[ { "path": ".agents/skills/claude-on-vertex-ci/SKILL.md", "content": "# Claude on Vertex AI from GitHub Actions\n\nReusable infrastructure for invoking Claude (via [`anthropics/claude-code-action`](https://github.com/anthropics/claude-code-action))\non Google Vertex AI from GitHub Actions workflows in this repo. Authentication\nis via Workload Identity Federation — no long-lived secrets.\n\n## When to Use\n\nAdd a new Claude-in-CI use case (PR review, CVE triage, dependency-update\nanalysis, automated docs generation, etc.) when:\n\n- The task is well-suited to an LLM with tool use (reading files, running CLI\n commands, calling `gh`)\n- The task fires on a GitHub event (schedule, workflow_dispatch, push, PR)\n- You want an issue, PR comment, or artifact as the output\n\nThe first use case (and template) is the **CVE triage step in\n`container-scan.yml`** — see `.agents/skills/container-vulns/SKILL.md`.\n\n## What's Already Provisioned\n\n**GCP project: `viral-seq-ai`**\n\n| Resource | Identifier |\n|---|---|\n| Workload Identity Pool | `github-actions-pool` (global) |\n| OIDC provider | `broadinstitute-github` |\n| Provider attribute condition | `assertion.repository_owner == 'broadinstitute'` |\n| Required APIs | `aiplatform.googleapis.com`, `iamcredentials.googleapis.com` |\n\n**Service accounts (one per use case):**\n\n| SA email | Use case | Workflow |\n|---|---|---|\n| `viral-ngs-cve-triage@viral-seq-ai.iam.gserviceaccount.com` | Weekly CVE triage | `.github/workflows/container-scan.yml` |\n\nThe pool + provider are reusable across use cases. Add a new SA per use case\n(principle of least privilege; easier to audit and disable individually).\n\n## Adding a New Claude-in-CI Use Case\n\nYou need GCP IAM Admin on `viral-seq-ai` for steps 1–3.\n\n### 1. Create a service account scoped to the use case\n\n```bash\ngcloud iam service-accounts create \\\n --project=viral-seq-ai \\\n --display-name=\"\" \\\n --description=\"Used by .yml to invoke Claude on Vertex AI for \"\n```\n\n### 2. Grant minimum roles\n\nVertex invocation requires both:\n\n```bash\ngcloud projects add-iam-policy-binding viral-seq-ai \\\n --member=\"serviceAccount:@viral-seq-ai.iam.gserviceaccount.com\" \\\n --role=\"roles/aiplatform.user\" \\\n --condition=None\n\ngcloud projects add-iam-policy-binding viral-seq-ai \\\n --member=\"serviceAccount:@viral-seq-ai.iam.gserviceaccount.com\" \\\n --role=\"roles/serviceusage.serviceUsageConsumer\" \\\n --condition=None\n```\n\n### 3. Bind the GitHub repo to the SA via WIF\n\n```bash\nPROJECT_NUMBER=$(gcloud projects describe viral-seq-ai --format='value(projectNumber)')\n\ngcloud iam service-accounts add-iam-policy-binding \\\n @viral-seq-ai.iam.gserviceaccount.com \\\n --project=viral-seq-ai \\\n --role=\"roles/iam.workloadIdentityUser\" \\\n --member=\"principalSet://iam.googleapis.com/projects/${PROJECT_NUMBER}/locations/global/workloadIdentityPools/github-actions-pool/attribute.repository/broadinstitute/viral-ngs\"\n```\n\nFor tighter scope, use `attribute.ref` (branch) or `attribute.workflow` (specific\nworkflow file) in place of (or in addition to) `attribute.repository`.\n\n### 4. Set GitHub repo variables\n\nIf the new use case lives alongside the CVE triage one, you can reuse\n`GCP_PROJECT_ID` and `GCP_WIP_PROVIDER`. The SA email differs per use case —\neither create a use-case-specific variable (e.g., `GCP_PR_REVIEW_SA_EMAIL`) or\nhard-code it in the workflow file.\n\n```bash\ngh variable set GCP__SA_EMAIL \\\n --body \"@viral-seq-ai.iam.gserviceaccount.com\" \\\n --repo broadinstitute/viral-ngs\n```\n\n### 5. Add the workflow steps\n\nSee the canonical pattern below.\n\n## Canonical Workflow Pattern\n\n```yaml\npermissions:\n id-token: write # for OIDC token to GCP via WIF\n # plus whatever else your workflow needs (contents: read, issues: write, etc.)\n\nsteps:\n - name: Checkout repository\n uses: actions/checkout@v4\n with:\n # If Claude needs git history (`git log --grep`, `git show`), use 0.\n # Otherwise the default shallow clone is fine.\n fetch-depth: 0\n\n - name: Authenticate to GCP via Workload Identity Federation\n uses: google-github-actions/auth@v2\n with:\n workload_identity_provider: ${{ vars.GCP_WIP_PROVIDER }}\n service_account: ${{ vars.GCP__SA_EMAIL }}\n\n - name: Claude on Vertex AI\n # Pin to commit SHA for supply-chain safety; bump when picking up new releases.\n uses: anthropics/claude-code-action@ # v1\n env:\n CLAUDE_CODE_USE_VERTEX: '1'\n CLOUD_ML_REGION: global # Sonnet 4.6 supports the global endpoint\n ANTHROPIC_VERTEX_PROJECT_ID: ${{ vars.GCP_PROJECT_ID }}\n with:\n use_vertex: 'true'\n github_token: ${{ secrets.GITHUB_TOKEN }} # avoids needing the Claude Code GitHub App\n claude_args: '--model claude-sonnet-4-6 --max-turns 30'\n settings: |\n {\n \"permissions\": {\n \"allow\": [\n \"Read\",\n \"Write\",\n \"Bash(git log:*)\",\n \"Bash(grep:*)\",\n \"Bash(jq:*)\"\n # ... add only what the prompt actually needs\n ]\n }\n }\n prompt: |\n \n```\n\n## Gotchas (Things We Learned the Hard Way)\n\n- **`iamcredentials.googleapis.com` must be enabled.** WIF impersonation calls\n this API; without it you get `IAM Service Account Credentials API has not\n been used in project ... before or it is disabled` from the Claude action,\n AFTER auth appears to succeed. Confusing.\n\n- **Use `@v1`, not `@beta`.** `claude-code-action@beta` is the older API shape\n with separate `direct_prompt`, `max_turns`, `allowed_tools` inputs. `@v1`\n consolidates everything into `prompt` + `claude_args` + `settings`. Pin to a\n commit SHA, not the floating tag.\n\n- **Both `use_vertex: 'true'` AND `CLAUDE_CODE_USE_VERTEX=1` are needed** —\n the input goes to the action wrapper, the env var goes to the underlying\n `claude-code` CLI.\n\n- **Pass `github_token: ${{ secrets.GITHUB_TOKEN }}`** to skip the Claude\n Code GitHub App requirement. Without this you get\n `Error: Claude Code is not installed on this repository`.\n\n- **The permission DSL doesn't take path globs on `Write` or paths on `Bash`\n command names.** `Write(/tmp/issues/**)` and `Bash(mkdir:/tmp/issues*)` are\n silently rejected and Claude hits `permission_denials_count > 0`. The\n `Bash(:*)` pattern is for the *args after the command*, not paths\n embedded in the command name. For now, use unrestricted `Write` and rely\n on prompt instructions to constrain output paths.\n\n- **Region `global` (recommended) gives dynamic routing across regions for\n Sonnet 4.6.** Pin to a specific region (e.g., `us-east5`, `europe-west1`)\n only if you need data-residency control.\n\n- **`fetch-depth: 0` if Claude needs git history.** Default `actions/checkout`\n is shallow (depth=1); `git log --all --grep` and `git show ` will\n produce empty results without unshallowing.\n\n- **Always `jq`-query authoritative data sources in the prompt.** When Claude\n has multiple ways to learn a fact (training data vs reading a workspace\n file), tell it explicitly which is canonical and require the tool call.\n Otherwise it sometimes infers from training data.\n\n## Cost / Safety\n\n- **Cost gate:** invoke Claude only when the workflow has real work to do\n (e.g., new CVEs detected, PR opened by non-bot). Don't invoke on every\n schedule tick unconditionally.\n- **Turn cap:** `--max-turns 30` is generous for triage-style tasks; tighten\n if you can. Observed: 6–10 turns for one-CVE analyses.\n- **Cost order of magnitude:** Sonnet 4.6 ≈ $0.10–1 per non-trivial task\n (one-CVE analysis with full repo reading). Opus 4.7 is ~5× more expensive\n for marginal quality gain on most CI tasks.\n- **Provider gate:** the OIDC provider attribute condition limits token\n minting to repos owned by `broadinstitute`. Other GitHub orgs cannot use\n this pool.\n- **SA gate:** each SA's `workloadIdentityUser` binding limits which repos\n can impersonate it. Default scope: `attribute.repository/broadinstitute/viral-ngs`.\n Tighten with `attribute.ref` or `attribute.workflow` if needed.\n- **Tool allowlist:** only allow tools the prompt actually uses. Avoid wildcard\n `Bash(*:*)` — name specific commands like `Bash(git log:*)`.\n\n## Key Files\n\n| File | Purpose |\n|------|---------|\n| `.github/workflows/container-scan.yml` | First use case (CVE triage); reference for the workflow pattern |\n| `.agents/skills/container-vulns/SKILL.md` | The CVE triage playbook this infra serves |\n\n## References\n\n- [`anthropics/claude-code-action`](https://github.com/anthropics/claude-code-action)\n- [Claude Code on Google Vertex AI](https://code.claude.com/docs/en/google-vertex-ai)\n- [`google-github-actions/auth`](https://github.com/google-github-actions/auth) (WIF action)\n" }, { "path": ".agents/skills/container-vulns/SKILL.md", "content": "# Container Vulnerability Management\n\nGuidance for scanning, triaging, and mitigating container image vulnerabilities\nin the viral-ngs Docker image hierarchy.\n\n## Scanning\n\nContainer images are scanned for vulnerabilities using [Trivy](https://aquasecurity.github.io/trivy/):\n\n- **On every PR/push**: `docker.yml` scans each image flavor after build (SARIF -> GitHub Security tab, JSON -> artifact)\n- **Weekly schedule**: `container-scan.yml` scans the latest published images. When new\n fixable HIGH/CRITICAL CVEs are detected (i.e. CVE IDs not already present in any open\n or closed GH issue title), the workflow invokes Claude Sonnet 4.6 on Vertex AI to\n triage each one and files a GitHub issue per CVE (labels: `security`, `cve`). The\n Vertex/WIF infra used here is documented in `.agents/skills/claude-on-vertex-ci/SKILL.md`.\n- Scans filter to **CRITICAL/HIGH** severity, **ignore-unfixed**, and apply a Rego policy (`.trivy-ignore-policy.rego`)\n- Per-CVE exceptions go in `.trivyignore` with mandatory justification comments\n\n## Rego Policy (`.trivy-ignore-policy.rego`)\n\nThe Rego policy filters CVEs that are architecturally inapplicable to ephemeral batch containers:\n\n- **AV:P** (Physical access required) -- containers are cloud-hosted\n- **AV:A** (Adjacent network required) -- no attacker on same network segment\n- **AV:L + UI:R** (Local + user interaction) -- no interactive sessions\n- **AV:L + PR:H** (Local + high privileges) -- containers run non-root\n- **AV:L + S:U** (Local + scope unchanged) -- attacker already has code execution and impact stays within the ephemeral container\n\nChanges to this policy should be reviewed carefully. The comments in the file explain the rationale and risk for each rule.\n\n## Common Vulnerability Sources\n\n**Python transitive deps**: Pin minimum versions in `docker/requirements/*.txt`. Prefer conda packages over pip. Check conda-forge availability before assuming a version exists -- conda-forge often lags PyPI by days/weeks.\n\n**Java fat JARs** (picard, gatk, snpeff, fgbio): Bioinformatics Java tools are distributed as uber JARs with all dependencies bundled inside. Trivy detects vulnerable libraries (log4j, commons-compress, etc.) baked into these JARs. Version bumps can cause ARM64 conda solver conflicts because Java tools pull in openjdk -> harfbuzz -> icu version chains that clash with other packages (r-base, boost-cpp, pyicu). Always check:\n1. Whether the tool is actually flagged by Trivy (don't bump versions unnecessarily)\n2. Whether the CVE applies (e.g., log4j 1.x is NOT vulnerable to Log4Shell)\n3. Whether the desired version resolves on ARM64 before pushing\n\n**Go binaries**: Some conda packages bundle compiled Go binaries (e.g., mafft's `dash_client`, google-cloud-sdk's `gcloud-crc32c`). If the binary is unused, delete it in the Dockerfile. Delete from **both** the installed location and `/opt/conda/pkgs/*/` (conda package cache) -- Trivy scans the full filesystem.\n\n**Vendored copies**: Packages like google-cloud-sdk and setuptools bundle their own copies of Python libraries that may be older than what's in the conda environment. Trivy flags these vendored copies separately. Options: delete the vendored directory (if not needed at runtime), or accept the risk in `.trivyignore` with justification.\n\n## ARM64 Solver Conflicts\n\nThe conda solver on ARM64 (linux-aarch64) is more constrained than amd64 because fewer package builds exist. Common conflict patterns:\n\n- **icu version conflicts**: Many packages (openjdk, r-base, boost-cpp, pyicu) pin specific icu version ranges. Bumping one package can make the entire environment unsolvable.\n- **libdeflate/htslib conflicts**: lofreq 2.1.5 pins old htslib/libdeflate versions that conflict with newer pillow/libtiff.\n- **openjdk version escalation**: snpeff 5.2+ requires openjdk>=11, 5.3+ requires openjdk>=21. Higher openjdk versions pull in harfbuzz->icu chains that conflict with everything.\n\nWhen a solver conflict occurs: revert the change, check what version the solver was picking before, and pin to that exact version if it already addresses the CVE.\n\n## Mitigation Decision Process\n\nWhen triaging a CVE:\n\n1. **Check the CVSS vector** -- does the Rego policy already filter it?\n2. **Identify the source package** -- use Trivy JSON output (`PkgName`, `PkgPath`, `InstalledVersion`)\n3. **Check if a fix version exists on conda-forge/bioconda** -- not just on PyPI\n4. **Test on ARM64** -- solver conflicts are the most common failure mode\n5. **If the fix version conflicts**: consider whether the CVE is exploitable in your deployment model. Document the risk assessment in `.trivyignore` or `vulnerability-mitigation-status.md`.\n6. **If the vulnerable code is unused**: delete the binary/file inline in the Dockerfile (same RUN layer as install to avoid bloating images)\n\n## Key Files\n\n| File | Purpose |\n|------|---------|\n| `.trivy-ignore-policy.rego` | Rego policy for class-level CVE filtering |\n| `.trivyignore` | Per-CVE exceptions with justifications |\n| `.github/workflows/docker.yml` | Build-time scanning (SARIF + JSON) |\n| `.github/workflows/container-scan.yml` | Weekly scheduled scanning |\n| `vulnerability-mitigation-status.md` | Local-only tracking doc (not committed) |\n" }, { "path": ".agents/skills/dsub-batch-jobs/SKILL.md", "content": "# Running Batch Jobs on GCP via dsub\n\nUse dsub to run one-off compute jobs on Google Cloud when your analysis requires\nmore compute/memory than the local environment, or needs specific Docker images\nthat are impractical to run locally.\n\n## When to Use\n\n- Analysis tools need >8GB RAM (e.g., VADR, BLAST, assembly)\n- Need to run many independent jobs in parallel (batch processing)\n- Need a specific Docker image with pre-installed tools\n- Data lives in GCS and is most efficiently processed in-cloud\n\n## Prerequisites\n\n- **dsub** installed (ask the user where their dsub installation or venv is located)\n- **gcloud CLI** authenticated with a GCP project that has Batch API enabled\n- **GCS bucket** accessible by the project's default service account\n\n## Generic Invocation\n\n```bash\ndsub --provider google-cls-v2 \\\n --project \\\n --regions \\\n --image \\\n --machine-type \\\n --script \\\n --tasks \\\n --logging gs:///logs//\n```\n\n### Key Parameters\n\n| Parameter | Description |\n|-----------|-------------|\n| `--provider google-cls-v2` | Use Google Cloud Batch (recommended over Life Sciences) |\n| `--project` | GCP project with Batch API enabled |\n| `--regions` | Compute region (e.g., `us-central1`) |\n| `--image` | Docker image to run (e.g., `staphb/vadr:1.6.4`) |\n| `--machine-type` | VM type (e.g., `n1-highmem-4` for 26GB RAM) |\n| `--script` | Local shell script to execute inside the container |\n| `--tasks` | TSV file defining one row per job (batch mode) |\n| `--logging` | GCS path for stdout/stderr logs |\n\n## Task TSV Format\n\nThe tasks TSV defines inputs, outputs, and environment variables for each job.\nHeader row uses column prefixes to declare types:\n\n```\n--env VAR1\t--env VAR2\t--input FASTA\t--output RESULT\t--output LOG\nvalue1\tvalue2\tgs://bucket/input.fasta\tgs://bucket/output.txt\tgs://bucket/log.txt\n```\n\n- `--env NAME` -- environment variable passed to the script\n- `--input NAME` -- GCS file downloaded to a local path; the env var is set to the local path\n- `--output NAME` -- local path; after the script finishes, the file is uploaded to GCS\n\nEach non-header row is one job. All jobs run independently in parallel.\n\n## GCP Project and Bucket Scoping\n\nThe service account running dsub jobs must have read/write access to all GCS paths\nreferenced in the tasks TSV. The simplest approach:\n\n1. Use a GCP project whose default service account already has access to your data\n2. Use a bucket within that same project for staging intermediate/output files\n3. For ephemeral results, use a temp bucket with a lifecycle policy (e.g., 30-day auto-delete)\n\n### Broad Viral Genomics Defaults\n\nMost developers on the viral-ngs codebase use:\n- **GCP project**: `gcid-viral-seq`\n- **Staging bucket**: `gs://viral-temp-30d` (30-day auto-delete lifecycle)\n\nThese are not universal -- always confirm with the user before using them.\n\n## Monitoring Jobs\n\n```bash\n# Check job status\ndsub --provider google-cls-v2 --project --jobs --status\n\n# Or use dstat\ndstat --provider google-cls-v2 --project --jobs --status '*'\n\n# View logs\ngcloud storage cat gs:///logs//.log\n```\n\n## Tips\n\n- **Batch over single jobs**: Always prefer `--tasks` with a TSV over individual\n `dsub` invocations. One TSV row per job is cleaner and easier to track.\n- **Machine sizing**: Check your tool's memory requirements. VADR needs ~16GB;\n use `n1-highmem-4` (26GB). Most tools work fine with `n1-standard-4` (15GB).\n- **Script portability**: Write the `--script` to be self-contained. It receives\n inputs/outputs as environment variables. Don't assume any local state.\n- **Logging**: Always set `--logging` to a GCS path so you can debug failures.\n- **Idempotency**: If re-running, dsub will create new jobs. Check for existing\n outputs before re-submitting to avoid redundant computation.\n\n## Example: VADR Batch Analysis\n\nFrom the GATK-to-FreeBayes regression testing (PR #1053), we ran VADR on 30 FASTAs\n(15 assemblies x old/new) using dsub:\n\n```bash\nsource ~/venvs/dsub/bin/activate # or wherever dsub is installed\n\ndsub --provider google-cls-v2 \\\n --project gcid-viral-seq \\\n --regions us-central1 \\\n --image staphb/vadr:1.6.4 \\\n --machine-type n1-highmem-4 \\\n --script run_vadr.sh \\\n --tasks vadr_tasks.tsv \\\n --logging gs://viral-temp-30d/vadr_regression/logs/\n```\n\nThe tasks TSV had columns for VADR options (`--env VADR_OPTS`), model URL\n(`--env MODEL_URL`), input FASTA (`--input FASTA`), and outputs\n(`--output NUM_ALERTS`, `--output ALERTS_TSV`, `--output VADR_TGZ`).\n\nAll 30 jobs completed in ~15 minutes total (running in parallel on GCP).\n" }, { "path": ".agents/skills/regression-testing/SKILL.md", "content": "# Assembly Regression Testing\n\nEnd-to-end regression testing for assembly pipeline changes against Terra submissions.\n\n## When to Use\n\nUse this playbook when a PR makes functional changes to the assembly or variant-calling\npipeline (e.g., swapping variant callers, changing alignment parameters, modifying\nconsensus logic). It compares assembly outputs from old vs new code across hundreds\nof real samples to validate equivalence or improvement.\n\n## Prerequisites\n\n- **gcloud CLI** -- authenticated with access to Terra workspace GCS buckets\n- **mafft** -- for pairwise sequence alignment\n- **Python** with pandas and matplotlib (e.g., a dataviz venv)\n- **dsub** -- for running VADR batch jobs on GCP (see the `dsub-batch-jobs` skill)\n\n## Workflow\n\n### Step 1: Set Up Terra Submissions (Manual)\n\nThe user must manually launch Terra submissions with old and new code:\n1. Run the pipeline on a representative dataset using the **main branch** Docker image\n2. Run the same pipeline on the same dataset using the **feature branch** Docker image\n3. Note the submission IDs and workspace bucket for both runs\n\n### Step 2: Discover Paired Samples\n\nUse `discover_pairs.py` to find all comparable old/new sample pairs by crawling\nGCS Cromwell output directories.\n\n```bash\npython discover_pairs.py \\\n --bucket \\\n --old-sub \\\n --new-sub \\\n --output pairs.json\n```\n\nThis produces a JSON mapping sample_name -> {old_tsv, new_tsv} for all samples\npresent in both submissions.\n\n### Step 3: Compare Assembly Outputs\n\nUse `compare_sample_pair.py` to compare each sample pair. This script:\n- Downloads assembly_stats TSVs from GCS\n- Compares metrics (coverage, % reference covered, length, etc.)\n- Downloads FASTA assemblies and aligns them with mafft\n- Reports SNPs, indels (events and bp), ambiguity diffs, and terminal extensions\n\n```bash\npython compare_sample_pair.py \\\n --old-tsv --new-tsv \\\n --work-dir ./results/ \\\n --output-json ./results/.json\n```\n\nFor batch processing, iterate over all entries in `pairs.json` and invoke\n`compare_sample_pair.py` for each sample pair (e.g., via a small wrapper\nscript using `concurrent.futures` or `xargs`/GNU `parallel`).\n\n### Step 4: Generate Report\n\nUse `generate_report.py` to aggregate all per-sample JSONs into plots and a markdown report.\n\n```bash\npython generate_report.py \\\n --results-dir ./results/ \\\n --report-dir ./report/ \\\n --workspace-name \n```\n\nOutputs:\n- Summary TSV with per-assembly metrics\n- 8 plots (scatter plots, histograms, identity distribution)\n- Markdown report with summary tables and divergent assembly details\n\n### Step 5: (Optional) VADR Annotation Quality\n\nFor assemblies with internal indel differences, run VADR to assess whether indels\ncause frameshifts or other annotation problems. See the `dsub-batch-jobs` skill for\ndetails on running batch jobs via dsub.\n\nUse `run_vadr.sh` with dsub to run VADR on each FASTA:\n\n```bash\ndsub --provider google-cls-v2 \\\n --project --regions us-central1 \\\n --image staphb/vadr:1.6.4 \\\n --machine-type n1-highmem-4 \\\n --script run_vadr.sh \\\n --tasks vadr_tasks.tsv \\\n --logging gs:///vadr_logs/\n```\n\nVADR model parameters come from the viral-references repo:\nhttps://github.com/broadinstitute/viral-references/blob/main/annotation/vadr/vadr-by-taxid.tsv\n\nUse the taxid from the assembly_id (format: `sample_id-taxid`) to look up the\ncorrect `vadr_opts`, `min_seq_len`, `max_seq_len`, `vadr_model_tar_url`, and\n`vadr_model_tar_subdir`.\n\n### Step 6: Post Results\n\nPost the report as a PR comment. Before posting:\n- **Self-review the proposed comment for confidential information** (sample names,\n internal paths, credentials, etc.). Ask the user if in doubt about what is safe\n to share publicly.\n- Include plots as image attachments if the PR is on GitHub\n- Attribute the analysis appropriately\n\n## Key Patterns\n\n### Per-Segment Alignment\n\nMulti-segment genomes (e.g., influenza with 8 segments) must be aligned\n**per-segment**, not as a single concatenated sequence. Otherwise, terminal\neffects at segment boundaries get misclassified as internal indels.\n\nThe `compare_sample_pair.py` script handles this automatically: it pairs\nsegments by FASTA header, aligns each pair independently, analyzes each\nalignment separately (so terminal effects stay terminal), and aggregates\nthe statistics.\n\n### Event Counting vs BP Counting\n\nFor indels, both counts matter:\n- **BP count**: Total gap positions (e.g., \"49 bp of indels\")\n- **Event count**: Contiguous gap runs (e.g., \"13 indel events\")\n\nA single 26bp insertion is 1 event but 26 bp. Event counts better reflect\nthe number of variant-calling decisions that differ between old and new code.\n\n### VADR Frameshift Cascade Detection\n\nA single spurious 1bp indel in a coding region causes a cascade of VADR alerts:\n1. `FRAMESHIFT` -- the indel shifts the reading frame\n2. `STOP_CODON` -- premature stop codon in the shifted frame\n3. `UNEXPECTED_LENGTH` -- protein length doesn't match model\n4. `PEPTIDE_TRANSLATION_PROBLEM` -- for each downstream mature peptide\n\nWhen comparing VADR alert counts, a large delta (e.g., 32 -> 1) usually means\none version has frameshift-causing indels that the other avoids. Check the\n`.alt.list` files to confirm which genes are affected.\n\n## Interpreting Results\n\n### What to Look For\n\n1. **Identity distribution**: Most assemblies should be 100% identical. Any\n below 99.9% warrant investigation.\n2. **SNP count = 0 for all assemblies**: Pipeline changes that only affect\n indel calling (e.g., swapping variant callers) should produce zero SNPs.\n3. **Indel events**: The number and nature of indel differences. Are they in\n coding regions? Do they cause frameshifts?\n4. **Coverage correlation**: Low-coverage samples (<10x) are most likely to\n show differences between variant callers.\n5. **VADR alert deltas**: Fewer alerts = more biologically plausible assembly.\n Large improvements (e.g., -31 alerts) strongly favor the new code.\n\n### Red Flags\n\n- Assemblies present in old but missing in new (or vice versa)\n- SNPs introduced where none existed before\n- VADR alerts increasing significantly for the new code\n- Differences concentrated in specific organisms/taxids\n" }, { "path": ".agents/skills/regression-testing/compare_sample_pair.py", "content": "#!/usr/bin/env python3\n\"\"\"Compare assembly outputs between old and new code for a single sample pair.\n\nTakes two GCS URIs pointing at assembly_metadata TSV files (old and new),\ndownloads them, compares metrics, aligns FASTAs with mafft, and outputs a JSON result.\n\"\"\"\nimport argparse\nimport csv\nimport io\nimport json\nimport logging\nimport os\nimport subprocess\n\nlogging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s')\nlog = logging.getLogger(__name__)\n\nMETRICS_COLS = [\n 'assembly_length', 'assembly_length_unambiguous', 'reads_aligned',\n 'mean_coverage', 'percent_reference_covered', 'reference_length',\n 'scaffolding_num_segments_recovered', 'reference_num_segments_required',\n]\nFLOAT_COLS = {'mean_coverage', 'percent_reference_covered'}\nINT_COLS = {'assembly_length', 'assembly_length_unambiguous', 'reads_aligned',\n 'reference_length', 'scaffolding_num_segments_recovered',\n 'reference_num_segments_required'}\n\n\ndef gcloud_cat(gcs_uri):\n \"\"\"Read a GCS file's contents as a string.\"\"\"\n result = subprocess.run(\n ['gcloud', 'storage', 'cat', gcs_uri],\n capture_output=True, text=True, timeout=120\n )\n if result.returncode != 0:\n raise RuntimeError(f\"gcloud storage cat failed for {gcs_uri}: {result.stderr.strip()}\")\n return result.stdout\n\n\ndef gcloud_cp(gcs_uri, local_path):\n \"\"\"Download a GCS file to local path.\"\"\"\n result = subprocess.run(\n ['gcloud', 'storage', 'cp', gcs_uri, local_path],\n capture_output=True, text=True, timeout=120\n )\n if result.returncode != 0:\n raise RuntimeError(f\"gcloud storage cp failed for {gcs_uri}: {result.stderr.strip()}\")\n\n\ndef parse_tsv(content):\n \"\"\"Parse assembly_metadata TSV content into a dict keyed by assembly_id.\n\n Returns dict: assembly_id -> {col: value, ...}\n \"\"\"\n reader = csv.DictReader(io.StringIO(content), delimiter='\\t')\n rows = {}\n for row in reader:\n # The first column is 'entity:assembly_id'\n assembly_id = row.get('entity:assembly_id', '').strip()\n if not assembly_id:\n continue\n # Parse numeric columns\n parsed = dict(row)\n for col in FLOAT_COLS:\n if col in parsed and parsed[col]:\n try:\n parsed[col] = float(parsed[col])\n except (ValueError, TypeError):\n parsed[col] = None\n for col in INT_COLS:\n if col in parsed and parsed[col]:\n try:\n parsed[col] = int(parsed[col])\n except (ValueError, TypeError):\n parsed[col] = None\n rows[assembly_id] = parsed\n return rows\n\n\ndef parse_fasta(content):\n \"\"\"Parse a FASTA string into list of (header, sequence) tuples.\"\"\"\n sequences = []\n current_header = None\n current_seq = []\n for line in content.strip().split('\\n'):\n line = line.strip()\n if not line:\n continue\n if line.startswith('>'):\n if current_header is not None:\n sequences.append((current_header, ''.join(current_seq)))\n current_header = line[1:].strip()\n current_seq = []\n else:\n current_seq.append(line)\n if current_header is not None:\n sequences.append((current_header, ''.join(current_seq)))\n return sequences\n\n\ndef run_mafft_pair(old_seq, new_seq, work_dir, pair_id='0'):\n \"\"\"Run mafft on a single pair of sequences. Returns aligned (old_seq, new_seq) strings.\"\"\"\n combined = os.path.join(work_dir, f'combined_{pair_id}.fasta')\n with open(combined, 'w') as f:\n f.write(f'>old_{pair_id}\\n{old_seq}\\n>new_{pair_id}\\n{new_seq}\\n')\n\n try:\n result = subprocess.run(\n ['mafft', '--auto', '--preservecase', '--quiet', '--thread', '1', combined],\n capture_output=True, text=True, timeout=300\n )\n finally:\n os.unlink(combined)\n if result.returncode != 0:\n raise RuntimeError(f\"mafft failed: {result.stderr.strip()}\")\n\n seqs = parse_fasta(result.stdout)\n if len(seqs) != 2:\n raise RuntimeError(f\"Expected 2 sequences from mafft, got {len(seqs)}\")\n return seqs[0][1], seqs[1][1]\n\n\ndef align_and_analyze_fastas(old_fasta_path, new_fasta_path, work_dir):\n \"\"\"Align old vs new FASTAs, handling multi-segment genomes.\n\n For single-segment: runs one mafft alignment and analyzes it.\n For multi-segment: pairs segments by header, aligns each pair separately,\n analyzes each independently (so terminal effects stay terminal), and\n aggregates the stats.\n\n Returns (aligned_fasta_path, stats_dict).\n \"\"\"\n with open(old_fasta_path) as f:\n old_fasta_text = f.read()\n with open(new_fasta_path) as f:\n new_fasta_text = f.read()\n old_seqs = parse_fasta(old_fasta_text)\n new_seqs = parse_fasta(new_fasta_text)\n\n if len(old_seqs) == 1 and len(new_seqs) == 1:\n # Simple case: single segment\n aln_old, aln_new = run_mafft_pair(old_seqs[0][1], new_seqs[0][1], work_dir)\n aligned = os.path.join(work_dir, 'aligned.fasta')\n with open(aligned, 'w') as f:\n f.write(f'>old_{old_seqs[0][0]}\\n{aln_old}\\n>new_{new_seqs[0][0]}\\n{aln_new}\\n')\n stats = analyze_alignment_seqs(aln_old, aln_new)\n return aligned, stats\n\n # Multi-segment: pair by header name\n old_dict = {h: s for h, s in old_seqs}\n new_dict = {h: s for h, s in new_seqs}\n common_headers = [h for h in old_dict if h in new_dict]\n\n if not common_headers:\n if len(old_seqs) == len(new_seqs):\n log.info(f\" Multi-segment: headers don't match, pairing by position ({len(old_seqs)} segments)\")\n common_headers = None\n else:\n raise RuntimeError(\n f\"Cannot pair segments: {len(old_seqs)} old vs {len(new_seqs)} new, no matching headers\")\n\n # Align each pair and analyze independently\n segment_pairs = []\n if common_headers is not None:\n for i, h in enumerate(common_headers):\n aln_old, aln_new = run_mafft_pair(old_dict[h], new_dict[h], work_dir, pair_id=str(i))\n segment_pairs.append((h, aln_old, aln_new))\n else:\n for i in range(len(old_seqs)):\n aln_old, aln_new = run_mafft_pair(old_seqs[i][1], new_seqs[i][1], work_dir, pair_id=str(i))\n segment_pairs.append((old_seqs[i][0], aln_old, aln_new))\n\n n_segments = len(segment_pairs)\n log.info(f\" Multi-segment alignment: {n_segments} segments aligned\")\n\n # Analyze each segment independently, then aggregate\n agg = {\n 'alignment_length': 0, 'internal_length': 0,\n 'matches': 0, 'snps': 0,\n 'internal_insertions': 0, 'internal_deletions': 0,\n 'internal_insertion_events': 0, 'internal_deletion_events': 0,\n 'ambiguity_diffs': 0,\n 'terminal_old_left': 0, 'terminal_new_left': 0,\n 'terminal_old_right': 0, 'terminal_new_right': 0,\n 'terminal_extensions_old': 0, 'terminal_extensions_new': 0,\n 'terminal_extension_events_old': 0, 'terminal_extension_events_new': 0,\n }\n per_segment = []\n for header, aln_old, aln_new in segment_pairs:\n seg_stats = analyze_alignment_seqs(aln_old, aln_new)\n per_segment.append({'segment': header, **seg_stats})\n for key in agg:\n agg[key] += seg_stats.get(key, 0)\n\n # Compute aggregate identity\n total_bases_compared = agg['matches'] + agg['snps'] + agg['ambiguity_diffs']\n agg['identity'] = agg['matches'] / total_bases_compared if total_bases_compared > 0 else 1.0\n agg['n_segments'] = n_segments\n agg['per_segment'] = per_segment\n\n # Write per-segment alignment file (for review)\n aligned = os.path.join(work_dir, 'aligned.fasta')\n with open(aligned, 'w') as f:\n for header, aln_old, aln_new in segment_pairs:\n f.write(f'>old_{header}\\n{aln_old}\\n>new_{header}\\n{aln_new}\\n')\n\n return aligned, agg\n\n\ndef analyze_alignment_seqs(old_seq_str, new_seq_str):\n \"\"\"Analyze a pairwise alignment given two aligned sequence strings.\n\n Returns dict with alignment statistics.\n \"\"\"\n old_seq = old_seq_str.upper()\n new_seq = new_seq_str.upper()\n aln_len = len(old_seq)\n\n if len(new_seq) != aln_len:\n raise RuntimeError(f\"Alignment sequences differ in length: {aln_len} vs {len(new_seq)}\")\n\n ACGT = set('ACGT')\n\n # Find the internal region (where both sequences have bases)\n left_bound = 0\n while left_bound < aln_len and (old_seq[left_bound] == '-' or new_seq[left_bound] == '-'):\n left_bound += 1\n\n right_bound = aln_len - 1\n while right_bound >= 0 and (old_seq[right_bound] == '-' or new_seq[right_bound] == '-'):\n right_bound -= 1\n\n # Terminal extension counts (bp and events)\n terminal_old_left = 0\n terminal_new_left = 0\n terminal_old_right = 0\n terminal_new_right = 0\n # Track events: a contiguous run of gaps on one side = 1 event\n terminal_old_left_events = 0\n terminal_new_left_events = 0\n terminal_old_right_events = 0\n terminal_new_right_events = 0\n\n prev_old_gap = False\n prev_new_gap = False\n for i in range(left_bound):\n if old_seq[i] != '-' and new_seq[i] == '-':\n terminal_old_left += 1\n if not prev_old_gap:\n terminal_old_left_events += 1\n prev_old_gap = True\n prev_new_gap = False\n elif new_seq[i] != '-' and old_seq[i] == '-':\n terminal_new_left += 1\n if not prev_new_gap:\n terminal_new_left_events += 1\n prev_new_gap = True\n prev_old_gap = False\n else:\n prev_old_gap = False\n prev_new_gap = False\n\n prev_old_gap = False\n prev_new_gap = False\n for i in range(right_bound + 1, aln_len):\n if old_seq[i] != '-' and new_seq[i] == '-':\n terminal_old_right += 1\n if not prev_old_gap:\n terminal_old_right_events += 1\n prev_old_gap = True\n prev_new_gap = False\n elif new_seq[i] != '-' and old_seq[i] == '-':\n terminal_new_right += 1\n if not prev_new_gap:\n terminal_new_right_events += 1\n prev_new_gap = True\n prev_old_gap = False\n else:\n prev_old_gap = False\n prev_new_gap = False\n\n # Analyze internal region (bp counts and event counts)\n matches = 0\n snps = 0\n internal_insertions = 0 # bp count\n internal_deletions = 0 # bp count\n internal_insertion_events = 0\n internal_deletion_events = 0\n ambiguity_diffs = 0\n in_insertion = False\n in_deletion = False\n\n for i in range(left_bound, right_bound + 1):\n o = old_seq[i]\n n = new_seq[i]\n\n if o == '-' and n != '-':\n internal_insertions += 1\n if not in_insertion:\n internal_insertion_events += 1\n in_insertion = True\n in_deletion = False\n elif o != '-' and n == '-':\n internal_deletions += 1\n if not in_deletion:\n internal_deletion_events += 1\n in_deletion = True\n in_insertion = False\n else:\n in_insertion = False\n in_deletion = False\n if o == n:\n if o != '-':\n matches += 1\n elif o in ACGT and n in ACGT:\n snps += 1\n else:\n ambiguity_diffs += 1\n\n total_internal = right_bound - left_bound + 1 if right_bound >= left_bound else 0\n total_bases_compared = matches + snps + ambiguity_diffs\n identity = matches / total_bases_compared if total_bases_compared > 0 else 1.0\n\n return {\n 'alignment_length': aln_len,\n 'internal_length': total_internal,\n 'matches': matches,\n 'snps': snps,\n 'internal_insertions': internal_insertions,\n 'internal_deletions': internal_deletions,\n 'internal_insertion_events': internal_insertion_events,\n 'internal_deletion_events': internal_deletion_events,\n 'ambiguity_diffs': ambiguity_diffs,\n 'terminal_old_left': terminal_old_left,\n 'terminal_new_left': terminal_new_left,\n 'terminal_old_right': terminal_old_right,\n 'terminal_new_right': terminal_new_right,\n 'terminal_extensions_old': terminal_old_left + terminal_old_right,\n 'terminal_extensions_new': terminal_new_left + terminal_new_right,\n 'terminal_extension_events_old': terminal_old_left_events + terminal_old_right_events,\n 'terminal_extension_events_new': terminal_new_left_events + terminal_new_right_events,\n 'identity': identity,\n }\n\n\ndef analyze_alignment(aligned_fasta_path):\n \"\"\"Analyze pairwise alignment from mafft output file. Thin wrapper around analyze_alignment_seqs.\"\"\"\n with open(aligned_fasta_path) as f:\n seqs = parse_fasta(f.read())\n if len(seqs) != 2:\n raise RuntimeError(f\"Expected 2 sequences in alignment, got {len(seqs)}\")\n return analyze_alignment_seqs(seqs[0][1], seqs[1][1])\n\n\ndef compare_assembly(assembly_id, old_row, new_row, work_dir):\n \"\"\"Compare one assembly (old vs new). Downloads FASTAs, runs mafft, returns result dict.\"\"\"\n result = {\n 'assembly_id': assembly_id,\n 'taxid': old_row.get('taxid', ''),\n 'tax_name': old_row.get('tax_name', ''),\n 'old_metrics': {},\n 'new_metrics': {},\n 'deltas': {},\n 'alignment': None,\n 'error': None,\n }\n\n # Extract metrics\n for col in METRICS_COLS:\n old_val = old_row.get(col)\n new_val = new_row.get(col)\n result['old_metrics'][col] = old_val\n result['new_metrics'][col] = new_val\n if old_val is not None and new_val is not None:\n try:\n result['deltas'][col] = float(new_val) - float(old_val)\n except (ValueError, TypeError):\n result['deltas'][col] = None\n\n # Get FASTA paths\n old_fasta_uri = old_row.get('assembly_fasta', '').strip()\n new_fasta_uri = new_row.get('assembly_fasta', '').strip()\n\n if not old_fasta_uri or not new_fasta_uri:\n log.info(f\" {assembly_id}: skipping alignment (missing FASTA URI)\")\n return result\n\n # Download FASTAs\n aln_dir = os.path.join(work_dir, f'aln_{assembly_id}')\n os.makedirs(aln_dir, exist_ok=True)\n\n old_fasta_local = os.path.join(aln_dir, 'old.fasta')\n new_fasta_local = os.path.join(aln_dir, 'new.fasta')\n\n try:\n log.debug(f\" Downloading old FASTA: {old_fasta_uri}\")\n gcloud_cp(old_fasta_uri, old_fasta_local)\n log.debug(f\" Downloading new FASTA: {new_fasta_uri}\")\n gcloud_cp(new_fasta_uri, new_fasta_local)\n\n # Check if FASTAs are non-empty\n if os.path.getsize(old_fasta_local) == 0 or os.path.getsize(new_fasta_local) == 0:\n log.info(f\" {assembly_id}: skipping alignment (empty FASTA)\")\n return result\n\n # Align and analyze (handles multi-segment genomes independently)\n log.debug(f\" Running alignment for {assembly_id}\")\n aligned_path, alignment_stats = align_and_analyze_fastas(old_fasta_local, new_fasta_local, aln_dir)\n result['alignment'] = alignment_stats\n\n identity = alignment_stats['identity']\n snps = alignment_stats['snps']\n indels = alignment_stats['internal_insertions'] + alignment_stats['internal_deletions']\n log.info(f\" {assembly_id}: identity={identity:.6f}, snps={snps}, indels={indels}, \"\n f\"terminal_ext_old={alignment_stats['terminal_extensions_old']}, \"\n f\"terminal_ext_new={alignment_stats['terminal_extensions_new']}\")\n\n except Exception as e:\n log.error(f\" {assembly_id}: alignment failed: {e}\")\n result['error'] = str(e)\n finally:\n # Cleanup downloaded files\n for f in [old_fasta_local, new_fasta_local]:\n if os.path.exists(f):\n os.unlink(f)\n # Keep aligned file only if identity < 99.9%\n aligned_file = os.path.join(aln_dir, 'aligned.fasta')\n if os.path.exists(aligned_file):\n if result['alignment'] and result['alignment']['identity'] >= 0.999:\n os.unlink(aligned_file)\n else:\n log.info(f\" Keeping alignment file for review: {aligned_file}\")\n # Remove empty dir\n try:\n os.rmdir(aln_dir)\n except OSError:\n pass # dir not empty (kept alignment file)\n\n return result\n\n\ndef main():\n parser = argparse.ArgumentParser(description=__doc__)\n parser.add_argument('--old-tsv', required=True, help='GCS URI of old assembly_metadata TSV')\n parser.add_argument('--new-tsv', required=True, help='GCS URI of new assembly_metadata TSV')\n parser.add_argument('--work-dir', required=True, help='Working directory for temp files')\n parser.add_argument('--output-json', required=True, help='Output JSON file path')\n parser.add_argument('--verbose', '-v', action='store_true', help='Enable debug logging')\n args = parser.parse_args()\n\n if args.verbose:\n logging.getLogger().setLevel(logging.DEBUG)\n\n os.makedirs(args.work_dir, exist_ok=True)\n\n # Download and parse TSVs\n log.info(f\"Downloading old TSV: {args.old_tsv}\")\n old_content = gcloud_cat(args.old_tsv)\n old_rows = parse_tsv(old_content)\n\n log.info(f\"Downloading new TSV: {args.new_tsv}\")\n new_content = gcloud_cat(args.new_tsv)\n new_rows = parse_tsv(new_content)\n\n # Extract sample_id from first row (or from TSV filename)\n sample_id = 'unknown'\n if old_rows:\n first_row = next(iter(old_rows.values()))\n sample_id = first_row.get('sample_id', 'unknown')\n elif new_rows:\n first_row = next(iter(new_rows.values()))\n sample_id = first_row.get('sample_id', 'unknown')\n\n log.info(f\"Sample: {sample_id}\")\n log.info(f\"Old assemblies: {len(old_rows)}, New assemblies: {len(new_rows)}\")\n\n # Find intersecting assembly_ids\n common_ids = sorted(set(old_rows.keys()) & set(new_rows.keys()))\n old_only_ids = sorted(set(old_rows.keys()) - set(new_rows.keys()))\n new_only_ids = sorted(set(new_rows.keys()) - set(old_rows.keys()))\n\n if old_only_ids:\n log.info(f\" Assemblies only in old: {old_only_ids}\")\n if new_only_ids:\n log.info(f\" Assemblies only in new: {new_only_ids}\")\n log.info(f\" Assemblies in common: {len(common_ids)}\")\n\n # Compare each intersecting assembly\n comparisons = []\n for aid in common_ids:\n comp = compare_assembly(aid, old_rows[aid], new_rows[aid], args.work_dir)\n comparisons.append(comp)\n\n # Build output\n output = {\n 'sample_id': sample_id,\n 'old_tsv_uri': args.old_tsv,\n 'new_tsv_uri': args.new_tsv,\n 'old_assembly_count': len(old_rows),\n 'new_assembly_count': len(new_rows),\n 'assembly_count_match': len(old_rows) == len(new_rows),\n 'assemblies_only_in_old': old_only_ids,\n 'assemblies_only_in_new': new_only_ids,\n 'comparisons': comparisons,\n }\n\n with open(args.output_json, 'w') as f:\n json.dump(output, f, indent=2)\n\n log.info(f\"Wrote results to {args.output_json}\")\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": ".agents/skills/regression-testing/discover_pairs.py", "content": "#!/usr/bin/env python3\n\"\"\"Discover comparable old/new sample pairs by crawling GCS Cromwell output directories.\n\nFor each submission, finds assembly_metadata TSV files named\n``assembly_metadata-.tsv``, extracts sample names from filenames,\nand outputs the intersection as a JSON mapping.\n\nUsage:\n python discover_pairs.py \\\n --bucket fc-XXXXXXXX-... \\\n --old-sub \\\n --new-sub \\\n -o pairs.json\n\"\"\"\nimport argparse\nimport json\nimport logging\nimport re\nimport subprocess\n\nlogging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s')\nlog = logging.getLogger(__name__)\n\n\ndef gcloud_ls(path):\n \"\"\"List GCS path, return list of URIs. Returns [] on error.\"\"\"\n try:\n result = subprocess.run(\n ['gcloud', 'storage', 'ls', path],\n capture_output=True, text=True, timeout=60\n )\n if result.returncode != 0:\n log.warning(f\"gcloud ls non-zero exit for {path}: {result.stderr.strip()}\")\n return []\n return [line.strip() for line in result.stdout.strip().split('\\n') if line.strip()]\n except Exception as e:\n log.warning(f\"gcloud ls failed for {path}: {e}\")\n return []\n\n\ndef find_tsv_in_call_dir(call_dir_uri):\n \"\"\"Find assembly_metadata TSV in a call directory, handling attempt-N subdirs.\n\n Returns (sample_name, tsv_uri) or (None, None).\n \"\"\"\n items = gcloud_ls(call_dir_uri)\n\n # Check for attempt-N subdirectories\n def attempt_sort_key(path):\n match = re.search(r'/attempt-(\\d+)', path)\n return int(match.group(1)) if match else 0\n attempt_dirs = sorted([i for i in items if '/attempt-' in i],\n key=attempt_sort_key, reverse=True)\n tsv_files = [i for i in items if i.endswith('.tsv')]\n\n # If there are attempt dirs, check the highest attempt first\n if attempt_dirs:\n for attempt_dir in attempt_dirs:\n attempt_items = gcloud_ls(attempt_dir)\n attempt_tsvs = [i for i in attempt_items if i.endswith('.tsv')]\n if attempt_tsvs:\n tsv_files = attempt_tsvs\n break\n\n for tsv in tsv_files:\n match = re.search(r'assembly_metadata-(.+)\\.tsv$', tsv)\n if match:\n return match.group(1), tsv\n\n return None, None\n\n\ndef discover_submission_tsvs(bucket, submission_id):\n \"\"\"Find all assembly_metadata TSVs for a submission.\n\n Returns dict: sample_name -> tsv_gcs_uri\n \"\"\"\n base = f\"gs://{bucket}/submissions/{submission_id}/assemble_denovo_metagenomic/\"\n log.info(f\"Listing workflow directories in {base}\")\n\n wf_dirs = gcloud_ls(base)\n log.info(f\"Found {len(wf_dirs)} workflow directories\")\n\n results = {}\n for i, wf_dir in enumerate(wf_dirs):\n if i % 20 == 0:\n log.info(f\" Scanning workflow {i+1}/{len(wf_dirs)}...\")\n\n for call_name in ['call-assembly_stats_non_empty', 'call-assembly_stats_empty']:\n call_dir = f\"{wf_dir}{call_name}/\"\n sample_name, tsv_uri = find_tsv_in_call_dir(call_dir)\n if sample_name:\n if sample_name in results:\n log.warning(f\"Duplicate sample {sample_name} -- keeping first occurrence\")\n else:\n results[sample_name] = tsv_uri\n break\n\n log.info(f\"Found TSVs for {len(results)} samples in submission {submission_id[:8]}\")\n return results\n\n\ndef main():\n parser = argparse.ArgumentParser(description=__doc__,\n formatter_class=argparse.RawDescriptionHelpFormatter)\n parser.add_argument('--bucket', required=True,\n help='Terra workspace GCS bucket ID (e.g., fc-XXXXXXXX-...)')\n parser.add_argument('--old-sub', required=True,\n help='Old submission ID (main branch)')\n parser.add_argument('--new-sub', required=True,\n help='New submission ID (feature branch)')\n parser.add_argument('--output', '-o', required=True,\n help='Output JSON file path')\n args = parser.parse_args()\n\n log.info(f\"Old submission: {args.old_sub[:8]}\")\n log.info(f\"New submission: {args.new_sub[:8]}\")\n\n old_tsvs = discover_submission_tsvs(args.bucket, args.old_sub)\n new_tsvs = discover_submission_tsvs(args.bucket, args.new_sub)\n\n # Find intersection\n common_samples = sorted(set(old_tsvs.keys()) & set(new_tsvs.keys()))\n old_only = sorted(set(old_tsvs.keys()) - set(new_tsvs.keys()))\n new_only = sorted(set(new_tsvs.keys()) - set(old_tsvs.keys()))\n\n log.info(f\"Old-only samples: {len(old_only)}\")\n log.info(f\"New-only samples: {len(new_only)}\")\n log.info(f\"Intersecting samples: {len(common_samples)}\")\n\n if old_only:\n log.info(f\" Old-only: {old_only[:5]}{'...' if len(old_only) > 5 else ''}\")\n if new_only:\n log.info(f\" New-only: {new_only[:5]}{'...' if len(new_only) > 5 else ''}\")\n\n pairs = {}\n for sample in common_samples:\n pairs[sample] = {\n 'old_tsv': old_tsvs[sample],\n 'new_tsv': new_tsvs[sample],\n }\n\n output = {\n 'bucket': args.bucket,\n 'old_submission': args.old_sub,\n 'new_submission': args.new_sub,\n 'old_sample_count': len(old_tsvs),\n 'new_sample_count': len(new_tsvs),\n 'paired_count': len(pairs),\n 'old_only': old_only,\n 'new_only': new_only,\n 'pairs': pairs,\n }\n\n with open(args.output, 'w') as f:\n json.dump(output, f, indent=2)\n\n log.info(f\"Wrote {len(pairs)} pairs to {args.output}\")\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": ".agents/skills/regression-testing/generate_report.py", "content": "#!/usr/bin/env python3\n\"\"\"Generate regression testing report with plots from per-sample JSON results.\n\nAggregates all comparison results, produces summary TSV, plots, and markdown report.\n\"\"\"\nimport argparse\nimport glob\nimport json\nimport logging\nimport os\n\nlogging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s')\nlog = logging.getLogger(__name__)\n\n# Delay imports so script can show usage without these deps\ndef get_deps():\n import pandas as pd\n import matplotlib\n matplotlib.use('Agg')\n import matplotlib.pyplot as plt\n return pd, plt\n\n\ndef load_results(results_dir):\n \"\"\"Load all per-sample JSON results.\"\"\"\n results = []\n for path in sorted(glob.glob(os.path.join(results_dir, '*.json'))):\n try:\n with open(path) as f:\n results.append(json.load(f))\n except Exception as e:\n log.warning(f\"Failed to load {path}: {e}\")\n return results\n\n\ndef build_comparison_table(results, workspace_name):\n \"\"\"Build a flat table of per-assembly comparisons.\"\"\"\n rows = []\n for r in results:\n sample_id = r.get('sample_id', 'unknown')\n for comp in r.get('comparisons', []):\n row = {\n 'workspace': workspace_name,\n 'sample_id': sample_id,\n 'assembly_id': comp.get('assembly_id', ''),\n 'taxid': comp.get('taxid', ''),\n 'tax_name': comp.get('tax_name', ''),\n }\n # Metrics\n for col in ['percent_reference_covered', 'mean_coverage',\n 'assembly_length_unambiguous', 'assembly_length',\n 'reads_aligned', 'reference_length']:\n old_val = comp.get('old_metrics', {}).get(col)\n new_val = comp.get('new_metrics', {}).get(col)\n delta = comp.get('deltas', {}).get(col)\n row[f'old_{col}'] = old_val\n row[f'new_{col}'] = new_val\n row[f'delta_{col}'] = delta\n\n # Alignment stats\n aln = comp.get('alignment')\n if aln:\n row['alignment_identity'] = aln.get('identity')\n row['snp_count'] = aln.get('snps', 0)\n row['internal_insertions'] = aln.get('internal_insertions', 0)\n row['internal_deletions'] = aln.get('internal_deletions', 0)\n row['indel_count_bp'] = aln.get('internal_insertions', 0) + aln.get('internal_deletions', 0)\n row['indel_count_events'] = aln.get('internal_insertion_events', 0) + aln.get('internal_deletion_events', 0)\n row['terminal_extensions_old'] = aln.get('terminal_extensions_old', 0)\n row['terminal_extensions_new'] = aln.get('terminal_extensions_new', 0)\n row['terminal_extension_events_old'] = aln.get('terminal_extension_events_old', 0)\n row['terminal_extension_events_new'] = aln.get('terminal_extension_events_new', 0)\n row['ambiguity_diffs'] = aln.get('ambiguity_diffs', 0)\n else:\n row['alignment_identity'] = None\n row['snp_count'] = None\n row['indel_count_bp'] = None\n row['indel_count_events'] = None\n row['terminal_extensions_old'] = None\n row['terminal_extensions_new'] = None\n row['terminal_extension_events_old'] = None\n row['terminal_extension_events_new'] = None\n row['ambiguity_diffs'] = None\n\n row['error'] = comp.get('error')\n rows.append(row)\n return rows\n\n\ndef build_sample_summary(results):\n \"\"\"Build sample-level summary table.\"\"\"\n rows = []\n for r in results:\n rows.append({\n 'sample_id': r.get('sample_id', 'unknown'),\n 'old_assembly_count': r.get('old_assembly_count', 0),\n 'new_assembly_count': r.get('new_assembly_count', 0),\n 'assembly_count_match': r.get('assembly_count_match', False),\n 'assemblies_only_in_old': len(r.get('assemblies_only_in_old', [])),\n 'assemblies_only_in_new': len(r.get('assemblies_only_in_new', [])),\n 'num_comparisons': len(r.get('comparisons', [])),\n })\n return rows\n\n\ndef generate_plots(df, plot_dir):\n \"\"\"Generate all plots from the comparison dataframe.\"\"\"\n _, plt = get_deps()\n os.makedirs(plot_dir, exist_ok=True)\n\n # Filter to rows with actual assemblies\n df_asm = df[df['old_percent_reference_covered'].notna() &\n df['new_percent_reference_covered'].notna()].copy()\n\n if len(df_asm) == 0:\n log.warning(\"No assembly comparisons with metrics — skipping plots\")\n return\n\n # 1. Percent reference covered scatter\n fig, ax = plt.subplots(figsize=(8, 8))\n ax.scatter(df_asm['old_percent_reference_covered'] * 100,\n df_asm['new_percent_reference_covered'] * 100,\n alpha=0.5, s=20)\n lims = [0, 105]\n ax.plot(lims, lims, 'r--', alpha=0.5, label='y=x')\n ax.set_xlabel('Old % Reference Covered')\n ax.set_ylabel('New % Reference Covered')\n ax.set_title('Percent Reference Covered: Old vs New')\n ax.set_xlim(lims)\n ax.set_ylim(lims)\n ax.legend()\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'pct_ref_covered_scatter.png'), dpi=150)\n plt.close(fig)\n\n # 2. Mean coverage scatter (log scale)\n df_cov = df_asm[df_asm['old_mean_coverage'].notna() &\n df_asm['new_mean_coverage'].notna() &\n (df_asm['old_mean_coverage'] > 0) &\n (df_asm['new_mean_coverage'] > 0)].copy()\n if len(df_cov) > 0:\n fig, ax = plt.subplots(figsize=(8, 8))\n ax.scatter(df_cov['old_mean_coverage'], df_cov['new_mean_coverage'],\n alpha=0.5, s=20)\n min_v = min(df_cov['old_mean_coverage'].min(), df_cov['new_mean_coverage'].min()) * 0.8\n max_v = max(df_cov['old_mean_coverage'].max(), df_cov['new_mean_coverage'].max()) * 1.2\n ax.plot([min_v, max_v], [min_v, max_v], 'r--', alpha=0.5, label='y=x')\n ax.set_xscale('log')\n ax.set_yscale('log')\n ax.set_xlabel('Old Mean Coverage')\n ax.set_ylabel('New Mean Coverage')\n ax.set_title('Mean Coverage: Old vs New')\n ax.legend()\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'mean_coverage_scatter.png'), dpi=150)\n plt.close(fig)\n\n # 3. Assembly length scatter\n df_len = df_asm[df_asm['old_assembly_length_unambiguous'].notna() &\n df_asm['new_assembly_length_unambiguous'].notna()].copy()\n if len(df_len) > 0:\n fig, ax = plt.subplots(figsize=(8, 8))\n ax.scatter(df_len['old_assembly_length_unambiguous'],\n df_len['new_assembly_length_unambiguous'],\n alpha=0.5, s=20)\n min_v = min(df_len['old_assembly_length_unambiguous'].min(),\n df_len['new_assembly_length_unambiguous'].min()) * 0.95\n max_v = max(df_len['old_assembly_length_unambiguous'].max(),\n df_len['new_assembly_length_unambiguous'].max()) * 1.05\n ax.plot([min_v, max_v], [min_v, max_v], 'r--', alpha=0.5, label='y=x')\n ax.set_xlabel('Old Unambiguous Length')\n ax.set_ylabel('New Unambiguous Length')\n ax.set_title('Assembly Length (Unambiguous): Old vs New')\n ax.legend()\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'assembly_length_scatter.png'), dpi=150)\n plt.close(fig)\n\n # 4. Delta pct_ref_covered histogram\n deltas = df_asm['delta_percent_reference_covered'].dropna() * 100\n if len(deltas) > 0:\n fig, ax = plt.subplots(figsize=(8, 5))\n ax.hist(deltas, bins=50, edgecolor='black', alpha=0.7)\n ax.axvline(0, color='r', linestyle='--', alpha=0.5)\n ax.set_xlabel('Delta % Reference Covered (New - Old)')\n ax.set_ylabel('Count')\n ax.set_title(f'Distribution of % Reference Covered Changes (n={len(deltas)})')\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'delta_pct_ref_covered_hist.png'), dpi=150)\n plt.close(fig)\n\n # 5. Alignment identity histogram\n df_aln = df_asm[df_asm['alignment_identity'].notna()].copy()\n if len(df_aln) > 0:\n fig, ax = plt.subplots(figsize=(8, 5))\n identities = df_aln['alignment_identity'] * 100\n ax.hist(identities, bins=50, edgecolor='black', alpha=0.7)\n ax.set_xlabel('Pairwise Identity (%)')\n ax.set_ylabel('Count')\n ax.set_title(f'Assembly Identity Distribution (n={len(identities)})')\n ax.axvline(100, color='r', linestyle='--', alpha=0.3)\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'alignment_identity_hist.png'), dpi=150)\n plt.close(fig)\n\n # 6. SNP and indel count histograms\n if len(df_aln) > 0:\n fig, axes = plt.subplots(1, 2, figsize=(14, 5))\n\n snps = df_aln['snp_count'].dropna()\n if len(snps) > 0:\n max_snp = int(snps.max())\n bins_snp = range(0, max(max_snp + 2, 3))\n axes[0].hist(snps, bins=bins_snp, edgecolor='black', alpha=0.7)\n axes[0].set_xlabel('SNP Count')\n axes[0].set_ylabel('Number of Assemblies')\n axes[0].set_title(f'SNPs per Assembly (n={len(snps)})')\n\n indels = df_aln['indel_count_events'].dropna()\n if len(indels) > 0:\n max_indel = int(indels.max())\n bins_indel = range(0, max(max_indel + 2, 3))\n axes[1].hist(indels, bins=bins_indel, edgecolor='black', alpha=0.7)\n axes[1].set_xlabel('Indel Count (internal)')\n axes[1].set_ylabel('Number of Assemblies')\n axes[1].set_title(f'Internal Indels per Assembly (n={len(indels)})')\n\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'snp_indel_counts.png'), dpi=150)\n plt.close(fig)\n\n # 7. Terminal extensions histogram\n if len(df_aln) > 0:\n ext_old = df_aln['terminal_extensions_old'].dropna()\n ext_new = df_aln['terminal_extensions_new'].dropna()\n has_ext = (ext_old > 0) | (ext_new > 0)\n if has_ext.any():\n fig, ax = plt.subplots(figsize=(8, 5))\n ax.hist(ext_new[has_ext], bins=30, alpha=0.6, label='New extends beyond Old', edgecolor='black')\n ax.hist(ext_old[has_ext], bins=30, alpha=0.6, label='Old extends beyond New', edgecolor='black')\n ax.set_xlabel('Terminal Extension (bp)')\n ax.set_ylabel('Count')\n ax.set_title('Terminal Extensions')\n ax.legend()\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'terminal_extensions_hist.png'), dpi=150)\n plt.close(fig)\n\n # 8. Coverage vs identity\n if len(df_aln) > 0:\n df_ci = df_aln[df_aln['old_mean_coverage'].notna() & (df_aln['old_mean_coverage'] > 0)].copy()\n if len(df_ci) > 0:\n fig, ax = plt.subplots(figsize=(8, 5))\n ax.scatter(df_ci['old_mean_coverage'], df_ci['alignment_identity'] * 100,\n alpha=0.5, s=20)\n ax.set_xscale('log')\n ax.set_xlabel('Mean Coverage')\n ax.set_ylabel('Pairwise Identity (%)')\n ax.set_title('Coverage vs Assembly Identity')\n fig.tight_layout()\n fig.savefig(os.path.join(plot_dir, 'coverage_vs_identity.png'), dpi=150)\n plt.close(fig)\n\n log.info(f\"Generated plots in {plot_dir}\")\n\n\ndef generate_markdown_report(df, sample_df, workspace_name, report_dir, plot_dir):\n \"\"\"Generate markdown report.\"\"\"\n pd, _ = get_deps()\n\n total_samples = len(sample_df)\n if sample_df.empty or 'old_assembly_count' not in sample_df.columns:\n samples_with_assemblies = 0\n samples_count_match = 0\n else:\n samples_with_assemblies = len(sample_df[sample_df['old_assembly_count'] > 0])\n samples_count_match = len(sample_df[sample_df['assembly_count_match']])\n samples_count_mismatch = total_samples - samples_count_match\n\n total_assemblies = len(df)\n if df.empty or 'alignment_identity' not in df.columns:\n df_aln = pd.DataFrame()\n else:\n df_aln = df[df['alignment_identity'].notna()]\n\n identical = len(df_aln[df_aln['alignment_identity'] >= 1.0]) if len(df_aln) > 0 else 0\n near_identical = len(df_aln[(df_aln['alignment_identity'] >= 0.999) & (df_aln['alignment_identity'] < 1.0)]) if len(df_aln) > 0 else 0\n minor_diff = len(df_aln[(df_aln['alignment_identity'] >= 0.99) & (df_aln['alignment_identity'] < 0.999)]) if len(df_aln) > 0 else 0\n significant_diff = len(df_aln[df_aln['alignment_identity'] < 0.99]) if len(df_aln) > 0 else 0\n\n if len(df_aln) > 0 and 'snp_count' in df_aln.columns:\n with_snps = len(df_aln[df_aln['snp_count'] > 0])\n with_indels = len(df_aln[df_aln['indel_count_events'] > 0])\n with_ambig = len(df_aln[df_aln['ambiguity_diffs'] > 0])\n with_terminal = len(df_aln[(df_aln['terminal_extensions_old'] > 0) | (df_aln['terminal_extensions_new'] > 0)])\n total_snps = int(df_aln['snp_count'].sum())\n total_indel_bp = int(df_aln['indel_count_bp'].sum())\n total_indel_events = int(df_aln['indel_count_events'].sum())\n total_ambig = int(df_aln['ambiguity_diffs'].sum())\n total_terminal_bp_old = int(df_aln['terminal_extensions_old'].sum())\n total_terminal_bp_new = int(df_aln['terminal_extensions_new'].sum())\n total_terminal_events_old = int(df_aln['terminal_extension_events_old'].sum())\n total_terminal_events_new = int(df_aln['terminal_extension_events_new'].sum())\n else:\n with_snps = with_indels = with_ambig = with_terminal = 0\n total_snps = total_indel_bp = total_indel_events = total_ambig = 0\n total_terminal_bp_old = total_terminal_bp_new = 0\n total_terminal_events_old = total_terminal_events_new = 0\n\n report_path = os.path.join(report_dir, f'report_{workspace_name}.md')\n with open(report_path, 'w') as f:\n f.write(f\"# Regression Report: {workspace_name}\\n\\n\")\n f.write(f\"## Summary\\n\\n\")\n f.write(f\"| Metric | Value |\\n\")\n f.write(f\"|--------|-------|\\n\")\n f.write(f\"| Total samples compared | {total_samples} |\\n\")\n f.write(f\"| Samples with assemblies (old) | {samples_with_assemblies} |\\n\")\n f.write(f\"| Samples with matching assembly count | {samples_count_match} |\\n\")\n f.write(f\"| Samples with mismatched assembly count | {samples_count_mismatch} |\\n\")\n f.write(f\"| Total assembly comparisons | {total_assemblies} |\\n\")\n f.write(f\"| Assemblies aligned | {len(df_aln)} |\\n\\n\")\n\n f.write(f\"## Assembly Identity\\n\\n\")\n f.write(f\"| Category | Count | % |\\n\")\n f.write(f\"|----------|-------|---|\\n\")\n if len(df_aln) > 0:\n f.write(f\"| Identical (100%) | {identical} | {100*identical/len(df_aln):.1f}% |\\n\")\n f.write(f\"| Near-identical (99.9-100%) | {near_identical} | {100*near_identical/len(df_aln):.1f}% |\\n\")\n f.write(f\"| Minor differences (99-99.9%) | {minor_diff} | {100*minor_diff/len(df_aln):.1f}% |\\n\")\n f.write(f\"| Significant differences (<99%) | {significant_diff} | {100*significant_diff/len(df_aln):.1f}% |\\n\")\n f.write(f\"\\n\")\n\n f.write(f\"## Variant Counts\\n\\n\")\n f.write(f\"| Metric | Assemblies affected | Events | Bases |\\n\")\n f.write(f\"|--------|--------------------:|-------:|------:|\\n\")\n f.write(f\"| SNPs (A/C/G/T ↔ A/C/G/T) | {with_snps} | {total_snps} | {total_snps} |\\n\")\n f.write(f\"| Internal indels | {with_indels} | {total_indel_events} | {total_indel_bp} |\\n\")\n f.write(f\"| Ambiguity diffs (N ↔ A/C/G/T) | {with_ambig} | {total_ambig} | {total_ambig} |\\n\")\n f.write(f\"| Terminal extensions (old only) | {with_terminal} | {total_terminal_events_old} | {total_terminal_bp_old} |\\n\")\n f.write(f\"| Terminal extensions (new only) | {with_terminal} | {total_terminal_events_new} | {total_terminal_bp_new} |\\n\\n\")\n\n # Metrics summary\n if len(df_aln) > 0:\n f.write(f\"## Metrics Summary\\n\\n\")\n f.write(f\"| Metric | Median delta | Mean delta | Min | Max |\\n\")\n f.write(f\"|--------|-------------|------------|-----|-----|\\n\")\n for col, label in [\n ('delta_percent_reference_covered', '% Ref Covered'),\n ('delta_mean_coverage', 'Mean Coverage'),\n ('delta_assembly_length_unambiguous', 'Unambig Length'),\n ]:\n vals = df[col].dropna()\n if len(vals) > 0:\n f.write(f\"| {label} | {vals.median():.4f} | {vals.mean():.4f} | {vals.min():.4f} | {vals.max():.4f} |\\n\")\n f.write(f\"\\n\")\n\n # Divergent assemblies\n if len(df_aln) > 0 and 'alignment_identity' in df_aln.columns:\n divergent = df_aln[df_aln['alignment_identity'] < 0.999].sort_values('alignment_identity')\n else:\n divergent = pd.DataFrame()\n if len(divergent) > 0:\n f.write(f\"## Divergent Assemblies (identity < 99.9%)\\n\\n\")\n f.write(f\"| Assembly ID | Tax Name | Identity | SNPs | Indel events (bp) | Ambig Diffs | Term Ext Old events (bp) | Term Ext New events (bp) |\\n\")\n f.write(f\"|-------------|----------|----------|------|-------------------|-------------|--------------------------|---------------------------|\\n\")\n for _, row in divergent.iterrows():\n indel_ev = int(row.get('indel_count_events', 0))\n indel_bp = int(row.get('indel_count_bp', 0))\n term_old_ev = int(row.get('terminal_extension_events_old', 0))\n term_old_bp = int(row.get('terminal_extensions_old', 0))\n term_new_ev = int(row.get('terminal_extension_events_new', 0))\n term_new_bp = int(row.get('terminal_extensions_new', 0))\n f.write(f\"| {row['assembly_id']} | {row['tax_name']} | \"\n f\"{row['alignment_identity']*100:.3f}% | {row['snp_count']:.0f} | \"\n f\"{indel_ev} ({indel_bp}) | {row['ambiguity_diffs']:.0f} | \"\n f\"{term_old_ev} ({term_old_bp}) | \"\n f\"{term_new_ev} ({term_new_bp}) |\\n\")\n f.write(f\"\\n\")\n\n # Assembly count mismatches\n if 'assembly_count_match' not in sample_df.columns:\n mismatches = pd.DataFrame()\n else:\n mismatches = sample_df[~sample_df['assembly_count_match']]\n if len(mismatches) > 0:\n f.write(f\"## Assembly Count Mismatches\\n\\n\")\n f.write(f\"| Sample | Old Count | New Count | Only Old | Only New |\\n\")\n f.write(f\"|--------|-----------|-----------|----------|----------|\\n\")\n for _, row in mismatches.iterrows():\n f.write(f\"| {row['sample_id']} | {row['old_assembly_count']} | \"\n f\"{row['new_assembly_count']} | {row['assemblies_only_in_old']} | \"\n f\"{row['assemblies_only_in_new']} |\\n\")\n f.write(f\"\\n\")\n\n # Plot references\n f.write(f\"## Plots\\n\\n\")\n plot_files = sorted(os.listdir(plot_dir)) if os.path.isdir(plot_dir) else []\n for pf in plot_files:\n if pf.endswith('.png'):\n rel_plot_dir = os.path.basename(plot_dir)\n f.write(f\"![{pf}]({rel_plot_dir}/{pf})\\n\\n\")\n\n log.info(f\"Report written to {report_path}\")\n return report_path\n\n\ndef main():\n parser = argparse.ArgumentParser(description=__doc__)\n parser.add_argument('--results-dir', required=True, help='Directory with per-sample JSON results')\n parser.add_argument('--report-dir', required=True, help='Output directory for report')\n parser.add_argument('--workspace-name', required=True, help='Workspace name for report title')\n args = parser.parse_args()\n\n pd, plt = get_deps()\n\n results = load_results(args.results_dir)\n log.info(f\"Loaded {len(results)} sample results\")\n\n # Build comparison table\n comp_rows = build_comparison_table(results, args.workspace_name)\n df = pd.DataFrame(comp_rows)\n log.info(f\"Total assembly comparisons: {len(df)}\")\n\n # Build sample summary\n sample_rows = build_sample_summary(results)\n sample_df = pd.DataFrame(sample_rows)\n\n # Save summary TSV\n os.makedirs(args.report_dir, exist_ok=True)\n tsv_path = os.path.join(args.report_dir, f'summary_{args.workspace_name}.tsv')\n if len(df) > 0:\n df.to_csv(tsv_path, sep='\\t', index=False)\n log.info(f\"Summary TSV written to {tsv_path}\")\n\n # Generate plots\n plot_dir = os.path.join(args.report_dir, f'plots_{args.workspace_name}')\n if len(df) > 0:\n generate_plots(df, plot_dir)\n\n # Generate markdown report\n generate_markdown_report(df, sample_df, args.workspace_name, args.report_dir, plot_dir)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": ".agents/skills/regression-testing/run_vadr.sh", "content": "#!/bin/bash\n# Run VADR on a single FASTA file.\n# Inputs (env vars set by dsub):\n# FASTA - input FASTA file (localized by dsub)\n# VADR_OPTS - vadr options string\n# MIN_LEN - minimum sequence length (optional)\n# MAX_LEN - maximum sequence length (optional)\n# MODEL_URL - URL to vadr model tarball\n# MODEL_SUB - subdirectory within model tarball (optional)\n# Outputs (env vars set by dsub):\n# NUM_ALERTS - file to write num_alerts integer\n# ALERTS_TSV - file to write alerts TSV\n# VADR_TGZ - file to write full vadr output tarball\n\nset -euo pipefail\n\n# Default optional env vars to empty\nMODEL_URL=\"${MODEL_URL:-}\"\nMODEL_SUB=\"${MODEL_SUB:-}\"\nMIN_LEN=\"${MIN_LEN:-}\"\nMAX_LEN=\"${MAX_LEN:-}\"\n\nBASENAME=$(basename \"${FASTA}\" .fasta)\n\n# Download and unpack VADR models\nif [ -n \"${MODEL_URL}\" ]; then\n mkdir -p vadr-untar\n curl -fsSL \"${MODEL_URL}\" | tar -C vadr-untar -xzf -\n MODEL_DIR=$(find vadr-untar -mindepth 1 -maxdepth 1 -type d | head -1)\n ln -s \"${MODEL_DIR}\" vadr-models\nelse\n ln -s /opt/vadr/vadr-models vadr-models\nfi\n\nif [ -n \"${MODEL_SUB}\" ]; then\n VADR_MODEL_DIR=\"vadr-models/${MODEL_SUB}\"\nelse\n VADR_MODEL_DIR=\"vadr-models\"\nfi\n\n# Build trim args\nTRIM_ARGS=\"\"\nif [ -n \"${MIN_LEN}\" ]; then\n TRIM_ARGS=\"${TRIM_ARGS} --minlen ${MIN_LEN}\"\nfi\nif [ -n \"${MAX_LEN}\" ]; then\n TRIM_ARGS=\"${TRIM_ARGS} --maxlen ${MAX_LEN}\"\nfi\n\n# Remove terminal ambiguous nucleotides\n/opt/vadr/vadr/miniscripts/fasta-trim-terminal-ambigs.pl \\\n \"${FASTA}\" ${TRIM_ARGS} > \"${BASENAME}.trimmed.fasta\"\n\n# Run VADR\nv-annotate.pl \\\n ${VADR_OPTS} \\\n --split --cpu $(nproc) \\\n --mdir \"${VADR_MODEL_DIR}\" \\\n \"${BASENAME}.trimmed.fasta\" \\\n \"${BASENAME}\"\n\n# Package outputs\ntar -C \"${BASENAME}\" -czf \"${VADR_TGZ}\" .\n\n# Extract alerts\ncut -f 5 \"${BASENAME}/${BASENAME}.vadr.alt.list\" | tail -n +2 > alerts.tsv\ncp alerts.tsv \"${ALERTS_TSV}\"\nwc -l < alerts.tsv > \"${NUM_ALERTS}\"\n\necho \"VADR complete. Alerts: $(cat \"${NUM_ALERTS}\")\"\n" }, { "path": ".claude/rules/container-vulns.md", "content": "---\npaths:\n - \"docker/**\"\n - \".trivyignore\"\n - \".trivy-ignore-policy.rego\"\n - \"vulnerability-mitigation-status.md\"\n - \".github/workflows/container-scan.yml\"\n - \".github/workflows/docker.yml\"\n---\n\nFor container vulnerability management guidance, see\n.agents/skills/container-vulns/SKILL.md\n" }, { "path": ".codecov.yml", "content": "# Codecov configuration\n# https://docs.codecov.com/docs/codecov-yaml\n\ncoverage:\n status:\n project:\n default:\n informational: true # Never fails, just shows coverage info\n patch:\n default:\n informational: true # Never fails, just shows patch coverage\n\n# Flag configuration for multi-component coverage\nflags:\n core:\n paths:\n - src/viral_ngs/core/\n - src/viral_ngs/util/\n - src/viral_ngs/*.py\n carryforward: true\n assemble:\n paths:\n - src/viral_ngs/assemble/\n - src/viral_ngs/assembly.py\n carryforward: true\n classify:\n paths:\n - src/viral_ngs/classify/\n - src/viral_ngs/metagenomics.py\n - src/viral_ngs/taxon_filter.py\n - src/viral_ngs/kmer_utils.py\n carryforward: true\n phylo:\n paths:\n - src/viral_ngs/phylo/\n - src/viral_ngs/interhost.py\n - src/viral_ngs/intrahost.py\n - src/viral_ngs/ncbi.py\n carryforward: true\n\ncomment:\n layout: \"reach,diff,flags,files\"\n behavior: default\n require_changes: true # Only comment if coverage changes\n" }, { "path": ".dockerignore", "content": "*.pyc\n__pycache__\n" }, { "path": ".gitattributes", "content": "*.rules linguist-language=Python\n" }, { "path": ".github/actions/create-manifest/action.yml", "content": "name: 'Create Multi-Arch Manifest'\ndescription: 'Create multi-arch Docker manifest'\ninputs:\n ghcr-repo:\n description: 'GHCR repository base (e.g., ghcr.io/broadinstitute/viral-ngs)'\n required: true\n target-tag:\n description: 'Target manifest tag (just the tag, not full URL)'\n required: true\n source-amd64:\n description: 'Source AMD64 image tag'\n required: true\n source-arm64:\n description: 'Source ARM64 image tag'\n required: true\n description:\n description: 'Image description (reserved for future use)'\n required: false\n\nruns:\n using: 'composite'\n steps:\n - name: Create manifest\n shell: bash\n run: |\n docker buildx imagetools create \\\n --tag \"${{ inputs.ghcr-repo }}:${{ inputs.target-tag }}\" \\\n \"${{ inputs.ghcr-repo }}:${{ inputs.source-amd64 }}\" \\\n \"${{ inputs.ghcr-repo }}:${{ inputs.source-arm64 }}\"\n\n - name: Verify Docker Manifest List v2 format\n shell: bash\n run: |\n set -euo pipefail\n\n REPO_PATH=\"${REPO#ghcr.io/}\"\n\n # Fetch registry access token\n TOKEN=$(curl -fsS \"https://ghcr.io/token?service=ghcr.io&scope=repository:${REPO_PATH}:pull\" | jq -er .token) || {\n echo \"FAIL: Unable to retrieve token from ghcr.io\"\n exit 1\n }\n\n # Fetch manifest and capture HTTP status code + content type\n HTTP_STATUS=$(curl -sS -o /dev/null -w '%{http_code}' \\\n -H \"Authorization: Bearer $TOKEN\" \\\n -H \"Accept: application/vnd.docker.distribution.manifest.list.v2+json\" \\\n \"https://ghcr.io/v2/${REPO_PATH}/manifests/${{ inputs.target-tag }}\") || {\n echo \"FAIL: Unable to retrieve manifest from ghcr.io for tag '${{ inputs.target-tag }}'\"\n exit 1\n }\n\n if [ \"$HTTP_STATUS\" != \"200\" ]; then\n echo \"FAIL: Expected HTTP 200 when fetching manifest, got: $HTTP_STATUS\"\n exit 1\n fi\n\n CONTENT_TYPE=$(curl -sS -D- -o /dev/null \\\n -H \"Authorization: Bearer $TOKEN\" \\\n -H \"Accept: application/vnd.docker.distribution.manifest.list.v2+json\" \\\n \"https://ghcr.io/v2/${REPO_PATH}/manifests/${{ inputs.target-tag }}\" | grep -i content-type)\n\n if echo \"$CONTENT_TYPE\" | grep -qi \"manifest.list.v2\"; then\n echo \"OK: Docker Manifest List v2 format confirmed\"\n else\n echo \"FAIL: Expected Docker Manifest List v2, got: $CONTENT_TYPE\"\n exit 1\n fi\n env:\n REPO: ${{ inputs.ghcr-repo }}\n" }, { "path": ".github/actions/pull-with-retry/action.yml", "content": "name: 'Pull Docker Image with Retry'\ndescription: 'Pull a Docker image with retry logic'\ninputs:\n image:\n description: 'Full image reference to pull'\n required: true\n max-retries:\n description: 'Maximum number of retry attempts'\n default: '5'\n retry-delay:\n description: 'Delay between retries in seconds'\n default: '10'\n\nruns:\n using: 'composite'\n steps:\n - name: Pull image with retries\n shell: bash\n run: |\n for i in $(seq 1 ${{ inputs.max-retries }}); do\n echo \"Attempt $i: Pulling ${{ inputs.image }}...\"\n if docker pull \"${{ inputs.image }}\"; then\n echo \"Successfully pulled image\"\n exit 0\n fi\n echo \"Pull failed, waiting ${{ inputs.retry-delay }} seconds before retry...\"\n sleep ${{ inputs.retry-delay }}\n done\n echo \"Failed to pull image after ${{ inputs.max-retries }} attempts\"\n exit 1\n" }, { "path": ".github/actions/setup-docker-build/action.yml", "content": "name: 'Setup Docker Build'\ndescription: 'Checkout, setup buildx, and login to GHCR'\ninputs:\n github-token:\n description: 'GitHub token for GHCR login'\n required: true\n checkout:\n description: 'Whether to checkout repository'\n default: 'true'\n fetch-depth:\n description: 'Git fetch depth'\n default: '1'\n fetch-tags:\n description: 'Whether to fetch tags'\n default: 'false'\n\nruns:\n using: 'composite'\n steps:\n - name: Checkout repository\n if: ${{ inputs.checkout == 'true' }}\n uses: actions/checkout@v4\n with:\n fetch-depth: ${{ inputs.fetch-depth }}\n fetch-tags: ${{ inputs.fetch-tags }}\n\n - name: Set up Docker Buildx\n uses: docker/setup-buildx-action@v3\n\n - name: Log in to GitHub Container Registry\n uses: docker/login-action@v3\n with:\n registry: ghcr.io\n username: ${{ github.actor }}\n password: ${{ inputs.github-token }}\n" }, { "path": ".github/copilot-instructions.md", "content": "# Copilot Instructions\n\nThis file provides guidance to GitHub Copilot when working with code in this repository.\n\n**IMPORTANT**: Always read [AGENTS.md](../AGENTS.md) at the start of every session before doing any work. It contains comprehensive project context and development guidelines that are essential for working in this codebase.\n\n## Quick Reference\n\n- **Docker-centric development**: Run tests inside containers, not on host\n- **Import pattern**: `from viral_ngs import core` then `core.samtools.SamtoolsTool()`\n- **Test location**: `tests/unit//`\n- **Dependencies**: ALL via conda, not pip (see `docker/requirements/*.txt`)\n\n## Running Tests\n\n```bash\ndocker run --rm \\\n -v $(pwd):/opt/viral-ngs/source \\\n quay.io/broadinstitute/viral-ngs:main-core \\\n pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit\n```\n\n## Key Files\n\n| File | Purpose |\n|------|---------|\n| [AGENTS.md](../AGENTS.md) | Full AI assistant guidance |\n| [pyproject.toml](../pyproject.toml) | Package configuration |\n| [docker/](../docker/) | Dockerfiles and requirements |\n| [src/viral_ngs/](../src/viral_ngs/) | Source code |\n| [tests/](../tests/) | Test files |\n| [.agents/skills/](../.agents/skills/) | Reusable agent playbooks and scripts |\n" }, { "path": ".github/workflows/audit-quay-tags.yml", "content": "name: Audit Quay.io Tags\n\non:\n schedule:\n - cron: '0 8 * * 1' # Monday 8:00 UTC\n workflow_dispatch:\n\npermissions: {}\n\njobs:\n audit-tags:\n runs-on: ubuntu-latest\n permissions: {}\n\n steps:\n - name: Install crane\n uses: imjasonh/setup-crane@v0.4\n\n - name: Log in to Quay.io\n uses: docker/login-action@v3\n with:\n registry: quay.io\n username: ${{ secrets.QUAY_USERNAME }}\n password: ${{ secrets.QUAY_TOKEN }}\n\n - name: Audit version tags\n run: |\n set -euo pipefail\n REPO=\"quay.io/broadinstitute/viral-ngs\"\n FLAVORS=\"baseimage core assemble classify phylo\"\n FAILED=0\n\n # Check the 5 most recent version tags\n VERSIONS=$(crane ls \"$REPO\" | grep -E '^[0-9]+\\.[0-9]+\\.[0-9]+$' | sort -V | tail -5)\n\n if [[ -z \"$VERSIONS\" ]]; then\n echo \"::error::No version tags found on ${REPO}\"\n exit 1\n fi\n\n check_tag() {\n local TAG=\"$1\"\n if ! crane manifest \"${REPO}:${TAG}\" > /dev/null 2>&1; then\n echo \"::error::MISSING: ${REPO}:${TAG}\"\n FAILED=1\n else\n echo \"OK: ${REPO}:${TAG}\"\n fi\n }\n\n for VERSION in $VERSIONS; do\n MAJOR_MINOR=$(echo \"$VERSION\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n\n # Check mega tag (no suffix) — both X.Y.Z and X.Y\n check_tag \"${VERSION}\"\n check_tag \"${MAJOR_MINOR}\"\n\n # Check each flavor — both X.Y.Z-flavor and X.Y-flavor\n for FLAVOR in $FLAVORS; do\n check_tag \"${VERSION}-${FLAVOR}\"\n check_tag \"${MAJOR_MINOR}-${FLAVOR}\"\n done\n done\n\n if [[ $FAILED -ne 0 ]]; then\n echo \"::error::Some version tags are missing from Quay.io!\"\n exit 1\n fi\n echo \"All version tags verified.\"\n" }, { "path": ".github/workflows/cleanup-images.yml", "content": "name: Cleanup Feature Branch Images\n\non:\n delete:\n\njobs:\n cleanup-quay-images:\n # Only run for branch deletions (not tags), and skip main\n if: github.event.ref_type == 'branch' && github.event.ref != 'main'\n runs-on: ubuntu-latest\n permissions: {}\n\n steps:\n - name: Compute tag prefix\n id: tag-prefix\n run: |\n # Apply the same sanitization as docker.yml's \"Compute Docker image tag prefix\":\n # replace \"/\" with \"-\" and strip leading \"v\"\n RAW=\"${{ github.event.ref }}\"\n PREFIX=$(echo \"$RAW\" | sed 's|/|-|g')\n PREFIX=${PREFIX#v}\n echo \"prefix=${PREFIX}\" >> $GITHUB_OUTPUT\n echo \"Tag prefix: ${PREFIX} (from branch: ${RAW})\"\n\n - name: Safety check - refuse version-like branch names\n run: |\n PREFIX=\"${{ steps.tag-prefix.outputs.prefix }}\"\n if [[ \"$PREFIX\" =~ ^[0-9]+\\.[0-9]+ ]]; then\n echo \"::error::Refusing to delete tags for version-like branch: $PREFIX\"\n exit 1\n fi\n\n - name: Install crane\n uses: imjasonh/setup-crane@v0.4\n\n - name: Log in to Quay.io\n uses: docker/login-action@v3\n with:\n registry: quay.io\n username: ${{ secrets.QUAY_USERNAME }}\n password: ${{ secrets.QUAY_TOKEN }}\n\n - name: Delete feature branch tags from Quay\n run: |\n TAG_PREFIX=\"${{ steps.tag-prefix.outputs.prefix }}\"\n QUAY_REPO=\"quay.io/broadinstitute/viral-ngs\"\n\n # Image tag suffixes - must be kept in sync with deploy-to-quay in docker.yml\n # See: .github/workflows/docker.yml deploy-to-quay job matrix\n SUFFIXES=(\"-baseimage\" \"-core\" \"-assemble\" \"-classify\" \"-phylo\" \"\")\n\n for SUFFIX in \"${SUFFIXES[@]}\"; do\n TAG=\"${TAG_PREFIX}${SUFFIX}\"\n echo \"Deleting ${QUAY_REPO}:${TAG}...\"\n # Use crane delete instead of skopeo delete. crane removes only the tag\n # reference, not the underlying manifest. This prevents cascade deletion\n # of other tags sharing the same digest (which caused the 3.0.10-baseimage\n # incident: skopeo deleted the manifest by digest, expiring all tags\n # pointing to it).\n crane delete \"${QUAY_REPO}:${TAG}\" 2>&1 || echo \" Tag ${TAG} not found or already deleted\"\n done\n" }, { "path": ".github/workflows/container-scan.yml", "content": "name: Scheduled Container Vulnerability Scan\n\non:\n schedule:\n # Weekly scan of main branch mega image every Monday at 06:00 UTC\n - cron: '0 6 * * 1'\n workflow_dispatch:\n inputs:\n test_cve_id:\n description: 'Optional: bypass new-CVE detection and force-analyze this specific CVE ID (for testing the Claude pipeline)'\n required: false\n type: string\n default: ''\n dry_run:\n description: 'Run Claude analysis but do NOT file GitHub issues (artifact still uploaded)'\n required: false\n type: boolean\n default: false\n\npermissions: {}\n\nenv:\n GHCR_REPO: ghcr.io/broadinstitute/viral-ngs\n\njobs:\n scan:\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: read\n security-events: write\n issues: write # for filing CVE issues\n id-token: write # for OIDC token to GCP via WIF\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n with:\n # Full history so the Claude analysis step can `git log --grep` and `git show`\n # precedent CVE-fix commits (e.g., to mirror past mitigation patterns exactly).\n fetch-depth: 0\n\n - name: Log in to GHCR\n uses: docker/login-action@v3\n with:\n registry: ghcr.io\n username: ${{ github.actor }}\n password: ${{ secrets.GITHUB_TOKEN }}\n\n - name: Run Trivy vulnerability scanner\n uses: aquasecurity/trivy-action@master\n with:\n image-ref: '${{ env.GHCR_REPO }}:main-mega-amd64'\n format: 'sarif'\n output: 'trivy-results.sarif'\n severity: 'CRITICAL,HIGH'\n limit-severities-for-sarif: true\n exit-code: '0'\n ignore-unfixed: true\n trivyignores: '.trivyignore'\n ignore-policy: '.trivy-ignore-policy.rego'\n\n - name: Run Trivy vulnerability scanner (JSON)\n uses: aquasecurity/trivy-action@master\n with:\n image-ref: '${{ env.GHCR_REPO }}:main-mega-amd64'\n format: 'json'\n output: 'trivy-results.json'\n severity: 'CRITICAL,HIGH'\n exit-code: '0' # don't fail here — Claude pipeline + final-step gate handles signaling\n ignore-unfixed: true\n trivyignores: '.trivyignore'\n ignore-policy: '.trivy-ignore-policy.rego'\n\n - name: Log scan result count\n if: always()\n run: |\n if [ -f trivy-results.sarif ]; then\n COUNT=$(jq '[.runs[].results[]] | length' trivy-results.sarif)\n echo \"::notice::Trivy found $COUNT findings for mega-scheduled (after policy filtering)\"\n fi\n\n - name: Upload Trivy scan results to GitHub Security tab\n if: always()\n uses: github/codeql-action/upload-sarif@v3\n with:\n sarif_file: 'trivy-results.sarif'\n category: 'container-mega-scheduled'\n\n - name: Upload Trivy JSON results\n if: always()\n uses: actions/upload-artifact@v4\n with:\n name: trivy-mega-scheduled\n path: trivy-results.json\n\n # === Claude triage pipeline ===\n # If new fixable HIGH/CRITICAL CVEs are found, hand them to Claude (Sonnet 4.6\n # on Vertex AI) for analysis, then file GitHub issues. Source of truth for\n # \"new\" is GH issues themselves: a CVE is new if no existing issue (open OR\n # closed) has the CVE ID in its title.\n\n - name: Identify new fixable CVEs\n id: triage\n env:\n GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}\n # Use github.event.inputs (not inputs) so this is well-defined on schedule too.\n TEST_CVE_ID: ${{ github.event.inputs.test_cve_id || '' }}\n run: |\n set -euo pipefail\n\n # Test mode: bypass scan-diff and use the provided CVE ID directly.\n if [ -n \"${TEST_CVE_ID:-}\" ]; then\n echo \"::notice::Test mode active — analyzing TEST_CVE_ID=$TEST_CVE_ID\"\n echo \"cve_ids=$TEST_CVE_ID\" >> \"$GITHUB_OUTPUT\"\n echo \"test_mode=true\" >> \"$GITHUB_OUTPUT\"\n exit 0\n fi\n\n # Production mode: parse trivy JSON for fixable HIGH/CRITICAL CVEs.\n all_cves=$(jq -r '\n [.Results[]?.Vulnerabilities[]?\n | select((.Severity == \"HIGH\" or .Severity == \"CRITICAL\")\n and (.FixedVersion // \"\") != \"\")\n | .VulnerabilityID]\n | unique[]\n ' trivy-results.json)\n\n if [ -z \"$all_cves\" ]; then\n echo \"::notice::No fixable HIGH/CRITICAL CVEs in scan.\"\n echo \"cve_ids=\" >> \"$GITHUB_OUTPUT\"\n echo \"test_mode=false\" >> \"$GITHUB_OUTPUT\"\n exit 0\n fi\n\n # Dedup against existing GH issues (open + closed) by title-substring search.\n new_cves=()\n for cve in $all_cves; do\n count=$(gh search issues \\\n --repo \"$GITHUB_REPOSITORY\" \\\n --state=all \\\n \"\\\"$cve\\\" in:title\" \\\n --json url --jq 'length')\n if [ \"$count\" = \"0\" ]; then\n new_cves+=(\"$cve\")\n echo \" NEW: $cve\"\n else\n echo \" existing issue for $cve, skipping\"\n fi\n done\n\n new_list=\"${new_cves[*]:-}\"\n echo \"::notice::Found ${#new_cves[@]} new fixable CVE(s)\"\n echo \"cve_ids=$new_list\" >> \"$GITHUB_OUTPUT\"\n echo \"test_mode=false\" >> \"$GITHUB_OUTPUT\"\n\n - name: Authenticate to GCP via Workload Identity Federation\n if: steps.triage.outputs.cve_ids != ''\n uses: google-github-actions/auth@v2\n with:\n workload_identity_provider: ${{ vars.GCP_WIP_PROVIDER }}\n service_account: ${{ vars.GCP_SA_EMAIL }}\n\n - name: Ensure issue labels exist\n if: steps.triage.outputs.cve_ids != '' && (github.event.inputs.dry_run || 'false') != 'true'\n env:\n GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}\n run: |\n # Idempotent: gh label create exits non-zero if label exists; ignore that.\n gh label create security --color B60205 --description \"Security-related issue\" --repo \"$GITHUB_REPOSITORY\" 2>/dev/null || true\n gh label create cve --color B60205 --description \"CVE tracked in container scans\" --repo \"$GITHUB_REPOSITORY\" 2>/dev/null || true\n gh label create test --color FBCA04 --description \"Test issue (filed by workflow_dispatch test_cve_id)\" --repo \"$GITHUB_REPOSITORY\" 2>/dev/null || true\n\n - name: Claude analysis on Vertex AI\n if: steps.triage.outputs.cve_ids != ''\n # Pinned to commit SHA (== v1 as of 2026-04-27) for supply-chain safety;\n # bump this SHA when picking up new claude-code-action releases.\n uses: anthropics/claude-code-action@567fe954a4527e81f132d87d1bdbcc94f7737434 # v1\n env:\n CLAUDE_CODE_USE_VERTEX: '1'\n CLOUD_ML_REGION: global\n ANTHROPIC_VERTEX_PROJECT_ID: ${{ vars.GCP_PROJECT_ID }}\n with:\n use_vertex: 'true'\n github_token: ${{ secrets.GITHUB_TOKEN }}\n claude_args: '--model claude-sonnet-4-6 --max-turns 30'\n settings: |\n {\n \"permissions\": {\n \"allow\": [\n \"Read\",\n \"Write\",\n \"Bash(mkdir:*)\",\n \"Bash(git log:*)\",\n \"Bash(git show:*)\",\n \"Bash(git rev-parse:*)\",\n \"Bash(git grep:*)\",\n \"Bash(grep:*)\",\n \"Bash(find:*)\",\n \"Bash(jq:*)\",\n \"Bash(ls:*)\",\n \"Bash(cat:*)\",\n \"Bash(head:*)\",\n \"Bash(tail:*)\"\n ]\n }\n }\n prompt: |\n You are triaging container vulnerabilities for the broadinstitute/viral-ngs repo.\n\n ## Your task\n\n For each CVE ID listed below, write a triage report to `/tmp/issues/.md`.\n The reports will be filed verbatim as GitHub issues by the next workflow step.\n\n **CVE IDs to analyze:** ${{ steps.triage.outputs.cve_ids }}\n\n **Test mode:** ${{ steps.triage.outputs.test_mode }}\n (If `true`, the CVE was supplied manually via `test_cve_id` and may not appear in\n the current scan's `trivy-results.json`. Use your training knowledge in that case\n and add a `> _Test analysis_` blockquote at the top of the report so reviewers\n know it was generated for pipeline validation, not from a real scan finding.)\n\n ## Required reading (do this BEFORE writing reports)\n\n 1. `trivy-results.json` (in the workspace root) — **the authoritative source for\n CVSS score, CVSS vector, package path, fix version, and references.** Query\n it with `jq` before writing any report. Example:\n ```\n jq '.Results[]?.Vulnerabilities[]? | select(.VulnerabilityID == \"\")' trivy-results.json\n ```\n You MUST cite the exact CVSS score and vector from this file in the\n \"Vulnerability details\" section — do NOT infer or estimate them from your\n own knowledge if the CVE is present in the JSON. If the CVE is NOT in the\n JSON (test mode, or scan-target divergence), explicitly say so in the report\n and use your training knowledge as a clearly-labeled fallback.\n 2. `.agents/skills/container-vulns/SKILL.md` — read fully. This is the repo's\n container-vulnerability playbook and tells you what the maintainers consider\n actionable vs. accepted risk.\n 3. `.trivyignore` — existing per-CVE exceptions with their justifications. Mirror\n the writing style and depth of justification when you recommend `.trivyignore`\n additions.\n 4. `.trivy-ignore-policy.rego` — Rego policy for class-level CVE filtering.\n Understand what it filters and why.\n 5. `docker/Dockerfile.*` — container build files showing dep installs and inline\n mitigations. Look for prior fixups (`find ... -exec rm`, `gem install`, etc.)\n applied to similar packages.\n 6. `docker/requirements/*.txt` — conda dependency lists. Use `grep` to find\n which file pulls in the affected package.\n 7. Recent git history — full history is available (the workflow checks out\n with `fetch-depth: 0`). Use:\n - `git log --all --oneline --grep ` to find prior commits\n touching the affected package\n - `git log --all --oneline --grep CVE-` to find prior CVE-fix commits\n - **`git show ` to inspect the FULL DIFF of any precedent fix you\n plan to cite. Read the diff, not just the commit message.** Many fixes\n combine multiple elements (e.g., file removal + reinstall) — your\n recommendation must mirror ALL elements of the precedent, not just the\n headline change.\n - ALWAYS verify a commit SHA exists with `git show ` before citing it\n in the report.\n\n ## Required structure for each report\n\n File path: `/tmp/issues/.md` (filename MUST match the CVE ID exactly).\n **First line MUST be a single H1 used as the issue title:**\n `# [CVE-YYYY-NNNN] : `\n\n Then sections (use H2 `##` headers):\n\n 1. **Summary** — 2–3 sentences: what it is, severity, where it came from.\n 2. **Vulnerability details** — CVSS score + vector + plain-English meaning;\n 2–4 sentences explaining the bug technically.\n 3. **Dependency chain** — name the direct conda package or Docker layer that\n pulls this in. Trace transitive deps where you can. If you can't determine\n this confidently, say so explicitly — do NOT guess.\n 4. **Why the Rego policy didn't suppress it** — explain in terms of the AV/PR/UI/S\n vector classes the policy filters and why this CVE's vector doesn't match.\n 5. **Recommended fix** — concrete and actionable. Options:\n - Version bump (which file, which floor)\n - Inline Dockerfile mitigation (which Dockerfile, what RUN-block addition)\n - `.trivyignore` entry (with justification matching the existing style)\n Cite historical precedent when applicable: `(mirror the fix in commit )`.\n 6. **Practical exploitability** — in this deployment model (ephemeral batch\n containers, no network-facing services, no untrusted user input at runtime),\n is this actually reachable? Be honest and specific.\n 7. **References** — GHSA URL, NVD URL, vendor advisory.\n 8. **Attribution footer** — at the very end of the report, add a horizontal\n rule (`---`) on its own line, then this exact paragraph (italicized):\n\n `*This analysis and report were authored entirely by Claude Sonnet 4.6 (running on Google Vertex AI via the `container-scan.yml` triage pipeline). Independently verify the CVSS data, dependency chain, recommended fix, and commit SHAs before acting on this report.*`\n\n ## Constraints\n\n - `mkdir -p /tmp/issues` first.\n - One file per CVE.\n - Be concise. Each report should be readable in 1–2 minutes (target: 300–600 words).\n - Do NOT hallucinate package versions, file paths, or commit SHAs. Verify with\n tools when in doubt.\n - If you finish all reports with budget remaining, do NOT pad — stop.\n\n - name: Upload Claude analysis as artifact\n if: steps.triage.outputs.cve_ids != '' && always()\n uses: actions/upload-artifact@v4\n with:\n name: claude-cve-analysis\n path: /tmp/issues/\n if-no-files-found: warn\n\n - name: File GitHub issues\n if: steps.triage.outputs.cve_ids != '' && (github.event.inputs.dry_run || 'false') != 'true'\n env:\n GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}\n TEST_MODE: ${{ steps.triage.outputs.test_mode }}\n run: |\n set -uo pipefail\n shopt -s nullglob\n\n if [ ! -d /tmp/issues ]; then\n echo \"::error::/tmp/issues does not exist — Claude analysis step likely failed\"\n exit 1\n fi\n\n md_files=(/tmp/issues/*.md)\n if [ ${#md_files[@]} -eq 0 ]; then\n echo \"::error::No .md analysis files in /tmp/issues — Claude may have failed silently\"\n exit 1\n fi\n\n failed=0\n for f in \"${md_files[@]}\"; do\n cve=$(basename \"$f\" .md)\n title=$(head -1 \"$f\" | sed 's/^# *//')\n body=$(tail -n +2 \"$f\")\n\n # Dedup-integrity guard: title MUST contain the CVE ID, otherwise the next\n # scheduled run won't recognize it as already-triaged via title-substring search.\n if ! echo \"$title\" | grep -qF \"$cve\"; then\n echo \"::error::Issue title for $cve does not contain the CVE ID — refusing to file (would break dedup)\"\n echo \" Title was: $title\"\n failed=$((failed+1))\n continue\n fi\n\n label_args=(--label security --label cve)\n if [ \"$TEST_MODE\" = \"true\" ]; then\n label_args+=(--label test)\n fi\n\n echo \"Creating issue for $cve: $title\"\n if ! gh issue create \\\n --repo \"$GITHUB_REPOSITORY\" \\\n --title \"$title\" \\\n --body \"$body\" \\\n \"${label_args[@]}\"; then\n echo \"::error::Failed to create issue for $cve\"\n failed=$((failed+1))\n fi\n done\n\n if [ $failed -gt 0 ]; then\n echo \"::error::$failed issue(s) failed to create\"\n exit 1\n fi\n\n - name: Fail job if new CVEs were found (production mode only)\n if: steps.triage.outputs.cve_ids != '' && steps.triage.outputs.test_mode != 'true'\n run: |\n echo \"::error::Scan found new fixable HIGH/CRITICAL CVEs. See filed issues for details.\"\n exit 1\n" }, { "path": ".github/workflows/docker.yml", "content": "name: Build and Test\n\non:\n push:\n branches:\n - main\n - '**'\n tags:\n - '**'\n pull_request:\n branches:\n - main\n\nenv:\n QUAY_REPO: quay.io/broadinstitute/viral-ngs\n GHCR_REPO: ghcr.io/broadinstitute/viral-ngs\n\njobs:\n # Determine which paths changed to enable smart test filtering\n paths-filter:\n runs-on: ubuntu-latest\n permissions:\n contents: read\n outputs:\n core: ${{ steps.filter.outputs.core }}\n assemble: ${{ steps.filter.outputs.assemble }}\n classify: ${{ steps.filter.outputs.classify }}\n phylo: ${{ steps.filter.outputs.phylo }}\n docker: ${{ steps.filter.outputs.docker }}\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Check changed paths\n uses: dorny/paths-filter@v3\n id: filter\n with:\n filters: |\n core:\n - 'src/viral_ngs/*.py'\n - 'src/viral_ngs/core/**'\n - 'src/viral_ngs/util/**'\n - 'tests/unit/core/**'\n - 'tests/conftest.py'\n - 'docker/requirements/core.txt'\n - 'docker/requirements/core-x86.txt'\n - 'docker/requirements/baseimage.txt'\n - 'docker/Dockerfile.core'\n - 'docker/Dockerfile.baseimage'\n - 'pyproject.toml'\n assemble:\n - 'src/viral_ngs/assemble/**'\n - 'src/viral_ngs/assembly.py'\n - 'tests/unit/assemble/**'\n - 'docker/requirements/assemble.txt'\n - 'docker/Dockerfile.assemble'\n classify:\n - 'src/viral_ngs/classify/**'\n - 'src/viral_ngs/metagenomics.py'\n - 'src/viral_ngs/taxon_filter.py'\n - 'src/viral_ngs/kmer_utils.py'\n - 'tests/unit/classify/**'\n - 'docker/requirements/classify.txt'\n - 'docker/Dockerfile.classify'\n phylo:\n - 'src/viral_ngs/phylo/**'\n - 'src/viral_ngs/interhost.py'\n - 'src/viral_ngs/intrahost.py'\n - 'src/viral_ngs/ncbi.py'\n - 'tests/unit/phylo/**'\n - 'docker/requirements/phylo.txt'\n - 'docker/requirements/phylo-x86.txt'\n - 'docker/Dockerfile.phylo'\n docker:\n - 'docker/**'\n - '.github/workflows/docker.yml'\n\n # Calculate version from git describe (once, shared by all jobs)\n get-version:\n runs-on: ubuntu-latest\n permissions:\n contents: read\n outputs:\n version: ${{ steps.version.outputs.version }}\n image-tag-prefix: ${{ steps.image-tag.outputs.prefix }}\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n with:\n fetch-depth: 0 # Full history for accurate git describe\n fetch-tags: true\n\n - name: Get version from git describe\n id: version\n run: |\n # Get version like: v1.25.0, 3.0.0, or v1.25.0-42-gabcdef\n # Match version tags with or without 'v' prefix, excluding archive/* tags\n RAW_VERSION=$(git describe --tags --always --match 'v*' --match '[0-9]*')\n # Strip leading 'v' if present\n RAW_VERSION=${RAW_VERSION#v}\n\n # Convert to PEP 440 format for setuptools_scm\n # git describe: 1.25.0-42-gabcdef -> PEP 440: 1.25.0.dev42+gabcdef\n if [[ \"$RAW_VERSION\" =~ ^([0-9]+\\.[0-9]+\\.[0-9]+)-([0-9]+)-g([a-f0-9]+)$ ]]; then\n VERSION=\"${BASH_REMATCH[1]}.dev${BASH_REMATCH[2]}+g${BASH_REMATCH[3]}\"\n else\n # Clean version tag (e.g., 1.25.0)\n VERSION=\"$RAW_VERSION\"\n fi\n\n echo \"version=${VERSION}\" >> $GITHUB_OUTPUT\n echo \"Detected version: ${VERSION}\"\n\n - name: Compute Docker image tag prefix\n id: image-tag\n run: |\n # For PRs, github.ref_name is \"1020/merge\" which contains \"/\" - invalid in Docker tags\n # Convert to a valid tag prefix: \"pr-1020\" for PRs, sanitized branch name for branches\n if [[ \"${{ github.event_name }}\" == \"pull_request\" ]]; then\n # Extract PR number from github.ref (refs/pull/1020/merge -> 1020)\n PR_NUMBER=\"${{ github.event.pull_request.number }}\"\n PREFIX=\"pr-${PR_NUMBER}\"\n else\n # For branches/tags, replace \"/\" with \"-\" to create valid Docker tags\n PREFIX=$(echo \"${{ github.ref_name }}\" | sed 's|/|-|g')\n # Strip leading 'v' for version tags (e.g., v3.0.1 -> 3.0.1)\n PREFIX=${PREFIX#v}\n fi\n echo \"prefix=${PREFIX}\" >> $GITHUB_OUTPUT\n echo \"Image tag prefix: ${PREFIX}\"\n\n # ============================================================================\n # BASEIMAGE BUILD JOBS - Native multi-arch builds (no QEMU)\n # AMD64 and ARM64 build in parallel on native runners, then combined\n # ============================================================================\n\n # Build baseimage for AMD64\n build-baseimage-amd64:\n needs: get-version\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (amd64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.baseimage\n platforms: linux/amd64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-amd64\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-amd64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-amd64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Build baseimage for ARM64 (native runner)\n build-baseimage-arm64:\n needs: get-version\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (arm64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.baseimage\n platforms: linux/arm64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-arm64\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-arm64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-arm64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Create multi-arch manifest for baseimage\n create-manifest-baseimage:\n needs: [get-version, build-baseimage-amd64, build-baseimage-arm64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n baseimage-tag: ${{ steps.get-tag.outputs.tag }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Get baseimage tag\n id: get-tag\n run: echo \"tag=${{ needs.get-version.outputs.image-tag-prefix }}-baseimage\" >> $GITHUB_OUTPUT\n\n - name: Create multi-arch manifest\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: ${{ steps.get-tag.outputs.tag }}\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-arm64\n description: 'Viral genomics analysis tools - base image'\n\n - name: Create additional tags for main branch\n if: github.ref == 'refs/heads/main'\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: baseimage\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-arm64\n description: 'Viral genomics analysis tools - base image'\n\n - name: Create version tags\n if: github.ref_type == 'tag'\n run: |\n VERSION=\"${{ needs.get-version.outputs.image-tag-prefix }}\"\n MAJOR_MINOR=$(echo \"$VERSION\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n\n # Create version tag\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${VERSION}-baseimage \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-arm64\n\n # Create major.minor tag\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${MAJOR_MINOR}-baseimage \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-arm64\n\n # ============================================================================\n # CORE BUILD JOBS - Native multi-arch builds\n # ============================================================================\n\n # Build core for AMD64 (depends on baseimage-amd64, not manifest)\n build-core-amd64:\n needs: [get-version, build-baseimage-amd64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (amd64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.core\n platforms: linux/amd64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-amd64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-amd64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Build core for ARM64 (depends on baseimage-arm64, not manifest)\n build-core-arm64:\n needs: [get-version, build-baseimage-arm64]\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (arm64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.core\n platforms: linux/arm64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-baseimage-arm64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-baseimage-arm64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Create multi-arch manifest for core\n create-manifest-core:\n needs: [get-version, build-core-amd64, build-core-arm64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n core-tag: ${{ steps.get-tag.outputs.tag }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Get core tag\n id: get-tag\n run: echo \"tag=${{ needs.get-version.outputs.image-tag-prefix }}-core\" >> $GITHUB_OUTPUT\n\n - name: Create multi-arch manifest\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: ${{ steps.get-tag.outputs.tag }}\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n description: 'Viral genomics analysis tools - core utilities'\n\n - name: Create additional tags for main branch\n if: github.ref == 'refs/heads/main'\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: core\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n description: 'Viral genomics analysis tools - core utilities'\n\n - name: Create version tags\n if: github.ref_type == 'tag'\n run: |\n VERSION=\"${{ needs.get-version.outputs.image-tag-prefix }}\"\n MAJOR_MINOR=$(echo \"$VERSION\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${VERSION}-core \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${MAJOR_MINOR}-core \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n\n # ============================================================================\n # ASSEMBLE BUILD JOBS - Native multi-arch builds\n # ============================================================================\n\n # Build assemble for AMD64\n build-assemble-amd64:\n needs: [get-version, build-core-amd64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (amd64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.assemble\n platforms: linux/amd64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-assemble-amd64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-assemble-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-assemble-amd64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-assemble-amd64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Build assemble for ARM64\n build-assemble-arm64:\n needs: [get-version, build-core-arm64]\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (arm64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.assemble\n platforms: linux/arm64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-assemble-arm64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-assemble-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-assemble-arm64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-assemble-arm64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Create multi-arch manifest for assemble\n create-manifest-assemble:\n needs: [get-version, build-assemble-amd64, build-assemble-arm64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n assemble-tag: ${{ steps.get-tag.outputs.tag }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Get assemble tag\n id: get-tag\n run: echo \"tag=${{ needs.get-version.outputs.image-tag-prefix }}-assemble\" >> $GITHUB_OUTPUT\n\n - name: Create multi-arch manifest\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: ${{ steps.get-tag.outputs.tag }}\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-assemble-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-assemble-arm64\n description: 'Viral genomics analysis tools - assembly'\n\n - name: Create additional tags for main branch\n if: github.ref == 'refs/heads/main'\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: assemble\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-assemble-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-assemble-arm64\n description: 'Viral genomics analysis tools - assembly'\n\n - name: Create version tags\n if: github.ref_type == 'tag'\n run: |\n VERSION=\"${{ needs.get-version.outputs.image-tag-prefix }}\"\n MAJOR_MINOR=$(echo \"$VERSION\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${VERSION}-assemble \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-assemble-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-assemble-arm64\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${MAJOR_MINOR}-assemble \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-assemble-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-assemble-arm64\n\n # ============================================================================\n # CLASSIFY BUILD JOBS - Native multi-arch builds\n # ============================================================================\n\n # Build classify for AMD64\n build-classify-amd64:\n needs: [get-version, build-core-amd64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (amd64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.classify\n platforms: linux/amd64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-classify-amd64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-classify-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-classify-amd64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-classify-amd64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Build classify for ARM64\n build-classify-arm64:\n needs: [get-version, build-core-arm64]\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (arm64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.classify\n platforms: linux/arm64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-classify-arm64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-classify-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-classify-arm64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-classify-arm64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Create multi-arch manifest for classify\n create-manifest-classify:\n needs: [get-version, build-classify-amd64, build-classify-arm64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n classify-tag: ${{ steps.get-tag.outputs.tag }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Get classify tag\n id: get-tag\n run: echo \"tag=${{ needs.get-version.outputs.image-tag-prefix }}-classify\" >> $GITHUB_OUTPUT\n\n - name: Create multi-arch manifest\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: ${{ steps.get-tag.outputs.tag }}\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-classify-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-classify-arm64\n description: 'Viral genomics analysis tools - metagenomic classification'\n\n - name: Create additional tags for main branch\n if: github.ref == 'refs/heads/main'\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: classify\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-classify-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-classify-arm64\n description: 'Viral genomics analysis tools - metagenomic classification'\n\n - name: Create version tags\n if: github.ref_type == 'tag'\n run: |\n VERSION=\"${{ needs.get-version.outputs.image-tag-prefix }}\"\n MAJOR_MINOR=$(echo \"$VERSION\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${VERSION}-classify \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-classify-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-classify-arm64\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${MAJOR_MINOR}-classify \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-classify-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-classify-arm64\n\n # ============================================================================\n # PHYLO BUILD JOBS - Native multi-arch builds\n # ============================================================================\n\n # Build phylo for AMD64\n build-phylo-amd64:\n needs: [get-version, build-core-amd64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (amd64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.phylo\n platforms: linux/amd64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-phylo-amd64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-phylo-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-phylo-amd64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-phylo-amd64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Build phylo for ARM64\n build-phylo-arm64:\n needs: [get-version, build-core-arm64]\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (arm64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.phylo\n platforms: linux/arm64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-phylo-arm64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-phylo-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-phylo-arm64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-phylo-arm64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Create multi-arch manifest for phylo\n create-manifest-phylo:\n needs: [get-version, build-phylo-amd64, build-phylo-arm64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n phylo-tag: ${{ steps.get-tag.outputs.tag }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Get phylo tag\n id: get-tag\n run: echo \"tag=${{ needs.get-version.outputs.image-tag-prefix }}-phylo\" >> $GITHUB_OUTPUT\n\n - name: Create multi-arch manifest\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: ${{ steps.get-tag.outputs.tag }}\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-phylo-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-phylo-arm64\n description: 'Viral genomics analysis tools - phylogenetics'\n\n - name: Create additional tags for main branch\n if: github.ref == 'refs/heads/main'\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: phylo\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-phylo-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-phylo-arm64\n description: 'Viral genomics analysis tools - phylogenetics'\n\n - name: Create version tags\n if: github.ref_type == 'tag'\n run: |\n VERSION=\"${{ needs.get-version.outputs.image-tag-prefix }}\"\n MAJOR_MINOR=$(echo \"$VERSION\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${VERSION}-phylo \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-phylo-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-phylo-arm64\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${MAJOR_MINOR}-phylo \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-phylo-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-phylo-arm64\n\n # ============================================================================\n # MEGA BUILD JOBS - Native multi-arch builds (all tools combined)\n # ============================================================================\n\n # Build mega for AMD64\n build-mega-amd64:\n needs: [get-version, build-core-amd64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (amd64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.mega\n platforms: linux/amd64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-mega-amd64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-amd64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-mega-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-mega-amd64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-amd64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-mega-amd64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Build mega for ARM64\n build-mega-arm64:\n needs: [get-version, build-core-arm64]\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n packages: write\n outputs:\n digest: ${{ steps.build.outputs.digest }}\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Build and push (arm64)\n id: build\n uses: docker/build-push-action@v6\n with:\n context: .\n file: docker/Dockerfile.mega\n platforms: linux/arm64\n provenance: false\n sbom: false\n outputs: type=image,push=true,oci-mediatypes=false\n tags: ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-mega-arm64\n build-args: |\n BASEIMAGE=${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-core-arm64\n VERSION=${{ needs.get-version.outputs.version }}\n cache-from: |\n type=registry,ref=${{ env.GHCR_REPO }}:cache-mega-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-mega-arm64-main\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-${{ needs.get-version.outputs.image-tag-prefix }}\n type=registry,ref=${{ env.GHCR_REPO }}:cache-core-arm64-main\n cache-to: type=registry,ref=${{ env.GHCR_REPO }}:cache-mega-arm64-${{ needs.get-version.outputs.image-tag-prefix }},mode=max\n\n # Create multi-arch manifest for mega\n create-manifest-mega:\n needs: [get-version, build-mega-amd64, build-mega-arm64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: write\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Setup Docker build environment\n uses: ./.github/actions/setup-docker-build\n with:\n github-token: ${{ secrets.GITHUB_TOKEN }}\n checkout: 'false'\n\n - name: Create multi-arch manifest\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: ${{ needs.get-version.outputs.image-tag-prefix }}\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-mega-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-mega-arm64\n description: 'Viral genomics analysis tools - all tools combined'\n\n - name: Create additional tags for main branch\n if: github.ref == 'refs/heads/main'\n uses: ./.github/actions/create-manifest\n with:\n ghcr-repo: ${{ env.GHCR_REPO }}\n target-tag: latest\n source-amd64: ${{ needs.get-version.outputs.image-tag-prefix }}-mega-amd64\n source-arm64: ${{ needs.get-version.outputs.image-tag-prefix }}-mega-arm64\n description: 'Viral genomics analysis tools - all tools combined'\n\n - name: Create version tags\n if: github.ref_type == 'tag'\n run: |\n VERSION=\"${{ needs.get-version.outputs.image-tag-prefix }}\"\n MAJOR_MINOR=$(echo \"$VERSION\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${VERSION} \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-mega-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-mega-arm64\n\n docker buildx imagetools create \\\n --tag ${{ env.GHCR_REPO }}:${MAJOR_MINOR} \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-mega-amd64 \\\n ${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-mega-arm64\n\n # ============================================================================\n # VULNERABILITY SCAN JOBS - Trivy scans of amd64 images after build\n # Scans all 6 flavors in parallel; results uploaded as SARIF to Security tab\n # ============================================================================\n\n scan-containers:\n needs: [get-version, build-baseimage-amd64, build-core-amd64, build-assemble-amd64, build-classify-amd64, build-phylo-amd64, build-mega-amd64]\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: read\n security-events: write\n strategy:\n fail-fast: false\n matrix:\n flavor: [baseimage, core, assemble, classify, phylo, mega]\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Log in to GHCR\n uses: docker/login-action@v3\n with:\n registry: ghcr.io\n username: ${{ github.actor }}\n password: ${{ secrets.GITHUB_TOKEN }}\n\n - name: Run Trivy vulnerability scanner\n uses: aquasecurity/trivy-action@master\n with:\n image-ref: '${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-${{ matrix.flavor }}-amd64'\n format: 'sarif'\n output: 'trivy-results.sarif'\n severity: 'CRITICAL,HIGH'\n limit-severities-for-sarif: true\n exit-code: '0'\n ignore-unfixed: true\n trivyignores: '.trivyignore'\n ignore-policy: '.trivy-ignore-policy.rego'\n\n - name: Run Trivy vulnerability scanner (JSON)\n uses: aquasecurity/trivy-action@master\n with:\n image-ref: '${{ env.GHCR_REPO }}:${{ needs.get-version.outputs.image-tag-prefix }}-${{ matrix.flavor }}-amd64'\n format: 'json'\n output: 'trivy-results.json'\n severity: 'CRITICAL,HIGH'\n exit-code: '1'\n ignore-unfixed: true\n trivyignores: '.trivyignore'\n ignore-policy: '.trivy-ignore-policy.rego'\n\n - name: Log scan result count\n if: always()\n run: |\n if [ -f trivy-results.sarif ]; then\n COUNT=$(jq '[.runs[].results[]] | length' trivy-results.sarif)\n echo \"::notice::Trivy found $COUNT findings for ${{ matrix.flavor }} (after policy filtering)\"\n fi\n\n - name: Upload Trivy scan results to GitHub Security tab\n if: always()\n uses: github/codeql-action/upload-sarif@v3\n with:\n sarif_file: 'trivy-results.sarif'\n category: 'container-${{ matrix.flavor }}'\n\n - name: Upload Trivy JSON results\n if: always()\n uses: actions/upload-artifact@v4\n with:\n name: trivy-${{ matrix.flavor }}\n path: trivy-results.json\n\n # ============================================================================\n # TEST JOBS - Run after corresponding manifests are created\n # Each test runs in its flavor's Docker container (x86 only)\n # ============================================================================\n\n # Test core (x86)\n test-core:\n needs: [paths-filter, get-version, create-manifest-core]\n if: |\n github.event_name == 'pull_request' ||\n github.ref == 'refs/heads/main' ||\n github.ref_type == 'tag' ||\n needs.paths-filter.outputs.core == 'true' ||\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-latest\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-core.outputs.core-tag }}\n\n - name: Run core tests\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-core.outputs.core-tag }} \\\n pytest tests/unit/core/ \\\n -v --tb=short \\\n --cov=viral_ngs \\\n --cov-report=xml:/workspace/coverage-core.xml \\\n -n auto\n\n - name: Upload coverage to Codecov\n if: github.event_name == 'pull_request' || github.ref == 'refs/heads/main' || github.ref_type == 'tag'\n uses: codecov/codecov-action@v4\n with:\n token: ${{ secrets.CODECOV_TOKEN }}\n files: ./coverage-core.xml\n flags: core\n name: codecov-core\n fail_ci_if_error: false\n\n # Test core (ARM64) - only on PRs with docker changes\n test-core-arm64:\n needs: [paths-filter, get-version, create-manifest-core]\n if: |\n github.event_name == 'pull_request' &&\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-core.outputs.core-tag }}\n\n - name: Run core tests (ARM64)\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-core.outputs.core-tag }} \\\n pytest tests/unit/core/ \\\n -v --tb=short \\\n -n auto\n\n # Test assemble (x86)\n test-assemble:\n needs: [paths-filter, get-version, create-manifest-assemble]\n if: |\n github.event_name == 'pull_request' ||\n github.ref == 'refs/heads/main' ||\n github.ref_type == 'tag' ||\n needs.paths-filter.outputs.assemble == 'true' ||\n needs.paths-filter.outputs.core == 'true' ||\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-latest\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-assemble.outputs.assemble-tag }}\n\n - name: Run assemble tests\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-assemble.outputs.assemble-tag }} \\\n pytest tests/unit/assemble/ \\\n -v --tb=short \\\n --cov=viral_ngs \\\n --cov-report=xml:/workspace/coverage-assemble.xml \\\n -n auto\n\n - name: Upload coverage to Codecov\n if: github.event_name == 'pull_request' || github.ref == 'refs/heads/main' || github.ref_type == 'tag'\n uses: codecov/codecov-action@v4\n with:\n token: ${{ secrets.CODECOV_TOKEN }}\n files: ./coverage-assemble.xml\n flags: assemble\n name: codecov-assemble\n fail_ci_if_error: false\n\n # Test assemble (ARM64) - only on PRs with docker changes\n test-assemble-arm64:\n needs: [paths-filter, get-version, create-manifest-assemble]\n if: |\n github.event_name == 'pull_request' &&\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-assemble.outputs.assemble-tag }}\n\n - name: Run assemble tests (ARM64)\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-assemble.outputs.assemble-tag }} \\\n pytest tests/unit/assemble/ \\\n -v --tb=short \\\n -n auto\n\n # Test classify (x86)\n test-classify:\n needs: [paths-filter, get-version, create-manifest-classify]\n if: |\n github.event_name == 'pull_request' ||\n github.ref == 'refs/heads/main' ||\n github.ref_type == 'tag' ||\n needs.paths-filter.outputs.classify == 'true' ||\n needs.paths-filter.outputs.core == 'true' ||\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-latest\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-classify.outputs.classify-tag }}\n\n - name: Run classify tests\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-classify.outputs.classify-tag }} \\\n pytest tests/unit/classify/ \\\n -v --tb=short \\\n --cov=viral_ngs \\\n --cov-report=xml:/workspace/coverage-classify.xml \\\n -n auto\n\n - name: Upload coverage to Codecov\n if: github.event_name == 'pull_request' || github.ref == 'refs/heads/main' || github.ref_type == 'tag'\n uses: codecov/codecov-action@v4\n with:\n token: ${{ secrets.CODECOV_TOKEN }}\n files: ./coverage-classify.xml\n flags: classify\n name: codecov-classify\n fail_ci_if_error: false\n\n # Test classify (ARM64) - only on PRs with docker changes\n test-classify-arm64:\n needs: [paths-filter, get-version, create-manifest-classify]\n if: |\n github.event_name == 'pull_request' &&\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-classify.outputs.classify-tag }}\n\n - name: Run classify tests (ARM64)\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-classify.outputs.classify-tag }} \\\n pytest tests/unit/classify/ \\\n -v --tb=short \\\n -n auto\n\n # Test phylo (x86)\n test-phylo:\n needs: [paths-filter, get-version, create-manifest-phylo]\n if: |\n github.event_name == 'pull_request' ||\n github.ref == 'refs/heads/main' ||\n github.ref_type == 'tag' ||\n needs.paths-filter.outputs.phylo == 'true' ||\n needs.paths-filter.outputs.core == 'true' ||\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-latest\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-phylo.outputs.phylo-tag }}\n\n - name: Run phylo tests\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-phylo.outputs.phylo-tag }} \\\n pytest tests/unit/phylo/ \\\n -v --tb=short \\\n --cov=viral_ngs \\\n --cov-report=xml:/workspace/coverage-phylo.xml \\\n -n auto\n\n - name: Upload coverage to Codecov\n if: github.event_name == 'pull_request' || github.ref == 'refs/heads/main' || github.ref_type == 'tag'\n uses: codecov/codecov-action@v4\n with:\n token: ${{ secrets.CODECOV_TOKEN }}\n files: ./coverage-phylo.xml\n flags: phylo\n name: codecov-phylo\n fail_ci_if_error: false\n\n # Test phylo (ARM64) - only on PRs with docker changes\n test-phylo-arm64:\n needs: [paths-filter, get-version, create-manifest-phylo]\n if: |\n github.event_name == 'pull_request' &&\n needs.paths-filter.outputs.docker == 'true'\n runs-on: ubuntu-24.04-arm\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n\n - name: Pull test image (with retries)\n uses: ./.github/actions/pull-with-retry\n with:\n image: ${{ env.GHCR_REPO }}:${{ needs.create-manifest-phylo.outputs.phylo-tag }}\n\n - name: Run phylo tests (ARM64)\n run: |\n docker run --rm \\\n -v ${{ github.workspace }}:/workspace \\\n -w /workspace \\\n ${{ env.GHCR_REPO }}:${{ needs.create-manifest-phylo.outputs.phylo-tag }} \\\n pytest tests/unit/phylo/ \\\n -v --tb=short \\\n -n auto\n\n # ============================================================================\n # AGGREGATOR JOB - Single status check for branch protection\n # This job always runs and reports combined test status, allowing conditional\n # test jobs to be skipped without blocking PRs that don't need those tests.\n # ============================================================================\n\n all-tests-pass:\n if: always()\n needs:\n - test-core\n - test-core-arm64\n - test-assemble\n - test-assemble-arm64\n - test-classify\n - test-classify-arm64\n - test-phylo\n - test-phylo-arm64\n runs-on: ubuntu-latest\n permissions: {}\n steps:\n - name: Check test results\n run: |\n # Get all job results\n results=\"${{ join(needs.*.result, ' ') }}\"\n echo \"Job results: $results\"\n\n # Fail if any job failed or was cancelled\n for result in $results; do\n if [[ \"$result\" == \"failure\" || \"$result\" == \"cancelled\" ]]; then\n echo \"One or more test jobs failed or were cancelled\"\n exit 1\n fi\n done\n\n echo \"All test jobs passed or were skipped\"\n\n # ============================================================================\n # DEPLOY JOBS - Copy images from GHCR to Quay after tests pass\n # Uses crane to efficiently copy multi-arch manifests without re-pulling layers\n # ============================================================================\n\n deploy-to-quay:\n needs: [\n get-version,\n create-manifest-baseimage,\n create-manifest-core,\n create-manifest-assemble,\n create-manifest-classify,\n create-manifest-phylo,\n create-manifest-mega,\n all-tests-pass\n ]\n # Use always() to evaluate condition even when upstream jobs were skipped.\n # Without this, GitHub skips this job if any job in the dependency chain was skipped,\n # even if all direct dependencies succeeded.\n if: |\n always() &&\n !cancelled() &&\n needs.all-tests-pass.result == 'success' &&\n needs.create-manifest-baseimage.result == 'success' &&\n needs.create-manifest-core.result == 'success' &&\n needs.create-manifest-assemble.result == 'success' &&\n needs.create-manifest-classify.result == 'success' &&\n needs.create-manifest-phylo.result == 'success' &&\n needs.create-manifest-mega.result == 'success' &&\n github.event_name != 'pull_request'\n runs-on: ubuntu-latest\n permissions:\n contents: read\n packages: read\n\n strategy:\n fail-fast: false\n matrix:\n include:\n - flavor: baseimage\n - flavor: core\n - flavor: assemble\n - flavor: classify\n - flavor: phylo\n - flavor: mega\n\n steps:\n - name: Install crane\n uses: imjasonh/setup-crane@v0.4\n\n - name: Log in to GitHub Container Registry\n uses: docker/login-action@v3\n with:\n registry: ghcr.io\n username: ${{ github.actor }}\n password: ${{ secrets.GITHUB_TOKEN }}\n\n - name: Log in to Quay.io\n uses: docker/login-action@v3\n with:\n registry: quay.io\n username: ${{ secrets.QUAY_USERNAME }}\n password: ${{ secrets.QUAY_TOKEN }}\n\n - name: Determine tags to copy\n id: tags\n run: |\n FLAVOR=\"${{ matrix.flavor }}\"\n\n # Determine the suffix (mega has no suffix)\n if [[ \"$FLAVOR\" == \"mega\" ]]; then\n SUFFIX=\"\"\n else\n SUFFIX=\"-${FLAVOR}\"\n fi\n\n # Use image-tag-prefix which handles both branches and version tags\n # (strips 'v' prefix from version tags, sanitizes '/' in branch names)\n TAG_PREFIX=\"${{ needs.get-version.outputs.image-tag-prefix }}\"\n echo \"src_tag=${TAG_PREFIX}${SUFFIX}\" >> $GITHUB_OUTPUT\n echo \"dest_tags=${TAG_PREFIX}${SUFFIX}\" >> $GITHUB_OUTPUT\n\n # For version tags, also create major.minor tag\n if [[ \"${{ github.ref_type }}\" == \"tag\" ]]; then\n MAJOR_MINOR=$(echo \"$TAG_PREFIX\" | sed -E 's/^([0-9]+\\.[0-9]+).*/\\1/')\n echo \"extra_dest_tag=${MAJOR_MINOR}${SUFFIX}\" >> $GITHUB_OUTPUT\n else\n echo \"extra_dest_tag=\" >> $GITHUB_OUTPUT\n fi\n\n # For main branch, also create the \"latest\" style tag\n if [[ \"${{ github.ref }}\" == \"refs/heads/main\" ]]; then\n if [[ \"$FLAVOR\" == \"mega\" ]]; then\n echo \"latest_tag=latest\" >> $GITHUB_OUTPUT\n else\n echo \"latest_tag=${FLAVOR}\" >> $GITHUB_OUTPUT\n fi\n else\n echo \"latest_tag=\" >> $GITHUB_OUTPUT\n fi\n\n - name: Copy image to Quay.io\n run: |\n SRC=\"${{ env.GHCR_REPO }}:${{ steps.tags.outputs.src_tag }}\"\n DEST=\"${{ env.QUAY_REPO }}:${{ steps.tags.outputs.dest_tags }}\"\n\n echo \"Copying $SRC -> $DEST\"\n crane copy \"$SRC\" \"$DEST\"\n\n # Copy extra version tag if present (e.g., v1.25 for v1.25.0)\n if [[ -n \"${{ steps.tags.outputs.extra_dest_tag }}\" ]]; then\n EXTRA_DEST=\"${{ env.QUAY_REPO }}:${{ steps.tags.outputs.extra_dest_tag }}\"\n echo \"Copying $SRC -> $EXTRA_DEST\"\n crane copy \"$SRC\" \"$EXTRA_DEST\"\n fi\n\n # Copy \"latest\" style tag for main branch\n if [[ -n \"${{ steps.tags.outputs.latest_tag }}\" ]]; then\n LATEST_DEST=\"${{ env.QUAY_REPO }}:${{ steps.tags.outputs.latest_tag }}\"\n echo \"Copying $SRC -> $LATEST_DEST\"\n crane copy \"$SRC\" \"$LATEST_DEST\"\n fi\n" }, { "path": ".github/workflows/docs.yml", "content": "name: Documentation\n\non:\n push:\n branches:\n - main\n - '**'\n paths:\n - 'docs/**'\n - 'src/viral_ngs/**'\n - '.readthedocs.yml'\n - '.github/workflows/docs.yml'\n pull_request:\n branches:\n - main\n paths:\n - 'docs/**'\n - 'src/viral_ngs/**'\n - '.readthedocs.yml'\n - '.github/workflows/docs.yml'\n\njobs:\n build-docs:\n runs-on: ubuntu-latest\n permissions:\n contents: read\n\n steps:\n - name: Checkout repository\n uses: actions/checkout@v4\n with:\n fetch-depth: 0 # Full history for git describe version\n\n - name: Set up Python\n uses: actions/setup-python@v5\n with:\n python-version: '3.10'\n\n - name: Install dependencies\n run: |\n pip install -r docs/requirements.txt\n pip install -e .\n\n - name: Build documentation\n run: |\n cd docs\n sphinx-build -W -b html . _build/html\n\n - name: Upload documentation artifact\n uses: actions/upload-artifact@v4\n with:\n name: documentation\n path: docs/_build/html/\n retention-days: 7\n" }, { "path": ".gitignore", "content": "VERSION\ntest/output/\n\n# Sphinx documentation\ndocs/_build/\n\n# Mac OSX\n.DS_Store\n\n# Byte-compiled / optimized / DLL files\n__pycache__/\n*.py[cod]\n\n# C extensions\n*.so\n\n# WIP/dev temporary backup copies\n*.bak\n*.bak[0-9]\n\n# Distribution / packaging\n.Python\nenv/\nbuild/\ndevelop-eggs/\ndist/\ndownloads/\neggs/\nlib/\nlib64/\nparts/\nsdist/\nvar/\n*.egg-info/\n.installed.cfg\n*.egg\n\n# PyInstaller\n# Usually these files are written by a python script from a template\n# before PyInstaller builds the exe, so as to inject date/other infos into it.\n*.manifest\n*.spec\n\n# Installer logs\npip-log.txt\npip-delete-this-directory.txt\n\n# Pyenv local\n.python-version\n\n# Unit test / coverage reports\nhtmlcov/\n.tox/\n.coverage\n.coverage*\n.cache\n.noseids\nnosetests.xml\npytest.xml\ncoverage.xml\ncoverage/\n\ntest/input/TestVPhaser2/in.bam.bti\n\neasy-deploy/data/Snakefile\neasy-deploy-virtualized/data/Snakefile\n\neasy-deploy-virtualized/data/config.json\neasy-deploy-virtualized/data/config.yaml\n\neasy-deploy-virtualized/data/viral-ngs/\n\n**/.vagrant/\n\ntools/build/\ntools/conda-cache/\ntools/conda-tools/\n\n*.snakemake/\n\n.pytest_cache/\n\n.vscode/\nvulnerability-mitigation-status.md\n" }, { "path": ".readthedocs.yml", "content": "# .readthedocs.yml\n# Read the Docs configuration file\n# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details\n\n# Required\nversion: 2\n\n# Set the version of Python\nbuild:\n os: ubuntu-22.04\n tools:\n python: \"3.10\"\n\n# Build documentation in the docs/ directory with Sphinx\nsphinx:\n builder: html\n configuration: docs/conf.py\n\n# Build documentation with MkDocs\n#mkdocs:\n# configuration: mkdocs.yml\n\n# Optionally build your docs in additional formats such as PDF and ePub\nformats: all\n\n# Optionally set the version of Python and requirements required to build your docs\npython:\n install:\n - requirements: docs/requirements.txt\n - method: pip\n path: .\n extra_requirements: []" }, { "path": ".trivy-ignore-policy.rego", "content": "#\n# bioinformatics-platform.rego\n#\n# Conservative Trivy ignore policy for bioinformatics container images\n# running on genomics PaaS platforms as batch pipeline tasks.\n#\n# ASSUMPTIONS (document and verify these match your platform):\n# 1. Containers run as non-interactive batch jobs (no shell sessions,\n# no web UIs, no Jupyter notebooks served from pipeline containers)\n# 2. Containers have no inbound network listeners (no ports exposed)\n# 3. Containers run with dropped capabilities (no CAP_SYS_ADMIN, etc.)\n# 4. Containers do not run in privileged mode\n# 5. Pipeline inputs are data files (FASTQ, BAM, VCF, reference genomes)\n# which may be untrusted or malformed\n#\n# If any assumption does not hold for a given image or use case,\n# DO NOT apply this policy to that image.\n#\n# USAGE:\n# trivy image --ignore-policy bioinformatics-platform.rego \\\n# --severity CRITICAL,HIGH --ignore-unfixed \n#\n# IMPORTANT: Before using this policy, run your image with:\n# trivy image --format json > scan.json\n# and inspect the CVSS field structure. The field paths below\n# (input.CVSS, input.CweIDs, etc.) reflect the Trivy JSON output\n# structure. If your Trivy version uses different paths, adjust\n# accordingly. The CVSS vector string location has changed across\n# Trivy versions (see https://github.com/aquasecurity/trivy/issues/1627).\n#\n# CVSS VERSION SUPPORT:\n# This policy supports both CVSS v3.1 and CVSS v4.0 vector strings.\n# Trivy is transitioning to v4.0 for newer advisories. Some CVEs may\n# have only a v4.0 vector (no v3.1). The helper functions at the bottom\n# extract vectors from both versions and the rules are written to match\n# either format.\n#\n# VERSION: 2.0\n# LAST REVIEWED: 2026-03-20\n# REVIEW CADENCE: Quarterly, or when platform architecture changes\n#\n\npackage trivy\n\ndefault ignore = false\n\n###############################################################################\n# SECTION 1: PHYSICAL ACCESS REQUIRED (AV:P)\n#\n# Rationale: Cloud-hosted containers are never physically accessible.\n# These CVEs require hands-on hardware interaction (USB, Firewire,\n# JTAG, etc.) which is impossible in any cloud PaaS context.\n#\n# CVSS v3.1: AV:P\n# CVSS v4.0: AV:P (same field name)\n#\n# Risk of false negative: Essentially zero. There is no scenario\n# in which a pipeline container is physically accessible to an attacker.\n# Confidence: Very High\n###############################################################################\n\nignore {\n has_v3_field(input, \"AV:P\")\n}\n\nignore {\n has_v4_field(input, \"AV:P\")\n}\n\n###############################################################################\n# SECTION 2: ADJACENT NETWORK REQUIRED (AV:A)\n#\n# Rationale: Adjacent-network attacks require the attacker to be on\n# the same physical or logical network segment (e.g., same VLAN,\n# Bluetooth, local WiFi). In a cloud PaaS, pipeline containers run\n# on orchestrated infrastructure where the attacker cannot place\n# themselves on an adjacent segment.\n#\n# CVSS v3.1: AV:A\n# CVSS v4.0: AV:A (same field name)\n#\n# Risk of false negative: Very low. Cloud networking abstractions\n# make adjacent-network attacks impractical against pipeline containers.\n# Confidence: Very High\n###############################################################################\n\nignore {\n has_v3_field(input, \"AV:A\")\n}\n\nignore {\n has_v4_field(input, \"AV:A\")\n}\n\n###############################################################################\n# SECTION 3: USER INTERACTION REQUIRED (UI:R) + LOCAL VECTOR (AV:L)\n#\n# Rationale: Batch pipeline containers have no interactive user sessions.\n# No human is clicking links, opening files in a GUI, or interacting\n# with the container during execution. CVEs that require BOTH local\n# access AND user interaction (e.g., tricking a user into opening a\n# malicious file in a desktop app) are not exploitable in this context.\n#\n# NOTE: We require BOTH conditions (AV:L AND UI:R), not either alone.\n# - AV:L alone is NOT safe to ignore (local privilege escalation\n# could be triggered by pipeline code)\n# - UI:R alone is NOT safe to ignore for AV:N vulns (some network\n# vulns with UI:R involve clicking a link, which doesn't apply,\n# but others are ambiguous)\n# - AV:L + UI:R together means \"must have local access AND a human\n# must do something\" - genuinely inapplicable in batch containers.\n#\n# CVSS v3.1: AV:L + UI:R\n# CVSS v4.0: AV:L + UI:P (Passive) or UI:A (Active)\n# v4.0 splits \"Required\" into Passive (viewing content) and Active\n# (clicking/interacting). Both require a human, so both are safe to\n# ignore in batch containers.\n#\n# Risk of false negative: Very low for true batch pipeline containers.\n# Confidence: High\n###############################################################################\n\n# v3: AV:L + UI:R\nignore {\n has_v3_field(input, \"AV:L\")\n has_v3_field(input, \"UI:R\")\n}\n\n# v4: AV:L + UI:P (Passive user interaction)\nignore {\n has_v4_field(input, \"AV:L\")\n has_v4_field(input, \"UI:P\")\n}\n\n# v4: AV:L + UI:A (Active user interaction)\nignore {\n has_v4_field(input, \"AV:L\")\n has_v4_field(input, \"UI:A\")\n}\n\n###############################################################################\n# SECTION 4: HIGH PRIVILEGES REQUIRED + LOCAL VECTOR\n#\n# Rationale: CVEs requiring both local access and high (administrative)\n# privileges assume the attacker already has elevated access to the\n# system. In a properly configured container (non-root user, dropped\n# capabilities), the process inside the container does not have high\n# privileges to begin with. Combined with the local access requirement,\n# this class of CVE is not practically exploitable.\n#\n# NOTE: We only ignore AV:L + PR:H, not AV:N + PR:H. A network-\n# accessible vulnerability requiring high privileges may still be\n# relevant if the service runs as a privileged user.\n#\n# CVSS v3.1: AV:L + PR:H\n# CVSS v4.0: AV:L + PR:H (same field names)\n#\n# Risk of false negative: Low, assuming containers run as non-root.\n# If your containers run as root, REMOVE THIS RULE.\n# Confidence: High (conditional on non-root execution)\n###############################################################################\n\nignore {\n has_v3_field(input, \"AV:L\")\n has_v3_field(input, \"PR:H\")\n}\n\nignore {\n has_v4_field(input, \"AV:L\")\n has_v4_field(input, \"PR:H\")\n}\n\n###############################################################################\n# SECTION 5: LOCAL ATTACK, SCOPE UNCHANGED (AV:L + S:U)\n#\n# Rationale: AV:L means the attacker already has local code execution\n# inside the container. S:U (Scope Unchanged) means the impact does not\n# cross a security boundary — it stays within the container.\n#\n# In an ephemeral batch container, this combination means: the attacker\n# can already execute arbitrary code, and the vulnerability only lets\n# them affect things inside a container that will be destroyed when the\n# job completes. The vulnerability grants no capability the attacker\n# does not already have.\n#\n# Contrast with S:C (Scope Changed): a local vulnerability that crosses\n# the container-host boundary (e.g., container escape via kernel exploit)\n# IS dangerous and is NOT ignored by this rule.\n#\n# CVSS v3.1: AV:L + S:U\n# CVSS v4.0: AV:L + SC:N + SI:N + SA:N\n# v4.0 replaced the binary S:U/S:C with three subsequent-component\n# impact fields. SC:N + SI:N + SA:N means no impact on any component\n# beyond the vulnerable one — equivalent to v3's S:U.\n#\n# Risk of false negative: Low. The theoretical concern is that AV:L+S:U\n# could include reading mounted secrets, but an attacker with code\n# execution can already read those secrets directly.\n# Confidence: High\n###############################################################################\n\n# v3: AV:L + S:U\nignore {\n has_v3_field(input, \"AV:L\")\n has_v3_field(input, \"S:U\")\n}\n\n# v4: AV:L + no subsequent-component impact\nignore {\n has_v4_field(input, \"AV:L\")\n has_v4_field(input, \"SC:N\")\n has_v4_field(input, \"SI:N\")\n has_v4_field(input, \"SA:N\")\n}\n\n###############################################################################\n# SECTION 6: AVAILABILITY-ONLY IMPACT, SCOPE UNCHANGED\n#\n# Rationale: CVEs where the only impact is availability (DoS/resource\n# exhaustion) and scope is unchanged mean: processing crafted input can\n# crash or hang the affected process, but cannot read data (C:N),\n# modify data (I:N), or affect other components (S:U).\n#\n# In ephemeral batch containers, a DoS means a single pipeline job\n# fails or hangs until it hits its timeout or memory limit. This is\n# operationally equivalent to a corrupted input file or OOM — the job\n# fails, the container is destroyed, and the next job runs on a fresh\n# container. There is no persistent state corruption, no data\n# exfiltration, and no lateral movement.\n#\n# This rule applies regardless of attack vector (including AV:N),\n# because the impact is strictly contained: even if triggered by\n# network-delivered data, the worst outcome is one failed job.\n#\n# NOTE: This does NOT ignore:\n# - DoS with S:C / SC≠N / SI≠N / SA≠N (scope changed — could\n# affect host or other containers)\n# - DoS combined with any confidentiality or integrity impact\n# (C≠N or I≠N), which could indicate data leaks or corruption\n# alongside the crash\n#\n# CVSS v3.1: C:N + I:N + S:U (with any A value)\n# CVSS v4.0: VC:N + VI:N + SC:N + SI:N + SA:N (with any VA value)\n#\n# Risk of false negative: Low. The concern would be if a DoS could be\n# weaponized into a resource exhaustion attack against the compute\n# platform (e.g., repeatedly submitting jobs with crafted inputs to\n# burn credits). This is a business logic concern mitigated by job\n# submission controls and cost alerts, not by container hardening.\n# Confidence: High\n###############################################################################\n\n# v3: C:N + I:N + S:U (availability-only, scope unchanged)\nignore {\n has_v3_field(input, \"C:N\")\n has_v3_field(input, \"I:N\")\n has_v3_field(input, \"S:U\")\n}\n\n# v4: VC:N + VI:N + no subsequent-component impact (availability-only)\nignore {\n has_v4_field(input, \"VC:N\")\n has_v4_field(input, \"VI:N\")\n has_v4_field(input, \"SC:N\")\n has_v4_field(input, \"SI:N\")\n has_v4_field(input, \"SA:N\")\n}\n\n###############################################################################\n# HELPER FUNCTIONS: Extract and match CVSS vector strings\n#\n# Trivy's JSON structure nests CVSS data under input.CVSS with vendor\n# keys. The vector string location varies by data source. We check\n# multiple common paths and prefer NVD.\n#\n# CVSS v3.1 vectors look like: CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H\n# CVSS v4.0 vectors look like: CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:N/VA:H/SC:N/SI:N/SA:N\n#\n# Fields are slash-delimited key:value pairs. The has_vX_field helpers\n# check for a field anywhere in the vector, handling both mid-string\n# (/field/) and end-of-string (/field) positions.\n#\n# IMPORTANT: Run `trivy image --format json ` and inspect\n# the .Vulnerabilities[].CVSS structure to confirm these paths work\n# for your Trivy version. If the structure differs, update these\n# functions accordingly.\n###############################################################################\n\n# --- CVSS v3.1 vector extraction ---\n\nget_v3_vector(vuln) = vector {\n vector := vuln.CVSS.nvd.V3Vector\n} else = vector {\n vector := vuln.CVSS.redhat.V3Vector\n} else = vector {\n vector := vuln.CVSS.ghsa.V3Vector\n} else = vector {\n some vendor\n vector := vuln.CVSS[vendor].V3Vector\n} else = \"\" {\n true\n}\n\n# --- CVSS v4.0 vector extraction ---\n\nget_v4_vector(vuln) = vector {\n vector := vuln.CVSS.nvd.V40Vector\n} else = vector {\n vector := vuln.CVSS.redhat.V40Vector\n} else = vector {\n vector := vuln.CVSS.ghsa.V40Vector\n} else = vector {\n some vendor\n vector := vuln.CVSS[vendor].V40Vector\n} else = \"\" {\n true\n}\n\n# --- Field matching helpers ---\n# Check if a CVSS vector contains a specific field value.\n# Handles both mid-string (/AV:N/) and end-of-string (/AV:N) positions.\n\nhas_v3_field(vuln, field) {\n cvss_vector := get_v3_vector(vuln)\n cvss_vector != \"\"\n contains(cvss_vector, concat(\"\", [\"/\", field, \"/\"]))\n}\n\nhas_v3_field(vuln, field) {\n cvss_vector := get_v3_vector(vuln)\n cvss_vector != \"\"\n endswith(cvss_vector, concat(\"\", [\"/\", field]))\n}\n\nhas_v4_field(vuln, field) {\n cvss_vector := get_v4_vector(vuln)\n cvss_vector != \"\"\n contains(cvss_vector, concat(\"\", [\"/\", field, \"/\"]))\n}\n\nhas_v4_field(vuln, field) {\n cvss_vector := get_v4_vector(vuln)\n cvss_vector != \"\"\n endswith(cvss_vector, concat(\"\", [\"/\", field]))\n}\n\n###############################################################################\n# RULES INTENTIONALLY NOT INCLUDED (and why):\n#\n# 1. AV:N (Network attack vector) — NOT blanket-ignored.\n# Even though batch pipeline containers typically have no inbound\n# listeners, some AV:N CVEs involve outbound connections triggered\n# by processing attacker-influenced data (e.g., Log4Shell). We\n# cannot safely blanket-ignore network-vector CVEs. However,\n# Section 6 does ignore AV:N CVEs that are availability-only with\n# no scope change, since the worst outcome is a crashed job.\n#\n# 2. UI:R alone (without AV:L) — NOT ignored.\n# Some AV:N + UI:R vulnerabilities involve scenarios like processing\n# a crafted file that triggers a callback, which could be borderline\n# relevant if pipeline inputs are not fully trusted.\n#\n# 3. CWE-based filters — NOT included by default.\n# Filtering by CWE class (e.g., ignoring all CWE-79 XSS in a\n# non-web context) is tempting but risky as a default policy.\n# CWE classifications can be inaccurate, and a single misclassified\n# CVE could slip through. If your platform has specific architectural\n# mitigations (e.g., provably no web server in any image), you may\n# add CWE rules, but this should be a deliberate per-platform choice.\n#\n# 4. Specific CVE IDs — NOT included.\n# Use a .trivyignore.yaml or VEX document for individual CVE\n# exceptions with per-CVE justifications. The Rego policy should\n# capture architectural/class-level mitigations, not one-off\n# exceptions.\n#\n# 5. AV:L + S:C — NOT ignored.\n# Local vulnerabilities with Scope Changed (S:C) can cross security\n# boundaries (e.g., container escape via kernel exploit). These are\n# dangerous even in ephemeral containers. Only AV:L + S:U (Scope\n# Unchanged) is ignored — see Section 5 above.\n#\n# 6. Inbound-listener-only server CVEs — NOT categorically ignored.\n# Many AV:N CVEs in fat JARs (Jetty, ZooKeeper, Netty server-side)\n# require an active network listener that we never start. However,\n# CVSS does not distinguish inbound-listener vs. data-processing\n# attack surfaces within AV:N. Adding package-name-based exceptions\n# here would be fragile and is better handled in .trivyignore with\n# per-CVE justification documenting that the server component is\n# never instantiated.\n###############################################################################\n" }, { "path": ".trivyignore", "content": "# Trivy ignore file — per-CVE exceptions with justifications\n#\n# This file documents individual CVE exceptions that cannot be addressed by\n# version bumps or by the Rego policy (.trivy-ignore-policy.rego). Each entry\n# MUST include a justification explaining why the CVE is accepted.\n#\n# Format: CVE-YYYY-NNNNN (one per line, # for comments)\n# See: https://aquasecurity.github.io/trivy/latest/docs/configuration/filtering/#by-finding-ids\n#\n# Review cadence: Re-evaluate all entries quarterly or when the affected\n# package is upgraded. Remove entries once the underlying package ships a fix.\n#\n# =============================================================================\n\n# -----------------------------------------------------------------------------\n# CVE-2026-23949 — jaraco.context path traversal in tarball extraction\n# Severity: HIGH (NVD scored AV:N/S:C — see scoring dispute below)\n# Package: setuptools (vendored at setuptools/_vendor/jaraco/context.py)\n# Installed: setuptools 79.x (vendored jaraco.context 5.3.0)\n# Fix: jaraco.context >= 6.1.0 (installed in conda env, but setuptools\n# vendors its own copy which we cannot delete — setuptools imports\n# jaraco.text and jaraco.context at runtime for pkg_resources)\n#\n# JUSTIFICATION:\n# 1. The vulnerability is in archive extraction (tarball() context manager).\n# setuptools uses this only during \"pip install\" of source distributions.\n# Our containers run pip install at BUILD TIME only, from trusted sources\n# (PyPI, conda-forge). No pip installs happen at runtime.\n#\n# 2. Even if an attacker could trigger pip install at runtime (which would\n# require code execution inside the container), the path traversal only\n# writes files WITHIN the container. The attacker already has code\n# execution — they can write files anywhere in the container without\n# needing this vulnerability. It grants no new capability.\n#\n# 3. Containers are ephemeral batch jobs. Any files written (malicious or\n# otherwise) are destroyed when the job completes. There is no\n# persistence, no lateral movement, and no host boundary crossing.\n#\n# 4. NVD SCORING DISPUTE: NVD scored this AV:N/AC:L/PR:N/UI:N/S:C/C:H,\n# which assumes a network-facing service extracting untrusted archives\n# where the traversal crosses a trust boundary. In our deployment model,\n# there is no network-facing service, the archives come from trusted\n# sources, and the \"boundary\" is a container that will be destroyed.\n# The Rego policy cannot filter this because NVD mis-scored the attack\n# vector as Network (AV:N) rather than Local (AV:L).\n#\n# RESOLUTION: Will self-resolve when setuptools releases a version with\n# updated vendored dependencies (jaraco.context >= 6.1.0).\n# ADDED: 2026-03-19\n# -----------------------------------------------------------------------------\nCVE-2026-23949\n\n# -----------------------------------------------------------------------------\n# CVE-2020-25649 — jackson-databind XXE in DOMDeserializer\n# Severity: HIGH (AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:H/A:N)\n# Package: com.fasterxml.jackson.core:jackson-databind 2.10.5\n# Location: opt/conda/share/snpeff-5.2-3/snpEff.jar\n#\n# JUSTIFICATION:\n# The vulnerable code path is DOMDeserializer, which is invoked when\n# jackson-databind deserializes XML input into DOM objects without\n# disabling external entity resolution. This enables XXE attacks\n# (SSRF, local file read) when processing attacker-controlled XML.\n#\n# snpEff uses jackson-databind for JSON parsing only (config metadata,\n# database indices). snpEff's input formats are VCF (tab-delimited),\n# GenBank (flat text), and Java properties files. It never parses XML\n# through Jackson's DOMDeserializer. The vulnerable code is present in\n# the fat JAR but the code path is never traversed.\n#\n# This exclusion applies only to snpEff's bundled copy. If jackson-\n# databind 2.10.5 appears in other JARs, this entry will NOT suppress\n# those findings — Trivy matches .trivyignore by CVE ID globally, but\n# we accept this because no other JAR in our images bundles this old\n# version. If that changes, re-evaluate this entry.\n#\n# RESOLUTION: Upstream snpEff must update its bundled jackson-databind.\n# ADDED: 2026-03-20\n# -----------------------------------------------------------------------------\nCVE-2020-25649\n" }, { "path": "AGENTS.md", "content": "# AGENTS.md\n\nThis document provides guidance for AI assistants (Claude Code, GitHub Copilot, etc.) working on this repository.\n\n## Overview\n\nviral-ngs is a consolidated monorepo for viral NGS (Next-Generation Sequencing) analysis tools. It provides:\n\n- **Core utilities**: Read manipulation, Illumina demultiplexing, file handling, QC\n- **Assembly**: Genome assembly, scaffolding, gap filling\n- **Classification**: Metagenomic classification, taxonomy filtering, k-mer analysis\n- **Phylogenetics**: Variant calling, consensus generation, annotation\n\n**Related resources:**\n- Command-line documentation: https://viral-ngs.readthedocs.org/\n- Higher-level pipelines: https://github.com/broadinstitute/viral-pipelines\n\n---\n\n## Development Environment\n\n### Docker-Centric Development\n\nDevelopment is **intentionally docker-centric**. Developers need:\n- Docker\n- Git\n- Text/code editor\n\n### Development Workflow\n\n1. Clone the repository:\n ```bash\n git clone https://github.com/broadinstitute/viral-ngs.git\n ```\n\n2. Run the container with local checkout mounted:\n ```bash\n docker run -it --rm \\\n -v $(pwd):/opt/viral-ngs/source \\\n quay.io/broadinstitute/viral-ngs:main-core\n ```\n\n3. If modifying conda dependencies, install them inside the container:\n ```bash\n micromamba install \n ```\n\n4. Test code interactively:\n ```bash\n cd /opt/viral-ngs/source\n pytest -rsxX -n auto tests/unit\n ```\n\n5. Push changes to GitHub for automated CI testing\n\n### Running Tests\n\n```bash\n# Run all unit tests in the core image\ndocker run --rm \\\n -v $(pwd):/opt/viral-ngs/source \\\n quay.io/broadinstitute/viral-ngs:main-core \\\n pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit\n\n# Run specific module tests\ndocker run --rm \\\n -v $(pwd):/opt/viral-ngs/source \\\n quay.io/broadinstitute/viral-ngs:main-classify \\\n pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit/classify\n```\n\n**Important: Testing source code changes requires re-installing the package.**\nThe `-v` mount makes your local files visible on disk, but `viral_ngs` is already installed as a package inside the container image. Python imports resolve to the *installed* copy, not your mounted source files. If you've modified files under `src/viral_ngs/`, you must re-install before running tests:\n\n```bash\n# Run tests with local source changes applied\ndocker run --rm \\\n -v $(pwd):/opt/viral-ngs/source \\\n quay.io/broadinstitute/viral-ngs:main-core \\\n bash -c \"pip install -e /opt/viral-ngs/source --quiet && pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit\"\n```\n\nChanges to test files (`tests/`) and test inputs (`tests/input/`) are picked up automatically via the volume mount — the re-install is only needed when modifying the `src/viral_ngs/` package code.\n\nRunning pytest directly on the host will generally not work — most dependencies (bioinformatics tools, conda packages) are only available inside the Docker containers. Always test inside Docker.\n\n**Test conventions:**\n- Uses pytest (not nose or unittest)\n- Test files in `tests/unit//`\n- Test input files in `tests/input//`\n- Access via `viral_ngs.core.file.get_test_input_path(self)`\n- Custom marker: `@pytest.mark.slow` for slow tests\n\n---\n\n## Code Architecture\n\n### Directory Structure\n\n```\nviral-ngs/\n├── pyproject.toml # Package configuration\n├── src/viral_ngs/\n│ ├── __init__.py # Version detection\n│ ├── py.typed # PEP 561 marker\n│ │\n│ ├── # Command modules (CLI entry points)\n│ ├── illumina.py # Illumina demux commands\n│ ├── read_utils.py # Read manipulation commands\n│ ├── assembly.py # Assembly commands\n│ ├── metagenomics.py # Classification commands\n│ ├── interhost.py # Phylo commands\n│ │\n│ ├── core/ # Core library (shared utilities + tool wrappers)\n│ │ ├── __init__.py # Tool/InstallMethod classes\n│ │ ├── samtools.py # Tool wrapper\n│ │ ├── picard.py # Tool wrapper\n│ │ ├── file.py # File utilities\n│ │ ├── misc.py # General utilities\n│ │ └── ...\n│ │\n│ ├── assemble/ # Assembly tool wrappers\n│ │ ├── __init__.py\n│ │ ├── spades.py\n│ │ └── ...\n│ │\n│ ├── classify/ # Classification tool wrappers\n│ │ ├── __init__.py\n│ │ ├── kraken2.py\n│ │ └── ...\n│ │\n│ └── phylo/ # Phylogenetics tool wrappers\n│ ├── __init__.py\n│ ├── mafft.py\n│ └── ...\n│\n├── docker/\n│ ├── Dockerfile.baseimage # Base with conda/python\n│ ├── Dockerfile.core # Core tools\n│ ├── Dockerfile.assemble # + assembly tools\n│ ├── Dockerfile.classify # + classification tools\n│ ├── Dockerfile.phylo # + phylo tools\n│ ├── Dockerfile.mega # All tools combined\n│ ├── install-conda-deps.sh\n│ └── requirements/\n│ ├── baseimage.txt\n│ ├── core.txt\n│ ├── core-x86.txt # x86-only core packages\n│ ├── assemble.txt\n│ ├── assemble-x86.txt # x86-only assembly packages\n│ ├── classify.txt\n│ ├── classify-x86.txt # x86-only classify packages\n│ ├── phylo.txt\n│ └── phylo-x86.txt # x86-only phylo packages\n│\n├── tests/\n│ ├── conftest.py\n│ ├── unit/\n│ │ ├── core/\n│ │ ├── assemble/\n│ │ ├── classify/\n│ │ └── phylo/\n│ └── input/\n│\n├── scripts/ # Utility scripts\n├── .github/workflows/\n│ └── docker.yml # CI/CD workflow\n└── docs/\n```\n\n### Command Module Pattern\n\nCommand modules define CLI entry points:\n\n```python\n__commands__ = []\n\ndef parser_(parser=argparse.ArgumentParser()):\n # Define arguments\n return parser\n\ndef main_(args):\n # Implementation\n pass\n\n__commands__.append(('command_name', parser_command_name))\n```\n\n### Tool Wrapper Pattern\n\nTool wrappers in `core/`, `assemble/`, `classify/`, `phylo/`:\n\n```python\nimport viral_ngs.core as core\n\nclass SamtoolsTool(core.Tool):\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand('samtools')]\n super().__init__(install_methods=install_methods)\n\n def execute(self, command, *args):\n # Run samtools with arguments\n pass\n```\n\n---\n\n## Import Patterns\n\n### Standard imports\n\n```python\n# Within command modules (illumina.py, assembly.py, etc.)\nimport viral_ngs.core as core\nimport viral_ngs.core.file as util_file\nimport viral_ngs.core.misc as util_misc\n\n# Using tools\nsamtools = core.samtools.SamtoolsTool()\nbwa = core.bwa.BwaTool()\n\n# Using utilities\nutil_file.mkstempfname()\nutil_misc.available_cpu_count()\n```\n\n### Within core/ modules (use relative imports)\n\n```python\nfrom . import samtools, picard\nfrom .file import mkstempfname\nfrom .misc import available_cpu_count\n```\n\n### Within subpackages (assemble/, classify/, phylo/)\n\n```python\nimport viral_ngs.core as core\nimport viral_ngs.core.file as util_file\n\n# For other tools in same subpackage\nfrom . import mummer, mafft\n```\n\n### Key rules\n\n1. **Prefer full imports**: `import viral_ngs.core.samtools` over `from viral_ngs.core import samtools`\n2. **Use relative imports within packages**: `from . import X` inside core/, assemble/, etc.\n3. **No backward compat stubs**: `viral_ngs.tools` and `viral_ngs.util` don't exist\n\n---\n\n## Dependencies\n\n### Conda-First Approach\n\nALL runtime dependencies are installed via conda for speed and binary compatibility.\nThe `pyproject.toml` has empty dependencies - conda handles everything.\n\n### Adding Dependencies\n\n1. Check conda availability:\n ```bash\n micromamba search # default channel\n micromamba search -c bioconda # bioconda channel\n ```\n\n2. Add to appropriate requirements file:\n - `docker/requirements/core.txt` - core dependencies\n - `docker/requirements/assemble.txt` - assembly-specific\n - `docker/requirements/classify.txt` - classification-specific\n - `docker/requirements/phylo.txt` - phylo-specific\n\n3. For x86-only packages (no ARM64 build), add to the appropriate `-x86.txt` file:\n - `core-x86.txt` - novoalign, mvicuna\n - `classify-x86.txt` - bmtagger, kallisto, kb-python\n - `phylo-x86.txt` - table2asn\n\n### Dependency Resolution\n\nWhen building derivative images, ALL dependencies (including x86-only) must be installed in a **single resolver call** using the `--x86-only:` prefix:\n\n```bash\n# Single resolver call - x86-only files skipped on ARM64\n/tmp/install-conda-deps.sh \\\n /tmp/requirements/baseimage.txt \\\n /tmp/requirements/core.txt \\\n /tmp/requirements/classify.txt \\\n --x86-only:/tmp/requirements/classify-x86.txt\n```\n\nThis prevents version regressions. **Never install incrementally.**\n\nThe `install-conda-deps.sh` script:\n- On x86: Includes all files in one micromamba call\n- On ARM64: Skips files tagged with `--x86-only:` but includes others\n\n---\n\n## Docker Images\n\n### Image Hierarchy\n\n```\nbaseimage (conda/python)\n └── core (core tools)\n ├── assemble (+ assembly tools)\n ├── classify (+ classification tools)\n ├── phylo (+ phylo tools)\n └── mega (all tools)\n```\n\n### Tag Format\n\n```\nquay.io/broadinstitute/viral-ngs:2.6.0-core\nquay.io/broadinstitute/viral-ngs:2.6.0-classify\nquay.io/broadinstitute/viral-ngs:2.6.0 # mega (no suffix)\nquay.io/broadinstitute/viral-ngs:main-core # main branch\nquay.io/broadinstitute/viral-ngs:latest # alias for main mega\n```\n\n### Building Locally\n\n```bash\n# Build baseimage\ndocker build -t viral-ngs:baseimage -f docker/Dockerfile.baseimage .\n\n# Build core (needs baseimage)\ndocker build --build-arg BASEIMAGE=viral-ngs:baseimage \\\n -t viral-ngs:core -f docker/Dockerfile.core .\n\n# Build derivatives (need core)\ndocker build --build-arg BASEIMAGE=viral-ngs:core \\\n -t viral-ngs:classify -f docker/Dockerfile.classify .\n```\n\n---\n\n## CI/CD\n\n### GitHub Actions Workflow\n\nThe `.github/workflows/docker.yml` workflow handles building and testing:\n\n**Build Architecture:**\nEach image flavor is built using 3 parallel jobs for native multi-arch support:\n1. `build-{flavor}-amd64` - runs on `ubuntu-latest`\n2. `build-{flavor}-arm64` - runs on `ubuntu-24.04-arm` (native ARM runner)\n3. `create-manifest-{flavor}` - combines arch-specific images into multi-arch manifest\n\nThis approach is 3-5x faster than QEMU emulation for ARM builds.\n\n**Build Job Flow:**\n```\npaths-filter + get-version (parallel)\n ↓\nbuild-baseimage-amd64 ←→ build-baseimage-arm64 (parallel)\n ↓ ↓\n create-manifest-baseimage\n ↓\nbuild-core-amd64 ←→ build-core-arm64 (parallel)\n ↓ ↓\n create-manifest-core\n ↓\nbuild-{assemble,classify,phylo,mega}-amd64 ←→ build-{...}-arm64 (parallel)\n ↓\n create-manifest-{flavor}\n ↓\n test-{flavor} + test-{flavor}-arm64 (ARM64 tests only on PRs with docker changes)\n ↓\n deploy-to-quay (push/tag events only)\n```\n\n**Test Jobs:**\n- **test-core**: Runs on x86, tests `tests/unit/core/`\n- **test-assemble**: Runs on x86, tests `tests/unit/assemble/`\n- **test-classify**: Runs on x86, tests `tests/unit/classify/`\n- **test-phylo**: Runs on x86, tests `tests/unit/phylo/`\n- **test-{flavor}-arm64**: Runs on native ARM, only on PRs when docker files change\n\n**Smart Test Scoping:**\nTests only run when relevant code changes:\n- Core tests: `src/viral_ngs/*.py`, `core/**`, `util/**`, `tests/unit/core/**`\n- Assemble tests: `assemble/**`, `assembly.py`, or core changes\n- Classify tests: `classify/**`, `metagenomics.py`, `taxon_filter.py`, or core changes\n- Phylo tests: `phylo/**`, `interhost.py`, `intrahost.py`, `ncbi.py`, or core changes\n- Docker changes trigger all tests (including ARM64 tests on PRs)\n\n**Coverage:**\nEach x86 test job uploads coverage to Codecov with flavor-specific flags.\n\n### Multi-Architecture Support\n\n- Images built natively for `linux/amd64` and `linux/arm64` using parallel runners\n- Multi-arch manifests created with OCI annotations using `docker buildx imagetools create`\n- x86-only packages (novoalign, mvicuna, bmtagger, kallisto, kb-python, table2asn) handled via `--x86-only:` prefix in `install-conda-deps.sh`\n- Python tool wrappers still importable on ARM64; only runtime execution fails for missing binaries\n- Tests using x86-only tools have `@unittest.skipIf(IS_ARM, ...)` decorators\n- Architecture-specific caches prevent cross-arch cache pollution\n\n### ARM Test Skipping\n\nTests that use x86-only bioconda packages must be decorated to skip on ARM:\n\n```python\nfrom tests import IS_ARM\n\nSKIP_X86_ONLY_REASON = \"tool requires x86-only bioconda package (not available on ARM)\"\n\n@unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\nclass TestSomeTool(TestCaseWithTmp):\n ...\n\n# Or at method level:\n@unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\ndef test_specific_tool(self):\n ...\n```\n\n### Documentation Build\n\nThe `docs.yml` workflow builds Sphinx documentation. Key points:\n- Uses `mock` to stub heavy dependencies (`Bio`, `pysam`, `scipy`, etc.) in `docs/conf.py`\n- When adding new imports to source code, add corresponding mocks to `MOCK_MODULES` in `docs/conf.py`\n- Runs `sphinx-build -W` (warnings as errors)\n\n### Registry Strategy\n\n- **GHCR (ghcr.io)**: Primary build registry, images pushed during CI for all events including PRs\n- **Quay.io**: Production registry, images copied from GHCR after tests pass (push/tag events only)\n- Feature branch images should be cleaned up periodically from Quay.io\n\n---\n\n## Coding Guidelines\n\n### Agent Attribution\n\n**Commit messages**: By default, do NOT include agent/model credits (e.g., \"Co-Authored-By: Claude\") in commit messages. This reduces noise in the git history.\n\n**Code review comments**: DO include notes about agent/model involvement when writing code review comments (e.g., PR reviews, inline comments). This provides useful context about how the review was conducted.\n\n**Explicit requests**: Include agent attribution in commits or elsewhere when explicitly requested by a human reviewer or contributor.\n\n**Avoid amending pushed commits**: Do not use `git commit --amend` after a commit has been pushed to the remote. Amending pushed commits causes problems for collaboration. Instead, create a new commit with the fix. Amending is fine for local commits that haven't been pushed yet.\n\n### Test-Driven Development\n\n1. Write tests first\n2. Verify tests fail\n3. Implement feature\n4. Verify tests pass\n5. Refactor if needed\n\n### Avoid Over-Engineering\n\n- Only make changes directly requested\n- Don't add features beyond what was asked\n- Don't add comments/docstrings to unchanged code\n- Don't create abstractions for one-time operations\n\n### Security\n\n- Never introduce command injection, XSS, SQL injection vulnerabilities\n- Validate at system boundaries (user input, external APIs)\n- Trust internal code and framework guarantees\n\n### Code Style\n\n- Use explicit imports (prefer `import x.y.z` over `from x.y import z`)\n- Follow existing patterns in the codebase\n- Run tests before committing\n\n---\n\n## Common Operations\n\n### Verify Python imports\n\n```bash\ndocker run --rm viral-ngs:core python -c \"\nimport viral_ngs.core\nimport viral_ngs.core.samtools\nimport viral_ngs.core.picard\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\nprint('Core imports OK')\n\"\n```\n\n### Run syntax check on all files\n\n```bash\nfind src tests -name \"*.py\" -exec python -m py_compile {} \\;\n```\n\n### Check ARM64 package availability\n\n```bash\nmicromamba search -c bioconda --subdir linux-aarch64\n```\n\n---\n\n## Reusable Agent Skills\n\nEstablished workflows and playbooks live in `.agents/skills/`. Each skill\ndirectory contains a `SKILL.md` with the playbook and companion scripts.\nCheck there before building analysis pipelines from scratch.\n\nAvailable skills:\n- **regression-testing** -- End-to-end assembly regression testing against Terra submissions\n- **dsub-batch-jobs** -- Running one-off compute jobs on GCP via dsub\n- **container-vulns** -- Container vulnerability scanning, triage, and mitigation\n- **claude-on-vertex-ci** -- Invoking Claude (via claude-code-action) on Vertex AI from\n GitHub Actions workflows. Covers the WIF infra in `viral-seq-ai`, how to add a new\n Claude-in-CI use case, the canonical workflow YAML pattern, and gotchas.\n\n---\n\n## Container Vulnerability Management\n\nSee `.agents/skills/container-vulns/SKILL.md` for detailed guidance on vulnerability\nscanning, triaging CVEs, Rego policy, and ARM64 solver conflicts.\n\n---\n\n## Troubleshooting\n\n### Circular Import Errors\n\n- Use relative imports within packages (`from . import X`)\n- Check import order in `__init__.py` files\n- Don't import parent package from child modules\n\n### Missing Tool Errors\n\n- Verify tool is in the appropriate requirements file\n- Check if tool is x86-only (add to `core-x86.txt`)\n- Tool wrappers should fail gracefully at runtime, not import time\n\n### Docker Build Failures\n\n- Check that BASEIMAGE arg points to existing image\n- Verify all requirements files exist\n- Check for conda resolution conflicts (install all deps together)\n" }, { "path": "CLAUDE.md", "content": "# CLAUDE.md\n\nThis file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.\n\n**IMPORTANT**: Always read [AGENTS.md](AGENTS.md) at the start of every session before doing any work. It contains comprehensive project context and development guidelines that are essential for working in this codebase.\n\n## Quick Reference\n\n- **Docker-centric development**: Run tests inside containers, not on host\n- **Import pattern**: `from viral_ngs import core` then `core.samtools.SamtoolsTool()`\n- **Test location**: `tests/unit//`\n- **Dependencies**: ALL via conda, not pip (see `docker/requirements/*.txt`)\n\n## Running Tests\n\n```bash\ndocker run --rm \\\n -v $(pwd):/opt/viral-ngs/source \\\n quay.io/broadinstitute/viral-ngs:main-core \\\n pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit\n```\n\n## Key Files\n\n| File | Purpose |\n|------|---------|\n| [AGENTS.md](AGENTS.md) | Full AI assistant guidance |\n| [pyproject.toml](pyproject.toml) | Package configuration |\n| [docker/](docker/) | Dockerfiles and requirements |\n| [src/viral_ngs/](src/viral_ngs/) | Source code |\n| [tests/](tests/) | Test files |\n| [.agents/skills/](.agents/skills/) | Reusable agent playbooks and scripts |\n" }, { "path": "LICENSE", "content": "MIT License\n\nCopyright (c) 2014-2025 Broad Institute, Inc.\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n" }, { "path": "README.md", "content": "# viral-ngs\n\n[![Build and Test](https://github.com/broadinstitute/viral-ngs/actions/workflows/docker.yml/badge.svg)](https://github.com/broadinstitute/viral-ngs/actions/workflows/docker.yml)\n[![codecov](https://codecov.io/gh/broadinstitute/viral-ngs/graph/badge.svg)](https://codecov.io/gh/broadinstitute/viral-ngs)\n[![Documentation Status](https://readthedocs.org/projects/viral-ngs/badge/?version=latest)](https://viral-ngs.readthedocs.io/en/latest/?badge=latest)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n\nConsolidated tools for viral NGS (Next-Generation Sequencing) data analysis.\n\n## Overview\n\nviral-ngs provides a comprehensive suite of bioinformatics tools for viral genomics:\n\n- **Core utilities**: Read manipulation, Illumina demultiplexing, file handling, quality control\n- **Assembly**: Genome assembly, scaffolding, gap filling (SPAdes, MUMmer, MAFFT)\n- **Classification**: Metagenomic classification, taxonomy filtering (Kraken2, BLAST, BMTagger)\n- **Phylogenetics**: Variant calling, consensus generation, annotation (LoFreq, SnpEff, MUSCLE)\n\n## Docker Images\n\nPre-built Docker images are available on [Quay.io](https://quay.io/repository/broadinstitute/viral-ngs) and [GitHub Container Registry](https://github.com/broadinstitute/viral-ngs/pkgs/container/viral-ngs):\n\n| Image | Description |\n|-------|-------------|\n| `viral-ngs:latest` | All tools (mega image) |\n| `viral-ngs:core` | Core utilities only |\n| `viral-ngs:assemble` | Core + assembly tools |\n| `viral-ngs:classify` | Core + classification tools |\n| `viral-ngs:phylo` | Core + phylogenetics tools |\n\n### Quick Start\n\n```bash\n# Pull the latest image\ndocker pull quay.io/broadinstitute/viral-ngs:latest\n\n# Run interactively\ndocker run -it --rm quay.io/broadinstitute/viral-ngs:latest\n\n# Mount local data directory\ndocker run -it --rm -v $(pwd)/data:/data quay.io/broadinstitute/viral-ngs:latest\n```\n\n### Version Tags\n\n```bash\n# Specific version\ndocker pull quay.io/broadinstitute/viral-ngs:2.6.0-core\n\n# Main branch\ndocker pull quay.io/broadinstitute/viral-ngs:main-classify\n\n# GitHub Container Registry (alternative)\ndocker pull ghcr.io/broadinstitute/viral-ngs:latest\n```\n\n## Installation\n\n### Docker (Recommended)\n\nThe recommended way to use viral-ngs is via Docker images, which include all bioinformatics tool dependencies pre-configured.\n\n### Conda + pip (Development)\n\nFor local development with bioinformatics tools:\n\n1. **Clone the repository:**\n ```bash\n git clone https://github.com/broadinstitute/viral-ngs.git\n cd viral-ngs\n ```\n\n2. **Create and activate a conda environment:**\n ```bash\n conda create -n viral-ngs python=3.12\n conda activate viral-ngs\n ```\n\n Or using micromamba (faster):\n ```bash\n micromamba create -n viral-ngs python=3.12\n micromamba activate viral-ngs\n ```\n\n3. **Install bioinformatics tools via conda:**\n ```bash\n # Core tools only\n conda install -c conda-forge -c bioconda \\\n --file docker/requirements/baseimage.txt \\\n --file docker/requirements/core.txt\n\n # Or for all tools (mega)\n conda install -c conda-forge -c bioconda \\\n --file docker/requirements/baseimage.txt \\\n --file docker/requirements/core.txt \\\n --file docker/requirements/assemble.txt \\\n --file docker/requirements/classify.txt \\\n --file docker/requirements/phylo.txt\n ```\n\n4. **Install the viral-ngs Python package:**\n ```bash\n pip install -e .\n ```\n\n Note: Installing into an activated conda environment is safe - pip installs into the conda environment, not system Python.\n\n5. **Verify installation:**\n ```bash\n read_utils --version\n python -c \"from viral_ngs.core import samtools; print(samtools.SamtoolsTool().version())\"\n ```\n\n### pip (Python package only)\n\nFor use as a Python library without bioinformatics tools:\n\n```bash\npip install viral-ngs\n```\n\nNote: pip installation does not include external tools (samtools, bwa, etc.). Use Docker or Conda for the complete toolset.\n\n## Documentation\n\n- **Command-line documentation**: https://viral-ngs.readthedocs.org/\n- **Developer guide**: [AGENTS.md](AGENTS.md)\n- **Higher-level pipelines**: https://github.com/broadinstitute/viral-pipelines\n\n## Development\n\n### Running Tests\n\n```bash\ndocker run --rm \\\n -v $(pwd):/opt/viral-ngs/source \\\n quay.io/broadinstitute/viral-ngs:main-core \\\n pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit\n```\n\n### Building Docker Images Locally\n\n```bash\n# Build baseimage\ndocker build -t viral-ngs:baseimage -f docker/Dockerfile.baseimage .\n\n# Build core (requires baseimage)\ndocker build --build-arg BASEIMAGE=viral-ngs:baseimage \\\n -t viral-ngs:core -f docker/Dockerfile.core .\n\n# Build derivatives (require core)\ndocker build --build-arg BASEIMAGE=viral-ngs:core \\\n -t viral-ngs:classify -f docker/Dockerfile.classify .\n```\n\nSee [AGENTS.md](AGENTS.md) for comprehensive development documentation.\n\n## Architecture\n\n### Multi-Architecture Support\n\nImages are built for both `linux/amd64` and `linux/arm64` (Apple Silicon, ARM servers).\n\nSome tools (novoalign, mvicuna) are x86-only and will be skipped on ARM builds.\n\n### Module Structure\n\n```\nsrc/viral_ngs/\n├── core/ # Core utilities and tool wrappers\n├── assemble/ # Assembly tool wrappers\n├── classify/ # Classification tool wrappers\n└── phylo/ # Phylogenetics tool wrappers\n```\n\n## Related Projects\n\n- [viral-pipelines](https://github.com/broadinstitute/viral-pipelines) - WDL workflows using viral-ngs\n- [Terra](https://terra.bio/) - Cloud platform for running viral-pipelines\n\n## License\n\nMIT License - see [LICENSE](LICENSE)\n\n## Contributing\n\nContributions are welcome! Please see [AGENTS.md](AGENTS.md) for development guidelines.\n\n## Citation\n\nIf you use viral-ngs in your research, please cite:\n\n> Broad Institute viral-ngs: Tools for viral NGS data analysis.\n> https://github.com/broadinstitute/viral-ngs\n" }, { "path": "docker/Dockerfile.assemble", "content": "# viral-ngs assemble image\n# Builds on core, adds genome assembly tools\n#\n# This provides:\n# - All core bioinformatics tools (from core image)\n# - Assembly tools: SPAdes, MUMmer, MAFFT, Muscle, Gap2Seq, etc.\n# - ANI/clustering tools: skani, fastani, sourmash\n#\n# Usage:\n# docker build --build-arg BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core -t viral-ngs:assemble -f docker/Dockerfile.assemble .\n\nARG BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core\nFROM ${BASEIMAGE}\n\nLABEL maintainer=\"viral-ngs@broadinstitute.org\"\nLABEL org.opencontainers.image.source=\"https://github.com/broadinstitute/viral-ngs\"\n\n# Enable conda environment activation for RUN commands\nARG MAMBA_DOCKERFILE_ACTIVATE=1\n\n# Workaround: add sequip lib directory to PERL5LIB\n# NOTE: sequip version here must match the version in requirements/assemble.txt\nENV PERL5LIB=$PERL5LIB:/opt/conda/share/sequip-0.11/lib\n\n# Copy requirements and dependency installation script\nCOPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/assemble.txt docker/requirements/assemble-x86.txt /tmp/requirements/\nCOPY docker/install-conda-deps.sh /tmp/\n\n# Install conda dependencies (assembly tools)\n# All files resolved together in single micromamba call; x86-only files skipped on ARM\n# Post-install fixups (inline so vulnerable files never appear in a committed layer):\n# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode\n# - Ruby json gem: mummer4/sequip pull in Ruby (via yaggo), whose bundled json gem\n# has CVE-2026-33210; remove the old default gem and install patched version (>=2.19.2)\n# - Ruby erb gem: same chain (mummer4 → yaggo → ruby), CVE-2026-41316 (Marshal\n# deserialization bypass via ERB#def_module); remove default gem and install >=6.0.4\nRUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/assemble.txt \\\n --x86-only:/tmp/requirements/assemble-x86.txt && \\\n rm -f /opt/conda/libexec/mafft/dash_client && \\\n find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \\\n rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \\\n gem install json --version '>=2.19.2' --no-document && \\\n find /opt/conda/lib/ruby -maxdepth 3 -name 'erb*' -exec rm -rf {} + && \\\n rm -f /opt/conda/lib/ruby/gems/*/specifications/default/erb-*.gemspec && \\\n gem install erb --version '>=6.0.4' --no-document\n\n# Copy source code (includes assembly module)\nCOPY src/ /opt/viral-ngs/source/src/\nCOPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/\n\n# Install viral-ngs package\n# VERSION is passed from GitHub Actions via git describe\nWORKDIR /opt/viral-ngs/source\nARG VERSION\nENV SETUPTOOLS_SCM_PRETEND_VERSION=${VERSION}\nRUN pip install --no-cache-dir . && \\\n echo \"${VERSION}\" > /opt/viral-ngs/source/VERSION\n\n# Verify installation\nRUN python -c \"from viral_ngs import read_utils, illumina; print('Core modules OK')\" && \\\n python -c \"from viral_ngs import assembly; print('Assembly module OK')\" && \\\n python -c \"from viral_ngs.assemble import spades, mummer, mafft, skani; print('Assembly tools OK')\"\n\n# Clean up\nRUN rm -rf /tmp/requirements /tmp/install-conda-deps.sh\n\nCMD [\"/bin/bash\"]\n" }, { "path": "docker/Dockerfile.baseimage", "content": "# viral-ngs baseimage\n# Base image with micromamba, Python, and general utilities for viral-ngs tools\n#\n# This provides a foundation with:\n# - micromamba (conda-compatible package manager)\n# - Python 3.12\n# - General utilities (miniwdl, udocker, cloud CLIs, etc.)\n#\n# Derivative images (core, classify, assemble, phylo) build on this.\n\nFROM mambaorg/micromamba:2.5.0-ubuntu25.10\n\nLABEL maintainer=\"viral-ngs@broadinstitute.org\"\nLABEL org.opencontainers.image.source=\"https://github.com/broadinstitute/viral-ngs\"\n\n# Enable conda environment activation for RUN commands\nARG MAMBA_DOCKERFILE_ACTIVATE=1\n\nUSER root\n\n# Set locale\nENV LANG=\"en_US.UTF-8\" \\\n LANGUAGE=\"en_US:en\" \\\n LC_ALL=\"en_US.UTF-8\" \\\n TZ=\"UTC\"\n\n# Install system packages\nRUN apt-get update && apt-get install -y --no-install-recommends \\\n ca-certificates \\\n curl \\\n git \\\n locales \\\n && apt-get upgrade -y gpgv \\\n && locale-gen en_US.UTF-8 \\\n && apt-get clean \\\n && rm -rf /var/lib/apt/lists/*\n\n# Configure micromamba channels\nRUN micromamba config append channels bioconda && \\\n micromamba config append channels conda-forge && \\\n micromamba config set always_yes yes && \\\n micromamba config set changeps1 no\n\n# Install Python in base environment\nRUN micromamba install -y -n base python=3.12 pip && \\\n micromamba clean --all --yes\n\n# Set up paths - include /opt/conda/bin for conda environment binaries\nENV VIRAL_NGS_PATH=\"/opt/viral-ngs/source\" \\\n PYTHONPATH=\"/opt/viral-ngs/source\" \\\n PATH=\"/opt/conda/bin:/usr/local/bin:$PATH\"\n\n# Configure miniwdl to use udocker as container backend\nENV MINIWDL__SCHEDULER__CONTAINER_BACKEND=\"udocker\"\n\n# Copy requirements and install script\nCOPY docker/requirements/baseimage.txt /tmp/requirements/\nCOPY docker/install-conda-deps.sh /tmp/\n\n# Install baseimage dependencies (miniwdl, udocker, cloud CLIs, utilities)\n# Remove google-cloud-sdk's bundled Python — it contains vendored copies of\n# cryptography, pyOpenSSL, etc. that are older than what we install via conda.\n# Remove gcloud-crc32c — Go binary compiled with old Go stdlib (CVEs).\n# Remove gsutil's vendored urllib3 dummyserver — contains a dummy private key\n# that triggers secret-detection scanners (e.g. Trivy).\n# gcloud/gsutil use the conda environment Python, not the bundled one.\nRUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt && \\\n rm -rf /opt/conda/share/google-cloud-sdk-*/platform/bundledpythonunix && \\\n rm -f /opt/conda/share/google-cloud-sdk-*/bin/gcloud-crc32c && \\\n rm -rf /opt/conda/share/google-cloud-sdk-*/platform/gsutil/third_party/urllib3/dummyserver && \\\n rm -rf /tmp/requirements /tmp/install-conda-deps.sh\n\n# Install firecloud via pip instead of conda because the conda noarch\n# package bundles x86_64-only wheels (cryptography, cffi, grpcio, etc.)\n# that overwrite conda's native packages and break on arm64 (#1042).\n# Requires setuptools<80 due to firecloud's use of deprecated setuptools\n# APIs (broadinstitute/fiss#192).\nRUN pip install --no-cache-dir --upgrade pip wheel && \\\n pip install --no-cache-dir 'setuptools<80' && \\\n pip install --no-cache-dir --no-build-isolation 'firecloud>=0.16.35'\n\nWORKDIR /opt/viral-ngs/source\n\n# Verify installation\nRUN python --version && \\\n micromamba --version && \\\n miniwdl --version && \\\n udocker --allow-root version && \\\n python -c \"from cryptography.hazmat.bindings._rust import _openssl; print('cryptography Rust binding OK')\" && \\\n python -c \"from firecloud import api as fapi; print('firecloud OK')\"\n\nCMD [\"/bin/bash\"]\n" }, { "path": "docker/Dockerfile.classify", "content": "# viral-ngs classify image\n# Builds on core, adds metagenomic classification tools\n#\n# This provides:\n# - All core bioinformatics tools (from core image)\n# - Classification: Kraken2, Krona, BLAST, LAST, BMTagger\n# - K-mer tools: KMC, KMA\n# - Pseudoalignment: kallisto/kb-python\n#\n# Usage:\n# docker build --build-arg BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core -t viral-ngs:classify -f docker/Dockerfile.classify .\n\nARG BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core\nFROM ${BASEIMAGE}\n\nLABEL maintainer=\"viral-ngs@broadinstitute.org\"\nLABEL org.opencontainers.image.source=\"https://github.com/broadinstitute/viral-ngs\"\n\n# Enable conda environment activation for RUN commands\nARG MAMBA_DOCKERFILE_ACTIVATE=1\n\n# Copy requirements and dependency installation script\nCOPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/classify.txt docker/requirements/classify-x86.txt /tmp/requirements/\nCOPY docker/install-conda-deps.sh /tmp/\n\n# Install conda dependencies (classify tools)\n# All files resolved together in single micromamba call; x86-only files skipped on ARM\nRUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/classify.txt \\\n --x86-only:/tmp/requirements/classify-x86.txt\n\n# Copy source code (includes classify module)\nCOPY src/ /opt/viral-ngs/source/src/\nCOPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/\n\n# Install viral-ngs package\n# VERSION is passed from GitHub Actions via git describe\nWORKDIR /opt/viral-ngs/source\nARG VERSION\nENV SETUPTOOLS_SCM_PRETEND_VERSION=${VERSION}\nRUN pip install --no-cache-dir . && \\\n echo \"${VERSION}\" > /opt/viral-ngs/source/VERSION\n\n# Verify installation\nRUN python -c \"from viral_ngs import read_utils, illumina; print('Core modules OK')\" && \\\n python -c \"from viral_ngs import metagenomics, taxon_filter, kmer_utils; print('Classify command modules OK')\" && \\\n python -c \"from viral_ngs.classify import blast, bmtagger, kraken2, krona, kma, kmc, last; print('Classify tools OK')\"\n\n# Clean up\nRUN rm -rf /tmp/requirements /tmp/install-conda-deps.sh\n\nCMD [\"/bin/bash\"]\n" }, { "path": "docker/Dockerfile.core", "content": "# viral-ngs core image\n# Builds on baseimage, adds core bioinformatics tools and viral-ngs package\n#\n# This provides:\n# - All core bioinformatics tools (samtools, picard, bwa, etc.)\n# - The viral-ngs Python package installed in editable mode\n#\n# Usage:\n# docker build --build-arg BASEIMAGE_TAG=main-baseimage -t viral-ngs:core -f docker/Dockerfile.core .\n\nARG BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-baseimage\nFROM ${BASEIMAGE}\n\nLABEL maintainer=\"viral-ngs@broadinstitute.org\"\nLABEL org.opencontainers.image.source=\"https://github.com/broadinstitute/viral-ngs\"\n\n# Enable conda environment activation for RUN commands\nARG MAMBA_DOCKERFILE_ACTIVATE=1\n\n# Copy requirements and dependency installation script\nCOPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/core-x86.txt /tmp/requirements/\nCOPY docker/install-conda-deps.sh /tmp/\n\n# Install conda dependencies (bioinformatics tools)\n# All files resolved together in single micromamba call; x86-only files skipped on ARM\nRUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt \\\n --x86-only:/tmp/requirements/core-x86.txt\n\n# Copy source code\nCOPY src/ /opt/viral-ngs/source/src/\nCOPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/\n\n# Copy utility scripts\nCOPY docker/scripts/ /opt/viral-ngs/scripts/\n\n# Install viral-ngs package\n# VERSION is passed from GitHub Actions via git describe\nWORKDIR /opt/viral-ngs/source\nARG VERSION\nENV SETUPTOOLS_SCM_PRETEND_VERSION=${VERSION}\nRUN pip install --no-cache-dir . && \\\n echo \"${VERSION}\" > /opt/viral-ngs/source/VERSION\n\n# Verify installation\nRUN python -c \"from viral_ngs import read_utils, illumina, reports; print('Command modules OK')\" && \\\n python -c \"from viral_ngs.core import samtools, picard, bwa; print('Tool wrappers OK')\" && \\\n python -c \"from viral_ngs.core import file, misc, cmd; print('Utilities OK')\" && \\\n read_utils --version\n\n# Clean up\nRUN rm -rf /tmp/requirements /tmp/install-conda-deps.sh\n\nCMD [\"/bin/bash\"]\n" }, { "path": "docker/Dockerfile.mega", "content": "# viral-ngs mega image\n# Builds on core, adds ALL tools (assembly, classification, phylogenetics)\n#\n# This provides:\n# - All core bioinformatics tools (from core image)\n# - All assembly tools (SPAdes, MUMmer, MAFFT, skani, etc.)\n# - All classification tools (Kraken2, BLAST, BMTagger, KMC, etc.)\n# - All phylogenetics tools (LoFreq, SnpEff, MUSCLE, V-Phaser2, etc.)\n#\n# Usage:\n# docker build --build-arg BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core -t viral-ngs:mega -f docker/Dockerfile.mega .\n\nARG BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core\nFROM ${BASEIMAGE}\n\nLABEL maintainer=\"viral-ngs@broadinstitute.org\"\nLABEL org.opencontainers.image.source=\"https://github.com/broadinstitute/viral-ngs\"\n\n# Enable conda environment activation for RUN commands\nARG MAMBA_DOCKERFILE_ACTIVATE=1\n\n# Copy requirements and dependency installation script\nCOPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/assemble.txt docker/requirements/assemble-x86.txt docker/requirements/classify.txt docker/requirements/classify-x86.txt docker/requirements/phylo.txt docker/requirements/phylo-x86.txt /tmp/requirements/\nCOPY docker/install-conda-deps.sh /tmp/\n\n# Install ALL conda dependencies in single resolver call for proper dependency resolution\n# All files resolved together; x86-only files skipped on ARM\n# Post-install fixups (inline so vulnerable files never appear in a committed layer):\n# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode\n# - Ruby json gem: mummer4 → yaggo → Ruby, whose bundled json gem has CVE-2026-33210;\n# remove the old default gem and install patched version (>=2.19.2)\n# - Ruby erb gem: same chain (mummer4 → yaggo → ruby), CVE-2026-41316 (Marshal\n# deserialization bypass via ERB#def_module); remove default gem and install >=6.0.4\nRUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/assemble.txt /tmp/requirements/classify.txt /tmp/requirements/phylo.txt \\\n --x86-only:/tmp/requirements/assemble-x86.txt \\\n --x86-only:/tmp/requirements/classify-x86.txt \\\n --x86-only:/tmp/requirements/phylo-x86.txt && \\\n rm -f /opt/conda/libexec/mafft/dash_client && \\\n find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \\\n rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \\\n gem install json --version '>=2.19.2' --no-document && \\\n find /opt/conda/lib/ruby -maxdepth 3 -name 'erb*' -exec rm -rf {} + && \\\n rm -f /opt/conda/lib/ruby/gems/*/specifications/default/erb-*.gemspec && \\\n gem install erb --version '>=6.0.4' --no-document\n\n# Copy source code (includes all modules)\nCOPY src/ /opt/viral-ngs/source/src/\nCOPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/\n\n# Install viral-ngs package\n# VERSION is passed from GitHub Actions via git describe\nWORKDIR /opt/viral-ngs/source\nARG VERSION\nENV SETUPTOOLS_SCM_PRETEND_VERSION=${VERSION}\nRUN pip install --no-cache-dir . && \\\n echo \"${VERSION}\" > /opt/viral-ngs/source/VERSION\n\n# Verify installation - all modules\nRUN python -c \"from viral_ngs import read_utils, illumina; print('Core command modules OK')\" && \\\n python -c \"from viral_ngs import assembly; print('Assembly command modules OK')\" && \\\n python -c \"from viral_ngs import metagenomics, taxon_filter, kmer_utils; print('Classify command modules OK')\" && \\\n python -c \"from viral_ngs import interhost, intrahost, ncbi; print('Phylo command modules OK')\" && \\\n python -c \"from viral_ngs.core import samtools, picard, bwa; print('Core tools OK')\" && \\\n python -c \"from viral_ngs.assemble import spades, mummer, mafft; print('Assemble tools OK')\" && \\\n python -c \"from viral_ngs.classify import kraken2, blast, bmtagger; print('Classify tools OK')\" && \\\n python -c \"from viral_ngs.phylo import mafft, muscle, snpeff; print('Phylo tools OK')\"\n\n# Clean up\nRUN rm -rf /tmp/requirements /tmp/install-conda-deps.sh\n\nCMD [\"/bin/bash\"]\n" }, { "path": "docker/Dockerfile.phylo", "content": "# viral-ngs phylo image\n# Builds on core, adds phylogenetic analysis tools\n#\n# This provides:\n# - All core bioinformatics tools (from core image)\n# - Alignment tools: MAFFT, MUMmer, MUSCLE\n# - Variant calling: V-Phaser2, LoFreq\n# - Annotation: SnpEff, table2asn (x86-only)\n#\n# Usage:\n# docker build --build-arg BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core -t viral-ngs:phylo -f docker/Dockerfile.phylo .\n\nARG BASEIMAGE=quay.io/broadinstitute/viral-ngs:main-core\nFROM ${BASEIMAGE}\n\nLABEL maintainer=\"viral-ngs@broadinstitute.org\"\nLABEL org.opencontainers.image.source=\"https://github.com/broadinstitute/viral-ngs\"\n\n# Enable conda environment activation for RUN commands\nARG MAMBA_DOCKERFILE_ACTIVATE=1\n\n# Copy requirements and dependency installation script\nCOPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/phylo.txt docker/requirements/phylo-x86.txt /tmp/requirements/\nCOPY docker/install-conda-deps.sh /tmp/\n\n# Install conda dependencies (phylo tools)\n# All files resolved together in single micromamba call; x86-only files skipped on ARM\n# Post-install fixups (inline so vulnerable files never appear in a committed layer):\n# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode\n# - Ruby json gem: mummer4 pulls in yaggo → Ruby, whose bundled json gem has\n# CVE-2026-33210; remove the old default gem and install patched version (>=2.19.2)\n# - Ruby erb gem: same chain (mummer4 → yaggo → ruby), CVE-2026-41316 (Marshal\n# deserialization bypass via ERB#def_module); remove default gem and install >=6.0.4\nRUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/phylo.txt \\\n --x86-only:/tmp/requirements/phylo-x86.txt && \\\n rm -f /opt/conda/libexec/mafft/dash_client && \\\n find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \\\n rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \\\n gem install json --version '>=2.19.2' --no-document && \\\n find /opt/conda/lib/ruby -maxdepth 3 -name 'erb*' -exec rm -rf {} + && \\\n rm -f /opt/conda/lib/ruby/gems/*/specifications/default/erb-*.gemspec && \\\n gem install erb --version '>=6.0.4' --no-document\n\n# Copy source code (includes phylo module)\nCOPY src/ /opt/viral-ngs/source/src/\nCOPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/\n\n# Install viral-ngs package\n# VERSION is passed from GitHub Actions via git describe\nWORKDIR /opt/viral-ngs/source\nARG VERSION\nENV SETUPTOOLS_SCM_PRETEND_VERSION=${VERSION}\nRUN pip install --no-cache-dir . && \\\n echo \"${VERSION}\" > /opt/viral-ngs/source/VERSION\n\n# Verify installation\nRUN python -c \"from viral_ngs import read_utils, illumina; print('Core modules OK')\" && \\\n python -c \"from viral_ngs import interhost, intrahost, ncbi; print('Phylo command modules OK')\" && \\\n python -c \"from viral_ngs.phylo import mafft, mummer, muscle, snpeff, vphaser2; print('Phylo tools OK')\"\n\n# Clean up\nRUN rm -rf /tmp/requirements /tmp/install-conda-deps.sh\n\nCMD [\"/bin/bash\"]\n" }, { "path": "docker/install-conda-deps.sh", "content": "#!/bin/bash\n#\n# Install conda dependencies from one or more requirements files.\n#\n# Usage: install-conda-deps.sh [options] file1.txt [--x86-only:file2.txt] [file3.txt ...]\n#\n# Arguments:\n# file.txt Regular requirements file (installed on all architectures)\n# --x86-only:file.txt x86-only requirements file (skipped on ARM64)\n#\n# This script installs all dependencies in a SINGLE resolver call to prevent\n# version regressions when derivative images add packages. x86-only files are\n# included in the same resolver call on x86, ensuring consistent dependency\n# resolution across all packages.\n#\n# Examples:\n# # Install core packages only\n# install-conda-deps.sh baseimage.txt core.txt\n#\n# # Install with x86-only packages (single resolver call on x86, skips x86-only on ARM)\n# install-conda-deps.sh baseimage.txt core.txt --x86-only:core-x86.txt\n#\n# # Multiple x86-only files\n# install-conda-deps.sh baseimage.txt core.txt classify.txt --x86-only:classify-x86.txt phylo.txt --x86-only:phylo-x86.txt\n\nset -e -o pipefail\n\n# Architecture detection\nARCH=$(uname -m)\n\nis_x86() {\n [[ \"$ARCH\" == \"x86_64\" || \"$ARCH\" == \"amd64\" ]]\n}\n\n# Keepalive function for long-running installs (prevents CI timeout)\nKEEPALIVE_PID=\"\"\n\nstart_keepalive() {\n if [ -n \"$KEEPALIVE_PID\" ]; then\n return\n fi\n (\n local start_time=$(date +%s)\n while true; do\n sleep 60\n local elapsed=$(($(date +%s) - start_time))\n >&2 echo \"Still installing... (${elapsed}s elapsed)\"\n done\n ) &\n KEEPALIVE_PID=$!\n disown\n}\n\nstop_keepalive() {\n if [ -n \"$KEEPALIVE_PID\" ]; then\n kill $KEEPALIVE_PID 2>/dev/null || true\n unset KEEPALIVE_PID\n fi\n}\n\ntrap stop_keepalive EXIT SIGINT SIGQUIT SIGTERM\n\n# Parse arguments and build requirements list\nREQUIREMENTS=\"\"\nSKIPPED_X86_FILES=\"\"\n\nfor arg in \"$@\"; do\n if [[ \"$arg\" == --x86-only:* ]]; then\n # Extract filename from --x86-only:filename.txt\n file=\"${arg#--x86-only:}\"\n if is_x86; then\n if [ -f \"$file\" ]; then\n echo \"Adding x86-only requirements from: $file\"\n REQUIREMENTS=\"$REQUIREMENTS --file $file\"\n else\n echo \"Warning: x86-only requirements file not found: $file\" >&2\n fi\n else\n echo \"Skipping x86-only file on $ARCH: $file\"\n SKIPPED_X86_FILES=\"$SKIPPED_X86_FILES $file\"\n fi\n else\n # Regular requirements file\n if [ -f \"$arg\" ]; then\n echo \"Adding requirements from: $arg\"\n REQUIREMENTS=\"$REQUIREMENTS --file $arg\"\n else\n echo \"Warning: requirements file not found: $arg\" >&2\n fi\n fi\ndone\n\nif [ -z \"$REQUIREMENTS\" ]; then\n if [ -n \"$SKIPPED_X86_FILES\" ]; then\n echo \"No packages to install (all files were x86-only and skipped on $ARCH)\"\n exit 0\n fi\n echo \"Error: No valid requirements files provided\" >&2\n exit 1\nfi\n\necho \"\"\necho \"Installing conda dependencies...\"\necho \"Architecture: $ARCH\"\necho \"micromamba version: $(micromamba --version)\"\necho \"\"\n\n# Install all dependencies together in single resolver call\nstart_keepalive\nmicromamba install -y -n base $REQUIREMENTS\nstop_keepalive\n\necho \"\"\necho \"Installed packages:\"\nmicromamba list\n\n# Clean up: micromamba clean removes tarballs and index cache, but leaves\n# extracted packages in /opt/conda/pkgs/ for hardlink-installed files.\n# Trivy scans the full filesystem and flags CVEs in cached JARs/binaries,\n# so we nuke the entire pkgs cache to avoid false positives.\nmicromamba clean -y --all\nrm -rf /opt/conda/pkgs/*\n\necho \"\"\necho \"Done installing conda dependencies.\"\n" }, { "path": "docker/requirements/assemble-x86.txt", "content": "# Assembly tools - x86-only (ARM64 build has resolver conflicts)\n# These packages are skipped on ARM64 architecture\n# Install with: install-conda-deps.sh --x86-only:assemble-x86.txt\n\n# Gap2Seq: Fills gaps in genome assemblies using short reads\n# ARM64 build conflicts with pillow/libtiff due to old htslib/libdeflate pins\ngap2seq>=3.1.1a\n" }, { "path": "docker/requirements/assemble.txt", "content": "# Conda dependencies for viral-ngs assemble module\n#\n# These are bioinformatics tools used for genome assembly.\n# Install with core.txt in a single resolver call for proper dependency resolution.\n\n# Variant calling (replaces GATK)\nfreebayes>=1.3.6\n\n# Assemblers and alignment tools\n# Note: gap2seq is x86-only (ARM64 build conflicts with pillow/libtiff), see assemble-x86.txt\nmafft>=7.525\nmummer4>=4.0.1\nmuscle>=3.8,<4\nspades>=4.2.0\n\n# Read simulation and sampling\nrasusa>=3.0.0\nwgsim>=1.0\n\n# Sequence comparison / ANI tools\nfastani>=1.34\nskani>=0.3.0\nsourmash-minimal>=4.8.11\n\n# Perl packages for FASTA trimming script\nperl-bio-easel\nsequip>=0.11\n\n# Note: sourmash_plugin_branchwater has resolver problems, excluded for now\n# Note: mashtree, kwip excluded (compatibility issues)\n" }, { "path": "docker/requirements/baseimage.txt", "content": "# Conda dependencies for viral-ngs baseimage\n#\n# These are general-purpose tools installed in the base image that are\n# useful across all derivative images (core, classify, assemble, phylo).\n#\n# All packages are from conda-forge unless noted.\n\n# WDL local execution (miniwdl + udocker for containerized task execution)\nminiwdl>=1.11.1\nudocker>=1.3.16\n\n# Cloud CLIs\nawscli>=1.32.0\ngoogle-cloud-sdk>=561.0.0\ngoogle-cloud-storage>=2.14.0\n# Note: firecloud is installed via pip in Dockerfile.baseimage because the\n# conda noarch package bundles x86_64-only wheels that break on arm64 (#1042)\n\n# Python security libraries (pinned to address CVEs in transitive deps of firecloud)\ncryptography>=46.0.5\njaraco.context>=6.1.0\npyopenssl>=26.0.0\npyasn1>=0.6.3\ntornado>=6.5.4\n\n# General utilities\ncsvkit>=1.0.4\njq>=1.6\nparallel>=20190922\npigz>=2.4\nunzip>=6.0\nzstd>=1.5.7\n\n# Note: qsv is x86-only (no linux-aarch64 build), skipping for multi-arch support\n" }, { "path": "docker/requirements/classify-x86.txt", "content": "# Classification tools - x86-only (no ARM64 builds available)\n# These packages are skipped on ARM64 architecture\n# Install with: install-conda-deps.sh --x86-only:classify-x86.txt\n\n# BMTagger: Host sequence filtering tool\nbmtagger>=3.101\n\n# Kallisto/kb-python: Pseudoalignment for RNA-seq\n# kb-python depends on ngs-tools -> pyseq-align which has no ARM64 build\nkallisto>=0.51.1\nkb-python>=0.29.5\n" }, { "path": "docker/requirements/classify.txt", "content": "# Metagenomic classification tools\n# Note: x86-only packages (bmtagger, kallisto, kb-python) are in classify-x86.txt\nanndata>=0.10\nblast>=2.15.0\nkma>=1.4.0\nkmc>=3.2.1\nkraken2>=2.1.3\nkrona>=2.8.1\nlast>=1541" }, { "path": "docker/requirements/core-x86.txt", "content": "# x86-only bioinformatics tools\n# These packages are only available on x86_64 architecture (no ARM64 builds in bioconda)\n# They are installed separately from the main core requirements\n# Install with: install-conda-deps.sh --x86-only requirements/core-x86.txt\n\n# Aligners (bioconda, x86 only)\nmvicuna>=1.0\nnovoalign>=3.09.04,<4\n\n# CD-HIT auxiliary tools (includes cd-hit-dup for duplicate removal)\ncd-hit-auxtools>=4.6.8\n" }, { "path": "docker/requirements/core.txt", "content": "# Conda dependencies for viral-ngs core\n#\n# All Python runtime dependencies are installed via conda for faster\n# installation and better binary compatibility. This includes packages\n# with C extensions that would otherwise require compilation.\n#\n# Note: General utilities (parallel, pigz, jq, etc.) are in baseimage.txt\n# Note: x86-only packages (novoalign, mvicuna) are in core-x86.txt\n\n# Testing framework\npytest>=7.0.0\npytest-cov>=4.0.0\npytest-xdist>=3.0.0\n\n# Python runtime dependencies\narrow>=0.12.1\nbiopython>=1.72\njinja2>=2.11.3\nlz4>=2.2.1\nmatplotlib>=3.9.0\npandas>=2.0.0\npillow>=11.0\npsutil>=6.1.0\npybedtools>=0.7.10\npysam>=0.23.0\npyyaml>=6.0\nscipy>=1.10.0\nseaborn>=0.12.0\nzstandard>=0.23.0\n\n# Bioinformatics tools\nbbmap>=39.10\nbcftools>=1.10\nbedtools>=2.31.1\nbwa>=0.7.19\ncd-hit>=4.8.1\nfastqc>=0.12.1\nfgbio>=3.1.2\nillumina-interop=1.5.0\nlbzip2>=2.5\nlz4-c>=1.9.4\nminimap2>=2.30\npicard>=3.4.0\nprinseq>=0.20.4\nsambamba>=1.0.1\nsamtools>=1.21\nsplitcode>=0.31.6\ntrimmomatic>=0.40\n" }, { "path": "docker/requirements/phylo-x86.txt", "content": "# Phylogenetic tools - x86-only (no ARM64 builds available)\n# These packages are skipped on ARM64 architecture\n\n# table2asn: Creates sequence records for GenBank submission\n# Replaces tbl2asn, but binary-only x86 distribution\ntable2asn>=1.28\n" }, { "path": "docker/requirements/phylo.txt", "content": "# Phylogenetic analysis tools\nbamtools>=2.5.3\nlofreq>=2.1.5\nmafft>=7.525\nmummer4>=4.0.1\nmuscle>=3.8,<4\nsnpeff>=5.2\nvphaser2>=2.0\n" }, { "path": "docker/scripts/calc_mem.py", "content": "#!/usr/bin/env python\n\n\"\"\"Calculate the memory allocated to the process, taking account of cgroups.\nPrint result to stdout.\n\"\"\"\n\nimport math\nimport argparse\nimport sys\nimport os\nimport re\nimport logging\nimport os.path\nimport multiprocessing\n\nimport psutil\n\n#from util.misc import available_cpu_count # use the version of available_cpu_count() from viral-core/util/misc.py\n\nlog = logging.getLogger(__name__)\n\nparser = argparse.ArgumentParser('Calculated memory allocated to the process')\nparser.add_argument('mem_unit', choices=('b', 'kb', 'mb', 'gb'), help='memory units')\nparser.add_argument('mem_fraction', type=int, help='what fraction of total memory to report')\nparser.add_argument('--per-cpu', dest=\"per_cpu\", action='store_true', help='Calculate memory per-CPU.')\nargs = parser.parse_args()\n\nif not (1 <= args.mem_fraction <= 100):\n raise RuntimeError(\"mem_fraction should be in the range [1,100]\")\n\nunit2factor = {'b': 1, 'k': 1024, 'm': 1024*1024, 'g': 1024*1024*1024}\nMAX_INT32 = (2 ** 31)-1\n\ndef available_cpu_count():\n \"\"\"\n Return the number of available virtual or physical CPUs on this system.\n The number of available CPUs can be smaller than the total number of CPUs\n when the cpuset(7) mechanism is in use, as is the case on some cluster\n systems.\n\n Adapted from http://stackoverflow.com/a/1006301/715090\n \"\"\"\n\n cgroup_cpus = MAX_INT32\n try:\n def _load(path, encoding=\"utf-8\"):\n \"\"\" Loads a file content \"\"\"\n with open(path, 'r', encoding=encoding, newline=\"\") as handle:\n tmp = handle.read()\n return tmp\n\n # cgroup CPU count determination (w/ v2) adapted from:\n # https://github.com/conan-io/conan/blob/2.9.2/conan/tools/build/cpu.py#L31-L54\n #\n # see also:\n # https://docs.kernel.org/scheduler/sched-bwc.html\n\n # This is necessary to determine docker cpu_count\n cfs_quota_us = cfs_period_us = 0\n # cgroup v2\n if os.path.exists(\"/sys/fs/cgroup/cgroup.controllers\"):\n cpu_max = _load(\"/sys/fs/cgroup/cpu.max\").split()\n if cpu_max[0] != \"max\":\n if len(cpu_max) == 1:\n cfs_quota_us, cfs_period_us = int(cpu_max[0]), 100_000\n else:\n cfs_quota_us, cfs_period_us = map(int, cpu_max)\n # cgroup v1\n else:\n cfs_quota_us = int(_load(\"/sys/fs/cgroup/cpu/cpu.cfs_quota_us\"))\n cfs_period_us = int(_load(\"/sys/fs/cgroup/cpu/cpu.cfs_period_us\"))\n\n log.debug('cfs_quota_us %s, cfs_period_us %s', cfs_quota_us, cfs_period_us)\n if cfs_quota_us > 0 and cfs_period_us > 0:\n cgroup_cpus = max(1, int(math.ceil(cfs_quota_us / cfs_period_us)))\n except Exception as e:\n pass\n\n proc_cpus = MAX_INT32\n try:\n m = re.search(r'(?m)^Cpus_allowed:\\s*(.*)$', _load('/proc/self/status'))\n if m:\n res = bin(int(m.group(1).replace(',', ''), 16)).count('1')\n if res > 0:\n proc_cpus = res\n except IOError:\n pass\n\n log.debug('cgroup_cpus %d, proc_cpus %d, multiprocessing cpus %d',\n cgroup_cpus, proc_cpus, multiprocessing.cpu_count())\n return min(cgroup_cpus, proc_cpus, multiprocessing.cpu_count())\n\ndef mem_from_proc_meminfo():\n \"\"\"Return the total memory, in bytes, as given by /proc/meminfo\"\"\"\n with open('/proc/meminfo') as f:\n for line in f:\n if line.startswith('MemTotal:'):\n parts = line.strip().split()\n val, unit = parts[1:3]\n unit_factor = unit2factor[unit[0].lower()]\n return int(val) * unit_factor\n raise RuntimeError('Could not get MemTotal from /proc/meminfo')\n\ndef mem_from_cgroups():\n \"\"\"Return the total memory, in bytes, as given by cgroups (or sys.maxsize if not given)\"\"\"\n # list of potential cgroup paths to max mem info\n # see:\n # (cgroup v1) https://www.kernel.org/doc/Documentation/cgroup-v1/memory.txt\n # (cgroup v2) https://www.kernel.org/doc/Documentation/cgroup-v2.txt\n cgroups_memlimit_fnames = [\n '/sys/fs/cgroup/memory/memory.limit_in_bytes', # cgroup v1\n '/sys/fs/cgroup/memory.max' # cgroup v2\n ]\n # try the various potential cgroup memory info paths\n for cgroups_memlimit_fname in cgroups_memlimit_fnames:\n if os.path.isfile(cgroups_memlimit_fname):\n with open(cgroups_memlimit_fname) as f:\n val = f.read().strip()\n if val != \"max\":\n return int(val) * unit2factor.get(val[-1], 1)\n\n return sys.maxsize\n\ndef mem_from_psutil(metric_name=\"total\"):\n \"\"\" Use psutil to get a memory metric by name in a cross-platform way\n Returning sys.maxsize (obviously wrong large value) \n in the event the value cannot be obtained.\n\n For available metrics, see:\n https://psutil.readthedocs.io/en/latest/#psutil.virtual_memory\n \"\"\"\n mem_info = psutil.virtual_memory()\n\n return int(getattr(mem_info,metric_name,sys.maxsize))\n\n# of the memory values obtained, use the smallest value\n# this results in obviously-wrong values obtained from sys.maxsize\n# in mem_from_cgroups() or mem_from_psutil() falling in precedence \nmem_in_bytes = min(\n mem_from_psutil(),\n mem_from_proc_meminfo(),\n mem_from_cgroups()\n )\n\nif args.per_cpu:\n mem_in_bytes = mem_in_bytes/available_cpu_count()\n\nmem_in_units = float(mem_in_bytes) / float(unit2factor[args.mem_unit[0]])\nprint(int(mem_in_units * (float(args.mem_fraction) / 100.0)))\n" }, { "path": "docker/scripts/fasta-trim-terminal-ambigs.pl", "content": "#!/usr/bin/env perl\n\nuse strict;\nuse warnings;\nuse Getopt::Long;\nuse Bio::Easel::MSA;\nuse Bio::Easel::SqFile;\nrequire \"sqp_seq.pm\";\nrequire \"sqp_utils.pm\";\n\nmy $usage;\n$usage = \"fasta-trim-terminal-ambigs.pl\\n\\n\";\n$usage .= \"Usage:\\n\\n\";\n$usage .= \"perl fasta-trim-terminal-ambigs.pl [OPTIONS] \\n\\n\";\n$usage .= \"OPTIONS:\\n\";\n$usage .= \" --minlen : min allowed sequence length after trimming [default (df): 1]\\n\";\n$usage .= \" --maxlen : max allowed sequence length after trimming [df: 1Gb]\\n\";\n$usage .= \" --sfx : suffix to add to each sequence name is [df: do not change names]\\n\";\n$usage .= \" --strict : die (instead of skipping a seq) if any seq is not within minlen..maxlen range after trimming\\n\";\n$usage .= \"\\nAlternatively, use the --3rules option to trim using a more sophisticated method that removes\\n\";\n$usage .= \"terminal nucleotides (nts) using the following three rules:\\n\\n\";\n\n$usage .= \"Rule 1. remove the 10 terminal nts if > ambiguous nt exist in 10 terminal nt ( from --ten )\\n\";\n$usage .= \"Rule 2. remove the 50 terminal nts if > ambiguous nt exist in 50 terminal nt ( from --fifty )\\n\";\n$usage .= \"Continue to enforce rule 1 until it no longer applies, then enforce rule 2 and if rule 2 applies\\n\";\n$usage .= \"we go back and try to apply rule 1 again, and continue until neither rule 1 or 2 applies. Then\\n\";\n$usage .= \"move on to rule 3.\\n\";\n\n$usage .= \"Rule 3. remove all terminal ambiguous nt (such that sequence starts/ends with non-ambiguous nt)\\n\\n\";\n$usage .= \"Then output sequence only if it has length between the minimum and maximum (from --minlen and\\n\";\n$usage .= \"--maxlen) and is less than fraction Ns ( from --maxfrac ).\\n\\n\";\n\n$usage .= \"Options related to the alternative '3 rules' strategy:\\n\";\n$usage .= \" --3rules : use the 3 rules strategy described above [df: do not]\\n\";\n$usage .= \" --ten : max number of ambiguous nucleotides allowed in first/final 10 [df: 5]\\n\";\n$usage .= \" --fifty : max number of ambiguous nucleotides allowed in first/final 50 [df: 15]\\n\";\n$usage .= \" --maxfrac : max allowed fraction of sequence that can be Ns after trimming [df: 0.5]\\n\";\n\n# set defaults, for SC2 processing, GenBank used min of 50 and max of 30000 (as of May 2021)\nmy $minlen = 1;\nmy $maxlen = 1000000000; # 1Gb\n\nmy $sfx = undef;\nmy $do_strict = 0;\nmy $do_3rules = 0; # set to 1 if --3rules used\n\n# variables only relevant if --3rules is used\nmy $df_ten_max_ambig = 5;\nmy $df_fifty_max_ambig = 15;\nmy $df_maxfrac_Ns = 0.5;\nmy $ten_max_ambig = undef;\nmy $fifty_max_ambig = undef;\nmy $maxfrac_Ns = undef;\n\n&GetOptions( \"minlen=s\" => \\$minlen,\n \"maxlen=s\" => \\$maxlen,\n \"sfx=s\" => \\$sfx, \n \"strict\" => \\$do_strict,\n \"3rules\" => \\$do_3rules,\n \"ten=s\" => \\$ten_max_ambig,\n \"fifty=s\" => \\$fifty_max_ambig,\n \"maxfrac=s\"=> \\$maxfrac_Ns);\n\nif(scalar(@ARGV) != 1) { die $usage; }\nmy ($fasta_file) = @ARGV;\n\n# enforce --3rules related options only used if --3rules also used\nif(! $do_3rules) {\n if(defined $ten_max_ambig) {\n die \"ERROR, using --ten only makes sense if --3rules is also used\";\n }\n if(defined $fifty_max_ambig) {\n die \"ERROR, using --fifty only makes sense if --3rules is also used\";\n }\n if(defined $maxfrac_Ns) { \n die \"ERROR, using --maxfrac only makes sense if --3rules is also used\";\n }\n}\nif(! defined $ten_max_ambig) {\n $ten_max_ambig = $df_ten_max_ambig;\n}\nif(! defined $fifty_max_ambig) {\n $fifty_max_ambig = $df_fifty_max_ambig;\n}\nif(! defined $maxfrac_Ns) { \n $maxfrac_Ns = $df_maxfrac_Ns;\n}\n\n# enforce ranges that make sense for options\nif($minlen < 0) { \n die \"ERROR with --minlen , must be >= 0\";\n}\nif($maxlen < 0) { \n die \"ERROR with --maxlen , must be >= 0\";\n}\nif(($ten_max_ambig < 0) || ($ten_max_ambig >= 10)) { \n die \"ERROR with --ten , must in range [0..9]\";\n}\nif(($fifty_max_ambig < 0) || ($fifty_max_ambig >= 50)) { \n die \"ERROR with --ten , must in range [0..49]\";\n}\nif($minlen > $maxlen) { \n die \"ERROR with --minlen and --maxlen , must not be greater than \";\n}\nif($ten_max_ambig > $fifty_max_ambig) { \n die \"ERROR with --ten and --fifty , must not be greater than \";\n}\nif(($maxfrac_Ns < -0.00001) || ($maxfrac_Ns > 1.00001)) { \n die \"ERROR with --maxfrac , must be between 0 and 1\";\n}\n\nif(! -s $fasta_file) { \n die \"ERROR fasta file $fasta_file does not exist or is empty\";\n}\n\n# determine number of sequences in file\nmy $nseq = `grep ^\\\\> $fasta_file | wc -l`;\nchomp $nseq;\n$nseq =~ s/^\\s+//; # remove leading whitespace\n$nseq =~ s/\\s+$//; # remove trailing whitespace\nif($nseq !~ /^\\s*\\d+\\s*$/) { \n die \"ERROR could not determine number of sequences in file using grep and wc\";\n}\n\n# open Bio::Easel SqFile object\nmy $sqfile = Bio::Easel::SqFile->new({ fileLocation => $fasta_file }); # the sequence file object\n\nmy $fasta_seq = undef;\nmy @fasta_seq_A = ();\nmy ($header, $sqstring, $out_header) = (undef, undef, undef);\n\n# for each sequence, remove Ns and output to STDOUT\nfor(my $i = 0; $i < $nseq; $i++) { \n $fasta_seq = $sqfile->fetch_consecutive_seqs(1, \"\", -1); # -1: unlimited line length\n @fasta_seq_A = split(/\\n/, $fasta_seq);\n if(scalar(@fasta_seq_A) != 2) { \n die \"ERROR fetching sequence, could not split into header and sequence lines:\\n$fasta_seq\\n\"; \n }\n ($header, $sqstring) = (@fasta_seq_A);\n\n # add sfx to sequence name, if --sfx used\n if(defined $sfx) { \n if($header =~ /^\\>(\\S+)(\\s*.*)$/) { \n $out_header = \">\" . $1 . $sfx . $2;\n }\n else { \n die \"ERROR unable to parse header line:\\n$header\\n\";\n } \n } \n else { # --sfx not used\n $out_header = $header;\n }\n\n # two modes:\n # ! do_3rules (--3rules not used): remove leading and trailing ambigs only\n # do_3rules (--3rules): enforce the three rules\n\n if(! $do_3rules) { \n $sqstring =~ s/^[^ACGTUacgtu]+//; # remove any 5'-terminal ambiguous nts\n $sqstring =~ s/[^ACGTUacgtu]+$//; # remove any 3'-terminal ambiguous nts\n }\n else { \n # --3rules used, enforce the 3 rules \n # We trim the sequence at 5' end, then reverse it and trim at 3' end\n # (this makes it so we can reuse same code for both ends)\n # then reverse it back and output it (if there's any sequence left after trimming)\n $sqstring = trim_5p_end_using_three_rules($sqstring, $ten_max_ambig, $fifty_max_ambig);\n ##printf(\"5' trimmed length: %d\\n\", length($sqstring));\n if($sqstring ne \"\") { \n $sqstring = reverse($sqstring);\n $sqstring = trim_5p_end_using_three_rules($sqstring, $ten_max_ambig, $fifty_max_ambig);\n ##printf(\"3' trimmed length: %d\\n\", length($sqstring));\n if($sqstring ne \"\") { # reverse it back to original forward direction\n $sqstring = reverse($sqstring);\n }\n }\n }\n my $seqlen = length($sqstring);\n my $n_N = () = $sqstring =~ /[Nn]/g; # count Ns\n my $frac_N = ($seqlen > 0) ? ($n_N / $seqlen) : 0.;\n\n if(($seqlen < $minlen) || # too short (after trimming)\n ($seqlen > $maxlen) || # too long (after trimming)\n (($do_3rules) && ($frac_N > $maxfrac_Ns))) { # --3rules used and too many Ns (after trimming)\n # do not output sequence\n if(! $do_strict) { \n ; # --strict not used, it's ok to skip seqs, do nothing\n }\n else { \n # --strict used, it's not ok to skip seqs, die\n if($seqlen < $minlen) { \n die \"ERROR sequence with the header line below is too short (after trimming) length is $seqlen minlen is $minlen.\\n$header\\n\";\n }\n elsif($seqlen > $maxlen) { \n die \"ERROR sequence with the header line below is too short (after trimming) length is $seqlen minlen is $minlen.\\n$header\\n\";\n }\n else { \n die \"ERROR sequence with the header line below has too many Ns (after trimming) fraction Ns is $frac_N, max allowed is $maxfrac_Ns\\n$header\\n\";\n }\n }\n }\n else { \n # $sqstring is not too short, not too long, and doesn't have too many Ns (if --3rules)\n print $out_header . \"\\n\";\n print seq_SqstringAddNewlines($sqstring, 60);\n }\n}\n\nexit 0;\n\n#################################################################\n# Subroutine: trim_5p_end_using_three_rules()\n# Incept: EPN, Wed Apr 7 07:22:43 2021\n#\n# Purpose: Given a sequence string <$sqstring>, remove ambiguous\n# nts from the 5' end the same way that GenBank processing \n# does, using 3 rules:\n# while any rule results in trimming:\n# - rule 1: remove the 10 5'-most nt if > $ten_max_ambig \n# ambiguous nt exist in 10 5'-most nt [5 by default]\n# - rule 2: remove the 50 5'-most nt if > $fifty_max_ambig \n# ambiguous nt exist in 50 5'-most nt [15 by default]\n# - rule 3: after rule 1 and rule 2 trimming is finished,\n# trim terminal ambiguous nucleotides before returning.\n#\n# Arguments:\n# $sqstring: the nucleotide sequence string\n# $ten_max_ambig: max number of ambiguous nucleotides allowed in first 10\n# $fifty_max_ambig: max number of ambiguous nucleotides allowed in first 50\n#\n# Returns: the input <$sqstring> trimmed as above, or \"\" if none is left after trimming\n#\n#################################################################\nsub trim_5p_end_using_three_rules { \n my $sub_name = \"trim_5p_end_using_three_rules\";\n my $nargs_expected = 3;\n if(scalar(@_) != $nargs_expected) { printf STDERR (\"ERROR, $sub_name entered with %d != %d input arguments.\\n\", scalar(@_), $nargs_expected); exit(1); } \n\n my ($sqstring, $ten_max_ambig, $fifty_max_ambig) = @_;\n\n my $keep_going = 1;\n my ($next_10, $next_50, $nambig, $trim_offset); \n my $ntrimmed = 0;\n while(($keep_going) && ($sqstring ne \"\")) { \n $keep_going = 0; # set to 1 if we use any rules below\n # rule 1: remove the 10 5'-most nt if > $ten_max_ambig ambiguous nt exist in 10 5'-most nt\n $next_10 = substr($sqstring, 0, 10);\n $nambig = () = $next_10 =~ /[^ACGTUacgtu]/g;\n if($nambig > $ten_max_ambig) { \n # determine how many to trim, stop trimming at final ambig char in region\n # remove all non-ambiguous nt from the end to determine length to trim\n $next_10 =~ s/[ACGTUacgtu]+$//;\n $trim_offset = length($next_10);\n\n $ntrimmed += $trim_offset;\n ##printf(\"nambig: $nambig, trimming $trim_offset: %s (ntrimmed: $ntrimmed)\\n\", substr($sqstring, 0, $trim_offset));\n\n $sqstring = substr($sqstring, $trim_offset);\n $keep_going = 1;\n }\n # rule 2: remove the 50 5'-most nt if > $fifty_max_ambig ambiguous nt exist in 50 5'-most nt\n if(! $keep_going) { # only enforce this rule if we didn't use rule 1\n $next_50 = substr($sqstring, 0, 50);\n $nambig = () = $next_50 =~ /[^ACGTUacgtu]/g;\n if($nambig > $fifty_max_ambig) { \n # determine how many to trim, stop trimming at final ambig char in region\n # remove all non-ambiguous nt from the end to determine length to trim\n $next_50 =~ s/[ACGTUacgtu]+$//;\n $trim_offset = length($next_50);\n\n $ntrimmed += $trim_offset;\n ##printf(\"nambig: $nambig, trimming $trim_offset: %s (ntrimmed: $ntrimmed)\\n\", substr($sqstring, 0, $trim_offset));\n $sqstring = substr($sqstring, $trim_offset);\n $keep_going = 1;\n }\n }\n }\n\n # finally, trim any leading (terminal) ambiguities\n $sqstring =~ s/^[^ACGTUacgtu]+//;\n\n return $sqstring;\n}\n\n" }, { "path": "docs/Makefile", "content": "# Makefile for Sphinx documentation\n#\n\n# You can set these variables from the command line.\nSPHINXOPTS = --jobs auto\nSPHINXBUILD = sphinx-build\nPAPER =\nBUILDDIR = _build\n\n# User-friendly check for sphinx-build\nifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)\n$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)\nendif\n\n# Internal variables.\nPAPEROPT_a4 = -D latex_paper_size=a4\nPAPEROPT_letter = -D latex_paper_size=letter\nALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .\n# the i18n builder cannot share the environment and doctrees with the others\nI18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .\n\n.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext\n\nhelp:\n\t@echo \"Please use \\`make ' where is one of\"\n\t@echo \" html to make standalone HTML files\"\n\t@echo \" dirhtml to make HTML files named index.html in directories\"\n\t@echo \" singlehtml to make a single large HTML file\"\n\t@echo \" pickle to make pickle files\"\n\t@echo \" json to make JSON files\"\n\t@echo \" htmlhelp to make HTML files and a HTML help project\"\n\t@echo \" qthelp to make HTML files and a qthelp project\"\n\t@echo \" devhelp to make HTML files and a Devhelp project\"\n\t@echo \" epub to make an epub\"\n\t@echo \" latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter\"\n\t@echo \" latexpdf to make LaTeX files and run them through pdflatex\"\n\t@echo \" latexpdfja to make LaTeX files and run them through platex/dvipdfmx\"\n\t@echo \" text to make text files\"\n\t@echo \" man to make manual pages\"\n\t@echo \" texinfo to make Texinfo files\"\n\t@echo \" info to make Texinfo files and run them through makeinfo\"\n\t@echo \" gettext to make PO message catalogs\"\n\t@echo \" changes to make an overview of all changed/added/deprecated items\"\n\t@echo \" xml to make Docutils-native XML files\"\n\t@echo \" pseudoxml to make pseudoxml-XML files for display purposes\"\n\t@echo \" linkcheck to check all external links for integrity\"\n\t@echo \" doctest to run all doctests embedded in the documentation (if enabled)\"\n\nclean:\n\trm -rf $(BUILDDIR)/*\n\nhtml:\n\t$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html\n\t@echo\n\t@echo \"Build finished. The HTML pages are in $(BUILDDIR)/html.\"\n\ndirhtml:\n\t$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml\n\t@echo\n\t@echo \"Build finished. The HTML pages are in $(BUILDDIR)/dirhtml.\"\n\nsinglehtml:\n\t$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml\n\t@echo\n\t@echo \"Build finished. The HTML page is in $(BUILDDIR)/singlehtml.\"\n\npickle:\n\t$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle\n\t@echo\n\t@echo \"Build finished; now you can process the pickle files.\"\n\njson:\n\t$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json\n\t@echo\n\t@echo \"Build finished; now you can process the JSON files.\"\n\nhtmlhelp:\n\t$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp\n\t@echo\n\t@echo \"Build finished; now you can run HTML Help Workshop with the\" \\\n\t \".hhp project file in $(BUILDDIR)/htmlhelp.\"\n\nqthelp:\n\t$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp\n\t@echo\n\t@echo \"Build finished; now you can run \"qcollectiongenerator\" with the\" \\\n\t \".qhcp project file in $(BUILDDIR)/qthelp, like this:\"\n\t@echo \"# qcollectiongenerator $(BUILDDIR)/qthelp/viral-ngs.qhcp\"\n\t@echo \"To view the help file:\"\n\t@echo \"# assistant -collectionFile $(BUILDDIR)/qthelp/viral-ngs.qhc\"\n\ndevhelp:\n\t$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp\n\t@echo\n\t@echo \"Build finished.\"\n\t@echo \"To view the help file:\"\n\t@echo \"# mkdir -p $$HOME/.local/share/devhelp/viral-ngs\"\n\t@echo \"# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/viral-ngs\"\n\t@echo \"# devhelp\"\n\nepub:\n\t$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub\n\t@echo\n\t@echo \"Build finished. The epub file is in $(BUILDDIR)/epub.\"\n\nlatex:\n\t$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex\n\t@echo\n\t@echo \"Build finished; the LaTeX files are in $(BUILDDIR)/latex.\"\n\t@echo \"Run \\`make' in that directory to run these through (pdf)latex\" \\\n\t \"(use \\`make latexpdf' here to do that automatically).\"\n\nlatexpdf:\n\t$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex\n\t@echo \"Running LaTeX files through pdflatex...\"\n\t$(MAKE) -C $(BUILDDIR)/latex all-pdf\n\t@echo \"pdflatex finished; the PDF files are in $(BUILDDIR)/latex.\"\n\nlatexpdfja:\n\t$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex\n\t@echo \"Running LaTeX files through platex and dvipdfmx...\"\n\t$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja\n\t@echo \"pdflatex finished; the PDF files are in $(BUILDDIR)/latex.\"\n\ntext:\n\t$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text\n\t@echo\n\t@echo \"Build finished. The text files are in $(BUILDDIR)/text.\"\n\nman:\n\t$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man\n\t@echo\n\t@echo \"Build finished. The manual pages are in $(BUILDDIR)/man.\"\n\ntexinfo:\n\t$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo\n\t@echo\n\t@echo \"Build finished. The Texinfo files are in $(BUILDDIR)/texinfo.\"\n\t@echo \"Run \\`make' in that directory to run these through makeinfo\" \\\n\t \"(use \\`make info' here to do that automatically).\"\n\ninfo:\n\t$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo\n\t@echo \"Running Texinfo files through makeinfo...\"\n\tmake -C $(BUILDDIR)/texinfo info\n\t@echo \"makeinfo finished; the Info files are in $(BUILDDIR)/texinfo.\"\n\ngettext:\n\t$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale\n\t@echo\n\t@echo \"Build finished. The message catalogs are in $(BUILDDIR)/locale.\"\n\nchanges:\n\t$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes\n\t@echo\n\t@echo \"The overview file is in $(BUILDDIR)/changes.\"\n\nlinkcheck:\n\t$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck\n\t@echo\n\t@echo \"Link check complete; look for any errors in the above output \" \\\n\t \"or in $(BUILDDIR)/linkcheck/output.txt.\"\n\ndoctest:\n\t$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest\n\t@echo \"Testing of doctests in the sources finished, look at the \" \\\n\t \"results in $(BUILDDIR)/doctest/output.txt.\"\n\nxml:\n\t$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml\n\t@echo\n\t@echo \"Build finished. The XML files are in $(BUILDDIR)/xml.\"\n\npseudoxml:\n\t$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml\n\t@echo\n\t@echo \"Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml.\"\n" }, { "path": "docs/assembly.rst", "content": "assembly.py - viral sequence assembly from NGS reads\n====================================================\n\n.. argparse::\n :module: viral_ngs.assembly\n :func: full_parser\n :prog: assembly.py\n" }, { "path": "docs/broad_utils.rst", "content": "broad_utils.py - for data generated at the Broad Institute\n==========================================================\n\n.. argparse::\n :module: viral_ngs.broad_utils\n :func: full_parser\n :prog: broad_utils.py\n" }, { "path": "docs/cmdline.rst", "content": "Command line tools\n==================\n\n.. toctree::\n\n illumina\n read_utils\n assembly\n taxon_filter\n metagenomics\n kmer_utils\n interhost\n intrahost\n ncbi\n reports\n file_utils\n broad_utils\n" }, { "path": "docs/conf.py", "content": "#!/usr/bin/env python3\n# -*- coding: utf-8 -*-\n#\n# viral-ngs documentation build configuration file, created by\n# sphinx-quickstart on Fri Jan 16 00:23:17 2015.\n#\n# This file is execfile()d with the current directory set to its\n# containing dir.\n#\n# Note that not all possible configuration values are present in this\n# autogenerated file.\n#\n# All configuration values have a default; values that are commented out\n# serve to show the default.\n\nimport sys\nimport os\n\n# If extensions (or modules to document with autodoc) are in another directory,\n# add these directories to sys.path here. If the directory is relative to the\n# documentation root, use os.path.abspath to make it absolute, like shown here.\n# Add the project root to sys.path so viral_ngs package can be found\nproject_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))\nsys.path.insert(0, os.path.join(project_root, 'src'))\n\n# -- Mock out the heavyweight pip packages, esp those that require C ----\nfrom unittest import mock\nMOCK_MODULES = [\n 'scipy', 'pysam',\n 'Bio', 'Bio.AlignIO', 'Bio.Alphabet', 'Bio.Alphabet.IUPAC',\n 'Bio.SeqIO', 'Bio.SeqIO.FastaIO', 'Bio.Data.IUPACData',\n 'Bio.Seq', 'Bio.SeqRecord',\n 'pybedtools', 'pybedtools.BedTool',\n 'arrow', 'zstandard', 'bz2', 'lz4', 'lz4.frame',\n 'anndata',\n]\nfor mod_name in MOCK_MODULES:\n sys.modules[mod_name] = mock.Mock()\n\n # -- Obtain GIT version --\nimport subprocess\n\n\ndef _git_version():\n cmd = ['git', 'describe', '--tags', '--always'] # omit \"--dirty\" from doc build\n out = subprocess.check_output(cmd)\n if type(out) != str:\n out = out.decode('utf-8')\n return out.strip()\n\n\n__version__ = _git_version()\n\n# -- General configuration ------------------------------------------------\n\n# If your documentation needs a minimal Sphinx version, state it here.\n#needs_sphinx = '1.0'\n\n# Add any Sphinx extension module names here, as strings. They can be\n# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom\n# ones.\nextensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.imgmath', 'sphinxarg.ext', 'sphinx_rtd_theme']\n\n# Add any paths that contain templates here, relative to this directory.\ntemplates_path = ['_templates']\n\n# The suffix of source filenames.\nsource_suffix = '.rst'\n\n# The encoding of source files.\n#source_encoding = 'utf-8-sig'\n\n# The master toctree document.\nmaster_doc = 'index'\n\n# General information about the project.\nproject = 'viral-ngs'\ncopyright = '2026, Broad Institute Viral Genomics'\n\n# The version info for the project you're documenting, acts as replacement for\n# |version| and |release|, also used in various other places throughout the\n# built documents.\n#\nrelease = __version__\nversion = '.'.join(release.split('.')[:2])\n\n# The language for content autogenerated by Sphinx. Refer to documentation\n# for a list of supported languages.\n#language = None\n\n# There are two options for replacing |today|: either, you set today to some\n# non-false value, then it is used:\n#today = ''\n# Else, today_fmt is used as the format for a strftime call.\ntoday_fmt = '%Y-%m-%d'\n\n# List of patterns, relative to source directory, that match files and\n# directories to ignore when looking for source files.\nexclude_patterns = ['_build']\n\n# The reST default role (used for this markup: `text`) to use for all\n# documents.\n#default_role = None\n\n# If true, '()' will be appended to :func: etc. cross-reference text.\n#add_function_parentheses = True\n\n# If true, the current module name will be prepended to all description\n# unit titles (such as .. function::).\n#add_module_names = True\n\n# If true, sectionauthor and moduleauthor directives will be shown in the\n# output. They are ignored by default.\n#show_authors = False\n\n# The name of the Pygments (syntax highlighting) style to use.\npygments_style = 'sphinx'\n\n# A list of ignored prefixes for module index sorting.\n#modindex_common_prefix = []\n\n# If true, keep warnings as \"system message\" paragraphs in the built documents.\n#keep_warnings = False\n\n# -- Options for HTML output ----------------------------------------------\n\n# The theme to use for HTML and HTML Help pages. See the documentation for\n# a list of builtin themes.\nhtml_theme = 'sphinx_rtd_theme'\n# on_rtd = os.environ.get('READTHEDOCS') == 'True'\n# if on_rtd:\n# html_theme = 'sphinx_rtd_theme'\n# else:\n# import sphinx_rtd_theme\n# html_theme = \"sphinx_rtd_theme\"\n# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]\n\n# Theme options are theme-specific and customize the look and feel of a theme\n# further. For a list of options available for each theme, see the\n# documentation.\n#html_theme_options = {}\n\n# Add any paths that contain custom themes here, relative to this directory.\n#html_theme_path = []\n\n# The name for this set of Sphinx documents. If None, it defaults to\n# \" v documentation\".\n#html_title = None\n\n# A shorter title for the navigation bar. Default is the same as html_title.\n#html_short_title = None\n\n# The name of an image file (relative to this directory) to place at the top\n# of the sidebar.\n#html_logo = None\n\n# The name of an image file (within the static path) to use as favicon of the\n# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32\n# pixels large.\n#html_favicon = None\n\n# Add any paths that contain custom static files (such as style sheets) here,\n# relative to this directory. They are copied after the builtin static files,\n# so a file named \"default.css\" will overwrite the builtin \"default.css\".\n# html_static_path = ['_static']\n\n# Add any extra paths that contain custom files (such as robots.txt or\n# .htaccess) here, relative to this directory. These files are copied\n# directly to the root of the documentation.\n#html_extra_path = []\n\n# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,\n# using the given strftime format.\nhtml_last_updated_fmt = '%Y-%m-%d. {}'.format(release)\n\n# If true, SmartyPants will be used to convert quotes and dashes to\n# typographically correct entities.\n#html_use_smartypants = True\n\n# Custom sidebar templates, maps document names to template names.\n#html_sidebars = {}\n\n# Additional templates that should be rendered to pages, maps page names to\n# template names.\n#html_additional_pages = {}\n\n# If false, no module index is generated.\n#html_domain_indices = True\n\n# If false, no index is generated.\n#html_use_index = True\n\n# If true, the index is split into individual pages for each letter.\n#html_split_index = False\n\n# If true, links to the reST sources are added to the pages.\n#html_show_sourcelink = True\n\n# If true, \"Created using Sphinx\" is shown in the HTML footer. Default is True.\n#html_show_sphinx = True\n\n# If true, \"(C) Copyright ...\" is shown in the HTML footer. Default is True.\n#html_show_copyright = True\n\n# If true, an OpenSearch description file will be output, and all pages will\n# contain a tag referring to it. The value of this option must be the\n# base URL from which the finished HTML is served.\n#html_use_opensearch = ''\n\n# This is the file name suffix for HTML files (e.g. \".xhtml\").\n#html_file_suffix = None\n\n# Output file base name for HTML help builder.\nhtmlhelp_basename = 'viral-ngsdoc'\n\n# -- Options for LaTeX output ---------------------------------------------\n\nlatex_elements = {\n # The paper size ('letterpaper' or 'a4paper').\n #'papersize': 'letterpaper',\n # The font size ('10pt', '11pt' or '12pt').\n #'pointsize': '10pt',\n # Additional stuff for the LaTeX preamble.\n #'preamble': '',\n}\n\n# Grouping the document tree into LaTeX files. List of tuples\n# (source start file, target name, title,\n# author, documentclass [howto, manual, or own class]).\nlatex_documents = [('index', 'viral-ngs.tex', 'viral-ngs Documentation', 'Broad Institute Viral Genomics', 'manual'),]\n\n# The name of an image file (relative to this directory) to place at the top of\n# the title page.\n#latex_logo = None\n\n# For \"manual\" documents, if this is true, then toplevel headings are parts,\n# not chapters.\n#latex_use_parts = False\n\n# If true, show page references after internal links.\n#latex_show_pagerefs = False\n\n# If true, show URL addresses after external links.\n#latex_show_urls = False\n\n# Documents to append as an appendix to all manuals.\n#latex_appendices = []\n\n# If false, no module index is generated.\n#latex_domain_indices = True\n\n# -- Options for manual page output ---------------------------------------\n\n# One entry per manual page. List of tuples\n# (source start file, name, description, authors, manual section).\nman_pages = [('index', 'viral-ngs', 'viral-ngs Documentation', ['Broad Institute Viral Genomics'], 1)]\n\n# If true, show URL addresses after external links.\n#man_show_urls = False\n\n# -- Options for Texinfo output -------------------------------------------\n\n# Grouping the document tree into Texinfo files. List of tuples\n# (source start file, target name, title, author,\n# dir menu entry, description, category)\ntexinfo_documents = [\n ('index', 'viral-ngs', 'viral-ngs Documentation', 'Broad Institute Viral Genomics', 'viral-ngs',\n 'Viral genomics analysis pipelines', 'Miscellaneous'),\n]\n\n# Documents to append as an appendix to all manuals.\n#texinfo_appendices = []\n# If false, no module index is generated.\n#texinfo_domain_indices = True\n# How to display URL addresses: 'footnote', 'no', or 'inline'.\n#texinfo_show_urls = 'footnote'\n# If true, do not generate a @detailmenu in the \"Top\" node's menu.\n#texinfo_no_detailmenu = False\n" }, { "path": "docs/description.rst", "content": "Description of the methods\n==========================\n\nThis is a base module that provides basic utility functions,\nsome short read aligners, and samtools and Picard.\n" }, { "path": "docs/file_utils.rst", "content": "file_utils.py - utilities to perform various file manipulations\n================================================================\n\n.. argparse::\n :module: viral_ngs.file_utils\n :func: full_parser\n :prog: file_utils.py\n" }, { "path": "docs/illumina.rst", "content": "illumina.py - for raw Illumina outputs\n======================================\n\n.. argparse::\n :module: viral_ngs.illumina\n :func: full_parser\n :prog: illumina.py\n" }, { "path": "docs/index.rst", "content": ".. viral-ngs documentation master file, created by\n sphinx-quickstart on Fri Jan 16 00:23:17 2015.\n You can adapt this file completely to your liking, but it should at least\n contain the root `toctree` directive.\n\nviral-ngs: genomic analysis pipelines for viral sequencing\n==========================================================\n\n\nContents\n--------\n\n.. toctree::\n :maxdepth: 2\n :numbered:\n \n description\n cmdline\n" }, { "path": "docs/interhost.rst", "content": "interhost.py - SNP calling, multi-alignment, and phylogenetics\n==============================================================\n\n.. argparse::\n :module: viral_ngs.interhost\n :func: full_parser\n :prog: interhost.py\n" }, { "path": "docs/intrahost.rst", "content": "intrahost.py - intrahost variant calling and annotation\n=======================================================\n\n.. argparse::\n :module: viral_ngs.intrahost\n :func: full_parser\n :prog: intrahost.py\n" }, { "path": "docs/kmer_utils.rst", "content": "kmer_utils.py - commands for working with sets of kmers\n=======================================================\n\n.. argparse::\n :module: viral_ngs.kmer_utils\n :func: full_parser\n :prog: kmer_utils.py\n" }, { "path": "docs/metagenomics.rst", "content": "metagenomics.py - utilities for metagenomic analyses\n====================================================\n\n.. argparse::\n :module: viral_ngs.metagenomics\n :func: full_parser\n :prog: metagenomics.py\n" }, { "path": "docs/ncbi.rst", "content": "ncbi.py - NCBI Genbank and SRA utilities\n========================================\n\n.. argparse::\n :module: viral_ngs.ncbi\n :func: full_parser\n :prog: ncbi.py\n" }, { "path": "docs/read_utils.rst", "content": "read_utils.py - utilities that manipulate bam and fastq files\n=============================================================\n\n.. argparse::\n :module: viral_ngs.read_utils\n :func: full_parser\n :prog: read_utils.py\n" }, { "path": "docs/reports.rst", "content": "reports.py - produce various metrics and reports\n================================================\n\n.. argparse::\n :module: viral_ngs.reports\n :func: full_parser\n :prog: reports.py\n" }, { "path": "docs/requirements.txt", "content": "jinja2==3.1.4 # https://github.com/readthedocs/readthedocs.org/issues/9037#issuecomment-1077818554\nSphinx==7.4.7 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies\nsphinx-argparse==0.5.2\nsphinx-rtd-theme>=2.0.0\nmatplotlib>=2.2.4\nPyYAML==6.0.1\nmock==5.0.1\nrecommonmark\n" }, { "path": "docs/taxon_filter.rst", "content": "taxon_filter.py - filter reads by taxonomic membership\n======================================================\n\n.. argparse::\n :module: viral_ngs.taxon_filter\n :func: full_parser\n :prog: taxon_filter.py\n" }, { "path": "pyproject.toml", "content": "[build-system]\nrequires = [\"setuptools>=61.0\", \"setuptools-scm\"]\nbuild-backend = \"setuptools.build_meta\"\n\n[project]\nname = \"viral-ngs\"\ndynamic = [\"version\"]\ndescription = \"Consolidated tools for viral NGS data analysis\"\nreadme = \"README.md\"\nlicense = \"MIT\"\nrequires-python = \">=3.10\"\nauthors = [\n { name = \"Broad Institute Viral Genomics\", email = \"viral-ngs@broadinstitute.org\" }\n]\nclassifiers = [\n \"Development Status :: 4 - Beta\",\n \"Intended Audience :: Science/Research\",\n \"Operating System :: POSIX :: Linux\",\n \"Operating System :: MacOS :: MacOS X\",\n \"Programming Language :: Python :: 3\",\n \"Programming Language :: Python :: 3.10\",\n \"Programming Language :: Python :: 3.11\",\n \"Programming Language :: Python :: 3.12\",\n \"Topic :: Scientific/Engineering :: Bio-Informatics\",\n]\nkeywords = [\"bioinformatics\", \"genomics\", \"viral\", \"ngs\", \"sequencing\"]\n# Python dependencies for pip-based installs\n# Note: For Docker-based usage, all deps (including bioinformatics tools) are\n# installed via conda. See docker/requirements/core.txt\ndependencies = [\n \"arrow>=0.12.1\",\n \"biopython>=1.72\",\n \"jinja2>=2.11.3\",\n \"lz4>=2.2.1\",\n \"matplotlib>=2.2.4\",\n \"pandas>=2.0.0\",\n \"psutil>=6.1.0\",\n \"pybedtools>=0.7.10\",\n \"pysam>=0.23.0\",\n \"pyyaml>=6.0\",\n \"scipy>=1.10.0\",\n \"seaborn>=0.12.0\",\n \"zstandard>=0.23.0\",\n]\n\n[project.optional-dependencies]\ndev = [\n \"pytest>=7.0\",\n \"pytest-xdist\",\n \"pytest-cov\",\n]\n\n[project.scripts]\n# Command-line entry points for viral-ngs tools\n# Core commands\nillumina = \"viral_ngs.illumina:main\"\nread_utils = \"viral_ngs.read_utils:main\"\nreports = \"viral_ngs.reports:main\"\nfile_utils = \"viral_ngs.file_utils:main\"\nbroad_utils = \"viral_ngs.broad_utils:main\"\n# Assembly commands\nassembly = \"viral_ngs.assembly:main\"\n# Classification commands\nmetagenomics = \"viral_ngs.metagenomics:main\"\ntaxon_filter = \"viral_ngs.taxon_filter:main\"\nkmer_utils = \"viral_ngs.kmer_utils:main\"\n# Phylogenetics commands\ninterhost = \"viral_ngs.interhost:main\"\nintrahost = \"viral_ngs.intrahost:main\"\nncbi = \"viral_ngs.ncbi:main\"\n\n[project.urls]\nHomepage = \"https://github.com/broadinstitute/viral-ngs\"\nRepository = \"https://github.com/broadinstitute/viral-ngs\"\nIssues = \"https://github.com/broadinstitute/viral-ngs/issues\"\n\n[tool.setuptools_scm]\n\n[tool.setuptools.packages.find]\nwhere = [\"src\"]\n\n[tool.pytest.ini_options]\ntestpaths = [\"tests\"]\npython_files = [\"test_*.py\"]\naddopts = \"-v --tb=short\"\nmarkers = [\n \"slow: marks tests as slow (deselect with '-m \\\"not slow\\\"')\",\n]\n" }, { "path": "src/viral_ngs/__init__.py", "content": "\"\"\"\nviral-ngs: Consolidated tools for viral NGS data analysis.\n\nThis package provides utilities for viral genome sequencing data analysis,\nincluding read processing, assembly, classification, and phylogenetics.\n\nAll modules are in the `core` subpackage:\n import viral_ngs.core.samtools\n import viral_ngs.core.picard\n import viral_ngs.core.file\n import viral_ngs.core.misc\n\"\"\"\n\ntry:\n from importlib.metadata import version, PackageNotFoundError\n try:\n __version__ = version(\"viral-ngs\")\n except PackageNotFoundError:\n __version__ = \"0.0.0.dev0\"\nexcept ImportError:\n __version__ = \"0.0.0.dev0\"\n\n# Import core module - all functionality is in viral_ngs.core.*\nfrom . import core\n" }, { "path": "src/viral_ngs/assemble/__init__.py", "content": "\"\"\"\nviral_ngs.assemble - Tool wrappers for genome assembly.\n\nContains wrappers for assembly-related bioinformatics tools:\n- SPAdes, Gap2Seq, MAFFT, MUMmer, Muscle, etc.\n\"\"\"\n\n# Import tool wrappers for convenient access\nfrom . import gap2seq\nfrom . import mafft\nfrom . import mummer\nfrom . import muscle\nfrom . import skani\nfrom . import spades\nfrom . import freebayes\nfrom . import rasusa\nfrom . import vcf\nfrom . import wgsim\n" }, { "path": "src/viral_ngs/assemble/freebayes.py", "content": "'''\n FreeBayes variant caller — a Bayesian genetic variant detector.\n\n Replaces GATK3 UnifiedGenotyper for consensus refinement.\n Uses --report-monomorphic to emit all sites (equivalent to EMIT_ALL_SITES).\n'''\n\nimport logging\nimport os\nimport shutil\nimport subprocess\n\nimport pysam\n\nfrom ..core import Tool, PrexistingUnixCommand\nfrom ..core.file import mkstempfname\n\n_log = logging.getLogger(__name__)\n\nTOOL_NAME = 'freebayes'\n\n\nclass FreeBayesTool(Tool):\n\n def __init__(self):\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n Tool.__init__(self, install_methods=install_methods)\n\n def call(self, inBam, refFasta, outVcf, options=None):\n \"\"\"Call variants with FreeBayes, emitting all sites.\n\n If outVcf ends with .vcf.gz, the output is bgzipped and tabix-indexed\n (FreeBayes always writes plain VCF, so we compress and index afterward).\n \"\"\"\n options = options or [\"--min-base-quality\", \"15\", \"--pooled-continuous\"]\n\n if outVcf.endswith('.vcf.gz'):\n plainVcf = mkstempfname('.vcf')\n else:\n plainVcf = outVcf\n\n opts = [\n '-b', inBam,\n '-f', refFasta,\n '-v', plainVcf,\n '--use-best-n-alleles', '0',\n '--report-monomorphic',\n ]\n tool_cmd = [self.install_and_get_path()] + opts + options\n _log.debug(' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n\n if outVcf.endswith('.vcf.gz'):\n pysam.tabix_compress(plainVcf, outVcf, force=True)\n pysam.tabix_index(outVcf, preset='vcf', force=True)\n os.unlink(plainVcf)\n" }, { "path": "src/viral_ngs/assemble/gap2seq.py", "content": "'''\n Gap2Seq - assembly gap closing tool\n'''\n\nimport itertools\nimport functools\nimport operator\nimport logging\nimport os\nimport os.path\nimport subprocess\nimport shlex\nimport shutil\nimport tempfile\nimport time\n\nimport Bio.Seq\n\nimport viral_ngs.core\nimport viral_ngs.core.samtools\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\n\nTOOL_NAME = 'Gap2Seq'\n\nlog = logging.getLogger(__name__)\n\nclass Gap2SeqTool(viral_ngs.core.Tool):\n \"\"\"Tool wrapper for the Gap2Seq gap-closing tool.\"\"\"\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [viral_ngs.core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(Gap2SeqTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n return None\n\n def execute(self, args): # pylint: disable=W0221\n tool_cmd = [self.install_and_get_path()] + list(args)\n log.debug('running gap2seq: ' + ' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n\n def _run_gap2seq(self, reads, scaffolds, filled, *args, **kwargs):\n # gap2seq (or rather the gatb library it uses) currently has a bug where tempfiles are left in the\n # current working directory. So we run it in its own temp dir, but then must give absolute paths\n # for all files.\n\n abspath = os.path.abspath\n file_args = ('-s', abspath(scaffolds), '--filled', abspath(filled), \n '--reads', ','.join(map(abspath,reads)))\n more_args = functools.reduce(operator.concat, \n [(('--' if len(arg) > 1 else '-') + arg.replace('_','-'), str(val))\n for arg, val in kwargs.items()], ())\n with viral_ngs.core.file.tmp_dir('_gap2seq_run_dir') as gap2seq_run_dir:\n with viral_ngs.core.file.pushd_popd(gap2seq_run_dir):\n self.execute(file_args+args+more_args)\n\n def gapfill(self, in_scaffold, in_bam, out_scaffold, solid_kmer_thresholds=(3,), kmer_sizes=(90, 80, 70, 60, 50, 40, 31),\n min_gap_to_close=4, gap2seq_opts='', mem_limit_gb=4.0, threads=None, time_soft_limit_minutes=60.0, random_seed=0):\n \"\"\"Try to fill the gaps in the given scaffold, using the reads.\n\n Inputs:\n in_scaffold: a FASTA file containing the scaffold. Each FASTA record corresponds to one\n segment (for multi-segment genomes). Contigs within each segment are\n separated by Ns. The exact number of Ns between contigs does not matter, as the length of the gap is one \n of the things determined by the gap-filling tool. (But see `min_gap_to_close`).\n in_bam: reads to use for filling the gaps. Only paired-end reads from the bam file are used, any unpaired reads\n are ignored.\n \n Outputs:\n out_scaffold: the input scaffold, with some of the gaps between contigs possibly filled.\n\n Params:\n solid_kmer_thresholds: kmers must appear at least this many times in the reads to be considered solid.\n We try gapfilling for all combinations of values of solid_kmer_thresholds and kmer_sizes.\n kmer_sizes: kmer sizes to use. We try gapfilling for all combinations of values of solid_kmer_thresholds and kmer_sizes.\n min_gap_to_close: stop gap-closing if all gaps are no longer than this many Ns\n gap2seq_opts: extra command-line flags to pass to Gap2Seq\n mem_limit_gb: max memory to use, in gigabytes\n threads: number of threads to use; None means use all available cores.\n time_soft_limit_minutes: stop trying to close more gaps after this many minutes (currently this is a soft/advisory limit)\n random_seed: random seed for choosing random paths (0 to use current time)\n \n \"\"\"\n solid_kmer_thresholds = sorted(viral_ngs.core.misc.make_seq(solid_kmer_thresholds), reverse=True)\n kmer_sizes = sorted(viral_ngs.core.misc.make_seq(kmer_sizes), reverse=True)\n stop_time = time.time() + 60*time_soft_limit_minutes\n threads = viral_ngs.core.misc.sanitize_thread_count(threads, tool_max_cores_value=0)\n viral_ngs.core.misc.chk(out_scaffold != in_scaffold)\n with viral_ngs.core.samtools.SamtoolsTool().bam2fq_tmp(in_bam) as reads, viral_ngs.core.file.tmp_dir('_gap2seq_dir') as gap2seq_dir:\n\n # We call Gap2Seq for a range of parameter combinations. Output of each call is input to the next call, so\n # each call only deals with gaps not closed by prior calls. We first try to close using higher-quality kmers,\n # and if that fails try with lower-quality ones.\n prev_scaffold = in_scaffold\n for solid_kmer_threshold, kmer_size in itertools.product(solid_kmer_thresholds, kmer_sizes):\n\n if not any('N'*min_gap_to_close in str(rec.seq) for rec in Bio.SeqIO.parse(prev_scaffold, 'fasta')):\n log.info('no gaps left, quittting gap2seq early')\n break\n if time.time() > stop_time:\n log.info('Time limit for gap closing reached')\n break\n\n filled_scaffold = os.path.join(gap2seq_dir, 'gap2seq-filled.s{}.k{}.fasta'.format(solid_kmer_threshold, kmer_size))\n self._run_gap2seq(reads, prev_scaffold, filled_scaffold,\n *(['--all-upper']+shlex.split(gap2seq_opts)),\n solid=solid_kmer_threshold, k=kmer_size, threads=threads,\n max_mem=mem_limit_gb, randseed=random_seed)\n\n prev_scaffold = filled_scaffold\n\n Bio.SeqIO.convert(prev_scaffold, 'fasta', out_scaffold, 'fasta')\n\n" }, { "path": "src/viral_ngs/assemble/mafft.py", "content": "'''\n MAFFT - Multiple alignment program for amino acid or nucleotide sequences\n http://mafft.cbrc.jp/alignment/software/\n'''\n\n__author__ = \"tomkinsc@broadinstitute.org\"\n\nfrom Bio import SeqIO\nimport logging\nimport viral_ngs.core\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\nimport os\nimport os.path\nimport shutil\nimport subprocess\n\nTOOL_NAME = \"mafft\"\n\n_log = logging.getLogger(__name__)\n\n\nclass MafftTool(viral_ngs.core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [viral_ngs.core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(MafftTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').strip().split()[0]\n\n def __seqIdsAreAllUnique(self, filePath, inputFormat=\"fasta\"):\n seqIds = []\n with open(filePath, \"r\") as inFile:\n fastaFile = SeqIO.parse(inFile, inputFormat)\n seqIds = [x.id for x in fastaFile]\n\n # collapse like IDs using set()\n if len(seqIds) > len(set(seqIds)):\n raise LookupError(\n \"Not all sequence IDs in input are unique for file: {}\".format(\n os.path.basename(filePath)\n )\n )\n\n # pylint: disable=W0221\n def execute(\n self,\n inFastas,\n outFile,\n localpair,\n globalpair,\n preservecase,\n reorder,\n outputAsClustal,\n maxiters,\n gapOpeningPenalty=None,\n offset=None,\n threads=None,\n verbose=True,\n retree=None\n ):\n inputFileName = \"\"\n tempCombinedInputFile = \"\"\n\n # get the full paths of input and output files in case the user has specified relative paths\n inputFiles = []\n for f in inFastas:\n inputFiles.append(os.path.abspath(f))\n outFile = os.path.abspath(outFile)\n\n # ensure that all sequence IDs in each input file are unique\n # (otherwise the alignment result makes little sense)\n # we can check before combining to localize duplications to a specific file\n for filePath in inputFiles:\n self.__seqIdsAreAllUnique(filePath)\n\n # if multiple fasta files are specified for input\n if len(inputFiles) > 1:\n # combined specified input files into a single temp FASTA file so MAFFT can read them\n tempFileSuffix = \"\"\n for filePath in inputFiles:\n tempFileSuffix += \"__\" + os.path.basename(filePath)\n tempCombinedInputFile = viral_ngs.core.file.mkstempfname('__combined.{}'.format(tempFileSuffix))\n with open(tempCombinedInputFile, \"w\") as outfile:\n for f in inputFiles:\n with open(f, \"r\") as infile:\n outfile.write(infile.read())\n inputFileName = tempCombinedInputFile\n # if there is only one file specified, just use it\n else:\n inputFileName = inputFiles[0]\n\n # check that all sequence IDs in a file are unique\n self.__seqIdsAreAllUnique(inputFileName)\n\n # change the pwd, since the shell script that comes with mafft depends on the pwd\n # being correct\n pwdBeforeMafft = os.getcwd()\n os.chdir(os.path.dirname(self.install_and_get_path()))\n\n # build the MAFFT command\n tool_cmd = [self.install_and_get_path()]\n\n if not (retree or localpair or globalpair):\n tool_cmd.append(\"--auto\")\n tool_cmd.extend([\"--thread\", \"{}\".format(viral_ngs.core.misc.sanitize_thread_count(threads))])\n\n if localpair and globalpair:\n raise Exception(\"Alignment type must be either local or global, not both.\")\n\n if localpair:\n tool_cmd.append(\"--localpair\")\n if not maxiters:\n maxiters = 1000\n if globalpair:\n tool_cmd.append(\"--globalpair\")\n if not maxiters:\n maxiters = 1000\n if preservecase:\n tool_cmd.append(\"--preservecase\")\n if reorder:\n tool_cmd.append(\"--reorder\")\n if retree:\n tool_cmd.extend([\"--retree\", \"{}\".format(retree)])\n if gapOpeningPenalty:\n tool_cmd.extend([\"--op\", \"{penalty}\".format(penalty=gapOpeningPenalty)])\n if offset:\n tool_cmd.extend([\"--ep\", \"{num}\".format(num=offset)])\n if not verbose:\n tool_cmd.append(\"--quiet\")\n if outputAsClustal:\n tool_cmd.append(\"--clustalout\")\n if maxiters:\n tool_cmd.extend([\"--maxiterate\", \"{iters}\".format(iters=maxiters)])\n\n tool_cmd.append(inputFileName)\n\n _log.debug(' '.join(tool_cmd))\n\n # run the MAFFT alignment\n with open(outFile, 'w') as outf:\n viral_ngs.core.misc.run_and_save(tool_cmd, outf=outf)\n\n if len(tempCombinedInputFile):\n # remove temp FASTA file\n os.unlink(tempCombinedInputFile)\n\n # restore pwd\n os.chdir(pwdBeforeMafft)\n\n return outFile\n # pylint: enable=W0221\n" }, { "path": "src/viral_ngs/assemble/mummer.py", "content": "'''\n The MUMMER aligner\n http://mummer.sourceforge.net/\n'''\n\nimport logging\nimport viral_ngs.core\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\nimport os\nimport os.path\nimport random\nimport shutil\nimport subprocess\nimport Bio.SeqIO\n\nTOOL_NAME = \"mummer\"\n\nlog = logging.getLogger(__name__)\n\n\nclass MummerTool(viral_ngs.core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [viral_ngs.core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(MummerTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip()\n\n def executable_path(self):\n exec_path = viral_ngs.core.Tool.executable_path(self)\n if os.path.isdir(exec_path):\n return exec_path\n else:\n return os.path.dirname(exec_path)\n\n def execute(self, refFasta, qryFastas):\n toolCmd = [os.path.join(self.install_and_get_path(), 'mummer'),\n refFasta] + qryFastas\n log.debug(' '.join(toolCmd))\n subprocess.check_call(toolCmd)\n\n def nucmer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None):\n if not outDelta.endswith('.delta'):\n raise Exception()\n outDelta = outDelta[:-6]\n toolCmd = [os.path.join(self.install_and_get_path(), 'nucmer'),\n '--prefix={}'.format(outDelta)]\n if extend is not None:\n if not extend:\n # default behavior is --extend\n # mummer4 no longer recognizes --extend and we should only\n # specify an argument here if we want non-default behavior\n toolCmd.append('--noextend')\n if breaklen is not None:\n toolCmd.extend(['--breaklen', str(breaklen)])\n if maxgap is not None:\n toolCmd.extend(['--maxgap', str(maxgap)])\n if minmatch is not None:\n toolCmd.extend(['--minmatch', str(minmatch)])\n if mincluster is not None:\n toolCmd.extend(['--mincluster', str(mincluster)])\n toolCmd.extend([refFasta, qryFasta])\n log.debug(' '.join(toolCmd))\n subprocess.check_call(toolCmd)\n\n def promer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None):\n if not outDelta.endswith('.delta'):\n raise Exception()\n outDelta = outDelta[:-6]\n toolCmd = [os.path.join(self.install_and_get_path(), 'promer'),\n '--prefix={}'.format(outDelta)]\n if extend is not None:\n if not extend:\n # default behavior is --extend\n # mummer4 no longer recognizes --extend and we should only\n # specify an argument here if we want non-default behavior\n toolCmd.append('--noextend')\n if breaklen is not None:\n toolCmd.extend(['--breaklen', str(breaklen)])\n if maxgap is not None:\n toolCmd.extend(['--maxgap', str(maxgap)])\n if minmatch is not None:\n toolCmd.extend(['--minmatch', str(minmatch)])\n if mincluster is not None:\n toolCmd.extend(['--mincluster', str(mincluster)])\n toolCmd.extend([refFasta, qryFasta])\n log.debug(' '.join(toolCmd))\n subprocess.check_call(toolCmd)\n\n def delta_filter(self, inDelta, outDelta):\n toolCmd = [os.path.join(self.install_and_get_path(), 'delta-filter'),\n '-q', inDelta]\n log.debug(' '.join(toolCmd))\n with open(outDelta, 'w') as outf:\n subprocess.check_call(toolCmd, stdout=outf)\n\n def show_tiling(self, inDelta, outTiling, outFasta=None,\n circular=False, min_pct_id=None, min_contig_len=None,\n min_pct_contig_aligned=None, tab_delim=False,\n min_contig_coverage_diff=None):\n opts = []\n if circular:\n opts.append('-c')\n if tab_delim:\n opts.append('-a')\n if min_pct_id is not None:\n opts.append('-i')\n opts.append(str(100.0 * min_pct_id))\n if min_contig_len is not None:\n opts.append('-l')\n opts.append(str(min_contig_len))\n if min_pct_contig_aligned is not None:\n opts.append('-v')\n opts.append(str(100.0 * min_pct_contig_aligned))\n if min_contig_coverage_diff is not None:\n opts.append('-V')\n opts.append(str(100.0 * min_contig_coverage_diff))\n toolCmd = [os.path.join(self.install_and_get_path(), 'show-tiling')]\n if outFasta:\n toolCmd = toolCmd + ['-p', outFasta]\n toolCmd = toolCmd + opts + [inDelta]\n log.debug(' '.join(toolCmd))\n with open(outTiling, 'w') as outf:\n subprocess.check_call(toolCmd, stdout=outf)\n\n def trim_contigs(self, refFasta, contigsFasta, outFasta,\n aligner='nucmer', circular=False, extend=False, breaklen=None,\n min_pct_id=0.6, min_pct_contig_aligned=0.5, min_contig_len=200):\n ''' Align contigs with MUMmer and trim off the unused portions.\n '''\n # run MUMmer to get best alignments\n if aligner=='nucmer':\n aligner = self.nucmer\n elif aligner=='promer':\n aligner = self.promer\n else:\n raise NameError()\n delta_1 = viral_ngs.core.file.mkstempfname('.delta')\n delta_2 = viral_ngs.core.file.mkstempfname('.delta')\n tiling = viral_ngs.core.file.mkstempfname('.tiling')\n aligner(refFasta, contigsFasta, delta_1, extend=extend, breaklen=breaklen)\n self.delta_filter(delta_1, delta_2)\n self.show_tiling(delta_2, tiling, circular=circular, tab_delim=True,\n min_pct_id=min_pct_id, min_contig_len=min_contig_len,\n min_pct_contig_aligned=min_pct_contig_aligned)\n os.unlink(delta_1)\n os.unlink(delta_2)\n\n # get trim boundaries per contig\n seq_bounds = {}\n with open(tiling, 'rt') as inf:\n for line in inf:\n row = line.rstrip().split('\\t')\n seq_bounds.setdefault(row[-1], [float('inf'), 0])\n start = min(int(row[2]), int(row[3]))\n stop = max(int(row[2]), int(row[3]))\n seq_bounds[row[-1]][0] = min(seq_bounds[row[-1]][0], start)\n seq_bounds[row[-1]][1] = max(seq_bounds[row[-1]][1], stop)\n os.unlink(tiling)\n\n # trim contigs\n out = []\n with open(contigsFasta, 'rt') as inf:\n for record in Bio.SeqIO.parse(inf, 'fasta'):\n if record.id in seq_bounds:\n seq = record.seq[seq_bounds[record.id][0]-1:seq_bounds[record.id][1]]\n record.seq = seq\n out.append(record)\n with open(outFasta, 'wt') as outf:\n Bio.SeqIO.write(out, outf, 'fasta')\n\n def scaffold_contigs(self, refFasta, contigsFasta, outFasta,\n aligner='nucmer', circular=False, extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None,\n min_contig_coverage_diff=0.0,\n min_pct_id=0.6, min_pct_contig_aligned=None, min_contig_len=200):\n ''' Use MUMmer's pseudomolecule feature to scaffold contigs\n onto a reference genome.\n '''\n if aligner=='nucmer':\n aligner = self.nucmer\n elif aligner=='promer':\n aligner = self.promer\n else:\n raise NameError()\n delta_1 = viral_ngs.core.file.mkstempfname('.delta')\n delta_2 = viral_ngs.core.file.mkstempfname('.delta')\n tiling = viral_ngs.core.file.mkstempfname('.tiling')\n aligner(refFasta, contigsFasta, delta_1, extend=extend, breaklen=breaklen,\n maxgap=maxgap, minmatch=minmatch, mincluster=mincluster)\n self.delta_filter(delta_1, delta_2)\n self.show_tiling(delta_2, tiling, outFasta=outFasta, circular=circular,\n min_pct_id=min_pct_id, min_contig_len=min_contig_len,\n min_contig_coverage_diff=min_contig_coverage_diff,\n min_pct_contig_aligned=min_pct_contig_aligned)\n os.unlink(delta_1)\n os.unlink(delta_2)\n os.unlink(tiling)\n\n def scaffold_contigs_custom(self, refFasta, contigsFasta, outFasta,\n outAlternateContigs=None,\n aligner='nucmer', extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None,\n min_contig_coverage_diff=0.0,\n min_pct_id=0.6, min_pct_contig_aligned=None, min_contig_len=200,\n ambig_max_aligns=2, ambig_max_lens=1, ambig_max_frac=.01):\n ''' Re-implement a less buggy version of MUMmer's pseudomolecule\n feature to scaffold contigs onto a reference genome.\n '''\n\n # create tiling path with nucmer/promer and show-tiling\n if aligner=='nucmer':\n aligner = self.nucmer\n elif aligner=='promer':\n aligner = self.promer\n raise NotImplementedError('we have not implemented a show-aligns file reader that works for protein alignments')\n else:\n raise NameError()\n delta_1 = viral_ngs.core.file.mkstempfname('.delta')\n delta_2 = viral_ngs.core.file.mkstempfname('.delta')\n tiling = viral_ngs.core.file.mkstempfname('.tiling')\n aligner(refFasta, contigsFasta, delta_1, extend=extend, breaklen=breaklen,\n maxgap=maxgap, minmatch=minmatch, mincluster=mincluster)\n self.delta_filter(delta_1, delta_2)\n self.show_tiling(delta_2, tiling, tab_delim=True,\n min_pct_id=min_pct_id,\n min_contig_len=min_contig_len,\n min_contig_coverage_diff=min_contig_coverage_diff,\n min_pct_contig_aligned=min_pct_contig_aligned)\n os.unlink(delta_1)\n\n # load intervals into a FeatureSorter\n fs = viral_ngs.core.misc.FeatureSorter()\n with viral_ngs.core.file.open_or_gzopen(tiling, 'rU') as inf:\n for line in inf:\n row = line.rstrip('\\n\\r').split('\\t')\n c = row[11]\n start, stop = (int(row[0]), int(row[1]))\n alt_seq = (row[12], int(row[2]), int(row[3]))\n if stop1 not currently supported')\n n_tot = len(seqs[0])\n n_unambig = list(map(n_diff_vals, *seqs)).count(1)\n return float(n_unambig) / float(n_tot or 1.0)\n\n # construct scaffolded sequence for this chromosome\n seq = []\n for _, left, right, n_features, features in fs.get_intervals(c):\n # get all proposed sequences for this specific region\n alt_seqs = []\n for consider_ambig_aligns in (False, True):\n for f in features:\n alt_seqs_f = alnReaders[(c, f[-1][0])].retrieve_alts_by_ref(left, right, aln_start=f[1], aln_stop=f[2])\n if len(alt_seqs_f) == 1:\n alt_seqs.append(alt_seqs_f[0])\n elif consider_ambig_aligns:\n if len(alt_seqs_f) <= ambig_max_aligns and n_diff_lens(alt_seqs_f) <= ambig_max_lens and \\\n frac_unambig(alt_seqs_f) > (1.0 - ambig_max_frac):\n alt_seqs.append(alt_seqs_f[0])\n log.info(\"using ambiguous alignment to ref seq {} at [{},{}]\".format(c, f[1], f[2]))\n else:\n log.warning(\"dropping ambiguous alignment to ref seq {} at [{},{}]\".format(c, f[1], f[2]))\n if alt_seqs:\n # if have a non-unambiguous alignment, don't consider ambiguous ones\n break\n\n # pick the \"right\" one and glue together into a chromosome\n ranked_unique_seqs = contig_chooser(alt_seqs, right-left+1, \"%s:%d-%d\" % (c, left, right))\n seq.append(ranked_unique_seqs[0])\n # emit the \"alternates\" in a separate file\n if outAlternateContigs and len(ranked_unique_seqs) > 1:\n alternate_contigs.append((c, left, right, ranked_unique_seqs))\n\n # write this chromosome to fasta file\n for line in viral_ngs.core.file.fastaMaker([(str(c)+\"_contigs_ordered_and_oriented\", ''.join(seq))]):\n outf.write(line)\n\n # if alternate scaffolds exist, emit to output fasta file (if specified)\n if outAlternateContigs and alternate_contigs:\n log.info(\"emitting alternative scaffold sequences to {}\".format(outAlternateContigs))\n with open(outAlternateContigs, 'wt') as outf:\n for c, left, right, seqs in alternate_contigs:\n for line in viral_ngs.core.file.fastaMaker([\n (\"{}:{}-{}_option_{}\".format(c,left,right,i), s)\n for i,s in enumerate(seqs)]):\n outf.write(line)\n\n\n def align_one_to_one(self, refFasta, otherFasta, outFasta):\n ''' Take two sequences, align with nucmer, and produce\n an aligned-fasta file of the two based on show-aligns\n output.\n '''\n # grab seq_ids (very inefficient, but whatever)\n ref_id = Bio.SeqIO.read(refFasta, 'fasta').id\n query_id = Bio.SeqIO.read(otherFasta, 'fasta').id\n\n # run nucmer\n delta_1 = viral_ngs.core.file.mkstempfname('.delta')\n delta_2 = viral_ngs.core.file.mkstempfname('.delta')\n self.nucmer(refFasta, otherFasta, delta_1)\n self.delta_filter(delta_1, delta_2)\n\n # run show-aligns\n aln_file = viral_ngs.core.file.mkstempfname('.aligns')\n toolCmd = [os.path.join(self.install_and_get_path(), 'show-aligns'),\n '-r', delta_2, ref_id, query_id]\n log.debug(' '.join(toolCmd))\n with open(aln_file, 'wt') as outf:\n subprocess.check_call(toolCmd, stdout=outf)\n alns = AlignsReader(aln_file, refFasta)\n\n # write fasta\n seqs = [[alns.seq_ids[0], []], [alns.seq_ids[1], []]]\n for a in alns.get_intervals():\n seqs[0][1].append(a[6])\n seqs[1][1].append(a[7])\n seqs[0][1] = ''.join(seqs[0][1])\n seqs[1][1] = ''.join(seqs[1][1])\n viral_ngs.core.file.makeFastaFile(seqs, outFasta)\n\n # cleanup\n for fn in (delta_1, delta_2, aln_file):\n os.unlink(fn)\n\ndef contig_chooser(alt_seqs, ref_len, coords_debug=\"\"):\n ''' Our little heuristic to choose an alternative sequence from a pile\n of alignments to a reference. Takes a list of strings (one string per\n contig). This method will choose a single sequence from the input:\n 1. if there are no alt_seqs, emit a stretch of Ns, same length as ref\n 2. if there is only one alt_seq, emit that one\n 3. if there are many alt_seqs, emit the most popular (if there is one)\n 4. otherwise, if there is a most popular sequence length (including\n the ref_len as one vote), filter the alt_seqs to those of the\n most popular length and emit the most popular sequence (if there\n is one), otherwise, choose randomly amongst the remainder\n 5. otherwise, choose randomly amongst the same-as-ref length sequences\n 6. or just choose randomly if there are no same-as-ref length sequences\n The output will be a list of unique strings, where the first string\n is the \"chosen\" sequence, and the remaining strings are the alternative\n sequences (in no particular order, but guaranteed to be unique).\n '''\n if not alt_seqs:\n # no contigs align here, emit Ns of appropriate length\n new_seq = 'N' * ref_len\n other_seqs = []\n elif len(alt_seqs) == 1:\n # only one contig aligns here\n new_seq = alt_seqs[0]\n other_seqs = []\n else:\n # multiple contigs align here\n ranks = list(sorted(viral_ngs.core.misc.histogram(alt_seqs).items(),\n key=lambda x:x[1], reverse=True))\n other_seqs = list(s for s,n in ranks)\n if len(ranks)==1:\n # only one unique sequence exists\n new_seq = ranks[0][0]\n elif ranks[0][1]>ranks[1][1]:\n # clear winner: a most popular sequence exists\n new_seq = ranks[0][0]\n else:\n # multiple possible replacement sequences\n len_ranks = list(sorted(viral_ngs.core.misc.histogram(\n [len(s) for s in alt_seqs] + [ref_len] # let the reference have one vote\n ).items(), key=lambda x:x[1], reverse=True))\n if len(len_ranks)==1 or len_ranks[0][1]>len_ranks[1][1]:\n # a most popular replacement length exists\n # remove all alt_seqs that don't use that length\n alt_seqs = list(s for s in alt_seqs if len(s)==len_ranks[0][0])\n assert alt_seqs\n ranks = list(sorted(viral_ngs.core.misc.histogram(alt_seqs).items(),\n key=lambda x:x[1], reverse=True))\n if len(ranks)==1 or ranks[0][1]>ranks[1][1]:\n # clear winner amongst remaining sequences of most popular length\n new_seq = ranks[0][0]\n else:\n # more complicated scenario. choose randomly.\n # perhaps in future, vote based on aligned read count?\n if len(alt_seqs)>1:\n log.warning(\"choosing random contig from %d choices of most popular length in %s\" % (len(alt_seqs), coords_debug))\n new_seq = random.choice(alt_seqs)\n else:\n # no clear winner on replacement length\n alt_ref_len_seqs = list(s for s in alt_seqs if len(s)==ref_len)\n if alt_ref_len_seqs:\n # choose randomly among same-as-ref-length sequences\n alt_seqs = alt_ref_len_seqs\n if len(alt_seqs)>1:\n log.warning(\"choosing random contig from %d choices of reference length in %s\" % (len(alt_seqs), coords_debug))\n new_seq = random.choice(alt_seqs)\n else:\n # no clear winner and all replacement lengths are different from reference length\n # just choose randomly\n if len(alt_seqs)>1:\n log.warning(\"choosing random contig from %d choices in %s\" % (len(alt_seqs), coords_debug))\n new_seq = random.choice(alt_seqs)\n other_seqs = list(s for s in other_seqs if s!=new_seq)\n return [new_seq] + other_seqs\n\n\nclass AmbiguousAlignmentException(Exception):\n pass\n\nclass AlignsReader(object):\n ''' This class assists in the parsing and reading of show-aligns output.\n '''\n def __init__(self, aligns_file, ref_fasta=None):\n self.aligns_file = aligns_file\n self.ref_fasta = ref_fasta\n self.reference_seq = None\n self.alignments = []\n self.seq_ids = []\n self._load_align()\n self._load_fastas()\n\n def _load_align(self):\n with open(self.aligns_file, 'rt') as inf:\n # read ref_fasta, query_fasta from header\n header = inf.readline().strip().split()\n assert len(header) == 2\n if self.ref_fasta is None:\n self.ref_fasta = header[0]\n\n # iterate row by row\n mode = 'start'\n coords = None\n seqs = None\n for line in inf:\n line = line.rstrip()\n if not line:\n pass # empty lines\n elif not line.strip('='):\n pass # header and footer of file\n elif line[0] in (' ', '\\t'):\n pass # describes mismatches in alignment\n elif line.startswith('--'):\n if line.startswith('-- Alignments between '):\n assert mode == 'start'\n mode = 'between'\n self.seq_ids = line[22:].split(' and ')\n assert len(self.seq_ids) == 2\n elif line.startswith('-- BEGIN alignment [ '):\n assert mode == 'between'\n mode = 'align'\n coords = list(x.split() for x in line[21:-2].split(' | '))\n assert len(coords) == 2 and coords[0][2] == coords[1][2] == '-'\n assert coords[0][0] == '+1', \"error with line: %s\" % line\n seqs = [[], []]\n align_lines = 0\n elif line.startswith('-- END alignment [ '):\n assert mode == 'align'\n mode = 'between'\n new_coords = list(x.split() for x in line[21:-2].split(' | '))\n assert coords == new_coords, \"error: %s != %s\" % (new_coords, coords)\n assert len(seqs[0]) == len(seqs[1])\n seqs = list(''.join(x) for x in seqs)\n assert len(seqs[0]) == len(seqs[1])\n self.alignments.append([coords[0][0], int(coords[0][1]), int(coords[0][3]),\n coords[1][0], int(coords[1][1]), int(coords[1][3]),\n seqs[0], seqs[1]])\n coords = None\n seqs = None\n else:\n raise AssertionError(\"file format: line '%s'\" % line)\n else:\n # read in one line of an alignment\n assert mode == 'align', \"file format: line '%s' before alignment begins\" % line\n seq_str = line.split()[1].upper().replace('.','-')\n seqs[align_lines % 2].append(seq_str)\n align_lines += 1\n\n def _load_fastas(self):\n assert self.ref_fasta and self.seq_ids\n self.reference_seq = Bio.SeqIO.index(self.ref_fasta, 'fasta')[self.seq_ids[0]]\n\n def get_alignments(self):\n for a in self.alignments:\n yield a\n\n def get_intervals(self):\n prev = None\n for a in self.alignments:\n cur = a[1:3]\n assert cur[1] >= cur[0]\n if prev is None:\n if cur[0] > 1:\n # emit leading reference sequence before first alignment\n yield self._dummy_row(1, cur[0]-1, '-')\n else:\n assert cur[0] > prev[1], \"overlaps not allowed\"\n if cur[0] > prev[1] + 1:\n # emit gap between alignments\n yield self._dummy_row(prev[1]+1, cur[0]-1, 'N')\n # emit actual alignment\n yield a\n prev = cur\n if prev and prev[1] < len(self.reference_seq):\n # emit trailing reference sequence after last alignment\n yield self._dummy_row(prev[1]+1, len(self.reference_seq), '-')\n\n def _dummy_row(self, start, stop, filler='N'):\n return ['+1', start, stop, '+1', start, stop,\n self.get_ref_seq(start, stop),\n filler * (stop-start+1)]\n\n def get_ref_seq(self, start, stop):\n ''' Retrieve a sub-sequence from the reference (1st) sequence in the\n alignment using coordinates relative to the reference sequence.\n No gaps will be emitted.\n '''\n return str(self.reference_seq.seq[start-1:stop])\n\n def retrieve_alts_by_ref(self, start, stop, aln_start=None, aln_stop=None):\n ''' Retrieve sub-sequence(s) from the alternate (2nd) sequence in the\n alignment using coordinates relative to the reference sequence.\n No gaps will be emitted.\n Required: start-stop interval must be wholly contained within\n an alignment.\n '''\n\n # grab the one alignment that contains this window\n alns = list(a for a in self.alignments if a[1]<=start and a[2]>=stop)\n if aln_start is not None and aln_stop is not None:\n # if specified, restrict to a specific alignment that comes from show-tiling\n # (sometimes show-aligns is more promiscuous than show-tiling)\n new_alns = []\n for a in alns:\n if a[1] > aln_start or a[2] < aln_stop:\n log.debug(\"dropping undesired alignment: %s(%s):%s-%s to %s(%s):%s-%s (%s:%s-%s requested)\",\n self.seq_ids[0], a[0], a[1], a[2],\n self.seq_ids[1], a[3], a[4], a[5],\n self.seq_ids[0], aln_start, aln_stop)\n else:\n new_alns.append(a)\n alns = new_alns\n if len(alns) != 1:\n log.warning(\"invalid %s:%d-%d -> %s specified, %d alignments found that contain it\",\n self.seq_ids[0], start, stop, self.seq_ids[1], len(alns))\n for aln in alns:\n log.debug(\"alignment: %s\", str(aln[:6]))\n\n return [self._aln_to_alt_seq(aln, start, stop) for aln in alns]\n\n def _aln_to_alt_seq(self, aln, start, stop):\n \"\"\"Given an alignment of a contig to ref, return the contig sequence aligned to a given stretch of ref\"\"\"\n ref_l, ref_r, ref_seq, alt_seq = (aln[1], aln[2], aln[-2], aln[-1])\n\n # convert desired start/stop relative to this reference window\n # such that 0 <= start <= stop <= ref_r-ref_l+1\n aln_start = start - ref_l\n aln_stop = stop - ref_l\n\n # travel down alignment until we've reached the left edge\n # (because of gaps, you must check each position one by one)\n # end loop when ref_seq[:i_left] contains {aln_start} bases\n n_ref_bases = 0\n i_left = 0\n while n_ref_bases < aln_start:\n if ref_seq[i_left] != '-':\n n_ref_bases += 1\n i_left += 1\n\n # travel down alignment until we've reached the right edge\n # (because of gaps, you must check each position one by one)\n # end loop when ref_seq[:i_right] contains {aln_stop} bases\n i_right = i_left\n while n_ref_bases < aln_stop:\n if ref_seq[i_right] != '-':\n n_ref_bases += 1\n i_right += 1\n # consume and include any trailing gaps\n while i_right < len(ref_seq) and ref_seq[i_right] == '-':\n i_right += 1\n\n # grab the alternate sequence and strip gaps\n return alt_seq[i_left:i_right+1].replace('-','')\n" }, { "path": "src/viral_ngs/assemble/muscle.py", "content": "'''\n The MUSCLE aligner\n http://www.drive5.com/muscle\n'''\n\n\nimport viral_ngs.core\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\n\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport logging\n\nTOOL_NAME = \"muscle\"\n\n_log = logging.getLogger(__name__)\n\n\nclass MuscleTool(viral_ngs.core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [viral_ngs.core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(MuscleTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip().split()[1]\n\n # pylint: disable=W0221\n def execute(\n self,\n inFasta,\n outFasta,\n maxiters=None,\n maxhours=None,\n fmt='fasta',\n diags=None,\n quiet=True,\n logFile=None\n ):\n tool_cmd = [self.install_and_get_path(), '-in', inFasta, '-out', outFasta]\n\n if fmt in ('html', 'msf', 'clw', 'clwstrict'):\n tool_cmd.append('-' + fmt)\n else:\n if fmt != 'fasta':\n raise Exception()\n if quiet:\n tool_cmd.append('-quiet')\n if diags:\n tool_cmd.append('-diags')\n if maxiters:\n tool_cmd.extend(('-maxiters', str(maxiters)))\n if maxhours:\n tool_cmd.extend(('-maxhours', str(maxhours)))\n if logFile:\n tool_cmd.extend(('-log', logFile))\n\n _log.debug(' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n # pylint: enable=W0221\n\n" }, { "path": "src/viral_ngs/assemble/rasusa.py", "content": "'''\n Rasusa — randomly subsample sequencing reads or alignments to a\n specified coverage depth.\n\n https://github.com/mbhall88/rasusa\n'''\n\nimport logging\nimport shutil\nimport subprocess\n\nfrom ..core import Tool, PrexistingUnixCommand\n\n_log = logging.getLogger(__name__)\n\nTOOL_NAME = 'rasusa'\n\n\nclass RasusaTool(Tool):\n\n def __init__(self):\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n Tool.__init__(self, install_methods=install_methods)\n\n def downsample_bam(self, inBam, outBam, coverage, seed=None):\n \"\"\"Downsample aligned reads in a BAM to a target coverage depth\n using ``rasusa aln``.\n\n The input BAM must be coordinate-sorted. The output BAM is\n **not** guaranteed to be sorted — the caller is responsible for\n sorting and indexing if downstream tools require it.\n\n Args:\n inBam: Input BAM file (coordinate-sorted).\n outBam: Output BAM file path.\n coverage: Target coverage depth (integer).\n seed: Random seed for reproducibility (optional).\n \"\"\"\n tool_cmd = [\n self.install_and_get_path(), 'aln',\n '--coverage', str(coverage),\n '-o', outBam,\n inBam,\n ]\n if seed is not None:\n tool_cmd.extend(['--seed', str(seed)])\n _log.debug(' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n" }, { "path": "src/viral_ngs/assemble/skani.py", "content": "'''\n SKANI - accurate, fast nucleotide identity calculation for MAGs and databases\n https://github.com/bluenote-1577/skani\n'''\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport logging\nimport viral_ngs.core\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\nimport csv\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport Bio.SeqIO\n\nTOOL_NAME = \"skani\"\n\n_log = logging.getLogger(__name__)\n\n# Standard output header for skani dist command\nSKANI_DIST_HEADER = ['Ref_file','Query_file','ANI','Align_fraction_ref','Align_fraction_query',\n 'Ref_name','Query_name','Num_ref_contigs','Num_query_contigs',\n 'ANI_5_percentile','ANI_95_percentile','Standard_deviation',\n 'Ref_90_ctg_len','Ref_50_ctg_len','Ref_10_ctg_len',\n 'Query_90_ctg_len','Query_50_ctg_len','Query_10_ctg_len',\n 'Avg_chain_len','Total_bases_covered']\n\nclass UndirectedGraph:\n ''' Simple utility class for finding clusters from pairwise relationships\n '''\n def __init__(self):\n self.edges = {}\n\n def add_node(self, node):\n self.edges.setdefault(node, set())\n\n def add_edge(self, node1, node2):\n self.edges.setdefault(node1, set()).add(node2)\n self.edges.setdefault(node2, set()).add(node1)\n\n def _dfs(self, node, visited):\n visited.add(node)\n cluster = set()\n cluster.add(node)\n for neighbor in self.edges[node]:\n if neighbor not in visited:\n cluster.update(self._dfs(neighbor, visited))\n return cluster\n\n def get_clusters(self):\n visited = set()\n clusters = []\n for node in self.edges.keys():\n if node not in visited:\n clusters.append(self._dfs(node, visited))\n return clusters\n\n\nclass SkaniTool(viral_ngs.core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [viral_ngs.core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(SkaniTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').strip().split()[1]\n\n def _is_fasta_basically_empty(self, inFasta, min_length=500):\n ''' Check if a fasta file contains no sequences longer than min_length.\n If the fasta contains only sequences < min_length, return True\n '''\n with open(inFasta, 'r') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n if len(seq.seq.replace(\"-\",\"\").replace(\"N\",\"\")) >= min_length:\n return False\n return True\n\n def _sort_skani_table_by_product(self, in_tsv, out_tsv):\n ''' Sort the skani output tsv by the product of ANI and Total_bases_covered\n '''\n with open(in_tsv, 'r') as inf:\n reader = csv.DictReader(inf, delimiter='\\t')\n sorted_rows = sorted(reader, key=lambda row: float(row['ANI']) * float(row['Total_bases_covered']), reverse=True)\n fieldnames = reader.fieldnames # Capture while file is still open\n\n # Handle empty file case (no header, no data) - write header-only output\n if fieldnames is None:\n with open(out_tsv, 'w') as outf:\n outf.write('\\t'.join(SKANI_DIST_HEADER) + '\\n')\n return\n\n with open(out_tsv, 'w') as outf:\n writer = csv.DictWriter(outf, fieldnames=fieldnames, delimiter='\\t', dialect=csv.unix_dialect, quoting=csv.QUOTE_MINIMAL)\n writer.writeheader()\n writer.writerows(sorted_rows)\n\n def execute(self, subcommand, args, outfile, threads=None):\n ''' generic execution of skani\n '''\n\n # build the skani command\n tool_cmd = [self.install_and_get_path(), subcommand]\n tool_cmd.extend(map(str, args))\n tool_cmd.extend([\"-t\", \"{}\".format(viral_ngs.core.misc.sanitize_thread_count(threads))])\n\n # run the command\n _log.debug(' '.join(tool_cmd) + ' > ' + outfile)\n with open(outfile, 'w') as outf:\n viral_ngs.core.misc.run_and_save(tool_cmd, outf=outf)\n\n def triangle(self, ref_fastas, outfile_ani, other_args = (), threads=None):\n ''' skani triangle computes an all-to-all ANI distance matrix for a set of sequences\n '''\n self.execute('triangle', list(ref_fastas) + list(other_args), outfile_ani, threads=threads)\n\n def dist(self, query_fasta, ref_fastas, outfile, other_args = (), threads=None):\n ''' skani dist computes ANI distance between a specified query set of\n sequences (MAGs) and reference genomes (database)\n '''\n if self._is_fasta_basically_empty(query_fasta):\n _log.warning(\"Query fasta file is empty or contains only very short sequences. Skipping skani dist (which will fail in this scenario).\")\n with open(outfile, 'w') as outf:\n outf.write('\\t'.join(SKANI_DIST_HEADER) + '\\n')\n else:\n self.execute('dist', ['-q', query_fasta, '-r'] + list(ref_fastas) + list(other_args), outfile, threads=threads)\n\n def find_reference_clusters(self, ref_fastas,\n m=15, s=50, c=10, min_af=15,\n other_args = ('--no-learned-ani', '--robust', '--detailed', '--ci', '--sparse'),\n threads=None):\n ''' use skani triangle to define clusters of highly-related genomes\n (default settings here are for viral genomes)\n '''\n g = UndirectedGraph()\n for ref_fasta in ref_fastas:\n g.add_node(ref_fasta)\n\n with viral_ngs.core.file.tempfname('.skani_matrix.ani') as tmp_matrix_ani:\n # run skani triangle\n self.triangle(ref_fastas, tmp_matrix_ani,\n ['-m', m, '-c', c, '-s', s, '--min-af', min_af] + list(other_args), threads=threads)\n\n # parse the skani triangle results and define clusters\n with open(tmp_matrix_ani, 'r') as inf:\n for row in csv.DictReader(inf, delimiter='\\t'):\n g.add_edge(row['Ref_file'], row['Query_file'])\n\n return g.get_clusters()\n\n def find_closest_reference(self, contigs_fasta, ref_fastas, out_file,\n m=50, s=50, c=20, min_af=15, n=None,\n other_args = ('--no-learned-ani', '--robust', '--detailed', '--ci', '--no-marker-index'),\n threads=None):\n ''' use skani dist to find the closest reference genome for each contig\n (default settings here are for viral genomes)\n '''\n\n max_hits_args = [] if n is None else ['-n', n]\n with viral_ngs.core.file.tempfname('.skani_dist.tsv') as tmp_tsv:\n self.dist(contigs_fasta, ref_fastas, tmp_tsv,\n ['-m', m, '-c', c, '-s', s, '--min-af', min_af] + max_hits_args + list(other_args), threads=threads)\n self._sort_skani_table_by_product(tmp_tsv, out_file)\n\n with open(out_file, 'r') as inf:\n top_row = None\n for row in csv.DictReader(inf, delimiter='\\t'):\n top_row = row\n break\n return (top_row['Ref_file'], top_row['ANI'], top_row['Align_fraction_ref'], top_row['Total_bases_covered']) if top_row is not None else None\n" }, { "path": "src/viral_ngs/assemble/spades.py", "content": "'''\n Tool wrapper for SPAdes, St. Petersburg Assembler ( http://cab.spbu.ru/software/spades/ )\n'''\n\nimport logging\nimport os\nimport os.path\nimport subprocess\nimport shutil\nimport random\nimport shlex\nimport tempfile\n\nimport Bio.SeqIO\n\nimport viral_ngs.core\nimport viral_ngs.core.samtools\nimport viral_ngs.core.picard\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\n\nTOOL_NAME = 'spades.py'\n\nlog = logging.getLogger(__name__)\n\nclass SpadesTool(viral_ngs.core.Tool):\n '''Tool wrapper for SPAdes tool (St. Petersburg Assembler)'''\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [viral_ngs.core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(SpadesTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').strip().split()[1]\n\n def execute(self, args): # pylint: disable=W0221\n tool_cmd = [self.install_and_get_path()] + list(map(str, args))\n log.debug(' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n\n def assemble(self, reads_fwd, reads_bwd, contigs_out, reads_unpaired=None, contigs_trusted=None,\n contigs_untrusted=None, kmer_sizes=None, always_succeed=True,\n filter_contigs=False, min_contig_len=0, mem_limit_gb=8, threads=None, spades_opts=''):\n '''Assemble contigs from RNA-seq reads and (optionally) pre-existing contigs.\n\n Inputs:\n Required:\n reads_fwd, reads_bwd (fasta/q): paired reads\n Optional:\n reads_unpaired (fasta/q): optionally, additional unpaired reads\n contigs_trusted (fasta/q): optionally, already-assembled contigs of high quality\n contigs_untrusted (fasta/q): optionally, already-assembled contigs of average quality\n Params:\n kmer_sizes: if given, use these comma-separated ascending kmer sizes--all values must be odd and < 127. kmer size of 0 or None means use size auto-selected\n by SPAdes based on read length.\n always_succeed: if True, if spades fails with an error, pretend it just produced no contigs\n filter_contigs: if True, outputs only \"long and reliable transcripts with rather high expression\" (per SPAdes docs)\n min_contig_len: drop contigs shorter than this many bp\n mem_limit_gb: max memory to use, in gigabytes\n threads: number of threads to use\n spades_opts: additional options to pass to spades\n Outputs:\n contigs_out: assembled contigs in fasta format. Note that, since we use the\n RNA-seq assembly mode, for some genome regions we may get several contigs\n representing alternative transcripts. Fasta record name of each contig indicates\n its length, coverage, and the group of alternative transcripts to which it belongs.\n See details at \n http://cab.spbu.ru/files/release3.11.1/rnaspades_manual.html#sec2.4 .\n '''\n\n threads = viral_ngs.core.misc.sanitize_thread_count(threads)\n\n viral_ngs.core.file.make_empty(contigs_out)\n contigs_cumul_count = 0\n\n if ((reads_fwd and reads_bwd and os.path.getsize(reads_fwd) > 0 and os.path.getsize(reads_bwd) > 0) or\n (reads_unpaired and os.path.getsize(reads_unpaired) > 0)):\n\n with viral_ngs.core.file.tmp_dir('_spades') as spades_dir:\n log.debug('spades_dir=' + spades_dir)\n args = []\n if reads_fwd and reads_bwd and os.path.getsize(reads_fwd) > 0 and os.path.getsize(reads_bwd) > 0:\n args += ['-1', reads_fwd, '-2', reads_bwd ]\n if reads_unpaired and os.path.getsize(reads_unpaired) > 0:\n args += [ '--s1', reads_unpaired ]\n if contigs_trusted: args += [ '--trusted-contigs', contigs_trusted ]\n if contigs_untrusted: args += [ '--untrusted-contigs', contigs_untrusted ]\n if kmer_sizes: args += [ '-k', kmer_sizes ]\n if spades_opts: args += shlex.split(spades_opts)\n args += [ '-m' + str(mem_limit_gb), '-t', str(threads), '-o', spades_dir ]\n\n transcripts_fname = os.path.join(spades_dir, ('hard_filtered_' if filter_contigs else '') + 'contigs.fasta')\n\n try:\n self.execute(args=args)\n except Exception as e:\n if always_succeed:\n log.warning('SPAdes failed: {}'.format(e))\n viral_ngs.core.file.make_empty(transcripts_fname)\n else:\n raise\n\n # work around the bug that spades may succeed yet not create the contigs.fasta file\n if not os.path.isfile(transcripts_fname):\n msg = 'SPAdes failed to make contigs.fasta'\n if always_succeed:\n log.warning(msg)\n viral_ngs.core.file.make_empty(transcripts_fname)\n else:\n raise RuntimeError(msg)\n\n if min_contig_len:\n transcripts = Bio.SeqIO.parse(transcripts_fname, 'fasta')\n transcripts_sans_short = [r for r in transcripts if len(r.seq) >= min_contig_len]\n transcripts_fname = os.path.join(spades_dir, 'contigs_over_{}bp.fasta'.format(min_contig_len))\n Bio.SeqIO.write(transcripts_sans_short, transcripts_fname, 'fasta')\n\n contigs_cumul = os.path.join(spades_dir, 'contigs_cumul.{}.fasta'.format(contigs_cumul_count))\n contigs_cumul_count += 1\n\n viral_ngs.core.file.concat(inputFilePaths=(contigs_out, transcripts_fname), outputFilePath=contigs_cumul, append=True)\n shutil.copyfile(contigs_cumul, contigs_out)\n\n # end: with viral_ngs.core.file.tmp_dir('_spades') as spades_dir\n # if input non-empty\n # end: def assemble(self, reads_fwd, reads_bwd, contigs_out, reads_unpaired=None, contigs_trusted=None, ...)\n# end: class SpadesTool(viral_ngs.core.Tool)\n\n\n" }, { "path": "src/viral_ngs/assemble/vcf.py", "content": "'''This gives a number of useful quick methods for dealing with VCF files.\n'''\n\n__author__ = \"dpark@broadinstitute.org\"\n__version__ = \"PLACEHOLDER\"\n__date__ = \"PLACEHOLDER\"\n\nimport logging\nimport re\nimport pysam\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\n\nlog = logging.getLogger(__name__)\n\n\ndef make_intervals(i, n, fasta, chr_prefix='', verbose=False):\n ''' Divide a sorted genome into n equally sized parts and return the i'th\n part. We will return a list of intervals: chr, start, stop. It may\n contain multiple chromosomes in order to fill out a total length equal\n to the other parts. Each part will be adjacent and non-overlapping with\n the next part. i must be a number from 1 to n.\n '''\n assert 1 <= i <= n\n\n # read genome dict file\n tot = 0\n chrlens = []\n for c, c_len in get_chrlens(fasta):\n if c.startswith(chr_prefix):\n chrlens.append((c, c_len, tot))\n tot += c_len\n\n # define our chunk by gpos:\n part_size = tot // n\n g_start = 1 + part_size * (i - 1)\n g_stop = part_size * i\n if i == n:\n g_stop = tot\n\n # find the genomic intervals that correspond to our gpos window\n out = []\n for c, c_len, c_g_start in chrlens:\n c_g_stop = c_g_start + c_len\n c_g_start += 1\n if c_g_stop >= g_start and c_g_start <= g_stop:\n start = max(g_start, c_g_start) - c_g_start + 1\n stop = min(g_stop, c_g_stop) - c_g_start + 1\n out.append((c, start, stop))\n\n if verbose:\n log.info(\n \"Dividing the %d bp genome into %d chunks of %d bp each. The %dth chunk contains the following %d intervals: %s\",\n tot, n, part_size, i, len(out), ', '.join([\"%s:%d-%d\" % x for x in out]))\n return out\n\n\ndef sliding_windows(fasta, width, offset, chr_prefix=''):\n ''' Divide a genome into sliding windows and return as an iterator of\n intervals (chr, start, stop). The windows are of fixed width\n (except maybe the last window on each chromosome) and may overlap\n (offsetwidth).\n '''\n assert width > 0 and offset > 0\n for c, c_len in get_chrlens(fasta):\n if c.startswith(chr_prefix):\n start = 1\n while start <= c_len:\n stop = min(c_len, start + width - 1)\n yield (c, start, stop)\n start += offset\n\n\nclass GenomePosition(object):\n ''' Provide a mapping from chr:pos to genomic position.\n Read chromosome lengths and order from either a Picard/GATK-index for\n a FASTA file (a .dict file) or from a VCF header.\n '''\n\n def __init__(self, seqDb):\n self.gpos_map = {}\n self.clen_map = {}\n self.chrs = []\n totlen = 0\n for c, clen in get_chrlens(seqDb):\n self.chrs.append((c, clen))\n self.gpos_map[c] = totlen\n self.clen_map[c] = clen\n totlen += clen\n self.total = totlen\n\n def get_gpos(self, c, p):\n assert isinstance(p, int)\n assert c in self.gpos_map\n assert 1 <= p <= self.clen_map[c]\n return p + self.gpos_map[c]\n\n def get_chr_pos(self, gpos):\n assert isinstance(gpos, int)\n assert 1 <= gpos <= self.total\n totlen = 0\n for c, clen in self.chrs:\n if gpos <= totlen + clen:\n break\n totlen += clen\n return (c, gpos - totlen)\n\n\ndef parse_contig_header(line):\n '''Parse a VCF ##contig header line and return (contig_id, length).\n\n Handles headers with multiple attributes like:\n ##contig=\n\n Raises ValueError if the line has no length= attribute.\n '''\n if not (line.startswith('##contig=')):\n raise ValueError(\"not a valid ##contig header: %s\" % line)\n inner = line[13:-1]\n contig_id = inner.split(',')[0]\n m = re.search(r'length=(\\d+)', inner)\n if not m:\n raise ValueError(\"##contig header missing length= attribute: %s\" % line)\n return (contig_id, int(m.group(1)))\n\n\ndef get_chrlens(inFile):\n ''' Read chromosome lengths and order from either a Picard/GATK-index for\n a FASTA file (a .dict file) or from \"contig\" rows in the VCF header.\n '''\n chrlens = []\n if hasattr(inFile, 'chrlens'):\n chrlens = inFile.chrlens()\n else:\n if inFile.endswith('.fasta'):\n inFile = inFile[:-len('.fasta')] + '.dict'\n elif inFile.endswith('.fa'):\n inFile = inFile[:-len('.fa')] + '.dict'\n if inFile.endswith('.dict'):\n with open(inFile, 'rt') as inf:\n for line in inf:\n row = line.rstrip('\\n').split('\\t')\n if row[0] == '@SQ':\n assert row[1].startswith('SN:') and row[2].startswith('LN:')\n c = row[1][3:]\n c_len = int(row[2][3:])\n chrlens.append((c, c_len))\n elif inFile.endswith('.vcf') or inFile.endswith('.vcf.gz'):\n with viral_ngs.core.file.open_or_gzopen(inFile, 'rt') as inf:\n for line in inf:\n line = line.rstrip('\\n')\n if line.startswith('##contig='):\n chrlens.append(parse_contig_header(line))\n elif line.startswith('#CHROM'):\n break\n else:\n raise AssertionError(\"unrecognized file type %s\" % inFile)\n assert chrlens, \"no sequence data found in %s % inFile\"\n return chrlens\n\n\ndef calc_maf(genos, ancestral=None, ploidy=1):\n # get list of alleles\n if ploidy == 1:\n alleles = genos\n else:\n alleles = []\n for g in genos:\n g = g.split('/')\n assert len(g) == ploidy\n alleles += g\n\n # count up\n out = {'n_tot': len(alleles)}\n acounts = viral_ngs.core.misc.histogram(alleles)\n alist = sorted([(n, a) for a, n in acounts.items()])\n\n # daf\n if ancestral is not None:\n out['a_ancestral'] = ancestral\n derived = list(sorted([a for a in acounts.keys() if a != ancestral]))\n out['a_derived'] = ','.join(derived)\n out['dac'] = sum(acounts[a] for a in derived)\n out['daf'] = out['n_tot'] and float(out['dac']) / out['n_tot'] or None\n\n # maf\n if out['n_tot']:\n out['a_major'] = alist[-1][1]\n out['a_minor'] = ','.join([a for n, a in alist[:-1]])\n out['mac'] = out['n_tot'] - alist[-1][0]\n out['maf'] = float(out['mac']) / out['n_tot']\n else:\n out['a_major'] = None\n out['a_minor'] = None\n out['mac'] = None\n out['maf'] = None\n\n return out\n\nclass TabixReader(pysam.TabixFile):\n ''' A wrapper around pysam.TabixFile that provides a context and\n allows us to query using 1-based coordinates.\n\n We should request upstream to the Pysam people to implement\n methods __reversed__() and __len__() in pysam.TabixIterator.\n __getitem__ could be a bonus, but prob unnecessary.\n '''\n\n def __init__(self, inFile, parser=pysam.asTuple()):\n # inFile is passed in but is never used, and yet the TabixReader works. How?!\n # This inFile magic is because Tabixfile is a Cython object that uses def __cinit__ \n # rather than def __init__; the former is called automatically exactly once for the \n # base class prior to any use of __init__. Use of subsequent __init__ should obey \n # normal inheritance rules (assuming inheritance from object and it's not an old-style class). \n # So __cinit__ sets the input file, and then our __init__ (which doesn't override a base method) \n # is called and sets the parser. \n # This could all break in the future if pysam moves away from __cinit__, but doing so would\n # reduce performance and so it seems unlikely.\n # See:\n # https://github.com/cython/cython/blob/master/docs/src/userguide/special_methods.rst#id19\n # https://github.com/pysam-developers/pysam/blob/master/pysam/libctabix.pyx#L331\n #super(TabixReader, self).__init__(inFile, parser=parser)\n self.parser = parser\n\n def __enter__(self):\n return self\n\n def __exit__(self, exc_type, exc_val, exc_tb):\n self.close() # pylint: disable=E1101\n return 0\n\n # close() is being inherited from pysam.Tabixfile, why call it ourselves?\n # def close(self):\n # super(TabixReader, self).close()\n\n def chroms(self):\n return self.contigs # pylint: disable=E1101\n\n def get(self, chrom=None, start=None, stop=None, region=None):\n if start is not None:\n start -= 1\n return self.fetch(reference=chrom, start=start, end=stop, region=region, parser=self.parser) # pylint: disable=E1101\n\n\ndef get_pos_from_vcf_record(vcfrec):\n # new versions of pysam return a zero-based position here\n return vcfrec.pos + 1\n\n\ndef bytes_to_string(o):\n if isinstance(o, bytes):\n o = o.decode('utf-8')\n return o\n\n\nclass VcfReader(TabixReader):\n ''' Same as TabixReader with a few more perks for VCF files:\n - emit results parsed as pysam VCF rows\n - provide self.chrlens(), a dict mapping chrom name to chrom length\n - provide self.samples(), a list of sample names in order of appearance\n - provide get_range(c,start,stop) and get_snp_genos(c,pos)\n '''\n\n def __init__(self, inFile, ploidy=1, parser=pysam.asVCF()):\n # using old-style class superclass calling here\n # since TabixReader is derived from pysam.TabixFile\n # which is itself an old-style class (due to Cython version?)\n TabixReader.__init__(self, inFile, parser=parser)\n # when pysam uses new-style classes, we can replace with:\n #super(VcfReader, self).__init__(inFile, parser=parser)\n assert ploidy in (1, 2)\n self.ploidy = ploidy\n self.clens = []\n self.sample_names = None\n for line in self.header: # pylint: disable=E1101\n line = bytes_to_string(line)\n if line.startswith('##contig='):\n self.clens.append(parse_contig_header(line))\n elif line.startswith('#CHROM'):\n row = line.split('\\t')\n self.sample_names = row[9:]\n self.clens = dict(self.clens)\n assert self.sample_names\n\n def samples(self):\n return self.sample_names\n\n def chrlens(self):\n return self.clens\n\n def get_positions(self, c=None, start=None, stop=None, region=None):\n for snp in self.get(c, start, stop, region):\n yield (bytes_to_string(snp.contig), get_pos_from_vcf_record(snp),\n get_pos_from_vcf_record(snp) + len(snp.ref) - 1)\n\n def get_range(self, c=None, start=None, stop=None, region=None, as_strings=True, more=False):\n ''' Read a VCF file (optionally just a piece of it) and return contents\n as an iterator with parsed contents. Each row is returned as\n a 4-tuple:\n 1: chr\n 2: pos (int)\n 3: list of allele strings (in order)\n 4: list of genotypes as 2-tuples:\n haploid: (sample, allele)\n diploid: (sample, [allele, allele])\n If as_strings, the alleles will be actual alleles. Otherwise,\n alleles will be integers.\n If more is true, a fifth column will be emitted with the pysam VCF object.\n '''\n for snp in self.get(c, start, stop, region):\n alleles = [bytes_to_string(snp.ref)] + bytes_to_string(snp.alt).split(',')\n alleles = [a for a in alleles if a != '.']\n if self.ploidy == 1:\n genos = [(self.sample_names[i], int(bytes_to_string(snp[i])[0])) for i in range(len(self.sample_names))\n if bytes_to_string(snp[i])[0] != '.']\n if as_strings:\n genos = [(s, alleles[a]) for s, a in genos]\n else:\n genos = [(self.sample_names[i], [int(bytes_to_string(snp[i])[j * 2]) for j in range(self.ploidy)])\n for i in range(len(self.sample_names)) if bytes_to_string(snp[i])[0] != '.']\n if as_strings:\n genos = [(s, [alleles[a] for a in g]) for s, g in genos]\n if more:\n yield (bytes_to_string(snp.contig), get_pos_from_vcf_record(snp), alleles, genos, snp)\n else:\n yield (bytes_to_string(snp.contig), get_pos_from_vcf_record(snp), alleles, genos)\n\n def get_snp_genos(self, c, p, as_strings=True):\n ''' Read a single position from a VCF file and return the genotypes\n as a sample -> allele map. If there is not exactly one matching\n row in the VCF file at this position (if there are none or multiple)\n then we return an empty map: {}.\n '''\n snps = [x for x in self.get_range(c, p, p, as_strings=as_strings)]\n return len(snps) == 1 and dict(snps[0][3]) or {}\n\n def getFullSequences(self, c, start, stop, samples,\n na='-', refSeq=None, refInvariantsOnly=False, ignoreIndels=False):\n ''' chr - chromosome name\n start - start position\n stop - default = start\n samples is a list of samples. None can be used for the ref sample.\n if refSeq is a string with length = stop-start+1, then use this as the\n base sequence for missing data, otherwise, use the na string.\n if refInvariantsOnly is True, refSeq is only used for invariant\n sites or sites with no entries for any samples. if False, refSeq\n is used for all missing data.\n '''\n assert 1 <= start <= stop\n assert len(na) == 1\n\n # get all the VCF records\n vcf_records = [(p - start, alleles, dict(genos))\n for _, p, alleles, genos in self.get_range(c,\n start,\n stop,\n as_strings=True)\n if not ignoreIndels or set(map(len, alleles)) == set([1])]\n\n # Construct a list called \"seq\" into which we will replace alleles as\n # we discover them. This is a list, not a string, because each position\n # might be replaced with an arbitrary length string (deletions will be\n # empty strings, insertions will be strings > length 1). This all gets\n # converted to a string at the end.\n if refSeq:\n # assume refSeq alleles as a baseline for missing data\n assert len(refSeq) == (stop - start + 1)\n seq = list(refSeq)\n if refInvariantsOnly:\n # but don't assume refSeq alleles for any known variant sites\n for i, alleles, genos in vcf_records:\n if len(set(genos[s] for s in samples if s in genos)) > 1:\n for j in range(len(alleles[0])):\n if i + j < len(seq):\n seq[i + j] = na\n else:\n # assume nothing when data is missing\n seq = list(na * (stop - start + 1))\n\n for sample in samples:\n assert sample is None or sample in self.samples()\n\n # Make copy of reference sequence\n newseq = [s for s in seq]\n\n # Replace alleles, one site at a time.\n replaceAlleles(sample, newseq, vcf_records)\n\n # Convert list back to string. This string may or may not be the same\n # length as the original (if ignoreIndels is True, it must be the same\n # length as the original).\n newseq = ''.join(newseq)\n assert len(newseq) == (stop - start + 1) or not ignoreIndels\n yield (sample, newseq)\n\n\ndef replaceAlleles(sample, seq, vcf_records):\n ''' Replace alleles, one site at a time. '''\n for i, alleles, genos in vcf_records:\n\n # set allele to the DNA sequence we will replace at positions i through i+len(refallele)-1\n if sample is None:\n # caller is asking for the reference sample's sequence\n allele = alleles[0]\n alleles = [allele]\n else:\n # caller is asking for a normal sample\n samp_geno = genos.get(sample)\n if not samp_geno:\n continue\n if isinstance(samp_geno, list):\n log.warning(\n \"TO DO: add code to turn hets into IUPAC ambiguity codes (%s %s = %s).\",\n i, sample, '/'.join(samp_geno))\n continue\n allele = samp_geno\n\n # replace portion of sequence with allele\n # NEED BUGFIXES HERE for overlapping VCF records\n if allele is None:\n # nothing here ... is this even possible anymore?\n pass\n elif len(alleles[0]) == 1:\n # the most common cases: SNP, novar, or indel replacing one ref base (with zero or more bases)\n seq[i] = allele\n else:\n # most complicated case: something replacing multiple ref bases\n # TODO: beware--this is all untested!\n for j in range(max(len(alleles[0]), len(allele))):\n if i + j < len(seq):\n if j < len(allele):\n if j == len(alleles[0]) - 1:\n # new allele is >= ref length, fill out the rest of the bases\n seq[i + j] = allele[j:]\n else:\n seq[i + j] = allele[j]\n else:\n # new allele is shorter than ref, so delete extra bases\n seq[i + j] = ''\n return seq\n" }, { "path": "src/viral_ngs/assemble/wgsim.py", "content": "'''\n WGSIM - read simulator for next-generation sequencing\n https://github.com/lh3/wgsim\n'''\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport logging\nimport math\nimport viral_ngs.core\nimport viral_ngs.core.picard\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport Bio.SeqIO\nimport Bio.Seq\n\nTOOL_NAME = \"wgsim\"\n\n_log = logging.getLogger(__name__)\n\nclass WgsimTool(viral_ngs.core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [viral_ngs.core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(WgsimTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n # wgsim doesn't have a clean version flag, parse from help output\n try:\n output = subprocess.check_output([self.install_and_get_path()], stderr=subprocess.STDOUT).decode('UTF-8')\n # Look for \"Version:\" in output\n for line in output.split('\\n'):\n if 'Version:' in line:\n self.tool_version = line.split('Version:')[1].strip()\n return\n self.tool_version = 'unknown'\n except subprocess.CalledProcessError as e:\n # wgsim returns non-zero when called with no args, but outputs help\n output = e.output.decode('UTF-8')\n for line in output.split('\\n'):\n if 'Version:' in line:\n self.tool_version = line.split('Version:')[1].strip()\n return\n self.tool_version = 'unknown'\n\n def slice_fasta(self, in_fasta, out_fasta, seq_id=None, start=None, end=None):\n ''' Slice a fasta file to extract a specific sequence and optional coordinate range.\n\n Args:\n in_fasta: Input fasta file\n out_fasta: Output fasta file with sliced sequence\n seq_id: Sequence ID to extract (default: None). If None, all sequences are copied.\n start: Start coordinate (1-based, inclusive). None means start of sequence.\n end: End coordinate (1-based, inclusive). None means end of sequence.\n\n If all optional parameters are None, this is a no-op (output identical to input).\n '''\n # If no filtering/slicing requested, just copy the file\n if seq_id is None and start is None and end is None:\n shutil.copyfile(in_fasta, out_fasta)\n return\n\n found = False\n with open(out_fasta, 'w') as outf:\n for record in Bio.SeqIO.parse(in_fasta, 'fasta'):\n if seq_id is None or record.id == seq_id:\n found = True\n # Convert to 0-based for python slicing\n start_idx = (start - 1) if start is not None else None\n end_idx = end if end is not None else None\n sliced_seq = record.seq[start_idx:end_idx]\n sliced_record = Bio.SeqRecord.SeqRecord(\n sliced_seq,\n id=record.id,\n description=record.description\n )\n Bio.SeqIO.write(sliced_record, outf, 'fasta')\n if seq_id is not None:\n break\n\n if seq_id is not None and not found:\n raise ValueError(f\"Sequence ID '{seq_id}' not found in {in_fasta}\")\n\n def coverage_to_read_pairs(self, coverage, sequence_length, read_length):\n ''' Convert coverage depth to number of read pairs needed.\n\n Args:\n coverage: Desired coverage depth (e.g., 20 for 20X)\n sequence_length: Length of the sequence to cover\n read_length: Length of each read\n\n Returns:\n Number of read pairs (rounded up to nearest integer)\n '''\n # Each read pair contributes 2 * read_length bases\n total_bases_needed = coverage * sequence_length\n read_pairs = total_bases_needed / (2 * read_length)\n return math.ceil(read_pairs)\n\n def fastqs_to_bam(self, in_fastq1, in_fastq2, out_bam, sample_name='sample', library_name='lib1',\n platform='ILLUMINA', platform_unit='wgsim'):\n ''' Convert paired fastq files to unaligned BAM with read group headers.\n\n Args:\n in_fastq1: Input fastq file for read 1\n in_fastq2: Input fastq file for read 2\n out_bam: Output unaligned BAM file\n sample_name: Sample name for read group\n library_name: Library name for read group\n platform: Platform for read group (default: ILLUMINA)\n platform_unit: Platform unit for read group (default: wgsim)\n '''\n picard = viral_ngs.core.picard.FastqToSamTool()\n picard.execute(\n in_fastq1, in_fastq2, sample_name, out_bam,\n picardOptions=[\n 'LIBRARY_NAME=' + library_name,\n 'PLATFORM=' + platform,\n 'PLATFORM_UNIT=' + platform_unit\n ]\n )\n\n def execute(self, in_fasta, out_fastq1, out_fastq2,\n read_length=150, outer_distance=500, error_rate=0.02, mutation_rate=0.001,\n indel_fraction=0.15, indel_extended_prob=0.3, num_read_pairs=None,\n random_seed=None, other_opts=()):\n ''' Execute wgsim to generate simulated paired-end reads.\n\n Args:\n in_fasta: Input reference fasta file\n out_fastq1: Output fastq file for read 1\n out_fastq2: Output fastq file for read 2\n read_length: Length of each read (default: 150 for Illumina)\n outer_distance: Outer distance between the two ends (default: 500)\n error_rate: Base error rate (default: 0.02)\n mutation_rate: Rate of mutations (default: 0.001)\n indel_fraction: Fraction of indels (default: 0.15)\n indel_extended_prob: Probability an indel is extended (default: 0.3)\n num_read_pairs: Number of read pairs to generate (required)\n random_seed: Random seed for reproducibility\n other_opts: Additional command line options\n '''\n\n if num_read_pairs is None:\n raise ValueError(\"num_read_pairs must be specified\")\n\n tool_cmd = [\n self.install_and_get_path(),\n '-e', str(error_rate),\n '-d', str(outer_distance),\n '-N', str(num_read_pairs),\n '-1', str(read_length),\n '-2', str(read_length),\n '-r', str(mutation_rate),\n '-R', str(indel_fraction),\n '-X', str(indel_extended_prob),\n ]\n\n if random_seed is not None:\n tool_cmd.extend(['-S', str(random_seed)])\n\n tool_cmd.extend(other_opts)\n tool_cmd.extend([in_fasta, out_fastq1, out_fastq2])\n\n _log.debug('running wgsim: ' + ' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n" }, { "path": "src/viral_ngs/assembly.py", "content": "#!/usr/bin/env python3\n''' This script contains a number of utilities for viral sequence assembly\n from NGS reads. Primarily used for Lassa and Ebola virus analysis in\n the Sabeti Lab / Broad Institute Viral Genomics.\n'''\n\n__author__ = \"dpark@broadinstitute.org, rsealfon@broadinstitute.org\"\n__commands__ = []\n\n# built-ins\nimport argparse\nimport logging\nimport random\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport functools\nimport operator\nimport concurrent.futures\nimport csv\nimport itertools\nfrom collections import OrderedDict, defaultdict\n\n# from viral_ngs.core\nimport viral_ngs.core.cmd\nimport viral_ngs.core.file\nimport viral_ngs.core.misc\nimport viral_ngs.read_utils\nimport viral_ngs.core.picard\nimport viral_ngs.core.samtools\nimport viral_ngs.core.novoalign\nimport viral_ngs.assemble.freebayes\nimport viral_ngs.assemble.rasusa\n\n# intra-module (assembly tool wrappers)\nimport viral_ngs.assemble.vcf\nimport viral_ngs.assemble.spades\nimport viral_ngs.assemble.mafft\nimport viral_ngs.assemble.mummer\nimport viral_ngs.assemble.muscle\nimport viral_ngs.assemble.gap2seq\nimport viral_ngs.assemble.skani\nimport viral_ngs.assemble.wgsim\n\n# third-party\nimport numpy\nimport Bio.AlignIO\nimport Bio.SeqIO\nimport Bio.Data.IUPACData\n\nlog = logging.getLogger(__name__)\n\n\nclass DenovoAssemblyError(RuntimeError):\n\n '''Indicates a failure of the de novo assembly step. Can indicate an internal error in the assembler, but also\n insufficient input data (for assemblers which cannot report that condition separately).'''\n\n def __init__(self, reason):\n super(DenovoAssemblyError, self).__init__(reason)\n\n\ndef assemble_spades(\n in_bam,\n clip_db,\n out_fasta,\n spades_opts='--rnaviral',\n contigs_trusted=None, contigs_untrusted=None,\n filter_contigs=False,\n min_contig_len=0,\n kmer_sizes=None,\n n_reads=10000000,\n outReads=None,\n always_succeed=False,\n mem_limit_gb=8,\n threads=None,\n):\n '''De novo RNA-seq assembly with the SPAdes assembler.\n '''\n\n if outReads:\n trim_rmdup_bam = outReads\n else:\n trim_rmdup_bam = viral_ngs.core.file.mkstempfname('.subsamp.bam')\n\n viral_ngs.read_utils.trim_rmdup_subsamp_reads(in_bam, clip_db, trim_rmdup_bam, n_reads=n_reads,\n trim_opts=dict(maxinfo_target_length=35, maxinfo_strictness=.2))\n\n with viral_ngs.core.picard.SamToFastqTool().execute_tmp(trim_rmdup_bam, includeUnpaired=True, illuminaClipping=True\n ) as (reads_fwd, reads_bwd, reads_unpaired):\n try:\n viral_ngs.assemble.spades.SpadesTool().assemble(reads_fwd=reads_fwd, reads_bwd=reads_bwd, reads_unpaired=reads_unpaired,\n contigs_untrusted=contigs_untrusted, contigs_trusted=contigs_trusted,\n contigs_out=out_fasta, filter_contigs=filter_contigs,\n min_contig_len=min_contig_len,\n kmer_sizes=kmer_sizes, always_succeed=always_succeed,\n spades_opts=spades_opts, mem_limit_gb=mem_limit_gb,\n threads=threads)\n except subprocess.CalledProcessError as e:\n raise DenovoAssemblyError('SPAdes assembler failed: ' + str(e))\n\n if not outReads:\n os.unlink(trim_rmdup_bam)\n\n\n\ndef parser_assemble_spades(parser=argparse.ArgumentParser()):\n parser.add_argument('in_bam', help='Input unaligned reads, BAM format. May include both paired and unpaired reads.')\n parser.add_argument('clip_db', help='Trimmomatic clip db')\n parser.add_argument('out_fasta', help='Output assembled contigs. Note that, since this is RNA-seq assembly, for each assembled genomic region there may be several contigs representing different variants of that region.')\n parser.add_argument('--contigsTrusted', dest='contigs_trusted', \n help='Optional input contigs of high quality, previously assembled from the same sample')\n parser.add_argument('--contigsUntrusted', dest='contigs_untrusted', \n help='Optional input contigs of high medium quality, previously assembled from the same sample')\n parser.add_argument('--nReads', dest='n_reads', type=int, default=10000000, \n help='Before assembly, subsample the reads to at most this many')\n parser.add_argument('--kmerSizes', dest='kmer_sizes', default=None,\n help='Comma-separated ascending order list of odd-value kmer sizes to attempt')\n parser.add_argument('--outReads', default=None, help='Save the trimmomatic/prinseq/subsamp reads to a BAM file')\n parser.add_argument('--filterContigs', dest='filter_contigs', default=False, action='store_true', \n help='only output contigs SPAdes is sure of (drop lesser-quality contigs from output)')\n parser.add_argument('--alwaysSucceed', dest='always_succeed', default=True, action='store_true',\n help='if assembly fails for any reason, output an empty contigs file, rather than failing with '\n 'an error code')\n parser.add_argument('--minContigLen', dest='min_contig_len', type=int, default=0,\n help='only output contigs longer than this many bp')\n parser.add_argument('--spadesOpts', dest='spades_opts', default='--rnaviral', help='(advanced) Extra flags to pass to the SPAdes assembler')\n parser.add_argument('--memLimitGb', dest='mem_limit_gb', default=4, type=int, help='Max memory to use, in GB (default: %(default)s)')\n viral_ngs.core.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, assemble_spades, split_args=True)\n return parser\n\n\n__commands__.append(('assemble_spades', parser_assemble_spades))\n\ndef gapfill_gap2seq(in_scaffold, in_bam, out_scaffold, threads=None, mem_limit_gb=4, time_soft_limit_minutes=60.0,\n random_seed=0, gap2seq_opts='', always_succeed=False):\n ''' This step runs the Gap2Seq tool to close gaps between contigs in a scaffold.\n '''\n try:\n viral_ngs.assemble.gap2seq.Gap2SeqTool().gapfill(in_scaffold, in_bam, out_scaffold, gap2seq_opts=gap2seq_opts, threads=threads,\n mem_limit_gb=mem_limit_gb, time_soft_limit_minutes=time_soft_limit_minutes, \n random_seed=random_seed)\n except Exception as e:\n if not always_succeed:\n raise\n log.warning('Gap-filling failed (%s); ignoring error, emulating successful run where simply no gaps were filled.')\n shutil.copyfile(in_scaffold, out_scaffold)\n\ndef parser_gapfill_gap2seq(parser=argparse.ArgumentParser(description='Close gaps between contigs in a scaffold')):\n parser.add_argument('in_scaffold', help='FASTA file containing the scaffold. Each FASTA record corresponds to one '\n 'segment (for multi-segment genomes). Contigs within each segment are separated by Ns.')\n parser.add_argument('in_bam', help='Input unaligned reads, BAM format.')\n parser.add_argument('out_scaffold', help='Output assemble.')\n parser.add_argument('--memLimitGb', dest='mem_limit_gb', default=4.0, help='Max memory to use, in gigabytes %(default)s')\n parser.add_argument('--timeSoftLimitMinutes', dest='time_soft_limit_minutes', default=60.0,\n help='Stop trying to close more gaps after this many minutes (default: %(default)s); this is a soft/advisory limit')\n parser.add_argument('--maskErrors', dest='always_succeed', default=False, action='store_true',\n help='In case of any error, just copy in_scaffold to out_scaffold, emulating a successful run that simply could not '\n 'fill any gaps.')\n parser.add_argument('--gap2seqOpts', dest='gap2seq_opts', default='', help='(advanced) Extra command-line options to pass to Gap2Seq')\n parser.add_argument('--randomSeed', dest='random_seed', default=0, help='Random seed; 0 means use current time')\n viral_ngs.core.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, gapfill_gap2seq, split_args=True)\n return parser\n\n__commands__.append(('gapfill_gap2seq', parser_gapfill_gap2seq))\n\n\ndef cluster_references_ani(inRefs, outClusters, m=15, s=50, c=10, min_af=15, threads=None):\n ''' This step uses the skani triangle tool to define clusters of highly-related genomes.\n '''\n skani = viral_ngs.assemble.skani.SkaniTool()\n clusters = skani.find_reference_clusters(inRefs, m=m, s=s, c=c, min_af=min_af, threads=threads)\n with open(outClusters, 'w') as outf:\n for cluster in clusters:\n outf.write('\\t'.join(cluster) + '\\n')\n\ndef parser_cluster_references_ani(parser=argparse.ArgumentParser(description='Cluster references')):\n parser.add_argument('inRefs', nargs='+', help='FASTA files containing reference genomes')\n parser.add_argument('outClusters', help='Output file containing clusters of highly-related genomes. Each line contains the filenames of the genomes in one cluster.')\n parser.add_argument('-m', type=int, default=15, help='marker k-mer compression factor (default: %(default)s)')\n parser.add_argument('-s', type=int, default=50, help='screen out pairs with < percent identity using k-mer sketching (default: %(default)s)')\n parser.add_argument('-c', type=int, default=10, help='compression factor (k-mer subsampling ratio) (default: %(default)s)')\n parser.add_argument('--min_af', dest='min_af', type=int, default=15, help='minimum alignment fraction (default: %(default)s)')\n viral_ngs.core.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, cluster_references_ani, split_args=True)\n return parser\n\n__commands__.append(('cluster_references_ani', parser_cluster_references_ani))\n\n\ndef skani_contigs_to_refs(inContigs, inRefs, out_skani_dist, out_skani_dist_filtered, out_clusters_filtered, m=15, s=50, c=10, min_af=15, n=None, threads=None):\n\n skani = viral_ngs.assemble.skani.SkaniTool()\n clusters = skani.find_reference_clusters(inRefs, m=m, s=s, c=c, min_af=min_af, threads=threads)\n skani.find_closest_reference(inContigs, inRefs, out_skani_dist, m=m, s=s, c=c, n=n, min_af=min_af, threads=threads)\n refs_hit = set()\n refs_hit_by_cluster = set()\n\n dist_header = viral_ngs.core.file.readFlatFileHeader(out_skani_dist)\n with open(out_skani_dist, 'r') as inf:\n with open(out_skani_dist_filtered, 'w') as outf:\n writer = csv.DictWriter(outf, dist_header, delimiter='\\t', dialect=csv.unix_dialect, quoting=csv.QUOTE_MINIMAL)\n writer.writeheader()\n for row in csv.DictReader(inf, delimiter='\\t'):\n refs_hit.add(row['Ref_file'])\n if row['Ref_file'] not in refs_hit_by_cluster:\n writer.writerow(row)\n for cluster in clusters:\n if row['Ref_file'] in cluster:\n refs_hit_by_cluster.update(cluster)\n break\n\n with open(out_clusters_filtered, 'w') as outf:\n for cluster in clusters:\n hits = list([ref for ref in cluster if ref in refs_hit])\n if hits:\n outf.write('\\t'.join(hits) + '\\n')\n\ndef parser_skani_contigs_to_refs(parser=argparse.ArgumentParser(description='Find closest references for contigs')):\n parser.add_argument('inContigs', help='FASTA file containing contigs')\n parser.add_argument('inRefs', nargs='+', help='FASTA files containing reference genomes')\n parser.add_argument('out_skani_dist', help='Output file containing ANI distances between contigs and references')\n parser.add_argument('out_skani_dist_filtered', help='Output file containing ANI distances between contigs and references, with only the top reference hit per cluster')\n parser.add_argument('out_clusters_filtered', help='Output file containing clusters of highly-related genomes, with only clusters that have a hit to the contigs')\n parser.add_argument('-m', type=int, default=15, help='marker k-mer compression factor (default: %(default)s)')\n parser.add_argument('-s', type=int, default=50, help='screen out pairs with < percent identity using k-mer sketching (default: %(default)s)')\n parser.add_argument('-c', type=int, default=10, help='compression factor (k-mer subsampling ratio) (default: %(default)s)')\n parser.add_argument('-n', type=int, default=None, help='maximum number of hits to report (default: unlimited)')\n parser.add_argument('--min_af', dest='min_af', type=int, default=15, help='minimum alignment fraction (default: %(default)s)')\n viral_ngs.core.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, skani_contigs_to_refs, split_args=True)\n return parser\n\n__commands__.append(('skani_contigs_to_refs', parser_skani_contigs_to_refs)) \n\n\n\ndef _order_and_orient_orig(inFasta, inReference, outFasta,\n outAlternateContigs=None,\n breaklen=None, # aligner='nucmer', circular=False, trimmed_contigs=None,\n maxgap=200, minmatch=10, mincluster=None,\n min_pct_id=0.6, min_contig_len=200, min_pct_contig_aligned=0.3):\n ''' This step cleans up the de novo assembly with a known reference genome.\n Uses MUMmer (nucmer or promer) to create a reference-based consensus\n sequence of aligned contigs (with runs of N's in between the de novo\n contigs).\n '''\n mummer = viral_ngs.assemble.mummer.MummerTool()\n #if trimmed_contigs:\n # trimmed = trimmed_contigs\n #else:\n # trimmed = viral_ngs.core.file.mkstempfname('.trimmed.contigs.fasta')\n #mummer.trim_contigs(inReference, inFasta, trimmed,\n # aligner=aligner, circular=circular, extend=False, breaklen=breaklen,\n # min_pct_id=min_pct_id, min_contig_len=min_contig_len,\n # min_pct_contig_aligned=min_pct_contig_aligned)\n #mummer.scaffold_contigs(inReference, trimmed, outFasta,\n # aligner=aligner, circular=circular, extend=True, breaklen=breaklen,\n # min_pct_id=min_pct_id, min_contig_len=min_contig_len,\n # min_pct_contig_aligned=min_pct_contig_aligned)\n mummer.scaffold_contigs_custom(\n inReference,\n inFasta,\n outFasta,\n outAlternateContigs=outAlternateContigs,\n extend=True,\n breaklen=breaklen,\n min_pct_id=min_pct_id,\n min_contig_len=min_contig_len,\n maxgap=maxgap,\n minmatch=minmatch,\n mincluster=mincluster,\n min_pct_contig_aligned=min_pct_contig_aligned\n )\n #if not trimmed_contigs:\n # os.unlink(trimmed)\n return 0\n\ndef _call_order_and_orient_orig(inReference, outFasta, outAlternateContigs, **kwargs):\n return _order_and_orient_orig(inReference=inReference, outFasta=outFasta, outAlternateContigs=outAlternateContigs, **kwargs)\n\ndef order_and_orient(inFasta, inReference, outFasta,\n outAlternateContigs=None, outReference=None,\n breaklen=None, # aligner='nucmer', circular=False, trimmed_contigs=None,\n maxgap=200, minmatch=10, mincluster=None,\n min_pct_id=0.6, min_contig_len=200, min_pct_contig_aligned=0.3, n_genome_segments=0, \n allow_incomplete_output=False, outStats=None, threads=None):\n ''' This step cleans up the de novo assembly with a known reference genome.\n Uses MUMmer (nucmer or promer) to create a reference-based consensus\n sequence of aligned contigs (with runs of N's in between the de novo\n contigs).\n '''\n\n chk = viral_ngs.core.cmd.check_input\n\n ref_segments_all = [tuple(Bio.SeqIO.parse(inRef, 'fasta')) for inRef in viral_ngs.core.misc.make_seq(inReference)]\n chk(ref_segments_all, 'No references given')\n chk(len(set(map(len, ref_segments_all))) == 1, 'All references must have the same number of segments')\n if n_genome_segments:\n if len(ref_segments_all) == 1:\n chk((len(ref_segments_all[0]) % n_genome_segments) == 0,\n 'Number of reference sequences in must be a multiple of the number of genome segments')\n else:\n chk(len(ref_segments_all[0]) == n_genome_segments,\n 'Number of reference segments must match the n_genome_segments parameter')\n else:\n n_genome_segments = len(ref_segments_all[0])\n ref_segments_all = functools.reduce(operator.concat, ref_segments_all, ())\n\n n_refs = len(ref_segments_all) // n_genome_segments\n log.info('n_genome_segments={} n_refs={}'.format(n_genome_segments, n_refs))\n ref_ids = []\n\n with viral_ngs.core.file.tempfnames(suffixes=[ '.{}.ref.fasta'.format(ref_num) for ref_num in range(n_refs)]) as refs_fasta, \\\n viral_ngs.core.file.tempfnames(suffixes=[ '.{}.scaffold.fasta'.format(ref_num) for ref_num in range(n_refs)]) as scaffolds_fasta, \\\n viral_ngs.core.file.tempfnames(suffixes=[ '.{}.altcontig.fasta'.format(ref_num) for ref_num in range(n_refs)]) as alt_contigs_fasta:\n\n for ref_num in range(n_refs):\n this_ref_segs = ref_segments_all[ref_num*n_genome_segments : (ref_num+1)*n_genome_segments]\n ref_ids.append(this_ref_segs[0].id)\n Bio.SeqIO.write(this_ref_segs, refs_fasta[ref_num], 'fasta')\n\n with concurrent.futures.ProcessPoolExecutor(max_workers=viral_ngs.core.misc.sanitize_thread_count(threads)) as executor:\n retvals = executor.map(functools.partial(_call_order_and_orient_orig, inFasta=inFasta,\n breaklen=breaklen, maxgap=maxgap, minmatch=minmatch, mincluster=mincluster, min_pct_id=min_pct_id,\n min_contig_len=min_contig_len, min_pct_contig_aligned=min_pct_contig_aligned),\n refs_fasta, scaffolds_fasta, alt_contigs_fasta)\n for r in retvals:\n # if an exception is raised by _call_order_and_orient_contig, the\n # concurrent.futures.Executor.map function documentations states\n # that the same exception will be raised when retrieving that entry\n # of the retval iterator. This for loop is intended to reveal any\n # CalledProcessErrors from mummer itself.\n assert r==0\n\n scaffolds = [tuple(Bio.SeqIO.parse(scaffolds_fasta[ref_num], 'fasta')) for ref_num in range(n_refs)]\n base_counts = [sum([len(seg.seq.replace(\"N\",\"\")) for seg in scaffold]) \\\n if len(scaffold)==n_genome_segments else 0 for scaffold in scaffolds]\n best_ref_num = numpy.argmax(base_counts)\n if (len(scaffolds[best_ref_num]) != n_genome_segments) and not allow_incomplete_output:\n raise IncompleteAssemblyError(len(scaffolds[best_ref_num]), n_genome_segments)\n log.info('base_counts={} best_ref_num={}'.format(base_counts, best_ref_num))\n shutil.copyfile(scaffolds_fasta[best_ref_num], outFasta)\n if outAlternateContigs:\n shutil.copyfile(alt_contigs_fasta[best_ref_num], outAlternateContigs)\n if outReference:\n shutil.copyfile(refs_fasta[best_ref_num], outReference)\n if outStats:\n ref_ranks = (-numpy.array(base_counts)).argsort().argsort()\n with open(outStats, 'w') as stats_f:\n stats_w = csv.DictWriter(stats_f, fieldnames='ref_num ref_name base_count rank'.split(), delimiter='\\t')\n stats_w.writeheader()\n for ref_num, (ref_id, base_count, rank) in enumerate(zip(ref_ids, base_counts, ref_ranks)):\n stats_w.writerow({'ref_num': ref_num, 'ref_name': ref_id, 'base_count': base_count, 'rank': rank})\n\n\ndef parser_order_and_orient(parser=argparse.ArgumentParser()):\n parser.add_argument('inFasta', help='Input de novo assembly/contigs, FASTA format.')\n parser.add_argument(\n 'inReference', nargs='+',\n help=('Reference genome for ordering, orienting, and merging contigs, FASTA format. Multiple filenames may be listed, each '\n 'containing one reference genome. Alternatively, multiple references may be given by specifying a single filename, '\n 'and giving the number of reference segments with the nGenomeSegments parameter. If multiple references are given, '\n 'they must all contain the same number of segments listed in the same order.')\n )\n parser.add_argument(\n 'outFasta',\n help=\"\"\"Output assembly, FASTA format, with the same number of\n chromosomes as inReference, and in the same order.\"\"\"\n )\n parser.add_argument(\n '--outAlternateContigs',\n help=\"\"\"Output sequences (FASTA format) from alternative contigs that mapped,\n but were not chosen for the final output.\"\"\",\n default=None\n )\n\n parser.add_argument('--nGenomeSegments', dest='n_genome_segments', type=int, default=0,\n help=\"\"\"Number of genome segments. If 0 (the default), the `inReference` parameter is treated as one genome.\n If positive, the `inReference` parameter is treated as a list of genomes of nGenomeSegments each.\"\"\")\n\n parser.add_argument('--outReference', help='Output the reference chosen for scaffolding to this file')\n parser.add_argument('--outStats', help='Output stats used in reference selection')\n parser.add_argument(\n \"--allow_incomplete_output\",\n help=\"Do not fail with IncompleteAssemblyError if we fail to recover all segments of the desired genome.\",\n default=False,\n action=\"store_true\",\n dest=\"allow_incomplete_output\"\n )\n #parser.add_argument('--aligner',\n # help='nucmer (nucleotide) or promer (six-frame translations) [default: %(default)s]',\n # choices=['nucmer', 'promer'],\n # default='nucmer')\n #parser.add_argument(\"--circular\",\n # help=\"\"\"Allow contigs to wrap around the ends of the chromosome.\"\"\",\n # default=False,\n # action=\"store_true\",\n # dest=\"circular\")\n parser.add_argument(\n \"--breaklen\",\n \"-b\",\n help=\"\"\"Amount to extend alignment clusters by (if --extend).\n nucmer default 200, promer default 60.\"\"\",\n type=int,\n default=None,\n dest=\"breaklen\"\n )\n parser.add_argument(\n \"--maxgap\",\n \"-g\",\n help=\"\"\"Maximum gap between two adjacent matches in a cluster.\n Our default is %(default)s.\n nucmer default 90, promer default 30. Manual suggests going to 1000.\"\"\",\n type=int,\n default=200,\n dest=\"maxgap\"\n )\n parser.add_argument(\n \"--minmatch\",\n \"-l\",\n help=\"\"\"Minimum length of an maximal exact match.\n Our default is %(default)s.\n nucmer default 20, promer default 6.\"\"\",\n type=int,\n default=10,\n dest=\"minmatch\"\n )\n parser.add_argument(\n \"--mincluster\",\n \"-c\",\n help=\"\"\"Minimum cluster length.\n nucmer default 65, promer default 20.\"\"\",\n type=int,\n default=None,\n dest=\"mincluster\"\n )\n parser.add_argument(\n \"--min_pct_id\",\n \"-i\",\n type=float,\n default=0.6,\n help=\"show-tiling: minimum percent identity for contig alignment (0.0 - 1.0, default: %(default)s)\"\n )\n parser.add_argument(\n \"--min_contig_len\",\n type=int,\n default=200,\n help=\"show-tiling: reject contigs smaller than this (default: %(default)s)\"\n )\n parser.add_argument(\n \"--min_pct_contig_aligned\",\n \"-v\",\n type=float,\n default=0.3,\n help=\"show-tiling: minimum percent of contig length in alignment (0.0 - 1.0, default: %(default)s)\"\n )\n #parser.add_argument(\"--trimmed_contigs\",\n # default=None,\n # help=\"optional output file for trimmed contigs\")\n viral_ngs.core.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, order_and_orient, split_args=True)\n return parser\n\n\n__commands__.append(('order_and_orient', parser_order_and_orient))\n\n\nclass IncompleteAssemblyError(Exception):\n def __init__(self, actual_n, expected_n):\n super(IncompleteAssemblyError, self).__init__(\n 'All computed scaffolds are incomplete. Best assembly has {} contigs, expected {}'.format(\n actual_n, expected_n)\n )\n\nclass PoorAssemblyError(Exception):\n def __init__(self, chr_idx, seq_len, non_n_count, min_length, segment_length):\n super(PoorAssemblyError, self).__init__(\n 'Error: poor assembly quality, chr {}: contig length {}, unambiguous bases {}; bases required of reference segment length: {}/{} ({:.0%})'.format(\n chr_idx, seq_len, non_n_count, min_length, int(segment_length), float(min_length)/float(segment_length)\n )\n )\n\n\ndef impute_from_reference(\n inFasta,\n inReference,\n outFasta,\n minLengthFraction,\n minUnambig,\n replaceLength,\n newName=None,\n aligner='muscle',\n index=False\n):\n '''\n This takes a de novo assembly, aligns against a reference genome, and\n imputes all missing positions (plus some of the chromosome ends)\n with the reference genome. This provides an assembly with the proper\n structure (but potentially wrong sequences in areas) from which\n we can perform further read-based refinement.\n Two steps:\n filter_short_seqs: We then toss out all assemblies that come out to\n < 15kb or < 95% unambiguous and fail otherwise.\n modify_contig: Finally, we trim off anything at the end that exceeds\n the length of the known reference assemble. We also replace all\n Ns and everything within 55bp of the chromosome ends with the\n reference sequence. This is clearly incorrect consensus sequence,\n but it allows downstream steps to map reads in parts of the genome\n that would otherwise be Ns, and we will correct all of the inferred\n positions with two steps of read-based refinement (below), and\n revert positions back to Ns where read support is lacking.\n FASTA indexing: output assembly is indexed for Picard, Samtools, Novoalign.\n '''\n tempFastas = []\n\n pmc = parser_modify_contig(argparse.ArgumentParser())\n assert aligner in ('muscle', 'mafft', 'mummer')\n\n with open(inFasta, 'r') as asmFastaFile:\n with open(inReference, 'r') as refFastaFile:\n asmFasta = list(Bio.SeqIO.parse(asmFastaFile, 'fasta'))\n refFasta = Bio.SeqIO.parse(refFastaFile, 'fasta')\n if asmFasta:\n for idx, (refSeqObj, asmSeqObj) in enumerate(itertools.zip_longest(refFasta, asmFasta)):\n # our zip fails if one file has more seqs than the other\n if not refSeqObj or not asmSeqObj:\n raise KeyError(\"inFasta and inReference do not have the same number of sequences. This could be because the de novo assembly process was unable to create contigs for all segments.\")\n\n # error if PoorAssembly\n minLength = len(refSeqObj) * minLengthFraction\n non_n_count = viral_ngs.core.misc.unambig_count(asmSeqObj.seq)\n seq_len = len(asmSeqObj)\n log.info(\n \"Assembly Quality - segment {idx} - name {segname} - contig len {len_actual} / {len_desired} ({min_frac}) - unambiguous bases {unamb_actual} / {unamb_desired} ({min_unamb})\".format(\n idx=idx + 1,\n segname=refSeqObj.id,\n len_actual=seq_len,\n len_desired=len(refSeqObj),\n min_frac=minLengthFraction,\n unamb_actual=non_n_count,\n unamb_desired=seq_len,\n min_unamb=minUnambig\n )\n )\n if seq_len < minLength or non_n_count < seq_len * minUnambig:\n raise PoorAssemblyError(idx + 1, seq_len, non_n_count, minLength, len(refSeqObj))\n\n # prepare temp input and output files\n tmpOutputFile = viral_ngs.core.file.mkstempfname(prefix='seq-out-{idx}-'.format(idx=idx), suffix=\".fasta\")\n concat_file = viral_ngs.core.file.mkstempfname('.ref_and_actual.fasta')\n ref_file = viral_ngs.core.file.mkstempfname('.ref.fasta')\n actual_file = viral_ngs.core.file.mkstempfname('.actual.fasta')\n aligned_file = viral_ngs.core.file.mkstempfname('.'+aligner+'.fasta')\n refName = refSeqObj.id\n with open(concat_file, 'wt') as outf:\n Bio.SeqIO.write([refSeqObj, asmSeqObj], outf, \"fasta\")\n with open(ref_file, 'wt') as outf:\n Bio.SeqIO.write([refSeqObj], outf, \"fasta\")\n with open(actual_file, 'wt') as outf:\n Bio.SeqIO.write([asmSeqObj], outf, \"fasta\")\n\n # align scaffolded genome to reference (choose one of three aligners)\n if aligner == 'mafft':\n viral_ngs.assemble.mafft.MafftTool().execute(\n [ref_file, actual_file], aligned_file, False, True, True, False, False, None\n )\n elif aligner == 'muscle':\n if len(refSeqObj) > 40000:\n viral_ngs.assemble.muscle.MuscleTool().execute(\n concat_file, aligned_file, quiet=False,\n maxiters=2, diags=True\n )\n else:\n viral_ngs.assemble.muscle.MuscleTool().execute(concat_file, aligned_file, quiet=False)\n elif aligner == 'mummer':\n viral_ngs.assemble.mummer.MummerTool().align_one_to_one(ref_file, actual_file, aligned_file)\n\n # run modify_contig\n args = [\n aligned_file, tmpOutputFile, refName, '--call-reference-ns', '--trim-ends', '--replace-5ends',\n '--replace-3ends', '--replace-length', str(replaceLength), '--replace-end-gaps'\n ]\n if newName:\n # renames the segment name \"sampleName-idx\" where idx is the segment number\n args.extend(['--name', newName + \"-\" + str(idx + 1)])\n args = pmc.parse_args(args)\n args.func_main(args)\n\n # clean up\n os.unlink(concat_file)\n os.unlink(ref_file)\n os.unlink(actual_file)\n os.unlink(aligned_file)\n tempFastas.append(tmpOutputFile)\n\n # merge outputs\n viral_ngs.core.file.concat(tempFastas, outFasta)\n for tmpFile in tempFastas:\n os.unlink(tmpFile)\n\n # Index final output FASTA for Picard, Samtools, and Novoalign\n if index:\n viral_ngs.core.samtools.SamtoolsTool().faidx(outFasta, overwrite=True)\n viral_ngs.core.picard.CreateSequenceDictionaryTool().execute(outFasta, overwrite=True)\n viral_ngs.core.novoalign.NovoalignTool().index_fasta(outFasta)\n\n return 0\n\n\ndef parser_impute_from_reference(parser=argparse.ArgumentParser()):\n parser.add_argument(\n 'inFasta',\n help='Input assembly/contigs, FASTA format, already ordered, oriented and merged with inReference.'\n )\n parser.add_argument('inReference', help='Reference genome to impute with, FASTA format.')\n parser.add_argument('outFasta', help='Output assembly, FASTA format.')\n parser.add_argument(\"--newName\", default=None, help=\"rename output chromosome (default: do not rename)\")\n parser.add_argument(\n \"--minLengthFraction\",\n type=float,\n default=0.5,\n help=\"minimum length for contig, as fraction of reference (default: %(default)s)\"\n )\n parser.add_argument(\n \"--minUnambig\",\n type=float,\n default=0.5,\n help=\"minimum percentage unambiguous bases for contig (default: %(default)s)\"\n )\n parser.add_argument(\n \"--replaceLength\",\n type=int,\n default=0,\n help=\"length of ends to be replaced with reference (default: %(default)s)\"\n )\n parser.add_argument(\n '--aligner',\n help=\"\"\"which method to use to align inFasta to\n inReference. \"muscle\" = MUSCLE, \"mafft\" = MAFFT,\n \"mummer\" = nucmer. [default: %(default)s]\"\"\",\n choices=['muscle', 'mafft', 'mummer'],\n default='muscle'\n )\n parser.add_argument(\n \"--index\",\n help=\"\"\"Index outFasta for Picard/GATK, Samtools, and Novoalign.\"\"\",\n default=False,\n action=\"store_true\",\n dest=\"index\"\n )\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, impute_from_reference, split_args=True)\n return parser\n\n\n__commands__.append(('impute_from_reference', parser_impute_from_reference))\n\n\ndef refine_assembly(\n inFasta,\n inBam,\n outFasta,\n outVcf=None,\n outBam=None,\n novo_params='',\n min_coverage=2,\n major_cutoff=0.5,\n chr_names=None,\n keep_all_reads=False,\n max_coverage=None,\n rasusa_seed=None,\n already_realigned_bam=None,\n JVMmemory=None,\n threads=None,\n novoalign_license_path=None\n):\n ''' This a refinement step where we take a crude assembly, align\n all reads back to it, and modify the assembly to the majority\n allele at each position based on read pileups.\n This step considers both SNPs as well as indels called by FreeBayes\n and will correct the consensus based on variant calls.\n Reads are aligned with Novoalign, then PCR duplicates are removed\n with Picard (in order to debias the allele counts in the pileups).\n Output FASTA file is indexed for Picard, Samtools, and Novoalign.\n '''\n chr_names = chr_names or []\n\n # if the input fasta is empty, create an empty output fasta and return\n if (os.path.getsize(inFasta) == 0):\n viral_ngs.core.file.touch(outFasta)\n if outVcf:\n with viral_ngs.core.file.open_or_gzopen(outVcf, 'wt') as outf:\n outf.write('##fileformat=VCFv4.3')\n outf.write('\\t'.join(('#CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT'))+'\\n')\n return 0\n\n # Get tools\n picard_index = viral_ngs.core.picard.CreateSequenceDictionaryTool()\n picard_mkdup = viral_ngs.core.picard.MarkDuplicatesTool()\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n fb = viral_ngs.assemble.freebayes.FreeBayesTool()\n novoalign = None\n if not already_realigned_bam:\n novoalign = viral_ngs.core.novoalign.NovoalignTool(license_path=novoalign_license_path)\n\n # Sanitize fasta header & create deambiguated genome for variant calling\n deambigFasta = viral_ngs.core.file.mkstempfname('.deambig.fasta')\n with viral_ngs.core.file.fastas_with_sanitized_ids(inFasta, use_tmp=True) as sanitized_fastas:\n deambig_fasta(sanitized_fastas[0], deambigFasta)\n picard_index.execute(deambigFasta, overwrite=True)\n samtools.faidx(deambigFasta, overwrite=True)\n\n if already_realigned_bam:\n realignBam = already_realigned_bam\n if samtools.isEmpty(realignBam):\n viral_ngs.core.file.touch(outFasta)\n if outVcf:\n with viral_ngs.core.file.open_or_gzopen(outVcf, 'wt') as outf:\n outf.write('##fileformat=VCFv4.3')\n outf.write('\\t'.join(('#CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT'))+'\\n')\n return 0\n else:\n # Novoalign reads to self\n novoBam = viral_ngs.core.file.mkstempfname('.novoalign.bam')\n min_qual = 0 if keep_all_reads else 1\n novoalign.index_fasta(deambigFasta)\n novoalign.execute(inBam, deambigFasta, novoBam, options=novo_params.split(), min_qual=min_qual, JVMmemory=JVMmemory)\n rmdupBam = viral_ngs.core.file.mkstempfname('.rmdup.bam')\n opts = ['CREATE_INDEX=true']\n if not keep_all_reads:\n opts.append('REMOVE_DUPLICATES=true')\n picard_mkdup.execute([novoBam], rmdupBam, picardOptions=opts, JVMmemory=JVMmemory)\n os.unlink(novoBam)\n realignBam = rmdupBam\n if outBam:\n shutil.copyfile(realignBam, outBam)\n\n # Modify original assembly with VCF calls from FreeBayes\n with viral_ngs.core.file.tempfname('.vcf.gz') as tmpVcf, \\\n viral_ngs.core.file.tempfname('.fasta') as tmpFasta:\n\n # Optionally downsample coverage for variant calling only\n if max_coverage:\n rasusa_tool = viral_ngs.assemble.rasusa.RasusaTool()\n with viral_ngs.core.file.tempfname('.downsampled.unsorted.bam') as downsampledUnsortedBam, \\\n viral_ngs.core.file.tempfname('.downsampled.sorted.bam') as downsampledBam:\n rasusa_tool.downsample_bam(realignBam, downsampledUnsortedBam, max_coverage, seed=rasusa_seed)\n samtools.sort(downsampledUnsortedBam, downsampledBam, threads=threads)\n samtools.index(downsampledBam, threads=threads)\n fb.call(downsampledBam, deambigFasta, tmpVcf)\n # clean up samtools index sidecar\n if os.path.isfile(downsampledBam + '.bai'):\n os.unlink(downsampledBam + '.bai')\n else:\n fb.call(realignBam, deambigFasta, tmpVcf)\n\n if already_realigned_bam is None:\n os.unlink(realignBam)\n os.unlink(deambigFasta)\n name_opts = []\n if chr_names:\n name_opts = ['--name'] + chr_names\n main_vcf_to_fasta(\n parser_vcf_to_fasta(argparse.ArgumentParser(\n )).parse_args([\n tmpVcf,\n tmpFasta,\n '--trim_ends',\n '--min_coverage',\n str(min_coverage),\n '--major_cutoff',\n str(major_cutoff)\n ] + name_opts)\n )\n if outVcf:\n shutil.copyfile(tmpVcf, outVcf)\n if outVcf.endswith('.gz'):\n shutil.copyfile(tmpVcf + '.tbi', outVcf + '.tbi')\n shutil.copyfile(tmpFasta, outFasta)\n # clean up tabix index sidecar created by FreeBayes/tabix\n if os.path.isfile(tmpVcf + '.tbi'):\n os.unlink(tmpVcf + '.tbi')\n\n # Index final output FASTA for Picard, Samtools, and Novoalign\n picard_index.execute(outFasta, overwrite=True)\n # if the input bam is empty, an empty fasta will be created, however\n # faidx cannot index an empty fasta file, so only index if the fasta\n # has a non-zero size\n if (os.path.getsize(outFasta) > 0):\n samtools.faidx(outFasta, overwrite=True)\n if already_realigned_bam is None:\n novoalign.index_fasta(outFasta)\n \n return 0\n\n\ndef parser_refine_assembly(parser=argparse.ArgumentParser()):\n parser.add_argument(\n 'inFasta', help='Input assembly, FASTA format, pre-indexed for Picard, Samtools, and Novoalign.'\n )\n parser.add_argument('inBam', help='Input reads, unaligned BAM format.')\n parser.add_argument(\n 'outFasta',\n help='Output refined assembly, FASTA format, indexed for Picard, Samtools, and Novoalign.'\n )\n parser.add_argument(\n '--already_realigned_bam',\n default=None,\n help=\"\"\"BAM with reads that are already aligned to inFasta.\n This bypasses the alignment process by novoalign and instead uses the given\n BAM to make an assemble. When set, outBam is ignored.\"\"\"\n )\n parser.add_argument(\n '--outBam',\n default=None,\n help='Reads aligned to inFasta. Unaligned and duplicate reads have been removed.'\n )\n parser.add_argument('--outVcf', default=None, help='Variant calls for genome in inFasta coordinate space.')\n parser.add_argument(\n '--min_coverage',\n default=3,\n type=int,\n help='Minimum read coverage required to call a position unambiguous.'\n )\n parser.add_argument(\n '--major_cutoff',\n default=0.5,\n type=float,\n help=\"\"\"If the major allele is present at a frequency higher than this cutoff,\n we will call an unambiguous base at that position. If it is equal to or below\n this cutoff, we will call an ambiguous base representing all possible alleles at\n that position. [default: %(default)s]\"\"\"\n )\n parser.add_argument(\n '--novo_params',\n default='-r Random -l 40 -g 40 -x 20 -t 100',\n help='Alignment parameters for Novoalign.'\n )\n parser.add_argument(\n \"--chr_names\",\n dest=\"chr_names\",\n nargs=\"*\",\n help=\"Rename all output chromosomes (default: retain original chromosome names)\",\n default=[]\n )\n parser.add_argument(\n \"--keep_all_reads\",\n help=\"\"\"Retain all reads in BAM file? Default is to remove unaligned and duplicate reads.\"\"\",\n default=False,\n action=\"store_true\",\n dest=\"keep_all_reads\"\n )\n parser.add_argument(\n '--max_coverage',\n default=None,\n type=int,\n help=\"\"\"Maximum read coverage depth for variant calling. If specified,\n reads are downsampled to this coverage using rasusa before\n FreeBayes variant calling. The downsampled BAM is internal only\n and not included in any output. [default: %(default)s]\"\"\"\n )\n parser.add_argument(\n '--rasusa_seed',\n default=None,\n type=int,\n help=\"\"\"Random seed for rasusa downsampling reproducibility.\n Only used when --max_coverage is set. [default: %(default)s]\"\"\"\n )\n parser.add_argument(\n '--JVMmemory',\n default='2g',\n help='JVM virtual memory size for Picard/Novoalign (default: %(default)s)'\n )\n parser.add_argument(\n '--NOVOALIGN_LICENSE_PATH',\n default=None,\n dest=\"novoalign_license_path\",\n help='A path to the novoalign.lic file. This overrides the NOVOALIGN_LICENSE_PATH environment variable. (default: %(default)s)'\n )\n viral_ngs.core.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, refine_assembly, split_args=True)\n return parser\n\n\n__commands__.append(('refine_assembly', parser_refine_assembly))\n\n\ndef normalize_coverage(inBam, outBam, max_coverage, seed=None, threads=None):\n '''Downsample an aligned BAM to a maximum coverage depth using rasusa.\n The output BAM is coordinate-sorted and indexed.\n '''\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n rasusa_tool = viral_ngs.assemble.rasusa.RasusaTool()\n\n with viral_ngs.core.file.tempfname('.rasusa.unsorted.bam') as tmpBam:\n rasusa_tool.downsample_bam(inBam, tmpBam, max_coverage, seed=seed)\n samtools.sort(tmpBam, outBam, threads=threads)\n\n samtools.index(outBam, threads=threads)\n return outBam\n\n\ndef parser_normalize_coverage(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input aligned BAM file, coordinate-sorted.')\n parser.add_argument('outBam', help='Output downsampled BAM file, coordinate-sorted and indexed.')\n parser.add_argument('max_coverage', type=int, help='Maximum coverage depth to downsample to.')\n parser.add_argument(\n '--seed',\n default=None,\n type=int,\n help='Random seed for rasusa reproducibility. [default: %(default)s]'\n )\n viral_ngs.core.cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, normalize_coverage, split_args=True)\n return parser\n\n\n__commands__.append(('normalize_coverage', parser_normalize_coverage))\n\n\ndef parser_filter_short_seqs(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inFile\", help=\"input sequence file\")\n parser.add_argument(\"minLength\", help=\"minimum length for contig\", type=int)\n parser.add_argument(\"minUnambig\", help=\"minimum percentage unambiguous bases for contig\", type=float)\n parser.add_argument(\"outFile\", help=\"output file\")\n parser.add_argument(\"-f\", \"--format\", help=\"Format for input sequence (default: %(default)s)\", default=\"fasta\")\n parser.add_argument(\n \"-of\", \"--output-format\",\n help=\"Format for output sequence (default: %(default)s)\",\n default=\"fasta\"\n )\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None)))\n viral_ngs.core.cmd.attach_main(parser, main_filter_short_seqs)\n return parser\n\n\ndef main_filter_short_seqs(args):\n '''Check sequences in inFile, retaining only those that are at least minLength'''\n # orig by rsealfon, edited by dpark\n # TO DO: make this more generalized to accept multiple minLengths (for multiple chromosomes/segments)\n with viral_ngs.core.file.open_or_gzopen(args.inFile) as inf:\n with viral_ngs.core.file.open_or_gzopen(args.outFile, 'w') as outf:\n Bio.SeqIO.write(\n [\n s for s in Bio.SeqIO.parse(inf, args.format)\n if len(s) >= args.minLength and viral_ngs.core.misc.unambig_count(s.seq) >= len(s) * args.minUnambig\n ], outf, args.output_format\n )\n return 0\n\n\n__commands__.append(('filter_short_seqs', parser_filter_short_seqs))\n\n\ndef parser_modify_contig(parser=argparse.ArgumentParser()):\n parser.add_argument(\"input\", help=\"input alignment of reference and contig (should contain exactly 2 sequences)\")\n parser.add_argument(\"output\", help=\"Destination file for modified contigs\")\n parser.add_argument(\"ref\", help=\"reference sequence name (exact match required)\")\n parser.add_argument(\n \"-n\", \"--name\",\n type=str, help=\"fasta header output name (default: existing header)\",\n default=None\n )\n parser.add_argument(\n \"-cn\",\n \"--call-reference-ns\",\n help=\"\"\"should the reference sequence be called if there is an\n N in the contig and a more specific base in the reference (default: %(default)s)\"\"\",\n default=False,\n action=\"store_true\",\n dest=\"call_reference_ns\"\n )\n parser.add_argument(\n \"-t\",\n \"--trim-ends\",\n help=\"should ends of contig.fasta be trimmed to length of reference (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"trim_ends\"\n )\n parser.add_argument(\n \"-r5\",\n \"--replace-5ends\",\n help=\"should the 5'-end of contig.fasta be replaced by reference (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"replace_5ends\"\n )\n parser.add_argument(\n \"-r3\",\n \"--replace-3ends\",\n help=\"should the 3'-end of contig.fasta be replaced by reference (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"replace_3ends\"\n )\n parser.add_argument(\n \"-l\",\n \"--replace-length\",\n help=\"length of ends to be replaced (if replace-ends is yes) (default: %(default)s)\",\n default=10,\n type=int\n )\n parser.add_argument(\"-f\", \"--format\", help=\"Format for input alignment (default: %(default)s)\", default=\"fasta\")\n parser.add_argument(\n \"-r\",\n \"--replace-end-gaps\",\n help=\"Replace gaps at the beginning and end of the sequence with reference sequence (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"replace_end_gaps\"\n )\n parser.add_argument(\n \"-rn\",\n \"--remove-end-ns\",\n help=\"Remove leading and trailing N's in the contig (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"remove_end_ns\"\n )\n parser.add_argument(\n \"-ca\",\n \"--call-reference-ambiguous\",\n help=\"\"\"should the reference sequence be called if the contig seq is ambiguous and\n the reference sequence is more informative & consistant with the ambiguous base\n (ie Y->C) (default: %(default)s)\"\"\",\n default=False,\n action=\"store_true\",\n dest=\"call_reference_ambiguous\"\n )\n viral_ngs.core.cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n viral_ngs.core.cmd.attach_main(parser, main_modify_contig)\n return parser\n\n\ndef main_modify_contig(args):\n ''' Modifies an input contig. Depending on the options\n selected, can replace N calls with reference calls, replace ambiguous\n calls with reference calls, trim to the length of the reference, replace\n contig ends with reference calls, and trim leading and trailing Ns.\n Author: rsealfon.\n '''\n aln = Bio.AlignIO.read(args.input, args.format)\n\n # TODO?: take list of alignments in, one per chromosome, rather than\n # single alignment\n\n if len(aln) != 2:\n raise Exception(\"alignment does not contain exactly 2 sequences, %s found\" % len(aln))\n elif aln[0].name == args.ref:\n ref_idx = 0\n consensus_idx = 1\n elif aln[1].name == args.ref:\n ref_idx = 1\n consensus_idx = 0\n else:\n raise NameError(\"reference name '%s' not in alignment\" % args.ref)\n\n mc = ContigModifier(str(aln[ref_idx].seq), str(aln[consensus_idx].seq))\n if args.remove_end_ns:\n mc.remove_end_ns()\n if args.call_reference_ns:\n mc.call_reference_ns()\n if args.call_reference_ambiguous:\n mc.call_reference_ambiguous()\n if args.trim_ends:\n mc.trim_ends()\n if args.replace_end_gaps:\n mc.replace_end_gaps()\n if args.replace_5ends:\n mc.replace_5ends(args.replace_length)\n if args.replace_3ends:\n mc.replace_3ends(args.replace_length)\n\n with open(args.output, \"wt\") as f:\n if hasattr(args, \"name\"):\n name = args.name\n else:\n name = aln[consensus_idx].name\n for line in viral_ngs.core.file.fastaMaker([(name, mc.get_stripped_consensus())]):\n f.write(line)\n return 0\n\n\n__commands__.append(('modify_contig', parser_modify_contig))\n\n\nclass ContigModifier(object):\n ''' Initial modifications to spades+MUMmer assembly output based on\n MUSCLE alignment to known reference genome\n author: rsealfon\n '''\n\n def __init__(self, ref, consensus):\n if len(ref) != len(consensus):\n raise Exception(\"improper alignment\")\n self.ref = list(ref)\n self.consensus = list(consensus)\n self.len = len(ref)\n\n def get_stripped_consensus(self):\n return ''.join(self.consensus).replace('-', '')\n\n def call_reference_ns(self):\n log.debug(\"populating N's from reference...\")\n for i in range(self.len):\n if self.consensus[i].upper() == \"N\":\n self.consensus[i] = self.ref[i]\n\n def call_reference_ambiguous(self):\n ''' This is not normally used by default in our pipeline '''\n log.debug(\"populating ambiguous bases from reference...\")\n for i in range(self.len):\n if self.ref[i].upper() in Bio.Data.IUPACData.ambiguous_dna_values.get(self.consensus[i].upper(), []):\n self.consensus[i] = self.ref[i]\n\n def trim_ends(self):\n ''' This trims down the consensus so it cannot go beyond the given reference genome '''\n log.debug(\"trimming ends...\")\n for end_iterator in (range(self.len), reversed(range(self.len))):\n for i in end_iterator:\n if self.ref[i] != \"-\":\n break\n else:\n self.consensus[i] = \"-\"\n\n def replace_end_gaps(self):\n ''' This fills out the ends of the consensus with reference sequence '''\n log.debug(\"populating leading and trailing gaps from reference...\")\n for end_iterator in (range(self.len), reversed(range(self.len))):\n for i in end_iterator:\n if self.consensus[i] != \"-\":\n break\n self.consensus[i] = self.ref[i]\n\n def replace_5ends(self, replace_length):\n ''' This replaces everything within of the ends of the\n reference genome with the reference genome.\n '''\n log.debug(\"replacing 5' ends...\")\n ct = 0\n for i in range(self.len):\n if self.ref[i] != \"-\":\n ct = ct + 1\n if ct == replace_length:\n for j in range(i + 1):\n self.consensus[j] = self.ref[j]\n break\n\n def replace_3ends(self, replace_length):\n log.debug(\"replacing 3' ends...\")\n ct = 0\n for i in reversed(range(self.len)):\n if self.ref[i] != \"-\":\n ct = ct + 1\n if ct == replace_length:\n for j in range(i, self.len):\n self.consensus[j] = self.ref[j]\n break\n\n def remove_end_ns(self):\n ''' This clips off any N's that begin or end the consensus.\n Not normally used in our pipeline\n '''\n log.debug(\"removing leading and trailing N's...\")\n for end_iterator in (range(self.len), reversed(range(self.len))):\n for i in end_iterator:\n if (self.consensus[i].upper() == \"N\" or self.consensus[i] == \"-\"):\n self.consensus[i] = \"-\"\n else:\n break\n\n\nclass MutableSequence(object):\n\n def __init__(self, name, start, stop, init_seq=None):\n if not (stop >= start >= 1):\n raise IndexError(\"coords out of bounds\")\n if init_seq is None:\n self.seq = list('N' * (stop - start + 1))\n else:\n self.seq = list(init_seq)\n if stop - start + 1 != len(self.seq):\n raise Exception(\"wrong length\")\n self.start = start\n self.stop = stop\n self.name = name\n self.deletions = []\n\n def modify(self, p, new_base):\n if not (self.start <= p <= self.stop):\n raise IndexError(\"position out of bounds\")\n i = p - self.start\n self.seq[i] = new_base\n\n def replace(self, start, stop, new_seq):\n if stop > start:\n self.deletions.append((start, stop, new_seq))\n self.__change__(start, stop, new_seq)\n\n def __change__(self, start, stop, new_seq):\n if not (self.start <= start <= stop <= self.stop):\n raise IndexError(\"positions out of bounds\")\n start -= self.start\n stop -= self.start\n if start == stop:\n self.seq[start] = new_seq\n for i in range(max(stop - start + 1, len(new_seq))):\n if start + i <= stop:\n if i < len(new_seq):\n if start + i == stop:\n # new allele is >= ref length, fill out the rest of the bases\n self.seq[start + i] = new_seq[i:]\n else:\n self.seq[start + i] = new_seq[i]\n else:\n # new allele is shorter than ref, so delete extra bases\n self.seq[start + i] = ''\n\n def replay_deletions(self):\n for start, stop, new_seq in self.deletions:\n self.__change__(start, stop, new_seq)\n\n def emit(self):\n return (self.name, ''.join(self.seq))\n\n\ndef alleles_to_ambiguity(allelelist):\n ''' Convert a list of DNA bases to a single ambiguity base.\n All alleles must be one base long. '''\n for a in allelelist:\n if len(a) != 1:\n raise Exception(\"all alleles must be one base long\")\n if len(allelelist) == 1:\n return allelelist[0]\n else:\n convert = dict([(tuple(sorted(v)), k) for k, v in Bio.Data.IUPACData.ambiguous_dna_values.items() if k != 'X'])\n key = tuple(sorted(set(a.upper() for a in allelelist)))\n return convert[key]\n\n\ndef vcfrow_parse_and_call_snps(vcfrow, samples, min_dp=0, major_cutoff=0.5, min_dp_ratio=0.0):\n ''' Parse a single row of a VCF file, emit an iterator over each sample,\n call SNP genotypes using custom viral method based on read counts.\n '''\n # process this row\n c = vcfrow[0]\n alleles = [vcfrow[3]] + [a for a in vcfrow[4].split(',') if a not in '.']\n start = int(vcfrow[1])\n stop = start + len(vcfrow[3]) - 1\n format_col = vcfrow[8].split(':')\n format_col = dict((format_col[i], i) for i in range(len(format_col)))\n assert 'GT' in format_col and format_col['GT'] == 0 # required by VCF spec\n assert len(vcfrow) == 9 + len(samples)\n info = [x.split('=') for x in vcfrow[7].split(';') if x != '.']\n info = dict(x for x in info if len(x) == 2)\n info_dp = int(info.get('DP', 0))\n\n # process each sample\n for i in range(len(samples)):\n sample = samples[i]\n rec = vcfrow[i + 9].split(':')\n\n # require a minimum read coverage\n if len(alleles) == 1:\n # simple invariant case\n dp = ('DP' in format_col and len(rec) > format_col['DP']) and int(rec[format_col['DP']]) or 0\n if dp < min_dp:\n continue\n geno = alleles\n if info_dp and float(dp) / info_dp < min_dp_ratio:\n log.warning(\n \"dropping invariant call at %s:%s-%s %s (%s) due to low DP ratio (%s / %s = %s < %s)\", c, start,\n stop, sample, geno, dp, info_dp, float(dp) / info_dp, min_dp_ratio\n )\n continue\n else:\n # variant: manually call the highest read count allele if it exceeds a threshold\n assert ('AD' in format_col and len(rec) > format_col['AD'])\n allele_depths = list(map(int, rec[format_col['AD']].split(',')))\n assert len(allele_depths) == len(alleles)\n allele_depths = [(allele_depths[i], alleles[i]) for i in range(len(alleles)) if allele_depths[i] > 0]\n allele_depths = list(reversed(sorted((n, a) for n, a in allele_depths if n >= min_dp)))\n if not allele_depths:\n continue\n dp = sum(n for n, a in allele_depths)\n\n if allele_depths[0][0] > (dp * major_cutoff):\n # call a single allele at this position if it is a clear winner\n geno = [allele_depths[0][1]]\n else:\n # call multiple alleles at this position if there is no clear winner\n geno = [a for _, a in allele_depths]\n if geno:\n yield (c, start, stop, sample, geno)\n\n\ndef vcf_to_seqs(vcfIter, chrlens, samples, min_dp=0, major_cutoff=0.5, min_dp_ratio=0.0):\n ''' Take a VCF iterator and produce an iterator of chromosome x sample full sequences.'''\n seqs = {}\n cur_c = None\n for vcfrow in vcfIter:\n try:\n for c, start, stop, s, alleles in vcfrow_parse_and_call_snps(\n vcfrow, samples, min_dp=min_dp,\n major_cutoff=major_cutoff,\n min_dp_ratio=min_dp_ratio\n ):\n # changing chromosome?\n if c != cur_c:\n if cur_c is not None:\n # dump the previous chromosome before starting a new one\n for s in samples:\n seqs[s].replay_deletions() # because of the order of VCF rows with indels\n yield seqs[s].emit()\n\n # prepare base sequences for this chromosome\n cur_c = c\n for s in samples:\n name = len(samples) > 1 and (\"%s-%s\" % (c, s)) or c\n seqs[s] = MutableSequence(name, 1, chrlens[c])\n\n # modify sequence for this chromosome/sample/position\n if len(alleles) == 1:\n # call a single allele\n seqs[s].replace(start, stop, alleles[0])\n elif all(len(a) == 1 for a in alleles):\n # call an ambiguous SNP\n seqs[s].replace(start, stop, alleles_to_ambiguity(alleles))\n else:\n # mix of indels with no clear winner... force the most popular one\n seqs[s].replace(start, stop, alleles[0])\n except:\n log.exception(\"Exception occurred while parsing VCF file. Row: '%s'\", vcfrow)\n raise\n\n # at the end, dump the last chromosome\n if cur_c is not None:\n for s in samples:\n seqs[s].replay_deletions() # because of the order of VCF rows with indels\n yield seqs[s].emit()\n\n\ndef parser_vcf_to_fasta(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inVcf\", help=\"Input VCF file\")\n parser.add_argument(\"outFasta\", help=\"Output FASTA file\")\n parser.add_argument(\n \"--trim_ends\",\n action=\"store_true\",\n dest=\"trim_ends\",\n default=False,\n help=\"\"\"If specified, we will strip off continuous runs of N's from the beginning\n and end of the sequences before writing to output. Interior N's will not be\n changed.\"\"\"\n )\n parser.add_argument(\n \"--min_coverage\",\n dest=\"min_dp\",\n type=int,\n help=\"\"\"Specify minimum read coverage (with full agreement) to make a call.\n [default: %(default)s]\"\"\",\n default=3\n )\n parser.add_argument(\n \"--major_cutoff\",\n dest=\"major_cutoff\",\n type=float,\n help=\"\"\"If the major allele is present at a frequency higher than this cutoff,\n we will call an unambiguous base at that position. If it is equal to or below\n this cutoff, we will call an ambiguous base representing all possible alleles at\n that position. [default: %(default)s]\"\"\",\n default=0.5\n )\n parser.add_argument(\n \"--min_dp_ratio\",\n dest=\"min_dp_ratio\",\n type=float,\n help=\"\"\"The input VCF file often reports two read depth values (DP)--one for\n the position as a whole, and one for the sample in question. We can optionally\n reject calls in which the sample read count is below a specified fraction of the\n total read count. This filter will not apply to any sites unless both DP values\n are reported. [default: %(default)s]\"\"\",\n default=0.0\n )\n parser.add_argument(\n \"--name\",\n dest=\"name\",\n nargs=\"*\",\n help=\"output sequence names (default: reference names in VCF file)\",\n default=[]\n )\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None)))\n viral_ngs.core.cmd.attach_main(parser, main_vcf_to_fasta)\n return parser\n\n\ndef main_vcf_to_fasta(args):\n ''' Take input genotypes (VCF) and construct a consensus sequence\n (fasta) by using majority-read-count alleles in the VCF.\n Genotypes in the VCF will be ignored--we will use the allele\n with majority read support (or an ambiguity base if there is no clear majority).\n Uncalled positions will be emitted as N's.\n Author: dpark.\n '''\n assert args.min_dp >= 0\n assert 0.0 <= args.major_cutoff < 1.0\n\n with viral_ngs.assemble.vcf.VcfReader(args.inVcf) as vcf:\n chrlens = dict(vcf.chrlens())\n samples = vcf.samples()\n\n assert len(\n samples\n ) == 1, \"\"\"Multiple sample columns were found in the intermediary VCF file\n of the refine_assembly step, suggesting multiple sample names are present\n upstream in the BAM file. Please correct this so there is only one sample in the BAM file.\"\"\"\n\n with open(args.outFasta, 'wt') as outf:\n chr_idx = 0\n for chr_idx, (header, seq) in enumerate(\n vcf_to_seqs(\n viral_ngs.core.file.read_tabfile(args.inVcf),\n chrlens,\n samples,\n min_dp=args.min_dp,\n major_cutoff=args.major_cutoff,\n min_dp_ratio=args.min_dp_ratio\n )\n ):\n if args.trim_ends:\n seq = seq.strip('Nn')\n if args.name:\n header = args.name[chr_idx % len(args.name)]\n for line in viral_ngs.core.file.fastaMaker([(header, seq)]):\n outf.write(line)\n\n # done\n log.info(\"done\")\n return 0\n\n\n__commands__.append(('vcf_to_fasta', parser_vcf_to_fasta))\n\n\ndef parser_trim_fasta(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inFasta\", help=\"Input fasta file\")\n parser.add_argument(\"outFasta\", help=\"Output (trimmed) fasta file\")\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None)))\n viral_ngs.core.cmd.attach_main(parser, trim_fasta, split_args=True)\n return parser\n\n\ndef trim_fasta(inFasta, outFasta):\n ''' Take input sequences (fasta) and trim any continuous sections of\n N's from the ends of them. Write trimmed sequences to an output fasta file.\n '''\n with open(outFasta, 'wt') as outf:\n with open(inFasta, 'rt') as inf:\n for record in Bio.SeqIO.parse(inf, 'fasta'):\n for line in viral_ngs.core.file.fastaMaker([(record.id, str(record.seq).strip('Nn'))]):\n outf.write(line)\n log.info(\"done\")\n return 0\n\n\n__commands__.append(('trim_fasta', parser_trim_fasta))\n\n\ndef deambig_base(base):\n ''' Take a single base (possibly a IUPAC ambiguity code) and return a random\n non-ambiguous base from among the possibilities '''\n return random.choice(Bio.Data.IUPACData.ambiguous_dna_values[base.upper()])\n\n\ndef deambig_fasta(inFasta, outFasta):\n ''' Take input sequences (fasta) and replace any ambiguity bases with a\n random unambiguous base from among the possibilities described by the ambiguity\n code. Write output to fasta file.\n '''\n with viral_ngs.core.file.open_or_gzopen(outFasta, 'wt') as outf:\n with viral_ngs.core.file.open_or_gzopen(inFasta, 'rt') as inf:\n for record in Bio.SeqIO.parse(inf, 'fasta'):\n for line in viral_ngs.core.file.fastaMaker([(record.id, ''.join(map(deambig_base, str(record.seq))))]):\n outf.write(line)\n return 0\n\n\ndef parser_deambig_fasta(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inFasta\", help=\"Input fasta file\")\n parser.add_argument(\"outFasta\", help=\"Output fasta file\")\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None)))\n viral_ngs.core.cmd.attach_main(parser, deambig_fasta, split_args=True)\n return parser\n\n\n__commands__.append(('deambig_fasta', parser_deambig_fasta))\n\n\ndef vcf_dpdiff(vcfs):\n for vcf in vcfs:\n with viral_ngs.assemble.vcf.VcfReader(vcf) as v:\n samples = v.samples()\n assert len(samples) == 1\n for row in viral_ngs.core.file.read_tabfile(vcf):\n dp1 = int(dict(x.split('=') for x in row[7].split(';') if x != '.').get('DP', 0))\n dp2 = 0\n if 'DP' in row[8].split(':'):\n dpidx = row[8].split(':').index('DP')\n if len(row[9].split(':')) > dpidx:\n dp2 = int(row[9].split(':')[dpidx])\n ratio = ''\n if dp1:\n ratio = float(dp2) / dp1\n yield (row[0], row[1], samples[0], dp1, dp2, dp1 - dp2, ratio)\n\n\ndef parser_dpdiff(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inVcfs\", help=\"Input VCF file\", nargs='+')\n parser.add_argument(\"outFile\", help=\"Output flat file\")\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None)))\n viral_ngs.core.cmd.attach_main(parser, dpdiff, split_args=True)\n return parser\n\n\ndef dpdiff(inVcfs, outFile):\n ''' Take input VCF files (all with only one sample each) and report\n on the discrepancies between the two DP fields (one in INFO and one in the\n sample's genotype column).\n '''\n header = ['chr', 'pos', 'sample', 'dp_info', 'dp_sample', 'diff', 'ratio']\n with open(outFile, 'wt') as outf:\n outf.write('#' + '\\t'.join(header) + '\\n')\n for row in vcf_dpdiff(inVcfs):\n outf.write('\\t'.join(map(str, row)) + '\\n')\n return 0\n\n\n#__commands__.append(('dpdiff', parser_dpdiff))\n\n\n\ndef alignment_summary(inFastaFileOne, inFastaFileTwo, outfileName=None, printCounts=False):\n \"\"\" Write or print pairwise alignment summary information for sequences in two FASTA\n files, including SNPs, ambiguous bases, and indels.\n \"\"\"\n gap = '-'\n ambiguous = 'N'\n unambiguous = set(list(\"GATCgatc\"))\n aligner = viral_ngs.assemble.muscle.MuscleTool()\n\n per_chr_fastas = viral_ngs.core.file.transposeChromosomeFiles([inFastaFileOne, inFastaFileTwo])\n\n results = OrderedDict()\n results[\"same_unambig\"] = 0\n results[\"snp_unambig\"] = 0\n results[\"indel_unambig\"] = 0\n results[\"indel_ambig\"] = 0\n results[\"ambig_one\"] = 0\n results[\"ambig_two\"] = 0\n results[\"ambig_both\"] = 0\n results[\"unambig_both\"] = 0\n\n for chr_fasta in per_chr_fastas:\n same_unambig = 0\n snp_unambig = 0\n indel_unambig = 0\n indel_ambig = 0\n ambig_one = 0\n ambig_two = 0\n ambig_both = 0\n unambig_both = 0\n\n alignOutFileName = viral_ngs.core.file.mkstempfname('.fasta')\n aligner.execute(chr_fasta, alignOutFileName, fmt=\"clw\")\n\n with open(alignOutFileName, \"r\") as f:\n alignment = Bio.AlignIO.read(f, \"clustal\")\n\n for col_idx in range(0, alignment.get_alignment_length()):\n col = alignment[:, col_idx]\n c1 = col[0]\n c2 = col[1]\n\n if (c1 in ambiguous\n and c2 in ambiguous):\n ambig_both +=1\n elif c1 in ambiguous:\n ambig_one += 1\n elif c2 in ambiguous:\n ambig_two += 1\n\n if (c1 in unambiguous\n and c2 in unambiguous):\n unambig_both += 1\n if c1 == c2:\n same_unambig += 1\n else:\n snp_unambig += 1\n\n if ((c1 == gap and\n c2 in unambiguous) or\n (c2 == gap and\n c1 in unambiguous)):\n indel_unambig += 1\n\n if ((c1 == gap and\n c2 in ambiguous) or\n (c2 == gap and\n c1 in ambiguous)):\n indel_ambig += 1\n\n if printCounts:\n print(\"Counts for this segment/chromosome:\")\n print(\"same_unambig \", same_unambig)\n print(\"snp_unambig \", snp_unambig)\n print(\"indel_unambig\", indel_unambig)\n print(\"indel_ambig \", indel_ambig)\n print(\"ambig_one \", ambig_one)\n print(\"ambig_two \", ambig_two)\n print(\"ambig_both \", ambig_both)\n print(\"unambig_both \", unambig_both)\n\n results[\"same_unambig\"] += same_unambig\n results[\"snp_unambig\"] += snp_unambig\n results[\"indel_unambig\"] += indel_unambig\n results[\"indel_ambig\"] += indel_ambig\n results[\"ambig_one\"] += ambig_one\n results[\"ambig_two\"] += ambig_two\n results[\"ambig_both\"] += ambig_both\n results[\"unambig_both\"] += unambig_both\n\n if printCounts:\n print(\"\\nCounts for this sample:\")\n print(\"same_unambig \", results[\"same_unambig\"])\n print(\"snp_unambig \", results[\"snp_unambig\"])\n print(\"indel_unambig\", results[\"indel_unambig\"])\n print(\"indel_ambig \", results[\"indel_ambig\"])\n print(\"ambig_one \", results[\"ambig_one\"])\n print(\"ambig_two \", results[\"ambig_two\"])\n print(\"ambig_both \", results[\"ambig_both\"])\n print(\"unambig_both \", results[\"unambig_both\"])\n\n if outfileName:\n with open(outfileName, \"wt\") as of:\n csvout = csv.writer(of, delimiter='\\t')\n csvout.writerow(list(results.keys()))\n csvout.writerow(list(results.values()))\n\ndef parser_alignment_summary(parser=argparse.ArgumentParser()):\n parser.add_argument('inFastaFileOne', help='First fasta file for an alignment')\n parser.add_argument('inFastaFileTwo', help='First fasta file for an alignment')\n parser.add_argument('--outfileName', help='Output file for counts in TSV format')\n parser.add_argument('--printCounts', help='', action='store_true')\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, alignment_summary, split_args=True)\n return parser\n__commands__.append(('alignment_summary', parser_alignment_summary))\n\n\ndef simulate_illumina_reads(\n in_fasta, out_bam, coverage,\n read_length=150, outer_distance=500, error_rate=0.02,\n mutation_rate=0.001, indel_fraction=0.15, indel_extended_prob=0.3,\n random_seed=None, sample_name='sample', library_name='lib1'\n):\n ''' Simulate Illumina paired-end reads using wgsim.\n\n Args:\n in_fasta: Input reference fasta file\n out_bam: Output unaligned BAM file\n coverage: Coverage specification in one of three formats:\n 1. Single float value (e.g., 20.0) for uniform coverage across all sequences\n 2. Space-separated string with per-sequence depths (e.g., \"chr1:20x chr2:2x\")\n 3. Path to BED file with 5th column containing depth values\n read_length: Length of each simulated read (default: 150)\n outer_distance: Outer distance between read pairs (default: 500)\n error_rate: Base error rate (default: 0.02)\n mutation_rate: Mutation rate (default: 0.001)\n indel_fraction: Fraction of errors that are indels (default: 0.15)\n indel_extended_prob: Probability an indel is extended (default: 0.3)\n random_seed: Random seed for reproducibility\n sample_name: Sample name for read group\n library_name: Library name for read group\n '''\n wgsim = viral_ngs.assemble.wgsim.WgsimTool()\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n # Parse coverage specification into normalized format:\n # coverage_map[seq_id] = [(start, end, depth), ...]\n # where start/end are None to indicate whole sequence\n coverage_map = {}\n\n # Check if coverage is a path to a BED file\n if os.path.exists(str(coverage)):\n # Parse BED file (5th column is depth)\n with open(coverage, 'r') as f:\n for line in f:\n if line.startswith('#') or not line.strip():\n continue\n fields = line.strip().split('\\t')\n if len(fields) < 5:\n raise ValueError(f\"BED file must have at least 5 columns, found {len(fields)}\")\n seq_id = fields[0]\n start = int(fields[1]) + 1 # BED is 0-based, convert to 1-based\n end = int(fields[2]) # BED end is exclusive, so this is correct for 1-based inclusive\n depth = float(fields[4].rstrip('xX'))\n if seq_id not in coverage_map:\n coverage_map[seq_id] = []\n coverage_map[seq_id].append((start, end, depth))\n elif isinstance(coverage, str) and (':' in coverage or ' ' in coverage):\n # Parse per-sequence string format (e.g., \"chr1:20x chr2:2x\")\n for spec in coverage.split():\n if ':' in spec:\n seq_id, depth_str = spec.split(':', 1)\n depth = float(depth_str.rstrip('xX'))\n # Use None to indicate whole sequence\n coverage_map[seq_id] = [(None, None, depth)]\n else:\n # Single coverage value for all sequences\n try:\n uniform_depth = float(str(coverage).rstrip('xX'))\n # Read all sequence IDs from input fasta\n for record in Bio.SeqIO.parse(in_fasta, 'fasta'):\n # Use None to indicate whole sequence\n coverage_map[record.id] = [(None, None, uniform_depth)]\n except ValueError:\n raise ValueError(f\"Invalid coverage specification: {coverage}\")\n\n # Generate reads for each sequence/region\n temp_fastqs = []\n for record in Bio.SeqIO.parse(in_fasta, 'fasta'):\n seq_id = record.id\n seq_len = len(record.seq)\n\n if seq_id not in coverage_map:\n continue\n\n # Process all regions for this sequence\n for start, end, depth in coverage_map[seq_id]:\n if depth == 0:\n continue\n\n # Use whole sequence if start/end are None\n region_start = start if start is not None else 1\n region_end = end if end is not None else seq_len\n region_len = region_end - region_start + 1\n\n num_pairs = wgsim.coverage_to_read_pairs(depth, region_len, read_length)\n\n # Slice fasta to region (will be no-op if region is whole sequence)\n region_fasta = viral_ngs.core.file.mkstempfname('.region.fasta')\n wgsim.slice_fasta(in_fasta, region_fasta, seq_id, start, end)\n\n # Generate reads for this region\n fq1 = viral_ngs.core.file.mkstempfname('.1.fastq')\n fq2 = viral_ngs.core.file.mkstempfname('.2.fastq')\n wgsim.execute(\n region_fasta, fq1, fq2,\n read_length=read_length,\n outer_distance=outer_distance,\n error_rate=error_rate,\n mutation_rate=mutation_rate,\n indel_fraction=indel_fraction,\n indel_extended_prob=indel_extended_prob,\n num_read_pairs=num_pairs,\n random_seed=random_seed\n )\n temp_fastqs.append((fq1, fq2))\n\n # Merge all fastq files\n if not temp_fastqs:\n raise ValueError(\"No reads generated - check coverage specification matches sequences in fasta\")\n\n merged_fq1 = viral_ngs.core.file.mkstempfname('.merged.1.fastq')\n merged_fq2 = viral_ngs.core.file.mkstempfname('.merged.2.fastq')\n\n with open(merged_fq1, 'wb') as outf:\n for fq1, _ in temp_fastqs:\n with open(fq1, 'rb') as inf:\n shutil.copyfileobj(inf, outf)\n\n with open(merged_fq2, 'wb') as outf:\n for _, fq2 in temp_fastqs:\n with open(fq2, 'rb') as inf:\n shutil.copyfileobj(inf, outf)\n\n # Convert to BAM with proper read group headers\n wgsim.fastqs_to_bam(\n merged_fq1, merged_fq2, out_bam,\n sample_name=sample_name,\n library_name=library_name\n )\n\ndef parser_simulate_illumina_reads(parser=argparse.ArgumentParser()):\n parser.add_argument('in_fasta', help='Input reference genome (fasta format)')\n parser.add_argument('out_bam', help='Output unaligned BAM file')\n parser.add_argument(\n 'coverage',\n help='''Coverage specification in one of three formats:\n 1) Single value (e.g., \"20\" for 20X across all sequences)\n 2) Per-sequence string (e.g., \"chr1:20x chr2:2x chr3:0.48x\")\n 3) Path to BED file where 5th column contains depth values'''\n )\n parser.add_argument('--read_length', type=int, default=150, help='Length of each read (default: %(default)s)')\n parser.add_argument('--outer_distance', type=int, default=500, help='Outer distance between read pairs (default: %(default)s)')\n parser.add_argument('--error_rate', type=float, default=0.02, help='Base error rate (default: %(default)s)')\n parser.add_argument('--mutation_rate', type=float, default=0.001, help='Mutation rate (default: %(default)s)')\n parser.add_argument('--indel_fraction', type=float, default=0.15, help='Fraction of errors that are indels (default: %(default)s)')\n parser.add_argument('--indel_extended_prob', type=float, default=0.3, help='Probability an indel is extended (default: %(default)s)')\n parser.add_argument('--random_seed', type=int, default=None, help='Random seed for reproducibility (default: current time)')\n parser.add_argument('--sample_name', default='sample', help='Sample name for read group (default: %(default)s)')\n parser.add_argument('--library_name', default='lib1', help='Library name for read group (default: %(default)s)')\n viral_ngs.core.cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n viral_ngs.core.cmd.attach_main(parser, simulate_illumina_reads, split_args=True)\n return parser\n__commands__.append(('simulate_illumina_reads', parser_simulate_illumina_reads))\n\n\ndef full_parser():\n return viral_ngs.core.cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n viral_ngs.core.cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/broad_utils.py", "content": "#!/usr/bin/env python3\n\"\"\"\nUtilities for getting sequences out of the Broad walk-up sequencing pipeline.\nThese utilities are probably not of much use outside the Broad.\n\"\"\"\n\n__author__ = \"dpark@broadinstitute.org\"\n__commands__ = []\n\nimport argparse\nimport logging\nimport os\nimport os.path\nimport json\nimport glob\nfrom .core import file as util_file, misc as util_misc, cmd as util_cmd\n\nlog = logging.getLogger(__name__)\n\n# ==========================================\n# *** get stuff from Picard json file ***\n# ==========================================\n\n\ndef get_json_from_picard(picardDir):\n ''' for example, /seq/walkup/picard/{flowcell_minus_first_char} '''\n analysisDir = max(\n (os.path.getmtime(os.path.join(picardDir, d)), d) for d in os.listdir(picardDir)\n if os.path.isdir(os.path.join(picardDir, d)))[1]\n jsonfile = list(glob.glob(os.path.join(picardDir, analysisDir, 'info', 'logs', '*.json')))\n if len(jsonfile) != 1:\n raise Exception(\"error\")\n return jsonfile[0]\n\ndef get_run_date(jsonfile):\n with open(jsonfile, 'rt') as inf:\n runDate = json.load(inf)['workflow']['runDate']\n return runDate\n\ndef get_bustard_dir(jsonfile):\n with open(jsonfile, 'rt') as inf:\n bustard = json.load(inf)['workflow']['runFolder']\n return bustard\n\n\ndef parser_get_bustard_dir(parser=argparse.ArgumentParser()):\n parser.add_argument('inDir', help='Picard directory')\n util_cmd.common_args(parser, (('loglevel', 'ERROR'),))\n util_cmd.attach_main(parser, main_get_bustard_dir)\n return parser\ndef main_get_bustard_dir(args):\n 'Find the basecalls directory from a Picard directory'\n print(get_bustard_dir(get_json_from_picard(args.inDir)))\n return 0\n__commands__.append(('get_bustard_dir', parser_get_bustard_dir))\n\n\ndef parser_get_run_date(parser=argparse.ArgumentParser()):\n parser.add_argument('inDir', help='Picard directory')\n util_cmd.common_args(parser, (('loglevel', 'ERROR'),))\n util_cmd.attach_main(parser, main_get_run_date)\n return parser\ndef main_get_run_date(args):\n 'Find the sequencing run date from a Picard directory'\n print(get_run_date(get_json_from_picard(args.inDir)))\n return 0\n__commands__.append(('get_run_date', parser_get_run_date))\n\n\n# ===============\n# *** misc ***\n# ===============\n\ndef iterate_wells(runfile):\n for lane in util_file.read_tabfile_dict(runfile):\n for well in util_file.read_tabfile_dict(lane['barcode_file']):\n yield (lane, well)\n\n\ndef get_all_samples(runfile):\n return list(sorted(set(well['sample'] for lane, well in iterate_wells(runfile))))\n\n\ndef get_all_libraries(runfile):\n return list(sorted(set(well['sample'] + '.l' + well['library_id_per_sample'] for lane, well in iterate_wells(\n runfile))))\n\n\ndef get_run_id(well):\n run_id = well['sample']\n if well.get('library_id_per_sample'):\n run_id += '.l' + well['library_id_per_sample']\n if well.get('run_id_per_library'):\n run_id += '.r' + well['run_id_per_library']\n return run_id\n\n\ndef get_all_runs(runfile):\n return list(sorted(get_run_id(well) + '.' + lane['flowcell'] + '.' + lane['lane'] for lane, well in iterate_wells(\n runfile)))\n\n\ndef parser_get_all_names(parser=argparse.ArgumentParser()):\n parser.add_argument('type', help='Type of name', choices=['samples', 'libraries', 'runs'])\n parser.add_argument('runfile', help='File with seq run information')\n util_cmd.common_args(parser, (('loglevel', 'ERROR'),))\n util_cmd.attach_main(parser, main_get_all_names)\n return parser\ndef main_get_all_names(args):\n 'Get all samples'\n if args.type == 'samples':\n method = get_all_samples\n elif args.type == 'libraries':\n method = get_all_libraries\n elif args.type == 'runs':\n method = get_all_runs\n for s in method(args.runfile):\n print(s)\n return 0\n__commands__.append(('get_all_names', parser_get_all_names))\n\n\n# =======================\ndef full_parser():\n return util_cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n util_cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/classify/__init__.py", "content": "\"\"\"viral_ngs.classify - Metagenomic classification tools and utilities.\"\"\"\n\nfrom . import blast\nfrom . import bmtagger\nfrom . import kb\nfrom . import kma\nfrom . import kmc\nfrom . import kraken2\nfrom . import krona\nfrom . import last\nfrom . import taxonomy\n" }, { "path": "src/viral_ngs/classify/blast.py", "content": "\"Tools in the blast+ suite.\"\n\nimport logging\nimport os\nimport shutil\nimport subprocess\n\nfrom viral_ngs import core\nfrom viral_ngs.core import samtools\nfrom viral_ngs.core import misc\n\nTOOL_NAME = \"blastn\"\n\n'''\n#Creating task.log\nlogging.basicConfig(\n level=logging.DEBUG,\n format='%(asctime)s - %(levelname)s - %(message)s',\n handlers=[\n logging.FileHandler(\"blast_py.log\"), \n logging.StreamHandler() \n ]\n)\n'''\n_log = logging.getLogger(__name__)\n\nclass BlastTools(core.Tool):\n \"\"\"'Abstract' base class for tools in the blast+ suite.\n Subclasses must define class member subtool_name.\"\"\"\n\n def __init__(self, install_methods=None):\n unwanted = [\n 'blast_formatter', 'blastdb_aliastool', 'blastdbcheck', 'blastdbcmd', 'convert2blastmask', 'deltablast',\n 'legacy_blast.pl', 'makembindex', 'makeprofiledb', 'psiblast', 'rpsblast', 'rpstblastn', 'segmasker',\n 'tblastn', 'tblastx', 'update_blastdb.pl', 'windowmasker'\n ]\n self.subtool_name = self.subtool_name if hasattr(self, \"subtool_name\") else \"blastn\"\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand(shutil.which(self.subtool_name), require_executability=False)]\n super(BlastTools, self).__init__(install_methods=install_methods)\n\n def execute(self, *args):\n cmd = [self.install_and_get_path()]\n cmd.extend(args)\n misc.run_and_print(cmd, buffered=True, check=True)\n\n\nclass BlastnTool(BlastTools):\n \"\"\" Tool wrapper for blastn \"\"\"\n subtool_name = 'blastn'\n\n def get_hits_pipe(self, inPipe, db, threads=None, task=None, outfmt='6', max_target_seqs=1, output_type=\"read_id\"):\n _log.debug(f\"Executing get_hits_pipe function. Called with outfmt: {outfmt}\")\n #toggle between extracting read IDs only or full blast output (all lines)\n if output_type not in ['read_id', 'full_line']:\n _log.warning(f\"Invalid output_type '{output_type}' specified. Defaulting to 'read_id'.\")\n output_type = 'read_id'\n # run blastn and emit list of read IDs\n threads = misc.sanitize_thread_count(threads)\n cmd = [self.install_and_get_path(),\n '-db', db,\n '-word_size', 16,\n '-num_threads', threads,\n '-evalue', '1e-6',\n '-outfmt', str(outfmt),\n '-max_target_seqs', str(max_target_seqs),\n '-task', str(task) if task else 'blastn',\n ]\n cmd = [str(x) for x in cmd]\n #Log BLAST command executed\n _log.debug('Running blastn command: {}'.format(' '.join(cmd)))\n _log.debug('| ' + ' '.join(cmd) + ' |')\n blast_pipe = subprocess.Popen(cmd, stdin=inPipe, stdout=subprocess.PIPE)\n output, error = blast_pipe.communicate()\n\n #Display error message if BLAST failed\n if blast_pipe.returncode!= 0:\n _log.error('Error running blastn command: {}'.format(error))\n raise subprocess.CalledProcessError(blast_pipe.returncode, cmd)\n \n # If read_id is defined, strip tab output to just query read ID names and emit (default)\n last_read_id = None\n for line in output.decode('UTF-8').splitlines():\n if output_type == 'read_id':\n #Split line by tab, and take the first element\n read_id = line.split('\\t')[0]\n # Only emit if it is not a duplicate of the previous read ID\n if read_id != last_read_id:\n last_read_id = read_id\n yield read_id\n #Yield the full line without stripping whitespace\n elif output_type == 'full_line':\n yield line\n\n #Display on CMD if BLAST fails\n if blast_pipe.returncode!= 0:\n _log.error('Error running blastn command: {}'.format(error))\n raise subprocess.CalledProcessError(blast_pipe.returncode, cmd)\n #Logging configuration written to blast_py.log if BLAST passes/fails\n if blast_pipe.returncode == 0:\n _log.info(\"Blastn process completed succesfully.\")\n else:\n _log.error(\"Blastn process failed with exit code: %s\", blast_pipe.returncode)\n raise subprocess.CalledProcessError(blast_pipe.returncode, cmd)\n \n def get_hits_bam(self, inBam, db, threads=None):\n return self.get_hits_pipe(\n samtools.SamtoolsTool().bam2fa_pipe(inBam),\n db,\n threads=threads)\n\n def get_hits_fasta(self, inFasta, db, threads=None, task=None, outfmt='6', max_target_seqs=1, output_type='read_id'):\n _log.debug(f\"Executing get_hits_fasta function. Called with outfmt: {outfmt}\")\n with open(inFasta, 'rt') as inf:\n for hit in self.get_hits_pipe(inf, db, threads=threads, task=None, outfmt=outfmt, max_target_seqs=max_target_seqs, output_type=output_type):\n yield hit\n\n\nclass MakeblastdbTool(BlastTools):\n \"\"\" Tool wrapper for makeblastdb \"\"\"\n subtool_name = 'makeblastdb'\n\n def build_database(self, fasta_files, database_prefix_path):\n \"\"\" builds a srprism database \"\"\"\n\n input_fasta = \"\"\n\n # we can pass in a string containing a fasta file path\n # or a list of strings\n if 'basestring' not in globals():\n basestring = str\n if isinstance(fasta_files, basestring):\n fasta_files = [fasta_files]\n elif isinstance(fasta_files, list):\n pass\n else:\n raise TypeError(\"fasta_files was not a single fasta file, nor a list of fasta files\") # or something along that line\n\n # if more than one fasta file is specified, join them\n # otherwise if only one is specified, just use it\n if len(fasta_files) > 1:\n input_fasta = file.mkstempfname(\"fasta\")\n file.cat(input_fasta, fasta_files)\n elif len(fasta_files) == 1:\n input_fasta = fasta_files[0]\n else:\n raise IOError(\"No fasta file provided\")\n\n args = ['-dbtype', 'nucl', '-in', input_fasta, '-out', database_prefix_path]\n self.execute(*args)\n\n return database_prefix_path\n" }, { "path": "src/viral_ngs/classify/bmtagger.py", "content": "\"core.Tool for bmtagger.sh.\"\n\nfrom viral_ngs import core\nfrom viral_ngs.core import file\nimport os\nimport logging\nimport shutil\nimport subprocess\nfrom urllib.request import urlretrieve\n_log = logging.getLogger(__name__)\n\nTOOL_NAME = \"bmtagger\"\nTOOL_VERSION = \"3.101\"\n\n\nclass BmtaggerTools(core.Tool):\n '''\n \"Abstract\" base class for bmtagger.sh, bmfilter, extract_fullseq, srprism.\n Subclasses must define class member subtool_name.\n\n Note: bmtagger calls blastn so that must be installed somewhere in $PATH.\n\n WARNING: bmtagger.sh does not work with the version of getopt that ships\n with Mac OS X. This can be worked around by installing linux getopt\n using fink and assuring that /sw/bin comes before /usr/bin in $PATH.\n\n '''\n\n # subtool_name must be defined in subclass\n\n def __init__(self, install_methods=None):\n self.subtool_name = self.subtool_name if hasattr(self, \"subtool_name\") else \"bmtagger.sh\"\n if install_methods is None:\n install_methods = []\n install_methods = [core.PrexistingUnixCommand(shutil.which(self.subtool_name), require_executability=False)]\n core.Tool.__init__(self, install_methods=install_methods)\n\n def execute(self, *args):\n cmd = [self.install_and_get_path()]\n cmd.extend(args)\n subprocess.check_call(cmd)\n\n def silent_execute(self, *args):\n cmd = [self.install_and_get_path()]\n cmd.extend(args)\n with open(os.devnull, 'w') as fnull:\n subprocess.check_call(cmd, stderr=fnull)\n\n\nclass BmtaggerShTool(BmtaggerTools):\n \"\"\" tool wrapper for bmtagger \"\"\"\n subtool_name = 'bmtagger.sh'\n\n\nclass BmfilterTool(BmtaggerTools):\n \"\"\" tool wrapper for bmfilter \"\"\"\n subtool_name = 'bmfilter'\n\n\nclass BmtoolTool(BmtaggerTools):\n \"\"\" tool wrapper for bmtool \"\"\"\n subtool_name = 'bmtool'\n\n def build_database(self, fasta_files, bitmask_file_path, max_ambig=0, word_size=18):\n \"\"\" builds a bmtool database (*.bitmask file) \"\"\"\n\n input_fasta = \"\"\n\n # we can pass in a string containing a fasta file path\n # or a list of strings\n if 'basestring' not in globals():\n basestring = str\n if isinstance(fasta_files, basestring):\n fasta_files = [fasta_files]\n elif isinstance(fasta_files, list):\n pass\n else:\n raise TypeError(\"fasta_files was not a single fasta file, nor a list of fasta files\") # or something along that line\n\n # if more than one fasta file is specified, join them\n # otherwise if only one is specified, just use it\n if len(fasta_files) > 1:\n input_fasta = file.mkstempfname(\"fasta\")\n file.cat(input_fasta, fasta_files)\n elif len(fasta_files) == 1:\n input_fasta = fasta_files[0]\n else:\n raise IOError(\"No fasta file provided\")\n\n args = ['-d', input_fasta, '-o', bitmask_file_path, '-A', str(max_ambig), '-w', str(word_size)]\n self.silent_execute(*args)\n\n return bitmask_file_path\n\nclass ExtractFullseqTool(BmtaggerTools):\n \"\"\" tool wrapper for extract_fullseq \"\"\"\n subtool_name = 'extract_fullseq'\n\n\nclass SrprismTool(BmtaggerTools):\n \"\"\" tool wrapper for srprism \"\"\"\n subtool_name = 'srprism'\n\n def build_database(self, fasta_files, database_prefix_path):\n \"\"\" builds a srprism database \"\"\"\n\n input_fasta = \"\"\n\n # we can pass in a string containing a fasta file path\n # or a list of strings\n if 'basestring' not in globals():\n basestring = str\n if isinstance(fasta_files, basestring):\n fasta_files = [fasta_files]\n elif isinstance(fasta_files, list):\n pass\n else:\n raise TypeError(\"fasta_files was not a single fasta file, nor a list of fasta files\") # or something along that line\n\n # if more than one fasta file is specified, join them\n # otherwise if only one is specified, just use it\n if len(fasta_files) > 1:\n input_fasta = file.mkstempfname(\"fasta\")\n file.cat(input_fasta, fasta_files)\n elif len(fasta_files) == 1:\n input_fasta = fasta_files[0]\n else:\n raise IOError(\"No fasta file provided\")\n\n args = ['mkindex', '-i', input_fasta, '-o', database_prefix_path]\n self.execute(*args)\n\n return database_prefix_path\n" }, { "path": "src/viral_ngs/classify/kb.py", "content": "'''\nkb_python classification tool\n'''\nimport itertools\nimport glob\nimport logging\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport tarfile\n\nimport anndata\nimport pandas as pd\n\nfrom viral_ngs import core\nfrom viral_ngs.core import picard\nfrom viral_ngs.core import samtools\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nfrom builtins import super\n\nlog = logging.getLogger(__name__)\n\nclass kb(core.Tool):\n SUBCOMMANDS = ['count', 'ref', 'extract']\n\n def __init__(self, install_methods=None):\n if not install_methods:\n install_methods = []\n install_methods.append(core.PrexistingUnixCommand(shutil.which('kb'), require_executability=False))\n super(kb, self).__init__(install_methods=install_methods)\n\n def version(self):\n return '1'\n\n @property\n def libexec(self):\n if not self.executable_path():\n self.install_and_get_path()\n return os.path.dirname(self.executable_path())\n\n\n def execute(self, command,output, args=None, options=None):\n '''Run a kb * command.\n\n Args:\n command: Subcommand to run.\n input: Input file kb_python/kallisto operates on.\n output: Output file to send to command.\n args: List of positional args.\n options: List of keyword options. Values can be single items or lists for multi-value options.\n '''\n options = options or {}\n\n if output:\n options['-o'] = output\n args = args or []\n\n cmd = command.split()\n\n # Build options, handling both single values and lists\n for key, value in options.items():\n if value is None:\n # Empty flag like --aa\n cmd.append(key)\n elif isinstance(value, list):\n # Multi-value option like -ts target1 target2\n cmd.append(key)\n cmd.extend([str(v) for v in value])\n else:\n # Single value option\n cmd.extend([key, str(value)])\n \n cmd.extend(args)\n log.debug('Calling %s: %s', command, ' '.join(cmd))\n\n # Use Popen to capture both stdout and stderr for better error reporting\n process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)\n stdout, stderr = process.communicate()\n \n # Log output\n if stdout:\n log.info(\"kb output: %s\", stdout)\n if stderr:\n log.info(\"kb stderr: %s\", stderr)\n \n # Check for errors: kb_python sometimes catches exceptions without proper exit codes\n # Look for Python tracebacks or subprocess errors in stderr\n has_error = stderr and ('Traceback (most recent call last)' in stderr or 'CalledProcessError' in stderr)\n \n # Raise exception if command failed or error detected\n if process.returncode != 0 or has_error:\n error_msg = f\"Command failed with return code {process.returncode}: {' '.join(cmd)}\"\n if stderr:\n error_msg += f\"\\nStderr: {stderr}\"\n log.error(error_msg)\n raise subprocess.CalledProcessError(process.returncode if process.returncode != 0 else 1, cmd, output=stdout, stderr=stderr)\n \n def build(self, ref_fasta, index, workflow='standard', kmer_len=31, protein=False, num_threads=None):\n '''Create a kb_python index.\n Args:\n ref_fasta: reference fasta file\n index: output index file\n workflow: one of 'standard', 'nac', 'kite', 'custom'\n kmer_len: kmer size (default 31)\n protein: ref_fasta file contains amino acid sequences\n '''\n # build db\n build_opts = {\n '-t': misc.sanitize_thread_count(num_threads)\n }\n if kmer_len:\n build_opts['-k'] = kmer_len\n if index:\n build_opts['-i'] = index\n if protein:\n build_opts['--aa'] = None\n if workflow:\n build_opts['--workflow'] = workflow\n self.execute('kb ref', None, args=[ref_fasta], options=build_opts)\n \n def classify(self, in_bam, index_file, out_dir, t2g_file, k=31, parity='single', technology='bulk', h5ad=False, loom=False, protein=False, num_threads=None):\n \"\"\"Classify input reads (bam)\n\n Args:\n in_bam: unaligned reads (single or paired-end) in BAM or FASTQ format.\n index_file: kb_python index file\n out_dir: output directory\n t2g_file: transcript to gene mapping file\n k: kmer size (default 31)\n parity: one of 'single', 'paired'\n technology: one of '10xv2', '10xv3', '10xv3cr', '10xv3multiome', '10xv1', 'dropseq', 'indrop', 'sci-rna-seq', 'bulk'\n h5ad: output h5ad file\n loom: output loom file\n protein: ref_fasta file contains amino acid sequences\n num_threads: number of threads to use\n \"\"\"\n if samtools.SamtoolsTool().isEmpty(in_bam):\n return\n\n opts = {\n '-i': index_file,\n '-g': t2g_file,\n '-t': misc.sanitize_thread_count(num_threads),\n '--parity': parity\n }\n if k:\n opts['-k'] = k\n if technology:\n opts['-x'] = technology\n if h5ad:\n opts['--h5ad'] = None\n if loom:\n opts['--loom'] = None \n if protein:\n opts['--aa'] = None\n \n tmp_fastq1 = file.mkstempfname('.1.fastq')\n tmp_fastq2 = file.mkstempfname('.2.fastq')\n tmp_fastq3 = file.mkstempfname('.s.fastq')\n tmp_interleaved = None\n try:\n if in_bam.lower().endswith('.fastq') or in_bam.lower().endswith('.fq') or in_bam.lower().endswith('.fastq.gz') or in_bam.lower().endswith('.fq.gz'):\n if not os.path.exists(in_bam):\n return\n \n # Input is already FASTQ, use it directly (don't delete it later)\n self.execute('kb count', out_dir, args=[in_bam], options=opts)\n else:\n if samtools.SamtoolsTool().isEmpty(in_bam):\n return\n\n # Do not convert this to samtools bam2fq unless we can figure out how to replicate\n # the clipping functionality of Picard SamToFastq\n picard_tool = picard.SamToFastqTool()\n picard_opts = {\n 'CLIPPING_ATTRIBUTE': picard.SamToFastqTool.illumina_clipping_attribute,\n 'CLIPPING_ACTION': 'X'\n }\n picard_tool.execute(in_bam, tmp_fastq1, tmp_fastq2, outFastq0=tmp_fastq3,\n picardOptions=picard.PicardTools.dict_to_picard_opts(picard_opts),\n JVMmemory=picard_tool.jvmMemDefault)\n\n # Detect if input bam was paired by checking fastq 2\n if os.path.getsize(tmp_fastq2) < os.path.getsize(tmp_fastq3):\n self.execute('kb count', out_dir, args=[tmp_fastq3], options=opts)\n else:\n tmp_interleaved = file.mkstempfname('.interleaved.fastq')\n with open(tmp_fastq1, 'rb') as fastq1, open(tmp_fastq2, 'rb') as fastq2, open(tmp_interleaved, 'wb') as interleaved:\n while True:\n read1 = [fastq1.readline() for _ in range(4)]\n if not read1[0]:\n break\n if any(line == b'' for line in read1[1:]):\n raise ValueError(\"Unexpected end of read 1 FASTQ while interleaving paired data\")\n read2 = [fastq2.readline() for _ in range(4)]\n if any(line == b'' for line in read2):\n raise ValueError(\"Unexpected end of read 2 FASTQ while interleaving paired data\")\n interleaved.writelines(read1)\n interleaved.writelines(read2)\n if fastq2.readline():\n raise ValueError(\"Read 2 FASTQ contains extra data after interleaving paired data\")\n\n self.execute('kb count', out_dir, args=[tmp_interleaved], options=opts)\n except Exception as e:\n log.error(\"Error during kb count: %s\", e)\n raise\n finally:\n for path in (tmp_fastq1, tmp_fastq2, tmp_fastq3, tmp_interleaved):\n if path and os.path.exists(path):\n try:\n os.unlink(path)\n except OSError as e:\n log.warning(\"Failed to delete temporary file %s: %s\", path, e)\n\n # Add sample metadata to h5ad file if it was generated\n if h5ad:\n h5ad_files = glob.glob(os.path.join(out_dir, \"counts_unfiltered\", \"*.h5ad\"))\n if h5ad_files:\n for h5ad_file in h5ad_files:\n # Use the input bam filename (without extension) as sample name\n sample_name = os.path.splitext(os.path.basename(in_bam))[0]\n # Remove .bam if it's still there (handles .fastq.gz cases)\n if sample_name.endswith('.bam'):\n sample_name = os.path.splitext(sample_name)[0]\n self._add_sample_metadata_to_h5ad(h5ad_file, sample_name=sample_name)\n \n def extract(self, in_bam, index_file, target_ids, out_dir, t2g_file, protein=False, num_threads=None):\n \"\"\"Extracts reads mapping to target ids from input reads (bam)\n \n Args:\n in_bam: unaligned read to extract reads from (FASTQ or BAM)\n index_file: kb_python index file\n out_dir: output directory\n t2g_file: transcript to gene mapping file\n protein: ref_fasta file contains amino acid sequences\n target_ids: list of target ids to extract\n num_threads: number of threads to use\n \"\"\"\n opts = {\n '-i': index_file,\n '-g': t2g_file,\n '-ts': target_ids, # Pass as list for multi-value option\n '-t': misc.sanitize_thread_count(num_threads)\n }\n if protein:\n opts['--aa'] = None\n \n tmp_fastq1 = file.mkstempfname('.1.fastq')\n tmp_fastq2 = file.mkstempfname('.2.fastq')\n tmp_fastq3 = file.mkstempfname('.s.fastq')\n tmp_interleaved = None\n try:\n if in_bam.lower().endswith('.fastq') or in_bam.lower().endswith('.fq') or in_bam.lower().endswith('.fastq.gz') or in_bam.lower().endswith('.fq.gz'):\n if not os.path.exists(in_bam):\n return\n \n # Input is already FASTQ, use it directly (don't delete it later)\n self.execute('kb extract', out_dir, args=[in_bam], options=opts)\n else:\n if samtools.SamtoolsTool().isEmpty(in_bam):\n return\n\n # Do not convert this to samtools bam2fq unless we can figure out how to replicate\n # the clipping functionality of Picard SamToFastq\n picard_tool = picard.SamToFastqTool()\n picard_opts = {\n 'CLIPPING_ATTRIBUTE': picard.SamToFastqTool.illumina_clipping_attribute,\n 'CLIPPING_ACTION': 'X'\n }\n picard_tool.execute(in_bam, tmp_fastq1, tmp_fastq2, outFastq0=tmp_fastq3,\n picardOptions=picard.PicardTools.dict_to_picard_opts(picard_opts),\n JVMmemory=picard_tool.jvmMemDefault)\n\n # Detect if input bam was paired by checking fastq 2\n if os.path.getsize(tmp_fastq2) < os.path.getsize(tmp_fastq3):\n self.execute('kb extract', out_dir, args=[tmp_fastq3], options=opts)\n else:\n tmp_interleaved = file.mkstempfname('.interleaved.fastq')\n with open(tmp_fastq1, 'rb') as fastq1, open(tmp_fastq2, 'rb') as fastq2, open(tmp_interleaved, 'wb') as interleaved:\n while True:\n read1 = [fastq1.readline() for _ in range(4)]\n if not read1[0]:\n break\n if any(line == b'' for line in read1[1:]):\n raise ValueError(\"Unexpected end of read 1 FASTQ while interleaving paired data\")\n read2 = [fastq2.readline() for _ in range(4)]\n if any(line == b'' for line in read2):\n raise ValueError(\"Unexpected end of read 2 FASTQ while interleaving paired data\")\n interleaved.writelines(read1)\n interleaved.writelines(read2)\n if fastq2.readline():\n raise ValueError(\"Read 2 FASTQ contains extra data after interleaving paired data\")\n\n self.execute('kb extract', out_dir, args=[tmp_interleaved], options=opts)\n except Exception as e:\n log.error(\"Error during kb extract: %s\", e)\n raise\n finally:\n for path in (tmp_fastq1, tmp_fastq2, tmp_fastq3, tmp_interleaved):\n if path and os.path.exists(path):\n try:\n os.unlink(path)\n except OSError as e:\n log.warning(\"Failed to delete temporary file %s: %s\", path, e)\n \n\n def _extract_h5ad_from_tarball_to_tmpdir(self, count_tar, tmp_dir):\n \"\"\"Helper function to extract h5ad file from a tarball into a temporary directory.\n \n Args:\n count_tar: input kb count tarball file (tar.gz or tar.zst format)\n tmp_dir: temporary directory to extract into\n \n Returns:\n Path to the extracted h5ad file\n \"\"\"\n file.extract_tarball(count_tar, tmp_dir)\n \n # Find h5ad file in counts_unfiltered folder\n h5ad_files = glob.glob(os.path.join(tmp_dir, \"counts_unfiltered\", \"*.h5ad\"))\n log.debug(f\"Found h5ad files in {count_tar}: {h5ad_files}\")\n if len(h5ad_files) == 0:\n raise FileNotFoundError(f\"No .h5ad file found in counts_unfiltered/ directory of {count_tar}\")\n if len(h5ad_files) > 1:\n log.warning(f\"Multiple .h5ad files found in {count_tar}, using first one: {h5ad_files[0]}\")\n \n return h5ad_files[0]\n \n def _add_sample_metadata_to_h5ad(self, h5ad_or_tarball, sample_name=None, tmp_dir_parent=None):\n \"\"\"Add sample metadata to an h5ad file (in-place modification).\n \n Args:\n h5ad_or_tarball: path to h5ad file or tarball containing h5ad file\n sample_name: optional sample name to use. If not provided, will try to read from matrix.cells\n or use the filename as fallback\n tmp_dir_parent: parent directory for temporary files (optional, only used for tarballs)\n \"\"\"\n # Check if input is a tarball\n if tarfile.is_tarfile(h5ad_or_tarball) or h5ad_or_tarball.endswith('.tar.zst'):\n with file.tmp_dir(dir=tmp_dir_parent) as tmp_dir:\n log.debug(f\"Extracting {h5ad_or_tarball} to temporary directory {tmp_dir}\")\n h5ad_file = self._extract_h5ad_from_tarball_to_tmpdir(h5ad_or_tarball, tmp_dir)\n \n # Read sample name from matrix.cells file if not provided\n if sample_name is None:\n cells_file = os.path.join(tmp_dir, \"matrix.cells\")\n if os.path.exists(cells_file):\n with open(cells_file, 'r') as f:\n sample_name = f.read().strip()\n else:\n # Fallback to tarball basename if matrix.cells doesn't exist\n sample_name = os.path.splitext(os.path.splitext(os.path.basename(h5ad_or_tarball))[0])[0]\n log.warning(f\"matrix.cells not found in {h5ad_or_tarball}, using filename as sample name: {sample_name}\")\n \n # Load h5ad file\n adata = anndata.read_h5ad(h5ad_file)\n \n # Check if matrix.sample.barcodes exists and read barcodes\n barcodes = None\n barcodes_file = os.path.join(tmp_dir, \"matrix.sample.barcodes\")\n if os.path.exists(barcodes_file):\n with open(barcodes_file, 'r') as f:\n barcodes = [line.strip() for line in f]\n else:\n # Direct h5ad file\n h5ad_file = h5ad_or_tarball\n if sample_name is None:\n # Use filename as fallback\n sample_name = os.path.splitext(os.path.basename(h5ad_file))[0]\n log.warning(f\"No sample name provided for {h5ad_file}, using filename as sample name: {sample_name}\")\n \n adata = anndata.read_h5ad(h5ad_file)\n barcodes = None\n \n # Add sample metadata to observations\n adata.obs['sample'] = sample_name\n adata.obs['batch_name'] = sample_name\n \n # Add barcode info if available\n if barcodes is not None and len(barcodes) == adata.n_obs:\n adata.obs['batch_barcode'] = barcodes\n \n # Write back to the h5ad file\n adata.write_h5ad(h5ad_file)\n log.debug(f\"Added sample metadata to {h5ad_file}: sample={sample_name}\")\n \n def merge_h5ads(self, in_count_tars, out_h5ad, tmp_dir_parent=None):\n \"\"\"Merge multiple kb count output tarballs into a single h5ad file.\n\n Args:\n in_count_tars: list of input kb count tarball files (tar.zst format)\n out_h5ad: output h5ad file path\n tmp_dir_parent: parent directory for temporary files (optional)\n \"\"\"\n\n assert len(in_count_tars) > 0, \"no input count tarballs provided\"\n\n adatas = []\n\n for count_tar in in_count_tars:\n # Extract tarball to temporary directory\n with file.tmp_dir(dir=tmp_dir_parent) as tmp_dir:\n log.debug(f\"Extracting {count_tar} to temporary directory {tmp_dir}\")\n h5ad_file = self._extract_h5ad_from_tarball_to_tmpdir(count_tar, tmp_dir)\n log.debug(f\"Extracted h5ad file: {h5ad_file}\")\n \n # Load h5ad file without metadata\n adata = anndata.read_h5ad(h5ad_file)\n adatas.append(adata)\n\n # Handle single file case\n if len(adatas) == 1:\n log.warning(\"Only one count tarball provided - writing single file instead of merging\")\n adatas[0].write_h5ad(out_h5ad)\n return\n\n # Check that all h5ad files have the same number of variables (genes)\n n_vars_ref = adatas[0].n_vars\n var_names_ref = adatas[0].var_names\n for i, adata in enumerate(adatas[1:], 1):\n if adata.n_vars != n_vars_ref:\n raise ValueError(f\"Dimension mismatch: file {in_count_tars[0]} has {n_vars_ref} variables, \"\n f\"but file {in_count_tars[i]} has {adata.n_vars} variables\")\n if not adata.var_names.equals(var_names_ref):\n raise ValueError(f\"Variable names mismatch: file {in_count_tars[0]} and file {in_count_tars[i]} have different variable names\")\n\n # Straight merge of all anndata objects without metadata\n combined = anndata.concat(adatas, join='outer', axis=0, fill_value=0)\n combined.write_h5ad(out_h5ad)\n\n def parse_h5ad_counts(self, h5ad_file):\n \"\"\"Parse h5ad file and return gene IDs with their total counts.\n\n Args:\n h5ad_file: path to h5ad file\n\n Returns:\n List of tuples (gene_id, count) sorted by gene ID\n \"\"\"\n adata = anndata.read_h5ad(h5ad_file)\n\n counts_mtx = adata.X.toarray() if hasattr(adata.X, 'toarray') else adata.X\n\n gene_ids = adata.var.index.tolist()\n gene_totals = counts_mtx.sum(axis=0)\n\n if hasattr(gene_totals, 'A1'): # numpy matrix\n gene_totals = gene_totals.A1\n\n return list(zip(gene_ids, gene_totals))\n\n def extract_hit_ids_from_h5ad(self, h5ad_file, threshold=1):\n \"\"\"Parse h5ad file and extract all target IDs with 1 or more hits.\n \n Assumes h5ad contains a single sample (single row).\n\n Args:\n h5ad_file: path to h5ad file or tarball containing h5ad file\n threshold: minimum count threshold to consider a target ID to return (default 1)\n\n Returns:\n List of target IDs (strings) with counts > 0\n \"\"\"\n ## Check if file passed in is a tarball, if so we need to grab the h5ad\n if tarfile.is_tarfile(h5ad_file) or h5ad_file.endswith('.tar.zst'):\n with file.tmp_dir() as tmp_dir:\n h5ad_file = self._extract_h5ad_from_tarball_to_tmpdir(h5ad_file, tmp_dir)\n log.debug(f\"Reading h5ad file from tarball: {h5ad_file}\")\n adata = anndata.read_h5ad(h5ad_file)\n else:\n log.debug(f\"Reading h5ad file: {h5ad_file}\")\n adata = anndata.read_h5ad(h5ad_file)\n\n # Get count matrix and sum across all observations (rows)\n counts_mtx = adata.X.toarray() if hasattr(adata.X, 'toarray') else adata.X\n gene_totals = counts_mtx.sum(axis=0)\n\n if hasattr(gene_totals, 'A1'): # numpy matrix\n gene_totals = gene_totals.A1\n\n # Extract gene IDs and filter to those with counts > 0\n gene_ids = adata.var.index.tolist()\n hit_ids = [gene_id for gene_id, count in zip(gene_ids, gene_totals) if count > 0]\n if threshold is not None:\n hit_ids = [gene_id for gene_id, count in zip(gene_ids, gene_totals) if count >= threshold]\n\n return hit_ids\n" }, { "path": "src/viral_ngs/classify/kma.py", "content": "'''\nKMA k-mer alignment tool\n'''\nimport logging\nimport os\nimport os.path\nimport shutil\nimport subprocess\n\nfrom viral_ngs import core\nfrom viral_ngs.core import picard\nfrom viral_ngs.core import samtools\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nfrom builtins import super\n\nlog = logging.getLogger(__name__)\n\nclass KMA(core.Tool):\n\n def __init__(self, install_methods=None):\n if not install_methods:\n install_methods = []\n install_methods.append(core.PrexistingUnixCommand(shutil.which('kma'), require_executability=False))\n super(KMA, self).__init__(install_methods=install_methods)\n\n def version(self):\n '''Parse version from kma -v output'''\n try:\n result = subprocess.run(['kma', '-v'], capture_output=True, text=True, check=True)\n version_line = result.stdout.strip() or result.stderr.strip()\n if version_line:\n parts = version_line.split()\n if len(parts) >= 2:\n return parts[1]\n return 'unknown'\n except (subprocess.CalledProcessError, FileNotFoundError, IndexError):\n return 'unknown'\n\n @property\n def libexec(self):\n if not self.executable_path():\n self.install_and_get_path()\n return os.path.dirname(self.executable_path())\n\n def execute(self, command, args=None, options=None):\n '''Run a kma command.\n\n Args:\n command: Command to run (e.g., 'kma', 'kma_index').\n args: List of positional args.\n options: Dict of keyword options.\n '''\n options = options or {}\n args = args or []\n\n cmd = [command]\n\n for key, value in options.items():\n if value is None:\n cmd.append(key)\n else:\n cmd.extend([key, str(value)])\n\n cmd.extend(args)\n log.debug('Calling %s: %s', command, ' '.join(cmd))\n\n subprocess.check_call(cmd)\n\n def build(self, ref_fasta, db_prefix, num_threads=None):\n '''Build a KMA database from a reference FASTA file.\n\n Args:\n ref_fasta: Input reference FASTA file.\n db_prefix: Output database prefix.\n num_threads: Number of threads to use.\n '''\n opts = {\n '-i': ref_fasta,\n '-o': db_prefix\n }\n if num_threads:\n opts['-t'] = misc.sanitize_thread_count(num_threads)\n\n self.execute('kma_index', options=opts)\n\n def classify(self, in_bam, db, out_prefix, num_threads=None):\n '''Classify reads from BAM file using KMA.\n\n Args:\n in_bam: Input unaligned reads in BAM format.\n db: KMA database prefix (without file extensions).\n out_prefix: Output prefix for KMA result files.\n num_threads: Number of threads to use.\n '''\n if samtools.SamtoolsTool().isEmpty(in_bam):\n log.warning(\"Input BAM is empty, skipping KMA classification\")\n with open(out_prefix + '.res', 'wt') as outf:\n pass\n return\n\n tmp_fastq1 = file.mkstempfname('.1.fastq')\n tmp_fastq2 = file.mkstempfname('.2.fastq')\n tmp_fastq3 = file.mkstempfname('.s.fastq')\n\n try:\n picard_tool = picard.SamToFastqTool()\n picard_opts = {\n 'CLIPPING_ATTRIBUTE': picard.SamToFastqTool.illumina_clipping_attribute,\n 'CLIPPING_ACTION': 'X'\n }\n picard_tool.execute(in_bam, tmp_fastq1, tmp_fastq2, outFastq0=tmp_fastq3,\n picardOptions=picard.PicardTools.dict_to_picard_opts(picard_opts),\n JVMmemory=picard_tool.jvmMemDefault)\n\n opts = {\n '-t_db': db,\n '-o': out_prefix\n }\n if num_threads:\n opts['-t'] = misc.sanitize_thread_count(num_threads)\n\n # SamToFastq outputs paired reads to tmp_fastq1/2 and unpaired to tmp_fastq3.\n # For true paired-end data, tmp_fastq2 will be larger than tmp_fastq3.\n # For single-end data, tmp_fastq2 is empty/tiny and tmp_fastq3 contains all reads.\n if os.path.getsize(tmp_fastq2) < os.path.getsize(tmp_fastq3):\n log.warning(\"running in single-end read mode\")\n opts['-i'] = tmp_fastq3\n else:\n opts['-ipe'] = ' '.join([tmp_fastq1, tmp_fastq2])\n\n self.execute('kma', options=opts)\n\n finally:\n if os.path.exists(tmp_fastq1):\n os.unlink(tmp_fastq1)\n if os.path.exists(tmp_fastq2):\n os.unlink(tmp_fastq2)\n if os.path.exists(tmp_fastq3):\n os.unlink(tmp_fastq3)\n" }, { "path": "src/viral_ngs/classify/kmc.py", "content": "'''\n Tool wrapper for the KMC kmer counter\n ( http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about )\n'''\n\nimport logging\nimport os\nimport os.path\nimport sys\nimport subprocess\nimport shlex\nimport argparse\nimport shutil\nimport re\nimport collections\n\nimport Bio.SeqIO\n\nfrom viral_ngs import core\nfrom viral_ngs import read_utils\nfrom viral_ngs.core import samtools\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\n\n\nTOOL_NAME = 'kmc'\nTOOL_VERSION = '3.1.1rc1'\n\n_log = logging.getLogger(__name__) # pylint: disable=invalid-name\n\n_chk = misc.chk\n\nDEFAULT_KMER_SIZE = 25\nDEFAULT_COUNTER_CAP = 255 # default for \"cap counter values at\" params\n\nclass KmcTool(core.Tool):\n '''Tool wrapper for KMC kmer counter'''\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=False)]\n\n core.Tool.__init__(self, install_methods=install_methods)\n\n def version(self):\n return TOOL_VERSION\n\n def _kmer_db_name(self, kmer_db):\n \"\"\"Return the kmer database path, given either the db path of the file name of the .kmc_pre or .kmc_suf file\"\"\"\n base, ext = os.path.splitext(kmer_db)\n return base if ext in ('.kmc_pre', '.kmc_suf') else kmer_db\n\n def is_kmer_db(self, kmer_db):\n \"\"\"Quickly check that the given kmer database exists\"\"\"\n kmer_db = self._kmer_db_name(kmer_db)\n return os.path.isfile(kmer_db + '.kmc_pre') and os.path.isfile(kmer_db + '.kmc_suf')\n\n def _get_file_format_opt(self, fname):\n \"\"\"Get the KMC command-line option to specify file format\"\"\"\n file_type = file.uncompressed_file_type(fname)\n if file_type in ('.fasta', '.fa'):\n return 'm'\n elif file_type in ('.fastq', '.fq'):\n return 'q'\n elif file_type == '.bam':\n return 'bam'\n else:\n raise RuntimeError('Unknown seq file format: {}'.format(file_type))\n\n def build_kmer_db(self, seq_files, kmer_db, kmer_size=DEFAULT_KMER_SIZE, min_occs=1, max_occs=misc.MAX_INT32,\n counter_cap=DEFAULT_COUNTER_CAP, single_strand=False, mem_limit_gb=8, mem_limit_laxness=0,\n threads=None, kmc_opts=''):\n \"\"\"Build a database of kmers occurring in the given sequence files.\n\n Inputs:\n seq_files: filename(s) of files from which to gather kmers. Files can be fasta, fastq or bam; fasta and fastq\n may be compressed with gzip or bzip2.\n\n Outputs:\n kmer_db: kmer database path, with or without the .kmc_pre/.kmc_suf extension.\n\n Params:\n kmer_size: kmer size\n\n min_occs: ignore kmers occurring fewer than this many times\n max_occs: ignore kmers occurring more than this many times\n\n counter_cap: when writing kmer counts to the database, cap the values at this number\n\n single_strand: if True, do not include kmers from reverse complements of input sequences\n\n mem_limit_gb: max RAM to use when building kmer database. Might be exceeded unless `mem_limit_strict`\n is True.\n mem_limit_laxness: how strictly to adhere to `mem_limit_gb`: 0=strictly, higher values permit more laxness\n\n kmc_opts: any additional kmc flags\n \"\"\"\n seq_files = misc.make_seq(seq_files)\n kmer_db = self._kmer_db_name(kmer_db)\n threads = misc.sanitize_thread_count(threads)\n with file.tmp_dir(suffix='_kmc_db') as t_dir, \\\n file.tempfname(suffix='_kmc_seq_files') as seq_file_list:\n file.dump_file(seq_file_list, '\\n'.join(seq_files))\n args = ['-v']\n\n input_fmt_opts_set = set(map(self._get_file_format_opt, seq_files))\n _chk(len(input_fmt_opts_set) == 1, \"All input sequence files must be in the same format\")\n input_fmt_opt = list(input_fmt_opts_set)[0]\n\n args += '-f{} -k{} -ci{} -cx{} -cs{} -m{} -t{}'.format(input_fmt_opt, kmer_size, min_occs, max_occs,\n counter_cap, mem_limit_gb, threads).split()\n if single_strand:\n args += ['-b']\n if mem_limit_laxness == 0:\n args += ['-sm'] # strict memory mode\n elif mem_limit_laxness == 2:\n args += ['-r'] # RAM-only mode\n\n if kmc_opts:\n args += shlex.split(kmc_opts)\n\n args += ['@'+seq_file_list, kmer_db, t_dir]\n tool_cmd = [self.install_and_get_path()] + args\n _log.info('Building kmer database with command: %s', ' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n _chk(os.path.isfile(kmer_db+'.kmc_pre') and os.path.isfile(kmer_db+'.kmc_suf'),\n 'kmer database files not created: {}'.format(kmer_db))\n\n def execute(self, args, threads=None, return_output=False): # pylint: disable=arguments-differ\n \"\"\"Run kmc_tools with the given args. If `return_output` is True, returns the stdout output.\"\"\"\n threads = misc.sanitize_thread_count(threads)\n tool_cmd = [self.install_and_get_path()+'_tools'] + ['-t{}'.format(threads)] + list(map(str, args))\n _log.info('Running kmc_tools command: %s', ' '.join(tool_cmd))\n\n result = None\n if not return_output:\n subprocess.check_call(tool_cmd)\n else:\n result = subprocess.check_output(tool_cmd).decode('utf-8')\n _log.info('Done running kmc_tools command: %s', ' '.join(tool_cmd))\n return result\n\n\n def dump_kmer_counts(self, kmer_db, out_kmers, min_occs=1, max_occs=misc.MAX_INT32, threads=None):\n \"\"\"Dump the kmers from the database, with their counts, to a text file. Kmers with counts\n below `min_occs` or above `max_occs` are ignored.\"\"\"\n self.execute('transform {} -ci{} -cx{} dump {}'.format(self._kmer_db_name(kmer_db),\n min_occs, max_occs, out_kmers).split(),\n threads=threads)\n _chk(os.path.isfile(out_kmers), 'dump_kmer_counts: output file not created')\n\n def read_kmer_counts(self, kmer_counts_txt):\n \"\"\"Read kmer counts from a file written by dump_kmer_counts, as collections.Counter\"\"\"\n counts = collections.Counter()\n with file.open_or_gzopen(kmer_counts_txt) as kmers_f:\n for line in kmers_f:\n kmer, count = line.strip().split()\n counts[kmer] = int(count)\n return counts\n\n def get_kmer_counts(self, kmer_db, **kwargs):\n \"\"\"Extract and return the kmer counts from the kmer database as a dict. `kwargs` are passed through\n to read_kmer_counts().\"\"\"\n with file.tempfname(suffix='_kmer_cnts.txt') as kmer_counts_file:\n self.dump_kmer_counts(kmer_db, out_kmers=kmer_counts_file, **kwargs)\n return self.read_kmer_counts(kmer_counts_file)\n\n def get_kmer_db_info(self, kmer_db):\n \"\"\"Return params of a kmer db.\n This functionality is not documented in KMC docs but is supported\n ( https://github.com/refresh-bio/KMC/issues/83 )\n\n Returns: an argparse.Namespace() with attributes kmer_size, min_occs, max_occs,\n counter_size_bytes, and total_kmers.\n \"\"\"\n output = self.execute(['info', self._kmer_db_name(kmer_db)], return_output=True, threads=1)\n db_info = dict(re.split('\\\\s+:\\\\s+', line.strip()) for line in output.strip().split('\\n'))\n def fix_val(v):\n return v=='yes' if v in ('yes', 'no') else misc.as_type(v, (int, str))\n db_info = {k: fix_val(v) for k, v in db_info.items()}\n\n return argparse.Namespace(kmer_size=db_info['k'], single_strand=not db_info['both strands'],\n min_occs=db_info['cutoff min'],\n max_occs=db_info['cutoff max'],\n counter_size_bytes=int(db_info['counter size'].split()[0]),\n total_kmers=db_info['total k-mers'])\n\n def filter_reads(self, kmer_db, in_reads, out_reads, db_min_occs=1, db_max_occs=misc.MAX_INT32,\n read_min_occs=0, read_max_occs=misc.MAX_INT32,\n read_min_occs_frac=0.0, read_max_occs_frac=1.0, hard_mask=False, threads=None):\n \"\"\"Filter reads based on their kmer contents.\n\n Note that \"occurrence of a kmer\" means \"occurrence of the kmer or its reverse complement\" if kmer_db was built\n with single_strand==False.\n\n Inputs:\n kmer_db: the kmc kmer database\n in_reads: the reads to filter. can be a .fasta or .fastq or .bam; fasta or fastq can be compressed\n with gzip or bzip2. If a .bam, a read pair is kept if either mate passes the filter.\n\n Outputs:\n out_reads: file to which filtered reads are written. type is determined from extension,\n same types as above are supported.\n\n Params:\n db_min_occs: only consider database kmers with at least this count\n db_max_occs: only consider database kmers with at most this count\n\n read_min_occs: only keep reads with at least this many occurrences of kmers from database.\n read_max_occs: only keep reads with no more than this many occurrence of kmers from the database.\n read_min_occs_frac: only keep reads with at least this many occurrences of kmers from database,\n interpreted as a fraction of read length in kmers\n read_max_occs_frac: only keep reads with no more than this many occurrence of kmers from the database.\n interpreted as a fraction of read length in kmers.\n\n (Note: minimal read kmer content can be given as absolute counts or fraction of read length, but not both).\n\n hard_mask: if True, in the output reads, kmers not passing the filter are replaced by Ns\n threads: use this many threads\n \"\"\"\n _log.debug('FILTER_READS: locals=%s dbinfo=%s', locals(), self.get_kmer_db_info(kmer_db))\n\n abs_thresholds = (read_min_occs, read_max_occs) != (0, misc.MAX_INT32)\n rel_thresholds = (read_min_occs_frac, read_max_occs_frac) != (0., 1.)\n if not (abs_thresholds or rel_thresholds): abs_thresholds = True\n _chk(not (abs_thresholds and rel_thresholds),\n \"Mixing absolute and relative thresholds for kmer content not currently supported\")\n _chk(0 <= read_min_occs <= read_max_occs <= misc.MAX_INT32,\n 'Invalid kmer contents thresholds')\n _chk(0.0 <= read_min_occs_frac <= read_max_occs_frac <= 1.0,\n 'Invalid kmer contents thresholds')\n\n in_reads_type = file.uncompressed_file_type(in_reads)\n _in_reads = in_reads\n _out_reads = out_reads\n with file.tmp_dir(suffix='_kmcfilt') as t_dir:\n if in_reads_type in ('.fa', '.fasta'):\n # kmc_tools filter currently requires fasta files to be in fasta-2line format\n # https://github.com/refresh-bio/KMC/issues/57\n _in_reads = os.path.join(t_dir, 'in_reads.fasta')\n Bio.SeqIO.convert(in_reads, 'fasta', _in_reads, 'fasta-2line')\n if in_reads_type == '.bam':\n # kmc_tools filter currently does not support .bam files\n # https://github.com/refresh-bio/KMC/issues/66\n _in_reads = os.path.join(t_dir, 'in_reads.fasta')\n samtools.SamtoolsTool().bam2fa(in_reads, _in_reads)\n _out_reads = os.path.join(t_dir, 'out_reads.fasta')\n\n # TODO: if db is single-strand, reverse-complement read2's?\n\n in_reads_fmt = 'q' if in_reads_type in ('.fq', '.fastq') else 'a'\n\n if os.path.getsize(self._kmer_db_name(kmer_db)+'.kmc_suf') == 8:\n _chk(self.get_kmer_db_info(kmer_db).total_kmers == 0,\n 'Something odd: did kmc file format change?')\n # kmc has a bug filtering on empty kmer databases:\n # https://github.com/refresh-bio/KMC/issues/86\n if read_min_occs > 0 or read_min_occs_frac > 0.0:\n file.make_empty(_out_reads)\n else:\n shutil.copyfile(_in_reads, _out_reads)\n else:\n thresholds_opt = ' -ci{} -cx{}'.format(*((read_min_occs, read_max_occs) if abs_thresholds else \\\n (read_min_occs_frac, read_max_occs_frac)))\n self.execute('filter {} {} -ci{} -cx{} {} -f{} {} {}'.format('-hm' if hard_mask else '',\n self._kmer_db_name(kmer_db),\n db_min_occs, db_max_occs,\n _in_reads, in_reads_fmt,\n thresholds_opt,\n _out_reads).split(),\n threads=threads)\n\n if in_reads_type == '.bam':\n _chk(out_reads.endswith('.bam'), 'output from .bam to non-.bam not yet supported')\n passing_read_names = os.path.join(t_dir, 'passing_read_names.txt')\n read_utils.fasta_read_names(_out_reads, passing_read_names)\n # Load passing read names into ReadIdStore and filter BAM (keep matching reads)\n db_path = os.path.join(t_dir, 'read_ids.db')\n with read_utils.ReadIdStore(db_path) as store:\n store.add_from_readlist(passing_read_names)\n store.filter_bam_by_ids(in_reads, out_reads, include=True)\n # end: with file.tmp_dir(suffix='kmcfilt') as t_dir\n # end: def filter_reads(self, kmer_db, in_reads, out_reads, db_min_occs=1, db_max_occs=misc.MAX_INT32, ...)\n\n def kmers_binary_op(self, op, kmer_db1, kmer_db2, kmer_db_out,\n result_min_occs=1, result_max_occs=misc.MAX_INT32,\n result_counter_cap=DEFAULT_COUNTER_CAP,\n threads=None):\n \"\"\"Perform a simple binary operation on two kmer sets\"\"\"\n kmer_db1, kmer_db2, kmer_db_out = map(self._kmer_db_name, (kmer_db1, kmer_db2, kmer_db_out))\n # db1_min_occs, db1_max_occs, db2_min_occs, db2_max_occs, db_out_min_occs, db_out_max_occs,\n self.execute(['simple', kmer_db1, kmer_db2, op, kmer_db_out,\n '-ci{}'.format(result_min_occs),\n '-cx{}'.format(result_max_occs),\n '-cs{}'.format(result_counter_cap)], threads=threads)\n _chk(self.is_kmer_db(kmer_db_out), 'kmer_binary_op: output not created')\n\n def set_kmer_counts(self, kmer_db_in, value, kmer_db_out, threads=None):\n \"\"\"Create a copy of the kmer database with all counts set to specified value\"\"\"\n _chk(1 <= value <= misc.MAX_INT32, 'can only set kmer counts to a positive 32-bit int')\n kmer_db_in, kmer_db_out = map(self._kmer_db_name, (kmer_db_in, kmer_db_out))\n # db1_min_occs, db1_max_occs, db2_min_occs, db2_max_occs, db_out_min_occs, db_out_max_occs,\n self.execute(['transform', kmer_db_in, 'set_counts', value, kmer_db_out], threads=threads)\n _chk(self.is_kmer_db(kmer_db_out), 'set_kmer_counts: output not created')\n\n# end: class KmcTool(core.Tool)\n" }, { "path": "src/viral_ngs/classify/kraken2.py", "content": "'''\nKRAKEN metagenomics classifier\n'''\nimport collections\nimport concurrent.futures\nimport itertools\nimport logging\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport sys\nimport tempfile\n\nfrom viral_ngs import core\nfrom viral_ngs.core import picard\nfrom viral_ngs.core import samtools\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nfrom builtins import super\n\nlog = logging.getLogger(__name__)\n\nclass Kraken2(core.Tool):\n\n def __init__(self, install_methods=None):\n if not install_methods:\n install_methods = []\n install_methods.append(core.PrexistingUnixCommand(shutil.which('kraken2'), require_executability=False))\n super(Kraken2, self).__init__(install_methods=install_methods)\n\n def version(self):\n return '2'\n\n @property\n def libexec(self):\n if not self.executable_path():\n self.install_and_get_path()\n return os.path.dirname(self.executable_path())\n\n def build(self, db, standard_libraries=(), custom_libraries=(), taxdump_out=None,\n k=None, l=None, s=None, protein=False, max_db_size=None, tax_db=None,\n num_threads=None):\n '''Create a kraken2 database.\n\n Args:\n db: output directory\n standard_libraries: a list of strings from the set of:\n \"archaea\", \"bacteria\", \"plasmid\",\n \"viral\", \"human\", \"fungi\", \"plant\", \"protozoa\",\n \"nr\", \"nt\", \"env_nr\", \"env_nt\", \"UniVec\",\n \"UniVec_Core\"\n '''\n\n # all the library download and dustmasking can be *easily* parallelized\n with concurrent.futures.ProcessPoolExecutor(\n max_workers=misc.sanitize_thread_count(num_threads)) as executor:\n\n futs = []\n # use or fetch taxonomy database\n if tax_db:\n file.mkdir_p(db)\n futs.append(executor.submit(shutil.copytree, tax_db, os.path.join(db, 'taxonomy')))\n else:\n if protein:\n futs.append(executor.submit(self.execute, 'kraken2-build', db, None,\n options={'--download-taxonomy': None, '--protein': None}))\n else:\n futs.append(executor.submit(self.execute, 'kraken2-build', db, None,\n options={'--download-taxonomy': None}))\n # add standard libraries:\n if standard_libraries:\n for lib in standard_libraries:\n if protein:\n futs.append(executor.submit(self.execute, 'kraken2-build', db, None,\n options={'--download-library': lib, '--protein':None}))\n else:\n futs.append(executor.submit(self.execute, 'kraken2-build', db, None,\n options={'--download-library': lib}))\n # add custom libraries:\n if custom_libraries:\n for lib in custom_libraries:\n if protein:\n futs.append(executor.submit(self.execute, 'kraken2-build', db, None,\n options={'--add-to-library': lib, '--protein': None}))\n else:\n futs.append(executor.submit(self.execute, 'kraken2-build', db, None,\n options={'--add-to-library': lib}))\n\n # properly raise exceptions from any of the above jobs\n for fut in concurrent.futures.as_completed(futs):\n fut.result()\n\n # build db\n build_opts = {\n '--build': None,\n '--threads': misc.sanitize_thread_count(num_threads)\n }\n if k:\n build_opts['--kmer-len'] = k\n if l:\n build_opts['--minimizer-len'] = l\n if s:\n build_opts['--minimizer-spaces'] = s\n if protein:\n build_opts['--protein'] = None\n if max_db_size:\n build_opts['--max-db-size'] = max_db_size\n self.execute('kraken2-build', db, None, options=build_opts)\n\n # grab the taxdump for krona!\n if taxdump_out:\n shutil.copyfile(os.path.join(db, 'taxonomy', 'taxdump.tar.gz'), taxdump_out)\n\n # clean db\n self.execute('kraken2-build', db, None, options={\n '--threads':misc.sanitize_thread_count(num_threads),\n '--clean': None\n })\n\n def inspect(self, db, output, num_threads=None):\n with open(output, 'wt') as outf:\n subprocess.check_call('kraken2-inspect',\n '--db', db,\n '--threads', misc.sanitize_thread_count(num_threads),\n stdout=outf)\n\n def execute(self, command, db, output, args=None, options=None):\n '''Run a kraken-* command.\n\n Args:\n db: Kraken database directory.\n output: Output file of command.\n args: List of positional args.\n options: List of keyword options.\n '''\n options = options or {}\n\n if output:\n options['--output'] = output\n args = args or []\n\n cmd = [command, '--db', db]\n # We need some way to allow empty options args like --build, hence\n # we filter out on 'x is None'.\n cmd.extend([str(x) for x in itertools.chain(*options.items())\n if x is not None])\n cmd.extend(args)\n log.debug('Calling %s: %s', command, ' '.join(cmd))\n\n subprocess.check_call(cmd)\n\n def pipeline(self, db, in_bams, out_reports=None, out_reads=None,\n min_base_qual=None, confidence=None, minimum_hit_groups=None, num_threads=None):\n\n assert out_reads is not None or out_reports is not None\n out_reports = out_reports or []\n out_reads = out_reads or []\n\n for in_bam, out_read, out_report in itertools.zip_longest(in_bams, out_reads, out_reports):\n self.classify(in_bam, db, out_reads=out_read, out_report=out_report,\n min_base_qual=min_base_qual, confidence=confidence,\n minimum_hit_groups=minimum_hit_groups, num_threads=None)\n\n def classify(self, in_bam, db, out_reads=None, out_report=None,\n confidence=None, min_base_qual=None, minimum_hit_groups=None, num_threads=None):\n \"\"\"Classify input reads (bam)\n\n Args:\n in_bam: unaligned reads\n db: Kraken built database directory.\n out_reads: Output file of command.\n \"\"\"\n\n if samtools.SamtoolsTool().isEmpty(in_bam):\n # kraken cannot deal with empty input\n if out_reads:\n with open(out_reads, 'wt') as outf:\n pass\n if out_report:\n with open(out_report, 'wt') as outf:\n pass\n return\n\n opts = {\n '--threads': misc.sanitize_thread_count(num_threads)\n }\n if out_report:\n opts['--report'] = out_report\n if not out_reads:\n out_reads = '-' # in kraken2, this suppresses normal output\n if min_base_qual:\n opts['--minimum-base-quality'] = min_base_qual\n if confidence:\n opts['--confidence'] = confidence\n if minimum_hit_groups:\n opts['--minimum-hit-groups'] = minimum_hit_groups\n\n tmp_fastq1 = file.mkstempfname('.1.fastq')\n tmp_fastq2 = file.mkstempfname('.2.fastq')\n tmp_fastq3 = file.mkstempfname('.s.fastq')\n # Do not convert this to samtools bam2fq unless we can figure out how to replicate\n # the clipping functionality of Picard SamToFastq\n picard_tool = picard.SamToFastqTool()\n picard_opts = {\n 'CLIPPING_ATTRIBUTE': picard.SamToFastqTool.illumina_clipping_attribute,\n 'CLIPPING_ACTION': 'X'\n }\n picard_tool.execute(in_bam, tmp_fastq1, tmp_fastq2, outFastq0=tmp_fastq3,\n picardOptions=picard.PicardTools.dict_to_picard_opts(picard_opts),\n JVMmemory=picard_tool.jvmMemDefault)\n\n if out_report:\n opts['--report'] = out_report\n # Detect if input bam was paired by checking fastq 2\n if os.path.getsize(tmp_fastq2) < os.path.getsize(tmp_fastq3):\n log.warn(\"running in single-end read mode!\")\n res = self.execute('kraken2', db, out_reads, args=[tmp_fastq3], options=opts)\n else:\n opts['--paired'] = None\n res = self.execute('kraken2', db, out_reads, args=[tmp_fastq1, tmp_fastq2], options=opts)\n os.unlink(tmp_fastq1)\n os.unlink(tmp_fastq2)\n os.unlink(tmp_fastq3)\n\n" }, { "path": "src/viral_ngs/classify/krona.py", "content": "from viral_ngs import core\nimport os.path\nimport subprocess\nimport shutil\nfrom builtins import super\nfrom viral_ngs.core import file\n\nTOOL_NAME = 'krona'\n\nclass Krona(core.Tool):\n def __init__(self, install_methods=None):\n if not install_methods:\n install_methods = [core.PrexistingUnixCommand(shutil.which('ktImportTaxonomy'))]\n super(Krona, self).__init__(install_methods=install_methods)\n\n @property\n def opt(self):\n if not self.executable_path():\n self.install_and_get_path()\n bin_path = os.path.dirname(self.executable_path())\n # Get at the opt directory from the conda env root\n opt = os.path.abspath(os.path.join(bin_path, '..', 'opt', 'krona'))\n return opt\n\n def import_taxonomy(self,\n db,\n input_tsvs,\n output,\n query_column=None,\n taxid_column=None,\n score_column=None,\n magnitude_column=None,\n root_name=None,\n no_hits=None,\n no_rank=None):\n if not self.executable_path():\n self.install_and_get_path()\n bin_path = os.path.dirname(self.executable_path())\n env = os.environ.copy()\n env['PATH'] = '{}:{}'.format(bin_path, env['PATH'])\n cmd = ['ktImportTaxonomy', '-tax', db, '-o', output]\n if query_column is not None:\n cmd.extend(['-q', str(query_column)])\n if taxid_column is not None:\n cmd.extend(['-t', str(taxid_column)])\n if score_column is not None:\n cmd.extend(['-s', str(score_column)])\n if magnitude_column is not None:\n cmd.extend(['-m', str(magnitude_column)])\n if root_name is not None:\n cmd.extend(['-n', root_name])\n if no_hits is not None:\n cmd.append('-i')\n if no_rank is not None:\n cmd.append('-k')\n cmd.extend(input_tsvs)\n\n subprocess.check_call(cmd, env=env)\n\n def create_db(self, db_dir):\n \"\"\"Caution - this deletes the original .dmp files.\"\"\"\n if not self.executable_path():\n self.install_and_get_path()\n bin_path = os.path.dirname(self.executable_path())\n env = os.environ.copy()\n env['PATH'] = '{}:{}'.format(bin_path, env['PATH'])\n\n sh = os.path.join(self.opt, 'updateTaxonomy.sh')\n cmd = [sh, '--only-build', os.path.abspath(db_dir)]\n subprocess.check_call(cmd, env=env)\n\n def build_db(self, db_dir, taxdump_tar_gz=None, get_accessions=False):\n \"\"\"More all-in-one version of above\"\"\"\n if not self.executable_path():\n self.install_and_get_path()\n bin_path = os.path.dirname(self.executable_path())\n env = os.environ.copy()\n env['PATH'] = '{}:{}'.format(bin_path, env['PATH'])\n\n file.mkdir_p(db_dir)\n\n # get taxdump.tar.gz\n if taxdump_tar_gz:\n shutil.copyfile(taxdump_tar_gz, os.path.join(db_dir, 'taxdump.tar.gz'))\n else:\n cmd = [os.path.join(self.opt, 'updateTaxonomy.sh'),\n '--only-fetch', os.path.abspath(db_dir)]\n subprocess.check_call(cmd, env=env)\n\n # get accessions\n if get_accessions:\n cmd = [os.path.join(self.opt, 'updateAccessions.sh'),\n '--only-fetch', os.path.abspath(db_dir)]\n subprocess.check_call(cmd, env=env)\n\n # build taxdb\n cmd = [os.path.join(self.opt, 'updateTaxonomy.sh'),\n '--only-build', os.path.abspath(db_dir)]\n subprocess.check_call(cmd, env=env)\n\n # build accessions\n if get_accessions:\n cmd = [os.path.join(self.opt, 'updateAccessions.sh'),\n '--only-build', os.path.abspath(db_dir)]\n subprocess.check_call(cmd, env=env)\n" }, { "path": "src/viral_ngs/classify/last.py", "content": "\"Tools in the 'last' suite.\"\n\n# built-ins\nimport os\nimport logging\nimport shutil\nimport subprocess\n\n# within this module\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nfrom viral_ngs import core\nfrom viral_ngs.core import samtools\n\n_log = logging.getLogger(__name__)\n\nTOOL_NAME = \"last\"\n\n\nclass LastTools(core.Tool):\n \"\"\"\n \"Abstract\" base class for tools in the 'last' suite.\n Subclasses must define class members subtool_name #and subtool_name_on_broad.\n \"\"\"\n\n def __init__(self, install_methods=None):\n self.subtool_name = self.subtool_name if hasattr(self, \"subtool_name\") else TOOL_NAME\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand(shutil.which(self.subtool_name), require_executability=False)]\n core.Tool.__init__(self, install_methods=install_methods)\n\n\nclass Lastal(LastTools):\n \"\"\" wrapper for lastal subtool \"\"\"\n subtool_name = 'lastal'\n\n def get_hits(self, inBam, db,\n max_gapless_alignments_per_position=1,\n min_length_for_initial_matches=5,\n max_length_for_initial_matches=50,\n max_initial_matches_per_position=100,\n threads=None\n ):\n\n # convert BAM to interleaved FASTQ with no /1 /2 appended to the read IDs\n fastq_pipe = samtools.SamtoolsTool().bam2fq_pipe(inBam)\n\n # run lastal and emit list of read IDs\n # -P 0 = use threads = core count\n # -N 1 = report at most one alignment per query sequence\n # -i 1G = perform work in batches of at most 1GB of query sequence at a time\n # -f tab = write output in tab format instead of maf format\n cmd = [self.install_and_get_path(),\n '-n', max_gapless_alignments_per_position,\n '-l', min_length_for_initial_matches,\n '-L', max_length_for_initial_matches,\n '-m', max_initial_matches_per_position,\n '-Q', '1',\n '-P', str(misc.sanitize_thread_count(threads, tool_max_cores_value=0)),\n '-N', '1', '-i', '1G', '-f', 'tab',\n db,\n ]\n cmd = [str(x) for x in cmd]\n _log.debug('| ' + ' '.join(cmd) + ' |')\n lastal_pipe = subprocess.Popen(cmd, stdin=fastq_pipe.stdout, stdout=subprocess.PIPE)\n\n if fastq_pipe.poll():\n raise subprocess.CalledProcessError(fastq_pipe.returncode, \"SamtoolsTool().bam2fq_pipe({})\".format(inBam))\n\n # strip tab output to just query read ID names and emit\n last_read_id = None\n for line in lastal_pipe.stdout:\n line = line.decode('UTF-8').rstrip('\\n\\r')\n if not line.startswith('#'):\n read_id = line.split('\\t')[6]\n # only emit if it is not a duplicate of the previous read ID\n if read_id != last_read_id:\n last_read_id = read_id\n yield read_id\n\n if lastal_pipe.poll():\n raise subprocess.CalledProcessError(lastal_pipe.returncode, cmd)\n\n\nclass Lastdb(LastTools):\n \"\"\" wrapper for lastdb subtool \"\"\"\n subtool_name = 'lastdb'\n\n def is_indexed(self, db_prefix):\n return all(os.path.exists(db_prefix + x)\n for x in ('.bck', '.des', '.prj', '.sds', '.ssp', '.suf', '.tis'))\n\n def build_database(self, fasta_files, database_prefix_path=None): # pylint: disable=W0221\n if database_prefix_path is None:\n output_file_prefix = \"lastdb\"\n output_directory = tempfile.mkdtemp()\n else:\n output_file_prefix = os.path.basename(os.path.abspath(database_prefix_path))\n output_directory = os.path.dirname(os.path.abspath(database_prefix_path))\n\n # we can pass in a string containing a fasta file path\n # or a list of strings\n if isinstance(fasta_files, str):\n fasta_files = [fasta_files]\n elif isinstance(fasta_files, list) and fasta_files:\n pass\n else:\n raise TypeError(\"fasta_files was not a single fasta file, nor a list of fasta files\") # or something along that line\n\n # if more than one fasta file is specified, join them\n # otherwise if only one is specified, just use it\n if len(fasta_files) == 1 and not fasta_files[0].endswith('.gz'):\n input_fasta = fasta_files[0]\n else:\n input_fasta = file.mkstempfname(\".fasta\")\n file.cat(input_fasta, fasta_files) # automatically decompresses gz inputs\n\n self.execute(input_fasta, output_directory, output_file_prefix) \n\n return os.path.join(output_directory, output_file_prefix)\n\n\n def execute(self, inputFasta, outputDirectory, outputFilePrefix): # pylint: disable=W0221\n # get the path to the binary\n tool_cmd = [self.install_and_get_path()]\n\n # if the output directory (and its parents) do not exist, create them\n if not os.path.exists(outputDirectory):\n os.makedirs(outputDirectory)\n\n # append the prefix given to files created by lastdb\n tool_cmd.append(outputFilePrefix)\n\n # append the input filepath\n tool_cmd.append(os.path.realpath(inputFasta))\n\n # execute the lastdb command\n # lastdb writes files to the current working directory, so we need to set\n # it to the desired output location\n with file.pushd_popd(os.path.realpath(outputDirectory)):\n _log.debug(\" \".join(tool_cmd))\n subprocess.check_call(tool_cmd)\n\n\n" }, { "path": "src/viral_ngs/classify/taxonomy.py", "content": "\"\"\"\nNCBI Taxonomy database utilities.\n\nThis module provides classes and functions for working with NCBI taxonomy data,\nincluding taxonomy ID lookups, LCA calculations, and tree traversal.\n\"\"\"\n\nimport collections\nimport itertools\nimport logging\nimport operator\nimport os\n\nimport pysam\n\nfrom ..core import file as util_file\n\nlog = logging.getLogger(__name__)\n\n\nclass TaxIdError(ValueError):\n '''Taxonomy ID couldn't be determined.'''\n\n\ndef maybe_compressed(fn):\n \"\"\"Check for file existence, returning .gz version if original not found.\"\"\"\n fn_gz = fn + '.gz'\n if os.path.exists(fn):\n return fn\n elif os.path.exists(fn_gz):\n return fn_gz\n else:\n raise FileNotFoundError(fn)\n\n\nBlastRecord = collections.namedtuple(\n 'BlastRecord', [\n 'query_id', 'subject_id', 'percent_identity', 'aln_length', 'mismatch_count', 'gap_open_count', 'query_start',\n 'query_end', 'subject_start', 'subject_end', 'e_val', 'bit_score', 'extra'\n ]\n)\n\n\ndef blast_records(f):\n '''Yield blast m8 records line by line'''\n for line in f:\n if line.startswith('#'):\n continue\n parts = line.strip().split()\n for field in range(3, 10):\n parts[field] = int(parts[field])\n for field in (2, 10, 11):\n parts[field] = float(parts[field])\n args = parts[:12]\n extra = parts[12:]\n args.append(extra)\n\n yield BlastRecord(*args)\n\n\ndef paired_query_id(record):\n '''Replace paired suffixes in query ids.'''\n suffixes = ('/1', '/2')\n for suffix in suffixes:\n if record.query_id.endswith(suffix):\n rec_list = list(record)\n rec_list[0] = record.query_id[:-len(suffix)]\n return BlastRecord(*rec_list)\n return record\n\n\ndef blast_m8_taxids(record):\n return [int(record.subject_id)]\n\n\ndef extract_tax_id(sam1):\n '''Replace gi headers in subject ids to int taxonomy ids.'''\n parts = sam1.reference_name.split('|')\n if parts[0] == 'taxid':\n return int(parts[1])\n else:\n raise TaxIdError(parts)\n\n\ndef coverage_lca(query_ids, parents, lca_percent=100):\n '''Calculate the lca that will cover at least this percent of queries.\n\n Args:\n query_ids: []int list of nodes.\n parents: []int array of parents.\n lca_percent: (float) Cover at least this percent of queries.\n\n Return:\n (int) LCA\n '''\n lca_needed = lca_percent / 100 * len(query_ids)\n paths = []\n for query_id in query_ids:\n path = []\n while query_id != 1:\n path.append(query_id)\n if parents.get(query_id, 0) == 0:\n log.warning('Parent for query id: {} missing'.format(query_id))\n break\n query_id = parents[query_id]\n if query_id == 1:\n path.append(1)\n path = list(reversed(path))\n paths.append(path)\n if not paths:\n return\n\n last_common = 1\n max_path_length = max(len(path) for path in paths)\n for level in range(max_path_length):\n valid_paths = (path for path in paths if len(path) > level)\n max_query_id, hits_covered = collections.Counter(path[level] for path in valid_paths).most_common(1)[0]\n if hits_covered >= lca_needed:\n last_common = max_query_id\n else:\n break\n return last_common\n\n\ndef parents_to_children(parents):\n '''Convert an array of parents to lists of children for each parent.\n\n Returns:\n (dict[list]) Lists of children\n '''\n children = collections.defaultdict(list)\n for node, parent in parents.items():\n if node == 1:\n continue\n if parent != 0:\n children[parent].append(node)\n return children\n\n\ndef rank_code(rank):\n '''Get the short 1 letter rank code for named ranks.'''\n if rank == \"species\":\n return \"S\"\n elif rank == \"genus\":\n return \"G\"\n elif rank == \"family\":\n return \"F\"\n elif rank == \"order\":\n return \"O\"\n elif rank == \"class\":\n return \"C\"\n elif rank == \"phylum\":\n return \"P\"\n elif rank == \"kingdom\":\n return \"K\"\n elif rank == \"superkingdom\":\n return \"D\"\n elif rank == \"unclassified\":\n return \"U\"\n else:\n return \"-\"\n\n\nclass TaxonomyDb(object):\n \"\"\"\n NCBI Taxonomy database handler.\n\n This class loads NCBI taxonomy information from:\n ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/\n \"\"\"\n\n def __init__(\n self,\n tax_dir=None,\n gis=None,\n nodes=None,\n names=None,\n gis_paths=None,\n nodes_path=None,\n names_path=None,\n load_gis=False,\n load_nodes=False,\n load_names=False\n ):\n if tax_dir:\n if load_gis and not gis:\n gis_paths = [maybe_compressed(os.path.join(tax_dir, 'gi_taxid_nucl.dmp')),\n maybe_compressed(os.path.join(tax_dir, 'gi_taxid_prot.dmp'))]\n else:\n gis_paths = []\n nodes_path = load_nodes and maybe_compressed(os.path.join(tax_dir, 'nodes.dmp')) or None\n names_path = load_names and maybe_compressed(os.path.join(tax_dir, 'names.dmp')) or None\n self.tax_dir = tax_dir\n self.gis_paths = gis_paths\n self.nodes_path = nodes_path\n self.names_path = names_path\n if load_gis:\n if gis:\n self.gis = gis\n elif gis_paths:\n self.gis = {}\n for gi_path in gis_paths:\n log.info('Loading taxonomy gis: %s', gi_path)\n self.gis.update(self.load_gi_single_dmp(gi_path))\n if load_nodes:\n if nodes:\n self.ranks, self.parents = nodes\n elif nodes_path:\n log.info('Loading taxonomy nodes: %s', nodes_path)\n self.ranks, self.parents = self.load_nodes(nodes_path)\n if load_names:\n if names:\n self.names = names\n elif names_path:\n log.info('Loading taxonomy names: %s', names_path)\n self.names = self.load_names(names_path)\n\n def load_gi_single_dmp(self, dmp_path):\n '''Load a gi->taxid dmp file from NCBI taxonomy.'''\n gi_array = {}\n with util_file.open_or_gzopen(dmp_path) as f:\n for i, line in enumerate(f):\n gi, taxid = line.strip().split('\\t')\n gi = int(gi)\n taxid = int(taxid)\n gi_array[gi] = taxid\n if (i + 1) % 1000000 == 0:\n log.info('Loaded %s gis', i)\n return gi_array\n\n def load_names(self, names_db, scientific_only=True):\n '''Load the names.dmp file from NCBI taxonomy.'''\n if scientific_only:\n names = {}\n else:\n names = collections.defaultdict(list)\n for line in util_file.open_or_gzopen(names_db):\n parts = line.strip().split('|')\n taxid = int(parts[0])\n name = parts[1].strip()\n class_ = parts[3].strip()\n if scientific_only:\n if class_ == 'scientific name':\n names[taxid] = name\n else:\n names[taxid].append(name)\n return names\n\n def load_nodes(self, nodes_db):\n '''Load ranks and parents arrays from NCBI taxonomy.'''\n ranks = {}\n parents = {}\n with util_file.open_or_gzopen(nodes_db) as f:\n for line in f:\n parts = line.strip().split('|')\n taxid = int(parts[0])\n parent_taxid = int(parts[1])\n rank = parts[2].strip()\n parents[taxid] = parent_taxid\n ranks[taxid] = rank\n return ranks, parents\n\n def get_ordered_ancestors(self, taxid):\n ''' returns all ancestors of a taxid in proximity order: [parent, grandparent, greatgrandparent, etc] '''\n if taxid in self.parents and taxid != self.parents[taxid]:\n return [self.parents[taxid]] + self.get_ordered_ancestors(self.parents[taxid])\n else:\n return []\n\n def process_blast_hits(self, hits, top_percent):\n '''Filter groups of blast hits and perform lca.\n\n Args:\n hits: []BlastRecord groups of hits.\n top_percent: (float) Only consider hits within this percent of top bit score.\n\n Return:\n (int) Tax id of LCA.\n '''\n hits = (self.translate_gi_to_tax_id(hit) for hit in hits)\n\n hits = [hit for hit in hits if hit.subject_id != 0]\n if len(hits) == 0:\n return\n\n best_score = max(hit.bit_score for hit in hits)\n cutoff_bit_score = (100 - top_percent) / 100 * best_score\n valid_hits = (hit for hit in hits if hit.bit_score >= cutoff_bit_score)\n valid_hits = list(valid_hits)\n # Sort requires realized list\n valid_hits.sort(key=operator.attrgetter('bit_score'), reverse=True)\n if valid_hits:\n tax_ids = tuple(itertools.chain(*(blast_m8_taxids(hit) for hit in valid_hits)))\n return coverage_lca(tax_ids, self.parents)\n\n def process_sam_hits(self, sam_hits, top_percent):\n '''Filter groups of blast hits and perform lca.\n\n Args:\n sam_hits: []Sam groups of hits.\n top_percent: (float) Only consider hits within this percent of top bit score.\n\n Return:\n (int) Tax id of LCA.\n '''\n best_score = max(hit.get_tag('AS') for hit in sam_hits)\n cutoff_alignment_score = (100 - top_percent) / 100 * best_score\n valid_hits = (hit for hit in sam_hits if hit.get_tag('AS') >= cutoff_alignment_score)\n valid_hits = list(valid_hits)\n # Sort requires realized list\n valid_hits.sort(key=lambda sam1: sam1.get_tag('AS'), reverse=True)\n\n tax_ids = [extract_tax_id(hit) for hit in valid_hits]\n return coverage_lca(tax_ids, self.parents)\n\n def translate_gi_to_tax_id(self, record):\n '''Replace gi headers in subject ids to int taxonomy ids.'''\n gi = int(record.subject_id.split('|')[1])\n tax_id = self.gis[gi]\n rec_list = list(record)\n rec_list[1] = tax_id\n return BlastRecord(*rec_list)\n\n def sam_lca(self, sam_file, output=None, top_percent=10, unique_only=True):\n ''' Calculate the LCA taxonomy id for multi-mapped reads in a samfile.\n\n Assumes the sam is sorted by query name. Writes tsv output: query_id \\t tax_id.\n\n Args:\n sam_file: (path) Sam file.\n output: (io) Output file.\n top_percent: (float) Only this percent within top hit are used.\n unique_only: (bool) If true, only output assignments for unique, mapped reads. If False, set unmapped or duplicate reads as unclassified.\n\n Return:\n (collections.Counter) Counter of taxid hits\n '''\n\n c = collections.Counter()\n with pysam.AlignmentFile(sam_file, 'rb') as sam:\n seg_groups = (v for k, v in itertools.groupby(sam, operator.attrgetter('query_name')))\n for seg_group in seg_groups:\n segs = list(seg_group)\n query_name = segs[0].query_name\n # 0x4 is unmapped, 0x400 is duplicate\n mapped_segs = [seg for seg in segs if seg.flag & 0x4 == 0 and seg.flag & 0x400 == 0]\n if unique_only and not mapped_segs:\n continue\n\n if mapped_segs:\n tax_id = self.process_sam_hits(mapped_segs, top_percent)\n if tax_id is None:\n log.warning('Query: {} has no valid taxonomy paths.'.format(query_name))\n if unique_only:\n continue\n else:\n tax_id = 0\n else:\n tax_id = 0\n\n if output:\n classified = 'C' if tax_id else 'U'\n output.write('{}\\t{}\\t{}\\n'.format(classified, query_name, tax_id))\n c[tax_id] += 1\n return c\n\n def sam_lca_report(self, bam_aligned, outReport, outReads=None, unique_only=None):\n if outReads:\n lca_tsv = outReads\n else:\n lca_tsv = util_file.mkstempfname('.tsv')\n with util_file.open_or_gzopen(lca_tsv, 'wt') as lca:\n hits = self.sam_lca(bam_aligned, lca, top_percent=10, unique_only=unique_only)\n with open(outReport, 'w') as f:\n for line in self.kraken_dfs_report(hits):\n print(line, file=f)\n\n def blast_lca(self,\n m8_file,\n output,\n paired=False,\n min_bit_score=50,\n max_expected_value=0.01,\n top_percent=10,):\n '''Calculate the LCA taxonomy id for groups of blast hits.\n\n Writes tsv output: query_id \\t tax_id\n\n Args:\n m8_file: (io) Blast m8 file to read.\n output: (io) Output file.\n paired: (bool) Whether to count paired suffixes /1,/2 as one group.\n min_bit_score: (float) Minimum bit score or discard.\n max_expected_value: (float) Maximum e-val or discard.\n top_percent: (float) Only this percent within top hit are used.\n '''\n records = blast_records(m8_file)\n records = (r for r in records if r.e_val <= max_expected_value)\n records = (r for r in records if r.bit_score >= min_bit_score)\n if paired:\n records = (paired_query_id(rec) for rec in records)\n blast_groups = (v for k, v in itertools.groupby(records, operator.attrgetter('query_id')))\n for blast_group in blast_groups:\n blast_group = list(blast_group)\n tax_id = self.process_blast_hits(blast_group, top_percent)\n query_id = blast_group[0].query_id\n if not tax_id:\n log.debug('Query: {} has no valid taxonomy paths.'.format(query_id))\n classified = 'C' if tax_id else 'U'\n output.write('{}\\t{}\\t{}\\n'.format(classified, query_id, tax_id))\n\n def kraken_dfs(self, lines, taxa_hits, total_hits, taxid, level):\n '''Recursively do DFS for number of hits per taxa.'''\n cum_hits = num_hits = taxa_hits.get(taxid, 0)\n for child_taxid in self.children[taxid]:\n cum_hits += self.kraken_dfs(lines, taxa_hits, total_hits, child_taxid, level + 1)\n percent_covered = '%.2f' % (cum_hits / total_hits * 100)\n rank = rank_code(self.ranks[taxid])\n name = self.names[taxid]\n if cum_hits > 0:\n lines.append('\\t'.join([percent_covered, str(cum_hits), str(num_hits), rank, str(taxid), ' ' * level + name]))\n return cum_hits\n\n def kraken_dfs_report(self, taxa_hits):\n '''Return a kraken compatible DFS report of taxa hits.\n\n Warning: this potentially mutates the self.children variable\n\n Args:\n taxa_hits: (collections.Counter) # of hits per tax id.\n\n Return:\n []str lines of the report\n '''\n\n self.children = parents_to_children(self.parents) # huh??? are we sure we want to mutate?\n total_hits = sum(taxa_hits.values())\n if total_hits == 0:\n return ['\\t'.join(['100.00', '0', '0', 'U', '0', 'unclassified'])]\n\n lines = []\n self.kraken_dfs(lines, taxa_hits, total_hits, 1, 0)\n unclassified_hits = taxa_hits.get(0, 0)\n unclassified_hits += taxa_hits.get(-1, 0)\n\n if unclassified_hits > 0:\n percent_covered = '%.2f' % (unclassified_hits / total_hits * 100)\n lines.append(\n '\\t'.join([\n str(percent_covered), str(unclassified_hits), str(unclassified_hits), 'U', '0', 'unclassified'\n ])\n )\n return reversed(lines)\n" }, { "path": "src/viral_ngs/core/__init__.py", "content": "'''Core module containing Tool base classes, utilities, and bioinformatics tool wrappers.\n\nThis module consolidates what was previously in tools/ and util/ directories.\n'''\n\n__author__ = \"dpark@broadinstitute.org,irwin@broadinstitute.org\"\n\nimport collections\nimport json\nimport operator\nimport os\nimport re\nimport logging\nimport tempfile\nimport shutil\nimport shlex\nimport subprocess\n\nfrom urllib.request import urlretrieve\nfrom urllib.parse import urlparse\n\n_log = logging.getLogger(__name__)\n\n# Registry of installed tools\ninstalled_tools = {}\n\n\ndef iter_leaf_subclasses(a_class):\n \"Iterate over subclasses at all levels that don't themselves have a subclass\"\n is_leaf = True\n for subclass in sorted(a_class.__subclasses__(), key=operator.attrgetter(\"__name__\")):\n is_leaf = False\n for leaf_class in iter_leaf_subclasses(subclass):\n if not getattr(leaf_class, '_skiptest', False):\n yield leaf_class\n if is_leaf:\n yield a_class\n\n\ndef all_tool_classes():\n return iter_leaf_subclasses(Tool)\n\n\ndef get_tool_by_name(name):\n if name not in installed_tools:\n raise NotImplementedError\n return installed_tools[name]\n\n\ndef skip_install_test(condition=None):\n '''Decorate the Tool class to skip the installation test.'''\n\n def decorator(klass):\n if callable(condition) and not condition():\n return klass\n klass._skiptest = True\n return klass\n\n return decorator\n\n\ndef is_osx():\n return os.uname()[0] == 'Darwin'\n\n\nclass Tool(object):\n ''' Base tool class that includes install machinery.\n '''\n\n def __init__(self, install_methods=None):\n install_methods = install_methods or []\n\n self.install_methods = install_methods\n self.installed_method = None\n self.exec_path = None\n self.tool_version = None\n\n def is_installed(self):\n return (self.installed_method is not None)\n\n def install(self):\n if not self.is_installed():\n for m in self.install_methods:\n if not m.is_attempted():\n m.attempt_install()\n if m.is_installed():\n self.installed_method = m\n self.exec_path = m.executable_path()\n installed_tools[self.__class__.__name__] = self\n break\n\n def get_install_methods(self):\n return self.install_methods\n\n def set_install_methods(self, methods):\n self.install_methods = methods\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n raise NotImplementedError\n\n def executable_path(self):\n return self.exec_path\n\n def execute(self, *args):\n assert not os.system(self.exec_path + ' ' + args)\n\n def install_and_get_path(self):\n self.install()\n if self.executable_path() == None:\n raise NameError(\"unsuccessful in installing \" + type(self).__name__)\n return self.executable_path()\n\n\nclass InstallMethod(object):\n ''' Base class for installation methods for a given tool.\n None of these methods should ever fail/error. attempt_install should\n return silently regardless of the outcome (is_installed must be\n called to verify success or failure).\n '''\n\n def __init__(self):\n self.attempts = 0\n\n def is_attempted(self):\n return self.attempts\n\n def attempt_install(self): # Override _attempt_install, not this.\n self.attempts += 1\n self._attempt_install()\n\n def _attempt_install(self):\n raise NotImplementedError\n\n def is_installed(self):\n raise NotImplementedError\n\n def executable_path(self):\n raise NotImplementedError\n\n\nclass PrexistingUnixCommand(InstallMethod):\n ''' This is an install method that tries to find whether an executable\n binary already exists for free on the unix file system--it doesn't\n actually try to install anything.\n '''\n\n def __init__(self, path, verifycmd=None, verifycode=0, require_executability=True):\n self.path = path\n self.verifycmd = verifycmd\n self.verifycode = verifycode\n self.installed = False\n self.require_executability = require_executability\n InstallMethod.__init__(self)\n\n def _attempt_install(self):\n if os.access(self.path, (os.X_OK | os.R_OK) if self.require_executability else os.R_OK):\n if self.verifycmd:\n self.installed = (os.system(self.verifycmd) == self.verifycode)\n else:\n self.installed = True\n else:\n self.installed = False\n\n def is_installed(self):\n if not self.is_attempted():\n self.attempt_install()\n return self.installed\n\n def executable_path(self):\n return self.installed and self.path or None\n\n\n# Import submodules to make them accessible as viral_ngs.core.file, etc.\n# Note: version must be imported before cmd because cmd uses version at module level\nfrom . import version\nfrom . import misc\nfrom . import file\nfrom . import stats\nfrom . import cmd\nfrom . import illumina_indices\nfrom . import illumina_utils\n\n# Remaining core modules\nfrom . import errors\nfrom . import priorities\n\n# Tool wrappers\nfrom . import bbmap\nfrom . import bwa\nfrom . import cdhit\nfrom . import fastqc\nfrom . import minimap2\nfrom . import mvicuna\nfrom . import novoalign\nfrom . import picard\nfrom . import prinseq\nfrom . import sambamba\nfrom . import samtools\nfrom . import splitcode\nfrom . import trimmomatic\n" }, { "path": "src/viral_ngs/core/bbmap.py", "content": "'''\n Tool wrapper for the BBMap aligner and related tools.\n'''\n\nimport logging\nimport os\nimport os.path\nimport shutil\nimport subprocess\n\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = 'bbmap.sh'\n\n_log = logging.getLogger(__name__) # pylint: disable=invalid-name\n\nclass BBMapTool(Tool):\n '''Tool wrapper for the BBMap aligner and related tools.'''\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(BBMapTool, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([os.path.join(os.path.dirname(self.install_and_get_path()), 'bbversion.sh')]).decode('UTF-8').strip()\n\n def execute(self, tool, **kwargs): # pylint: disable=arguments-differ\n tool_dir = os.path.dirname(self.install_and_get_path())\n tool_cmd = [os.path.join(tool_dir, tool)] + \\\n ['{}={}'.format('in' if arg=='in_' else arg,\n (val is True and 't') or (val is False and 'f') or val)\n for arg, val in kwargs.items()]\n _log.debug('Running BBMap tool: %s', ' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n\n def align(self, inBam, refFasta, outBam, min_qual=0, nodisk=True, JVMmemory=None, **kwargs):\n with samtools.SamtoolsTool().bam2fq_tmp(inBam) as (in1, in2), \\\n util_file.tmp_dir('_bbmap_align') as t_dir:\n tmp_bam = os.path.join(t_dir, 'bbmap_out.bam')\n self.execute(tool='bbmap.sh', in1=in1, in2=in2, ref=refFasta, out=tmp_bam, nodisk=nodisk, **kwargs)\n \n # Samtools filter (optional)\n if min_qual:\n tmp_bam2 = os.path.join(tdir, 'bbmap.filtered.bam')\n cmd = [samtools.install_and_get_path(), 'view', '-b', '-S', '-1', '-q', str(min_qual), tmp_bam]\n _log.debug('%s > %s', ' '.join(cmd), tmp_bam2)\n with open(tmp_bam2, 'wb') as outf:\n util_misc.run_and_save(cmd, outf=outf)\n os.unlink(tmp_bam)\n tmp_bam = tmp_bam2\n\n # Picard SortSam\n sorter = picard.SortSamTool()\n sorter.execute(\n tmp_bam,\n outBam,\n sort_order='coordinate',\n picardOptions=['CREATE_INDEX=true', 'VALIDATION_STRINGENCY=SILENT'],\n JVMmemory=JVMmemory\n )\n\n def bbnorm(self, inFastq, outFastq, tmpdir=None, target=None, k=None,\n passes=None, mindepth=0, threads=None, memory=None):\n \"\"\"\n Run bbnorm for read normalization/deduplication.\n\n Args:\n inFastq: Input FASTQ file (interleaved for paired-end, or single-end)\n outFastq: Output FASTQ file (same format as input)\n tmpdir: Temporary directory for multipass processing\n target: Target normalization depth (default: bbnorm default of 100)\n k: Kmer length (default: bbnorm default of 31)\n passes: Number of passes (default: bbnorm default of 2)\n mindepth: Min kmer depth threshold (default: 0 to include all)\n threads: Number of threads (default: auto)\n memory: Java memory allocation string (e.g., \"4g\")\n\n Note: bbnorm auto-detects interleaved vs single-end format.\n \"\"\"\n tool_dir = os.path.dirname(self.install_and_get_path())\n tool_cmd = [os.path.join(tool_dir, 'bbnorm.sh'), '-eoom']\n\n if memory:\n tool_cmd.append('-Xmx{}'.format(memory))\n\n # Build arguments\n tool_cmd.append('in={}'.format(inFastq))\n tool_cmd.append('out={}'.format(outFastq))\n tool_cmd.append('mindepth={}'.format(mindepth))\n\n if tmpdir is not None:\n tool_cmd.append('tmpdir={}'.format(tmpdir))\n if target is not None:\n tool_cmd.append('target={}'.format(target))\n if k is not None:\n tool_cmd.append('k={}'.format(k))\n if passes is not None:\n tool_cmd.append('passes={}'.format(passes))\n if threads is not None:\n tool_cmd.append('threads={}'.format(threads))\n\n _log.debug('Running bbnorm: %s', ' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n\n" }, { "path": "src/viral_ngs/core/bwa.py", "content": "'''\n The BWA aligner.\n\n'''\n\nfrom collections import defaultdict\nimport logging\nimport os\nimport os.path\nimport subprocess\nimport shutil\nimport concurrent.futures\n\nfrom . import samtools\nfrom . import picard\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom .errors import *\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = 'bwa'\n\nlog = logging.getLogger(__name__)\n\n\nclass Bwa(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(Bwa, self).__init__(install_methods=install_methods)\n\n def execute(self, command, args, stdout=None, stdin=None, background=False): # pylint: disable=W0221\n tool_cmd = [self.install_and_get_path(), command] + args\n log.debug(' '.join(tool_cmd))\n if stdout:\n stdout = open(stdout, 'w')\n if background:\n subprocess.Popen(tool_cmd, stdout=stdout, stdin=stdin)\n else:\n subprocess.check_call(tool_cmd, stdout=stdout, stdin=stdin)\n if stdout:\n stdout.close()\n\n def index(self, inFasta, output=None, algorithm=None):\n cmd = []\n if algorithm is not None:\n if algorithm not in ('is', 'bwtsw'):\n raise NameError(algorithm + \" is not a recognized algorithm\")\n cmd.extend(('-a', algorithm))\n if output:\n cmd.extend(('-p', output))\n cmd.append(inFasta)\n self.execute('index', cmd)\n return output\n\n def align_mem_bam(self, inBam, refDb, outBam, options=None,\n min_score_to_filter=None, threads=None, JVMmemory=None, invert_filter=False, should_index=True):\n options = options or []\n\n samtools_tool = samtools.SamtoolsTool()\n threads = util_misc.sanitize_thread_count(threads)\n\n # fetch list of RGs\n rgs = list(samtools_tool.getReadGroups(inBam).keys())\n\n if len(rgs) == 0:\n # Can't do this\n raise InvalidBamHeaderError(\"{} lacks read groups\".format(inBam))\n\n elif len(rgs) == 1:\n # Only one RG, keep it simple\n self.align_mem_one_rg(inBam, refDb, outBam, options=options,\n min_score_to_filter=min_score_to_filter,\n threads=threads, invert_filter=invert_filter)\n\n else:\n # Multiple RGs, align one at a time and merge\n align_bams = []\n\n threads_for_chunk = int(round(min(max(threads / len(rgs),1),threads),0))+1\n # worker count limited to 1 for now to reduce in-memory index size resulting from\n # running multiple copies of bwa in parallel\n workers = 1 #len(rgs) if len(rgs) 0:\n align_bams.append(aln_bam)\n else:\n log.warning(\"No alignment output for RG %s in file %s against %s\", rg, inBam, refDb)\n\n if len(align_bams) == 0:\n util_file.touch(outBam)\n else:\n # Merge BAMs, sort, and index\n picardOptions = ['SORT_ORDER=coordinate', 'USE_THREADING=true']\n if should_index:\n picardOptions.append('CREATE_INDEX=true')\n picard.MergeSamFilesTool().execute(\n align_bams,\n outBam,\n picardOptions=picardOptions,\n JVMmemory=JVMmemory\n )\n # no longer required since MergeSamFiles creates the index\n #if outBam.endswith(\".bam\") or outBam.endswith(\".cram\"):\n # samtools.index(outBam)\n for bam in align_bams:\n os.unlink(bam)\n\n def align_mem_one_rg(self, inBam, refDb, outBam, rgid=None, options=None,\n min_score_to_filter=None, threads=None, JVMmemory=None, invert_filter=False, should_index=True):\n \"\"\"\n Performs an alignment of one read group in a bam file to a reference fasta file\n\n TODO: With the addition of a third aligner to viral-ngs, the functionality\n common to this method and to the comparable method in the Novoalign wrapper should\n be broken out as an \"aligner\" superclass, capable of aligning bam or fastq files with an arbitrary\n aligner, while preserving read groups. \n \"\"\"\n options = options or []\n\n samtools_tool = samtools.SamtoolsTool()\n\n # Require exactly one RG\n rgs = samtools_tool.getReadGroups(inBam)\n if len(rgs) == 0:\n raise InvalidBamHeaderError(\"{} lacks read groups\".format(inBam))\n elif len(rgs) == 1:\n if not rgid:\n rgid = list(rgs.keys())[0]\n elif not rgid:\n raise InvalidBamHeaderError(\"{} has {} read groups, but we require exactly one\".format(inBam, len(rgs)))\n if rgid not in rgs:\n raise InvalidBamHeaderError(\"{} has read groups, but not {}\".format(inBam, rgid))\n\n headerFile = util_file.mkstempfname('.{}.header.txt'.format(rgid))\n # Strip inBam to just one RG (if necessary)\n removeInput = False\n if len(rgs) == 1:\n one_rg_inBam = inBam\n samtools_tool.dumpHeader(one_rg_inBam, headerFile)\n else:\n # strip inBam to one read group\n with util_file.tempfname('.onebam.bam') as tmp_bam:\n samtools_tool.view(['-b', '-r', rgid], inBam, tmp_bam)\n # special exit if this file is empty\n if samtools_tool.count(tmp_bam) == 0:\n log.warning(\"No reads present for RG %s in file: %s\", rgid, inBam)\n return\n # simplify BAM header otherwise Novoalign gets confused\n one_rg_inBam = util_file.mkstempfname('.{}.in.bam'.format(rgid))\n removeInput = True\n\n with open(headerFile, 'wt') as outf:\n for row in samtools_tool.getHeader(inBam):\n if len(row) > 0 and row[0] == '@RG':\n if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]:\n # skip all read groups that are not rgid\n continue\n outf.write('\\t'.join(row) + '\\n')\n samtools_tool.reheader(tmp_bam, headerFile, one_rg_inBam)\n\n # perform actual alignment\n\n # get the read group line to give to BWA\n readgroup_line = \"\"\n with open(headerFile) as inf:\n for line in inf:\n if line.startswith(\"@RG\"):\n readgroup_line = line\n\n assert len(readgroup_line) > 0\n\n #with util_file.tempfname('.aligned.bam') as tmp_bam_aligned:\n # rather than reheader the alignment bam file later so it has the readgroup information\n # from the original bam file, we'll pass the RG line to bwa to write out\n self.mem(one_rg_inBam, refDb, outBam, options=options+['-R',\n readgroup_line.rstrip(\"\\r\\n\").replace('\\t','\\\\t')],\n min_score_to_filter=min_score_to_filter, threads=threads, invert_filter=invert_filter, should_index=should_index)\n\n return (rgid, outBam)\n # if there was more than one RG in the input, we had to create a temporary file with the one RG specified\n # and we can safely delete it this file\n # if there was only one RG in the input, we used it directly and should not delete it\n if removeInput:\n os.unlink(one_rg_inBam)\n\n def mem(self, inReads, refDb, outAlign, options=None, min_score_to_filter=None,\n threads=None, invert_filter=False, should_index=True):\n options = [] if not options else options\n\n threads = util_misc.sanitize_thread_count(threads)\n if '-t' not in options:\n options.extend(('-t', str(threads)))\n\n samtools_tool = samtools.SamtoolsTool()\n\n aln_sam = util_file.mkstempfname('.aligned.sam')\n fastq_pipe = samtools_tool.bam2fq_pipe(inReads)\n self.execute('mem', options + ['-p', refDb, '-'], stdout=aln_sam, stdin=fastq_pipe.stdout)\n\n if fastq_pipe.poll():\n raise subprocess.CalledProcessError(fastq_pipe.returncode, \"samtools.bam2fq_pipe() for {}\".format(inReads))\n\n if min_score_to_filter:\n # Filter reads in the alignment based on on their alignment score\n aln_sam_filtered = util_file.mkstempfname('.sam')\n self.filter_sam_on_alignment_score(aln_sam, aln_sam_filtered,\n min_score_to_filter, options, invert_filter=invert_filter)\n os.unlink(aln_sam)\n else:\n aln_sam_filtered = aln_sam\n\n \n samtools_tool.sort(aln_sam_filtered, outAlign, threads=threads)\n os.unlink(aln_sam_filtered)\n\n # cannot index sam files; only do so if a bam/cram is desired\n if should_index and (outAlign.endswith(\".bam\") or outAlign.endswith(\".cram\")):\n samtools_tool.index(outAlign)\n\n def filter_sam_on_alignment_score(self, in_sam, out_sam, min_score_to_filter,\n bwa_options, invert_filter=False):\n \"\"\"Filter reads in an alignment based on their alignment score.\n\n This is useful because bwa mem ignores its -T option on paired-end\n data (https://github.com/lh3/bwa/issues/133); -T normally specifies\n the threshold on score below which alignments are not output.\n\n This sums the alignment score across all alignments for each\n query name in the aligned SAM. This has the effect of summing\n the score across both reads in a pair (their query name is the same)\n as well as supplementary alignments (SAM flag 2048) and secondary\n alignments (SAM flag 256). The use of a summed score is reasonable for\n supplementary alignments, which bwa mem outputs. bwa mem normally\n does not output secondary alignments, but if it does then the\n use of a summed score might not be reasonable.\n \"\"\"\n if '-a' in bwa_options:\n log.warning((\"'bwa mem -a' will output secondary alignments, \"\n \"and the filter on alignment score will use \"\n \"a score that is summed across the primary and \"\n \"secondary alignments for each read; this might \"\n \"not be desired\"))\n\n # Determine an alignment score for each query name\n qname_alignment_scores = defaultdict(int)\n with open(in_sam) as in_sam_f:\n for line in in_sam_f:\n line = line.rstrip()\n if line.startswith('@'):\n # Skip headers\n continue\n ls = line.split('\\t')\n\n # bwa's output should have optional fields for all\n # alignments\n assert len(ls) >= 12\n\n qname = ls[0]\n aln_score = None\n for opt_field in ls[11:]:\n opt_field_tag, opt_field_type, opt_field_val = opt_field.split(':')\n if opt_field_tag == 'AS':\n # The alignment score output by bwa should be a\n # signed integer\n assert opt_field_type == 'i'\n aln_score = int(opt_field_val)\n break\n if aln_score is None:\n raise Exception((\"Unknown alignment score for query \"\n \"name %s\") % qname)\n qname_alignment_scores[qname] += aln_score\n\n # Write a SAM file that only includes reads whose query has a\n # sufficient alignment score summed across its alignments\n with open(out_sam, 'w') as out_sam_f:\n with open(in_sam) as in_sam_f:\n for line in in_sam_f:\n line = line.rstrip()\n if line.startswith('@'):\n # Rewrite all headers\n out_sam_f.write(line + '\\n')\n continue\n ls = line.split('\\t')\n\n qname = ls[0]\n if ((qname_alignment_scores[qname] >= min_score_to_filter and not invert_filter) or \n (qname_alignment_scores[qname] < min_score_to_filter and invert_filter)):\n # Write this query name\n out_sam_f.write(line + '\\n')\n" }, { "path": "src/viral_ngs/core/cdhit.py", "content": "'''\nCD-HIT\n'''\nfrom builtins import super\nimport itertools\nimport logging\nimport os\nimport os.path\nimport shlex\nimport shutil\nimport subprocess\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file\nfrom . import Tool, PrexistingUnixCommand\n\nlog = logging.getLogger(__name__)\n\nclass CdHit(Tool):\n\n COMMANDS = [\n 'cd-hit',\n 'cd-hit-est',\n 'cd-hit-2d',\n 'cd-hit-est-2d',\n 'cd-hit-dup',\n ]\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which('cd-hit'), require_executability=True)]\n super(CdHit, self).__init__(install_methods=install_methods)\n\n def execute(self, command, input_fn, output_fn, options=None, option_string=None, background=None):\n '''Perform a clustering on DNA/RNA sequences\n\n Args:\n input_fn: Input fasta filename\n output_fn: Output fasta filename\n '''\n assert command in self.COMMANDS\n cmd = [command]\n cmd.extend(['-i', input_fn])\n cmd.extend(['-o', output_fn])\n\n options = options or {}\n if options:\n # We need some way to allow empty options args like --log, hence\n # we filter out on 'x is None'.\n cmd.extend([str(x) for x in itertools.chain(*options.items()) if x is not None])\n if option_string:\n cmd.extend(shlex.split(option_string))\n log.debug(\"Calling {}: {}\".format(command, \" \".join(cmd)))\n if background:\n return subprocess.Popen(cmd)\n else:\n return subprocess.check_call(cmd)\n" }, { "path": "src/viral_ngs/core/cmd.py", "content": "'''This gives a main() function that serves as a nice wrapper\naround other commands and presents the ability to serve up multiple\ncommand-line functions from a single python script.\n'''\n\nimport os\nimport os.path\nimport tempfile\nimport textwrap\nimport sys\nimport shutil\nimport logging\nimport argparse\nimport importlib\nimport inspect\nimport collections\n\n# Note: avoid circular import by importing submodules directly, not the util package\nfrom . import version as util_version\nfrom . import misc as util_misc\nfrom . import file as util_file\n\n__author__ = \"dpark@broadinstitute.org\"\n__version__ = util_version.get_version()\n\nlog = logging.getLogger()\ntmp_dir = None\n\nclass color(object):\n \"\"\" *nix terminal control characters for altering text display\n \"\"\"\n PURPLE = '\\033[95m'\n CYAN = '\\033[96m'\n DARKCYAN = '\\033[36m'\n BLUE = '\\033[94m'\n GREEN = '\\033[92m'\n YELLOW = '\\033[93m'\n RED = '\\033[91m'\n BOLD = '\\033[1m'\n UNDERLINE = '\\033[4m'\n END = '\\033[0m'\n\ndef setup_logger(log_level):\n loglevel = getattr(logging, log_level.upper(), None)\n assert loglevel, \"unrecognized log level: %s\" % log_level\n log.setLevel(loglevel)\n h = logging.StreamHandler()\n h.setFormatter(logging.Formatter(\"%(asctime)s - %(module)s:%(lineno)d:%(funcName)s - %(levelname)s - %(message)s\"))\n log.addHandler(h)\n\n\ndef script_name():\n return os.path.basename(sys.argv[0]).rsplit('.', 1)[0]\n\n\ndef common_args(parser, arglist=(('tmp_dir', None), ('loglevel', None))):\n for k, v in arglist:\n if k == 'loglevel':\n if not v:\n v = 'INFO'\n parser.add_argument(\"--loglevel\",\n dest=\"loglevel\",\n help=\"Verboseness of output. [default: %(default)s]\",\n default=v,\n choices=('DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL', 'EXCEPTION'))\n elif k == 'tmp_dir':\n if not v:\n v = find_tmp_dir()\n parser.add_argument(\"--tmp_dir\",\n dest=\"tmp_dir\",\n help=\"Base directory for temp files. [default: %(default)s]\",\n default=v)\n parser.add_argument(\"--tmp_dirKeep\",\n action=\"store_true\",\n dest=\"tmp_dirKeep\",\n help=\"\"\"Keep the tmp_dir if an exception occurs while\n running. Default is to delete all temp files at\n the end, even if there's a failure.\"\"\",\n default=False)\n elif k == 'threads':\n # if v is None, sanitize_thread_count() sets count to all available cores\n thread_count = util_misc.sanitize_thread_count(v)\n parser.add_argument('--threads',\n dest=\"threads\",\n type=int,\n help=\"Number of threads; by default all cores are used\",\n default=thread_count)\n elif k == 'version':\n if not v:\n v = __version__\n parser.add_argument('--version', '-V', action='version', version=v)\n else:\n raise Exception(\"unrecognized argument %s\" % k)\n return parser\n\n\ndef main_command(mainfunc):\n ''' This wraps a python method in another method that can be called\n with an argparse.Namespace object. When called, it will pass all\n the values of the object on as parameters to the function call.\n '''\n\n def _main(args):\n args2 = dict((k, v) for k, v in vars(args).items() if k not in (\n 'loglevel', 'tmp_dir', 'tmp_dirKeep', 'version', 'func_main', 'command'))\n mainfunc(**args2)\n\n _main.__doc__ = mainfunc.__doc__\n return _main\n\n\ndef attach_main(parser, cmd_main, split_args=False):\n ''' This attaches the main function call to a parser object.\n '''\n if split_args:\n cmd_main = main_command(cmd_main)\n parser.description = cmd_main.__doc__\n parser.set_defaults(func_main=cmd_main)\n return parser\n\nclass _HelpAction(argparse._HelpAction):\n\n def __call__(self, parser, namespace, values, option_string=None):\n\n print(\"\\nEnter a subcommand to view additional information:\")\n\n # retrieve subparser actions from parser\n subparsers_actions = [\n action for action in parser._actions\n if isinstance(action, argparse._SubParsersAction)]\n\n indent_space = \" \" * 5\n for subparsers_action in subparsers_actions:\n # get all subparsers and print descriptions for each\n for choice, subparser in subparsers_action.choices.items():\n print(\"\\n{indent}{filename} {cmd} [...]\".format(indent=indent_space, filename=os.path.basename(sys.argv[0]), cmd=color.BOLD+choice+color.END))\n\n # if the subparser has a description string, format and print it\n if subparser.description:\n # clean up line breaks and spaces in the triple-quoted string\n help_description = subparser.description.replace(\"\\n\",\"\").replace(\". \",\". \").replace(\" \",\"\").replace(\"\\t\",\"\")\n help_description = help_description.strip()\n # wrap text to a set width\n help_description = textwrap.fill(help_description, 60)\n # indent each line\n help_description = help_description.replace(\"\\n\",\"\\n{}\".format(indent_space*2))\n print(\"{}{}\".format(indent_space*2, help_description))\n\n print()\n parser.print_help()\n\n parser.exit()\n\n\n\nclass storeMultiArgsOrFallBackToConst(argparse.Action):\n \"\"\"\n Custom argparse action to allow multiple values \n to be stored in a list for an optional argument, with a fallback\n const value in the event the arg flag is passed without one or more\n values. Equivalent to using:\n nargs='?',const=1\n (but for multiple values)\n\n 1) If --arg is NOT passed: set to self.default (None)\n 2) If --arg IS passed:\n a) If values are supplied:\n set arg to list of values supplied\n b) If no values are supplied:\n set arg to self.const\n\n Usage:\n p.add_argument('--option',\n nargs='*',\n action=customAction,\n type=int,\n const=[1, 2, 3]\n )\n \"\"\"\n def __call__(self, parser, namespace, values, option_string=None):\n if not option_string:\n setattr(namespace, self.dest, self.default) #default=None\n else:\n if not values:\n setattr(namespace, self.dest, self.const)\n else:\n setattr(namespace, self.dest, values)\n\ndef make_parser(commands, description):\n ''' commands: a list of pairs containing the following:\n 1. name of command (string, no whitespace)\n 2. method to call (no arguments) that returns an argparse parser.\n If commands contains exactly one member and the name of the\n only command is None, then we get rid of the whole multi-command\n thing and just present the options for that one function.\n description: a long string to present as a description of your script\n as a whole if the script is run with no arguments\n '''\n if len(commands) == 1 and commands[0][0] == None:\n # only one (nameless) command in this script, simplify\n parser = commands[0][1]()\n parser.set_defaults(command='')\n else:\n # multiple commands available\n parser = argparse.ArgumentParser(description=description, usage='%(prog)s subcommand', add_help=False)\n parser.add_argument('--help', '-h', action=_HelpAction, help=argparse.SUPPRESS)\n parser.add_argument('--version', '-V', action='version', version=__version__, help=argparse.SUPPRESS)\n subparsers = parser.add_subparsers(title='subcommands', dest='command', metavar='\\033[F') # \\033[F moves cursor up\n for cmd_name, cmd_parser in commands:\n help_str = cmd_parser.__doc__ if cmd_parser.__doc__ and len(cmd_parser.__doc__) else None\n # give a blank string for help if the parser docstring is null\n # so sphinx-argparse doesnt't render \"Undocumented\"\n if (not help_str) and os.environ.get('READTHEDOCS') or 'sphinx' in sys.modules:\n help_str = \" \"\n p = subparsers.add_parser(cmd_name, help=help_str, formatter_class=argparse.ArgumentDefaultsHelpFormatter)\n cmd_parser(p)\n return parser\n\n\ndef main_argparse(commands, description):\n parser = make_parser(commands, description)\n\n # if called with no arguments, print help\n if len(sys.argv) == 1:\n parser.parse_args(['--help'])\n elif len(sys.argv) == 2 and (len(commands) > 1 or commands[0][0] != None):\n parser.parse_args([sys.argv[1], '--help'])\n args = parser.parse_args()\n\n setup_logger(not hasattr(args, 'loglevel') and 'DEBUG' or args.loglevel)\n log.info(\"software version: %s, python version: %s\", __version__, sys.version)\n log.info(\"command: %s %s %s\", sys.argv[0], sys.argv[1],\n ' '.join([\"%s=%s\" % (k, v) for k, v in vars(args).items() if k not in ('command', 'func_main')]))\n\n if hasattr(args, 'tmp_dir'):\n # If this command has a tmp_dir option, use that as a base directory\n # and create a subdirectory within it which we will then destroy at\n # the end of execution.\n\n proposed_dir = 'tmp-%s-%s' % (script_name(), args.command)\n for e in ('LSB_JOBID', 'JOB_ID'): # LSB_JOBID is for LSF, JOB_ID is for UGER/GridEngine\n if e in os.environ:\n proposed_dir = 'tmp-%s-%s-%s-%s' % (script_name(), args.command, os.environ[e],\n os.environ.get('LSB_JOBINDEX','0'))\n break\n tempfile.tempdir = tempfile.mkdtemp(prefix='%s-' % proposed_dir, dir=args.tmp_dir)\n log.debug(\"using tempDir: %s\", tempfile.tempdir)\n os.environ['TMPDIR'] = tempfile.tempdir # this is for running R\n try:\n ret = args.func_main(args)\n finally:\n if (hasattr(args, 'tmp_dirKeep') and args.tmp_dirKeep) or util_file.keep_tmp():\n log.debug(\"After running %s, saving tmp_dir at %s\", args.command, tempfile.tempdir)\n else:\n shutil.rmtree(tempfile.tempdir)\n else:\n # otherwise just run the command\n ret = args.func_main(args)\n if ret is None:\n ret = 0\n return ret\n\n\ndef find_tmp_dir():\n ''' This provides a suggested base directory for a temp dir for use in your\n argparse-based tmp_dir option.\n '''\n tmpdir = '/tmp'\n if os.access('/local/scratch', os.X_OK | os.W_OK | os.R_OK) and os.path.isdir('/local/scratch'):\n tmpdir = '/local/scratch'\n # LSB_JOBID is for LSF, JOB_ID is for UGER/GridEngine\n for e in ('LSB_JOBID', 'JOB_ID'):\n if e in os.environ:\n # this directory often exists for LSF jobs, but not always.\n # for example, if the job is part of a job array, this directory is called\n # something unpredictable and unfindable, so just use /local/scratch\n proposed_dir = '/local/scratch/%s.tmpdir' % os.environ[e]\n if os.access(proposed_dir, os.X_OK | os.W_OK | os.R_OK):\n tmpdir = proposed_dir\n break\n if 'TMPDIR' in os.environ and os.path.isdir(os.environ['TMPDIR']):\n tmpdir = os.environ['TMPDIR']\n return tmpdir\n\nclass BadInputError(RuntimeError):\n\n '''Indicates that an invalid input was given to a command'''\n\n def __init__(self, reason):\n super(BadInputError, self).__init__(reason)\n\ndef check_input(condition, error_msg):\n '''Check input to a command'''\n if not condition:\n raise BadInputError(error_msg)\n\ndef parse_cmd(module, cmd, args):\n \"\"\"Parse arguments `args` to command `cmd` from module `module`.\"\"\"\n if isinstance(module, str): \n module = importlib.import_module(module)\n assert inspect.ismodule(module)\n parser_fn = dict(getattr(module, '__commands__'))[cmd]\n return parser_fn(argparse.ArgumentParser()).parse_args(list(map(str, args)))\n \nCmdRunInfo = collections.namedtuple('CmdRunInfo', ['result', 'args_parsed'])\n\ndef run_cmd(module, cmd, args):\n \"\"\"Run command after parsing its arguments with the command's parser.\n \n Args:\n module: the module object for the script containing the command\n cmd: the command name\n args: list of args to the command\n\n Returns:\n a CmdRunInfo namedtuple with info about the run\n \"\"\"\n log.info('Calling command {} with args {}'.format(cmd, args))\n args_parsed = parse_cmd(module, cmd, args)\n result = args_parsed.func_main(args_parsed)\n return CmdRunInfo(result=result, args_parsed=args_parsed)\n" }, { "path": "src/viral_ngs/core/errors.py", "content": "#!/usr/bin/env python\n\nclass QCError(RuntimeError):\n '''Indicates a failure at a QC step.'''\n \n def __init__(self, reason):\n super(QCError, self).__init__(reason)\n\nclass InvalidBamHeaderError(ValueError):\n '''Indicates a malformed or otherwise unusable bam file header'''\n pass" }, { "path": "src/viral_ngs/core/fastqc.py", "content": "'''\n FastQC\n'''\n\nimport logging\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport sys\nimport zipfile\n\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = 'fastqc'\n\nlog = logging.getLogger(__name__)\n\nclass FastQC(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(FastQC, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-v']).decode('UTF-8').strip().split()[1]\n\n def execute(self, inBam, out_html, out_zip=None, threads=None): # pylint: disable=W0221\n threads = util_misc.sanitize_thread_count(threads)\n\n if samtools.SamtoolsTool().isEmpty(inBam):\n # fastqc can't deal with empty input\n with open(out_html, 'wt') as outf:\n outf.write(\"Input BAM has zero reads.\\n\")\n if out_zip:\n with zipfile.ZipFile(out_zip, 'w') as zf:\n pass\n\n else:\n # run fastqc\n with util_file.tmp_dir() as out_dir:\n\n # fastqc sets java \"-Xmx\" (max java heap size) to 250mb/thread\n tool_cmd = [self.install_and_get_path(),\n '-t', str(threads),\n '-o', out_dir,\n inBam]\n log.debug(' '.join(tool_cmd))\n subprocess.check_call(tool_cmd, stdout=sys.stderr)\n expected_out = os.path.join(out_dir, os.path.basename(inBam)[:-4]) + \"_fastqc.html\"\n shutil.copyfile(expected_out, out_html)\n if out_zip:\n expected_out_zip = os.path.join(out_dir, os.path.basename(inBam)[:-4]) + \"_fastqc.zip\"\n shutil.copyfile(expected_out_zip, out_zip)\n log.debug(\"complete\")\n" }, { "path": "src/viral_ngs/core/file.py", "content": "'''This gives a number of useful quick methods for dealing with\ntab-text files and gzipped files, as well as fasta files, plus\ngeneral file-handling routines.\n'''\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport codecs\nimport concurrent.futures\nimport contextlib\nimport csv\nimport errno\nimport gzip\nimport inspect\nimport io\nimport io\nimport itertools\nimport json\nimport logging\nimport os\nimport re\nimport shutil\nimport sqlite3\nimport subprocess\nimport sys\nimport tarfile\nimport tempfile\nimport urllib.request\n\nfrom Bio import SeqIO\nfrom Bio.Seq import Seq\nfrom Bio.SeqIO import FastaIO\nfrom Bio.SeqRecord import SeqRecord\nimport bz2\nimport lz4.frame\nimport pysam\nimport zstandard as zstd\n\nfrom . import misc as util_misc # was: from viral_ngs import util\n\nlog = logging.getLogger(__name__)\n\nif sys.version_info >= (3, 10, 12):\n '''\n Set the default extraction filter at class instance level for the tarfile\n module, to avoid needing to specify it every time we extract a tarball.\n The extraction filter avoids extracting \"unsafe\" items from tarballs, and\n is available in Python 3.10.12+. This sets the default to \"tar_filter\".\n For other filter types and general info on the tarfile module, see:\n https://docs.python.org/3.12/library/tarfile.html#tarfile.TarFile.extraction_filter\n https://docs.python.org/3.12/library/tarfile.html#tarfile.tar_filter\n https://docs.python.org/3.12/library/tarfile.html#extraction-filters\n '''\n log.debug(\"Setting extraction filter for tarfile module to tar_filter\")\n tarfile.TarFile.extraction_filter = staticmethod(tarfile.tar_filter) if hasattr(tarfile, 'data_filter') else (lambda member, path: member)\n\nclass StringNotFoundException(Exception):\n \"\"\"When a substring is not found.\"\"\"\n pass\n\n\ndef get_project_path():\n '''Return the absolute path of the top-level project, assumed to be the\n parent of the directory containing this script.\n\n When package is pip-installed (e.g., in Docker), the relative path from\n __file__ won't work. In that case, check for VIRAL_NGS_SOURCE_DIR env var\n or fall back to cwd if it contains a tests/ directory.\n '''\n # Check for explicit environment variable first (useful for Docker/CI)\n if 'VIRAL_NGS_SOURCE_DIR' in os.environ:\n return os.environ['VIRAL_NGS_SOURCE_DIR']\n\n # Try relative path from this file (works in source checkout)\n path = __file__ # path to this script\n path = os.path.expanduser(path) # interpret ~\n path = os.path.abspath(path) # convert to absolute path\n path = os.path.dirname(path) # containing directory: util\n path = os.path.dirname(path) # containing directory: viral_ngs\n path = os.path.dirname(path) # containing directory: src\n path = os.path.dirname(path) # containing directory: project root\n\n # If tests directory exists at calculated path, use it\n if os.path.isdir(os.path.join(path, 'tests')):\n return path\n\n # Fall back to current working directory if it has tests/\n cwd = os.getcwd()\n if os.path.isdir(os.path.join(cwd, 'tests')):\n return cwd\n\n # Last resort: return calculated path even if tests/ doesn't exist\n return path\n\n\ndef get_build_path():\n raise Exception('deprecated')\n return os.path.join(get_project_path(), 'tools', 'build')\n\n\ndef get_test_path():\n '''Return absolute path of \"tests\" directory'''\n return os.path.join(get_project_path(), 'tests')\n\n\ndef get_test_input_path(testClassInstance=None):\n '''Return the path to the directory containing input files for the specified\n test class\n '''\n if testClassInstance is not None:\n return os.path.join(get_test_path(), 'input', type(testClassInstance).__name__)\n else:\n return os.path.join(get_test_path(), 'input')\n\ndef check_paths(read=(), write=(), read_and_write=()):\n '''Check that we can read and write the specified files, throw an exception if not. Useful for checking\n error conditions early in the execution of a command. Each arg can be a filename or iterable of filenames.\n '''\n read, write, read_and_write = map(util_misc.make_seq, (read, write, read_and_write))\n assert not (set(read) & set(write))\n assert not (set(read) & set(read_and_write))\n assert not (set(write) & set(read_and_write))\n\n for fname in read+read_and_write:\n with open(fname):\n pass\n\n for fname in write+read_and_write:\n if not os.path.exists(fname):\n with open(fname, 'w'):\n pass\n os.unlink(fname)\n else:\n if not (os.path.isfile(fname) and os.access(fname, os.W_OK)):\n raise PermissionError('Cannot write ' + fname)\n\ndef mkstempfname(suffix='', prefix='tmp', directory=None, text=False):\n ''' There's no other one-liner way to securely ask for a temp file by\n filename only. This calls mkstemp, which does what we want, except\n that it returns an open file handle, which causes huge problems on NFS\n if we don't close it. So close it first then return the name part only.\n '''\n fd, fn = tempfile.mkstemp(prefix=prefix, suffix=suffix, dir=directory, text=text)\n os.close(fd)\n return fn\n\n\n@contextlib.contextmanager\ndef tempfname(*args, **kwargs):\n '''Create a tempfile name on context entry, delete the file (if it exists) on context exit.\n The file is kept for debugging purposes if the environment variable VIRAL_NGS_TMP_DIRKEEP is set.\n '''\n fn = mkstempfname(*args, **kwargs)\n try:\n yield fn\n finally:\n if os.path.isfile(fn) and not keep_tmp():\n os.unlink(fn)\n\n\n@contextlib.contextmanager\ndef tempfnames(suffixes, *args, **kwargs):\n '''Create a set of tempfile names on context entry, delete the files (if they exist) on context exit.\n The files are kept for debugging purposes if the environment variable VIRAL_NGS_TMP_DIRKEEP is set.\n '''\n fns = [mkstempfname(sfx, *args, **kwargs) for sfx in suffixes]\n try:\n yield fns\n finally:\n if not keep_tmp():\n for fn in fns:\n if os.path.isfile(fn):\n os.unlink(fn)\n\n@contextlib.contextmanager\ndef tmp_dir(*args, **kwargs):\n \"\"\"Create and return a temporary directory, which is cleaned up on context exit\n unless keep_tmp() is True.\"\"\"\n\n _args = inspect.getcallargs(tempfile.mkdtemp, *args, **kwargs)\n length_margin = 6\n for pfx_sfx in ('prefix', 'suffix'):\n if _args[pfx_sfx]:\n _args[pfx_sfx] = string_to_file_name(_args[pfx_sfx], file_system_path=_args['dir'], length_margin=length_margin)\n length_margin += len(_args[pfx_sfx].encode('utf-8'))\n\n name = None\n try:\n name = tempfile.mkdtemp(**_args)\n yield name\n finally:\n if name is not None:\n if keep_tmp():\n log.debug('keeping tempdir ' + name)\n else:\n shutil.rmtree(name, ignore_errors=True)\n\n@contextlib.contextmanager\ndef pushd_popd(target_dir):\n '''Temporary change to the specified directory, restoring current directory on context exit.'''\n save_cwd = os.getcwd()\n try:\n os.chdir(target_dir)\n yield target_dir\n finally:\n os.chdir(save_cwd)\n\ndef keep_tmp():\n \"\"\"Whether to preserve temporary directories and files (useful during debugging).\n Return True if the environment variable VIRAL_NGS_TMP_DIRKEEP is set.\n \"\"\"\n return 'VIRAL_NGS_TMP_DIRKEEP' in os.environ\n\ndef set_tmp_dir(name):\n from . import cmd as util_cmd # lazy import to avoid circular dependency\n proposed_prefix = ['tmp']\n if name:\n proposed_prefix.append(name)\n for e in ('LSB_JOBID', 'LSB_JOBINDEX', 'JOB_ID'):\n if e in os.environ:\n proposed_prefix.append(os.environ[e])\n break\n tempfile.tempdir = tempfile.mkdtemp(prefix='-'.join(proposed_prefix) + '-', dir=util_cmd.find_tmp_dir())\n os.environ['TMPDIR'] = tempfile.tempdir\n return tempfile.tempdir\n\n\ndef destroy_tmp_dir(tempdir=None):\n if not keep_tmp():\n if tempdir:\n shutil.rmtree(tempdir)\n elif tempfile.tempdir:\n shutil.rmtree(tempfile.tempdir)\n tempfile.tempdir = None\n\n\ndef extract_tarball(tarfile, out_dir=None, threads=None, compression='auto', pipe_hint=None):\n if not (tarfile == '-' or (os.path.exists(tarfile) and not os.path.isdir(tarfile))):\n raise Exception('file does not exist: %s' % tarfile)\n if out_dir is None:\n out_dir = tempfile.mkdtemp(prefix='extract_tarball-')\n else:\n mkdir_p(out_dir)\n assert compression in ('gz', 'bz2', 'lz4', 'zip', 'zst', 'none', 'auto')\n if compression == 'auto':\n assert tarfile != '-' or pipe_hint, \"cannot autodetect on stdin input unless pipe_hint provided\"\n # auto-detect compression type based on file name\n if tarfile=='-':\n lower_fname = pipe_hint\n else:\n lower_fname = os.path.basename(tarfile).lower()\n if lower_fname.endswith('.tar'):\n compression = 'none'\n elif lower_fname.endswith('.zip'):\n compression = 'zip'\n elif lower_fname.endswith('.tgz') or lower_fname.endswith('.tar.gz'):\n compression = 'gz'\n elif lower_fname.endswith('.tar.lz4'):\n compression = 'lz4'\n elif lower_fname.endswith('.tar.bz2'):\n compression = 'bz2'\n elif lower_fname.endswith('.tar.zst'):\n compression = 'zst'\n else:\n raise Exception(\"unsupported file type: %s\" % tarfile)\n\n if compression == 'zip':\n assert tarfile != '-'\n cmd = ['unzip', '-q', tarfile, '-d', out_dir]\n with open(os.devnull, 'w') as fnull:\n subprocess.check_call(cmd, stderr=fnull)\n else:\n if compression == 'gz':\n decompressor = ['pigz', '-dc', '-p', str(util_misc.sanitize_thread_count(threads))]\n elif compression == 'bz2':\n decompressor = ['lbzip2', '-dc', '-n', str(util_misc.sanitize_thread_count(threads))]\n elif compression == 'lz4':\n decompressor = ['lz4', '-d']\n elif compression == 'zst':\n decompressor = ['zstd', '-dc']\n elif compression == 'none':\n decompressor = ['cat']\n\n untar_cmd = ['tar']\n # always tolerate concatenated tarballs \n # (remove \"True\" to only allow for non-piped input)\n if True or tarfile != '-': \n # --ignore-zeros to allow tarballs that have been made of other tarballs merged via simply\n # calling 'cat' on them all\n untar_cmd.extend(['--ignore-zeros'])\n untar_cmd.extend(['-C', out_dir, '-x'])\n\n if os.getuid() == 0:\n # GNU tar behaves differently when run as root vs normal user\n # we want normal user behavior always\n if 'GNU' in subprocess.check_output(['tar', '--version']).decode('UTF-8'):\n untar_cmd.append('--no-same-owner')\n log.debug(\"cat {} | {} | {}\".format(tarfile, ' '.join(decompressor), ' '.join(untar_cmd)))\n with open(os.devnull, 'w') as fnull:\n if tarfile == '-':\n inf = None\n else:\n inf = open(tarfile, 'rb')\n decompress_proc = subprocess.Popen(decompressor,\n stdin=inf, stdout=subprocess.PIPE)\n untar_proc = subprocess.Popen(untar_cmd,\n stdin=decompress_proc.stdout) #, stderr=fnull)\n if untar_proc.wait():\n raise subprocess.CalledProcessError(untar_proc.returncode, untar_cmd)\n if decompress_proc.wait():\n raise subprocess.CalledProcessError(decompress_proc.returncode, decompressor)\n if inf is not None:\n inf.close()\n log.debug(\"completed unpacking of {} into {}\".format(tarfile, out_dir))\n\n return out_dir\n\n\n@contextlib.contextmanager\ndef fifo(num_pipes=1, names=None, name=None):\n pipe_dir = tempfile.mkdtemp()\n pipe_paths = []\n if name is not None:\n names = [name]\n if names:\n num_pipes = len(names)\n for i in range(num_pipes):\n if names is not None:\n fn = names[i]\n else:\n fn = '{}.pipe'.format(i)\n pipe_path = os.path.join(pipe_dir, fn)\n os.mkfifo(pipe_path)\n pipe_paths.append(pipe_path)\n\n if num_pipes == 1:\n yield pipe_paths[0]\n else:\n yield pipe_paths\n shutil.rmtree(pipe_dir)\n\n\ndef mkdir_p(dirpath):\n ''' Verify that the directory given exists, and if not, create it.\n '''\n try:\n os.makedirs(dirpath)\n except OSError as exc: # Python >2.5\n if exc.errno == errno.EEXIST and os.path.isdir(dirpath):\n pass\n else:\n raise\n\n\ndef touch_p(path, times=None):\n '''Touch file, making parent directories if they don't exist.'''\n mkdir_p(os.path.dirname(path))\n touch(path, times=times)\n\n\n@contextlib.contextmanager\ndef zstd_open(fname, mode='r', **kwargs):\n '''Handle both text and byte decompression of the file.'''\n if 'r' in mode:\n with open(fname, 'rb') as fh:\n dctx = zstd.ZstdDecompressor()\n stream_reader = dctx.stream_reader(fh)\n if 'b' not in mode:\n text_stream = io.TextIOWrapper(stream_reader, encoding='utf-8-sig')\n yield text_stream\n return\n yield stream_reader\n else:\n with open(fname, 'wb') as fh:\n cctx = zstd.ZstdCompressor(level=kwargs.get('level', 10),\n threads=util_misc.sanitize_thread_count(kwargs.get('threads', None)))\n stream_writer = cctx.stream_writer(fh)\n if 'b' not in mode:\n text_stream = io.TextIOWrapper(stream_reader, encoding='utf-8')\n yield text_stream\n return\n yield stream_writer\n\ndef open_or_gzopen(fname, mode='r', **kwargs):\n assert type(mode) == str, \"open mode must be of type str\"\n\n # 'U' mode is deprecated in py3 and may be unsupported in future versions,\n # so use newline=None when 'U' is specified\n if 'U' in mode:\n if 'newline' not in kwargs:\n kwargs['newline'] = None\n mode = mode.replace(\"U\",\"t\")\n\n if fname.endswith('.gz'):\n # Allow using 'level' kwarg as an alias for gzip files.\n if 'level' in kwargs:\n kwargs['compresslevel'] = kwargs.pop('level')\n return gzip.open(fname, mode=mode, **kwargs)\n elif fname.endswith('.bz2'):\n return bz2.open(fname, mode=mode, **kwargs)\n elif fname.endswith('.zst'):\n return zstd_open(fname, mode=mode, **kwargs)\n elif fname.endswith('.lz4'):\n return lz4.frame.open(fname, mode=mode, **kwargs)\n else:\n return open(fname, mode=mode, **kwargs)\n\n\ndef read_tabfile_dict(inFile, header_prefix=\"#\", skip_prefix=None, rowcount_limit=None):\n ''' Read a tab text file (possibly gzipped) and return contents as an\n iterator of dicts.\n '''\n with open_or_gzopen(inFile, 'rt', encoding='utf-8-sig', newline=None) as inf:\n header = None\n lines_read=0\n for line_no,line in enumerate(inf):\n lines_read+=1\n row = [item.strip() for item in line.rstrip('\\r\\n').split('\\t')]\n # skip empty lines/rows\n if len(\"\".join(row)) == 0 or (skip_prefix and line.startswith(skip_prefix)):\n continue\n if line.startswith(header_prefix):\n row[0] = row[0][1:]\n header = [item for item in row if len(item)]\n elif header is None:\n header = [item for item in row if len(item)]\n else:\n # if a row is longer than the header\n if len(row) > len(header):\n # truncate the row to the header length, and only include extra items if they are not spaces\n # (takes care of the case where the user may enter an extra space at the end of a row)\n row = row[:len(header)] + [item for item in row[len(header):] if len(item)]\n assert len(header) == len(row), \"%s != %s\" % (len(header), len(row))\n yield dict((k, v) for k, v in zip(header, row) if v)\n\n if rowcount_limit and lines_read==rowcount_limit:\n break\n\n\ndef read_tabfile(inFile):\n ''' Read a tab text file (possibly gzipped) and return contents as an\n iterator of arrays.\n '''\n with open_or_gzopen(inFile, 'rt', encoding='utf-8-sig', newline=None) as inf:\n for line_no,line in enumerate(inf):\n if not line.startswith('#'):\n yield list(item.strip() for item in line.rstrip('\\r\\n').split('\\t'))\n\n\ndef readFlatFileHeader(filename, headerPrefix='#', delim='\\t'):\n with open_or_gzopen(filename, 'rt', encoding='utf-8-sig', newline=None) as inf:\n header = inf.readline().rstrip('\\n').split(delim)\n if header and header[0].startswith(headerPrefix):\n header[0] = header[0][len(headerPrefix):]\n return header\n\n\nclass FlatFileParser(object):\n ''' Generic flat file parser that parses tabular text input\n '''\n\n def __init__(self, lineIter=None, name=None, outType='dict',\n readHeader=True, headerPrefix='#', delim='\\t',\n requireUniqueHeader=False):\n self.lineIter = lineIter\n self.header = None\n self.name = name\n self.headerPrefix = headerPrefix\n self.readHeader = readHeader\n self.delim = delim\n self.requireUniqueHeader = requireUniqueHeader\n self.line_num = 0\n assert outType in ('dict', 'arrayStrict', 'arrayLoose', 'both')\n self.outType = outType\n assert readHeader or outType in ('arrayStrict', 'arrayLoose')\n\n def __enter__(self):\n return self\n\n def __exit__(self, exc_type, exc_val, exc_tb):\n return 0\n\n def __iter__(self):\n assert self.lineIter\n for row in self.lineIter:\n out = self.parse(row)\n if out is not None:\n yield out\n\n def parse(self, row):\n self.line_num += 1\n try:\n line = row.rstrip('\\n').split(self.delim)\n if self.readHeader:\n if self.headerPrefix and row.startswith(self.headerPrefix):\n line[0] = line[0][len(self.headerPrefix):]\n assert not (self.requireUniqueHeader and self.header)\n self.parseHeader(line)\n return None\n elif not self.header:\n self.parseHeader(line)\n return None\n else:\n return self.parseRow(line)\n else:\n return self.parseRow(line)\n except Exception:\n template = \"Exception parsing file at line {}. Line contents: '{}'\"\n message = template.format(self.line_num, row)\n if self.name:\n log.exception(\"%s File: %s\", message, self.name)\n else:\n log.exception(message)\n raise\n\n def parseHeader(self, row):\n assert row\n self.header = row\n if self.outType != 'arrayLoose':\n assert len(row) == len(dict([(x, 0) for x in row]))\n\n def parseRow(self, row):\n assert self.outType == 'arrayLoose' or (self.header and len(self.header) == len(row))\n\n if self.outType == 'arrayLoose' or self.outType == 'arrayStrict':\n return row\n out = {self.header[i]: row[i] for i in range(len(self.header))}\n if self.outType == 'both':\n for i in range(len(self.header)):\n out[i] = row[i]\n return out\n\n\ndef fastaMaker(seqs, linewidth=60):\n assert linewidth > 0\n\n for idVal, seq in seqs:\n yield \">{}\\n\".format(idVal)\n\n while len(seq) > linewidth:\n line = seq[:linewidth]\n seq = seq[linewidth:]\n yield \"{}\\n\".format(line)\n\n if seq:\n yield seq + \"\\n\"\n\n\ndef makeFastaFile(seqs, outFasta):\n with open(outFasta, 'wt') as outf:\n for line in fastaMaker(seqs):\n outf.write(line)\n\n return outFasta\n\n\ndef bam_is_sorted(bam_file_path):\n # Should perhaps be in samtools.py once it moves to pysam\n samfile = pysam.AlignmentFile(bam_file_path, \"rb\", check_sq=False)\n if \"HD\" in samfile.header and \"SO\" in samfile.header[\"HD\"]:\n return samfile.header[\"HD\"][\"SO\"] in (\"coordinate\") # also: \"queryname\"\n else:\n raise KeyError(\"Could not locate the SO field in the SAM/BAM file header.\")\n\n\ndef concat(inputFilePaths, outputFilePath, append=False):\n '''\n This function creates an output file containing the\n lines present in the input file(s), in the order specified\n by the inputFilePaths list. If `append` is True,\n appends to the output file instead of overwriting it.\n '''\n with open(outputFilePath, 'a' if append else 'w') as outfile:\n for filePath in util_misc.make_seq(inputFilePaths):\n with open(filePath) as infile:\n for line in infile:\n outfile.write(line)\n\n\ndef download_file(uriToGet, dest, destFileName=None):\n destDir = os.path.realpath(os.path.expanduser(dest))\n\n req = urllib.request.urlopen(uriToGet)\n\n if not destFileName:\n m = re.search('filename=\"(?P.+)\"', req.info()['Content-Disposition'])\n\n if m:\n destFileName = m.group(\"filename\")\n else:\n destFileName = \"file\"\n\n destPath = os.path.join(destDir, destFileName)\n\n with open(destPath, \"wb\") as outf:\n while True:\n chunk = req.read(1024)\n if not chunk:\n break\n outf.write(chunk)\n\n return destPath\n\n\ndef webfile_readlines(uriToGet):\n\n for line in urllib.request.urlopen(uriToGet): # .readlines():\n cleanedLine = line.decode(\"utf-8\").strip()\n if len(cleanedLine) > 0:\n yield cleanedLine\n\n\ndef replace_in_file(filename, original, new):\n '''Replace the original string with new in file.\n\n Raises error if the original is not in the file.\n '''\n with open(filename) as f:\n s = f.read()\n if original not in s:\n raise StringNotFoundException(\"String '%s' not found.\" % s)\n s = s.replace(original, new)\n with open(filename, 'w') as f:\n f.write(s)\n\n\ndef cat(output_file, input_files):\n '''Cat list of input filenames to output filename.'''\n with open_or_gzopen(output_file, 'wb') as wfd:\n for f in input_files:\n with open_or_gzopen(f, 'rb') as fd:\n shutil.copyfileobj(fd, wfd, 1024*1024*10)\n\n\n@contextlib.contextmanager\ndef temp_catted_files(input_files, suffix=None, prefix=None):\n '''Create a temporary file holding catted contents of input_files.'''\n fn = mkstempfname(suffix=suffix, prefix=prefix)\n try:\n cat(fn, input_files)\n yield fn\n finally:\n os.remove(fn)\n\ndef _get_pathconf(file_system_path, param_suffix, default):\n \"\"\"Return a pathconf parameter value for a filesystem.\n \"\"\"\n param_str = [s for s in os.pathconf_names if s.endswith(param_suffix)]\n if len(param_str) == 1:\n try:\n return os.pathconf(file_system_path, param_str[0])\n except OSError:\n pass\n return default\n\ndef max_file_name_length(file_system_path):\n \"\"\"Return the maximum valid length of a filename (path component) on the given filesystem.\"\"\"\n return _get_pathconf(file_system_path, '_NAME_MAX', 80)-1\n\ndef max_path_length(file_system_path):\n \"\"\"Return the maximum valid length of a path on the given filesystem.\"\"\"\n return _get_pathconf(file_system_path, '_PATH_MAX', 255)-1\n\ndef sanitize_id_for_sam_rname(string_in):\n #[0-9A-Za-z!#$%&+./:;?@^_|~-]\n # See character set restrictions in SAM/BAM RNAME spec:\n # https://samtools.github.io/hts-specs/SAMv1.pdf\n # [0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*\n # Here we are being conservative and replacing anything disallowed:\n # [^0-9A-Za-z!#$%&+./:;?@^_|~-]\n disallowed_char_re = re.compile(r'[^0-9A-Za-z!#$%&+./:;?@^_|~-]')\n string_value = disallowed_char_re.sub(\"_\", string_in)\n\n # condense runs of underscores\n double_underscore_re = re.compile(r'_{2,}')\n string_value = double_underscore_re.sub(\"_\", string_value)\n\n # ensure all the character removals did not make the name empty\n string_value = string_value or '_'\n print(\"sanitizing: %s ====> %s \" % (string_in, string_value))\n return string_value\n\ndef write_fasta_with_sanitized_ids(fasta_in, out_filepath):\n with open(out_filepath, \"wt\") as outf:\n with open(fasta_in, \"rt\") as inf:\n for line in inf:\n line = line.strip()\n if line.startswith(\">\"):\n line = \">\"+sanitize_id_for_sam_rname(line[1:])\n outf.write(line + '\\n')\n print(\"out_filepath\",out_filepath)\n print(\"os.path.dirname(out_filepath)\",os.path.dirname(out_filepath))\n return out_filepath\n\n@contextlib.contextmanager\ndef fastas_with_sanitized_ids(input_fasta_paths, use_tmp=False):\n \"\"\" Returns a list of file paths for fasta files with\n sanitized IDs \n ( Suitable for Picard; see: https://github.com/samtools/hts-specs/pull/333 )\n\n input_fasta_paths is a list of file paths to fasta files\n\n if use_tmp==False, companion fasta files will be created with \".sanitized_ids.fasta\" appended\n in the same location as the input\n if use_tmp==True, temp files will be written instead\n \"\"\"\n sanitized_fasta_paths=[]\n if use_tmp:\n with tempfnames([\"_{inf_name}\".format(inf_name=os.path.basename(inf_path)) for inf_path in [input_fasta_paths]]) as temp_fasta_paths:\n for fasta_in, out_filepath in zip([input_fasta_paths], temp_fasta_paths):\n sanitized_fasta_paths.append(write_fasta_with_sanitized_ids(fasta_in, out_filepath))\n yield sanitized_fasta_paths\n else:\n for fasta_in in [input_fasta_paths]:\n in_fasta_basename = os.path.splitext(os.path.basename(fasta_in))[0]\n out_basedir = os.path.realpath(os.path.dirname(fasta_in))\n new_basename = in_fasta_basename\n if new_basename.lower().endswith('.fa'):\n new_basename = new_basename[:-3] + '.sanitized_ids.fa'\n elif new_basename.lower().endswith('.fasta'):\n new_basename = new_basename[:-6] + '.sanitized_ids.fasta'\n else:\n new_basename = new_basename + '.sanitized_ids.fasta'\n out_filepath = os.path.join(out_basedir,new_basename)\n sanitized_fasta_paths.append(write_fasta_with_sanitized_ids(fasta_in, out_filepath))\n yield sanitized_fasta_paths\n\nclass TranspositionError(Exception):\n def __init___(self, *args, **kwargs):\n super(TranspositionError, self).__init__(self, *args, **kwargs)\n\ndef transposeChromosomeFiles(inputFilenamesList, sampleRelationFile=None, sampleNameListFile=None):\n ''' Input: a list of FASTA files representing a genome for each sample.\n Each file contains the same number of sequences (chromosomes, segments,\n etc) in the same order.\n If the parameter sampleRelationFile is specified (as a file path),\n a JSON file will be written mapping sample name to sequence position\n in the output.\n Output: a list of FASTA files representing all samples for each\n chromosome/segment for input to a multiple sequence aligner.\n The number of FASTA files corresponds to the number of chromosomes\n in the genome. Each file contains the same number of samples\n in the same order. Each output file is a tempfile.\n '''\n outputFilenames = []\n\n # open all files\n inputFilesList = [open_or_gzopen(x, 'r') for x in inputFilenamesList]\n # get BioPython iterators for each of the FASTA files specified in the input\n fastaFiles = [SeqIO.parse(x, 'fasta') for x in inputFilesList]\n\n # write out json file containing relation of\n # sample name to position in output\n if sampleRelationFile:\n with open(os.path.realpath(sampleRelationFile), \"w\") as outFile:\n # dict mapping sample->index, zero indexed\n sampleIdxMap = dict((os.path.basename(v).replace(\".fasta\", \"\"), k)\n for k, v in enumerate(inputFilenamesList))\n json.dump(sampleIdxMap, outFile, sort_keys=True, indent=4, separators=(',', ': '))\n\n if sampleNameListFile:\n with open(os.path.realpath(sampleNameListFile), \"w\") as outFile:\n sampleNameList = [os.path.basename(v).replace(\".fasta\", \"\\n\") for v in inputFilenamesList]\n outFile.writelines(sampleNameList)\n\n # for each interleaved record\n for chrRecordList in itertools.zip_longest(*fastaFiles):\n if any(rec is None for rec in chrRecordList):\n raise TranspositionError(\"input fasta files must all have the same number of sequences\")\n\n outputFilename = mkstempfname('.fasta')\n outputFilenames.append(outputFilename)\n with open(outputFilename, \"w\") as outf:\n # write the corresonding records to a new FASTA file\n SeqIO.write(chrRecordList, outf, 'fasta')\n\n # close all input files\n for x in inputFilesList:\n x.close()\n\n return outputFilenames\n\ndef string_to_file_name(string_value, file_system_path=None, length_margin=0):\n \"\"\"Constructs a valid file name from a given string, replacing or deleting invalid characters.\n If `file_system_path` is given, makes sure the file name is valid on that file system.\n If `length_margin` is given, ensure a string that long can be added to filename without breaking length limits.\n \"\"\"\n replacements_dict = {\n \"\\\\\": \"-\", # win directory separator\n \"/\": \"-\", # posix directory separator\n os.sep: \"-\", # directory separator\n \"^\": \"_\", # caret\n \"&\": \"_and_\", # background\n \"\\\"\": \"\", # double quotes\n r\"'\": \"\", # single quotes\n r\":\": \"_\", # colon (problem for ntfs)\n r\" \": \"_\", # spaces\n r\"|\": \"-\", # shouldn't confuse a vertical bar for a shell pipe\n r\"!\": \".\", # not a bash operator\n r\";\": \".\", # not a terminator\n r\"?\": \"_\", # could be mistaken for a wildcard\n r\"*\": \"_\", # could be mistaken for a wildcard\n r\"`\": \"_\", # no subshells\n r\" -\": \"_-\", # could be mistaken for an argument\n r\" --\": \"_--\", # could be mistaken for an argument\n r\">\": \"_\", # no redirect chars\n r\"<\": \"_\", # no redirect chars\n r\"(\": \"__\", # special character\n r\")\": \"__\", # special character\n r\"\\\\x\": \"_\", # hex char\n r\"\\\\o\": \"_\", # octal char\n #r\"\\\\u\": \"\", # unicode char\n #\"\": \"\", # other illegal strings to replace\n }\n\n # group of ascii control and non-printable characters\n control_chars = ''.join( map(chr, list(range(0,32)) + list(range(127,160)) ) )\n control_char_re = re.compile('[%s]' % re.escape(control_chars))\n string_value = control_char_re.sub(\"_\", string_value)\n\n # replacements from the dictionary above\n strs_to_replace_re = re.compile(r'|'.join(re.escape(key) for key in replacements_dict.keys()))\n string_value = strs_to_replace_re.sub(lambda x: replacements_dict.get(x.group(), \"_\"), string_value)\n\n # condense runs of underscores\n double_underscore_re = re.compile(r'_{2,}')\n string_value = double_underscore_re.sub(\"_\", string_value)\n\n # condense runs of dashes\n double_dash_re = re.compile(r'-{2,}')\n string_value = double_dash_re.sub(\"-\", string_value)\n\n # remove leading or trailing periods (no hidden files (*NIX) or missing file extensions (NTFS))\n string_value = string_value.strip(\".\")\n\n # comply with file name length limits\n if file_system_path is not None:\n max_len = max(1, max_file_name_length(file_system_path) - length_margin)\n string_value = string_value[:max_len]\n while len(string_value.encode('utf-8')) > max_len:\n string_value = string_value[:-1]\n\n # ensure all the character removals did not make the name empty\n string_value = string_value or '_'\n\n return string_value\n\ndef grep_count(file_path, to_match, additional_flags=None, fixed_mode=True, starts_with=False):\n '''\n This uses grep for fast counting of strings in a file\n '''\n if not os.path.isfile(file_path) or os.path.getsize(file_path)==0:\n return 0\n\n env = os.environ.copy()\n env['LC_ALL'] = 'C' #use C locale rather than UTF8 for faster grep\n\n cmd = [\"grep\"]\n # '-c' returns the match count\n cmd.append(\"-c\")\n if additional_flags:\n cmd.extend(additional_flags)\n\n # fixed mode cannot be used with starts_with, since it does not match regular expressions\n # only add the fixed_mode flag if we're not using starts_with\n if not starts_with:\n if fixed_mode:\n cmd.append(\"-F\")\n cmd.append(to_match)\n else:\n cmd.append(\"^\"+to_match)\n\n cmd.append(file_path)\n\n number_of_seqs = subprocess.check_output(cmd, env=env)\n return int(number_of_seqs.decode(\"utf-8\").rstrip(os.linesep))\n\n# used by count_and_sort_barcodes\ndef count_occurrences_in_tsv(filePath, \n col=0, \n noise_chr='.',\n delimiter='\\t',\n include_noise=False):\n file_occurrence_counts = {}\n with open(filePath) as infile:\n for row in csv.reader(infile, delimiter=delimiter):\n if noise_chr not in row[col] or include_noise:\n file_occurrence_counts[row[col]] = file_occurrence_counts.get(row[col], 0) + 1\n return file_occurrence_counts\n\n# used by count_and_sort_barcodes\ndef count_occurrences_in_tsv_sqlite_backed(db_file_path, \n file_path, \n col=0, \n noise_chr='.', \n delimiter='\\t', \n include_noise=False):\n db = CountDB(db_file_path)\n db.start()\n with open(file_path) as infile:\n for chunk in util_misc.batch_iterator(csv.reader(infile, delimiter=delimiter), 40000):\n db.increment_count_for_multiple_IDs([row[0] for row in chunk if noise_chr not in row[col] or include_noise ])\n log.info(\"unique barcodes seen and counted in SQLite: %s for file %s\", db.get_num_IDS(), file_path)\n db.close()\n return (db_file_path,file_path) #file_occurrence_counts\n\ndef count_str_in_file(in_file, query_str, starts_with=False):\n if not os.path.isfile(in_file) or os.path.getsize(in_file)==0:\n return 0\n\n if in_file.endswith('.gz'):\n n = 0\n with gzip.open(in_file, 'rt') as inf:\n if starts_with:\n n = sum(1 for line in inf if line.startswith(query_str))\n else:\n n = sum(1 for line in inf if query_str in line)\n return n\n # use grep count for non-gzip files since it seems to be faster than native on Pythons <3.5\n else:\n return grep_count(in_file, query_str, starts_with=starts_with)\n\ndef fasta_length(fasta_path):\n '''\n Count number of records in fasta file\n '''\n return count_str_in_file(fasta_path, '>', starts_with=True)\n\ndef count_fastq_reads(inFastq):\n '''\n Count number of reads in fastq file\n '''\n n = line_count(inFastq)\n if n % 4 != 0:\n raise Exception(\"cannot count reads in a fastq with wrapped lines\")\n return n // 4\n # unfortunately, both @ and + are potential quality characters and cannot be used in a\n # fastq counting approach....\n #return count_str_in_file(inFastq, '@', starts_with=True)\n\ndef line_count(infname):\n n = 0\n with open_or_gzopen(infname, 'rt') as inf:\n for line in inf:\n n += 1\n return n\n\ndef touch(fname, times=None):\n with open(fname, 'a'):\n os.utime(fname, times)\n\ndef make_empty(fname):\n '''Make `fname` a zero-length file with the current timestamp.'''\n with open(fname, 'w'):\n pass\n\ndef dump_file(fname, value):\n \"\"\"store string in file\"\"\"\n with open(fname, 'w') as out:\n out.write(str(value))\n\ndef slurp_file(fname, maxSizeMb=50):\n \"\"\"Read entire file into one string. If file is gzipped, uncompress it on-the-fly. If file is larger\n than `maxSizeMb` megabytes, throw an error; this is to encourage proper use of iterators for reading\n large files. If `maxSizeMb` is None or 0, file size is unlimited.\"\"\"\n fileSize = os.path.getsize(fname)\n if maxSizeMb and fileSize > maxSizeMb*1024*1024:\n raise RuntimeError('Tried to slurp large file {} (size={}); are you sure? Increase `maxSizeMb` param if yes'.\n format(fname, fileSize))\n with open_or_gzopen(fname) as f:\n return f.read()\n\ndef is_broken_link(filename):\n # isfile() returns True if a file, or a working link\n if os.path.isfile(filename) or os.path.isdir(filename):\n return False\n # otherwise if this is a link\n if os.path.islink(filename):\n # os.path.exists() returns false in the case of broken symlinks\n return not os.path.exists(filename)\n return False\n\n\ndef find_broken_symlinks(rootdir, followlinks=False):\n \"\"\"\n This function removes broken symlinks within a directory,\n doing the same in each child directory as well (though not following\n functional symlinks, unless they're directories and followlinks=True).\n @param followlinks: only applies to directory links as per os.walk\n \"\"\"\n\n broken_links_to_remove = []\n\n # first check to see if the input is itself a broken link\n if is_broken_link(rootdir):\n broken_links_to_remove.append(rootdir.rstrip(\"/\"))\n else:\n # otherwise traverse the directory hierarchy\n for rootpath, subfolders, files in os.walk(rootdir, followlinks=followlinks):\n for filename in files:\n fpath = os.path.join(rootpath, filename)\n if is_broken_link(fpath):\n broken_links_to_remove.append(fpath.rstrip(\"/\"))\n\n return broken_links_to_remove\n\n\ndef uncompressed_file_type(fname):\n \"\"\"Return the original file extension of either a compressed or an uncompressed file.\"\"\"\n base, ext = os.path.splitext(fname)\n if ext in ('.gz', '.bz2', '.lz4', '.zst'):\n base, ext = os.path.splitext(base)\n return ext\n\ndef repack_tarballs(out_compressed_tarball,\n input_compressed_tarballs,\n extract_to_disk_path=None,\n extract_numeric_owner=False,\n avoid_disk_roundtrip=True,\n ignore_zeros=True,\n pipe_hint_in=None,\n pipe_hint_out=None,\n threads=None):\n threads = util_misc.sanitize_thread_count(threads)\n\n def choose_compressor(filepath, threads=8):\n return_obj = {}\n filepath = filepath.lower()\n if re.search(r'(\\.?tgz|\\.?gz)$', filepath):\n compressor = 'pigz {threads}'.format(threads=\"-p \"+str(threads) if threads else \"\").split()\n return_obj[\"decompress_cmd\"] = compressor + [\"-dc\"]\n return_obj[\"compress_cmd\"] = compressor + [\"-c\"]\n elif re.search(r'\\.?bz2$', filepath):\n compressor = 'lbzip2 {threads}'.format(threads=\"-n \"+str(threads) if threads else \"\").split()\n return_obj[\"decompress_cmd\"] = compressor + [\"-dc\"]\n return_obj[\"compress_cmd\"] = compressor + [\"-c\"]\n elif re.search(r'\\.?lz4$', filepath):\n compressor = ['lz4']\n return_obj[\"decompress_cmd\"] = compressor + [\"-dc\"]\n return_obj[\"compress_cmd\"] = compressor + [\"-c\"]\n elif re.search(r'\\.?zst$', filepath):\n compressor = ['zstd']\n return_obj[\"decompress_cmd\"] = compressor + [\"-qdc\"]\n return_obj[\"compress_cmd\"] = compressor + [\"-c19\", \"-T\"+str(threads)]\n elif re.search(r'\\.?tar$', filepath):\n compressor = ['cat']\n return_obj[\"decompress_cmd\"] = compressor\n return_obj[\"compress_cmd\"] = compressor\n else:\n raise IOError(\"An input file of unknown type was provided: %s\" % filepath)\n return return_obj\n\n class FileDiverter(object):\n \"\"\"\n This reads bytes from a TarInfo file stream, writes them to a disk file\n and returns the buffered bytes as they are read\n \"\"\"\n def __init__(self, fileinfo, fileobj, written_mirror_file=None, extract_numeric_owner=False):\n self.written_mirror_file = open(written_mirror_file,\"wb\")\n self.fileinfo = fileinfo\n self.fileobj = fileobj\n self.extract_numeric_owner = extract_numeric_owner\n\n def __del__(self):\n self.written_mirror_file.close()\n\n tar_in.chown(self.fileinfo, self.written_mirror_file.name, self.extract_numeric_owner)\n if not self.fileinfo.issym():\n tar_in.chmod(self.fileinfo, self.written_mirror_file.name)\n tar_in.utime(self.fileinfo, self.written_mirror_file.name)\n\n def read(self, size):\n assert size is not None\n\n buf = self.fileobj.read(size)\n self.written_mirror_file.write(buf)\n return buf\n\n if extract_to_disk_path and not os.path.isdir(extract_to_disk_path):\n mkdir_p(extract_to_disk_path)\n\n if out_compressed_tarball == \"-\":\n if not pipe_hint_out:\n raise IOError(\"cannot autodetect compression for stdoud unless pipeOutHint provided\")\n compressor = choose_compressor(pipe_hint_out, threads=threads)[\"compress_cmd\"]\n outfile = None\n else:\n compressor = choose_compressor(out_compressed_tarball, threads=threads)[\"compress_cmd\"]\n outfile = open(out_compressed_tarball, \"w\")\n\n out_compress_ps = subprocess.Popen(compressor, stdout=sys.stdout if out_compressed_tarball == \"-\" else outfile, stdin=subprocess.PIPE)\n\n tar_out = tarfile.open(fileobj=out_compress_ps.stdin, mode=\"w|\")\n\n for in_compressed_tarball in input_compressed_tarballs:\n if in_compressed_tarball != \"-\":\n pigz_ps = subprocess.Popen(choose_compressor(in_compressed_tarball)[\"decompress_cmd\"] + [in_compressed_tarball], stdout=subprocess.PIPE)\n else:\n if not pipe_hint_in:\n raise IOError(\"cannot autodetect compression for stdin unless pipeInHint provided\")\n pigz_ps = subprocess.Popen(choose_compressor(pipe_hint_in)[\"decompress_cmd\"] + [in_compressed_tarball], stdout=subprocess.PIPE, stdin=sys.stdin)\n tar_in = tarfile.open(fileobj=pigz_ps.stdout, mode=\"r|\", ignore_zeros=True)\n\n fileinfo = tar_in.next()\n while fileinfo is not None:\n if extract_to_disk_path:\n target_path = os.path.normpath(os.path.join(extract_to_disk_path, fileinfo.name).rstrip(\"/\"))\n containing_path = os.path.dirname(target_path)\n mkdir_p(containing_path)\n\n if avoid_disk_roundtrip and fileinfo.isreg():\n # avoid disk round trip for regular files (don't re-read from disk to write to new tar)\n fileobj = tar_in.extractfile(fileinfo)\n tar_out.addfile(fileinfo, fileobj=FileDiverter(fileinfo, fileobj, written_mirror_file=target_path))\n else:\n # write to disk, add to new tarball from disk\n outfile = tar_in.extract(fileinfo, path=extract_to_disk_path)\n with pushd_popd(extract_to_disk_path):\n tar_out.add(fileinfo.name)\n else:\n # if we're not extracting to disk, stream directly between tarballs\n fileobj = tar_in.extractfile(fileinfo)\n tar_out.addfile(fileinfo, fileobj=fileobj)\n\n fileinfo = tar_in.next()\n pigz_ps.wait()\n tar_in.close()\n if pigz_ps.returncode != 0:\n raise subprocess.CalledProcessError(pigz_ps.returncode, \"Call error %s\" % pigz_ps.returncode)\n\n tar_out.close()\n out_compress_ps.stdin.close()\n out_compress_ps.wait()\n if out_compress_ps.returncode != 0:\n raise subprocess.CalledProcessError(out_compress_ps.returncode, \"Call error %s\" % out_compress_ps.returncode)\n\n if outfile is not None:\n outfile.close()\n\nclass DBConnection:\n def __init__(self, db_file=None):\n self.should_unlink_on_exit=False\n if db_file==None:\n self.db_file = mkstempfname(suffix='.db')\n self.should_unlink_on_exit=True\n else:\n self.db_file=db_file\n self.conn = sqlite3.connect(self.db_file, isolation_level='DEFERRED')\n assert self.conn.isolation_level\n self.conn.text_factory = str\n self.cur = self.conn.cursor()\n self.cur.execute(\"PRAGMA foreign_keys=ON\")\n self.cur.execute(\"PRAGMA foreign_keys\")\n fk = self.cur.fetchone()\n #log.debug(\"SQLite version: %s\" % sqlite3.sqlite_version)\n #log.debug(\"SQLite foreign key support: %s\" % ((fk and fk[0]) and 'true' or 'false'))\n self.start()\n def start(self):\n pass\n def __enter__(self):\n return self\n def __exit__(self, exc_type, exc_val, exc_tb):\n self.close()\n return False # ensure exceptions are propagated\n def close(self):\n if not self.conn:\n return\n self.conn.commit()\n self.cur.close()\n self.conn.close()\n self.conn = None\n self.cur = None\n if self.should_unlink_on_exit==True:\n os.unlink(self.db_file)\n\nclass CountDB(DBConnection):\n \"\"\"\n This is a simple SQLite class for counting large\n numbers of strings where storing counts in memory\n would be prohibitive.\n \"\"\"\n def __init__(self, db_file=None):\n DBConnection.__init__(self,db_file=db_file)\n\n def start(self):\n DBConnection.start(self)\n self.cur.execute(\"\"\"CREATE TABLE IF NOT EXISTS counts (\n id TEXT PRIMARY KEY,\n count INTEGER DEFAULT 1)\"\"\")\n\n def get_count_for_ID(self, idval):\n self.cur.execute(\"SELECT id,count FROM counts WHERE id=?\", [idval])\n row = self.cur.fetchone()\n yield row or None\n\n def get_count_for_multiple_IDs(self, idvals):\n self.cur.execute(\"SELECT id,count from counts WHERE id IN (%s)\" % ','.join('?'*len(idvals)), *idvals)\n for row in self.cur.fetchone():\n yield row or None\n\n def set_count_for_ID(self, idval, count):\n with self.conn:\n # make use of UPSERT to insert or update: https://www.sqlite.org/lang_UPSERT.html\n self.cur.execute(\"INSERT INTO counts(id) VALUES (?) ON CONFLICT(id) UPDATE SET count=?\", (idval, count))\n\n def set_count_for_multiple_IDs(self, idvals, count):\n with self.conn:\n # make use of UPSERT to insert or update: https://www.sqlite.org/lang_UPSERT.html\n values_str=\",\".join([\"('{}')\".format(idval) for idval in idvals])\n self.cur.execute(\"INSERT INTO counts(id) VALUES %s ON CONFLICT(id) DO UPDATE SET count=?\" % values_str, (count,))\n\n def increment_count_for_multiple_IDs(self, idvals, increment_val=1):\n with self.conn:\n for idvals_chunk in util_misc.batch_iterator(idvals, 600):\n values_str=\",\".join([\"('{}')\".format(idval) for idval in idvals_chunk])\n # make use of \"UPSERT\" to insert or update: https://www.sqlite.org/lang_UPSERT.html\n # This string interpolation form is limited to ~1000 ids\n self.cur.execute(\"INSERT INTO counts(id) VALUES %s ON CONFLICT(id) DO UPDATE SET count=count+?\" % values_str, (increment_val,))\n # This is more proper, but slower and uses more memory:\n #self.cur.executemany(\"INSERT INTO counts(id) VALUES (?) ON CONFLICT(id) DO UPDATE SET count=count+?\", zip(idvals_chunk, [increment_val]*len(idvals_chunk)))\n\n def add_counts_from_other_db(self, other_db):\n log.debug(\"attaching DB for merge: %s\",other_db)\n otherdb_basename=os.path.basename(other_db)\n otherdb_basename = otherdb_basename[:-3] if otherdb_basename.endswith(\".db\") else otherdb_basename\n self.conn.execute(\"ATTACH DATABASE ? AS ?\", [other_db,otherdb_basename])\n with self.conn:\n # in \"DO UPDATE SET count=excluded.count\", \"count\" is the column the value would have been inserted into; excluded applies to the conflicting row; see: https://www.sqlite.org/lang_UPSERT.html\n query = \"\"\" \n INSERT INTO counts SELECT * FROM \n (SELECT id, SUM(count) sumval FROM ( \n SELECT id,count FROM counts UNION ALL \n SELECT id,count FROM %s.counts \n ) group by id) as p \n WHERE true ON CONFLICT(id) DO UPDATE SET count=excluded.count; \n \"\"\" % otherdb_basename\n self.conn.executescript(query)\n self.conn.execute(\"DETACH DATABASE ?;\",[otherdb_basename])\n\n def increment_count_for_ID(self, idval, increment_val=1):\n self.increment_count_for_multiple_IDs([idval], increment_val)\n\n def decrement_count_for_multiple_IDs(self, idvals, decrement_val=-1):\n self.increment_count_for_multiple_IDs(idvals, deccrement_val)\n\n def decrement_count_for_ID(self, idval, decrement_val=-1):\n self.increment_count_for_multiple_IDs([idval], decrement_val)\n\n def get_counts_descending(self):\n self.cur.execute(\"SELECT id,count FROM counts ORDER BY count DESC\")\n for row in self.cur:\n yield row or None\n\n def get_num_IDS(self):\n return self.cur.execute(\"SELECT COUNT() FROM counts\").fetchone()[0]\n \n\n" }, { "path": "src/viral_ngs/core/illumina_indices.py", "content": "#!/usr/bin/env python\n\n\"\"\"\n Related only to sequence data within this file: \n \"Oligonucleotide sequences Copyright 2016 Illumina, Inc. All rights reserved.\"\n See: https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf\n Python code below is under the license of this repository:\n https://raw.githubusercontent.com/broadinstitute/viral-ngs/master/LICENSE\n\"\"\"\n\nimport re, functools\nimport csv\nimport copy\nimport math\nimport logging\nfrom collections import OrderedDict, defaultdict\n\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\n\nlog = logging.getLogger(__name__)\n\ndef memoize(obj):\n cache = obj.cache = {}\n\n @functools.wraps(obj)\n def memoizer(*args, **kwargs):\n key = \"\".join([str(args),str(kwargs)])\n if key not in cache:\n cache[key] = obj(*args, **kwargs)\n return cache[key]\n return memoizer\n\nclass IlluminaIndexReference(object):\n\n def __init__(self, kit=None, instrument=None):\n self.kit = kit\n self.instrument = instrument\n\n _kits = {\n \"TruSight Amplicon Panels\":{\n \"_short_name\":\"trusight_amp\",\n \"i7\":{\n \"A701\":[{\"seq\":\"ATCACGAC\",\"instruments\":[]}],\n \"A702\":[{\"seq\":\"ACAGTGGT\",\"instruments\":[]}],\n \"A703\":[{\"seq\":\"CAGATCCA\",\"instruments\":[]}],\n \"A704\":[{\"seq\":\"ACAAACGG\",\"instruments\":[]}],\n \"A705\":[{\"seq\":\"ACCCAGCA\",\"instruments\":[]}],\n \"A706\":[{\"seq\":\"AACCCCTC\",\"instruments\":[]}],\n \"A707\":[{\"seq\":\"CCCAACCT\",\"instruments\":[]}],\n \"A708\":[{\"seq\":\"CACCACAC\",\"instruments\":[]}],\n \"A709\":[{\"seq\":\"GAAACCCA\",\"instruments\":[]}],\n \"A710\":[{\"seq\":\"TGTGACCA\",\"instruments\":[]}],\n \"A711\":[{\"seq\":\"AGGGTCAA\",\"instruments\":[]}],\n \"A712\":[{\"seq\":\"AGGAGTGG\",\"instruments\":[]}]\n },\n \"i5\":{\n \"A501\": [{\"seq\":\"TGAACCTT\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AAGGTTCA\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A502\": [{\"seq\":\"TGCTAAGT\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"ACTTAGCA\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A503\": [{\"seq\":\"TGTTCTCT\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AGAGAACA\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A504\": [{\"seq\":\"TAAGACAC\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GTGTCTTA\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A505\": [{\"seq\":\"CTAATCGA\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TCGATTAG\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A506\": [{\"seq\":\"CTAGAACA\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TGTTCTAG\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A507\": [{\"seq\":\"TAAGTTCC\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GGAACTTA\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A508\": [{\"seq\":\"TAGACCTA\", \"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TAGGTCTA\", \"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}]\n }\n },\n \"TruSight Cardio\":{\n \"_short_name\":\"trusight_cardio\",\n \"i7\":{\n \"N701\": [{\"seq\":\"TAAGGCGA\",\"instruments\":[]}],\n \"N702\": [{\"seq\":\"CGTACTAG\",\"instruments\":[]}],\n \"N703\": [{\"seq\":\"AGGCAGAA\",\"instruments\":[]}],\n \"N704\": [{\"seq\":\"TCCTGAGC\",\"instruments\":[]}],\n \"N705\": [{\"seq\":\"GGACTCCT\",\"instruments\":[]}],\n \"N706\": [{\"seq\":\"TAGGCATG\",\"instruments\":[]}],\n \"N707\": [{\"seq\":\"CTCTCTAC\",\"instruments\":[]}],\n \"N708\": [{\"seq\":\"CAGAGAGG\",\"instruments\":[]}],\n \"N709\": [{\"seq\":\"GCTACGCT\",\"instruments\":[]}],\n \"N710\": [{\"seq\":\"CGAGGCTG\",\"instruments\":[]}],\n \"N711\": [{\"seq\":\"AAGAGGCA\",\"instruments\":[]}],\n \"N712\": [{\"seq\":\"GTAGAGGA\",\"instruments\":[]}]\n } ,\n \"i5\":{\n \"E505\": [{\"seq\":\"GTAAGGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"CTCCTTAC\",\"instruments\":[\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}]\n }\n },\n \"TruSight One\":{\n \"_short_name\":\"trusight_one\",\n \"i7\":{\n \"N701\":[{\"seq\":\"TAAGGCGA\",\"instruments\":[]}],\n \"N702\":[{\"seq\":\"CGTACTAG\",\"instruments\":[]}],\n \"N703\":[{\"seq\":\"AGGCAGAA\",\"instruments\":[]}],\n \"N704\":[{\"seq\":\"TCCTGAGC\",\"instruments\":[]}],\n \"N705\":[{\"seq\":\"GGACTCCT\",\"instruments\":[]}],\n \"N706\":[{\"seq\":\"TAGGCATG\",\"instruments\":[]}],\n \"N707\":[{\"seq\":\"CTCTCTAC\",\"instruments\":[]}],\n \"N708\":[{\"seq\":\"CAGAGAGG\",\"instruments\":[]}],\n \"N709\":[{\"seq\":\"GCTACGCT\",\"instruments\":[]}],\n \"N710\":[{\"seq\":\"CGAGGCTG\",\"instruments\":[]}],\n \"N711\":[{\"seq\":\"AAGAGGCA\",\"instruments\":[]}],\n \"N712\":[{\"seq\":\"GTAGAGGA\",\"instruments\":[]}]\n },\n \"i5\":{\n \"E502\": [{\"seq\":\"CTCTCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"ATAGAGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"E503\": [{\"seq\":\"TATCCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AGAGGATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"E504\": [{\"seq\":\"AGAGTAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TCTACTCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"E505\": [{\"seq\":\"GTAAGGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"CTCCTTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}]\n }\n },\n \"TruSight Rapid Capture\":{\n \"_short_name\":\"trusight_rapid_capture\",\n \"i7\":{\n \"N701\":[{\"seq\":\"TAAGGCGA\",\"instruments\":[]}],\n \"N702\":[{\"seq\":\"CGTACTAG\",\"instruments\":[]}],\n \"N703\":[{\"seq\":\"AGGCAGAA\",\"instruments\":[]}],\n \"N704\":[{\"seq\":\"TCCTGAGC\",\"instruments\":[]}],\n \"N705\":[{\"seq\":\"GGACTCCT\",\"instruments\":[]}],\n \"N706\":[{\"seq\":\"TAGGCATG\",\"instruments\":[]}],\n \"N707\":[{\"seq\":\"CTCTCTAC\",\"instruments\":[]}],\n \"N708\":[{\"seq\":\"CAGAGAGG\",\"instruments\":[]}],\n \"N709\":[{\"seq\":\"GCTACGCT\",\"instruments\":[]}],\n \"N710\":[{\"seq\":\"CGAGGCTG\",\"instruments\":[]}],\n \"N711\":[{\"seq\":\"AAGAGGCA\",\"instruments\":[]}],\n \"N712\":[{\"seq\":\"GTAGAGGA\",\"instruments\":[]}]\n },\n \"i5\":{\n \"E502\": [{\"seq\":\"CTCTCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"ATAGAGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"E505\": [{\"seq\":\"GTAAGGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"CTCCTTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"E506\": [{\"seq\":\"ACTGCATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TATGCAGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"E517\": [{\"seq\":\"GCGTAAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TCTTACGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}]\n }\n },\n \"TruSight Tumor 15\":{\n \"_short_name\":\"trusight_tumor_15\",\n \"i7\":{\n \"R701\": [{\"seq\":\"ATCACG\",\"instruments\":[]}],\n \"R702\": [{\"seq\":\"CGATGT\",\"instruments\":[]}],\n \"R703\": [{\"seq\":\"TTAGGC\",\"instruments\":[]}],\n \"R704\": [{\"seq\":\"TGACCA\",\"instruments\":[]}],\n \"R705\": [{\"seq\":\"ACAGTG\",\"instruments\":[]}],\n \"R706\": [{\"seq\":\"GCCAAT\",\"instruments\":[]}],\n \"R707\": [{\"seq\":\"CAGATC\",\"instruments\":[]}],\n \"R708\": [{\"seq\":\"ACTTGA\",\"instruments\":[]}],\n \"R709\": [{\"seq\":\"GATCAG\",\"instruments\":[]}],\n \"R711\": [{\"seq\":\"GGCTAC\",\"instruments\":[]}],\n \"R712\": [{\"seq\":\"CTTGTA\",\"instruments\":[]}],\n \"R725\": [{\"seq\":\"ACTGAT\",\"instruments\":[]}],\n \"R726\": [{\"seq\":\"ATGAGC\",\"instruments\":[]}],\n \"R727\": [{\"seq\":\"ATTCCT\",\"instruments\":[]}],\n \"R728\": [{\"seq\":\"CAAAAG\",\"instruments\":[]}],\n \"R729\": [{\"seq\":\"CAACTA\",\"instruments\":[]}],\n \"R730\": [{\"seq\":\"CACCGG\",\"instruments\":[]}],\n \"R731\": [{\"seq\":\"CACGAT\",\"instruments\":[]}],\n \"R732\": [{\"seq\":\"CACTCA\",\"instruments\":[]}],\n \"R733\": [{\"seq\":\"CAGGCG\",\"instruments\":[]}],\n \"R734\": [{\"seq\":\"CATGGC\",\"instruments\":[]}],\n \"R735\": [{\"seq\":\"CATTTT\",\"instruments\":[]}],\n \"R736\": [{\"seq\":\"CCAACA\",\"instruments\":[]}],\n \"R749\": [{\"seq\":\"GATGCT\",\"instruments\":[]}]\n },\n \"i5\":{\n \"A501\": [{\"seq\":\"TGAACCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AAGGTTCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A502\": [{\"seq\":\"TGCTAAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"ACTTAGCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}]\n }\n },\n \"TruSight RNA Pan-Cancer Panel\":{\n \"_short_name\":\"trusight_rna_pan_cancer\",\n \"indices\":{\n \"AR001\": [{\"seq\":\"ATCACG\", \"instruments\":[], \"LT_set\":\"B\"}],\n \"AR002\": [{\"seq\":\"CGATGT\", \"instruments\":[], \"LT_set\":\"A\"}],\n \"AR003\": [{\"seq\":\"TTAGGC\", 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{\"seq\":\"GCGATCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TAGATCGC\"}],\n \"[N|S|E]502\":[{\"seq\":\"CTCTCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCTCTAT\"}, {\"seq\":\"ATAGAGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTCTCTAT\"}],\n \"[N|S|E]503\":[{\"seq\":\"TATCCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TATCCTCT\"}, {\"seq\":\"AGAGGATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TATCCTCT\"}],\n \"[N|S|E]504\":[{\"seq\":\"AGAGTAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AGAGTAGA\"}, {\"seq\":\"TCTACTCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AGAGTAGA\"}],\n \"[N|S|E]505\":[{\"seq\":\"GTAAGGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GTAAGGAG\"}, {\"seq\":\"CTCCTTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GTAAGGAG\"}],\n \"[N|S|E]506\":[{\"seq\":\"ACTGCATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ACTGCATA\"}, {\"seq\":\"TATGCAGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ACTGCATA\"}],\n \"[N|S|E]507\":[{\"seq\":\"AAGGAGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AAGGAGTA\"}, {\"seq\":\"TACTCCTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AAGGAGTA\"}],\n \"[N|S|E]508\":[{\"seq\":\"CTAAGCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTAAGCCT\"}, {\"seq\":\"AGGCTTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTAAGCCT\"}],\n \"[N|S|E]517\":[{\"seq\":\"GCGTAAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGTAAGA\"}, {\"seq\":\"TCTTACGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCGTAAGA\"}],\n }\n },\n \"Nextera XT Index Kit v2\":{\n \"_short_name\":\"nextera_v2\",\n \"i7\":{\n \"N701\": [{\"seq\":\"TAAGGCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGCCTTA\"}],\n \"N702\": [{\"seq\":\"CGTACTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAGTACG\"}],\n \"N703\": [{\"seq\":\"AGGCAGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCTGCCT\"}],\n \"N704\": [{\"seq\":\"TCCTGAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTCAGGA\"}],\n \"N705\": [{\"seq\":\"GGACTCCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGAGTCC\"}],\n \"N706\": [{\"seq\":\"TAGGCATG\",\"instruments\":[],\"seq_in_adapter\":\"CATGCCTA\"}],\n \"N707\": [{\"seq\":\"CTCTCTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAGAGAG\"}],\n \"N710\": [{\"seq\":\"CGAGGCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGCCTCG\"}],\n \"N711\": [{\"seq\":\"AAGAGGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCCTCTT\"}],\n \"N712\": [{\"seq\":\"GTAGAGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCTCTAC\"}],\n \"N714\": [{\"seq\":\"GCTCATGA\",\"instruments\":[],\"seq_in_adapter\":\"TCATGAGC\"}],\n \"N715\": [{\"seq\":\"ATCTCAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTGAGAT\"}],\n \"N716\": [{\"seq\":\"ACTCGCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGCGAGT\"}],\n \"N718\": [{\"seq\":\"GGAGCTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAGCTCC\"}],\n \"N719\": [{\"seq\":\"GCGTAGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACTACGC\"}],\n \"N720\": [{\"seq\":\"CGGAGCCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGCTCCG\"}],\n \"N721\": [{\"seq\":\"TACGCTGC\",\"instruments\":[],\"seq_in_adapter\":\"GCAGCGTA\"}],\n \"N722\": [{\"seq\":\"ATGCGCAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGCGCAT\"}],\n \"N723\": [{\"seq\":\"TAGCGCTC\",\"instruments\":[],\"seq_in_adapter\":\"GAGCGCTA\"}],\n \"N724\": [{\"seq\":\"ACTGAGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCTCAGT\"}],\n \"N726\": [{\"seq\":\"CCTAAGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCTTAGG\"}],\n \"N727\": [{\"seq\":\"CGATCAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTGATCG\"}],\n \"N728\": [{\"seq\":\"TGCAGCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGCTGCA\"}],\n \"N729\": [{\"seq\":\"TCGACGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACGTCGA\"}]\n },\n \"i5\":{\n \"S502\":[{\"seq\":\"CTCTCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCTCTAT\"}, {\"seq\":\"ATAGAGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTCTCTAT\"}],\n \"S503\":[{\"seq\":\"TATCCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TATCCTCT\"}, {\"seq\":\"AGAGGATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TATCCTCT\"}],\n \"S505\":[{\"seq\":\"GTAAGGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GTAAGGAG\"}, {\"seq\":\"CTCCTTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GTAAGGAG\"}],\n \"S506\":[{\"seq\":\"ACTGCATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ACTGCATA\"}, {\"seq\":\"TATGCAGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ACTGCATA\"}],\n \"S507\":[{\"seq\":\"AAGGAGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AAGGAGTA\"}, {\"seq\":\"TACTCCTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AAGGAGTA\"}],\n \"S508\":[{\"seq\":\"CTAAGCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTAAGCCT\"}, {\"seq\":\"AGGCTTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTAAGCCT\"}],\n \"S510\":[{\"seq\":\"CGTCTAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CGTCTAAT\"}, {\"seq\":\"ATTAGACG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CGTCTAAT\"}],\n \"S511\":[{\"seq\":\"TCTCTCCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTCTCCG\"}, {\"seq\":\"CGGAGAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCTCTCCG\"}],\n \"S513\":[{\"seq\":\"TCGACTAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCGACTAG\"}, {\"seq\":\"CTAGTCGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCGACTAG\"}],\n \"S515\":[{\"seq\":\"TTCTAGCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCTAGCT\"}, {\"seq\":\"AGCTAGAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTCTAGCT\"}],\n \"S516\":[{\"seq\":\"CCTAGAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTAGAGT\"}, {\"seq\":\"ACTCTAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CCTAGAGT\"}],\n \"S517\":[{\"seq\":\"GCGTAAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGTAAGA\"}, {\"seq\":\"TCTTACGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCGTAAGA\"}],\n \"S518\":[{\"seq\":\"CTATTAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTATTAAG\"}, {\"seq\":\"CTTAATAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTATTAAG\"}],\n \"S520\":[{\"seq\":\"AAGGCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AAGGCTAT\"}, {\"seq\":\"ATAGCCTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AAGGCTAT\"}],\n \"S521\":[{\"seq\":\"GAGCCTTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GAGCCTTA\"}, {\"seq\":\"TAAGGCTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GAGCCTTA\"}],\n \"S522\":[{\"seq\":\"TTATGCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTATGCGA\"}, {\"seq\":\"TCGCATAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTATGCGA\"}],\n }\n },\n \"TruSeq Amplicon Kits\":{\n \"_short_name\":\"truseq_amplicon\",\n \"i7\":{\n \"A701\":[{\"seq\":\"ATCACGAC\",\"instruments\":[]}],\n \"A702\":[{\"seq\":\"ACAGTGGT\",\"instruments\":[]}],\n \"A703\":[{\"seq\":\"CAGATCCA\",\"instruments\":[]}],\n \"A704\":[{\"seq\":\"ACAAACGG\",\"instruments\":[]}],\n \"A705\":[{\"seq\":\"ACCCAGCA\",\"instruments\":[]}],\n \"A706\":[{\"seq\":\"AACCCCTC\",\"instruments\":[]}],\n \"A707\":[{\"seq\":\"CCCAACCT\",\"instruments\":[]}],\n \"A708\":[{\"seq\":\"CACCACAC\",\"instruments\":[]}],\n \"A709\":[{\"seq\":\"GAAACCCA\",\"instruments\":[]}],\n \"A710\":[{\"seq\":\"TGTGACCA\",\"instruments\":[]}],\n \"A711\":[{\"seq\":\"AGGGTCAA\",\"instruments\":[]}],\n \"A712\":[{\"seq\":\"AGGAGTGG\",\"instruments\":[]}],\n },\n \"i5\":{\n \"A501\":[{\"seq\":\"TGAACCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AAGGTTCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A502\":[{\"seq\":\"TGCTAAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"ACTTAGCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A503\":[{\"seq\":\"TGTTCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AGAGAACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A504\":[{\"seq\":\"TAAGACAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GTGTCTTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A505\":[{\"seq\":\"CTAATCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TCGATTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A506\":[{\"seq\":\"CTAGAACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TGTTCTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A507\":[{\"seq\":\"TAAGTTCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GGAACTTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A508\":[{\"seq\":\"TAGACCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TAGGTCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n }\n },\n \"TruSeq DNA Methylation\":{\n \"_short_name\":\"truseq_methylation\",\n \"indices\":{\n \"Index 1\": [{\"seq\":\"ATCACG\",\"instruments\":[]}],\n \"Index 2\": [{\"seq\":\"CGATGT\",\"instruments\":[]}],\n \"Index 3\": [{\"seq\":\"TTAGGC\",\"instruments\":[]}],\n \"Index 4\": [{\"seq\":\"TGACCA\",\"instruments\":[]}],\n \"Index 5\": [{\"seq\":\"ACAGTG\",\"instruments\":[]}],\n \"Index 6\": [{\"seq\":\"GCCAAT\",\"instruments\":[]}],\n \"Index 7\": [{\"seq\":\"CAGATC\",\"instruments\":[]}],\n \"Index 8\": [{\"seq\":\"ACTTGA\",\"instruments\":[]}],\n \"Index 9\": [{\"seq\":\"GATCAG\",\"instruments\":[]}],\n \"Index 10\": [{\"seq\":\"TAGCTT\",\"instruments\":[]}],\n \"Index 11\": [{\"seq\":\"GGCTAC\",\"instruments\":[]}],\n \"Index 12\": [{\"seq\":\"CTTGTA\",\"instruments\":[]}],\n },\n },\n \"TruSeq HT Kits\":{\n \"_short_name\":\"truseq_ht\",\n \"i7\":{\n \"D701\":[{\"seq\":\"ATTACTCG\",\"instruments\":[]}],\n \"D702\":[{\"seq\":\"TCCGGAGA\",\"instruments\":[]}],\n \"D703\":[{\"seq\":\"CGCTCATT\",\"instruments\":[]}],\n \"D704\":[{\"seq\":\"GAGATTCC\",\"instruments\":[]}],\n \"D705\":[{\"seq\":\"ATTCAGAA\",\"instruments\":[]}],\n \"D706\":[{\"seq\":\"GAATTCGT\",\"instruments\":[]}],\n \"D707\":[{\"seq\":\"CTGAAGCT\",\"instruments\":[]}],\n \"D708\":[{\"seq\":\"TAATGCGC\",\"instruments\":[]}],\n \"D709\":[{\"seq\":\"CGGCTATG\",\"instruments\":[]}],\n \"D710\":[{\"seq\":\"TCCGCGAA\",\"instruments\":[]}],\n \"D711\":[{\"seq\":\"TCTCGCGC\",\"instruments\":[]}],\n \"D712\":[{\"seq\":\"AGCGATAG\",\"instruments\":[]}],\n },\n \"i5\":{\n \"D501\":[{\"seq\":\"TATAGCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AGGCTATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"D502\":[{\"seq\":\"ATAGAGGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GCCTCTAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"D503\":[{\"seq\":\"CCTATCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AGGATAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"D504\":[{\"seq\":\"GGCTCTGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TCAGAGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"D505\":[{\"seq\":\"AGGCGAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"CTTCGCCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"D506\":[{\"seq\":\"TAATCTTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TAAGATTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"D507\":[{\"seq\":\"CAGGACGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"ACGTCCTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"D508\":[{\"seq\":\"GTACTGAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GTCAGTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n }\n },\n # \"TruSeq LT Kits\":{\n # \"_short_name\":\"\",\n # },\n # \"TruSeq v1/v2 Kits\":{\n # \"_short_name\":\"\",\n # },\n \"TruSeq Ribo Profile\":{\n \"_short_name\":\"truseq_ribo\",\n \"indices\":{\n \"A001\": [{\"seq\":\"ATCACG\",\"instruments\":[]}],\n \"A002\": [{\"seq\":\"CGATGT\",\"instruments\":[]}],\n \"A003\": [{\"seq\":\"TTAGGC\",\"instruments\":[]}],\n \"A004\": [{\"seq\":\"TGACCA\",\"instruments\":[]}],\n \"A005\": [{\"seq\":\"ACAGTG\",\"instruments\":[]}],\n \"A006\": [{\"seq\":\"GCCAAT\",\"instruments\":[]}],\n \"A007\": [{\"seq\":\"CAGATC\",\"instruments\":[]}],\n \"A008\": [{\"seq\":\"ACTTGA\",\"instruments\":[]}],\n \"A009\": [{\"seq\":\"GATCAG\",\"instruments\":[]}],\n \"A010\": [{\"seq\":\"TAGCTT\",\"instruments\":[]}],\n \"A011\": [{\"seq\":\"GGCTAC\",\"instruments\":[]}],\n \"A012\": [{\"seq\":\"CTTGTA\",\"instruments\":[]}],\n },\n },\n # \"TruSeq Synthetic Long-Read DNA\":{\n # \"_short_name\":\"\",\n # },\n # \"TruSeq Small RNA\":{\n # \"_short_name\":\"\",\n # },\n \"TruSeq Targeted RNA Expression\":{\n \"_short_name\":\"truseq_rna_expression\",\n \"i7\":{\n \"R701\": [{\"seq\":\"ATCACG\",\"instruments\":[]}],\n \"R702\": [{\"seq\":\"CGATGT\",\"instruments\":[]}],\n \"R703\": [{\"seq\":\"TTAGGC\",\"instruments\":[]}],\n \"R704\": [{\"seq\":\"TGACCA\",\"instruments\":[]}],\n \"R705\": [{\"seq\":\"ACAGTG\",\"instruments\":[]}],\n \"R706\": [{\"seq\":\"GCCAAT\",\"instruments\":[]}],\n \"R707\": [{\"seq\":\"CAGATC\",\"instruments\":[]}],\n \"R708\": [{\"seq\":\"ACTTGA\",\"instruments\":[]}],\n \"R709\": [{\"seq\":\"GATCAG\",\"instruments\":[]}],\n \"R710\": [{\"seq\":\"TAGCTT\",\"instruments\":[]}],\n \"R711\": [{\"seq\":\"GGCTAC\",\"instruments\":[]}],\n \"R712\": [{\"seq\":\"CTTGTA\",\"instruments\":[]}],\n \"R713\": [{\"seq\":\"AGTCAA\",\"instruments\":[]}],\n \"R714\": [{\"seq\":\"AGTTCC\",\"instruments\":[]}],\n \"R715\": [{\"seq\":\"ATGTCA\",\"instruments\":[]}],\n \"R716\": [{\"seq\":\"CCGTCC\",\"instruments\":[]}],\n \"R717\": [{\"seq\":\"GTAGAG\",\"instruments\":[]}],\n \"R718\": [{\"seq\":\"GTCCGC\",\"instruments\":[]}],\n \"R719\": [{\"seq\":\"GTGAAA\",\"instruments\":[]}],\n \"R720\": [{\"seq\":\"GTGGCC\",\"instruments\":[]}],\n \"R721\": [{\"seq\":\"GTTTCG\",\"instruments\":[]}],\n \"R722\": [{\"seq\":\"CGTACG\",\"instruments\":[]}],\n \"R723\": [{\"seq\":\"GAGTGG\",\"instruments\":[]}],\n \"R724\": [{\"seq\":\"GGTAGC\",\"instruments\":[]}],\n \"R725\": [{\"seq\":\"ACTGAT\",\"instruments\":[]}],\n \"R726\": [{\"seq\":\"ATGAGC\",\"instruments\":[]}],\n \"R727\": [{\"seq\":\"ATTCCT\",\"instruments\":[]}],\n \"R728\": [{\"seq\":\"CAAAAG\",\"instruments\":[]}],\n \"R729\": [{\"seq\":\"CAACTA\",\"instruments\":[]}],\n \"R730\": [{\"seq\":\"CACCGG\",\"instruments\":[]}],\n \"R731\": [{\"seq\":\"CACGAT\",\"instruments\":[]}],\n \"R732\": [{\"seq\":\"CACTCA\",\"instruments\":[]}],\n \"R733\": [{\"seq\":\"CAGGCG\",\"instruments\":[]}],\n \"R734\": [{\"seq\":\"CATGGC\",\"instruments\":[]}],\n \"R735\": [{\"seq\":\"CATTTT\",\"instruments\":[]}],\n \"R736\": [{\"seq\":\"CCAACA\",\"instruments\":[]}],\n \"R737\": [{\"seq\":\"CGGAAT\",\"instruments\":[]}],\n \"R738\": [{\"seq\":\"CTAGCT\",\"instruments\":[]}],\n \"R739\": [{\"seq\":\"CTATAC\",\"instruments\":[]}],\n \"R740\": [{\"seq\":\"CTCAGA\",\"instruments\":[]}],\n \"R741\": [{\"seq\":\"GACGAC\",\"instruments\":[]}],\n \"R742\": [{\"seq\":\"TAATCG\",\"instruments\":[]}],\n \"R743\": [{\"seq\":\"TACAGC\",\"instruments\":[]}],\n \"R744\": [{\"seq\":\"TATAAT\",\"instruments\":[]}],\n \"R745\": [{\"seq\":\"TCATTC\",\"instruments\":[]}],\n \"R746\": [{\"seq\":\"TCCCGA\",\"instruments\":[]}],\n \"R747\": [{\"seq\":\"TCGAAG\",\"instruments\":[]}],\n \"R748\": [{\"seq\":\"TCGGCA\",\"instruments\":[]}],\n },\n \"i5\":{\n \"A501\":[{\"seq\":\"TGAACCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AAGGTTCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A502\":[{\"seq\":\"TGCTAAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"ACTTAGCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A503\":[{\"seq\":\"TGTTCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"AGAGAACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A504\":[{\"seq\":\"TAAGACAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GTGTCTTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A505\":[{\"seq\":\"CTAATCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TCGATTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A506\":[{\"seq\":\"CTAGAACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TGTTCTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A507\":[{\"seq\":\"TAAGTTCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"GGAACTTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n \"A508\":[{\"seq\":\"TAGACCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"]}, {\"seq\":\"TAGGTCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"]}],\n }\n },\n # \"Process Controls for TruSeq Kits\":{\n # \"_short_name\":\"\",\n # },\n # \"Nextera DNA Sample Prep Kit\":{\n # \"_short_name\":\"\",\n # },\n # \"Oligonucleotide Sequences for Genomic DNA\":{\n # \"_short_name\":\"\",\n # },\n # \"Oligonucleotide Sequences for Paired End DNA\":{\n # \"_short_name\":\"\",\n # },\n # \"Oligonucleotide Sequences for the Multiplexing Sample Prep Oligo Only Kit\":{\n # \"_short_name\":\"\",\n # },\n # \"Oligonucleotide Sequences for the v1 and v1.5 Small RNA Kits\":{\n # \"_short_name\":\"\",\n # }\n \"Broad Institute NEXTERAINDEXPL\":{\n \"_short_name\":\"BI_nextera\",\n \"i7\":{\n \"BI7A01\":[{\"seq\":\"AAGTAGAG\",\"instruments\":[],\"seq_in_adapter\":\"CTCTACTT\"}],\n \"BI7A02\":[{\"seq\":\"ACACGATC\",\"instruments\":[],\"seq_in_adapter\":\"GATCGTGT\"}],\n \"BI7A03\":[{\"seq\":\"TGTTCCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGGAACA\"}],\n \"BI7A04\":[{\"seq\":\"CATGATCG\",\"instruments\":[],\"seq_in_adapter\":\"CGATCATG\"}],\n \"BI7A05\":[{\"seq\":\"CGTTACCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGTAACG\"}],\n \"BI7A06\":[{\"seq\":\"CAGAGAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTCTCTG\"}],\n \"BI7A07\":[{\"seq\":\"AACGCATT\",\"instruments\":[],\"seq_in_adapter\":\"AATGCGTT\"}],\n \"BI7A08\":[{\"seq\":\"ACAGGTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATACCTGT\"}],\n \"BI7A09\":[{\"seq\":\"AGGTAAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTTACCT\"}],\n \"BI7A10\":[{\"seq\":\"AACAATGG\",\"instruments\":[],\"seq_in_adapter\":\"CCATTGTT\"}],\n \"BI7A11\":[{\"seq\":\"ACTGTATC\",\"instruments\":[],\"seq_in_adapter\":\"GATACAGT\"}],\n \"BI7A12\":[{\"seq\":\"AGGTCGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCGACCT\"}],\n \"BI7B01\":[{\"seq\":\"GGTCCAGA\",\"instruments\":[],\"seq_in_adapter\":\"TCTGGACC\"}],\n \"BI7B02\":[{\"seq\":\"CATGCTTA\",\"instruments\":[],\"seq_in_adapter\":\"TAAGCATG\"}],\n \"BI7B03\":[{\"seq\":\"AGGATCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGATCCT\"}],\n \"BI7B04\":[{\"seq\":\"TCTGGCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGCCAGA\"}],\n \"BI7B05\":[{\"seq\":\"AGGTTATC\",\"instruments\":[],\"seq_in_adapter\":\"GATAACCT\"}],\n \"BI7B06\":[{\"seq\":\"GTCTGATG\",\"instruments\":[],\"seq_in_adapter\":\"CATCAGAC\"}],\n \"BI7B07\":[{\"seq\":\"CCAACATT\",\"instruments\":[],\"seq_in_adapter\":\"AATGTTGG\"}],\n \"BI7B08\":[{\"seq\":\"CAACTCTC\",\"instruments\":[],\"seq_in_adapter\":\"GAGAGTTG\"}],\n \"BI7B09\":[{\"seq\":\"ATTCCTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAGGAAT\"}],\n \"BI7B10\":[{\"seq\":\"CTAACTCG\",\"instruments\":[],\"seq_in_adapter\":\"CGAGTTAG\"}],\n \"BI7B11\":[{\"seq\":\"CTGCGGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCCGCAG\"}],\n \"BI7B12\":[{\"seq\":\"CTACCAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTGGTAG\"}],\n \"BI7C01\":[{\"seq\":\"GCACATCT\",\"instruments\":[],\"seq_in_adapter\":\"AGATGTGC\"}],\n \"BI7C02\":[{\"seq\":\"GTATAACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTTATAC\"}],\n \"BI7C03\":[{\"seq\":\"CATAGCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGCTATG\"}],\n \"BI7C04\":[{\"seq\":\"GACAGTAA\",\"instruments\":[],\"seq_in_adapter\":\"TTACTGTC\"}],\n \"BI7C05\":[{\"seq\":\"TTACGCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGCGTAA\"}],\n \"BI7C06\":[{\"seq\":\"GTCATCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGATGAC\"}],\n \"BI7C07\":[{\"seq\":\"CTGTAATC\",\"instruments\":[],\"seq_in_adapter\":\"GATTACAG\"}],\n \"BI7C08\":[{\"seq\":\"GCCGTCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGACGGC\"}],\n \"BI7C09\":[{\"seq\":\"GTAACATC\",\"instruments\":[],\"seq_in_adapter\":\"GATGTTAC\"}],\n \"BI7C10\":[{\"seq\":\"GAAGGAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTCCTTC\"}],\n \"BI7C11\":[{\"seq\":\"GACCTAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTAGGTC\"}],\n \"BI7C12\":[{\"seq\":\"ACCAACTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGTTGGT\"}],\n \"BI7D01\":[{\"seq\":\"TTCGCTGA\",\"instruments\":[],\"seq_in_adapter\":\"TCAGCGAA\"}],\n \"BI7D02\":[{\"seq\":\"TGCTCGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCGAGCA\"}],\n \"BI7D03\":[{\"seq\":\"GGACTCCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGAGTCC\"}],\n \"BI7D04\":[{\"seq\":\"CAGGAGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCTCCTG\"}],\n \"BI7D05\":[{\"seq\":\"CCTTCGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCGAAGG\"}],\n \"BI7D06\":[{\"seq\":\"TTGAATAG\",\"instruments\":[],\"seq_in_adapter\":\"CTATTCAA\"}],\n \"BI7D07\":[{\"seq\":\"TATCTGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCAGATA\"}],\n \"BI7D08\":[{\"seq\":\"TAAGCACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTGCTTA\"}],\n \"BI7D09\":[{\"seq\":\"TCGCTAGA\",\"instruments\":[],\"seq_in_adapter\":\"TCTAGCGA\"}],\n \"BI7D10\":[{\"seq\":\"TGTAATCA\",\"instruments\":[],\"seq_in_adapter\":\"TGATTACA\"}],\n \"BI7D11\":[{\"seq\":\"TTAATCAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGATTAA\"}],\n \"BI7D12\":[{\"seq\":\"TGCAAGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACTTGCA\"}],\n \"BI7E01\":[{\"seq\":\"AGCAATTC\",\"instruments\":[],\"seq_in_adapter\":\"GAATTGCT\"}],\n \"BI7E02\":[{\"seq\":\"AACTTGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCAAGTT\"}],\n \"BI7E03\":[{\"seq\":\"TGTCGGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCCGACA\"}],\n \"BI7E04\":[{\"seq\":\"TCGCCTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAAGGCGA\"}],\n \"BI7E05\":[{\"seq\":\"AAGACACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTGTCTT\"}],\n \"BI7E06\":[{\"seq\":\"TCTCGGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACCGAGA\"}],\n \"BI7E07\":[{\"seq\":\"AATGTTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAACATT\"}],\n \"BI7E08\":[{\"seq\":\"ACTAAGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCTTAGT\"}],\n \"BI7E09\":[{\"seq\":\"ATTATCAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGATAAT\"}],\n \"BI7E10\":[{\"seq\":\"ACAGTTGA\",\"instruments\":[],\"seq_in_adapter\":\"TCAACTGT\"}],\n \"BI7E11\":[{\"seq\":\"AGCATGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCATGCT\"}],\n \"BI7E12\":[{\"seq\":\"AGGTGCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGCACCT\"}],\n \"BI7F01\":[{\"seq\":\"CACATCCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGATGTG\"}],\n \"BI7F02\":[{\"seq\":\"AGTTGCTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGCAACT\"}],\n \"BI7F03\":[{\"seq\":\"ATAGCGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACGCTAT\"}],\n \"BI7F04\":[{\"seq\":\"ATTATGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACATAAT\"}],\n \"BI7F05\":[{\"seq\":\"ATTGTCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGACAAT\"}],\n \"BI7F06\":[{\"seq\":\"CAGCAAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTTGCTG\"}],\n \"BI7F07\":[{\"seq\":\"CGCCTTCC\",\"instruments\":[],\"seq_in_adapter\":\"GGAAGGCG\"}],\n \"BI7F08\":[{\"seq\":\"CAGCGGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACCGCTG\"}],\n \"BI7F09\":[{\"seq\":\"CAATAGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACTATTG\"}],\n \"BI7F10\":[{\"seq\":\"CTATGCGT\",\"instruments\":[],\"seq_in_adapter\":\"ACGCATAG\"}],\n \"BI7F11\":[{\"seq\":\"CTGTGGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCCACAG\"}],\n \"BI7F12\":[{\"seq\":\"CGCTATGT\",\"instruments\":[],\"seq_in_adapter\":\"ACATAGCG\"}],\n \"BI7G01\":[{\"seq\":\"CCAGTTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAACTGG\"}],\n \"BI7G02\":[{\"seq\":\"CTCTCTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAGAGAG\"}],\n \"BI7G03\":[{\"seq\":\"CCTACCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGGTAGG\"}],\n \"BI7G04\":[{\"seq\":\"GAAGAAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTTCTTC\"}],\n \"BI7G05\":[{\"seq\":\"TCCAGCAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGCTGGA\"}],\n \"BI7G06\":[{\"seq\":\"AAGAGGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCCTCTT\"}],\n \"BI7G07\":[{\"seq\":\"GACCAGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCTGGTC\"}],\n \"BI7G08\":[{\"seq\":\"GCCTAGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCTAGGC\"}],\n \"BI7G09\":[{\"seq\":\"GTCCACAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGTGGAC\"}],\n \"BI7G10\":[{\"seq\":\"GACCGTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAACGGTC\"}],\n \"BI7G11\":[{\"seq\":\"GATATCCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGATATC\"}],\n \"BI7G12\":[{\"seq\":\"GCCGCAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTGCGGC\"}],\n \"BI7H01\":[{\"seq\":\"AAGGATGT\",\"instruments\":[],\"seq_in_adapter\":\"ACATCCTT\"}],\n \"BI7H02\":[{\"seq\":\"AGGCAGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCTGCCT\"}],\n \"BI7H03\":[{\"seq\":\"ATTCTAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTAGAAT\"}],\n \"BI7H04\":[{\"seq\":\"TCCTGAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTCAGGA\"}],\n \"BI7H05\":[{\"seq\":\"TAATGAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTCATTA\"}],\n \"BI7H06\":[{\"seq\":\"CCAGAGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCTCTGG\"}],\n \"BI7H07\":[{\"seq\":\"CGTACTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAGTACG\"}],\n \"BI7H08\":[{\"seq\":\"TATCCAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTGGATA\"}],\n \"BI7H09\":[{\"seq\":\"TCTGCAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTGCAGA\"}],\n \"BI7H10\":[{\"seq\":\"TTGTCTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAGACAA\"}],\n \"BI7H11\":[{\"seq\":\"TTATATCT\",\"instruments\":[],\"seq_in_adapter\":\"AGATATAA\"}],\n \"BI7H12\":[{\"seq\":\"TAGGCATG\",\"instruments\":[],\"seq_in_adapter\":\"CATGCCTA\"}],\n },\n \"i5\":{\n \"BI5A01\":[{\"seq\":\"ATCGACTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCGACTG\"}, {\"seq\":\"CAGTCGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ATCGACTG\"}],\n \"BI5A02\":[{\"seq\":\"CGGTTCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGTTCTT\"}, {\"seq\":\"AAGAACCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CGGTTCTT\"}],\n \"BI5A03\":[{\"seq\":\"AACCTCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AACCTCTT\"}, {\"seq\":\"AAGAGGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AACCTCTT\"}],\n \"BI5A04\":[{\"seq\":\"CGCATATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCATATT\"}, {\"seq\":\"AATATGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CGCATATT\"}],\n \"BI5A05\":[{\"seq\":\"CTGCTCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGCTCCT\"}, {\"seq\":\"AGGAGCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTGCTCCT\"}],\n \"BI5A06\":[{\"seq\":\"TAGATCGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGATCGC\"}, {\"seq\":\"GCGATCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TAGATCGC\"}],\n \"BI5A07\":[{\"seq\":\"CCTGTCAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTGTCAT\"}, {\"seq\":\"ATGACAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CCTGTCAT\"}],\n \"BI5A08\":[{\"seq\":\"CACTTCAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CACTTCAT\"}, {\"seq\":\"ATGAAGTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CACTTCAT\"}],\n \"BI5A09\":[{\"seq\":\"AATACCAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AATACCAT\"}, {\"seq\":\"ATGGTATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AATACCAT\"}],\n \"BI5A10\":[{\"seq\":\"ATGAATTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ATGAATTA\"}, {\"seq\":\"TAATTCAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ATGAATTA\"}],\n \"BI5A11\":[{\"seq\":\"TGCTTCAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TGCTTCAC\"}, {\"seq\":\"GTGAAGCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TGCTTCAC\"}],\n \"BI5A12\":[{\"seq\":\"ATCCTTAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCCTTAA\"}, {\"seq\":\"TTAAGGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ATCCTTAA\"}],\n \"BI5B01\":[{\"seq\":\"GCTAGCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTAGCAG\"}, {\"seq\":\"CTGCTAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCTAGCAG\"}],\n \"BI5B02\":[{\"seq\":\"TAGCATTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGCATTG\"}, {\"seq\":\"CAATGCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TAGCATTG\"}],\n \"BI5B03\":[{\"seq\":\"CTACATTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTACATTG\"}, {\"seq\":\"CAATGTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTACATTG\"}],\n \"BI5B04\":[{\"seq\":\"TCATTCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCATTCGA\"}, {\"seq\":\"TCGAATGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCATTCGA\"}],\n \"BI5B05\":[{\"seq\":\"TTAGCCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTAGCCAG\"}, {\"seq\":\"CTGGCTAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTAGCCAG\"}],\n \"BI5B06\":[{\"seq\":\"GAACTTCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GAACTTCG\"}, {\"seq\":\"CGAAGTTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GAACTTCG\"}],\n \"BI5B07\":[{\"seq\":\"GACGGTTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GACGGTTA\"}, {\"seq\":\"TAACCGTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GACGGTTA\"}],\n \"BI5B08\":[{\"seq\":\"CAAGCTTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CAAGCTTA\"}, {\"seq\":\"TAAGCTTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CAAGCTTA\"}],\n \"BI5B09\":[{\"seq\":\"TCAGGCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCAGGCTT\"}, {\"seq\":\"AAGCCTGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCAGGCTT\"}],\n \"BI5B10\":[{\"seq\":\"TACTCCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TACTCCAG\"}, {\"seq\":\"CTGGAGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TACTCCAG\"}],\n \"BI5B11\":[{\"seq\":\"GCTTCCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTTCCTA\"}, {\"seq\":\"TAGGAAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCTTCCTA\"}],\n \"BI5B12\":[{\"seq\":\"TTCTTGGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCTTGGC\"}, {\"seq\":\"GCCAAGAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTCTTGGC\"}],\n \"BI5C01\":[{\"seq\":\"TACTCTCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TACTCTCC\"}, {\"seq\":\"GGAGAGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TACTCTCC\"}],\n \"BI5C02\":[{\"seq\":\"AATTCAAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AATTCAAC\"}, {\"seq\":\"GTTGAATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AATTCAAC\"}],\n \"BI5C03\":[{\"seq\":\"GCGATTAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGATTAC\"}, {\"seq\":\"GTAATCGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCGATTAC\"}],\n \"BI5C04\":[{\"seq\":\"GTCCAATC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GTCCAATC\"}, {\"seq\":\"GATTGGAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GTCCAATC\"}],\n \"BI5C05\":[{\"seq\":\"GCTGATTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTGATTC\"}, {\"seq\":\"GAATCAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCTGATTC\"}],\n \"BI5C06\":[{\"seq\":\"CTGTATTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGTATTC\"}, {\"seq\":\"GAATACAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTGTATTC\"}],\n \"BI5C07\":[{\"seq\":\"CTATTAGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTATTAGC\"}, {\"seq\":\"GCTAATAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTATTAGC\"}],\n \"BI5C08\":[{\"seq\":\"AGGTACCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AGGTACCA\"}, {\"seq\":\"TGGTACCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AGGTACCA\"}],\n \"BI5C09\":[{\"seq\":\"GAACGCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GAACGCTA\"}, {\"seq\":\"TAGCGTTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GAACGCTA\"}],\n \"BI5C10\":[{\"seq\":\"ATCATACC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCATACC\"}, {\"seq\":\"GGTATGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ATCATACC\"}],\n \"BI5C11\":[{\"seq\":\"GACCATCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GACCATCT\"}, {\"seq\":\"AGATGGTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GACCATCT\"}],\n \"BI5C12\":[{\"seq\":\"CATCACTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CATCACTT\"}, {\"seq\":\"AAGTGATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CATCACTT\"}],\n \"BI5D01\":[{\"seq\":\"TGACAGCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TGACAGCA\"}, {\"seq\":\"TGCTGTCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TGACAGCA\"}],\n \"BI5D02\":[{\"seq\":\"TTCACAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCACAGA\"}, {\"seq\":\"TCTGTGAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTCACAGA\"}],\n \"BI5D03\":[{\"seq\":\"CTCTCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCTCTAT\"}, {\"seq\":\"ATAGAGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTCTCTAT\"}],\n \"BI5D04\":[{\"seq\":\"CTTGGCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTTGGCTT\"}, {\"seq\":\"AAGCCAAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTTGGCTT\"}],\n \"BI5D05\":[{\"seq\":\"GAATCGAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GAATCGAC\"}, {\"seq\":\"GTCGATTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GAATCGAC\"}],\n \"BI5D06\":[{\"seq\":\"ATATCCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ATATCCGA\"}, {\"seq\":\"TCGGATAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ATATCCGA\"}],\n \"BI5D07\":[{\"seq\":\"TCCAACCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCAACCA\"}, {\"seq\":\"TGGTTGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCCAACCA\"}],\n \"BI5D08\":[{\"seq\":\"TCCATAAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCATAAC\"}, {\"seq\":\"GTTATGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCCATAAC\"}],\n \"BI5D09\":[{\"seq\":\"CTGACATC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGACATC\"}, {\"seq\":\"GATGTCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTGACATC\"}],\n \"BI5D10\":[{\"seq\":\"CCTCTAAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTCTAAC\"}, {\"seq\":\"GTTAGAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CCTCTAAC\"}],\n \"BI5D11\":[{\"seq\":\"CTGGTATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGGTATT\"}, {\"seq\":\"AATACCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTGGTATT\"}],\n \"BI5D12\":[{\"seq\":\"CGAACTTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CGAACTTC\"}, {\"seq\":\"GAAGTTCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CGAACTTC\"}],\n \"BI5E01\":[{\"seq\":\"GCAGGTTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCAGGTTG\"}, {\"seq\":\"CAACCTGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCAGGTTG\"}],\n \"BI5E02\":[{\"seq\":\"GCTCTCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTCTCTT\"}, {\"seq\":\"AAGAGAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCTCTCTT\"}],\n \"BI5E03\":[{\"seq\":\"AATTGCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AATTGCTT\"}, {\"seq\":\"AAGCAATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AATTGCTT\"}],\n \"BI5E04\":[{\"seq\":\"CCAACGCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CCAACGCT\"}, {\"seq\":\"AGCGTTGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CCAACGCT\"}],\n \"BI5E05\":[{\"seq\":\"AGTCACCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AGTCACCT\"}, {\"seq\":\"AGGTGACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AGTCACCT\"}],\n \"BI5E06\":[{\"seq\":\"GCGGACTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGGACTT\"}, {\"seq\":\"AAGTCCGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCGGACTT\"}],\n \"BI5E07\":[{\"seq\":\"CTGGCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGGCTAT\"}, {\"seq\":\"ATAGCCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTGGCTAT\"}],\n \"BI5E08\":[{\"seq\":\"GTCCTCAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GTCCTCAT\"}, {\"seq\":\"ATGAGGAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GTCCTCAT\"}],\n \"BI5E09\":[{\"seq\":\"GCCACCAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCCACCAT\"}, {\"seq\":\"ATGGTGGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCCACCAT\"}],\n \"BI5E10\":[{\"seq\":\"ATCTTCTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCTTCTC\"}, {\"seq\":\"GAGAAGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ATCTTCTC\"}],\n \"BI5E11\":[{\"seq\":\"TTAATCAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTAATCAC\"}, {\"seq\":\"GTGATTAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTAATCAC\"}],\n \"BI5E12\":[{\"seq\":\"GACATTAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GACATTAA\"}, {\"seq\":\"TTAATGTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GACATTAA\"}],\n \"BI5F01\":[{\"seq\":\"TTCCAGCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCCAGCT\"}, {\"seq\":\"AGCTGGAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTCCAGCT\"}],\n \"BI5F02\":[{\"seq\":\"TGACTTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TGACTTGG\"}, {\"seq\":\"CCAAGTCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TGACTTGG\"}],\n \"BI5F03\":[{\"seq\":\"TTGGTCTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGGTCTG\"}, {\"seq\":\"CAGACCAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTGGTCTG\"}],\n \"BI5F04\":[{\"seq\":\"TCCACTTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCACTTC\"}, {\"seq\":\"GAAGTGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCCACTTC\"}],\n \"BI5F05\":[{\"seq\":\"CACGATTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CACGATTC\"}, {\"seq\":\"GAATCGTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CACGATTC\"}],\n \"BI5F06\":[{\"seq\":\"GCGATATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGATATT\"}, {\"seq\":\"AATATCGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCGATATT\"}],\n \"BI5F07\":[{\"seq\":\"CAGCGATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CAGCGATT\"}, {\"seq\":\"AATCGCTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CAGCGATT\"}],\n \"BI5F08\":[{\"seq\":\"AGTACTGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AGTACTGC\"}, {\"seq\":\"GCAGTACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AGTACTGC\"}],\n \"BI5F09\":[{\"seq\":\"CGACTCTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CGACTCTC\"}, {\"seq\":\"GAGAGTCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CGACTCTC\"}],\n \"BI5F10\":[{\"seq\":\"CAGCTCAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CAGCTCAC\"}, {\"seq\":\"GTGAGCTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CAGCTCAC\"}],\n \"BI5F11\":[{\"seq\":\"CGCGAATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCGAATA\"}, {\"seq\":\"TATTCGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CGCGAATA\"}],\n \"BI5F12\":[{\"seq\":\"TTCACCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCACCTT\"}, {\"seq\":\"AAGGTGAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTCACCTT\"}],\n \"BI5G01\":[{\"seq\":\"TAGTTAGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGTTAGC\"}, {\"seq\":\"GCTAACTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TAGTTAGC\"}],\n \"BI5G02\":[{\"seq\":\"TATCCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TATCCTCT\"}, {\"seq\":\"AGAGGATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TATCCTCT\"}],\n \"BI5G03\":[{\"seq\":\"CATCCTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CATCCTGG\"}, {\"seq\":\"CCAGGATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CATCCTGG\"}],\n \"BI5G04\":[{\"seq\":\"AATCTCCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AATCTCCA\"}, {\"seq\":\"TGGAGATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AATCTCCA\"}],\n \"BI5G05\":[{\"seq\":\"GCTCCGAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTCCGAT\"}, {\"seq\":\"ATCGGAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GCTCCGAT\"}],\n 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\"X7323\":[{\"seq\":\"CTCAGAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTCTGAG\"}],\n \"X7324\":[{\"seq\":\"GCCATAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTATGGC\"}],\n \"X7325\":[{\"seq\":\"TTACCGAG\",\"instruments\":[],\"seq_in_adapter\":\"CTCGGTAA\"}],\n \"X7326\":[{\"seq\":\"GCTCTGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACAGAGC\"}],\n \"X7327\":[{\"seq\":\"CGTTATGC\",\"instruments\":[],\"seq_in_adapter\":\"GCATAACG\"}],\n \"X7328\":[{\"seq\":\"GTCTGATC\",\"instruments\":[],\"seq_in_adapter\":\"GATCAGAC\"}],\n \"X7329\":[{\"seq\":\"TAGTTGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCAACTA\"}],\n \"X7330\":[{\"seq\":\"TGATCGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCGATCA\"}],\n \"X7331\":[{\"seq\":\"CCAAGTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAACTTGG\"}],\n \"X7332\":[{\"seq\":\"CCTACTGA\",\"instruments\":[],\"seq_in_adapter\":\"TCAGTAGG\"}],\n \"X7333\":[{\"seq\":\"CTTGCTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACAGCAAG\"}],\n \"X7334\":[{\"seq\":\"TGCCATTC\",\"instruments\":[],\"seq_in_adapter\":\"GAATGGCA\"}],\n \"X7335\":[{\"seq\":\"TTGATCCG\",\"instruments\":[],\"seq_in_adapter\":\"CGGATCAA\"}],\n \"X7336\":[{\"seq\":\"AGTGCAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTGCACT\"}],\n \"X7337\":[{\"seq\":\"GACTTAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTAAGTC\"}],\n \"X7338\":[{\"seq\":\"CGTACGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCGTACG\"}],\n \"X7339\":[{\"seq\":\"TACCAGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCTGGTA\"}],\n \"X7340\":[{\"seq\":\"CGTCAATG\",\"instruments\":[],\"seq_in_adapter\":\"CATTGACG\"}],\n \"X7341\":[{\"seq\":\"GAAGAGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCTCTTC\"}],\n \"X7342\":[{\"seq\":\"GACGAATG\",\"instruments\":[],\"seq_in_adapter\":\"CATTCGTC\"}],\n \"X7343\":[{\"seq\":\"AGGAGGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCCTCCT\"}],\n \"X7344\":[{\"seq\":\"CTTACAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTGTAAG\"}],\n \"X7345\":[{\"seq\":\"GAGATGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACATCTC\"}],\n \"X7346\":[{\"seq\":\"TACGGTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAACCGTA\"}],\n \"X7347\":[{\"seq\":\"CTATCGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCGATAG\"}],\n \"X7348\":[{\"seq\":\"TCGAACCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGTTCGA\"}],\n \"X7349\":[{\"seq\":\"GAACGCTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGCGTTC\"}],\n \"X7350\":[{\"seq\":\"CAGAATCG\",\"instruments\":[],\"seq_in_adapter\":\"CGATTCTG\"}],\n \"X7351\":[{\"seq\":\"ATGGTTGC\",\"instruments\":[],\"seq_in_adapter\":\"GCAACCAT\"}],\n \"X7352\":[{\"seq\":\"GCTGGATT\",\"instruments\":[],\"seq_in_adapter\":\"AATCCAGC\"}],\n \"X7353\":[{\"seq\":\"GATGCACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTGCATC\"}],\n \"X7354\":[{\"seq\":\"ACCAATGC\",\"instruments\":[],\"seq_in_adapter\":\"GCATTGGT\"}],\n \"X7355\":[{\"seq\":\"GTCCTAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTAGGAC\"}],\n \"X7356\":[{\"seq\":\"CCGACTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAGTCGG\"}],\n \"X7357\":[{\"seq\":\"TTGGTCTC\",\"instruments\":[],\"seq_in_adapter\":\"GAGACCAA\"}],\n \"X7358\":[{\"seq\":\"GCCTTGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACAAGGC\"}],\n \"X7359\":[{\"seq\":\"GATACTGG\",\"instruments\":[],\"seq_in_adapter\":\"CCAGTATC\"}],\n \"X7360\":[{\"seq\":\"ATTCGAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTCGAAT\"}],\n \"X7361\":[{\"seq\":\"GTCAGTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAACTGAC\"}],\n \"X7362\":[{\"seq\":\"GTAGAGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCTCTAC\"}],\n \"X7363\":[{\"seq\":\"ACGTGATG\",\"instruments\":[],\"seq_in_adapter\":\"CATCACGT\"}],\n \"X7364\":[{\"seq\":\"TAAGTGGC\",\"instruments\":[],\"seq_in_adapter\":\"GCCACTTA\"}],\n \"X7365\":[{\"seq\":\"TGTGAAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTTCACA\"}],\n \"X7366\":[{\"seq\":\"CATTCGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCGAATG\"}],\n \"X7367\":[{\"seq\":\"TTGGTGAG\",\"instruments\":[],\"seq_in_adapter\":\"CTCACCAA\"}],\n \"X7368\":[{\"seq\":\"CAGTTCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGAACTG\"}],\n \"X7369\":[{\"seq\":\"AGGCTTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAAGCCT\"}],\n \"X7370\":[{\"seq\":\"GAATCGTG\",\"instruments\":[],\"seq_in_adapter\":\"CACGATTC\"}],\n \"X7371\":[{\"seq\":\"ACCAGCTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGCTGGT\"}],\n \"X7372\":[{\"seq\":\"CTCATTGC\",\"instruments\":[],\"seq_in_adapter\":\"GCAATGAG\"}],\n \"X7373\":[{\"seq\":\"CGATAGAG\",\"instruments\":[],\"seq_in_adapter\":\"CTCTATCG\"}],\n \"X7374\":[{\"seq\":\"TGGAGAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTCTCCA\"}],\n \"X7375\":[{\"seq\":\"GTATGCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGCATAC\"}],\n \"X7376\":[{\"seq\":\"CTGGAGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACTCCAG\"}],\n \"X7377\":[{\"seq\":\"AATGCCTC\",\"instruments\":[],\"seq_in_adapter\":\"GAGGCATT\"}],\n 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4000\"],\"seq_in_adapter\":\"GAGCTCTA\"}],\n \"X5370\":[{\"seq\":\"TCCGTGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCACGGA\"}, {\"seq\":\"TTCACGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTCACGGA\"}],\n \"X5371\":[{\"seq\":\"CTCGATAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GTATCGAG\"}, {\"seq\":\"GTATCGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GTATCGAG\"}],\n \"X5372\":[{\"seq\":\"CTTACCTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CAGGTAAG\"}, {\"seq\":\"CAGGTAAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CAGGTAAG\"}],\n \"X5373\":[{\"seq\":\"ATGGCGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCGCCAT\"}, {\"seq\":\"TTCGCCAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TTCGCCAT\"}],\n \"X5374\":[{\"seq\":\"TCCTACCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AGGTAGGA\"}, {\"seq\":\"AGGTAGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AGGTAGGA\"}],\n \"X5375\":[{\"seq\":\"CCTCAGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AACTGAGG\"}, {\"seq\":\"AACTGAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AACTGAGG\"}],\n \"X5376\":[{\"seq\":\"CTACTTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CCAAGTAG\"}, {\"seq\":\"CCAAGTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CCAAGTAG\"}],\n \"X5377\":[{\"seq\":\"TCACAGCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TGCTGTGA\"}, {\"seq\":\"TGCTGTGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TGCTGTGA\"}],\n \"X5378\":[{\"seq\":\"CACGTTGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ACAACGTG\"}, {\"seq\":\"ACAACGTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ACAACGTG\"}],\n \"X5379\":[{\"seq\":\"AAGTCGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCGACTT\"}, {\"seq\":\"CTCGACTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTCGACTT\"}],\n \"X5380\":[{\"seq\":\"TGTACCGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"ACGGTACA\"}, {\"seq\":\"ACGGTACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"ACGGTACA\"}],\n \"X5381\":[{\"seq\":\"CTCATCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGATGAG\"}, {\"seq\":\"CTGATGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTGATGAG\"}],\n \"X5382\":[{\"seq\":\"AGTCTCAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GTGAGACT\"}, {\"seq\":\"GTGAGACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GTGAGACT\"}],\n \"X5383\":[{\"seq\":\"CTTGGATG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CATCCAAG\"}, {\"seq\":\"CATCCAAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CATCCAAG\"}],\n \"X5384\":[{\"seq\":\"GCCTATCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TGATAGGC\"}, {\"seq\":\"TGATAGGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TGATAGGC\"}],\n }\n },\n # See: https://support-docs.illumina.com/SHARE/AdapterSeq/Content/SHARE/AdapterSeq/Nextera/UDIndexesSequencesNXT.htm\n \"IDT for Illumina UD Indexes Plate A\":{\n \"_short_name\":\"IDT_for_Illumina_UDI-A\",\n \"i7\":{\n \"IDT_UDI-A_i7-UDP0001\":[{\"seq\":\"GAACTGAGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCTCAGTTC\"}],\n \"IDT_UDI-A_i7-UDP0002\":[{\"seq\":\"AGGTCAGATA\",\"instruments\":[],\"seq_in_adapter\":\"TATCTGACCT\"}],\n \"IDT_UDI-A_i7-UDP0003\":[{\"seq\":\"CGTCTCATAT\",\"instruments\":[],\"seq_in_adapter\":\"ATATGAGACG\"}],\n \"IDT_UDI-A_i7-UDP0004\":[{\"seq\":\"ATTCCATAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTATGGAAT\"}],\n \"IDT_UDI-A_i7-UDP0005\":[{\"seq\":\"GACGAGATTA\",\"instruments\":[],\"seq_in_adapter\":\"TAATCTCGTC\"}],\n \"IDT_UDI-A_i7-UDP0006\":[{\"seq\":\"AACATCGCGC\",\"instruments\":[],\"seq_in_adapter\":\"GCGCGATGTT\"}],\n \"IDT_UDI-A_i7-UDP0007\":[{\"seq\":\"CTAGTGCTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAGCACTAG\"}],\n \"IDT_UDI-A_i7-UDP0008\":[{\"seq\":\"GATCAAGGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCCTTGATC\"}],\n \"IDT_UDI-A_i7-UDP0009\":[{\"seq\":\"GACTGAGTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTACTCAGTC\"}],\n \"IDT_UDI-A_i7-UDP0010\":[{\"seq\":\"AGTCAGACGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGTCTGACT\"}],\n \"IDT_UDI-A_i7-UDP0011\":[{\"seq\":\"CCGTATGTTC\",\"instruments\":[],\"seq_in_adapter\":\"GAACATACGG\"}],\n \"IDT_UDI-A_i7-UDP0012\":[{\"seq\":\"GAGTCATAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTATGACTC\"}],\n \"IDT_UDI-A_i7-UDP0013\":[{\"seq\":\"CTTGCCATTA\",\"instruments\":[],\"seq_in_adapter\":\"TAATGGCAAG\"}],\n \"IDT_UDI-A_i7-UDP0014\":[{\"seq\":\"GAAGCGGCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGCCGCTTC\"}],\n \"IDT_UDI-A_i7-UDP0015\":[{\"seq\":\"TCCATTGCCG\",\"instruments\":[],\"seq_in_adapter\":\"CGGCAATGGA\"}],\n \"IDT_UDI-A_i7-UDP0016\":[{\"seq\":\"CGGTTACGGC\",\"instruments\":[],\"seq_in_adapter\":\"GCCGTAACCG\"}],\n \"IDT_UDI-A_i7-UDP0017\":[{\"seq\":\"GAGAATGGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACCATTCTC\"}],\n \"IDT_UDI-A_i7-UDP0018\":[{\"seq\":\"AGAGGCAACC\",\"instruments\":[],\"seq_in_adapter\":\"GGTTGCCTCT\"}],\n \"IDT_UDI-A_i7-UDP0019\":[{\"seq\":\"CCATCATTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAATGATGG\"}],\n \"IDT_UDI-A_i7-UDP0020\":[{\"seq\":\"GATAGGCCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGGCCTATC\"}],\n \"IDT_UDI-A_i7-UDP0021\":[{\"seq\":\"ATGGTTGACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTCAACCAT\"}],\n \"IDT_UDI-A_i7-UDP0022\":[{\"seq\":\"TATTGCGCTC\",\"instruments\":[],\"seq_in_adapter\":\"GAGCGCAATA\"}],\n \"IDT_UDI-A_i7-UDP0023\":[{\"seq\":\"ACGCCTTGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACAAGGCGT\"}],\n \"IDT_UDI-A_i7-UDP0024\":[{\"seq\":\"TTCTACATAC\",\"instruments\":[],\"seq_in_adapter\":\"GTATGTAGAA\"}],\n \"IDT_UDI-A_i7-UDP0025\":[{\"seq\":\"AACCATAGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCTATGGTT\"}],\n \"IDT_UDI-A_i7-UDP0026\":[{\"seq\":\"GGTTGCGAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTCGCAACC\"}],\n \"IDT_UDI-A_i7-UDP0027\":[{\"seq\":\"TAAGCATCCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGATGCTTA\"}],\n \"IDT_UDI-A_i7-UDP0028\":[{\"seq\":\"ACCACGACAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGTCGTGGT\"}],\n \"IDT_UDI-A_i7-UDP0029\":[{\"seq\":\"GCCGCACTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAGTGCGGC\"}],\n \"IDT_UDI-A_i7-UDP0030\":[{\"seq\":\"CCACCAGGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCCTGGTGG\"}],\n \"IDT_UDI-A_i7-UDP0031\":[{\"seq\":\"GTGACACGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCGTGTCAC\"}],\n \"IDT_UDI-A_i7-UDP0032\":[{\"seq\":\"ACAGTGTATG\",\"instruments\":[],\"seq_in_adapter\":\"CATACACTGT\"}],\n \"IDT_UDI-A_i7-UDP0033\":[{\"seq\":\"TGATTATACG\",\"instruments\":[],\"seq_in_adapter\":\"CGTATAATCA\"}],\n \"IDT_UDI-A_i7-UDP0034\":[{\"seq\":\"CAGCCGCGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACGCGGCTG\"}],\n \"IDT_UDI-A_i7-UDP0035\":[{\"seq\":\"GGTAACTCGC\",\"instruments\":[],\"seq_in_adapter\":\"GCGAGTTACC\"}],\n \"IDT_UDI-A_i7-UDP0036\":[{\"seq\":\"ACCGGCCGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACGGCCGGT\"}],\n \"IDT_UDI-A_i7-UDP0037\":[{\"seq\":\"TGTAATCGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCGATTACA\"}],\n \"IDT_UDI-A_i7-UDP0038\":[{\"seq\":\"GTGCAGACAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGTCTGCAC\"}],\n \"IDT_UDI-A_i7-UDP0039\":[{\"seq\":\"CAATCGGCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGCCGATTG\"}],\n \"IDT_UDI-A_i7-UDP0040\":[{\"seq\":\"TATGTAGTCA\",\"instruments\":[],\"seq_in_adapter\":\"TGACTACATA\"}],\n \"IDT_UDI-A_i7-UDP0041\":[{\"seq\":\"ACTCGGCAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTGCCGAGT\"}],\n \"IDT_UDI-A_i7-UDP0042\":[{\"seq\":\"GTCTAATGGC\",\"instruments\":[],\"seq_in_adapter\":\"GCCATTAGAC\"}],\n \"IDT_UDI-A_i7-UDP0043\":[{\"seq\":\"CCATCTCGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCGAGATGG\"}],\n \"IDT_UDI-A_i7-UDP0044\":[{\"seq\":\"CTGCGAGCCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGCTCGCAG\"}],\n \"IDT_UDI-A_i7-UDP0045\":[{\"seq\":\"CGTTATTCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGAATAACG\"}],\n \"IDT_UDI-A_i7-UDP0046\":[{\"seq\":\"AGATCCATTA\",\"instruments\":[],\"seq_in_adapter\":\"TAATGGATCT\"}],\n \"IDT_UDI-A_i7-UDP0047\":[{\"seq\":\"GTCCTGGATA\",\"instruments\":[],\"seq_in_adapter\":\"TATCCAGGAC\"}],\n \"IDT_UDI-A_i7-UDP0048\":[{\"seq\":\"CAGTGGCACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTGCCACTG\"}],\n \"IDT_UDI-A_i7-UDP0049\":[{\"seq\":\"AGTGTTGCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGCAACACT\"}],\n \"IDT_UDI-A_i7-UDP0050\":[{\"seq\":\"GACACCATGT\",\"instruments\":[],\"seq_in_adapter\":\"ACATGGTGTC\"}],\n \"IDT_UDI-A_i7-UDP0051\":[{\"seq\":\"CCTGTCTGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACAGACAGG\"}],\n \"IDT_UDI-A_i7-UDP0052\":[{\"seq\":\"TGATGTAAGA\",\"instruments\":[],\"seq_in_adapter\":\"TCTTACATCA\"}],\n \"IDT_UDI-A_i7-UDP0053\":[{\"seq\":\"GGAATTGTAA\",\"instruments\":[],\"seq_in_adapter\":\"TTACAATTCC\"}],\n \"IDT_UDI-A_i7-UDP0054\":[{\"seq\":\"GCATAAGCTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGCTTATGC\"}],\n \"IDT_UDI-A_i7-UDP0055\":[{\"seq\":\"CTGAGGAATA\",\"instruments\":[],\"seq_in_adapter\":\"TATTCCTCAG\"}],\n \"IDT_UDI-A_i7-UDP0056\":[{\"seq\":\"AACGCACGAG\",\"instruments\":[],\"seq_in_adapter\":\"CTCGTGCGTT\"}],\n \"IDT_UDI-A_i7-UDP0057\":[{\"seq\":\"TCTATCCTAA\",\"instruments\":[],\"seq_in_adapter\":\"TTAGGATAGA\"}],\n \"IDT_UDI-A_i7-UDP0058\":[{\"seq\":\"CTCGCTTCGG\",\"instruments\":[],\"seq_in_adapter\":\"CCGAAGCGAG\"}],\n \"IDT_UDI-A_i7-UDP0059\":[{\"seq\":\"CTGTTGGTCC\",\"instruments\":[],\"seq_in_adapter\":\"GGACCAACAG\"}],\n \"IDT_UDI-A_i7-UDP0060\":[{\"seq\":\"TTACCTGGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCCAGGTAA\"}],\n \"IDT_UDI-A_i7-UDP0061\":[{\"seq\":\"TGGCTAATCA\",\"instruments\":[],\"seq_in_adapter\":\"TGATTAGCCA\"}],\n \"IDT_UDI-A_i7-UDP0062\":[{\"seq\":\"AACACTGTTA\",\"instruments\":[],\"seq_in_adapter\":\"TAACAGTGTT\"}],\n \"IDT_UDI-A_i7-UDP0063\":[{\"seq\":\"ATTGCGCGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCGCGCAAT\"}],\n \"IDT_UDI-A_i7-UDP0064\":[{\"seq\":\"TGGCGCGAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTCGCGCCA\"}],\n \"IDT_UDI-A_i7-UDP0065\":[{\"seq\":\"TAATGTGTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGACACATTA\"}],\n \"IDT_UDI-A_i7-UDP0066\":[{\"seq\":\"ATACCAACGC\",\"instruments\":[],\"seq_in_adapter\":\"GCGTTGGTAT\"}],\n \"IDT_UDI-A_i7-UDP0067\":[{\"seq\":\"AGGATGTGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCACATCCT\"}],\n \"IDT_UDI-A_i7-UDP0068\":[{\"seq\":\"CACGGAACAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGTTCCGTG\"}],\n \"IDT_UDI-A_i7-UDP0069\":[{\"seq\":\"TGGAGTACTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGTACTCCA\"}],\n \"IDT_UDI-A_i7-UDP0070\":[{\"seq\":\"GTATTGACGT\",\"instruments\":[],\"seq_in_adapter\":\"ACGTCAATAC\"}],\n \"IDT_UDI-A_i7-UDP0071\":[{\"seq\":\"CTTGTACACC\",\"instruments\":[],\"seq_in_adapter\":\"GGTGTACAAG\"}],\n \"IDT_UDI-A_i7-UDP0072\":[{\"seq\":\"ACACAGGTGG\",\"instruments\":[],\"seq_in_adapter\":\"CCACCTGTGT\"}],\n \"IDT_UDI-A_i7-UDP0073\":[{\"seq\":\"CCTGCGGAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTCCGCAGG\"}],\n \"IDT_UDI-A_i7-UDP0074\":[{\"seq\":\"TTCATAAGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCTTATGAA\"}],\n \"IDT_UDI-A_i7-UDP0075\":[{\"seq\":\"CTCTGCAGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCTGCAGAG\"}],\n \"IDT_UDI-A_i7-UDP0076\":[{\"seq\":\"CTGACTCTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAGAGTCAG\"}],\n \"IDT_UDI-A_i7-UDP0077\":[{\"seq\":\"TCTGGTATCC\",\"instruments\":[],\"seq_in_adapter\":\"GGATACCAGA\"}],\n \"IDT_UDI-A_i7-UDP0078\":[{\"seq\":\"CATTAGTGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCACTAATG\"}],\n \"IDT_UDI-A_i7-UDP0079\":[{\"seq\":\"ACGGTCAGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCTGACCGT\"}],\n \"IDT_UDI-A_i7-UDP0080\":[{\"seq\":\"GGCAAGCCAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGGCTTGCC\"}],\n \"IDT_UDI-A_i7-UDP0081\":[{\"seq\":\"TGTCGCTGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCAGCGACA\"}],\n \"IDT_UDI-A_i7-UDP0082\":[{\"seq\":\"ACCGTTACAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGTAACGGT\"}],\n \"IDT_UDI-A_i7-UDP0083\":[{\"seq\":\"TATGCCTTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAAGGCATA\"}],\n \"IDT_UDI-A_i7-UDP0084\":[{\"seq\":\"ACAAGTGGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCCACTTGT\"}],\n \"IDT_UDI-A_i7-UDP0085\":[{\"seq\":\"TGGTACCTAA\",\"instruments\":[],\"seq_in_adapter\":\"TTAGGTACCA\"}],\n \"IDT_UDI-A_i7-UDP0086\":[{\"seq\":\"TTGGAATTCC\",\"instruments\":[],\"seq_in_adapter\":\"GGAATTCCAA\"}],\n \"IDT_UDI-A_i7-UDP0087\":[{\"seq\":\"CCTCTACATG\",\"instruments\":[],\"seq_in_adapter\":\"CATGTAGAGG\"}],\n \"IDT_UDI-A_i7-UDP0088\":[{\"seq\":\"GGAGCGTGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACACGCTCC\"}],\n \"IDT_UDI-A_i7-UDP0089\":[{\"seq\":\"GTCCGTAAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTTACGGAC\"}],\n \"IDT_UDI-A_i7-UDP0090\":[{\"seq\":\"ACTTCAAGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCTTGAAGT\"}],\n \"IDT_UDI-A_i7-UDP0091\":[{\"seq\":\"TCAGAAGGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCCTTCTGA\"}],\n \"IDT_UDI-A_i7-UDP0092\":[{\"seq\":\"GCGTTGGTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATACCAACGC\"}],\n \"IDT_UDI-A_i7-UDP0093\":[{\"seq\":\"ACATATCCAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGGATATGT\"}],\n \"IDT_UDI-A_i7-UDP0094\":[{\"seq\":\"TCATAGATTG\",\"instruments\":[],\"seq_in_adapter\":\"CAATCTATGA\"}],\n \"IDT_UDI-A_i7-UDP0095\":[{\"seq\":\"GTATTCCACC\",\"instruments\":[],\"seq_in_adapter\":\"GGTGGAATAC\"}],\n \"IDT_UDI-A_i7-UDP0096\":[{\"seq\":\"CCTCCGTCCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGACGGAGG\"}],\n },\n \"i5\":{\n \"IDT_UDI-A_i5-UDP0001\":[{\"seq\":\"TCGTGGAGCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCGTGGAGCG\"}, {\"seq\":\"CGCTCCACGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCGTGGAGCG\"}],\n \"IDT_UDI-A_i5-UDP0002\":[{\"seq\":\"CTACAAGATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTACAAGATA\"}, {\"seq\":\"TATCTTGTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTACAAGATA\"}],\n \"IDT_UDI-A_i5-UDP0003\":[{\"seq\":\"TATAGTAGCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TATAGTAGCT\"}, {\"seq\":\"AGCTACTATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TATAGTAGCT\"}],\n \"IDT_UDI-A_i5-UDP0004\":[{\"seq\":\"TGCCTGGTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGCCTGGTGG\"}, {\"seq\":\"CCACCAGGCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGCCTGGTGG\"}],\n \"IDT_UDI-A_i5-UDP0005\":[{\"seq\":\"ACATTATCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACATTATCCT\"}, {\"seq\":\"AGGATAATGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACATTATCCT\"}],\n \"IDT_UDI-A_i5-UDP0006\":[{\"seq\":\"GTCCACTTGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTCCACTTGT\"}, {\"seq\":\"ACAAGTGGAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTCCACTTGT\"}],\n \"IDT_UDI-A_i5-UDP0007\":[{\"seq\":\"TGGAACAGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGAACAGTA\"}, {\"seq\":\"TACTGTTCCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGAACAGTA\"}],\n \"IDT_UDI-A_i5-UDP0008\":[{\"seq\":\"CCTTGTTAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTTGTTAAT\"}, {\"seq\":\"ATTAACAAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTTGTTAAT\"}],\n \"IDT_UDI-A_i5-UDP0009\":[{\"seq\":\"GTTGATAGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTTGATAGTG\"}, {\"seq\":\"CACTATCAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTTGATAGTG\"}],\n \"IDT_UDI-A_i5-UDP0010\":[{\"seq\":\"ACCAGCGACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACCAGCGACA\"}, {\"seq\":\"TGTCGCTGGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACCAGCGACA\"}],\n \"IDT_UDI-A_i5-UDP0011\":[{\"seq\":\"CATACACTGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CATACACTGT\"}, {\"seq\":\"ACAGTGTATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 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{\"seq\":\"GCCATGTGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCACATGGC\"}],\n \"IDT_UDI-A_i5-UDP0021\":[{\"seq\":\"GGCCTGTCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCCTGTCCT\"}, {\"seq\":\"AGGACAGGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCCTGTCCT\"}],\n \"IDT_UDI-A_i5-UDP0022\":[{\"seq\":\"CTGTGTTAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTGTGTTAGG\"}, {\"seq\":\"CCTAACACAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGTGTTAGG\"}],\n \"IDT_UDI-A_i5-UDP0023\":[{\"seq\":\"TAAGGAACGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAAGGAACGT\"}, {\"seq\":\"ACGTTCCTTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAAGGAACGT\"}],\n \"IDT_UDI-A_i5-UDP0024\":[{\"seq\":\"CTAACTGTAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTAACTGTAA\"}, {\"seq\":\"TTACAGTTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTAACTGTAA\"}],\n \"IDT_UDI-A_i5-UDP0025\":[{\"seq\":\"GGCGAGATGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCGAGATGG\"}, {\"seq\":\"CCATCTCGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCGAGATGG\"}],\n \"IDT_UDI-A_i5-UDP0026\":[{\"seq\":\"AATAGAGCAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 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2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCCGACCTCG\"}, {\"seq\":\"CGAGGTCGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCGACCTCG\"}],\n \"IDT_UDI-A_i5-UDP0030\":[{\"seq\":\"CTTATGGAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTTATGGAAT\"}, {\"seq\":\"ATTCCATAAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTTATGGAAT\"}],\n \"IDT_UDI-A_i5-UDP0031\":[{\"seq\":\"GCTTACGGAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCTTACGGAC\"}, {\"seq\":\"GTCCGTAAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTTACGGAC\"}],\n \"IDT_UDI-A_i5-UDP0032\":[{\"seq\":\"GAACATACGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAACATACGG\"}, {\"seq\":\"CCGTATGTTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAACATACGG\"}],\n \"IDT_UDI-A_i5-UDP0033\":[{\"seq\":\"GTCGATTACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTCGATTACA\"}, {\"seq\":\"TGTAATCGAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTCGATTACA\"}],\n \"IDT_UDI-A_i5-UDP0034\":[{\"seq\":\"ACTAGCCGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACTAGCCGTG\"}, {\"seq\":\"CACGGCTAGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACTAGCCGTG\"}],\n \"IDT_UDI-A_i5-UDP0035\":[{\"seq\":\"AAGTTGGTGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AAGTTGGTGA\"}, {\"seq\":\"TCACCAACTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AAGTTGGTGA\"}],\n \"IDT_UDI-A_i5-UDP0036\":[{\"seq\":\"TGGCAATATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGCAATATT\"}, {\"seq\":\"AATATTGCCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGCAATATT\"}],\n \"IDT_UDI-A_i5-UDP0037\":[{\"seq\":\"GATCACCGCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATCACCGCG\"}, {\"seq\":\"CGCGGTGATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATCACCGCG\"}],\n \"IDT_UDI-A_i5-UDP0038\":[{\"seq\":\"TACCATCCGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TACCATCCGT\"}, {\"seq\":\"ACGGATGGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TACCATCCGT\"}],\n \"IDT_UDI-A_i5-UDP0039\":[{\"seq\":\"GCTGTAGGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCTGTAGGAA\"}, {\"seq\":\"TTCCTACAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTGTAGGAA\"}],\n \"IDT_UDI-A_i5-UDP0040\":[{\"seq\":\"CGCACTAATG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGCACTAATG\"}, {\"seq\":\"CATTAGTGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 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500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCTATGGTT\"}],\n \"IDT_UDI-A_i5-UDP0044\":[{\"seq\":\"AATCCGGCCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AATCCGGCCA\"}, {\"seq\":\"TGGCCGGATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AATCCGGCCA\"}],\n \"IDT_UDI-A_i5-UDP0045\":[{\"seq\":\"CCATAAGGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCATAAGGTT\"}, {\"seq\":\"AACCTTATGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCATAAGGTT\"}],\n \"IDT_UDI-A_i5-UDP0046\":[{\"seq\":\"ATCTCTACCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATCTCTACCA\"}, {\"seq\":\"TGGTAGAGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCTCTACCA\"}],\n \"IDT_UDI-A_i5-UDP0047\":[{\"seq\":\"CGGTGGCGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGTGGCGAA\"}, {\"seq\":\"TTCGCCACCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGTGGCGAA\"}],\n \"IDT_UDI-A_i5-UDP0048\":[{\"seq\":\"TAACAATAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAACAATAGG\"}, {\"seq\":\"CCTATTGTTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAACAATAGG\"}],\n \"IDT_UDI-A_i5-UDP0049\":[{\"seq\":\"CTGGTACACG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTGGTACACG\"}, {\"seq\":\"CGTGTACCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGGTACACG\"}],\n \"IDT_UDI-A_i5-UDP0050\":[{\"seq\":\"TCAACGTGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCAACGTGTA\"}, {\"seq\":\"TACACGTTGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCAACGTGTA\"}],\n \"IDT_UDI-A_i5-UDP0051\":[{\"seq\":\"ACTGTTGTGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACTGTTGTGA\"}, {\"seq\":\"TCACAACAGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACTGTTGTGA\"}],\n \"IDT_UDI-A_i5-UDP0052\":[{\"seq\":\"GTGCGTCCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 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\"IDT_UDI-A_i5-UDP0058\":[{\"seq\":\"TACTAGTCAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TACTAGTCAA\"}, {\"seq\":\"TTGACTAGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TACTAGTCAA\"}],\n \"IDT_UDI-A_i5-UDP0059\":[{\"seq\":\"ATAGACCGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATAGACCGTT\"}, {\"seq\":\"AACGGTCTAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATAGACCGTT\"}],\n \"IDT_UDI-A_i5-UDP0060\":[{\"seq\":\"ACAGTTCCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACAGTTCCAG\"}, {\"seq\":\"CTGGAACTGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 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3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGGCTCCGC\"}],\n \"IDT_UDI-A_i5-UDP0064\":[{\"seq\":\"AACTGATACT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACTGATACT\"}, {\"seq\":\"AGTATCAGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACTGATACT\"}],\n \"IDT_UDI-A_i5-UDP0065\":[{\"seq\":\"GTAAGGCATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTAAGGCATA\"}, {\"seq\":\"TATGCCTTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTAAGGCATA\"}],\n \"IDT_UDI-A_i5-UDP0066\":[{\"seq\":\"AATTGCTGCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AATTGCTGCG\"}, {\"seq\":\"CGCAGCAATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AATTGCTGCG\"}],\n \"IDT_UDI-A_i5-UDP0067\":[{\"seq\":\"TTACAATTCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTACAATTCC\"}, {\"seq\":\"GGAATTGTAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTACAATTCC\"}],\n \"IDT_UDI-A_i5-UDP0068\":[{\"seq\":\"AACCTAGCAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACCTAGCAC\"}, {\"seq\":\"GTGCTAGGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACCTAGCAC\"}],\n \"IDT_UDI-A_i5-UDP0069\":[{\"seq\":\"TCTGTGTGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTGTGTGGA\"}, {\"seq\":\"TCCACACAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTGTGTGGA\"}],\n \"IDT_UDI-A_i5-UDP0070\":[{\"seq\":\"GGAATTCCAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGAATTCCAA\"}, {\"seq\":\"TTGGAATTCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGAATTCCAA\"}],\n \"IDT_UDI-A_i5-UDP0071\":[{\"seq\":\"AAGCGCGCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AAGCGCGCTT\"}, {\"seq\":\"AAGCGCGCTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AAGCGCGCTT\"}],\n \"IDT_UDI-A_i5-UDP0072\":[{\"seq\":\"TGAGCGTTGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGAGCGTTGT\"}, {\"seq\":\"ACAACGCTCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGAGCGTTGT\"}],\n \"IDT_UDI-A_i5-UDP0073\":[{\"seq\":\"ATCATAGGCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATCATAGGCT\"}, {\"seq\":\"AGCCTATGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCATAGGCT\"}],\n \"IDT_UDI-A_i5-UDP0074\":[{\"seq\":\"TGTTAGAAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGTTAGAAGG\"}, {\"seq\":\"CCTTCTAACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGTTAGAAGG\"}],\n \"IDT_UDI-A_i5-UDP0075\":[{\"seq\":\"GATGGATGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATGGATGTA\"}, {\"seq\":\"TACATCCATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATGGATGTA\"}],\n \"IDT_UDI-A_i5-UDP0076\":[{\"seq\":\"ACGGCCGTCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACGGCCGTCA\"}, {\"seq\":\"TGACGGCCGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACGGCCGTCA\"}],\n \"IDT_UDI-A_i5-UDP0077\":[{\"seq\":\"CGTTGCTTAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGTTGCTTAC\"}, {\"seq\":\"GTAAGCAACG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGTTGCTTAC\"}],\n \"IDT_UDI-A_i5-UDP0078\":[{\"seq\":\"TGACTACATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGACTACATA\"}, {\"seq\":\"TATGTAGTCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGACTACATA\"}],\n \"IDT_UDI-A_i5-UDP0079\":[{\"seq\":\"CGGCCTCGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGCCTCGTT\"}, {\"seq\":\"AACGAGGCCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGCCTCGTT\"}],\n \"IDT_UDI-A_i5-UDP0080\":[{\"seq\":\"CAAGCATCCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CAAGCATCCG\"}, {\"seq\":\"CGGATGCTTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CAAGCATCCG\"}],\n \"IDT_UDI-A_i5-UDP0081\":[{\"seq\":\"TCGTCTGACT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCGTCTGACT\"}, {\"seq\":\"AGTCAGACGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCGTCTGACT\"}],\n \"IDT_UDI-A_i5-UDP0082\":[{\"seq\":\"CTCATAGCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCATAGCGA\"}, {\"seq\":\"TCGCTATGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCATAGCGA\"}],\n \"IDT_UDI-A_i5-UDP0083\":[{\"seq\":\"AGACACATTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGACACATTA\"}, {\"seq\":\"TAATGTGTCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGACACATTA\"}],\n \"IDT_UDI-A_i5-UDP0084\":[{\"seq\":\"GCGCGATGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCGCGATGTT\"}, {\"seq\":\"AACATCGCGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGCGATGTT\"}],\n \"IDT_UDI-A_i5-UDP0085\":[{\"seq\":\"CATGAGTACT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CATGAGTACT\"}, {\"seq\":\"AGTACTCATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CATGAGTACT\"}],\n \"IDT_UDI-A_i5-UDP0086\":[{\"seq\":\"ACGTCAATAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACGTCAATAC\"}, {\"seq\":\"GTATTGACGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACGTCAATAC\"}],\n \"IDT_UDI-A_i5-UDP0087\":[{\"seq\":\"GATACCTCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATACCTCCT\"}, {\"seq\":\"AGGAGGTATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATACCTCCT\"}],\n \"IDT_UDI-A_i5-UDP0088\":[{\"seq\":\"ATCCGTAAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATCCGTAAGT\"}, {\"seq\":\"ACTTACGGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCCGTAAGT\"}],\n \"IDT_UDI-A_i5-UDP0089\":[{\"seq\":\"CGTGTATCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGTGTATCTT\"}, {\"seq\":\"AAGATACACG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGTGTATCTT\"}],\n \"IDT_UDI-A_i5-UDP0090\":[{\"seq\":\"GAACCATGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAACCATGAA\"}, {\"seq\":\"TTCATGGTTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAACCATGAA\"}],\n \"IDT_UDI-A_i5-UDP0091\":[{\"seq\":\"GGCCATCATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCCATCATA\"}, {\"seq\":\"TATGATGGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCCATCATA\"}],\n \"IDT_UDI-A_i5-UDP0092\":[{\"seq\":\"ACATACTTCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACATACTTCC\"}, {\"seq\":\"GGAAGTATGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACATACTTCC\"}],\n \"IDT_UDI-A_i5-UDP0093\":[{\"seq\":\"TATGTGCAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TATGTGCAAT\"}, {\"seq\":\"ATTGCACATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TATGTGCAAT\"}],\n \"IDT_UDI-A_i5-UDP0094\":[{\"seq\":\"GATTAAGGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATTAAGGTG\"}, {\"seq\":\"CACCTTAATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATTAAGGTG\"}],\n \"IDT_UDI-A_i5-UDP0095\":[{\"seq\":\"ATGTAGACAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATGTAGACAA\"}, {\"seq\":\"TTGTCTACAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATGTAGACAA\"}],\n \"IDT_UDI-A_i5-UDP0096\":[{\"seq\":\"CACATCGGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CACATCGGTG\"}, {\"seq\":\"CACCGATGTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CACATCGGTG\"}],\n }\n },\n \"IDT for Illumina UD Indexes Plate B\":{\n \"_short_name\":\"IDT_for_Illumina_UDI-B\",\n \"i7\":{\n \"IDT_UDI-B_i7-UDP0097\":[{\"seq\":\"TGCCGGTCAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGACCGGCA\"}],\n \"IDT_UDI-B_i7-UDP0098\":[{\"seq\":\"CACTCAATTC\",\"instruments\":[],\"seq_in_adapter\":\"GAATTGAGTG\"}],\n \"IDT_UDI-B_i7-UDP0099\":[{\"seq\":\"TCTCACACGC\",\"instruments\":[],\"seq_in_adapter\":\"GCGTGTGAGA\"}],\n \"IDT_UDI-B_i7-UDP0100\":[{\"seq\":\"TCAATGGAGA\",\"instruments\":[],\"seq_in_adapter\":\"TCTCCATTGA\"}],\n \"IDT_UDI-B_i7-UDP0101\":[{\"seq\":\"ATATGCATGT\",\"instruments\":[],\"seq_in_adapter\":\"ACATGCATAT\"}],\n \"IDT_UDI-B_i7-UDP0102\":[{\"seq\":\"ATGGCGCCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGGCGCCAT\"}],\n \"IDT_UDI-B_i7-UDP0103\":[{\"seq\":\"TCCGTTATGT\",\"instruments\":[],\"seq_in_adapter\":\"ACATAACGGA\"}],\n \"IDT_UDI-B_i7-UDP0104\":[{\"seq\":\"GGTCTATTAA\",\"instruments\":[],\"seq_in_adapter\":\"TTAATAGACC\"}],\n \"IDT_UDI-B_i7-UDP0105\":[{\"seq\":\"CAGCAATCGT\",\"instruments\":[],\"seq_in_adapter\":\"ACGATTGCTG\"}],\n \"IDT_UDI-B_i7-UDP0106\":[{\"seq\":\"TTCTGTAGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCTACAGAA\"}],\n \"IDT_UDI-B_i7-UDP0107\":[{\"seq\":\"GAACGCAATA\",\"instruments\":[],\"seq_in_adapter\":\"TATTGCGTTC\"}],\n \"IDT_UDI-B_i7-UDP0108\":[{\"seq\":\"AGTACTCATG\",\"instruments\":[],\"seq_in_adapter\":\"CATGAGTACT\"}],\n \"IDT_UDI-B_i7-UDP0109\":[{\"seq\":\"GGTAGAATTA\",\"instruments\":[],\"seq_in_adapter\":\"TAATTCTACC\"}],\n \"IDT_UDI-B_i7-UDP0110\":[{\"seq\":\"TAATTAGCGT\",\"instruments\":[],\"seq_in_adapter\":\"ACGCTAATTA\"}],\n \"IDT_UDI-B_i7-UDP0111\":[{\"seq\":\"ATTAACAAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTTGTTAAT\"}],\n \"IDT_UDI-B_i7-UDP0112\":[{\"seq\":\"TGATGGCTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAGCCATCA\"}],\n \"IDT_UDI-B_i7-UDP0113\":[{\"seq\":\"GAATTACAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTGTAATTC\"}],\n \"IDT_UDI-B_i7-UDP0114\":[{\"seq\":\"TAGAATTGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCAATTCTA\"}],\n \"IDT_UDI-B_i7-UDP0115\":[{\"seq\":\"AGGCAGCTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAGCTGCCT\"}],\n \"IDT_UDI-B_i7-UDP0116\":[{\"seq\":\"ATCGGCGAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTCGCCGAT\"}],\n \"IDT_UDI-B_i7-UDP0117\":[{\"seq\":\"CCGTGACCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGGTCACGG\"}],\n \"IDT_UDI-B_i7-UDP0118\":[{\"seq\":\"ATACTTGTTC\",\"instruments\":[],\"seq_in_adapter\":\"GAACAAGTAT\"}],\n \"IDT_UDI-B_i7-UDP0119\":[{\"seq\":\"TCCGCCAATT\",\"instruments\":[],\"seq_in_adapter\":\"AATTGGCGGA\"}],\n \"IDT_UDI-B_i7-UDP0120\":[{\"seq\":\"AGGACAGGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCCTGTCCT\"}],\n \"IDT_UDI-B_i7-UDP0121\":[{\"seq\":\"AGAGAACCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGGTTCTCT\"}],\n \"IDT_UDI-B_i7-UDP0122\":[{\"seq\":\"GATATTGTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACACAATATC\"}],\n \"IDT_UDI-B_i7-UDP0123\":[{\"seq\":\"CGTACAGGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCCTGTACG\"}],\n \"IDT_UDI-B_i7-UDP0124\":[{\"seq\":\"CTGCGTTACC\",\"instruments\":[],\"seq_in_adapter\":\"GGTAACGCAG\"}],\n \"IDT_UDI-B_i7-UDP0125\":[{\"seq\":\"AGGCCGTGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCACGGCCT\"}],\n \"IDT_UDI-B_i7-UDP0126\":[{\"seq\":\"AGGAGGTATC\",\"instruments\":[],\"seq_in_adapter\":\"GATACCTCCT\"}],\n \"IDT_UDI-B_i7-UDP0127\":[{\"seq\":\"GCTGACGTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAACGTCAGC\"}],\n \"IDT_UDI-B_i7-UDP0128\":[{\"seq\":\"CTAATAACCG\",\"instruments\":[],\"seq_in_adapter\":\"CGGTTATTAG\"}],\n \"IDT_UDI-B_i7-UDP0129\":[{\"seq\":\"TCTAGGCGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCGCCTAGA\"}],\n \"IDT_UDI-B_i7-UDP0130\":[{\"seq\":\"ATAGCCAAGA\",\"instruments\":[],\"seq_in_adapter\":\"TCTTGGCTAT\"}],\n \"IDT_UDI-B_i7-UDP0131\":[{\"seq\":\"TTCGGTGTGA\",\"instruments\":[],\"seq_in_adapter\":\"TCACACCGAA\"}],\n \"IDT_UDI-B_i7-UDP0132\":[{\"seq\":\"ATGTAACGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACGTTACAT\"}],\n \"IDT_UDI-B_i7-UDP0133\":[{\"seq\":\"AACGAGGCCG\",\"instruments\":[],\"seq_in_adapter\":\"CGGCCTCGTT\"}],\n \"IDT_UDI-B_i7-UDP0134\":[{\"seq\":\"TGGTGTTATG\",\"instruments\":[],\"seq_in_adapter\":\"CATAACACCA\"}],\n \"IDT_UDI-B_i7-UDP0135\":[{\"seq\":\"TGGCCTCTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACAGAGGCCA\"}],\n \"IDT_UDI-B_i7-UDP0136\":[{\"seq\":\"CCAGGCACCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGTGCCTGG\"}],\n \"IDT_UDI-B_i7-UDP0137\":[{\"seq\":\"CCGGTTCCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGGAACCGG\"}],\n \"IDT_UDI-B_i7-UDP0138\":[{\"seq\":\"GGCCAATATT\",\"instruments\":[],\"seq_in_adapter\":\"AATATTGGCC\"}],\n \"IDT_UDI-B_i7-UDP0139\":[{\"seq\":\"GAATACCTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAGGTATTC\"}],\n \"IDT_UDI-B_i7-UDP0140\":[{\"seq\":\"TACGTGAAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTTCACGTA\"}],\n \"IDT_UDI-B_i7-UDP0141\":[{\"seq\":\"CTTATTGGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCCAATAAG\"}],\n \"IDT_UDI-B_i7-UDP0142\":[{\"seq\":\"ACAACTACTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGTAGTTGT\"}],\n \"IDT_UDI-B_i7-UDP0143\":[{\"seq\":\"GTTGGATGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCATCCAAC\"}],\n \"IDT_UDI-B_i7-UDP0144\":[{\"seq\":\"AATCCAATTG\",\"instruments\":[],\"seq_in_adapter\":\"CAATTGGATT\"}],\n \"IDT_UDI-B_i7-UDP0145\":[{\"seq\":\"TATGATGGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCCATCATA\"}],\n \"IDT_UDI-B_i7-UDP0146\":[{\"seq\":\"CGCAGCAATT\",\"instruments\":[],\"seq_in_adapter\":\"AATTGCTGCG\"}],\n \"IDT_UDI-B_i7-UDP0147\":[{\"seq\":\"ACGTTCCTTA\",\"instruments\":[],\"seq_in_adapter\":\"TAAGGAACGT\"}],\n \"IDT_UDI-B_i7-UDP0148\":[{\"seq\":\"CCGCGTATAG\",\"instruments\":[],\"seq_in_adapter\":\"CTATACGCGG\"}],\n \"IDT_UDI-B_i7-UDP0149\":[{\"seq\":\"GATTCTGAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTCAGAATC\"}],\n \"IDT_UDI-B_i7-UDP0150\":[{\"seq\":\"TAGAGAATAC\",\"instruments\":[],\"seq_in_adapter\":\"GTATTCTCTA\"}],\n \"IDT_UDI-B_i7-UDP0151\":[{\"seq\":\"TTGTATCAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTGATACAA\"}],\n \"IDT_UDI-B_i7-UDP0152\":[{\"seq\":\"CACAGCGGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACCGCTGTG\"}],\n \"IDT_UDI-B_i7-UDP0153\":[{\"seq\":\"CCACGCTGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCAGCGTGG\"}],\n \"IDT_UDI-B_i7-UDP0154\":[{\"seq\":\"GTTCGGAGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACTCCGAAC\"}],\n \"IDT_UDI-B_i7-UDP0155\":[{\"seq\":\"ATAGCGGAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTCCGCTAT\"}],\n \"IDT_UDI-B_i7-UDP0156\":[{\"seq\":\"GCAATATTCA\",\"instruments\":[],\"seq_in_adapter\":\"TGAATATTGC\"}],\n \"IDT_UDI-B_i7-UDP0157\":[{\"seq\":\"CTAGATTGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCAATCTAG\"}],\n \"IDT_UDI-B_i7-UDP0158\":[{\"seq\":\"CGATGCGGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACCGCATCG\"}],\n \"IDT_UDI-B_i7-UDP0159\":[{\"seq\":\"TCCGGACTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAGTCCGGA\"}],\n \"IDT_UDI-B_i7-UDP0160\":[{\"seq\":\"GTGACGGAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTCCGTCAC\"}],\n \"IDT_UDI-B_i7-UDP0161\":[{\"seq\":\"AATTCCATCT\",\"instruments\":[],\"seq_in_adapter\":\"AGATGGAATT\"}],\n \"IDT_UDI-B_i7-UDP0162\":[{\"seq\":\"TTAACGGTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACACCGTTAA\"}],\n \"IDT_UDI-B_i7-UDP0163\":[{\"seq\":\"ACTTGTTATC\",\"instruments\":[],\"seq_in_adapter\":\"GATAACAAGT\"}],\n \"IDT_UDI-B_i7-UDP0164\":[{\"seq\":\"CGTGTACCAG\",\"instruments\":[],\"seq_in_adapter\":\"CTGGTACACG\"}],\n \"IDT_UDI-B_i7-UDP0165\":[{\"seq\":\"TTAACCTTCG\",\"instruments\":[],\"seq_in_adapter\":\"CGAAGGTTAA\"}],\n \"IDT_UDI-B_i7-UDP0166\":[{\"seq\":\"CATATGCGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCGCATATG\"}],\n \"IDT_UDI-B_i7-UDP0167\":[{\"seq\":\"AGCCTATGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCATAGGCT\"}],\n \"IDT_UDI-B_i7-UDP0168\":[{\"seq\":\"TATGACAATC\",\"instruments\":[],\"seq_in_adapter\":\"GATTGTCATA\"}],\n \"IDT_UDI-B_i7-UDP0169\":[{\"seq\":\"ATGTTGTTGG\",\"instruments\":[],\"seq_in_adapter\":\"CCAACAACAT\"}],\n \"IDT_UDI-B_i7-UDP0170\":[{\"seq\":\"GCACCACCAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGGTGGTGC\"}],\n \"IDT_UDI-B_i7-UDP0171\":[{\"seq\":\"AGGCGTTCGC\",\"instruments\":[],\"seq_in_adapter\":\"GCGAACGCCT\"}],\n \"IDT_UDI-B_i7-UDP0172\":[{\"seq\":\"CCTCCGGTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAACCGGAGG\"}],\n \"IDT_UDI-B_i7-UDP0173\":[{\"seq\":\"GTCCACCGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCGGTGGAC\"}],\n \"IDT_UDI-B_i7-UDP0174\":[{\"seq\":\"ATTGTTCGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACGAACAAT\"}],\n \"IDT_UDI-B_i7-UDP0175\":[{\"seq\":\"GGACCAGTGG\",\"instruments\":[],\"seq_in_adapter\":\"CCACTGGTCC\"}],\n \"IDT_UDI-B_i7-UDP0176\":[{\"seq\":\"CCTTCTAACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTTAGAAGG\"}],\n \"IDT_UDI-B_i7-UDP0177\":[{\"seq\":\"CTCGAATATA\",\"instruments\":[],\"seq_in_adapter\":\"TATATTCGAG\"}],\n \"IDT_UDI-B_i7-UDP0178\":[{\"seq\":\"GATCGTCGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCGACGATC\"}],\n \"IDT_UDI-B_i7-UDP0179\":[{\"seq\":\"TATCCGAGGC\",\"instruments\":[],\"seq_in_adapter\":\"GCCTCGGATA\"}],\n \"IDT_UDI-B_i7-UDP0180\":[{\"seq\":\"CGCTGTCTCA\",\"instruments\":[],\"seq_in_adapter\":\"TGAGACAGCG\"}],\n \"IDT_UDI-B_i7-UDP0181\":[{\"seq\":\"AATGCGAACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTTCGCATT\"}],\n \"IDT_UDI-B_i7-UDP0182\":[{\"seq\":\"AATTCTTGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCAAGAATT\"}],\n \"IDT_UDI-B_i7-UDP0183\":[{\"seq\":\"TTCCTACAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTGTAGGAA\"}],\n \"IDT_UDI-B_i7-UDP0184\":[{\"seq\":\"ATCCAGGTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATACCTGGAT\"}],\n \"IDT_UDI-B_i7-UDP0185\":[{\"seq\":\"ACGGTCCAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTGGACCGT\"}],\n \"IDT_UDI-B_i7-UDP0186\":[{\"seq\":\"GTAACTTGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCAAGTTAC\"}],\n \"IDT_UDI-B_i7-UDP0187\":[{\"seq\":\"AGCGCCACAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGTGGCGCT\"}],\n \"IDT_UDI-B_i7-UDP0188\":[{\"seq\":\"TGCTACTGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCAGTAGCA\"}],\n \"IDT_UDI-B_i7-UDP0189\":[{\"seq\":\"CAACACCGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCGGTGTTG\"}],\n \"IDT_UDI-B_i7-UDP0190\":[{\"seq\":\"CACCTTAATC\",\"instruments\":[],\"seq_in_adapter\":\"GATTAAGGTG\"}],\n \"IDT_UDI-B_i7-UDP0191\":[{\"seq\":\"TTGAATGTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAACATTCAA\"}],\n \"IDT_UDI-B_i7-UDP0192\":[{\"seq\":\"CCGGTAACAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGTTACCGG\"}],\n },\n \"i5\":{\n \"IDT_UDI-B_i5-UDP0097\":[{\"seq\":\"CCTGATACAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTGATACAA\"}, {\"seq\":\"TTGTATCAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTGATACAA\"}],\n \"IDT_UDI-B_i5-UDP0098\":[{\"seq\":\"TTAAGTTGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTAAGTTGTG\"}, {\"seq\":\"CACAACTTAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTAAGTTGTG\"}],\n \"IDT_UDI-B_i5-UDP0099\":[{\"seq\":\"CGGACAGTGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGACAGTGA\"}, {\"seq\":\"TCACTGTCCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGACAGTGA\"}],\n \"IDT_UDI-B_i5-UDP0100\":[{\"seq\":\"GCACTACAAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCACTACAAC\"}, {\"seq\":\"GTTGTAGTGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCACTACAAC\"}],\n \"IDT_UDI-B_i5-UDP0101\":[{\"seq\":\"TGGTGCCTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGTGCCTGG\"}, {\"seq\":\"CCAGGCACCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGTGCCTGG\"}],\n \"IDT_UDI-B_i5-UDP0102\":[{\"seq\":\"TCCACGGCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCCACGGCCT\"}, {\"seq\":\"AGGCCGTGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCACGGCCT\"}],\n \"IDT_UDI-B_i5-UDP0103\":[{\"seq\":\"TTGTAGTGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTGTAGTGTA\"}, {\"seq\":\"TACACTACAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGTAGTGTA\"}],\n \"IDT_UDI-B_i5-UDP0104\":[{\"seq\":\"CCACGACACG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCACGACACG\"}, {\"seq\":\"CGTGTCGTGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCACGACACG\"}],\n \"IDT_UDI-B_i5-UDP0105\":[{\"seq\":\"TGTGATGTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGTGATGTAT\"}, {\"seq\":\"ATACATCACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGTGATGTAT\"}],\n \"IDT_UDI-B_i5-UDP0106\":[{\"seq\":\"GAGCGCAATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAGCGCAATA\"}, {\"seq\":\"TATTGCGCTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAGCGCAATA\"}],\n \"IDT_UDI-B_i5-UDP0107\":[{\"seq\":\"ATCTTACTGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATCTTACTGT\"}, {\"seq\":\"ACAGTAAGAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATCTTACTGT\"}],\n \"IDT_UDI-B_i5-UDP0108\":[{\"seq\":\"ATGTCGTGGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATGTCGTGGT\"}, {\"seq\":\"ACCACGACAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATGTCGTGGT\"}],\n \"IDT_UDI-B_i5-UDP0109\":[{\"seq\":\"GTAGCCATCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTAGCCATCA\"}, {\"seq\":\"TGATGGCTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTAGCCATCA\"}],\n \"IDT_UDI-B_i5-UDP0110\":[{\"seq\":\"TGGTTAAGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGTTAAGAA\"}, {\"seq\":\"TTCTTAACCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGTTAAGAA\"}],\n \"IDT_UDI-B_i5-UDP0111\":[{\"seq\":\"TGTTGTTCGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGTTGTTCGT\"}, {\"seq\":\"ACGAACAACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGTTGTTCGT\"}],\n \"IDT_UDI-B_i5-UDP0112\":[{\"seq\":\"CCAACAACAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCAACAACAT\"}, {\"seq\":\"ATGTTGTTGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCAACAACAT\"}],\n \"IDT_UDI-B_i5-UDP0113\":[{\"seq\":\"ACCGGCTCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACCGGCTCAG\"}, {\"seq\":\"CTGAGCCGGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACCGGCTCAG\"}],\n \"IDT_UDI-B_i5-UDP0114\":[{\"seq\":\"GTTAATCTGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTTAATCTGA\"}, {\"seq\":\"TCAGATTAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTTAATCTGA\"}],\n \"IDT_UDI-B_i5-UDP0115\":[{\"seq\":\"CGGCTAACGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGCTAACGT\"}, {\"seq\":\"ACGTTAGCCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGCTAACGT\"}],\n \"IDT_UDI-B_i5-UDP0116\":[{\"seq\":\"TCCAAGAATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCCAAGAATT\"}, {\"seq\":\"AATTCTTGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCAAGAATT\"}],\n \"IDT_UDI-B_i5-UDP0117\":[{\"seq\":\"CCGAACGTTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCGAACGTTG\"}, {\"seq\":\"CAACGTTCGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCGAACGTTG\"}],\n \"IDT_UDI-B_i5-UDP0118\":[{\"seq\":\"TAACCGCCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAACCGCCGA\"}, {\"seq\":\"TCGGCGGTTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAACCGCCGA\"}],\n \"IDT_UDI-B_i5-UDP0119\":[{\"seq\":\"CTCCGTGCTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCCGTGCTG\"}, {\"seq\":\"CAGCACGGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCCGTGCTG\"}],\n \"IDT_UDI-B_i5-UDP0120\":[{\"seq\":\"CATTCCAGCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CATTCCAGCT\"}, {\"seq\":\"AGCTGGAATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CATTCCAGCT\"}],\n \"IDT_UDI-B_i5-UDP0121\":[{\"seq\":\"GGTTATGCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGTTATGCTA\"}, {\"seq\":\"TAGCATAACC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGTTATGCTA\"}],\n \"IDT_UDI-B_i5-UDP0122\":[{\"seq\":\"ACCACACGGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACCACACGGT\"}, {\"seq\":\"ACCGTGTGGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACCACACGGT\"}],\n \"IDT_UDI-B_i5-UDP0123\":[{\"seq\":\"TAGGTTCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAGGTTCTCT\"}, {\"seq\":\"AGAGAACCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGGTTCTCT\"}],\n \"IDT_UDI-B_i5-UDP0124\":[{\"seq\":\"TATGGCTCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TATGGCTCGA\"}, {\"seq\":\"TCGAGCCATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TATGGCTCGA\"}],\n \"IDT_UDI-B_i5-UDP0125\":[{\"seq\":\"CTCGTGCGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCGTGCGTT\"}, {\"seq\":\"AACGCACGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCGTGCGTT\"}],\n \"IDT_UDI-B_i5-UDP0126\":[{\"seq\":\"CCAGTTGGCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCAGTTGGCA\"}, {\"seq\":\"TGCCAACTGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCAGTTGGCA\"}],\n \"IDT_UDI-B_i5-UDP0127\":[{\"seq\":\"TGTTCGCATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGTTCGCATT\"}, {\"seq\":\"AATGCGAACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGTTCGCATT\"}],\n \"IDT_UDI-B_i5-UDP0128\":[{\"seq\":\"AACCGCATCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACCGCATCG\"}, {\"seq\":\"CGATGCGGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACCGCATCG\"}],\n \"IDT_UDI-B_i5-UDP0129\":[{\"seq\":\"CGAAGGTTAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGAAGGTTAA\"}, {\"seq\":\"TTAACCTTCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGAAGGTTAA\"}],\n \"IDT_UDI-B_i5-UDP0130\":[{\"seq\":\"AGTGCCACTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGTGCCACTG\"}, {\"seq\":\"CAGTGGCACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 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550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACGCTAATTA\"}],\n \"IDT_UDI-B_i5-UDP0137\":[{\"seq\":\"TATATTCGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TATATTCGAG\"}, {\"seq\":\"CTCGAATATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TATATTCGAG\"}],\n \"IDT_UDI-B_i5-UDP0138\":[{\"seq\":\"CGGTCCGATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGTCCGATA\"}, {\"seq\":\"TATCGGACCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGTCCGATA\"}],\n \"IDT_UDI-B_i5-UDP0139\":[{\"seq\":\"ACAATAGAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACAATAGAGT\"}, {\"seq\":\"ACTCTATTGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACAATAGAGT\"}],\n \"IDT_UDI-B_i5-UDP0140\":[{\"seq\":\"CGGTTATTAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGTTATTAG\"}, {\"seq\":\"CTAATAACCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGTTATTAG\"}],\n \"IDT_UDI-B_i5-UDP0141\":[{\"seq\":\"GATAACAAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATAACAAGT\"}, {\"seq\":\"ACTTGTTATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATAACAAGT\"}],\n \"IDT_UDI-B_i5-UDP0142\":[{\"seq\":\"AGTTATCACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGTTATCACA\"}, {\"seq\":\"TGTGATAACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGTTATCACA\"}],\n \"IDT_UDI-B_i5-UDP0143\":[{\"seq\":\"TTCCAGGTAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTCCAGGTAA\"}, {\"seq\":\"TTACCTGGAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCCAGGTAA\"}],\n \"IDT_UDI-B_i5-UDP0144\":[{\"seq\":\"CATGTAGAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CATGTAGAGG\"}, {\"seq\":\"CCTCTACATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CATGTAGAGG\"}],\n \"IDT_UDI-B_i5-UDP0145\":[{\"seq\":\"GATTGTCATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATTGTCATA\"}, {\"seq\":\"TATGACAATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATTGTCATA\"}],\n \"IDT_UDI-B_i5-UDP0146\":[{\"seq\":\"ATTCCGCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATTCCGCTAT\"}, {\"seq\":\"ATAGCGGAAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATTCCGCTAT\"}],\n \"IDT_UDI-B_i5-UDP0147\":[{\"seq\":\"GACCGCTGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GACCGCTGTG\"}, {\"seq\":\"CACAGCGGTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GACCGCTGTG\"}],\n \"IDT_UDI-B_i5-UDP0148\":[{\"seq\":\"TAGGAACCGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAGGAACCGG\"}, {\"seq\":\"CCGGTTCCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGGAACCGG\"}],\n \"IDT_UDI-B_i5-UDP0149\":[{\"seq\":\"AGCGGTGGAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGCGGTGGAC\"}, {\"seq\":\"GTCCACCGCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGCGGTGGAC\"}],\n \"IDT_UDI-B_i5-UDP0150\":[{\"seq\":\"TATAGATTCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TATAGATTCG\"}, {\"seq\":\"CGAATCTATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TATAGATTCG\"}],\n \"IDT_UDI-B_i5-UDP0151\":[{\"seq\":\"ACAGAGGCCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACAGAGGCCA\"}, {\"seq\":\"TGGCCTCTGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACAGAGGCCA\"}],\n \"IDT_UDI-B_i5-UDP0152\":[{\"seq\":\"ATTCCTATTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATTCCTATTG\"}, {\"seq\":\"CAATAGGAAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATTCCTATTG\"}],\n \"IDT_UDI-B_i5-UDP0153\":[{\"seq\":\"TATTCCTCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TATTCCTCAG\"}, {\"seq\":\"CTGAGGAATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TATTCCTCAG\"}],\n \"IDT_UDI-B_i5-UDP0154\":[{\"seq\":\"CGCCTTCTGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGCCTTCTGA\"}, {\"seq\":\"TCAGAAGGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCCTTCTGA\"}],\n \"IDT_UDI-B_i5-UDP0155\":[{\"seq\":\"GCGCAGAGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCGCAGAGTA\"}, {\"seq\":\"TACTCTGCGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGCAGAGTA\"}],\n \"IDT_UDI-B_i5-UDP0156\":[{\"seq\":\"GGCGCCAATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCGCCAATT\"}, {\"seq\":\"AATTGGCGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCGCCAATT\"}],\n \"IDT_UDI-B_i5-UDP0157\":[{\"seq\":\"AGATATGGCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGATATGGCG\"}, {\"seq\":\"CGCCATATCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGATATGGCG\"}],\n \"IDT_UDI-B_i5-UDP0158\":[{\"seq\":\"CCTGCTTGGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTGCTTGGT\"}, {\"seq\":\"ACCAAGCAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTGCTTGGT\"}],\n \"IDT_UDI-B_i5-UDP0159\":[{\"seq\":\"GACGAACAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GACGAACAAT\"}, {\"seq\":\"ATTGTTCGTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GACGAACAAT\"}],\n \"IDT_UDI-B_i5-UDP0160\":[{\"seq\":\"TGGCGGTCCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGCGGTCCA\"}, {\"seq\":\"TGGACCGCCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGCGGTCCA\"}],\n \"IDT_UDI-B_i5-UDP0161\":[{\"seq\":\"CTTCAGTTAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTTCAGTTAC\"}, {\"seq\":\"GTAACTGAAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTTCAGTTAC\"}],\n \"IDT_UDI-B_i5-UDP0162\":[{\"seq\":\"TCCTGACCGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCCTGACCGT\"}, {\"seq\":\"ACGGTCAGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCTGACCGT\"}],\n \"IDT_UDI-B_i5-UDP0163\":[{\"seq\":\"CGCGCCTAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGCGCCTAGA\"}, {\"seq\":\"TCTAGGCGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCGCCTAGA\"}],\n \"IDT_UDI-B_i5-UDP0164\":[{\"seq\":\"AGGATAAGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGGATAAGTT\"}, {\"seq\":\"AACTTATCCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGGATAAGTT\"}],\n \"IDT_UDI-B_i5-UDP0165\":[{\"seq\":\"AGGCCAGACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGGCCAGACA\"}, {\"seq\":\"TGTCTGGCCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGGCCAGACA\"}],\n \"IDT_UDI-B_i5-UDP0166\":[{\"seq\":\"CCTTGAACGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTTGAACGG\"}, {\"seq\":\"CCGTTCAAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTTGAACGG\"}],\n \"IDT_UDI-B_i5-UDP0167\":[{\"seq\":\"CACCACCTAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CACCACCTAC\"}, {\"seq\":\"GTAGGTGGTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CACCACCTAC\"}],\n \"IDT_UDI-B_i5-UDP0168\":[{\"seq\":\"TTGCTTGTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTGCTTGTAT\"}, {\"seq\":\"ATACAAGCAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGCTTGTAT\"}],\n \"IDT_UDI-B_i5-UDP0169\":[{\"seq\":\"CAATCTATGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CAATCTATGA\"}, {\"seq\":\"TCATAGATTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CAATCTATGA\"}],\n \"IDT_UDI-B_i5-UDP0170\":[{\"seq\":\"TGGTACTGAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGTACTGAT\"}, {\"seq\":\"ATCAGTACCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGTACTGAT\"}],\n \"IDT_UDI-B_i5-UDP0171\":[{\"seq\":\"TTCATCCAAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTCATCCAAC\"}, {\"seq\":\"GTTGGATGAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTCATCCAAC\"}],\n \"IDT_UDI-B_i5-UDP0172\":[{\"seq\":\"CATAACACCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CATAACACCA\"}, {\"seq\":\"TGGTGTTATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CATAACACCA\"}],\n \"IDT_UDI-B_i5-UDP0173\":[{\"seq\":\"TCCTATTAGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCCTATTAGC\"}, {\"seq\":\"GCTAATAGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCTATTAGC\"}],\n \"IDT_UDI-B_i5-UDP0174\":[{\"seq\":\"TCTCTAGATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTCTAGATT\"}, {\"seq\":\"AATCTAGAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTCTAGATT\"}],\n \"IDT_UDI-B_i5-UDP0175\":[{\"seq\":\"CGCGAGCCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGCGAGCCTA\"}, {\"seq\":\"TAGGCTCGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCGAGCCTA\"}],\n \"IDT_UDI-B_i5-UDP0176\":[{\"seq\":\"GATAAGCTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATAAGCTCT\"}, {\"seq\":\"AGAGCTTATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATAAGCTCT\"}],\n \"IDT_UDI-B_i5-UDP0177\":[{\"seq\":\"GAGATGTCGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAGATGTCGA\"}, {\"seq\":\"TCGACATCTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAGATGTCGA\"}],\n \"IDT_UDI-B_i5-UDP0178\":[{\"seq\":\"CTGGATATGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTGGATATGT\"}, {\"seq\":\"ACATATCCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGGATATGT\"}],\n \"IDT_UDI-B_i5-UDP0179\":[{\"seq\":\"GGCCAATAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCCAATAAG\"}, {\"seq\":\"CTTATTGGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCCAATAAG\"}],\n \"IDT_UDI-B_i5-UDP0180\":[{\"seq\":\"ATTACTCACC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATTACTCACC\"}, {\"seq\":\"GGTGAGTAAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATTACTCACC\"}],\n \"IDT_UDI-B_i5-UDP0181\":[{\"seq\":\"AATTGGCGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AATTGGCGGA\"}, {\"seq\":\"TCCGCCAATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AATTGGCGGA\"}],\n \"IDT_UDI-B_i5-UDP0182\":[{\"seq\":\"TTGTCAACTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTGTCAACTT\"}, {\"seq\":\"AAGTTGACAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGTCAACTT\"}],\n \"IDT_UDI-B_i5-UDP0183\":[{\"seq\":\"GGCGAATTCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCGAATTCT\"}, {\"seq\":\"AGAATTCGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCGAATTCT\"}],\n \"IDT_UDI-B_i5-UDP0184\":[{\"seq\":\"CAACGTCAGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CAACGTCAGC\"}, {\"seq\":\"GCTGACGTTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CAACGTCAGC\"}],\n \"IDT_UDI-B_i5-UDP0185\":[{\"seq\":\"TCTTACATCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTTACATCA\"}, {\"seq\":\"TGATGTAAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTTACATCA\"}],\n \"IDT_UDI-B_i5-UDP0186\":[{\"seq\":\"CGCCATACCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGCCATACCT\"}, {\"seq\":\"AGGTATGGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCCATACCT\"}],\n \"IDT_UDI-B_i5-UDP0187\":[{\"seq\":\"CTAATGTCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTAATGTCTT\"}, {\"seq\":\"AAGACATTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTAATGTCTT\"}],\n \"IDT_UDI-B_i5-UDP0188\":[{\"seq\":\"CAACCGGAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CAACCGGAGG\"}, {\"seq\":\"CCTCCGGTTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CAACCGGAGG\"}],\n \"IDT_UDI-B_i5-UDP0189\":[{\"seq\":\"GGCAGTAGCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCAGTAGCA\"}, {\"seq\":\"TGCTACTGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCAGTAGCA\"}],\n \"IDT_UDI-B_i5-UDP0190\":[{\"seq\":\"TTAGGATAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTAGGATAGA\"}, {\"seq\":\"TCTATCCTAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTAGGATAGA\"}],\n \"IDT_UDI-B_i5-UDP0191\":[{\"seq\":\"CGCAATCTAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGCAATCTAG\"}, {\"seq\":\"CTAGATTGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCAATCTAG\"}],\n \"IDT_UDI-B_i5-UDP0192\":[{\"seq\":\"GAGTTGTACT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAGTTGTACT\"}, {\"seq\":\"AGTACAACTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAGTTGTACT\"}],\n }\n },\n \"IDT for Illumina UD Indexes Plate C\":{\n \"_short_name\":\"IDT_for_Illumina_UDI-C\",\n \"i7\":{\n \"IDT_UDI-C_i7-UDP0193\":[{\"seq\":\"TCTCATGATA\",\"instruments\":[],\"seq_in_adapter\":\"TATCATGAGA\"}],\n \"IDT_UDI-C_i7-UDP0194\":[{\"seq\":\"CGAGGCCAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTGGCCTCG\"}],\n \"IDT_UDI-C_i7-UDP0195\":[{\"seq\":\"TTCACGAGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCTCGTGAA\"}],\n \"IDT_UDI-C_i7-UDP0196\":[{\"seq\":\"GCGTGGATGG\",\"instruments\":[],\"seq_in_adapter\":\"CCATCCACGC\"}],\n \"IDT_UDI-C_i7-UDP0197\":[{\"seq\":\"TCCTGGTTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACAACCAGGA\"}],\n \"IDT_UDI-C_i7-UDP0198\":[{\"seq\":\"TAATTCTGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCAGAATTA\"}],\n \"IDT_UDI-C_i7-UDP0199\":[{\"seq\":\"CGCACGACTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGTCGTGCG\"}],\n \"IDT_UDI-C_i7-UDP0200\":[{\"seq\":\"GAGGTTAGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCTAACCTC\"}],\n \"IDT_UDI-C_i7-UDP0201\":[{\"seq\":\"AACCGAGTTC\",\"instruments\":[],\"seq_in_adapter\":\"GAACTCGGTT\"}],\n \"IDT_UDI-C_i7-UDP0202\":[{\"seq\":\"TGTGATAACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTTATCACA\"}],\n \"IDT_UDI-C_i7-UDP0203\":[{\"seq\":\"AGTATGCTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAGCATACT\"}],\n \"IDT_UDI-C_i7-UDP0204\":[{\"seq\":\"GTAACTGAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTCAGTTAC\"}],\n \"IDT_UDI-C_i7-UDP0205\":[{\"seq\":\"TCCTCGGACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTCCGAGGA\"}],\n \"IDT_UDI-C_i7-UDP0206\":[{\"seq\":\"CTGGAACTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACAGTTCCAG\"}],\n \"IDT_UDI-C_i7-UDP0207\":[{\"seq\":\"GAATATGCGG\",\"instruments\":[],\"seq_in_adapter\":\"CCGCATATTC\"}],\n \"IDT_UDI-C_i7-UDP0208\":[{\"seq\":\"GATCGGATAA\",\"instruments\":[],\"seq_in_adapter\":\"TTATCCGATC\"}],\n \"IDT_UDI-C_i7-UDP0209\":[{\"seq\":\"GCTAGACTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAGTCTAGC\"}],\n \"IDT_UDI-C_i7-UDP0210\":[{\"seq\":\"AGCTACTATA\",\"instruments\":[],\"seq_in_adapter\":\"TATAGTAGCT\"}],\n \"IDT_UDI-C_i7-UDP0211\":[{\"seq\":\"CCACCGGAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTCCGGTGG\"}],\n \"IDT_UDI-C_i7-UDP0212\":[{\"seq\":\"CTTACCGCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGCGGTAAG\"}],\n \"IDT_UDI-C_i7-UDP0213\":[{\"seq\":\"TTAGGATATC\",\"instruments\":[],\"seq_in_adapter\":\"GATATCCTAA\"}],\n \"IDT_UDI-C_i7-UDP0214\":[{\"seq\":\"TTATACGCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGCGTATAA\"}],\n \"IDT_UDI-C_i7-UDP0215\":[{\"seq\":\"CGCTTAGAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTCTAAGCG\"}],\n \"IDT_UDI-C_i7-UDP0216\":[{\"seq\":\"CCGAAGCGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCGCTTCGG\"}],\n \"IDT_UDI-C_i7-UDP0217\":[{\"seq\":\"CACTATCAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTGATAGTG\"}],\n \"IDT_UDI-C_i7-UDP0218\":[{\"seq\":\"TTGCTCTATT\",\"instruments\":[],\"seq_in_adapter\":\"AATAGAGCAA\"}],\n \"IDT_UDI-C_i7-UDP0219\":[{\"seq\":\"TTACAGTTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAACTGTAA\"}],\n \"IDT_UDI-C_i7-UDP0220\":[{\"seq\":\"CTAAGTACGC\",\"instruments\":[],\"seq_in_adapter\":\"GCGTACTTAG\"}],\n \"IDT_UDI-C_i7-UDP0221\":[{\"seq\":\"TAGTTCGGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACCGAACTA\"}],\n \"IDT_UDI-C_i7-UDP0222\":[{\"seq\":\"CTATTACTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAGTAATAG\"}],\n \"IDT_UDI-C_i7-UDP0223\":[{\"seq\":\"TAGCATAACC\",\"instruments\":[],\"seq_in_adapter\":\"GGTTATGCTA\"}],\n \"IDT_UDI-C_i7-UDP0224\":[{\"seq\":\"ACTCTATTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACAATAGAGT\"}],\n \"IDT_UDI-C_i7-UDP0225\":[{\"seq\":\"TAGTGGAAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTTCCACTA\"}],\n \"IDT_UDI-C_i7-UDP0226\":[{\"seq\":\"CGCCATATCT\",\"instruments\":[],\"seq_in_adapter\":\"AGATATGGCG\"}],\n \"IDT_UDI-C_i7-UDP0227\":[{\"seq\":\"GCTTCATATT\",\"instruments\":[],\"seq_in_adapter\":\"AATATGAAGC\"}],\n \"IDT_UDI-C_i7-UDP0228\":[{\"seq\":\"ACTAGCGCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGCGCTAGT\"}],\n \"IDT_UDI-C_i7-UDP0229\":[{\"seq\":\"GCTCTTAACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTTAAGAGC\"}],\n \"IDT_UDI-C_i7-UDP0230\":[{\"seq\":\"GTGGTATCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGATACCAC\"}],\n \"IDT_UDI-C_i7-UDP0231\":[{\"seq\":\"TGACGGCCGT\",\"instruments\":[],\"seq_in_adapter\":\"ACGGCCGTCA\"}],\n \"IDT_UDI-C_i7-UDP0232\":[{\"seq\":\"CAGTAATTAC\",\"instruments\":[],\"seq_in_adapter\":\"GTAATTACTG\"}],\n \"IDT_UDI-C_i7-UDP0233\":[{\"seq\":\"TACAAGACTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGTCTTGTA\"}],\n \"IDT_UDI-C_i7-UDP0234\":[{\"seq\":\"CTGTGGTGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCACCACAG\"}],\n \"IDT_UDI-C_i7-UDP0235\":[{\"seq\":\"CTCCACTAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTAGTGGAG\"}],\n \"IDT_UDI-C_i7-UDP0236\":[{\"seq\":\"ATAGTTAGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCTAACTAT\"}],\n \"IDT_UDI-C_i7-UDP0237\":[{\"seq\":\"ATAGGTCTTA\",\"instruments\":[],\"seq_in_adapter\":\"TAAGACCTAT\"}],\n \"IDT_UDI-C_i7-UDP0238\":[{\"seq\":\"TTCTTAACCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGTTAAGAA\"}],\n \"IDT_UDI-C_i7-UDP0239\":[{\"seq\":\"AAGGAAGAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTCTTCCTT\"}],\n \"IDT_UDI-C_i7-UDP0240\":[{\"seq\":\"GGAAGGAGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCTCCTTCC\"}],\n \"IDT_UDI-C_i7-UDP0241\":[{\"seq\":\"TGAACGCGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCGCGTTCA\"}],\n \"IDT_UDI-C_i7-UDP0242\":[{\"seq\":\"CCTGCAACCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGTTGCAGG\"}],\n \"IDT_UDI-C_i7-UDP0243\":[{\"seq\":\"TTCATGGTTC\",\"instruments\":[],\"seq_in_adapter\":\"GAACCATGAA\"}],\n \"IDT_UDI-C_i7-UDP0244\":[{\"seq\":\"ATCCTCTCAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGAGAGGAT\"}],\n \"IDT_UDI-C_i7-UDP0245\":[{\"seq\":\"CACTAGACCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGTCTAGTG\"}],\n \"IDT_UDI-C_i7-UDP0246\":[{\"seq\":\"ATTATCCACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTGGATAAT\"}],\n \"IDT_UDI-C_i7-UDP0247\":[{\"seq\":\"ATGGCGTGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCACGCCAT\"}],\n \"IDT_UDI-C_i7-UDP0248\":[{\"seq\":\"TCCAGAGATC\",\"instruments\":[],\"seq_in_adapter\":\"GATCTCTGGA\"}],\n \"IDT_UDI-C_i7-UDP0249\":[{\"seq\":\"ATGTCCAGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCTGGACAT\"}],\n \"IDT_UDI-C_i7-UDP0250\":[{\"seq\":\"CAACGTTCGG\",\"instruments\":[],\"seq_in_adapter\":\"CCGAACGTTG\"}],\n \"IDT_UDI-C_i7-UDP0251\":[{\"seq\":\"GCGTATTAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTAATACGC\"}],\n \"IDT_UDI-C_i7-UDP0252V2\":[{\"seq\":\"CCGAATCTGG\",\"instruments\":[],\"seq_in_adapter\":\"CCAGATTCGG\"}],\n \"IDT_UDI-C_i7-UDP0252\":[{\"seq\":\"GTTGTGACTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGTCACAAC\"}],\n \"IDT_UDI-C_i7-UDP0253\":[{\"seq\":\"TCTCAATACC\",\"instruments\":[],\"seq_in_adapter\":\"GGTATTGAGA\"}],\n \"IDT_UDI-C_i7-UDP0254\":[{\"seq\":\"AAGCATCTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAAGATGCTT\"}],\n \"IDT_UDI-C_i7-UDP0255\":[{\"seq\":\"TCAGTCTCGT\",\"instruments\":[],\"seq_in_adapter\":\"ACGAGACTGA\"}],\n \"IDT_UDI-C_i7-UDP0256\":[{\"seq\":\"TGCAAGATAA\",\"instruments\":[],\"seq_in_adapter\":\"TTATCTTGCA\"}],\n \"IDT_UDI-C_i7-UDP0257\":[{\"seq\":\"GTAACAATCT\",\"instruments\":[],\"seq_in_adapter\":\"AGATTGTTAC\"}],\n \"IDT_UDI-C_i7-UDP0258V2\":[{\"seq\":\"CCATGGTATA\",\"instruments\":[],\"seq_in_adapter\":\"TATACCATGG\"}],\n \"IDT_UDI-C_i7-UDP0258\":[{\"seq\":\"CAGCGGTAGA\",\"instruments\":[],\"seq_in_adapter\":\"TCTACCGCTG\"}],\n \"IDT_UDI-C_i7-UDP0259\":[{\"seq\":\"TCATACCGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACGGTATGA\"}],\n \"IDT_UDI-C_i7-UDP0260\":[{\"seq\":\"GGCGCCATTG\",\"instruments\":[],\"seq_in_adapter\":\"CAATGGCGCC\"}],\n \"IDT_UDI-C_i7-UDP0261\":[{\"seq\":\"AGCGAATTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAATTCGCT\"}],\n \"IDT_UDI-C_i7-UDP0262\":[{\"seq\":\"TTAGACCATG\",\"instruments\":[],\"seq_in_adapter\":\"CATGGTCTAA\"}],\n \"IDT_UDI-C_i7-UDP0263\":[{\"seq\":\"CACACAGTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATACTGTGTG\"}],\n \"IDT_UDI-C_i7-UDP0264\":[{\"seq\":\"TCTTGTCGGC\",\"instruments\":[],\"seq_in_adapter\":\"GCCGACAAGA\"}],\n \"IDT_UDI-C_i7-UDP0265\":[{\"seq\":\"TACCGCCTCG\",\"instruments\":[],\"seq_in_adapter\":\"CGAGGCGGTA\"}],\n \"IDT_UDI-C_i7-UDP0266\":[{\"seq\":\"CTGTTATATC\",\"instruments\":[],\"seq_in_adapter\":\"GATATAACAG\"}],\n \"IDT_UDI-C_i7-UDP0267\":[{\"seq\":\"TAACCGGCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGCCGGTTA\"}],\n \"IDT_UDI-C_i7-UDP0268\":[{\"seq\":\"AAGAGAGTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGACTCTCTT\"}],\n \"IDT_UDI-C_i7-UDP0269\":[{\"seq\":\"GTAGGCGAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTCGCCTAC\"}],\n \"IDT_UDI-C_i7-UDP0270\":[{\"seq\":\"AACTTATCCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGATAAGTT\"}],\n \"IDT_UDI-C_i7-UDP0271\":[{\"seq\":\"ATTATGTCTC\",\"instruments\":[],\"seq_in_adapter\":\"GAGACATAAT\"}],\n \"IDT_UDI-C_i7-UDP0272\":[{\"seq\":\"TATAACAGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCTGTTATA\"}],\n \"IDT_UDI-C_i7-UDP0273\":[{\"seq\":\"CCAATGATAC\",\"instruments\":[],\"seq_in_adapter\":\"GTATCATTGG\"}],\n \"IDT_UDI-C_i7-UDP0274\":[{\"seq\":\"GAGGCCTATT\",\"instruments\":[],\"seq_in_adapter\":\"AATAGGCCTC\"}],\n \"IDT_UDI-C_i7-UDP0275\":[{\"seq\":\"AGCTAAGCGG\",\"instruments\":[],\"seq_in_adapter\":\"CCGCTTAGCT\"}],\n \"IDT_UDI-C_i7-UDP0276\":[{\"seq\":\"CTTCCTAGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCTAGGAAG\"}],\n \"IDT_UDI-C_i7-UDP0277\":[{\"seq\":\"CGATCTGTGA\",\"instruments\":[],\"seq_in_adapter\":\"TCACAGATCG\"}],\n \"IDT_UDI-C_i7-UDP0278\":[{\"seq\":\"GTGGACAAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTTGTCCAC\"}],\n \"IDT_UDI-C_i7-UDP0279\":[{\"seq\":\"AACAAGTACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTACTTGTT\"}],\n \"IDT_UDI-C_i7-UDP0280\":[{\"seq\":\"AGATTAAGTG\",\"instruments\":[],\"seq_in_adapter\":\"CACTTAATCT\"}],\n \"IDT_UDI-C_i7-UDP0281\":[{\"seq\":\"TATCACTCTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGAGTGATA\"}],\n \"IDT_UDI-C_i7-UDP0282\":[{\"seq\":\"AGAATTCGCC\",\"instruments\":[],\"seq_in_adapter\":\"GGCGAATTCT\"}],\n \"IDT_UDI-C_i7-UDP0283\":[{\"seq\":\"CCTGACCACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTGGTCAGG\"}],\n \"IDT_UDI-C_i7-UDP0284\":[{\"seq\":\"AGCTGGAATG\",\"instruments\":[],\"seq_in_adapter\":\"CATTCCAGCT\"}],\n \"IDT_UDI-C_i7-UDP0285\":[{\"seq\":\"TGATAACGAG\",\"instruments\":[],\"seq_in_adapter\":\"CTCGTTATCA\"}],\n \"IDT_UDI-C_i7-UDP0286\":[{\"seq\":\"CATAGTAAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTTACTATG\"}],\n \"IDT_UDI-C_i7-UDP0287\":[{\"seq\":\"ATTGGCTTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAAGCCAAT\"}],\n \"IDT_UDI-C_i7-UDP0288\":[{\"seq\":\"GTACCGATTA\",\"instruments\":[],\"seq_in_adapter\":\"TAATCGGTAC\"}],\n },\n \"i5\":{\n \"IDT_UDI-C_i5-UDP0193\":[{\"seq\":\"AACACGTGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACACGTGGA\"}, {\"seq\":\"TCCACGTGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACACGTGGA\"}],\n \"IDT_UDI-C_i5-UDP0194\":[{\"seq\":\"GTGTTACCGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTGTTACCGG\"}, {\"seq\":\"CCGGTAACAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTGTTACCGG\"}],\n \"IDT_UDI-C_i5-UDP0195\":[{\"seq\":\"AGATTGTTAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGATTGTTAC\"}, {\"seq\":\"GTAACAATCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGATTGTTAC\"}],\n \"IDT_UDI-C_i5-UDP0196\":[{\"seq\":\"TTGACCAATG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTGACCAATG\"}, {\"seq\":\"CATTGGTCAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGACCAATG\"}],\n \"IDT_UDI-C_i5-UDP0197\":[{\"seq\":\"CTGACCGGCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTGACCGGCA\"}, {\"seq\":\"TGCCGGTCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGACCGGCA\"}],\n \"IDT_UDI-C_i5-UDP0198\":[{\"seq\":\"TCTCATCAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTCATCAAT\"}, {\"seq\":\"ATTGATGAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTCATCAAT\"}],\n \"IDT_UDI-C_i5-UDP0199\":[{\"seq\":\"GGACCAACAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGACCAACAG\"}, {\"seq\":\"CTGTTGGTCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGACCAACAG\"}],\n \"IDT_UDI-C_i5-UDP0200\":[{\"seq\":\"AATGTATTGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 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{\"seq\":\"TAGGTATGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACATACCTA\"}],\n \"IDT_UDI-C_i5-UDP0221\":[{\"seq\":\"CCATGTGTAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCATGTGTAG\"}, {\"seq\":\"CTACACATGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCATGTGTAG\"}],\n \"IDT_UDI-C_i5-UDP0222\":[{\"seq\":\"GAGTCTCTCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAGTCTCTCC\"}, {\"seq\":\"GGAGAGACTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAGTCTCTCC\"}],\n \"IDT_UDI-C_i5-UDP0223\":[{\"seq\":\"GCTATGCGCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 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\"IDT_UDI-C_i5-UDP0232\":[{\"seq\":\"CGAGGCGGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGAGGCGGTA\"}, {\"seq\":\"TACCGCCTCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGAGGCGGTA\"}],\n \"IDT_UDI-C_i5-UDP0233\":[{\"seq\":\"CAGGTGTTCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CAGGTGTTCA\"}, {\"seq\":\"TGAACACCTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CAGGTGTTCA\"}],\n \"IDT_UDI-C_i5-UDP0234\":[{\"seq\":\"GACAGACAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GACAGACAGG\"}, {\"seq\":\"CCTGTCTGTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 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{\"seq\":\"TACGTGCGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TACGCACGTA\"}],\n \"IDT_UDI-C_i5-UDP0247\":[{\"seq\":\"CGCTTGAAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGCTTGAAGT\"}, {\"seq\":\"ACTTCAAGCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGCTTGAAGT\"}],\n \"IDT_UDI-C_i5-UDP0248\":[{\"seq\":\"CTGCACTTCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTGCACTTCA\"}, {\"seq\":\"TGAAGTGCAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGCACTTCA\"}],\n \"IDT_UDI-C_i5-UDP0249\":[{\"seq\":\"CAGCGGACAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 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2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATGAATCAAG\"}, {\"seq\":\"CTTGATTCAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATGAATCAAG\"}],\n \"IDT_UDI-C_i5-UDP0252\":[{\"seq\":\"ACATAACGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACATAACGGA\"}, {\"seq\":\"TCCGTTATGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACATAACGGA\"}],\n \"IDT_UDI-C_i5-UDP0253\":[{\"seq\":\"GACGTTCGCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GACGTTCGCG\"}, {\"seq\":\"CGCGAACGTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GACGTTCGCG\"}],\n \"IDT_UDI-C_i5-UDP0254\":[{\"seq\":\"CATTCAACAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CATTCAACAA\"}, {\"seq\":\"TTGTTGAATG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CATTCAACAA\"}],\n \"IDT_UDI-C_i5-UDP0255\":[{\"seq\":\"CACGGATTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CACGGATTAT\"}, {\"seq\":\"ATAATCCGTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CACGGATTAT\"}],\n \"IDT_UDI-C_i5-UDP0256\":[{\"seq\":\"TTGAGGACGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTGAGGACGG\"}, {\"seq\":\"CCGTCCTCAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGAGGACGG\"}],\n \"IDT_UDI-C_i5-UDP0257\":[{\"seq\":\"CTCTGTATAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCTGTATAC\"}, {\"seq\":\"GTATACAGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCTGTATAC\"}],\n \"IDT_UDI-C_i5-UDP0258V2\":[{\"seq\":\"TCTCGCGGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTCGCGGAG\"}, {\"seq\":\"CTCCGCGAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTCGCGGAG\"}],\n \"IDT_UDI-C_i5-UDP0258\":[{\"seq\":\"GCAACAGGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCAACAGGTG\"}, {\"seq\":\"CACCTGTTGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCAACAGGTG\"}],\n \"IDT_UDI-C_i5-UDP0259\":[{\"seq\":\"GGTAACGCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGTAACGCAG\"}, {\"seq\":\"CTGCGTTACC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGTAACGCAG\"}],\n \"IDT_UDI-C_i5-UDP0260\":[{\"seq\":\"ACCGCGCAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACCGCGCAAT\"}, {\"seq\":\"ATTGCGCGGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACCGCGCAAT\"}],\n \"IDT_UDI-C_i5-UDP0261\":[{\"seq\":\"AGCCGGAACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGCCGGAACA\"}, {\"seq\":\"TGTTCCGGCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGCCGGAACA\"}],\n \"IDT_UDI-C_i5-UDP0262\":[{\"seq\":\"TCCTAGGAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCCTAGGAAG\"}, {\"seq\":\"CTTCCTAGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCTAGGAAG\"}],\n \"IDT_UDI-C_i5-UDP0263\":[{\"seq\":\"TTGAGCCTAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTGAGCCTAA\"}, {\"seq\":\"TTAGGCTCAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGAGCCTAA\"}],\n \"IDT_UDI-C_i5-UDP0264\":[{\"seq\":\"CCACCTGTGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCACCTGTGT\"}, {\"seq\":\"ACACAGGTGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCACCTGTGT\"}],\n \"IDT_UDI-C_i5-UDP0265\":[{\"seq\":\"CCTCGCAACC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTCGCAACC\"}, {\"seq\":\"GGTTGCGAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTCGCAACC\"}],\n \"IDT_UDI-C_i5-UDP0266\":[{\"seq\":\"GTATAGCTGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTATAGCTGT\"}, {\"seq\":\"ACAGCTATAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTATAGCTGT\"}],\n \"IDT_UDI-C_i5-UDP0267\":[{\"seq\":\"GCTACATTAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCTACATTAG\"}, {\"seq\":\"CTAATGTAGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCTACATTAG\"}],\n \"IDT_UDI-C_i5-UDP0268\":[{\"seq\":\"TACGAATCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TACGAATCTT\"}, {\"seq\":\"AAGATTCGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TACGAATCTT\"}],\n \"IDT_UDI-C_i5-UDP0269\":[{\"seq\":\"TAGGAGCGCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAGGAGCGCA\"}, {\"seq\":\"TGCGCTCCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGGAGCGCA\"}],\n \"IDT_UDI-C_i5-UDP0270\":[{\"seq\":\"GTACTGGCGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTACTGGCGT\"}, {\"seq\":\"ACGCCAGTAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTACTGGCGT\"}],\n \"IDT_UDI-C_i5-UDP0271\":[{\"seq\":\"AGTTAAGAGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGTTAAGAGC\"}, {\"seq\":\"GCTCTTAACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGTTAAGAGC\"}],\n \"IDT_UDI-C_i5-UDP0272\":[{\"seq\":\"TCGCGTATAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCGCGTATAA\"}, {\"seq\":\"TTATACGCGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCGCGTATAA\"}],\n \"IDT_UDI-C_i5-UDP0273\":[{\"seq\":\"GAGTGTGCCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAGTGTGCCG\"}, {\"seq\":\"CGGCACACTC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAGTGTGCCG\"}],\n \"IDT_UDI-C_i5-UDP0274\":[{\"seq\":\"CTAGTCCGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTAGTCCGGA\"}, {\"seq\":\"TCCGGACTAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTAGTCCGGA\"}],\n \"IDT_UDI-C_i5-UDP0275\":[{\"seq\":\"ATTAATACGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATTAATACGC\"}, {\"seq\":\"GCGTATTAAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATTAATACGC\"}],\n \"IDT_UDI-C_i5-UDP0276\":[{\"seq\":\"CCTAGAGTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTAGAGTAT\"}, {\"seq\":\"ATACTCTAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTAGAGTAT\"}],\n \"IDT_UDI-C_i5-UDP0277\":[{\"seq\":\"TAGGAAGACT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAGGAAGACT\"}, {\"seq\":\"AGTCTTCCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGGAAGACT\"}],\n \"IDT_UDI-C_i5-UDP0278\":[{\"seq\":\"CCGTGGCCTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCGTGGCCTT\"}, {\"seq\":\"AAGGCCACGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCGTGGCCTT\"}],\n \"IDT_UDI-C_i5-UDP0279\":[{\"seq\":\"GGATATATCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGATATATCC\"}, {\"seq\":\"GGATATATCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGATATATCC\"}],\n \"IDT_UDI-C_i5-UDP0280\":[{\"seq\":\"CACCTCTTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CACCTCTTGG\"}, {\"seq\":\"CCAAGAGGTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CACCTCTTGG\"}],\n \"IDT_UDI-C_i5-UDP0281\":[{\"seq\":\"AACGTTACAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACGTTACAT\"}, {\"seq\":\"ATGTAACGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACGTTACAT\"}],\n \"IDT_UDI-C_i5-UDP0282\":[{\"seq\":\"CGGCAAGCTC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGCAAGCTC\"}, {\"seq\":\"GAGCTTGCCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGCAAGCTC\"}],\n \"IDT_UDI-C_i5-UDP0283\":[{\"seq\":\"TCTTGGCTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTTGGCTAT\"}, {\"seq\":\"ATAGCCAAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTTGGCTAT\"}],\n \"IDT_UDI-C_i5-UDP0284\":[{\"seq\":\"ACGGAATGCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACGGAATGCG\"}, {\"seq\":\"CGCATTCCGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACGGAATGCG\"}],\n \"IDT_UDI-C_i5-UDP0285\":[{\"seq\":\"GTTCCGCAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTTCCGCAGG\"}, {\"seq\":\"CCTGCGGAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTTCCGCAGG\"}],\n \"IDT_UDI-C_i5-UDP0286\":[{\"seq\":\"ACCAAGTTAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACCAAGTTAC\"}, {\"seq\":\"GTAACTTGGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACCAAGTTAC\"}],\n \"IDT_UDI-C_i5-UDP0287\":[{\"seq\":\"TGGCTCGCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGCTCGCAG\"}, {\"seq\":\"CTGCGAGCCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGCTCGCAG\"}],\n \"IDT_UDI-C_i5-UDP0288\":[{\"seq\":\"AACTAACGTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACTAACGTT\"}, {\"seq\":\"AACGTTAGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACTAACGTT\"}],\n }\n },\n \"IDT for Illumina UD Indexes Plate D\":{\n \"_short_name\":\"IDT_for_Illumina_UDI-D\",\n \"i7\":{\n \"IDT_UDI-D_i7-UDP0289V2\":[{\"seq\":\"AGATAGTAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTACTATCT\"}],\n \"IDT_UDI-D_i7-UDP0289\":[{\"seq\":\"GAACAATTCC\",\"instruments\":[],\"seq_in_adapter\":\"GGAATTGTTC\"}],\n \"IDT_UDI-D_i7-UDP0290V2\":[{\"seq\":\"ATTAGAAGAC\",\"instruments\":[],\"seq_in_adapter\":\"GTCTTCTAAT\"}],\n \"IDT_UDI-D_i7-UDP0290\":[{\"seq\":\"TGTGGTCCGG\",\"instruments\":[],\"seq_in_adapter\":\"CCGGACCACA\"}],\n \"IDT_UDI-D_i7-UDP0291V2\":[{\"seq\":\"GCTCGCACAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGTGCGAGC\"}],\n \"IDT_UDI-D_i7-UDP0291\":[{\"seq\":\"CTTCTAAGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACTTAGAAG\"}],\n \"IDT_UDI-D_i7-UDP0292\":[{\"seq\":\"AATATTGCCA\",\"instruments\":[],\"seq_in_adapter\":\"TGGCAATATT\"}],\n \"IDT_UDI-D_i7-UDP0293\":[{\"seq\":\"TCGTGCATTC\",\"instruments\":[],\"seq_in_adapter\":\"GAATGCACGA\"}],\n \"IDT_UDI-D_i7-UDP0294\":[{\"seq\":\"AAGATACACG\",\"instruments\":[],\"seq_in_adapter\":\"CGTGTATCTT\"}],\n \"IDT_UDI-D_i7-UDP0295\":[{\"seq\":\"TGCAATGAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTCATTGCA\"}],\n \"IDT_UDI-D_i7-UDP0296\":[{\"seq\":\"CTATGAAGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCTTCATAG\"}],\n \"IDT_UDI-D_i7-UDP0297\":[{\"seq\":\"GAAGACTAGA\",\"instruments\":[],\"seq_in_adapter\":\"TCTAGTCTTC\"}],\n \"IDT_UDI-D_i7-UDP0298\":[{\"seq\":\"AGGAGTCGAG\",\"instruments\":[],\"seq_in_adapter\":\"CTCGACTCCT\"}],\n \"IDT_UDI-D_i7-UDP0299\":[{\"seq\":\"TTCACTCACT\",\"instruments\":[],\"seq_in_adapter\":\"AGTGAGTGAA\"}],\n \"IDT_UDI-D_i7-UDP0300\":[{\"seq\":\"GGTCCGCTTC\",\"instruments\":[],\"seq_in_adapter\":\"GAAGCGGACC\"}],\n \"IDT_UDI-D_i7-UDP0301V2\":[{\"seq\":\"TAGTGGCTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAAGCCACTA\"}],\n \"IDT_UDI-D_i7-UDP0301\":[{\"seq\":\"CAACGAGAGC\",\"instruments\":[],\"seq_in_adapter\":\"GCTCTCGTTG\"}],\n \"IDT_UDI-D_i7-UDP0302\":[{\"seq\":\"ATTGAGGTCC\",\"instruments\":[],\"seq_in_adapter\":\"GGACCTCAAT\"}],\n \"IDT_UDI-D_i7-UDP0303\":[{\"seq\":\"GGAGAGACTC\",\"instruments\":[],\"seq_in_adapter\":\"GAGTCTCTCC\"}],\n \"IDT_UDI-D_i7-UDP0304\":[{\"seq\":\"CCGCTCCGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACGGAGCGG\"}],\n \"IDT_UDI-D_i7-UDP0305\":[{\"seq\":\"ATACATCACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTGATGTAT\"}],\n \"IDT_UDI-D_i7-UDP0306\":[{\"seq\":\"TAGGTATGTT\",\"instruments\":[],\"seq_in_adapter\":\"AACATACCTA\"}],\n \"IDT_UDI-D_i7-UDP0307\":[{\"seq\":\"CACCTAGCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGCTAGGTG\"}],\n \"IDT_UDI-D_i7-UDP0308\":[{\"seq\":\"TTCAAGTATG\",\"instruments\":[],\"seq_in_adapter\":\"CATACTTGAA\"}],\n \"IDT_UDI-D_i7-UDP0309\":[{\"seq\":\"TTAAGACAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTGTCTTAA\"}],\n \"IDT_UDI-D_i7-UDP0310\":[{\"seq\":\"CACCTCTCTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGAGAGGTG\"}],\n \"IDT_UDI-D_i7-UDP0311\":[{\"seq\":\"TTCTCGTGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCACGAGAA\"}],\n \"IDT_UDI-D_i7-UDP0312\":[{\"seq\":\"GCTAGGAAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTTCCTAGC\"}],\n \"IDT_UDI-D_i7-UDP0313\":[{\"seq\":\"TTAATAGCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGCTATTAA\"}],\n \"IDT_UDI-D_i7-UDP0314\":[{\"seq\":\"CATTCACGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCGTGAATG\"}],\n \"IDT_UDI-D_i7-UDP0315\":[{\"seq\":\"GGCACTAAGG\",\"instruments\":[],\"seq_in_adapter\":\"CCTTAGTGCC\"}],\n \"IDT_UDI-D_i7-UDP0316\":[{\"seq\":\"ATTCGGTACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTACCGAAT\"}],\n \"IDT_UDI-D_i7-UDP0317\":[{\"seq\":\"ACTAATCTCC\",\"instruments\":[],\"seq_in_adapter\":\"GGAGATTAGT\"}],\n \"IDT_UDI-D_i7-UDP0318\":[{\"seq\":\"TGTGTTAGTA\",\"instruments\":[],\"seq_in_adapter\":\"TACTAACACA\"}],\n \"IDT_UDI-D_i7-UDP0319\":[{\"seq\":\"CAACGACCTA\",\"instruments\":[],\"seq_in_adapter\":\"TAGGTCGTTG\"}],\n \"IDT_UDI-D_i7-UDP0320\":[{\"seq\":\"CGGTCGGCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGCCGACCG\"}],\n \"IDT_UDI-D_i7-UDP0321\":[{\"seq\":\"TCGACGCTAG\",\"instruments\":[],\"seq_in_adapter\":\"CTAGCGTCGA\"}],\n \"IDT_UDI-D_i7-UDP0322\":[{\"seq\":\"CTCGTAGGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCCTACGAG\"}],\n \"IDT_UDI-D_i7-UDP0323\":[{\"seq\":\"AAGTTCTAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTAGAACTT\"}],\n \"IDT_UDI-D_i7-UDP0324\":[{\"seq\":\"CCAAGAGGTG\",\"instruments\":[],\"seq_in_adapter\":\"CACCTCTTGG\"}],\n \"IDT_UDI-D_i7-UDP0325\":[{\"seq\":\"ATATCTGCTT\",\"instruments\":[],\"seq_in_adapter\":\"AAGCAGATAT\"}],\n \"IDT_UDI-D_i7-UDP0326\":[{\"seq\":\"TGGATCTGGC\",\"instruments\":[],\"seq_in_adapter\":\"GCCAGATCCA\"}],\n \"IDT_UDI-D_i7-UDP0327\":[{\"seq\":\"TTGAATCCAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGGATTCAA\"}],\n \"IDT_UDI-D_i7-UDP0328\":[{\"seq\":\"CACGGCTAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTAGCCGTG\"}],\n \"IDT_UDI-D_i7-UDP0329\":[{\"seq\":\"GAGCTTGCCG\",\"instruments\":[],\"seq_in_adapter\":\"CGGCAAGCTC\"}],\n \"IDT_UDI-D_i7-UDP0330\":[{\"seq\":\"AGCTAGCTTC\",\"instruments\":[],\"seq_in_adapter\":\"GAAGCTAGCT\"}],\n \"IDT_UDI-D_i7-UDP0331\":[{\"seq\":\"CAATCCTTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACAAGGATTG\"}],\n \"IDT_UDI-D_i7-UDP0332\":[{\"seq\":\"CACCTGTTGC\",\"instruments\":[],\"seq_in_adapter\":\"GCAACAGGTG\"}],\n \"IDT_UDI-D_i7-UDP0333\":[{\"seq\":\"CGTCACCTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAAGGTGACG\"}],\n \"IDT_UDI-D_i7-UDP0334\":[{\"seq\":\"AATGACTGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCAGTCATT\"}],\n \"IDT_UDI-D_i7-UDP0335\":[{\"seq\":\"ATGATTCCGG\",\"instruments\":[],\"seq_in_adapter\":\"CCGGAATCAT\"}],\n \"IDT_UDI-D_i7-UDP0336\":[{\"seq\":\"TTAGGCTCAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGAGCCTAA\"}],\n \"IDT_UDI-D_i7-UDP0337\":[{\"seq\":\"TGTAAGGTGG\",\"instruments\":[],\"seq_in_adapter\":\"CCACCTTACA\"}],\n \"IDT_UDI-D_i7-UDP0338\":[{\"seq\":\"CAACTGCAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTGCAGTTG\"}],\n \"IDT_UDI-D_i7-UDP0339\":[{\"seq\":\"ACATGAGTGA\",\"instruments\":[],\"seq_in_adapter\":\"TCACTCATGT\"}],\n \"IDT_UDI-D_i7-UDP0340\":[{\"seq\":\"GCAACCAGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACTGGTTGC\"}],\n \"IDT_UDI-D_i7-UDP0341\":[{\"seq\":\"GAGCGACGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCGTCGCTC\"}],\n \"IDT_UDI-D_i7-UDP0342\":[{\"seq\":\"CGAACGCACC\",\"instruments\":[],\"seq_in_adapter\":\"GGTGCGTTCG\"}],\n \"IDT_UDI-D_i7-UDP0343\":[{\"seq\":\"TCTTACGCCG\",\"instruments\":[],\"seq_in_adapter\":\"CGGCGTAAGA\"}],\n \"IDT_UDI-D_i7-UDP0344\":[{\"seq\":\"AGCTGATGTC\",\"instruments\":[],\"seq_in_adapter\":\"GACATCAGCT\"}],\n \"IDT_UDI-D_i7-UDP0345\":[{\"seq\":\"CTGAATTAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTAATTCAG\"}],\n \"IDT_UDI-D_i7-UDP0346\":[{\"seq\":\"TAAGGAGGAA\",\"instruments\":[],\"seq_in_adapter\":\"TTCCTCCTTA\"}],\n \"IDT_UDI-D_i7-UDP0347\":[{\"seq\":\"AGCTTACACA\",\"instruments\":[],\"seq_in_adapter\":\"TGTGTAAGCT\"}],\n \"IDT_UDI-D_i7-UDP0348\":[{\"seq\":\"AACCAGCCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGGCTGGTT\"}],\n \"IDT_UDI-D_i7-UDP0349\":[{\"seq\":\"CTTAAGTCGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGACTTAAG\"}],\n \"IDT_UDI-D_i7-UDP0350\":[{\"seq\":\"GCCTAACGTG\",\"instruments\":[],\"seq_in_adapter\":\"CACGTTAGGC\"}],\n \"IDT_UDI-D_i7-UDP0351\":[{\"seq\":\"ACTTACTTCA\",\"instruments\":[],\"seq_in_adapter\":\"TGAAGTAAGT\"}],\n \"IDT_UDI-D_i7-UDP0352\":[{\"seq\":\"CGCATTCCGT\",\"instruments\":[],\"seq_in_adapter\":\"ACGGAATGCG\"}],\n \"IDT_UDI-D_i7-UDP0353\":[{\"seq\":\"GATATCACAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGTGATATC\"}],\n \"IDT_UDI-D_i7-UDP0354\":[{\"seq\":\"AGCGCTGTGT\",\"instruments\":[],\"seq_in_adapter\":\"ACACAGCGCT\"}],\n \"IDT_UDI-D_i7-UDP0355\":[{\"seq\":\"TCACCGCGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCGCGGTGA\"}],\n \"IDT_UDI-D_i7-UDP0356\":[{\"seq\":\"GATAGCCTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAAGGCTATC\"}],\n \"IDT_UDI-D_i7-UDP0357\":[{\"seq\":\"CCTGGACGCA\",\"instruments\":[],\"seq_in_adapter\":\"TGCGTCCAGG\"}],\n \"IDT_UDI-D_i7-UDP0358\":[{\"seq\":\"TTACGCACCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGTGCGTAA\"}],\n \"IDT_UDI-D_i7-UDP0359\":[{\"seq\":\"TCGTTGCTGC\",\"instruments\":[],\"seq_in_adapter\":\"GCAGCAACGA\"}],\n \"IDT_UDI-D_i7-UDP0360\":[{\"seq\":\"CGACAAGGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCCTTGTCG\"}],\n \"IDT_UDI-D_i7-UDP0361\":[{\"seq\":\"GTGTACCTTC\",\"instruments\":[],\"seq_in_adapter\":\"GAAGGTACAC\"}],\n \"IDT_UDI-D_i7-UDP0362\":[{\"seq\":\"ACCTGGCCAA\",\"instruments\":[],\"seq_in_adapter\":\"TTGGCCAGGT\"}],\n \"IDT_UDI-D_i7-UDP0363\":[{\"seq\":\"TGTCTGGCCT\",\"instruments\":[],\"seq_in_adapter\":\"AGGCCAGACA\"}],\n \"IDT_UDI-D_i7-UDP0364\":[{\"seq\":\"AGTTAATGCT\",\"instruments\":[],\"seq_in_adapter\":\"AGCATTAACT\"}],\n \"IDT_UDI-D_i7-UDP0365\":[{\"seq\":\"GGTGAGTAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTACTCACC\"}],\n \"IDT_UDI-D_i7-UDP0366\":[{\"seq\":\"TACTCTGCGC\",\"instruments\":[],\"seq_in_adapter\":\"GCGCAGAGTA\"}],\n \"IDT_UDI-D_i7-UDP0367\":[{\"seq\":\"AGGTATGGCG\",\"instruments\":[],\"seq_in_adapter\":\"CGCCATACCT\"}],\n \"IDT_UDI-D_i7-UDP0368\":[{\"seq\":\"TCCAGCCTGC\",\"instruments\":[],\"seq_in_adapter\":\"GCAGGCTGGA\"}],\n \"IDT_UDI-D_i7-UDP0369\":[{\"seq\":\"GCCATATAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTATATGGC\"}],\n \"IDT_UDI-D_i7-UDP0370\":[{\"seq\":\"AGTGCGAGTG\",\"instruments\":[],\"seq_in_adapter\":\"CACTCGCACT\"}],\n \"IDT_UDI-D_i7-UDP0371\":[{\"seq\":\"CTGAGCCGGT\",\"instruments\":[],\"seq_in_adapter\":\"ACCGGCTCAG\"}],\n \"IDT_UDI-D_i7-UDP0372\":[{\"seq\":\"AACGGTCTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAGACCGTT\"}],\n \"IDT_UDI-D_i7-UDP0373\":[{\"seq\":\"GTTGCGTTCA\",\"instruments\":[],\"seq_in_adapter\":\"TGAACGCAAC\"}],\n \"IDT_UDI-D_i7-UDP0374\":[{\"seq\":\"CTTCAACCAC\",\"instruments\":[],\"seq_in_adapter\":\"GTGGTTGAAG\"}],\n \"IDT_UDI-D_i7-UDP0375\":[{\"seq\":\"TCTATTCAGT\",\"instruments\":[],\"seq_in_adapter\":\"ACTGAATAGA\"}],\n \"IDT_UDI-D_i7-UDP0376\":[{\"seq\":\"CAAGACGTCC\",\"instruments\":[],\"seq_in_adapter\":\"GGACGTCTTG\"}],\n \"IDT_UDI-D_i7-UDP0377\":[{\"seq\":\"TGAGTACAAC\",\"instruments\":[],\"seq_in_adapter\":\"GTTGTACTCA\"}],\n \"IDT_UDI-D_i7-UDP0378\":[{\"seq\":\"CCGCGGTTCT\",\"instruments\":[],\"seq_in_adapter\":\"AGAACCGCGG\"}],\n \"IDT_UDI-D_i7-UDP0379\":[{\"seq\":\"ATTGATACTG\",\"instruments\":[],\"seq_in_adapter\":\"CAGTATCAAT\"}],\n \"IDT_UDI-D_i7-UDP0380\":[{\"seq\":\"GGATTATGGA\",\"instruments\":[],\"seq_in_adapter\":\"TCCATAATCC\"}],\n \"IDT_UDI-D_i7-UDP0381\":[{\"seq\":\"TGGTTCTCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGAGAACCA\"}],\n \"IDT_UDI-D_i7-UDP0382\":[{\"seq\":\"TCAACCACGA\",\"instruments\":[],\"seq_in_adapter\":\"TCGTGGTTGA\"}],\n \"IDT_UDI-D_i7-UDP0383\":[{\"seq\":\"TATGAACTTG\",\"instruments\":[],\"seq_in_adapter\":\"CAAGTTCATA\"}],\n \"IDT_UDI-D_i7-UDP0384\":[{\"seq\":\"AGTGGTTAAG\",\"instruments\":[],\"seq_in_adapter\":\"CTTAACCACT\"}],\n },\n \"i5\":{\n \"IDT_UDI-D_i5-UDP0289V2\":[{\"seq\":\"GGCACGCCAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCACGCCAT\"}, {\"seq\":\"ATGGCGTGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCACGCCAT\"}],\n \"IDT_UDI-D_i5-UDP0289\":[{\"seq\":\"TAGAGTTGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAGAGTTGGA\"}, {\"seq\":\"ATCTCAACCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGAGTTGGA\"}],\n \"IDT_UDI-D_i5-UDP0290V2\":[{\"seq\":\"GCAGGCTGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCAGGCTGGA\"}, {\"seq\":\"TCCAGCCTGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCAGGCTGGA\"}],\n \"IDT_UDI-D_i5-UDP0290\":[{\"seq\":\"AGAGCACTAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGAGCACTAG\"}, {\"seq\":\"TCTCGTGATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGAGCACTAG\"}],\n \"IDT_UDI-D_i5-UDP0291V2\":[{\"seq\":\"ATGGCTTAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATGGCTTAAT\"}, {\"seq\":\"ATTAAGCCAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATGGCTTAAT\"}],\n \"IDT_UDI-D_i5-UDP0291\":[{\"seq\":\"ACTCTACAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACTCTACAGG\"}, {\"seq\":\"TGAGATGTCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACTCTACAGG\"}],\n \"IDT_UDI-D_i5-UDP0292\":[{\"seq\":\"CGGTGACACC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGTGACACC\"}, {\"seq\":\"GGTGTCACCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGTGACACC\"}],\n \"IDT_UDI-D_i5-UDP0293\":[{\"seq\":\"GCGTTGGTAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCGTTGGTAT\"}, {\"seq\":\"ATACCAACGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCGTTGGTAT\"}],\n \"IDT_UDI-D_i5-UDP0294\":[{\"seq\":\"TGTGCTAACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGTGCTAACA\"}, {\"seq\":\"TGTTAGCACA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGTGCTAACA\"}],\n \"IDT_UDI-D_i5-UDP0295\":[{\"seq\":\"CCAGAAGTAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCAGAAGTAA\"}, {\"seq\":\"TTACTTCTGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCAGAAGTAA\"}],\n \"IDT_UDI-D_i5-UDP0296\":[{\"seq\":\"CTTATACCTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTTATACCTG\"}, {\"seq\":\"CAGGTATAAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTTATACCTG\"}],\n \"IDT_UDI-D_i5-UDP0297\":[{\"seq\":\"ACTAGAACTT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACTAGAACTT\"}, {\"seq\":\"AAGTTCTAGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACTAGAACTT\"}],\n \"IDT_UDI-D_i5-UDP0298\":[{\"seq\":\"TTAGGCTTAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTAGGCTTAC\"}, {\"seq\":\"GTAAGCCTAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTAGGCTTAC\"}],\n \"IDT_UDI-D_i5-UDP0299\":[{\"seq\":\"TATCATGAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TATCATGAGA\"}, {\"seq\":\"TCTCATGATA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TATCATGAGA\"}],\n \"IDT_UDI-D_i5-UDP0300\":[{\"seq\":\"CTCACACAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCACACAAG\"}, {\"seq\":\"CTTGTGTGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCACACAAG\"}],\n \"IDT_UDI-D_i5-UDP0301V2\":[{\"seq\":\"AGTTACTTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGTTACTTGG\"}, {\"seq\":\"CCAAGTAACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGTTACTTGG\"}],\n \"IDT_UDI-D_i5-UDP0301\":[{\"seq\":\"GAATTGAGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GAATTGAGTG\"}, {\"seq\":\"CTTAACTCAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GAATTGAGTG\"}],\n \"IDT_UDI-D_i5-UDP0302\":[{\"seq\":\"CGGATTATAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGGATTATAT\"}, {\"seq\":\"ATATAATCCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGGATTATAT\"}],\n \"IDT_UDI-D_i5-UDP0303\":[{\"seq\":\"TTGAAGCAGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTGAAGCAGA\"}, {\"seq\":\"TCTGCTTCAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTGAAGCAGA\"}],\n \"IDT_UDI-D_i5-UDP0304\":[{\"seq\":\"TACGGCGAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TACGGCGAAG\"}, {\"seq\":\"CTTCGCCGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TACGGCGAAG\"}],\n \"IDT_UDI-D_i5-UDP0305\":[{\"seq\":\"TCTCCATTGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTCCATTGA\"}, {\"seq\":\"TCAATGGAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTCCATTGA\"}],\n \"IDT_UDI-D_i5-UDP0306\":[{\"seq\":\"CGAGACCAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CGAGACCAAG\"}, {\"seq\":\"CTTGGTCTCG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CGAGACCAAG\"}],\n \"IDT_UDI-D_i5-UDP0307\":[{\"seq\":\"TGCTGGACAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGCTGGACAT\"}, {\"seq\":\"ATGTCCAGCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGCTGGACAT\"}],\n \"IDT_UDI-D_i5-UDP0308\":[{\"seq\":\"GATGGTATCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GATGGTATCG\"}, {\"seq\":\"CGATACCATC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GATGGTATCG\"}],\n \"IDT_UDI-D_i5-UDP0309\":[{\"seq\":\"GGCTTAATTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGCTTAATTG\"}, {\"seq\":\"CAATTAAGCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGCTTAATTG\"}],\n \"IDT_UDI-D_i5-UDP0310\":[{\"seq\":\"CTCGACTCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCGACTCCT\"}, {\"seq\":\"AGGAGTCGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCGACTCCT\"}],\n \"IDT_UDI-D_i5-UDP0311\":[{\"seq\":\"ATACACAGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ATACACAGAG\"}, {\"seq\":\"CTCTGTGTAT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ATACACAGAG\"}],\n \"IDT_UDI-D_i5-UDP0312\":[{\"seq\":\"TCTCGGACGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTCGGACGA\"}, {\"seq\":\"TCGTCCGAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTCGGACGA\"}],\n \"IDT_UDI-D_i5-UDP0313\":[{\"seq\":\"ACCACGTCTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACCACGTCTG\"}, {\"seq\":\"CAGACGTGGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACCACGTCTG\"}],\n \"IDT_UDI-D_i5-UDP0314\":[{\"seq\":\"GTTGTACTCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTTGTACTCA\"}, {\"seq\":\"TGAGTACAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 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{\"seq\":\"TTATCTTACC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGTAAGATAA\"}],\n \"IDT_UDI-D_i5-UDP0324\":[{\"seq\":\"AACGAGCCAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACGAGCCAG\"}, {\"seq\":\"CTGGCTCGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACGAGCCAG\"}],\n \"IDT_UDI-D_i5-UDP0325\":[{\"seq\":\"TAGACAATCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TAGACAATCT\"}, {\"seq\":\"AGATTGTCTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TAGACAATCT\"}],\n \"IDT_UDI-D_i5-UDP0326\":[{\"seq\":\"CAATGCTGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 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\"IDT_UDI-D_i5-UDP0335\":[{\"seq\":\"CTCTGACGTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCTGACGTG\"}, {\"seq\":\"CACGTCAGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCTGACGTG\"}],\n \"IDT_UDI-D_i5-UDP0336\":[{\"seq\":\"TCGAATGGAA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCGAATGGAA\"}, {\"seq\":\"TTCCATTCGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCGAATGGAA\"}],\n \"IDT_UDI-D_i5-UDP0337\":[{\"seq\":\"AAGGCCTTGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AAGGCCTTGG\"}, {\"seq\":\"CCAAGGCCTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 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{\"seq\":\"ACAACTACTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CAGTAGTTGT\"}],\n \"IDT_UDI-D_i5-UDP0350\":[{\"seq\":\"AGCTCTCAAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGCTCTCAAG\"}, {\"seq\":\"CTTGAGAGCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGCTCTCAAG\"}],\n \"IDT_UDI-D_i5-UDP0351\":[{\"seq\":\"TCTGGAATTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTGGAATTA\"}, {\"seq\":\"TAATTCCAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTGGAATTA\"}],\n \"IDT_UDI-D_i5-UDP0352\":[{\"seq\":\"ATTAGTGGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 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\"IDT_UDI-D_i5-UDP0361\":[{\"seq\":\"CTGTGAGCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTGTGAGCTA\"}, {\"seq\":\"TAGCTCACAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTGTGAGCTA\"}],\n \"IDT_UDI-D_i5-UDP0362\":[{\"seq\":\"TCACAGATCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCACAGATCG\"}, {\"seq\":\"CGATCTGTGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCACAGATCG\"}],\n \"IDT_UDI-D_i5-UDP0363\":[{\"seq\":\"AGAAGCCAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGAAGCCAAT\"}, {\"seq\":\"ATTGGCTTCT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGAAGCCAAT\"}],\n \"IDT_UDI-D_i5-UDP0364\":[{\"seq\":\"ACTGCAGCCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACTGCAGCCG\"}, {\"seq\":\"CGGCTGCAGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACTGCAGCCG\"}],\n \"IDT_UDI-D_i5-UDP0365\":[{\"seq\":\"AACATCTAGT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AACATCTAGT\"}, {\"seq\":\"ACTAGATGTT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AACATCTAGT\"}],\n \"IDT_UDI-D_i5-UDP0366\":[{\"seq\":\"CCTTACTATG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTTACTATG\"}, {\"seq\":\"CATAGTAAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTTACTATG\"}],\n \"IDT_UDI-D_i5-UDP0367\":[{\"seq\":\"GTGGCGAGAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTGGCGAGAC\"}, {\"seq\":\"GTCTCGCCAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTGGCGAGAC\"}],\n \"IDT_UDI-D_i5-UDP0368\":[{\"seq\":\"GCCAGATCCA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GCCAGATCCA\"}, {\"seq\":\"TGGATCTGGC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GCCAGATCCA\"}],\n \"IDT_UDI-D_i5-UDP0369\":[{\"seq\":\"ACACAATATC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACACAATATC\"}, {\"seq\":\"GATATTGTGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACACAATATC\"}],\n \"IDT_UDI-D_i5-UDP0370\":[{\"seq\":\"TGGAGGTAAT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TGGAGGTAAT\"}, {\"seq\":\"ATTACCTCCA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TGGAGGTAAT\"}],\n \"IDT_UDI-D_i5-UDP0371\":[{\"seq\":\"CCTTCACGTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CCTTCACGTA\"}, {\"seq\":\"TACGTGAAGG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CCTTCACGTA\"}],\n \"IDT_UDI-D_i5-UDP0372\":[{\"seq\":\"CTATACGCGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTATACGCGG\"}, {\"seq\":\"CCGCGTATAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTATACGCGG\"}],\n \"IDT_UDI-D_i5-UDP0373\":[{\"seq\":\"GTTGCAGTTG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GTTGCAGTTG\"}, {\"seq\":\"CAACTGCAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GTTGCAGTTG\"}],\n \"IDT_UDI-D_i5-UDP0374\":[{\"seq\":\"TTATGCGCCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TTATGCGCCT\"}, {\"seq\":\"AGGCGCATAA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TTATGCGCCT\"}],\n \"IDT_UDI-D_i5-UDP0375\":[{\"seq\":\"TCTCAGTACA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCTCAGTACA\"}, {\"seq\":\"TGTACTGAGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCTCAGTACA\"}],\n \"IDT_UDI-D_i5-UDP0376\":[{\"seq\":\"AGTATACGGA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AGTATACGGA\"}, {\"seq\":\"TCCGTATACT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AGTATACGGA\"}],\n \"IDT_UDI-D_i5-UDP0377\":[{\"seq\":\"ACGCTTGGAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"ACGCTTGGAC\"}, {\"seq\":\"GTCCAAGCGT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"ACGCTTGGAC\"}],\n \"IDT_UDI-D_i5-UDP0378\":[{\"seq\":\"GGAGTAGATT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGAGTAGATT\"}, {\"seq\":\"AATCTACTCC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGAGTAGATT\"}],\n \"IDT_UDI-D_i5-UDP0379\":[{\"seq\":\"TACACGCTCC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TACACGCTCC\"}, {\"seq\":\"GGAGCGTGTA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TACACGCTCC\"}],\n \"IDT_UDI-D_i5-UDP0380\":[{\"seq\":\"TCCGATAGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"TCCGATAGAG\"}, {\"seq\":\"CTCTATCGGA\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"TCCGATAGAG\"}],\n \"IDT_UDI-D_i5-UDP0381\":[{\"seq\":\"CTCAAGGCCG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CTCAAGGCCG\"}, {\"seq\":\"CGGCCTTGAG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCAAGGCCG\"}],\n \"IDT_UDI-D_i5-UDP0382\":[{\"seq\":\"CAAGTTCATA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"CAAGTTCATA\"}, {\"seq\":\"TATGAACTTG\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"CAAGTTCATA\"}],\n \"IDT_UDI-D_i5-UDP0383\":[{\"seq\":\"AATCCTTAGG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"AATCCTTAGG\"}, {\"seq\":\"CCTAAGGATT\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"AATCCTTAGG\"}],\n \"IDT_UDI-D_i5-UDP0384\":[{\"seq\":\"GGTGGAATAC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NextSeq 2000\"],\"seq_in_adapter\":\"GGTGGAATAC\"}, {\"seq\":\"GTATTCCACC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq 500\",\"NextSeq 550\",\"HiSeq 3000\",\"HiSeq 4000\",\"NovaSeq\"],\"seq_in_adapter\":\"GGTGGAATAC\"}],\n }\n },\n \"Sabeti Lab Custom RNA-seq v5\":{\n \"_short_name\":\"sabeti-nextera\",\n \"i7\":{\n \"RPI1\":[{\"seq\":\"ATCACGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCGTGAT\"}],\n \"RPI2\":[{\"seq\":\"CGATGTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATACATCG\"}],\n \"RPI3\":[{\"seq\":\"TTAGGCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGCCTAA\"}],\n \"RPI4\":[{\"seq\":\"TGACCAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTGGTCA\"}],\n \"RPI5\":[{\"seq\":\"ACAGTGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCACTGT\"}],\n \"RPI6\":[{\"seq\":\"GCCAATAT\",\"instruments\":[],\"seq_in_adapter\":\"ATATTGGC\"}],\n \"RPI7\":[{\"seq\":\"CAGATCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGATCTG\"}],\n \"RPI8\":[{\"seq\":\"ACTTGAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTCAAGT\"}],\n \"RPI9\":[{\"seq\":\"GATCAGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCTGATC\"}],\n \"RPI10\":[{\"seq\":\"TAGCTTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAAGCTA\"}],\n \"RPI11\":[{\"seq\":\"GGCTACAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGTAGCC\"}],\n \"RPI12\":[{\"seq\":\"CTTGTAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTACAAG\"}],\n \"RPI13\":[{\"seq\":\"AGTCAAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTTGACT\"}],\n \"RPI14\":[{\"seq\":\"AGTTCCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGGAACT\"}],\n \"RPI15\":[{\"seq\":\"ATGTCAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTGACAT\"}],\n \"RPI16\":[{\"seq\":\"CCGTCCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGGACGG\"}],\n \"RPI17\":[{\"seq\":\"GTAGAGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCTCTAC\"}],\n \"RPI18\":[{\"seq\":\"GTCCGCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGCGGAC\"}],\n \"RPI19\":[{\"seq\":\"GTGAAAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTTTCAC\"}],\n \"RPI20\":[{\"seq\":\"GTGGCCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGGCCAC\"}],\n \"RPI21\":[{\"seq\":\"GTTTCGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCGAAAC\"}],\n \"RPI22\":[{\"seq\":\"CGTACGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCGTACG\"}],\n \"RPI23\":[{\"seq\":\"GAGTGGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCCACTC\"}],\n \"RPI24\":[{\"seq\":\"GGTAGCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGCTACC\"}],\n \"RPI25\":[{\"seq\":\"ACTGATAT\",\"instruments\":[],\"seq_in_adapter\":\"ATATCAGT\"}],\n \"RPI26\":[{\"seq\":\"ATGAGCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGCTCAT\"}],\n \"RPI27\":[{\"seq\":\"ATTCCTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAGGAAT\"}],\n \"RPI28\":[{\"seq\":\"CAAAAGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCTTTTG\"}],\n \"RPI29\":[{\"seq\":\"CAACTAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTAGTTG\"}],\n \"RPI30\":[{\"seq\":\"CACCGGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCCGGTG\"}],\n \"RPI31\":[{\"seq\":\"CACGATAT\",\"instruments\":[],\"seq_in_adapter\":\"ATATCGTG\"}],\n \"RPI32\":[{\"seq\":\"CACTCAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTGAGTG\"}],\n \"RPI33\":[{\"seq\":\"CAGGCGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCGCCTG\"}],\n \"RPI34\":[{\"seq\":\"CATGGCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGCCATG\"}],\n \"RPI35\":[{\"seq\":\"CATTTTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAAAATG\"}],\n \"RPI36\":[{\"seq\":\"CCAACAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTGTTGG\"}],\n \"RPI37\":[{\"seq\":\"CGGAATAT\",\"instruments\":[],\"seq_in_adapter\":\"ATATTCCG\"}],\n \"RPI38\":[{\"seq\":\"CTAGCTAT\",\"instruments\":[],\"seq_in_adapter\":\"ATAGCTAG\"}],\n \"RPI39\":[{\"seq\":\"CTATACAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGTATAG\"}],\n \"RPI40\":[{\"seq\":\"CTCAGAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTCTGAG\"}],\n \"RPI41\":[{\"seq\":\"GACGACAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGTCGTC\"}],\n \"RPI42\":[{\"seq\":\"TAATCGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCGATTA\"}],\n \"RPI43\":[{\"seq\":\"TACAGCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGCTGTA\"}],\n \"RPI44\":[{\"seq\":\"TATAATAT\",\"instruments\":[],\"seq_in_adapter\":\"ATATTATA\"}],\n \"RPI45\":[{\"seq\":\"TCATTCAT\",\"instruments\":[],\"seq_in_adapter\":\"ATGAATGA\"}],\n \"RPI46\":[{\"seq\":\"TCCCGAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTCGGGA\"}],\n \"RPI47\":[{\"seq\":\"TCGAAGAT\",\"instruments\":[],\"seq_in_adapter\":\"ATCTTCGA\"}],\n \"RPI48\":[{\"seq\":\"TCGGCAAT\",\"instruments\":[],\"seq_in_adapter\":\"ATTGCCGA\"}],\n },\n \"i5\":{\n \"RP1\":[{\"seq\":\"GTTCAGAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GTTCAGAG\"}, {\"seq\":\"CTCTGAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GTTCAGAG\"}],\n \"RP1-v4\":[{\"seq\":\"AAGTGCTA\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"AAGTGCTA\"}, {\"seq\":\"CTCTGAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"AAGTGCTA\"}],\n \"RP2-v4\":[{\"seq\":\"CTCGAAGC\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"CTCGAAGC\"}, {\"seq\":\"CTCTGAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"CTCGAAGC\"}],\n \"RP3-v4\":[{\"seq\":\"TCACTGCT\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"TCACTGCT\"}, {\"seq\":\"CTCTGAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"TCACTGCT\"}],\n \"RP4-v4\":[{\"seq\":\"GGTACTAG\",\"instruments\":[\"MiSeq\",\"HiSeq 2000\",\"HiSeq 2500\",\"NovaSeq\"],\"seq_in_adapter\":\"GGTACTAG\"}, {\"seq\":\"CTCTGAAC\",\"instruments\":[\"iSeq\",\"MiniSeq\",\"NextSeq\",\"HiSeq 3000\",\"HiSeq 4000\"],\"seq_in_adapter\":\"GGTACTAG\"}],\n }\n },\n }\n\n @classmethod\n @memoize\n def neighbors(cls, seq, distance=1):\n ''' Returns a list Hamming-distance of 1 from the input seq'''\n neighbor_list = []\n\n seq = seq.rstrip()\n for i in range(0, len(seq.rstrip())):\n for j in [\"A\", \"C\", \"G\", \"T\", \"N\"]:\n if j == seq[i].upper():\n continue # Do not include the seq itself\n q = seq[0:i] + j + seq[i+1:]\n neighbor_list.append(q)\n\n if distance==1:\n return sorted(neighbor_list)\n else:\n return sorted(list(set([item for sublist in (cls.neighbors(s, distance=distance-1) for s in neighbor_list) for item in sublist if item!=seq])))\n\n @staticmethod\n def reverse_complement(seq):\n \"\"\"\n Returns the reverse complement using string.maketrans\n \"\"\"\n table = bytearray.maketrans(b\"ACTGN\",b\"TGACN\")\n return bytearray(seq.encode(\"UTF8\")).translate(table)[::-1].decode(\"UTF8\")\n\n @property\n @memoize\n def _barcodes_meta_all(self):\n barcodes = []\n for kit_name,kit_value in self._kits.items():\n for item_key,item_value in kit_value.items():\n\n if type(item_value) == dict:\n for index_name,index_value in item_value.items():\n for barcode_meta in index_value:\n barcodes.append(barcode_meta)\n return barcodes\n\n @classmethod\n @memoize\n def kits(cls):\n return sorted(list(cls._kits.keys()))\n\n @property\n def instruments(self):\n instruments = set()\n for barcode_meta in self._barcodes_meta_all:\n ins_for_barcode = barcode_meta.get(\"instruments\",\"\")\n if len(ins_for_barcode):\n \n instruments |= set(ins_for_barcode)\n return sorted(list(instruments))\n\n @memoize\n def index_for_seq(self, seq, kit=None, instrument=None):\n # use kit/instrument passed in if present\n # value forinstrument, if present, if neither return list of options\n possible_indices = set()\n for kit_name,kit_value in self._kits.items():\n if not kit or (kit_name == kit) or (kit_value[\"_short_name\"]==kit):\n for item_key,item_value in kit_value.items():\n if type(item_value) == dict:\n for index_name,index_value in item_value.items():\n for barcode_meta in index_value:\n if barcode_meta[\"seq\"] == seq:\n if not instrument or instrument in barcode_meta[\"instruments\"]:\n possible_indices |= set([index_name])\n return sorted(list(possible_indices))\n\n @memoize\n def seq_for_index(self, index, kit=None, instrument=None):\n # use kit/instrument passed in if present\n # value forinstrument, if present, if neither return list of options\n possible_seqs = set()\n for kit_name,kit_value in self._kits.items():\n if not kit or (kit_name == kit) or (kit_value[\"_short_name\"]==kit):\n for item_key,item_value in kit_value.items():\n if type(item_value) == dict:\n for index_name,index_value in item_value.items():\n matches = re.match(\"(?P\"+index_name+\")\", index)\n if matches:\n for barcode_meta in index_value:\n if not instrument or instrument in barcode_meta[\"instruments\"]:\n possible_seqs |= set([barcode_meta[\"seq\"]])\n return sorted(list(possible_seqs))\n\n @memoize\n def guess_index(self, seq, distance=1, kit=None, instrument=None):\n # using neighbors()...\n # use kit/instrument if present\n possible_indices = set()\n # first include exact matches\n exact_matches = self.index_for_seq(seq, kit=kit, instrument=instrument)\n if len(exact_matches):\n possible_indices |= set(exact_matches)\n else:\n # then include barcodes _distance_ away\n for neighbor_seq in self.neighbors(seq, distance=distance):\n possible_indices |= set(self.index_for_seq(neighbor_seq, kit=kit, instrument=instrument))\n return sorted(list(possible_indices))\n\nclass UncertainSamplesheetError(Exception):\n pass\n\nclass IlluminaBarcodeHelper(object):\n index_reference = IlluminaIndexReference()\n def __init__(self, barcode_counts, picard_metrics, sample_name, rows_limit=1000):\n # (barcode1,barcode2): count\n self.barcodes_seen = OrderedDict()\n # barcode: illumina index name (N507, etc.)\n self.barcode_name_map = OrderedDict()\n # sample_name: (barcode1,barcode2)\n self.sample_to_barcodes = OrderedDict()\n # list of all sample names (barcode_name from Picard metrics file)\n self.samples = []\n # sample_name: count\n self.sample_to_read_counts = OrderedDict()\n # unresolved barcode pair count\n self.unassigned_read_count = 0\n\n # read Picard demux metrics file\n for row in util_file.read_tabfile_dict(picard_metrics, skip_prefix=\"#\"):\n barcodes = tuple(row[\"BARCODE\"].split(\"-\"))\n if \"BARCODE_NAME\" in row:\n self.sample_to_barcodes[row[\"BARCODE_NAME\"]] = barcodes\n self.samples.append(row[\"BARCODE_NAME\"])\n self.sample_to_read_counts[row[\"BARCODE_NAME\"]] = int(row[\"READS\"])\n elif all(re.match(r'^N+$',barcode) for barcode in barcodes):\n self.unassigned_read_count = int(row[\"READS\"])\n continue\n\n # read barcodes seen in the file, in the format:\n #Barcode1 Likely_Index_Names1 Barcode2 Likely_Index_Names2 Count\n #CTCTCTAC N707 AAGGAGTA S507,[N|S|E]507 40324834\n for row in util_file.read_tabfile_dict(barcode_counts, rowcount_limit=rows_limit):\n if (row[\"Barcode1\"],row.get(\"Barcode2\",None)) not in self.barcodes_seen:\n self.barcodes_seen[(row[\"Barcode1\"],row.get(\"Barcode2\",None))] = int(row[\"Count\"])\n self.barcode_name_map[row[\"Barcode1\"]] = row[\"Likely_Index_Names1\"]\n if \"Barcode2\" in row and row[\"Barcode2\"]:\n self.barcode_name_map[row[\"Barcode2\"]] = row[\"Likely_Index_Names2\"]\n\n def outlier_barcodes(self, outlier_threshold=0.775, expected_assigned_fraction=0.7, number_of_negative_controls=1):\n \"\"\"\n This identifies samples listed in the Picard metrics (derived from \n the sample sheet) that are believed to have an anomalously low \n number of reads after demultiplexing, based on the following assumptions:\n - The pool of samples will have (at least) one negative control that should yield zero reads\n - The total number of reads should be evenly distributed among the rest of the samples\n since the nucleic acid concentration should be roughly balanced in the pool\n - The variation among what should be evenly distributed is gaussian\n \n\n A warning is raised if <70% of the total reads are assigned (likely indicating\n multiple problems with the samplesheet).\n\n Loosely based on the method for outlier detection specified in\n Boris Iglewicz and David Hoaglin (1993), \n \"Volume 16: How to Detect and Handle Outliers\", \n The ASQC Basic References in Quality Control: Statistical Techniques\n\n Params:\n outlier_threshold (float): 0.675, corresponds to 75th percentile\n expected_assigned_fraction (float): fraction of reads assigned to samples\n number_of_negative_controls (int): the number of samples in the pool expected to have zero reads\n \"\"\"\n ##log.debug(f\"outlier_threshold {outlier_threshold}\")\n assigned_read_count = sum(self.sample_to_read_counts.values())\n total_read_count = assigned_read_count+self.unassigned_read_count\n fraction_assigned = float(assigned_read_count)/float(total_read_count)\n log.info(\"fraction_assigned %s\", fraction_assigned)\n if fraction_assigned < expected_assigned_fraction:\n raise UncertainSamplesheetError(\"Only {:.0%} of reads were assigned to barcode pairs listed in the samplesheet. Check the sample sheet for errors.\".format(fraction_assigned))\n\n num_samples = len(self.sample_to_read_counts)\n assert number_of_negative_controls0 \n else 0\n for x in \n list(self.sample_to_read_counts.values())\n ]\n ##log.debug(f\"log_obs_fractions_of_pool {log_obs_fractions_of_pool}\")\n log_exp_fractions_of_pool = [-math.log(1.0/float(num_samples-number_of_negative_controls),10)]*num_samples\n ##log.warning(f\"log_exp_fractions_of_pool {log_exp_fractions_of_pool}\")\n residuals = [obs-exp for (obs,exp) in zip(log_obs_fractions_of_pool,log_exp_fractions_of_pool)]\n resid_stdev = self.stddevp(residuals) #essentially RMSE\n resid_mean = self.mean(residuals) # mean error\n resid_median = self.median(residuals) # median error\n\n # set stdev to 1 if it is zero to cause no standardization below\n # (zero will cause div-by-zero error)\n # stdev is an edge case where read counts are all the same\n # across the board\n resid_stdev = resid_stdev if resid_stdev!=0 else 1.0\n\n ##log.debug(f\"residuals {residuals}\")\n ##log.debug(f\"resid_stdev {resid_stdev}\")\n ##log.debug(f\"resid_mean {resid_mean}\")\n ##log.debug(f\"resid_median {resid_median}\")\n\n # modifed zscore using median to reduce influence of outliers\n zscores_residual_relative_to_median = [float(1.0 * (x-resid_median))/resid_stdev for x in residuals]\n ##log.debug(f\"zscores_residual_relative_to_median {zscores_residual_relative_to_median}\")\n # only consider LOW variance\n indices_of_outliers = [i for i,v in enumerate(zscores_residual_relative_to_median) if v > outlier_threshold]\n indices_of_outliers += [i for i,v in enumerate(list(self.sample_to_read_counts.values())) if v==0]\n ##log.debug(\"self.sample_to_read_counts.keys() {}\".format(self.sample_to_read_counts.keys()))\n names_of_outlier_samples = [(list(self.sample_to_read_counts.keys()))[i] for i in indices_of_outliers]\n log.warning(\"outlier samples\")\n for s in names_of_outlier_samples:\n log.warning(\"\\t%s (%s reads)\", s,self.sample_to_read_counts[s])\n\n return names_of_outlier_samples\n\n @classmethod\n def mean(cls, nums):\n return sum(nums) / len(nums)\n\n @classmethod\n def stddevp(cls, nums):\n \"\"\"population standard deviation of nums\"\"\"\n mn = cls.mean(nums)\n variance = sum([(e-mn)**2 for e in nums]) / len(nums)\n return math.sqrt(variance)\n\n @classmethod\n def median(cls, nums):\n length = len(nums)\n if length < 1:\n return None\n if length % 2 == 1:\n # if this is a list with an odd number of elements, \n # return the middle element from a sorted version of the list\n return sorted(nums)[length//2]\n else:\n # otherwise if the list has an even number of elements\n # return the interpolated mean of the middle two numbers\n return sum(sorted(nums)[length//2-1:length//2+1])/2.0\n\n\n def guess_barcodes_for_sample(self, sample_name):\n \"\"\"\n This guesses the barcode value for a sample name,\n based on the following:\n - a list is made of novel barcode pairs seen in the data, but not in the picard metrics\n - for the sample in question, get the most abundant novel barcode pair where one of the \n barcodes seen in the data matches one of the barcodes in the picard metrics (partial match)\n - if there are no partial matches, get the most abundant novel barcode pair \n\n Limitations:\n - If multiple samples share a barcode with multiple novel barcodes, disentangling them\n is difficult or impossible\n \"\"\"\n # output_header = [\"sample_name\",\n # \"expected_barcode_1\",\"expected_barcode_1_name\",\n # \"expected_barcode_2\",\"expected_barcode_2_name\"\n # \"expected_barcodes_read_count\",\n # \"guessed_barcode_1\",\"guessed_barcode_1_name\",\n # \"guessed_barcode_2\",\"guessed_barcode_2_name\"\n # \"guessed_barcodes_read_count\",\n # \"match_type\"\n # ]\n\n out_dict = OrderedDict()\n out_dict[\"sample_name\"] = sample_name\n out_dict[\"match_type\"] = \"not_found\"\n \n barcodes_seen_novel = copy.deepcopy(self.barcodes_seen)\n\n # From barcodes seen in data, collect barcode pairs not expected based on sample sheet\n novel_barcode_pairs = []\n\n for barcode_pair in self.barcodes_seen.keys():\n barcode = tuple((b for b in barcode_pair if b is not None))\n if barcode not in self.sample_to_barcodes.values():\n novel_barcode_pairs.append(barcode_pair)\n else:\n del barcodes_seen_novel[barcode_pair]\n\n is_dual_index = len(self.sample_to_barcodes[sample_name]) > 1\n\n out_dict[\"expected_barcode_1\"] = self.sample_to_barcodes[sample_name][0]\n out_dict[\"expected_barcode_1_name\"] = \",\".join(self.index_reference.guess_index(self.sample_to_barcodes[sample_name][0]))\n if is_dual_index:\n out_dict[\"expected_barcode_2\"] = self.sample_to_barcodes[sample_name][1]\n out_dict[\"expected_barcode_2_name\"] = \",\".join(self.index_reference.guess_index(self.sample_to_barcodes[sample_name][1]))\n out_dict[\"expected_barcodes_read_count\"] = self.sample_to_read_counts[sample_name]\n\n claimed_barcodes = self.sample_to_barcodes[sample_name]\n\n found_partial_match = False\n putative_match = None\n\n if is_dual_index:\n # barcodes_seen_novel is sorted by read count, desc\n for (barcode_pair,count) in barcodes_seen_novel.items():\n if barcode_pair[0]==claimed_barcodes[0] or barcode_pair[1]==claimed_barcodes[1]:\n found_partial_match=True\n putative_match = barcode_pair\n out_dict[\"match_type\"] = \"one_barcode_match\"\n break\n else:\n # barcodes_seen_novel is sorted by read count, desc\n for (barcode_pair,count) in barcodes_seen_novel.items():\n # get barcode with greatest count that isn't the one we're looking for\n if barcode_pair[0]!=claimed_barcodes[0]:\n found_partial_match=True\n putative_match = barcode_pair\n out_dict[\"match_type\"] = \"one_barcode_match\"\n break\n\n # find index of match to help determine if it is a reasonable guess\n idx_of_match = -1\n for (idx,(barcode_pair,count)) in enumerate(self.barcodes_seen.items()):\n if barcode_pair==putative_match:\n idx_of_match=idx\n break\n\n # if the one-barcode match is too far down the list of barcode pairs seen\n # (farther down than 1.5x the number of samples)\n if not found_partial_match or idx_of_match>(len(self.sample_to_read_counts)*1.5):\n for (barcode_pair,count) in barcodes_seen_novel.items():\n # return the most pair with greatest count\n putative_match = barcode_pair\n out_dict[\"match_type\"] = \"high_count_novel_barcode\"\n break\n \n out_dict[\"guessed_barcode_1\"] = \"unknown\"\n out_dict[\"guessed_barcode_1_name\"] = \"unknown\"\n #out_dict[\"guessed_barcodes_read_count\"] = 0\n if is_dual_index and (putative_match is not None and putative_match[1] != None):\n out_dict[\"guessed_barcode_2\"] = \"unknown\"\n out_dict[\"guessed_barcode_2_name\"] = \"unknown\"\n\n if putative_match is not None and putative_match[0]!=None:\n out_dict[\"guessed_barcode_1\"] = putative_match[0]\n out_dict[\"guessed_barcode_1_name\"] = self.barcode_name_map[putative_match[0]]\n if is_dual_index and putative_match[1] != None:\n out_dict[\"guessed_barcode_2\"] = putative_match[1]\n out_dict[\"guessed_barcode_2_name\"] = self.barcode_name_map[putative_match[1]]\n out_dict[\"guessed_barcodes_read_count\"] = self.barcodes_seen[(putative_match[0],putative_match[1])]\n\n return out_dict\n\n\n def find_uncertain_barcodes(self, sample_names=None, outlier_threshold=0.675, expected_assigned_fraction=0.7, number_of_negative_controls=None, readcount_threshold=None, neg_control_prefixes=None):\n \"\"\"\n If sample_names is specified, barcodes for the named samples \n will be re-examined. \n\n If readcount_threshold is specified, this will be used as the\n cutoff above which sample barcodes will not be re-examined.\n If this is not specified, outliers will be detected automatically.\n \"\"\"\n samples_to_examine = sample_names or []\n neg_control_prefixes = neg_control_prefixes or [\"neg\", \"water\", \"NTC\", \"H2O\"]\n\n inferred_ntc_count = [s.upper().startswith(tuple([p.upper() for p in neg_control_prefixes])) for s in self.sample_to_read_counts.keys()].count(True)\n\n number_of_negative_controls = number_of_negative_controls or inferred_ntc_count\n\n guessed_barcodes = []\n\n if not samples_to_examine:\n if readcount_threshold:\n for sample_name,count in self.sample_to_read_counts.items():\n if count < readcount_threshold:\n samples_to_examine.append(sample_name)\n else:\n samples_to_examine = self.outlier_barcodes(outlier_threshold=outlier_threshold, expected_assigned_fraction=expected_assigned_fraction, number_of_negative_controls=number_of_negative_controls)\n\n for s in samples_to_examine:\n guessed_barcodes.append(self.guess_barcodes_for_sample(s))\n\n consolidated_guesses = defaultdict(list)\n\n for row in guessed_barcodes:\n consolidated_guesses[(row[\"guessed_barcode_1\"],row.get(\"guessed_barcode_2\",None))].append(row)\n\n final_guesses = []\n\n def clear_guessed_fields(sample,match_reason,fields_to_clear=None):\n fields_to_clear = fields_to_clear or [\"guessed_barcode_1\", \"guessed_barcode_2\",\n \"guessed_barcode_1_name\", \"guessed_barcode_2_name\",\n \"guessed_barcodes_read_count\"]\n for field in fields_to_clear:\n if field in sample:\n sample[field] = None\n sample[\"match_type\"] = match_reason\n return sample\n\n for barcode_pair,samples in consolidated_guesses.items():\n if len(samples) > 1:\n log.warning(\"Ambiguous! Multiple samples corresponding to guessed barcodes %s:\", barcode_pair)\n for sample in samples:\n log.warning(\"\\t%s expected (%s,%s); -> Guessed (%s,%s); match type: %s\", sample[\"sample_name\"], sample[\"expected_barcode_1\"],sample.get(\"expected_barcode_2\",\"\"),sample[\"guessed_barcode_1\"],sample.get(\"guessed_barcode_2\",\"\"),sample[\"match_type\"])\n\n final_guesses.append(clear_guessed_fields(sample, \"alternative_indices_uncertain\"))\n else:\n for sample in samples:\n if sample[\"guessed_barcodes_read_count\"] < sample[\"expected_barcodes_read_count\"]:\n final_guesses.append(clear_guessed_fields(sample, \"alternatives_have_lower_read_counts\"))\n else:\n final_guesses.append(sample)\n return final_guesses\n\n def write_guessed_barcodes(self, out_tsv, guessed_barcodes):\n possible_header_cols = [\"sample_name\",\n \"expected_barcode_1\",\"expected_barcode_2\",\n \"expected_barcode_1_name\",\"expected_barcode_2_name\",\n \"expected_barcodes_read_count\",\n \"guessed_barcode_1\", \"guessed_barcode_2\",\n \"guessed_barcode_1_name\", \"guessed_barcode_2_name\",\n \"guessed_barcodes_read_count\",\n \"match_type\"\n ]\n output_header_columns = []\n for header_key in possible_header_cols:\n for row in guessed_barcodes:\n if header_key in row.keys() and header_key not in output_header_columns:\n output_header_columns.append(header_key)\n\n with open(out_tsv, 'w') as tsvfile:\n csv.register_dialect('dict_tsv', quoting=csv.QUOTE_MINIMAL, delimiter=\"\\t\")\n writer = csv.DictWriter(tsvfile, fieldnames=output_header_columns, dialect=\"dict_tsv\")\n\n writer.writeheader()\n writer.writerows(guessed_barcodes)\n" }, { "path": "src/viral_ngs/core/illumina_utils.py", "content": "#!/usr/bin/env python3\n\"\"\"\nUtilities for Illumina data handling, including directory management,\nrun information parsing, and sample sheet processing.\n\"\"\"\n\nimport csv\nimport logging\nimport os\nimport re\nimport shutil\nimport tempfile\nimport xml.etree.ElementTree\n\nimport arrow\nimport pandas as pd\n\nfrom . import file as util_file\nfrom . import misc as util_misc\n\nlog = logging.getLogger(__name__)\n\n\n# ============================\n# *** IlluminaDirectory ***\n# ============================\n\n\nclass IlluminaDirectory(object):\n \"\"\"A class that handles Illumina data directories\"\"\"\n\n def __init__(self, uri):\n self.uri = uri\n self.path = None\n self.tempDir = None\n self.runinfo = None\n self.samplesheet = None\n\n def __enter__(self):\n self.load()\n return self\n\n def __exit__(self, exc_type, exc_val, exc_tb):\n self.close()\n return 0\n\n def load(self):\n if self.path is None:\n if \"://\" in self.uri:\n raise NotImplementedError(\"boto s3 download here uri -> tarball\")\n else:\n if os.path.isdir(self.uri):\n self.path = self.uri\n else:\n self._extract_tarball(self.uri)\n self._fix_path()\n\n def _fix_path(self):\n assert self.path is not None\n # this is not the correct root-level directory\n # sometimes this points to one level up\n while True:\n if os.path.isdir(\n os.path.join(self.path, \"Data\", \"Intensities\", \"BaseCalls\")\n ):\n # found it! self.path is correct\n break\n else:\n subdirs = list(\n os.path.join(self.path, x)\n for x in os.listdir(self.path)\n if os.path.isdir(os.path.join(self.path, x))\n )\n if len(subdirs) == 1:\n # follow the rabbit hole\n self.path = subdirs[0]\n else:\n # don't know where to go now!\n raise Exception(\n \"cannot find Data/Intensities/BaseCalls/ inside %s (%s)\"\n % (self.uri, self.path)\n )\n\n def _extract_tarball(self, tarfile):\n self.tempDir = tempfile.mkdtemp(prefix=\"IlluminaDirectory-\")\n self.path = self.tempDir\n util_file.extract_tarball(tarfile, self.tempDir)\n\n def close(self):\n if self.tempDir:\n shutil.rmtree(self.tempDir)\n self.tempDir = None\n\n def get_RunInfo(self):\n if self.runinfo is None:\n runinfo_file = os.path.join(self.path, \"RunInfo.xml\")\n util_file.check_paths(runinfo_file)\n self.runinfo = RunInfo(runinfo_file)\n return self.runinfo\n\n def get_SampleSheet(self, only_lane=None, append_run_id=None, **kwargs):\n if self.samplesheet is None:\n samplesheet_file = os.path.join(self.path, \"SampleSheet.csv\")\n util_file.check_paths(samplesheet_file)\n self.samplesheet = SampleSheet(\n samplesheet_file,\n only_lane=only_lane,\n append_run_id=append_run_id,\n **kwargs\n )\n return self.samplesheet\n\n def get_intensities_dir(self):\n return os.path.join(self.path, \"Data\", \"Intensities\")\n\n def get_BCLdir(self):\n return os.path.join(self.get_intensities_dir(), \"BaseCalls\")\n\n\n# ==================\n# *** RunInfo ***\n# ==================\n\n\nclass RunInfo(object):\n \"\"\"A class that reads the RunInfo.xml file emitted by Illumina\n MiSeq and HiSeq machines.\n \"\"\"\n\n def __init__(self, xml_fname):\n self.fname = xml_fname\n self.root = xml.etree.ElementTree.parse(xml_fname).getroot()\n\n def get_fname(self):\n return self.fname\n\n def get_run_id(self):\n return self.root[0].attrib[\"Id\"]\n\n def get_flowcell_raw(self):\n return self.root[0].find(\"Flowcell\").text\n\n def get_flowcell(self):\n fc = self.get_flowcell_raw()\n # slice in the case where the ID has a prefix of zeros\n if re.match(r\"^0+-\", fc):\n if \"-\" in fc:\n # miseq often adds a bunch of leading zeros and a dash in front\n fc = \"-\".join(fc.split(\"-\")[1:])\n # >=5 to avoid an exception here\n # <= 15 to limit the bytes added to each bam record\n assert len(fc) >= 5, \"The flowcell ID must be five or more characters in length\"\n if len(fc) > 15:\n log.warning(\n \"The provided flowcell ID is longer than 15 characters. Is that correct?\"\n )\n return fc\n\n def _get_rundate_obj(self):\n \"\"\"\n Access the text of the node in the RunInfo.xml file\n and returns an arrow date object.\n \"\"\"\n rundate = self.root[0].find(\"Date\").text\n datestring_formats = [\n \"YYMMDD\",\n \"YYYYMMDD\",\n \"M/D/YYYY h:mm:ss A\",\n \"YYYY-MM-DDTHH:mm:ssZ\",\n ]\n for datestring_format in datestring_formats:\n try:\n date_parsed = arrow.get(rundate, datestring_format)\n return date_parsed\n except arrow.parser.ParserError:\n pass\n raise arrow.parser.ParserError(\n \"The date string seen in RunInfo.xml ('%s') did not match known Illumina formats: %s\"\n % (rundate, datestring_formats)\n )\n\n def get_rundate_american(self):\n return str(self._get_rundate_obj().format(\"MM/DD/YYYY\"))\n\n def get_rundate_iso(self):\n return str(self._get_rundate_obj().format(\"YYYY-MM-DD\"))\n\n def get_machine(self):\n return self.root[0].find(\"Instrument\").text\n\n def get_read_structure(self):\n reads = []\n for x in self.root[0].find(\"Reads\").findall(\"Read\"):\n order = int(x.attrib[\"Number\"])\n read = x.attrib[\"NumCycles\"] + (\n x.attrib[\"IsIndexedRead\"] == \"Y\" and \"B\" or \"T\"\n )\n reads.append((order, read))\n return \"\".join([r for _, r in sorted(reads)])\n\n def num_reads(self):\n return sum(\n 1\n for x in self.root[0].find(\"Reads\").findall(\"Read\")\n if x.attrib[\"IsIndexedRead\"] == \"N\"\n )\n\n def get_lane_count(self):\n layout = self.root[0].find(\"FlowcellLayout\")\n return int(layout.attrib[\"LaneCount\"])\n\n def get_surface_count(self):\n layout = self.root[0].find(\"FlowcellLayout\")\n return int(layout.attrib[\"SurfaceCount\"])\n\n def get_swath_count(self):\n layout = self.root[0].find(\"FlowcellLayout\")\n return int(layout.attrib[\"SwathCount\"])\n\n def get_tile_count(self):\n layout = self.root[0].find(\"FlowcellLayout\")\n return int(layout.attrib[\"TileCount\"])\n\n def get_section_count(self):\n layout = self.root[0].find(\"FlowcellLayout\")\n return int(layout.attrib.get(\"SectionPerLane\", 1))\n\n def tile_count(self):\n lane_count = self.get_lane_count()\n surface_count = self.get_surface_count()\n swath_count = self.get_swath_count()\n tile_count = self.get_tile_count()\n section_count = self.get_section_count()\n\n total_tile_count = (\n lane_count * surface_count * swath_count * tile_count * section_count\n )\n return total_tile_count\n\n def machine_model_from_tile_count(self):\n \"\"\"Return machine name and lane count based on tile count\"\"\"\n tc = self.tile_count()\n\n machine = None\n if tc == 2:\n log.info(\"Detected %s tiles, interpreting as MiSeq nano run.\", tc)\n machine = {\"machine\": \"Illumina MiSeq\", \"lane_count\": 1}\n elif tc == 8:\n log.info(\"Detected %s tiles, interpreting as MiSeq micro run.\", tc)\n machine = {\"machine\": \"Illumina MiSeq\", \"lane_count\": 1}\n elif tc == 16:\n log.info(\"Detected %s tiles, interpreting as iSeq run.\", tc)\n machine = {\"machine\": \"Illumina iSeq 100\", \"lane_count\": 1}\n elif tc == 28:\n log.info(\"Detected %s tiles, interpreting as MiSeq run.\", tc)\n machine = {\"machine\": \"Illumina MiSeq\", \"lane_count\": 1}\n elif tc == 38:\n log.info(\"Detected %s tiles, interpreting as MiSeq run.\", tc)\n machine = {\"machine\": \"Illumina MiSeq\", \"lane_count\": 1}\n elif tc == 32:\n log.info(\"Detected %s tiles, interpreting as NextSeq 1000/2000 P1 run.\", tc)\n machine = {\"machine\": \"NextSeq 1000/2000\", \"lane_count\": 1}\n elif tc == 128:\n log.info(\"Detected %s tiles, interpreting as HiSeq2k run.\", tc)\n machine = {\"machine\": \"Illumina HiSeq 2500\", \"lane_count\": 2}\n elif tc == 132:\n log.info(\"Detected %s tiles, interpreting as NextSeq 1000/2000 P2 run.\", tc)\n machine = {\"machine\": \"NextSeq 1000/2000\", \"lane_count\": 1}\n elif tc == 264:\n log.info(\"Detected %s tiles, interpreting as NextSeq 2000 P3 run.\", tc)\n machine = {\"machine\": \"NextSeq 2000\", \"lane_count\": 2}\n elif tc == 288:\n log.info(\"Detected %s tiles, interpreting as NextSeq 550 (mid-output) run.\", tc)\n machine = {\"machine\": \"NextSeq 550\", \"lane_count\": 4}\n elif tc == 624:\n log.info(\"Detected %s tiles, interpreting as Illumina NovaSeq 6000 run.\", tc)\n machine = {\"machine\": \"Illumina NovaSeq 6000\", \"lane_count\": 2}\n elif tc == 768:\n log.info(\"Detected %s tiles, interpreting as HiSeq2500 run.\", tc)\n machine = {\"machine\": \"Illumina HiSeq 2500\", \"lane_count\": 8}\n elif tc == 864:\n log.info(\"Detected %s tiles, interpreting as NextSeq 550 (high-output) run.\", tc)\n machine = {\"machine\": \"NextSeq 550\", \"lane_count\": 4}\n elif tc == 896:\n log.info(\"Detected %s tiles, interpreting as HiSeq4k run.\", tc)\n machine = {\"machine\": \"Illumina HiSeq 4000\", \"lane_count\": 8}\n elif tc == 1408:\n log.info(\"Detected %s tiles, interpreting as Illumina NovaSeq 6000 run.\", tc)\n machine = {\"machine\": \"Illumina NovaSeq 6000\", \"lane_count\": 2}\n elif tc == 3744:\n log.info(\"Detected %s tiles, interpreting as Illumina NovaSeq 6000 run.\", tc)\n machine = {\"machine\": \"Illumina NovaSeq 6000\", \"lane_count\": 4}\n elif tc == 6272:\n log.info(\"Detected %s tiles, interpreting as Illumina NovaSeq X Plus run.\", tc)\n machine = {\"machine\": \"Illumina NovaSeq X Plus\", \"lane_count\": 8}\n else:\n log.info(\"Tile count: %s tiles (unknown instrument type).\", tc)\n return machine\n\n def get_flowcell_chemistry(self):\n guessed_sequencer = self.infer_sequencer_model()\n return guessed_sequencer[\"chemistry\"]\n\n def get_flowcell_lane_count(self):\n guessed_sequencer = self.infer_sequencer_model()\n try:\n return self.get_lane_count()\n except Exception:\n return guessed_sequencer.get(\"lane_count\", None)\n\n def get_machine_model(self):\n guessed_sequencer = self.infer_sequencer_model()\n return guessed_sequencer[\"machine\"]\n\n @classmethod\n def get_machines_for_flowcell_id(cls, fcid):\n sequencer_by_fcid = []\n for key in cls.flowcell_to_machine_model_and_chemistry:\n if re.search(key, fcid):\n sequencer_by_fcid.append(\n cls.flowcell_to_machine_model_and_chemistry[key]\n )\n return sequencer_by_fcid\n\n def infer_sequencer_model(self):\n fcid = self.get_flowcell_raw()\n sequencer_by_tile_count = self.machine_model_from_tile_count()\n sequencers_by_fcid = self.get_machines_for_flowcell_id(fcid)\n\n if len(sequencers_by_fcid) > 1:\n raise LookupError(\"Multiple sequencers possible: %s\", fcid)\n\n log.debug(\"self.tile_count(): %s\", self.tile_count())\n\n if len(sequencers_by_fcid) > 0:\n if (\n sequencer_by_tile_count is not None\n and sequencers_by_fcid[0][\"machine\"]\n != sequencer_by_tile_count[\"machine\"]\n ):\n log.warning(\n \"Sequencer type inferred from flowcell ID: %s does not match sequencer inferred from tile count: %s; is this a new machine type?\"\n % (\n sequencers_by_fcid[0][\"machine\"],\n sequencer_by_tile_count[\"machine\"],\n )\n )\n return sequencers_by_fcid[0]\n elif sequencer_by_tile_count is not None:\n log.warning(\n \"Sequencer type unknown flowcell ID: %s, yet sequencer type was inferred for tile count: %s; is this a new flowcell ID pattern?\"\n % (fcid, self.tile_count())\n )\n return sequencer_by_tile_count\n else:\n log.warning(\n \"Tile count: %s and flowcell ID: %s are both novel; is this a new machine type?\"\n % (self.tile_count(), fcid)\n )\n return {\"machine\": \"UNKNOWN\", \"lane_count\": self.get_lane_count()}\n\n flowcell_to_machine_model_and_chemistry = {\n r\"[A-Z,0-9]{5}AAXX\": {\n \"machine\" : \"Illumina Genome Analyzer IIx\",\n \"chemistry\" : \"All\",\n \"lane_count\" : 8,\n \"note\" : \"\",\n },\n r\"[A-Z,0-9]{5}ABXX\": {\n \"machine\" : \"Illumina HiSeq 2000\",\n \"chemistry\" : \"V2 Chemistry\",\n \"lane_count\" : 8,\n \"note\" : \"\",\n },\n r\"[A-Z,0-9]{5}ACXX\": {\n \"machine\" : \"Illumina HiSeq 2000\",\n \"chemistry\" : \"V3 Chemistry\",\n \"lane_count\" : 8,\n \"note\" : \"Also used on transient 2000E\",\n },\n r\"[A-Z,0-9]{5}(?:ANXX|AN\\w\\w)\": {\n \"machine\" : \"Illumina HiSeq 2500\",\n \"chemistry\" : \"V4 Chemistry\",\n \"lane_count\" : 8,\n \"note\" : \"High output\",\n },\n r\"[A-Z,0-9]{5}(?:ADXX|AD\\w\\w)\": {\n \"machine\" : \"Illumina HiSeq 2500\",\n \"chemistry\" : \"V1 Chemistry\",\n \"lane_count\" : 2,\n \"note\" : \"Rapid run\",\n },\n r\"[A-Z,0-9]{5}AMXX\": {\n \"machine\" : \"Illumina HiSeq 2500\",\n \"chemistry\" : \"V2 Chemistry (beta)\",\n \"lane_count\" : 2,\n \"note\" : \"Rapid run\",\n },\n r\"[A-Z,0-9]{5}(?:BCXX|BC\\w\\w)\": {\n \"machine\" : \"Illumina HiSeq 2500\",\n \"chemistry\" : \"V2 Chemistry\",\n \"lane_count\" : 2,\n \"note\" : \"Rapid run\",\n },\n r\"[A-Z,0-9]{5}AFX\\w\": {\n \"machine\" : \"NextSeq 550\",\n \"chemistry\" : \"Mid-Output NextSeq\",\n \"lane_count\" : 4,\n \"note\" : \"\",\n },\n r\"[A-Z,0-9]{5}AGXX\": {\n \"machine\" : \"NextSeq 550\",\n \"chemistry\" : \"V1 Chemistry\",\n \"lane_count\" : 4,\n \"note\" : \"High-output\",\n },\n r\"[A-Z,0-9]{5}(?:BGXX|BG\\w\\w)\": {\n \"machine\" : \"NextSeq 550\",\n \"chemistry\" : \"V2/V2.5 Chemistry\",\n \"lane_count\" : 4,\n \"note\" : \"High-output\",\n },\n r\"[A-Z,0-9]{5}(?:BBXX|BB\\w\\w)\": {\n \"machine\" : \"Illumina HiSeq 4000\",\n \"chemistry\" : \"Illumina HiSeq 4000\",\n \"lane_count\" : 8,\n \"note\" : \"\",\n },\n r\"[A-Z,0-9]{5}(?:ALXX:AL\\w\\w)\": {\n \"machine\" : \"HiSeq X Ten\",\n \"chemistry\" : \"V1/V2.5 Chemistry\",\n \"lane_count\" : 8,\n \"note\" : \"\",\n },\n r\"[A-Z,0-9]{5}(?:CCXX:CC\\w\\w)\": {\n \"machine\" : \"HiSeq X Ten\",\n \"chemistry\" : \"V2/V2.5 Chemistry\",\n \"lane_count\" : 8,\n \"note\" : \"\",\n },\n r\"[A-Z,0-9]{5}DR\\w\\w\": {\n \"machine\" : \"Illumina NovaSeq 6000\",\n \"chemistry\" : \"V1 Chemistry\",\n \"lane_count\" : 2,\n \"note\" : \"S1/SP\",\n },\n r\"[A-Z,0-9]{5}DM\\w\\w\": {\n \"machine\" : \"Illumina NovaSeq 6000\",\n \"chemistry\" : \"V1 Chemistry\",\n \"lane_count\" : 2,\n \"note\" : \"S2\",\n },\n r\"[A-Z,0-9]{5}DS\\w\\w\": {\n \"machine\" : \"Illumina NovaSeq 6000\",\n \"chemistry\" : \"V1 Chemistry\",\n \"lane_count\" : 4,\n \"note\" : \"S4\",\n },\n r\"BNS417.*\": {\n \"machine\" : \"Illumina iSeq 100\",\n \"chemistry\" : \"V1\",\n \"lane_count\" : 1,\n \"note\" : \"AKA Firefly\",\n },\n r\"[0-9]{9}-\\w{5}\": {\n \"machine\" : \"Illumina MiSeq\",\n \"chemistry\" : \"V1/V2/V3 Chemistry\",\n \"lane_count\" : 1,\n \"note\" : \"\",\n },\n }\n\n\n# ======================\n# *** SampleSheet ***\n# ======================\n\n\nclass SampleSheetError(Exception):\n def __init__(self, message, fname):\n super(SampleSheetError, self).__init__(\n \"Failed to load {} ({})\".format(fname, message)\n )\n\n\nclass SampleSheet(object):\n \"\"\"A class that reads an Illumina SampleSheet.csv or alternative/simplified\n tab-delimited versions as well.\n \"\"\"\n\n def __init__(\n self,\n infile,\n use_sample_name = True,\n only_lane = None,\n allow_non_unique = False,\n append_run_id = None,\n collapse_duplicates = False,\n rev_comp_barcode_2 = False,\n barcode_columns_to_revcomp = None\n ):\n self.fname = infile\n self.use_sample_name = use_sample_name\n if only_lane is not None:\n only_lane = str(only_lane)\n self.only_lane = only_lane\n self.allow_non_unique = allow_non_unique\n self.append_run_id = append_run_id\n self.rows = []\n self._rowsOriginal = []\n self.duplicate_rows_collapsed = False\n self.barcodes_revcomped_relative_to_input = False\n self.barcodes_revcomped_column_names = set()\n\n self._detect_and_load_sheet(infile)\n\n barcode_columns_to_revcomp = barcode_columns_to_revcomp or []\n\n if rev_comp_barcode_2 or (barcode_columns_to_revcomp and isinstance(barcode_columns_to_revcomp, (list, tuple, set, str))):\n columns_to_revcomp = ['barcode_2'] if rev_comp_barcode_2 else []\n columns_to_revcomp += barcode_columns_to_revcomp\n self.rev_comp_barcode_values(barcode_columns_to_revcomp=columns_to_revcomp, inplace=True)\n\n if self.can_be_collapsed:\n if not allow_non_unique:\n raise SampleSheetError(\"Duplicate indices found in sample sheet\", infile)\n else:\n if collapse_duplicates:\n self.collapse_sample_index_duplicates()\n\n def _detect_and_load_sheet(self, infile):\n if infile.endswith((\".csv\", \".csv.gz\")):\n with util_file.open_or_gzopen(infile, \"rU\") as inf:\n header = None\n miseq_skip = False\n row_num = 0\n for line_no, line in enumerate(inf):\n if line_no == 0:\n line = line.replace(\"\\ufeff\", \"\")\n\n if len(line.rstrip(\"\\r\\n\").strip()) == 0:\n continue\n csv.register_dialect(\n \"samplesheet\", quoting=csv.QUOTE_MINIMAL, escapechar=\"\\\\\"\n )\n row = next(\n csv.reader([line.strip().rstrip(\"\\n\")], dialect=\"samplesheet\")\n )\n row = [item.strip() for item in row]\n if miseq_skip:\n if line.startswith(\"[Data]\"):\n miseq_skip = False\n elif line.startswith(\"[\"):\n miseq_skip = True\n elif header is None:\n header = row\n if all(x in header for x in [\"Sample_ID\", \"Index\"]):\n keymapper = {\n \"Sample_ID\" : \"sample\",\n \"Index\" : \"barcode_1\",\n \"Index2\" : \"barcode_2\",\n \"Sample_Name\" : \"sample_name\",\n }\n header = list(map(keymapper.get, header))\n elif \"Sample_ID\" in header:\n keymapper = {\n \"Sample_ID\" : \"sample\",\n \"index\" : \"barcode_1\",\n \"index2\" : \"barcode_2\",\n \"Sample_Name\" : \"sample_name\",\n }\n header = list(map(keymapper.get, header))\n elif \"SampleID\" in header:\n keymapper = {\n \"SampleID\" : \"sample\",\n \"Index\" : \"barcode_1\",\n \"Index2\" : \"barcode_2\",\n \"libraryName\" : \"library_id_per_sample\",\n \"FCID\" : \"flowcell\",\n \"Lane\" : \"lane\",\n }\n header = list(map(keymapper.get, header))\n elif len(row) == 3:\n header = [\"sample\", \"barcode_1\", \"barcode_2\"]\n if \"sample\" not in row[0].lower():\n row_num += 1\n self.rows.append({\n \"sample\" : row[0],\n \"barcode_1\" : row[1],\n \"barcode_2\" : row[2],\n \"row_num\" : str(row_num),\n })\n else:\n raise SampleSheetError(\"unrecognized filetype\", infile)\n for h in (\"sample\", \"barcode_1\"):\n assert h in header\n else:\n row_num += 1\n while len(row) < len(header):\n row.append(\"\")\n assert len(header) == len(row)\n row = dict((k, v) for k, v in zip(header, row) if k and v)\n row[\"row_num\"] = str(row_num)\n if (\n self.only_lane is not None\n and row.get(\"lane\")\n and self.only_lane != row[\"lane\"]\n ):\n continue\n if (\"sample\" in row and row[\"sample\"]) and (\n \"barcode_1\" in row and row[\"barcode_1\"]\n ):\n self.rows.append(row)\n if (\n self.use_sample_name\n and \"sample_name\" in header\n and all(row.get(\"sample_name\") for row in self.rows)\n ):\n for row in self.rows:\n row[\"library_id_per_sample\"] = row[\"sample\"]\n row[\"sample\"] = row[\"sample_name\"]\n for row in self.rows:\n if \"sample_name\" in row:\n del row[\"sample_name\"]\n\n elif infile.endswith((\".txt\", \".txt.gz\", \".tsv\")):\n self.rows = []\n row_num = 0\n for row in util_file.read_tabfile_dict(infile):\n assert row.get(\"sample\") and row.get(\"barcode_1\")\n row_num += 1\n row[\"row_num\"] = str(row_num)\n self.rows.append(row)\n else:\n raise SampleSheetError(\"unrecognized filetype\", infile)\n\n if not self.rows:\n raise SampleSheetError(\"empty file\", infile)\n\n for row in self.rows:\n row[\"library\"] = row[\"sample\"]\n if row.get(\"library_id_per_sample\"):\n row[\"library\"] += \".l\" + row[\"library_id_per_sample\"]\n row[\"run\"] = row[\"library\"]\n if len(set(row[\"run\"] for row in self.rows)) != len(self.rows):\n if self.allow_non_unique:\n log.warning(\"non-unique library IDs in this lane\")\n unique_count = {}\n for row in self.rows:\n unique_count.setdefault(row[\"library\"], 0)\n unique_count[row[\"library\"]] += 1\n row[\"run\"] += \".r\" + str(unique_count[row[\"library\"]])\n else:\n raise SampleSheetError(\"non-unique library IDs in this lane\", infile)\n if self.append_run_id:\n for row in self.rows:\n row[\"run\"] += \".\" + self.append_run_id\n\n for row in self.rows:\n row[\"sample_original\"] = row[\"sample\"]\n row[\"sample\"] = util_file.string_to_file_name(row[\"sample\"])\n row[\"library\"] = util_file.string_to_file_name(row[\"library\"])\n row[\"run\"] = util_file.string_to_file_name(row[\"run\"])\n\n if all(row.get(\"barcode_2\") for row in self.rows):\n self.indexes = 2\n elif any(row.get(\"barcode_2\") for row in self.rows):\n raise SampleSheetError(\n \"inconsistent single/double barcoding in sample sheet\", infile\n )\n else:\n self.indexes = 1\n\n @property\n def can_be_collapsed(self) -> bool:\n \"\"\"Return True if duplicate barcodes exist that could be collapsed.\"\"\"\n assert len(self.rows) > 0, \"No sample sheet rows to collapse\"\n df = pd.json_normalize(self.rows).astype(str).fillna(\"\")\n grouping_cols = [\"barcode_1\"]\n if \"barcode_2\" in df.columns:\n grouping_cols.append(\"barcode_2\")\n duplicated_mask = df.duplicated(subset=grouping_cols, keep=False)\n return duplicated_mask.any()\n\n def collapse_sample_index_duplicates(self, output_tsv=None, overwrite_instance_data=True):\n \"\"\"Collapse duplicate barcode rows into single entries.\"\"\"\n assert len(self.rows) > 0, \"No sample sheet rows to collapse\"\n hash_if_longer_than = 32\n\n df = pd.json_normalize(self.rows).astype(str).fillna(\"\")\n original_cols = df.columns.tolist()\n\n grouping_cols = [\"barcode_1\"]\n has_barcode2 = \"barcode_2\" in df.columns\n if has_barcode2:\n grouping_cols.append(\"barcode_2\")\n\n duplicated_mask = df.duplicated(subset=grouping_cols, keep=False)\n df_unique = df[~duplicated_mask].copy()\n df_duplicates = df[duplicated_mask].copy()\n grouped_dups = df_duplicates.groupby(grouping_cols, sort=False)\n\n collapsed_rows = []\n for group_keys, group_df in grouped_dups:\n if not isinstance(group_keys, tuple):\n group_keys = (group_keys,)\n\n b1 = group_keys[0]\n b2 = group_keys[1] if has_barcode2 else None\n\n if len(group_df) == 1:\n collapsed_rows.append(group_df.iloc[0])\n else:\n row_dict = {}\n if \"barcode_1\" in df.columns:\n row_dict[\"barcode_1\"] = b1\n if has_barcode2:\n row_dict[\"barcode_2\"] = b2\n\n if not has_barcode2:\n row_dict[\"sample\"] = f\"{b1}\"\n else:\n if b2 and b2.strip() != \"\":\n row_dict[\"sample\"] = f\"{b1}-{b2}\"\n else:\n row_dict[\"sample\"] = f\"{b1}\"\n\n for col in original_cols:\n if col in (\"barcode_1\", \"barcode_2\", \"sample\"):\n continue\n col_values = group_df[col].tolist()\n row_dict[col] = util_misc.collapse_dup_strs_to_str_or_md5(\n col_values,\n suffix=\"_muxed\",\n hash_if_longer_than=hash_if_longer_than\n )\n\n row_dict[\"run\"] = f\"{row_dict['sample']}.l{row_dict['library_id_per_sample']}\"\n if self.append_run_id:\n row_dict[\"run\"] += \".\" + self.append_run_id\n\n collapsed_rows.append(pd.Series(row_dict))\n\n df_collapsed = pd.DataFrame(collapsed_rows, dtype=str) if collapsed_rows else pd.DataFrame(columns=original_cols, dtype=str)\n out_df = pd.concat([df_collapsed, df_unique], ignore_index=True)\n out_df = out_df[original_cols]\n\n rows_collapsed = out_df.to_dict(orient=\"records\")\n\n if len(rows_collapsed) < len(self.rows):\n log.info(\"%s: %i rows collapsed ----> %i rows\", os.path.basename(self.fname), len(self.rows), len(rows_collapsed))\n self.duplicate_rows_collapsed = True\n else:\n log.info(\"%s: ZERO rows collapsed\", os.path.basename(self.fname))\n\n excluded_tsv_output_columns = ('row_num', 'library', 'run', 'sample_original')\n filtered_cols = [col for col in original_cols if col not in excluded_tsv_output_columns]\n if output_tsv is not None:\n log.info(\"Saving collapsed sample sheet to: %s\", os.path.realpath(output_tsv))\n out_df[filtered_cols].to_csv(output_tsv, sep=\"\\t\", index=False)\n\n if overwrite_instance_data:\n self._rowsOriginal = self.rows\n self.rows = rows_collapsed\n\n return rows_collapsed\n\n def inner_demux_mapper(self):\n \"\"\"Build a DataFrame mapping barcode groups to barcode_3 values.\"\"\"\n df = pd.json_normalize(self.rows).astype(str)\n has_barcode2 = (\"barcode_2\" in df.columns)\n columns = df.columns\n\n grouping_cols = [\"barcode_1\"]\n if has_barcode2:\n grouping_cols.append(\"barcode_2\")\n\n def fill_inline_index_ids(group):\n if \"Inline_Index_ID\" not in group.columns:\n group[\"Inline_Index_ID\"] = [str(i + 1) for i in range(len(group))]\n else:\n mask = (group[\"Inline_Index_ID\"].isna()) | (group[\"Inline_Index_ID\"] == \"\")\n next_ids = (str(i + 1) for i in range(len(group)))\n group.loc[mask, \"Inline_Index_ID\"] = [next(next_ids) for _ in range(sum(mask))]\n return group\n\n df = df.groupby(grouping_cols, group_keys=False, as_index=False)\n df = df[columns].apply(fill_inline_index_ids, include_groups=False)\n\n def build_run_string(row):\n sample_val = row.get(\"sample\", \"\")\n lib_val = row.get(\"library_id_per_sample\", \"\")\n run_str = f\"{sample_val}.l{lib_val}\"\n if self.append_run_id:\n run_str += f\".{self.append_run_id}\"\n return run_str\n\n df[\"run\"] = df.apply(build_run_string, axis=1)\n\n def build_muxed_run_string(row):\n b1 = row.get(\"barcode_1\", \"\")\n b2 = row.get(\"barcode_2\", \"\") if has_barcode2 else None\n if b2 and b2.strip():\n muxed_sample = f\"{b1}-{b2}\"\n else:\n muxed_sample = b1\n lib_val = row.get(\"library_id_per_sample\", \"\")\n muxed_run_str = f\"{muxed_sample}.l{lib_val}\"\n if self.append_run_id:\n muxed_run_str += f\".{self.append_run_id}\"\n return muxed_run_str\n\n df[\"muxed_run\"] = df.apply(build_muxed_run_string, axis=1)\n\n out_cols = [\"barcode_1\"]\n if has_barcode2:\n out_cols.append(\"barcode_2\")\n out_cols.extend([\"barcode_3\", \"sample\", \"library_id_per_sample\", \"Inline_Index_ID\", \"run\", \"muxed_run\"])\n\n existing_cols = [c for c in out_cols if c in df.columns]\n out_df = df[existing_cols].copy()\n out_df.set_index(\"sample\", inplace=True)\n return out_df\n\n def make_barcodes_file(self, outFile):\n \"\"\"Create input file for Picard ExtractBarcodes\"\"\"\n if self.num_indexes() == 2:\n header = [\"barcode_name\", \"library_name\", \"barcode_sequence_1\", \"barcode_sequence_2\"]\n else:\n header = [\"barcode_name\", \"library_name\", \"barcode_sequence_1\"]\n with open(outFile, \"wt\") as outf:\n outf.write(\"\\t\".join(header) + \"\\n\")\n for row in self.rows:\n out = {\n \"barcode_sequence_1\": row[\"barcode_1\"],\n \"barcode_sequence_2\": row.get(\"barcode_2\", \"\"),\n \"barcode_name\": row[\"sample\"],\n \"library_name\": row[\"library\"],\n }\n outf.write(\"\\t\".join(out[h] for h in header) + \"\\n\")\n\n def write_tsv(self, outFile, force=False):\n \"\"\"Write sample sheet to a tab-delimited file.\"\"\"\n if os.path.exists(outFile) and not force:\n raise FileExistsError(f\"Output file {outFile} already exists. Use force=True to overwrite.\")\n with open(outFile, \"wt\") as outf:\n writer = csv.DictWriter(outf, self.rows[0].keys(), delimiter=\"\\t\")\n writer.writeheader()\n for row in self.rows:\n writer.writerow(row)\n\n def rev_comp_barcode_values(self, barcode_columns_to_revcomp=None, inplace=True):\n \"\"\"Reverse-complement barcode values in specified columns.\"\"\"\n barcode_columns_to_revcomp = barcode_columns_to_revcomp or [\"barcode_2\"]\n\n if type(barcode_columns_to_revcomp) is str:\n barcode_columns_to_revcomp = [barcode_columns_to_revcomp]\n\n if inplace:\n self._rowsOriginal = self.rows.copy()\n for row_idx, row in enumerate(self.rows):\n for column_name in barcode_columns_to_revcomp:\n if column_name in row:\n try:\n row[column_name] = util_misc.reverse_complement(row[column_name])\n except Exception:\n log.warning(\"Failed to reverse-complement barcode value on line %s of %s: '%s'\",\n row_idx + 1, self.fname, row[column_name])\n pass\n self.barcodes_revcomped_relative_to_input = True\n self.barcodes_revcomped_column_names.add(column_name)\n return self\n else:\n new_sheet_fp = util_file.mkstempfname(f'{os.path.basename(self.fname)}_rev-comped-{\"-\".join(barcode_columns_to_revcomp)}.txt')\n log.debug(\"Creating a new SampleSheet object with reverse-complemented barcodes: %s\", new_sheet_fp)\n shutil.copyfile(self.fname, new_sheet_fp)\n new_ss = SampleSheet(\n new_sheet_fp,\n barcode_columns_to_revcomp=barcode_columns_to_revcomp,\n allow_non_unique=self.allow_non_unique\n )\n return new_ss\n\n def make_params_file(self, bamDir, outFile):\n \"\"\"Create input file for Picard IlluminaBasecallsToXXX\"\"\"\n if self.num_indexes() == 2:\n header = [\"OUTPUT\", \"SAMPLE_ALIAS\", \"LIBRARY_NAME\", \"BARCODE_1\", \"BARCODE_2\"]\n else:\n header = [\"OUTPUT\", \"SAMPLE_ALIAS\", \"LIBRARY_NAME\", \"BARCODE_1\"]\n with open(outFile, \"wt\") as outf:\n outf.write(\"\\t\".join(header) + \"\\n\")\n rows = self.rows + [{\n \"barcode_1\": \"N\",\n \"barcode_2\": \"N\",\n \"sample\": \"Unmatched\",\n \"library\": \"Unmatched\",\n \"run\": \"Unmatched\",\n }]\n for row in rows:\n out = {\n \"BARCODE_1\": row[\"barcode_1\"],\n \"BARCODE_2\": row.get(\"barcode_2\", \"\"),\n \"SAMPLE_ALIAS\": row[\"sample\"],\n \"LIBRARY_NAME\": row[\"library\"],\n }\n out[\"OUTPUT\"] = os.path.join(bamDir, row[\"run\"] + \".bam\")\n outf.write(\"\\t\".join(out[h] for h in header) + \"\\n\")\n\n def get_fname(self):\n return self.fname\n\n def get_rows(self):\n return self.rows\n\n def print_rows(self, row_indices=None):\n \"\"\"Print rows, optionally only a subset.\"\"\"\n rows_selected = [self.rows[i] for i in row_indices] if row_indices else self.rows\n for r in rows_selected:\n longest_key_len = len(max(r.keys(), key=len))\n print(f\"Sample: {r['sample']}\")\n for k, v in r.items():\n if k != 'sample':\n print(f\"\\t{k:<{longest_key_len + 1}}: {v}\")\n print(\"\")\n\n def num_indexes(self):\n \"\"\"Return 1 or 2 depending on whether pools are single or double indexed.\"\"\"\n return self.indexes\n\n @property\n def num_samples(self):\n return len(self.rows)\n\n def fetch_by_index(self, idx):\n idx = str(idx)\n for row in self.rows:\n if idx == row[\"row_num\"]:\n return row\n return None\n" }, { "path": "src/viral_ngs/core/minimap2.py", "content": "'''\n The minimap2 aligner.\n\n'''\n\nimport collections\nimport logging\nimport os\nimport os.path\nimport shutil\nimport subprocess\n\nfrom Bio import SeqIO\n\nfrom . import samtools\nfrom . import picard\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom .errors import *\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = 'minimap2'\n\nlog = logging.getLogger(__name__)\n\nclass Minimap2(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = []\n install_methods.append(PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True))\n super(Minimap2, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([TOOL_NAME ,'--version']).decode('UTF-8').strip()\n\n def execute(self, args, stdout=None, stdin=None, background=False): # pylint: disable=W0221\n tool_cmd = [self.install_and_get_path()] + args\n log.debug(' '.join(tool_cmd))\n if stdout:\n stdout = open(stdout, 'w')\n if background:\n subprocess.Popen(tool_cmd, stdout=stdout, stdin=stdin)\n else:\n subprocess.check_call(tool_cmd, stdout=stdout, stdin=stdin)\n if stdout:\n stdout.close()\n\n def align_bam(self, inBam, refDb, outBam, options=None,\n threads=None, JVMmemory=None, should_index=True):\n options = options or []\n\n samtools_tool = samtools.SamtoolsTool()\n threads = util_misc.sanitize_thread_count(threads)\n\n # fetch list of RGs\n rgs = list(samtools_tool.getReadGroups(inBam).keys())\n\n if len(rgs) == 0:\n # Can't do this\n raise InvalidBamHeaderError(\"{} lacks read groups\".format(inBam))\n\n elif len(rgs) == 1:\n # Only one RG, keep it simple\n self.align_one_rg(inBam, refDb, outBam, options=options, threads=threads, should_index=should_index)\n\n else:\n # Multiple RGs, align one at a time and merge\n align_bams = []\n\n for rg in rgs:\n tmp_bam = util_file.mkstempfname('.{}.bam'.format(rg))\n self.align_one_rg(\n inBam,\n refDb,\n tmp_bam,\n rgid=rg,\n options=options,\n threads=threads,\n should_index=False # Don't index intermediate BAMs that will be merged\n )\n if not samtools_tool.isEmpty(tmp_bam):\n align_bams.append(tmp_bam)\n else:\n log.warning(\"No alignment output for RG %s in file %s against %s\", rg, inBam, refDb)\n\n if len(align_bams)==0:\n log.warning(\"All read groups in file %s appear to be empty.\", inBam)\n with util_file.tempfname('.empty.sam') as empty_sam:\n samtools_tool.dumpHeader(inBam, empty_sam)\n samtools_tool.sort(empty_sam, outBam)\n else:\n # Merge BAMs, sort, and index\n picardOptions = ['SORT_ORDER=coordinate', 'USE_THREADING=true', 'CREATE_INDEX=true']\n picard.MergeSamFilesTool().execute(\n align_bams,\n outBam,\n picardOptions=picardOptions,\n JVMmemory=JVMmemory\n )\n\n for bam in align_bams:\n os.unlink(bam)\n\n def align_one_rg(self, inBam, refDb, outBam, rgid=None, preset=None, options=None,\n threads=None, JVMmemory=None, should_index=True):\n \"\"\"\n Performs an alignment of one read group in a bam file to a reference fasta file using minimap2.\n Emits alignments in sorted, index bam files.\n inBam may contain more read groups, but we will subset input to the specified rgid.\n preset may be specified as a valid value for \"minimap2 -x\" which depends on the type of\n data (short accurate reads vs long noisy reads). If preset is set to None, we will autodetect\n based on the PL (platform) tag in the read group header (e.g. illumina, ont, pacbio)\n \"\"\"\n options = list(options).copy() or []\n\n samtools_tool = samtools.SamtoolsTool()\n\n # Require exactly one RG\n rgs = samtools_tool.getReadGroups(inBam)\n if len(rgs) == 0:\n raise InvalidBamHeaderError(\"{} lacks read groups\".format(inBam))\n elif len(rgs) == 1:\n if not rgid:\n rgid = list(rgs.keys())[0]\n elif not rgid:\n raise InvalidBamHeaderError(\"{} has {} read groups, but we require exactly one\".format(inBam, len(rgs)))\n if rgid not in rgs:\n raise InvalidBamHeaderError(\"{} has read groups, but not {}\".format(inBam, rgid))\n\n headerFile = util_file.mkstempfname('.{}.header.txt'.format(rgid))\n # Strip inBam to just one RG (if necessary)\n removeInput = False\n if len(rgs) == 1:\n one_rg_inBam = inBam\n samtools_tool.dumpHeader(one_rg_inBam, headerFile)\n else:\n # strip inBam to one read group\n with util_file.tempfname('.onebam.bam') as tmp_bam:\n samtools_tool.view(['-1', '-r', rgid], inBam, tmp_bam)\n # special exit if this file is empty\n if samtools_tool.isEmpty(tmp_bam):\n log.warning(\"No reads present for RG %s in file: %s\", rgid, inBam)\n shutil.copyfile(tmp_bam, outBam)\n return\n # simplify BAM header otherwise Novoalign gets confused\n one_rg_inBam = util_file.mkstempfname('.{}.in.bam'.format(rgid))\n removeInput = True\n \n with open(headerFile, 'wt') as outf:\n for row in samtools_tool.getHeader(inBam):\n if len(row) > 0 and row[0] == '@RG':\n if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]:\n # skip all read groups that are not rgid\n continue\n outf.write('\\t'.join(row) + '\\n')\n samtools_tool.reheader(tmp_bam, headerFile, one_rg_inBam)\n\n # get the read group line to give to mm2\n readgroup_line = \"\"\n with open(headerFile) as inf:\n for line in inf:\n if line.startswith(\"@RG\"):\n readgroup_line = line.rstrip(\"\\r\\n\")\n if not readgroup_line:\n raise Exception()\n # rather than reheader the alignment bam file later so it has the readgroup information\n # from the original bam file, we'll pass the RG line to minimap2 to write out\n options.extend(('-R', readgroup_line.replace('\\t','\\\\t')))\n\n # dynamically determine the mode of operation\n if '-x' not in options:\n if preset is None:\n platform = list(x for x in readgroup_line.split('\\t') if x.startswith('PL:'))\n if len(platform) != 1:\n raise Exception(\"cannot autodetect minimap2 aligner mode when PL: tag is not set in the read group header for {}: {}\".format(inBam, readgroup_line))\n else:\n platform = platform[0][3:].lower()\n if platform == 'illumina':\n preset = 'sr'\n elif platform == 'ont':\n preset = 'map-ont'\n elif platform == 'pacbio':\n preset = 'map-pb'\n else:\n raise Exception(\"PL: tag {} for read group {} in bam {} refers to a data type we do not know how to map with minimap2\".format(platform, rgid, inBam))\n options.extend(('-x', preset))\n\n # perform actual alignment\n if samtools_tool.isEmpty(one_rg_inBam):\n log.warning(\"Input file %s appears to lack reads for RG '%s'\", inBam, rgid)\n # minimap doesn't like empty inputs, so copy empty bam through\n # samtools.sort(one_rg_inBam, outBam)\n self.align_cmd(one_rg_inBam, refDb, outBam, options=options, threads=threads, should_index=should_index)\n else:\n self.align_cmd(one_rg_inBam, refDb, outBam, options=options, threads=threads, should_index=should_index)\n\n # if there was more than one RG in the input, we had to create a temporary file with the one RG specified\n # and we can safely delete it this file\n # if there was only one RG in the input, we used it directly and should not delete it\n if removeInput:\n os.unlink(one_rg_inBam)\n\n def align_cmd(self, inReads, refDb, outAlign, options=None, threads=None, should_index=True):\n options = [] if not options else options\n\n threads = util_misc.sanitize_thread_count(threads)\n if '-t' not in options:\n options.extend(('-t', str(threads)))\n if '-2' not in options:\n options.append('-2')\n\n samtools_tool = samtools.SamtoolsTool()\n\n with util_file.tempfname('.aligned.sam') as aln_sam:\n fastq_pipe = samtools_tool.bam2fq_pipe(inReads)\n options.extend(('-a', refDb, '-', '-o', aln_sam))\n self.execute(options, stdin=fastq_pipe.stdout)\n if fastq_pipe.wait():\n raise subprocess.CalledProcessError(fastq_pipe.returncode, \"samtools.bam2fq_pipe() for {}\".format(inReads))\n samtools_tool.sort(aln_sam, outAlign, threads=threads)\n\n # cannot index sam files; only do so if a bam/cram is desired\n if should_index and (outAlign.endswith(\".bam\") or outAlign.endswith(\".cram\")):\n samtools_tool.index(outAlign, threads=threads)\n\n def scaffold(self, contigs_fasta, ref_fasta, outAlign, divergence=20, options=None, threads=None):\n options = [] if not options else options\n\n samtools_tool = samtools.SamtoolsTool()\n threads = util_misc.sanitize_thread_count(threads)\n if '-t' not in options:\n options.extend(('-t', str(threads)))\n if '-2' not in options:\n options.append('-2')\n\n if divergence >= 20:\n options.extend(('-x', 'asm20'))\n elif divergence >= 10:\n options.extend(('-x', 'asm10'))\n else:\n options.extend(('-x', 'asm5'))\n\n with util_file.tempfname('.aligned.sam') as aln_sam:\n options.extend(('-a', ref_fasta, contigs_fasta, '-o', aln_sam))\n self.execute(options)\n samtools_tool.sort(aln_sam, outAlign, threads=threads)\n\n # cannot index sam files; only do so if a bam/cram is desired\n if (outAlign.endswith(\".bam\") or outAlign.endswith(\".cram\")):\n samtools_tool.index(outAlign)\n\n def idxstats(self, inReads, refDb, outIdxstats, outReadlist=None, threads=None):\n \"\"\"\n Align reads and produce idxstats-like counts and optional read list.\n\n This method is optimized for counting reads per reference by:\n - Using PAF output (no -a flag) for faster alignment\n - Streaming and parsing PAF directly without intermediate files\n - Only counting primary alignments\n - For paired-end reads: requiring both R1 and R2 to have primary alignments\n (properly paired behavior)\n - For single-end reads: counting any primary alignment\n\n Args:\n inReads: Input reads (BAM format)\n refDb: Reference database (FASTA format)\n outIdxstats: Output file in samtools idxstats format (tab-separated:\n seq_name, seq_length, mapped_count, unmapped_count)\n Note: unmapped_count will always be 0 in this implementation\n outReadlist: Optional output file listing all read IDs that mapped\n as primary alignments. If None, this output is skipped.\n threads: Number of threads for minimap2 (default: auto-detect)\n \"\"\"\n log.info(\"Starting idxstats: aligning %s to %s\", inReads, refDb)\n\n threads = util_misc.sanitize_thread_count(threads)\n samtools_tool = samtools.SamtoolsTool()\n\n # Parse reference FASTA for sequence lengths\n ref_lengths = collections.OrderedDict()\n for record in SeqIO.parse(refDb, 'fasta'):\n ref_lengths[record.id] = len(record.seq)\n\n # Handle empty reference case\n if not ref_lengths:\n log.warning(\"Reference FASTA %s contains no sequences\", refDb)\n with util_file.open_or_gzopen(outIdxstats, 'wt') as outf:\n pass # write empty file\n if outReadlist:\n with util_file.open_or_gzopen(outReadlist, 'wt') as outf:\n pass # write empty file\n return\n\n # Initialize counter for reads per reference\n reads_per_ref = collections.Counter()\n\n # Build minimap2 command for PAF output (no -a flag)\n options = ['-t', str(threads), '-2', '-x', 'sr', refDb, '-']\n\n # Open readlist file for streaming if requested\n readlist_file = util_file.open_or_gzopen(outReadlist, 'wt') if outReadlist else None\n\n try:\n # Start samtools bam2fq pipe for input (use 4 threads for BAM decompression)\n fastq_pipe = samtools_tool.bam2fq_pipe(inReads, threads=4)\n\n # Start minimap2 process with PAF output to stdout\n tool_cmd = [self.install_and_get_path()] + options\n log.debug(' '.join(tool_cmd))\n mm2_proc = subprocess.Popen(\n tool_cmd,\n stdin=fastq_pipe.stdout,\n stdout=subprocess.PIPE,\n text=True\n )\n\n # Parse PAF output line by line\n # For paired-end reads: require both R1 and R2 to have primary alignments\n # (properly paired behavior). For single-end reads: count any primary alignment.\n # Track recent read names to deduplicate readlist output.\n recent_reads = collections.deque(maxlen=4)\n pending_alignment = None # Tuple: (base_read_id, target_name, is_r1) for paired-end\n lines_processed = 0\n paired_count = 0\n single_count = 0\n for line in mm2_proc.stdout:\n lines_processed += 1\n if lines_processed % 100000 == 0:\n log.info(\"Processed %d PAF lines, %d paired + %d single reads so far\",\n lines_processed, paired_count, single_count)\n\n fields = line.rstrip('\\n').split('\\t')\n if len(fields) < 12:\n continue\n\n read_id = fields[0]\n target_name = fields[5]\n\n # Check for primary alignment tag (tp:A:P)\n is_primary = False\n for field in fields[12:]:\n if field == 'tp:A:P':\n is_primary = True\n break\n\n if not is_primary:\n continue\n\n # Detect if paired-end by checking for /1 or /2 suffix\n # bam2fq -n adds these suffixes for paired-end reads\n if read_id.endswith('/1'):\n is_paired = True\n is_r1 = True\n base_read_id = read_id[:-2]\n elif read_id.endswith('/2'):\n is_paired = True\n is_r1 = False\n base_read_id = read_id[:-2]\n else:\n is_paired = False\n base_read_id = read_id\n\n if not is_paired:\n # SINGLE-END: count immediately\n single_count += 1\n reads_per_ref[target_name] += 1\n if readlist_file and base_read_id not in recent_reads:\n recent_reads.append(base_read_id)\n readlist_file.write(base_read_id + '\\n')\n else:\n # PAIRED-END: require both R1 and R2 to have primary alignments\n if pending_alignment is None:\n # First of pair: store it\n pending_alignment = (base_read_id, target_name, is_r1)\n else:\n pending_base, pending_target, pending_is_r1 = pending_alignment\n\n if base_read_id == pending_base and is_r1 != pending_is_r1:\n # Mate found! Both R1 and R2 aligned - count BOTH\n paired_count += 2\n reads_per_ref[pending_target] += 1\n reads_per_ref[target_name] += 1\n if readlist_file and base_read_id not in recent_reads:\n recent_reads.append(base_read_id)\n readlist_file.write(base_read_id + '\\n')\n pending_alignment = None\n else:\n # Not a matching mate - discard pending (singleton), store current\n pending_alignment = (base_read_id, target_name, is_r1)\n\n # Wait for processes to complete\n mm2_proc.wait()\n if fastq_pipe.wait():\n raise subprocess.CalledProcessError(\n fastq_pipe.returncode,\n \"samtools.bam2fq_pipe() for {}\".format(inReads)\n )\n\n finally:\n if readlist_file:\n readlist_file.close()\n\n # Write idxstats output\n with util_file.open_or_gzopen(outIdxstats, 'wt') as outf:\n for ref_name, ref_len in ref_lengths.items():\n mapped_count = reads_per_ref.get(ref_name, 0)\n outf.write('{}\\t{}\\t{}\\t0\\n'.format(ref_name, ref_len, mapped_count))\n\n log.info(\"Completed idxstats: %d paired + %d single-end reads counted from %d PAF lines\",\n paired_count, single_count, lines_processed)\n" }, { "path": "src/viral_ngs/core/misc.py", "content": "'''A few miscellaneous tools. '''\nimport array\nimport bisect\nimport collections\nimport collections.abc\nimport contextlib\nimport copy\nimport functools\nimport hashlib\nimport itertools\nimport json\nimport logging\nimport math\nimport multiprocessing\nimport operator\nimport os, os.path\nimport re\nimport shutil\nimport sqlite3\nimport subprocess\nimport sys\nimport threading\nimport time\nimport yaml\n\nimport Bio.SeqIO\nimport pysam\n\nfrom . import file as util_file # was: from viral_ngs import util\n\nlog = logging.getLogger(__name__)\n\n__author__ = \"dpark@broadinstitute.org\"\n\nMAX_INT32 = (2 ** 31)-1\n\ndef unambig_count(seq):\n unambig = set(('A', 'T', 'C', 'G'))\n return sum(1 for s in seq if s.upper() in unambig)\n\n@contextlib.contextmanager\ndef timer(prefix):\n start = time.time()\n yield\n finish = time.time()\n elapsed = '{:.2f}'.format(finish - start)\n print(prefix + ' - ' + elapsed, file=sys.stderr)\n\n\ndef memoize(obj):\n cache = obj.cache = {}\n\n @functools.wraps(obj)\n def memoizer(*args, **kwargs):\n key = \"\".join([str(args),str(kwargs)])\n if key not in cache:\n cache[key] = obj(*args, **kwargs)\n return cache[key]\n return memoizer\n\n\ndef unique(items):\n ''' Return unique items in the same order as seen in the input. '''\n seen = set()\n for i in items:\n if i not in seen:\n seen.add(i)\n yield i\n\ndef collapse_dup_strs_to_str_or_md5(values,\n suffix = \"\",\n delimiter = \"_\",\n hash_if_longer_than = -1,\n sort_plural_vals = False,\n calculate_md5_including_suffix = False,\n append_suffix_to_delimited_str = True,\n append_suffix_to_one_unique_str = False,\n ):\n \"\"\"\n Collapse multiple string values into one string value\n\n Given a list of values (ex. from a column in a duplicated group of >=2 rows):\n 1) If all values are empty (\"\"), return \"\".\n 2) Otherwise, if there's exactly 1 unique value (non-empty or empty), return that value + (suffix, optionally)\n 3) Otherwise (>=2 distinct values), join with delimiter. \n If (length with delimiters + suffix, if appending) > max_length, \n compute the MD5 hash of the joined values (without delimiters, optionally including the suffix),\n and only return the last 8 characters of that MD5 hash plus suffix.\n The default is to always return MD5+suffix (default max_length is -1)\n\n Note that the MD5 hash will *not* be affected by \n any empty strings present in the input\n (and when returning a delimited string of the joined values,\n such empty strings will be omitted).\n \"\"\"\n # If all values are empty, return \"\"\n if all(v == \"\" for v in values):\n return \"\"\n\n # Get the unique values, in the original order\n unique_vals = list(unique(values))\n\n # Exactly 1 unique value => \n if len(unique_vals) == 1:\n return f\"{unique_vals[0]}{suffix if append_suffix_to_one_unique_str else ''}\"\n\n # Otherwise, return joined values\n # or if that would be too long, return (MD5 of joined values)[-8:]+(optional suffix)\n # the input values are optionally sorted after removing empty strings\n joined_values_delimited = f\"{delimiter}\".join(sorted([s for s in unique_vals if len(s)>0]) if sort_plural_vals else unique_vals) + (suffix if append_suffix_to_delimited_str else \"\")\n \n\n if len(joined_values_delimited) <= int(hash_if_longer_than):\n return joined_values_delimited\n else:\n # If the joined string is too long, compute MD5 of joined values\n #joined_values = f\"\".join(sorted(unique_vals)) + (suffix if calculate_md5_including_suffix else \"\")\n joined_values = f\"\".join(unique_vals) + (suffix if calculate_md5_including_suffix else \"\")\n # Use only the last 8 characters of the MD5\n short_md5 = md5_digest(joined_values)\n return f\"{short_md5}{suffix}\"\n\ndef md5_digest(in_str, last_n_chr=8):\n '''Return the last `last_n_chr` characters of the md5 digest of `str`.'''\n return hashlib.md5(in_str.encode('utf-8')).hexdigest()[-last_n_chr:]\n\ndef reverse_complement(seq):\n \"\"\"\n Returns the reverse complement using string.maketrans\n \"\"\"\n table = bytearray.maketrans(b\"ACTGN\",b\"TGACN\")\n return bytearray(seq.encode(\"UTF8\")).translate(table)[::-1].decode(\"UTF8\")\n\n\ndef histogram(items):\n ''' I count the number of times I see stuff and return a dict of counts. '''\n out = {}\n for i in items:\n out.setdefault(i, 0)\n out[i] += 1\n return out\n\n\ndef freqs(items, zero_checks=None):\n ''' Given a list of comparable, non-unique items, produce an iterator of\n (item, count, freq) tuples.\n item is a unique instance of one of the items seen on input\n count is a positive integer describing the number of times this item was observed\n freq is count / sum(count) for all outputs.\n If zero_checks is specified, then the output iterator will emit tuples for the\n items in zero_checks even if they do not appear in the input. If they are not in\n the input, they will be emitted with a zero count and freq.\n See histogram(items)\n '''\n zero_checks = zero_checks or set()\n\n tot = 0\n out = {}\n for i in items:\n out.setdefault(i, 0)\n out[i] += 1\n tot += 1\n for k, v in out.items():\n yield (k, v, float(v) / tot)\n for i in zero_checks:\n if i not in out:\n yield (i, 0, 0.0)\n\n\ndef intervals(i, n, l):\n ''' Divide something of length l into n equally sized parts and return the\n start-stop values of the i'th part. Values are 1-based. Each part\n will be adjacent and non-overlapping with the next part. i must be a\n number from 1 to n.\n '''\n assert 1 <= i <= n and l >= n\n part_size = l // n\n start = 1 + part_size * (i - 1)\n stop = part_size * i\n if i == n:\n stop = l\n return (start, stop)\n\n# from http://stackoverflow.com/a/312467\n\n\ndef pairwise(iterable):\n \"\"\" from itertools recipes\n s -> (s0,s1), (s1,s2), (s2, s3), ...\"\"\"\n a, b = itertools.tee(iterable)\n next(b, None)\n return zip(a, b)\n\n\ndef batch_iterator(iterator, batch_size):\n \"\"\"Returns lists of length batch_size.\n\n This can be used on any iterator, for example to batch up\n SeqRecord objects from Bio.SeqIO.parse(...), or to batch\n Alignment objects from Bio.AlignIO.parse(...), or simply\n lines from a file handle.\n\n This is a generator function, and it returns lists of the\n entries from the supplied iterator. Each list will have\n batch_size entries, although the final list may be shorter.\n \"\"\"\n it = iter(iterator)\n item = list(itertools.islice(it, batch_size))\n while item:\n yield item\n item = list(itertools.islice(it, batch_size))\n\n\ndef list_contains(sublist, list_):\n \"\"\"Tests whether sublist is contained in full list_.\"\"\"\n\n for i in range(len(list_)-len(sublist)+1):\n if sublist == list_[i:i+len(sublist)]:\n return True\n return False\n\n\ndef run_and_print(args, stdout=None, stderr=subprocess.STDOUT,\n stdin=None, shell=False, env=None, cwd=None,\n timeout=None, silent=False, buffered=False, check=False,\n loglevel=None):\n '''Capture stdout+stderr and print.\n\n This is useful for nose, which has difficulty capturing stdout of\n subprocess invocations.\n '''\n if not buffered:\n if check and not silent:\n try:\n result = subprocess.run(\n args,\n stdin=stdin,\n stdout=subprocess.PIPE,\n stderr=stderr,\n env=env,\n cwd=cwd,\n timeout=timeout,\n check=check\n )\n print(result.stdout.decode('utf-8'))\n try:\n print(result.stderr.decode('utf-8'))\n except AttributeError:\n pass\n except subprocess.CalledProcessError as e:\n if loglevel:\n try:\n log.log(loglevel, result.stdout.decode('utf-8'))\n except NameError:\n # in some situations, result does not get assigned anything\n pass\n except AttributeError:\n log.log(loglevel, result.output.decode('utf-8'))\n else:\n print(e.output.decode('utf-8'))\n try:\n print(e.stderr.decode('utf-8'))\n except AttributeError:\n pass\n sys.stdout.flush()\n raise(e)\n else:\n result = subprocess.run(args, stdin=stdin, stdout=subprocess.PIPE,\n stderr=stderr, env=env, cwd=cwd,\n timeout=timeout, check=check)\n if not silent and not loglevel:\n print(result.stdout.decode('utf-8'))\n sys.stdout.flush()\n elif loglevel:\n log.log(loglevel, result.stdout.decode('utf-8'))\n\n else:\n CompletedProcess = collections.namedtuple(\n 'CompletedProcess', ['args', 'returncode', 'stdout', 'stderr'])\n\n process = subprocess.Popen(args, stdin=stdin, stdout=subprocess.PIPE,\n stderr=stderr, env=env,\n cwd=cwd)\n output = []\n while process.poll() is None:\n for c in iter(process.stdout.read, b\"\"):\n output.append(c)\n if not silent:\n print(c.decode('utf-8'), end=\"\") # print for py3 / p2 from __future__\n sys.stdout.flush() # flush buffer to stdout\n\n # in case there are still chars in the pipe buffer\n for c in iter(lambda: process.stdout.read(1), b\"\"):\n if not silent:\n print(c, end=\"\")\n sys.stdout.flush() # flush buffer to stdout\n\n if check and process.returncode != 0:\n raise subprocess.CalledProcessError(process.returncode, args,\n b''.join(output))\n result = CompletedProcess(\n args, process.returncode, b''.join(output), b'')\n\n return result\n\n\ndef run_and_save(args, stdout=None, stdin=None,\n outf=None, stderr=None, preexec_fn=None,\n close_fds=False, shell=False, cwd=None, env=None, check=True):\n assert outf is not None\n\n sp = subprocess.Popen(args,\n stdin=stdin,\n stdout=outf,\n stderr=subprocess.PIPE,\n preexec_fn=preexec_fn,\n close_fds=close_fds,\n shell=shell,\n cwd=cwd,\n env=env)\n out, err = sp.communicate()\n\n # redirect stderror to stdout so it can be captured by nose\n if err:\n sys.stdout.write(err.decode(\"UTF-8\"))\n\n if sp.returncode != 0 and check:\n raise subprocess.CalledProcessError(sp.returncode, str(args[0]))\n\n return sp\n\n\nclass FeatureSorter(object):\n ''' This class helps sort genomic features. It's not terribly optimized\n for speed or anything. Slightly inspired by calhoun's MultiSequenceRangeMap.\n '''\n def __init__(self, collection=None):\n self.seqids = []\n self.seq_to_features = {}\n self.seq_to_breakpoints = {}\n self.dirty = False\n if collection is not None:\n for args in collection:\n self.add(*args)\n\n def add(self, c, start, stop, strand='+', other=None):\n ''' Add a \"feature\", which is a chrom,start,stop,strand tuple (with\n optional other info attached)\n '''\n if c not in self.seq_to_features:\n self.seqids.append(c)\n self.seq_to_features[c] = []\n self.seq_to_breakpoints[c] = set()\n #self.seq_to_breakpoints[c].add(1) # do we want the empty interval in front?\n self.seq_to_features[c].append((int(start), int(stop), strand, other))\n self.seq_to_breakpoints[c].add(start)\n self.seq_to_breakpoints[c].add(stop+1)\n self.dirty = True\n\n def _cleanup(self):\n if self.dirty:\n self.dirty = False\n for c in self.seqids:\n self.seq_to_features[c].sort()\n\n def get_seqids(self):\n return tuple(self.seqids)\n\n def get_features(self, c=None, left=0, right=float('inf')):\n ''' Get all features on all chromosomes in sorted order. Chromosomes\n are emitted in order of first appearance (via add). Features on\n each chromosome are emitted in start, then stop order. If\n boundaries are specified, we restrict to features that contain\n the specified interval.\n '''\n self._cleanup()\n if c is not None:\n seqlist = [c]\n else:\n seqlist = self.seqids\n for c in seqlist:\n for start, stop, strand, other in self.seq_to_features[c]:\n if stop>=left and start<=right:\n yield (c, start, stop, strand, other)\n\n def get_intervals(self, c=None):\n ''' Get all intervals on the reference where the overlapping feature\n set remains the same. Output will be sorted, adjacent intervals\n and will describe how many and which features overlap it.\n '''\n self._cleanup()\n if c is not None:\n seqlist = [c]\n else:\n seqlist = self.seqids\n for c in seqlist:\n for left, right in pairwise(sorted(self.seq_to_breakpoints[c])):\n right = right - 1\n features = list(self.get_features(c, left, right))\n yield (c, left, right, len(features), features)\n\n\ndef available_cpu_count():\n \"\"\"\n Return the number of available virtual or physical CPUs on this system.\n The number of available CPUs can be smaller than the total number of CPUs\n when the cpuset(7) mechanism is in use, as is the case on some cluster\n systems.\n\n Adapted from http://stackoverflow.com/a/1006301/715090\n \"\"\"\n\n cgroup_cpus = MAX_INT32\n try:\n # cgroup CPU count determination (w/ v2) adapted from:\n # https://github.com/conan-io/conan/blob/2.9.2/conan/tools/build/cpu.py#L31-L54\n #\n # see also:\n # https://docs.kernel.org/scheduler/sched-bwc.html\n\n # This is necessary to determine docker cpu_count\n cfs_quota_us = cfs_period_us = 0\n # cgroup v2\n if os.path.exists(\"/sys/fs/cgroup/cgroup.controllers\"):\n log.debug(\"cgroup v2 detected\")\n cpu_max = util_file.slurp_file(\"/sys/fs/cgroup/cpu.max\").split()\n if cpu_max[0] != \"max\":\n if len(cpu_max) == 1:\n cfs_quota_us, cfs_period_us = int(cpu_max[0]), 100_000\n else:\n cfs_quota_us, cfs_period_us = map(int, cpu_max)\n # cgroup v1\n else:\n log.debug(\"cgroup v1 detected\")\n cfs_quota_us = int(util_file.slurp_file(\"/sys/fs/cgroup/cpu/cpu.cfs_quota_us\"))\n cfs_period_us = int(util_file.slurp_file(\"/sys/fs/cgroup/cpu/cpu.cfs_period_us\"))\n\n log.debug('cfs_quota_us %s, cfs_period_us %s', cfs_quota_us, cfs_period_us)\n if cfs_quota_us > 0 and cfs_period_us > 0:\n cgroup_cpus = max(1, int(math.ceil(cfs_quota_us / cfs_period_us)))\n except Exception as e:\n pass\n\n proc_cpus = MAX_INT32\n try:\n m = re.search(r'(?m)^Cpus_allowed:\\s*(.*)$', util_file.slurp_file('/proc/self/status'))\n if m:\n res = bin(int(m.group(1).replace(',', ''), 16)).count('1')\n if res > 0:\n proc_cpus = res\n except IOError:\n pass\n\n min_cpu_count_reported = min(cgroup_cpus, proc_cpus, multiprocessing.cpu_count())\n log.debug('min(cgroup_cpus %d, proc_cpus %d, multiprocessing cpus %d) = %d',\n cgroup_cpus, proc_cpus, multiprocessing.cpu_count(), min_cpu_count_reported)\n return min_cpu_count_reported\n\ndef sanitize_thread_count(threads=None, tool_max_cores_value=available_cpu_count):\n ''' Given a user specified thread count, this function will:\n - ensure that 1 <= threads <= available_cpu_count()\n - interpret None values to mean max available cpus\n unless PYTEST_XDIST_WORKER_COUNT is defined as an environment\n variable, in which case we always return 1\n - allow for various, tool-specific ways of specifying\n max available cores (tool_max_value)\n tool_max_cores_value can be one of:\n available_cpu_count - this function will return available_cpu_count()\n any other value - this function will return that value.\n some commonly used values for tools are -1, 0, and None.\n '''\n if 'PYTEST_XDIST_WORKER_COUNT' in os.environ:\n threads = 1\n\n max_cores = available_cpu_count()\n\n if threads is None:\n threads = max_cores\n\n assert type(threads) == int\n\n if threads >= max_cores:\n if tool_max_cores_value == available_cpu_count:\n threads = max_cores\n else:\n threads = tool_max_cores_value\n else:\n if threads < 1:\n threads = 1\n return threads\n\ndef which(application_binary_name):\n \"\"\"\n Similar to the *nix \"which\" command,\n this function finds the first executable binary present\n in the system PATH for the binary specified.\n It differs in that it resolves symlinks.\n \"\"\"\n path=os.getenv('PATH')\n for path in path.split(os.path.pathsep):\n full_path=os.path.join(path, application_binary_name)\n if os.path.exists(full_path) and os.access(full_path, os.X_OK):\n link_resolved_path = os.path.realpath(full_path)\n return link_resolved_path\n\ndef is_nonstr_iterable(x, str_types=str):\n '''Tests whether `x` is an Iterable other than a string. `str_types` gives the type(s) to treat as strings.'''\n return isinstance(x, collections.abc.Iterable) and not isinstance(x, str_types)\n\ndef make_seq(x, str_types=str):\n '''Return a tuple containing the items in `x`, or containing just `x` if `x` is a non-string iterable. Convenient\n for uniformly writing iterations over parameters that may be passed in as either an item or a tuple/list of items.\n Note that if `x` is an iterator, it will be concretized. `str_types` gives the type(s) to treat as strings.'\n '''\n return tuple(x) if is_nonstr_iterable(x, str_types) else (x,)\n\ndef load_yaml_or_json(fname):\n '''Load a dictionary from either a yaml or a json file'''\n with open(fname) as f:\n if fname.upper().endswith('.YAML'): return yaml.safe_load(f) or {}\n if fname.upper().endswith('.JSON'): return json.load(f) or {}\n raise TypeError('Unsupported dict file format: ' + fname)\n\n\ndef load_config(cfg, include_directive='include', std_includes=(), param_renamings=None):\n '''Load a configuration, with support for some extra functionality that lets project configurations evolve\n without breaking backwards compatibility.\n\n The configuration `cfg` is either a dict (possibly including nested dicts) or a yaml/json file containing one.\n A configuration parameter or config param is a sequence of one or more keys; the value of the corresponding\n parameter is accessed as \"cfg[k1][k2]...[kN]\". Note, by \"parameter\" we denote the entire sequence of keys.\n\n This function implements extensions to the standard way of specifying configuration parameters via (possibly nested)\n dictionaries. These extensions make it easier to add or rename config params without breaking backwards\n compatibility.\n\n One extension lets config files include other config files, and lets you specify \"standard\" config file(s) to\n be included before all others. If the \"default\" config file from the project distribution is made a standard\n include, new parameters can be added to it (and referenced from project code) without breaking compatibility\n with old config files that omit these parameters.\n\n Another extension lets you, when loading a config file, recognize parameters specified under old or legacy names.\n This lets you change parameter names in new program versions while still accepting legacy config files that\n use older names.\n\n Args:\n cfg: either a config mapping, or the name of a file containing one (in yaml or json format).\n A config mapping is just a dict, possibly including nested dicts, specifying config params.\n The mapping can include an entry pointing to other config files to include.\n The key of the entry is `include_directive`, and the value is a filename or list of filenames of config files.\n Relative filenames are interpreted relative to the directory containing `cfg`, if `cfg` is a filename,\n else relative to the current directory. Any files from `std_includes` are prepended to the list of\n included config files. Parameter values from `cfg` override ones from any included files, and parameter values\n from included files listed later in the include list override parameter values from included files listed\n earlier.\n\n include_directive: key used to specify included config files\n std_includes: config file(s) implicitly included before all others and before `cfg`\n param_renamings: optional map of old/legacy config param names to new ones. 'Param names' here are\n either keys or sequences of keys. Example value: {'trinity_kmer_size': ('de_novo_assembly', 'kmer_size')};\n new code can access the parameter as cfg[\"de_novo_assembly\"][\"kmer_size\"] while legacy users can keep\n specifying it as \"trinity_kmer_size: 31\".\n '''\n\n param_renamings = param_renamings or {}\n\n result = dict()\n\n base_dir_for_includes = None\n if isinstance(cfg, str):\n cfg_fname = os.path.realpath(cfg)\n base_dir_for_includes = os.path.dirname(cfg_fname)\n cfg = load_yaml_or_json(cfg_fname)\n\n def _update_config(config, overwrite_config):\n \"\"\"Recursively update dictionary config with overwrite_config.\n\n Adapted from snakemake.utils.\n See\n http://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth\n for details.\n\n Args:\n config (dict): dictionary to update\n overwrite_config (dict): dictionary whose items will overwrite those in config\n\n \"\"\"\n\n def _update(d, u):\n def fix_None(v): return {} if v is None else v\n for (key, value) in u.items():\n if (isinstance(value, collections.abc.Mapping)):\n d[key] = _update(fix_None(d.get(key, {})), value)\n else:\n d[key] = fix_None(value)\n return d\n\n _update(config, overwrite_config)\n\n\n includes = make_seq(std_includes) + make_seq(cfg.get(include_directive, []))\n for included_cfg_fname in includes:\n if (not os.path.isabs(included_cfg_fname)) and base_dir_for_includes:\n included_cfg_fname = os.path.join(base_dir_for_includes, included_cfg_fname)\n _update_config(result, load_config(cfg=included_cfg_fname, \n include_directive=include_directive,\n param_renamings=param_renamings))\n\n # mappings in the current (top-level) config override any mappings from included configs\n _update_config(result, cfg)\n\n # load any params specified under legacy names, for backwards compatibility\n param_renamings_seq = dict(map(lambda kv: map(make_seq, kv), param_renamings.items()))\n\n for old_param, new_param in param_renamings_seq.items():\n\n # handle chains of param renamings\n while new_param in param_renamings_seq:\n new_param = param_renamings_seq[new_param]\n\n old_val = functools.reduce(lambda d, k: d.get(k, {}), old_param, result)\n new_val = functools.reduce(lambda d, k: d.get(k, {}), new_param, result)\n\n if old_val != {} and new_val == {}:\n _update_config(result, functools.reduce(lambda d, k: {k: d}, new_param[::-1], old_val))\n log.warning('Config param {} has been renamed to {}; old name accepted for now'.format(old_param, new_param))\n\n return result\n\ndef as_type(val, types):\n \"\"\"Try converting `val`to each of `types` in turn, returning the first one that succeeds.\"\"\"\n errs = []\n for type in make_seq(types):\n try:\n return type(val)\n except Exception as e:\n errs.append(e)\n pass\n raise TypeError('Could not convert {} to any of {}: {}'.format(val, types, errs))\n\ndef subdict(d, keys):\n \"\"\"Return a newly allocated shallow copy of a mapping `d` restricted to keys in `keys`.\"\"\"\n d = dict(d)\n keys = set(keys)\n return {k: v for k, v in d.items() if k in keys}\n\ndef chk(condition, message='Check failed', exc=RuntimeError):\n \"\"\"Check a condition, raise an exception if condition is False.\"\"\"\n if not condition:\n raise exc(message)\n\ndef wraps(f):\n \"\"\"Like functools.wraps but sets __wrapped__ even on Python 2.7\"\"\"\n wrapper = functools.wraps(f)\n wrapper.__wrapped__ = f\n return wrapper\n\ndef unwrap(f):\n \"\"\"Find the original function under layers of wrappers\"\"\"\n return f if not hasattr(f, '__wrapped__') else unwrap(f.__wrapped__)\n\ndef convert_size_str(input_size_str, output_unit=\"m\", round_number=True):\n \"\"\" intended to convert a jvm-style size spec to an int value of the desired unit \"\"\"\n unit2factor = {'k': 1024, 'm': 1024**2, 'g': 1024**3, 't': 1024**4}\n output_unit = output_unit.lower()\n\n size_spec_pattern = re.compile(r\"(.*)([kmgt])\")\n\n m = re.search(size_spec_pattern, input_size_str)\n if m:\n if m.group(1) and m.group(2):\n input_size=float(m.group(1))\n input_unit=m.group(2).lower()\n \n if input_unit not in unit2factor.keys():\n raise TypeError(\"Error parsing size from string: %s\" % input_size_str)\n\n # convert to bytes\n size_in_bytes = input_size * unit2factor[input_unit]\n\n # convert to desired size\n if round_number:\n return str(round(max(1,float(size_in_bytes)/unit2factor[output_unit])))+output_unit\n else:\n return str(float(size_in_bytes)/unit2factor[output_unit])+output_unit\n\n\n# =========== ReadIdStore =================\n\nclass ReadIdStore:\n \"\"\"\n SQLite-backed store for read IDs with O(1) memory footprint.\n\n Uses SQLite for disk-based storage with automatic deduplication via\n UNIQUE constraint. Supports random sampling for downsampling operations.\n \"\"\"\n\n def __init__(self, db_path):\n \"\"\"\n Initialize the read ID store.\n\n Args:\n db_path: Path to SQLite database file (typically in tmpdir)\n \"\"\"\n self.db_path = db_path\n self.conn = sqlite3.connect(db_path)\n # Performance pragmas (safe since db_path is in tmpdir)\n self.conn.execute('PRAGMA synchronous = OFF')\n self.conn.execute('PRAGMA journal_mode = OFF')\n self.conn.execute('PRAGMA cache_size = -64000') # 64MB cache (negative = KiB)\n self.conn.execute('PRAGMA temp_store = MEMORY')\n self.conn.execute('''\n CREATE TABLE IF NOT EXISTS read_ids (\n id INTEGER PRIMARY KEY AUTOINCREMENT,\n read_id TEXT UNIQUE NOT NULL\n )\n ''')\n self.conn.commit()\n\n def add_from_fastq(self, fastq_path):\n \"\"\"\n Extract read IDs from a FASTQ file and add to the store.\n\n Handles paired-end reads by stripping /1 or /2 suffixes.\n Duplicates are automatically ignored via INSERT OR IGNORE.\n\n Args:\n fastq_path: Path to FASTQ file (can be gzipped)\n\n Returns:\n Number of new read IDs added\n \"\"\"\n cursor = self.conn.cursor()\n count_before = len(self)\n\n with util_file.open_or_gzopen(fastq_path, 'rt') as inf:\n line_num = 0\n batch = []\n for line in inf:\n if (line_num % 4) == 0:\n idVal = line.rstrip('\\n')[1:]\n # Remove /1 or /2 suffix if present (paired-end reads)\n if idVal.endswith('/1') or idVal.endswith('/2'):\n idVal = idVal[:-2]\n batch.append((idVal,))\n\n # Batch inserts for performance\n if len(batch) >= 10000:\n cursor.executemany(\n 'INSERT OR IGNORE INTO read_ids (read_id) VALUES (?)',\n batch\n )\n batch = []\n line_num += 1\n\n # Insert remaining batch\n if batch:\n cursor.executemany(\n 'INSERT OR IGNORE INTO read_ids (read_id) VALUES (?)',\n batch\n )\n\n self.conn.commit()\n return len(self) - count_before\n\n def add_from_readlist(self, readlist_path):\n \"\"\"\n Add read IDs from a text file (one ID per line).\n\n Args:\n readlist_path: Path to text file with one read ID per line.\n Empty lines and whitespace are stripped.\n \"\"\"\n with util_file.open_or_gzopen(readlist_path, 'rt') as f:\n self.extend(line.strip() for line in f if line.strip())\n\n def __len__(self):\n \"\"\"Return the number of unique read IDs in the store.\"\"\"\n cursor = self.conn.execute('SELECT COUNT(*) FROM read_ids')\n return cursor.fetchone()[0]\n\n def __iter__(self):\n \"\"\"Iterate over all read IDs in insertion order. O(1) memory.\"\"\"\n cursor = self.conn.execute('SELECT read_id FROM read_ids ORDER BY id')\n for row in cursor:\n yield row[0]\n\n def __contains__(self, read_id):\n \"\"\"Check if a read ID exists in the store.\"\"\"\n cursor = self.conn.execute(\n 'SELECT 1 FROM read_ids WHERE read_id = ? LIMIT 1',\n (read_id,)\n )\n return cursor.fetchone() is not None\n\n def contains_batch(self, read_ids, batch_size=10000):\n \"\"\"\n Check multiple read IDs for membership in batched queries.\n\n Args:\n read_ids: List of read ID strings to check\n batch_size: Number of IDs to query at once (default 10000)\n\n Returns:\n Set of read IDs that exist in the store\n \"\"\"\n found = set()\n batch = []\n for read_id in read_ids:\n batch.append(read_id)\n if len(batch) >= batch_size:\n placeholders = ','.join('?' * len(batch))\n cursor = self.conn.execute(\n f'SELECT read_id FROM read_ids WHERE read_id IN ({placeholders})',\n batch\n )\n found.update(row[0] for row in cursor)\n batch = []\n if batch:\n placeholders = ','.join('?' * len(batch))\n cursor = self.conn.execute(\n f'SELECT read_id FROM read_ids WHERE read_id IN ({placeholders})',\n batch\n )\n found.update(row[0] for row in cursor)\n return found\n\n def add(self, read_id):\n \"\"\"\n Add a single read ID to the store.\n\n Args:\n read_id: The read ID string to add\n\n Returns:\n True if the read ID was added, False if it already existed\n \"\"\"\n cursor = self.conn.execute(\n 'INSERT OR IGNORE INTO read_ids (read_id) VALUES (?)',\n (read_id,)\n )\n self.conn.commit()\n return cursor.rowcount > 0\n\n def extend(self, read_ids):\n \"\"\"\n Add multiple read IDs to the store efficiently.\n\n Uses executemany for batch insertion. O(1) memory - processes\n the input iterable in chunks.\n\n Args:\n read_ids: Iterable of read ID strings\n\n Returns:\n Number of new read IDs added\n \"\"\"\n count_before = len(self)\n cursor = self.conn.cursor()\n\n # Process in batches for memory efficiency\n batch = []\n for read_id in read_ids:\n batch.append((read_id,))\n if len(batch) >= 10000:\n cursor.executemany(\n 'INSERT OR IGNORE INTO read_ids (read_id) VALUES (?)',\n batch\n )\n batch = []\n\n # Insert remaining batch\n if batch:\n cursor.executemany(\n 'INSERT OR IGNORE INTO read_ids (read_id) VALUES (?)',\n batch\n )\n\n self.conn.commit()\n return len(self) - count_before\n\n def __delitem__(self, read_id):\n \"\"\"\n Delete a read ID from the store.\n\n Args:\n read_id: The read ID string to delete\n\n Raises:\n KeyError: If the read ID does not exist\n \"\"\"\n cursor = self.conn.execute(\n 'DELETE FROM read_ids WHERE read_id = ?',\n (read_id,)\n )\n self.conn.commit()\n if cursor.rowcount == 0:\n raise KeyError(read_id)\n\n def discard(self, read_id):\n \"\"\"\n Remove a read ID if it exists, without raising an error if absent.\n\n Args:\n read_id: The read ID string to remove\n \"\"\"\n self.conn.execute(\n 'DELETE FROM read_ids WHERE read_id = ?',\n (read_id,)\n )\n self.conn.commit()\n\n def write_to_file(self, out_path, max_reads=None):\n \"\"\"\n Write read IDs to a file.\n\n Args:\n out_path: Output file path\n max_reads: If specified, randomly sample this many read IDs\n\n Returns:\n Number of read IDs written\n \"\"\"\n if max_reads is not None and max_reads < len(self):\n # Random sampling using ORDER BY RANDOM()\n query = 'SELECT read_id FROM read_ids ORDER BY RANDOM() LIMIT ?'\n cursor = self.conn.execute(query, (max_reads,))\n else:\n # Return all in insertion order\n query = 'SELECT read_id FROM read_ids ORDER BY id'\n cursor = self.conn.execute(query)\n\n count = 0\n with open(out_path, 'wt') as outf:\n for row in cursor:\n outf.write(row[0] + '\\n')\n count += 1\n\n return count\n\n def shrink_to_subsample(self, n):\n \"\"\"\n Destructively shrink the store to a random subsample of n elements.\n\n This modifies the store in-place, keeping exactly n randomly selected\n read IDs and deleting all others. If the store has n or fewer elements,\n no changes are made.\n\n Args:\n n: Number of read IDs to keep\n\n Note:\n Uses SQLite's ORDER BY RANDOM() for random selection. The operation\n is O(N log N) where N is the current store size due to random sorting.\n \"\"\"\n current_size = len(self)\n if current_size <= n:\n return # Nothing to do\n\n # Delete all rows except n randomly selected ones\n self.conn.execute('''\n DELETE FROM read_ids\n WHERE id NOT IN (\n SELECT id FROM read_ids\n ORDER BY RANDOM()\n LIMIT ?\n )\n ''', (n,))\n self.conn.commit()\n\n def filter_bam_by_ids(self, inBam, outBam, include=True):\n \"\"\"\n Filter a BAM file to reads matching (or not matching) IDs in this store.\n\n This is a faster, O(1) memory replacement for picard.FilterSamReadsTool.\n Headers are fully preserved from input to output.\n\n Args:\n inBam: Input BAM file path\n outBam: Output BAM file path\n include: If True, keep only reads with IDs in the store (inclusion list).\n If False, keep only reads with IDs NOT in the store (exclusion list).\n\n Note:\n For paired-end reads, both mates share the same QNAME so both will be\n kept or excluded together based on whether the QNAME is in the store.\n \"\"\"\n # Lazy import to avoid circular dependency\n from . import samtools as samtools_module\n\n # Handle empty input BAM\n samtools_tool = samtools_module.SamtoolsTool()\n if samtools_tool.isEmpty(inBam):\n shutil.copyfile(inBam, outBam)\n return\n\n # Handle empty read ID store\n if len(self) == 0:\n if include:\n # Include mode with empty list = empty output (keep header only)\n with pysam.AlignmentFile(inBam, 'rb', check_sq=False) as inb:\n with pysam.AlignmentFile(outBam, 'wb', header=inb.header) as outf:\n pass # Write header only, no reads\n else:\n # Exclude mode with empty list = keep all reads\n shutil.copyfile(inBam, outBam)\n return\n\n # Hybrid approach: samtools subprocess pipes + batched SQLite queries\n start = time.time()\n read_count = 0\n write_count = 0\n lookup_time = 0.0\n batch_size = 50000\n\n samtools_path = samtools_tool.install_and_get_path()\n\n # Read: samtools view -h --no-PG input.bam -> SAM text (with header, no PG added)\n # Write: samtools view -b --no-PG -o output.bam - (converts SAM to BAM, no PG added)\n read_proc = subprocess.Popen(\n [samtools_path, 'view', '-h', '--no-PG', inBam],\n stdout=subprocess.PIPE)\n write_proc = subprocess.Popen(\n [samtools_path, 'view', '-b', '-@', '2', '--no-PG', '-o', outBam, '-'],\n stdin=subprocess.PIPE)\n\n try:\n batch = [] # [(line, qname), ...]\n for line in read_proc.stdout:\n # Header lines (start with @) are passed through unchanged\n if line.startswith(b'@'):\n write_proc.stdin.write(line)\n continue\n\n read_count += 1\n\n # Parse only QNAME (first field before tab)\n tab_pos = line.find(b'\\t')\n qname = line[:tab_pos].decode()\n batch.append((line, qname))\n\n if len(batch) >= batch_size:\n t0 = time.time()\n found = self.contains_batch([q for _, q in batch])\n lookup_time += time.time() - t0\n\n for ln, q in batch:\n if (include and q in found) or (not include and q not in found):\n write_proc.stdin.write(ln)\n write_count += 1\n batch = []\n\n # Process remaining batch\n if batch:\n t0 = time.time()\n found = self.contains_batch([q for _, q in batch])\n lookup_time += time.time() - t0\n\n for ln, q in batch:\n if (include and q in found) or (not include and q not in found):\n write_proc.stdin.write(ln)\n write_count += 1\n finally:\n write_proc.stdin.close()\n write_proc.wait()\n read_proc.wait()\n\n elapsed = time.time() - start\n log.debug(f\"PERF: filter_time={elapsed:.2f}s lookup_time={lookup_time:.2f}s \"\n f\"reads={read_count} written={write_count} batch_size={batch_size}\")\n\n def close(self):\n \"\"\"Close the database connection.\"\"\"\n self.conn.close()\n\n def __enter__(self):\n return self\n\n def __exit__(self, exc_type, exc_val, exc_tb):\n self.close()\n return False\n\n\n# =========== CoordMapper =================\n\nclass CoordMapperError(Exception):\n def __init___(self, *args, **kwargs):\n super(CoordMapperError, self).__init__(self, *args, **kwargs)\n\n\nclass CoordMapper(collections.abc.MutableMapping):\n \"\"\" Map (chrom, coordinate) between genome A and genome B.\n Coordinates are 1-based.\n Indels are handled as follows after corresponding sequences are aligned:\n Return (chrom, None) if base is past either end of other sequence.\n If a base maps to a gap in the other species, return the index\n of the closest upstream non-gap base.\n If a base is followed by a gap then instead of returning an integer,\n return a two-element list representing the interval in the\n other species that aligns to this base and the subsequent gap.\n Assumption: the aligner tool will never align two gaps, and will never\n put gaps in opposite species adjacent to each other without aligning\n a pair of real bases in between.\n \"\"\"\n\n def __init__(self, alignerTool=None):\n \"\"\" The two genomes are described by fasta files with the same number of\n chromosomes, and corresponding chromosomes must be in same order.\n\n Args:\n alignerTool: Aligner tool class (e.g., muscle.MuscleTool).\n If None, defaults to muscle.MuscleTool (lazy import).\n \"\"\"\n from collections import OrderedDict\n\n # {\n # chrA : {chrB: mapperAB, chrC: mapperAC},\n # chrB : {chrA: mapperBA, chrC: mapperBC},\n # chrC : {chrA: mapperCA, chrB: mapperCB}\n # }\n self.chrMaps = OrderedDict()\n self.chrMapsUngapped = OrderedDict()\n\n if alignerTool is None:\n # Lazy import to avoid circular dependency\n from ..phylo import muscle\n alignerTool = muscle.MuscleTool\n self.alignerTool = alignerTool()\n\n def __getitem__(self, key):\n return self.chrMaps[key]\n\n def __setitem__(self, key, value):\n raise TypeError(\"'%s' object does not support item assignment\" % self.__class__.__name__)\n\n def __delitem__(self, key):\n raise TypeError(\"'%s' object does not support item deletion\" % self.__class__.__name__)\n\n def __len__(self):\n return len(self.chrMaps)\n\n def __iter__(self):\n for i in self.chrMaps:\n yield i\n\n def __contains__(self, key):\n if key in self.chrMaps:\n return True\n else:\n return False\n\n def keys(self):\n return self.chrMaps.keys()\n\n def mapAtoB(self, fromChrom, fromPos=None, side=0):\n \"\"\" Map (chrom, coordinate) from genome A to genome B.\n If fromPos is None, map only the chromosome name\n If side is:\n < 0, return the left-most position on B\n ==0, return either the unique position on B or a [left,right] list\n > 0, return the right-most position on B\n \"\"\"\n if len(self.chrMaps.keys()) != 4:\n raise LookupError(\n \"CoordMapper.mapAtoB expects two input sequences and is provided only as a legacy function\")\n\n return self.mapChr(fromChrom, list(self.chrMaps[fromChrom].keys())[0], fromPos, side)\n\n def mapBtoA(self, fromChrom, fromPos=None, side=0):\n \"\"\" Map (chrom, coordinate) from genome B to genome A.\n If fromPos is None, map only the chromosome name\n If side is:\n < 0, return the left-most position on A\n ==0, return either the unique position on A or a [left,right] list\n > 0, return the right-most position on A\n \"\"\"\n if len(self.chrMaps.keys()) != 4:\n raise LookupError(\n \"CoordMapper.mapBtoA expects two input sequences and is provided only as a legacy function\")\n\n return self.mapChr(fromChrom, list(self.chrMaps[fromChrom].keys())[0], fromPos, side)\n\n def mapChr(self, fromChrom, toChrom, fromPos=None, side=0):\n \"\"\" Map (chrom, coordinate) from seq \"fromChrom\" to seq \"toChrom\".\n If fromPos is None, map only the chromosome name\n If side is:\n < 0, return the left-most position on A\n ==0, return either the unique position on A or a [left,right] list\n > 0, return the right-most position on A\n \"\"\"\n\n if fromChrom not in self.chrMaps:\n raise KeyError(\"chr '%s' not found in CoordMapper relation map\" % fromChrom)\n if toChrom not in self.chrMaps[fromChrom].keys():\n raise KeyError(\"chr '%s' not found in CoordMapper relation map\" % toChrom)\n\n mapper = self.chrMaps[fromChrom][toChrom]\n\n if fromPos is None:\n return toChrom\n toPos = mapper(fromPos, 0)\n if isinstance(toPos, collections.abc.Sequence) and side != 0:\n toPos = toPos[0] if side < 0 else toPos[1]\n return (toChrom, toPos)\n\n def load_alignments(self, aligned_files, a_idx=None, b_idx=None):\n \"\"\" Loads aligned sequences into a CoordMapper instance.\n Any number of sequences >1 may be read in.\n Mappers may be accessed via CoordMapper.chrMaps where chrMaps may look like:\n ```\n {\n chrA : {chrB: mapperAB, chrC: mapperAC},\n chrB : {chrA: mapperBA, chrC: mapperBC},\n chrC : {chrA: mapperCA, chrB: mapperCB}\n }\n ```\n \"\"\"\n from collections import OrderedDict\n\n for alignOutFileName in aligned_files:\n with open(alignOutFileName, 'rt') as alignOutFile:\n seqs = list(Bio.SeqIO.parse(alignOutFile, 'fasta'))\n\n # if mapping between specific sequences is specified\n if a_idx is not None and b_idx is not None:\n assert a_idx >= 0 and b_idx >= 0\n assert a_idx < len(seqs) and b_idx < len(seqs)\n\n mapper = CoordMapper2Seqs(seqs[a_idx].seq, seqs[b_idx].seq)\n self.chrMaps.setdefault(seqs[a_idx].id, OrderedDict())\n mapDict = OrderedDict()\n mapDict[seqs[b_idx].id] = mapper\n self.chrMaps[seqs[a_idx].id] = mapDict\n\n mapper = CoordMapper2Seqs(seqs[b_idx].seq, seqs[a_idx].seq)\n self.chrMaps.setdefault(seqs[b_idx].id, OrderedDict())\n mapDict = OrderedDict()\n mapDict[seqs[a_idx].id] = mapper\n self.chrMaps[seqs[b_idx].id] = mapDict\n # otherwise, map all possible pairwise itertools.permutations\n else:\n for (seq1, seq2) in itertools.permutations(seqs, 2):\n if (seq1.id == seq2.id):\n raise KeyError(\"duplicate sequence names '%s', '%s'\" % (seq1.id, seq2.id))\n\n self.chrMaps.setdefault(seq1.id, OrderedDict())\n self.chrMapsUngapped.setdefault(seq1.id, OrderedDict())\n # if the sequence we are mapping onto is already in the map\n # raise an error\n # (could occur if same sequence is read in from multiple files)\n if (seq2.id in self.chrMaps[seq1.id]):\n raise KeyError(\n \"duplicate sequence name '%s' already in chrMap for %s\" % (seq2.id, seq1.id))\n\n mapper = CoordMapper2Seqs(seq1.seq, seq2.seq)\n mapDict = self.chrMaps[seq1.id]\n mapDict[seq2.id] = mapper\n self.chrMaps[seq1.id] = mapDict\n\n def align_and_load_sequences(self, unaligned_fasta_files, aligner=None):\n aligner = self.alignerTool if aligner is None else aligner\n\n # transpose\n per_chr_fastas = util_file.transposeChromosomeFiles(unaligned_fasta_files)\n if not per_chr_fastas:\n raise Exception('no input sequences')\n # align\n alignOutFileNames = []\n for alignInFileName in per_chr_fastas:\n alignOutFileName = util_file.mkstempfname('.fasta')\n aligner.execute(alignInFileName, alignOutFileName)\n alignOutFileNames.append(alignOutFileName)\n os.unlink(alignInFileName)\n # read in\n self.load_alignments(alignOutFileNames)\n # clean up\n for f in alignOutFileNames:\n os.unlink(f)\n\n\nclass CoordMapper2Seqs(object):\n \"\"\" Map 1-based coordinates between two aligned sequences.\n Result is a coordinate or an interval, as described in CoordMapper main\n comment string.\n Return None if beyond end.\n Input sequences must be already-aligned iterators through bases with\n gaps represented by dashes and all other characters assumed to be\n real bases.\n Assumptions:\n - Sequences (including gaps) are same length.\n - Each sequence has at least one real base.\n - A gap is never aligned to a gap.\n - A gap in one sequence is never adjacent to a gap in the other;\n there must always be an intervening real base between two gaps.\n \"\"\"\n #\n # Implementation:\n # mapArrays is a pair of arrays of equal length such that\n # (mapArrays[0][n], mapArrays[1][n]) are the coordinates of a pair of\n # aligned real bases on the two sequences. The only pairs that are\n # included are the first, the last, and the pair immediately following\n # any gap. Pairs are in increasing order. Coordinate mapping\n # requires binary search in one of the arrays.\n # Total space required, in bytes, is const + 8 * (number of indels).\n # Time for a map in either direction is O(log(number of indels)).\n #\n\n def __init__(self, seq0, seq1):\n self.mapArrays = [array.array('I'), array.array('I')]\n baseCount0 = 0 # Number of real bases in seq0 up to and including cur pos\n baseCount1 = 0 # Number of real bases in seq1 up to and including cur pos\n beforeStart = True # Haven't yet reached first pair of aligned real bases\n gapSinceLast = False # Have encounted a gap since last pair in mapArrays\n for b0, b1 in itertools.zip_longest(seq0, seq1):\n if b0 is None or b1 is None:\n raise Exception('CoordMapper2Seqs: sequences must be same length.')\n realBase0 = b0 != '-'\n realBase1 = b1 != '-'\n baseCount0 += realBase0\n baseCount1 += realBase1\n if realBase0 and realBase1:\n if beforeStart or gapSinceLast:\n self.mapArrays[0].append(baseCount0)\n self.mapArrays[1].append(baseCount1)\n gapSinceLast = False\n beforeStart = False\n finalPos0 = baseCount0 # Last pair of aligned real bases so far\n finalPos1 = baseCount1 # Last pair of aligned real bases so far\n else:\n gapSinceLast = True\n if len(self.mapArrays[0]) > 0:\n if self.mapArrays[0][-1] != finalPos0:\n self.mapArrays[0].append(finalPos0)\n self.mapArrays[1].append(finalPos1)\n\n def __call__(self, fromPos, fromWhich):\n \"\"\" fromPos: 1-based coordinate\n fromWhich: if 0, map from 1st sequence to 2nd, o.w. 2nd to 1st.\"\"\"\n if len(self.mapArrays[0]) == 0:\n raise Exception('CoordMapper2Seqs: no aligned bases.')\n if fromPos != int(fromPos):\n raise TypeError('CoordMapper2Seqs: pos %s is not an integer' % fromPos)\n fromArray = self.mapArrays[fromWhich]\n toArray = self.mapArrays[1 - fromWhich]\n if fromPos < fromArray[0] or fromPos > fromArray[-1]:\n result = None\n elif fromPos == fromArray[-1]:\n result = toArray[-1]\n else:\n insertInd = bisect.bisect(fromArray, fromPos)\n prevFromPos = fromArray[insertInd - 1]\n nextFromPos = fromArray[insertInd]\n prevToPos = toArray[insertInd - 1]\n nextToPos = toArray[insertInd]\n assert (prevFromPos <= fromPos < nextFromPos)\n prevPlusOffset = prevToPos + (fromPos - prevFromPos)\n if fromPos == nextFromPos - 1 and prevPlusOffset < nextToPos - 1:\n result = [prevPlusOffset, nextToPos - 1]\n else:\n result = min(prevPlusOffset, nextToPos - 1)\n return result\n" }, { "path": "src/viral_ngs/core/mvicuna.py", "content": "\"Tool for mvicuna.\"\n\nimport logging\nimport os\nimport subprocess\nimport shutil\n\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = \"mvicuna\"\n\n_log = logging.getLogger(__name__)\n\n\nclass MvicunaTool(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME))]\n Tool.__init__(self, install_methods=install_methods)\n\n def rmdup(self, inPair, outPair, outUnpaired=None):\n \"\"\"\n Run mvicuna's duplicate removal operation on paired-end input reads in\n fastq format, producing various outputs in fastq format.\n inPair, pairedOutPair are pairs of file names,\n while unpairedOut is a single file name.\n Notes on weird behaviors of M-Vicuna DupRm:\n For some reason, it requires you to specify both -opfq and -drm_op.\n The -drm_op pair (here, tmp1OutPair) is where the output is initially written.\n Then M-Vicuna renames the -drm_op files to the -opfq filenames (here, tmp2OutPair).\n So obviously, we use throwaway (tempfile) names for -drm_op and use the real\n desired output file names in -opfq.\n The problem is that M-Vicuna uses a rename/move operating system function, which\n means your tempfiles cannot be on a different file system than the final output\n files. This is our typical use case (local disks for tempfile.tempdir and\n network file systems for final output). Hence, our wrapper sets -opfq to yet\n another set of temp file names, and we move the final output files ourselves\n using shutil.move (which is capable of crossing file system boundaries).\n \"\"\"\n if not outUnpaired:\n outUnpaired = util_file.mkstempfname(suffix='.unpaired.fastq')\n tmp1OutPair = (\n util_file.mkstempfname(suffix='.tmp1out.1.fastq'), util_file.mkstempfname(suffix='.tmp1out.2.fastq')\n )\n tmp2OutPair = (\n util_file.mkstempfname(suffix='.tmp2out.1.fastq'), util_file.mkstempfname(suffix='.tmp2out.2.fastq')\n )\n cmdline = [\n self.install_and_get_path(), '-ipfq', ','.join(inPair), '-opfq', ','.join(tmp2OutPair), '-osfq',\n outUnpaired, '-drm_op', ','.join(tmp1OutPair), '-tasks', 'DupRm'\n ]\n _log.debug(' '.join(cmdline))\n subprocess.check_call(cmdline)\n for tmpfname, outfname in zip(tmp2OutPair, outPair):\n shutil.copyfile(tmpfname, outfname)\n\n def rmdup_single(self, inFastq, outFastq):\n \"\"\"\n Run mvicuna's duplicate removal operation on single-end input reads in\n fastq format, producing output in fastq format.\n Notes on weird behaviors of M-Vicuna DupRm:\n For some reason, it requires you to specify both -opfq and -drm_op even for\n single-end input.\n\n Actually, more interestingly, this doesn't work at all.\n \"\"\"\n _log.warning(\"MVicuna duplicate removal doesn't work for single-end reads. Copying input to output and allowing all reads to pass.\")\n shutil.copyfile(inFastq, outFastq)\n '''\n tmp1OutPair = (\n util_file.mkstempfname(suffix='.tmp1out.1.fastq'), util_file.mkstempfname(suffix='.tmp1out.2.fastq')\n )\n tmp2OutPair = (\n util_file.mkstempfname(suffix='.tmp2out.1.fastq'), util_file.mkstempfname(suffix='.tmp2out.2.fastq')\n )\n cmdline = [\n self.install_and_get_path(), '-isfq', inFastq, '-osfq', outFastq,\n '-opfq', ','.join(tmp2OutPair), '-drm_op', ','.join(tmp1OutPair),\n '-tasks', 'DupRm'\n ]\n _log.debug(' '.join(cmdline))\n subprocess.check_call(cmdline)\n '''\n" }, { "path": "src/viral_ngs/core/novoalign.py", "content": "'''\n Novoalign aligner by Novocraft\n\n This is commercial software that has different licenses depending\n on use cases. As such, we do not have an auto-downloader. The user\n must have Novoalign pre-installed on their own and available\n either in $PATH or $NOVOALIGN_PATH.\n'''\n\nimport logging\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport stat\nimport sys\n\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom .errors import *\nfrom . import Tool, PrexistingUnixCommand\n\n_log = logging.getLogger(__name__)\n\nTOOL_NAME = \"novoalign\"\n\nclass NovoalignTool(Tool):\n\n def __init__(self, path=None, license_path=None):\n self.tool_version = None\n install_methods = []\n for novopath in [path, os.environ.get('NOVOALIGN_PATH')]:\n if novopath is not None:\n install_methods.append(\n PrexistingUnixCommand(\n os.path.join(novopath, TOOL_NAME),\n require_executability=True\n )\n )\n install_methods.append(PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True))\n\n post_verify_command = None\n for novo_license_path in [license_path, os.environ.get(\"NOVOALIGN_LICENSE_PATH\"), '']:\n if novo_license_path is not None and os.path.isfile(novo_license_path):\n # called relative to the conda bin/ directory\n uname = os.uname()\n # we ideally want the \"update\" copy operation\n # but only GNU cp has it. On OSX, the license will be copied each time.\n if uname[0] == 'Darwin':\n copy_operation = ''\n else:\n copy_operation = '-u'\n\n post_verify_command = \"cp {copy_operation} {lic_path} ./\".format(copy_operation=copy_operation, lic_path=novo_license_path)\n break # if we've found a license file, stop looking\n\n #install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, post_verify_command=post_verify_command))\n Tool.__init__(self, install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-V']).decode('UTF-8').strip().split()[1]\n\n def _fasta_to_idx_name(self, fasta):\n if not fasta.endswith('.fasta'):\n raise ValueError('input file %s must end with .fasta' % fasta)\n return fasta[:-6] + '.nix'\n\n def execute(self, inBam, refFasta, outBam, options=None, min_qual=0, JVMmemory=None): # pylint: disable=W0221\n ''' Execute Novoalign on BAM inputs and outputs.\n If the BAM contains multiple read groups, break up\n the input and perform Novoalign separately on each one\n (because Novoalign mangles read groups).\n Use Picard to sort and index the output BAM.\n If min_qual>0, use Samtools to filter on mapping quality.\n '''\n options = options or [\"-r\", \"Random\"]\n\n samtools_tool = samtools.SamtoolsTool()\n\n # fetch list of RGs\n rgs = samtools_tool.getReadGroups(inBam)\n\n rgs_list = list(samtools_tool.getReadGroups(inBam).keys())\n if len(rgs) == 0:\n # Can't do this\n raise InvalidBamHeaderError(\"{} lacks read groups\".format(inBam))\n\n elif len(rgs) == 1:\n # Only one RG, keep it simple\n self.align_one_rg_bam(inBam, refFasta, outBam, rgs=rgs, options=options, min_qual=min_qual, JVMmemory=JVMmemory)\n\n else:\n # Multiple RGs, align one at a time and merge\n align_bams = []\n for rg in rgs:\n tmp_bam = util_file.mkstempfname('.{}.bam'.format(rg))\n self.align_one_rg_bam(\n inBam,\n refFasta,\n tmp_bam,\n rgid=rg,\n rgs=rgs,\n options=options,\n min_qual=min_qual,\n JVMmemory=JVMmemory\n )\n if os.path.getsize(tmp_bam) > 0:\n align_bams.append(tmp_bam)\n\n # Merge BAMs, sort, and index\n picard.MergeSamFilesTool().execute(\n align_bams,\n outBam,\n picardOptions=['SORT_ORDER=coordinate', 'USE_THREADING=true', 'CREATE_INDEX=true'],\n JVMmemory=JVMmemory\n )\n for bam in align_bams:\n os.unlink(bam)\n\n def align_one_rg_bam(self, inBam, refFasta, outBam, rgid=None, rgs=None, options=None, min_qual=0, JVMmemory=None):\n ''' Execute Novoalign on BAM inputs and outputs.\n Requires that only one RG exists (will error otherwise).\n Use Picard to sort and index the output BAM.\n If min_qual>0, use Samtools to filter on mapping quality.\n '''\n options = options or [\"-r\", \"Random\"]\n\n samtools_tool = samtools.SamtoolsTool()\n\n # Require exactly one RG\n rgs = rgs if rgs is not None else samtools_tool.getReadGroups(inBam)\n if len(rgs) == 0:\n raise InvalidBamHeaderError(\"{} lacks read groups\".format(inBam))\n elif len(rgs) == 1:\n if not rgid:\n rgid = list(rgs.keys())[0]\n elif not rgid:\n raise InvalidBamHeaderError(\"{} has {} read groups, but we require exactly one\".format(inBam, len(rgs)))\n if rgid not in rgs:\n raise InvalidBamHeaderError(\"{} has read groups, but not {}\".format(inBam, rgid))\n #rg = rgs[rgid]\n\n # Strip inBam to just one RG (if necessary)\n if len(rgs) == 1:\n one_rg_inBam = inBam\n else:\n # strip inBam to one read group\n tmp_bam = util_file.mkstempfname('.onebam.bam')\n samtools_tool.view(['-b', '-r', rgid], inBam, tmp_bam)\n # special exit if this file is empty\n if samtools_tool.count(tmp_bam) == 0:\n return\n\n # simplify BAM header otherwise Novoalign gets confused\n one_rg_inBam = util_file.mkstempfname('.{}.in.bam'.format(rgid))\n headerFile = util_file.mkstempfname('.{}.header.txt'.format(rgid))\n with open(headerFile, 'wt') as outf:\n for row in samtools_tool.getHeader(inBam):\n if len(row) > 0 and row[0] == '@RG':\n if rgid != list(x[3:] for x in row if x.startswith('ID:'))[0]:\n # skip all read groups that are not rgid\n continue\n outf.write('\\t'.join(row) + '\\n')\n samtools_tool.reheader(tmp_bam, headerFile, one_rg_inBam)\n os.unlink(tmp_bam)\n os.unlink(headerFile)\n\n # Novoalign\n _log.info(\"novoalign on {} ({}B), read group {}\".format(one_rg_inBam, os.path.getsize(one_rg_inBam), rgid))\n tmp_sam = util_file.mkstempfname('.novoalign.sam')\n cmd = [self.install_and_get_path(), '-f', one_rg_inBam] + list(map(str, options))\n cmd = cmd + ['-F', 'BAM', '-d', self._fasta_to_idx_name(refFasta), '-o', 'SAM']\n _log.debug(' '.join(cmd))\n with open(tmp_sam, 'wt') as outf:\n util_misc.run_and_save(cmd, outf=outf)\n\n # Samtools filter (optional)\n if min_qual:\n tmp_bam2 = util_file.mkstempfname('.filtered.bam')\n samtools_tool.view(['-b', '-S', '-1', '-q', str(min_qual)], tmp_sam, tmp_bam2)\n os.unlink(tmp_sam)\n tmp_sam = tmp_bam2\n\n # Picard SortSam\n sorter = picard.SortSamTool()\n sorter.execute(\n tmp_sam,\n outBam,\n sort_order='coordinate',\n picardOptions=['CREATE_INDEX=true', 'VALIDATION_STRINGENCY=SILENT'],\n JVMmemory=JVMmemory\n )\n\n def index_fasta(self, refFasta, k=None, s=None):\n ''' Index a FASTA file (reference genome) for use with Novoalign.\n The input file name must end in \".fasta\". This will create a\n new \".nix\" file in the same directory. If it already exists,\n it will be deleted and regenerated.\n '''\n novoindex = os.path.join(os.path.dirname(self.install_and_get_path()), 'novoindex')\n outfname = self._fasta_to_idx_name(refFasta)\n if os.path.isfile(outfname):\n os.unlink(outfname)\n cmd = [novoindex]\n if k is not None:\n cmd.extend(['-k', str(k)])\n if s is not None:\n cmd.extend(['-s', str(s)])\n cmd.extend([outfname, refFasta])\n _log.debug(' '.join(cmd))\n subprocess.check_call(cmd)\n try:\n mode = os.stat(outfname).st_mode & ~stat.S_IXUSR & ~stat.S_IXGRP & ~stat.S_IXOTH\n os.chmod(outfname, mode)\n except (IOError, OSError):\n _log.warning('could not chmod \"%s\", this is likely OK', refFasta)\n" }, { "path": "src/viral_ngs/core/picard.py", "content": "'''\n Tools in the Picard suite\n'''\n\nimport logging\nimport os\nimport os.path\nimport tempfile\nimport shutil\nimport subprocess\nimport contextlib\nfrom decimal import *\n\nimport pysam\n\nfrom . import samtools # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool\n\nTOOL_NAME = \"picard\"\n\n_log = logging.getLogger(__name__)\n\n\nclass PicardTools(Tool):\n \"\"\"Base class for tools in the picard suite.\"\"\"\n jvmMemDefault = '2g'\n\n def is_installed(self):\n return True\n\n def __init__(self, install_methods=None):\n self.subtool_name = self.subtool_name if hasattr(self, \"subtool_name\") else None\n self.installed_method = True\n self.exec_path = shutil.which(TOOL_NAME)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.exec_path, 'BamIndexStats', '--version']).decode('UTF-8').rstrip()\n\n def execute(self, command, picardOptions=None, JVMmemory=None, background=False, **kwargs): # pylint: disable=W0221\n picardOptions = picardOptions or []\n\n if JVMmemory is None:\n JVMmemory = self.jvmMemDefault\n\n # the conda version wraps the jar file with a shell script\n path = self.install_and_get_path()\n tool_cmd = [path, '-Xmx' + JVMmemory, '-Djava.io.tmpdir=' + tempfile.gettempdir(), command] + picardOptions # + ['USE_JDK_DEFLATER=true','USE_JDK_INFLATER=true']\n _log.debug(' '.join(tool_cmd))\n\n env = os.environ.copy()\n env.pop('JAVA_HOME', None)\n if background:\n return subprocess.Popen(tool_cmd, env=env, **kwargs)\n else:\n return subprocess.check_call(tool_cmd, env=env, **kwargs)\n\n @staticmethod\n def dict_to_picard_opts(options):\n return [\"%s=%s\" % (k, v) for k, v in options.items()]\n\n\nclass RevertSamTool(PicardTools):\n subtoolName = 'RevertSam'\n\n def execute(self, inBam, outBam, picardOptions=None, JVMmemory=None, background=False): # pylint: disable=W0221\n if samtools.SamtoolsTool().isEmpty(inBam):\n shutil.copyfile(inBam, outBam)\n else:\n picardOptions = picardOptions or []\n opts = ['INPUT=' + inBam, 'OUTPUT=' + outBam]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory, background=background)\n\n\nclass CheckIlluminaDirectoryTool(PicardTools):\n subtoolName = 'CheckIlluminaDirectory'\n\n def execute(self, \n basecalls_dir, \n lanes, \n read_structure, \n data_types = None, \n fake_files = False, \n tile_numbers = None, \n link_locs = False, \n picardOptions = None, \n JVMmemory = None): # pylint: disable=W0221\n picardOptions = picardOptions or []\n opts = [\n 'BASECALLS_DIR=' + basecalls_dir,\n 'READ_STRUCTURE=' + read_structure\n ]\n\n if fake_files:\n opts += ['FAKE_FILES=true']\n\n if tile_numbers is not None:\n if type(tile_numbers)==int:\n tile_numbers = [tile_numbers]\n for tile_number in set(tile_numbers):\n opts += ['TILE_NUMBERS=' + str(tile_number)]\n\n if data_types is not None:\n if isinstance(arg, str):\n data_types = [data_types]\n for data_type in set(data_types):\n opts += ['DATA_TYPES=' + data_type]\n\n # if lanes is a single int, cast it to a list\n if type(lanes)==int:\n lanes = [lanes]\n\n assert type(lanes)==list, \"Lanes must be a list specifying the lanes\"\n for lane in set(lanes):\n opts += ['LANES=' + str(lane)]\n\n if link_locs:\n opts += ['LINK_LOCS=true']\n\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\nclass MarkDuplicatesTool(PicardTools):\n subtoolName = 'MarkDuplicates'\n\n def execute(\n self, inBams, outBam, outMetrics=None, taggingPolicy=None, picardOptions=None, JVMmemory=None\n ): # pylint: disable=W0221\n picardOptions = picardOptions or []\n\n if not outMetrics:\n outMetrics = util_file.mkstempfname('.metrics')\n opts = ['INPUT=' + bam for bam in inBams] + ['OUTPUT=' + outBam, 'METRICS_FILE=' + outMetrics]\n if taggingPolicy:\n opts += ['TAGGING_POLICY={}'.format(taggingPolicy)]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\nclass SplitSamByLibraryTool(PicardTools):\n subtoolName = 'SplitSamByLibrary'\n\n def execute(\n self, in_bam, out_dir, picardOptions=None, JVMmemory=None\n ): # pylint: disable=W0221\n\n if samtools.SamtoolsTool().isEmpty(in_bam):\n # Picard SplitSamByLibrary cannot deal with an empty input BAM file\n shutil.copyfile(in_bam, os.path.join(out_dir, 'output.bam'))\n return\n\n opts = ['INPUT=' + in_bam, 'OUTPUT=' + out_dir]\n PicardTools.execute(self, self.subtoolName, opts, JVMmemory=JVMmemory)\n\n\nclass SamToFastqTool(PicardTools):\n subtoolName = 'SamToFastq'\n illumina_clipping_attribute = 'XT'\n\n def execute(self, inBam, outFastq1, outFastq2=None, outFastq0=None,\n illuminaClipping=False, interleave=False,\n picardOptions=None, JVMmemory=None, background=None, **kwargs): # pylint: disable=W0221\n '''Write paired reads from `inBam` to `outFastq1` and `outFastq1`. If `outFastq0` is given, write\n any unpaired reads from `inBam` there, else ignore them. If `illuminaClipping` is True,\n trim reads at the clipping position specified by the Illumina clipping attribute\n (which is defined by the class variable SamToFastqTool.illumina_clipping_attribute).'''\n\n picardOptions = picardOptions or []\n\n opts = [\n 'INPUT=' + inBam, 'VALIDATION_STRINGENCY=SILENT', 'FASTQ=' + outFastq1,\n ]\n if outFastq2:\n opts.append('SECOND_END_FASTQ=' + outFastq2)\n else:\n if interleave:\n opts.append('INTERLEAVE=true')\n\n if outFastq0:\n assert outFastq2, \"outFastq0 option only applies in paired-end output mode\"\n opts.append('UNPAIRED_FASTQ=' + outFastq0)\n\n if illuminaClipping:\n opts += PicardTools.dict_to_picard_opts({\n 'CLIPPING_ATTRIBUTE': SamToFastqTool.illumina_clipping_attribute,\n 'CLIPPING_ACTION': 'X'\n })\n\n return PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory,\n background=background, **kwargs)\n\n @contextlib.contextmanager\n def execute_tmp(self, inBam, sfx='', includeUnpaired=False, **kwargs):\n '''Output reads from `inBam` to temp fastq files, and yield their filenames as a tuple.\n If `includeUnpaired` is True, output unpaired reads to a third temp fastq file and yield it as a third\n element of the tuple.\n '''\n if not includeUnpaired:\n with util_file.tempfnames((sfx+'.1.fq', sfx+'.2.fq')) as (outFastq1, outFastq2):\n self.execute(inBam, outFastq1, outFastq2, **kwargs)\n yield outFastq1, outFastq2\n else:\n with util_file.tempfnames((sfx+'.1.fq', sfx+'.2.fq', sfx+'.0.fq')) as (outFastq1, outFastq2, outFastq0):\n self.execute(inBam, outFastq1, outFastq2, outFastq0=outFastq0, **kwargs)\n yield outFastq1, outFastq2, outFastq0\n\n def per_read_group(self, inBam, outDir, picardOptions=None, JVMmemory=None):\n if samtools.SamtoolsTool().isEmpty(inBam):\n # Picard SamToFastq cannot deal with an empty input BAM file\n if not os.path.isdir(outDir):\n os.mkdir(outDir)\n else:\n picardOptions = picardOptions or []\n opts = ['INPUT=' + inBam, 'OUTPUT_DIR=' + outDir, 'OUTPUT_PER_RG=true', 'RG_TAG=ID']\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\nclass FastqToSamTool(PicardTools):\n subtoolName = 'FastqToSam'\n jvmMemDefault = '4g'\n\n @staticmethod\n def isFastqEmpty(fastq_file):\n \"\"\"\n Check if a FASTQ file is semantically empty (contains no reads).\n\n A FASTQ file is considered empty if:\n - The file does not exist\n - The file is zero bytes\n - The file is small (< 1024 bytes) and contains only whitespace\n\n For performance, files >= 1024 bytes are assumed to be non-empty without\n reading their contents.\n\n Args:\n fastq_file (str): Path to FASTQ file\n\n Returns:\n bool: True if file is empty, False if it contains data\n \"\"\"\n if not fastq_file or not os.path.exists(fastq_file):\n return True\n\n # Large files are assumed to be non-empty (avoid reading huge files)\n if os.path.getsize(fastq_file) > 1024:\n return False\n\n # Small files: check if they contain only whitespace\n # Handle both gzipped and plain text files\n with util_file.open_or_gzopen(fastq_file, 'r') as f:\n return len(f.read().strip()) == 0\n\n def execute(\n self,\n inFastq1,\n inFastq2,\n sampleName,\n outBam,\n picardOptions=None,\n JVMmemory=None\n ): # pylint: disable=W0221\n picardOptions = picardOptions or []\n\n # Check if FASTQ inputs are empty (defensive code to handle edge cases)\n # Picard's FastqToSam crashes on empty FASTQs because it cannot determine quality encoding\n fastq1_empty = self.isFastqEmpty(inFastq1)\n fastq2_empty = self.isFastqEmpty(inFastq2) if inFastq2 else True\n\n # If inFastq2 is specified but empty, treat as single-read input\n if inFastq2 and fastq2_empty and not fastq1_empty:\n _log.warning(\"FASTQ2 file is empty; treating as single-read input: %s\", inFastq1)\n inFastq2 = None\n fastq2_empty = True\n\n # If inFastq1 is empty, create an empty BAM file manually\n if fastq1_empty:\n _log.warning(\"FASTQ1 file is empty; creating empty BAM file: %s\", outBam)\n # Parse picardOptions to extract header information\n picard_opts_dict = {}\n for opt in picardOptions:\n if '=' in opt:\n key, value = opt.split('=', 1)\n picard_opts_dict[key] = value\n\n # Create a minimal BAM header\n header = {\n 'HD': {'VN': '1.6', 'SO': 'queryname'},\n 'RG': [{\n 'ID': picard_opts_dict.get('READ_GROUP_NAME', 'A'),\n 'SM': sampleName,\n 'LB': picard_opts_dict.get('LIBRARY_NAME', sampleName),\n 'PL': picard_opts_dict.get('PLATFORM', 'ILLUMINA'),\n }]\n }\n\n # Add optional header fields if present\n if 'PLATFORM_UNIT' in picard_opts_dict:\n header['RG'][0]['PU'] = picard_opts_dict['PLATFORM_UNIT']\n if 'PLATFORM_MODEL' in picard_opts_dict:\n header['RG'][0]['PM'] = picard_opts_dict['PLATFORM_MODEL']\n if 'SEQUENCING_CENTER' in picard_opts_dict:\n header['RG'][0]['CN'] = picard_opts_dict['SEQUENCING_CENTER']\n if 'RUN_DATE' in picard_opts_dict:\n header['RG'][0]['DT'] = picard_opts_dict['RUN_DATE']\n if 'DESCRIPTION' in picard_opts_dict:\n header['RG'][0]['DS'] = picard_opts_dict['DESCRIPTION']\n\n # Write empty BAM file with pysam\n with pysam.AlignmentFile(outBam, 'wb', header=header) as outf:\n pass # No reads to write\n\n _log.info(\"Created empty BAM file with header: %s\", outBam)\n return\n\n # Normal case: non-empty FASTQs, call Picard\n if inFastq2:\n opts = ['FASTQ=' + inFastq1, 'FASTQ2=' + inFastq2, 'OUTPUT=' + outBam, 'SAMPLE_NAME=' + sampleName]\n else:\n opts = ['FASTQ=' + inFastq1, 'OUTPUT=' + outBam, 'SAMPLE_NAME=' + sampleName]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\nclass SortSamTool(PicardTools):\n subtoolName = 'SortSam'\n valid_sort_orders = ['unsorted', 'queryname', 'coordinate']\n default_sort_order = 'coordinate'\n\n def execute(\n self, inBam, outBam, sort_order=default_sort_order,\n picardOptions=None, JVMmemory=None\n ): # pylint: disable=W0221\n picardOptions = picardOptions or []\n\n if sort_order not in self.valid_sort_orders:\n raise Exception(\"invalid sort order\")\n opts = ['INPUT=' + inBam, 'OUTPUT=' + outBam, 'SORT_ORDER=' + sort_order]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\nclass DownsampleSamTool(PicardTools):\n subtoolName = 'DownsampleSam'\n valid_strategies = ['HighAccuracy', 'ConstantMemory', 'Chained']\n default_strategy = 'Chained' # ConstantMemory first, then HighAccuracy to get closer to the target probability\n default_random_seed = 1 # Set to constant int for deterministic results\n jvmMemDefault = '4g'\n\n def execute(self,\n inBam,\n outBam,\n probability,\n accuracy=None, #Picard default is 1.0E-4\n strategy=default_strategy,\n random_seed=default_random_seed,\n picardOptions=None,\n JVMmemory=None): # pylint: disable=W0221\n picardOptions = picardOptions or []\n JVMmemory = JVMmemory or self.jvmMemDefault\n\n if strategy not in self.valid_strategies:\n raise Exception(\"invalid subsample strategy: %s\" % strategy)\n if not probability:\n raise Exception(\"Probability must be defined\")\n if float(probability) <= 0 or float(probability) > 1:\n raise Exception(\"Probability must be in range (0,1]. This value was given: %s\" % probability)\n\n opts = ['INPUT=' + inBam, 'OUTPUT=' + outBam, 'PROBABILITY=' + str(probability)]\n\n if accuracy:\n opts.extend(['ACCURACY=' + str(accuracy)])\n\n if strategy:\n opts.extend(['STRATEGY=' + strategy])\n\n if not random_seed:\n _log.info(\"No random seed is set for subsample operation; results will be non-deterministic\")\n opts.extend([\"RANDOM_SEED=null\"])\n raise Exception(\n \"Setting RANDOM_SEED=null crashes Picard 1.141, though it may be available when viral-ngs updates to a later version of Picard.\"\n )\n else:\n _log.info(\"Random seed is set for subsample operation; results will be deterministic\")\n opts.extend(['RANDOM_SEED=' + str(random_seed)])\n\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\n def downsample_to_approx_count(\n self, inBam, outBam, read_count, picardOptions=None,\n JVMmemory=None\n ): # pylint: disable=W0221):\n\n samtools_tool = samtools.SamtoolsTool()\n total_read_count = samtools_tool.count(inBam)\n\n if total_read_count == 0:\n _log.info(\"Input BAM has no reads. Copying to output.\")\n shutil.copyfile(inBam, outBam)\n\n probability = Decimal(int(read_count)) / Decimal(total_read_count)\n probability = 1 if probability > 1 else probability\n\n assert probability >= 0\n\n if probability < 1:\n # per the Picard docs, HighAccuracy is recommended for read counts <50k\n strategy = \"HighAccuracy\" if total_read_count < 50000 else \"Chained\"\n _log.info(\"Setting downsample accuracy to %s based on read count of %s\" % (strategy, total_read_count))\n\n self.execute(inBam, outBam, probability, strategy=strategy, accuracy=0.00001, picardOptions=picardOptions, JVMmemory=JVMmemory)\n else:\n _log.info(\"Requested downsample count exceeds number of reads. Including all reads in output.\")\n shutil.copyfile(inBam, outBam)\n\n\nclass MergeSamFilesTool(PicardTools):\n subtoolName = 'MergeSamFiles'\n\n def execute(self, inBams, outBam, picardOptions=None, JVMmemory=None, background=None): # pylint: disable=W0221\n picardOptions = picardOptions or []\n\n if not any(opt.startswith('USE_THREADING') for opt in picardOptions):\n picardOptions.append('USE_THREADING=true')\n\n opts = ['INPUT=' + bam for bam in inBams] + ['OUTPUT=' + outBam]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory=JVMmemory, background=background)\n\n\nclass ReplaceSamHeaderTool(PicardTools):\n subtoolName = 'ReplaceSamHeader'\n\n def execute(self, inBam, headerBam, outBam, picardOptions=None, JVMmemory=None, background=None): # pylint: disable=W0221\n\n opts = ['INPUT=' + inBam,\n 'HEADER=' + headerBam,\n 'OUTPUT=' + outBam]\n PicardTools.execute(self, self.subtoolName, opts, JVMmemory=JVMmemory, background=background)\n\n\nclass FilterSamReadsTool(PicardTools):\n '''\n DEPRECATED: This Picard-based tool is deprecated in favor of\n ReadIdStore.filter_bam_by_ids() in read_utils.py which uses\n pysam/sqlite with O(1) memory and is significantly faster.\n\n This class is retained for backwards compatibility but new code\n should use ReadIdStore instead.\n '''\n subtoolName = 'FilterSamReads'\n jvmMemDefault = '4g'\n\n def execute(self, inBam, exclude, readList, outBam, picardOptions=None, JVMmemory=None): # pylint: disable=W0221\n _log.warning(\n \"DEPRECATED: FilterSamReadsTool is deprecated. \"\n \"Use ReadIdStore.filter_bam_by_ids() from read_utils.py instead \"\n \"for faster O(1) memory filtering.\"\n )\n picardOptions = picardOptions or []\n\n if samtools.SamtoolsTool().isEmpty(inBam):\n # Picard FilterSamReads cannot deal with an empty input BAM file\n shutil.copyfile(inBam, outBam)\n elif os.path.getsize(readList) == 0:\n # Picard FilterSamReads cannot deal with an empty READ_LIST_FILE\n if exclude:\n shutil.copyfile(inBam, outBam)\n else:\n tmpf = util_file.mkstempfname('.sam')\n if inBam.endswith('.sam'):\n # output format (sam/bam) is inferred by samtools based on file extension\n header = pysam.view('-o', tmpf, '-H', '-S', inBam, catch_stdout=False)\n else:\n header = pysam.view('-o', tmpf, '-H', inBam, catch_stdout=False)\n # pysam.AlignmentFile cannot write an empty file\n # samtools cannot convert SAM -> BAM on an empty file\n # but Picard SamFormatConverter can deal with empty files\n opts = ['INPUT=' + tmpf, 'OUTPUT=' + outBam, 'VERBOSITY=ERROR']\n PicardTools.execute(self, 'SamFormatConverter', opts, JVMmemory='50m')\n else:\n opts = [\n 'INPUT=' + inBam, 'OUTPUT=' + outBam, 'READ_LIST_FILE=' + readList,\n 'FILTER=' + (exclude and 'excludeReadList' or 'includeReadList'), 'WRITE_READS_FILES=false'\n ]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\nclass CreateSequenceDictionaryTool(PicardTools):\n subtoolName = 'CreateSequenceDictionary'\n jvmMemDefault = '512m'\n\n def execute(\n self, inFasta, outDict=None, overwrite=False,\n picardOptions=None, JVMmemory=None\n ): # pylint: disable=W0221\n picardOptions = picardOptions or []\n\n if not outDict:\n if inFasta.lower().endswith('.fa'):\n outDict = inFasta[:-3] + '.dict'\n elif inFasta.lower().endswith('.fasta'):\n outDict = inFasta[:-6] + '.dict'\n else:\n raise Exception(\"bad input\")\n if os.path.isfile(outDict):\n if overwrite:\n os.unlink(outDict)\n else:\n return\n with util_file.fastas_with_sanitized_ids(inFasta, use_tmp=False) as sanitized_fastas:\n opts = ['REFERENCE=' + sanitized_fastas[0], 'OUTPUT=' + outDict]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\n\nclass BuildBamIndexTool(PicardTools):\n subtoolName = 'BuildBamIndex'\n jvmMemDefault = '512m'\n\n def execute(self, inBam, picardOptions=None, JVMmemory=None): # pylint: disable=W0221\n picardOptions = picardOptions or []\n\n opts = ['INPUT=' + inBam]\n PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory)\n\nclass CollectIlluminaLaneMetricsTool(PicardTools):\n subtoolName = 'CollectIlluminaLaneMetrics'\n jvmMemDefault = '8g'\n defaults = {'read_structure': '101T8B8B101T'}\n option_list = (\n 'read_structure',\n )\n\n def execute(\n self, run_dir,\n output_dir, output_prefix,\n picardOptions=None,\n JVMmemory=None\n ): # pylint: disable=W0221\n picardOptions = picardOptions or {}\n\n opts_dict = self.defaults.copy()\n for k, v in picardOptions.items():\n opts_dict[k] = v\n opts = []\n for k, v in opts_dict.items():\n if v is not None:\n if type(v) in (list, tuple):\n for x in v:\n opts.append('='.join((k.upper(), str(x))))\n else:\n opts.append('='.join((k.upper(), str(v))))\n\n opts += ['RUN_DIRECTORY=' + run_dir]\n opts += ['OUTPUT_DIRECTORY=' + output_dir]\n opts += ['OUTPUT_PREFIX=' + output_prefix]\n PicardTools.execute(self, self.subtoolName, opts, JVMmemory)\n\nclass ExtractIlluminaBarcodesTool(PicardTools):\n subtoolName = 'ExtractIlluminaBarcodes'\n jvmMemDefault = '8g'\n # minimum_base_quality=20 used to accommodate NovaSeq, which with RTA3 writes only four Q-score values: 2, 12, 23, and 37\n defaults = {\n 'read_structure': '101T8B8B101T', \n 'max_mismatches': 0, \n 'minimum_base_quality': 20, \n 'num_processors': 0\n }\n option_list = (\n 'read_structure', 'max_mismatches', 'minimum_base_quality', 'min_mismatch_delta', 'max_no_calls',\n 'minimum_quality', 'compress_outputs', 'num_processors'\n )\n\n def execute(\n self, \n basecalls_dir,\n lane, \n barcode_file,\n output_dir, \n metrics,\n picardOptions=None,\n JVMmemory=None\n ): # pylint: disable=W0221\n picardOptions = picardOptions or {}\n\n opts_dict = self.defaults.copy()\n for k, v in picardOptions.items():\n opts_dict[k] = v\n opts = []\n for k, v in opts_dict.items():\n if v is not None:\n if type(v) in (list, tuple):\n for x in v:\n opts.append('='.join((k.upper(), str(x))))\n else:\n opts.append('='.join((k.upper(), str(v))))\n opts += [\n 'BASECALLS_DIR=' + basecalls_dir, 'LANE=' + str(lane), 'BARCODE_FILE=' + barcode_file,\n 'METRICS_FILE=' + metrics\n ]\n if output_dir is not None:\n opts += ['OUTPUT_DIR=' + output_dir]\n PicardTools.execute(self, self.subtoolName, opts, JVMmemory)\n\n\nclass AddCommentsToBamTool(PicardTools):\n # https://broadinstitute.github.io/picard/command-line-overview.html#AddCommentsToBam\n subtoolName = 'AddCommentsToBam'\n jvmMemDefault = '8g'\n\n def execute(self, \n inBam, \n outBam,\n comments, \n picardOptions = None, \n JVMmemory = None\n ): # pylint: disable=W0221\n picardOptions = picardOptions or {}\n\n # check that comments are provided\n if not comments:\n raise Exception(\"comments must be provided to AddCommentsToBam \")\n\n comments_to_add = []\n if type(comments) in (list, tuple, set):\n # if we have an iterable, check that all comments are strings or can be cast to strings\n # and have a length > 0 before adding to comments_to_add\n comments_to_add = [str(comment) for comment in comments if len(str(comment)) > 0]\n elif type(comments) == str:\n comments_to_add = [comments]\n else:\n raise Exception(\"comments provided to AddCommentsToBam must be in the form of a string or a list of strings\")\n\n opts = ['INPUT=' + inBam, 'OUTPUT=' + outBam] \n\n for comment in comments_to_add:\n opts += ['COMMENT=' + comment]\n\n PicardTools.execute(self, self.subtoolName, opts, JVMmemory)\n\nclass IlluminaBasecallsToSamTool(PicardTools):\n # https://broadinstitute.github.io/picard/command-line-overview.html#IlluminaBasecallsToSam\n subtoolName = 'IlluminaBasecallsToSam'\n jvmMemDefault = '7g'\n defaults = {\n 'read_structure': '101T8B8B101T',\n 'adapters_to_check': ('PAIRED_END', 'NEXTERA_V1', 'NEXTERA_V2'),\n # MAX_READS_IN_RAM_PER_TILE is deprecated in newer versions of Picard in favor of MAX_RECORDS_IN_RAM\n # commenting out for now until fully removed from picard\n #'max_reads_in_ram_per_tile': 1000000, \n 'max_records_in_ram': 2000000,\n 'num_processors': 0,\n 'include_non_pf_reads': False,\n 'compression_level': 7,\n 'sort': True\n }\n option_list = (\n 'read_structure', 'sequencing_center', 'adapters_to_check', 'platform',\n 'max_records_in_ram', 'num_processors', 'apply_eamss_filter', 'force_gc', 'first_tile', 'tile_limit',\n 'include_non_pf_reads', 'run_start_date', 'read_group_id', 'compression_level', 'sort'\n )\n\n # pylint: disable=W0221\n def execute(self, \n basecalls_dir,\n barcodes_dir,\n read_group_id_precursor,\n lane, library_params,\n picardOptions=None,\n JVMmemory=None\n ):\n picardOptions = picardOptions or {}\n\n opts_dict = self.defaults.copy()\n for k, v in picardOptions.items():\n opts_dict[k] = v\n opts = []\n for k, v in opts_dict.items():\n if v is not None:\n if type(v) in (list, tuple):\n for x in v:\n opts.append('='.join((k.upper(), str(x))))\n else:\n opts.append('='.join((k.upper(), str(v))))\n opts += [\n 'BASECALLS_DIR=' + basecalls_dir, 'BARCODES_DIR=' + barcodes_dir, 'LANE=' + str(lane),\n 'RUN_BARCODE=' + read_group_id_precursor, 'LIBRARY_PARAMS=' + library_params\n ]\n # MAX_READS_IN_RAM_PER_TILE is deprecated in newer versions of Picard in favor of MAX_RECORDS_IN_RAM\n # remove from opts; this list comprehension can be removed once MAX_READS_IN_RAM_PER_TILE is removed\n # from picard\n opts = [opt for opt in opts if \"MAX_READS_IN_RAM_PER_TILE\" not in opt]\n PicardTools.execute(self, self.subtoolName, opts, JVMmemory)\n\n def execute_single_sample(self, \n basecalls_dir,\n output_file,\n read_group_id_precursor, # this is a run-specific ID, ex. the flowcell ID\n lane,\n sample_alias,\n picardOptions=None,\n JVMmemory=None\n ):\n picardOptions = picardOptions or {}\n\n assert len(read_group_id_precursor) >= 5, \"read_group_id_precursor must be >=5 chars per https://github.com/broadinstitute/picard/blob/2.17.6/src/main/java/picard/illumina/IlluminaBasecallsToSam.java#L510\"\n\n opts_dict = self.defaults.copy()\n for k, v in picardOptions.items():\n opts_dict[k] = v\n opts = []\n for k, v in opts_dict.items():\n if v is not None:\n if type(v) in (list, tuple):\n for x in v:\n opts.append('='.join((k.upper(), str(x))))\n else:\n opts.append('='.join((k.upper(), str(v))))\n opts += [\n 'OUTPUT=' + output_file,\n 'BASECALLS_DIR=' + basecalls_dir, \n 'LANE=' + str(lane),\n 'RUN_BARCODE=' + read_group_id_precursor, #\n 'SAMPLE_ALIAS=' + sample_alias,\n 'LIBRARY_NAME=' + sample_alias\n ]\n PicardTools.execute(self, self.subtoolName, opts, JVMmemory)\n # pylint: enable=W0221\n" }, { "path": "src/viral_ngs/core/prinseq.py", "content": "\"Tool for prinseq.\"\n\nimport logging\nimport os.path\nimport shutil\nimport subprocess\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = \"prinseq-lite.pl\"\n\nlog = logging.getLogger(__name__)\n\nclass PrinseqTool(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(PrinseqTool, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip().split()[1]\n\n def rmdup_fastq_single(self, inFastq, outFastq):\n ''' remove duplicate reads and reads with multiple Ns '''\n\n if os.path.getsize(inFastq) == 0:\n # prinseq-lite fails on empty file input so handle this scenario specially\n log.debug(\"prinseq input is empty\")\n shutil.copyfile(inFastq, outFastq)\n else:\n outprefix = util_file.mkstempfname(\"-prinseq-rmdup-out\")\n cmd = [\n 'perl', self.install_and_get_path(), '-verbose',\n '-ns_max_n', '1', '-derep', '1',\n '-fastq', inFastq,\n '-out_bad', 'null', '-line_width', '0', '-out_good', outprefix\n ]\n log.debug(' '.join(cmd))\n subprocess.check_call(cmd)\n shutil.copyfile(outprefix+'.fastq', outFastq)\n os.unlink(outprefix+'.fastq')\n\n def rmdup_fastq_paired(self, inFastq1, inFastq2, outFastq1, outFastq2, includeUnmated=False, unpairedOutFastq1=None, unpairedOutFastq2=None):\n ''' remove duplicate reads and reads with multiple Ns '''\n\n if not os.path.exists(inFastq2) or os.path.getsize(inFastq2) == 0:\n # input is single-end\n log.debug(\"prinseq input is unpaired\")\n util_file.touch(outFastq2)\n if not includeUnmated:\n # excluding unmated on unpaired input implies no output\n util_file.touch(outFastq1)\n else:\n self.rmdup_fastq_single(inFastq1, outFastq1)\n elif os.path.getsize(inFastq1) == 0:\n # prinseq-lite fails on empty file input so handle this scenario specially\n log.debug(\"prinseq input is empty\")\n util_file.touch(outFastq1)\n util_file.touch(outFastq2)\n else:\n outprefix = util_file.mkstempfname(\"-prinseq-rmdup-out\")\n cmd = [\n 'perl', self.install_and_get_path(), '-verbose',\n '-ns_max_n', '1', '-derep', '1',\n '-fastq', inFastq1, '-fastq2', inFastq2,\n '-out_bad', 'null', '-line_width', '0', '-out_good', outprefix\n ]\n log.debug(' '.join(cmd))\n subprocess.check_call(cmd)\n for fn in (outprefix+'_1.fastq', outprefix+'_1_singletons.fastq',\n outprefix+'_2.fastq', outprefix+'_2_singletons.fastq'):\n # if any of the four output files is empty, prinseq doesn't create it at all, which is bad for us\n util_file.touch(fn)\n \n # if the user desires the unmated reads to be included in the output fastqs\n if includeUnmated:\n util_file.cat(outFastq1, (outprefix+'_1.fastq', outprefix+'_1_singletons.fastq'))\n util_file.cat(outFastq2, (outprefix+'_2.fastq', outprefix+'_2_singletons.fastq'))\n else:\n shutil.copyfile(outprefix+'_1.fastq', outFastq1)\n shutil.copyfile(outprefix+'_2.fastq', outFastq2)\n\n # if a path is specified for the unmated reads\n if unpairedOutFastq1 is not None:\n shutil.copyfile(outprefix+'_1_singletons.fastq', unpairedOutFastq1)\n\n if unpairedOutFastq2 is not None:\n shutil.copyfile(outprefix+'_2_singletons.fastq', unpairedOutFastq2)\n\n os.unlink(outprefix+'_1.fastq')\n os.unlink(outprefix+'_2.fastq')\n os.unlink(outprefix+'_1_singletons.fastq')\n os.unlink(outprefix+'_2_singletons.fastq')\n" }, { "path": "src/viral_ngs/core/priorities.py", "content": "#!/usr/bin/env python3\n\"\"\"\nMask initial bases from alignment FASTA\n\"\"\"\nimport argparse\nfrom random import shuffle\nfrom collections import defaultdict\nimport Bio\nimport numpy as np\nfrom Bio.SeqIO.FastaIO import SimpleFastaParser\nfrom Bio.Seq import Seq\nfrom Bio import AlignIO, SeqIO\nfrom scipy import sparse\n\n\ndef compactify_sequences(sparse_matrix, sequence_names):\n sequence_groups = defaultdict(list)\n for s, snps in zip(sequence_names, sparse_matrix):\n ind = snps.nonzero()\n vals = np.array(snps[ind])\n if len(ind[1]):\n sequence_groups[tuple(zip(ind[1], vals[0]))].append(s)\n else:\n sequence_groups[tuple()].append(s)\n\n return sequence_groups\n\nINITIALISATION_LENGTH = 1000000\n\ndef sequence_to_int_array(s, fill_value=110, fill_gaps=True):\n seq = np.frombuffer(str(s).lower().encode('utf-8'), dtype=np.int8).copy()\n if fill_gaps:\n seq[(seq!=97) & (seq!=99) & (seq!=103) & (seq!=116)] = fill_value\n else:\n seq[(seq!=97) & (seq!=99) & (seq!=103) & (seq!=116) & (seq!=45)] = fill_value\n return seq\n\n# Function adapted from https://github.com/gtonkinhill/pairsnp-python\ndef calculate_snp_matrix(fastafile, consensus=None, zipped=False, fill_value=110):\n # This function generate a sparse matrix where differences to the consensus are coded as integers.\n\n row = np.empty(INITIALISATION_LENGTH)\n col = np.empty(INITIALISATION_LENGTH, dtype=np.int64)\n val = np.empty(INITIALISATION_LENGTH, dtype=np.int8)\n\n r = 0\n n_snps = 0\n nseqs = 0\n seq_names = []\n filled_positions = []\n current_length = INITIALISATION_LENGTH\n if zipped:\n fh = gzip.open(fastafile, 'rt')\n else:\n fh = open(fastafile, 'rt')\n with fh as fasta:\n for h,s in SimpleFastaParser(fasta):\n if consensus is None:\n align_length = len(s)\n # Take consensus as first sequence\n consensus = sequence_to_int_array(s, fill_value=fill_value)\n else:\n align_length = len(consensus)\n\n nseqs +=1\n seq_names.append(h)\n\n if(len(s)!=align_length):\n raise ValueError('Fasta file appears to have sequences of different lengths!')\n\n s = sequence_to_int_array(s, fill_value=fill_value)\n snps = (consensus!=s) & (s!=fill_value)\n right = n_snps + np.sum(snps)\n filled_positions.append(np.where(s==fill_value)[0])\n\n if right >= (current_length/2):\n current_length = current_length + INITIALISATION_LENGTH\n row.resize(current_length)\n col.resize(current_length)\n val.resize(current_length)\n\n row[n_snps:right] = r\n col[n_snps:right] = np.flatnonzero(snps)\n val[n_snps:right] = s[snps]\n r += 1\n n_snps = right\n fh.close()\n\n if nseqs==0:\n raise ValueError('No sequences found!')\n\n row = row[0:right]\n col = col[0:right]\n val = val[0:right]\n\n sparse_snps = sparse.csc_matrix((val, (row, col)), shape=(nseqs, align_length))\n\n return {'snps': sparse_snps, 'consensus': consensus, 'names': seq_names, 'filled_positions': filled_positions}\n\n# Function adapted from https://github.com/gtonkinhill/pairsnp-python\ndef calculate_distance_matrix(sparse_matrix_A, sparse_matrix_B, consensus):\n\n n_seqs_A = sparse_matrix_A.shape[0]\n n_seqs_B = sparse_matrix_B.shape[0]\n\n d = (1*(sparse_matrix_A==97)) * (sparse_matrix_B.transpose()==97)\n d = d + (1*(sparse_matrix_A==99) * (sparse_matrix_B.transpose()==99))\n d = d + (1*(sparse_matrix_A==103) * (sparse_matrix_B.transpose()==103))\n d = d + (1*(sparse_matrix_A==116) * (sparse_matrix_B.transpose()==116))\n\n d = d.todense()\n\n n_comp = (1*(sparse_matrix_A==110) * ((sparse_matrix_B==110).transpose())).todense()\n d = d + n_comp\n\n temp_total = np.zeros((n_seqs_A, n_seqs_B))\n temp_total[:] = (1*(sparse_matrix_A>0)).sum(1)\n temp_total += (1*(sparse_matrix_B>0)).sum(1).transpose()\n\n total_differences_shared = (1*(sparse_matrix_A>0)) * (sparse_matrix_B.transpose()>0)\n\n n_total = np.zeros((n_seqs_A, n_seqs_B))\n n_sum = (1*(sparse_matrix_A==110)).sum(1)\n n_total[:] = n_sum\n n_total += (1*(sparse_matrix_B==110)).sum(1).transpose()\n\n diff_n = n_total - 2*n_comp\n d = temp_total - total_differences_shared.todense() - d - diff_n\n\n return d\n\nif __name__ == '__main__':\n parser = argparse.ArgumentParser(\n description=\"generate priorities files based on genetic proximity to focal sample\",\n formatter_class=argparse.ArgumentDefaultsHelpFormatter\n )\n parser.add_argument(\"--alignment\", type=str, required=True, help=\"FASTA file of alignment\")\n parser.add_argument(\"--reference\", type = str, required=True, help=\"reference sequence\")\n parser.add_argument(\"--metadata\", type = str, required=True, help=\"metadata\")\n parser.add_argument(\"--focal-alignment\", type = str, required=True, help=\"focal smaple of sequences\")\n parser.add_argument(\"--output\", type=str, required=True, help=\"FASTA file of output alignment\")\n args = parser.parse_args()\n\n # load entire alignment and the alignment of focal sequences (upper case -- probably not necessary)\n ref = sequence_to_int_array(SeqIO.read(args.reference, 'genbank').seq)\n context_seqs_dict = calculate_snp_matrix(args.alignment, consensus=ref)\n focal_seqs_dict = calculate_snp_matrix(args.focal_alignment, consensus = ref)\n alignment_length = len(ref)\n print(\"Done reading the alignments.\")\n\n # calculate number of masked sites in either set\n mask_count_focal = np.array([len(x) for x in focal_seqs_dict['filled_positions']])\n mask_count_context = {s: len(x) for s,x in zip(context_seqs_dict['names'], context_seqs_dict['filled_positions'])}\n\n # for each context sequence, calculate minimal distance to focal set, weigh with number of N/- to pick best sequence\n d = np.array(calculate_distance_matrix(context_seqs_dict['snps'], focal_seqs_dict['snps'], consensus = context_seqs_dict['consensus']))\n closest_match = np.argmin(d+mask_count_focal/alignment_length, axis=1)\n print(\"Done finding closest matches.\")\n\n minimal_distance_to_focal_set = {}\n for context_index, focal_index in enumerate(closest_match):\n minimal_distance_to_focal_set[context_seqs_dict['names'][context_index]] = (d[context_index, focal_index], focal_seqs_dict[\"names\"][focal_index])\n\n # for each focal sequence with close matches (using the index), we list all close contexts\n close_matches = defaultdict(list)\n for seq in minimal_distance_to_focal_set:\n close_matches[minimal_distance_to_focal_set[seq][1]].append(seq)\n\n for f in close_matches:\n shuffle(close_matches[f])\n close_matches[f].sort(key=lambda x: minimal_distance_to_focal_set[x][0] + mask_count_context[x]/alignment_length)\n\n # export priorities\n with open(args.output, 'w') as fh:\n for i, seqid in enumerate(context_seqs_dict['names']):\n # use distance as negative priority\n # penalize masked (N or -) -- 333 masked sites==one mutations\n # penalize if many sequences are close to the same focal one by using the index of the shuffled list of neighbours\n # currently each position in this lists reduced priority by 0.2, i.e. 5 other sequences == one mutation\n position = close_matches[minimal_distance_to_focal_set[seqid][1]].index(seqid)\n priority = -minimal_distance_to_focal_set[seqid][0] - 0.1*position\n fh.write(f\"{seqid}\\t{priority:1.2f}\\n\")\n" }, { "path": "src/viral_ngs/core/sambamba.py", "content": "'''\n Sambamba - high-performance BAM processing tool.\n\n Sambamba is a tool for processing BAM files that provides multi-threaded\n implementations of common operations like sorting, indexing, merging,\n and duplicate marking. It is significantly faster than single-threaded\n alternatives like Picard for many operations.\n\n https://github.com/biod/sambamba\n'''\n\nimport logging\nimport os\nimport re\nimport shutil\nimport subprocess\n\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = 'sambamba'\n\nlog = logging.getLogger(__name__)\n\n\nclass SambambaTool(Tool):\n \"\"\"Tool wrapper for sambamba - high-performance SAM/BAM processing\"\"\"\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [\n PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)\n ]\n super(SambambaTool, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n output = subprocess.check_output(\n [self.install_and_get_path(), '--version'],\n stderr=subprocess.STDOUT\n ).decode('UTF-8')\n # Parse version from output like \"sambamba 1.0.1\"\n match = re.search(r'sambamba\\s+(\\d+\\.\\d+\\.\\d+)', output)\n if match:\n self.tool_version = match.group(1)\n else:\n # Fallback: try to get first version-like string\n for line in output.split('\\n'):\n if 'sambamba' in line.lower():\n parts = line.split()\n for part in parts:\n if re.match(r'\\d+\\.\\d+', part):\n self.tool_version = part\n return\n self.tool_version = 'unknown'\n\n def execute(self, command, args, stdout=None, stderr=None):\n \"\"\"Execute a sambamba subcommand with arguments\"\"\"\n tool_cmd = [self.install_and_get_path(), command] + [str(a) for a in args]\n log.debug(' '.join(tool_cmd))\n\n stdout_fh = open(stdout, 'w') if stdout else None\n stderr_fh = open(stderr, 'w') if stderr else None\n\n try:\n subprocess.check_call(tool_cmd, stdout=stdout_fh, stderr=stderr_fh)\n finally:\n if stdout_fh:\n stdout_fh.close()\n if stderr_fh:\n stderr_fh.close()\n\n def sort(self, inBam, outBam, sort_order='coordinate', threads=None):\n \"\"\"\n Sort a BAM file.\n\n Args:\n inBam: Input BAM file path\n outBam: Output sorted BAM file path\n sort_order: 'coordinate' (default) or 'queryname'\n threads: Number of threads to use (default: auto)\n \"\"\"\n threads = util_misc.sanitize_thread_count(threads)\n\n args = []\n\n # Thread count\n args.extend(['-t', str(threads)])\n\n # Sort order: -n for queryname, default is coordinate\n if sort_order == 'queryname':\n args.append('-n')\n elif sort_order != 'coordinate':\n raise ValueError(f\"Invalid sort_order: {sort_order}. Must be 'coordinate' or 'queryname'\")\n\n # Output file\n args.extend(['-o', outBam])\n\n # Input file\n args.append(inBam)\n\n self.execute('sort', args)\n\n def index(self, inBam, threads=None):\n \"\"\"\n Create an index (.bai) for a coordinate-sorted BAM file.\n\n Sambamba creates {inBam}.bai by default (e.g., sample.bam.bai).\n We rename it to match the expected convention of {basename}.bai\n (e.g., sample.bai) for compatibility with WDL workflows.\n\n Args:\n inBam: Input BAM file path (must be coordinate-sorted)\n threads: Number of threads to use (default: auto)\n \"\"\"\n threads = util_misc.sanitize_thread_count(threads)\n\n args = ['-t', str(threads), inBam]\n\n self.execute('index', args)\n\n # Sambamba creates .bam.bai, rename to .bai for compatibility\n bam_bai = inBam + '.bai'\n expected_bai = inBam[:-4] + '.bai' # sample.bam -> sample.bai\n if os.path.exists(bam_bai) and bam_bai != expected_bai:\n shutil.move(bam_bai, expected_bai)\n\n def merge(self, inBams, outBam, threads=None):\n \"\"\"\n Merge multiple sorted BAM files into a single BAM file.\n\n NOTE: This function is currently disabled due to a segfault bug in\n sambamba 1.0.1 merge. Use samtools merge or Picard MergeSamFiles instead.\n\n Args:\n inBams: List of input BAM file paths (must be coordinate-sorted)\n outBam: Output merged BAM file path\n threads: Number of threads to use (default: auto)\n\n Raises:\n NotImplementedError: Always raised - sambamba merge has a known bug\n \"\"\"\n raise NotImplementedError(\n \"sambamba merge is disabled due to a segfault bug in sambamba 1.0.1. \"\n \"Use samtools merge or Picard MergeSamFiles instead.\"\n )\n\n def flagstat(self, inBam, threads=None):\n \"\"\"\n Get alignment statistics from a BAM file.\n\n Args:\n inBam: Input BAM file path\n threads: Number of threads to use (default: auto)\n\n Returns:\n Dictionary with parsed flagstat statistics\n \"\"\"\n threads = util_misc.sanitize_thread_count(threads)\n\n args = ['-t', str(threads), inBam]\n\n # Capture output\n tool_cmd = [self.install_and_get_path(), 'flagstat'] + [str(a) for a in args]\n log.debug(' '.join(tool_cmd))\n\n output = subprocess.check_output(tool_cmd).decode('UTF-8')\n\n return self._parse_flagstat(output)\n\n def _parse_flagstat(self, output):\n \"\"\"\n Parse sambamba flagstat output into a dictionary.\n\n The output format is similar to samtools flagstat:\n 123 + 0 in total (QC-passed reads + QC-failed reads)\n 0 + 0 secondary\n ...\n \"\"\"\n stats = {}\n\n for line in output.strip().split('\\n'):\n if not line.strip():\n continue\n\n # Parse lines like \"123 + 0 in total...\"\n match = re.match(r'(\\d+)\\s*\\+\\s*(\\d+)\\s+(.*)', line)\n if match:\n passed = int(match.group(1))\n failed = int(match.group(2))\n description = match.group(3).strip()\n\n # Create clean key from description\n if 'in total' in description:\n key = 'total'\n elif 'secondary' in description:\n key = 'secondary'\n elif 'supplementary' in description:\n key = 'supplementary'\n elif 'duplicates' in description:\n key = 'duplicates'\n elif 'mapped' in description and 'mate' not in description:\n key = 'mapped'\n elif 'paired in sequencing' in description:\n key = 'paired'\n elif 'read1' in description:\n key = 'read1'\n elif 'read2' in description:\n key = 'read2'\n elif 'properly paired' in description:\n key = 'properly_paired'\n elif 'with itself and mate mapped' in description:\n key = 'both_mapped'\n elif 'singletons' in description:\n key = 'singletons'\n elif 'mate mapped to a different chr' in description:\n if 'mapQ>=5' in description:\n key = 'mate_diff_chr_mapq5'\n else:\n key = 'mate_diff_chr'\n else:\n # Fallback: use cleaned description as key\n key = re.sub(r'[^a-z0-9]+', '_', description.lower()).strip('_')\n\n stats[key] = passed\n stats[f'{key}_qcfailed'] = failed\n\n return stats\n\n def markdup(self, inBam, outBam, remove_duplicates=False, threads=None,\n hash_table_size=None, overflow_list_size=None):\n \"\"\"\n Mark or remove duplicate reads using sambamba markdup.\n\n Args:\n inBam: Input BAM file (must be coordinate-sorted)\n outBam: Output BAM file\n remove_duplicates: If True, remove duplicates; if False, mark them (default: False)\n threads: Number of threads to use (default: auto)\n hash_table_size: Size of hash table for finding read pairs (optional)\n overflow_list_size: Size of overflow list (optional)\n \"\"\"\n threads = util_misc.sanitize_thread_count(threads)\n\n args = []\n\n # Remove duplicates flag\n if remove_duplicates:\n args.append('-r')\n\n # Thread count\n args.extend(['-t', str(threads)])\n\n # Optional tuning parameters\n if hash_table_size:\n args.extend(['--hash-table-size', str(hash_table_size)])\n if overflow_list_size:\n args.extend(['--overflow-list-size', str(overflow_list_size)])\n\n # Input and output files\n args.append(inBam)\n args.append(outBam)\n\n self.execute('markdup', args)\n" }, { "path": "src/viral_ngs/core/samtools.py", "content": "'''\n The Samtools package.\n\n TO DO: much of this stuff can be all eliminated by using pysam instead, as\n pysam (in its current versions) is meant to be the complete python\n implementation of htslib/samtools.\n\n http://pysam.readthedocs.org/en/latest/usage.html#using-samtools-commands-within-python\n\n Current bug with pysam 0.8.1: nosetests does not work unless you use --nocapture.\n python -m unittest works. Something about redirecting stdout.\n Actually, Travis CI still has issues with pysam and stdout even with --nocapture.\n\n pysam 0.9.1 stops redirecting stdout which makes things much easier,\n but it's a pain to pip install.\n'''\n\nimport logging\nimport shutil\nimport os\nimport re\nimport os.path\nimport subprocess\nimport tempfile\nimport contextlib\nfrom collections import OrderedDict\nfrom decimal import *\n\nimport pysam\n\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = 'samtools'\n\nlog = logging.getLogger(__name__)\n\nclass SamtoolsTool(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(SamtoolsTool, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').split('\\n')[0].split()[1]\n\n def execute(self, command, args, stdout=None, stderr=None, background=False): # pylint: disable=W0221\n tool_cmd = [self.install_and_get_path(), command] + args\n log.debug(' '.join(tool_cmd))\n if stdout:\n stdout = open(stdout, 'w')\n if stderr:\n stderr = open(stderr, 'w')\n\n env = os.environ.copy()\n env.pop('JAVA_HOME', None)\n if background:\n subprocess.Popen(tool_cmd, stdout=stdout, stderr=stderr, env=env)\n else:\n subprocess.check_call(tool_cmd, stdout=stdout, stderr=stderr, env=env)\n\n if stdout:\n stdout.close()\n if stderr:\n stderr.close()\n\n def view(self, args, inFile, outFile, regions=None, threads=None, background=False):\n regions = regions or []\n args = args or []\n\n # -@ seems to result in segfaults in some cases\n # so this is commented out for now...\n\n self.execute('view', args + ['-o', outFile, inFile] + regions, background=background)\n #opts = args + ['-o', outFile, inFile] + regions\n #pysam.view(*opts)\n\n def bam2fq(self, inBam, outFq1, outFq2=None):\n if outFq2 is None:\n self.execute('bam2fq', ['-n', inBam], stdout=outFq1)\n else:\n self.execute('bam2fq', ['-1', outFq1, '-2', outFq2, inBam])\n\n def bam2fq_pipe(self, inBam, threads=None):\n tool_cmd = [self.install_and_get_path(), 'bam2fq']\n if threads is not None:\n tool_cmd.extend(['-@', str(threads)])\n tool_cmd.extend(['-n', inBam])\n log.debug(' '.join(tool_cmd) + ' |')\n p = subprocess.Popen(tool_cmd, stdout=subprocess.PIPE)\n return p\n\n def bam2fa(self, inBam, outFa1, outFa2=None, outFa0=None, append_mate_num=False):\n if outFa2 is None:\n args = ['-N' if append_mate_num else '-n']\n else:\n args = ['-1', outFa1, '-2', outFa2]\n if outFa0:\n args += ['-0', outFa0]\n args += [inBam]\n if outFa2 is None:\n self.execute('fasta', args, stdout=outFa1)\n else:\n self.execute('fasta', args)\n\n def bam2fa_pipe(self, inBam):\n tool_cmd = [self.install_and_get_path(), 'fasta', '-n', inBam]\n log.debug(' '.join(tool_cmd) + ' |')\n p = subprocess.Popen(tool_cmd, stdout=subprocess.PIPE)\n return p.stdout\n\n @contextlib.contextmanager\n def bam2fq_tmp(self, inBam):\n with util_file.tempfnames(('.1.fq', '.2.fq')) as (reads1, reads2):\n self.bam2fq(inBam, reads1, reads2)\n yield reads1, reads2\n\n @contextlib.contextmanager\n def bam2fa_tmp(self, inBam):\n with util_file.tempfnames(('.1.fa', '.2.fa')) as (reads1, reads2):\n self.bam2fa(inBam, reads1, reads2)\n yield reads1, reads2\n\n def import_fastq(self, inFastq1, inFastq2, outBam,\n sample_name, library_name=None, platform='illumina',\n read_group_id=None, platform_unit=None,\n sequencing_center=None, run_date=None,\n threads=None):\n \"\"\"\n Convert paired FASTQ files to unaligned BAM using samtools import.\n\n Multi-threaded alternative to Picard FastqToSam with 3-4x speedup.\n\n Args:\n inFastq1: R1 FASTQ file path\n inFastq2: R2 FASTQ file path (can be None for single-end)\n outBam: Output BAM file path\n sample_name: Sample name (SM tag, required)\n library_name: Library name (LB tag, defaults to sample_name)\n platform: Sequencing platform (PL tag, default: 'illumina')\n read_group_id: Read group ID (ID tag, defaults to 'A')\n platform_unit: Platform unit (PU tag, e.g., flowcell.lane.barcode)\n sequencing_center: Sequencing center (CN tag)\n run_date: Run date in ISO format (DT tag)\n threads: Number of threads for compression (default: auto)\n \"\"\"\n # Handle empty FASTQ edge case\n if self._is_fastq_empty(inFastq1):\n log.warning(\"FASTQ1 file is empty; creating empty BAM file: %s\", outBam)\n self._create_empty_bam_with_header(\n outBam, sample_name, library_name, platform,\n read_group_id, platform_unit, sequencing_center, run_date\n )\n return\n\n # Build read group string\n rg_id = read_group_id or 'A'\n lib_name = library_name or sample_name\n rg_parts = [f'@RG', f'ID:{rg_id}', f'SM:{sample_name}', f'LB:{lib_name}', f'PL:{platform}']\n\n if platform_unit:\n rg_parts.append(f'PU:{platform_unit}')\n if sequencing_center:\n rg_parts.append(f'CN:{sequencing_center}')\n if run_date:\n rg_parts.append(f'DT:{run_date}')\n\n rg_string = '\\t'.join(rg_parts)\n\n # Build command\n args = ['-r', rg_string]\n\n # Add threading if specified\n if threads:\n args.extend(['-@', str(threads)])\n\n # Add input files\n args.extend(['-1', inFastq1])\n if inFastq2 and not self._is_fastq_empty(inFastq2):\n args.extend(['-2', inFastq2])\n\n # Add output\n args.extend(['-o', outBam])\n\n self.execute('import', args)\n\n def _is_fastq_empty(self, fastq_file):\n \"\"\"\n Check if a FASTQ file is semantically empty (contains no reads).\n\n Args:\n fastq_file: Path to FASTQ file\n\n Returns:\n bool: True if file is empty, False if it contains data\n \"\"\"\n if not fastq_file or not os.path.exists(fastq_file):\n return True\n\n # Large files are assumed to be non-empty\n if os.path.getsize(fastq_file) > 1024:\n return False\n\n # Small files: check if they contain only whitespace\n with util_file.open_or_gzopen(fastq_file, 'r') as f:\n return len(f.read().strip()) == 0\n\n def _create_empty_bam_with_header(self, outBam, sample_name, library_name=None,\n platform='illumina', read_group_id=None,\n platform_unit=None, sequencing_center=None,\n run_date=None):\n \"\"\"\n Create an empty BAM file with a proper header including RG tags.\n\n Args:\n outBam: Output BAM file path\n sample_name: Sample name (SM tag)\n library_name: Library name (LB tag, defaults to sample_name)\n platform: Sequencing platform (PL tag)\n read_group_id: Read group ID (ID tag, defaults to 'A')\n platform_unit: Platform unit (PU tag)\n sequencing_center: Sequencing center (CN tag)\n run_date: Run date in ISO format (DT tag)\n \"\"\"\n rg_id = read_group_id or 'A'\n lib_name = library_name or sample_name\n\n header = {\n 'HD': {'VN': '1.6', 'SO': 'queryname'},\n 'RG': [{\n 'ID': rg_id,\n 'SM': sample_name,\n 'LB': lib_name,\n 'PL': platform,\n }]\n }\n\n # Add optional fields if present\n if platform_unit:\n header['RG'][0]['PU'] = platform_unit\n if sequencing_center:\n header['RG'][0]['CN'] = sequencing_center\n if run_date:\n header['RG'][0]['DT'] = run_date\n\n # Write empty BAM file with pysam\n with pysam.AlignmentFile(outBam, 'wb', header=header) as outf:\n pass # No reads to write\n\n log.info(\"Created empty BAM file with header: %s\", outBam)\n\n def sort(self, inFile, outFile, args=None, threads=None):\n # inFile can be .sam, .bam, .cram\n # outFile can be .sam, .bam, .cram\n args = args or []\n if '-@' not in args:\n args.extend(('-@', str(util_misc.sanitize_thread_count(threads))))\n if '-T' not in args and os.path.isdir(tempfile.tempdir):\n args.extend(('-T', tempfile.tempdir))\n\n args.extend(('-o', outFile, inFile))\n self.execute('sort', args)\n\n def merge(self, inFiles, outFile, options=None):\n \"Merge a list of inFiles to create outFile.\"\n options = options or ['-f']\n\n # We are using -f for now because mkstempfname actually makes an empty\n # file, and merge fails with that as output target without the -f.\n # When mkstempfname is fixed, we should remove the -f.\n self.execute('merge', options + [outFile] + inFiles)\n\n def index(self, inBam, threads=None):\n # inBam can be .bam or .cram\n args = []\n if threads:\n threads = util_misc.sanitize_thread_count(threads)\n args.extend(['-@', str(threads)])\n args.append(inBam)\n self.execute('index', args)\n\n def faidx(self, inFasta, overwrite=False):\n ''' Index reference genome for samtools '''\n outfname = inFasta + '.fai'\n if os.path.isfile(outfname):\n if overwrite:\n os.unlink(outfname)\n else:\n return\n #pysam.faidx(inFasta)\n with util_file.fastas_with_sanitized_ids(inFasta, use_tmp=True) as sanitized_fastas:\n sanitized_fasta = sanitized_fastas[0]\n self.execute('faidx', [sanitized_fasta])\n shutil.copyfile(sanitized_fasta + '.fai', outfname)\n\n def depth(self, inBam, outFile, options=None):\n \"\"\" Write a TSV file with coverage depth by position \"\"\"\n options = options or [\"-aa\", \"-m\", \"1000000\"]\n\n self.execute('depth', options + [inBam], stdout=outFile)\n\n def idxstats(self, inBam, statsFile, threads=None):\n args = []\n if threads:\n threads = util_misc.sanitize_thread_count(threads)\n args.extend(['-@', str(threads)])\n args.append(inBam)\n self.execute('idxstats', args, stdout=statsFile)\n\n def reheader(self, inBam, headerFile, outBam):\n self.execute('reheader', [headerFile, inBam], stdout=outBam)\n\n def dumpHeader(self, inBam, outHeader):\n opts = []\n if inBam.endswith('.bam'):\n opts = ['-H']\n elif inBam.endswith('.sam'):\n opts = ['-H', '-S']\n #header = pysam.view(*opts)\n self.view(opts, inBam, outHeader)\n\n def removeDoublyMappedReads(self, inBam, outBam):\n #opts = ['-b', '-f 2']\n opts = ['-b', '-F' '1028', '-f', '2', '-@', '3']\n self.view(opts, inBam, outBam)\n\n def filter_to_proper_primary_mapped_reads(self, inBam, outBam, require_pairs_to_be_proper=True, reject_singletons=True, reject_duplicates=True):\n '''\n This function writes a bam file filtered to include only reads that are:\n - not flagged as duplicates\n - not secondary or supplementary (split/chimeric reads)\n - For paired-end reads:\n - marked as proper pair (if require_pairs_to_be_proper=True) OR\n both not unmapped (if require_pairs_to_be_proper=False) OR\n not a member of a pair with a singleton (if reject_singletons=True)\n - For single-end reads:\n mapped\n\n '''\n\n with pysam.AlignmentFile(inBam, 'rb', check_sq=False) as inb:\n with pysam.AlignmentFile(outBam, 'wb', header=inb.header) as outf:\n # process the lines individually and write them or not, depending on the flags\n # For explanation of flags, see:\n # https://broadinstitute.github.io/picard/explain-flags.html\n # https://pysam.readthedocs.io/en/latest/api.html\n # https://samtools.github.io/hts-specs/SAMv1.pdf\n # https://github.com/pysam-developers/pysam/blob/31183d7fac52b529b304bdf61ff933818ae4a71f/samtools/stats.c#L72-L81\n\n for read in inb:\n # check if a read is paired\n is_single_end=not read.is_paired\n\n # if a PCR/optical duplicate, do not write\n if reject_duplicates and read.is_duplicate:\n continue\n\n # if a read is a secondary or supplementary mapping (split/chimeric), do not write\n if read.is_secondary or read.is_supplementary:\n continue\n\n # do not write if\n # paired-end\n if (read.is_paired and \n # reject anything not marked as proper pair (this bit is not guaranteed)\n (require_pairs_to_be_proper and not read.is_proper_pair) or\n # reject pairs where both mates are unmapped\n (read.mate_is_unmapped and read.is_unmapped) or\n # reject reads where only one mate is mapped (singletons)\n (reject_singletons and (read.mate_is_unmapped or read.is_unmapped))):\n continue \n\n if is_single_end and read.is_unmapped: # or if this is single-end and unmapped, reject\n continue\n\n # otherwise write the read to the output\n outf.write(read)\n\n def filterByCigarString(self, inBam, outBam, \n regexToMatchForRemoval='^((?:[0-9]+[ID]){1}(?:[0-9]+[MNIDSHPX=])+)|((?:[0-9]+[MNIDSHPX=])+(?:[0-9]+[ID]){1})$', \n invertResult=False):\n '''\n This function applies a regex to the cigar string for each read.\n If the regex matches, the read is not written to the output unless\n invertResult is True.\n The default regex matches cigar strings with trailing or leading indels:\n '^((?:[0-9]+[ID]){1}(?:[0-9]+[MNIDSHPX=])+)|((?:[0-9]+[MNIDSHPX=])+(?:[0-9]+[ID]){1})$'\n\n '''\n regex = re.compile(regexToMatchForRemoval)\n with pysam.AlignmentFile(inBam, 'rb', check_sq=False) as inb:\n with pysam.AlignmentFile(outBam, 'wb', header=inb.header) as outf:\n # process the lines individually and write them or not, depending on \n # whether they match regexToMatchForRemoval\n for read in inb:\n if read.cigarstring:\n # perform a regex match\n matches = regex.search(read.cigarstring)\n # if the regex was found (or not, if inverted)\n if (not invertResult and matches) or (invertResult and not matches):\n # continue to the next read (don't write out this one)\n continue\n else:\n if invertResult:\n continue\n # otherwise write out the line\n outf.write(read)\n\n\n def downsample(self, inBam, outBam, probability):\n\n if not probability:\n raise Exception(\"Probability must be defined\")\n if float(probability) <= 0 or float(probability) > 1:\n raise Exception(\"Probability must be in range (0,1]. This value was given: %s\" % probability)\n\n opts = ['-s', str(1) + '.' + str(probability).split('.')[1], '-@', '3'] # -s subsamples: seed.fraction\n self.view(opts, inBam, outBam)\n\n def downsample_to_approx_count(self, inBam, outBam, read_count):\n total_read_count = self.count(inBam)\n probability = Decimal(int(read_count)) / Decimal(total_read_count)\n probability = 1 if probability > 1 else probability\n\n if probability < 1:\n self.downsample(inBam, outBam, probability)\n else:\n _log.info(\"Requested downsample count exceeds number of reads. Including all reads in output.\")\n shutil.copyfile(inBam, outBam)\n\n def getHeader(self, inBam):\n ''' fetch BAM header as a list of tuples (already split on tabs) '''\n tmpf = util_file.mkstempfname('.txt')\n self.dumpHeader(inBam, tmpf)\n with open(tmpf, 'rb') as inf:\n header = list(line.decode(\"latin-1\").rstrip('\\n').split('\\t') for line in inf)\n os.unlink(tmpf)\n return header\n\n def getReadGroups(self, inBam):\n ''' fetch all read groups from the BAM header as an OrderedDict of\n RG ID -> RG dict. The RG dict is a mapping of read group keyword\n (like ID, DT, PU, LB, SM, CN, PL, etc) to value. ID is included\n and not stripped out. ID is required for all read groups.\n Resulting keys are in same order as @RG lines in bam file.\n '''\n rgs = [\n dict(x.split(':', 1) for x in row[1:]) for row in self.getHeader(inBam) if len(row) > 0 and row[0] == '@RG'\n ]\n return OrderedDict((rg['ID'], rg) for rg in rgs)\n\n def count(self, inBam, opts=None, regions=None):\n opts = opts or []\n regions = regions or []\n\n cmd = [self.install_and_get_path(), 'view', '-c'] + opts + [inBam] + regions\n return int(subprocess.check_output(cmd).strip())\n #if inBam.endswith('.sam') and '-S' not in opts:\n # opts = ['-S'] + opts\n #cmd = ['-c'] + opts + [inBam] + regions\n #return int(pysam.view(*cmd)[0].strip())\n\n def mpileup(self, inBam, outPileup, opts=None):\n opts = opts or []\n\n self.execute('mpileup', opts + [inBam], stdout=outPileup, stderr='/dev/null') # Suppress info messages\n\n def isEmpty(self, inBam):\n if not os.path.isfile(inBam):\n return True\n else:\n tmpf = util_file.mkstempfname('.txt')\n self.dumpHeader(inBam, tmpf)\n header_size = os.path.getsize(tmpf)\n if (os.path.getsize(inBam) > (100 + 5 * header_size)):\n # large BAM file: assume it is not empty\n # a BAM file definitely has reads in it if its filesize is larger\n # than just the header itself\n return False\n else:\n # small BAM file: just count and see if it's non-zero\n return (0 == self.count(inBam))\n" }, { "path": "src/viral_ngs/core/splitcode.py", "content": "import csv\nimport glob\nimport json\nimport logging\nimport os\nimport shutil\nimport subprocess\nimport tempfile\n\nimport matplotlib.pyplot as plt\nimport numpy as np\nimport pandas as pd\n\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = 'splitcode'\n\nlog = logging.getLogger(__name__)\n\nclass SplitCodeTool(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(SplitCodeTool, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').strip()\n\n def execute( self,\n n_fastqs,\n threads,\n config_file,\n keep_file,\n unassigned_r1,\n unassigned_r2,\n summary_stats,\n r1,\n r2,\n splitcode_opts=None,\n gzip_output=False,\n keep_r1_r2_suffixes=True,\n predemux_r1_trim_5prime_num_bp=None,\n predemux_r1_trim_3prime_num_bp=None,\n predemux_r2_trim_5prime_num_bp=None,\n predemux_r2_trim_3prime_num_bp=None\n ):\n \"\"\"\n Execute the splitcode command with the provided parameters.\n\n :param n_fastqs: Number of FASTQ files (e.g., 2 for paired-end reads).\n :param threads: Number of threads to use.\n :param config_file: Path to the configuration file.\n :param keep_file: Path to the keep file.\n :param unassigned_r1: Path for unassigned R1 reads.\n :param unassigned_r2: Path for unassigned R2 reads.\n :param summary_stats: Path to the summary statistics file.\n :param r1: Input FASTQ file for R1 reads.\n :param r2: Input FASTQ file for R2 reads.\n :param splitcode_opts: additional parameters to pass to splitcode\n \"\"\"\n splitcode_opts = splitcode_opts or []\n\n # documentation: \n # https://splitcode.readthedocs.io/en/latest/reference_guide.html#command-line-config-optional\n\n tool_cmd = [\n self.install_and_get_path(),\n f\"--nFastqs={n_fastqs}\",\n f\"-t\", str(threads),\n f\"-c\", config_file,\n f\"--keep={keep_file}\",\n f\"--unassigned={unassigned_r1},{unassigned_r2}\",\n f\"--summary\", summary_stats\n ]\n if gzip_output and \"--gzip\" not in splitcode_opts:\n tool_cmd.append(\"--gzip\")\n if keep_r1_r2_suffixes and \"--keep-r1-r2\" not in splitcode_opts:\n tool_cmd.append(\"--keep-r1-r2\")\n if predemux_r1_trim_3prime_num_bp or predemux_r2_trim_3prime_num_bp:\n r1_3prime_bp_to_remove = predemux_r1_trim_3prime_num_bp or 0\n r2_3prime_bp_to_remove = predemux_r2_trim_3prime_num_bp or 0\n tool_cmd.extend([\"--trim-3\",\n f\"{r1_3prime_bp_to_remove},{r2_3prime_bp_to_remove}\"])\n if predemux_r1_trim_5prime_num_bp or predemux_r2_trim_5prime_num_bp:\n r1_5prime_bp_to_remove = predemux_r1_trim_5prime_num_bp or 0\n r2_5prime_bp_to_remove = predemux_r2_trim_5prime_num_bp or 0\n tool_cmd.extend([\"--trim-5\", \n f\"{r1_5prime_bp_to_remove},{r2_5prime_bp_to_remove}\"])\n\n tool_cmd.extend(splitcode_opts)\n tool_cmd.extend([r1,r2])\n\n log.debug('Running splitcode with command: %s', ' '.join(tool_cmd))\n try:\n return subprocess.check_call(tool_cmd)\n except subprocess.CalledProcessError as e:\n log.error(f'Splitcode failed with return code {e.returncode}')\n log.error(f'Command was: {\" \".join(tool_cmd)}')\n raise\n\n def check_installation(self):\n \"\"\"Ensure the tool is properly installed.\"\"\"\n if not shutil.which(TOOL_NAME):\n raise FileNotFoundError(f\"{TOOL_NAME} is not installed or not in PATH.\")\n\n def run_splitcode(self, **kwargs):\n \"\"\"\n Wrapper method to execute the splitcode command with named parameters.\n\n Expected kwargs:\n - n_fastqs, threads, config_file, keep_file, unassigned_r1, unassigned_r2, summary_stats, r1, r2\n \"\"\"\n self.execute(\n kwargs.get('n_fastqs', 2),\n kwargs.get('threads', 1),\n kwargs['config_file'],\n kwargs['keep_file'],\n kwargs['unassigned_r1'],\n kwargs['unassigned_r2'],\n kwargs['summary_stats'],\n kwargs['r1'],\n kwargs['r2']\n )\n\n\n# ==================\n# *** Splitcode helper functions ***\n# ==================\n\n\ndef create_splitcode_lookup_table(sample_sheet_or_dataframe, csv_out, unmatched_name, pool_ids=None, append_run_id=None, check_sample_sheet_consistency=False):\n \"\"\"\n Create a lookup table (LUT) consolidating splitcode demux results with sample metadata.\n\n After splitcode demultiplexes pooled samples by inner barcodes (barcode_3), this function\n reads the splitcode summary JSON files, joins them with the sample sheet, and creates a\n unified CSV mapping samples to barcodes to read counts. This LUT is used by downstream\n plotting and metrics functions.\n\n The function performs 3-barcode demux integration by:\n 1. Loading sample sheet with all barcode mappings (barcode_1, barcode_2, barcode_3)\n 2. Building pool identifiers from outer barcode pairs (barcode_1 + barcode_2)\n 3. Loading splitcode summary JSONs for each pool\n 4. Extracting read counts at Hamming distance 0 (perfect match) and 1 (1-mismatch)\n 5. Joining splitcode counts with sample metadata based on run identifiers\n 6. Creating unmatched read entries for reads that didn't match any barcode\n 7. Outputting a CSV with unified sample-to-barcode-to-count mappings\n\n Parameters\n ----------\n sample_sheet_or_dataframe : str or pd.DataFrame\n Either:\n - Path to TSV file with barcode mappings (str), OR\n - DataFrame from SampleSheet.inner_demux_mapper() (pd.DataFrame)\n\n If DataFrame, must already contain columns:\n - barcode_1, barcode_2, barcode_3, sample, library_id_per_sample\n - run: Sample run identifier (sample.lLibrary[.FlowcellID])\n - muxed_run: Pool identifier (barcode_1-barcode_2.lLibrary[.FlowcellID])\n\n If str (file path), must be TSV with columns:\n - barcode_1, barcode_2, barcode_3, sample, library_id_per_sample\n csv_out : str\n Output path for the lookup table CSV file\n unmatched_name : str\n Name prefix for unmatched/unassigned reads (e.g., \"Unmatched\")\n pool_ids : list, optional\n List of pool IDs to process. If None/empty, processes all pools found.\n append_run_id : str, optional\n Suffix to append to run identifiers (typically flowcell ID).\n Only used when sample_sheet_or_dataframe is a file path (str).\n Ignored when a DataFrame is provided (which already has run/muxed_run).\n check_sample_sheet_consistency : bool, optional\n If True, validates sample sheet for duplicate barcode combinations\n\n Returns\n -------\n str\n Path to the output CSV file containing the lookup table\n\n Output CSV Schema\n -----------------\n The output CSV contains columns:\n - sample: Sample identifier\n - library_id: Library/pool identifier\n - barcode_1: Outer barcode (i7 index)\n - barcode_2: Outer barcode (i5 index)\n - inline_barcode: Inner barcode (barcode_3)\n - run: Sample run identifier (sample.lLibrary[.FlowcellID])\n - muxed_pool: Pool identifier (barcode_1-barcode_2.lLibrary)\n - num_reads_hdistance0: Read count with perfect barcode match\n - num_reads_hdistance1: Read count with 1-mismatch to barcode\n - num_reads_total: Total reads (hdistance0 + hdistance1)\n\n Notes\n -----\n - Expects splitcode summary JSON files named \"{pool}_summary.json\" in csv_out directory\n - Validates that (barcode_1, barcode_2) pairs don't have duplicate barcode_3 values\n - Handles pools with 0 reads gracefully by creating empty metrics\n - Unmatched reads get barcode_3 set to all \"N\"s matching expected barcode length\n \"\"\"\n pool_ids = pool_ids or []\n\n outDir=os.path.dirname(csv_out)\n\n # Load or reuse barcode data\n # If we receive a DataFrame (from SampleSheet.inner_demux_mapper()), use it directly\n # This ensures pool IDs match exactly what was used to create summary JSON files\n if isinstance(sample_sheet_or_dataframe, pd.DataFrame):\n log.debug(\"Using provided DataFrame for barcode lookup table\")\n barcodes_df = sample_sheet_or_dataframe.copy()\n # Reset index to make 'sample' a regular column (inner_demux_mapper sets it as index)\n barcodes_df.reset_index(inplace=True)\n\n # Rename 'muxed_run' to 'muxed_pool' for consistency with legacy code\n # The inner_demux_mapper() creates 'muxed_run' column, but this function expects 'muxed_pool'\n if 'muxed_run' in barcodes_df.columns and 'muxed_pool' not in barcodes_df.columns:\n barcodes_df['muxed_pool'] = barcodes_df['muxed_run']\n else:\n # Legacy path: read from file and build columns\n log.debug(\"Reading sample sheet from file: %s\", sample_sheet_or_dataframe)\n barcodes_df = pd.read_csv(sample_sheet_or_dataframe, sep=\"\\t\", dtype=str)\n\n # Build \"run\" column = \".l[.]\"\n def build_sample_library_id_string(row):\n sample_val = row.get(\"sample\", \"\")\n lib_val = row.get(\"library_id_per_sample\", \"\")\n run_str = f\"{sample_val}.l{lib_val}\"\n if append_run_id:\n run_str += f\".{append_run_id}\"\n return run_str\n barcodes_df[\"run\"] = barcodes_df.apply(build_sample_library_id_string, axis=1)\n\n def build_muxed_run_string(row):\n b1 = row.get(\"barcode_1\", \"\")\n b2 = row.get(\"barcode_2\", None)\n if b2 and b2.strip():\n muxed_sample = f\"{b1}-{b2}\"\n else:\n muxed_sample = b1\n\n lib_val = row.get(\"library_id_per_sample\", \"\")\n muxed_run_str = f\"{muxed_sample}.l{lib_val}\"\n if append_run_id:\n muxed_run_str += f\".{append_run_id}\"\n return muxed_run_str\n barcodes_df[\"muxed_pool\"] = barcodes_df.apply(build_muxed_run_string, axis=1)\n\n df_csv_out = f\"{csv_out}\"\n\n i7_barcodes = list(set(barcodes_df[\"barcode_1\"].values))\n barcodes = sorted(list(set(barcodes_df[\"barcode_3\"].values)))\n\n def duplication_check(df, primary_cols, secondary_col, error_message_header=None, error_message=None):\n default_error_message_header = \"Error: More than one '{column_to_check_for_duplicates}' value present for distinct combinations of the columns {affected_column_names}:\"\n default_error_message = \"'{duplicated_values}' appears {duplicate_count} times, for {affected_values}.\"\n\n error_message_header = error_message_header or default_error_message_header\n error_message = error_message or default_error_message\n\n # Check which placeholders are actually present in the template\n err_header_has_dup_check_col = '{column_to_check_for_duplicates}' in error_message_header\n err_header_has_affected_column_names = '{affected_column_names}' in error_message_header\n\n err_msg_has_affected_values = '{affected_values}' in error_message\n err_msg_has_dup_val = '{duplicated_values}' in error_message\n err_msg_has_count = '{duplicate_count}' in error_message\n\n\n # To store all generated error messages\n errors = []\n\n # Group the dataframe by the primary columns\n grouped = df.groupby(primary_cols, dropna=False)\n\n error_header_out=None\n for group_key, subdf in grouped:\n # If there's only one primary column, group_key is a single value\n # Otherwise, it's a tuple of values\n if isinstance(group_key, tuple):\n # E.g.: (\"North\", \"A\")\n group_str = ','.join(\n f\"{col}={val}\" for col, val in zip(primary_cols, group_key)\n )\n else:\n # E.g.: \"North\" when there's only one primary column\n group_str = f\"{primary_cols[0]}={group_key}\"\n\n # Count occurrences of each value in secondary_col\n value_counts = subdf[secondary_col].value_counts(dropna=True)\n # Identify duplicates: values with count > 1\n duplicates = value_counts[value_counts > 1]\n\n\n # Build a separate message for each duplicated value\n for val, count_ in duplicates.items():\n msg_dict = {}\n header_msg_dict = {}\n\n if err_msg_has_affected_values:\n msg_dict['affected_values'] = group_str\n if err_msg_has_dup_val:\n msg_dict['duplicated_values'] = val\n if err_msg_has_count:\n msg_dict['duplicate_count'] = count_\n if err_header_has_dup_check_col:\n header_msg_dict['column_to_check_for_duplicates'] = secondary_col\n if err_header_has_affected_column_names:\n header_msg_dict['affected_column_names'] = f\"{'+'.join([f'{chr(39)+c+chr(39)}' for c in primary_cols])}\"\n\n if error_header_out is None:\n error_header_out = error_message_header.format(**header_msg_dict)\n message = error_message.format(**msg_dict)\n errors.append(message)\n return (error_header_out, errors)\n\n\n duplication_check_conditions = [\n {\n \"columns\": [\"barcode_1\",\"barcode_2\"],\n \"column_to_check_for_duplicates\": \"barcode_3\",\n }\n ]\n\n for dup_condition in duplication_check_conditions:\n\n problem_header, problems = duplication_check( barcodes_df,\n dup_condition[\"columns\"],\n dup_condition[\"column_to_check_for_duplicates\"],\n dup_condition.get(\"error_message_header\", None),\n dup_condition.get(\"error_message\", None) )\n problem_found = False\n if len(problems):\n log.warning(problem_header)\n for problem in problems:\n log.warning(f\"\\t{problem}\")\n problem_found = True\n if problem_found:\n raise ValueError(\"Problem(s) found in sample sheet; see above for details.\")\n\n pool_dfs = []\n unmatched_dfs = []\n\n # Build barcode_group column for JSON lookup: outer barcodes only, no library_id.\n # Splitcode produces ONE summary JSON per outer barcode group (barcode_1+barcode_2),\n # but muxed_pool includes library_id_per_sample. When samples have unique library_ids,\n # there are multiple muxed_pool values per barcode group but only one JSON file.\n def _barcode_group(row):\n b1 = row.get(\"barcode_1\", \"\")\n b2 = row.get(\"barcode_2\", \"\")\n if b2 and str(b2).strip():\n return f\"{b1}-{b2}\"\n return b1\n barcodes_df[\"barcode_group\"] = barcodes_df.apply(_barcode_group, axis=1)\n\n for barcode_group in barcodes_df[\"barcode_group\"].unique():\n samplesheet_rows_for_pool_df = barcodes_df[barcodes_df[\"barcode_group\"] == barcode_group]\n\n # Find the splitcode summary JSON file for this barcode group.\n # Try each muxed_pool value in the group until we find a matching JSON.\n # This handles the case where library_id_per_sample differs per sample:\n # splitcode produces one JSON named after whichever muxed_pool was used as pool_id.\n splitcode_summary_file = None\n tried_patterns = []\n try:\n for candidate_pool in samplesheet_rows_for_pool_df[\"muxed_pool\"].unique():\n summary_pattern = f\"{outDir}/{candidate_pool}_summary.json\"\n tried_patterns.append(summary_pattern)\n matching_files = glob.glob(summary_pattern)\n if matching_files:\n splitcode_summary_file = matching_files[0]\n if len(matching_files) > 1:\n log.warning(f\"Multiple summary JSON files match pattern '{summary_pattern}':\")\n for f in matching_files:\n log.warning(f\" - {f}\")\n log.warning(f\"Using first match: {splitcode_summary_file}\")\n break\n\n if splitcode_summary_file is None:\n # JSON file not found - list directory contents for debugging\n log.error(f\"Splitcode summary JSON not found for barcode group '{barcode_group}'\")\n log.error(f\" Tried patterns: {tried_patterns}\")\n log.error(f\" Searching in directory: {outDir}\")\n\n # List all files in the output directory to help debug\n try:\n dir_contents = os.listdir(outDir)\n log.error(f\" Directory contents ({len(dir_contents)} files):\")\n # List JSON files first (most relevant)\n json_files = [f for f in dir_contents if f.endswith('.json')]\n if json_files:\n log.error(f\" JSON files found ({len(json_files)}):\")\n for f in sorted(json_files):\n log.error(f\" - {f}\")\n else:\n log.error(f\" No JSON files found in directory\")\n\n # List first 20 other files for context\n other_files = [f for f in dir_contents if not f.endswith('.json')]\n if other_files:\n log.error(f\" Other files (showing first 20 of {len(other_files)}):\")\n for f in sorted(other_files)[:20]:\n log.error(f\" - {f}\")\n except OSError as list_err:\n log.error(f\" Could not list directory contents: {list_err}\")\n\n raise FileNotFoundError(\n f\"Splitcode summary JSON not found for barcode group '{barcode_group}'. \"\n f\"Tried patterns: {tried_patterns}. \"\n f\"Check logs above for directory contents.\"\n )\n\n log.debug(f\"Loading splitcode summary from: {splitcode_summary_file}\")\n\n with open(splitcode_summary_file, \"r\") as f:\n splitcode_summary = json.load(f)\n\n except (FileNotFoundError, IndexError) as e:\n # Re-raise with more context (directory listing already logged above)\n raise\n except json.JSONDecodeError as e:\n log.error(f\"Failed to parse JSON from {splitcode_summary_file}\")\n log.error(f\" JSON decode error: {e}\")\n # Try to show first few lines of the file for debugging\n try:\n with open(splitcode_summary_file, \"r\") as f:\n lines = f.readlines()\n log.error(f\" File contents (first 10 lines):\")\n for i, line in enumerate(lines[:10], 1):\n log.error(f\" {i}: {line.rstrip()}\")\n if len(lines) > 10:\n log.error(f\" ... ({len(lines) - 10} more lines)\")\n except Exception as read_err:\n log.error(f\" Could not read file for debugging: {read_err}\")\n raise\n except Exception as e:\n log.error(f\"Unexpected error loading splitcode summary for barcode group '{barcode_group}'\")\n log.error(f\" File: {splitcode_summary_file if splitcode_summary_file else 'not determined'}\")\n log.error(f\" Error type: {type(e).__name__}\")\n log.error(f\" Error message: {e}\")\n raise\n\n # Parse splitcode summary JSON\n # IMPORTANT: The tag_qc array has MULTIPLE entries per barcode tag!\n # Each barcode appears once for each hamming distance level (0, 1, 2, 3).\n # Example tag_qc structure:\n # [\n # {\"tag\": \"Sample1_R1\", \"distance\": 0, \"count\": 5}, # Perfect matches\n # {\"tag\": \"Sample1_R1\", \"distance\": 1, \"count\": 2}, # 1 mismatch\n # {\"tag\": \"Sample1_R1\", \"distance\": 2, \"count\": 0}, # 2 mismatches\n # {\"tag\": \"Sample1_R1\", \"distance\": 3, \"count\": 0}, # 3 mismatches\n # {\"tag\": \"Sample2_R1\", \"distance\": 0, \"count\": 3},\n # ...\n # ]\n #\n # Here we filter to distance=0 (perfect matches) and distance=1 (1-mismatch) separately\n # for downstream metrics and QC analysis.\n if len(splitcode_summary.get(\"tag_qc\", [])) > 0:\n splitcode_summary_df = pd.DataFrame.from_records(splitcode_summary[\"tag_qc\"])\n # Convert only the tag column to string, keep count/distance as numeric\n splitcode_summary_df['tag'] = splitcode_summary_df['tag'].astype(str)\n\n splitcode_summary_df['run'] = splitcode_summary_df['tag'].copy()\n splitcode_summary_df['run'] = splitcode_summary_df['run'].str.removesuffix('_R1')\n\n # Extract perfect matches (hamming distance = 0)\n splitcode_summary_df_h0_df = splitcode_summary_df[splitcode_summary_df[\"distance\"] == 0]\n # Extract 1-mismatch reads (hamming distance = 1)\n splitcode_summary_df_h1_df = splitcode_summary_df[splitcode_summary_df[\"distance\"] == 1].copy()\n\n splitcode_summary_df_h1_df = splitcode_summary_df_h1_df.rename(columns={\"count\": \"count_h1\"})\n\n samplesheet_rows_for_pool_hx_df = samplesheet_rows_for_pool_df.join(\n splitcode_summary_df_h0_df.set_index('run'),\n on='run')\n\n samplesheet_rows_for_pool_hx_df = pd.merge(samplesheet_rows_for_pool_hx_df,\n splitcode_summary_df_h1_df[['run','count_h1']].rename(columns={'run':'run_h1'}),\n left_on = 'run',\n right_on = 'run_h1',\n how = 'left')\n samplesheet_rows_for_pool_hx_df = samplesheet_rows_for_pool_hx_df.drop(columns=['run_h1','distance','tag']) # dropping distance since we've added a col with different distance (as indicated by _h1 suffix)\n # fil NA values in 'count_h1' and cast to int\n samplesheet_rows_for_pool_hx_df[\"count_h1\"] = samplesheet_rows_for_pool_hx_df[\"count_h1\"].fillna(0).astype(int)\n else:\n # No reads were processed by splitcode for this pool\n # Create a dataframe with the expected schema but all counts set to 0\n log.warning(f\"Barcode group {barcode_group} has 0 reads processed by splitcode. Creating empty metrics.\")\n samplesheet_rows_for_pool_hx_df = samplesheet_rows_for_pool_df.copy()\n samplesheet_rows_for_pool_hx_df['count'] = 0\n samplesheet_rows_for_pool_hx_df['count_h1'] = 0\n\n pool_dfs.append(samplesheet_rows_for_pool_hx_df)\n\n unmatched_dict = {\n \"sample\" : f\"{unmatched_name}.{barcode_group}\",\n \"library_id_per_sample\" : list(set(samplesheet_rows_for_pool_hx_df[\"library_id_per_sample\"]))[0],\n \"run\" : f\"{unmatched_name}.{barcode_group}\",\n \"muxed_pool\" : barcode_group,\n \"count\" : splitcode_summary[\"n_processed\"] - splitcode_summary[\"n_assigned\"],\n \"count_h1\" : 0,\n \"barcode_1\" : list(samplesheet_rows_for_pool_hx_df[\"barcode_1\"])[0],\n \"barcode_2\" : list(samplesheet_rows_for_pool_hx_df[\"barcode_2\"])[0],\n \"barcode_3\" : \"N\" * len(list(samplesheet_rows_for_pool_hx_df[\"barcode_3\"])[0]),\n }\n unmatched_df = pd.DataFrame.from_dict([unmatched_dict], dtype=str)\n unmatched_dfs.append(unmatched_df)\n\n all_pools_and_unmatched_df = pd.concat(pool_dfs + unmatched_dfs, ignore_index=True)\n\n df_lut = all_pools_and_unmatched_df.copy()\n # rename columns to values expected by downstream plotting code\n df_lut = df_lut.rename(columns={\n \"count\": \"num_reads_hdistance0\",\n \"count_h1\": \"num_reads_hdistance1\",\n \"barcode_3\":\"inline_barcode\",\n \"library_id_per_sample\":\"library_id\"\n })\n\n df_lut[\"num_reads_total\"] = (\n df_lut[\"num_reads_hdistance0\"] + df_lut[\"num_reads_hdistance1\"]\n )\n\n # TO-DO: Adjust the table outputted by this function to match Picard output\n\n df_lut.to_csv(df_csv_out, index=False)\n\n return df_csv_out\n\ndef plot_read_counts(df_csv_path, outDir):\n df_lut = pd.read_csv(df_csv_path, dtype=str)\n # Convert numeric columns explicitly\n numeric_cols = ['num_reads_total', 'num_reads_hdistance0', 'num_reads_hdistance1']\n for col in numeric_cols:\n if col in df_lut.columns:\n df_lut[col] = pd.to_numeric(df_lut[col], errors='coerce').fillna(0)\n\n fig, axs = plt.subplots(figsize=(10, 10), nrows=3, sharex=True)\n fontsize = 14\n\n df_grouped = (\n df_lut.groupby([\"inline_barcode\", \"library_id\"])[\"num_reads_total\"]\n .sum()\n .unstack(fill_value=0)\n )\n df_grouped_fracs = df_grouped.div(df_grouped.sum(axis=0), axis=1)\n\n bar_width = 0.2\n bar_positions = np.arange(len(df_grouped))\n\n # Define colors\n unique_library_ids = df_lut[\"library_id\"].nunique()\n tab20_colors = plt.cm.tab20.colors\n pool_colors = (tab20_colors * (unique_library_ids // 20 + 1))[:unique_library_ids]\n\n for i, pool in enumerate(df_grouped.columns):\n axs[0].bar(\n bar_positions + i * bar_width,\n df_grouped[pool],\n width=bar_width,\n label=f'{pool.split(\"_\")[-1]}',\n color=pool_colors[i],\n )\n axs[1].bar(\n bar_positions + i * bar_width,\n df_grouped[pool],\n width=bar_width,\n color=pool_colors[i],\n )\n axs[2].bar(\n bar_positions + i * bar_width,\n df_grouped_fracs[pool],\n width=bar_width,\n color=pool_colors[i],\n )\n\n # Only set log scale if there are positive values\n if df_grouped.values.max() > 0:\n axs[1].set_yscale(\"log\")\n else:\n log.warning(\"All read counts are zero; skipping log scale for plot\")\n\n for ax in axs[:2]:\n ax.set_ylabel(\"# Reads\", fontsize=fontsize)\n axs[2].set_ylabel(\"Fraction of Reads\", fontsize=fontsize)\n\n for ax in axs:\n ax.set_xticks(bar_positions + 1.5 * bar_width)\n ax.set_xticklabels(df_grouped.index, rotation=45, ha=\"right\")\n ax.tick_params(axis=\"both\", labelsize=fontsize - 2)\n ax.grid(True, axis=\"y\", linestyle=\"--\", alpha=0.7)\n ax.margins(x=0.01)\n\n axs[0].legend(title=\"Pool\", fontsize=fontsize - 2, title_fontsize=fontsize)\n axs[0].set_title(\"# Reads per inline barcode\", fontsize=fontsize)\n axs[2].set_xlabel(\"Inline Barcode\", fontsize=fontsize)\n\n plt.tight_layout()\n\n fig.savefig(f\"{outDir}/reads_per_pool.pdf\", bbox_inches=\"tight\", dpi=300)\n fig.savefig(f\"{outDir}/reads_per_pool.png\", bbox_inches=\"tight\", dpi=300)\n\n\ndef plot_sorted_curve(df_csv_path, out_dir, unmatched_name, out_basename=None):\n out_basename = out_basename or \"reads_per_pool_sorted_curve\"\n\n df_lut = pd.read_csv(df_csv_path, dtype=str)\n # Convert numeric columns explicitly\n numeric_cols = ['num_reads_total', 'num_reads_hdistance0', 'num_reads_hdistance1']\n for col in numeric_cols:\n if col in df_lut.columns:\n df_lut[col] = pd.to_numeric(df_lut[col], errors='coerce').fillna(0)\n\n log.debug(f\"Reading in metrics file for plotting barcode read counts per pool: {df_csv_path}\")\n log.debug(f\"unmatched_name: {unmatched_name}\")\n\n fig, axs = plt.subplots(figsize=(10, 10), nrows=4, sharex=True)\n fontsize = 14\n\n # Define colors\n unique_library_ids = df_lut[\"library_id\"].nunique()\n log.debug(f\"Number of distinct library_id values (pools) present: {unique_library_ids}\")\n log.debug(f\"library_id values (pools): {', '.join(sorted(list(set(df_lut['library_id'].astype(str)))))}\")\n\n tab20_colors = plt.cm.tab20.colors\n pool_colors = (tab20_colors * (unique_library_ids // 20 + 1))[:unique_library_ids]\n\n for i, pool in enumerate(sorted(df_lut[\"library_id\"].unique())):\n log.debug(f\"Processing read counts to plot for library_id (pool): {pool}\")\n # pool_metrics = df_lut[\n # (df_lut[\"library_id\"] == str(pool))\n # & (df_lut[\"inline_barcode\"] != unmatched_name)\n # ]\n pool_metrics = df_lut[\n (df_lut[\"library_id\"] == pool)\n & (~df_lut['inline_barcode'].str.match(r'^N+$', na=False))\n ]\n num_reads = pool_metrics[\"num_reads_total\"]\n num_reads = sorted(num_reads, reverse=True)\n for ax in axs[:2]:\n ax.scatter(\n np.arange(len(num_reads)),\n num_reads,\n label=f'{pool.split(\"_\")[-1]}',\n color=pool_colors[i],\n )\n ax.plot(np.arange(len(num_reads)), num_reads, color=pool_colors[i])\n\n # Calculate total and fractions (handle division by zero)\n total_reads = sum(num_reads)\n if total_reads > 0:\n fractions = np.array([read / total_reads for read in num_reads])\n else:\n fractions = np.zeros(len(num_reads))\n log.warning(f\"Pool {pool} has 0 total reads; setting all fractions to 0\")\n\n for ax in axs[2:]:\n ax.scatter(np.arange(len(fractions)), fractions * 100, color=pool_colors[i])\n ax.plot(np.arange(len(fractions)), fractions * 100, color=pool_colors[i])\n\n axs[1].set_yscale(\"symlog\")\n axs[1].set_ylim(bottom=0)\n axs[3].set_ylim(bottom=0, top=0.5)\n axs[3].set_xlabel(\"Inline Barcode\", fontsize=fontsize)\n axs[0].set_title(\"Reads per Inline Barcode (Sorted Curve)\", fontsize=fontsize)\n axs[0].legend(title=\"Pool\", fontsize=fontsize - 2, title_fontsize=fontsize)\n\n for ax in axs[:2]:\n ax.set_ylabel(\"# Reads\", fontsize=fontsize)\n\n for ax in axs[2:]:\n ax.set_ylabel(\"% Reads\", fontsize=fontsize)\n\n for ax in axs:\n ax.tick_params(axis=\"both\", labelsize=fontsize - 2)\n ax.grid(True, axis=\"y\", linestyle=\"--\", alpha=0.7)\n ax.margins(x=0.01)\n\n plt.tight_layout()\n\n fig.savefig(\n f\"{out_dir}/{out_basename}.pdf\", bbox_inches=\"tight\", dpi=300\n )\n fig.savefig(\n f\"{out_dir}/{out_basename}.png\", bbox_inches=\"tight\", dpi=300\n )\n\n# this function is called in new processes\n# and must remain at the top level (global scope) of this file\n# to be picklable and thus compatible\n# with concurrent.futures.ProcessPoolExecutor()\n# see: https://docs.python.org/3/library/concurrent.futures.html#processpoolexecutor\n# https://stackoverflow.com/a/72776044\ndef run_splitcode_on_pool( pool_id,\n pool_bam_file,\n splitcode_config,\n splitcode_keepfile,\n out_demux_dir_path,\n unmatched_name = \"unmatched\",\n threads_per_worker = None,\n out_dir_path = None,\n out_demux_dir_path_tmp = None,\n string_to_log = None,\n predemux_r1_trim_5prime_num_bp=None,\n predemux_r1_trim_3prime_num_bp=None,\n predemux_r2_trim_5prime_num_bp=None,\n predemux_r2_trim_3prime_num_bp=None\n ):\n \"\"\"\n Execute splitcode demultiplexing on a single BAM pool.\n\n This function converts the input BAM to FASTQ, runs splitcode to demultiplex based on\n inline barcodes, and generates a summary JSON with barcode matching statistics.\n\n Args:\n pool_id: Identifier for this pool (used in output filenames)\n pool_bam_file: Path to input BAM file containing multiplexed reads\n splitcode_config: Path to splitcode config file (TSV format with columns:\n tag, id, locations, distance, left, right)\n splitcode_keepfile: Path to keep file (TSV: barcode_idoutput_prefix)\n out_demux_dir_path: Directory for demultiplexed output FASTQs\n unmatched_name: Prefix for unmatched/unassigned reads output\n out_dir_path: Directory for summary JSON (defaults to out_demux_dir_path)\n out_demux_dir_path_tmp: Temporary directory for intermediate files\n\n Returns:\n tuple: (return_code, pool_id) where return_code is 0 on success\n\n Output files:\n - Summary JSON: {out_dir_path}/{pool_id}_summary.json\n Contains 'tag_qc' array with barcode matching statistics. Each barcode has\n multiple entries (one per hamming distance level 0-3) with 'tag', 'distance',\n and 'count' fields.\n - Demuxed FASTQs: {output_prefix}_R1.fastq, {output_prefix}_R2.fastq\n (output_prefix comes from keepfile, one pair per barcode)\n - Unmatched FASTQs: {unmatched_name}.{pool_id}_R1.fastq, {unmatched_name}.{pool_id}_R2.fastq\n\n Notes:\n - Splitcode config locations format: FILE_NUMBER:START_BP:END_BP\n Example: \"0:0:8\" means file 0 (R1), positions 0-8 (8bp barcode)\n - The 'id' column in config file must match the first column in keepfile\n - By convention, we use f\"{sample_library_id}_R1\" as the ID\n - tag_qc in summary JSON has multiple entries per tag (one for each distance level),\n so downstream code must sum counts across all distance levels if needed\n\n See test/unit/test_illumina_splitcode.py for detailed examples and validation of\n splitcode behavior assumptions.\n \"\"\"\n with samtools.SamtoolsTool().bam2fq_tmp(pool_bam_file) as (fqin1, fqin2):\n n_fastqs = 2\n splitcode_tool = SplitCodeTool()\n\n # output args\n unmapped_r1 = f\"{out_demux_dir_path_tmp}/{unmatched_name}.{pool_id}_R1.fastq\"\n unmapped_r2 = f\"{out_demux_dir_path_tmp}/{unmatched_name}.{pool_id}_R2.fastq\"\n # write the stats to the output directory rather than tmp\n summary_stats = f\"{out_dir_path}/{pool_id}_summary.json\"\n\n # Dummy output files for --output parameter\n # Note: --no-output flag prevents --keep files from being written, so we must\n # provide --output even though we don't use these files\n dummy_output_r1 = f\"{out_demux_dir_path_tmp}/_dummy_main_output_{pool_id}_R1.fastq\"\n dummy_output_r2 = f\"{out_demux_dir_path_tmp}/_dummy_main_output_{pool_id}_R2.fastq\"\n\n # Optional: Pass 'predemux_r2_trim_3prime_num_bp':8 for '--trim-3 0,8'\n # to remove 8 bases from end of R2 read\n # (note: trimming happens before demuxing)\n # valid options:\n # predemux_r1_trim_5prime_num_bp\n # predemux_r1_trim_3prime_num_bp\n # predemux_r2_trim_5prime_num_bp\n # predemux_r2_trim_3prime_num_bp\n # see splitcode.py wrapper for more details, and also:\n # https://splitcode.readthedocs.io/en/latest/reference_guide.html#command-line-config-optional\n splitcode_kwargs={\n \"n_fastqs\" : n_fastqs,\n \"threads\" : threads_per_worker,\n \"config_file\" : splitcode_config,\n \"keep_file\" : splitcode_keepfile,\n \"unassigned_r1\" : unmapped_r1,\n \"unassigned_r2\" : unmapped_r2,\n \"summary_stats\" : summary_stats,\n \"r1\" : fqin1,\n \"r2\" : fqin2,\n \"predemux_r1_trim_5prime_num_bp\" : predemux_r1_trim_5prime_num_bp,\n \"predemux_r1_trim_3prime_num_bp\" : predemux_r1_trim_3prime_num_bp,\n \"predemux_r2_trim_5prime_num_bp\" : predemux_r2_trim_5prime_num_bp,\n \"predemux_r2_trim_3prime_num_bp\" : predemux_r2_trim_3prime_num_bp,\n \"keep_r1_r2_suffixes\" : True, # Add --keep-r1-r2 flag for _R1/_R2 suffixes\n \"splitcode_opts\" : [f\"--output={dummy_output_r1},{dummy_output_r2}\"], # Required for --keep to work\n }\n if string_to_log:\n log.info(string_to_log)\n return (splitcode_tool.execute(**splitcode_kwargs), pool_id)\n\ndef generate_splitcode_config_and_keep_files(\n inner_demux_barcode_map_df,\n pool_id,\n output_dir,\n max_hamming_dist=1,\n r1_trim_bp_right_of_barcode=None,\n r2_trim_bp_left_of_barcode=None\n):\n \"\"\"\n Generate splitcode config and keep files for a single pool.\n\n This function creates the TSV files needed by splitcode to demultiplex reads\n based on inline barcodes (barcode_3). It takes sample metadata from a DataFrame\n and generates both the config file (which specifies barcode sequences and matching\n parameters) and the keep file (which maps barcodes to output file prefixes).\n\n Args:\n inner_demux_barcode_map_df (pd.DataFrame): DataFrame with sample metadata.\n Required columns:\n - 'barcode_3': Inline barcode sequence\n - 'run': Sample library ID (e.g., \"Sample1.lLib1.FLOWCELL.1\")\n - 'muxed_run': Pool ID for grouping samples\n Index: sample names\n pool_id (str): Pool identifier to filter samples and name output files\n output_dir (str): Directory where demultiplexed FASTQs will be written\n max_hamming_dist (int): Maximum Hamming distance for fuzzy barcode matching.\n Default: 1 (allows 1 mismatch)\n r1_trim_bp_right_of_barcode (int, optional): Additional bases to trim from R1\n after removing the barcode. If None, only the barcode is trimmed.\n r2_trim_bp_left_of_barcode (int, optional): Bases to trim from R2 left side\n (currently unused - R2 barcodes not implemented)\n\n Returns:\n tuple: (config_file_path, keep_file_path, sample_library_ids)\n - config_file_path (str): Path to generated splitcode config TSV\n - keep_file_path (str): Path to generated splitcode keep TSV\n - sample_library_ids (list): List of sample_library_id values for this pool\n\n Config file format (TSV with header):\n tag - Barcode sequence (e.g., \"AAAAAAAA\")\n id - Barcode identifier (e.g., \"Sample1_R1\") - MUST match keep file\n locations - FILE_NUMBER:START_BP:END_BP (e.g., \"0:0:8\" for R1 positions 0-8)\n distance - Max hamming distance for fuzzy matching (0=exact, 1=1 mismatch, etc.)\n left - Trim from left: \"1\" removes barcode, \"1:N\" removes barcode + N more bp\n right - Trim from right (typically \"0\" for R1 barcodes)\n\n Keep file format (TSV, NO header):\n Column 1: barcode_id - MUST match \"id\" from config file\n Column 2: output_prefix - Path prefix for output FASTQs (without _R1/_R2.fastq)\n\n Example:\n >>> df = pd.DataFrame({\n ... 'barcode_3': ['AAAAAAAA', 'CCCCCCCC'],\n ... 'run': ['Sample1.lLib1', 'Sample2.lLib1'],\n ... 'muxed_run': ['Pool1', 'Pool1']\n ... }, index=['Sample1', 'Sample2'])\n >>> config, keep, ids = generate_splitcode_config_and_keep_files(\n ... df, 'Pool1', '/output', max_hamming_dist=1\n ... )\n >>> # config file contains:\n >>> # tag id locations distance left right\n >>> # AAAAAAAA Sample1.lLib1_R1 0:0:8 1 1 0\n >>> # CCCCCCCC Sample2.lLib1_R1 0:0:8 1 1 0\n >>> # keep file contains:\n >>> # Sample1.lLib1_R1 /output/Sample1.lLib1\n >>> # Sample2.lLib1_R1 /output/Sample2.lLib1\n\n See test/unit/test_illumina_splitcode.py for validation of splitcode's behavior\n with these file formats.\n \"\"\"\n # Filter DataFrame to only samples in this pool\n pool_samples_df = inner_demux_barcode_map_df[\n inner_demux_barcode_map_df['muxed_run'] == pool_id\n ]\n\n if len(pool_samples_df) == 0:\n raise ValueError(f\"No samples found for pool_id '{pool_id}'\")\n\n # ======== Create splitcode config file ========\n # For more information on config format and parameters see:\n # https://splitcode.readthedocs.io/en/latest/reference_guide.html#table-options\n # https://splitcode.readthedocs.io/en/latest/user_guide_tags.html#locations\n # https://splitcode.readthedocs.io/en/latest/user_guide_tags.html#left-and-right-trimming\n\n config_file = util_file.mkstempfname(f'splitcode_{pool_id}_config.txt')\n\n with open(config_file, \"w\") as config_fh:\n config_tsv_writer = csv.writer(config_fh, delimiter=\"\\t\", lineterminator='\\n')\n\n # Write header columns\n config_header = [\n \"tag\", # Barcode sequence\n \"id\", # Barcode identifier (must match keep file)\n \"locations\", # FILE:START:END format\n \"distance\", # Max hamming distance\n \"left\", # Trim from left\n \"right\" # Trim from right\n ]\n config_tsv_writer.writerow(config_header)\n\n # Write config lines for each sample in this pool\n for sample_name, sample_row in pool_samples_df.iterrows():\n barcode_sequence = sample_row[\"barcode_3\"]\n barcode_len = len(barcode_sequence)\n sample_library_id = sample_row[\"run\"]\n\n # R1 barcode configuration\n # The \"left\" column controls trimming from the left side of R1\n # Format: \"1\" (trim barcode only) or \"1:N\" (trim barcode + N more bp)\n left_trim = \"1\" if r1_trim_bp_right_of_barcode is None else f\"1:{r1_trim_bp_right_of_barcode}\"\n\n # When using --keep-r1-r2 flag, splitcode automatically adds _R1/_R2 suffixes\n # to output filenames, so the ID should NOT include _R1 suffix\n config_line_r1 = [\n barcode_sequence, # The barcode sequence to search for\n sample_library_id, # ID (MUST match keep file column 1)\n f\"0:0:{barcode_len}\", # locations: FILE:START:END (0=R1, 0-barcode_len)\n str(max_hamming_dist), # Maximum hamming distance\n left_trim, # Trim from left (barcode + optional extra bp)\n \"0\" # Trim from right (not used for R1)\n ]\n config_tsv_writer.writerow(config_line_r1)\n\n # TODO: R2 barcode support (currently commented out in splitcode_demux)\n # If needed, would add config_line_r2 here using r2_trim_bp_left_of_barcode\n\n # ======== Create splitcode keep file ========\n # Keep file maps barcode IDs to output file prefixes\n # NO header row (unlike config file)\n\n keep_file = util_file.mkstempfname(f\"splitcode_{pool_id}_keepfile.txt\")\n sample_library_ids = []\n\n with open(keep_file, \"w\") as keep_fh:\n keep_tsv_writer = csv.writer(keep_fh, delimiter=\"\\t\", lineterminator='\\n')\n\n for sample_name, sample_row in pool_samples_df.iterrows():\n sample_library_id = sample_row[\"run\"]\n sample_library_ids.append(sample_library_id)\n\n # Output prefix: /output/dir/Sample1.lLib1\n # When using --keep-r1-r2, splitcode will create:\n # /output/dir/Sample1.lLib1_R1.fastq, ...R2.fastq\n sample_output_prefix = f\"{output_dir}/{sample_library_id}\"\n\n keep_row = [\n sample_library_id, # MUST match config file \"id\" column (no _R1 suffix)\n sample_output_prefix, # Output prefix (without _R1/_R2.fastq)\n ]\n keep_tsv_writer.writerow(keep_row)\n\n return (config_file, keep_file, sample_library_ids)\n\ndef convert_splitcode_demux_metrics_to_picard_style(\n in_splitcode_csv_path,\n out_splitcode_tsv_metrics_path,\n demux_function = \"viral-core.SplitcodeMetrics\",\n catchall_name = \"unmatched\",\n combine_innerbarcode_unmatched = False,\n report_within_pools = True\n):\n \"\"\"\n Convert a custom Splitcode demux CSV file into a Picard-style\n ExtractIlluminaBarcodes.BarcodeMetric TSV file.\n\n :param in_splitcode_csv_path: Path to the Splitcode-format CSV input\n :param out_splitcode_tsv_metrics_path: Path to the desired Picard-style metrics TSV output\n :param demux_function: The string to insert after 'ExtractIlluminaBarcodes$' in\n the '## METRICS CLASS' comment line\n :param catchall_name: A placeholder name for collapsed 'N' rows (not strictly used here)\n :param combine_innerbarcode_unmatched: If True, we collapse \"all-N\" rows into one single row.\n If False, we leave them as-is (no collapsing).\n :param report_within_pools: If True, the ratio/percentage columns are computed for each unique\n (barcode_1, barcode_2) group. If False, they are computed globally.\n Also, if True, we check only the *last* barcode segment for 'N's.\n If False, we check the entire combined barcode for 'N's.\n \"\"\"\n\n # Required columns for the first set of metrics\n required_cols = [\n \"sample\", # -> BARCODE_NAME\n \"barcode_1\", # -> part of BARCODE\n \"barcode_2\", # -> part of BARCODE\n \"num_reads_hdistance0\", # -> PERFECT_MATCHES, PF_PERFECT_MATCHES\n \"num_reads_hdistance1\", # -> ONE_MISMATCH_MATCHES, PF_ONE_MISMATCH_MATCHES\n \"num_reads_total\" # -> READS, PF_READS\n ]\n\n # Read the CSV\n df = pd.read_csv(in_splitcode_csv_path, dtype=str)\n\n # Check for presence of required columns\n for col in required_cols:\n if col not in df.columns:\n raise ValueError(f\"Required column '{col}' is missing in the input file.\")\n # Also check that these columns are not all empty\n for col in required_cols:\n if df[col].dropna().empty:\n raise ValueError(\n f\"Required column '{col}' is present but entirely empty (no usable data).\"\n )\n\n # Convert numeric columns from string to numeric\n # These columns are read as strings but need to be numeric for calculations\n numeric_cols = [\"num_reads_hdistance0\", \"num_reads_hdistance1\", \"num_reads_total\"]\n for col in numeric_cols:\n if col in df.columns:\n df[col] = pd.to_numeric(df[col], errors='coerce').fillna(0).astype(int)\n\n # If 'inline_barcode' is present, treat it as a potential \"third\" barcode\n barcode_3_col = \"inline_barcode\" if \"inline_barcode\" in df.columns else None\n\n # Combine up to 3 barcodes into 'BARCODE' (with '-') and 'BARCODE_WITHOUT_DELIMITER' (concatenated)\n def combine_barcodes(row):\n bcs = []\n for bc_col in [\"barcode_1\", \"barcode_2\"]:\n val = row.get(bc_col, \"\")\n if pd.notnull(val) and val != \"\":\n bcs.append(val)\n if barcode_3_col and pd.notnull(row.get(barcode_3_col, \"\")) and row[barcode_3_col] != \"\":\n bcs.append(row[barcode_3_col])\n barcode = \"-\".join(bcs)\n barcode_no_delim = \"\".join(bcs)\n return pd.Series([barcode, barcode_no_delim])\n\n df[[\"BARCODE\", \"BARCODE_WITHOUT_DELIMITER\"]] = df.apply(combine_barcodes, axis=1)\n\n # Assign 'BARCODE_NAME' and 'LIBRARY_NAME'\n df[\"BARCODE_NAME\"] = df[\"sample\"]\n if \"run\" in df.columns and not df[\"run\"].dropna().empty:\n df[\"LIBRARY_NAME\"] = df[\"run\"]\n elif \"library_id\" in df.columns and not df[\"library_id\"].dropna().empty:\n df[\"LIBRARY_NAME\"] = df[\"library_id\"]\n else:\n df[\"LIBRARY_NAME\"] = df[\"BARCODE_NAME\"]\n\n # Fill the first set of columns (READS, PF_READS, etc.)\n df[\"READS\"] = df[\"num_reads_total\"]\n df[\"PF_READS\"] = df[\"num_reads_total\"]\n df[\"PERFECT_MATCHES\"] = df[\"num_reads_hdistance0\"]\n df[\"PF_PERFECT_MATCHES\"] = df[\"num_reads_hdistance0\"]\n df[\"ONE_MISMATCH_MATCHES\"] = df[\"num_reads_hdistance1\"]\n df[\"PF_ONE_MISMATCH_MATCHES\"] = df[\"num_reads_hdistance1\"]\n\n # Define the \"all N\" checkers\n def is_all_N(barcode_str: str) -> bool:\n \"\"\"\n Return True if the entire (combined) barcode is all 'N' and non-empty.\n Ignores delimiter characters ('-').\n \"\"\"\n if not isinstance(barcode_str, str):\n return False\n # Remove delimiters before checking\n barcode_no_delim = barcode_str.replace('-', '')\n return len(barcode_no_delim) > 0 and all(ch == 'N' for ch in barcode_no_delim)\n\n def last_barcode_is_all_N(barcode_str: str) -> bool:\n \"\"\"\n Return True if the final piece (e.g. inline barcode) is non-empty and all 'N'.\n For example, 'ACTGATCG-NNNNNNNNN' => True for that last piece.\n \"\"\"\n if not isinstance(barcode_str, str):\n return False\n parts = barcode_str.split(\"-\")\n if not parts:\n return False\n return is_all_N(parts[-1])\n\n # Row Collapsing for \"all-N\" if combine_innerbarcode_unmatched == True\n if combine_innerbarcode_unmatched:\n # The definition of \"all-N\" changes depending on report_within_pools:\n # - If report_within_pools=True => check ONLY the last barcode piece\n # - Otherwise => check entire combined barcode\n check_all_n_func = last_barcode_is_all_N if report_within_pools else is_all_N\n\n # Identify any rows that are \"all N\" by that definition\n df[\"IS_ALL_N\"] = df[\"BARCODE\"].apply(check_all_n_func)\n\n # Separate them out\n df_all_n = df[df[\"IS_ALL_N\"]]\n df_not_all_n = df[~df[\"IS_ALL_N\"]]\n\n if not df_all_n.empty:\n # Sum their metric columns\n sum_reads = df_all_n[\"READS\"].sum()\n sum_pf_reads = df_all_n[\"PF_READS\"].sum()\n sum_perfect_matches = df_all_n[\"PERFECT_MATCHES\"].sum()\n sum_pf_perfect_matches = df_all_n[\"PF_PERFECT_MATCHES\"].sum()\n sum_one_mismatch = df_all_n[\"ONE_MISMATCH_MATCHES\"].sum()\n sum_pf_one_mismatch = df_all_n[\"PF_ONE_MISMATCH_MATCHES\"].sum()\n\n collapsed = df_all_n.iloc[0].copy()\n collapsed[\"BARCODE\"] = \"N\"\n collapsed[\"BARCODE_WITHOUT_DELIMITER\"] = \"N\"\n collapsed[\"BARCODE_NAME\"] = \"\"\n collapsed[\"LIBRARY_NAME\"] = \"\"\n collapsed[\"READS\"] = sum_reads\n collapsed[\"PF_READS\"] = sum_pf_reads\n collapsed[\"PERFECT_MATCHES\"] = sum_perfect_matches\n collapsed[\"PF_PERFECT_MATCHES\"] = sum_pf_perfect_matches\n collapsed[\"ONE_MISMATCH_MATCHES\"] = sum_one_mismatch\n collapsed[\"PF_ONE_MISMATCH_MATCHES\"] = sum_pf_one_mismatch\n\n # Recombine the \"not all-N\" rows plus this one collapsed row\n df = pd.concat([df_not_all_n, pd.DataFrame([collapsed], dtype=str)], ignore_index=True)\n\n # After concat with dtype=str, re-convert numeric columns\n numeric_cols_to_reconvert = [\n \"READS\", \"PF_READS\", \"PERFECT_MATCHES\", \"PF_PERFECT_MATCHES\",\n \"ONE_MISMATCH_MATCHES\", \"PF_ONE_MISMATCH_MATCHES\"\n ]\n for col in numeric_cols_to_reconvert:\n if col in df.columns:\n df[col] = pd.to_numeric(df[col], errors='coerce').fillna(0).astype(int)\n\n # Drop helper column\n df.drop(columns=[\"IS_ALL_N\"], inplace=True, errors=\"ignore\")\n\n #\n # Now define how we compute the ratio/percentage columns\n #\n # Because you specifically want \"if report_within_pools=True, only the last barcode is considered\n # for 'N's in the PF_NORMALIZED_MATCHES exclusion,\" we will conditionally pick which function\n # to use in that step too.\n #\n exclude_for_mean_func = last_barcode_is_all_N if report_within_pools else is_all_N\n\n def compute_stats_per_group(group: pd.DataFrame) -> pd.DataFrame:\n # Compute sums, maxima, etc. *within* the group, fill ratio/percentage columns.\n sum_of_reads = group[\"READS\"].sum()\n max_of_reads = group[\"READS\"].max() if len(group) > 0 else 1\n sum_of_pf_reads = group[\"PF_READS\"].sum()\n max_of_pf_reads = group[\"PF_READS\"].max() if len(group) > 0 else 1\n\n # For PF_NORMALIZED_MATCHES, exclude rows that pass `exclude_for_mean_func`\n # (which is either last_barcode_is_all_N or is_all_N, depending on 'report_within_pools').\n group_for_mean = group[~group[\"BARCODE\"].apply(exclude_for_mean_func)]\n mean_pf_reads = group_for_mean[\"PF_READS\"].mean() if len(group_for_mean) > 0 else 1\n\n out = group.copy()\n if sum_of_reads == 0:\n out[\"PCT_MATCHES\"] = 0\n else:\n out[\"PCT_MATCHES\"] = out[\"PERFECT_MATCHES\"] / sum_of_reads\n\n if max_of_reads == 0:\n out[\"RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\"] = 0\n else:\n out[\"RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\"] = out[\"READS\"] / max_of_reads\n\n if sum_of_pf_reads == 0:\n out[\"PF_PCT_MATCHES\"] = 0\n else:\n out[\"PF_PCT_MATCHES\"] = out[\"PF_PERFECT_MATCHES\"] / sum_of_pf_reads\n\n if max_of_pf_reads == 0:\n out[\"PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\"] = 0\n else:\n out[\"PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\"] = out[\"PF_READS\"] / max_of_pf_reads\n\n if mean_pf_reads == 0:\n out[\"PF_NORMALIZED_MATCHES\"] = 0\n else:\n out[\"PF_NORMALIZED_MATCHES\"] = out[\"PF_PERFECT_MATCHES\"] / mean_pf_reads\n\n return out\n\n # Perform the group-based or global stats\n if report_within_pools:\n # Group by (barcode_1, barcode_2)\n grouped = df.groupby([\"barcode_1\", \"barcode_2\"], group_keys=False)\n df = grouped[df.columns].apply(compute_stats_per_group)\n else:\n # Global\n df = compute_stats_per_group(df)\n\n # Add DEMUX_TYPE column to all rows\n df[\"DEMUX_TYPE\"] = \"inline_splitcode\"\n\n # Prepare the output\n columns_out = [\n \"BARCODE\",\n \"BARCODE_WITHOUT_DELIMITER\",\n \"BARCODE_NAME\",\n \"LIBRARY_NAME\",\n \"READS\",\n \"PF_READS\",\n \"PERFECT_MATCHES\",\n \"PF_PERFECT_MATCHES\",\n \"ONE_MISMATCH_MATCHES\",\n \"PF_ONE_MISMATCH_MATCHES\",\n \"PCT_MATCHES\",\n \"RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\",\n \"PF_PCT_MATCHES\",\n \"PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\",\n \"PF_NORMALIZED_MATCHES\",\n \"DEMUX_TYPE\",\n ]\n\n with open(out_splitcode_tsv_metrics_path, \"w\") as f:\n # Write the Picard-style \"## METRICS CLASS\" header line\n f.write(f\"## METRICS CLASS\\t{demux_function}\\n\")\n # Write column header\n f.write(\"\\t\".join(columns_out) + \"\\n\")\n\n # Write data rows\n for _, row in df.iterrows():\n row_values = [str(row.get(col, \"\")) for col in columns_out]\n f.write(\"\\t\".join(row_values) + \"\\n\")\n" }, { "path": "src/viral_ngs/core/stats.py", "content": "'''A few pure-python statistical tools to avoid the need to install scipy. '''\n__author__ = \"dpark@broadinstitute.org, irwin@broadinstitute.org\"\n\nfrom math import exp, log, sqrt, gamma, lgamma, erf\nfrom statistics import mean, median\nimport itertools\n\n\ndef product(iterable):\n prod = 1\n for x in iterable:\n prod *= x\n return prod\n\n\ndef chi2_contingency(contingencyTable, correction=True):\n \"\"\" contingencyTable is a sequence of m sequences, each of length n.\n Return an estimate using the chi-square distribution of the two-tailed\n p-value for an m x n contingency table against the null hypothesis\n that the row and column criteria are independent. This is not as\n accurate as fisher_exact, but is faster (and is implemented for all\n m and n).\n If correction is True and there is 1 degree of freedom, apply Yates's\n correction for continuity, i.e., adjust each observed value\n by 0.5 towards the corresponding expected value, which brings\n the result closer to the Fisher exact test result.\n Not recommended if any of the counts or expected counts are\n less than 5.\n \"\"\"\n # scipy equivalent: scipy.stats.chi2_contingency(contingencyTable)[1]\n\n if len(contingencyTable) == 0:\n return 1.0\n if len(set(map(len, contingencyTable))) != 1:\n raise ValueError('Not all rows have the same length')\n\n # Eliminate rows and columns with 0 sum\n colSums = [sum(row[col] for row in contingencyTable) for col in range(len(contingencyTable[0]))]\n table = [[x for x, colSum in zip(row, colSums) if colSum != 0] for row in contingencyTable if sum(row) != 0]\n\n if len(table) < 2 or len(table[0]) < 2:\n return 1.0\n\n m = len(table)\n n = len(table[0])\n rowSums = [sum(row) for row in table]\n colSums = [sum(row[col] for row in table) for col in range(n)]\n N = sum(rowSums)\n expect = [[rowSums[i] * colSums[j] / N for j in range(n)] for i in range(m)]\n if correction and m == n == 2:\n\n def corr(i, j):\n if expect[i][j] > table[i][j]:\n return min(table[i][j] + 0.5, expect[i][j])\n else:\n return max(table[i][j] - 0.5, expect[i][j])\n\n table = [[corr(i, j) for j in range(n)] for i in range(m)]\n chisq = sum((table[i][j] - expect[i][j]) ** 2 / expect[i][j] for j in range(n) for i in range(m))\n pval = 1 - pchisq(chisq, (m - 1) * (n - 1))\n return pval\n\n\ndef fisher_exact(contingencyTable):\n \"\"\" Fisher exact test for the 2 x n case.\n contingencyTable is a sequence of 2 length-n sequences of integers.\n Return the two-tailed p-value against the null hypothesis that the row\n and column criteria are independent, using Fisher's exact test.\n For n larger than 2, this is very slow, O(S^(n-1)), where S is the\n smaller of the two row sums. Better to use chi2_contingency unless\n one of the row sums is small.\n Handles m x n contingencyTable with m > 2 if it can be reduced to the\n 2 x n case by transposing or by removing rows that are all 0s. Also\n handles degenerate cases of 0 or 1 row by returning 1.0.\n \"\"\"\n if len(contingencyTable) == 0:\n return 1.0\n if len(set(map(len, contingencyTable))) != 1:\n raise ValueError('Not all rows have the same length')\n if any(x != int(x) for row in contingencyTable for x in row):\n raise ValueError('Some table entry is not an integer')\n if any(x < 0 for row in contingencyTable for x in row):\n raise ValueError('Some table entry is negative')\n\n # Eliminate rows and columns with 0 sum\n colSums = [sum(row[col] for row in contingencyTable) for col in range(len(contingencyTable[0]))]\n table = [[x for x, colSum in zip(row, colSums) if colSum != 0] for row in contingencyTable if sum(row) != 0]\n\n if len(table) < 2 or len(table[0]) < 2:\n return 1.0\n\n if len(table) > len(table[0]):\n table = list(zip(*table)) # Transpose\n\n m = len(table)\n n = len(table[0])\n if m != 2:\n raise NotImplementedError('More than 2 non-zero rows and columns.')\n\n # Put row with smaller sum first. Makes the loop iterations simpler.\n table.sort(key=sum)\n # Put column with largest sum last. Makes loop quick rejection faster.\n table = list(zip(*table)) # Transpose\n table.sort(key=sum)\n table = list(zip(*table)) # Transpose back\n\n # There are many optimizations possible for the following code, but it would\n # still be O(S^(n-1)) so it would still be too slow for anything\n # sizeable, and it's usable as it for small things.\n\n rowSums = [sum(row) for row in table]\n colSums = [sum(row[col] for row in table) for col in range(n)]\n\n logChooseNrowSum = log_choose(sum(rowSums), rowSums[0])\n\n def prob_of_table(firstRow):\n return exp(sum(log_choose(cs, a) for cs, a in zip(colSums, firstRow)) - logChooseNrowSum)\n\n p0 = prob_of_table(table[0])\n result = 0\n for firstRowM1 in itertools.product(*[range(min(rowSums[0], colSums[i]) + 1) for i in range(n - 1)]):\n lastElmt = rowSums[0] - sum(firstRowM1)\n if lastElmt < 0 or lastElmt > colSums[-1]:\n continue\n prob = prob_of_table(firstRowM1 + (lastElmt,))\n if prob <= p0 + 1e-9: # (1e-9 handles floating point round off)\n result += prob\n\n return result\n\n\ndef log_choose(n, k):\n # Return log(n choose k). Compute using lgamma(x + 1) = log(x!)\n if not (0 <= k <= n):\n raise ValueError('%d is negative or more than %d' % (k, n))\n return lgamma(n + 1) - lgamma(k + 1) - lgamma(n - k + 1)\n\n\ndef gammainc_halfint(s, x):\n \"\"\" Lower incomplete gamma function =\n integral from 0 to x of t ** (s-1) exp(-t) dt divided by gamma(s),\n i.e., the fraction of gamma that you get if you integrate only until\n x instead of all the way to infinity.\n Implemented here only if s is a positive multiple of 0.5.\n \"\"\"\n # scipy equivalent: scipy.special.gammainc(s,x)\n\n if s <= 0:\n raise ValueError('%s is not positive' % s)\n if x < 0:\n raise ValueError('%s < 0' % x)\n if s * 2 != int(s * 2):\n raise NotImplementedError('%s is not a multiple of 0.5' % s)\n\n # Handle integers analytically\n if s == int(s):\n term = 1\n total = 1\n for k in range(1, int(s)):\n term *= x / k\n total += term\n return 1 - exp(-x) * total\n\n # Otherwise s is integer + 0.5. Decrease to 0.5 using recursion formula:\n result = 0.0\n while s > 1:\n result -= x ** (s - 1) * exp(-x) / gamma(s)\n s = s - 1\n # Then use gammainc(0.5, x) = erf(sqrt(x))\n result += erf(sqrt(x))\n return result\n\n\ndef pchisq(x, k):\n \"Cumulative distribution function of chi squared with k degrees of freedom.\"\n if k < 1 or k != int(k):\n raise ValueError('%s is not a positive integer' % k)\n if x < 0:\n raise ValueError('%s < 0' % x)\n return gammainc_halfint(k / 2, x / 2)\n" }, { "path": "src/viral_ngs/core/trimmomatic.py", "content": "\"Tool for trimmomatic.\"\n\nimport logging\nimport os\nimport shutil\nimport subprocess\nfrom . import samtools, picard # was: from viral_ngs import tools\nfrom . import file as util_file, misc as util_misc # was: from viral_ngs import util\nfrom . import Tool, PrexistingUnixCommand\n\nTOOL_NAME = \"trimmomatic\"\n\n_log = logging.getLogger(__name__)\n\nclass TrimmomaticTool(Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(TrimmomaticTool, self).__init__(install_methods=install_methods)\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip()\n\n def execute(self,\n inFastq1,\n inFastq2,\n pairedOutFastq1,\n pairedOutFastq2,\n clipFasta,\n unpairedOutFastq1=None,\n unpairedOutFastq2=None,\n leading_q_cutoff=15,\n trailing_q_cutoff=15,\n minlength_to_keep=30,\n sliding_window_size=4,\n sliding_window_q_cutoff=25,\n maxinfo_target_length=None,\n maxinfo_strictness=None,\n threads=None\n ):\n '''Trim read sequences with Trimmomatic.\n\n Args:\n threads: Number of CPU threads to use. If None, Trimmomatic uses its default.\n '''\n trimmomaticPath = self.install_and_get_path()\n unpairedFastq1 = unpairedOutFastq1 or util_file.mkstempfname()\n unpairedFastq2 = unpairedOutFastq2 or util_file.mkstempfname()\n javaCmd = [trimmomaticPath]\n\n # Build thread arguments if specified\n thread_args = []\n if threads is not None:\n thread_count = util_misc.sanitize_thread_count(threads)\n thread_args = ['-threads', str(thread_count)]\n\n if inFastq2 is None or os.path.getsize(inFastq2) < 10:\n # Unpaired reads\n javaCmd.extend(['SE'] + thread_args + ['-phred33', inFastq1, unpairedFastq1])\n else:\n # Paired reads\n javaCmd.extend(['PE'] + thread_args + ['-phred33',\n inFastq1, inFastq2,\n pairedOutFastq1, unpairedFastq1, pairedOutFastq2, unpairedFastq2\n ])\n\n # all the options\n javaCmd.extend(\n [\n 'LEADING:{leading_q_cutoff}'.format(leading_q_cutoff=leading_q_cutoff),\n 'TRAILING:{trailing_q_cutoff}'.format(trailing_q_cutoff=trailing_q_cutoff),\n 'SLIDINGWINDOW:{sliding_window_size}:{sliding_window_q_cutoff}'.format(\n sliding_window_size=sliding_window_size,\n sliding_window_q_cutoff=sliding_window_q_cutoff,\n ) if not maxinfo_target_length else \\\n 'MAXINFO:{maxinfo_target_length}:{maxinfo_strictness}'.format(\n maxinfo_target_length=maxinfo_target_length,\n maxinfo_strictness=maxinfo_strictness,\n ), \n 'MINLEN:{minlength_to_keep}'.format(minlength_to_keep=minlength_to_keep),\n 'ILLUMINACLIP:{clipFasta}:2:30:12'.format(clipFasta=clipFasta)\n ]\n )\n\n _log.debug(' '.join(javaCmd))\n util_misc.run_and_print(javaCmd, check=True)\n\n if not unpairedOutFastq1:\n os.unlink(unpairedFastq1)\n if not unpairedOutFastq2:\n os.unlink(unpairedFastq2)\n" }, { "path": "src/viral_ngs/core/version.py", "content": "#!/usr/bin/python\n''' This gets the git version into python-land\n'''\n\n__author__ = \"dpark@broadinstitute.org\"\n__version__ = None\n\n# import built-in\nimport subprocess\nimport os\nimport re\nimport time, datetime\nimport os.path\nimport inspect\n\n# module-level imports\n# Note: avoid circular import by importing misc directly, not the util package\nfrom . import misc as util_misc\n\n\ndef get_project_path(include_derived_modules=True):\n '''Return the absolute path of the top-level project,\n if include_derived_modules==False:\n path is assumed to be the parent of the directory containing this script.'''\n\n # obtain path to this script (i.e. the script you're currently reading)\n path = __file__\n\n path = os.path.expanduser(path) # interpret ~\n path = os.path.abspath(path) # abspath converts relative to absolute path\n\n path = os.path.dirname(path) # containing directory: util\n path = os.path.dirname(path) # containing directory: main project dir\n\n # If we want to be more careful, look at derived Python\n # modules calling this one, look for a VERSION file to\n # determine validity of the various containing directories\n if include_derived_modules:\n '''\n find a VERSION file relative to scripts in the Python call stack,\n looking from the outermost layer (closest to initial invocation)\n to the innermost call, and use the path of the first VERSION file found.\n\n This allows a derived module with its own VERSION file\n to report its versions rather than the core version.\n\n This falls back to using/finding the core path\n '''\n for called_item in inspect.stack()[::-1]:\n # resolve symlinks so the project_path is relative to the actual location of the invoked script\n # (i.e. taxon_filter.py --version should resolve viral-classify/VERSION, not viral-core/VERSION)\n called_item_realpath = os.path.realpath(called_item.filename)\n dir_containing_called_item = os.path.dirname(called_item_realpath)\n potential_version_file_path = f\"{dir_containing_called_item}/VERSION\"\n\n if os.path.isfile(potential_version_file_path):\n path = dir_containing_called_item\n break\n\n return path\n\n\ndef call_git_describe():\n cwd = os.getcwd()\n try:\n os.chdir(get_project_path())\n cmd = ['git', 'describe', '--tags', '--always', '--dirty']\n result = util_misc.run_and_print(cmd, silent=True)\n ver = None\n if result.returncode == 0:\n out = result.stdout \n if not isinstance(out, str):\n out = out.decode('utf-8')\n ver = out.strip()\n except Exception:\n ver = None\n os.chdir(cwd)\n return ver\n\ndef release_file():\n return os.path.join(get_project_path(), 'VERSION')\n\n\ndef read_release_version():\n try:\n with open(release_file(), 'rt') as inf:\n version = inf.readlines()[0].strip()\n except Exception:\n version = None\n return version\n\n\ndef write_release_version(version):\n with open(release_file(), 'wt') as outf:\n outf.write(version + '\\n')\n\n\ndef approx_version_number():\n \"\"\"\n In the event that git is unavailable and the VERSION file is not present\n this returns a \"version number\" in the following precedence:\n - version number from path\n downloads of viral-ngs from GitHub tagged releases\n are likely to be extracted into directories containing\n the version number. If they contain a version number\n in the form d.d.d, we can use it\n - modification time of this file (unix timestamp)\n file modification time for github releases corresponds to\n when the release archives were created, a rough way to ballpark\n the release date. If we can't get the version number from the path\n we can at least use the modification time of this file as a proxy\n for the true version number\n - the current time (unix timestamp)\n the current time is better than not having any version number\n \"\"\"\n version = \"\"\n\n version_re = re.compile(r\"(?:(\\d+)\\.)?(?:(\\d+)\\.)?(?:(\\d+))\")\n # path relative to version.py\n viral_ngs_path = os.path.basename(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))\n\n # for tagged releases, it is likely the version number is part of\n # the viral-ngs root directory name\n matches = version_re.search(viral_ngs_path)\n\n if matches and len([n for n in matches.groups() if n]) == 3:\n version = \".\".join( map(str,matches.groups()) )\n else:\n try:\n mtime = os.path.getmtime(__file__)\n except OSError:\n mtime = 0\n\n if mtime > 0:\n # if we could get the modification time of the current file, use it\n version = str(int(mtime))\n else:\n # just use the current time\n version = str(int(time.time()))\n\n return version\n\ndef get_version():\n global __version__\n if __version__ is None:\n # First, try importlib.metadata (works for pip-installed packages\n # regardless of the current working directory)\n try:\n from importlib.metadata import version, PackageNotFoundError\n __version__ = version(\"viral-ngs\")\n except (ImportError, PackageNotFoundError):\n pass\n\n # Fall back to git describe (for development in git clones)\n if __version__ is None:\n from_git = call_git_describe()\n from_file = read_release_version()\n\n if from_git:\n if from_file != from_git:\n write_release_version(from_git)\n __version__ = from_git\n else:\n __version__ = from_file\n\n # Last resort fallback\n if __version__ is None:\n __version__ = approx_version_number()\n\n return __version__\n\n\nif __name__ == \"__main__\":\n print(get_version())\n" }, { "path": "src/viral_ngs/file_utils.py", "content": "#!/usr/bin/env python3\n\"\"\"\nUtilities for dealing with files.\n\"\"\"\n\n__author__ = \"tomkinsc@broadinstitute.org\"\n__commands__ = []\n\nimport argparse\nimport csv\nimport logging\n\nimport pandas\n\nfrom .core import file as util_file, misc as util_misc, cmd as util_cmd\n\nlog = logging.getLogger(__name__)\n\n\n# ==============================\n# *** merge_tarballs ***\n# ==============================\n\ndef merge_tarballs(out_tarball, in_tarballs, threads=None, extract_to_disk_path=None, pipe_hint_in=None, pipe_hint_out=None):\n ''' Merges separate tarballs into one tarball\n data can be piped in and/or out\n '''\n util_file.repack_tarballs(out_tarball, in_tarballs, threads=threads, extract_to_disk_path=extract_to_disk_path, pipe_hint_in=pipe_hint_in, pipe_hint_out=pipe_hint_out)\n return 0\ndef parser_merge_tarballs(parser=argparse.ArgumentParser()):\n parser.add_argument(\n 'out_tarball', \n help='''output tarball (*.tar.gz|*.tar.lz4|*.tar.bz2|*.tar.zst|-);\n compression is inferred by the file extension.\n Note: if \"-\" is used, output will be written to stdout and\n --pipeOutHint must be provided to indicate compression type\n when compression type is not gzip (gzip is used by default).\n ''')\n parser.add_argument(\n 'in_tarballs', nargs='+',\n help=('input tarballs (*.tar.gz|*.tar.lz4|*.tar.bz2|*.tar.zst)')\n )\n parser.add_argument('--extractToDiskPath',\n dest=\"extract_to_disk_path\",\n help='If specified, the tar contents will also be extracted to a local directory.')\n parser.add_argument('--pipeInHint',\n dest=\"pipe_hint_in\",\n default=\"gz\",\n help='If specified, the compression type used is used for piped input.')\n parser.add_argument('--pipeOutHint',\n dest=\"pipe_hint_out\",\n default=\"gz\",\n help='If specified, the compression type used is used for piped output.')\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, merge_tarballs, split_args=True)\n return parser\n__commands__.append(('merge_tarballs', parser_merge_tarballs))\n\n\ndef parser_rename_fasta_sequences(parser=argparse.ArgumentParser()):\n parser.add_argument(\"in_fasta\", help=\"input fasta sequences\")\n parser.add_argument(\"out_fasta\", help=\"output (renamed) fasta sequences\")\n parser.add_argument(\"new_name\", help=\"new sequence base name\")\n parser.add_argument(\n \"--suffix_always\",\n help=\"append numeric index '-1' to if only one sequence exists in (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"suffix_always\"\n )\n\n util_cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n util_cmd.attach_main(parser, main_rename_fasta_sequences)\n return parser\ndef main_rename_fasta_sequences(args):\n ''' Renames the sequences in a fasta file. Behavior modes:\n 1. If input file has exactly one sequence and suffix_always is False,\n then the output file's sequence is named new_name.\n 2. In all other cases,\n the output file's sequences are named - where is an increasing number from 1..<# of sequences>\n '''\n n_seqs = util_file.fasta_length(args.in_fasta)\n with open(args.in_fasta, 'rt') as inf:\n with open(args.out_fasta, 'wt') as outf:\n if (n_seqs == 1) and not args.suffix_always:\n inf.readline()\n outf.write('>' + args.new_name + '\\n')\n for line in inf:\n outf.write(line)\n else:\n i = 1\n for line in inf:\n if line.startswith('>'):\n line = \">{}-{}\\n\".format(args.new_name, i)\n i += 1\n outf.write(line)\n\n return 0\n__commands__.append(('rename_fasta_sequences', parser_rename_fasta_sequences))\n\n## derived cols\n\nclass Adder_Table_Map:\n def __init__(self, tab_file):\n self._mapper = {}\n self._default_col = None\n with open(tab_file, 'rt') as inf:\n reader = csv.DictReader(inf, delimiter='\\t')\n self._col_name = reader.fieldnames[0]\n self._orig_cols = reader.fieldnames[1:]\n for row in reader:\n if all(v=='*' for k,v in row.items() if k in self._orig_cols):\n self._default_col = row.get(self._col_name)\n else:\n k = self._make_key_str(row)\n v = row.get(self._col_name, '')\n log.debug(\"setting {}={} if {}\".format(self._col_name, v, k))\n self._mapper[k] = v\n def _make_key_str(self, row):\n key_str = ':'.join('='.join((k,row.get(k,''))) for k in self._orig_cols)\n return key_str\n def extra_headers(self):\n return (self._col_name,)\n def modify_row(self, row):\n k = self._make_key_str(row)\n v = self._mapper.get(k)\n if v is None and self._default_col:\n v = row.get(self._default_col, '')\n row[self._col_name] = v\n return row\n\nclass Adder_Source_Lab_Subset:\n def __init__(self, restrict_string):\n self._prefix = restrict_string.split(';')[0]\n self._restrict_map = dict(kv.split('=') for kv in restrict_string.split(';')[1].split(':'))\n def extra_headers(self):\n return (self._prefix + '_originating_lab', self._prefix + '_submitting_lab')\n def modify_row(self, row):\n if all((row.get(k) == v) for k,v in self._restrict_map.items()):\n row[self._prefix + '_originating_lab'] = row['originating_lab']\n row[self._prefix + '_submitting_lab'] = row['submitting_lab']\n return row\n\ndef parser_tsv_derived_cols(parser=argparse.ArgumentParser()):\n parser.add_argument(\"in_tsv\", type=str, help=\"input metadata\")\n parser.add_argument(\"out_tsv\", type=str, help=\"output metadata\")\n parser.add_argument(\"--table_map\", type=str, nargs='*', help=\"Mapping tables. Each mapping table is a tsv with a header. The first column is the output column name for this mapping (it will be created or overwritten). The subsequent columns are matching criteria. The value in the first column is written to the output column. The exception is in the case where all match columns are '*' -- in this case, the value in the first column is the column header name to copy over.\")\n parser.add_argument(\"--lab_highlight_loc\", type=str, help=\"This option copies the 'originating_lab' and 'submitting_lab' columns to new ones including a prefix, but only if they match certain criteria. The value of this string must be of the form prefix;col_header=value:col_header=value. For example, 'MA;country=USA:division=Massachusetts' will copy the originating_lab and submitting_lab columns to MA_originating_lab and MA_submitting_lab, but only for those rows where country=USA and division=Massachusetts.\")\n util_cmd.common_args(parser, (('loglevel', None), ('version', None)))\n util_cmd.attach_main(parser, tsv_derived_cols, split_args=True)\n return parser\ndef tsv_derived_cols(in_tsv, out_tsv, table_map=None, lab_highlight_loc=None):\n ''' Modify metadata table to compute derivative columns on the fly and add or replace new columns\n '''\n adders = []\n if table_map:\n for t in table_map:\n adders.append(Adder_Table_Map(t))\n if lab_highlight_loc:\n adders.append(Adder_Source_Lab_Subset(lab_highlight_loc))\n\n with open(in_tsv, 'rt') as inf:\n reader = csv.DictReader(inf, delimiter='\\t')\n out_headers = reader.fieldnames\n for adder in adders:\n out_headers.extend(adder.extra_headers())\n\n with open(out_tsv, 'wt') as outf:\n writer = csv.DictWriter(outf, out_headers, delimiter='\\t')\n writer.writeheader()\n for row in reader:\n for adder in adders:\n adder.modify_row(row)\n writer.writerow(row)\n__commands__.append(('tsv_derived_cols', parser_tsv_derived_cols))\n\n\ndef parser_tsv_join(parser=argparse.ArgumentParser()):\n parser.add_argument(\"in_tsvs\", nargs=\"+\", type=str, help=\"input tsvs\")\n parser.add_argument(\"out_tsv\", type=str, help=\"output tsv\")\n parser.add_argument(\"--join_id\", type=str, required=True, help=\"column name to join on\")\n util_cmd.common_args(parser, (('loglevel', None), ('version', None)))\n util_cmd.attach_main(parser, tsv_join, split_args=True)\n return parser\ndef tsv_join(in_tsvs, out_tsv, join_id=None):\n ''' full outer join of tables\n '''\n\n ''' schaluva implementation:\n df_list = list(pandas.read_csv(f, sep=\"\\t\") for f in in_tsvs)\n df_concat = pandas.concat(df_list, axis=0, ignore_index=True, sort=False).fillna('NA')\n pandas.DataFrame.to_csv(df_concat, out_tsv, sep='\\t', na_rep='NA', index=False)\n\n but the above causes types to be parsed and re-outputted slightly differently (e.g. ints become floats)\n and importantly it doesn't actually join on a join key\n\n attempt to reimplement by hand\n '''\n\n # prep all readers\n readers = list(csv.DictReader(open(fn, 'rt'), delimiter='\\t') for fn in in_tsvs)\n\n # prep the output header\n header = []\n for reader in readers:\n header.extend(reader.fieldnames)\n header = list(util_misc.unique(header))\n if not join_id or join_id not in header:\n raise Exception()\n\n # merge everything in-memory\n out_ids = []\n out_row_by_id = {}\n for reader in readers:\n for row in reader:\n row_id = row[join_id]\n row_out = out_row_by_id.get(row_id, {})\n for h in header:\n # prefer non-empty values from earlier files in in_tsvs, populate from subsequent files only if missing\n if not row_out.get(h):\n row_out[h] = row.get(h, '')\n out_row_by_id[row_id] = row_out\n out_ids.append(row_id)\n out_ids = list(util_misc.unique(out_ids))\n\n # write output\n with open(out_tsv, 'w', newline='') as outf:\n writer = csv.DictWriter(outf, header, delimiter='\\t', dialect=csv.unix_dialect, quoting=csv.QUOTE_MINIMAL)\n writer.writeheader()\n writer.writerows(out_row_by_id[row_id] for row_id in out_ids)\n__commands__.append(('tsv_join', parser_tsv_join))\n\n\n# =======================\ndef full_parser():\n return util_cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n util_cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/illumina.py", "content": "#!/usr/bin/env python3\n\"\"\"\nUtilities for demultiplexing Illumina data.\n\"\"\"\n\n__author__ = \"dpark@broadinstitute.org\"\n__commands__ = []\n\nimport argparse\nimport concurrent.futures\nimport csv\nimport gc\nimport glob\nimport gzip\nimport itertools\nimport json\nimport logging\nimport os\nimport os.path\nimport re\nimport shutil\nimport sqlite3\nimport subprocess\nimport tempfile\nimport xml.etree.ElementTree\nfrom collections import Counter, defaultdict\n\nimport arrow\nimport matplotlib.pyplot as plt\nimport numpy as np\nimport pandas as pd\n\nfrom .core import picard\nfrom .core import samtools\nfrom .core import splitcode\nfrom . import read_utils\nfrom .core import file as util_file, misc as util_misc, cmd as util_cmd\nfrom .core.illumina_indices import IlluminaIndexReference, IlluminaBarcodeHelper\nfrom .core.illumina_utils import IlluminaDirectory, RunInfo, SampleSheet, SampleSheetError\n\nlog = logging.getLogger(__name__)\n\n\n# =============================\n# *** Utility Functions ***\n# =============================\n\n\ndef parse_illumina_fastq_filename(filename):\n \"\"\"Parse Illumina FASTQ filename to extract metadata.\n\n Supports two filename formats:\n 1. DRAGEN format (with flowcell ID):\n {flowcell}_{lane}_{numeric_id}_{sample_name}_{S#}_{L00#}_{R#}_{chunk}.fastq[.gz]\n Example: 22J5GLLT4_6_0420593812_B13Pool1a_S1_L006_R1_001.fastq.gz\n\n 2. Simple bcl2fastq format (without flowcell ID):\n {sample_name}_{S#}_{L00#}_{R#}_{chunk}.fastq[.gz]\n Example: mebv-48-5_S17_L001_R1_001.fastq.gz\n\n Args:\n filename (str): FASTQ filename (with or without path)\n\n Returns:\n dict: Dictionary with extracted metadata fields:\n For DRAGEN format:\n - flowcell (str): Flowcell ID (typically 9 alphanumeric characters)\n - lane_short (int): Short lane number (1-8)\n - numeric_id (str): Numeric identifier\n - sample_name (str): Sample name (may contain underscores)\n - sample_number (int): Sample number (from S#)\n - lane (int): Full lane number (from L00#)\n - read (int): Read number (1 or 2)\n - chunk (int): Chunk number (typically 001)\n For simple format:\n - sample_name (str): Sample name\n - sample_number (int): Sample number (from S#)\n - lane (int): Lane number (from L00#)\n - read (int): Read number (1 or 2)\n - chunk (int): Chunk number (typically 001)\n\n Raises:\n ValueError: If filename doesn't match expected format\n \"\"\"\n if not filename:\n raise ValueError(\"Filename cannot be empty\")\n\n # Extract basename and remove extensions\n basename = os.path.basename(filename)\n basename = basename.replace('.fastq.gz', '').replace('.fastq', '')\n\n # Try DRAGEN format first (with flowcell ID)\n # Pattern: {flowcell}_{lane}_{numeric_id}_{sample_name}_{S#}_{L00#}_{R#}_{chunk}\n # The tricky part: sample_name can contain underscores!\n # Strategy: Match from both ends and extract the middle as sample_name\n\n # DRAGEN pattern: we know the last 4 fields are always S#_L00#_R#_chunk\n # and the first 3 fields are flowcell_lane_numeric_id\n # Everything in between is the sample name\n dragen_pattern = r'^([A-Z0-9]{5,15})_(\\d)_(\\d{10})_(.+)_S(\\d+)_L00(\\d)_(R|I)(\\d)_(\\d{3})$'\n match = re.match(dragen_pattern, basename)\n\n if match:\n return {\n 'flowcell': match.group(1),\n 'lane_short': int(match.group(2)),\n 'numeric_id': match.group(3),\n 'sample_name': match.group(4),\n 'sample_number': int(match.group(5)),\n 'lane': int(match.group(6)),\n 'read': int(match.group(8)),\n 'chunk': int(match.group(9)),\n 'is_index': match.group(7) == 'I'\n }\n\n # Try simple bcl2fastq format (without flowcell ID)\n # Pattern: {sample_name}_{S#}_{L00#}_{R#}_{chunk}\n # Sample name cannot contain underscores followed by S# pattern\n simple_pattern = r'^(.+)_S(\\d+)_L00(\\d)_(R|I)(\\d)_(\\d{3})$'\n match = re.match(simple_pattern, basename)\n\n if match:\n return {\n 'sample_name': match.group(1),\n 'sample_number': int(match.group(2)),\n 'lane': int(match.group(3)),\n 'read': int(match.group(5)),\n 'chunk': int(match.group(6)),\n 'is_index': match.group(4) == 'I'\n }\n\n # If neither pattern matches, raise an error\n raise ValueError(\n f\"Filename '{basename}' does not match expected Illumina FASTQ format. \"\n f\"Expected formats:\\n\"\n f\" DRAGEN: {{flowcell}}_{{lane}}_{{numeric_id}}_{{sample_name}}_S#_L00#_R#_###.fastq[.gz]\\n\"\n f\" Simple: {{sample_name}}_S#_L00#_R#_###.fastq[.gz]\"\n )\n\n\ndef normalize_barcode(barcode):\n \"\"\"Normalize an Illumina barcode sequence.\n\n Performs the following normalizations:\n 1. Converts to uppercase\n 2. Strips leading and trailing whitespace\n 3. Validates that only ACGTN characters are present\n\n Args:\n barcode (str): Barcode sequence to normalize\n\n Returns:\n str: Normalized barcode (uppercase, no whitespace)\n\n Raises:\n ValueError: If barcode contains invalid characters (not ACGTN)\n TypeError: If barcode is not a string\n\n Examples:\n >>> normalize_barcode(\"acgt\")\n 'ACGT'\n >>> normalize_barcode(\" CTGATCGT \")\n 'CTGATCGT'\n >>> normalize_barcode(\"acgtn\")\n 'ACGTN'\n \"\"\"\n if not isinstance(barcode, str):\n raise TypeError(f\"Barcode must be a string, got {type(barcode).__name__}\")\n\n # Strip whitespace and convert to uppercase\n normalized = barcode.strip().upper()\n\n # Empty string is valid (allows for missing barcodes)\n if not normalized:\n return normalized\n\n # Validate characters (only ACGTN allowed)\n valid_chars = set('ACGTN')\n invalid_chars = set(normalized) - valid_chars\n\n if invalid_chars:\n raise ValueError(\n f\"Barcode contains invalid characters: {sorted(invalid_chars)}. \"\n f\"Only ACGTN characters are allowed. Got: '{barcode}'\"\n )\n\n return normalized\n\n\ndef barcode_n_fraction(barcode):\n \"\"\"Calculate the fraction of N bases in a barcode.\n\n Args:\n barcode: Normalized barcode string\n\n Returns:\n float: Fraction of bases that are N (0.0 to 1.0)\n \"\"\"\n if not barcode:\n return 0.0\n return barcode.count('N') / len(barcode)\n\n\ndef barcode_matches_with_n(observed, expected):\n \"\"\"Check if an observed barcode matches expected, treating N as wildcard.\n\n N bases in the observed barcode (from FASTQ header) are treated as wildcards\n that match any base. This handles sequencer no-call bases where a position\n couldn't be confidently determined.\n\n Note: N in the expected barcode (from samplesheet) is NOT a wildcard -\n it requires an exact N match in the observed barcode.\n\n Args:\n observed: Barcode from FASTQ header (may contain N wildcards)\n expected: Barcode from samplesheet (N requires exact match)\n\n Returns:\n bool: True if barcodes match (accounting for N wildcards in observed)\n\n Examples:\n >>> barcode_matches_with_n('ATCGATCG', 'ATCGATCG')\n True\n >>> barcode_matches_with_n('ATCNATCG', 'ATCGATCG') # N matches G\n True\n >>> barcode_matches_with_n('ATCGATCG', 'ATCNATCG') # N in expected requires exact N\n False\n >>> barcode_matches_with_n('NNNNNNNN', 'ATCGATCG') # All N matches anything\n True\n \"\"\"\n if len(observed) != len(expected):\n return False\n\n for obs_base, exp_base in zip(observed, expected):\n # N in observed matches any base in expected\n if obs_base == 'N':\n continue\n # Otherwise require exact match\n if obs_base != exp_base:\n return False\n\n return True\n\n\ndef barcode_matches_fuzzy(observed, expected, max_mismatches=1):\n \"\"\"Check if observed barcode matches expected, with N wildcards and mismatch tolerance.\n\n N bases in the observed barcode (from FASTQ header) are treated as wildcards\n and are NOT counted as mismatches. Non-N bases that differ from expected are\n counted as mismatches. Match succeeds if total mismatches <= max_mismatches.\n\n Args:\n observed: Barcode from FASTQ header (may contain N wildcards)\n expected: Barcode from samplesheet\n max_mismatches: Maximum allowed non-N mismatches (default: 1)\n\n Returns:\n tuple: (matches: bool, mismatch_count: int)\n\n Examples:\n >>> barcode_matches_fuzzy('ATCGATCG', 'ATCGATCG', 1)\n (True, 0)\n >>> barcode_matches_fuzzy('ATCGATCG', 'ATCAATCG', 1) # G->A at pos 3\n (True, 1)\n >>> barcode_matches_fuzzy('ATCGATCG', 'ATAAATCG', 1) # 2 mismatches\n (False, 2)\n >>> barcode_matches_fuzzy('ATCNATCG', 'ATCGATCG', 0) # N is wildcard, not mismatch\n (True, 0)\n \"\"\"\n if len(observed) != len(expected):\n return False, len(observed)\n\n mismatches = 0\n for obs_base, exp_base in zip(observed, expected):\n if obs_base == 'N':\n continue # wildcard, not a mismatch\n if obs_base != exp_base:\n mismatches += 1\n if mismatches > max_mismatches:\n return False, mismatches # early exit\n\n return True, mismatches\n\n\ndef match_barcodes_with_orientation(target_bc1, target_bc2, sample_rows,\n barcode_columns=('barcode_1', 'barcode_2'),\n max_mismatches=1):\n \"\"\"\n Match FASTQ barcodes against samplesheet with automatic i5 orientation detection.\n\n Due to Illumina chemistry changes over the years, the i5 index (barcode_2) may be\n written to FASTQ headers in either forward or reverse complement orientation\n depending on the sequencer model. This function automatically tries both orientations.\n\n N bases in FASTQ barcodes are treated as wildcards (sequencer no-call bases).\n However, barcodes with >50% N bases are rejected as too low confidence.\n\n Non-N mismatches up to max_mismatches are tolerated to handle cases where\n DRAGEN demultiplexing accepted reads with index mismatches. When multiple\n samplesheet barcode pairs match, the one with fewest total mismatches is\n preferred. If multiple distinct pairs tie at the same mismatch distance,\n the match is considered ambiguous.\n\n Note: Only barcode_2 orientation is auto-detected. barcode_1 (i7) orientation is\n consistent across all Illumina platforms.\n\n Tries matching in this order:\n 1. Direct match (both barcodes as-is)\n 2. Reverse complement barcode_2 only (i5 orientation difference)\n\n Args:\n target_bc1: Normalized barcode_1 from FASTQ header\n target_bc2: Normalized barcode_2 from FASTQ header (or None)\n sample_rows: List of sample row dicts from samplesheet\n barcode_columns: Tuple of column names to match against\n max_mismatches: Maximum allowed non-N mismatches per barcode (default: 1)\n\n Returns:\n tuple: (matched_rows, orientation_info)\n matched_rows: List of matching sample rows (empty if no match, ambiguous, or high N fraction)\n orientation_info: dict with keys:\n - 'barcode_2_revcomp': bool (True if reverse complement was needed)\n - 'matched_bc1': str. On successful match (no 'skipped_reason'), this is\n the samplesheet barcode_1 value. When 'skipped_reason' is set, this\n is the normalized barcode_1 observed in the FASTQ header.\n - 'matched_bc2': str. On successful match (no 'skipped_reason'), this is\n the samplesheet barcode_2 value. When 'skipped_reason' is set, this\n is the normalized barcode_2 observed in the FASTQ header.\n - 'skipped_reason': str (if empty results, why - 'high_n_fraction', 'ambiguous', or 'no_match')\n \"\"\"\n log = logging.getLogger(__name__)\n bc1_col, bc2_col = barcode_columns\n\n # Normalize input barcodes for case-insensitive matching\n target_bc1 = normalize_barcode(target_bc1) if target_bc1 else None\n target_bc2 = normalize_barcode(target_bc2) if target_bc2 else None\n\n # Check if barcodes have too many N bases (>50% = low confidence)\n bc1_n_frac = barcode_n_fraction(target_bc1) if target_bc1 else 0.0\n bc2_n_frac = barcode_n_fraction(target_bc2) if target_bc2 else 0.0\n\n if bc1_n_frac > 0.5 or bc2_n_frac > 0.5:\n log.warning(f\"Skipping barcode match: too many N bases (bc1={bc1_n_frac:.0%}, bc2={bc2_n_frac:.0%}). \"\n f\"Barcodes: {target_bc1}+{target_bc2}\")\n return [], {\n 'barcode_2_revcomp': False,\n 'matched_bc1': target_bc1,\n 'matched_bc2': target_bc2,\n 'skipped_reason': 'high_n_fraction',\n }\n\n def try_match(check_bc1, check_bc2):\n \"\"\"Try matching with given barcode values using fuzzy matching.\n\n Uses barcode_matches_fuzzy() to handle N wildcards and tolerate mismatches.\n Returns matches with the fewest total mismatches.\n \"\"\"\n candidates = []\n for row in sample_rows:\n sheet_bc1 = normalize_barcode(row.get(bc1_col, ''))\n sheet_bc2 = normalize_barcode(row.get(bc2_col, ''))\n\n bc1_ok, bc1_mm = barcode_matches_fuzzy(check_bc1, sheet_bc1, max_mismatches)\n if not bc1_ok:\n continue\n\n if check_bc2 is not None:\n bc2_ok, bc2_mm = barcode_matches_fuzzy(check_bc2, sheet_bc2, max_mismatches)\n if not bc2_ok:\n continue\n else:\n bc2_mm = 0\n\n candidates.append((row, bc1_mm + bc2_mm))\n\n if not candidates:\n return []\n\n # Prefer matches with fewest total mismatches\n best_mm = min(mm for _, mm in candidates)\n return [row for row, mm in candidates if mm == best_mm]\n\n def check_ambiguous(matched_rows):\n \"\"\"Check if matching produced ambiguous results.\n\n Returns True if matched rows have multiple distinct barcode pairs.\n \"\"\"\n if not matched_rows:\n return False\n\n unique_pairs = set()\n for row in matched_rows:\n sheet_bc1 = normalize_barcode(row.get(bc1_col, ''))\n sheet_bc2 = normalize_barcode(row.get(bc2_col, ''))\n unique_pairs.add((sheet_bc1, sheet_bc2))\n\n return len(unique_pairs) > 1\n\n def _samplesheet_barcodes(matched_rows):\n \"\"\"Get authoritative samplesheet barcode values from matched rows.\"\"\"\n sheet_bc1 = normalize_barcode(matched_rows[0].get(bc1_col, ''))\n sheet_bc2 = normalize_barcode(matched_rows[0].get(bc2_col, ''))\n return sheet_bc1, sheet_bc2\n\n # Try direct match first\n matched = try_match(target_bc1, target_bc2)\n if matched:\n if check_ambiguous(matched):\n log.warning(f\"Skipping barcode match: fuzzy matching is ambiguous \"\n f\"(matched multiple distinct barcode pairs). Barcodes: {target_bc1}+{target_bc2}\")\n return [], {\n 'barcode_2_revcomp': False,\n 'matched_bc1': target_bc1,\n 'matched_bc2': target_bc2,\n 'skipped_reason': 'ambiguous',\n }\n sheet_bc1, sheet_bc2 = _samplesheet_barcodes(matched)\n return matched, {\n 'barcode_2_revcomp': False,\n 'matched_bc1': sheet_bc1,\n 'matched_bc2': sheet_bc2,\n }\n\n # Try reverse complement of barcode_2 (i5 orientation issue)\n if target_bc2:\n target_bc2_rc = util_misc.reverse_complement(target_bc2)\n matched = try_match(target_bc1, target_bc2_rc)\n if matched:\n if check_ambiguous(matched):\n log.warning(f\"Skipping barcode match: fuzzy matching is ambiguous \"\n f\"(matched multiple distinct barcode pairs). Barcodes: {target_bc1}+{target_bc2_rc}\")\n return [], {\n 'barcode_2_revcomp': True,\n 'matched_bc1': target_bc1,\n 'matched_bc2': target_bc2_rc,\n 'skipped_reason': 'ambiguous',\n }\n sheet_bc1, sheet_bc2 = _samplesheet_barcodes(matched)\n return matched, {\n 'barcode_2_revcomp': True,\n 'matched_bc1': sheet_bc1,\n 'matched_bc2': sheet_bc2,\n }\n\n # No match found - return empty list with skipped_reason\n unique_bc_pairs = set()\n for row in sample_rows:\n bc1 = normalize_barcode(row.get(bc1_col, ''))\n bc2 = normalize_barcode(row.get(bc2_col, ''))\n unique_bc_pairs.add(f\"{bc1}+{bc2}\")\n\n log.warning(\n f\"No samples found matching barcodes {target_bc1}+{target_bc2} \"\n f\"(also tried reverse complement of barcode_2). \"\n f\"Samplesheet contains barcode pairs: {sorted(unique_bc_pairs)[:10]}...\"\n )\n return [], {\n 'barcode_2_revcomp': False,\n 'matched_bc1': target_bc1,\n 'matched_bc2': target_bc2,\n 'skipped_reason': 'no_match',\n }\n\n\ndef build_run_info_json(\n sequencing_center,\n run_start_date,\n read_structure,\n indexes,\n run_id,\n lane,\n flowcell,\n lane_count=None,\n surface_count=None,\n swath_count=None,\n tile_count=None,\n total_tile_count=None,\n sequencer_model=None\n):\n \"\"\"Build a run_info.json dictionary with standardized schema.\n\n This function consolidates run info JSON construction logic used by\n illumina_demux, splitcode_demux, and other demultiplexing functions.\n\n Args:\n sequencing_center (str): Sequencing center name\n run_start_date (str): Run start date in ISO format (YYYY-MM-DD)\n read_structure (str): Picard-style read structure (e.g., \"76T8B8B76T\")\n indexes (int): Number of index reads\n run_id (str): Run identifier (often flowcell.lane)\n lane (int): Lane number\n flowcell (str): Flowcell identifier\n lane_count (int, optional): Number of lanes in the flowcell\n surface_count (int, optional): Number of surfaces\n swath_count (int, optional): Number of swaths\n tile_count (int, optional): Number of tiles per lane\n total_tile_count (int, optional): Total number of tiles\n sequencer_model (str, optional): Sequencer model name\n\n Returns:\n dict: Dictionary with run metadata matching the standard schema.\n All numeric fields are converted to strings for JSON consistency.\n\n Examples:\n >>> info = build_run_info_json(\n ... sequencing_center=\"BROAD\",\n ... run_start_date=\"2024-01-15\",\n ... read_structure=\"76T8B76T\",\n ... indexes=1,\n ... run_id=\"FC123.1\",\n ... lane=1,\n ... flowcell=\"FC123\"\n ... )\n >>> info['flowcell']\n 'FC123'\n \"\"\"\n run_info_data = {\n \"sequencing_center\": sequencing_center,\n \"run_start_date\": run_start_date,\n \"read_structure\": read_structure,\n \"indexes\": str(indexes),\n \"run_id\": run_id,\n \"lane\": str(lane),\n \"flowcell\": str(flowcell),\n }\n\n # Add optional fields if provided\n if lane_count is not None:\n run_info_data[\"lane_count\"] = str(lane_count)\n if surface_count is not None:\n run_info_data[\"surface_count\"] = str(surface_count)\n if swath_count is not None:\n run_info_data[\"swath_count\"] = str(swath_count)\n if tile_count is not None:\n run_info_data[\"tile_count\"] = str(tile_count)\n if total_tile_count is not None:\n run_info_data[\"total_tile_count\"] = str(total_tile_count)\n if sequencer_model is not None:\n run_info_data[\"sequencer_model\"] = sequencer_model\n\n return run_info_data\n\n\n# ==============================\n# *** illumina_metadata ***\n# ==============================\n\n\ndef illumina_metadata(\n runinfo,\n samplesheet,\n lane=None,\n sequencing_center=None,\n append_run_id=False,\n out_runinfo=None,\n out_meta_by_sample=None,\n out_meta_by_filename=None\n):\n \"\"\"\n Generate metadata JSON files from Illumina run files without processing reads.\n\n This function extracts metadata from RunInfo.xml and SampleSheet, generating\n standardized JSON output files. It is designed to be run once per sequencing run\n to create metadata that's shared across all parallel demux jobs.\n\n Args:\n runinfo (str): Path to RunInfo.xml file\n samplesheet (str): Path to Illumina SampleSheet.csv file\n lane (int, optional): Lane number to process. If not specified:\n - All lanes from samplesheet will be processed\n - Output run_info.json will use lane=\"0\"\n - Sample metadata will preserve lane values from samplesheet if present, else use \"0\"\n sequencing_center (str, optional): Sequencing center name. If not provided,\n will be derived from the instrument ID in RunInfo.xml.\n append_run_id (bool, optional): If True, append flowcell ID and lane to\n library IDs in the format: {sample}.l{library_id}.{flowcell}.{lane}\n This matches the behavior of illumina_demux and splitcode_demux_fastqs\n when using --append_run_id, ensuring metadata 'run' fields match BAM\n filenames. Default: False.\n out_runinfo (str, optional): Output path for run_info.json\n out_meta_by_sample (str, optional): Output path for meta_by_sample.json\n out_meta_by_filename (str, optional): Output path for meta_by_filename.json\n\n Returns:\n dict: Dictionary containing paths to generated files\n\n Raises:\n FileNotFoundError: If runinfo or samplesheet files don't exist\n IOError: If there are issues reading input files or writing output files\n\n Example:\n >>> illumina_metadata(\n ... runinfo='RunInfo.xml',\n ... samplesheet='SampleSheet.csv',\n ... lane=1,\n ... out_runinfo='run_info.json',\n ... out_meta_by_sample='meta_by_sample.json',\n ... out_meta_by_filename='meta_by_filename.json'\n ... )\n \"\"\"\n # Validate input files exist\n if not os.path.exists(runinfo):\n raise FileNotFoundError(f\"RunInfo.xml not found: {runinfo}\")\n\n # Samplesheet is only required when sample metadata is requested\n if out_meta_by_sample or out_meta_by_filename:\n if samplesheet is None:\n raise ValueError(\"--samplesheet is required when generating sample metadata \"\n \"(--out_meta_by_sample or --out_meta_by_filename)\")\n if not os.path.exists(samplesheet):\n raise FileNotFoundError(f\"SampleSheet not found: {samplesheet}\")\n elif samplesheet is not None and not os.path.exists(samplesheet):\n raise FileNotFoundError(f\"SampleSheet not found: {samplesheet}\")\n\n # Parse RunInfo.xml\n runinfo_obj = RunInfo(runinfo)\n\n # Derive sequencing center from RunInfo if not provided\n if sequencing_center is None:\n sequencing_center = runinfo_obj.get_machine()\n log.info(f\"Using sequencing center from RunInfo.xml: {sequencing_center}\")\n\n # Build run_id string for library IDs if requested (matches demux commands)\n if append_run_id:\n flowcell = runinfo_obj.get_flowcell()\n run_id_str = f\"{flowcell}.{lane if lane is not None else 0}\"\n else:\n run_id_str = None\n\n # Parse SampleSheet only when needed (sample metadata requested or provided)\n samples = None\n if samplesheet is not None:\n # Note: allow_non_unique=True is needed for 3-barcode samplesheets where\n # multiple samples share outer barcodes (barcode_1 + barcode_2) and differ\n # only in inner barcodes (barcode_3)\n samples = SampleSheet(\n samplesheet,\n only_lane=lane,\n allow_non_unique=True,\n append_run_id=run_id_str\n )\n\n output_files = {}\n\n # Generate run_info.json using utility function\n if out_runinfo:\n run_info_dict = build_run_info_json(\n sequencing_center=sequencing_center,\n run_start_date=runinfo_obj.get_rundate_iso(),\n read_structure=runinfo_obj.get_read_structure(),\n indexes=str(runinfo_obj.get_read_structure().count('B')),\n run_id=runinfo_obj.get_run_id(),\n lane=str(lane if lane is not None else 0),\n flowcell=str(runinfo_obj.get_flowcell()),\n lane_count=runinfo_obj.get_lane_count(),\n surface_count=runinfo_obj.get_surface_count(),\n swath_count=runinfo_obj.get_swath_count(),\n tile_count=runinfo_obj.get_tile_count(),\n total_tile_count=runinfo_obj.tile_count(),\n sequencer_model=runinfo_obj.get_machine_model()\n )\n\n with open(out_runinfo, 'wt') as outf:\n json.dump(run_info_dict, outf, indent=2)\n output_files['run_info'] = out_runinfo\n\n # Generate sample metadata JSONs\n if out_meta_by_sample or out_meta_by_filename:\n # Get sample metadata and add lane\n sample_meta = list(samples.get_rows())\n for row in sample_meta:\n row[\"lane\"] = str(lane) if lane is not None else row.get(\"lane\", \"0\")\n\n if out_meta_by_sample:\n with open(out_meta_by_sample, 'wt') as outf:\n json.dump(dict((r[\"sample\"], r) for r in sample_meta), outf, indent=2)\n output_files['meta_by_sample'] = out_meta_by_sample\n\n if out_meta_by_filename:\n with open(out_meta_by_filename, 'wt') as outf:\n json.dump(dict((r[\"run\"], r) for r in sample_meta), outf, indent=2)\n output_files['meta_by_filename'] = out_meta_by_filename\n\n # Log generated files\n log.info(f\"Generated {len(output_files)} metadata file(s):\")\n for key, path in output_files.items():\n log.info(f\" {key}: {path}\")\n\n return output_files\n\n\ndef parser_illumina_metadata(parser=argparse.ArgumentParser()):\n \"\"\"\n Argument parser for illumina_metadata entry point.\n \"\"\"\n parser.add_argument(\n '--runinfo',\n required=True,\n help='Path to RunInfo.xml file'\n )\n parser.add_argument(\n '--samplesheet',\n required=False,\n default=None,\n help='Path to Illumina SampleSheet.csv file (required for --out_meta_by_sample and --out_meta_by_filename)'\n )\n parser.add_argument(\n '--lane',\n required=False,\n type=int,\n default=None,\n help='Lane number to process (optional; if not specified, processes all lanes and uses default value of 0 in outputs)'\n )\n parser.add_argument(\n '--sequencing_center',\n default=None,\n help='Sequencing center name (default: derived from instrument ID in RunInfo.xml)'\n )\n parser.add_argument(\n '--append_run_id',\n action='store_true',\n help='Append flowcell ID and lane to library IDs (e.g., sample.l1.FLOWCELL.1) for SRA compatibility'\n )\n parser.add_argument(\n '--out_runinfo',\n help='Output path for run_info.json'\n )\n parser.add_argument(\n '--out_meta_by_sample',\n help='Output path for meta_by_sample.json (sample metadata indexed by sample name)'\n )\n parser.add_argument(\n '--out_meta_by_filename',\n help='Output path for meta_by_filename.json (sample metadata indexed by library ID)'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, illumina_metadata, split_args=True)\n return parser\n\n\n__commands__.append(('illumina_metadata', parser_illumina_metadata))\n\n\n# ===================================\n# *** splitcode_demux_fastqs ***\n# ===================================\n\n\n# This function is called in new processes and must remain at the top level\n# (global scope) of this file to be picklable and thus compatible with\n# concurrent.futures.ProcessPoolExecutor()\n# See: https://docs.python.org/3/library/concurrent.futures.html#processpoolexecutor\ndef run_picard_fastq_to_sam_for_splitcode_demux(\n sample_library_id,\n sample_name,\n bc_r1,\n bc_r2,\n outdir,\n picard_opts_dict,\n jvm_memory='2g',\n string_to_log=None\n):\n \"\"\"\n Convert a pair of splitcode-demuxed FASTQs to an unaligned BAM file.\n\n This function is designed to be called in parallel worker processes via\n ProcessPoolExecutor. It encapsulates all the logic for converting a single\n sample's FASTQs to BAM.\n\n Args:\n sample_library_id (str): Library ID from samplesheet (used for logging)\n sample_name (str): Sample name for BAM (SAMPLE field in @RG)\n bc_r1 (str): Path to R1 FASTQ file\n bc_r2 (str): Path to R2 FASTQ file\n outdir (str): Output directory for BAM\n picard_opts_dict (dict): Picard options as dict (will be converted to list)\n jvm_memory (str): JVM memory allocation (e.g., '2g')\n string_to_log (str): Optional message to log when starting\n\n Returns:\n tuple: (sample_name, output_bam, read_pairs, sample_library_id)\n - sample_name: Sample name from input\n - output_bam: Path to created BAM file\n - read_pairs: Number of read pairs in the BAM\n - sample_library_id: Library ID from input (for error tracking)\n\n Raises:\n FileNotFoundError: If input FASTQs don't exist\n subprocess.CalledProcessError: If Picard or samtools fails\n \"\"\"\n if string_to_log:\n log.info(string_to_log)\n\n # Verify input FASTQs exist\n if not os.path.exists(bc_r1) or not os.path.exists(bc_r2):\n raise FileNotFoundError(\n f\"Input FASTQs not found for {sample_library_id}: {bc_r1}, {bc_r2}\"\n )\n\n output_bam = os.path.join(outdir, f\"{sample_library_id}.bam\")\n\n # Convert dict to Picard options list\n picard_tool = picard.FastqToSamTool()\n picard_opts = picard_tool.dict_to_picard_opts(picard_opts_dict)\n\n # Execute Picard FastqToSam\n picard_tool.execute(\n bc_r1,\n bc_r2,\n sample_name,\n output_bam,\n picardOptions=picard_opts,\n JVMmemory=jvm_memory\n )\n\n # Count read pairs\n samtools_tool = samtools.SamtoolsTool()\n total_reads = samtools_tool.count(output_bam)\n read_pairs = total_reads // 2\n\n return (sample_name, output_bam, read_pairs, sample_library_id)\n\n\ndef _parse_barcode_from_header(header_line):\n \"\"\"Parse barcode sequences from an Illumina FASTQ header line.\n\n Expects the standard Illumina format:\n @INST:RUN:FC:LANE:TILE:X:Y READ:FILTERED:CONTROL:BARCODE\n\n Args:\n header_line: A single FASTQ header line (with or without leading @)\n\n Returns:\n tuple: (bc1_raw, bc2_raw_or_None) raw barcode strings,\n or (None, None) if the header cannot be parsed.\n \"\"\"\n parts = header_line.strip().split()\n if len(parts) < 2:\n return None, None\n\n metadata_field = parts[-1]\n metadata_parts = metadata_field.split(':')\n if len(metadata_parts) < 4:\n return None, None\n\n barcode_field = metadata_parts[3]\n if '+' in barcode_field:\n bc1_raw, bc2_raw = barcode_field.split('+', 1)\n return bc1_raw, bc2_raw\n else:\n return barcode_field, None\n\n\ndef consensus_barcode_from_fastq(fastq_path, num_reads=10):\n \"\"\"Read first N reads from a FASTQ and form a consensus barcode sequence.\n\n For each position in the barcode, takes the majority base across all reads.\n N bases are excluded from the vote (treated as missing data). If all reads\n have N at a position, the consensus is N.\n\n Args:\n fastq_path: Path to FASTQ file (may be gzipped)\n num_reads: Number of reads to examine (default: 10)\n\n Returns:\n tuple: (barcode_1, barcode_2_or_None) normalized consensus barcodes,\n or (None, None) if file is empty (no reads).\n\n Raises:\n ValueError: If the FASTQ has reads but none have parseable barcode headers.\n \"\"\"\n log = logging.getLogger(__name__)\n\n bc1_list = []\n bc2_list = []\n headers_seen = 0\n\n with util_file.open_or_gzopen(fastq_path, 'rt') as f:\n reads_found = 0\n for line_num, line in enumerate(f):\n # FASTQ format: header is every 4th line starting at line 0\n if line_num % 4 != 0:\n continue\n headers_seen += 1\n if reads_found >= num_reads:\n break\n\n bc1_raw, bc2_raw = _parse_barcode_from_header(line)\n if bc1_raw is None:\n continue\n\n try:\n bc1_list.append(normalize_barcode(bc1_raw))\n if bc2_raw is not None:\n bc2_list.append(normalize_barcode(bc2_raw))\n except ValueError:\n continue # skip reads with invalid barcode characters\n\n reads_found += 1\n\n if not bc1_list:\n if headers_seen > 0:\n raise ValueError(\n f\"FASTQ file has reads but no parseable barcode headers in first \"\n f\"{headers_seen} reads: {fastq_path}\"\n )\n return None, None\n\n def _position_consensus(bases_at_position):\n \"\"\"Return majority base at a position, ignoring N.\n\n Requires strict majority (>50% of non-N bases). Returns N if\n there is no clear winner (e.g., a tie).\n \"\"\"\n non_n = [b for b in bases_at_position if b != 'N']\n if not non_n:\n return 'N'\n counts = Counter(non_n)\n top_base, top_count = counts.most_common(1)[0]\n if top_count * 2 <= len(non_n):\n return 'N' # no strict majority (tie or split)\n return top_base\n\n # Build consensus for bc1\n bc1_len = len(bc1_list[0])\n consensus_bc1 = ''.join(\n _position_consensus([bc[i] for bc in bc1_list if len(bc) > i])\n for i in range(bc1_len)\n )\n\n # Build consensus for bc2 if present\n consensus_bc2 = None\n if bc2_list:\n bc2_len = len(bc2_list[0])\n consensus_bc2 = ''.join(\n _position_consensus([bc[i] for bc in bc2_list if len(bc) > i])\n for i in range(bc2_len)\n )\n\n log.debug(f\"Consensus barcode from {len(bc1_list)} reads: {consensus_bc1}+{consensus_bc2}\")\n return consensus_bc1, consensus_bc2\n\n\ndef splitcode_demux_fastqs(\n fastq_r1,\n fastq_r2,\n samplesheet,\n outdir,\n runinfo=None,\n sequencing_center=None,\n flowcell_id=None,\n run_date=None,\n append_run_id=False,\n max_hamming_dist=1,\n r1_trim_bp_right_of_barcode=None,\n r2_trim_bp_left_of_barcode=None,\n predemux_r1_trim_5prime_num_bp=None,\n predemux_r1_trim_3prime_num_bp=None,\n predemux_r2_trim_5prime_num_bp=None,\n predemux_r2_trim_3prime_num_bp=None,\n threads=None,\n picard_jvm_memory='2g',\n out_meta_by_sample=None,\n out_meta_by_filename=None,\n max_barcode_mismatches=1,\n num_reads_for_barcode=10\n):\n \"\"\"\n Simplified splitcode demultiplexing from paired DRAGEN FASTQ files.\n\n This function performs 3-barcode demultiplexing directly from paired FASTQ files.\n It's designed to run in parallel across multiple FASTQ pairs.\n\n For samples with empty barcode_3 (2-barcode samples), it skips splitcode and\n performs direct FASTQ → BAM conversion.\n\n Picard FastqToSam conversions are parallelized using ProcessPoolExecutor with\n the number of workers controlled by the 'threads' parameter. For optimal\n performance with N samples, use threads=min(N, num_cpus).\n\n Args:\n fastq_r1 (str): Path to R1 FASTQ file\n fastq_r2 (str): Path to R2 FASTQ file\n samplesheet (str): Path to custom 3-barcode samplesheet (TSV format)\n outdir (str): Output directory for BAM files and metrics\n runinfo (str): Path to RunInfo.xml (optional, but recommended for richer BAM metadata\n including RUN_DATE, SEQUENCING_CENTER, and PLATFORM_UNIT)\n sequencing_center (str): Sequencing center name (default: None, uses runinfo.get_machine() if available)\n flowcell_id (str): Override flowcell ID (default: None, extracted from FASTQ filename or RunInfo.xml)\n run_date (str): Override run date in YYYY-MM-DD format (default: None, read from RunInfo.xml)\n append_run_id (bool): If True, output BAM filenames will include flowcell ID and lane\n in the format: {sample}.l{library_id}.{flowcell}.{lane}.bam\n If False (default): {sample}.l{library_id}.bam\n max_hamming_dist (int): Maximum Hamming distance for barcode matching (default: 1)\n r1_trim_bp_right_of_barcode (int): Additional bp to trim from R1 after barcode\n r2_trim_bp_left_of_barcode (int): Additional bp to trim from R2 before barcode\n predemux_r1_trim_5prime_num_bp (int): Trim from R1 5' end before demux\n predemux_r1_trim_3prime_num_bp (int): Trim from R1 3' end before demux\n predemux_r2_trim_5prime_num_bp (int): Trim from R2 5' end before demux\n predemux_r2_trim_3prime_num_bp (int): Trim from R2 3' end before demux\n threads (int): Number of threads for splitcode and parallel Picard conversions\n (default: auto-detect)\n picard_jvm_memory (str): JVM memory allocation per Picard worker (default: '2g')\n out_meta_by_sample (str, optional): Output path for meta_by_sample.json.\n Contains sample metadata keyed by sample name.\n out_meta_by_filename (str, optional): Output path for meta_by_filename.json.\n Contains sample metadata keyed by 'run' field (matches BAM basenames when\n append_run_id=True). This is the critical output for fixing metadata/BAM\n filename mismatches in Terra table insertion.\n max_barcode_mismatches (int): Maximum allowed non-N mismatches per outer barcode\n when matching FASTQ barcodes to samplesheet (default: 1). DRAGEN tolerates\n index mismatches during demux, so FASTQ reads may carry barcodes that differ\n by 1-2 bases from the samplesheet.\n num_reads_for_barcode (int): Number of reads to examine from the FASTQ to form\n a consensus barcode sequence (default: 10). Using multiple reads avoids\n relying on a single read that may have a mismatched index.\n\n Raises:\n FileNotFoundError: If FASTQ or samplesheet files don't exist\n ValueError: If samplesheet format is invalid\n\n Example:\n >>> splitcode_demux_fastqs(\n ... fastq_r1='Pool1_R1.fastq.gz',\n ... fastq_r2='Pool1_R2.fastq.gz',\n ... samplesheet='samples_3bc.tsv',\n ... outdir='demux_out'\n ... )\n\n Outputs:\n - Per-sample unaligned BAMs (zero to many, depending on samplesheet matches)\n - demux_metrics.json: Read counts per sample (or reason for no output)\n - demux_metrics_picard-style.txt: Picard-style metrics\n\n Note:\n - If the input FASTQ is empty or its barcodes don't match the samplesheet,\n zero BAMs are produced but metrics files are still generated to document\n the reason (demux_type field).\n - This simplified function does NOT generate barcodes_common.txt or\n barcodes_outliers.txt. For comprehensive barcode reporting, use\n illumina_demux or splitcode_demux instead.\n \"\"\"\n # Validate inputs\n if not os.path.exists(fastq_r1):\n raise FileNotFoundError(f\"R1 FASTQ not found: {fastq_r1}\")\n if not os.path.exists(fastq_r2):\n raise FileNotFoundError(f\"R2 FASTQ not found: {fastq_r2}\")\n if not os.path.exists(samplesheet):\n raise FileNotFoundError(f\"Samplesheet not found: {samplesheet}\")\n if max_barcode_mismatches < 0:\n raise ValueError(f\"max_barcode_mismatches must be >= 0, got {max_barcode_mismatches}\")\n if num_reads_for_barcode < 1:\n raise ValueError(f\"num_reads_for_barcode must be >= 1, got {num_reads_for_barcode}\")\n\n # Parse RunInfo.xml if provided (unless flowcell_id and run_date both overridden)\n runinfo_obj = None\n flowcell = flowcell_id # Use CLI override if provided\n run_date_val = run_date # Use CLI override if provided\n\n if runinfo or flowcell is None or run_date_val is None or sequencing_center is None:\n if runinfo:\n if not os.path.exists(runinfo):\n raise FileNotFoundError(f\"RunInfo.xml not found: {runinfo}\")\n runinfo_obj = RunInfo(runinfo)\n\n # Only extract from RunInfo if not provided via CLI\n if flowcell is None:\n flowcell = runinfo_obj.get_flowcell()\n if run_date_val is None:\n run_date_val = runinfo_obj.get_rundate_iso()\n\n # Use machine as sequencing_center if not specified\n if sequencing_center is None:\n sequencing_center = runinfo_obj.get_machine()\n log.info(f\"Using sequencing center from RunInfo: {sequencing_center}\")\n\n # Set default threads if not provided\n threads = threads or util_misc.available_cpu_count()\n\n # Create output directory\n os.makedirs(outdir, exist_ok=True)\n\n # Parse FASTQ filename to extract metadata\n fastq_metadata = parse_illumina_fastq_filename(fastq_r1)\n pool_name = fastq_metadata['sample_name']\n lane = fastq_metadata['lane']\n\n log.info(f\"Processing pool: {pool_name}, lane: {lane}\")\n\n # Build run_id for BAM filenames if requested\n if append_run_id:\n if not flowcell:\n raise ValueError(\"append_run_id=True requires flowcell (from RunInfo.xml or --flowcell_id)\")\n run_id_str = f\"{flowcell}.{lane}\"\n else:\n run_id_str = None\n\n # Extract outer barcodes (barcode_1 + barcode_2) from FASTQ headers\n # DRAGEN FASTQs have headers like: @INSTRUMENT:...:BARCODE where BARCODE is \"BC1+BC2\"\n # We read multiple reads and form a consensus to avoid relying on a single read\n # that may have a mismatched index (DRAGEN tolerates index mismatches).\n target_bc1, target_bc2 = consensus_barcode_from_fastq(fastq_r1, num_reads=num_reads_for_barcode)\n\n # Handle empty FASTQ files (e.g., NTC samples with zero reads)\n # Since we can't read barcode from an empty FASTQ, we emit zero BAMs but still\n # generate metrics to document why no output was produced.\n if target_bc1 is None:\n log.warning(f\"FASTQ file contains no reads (or no parseable barcodes): {fastq_r1}\")\n log.info(\"Producing metrics files with zero read counts (no BAM output)\")\n\n # Create output directory if needed\n os.makedirs(outdir, exist_ok=True)\n\n # Generate metrics showing 0 reads\n metrics = {\n 'demux_type': 'empty_input',\n 'samples': {\n pool_name: {\n 'sample_library_id': pool_name,\n 'read_count': 0\n }\n }\n }\n metrics_file = os.path.join(outdir, 'demux_metrics.json')\n with open(metrics_file, 'w') as f:\n json.dump(metrics, f, indent=2)\n\n # Generate Picard-style metrics with 0 reads\n picard_style_metrics_path = os.path.join(outdir, 'demux_metrics_picard-style.txt')\n with open(picard_style_metrics_path, 'w') as f:\n f.write(\"## METRICS CLASS\\tviral-core.splitcode_demux_fastqs.empty\\n\")\n columns = [\n \"BARCODE\", \"BARCODE_WITHOUT_DELIMITER\", \"BARCODE_NAME\", \"LIBRARY_NAME\",\n \"READS\", \"PF_READS\", \"PERFECT_MATCHES\", \"PF_PERFECT_MATCHES\",\n \"ONE_MISMATCH_MATCHES\", \"PF_ONE_MISMATCH_MATCHES\", \"PCT_MATCHES\",\n \"RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_PCT_MATCHES\",\n \"PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_NORMALIZED_MATCHES\",\n \"DEMUX_TYPE\"\n ]\n f.write(\"\\t\".join(columns) + \"\\n\")\n values = [\n \"N/A\", \"N/A\", pool_name, pool_name,\n \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"empty_input\"\n ]\n f.write(\"\\t\".join(values) + \"\\n\")\n\n return\n\n log.info(f\"Consensus outer barcodes from FASTQ ({num_reads_for_barcode} reads): {target_bc1}+{target_bc2}\")\n\n # Load custom 3-barcode samplesheet\n # Note: The samplesheet may contain multiple pools, filter to only this pool's outer barcodes\n samples = SampleSheet(samplesheet, allow_non_unique=True, append_run_id=run_id_str)\n\n # Filter sample_rows to only those matching the outer barcodes from the FASTQ\n # Uses auto-detection for i5 (barcode_2) orientation differences across Illumina platforms\n all_sample_rows = list(samples.get_rows())\n sample_rows, orientation_info = match_barcodes_with_orientation(\n target_bc1, target_bc2, all_sample_rows,\n max_mismatches=max_barcode_mismatches\n )\n\n # Log if i5 orientation auto-detection was used\n if orientation_info.get('barcode_2_revcomp'):\n log.info(f\"Auto-detected i5 reverse complement orientation: \"\n f\"FASTQ barcode_2 {target_bc2} matched samplesheet {orientation_info['matched_bc2']}\")\n\n log.info(f\"Filtered samplesheet to {len(sample_rows)} samples matching outer barcodes\")\n\n # Handle case where no samples matched the barcodes\n # This can happen due to:\n # - Barcodes not in samplesheet (e.g., contaminant reads, barcode hopping)\n # - High N fraction in observed barcodes (low sequencer confidence)\n # - Ambiguous N-wildcard matching (matched multiple distinct barcode pairs)\n # We emit zero BAMs but still generate metrics to document why no output was produced.\n if not sample_rows:\n skipped_reason = orientation_info.get('skipped_reason', 'no_match')\n log.warning(f\"No samples matched barcodes {target_bc1}+{target_bc2} (reason: {skipped_reason})\")\n log.info(\"Producing metrics files with zero read counts (no BAM output)\")\n\n # Create output directory if needed\n os.makedirs(outdir, exist_ok=True)\n\n # Generate metrics showing 0 reads\n metrics = {\n 'demux_type': f'no_barcode_match ({skipped_reason})',\n 'samples': {\n pool_name: {\n 'sample_library_id': pool_name,\n 'read_count': 0\n }\n }\n }\n metrics_file = os.path.join(outdir, 'demux_metrics.json')\n with open(metrics_file, 'w') as f:\n json.dump(metrics, f, indent=2)\n\n # Generate Picard-style metrics with 0 reads\n picard_style_metrics_path = os.path.join(outdir, 'demux_metrics_picard-style.txt')\n with open(picard_style_metrics_path, 'w') as f:\n f.write(f\"## METRICS CLASS\\tviral-core.splitcode_demux_fastqs.no_match\\n\")\n columns = [\n \"BARCODE\", \"BARCODE_WITHOUT_DELIMITER\", \"BARCODE_NAME\", \"LIBRARY_NAME\",\n \"READS\", \"PF_READS\", \"PERFECT_MATCHES\", \"PF_PERFECT_MATCHES\",\n \"ONE_MISMATCH_MATCHES\", \"PF_ONE_MISMATCH_MATCHES\", \"PCT_MATCHES\",\n \"RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_PCT_MATCHES\",\n \"PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_NORMALIZED_MATCHES\",\n \"DEMUX_TYPE\"\n ]\n f.write(\"\\t\".join(columns) + \"\\n\")\n barcode_str = f\"{target_bc1}+{target_bc2}\" if target_bc2 else target_bc1\n values = [\n barcode_str, barcode_str.replace('+', ''), pool_name, pool_name,\n \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", skipped_reason\n ]\n f.write(\"\\t\".join(values) + \"\\n\")\n\n return\n\n # Extract samplesheet-authoritative barcode values for use in metrics and platform_unit.\n # These are the ground truth from the samplesheet, not the FASTQ-observed values\n # which may contain Ns or mismatches.\n auth_bc1 = orientation_info.get('matched_bc1', target_bc1)\n auth_bc2 = orientation_info.get('matched_bc2', target_bc2)\n\n # Now check if the FILTERED samples are 2-barcode or 3-barcode\n has_3bc_samples = any(row.get('barcode_3', '').strip() for row in sample_rows)\n has_2bc_samples = any(not row.get('barcode_3', '').strip() for row in sample_rows)\n\n if has_2bc_samples and not has_3bc_samples:\n # All samples are 2-barcode → skip splitcode, do direct FASTQ→BAM\n log.info(\"2-barcode sample detected - bypassing splitcode, performing direct FASTQ→BAM conversion\")\n\n # Get the sample name and library ID from the 'run' column (includes run_id if append_run_id was set)\n sample_name = sample_rows[0]['sample']\n sample_library_id = sample_rows[0]['run']\n output_bam = os.path.join(outdir, f\"{sample_library_id}.bam\")\n\n # Build platform unit: ..\n # Uses samplesheet-authoritative barcode values (auth_bc1/auth_bc2)\n platform_unit = None\n if flowcell and auth_bc1:\n if auth_bc2:\n barcode_str = f\"{auth_bc1}-{auth_bc2}\"\n else:\n barcode_str = auth_bc1\n platform_unit = f\"{flowcell}.{lane}.{barcode_str}\"\n\n # Use samtools import for multi-threaded FASTQ→BAM conversion\n samtools_tool = samtools.SamtoolsTool()\n samtools_tool.import_fastq(\n fastq_r1,\n fastq_r2,\n output_bam,\n sample_name=sample_name,\n library_name=sample_library_id,\n platform='illumina',\n platform_unit=platform_unit,\n sequencing_center=sequencing_center,\n run_date=run_date_val,\n threads=threads\n )\n\n # Generate metrics with consistent schema (nested samples dict)\n total_reads = samtools_tool.count(output_bam)\n # Divide by 2 because samtools.count() returns total reads (R1+R2),\n # but we want to report read pairs\n read_pairs = total_reads // 2\n\n metrics = {\n 'demux_type': '2-barcode (no splitcode)',\n 'samples': {\n sample_name: {\n 'sample_library_id': sample_library_id,\n 'read_count': read_pairs\n }\n }\n }\n\n metrics_file = os.path.join(outdir, 'demux_metrics.json')\n with open(metrics_file, 'w') as f:\n json.dump(metrics, f, indent=2)\n\n # Generate Picard-style TSV metrics for 2-barcode case\n # Create a simple single-row metrics file\n picard_style_metrics_path = os.path.join(outdir, 'demux_metrics_picard-style.txt')\n try:\n with open(picard_style_metrics_path, 'w') as f:\n # Write Picard-style header\n f.write(\"## METRICS CLASS\\tviral-core.splitcode_demux_fastqs.dragen\\n\")\n\n # Column headers\n columns = [\n \"BARCODE\", \"BARCODE_WITHOUT_DELIMITER\", \"BARCODE_NAME\", \"LIBRARY_NAME\",\n \"READS\", \"PF_READS\", \"PERFECT_MATCHES\", \"PF_PERFECT_MATCHES\",\n \"ONE_MISMATCH_MATCHES\", \"PF_ONE_MISMATCH_MATCHES\", \"PCT_MATCHES\",\n \"RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_PCT_MATCHES\",\n \"PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_NORMALIZED_MATCHES\",\n \"DEMUX_TYPE\"\n ]\n f.write(\"\\t\".join(columns) + \"\\n\")\n\n # Data row - for 2-barcode case, all reads belong to this one sample (100%)\n # Use samplesheet-authoritative barcode values (not FASTQ-observed)\n barcode_str = f\"{auth_bc1}-{auth_bc2}\" if auth_bc2 else auth_bc1\n values = [\n barcode_str, # BARCODE\n barcode_str.replace('-', ''), # BARCODE_WITHOUT_DELIMITER\n sample_name, # BARCODE_NAME\n sample_library_id, # LIBRARY_NAME\n str(read_pairs), # READS\n str(read_pairs), # PF_READS (assume all pass filter)\n str(read_pairs), # PERFECT_MATCHES (assume all reads match perfectly)\n str(read_pairs), # PF_PERFECT_MATCHES\n \"0\", # ONE_MISMATCH_MATCHES (none, since all are perfect)\n \"0\", # PF_ONE_MISMATCH_MATCHES\n \"1.0\", # PCT_MATCHES (100%)\n \"1.0\", # RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT (100%, it's the only one)\n \"1.0\", # PF_PCT_MATCHES (100%)\n \"1.0\", # PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT (100%)\n \"1.0\", # PF_NORMALIZED_MATCHES\n \"dragen\" # DEMUX_TYPE\n ]\n f.write(\"\\t\".join(values) + \"\\n\")\n\n log.info(f\"Generated Picard-style metrics: {picard_style_metrics_path}\")\n\n except Exception as e:\n log.warning(f\"Failed to generate Picard-style metrics for 2-barcode case: {e}\")\n\n # Generate sample metadata JSONs if requested\n # The sample_rows already have 'run' field set from SampleSheet with append_run_id\n # We just need to update the 'lane' field to use actual lane from FASTQ filename\n if out_meta_by_sample or out_meta_by_filename:\n sample_meta = []\n for row in sample_rows:\n meta_row = dict(row) # Copy all samplesheet columns\n meta_row['lane'] = str(lane) # Use actual lane from FASTQ filename (critical fix)\n sample_meta.append(meta_row)\n\n if out_meta_by_sample:\n with open(out_meta_by_sample, 'wt') as outf:\n json.dump(dict((r['sample'], r) for r in sample_meta), outf, indent=2)\n log.info(f\"Generated meta_by_sample.json: {out_meta_by_sample}\")\n\n if out_meta_by_filename:\n with open(out_meta_by_filename, 'wt') as outf:\n json.dump(dict((r['run'], r) for r in sample_meta), outf, indent=2)\n log.info(f\"Generated meta_by_filename.json: {out_meta_by_filename}\")\n\n elif has_3bc_samples:\n # 3-barcode samples → run splitcode demux\n log.info(\"3-barcode samples detected - running splitcode demultiplexing\")\n\n # Check if the FILTERED samples can be collapsed (outer barcodes are collapsible)\n # We need to check only the filtered sample_rows, not the entire samplesheet\n # Create a temporary dataframe from filtered sample_rows to check collapsibility\n sample_rows_df = pd.DataFrame(sample_rows)\n\n # Group by outer barcodes to verify all samples in this pool share the same outer barcodes\n grouping_cols = [\"barcode_1\"]\n if \"barcode_2\" in sample_rows_df.columns:\n grouping_cols.append(\"barcode_2\")\n\n # For 3-barcode demux, all samples must share the same outer barcodes (be collapsible)\n duplicated_mask = sample_rows_df.duplicated(subset=grouping_cols, keep=False)\n if not duplicated_mask.any():\n raise ValueError(\n \"The outer (barcode_1, barcode_2) sequences in the filtered sample rows do not appear to be collapsible. \"\n \"For 3-barcode demux, all samples in a pool must share the same outer barcodes.\"\n )\n\n # Create the inner demux barcode map using SampleSheet method\n # This creates a dataframe with all samples from the samplesheet\n inner_demux_barcode_map_df = samples.inner_demux_mapper()\n\n # Filter the dataframe to only samples matching the outer barcodes from FASTQ header\n # Use orientation-corrected barcodes from match_barcodes_with_orientation (issue #133)\n # AND use N-wildcard matching to handle N bases in observed barcodes\n matched_bc1 = orientation_info.get('matched_bc1', target_bc1)\n matched_bc2 = orientation_info.get('matched_bc2', target_bc2)\n\n # Filter using N-wildcard aware matching (not exact string ==)\n # This handles N bases in the FASTQ barcodes (sequencer no-calls)\n if matched_bc2:\n # Use apply() with barcode_matches_with_n() for N-wildcard matching\n # Note: observed barcode (from FASTQ) may have N, expected (from samplesheet) should not\n filtered_df = inner_demux_barcode_map_df[\n inner_demux_barcode_map_df.apply(\n lambda row: (\n barcode_matches_with_n(matched_bc1, normalize_barcode(row['barcode_1'])) and\n barcode_matches_with_n(matched_bc2, normalize_barcode(row['barcode_2']))\n ),\n axis=1\n )\n ]\n else:\n filtered_df = inner_demux_barcode_map_df[\n inner_demux_barcode_map_df.apply(\n lambda row: barcode_matches_with_n(matched_bc1, normalize_barcode(row['barcode_1'])),\n axis=1\n )\n ]\n\n # Verify we have 3-barcode samples after filtering\n samples_with_bc3 = filtered_df[\n (filtered_df['barcode_3'].notna()) &\n (filtered_df['barcode_3'].str.strip() != '')\n ]\n\n if len(samples_with_bc3) == 0:\n # Get the matched barcodes for logging (with RC correction if applicable)\n matched_bc1 = orientation_info.get('matched_bc1', target_bc1)\n matched_bc2 = orientation_info.get('matched_bc2', target_bc2)\n log.warning(f\"No 3-barcode samples found matching outer barcodes {matched_bc1}+{matched_bc2}\")\n log.info(\"Producing metrics files with zero read counts (no BAM output)\")\n\n # Generate metrics showing 0 reads\n metrics = {\n 'demux_type': 'no_3bc_match',\n 'samples': {\n pool_name: {\n 'sample_library_id': pool_name,\n 'read_count': 0\n }\n }\n }\n metrics_file = os.path.join(outdir, 'demux_metrics.json')\n with open(metrics_file, 'w') as f:\n json.dump(metrics, f, indent=2)\n\n # Generate Picard-style metrics with 0 reads\n picard_style_metrics_path = os.path.join(outdir, 'demux_metrics_picard-style.txt')\n with open(picard_style_metrics_path, 'w') as f:\n f.write(\"## METRICS CLASS\\tviral-core.splitcode_demux_fastqs.no_3bc_match\\n\")\n columns = [\n \"BARCODE\", \"BARCODE_WITHOUT_DELIMITER\", \"BARCODE_NAME\", \"LIBRARY_NAME\",\n \"READS\", \"PF_READS\", \"PERFECT_MATCHES\", \"PF_PERFECT_MATCHES\",\n \"ONE_MISMATCH_MATCHES\", \"PF_ONE_MISMATCH_MATCHES\", \"PCT_MATCHES\",\n \"RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_PCT_MATCHES\",\n \"PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\", \"PF_NORMALIZED_MATCHES\",\n \"DEMUX_TYPE\"\n ]\n f.write(\"\\t\".join(columns) + \"\\n\")\n barcode_str = f\"{auth_bc1}+{auth_bc2}\" if auth_bc2 else auth_bc1\n values = [\n barcode_str, barcode_str.replace('+', ''), pool_name, pool_name,\n \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"0\", \"no_3bc_match\"\n ]\n f.write(\"\\t\".join(values) + \"\\n\")\n\n return\n\n log.info(f\"Filtered to {len(samples_with_bc3)} samples with 3-barcode scheme\")\n\n # Use the filtered dataframe\n inner_demux_barcode_map_df = filtered_df\n\n # The pool_id is the unique muxed_run for this outer barcode pair\n pool_id = filtered_df['muxed_run'].iloc[0]\n\n # Generate splitcode config and keep files using existing helper function\n splitcode_config, splitcode_keep_file, sample_library_ids = splitcode.generate_splitcode_config_and_keep_files(\n inner_demux_barcode_map_df,\n pool_id,\n outdir,\n max_hamming_dist=max_hamming_dist,\n r1_trim_bp_right_of_barcode=r1_trim_bp_right_of_barcode,\n r2_trim_bp_left_of_barcode=r2_trim_bp_left_of_barcode\n )\n\n log.info(f\"Generated splitcode config: {splitcode_config}\")\n log.info(f\"Generated splitcode keep file: {splitcode_keep_file}\")\n log.info(f\"Will demux {len(sample_library_ids)} samples\")\n\n # Run splitcode\n splitcode_tool = splitcode.SplitCodeTool()\n\n # Prepare splitcode output paths\n unassigned_r1 = os.path.join(outdir, 'unassigned_R1.fastq.gz')\n unassigned_r2 = os.path.join(outdir, 'unassigned_R2.fastq.gz')\n # Name the summary file with pool_id to match create_splitcode_lookup_table() expectations\n summary_stats = os.path.join(outdir, f'{pool_id}_summary.json')\n\n # Dummy output files required for --keep to work (splitcode quirk)\n dummy_output_r1 = os.path.join(outdir, 'dummy_R1.fastq.gz')\n dummy_output_r2 = os.path.join(outdir, 'dummy_R2.fastq.gz')\n\n # Run splitcode with the generated config\n splitcode_tool.execute(\n n_fastqs=2,\n threads=threads,\n config_file=splitcode_config,\n keep_file=splitcode_keep_file,\n unassigned_r1=unassigned_r1,\n unassigned_r2=unassigned_r2,\n summary_stats=summary_stats,\n r1=fastq_r1,\n r2=fastq_r2,\n predemux_r1_trim_5prime_num_bp=predemux_r1_trim_5prime_num_bp,\n predemux_r1_trim_3prime_num_bp=predemux_r1_trim_3prime_num_bp,\n predemux_r2_trim_5prime_num_bp=predemux_r2_trim_5prime_num_bp,\n predemux_r2_trim_3prime_num_bp=predemux_r2_trim_3prime_num_bp,\n keep_r1_r2_suffixes=True,\n splitcode_opts=[f\"--output={dummy_output_r1},{dummy_output_r2}\"]\n )\n\n # Convert splitcode FASTQs to BAMs in parallel\n # Build mapping from sample_library_id to sample name\n # Note: inner_demux_barcode_map_df is already filtered to this pool, so no need to check pool_id\n sample_library_to_sample = {}\n for sample_name, row in inner_demux_barcode_map_df.iterrows():\n sample_library_to_sample[row['run']] = sample_name\n\n # Build list of conversion jobs with all metadata\n conversion_jobs = []\n for sample_library_id in sample_library_ids:\n sample_name = sample_library_to_sample.get(sample_library_id)\n if not sample_name:\n log.warning(f\"No sample name found for library ID: {sample_library_id}\")\n continue\n\n # Find splitcode output FASTQs for this sample\n # With keep_r1_r2_suffixes=True, splitcode outputs: {outdir}/{sample_library_id}_R1.fastq.gz and _R2.fastq.gz\n bc_r1 = os.path.join(outdir, f\"{sample_library_id}_R1.fastq.gz\")\n bc_r2 = os.path.join(outdir, f\"{sample_library_id}_R2.fastq.gz\")\n\n # Only queue jobs for samples that have FASTQ outputs\n if not (os.path.exists(bc_r1) and os.path.exists(bc_r2)):\n log.warning(f\"Splitcode output FASTQs not found for {sample_library_id}: {bc_r1}, {bc_r2}\")\n continue\n\n # Get inline barcode for this sample from the dataframe\n sample_row = inner_demux_barcode_map_df.loc[sample_name]\n inline_barcode = sample_row.get('barcode_3', '')\n\n # Build Picard options dict with richer metadata\n picard_opts = {\n 'PLATFORM': 'illumina',\n 'LIBRARY_NAME': sample_library_id,\n 'VERBOSITY': 'WARNING',\n 'QUIET': 'TRUE',\n 'COMPRESSION_LEVEL': '1' # Faster BAM writes\n }\n\n # Add run date from RunInfo or CLI override\n if run_date_val:\n picard_opts['RUN_DATE'] = run_date_val\n\n # Add sequencing center\n if sequencing_center:\n picard_opts['SEQUENCING_CENTER'] = sequencing_center\n\n # Add platform unit: ..\n # For 3-barcode samples, include all three barcodes\n # Use samplesheet-authoritative barcode values (not FASTQ-observed)\n if flowcell and auth_bc1:\n if auth_bc2:\n barcode_str = f\"{auth_bc1}-{auth_bc2}-{inline_barcode}\"\n else:\n barcode_str = f\"{auth_bc1}-{inline_barcode}\"\n picard_opts['PLATFORM_UNIT'] = f\"{flowcell}.{lane}.{barcode_str}\"\n\n conversion_jobs.append({\n 'sample_library_id': sample_library_id,\n 'sample_name': sample_name,\n 'bc_r1': bc_r1,\n 'bc_r2': bc_r2,\n 'picard_opts': picard_opts\n })\n\n # Execute Picard conversions in parallel\n workers = max(threads, 1)\n log.info(f\"Converting {len(conversion_jobs)} splitcode outputs to BAM using \"\n f\"{workers} parallel worker{'s' if workers != 1 else ''}\")\n\n sample_metrics = {}\n\n with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:\n futures = []\n\n # Submit all conversion jobs\n for idx, job in enumerate(conversion_jobs):\n string_to_log = (f\"Processing sample {idx+1}/{len(conversion_jobs)}: \"\n f\"{job['sample_name']} (library: {job['sample_library_id']})\")\n\n future = executor.submit(\n run_picard_fastq_to_sam_for_splitcode_demux,\n job['sample_library_id'],\n job['sample_name'],\n job['bc_r1'],\n job['bc_r2'],\n outdir,\n job['picard_opts'],\n jvm_memory=picard_jvm_memory,\n string_to_log=string_to_log\n )\n futures.append(future)\n\n # Collect results as they complete\n for future in concurrent.futures.as_completed(futures):\n try:\n sample_name, output_bam, read_pairs, sample_library_id = future.result()\n\n log.info(f\"Conversion complete: {sample_name} -> {output_bam} \"\n f\"({read_pairs} read pairs)\")\n\n # Store metrics\n sample_metrics[sample_name] = {\n 'sample_library_id': sample_library_id,\n 'read_count': read_pairs\n }\n\n except subprocess.CalledProcessError as e:\n log.error(f\"Picard FastqToSam failed: {e}\")\n raise\n except Exception as e:\n log.error(f\"Unexpected error during FASTQ to BAM conversion: {e}\")\n raise\n\n # Write JSON metrics (backward compatibility)\n metrics_file = os.path.join(outdir, 'demux_metrics.json')\n with open(metrics_file, 'w') as f:\n json.dump({\n 'demux_type': '3-barcode (splitcode)',\n 'samples': sample_metrics\n }, f, indent=2)\n\n # Generate Picard-style TSV metrics using existing helper functions\n # Use splitcode.create_splitcode_lookup_table() to parse splitcode JSON summary and create CSV\n splitcode_csv_path = os.path.join(outdir, 'splitcode_metrics.csv')\n try:\n splitcode.create_splitcode_lookup_table(\n sample_sheet_or_dataframe=inner_demux_barcode_map_df,\n csv_out=splitcode_csv_path,\n unmatched_name='unmatched',\n pool_ids=[pool_id], # Only process this single pool\n check_sample_sheet_consistency=False\n )\n\n # Convert CSV to Picard-style TSV\n picard_style_metrics_path = os.path.join(outdir, 'demux_metrics_picard-style.txt')\n splitcode.convert_splitcode_demux_metrics_to_picard_style(\n splitcode_csv_path,\n picard_style_metrics_path,\n demux_function=\"viral-core.splitcode_demux_fastqs\",\n report_within_pools=False # Global stats since we're processing one pool\n )\n log.info(f\"Generated Picard-style metrics: {picard_style_metrics_path}\")\n\n except Exception as e:\n log.warning(f\"Failed to generate Picard-style metrics from splitcode summary: {e}\")\n log.warning(\"Continuing with JSON metrics only\")\n\n # Note: We don't generate barcodes_common.txt or barcodes_outliers.txt here.\n # Those files require full barcode analysis which is handled by illumina_demux\n # or splitcode_demux workflows. The simplified splitcode_demux_fastqs is designed\n # for quick per-FASTQ-pair demux without comprehensive barcode reporting.\n\n # Generate sample metadata JSONs if requested\n # The sample_rows already have 'run' field set from SampleSheet with append_run_id\n # We just need to update the 'lane' field to use actual lane from FASTQ filename\n if out_meta_by_sample or out_meta_by_filename:\n sample_meta = []\n for row in sample_rows:\n meta_row = dict(row) # Copy all samplesheet columns\n meta_row['lane'] = str(lane) # Use actual lane from FASTQ filename (critical fix)\n sample_meta.append(meta_row)\n\n if out_meta_by_sample:\n with open(out_meta_by_sample, 'wt') as outf:\n json.dump(dict((r['sample'], r) for r in sample_meta), outf, indent=2)\n log.info(f\"Generated meta_by_sample.json: {out_meta_by_sample}\")\n\n if out_meta_by_filename:\n with open(out_meta_by_filename, 'wt') as outf:\n json.dump(dict((r['run'], r) for r in sample_meta), outf, indent=2)\n log.info(f\"Generated meta_by_filename.json: {out_meta_by_filename}\")\n\n else:\n raise ValueError(\"Samplesheet contains no valid samples (all barcode_3 values are empty)\")\n\n\ndef parser_splitcode_demux_fastqs(parser=argparse.ArgumentParser()):\n \"\"\"\n Argument parser for splitcode_demux_fastqs entry point.\n \"\"\"\n parser.add_argument(\n '--fastq_r1',\n required=True,\n help='Path to R1 FASTQ file'\n )\n parser.add_argument(\n '--fastq_r2',\n required=True,\n help='Path to R2 FASTQ file'\n )\n parser.add_argument(\n '--samplesheet',\n required=True,\n help='Path to custom 3-barcode samplesheet (TSV format)'\n )\n parser.add_argument(\n '--outdir',\n required=True,\n help='Output directory for BAM files and metrics'\n )\n parser.add_argument(\n '--runinfo',\n default=None,\n help='Path to RunInfo.xml (optional, for richer BAM metadata)'\n )\n parser.add_argument(\n '--sequencing_center',\n default=None,\n help='Sequencing center name (default: None, uses runinfo.get_machine() if RunInfo.xml provided)'\n )\n parser.add_argument(\n '--flowcell_id',\n default=None,\n help='Override flowcell ID (default: extracted from FASTQ filename or RunInfo.xml)'\n )\n parser.add_argument(\n '--run_date',\n default=None,\n help='Override run date in YYYY-MM-DD format (default: read from RunInfo.xml)'\n )\n parser.add_argument(\n '--append_run_id',\n action='store_true',\n help='Append flowcell ID and lane to output BAM filenames for SRA compatibility'\n )\n parser.add_argument(\n '--picard_jvm_memory',\n default='2g',\n help='JVM memory allocation per Picard FastqToSam worker (default: %(default)s)'\n )\n parser.add_argument(\n '--out_meta_by_sample',\n default=None,\n help='Output path for meta_by_sample.json (sample metadata indexed by sample name)'\n )\n parser.add_argument(\n '--out_meta_by_filename',\n default=None,\n help='Output path for meta_by_filename.json (sample metadata indexed by run/library ID, matches BAM basenames)'\n )\n parser.add_argument(\n '--max_barcode_mismatches',\n type=int,\n default=1,\n help='Maximum allowed non-N mismatches per outer barcode when matching FASTQ barcodes '\n 'to samplesheet. DRAGEN tolerates index mismatches, so FASTQ reads may carry '\n 'barcodes that differ from the samplesheet. (default: %(default)s)'\n )\n parser.add_argument(\n '--num_reads_for_barcode',\n type=int,\n default=10,\n help='Number of reads to examine from the FASTQ to form a consensus barcode sequence. '\n 'Using multiple reads avoids relying on a single read that may have a mismatched '\n 'index. (default: %(default)s)'\n )\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, splitcode_demux_fastqs, split_args=True)\n return parser\n\n\n__commands__.append(('splitcode_demux_fastqs', parser_splitcode_demux_fastqs))\n\n\n# =========================\n# *** illumina_demux ***\n# =========================\n\n\ndef parser_illumina_demux(parser=argparse.ArgumentParser()):\n parser.add_argument(\n \"inDir\",\n help=\"Illumina BCL directory (or tar.gz of BCL directory). This is the top-level run directory.\",\n )\n parser.add_argument(\"lane\", help=\"Lane number.\", type=int)\n parser.add_argument(\"outDir\", help=\"Output directory for BAM files.\")\n\n parser.add_argument(\n \"--outMetrics\",\n help=\"Output ExtractIlluminaBarcodes metrics file. Default is to dump to a temp file.\",\n default=None,\n )\n parser.add_argument(\n \"--commonBarcodes\",\n help='''Write a TSV report of all barcode counts, in descending order. \n Only applicable for read structures containing \"B\"''',\n default=None,\n )\n parser.add_argument(\n \"--max_barcodes\",\n help=\"\"\"Cap the commonBarcodes report length to this size (default: %(default)s)\"\"\",\n default=10000,\n type=int,\n )\n parser.add_argument(\n \"--sampleSheet\",\n default=None,\n help=\"\"\"Override SampleSheet. Input TSV or CSV file w/header and four named columns:\n barcode_name, library_name, barcode_sequence_1, barcode_sequence_2.\n Default is to look for a SampleSheet.csv in the inDir.\"\"\",\n )\n parser.add_argument(\n \"--runInfo\",\n default=None,\n dest=\"runinfo\",\n help=\"\"\"Override RunInfo. Input xml file.\n Default is to look for a RunInfo.xml file in the inDir.\"\"\",\n )\n parser.add_argument(\n \"--flowcell\",\n help=\"Override flowcell ID (default: read from RunInfo.xml).\",\n default=None,\n )\n parser.add_argument(\n \"--read_structure\",\n help=\"Override read structure (default: read from RunInfo.xml).\",\n default=None,\n )\n parser.add_argument(\n \"--append_run_id\",\n help=\"If specified, output filenames will include the flowcell ID and lane number.\",\n action=\"store_true\",\n )\n parser.add_argument(\n \"--collapse_duplicated_barcodes\",\n help=\"\"\"If specified, reads from samples with duplicated barcodes or barcode pairs \n will be collapsed into a single output for each distinct barcode (or distinct barcode pair). \n Intended for protocols allowing additional demultiplexing downstream by other means \n (ex. breaking out samples based on a third, inner barcode, added via swift-seq). \n If not specified, an error will be raised if duplicated barcodes (or barcode pairs) \n are present in the sample sheet. If a value is specified, it will be used as \n the path to store output sample sheet with barcodes collapsed\"\"\",\n default=False,\n const=None,\n nargs='?',\n #action=\"store_true\"\n )\n parser.add_argument(\n \"--rev_comp_barcodes_before_demux\",\n help=\"\"\"Reverse complement barcodes before demultiplexing.\n If specified without setting a value, \n the \"barcode_2\" column will be reverse-complemented.\n If one or more values are specified, \n the columns with those names will be reverse-complemented.\n (and if not specified, barcodes will not be reverse-complemented)\"\"\",\n nargs='*',\n action=util_cmd.storeMultiArgsOrFallBackToConst,\n type=str,\n const=[\"barcode_2\"],\n )\n parser.add_argument(\n \"--out_meta_by_sample\", help=\"Output json metadata by sample\", default=None\n )\n parser.add_argument(\n \"--out_meta_by_filename\",\n help=\"Output json metadata by bam file basename\",\n default=None,\n )\n parser.add_argument(\n \"--out_runinfo\", help=\"Output json metadata about the run\", default=None\n )\n\n for opt in picard.ExtractIlluminaBarcodesTool.option_list:\n if opt not in (\"read_structure\", \"num_processors\"):\n parser.add_argument(\n \"--\" + opt,\n help=\"Picard ExtractIlluminaBarcodes \"\n + opt.upper()\n + \" (default: %(default)s)\",\n default=picard.ExtractIlluminaBarcodesTool.defaults.get(opt),\n )\n for opt in picard.IlluminaBasecallsToSamTool.option_list:\n if opt == \"adapters_to_check\":\n parser.add_argument(\n \"--\" + opt,\n nargs=\"*\",\n help=\"Picard IlluminaBasecallsToSam \"\n + opt.upper()\n + \" (default: %(default)s)\",\n default=picard.IlluminaBasecallsToSamTool.defaults.get(opt),\n )\n elif opt in (\"read_structure\", \"num_processors\"):\n pass\n else:\n parser.add_argument(\n \"--\" + opt,\n help=\"Picard IlluminaBasecallsToSam \"\n + opt.upper()\n + \" (default: %(default)s)\",\n default=picard.IlluminaBasecallsToSamTool.defaults.get(opt),\n )\n\n parser.add_argument(\n \"--JVMmemory\",\n help=\"JVM virtual memory size (default: %(default)s)\",\n default=picard.IlluminaBasecallsToSamTool.jvmMemDefault,\n )\n util_cmd.common_args(\n parser,\n (\n (\n \"threads\",\n picard.IlluminaBasecallsToSamTool.defaults[\"num_processors\"],\n ),\n (\"loglevel\", None),\n (\"version\", None),\n (\"tmp_dir\", None),\n ),\n )\n util_cmd.attach_main(parser, main_illumina_demux)\n return parser\n\n\ndef main_illumina_demux(args):\n \"\"\"Read Illumina runs & produce BAM files, demultiplexing to one bam per sample, or\n for simplex runs, a single bam will be produced bearing the flowcell ID.\n Wraps together Picard's ExtractBarcodes (for multiplexed samples) and IlluminaBasecallsToSam\n while handling the various required input formats. Also can\n read Illumina BCL directories, tar.gz BCL directories.\n \"\"\"\n\n # prepare\n illumina = IlluminaDirectory(args.inDir)\n illumina.load()\n\n if args.runinfo:\n runinfo = RunInfo(args.runinfo)\n else:\n runinfo = illumina.get_RunInfo()\n if args.flowcell:\n flowcell = args.flowcell\n else:\n flowcell = runinfo.get_flowcell()\n if args.run_start_date:\n run_date = args.run_start_date\n else:\n run_date = runinfo.get_rundate_american()\n if args.read_structure:\n read_structure = args.read_structure\n else:\n read_structure = runinfo.get_read_structure()\n if args.append_run_id:\n run_id = \"{}.{}\".format(flowcell, args.lane)\n else:\n run_id = None\n if args.sampleSheet:\n samples = SampleSheet(\n args.sampleSheet,\n only_lane = args.lane,\n append_run_id = run_id,\n allow_non_unique = True if args.collapse_duplicated_barcodes != False else False,\n # barcode_columns_to_revcomp:\n # For --rev_comp_barcodes_before_demux: \n # 1) None if not passed\n # 2) 'barcode_2' if passed without value\n # 3) barcodes specified if values passed with --rev_comp_barcodes_before_demux\n barcode_columns_to_revcomp = args.rev_comp_barcodes_before_demux \n )\n else:\n samples = illumina.get_SampleSheet(\n only_lane = args.lane,\n append_run_id = run_id,\n allow_non_unique = True if args.collapse_duplicated_barcodes != False else False,\n # barcode_columns_to_revcomp:\n # For --rev_comp_barcodes_before_demux: \n # 1) None if not passed\n # 2) 'barcode_2' if passed without value\n # 3) barcodes specified if values passed with --rev_comp_barcodes_before_demux\n barcode_columns_to_revcomp = args.rev_comp_barcodes_before_demux\n )\n\n collapse_requested = (args.collapse_duplicated_barcodes is not False)\n if not samples.can_be_collapsed:\n if collapse_requested:\n log.warning(\n \"'--collapse_duplicated_barcodes' specified, but no duplicated barcodes \"\n \"(or barcode pairs) were found in the sample sheet.\"\n )\n else:\n log.warning(\"Duplicated barcodes (or barcode pairs) found in the sample sheet.\")\n if collapse_requested:\n log.info(\n \"'--collapse_duplicated_barcodes' specified; collapsing each duplicated barcode into \"\n \"a distinct barcode (or barcode pair)...\"\n )\n samples.collapse_sample_index_duplicates(output_tsv=args.collapse_duplicated_barcodes)\n\n link_locs = False\n # For HiSeq-4000/X runs, If Picard's CheckIlluminaDirectory is\n # called with LINK_LOCS=true, symlinks with absolute paths\n # may be created, pointing from tile-specific *.locs to the\n # single s.locs file in the Intensities directory.\n # These links may break if the run directory is moved.\n # We should begin by removing broken links, if present,\n # and call CheckIlluminaDirectory ourselves if a 's.locs'\n # file is present, but only if the directory check fails\n # since link_locs=true tries to create symlinks even if they\n # (or the files) already exist\n try:\n picard.CheckIlluminaDirectoryTool().execute(\n illumina.get_BCLdir(), args.lane, read_structure, link_locs=link_locs\n )\n except subprocess.CalledProcessError as e:\n log.warning(\"CheckIlluminaDirectory failed for %s\", illumina.get_BCLdir())\n if os.path.exists(os.path.join(illumina.get_intensities_dir(), \"s.locs\")):\n # recurse to remove broken links in directory\n log.info(\n \"This run has an 's.locs' file; checking for and removing broken per-tile symlinks...\"\n )\n broken_links = util_file.find_broken_symlinks(\n illumina.get_intensities_dir()\n )\n if len(broken_links):\n for lpath in broken_links:\n log.info(\"Removing broken symlink: %s\", lpath)\n os.unlink(lpath)\n\n # call CheckIlluminaDirectory with LINK_LOCS=true\n link_locs = True\n\n log.info(\"Checking run directory with Picard...\")\n picard.CheckIlluminaDirectoryTool().execute(\n illumina.get_BCLdir(), args.lane, read_structure, link_locs=link_locs\n )\n else:\n log.error(\"CheckIlluminaDirectory failed for %s\", illumina.get_BCLdir())\n\n multiplexed_samples = True if \"B\" in read_structure else False\n\n if multiplexed_samples:\n assert (\n samples is not None\n ), \"This looks like a multiplexed run since 'B' is in the read_structure: a SampleSheet must be given.\"\n else:\n assert (\n samples == None\n ), \"A SampleSheet may not be provided unless 'B' is present in the read_structure\"\n if args.commonBarcodes:\n log.warning(\n \"--commonBarcodes was set but 'B' is not present in the read_structure; emitting an empty file.\"\n )\n util_file.touch(args.commonBarcodes)\n\n executor = concurrent.futures.ProcessPoolExecutor()\n async_execution_futures = []\n\n # B in read structure indicates barcoded multiplexed samples\n if multiplexed_samples:\n # Picard ExtractIlluminaBarcodes\n extract_input = util_file.mkstempfname(\n \".txt\", prefix=\".\".join([\"barcodeData\", flowcell, str(args.lane)])\n )\n barcodes_tmpdir = tempfile.mkdtemp(prefix=\"extracted_barcodes-\")\n samples.make_barcodes_file(extract_input)\n out_metrics = (\n (args.outMetrics is None)\n and util_file.mkstempfname(\".metrics.txt\")\n or args.outMetrics\n )\n picardOpts = dict(\n (opt, getattr(args, opt))\n for opt in picard.ExtractIlluminaBarcodesTool.option_list\n if hasattr(args, opt) and getattr(args, opt) != None\n )\n picardOpts[\"read_structure\"] = read_structure\n picard.ExtractIlluminaBarcodesTool().execute(\n illumina.get_BCLdir(),\n args.lane,\n extract_input,\n barcodes_tmpdir,\n out_metrics,\n picardOptions=picardOpts,\n JVMmemory=args.JVMmemory,\n )\n\n # Add DEMUX_TYPE column to Picard metrics file\n add_constant_column_to_metrics(out_metrics, 'DEMUX_TYPE', 'picard')\n\n if args.commonBarcodes:\n barcode_lengths = re.findall(r\"(\\d+)B\", read_structure)\n try:\n barcode1_len = int(barcode_lengths[0])\n except IndexError:\n barcode1_len = 0\n try:\n barcode2_len = int(barcode_lengths[1])\n except IndexError:\n barcode2_len = 0\n\n # this step can take > 2 hours on a large high-output flowcell\n # so kick it to the background while we demux\n # count_and_sort_barcodes(barcodes_tmpdir, args.commonBarcodes)\n async_execution_futures.append(\n executor.submit(\n count_and_sort_barcodes,\n barcodes_tmpdir,\n args.commonBarcodes,\n barcode1_len,\n barcode2_len,\n truncateToLength=args.max_barcodes,\n threads=util_misc.sanitize_thread_count(args.threads),\n )\n )\n\n # Picard IlluminaBasecallsToSam\n basecalls_input = util_file.mkstempfname(\n \".txt\", prefix=\".\".join([\"library_params\", flowcell, str(args.lane)])\n )\n samples.make_params_file(args.outDir, basecalls_input)\n\n picardOpts = dict(\n (opt, getattr(args, opt))\n for opt in picard.IlluminaBasecallsToSamTool.option_list\n if hasattr(args, opt) and getattr(args, opt) != None\n )\n picardOpts[\"run_start_date\"] = run_date\n picardOpts[\"read_structure\"] = read_structure\n if args.threads:\n picardOpts[\"num_processors\"] = args.threads\n if not picardOpts.get(\"sequencing_center\") and runinfo:\n picardOpts[\"sequencing_center\"] = runinfo.get_machine()\n\n if picardOpts.get(\"sequencing_center\"):\n picardOpts[\"sequencing_center\"] = util_file.string_to_file_name(\n picardOpts[\"sequencing_center\"]\n )\n\n if args.out_runinfo:\n # Use build_run_info_json() utility function (eliminates code duplication)\n run_info_dict = build_run_info_json(\n sequencing_center=picardOpts[\"sequencing_center\"],\n run_start_date=runinfo.get_rundate_iso(),\n read_structure=picardOpts[\"read_structure\"],\n indexes=str(samples.indexes),\n run_id=runinfo.get_run_id(),\n lane=str(args.lane),\n flowcell=str(runinfo.get_flowcell()),\n lane_count=runinfo.get_lane_count(),\n surface_count=runinfo.get_surface_count(),\n swath_count=runinfo.get_swath_count(),\n tile_count=runinfo.get_tile_count(),\n total_tile_count=runinfo.tile_count(),\n sequencer_model=runinfo.get_machine_model()\n )\n with open(args.out_runinfo, \"wt\") as outf:\n json.dump(run_info_dict, outf, indent=2)\n\n # manually garbage collect to make sure we have as much RAM free as possible\n gc.collect()\n if multiplexed_samples:\n picard.IlluminaBasecallsToSamTool().execute(\n illumina.get_BCLdir(),\n barcodes_tmpdir,\n flowcell,\n args.lane,\n basecalls_input,\n picardOptions=picardOpts,\n JVMmemory=args.JVMmemory,\n )\n\n # organize samplesheet metadata as json\n sample_meta = list(samples.get_rows())\n for row in sample_meta:\n row[\"lane\"] = str(args.lane)\n if args.out_meta_by_sample:\n with open(args.out_meta_by_sample, \"wt\") as outf:\n json.dump(dict((r[\"sample\"], r) for r in sample_meta), outf, indent=2)\n if args.out_meta_by_filename:\n with open(args.out_meta_by_filename, \"wt\") as outf:\n json.dump(dict((r[\"run\"], r) for r in sample_meta), outf, indent=2)\n\n else:\n picard.IlluminaBasecallsToSamTool().execute_single_sample(\n illumina.get_BCLdir(),\n os.path.join(args.outDir, flowcell + \".bam\"),\n flowcell,\n args.lane,\n flowcell,\n picardOptions=picardOpts,\n JVMmemory=args.JVMmemory,\n )\n\n async_execution_results = []\n\n for future in concurrent.futures.as_completed(async_execution_results):\n try:\n result = future.result()\n async_execution_results.append(result)\n except Exception as e:\n log.error(f\"Exception in future: {e}\")\n async_execution_results.append({\"success\": False, \"error\": str(e)})\n log.debug(f\"async_execution_results: {async_execution_results}\")\n\n log.info(\"waiting for backgrounded async operations to finish...\")\n executor.shutdown(wait=True)\n log.info(\"backgrounded async operations finished\")\n\n # clean up\n if multiplexed_samples:\n #if args.commonBarcodes:\n # log.info(\"waiting for commonBarcodes output to finish...\")\n # executor.shutdown(wait=True)\n os.unlink(extract_input)\n os.unlink(basecalls_input)\n shutil.rmtree(barcodes_tmpdir)\n illumina.close()\n log.info(\"illumina_demux complete\")\n return 0\n\n\n__commands__.append((\"illumina_demux\", parser_illumina_demux))\n\n# ==========================\n# *** flowcell_metadata ***\n# ==========================\n\n\ndef parser_flowcell_metadata(parser=argparse.ArgumentParser()):\n parser.add_argument(\n \"outMetadataFile\", help=\"path of file to which metadata will be written.\"\n )\n group = parser.add_mutually_exclusive_group(required=True)\n group.add_argument(\n \"--inDir\",\n dest=\"in_dir\",\n help=\"Illumina BCL directory (or tar.gz of BCL directory). This is the top-level run directory.\",\n default=None,\n )\n group.add_argument(\n \"--runInfo\", default=None, dest=\"run_info\", help=\"\"\"RunInfo.xml file.\"\"\"\n )\n group.add_argument(\n \"--flowcellID\",\n dest=\"flowcell_id\",\n help=\"flowcell ID (default: read from RunInfo.xml).\",\n default=None,\n )\n util_cmd.common_args(\n parser,\n (\n (\n \"threads\",\n picard.IlluminaBasecallsToSamTool.defaults[\"num_processors\"],\n ),\n (\"loglevel\", None),\n (\"version\", None),\n (\"tmp_dir\", None),\n ),\n )\n util_cmd.attach_main(parser, main_flowcell_metadata)\n return parser\n\n\ndef main_flowcell_metadata(args):\n \"\"\"Writes run metadata to a file\"\"\"\n\n if args.flowcell_id:\n machine_matches = RunInfo.get_machines_for_flowcell_id(args.flowcell_id)\n machine_match = None\n if len(machine_matches) > 1:\n raise LookupError(\n \"Multiple sequencers found for flowcell ID: %s\"\n % \" \".join([m[\"machine\"] for m in machine_matches])\n )\n if len(machine_matches) == 0:\n raise LookupError(\n \"No sequencers found for flowcell ID '%s' \" % args.flowcell_id\n )\n machine_match = machine_matches[0]\n if args.run_info:\n runinfo = RunInfo(args.run_info)\n machine_match = runinfo.infer_sequencer_model()\n if args.in_dir:\n illumina = IlluminaDirectory(args.in_dir)\n illumina.load()\n runinfo = illumina.get_RunInfo()\n machine_match = runinfo.infer_sequencer_model()\n\n with open(args.outMetadataFile, \"w\") as outf:\n for k, v in machine_match.items():\n if type(v) == str and len(v) > 0 or type(v) != str:\n outline = \"{k}\\t{v}\\n\".format(k=k, v=v)\n print(outline, end=\"\")\n outf.writelines([outline])\n\n\n__commands__.append((\"flowcell_metadata\", parser_flowcell_metadata))\n\n# ==========================\n# *** lane_metrics ***\n# ==========================\n\n\ndef parser_lane_metrics(parser=argparse.ArgumentParser()):\n parser.add_argument(\n \"inDir\",\n help=\"Illumina BCL directory (or tar.gz of BCL directory). This is the top-level run directory.\",\n )\n parser.add_argument(\n \"outPrefix\",\n help=\"\"\"Prefix path to the *.illumina_lane_metrics and *.illumina_phasing_metrics files.\"\"\",\n )\n parser.add_argument(\n \"--read_structure\",\n help=\"Override read structure (default: read from RunInfo.xml).\",\n default=None,\n )\n parser.add_argument(\n \"--JVMmemory\",\n help=\"JVM virtual memory size (default: %(default)s)\",\n default=picard.ExtractIlluminaBarcodesTool.jvmMemDefault,\n )\n util_cmd.common_args(\n parser, ((\"loglevel\", None), (\"version\", None), (\"tmp_dir\", None))\n )\n util_cmd.attach_main(parser, main_lane_metrics)\n return parser\n\n\ndef main_lane_metrics(args):\n \"\"\"\n Write out lane metrics to a tsv file.\n \"\"\"\n # prepare\n illumina = IlluminaDirectory(args.inDir)\n illumina.load()\n if args.read_structure:\n read_structure = args.read_structure\n else:\n read_structure = illumina.get_RunInfo().get_read_structure()\n\n # Picard CollectIlluminaLaneMetrics\n output_dir = os.path.dirname(os.path.realpath(args.outPrefix))\n output_prefix = os.path.basename(os.path.realpath(args.outPrefix))\n\n picardOpts = dict(\n (opt, getattr(args, opt))\n for opt in picard.CollectIlluminaLaneMetricsTool.option_list\n if hasattr(args, opt) and getattr(args, opt) != None\n )\n picardOpts[\"read_structure\"] = read_structure\n picard.CollectIlluminaLaneMetricsTool().execute(\n illumina.path,\n output_dir,\n output_prefix,\n picardOptions=picardOpts,\n JVMmemory=args.JVMmemory,\n )\n\n illumina.close()\n return 0\n\n\n__commands__.append((\"lane_metrics\", parser_lane_metrics))\n\n\n# ==========================\n# *** common_barcodes ***\n# ==========================\n\n\ndef parser_common_barcodes(parser=argparse.ArgumentParser()):\n parser.add_argument(\n \"inDir\",\n help=\"Illumina BCL directory (or tar.gz of BCL directory). This is the top-level run directory.\",\n )\n parser.add_argument(\"lane\", help=\"Lane number.\", type=int)\n parser.add_argument(\n \"outSummary\",\n help=\"\"\"Path to the summary file (.tsv format). It includes several columns: \n (barcode1, likely_index_name1, barcode2, likely_index_name2, count), \n where likely index names are either the exact match index name for the barcode \n sequence, or those Hamming distance of 1 away.\"\"\",\n )\n\n parser.add_argument(\n \"--truncateToLength\",\n help=\"If specified, only this number of barcodes will be returned. Useful if you only want the top N barcodes.\",\n type=int,\n default=None,\n )\n parser.add_argument(\n \"--omitHeader\",\n help=\"If specified, a header will not be added to the outSummary tsv file.\",\n action=\"store_true\",\n )\n parser.add_argument(\n \"--includeNoise\",\n help='If specified, barcodes with periods (\".\") will be included.',\n action=\"store_true\",\n )\n parser.add_argument(\n \"--outMetrics\",\n help=\"Output ExtractIlluminaBarcodes metrics file. Default is to dump to a temp file.\",\n default=None,\n )\n parser.add_argument(\n \"--sampleSheet\",\n default=None,\n help=\"\"\"Override SampleSheet. Input tab or CSV file w/header and four named columns:\n barcode_name, library_name, barcode_sequence_1, barcode_sequence_2.\n Default is to look for a SampleSheet.csv in the inDir.\"\"\",\n )\n parser.add_argument(\n \"--flowcell\",\n help=\"Override flowcell ID (default: read from RunInfo.xml).\",\n default=None,\n )\n parser.add_argument(\n \"--read_structure\",\n help=\"Override read structure (default: read from RunInfo.xml).\",\n default=None,\n )\n\n for opt in picard.ExtractIlluminaBarcodesTool.option_list:\n if opt not in (\"read_structure\", \"num_processors\"):\n parser.add_argument(\n \"--\" + opt,\n help=\"Picard ExtractIlluminaBarcodes \"\n + opt.upper()\n + \" (default: %(default)s)\",\n default=picard.ExtractIlluminaBarcodesTool.defaults.get(opt),\n )\n\n parser.add_argument(\n \"--JVMmemory\",\n help=\"JVM virtual memory size (default: %(default)s)\",\n default=picard.ExtractIlluminaBarcodesTool.jvmMemDefault,\n )\n util_cmd.common_args(\n parser,\n ((\"threads\", None), (\"loglevel\", None), (\"version\", None), (\"tmp_dir\", None)),\n )\n util_cmd.attach_main(parser, main_common_barcodes)\n return parser\n\n\ndef main_common_barcodes(args):\n \"\"\"\n Extract Illumina barcodes for a run and write a TSV report\n of the barcode counts in descending order\n \"\"\"\n\n # prepare\n illumina = IlluminaDirectory(args.inDir)\n illumina.load()\n if args.flowcell:\n flowcell = args.flowcell\n else:\n flowcell = illumina.get_RunInfo().get_flowcell()\n if args.read_structure:\n read_structure = args.read_structure\n else:\n read_structure = illumina.get_RunInfo().get_read_structure()\n if args.sampleSheet:\n samples = SampleSheet(args.sampleSheet, only_lane=args.lane)\n else:\n samples = illumina.get_SampleSheet(only_lane=args.lane)\n\n # Picard ExtractIlluminaBarcodes\n barcode_file = util_file.mkstempfname(\n \".txt\", prefix=\".\".join([\"barcodeData\", flowcell, str(args.lane)])\n )\n barcodes_tmpdir = tempfile.mkdtemp(prefix=\"extracted_barcodes-\")\n samples.make_barcodes_file(barcode_file)\n out_metrics = (\n (args.outMetrics is None)\n and util_file.mkstempfname(\".metrics.txt\")\n or args.outMetrics\n )\n picardOpts = dict(\n (opt, getattr(args, opt))\n for opt in picard.ExtractIlluminaBarcodesTool.option_list\n if hasattr(args, opt) and getattr(args, opt) != None\n )\n picardOpts[\"read_structure\"] = read_structure\n picard.ExtractIlluminaBarcodesTool().execute(\n illumina.get_BCLdir(),\n args.lane,\n barcode_file,\n barcodes_tmpdir,\n out_metrics,\n picardOptions=picardOpts,\n JVMmemory=args.JVMmemory,\n )\n\n barcode_lengths = re.findall(r\"(\\d+)B\", read_structure)\n try:\n barcode1_len = int(barcode_lengths[0])\n except IndexError:\n barcode1_len = 0\n try:\n barcode2_len = int(barcode_lengths[1])\n except IndexError:\n barcode2_len = 0\n\n count_and_sort_barcodes(\n barcodes_tmpdir,\n args.outSummary,\n barcode1_len,\n barcode2_len,\n args.truncateToLength,\n args.includeNoise,\n args.omitHeader,\n args.threads,\n )\n\n # clean up\n os.unlink(barcode_file)\n shutil.rmtree(barcodes_tmpdir)\n illumina.close()\n return 0\n\n\n__commands__.append((\"common_barcodes\", parser_common_barcodes))\n\n\ndef count_and_sort_barcodes(\n barcodes_dir,\n outSummary,\n barcode1_len = 8,\n barcode2_len = 8,\n truncateToLength = None,\n includeNoise = False,\n omitHeader = False,\n threads = None,\n):\n # collect the barcode file paths for all tiles\n tile_barcode_files = [\n os.path.join(barcodes_dir, filename) for filename in os.listdir(barcodes_dir)\n ]\n\n # count all of the barcodes present in the tile files\n log.info(\"counting barcode occurrences in files containing all barcodes extracted from tiles present (%s tiles)\", len(tile_barcode_files))\n\n with util_file.CountDB() as reduce_db:\n barcodefile_tempfile_tuples = [\n (tile_barcode_file, util_file.mkstempfname(\"sqlite_.db\"))\n for tile_barcode_file in tile_barcode_files\n ]\n\n # scatter tile-specific barcode files among workers to store barcode counts in SQLite\n workers = util_misc.sanitize_thread_count(threads)\n with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:\n\n log.info(\"using %s workers to read barcodes from tile files\", workers)\n\n futures = []\n for bf, tf in barcodefile_tempfile_tuples:\n log.debug(\"creating separate process to read barcodes from %s and store the count of each distinct barcode in %s\", tf, bf)\n futures.append(\n executor.submit(\n util_file.count_occurrences_in_tsv_sqlite_backed,\n tf,\n bf,\n include_noise=includeNoise,\n )\n )\n\n # futures = [\n # executor.submit(\n # util_file.count_occurrences_in_tsv_sqlite_backed,\n # tf,\n # bf,\n # include_noise=includeNoise,\n # )\n # for bf, tf in barcodefile_tempfile_tuples\n # ]\n for future in concurrent.futures.as_completed(futures):\n try:\n tmp_db, barcode_file = future.result()\n log.debug(\n \"done reading barcodes from %s; adding to total...\", barcode_file\n )\n # gather and reduce counts from separate SQLite databases into one\n reduce_db.add_counts_from_other_db(tmp_db)\n os.unlink(tmp_db)\n except Exception as e:\n log.error(\n \"Error reading barcodes from tile file %s: %s\", barcode_file, e\n )\n raise\n\n illumina_reference = IlluminaIndexReference()\n\n log.info(\"Number of barcodes seen %s\", reduce_db.get_num_IDS())\n\n # write the barcodes and their corresponding counts\n with open(outSummary, \"w\") as tsvfile:\n log.info(\"sorting counts...\")\n log.info(\"writing output...\")\n writer = csv.writer(tsvfile, delimiter=\"\\t\")\n # write the header unless the user has specified not to do so\n if not omitHeader:\n writer.writerow(\n (\n \"Barcode1\",\n \"Likely_Index_Names1\",\n \"Barcode2\",\n \"Likely_Index_Names2\",\n \"Count\",\n )\n )\n\n for num_processed, row in enumerate(reduce_db.get_counts_descending()):\n\n if truncateToLength and num_processed > truncateToLength:\n break\n\n barcode, count = row\n\n writer.writerow(\n (\n barcode[:barcode1_len],\n \",\".join(\n [\n x\n for x in illumina_reference.guess_index(\n barcode[:barcode1_len], distance=1\n )\n ]\n or [\"Unknown\"]\n ),\n barcode[barcode1_len : len(barcode)],\n \",\".join(\n [\n x\n for x in illumina_reference.guess_index(\n barcode[barcode1_len : len(barcode)], distance=1\n )\n ]\n or [\"Unknown\"]\n ),\n count,\n )\n )\n\n if num_processed % 50000 == 0:\n log.debug(\n \"written %s barcode summaries to output file\", num_processed\n )\n\n log.info(\"done\")\n\n\n# ======================================\n# *** guess_low-abundance_barcodes ***\n# ======================================\n\n\ndef parser_guess_barcodes(parser=argparse.ArgumentParser()):\n parser.add_argument(\n \"in_barcodes\", help=\"The barcode counts file produced by common_barcodes.\"\n )\n parser.add_argument(\n \"in_picard_metrics\", help=\"The demultiplexing read metrics produced by Picard.\"\n )\n parser.add_argument(\n \"out_summary_tsv\",\n help=\"\"\"Path to the summary file (.tsv format). It includes several columns: \n (sample_name, expected_barcode_1, expected_barcode_2, \n expected_barcode_1_name, expected_barcode_2_name, \n expected_barcodes_read_count, guessed_barcode_1, \n guessed_barcode_2, guessed_barcode_1_name, \n guessed_barcode_2_name, guessed_barcodes_read_count, \n match_type), \n where the expected values are those used by Picard during demultiplexing\n and the guessed values are based on the barcodes seen among the data.\"\"\",\n )\n\n group = parser.add_mutually_exclusive_group()\n group.add_argument(\n \"--readcount_threshold\",\n default=None,\n type=int,\n help=\"\"\"If specified, guess barcodes for samples with fewer than this many reads.\"\"\",\n )\n group.add_argument(\n \"--sample_names\",\n nargs=\"*\",\n help=\"If specified, only guess barcodes for these sample names.\",\n type=str,\n default=None,\n )\n parser.add_argument(\n \"--outlier_threshold\",\n help=\"threshold of how far from unbalanced a sample must be to be considered an outlier.\",\n type=float,\n default=0.775,\n )\n parser.add_argument(\n \"--expected_assigned_fraction\",\n help=\"The fraction of reads expected to be assigned. An exception is raised if fewer than this fraction are assigned.\",\n type=float,\n default=0.7,\n )\n group2 = parser.add_mutually_exclusive_group()\n group2.add_argument(\n \"--number_of_negative_controls\",\n help=\"If specified, the number of negative controls in the pool, for calculating expected number of reads in the rest of the pool.\",\n type=int,\n )\n group2.add_argument(\n \"--neg_control_prefixes\",\n nargs=\"+\",\n help=\"If specified, the sample name prefixes assumed for counting negative controls. Case-insensitive.\",\n type=str,\n default=[\"neg\", \"water\", \"NTC\", \"H2O\"],\n )\n parser.add_argument(\n \"--rows_limit\",\n default=1000,\n type=int,\n help=\"\"\"The number of rows to use from the in_barcodes.\"\"\",\n )\n\n util_cmd.common_args(\n parser, ((\"loglevel\", None), (\"version\", None), (\"tmp_dir\", None))\n )\n util_cmd.attach_main(parser, main_guess_barcodes, split_args=True)\n return parser\n\n\ndef main_guess_barcodes(\n in_barcodes,\n in_picard_metrics,\n out_summary_tsv,\n sample_names,\n outlier_threshold,\n expected_assigned_fraction,\n number_of_negative_controls,\n readcount_threshold,\n rows_limit,\n neg_control_prefixes,\n):\n \"\"\"\n Guess the barcode value for a sample name,\n based on the following:\n - a list is made of novel barcode pairs seen in the data, but not in the picard metrics\n - for the sample in question, get the most abundant novel barcode pair where one of the\n barcodes seen in the data matches one of the barcodes in the picard metrics (partial match)\n - if there are no partial matches, get the most abundant novel barcode pair\n\n Limitations:\n - If multiple samples share a barcode with multiple novel barcodes, disentangling them\n is difficult or impossible\n\n The names of samples to guess are selected:\n - explicitly by name, passed via argument, OR\n - explicitly by read count threshold, OR\n - automatically (if names or count threshold are omitted)\n based on basic outlier detection of deviation from an assumed-balanced pool with\n some number of negative controls\n \"\"\"\n\n bh = IlluminaBarcodeHelper(\n in_barcodes, in_picard_metrics, rows_limit\n )\n guessed_barcodes = bh.find_uncertain_barcodes(\n sample_names = sample_names,\n outlier_threshold = outlier_threshold,\n expected_assigned_fraction = expected_assigned_fraction,\n number_of_negative_controls = number_of_negative_controls,\n readcount_threshold = readcount_threshold,\n neg_control_prefixes = neg_control_prefixes,\n )\n bh.write_guessed_barcodes(out_summary_tsv, guessed_barcodes)\n\n\n__commands__.append((\"guess_barcodes\", parser_guess_barcodes))\n\n\n# NOTE: IlluminaDirectory, RunInfo, SampleSheet, SampleSheetError classes\n# have been moved to core.illumina_utils\n\n\n# =============================\n# *** miseq_fastq_to_bam ***\n# =============================\n\n\ndef miseq_fastq_to_bam(\n outBam,\n sampleSheet,\n inFastq1,\n inFastq2=None,\n runInfo=None,\n sequencing_center=None,\n JVMmemory=picard.FastqToSamTool.jvmMemDefault,\n):\n \"\"\"Convert fastq read files to a single bam file. Fastq file names must conform\n to patterns emitted by Miseq machines. Sample metadata must be provided\n in a SampleSheet.csv that corresponds to the fastq filename. Specifically,\n the _S##_ index in the fastq file name will be used to find the corresponding\n row in the SampleSheet\n \"\"\"\n\n # match miseq based on fastq filenames\n mo = re.match(r\"^\\S+_S(\\d+)_L001_R(\\d)_001.fastq(?:.gz|)$\", inFastq1)\n assert mo, (\n \"fastq filename %s does not match the patterns used by an Illumina Miseq machine\"\n % inFastq1\n )\n assert (\n mo.group(2) == \"1\"\n ), \"fastq1 must correspond to read 1, not read %s\" % mo.group(2)\n sample_num = mo.group(1)\n if inFastq2:\n mo = re.match(r\"^\\S+_S(\\d+)_L001_R(\\d)_001.fastq(?:.gz|)$\", inFastq2)\n assert mo, (\n \"fastq filename %s does not match the patterns used by an Illumina Miseq machine\"\n % inFastq2\n )\n assert (\n mo.group(2) == \"2\"\n ), \"fastq2 must correspond to read 2, not read %s\" % mo.group(2)\n assert (\n mo.group(1) == sample_num\n ), \"fastq1 (%s) and fastq2 (%s) must have the same sample number\" % (\n sample_num,\n mo.group(1),\n )\n\n # load metadata\n samples = SampleSheet(sampleSheet, allow_non_unique=True)\n sample_info = samples.fetch_by_index(sample_num)\n assert sample_info, \"sample %s not found in %s\" % (sample_num, sampleSheet)\n sampleName = sample_info[\"sample\"]\n log.info(\"Using sample name: %s\", sampleName)\n if sample_info.get(\"barcode_2\"):\n barcode = \"-\".join((sample_info[\"barcode_1\"], sample_info[\"barcode_2\"]))\n else:\n barcode = sample_info[\"barcode_1\"]\n picardOpts = {\n \"LIBRARY_NAME\": sample_info[\"library\"],\n \"PLATFORM\": \"illumina\",\n \"VERBOSITY\": \"WARNING\",\n \"QUIET\": \"TRUE\",\n }\n if runInfo:\n runInfo = RunInfo(runInfo)\n flowcell = runInfo.get_flowcell()\n picardOpts[\"RUN_DATE\"] = runInfo.get_rundate_iso()\n if inFastq2:\n assert (\n runInfo.num_reads() == 2\n ), \"paired fastqs given for a single-end RunInfo.xml\"\n else:\n assert (\n runInfo.num_reads() == 1\n ), \"second fastq missing for a paired-end RunInfo.xml\"\n else:\n flowcell = \"A\"\n if sequencing_center is None and runInfo:\n sequencing_center = runInfo.get_machine()\n if sequencing_center:\n picardOpts[\"SEQUENCING_CENTER\"] = util_file.string_to_file_name(\n sequencing_center\n )\n picardOpts[\"PLATFORM_UNIT\"] = \".\".join((flowcell, \"1\", barcode))\n if len(flowcell) > 5:\n flowcell = flowcell[:5]\n picardOpts[\"READ_GROUP_NAME\"] = flowcell\n\n # run Picard\n picard_tool = picard.FastqToSamTool()\n picard_tool.execute(\n inFastq1,\n inFastq2,\n sampleName,\n outBam,\n picardOptions=picard_tool.dict_to_picard_opts(picardOpts),\n JVMmemory=JVMmemory,\n )\n return 0\n\n\ndef parser_miseq_fastq_to_bam(parser=argparse.ArgumentParser()):\n parser.add_argument(\"outBam\", help=\"Output BAM file.\")\n parser.add_argument(\"sampleSheet\", help=\"Input SampleSheet.csv file.\")\n parser.add_argument(\n \"inFastq1\", help=\"Input fastq file; 1st end of paired-end reads if paired.\"\n )\n parser.add_argument(\n \"--inFastq2\",\n help=\"Input fastq file; 2nd end of paired-end reads.\",\n default=None,\n )\n parser.add_argument(\"--runInfo\", help=\"Input RunInfo.xml file.\", default=None)\n parser.add_argument(\n \"--sequencing_center\",\n default=None,\n help=\"Name of your sequencing center (default is the sequencing machine ID from the RunInfo.xml)\",\n )\n parser.add_argument(\n \"--JVMmemory\",\n default=picard.FastqToSamTool.jvmMemDefault,\n help=\"JVM virtual memory size (default: %(default)s)\",\n )\n util_cmd.common_args(\n parser, ((\"loglevel\", None), (\"version\", None), (\"tmp_dir\", None))\n )\n util_cmd.attach_main(parser, miseq_fastq_to_bam, split_args=True)\n return parser\n\n\n__commands__.append((\"miseq_fastq_to_bam\", parser_miseq_fastq_to_bam))\n\n\n# ==============================\n# *** extract_fc_metadata ***\n# ==============================\ndef extract_fc_metadata(flowcell, outRunInfo, outSampleSheet):\n \"\"\"Extract RunInfo.xml and SampleSheet.csv from the provided Illumina directory\"\"\"\n illumina = IlluminaDirectory(flowcell)\n illumina.load()\n shutil.copy(illumina.get_RunInfo().get_fname(), outRunInfo)\n shutil.copy(illumina.get_SampleSheet().get_fname(), outSampleSheet)\n return 0\n\n\ndef parser_extract_fc_metadata(parser=argparse.ArgumentParser()):\n parser.add_argument(\"flowcell\", help=\"Illumina directory (possibly tarball)\")\n parser.add_argument(\"outRunInfo\", help=\"Output RunInfo.xml file.\")\n parser.add_argument(\"outSampleSheet\", help=\"Output SampleSheet.csv file.\")\n util_cmd.common_args(\n parser, ((\"loglevel\", None), (\"version\", None), (\"tmp_dir\", None))\n )\n util_cmd.attach_main(parser, extract_fc_metadata, split_args=True)\n return parser\n\n\n__commands__.append((\"extract_fc_metadata\", parser_extract_fc_metadata))\n\n\n# ==================\n# *** Swiftseq/cDNAtag-Seq demux ***\n# ==================\n\n\ndef write_barcode_metrics_for_pools(input_csv_path, \n out_dir, \n out_basename=None, \n out_format=None):\n \"\"\"\n Process sequencing data to calculate read metrics for each inline barcode across library pools\n and write results to a file.\n \n For each (library_id, inline_barcode) pair, calculates:\n - {library_id}_reads: Total reads for the pair\n - {library_id}_reads_pool_pct: Reads as fraction of total reads in that library\n - {library_id}_reads_all_pct: Reads as fraction of total reads across all libraries\n - {library_id}_barcode_reads_vs_all_reads_for_barcode_pct: Reads as fraction of total reads for that barcode across all libraries\n \n Parameters:\n -----------\n input_csv_path : str\n Path to the input CSV file\n out_dir : str\n Output directory for the results file\n out_basename : str, optional\n Base name for the output file (default: \"reads_per_bc\")\n out_format : str, optional\n Output file format (default: \"csv\")\n \n Returns:\n --------\n pd.DataFrame\n Processed dataframe with metrics for each inline barcode\n \"\"\"\n \n out_basename = out_basename or \"reads_per_bc\"\n out_format = out_format or \"csv\"\n output_csv_path = f\"{out_dir}/{out_basename}.{out_format}\"\n\n # Read the CSV file\n df = pd.read_csv(input_csv_path, dtype=str)\n # Convert numeric columns explicitly\n numeric_cols = ['num_reads_total', 'num_reads_hdistance0', 'num_reads_hdistance1']\n for col in numeric_cols:\n if col in df.columns:\n df[col] = pd.to_numeric(df[col], errors='coerce').fillna(0)\n\n # Filter out unmatched entries (those with inline_barcode containing only N characters)\n # This handles variable numbers of N's (e.g., \"N\", \"NN\", \"NNNNNNNNN\", etc.)\n df_filtered = df[~df['inline_barcode'].str.match(r'^N+$', na=False)].copy()\n\n # Get unique inline barcodes and library IDs\n unique_barcodes = df_filtered['inline_barcode'].unique()\n unique_libraries = df_filtered['library_id'].unique()\n\n # Calculate total reads across all libraries for percentage calculations\n total_reads_all = df_filtered['num_reads_total'].sum()\n \n # Calculate total reads per library for pool percentage calculations\n library_totals = df_filtered.groupby('library_id')['num_reads_total'].sum()\n \n # Calculate total reads per barcode across all libraries for barcode-specific percentages\n barcode_totals = df_filtered.groupby('inline_barcode')['num_reads_total'].sum()\n \n # Initialize result dataframe with inline_barcode as index\n result_df = pd.DataFrame(index=unique_barcodes, dtype=str)\n result_df.index.name = 'inline_barcode'\n \n # For each library, calculate metrics\n for library_id in unique_libraries:\n library_data = df_filtered[df_filtered['library_id'] == library_id]\n \n # Group by inline_barcode and sum reads for this library\n barcode_reads = library_data.groupby('inline_barcode')['num_reads_total'].sum()\n \n # Add columns for this library\n reads_col = f\"{library_id}_reads\"\n pool_pct_col = f\"{library_id}_reads_pool_pct\"\n all_pct_col = f\"{library_id}_reads_all_pct\"\n barcode_pct_col = f\"{library_id}_barcode_reads_vs_all_reads_for_barcode_pct\"\n \n # Initialize columns with 0\n result_df[reads_col] = 0\n result_df[pool_pct_col] = 0.0\n result_df[all_pct_col] = 0.0\n result_df[barcode_pct_col] = 0.0\n \n # Fill in values for barcodes that exist in this library\n for barcode in barcode_reads.index:\n reads = barcode_reads[barcode]\n result_df.loc[barcode, reads_col] = reads\n result_df.loc[barcode, pool_pct_col] = reads / library_totals[library_id] if library_totals[library_id] > 0 else 0.0\n result_df.loc[barcode, all_pct_col] = reads / total_reads_all if total_reads_all > 0 else 0.0\n result_df.loc[barcode, barcode_pct_col] = reads / barcode_totals[barcode] if barcode_totals[barcode] > 0 else 0.0\n \n # Sort by inline_barcode for consistent output\n result_df = result_df.sort_index()\n \n # Save to CSV\n result_df.to_csv(output_csv_path)\n \n return result_df\n\n# this function is called in new processes\n# and must remain at the top level (global scope) of this file\n# to be picklable and thus compatible\n# with concurrent.futures.ProcessPoolExecutor()\n# see: https://docs.python.org/3/library/concurrent.futures.html#processpoolexecutor\n# https://stackoverflow.com/a/72776044\ndef run_picard_fastq_to_ubam(fq1,\n fq2,\n library_name,\n sample_name,\n out_demux_dir_path,\n picardOptions,\n jvm_memory,\n string_to_log=None):\n # out_bam = f\"{out_demux_dir_path}/{sample}.l{library_name}.{flowcell}.{lane}.bam\"\n # sample in this case is the library ID, so the\n # output bam file named in the form: .l...bam\n out_bam = f\"{out_demux_dir_path}/{library_name}.bam\"\n\n if string_to_log:\n log.info(string_to_log)\n picard.FastqToSamTool().execute( fq1,\n fq2,\n sample_name,\n out_bam,\n picardOptions = picardOptions,\n JVMmemory = jvm_memory)\n return (sample_name, out_bam)\n\ndef splitcode_demux(\n inDir,\n lane,\n outDir,\n\n max_hamming_dist = 1,\n unmatched_name = None,\n\n illumina_run_directory = None,\n sampleSheet = None,\n runinfo = None,\n \n read_structure = None,\n platform_name = None,\n flowcell = None,\n run_id = None,\n run_date = None,\n #readgroup_name = None,\n sequencing_center = None,\n sequencer_model = None,\n\n rev_comp_barcodes_before_demux = None,\n out_runinfo = None,\n out_meta_by_filename = None,\n out_meta_by_sample = None,\n\n predemux_r1_trim_5prime_num_bp = None,\n predemux_r1_trim_3prime_num_bp = None,\n predemux_r2_trim_5prime_num_bp = None,\n predemux_r2_trim_3prime_num_bp = None,\n\n r1_trim_bp_right_of_barcode = None,\n r2_trim_bp_left_of_barcode = None,\n\n threads = None,\n jvm_memory = None\n):\n \"\"\"\n Args:\n inDir (str) File path to folder containing gzipped bam or fastq files from demux using outer barcodes\n outDir (str) Output directory for BAM files and other output files\n sampleSheet (str) Overwrite file path to csv samplesheet. Input tab or CSV file with columns:\n sample, library_id_per_sample, I7_Index_ID, barcode_1, I5_Index_ID, barcode_2, Inline_Index_ID, barcode_3.\n Default is to look for a SampleSheet.csv in the inDir.\n unmatched_name (str) ID for reads that don't match an inline barcode. Default: \"unmatched\"\n max_hamming_dist (int) Max allowed Hamming distance for inline barcode matching. Default: 1\n threads (int) Threads used by splitcode demultiplexing. Default: 32\n runinfo (str) Override RunInfo. Input xml file. Default: Look for a RunInfo.xml file in the inDir\n read_structure (str) Read structure. Default: read from RunInfo.xml\n platform_name (str) Platform name (used to populate BAM header). Default: read from RunInfo.xml\n flowcell (str) Flowcell ID (used to populate BAM header). Default: read from RunInfo.xml\n lane (str) Lane number (used to populate BAM header). Default: read from RunInfo.xml\n run_date (str) Run date (used to populate BAM header). Default: read from RunInfo.xml\n readgroup_name (str) Readgroup name (used to populate BAM header). Default: read from RunInfo.xml\n sequencing_center (str) Sequencing center (used to populate BAM header). Default: read from RunInfo.xml\n sequencer_model (str) Sequencer model (used to populate BAM header). Default: inferred from RunInfo.xml\n \n predemux_r1_trim_5prime_num_bp (int) number of bases to trim from the 5' end of read 1 (before demux)\n predemux_r1_trim_3prime_num_bp (int) number of bases to trim from the 3' end of read 1 (before demux)\n predemux_r2_trim_5prime_num_bp (int) number of bases to trim from the 5' end of read 2 (before demux)\n predemux_r2_trim_3prime_num_bp (int) number of bases to trim from the 3' end of read 2 (before demux)\n\n rev_comp_barcodes_before_demux (list(str)) List of barcode columns to reverse complement before demux.\n \"\"\"\n # Create temp directory for splitcode FASTQs inside outDir to prevent cleanup issues\n splitcode_out_tmp_dir = os.path.join(outDir, \".splitcode_tmp\")\n os.makedirs(splitcode_out_tmp_dir, exist_ok=True)\n\n threads = threads or util_misc.available_cpu_count()\n unmatched_name = unmatched_name or \"Unmatched\"\n\n illumina_dir=None\n if illumina_run_directory:\n illumina_dir = IlluminaDirectory(illumina_run_directory)\n illumina_dir.load()\n\n # ToDo: if illumina_run_directory is not provided, but we lack provided runinfo, \n # inspect the inDir to see if it looks like an illumina run directory\n # and try to load it as such (then interpreting Analysis/, fastq/ and other sub-dirs)\n # as potential locations for the fastq files (maybe recursively find them)\n\n if runinfo:\n log.info(f\"Loading RunInfo from supplied file {runinfo}\")\n runinfo = RunInfo(runinfo)\n else:\n assert illumina_dir, \"No Illumina Run Directory provided, and runinfo not provided.\"\n log.info(f\"Loading RunInfo from Illumina Run Directory: {illumina_dir.path}\")\n runinfo = illumina_dir.get_RunInfo()\n # data from RunInfo.xml is used in the absense of user input\n # so assert that we have runinfo available\n \n # if RunInfo.xml is needed to obtain any values not provided, \n # so unless all values are provided, assert that runinfo is available\n if not all([flowcell, run_date, read_structure, run_id, sequencing_center]):\n assert runinfo, \"No RunInfo.xml provided, nor found in a specified Illumina Run Directory.\"\n\n flowcell = flowcell or runinfo.get_flowcell()\n run_date = run_date or runinfo.get_rundate_iso()\n read_structure = read_structure or runinfo.get_read_structure()\n run_id = run_id or f\"{runinfo.get_flowcell()}.{lane}\" # runinfo.get_run_id()\n sequencing_center = sequencing_center or runinfo.get_machine() #f\"{runinfo.get_machine_model()}.{runinfo.get_machine()}\"\n platform_model = sequencer_model or runinfo.get_machine_model()\n sequencing_center = util_file.string_to_file_name(sequencing_center)\n platform_model = util_file.string_to_file_name(platform_model)\n\n log.info(f\"{'flowcell:':<19}{flowcell:<20}\")\n log.info(f\"{'run_date:':<19}{run_date:<20}\")\n log.info(f\"{'read_structure:':<19}{read_structure:<20}\")\n log.info(f\"{'run_id:':<19}{run_id:<20}\")\n log.info(f\"{'sequencing_center:':<19}{sequencing_center:<20}\")\n log.info(f\"{'platform_model:':<19}{platform_model:<20}\")\n\n if not platform_name:\n log.warning(\"No platform name provided. Defaulting to 'ILLUMINA'\")\n platform_name = \"ILLUMINA\"\n\n if sampleSheet:\n log.info(f\"Loading SampleSheet from supplied file {sampleSheet}\")\n samples = SampleSheet(\n sampleSheet,\n only_lane = lane,\n append_run_id = run_id,\n allow_non_unique = True,\n # barcode_columns_to_revcomp:\n # For --rev_comp_barcodes_before_demux: \n # 1) None if not passed\n # 2) 'barcode_2' if passed without value\n # 3) barcodes specified if values passed with --rev_comp_barcodes_before_demux\n barcode_columns_to_revcomp = rev_comp_barcodes_before_demux\n )\n else:\n log.info(f\"Loading SampleSheet from Illumina Run Directory: {illumina_dir.path}\")\n samples = illumina_dir.get_SampleSheet(\n only_lane = lane,\n append_run_id = run_id,\n allow_non_unique = True,\n # barcode_columns_to_revcomp:\n # For --rev_comp_barcodes_before_demux: \n # 1) None if not passed\n # 2) 'barcode_2' if passed without value\n # 3) barcodes specified if values passed with --rev_comp_barcodes_before_demux\n barcode_columns_to_revcomp = rev_comp_barcodes_before_demux\n )\n\n # debugging / perhaps useful later\n lane_count = runinfo.get_lane_count()\n\n # Create outDir\n os.makedirs(outDir, exist_ok=True)\n out_demux_dir_path = f\"{outDir}\"\n os.makedirs(out_demux_dir_path, exist_ok=True)\n\n if out_runinfo:\n # Use build_run_info_json() utility function (eliminates code duplication)\n run_info_dict = build_run_info_json(\n sequencing_center=sequencing_center,\n run_start_date=runinfo.get_rundate_iso(),\n read_structure=read_structure,\n indexes=str(samples.indexes),\n run_id=runinfo.get_run_id(),\n lane=str(lane),\n flowcell=str(runinfo.get_flowcell()),\n lane_count=runinfo.get_lane_count(),\n surface_count=runinfo.get_surface_count(),\n swath_count=runinfo.get_swath_count(),\n tile_count=runinfo.get_tile_count(),\n total_tile_count=runinfo.tile_count(),\n sequencer_model=runinfo.get_machine_model()\n )\n with open(out_runinfo, \"wt\") as outf:\n json.dump(run_info_dict, outf, indent=2)\n\n # Load samplesheet into dataframe\n barcodes_df = pd.json_normalize(samples.get_rows()).astype(str).fillna(\"\")\n\n inner_demux_barcode_map_df = None\n if samples.can_be_collapsed:\n #samples.collapse_sample_index_duplicates()\n #collapsed_barcodes_df = pd.json_normalize(samples.get_rows()).fillna(\"\")\n inner_demux_barcode_map_df = samples.inner_demux_mapper()\n else:\n log.error(\"The outer (barcode_1,barcode_2) sequences in the sample sheet do not appear to be collapsible.\")\n\n # TODO: guardrails around missing barcode_3 values or a mixture of rows with it present/absent\n\n # Load inline barcodes and inline barcode indices\n inline_barcodes = sorted(list(set(barcodes_df[\"barcode_3\"].values)))\n\n # Instantiate the splitcode and samtools tools\n samtools_tool = samtools.SamtoolsTool()\n\n demux_bams_to_sample_library_id_map = defaultdict(list)\n pool_id_to_sample_library_id_map = defaultdict(list)\n sample_to_demux_bam_map = {}\n pool_id_to_splitcode_keepfile = {}\n pool_id_to_splitcode_configfile = {}\n pool_id_to_pool_bam = {}\n sample_library_id_to_fastqs = {}\n pool_ids_successfully_demuxed_via_splitcode = []\n\n # Iterate over rows\n for sample_name, sample_row in inner_demux_barcode_map_df.iterrows():\n log.debug(f\"Looking for input pool bam files for '{sample_name}'\")\n #b1 = sample_row[\"barcode_1\"]\n #b3 = sample_row[\"barcode_3\"]\n #inline_index_id = sample_row[\"Inline_Index_ID\"]\n #run_str = sample_row[\"run\"]\n muxed_pool_str = sample_row[\"muxed_run\"]\n\n bam_to_glob_for = f\"{sample_row['muxed_run']}*.bam\"\n found_bam_files = glob.glob(f\"{inDir}/{bam_to_glob_for}\".replace(\"//\",\"/\"))\n found_bam_file = found_bam_files[0] if found_bam_files else None\n \n if found_bam_file:\n if muxed_pool_str not in pool_id_to_pool_bam:\n pool_id_to_pool_bam[muxed_pool_str] = found_bam_file\n log.info(f\"Found input pool bam file for {muxed_pool_str}: {found_bam_file}\")\n\n demux_bams_to_sample_library_id_map[found_bam_file].append(sample_row[\"run\"])\n sample_to_demux_bam_map[sample_name] = found_bam_file\n pool_id_to_sample_library_id_map[sample_row[\"muxed_run\"]].append(sample_row[\"run\"])\n else:\n raise FileNotFoundError(f\"No bam file found: for {bam_to_glob_for}\")\n\n demux_bams_to_sample_library_id_map = dict(demux_bams_to_sample_library_id_map)\n pool_id_to_sample_library_id_map = dict(pool_id_to_sample_library_id_map)\n\n\n \"\"\"\n ToDo: alternative code path to glob the input files for either fastq or bam patterns\n if the input is a bam file, convert to fastq files\n \n In an Illumina directory, a file manifest of fastq files (may, or may not—mush check) exists within:\n fastq/Reports/fastq_list.csv\n \n The manifest is formatted like this:\n RGID,RGSM,RGLB,Lane,Read1File,Read2File\n AGCGTGTTAT.CTTCGCAAGT.6,22J5GLLT4_6_0420593812_B13Pool1a,UnknownLibrary,6,/seq/dragen/fastqs/prod/SL-EXC/241217_SL-EXC_0433_B22J5GLLT4/dragen/2024-12-17--18-30-31/fastq/22J5GLLT4_6_0420593812_B13Pool1a_S1_L006_R1_001.fastq.gz,/seq/dragen/fastqs/prod/SL-EXC/241217_SL-EXC_0433_B22J5GLLT4/dragen/2024-12-17--18-30-31/fastq/22J5GLLT4_6_0420593812_B13Pool1a_S1_L006_R2_001.fastq.gz\n ATCGCCATAT.TGCGTAACGT.6,22J5GLLT4_6_0420593812_B13Pool2a,UnknownLibrary,6,/seq/dragen/fastqs/prod/SL-EXC/241217_SL-EXC_0433_B22J5GLLT4/dragen/2024-12-17--18-30-31/fastq/22J5GLLT4_6_0420593812_B13Pool2a_S2_L006_R1_001.fastq.gz,/seq/dragen/fastqs/prod/SL-EXC/241217_SL-EXC_0433_B22J5GLLT4/dragen/2024-12-17--18-30-31/fastq/22J5GLLT4_6_0420593812_B13Pool2a_S2_L006_R2_001.fastq.gz\n ...\n \n The long paths to the fastq files are local to the dragen server, whether dragen is running\n on the instrument (ex. NextSeq 2000) or on an external server (ex. NovaSeq X). \n \n It is unlikely that the splitcode demultiplexing performed by this function will be\n performed on the same machine as dragen, so we need to match samples we know from the input\n sample sheet tsv given to this function to a line in the manifest using the\n `RGID`,`RGSM`,`RGLB`, and `Lane` columns, and then find the fastq files based on their\n basenames, somewhere within the `inDir` directory provided to this function or its\n subdirectories.\n \n We cannot assume data will be being delivered in the same way by all sequencers or\n facilities, so the fastq files may be at varying subdirectory depths within `inDir`.\n \n We should be able to find them using a glob pattern looking for the fastq basenames given in\n the manifest.\n\n That said, the common case is that `inDir` will be an Illumina run directory, so after first\n checking within `inDir` itself, we should check `f\"{os.path.realpath(inDir)}/fastq/\"` for\n files matching the basenames, and if not found look elsewhere within `inDir`. We should\n check a list of subdirs of inDir for the fastq files, starting with `./fastq/`(iff present)\n before proceeding to (recursively) check the other subdirs within inDir. Once we find the\n first matching fastq files, the `os.path.realpath(os.path.dirname())` of that path should\n then be the first location checked for the other files listed in the file manifest, before\n checking the other subdirs of `inDir`(since they're probably all in the same subdir).\n \"\"\"\n\n # \n # \n #with samtools.SamtoolsTool().bam2fq_tmp(inBam) as (fqin1, fqin2), \\\n # util_file.tmp_dir('_splitcode') as t_dir:\n # pass\n\n # Unzip fastq files using pigz\n #fastq_files = \" \".join(f\"'{f}'\" for f in glob.glob(fastqs))\n #subprocess.run([\"pigz\", \"-d\", *fastq_files], check=True) \n\n # ======== Generate splitcode config and keep files for each pool ========\n for pool_id, sample_libraries in pool_id_to_sample_library_id_map.items():\n log.info(f\"pool to demux with splitcode: {pool_id} containing {len(sample_libraries)} libraries\")\n\n # Use the extracted function to generate config/keep files\n splitcode_config, splitcode_sample_keep_file, returned_sample_ids = splitcode.generate_splitcode_config_and_keep_files(\n inner_demux_barcode_map_df,\n pool_id,\n splitcode_out_tmp_dir,\n max_hamming_dist=max_hamming_dist,\n r1_trim_bp_right_of_barcode=r1_trim_bp_right_of_barcode,\n r2_trim_bp_left_of_barcode=r2_trim_bp_left_of_barcode\n )\n\n # Store paths for later use\n pool_id_to_splitcode_configfile[pool_id] = splitcode_config\n pool_id_to_splitcode_keepfile[pool_id] = splitcode_sample_keep_file\n\n # Build sample_library_id_to_fastqs mapping\n for sample_library_id in returned_sample_ids:\n assert (sample_library_id not in sample_library_id_to_fastqs), \"%s detected twice when it should be present only once\" % sample_library_id\n\n # Map sample_library_id to expected output FASTQ paths\n # ex. 'VGG_19883.lPool_3.HHJYWDRX5.1' ->\n # [\"VGG_19883.lPool_3.HHJYWDRX5.1_R1.fastq\", \"VGG_19883.lPool_3.HHJYWDRX5.1_R2.fastq\"]\n sample_output_prefix = f\"{splitcode_out_tmp_dir}/{sample_library_id}\"\n sample_library_id_to_fastqs[sample_library_id] = [\n f\"{sample_output_prefix}_R1.fastq\",\n f\"{sample_output_prefix}_R2.fastq\"\n ]\n\n # Add unmatched reads to the mapping\n unmatched_sample_name = f\"{unmatched_name}.{pool_id}\"\n unmatched_output_prefix = f\"{splitcode_out_tmp_dir}/{unmatched_sample_name}\"\n sample_library_id_to_fastqs[unmatched_sample_name] = [\n f\"{unmatched_output_prefix}_R1.fastq\",\n f\"{unmatched_output_prefix}_R2.fastq\"\n ]\n\n log.debug(f\"splitcode config and keep files created for {pool_id}\")\n \n\n # ======== run splitcode ==========\n workers = threads or util_misc.available_cpu_count()\n workers = min(workers, len(pool_id_to_sample_library_id_map)) # ensure we cannot have more workers than pools\n workers = max(workers,1) # ensure at least 1 worker\n\n threads_per_worker = 1\n if threads:\n threads_per_worker = threads // workers\n else:\n threads_per_worker = util_misc.available_cpu_count() // workers\n threads_per_worker = max(threads_per_worker,1) # ensure at least 1 thread per worker\n\n log.info(f\"Running splitcode using {workers} worker{'s'[:workers^1]} to process {len(pool_id_to_sample_library_id_map)} pools, with {threads_per_worker} thread{'s'[:threads_per_worker^1]} per worker\")\n with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:\n futures = []\n for pool_idx,pool_id in enumerate(sorted(pool_id_to_sample_library_id_map.keys())):\n splitcode_config = pool_id_to_splitcode_configfile[pool_id]\n splitcode_keepfile = pool_id_to_splitcode_keepfile[pool_id]\n\n pool_bam_file = pool_id_to_pool_bam[pool_id]\n\n string_to_log = f\"creating splitcode process {pool_idx+1} for: {pool_id}\"\n future = executor.submit(\n splitcode.run_splitcode_on_pool,\n pool_id,\n pool_bam_file,\n splitcode_config,\n splitcode_keepfile,\n out_demux_dir_path,\n threads_per_worker = threads_per_worker,\n out_dir_path = out_demux_dir_path,\n out_demux_dir_path_tmp = splitcode_out_tmp_dir,\n string_to_log = string_to_log,\n predemux_r1_trim_5prime_num_bp = predemux_r1_trim_5prime_num_bp,\n predemux_r1_trim_3prime_num_bp = predemux_r1_trim_3prime_num_bp,\n predemux_r2_trim_5prime_num_bp = predemux_r2_trim_5prime_num_bp,\n predemux_r2_trim_3prime_num_bp = predemux_r2_trim_3prime_num_bp,\n )\n futures.append(future)\n\n for future in concurrent.futures.as_completed(futures):\n try:\n return_code, pool_id = future.result()\n log.info(\"worker done processing with splitcode: %s \", pool_id)\n pool_ids_successfully_demuxed_via_splitcode.append(pool_id)\n\n except subprocess.CalledProcessError as e:\n log.error(\"Error running splitcode on pool; return code %s: %s\", e.returncode, e.output)\n raise e\n\n splitcode_demux_failures = list(set(pool_id_to_sample_library_id_map.keys()) - set(pool_ids_successfully_demuxed_via_splitcode))\n if len(splitcode_demux_failures)>0:\n log.warning(\"splitcode demux failed for: %s\", )\n\n # gather metrics and create output plots\n log.info(\"gathering splitcode demux metrics...\")\n # Create look-up table that shows number of reads for each sample and maps i7/i5/inline barcodes\n splitcode_csv_metrics_out = f\"{outDir}/bc2sample_lut.csv\"\n # Pass the inner_demux_barcode_map_df directly instead of re-reading the sample sheet\n # This ensures pool IDs match exactly what was used to create summary JSON files\n # (avoiding mismatch between SampleSheet.inner_demux_mapper() and splitcode.create_splitcode_lookup_table())\n df_csv_out_path = splitcode.create_splitcode_lookup_table(\n inner_demux_barcode_map_df, # Pass DataFrame directly (not file path)\n splitcode_csv_metrics_out,\n unmatched_name,\n pool_ids_successfully_demuxed_via_splitcode\n # Note: append_run_id not needed when passing DataFrame (it's already in the DataFrame)\n )\n log.info(\"splitcode demux metrics written to %s\", splitcode_csv_metrics_out)\n\n picard_style_splitcode_metrics_path = os.path.splitext(df_csv_out_path)[0] + \"_picard-style.txt\"\n splitcode.convert_splitcode_demux_metrics_to_picard_style(df_csv_out_path, picard_style_splitcode_metrics_path)\n log.info(\"picard-style splitcode demux metrics written to %s\", picard_style_splitcode_metrics_path)\n\n # ----- splitcode metrics plotting -----\n log.info(\"plotting splitcode demux metrics...\")\n # Plot number and fraction of reads per inline barcode per pool\n splitcode.plot_read_counts(df_csv_out_path, outDir)\n # Plot a sorted curve per pool and save csv file with sorted read numbers and fractions for QC\n splitcode.plot_sorted_curve(df_csv_out_path, outDir, unmatched_name)\n # Write metrics for barcode-pool pairs\n write_barcode_metrics_for_pools(df_csv_out_path, outDir)\n # --- end splitcode metrics plotting ---\n\n df = pd.read_csv(df_csv_out_path, dtype=str)\n df = df.rename(columns={\"inline_barcode\": \"barcode_3\"})\n\n # change index of df to 'run' column\n df = df.set_index('run')\n\n workers = threads or util_misc.available_cpu_count()\n workers = min(workers, len(sample_library_id_to_fastqs))\n workers = max(workers,1) # ensure at least 1 worker\n threads_per_worker = 1\n\n bams_successfully_created_for_samples = []\n bam_conversion_attempted_for_samples = []\n\n log.info(f\"Converting splitcode output to ubam using {workers} worker{'s'[:workers^1]} for {len(sample_library_id_to_fastqs)} samples, with {threads_per_worker} thread{'s'[:threads_per_worker^1]} per worker\")\n\n with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:\n futures = []\n # Generate bam files\n for sample_idx,(sample,(fq1,fq2)) in enumerate(sample_library_id_to_fastqs.items()):\n if sample not in df.index:\n log.warning(\"Sample %s not found in the samplesheet data.\", sample)\n continue\n\n samplesheet_row_for_sample = df.loc[sample]\n samplesheet_row_idx = df.index.get_loc(sample)\n samplesheet_row_idx = samplesheet_row_idx if type(samplesheet_row_idx)==int else None\n\n barcodes_for_sample_joined = \"-\".join([\n samplesheet_row_for_sample[\"barcode_1\"], \n samplesheet_row_for_sample[\"barcode_2\"], \n samplesheet_row_for_sample[\"barcode_3\"]])\n platform_unit = \".\".join([\n flowcell,\n str(lane), \n barcodes_for_sample_joined\n ])\n\n # this is the long-form name, in the form \"{sample}.l{library_name}.{flowcell}.{lane}\"\"\n sample = samplesheet_row_for_sample.name \n sample_name = samplesheet_row_for_sample[\"sample\"]\n library_name = samplesheet_row_for_sample[\"library_id\"]\n readgroup_name = \".\".join([\n flowcell[:4],\n str(lane),\n str(samplesheet_row_idx+1) if samplesheet_row_idx is not None else util_misc.md5_digest(barcodes_for_sample_joined,last_n_chr=4)\n ])\n picardOptions = [\n f\"LIBRARY_NAME={sample}\",\n f\"PLATFORM={platform_name}\",\n f\"PLATFORM_UNIT={platform_unit}\",\n f\"PLATFORM_MODEL={platform_model}\",\n f\"SEQUENCING_CENTER={sequencing_center}\",\n f\"RUN_DATE={run_date}\",\n f\"READ_GROUP_NAME={readgroup_name}\",\n # note in the read group (@RG) description (DS) tag \n # that this was a two-stage demux (since we don't necessarily know from a RG:PU value whether three barcodes means splitcode demux or atypical picard demux with three barcodes)\n # see:\n # https://samtools.github.io/hts-specs/SAMv1.pdf#page=4\n f\"DESCRIPTION=two-stage-demux_with_picard-on-illumina-indices_then_splitcode-on-inner-barcodes\"\n ]\n\n string_to_log = f\"creating picard FastqToSamTool process {sample_idx+1} for: {sample_name}\"\n future = executor.submit(\n run_picard_fastq_to_ubam,\n fq1,\n fq2,\n sample, # library name\n sample_name, \n out_demux_dir_path,\n picardOptions,\n jvm_memory,\n string_to_log\n )\n bam_conversion_attempted_for_samples.append(sample_name)\n futures.append(future)\n\n for future in concurrent.futures.as_completed(futures):\n try:\n sample_name, out_bam = future.result()\n log.info(\"worker done processing splitcode output to ubam: %s --> %s\", sample_name, out_bam)\n bams_successfully_created_for_samples.append(sample_name)\n except subprocess.CalledProcessError as e:\n log.error(\"Error running picard FastqToSamTool; return code %s: %s\", e.returncode, e.output)\n raise e\n bam_conversion_failures = list(set(bam_conversion_attempted_for_samples) - set(bams_successfully_created_for_samples))\n if len(bam_conversion_failures)>0:\n log.warning(\"picard FastqToSamTool failed for: %s\", bam_conversion_failures)\n\n # now that we have ubam output, \n # the fastq files and tabular splitcode inputs are no longer needed\n # so we can delete the splitcode_out_tmp_dir directory\n shutil.rmtree(splitcode_out_tmp_dir)\n\n #os.unlink(splitcode_out_tmp_dir)\n\n # organize samplesheet metadata as json\n sample_meta = list(samples.get_rows())\n for row in sample_meta:\n row[\"lane\"] = str(lane)\n if out_meta_by_sample:\n with open(out_meta_by_sample, \"wt\") as outf:\n json.dump(dict((r[\"sample\"], r) for r in sample_meta), outf, indent=2)\n if out_meta_by_filename:\n with open(out_meta_by_filename, \"wt\") as outf:\n json.dump(dict((r[\"run\"], r) for r in sample_meta), outf, indent=2)\n\n\ndef main_splitcode_demux(args):\n \"\"\"\n Main function to call splitcode_demux from the command line.\n \"\"\"\n splitcode_demux(\n inDir = args.inDir,\n lane = args.lane,\n outDir = args.outDir,\n sampleSheet = args.sampleSheet,\n illumina_run_directory = args.illumina_run_directory,\n unmatched_name = args.unmatched_name,\n max_hamming_dist = args.max_hamming_dist,\n threads = args.threads,\n runinfo = args.runinfo,\n platform_name = args.platform_name,\n flowcell = args.flowcell,\n run_date = args.run_date,\n sequencing_center = args.sequencing_center,\n rev_comp_barcodes_before_demux = args.rev_comp_barcodes_before_demux,\n out_runinfo = args.out_runinfo,\n out_meta_by_filename = args.out_meta_by_filename,\n out_meta_by_sample = args.out_meta_by_sample,\n predemux_r1_trim_5prime_num_bp = args.predemux_r1_trim_5prime_num_bp,\n predemux_r1_trim_3prime_num_bp = args.predemux_r1_trim_3prime_num_bp,\n predemux_r2_trim_5prime_num_bp = args.predemux_r2_trim_5prime_num_bp,\n predemux_r2_trim_3prime_num_bp = args.predemux_r2_trim_3prime_num_bp,\n r1_trim_bp_right_of_barcode = args.r1_trim_bp_right_of_barcode, \n r2_trim_bp_left_of_barcode = args.r2_trim_bp_left_of_barcode,\n jvm_memory = args.jvm_memory\n )\n\n\ndef parser_splitcode_demux(parser=None):\n if parser is None:\n parser = argparse.ArgumentParser(\n description=\"Demultiplex FASTQ files using inline barcodes with splitcode.\"\n )\n\n # Positional arguments\n parser.add_argument(\n \"inDir\", help=\"File path to folder containing gzipped FASTQ files.\"\n )\n parser.add_argument(\n \"lane\",\n default=None,\n help=\"Lane number (used to populate BAM header). Default: read from RunInfo.xml.\",\n )\n parser.add_argument(\n \"outDir\", help=\"Output directory for BAM files and other output files.\"\n )\n\n # Optional arguments\n parser.add_argument(\n \"--sampleSheet\",\n default=None,\n help=\"\"\"Override SampleSheet. Input tab or CSV file with columns:\n sample, library_id_per_sample, I7_Index_ID, barcode_1, I5_Index_ID, barcode_2, Inline_Index_ID, barcode_3..\n Default is to look for a SampleSheet.csv in the inDir.\"\"\",\n )\n parser.add_argument(\n \"--illuminaRunDirectory\",\n dest=\"illumina_run_directory\",\n default=None,\n help=\"\"\"Path to Illumina Run Directory. Default is to look for a RunInfo.xml file in the inDir.\"\"\",\n )\n\n # Optional arguments specific to splitcode_demux\n parser.add_argument(\n \"--unmatched_name\",\n default=\"unmatched\",\n help=\"ID for reads that don't match an inline barcode. Default: 'unmatched'.\",\n )\n parser.add_argument(\n \"--max_hamming_dist\",\n type=int,\n default=1,\n help=\"Max allowed Hamming distance for inline barcode matching. Default: 1.\",\n )\n\n # Additional BAM header fields\n parser.add_argument(\n \"--runInfo\",\n default=None,\n dest=\"runinfo\",\n help=\"\"\"Override RunInfo. Input xml file.\n Default is to look for a RunInfo.xml file in the inDir.\"\"\",\n )\n parser.add_argument(\n \"--platform_name\",\n default=None,\n help=\"Platform name (used to populate BAM header). Default: read from RunInfo.xml.\",\n )\n parser.add_argument(\n \"--flowcell\",\n default=None,\n help=\"Flowcell ID (used to populate BAM header). Default: read from RunInfo.xml.\",\n )\n parser.add_argument(\n \"--run_date\",\n default=None,\n help=\"Run date (used to populate BAM header). Default: read from RunInfo.xml.\",\n )\n # parser.add_argument(\n # \"--readgroup_name\",\n # default=None,\n # help=\"Readgroup name (used to populate BAM header). Default: read from RunInfo.xml.\",\n # )\n parser.add_argument(\n \"--sequencing_center\",\n default=None,\n help=\"Sequencing center (used to populate BAM header). Default: read from RunInfo.xml.\",\n )\n parser.add_argument(\n \"--rev_comp_barcodes_before_demux\",\n help=\"\"\"Reverse complement barcodes before demultiplexing.\n If specified without setting a value, \n the \"barcode_2\" column will be reverse-complemented.\n If one or more values are specified, \n the columns with those names will be reverse-complemented.\n (and if not specified, barcodes will not be reverse-complemented)\"\"\",\n nargs='*',\n action=util_cmd.storeMultiArgsOrFallBackToConst,\n type=str,\n const=[\"barcode_2\"],\n )\n # ----- pre-demux trimming -----\n # typical invocation usage: \n # '--trim_r1_right_of_barcode --predemux_trim_r1_3prime --predemux_trim_r2_5prime --predemux_trim_r2_3prime'\n parser.add_argument(\n \"--predemux_trim_r1_5prime\",\n dest=\"predemux_r1_trim_5prime_num_bp\",\n const=18,\n nargs=\"?\",\n help=\"number of bases to trim from the 5' end of read 1 (before demux)\",\n type=int,\n )\n parser.add_argument(\n \"--predemux_trim_r1_3prime\",\n dest=\"predemux_r1_trim_3prime_num_bp\",\n const=18,\n nargs=\"?\",\n help=\"number of bases to trim from the 3' end of read 1 (before demux)\",\n type=int,\n )\n parser.add_argument(\n \"--predemux_trim_r2_5prime\",\n dest=\"predemux_r2_trim_5prime_num_bp\",\n const=18,\n nargs=\"?\",\n help=\"number of bases to trim from the 5' end of read 2 (before demux)\",\n type=int,\n )\n parser.add_argument(\n \"--predemux_trim_r2_3prime\",\n dest=\"predemux_r2_trim_3prime_num_bp\",\n const=18,\n nargs=\"?\",\n help=\"number of bases to trim from the 3' end of read 2 (before demux)\",\n type=int,\n )\n # -------------------------------\n\n # ----- post-demux trimming (relative to barcode position) -----\n parser.add_argument(\n \"--trim_r1_right_of_barcode\",\n dest=\"r1_trim_bp_right_of_barcode\",\n const=10,\n nargs=\"?\",\n help=\"number of bases to trim after the barcode on the right (3') side of read 1 (after demux)\",\n type=int,\n )\n parser.add_argument(\n \"--trim_r2_left_of_barcode\",\n dest=\"r2_trim_bp_left_of_barcode\",\n const=10,\n nargs=\"?\",\n help=\"number of bases to trim after the barcode on the left (5') side of read 2 (after demux)\",\n type=int,\n )\n # -------------------------------\n\n parser.add_argument(\n \"--out_meta_by_sample\", help=\"Output json metadata by sample\", default=None\n )\n parser.add_argument(\n \"--out_meta_by_filename\",\n help=\"Output json metadata by bam file basename\",\n default=None,\n )\n parser.add_argument(\n \"--out_runinfo\", help=\"Output json metadata about the run\", default=None\n )\n parser.add_argument(\n \"--JVMmemory\",\n dest=\"jvm_memory\",\n help=\"JVM virtual memory size (default: %(default)s)\",\n default=picard.FastqToSamTool.jvmMemDefault,\n )\n\n # Attach common arguments. Adjust the default for threads if needed.\n util_cmd.common_args(\n parser,\n ((\"threads\", 32), (\"loglevel\", None), (\"version\", None), (\"tmp_dir\", None)),\n )\n\n # Attach main function so that the parser can execute the main when run from CLI.\n util_cmd.attach_main(parser, main_splitcode_demux)\n return parser\n\n\n__commands__.append((\"splitcode_demux\", parser_splitcode_demux))\n\ndef add_constant_column_to_metrics(\n metrics_file,\n column_name,\n column_value,\n output_file=None\n):\n \"\"\"\n Add a constant-value column to a Picard-style metrics file.\n\n Reads a tab-delimited Picard metrics file and adds a new column as the last column,\n with all data rows receiving the specified constant value.\n\n Args:\n metrics_file (str): Path to input metrics file (TSV format)\n column_name (str): Name of the new column (appears in header)\n column_value (str): Value to set for all rows in the new column\n output_file (str, optional): Path to output file. If None, overwrites input file.\n\n Returns:\n str: Path to the output file\n\n Raises:\n FileNotFoundError: If metrics_file doesn't exist\n\n Example:\n >>> add_constant_column_to_metrics('demux_metrics.txt', 'DEMUX_TYPE', 'picard')\n 'demux_metrics.txt'\n >>> add_constant_column_to_metrics('metrics.txt', 'BATCH', 'batch_1', 'metrics_with_batch.txt')\n 'metrics_with_batch.txt'\n \"\"\"\n import os\n\n if not os.path.exists(metrics_file):\n raise FileNotFoundError(f\"Metrics file not found: {metrics_file}\")\n\n if output_file is None:\n output_file = metrics_file\n\n # Read the file, modify it, write to temp, then move to output\n temp_file = output_file + '.tmp'\n\n with open(metrics_file, 'r') as inf, open(temp_file, 'w') as outf:\n for line in inf:\n # Preserve comment lines as-is\n if line.startswith('##'):\n outf.write(line)\n continue\n\n # Skip empty lines\n stripped = line.rstrip('\\n\\r')\n if not stripped or stripped.isspace():\n outf.write(line)\n continue\n\n # Check if this is a header line\n is_header = any(stripped.startswith(col) for col in [\n 'BARCODE', 'SAMPLE_ALIAS', 'OUTPUT', 'LIBRARY_NAME'\n ])\n\n if is_header:\n # Add column_name to header\n outf.write(f\"{stripped}\\t{column_name}\\n\")\n else:\n # Add column_value to data row\n outf.write(f\"{stripped}\\t{column_value}\\n\")\n\n # Move temp file to output file\n os.replace(temp_file, output_file)\n\n log.info(f\"Added column '{column_name}' (value: '{column_value}') to {output_file}\")\n return output_file\n\n\ndef merge_demux_metrics(\n input_metrics_files,\n output_metrics_file,\n skip_header_merge_check=False\n):\n \"\"\"\n Merge multiple Picard-style demux metrics tab files into a single file.\n\n This function takes multiple tab-delimited metrics files (e.g., from Illumina/Picard demux\n and splitcode demux) and combines them into a single output file. It preserves comment lines\n from the first file and combines data rows from all files.\n\n The function expects all input files to have the same column structure (same columns in the\n same order), and will raise an error if headers don't match (unless skip_header_merge_check=True).\n\n Args:\n input_metrics_files (list): List of paths to input metrics files (TSV format).\n Each file should be in Picard-style format with:\n - Optional comment lines starting with '##'\n - A header line with tab-separated column names\n - Data rows with tab-separated values\n output_metrics_file (str): Path to the output merged metrics file.\n skip_header_merge_check (bool): If True, skips validation that all files have\n matching headers. Use with caution - mismatched columns will produce invalid output.\n Default: False\n\n Returns:\n str: Path to the output metrics file\n\n Raises:\n ValueError: If input_metrics_files is empty or if headers don't match (when\n skip_header_merge_check=False)\n FileNotFoundError: If any input file doesn't exist\n\n Example:\n >>> merge_demux_metrics(\n ... input_metrics_files=[\n ... 'illumina_demux_metrics.txt',\n ... 'splitcode_demux_metrics_picard-style.txt'\n ... ],\n ... output_metrics_file='merged_demux_metrics.txt'\n ... )\n 'merged_demux_metrics.txt'\n\n Output format:\n The output file will have:\n - Comment lines from the first file (lines starting with '##')\n - The header line from the first file\n - All data rows from all input files (in order of input_metrics_files)\n\n Notes:\n - Skips empty lines and whitespace-only lines\n - Preserves all comment lines from the first file only\n - The DEMUX_TYPE column (if present) should differentiate rows from different sources\n - Files are processed in the order provided in input_metrics_files\n \"\"\"\n import os\n\n # Validate inputs\n if not input_metrics_files:\n raise ValueError(\"input_metrics_files cannot be empty\")\n\n # Check all input files exist\n for f in input_metrics_files:\n if not os.path.exists(f):\n raise FileNotFoundError(f\"Input metrics file not found: {f}\")\n\n reference_header = None\n first_file = True\n\n with open(output_metrics_file, 'w') as outf:\n for file_idx, metrics_file in enumerate(input_metrics_files):\n with open(metrics_file, 'r') as inf:\n current_file_header = None\n\n for line in inf:\n # Preserve comment lines from first file only\n if line.startswith('##'):\n if first_file:\n outf.write(line)\n continue\n\n # Skip empty lines\n stripped = line.rstrip('\\n\\r')\n if not stripped or stripped.isspace():\n continue\n\n # Detect header line (contains common column names)\n is_header = any(stripped.startswith(col) for col in [\n 'BARCODE', 'SAMPLE_ALIAS', 'OUTPUT', 'LIBRARY_NAME'\n ])\n\n if is_header:\n current_file_header = stripped\n if reference_header is None:\n # First header - write it and set as reference\n reference_header = stripped\n outf.write(f\"{stripped}\\n\")\n else:\n # Subsequent headers - validate they match\n if not skip_header_merge_check and current_file_header != reference_header:\n raise ValueError(\n f\"Header mismatch in file '{metrics_file}'.\\n\"\n f\"Expected: {reference_header}\\n\"\n f\"Got: {current_file_header}\\n\"\n f\"Use skip_header_merge_check=True to bypass this check.\"\n )\n # Don't write duplicate headers\n continue\n\n # Data line - write it\n outf.write(f\"{stripped}\\n\")\n\n first_file = False\n\n log.info(f\"Merged {len(input_metrics_files)} demux metrics files into {output_metrics_file}\")\n return output_metrics_file\n\n\ndef parser_merge_demux_metrics(parser=argparse.ArgumentParser()):\n \"\"\"\n Argument parser for merge_demux_metrics entry point.\n \"\"\"\n parser.add_argument(\n 'input_metrics_files',\n nargs='+',\n help='Input Picard-style demux metrics files to merge (TSV format). Specify multiple files separated by spaces.'\n )\n parser.add_argument(\n 'output_metrics_file',\n help='Output path for merged demux metrics file'\n )\n parser.add_argument(\n '--skip_header_merge_check',\n action='store_true',\n help='Skip validation that all input files have matching column headers. Use with caution.'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, merge_demux_metrics, split_args=True)\n return parser\n\n\n__commands__.append(('merge_demux_metrics', parser_merge_demux_metrics))\n\n\n# =======================\ndef full_parser():\n return util_cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n util_cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == \"__main__\":\n main()\n" }, { "path": "src/viral_ngs/interhost.py", "content": "#!/usr/bin/env python\n''' This script contains a number of utilities for SNP calling, multi-alignment,\n phylogenetics, etc.\n'''\n\n__author__ = \"PLACEHOLDER\"\n__commands__ = []\n\n# built-ins\nimport argparse\nimport logging\nimport os\nimport json\nfrom collections import OrderedDict\n\n# third-party libraries\nimport Bio.AlignIO, Bio.SeqIO\n\n# module-specific\nfrom .core import cmd\nfrom .core import file\nfrom .core.misc import CoordMapperError, CoordMapper, CoordMapper2Seqs\nfrom .phylo import muscle\nfrom .phylo import snpeff\nfrom .phylo import mafft\nfrom .phylo import vcf\n\nlog = logging.getLogger(__name__)\n\n# ========== snpEff annotation of VCF files ==================\n\n\ndef parser_snpEff(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inVcf\", help=\"Input VCF file\")\n parser.add_argument(\"genomes\", nargs='+', help=\"genome name (snpEff db name, or NCBI accessions)\")\n parser.add_argument(\"outVcf\", help=\"Output VCF file\")\n parser.add_argument(\"--emailAddress\",\n help=\"\"\"Your email address. To access the Genbank CoreNucleotide database,\n NCBI requires you to specify your email address with each request.\n In case of excessive usage of the E-utilities, NCBI will attempt to contact\n a user at the email address provided before blocking access.\"\"\")\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, snpeff.SnpEff().annotate_vcf, split_args=True)\n return parser\n\n\n__commands__.append(('snpEff', parser_snpEff))\n\n# =======================\n# *** align_mafft ***\n# =======================\n\n\ndef parser_general_mafft(parser=argparse.ArgumentParser()):\n parser.add_argument('inFastas', nargs='+', help='Input FASTA files.')\n\n group = parser.add_mutually_exclusive_group()\n group.add_argument('--localpair',\n default=None,\n action='store_true',\n help='All pairwise alignments are computed with the Smith-Waterman algorithm.')\n group.add_argument('--globalpair',\n default=None,\n action='store_true',\n help='All pairwise alignments are computed with the Needleman-Wunsch algorithm.')\n\n parser.add_argument('--preservecase',\n default=None,\n action='store_true',\n help='Preserve base or aa case, as well as symbols.')\n parser.add_argument('--reorder',\n default=None,\n action='store_true',\n help='Output is ordered aligned rather than in the order of the input (default: %(default)s).')\n parser.add_argument('--gapOpeningPenalty',\n default=1.53,\n type=float,\n help='Gap opening penalty (default: %(default)s).')\n parser.add_argument('--ep', type=float, help='Offset (works like gap extension penalty).')\n parser.add_argument('--verbose', default=False, action='store_true', help='Full output (default: %(default)s).')\n parser.add_argument('--outputAsClustal',\n default=None,\n action='store_true',\n help='Write output file in Clustal format rather than FASTA')\n parser.add_argument(\n '--maxiters',\n default=0,\n type=int,\n help=\"\"\"Maximum number of refinement iterations (default: %(default)s).\n Note: if \"--localpair\" or \"--globalpair\" is specified this defaults to 1000.\"\"\")\n return parser\n\n\ndef parser_align_mafft(parser):\n parser = parser_general_mafft(parser)\n\n parser.add_argument('outFile', help='Output file containing alignment result (default format: FASTA)')\n\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_align_mafft)\n return parser\n\n\ndef main_align_mafft(args):\n ''' Run the mafft alignment on the input FASTA file.'''\n\n mafft.MafftTool().execute(\n inFastas=args.inFastas,\n outFile=args.outFile,\n localpair=args.localpair,\n globalpair=args.globalpair,\n preservecase=args.preservecase,\n reorder=args.reorder,\n gapOpeningPenalty=args.gapOpeningPenalty,\n offset=args.ep,\n verbose=args.verbose,\n outputAsClustal=args.outputAsClustal,\n maxiters=args.maxiters,\n threads=args.threads)\n\n return 0\n\n\n__commands__.append(('align_mafft', parser_align_mafft))\n\n# =======================\n# *** multichr_mafft ***\n# =======================\n\n\ndef parser_multichr_mafft(parser):\n parser = parser_general_mafft(parser)\n\n parser.add_argument('outDirectory', help='Location for the output files (default is cwd: %(default)s)')\n parser.add_argument('--outFilePrefix',\n default=\"aligned\",\n help='Prefix for the output file name (default: %(default)s)')\n parser.add_argument('--sampleRelationFile',\n default=None,\n help=\"\"\"If the parameter sampleRelationFile is specified\n (as a file path), a JSON file will be written mapping\n sample name to sequence position in the output.\"\"\")\n parser.add_argument('--sampleNameListFile',\n default=None,\n help=\"\"\"If the parameter sampleRelationFile is specified\n (as a file path), a file will be written mapping\n sample names in the order of their sequence\n positions in the output.\"\"\")\n\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, multichr_mafft)\n return parser\n\n\ndef multichr_mafft(args):\n ''' Run the mafft alignment on a series of chromosomes provided in sample-partitioned FASTA files. Output as FASTA.\n (i.e. file1.fasta would contain chr1, chr2, chr3; file2.fasta would also contain chr1, chr2, chr3)'''\n\n # get the absolute path to the output directory in case it has been specified as a relative path,\n # since MAFFT relies on its CWD for path resolution\n absoluteOutDirectory = os.path.abspath(args.outDirectory)\n\n # make the output directory if it does not exist\n if not os.path.isdir(absoluteOutDirectory):\n os.makedirs(absoluteOutDirectory)\n\n # prefix for output files\n prefix = \"\" if args.outFilePrefix is None else args.outFilePrefix\n\n # reorder the data into new FASTA files, where each FASTA file has only variants of its respective chromosome\n transposedFiles = file.transposeChromosomeFiles(args.inFastas, args.sampleRelationFile, args.sampleNameListFile)\n\n # since the FASTA files are\n for idx, filePath in enumerate(transposedFiles):\n\n # execute MAFFT alignment. The input file is passed within a list, since argparse ordinarily\n # passes input files in this way, and the MAFFT tool expects lists,\n # but in this case we are creating the input file ourselves\n mafft.MafftTool().execute(\n inFastas=[os.path.abspath(filePath)],\n outFile=os.path.join(absoluteOutDirectory, \"{}_{}.fasta\".format(prefix, idx + 1)),\n localpair=args.localpair,\n globalpair=args.globalpair,\n preservecase=args.preservecase,\n reorder=args.reorder,\n gapOpeningPenalty=args.gapOpeningPenalty,\n offset=args.ep,\n verbose=args.verbose,\n outputAsClustal=args.outputAsClustal,\n maxiters=args.maxiters,\n threads=args.threads)\n\n return 0\n\n\n__commands__.append(('multichr_mafft', parser_multichr_mafft))\n\n# ============================\n\n# modified version of rachel's call_snps_3.py follows\n\n\ndef call_snps_3(inFasta, outVcf, REF=\"KJ660346.2\"):\n a = Bio.AlignIO.read(inFasta, \"fasta\")\n ref_idx = find_ref(a, REF)\n with open(outVcf, 'wt') as outf:\n outf.write(vcf_header(a))\n for row in make_vcf(a, ref_idx, REF):\n outf.write('\\t'.join(map(str, row)) + '\\n')\n\n\ndef find_ref(a, ref):\n for i in range(len(a)):\n if a[i].id == ref:\n return i\n return -1\n\n\ndef vcf_header(a):\n header = \"##fileformat=VCFv4.1\\n\"\n header += \"##FORMAT=\\n\"\n header += \"##contig=\\n\"\n header += '#' + '\\t'.join(['CHROM', 'POS', 'ID', 'REF', 'ALT',\n 'QUAL', 'FILTER', 'INFO', 'FORMAT'] + [x.id for x in a]) + '\\n' # pylint: disable=E1101\n\n return header\n\n\ndef make_vcf(a, ref_idx, chrom):\n bases = set([\"A\", \"C\", \"G\", \"T\"])\n for i in range(len(a[0])):\n alt = []\n for j in range(len(a)):\n if (a[j][i] != a[ref_idx][i]) and ((a[ref_idx][i] in bases) and (a[j][i] in bases)) and a[j][i] not in alt:\n alt.append(a[j][i])\n if len(alt) > 0:\n row = [chrom, i + 1, '.', a[ref_idx][i], ','.join(alt), '.', '.', '.', 'GT']\n genos = []\n for k in range(len(a)):\n if a[k][i] == a[ref_idx][i]:\n genos.append(0)\n elif a[k][i] not in bases:\n genos.append(\".\")\n else:\n for m in range(0, len(alt)):\n if a[k][i] == alt[m]:\n genos.append(m + 1)\n yield row + genos\n\n\n\ndef full_parser():\n return cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/intrahost.py", "content": "#!/usr/bin/env python\n'''This script contains a number of utilities for intrahost variant calling\nand annotation for viral genomes.\n'''\n\n__author__ = \"dpark@broadinstitute.org, rsealfon@broadinstitute.org, \"\\\n \"swohl@broadinstitute.org, irwin@broadinstitute.org\"\n__commands__ = []\n\n# built-ins\nimport argparse\nimport logging\nimport itertools\nimport re\nimport os\nimport collections\n\n# third-party\nimport Bio.AlignIO\nimport Bio.SeqIO\nimport Bio.Data.IUPACData\nimport pysam\n\n# module-specific\nfrom .core import samtools\nfrom .core import cmd\nfrom .core import file\nfrom .core import misc\nfrom .phylo import genbank\nfrom .phylo import vcf\nfrom .phylo import vphaser2\nfrom .core.stats import median, fisher_exact, chi2_contingency\nfrom . import interhost\n\nlog = logging.getLogger(__name__)\n\n# ============= class AlleleFieldParser =================\n\n\nclass AlleleFieldParser(object):\n \"\"\"\n Class for converting between the string and list representation\n of the fields in the allele columns of vphaser_one_sample output\n (corresponding to the SNP_or_LP_Profile columns in the V-Phaser 2 output).\n \"\"\"\n __slots__ = ('_allele', '_strandCounts', '_libBiasPval', '_libCounts')\n\n def __init__(self, field=None, allele=None, fcount=None, rcount=None, libBiasPval=None, libCounts=None):\n \"\"\" Input is either the string stored in one of the allele columns.\n or set field values.\n \"\"\"\n if field is None:\n self._allele = allele\n self._strandCounts = [fcount, rcount]\n self._libBiasPval = libBiasPval\n self._libCounts = libCounts # libCounts is a list of 2-element lists\n else:\n words = field.split(':')\n self._allele = words[0]\n self._strandCounts = [int(words[1]), int(words[2])]\n self._libCounts = [[int(words[ii]), int(words[ii + 1])] for ii in range(3, len(words) - 1, 2)]\n self._libBiasPval = float(words[-1])\n\n def __repr__(self):\n \"\"\"Convert to string representation.\"\"\"\n return ':'.join([self._allele] + list(map(str, self._strandCounts)) + sum((list(map(\n str, libCount)) for libCount in self._libCounts), []) + ['%.4g' % self._libBiasPval])\n\n def allele(self):\n \"\"\" Return allele:\n A, C, G, or T for SNVs,\n Dn with n > 0 for deletions,\n Ibases where bases is a string of two or more bases for inserts\n \"\"\"\n return self._allele\n\n def total(self):\n return sum(self._strandCounts)\n\n def strand_counts(self):\n \"Return [# forward reads (all libs), # reverse reads (all libs)]\"\n return self._strandCounts\n\n def allele_and_strand_counts(self):\n return [self.allele()] + self.strand_counts()\n\n def lib_counts(self):\n \"\"\"Yield [# forward reads, # reverse reads] for each library, in order\n of read groups in BAM file.\n \"\"\"\n for counts in self._libCounts:\n yield counts\n\n def lib_bias_pval(self):\n \"Return a p-value on whether there is a library bias for this allele.\"\n return self._libBiasPval\n\n# ========== vphaser_one_sample =================\n\ndefaultMinReads = 5\ndefaultMaxBias = 10\n\n\ndef vphaser_one_sample(inBam, inConsFasta, outTab, vphaserNumThreads=None,\n minReadsEach=None, maxBias=None, removeDoublyMappedReads=False):\n ''' Input: a single BAM file, representing reads from one sample, mapped to\n its own consensus assembly. It may contain multiple read groups and\n libraries.\n Output: a tab-separated file with no header containing filtered\n V Phaser-2 output variants with additional column for\n sequence/chrom name, and library counts and p-values appended to\n the counts for each allele.\n '''\n samtoolsTool = samtools.SamtoolsTool()\n\n if minReadsEach is not None and minReadsEach < 0:\n raise Exception('minReadsEach must be at least 0.')\n\n sorted_bam_file = inBam\n if not file.bam_is_sorted(inBam):\n sorted_bam_file = file.mkstempfname('.mapped-sorted.bam')\n sorted_bam_file_tmp = file.mkstempfname('.mapped-sorted.bam')\n samtoolsTool.sort(args=['-T', sorted_bam_file_tmp], inFile=inBam, outFile=sorted_bam_file)\n\n bam_to_process = sorted_bam_file\n if removeDoublyMappedReads:\n leading_or_trailing_indels_removed = file.mkstempfname('.mapped-leading_or_trailing_indels_removed.bam')\n # vphaser crashes when cigar strings have leading or trailing indels\n # so we will use filterByCigarString() with its default regex to remove such reads\n samtoolsTool.filterByCigarString(sorted_bam_file, leading_or_trailing_indels_removed)\n\n bam_to_process = file.mkstempfname('.mapped-withdoublymappedremoved.bam')\n samtoolsTool.removeDoublyMappedReads(leading_or_trailing_indels_removed, bam_to_process)\n os.unlink(leading_or_trailing_indels_removed)\n\n samtoolsTool.index(bam_to_process)\n\n # For low-quality data, the process of removing doubly-mapped reads\n # can remove all reads. In such cases, stub out an empty vphaser output\n # file to allow the pipeline to continue\n if samtoolsTool.count(bam_to_process) == 0:\n log.warning(\"The bam file %s has 0 reads after removing doubly-mapped reads. Writing blank V-Phaser output.\", bam_to_process)\n file.touch(outTab)\n return None\n\n variantIter = vphaser2.Vphaser2Tool().iterate(bam_to_process, vphaserNumThreads)\n filteredIter = filter_strand_bias(variantIter, minReadsEach, maxBias)\n\n libraryFilteredIter = compute_library_bias(filteredIter, bam_to_process, inConsFasta)\n with file.open_or_gzopen(outTab, 'wt') as outf:\n for row in libraryFilteredIter:\n outf.write('\\t'.join(row) + '\\n')\n\n\ndef filter_strand_bias(isnvs, minReadsEach=None, maxBias=None):\n ''' Take an iterator of V-Phaser output (plus chromosome name prepended)\n and perform hard filtering for strand bias\n '''\n alleleCol = 7 # First column of output with allele counts\n if minReadsEach is None:\n minReadsEach = defaultMinReads\n if maxBias is None:\n maxBias = defaultMaxBias\n for row in isnvs:\n #front = row[:alleleCol]\n for fieldInd in range(len(row) - 1, alleleCol - 1, -1):\n f, r = AlleleFieldParser(row[fieldInd]).strand_counts()\n if (int(f) < minReadsEach or int(r) < minReadsEach or\n (minReadsEach > 0 and not (maxBias >= (float(f) / float(r)) >= 1.0 / maxBias))):\n del row[fieldInd]\n if len(row) > alleleCol + 1:\n row[alleleCol:] = sorted(row[alleleCol:], key=lambda field: AlleleFieldParser(field).total(), reverse=True)\n mac = sum(AlleleFieldParser(field).total() for field in row[alleleCol + 1:])\n tot = sum(AlleleFieldParser(field).total() for field in row[alleleCol:])\n row[2] = AlleleFieldParser(row[alleleCol + 1]).allele()\n row[3] = AlleleFieldParser(row[alleleCol]).allele()\n row[6] = '%.6g' % (100.0 * mac / tot)\n yield row\n\n\ndef compute_library_bias(isnvs, inBam, inConsFasta):\n ''' For each variant, compute read counts in each library and p-value for\n library bias; append them to string for each variant.\n Format is allele:totalF:totalR:1stLibFCount:1stLibRCount:2ndLibFCount:...:p-val.\n Library counts are in alphabetical order of library IDs.\n Note: Total was computed by vphaser, library counts by samtools mpileup,\n so total might not be sum of library counts.\n '''\n alleleCol = 7 # First column of output with allele counts\n samtoolsTool = samtools.SamtoolsTool()\n rgs_by_lib = sorted((rg['LB'], rg['ID']) for rg in samtoolsTool.getReadGroups(inBam).values())\n rgs_by_lib = itertools.groupby(rgs_by_lib, lambda x: x[0])\n libBams = []\n header_sam = file.mkstempfname('.sam')\n samtoolsTool.dumpHeader(inBam, header_sam)\n for lib, rgs in rgs_by_lib:\n rgs = list(idVal for lb, idVal in rgs)\n\n # Create libBam containing all the readgroups in rgs.\n # In samtools 1.1, this can be done by including -r multiple times on\n # a single command line, but that doesn't work in 0.1.19, so instead\n # extract readgroups one by one and then concatenate.\n rgBams = []\n for idVal in rgs:\n rgBam = file.mkstempfname('.bam')\n samtoolsTool.view(['-b', '-r', idVal], inBam, rgBam)\n samtoolsTool.index(rgBam)\n if samtoolsTool.count(rgBam) > 0:\n rgBams.append(rgBam)\n else:\n # most samtools functions don't like empty input bams, so skip them\n os.unlink(rgBam)\n if rgBams:\n if len(rgBams) > 1:\n libBam = file.mkstempfname('.bam')\n samtoolsTool.merge(rgBams, libBam, ['-f', '-1', '-h', header_sam])\n for bam in rgBams:\n os.unlink(bam)\n else:\n # samtools merge cannot deal with only one (or zero) input bams\n libBam = rgBams[0]\n samtoolsTool.index(libBam)\n n_reads = samtoolsTool.count(libBam)\n log.debug(\"LB:%s has %s reads in %s read group(s) (%s)\", lib, n_reads, len(rgs), ', '.join(rgs))\n libBams.append(libBam)\n\n for row in isnvs:\n consensusAllele = row[3]\n pos = int(row[1]) if consensusAllele != 'i' else int(row[1]) - 1\n chrom = row[0]\n libCounts = [get_mpileup_allele_counts(libBamItem, chrom, pos, inConsFasta, samtools=samtoolsTool) for libBamItem in libBams]\n numAlleles = len(row) - alleleCol\n countsMatrix = [[0] * numAlleles for lib in libBams]\n libCountsByAllele = []\n for alleleInd in range(numAlleles):\n allele = row[alleleCol + alleleInd].split(':')[0]\n libCountsByAllele.append([])\n for libAlleleCounts, countsRow in zip(libCounts, countsMatrix):\n f, r = libAlleleCounts.get(allele, [0, 0])\n libCountsByAllele[-1].append([f, r])\n countsRow[alleleInd] += f + r\n for alleleInd in range(numAlleles):\n contingencyTable = [\n [countsRow[alleleInd] for countsRow in countsMatrix], [sum(countsRow) - countsRow[alleleInd]\n for countsRow in countsMatrix]\n ]\n rowSums = map(sum, contingencyTable)\n dofs = len(libCounts) - 1\n if dofs < 1:\n pval = 1.0\n elif min(rowSums) ** dofs / dofs < 10000:\n # At this cutoff, fisher_exact should take <~ 0.1 sec\n pval = fisher_exact(contingencyTable)\n else:\n pval = chi2_contingency(contingencyTable)\n row[alleleCol + alleleInd] = str(AlleleFieldParser(None, *(row[alleleCol + alleleInd].split(':') +\n [pval, libCountsByAllele[alleleInd]])))\n yield row\n for bam in libBams:\n os.unlink(bam)\n os.unlink(header_sam)\n\n\ndef parse_alleles_string(allelesStr):\n # Return {allele : [forwardCount, reverseCount]}\n # For reference, allele is '.' rather than real allele\n alleleCounts = {} # allele : [forwardCount, reverseCount]\n pos = -1\n digits = re.compile('[0-9]+')\n while pos < len(allelesStr) - 1:\n pos += 1\n c = allelesStr[pos]\n if c in '.,':\n allele = '.'\n isRev = c == ','\n elif c in '<>$*': # Reference skip, end of read, placeholder\n continue # Not interested in these\n elif c == '^': # Start of read\n pos += 1 # Skip quality character\n continue\n elif c in 'ACGTNacgtn':\n allele = c.upper()\n isRev = c == c.lower()\n elif c in '+-': # e.g., +3aaa\n mat = digits.match(allelesStr, pos + 1)\n indelLen = int(allelesStr[mat.start():mat.end()])\n indelStr = allelesStr[mat.end():mat.end() + indelLen]\n allele = 'I' + indelStr.upper() if c == '+' else 'D' + str(indelLen)\n isRev = indelStr == indelStr.lower()\n pos += mat.end() - mat.start() + indelLen\n else:\n raise Exception('Unknown allele type %s' % c)\n alleleCounts.setdefault(allele, [0, 0])\n alleleCounts[allele][isRev] += 1\n return alleleCounts\n\n\ndef get_mpileup_allele_counts(inBam, chrom, pos, inConsFasta, samtools=None):\n \"\"\" Return {allele : [forwardCount, reverseCount], ...}\n allele is:\n Iins for insertions where ins represents the inserted bases\n Dlen for deletions where len is the length of the deletion\n base itself for non-indels\n 'i' or 'd', in which case report count for consensus.\n \"\"\"\n samtools = samtools or samtools.SamtoolsTool()\n pileupFileName = file.mkstempfname('.txt')\n\n # bcftools params\n # https://samtools.github.io/bcftools/bcftools.html#mpileup\n # -A, --count-orphans Do not skip anomalous read pairs in variant calling.\n # -r, --regions Only generate mpileup output in given regions. Requires the alignment files to be indexed. \n # -B, --no-BAQ Disable probabilistic realignment for the computation of base alignment quality (BAQ).\n # -d, --max-depth At a position, read maximally INT reads per input file. \n # -L, --max-idepth Skip INDEL calling if the average per-sample depth is above INT \n # -Q, --min-BQ Minimum base quality for a base to be considered\n # -f, --fasta-ref The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by bgzip.\n # bcftools.mpileup(inBam, pileupFileName, ['-A', '-r', '%s:%d-%d' % (chrom, pos, pos), '-B', '-d', '50000',\n # '-L', '50000', '-Q', '0', '-O', 'v', '-f', inConsFasta])\n\n samtools.mpileup(inBam, pileupFileName, ['-A', '-r', '%s:%d-%d' % (chrom, pos, pos), '-B', '-d', '50000',\n '-Q', '0', '-f', inConsFasta])\n with open(pileupFileName) as pileupFile:\n words = pileupFile.readline().split('\\t')\n if len(words) < 5:\n # empty output files means no reads pile up on this position\n return {}\n alleleCounts = parse_alleles_string(words[4])\n\n # '.' is whatever mpileup thinks is the reference base (which might be\n # different from vphaser's consensus base). This is the count we want to\n # report for this base, but we also want to report this count for what\n # vphaser calls 'i' or 'd'.\n # This will probably be wrong in the unlikely case that there are both\n # an indel and a snp at the same position, and vphaser's consensus base\n # is different from mpileup's at that position.\n refAllele = words[2]\n alleleCounts['i'] = alleleCounts['d'] = alleleCounts[refAllele] = \\\n alleleCounts.get('.', [0, 0])\n\n return alleleCounts\n\n\ndef parser_vphaser_one_sample(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inBam\", help=\"Input Bam file.\")\n parser.add_argument(\"inConsFasta\", help=\"Consensus assembly fasta.\")\n parser.add_argument(\"outTab\", help=\"Tab-separated headerless output file.\")\n parser.add_argument(\"--vphaserNumThreads\", type=int, default=None, help=\"Number of threads in call to V-Phaser 2.\")\n parser.add_argument(\"--minReadsEach\",\n type=int,\n default=defaultMinReads,\n help=\"Minimum number of reads on each strand (default: %(default)s).\")\n parser.add_argument(\"--maxBias\",\n type=int,\n default=defaultMaxBias,\n help=\"\"\"Maximum allowable ratio of number of reads on the two strands\n (default: %(default)s). Ignored if minReadsEach = 0.\"\"\")\n parser.add_argument(\"--removeDoublyMappedReads\",\n default=False,\n action=\"store_true\",\n help=\"\"\"When calling V-Phaser, remove reads mapping to more than one contig. Default is to keep the reads.\"\"\")\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, vphaser_one_sample, split_args=True)\n return parser\n\n\n__commands__.append(('vphaser_one_sample', parser_vphaser_one_sample))\n\n# ========== vphaser =================\n\n\ndef parser_vphaser(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inBam\", help=\"Input Bam file.\")\n parser.add_argument(\"outTab\", help=\"Tab-separated headerless output file.\")\n parser.add_argument(\"--numThreads\", type=int, default=None, help=\"Number of threads in call to V-Phaser 2.\")\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, vphaser_main, split_args=True)\n return parser\n\n\ndef vphaser_main(inBam, outTab, numThreads=None):\n \"\"\" Run V-Phaser 2 on the input file without any additional filtering.\n Combine the non-header lines of the CHROM.var.raw.txt files it produces,\n adding CHROM as the first field on each line.\n \"\"\"\n with open(outTab, 'wt') as outf:\n for row in vphaser2.Vphaser2Tool().iterate(inBam, numThreads):\n outf.write('\\t'.join(row) + '\\n')\n\n\n__commands__.append(('vphaser', parser_vphaser))\n\n# ========== tabfile_values_rename =================\n\n\ndef tabfile_values_rename(inFile, mapFile, outFile, col=0):\n ''' Take input tab file and copy to an output file while changing\n the values in a specific column based on a mapping file.\n The first line will pass through untouched (it is assumed to be\n a header).\n '''\n # read map\n with open(mapFile, 'rt') as inf:\n name_map = dict(line.strip().split('\\t') for line in inf)\n # convert file\n with open(outFile, 'wt') as outf:\n with open(inFile, 'rt') as inf:\n # copy header row verbatim\n outf.write(inf.readline())\n # all other rows: remap the specified column's values\n for line in inf:\n row = line.rstrip('\\n').split('\\t')\n row[col] = name_map[row[col]]\n outf.write('\\t'.join(row) + '\\n')\n\n\ndef parser_tabfile_rename(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inFile\", help=\"Input flat file\")\n parser.add_argument(\"mapFile\",\n help=\"\"\"Map file. Two-column headerless file that maps input values to\n output values. This script will error if there are values in inFile that do\n not exist in mapFile.\"\"\")\n parser.add_argument(\"outFile\", help=\"Output flat file\")\n parser.add_argument(\"--col_idx\",\n dest=\"col\",\n type=int,\n help=\"\"\"Which column number to replace (0-based index). [default: %(default)s]\"\"\",\n default=0)\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, tabfile_values_rename, split_args=True)\n return parser\n\n\n__commands__.append(('tabfile_rename', parser_tabfile_rename))\n\n# ========== merge_to_vcf ===========================\n\n\ndef count_iter_items(iterable):\n \"\"\"\n Consume an iterable not reading it into memory; return the number of items.\n \"\"\"\n\n counter = itertools.count()\n collections.deque(zip(iterable, counter), maxlen=0) # (consume at C speed)\n return next(counter)\n\n\ndef strip_accession_version(acc):\n ''' If this is a Genbank accession with a version number,\n remove the version number.\n '''\n m = re.match(r\"^(\\S+)\\.\\d+$\", acc)\n if m:\n acc = m.group(1)\n return acc\n\n\n\n# def merge_to_vcf(refFasta, outVcf, samples, isnvs, assemblies, strip_chr_version=False, naive_filter=False):\n\n\ndef merge_to_vcf(\n refFasta,\n outVcf,\n samples,\n isnvs,\n alignments,\n strip_chr_version=False,\n naive_filter=False,\n parse_accession=False):\n ''' Combine and convert vPhaser2 parsed filtered output text files into VCF format.\n Assumption: consensus assemblies used in creating alignments do not extend beyond ends of reference.\n the number of alignment files equals the number of chromosomes / segments\n '''\n\n guessed_samples = []\n if not samples:\n samplenames_from_isnvs = []\n for isnvs_file in isnvs:\n for row in file.read_tabfile(isnvs_file):\n guessed_sample_ID = sampleIDMatch(row[0])\n if guessed_sample_ID not in samplenames_from_isnvs:\n samplenames_from_isnvs.append(guessed_sample_ID)\n \n samplenames_from_alignments = set()\n for alignmentFile in alignments:\n with file.open_or_gzopen(alignmentFile, 'r') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n samplenames_from_alignments.add(sampleIDMatch(seq.id))\n\n refnames = set()\n with file.open_or_gzopen(refFasta, 'r') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n refnames.add(sampleIDMatch(seq.id))\n\n # sample names from the isnv files, in that order, \n # followed by sample names seen in the alignments, minus the former and the reference IDs\n guessed_samples = samplenames_from_isnvs + list(samplenames_from_alignments-(refnames|set(samplenames_from_isnvs)))\n log.info(\"guessed sample names %s\" % guessed_samples)\n\n samples = samples if samples is not None and len(samples)>0 else guessed_samples\n\n samp_to_isnv = {}\n # if we had to guess sample names, match them up to isnv files\n if len(guessed_samples)>0:\n matched_samples = []\n matched_isnv_files = []\n for sample in samples:\n sample_found=False\n for isnvs_file in isnvs:\n for row in file.read_tabfile(isnvs_file):\n if sample==sampleIDMatch(row[0]):\n samp_to_isnv[sample] = isnvs_file\n sample_found=True\n matched_samples.append(sample)\n matched_isnv_files.append(isnvs_file)\n break\n if sample_found:\n break\n samples = matched_samples\n isnvs = matched_isnv_files\n else:\n samp_to_isnv = dict(zip(samples, isnvs))\n\n log.info(samp_to_isnv)\n\n # get IDs and sequence lengths for reference sequence\n with file.open_or_gzopen(refFasta, 'r') as inf:\n ref_chrlens = list((seq.id, len(seq)) for seq in Bio.SeqIO.parse(inf, 'fasta'))\n\n # use the output filepath specified if it is a .vcf, otherwise if it is gzipped we need\n # to write to a temp VCF and then compress to vcf.gz later\n if outVcf.endswith('.vcf.gz'):\n tmpVcf = file.mkstempfname('.vcf')\n elif outVcf.endswith('.vcf'):\n tmpVcf = outVcf\n else:\n raise ValueError(\"outVcf must end in .vcf or .vcf.gz\")\n\n log.info(\"loaded CoordMapper for all genomes, starting VCF merge...\")\n\n # write header\n with open(tmpVcf, 'w') as outf:\n # write header\n outf.write('##fileformat=VCFv4.1\\n')\n outf.write('##FORMAT=\\n')\n outf.write('##FORMAT=\\n')\n outf.write('##FORMAT=\\n')\n outf.write('##FORMAT=\\n')\n outf.write(\n '##FORMAT=\\n')\n # write out the contig lengths present in the reference genome\n for c, clen in ref_chrlens:\n if parse_accession:\n c = genbank.parse_accession_str(c)\n if strip_chr_version:\n c = strip_accession_version(c)\n outf.write('##contig=\\n' % (c, clen))\n # write out the name of the reference file used to generate the VCF\n outf.write('##reference=file://%s\\n' % refFasta)\n header = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT'] + samples\n outf.write('#' + '\\t'.join(header) + '\\n')\n\n # compress output if requested\n if outVcf.endswith('.vcf.gz'):\n pysam.tabix_compress(tmpVcf, outVcf, force=True)\n pysam.tabix_index(outVcf, force=True, preset='vcf')\n\n with open(tmpVcf, 'a') as outf:\n if not len(ref_chrlens) == len(alignments):\n raise LookupError(\"there must be an alignment file for each chromosome/segment present in the reference\")\n\n # we are assuming that the reference sequences have the same IDs in the alignments and in the\n # reference fasta, but we need to relate each reference sequence (chromosome/segment) to a specific\n # alignment file and index within the alignment\n ref_seq_id_to_alignment_file = dict()\n ref_seq_in_alignment_file = dict()\n\n # copy the list of alignment files\n alignmentFiles = list(alignments)\n\n with file.open_or_gzopen(refFasta, 'r') as inf:\n for refSeq in Bio.SeqIO.parse(inf, 'fasta'):\n for alignmentFile in alignmentFiles:\n with file.open_or_gzopen(alignmentFile, 'r') as inf2:\n for seq in Bio.SeqIO.parse(inf2, 'fasta'):\n if refSeq.id == seq.id:\n ref_seq_id_to_alignment_file[seq.id] = alignmentFile\n ref_seq_in_alignment_file[seq.id] = seq.seq.replace(\"-\",\"\")\n\n if len(ref_seq_id_to_alignment_file) < len(ref_chrlens):\n raise LookupError(\"Not all reference sequences found in alignments.\")\n\n if len(guessed_samples)==0 and not (len(samples) == len(isnvs)):\n raise LookupError(\n \"There must be an isnv file for each sample. %s samples, %s isnv files\" % (len(samples), len(isnvs)))\n\n for fileName in alignments:\n with file.open_or_gzopen(fileName, 'r') as inf:\n # get two independent iterators into the alignment file\n number_of_aligned_sequences = count_iter_items(Bio.SeqIO.parse(inf, 'fasta'))\n num_isnv_files = len(isnvs)\n # -1 is to account for inclusion of reference in the alignement in addition\n # to the assemblies\n\n # if we had to guess samples only check that the number of isnv files == number of alignments\n if len(guessed_samples)==0:\n if not (number_of_aligned_sequences - 1) == num_isnv_files == len(samples):\n raise LookupError(\n \"\"\"The number of isnv files provided (%s) and must equal the number of sequences\n seen in the alignment (%s) (plus an extra reference record in the alignment), \n as well as the number of sample names provided (%s)\n %s does not have the right number of sequences\"\"\" % (num_isnv_files,number_of_aligned_sequences - 1,len(samples),fileName))\n\n # one reference chrom at a time\n with open(refFasta, 'r') as inf:\n for ref_sequence in Bio.SeqIO.parse(inf, 'fasta'):\n samp_to_seqIndex = dict()\n\n #ref_sequence = ref_seq_in_alignment_file[refSequence.id]\n # make a coordmapper to map all alignments to this reference sequence\n cm = interhost.CoordMapper()\n cm.load_alignments([ref_seq_id_to_alignment_file[ref_sequence.id]])\n\n # ========================\n # to map from ref->sample\n # cm[ref_sequence.id][s]\n # to map sample->ref\n # cm[s][ref_sequence.id]\n\n # read in all iSNVs for this chrom and map to reference coords\n data = []\n\n # use conditional matching to only include the sequences that match the sample basename provided\n samplesToUse = [x for x in cm.chrMaps.keys() if sampleIDMatch(x) in samples]\n\n alignmentFile = ref_seq_id_to_alignment_file[ref_sequence.id]\n with file.open_or_gzopen(alignmentFile, 'r') as alignFileIn:\n for seq in Bio.SeqIO.parse(alignFileIn, 'fasta'):\n for sampleName in samplesToUse:\n if seq.id == sampleName:\n samp_to_seqIndex[sampleName] = seq.seq.replace(\"-\",\"\")\n break\n\n if not len(samp_to_seqIndex) == len(samplesToUse):\n raise LookupError(\n \"Sequence info not found in file %s for all sample names provided. Check alignment files.\" %\n alignmentFile)\n\n for s in samplesToUse:\n isnv_filepath = samp_to_isnv[sampleIDMatch(s)]\n\n for row in file.read_tabfile(isnv_filepath):\n # map ref->sample\n s_chrom = cm.mapChr(ref_sequence.id, s)\n if row[0] == s_chrom:\n allele_fields = list(AlleleFieldParser(x) for x in row[7:] if x)\n row = {\n 'sample': s,\n 'CHROM': ref_sequence.id,\n 's_chrom': s_chrom,\n 's_pos': int(row[1]),\n 's_alt': row[2],\n 's_ref': row[3],\n 'alleles': list(x.allele_and_strand_counts() for x in allele_fields),\n 'n_libs': dict(\n (x.allele(), sum(1 for f, r in x.lib_counts()\n if f + r > 0)) for x in allele_fields),\n 'lib_bias': dict(\n (x.allele(), x.lib_bias_pval()) for x in allele_fields),\n }\n # make a sorted allele list\n row['allele_counts'] = list(sorted(\n [(a, int(f) + int(r)) for a, f, r in row['alleles']],\n key=(lambda x: x[1]),\n reverse=True))\n # naive filter (quick and dirty)\n if naive_filter:\n # require 2 libraries for every allele call\n row['allele_counts'] = list((a, n) for a, n in row['allele_counts']\n if row['n_libs'][a] >= 2)\n # recompute total read counts for remaining\n tot_n = sum(n for a, n in row['allele_counts'])\n # require allele frequency >= 0.5%\n row['allele_counts'] = list((a, n) for a, n in row['allele_counts']\n if tot_n > 0 and float(n) / tot_n >= 0.005)\n # drop this position:sample if no variation left\n if len(row['allele_counts']) < 2:\n log.info(\n \"\"\"dropping iSNV at %s:%s (%s)\n because no variation remains after simple filtering\"\"\", row['s_chrom'],\n row['s_pos'], row['sample'])\n continue\n # reposition vphaser deletions minus one to be consistent with\n # VCF conventions\n if row['s_alt'].startswith('D'):\n for a, n in row['allele_counts']:\n if a[0] not in ('D', 'i'):\n log.error(\"allele_counts: \" + str(row['allele_counts']))\n raise Exception(\"deletion alleles must always start with D or i\")\n row['s_pos'] = row['s_pos'] - 1\n # map position back to reference coordinates\n row['POS'] = cm.mapChr(s, ref_sequence.id, row['s_pos'], side=-1)[1]\n row['END'] = cm.mapChr(s, ref_sequence.id, row['s_pos'], side=1)[1]\n if row['POS'] == None or row['END'] == None:\n raise Exception('consensus extends beyond start or end of reference.')\n data.append(row)\n\n # sort all iSNVs (across all samples) and group by position\n data = sorted(data, key=(lambda row: row['POS']))\n data = itertools.groupby(data, lambda row: row['POS'])\n\n # process one reference position at a time from\n for pos, rows in data:\n # each of the sample-specific variants for a given ref pos\n rows = list(rows)\n\n # define the length of this variation based on the largest deletion\n end = pos\n for row in rows:\n end = max(end, row['END'])\n for a, n in row['allele_counts']:\n if a.startswith('D'):\n # end of deletion in sample's coord space\n local_end = row['s_pos'] + int(a[1:])\n\n # end of deletion in reference coord space\n ref_end = cm.mapChr(row['s_chrom'], ref_sequence.id, local_end, side=1)[1]\n if ref_end is None:\n raise Exception('consensus extends ' 'beyond start or end of reference.')\n end = max(end, ref_end)\n\n # find reference allele and consensus alleles\n refAllele = str(ref_sequence[pos - 1:end].seq)\n consAlleles = {} # the full pos-to-end consensus assembly sequence for each sample\n samp_offsets = {} # {sample : isnv's index in its consAllele string}\n for row in rows:\n s_pos = row['s_pos']\n sample = row['sample']\n if samp_offsets.get(sample, s_pos) != s_pos:\n raise NotImplementedError('Sample %s has variants at 2 '\n 'positions %s mapped to same reference position (%s:%s)' %\n (sample, (s_pos, samp_offsets[sample]), ref_sequence.id, pos))\n samp_offsets[sample] = s_pos\n for s in samplesToUse:\n # map ref to s\n cons_start = cm.mapChr(ref_sequence.id, s, pos, side=-1)[1]\n cons_stop = cm.mapChr(ref_sequence.id, s, end, side=1)[1]\n if cons_start is None or cons_stop is None:\n log.info(\"variant is outside consensus assembly \"\n \"for %s at %s:%s-%s.\", s, ref_sequence.id, pos, end)\n continue\n\n cons = samp_to_seqIndex[s] # .seq.replace(\"-\",\"\")#[ cm.mapChr(ref_sequence.id, s) ]\n\n allele = str(cons[cons_start - 1:cons_stop]).upper()\n if s in samp_offsets:\n samp_offsets[s] -= cons_start\n if all(a in set(('A', 'C', 'T', 'G')) for a in allele):\n consAlleles[s] = allele\n else:\n log.warning(\"dropping ambiguous consensus for %s at %s:%s-%s: %s\", s, ref_sequence.id, pos,\n end, allele)\n\n # define genotypes and fractions\n iSNVs = {} # {sample : {allele : fraction, ...}, ...}\n iSNVs_read_depth = {} # {sample: read depth}\n iSNVs_n_libs = {} # {sample : {allele : n libraries > 0, ...}, ...}\n iSNVs_lib_bias = {} # {sample : {allele : pval, ...}, ...}\n for s in samplesToUse:\n # get all rows for this sample and merge allele counts together\n acounts = dict(itertools.chain.from_iterable(row['allele_counts'] for row in rows if\n row['sample'] == s))\n nlibs = dict(itertools.chain.from_iterable(row['n_libs'].items() for row in rows if\n row['sample'] == s))\n libbias = dict(itertools.chain.from_iterable(row['lib_bias'].items() for row in rows if\n row['sample'] == s))\n if 'i' in acounts and 'd' in acounts:\n # This sample has both an insertion line and a deletion line at the same spot!\n # To keep the reference allele from be counted twice, once as an i and once\n # as a d, average the counts and get rid of one of them.\n acounts['i'] = int(round((acounts['i'] + acounts['d']) / 2.0, 0))\n del acounts['d']\n nlibs['i'] = max(nlibs['i'], nlibs['d'])\n libbias['i'] = max(libbias['i'], libbias['d'])\n\n if acounts and s in consAlleles:\n # we have iSNV data on this sample\n consAllele = consAlleles[s]\n tot_n = sum(acounts.values())\n iSNVs[s] = {} # {allele : fraction, ...}\n iSNVs_read_depth[s] = tot_n\n iSNVs_n_libs[s] = {}\n iSNVs_lib_bias[s] = {}\n for orig_a, n in acounts.items():\n f = float(n) / tot_n\n a = orig_a\n if a.startswith('I'):\n # insertion point is relative to each sample\n insert_point = samp_offsets[s] + 1\n a = consAllele[:insert_point] + a[1:] + consAllele[insert_point:]\n elif a.startswith('D'):\n # deletion is the first consensus base, plus remaining\n # consensus seq with the first few positions dropped off\n cut_left = samp_offsets[s] + 1\n cut_right = samp_offsets[s] + 1 + int(a[1:])\n a = consAllele[:cut_left] + consAllele[cut_right:]\n elif a in ('i', 'd'):\n # this is vphaser's way of saying the \"reference\" (majority/consensus)\n # allele, in the face of other indel variants\n a = consAllele\n else:\n # this is a SNP\n if a not in set(('A', 'C', 'T', 'G')):\n raise Exception()\n if f > 0.5 and a != consAllele[samp_offsets[s]]:\n log.warning(\"vPhaser and assembly pipelines mismatch at \"\n \"%s:%d (%s) - consensus %s, vPhaser %s, f %.3f\", ref_sequence.id,\n pos, s, consAllele[samp_offsets[s]], a, f)\n new_allele = list(consAllele)\n new_allele[samp_offsets[s]] = a\n a = ''.join(new_allele)\n if not (a and a == a.upper()):\n raise Exception()\n iSNVs[s][a] = f\n iSNVs_n_libs[s][a] = nlibs[orig_a]\n iSNVs_lib_bias[s][a] = libbias[orig_a]\n if all(len(a) == 1 for a in iSNVs[s].keys()):\n if consAllele not in iSNVs[s]:\n raise Exception(\n \"\"\"at %s:%s (%s), consensus allele %s\n not among iSNV alleles %s -- other cons alleles: %s\"\"\" % (\n ref_sequence.id, pos, s, consAllele, ', '.join(\n iSNVs[s].keys()), ', '.join(\n consAlleles[s])))\n elif s in consAlleles:\n # there is no iSNV data for this sample, so substitute the consensus allele\n iSNVs[s] = {consAlleles[s]: 1.0}\n\n # get unique alleles list for this position, in this order:\n # first: reference allele,\n # next: consensus allele for each sample, in descending order of\n # number of samples with that consensus,\n # finally: all other alleles, sorted first by number of containing samples,\n # then by intrahost read frequency summed over the population,\n # then by the allele string itself.\n alleles_cons = [alleleItem for alleleItem, n in sorted(misc.histogram(consAlleles.values()).items(),\n key=lambda x: x[1],\n reverse=True) if alleleItem != refAllele]\n alleles_isnv = list(itertools.chain.from_iterable(\n [iSNVs[s].items() for s in samplesToUse if s in iSNVs]))\n alleles_isnv2 = []\n for a in set(a for a, n in alleles_isnv):\n counts = list(x[1] for x in alleles_isnv if x[0] == a)\n if len(counts) > 0 and sum(counts) > 0:\n # if we filtered any alleles above, make sure to omit absent alleles\n alleles_isnv2.append((len(counts), sum(counts), a))\n else:\n log.info(\"dropped allele %s at position %s:%s\", a, ref_sequence.id, pos)\n alleles_isnv = list(allele for n_samples, n_reads, allele in reversed(sorted(alleles_isnv2)))\n alleles = list(misc.unique([refAllele] + alleles_cons + alleles_isnv))\n\n # map alleles from strings to numeric indexes\n if not alleles:\n raise Exception()\n elif len(alleles) == 1:\n # if we filtered any alleles above, skip this position if there is no variation left here\n log.info(\"dropped position %s:%s due to lack of variation\", ref_sequence.id, pos)\n continue\n alleleMap = dict((a, i) for i, a in enumerate(alleles))\n # GT col emitted below\n genos = [str(alleleMap.get(consAlleles.get(s), '.')) for s in samplesToUse]\n # AF col emitted below, everything excluding the ref allele (one float per non-ref allele)\n freqs = [(s in iSNVs) and ','.join(map(str, [iSNVs[s].get(a, 0.0) for a in alleles[1:]])) or '.'\n for s in samplesToUse]\n # DP col emitted below\n depths = [str(iSNVs_read_depth.get(s, '.')) for s in samplesToUse]\n # NL col, everything including the ref allele (one int per allele)\n nlibs = [(s in iSNVs_n_libs) and ','.join([str(iSNVs_n_libs[s].get(a, 0)) for a in alleles]) or '.'\n for s in samplesToUse]\n # LB col, everything including the ref allele (one float per allele)\n pvals = [(s in iSNVs_lib_bias) and ','.join([str(iSNVs_lib_bias[s].get(a, '.')) for a in alleles])\n or '.' for s in samplesToUse]\n\n # prepare output row and write to file\n c = ref_sequence.id\n if parse_accession:\n c = genbank.parse_accession_str(c)\n if strip_chr_version:\n c = strip_accession_version(c)\n out = [c, pos, '.', alleles[0], ','.join(alleles[1:]), '.', '.', '.', 'GT:AF:DP:NL:LB']\n out = out + list(map(':'.join, zip(genos, freqs, depths, nlibs, pvals)))\n outf.write('\\t'.join(map(str, out)) + '\\n')\n # compress output if requested\n if outVcf.endswith('.vcf.gz'):\n pysam.tabix_compress(tmpVcf, outVcf, force=True)\n pysam.tabix_index(outVcf, force=True, preset='vcf')\n os.unlink(tmpVcf)\n\n\ndef parser_merge_to_vcf(parser=argparse.ArgumentParser()):\n parser.add_argument(\"refFasta\",\n help=\"\"\"The target reference genome. outVcf will use these\n chromosome names, coordinate spaces, and reference alleles\"\"\")\n parser.add_argument(\"outVcf\", help=\"Output VCF file containing all variants\")\n parser.add_argument(\"--samples\", nargs='*', help=\"A list of sample names\")\n parser.add_argument(\"--isnvs\",\n nargs='+',\n required=True,\n help=\"\"\"A list of file names from the output of vphaser_one_sample\n These must be in the SAME ORDER as samples.\"\"\")\n parser.add_argument(\"--alignments\",\n nargs='+',\n required=True,\n help=\"\"\"a list of fasta files containing multialignment of input\n assemblies, with one file per chromosome/segment. Each alignment\n file will contain a line for each sample, as well as the\n reference genome to which they were aligned.\"\"\")\n parser.add_argument(\"--strip_chr_version\",\n default=False,\n action=\"store_true\",\n dest=\"strip_chr_version\",\n help=\"\"\"If set, strip any trailing version numbers from the\n chromosome names. If the chromosome name ends with a period\n followed by integers, this is interepreted as a version number\n to be removed. This is because Genbank accession numbers are\n often used by SnpEff databases downstream, but without the\n corresponding version number. Default is false (leave\n chromosome names untouched).\"\"\")\n parser.add_argument(\"--naive_filter\",\n default=False,\n action=\"store_true\",\n dest=\"naive_filter\",\n help=\"\"\"If set, keep only the alleles that have at least\n two independent libraries of support and allele freq > 0.005.\n Default is false (do not filter at this stage).\"\"\")\n parser.add_argument(\"--parse_accession\",\n default=False,\n action=\"store_true\",\n dest=\"parse_accession\",\n help=\"\"\"If set, parse only the accession for the chromosome name.\n Helpful if snpEff has to create its own database\"\"\")\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, merge_to_vcf, split_args=True)\n return parser\n\n\n__commands__.append(('merge_to_vcf', parser_merge_to_vcf))\n\n# ===================================================\n\n\ndef compute_Fws(vcfrow):\n format_col = vcfrow[8].split(':')\n if 'AF' not in format_col:\n return None\n af_idx = format_col.index('AF')\n\n freqs = [dat.split(':') for dat in vcfrow[9:]]\n freqs = [float(dat[af_idx].split(',')[0]) for dat in freqs\n if len(dat) > af_idx and dat[af_idx] != '.' and dat[0] != '.' and int(dat[0]) <= 1]\n\n if len(freqs) < 2:\n return None\n\n p_s = sum(freqs) / len(freqs)\n H_s = 2 * p_s * (1.0 - p_s)\n\n if H_s == 0.0:\n return None\n\n H_w = [2 * p * (1.0 - p) for p in freqs]\n H_w = sum(H_w) / len(H_w)\n return (H_s, 1.0 - H_w / H_s)\n\n\ndef add_Fws_vcf(inVcf, outVcf):\n '''Compute the Fws statistic on iSNV data. See Manske, 2012 (Nature)'''\n with open(outVcf, 'wt') as outf:\n with file.open_or_gzopen(inVcf, 'rt') as inf:\n for line in inf:\n if line.startswith('##'):\n outf.write(line)\n elif line.startswith('#'):\n outf.write(\n '##INFO=\\n')\n outf.write(\n '##INFO=\\n')\n outf.write(line)\n else:\n row = line.strip('\\n').split('\\t')\n Fws = compute_Fws(row)\n if Fws is not None:\n row[7] = row[7] + \";PI=%s;FWS=%s\" % Fws\n outf.write('\\t'.join(row) + '\\n')\n\n\ndef parser_Fws(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inVcf\", help=\"Input VCF file\")\n parser.add_argument(\"outVcf\", help=\"Output VCF file\")\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, add_Fws_vcf, split_args=True)\n return parser\n\n\n__commands__.append(('Fws', parser_Fws))\n\n# =================== iSNV_table ================================\n\n\ndef parse_eff(eff_field):\n ''' parse the old snpEff \"EFF\" INFO field '''\n out = {}\n effs = [eff.rstrip(')').replace('(', '|').split('|') for eff in eff_field.split(',')]\n effs = [[eff[i] for i in (0, 3, 4, 5, 6, 9, 11)] for eff in effs]\n effs = [eff for eff in effs if eff[5] not in ('sGP', 'ssGP') and int(eff[6]) < 2]\n if not len(effs) == 1:\n raise Exception()\n eff = effs[0]\n if eff[2]:\n aa = eff[2].split('/')[0]\n assert aa.startswith('p.')\n aa = aa[2:]\n m = re.search(r\"(\\d+)\", aa)\n out['eff_aa_pos'] = int(m.group(1))\n (out['eff_type'], out['eff_codon_dna'], out['eff_aa'], out[\n 'eff_prot_len'\n ], out['eff_gene'], out['eff_protein'], _) = eff # _ is placeholder for rank\n return out\n\n\nclass SnpEffException(Exception):\n pass\n\n\ndef parse_ann(ann_field, alleles, transcript_blacklist=None):\n ''' parse the new snpEff \"ANN\" INFO field '''\n\n transcript_blacklist = transcript_blacklist or set(('GP.2', 'GP.3'))\n\n # only work on alt alleles\n alleles = alleles[1:]\n\n effs = [eff.split('|') for eff in ann_field.split(',')]\n effs = [(eff[0]+\"-\"+eff[6], dict((k, eff[i]) for k, i in (('eff_type', 1), ('eff_gene', 3), ('eff_protein', 6), (\n 'eff_codon_dna', 9), ('eff_aa', 10), ('eff_aa_pos', 13), ('eff_prot_len', 13)))) for eff in effs\n if eff[6] not in transcript_blacklist]\n effs_dict = dict(effs) # effs_dict contains key,val pairs where key is BOTH the alt allele plus each transcript being annotated\n effs_alleles = [ k[:k.index(\"-\")] for k in effs_dict ] # effs_alleles is a non-unique list of all alt alleles to keep track of how many ANNs were processed\n if not effs:\n return {}\n\n if len(effs) != len(effs_alleles): # raises an exception iff an alt allele has more than one annotation for the same transcript; does not error with overlapping transcripts being annotated\n raise SnpEffException(\"ANN field has non-unique alleles\")\n for a in alleles:\n if a not in effs_alleles: # raises an exception iff an alt allele is not found in the ANN field\n raise SnpEffException(\"ANN field is missing ALT allele: \" + a)\n if len(set(effs_alleles)) != len(set(alleles)): # raises an exception if ANN field has different number of unique alleles than alt alleles\n raise SnpEffException(\"ANN field has %s entries, but ALT field has %s unique alleles: %s\" % (\n len(effs), len(set(alleles)), ','.join(alleles)))\n\n out = {}\n for k in ('eff_type', 'eff_codon_dna', 'eff_aa', 'eff_aa_pos', 'eff_prot_len', 'eff_gene', 'eff_protein'):\n a_out = []\n for a in effs_dict:\n v = effs_dict[a][k]\n if k == 'eff_codon_dna' and v.startswith('c.'):\n v = v[2:]\n elif k == 'eff_aa' and v.startswith('p.'):\n v = v[2:]\n elif k == 'eff_aa_pos' and '/' in v:\n v = v.split('/')[0]\n elif k == 'eff_prot_len' and '/' in v:\n v = v.split('/')[1]\n elif k == 'eff_protein' and v == 'GP.1':\n v = 'Glycoprotein'\n if v:\n a_out.append(v)\n out[k] = ','.join(misc.unique(a_out))\n return out\n\n\ndef iSNV_table(vcf_iter):\n for row in vcf_iter:\n info = dict(kv.split('=') for kv in row['INFO'].split(';') if kv and kv != '.')\n samples = [\n k for k in row.keys() if k not in set(\n ('CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT'))\n ]\n # compute Hs: heterozygosity in population based on consensus genotypes alone\n genos = [row[s].split(':')[0] for s in samples]\n genos = misc.histogram(int(gt) for gt in genos if gt != '.')\n n = sum(genos.values())\n Hs = 1.0 - sum(k * k / float(n * n) for k in genos.values())\n try:\n for s in samples:\n f = row[s].split(':')[1]\n if f and f != '.':\n freqs = list(map(float, f.split(',')))\n f = sum(freqs)\n Hw = 1.0 - sum(p * p for p in [1.0 - f] + freqs)\n out = {\n 'chr': row['CHROM'],\n 'pos': row['POS'],\n 'alleles': \"%s,%s\" % (row['REF'], row['ALT']),\n 'sample': s,\n 'iSNV_freq': f,\n 'Hw': Hw,\n 'Hs': Hs\n }\n if 'EFF' in info:\n for k, v in parse_eff(info['EFF']).items():\n out[k] = v\n if 'ANN' in info:\n for k, v in parse_ann(info['ANN'], alleles=out['alleles'].split(',')).items():\n out[k] = v\n if 'PI' in info:\n out['Hs_snp'] = info['PI']\n if 'FWS' in info:\n out['Fws_snp'] = info['FWS']\n yield out\n except:\n log.error(\"VCF parsing error at %s:%s\", row['CHROM'], row['POS'])\n raise\n\n\ndef parser_iSNV_table(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inVcf\", help=\"Input VCF file\")\n parser.add_argument(\"outFile\", help=\"Output text file\")\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, main_iSNV_table)\n return parser\n\n\ndef main_iSNV_table(args):\n '''Convert VCF iSNV data to tabular text'''\n header = ['chr', 'pos', 'sample', 'patient', 'time', 'alleles', 'iSNV_freq', 'Hw', 'Hs', 'eff_type',\n 'eff_codon_dna', 'eff_aa', 'eff_aa_pos', 'eff_prot_len', 'eff_gene', 'eff_protein']\n with file.open_or_gzopen(args.outFile, 'wt') as outf:\n outf.write('\\t'.join(header) + '\\n')\n for row in iSNV_table(file.read_tabfile_dict(args.inVcf)):\n sample_parts = row['sample'].split('.')\n row['patient'] = sample_parts[0]\n if len(sample_parts) > 1:\n row['time'] = sample_parts[1]\n outf.write('\\t'.join(map(str, [row.get(h, '') for h in header])) + '\\n')\n return 0\n\n\n__commands__.append(('iSNV_table', parser_iSNV_table))\n\n# ===================================================\n\n\ndef iSNP_per_patient(table, agg_fun=median):\n data = sorted(table, key=lambda row: (int(row['pos']), row['patient']))\n data = itertools.groupby(data, lambda row: (int(row['pos']), row['patient']))\n for _, rows in data:\n rows = list(rows)\n row = rows[0]\n if set(r['time'] for r in rows if r.get('time')):\n f = agg_fun(list(float(r['iSNV_freq']) for r in rows))\n row['iSNV_freq'] = f\n row['Hw'] = 2 * f * (1.0 - f)\n row['sample'] = row['patient']\n else:\n assert len(rows) == 1, \"error, found multiple rows for %s:%s\" % (row['pos'], row['patient'])\n yield row\n\n\ndef parser_iSNP_per_patient(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inFile\", help=\"Input text file\")\n parser.add_argument(\"outFile\", help=\"Output text file\")\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, main_iSNP_per_patient)\n return parser\n\n\ndef main_iSNP_per_patient(args):\n '''Aggregate tabular iSNP data per patient x position (all time points averaged)'''\n header = ['pos', 'patient', 'alleles', 'iSNV_freq', 'Hw', 'eff_type', 'eff_codon_dna', 'eff_aa', 'eff_aa_pos',\n 'eff_prot_len', 'eff_gene', 'eff_protein']\n with open(args.outFile, 'wt') as outf:\n outf.write('\\t'.join(header) + '\\n')\n for row in iSNP_per_patient(file.read_tabfile_dict(args.inFile)):\n outf.write('\\t'.join(map(str, [row.get(h, '') for h in header])) + '\\n')\n return 0\n\n\n__commands__.append(('iSNP_per_patient', parser_iSNP_per_patient))\n\n# ===================================================\n\n# ===============[ Utility functions ]================\n\n\ndef sampleIDMatch(inputString):\n \"\"\"\n Given a sample name in the form of [sample] or [sample]-#,\n return only [sample]\n \"\"\"\n idRegex = re.compile(r\"(.*?)(?:-\\d+)?$\")\n m = idRegex.match(inputString)\n\n if m:\n return m.group(1)\n else:\n raise LookupError(r\"The ID was not of the form (.*?)(?:-\\d+|$)+, ex. 5985-0\")\n\n\ndef full_parser():\n return cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/kmer_utils.py", "content": "#!/usr/bin/env python3\n\n\"\"\"Commands for working with sets of kmers\"\"\"\n\n\nfrom __future__ import print_function\n__author__ = \"ilya@broadinstitute.org\"\n\n__commands__ = []\n\nimport argparse\nimport logging\nimport functools\n\nfrom .core import cmd\nfrom .core import file\nfrom .core import misc\nfrom . import core\nfrom .core import picard\nfrom .core import samtools\nfrom .classify import kmc\n\nlog = logging.getLogger(__name__) # pylint: disable=invalid-name\n\n# =================================\n\ndef build_kmer_db(seq_files, kmer_db, kmer_size=kmc.DEFAULT_KMER_SIZE, min_occs=1, max_occs=misc.MAX_INT32,\n counter_cap=kmc.DEFAULT_COUNTER_CAP, single_strand=False, mem_limit_gb=8, mem_limit_laxness=0,\n threads=None):\n \"\"\"Build a database of kmers occurring in given sequences.\"\"\"\n kmc.KmcTool().build_kmer_db(**locals())\n\ndef parser_build_kmer_db(parser=argparse.ArgumentParser()):\n \"\"\"Create parser for build_kmer_db\"\"\"\n parser.add_argument('seq_files', nargs='+',\n help='Files from which to extract kmers (fasta/fastq/bam, fasta/fastq may be .gz or .bz2)')\n parser.add_argument('kmer_db', help='kmer database (with or without .kmc_pre/.kmc_suf suffix)')\n parser.add_argument('--kmerSize', '-k', dest='kmer_size', type=int, default=kmc.DEFAULT_KMER_SIZE,\n help='kmer size')\n parser.add_argument('--minOccs', '-ci', dest='min_occs', type=int, default=1,\n help='drop kmers with fewer than this many occurrences')\n parser.add_argument('--maxOccs', '-cx', dest='max_occs', type=int, default=misc.MAX_INT32,\n help='drop kmers with more than this many occurrences')\n parser.add_argument('--counterCap', '-cs', dest='counter_cap', type=int,\n default=kmc.DEFAULT_COUNTER_CAP, help='cap kmer counts at this value')\n parser.add_argument('--singleStrand', '-b', dest='single_strand', default=False, action='store_true',\n help='do not add kmers from reverse complements of input sequences')\n parser.add_argument('--memLimitGb', dest='mem_limit_gb', default=8, type=int, help='Max memory to use, in GB')\n parser.add_argument('--memLimitLaxness', dest='mem_limit_laxness', default=0, type=int, choices=(0, 1, 2),\n help='How strict is --memLimitGb? 0=strict, 1=lax, 2=even more lax')\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, build_kmer_db, split_args=True)\n return parser\n\n__commands__.append(('build_kmer_db', parser_build_kmer_db))\n\n# =========================\n\ndef dump_kmer_counts(kmer_db, out_kmers, min_occs=1, max_occs=misc.MAX_INT32, threads=None):\n \"\"\"Dump kmers and their counts from kmer database to a text file\"\"\"\n kmc.KmcTool().dump_kmer_counts(**locals())\n\ndef parser_dump_kmer_counts(parser=argparse.ArgumentParser()):\n \"\"\"Create parser for dump_kmer_counts\"\"\"\n parser.add_argument('kmer_db', help='kmer database (with or without .kmc_pre/.kmc_suf suffix)')\n parser.add_argument('out_kmers', help='text file to which to write the kmers')\n parser.add_argument('--minOccs', '-ci', dest='min_occs', type=int, default=1,\n help='drop kmers with fewer than this many occurrences')\n parser.add_argument('--maxOccs', '-cx', dest='max_occs', type=int, default=misc.MAX_INT32,\n help='drop kmers with more than this many occurrences')\n\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, dump_kmer_counts, split_args=True)\n return parser\n\n__commands__.append(('dump_kmer_counts', parser_dump_kmer_counts))\n\n# =========================\n\ndef filter_reads(kmer_db, in_reads, out_reads, db_min_occs=1, db_max_occs=misc.MAX_INT32,\n read_min_occs=0, read_max_occs=misc.MAX_INT32, \n read_min_occs_frac=0.0, read_max_occs_frac=1.0, hard_mask=False, threads=None):\n \"\"\"Filter reads based on their kmer contents.\n\n Can also be used to filter contigs or reference sequences, but we'll refer to filtering of reads\n in the documentation.\n\n Note that \"occurrence of a kmer\" means \"occurrence of the kmer or its reverse complement\" if kmer_db was built\n with single_strand==False.\n\n Inputs:\n kmer_db: the kmc kmer database\n in_reads: the reads to filter. can be a .fasta or .fastq or .bam; fasta or fastq can be compressed\n with gzip or bzip2. If a .bam, a read pair is kept if either mate passes the filter.\n\n Outputs:\n out_reads: file to which filtered reads are written. type is determined from extension,\n same types as above are supported.\n\n Params:\n db_min_occs: only consider database kmers with at least this count\n db_max_occs: only consider database kmers with at most this count\n\n read_min_occs: only keep reads with at least this many occurrences of kmers from database.\n read_max_occs: only keep reads with no more than this many occurrence of kmers from the database.\n read_min_occs_frac: only keep reads with at least this many occurrences of kmers from database,\n interpreted as a fraction of read length in kmers\n read_max_occs_frac: only keep reads with no more than this many occurrence of kmers from the database.\n interpreted as a fraction of read length in kmers.\n\n (Note: minimal read kmer content can be given as absolute counts or fraction of read length, but not both).\n\n hard_mask: if True, in the output reads, kmers not passing the filter are replaced by Ns\n threads: use this many threads\n \"\"\"\n kmc.KmcTool().filter_reads(**locals())\n\ndef parser_filter_reads(parser=argparse.ArgumentParser()):\n \"\"\"Create parser for filter_reads\"\"\"\n parser.add_argument('kmer_db', help='kmer database (with or without .kmc_pre/.kmc_suf suffix)')\n parser.add_argument('in_reads', help='input reads, as fasta/fastq/bam')\n parser.add_argument('out_reads', help='output reads')\n parser.add_argument('--dbMinOccs', dest='db_min_occs', type=int, default=1,\n help='ignore datatbase kmers with count below this')\n parser.add_argument('--dbMaxOccs', dest='db_max_occs', type=int, default=misc.MAX_INT32,\n help='ignore datatbase kmers with count above this')\n parser.add_argument('--readMinOccs', dest='read_min_occs', type=int, default=0,\n help='filter out reads with fewer than this many db kmers')\n parser.add_argument('--readMaxOccs', dest='read_max_occs', type=int, default=misc.MAX_INT32,\n help='filter out reads with more than this many db kmers')\n parser.add_argument('--readMinOccsFrac', dest='read_min_occs_frac', type=float, default=0.0,\n help='filter out reads with fewer than this many db kmers, '\n 'interpreted as fraction of read length')\n parser.add_argument('--readMaxOccsFrac', dest='read_max_occs_frac', type=float, default=1.0,\n help='filter out reads with more than this many db kmers, '\n 'interpreted as fraction of read length')\n parser.add_argument('--hardMask', dest='hard_mask', default=False,\n action='store_true',\n help='In the output reads, mask the invalid kmers')\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, filter_reads, split_args=True)\n return parser\n\n__commands__.append(('filter_reads', parser_filter_reads))\n\n# =========================\n\ndef kmers_binary_op(op, kmer_db1, kmer_db2, kmer_db_out,\n result_min_occs=1, result_max_occs=misc.MAX_INT32,\n result_counter_cap=kmc.DEFAULT_COUNTER_CAP, threads=None): # pylint: disable=invalid-name\n \"\"\"Perform a simple binary operation on kmer sets.\"\"\"\n\n kmc.KmcTool().kmers_binary_op(**locals())\n\ndef parser_kmers_binary_op(parser=argparse.ArgumentParser()):\n \"\"\"Create parser forkmers_binary_op\"\"\"\n parser.add_argument('op', choices=('intersect', 'union', 'kmers_subtract', 'counters_subtract'),\n help='binary operation to perform')\n parser.add_argument('kmer_db1', help='first kmer set')\n parser.add_argument('kmer_db2', help='second kmer set')\n parser.add_argument('kmer_db_out', help='output kmer db')\n parser.add_argument('--resultMinOccs', dest='result_min_occs', type=int, default=1,\n help='from the result drop kmers with counts below this')\n parser.add_argument('--resultMaxOccs', dest='result_max_occs', type=int, default=misc.MAX_INT32,\n help='from the result drop kmers with counts above this')\n parser.add_argument('--resultCounterCap', dest='result_counter_cap', type=int, default=kmc.DEFAULT_COUNTER_CAP,\n help='cap output counters at this value')\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kmers_binary_op, split_args=True)\n return parser\n\n__commands__.append(('kmers_binary_op', parser_kmers_binary_op))\n\n# =========================\n\ndef kmers_set_counts(kmer_db_in, value, kmer_db_out, threads=None):\n \"\"\"Copy the kmer database, setting all kmer counts in the output to the given value.\"\"\"\n\n kmc.KmcTool().set_kmer_counts(**locals())\n\ndef parser_kmers_set_counts(parser=argparse.ArgumentParser()):\n \"\"\"Create parser for kmers_set_counts\"\"\"\n parser.add_argument('kmer_db_in', help='input kmer db')\n parser.add_argument('value', type=int, help='all kmer counts in the output will be set to this value')\n parser.add_argument('kmer_db_out', help='output kmer db')\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kmers_set_counts, split_args=True)\n return parser\n\n__commands__.append(('kmers_set_counts', parser_kmers_set_counts))\n\n# ========================\n\ndef full_parser():\n \"\"\"Create parser for all commands in kmers.py\"\"\"\n return cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/metagenomics.py", "content": "#!/usr/bin/env python3\n''' This script contains a number of utilities for metagenomic analyses.\n'''\nfrom __future__ import print_function\nfrom __future__ import division\n\n__author__ = \"yesimon@broadinstitute.org\"\n\nimport argparse\nimport collections\nimport csv\nimport glob\nimport gzip\nimport io\nimport itertools\nimport logging\nimport os.path\nimport operator\nimport queue\nimport re\nimport shutil\nimport sys\nimport tempfile\nimport json\n\nfrom Bio import SeqIO\nfrom Bio.Seq import Seq\nfrom Bio.SeqRecord import SeqRecord\n\nimport anndata\nimport numpy as np\nimport pandas as pd\nimport pysam\n\nfrom .core import cmd\nfrom .core import file\nfrom .core import misc\nfrom . import read_utils\n\nfrom .classify import kma\nfrom .classify import kraken2\nfrom .classify import krona\nfrom .classify import kb\nfrom .classify.taxonomy import (\n TaxIdError, TaxonomyDb, BlastRecord, blast_records, paired_query_id,\n blast_m8_taxids, extract_tax_id, coverage_lca, parents_to_children,\n maybe_compressed, rank_code\n)\n\n__commands__ = []\n\nlog = logging.getLogger(__name__)\n\n\ndef tree_level_lookup(parents, node, level_cache):\n '''Get the node level/depth.\n\n Args:\n parents: Array of node parents.\n node: Node to get level (root == 1).\n level_cache: Cache of previously found levels.\n\n Returns:\n (int) level of node\n '''\n path = []\n while True:\n level = level_cache.get(node)\n if level:\n for i, node in enumerate(reversed(path)):\n level_cache[node] = level + i + 1\n return level + len(path)\n path.append(node)\n node = parents[node]\n\n\ndef push_up_tree_hits(parents, hits, min_support_percent=None, min_support=None, update_assignments=False):\n '''Push up hits on nodes until min support is reached.\n\n Args:\n parents: Array of node parents.\n hits: Counter of hits on each node.\n min_support_percent: Push up hits until each node has\n this percent of the sum of all hits.\n min_support: Push up hits until each node has this number of hits.\n\n Returns:\n (counter) Hits mutated pushed up the tree.\n '''\n assert min_support_percent or min_support\n\n if update_assignments:\n pass\n\n total_hits = sum(hits.values())\n if not min_support:\n min_support = round(min_support_percent * 0.01 * total_hits)\n pq_level = queue.PriorityQueue()\n level_cache = {1: 1}\n for hit_id, num_hits in hits.items():\n if num_hits < min_support:\n pq_level.put((-tree_level_lookup(parents, hit_id, level_cache), hit_id))\n\n while not pq_level.empty() > 0:\n level, hit_id = pq_level.get()\n level = -level\n\n if hits[hit_id] >= min_support:\n continue\n if hit_id == 1:\n del hits[1]\n break\n\n parent_hit_id = parents[hit_id]\n num_hits = hits[hit_id]\n hits[parent_hit_id] += num_hits\n # Can't pop directly from hits because hit_id might not be stored in counter\n if hit_id in hits:\n del hits[hit_id]\n if hits[parent_hit_id] < min_support:\n pq_level.put((-tree_level_lookup(parents, parent_hit_id, level_cache), parent_hit_id))\n return hits\n\n\ndef file_lines(filename):\n if filename is not None:\n with open(filename) as f:\n for line in f:\n yield line\n\n\ndef collect_children(children, original_taxids):\n '''Collect nodes with all children recursively.'''\n taxids = original_taxids\n while taxids:\n taxid = taxids.pop()\n yield taxid\n for child_taxid in children[taxid]:\n taxids.add(child_taxid)\n\n\ndef collect_parents(parents, taxids):\n '''Collect nodes with all parents recursively.'''\n # The root taxid node is 1\n yield 1\n taxids_with_parents = set([1])\n for taxid in taxids:\n while taxid not in taxids_with_parents:\n yield taxid\n taxids_with_parents.add(taxid)\n taxid = parents[taxid]\n\n\ndef parser_subset_taxonomy(parser=argparse.ArgumentParser()):\n parser.add_argument(\n \"taxDb\",\n help=\"Taxonomy database directory (containing nodes.dmp, parents.dmp etc.)\",\n )\n parser.add_argument(\n \"outputDb\",\n help=\"Output taxonomy database directory\",\n )\n parser.add_argument(\n \"--whitelistTaxids\",\n help=\"List of taxids to add to taxonomy (with parents)\",\n nargs='+', type=int\n )\n parser.add_argument(\n \"--whitelistTaxidFile\",\n help=\"File containing taxids - one per line - to add to taxonomy with parents.\",\n )\n parser.add_argument(\n \"--whitelistTreeTaxids\",\n help=\"List of taxids to add to taxonomy (with parents and children)\",\n nargs='+', type=int\n )\n parser.add_argument(\n \"--whitelistTreeTaxidFile\",\n help=\"File containing taxids - one per line - to add to taxonomy with parents and children.\",\n )\n parser.add_argument(\n \"--whitelistGiFile\",\n help=\"File containing GIs - one per line - to add to taxonomy with nodes.\",\n )\n parser.add_argument(\n \"--whitelistAccessionFile\",\n help=\"File containing accessions - one per line - to add to taxonomy with nodes.\",\n )\n parser.add_argument(\n \"--skipGi\", action='store_true',\n help=\"Skip GI to taxid mapping files\"\n )\n parser.add_argument(\n \"--skipAccession\", action='store_true',\n help=\"Skip accession to taxid mapping files\"\n )\n parser.add_argument(\n \"--skipDeadAccession\", action='store_true',\n help=\"Skip dead accession to taxid mapping files\"\n )\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, subset_taxonomy, split_args=True)\n return parser\ndef subset_taxonomy(taxDb, outputDb, whitelistTaxids=None, whitelistTaxidFile=None,\n whitelistTreeTaxids=None, whitelistTreeTaxidFile=None,\n whitelistGiFile=None, whitelistAccessionFile=None,\n skipGi=None, skipAccession=None, skipDeadAccession=None,\n stripVersion=True):\n '''\n Generate a subset of the taxonomy db files filtered by the whitelist. The\n whitelist taxids indicate specific taxids plus their parents to add to\n taxonomy while whitelistTreeTaxids indicate specific taxids plus both\n parents and all children taxa. Whitelist GI and accessions can only be\n provided in file form and the resulting gi/accession2taxid files will be\n filtered to only include those in the whitelist files. Finally, taxids +\n parents for the gis/accessions will also be included.\n '''\n file.mkdir_p(os.path.join(outputDb, 'accession2taxid'))\n db = TaxonomyDb(tax_dir=taxDb, load_nodes=True)\n\n taxids = set()\n if whitelistTaxids is not None:\n taxids.update(set(whitelistTaxids))\n taxids.update((int(x) for x in file_lines(whitelistTaxidFile)))\n\n tree_taxids = set()\n if whitelistTreeTaxids is not None:\n tree_taxids.update(set(whitelistTreeTaxids))\n taxids.update((int(x) for x in file_lines(whitelistTreeTaxidFile)))\n keep_taxids = set(collect_parents(db.parents, taxids))\n\n if tree_taxids:\n db.children = parents_to_children(db.parents)\n children_taxids = collect_children(db.children, tree_taxids)\n keep_taxids.update(children_taxids)\n\n # Taxids kept based on GI or Accession. Get parents afterwards to not pull in all GIs/accessions.\n keep_seq_taxids = set()\n def filter_file(path, sep='\\t', taxid_column=0, gi_column=None, a2t=False, header=False):\n input_path = os.path.join(db.tax_dir, path)\n output_path = os.path.join(outputDb, path)\n\n input_path = maybe_compressed(input_path)\n with file.open_or_gzopen(input_path, 'rt') as f, \\\n file.open_or_gzopen(output_path, 'wt') as out_f:\n if header:\n out_f.write(f.readline()) # Cannot use next(f) for python2\n for line in f:\n parts = line.split(sep)\n taxid = int(parts[taxid_column])\n if gi_column is not None:\n gi = int(parts[gi_column])\n if gi in gis:\n keep_seq_taxids.add(taxid)\n out_f.write(line)\n continue\n if a2t:\n accession = parts[accession_column_i]\n if stripVersion:\n accession = accession.split('.', 1)[0]\n if accession in accessions:\n keep_seq_taxids.add(taxid)\n out_f.write(line)\n continue\n if taxid in keep_taxids:\n out_f.write(line)\n\n if not skipGi:\n gis = set(int(x) for x in file_lines(whitelistGiFile))\n\n filter_file('gi_taxid_nucl.dmp', taxid_column=1, gi_column=0)\n filter_file('gi_taxid_prot.dmp', taxid_column=1, gi_column=0)\n\n if not skipAccession:\n if stripVersion:\n accessions = set(x.strip().split('.', 1)[0] for x in file_lines(whitelistAccessionFile))\n accession_column_i = 0\n else:\n accessions = set(file_lines(whitelistAccessionFile))\n accession_column_i = 1\n\n acc_dir = os.path.join(db.tax_dir, 'accession2taxid')\n acc_paths = []\n for fn in os.listdir(acc_dir):\n if fn.endswith('.accession2taxid') or fn.endswith('.accession2taxid.gz'):\n if skipDeadAccession and fn.startswith('dead_'):\n continue\n acc_paths.append(os.path.join(acc_dir, fn))\n for acc_path in acc_paths:\n filter_file(os.path.relpath(acc_path, db.tax_dir), taxid_column=2, header=True, a2t=True)\n\n\n # Add in taxids found from processing GI/accession\n keep_seq_taxids = collect_parents(db.parents, keep_seq_taxids)\n keep_taxids.update(keep_seq_taxids)\n\n filter_file('nodes.dmp', sep='|')\n filter_file('names.dmp', sep='|')\n filter_file('merged.dmp')\n filter_file('delnodes.dmp')\n__commands__.append(('subset_taxonomy', parser_subset_taxonomy))\n\n\ndef parser_filter_taxids_to_focal_hits(parser=argparse.ArgumentParser()):\n parser.add_argument(\"taxids_tsv\", help=\"TSV file where first column is a taxid\")\n parser.add_argument(\"focal_report_tsv\", help=\"TSV produced by taxlevel_plurality\")\n parser.add_argument(\"taxdb_dir\", help=\"Taxonomy database directory (containing nodes.dmp, parents.dmp etc.)\")\n parser.add_argument(\"min_read_count\", type=int, help=\"ignore focal_report_tsv entries below this read count\")\n parser.add_argument(\"output_tsv\", help=\"Output TSV file where first column is a taxid\")\n\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, filter_taxids_to_focal_hits, split_args=True)\n return parser\ndef filter_taxids_to_focal_hits(taxids_tsv, focal_report_tsv, taxdb_dir, min_read_count, output_tsv):\n '''\n Generate a subset of the taxids_tsv file filtered by the focal_report_tsv.\n We will only emit rows from the taxids_tsv that contain taxids that are either\n contained within or are a child/descendant of nodes contained within the\n focal_report_tsv\n '''\n\n # load taxonomy database structure\n taxdb = TaxonomyDb(tax_dir=taxdb_dir, load_nodes=True, load_gis=False)\n\n # load focal hits\n hits = set()\n with file.open_or_gzopen(focal_report_tsv, \"rt\") as inf:\n for row in csv.DictReader(inf, delimiter='\\t'):\n if int(row['reads_excl_children']) >= min_read_count:\n hits.add(int(row['taxon_id']))\n\n # filter taxids_tsv -> output_tsv\n with file.open_or_gzopen(taxids_tsv, \"rt\") as inf:\n with file.open_or_gzopen(output_tsv, \"wt\") as outf:\n for line in inf:\n taxid = int(line.rstrip('\\r\\n').split('\\t')[0])\n ancestors = taxdb.get_ordered_ancestors(taxid)\n if any(node in hits for node in [taxid] + ancestors):\n outf.write(line)\n\n__commands__.append(('filter_taxids_to_focal_hits', parser_filter_taxids_to_focal_hits))\n\n\ndef taxa_hits_from_tsv(f, taxid_column=2):\n '''Return a counter of hits from tsv.'''\n c = collections.Counter()\n for row in csv.reader(f, delimiter='\\t'):\n tax_id = int(row[taxid_column - 1])\n c[tax_id] += 1\n return c\n\n\ndef parser_kraken2(parser=argparse.ArgumentParser()):\n parser.add_argument('db', help='Kraken database directory.')\n parser.add_argument('inBams', nargs='+', help='Input unaligned reads, BAM format.')\n parser.add_argument('--outReports', nargs='+', help='Kraken2 summary report output file. Multiple filenames space separated.')\n parser.add_argument('--outReads', nargs='+', help='Kraken2 per read classification output file. Multiple filenames space separated.')\n parser.add_argument(\n '--minimum_hit_groups', default=None, type=int, help='Minimum hit groups (Kraken2 default: 2)'\n )\n parser.add_argument(\n '--min_base_qual', default=None, type=int, help='Minimum base quality (default %(default)s)'\n )\n parser.add_argument(\n '--confidence', default=None, type=float, help='Kraken2 confidence score threshold (default %(default)s)'\n )\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_kraken2, split_args=True)\n return parser\ndef main_kraken2(db, inBams, outReports=None, outReads=None, min_base_qual=None, confidence=None, minimum_hit_groups=None, threads=None):\n '''\n Classify reads by taxon using Kraken2\n '''\n\n assert outReads or outReports, ('Either --outReads or --outReport must be specified.')\n kraken_tool = kraken2.Kraken2()\n kraken_tool.pipeline(db, inBams, out_reports=outReports, out_reads=outReads,\n min_base_qual=min_base_qual, confidence=confidence,\n minimum_hit_groups=minimum_hit_groups, num_threads=threads)\n__commands__.append(('kraken2', parser_kraken2))\n\n\ndef parser_kb(parser=argparse.ArgumentParser()):\n \"\"\"Argument parser for the kb_python wrapper.\n\n Args:\n parser (_type_, optional): _description_. Defaults to argparse.ArgumentParser().\n\n Returns:\n argparse.ArgumentParser: The parser with arguments added.\n \"\"\"\n parser.add_argument('in_bam', help='Input unaligned reads, BAM format.')\n parser.add_argument('--index', help='kb index file.')\n parser.add_argument('--t2g', help='Input unaligned reads, BAM format.')\n parser.add_argument('--kmer_len', type=int, help='k-mer size (default: 31bp)', default=31)\n parser.add_argument('--parity', choices=['single', 'paired'], help='Library parity (default: single)', default='single')\n parser.add_argument('--technology', choices=['10xv2', '10xv3', '10xv3-3prime', '10xv3-5prime', 'dropseq', \n 'indrop', 'celseq', 'celseq2', 'smartseq2', 'bulk'], \n help='Technology used to generate the data (default: bulk)', default='bulk')\n parser.add_argument('--h5ad', action='store_true', help='Output HDF5 file (default: False)', default=False)\n parser.add_argument('--loom', action='store_true', help='Output Loom file (default: False)', default=False)\n parser.add_argument('--protein', action='store_true', help='True if sequence contains amino acids (default: False).')\n parser.add_argument('--out_dir', help='Output directory (default: kb_out)', default='kb_out')\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kb_python, split_args=True)\n return parser\ndef kb_python(in_bam, index=None, t2g=None, kmer_len=31, parity='single', technology='bulk', h5ad=False, loom=False, protein=False, out_dir=None, threads=None):\n \"\"\"Runs kb count on the input BAM files.\n\n Args:\n in_bam (list): List of input BAM files.\n out_dir (str): Output directory. Defaults to None.\n index (str): Path to the kb index file.\n t2g (list|str): Transcript-to-gene mapping file(s).\n kmer_len (int, optional): K-mer size for the alignment. Defaults to 31.\n parity (str, optional): Library parity (default: single). Defaults to 'single'.\n technology (str, optional): Sequencing technology used. Defaults to 'bulk'.\n h5ad (bool, optional): Whether to output HDF5 file. Defaults to False.\n loom (bool, optional): Whether to output Loom file. Defaults to False.\n protein (bool, optional): Whether the sequence contains amino acids. Defaults to False.\n threads (int, optional): Number of threads to use. Defaults to None.\n \"\"\"\n\n assert out_dir, ('Output directory must be specified.')\n kb_tool = kb.kb()\n kb_tool.classify(\n in_bam=in_bam,\n out_dir=out_dir,\n index_file=index,\n t2g_file=t2g,\n k=kmer_len,\n parity=parity,\n technology=technology,\n h5ad=h5ad,\n loom=loom,\n protein=protein,\n num_threads=threads\n )\n__commands__.append(('kb', parser_kb))\n\ndef parser_kma(parser=argparse.ArgumentParser()):\n parser.add_argument('db', help='KMA database prefix.')\n parser.add_argument('inBams', nargs='+', help='Input unaligned reads, BAM format.')\n parser.add_argument('--outPrefixes', nargs='+', help='KMA output prefixes.')\n parser.add_argument('--threads', type=int, help='Number of threads.')\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_kma, split_args=True)\n return parser\n\ndef main_kma(db, inBams, outPrefixes=None, threads=None):\n if outPrefixes and len(inBams) != len(outPrefixes):\n raise ValueError(f\"Number of input BAMs ({len(inBams)}) must match number of output prefixes ({len(outPrefixes)})\")\n kma_tool = kma.KMA()\n for in_bam, out_prefix in itertools.zip_longest(inBams, outPrefixes):\n kma_tool.classify(in_bam, db, out_prefix, num_threads=threads)\n\n__commands__.append(('kma', parser_kma))\n\ndef parser_kma_build(parser=argparse.ArgumentParser()):\n parser.add_argument('ref_fasta', help='Reference FASTA file.')\n parser.add_argument('db_prefix', help='Output database prefix.')\n parser.add_argument('--threads', type=int, help='Number of threads.')\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_kma_build, split_args=True)\n return parser\n\ndef main_kma_build(ref_fasta, db_prefix, threads=None):\n kma_tool = kma.KMA()\n kma_tool.build(ref_fasta, db_prefix, num_threads=threads)\n\n__commands__.append(('kma_build', parser_kma_build))\n\n\ndef parser_krona(parser=argparse.ArgumentParser()):\n parser.add_argument('inReports', nargs='+', help='Input report file (default: tsv)')\n parser.add_argument('db', help='Krona taxonomy database directory.')\n parser.add_argument('outHtml', help='Output html report.')\n parser.add_argument('--sample_name', help='Title of dataset (default basename(inReport))', default=None)\n parser.add_argument('--queryColumn', help='Column of query id. (default %(default)s)', type=int, default=2)\n parser.add_argument('--taxidColumn', help='Column of taxonomy id. (default %(default)s)', type=int, default=3)\n parser.add_argument('--scoreColumn', help='Column of score. (default %(default)s)', type=int, default=None)\n parser.add_argument('--magnitudeColumn', help='Column of magnitude. (default %(default)s)', type=int, default=None)\n parser.add_argument('--noHits', help='Include wedge for no hits.', action='store_true')\n parser.add_argument('--noRank', help='Include no rank assignments.', action='store_true')\n parser.add_argument('--inputType', help='Handling for specialized report types.', default='tsv', choices=['tsv', 'kraken2'])\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, main_krona, split_args=True)\n return parser\ndef main_krona(inReports, db, outHtml, queryColumn=None, taxidColumn=None, scoreColumn=None, magnitudeColumn=None, noHits=None, noRank=None,\n inputType=None, sample_name=None):\n '''\n Create an interactive HTML report from a tabular metagenomic report\n '''\n\n krona_tool = krona.Krona()\n if sample_name is not None:\n dataset_names = list(sample_name for fn in inReports)\n else:\n dataset_names = list(os.path.basename(fn) for fn in inReports)\n\n with file.tmp_dir() as tmp_dir:\n to_import = []\n\n if inputType == 'tsv':\n for inReport in inReports:\n if inReport.endswith('.gz'):\n tmp_tsv = file.mkstempfname('.tsv', directory=tmp_dir)\n with gzip.open(inReport, 'rb') as f_in:\n with open(tmp_tsv, 'w') as f_out:\n shutil.copyfileobj(f_in, f_out)\n to_import.append(tmp_tsv)\n else:\n to_import.append(inReport)\n\n elif inputType == 'kraken2':\n queryColumn=None\n taxidColumn=5\n scoreColumn=None\n magnitudeColumn=3\n to_import = inReports\n\n else:\n raise NotImplementedError\n\n # run krona\n krona_tool.import_taxonomy(\n db,\n list(','.join(pair) for pair in zip(to_import, dataset_names)),\n outHtml,\n query_column=queryColumn,\n taxid_column=taxidColumn,\n score_column=scoreColumn,\n magnitude_column=magnitudeColumn,\n no_hits=noHits,\n no_rank=noRank\n )\n\n__commands__.append(('krona', parser_krona))\n\n\ndef parser_metagenomic_report_merge(parser=argparse.ArgumentParser()):\n parser.add_argument(\n \"metagenomic_reports\",\n help=\"Input metagenomic reports with the query ID and taxon ID in the 2nd and 3rd columns (Kraken format)\",\n nargs='+',\n type=argparse.FileType('r')\n )\n parser.add_argument(\n \"out_krona_input\",\n help=\"Output metagenomic report suitable for Krona input.\"\n )\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, metagenomic_report_merge, split_args=True)\n return parser\ndef metagenomic_report_merge(metagenomic_reports, out_krona_input):\n '''\n Merge multiple metagenomic reports into a single metagenomic report suitable for Krona input.\n '''\n with file.open_or_gzopen(out_krona_input, \"wt\") as outf:\n output_writer = csv.writer(outf, delimiter='\\t', lineterminator='\\n')\n for metag_file in metagenomic_reports:\n with file.open_or_gzopen(metag_file.name, \"rt\") as inf:\n file_reader = csv.reader(inf, delimiter='\\t')\n for row in file_reader:\n output_writer.writerow([f for f in row])\n__commands__.append(('report_merge', parser_metagenomic_report_merge))\n\n\ndef parser_filter_bam_to_taxa(parser=argparse.ArgumentParser()):\n parser.add_argument('in_bam', help='Input bam file.')\n parser.add_argument('read_IDs_to_tax_IDs', help='TSV file mapping read IDs to taxIDs, Kraken-format by default. Assumes bijective mapping of read ID to tax ID.')\n parser.add_argument('out_bam', help='Output bam file, filtered to the taxa specified')\n parser.add_argument('nodes_dmp', help='nodes.dmp file from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/')\n parser.add_argument('names_dmp', help='names.dmp file from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/')\n parser.add_argument('--exclude', action='store_true', dest=\"exclude\", help='Switch filtration to remove all reads falling under matching taxa (and keep all non-matching). Default is the inverse: keep all reads falling under matching taxa (and remove all non-matching).')\n parser.add_argument('--taxNames', nargs=\"+\", dest=\"tax_names\", help='The taxonomic names to include. More than one can be specified. Mapped to Tax IDs by lowercase exact match only. Ex. \"Viruses\" This is in addition to any taxonomic IDs provided.')\n parser.add_argument('--taxIDs', nargs=\"+\", type=int, dest=\"tax_ids\", help='The NCBI taxonomy IDs to include. More than one can be specified. This is in addition to any taxonomic names provided.')\n parser.add_argument('--without-children', action='store_true', dest=\"omit_children\", help='Omit reads classified more specifically than each taxon specified (without this a taxon and its children are included).')\n parser.add_argument('--read_id_col', type=int, dest=\"read_id_col\", help='The (zero-indexed) number of the column in read_IDs_to_tax_IDs containing read IDs. (default: %(default)s)', default=1)\n parser.add_argument('--tax_id_col', type=int, dest=\"tax_id_col\", help='The (zero-indexed) number of the column in read_IDs_to_tax_IDs containing Taxonomy IDs. (default: %(default)s)', default=2)\n parser.add_argument('--out_count', help='Write a file with the number of reads matching the specified taxa.')\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, filter_bam_to_taxa, split_args=True)\n return parser\n\ndef filter_bam_to_taxa(in_bam, read_IDs_to_tax_IDs, out_bam,\n nodes_dmp, names_dmp,\n exclude=False,\n tax_names=None, tax_ids=None,\n omit_children=False,\n read_id_col=1, tax_id_col=2,\n out_count=None):\n \"\"\"\n Filter an (already classified) input bam file to only include reads that have been mapped to specified\n taxonomic IDs or scientific names. This requires a classification file, as produced\n by tools such as Kraken, as well as the NCBI taxonomy database.\n \"\"\"\n tax_ids = set(tax_ids) if tax_ids else set()\n tax_names = tax_names or []\n # use TaxonomyDb() class above and tree traversal/collection functions above\n db = TaxonomyDb(nodes_path=nodes_dmp, names_path=names_dmp, load_nodes=True, load_names=True)\n db.children = parents_to_children(db.parents)\n\n paired_read_base_pattern = re.compile(r'^(.*?)(/[1-2])?$')\n\n # get taxIDs for each of the heading values specifed (exact matches only)\n tax_ids_from_headings = set()\n for heading in tax_names:\n # map heading to taxID\n name_pattern = re.compile(heading, flags=re.IGNORECASE)\n for row_tax_id, names in db.names.items():\n found_heading = False\n if type(names) != list:\n # if taxID->str, create list (of names) with cardinality=1\n names = [names]\n for name in names:\n if name_pattern.match(name):\n tax_ids_from_headings.add(row_tax_id)\n log.debug(\"Found taxName match: %s -> %s\" % (row_tax_id,name))\n found_heading = True\n break\n if found_heading:\n break\n\n tax_ids |= tax_ids_from_headings\n\n log.debug(\"tax_ids %s\", tax_ids)\n log.debug(\"tax_names %s\", tax_names)\n\n # extend tax_ids to include IDs of children\n tax_ids_to_include = set()\n for tax_id in tax_ids:\n tax_ids_to_include.add(tax_id)\n if not omit_children:\n child_ids = collect_children(db.children, set([tax_id]))\n tax_ids_to_include |= set(child_ids)\n\n tax_ids_to_include = frozenset(tax_ids_to_include) # frozenset membership check slightly faster\n log.info(\"matching against {} taxa\".format(len(tax_ids_to_include)))\n\n def _matching_read_ids():\n \"\"\"Generator that yields read IDs matching the specified taxa.\"\"\"\n for row in file.read_tabfile(read_IDs_to_tax_IDs):\n assert tax_id_col=count_threshold:\n sample_summary[currently_being_processed][row[\"sci_name\"]] = Abundance(float(row[\"pct_of_reads\"]), int(row[\"num_reads\"]),row.get(\"kmers\",None),row.get(\"dup\",None),row.get(\"cov\",None))\n\n\n for k,taxa in sample_summary.items():\n sample_summary[k] = collections.OrderedDict(sorted(taxa.items(), key=lambda item: (item[1][1]) , reverse=True)[:top_n_entries])\n\n if len(list(sample_summary[k].items()))>0:\n log.info(\"{f}: most abundant among {heading} at the {level} level: \"\n \"\\\"{name}\\\" with {reads} reads ({percent:.2%} of total); \"\n \"included since >{threshold} read{plural}\".format(\n f=f,\n heading=k,\n level=taxlevel_focus,\n name=list(sample_summary[k].items())[0][0],\n reads=list(sample_summary[k].items())[0][1].count,\n percent=list(sample_summary[k].items())[0][1].percent/100.0,\n threshold=count_threshold,\n plural=\"s\" if count_threshold>1 else \"\" )\n )\n\n if include_root:\n # include root-level bins (root, unclassified) in the returned data\n for k,taxa in sample_root_summary.items():\n assert (k not in sample_summary), \"{k} already in sample summary\".format(k=k)\n sample_summary[k] = taxa\n samples[sample_name] = sample_summary\n\n if json_out != None:\n json_summary = json.dumps(samples, sort_keys=True, indent=4, separators=(',', ': '))\n json_out.write(json_summary)\n json_out.close()\n\n\n if csv_out != None:\n\n # if we're writing out at the same level as the query header\n # write out the fractions and counts\n if same_level or no_hist:\n\n fieldnames = set()\n for sample, taxa in samples.items():\n for heading,taxon in taxa.items():\n if len(taxon):\n for k in taxon.keys():\n fieldnames |= set([k+\"-pt\",k+\"-ct\"])\n\n heading_columns = [\"sample\"]\n if include_root:\n root_fields = [\"root-pt\",\"root-ct\",\"unclassified-pt\",\"unclassified-ct\"]\n fieldnames -= set(root_fields)\n heading_columns += root_fields\n\n writer = csv.DictWriter(csv_out, restval=0 if zero_fill else '', fieldnames=heading_columns+sorted(list(fieldnames)))\n writer.writeheader()\n\n for sample, taxa in samples.items():\n sample_dict = {}\n sample_dict[\"sample\"] = sample\n for heading,taxon in taxa.items():\n for entry in taxon.keys():\n sample_dict[entry+\"-pt\"] = taxon[entry].percent\n sample_dict[entry+\"-ct\"] = taxon[entry].count\n writer.writerow(sample_dict)\n\n\n csv_out.close()\n\n # otherwise write out a histogram\n else:\n count = 0\n summary_counts = collections.defaultdict(dict)\n for sample, totals in samples.items():\n for heading,taxa in totals.items():\n for taxon in taxa.keys():\n if taxon not in summary_counts[heading].keys():\n summary_counts[heading][taxon] = 1\n else:\n summary_counts[heading][taxon] += 1\n\n for k,taxa in summary_counts.items():\n summary_counts[k] = collections.OrderedDict(sorted(taxa.items(), key=lambda item: (item[1]) , reverse=True))\n\n\n fieldnames = [\"heading\",\"taxon\",\"num_samples\"]\n writer = csv.DictWriter(csv_out, restval=0 if zero_fill else '', fieldnames=fieldnames)\n writer.writeheader()\n\n for heading,taxa_counts in summary_counts.items():\n writer.writerows([{\"heading\":heading,\"taxon\":taxon,\"num_samples\":count} for taxon,count in taxa_counts.items()])\n\n csv_out.close()\n\n\n__commands__.append(('taxlevel_summary', parser_kraken_taxlevel_summary))\n\n\ndef parser_kraken_taxlevel_plurality(parser=argparse.ArgumentParser()):\n parser.add_argument('summary_file', help='input Kraken-format summary text file with tab-delimited taxonomic levels.')\n parser.add_argument('tax_heading', help='The taxonomic heading to analyze.')\n parser.add_argument('out_report', help='tab-delimited output file.')\n parser.add_argument('--min_reads', type=int, dest=\"min_reads\", help='Only include hits with more than min_reads (default: %(default)s)', default=1)\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, taxlevel_plurality, split_args=True)\n return parser\n\ndef taxlevel_plurality(summary_file, tax_heading, out_report, min_reads):\n \"\"\"\n Identifies the most abundant taxon (of any rank) contributing to a node of interest in the taxonomic tree.\n It is intended to highlight the primary contributor of taxonomic signal within a taxonomic category of interest,\n for example, the most abundant virus among all viruses.\n \"\"\"\n\n keeper_rows = []\n with file.open_or_gzopen(summary_file, 'rt') as inf:\n report_type=None\n should_process = False\n indent_of_selection = -1\n def indent_len(in_string):\n return len(in_string)-len(in_string.lstrip())\n for lineno, line in enumerate(inf):\n if len(line.rstrip('\\r\\n').strip()) == 0 or ( report_type != None and line.startswith(\"#\") or line.startswith(\"%\")):\n continue\n\n if not report_type and \"KrakenUniq\" in line:\n report_type=\"krakenuniq\"\n continue\n elif not report_type:\n report_type=\"kraken\"\n\n csv.register_dialect('kraken_report', quoting=csv.QUOTE_MINIMAL, delimiter=\"\\t\")\n if report_type == \"kraken\":\n fieldnames = [ \"pct_of_total\",\n \"reads_cumulative\",\n \"reads_excl_children\",\n \"taxon_rank\",\n \"taxon_id\",\n \"taxon_sci_name\"\n ]\n elif report_type == \"krakenuniq\":\n fieldnames = [ \"pct_of_total\",\n \"reads_cumulative\",\n \"reads_excl_children\",\n \"uniq_kmers\",\n \"kmer_dups\",\n \"cov_of_clade_kmers\",\n \"taxon_id\",\n \"taxon_rank\",\n \"taxon_sci_name\"\n ]\n else:\n continue #never reached since we fall back to kraken above\n\n row = next(csv.DictReader([line.strip().rstrip('\\n')], fieldnames=fieldnames, dialect=\"kraken_report\"))\n\n try:\n indent_of_line = indent_len(row[\"taxon_sci_name\"])\n except AttributeError as e:\n log.warning(\"Report type: '{}'\".format(report_type))\n log.warning(\"Issue with line {}: '{}'\".format(lineno,line.strip().rstrip('\\n')))\n log.warning(\"From file: {}\".format(f))\n # remove leading/trailing whitespace from each item\n row = { k:v.strip() for k, v in row.items()}\n\n if indent_of_line <= indent_of_selection:\n should_process = False\n indent_of_selection=-1\n\n if indent_of_selection == -1:\n if row[\"taxon_sci_name\"].lower() == tax_heading.lower():\n should_process = True\n indent_of_selection = indent_of_line\n\n if should_process:\n keeper_rows.append(row)\n\n # find the top hits within the focal taxon (if any)\n out = []\n if not keeper_rows:\n # we didn't find anything under the tax_heading of interest\n out.append({'order_within_focal':0, 'focal_taxon_name':tax_heading, 'focal_taxon_count':0, 'pct_of_focal':0.0, 'pct_of_total':0.0, 'reads_cumulative':0, 'reads_excl_children':0, 'taxon_rank':'', 'taxon_id':'', 'taxon_sci_name':''})\n else:\n # find the most abundant taxon classified underneath (but not including) the tax_heading \n assert keeper_rows[0][\"taxon_sci_name\"].lower() == tax_heading.lower()\n keepers_sorted = enumerate(sorted(keeper_rows[1:], key=lambda row:int(row[\"reads_excl_children\"]), reverse=True))\n for i, hit in keepers_sorted:\n outrow = { 'order_within_focal': i+1,\n 'focal_taxon_name':keeper_rows[0][\"taxon_sci_name\"],\n 'focal_taxon_count':keeper_rows[0][\"reads_cumulative\"],\n 'pct_of_focal': 100.0 * float(hit[\"reads_excl_children\"]) / float(keeper_rows[0][\"reads_cumulative\"])}\n for k in (\"pct_of_total\", \"reads_cumulative\", \"reads_excl_children\", \"taxon_rank\", \"taxon_id\", \"taxon_sci_name\"):\n outrow[k] = hit[k]\n if int(outrow['reads_excl_children']) >= min_reads:\n out.append(outrow)\n\n # write outputs\n with file.open_or_gzopen(out_report, 'wt') as outf:\n header = ('focal_taxon_name', 'focal_taxon_count', 'order_within_focal', 'pct_of_focal', 'pct_of_total', 'reads_cumulative', 'reads_excl_children', 'taxon_rank', 'taxon_id', 'taxon_sci_name')\n writer = csv.DictWriter(outf, header, delimiter='\\t', dialect=csv.unix_dialect, quoting=csv.QUOTE_MINIMAL)\n writer.writeheader()\n writer.writerows(out)\n\n__commands__.append(('taxlevel_plurality', parser_kraken_taxlevel_plurality))\n\ndef parser_kb_extract(parser=argparse.ArgumentParser()):\n \"\"\"Argument parser for the kb_python extract command.\n\n Args:\n parser (argparse.ArgumentParser): Argument parser instance. Defaults to argparse.ArgumentParser().\n\n Returns:\n argparse.ArgumentParser: The parser with arguments added.\n \"\"\"\n parser.add_argument('in_bam', help='Input unaligned reads, BAM format.')\n parser.add_argument('--index', help='kb index file.')\n parser.add_argument('--t2g', help='Transcript to gene mapping file.')\n parser.add_argument('--out_dir', dest='out_dir', help='Output directory (default: kb_out)', default='kb_out')\n parser.add_argument('--protein', action='store_true', help='True if sequence contains amino acids (default: False).')\n parser.add_argument('--targets', help='Comma-separated list of target sequences to extract from input sequences.', default=None)\n parser.add_argument('--h5ad', help='Path to the output h5ad file. Can pull IDs to extract from this file.', default=None)\n parser.add_argument('--threshold', type=int, help='Minimum read count threshold for a target to be extracted (only used when extractin IDs from h5ad; default: %(default)s)', default=1)\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kb_extract, split_args=True)\n return parser\ndef kb_extract(in_bam, index, t2g, targets, protein=False, out_dir=None, h5ad=None, threads=None, threshold=None):\n \"\"\"Runs kb extract on the input BAM file.\n\n Args:\n in_bam (str): Input BAM file.\n index (str): Path to the kb index file.\n t2g (str): Path to the transcript-to-gene mapping file.\n targets (str): Comma-separated list of target sequences to extract.\n protein (bool): True if sequence contains amino acids. Defaults to False.\n out_dir (str): Output directory. Defaults to None.\n h5ad (str): Path to the output h5ad file. Can pull IDs to extract from this file. Defaults to None.\n threshold (int, optional): Minimum read count threshold for a target to be extracted. Defaults to 1.\n threads (int, optional): Number of threads to use. Defaults to None.\n \"\"\"\n assert out_dir, ('Output directory must be specified.')\n\n kb_tool = kb.kb()\n \n target_ids = targets.split(',') if targets else []\n if not target_ids or len(target_ids) == 0:\n # TODO: This extraction method expects only to have a single row h5ad (i.e. 1 sample). This should be handled more robustly.\n log.warning('No targets specified for extraction. Trying to extract IDs from h5ad.')\n target_ids = kb_tool.extract_hit_ids_from_h5ad(h5ad, threshold=threshold)\n log.info(\"Target IDs extracted from h5ad: {}\".format(target_ids))\n if len(target_ids) == 0:\n raise ValueError('No targets specified for extraction and no IDs found in h5ad.')\n\n kb_tool.extract(\n in_bam=in_bam,\n index_file=index,\n target_ids=target_ids,\n out_dir=out_dir,\n t2g_file=t2g,\n protein=protein,\n num_threads=threads\n )\n__commands__.append(('kb_extract', parser_kb_extract))\n\ndef parser_kb_top_taxa(parser=argparse.ArgumentParser()):\n parser.add_argument('counts_tar', help='Input kb count tarball (tar.zst format).')\n parser.add_argument('--id-to-tax-map', dest='id_to_tax_map', help='ID to taxonomy mapping file (CSV format).')\n parser.add_argument('--target-taxon', dest='target_taxon', default='Viruses', help='Target taxonomic category to analyze (default: Viruses).')\n parser.add_argument('out_report', help='Tab-delimited output file.')\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kb_top_taxa, split_args=True)\n return parser\n\ndef kb_top_taxa(counts_tar, out_report, id_to_tax_map=None, target_taxon='Viruses'):\n \"\"\"Identifies the most abundant taxon (of any rank) contributing to a taxa node of interest in kb count output.\n\n It is intended to highlight the primary contributor of taxonomic signal within a taxonomic category of interest,\n for example, the most abundant virus among all viruses.\n\n Args:\n counts_tar (str): Path to the input kb count tarball (tar.zst format).\n out_report (str): Path to the output report file.\n id_to_tax_map (str, optional): Path to the ID to taxonomy mapping file (CSV format).\n target_taxon (str): The taxonomic category to analyze (default: 'Viruses').\n \"\"\"\n kb_tool = kb.kb()\n\n # Extract and read h5ad file from tarball\n with file.tmp_dir() as tmp_dir:\n file.extract_tarball(counts_tar, tmp_dir)\n h5ad_files = glob.glob(os.path.join(tmp_dir, \"counts_unfiltered\", '*.h5ad'))\n\n assert len(h5ad_files) == 1, \"Expected exactly one .h5ad file in the counts tarball, found {}\".format(len(h5ad_files))\n h5ad_file = h5ad_files[0]\n\n # Use kb helper to parse h5ad file\n gene_counts = kb_tool.parse_h5ad_counts(h5ad_file)\n\n # Build results data with taxonomy information\n results_data = []\n\n if id_to_tax_map:\n # Load taxonomy mapping\n tax_map_df = pd.read_csv(id_to_tax_map)\n tax_map_df = tax_map_df.replace('.', np.nan)\n\n # Standardize column name: handle both 'ID' and 'id'\n if 'ID' in tax_map_df.columns:\n tax_map_df = tax_map_df.rename(columns={'ID': 'id'})\n elif 'id' not in tax_map_df.columns:\n # If neither exists, use the first column as 'id'\n tax_map_df = tax_map_df.rename(columns={tax_map_df.columns[0]: 'id'})\n\n # Get the farthest (most specific) non-empty taxonomy for each gene\n # Define taxonomy rank columns in order from broad to specific\n taxonomy_columns = [col for col in ['phylum', 'class', 'order', 'family', 'genus', 'species']\n if col in tax_map_df.columns]\n\n def get_farthest_taxa(row):\n # Only consider taxonomy columns, in reverse order (most specific first)\n for col in reversed(taxonomy_columns):\n if pd.notna(row[col]) and row[col] != '':\n return row[col]\n return 'Unknown'\n\n tax_map_df['farthest_taxa'] = tax_map_df.apply(get_farthest_taxa, axis=1)\n\n # Get the root taxonomy category\n if 'root' in tax_map_df.columns:\n tax_map_df['tax_category'] = tax_map_df['root']\n elif 'phylum' in tax_map_df.columns:\n tax_map_df['tax_category'] = tax_map_df['phylum']\n else:\n # Assume first column after 'id' is the root category\n tax_map_df['tax_category'] = tax_map_df.iloc[:, 1]\n\n # OPTIMIZATION: Set 'id' as index for O(1) lookups instead of O(n) filtering\n tax_map_df = tax_map_df.set_index('id')\n\n # Filter by target taxon - optimized with index-based lookup\n for gene_id, count in gene_counts:\n # Skip genes with 0 counts\n if count == 0:\n continue\n if gene_id in tax_map_df.index:\n tax_info = tax_map_df.loc[gene_id]\n tax_category = tax_info['tax_category']\n if tax_category == target_taxon:\n # Use species name if available, otherwise use farthest_taxa\n species_name = tax_info.get('species', tax_info['farthest_taxa']) if 'species' in tax_info.index else tax_info['farthest_taxa']\n if pd.isna(species_name) or species_name == '':\n species_name = tax_info['farthest_taxa']\n\n results_data.append({\n 'palmdb_id': gene_id,\n 'sotu_id': species_name,\n 'count': int(count),\n 'tax_category': tax_category,\n 'farthest_taxa': tax_info['farthest_taxa']\n })\n else:\n # No taxonomy mapping - report all genes\n for gene_id, count in gene_counts:\n # Skip genes with 0 counts\n if count == 0:\n continue\n results_data.append({\n 'palmdb_id': gene_id,\n 'sotu_id': gene_id,\n 'count': int(count),\n 'tax_category': 'Unknown',\n 'farthest_taxa': gene_id\n })\n\n # Create output\n if not results_data:\n out = [{'focal_taxon_name': target_taxon, 'focal_taxon_count': 0, 'pct_of_focal': 0.0,\n 'palmdb_id': '', 'hit_id': '', 'hit_lowest_taxa_name': '', 'hit_reads': 0}]\n else:\n results_df = pd.DataFrame(results_data)\n total_focal_count = results_df['count'].sum()\n results_df = results_df.sort_values(by='count', ascending=False).reset_index(drop=True)\n\n # OPTIMIZATION: Use vectorized operations instead of iterrows()\n results_df['focal_taxon_name'] = target_taxon\n results_df['focal_taxon_count'] = total_focal_count\n results_df['pct_of_focal'] = 100.0 * results_df['count'] / total_focal_count\n\n # Create output dict\n out = results_df.rename(columns={\n 'sotu_id': 'hit_id',\n 'farthest_taxa': 'hit_lowest_taxa_name',\n 'count': 'hit_reads'\n })[['focal_taxon_name', 'focal_taxon_count', 'palmdb_id', 'hit_id', 'hit_lowest_taxa_name', 'hit_reads', 'pct_of_focal']].to_dict('records')\n\n # Write output\n with file.open_or_gzopen(out_report, 'wt') as outf:\n header = ('focal_taxon_name', 'focal_taxon_count', 'palmdb_id', 'hit_id', 'hit_lowest_taxa_name', 'hit_reads', 'pct_of_focal')\n writer = csv.DictWriter(outf, header, delimiter='\\t', dialect=csv.unix_dialect, quoting=csv.QUOTE_MINIMAL)\n writer.writeheader()\n writer.writerows(out)\n\n__commands__.append(('kb_top_taxa', parser_kb_top_taxa))\n\ndef parser_kb_merge_h5ads(parser=argparse.ArgumentParser()):\n parser.add_argument('in_count_tars', nargs='+', help='Input kb count tarballs to merge (tar.zst format).')\n parser.add_argument('--out-h5ad', dest='out_h5ad', help='Output merged h5ad file.')\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kb_merge_h5ads, split_args=True)\n return parser\ndef kb_merge_h5ads(in_count_tars, out_h5ad, tmp_dir=None):\n '''\n Merge multiple kb count output tarballs into a single h5ad file with sample metadata.\n\n Extracts h5ad files from counts_unfiltered folder and adds sample names from matrix.cells.\n\n Args:\n in_count_tars (list): List of input kb count tarballs (tar.zst format).\n out_h5ad (str): Path to the output h5ad file.\n tmp_dir (str, optional): Temporary directory for extraction.\n '''\n assert out_h5ad, ('Output h5ad file must be specified.')\n kb_tool = kb.kb()\n kb_tool.merge_h5ads(\n in_count_tars=in_count_tars,\n out_h5ad=out_h5ad,\n tmp_dir_parent=tmp_dir\n )\n\n__commands__.append(('kb_merge_h5ads', parser_kb_merge_h5ads))\n\ndef parser_krona_build(parser=argparse.ArgumentParser()):\n parser.add_argument('db', help='Krona taxonomy database output directory.')\n parser.add_argument('--taxdump_tar_gz', help='NCBI taxdump.tar.gz file', default=None)\n parser.add_argument('--get_accessions', action='store_true', help='Fetch NCBI accession to taxid mappings. This is not required for processing kraken1/2/uniq hits, only for BLAST hits, and adds a significant amount of time and database space (default false).')\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, krona_build, split_args=True)\n return parser\ndef krona_build(db, taxdump_tar_gz=None, get_accessions=False):\n '''\n Builds a Krona taxonomy database\n '''\n krona.Krona().build_db(\n db, taxdump_tar_gz=taxdump_tar_gz, get_accessions=get_accessions)\n__commands__.append(('krona_build', parser_krona_build))\n\n\ndef parser_kraken2_build(parser=argparse.ArgumentParser()):\n parser.add_argument('db', help='Kraken database output directory.')\n parser.add_argument('--tax_db', help='Use pre-existing kraken2 taxonomy db structure', default=None)\n parser.add_argument('--taxdump_out', help='Save ncbi taxdump.tar.gz file', default=None)\n parser.add_argument('--standard_libraries',\n nargs='+',\n choices=[\"archaea\", \"bacteria\", \"plasmid\",\n \"viral\", \"human\", \"fungi\", \"plant\", \"protozoa\",\n \"nr\", \"nt\", \"env_nr\", \"env_nt\", \"UniVec\",\n \"UniVec_Core\"],\n help='A list of \"standard\" kraken libraries to download on the fly and add.')\n parser.add_argument('--custom_libraries', nargs='+', help='Custom fasta files with properly formatted headers.')\n parser.add_argument('--kmerLen', type=int, help='(k) k-mer length (kraken2 default: 35nt/15aa)')\n parser.add_argument('--minimizerLen', type=int, help='(l) Minimizer length (kraken2 default: 31nt/12aa)')\n parser.add_argument('--minimizerSpaces', type=int, help='(s) Number of characters in minimizer that are ignored in comparisons (kraken2 default: 7nt/0aa)')\n parser.add_argument('--protein', action='store_true', help='Build protein database (default false/nucleotide).')\n parser.add_argument('--maxDbSize', type=int, help='Maximum db size in GB (default: none)')\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kraken2_build, split_args=True)\n return parser\ndef kraken2_build(db,\n tax_db=None, taxdump_out=None,\n standard_libraries=(), custom_libraries=(),\n protein=False,\n minimizerLen=None, kmerLen=None, minimizerSpaces=None,\n maxDbSize=None, threads=None):\n '''\n Builds a kraken2 database from library directory of fastas and taxonomy db\n directory. The --subsetTaxonomy option allows shrinking the taxonomy to only\n include taxids associated with the library folders. For this to work, the\n library fastas must have the standard id names such as `>NC1234.1`\n accessions, `>gi|123456789|ref|XXXX||`, or custom kraken name\n `>kraken:taxid|1234|`.\n '''\n\n kraken_tool = kraken2.Kraken2()\n kraken_tool.build(db,\n tax_db=tax_db,\n standard_libraries=standard_libraries,\n custom_libraries=custom_libraries,\n taxdump_out=taxdump_out,\n k=kmerLen, l=minimizerLen, s=minimizerSpaces,\n protein=protein,\n max_db_size=maxDbSize,\n num_threads=threads)\n\n__commands__.append(('kraken2_build', parser_kraken2_build))\n\n\ndef parser_kb_build(parser=argparse.ArgumentParser()):\n parser.add_argument('ref_fasta', help='Reference sequence fasta file.')\n parser.add_argument('--index', help='kb output index file.')\n parser.add_argument('--workflow', choices=['standard', 'nac', 'kite', 'custom'],\n default='standard', help='Type of index to create (default: %(default)s).')\n parser.add_argument('--kmer_len', type=int, help='k-mer length (default: 31).')\n parser.add_argument('--protein', action='store_true', help='True if sequence contains amino acids(default: False).')\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, kb_build, split_args=True)\n return parser\ndef kb_build(ref_fasta, index, workflow='standard', kmer_len=31, protein=False, threads=None):\n '''\n Builds a kb index from a reference fasta file.\n\n Args:\n ref_fasta (str): Path to the reference sequence fasta file.\n index (str): Path to the output kb index file.\n workflow (str): Type of index to create. Options are 'standard', 'nac', 'kite', 'custom'.\n kmer_len (int): k-mer length (default: 31).\n protein (bool): True if sequence contains amino acids (default: False).\n threads (int): Number of threads to use (default: None).\n '''\n kb_tool = kb.kb()\n kb_tool.build(ref_fasta,\n index=index,\n workflow=workflow,\n kmer_len=kmer_len,\n protein=protein,\n num_threads=threads)\n__commands__.append(('kb_build', parser_kb_build))\n\n\ndef full_parser():\n return cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/ncbi.py", "content": "#!/usr/bin/env python\n'''This script contains a number of utilities for submitting our analyses\nto NCBI's Genbank and SRA databases, as well as retreiving records from Genbank.\n'''\n\n__author__ = \"tomkinsc@broadinstitute.org\"\n__commands__ = []\n\nimport argparse\nimport logging\nimport collections\nimport shutil\nimport os\nimport os.path\n\nimport arrow\nimport Bio.SeqIO\n\nfrom .core import cmd\nfrom .core import file\nfrom .core import version\nfrom .phylo import genbank\nfrom . import interhost\nfrom .phylo import feature_table\n\nlog = logging.getLogger(__name__)\n\n\ndef fasta_chrlens(fasta):\n out = collections.OrderedDict()\n with open(fasta, 'rt') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n out[seq.id] = len(seq)\n return out\n\ndef tbl_transfer_common(cmap, ref_tbl, out_tbl, alt_chrlens, oob_clip=False, ignore_ambig_feature_edge=False):\n \"\"\"\n This function is the feature transfer machinery used by tbl_transfer()\n and tbl_transfer_prealigned(). cmap is an instance of CoordMapper.\n \"\"\"\n\n ft = feature_table.FeatureTable(ref_tbl)\n remapped_ft = feature_table.FeatureTable()\n\n # sequence identifier\n refSeqID = [x for x in cmap.keys() if ft.refID in x][0]\n altid = list(set(cmap.keys()) - set([refSeqID]))[0]\n ft.refID = altid\n\n # feature with numeric coordinates (map them)\n def remap_function(start, end, feature):\n \"\"\"\n start/end are SeqPositions from phylo.feature_table\n \"\"\"\n strand = None\n if end.position >= start.position:\n strand = '+'\n start.position = cmap.mapChr(refSeqID, altid, start.position, -1)[1]\n end.position = cmap.mapChr(refSeqID, altid, end.position, 1)[1]\n else:\n # negative strand feature\n strand = '-'\n start.position = cmap.mapChr(refSeqID, altid, start.position, 1)[1]\n end.position = cmap.mapChr(refSeqID, altid, end.position, -1)[1]\n\n if ignore_ambig_feature_edge:\n start.location_operator = None\n end.location_operator = None\n \n if start.position and end.position:\n # feature completely within bounds\n return (start, end)\n elif start.position == None and end.position == None:\n # feature completely out of bounds\n return (None, None)\n else:\n # feature overhangs end of sequence\n if oob_clip:\n if feature.type == \"CDS\":\n feature.add_note(\"sequencing did not capture complete CDS\")\n if strand == '+':\n # clip pos strand feature\n if start.position == None:\n # clip the beginning\n if feature.type == 'CDS':\n # for CDS features, clip in multiples of 3\n r = (end.position if end.position is not None else alt_chrlens[altid])\n start.position = (r % 3) + 1\n start.location_operator = '<'\n else:\n start.position = 1\n start.location_operator = '<'\n if end.position == None:\n # clip the end\n end.position = alt_chrlens[altid]\n end.location_operator = '>'\n else:\n # clip neg strand feature\n if start.position == None:\n # clip the beginning (right side)\n r = alt_chrlens[altid]\n if feature.type == 'CDS':\n # for CDS features, clip in multiples of 3\n l = (end.position if end.position is not None else 1) # new left\n r = r - ((r-l+1) % 3) # create new right in multiples of 3 from left\n if (r-l) < 3:\n # less than a codon remains, drop it\n return (None, None)\n start.position = r\n start.location_operator = '<'\n if end.position == None:\n # clip the end (left side)\n end.position = 1\n end.location_operator = '>'\n else:\n return (None, None)\n\n # Validate final coordinates are within bounds\n if start.position and end.position:\n seq_len = alt_chrlens[altid]\n if start.position < 1 or start.position > seq_len:\n return (None, None)\n if end.position < 1 or end.position > seq_len:\n return (None, None)\n\n return (start, end)\n\n ft.remap_locations(remap_function)\n\n with open(out_tbl, 'wt') as outf:\n exclude_patterns = [\n # regexp, matched anywhere in line\n r\"protein_id\"\n ]\n for line in ft.lines(exclude_patterns=exclude_patterns):\n outf.write(str(line) + '\\n')\n # extra newline at the end\n outf.write('\\n')\n\n\ndef tbl_transfer(ref_fasta, ref_tbl, alt_fasta, out_tbl, oob_clip=False, ignore_ambig_feature_edge=False):\n ''' This function takes an NCBI TBL file describing features on a genome\n (genes, etc) and transfers them to a new genome.\n '''\n cmap = interhost.CoordMapper()\n cmap.align_and_load_sequences([ref_fasta, alt_fasta])\n alt_chrlens = fasta_chrlens(alt_fasta)\n\n tbl_transfer_common(cmap, ref_tbl, out_tbl, alt_chrlens, oob_clip, ignore_ambig_feature_edge)\n\n\ndef parser_tbl_transfer(parser=argparse.ArgumentParser()):\n parser.add_argument(\"ref_fasta\", help=\"Input sequence of reference genome\")\n parser.add_argument(\"ref_tbl\", help=\"Input reference annotations (NCBI TBL format)\")\n parser.add_argument(\"alt_fasta\", help=\"Input sequence of new genome\")\n parser.add_argument(\"out_tbl\", help=\"Output file with transferred annotations\")\n parser.add_argument('--oob_clip',\n default=False,\n action='store_true',\n help='''Out of bounds feature behavior.\n False: drop all features that are completely or partly out of bounds\n True: drop all features completely out of bounds\n but truncate any features that are partly out of bounds''')\n parser.add_argument('--ignoreAmbigFeatureEdge',\n dest=\"ignore_ambig_feature_edge\",\n default=False,\n action='store_true',\n help='''Ambiguous feature behavior.\n False: features specified as ambiguous (\"<####\" or \">####\") are mapped, \n where possible\n True: features specified as ambiguous (\"<####\" or \">####\") are interpreted\n as exact values''')\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, tbl_transfer, split_args=True)\n return parser\n\n\n__commands__.append(('tbl_transfer', parser_tbl_transfer))\n\n\n\ndef tbl_transfer_multichr(ref_fastas, ref_tbls, alt_fasta, out_dir, oob_clip=False, ignore_ambig_feature_edge=False):\n ''' This function takes an NCBI TBL file describing features on a genome\n (genes, etc) and transfers them to a new genome.\n '''\n\n # parse the alt_fasta into one-seg-per-file fastas\n alt_fastas = []\n alt_seqids = []\n with file.open_or_gzopen(alt_fasta, 'r') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n fname = os.path.join(out_dir, file.string_to_file_name(seq.id) + \".fasta\")\n alt_seqids.append(seq.id)\n alt_fastas.append(fname)\n Bio.SeqIO.write(seq, fname, \"fasta\")\n n_segs = len(alt_fastas)\n\n # input consistency check\n if not (n_segs == len(ref_fastas)) and (n_segs == len(ref_tbls)):\n raise Exception(\"The number of reference fastas ({}), reference feature tables ({}), and alt sequences ({}) must be exactly equal\".format(\n len(ref_fastas), len(ref_tbls), n_segs))\n\n # iterate over each segment and call tbl_transfer on each\n for i in range(n_segs):\n out_tbl = os.path.join(out_dir, file.string_to_file_name(alt_seqids[i]) + '.tbl')\n tbl_transfer(ref_fastas[i], ref_tbls[i], alt_fastas[i], out_tbl,\n oob_clip=oob_clip, ignore_ambig_feature_edge=ignore_ambig_feature_edge)\n\ndef parser_tbl_transfer_multichr(parser=argparse.ArgumentParser()):\n parser.add_argument(\"alt_fasta\", help=\"Input sequence of new genome, all chr/segs in one fasta file, in the same order as ref_fastas\")\n parser.add_argument(\"out_dir\", help=\"Output files include one fasta and tbl per sequence in alt_fasta, named according to the fasta header ID of each entry in alt_fasta.\")\n parser.add_argument(\"--ref_fastas\",\n nargs='+',\n help=\"Input sequences of reference genome, one chr/seg per fasta file\")\n parser.add_argument(\"--ref_tbls\",\n nargs='+',\n help=\"Input reference annotations (NCBI TBL format), one chr/seg per tbl file, in the same order as ref_fastas\")\n parser.add_argument('--oob_clip',\n default=False,\n action='store_true',\n help='''Out of bounds feature behavior.\n False: drop all features that are completely or partly out of bounds\n True: drop all features completely out of bounds\n but truncate any features that are partly out of bounds''')\n parser.add_argument('--ignoreAmbigFeatureEdge',\n dest=\"ignore_ambig_feature_edge\",\n default=False,\n action='store_true',\n help='''Ambiguous feature behavior.\n False: features specified as ambiguous (\"<####\" or \">####\") are mapped,\n where possible\n True: features specified as ambiguous (\"<####\" or \">####\") are interpreted\n as exact values''')\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, tbl_transfer_multichr, split_args=True)\n return parser\n\n__commands__.append(('tbl_transfer_multichr', parser_tbl_transfer_multichr))\n\n\ndef tbl_transfer_prealigned(inputFasta, refFasta, refAnnotTblFiles, outputDir, oob_clip=False, ignore_ambig_feature_edge=False):\n \"\"\"\n This breaks out the ref and alt sequences into separate fasta files, and then\n creates unified files containing the reference sequence first and the alt second. Each of these unified files\n is then passed as a cmap to tbl_transfer_common.\n\n This function expects to receive one fasta file containing a multialignment of a single segment/chromosome along\n with the respective reference sequence for that segment/chromosome. It also expects a reference containing all\n reference segments/chromosomes, so that the reference sequence can be identified in the input file by name. It\n also expects a list of reference tbl files, where each file is named according to the ID present for its\n corresponding sequence in the refFasta. For each non-reference sequence present in the inputFasta, two files are\n written: a fasta containing the segment/chromosome for the same, along with its corresponding feature table as\n created by tbl_transfer_common.\n \"\"\"\n\n ref_tbl = \"\" # must be identified in list of tables\n ref_fasta_filename = \"\"\n matchingRefSeq = None\n\n if not os.path.exists(outputDir):\n os.makedirs(outputDir)\n\n # identify which of the sequences in the multialignment is the reference,\n # matching by ID to one of the sequences in the refFasta\n with file.open_or_gzopen(inputFasta, 'r') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n with file.open_or_gzopen(refFasta, 'r') as reff:\n for refSeq in Bio.SeqIO.parse(reff, 'fasta'):\n if seq.id == refSeq.id:\n ref_fasta_filename = file.mkstempfname('.fasta')\n matchingRefSeq = seq\n break\n if matchingRefSeq:\n break\n\n if ref_fasta_filename == \"\":\n raise KeyError(\"No reference was found in the input file %s\" % (inputFasta))\n\n # identify the correct feature table source based on its filename,\n # which should correspond to a unique component of the ref sequence ID (i.e. the genbank accession)\n for tblFilename in refAnnotTblFiles:\n # identify the correct feature table as the one that has an ID that is\n # part of the ref seq ID\n fileAccession = genbank.get_feature_table_id(tblFilename)\n if fileAccession == matchingRefSeq.id.split('|')[0]:\n ref_tbl = tblFilename\n break\n if ref_tbl == \"\":\n raise KeyError(\"No reference table was found for the reference %s\" % (matchingRefSeq.id))\n\n # write out the desired sequences to separate fasta files\n with file.open_or_gzopen(inputFasta, 'r') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n # if we are looking at the reference sequence in the multialignment,\n # continue to the next sequence\n if seq.id == matchingRefSeq.id:\n continue\n\n combined_fasta_filename = \"\"\n\n combined_fasta_filename = file.mkstempfname('.fasta')\n # write ref and alt sequences to a combined fasta file, sourced from the\n # alignment so gaps are present for the CoordMapper instance, cmap\n with open(combined_fasta_filename, 'wt') as outf:\n Bio.SeqIO.write([matchingRefSeq, seq], outf, \"fasta\")\n\n # create a filepath for the output table\n out_tbl = os.path.join(outputDir, seq.id + \".tbl\")\n\n cmap = interhost.CoordMapper()\n cmap.load_alignments([combined_fasta_filename])\n # sequences in the fasta file here should NOT include gaps\n # since alt_chrlens is only used in the case where features would \n # extend beyond the genome (for reporting >{seq.len})\n alt_chrlens = {}#fasta_chrlens(combined_fasta_filename)\n alt_chrlens[seq.id] = len(seq.seq.replace(\"-\",\"\"))\n alt_chrlens[matchingRefSeq.id] = len(matchingRefSeq.seq.replace(\"-\",\"\"))\n\n tbl_transfer_common(cmap, ref_tbl, out_tbl, alt_chrlens, oob_clip, ignore_ambig_feature_edge)\n\ndef parser_tbl_transfer_prealigned(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inputFasta\",\n help=\"\"\"FASTA file containing input sequences,\n including pre-made alignments and reference sequence\"\"\")\n parser.add_argument(\"refFasta\", help=\"FASTA file containing the reference genome\")\n parser.add_argument(\"refAnnotTblFiles\",\n nargs='+',\n help=\"\"\"Name of the reference feature tables,\n each of which should have a filename comrised of [refId].tbl\n so they can be matched against the reference sequences\"\"\")\n parser.add_argument(\"outputDir\", help=\"The output directory\")\n parser.add_argument('--oob_clip',\n default=False,\n action='store_true',\n help='''Out of bounds feature behavior.\n False: drop all features that are completely or partly out of bounds\n True: drop all features completely out of bounds\n but truncate any features that are partly out of bounds''')\n parser.add_argument('--ignoreAmbigFeatureEdge',\n dest=\"ignore_ambig_feature_edge\",\n default=False,\n action='store_true',\n help='''Ambiguous feature behavior.\n False: features specified as ambiguous (\"<####\" or \">####\") are mapped, \n where possible\n True: features specified as ambiguous (\"<####\" or \">####\") are interpreted\n as exact values''')\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, tbl_transfer_prealigned, split_args=True)\n return parser\n\n\n__commands__.append(('tbl_transfer_prealigned', parser_tbl_transfer_prealigned))\n\n\ndef fetch_fastas(accession_IDs, destinationDir, emailAddress, forceOverwrite, combinedFilePrefix, fileExt,\n removeSeparateFiles, chunkSize, api_key=None):\n '''\n This function downloads and saves the FASTA files\n from the Genbank CoreNucleotide database given a given list of accession IDs.\n '''\n genbank.fetch_fastas_from_genbank(accession_IDs,\n destinationDir,\n emailAddress,\n forceOverwrite,\n combinedFilePrefix,\n removeSeparateFiles,\n fileExt,\n \"fasta\",\n chunkSize=chunkSize,\n api_key=api_key)\n\n\ndef fetch_feature_tables(accession_IDs, destinationDir, emailAddress, forceOverwrite, combinedFilePrefix, fileExt,\n removeSeparateFiles, chunkSize, api_key=None):\n '''\n This function downloads and saves\n feature tables from the Genbank CoreNucleotide database given a given list of accession IDs.\n '''\n genbank.fetch_feature_tables_from_genbank(accession_IDs,\n destinationDir,\n emailAddress,\n forceOverwrite,\n combinedFilePrefix,\n removeSeparateFiles,\n fileExt,\n \"ft\",\n chunkSize=chunkSize,\n api_key=api_key)\n\n\ndef fetch_genbank_records(accession_IDs, destinationDir, emailAddress, forceOverwrite, combinedFilePrefix, fileExt,\n removeSeparateFiles, chunkSize, api_key=None):\n '''\n This function downloads and saves\n full flat text records from Genbank CoreNucleotide database given a given list of accession IDs.\n '''\n genbank.fetch_full_records_from_genbank(accession_IDs,\n destinationDir,\n emailAddress,\n forceOverwrite,\n combinedFilePrefix,\n removeSeparateFiles,\n fileExt,\n \"gb\",\n chunkSize=chunkSize,\n api_key=api_key)\n\n\ndef parser_fetch_reference_common(parser=argparse.ArgumentParser()):\n parser.add_argument(\"emailAddress\",\n help=\"\"\"Your email address. To access Genbank databases,\n NCBI requires you to specify your email address with each request.\n In case of excessive usage of the E-utilities, NCBI will attempt to contact\n a user at the email address provided before blocking access. This email address should\n be registered with NCBI. To register an email address, simply send\n an email to eutilities@ncbi.nlm.nih.gov including your email address and\n the tool name (tool='https://github.com/broadinstitute/viral-ngs').\"\"\")\n parser.add_argument(\"--api_key\",\n dest=\"api_key\",\n help=\"\"\"Your NCBI API key. If an API key is not provided, NCBI \n requests are limited to 3/second. If an API key is provided, \n requests may be submitted at a rate up to 10/second. \n For more information, see: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/\n \"\"\")\n parser.add_argument(\"destinationDir\", help=\"Output directory with where .fasta and .tbl files will be saved\")\n parser.add_argument(\"accession_IDs\", nargs='+', help=\"List of Genbank nuccore accession IDs\")\n parser.add_argument('--forceOverwrite',\n default=False,\n action='store_true',\n help='''Overwrite existing files, if present.''')\n parser.add_argument('--combinedFilePrefix',\n help='''The prefix of the file containing the combined concatenated\n results returned by the list of accession IDs, in the order provided.''')\n parser.add_argument('--fileExt', default=None, help='''The extension to use for the downloaded files''')\n parser.add_argument('--removeSeparateFiles',\n default=False,\n action='store_true',\n help='''If specified, remove the individual files and leave only the combined file.''')\n parser.add_argument('--chunkSize',\n default=1,\n type=int,\n help='''Causes files to be downloaded from GenBank in chunks of N accessions.\n Each chunk will be its own combined file, separate from any combined\n file created via --combinedFilePrefix (default: %(default)s). If chunkSize is\n unspecified and >500 accessions are provided, chunkSize will be set to 500 to\n adhere to the NCBI guidelines on information retreival.''')\n return parser\n\n\ndef parser_fetch_fastas(parser):\n parser = parser_fetch_reference_common(parser)\n\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, fetch_fastas, split_args=True)\n return parser\n\n\n__commands__.append(('fetch_fastas', parser_fetch_fastas))\n\n\ndef parser_fetch_feature_tables(parser):\n parser = parser_fetch_reference_common(parser)\n\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, fetch_feature_tables, split_args=True)\n return parser\n\n\n__commands__.append(('fetch_feature_tables', parser_fetch_feature_tables))\n\n\ndef parser_fetch_genbank_records(parser):\n parser = parser_fetch_reference_common(parser)\n\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, fetch_genbank_records, split_args=True)\n return parser\n\n\n__commands__.append(('fetch_genbank_records', parser_fetch_genbank_records))\n\n\ndef biosample_to_genbank(attributes, num_segments, taxid, out_genbank_smt, out_biosample_map, biosample_in_smt=False, iso_dates=False, filter_to_samples=None, sgtf_override=False):\n ''' Prepare a Genbank Source Modifier Table based on a BioSample registration table (since all of the values are there)\n '''\n header_key_map = {\n 'Sequence_ID':'sample_name',\n 'country':'geo_loc_name',\n 'BioProject':'bioproject_accession',\n 'BioSample':'accession',\n }\n datestring_formats = [\n \"YYYY-MM-DDTHH:mm:ss\", \"YYYY-MM-DD\", \"YYYY-MM\", \"DD-MMM-YYYY\", \"MMM-YYYY\", \"YYYY\"\n ]\n out_headers_total = ['Sequence_ID', 'isolate', 'collection_date', 'country', 'collected_by', 'isolation_source', 'organism', 'host', 'note', 'db_xref']\n if biosample_in_smt:\n out_headers_total.extend(['BioProject', 'BioSample'])\n if filter_to_samples:\n with open(filter_to_samples, 'rt') as inf:\n samples_to_filter_to = set(line.strip() for line in inf)\n with open(out_genbank_smt, 'wt') as outf_smt:\n in_headers = file.readFlatFileHeader(attributes)\n out_headers = list(h for h in out_headers_total if header_key_map.get(h,h) in in_headers)\n if 'db_xref' not in out_headers:\n out_headers.append('db_xref')\n if 'note' not in out_headers:\n out_headers.append('note')\n outf_smt.write('\\t'.join(out_headers)+'\\n')\n\n with open(out_biosample_map, 'wt') as outf_biosample:\n outf_biosample.write('BioSample\\tsample\\n')\n\n for row in file.read_tabfile_dict(attributes):\n if row['message'].startswith('Success'):\n # skip if this is not a sample we're interested in\n if filter_to_samples:\n if row['sample_name'] not in samples_to_filter_to:\n continue\n\n # write BioSample\n outf_biosample.write(\"{}\\t{}\\n\".format(row['accession'], row['sample_name']))\n\n # populate output row as a dict\n outrow = dict((h, row.get(header_key_map.get(h,h), '')) for h in out_headers)\n\n # custom reformat collection_date\n collection_date = outrow.get('collection_date', '')\n if collection_date:\n date_parsed = None\n for datestring_format in datestring_formats:\n try:\n date_parsed = arrow.get(collection_date, datestring_format)\n break\n except arrow.parser.ParserError:\n pass\n if date_parsed:\n if iso_dates:\n collection_date = str(date_parsed.format(\"YYYY-MM-DD\"))\n else:\n collection_date = str(date_parsed.format(\"DD-MMM-YYYY\"))\n outrow['collection_date'] = collection_date\n else:\n log.warn(\"unable to parse date {} from sample {}\".format(collection_date, outrow['Sequence_ID']))\n\n # custom db_xref/taxon\n outrow['db_xref'] = \"taxon:{}\".format(taxid)\n\n # load the purpose of sequencing (or if not, the purpose of sampling) in the note field\n outrow['note'] = row.get('purpose_of_sequencing', row.get('purpose_of_sampling', ''))\n\n # SARS-CoV-2 specific bits\n if sgtf_override and (outrow['note'] in set([\"Screening for Variants of Concern (VoC)\", \"SGTF Surveillance\"])):\n outrow['note'] = 'screened by S dropout'\n\n # write entry for this sample\n outf_smt.write('\\t'.join(outrow[h] for h in out_headers)+'\\n')\n\n # also write numbered versions for every segment/chromosome\n sample_name = outrow['Sequence_ID']\n if num_segments>1:\n for i in range(num_segments):\n outrow['Sequence_ID'] = \"{}-{}\".format(sample_name, i+1)\n outf_smt.write('\\t'.join(outrow[h] for h in out_headers)+'\\n')\n\ndef parser_biosample_to_genbank(parser=argparse.ArgumentParser()):\n parser.add_argument('attributes', help='Input BioSample metadata table -- the attributes.tsv returned by BioSample after successful registration')\n parser.add_argument(\"num_segments\", type=int, help=\"number of chromosomes/segments per genome for this species\")\n parser.add_argument(\"taxid\", type=int, help=\"NCBI Taxonomy numeric taxid to assign to all entries\")\n parser.add_argument(\"out_genbank_smt\", help=\"Output tab table in Genbank Source Modifier Table format, suitable for prep_genbank_files\")\n parser.add_argument(\"out_biosample_map\", help=\"Output two-column biosample accession to sample name map, suitable for prep_genbank_files\")\n parser.add_argument('--biosample_in_smt',\n dest=\"biosample_in_smt\",\n default=False,\n action='store_true',\n help='Add BioSample and BioProject columns to source modifier table output')\n parser.add_argument('--iso_dates',\n dest=\"iso_dates\",\n default=False,\n action='store_true',\n help='write collection_date in ISO format (YYYY-MM-DD). default (false) is to write in tbl2asn format (DD-Mmm-YYYY)')\n parser.add_argument('--sgtf_override',\n dest=\"sgtf_override\",\n default=False,\n action='store_true',\n help='replace \"Screening for Variants of Concern (VoC)\" with \"screened by S dropout\" in the note field')\n parser.add_argument('--filter_to_samples', help=\"Filter output to specified sample IDs in this input file (one ID per line).\")\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, biosample_to_genbank, split_args=True)\n return parser\n__commands__.append(('biosample_to_genbank', parser_biosample_to_genbank))\n\n\ndef fasta2fsa(infname, outdir, biosample=None):\n ''' copy a fasta file to a new directory and change its filename to end in .fsa\n for NCBI's sake. '''\n outfname = os.path.basename(infname)\n if outfname.endswith('.fasta'):\n outfname = outfname[:-6]\n elif outfname.endswith('.fa'):\n outfname = outfname[:-3]\n if not outfname.endswith('.fsa'):\n outfname = outfname + '.fsa'\n outfname = os.path.join(outdir, outfname)\n with open(infname, 'r') as inf:\n with open(outfname, 'wt') as outf:\n for line in inf:\n if line.startswith('>') and biosample:\n line = line.rstrip('\\n\\r')\n line = '{} [biosample={}]\\n'.format(line, biosample)\n outf.write(line)\n return outfname\n\n\ndef multi_smt_table(in_table, out_cmt):\n header_key_map = {\n }\n out_headers_total = ('SeqID', 'StructuredCommentPrefix', 'Assembly Method', 'Coverage', 'Sequencing Technology', 'StructuredCommentSuffix')\n with open(out_cmt, 'wt') as outf:\n for row in file.read_tabfile_dict(in_table):\n outrow = dict((h, row.get(header_key_map.get(h,h), '')) for h in out_headers)\n outrow['StructuredCommentPrefix'] = 'Assembly-Data'\n outrow['StructuredCommentSuffix'] = 'Assembly-Data'\n outf.write('\\t'.join(outrow[h] for h in out_headers)+'\\n')\n\n\n\ndef make_structured_comment_file(cmt_fname, name=None, seq_tech=None, coverage=None, assembly_method=None, assembly_method_version=None):\n if assembly_method is None and assembly_method_version is None:\n assembly_method = \"github.com/broadinstitute/viral-ngs\"\n assembly_method_version = version.get_version()\n elif assembly_method is None or assembly_method_version is None:\n raise Exception(\"if either the assembly_method or assembly_method_version are specified, both most be specified\")\n with open(cmt_fname, 'wt') as outf:\n outf.write(\"StructuredCommentPrefix\\t##Genome-Assembly-Data-START##\\n\")\n # note: the v. format is required by NCBI, don't remove the \" v. \"\n\n outf.write(\"Assembly Method\\t{} v. {}\\n\".format(assembly_method, assembly_method_version))\n if name:\n outf.write(\"Assembly Name\\t{}\\n\".format(name))\n if coverage:\n coverage = str(coverage)\n if not coverage.endswith('x') or coverage.endswith('X'):\n coverage = coverage + 'x'\n outf.write(\"Genome Coverage\\t{}\\n\".format(coverage))\n if seq_tech:\n outf.write(\"Sequencing Technology\\t{}\\n\".format(seq_tech))\n outf.write(\"StructuredCommentSuffix\\t##Genome-Assembly-Data-END##\\n\")\n\n\ndef prep_genbank_files(templateFile, fasta_files, annotDir,\n master_source_table=None, comment=None, sequencing_tech=None,\n coverage_table=None, biosample_map=None, organism=None, mol_type=None,\n assembly_method=None, assembly_method_version=None):\n ''' Prepare genbank submission files. Requires .fasta and .tbl files as input,\n as well as numerous other metadata files for the submission. Creates a\n directory full of files (.sqn in particular) that can be sent to GenBank.\n '''\n # get coverage map\n coverage = {}\n if coverage_table:\n for row in file.read_tabfile_dict(coverage_table):\n if row.get('sample') and row.get('aln2self_cov_median'):\n coverage[row['sample']] = row['aln2self_cov_median']\n\n # get biosample id map\n biosample = {}\n if biosample_map:\n for row in file.read_tabfile_dict(biosample_map):\n if row.get('sample') and row.get('BioSample'):\n biosample[row['sample']] = row['BioSample']\n\n # make output directory\n file.mkdir_p(annotDir)\n for fn in fasta_files:\n if not fn.endswith('.fasta'):\n raise Exception(\"fasta files must end in .fasta\")\n sample_base = os.path.basename(fn)[:-6]\n\n # for each segment/chromosome in the fasta file,\n # create a separate new *.fsa file\n n_segs = file.fasta_length(fn)\n with open(fn, \"r\") as inf:\n asm_fasta = Bio.SeqIO.parse(inf, 'fasta')\n for idx, seq_obj in enumerate(asm_fasta):\n seq_obj.id\n if n_segs>1:\n sample = sample_base + \"-\" + str(idx+1)\n else:\n sample = sample_base\n\n # write the segment to a temp .fasta file\n # in the same dir so fasta2fsa functions as expected\n with file.tmp_dir() as tdir:\n temp_fasta_fname = os.path.join(tdir,file.string_to_file_name(seq_obj.id)+\".fasta\")\n with open(temp_fasta_fname, \"w\") as out_chr_fasta:\n Bio.SeqIO.write(seq_obj, out_chr_fasta, \"fasta\")\n # make .fsa files\n fasta2fsa(temp_fasta_fname, annotDir, biosample=biosample.get(seq_obj.id))\n\n # make .src files\n if master_source_table:\n out_src_fname = os.path.join(annotDir, file.string_to_file_name(seq_obj.id) + '.src')\n with open(master_source_table, 'rt') as inf:\n with open(out_src_fname, 'wt') as outf:\n outf.write(inf.readline())\n for line in inf:\n row = line.rstrip('\\n').split('\\t')\n if row[0] in set((seq_obj.id, sample_base, file.string_to_file_name(seq_obj.id))):\n row[0] = seq_obj.id\n outf.write('\\t'.join(row) + '\\n')\n\n # make .cmt files\n make_structured_comment_file(os.path.join(annotDir, file.string_to_file_name(seq_obj.id) + '.cmt'),\n name=seq_obj.id,\n coverage=coverage.get(seq_obj.id, coverage.get(sample_base, coverage.get(file.string_to_file_name(seq_obj.id)))),\n seq_tech=sequencing_tech,\n assembly_method=assembly_method,\n assembly_method_version=assembly_method_version)\n\n # TODO: Migrate to table2asn (tbl2asn is deprecated by NCBI)\n # The old tbl2asn tool wrapper was removed during monorepo migration.\n # table2asn has a different command-line interface and needs a new wrapper.\n log.warning(\"tbl2asn step skipped - tool deprecated. Use table2asn manually or implement wrapper.\")\n\n\ndef parser_prep_genbank_files(parser=argparse.ArgumentParser()):\n parser.add_argument('templateFile', help='Submission template file (.sbt) including author and contact info')\n parser.add_argument(\"fasta_files\", nargs='+', help=\"Input fasta files\")\n parser.add_argument(\"annotDir\",\n help=\"Output directory with genbank submission files (.tbl files must already be there)\")\n parser.add_argument('--comment', default=None, help='comment field')\n parser.add_argument('--sequencing_tech', default=None, help='sequencing technology (e.g. Illumina HiSeq 2500)')\n parser.add_argument('--master_source_table', default=None, help='source modifier table')\n parser.add_argument('--organism', default=None, help='species name')\n parser.add_argument('--mol_type', default=None, help='molecule type')\n parser.add_argument(\"--biosample_map\",\n help=\"\"\"A file with two columns and a header: sample and BioSample.\n This file may refer to samples that are not included in this submission.\"\"\")\n parser.add_argument('--coverage_table',\n default=None,\n help='''A genome coverage report file with a header row. The table must\n have at least two columns named sample and aln2self_cov_median. All other\n columns are ignored. Rows referring to samples not in this submission are\n ignored.''')\n parser.add_argument('--assembly_method', default=None, help='short description of informatic assembly method')\n parser.add_argument('--assembly_method_version', default=None, help='version of assembly method used')\n cmd.common_args(parser, (('tmp_dir', None), ('loglevel', None), ('version', None)))\n cmd.attach_main(parser, prep_genbank_files, split_args=True)\n return parser\n\n\n__commands__.append(('prep_genbank_files', parser_prep_genbank_files))\n\n\ndef prep_sra_table(lib_fname, biosampleFile, md5_fname, outFile):\n ''' This is a very lazy hack that creates a basic table that can be\n pasted into various columns of an SRA submission spreadsheet. It probably\n doesn't work in all cases.\n '''\n metadata = {}\n\n with file.open_or_gzopen(biosampleFile, 'r') as inf:\n header = inf.readline()\n for line in inf:\n row = line.rstrip('\\n\\r').split('\\t')\n metadata.setdefault(row[0], {})\n metadata[row[0]]['biosample_accession'] = row[1]\n\n with file.open_or_gzopen(md5_fname, 'r') as inf:\n for line in inf:\n row = line.rstrip('\\n\\r').split()\n s = os.path.basename(row[1])\n assert s.endswith('.cleaned.bam')\n s = s[:-len('.cleaned.bam')]\n metadata.setdefault(s, {})\n metadata[s]['filename'] = row[1]\n metadata[s]['MD5_checksum'] = row[0]\n\n with open(outFile, 'wt') as outf:\n header = ['biosample_accession', 'sample_name', 'library_ID', 'filename', 'MD5_checksum']\n outf.write('\\t'.join(header) + '\\n')\n with open(lib_fname, 'r') as inf:\n for line in inf:\n lib = line.rstrip('\\n\\r')\n parts = lib.split('.')\n assert len(parts) > 1 and parts[-1].startswith('l')\n s = '.'.join(parts[:-1])\n metadata.setdefault(s, {})\n metadata[s]['library_ID'] = lib\n metadata[s]['sample_name'] = s\n outf.write('\\t'.join(metadata[s].get(h, '') for h in header) + '\\n')\n\n\ndef parser_prep_sra_table(parser=argparse.ArgumentParser()):\n parser.add_argument('lib_fname',\n help='A file that lists all of the library IDs that will be submitted in this batch')\n parser.add_argument(\"biosampleFile\",\n help=\"\"\"A file with two columns and a header: sample and BioSample.\n This file may refer to samples that are not included in this submission.\"\"\")\n parser.add_argument(\"md5_fname\",\n help=\"\"\"A file with two columns and no header. Two columns are MD5 checksum and filename.\n Should contain an entry for every bam file being submitted in this batch.\n This is typical output from \"md5sum *.cleaned.bam\".\"\"\")\n parser.add_argument(\"outFile\",\n help=\"Output table that contains most of the variable columns needed for SRA submission.\")\n cmd.common_args(parser, (('loglevel', None), ('version', None)))\n cmd.attach_main(parser, prep_sra_table, split_args=True)\n return parser\n\n\n__commands__.append(('prep_sra_table', parser_prep_sra_table))\n\n\ndef full_parser():\n return cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/phylo/__init__.py", "content": "\"\"\"\nviral_ngs.phylo - Phylogenetic analysis tools and utilities.\n\nThis package contains tool wrappers and utilities for:\n- Multiple sequence alignment (MAFFT, MUMmer, MUSCLE)\n- Variant calling and annotation (V-Phaser2, SnpEff)\n- GenBank feature table manipulation\n- VCF file utilities\n\"\"\"\nfrom . import feature_table\nfrom . import feature_table_types\nfrom . import genbank\nfrom . import mafft\nfrom . import mummer\nfrom . import muscle\nfrom . import snpeff\nfrom . import vcf\nfrom . import vphaser2\n" }, { "path": "src/viral_ngs/phylo/feature_table.py", "content": "#!/usr/bin/env python\n\nimport re\nimport os\n\nfrom . import feature_table_types\n\nclass SeqPosition(object):\n def __init__(self, position, location_operator=None, allow_fuzzy=True):\n self.position = int(position)\n self.location_operator = location_operator\n self.allow_fuzzy = allow_fuzzy\n\n def __str__(self):\n if self.allow_fuzzy:\n return \"{op}{pos}\".format(op=self.location_operator if self.location_operator else \"\", pos=str(self.position))\n else:\n return str(self.position)\n\n def __int__(self):\n return self.position\n\n def is_fuzzy(self):\n return self.locaton_operator\n\n def __eq__(self, other):\n return self.position == other.position\n\n def __ne__(self, other):\n return self.position != other.position\n\n def __lt__(self, other):\n return self.position < other.position\n\n def __le__(self, other):\n return self.position <= other.position\n\n def __gt__(self, other):\n return self.position > other.position\n\n def __ge__(self, other):\n return self.position >= other.position\n\nclass SeqQualifier(object):\n def __init__(self, qualifier_key, qualifier_value):\n self.qualifier_key = qualifier_key\n self.qualifier_value = qualifier_value\n\n def __str__(self):\n if self.qualifier_value:\n return \"\\t\\t\\t{k}\\t{v}\".format(k=self.qualifier_key,v=self.qualifier_value)\n else:\n return \"\\t\\t\\t{k}\".format(k=self.qualifier_key)\n\nclass SeqLocation(object):\n def __init__(self, start_pos, end_pos, feature_type=None):\n self.start = start_pos\n self.end = end_pos\n self.feature_type = feature_type\n\n def __str__(self):\n if self.feature_type:\n return \"{start}\\t{end}\\t{type}\".format(\n start=self.start, end=self.end, type=self.feature_type\n )\n else:\n return \"{start}\\t{end}\".format(start=self.start, end=self.end)\n\n def __eq__(self, other):\n return ((self.start, self.end) == (other.start, other.end))\n\n def __ne__(self, other):\n return ((self.start, self.end) != (other.start, other.end))\n\n def __lt__(self, other):\n return self.start < other.start or (self.start==other.start and self.end < other.end)\n\n def __le__(self, other):\n return self.start <= other.start or (self.start==other.start and self.end <= other.end)\n\n def __gt__(self, other):\n return self.start > other.start or (self.start==other.start and self.end > other.end)\n\n def __ge__(self, other):\n return self.start >= other.start or (self.start==other.start and self.end >= other.end)\n\nclass SeqFeature(object):\n def __init__(self, locations=None, feature_type=None):\n self.locations = locations or []\n self.type = feature_type\n self.qualifiers = []\n\n def add_location(self, location):\n self.locations.append(location)\n\n def add_location(self, start, location_operator_start, end, location_operator_end, allow_fuzzy=True, *args, **kwargs):\n self.locations.append(SeqLocation(SeqPosition(start, location_operator_start, allow_fuzzy=allow_fuzzy), SeqPosition(end, location_operator_end, allow_fuzzy=allow_fuzzy)))\n # sort with each insertion\n self.sort()\n\n def sort(self):\n #pass\n self.locations = sorted(self.locations)\n\n def add_qualifier(self, qualifier_key, qualifier_value, *args, **kwargs):\n self.qualifiers.append(SeqQualifier(qualifier_key, qualifier_value))\n\n def add_note(self, note_text):\n self.add_qualifier(\"note\", note_text)\n\n @property\n def lines(self):\n if len(self.locations):\n first_loc = self.locations.pop(0)\n first_loc.feature_type = self.type\n yield first_loc\n for l in self.locations:\n yield l\n # yield notes first\n for q in self.qualifiers:\n if q.qualifier_key == \"note\":\n yield q\n for q in self.qualifiers:\n if q.qualifier_key != \"note\":\n yield q\n\nclass AttrDict(dict):\n \"\"\"\n Expose (string) dictionary keys as attributes.\n Danger: can cause collisions between dict item keys\n and dict built-ins (the former will override).\n Only to be used with trusted input for dict keys\n Note: memory leak Python < 2.7.4 / Python3 < 3.2.3\n see: https://bugs.python.org/issue1469629\n \"\"\"\n def __init__(self, *args, **kwargs):\n super(AttrDict, self).__init__(*args, **kwargs)\n self.__dict__ = self\n\nclass FeatureTable(object):\n # get feature table keys from extensive map\n _default_feature_types = sorted(feature_table_types.ft_types.keys())\n\n def __init__(self, filepath=None, valid_feature_types=None):\n self.refID = None\n self._features = []\n self.valid_feature_types = valid_feature_types or self._default_feature_types\n\n self.feature_line_regex_map = { \n \"feature_table_header\" : re.compile(r\"^>Feature (gb\\||ref\\||emb\\||dbj\\|)(?P.*)\\|.*$\"),\n \"feature_first_location_line\" : re.compile(r\"^(?P[<>])?(?P\\d+)\\t(?P[<>])?(?P\\d+)\\t(?P\" + \"|\".join(self.valid_feature_types) + \")$\"),\n \"feature_subsequent_location_line\" : re.compile(r\"^(?P[<>])?(?P\\d+)\\t(?P[<>])?(?P\\d+)\\t*$\"),\n \"offset_line\" : re.compile(r\"^(?:\\[offset=(?P-?\\d+)\\])$\"),\n \"feature_qualifier_line\" : re.compile(r\"^\\t{3}(?P[^\\t]*)(?:\\t(?P[^\\t]*))?$\")\n }\n\n if filepath:\n self.read_feature_table(filepath)\n\n def _parse_line(self, line):\n for k,r in self.feature_line_regex_map.items():\n m = r.match(line)\n if m:\n return_dict = AttrDict(m.groupdict())\n return_dict[\"line_type\"] = k\n #return_dict[\"raw_line\"] = line\n return return_dict\n raise LookupError(r\"Error parsing feature table line: '%s'\" % line)\n\n @property\n def features(self):\n return self._features\n\n @property\n def default_feature_types(self):\n return self._default_feature_values.keys()\n \n\n def add_feature(self, feature):\n self._features.append(feature)\n\n def read_feature_table(self, filepath, map_function=None, allow_fuzzy=True):\n \"\"\"\n Read a Genbank-style feature table in tsv/Sequin format\n This applies any offsets present in the input to the positions seen (no offsets in output).\n The map_function accepts two ints: a position interval, and returns two ints\n representing remapped feature coordinates. \n \"\"\"\n with open(os.path.realpath(os.path.normpath(filepath)), 'rt') as inf:\n feature_in_progress = None\n offset = 0\n for line in inf:\n line = line.rstrip('\\r\\n')\n if not line:\n continue\n\n l = self._parse_line(line)\n if not self.refID and l.line_type == \"feature_table_header\":\n self.refID = l.refID\n elif l.line_type == \"feature_first_location_line\":\n if feature_in_progress:\n self.features.append(feature_in_progress)\n feature_in_progress = None\n \n feature_in_progress = SeqFeature(feature_type=l.feature_type)\n l.start = int(l.start) + int(offset)\n l.end = int(l.end) + int(offset)\n\n if map_function:\n l.start, l.end = map_function(l.start, l.end)\n\n feature_in_progress.add_location(allow_fuzzy=allow_fuzzy,**l)\n elif l.line_type == \"feature_subsequent_location_line\":\n l.start = int(l.start) + int(offset)\n l.end = int(l.end) + int(offset)\n\n if map_function:\n l.start, l.end = map_function(l.start, l.end)\n\n feature_in_progress.add_location(allow_fuzzy=allow_fuzzy,**l)\n elif l.line_type == \"feature_qualifier_line\":\n feature_in_progress.add_qualifier(**l)\n elif l.line_type == \"offset_line\":\n offset = int(l.offset)\n\n if feature_in_progress:\n self.features.append(feature_in_progress)\n feature_in_progress = None\n\n if not self.refID:\n raise Exception(\"The feature table file did not have a header line in the format '%s'\" % self.feature_line_regex_map[\"feature_table_header\"].pattern)\n\n def _is_valid_location(self, location):\n \"\"\"Check if a location has valid, non-None coordinates.\"\"\"\n if location.start is None or location.end is None:\n return False\n if location.start.position is None or location.end.position is None:\n return False\n # Ensure positions are integers (not strings)\n try:\n int(location.start.position)\n int(location.end.position)\n except (ValueError, TypeError):\n return False\n return True\n\n def remap_locations(self, map_function=None):\n \"\"\"\n map_function should accept two SeqLocation objects and the containing feature, and return two (mapped) SeqLocation objects\n if (None,None) is returned, the location will not be included in the remapped location list\n \"\"\"\n if map_function:\n for feature in self.features:\n remapped_locations = []\n intervals_dropped = False\n for location in feature.locations:\n\n location.start, location.end = map_function(location.start,location.end, feature)\n # only include locations that are valid\n if self._is_valid_location(location):\n remapped_locations.append(location)\n else:\n # Mark that we've dropped intervals\n intervals_dropped = True\n # Add note when intervals are dropped\n if not any(q.qualifier_key == \"note\" and \"sequencing did not capture\" in q.qualifier_value\n for q in feature.qualifiers):\n feature.add_note(\"sequencing did not capture all intervals comprising CDS\")\n\n # Filter out invalid intervals for CDS features\n if feature.type == \"CDS\" and len(remapped_locations) > 0:\n filtered_locations = []\n seen_positions = set()\n for loc in remapped_locations:\n start_pos = int(loc.start.position)\n end_pos = int(loc.end.position)\n interval_key = (min(start_pos, end_pos), max(start_pos, end_pos))\n # Skip duplicate or single-base intervals\n if interval_key not in seen_positions and start_pos != end_pos:\n filtered_locations.append(loc)\n seen_positions.add(interval_key)\n else:\n # Mark that we dropped an interval\n intervals_dropped = True\n # If we filtered out intervals, add note\n if intervals_dropped and len(filtered_locations) < len(remapped_locations):\n if not any(q.qualifier_key == \"note\" and \"sequencing did not capture\" in q.qualifier_value\n for q in feature.qualifiers):\n feature.add_note(\"sequencing did not capture all intervals comprising CDS\")\n remapped_locations = filtered_locations\n\n feature.locations = remapped_locations\n\n # Drop CDS features with insufficient total length\n if feature.type == \"CDS\" and len(remapped_locations) > 0:\n total_length = sum(abs(int(loc.end.position) - int(loc.start.position)) + 1\n for loc in remapped_locations)\n if total_length < 3: # Less than one codon\n feature.locations = []\n\n # Drop multi-interval features with internal partial symbols\n # Per NCBI spec, < only valid at 5' end, > only at 3' end of entire feature\n # Issue #74: table2asn rejects \"Feature's location has internal partials\"\n if len(feature.locations) > 1:\n has_internal_partial = False\n for i, loc in enumerate(feature.locations):\n is_first = (i == 0)\n is_last = (i == len(feature.locations) - 1)\n\n # Check for partial symbols on non-terminal intervals\n # < should only appear on the first interval's start\n if loc.start.location_operator == '<' and not is_first:\n has_internal_partial = True\n # > should only appear on the last interval's end\n if loc.end.location_operator == '>' and not is_last:\n has_internal_partial = True\n # Also check reversed cases for strand considerations\n if loc.start.location_operator == '>' and not is_last:\n has_internal_partial = True\n if loc.end.location_operator == '<' and not is_first:\n has_internal_partial = True\n\n if has_internal_partial:\n feature.locations = [] # Drop the entire feature\n\n\n def lines(self, exclude_patterns=None):\n yield \">Feature {refID}\".format(refID=self.refID)\n for feature in self.features:\n for l in feature.lines:\n if not exclude_patterns:\n yield l\n else: \n if not any(re.search(pattern, str(l)) for pattern in exclude_patterns):\n yield l\n" }, { "path": "src/viral_ngs/phylo/feature_table_types.py", "content": "#!/usr/bin/env python\n\n# This is intended to assist with parsing Sequin-format feature tables.\n# \n# Note: Molecule scope, Organism scope, and qualifier conditions are not currently included here\n# Definitions and comments adapted from INSDC documentation.\n#\n# see the feature table key reference:\n# https://www.insdc.org/documents/feature-table#7.2\n# https://www.ncbi.nlm.nih.gov/Sequin/table.html\nft_types = {\n \"assembly_gap\":{\n # Definition gap between two components of a genome or transcriptome assembly;\n \"mandatory_qualifiers\":[\"estimated_length\",\"gap_type\",\"linkage_evidence\"]\n # Comment the location span of the assembly_gap feature for an unknown gap has \n # to be specified by the submitter; the specified gap length has to be \n # reasonable (less or = 1000) and will be indicated as \"n\"'s in sequence.\n # However, the value for the estimated_length of assembly_gap features \n # within a single (non-CON) transcriptome record must be an integer \n # and can not be \"unknown\";\n },\n \"C_region\":{\n # Definition constant region of immunoglobulin light and heavy \n # chains, and T-cell receptor alpha, beta, and gamma \n # chains; includes one or more exons depending on the \n # particular chain\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"CDS\":{\n # Definition coding sequence; sequence of nucleotides that\n # corresponds with the sequence of amino acids in a\n # protein (location includes stop codon); \n # feature includes amino acid conceptual translation.\n \"optional_qualifiers\":[\n \"allele\",\n \"artificial_location\",\n \"citation\",\n \"codon_start\",\n \"db_xref\",\n \"EC_number\",\n \"exception\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"number=unquoted text (single token)\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"protein_id\",\n \"pseudo\",\n \"pseudogene\",\n \"ribosomal_slippage\",\n \"standard_name\",\n \"translation\",\n \"transl_except=(pos:,aa:)\",\n \"transl_table \",\n \"trans_splicing\"\n ]\n # Comment codon_start has valid value of 1 or 2 or 3, indicating\n # the offset at which the first complete codon of a coding\n # feature can be found, relative to the first base of\n # that feature;\n # \"transl_table defines the genetic code table used if\",\n # other than the universal genetic code table;\n # genetic code exceptions outside the range of the specified\n # tables is reported in /transl_except qualifier;\n # \"protein_id consists of a stable ID portion (3+5 format\",\n # with 3 position letters and 5 numbers) plus a version \n # number after the decimal point; when the protein \n # sequence encoded by the CDS changes, only the version \n # number of the /protein_id value is incremented; the\n # stable part of the /protein_id remains unchanged and as \n # a result will permanently be associated with a given \n # protein; \n },\n \"centromere\":{\n # Definition region of biological interest identified as a centromere and\n # which has been experimentally characterized;\n \"optional_qualifiers\":[\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"inference\",\n \"note\",\n \"standard_name\"\n ]\n # Comment the centromere feature describes the interval of DNA \n # that corresponds to a region where chromatids are held \n # and a kinetochore is formed\n },\n \"D-loop\":{\n # Definition displacement loop; a region within mitochondrial DNA in\n # which a short stretch of RNA is paired with one strand\n # of DNA, displacing the original partner DNA strand in\n # this region; also used to describe the displacement of a\n # region of one strand of duplex DNA by a single stranded\n # invader in the reaction catalyzed by RecA protein\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\"\n ]\n },\n \"D_segment\":{\n # Definition Diversity segment of immunoglobulin heavy chain, and \n # T-cell receptor beta chain; \n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"exon\":{\n # Definition region of genome that codes for portion of spliced mRNA, \n # rRNA and tRNA; may contain 5'UTR, all CDSs and 3' UTR; \n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"EC_number\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"number=unquoted text (single token)\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n },\n \"gap\":{\n # Definition gap in the sequence\n \"mandatory_qualifiers\":[\n \"estimated_length\"\n ],\n \"optional_qualifiers\":[\n \"experiment\",\n \"inference\",\n \"map\",\n \"note\"\n ]\n # Comment the location span of the gap feature for an unknown \n # gap is 100 bp, with the 100 bp indicated as 100 \"n\"'s in \n # the sequence. Where estimated length is indicated by \n # an integer, this is indicated by the same number of \n # \"n\"'s in the sequence. \n # No upper or lower limit is set on the size of the gap.\n },\n \"gene\":{\n # Definition region of biological interest identified as a gene \n # and for which a name has been assigned;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"phenotype\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n # Comment the gene feature describes the interval of DNA that \n # corresponds to a genetic trait or phenotype; the feature is,\n # by definition, not strictly bound to it's positions at the \n # ends; it is meant to represent a region where the gene is \n # located.\n },\n \"iDNA\":{\n # Definition intervening DNA; DNA which is eliminated through any of\n # several kinds of recombination;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"number=unquoted text (single token)\",\n \"old_locus_tag\",\n \"standard_name\"\n ]\n # Comment e.g., in the somatic processing of immunoglobulin genes.\n },\n \"intron\":{\n # Definition a segment of DNA that is transcribed, but removed from\n # within the transcript by splicing together the sequences\n # (exons) on either side of it;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"number=unquoted text (single token)\",\n \"old_locus_tag\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n },\n \"J_segment\":{\n # Definition joining segment of immunoglobulin light and heavy \n # chains, and T-cell receptor alpha, beta, and gamma \n # chains; \n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"mat_peptide\":{\n # Definition mature peptide or protein coding sequence; coding\n # sequence for the mature or final peptide or protein\n # product following post-translational modification; the\n # location does not include the stop codon (unlike the\n # corresponding CDS);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"EC_number\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"misc_binding\":{\n # Definition site in nucleic acid which covalently or non-covalently\n # binds another moiety that cannot be described by any\n # other binding key (primer_bind or protein_bind);\n \"mandatory_qualifiers\":[\"bound_moiety\"],\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\"\n ]\n # Comment note that feature key regulatory with /regulatory_class\n # should be used for ribosome binding sites.\n },\n \"misc_difference\":{\n # Definition feature sequence is different from that presented \n # in the entry and cannot be described by any other \n # difference key (old_sequence, variation, or modified_base);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"clone\",\n \"compare\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map=\",\n \"note\",\n \"old_locus_tag\",\n \"phenotype\",\n \"replace\",\n \"standard_name\"\n ]\n # Comment the misc_difference feature key should be used to \n # describe variability that arises as a result of \n # genetic manipulation (e.g. site directed mutagenesis);\n # use /replace=\"\" to annotate deletion, e.g. \n # misc_difference 412..433\n # \"replace=\"\" \",\n },\n \"misc_feature\":{\n # Definition region of biological interest which cannot be described\n # by any other feature key; a new or rare feature;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"number=unquoted text (single token)\",\n \"old_locus_tag\",\n \"phenotype\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n # Comment this key should not be used when the need is merely to \n # mark a region in order to comment on it or to use it in \n # another feature's location\n },\n \"misc_recomb\":{\n # Definition site of any generalized, site-specific or replicative\n # recombination event where there is a breakage and\n # reunion of duplex DNA that cannot be described by other\n # recombination keys or qualifiers of source key \n # (/proviral);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"recombination_class\",\n \"standard_name\"\n ]\n },\n \"misc_RNA\":{\n # Definition any transcript or RNA product that cannot be defined by\n # other RNA keys (prim_transcript, precursor_RNA, mRNA,\n # 5'UTR, 3'UTR, exon, CDS, sig_peptide, transit_peptide,\n # mat_peptide, intron, polyA_site, ncRNA, rRNA and tRNA);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n },\n \"misc_structure\":{\n # Definition any secondary or tertiary nucleotide structure or \n # conformation that cannot be described by other Structure\n # keys (stem_loop and D-loop);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"standard_name\"\n ]\n },\n \"mobile_element\":{\n # Definition region of genome containing mobile elements;\n \"mandatory_qualifiers\":[\"mobile_element_type\"],\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"rpt_family\",\n \"rpt_type\",\n \"standard_name\"\n ]\n },\n \"modified_base\":{\n # Definition the indicated nucleotide is a modified nucleotide and\n # should be substituted for by the indicated molecule\n # (given in the mod_base qualifier value)\n \"mandatory_qualifiers\":[\"mod_base\"],\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"frequency\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\"\n ]\n # Comment value is limited to the restricted vocabulary for \n # modified base abbreviations;\n },\n \"mRNA\":{\n # Definition messenger RNA; includes 5'untranslated region (5'UTR),\n # coding sequences (CDS, exon) and 3'untranslated region\n # (3'UTR);\n \"optional_qualifiers\":[\n \"allele\",\n \"artificial_location\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n },\n \"ncRNA\":{\n # Definition a non-protein-coding gene, other than ribosomal RNA and\n # transfer RNA, the functional molecule of which is the RNA\n # transcript;\n \"mandatory_qualifiers\":[\"ncRNA_class\"],\n \n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n # Comment the ncRNA feature is not used for ribosomal and transfer\n # RNA annotation, for which the rRNA and tRNA feature keys\n # should be used, respectively;\n },\n \"N_region\":{\n # Definition extra nucleotides inserted between rearranged \n # immunoglobulin segments.\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"old_sequence\":{\n # Definition the presented sequence revises a previous version of the\n # sequence at this location;\n \"mandatory_qualifiers\":[\"citation\", \"compare\"],\n \"optional_qualifiers\":[\n \"allele\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"replace\"\n ]\n # Comment /replace=\"\" is used to annotate deletion, e.g. \n # old_sequence 12..15 \"replace=\"\" \",\n # NOTE: This feature key is not valid in entries/records\n # created from 15-Oct-2007.\n },\n \"operon\":{\n # Definition region containing polycistronic transcript including a cluster of\n # genes that are under the control of the same regulatory sequences/promoter\n # and in the same biological pathway\n \"mandatory_qualifiers\":[\"operon\"],\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"inference\",\n \"map\",\n \"note\",\n \"phenotype\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"oriT\":{\n # Definition origin of transfer; region of a DNA molecule where transfer is\n # initiated during the process of conjugation or mobilization\n \"optional_qualifiers\":[\n \"allele\",\n \"bound_moiety\",\n \"citation\",\n \"db_xref\",\n \"direction=value\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"rpt_family\",\n \"rpt_type\",\n \"rpt_unit_range\",\n \"rpt_unit_seq\",\n \"standard_name\"\n ]\n # Comment rep_origin should be used for origins of replication; \n # \"direction has legal values RIGHT, LEFT and BOTH, however only \",\n # RIGHT and LEFT are valid when used in conjunction with the oriT \n # feature;\n # origins of transfer can be present in the chromosome; \n # plasmids can contain multiple origins of transfer\n },\n \"polyA_site\":{\n # Definition site on an RNA transcript to which will be added adenine\n # residues by post-transcriptional polyadenylation;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\"\n ]\n },\n \"precursor_RNA\":{\n # Definition any RNA species that is not yet the mature RNA product;\n # may include ncRNA, rRNA, tRNA, 5' untranslated region\n # (5'UTR), coding sequences (CDS, exon), intervening\n # sequences (intron) and 3' untranslated region (3'UTR);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n # Comment used for RNA which may be the result of \n # post-transcriptional processing; if the RNA in question \n # is known not to have been processed, use the \n # prim_transcript key.\n },\n \"prim_transcript\":{\n # Definition primary (initial, unprocessed) transcript; \n # may include ncRNA, rRNA, tRNA, 5' untranslated region\n # (5'UTR), coding sequences (CDS, exon), intervening\n # sequences (intron) and 3' untranslated region (3'UTR);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"standard_name\"\n ]\n },\n \"primer_bind\":{\n # Definition non-covalent primer binding site for initiation of\n # replication, transcription, or reverse transcription;\n # includes site(s) for synthetic e.g., PCR primer elements;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"standard_name\",\n \"PCR_conditions\"\n ]\n # Comment used to annotate the site on a given sequence to which a primer \n # molecule binds - not intended to represent the sequence of the\n # primer molecule itself; PCR components and reaction times may \n # be stored under the \"/PCR_conditions\" qualifier; \n # since PCR reactions most often involve pairs of primers,\n # a single primer_bind key may use the order() operator\n # with two locations, or a pair of primer_bind keys may be\n # used.\n },\n \"propeptide\":{\n # Definition propeptide coding sequence; coding sequence for the domain of a \n # proprotein that is cleaved to form the mature protein product.\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"protein_bind\":{\n # Definition non-covalent protein binding site on nucleic acid;\n \"mandatory_qualifiers\":[\"bound_moiety\"],\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"standard_name\"\n ]\n # Comment note that feature key regulatory with /regulatory_class\n # should be used for ribosome binding sites.\n },\n \"regulatory\":{\n # Definition any region of sequence that functions in the regulation of\n # transcription, translation, replication or chromatin structure;\n \"mandatory_qualifiers\":[\"regulatory_class\"],\n \"optional_qualifiers\":[\n \"allele\",\n \"bound_moiety\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"phenotype\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n # Comment This feature has replaced the following Feature Keys on 15-DEC-2014:\n # enhancer, promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal,\n # RBS, GC_signal, polyA_signal, attenuator, terminator, misc_signal.\n }, \n \"repeat_region\":{\n # Definition region of genome containing repeating units;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"rpt_family\",\n \"rpt_type\",\n \"rpt_unit_range\",\n \"rpt_unit_seq\",\n \"satellite\",\n \"standard_name\"\n ]\n },\n \"rep_origin\":{\n # Definition origin of replication; starting site for duplication of\n # nucleic acid to give two identical copies; \n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"direction=value\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"standard_name\"\n ]\n # Comment /direction has valid values: RIGHT, LEFT, or BOTH.\n },\n \"rRNA\":{\n # Definition mature ribosomal RNA; RNA component of the\n # ribonucleoprotein particle (ribosome) which assembles\n # amino acids into proteins.\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n # Comment rRNA sizes should be annotated with the /product\n # qualifier.\n },\n \"S_region\":{\n # Definition switch region of immunoglobulin heavy chains; \n # involved in the rearrangement of heavy chain DNA leading \n # to the expression of a different immunoglobulin class \n # from the same B-cell;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"sig_peptide\":{\n # Definition signal peptide coding sequence; coding sequence for an\n # N-terminal domain of a secreted protein; this domain is\n # involved in attaching nascent polypeptide to the\n # membrane leader sequence;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"source\":{\n # Definition identifies the biological source of the specified span of\n # the sequence; this key is mandatory; more than one source\n # key per sequence is allowed; every entry/record will have, as a\n # minimum, either a single source key spanning the entire\n # sequence or multiple source keys, which together, span the\n # entire sequence.\n \"mandatory_qualifiers\":[\"organism\",\"mol_type\"],\n \"optional_qualifiers\":[\n \"altitude\",\n \"bio_material\",\n \"cell_line\",\n \"cell_type\",\n \"chromosome\",\n \"citation\",\n \"clone\",\n \"clone_lib\",\n \"collected_by\",\n \"collection_date\",\n \"country\",\n \"cultivar\",\n \"culture_collection\",\n \"db_xref\",\n \"dev_stage\",\n \"ecotype\",\n \"environmental_sample\",\n \"focus\",\n \"germline\",\n \"haplogroup\",\n \"haplotype\",\n \"host\",\n \"identified_by\",\n \"isolate\",\n \"isolation_source\",\n \"lab_host\",\n \"lat_lon\",\n \"macronuclear\",\n \"map\",\n \"mating_type\",\n \"note\",\n \"organelle\",\n \"PCR_primers\",\n \"plasmid\",\n \"pop_variant\",\n \"proviral\",\n \"rearranged\",\n \"segment\",\n \"serotype\",\n \"serovar\",\n \"sex\",\n \"specimen_voucher\",\n \"strain\",\n \"sub_clone\",\n \"submitter_seqid\",\n \"sub_species\",\n \"sub_strain\",\n \"tissue_lib\",\n \"tissue_type\",\n \"transgenic\",\n \"type_material\",\n \"variety\"\n ]\n # Comment transgenic sequences must have at least two source feature\n # keys; in a transgenic sequence the source feature key\n # describing the organism that is the recipient of the DNA\n # must span the entire sequence;\n # see Appendix III /organelle for a list of \n },\n \"stem_loop\":{\n # Definition hairpin; a double-helical region formed by base-pairing\n # between adjacent (inverted) complementary sequences in a\n # single strand of RNA or DNA. \n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"standard_name\"\n ]\n },\n \"STS\":{\n # Definition sequence tagged site; short, single-copy DNA sequence\n # that characterizes a mapping landmark on the genome and\n # can be detected by PCR; a region of the genome can be\n # mapped by determining the order of a series of STSs;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"standard_name\",\n ]\n # Comment STS location to include primer(s) in primer_bind key or\n # primers.\n },\n \"telomere\":{\n # Definition region of biological interest identified as a telomere \n # and which has been experimentally characterized;\n \"optional_qualifiers\":[\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"inference\",\n \"note\",\n \"rpt_type\",\n \"rpt_unit_range\",\n \"rpt_unit_seq\",\n \"standard_name\"\n ]\n # Comment the telomere feature describes the interval of DNA \n # that corresponds to a specific structure at the end of \n # the linear eukaryotic chromosome which is required for \n # the integrity and maintenance of the end; this region\n # is unique compared to the rest of the chromosome and \n # represent the physical end of the chromosome;\n },\n \"tmRNA\":{\n # Definition transfer messenger RNA; tmRNA acts as a tRNA first,\n # and then as an mRNA that encodes a peptide tag; the\n # ribosome translates this mRNA region of tmRNA and attaches\n # the encoded peptide tag to the C-terminus of the\n # unfinished protein; this attached tag targets the protein for\n # destruction or proteolysis;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n \"tag_peptide\"\n ]\n },\n \"transit_peptide\":{\n # Definition transit peptide coding sequence; coding sequence for an\n # N-terminal domain of a nuclear-encoded organellar\n # protein; this domain is involved in post-translational\n # import of the protein into the organelle;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"tRNA\":{\n # Definition mature transfer RNA, a small RNA molecule (75-85 bases\n # long) that mediates the translation of a nucleic acid\n # sequence into an amino acid sequence;\n \"optional_qualifiers\":[\n \"allele\",\n \"anticodon=(pos:,aa:,seq:)\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"operon\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n },\n \"unsure\":{\n # Definition a small region of sequenced bases, generally 10 or fewer in its length, which \n # could not be confidently identified. Such a region might contain called bases \n # (A, T, G, or C), or a mixture of called-bases and uncalled-bases ('N').\n # The unsure feature should not be used when annotating gaps in genome assemblies.\n # Please refer to assembly_gap feature for gaps within the sequence of an assembled\n # genome. For annotation of gaps in other sequences than assembled genomes use the \n # gap feature.\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"compare\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"replace\"\n ]\n # Comment use /replace=\"\" to annotate deletion, e.g. \n # unsure 11..15 \"replace=\"\" \",\n },\n \"V_region\":{\n # Definition variable region of immunoglobulin light and heavy\n # chains, and T-cell receptor alpha, beta, and gamma\n # chains; codes for the variable amino terminal portion;\n # can be composed of V_segments, D_segments, N_regions,\n # and J_segments;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\",\n ]\n },\n \"V_segment\":{\n # Definition variable segment of immunoglobulin light and heavy\n # chains, and T-cell receptor alpha, beta, and gamma\n # chains; codes for most of the variable region (V_region)\n # and the last few amino acids of the leader peptide;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"product\",\n \"pseudo\",\n \"pseudogene\",\n \"standard_name\"\n ]\n },\n \"variation\":{\n # Definition a related strain contains stable mutations from the same\n # gene (e.g., RFLPs, polymorphisms, etc.) which differ\n # from the presented sequence at this location (and\n # possibly others);\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"compare\",\n \"db_xref\",\n \"experiment\",\n \"frequency\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"phenotype\",\n \"product\",\n \"replace\",\n \"standard_name\"\n ]\n # Comment used to describe alleles, RFLP's,and other naturally occurring \n # mutations and polymorphisms; variability arising as a result \n # of genetic manipulation (e.g. site directed mutagenesis) should \n # be described with the misc_difference feature;\n # use /replace=\"\" to annotate deletion, e.g. \n },\n \"3'UTR\":{\n # Definition 1) region at the 3' end of a mature transcript (following \n # the stop codon) that is not translated into a protein;\n # 2) region at the 3' end of an RNA virus (following the last stop\n # codon) that is not translated into a protein;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n },\n \"5'UTR\":{\n # Definition 1) region at the 5' end of a mature transcript (preceding \n # the initiation codon) that is not translated into a protein;\n # 2) region at the 5' end of an RNA virus genome (preceding the first \n # initiation codon) that is not translated into a protein;\n \"optional_qualifiers\":[\n \"allele\",\n \"citation\",\n \"db_xref\",\n \"experiment\",\n \"function\",\n \"gene\",\n \"gene_synonym\",\n \"inference\",\n \"locus_tag\",\n \"map\",\n \"note\",\n \"old_locus_tag\",\n \"standard_name\",\n \"trans_splicing\"\n ]\n }\n }" }, { "path": "src/viral_ngs/phylo/genbank.py", "content": "#!/usr/bin/python\n\n# built-ins\nimport time\nimport os\nimport re\nimport logging\n\n# third-party\nfrom Bio import Entrez\n\nlog = logging.getLogger(__name__)\n\n\ndef parse_accession_str(chr_ref):\n '''\n This tries to match an NCBI accession as defined here:\n http://www.ncbi.nlm.nih.gov/Sequin/acc.html\n '''\n m = re.search(r\"(?P(?:[a-zA-Z]{1,6}|NC_)\\d{1,10})(?:\\.(?P\\d+))?.*\", chr_ref)\n if m:\n chr_ref = m.group(\"accession\")\n return chr_ref\n\ndef get_feature_table_id(featureTableFile):\n with open(featureTableFile, 'rt') as inf:\n for line in inf:\n line = line.rstrip('\\r\\n')\n if not line:\n pass\n elif line.startswith('>'):\n # sequence identifier\n if not line.startswith('>Feature '):\n raise Exception(\"not sure how to handle a non-Feature record\")\n seqid = line[len('>Feature '):].strip()\n if not (\n (seqid.startswith('gb|') or seqid.startswith('ref|') or seqid.startswith('emb|') or seqid.startswith('dbj|'))):\n raise Exception(\"reference annotation ID does not appear to refer to a GenBank, RefSeq, EMBL, or DDBJ accession: %s\" % seqid)\n m = re.search(r\"(?P(?:gb|ref|emb|dbj))\\|(?:(?P[a-zA-Z0-9\\._]+))+.*\", seqid)\n if m:\n seqid = m.group(\"accession\")\n else:\n raise Exception(\"Error parsing accession: %s\" % seqid)\n return seqid\n\ndef _seq_chunks(seq, n):\n # http://stackoverflow.com/a/312464/190597 (Ned Batchelder)\n \"\"\" Yield successive n-sized chunks from seq.\"\"\"\n for i in range(0, len(seq), n):\n yield seq[i:i + n]\n\ndef _fetch_from_nuccore(accessionList, destinationDir, emailAddress,\n forceOverwrite=False, rettype=\"fasta\", retmode=\"text\",\n fileExt=None, combinedFilePrefix=None, removeSeparateFiles=False,\n chunkSize=1, api_key=None):\n \"\"\"\n This function downloads and saves files from NCBI nuccore.\n \"\"\"\n db = \"nuccore\"\n Entrez.email = emailAddress\n if api_key is not None:\n Entrez.api_key = api_key\n Entrez.tool = \"https://github.com/broadinstitute/viral-ngs\"\n\n maxChunkSize = 500\n\n # Conform to NCBI retreival guidelines by chunking into 500-accession chunks if\n # >500 accessions are specified and chunkSize is set to 1\n # Also clamp chunk size to 500 if the user specified a larger value.\n if chunkSize > maxChunkSize or (len(accessionList) > maxChunkSize and chunkSize == 1):\n chunkSize = maxChunkSize\n\n outEx = {\"fasta\": \"fasta\", \"ft\": \"tbl\", \"gb\": \"gbk\"}\n\n assert rettype in outEx.keys(\n ), \"The return type requested, %s, is not compatible with the nuccore fetch.\" % rettype\n\n outputDirectory = os.path.abspath(os.path.expanduser(destinationDir))\n\n if not os.path.exists(outputDirectory):\n os.makedirs(outputDirectory)\n\n # if the file extension to use is specified as the fileExt arg, use it\n # otherwise, use the default for the rettype according to the outEx dict,\n # falling back to the retmode if there is no match\n if not fileExt:\n outputExtension = outEx.get(rettype, retmode)\n else:\n outputExtension = str(fileExt)\n\n # ensure the extension starts with a \".\", also allowing for passed-in\n # extensions that already have it\n if outputExtension[:1] != \".\":\n outputExtension = \".\" + outputExtension\n\n log.info(\"Fetching %s entries from GenBank: %s\\n\", str(len(accessionList)), \", \".join(accessionList[:10]))\n outputFiles = []\n\n for chunkNum, chunk in enumerate(_seq_chunks(accessionList, chunkSize)):\n\n accString = \",\".join(chunk)\n\n # if the filename would be longer than Linux allows, simply say \"chunk-chunkNum\"\n if len(accString) + len(outputExtension) <= 254:\n outputFilePath = os.path.join(outputDirectory, accString + outputExtension)\n else:\n outputFilePath = os.path.join(outputDirectory, \"chunk-{}\".format(chunkNum) + outputExtension)\n\n if not forceOverwrite:\n log.info(\"not overwriting, checking for existence\")\n assert not os.path.exists(outputFilePath), \"\"\"File %s already exists. Consider removing\n this file or specifying a different output directory. The files for the accessions specified\n can be overwritten if you add --forceOverwrite flag. Processing aborted.\"\"\" % outputFilePath\n\n tryCount = 1\n while True:\n try:\n log.info(\"Fetching file %s: %s, try #%s\", chunkNum + 1, accString, tryCount)\n handle = Entrez.efetch(db=db, rettype=rettype, id=accString)\n\n with open(outputFilePath, \"w\") as outf:\n for line in handle:\n outf.write(line)\n outputFiles.append(outputFilePath)\n except IOError:\n\n log.warning(\n \"Error fetching file %s: %s, try #%s probably because NCBI is too busy.\", chunkNum + 1, accString,\n tryCount)\n\n tryCount += 1\n if tryCount > 4:\n log.warning(\"Tried too many times. Aborting.\")\n raise\n\n # if the fetch failed, wait a few seconds and try again.\n log.info(\"Waiting and retrying...\")\n time.sleep(2)\n\n continue\n break\n\n # assert that we are not trying to remove the intermediate files without writing a combined file\n if removeSeparateFiles:\n assert combinedFilePrefix, \"\"\"The intermediate files\n can only be removed if a combined file is written via --combinedFilePrefix\"\"\"\n\n # build a path to the combined genome file\n if combinedFilePrefix:\n concatenatedGenomeFilepath = os.path.join(outputDirectory, combinedFilePrefix + outputExtension)\n\n if not forceOverwrite:\n assert not os.path.exists(concatenatedGenomeFilepath), \"\"\"File %s already exists. Consider removing\n this file or specifying a different output directory. The files for the accessions specified\n can be overwritten if you add --forceOverwrite flag. Processing aborted.\"\"\" % outputFilePath\n\n # concatenate the files together into one genome file\n with open(concatenatedGenomeFilepath, 'w') as outfile:\n for filePath in outputFiles:\n with open(filePath) as infile:\n for line in infile:\n outfile.write(line)\n\n # if the option is specified, remove the intermediate fasta files\n if removeSeparateFiles:\n while len(outputFiles) > 0:\n os.unlink(outputFiles.pop())\n\n # add the combined file to the list of files returned\n outputFiles.append(concatenatedGenomeFilepath)\n\n # return list of files\n return outputFiles\n\n\ndef fetch_fastas_from_genbank(\n accessionList,\n destinationDir,\n emailAddress,\n forceOverwrite,\n combinedFilePrefix,\n removeSeparateFiles,\n fileExt=None,\n rettype=\"fasta\",\n retmode=\"text\",\n chunkSize=1, \n api_key=None):\n return _fetch_from_nuccore(\n accessionList, destinationDir, emailAddress, forceOverwrite, rettype, retmode, fileExt, combinedFilePrefix,\n removeSeparateFiles, chunkSize, api_key=api_key)\n\n\ndef fetch_feature_tables_from_genbank(\n accessionList,\n destinationDir,\n emailAddress,\n forceOverwrite,\n combinedFilePrefix,\n removeSeparateFiles,\n fileExt=None,\n rettype=\"ft\",\n retmode=\"text\",\n chunkSize=1,\n api_key=None):\n return _fetch_from_nuccore(\n accessionList, destinationDir, emailAddress, forceOverwrite, rettype, retmode, fileExt, combinedFilePrefix,\n removeSeparateFiles, chunkSize, api_key=api_key)\n\n\ndef fetch_full_records_from_genbank(\n accessionList,\n destinationDir,\n emailAddress,\n forceOverwrite,\n combinedFilePrefix,\n removeSeparateFiles,\n fileExt=None,\n rettype=\"gb\",\n retmode=\"text\",\n chunkSize=1,\n api_key=None):\n return _fetch_from_nuccore(\n accessionList, destinationDir, emailAddress, forceOverwrite, rettype, retmode, fileExt, combinedFilePrefix,\n removeSeparateFiles, chunkSize, api_key=api_key)\n" }, { "path": "src/viral_ngs/phylo/mafft.py", "content": "'''\n MAFFT - Multiple alignment program for amino acid or nucleotide sequences\n http://mafft.cbrc.jp/alignment/software/\n'''\n\n__author__ = \"tomkinsc@broadinstitute.org\"\n\nfrom Bio import SeqIO\nimport logging\nfrom viral_ngs import core\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nimport os\nimport os.path\nimport shutil\nimport subprocess\n\nTOOL_NAME = \"mafft\"\n\n_log = logging.getLogger(__name__)\n\n\nclass MafftTool(core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(MafftTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').strip().split()[0]\n\n def __seqIdsAreAllUnique(self, filePath, inputFormat=\"fasta\"):\n seqIds = []\n with open(filePath, \"r\") as inFile:\n fastaFile = SeqIO.parse(inFile, inputFormat)\n seqIds = [x.id for x in fastaFile]\n\n # collapse like IDs using set()\n if len(seqIds) > len(set(seqIds)):\n raise LookupError(\n \"Not all sequence IDs in input are unique for file: {}\".format(\n os.path.basename(filePath)\n )\n )\n\n # pylint: disable=W0221\n def execute(\n self,\n inFastas,\n outFile,\n localpair,\n globalpair,\n preservecase,\n reorder,\n outputAsClustal,\n maxiters,\n gapOpeningPenalty=None,\n offset=None,\n threads=None,\n verbose=True,\n retree=None\n ):\n inputFileName = \"\"\n tempCombinedInputFile = \"\"\n\n # get the full paths of input and output files in case the user has specified relative paths\n inputFiles = []\n for f in inFastas:\n inputFiles.append(os.path.abspath(f))\n outFile = os.path.abspath(outFile)\n\n # ensure that all sequence IDs in each input file are unique\n # (otherwise the alignment result makes little sense)\n # we can check before combining to localize duplications to a specific file\n for filePath in inputFiles:\n self.__seqIdsAreAllUnique(filePath)\n\n # if multiple fasta files are specified for input\n if len(inputFiles) > 1:\n # combined specified input files into a single temp FASTA file so MAFFT can read them\n tempFileSuffix = \"\"\n for filePath in inputFiles:\n tempFileSuffix += \"__\" + os.path.basename(filePath)\n tempCombinedInputFile = file.mkstempfname('__combined.{}'.format(tempFileSuffix))\n with open(tempCombinedInputFile, \"w\") as outfile:\n for f in inputFiles:\n with open(f, \"r\") as infile:\n outfile.write(infile.read())\n inputFileName = tempCombinedInputFile\n # if there is only one file specified, just use it\n else:\n inputFileName = inputFiles[0]\n\n # check that all sequence IDs in a file are unique\n self.__seqIdsAreAllUnique(inputFileName)\n\n # change the pwd, since the shell script that comes with mafft depends on the pwd\n # being correct\n pwdBeforeMafft = os.getcwd()\n os.chdir(os.path.dirname(self.install_and_get_path()))\n\n # build the MAFFT command\n tool_cmd = [self.install_and_get_path()]\n\n if not (retree or localpair or globalpair):\n tool_cmd.append(\"--auto\")\n tool_cmd.extend([\"--thread\", \"{}\".format(misc.sanitize_thread_count(threads))])\n\n if localpair and globalpair:\n raise Exception(\"Alignment type must be either local or global, not both.\")\n\n if localpair:\n tool_cmd.append(\"--localpair\")\n if not maxiters:\n maxiters = 1000\n if globalpair:\n tool_cmd.append(\"--globalpair\")\n if not maxiters:\n maxiters = 1000\n if preservecase:\n tool_cmd.append(\"--preservecase\")\n if reorder:\n tool_cmd.append(\"--reorder\")\n if retree:\n tool_cmd.extend([\"--retree\", \"{}\".format(retree)])\n if gapOpeningPenalty:\n tool_cmd.extend([\"--op\", \"{penalty}\".format(penalty=gapOpeningPenalty)])\n if offset:\n tool_cmd.extend([\"--ep\", \"{num}\".format(num=offset)])\n if not verbose:\n tool_cmd.append(\"--quiet\")\n if outputAsClustal:\n tool_cmd.append(\"--clustalout\")\n if maxiters:\n tool_cmd.extend([\"--maxiterate\", \"{iters}\".format(iters=maxiters)])\n\n tool_cmd.append(inputFileName)\n\n _log.debug(' '.join(tool_cmd))\n\n # run the MAFFT alignment\n with open(outFile, 'w') as outf:\n misc.run_and_save(tool_cmd, outf=outf)\n\n if len(tempCombinedInputFile):\n # remove temp FASTA file\n os.unlink(tempCombinedInputFile)\n\n # restore pwd\n os.chdir(pwdBeforeMafft)\n\n return outFile\n # pylint: enable=W0221\n" }, { "path": "src/viral_ngs/phylo/mummer.py", "content": "'''\n The MUMMER aligner\n http://mummer.sourceforge.net/\n'''\n\nimport logging\nfrom viral_ngs import core\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nimport os\nimport os.path\nimport random\nimport shutil\nimport subprocess\nimport Bio.SeqIO\n\nTOOL_NAME = \"mummer\"\n\nlog = logging.getLogger(__name__)\n\n\nclass MummerTool(core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(MummerTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip()\n\n def executable_path(self):\n exec_path = core.Tool.executable_path(self)\n if os.path.isdir(exec_path):\n return exec_path\n else:\n return os.path.dirname(exec_path)\n\n def execute(self, refFasta, qryFastas):\n toolCmd = [os.path.join(self.install_and_get_path(), 'mummer'),\n refFasta] + qryFastas\n log.debug(' '.join(toolCmd))\n subprocess.check_call(toolCmd)\n\n def nucmer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None):\n if not outDelta.endswith('.delta'):\n raise Exception()\n outDelta = outDelta[:-6]\n toolCmd = [os.path.join(self.install_and_get_path(), 'nucmer'),\n '--prefix={}'.format(outDelta)]\n if extend is not None:\n if not extend:\n # default behavior is --extend\n # mummer4 no longer recognizes --extend and we should only\n # specify an argument here if we want non-default behavior\n toolCmd.append('--noextend')\n if breaklen is not None:\n toolCmd.extend(['--breaklen', str(breaklen)])\n if maxgap is not None:\n toolCmd.extend(['--maxgap', str(maxgap)])\n if minmatch is not None:\n toolCmd.extend(['--minmatch', str(minmatch)])\n if mincluster is not None:\n toolCmd.extend(['--mincluster', str(mincluster)])\n toolCmd.extend([refFasta, qryFasta])\n log.debug(' '.join(toolCmd))\n subprocess.check_call(toolCmd)\n\n def promer(self, refFasta, qryFasta, outDelta, extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None):\n if not outDelta.endswith('.delta'):\n raise Exception()\n outDelta = outDelta[:-6]\n toolCmd = [os.path.join(self.install_and_get_path(), 'promer'),\n '--prefix={}'.format(outDelta)]\n if extend is not None:\n if not extend:\n # default behavior is --extend\n # mummer4 no longer recognizes --extend and we should only\n # specify an argument here if we want non-default behavior\n toolCmd.append('--noextend')\n if breaklen is not None:\n toolCmd.extend(['--breaklen', str(breaklen)])\n if maxgap is not None:\n toolCmd.extend(['--maxgap', str(maxgap)])\n if minmatch is not None:\n toolCmd.extend(['--minmatch', str(minmatch)])\n if mincluster is not None:\n toolCmd.extend(['--mincluster', str(mincluster)])\n toolCmd.extend([refFasta, qryFasta])\n log.debug(' '.join(toolCmd))\n subprocess.check_call(toolCmd)\n\n def delta_filter(self, inDelta, outDelta):\n toolCmd = [os.path.join(self.install_and_get_path(), 'delta-filter'),\n '-q', inDelta]\n log.debug(' '.join(toolCmd))\n with open(outDelta, 'w') as outf:\n subprocess.check_call(toolCmd, stdout=outf)\n\n def show_tiling(self, inDelta, outTiling, outFasta=None,\n circular=False, min_pct_id=None, min_contig_len=None,\n min_pct_contig_aligned=None, tab_delim=False,\n min_contig_coverage_diff=None):\n opts = []\n if circular:\n opts.append('-c')\n if tab_delim:\n opts.append('-a')\n if min_pct_id is not None:\n opts.append('-i')\n opts.append(str(100.0 * min_pct_id))\n if min_contig_len is not None:\n opts.append('-l')\n opts.append(str(min_contig_len))\n if min_pct_contig_aligned is not None:\n opts.append('-v')\n opts.append(str(100.0 * min_pct_contig_aligned))\n if min_contig_coverage_diff is not None:\n opts.append('-V')\n opts.append(str(100.0 * min_contig_coverage_diff))\n toolCmd = [os.path.join(self.install_and_get_path(), 'show-tiling')]\n if outFasta:\n toolCmd = toolCmd + ['-p', outFasta]\n toolCmd = toolCmd + opts + [inDelta]\n log.debug(' '.join(toolCmd))\n with open(outTiling, 'w') as outf:\n subprocess.check_call(toolCmd, stdout=outf)\n\n def trim_contigs(self, refFasta, contigsFasta, outFasta,\n aligner='nucmer', circular=False, extend=False, breaklen=None,\n min_pct_id=0.6, min_pct_contig_aligned=0.5, min_contig_len=200):\n ''' Align contigs with MUMmer and trim off the unused portions.\n '''\n # run MUMmer to get best alignments\n if aligner=='nucmer':\n aligner = self.nucmer\n elif aligner=='promer':\n aligner = self.promer\n else:\n raise NameError()\n delta_1 = file.mkstempfname('.delta')\n delta_2 = file.mkstempfname('.delta')\n tiling = file.mkstempfname('.tiling')\n aligner(refFasta, contigsFasta, delta_1, extend=extend, breaklen=breaklen)\n self.delta_filter(delta_1, delta_2)\n self.show_tiling(delta_2, tiling, circular=circular, tab_delim=True,\n min_pct_id=min_pct_id, min_contig_len=min_contig_len,\n min_pct_contig_aligned=min_pct_contig_aligned)\n os.unlink(delta_1)\n os.unlink(delta_2)\n\n # get trim boundaries per contig\n seq_bounds = {}\n with open(tiling, 'rt') as inf:\n for line in inf:\n row = line.rstrip().split('\\t')\n seq_bounds.setdefault(row[-1], [float('inf'), 0])\n start = min(int(row[2]), int(row[3]))\n stop = max(int(row[2]), int(row[3]))\n seq_bounds[row[-1]][0] = min(seq_bounds[row[-1]][0], start)\n seq_bounds[row[-1]][1] = max(seq_bounds[row[-1]][1], stop)\n os.unlink(tiling)\n\n # trim contigs\n out = []\n with open(contigsFasta, 'rt') as inf:\n for record in Bio.SeqIO.parse(inf, 'fasta'):\n if record.id in seq_bounds:\n seq = record.seq[seq_bounds[record.id][0]-1:seq_bounds[record.id][1]]\n record.seq = seq\n out.append(record)\n with open(outFasta, 'wt') as outf:\n Bio.SeqIO.write(out, outf, 'fasta')\n\n def scaffold_contigs(self, refFasta, contigsFasta, outFasta,\n aligner='nucmer', circular=False, extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None,\n min_contig_coverage_diff=0.0,\n min_pct_id=0.6, min_pct_contig_aligned=None, min_contig_len=200):\n ''' Use MUMmer's pseudomolecule feature to scaffold contigs\n onto a reference genome.\n '''\n if aligner=='nucmer':\n aligner = self.nucmer\n elif aligner=='promer':\n aligner = self.promer\n else:\n raise NameError()\n delta_1 = file.mkstempfname('.delta')\n delta_2 = file.mkstempfname('.delta')\n tiling = file.mkstempfname('.tiling')\n aligner(refFasta, contigsFasta, delta_1, extend=extend, breaklen=breaklen,\n maxgap=maxgap, minmatch=minmatch, mincluster=mincluster)\n self.delta_filter(delta_1, delta_2)\n self.show_tiling(delta_2, tiling, outFasta=outFasta, circular=circular,\n min_pct_id=min_pct_id, min_contig_len=min_contig_len,\n min_contig_coverage_diff=min_contig_coverage_diff,\n min_pct_contig_aligned=min_pct_contig_aligned)\n os.unlink(delta_1)\n os.unlink(delta_2)\n os.unlink(tiling)\n\n def scaffold_contigs_custom(self, refFasta, contigsFasta, outFasta,\n outAlternateContigs=None,\n aligner='nucmer', extend=None, breaklen=None,\n maxgap=None, minmatch=None, mincluster=None,\n min_contig_coverage_diff=0.0,\n min_pct_id=0.6, min_pct_contig_aligned=None, min_contig_len=200,\n ambig_max_aligns=2, ambig_max_lens=1, ambig_max_frac=.01):\n ''' Re-implement a less buggy version of MUMmer's pseudomolecule\n feature to scaffold contigs onto a reference genome.\n '''\n\n # create tiling path with nucmer/promer and show-tiling\n if aligner=='nucmer':\n aligner = self.nucmer\n elif aligner=='promer':\n aligner = self.promer\n raise NotImplementedError('we have not implemented a show-aligns file reader that works for protein alignments')\n else:\n raise NameError()\n delta_1 = file.mkstempfname('.delta')\n delta_2 = file.mkstempfname('.delta')\n tiling = file.mkstempfname('.tiling')\n aligner(refFasta, contigsFasta, delta_1, extend=extend, breaklen=breaklen,\n maxgap=maxgap, minmatch=minmatch, mincluster=mincluster)\n self.delta_filter(delta_1, delta_2)\n self.show_tiling(delta_2, tiling, tab_delim=True,\n min_pct_id=min_pct_id,\n min_contig_len=min_contig_len,\n min_contig_coverage_diff=min_contig_coverage_diff,\n min_pct_contig_aligned=min_pct_contig_aligned)\n os.unlink(delta_1)\n\n # load intervals into a FeatureSorter\n fs = misc.FeatureSorter()\n with file.open_or_gzopen(tiling, 'r') as inf:\n for line in inf:\n row = line.rstrip('\\n\\r').split('\\t')\n c = row[11]\n start, stop = (int(row[0]), int(row[1]))\n alt_seq = (row[12], int(row[2]), int(row[3]))\n if stop1 not currently supported')\n n_tot = len(seqs[0])\n n_unambig = list(map(n_diff_vals, *seqs)).count(1)\n return float(n_unambig) / float(n_tot or 1.0)\n\n # construct scaffolded sequence for this chromosome\n seq = []\n for _, left, right, n_features, features in fs.get_intervals(c):\n # get all proposed sequences for this specific region\n alt_seqs = []\n for consider_ambig_aligns in (False, True):\n for f in features:\n alt_seqs_f = alnReaders[(c, f[-1][0])].retrieve_alts_by_ref(left, right, aln_start=f[1], aln_stop=f[2])\n if len(alt_seqs_f) == 1:\n alt_seqs.append(alt_seqs_f[0])\n elif consider_ambig_aligns:\n if len(alt_seqs_f) <= ambig_max_aligns and n_diff_lens(alt_seqs_f) <= ambig_max_lens and \\\n frac_unambig(alt_seqs_f) > (1.0 - ambig_max_frac):\n alt_seqs.append(alt_seqs_f[0])\n log.info(\"using ambiguous alignment to ref seq {} at [{},{}]\".format(c, f[1], f[2]))\n else:\n log.warning(\"dropping ambiguous alignment to ref seq {} at [{},{}]\".format(c, f[1], f[2]))\n if alt_seqs:\n # if have a non-unambiguous alignment, don't consider ambiguous ones\n break\n\n # pick the \"right\" one and glue together into a chromosome\n ranked_unique_seqs = contig_chooser(alt_seqs, right-left+1, \"%s:%d-%d\" % (c, left, right))\n seq.append(ranked_unique_seqs[0])\n # emit the \"alternates\" in a separate file\n if outAlternateContigs and len(ranked_unique_seqs) > 1:\n alternate_contigs.append((c, left, right, ranked_unique_seqs))\n\n # write this chromosome to fasta file\n for line in file.fastaMaker([(str(c)+\"_contigs_ordered_and_oriented\", ''.join(seq))]):\n outf.write(line)\n\n # if alternate scaffolds exist, emit to output fasta file (if specified)\n if outAlternateContigs and alternate_contigs:\n log.info(\"emitting alternative scaffold sequences to {}\".format(outAlternateContigs))\n with open(outAlternateContigs, 'wt') as outf:\n for c, left, right, seqs in alternate_contigs:\n for line in file.fastaMaker([\n (\"{}:{}-{}_option_{}\".format(c,left,right,i), s)\n for i,s in enumerate(seqs)]):\n outf.write(line)\n\n\n def align_one_to_one(self, refFasta, otherFasta, outFasta):\n ''' Take two sequences, align with nucmer, and produce\n an aligned-fasta file of the two based on show-aligns\n output.\n '''\n # grab seq_ids (very inefficient, but whatever)\n ref_id = Bio.SeqIO.read(refFasta, 'fasta').id\n query_id = Bio.SeqIO.read(otherFasta, 'fasta').id\n\n # run nucmer\n delta_1 = file.mkstempfname('.delta')\n delta_2 = file.mkstempfname('.delta')\n self.nucmer(refFasta, otherFasta, delta_1)\n self.delta_filter(delta_1, delta_2)\n\n # run show-aligns\n aln_file = file.mkstempfname('.aligns')\n toolCmd = [os.path.join(self.install_and_get_path(), 'show-aligns'),\n '-r', delta_2, ref_id, query_id]\n log.debug(' '.join(toolCmd))\n with open(aln_file, 'wt') as outf:\n subprocess.check_call(toolCmd, stdout=outf)\n alns = AlignsReader(aln_file, refFasta)\n\n # write fasta\n seqs = [[alns.seq_ids[0], []], [alns.seq_ids[1], []]]\n for a in alns.get_intervals():\n seqs[0][1].append(a[6])\n seqs[1][1].append(a[7])\n seqs[0][1] = ''.join(seqs[0][1])\n seqs[1][1] = ''.join(seqs[1][1])\n file.makeFastaFile(seqs, outFasta)\n\n # cleanup\n for fn in (delta_1, delta_2, aln_file):\n os.unlink(fn)\n\ndef contig_chooser(alt_seqs, ref_len, coords_debug=\"\"):\n ''' Our little heuristic to choose an alternative sequence from a pile\n of alignments to a reference. Takes a list of strings (one string per\n contig). This method will choose a single sequence from the input:\n 1. if there are no alt_seqs, emit a stretch of Ns, same length as ref\n 2. if there is only one alt_seq, emit that one\n 3. if there are many alt_seqs, emit the most popular (if there is one)\n 4. otherwise, if there is a most popular sequence length (including\n the ref_len as one vote), filter the alt_seqs to those of the\n most popular length and emit the most popular sequence (if there\n is one), otherwise, choose randomly amongst the remainder\n 5. otherwise, choose randomly amongst the same-as-ref length sequences\n 6. or just choose randomly if there are no same-as-ref length sequences\n The output will be a list of unique strings, where the first string\n is the \"chosen\" sequence, and the remaining strings are the alternative\n sequences (in no particular order, but guaranteed to be unique).\n '''\n if not alt_seqs:\n # no contigs align here, emit Ns of appropriate length\n new_seq = 'N' * ref_len\n other_seqs = []\n elif len(alt_seqs) == 1:\n # only one contig aligns here\n new_seq = alt_seqs[0]\n other_seqs = []\n else:\n # multiple contigs align here\n ranks = list(sorted(misc.histogram(alt_seqs).items(),\n key=lambda x:x[1], reverse=True))\n other_seqs = list(s for s,n in ranks)\n if len(ranks)==1:\n # only one unique sequence exists\n new_seq = ranks[0][0]\n elif ranks[0][1]>ranks[1][1]:\n # clear winner: a most popular sequence exists\n new_seq = ranks[0][0]\n else:\n # multiple possible replacement sequences\n len_ranks = list(sorted(misc.histogram(\n [len(s) for s in alt_seqs] + [ref_len] # let the reference have one vote\n ).items(), key=lambda x:x[1], reverse=True))\n if len(len_ranks)==1 or len_ranks[0][1]>len_ranks[1][1]:\n # a most popular replacement length exists\n # remove all alt_seqs that don't use that length\n alt_seqs = list(s for s in alt_seqs if len(s)==len_ranks[0][0])\n assert alt_seqs\n ranks = list(sorted(misc.histogram(alt_seqs).items(),\n key=lambda x:x[1], reverse=True))\n if len(ranks)==1 or ranks[0][1]>ranks[1][1]:\n # clear winner amongst remaining sequences of most popular length\n new_seq = ranks[0][0]\n else:\n # more complicated scenario. choose randomly.\n # perhaps in future, vote based on aligned read count?\n if len(alt_seqs)>1:\n log.warning(\"choosing random contig from %d choices of most popular length in %s\" % (len(alt_seqs), coords_debug))\n new_seq = random.choice(alt_seqs)\n else:\n # no clear winner on replacement length\n alt_ref_len_seqs = list(s for s in alt_seqs if len(s)==ref_len)\n if alt_ref_len_seqs:\n # choose randomly among same-as-ref-length sequences\n alt_seqs = alt_ref_len_seqs\n if len(alt_seqs)>1:\n log.warning(\"choosing random contig from %d choices of reference length in %s\" % (len(alt_seqs), coords_debug))\n new_seq = random.choice(alt_seqs)\n else:\n # no clear winner and all replacement lengths are different from reference length\n # just choose randomly\n if len(alt_seqs)>1:\n log.warning(\"choosing random contig from %d choices in %s\" % (len(alt_seqs), coords_debug))\n new_seq = random.choice(alt_seqs)\n other_seqs = list(s for s in other_seqs if s!=new_seq)\n return [new_seq] + other_seqs\n\n\nclass AmbiguousAlignmentException(Exception):\n pass\n\nclass AlignsReader(object):\n ''' This class assists in the parsing and reading of show-aligns output.\n '''\n def __init__(self, aligns_file, ref_fasta=None):\n self.aligns_file = aligns_file\n self.ref_fasta = ref_fasta\n self.reference_seq = None\n self.alignments = []\n self.seq_ids = []\n self._load_align()\n self._load_fastas()\n\n def _load_align(self):\n with open(self.aligns_file, 'rt') as inf:\n # read ref_fasta, query_fasta from header\n header = inf.readline().strip().split()\n assert len(header) == 2\n if self.ref_fasta is None:\n self.ref_fasta = header[0]\n\n # iterate row by row\n mode = 'start'\n coords = None\n seqs = None\n for line in inf:\n line = line.rstrip()\n if not line:\n pass # empty lines\n elif not line.strip('='):\n pass # header and footer of file\n elif line[0] in (' ', '\\t'):\n pass # describes mismatches in alignment\n elif line.startswith('--'):\n if line.startswith('-- Alignments between '):\n assert mode == 'start'\n mode = 'between'\n self.seq_ids = line[22:].split(' and ')\n assert len(self.seq_ids) == 2\n elif line.startswith('-- BEGIN alignment [ '):\n assert mode == 'between'\n mode = 'align'\n coords = list(x.split() for x in line[21:-2].split(' | '))\n assert len(coords) == 2 and coords[0][2] == coords[1][2] == '-'\n assert coords[0][0] == '+1', \"error with line: %s\" % line\n seqs = [[], []]\n align_lines = 0\n elif line.startswith('-- END alignment [ '):\n assert mode == 'align'\n mode = 'between'\n new_coords = list(x.split() for x in line[21:-2].split(' | '))\n assert coords == new_coords, \"error: %s != %s\" % (new_coords, coords)\n assert len(seqs[0]) == len(seqs[1])\n seqs = list(''.join(x) for x in seqs)\n assert len(seqs[0]) == len(seqs[1])\n self.alignments.append([coords[0][0], int(coords[0][1]), int(coords[0][3]),\n coords[1][0], int(coords[1][1]), int(coords[1][3]),\n seqs[0], seqs[1]])\n coords = None\n seqs = None\n else:\n raise AssertionError(\"file format: line '%s'\" % line)\n else:\n # read in one line of an alignment\n assert mode == 'align', \"file format: line '%s' before alignment begins\" % line\n seq_str = line.split()[1].upper().replace('.','-')\n seqs[align_lines % 2].append(seq_str)\n align_lines += 1\n\n def _load_fastas(self):\n assert self.ref_fasta and self.seq_ids\n self.reference_seq = Bio.SeqIO.index(self.ref_fasta, 'fasta')[self.seq_ids[0]]\n\n def get_alignments(self):\n for a in self.alignments:\n yield a\n\n def get_intervals(self):\n prev = None\n for a in self.alignments:\n cur = a[1:3]\n assert cur[1] >= cur[0]\n if prev is None:\n if cur[0] > 1:\n # emit leading reference sequence before first alignment\n yield self._dummy_row(1, cur[0]-1, '-')\n else:\n assert cur[0] > prev[1], \"overlaps not allowed\"\n if cur[0] > prev[1] + 1:\n # emit gap between alignments\n yield self._dummy_row(prev[1]+1, cur[0]-1, 'N')\n # emit actual alignment\n yield a\n prev = cur\n if prev and prev[1] < len(self.reference_seq):\n # emit trailing reference sequence after last alignment\n yield self._dummy_row(prev[1]+1, len(self.reference_seq), '-')\n\n def _dummy_row(self, start, stop, filler='N'):\n return ['+1', start, stop, '+1', start, stop,\n self.get_ref_seq(start, stop),\n filler * (stop-start+1)]\n\n def get_ref_seq(self, start, stop):\n ''' Retrieve a sub-sequence from the reference (1st) sequence in the\n alignment using coordinates relative to the reference sequence.\n No gaps will be emitted.\n '''\n return str(self.reference_seq.seq[start-1:stop])\n\n def retrieve_alts_by_ref(self, start, stop, aln_start=None, aln_stop=None):\n ''' Retrieve sub-sequence(s) from the alternate (2nd) sequence in the\n alignment using coordinates relative to the reference sequence.\n No gaps will be emitted.\n Required: start-stop interval must be wholly contained within\n an alignment.\n '''\n\n # grab the one alignment that contains this window\n alns = list(a for a in self.alignments if a[1]<=start and a[2]>=stop)\n if aln_start is not None and aln_stop is not None:\n # if specified, restrict to a specific alignment that comes from show-tiling\n # (sometimes show-aligns is more promiscuous than show-tiling)\n new_alns = []\n for a in alns:\n if a[1] > aln_start or a[2] < aln_stop:\n log.debug(\"dropping undesired alignment: %s(%s):%s-%s to %s(%s):%s-%s (%s:%s-%s requested)\",\n self.seq_ids[0], a[0], a[1], a[2],\n self.seq_ids[1], a[3], a[4], a[5],\n self.seq_ids[0], aln_start, aln_stop)\n else:\n new_alns.append(a)\n alns = new_alns\n if len(alns) != 1:\n log.warning(\"invalid %s:%d-%d -> %s specified, %d alignments found that contain it\",\n self.seq_ids[0], start, stop, self.seq_ids[1], len(alns))\n for aln in alns:\n log.debug(\"alignment: %s\", str(aln[:6]))\n\n return [self._aln_to_alt_seq(aln, start, stop) for aln in alns]\n\n def _aln_to_alt_seq(self, aln, start, stop):\n \"\"\"Given an alignment of a contig to ref, return the contig sequence aligned to a given stretch of ref\"\"\"\n ref_l, ref_r, ref_seq, alt_seq = (aln[1], aln[2], aln[-2], aln[-1])\n\n # convert desired start/stop relative to this reference window\n # such that 0 <= start <= stop <= ref_r-ref_l+1\n aln_start = start - ref_l\n aln_stop = stop - ref_l\n\n # travel down alignment until we've reached the left edge\n # (because of gaps, you must check each position one by one)\n # end loop when ref_seq[:i_left] contains {aln_start} bases\n n_ref_bases = 0\n i_left = 0\n while n_ref_bases < aln_start:\n if ref_seq[i_left] != '-':\n n_ref_bases += 1\n i_left += 1\n\n # travel down alignment until we've reached the right edge\n # (because of gaps, you must check each position one by one)\n # end loop when ref_seq[:i_right] contains {aln_stop} bases\n i_right = i_left\n while n_ref_bases < aln_stop:\n if ref_seq[i_right] != '-':\n n_ref_bases += 1\n i_right += 1\n # consume and include any trailing gaps\n while i_right < len(ref_seq) and ref_seq[i_right] == '-':\n i_right += 1\n\n # grab the alternate sequence and strip gaps\n return alt_seq[i_left:i_right+1].replace('-','')\n" }, { "path": "src/viral_ngs/phylo/muscle.py", "content": "'''\n The MUSCLE aligner\n http://www.drive5.com/muscle\n'''\n\n\nfrom viral_ngs import core\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\n\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport logging\n\nTOOL_NAME = \"muscle\"\n\n_log = logging.getLogger(__name__)\n\n\nclass MuscleTool(core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(MuscleTool, self).__init__(install_methods=install_methods)\n\n def version(self):\n if self.tool_version is None:\n self._get_tool_version()\n return self.tool_version\n\n def _get_tool_version(self):\n self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip().split()[1]\n\n # pylint: disable=W0221\n def execute(\n self,\n inFasta,\n outFasta,\n maxiters=None,\n maxhours=None,\n fmt='fasta',\n diags=None,\n quiet=True,\n logFile=None\n ):\n tool_cmd = [self.install_and_get_path(), '-in', inFasta, '-out', outFasta]\n\n if fmt in ('html', 'msf', 'clw', 'clwstrict'):\n tool_cmd.append('-' + fmt)\n else:\n if fmt != 'fasta':\n raise Exception()\n if quiet:\n tool_cmd.append('-quiet')\n if diags:\n tool_cmd.append('-diags')\n if maxiters:\n tool_cmd.extend(('-maxiters', str(maxiters)))\n if maxhours:\n tool_cmd.extend(('-maxhours', str(maxhours)))\n if logFile:\n tool_cmd.extend(('-log', logFile))\n\n _log.debug(' '.join(tool_cmd))\n subprocess.check_call(tool_cmd)\n # pylint: enable=W0221\n\n" }, { "path": "src/viral_ngs/phylo/snpeff.py", "content": "'''\nsnpEff - a tool for annotating genetic consequences of variants in VCF format\nhttp://snpeff.sourceforge.net/\n'''\n\n# built-ins\nimport hashlib\nimport os\nimport tempfile\nimport logging\nimport subprocess\nimport shutil\n\n# third-party\nimport pysam\n\n# module-specific\nfrom viral_ngs import core\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nfrom . import genbank\n\n_log = logging.getLogger(__name__)\n\nTOOL_NAME = 'snpEff'\nTOOL_VERSION = '5.1'\n\n\nclass SnpEff(core.Tool):\n\n def __init__(self, install_methods=None, extra_genomes=None):\n self.jvmMemDefault = '4g'\n if not install_methods:\n install_methods = [core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n self.known_dbs = set()\n self.installed_dbs = set()\n super(SnpEff, self).__init__(install_methods=install_methods)\n\n def version(self):\n return TOOL_VERSION\n\n def execute(self, command, args, JVMmemory=None, stdin=None, stdout=None, stderr=None): # pylint: disable=W0221\n if not JVMmemory:\n JVMmemory = self.jvmMemDefault\n\n # the conda version wraps the jar file with a shell script\n if self.install_and_get_path().endswith(\".jar\"):\n tool_cmd = [\n 'java', '-Xmx' + JVMmemory, '-Djava.io.tmpdir=' + tempfile.gettempdir(), '-jar', self.install_and_get_path(),\n command\n ] + args\n else:\n tool_cmd = [\n self.install_and_get_path(), '-Xmx' + JVMmemory, '-Djava.io.tmpdir=' + tempfile.gettempdir(), command\n ] + args\n\n _log.debug(' '.join(tool_cmd))\n return misc.run_and_print(tool_cmd, stdin=stdin, stderr=stderr, buffered=True, silent=command in (\"databases\",\"build\"), check=True)\n\n def has_genome(self, genome):\n if not self.known_dbs:\n for _ in self.available_databases():\n pass\n\n return genome in self.installed_dbs\n\n def download_db(self, dbname, verbose=False):\n opts = [dbname]\n if verbose:\n opts.append('-v')\n self.execute('download', opts)\n self.known_dbs.add(dbname)\n self.installed_dbs.add(dbname)\n\n def create_db(self, accessions, emailAddress=None, JVMmemory=None):\n sortedAccessionString = \", \".join([genbank.parse_accession_str(acc) for acc in sorted(accessions)])\n databaseId = hashlib.sha256(sortedAccessionString.encode('utf-8')).hexdigest()[:55]\n\n # if the database is not installed, we need to make it\n if not self.has_genome(databaseId):\n config_file = os.path.join(os.path.dirname(os.path.realpath(self.install_and_get_path())), 'snpEff.config')\n data_dir = get_data_dir(config_file)\n\n # if the data directory specified in the config is absolute, use it\n # otherwise get the data directory relative to the location of the config file\n if os.path.isabs(data_dir):\n outputDir = os.path.join(data_dir, databaseId)\n else:\n outputDir = os.path.realpath(os.path.join(os.path.dirname(config_file), data_dir, databaseId))\n\n genbank.fetch_full_records_from_genbank(\n sorted(accessions), \n outputDir,\n emailAddress,\n forceOverwrite=True,\n combinedFilePrefix=\"genes\",\n removeSeparateFiles=False\n )\n\n # create a temp config file in the same location as the original\n # since the data dir for the built database has a relative\n # location by default\n tmp_config_file = config_file+\".temp\"\n\n # build a new snpEff database using the downloaded genbank file\n # Note that if the snpEff command fails for some reason,\n # we should take care to not include an entry for the database\n # in the config file, which is the record of installed databases.\n # In the event the build fails, the config file must reflect\n # databases present in the data_dir, otherwise calls to execute snpEff will\n # fail if the data_dir lacks databases for entries listed in the config file.\n\n # make a temp copy of the old config file\n shutil.copyfile(config_file, tmp_config_file)\n\n # add the new genome to the temp config file\n # since snpEff will not attempt to build unless the\n # database is in the config file\n add_genomes_to_snpeff_config_file(tmp_config_file, [(databaseId, sortedAccessionString, sortedAccessionString)])\n\n try:\n args = ['-genbank', '-v', databaseId, \"-c\", tmp_config_file]\n self.execute('build', args, JVMmemory=JVMmemory)\n except:\n # remove temp config file if the database build failed\n shutil.unlink(tmp_config_file)\n raise\n\n # copy the temp config including the built database \n # if the execute('build') command did not raise an exception\n shutil.move(tmp_config_file, config_file)\n self.known_dbs.add(databaseId)\n self.installed_dbs.add(databaseId)\n\n def available_databases(self):\n # do not capture stderr, since snpEff writes 'Picked up _JAVA_OPTIONS'\n # which is not helpful for reading the stdout of the databases command\n with open(os.devnull, \"wb\") as devnull:\n command_ps = self.execute(\"databases\", args=[], stderr=devnull)\n\n split_points = []\n keys = ['Genome', 'Organism', 'Status', 'Bundle', 'Database']\n self.installed_dbs = set()\n self.known_dbs = set()\n for line in command_ps.stdout.decode(\"utf-8\").splitlines():\n line = line.strip()\n if not split_points:\n if not line.startswith('Genome'):\n raise Exception()\n split_points = list(line.index(key) for key in keys)\n elif not line.startswith('----'):\n indexes = split_points + [len(line)]\n row = dict((keys[i], line[indexes[i]:indexes[i + 1]].strip()) for i in range(len(split_points)))\n self.known_dbs.add(row['Genome'])\n if row.get('Status') == 'OK':\n self.installed_dbs.add(row['Genome'])\n yield row\n\n def annotate_vcf(self, inVcf, genomes, outVcf, emailAddress=None, JVMmemory=None):\n \"\"\"\n Annotate variants in VCF file with translation consequences using snpEff.\n \"\"\"\n if outVcf.endswith('.vcf.gz'):\n tmpVcf = file.mkstempfname(prefix='vcf_snpEff-', suffix='.vcf')\n elif outVcf.endswith('.vcf'):\n tmpVcf = outVcf\n else:\n raise Exception(\"invalid input\")\n\n sortedAccessionString = \", \".join([genbank.parse_accession_str(acc) for acc in sorted(genomes)])\n databaseId = hashlib.sha256(sortedAccessionString.encode('utf-8')).hexdigest()[:55]\n\n genomeToUse = \"\"\n\n # if we don't have the genome, by name (snpEff official) or by hash (custom)\n if (not self.has_genome(databaseId)):\n if (not self.has_genome(genomes[0])):\n _log.info(\"Checking for snpEff database online...\")\n # check to see if it is available for download, and if so install it\n for row in self.available_databases():\n if (genomes[0].lower() in row['Genome'].lower()) or (\n genomes[0].lower() in row['Bundle'].lower()\n ) or (\n genomes[0].lower() in row['Organism'].lower()\n ):\n self.download_db(row['Genome'])\n\n # backward compatability for where a single genome name is provided\n if self.has_genome(genomes[0]):\n genomeToUse = genomes[0]\n else:\n # if the hash of the accessions passed in is not present in the genomes db\n if not self.has_genome(databaseId):\n self.create_db(genomes, emailAddress, JVMmemory)\n\n if self.has_genome(databaseId):\n genomeToUse = databaseId\n\n if not genomeToUse:\n raise Exception()\n\n args = [\n '-treatAllAsProteinCoding', 'false', '-t', '-noLog', '-ud', '0', '-noStats', '-noShiftHgvs', genomeToUse,\n os.path.realpath(inVcf)\n ]\n\n command_ps = self.execute('ann', args, JVMmemory=JVMmemory)\n if command_ps.returncode == 0:\n with open(tmpVcf, 'wt') as outf:\n outf.write(command_ps.stdout.decode(\"utf-8\"))\n\n if outVcf.endswith('.vcf.gz'):\n pysam.tabix_compress(tmpVcf, outVcf, force=True)\n pysam.tabix_index(outVcf, force=True, preset='vcf')\n os.unlink(tmpVcf)\n else:\n raise subprocess.CalledProcessError(cmd=command_ps.args, returncode=command_ps.returncode, output=command_ps.stdout)\n\n\ndef get_data_dir(config_file):\n data_dir = \"\"\n with open(config_file, 'rt') as inf:\n for line in inf:\n if line.strip().startswith('data.dir'):\n data_dir = line[line.find(\"=\") + 1:].strip()\n break\n return data_dir\n\n\ndef add_genomes_to_snpeff_config_file(config_file, new_genomes):\n \"\"\"\n new_genomes is a 3-tuple (g,d,c):\n where g is the genome name\n d is the description\n c is a comma-separated list of chromosomes\n \"\"\"\n genomes = set()\n with open(config_file, 'rt') as inf:\n for line in inf:\n if not line.startswith('#') and line.strip():\n i = line.find('.genome : ')\n if i >= 0:\n genomes.add(line[:i])\n with open(config_file, 'at') as outf:\n for (g, d, c) in new_genomes:\n if g not in genomes:\n outf.write('{}.genome : {}\\n'.format(g, d))\n if g != c:\n outf.write(\"\\t{}.chromosomes : {}\\n\".format(g, c))\n\n" }, { "path": "src/viral_ngs/phylo/vcf.py", "content": "'''This gives a number of useful quick methods for dealing with VCF files.\n'''\n\n__author__ = \"dpark@broadinstitute.org\"\n__version__ = \"PLACEHOLDER\"\n__date__ = \"PLACEHOLDER\"\n\nimport logging\nimport re\nimport pysam\nfrom viral_ngs.core import file\nfrom viral_ngs.core import misc\nfrom viral_ngs.assemble.vcf import parse_contig_header\n\nlog = logging.getLogger(__name__)\n\n\ndef make_intervals(i, n, fasta, chr_prefix='', verbose=False):\n ''' Divide a sorted genome into n equally sized parts and return the i'th\n part. We will return a list of intervals: chr, start, stop. It may\n contain multiple chromosomes in order to fill out a total length equal\n to the other parts. Each part will be adjacent and non-overlapping with\n the next part. i must be a number from 1 to n.\n '''\n assert 1 <= i <= n\n\n # read genome dict file\n tot = 0\n chrlens = []\n for c, c_len in get_chrlens(fasta):\n if c.startswith(chr_prefix):\n chrlens.append((c, c_len, tot))\n tot += c_len\n\n # define our chunk by gpos:\n part_size = tot // n\n g_start = 1 + part_size * (i - 1)\n g_stop = part_size * i\n if i == n:\n g_stop = tot\n\n # find the genomic intervals that correspond to our gpos window\n out = []\n for c, c_len, c_g_start in chrlens:\n c_g_stop = c_g_start + c_len\n c_g_start += 1\n if c_g_stop >= g_start and c_g_start <= g_stop:\n start = max(g_start, c_g_start) - c_g_start + 1\n stop = min(g_stop, c_g_stop) - c_g_start + 1\n out.append((c, start, stop))\n\n if verbose:\n log.info(\n \"Dividing the %d bp genome into %d chunks of %d bp each. The %dth chunk contains the following %d intervals: %s\",\n tot, n, part_size, i, len(out), ', '.join([\"%s:%d-%d\" % x for x in out]))\n return out\n\n\ndef sliding_windows(fasta, width, offset, chr_prefix=''):\n ''' Divide a genome into sliding windows and return as an iterator of\n intervals (chr, start, stop). The windows are of fixed width\n (except maybe the last window on each chromosome) and may overlap\n (offsetwidth).\n '''\n assert width > 0 and offset > 0\n for c, c_len in get_chrlens(fasta):\n if c.startswith(chr_prefix):\n start = 1\n while start <= c_len:\n stop = min(c_len, start + width - 1)\n yield (c, start, stop)\n start += offset\n\n\nclass GenomePosition(object):\n ''' Provide a mapping from chr:pos to genomic position.\n Read chromosome lengths and order from either a Picard/GATK-index for\n a FASTA file (a .dict file) or from a VCF header.\n '''\n\n def __init__(self, seqDb):\n self.gpos_map = {}\n self.clen_map = {}\n self.chrs = []\n totlen = 0\n for c, clen in get_chrlens(seqDb):\n self.chrs.append((c, clen))\n self.gpos_map[c] = totlen\n self.clen_map[c] = clen\n totlen += clen\n self.total = totlen\n\n def get_gpos(self, c, p):\n assert isinstance(p, int)\n assert c in self.gpos_map\n assert 1 <= p <= self.clen_map[c]\n return p + self.gpos_map[c]\n\n def get_chr_pos(self, gpos):\n assert isinstance(gpos, int)\n assert 1 <= gpos <= self.total\n totlen = 0\n for c, clen in self.chrs:\n if gpos <= totlen + clen:\n break\n totlen += clen\n return (c, gpos - totlen)\n\n\ndef get_chrlens(inFile):\n ''' Read chromosome lengths and order from either a Picard/GATK-index for\n a FASTA file (a .dict file) or from \"contig\" rows in the VCF header.\n '''\n chrlens = []\n if hasattr(inFile, 'chrlens'):\n chrlens = inFile.chrlens()\n else:\n if inFile.endswith('.fasta'):\n inFile = inFile[:-len('.fasta')] + '.dict'\n elif inFile.endswith('.fa'):\n inFile = inFile[:-len('.fa')] + '.dict'\n if inFile.endswith('.dict'):\n with open(inFile, 'rt') as inf:\n for line in inf:\n row = line.rstrip('\\n').split('\\t')\n if row[0] == '@SQ':\n assert row[1].startswith('SN:') and row[2].startswith('LN:')\n c = row[1][3:]\n c_len = int(row[2][3:])\n chrlens.append((c, c_len))\n elif inFile.endswith('.vcf') or inFile.endswith('.vcf.gz'):\n with file.open_or_gzopen(inFile, 'rt') as inf:\n for line in inf:\n line = line.rstrip('\\n')\n if line.startswith('##contig='):\n chrlens.append(parse_contig_header(line))\n elif line.startswith('#CHROM'):\n break\n else:\n raise AssertionError(\"unrecognized file type %s\" % inFile)\n assert chrlens, \"no sequence data found in %s % inFile\"\n return chrlens\n\n\ndef calc_maf(genos, ancestral=None, ploidy=1):\n # get list of alleles\n if ploidy == 1:\n alleles = genos\n else:\n alleles = []\n for g in genos:\n g = g.split('/')\n assert len(g) == ploidy\n alleles += g\n\n # count up\n out = {'n_tot': len(alleles)}\n acounts = misc.histogram(alleles)\n alist = sorted([(n, a) for a, n in acounts.items()])\n\n # daf\n if ancestral is not None:\n out['a_ancestral'] = ancestral\n derived = list(sorted([a for a in acounts.keys() if a != ancestral]))\n out['a_derived'] = ','.join(derived)\n out['dac'] = sum(acounts[a] for a in derived)\n out['daf'] = out['n_tot'] and float(out['dac']) / out['n_tot'] or None\n\n # maf\n if out['n_tot']:\n out['a_major'] = alist[-1][1]\n out['a_minor'] = ','.join([a for n, a in alist[:-1]])\n out['mac'] = out['n_tot'] - alist[-1][0]\n out['maf'] = float(out['mac']) / out['n_tot']\n else:\n out['a_major'] = None\n out['a_minor'] = None\n out['mac'] = None\n out['maf'] = None\n\n return out\n\nclass TabixReader(pysam.TabixFile):\n ''' A wrapper around pysam.TabixFile that provides a context and\n allows us to query using 1-based coordinates.\n\n We should request upstream to the Pysam people to implement\n methods __reversed__() and __len__() in pysam.TabixIterator.\n __getitem__ could be a bonus, but prob unnecessary.\n '''\n\n def __init__(self, inFile, parser=pysam.asTuple()):\n # inFile is passed in but is never used, and yet the TabixReader works. How?!\n # This inFile magic is because Tabixfile is a Cython object that uses def __cinit__ \n # rather than def __init__; the former is called automatically exactly once for the \n # base class prior to any use of __init__. Use of subsequent __init__ should obey \n # normal inheritance rules (assuming inheritance from object and it's not an old-style class). \n # So __cinit__ sets the input file, and then our __init__ (which doesn't override a base method) \n # is called and sets the parser. \n # This could all break in the future if pysam moves away from __cinit__, but doing so would\n # reduce performance and so it seems unlikely.\n # See:\n # https://github.com/cython/cython/blob/master/docs/src/userguide/special_methods.rst#id19\n # https://github.com/pysam-developers/pysam/blob/master/pysam/libctabix.pyx#L331\n #super(TabixReader, self).__init__(inFile, parser=parser)\n self.parser = parser\n\n def __enter__(self):\n return self\n\n def __exit__(self, exc_type, exc_val, exc_tb):\n self.close() # pylint: disable=E1101\n return 0\n\n # close() is being inherited from pysam.Tabixfile, why call it ourselves?\n # def close(self):\n # super(TabixReader, self).close()\n\n def chroms(self):\n return self.contigs # pylint: disable=E1101\n\n def get(self, chrom=None, start=None, stop=None, region=None):\n if start is not None:\n start -= 1\n return self.fetch(reference=chrom, start=start, end=stop, region=region, parser=self.parser) # pylint: disable=E1101\n\n\ndef get_pos_from_vcf_record(vcfrec):\n # new versions of pysam return a zero-based position here\n return vcfrec.pos + 1\n\n\ndef bytes_to_string(o):\n if isinstance(o, bytes):\n o = o.decode('utf-8')\n return o\n\n\nclass VcfReader(TabixReader):\n ''' Same as TabixReader with a few more perks for VCF files:\n - emit results parsed as pysam VCF rows\n - provide self.chrlens(), a dict mapping chrom name to chrom length\n - provide self.samples(), a list of sample names in order of appearance\n - provide get_range(c,start,stop) and get_snp_genos(c,pos)\n '''\n\n def __init__(self, inFile, ploidy=1, parser=pysam.asVCF()):\n # using old-style class superclass calling here\n # since TabixReader is derived from pysam.TabixFile\n # which is itself an old-style class (due to Cython version?)\n TabixReader.__init__(self, inFile, parser=parser)\n # when pysam uses new-style classes, we can replace with:\n #super(VcfReader, self).__init__(inFile, parser=parser)\n assert ploidy in (1, 2)\n self.ploidy = ploidy\n self.clens = []\n self.sample_names = None\n for line in self.header: # pylint: disable=E1101\n line = bytes_to_string(line)\n if line.startswith('##contig='):\n self.clens.append(parse_contig_header(line))\n elif line.startswith('#CHROM'):\n row = line.split('\\t')\n self.sample_names = row[9:]\n self.clens = dict(self.clens)\n assert self.sample_names\n\n def samples(self):\n return self.sample_names\n\n def chrlens(self):\n return self.clens\n\n def get_positions(self, c=None, start=None, stop=None, region=None):\n for snp in self.get(c, start, stop, region):\n yield (bytes_to_string(snp.contig), get_pos_from_vcf_record(snp),\n get_pos_from_vcf_record(snp) + len(snp.ref) - 1)\n\n def get_range(self, c=None, start=None, stop=None, region=None, as_strings=True, more=False):\n ''' Read a VCF file (optionally just a piece of it) and return contents\n as an iterator with parsed contents. Each row is returned as\n a 4-tuple:\n 1: chr\n 2: pos (int)\n 3: list of allele strings (in order)\n 4: list of genotypes as 2-tuples:\n haploid: (sample, allele)\n diploid: (sample, [allele, allele])\n If as_strings, the alleles will be actual alleles. Otherwise,\n alleles will be integers.\n If more is true, a fifth column will be emitted with the pysam VCF object.\n '''\n for snp in self.get(c, start, stop, region):\n alleles = [bytes_to_string(snp.ref)] + bytes_to_string(snp.alt).split(',')\n alleles = [a for a in alleles if a != '.']\n if self.ploidy == 1:\n genos = [(self.sample_names[i], int(bytes_to_string(snp[i])[0])) for i in range(len(self.sample_names))\n if bytes_to_string(snp[i])[0] != '.']\n if as_strings:\n genos = [(s, alleles[a]) for s, a in genos]\n else:\n genos = [(self.sample_names[i], [int(bytes_to_string(snp[i])[j * 2]) for j in range(self.ploidy)])\n for i in range(len(self.sample_names)) if bytes_to_string(snp[i])[0] != '.']\n if as_strings:\n genos = [(s, [alleles[a] for a in g]) for s, g in genos]\n if more:\n yield (bytes_to_string(snp.contig), get_pos_from_vcf_record(snp), alleles, genos, snp)\n else:\n yield (bytes_to_string(snp.contig), get_pos_from_vcf_record(snp), alleles, genos)\n\n def get_snp_genos(self, c, p, as_strings=True):\n ''' Read a single position from a VCF file and return the genotypes\n as a sample -> allele map. If there is not exactly one matching\n row in the VCF file at this position (if there are none or multiple)\n then we return an empty map: {}.\n '''\n snps = [x for x in self.get_range(c, p, p, as_strings=as_strings)]\n return len(snps) == 1 and dict(snps[0][3]) or {}\n\n def getFullSequences(self, c, start, stop, samples,\n na='-', refSeq=None, refInvariantsOnly=False, ignoreIndels=False):\n ''' chr - chromosome name\n start - start position\n stop - default = start\n samples is a list of samples. None can be used for the ref sample.\n if refSeq is a string with length = stop-start+1, then use this as the\n base sequence for missing data, otherwise, use the na string.\n if refInvariantsOnly is True, refSeq is only used for invariant\n sites or sites with no entries for any samples. if False, refSeq\n is used for all missing data.\n '''\n assert 1 <= start <= stop\n assert len(na) == 1\n\n # get all the VCF records\n vcf_records = [(p - start, alleles, dict(genos))\n for _, p, alleles, genos in self.get_range(c,\n start,\n stop,\n as_strings=True)\n if not ignoreIndels or set(map(len, alleles)) == set([1])]\n\n # Construct a list called \"seq\" into which we will replace alleles as\n # we discover them. This is a list, not a string, because each position\n # might be replaced with an arbitrary length string (deletions will be\n # empty strings, insertions will be strings > length 1). This all gets\n # converted to a string at the end.\n if refSeq:\n # assume refSeq alleles as a baseline for missing data\n assert len(refSeq) == (stop - start + 1)\n seq = list(refSeq)\n if refInvariantsOnly:\n # but don't assume refSeq alleles for any known variant sites\n for i, alleles, genos in vcf_records:\n if len(set(genos[s] for s in samples if s in genos)) > 1:\n for j in range(len(alleles[0])):\n if i + j < len(seq):\n seq[i + j] = na\n else:\n # assume nothing when data is missing\n seq = list(na * (stop - start + 1))\n\n for sample in samples:\n assert sample is None or sample in self.samples()\n\n # Make copy of reference sequence\n newseq = [s for s in seq]\n\n # Replace alleles, one site at a time.\n replaceAlleles(sample, newseq, vcf_records)\n\n # Convert list back to string. This string may or may not be the same\n # length as the original (if ignoreIndels is True, it must be the same\n # length as the original).\n newseq = ''.join(newseq)\n assert len(newseq) == (stop - start + 1) or not ignoreIndels\n yield (sample, newseq)\n\n\ndef replaceAlleles(sample, seq, vcf_records):\n ''' Replace alleles, one site at a time. '''\n for i, alleles, genos in vcf_records:\n\n # set allele to the DNA sequence we will replace at positions i through i+len(refallele)-1\n if sample is None:\n # caller is asking for the reference sample's sequence\n allele = alleles[0]\n alleles = [allele]\n else:\n # caller is asking for a normal sample\n samp_geno = genos.get(sample)\n if not samp_geno:\n continue\n if isinstance(samp_geno, list):\n log.warning(\n \"TO DO: add code to turn hets into IUPAC ambiguity codes (%s %s = %s).\",\n i, sample, '/'.join(samp_geno))\n continue\n allele = samp_geno\n\n # replace portion of sequence with allele\n # NEED BUGFIXES HERE for overlapping VCF records\n if allele is None:\n # nothing here ... is this even possible anymore?\n pass\n elif len(alleles[0]) == 1:\n # the most common cases: SNP, novar, or indel replacing one ref base (with zero or more bases)\n seq[i] = allele\n else:\n # most complicated case: something replacing multiple ref bases\n # TODO: beware--this is all untested!\n for j in range(max(len(alleles[0]), len(allele))):\n if i + j < len(seq):\n if j < len(allele):\n if j == len(alleles[0]) - 1:\n # new allele is >= ref length, fill out the rest of the bases\n seq[i + j] = allele[j:]\n else:\n seq[i + j] = allele[j]\n else:\n # new allele is shorter than ref, so delete extra bases\n seq[i + j] = ''\n return seq\n" }, { "path": "src/viral_ngs/phylo/vphaser2.py", "content": "'''\n V-Phaser 2 variant caller\n'''\n\nimport logging\nimport subprocess\nimport os\nimport tempfile\nimport shutil\nimport pysam\nfrom viral_ngs import core\nfrom viral_ngs.core import file\n\nlog = logging.getLogger(__name__)\n\nTOOL_NAME = \"vphaser2\"\nTOOL_VERSION = \"2.0\"\n\nclass Vphaser2Tool(core.Tool):\n\n def __init__(self, install_methods=None):\n if install_methods is None:\n install_methods = [core.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]\n super(Vphaser2Tool, self).__init__(install_methods=install_methods)\n\n def execute(self, inBam, outDir, numThreads=None): # pylint: disable=W0221\n # index inBam\n samtoolsTool = tools.samtools.SamtoolsTool()\n samtoolsTool.index(inBam)\n\n log.debug(\"V-Phaser2 output directory: '%s'\", outDir)\n\n cmd = [self.install_and_get_path(), '-i', inBam, '-o', outDir]\n cmd_str = ' '.join(cmd)\n envCopy = os.environ.copy()\n if numThreads is not None:\n envCopy['OMP_NUM_THREADS'] = str(numThreads)\n cmd_str = 'OMP_NUM_THREADS=%d ' % numThreads + cmd_str\n log.debug(cmd_str)\n\n # Use check_output instead of check_call so that we get error information\n # if the executable can't run on GitHub Actions.\n # Also has the effect of suppressing informational messages from vphaser,\n # which is probably a good thing.\n try:\n subprocess.check_output(cmd, env=envCopy, stderr=subprocess.STDOUT)\n except subprocess.CalledProcessError as ex:\n log.error(ex.output if type(ex.output)==str else ex.output.decode('utf-8'))\n raise\n\n def iterate(self, inBam, numThreads=None):\n \"\"\"\n Run V-Phaser 2 on inBam. Interate through lines in files\n CHROM.var.raw.txt in order of chroms in the inBam header.\n For each line yield:\n [CHROM, Ref_Pos, Var, Cons, Strd_bias_pval, Type, Var_perc,\n SNP_or_LP_Profile1, SNP_or_LP_Profile2, ...]\n \"\"\"\n #outdir = tempfile.mkdtemp('vphaser2')\n with file.tmp_dir(prefix='vphaser2') as outdir:\n try:\n self.execute(inBam, outdir, numThreads)\n finally:\n # these V-Phaser droppings cause problems if they persist\n bti = inBam + '.bti'\n if os.path.isfile(bti):\n os.unlink(bti)\n chromNames = pysam.Samfile(inBam).references\n for chromName in chromNames:\n outfile = os.path.join(outdir, chromName + '.var.raw.txt')\n if not os.path.exists(outfile):\n continue\n with open(outfile, 'rt') as inf:\n for line in inf:\n if not line.startswith('#'):\n yield [chromName] + line.strip().split()\n" }, { "path": "src/viral_ngs/py.typed", "content": "" }, { "path": "src/viral_ngs/read_utils.py", "content": "#!/usr/bin/env python3\n\"\"\"\nUtilities for working with sequence reads, such as converting formats and\nfixing mate pairs.\n\"\"\"\n\n__author__ = \"irwin@broadinstitute.org, dpark@broadinstitute.org\"\n__commands__ = []\n\nimport argparse\nimport logging\nimport math\nimport os\nimport sqlite3\nimport subprocess\nimport tempfile\nimport time\nimport shutil\nimport sys\nimport concurrent.futures\nfrom contextlib import contextmanager\nimport functools\n\nfrom Bio import SeqIO\nimport pysam\n\nfrom .core import file as util_file, misc as util_misc, cmd as util_cmd\nfrom .core.file import mkstempfname\nfrom .core import bbmap\nfrom .core import bwa\nfrom .core import cdhit\nfrom .core import picard\nfrom .core import samtools\nfrom .core import minimap2\nfrom .core import mvicuna\nfrom .core import prinseq\nfrom .core import novoalign\nfrom .core import sambamba\nfrom .core import trimmomatic\nfrom .core import Tool\nfrom .core.misc import ReadIdStore\n\nlog = logging.getLogger(__name__)\n\n\n# ===============================\n# *** index_fasta_samtools ***\n# ===============================\n\n\ndef parser_index_fasta_samtools(parser=argparse.ArgumentParser()):\n parser.add_argument('inFasta', help='Reference genome, FASTA format.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None)))\n util_cmd.attach_main(parser, main_index_fasta_samtools)\n return parser\n\n\ndef main_index_fasta_samtools(args):\n '''Index a reference genome for Samtools.'''\n samtools.SamtoolsTool().faidx(args.inFasta, overwrite=True)\n return 0\n\n\n__commands__.append(('index_fasta_samtools', parser_index_fasta_samtools))\n\n# =============================\n# *** index_fasta_picard ***\n# =============================\n\n\ndef parser_index_fasta_picard(parser=argparse.ArgumentParser()):\n parser.add_argument('inFasta', help='Input reference genome, FASTA format.')\n parser.add_argument(\n '--JVMmemory',\n default=picard.CreateSequenceDictionaryTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='Optional arguments to Picard\\'s CreateSequenceDictionary, OPTIONNAME=value ...'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_index_fasta_picard)\n return parser\n\n\ndef main_index_fasta_picard(args):\n '''Create an index file for a reference genome suitable for Picard/GATK.'''\n picard.CreateSequenceDictionaryTool().execute(\n args.inFasta, overwrite=True,\n picardOptions=args.picardOptions,\n JVMmemory=args.JVMmemory\n )\n return 0\n\n\n__commands__.append(('index_fasta_picard', parser_index_fasta_picard))\n\n# =============================\n# *** mkdup_picard ***\n# =============================\n\n\ndef parser_mkdup_picard(parser=argparse.ArgumentParser()):\n parser.add_argument('inBams', help='Input reads, BAM format.', nargs='+')\n parser.add_argument('outBam', help='Output reads, BAM format.')\n parser.add_argument('--outMetrics', help='Output metrics file. Default is to dump to a temp file.', default=None)\n parser.add_argument(\n \"--remove\",\n help=\"Instead of marking duplicates, remove them entirely (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"remove\"\n )\n parser.add_argument(\n '--JVMmemory',\n default=picard.MarkDuplicatesTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='Optional arguments to Picard\\'s MarkDuplicates, OPTIONNAME=value ...'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_mkdup_picard)\n return parser\n\n\ndef main_mkdup_picard(args):\n '''Mark or remove duplicate reads from BAM file.'''\n opts = list(args.picardOptions)\n if args.remove:\n opts = ['REMOVE_DUPLICATES=true'] + opts\n picard.MarkDuplicatesTool().execute(\n args.inBams, args.outBam,\n args.outMetrics, picardOptions=opts,\n JVMmemory=args.JVMmemory\n )\n return 0\n\n\n__commands__.append(('mkdup_picard', parser_mkdup_picard))\n\n# =============================\n# *** revert_bam_picard ***\n# =============================\n\ndef parser_revert_sam_common(parser=argparse.ArgumentParser()):\n parser.add_argument('--clearTags', dest='clear_tags', default=False, action='store_true', \n help='When supplying an aligned input file, clear the per-read attribute tags')\n parser.add_argument(\"--tagsToClear\", type=str, nargs='+', dest=\"tags_to_clear\", default=[\"XT\", \"X0\", \"X1\", \"XA\", \n \"AM\", \"SM\", \"BQ\", \"CT\", \"XN\", \"OC\", \"OP\"], \n help='A space-separated list of tags to remove from all reads in the input bam file (default: %(default)s)')\n parser.add_argument(\n '--doNotSanitize',\n dest=\"do_not_sanitize\",\n action='store_true',\n help=\"\"\"When being reverted, picard's SANITIZE=true\n is set unless --doNotSanitize is given. \n Sanitization is a destructive operation that removes reads so the bam file is consistent.\n From the picard documentation:\n 'Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, \n records with mismatches in length of bases and qualities.'\n For more information see:\n https://broadinstitute.github.io/picard/command-line-overview.html#RevertSam\n \"\"\"\n )\n try:\n parser.add_argument(\n '--JVMmemory',\n default=picard.RevertSamTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n except argparse.ArgumentError:\n # if --JVMmemory is already present in the parser, continue on...\n pass\n return parser\n\ndef parser_revert_bam_picard(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, BAM format.')\n parser.add_argument('outBam', help='Output reads, BAM format.')\n parser.add_argument(\n '--JVMmemory',\n default=picard.RevertSamTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='Optional arguments to Picard\\'s RevertSam, OPTIONNAME=value ...'\n )\n parser = parser_revert_sam_common(parser)\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_revert_bam_picard, split_args=True)\n return parser\n\n\ndef main_revert_bam_picard(inBam, outBam, clear_tags=False, tags_to_clear=None, picardOptions=None, do_not_sanitize=False, JVMmemory=None):\n '''Revert BAM to raw reads'''\n picardOptions = picardOptions or []\n tags_to_clear = tags_to_clear or []\n\n if clear_tags:\n for tag in tags_to_clear:\n picardOptions.append(\"ATTRIBUTE_TO_CLEAR={}\".format(tag))\n \n if not do_not_sanitize and not any(opt.startswith(\"SANITIZE\") for opt in picardOptions):\n picardOptions.append('SANITIZE=true')\n\n picard.RevertSamTool().execute(inBam, outBam, picardOptions=picardOptions, JVMmemory=JVMmemory)\n return 0\n__commands__.append(('revert_bam_picard', parser_revert_bam_picard))\n\n@contextmanager\ndef revert_bam_if_aligned(inBam, revert_bam=None, clear_tags=True, tags_to_clear=None, picardOptions=None, JVMmemory=\"4g\", sanitize=False):\n '''\n revert the bam file if aligned. \n If a revertBam file path is specified, it is used, otherwise a temp file is created.\n '''\n\n revertBamOut = revert_bam if revert_bam else util_file.mkstempfname('.bam')\n picardOptions = picardOptions or []\n tags_to_clear = tags_to_clear or []\n\n outBam = inBam\n with pysam.AlignmentFile(inBam, 'rb', check_sq=False) as bam:\n # if it looks like the bam is aligned, revert it\n if 'SQ' in bam.header and len(bam.header['SQ'])>0:\n if clear_tags:\n for tag in tags_to_clear:\n picardOptions.append(\"ATTRIBUTE_TO_CLEAR={}\".format(tag))\n\n if not any(opt.startswith(\"SORT_ORDER\") for opt in picardOptions):\n picardOptions.append('SORT_ORDER=queryname')\n\n if sanitize and not any(opt.startswith(\"SANITIZE\") for opt in picardOptions):\n picardOptions.append('SANITIZE=true')\n\n picard.RevertSamTool().execute(\n inBam, revertBamOut, picardOptions=picardOptions \n )\n outBam = revertBamOut\n else:\n # if we don't need to produce a revertBam file\n # but the user has specified one anyway\n # simply touch the output\n if revert_bam:\n log.warning(\"An output was specified for 'revertBam', but the input is unaligned, so RevertSam was not needed. Touching the output.\")\n util_file.touch(revertBamOut)\n # TODO: error out? run RevertSam anyway?\n\n yield outBam\n\n if revert_bam == None:\n os.unlink(revertBamOut)\n\n# =========================\n# *** generic picard ***\n# =========================\n\n\ndef parser_picard(parser=argparse.ArgumentParser()):\n parser.add_argument('command', help='picard command')\n parser.add_argument(\n '--JVMmemory',\n default=picard.PicardTools.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[], nargs='*',\n help='Optional arguments to Picard, OPTIONNAME=value ...'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_picard)\n return parser\n\n\ndef main_picard(args):\n '''Generic Picard runner.'''\n picard.PicardTools().execute(args.command, picardOptions=args.picardOptions, JVMmemory=args.JVMmemory)\n return 0\n\n\n__commands__.append(('picard', parser_picard))\n\n# ===================\n# *** sort_bam ***\n# ===================\n\n\ndef parser_sort_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input bam file.')\n parser.add_argument('outBam', help='Output bam file, sorted.')\n parser.add_argument(\n 'sortOrder',\n help='How to sort the reads. [default: %(default)s]',\n choices=picard.SortSamTool.valid_sort_orders,\n default=picard.SortSamTool.default_sort_order\n )\n parser.add_argument(\n \"--index\",\n help=\"Index outBam (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"index\"\n )\n parser.add_argument(\n \"--md5\",\n help=\"MD5 checksum outBam (default: %(default)s)\",\n default=False,\n action=\"store_true\",\n dest=\"md5\"\n )\n parser.add_argument(\n '--JVMmemory',\n default=picard.SortSamTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='Optional arguments to Picard\\'s SortSam, OPTIONNAME=value ...'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_sort_bam)\n return parser\n\n\ndef main_sort_bam(args):\n '''Sort BAM file'''\n opts = list(args.picardOptions)\n if args.index:\n opts = ['CREATE_INDEX=true'] + opts\n if args.md5:\n opts = ['CREATE_MD5_FILE=true'] + opts\n picard.SortSamTool().execute(\n args.inBam, args.outBam, args.sortOrder,\n picardOptions=opts, JVMmemory=args.JVMmemory\n )\n return 0\n\n\n__commands__.append(('sort_bam', parser_sort_bam))\n\n# ====================\n# *** downsample_bams ***\n# ====================\n\ndef parser_downsample_bams(parser=argparse.ArgumentParser()):\n parser.add_argument('in_bams', help='Input bam files.', nargs='+')\n parser.add_argument('--outPath', dest=\"out_path\", type=str, help=\"\"\"Output path. If not provided, \n downsampled bam files will be written to the same paths as each \n source bam file\"\"\")\n parser.add_argument('--readCount', dest=\"specified_read_count\", type=int, help='The number of reads to downsample to.')\n group = parser.add_mutually_exclusive_group()\n group.add_argument('--deduplicateBefore', action='store_true', dest=\"deduplicate_before\", help='de-duplicate reads before downsampling.')\n group.add_argument('--deduplicateAfter', action='store_true', dest=\"deduplicate_after\", help='de-duplicate reads after downsampling.')\n parser.add_argument(\n '--JVMmemory',\n default=picard.DownsampleSamTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='Optional arguments to Picard\\'s DownsampleSam, OPTIONNAME=value ...'\n )\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_downsample_bams, split_args=True)\n return parser\n\n\ndef main_downsample_bams(in_bams, out_path, specified_read_count=None, deduplicate_before=False, deduplicate_after=False, picardOptions=None, threads=None, JVMmemory=None):\n '''Downsample multiple bam files to the smallest read count in common, or to the specified count.'''\n if picardOptions is None:\n picardOptions = []\n\n opts = list(picardOptions) + []\n\n def get_read_counts(bams):\n # get read counts for bam files provided\n read_counts = {}\n with concurrent.futures.ProcessPoolExecutor(max_workers=util_misc.sanitize_thread_count(threads)) as executor:\n samtools_tool = samtools.SamtoolsTool()\n for x, result in zip(bams, executor.map(samtools_tool.count, bams)):\n read_counts[x] = int(result)\n\n return read_counts\n\n def get_downsample_target_count(bams, readcount_requested):\n read_counts = get_read_counts(bams)\n downsample_target = 0\n if readcount_requested is not None:\n downsample_target = readcount_requested\n if downsample_target > min(read_counts.values()):\n raise ValueError(\"The smallest file has %s reads, which is less than the downsample target specified, %s. Please reduce the target count or omit it to use the read count of the smallest input file.\" % (min(read_counts.values()), downsample_target))\n else:\n downsample_target = min(read_counts.values())\n return downsample_target\n\n def downsample_bams(data_pairs, downsample_target, threads=None, JVMmemory=None):\n workers = min(util_misc.sanitize_thread_count(threads), len(data_pairs))\n JVMmemory = JVMmemory if JVMmemory else picard.DownsampleSamTool.jvmMemDefault\n jvm_worker_memory_mb = str(int(util_misc.convert_size_str(JVMmemory,\"m\")[:-1])//workers)+\"m\"\n with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:\n downsamplesam = picard.DownsampleSamTool()\n future_to_file = {executor.submit(downsamplesam.downsample_to_approx_count, *(list(fp)+[downsample_target]), JVMmemory=jvm_worker_memory_mb): fp[0] for fp in data_pairs}\n for future in concurrent.futures.as_completed(future_to_file):\n f = future_to_file[future]\n try:\n data = future.result()\n except Exception as exc:\n raise\n\n def dedup_bams(data_pairs, threads=None):\n workers = min(util_misc.sanitize_thread_count(threads), len(data_pairs))\n with concurrent.futures.ProcessPoolExecutor(max_workers=workers) as executor:\n future_to_file = {executor.submit(rmdup_mvicuna_bam, *fp): fp[0] for fp in data_pairs}\n for future in concurrent.futures.as_completed(future_to_file):\n f = future_to_file[future]\n try:\n data = future.result()\n except Exception as exc:\n raise\n\n data_pairs = []\n if deduplicate_before:\n with util_file.tempfnames(suffixes=[ '{}.dedup.bam'.format(os.path.splitext(os.path.basename(x))[0]) for x in in_bams]) as deduped_bams:\n data_pairs = list(zip(in_bams, deduped_bams))\n dedup_bams(data_pairs, threads=threads)\n downsample_target = get_downsample_target_count(deduped_bams, specified_read_count)\n \n if out_path:\n util_file.mkdir_p(out_path)\n data_pairs = list(zip(deduped_bams, [os.path.join(out_path, os.path.splitext(os.path.basename(x))[0]+\".dedup.downsampled-{}.bam\".format(downsample_target)) for x in in_bams]))\n else:\n data_pairs = list(zip(deduped_bams, [os.path.splitext(x)[0]+\".dedup.downsampled-{}.bam\".format(downsample_target) for x in in_bams]))\n downsample_bams(data_pairs, downsample_target, threads=threads, JVMmemory=JVMmemory)\n else:\n downsample_target = get_downsample_target_count(in_bams, specified_read_count)\n if deduplicate_after:\n log.warning(\"--deduplicateAfter has been specified. Read count of output files is not guaranteed.\")\n with util_file.tempfnames(suffixes=[ '{}.downsampled-{}.bam'.format(os.path.splitext(os.path.basename(x))[0], downsample_target) for x in in_bams]) as downsampled_tmp_bams:\n data_pairs = list(zip(in_bams, downsampled_tmp_bams))\n downsample_bams(data_pairs, downsample_target, threads=threads, JVMmemory=JVMmemory)\n \n if out_path:\n util_file.mkdir_p(out_path)\n data_pairs = list(zip(downsampled_tmp_bams, [os.path.join(out_path, os.path.splitext(os.path.basename(x))[0]+\".downsampled-{}.dedup.bam\").format(downsample_target) for x in in_bams]))\n else:\n data_pairs = list(zip(downsampled_tmp_bams, [os.path.splitext(x)[0]+\".downsampled-{}.dedup.bam\".format(downsample_target) for x in in_bams]))\n dedup_bams(data_pairs, threads=threads)\n else:\n if out_path:\n util_file.mkdir_p(out_path)\n data_pairs = list(zip(in_bams, [os.path.join(out_path, os.path.splitext(os.path.basename(x))[0]+\".downsampled-{}.bam\".format(downsample_target)) for x in in_bams]))\n else:\n data_pairs = list(zip(in_bams, [os.path.splitext(x)[0]+\".downsampled-{}.bam\".format(downsample_target) for x in in_bams]))\n downsample_bams(data_pairs, downsample_target, threads=threads, JVMmemory=JVMmemory)\n return 0\n\n__commands__.append(('downsample_bams', parser_downsample_bams))\n\n# ====================\n# *** merge_bams ***\n# ====================\n\n\ndef parser_merge_bams(parser=argparse.ArgumentParser()):\n parser.add_argument('inBams', help='Input bam files.', nargs='+')\n parser.add_argument('outBam', help='Output bam file.')\n parser.add_argument(\n '--JVMmemory',\n default=picard.MergeSamFilesTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='Optional arguments to Picard\\'s MergeSamFiles, OPTIONNAME=value ...'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_merge_bams)\n return parser\n\n\ndef main_merge_bams(args):\n '''Merge multiple BAMs into one'''\n opts = list(args.picardOptions) + ['USE_THREADING=true']\n picard.MergeSamFilesTool().execute(args.inBams, args.outBam, picardOptions=opts, JVMmemory=args.JVMmemory)\n return 0\n\n\n__commands__.append(('merge_bams', parser_merge_bams))\n\n# ====================\n# *** filter_bam ***\n# ====================\n\n\ndef parser_filter_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input bam file.')\n parser.add_argument('readList', help='Input file of read IDs.')\n parser.add_argument('outBam', help='Output bam file.')\n parser.add_argument(\n \"--exclude\",\n help=\"\"\"If specified, readList is a list of reads to remove from input.\n Default behavior is to treat readList as an inclusion list (all unnamed\n reads are removed).\"\"\",\n default=False,\n action=\"store_true\",\n dest=\"exclude\"\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_filter_bam)\n return parser\n\n\ndef main_filter_bam(args):\n '''Filter BAM file by read name'''\n with util_file.tmp_dir(suffix='_filter_bam') as tmpdir:\n db_path = os.path.join(tmpdir, 'read_ids.db')\n with ReadIdStore(db_path) as store:\n store.add_from_readlist(args.readList)\n store.filter_bam_by_ids(args.inBam, args.outBam, include=not args.exclude)\n return 0\n\n\n__commands__.append(('filter_bam', parser_filter_bam))\n\n\n\n# =======================\n# *** fastq_to_bam ***\n# =======================\n\n\ndef fastq_to_bam(\n inFastq1,\n inFastq2,\n outBam,\n sampleName=None,\n header=None,\n JVMmemory=None, # Kept for backwards compatibility, ignored (was for Picard)\n picardOptions=None, # Kept for backwards compatibility, parsed for RG tags\n threads=None\n):\n ''' Convert a pair of fastq paired-end read files and optional text header\n to a single bam file.\n\n Uses samtools import for multi-threaded FASTQ to BAM conversion.\n The JVMmemory parameter is kept for backwards compatibility but ignored.\n The picardOptions parameter is parsed for Picard-style RG tag options.\n '''\n picardOptions = picardOptions or []\n\n if header:\n fastqToSamOut = mkstempfname('.bam')\n else:\n fastqToSamOut = outBam\n if sampleName is None:\n sampleName = 'Dummy' # Will get overwritten by rehead command\n\n # Parse picardOptions to extract RG tag values\n # Supports Picard-style options like LIBRARY_NAME=Alexandria\n opts_dict = {}\n for opt in picardOptions:\n if '=' in opt:\n key, value = opt.split('=', 1)\n opts_dict[key.upper()] = value\n\n # Map Picard option names to import_fastq parameters\n library_name = opts_dict.get('LIBRARY_NAME')\n platform = opts_dict.get('PLATFORM', 'illumina')\n platform_unit = opts_dict.get('PLATFORM_UNIT')\n sequencing_center = opts_dict.get('SEQUENCING_CENTER')\n run_date = opts_dict.get('RUN_DATE')\n read_group_id = opts_dict.get('READ_GROUP_NAME')\n\n samtools.SamtoolsTool().import_fastq(\n inFastq1, inFastq2, fastqToSamOut,\n sample_name=sampleName,\n library_name=library_name,\n platform=platform,\n read_group_id=read_group_id,\n platform_unit=platform_unit,\n sequencing_center=sequencing_center,\n run_date=run_date,\n threads=threads\n )\n\n if header:\n samtools.SamtoolsTool().reheader(fastqToSamOut, header, outBam)\n\n return 0\n\n\ndef parser_fastq_to_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inFastq1', help='Input fastq file; 1st end of paired-end reads.')\n parser.add_argument('inFastq2', help='Input fastq file; 2nd end of paired-end reads.')\n parser.add_argument('outBam', help='Output bam file.')\n headerGroup = parser.add_mutually_exclusive_group(required=True)\n headerGroup.add_argument('--sampleName', help='Sample name to insert into the read group header.')\n headerGroup.add_argument('--header', help='Optional text file containing header.')\n parser.add_argument(\n '--JVMmemory',\n default=None,\n help='Deprecated: kept for backwards compatibility, ignored. (Was for Picard)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='''Read group options in Picard format (OPTIONNAME=value).\n Supported: LIBRARY_NAME, PLATFORM, PLATFORM_UNIT, SEQUENCING_CENTER,\n RUN_DATE, READ_GROUP_NAME. Note that header-related options will be\n overwritten by HEADER if present.'''\n )\n parser.add_argument(\n '--threads',\n type=int,\n default=None,\n help='Number of threads for BAM compression (default: auto)'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, fastq_to_bam, split_args=True)\n return parser\n\n\n__commands__.append(('fastq_to_bam', parser_fastq_to_bam))\n\n\ndef join_paired_fastq(\n inFastqs,\n output,\n outFormat\n):\n ''' Join paired fastq reads into single reads with Ns\n '''\n inFastqs = list(inFastqs)\n if output == '-':\n output = sys.stdout\n SeqIO.write(util_file.join_paired_fastq(inFastqs, output_format=outFormat), output, outFormat)\n return 0\n\n\ndef parser_join_paired_fastq(parser=argparse.ArgumentParser()):\n parser.add_argument('output', help='Output file.')\n parser.add_argument('inFastqs', nargs='+', help='Input fastq file (2 if paired, 1 if interleaved)')\n parser.add_argument('--outFormat', default='fastq', help='Output file format.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, join_paired_fastq, split_args=True)\n return parser\n\n__commands__.append(('join_paired_fastq', parser_join_paired_fastq))\n\n\n# ======================\n# *** split_reads ***\n# ======================\ndefaultIndexLen = 2\ndefaultMaxReads = 1000\ndefaultFormat = 'fastq'\n\n\ndef split_bam(inBam, outBams):\n '''Split BAM file equally into several output BAM files. '''\n samtools_tool = samtools.SamtoolsTool()\n picard_tool = picard.PicardTools()\n\n # get totalReadCount and maxReads\n # maxReads = totalReadCount / num files, but round up to the nearest\n # even number in order to keep read pairs together (assuming the input\n # is sorted in query order and has no unmated reads, which can be\n # accomplished by Picard RevertSam with SANITIZE=true)\n totalReadCount = samtools_tool.count(inBam)\n maxReads = int(math.ceil(float(totalReadCount) / len(outBams) / 2) * 2)\n log.info(\"splitting %d reads into %d files of %d reads each\", totalReadCount, len(outBams), maxReads)\n\n # load BAM header into memory\n header = samtools_tool.getHeader(inBam)\n if 'SO:queryname' not in header[0]:\n raise Exception('Input BAM file must be sorted in queryame order')\n\n # dump to bigsam\n bigsam = mkstempfname('.sam')\n samtools_tool.view(['-@', '3'], inBam, bigsam)\n\n # split bigsam into little ones\n with util_file.open_or_gzopen(bigsam, 'rt') as inf:\n for outBam in outBams:\n log.info(\"preparing file \" + outBam)\n tmp_sam_reads = mkstempfname('.sam')\n with open(tmp_sam_reads, 'wt') as outf:\n for row in header:\n outf.write('\\t'.join(row) + '\\n')\n for _ in range(maxReads):\n line = inf.readline()\n if not line:\n break\n outf.write(line)\n if outBam == outBams[-1]:\n for line in inf:\n outf.write(line)\n picard_tool.execute(\n \"SamFormatConverter\", [\n 'INPUT=' + tmp_sam_reads, 'OUTPUT=' + outBam, 'VERBOSITY=WARNING'\n ],\n JVMmemory='512m'\n )\n os.unlink(tmp_sam_reads)\n os.unlink(bigsam)\n\n\ndef parser_split_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input BAM file.')\n parser.add_argument('outBams', nargs='+', help='Output BAM files')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, split_bam, split_args=True)\n return parser\n\n\n__commands__.append(('split_bam', parser_split_bam))\n\n# =======================\n# *** reheader_bam ***\n# =======================\n\n\ndef parser_reheader_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, BAM format.')\n parser.add_argument('rgMap', help='Tabular file containing three columns: field, old, new.')\n parser.add_argument('outBam', help='Output reads, BAM format.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_reheader_bam)\n return parser\n\n\ndef main_reheader_bam(args):\n ''' Copy a BAM file (inBam to outBam) while renaming elements of the BAM header.\n The mapping file specifies which (key, old value, new value) mappings. For\n example:\n LB\tlib1\tlib_one\n SM\tsample1\tSample_1\n SM\tsample2\tSample_2\n SM\tsample3\tSample_3\n CN\tbroad\tBI\n '''\n # read mapping file\n mapper = dict((a + ':' + b, a + ':' + c) for a, b, c in util_file.read_tabfile(args.rgMap))\n # read and convert bam header\n header_file = mkstempfname('.sam')\n with open(header_file, 'wt') as outf:\n for row in samtools.SamtoolsTool().getHeader(args.inBam):\n if row[0] == '@RG':\n row = [mapper.get(x, x) for x in row]\n outf.write('\\t'.join(row) + '\\n')\n # write new bam with new header\n samtools.SamtoolsTool().reheader(args.inBam, header_file, args.outBam)\n os.unlink(header_file)\n return 0\n\n\n__commands__.append(('reheader_bam', parser_reheader_bam))\n\n\ndef parser_reheader_bams(parser=argparse.ArgumentParser()):\n parser.add_argument('rgMap', help='Tabular file containing three columns: field, old, new.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_reheader_bams)\n return parser\n\n\ndef main_reheader_bams(args):\n ''' Copy BAM files while renaming elements of the BAM header.\n The mapping file specifies which (key, old value, new value) mappings. For\n example:\n LB lib1 lib_one\n SM sample1 Sample_1\n SM sample2 Sample_2\n SM sample3 Sample_3\n CN broad BI\n FN in1.bam out1.bam\n FN in2.bam out2.bam\n '''\n # read mapping file\n mapper = dict((a + ':' + b, a + ':' + c) for a, b, c in util_file.read_tabfile(args.rgMap) if a != 'FN')\n files = list((b, c) for a, b, c in util_file.read_tabfile(args.rgMap) if a == 'FN')\n header_file = mkstempfname('.sam')\n # read and convert bam headers\n for inBam, outBam in files:\n if os.path.isfile(inBam):\n with open(header_file, 'wt') as outf:\n for row in samtools.SamtoolsTool().getHeader(inBam):\n if row[0] == '@RG':\n row = [mapper.get(x, x) for x in row]\n outf.write('\\t'.join(row) + '\\n')\n # write new bam with new header\n samtools.SamtoolsTool().reheader(inBam, header_file, outBam)\n os.unlink(header_file)\n return 0\n\n\n__commands__.append(('reheader_bams', parser_reheader_bams))\n\n# ============================\n# *** dup_remove_mvicuna ***\n# ============================\n\n\ndef mvicuna_fastqs_to_readlist(inFastq1, inFastq2, readList):\n # Run M-Vicuna on FASTQ files\n outFastq1 = mkstempfname('.1.fastq')\n outFastq2 = mkstempfname('.2.fastq')\n if inFastq2 is None or os.path.getsize(inFastq2) < 10:\n mvicuna.MvicunaTool().rmdup_single(inFastq1, outFastq1)\n else:\n mvicuna.MvicunaTool().rmdup((inFastq1, inFastq2), (outFastq1, outFastq2), None)\n\n # Make a list of reads to keep\n with open(readList, 'at') as outf:\n for fq in (outFastq1, outFastq2):\n with util_file.open_or_gzopen(fq, 'rt') as inf:\n line_num = 0\n for line in inf:\n if (line_num % 4) == 0:\n idVal = line.rstrip('\\n')[1:]\n if idVal.endswith('/1'):\n outf.write(idVal[:-2] + '\\n')\n # single-end reads do not have /1 /2 mate suffix\n # so pass through their IDs\n if not (idVal.endswith('/1') or idVal.endswith('/2')):\n outf.write(idVal + '\\n')\n line_num += 1\n os.unlink(outFastq1)\n os.unlink(outFastq2)\n\n\ndef rmdup_cdhit_bam(inBam, outBam, max_mismatches=None, jvm_memory=None):\n ''' Remove duplicate reads from BAM file using cd-hit-dup.\n '''\n max_mismatches = max_mismatches or 4\n tmp_dir = tempfile.mkdtemp()\n\n picard.SplitSamByLibraryTool().execute(inBam, tmp_dir)\n\n s2fq_tool = picard.SamToFastqTool()\n cdhit_tool = cdhit.CdHit()\n out_bams = []\n for f in os.listdir(tmp_dir):\n out_bam = mkstempfname('.bam')\n out_bams.append(out_bam)\n library_sam = os.path.join(tmp_dir, f)\n\n in_fastqs = mkstempfname('.1.fastq'), mkstempfname('.2.fastq')\n\n s2fq_tool.execute(library_sam, in_fastqs[0], in_fastqs[1])\n if not os.path.getsize(in_fastqs[0]) > 0 and not os.path.getsize(in_fastqs[1]) > 0:\n continue\n\n out_fastqs = mkstempfname('.1.fastq'), mkstempfname('.2.fastq')\n options = {\n '-e': max_mismatches,\n }\n if in_fastqs[1] is not None and os.path.getsize(in_fastqs[1]) > 10:\n options['-i2'] = in_fastqs[1]\n options['-o2'] = out_fastqs[1]\n\n log.info(\"executing cd-hit-dup on library \" + library_sam)\n # cd-hit-dup cannot operate on piped fastq input because it reads twice\n # Run cd-hit-dup synchronously (not in background) to ensure output files are complete\n # before FastqToSamTool tries to read them\n cdhit_tool.execute('cd-hit-dup', in_fastqs[0], out_fastqs[0], options=options, background=False)\n\n samtools.SamtoolsTool().import_fastq(\n out_fastqs[0], out_fastqs[1], out_bam,\n sample_name=f,\n )\n for fn in in_fastqs:\n os.unlink(fn)\n\n with util_file.fifo(name='merged.sam') as merged_bam:\n merge_opts = ['SORT_ORDER=queryname']\n picard.MergeSamFilesTool().execute(out_bams, merged_bam, picardOptions=merge_opts, JVMmemory=jvm_memory, background=True)\n picard.ReplaceSamHeaderTool().execute(merged_bam, inBam, outBam, JVMmemory=jvm_memory)\n\n\ndef parser_rmdup_cdhit_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, BAM format.')\n parser.add_argument('outBam', help='Output reads, BAM format.')\n parser.add_argument(\n '--JVMmemory',\n default=picard.FilterSamReadsTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)',\n dest='jvm_memory'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, rmdup_cdhit_bam, split_args=True)\n return parser\n\n\n__commands__.append(('rmdup_cdhit_bam', parser_rmdup_cdhit_bam))\n\ndef _merge_fastqs_and_mvicuna(lb, files):\n readList = mkstempfname('.keep_reads.txt')\n log.info(\"executing M-Vicuna DupRm on library \" + lb)\n\n # create merged FASTQs per library\n infastqs = (mkstempfname('.1.fastq'), mkstempfname('.2.fastq'))\n for d in range(2):\n with open(infastqs[d], 'wt') as outf:\n for fprefix in files:\n fn = '%s_%d.fastq' % (fprefix, d + 1)\n\n if os.path.isfile(fn):\n with open(fn, 'rt') as inf:\n for line in inf:\n outf.write(line)\n os.unlink(fn)\n else:\n log.warning(\n \"\"\"no reads found in %s,\n assuming that's because there's no reads in that read group\"\"\", fn\n )\n\n # M-Vicuna DupRm to see what we should keep (append IDs to running file)\n if os.path.getsize(infastqs[0]) > 0 or os.path.getsize(infastqs[1]) > 0:\n mvicuna_fastqs_to_readlist(infastqs[0], infastqs[1], readList)\n for fn in infastqs:\n os.unlink(fn)\n\n return readList\n\ndef rmdup_mvicuna_bam(inBam, outBam, threads=None):\n ''' Remove duplicate reads from BAM file using M-Vicuna. The\n primary advantage to this approach over Picard's MarkDuplicates tool\n is that Picard requires that input reads are aligned to a reference,\n and M-Vicuna can operate on unaligned reads.\n '''\n\n # Convert BAM -> FASTQ pairs per read group and load all read groups\n tempDir = tempfile.mkdtemp()\n picard.SamToFastqTool().per_read_group(inBam, tempDir, picardOptions=['VALIDATION_STRINGENCY=LENIENT'])\n read_groups = [x[1:] for x in samtools.SamtoolsTool().getHeader(inBam) if x[0] == '@RG']\n read_groups = [dict(pair.split(':', 1) for pair in rg) for rg in read_groups]\n\n # Collect FASTQ pairs for each library\n lb_to_files = {}\n for rg in read_groups:\n lb_to_files.setdefault(rg.get('LB', 'none'), set())\n fname = rg['ID']\n lb_to_files[rg.get('LB', 'none')].add(os.path.join(tempDir, fname))\n log.info(\"found %d distinct libraries and %d read groups\", len(lb_to_files), len(read_groups))\n\n # Create ReadIdStore and collect read IDs from all libraries\n with util_file.tmp_dir(suffix='_mvicuna_filter') as filter_tmpdir:\n db_path = os.path.join(filter_tmpdir, 'read_ids.db')\n with ReadIdStore(db_path) as store:\n # For each library, merge FASTQs and run M-Vicuna, collecting read IDs\n with concurrent.futures.ProcessPoolExecutor(\n max_workers=threads or util_misc.available_cpu_count()) as executor:\n futures = [executor.submit(_merge_fastqs_and_mvicuna, lb, files)\n for lb, files in lb_to_files.items()]\n for future in concurrent.futures.as_completed(futures):\n log.info(\"mvicuna finished processing library\")\n try:\n readList = future.result()\n # Stream read IDs directly into store (no intermediate concat)\n with open(readList, 'rt') as f:\n store.extend(line.strip() for line in f if line.strip())\n os.unlink(readList) # Clean up per-library file immediately\n except Exception as exc:\n log.error('mvicuna process call generated an exception: %s' % (exc))\n raise\n\n # Filter original input BAM against keep-list\n store.filter_bam_by_ids(inBam, outBam, include=True)\n\n return 0\n\n\ndef parser_rmdup_mvicuna_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, BAM format.')\n parser.add_argument('outBam', help='Output reads, BAM format.')\n util_cmd.common_args(parser, (('threads',None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, rmdup_mvicuna_bam, split_args=True)\n return parser\n\n\n__commands__.append(('rmdup_mvicuna_bam', parser_rmdup_mvicuna_bam))\n\n\ndef rmdup_bbnorm_bam(inBam, outBam,\n target=None, k=None, passes=None,\n memory=None, threads=None,\n min_input_reads=None, max_output_reads=None):\n \"\"\"\n Remove duplicate/normalize reads from BAM file using BBNorm.\n\n Convert BAM to interleaved FASTQ, run bbnorm, extract kept read IDs,\n and filter original BAM to those IDs using pysam (O(1) memory).\n\n Args:\n inBam: Input BAM file\n outBam: Output BAM file\n target: BBNorm target normalization depth (default: bbnorm default of 100)\n k: Kmer length (default: bbnorm default of 31)\n passes: Number of passes (default: bbnorm default of 2)\n memory: Java memory for bbnorm (e.g., \"4g\")\n threads: Number of threads for bbnorm\n min_input_reads: Skip processing if input has fewer reads (copy input to output)\n max_output_reads: Randomly downsample keep-list if larger than this\n \"\"\"\n samtools_tool = samtools.SamtoolsTool()\n\n # Count input reads\n input_read_count = samtools_tool.count(inBam)\n log.info(\"Input BAM has %d reads\", input_read_count)\n\n # Skip processing if empty or below min_input_reads threshold\n min_threshold = min_input_reads if min_input_reads is not None else 1\n if input_read_count < min_threshold:\n if min_input_reads is not None:\n log.info(\"Input read count %d below min_input_reads %d, copying input to output\",\n input_read_count, min_input_reads)\n else:\n log.info(\"Input BAM is empty, copying to output\")\n shutil.copyfile(inBam, outBam)\n return 0\n\n with util_file.tmp_dir(suffix='_bbnorm') as tmpdir:\n # Convert BAM to interleaved FASTQ using samtools bam2fq\n inFastq = os.path.join(tmpdir, 'input.fastq')\n samtools_tool.bam2fq(inBam, inFastq) # Single file = interleaved output\n\n # Run bbnorm\n outFastq = os.path.join(tmpdir, 'output.fastq')\n bbmap.BBMapTool().bbnorm(\n inFastq, outFastq,\n tmpdir=tmpdir, target=target, k=k, passes=passes,\n mindepth=0, threads=threads, memory=memory\n )\n\n # Extract read IDs from bbnorm output FASTQ using SQLite for O(1) memory\n db_path = os.path.join(tmpdir, 'read_ids.db')\n\n with ReadIdStore(db_path) as store:\n store.add_from_fastq(outFastq)\n num_ids = len(store)\n log.info(\"BBNorm retained %d read IDs\", num_ids)\n\n # Downsample if needed (modifies store in-place via SQL)\n if max_output_reads is not None and num_ids > max_output_reads:\n log.info(\"Downsampling from %d to %d read IDs\", num_ids, max_output_reads)\n store.shrink_to_subsample(max_output_reads)\n\n # Filter original BAM directly using ReadIdStore\n store.filter_bam_by_ids(inBam, outBam, include=True)\n\n # Count output reads\n output_read_count = samtools_tool.count(outBam)\n log.info(\"Output BAM has %d reads (%.1f%% of input)\",\n output_read_count, 100.0 * output_read_count / max(input_read_count, 1))\n\n return 0\n\n\ndef parser_rmdup_bbnorm_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, BAM format.')\n parser.add_argument('outBam', help='Output reads, BAM format.')\n parser.add_argument(\n '--target',\n type=int,\n default=None,\n help='BBNorm target normalization depth (default: bbnorm default of 100)'\n )\n parser.add_argument(\n '--kmerLength',\n dest='k',\n type=int,\n default=None,\n help='Kmer length for bbnorm (default: bbnorm default of 31)'\n )\n parser.add_argument(\n '--passes',\n type=int,\n default=None,\n help='Number of bbnorm passes (default: bbnorm default of 2)'\n )\n parser.add_argument(\n '--memory',\n default=None,\n help='Java memory for bbnorm (e.g., \"4g\", \"8g\")'\n )\n parser.add_argument(\n '--minInputReads',\n dest='min_input_reads',\n type=int,\n default=None,\n help='Skip processing if input has fewer than this many reads'\n )\n parser.add_argument(\n '--maxOutputReads',\n dest='max_output_reads',\n type=int,\n default=None,\n help='Randomly downsample output to at most this many read IDs'\n )\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, rmdup_bbnorm_bam, split_args=True)\n return parser\n\n\n__commands__.append(('rmdup_bbnorm_bam', parser_rmdup_bbnorm_bam))\n\n\ndef parser_rmdup_prinseq_fastq(parser=argparse.ArgumentParser()):\n parser.add_argument('inFastq1', help='Input fastq file; 1st end of paired-end reads.')\n parser.add_argument('inFastq2', help='Input fastq file; 2nd end of paired-end reads.')\n parser.add_argument('outFastq1', help='Output fastq file; 1st end of paired-end reads.')\n parser.add_argument('outFastq2', help='Output fastq file; 2nd end of paired-end reads.')\n parser.add_argument(\n \"--includeUnmated\",\n help=\"Include unmated reads in the main output fastq files (default: %(default)s)\",\n default=False,\n action=\"store_true\"\n )\n parser.add_argument('--unpairedOutFastq1', default=None, help='File name of output unpaired reads from 1st end of paired-end reads (independent of --includeUnmated)')\n parser.add_argument('--unpairedOutFastq2', default=None, help='File name of output unpaired reads from 2nd end of paired-end reads (independent of --includeUnmated)')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_rmdup_prinseq_fastq)\n return parser\n\n\ndef main_rmdup_prinseq_fastq(args):\n ''' Run prinseq-lite's duplicate removal operation on paired-end\n reads. Also removes reads with more than one N.\n '''\n prinseq_tool = prinseq.PrinseqTool()\n prinseq_tool.rmdup_fastq_paired(args.inFastq1, args.inFastq2, args.outFastq1, args.outFastq2, args.includeUnmated, args.unpairedOutFastq1, args.unpairedOutFastq2)\n return 0\n\n\n__commands__.append(('rmdup_prinseq_fastq', parser_rmdup_prinseq_fastq))\n\n\ndef filter_bam_mapped_only(inBam, outBam):\n ''' Samtools to reduce a BAM file to only reads that are\n aligned (-F 4) with a non-zero mapping quality (-q 1)\n and are not marked as a PCR/optical duplicate (-F 1024).\n '''\n samtools.SamtoolsTool().view(['-b', '-q', '1', '-F', '1028'], inBam, outBam)\n picard.BuildBamIndexTool().execute(outBam)\n return 0\n\n\ndef parser_filter_bam_mapped_only(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input aligned reads, BAM format.')\n parser.add_argument('outBam', help='Output sorted indexed reads, filtered to aligned-only, BAM format.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, filter_bam_mapped_only, split_args=True)\n return parser\n\n\n__commands__.append(('filter_bam_mapped_only', parser_filter_bam_mapped_only))\n\n# ======= Novoalign ========\n\n\ndef parser_novoalign(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, BAM format.')\n parser.add_argument('refFasta', help='Reference genome, FASTA format, pre-indexed by Novoindex.')\n parser.add_argument('outBam', help='Output reads, BAM format (aligned).')\n parser.add_argument('--options', default='-r Random', help='Novoalign options (default: %(default)s)')\n parser.add_argument('--min_qual', default=0, help='Filter outBam to minimum mapping quality (default: %(default)s)')\n parser.add_argument(\n '--JVMmemory',\n default=picard.SortSamTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--NOVOALIGN_LICENSE_PATH',\n default=None,\n dest=\"novoalign_license_path\",\n help='A path to the novoalign.lic file. This overrides the NOVOALIGN_LICENSE_PATH environment variable. (default: %(default)s)'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_novoalign)\n return parser\n\n\ndef main_novoalign(args):\n '''Align reads with Novoalign. Sort and index BAM output.'''\n novoalign.NovoalignTool(license_path=args.novoalign_license_path).execute(\n args.inBam,\n args.refFasta,\n args.outBam,\n options=args.options.split(),\n min_qual=args.min_qual,\n JVMmemory=args.JVMmemory\n )\n return 0\n\n\n__commands__.append(('novoalign', parser_novoalign))\n\n\ndef parser_novoindex(parser=argparse.ArgumentParser()):\n parser.add_argument('refFasta', help='Reference genome, FASTA format.')\n parser.add_argument(\n '--NOVOALIGN_LICENSE_PATH',\n default=None,\n dest=\"novoalign_license_path\",\n help='A path to the novoalign.lic file. This overrides the NOVOALIGN_LICENSE_PATH environment variable. (default: %(default)s)'\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None)))\n util_cmd.attach_main(parser, main_novoindex)\n return parser\n\ndef main_novoindex(args):\n novoalign.NovoalignTool(license_path=args.novoalign_license_path).index_fasta(args.refFasta)\n return 0\n\n\n__commands__.append(('novoindex', parser_novoindex))\n\n# ========= align_and_fix ==========\n\n\ndef align_and_fix(\n inBam, refFasta,\n outBamAll=None,\n outBamFiltered=None,\n aligner_options='',\n aligner=\"novoalign\",\n bwa_min_score=None,\n novoalign_amplicons_bed=None,\n amplicon_window=4,\n JVMmemory=None,\n threads=None,\n skip_mark_dupes=False,\n dup_marker='sambamba',\n novoalign_license_path=None,\n skip_realign=False,\n):\n ''' Take reads, align to reference with Novoalign, minimap2, or BWA-MEM.\n Optionally mark duplicates with Picard or sambamba,\n and optionally filter final file to mapped/non-dupe reads.\n '''\n if not (outBamAll or outBamFiltered):\n log.warning(\"are you sure you meant to do nothing?\")\n return\n\n assert aligner in [\"novoalign\", \"bwa\", \"minimap2\"]\n samtools_tool = samtools.SamtoolsTool()\n\n refFastaCopy = mkstempfname('.ref_copy.fasta')\n with util_file.fastas_with_sanitized_ids(refFasta, use_tmp=True) as sanitized_fastas:\n shutil.copyfile(sanitized_fastas[0], refFastaCopy)\n\n picard.CreateSequenceDictionaryTool().execute(refFastaCopy, overwrite=True, JVMmemory=JVMmemory)\n samtools_tool.faidx(refFastaCopy, overwrite=True)\n\n if aligner_options is None:\n if aligner==\"novoalign\":\n aligner_options = '-r Random'\n else:\n aligner_options = '' # use defaults\n\n if samtools_tool.isEmpty(inBam):\n log.warning(\"zero reads present in input\")\n\n bam_aligned = mkstempfname('.aligned.bam')\n if aligner==\"novoalign\":\n if novoalign_amplicons_bed is not None:\n aligner_options += ' --amplicons {} {}'.format(novoalign_amplicons_bed, amplicon_window)\n\n novoalign.NovoalignTool(license_path=novoalign_license_path).index_fasta(refFastaCopy)\n\n novoalign.NovoalignTool(license_path=novoalign_license_path).execute(\n inBam, refFastaCopy, bam_aligned,\n options=aligner_options.split(),\n JVMmemory=JVMmemory\n )\n\n elif aligner=='bwa':\n bwa_tool = bwa.Bwa()\n bwa_tool.index(refFastaCopy)\n\n opts = aligner_options.split()\n\n bwa_tool.align_mem_bam(inBam, refFastaCopy, bam_aligned, min_score_to_filter=bwa_min_score, threads=threads, options=opts)\n\n elif aligner=='minimap2':\n mm2 = minimap2.Minimap2()\n mm2.align_bam(inBam, refFastaCopy, bam_aligned, threads=threads, options=aligner_options.split())\n\n # Mark duplicates with sambamba (default) or Picard\n if skip_mark_dupes:\n bam_marked = bam_aligned\n else:\n bam_marked = mkstempfname('.mkdup.bam')\n if dup_marker == 'sambamba':\n sambamba.SambambaTool().markdup(\n bam_aligned, bam_marked, threads=threads\n )\n elif dup_marker == 'picard':\n picard.MarkDuplicatesTool().execute(\n [bam_aligned], bam_marked, picardOptions=['CREATE_INDEX=true'],\n JVMmemory=JVMmemory\n )\n else:\n raise ValueError(f\"Unknown dup_marker: {dup_marker}. Must be 'sambamba' or 'picard'\")\n os.unlink(bam_aligned)\n\n # Index the marked BAM\n if dup_marker == 'sambamba' and not skip_mark_dupes:\n sambamba.SambambaTool().index(bam_marked, threads=threads)\n else:\n samtools_tool.index(bam_marked)\n\n # Generate output files\n if outBamAll:\n shutil.copyfile(bam_marked, outBamAll)\n if dup_marker == 'sambamba':\n sambamba.SambambaTool().index(outBamAll, threads=threads)\n else:\n picard.BuildBamIndexTool().execute(outBamAll, JVMmemory=JVMmemory)\n if outBamFiltered:\n filtered_any_mapq = mkstempfname('.filtered_any_mapq.bam')\n # filter based on read flags\n samtools_tool.filter_to_proper_primary_mapped_reads(bam_marked, filtered_any_mapq)\n # remove reads with MAPQ <1\n samtools_tool.view(['-b', '-q', '1'], filtered_any_mapq, outBamFiltered)\n os.unlink(filtered_any_mapq)\n if dup_marker == 'sambamba':\n sambamba.SambambaTool().index(outBamFiltered, threads=threads)\n else:\n picard.BuildBamIndexTool().execute(outBamFiltered, JVMmemory=JVMmemory)\n os.unlink(bam_marked)\n\n\ndef parser_align_and_fix(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input unaligned reads, BAM format.')\n parser.add_argument('refFasta', help='Reference genome, FASTA format; will be indexed by Picard and Novoalign.')\n parser.add_argument(\n '--outBamAll',\n default=None,\n help='''Aligned, sorted, and indexed reads. Unmapped and duplicate reads are\n retained. By default, duplicate reads are marked. If \"--skipMarkDupes\"\n is specified duplicate reads are included in outout without being marked.'''\n )\n parser.add_argument(\n '--outBamFiltered',\n default=None,\n help='''Aligned, sorted, and indexed reads. Unmapped reads are removed from this file,\n as well as any marked duplicate reads. Note that if \"--skipMarkDupes\" is provided,\n duplicates will be not be marked and will be included in the output.'''\n )\n parser.add_argument('--aligner_options', default=None, help='aligner options (default for novoalign: \"-r Random\", bwa: \"-T 30\"')\n parser.add_argument('--aligner', choices=['novoalign', 'minimap2', 'bwa'], default='novoalign', help='aligner (default: %(default)s)')\n parser.add_argument('--bwa_min_score', type=int, default=None, help='BWA mem on paired reads ignores the -T parameter. Set a value here (e.g. 30) to invoke a custom post-alignment filter (default: no filtration)')\n parser.add_argument('--novoalign_amplicons_bed', default=None, help='Novoalign only: amplicon primer file (BED format) to soft clip')\n parser.add_argument('--amplicon_window', type=int, default=4, help='Novoalign only: amplicon primer window size (default: %(default)s)')\n parser.add_argument('--JVMmemory', default='4g', help='JVM virtual memory size (default: %(default)s)')\n parser.add_argument('--threads', type=int, default=None, help='Number of threads (default: all available cores)')\n parser.add_argument('--skipMarkDupes',\n help='If specified, duplicate reads will not be marked in the resulting output file.',\n dest=\"skip_mark_dupes\",\n action='store_true')\n parser.add_argument('--dupMarker',\n choices=['sambamba', 'picard'],\n default='sambamba',\n dest=\"dup_marker\",\n help='Tool to use for marking duplicates. Sambamba is multi-threaded and faster. '\n 'Picard is the legacy option. (default: %(default)s)')\n parser.add_argument(\n '--NOVOALIGN_LICENSE_PATH',\n default=None,\n dest=\"novoalign_license_path\",\n help='A path to the novoalign.lic file. This overrides the NOVOALIGN_LICENSE_PATH environment variable. (default: %(default)s)'\n )\n parser.add_argument('--skipRealign',\n dest=\"skip_realign\",\n action='store_true',\n default=False,\n help='Deprecated no-op. GATK realignment has been removed.')\n\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, align_and_fix, split_args=True)\n return parser\n\n\n__commands__.append(('align_and_fix', parser_align_and_fix))\n\n# =========================\n\ndef filter_bam_to_proper_primary_mapped_reads(inBam, outBam, doNotRequirePairsToBeProper=False, keepSingletons=False, keepDuplicates=False):\n ''' Take a BAM file and filter to only reads that are properly\n paired and mapped. Optionally reject singletons, and \n optionally require reads to be properly paired and mapped.\n\n Output includes reads that are:\n - not flagged as duplicates\n - not secondary or supplementary (split/chimeric reads)\n - For paired-end reads:\n - marked as proper pair (if require_pairs_to_be_proper=True) OR\n both not unmapped (if require_pairs_to_be_proper=False) OR\n not a member of a pair with a singleton (if reject_singletons=True)\n - For single-end reads:\n mapped\n '''\n samtools_tool = samtools.SamtoolsTool()\n samtools_tool.filter_to_proper_primary_mapped_reads(inBam,\n outBam,\n require_pairs_to_be_proper=not doNotRequirePairsToBeProper,\n reject_singletons=not keepSingletons,\n reject_duplicates=not keepDuplicates)\n return 0\n\ndef parser_filter_bam_to_proper_primary_mapped_reads(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input aligned reads, BAM format.')\n parser.add_argument('outBam', help='Output reads, BAM format.')\n parser.add_argument(\n '--doNotRequirePairsToBeProper',\n help='Do not require reads to be properly paired when filtering (default: %(default)s)',\n action='store_true'\n )\n parser.add_argument(\n '--keepSingletons',\n help='Keep singleton reads when filtering (default: %(default)s)',\n action='store_true'\n )\n parser.add_argument(\n '--keepDuplicates',\n help='When filtering, do not exclude reads due to being flagged as duplicates (default: %(default)s)',\n action='store_true'\n )\n\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, filter_bam_to_proper_primary_mapped_reads, split_args=True)\n return parser\n\n# =========================\n\n\ndef minimap2_idxstats(inBam, refFasta, outStats, outReadlist=None, threads=None):\n ''' Align reads to reference with minimap2 and produce idxstats-like counts.\n\n This uses PAF output format (no SAM/BAM generation) for faster alignment\n and streams the output directly without intermediate files.\n\n Args:\n inBam: Input reads (BAM format)\n refFasta: Reference genome (FASTA format)\n outStats: Output file in samtools idxstats format\n outReadlist: Optional output file with read IDs that mapped (or None to skip)\n threads: Number of threads for alignment (default: auto-detect)\n '''\n mm2 = minimap2.Minimap2()\n mm2.idxstats(inBam, refFasta, outStats, outReadlist=outReadlist, threads=threads)\n\n \n\ndef parser_minimap2_idxstats(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input unaligned reads, BAM format.')\n parser.add_argument('refFasta', help='Reference genome, FASTA format.')\n parser.add_argument('outStats', help='Output idxstats file (tab-separated: ref_name, ref_length, mapped_count, 0).')\n parser.add_argument('--outReadlist', help='Optional output file listing read IDs that mapped.', default=None)\n\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, minimap2_idxstats, split_args=True)\n return parser\n\n__commands__.append(('minimap2_idxstats', parser_minimap2_idxstats))\n\n\ndef bwamem_idxstats(inBam, refFasta, outBam=None, outStats=None,\n min_score_to_filter=None, aligner_options=None,\n filterReadsAfterAlignment=False, doNotRequirePairsToBeProper=False, keepSingletons=False, keepDuplicates=False):\n ''' Take reads, align to reference with BWA-MEM and perform samtools idxstats.\n Optionally filter reads after alignment, prior to reporting idxstats, to include only those flagged as properly paired.\n '''\n\n assert outBam or outStats, \"Either outBam or outStats must be specified\"\n\n bam_aligned = util_file.mkstempfname('.aligned.bam')\n if outBam is None:\n bam_filtered = mkstempfname('.filtered.bam')\n else:\n bam_filtered = outBam\n\n samtools_tool = samtools.SamtoolsTool()\n bwa_tool = bwa.Bwa()\n\n ref_indexed = util_file.mkstempfname('.reference.fasta')\n shutil.copyfile(refFasta, ref_indexed)\n bwa_tool.index(ref_indexed)\n\n bwa_opts = [] if aligner_options is None else aligner_options.split()\n bwa_tool.mem(inBam, ref_indexed, bam_aligned, options=bwa_opts,\n min_score_to_filter=min_score_to_filter)\n\n if filterReadsAfterAlignment:\n samtools_tool.filter_to_proper_primary_mapped_reads(bam_aligned,\n bam_filtered,\n require_pairs_to_be_proper=not doNotRequirePairsToBeProper,\n reject_singletons=not keepSingletons,\n reject_duplicates=not keepDuplicates)\n os.unlink(bam_aligned)\n else:\n shutil.move(bam_aligned, bam_filtered)\n\n if outStats is not None:\n samtools_tool.idxstats(bam_filtered, outStats)\n\n if outBam is None:\n os.unlink(bam_filtered)\n\n\ndef parser_bwamem_idxstats(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input unaligned reads, BAM format.')\n parser.add_argument('refFasta', help='Reference genome, FASTA format, pre-indexed by Picard and Novoalign.')\n parser.add_argument('--outBam', help='Output aligned, indexed BAM file', default=None)\n parser.add_argument('--outStats', help='Output idxstats file', default=None)\n parser.add_argument(\n '--minScoreToFilter',\n dest=\"min_score_to_filter\",\n type=int,\n help=(\"Filter bwa alignments using this value as the minimum allowed \"\n \"alignment score. Specifically, sum the alignment scores across \"\n \"all alignments for each query (including reads in a pair, \"\n \"supplementary and secondary alignments) and then only include, \"\n \"in the output, queries whose summed alignment score is at least \"\n \"this value. This is only applied when the aligner is 'bwa'. \"\n \"The filtering on a summed alignment score is sensible for reads \"\n \"in a pair and supplementary alignments, but may not be \"\n \"reasonable if bwa outputs secondary alignments (i.e., if '-a' \"\n \"is in the aligner options). (default: not set - i.e., do not \"\n \"filter bwa's output)\")\n )\n parser.add_argument(\n '--alignerOptions',\n dest=\"aligner_options\",\n help=\"bwa options (default: bwa defaults)\")\n parser.add_argument(\n '--filterReadsAfterAlignment',\n help=(\"If specified, reads till be filtered after alignment to include only those flagged as properly paired.\"\n \"This excludes secondary and supplementary alignments.\"),\n action='store_true'\n )\n parser.add_argument(\n '--doNotRequirePairsToBeProper',\n help='Do not require reads to be properly paired when filtering (default: %(default)s)',\n action='store_true'\n )\n parser.add_argument(\n '--keepSingletons',\n help='Keep singleton reads when filtering (default: %(default)s)',\n action='store_true'\n )\n parser.add_argument(\n '--keepDuplicates',\n help='When filtering, do not exclude reads due to being flagged as duplicates (default: %(default)s)',\n action='store_true'\n )\n\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, bwamem_idxstats, split_args=True)\n return parser\n\n__commands__.append(('bwamem_idxstats', parser_bwamem_idxstats))\n\n\ndef parser_extract_tarball(parser=argparse.ArgumentParser()):\n parser.add_argument('tarfile', help='Input tar file. May be \"-\" for stdin.')\n parser.add_argument('out_dir', help='Output directory')\n parser.add_argument('--compression',\n help='Compression type (default: %(default)s). Auto-detect is incompatible with stdin input unless pipe_hint is specified.',\n choices=('gz', 'bz2', 'lz4', 'zip', 'none', 'auto'),\n default='auto')\n parser.add_argument('--pipe_hint',\n help='If tarfile is stdin, you can provide a file-like URI string for pipe_hint which ends with a common compression file extension if you want to use compression=auto.',\n default=None)\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, main_extract_tarball, split_args=True)\n return parser\ndef main_extract_tarball(*args, **kwargs):\n ''' Extract an input .tar, .tgz, .tar.gz, .tar.bz2, .tar.lz4, or .zip file\n to a given directory (or we will choose one on our own). Emit the\n resulting directory path to stdout.\n '''\n print(util_file.extract_tarball(*args, **kwargs))\n__commands__.append(('extract_tarball', parser_extract_tarball))\n\n# =========================\n\ndef fasta_read_names(in_fasta, out_read_names):\n \"\"\"Save the read names of reads in a .fasta file to a text file\"\"\"\n with util_file.open_or_gzopen(in_fasta) as in_fasta_f, open(out_read_names, 'wt') as out_read_names_f:\n last_read_name = None\n for line in in_fasta_f:\n if line.startswith('>'):\n read_name = line[1:].strip()\n if read_name.endswith('/1') or read_name.endswith('/2'):\n read_name = read_name[:-2]\n if read_name != last_read_name:\n out_read_names_f.write(read_name+'\\n')\n last_read_name = read_name\n\n\ndef read_names(in_reads, out_read_names, threads=None):\n \"\"\"Extract read names from a sequence file\"\"\"\n _in_reads = in_reads\n with util_file.tmp_dir(suffix='_read_names.txt') as t_dir:\n if in_reads.endswith('.bam'):\n _in_reads = os.path.join(t_dir, 'reads.fasta')\n samtools.SamtoolsTool().bam2fa(in_reads, _in_reads)\n fasta_read_names(_in_reads, out_read_names)\n\ndef parser_read_names(parser=argparse.ArgumentParser()):\n parser.add_argument('in_reads', help='the input reads ([compressed] fasta or bam)')\n parser.add_argument('out_read_names', help='the read names')\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, read_names, split_args=True)\n return parser\n\n__commands__.append(('read_names', parser_read_names))\n\n\n# ================================\n# *** trim_rmdup_subsamp ***\n# ================================\n\n\ndef trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=100000, trim_opts=None, threads=None):\n '''Take reads through Trimmomatic, Prinseq, and subsampling.\n\n This function performs three main operations:\n 1. Trimmomatic: adapter trimming and quality filtering\n 2. Prinseq: duplicate read removal\n 3. Subsampling: reduce to target read count\n\n Args:\n inBam: Input unaligned BAM file\n clipDb: Trimmomatic adapter clip database (FASTA)\n outBam: Output unaligned BAM file\n n_reads: Target number of individual reads (default: 100000)\n trim_opts: Optional dict of Trimmomatic options\n threads: Number of threads for Trimmomatic (default: all available)\n\n Returns:\n Tuple of (n_input, n_trim, n_rmdup, n_output, n_paired_subsamp, n_unpaired_subsamp)\n where all counts are individual reads (not pairs).\n '''\n threads = util_misc.sanitize_thread_count(threads)\n\n downsamplesam = picard.DownsampleSamTool()\n samtools_tool = samtools.SamtoolsTool()\n prinseq_tool = prinseq.PrinseqTool()\n\n if n_reads < 1:\n raise ValueError(\"n_reads must be >= 1\")\n\n # Use nested context managers for all temp files\n with util_file.tempfnames(suffixes=['.in.1.fastq', '.in.2.fastq']) as infq, \\\n util_file.tempfnames(suffixes=['.trim.1.fastq', '.trim.2.fastq']) as trimfq, \\\n util_file.tempfnames(suffixes=['.trim.unpaired.1.fastq', '.trim.unpaired.2.fastq']) as trimfq_unpaired, \\\n util_file.tempfnames(suffixes=['.rmdup.1.fastq', '.rmdup.2.fastq']) as rmdupfq, \\\n util_file.tempfnames(suffixes=['.rmdup.unpaired.1.fastq', '.rmdup.unpaired.2.fastq']) as rmdupfq_unpaired_from_paired_rmdup, \\\n util_file.tempfname(suffix='.header.sam') as tmp_header, \\\n util_file.tempfname(suffix='.paired.bam') as tmp_bam_paired:\n\n # BAM -> fastq\n picard.SamToFastqTool().execute(inBam, infq[0], infq[1])\n n_input = util_file.count_fastq_reads(infq[0])\n\n # --- Trimmomatic ---\n if n_input == 0:\n for i in range(2):\n shutil.copyfile(infq[i], trimfq[i])\n else:\n trimmomatic.TrimmomaticTool().execute(\n infq[0],\n infq[1],\n trimfq[0],\n trimfq[1],\n clipDb,\n unpairedOutFastq1=trimfq_unpaired[0],\n unpairedOutFastq2=trimfq_unpaired[1],\n threads=threads,\n **(trim_opts or {})\n )\n\n n_trim = max(map(util_file.count_fastq_reads, trimfq)) # count is pairs\n n_trim_unpaired = sum(map(util_file.count_fastq_reads, trimfq_unpaired)) # count is individual reads\n\n # --- Prinseq duplicate removal ---\n prinseq_tool.rmdup_fastq_paired(\n trimfq[0],\n trimfq[1],\n rmdupfq[0],\n rmdupfq[1],\n includeUnmated=False,\n unpairedOutFastq1=rmdupfq_unpaired_from_paired_rmdup[0],\n unpairedOutFastq2=rmdupfq_unpaired_from_paired_rmdup[1]\n )\n\n n_rmdup_paired = max(map(util_file.count_fastq_reads, rmdupfq)) # count is pairs\n n_rmdup = n_rmdup_paired # count is pairs\n\n samtools_tool.dumpHeader(inBam, tmp_header)\n\n # convert paired reads to bam\n # stub out an empty file if the input fastqs are empty\n if all(os.path.getsize(x) > 0 for x in rmdupfq):\n picard.FastqToSamTool().execute(rmdupfq[0], rmdupfq[1], 'Dummy', tmp_bam_paired)\n else:\n opts = ['INPUT=' + tmp_header, 'OUTPUT=' + tmp_bam_paired, 'VERBOSITY=ERROR']\n picard.PicardTools().execute('SamFormatConverter', opts, JVMmemory='50m')\n\n n_paired_subsamp = 0\n n_unpaired_subsamp = 0\n n_rmdup_unpaired = 0\n did_include_subsampled_unpaired_reads = False\n\n # --- subsampling ---\n\n # if we have too few paired reads after trimming and de-duplication, we can incorporate unpaired reads\n if n_rmdup_paired * 2 < n_reads:\n # Need to include unpaired reads to reach target\n with util_file.tempfname(suffix='.unpaired.fastq') as unpaired_concat, \\\n util_file.tempfname(suffix='.unpaired.rmdup.fastq') as unpaired_concat_rmdup:\n\n # merge unpaired reads from trimmomatic and singletons left over from paired-mode prinseq\n util_file.cat(unpaired_concat, trimfq_unpaired + rmdupfq_unpaired_from_paired_rmdup)\n\n prinseq_tool.rmdup_fastq_single(unpaired_concat, unpaired_concat_rmdup)\n n_rmdup_unpaired = util_file.count_fastq_reads(unpaired_concat_rmdup)\n\n did_include_subsampled_unpaired_reads = True\n\n # if there are no unpaired reads, simply output the paired reads\n if n_rmdup_unpaired == 0:\n shutil.copyfile(tmp_bam_paired, outBam)\n n_output = samtools_tool.count(outBam)\n else:\n with util_file.tempfname(suffix='.unpaired.bam') as tmp_bam_unpaired, \\\n util_file.tempfname(suffix='.unpaired.subsamp.bam') as tmp_bam_unpaired_subsamp, \\\n util_file.tempfname(suffix='.merged.bam') as tmp_bam_merged:\n\n # take pooled unpaired reads and convert to bam\n picard.FastqToSamTool().execute(unpaired_concat_rmdup, None, 'Dummy', tmp_bam_unpaired)\n\n reads_to_add = (n_reads - (n_rmdup_paired * 2))\n downsamplesam.downsample_to_approx_count(tmp_bam_unpaired, tmp_bam_unpaired_subsamp, reads_to_add)\n n_unpaired_subsamp = samtools_tool.count(tmp_bam_unpaired_subsamp)\n\n # merge the subsampled unpaired reads into the bam\n picard.MergeSamFilesTool().execute([tmp_bam_paired, tmp_bam_unpaired_subsamp], tmp_bam_merged)\n\n samtools_tool.reheader(tmp_bam_merged, tmp_header, outBam)\n\n n_paired_subsamp = n_rmdup_paired # count is pairs\n n_output = n_rmdup_paired * 2 + n_unpaired_subsamp # count is individual reads\n\n else:\n did_include_subsampled_unpaired_reads = False\n log.info(\"PRE-SUBSAMPLE COUNT: %s read pairs\", n_rmdup_paired)\n\n with util_file.tempfname(suffix='.paired.subsamp.bam') as tmp_bam_paired_subsamp:\n downsamplesam.downsample_to_approx_count(tmp_bam_paired, tmp_bam_paired_subsamp, n_reads)\n n_paired_subsamp = samtools_tool.count(tmp_bam_paired_subsamp) // 2 # count is pairs\n n_output = n_paired_subsamp * 2 # count is individual reads\n\n samtools_tool.reheader(tmp_bam_paired_subsamp, tmp_header, outBam)\n\n n_final_individual_reads = samtools_tool.count(outBam)\n\n log.info(\"Pre-DeNovoAssembly read filters: \")\n log.info(\" %d read pairs at start\", n_input)\n log.info(\n \" %d read pairs after Trimmomatic %s\",\n n_trim, \"(and {} unpaired)\".format(n_trim_unpaired) if n_trim_unpaired > 0 else \"\"\n )\n log.info(\n \" %d read pairs after Prinseq rmdup %s\",\n n_rmdup, \"(and {} unpaired from Trimmomatic+Prinseq)\".format(n_rmdup_unpaired)\n if n_rmdup_unpaired > 0 else \"\"\n )\n if did_include_subsampled_unpaired_reads:\n log.info(\n \" Too few individual reads (%d*2=%d) from paired reads to reach desired threshold (%d), \"\n \"so including subsampled unpaired reads\",\n n_rmdup_paired, n_rmdup_paired * 2, n_reads\n )\n else:\n log.info(\" Paired read count sufficient to reach threshold (%d)\", n_reads)\n log.info(\n \" %d individual reads for de novo assembly (%s%s)\",\n n_output,\n \"paired subsampled {} -> {}\".format(n_rmdup_paired, n_paired_subsamp)\n if not did_include_subsampled_unpaired_reads else \"{} read pairs\".format(n_rmdup_paired),\n \" + unpaired subsampled {} -> {}\".format(n_rmdup_unpaired, n_unpaired_subsamp)\n if did_include_subsampled_unpaired_reads else \"\"\n )\n log.info(\" %d individual reads\", n_final_individual_reads)\n\n if did_include_subsampled_unpaired_reads:\n if n_final_individual_reads < n_reads:\n log.warning(\n \"NOTE: Even with unpaired reads included, there are fewer unique trimmed reads \"\n \"than requested for de novo assembly input.\"\n )\n\n # multiply counts so all reflect individual reads\n return (n_input * 2, n_trim * 2, n_rmdup * 2, n_output, n_paired_subsamp * 2, n_unpaired_subsamp)\n\n\ndef parser_trim_rmdup_subsamp(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, unaligned BAM format.')\n parser.add_argument('clipDb', help='Trimmomatic clip DB (FASTA with adapter sequences).')\n parser.add_argument(\n 'outBam',\n help='''Output reads, unaligned BAM format (currently, read groups and other\n header information are destroyed in this process).'''\n )\n parser.add_argument(\n '--n_reads',\n default=100000,\n type=int,\n help='''Subsample to no more than this many individual reads. Note that\n paired reads are given priority, and unpaired reads are included to\n reach the count if there are too few paired reads. (default: %(default)s)'''\n )\n util_cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, trim_rmdup_subsamp_reads, split_args=True)\n return parser\n\n\n__commands__.append(('trim_rmdup_subsamp', parser_trim_rmdup_subsamp))\n\n\n# =========================\n\ndef full_parser():\n return util_cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n util_cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/reports.py", "content": "#!/usr/bin/env python3\n''' Functions to create reports from genomics pipeline data.\n'''\n\n__author__ = \"dpark@broadinstitute.org\"\n__commands__ = []\n\nimport argparse\nimport logging\nimport glob\nimport os\nimport time\nfrom collections import OrderedDict, defaultdict\nimport csv\nimport math\nimport shutil\n\nimport pysam\nfrom pybedtools import BedTool\nimport Bio.SeqIO\nimport matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot\n\nfrom .core import file as util_file, misc as util_misc, cmd as util_cmd\nfrom .core import samtools\nfrom .core import bwa\nfrom .core import fastqc\nfrom .core import picard\nfrom .core.stats import mean, median\n\nlog = logging.getLogger(__name__)\n\n\ndef get_assembly_stats(sample,\n cov_thresholds=(1, 5, 20, 100),\n assembly_dir='data/02_assembly', assembly_tmp='tmp/02_assembly',\n align_dir='data/02_align_to_self', reads_dir='data/01_per_sample',\n raw_reads_dir='data/00_raw'):\n ''' Fetch assembly-level statistics for a given sample '''\n out = {'sample': sample}\n samtools_tool = samtools.SamtoolsTool()\n header = ['sample',\n 'reads_raw',\n 'reads_cleaned',\n 'reads_taxfilt',\n 'assembled_trinity',\n 'trinity_in_reads',\n 'n_contigs',\n 'contig_len',\n 'unambig_bases',\n 'pct_unambig',\n 'aln2self_reads_tot',\n 'aln2self_reads_aln',\n 'aln2self_reads_rmdup',\n 'aln2self_pct_nondup',\n 'aln2self_cov_median',\n 'aln2self_cov_mean',\n 'aln2self_cov_mean_non0',] + ['aln2self_cov_%dX' % t for t in cov_thresholds]\n\n # per-sample unaligned read stats\n for adj in ('cleaned', 'taxfilt'):\n reads_bam = os.path.join(reads_dir, '.'.join((sample, adj, 'bam')))\n if os.path.isfile(reads_bam):\n out['reads_' + adj] = samtools_tool.count(reads_bam)\n if os.path.isdir(raw_reads_dir):\n out['reads_raw'] = sum(samtools_tool.count(bam)\n # correct issue where sample names containing other sample names as substrings leads\n # to extra files being included in the count\n #\n # add a dot before the wildcard, and assume the sample name is found before the dot.\n # this works for now since dots are the filename field separators\n # and leading/trailing dots are stripped from sample names in util_file.string_to_file_name()\n # TODO: replace this with better filtering?\n for bam in glob.glob(os.path.join(raw_reads_dir, sample + \".*.bam\")))\n sample_raw_fname = os.path.join(raw_reads_dir, sample + \".bam\")\n if os.path.isfile(sample_raw_fname):\n # if \"00_raw/sample.bam\" exists, these were not demuxed by snakemake\n if out['reads_raw']:\n # if sample.bam AND sample.library.flowcell.lane.bam exist, we have a problem!\n out['reads_raw'] = 'ambiguous filenames in raw reads directory!'\n else:\n # just count the sample.bam reads\n out['reads_raw'] = samtools_tool.count(sample_raw_fname)\n\n # pre-assembly stats\n out['assembled_trinity'] = os.path.isfile(os.path.join(assembly_tmp, sample +\n '.assembly1-trinity.fasta')) and 1 or 0\n sub_bam = os.path.join(assembly_tmp, sample + '.subsamp.bam')\n if os.path.isfile(sub_bam):\n out['trinity_in_reads'] = samtools_tool.count(sub_bam)\n\n # assembly stats\n assembly_fname = os.path.join(assembly_dir, sample + '.fasta')\n if not os.path.isfile(assembly_fname):\n assembly_fname = os.path.join(assembly_tmp, sample + '.assembly2-scaffolded.fasta')\n if not os.path.isfile(assembly_fname):\n out['n_contigs'] = 0\n if os.path.isfile(assembly_fname):\n with open(assembly_fname, 'rt') as inf:\n counts = [(len(s), util_misc.unambig_count(s.seq)) for s in Bio.SeqIO.parse(inf, 'fasta') if len(s) > 0]\n out['n_contigs'] = len(counts)\n out['contig_len'] = ','.join(str(x) for x, y in counts)\n out['unambig_bases'] = ','.join(str(y) for x, y in counts)\n out['pct_unambig'] = ','.join(str(float(y) / x) for x, y in counts)\n\n # read counts from align-to-self\n bam_fname = os.path.join(align_dir, sample + '.bam')\n if os.path.isfile(bam_fname):\n out['aln2self_reads_tot'] = samtools_tool.count(bam_fname)\n out['aln2self_reads_aln'] = samtools_tool.count(bam_fname, opts=['-F', '4'])\n out['aln2self_reads_rmdup'] = samtools_tool.count(bam_fname, opts=['-F', '1028'])\n if out['aln2self_reads_aln']:\n out['aln2self_pct_nondup'] = float(out['aln2self_reads_rmdup']) / out['aln2self_reads_aln']\n\n # genome coverage stats\n bam_fname = os.path.join(align_dir, sample + '.mapped.bam')\n if os.path.isfile(bam_fname):\n with pysam.AlignmentFile(bam_fname, 'rb') as bam:\n coverages = list([pcol.nsegments for pcol in bam.pileup()])\n if coverages:\n out['aln2self_cov_median'] = median(coverages)\n out['aln2self_cov_mean'] = \"%0.3f\" % mean(coverages)\n out['aln2self_cov_mean_non0'] = \"%0.3f\" % mean([n for n in coverages if n > 0])\n for thresh in cov_thresholds:\n out['aln2self_cov_%dX' % thresh] = sum(1 for n in coverages if n >= thresh)\n\n return (header, out)\n\n\ndef genome_coverage_stats_only(mapped_bam, chr_name=None, cov_thresholds=(1, 5, 20, 100)):\n out = {}\n with pysam.AlignmentFile(mapped_bam, 'rb') as bam:\n coverages = list([pcol.nsegments for pcol in bam.pileup(chr_name)])\n if coverages:\n out['aln2self_cov_median'] = median(coverages)\n out['aln2self_cov_mean'] = \"%0.3f\" % mean(coverages)\n out['aln2self_cov_mean_non0'] = \"%0.3f\" % mean([n for n in coverages if n > 0])\n for thresh in cov_thresholds:\n out['aln2self_cov_%dX' % thresh] = sum(1 for n in coverages if n >= thresh)\n return out\n\n\ndef assembly_stats(samples, outFile, cov_thresholds, assembly_dir, assembly_tmp, align_dir, reads_dir, raw_reads_dir):\n ''' Fetch assembly-level statistics for a given sample '''\n header_written = False\n with open(outFile, 'wt') as outf:\n for sample in samples:\n log.info(\"fetching stats on \" + sample)\n header, out = get_assembly_stats(sample,\n cov_thresholds=cov_thresholds,\n assembly_dir=assembly_dir,\n assembly_tmp=assembly_tmp,\n align_dir=align_dir,\n reads_dir=reads_dir,\n raw_reads_dir=raw_reads_dir)\n if not header_written:\n outf.write('\\t'.join(map(str, header)) + '\\n')\n header_written = True\n outf.write('\\t'.join([str(out.get(h, '')) for h in header]) + '\\n')\n outf.flush()\n\n\ndef parser_assembly_stats(parser=argparse.ArgumentParser()):\n parser.add_argument('samples', nargs='+', help='Sample names.')\n parser.add_argument('outFile', help='Output report file.')\n parser.add_argument('--cov_thresholds',\n nargs='+',\n type=int,\n default=(1, 5, 20, 100),\n help='Genome coverage thresholds to report on. (default: %(default)s)')\n parser.add_argument('--assembly_dir',\n default='data/02_assembly',\n help='Directory with assembly outputs. (default: %(default)s)')\n parser.add_argument('--assembly_tmp',\n default='tmp/02_assembly',\n help='Directory with assembly temp files. (default: %(default)s)')\n parser.add_argument('--align_dir',\n default='data/02_align_to_self',\n help='Directory with reads aligned to own assembly. (default: %(default)s)')\n parser.add_argument('--reads_dir',\n default='data/01_per_sample',\n help='Directory with unaligned filtered read BAMs. (default: %(default)s)')\n parser.add_argument('--raw_reads_dir',\n default='data/00_raw',\n help='Directory with unaligned raw read BAMs. (default: %(default)s)')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, assembly_stats, split_args=True)\n return parser\n\n\n__commands__.append(('assembly_stats', parser_assembly_stats))\n\n\ndef _get_samples_from_bam(bam):\n with pysam.AlignmentFile(bam) as af:\n return set(rg['SM'] for rg in af.header['RG'])\ndef _get_chrs_from_bam(bam):\n with pysam.AlignmentFile(bam) as af:\n return list(sq['SN'] for sq in af.header['SQ'])\n\ndef parser_coverage_only(parser=argparse.ArgumentParser()):\n parser.add_argument('mapped_bams', nargs='+', help='Aligned-to-self mapped bam files.')\n parser.add_argument('out_report', help='Output report file.')\n parser.add_argument('--cov_thresholds',\n nargs='+',\n type=int,\n default=(1, 5, 20, 100),\n help='Genome coverage thresholds to report on. (default: %(default)s)')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, coverage_only, split_args=True)\n return parser\ndef coverage_only(mapped_bams, out_report, cov_thresholds=(1, 5, 20, 100)):\n header = ['sample','aln2self_cov_median', 'aln2self_cov_mean', 'aln2self_cov_mean_non0']\n header += ['aln2self_cov_%dX' % thresh for thresh in cov_thresholds]\n with open(out_report, 'wt') as outf:\n outf.write('\\t'.join(header)+'\\n')\n for bam in mapped_bams:\n # check for index and auto-create if needed\n with pysam.AlignmentFile(bam) as af:\n is_indexed = af.has_index()\n if not is_indexed:\n pysam.index(bam)\n # get unique sample name\n samples = _get_samples_from_bam(bam)\n if len(samples) != 1:\n raise Exception(\"input bam file {} has {} unique samples: {} (require one unique sample)\".format(bam, len(samples), str(samples)))\n sample_name = samples.pop()\n # get and write coverage stats\n row = genome_coverage_stats_only(bam, cov_thresholds=cov_thresholds)\n row['sample'] = sample_name\n outf.write('\\t'.join([str(row.get(h,'')) for h in header])+'\\n')\n # for multi-seg genomes, also do per-chr stats\n chrs = _get_chrs_from_bam(bam)\n if len(chrs) > 1:\n for i in range(len(chrs)):\n row = genome_coverage_stats_only(bam, chr_name=chrs[i], cov_thresholds=cov_thresholds)\n row['sample'] = \"{}-{}\".format(sample_name, i+1)\n outf.write('\\t'.join([str(row.get(h,'')) for h in header])+'\\n')\n__commands__.append(('coverage_only', parser_coverage_only))\n\n\n\ndef consolidate_fastqc(inDirs, outFile):\n '''Consolidate multiple FASTQC reports into one.'''\n with util_file.open_or_gzopen(outFile, 'wt') as outf:\n header = ['Sample']\n out_n = 0\n for sdir in inDirs:\n out = {}\n with open(os.path.join(sdir, 'summary.txt'), 'rt') as inf:\n for line in inf:\n v, k, fn = line.strip().split('\\t')\n out[k] = v\n if out_n == 0:\n header.append(k)\n if not fn.endswith('.bam'):\n raise TypeError(\"%s not a bam file\" % fn)\n out['Sample'] = fn[:-len('.bam')]\n if out_n == 0:\n outf.write('\\t'.join(header) + '\\n')\n outf.write('\\t'.join([out.get(h, '') for h in header]) + '\\n')\n out_n += 1\n\n\ndef parser_consolidate_fastqc(parser=argparse.ArgumentParser()):\n parser.add_argument('inDirs', help='Input FASTQC directories.', nargs='+')\n parser.add_argument('outFile', help='Output report file.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, consolidate_fastqc, split_args=True)\n return parser\n\n\n__commands__.append(('consolidate_fastqc', parser_consolidate_fastqc))\n\n\ndef get_bam_info(bamstats_dir):\n libs = {}\n for fn in glob.glob(os.path.join(bamstats_dir, \"*.txt\")):\n with util_file.open_or_gzopen(fn, 'rt') as inf:\n bam = {}\n for line in inf:\n k, v = line.rstrip('\\n').split('\\t')\n bam[k] = v\n libs.setdefault(bam['Sample'], {})\n libs[bam['Sample']][bam['BAM']] = bam['Total reads']\n return libs\n\n\ndef get_lib_info(runfile):\n libs = {}\n for lane in util_file.read_tabfile_dict(runfile):\n for well in util_file.read_tabfile_dict(lane['barcode_file']):\n libname = well['sample'] + '.l' + well['library_id_per_sample']\n libs.setdefault(libname, [])\n plate = well['Plate']\n if plate.lower().startswith('plate'):\n plate = plate[5:]\n well_id = well['Well'][0].upper() + \"%02d\" % int(well['Well'][1:])\n dat = [well['sample'], lane['flowcell'] + '.' + lane['lane'], well['barcode_1'] + '-' + well['barcode_2'],\n plate.strip() + ':' + well_id, get_earliest_date(lane['bustard_dir']), well.get('Tube_ID', '')]\n libs[libname].append(dat)\n return libs\n\n\ndef get_earliest_date(inDir):\n fnames = [inDir] + [os.path.join(inDir, x) for x in os.listdir(inDir)]\n earliest = min(os.path.getmtime(fn) for fn in fnames)\n return time.strftime(\"%Y-%m-%d\", time.localtime(earliest))\n\n\ndef consolidate_spike_count(in_dir, out_file):\n '''Consolidate multiple spike count reports into one.'''\n with open(out_file, 'wt') as outf:\n for fn in os.listdir(in_dir):\n fn = os.path.join(in_dir, fn)\n s = os.path.basename(fn)\n if not s.endswith('.spike_count.txt'):\n raise Exception()\n s = s[:-len('.spike_count.txt')]\n with open(fn, 'rt') as inf:\n for line in inf:\n if not line.startswith('Input bam') and not line.startswith('*'):\n spike, count = [line.strip().split('\\t')[i] for i in [0,2]]\n outf.write('\\t'.join([s, spike, count]) + '\\n')\n\n\ndef parser_consolidate_spike_count(parser=argparse.ArgumentParser()):\n parser.add_argument('in_dir', metavar=\"inDir\", help='Input spike count directory.')\n parser.add_argument('out_file', metavar=\"outFile\", help='Output report file.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, consolidate_spike_count, split_args=True)\n return parser\n\n\n__commands__.append(('consolidate_spike_count', parser_consolidate_spike_count))\n\n\ndef aggregate_spike_count(in_dir, out_file):\n '''aggregate multiple spike count reports into one.'''\n spike_in_sample_counts = defaultdict(dict) # For a given spikein ID, map to sample name and corresponding count\n samples_seen = []\n with open(out_file, 'wt') as outf:\n for fn in glob.glob(os.path.realpath(in_dir)+\"/*.spike_count.txt\"):# os.listdir():\n #fn = os.path.join(in_dir, fn)\n s = os.path.basename(fn)\n if not s.endswith('.spike_count.txt'):\n raise Exception()\n if s.find('.spike_count.txt'):\n s = s[:-len('.spike_count.txt')]\n if s not in samples_seen:\n samples_seen.append(s)\n with open(fn, 'rt') as inf:\n for line in inf:\n if not line.startswith('Input bam') and not line.startswith('*'):\n spike, count = [line.strip().split('\\t')[i] for i in [0,2]]\n spike_in_sample_counts[spike][s] = count\n #outf.write('\\t'.join([s, spike, count]) + '\\n')\n outf.write(\"\\t\".join([\"spike-in\"]+samples_seen)+\"\\n\")\n for spike in sorted(spike_in_sample_counts.keys()):\n row = []\n row.append(spike)\n for s in samples_seen:\n if s in spike_in_sample_counts[spike]:\n row.append(spike_in_sample_counts[spike][s])\n else:\n row.append(\"0\")\n outf.write(\"\\t\".join(row)+\"\\n\")\n\n\ndef parser_aggregate_spike_count(parser=argparse.ArgumentParser()):\n parser.add_argument('in_dir', metavar=\"inDir\", help='Input spike count directory.')\n parser.add_argument('out_file', metavar=\"outFile\", help='Output report file.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, aggregate_spike_count, split_args=True)\n return parser\n__commands__.append(('aggregate_spike_count', parser_aggregate_spike_count))\n\n\ndef aggregate_alignment_counts(in_reports, out_file):\n '''aggregate multiple reports from read_utils.py bwamem_idxstats into one report.'''\n seq_in_sample_counts = defaultdict(dict) # For a given ref sequence ID, map to input file and corresponding count\n input_files_seen = []\n with open(out_file, 'wt') as outf:\n for in_report in in_reports:\n short_name = os.path.basename(in_report)\n for suffix in ['.txt','.tsv']:\n if short_name.endswith(suffix):\n short_name = short_name[:-len(suffix)] \n if short_name not in input_files_seen:\n input_files_seen.append(short_name)\n with open(in_report, 'rt') as inf:\n for line in inf:\n if not line.startswith('Input bam') and not line.startswith('*'):\n seq_mapped_to, count = [line.strip().split('\\t')[i] for i in [0,2]]\n seq_in_sample_counts[seq_mapped_to][short_name] = count\n outf.write(\"\\t\".join([\"seq_mapped_to\"]+sorted(input_files_seen))+\"\\n\")\n for seq_mapped_to in sorted(seq_in_sample_counts.keys()):\n row = []\n row.append(seq_mapped_to)\n for s in sorted(input_files_seen):\n if s in seq_in_sample_counts[seq_mapped_to]:\n row.append(seq_in_sample_counts[seq_mapped_to][s])\n else:\n row.append(\"0\")\n outf.write(\"\\t\".join(row)+\"\\n\")\n\ndef parser_aggregate_alignment_counts(parser=argparse.ArgumentParser()):\n parser.add_argument('in_reports', nargs=\"+\", metavar=\"in_reports\", help='tsv reports with alignment counts from read_utils.py bwamem_idxstats')\n parser.add_argument('out_file', metavar=\"outFile\", help='Output report file.')\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, aggregate_alignment_counts, split_args=True)\n return parser\n__commands__.append(('aggregate_alignment_counts', parser_aggregate_alignment_counts))\n\n\n# =========================\n\n\ndef parser_plot_coverage_common(parser=argparse.ArgumentParser()): # parser needs add_help=False?\n parser.add_argument('in_bam', help='Input reads, BAM format.')\n parser.add_argument('out_plot_file', help='The generated chart file')\n parser.add_argument(\n '--plotFormat',\n dest=\"plot_format\",\n default=None,\n type=str,\n choices=list(matplotlib.pyplot.gcf().canvas.get_supported_filetypes().keys()),\n metavar='',\n help=\"File format of the coverage plot. By default it is inferred from the file extension of out_plot_file, but it can be set explicitly via --plotFormat. Valid formats include: \"\n + \", \".join(list(matplotlib.pyplot.gcf().canvas.get_supported_filetypes().keys()))\n )\n parser.add_argument(\n '--plotDataStyle',\n dest=\"plot_data_style\",\n default=\"filled\",\n type=str,\n choices=[\"filled\", \"line\", \"dots\"],\n metavar='',\n help=\"The plot data display style. Valid options: \" + \", \".join([\"filled\", \"line\", \"dots\"]) +\n \" (default: %(default)s)\"\n )\n parser.add_argument(\n '--plotStyle',\n dest=\"plot_style\",\n default=\"ggplot\",\n type=str,\n choices=matplotlib.pyplot.style.available,\n metavar='',\n help=\"The plot visual style. Valid options: \" + \", \".join(matplotlib.pyplot.style.available) + \" (default: %(default)s)\"\n )\n parser.add_argument(\n '--plotWidth',\n dest=\"plot_width\",\n default=880,\n type=int,\n help=\"Width of the plot in pixels (default: %(default)s)\"\n )\n parser.add_argument(\n '--plotHeight',\n dest=\"plot_height\",\n default=680,\n type=int,\n help=\"Width of the plot in pixels (default: %(default)s)\"\n )\n parser.add_argument(\n '--plotDPI',\n dest=\"plot_dpi\",\n default=matplotlib.pyplot.gcf().get_dpi(),\n type=int,\n help=\"dots per inch for rendered output, more useful for vector modes (default: %(default)s)\"\n )\n parser.add_argument(\n '--plotTitle',\n dest=\"plot_title\",\n default=\"Coverage Plot\",\n type=str,\n help=\"The title displayed on the coverage plot (default: '%(default)s')\"\n )\n parser.add_argument(\n '--plotXLimits',\n dest=\"plot_x_limits\",\n nargs=2,\n default=None,\n type=int,\n help=\"Limits on the x-axis of the coverage plot; args are ' '\"\n )\n parser.add_argument(\n '--plotYLimits',\n dest=\"plot_y_limits\",\n nargs=2,\n default=None,\n type=int,\n help=\"Limits on the y-axis of the coverage plot; args are ' '\"\n )\n parser.add_argument(\n '-q', dest=\"base_q_threshold\",\n default=None, type=int,\n help=\"The minimum base quality threshold\"\n )\n parser.add_argument(\n '-Q', dest=\"mapping_q_threshold\",\n default=None,\n type=int, help=\"The minimum mapping quality threshold\"\n )\n parser.add_argument(\n '-m',\n dest=\"max_coverage_depth\",\n default=None,\n type=int,\n help=\"The max coverage depth (default: %(default)s)\"\n )\n parser.add_argument('-l',\n dest=\"read_length_threshold\",\n default=None,\n type=int,\n help=\"Read length threshold\"\n )\n parser.add_argument(\n '--binLargePlots',\n dest=\"bin_large_plots\",\n action=\"store_true\",\n help=\"Plot summary read depth in one-pixel-width bins for large plots.\"\n )\n parser.add_argument(\n '--binningSummaryStatistic',\n dest=\"binning_summary_statistic\",\n choices=[\"max\", \"min\", \"mean\", \"median\"],\n type=str,\n default=\"max\",\n help=\"Statistic used to summarize each bin (max or min).\"\n )\n parser.add_argument(\n '--outSummary',\n dest=\"out_summary\",\n default=None,\n type=str,\n help=\"Coverage summary TSV file. Default is to write to temp.\"\n )\n return parser\n\n\ndef plot_coverage(\n in_bam,\n out_plot_file,\n plot_format,\n plot_data_style,\n plot_style,\n plot_width,\n plot_height,\n plot_dpi,\n plot_title,\n plot_x_limits,\n plot_y_limits,\n base_q_threshold,\n mapping_q_threshold,\n max_coverage_depth,\n read_length_threshold,\n plot_only_non_duplicates=False,\n bin_large_plots=False,\n binning_summary_statistic=\"max\",\n out_summary=None\n ):\n '''\n Generate a coverage plot from an aligned bam file\n '''\n samtools_tool = samtools.SamtoolsTool()\n\n # check if in_bam is aligned, if not raise an error\n num_mapped_reads = samtools_tool.count(in_bam, opts=[\"-F\", \"4\"])\n if num_mapped_reads == 0:\n raise Exception(\n \"\"\"The bam file specified appears to have zero mapped reads. 'plot_coverage' requires an aligned bam file. You can try 'align_and_plot_coverage' if the plot input bam file contains reads and you don't mind a simple bwa alignment. \\n File: %s\"\"\"\n % in_bam\n )\n\n if out_summary is None:\n coverage_tsv_file = util_file.mkstempfname('.summary.tsv')\n else:\n coverage_tsv_file = out_summary\n\n bam_dupe_processed = util_file.mkstempfname('.dupe_processed.bam')\n if plot_only_non_duplicates:\n # TODO: this is probably not necessary since \"samtools depth\" does not count marked duplicates\n # write a new bam file; exclude reads with the 1024 flag set (PCR or optical duplicates)\n samtools_tool.view([\"-F\", \"1024\", '-@', '3'], in_bam, bam_dupe_processed)\n else:\n bam_dupe_processed = in_bam\n\n # only sort if not sorted\n bam_sorted = util_file.mkstempfname('.sorted.bam')\n should_remove_sorted = True\n if not util_file.bam_is_sorted(bam_dupe_processed):\n samtools_tool.sort(bam_dupe_processed, bam_sorted, args=[\"-O\", \"bam\"])\n if plot_only_non_duplicates:\n os.unlink(bam_dupe_processed)\n else:\n bam_sorted = bam_dupe_processed\n if not plot_only_non_duplicates:\n # in this case we are passing through the original in_bam directly\n should_remove_sorted = False\n\n # call samtools index\n samtools_tool.index(bam_sorted)\n\n # call samtools depth\n opts = []\n opts += ['-aa'] # report coverate at \"absolutely all\" positions\n if base_q_threshold:\n if not plot_only_non_duplicates:\n # Note: \"bedtools genomecov\" will count depth including duplicates, but does\n # not expose options for filtering by quality. When duplicates\n # are excluded, \"samtools depth\" is used which does support quality filtering\n # We use either samtools or bedtools, because the former ignores marked duplicates\n # from its depth count while bedtools includes them. \n log.warning(\"'-q' ignored since --plotOnlyNonDuplicates is absent\")\n opts += [\"-q\", str(base_q_threshold)]\n if mapping_q_threshold:\n if not plot_only_non_duplicates:\n log.warning(\"'-Q' ignored since --plotOnlyNonDuplicates is absent\")\n opts += [\"-Q\", str(mapping_q_threshold)]\n if max_coverage_depth:\n if not plot_only_non_duplicates:\n log.warning(\"'-m' ignored since --plotOnlyNonDuplicates is absent\")\n opts += [\"-m\", str(max_coverage_depth)]\n if read_length_threshold:\n if not plot_only_non_duplicates:\n log.warning(\"'-l' ignored since --plotOnlyNonDuplicates is absent\")\n opts += [\"-l\", str(read_length_threshold)]\n\n # add option here for bedtools to report coverage w/ duplicates \n # (and then samtools for no-dups)\n #\n # Ex.\n # samtools depth -aa mapped-to-ref.with-dups.tmp.bam\n # bedtools genomecov -ibam mapped-to-ref.with-dups.tmp.bam -d\n if not plot_only_non_duplicates:\n bt = BedTool(bam_sorted)\n # \"d=True\" is the equivalent of passing \"-d\" to the bedtools CLI\n bt.genome_coverage(d=True).saveas(coverage_tsv_file)\n else:\n samtools_tool.depth(bam_sorted, coverage_tsv_file, opts)\n\n # only remove the sorted bam if it is not the original input bam\n # which we use directly in some casess \n if should_remove_sorted:\n os.unlink(bam_sorted)\n\n # ---- create plot based on coverage_tsv_file ----\n\n segment_depths = OrderedDict()\n domain_max = 0\n with open(coverage_tsv_file, \"r\") as tabfile:\n for row in csv.reader(tabfile, delimiter='\\t'):\n segment_depths.setdefault(row[0], []).append(float(row[2]))\n domain_max += 1\n\n with matplotlib.pyplot.style.context(plot_style):\n fig = matplotlib.pyplot.gcf()\n DPI = plot_dpi or fig.get_dpi()\n fig.set_size_inches(float(plot_width) / float(DPI), float(plot_height) / float(DPI))\n\n font_size = (2.5 * plot_height) / float(DPI)\n\n ax = matplotlib.pyplot.subplot() # Defines ax variable by creating an empty plot\n\n # Set the tick labels font\n for label in (ax.get_xticklabels() + ax.get_yticklabels()):\n label.set_fontsize(font_size)\n \n # Binning\n bin_size = 1\n if bin_large_plots:\n # Bin locations and take summary value (maximum or minimum) in each bin\n binning_fn = {\n \"min\": min,\n \"max\": max,\n \"mean\": mean,\n \"median\": median\n }\n binning_action = binning_fn.get(binning_summary_statistic, \"max\")\n \n inner_plot_width_inches = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted()).width\n inner_plot_width_px = inner_plot_width_inches * fig.dpi # width of actual plot (sans whitespace and y axis text)\n bins_per_pixel = 1 # increase to make smaller (but less visible) bins\n bin_size = 1 + int(domain_max/(inner_plot_width_px * bins_per_pixel))\n \n binned_segment_depths = OrderedDict()\n for segment_num, (segment_name, position_depths) in enumerate(segment_depths.items()):\n summary_depths_in_bins = [binning_action(position_depths[i:i + bin_size]) for i in range(0, len(position_depths), bin_size)]\n binned_segment_depths[segment_name] = summary_depths_in_bins\n segment_depths = binned_segment_depths\n \n # Plotting\n domain_max = 0\n for segment_num, (segment_name, position_depths) in enumerate(segment_depths.items()):\n prior_domain_max = domain_max\n domain_max += len(position_depths)\n\n colors = list(matplotlib.pyplot.rcParams['axes.prop_cycle'].by_key()['color']) # get the colors for this style\n segment_color = colors[segment_num % len(colors)] # pick a color, offset by the segment index\n\n x_values = range(prior_domain_max, domain_max)\n x_values = [x * bin_size for x in x_values]\n\n if plot_data_style == \"filled\":\n matplotlib.pyplot.fill_between(\n x_values,\n position_depths, [0] * len(position_depths),\n linewidth=0,\n antialiased=True,\n color=segment_color\n )\n elif plot_data_style == \"line\":\n matplotlib.pyplot.plot(\n x_values,\n position_depths,\n antialiased=True,\n color=segment_color\n )\n elif plot_data_style == \"dots\":\n matplotlib.pyplot.plot(\n x_values,\n position_depths,\n 'ro',\n antialiased=True,\n color=segment_color\n )\n\n matplotlib.pyplot.title(plot_title, fontsize=font_size * 1.2)\n matplotlib.pyplot.xlabel(\"bp\", fontsize=font_size * 1.1)\n \n ylabel = \"read depth\"\n if(bin_size > 1):\n \tylabel = \"read depth ({summary} in {size}-bp bin)\".format(size=bin_size, summary=binning_summary_statistic)\n matplotlib.pyplot.ylabel(ylabel, fontsize=font_size * 1.1)\n\n if plot_x_limits is not None:\n x_min, x_max = plot_x_limits\n matplotlib.pyplot.xlim(x_min, x_max)\n if plot_y_limits is not None:\n y_min, y_max = plot_y_limits\n matplotlib.pyplot.ylim(y_min, y_max)\n\n # to squash a backend renderer error on OSX related to tight layout\n if matplotlib.pyplot.get_backend().lower() in ['agg', 'macosx']:\n fig.set_tight_layout(True)\n else:\n fig.tight_layout()\n\n matplotlib.pyplot.savefig(out_plot_file, format=plot_format, dpi=DPI) #, bbox_inches='tight')\n log.info(\"Coverage plot saved to: \" + out_plot_file)\n\n if not out_summary:\n os.unlink(coverage_tsv_file)\n\n\ndef parser_plot_coverage(parser=argparse.ArgumentParser()):\n parser = parser_plot_coverage_common(parser)\n parser.add_argument(\n '--plotOnlyNonDuplicates',\n dest=\"plot_only_non_duplicates\",\n action=\"store_true\",\n help=\"Plot only non-duplicates (samtools -F 1024), coverage counted by bedtools rather than samtools.\"\n )\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, plot_coverage, split_args=True)\n return parser\n\n\n__commands__.append(('plot_coverage', parser_plot_coverage))\n\n\ndef align_and_plot_coverage(\n out_plot_file,\n plot_format,\n plot_data_style,\n plot_style,\n plot_width,\n plot_height,\n plot_dpi,\n plot_title,\n plot_x_limits,\n plot_y_limits,\n base_q_threshold,\n mapping_q_threshold,\n max_coverage_depth,\n read_length_threshold,\n out_summary,\n in_bam,\n ref_fasta,\n out_bam=None,\n sensitive=False,\n excludeDuplicates=False,\n bin_large_plots=False,\n binning_summary_statistic=\"max\",\n JVMmemory=None,\n picardOptions=None,\n min_score_to_filter=None,\n aligner=\"bwa\",\n aligner_options='',\n novoalign_license_path=None\n):\n ''' \n Take reads, align to reference with BWA-MEM, and generate a coverage plot\n '''\n\n # TODO: use read_utils.py::align_and_fix in place of the duplicated alignment code here\n # The main difference is the presence/absence of GATK's local_realign\n\n if out_bam is None:\n bam_aligned = util_file.mkstempfname('.aligned.bam')\n else:\n bam_aligned = out_bam\n\n assert aligner in [\"bwa\", \"novoalign\"]\n if aligner_options is None:\n if aligner==\"novoalign\":\n aligner_options = '-r Random -l 40 -g 40 -x 20 -t 100 -k'\n elif aligner=='bwa':\n aligner_options = '-1' # hidden option to work around kernel/cpu bug; disables multithreaded file read: https://github.com/lh3/bwa/issues/102\n\n samtools_tool = samtools.SamtoolsTool()\n\n ref_indexed = util_file.mkstempfname('.reference.fasta')\n shutil.copyfile(ref_fasta, ref_indexed)\n\n aln_bam = util_file.mkstempfname('.bam')\n if aligner==\"bwa\":\n bwa_tool = bwa.Bwa()\n\n\n bwa_tool.index(ref_indexed)\n\n bwa_opts = aligner_options.split()\n if sensitive:\n bwa_opts += \"-k 12 -A 1 -B 1 -O 1 -E 1\".split()\n\n bwa_tool.align_mem_bam(in_bam, ref_indexed, aln_bam, options=bwa_opts,\n min_score_to_filter=min_score_to_filter)\n elif aligner==\"novoalign\":\n \n novoalign.NovoalignTool(license_path=novoalign_license_path).index_fasta(ref_indexed)\n\n novoalign.NovoalignTool(license_path=novoalign_license_path).execute(\n in_bam, ref_indexed, aln_bam,\n options=aligner_options.split(),\n JVMmemory=JVMmemory\n )\n\n aln_bam_dupe_processed = util_file.mkstempfname('.filtered_dupe_processed.bam')\n if excludeDuplicates:\n opts = list(picardOptions)\n dupe_removal_out_metrics = util_file.mkstempfname('.metrics')\n picard.MarkDuplicatesTool().execute(\n [aln_bam], aln_bam_dupe_processed,\n dupe_removal_out_metrics, picardOptions=opts,\n JVMmemory=JVMmemory\n )\n else:\n aln_bam_dupe_processed = aln_bam\n\n samtools_tool.sort(aln_bam_dupe_processed, bam_aligned)\n os.unlink(aln_bam)\n \n if excludeDuplicates:\n os.unlink(aln_bam_dupe_processed)\n\n samtools.index(bam_aligned)\n\n # -- call plot function --\n plot_coverage(\n bam_aligned, out_plot_file, plot_format, plot_data_style, plot_style, plot_width, plot_height, plot_dpi, plot_title,\n plot_x_limits, plot_y_limits, base_q_threshold, mapping_q_threshold, max_coverage_depth, read_length_threshold,\n excludeDuplicates, bin_large_plots, binning_summary_statistic, out_summary\n )\n\n # remove the output bam, unless it is needed\n if out_bam is None:\n os.unlink(bam_aligned)\n\n # remove the files created by bwa index. \n # The empty extension causes the original fasta file to be removed\n for ext in [\".amb\", \".ann\", \".bwt\", \".bwa\", \".pac\", \".sa\", \"\"]:\n file_to_remove = ref_indexed + ext\n if os.path.isfile(file_to_remove):\n os.unlink(file_to_remove)\n\n\ndef parser_align_and_plot_coverage(parser=argparse.ArgumentParser()):\n parser = parser_plot_coverage_common(parser)\n parser.add_argument('ref_fasta', default=None, help='Reference genome, FASTA format.')\n parser.add_argument(\n '--outBam',\n dest=\"out_bam\",\n default=None,\n help='Output aligned, indexed BAM file. Default is to write to temp.'\n )\n parser.add_argument(\n '--sensitive', action=\"store_true\",\n help=\"Equivalent to giving bwa: '-k 12 -A 1 -B 1 -O 1 -E 1'. Only relevant if the bwa aligner is selected (the default). \"\n )\n parser.add_argument(\n '--excludeDuplicates', action=\"store_true\",\n help=\"MarkDuplicates with Picard and only plot non-duplicates\"\n )\n parser.add_argument(\n '--JVMmemory',\n default=picard.MarkDuplicatesTool.jvmMemDefault,\n help='JVM virtual memory size (default: %(default)s)'\n )\n parser.add_argument(\n '--picardOptions',\n default=[],\n nargs='*',\n help='Optional arguments to Picard\\'s MarkDuplicates, OPTIONNAME=value ...'\n )\n parser.add_argument(\n '--minScoreToFilter',\n dest=\"min_score_to_filter\",\n type=int,\n help=(\"Filter bwa alignments using this value as the minimum allowed \"\n \"alignment score. Specifically, sum the alignment scores across \"\n \"all alignments for each query (including reads in a pair, \"\n \"supplementary and secondary alignments) and then only include, \"\n \"in the output, queries whose summed alignment score is at least \"\n \"this value. This is only applied when the aligner is 'bwa'. \"\n \"The filtering on a summed alignment score is sensible for reads \"\n \"in a pair and supplementary alignments, but may not be \"\n \"reasonable if bwa outputs secondary alignments (i.e., if '-a' \"\n \"is in the aligner options). (default: not set - i.e., do not \"\n \"filter bwa's output)\")\n )\n parser.add_argument('--aligner', choices=['novoalign', 'bwa'], default='bwa', help='aligner (default: %(default)s)')\n parser.add_argument('--aligner_options', default=None, help='aligner options (default for novoalign: \"-r Random -l 40 -g 40 -x 20 -t 100 -k\", bwa: bwa defaults')\n parser.add_argument(\n '--NOVOALIGN_LICENSE_PATH',\n default=None,\n dest=\"novoalign_license_path\",\n help='A path to the novoalign.lic file. This overrides the NOVOALIGN_LICENSE_PATH environment variable. (default: %(default)s)'\n )\n\n util_cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n util_cmd.attach_main(parser, align_and_plot_coverage, split_args=True)\n return parser\n\n\n__commands__.append(('align_and_plot_coverage', parser_align_and_plot_coverage))\n\n\n\ndef parser_fastqc(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input reads, BAM format.')\n parser.add_argument('out_html', help='Output report, HTML format.')\n parser.add_argument('--out_zip', help='Output data, zip archive.')\n parser.add_argument('--threads', type=int, help='Number of threads.')\n util_cmd.attach_main(parser, fastqc.FastQC().execute, split_args=True)\n return parser\n__commands__.append(('fastqc', parser_fastqc))\n\n# =======================\n\n\ndef full_parser():\n return util_cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n util_cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "src/viral_ngs/taxon_filter.py", "content": "#!/usr/bin/env python3\n'''This script contains a number of utilities for filtering NGS reads based\non membership or non-membership in a species / genus / taxonomic grouping.\n'''\n\nfrom __future__ import print_function\n__author__ = \"dpark@broadinstitute.org, irwin@broadinstitute.org,\" \\\n + \"hlevitin@broadinstitute.org\"\n__commands__ = []\n\nimport argparse\nimport glob\nimport logging\nimport subprocess\nimport os\nimport math\nimport tempfile\nimport shutil\nimport concurrent.futures\nimport contextlib\n\nfrom Bio import SeqIO\nimport pysam\n\nfrom .core import cmd\nfrom .core import file\nfrom .core import misc\nfrom . import core\nfrom .core import minimap2\nfrom .core import prinseq\nfrom .core import picard\nfrom .core import samtools\nfrom .core.file import mkstempfname\nfrom .core.errors import QCError\n\nfrom .classify import blast\nfrom .classify import last\nfrom .classify import bmtagger\nfrom . import read_utils\n\n'''\n#Adding logging configuration to identify issues/ time spent\nlogging.basicConfig(\n level=logging.INFO,\n format='%(asctime)s - %(levelname)s - %(message)s',\n handlers=[\n logging.FileHandler(\"task.log\"), # Log file name\n logging.StreamHandler() # Keeps the console output if desired\n ]\n)\n'''\n\nlog = logging.getLogger(__name__)\n# =======================\n# *** deplete ***\n# =======================\n\ndef parser_deplete(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input BAM file.')\n parser.add_argument('revertBam', help='Output BAM: read markup reverted with Picard.')\n parser.add_argument('minimapBam', help='Output BAM: depleted of reads with minimap2.')\n parser.add_argument('bwaBam', help='Output BAM: depleted of reads with BWA.')\n parser.add_argument('bmtaggerBam', help='Output BAM: depleted of reads with BMTagger.')\n parser.add_argument(\n 'blastnBam', help='Output BAM: bmtaggerBam run through another depletion of reads with BLASTN.'\n )\n parser.add_argument(\n '--minimapDbs',\n nargs='*',\n default=(),\n help='Reference FASTA databases for minimap2 to deplete from input.'\n )\n parser.add_argument(\n '--bwaDbs',\n nargs='*',\n default=(),\n help='Reference databases for BWA to deplete from input.'\n )\n parser.add_argument(\n '--bmtaggerDbs',\n nargs='*',\n default=(),\n help='''Reference databases to deplete from input.\n For each db, requires prior creation of db.bitmask by bmtool,\n and db.srprism.idx, db.srprism.map, etc. by srprism mkindex.'''\n )\n parser.add_argument(\n '--blastDbs',\n nargs='*',\n default=(),\n help='Reference databases for BLASTN to deplete from input.'\n )\n parser.add_argument('--srprismMemory', dest=\"srprism_memory\", type=int, default=7168, help='Memory for srprism.')\n parser.add_argument(\"--chunkSize\", type=int, default=1000000, help='blastn chunk size (default: %(default)s)')\n parser.add_argument(\n '--JVMmemory',\n default=picard.PicardTools.jvmMemDefault,\n help='JVM virtual memory size for Picard RevertSam (default: %(default)s)'\n )\n parser = read_utils.parser_revert_sam_common(parser)\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_deplete)\n\n return parser\n\ndef main_deplete(args):\n ''' Run the entire depletion pipeline: minimap2, bwa, bmtagger, blastn.\n '''\n\n assert len(args.minimapDbs) + len(args.bmtaggerDbs) + len(args.blastDbs) + len(args.bwaDbs) > 0\n\n # only RevertSam if inBam is already aligned\n # Most of the time the input will be unaligned\n # so we can save save time if we can skip RevertSam in the unaligned case\n #\n # via the SAM/BAM spec, if the file is aligned, an SQ line should be present\n # in the header. Using pysam, we can check this if header['SQ'])>0\n # https://samcore.github.io/hts-specs/SAMv1.pdf\n\n # if the user has requested a revertBam\n\n with read_utils.revert_bam_if_aligned( args.inBam,\n revert_bam = args.revertBam,\n clear_tags = args.clear_tags,\n tags_to_clear = args.tags_to_clear,\n picardOptions = ['MAX_DISCARD_FRACTION=0.5'],\n JVMmemory = args.JVMmemory,\n sanitize = not args.do_not_sanitize) as bamToDeplete:\n multi_db_deplete_bam(\n bamToDeplete,\n args.minimapDbs,\n deplete_minimap2_bam,\n args.minimapBam,\n threads=args.threads\n )\n multi_db_deplete_bam(\n args.minimapBam,\n args.bwaDbs,\n deplete_bwa_bam,\n args.bwaBam,\n threads=args.threads\n )\n\n def bmtagger_wrapper(inBam, db, outBam):\n return deplete_bmtagger_bam(inBam, db, outBam, srprism_memory=args.srprism_memory)\n\n multi_db_deplete_bam(\n args.bwaBam,\n args.bmtaggerDbs,\n bmtagger_wrapper,\n args.bmtaggerBam\n )\n\n multi_db_deplete_bam(\n args.bmtaggerBam,\n args.blastDbs,\n deplete_blastn_bam,\n args.blastnBam,\n chunkSize=args.chunkSize,\n threads=args.threads\n )\n\n if os.path.getsize(args.revertBam) == 0:\n with file.tempfname('.empty.sam') as empty_sam:\n samtools_tool = samtools.SamtoolsTool()\n samtools_tool.dumpHeader(args.inBam, empty_sam)\n samtools_tool.view(['-b'], empty_sam, args.revertBam)\n\n return 0\n\n__commands__.append(('deplete', parser_deplete))\n\n\n# =======================\n# *** filter_lastal ***\n# =======================\n\n\ndef filter_lastal_bam(\n inBam,\n db,\n outBam,\n max_gapless_alignments_per_position=1,\n min_length_for_initial_matches=5,\n max_length_for_initial_matches=50,\n max_initial_matches_per_position=100,\n error_on_reads_in_neg_control=False,\n neg_control_prefixes=None, #set below: \"neg\",\"water\",\"NTC\"\n negative_control_reads_threshold=0,\n threads=None\n):\n ''' Restrict input reads to those that align to the given\n reference database using LASTAL.\n '''\n neg_control_prefixes = neg_control_prefixes or [\"neg\",\"water\",\"NTC\"]\n\n with file.tmp_dir('-lastdb') as tmp_db_dir:\n # index db if necessary\n lastdb = last.Lastdb()\n if not lastdb.is_indexed(db):\n db = lastdb.build_database(db, os.path.join(tmp_db_dir, 'lastdb'))\n\n # Stream lastal hits directly into ReadIdStore\n db_path = os.path.join(tmp_db_dir, 'read_ids.db')\n with read_utils.ReadIdStore(db_path) as store:\n store.extend(last.Lastal().get_hits(\n inBam, db,\n max_gapless_alignments_per_position,\n min_length_for_initial_matches,\n max_length_for_initial_matches,\n max_initial_matches_per_position,\n threads=threads\n ))\n\n if error_on_reads_in_neg_control:\n sample_name=os.path.basename(inBam)\n if any(sample_name.lower().startswith(prefix.lower()) for prefix in neg_control_prefixes):\n if len(store) > max(0,negative_control_reads_threshold):\n log.warning(\"Error raised due to reads in negative control; re-run this without '--errorOnReadsInNegControl' if this execution should succeed.\")\n raise QCError(\"The sample '{}' appears to be a negative control, but it contains {} reads after filtering to desired taxa.\".format(sample_name, len(store)))\n\n # filter original BAM file against keep list\n store.filter_bam_by_ids(inBam, outBam, include=True)\n\n\ndef parser_filter_lastal_bam(parser=argparse.ArgumentParser()):\n parser.add_argument(\"inBam\", help=\"Input reads\")\n parser.add_argument(\"db\", help=\"Database of taxa we keep\")\n parser.add_argument(\"outBam\", help=\"Output reads, filtered to refDb\")\n parser.add_argument(\n '-n',\n dest=\"max_gapless_alignments_per_position\",\n help='maximum gapless alignments per query position (default: %(default)s)',\n type=int,\n default=1\n )\n parser.add_argument(\n '-l',\n dest=\"min_length_for_initial_matches\",\n help='minimum length for initial matches (default: %(default)s)',\n type=int,\n default=5\n )\n parser.add_argument(\n '-L',\n dest=\"max_length_for_initial_matches\",\n help='maximum length for initial matches (default: %(default)s)',\n type=int,\n default=50\n )\n parser.add_argument(\n '-m',\n dest=\"max_initial_matches_per_position\",\n help='maximum initial matches per query position (default: %(default)s)',\n type=int,\n default=100\n )\n parser.add_argument(\n '--errorOnReadsInNegControl',\n dest=\"error_on_reads_in_neg_control\",\n help='If specified, the function will return an error if there are reads after filtering for samples with names containing: (water,neg,ntc) (default: %(default)s)',\n action=\"store_true\",\n )\n parser.add_argument(\n '--negativeControlReadsThreshold',\n dest=\"negative_control_reads_threshold\",\n help='maximum number of reads (single-end) or read pairs (paired-end) to tolerate in samples identified as negative controls (default: %(default)s)',\n type=int,\n default=0\n )\n parser.add_argument(\n '--negControlPrefixes',\n dest=\"neg_control_prefixes\",\n default=[\"neg\",\"water\",\"NTC\"],\n nargs='*',\n help='Bam file name prefixes to interpret as negative controls, space-separated (default: %(default)s)'\n )\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, filter_lastal_bam, split_args=True)\n return parser\n\n\n__commands__.append(('filter_lastal_bam', parser_filter_lastal_bam))\n\n\n# ==============================\n# *** deplete_bmtagger_bam ***\n# ==============================\n\n\ndef deplete_bmtagger_bam(inBam, db, outBam, srprism_memory=7168):\n \"\"\"\n Use bmtagger to partition the input reads into ones that match at least one\n of the databases and ones that don't match any of the databases.\n inBam: paired-end input reads in BAM format.\n db: bmtagger expects files\n db.bitmask created by bmtool, and\n db.srprism.idx, db.srprism.map, etc. created by srprism mkindex\n outBam: the output BAM files to hold the unmatched reads.\n srprism_memory: srprism memory in megabytes.\n \"\"\"\n bmtaggerPath = bmtagger.BmtaggerShTool().install_and_get_path()\n\n # bmtagger calls several executables in the same directory, and blastn;\n # make sure they are accessible through $PATH\n blastnPath = blast.BlastnTool().install_and_get_path()\n path = os.environ['PATH'].split(os.pathsep)\n for t in (bmtaggerPath, blastnPath):\n d = os.path.dirname(t)\n if d not in path:\n path = [d] + path\n path = os.pathsep.join(path)\n os.environ['PATH'] = path\n\n with file.tempfname('.1.fastq') as inReads1:\n samtools.SamtoolsTool().bam2fq(inBam, inReads1)\n\n with file.tempfname('.bmtagger.conf') as bmtaggerConf:\n with open(bmtaggerConf, 'w') as f:\n # Default srprismopts: \"-b 100000000 -n 5 -R 0 -r 1 -M 7168\"\n print('srprismopts=\"-b 100000000 -n 5 -R 0 -r 1 -M {srprism_memory} --paired false\"'.format(srprism_memory=srprism_memory), file=f)\n\n with extract_build_or_use_database(db, bmtagger_build_db, 'bitmask', tmp_suffix=\"-bmtagger\", db_prefix=\"bmtagger\") as (db_prefix,tempDir):\n matchesFile = mkstempfname('.txt')\n cmdline = [\n bmtaggerPath, '-b', db_prefix + '.bitmask', '-C', bmtaggerConf, '-x', db_prefix + '.srprism', '-T', tempDir, '-q1',\n '-1', inReads1, '-o', matchesFile\n ]\n log.debug(' '.join(cmdline))\n misc.run_and_print(cmdline, check=True)\n\n # Load matches into ReadIdStore and filter BAM (exclude matching reads)\n with file.tmp_dir(suffix='_bmtagger_filter') as filter_tmpdir:\n db_path = os.path.join(filter_tmpdir, 'read_ids.db')\n with read_utils.ReadIdStore(db_path) as store:\n store.add_from_readlist(matchesFile)\n store.filter_bam_by_ids(inBam, outBam, include=False)\n os.unlink(matchesFile)\n\ndef parser_deplete_bam_bmtagger(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input BAM file.')\n parser.add_argument(\n 'refDbs',\n nargs='+',\n help='''Reference databases (one or more) to deplete from input.\n For each db, requires prior creation of db.bitmask by bmtool,\n and db.srprism.idx, db.srprism.map, etc. by srprism mkindex.'''\n )\n parser.add_argument('outBam', help='Output BAM file.')\n parser.add_argument('--srprismMemory', dest=\"srprism_memory\", type=int, default=7168, help='Memory for srprism.')\n parser = read_utils.parser_revert_sam_common(parser)\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_deplete_bam_bmtagger)\n return parser\n\ndef main_deplete_bam_bmtagger(args):\n '''Use bmtagger to deplete input reads against several databases.'''\n\n def bmtagger_wrapper(inBam, db, outBam):\n return deplete_bmtagger_bam(inBam, db, outBam, srprism_memory=args.srprism_memory)\n\n with read_utils.revert_bam_if_aligned( args.inBam,\n clear_tags = args.clear_tags,\n tags_to_clear = args.tags_to_clear,\n picardOptions = ['MAX_DISCARD_FRACTION=0.5'],\n sanitize = not args.do_not_sanitize) as bamToDeplete:\n multi_db_deplete_bam(\n bamToDeplete,\n args.refDbs,\n bmtagger_wrapper,\n args.outBam\n )\n\n__commands__.append(('deplete_bam_bmtagger', parser_deplete_bam_bmtagger))\n\n\ndef multi_db_deplete_bam(inBam, refDbs, deplete_method, outBam, **kwargs):\n\n tmpDb = None\n if len(refDbs)>1 and not any(\n not os.path.exists(db) # indexed db prefix\n or os.path.isdir(db) # indexed db in directory\n or (os.path.isfile(db) and ('.tar' in db or '.tgz' in db or '.zip' in db)) # packaged indexed db\n for db in refDbs):\n # this is a scenario where all refDbs are unbuilt fasta\n # files. we can simplify and speed up execution by\n # concatenating them all and running deplete_method\n # just once\n tmpDb = mkstempfname('.fasta')\n merge_compressed_files(refDbs, tmpDb, sep='\\n')\n refDbs = [tmpDb]\n\n samtools_tool = samtools.SamtoolsTool()\n tmpBamIn = inBam\n for db in refDbs:\n if not samtools_tool.isEmpty(tmpBamIn):\n tmpBamOut = mkstempfname('.bam')\n deplete_method(tmpBamIn, db, tmpBamOut, **kwargs)\n if tmpBamIn != inBam:\n os.unlink(tmpBamIn)\n tmpBamIn = tmpBamOut\n shutil.copyfile(tmpBamIn, outBam)\n\n if tmpDb:\n os.unlink(tmpDb)\n\n\n# ========================\n# *** deplete_blastn ***\n# ========================\n\n\ndef _run_blastn_chunk(db, input_fasta, out_hits, blast_threads, task=None, outfmt='6', max_target_seqs=1, output_type='read_id'):\n \"\"\" run blastn on the input fasta file. this is intended to be run in parallel\n by blastn_chunked_fasta\n \"\"\"\n #Might need to remove this path, not absolute\n #os.environ['BLASTDB']= 'viral-classify/blast'\n try:\n with file.open_or_gzopen(out_hits, 'wt') as outf:\n for line in blast.BlastnTool().get_hits_fasta(input_fasta, db, threads=blast_threads, task=task, outfmt=outfmt, output_type=output_type):\n outf.write(line + '\\n')\n log.info(\"_run_blastn_chunk completed succesfully.\")\n except Exception as e:\n log.error(\"An error occurred in _run_blastn_chunk.:%s\", e)\n raise e\n\ndef blastn_chunked_fasta(fasta, db, out_hits, chunkSize=1000000, threads=None, task=None, outfmt='6', max_target_seqs=1, output_type='read_id'):\n \"\"\"\n Helper function: blastn a fasta file, overcoming apparent memory leaks on\n an input with many query sequences, by splitting it into multiple chunks\n and running a new blastn process on each chunk. Return a list of output\n filenames containing hits\n \"\"\"\n # the lower bound of how small a fasta chunk can be.\n # too small and the overhead of spawning a new blast process\n # will be detrimental relative to actual computation time\n\n #checks if the blastn_chunked_fasta function is being called\n log.info(\"Calling blastn_chunked_fasta function...\")\n MIN_CHUNK_SIZE = 20000\n\n # just in case blast is not installed, install it once, not many times in parallel!\n blast.BlastnTool().install()\n\n # clamp threadcount to number of CPU cores\n threads = misc.sanitize_thread_count(threads)\n\n # determine size of input data; records in fasta file\n number_of_reads = file.fasta_length(fasta)\n log.debug(\"number of reads in fasta file %s\" % number_of_reads)\n if number_of_reads == 0:\n file.make_empty(out_hits)\n\n # divide (max, single-thread) chunksize by thread count\n # to find the absolute max chunk size per thread\n chunk_max_size_per_thread = chunkSize // threads\n\n # find the chunk size if evenly divided among blast threads\n reads_per_thread = number_of_reads // threads\n\n # use the smaller of the two chunk sizes so we can run more copies of blast in parallel\n chunkSize = min(reads_per_thread, chunk_max_size_per_thread)\n\n # if the chunk size is too small, impose a sensible size\n chunkSize = max(chunkSize, MIN_CHUNK_SIZE)\n\n log.debug(\"chunk_max_size_per_thread %s\" % chunk_max_size_per_thread)\n\n # adjust chunk size so we don't have a small fraction\n # of a chunk running in its own blast process\n # if the size of the last chunk is <80% the size of the others,\n # decrease the chunk size until the last chunk is 80%\n # this is bounded by the MIN_CHUNK_SIZE\n while (number_of_reads / chunkSize) % 1 < 0.8 and chunkSize > MIN_CHUNK_SIZE:\n chunkSize = chunkSize - 1\n\n log.debug(\"blastn chunk size %s\" % chunkSize)\n log.debug(\"number of chunks to create %s\" % (number_of_reads / chunkSize))\n log.debug(\"blastn parallel instances %s\" % threads)\n log.debug(f\"outfmt value: {outfmt}\")\n # chunk the input file. This is a sequential operation\n input_fastas = []\n with open(fasta, \"rt\") as fastaFile:\n record_iter = SeqIO.parse(fastaFile, \"fasta\")\n for batch in misc.batch_iterator(record_iter, chunkSize):\n chunk_fasta = mkstempfname('.fasta')\n\n with open(chunk_fasta, \"wt\") as handle:\n count= SeqIO.write(batch, handle, \"fasta\")\n batch = None\n #detail chunk sizes being processed\n log.info(f\"Created chunk {chunk_fasta} with {count} records\")\n input_fastas.append(chunk_fasta)\n\n num_chunks = len(input_fastas)\n log.debug(\"number of chunk files to be processed by blastn %d\" % num_chunks)\n\n # run blastn on each of the fasta input chunks\n hits_files = list(mkstempfname('.hits.txt') for f in input_fastas)\n with concurrent.futures.ProcessPoolExecutor(max_workers=threads) as executor:\n # If we have so few chunks that there are cpus left over,\n # divide extra cpus evenly among chunks where possible\n # rounding to 1 if there are more chunks than extra threads.\n # Then double up this number to better maximize CPU usage.\n cpus_leftover = threads - num_chunks\n blast_threads = 2*max(1, int(cpus_leftover / num_chunks))\n for i in range(num_chunks):\n executor.submit(_run_blastn_chunk, db, input_fastas[i], hits_files[i], blast_threads, task=task, outfmt=outfmt, max_target_seqs=max_target_seqs, output_type=output_type)\n\n # merge results and clean up\n file.cat(out_hits, hits_files)\n for i in range(num_chunks):\n os.unlink(input_fastas[i])\n os.unlink(hits_files[i])\n\n\ndef deplete_blastn_bam(inBam, db, outBam, threads=None, chunkSize=1000000):\n 'Use blastn to remove reads that match at least one of the databases.'\n\n blast_hits = mkstempfname('.blast_hits.txt')\n\n with extract_build_or_use_database(db, blastn_build_db, 'nin', tmp_suffix=\"-blastn_db_unpack\", db_prefix=\"blastn\") as (db_prefix,tempDir):\n if chunkSize:\n ## chunk up input and perform blastn in several parallel threads\n with file.tempfname('.fasta') as reads_fasta:\n samtools.SamtoolsTool().bam2fa(inBam, reads_fasta)\n log.info(\"running blastn on %s against %s\", inBam, db)\n blastn_chunked_fasta(reads_fasta, db_prefix, blast_hits, chunkSize, threads)\n\n else:\n ## pipe tools together and run blastn multithreaded\n with open(blast_hits, 'wt') as outf:\n for read_id in blast.BlastnTool().get_hits_bam(inBam, db_prefix, threads=threads):\n outf.write(read_id + '\\n')\n\n # Load blast hits into ReadIdStore and filter BAM (exclude matching reads)\n with file.tmp_dir(suffix='_blastn_filter') as filter_tmpdir:\n db_path = os.path.join(filter_tmpdir, 'read_ids.db')\n with read_utils.ReadIdStore(db_path) as store:\n store.add_from_readlist(blast_hits)\n store.filter_bam_by_ids(inBam, outBam, include=False)\n os.unlink(blast_hits)\n\ndef chunk_blast_hits(inFasta, db, blast_hits_output, threads=None, chunkSize=1000000, task=None, outfmt='6', max_target_seqs=1, output_type= 'read_id'):\n 'Process BLAST hits from a FASTA file by dividing the file into smaller chunks for parallel processing (blastn_chunked_fasta).'\n if chunkSize:\n log.info(\"Running BLASTN on %s against database %s\", inFasta, db)\n #Execute blastn_chunked_fasta\n blastn_chunked_fasta(inFasta, db, blast_hits_output, chunkSize, threads, task, outfmt, max_target_seqs, output_type=output_type)\n else:\n #Pipe tools together and run blastn multithreaded\n with open(blast_hits_output, 'wt') as outf:\n for output in blast.BlastnTool().get_hits_fasta(inFasta, db, threads, task=task, outfmt=outfmt, max_target_seqs=max_target_seqs, output_type=output_type):\n #Account for read_ids extract only or full blast output run. Default = read_lines.\n if output_type == 'read_id':\n # Extract the first clmn in the output (assuming its the read ID)\n read_id = output.split('\\t')[0]\n outf.write(read_id + '\\n')\n else:\n #Extract and write full line if the output_type is not set to just read IDs\n outf.write(output + '\\n')\n\ndef parser_chunk_blast_hits(parser=argparse.ArgumentParser()):\n parser = argparse.ArgumentParser(description=\"Run BLASTN on chunks of a FASTA file.\")\n parser.add_argument('inBam', help='Input BAM file.')\n parser.add_argument('db', help='BLASTN database.')\n parser.add_argument('blast_hits_output', help='Stores hits found by BLASTN.')\n parser.add_argument(\"--chunkSize\", type=int, default=1000000, help='FASTA chunk size (default: %(default)s)')\n parser.add_argument(\"-task\", help=\"details the type of search (i.e. megablast,blatn,etc)\")\n parser.add_argument(\"-outfmt\", type=str, default=6, help=\"Custom output formats(default: %(default)s)\")\n parser.add_argument(\"-max_target_seqs\", type=int, default=1, help=\"BLAST will return the first (if set to default) database hits for a sequence query. (default: %(default)s)\")\n parser.add_argument(\"--output_type\", default= \"read_id\", choices=[\"read_id\", \"full_line\"], help=\"Specify the type of output: 'read_id' for read IDs only, or 'full_line' for full BLAST output lines. Default is 'read_id'. Useful when adding taxonomy IDs to outfmt type 6.\")\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, chunk_blast_hits)\n return parser\n\ndef parser_deplete_blastn_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input BAM file.')\n parser.add_argument('refDbs', nargs='+', help='One or more reference databases for blast. '\n 'An ephemeral database will be created if a fasta file is provided.')\n parser.add_argument('outBam', help='Output BAM file with matching reads removed.')\n parser.add_argument(\"--chunkSize\", type=int, default=1000000, help='FASTA chunk size (default: %(default)s)')\n parser = read_utils.parser_revert_sam_common(parser)\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_deplete_blastn_bam)\n return parser\n\n\ndef main_deplete_blastn_bam(args):\n '''Use blastn to remove reads that match at least one of the specified databases.'''\n\n def wrapper(inBam, db, outBam, threads):\n return deplete_blastn_bam(inBam, db, outBam, threads=threads, chunkSize=args.chunkSize)\n\n with read_utils.revert_bam_if_aligned( args.inBam,\n clear_tags = args.clear_tags,\n tags_to_clear = args.tags_to_clear,\n picardOptions = ['MAX_DISCARD_FRACTION=0.5'],\n sanitize = not args.do_not_sanitize) as bamToDeplete:\n multi_db_deplete_bam(bamToDeplete, args.refDbs, wrapper, args.outBam, threads=args.threads)\n return 0\n__commands__.append(('deplete_blastn_bam', parser_deplete_blastn_bam))\n\n\n@contextlib.contextmanager\ndef extract_build_or_use_database(db, db_build_command, db_extension_to_expect, tmp_suffix='db_unpack', db_prefix=\"db\"):\n '''\n db_extension_to_expect = file extension, sans dot prefix\n '''\n with file.tmp_dir(tmp_suffix) as tempDbDir:\n db_dir = \"\"\n if os.path.exists(db):\n if os.path.isfile(db):\n # this is a single file\n if db.endswith('.fasta') or db.endswith('.fa') or ('.fasta.' in db) or ('.fa.' in db):\n # this is an unindexed fasta file, we will need to index it\n # function should conform to the signature:\n # db_build_command(inputFasta, outputDirectory, outputFilePrefix)\n # the function will need to be able to handle lz4, etc.\n db_build_command(db, tempDbDir, db_prefix)\n db_dir = tempDbDir\n else:\n # this is a tarball with prebuilt indexes\n db_dir = file.extract_tarball(db, tempDbDir)\n else:\n # this is a directory\n db_dir = db\n # this directory should have a .{ext} file, where {ext} is specific to the type of db\n hits = list(glob.glob(os.path.join(db_dir, '*.{ext}'.format(ext=db_extension_to_expect))))\n if len(hits) == 0:\n raise Exception(\"The blast database does not appear to a *.{ext} file.\".format(ext=db_extension_to_expect))\n elif len(hits) == 1:\n db_prefix = hits[0][:-(len('.{ext}'.format(ext=db_extension_to_expect)))] # remove the '.extension'\n elif len(hits) >1:\n db_prefix = os.path.commonprefix(hits).rsplit('.', 1)[0] # remove extension and split-db prefix\n else:\n # this is simply a prefix to a bunch of files, not an actual file\n db_prefix = db.rsplit('.', 1)[0] if db.endswith('.') else db\n\n yield (db_prefix,tempDbDir)\n\n# ========================\n# *** deplete_bwa ***\n# ========================\n\ndef deplete_bwa_bam(inBam, db, outBam, threads=None, clear_tags=True, tags_to_clear=None, JVMmemory=None):\n 'Use bwa to remove reads from an unaligned bam that match at least one of the databases.'\n tags_to_clear = tags_to_clear or []\n\n threads = misc.sanitize_thread_count(threads)\n\n with extract_build_or_use_database(db, bwa_build_db, 'bwt', tmp_suffix=\"-bwa_db_unpack\", db_prefix=\"bwa\") as (db_prefix,tempDbDir):\n with file.tempfname('.aligned.sam') as aligned_sam:\n core.bwa.Bwa().align_mem_bam(inBam, db_prefix, aligned_sam, threads=threads, should_index=False, JVMmemory=JVMmemory)\n #with file.fifo(name='filtered.sam') as filtered_sam:\n with file.tempfname('.filtered.sam') as filtered_sam:\n # filter proper pairs\n samtools.SamtoolsTool().view(['-h','-F0x2'], aligned_sam, filtered_sam)\n\n picardOptions = []\n if clear_tags:\n for tag in tags_to_clear:\n picardOptions.append(\"ATTRIBUTE_TO_CLEAR={}\".format(tag))\n picard.RevertSamTool().execute(\n filtered_sam,\n outBam,\n picardOptions=['SORT_ORDER=queryname'] + picardOptions,\n JVMmemory=JVMmemory\n )\n # TODO: consider using Bwa().mem() so the input bam is not broken out by read group\n # TODO: pipe bwa input directly to samtools process (need to use Bwa().mem() directly, )\n # with Popen to background bwa process\n\ndef parser_deplete_bwa_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input BAM file.')\n parser.add_argument('refDbs', nargs='+', help='One or more reference databases for bwa. '\n 'An ephemeral database will be created if a fasta file is provided.')\n parser.add_argument('outBam', help='Ouput BAM file with matching reads removed.')\n parser.add_argument(\n '--JVMmemory',\n default=picard.PicardTools.jvmMemDefault,\n help='JVM virtual memory size for Picard RevertSam (default: %(default)s)'\n )\n parser = read_utils.parser_revert_sam_common(parser)\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_deplete_bwa_bam)\n return parser\n\ndef main_deplete_bwa_bam(args):\n '''Use BWA to remove reads that match at least one of the specified databases.'''\n with read_utils.revert_bam_if_aligned( args.inBam,\n clear_tags = args.clear_tags,\n tags_to_clear = args.tags_to_clear,\n picardOptions = ['MAX_DISCARD_FRACTION=0.5'],\n JVMmemory = args.JVMmemory,\n sanitize = not args.do_not_sanitize) as bamToDeplete:\n\n #def wrapper(inBam, db, outBam, threads, JVMmemory=None):\n # return deplete_bwa_bam(inBam, db, outBam, threads=threads, )\n multi_db_deplete_bam(bamToDeplete, args.refDbs, deplete_bwa_bam, args.outBam, threads=args.threads, clear_tags=args.clear_tags, tags_to_clear=args.tags_to_clear, JVMmemory=args.JVMmemory)\n return 0\n__commands__.append(('deplete_bwa_bam', parser_deplete_bwa_bam))\n\n\n# ========================\n# *** deplete_minimap2 ***\n# ========================\n\ndef deplete_minimap2_bam(inBam, db, outBam, threads=None):\n '''Use minimap2 to remove reads that match the reference database.\n\n inBam: input reads in BAM format.\n db: reference database in FASTA format.\n outBam: output BAM file with matching reads removed.\n threads: number of threads for minimap2 alignment.\n '''\n with file.tmp_dir(suffix='_minimap2_deplete') as tmpdir:\n idxstats_file = os.path.join(tmpdir, 'idxstats.txt')\n hitList = os.path.join(tmpdir, 'read_ids.txt')\n db_path = os.path.join(tmpdir, 'read_ids.db')\n\n # Use minimap2 idxstats to get list of mapped read IDs\n minimap2.Minimap2().idxstats(\n inBam, db, idxstats_file,\n outReadlist=hitList,\n threads=threads\n )\n\n # Load hit list into ReadIdStore and filter BAM (exclude matching reads)\n with read_utils.ReadIdStore(db_path) as store:\n store.add_from_readlist(hitList)\n store.filter_bam_by_ids(inBam, outBam, include=False)\n\n\ndef parser_deplete_minimap2_bam(parser=argparse.ArgumentParser()):\n parser.add_argument('inBam', help='Input BAM file.')\n parser.add_argument('refDbs', nargs='+', help='One or more reference FASTA files to deplete from input.')\n parser.add_argument('outBam', help='Output BAM file with matching reads removed.')\n parser = read_utils.parser_revert_sam_common(parser)\n cmd.common_args(parser, (('threads', None), ('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, main_deplete_minimap2_bam)\n return parser\n\n\ndef main_deplete_minimap2_bam(args):\n '''Use minimap2 to remove reads that match at least one of the specified databases.'''\n with read_utils.revert_bam_if_aligned(\n args.inBam,\n clear_tags=args.clear_tags,\n tags_to_clear=args.tags_to_clear,\n picardOptions=['MAX_DISCARD_FRACTION=0.5'],\n sanitize=not args.do_not_sanitize) as bamToDeplete:\n multi_db_deplete_bam(\n bamToDeplete,\n args.refDbs,\n deplete_minimap2_bam,\n args.outBam,\n threads=args.threads\n )\n return 0\n\n__commands__.append(('deplete_minimap2_bam', parser_deplete_minimap2_bam))\n\n\n# ========================\n# *** lastal_build_db ***\n# ========================\n\n\ndef lastal_build_db(inputFasta, outputDirectory, outputFilePrefix):\n ''' build a database for use with last based on an input fasta file '''\n if outputFilePrefix:\n outPrefix = outputFilePrefix\n else:\n baseName = os.path.basename(inputFasta)\n fileNameSansExtension = os.path.splitext(baseName)[0]\n outPrefix = fileNameSansExtension\n\n last.Lastdb().build_database(inputFasta, os.path.join(outputDirectory, outPrefix))\n\n\ndef parser_lastal_build_db(parser=argparse.ArgumentParser()):\n parser.add_argument('inputFasta', help='Location of the input FASTA file')\n parser.add_argument('outputDirectory', help='Location for the output files (default is cwd: %(default)s)')\n parser.add_argument(\n '--outputFilePrefix',\n help='Prefix for the output file name (default: inputFasta name, sans \".fasta\" extension)'\n )\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, lastal_build_db, split_args=True)\n return parser\n\n\n__commands__.append(('lastal_build_db', parser_lastal_build_db))\n\n# ================================\n# *** merge_compressed_files ***\n# ================================\n\ndef merge_compressed_files(inFiles, outFile, sep=''):\n ''' Take a collection of input text files, possibly compressed,\n and concatenate into a single output text file.\n '''\n with file.open_or_gzopen(outFile, 'wt') as outf:\n first = True\n for infname in inFiles:\n if not first:\n if sep:\n outf.write(sep)\n else:\n first = False\n with file.open_or_gzopen(infname, 'rt', newline=None) as inf:\n shutil.copyfileobj(inf, outf)\n\n# ========================\n# *** bwa_build_db ***\n# ========================\n\n\ndef bwa_build_db(inputFasta, outputDirectory, outputFilePrefix):\n \"\"\" Create a database for use with bwa from an input reference FASTA file\n \"\"\"\n\n new_fasta = None\n if not (inputFasta.endswith('.fasta') or inputFasta.endswith('.fa')):\n new_fasta = file.mkstempfname('.fasta')\n with file.open_or_gzopen(inputFasta, 'rt', newline=None) as inf, open(new_fasta, 'wt') as outf:\n shutil.copyfileobj(inf, outf)\n inputFasta = new_fasta\n\n # make the output path if it does not exist\n file.mkdir_p(outputDirectory)\n\n if outputFilePrefix:\n outPrefix = outputFilePrefix\n else:\n baseName = os.path.basename(inputFasta)\n fileNameSansExtension = os.path.splitext(baseName)[0]\n outPrefix = fileNameSansExtension\n\n core.bwa.Bwa().index(inputFasta, output=os.path.join(outputDirectory, outPrefix))\n\n if new_fasta is not None:\n os.unlink(new_fasta)\n\n\ndef parser_bwa_build_db(parser=argparse.ArgumentParser()):\n parser.add_argument('inputFasta', help='Location of the input FASTA file')\n parser.add_argument('outputDirectory', help='Location for the output files')\n parser.add_argument(\n '--outputFilePrefix',\n help='Prefix for the output file name (default: inputFasta name, sans \".fasta\" extension)'\n )\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, bwa_build_db, split_args=True)\n return parser\n\n\n__commands__.append(('bwa_build_db', parser_bwa_build_db))\n\n\n# ========================\n# *** blastn_build_db ***\n# ========================\n\n\ndef blastn_build_db(inputFasta, outputDirectory, outputFilePrefix):\n \"\"\" Create a database for use with blastn from an input reference FASTA file\n \"\"\"\n\n new_fasta = None\n if not (inputFasta.endswith('.fasta') or inputFasta.endswith('.fa')):\n new_fasta = file.mkstempfname('.fasta')\n with file.open_or_gzopen(inputFasta, 'rt', newline=None) as inf, open(new_fasta, 'wt') as outf:\n shutil.copyfileobj(inf, outf)\n inputFasta = new_fasta\n\n if outputFilePrefix:\n outPrefix = outputFilePrefix\n else:\n baseName = os.path.basename(inputFasta)\n fileNameSansExtension = os.path.splitext(baseName)[0]\n outPrefix = fileNameSansExtension\n\n blastdb_path = blast.MakeblastdbTool().build_database(inputFasta, os.path.join(outputDirectory, outPrefix))\n\n if new_fasta is not None:\n os.unlink(new_fasta)\n\n\ndef parser_blastn_build_db(parser=argparse.ArgumentParser()):\n parser.add_argument('inputFasta', help='Location of the input FASTA file')\n parser.add_argument('outputDirectory', help='Location for the output files')\n parser.add_argument(\n '--outputFilePrefix',\n help='Prefix for the output file name (default: inputFasta name, sans \".fasta\" extension)'\n )\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, blastn_build_db, split_args=True)\n return parser\n\n\n__commands__.append(('blastn_build_db', parser_blastn_build_db))\n\n# ========================\n# *** bmtagger_build_db ***\n# ========================\n\n\ndef bmtagger_build_db(inputFasta, outputDirectory, outputFilePrefix, word_size=18):\n \"\"\" Create a database for use with Bmtagger from an input FASTA file.\n \"\"\"\n\n new_fasta = None\n if not (inputFasta.endswith('.fasta') or inputFasta.endswith('.fa')):\n new_fasta = file.mkstempfname('.fasta')\n with file.open_or_gzopen(inputFasta, 'rt', newline=None) as inf, open(new_fasta, 'wt') as outf:\n shutil.copyfileobj(inf, outf)\n inputFasta = new_fasta\n\n if outputFilePrefix:\n outPrefix = outputFilePrefix\n else:\n baseName = os.path.basename(inputFasta)\n fileNameSansExtension = os.path.splitext(baseName)[0]\n outPrefix = fileNameSansExtension\n\n log.debug(\"building bmtagger and srprism databases on {}\".format(os.path.join(outputDirectory, outPrefix)))\n bmtooldb_path = bmtagger.BmtoolTool().build_database(\n inputFasta, os.path.join(outputDirectory, outPrefix + \".bitmask\"), word_size=word_size\n )\n srprismdb_path = bmtagger.SrprismTool().build_database(\n inputFasta, os.path.join(outputDirectory, outPrefix + \".srprism\")\n )\n\n if new_fasta is not None:\n os.unlink(new_fasta)\n\n\ndef parser_bmtagger_build_db(parser=argparse.ArgumentParser()):\n parser.add_argument('inputFasta', help='Location of the input FASTA file')\n parser.add_argument(\n 'outputDirectory',\n help='Location for the output files (Where *.bitmask and *.srprism files will be stored)'\n )\n parser.add_argument(\n '--outputFilePrefix',\n help='Prefix for the output file name (default: inputFasta name, sans \".fasta\" extension)'\n )\n parser.add_argument(\n '--word_size',\n type=int,\n default=18,\n help='Database word size (default: %(default)s)'\n )\n cmd.common_args(parser, (('loglevel', None), ('version', None), ('tmp_dir', None)))\n cmd.attach_main(parser, bmtagger_build_db, split_args=True)\n return parser\n\n\n__commands__.append(('bmtagger_build_db', parser_bmtagger_build_db))\n\n# ========================\n\n\ndef full_parser():\n return cmd.make_parser(__commands__, __doc__)\n\n\ndef main():\n cmd.main_argparse(__commands__, __doc__)\n\n\nif __name__ == '__main__':\n main()\n" }, { "path": "tests/__init__.py", "content": "'''utilities for tests'''\n\n__author__ = \"irwin@broadinstitute.org\"\n\n# built-ins\nimport filecmp\nimport os\nimport platform\nimport re\nimport unittest\nimport hashlib\nimport logging\nimport copy\n\n# third-party\nimport Bio.SeqIO\nimport pytest\nimport pysam\n\n# Platform detection for x86-only tools\nIS_ARM = platform.machine() in ('arm64', 'aarch64')\n\n# intra-project\nimport viral_ngs.core\nfrom viral_ngs.core.misc import available_cpu_count\nfrom viral_ngs.core.samtools import SamtoolsTool\n\nlogging.getLogger('botocore').setLevel(logging.WARNING)\nlogging.getLogger('boto3').setLevel(logging.WARNING)\n\n\nif 'PYTEST_XDIST_WORKER_COUNT' in os.environ:\n _CPUS = 1\nelse:\n _CPUS = available_cpu_count()\n\n\ndef assert_equal_contents(testCase, filename1, filename2):\n 'Assert contents of two files are equal for a unittest.TestCase'\n testCase.assertTrue(filecmp.cmp(filename1, filename2, shallow=False))\n\n\ndef assert_equal_bam_reads(testCase, bam_filename1, bam_filename2):\n ''' Assert that two bam files are equivalent\n\n This function converts each file to sam (plaintext) format,\n without header, since the header can be variable.\n\n Test data should be stored in bam format rather than sam\n to save space, and to ensure the bam->sam conversion\n is the same for both files.\n '''\n\n samtools = SamtoolsTool()\n\n sam_one = viral_ngs.core.file.mkstempfname(\".sam\")\n sam_two = viral_ngs.core.file.mkstempfname(\".sam\")\n\n # write the bam files to sam format, without header (no -h)\n samtools.view(args=[], inFile=bam_filename1, outFile=sam_one)\n samtools.view(args=[], inFile=bam_filename2, outFile=sam_two)\n\n try:\n if not filecmp.cmp(sam_one, sam_two, shallow=False):\n # Files are different - show debug output\n print(\"\\n\" + \"=\"*80)\n print(f\"DEBUG: BAM files are not equal\")\n print(f\" File 1: {bam_filename1}\")\n print(f\" File 2: {bam_filename2}\")\n print(\"\\nFirst 5 reads from each file:\")\n print(\"-\" * 80)\n print(\"File 1:\")\n with open(sam_one, 'r') as f:\n for i, line in enumerate(f):\n if i >= 5:\n break\n print(f\" {line.rstrip()}\")\n print(\"-\" * 80)\n print(\"File 2:\")\n with open(sam_two, 'r') as f:\n for i, line in enumerate(f):\n if i >= 5:\n break\n print(f\" {line.rstrip()}\")\n print(\"=\"*80 + \"\\n\")\n testCase.fail(\"BAM files are not equal (see debug output above)\")\n finally:\n for fname in [sam_one, sam_two]:\n if os.path.exists(fname):\n os.unlink(fname)\n\ndef assert_md5_equal_to_line_in_file(testCase, filename, checksum_file, msg=None):\n ''' Compare the checksum of a test file with the expected checksum\n stored in a second file\n compare md5(test_output.bam) with expected_output.bam.md5:1\n '''\n\n hash_md5 = hashlib.md5()\n with open(filename, \"rb\") as f:\n for chunk in iter(lambda: f.read(4096), b\"\"):\n hash_md5.update(chunk)\n\n expected_checksum = \"\"\n with open(checksum_file, \"rb\") as f:\n expected_checksum = str(f.readline().decode(\"utf-8\"))\n\n expected_checksum = expected_checksum.replace(\"\\r\",\"\").replace(\"\\n\",\"\")\n\n assert len(expected_checksum) > 0\n\n testCase.assertEqual(hash_md5.hexdigest(), expected_checksum, msg=msg)\n\n@pytest.mark.usefixtures('tmpdir_class')\nclass TestCaseWithTmp(unittest.TestCase):\n 'Base class for tests that use tempDir'\n\n def assertEqualContents(self, f1, f2):\n assert_equal_contents(self, f1, f2)\n\n def assertEqualFasta(self, f1, f2):\n '''Check that two fasta files have the same sequence ids and bases'''\n def seqIdPairs(f):\n return [(rec.id, rec.seq) for rec in Bio.SeqIO.parse(f, 'fasta')]\n self.assertEqual(seqIdPairs(f1), seqIdPairs(f2))\n\n def assertEqualFastaSeqs(self, f1, f2):\n '''Check that two fasta files have the same sequence bases (sequence ids may differ)'''\n def seqs(f):\n return [rec.seq for rec in Bio.SeqIO.parse(f, 'fasta')]\n self.assertEqual(seqs(f1), seqs(f2))\n\n def input(self, fname):\n '''Return the full filename for a file in the test input directory for this test class'''\n return os.path.join(viral_ngs.core.file.get_test_input_path(self), fname)\n\n def inputs(self, *fnames):\n '''Return the full filenames for files in the test input directory for this test class'''\n return [self.input(fname) for fname in fnames]\n\n def assertEqualSamHeaders(self, tested_samfile, expected_samfile, other_allowed_values=None):\n '''\n other_allowed_values is a dict that maps a key to a list of other accepted values\n '''\n other_allowed_values = other_allowed_values or {}\n\n test_sam = pysam.AlignmentFile(tested_samfile, \"rb\", check_sq=False)\n expected_sam = pysam.AlignmentFile(expected_samfile, \"rb\", check_sq=False)\n\n # check that the two sams contain the same types of header lines\n # note that pysam returns lists of dicts for\n # header lines types that appear more than once (ex. multiple 'RG' lines, etc.)\n self.assertEqual(sorted(test_sam.header.keys()),sorted(expected_sam.header.keys()))\n\n lines_tag_to_check = test_sam.header.keys()\n\n for line_tag in lines_tag_to_check:\n line_type = type(test_sam.header[line_tag])\n # for header lines that occur more than once\n if line_type == list: # if list of dicts\n # compose alterates for each line present, and check to see if exists in list of expected\n for test_dict in test_sam.header[line_tag]:\n alternate_allowed_test_dicts = []\n for key,val in test_dict.items():\n alterate_test_dict = copy.deepcopy(test_dict)\n if key in other_allowed_values.keys():\n for alternate_val in other_allowed_values[key]:\n alterate_test_dict[key] = alternate_val\n alternate_allowed_test_dicts.append(copy.deepcopy(alterate_test_dict))\n for expected_d in expected_sam.header[line_tag]:\n self.assertTrue(any(d==expected_d for d in alternate_allowed_test_dicts+[test_dict]), msg=\"{} expected but not seen in {}\".format(expected_d, alternate_allowed_test_dicts+[test_dict]))\n # for header lines that occur only once\n elif line_type in (dict,): # may need to change object type for pysam >=0.18\n test_dict = dict(test_sam.header[line_tag])\n alternate_allowed_test_dicts = []\n for key,val in test_dict.items():\n alterate_test_dict = copy.deepcopy(test_dict)\n if key in other_allowed_values.keys():\n for alternate_val in other_allowed_values[key]:\n alterate_test_dict[key] = alternate_val\n alternate_allowed_test_dicts.append(copy.deepcopy(alterate_test_dict))\n self.assertTrue(any(d==expected_sam.header[line_tag] for d in alternate_allowed_test_dicts+[test_dict]), msg=\"{} expected but not seen in {}\".format(expected_sam.header[line_tag],alternate_allowed_test_dicts+[test_dict]))\n\n\"\"\"\nWhen \"nose\" executes python scripts for automated testing, it excludes ones with\nthe executable bit set (in case they aren't import safe). To prevent any of the\ntests in this folder from being silently excluded, assure this bit is not set.\n\"\"\"\n\n\ndef assert_valid_feature_table(testCase, tbl_file, fasta_file, temp_dir):\n '''Validate a feature table file.\n\n This is a placeholder function that performs basic validation.\n Full validation with table2asn would require the tool to be installed.\n\n Note: table2asn is x86-only (no ARM64 builds in bioconda). When table2asn\n validation is implemented, it will be skipped on ARM platforms.\n '''\n # Basic check: the feature table file should exist and not be empty\n testCase.assertTrue(os.path.exists(tbl_file), f\"Feature table file does not exist: {tbl_file}\")\n testCase.assertTrue(os.path.getsize(tbl_file) > 0, f\"Feature table file is empty: {tbl_file}\")\n\n # TODO: When table2asn wrapper is implemented, add validation here\n # table2asn is x86-only, so skip validation on ARM:\n # if IS_ARM:\n # return # Skip table2asn validation on ARM\n # table2asn_tool = Table2AsnTool()\n # table2asn_tool.validate(tbl_file, fasta_file, temp_dir)\n\n\ndef assert_none_executable():\n testDir = os.path.dirname(__file__)\n assert all(not os.access(os.path.join(testDir, filename), os.X_OK) for filename in os.listdir(testDir)\n if filename.endswith('.py'))\n" }, { "path": "tests/conftest.py", "content": "import operator\nimport os\nimport shutil\nimport sys\nimport tempfile\nimport time\nimport contextlib\nimport string\nimport inspect\nimport copy\nimport functools\n\nimport viral_ngs.core\n\nimport pytest\n\nimport viral_ngs.core\n\ndef timer():\n if sys.version_info < (3, 3):\n return time.time()\n return time.perf_counter()\n\n\ndef pytest_addoption(parser):\n group = parser.getgroup(\"reporting\", description=\"terminal reporting\", after=\"general\")\n group.addoption(\n '--fixture-durations',\n action=\"store\",\n type=int,\n default=None,\n metavar=\"N\",\n help=\"show N slowest fixture durations (N=0 for all).\"\n )\n parser.addoption(\n \"--runslow\", action=\"store_true\", default=False, help=\"run slow tests\"\n )\n\n\ndef pytest_configure(config):\n reporter = FixtureReporter(config)\n config.pluginmanager.register(reporter, 'fixturereporter')\n\n config.addinivalue_line(\n \"markers\", \"slow: marks tests as slow (deselect with '-m \\\"not slow\\\"')\"\n )\n\n\ndef pytest_collection_modifyitems(config, items):\n if config.getoption(\"--runslow\"):\n # --runslow given in cli: do not skip slow tests\n return\n skip_slow = pytest.mark.skip(reason=\"need --runslow option to run\")\n for item in items:\n if \"slow\" in item.keywords:\n item.add_marker(skip_slow)\n\n\n# Fixtures for creating a temp dir at session/module/class/function scope.\n# Unlike pytest's tmpdir fixture, they use tempfile.mkdtemp to create a\n# tempdir in the most secure/race-condition-free manner possible.\n# Also, since viral_ngs.core.file.tmp_dir() is used, the tempdir contens can be\n# preserved for debugging by setting the environment variable VIRAL_NGS_TMP_DIRKEEP.\n\n\n@contextlib.contextmanager\ndef _tmpdir_aux(base_dir, scope, name):\n \"\"\"Create and return a temporary directory; remove it and its contents on context exit.\"\"\"\n with viral_ngs.core.file.tmp_dir(dir=base_dir,\n prefix='test-{}-{}-'.format(scope, name)) as tmpdir:\n yield tmpdir\n\n@pytest.fixture(scope='session')\ndef tmpdir_session(request, tmpdir_factory):\n \"\"\"Create a session-scope temporary directory.\"\"\"\n with _tmpdir_aux(str(tmpdir_factory.getbasetemp()),\n 'session', id(request.session)) as tmpdir:\n yield tmpdir\n\n@pytest.fixture(scope='module')\ndef tmpdir_module(request, tmpdir_session):\n \"\"\"Create a module-scope temporary directory.\"\"\"\n with _tmpdir_aux(tmpdir_session, 'module', request.module.__name__) as tmpdir:\n yield tmpdir\n\n@pytest.fixture(scope='class')\ndef tmpdir_class(request, tmpdir_module):\n \"\"\"Create a class-scope temporary directory.\"\"\"\n with _tmpdir_aux(tmpdir_module, 'class',\n request.cls.__name__ if request.cls else '__noclass__') as tmpdir:\n yield tmpdir\n\n@pytest.fixture(autouse=True)\ndef tmpdir_function(request, tmpdir_class, monkeypatch):\n \"\"\"Create a temporary directory and set it to be used by the tempfile module and as the TMPDIR environment variable.\"\"\"\n with _tmpdir_aux(tmpdir_class, 'node', request.node.name) as tmpdir:\n monkeypatch.setattr(tempfile, 'tempdir', tmpdir)\n monkeypatch.setenv('TMPDIR', tmpdir)\n yield tmpdir\n\n\n@pytest.fixture\ndef monkeypatch_function_result(monkeypatch):\n \"\"\"Patches result of a function for specified args\"\"\"\n\n @contextlib.contextmanager\n def _set_function_result(f, *patch_args, **patch_kwargs):\n \"\"\"Within the context, calls to function `f` with `patch_args` and `patch_kwargs` will return the\n `patch_result` (a keyword-only arg), or raise the `patch_exception` (a keyword-only arg) if that is given.\n Note that for the patched args, f will not be called, so any side effects of it won't happen.\n The function will be patched in the module `patch_module` (a keyword-only arg), or in `f` 's module\n if `patch_module` is None. The keyword-only args `patch_result`, `patch_exception` and `patch_module`\n will be removed from `patch_kwargs` before calling f. This context manager monkeypatches f for exactly\n one argument combination; multiple argument combos can be patched by nesting calls to this context manager.\n\n For a usage example, see test.unit.test_util_misc.test_available_cpu_count() .\n \"\"\"\n\n patch_kwargs = copy.copy(patch_kwargs)\n patch_result = patch_kwargs.pop('patch_result', None)\n patch_exception = patch_kwargs.pop('patch_exception', None)\n viral_ngs.core.misc.chk(patch_exception is None or patch_result is None)\n patch_module = patch_kwargs.pop('patch_module', inspect.getmodule(f))\n get_call_args = functools.partial(inspect.getcallargs, viral_ngs.core.misc.unwrap(f))\n patch_call_args = get_call_args(*patch_args, **patch_kwargs)\n\n @viral_ngs.core.misc.wraps(f)\n def patched_f(*args, **kwargs):\n if get_call_args(*args, **kwargs) != patch_call_args:\n return f(*args, **kwargs)\n\n if patch_exception:\n raise patch_exception\n\n return patch_result\n\n viral_ngs.core.misc.chk(inspect.ismodule(patch_module) and getattr(patch_module, f.__name__) == f)\n with monkeypatch.context() as m:\n m.setattr(patch_module, f.__name__, patched_f)\n yield\n\n return _set_function_result\n\n\n\nclass FixtureReporter:\n\n def __init__(self, config):\n import _pytest.config\n self.config = config\n self.stats = {}\n self.writer = _pytest.config.create_terminal_writer(config)\n self.durations = config.option.fixture_durations\n\n @pytest.hookimpl(hookwrapper=True)\n def pytest_fixture_setup(self, fixturedef, request):\n funcname = request._pyfuncitem.name\n fixname = fixturedef.argname\n\n fixturedef._timer_start = timer()\n yield\n duration = timer() - fixturedef._timer_start\n fixturedef._timer_duration = duration\n\n self.stats[(fixname, funcname)] = duration\n\n def pytest_terminal_summary(self, terminalreporter, exitstatus):\n if self.durations is None:\n return\n\n writer = terminalreporter\n\n slowest = sorted(self.stats.items(), key=operator.itemgetter(1), reverse=True)\n if not self.durations:\n writer.write_sep(\"=\", \"slowest fixture durations\")\n else:\n writer.write_sep(\"=\", \"slowest %s fixture durations\" % self.durations)\n slowest = slowest[:self.durations]\n\n\n rows = []\n for (fixname, funcname), duration in slowest:\n row = ['{:.2f}s'.format(duration), fixname, funcname]\n rows.append(row)\n\n widths = [max(map(len, col)) for col in zip(*rows)]\n for row in rows:\n writer.write(\" \".join((val.ljust(width) for val, width in zip(row, widths))))\n writer.line()\n" }, { "path": "tests/input/5kb_human_from_chr6.fasta", "content": ">human_5000bp random human subsequence\nGAAGTTTGGATTATGATATGCTCATTAATTATAAAACAGACTTCAGTAGTCAGAGAATAG\nTACACATAGGCCATTGAGCAAGTAGGAAATTAAAACAAAATGAAAAAATAAACACTTTCT\nGCTTTTTTTTTCTTCTTATGTATTGTGAAGAAAATCCAGGGATGGAGTGAATTATCAGTT\nTAGTTCCCACCTTTGTATATCTGATCTGTCACACACAAATCCACATATACACTTATATGT\nGAATATATGGCATTAAATGCTCACAAGCAGTCTATGCATATATTATTTGAAAAGATAATC\nATTTTTCAATAGTTTGAGAATATATTCCCTGTTAAACTGAATTTACTAACTAAATATTTA\nCTAAATATACTCTTAACCAGGGTGATTTATGAGATCATAGGAATAACAAAGAATAAAAAT\nACCTTCTGCAAAGGAAGCTTTAAATTTTAATTTGATTTGTTTGAAAATTCACATGAAGTC\nTTTGTAATCAATACATTCAGATCAGTATTCTACGAATCTTTCTGCATGTCAGAAATTAAA\nATTTTATTTAGGATTGAAGAGTAAATCATTTGCCAAGTAGGTTTCTAAAAGTGAAAACAA\nATGTCAGTTTCAAAAAAGAACAATTTAGTTTTACATTTCTGAGGAAGTCACATATATTAT\nGTATTAATAAATTAACAGTCTCACATTCTCTTTGATCATTGATTGTTTCTTGGCAGTTTG\nTTACATACTAGATTCTACACATCTCACAGCTATAAATTCAGTACCAGAATTTAGGGAGAT\nAATTTTAATGTAAAACAAAGATTGTTGTAAGAGacaacatgtcatagtgtttaagggtca\ngactccctgggttccagtcccaatttccagctctgtggcattgacacttttacacacttc\ntctaaacatcagggttttgttttgtttcgtttttttgttgtttctgttttctgtgaagtg\ngtgatgattttagtgaaataattggaagactgaatgaggtaatgcatgtaaaatacttag\ncataatgtttggactgtgtagtaaaggctcaataaatgttaaattccattaATTGGGTAA\nTCCTGGAACTCTTCACTGCAATTAGAATTCTTTATTACAACAAATAAAATTTTGATTCAT\nCATAAAAAGTAATCAATTTCTTTAATGGACCTCAGAGAAATTAAAATGCCTCCTGGACTG\nTTAAGTCCTCAGAAATGTATTGCATCTTTAATTCTTTATTTCCTCTGAATACTCATGCAC\nATGAGAAAAAATTTCTAAGTTAAGACATGTCTATTCTCCTTTAGTCCTCATTTCAAATAT\nCAACCACTGTTTACAGTATCACCACTTTTTCCTTTTAAAATGGACTAATCAGTTTTATTT\nAGAGATTGTTTGACAAAGGGTGATTGCCCCAAATGATGGTTTCCTGAAGACCAGGATATA\nCCAACCAAGAAAAGGCAAGTATATTTTGTCCACCTAAGTAACTTCTTCTTCTGTGTATTT\nTTCTGCAAATATGGATGTTCCTTTGGACTAGTCCTTTCTCAATCATATTGAAGTTTAAAT\nATATTTACTTTAATTGGTAAAATCAACTTAAAAATCTCTATTCTGATTTTTTCCTAAGGA\nTTGGTATGCATGTTAAAAGTAACCAAAGTATAATTTATGTCTTGGCCTGTATTGAATGCC\nTTTTTCCTCCTGAGCAGAGTCAATTGAAAAATATCTTGCTTGCTGCCTCCATTTTTAACA\nTTTATTCTTAGGCTTAATGTAGGAAACTAGCAATAAAATATAAATCCATATTCTATTTTT\nTAAAAGATCATACTGTTTTATTTTCAATTTTATGAAACTTTTACTTTTAGATATTACAAA\nCAAGAGAATTAGAAATGTGACGTTAGACTTTTAACTCTCTGTAGTCCTTTGTATTTAGGA\nGAGAATTTGGATTAGAAAACCACCTTCTGGAGGAGATTTTGACATTActgtgtgagcaaa\nttcaggcaagtcacataatctcttagagagaacttcagtttgctcagttataaagatcaa\naataatcatctgtaacacactggattatatggaaagtgtaatatacacgaaatctattta\ngaaaagtgaaaaccagcatgcaaaaatgttgttgtaattattattattGCCAACATAAAC\nTTGTAAATTTGTTCACATTTATTAGTTTAGTTCATTGGCCTGTATGTATGTGAAATAATG\nGTCCAGTCCTTTGATGATAAATATCACAAATTGTTGGATAGATTTGCTGGGTTTGACATT\nTTAAATTAAGACTCTGATATTCTGTTAGGAAAACATTTATTTCTTTGGTTTTTCTTTTTA\nCTTTCTATATCACTGGAAGCAATGAGTTTCggcttcatattcacatatttcagagttcca\nctcccaaccctgctttccactagtatgacctttggcagtttgcttcacagtttggttcat\nagaaaatatgaactttattttctgcatctgcaaaatagaaatcataTCTATTCTTTCTTA\nATATAGTCTGTACCAAAAGCAATATTAAGATTAATGCACAAATAATGCAGAAGTGGGAAG\nTTCTCTTAATTCAGGTTTTTTAAGTAATCTAAAACGTTGTTTTAGGCTGCCCATAGAAAA\nTGAAGTATAATGACTTCGATTTTATTCAATTCCAGTTTTACTCATCTGTAGATGAAGATC\nAGAAATATAATGAGTTGCTTTATAATAGGCTTCCACTCTTACATCAATCAGACAAGCAGC\nCTAAAAATAAACACATCCTTTCTGTCCTTGTGTTTCCTGGGAAAGTCAAGAGTTAGCATT\nAAAGGAAAATGAGTACAAATGAAGATTTATCAAAAAATTTCCCCAAGTGCTAAAAACAAA\nAATGGTCTGGGAGATATTGTAGTTTTACAGAACTATTTGTTTTCTGTAGGGGGCAAAGGC\nTATATATAAATAAGCCTAGGTCTCAGTGCCATGTCATGTAACTAAGAATTAAATGTATTA\nGTCTTTAAAGAATGCAAATGAGGTAAATTTTACATCAGTAAAAATTTTTAAACAGACGAA\nAATATGGAAACGTGTTAACAGAGCTTCAAAATTTTATGCTATGTTTTTGAATCAGTCTTG\nAAAATACTACAGATTGGTGTCTGTCCTCCTCTGCAGGTGATAGGTGGGACTATTTCAGAG\nGACAAATGTGATCAAGCAGCTGGCCATGGTTTTGTTCTGATGGGATTACTCAGCAAATTT\nAGTAGATAAACTAAACATTTTCCTATTACTTTCTACTTAAAATACTTACTCAACTTGTAA\nAGGGTTTTATCAAACCTTAGACTTTGTAAACACTTTTAAAAACACTCAGTTTTGTGCCTT\nTGAACAAGTGTAGCAAAATTAATAGGTGAATCTATATGCAAATTTGTATAGATCTTTGCT\nTAATTCAGGTAATATCAGCCTAATATATCTATTTTGATTAATTATGTATTTGATTAATTA\nAACACAACTGGCATTGCACAACTTAACCCCAAATGTATAAACTTTTCTGTTAACCTGGCA\nTCTATGGGAAATGGCTATTTTAGTAATCCGTTAATGGAAATTTACCATCTGTAGTAGATA\nTTTTGAGAATTCAAATGGAACAAACAACAGACTACTAAGCCCATACTTTGTATTTATTTA\nTTTGTGTATTTCataatcacaatactaatgaattattcctgtgtgtcagataaaatttta\naatattaactctttcattcttcctaagagccccatgagatagctgttattattacttttg\nttttctggatgaaaagactgagacacagaaaagttaagtgacttgcatagtatcacattg\nagaagaggcagagctgaattcaagttcattctctgagcccttacactataccaccactct\ngTAAAGATACATATAACACAATATTAGTTAAAAACTCAAAAAGAACTTAGCTTATCCCAT\nGTTTTGTAACTATAGGACGTTTCAAATAGAAAAATATATGTATTTTAAATCCTGCAAAGT\nACATCTCCAGATATGCTTAGTGGCCTCTGTCTGGTAATGTTTCTTCCACCTAGTGTTTTC\nCAAGCTATAGCCTGCATGTATCCTCACTAATAAAAGGACTTTCTTCTTTAACCAAGCCTA\nTTGCTCAAAGAATTCTGCAATCTCATCTCTCCCAGGAAACCTCCAAGTGATAAAAAATGG\nAGTATTGATTTCGACCTGCTATGAGACATGCAAAGTTTACTTTTTACTCACTAATACAAA\nGTTTTTTGGATTGCTACATTTTAAATTAGTATACATATTTATTTAGATATAAGTTTAGTC\nTATGTTTAACATTTTGTTTTAGAAAAATTTAAATGTCTTAGGTTACAGGGGCATAGATGT\nTAAAGGCTTTGCTGTTTAATTACCTTGAACTTTACTTAGCACCATATTAACACAACGAGC\nTGCTTAATCTTTTCTGTAATTATGATTATAGAAGATCAAAATAAAACTAGAATTACAATT\nATCTTTTAATGATTTTAAGTTGGTAAGATGTCATTTCTACTAGACAAAAATAATTTATAG\nTTAGATTAAGCATCTCTAGTACCAGAAGATACAGGATACCTGTAAAAGAAAGAGAGGTGA\nAAAGTTCATTCCCTGGCTTAGAGaatattttatttaatttttgtctttaaaataattttC\nATAAGTTCTTTTGTAACTCTCAACTTTTATTTACCTGAGAACCAAAAATAAATATCCTAT\nTAGAAAAAAATAAATCCTGATCCATTCTAACTAAAATAATTTTTTTGTGCTATTTTCTTA\nATTGTGGTAACACTCAATTACTGAAAATCAAGCTGATGCAATTTTTTTTAAATGATAAGT\nGATTCAATGTTTTGGGGATGTGACAGTTTCCTCAGAGGAACTAATCAAAACAAAATTATT\nTTTCTTGATAAAAAACAGCTACTTCATTTTTTCTAAAAAAAAAAGACAATTCAGAGAACT\nTATGTAGGTCATTGTCAGTA\n" }, { "path": "tests/input/G5012.3.fasta", "content": ">G5012.3\nATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCATAC\nCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGGGGC\nAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCAC\nAAATTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAACATTATTGTTAA\nAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACTTTGATTTTGAACC\nTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAACATTAGAAAT\nAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAA\nAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\nAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAA\nCAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCA\nAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATTA\nCAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGA\nAGTCAAGAAGTGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGG\nGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGC\nCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGC\nTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATA\nTCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAA\nTTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGCCGGACATGATGC\nCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGT\nCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCT\nTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCT\nGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAA\nTCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGCCCA\nCGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCAGC\nCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACTTGACCATCTTGG\nACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAG\nCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGA\nAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACAT\nTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGAC\nTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGATGATGGAGGCTACGG\nCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGA\nTCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGACCAAGGGTGGACA\nACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCACGCCAAC\nTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACTCACGGACAA\nTGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAACGA\nAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTAGAGTC\nAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCCACC\nGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACAAGA\nTCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCAGCCAGAACATTC\nTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCCGTTTTGTA\nTTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAAAGAGTACAC\nGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAA\nTGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAATCA\nCAGGAATAAATTCATGGCAATCCTGCAACACCATCAGTGAATGAGCATGTAATAATGGGA\nTGATTTAATCGACAAACAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTT\nTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTTTTGAATTTAAAG\nCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAAGCG\nTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCGATTTATCTAAAT\nTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTT\nTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTG\nAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGA\nTGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGC\nCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTGTAA\nACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAAC\nAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATC\nATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAA\nCCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAG\nTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAA\nAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGG\nCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGA\nTTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCA\nACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGG\nCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACC\nAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATG\nCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTA\nCAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAG\nGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGATTG\nATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTT\nGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAACTGCTGAAC\nTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCA\nATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGTAAT\nAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAAT\nGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCT\nTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTC\nCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTGGCA\nACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCATCGAATCCAC\nTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCAT\nCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGC\nAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAA\nCTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATC\nCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGC\nGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCCAGT\nATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTGCTGCAACAT\nGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATC\nCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATC\nTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTC\nCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGC\nTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAA\nAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATT\nGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAATTGCAATAAT\nTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAAT\nCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTG\nTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAA\nAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCAATA\nCGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCAAATTG\nCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAAAAA\nTCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTCTAATTAAGA\nAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTAT\nTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCA\nCTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTC\nGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACAT\nTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACAAAC\nTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCG\nAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCG\nGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATC\nTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGG\nGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACT\nTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCT\nACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGA\nAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGA\nGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAG\nAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCAC\nAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGG\nGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCT\nGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGT\nATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGA\nGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGT\nTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAAT\nCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCGTAATAC\nACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGC\nAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAA\nAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAG\nCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGA\nAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGG\nACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATG\nCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTG\nGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCA\nAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACT\nGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGA\nCTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGA\nACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGT\nTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATG\nGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTGTAT\nATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCAAAT\nCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAATGAT\nAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACA\nGTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACTTGA\nTGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTACAA\nTCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTGTAATAATCA\nGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAAAAG\nTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAGAGA\nGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCA\nCGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAA\nGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCA\nCCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAA\nAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAG\nACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCA\nAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCCAAAATTACCTTGTTGACACTG\nATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAATTA\nAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGT\nCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAGGCAGAACCCGTT\nCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGG\nCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTC\nCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAA\nTCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACC\nCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATA\nCCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCA\nCTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAAGAGGTATGATAT\nAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCAATATAACCTGCCAA\nGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTACAGGAGGTA\nGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAAAAT\nATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTATG\nGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTC\nAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGA\nTGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGC\nGAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCTGTATACCAGTTGCC\nCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATCTCATACATT\nGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAATCTG\nGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATTA\nCTTTGAGCACCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAGGTT\nACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAG\nACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAG\nGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACTATT\nCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCC\nCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAACCTA\nTTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTGAGA\nGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTA\nGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAAC\nATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCC\nAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAATGGATTA\nTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATG\nGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGG\nCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCG\nACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGG\nAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGC\nCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTT\nAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAG\nGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATAT\nTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACCCG\nCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAACTA\nACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGG\nGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACA\nCAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGAC\nCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATCCGCAACTACGCAAC\nTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACCAAGTTCTTA\nAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCA\nCTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATT\nATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCT\nCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAAT\nGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGTAGA\nTTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATTTAATAGACATCTTA\nGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTGAACACACAA\nGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAA\nGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGATTTA\nATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCAGTT\nTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTA\nCTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAACCATTGTGCTTG\nGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATG\nCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTAAAGCCTTCA\nCAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAA\nCAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGTGAA\nACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATCGTG\nATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAA\nGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTTAATTCTTATATC\nAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTATGGGAATTTTACCAC\nCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAA\nGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTG\nGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAGCAA\nGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCA\nCAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTC\nGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGAT\nGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAACAAAAAGAA\nAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAGCATGCCACA\nGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTATGAG\nTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAAT\nTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCG\nCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGT\nCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAA\nATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGACAAT\nCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAGCAGGAACAG\nAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGT\nGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAA\nAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCA\nCCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCT\nTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATAACCGCAGCTTTC\nCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTTAATAAAGGTTTT\nGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCATTGGCACTA\nGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGG\nAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATT\nGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATT\nGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTT\nCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACC\nTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGTGGCTCTTATCATCA\nACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGCGGGAAGCGA\nTTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAAC\nAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGGAGT\nCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATA\nACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAG\nGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTTTGG\nCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACCTGGTGGGAAACCA\nTTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCATCCCGAATA\nAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGG\nCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCG\nTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTT\nTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTAC\nTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAAT\nCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCA\nGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCA\nGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAATCGT\nGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTACTTAACATAC\nACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGACAAT\nAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGC\nAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTATCTGGATGGGAG\nCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCGTCTACAGACCCA\nATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAAATAGGA\nCTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACT\nAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCA\nCATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGATTA\nATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTC\nTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAG\nGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCATTAGAGGGT\nCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTGGTGCATGAT\nTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGACAAT\nCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGG\nAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGATCA\nAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCA\nCATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACGACA\nATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCTGCT\nTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTGAAATCTCAG\nGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTCCTA\nCCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACC\nCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTAT\nTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAA\nATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCCTTACTA\nTTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGCTACTGAGTCCAGT\nATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCA\nAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGAC\nATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTT\nATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTA\nCATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTC\nTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTTTTTGCC\nACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTATCTTTGT\nCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAG\nCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCAT\nTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCATCA\nTTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTAGTC\nTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTAT\nAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGA\nATCACAAAACTAGTCAATGATTACTTAAAATTCTTTCTTATTGTACAAGCATTAAAACAT\nAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGG\nTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTA\nCATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTA\nTTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTTGTA\nAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATCT\nTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTATACACTA\nTATTTGGCCTCTCTCCCTGCGTGATAATCAAAAATTCACAATACAGCATGTGTGACATAT\nTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATAATTAAGCTTT\nAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTTGCCA\nGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAAGATT\nAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTTAAAAATGGTGATAGCCTTAA\nTCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTAC\nTATTCCATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAATCAGAAATACCT\nTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGCATTGAC\nCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCCTGGAAAAATGGT\nCGCACACAAAAATTTAAAAATAAATCTATTTC\n" }, { "path": "tests/input/README.md", "content": "Description of input files:\n\n- ebola.fasta is a collection of Ebolavirus genomes from many Ebolavirus \nspecies (EBOV, SUDV, etc)\n\n- ebov-makona.fasta is our typical EBOV 2014 reference genome (the \nearliest Baize et al sequence from Guinea)\n\n- G5012.3.testreads.bam is a stripped down set of reads for one \nparticular Sierra Leone patient. These reads are unaligned. This only \ncontains 9179 read pairs that map to EBOV, none of which are PCR \nduplicates according to Picard after alignment. An additional 200 read \npairs that fail to map to EBOV are included here as well. This contains \nreads from 12 read groups: six from one library prep and six from \nanother independent prep. There are no non-EBOV reads here.\n\n- G5012.3.subset.bam is just 200 random reads from \nG5012.3.testreads.bam, only four read groups, one library. Just to\nspeed up unit tests that don't care about having a lot of reads.\nThis should be updated sometime to be an interesting set of 200\nreads (perhaps all aligning to an interesting iSNV) so as to make\nit more useful for certain kinds of unit tests.\n\n- G5012.3.fasta is the consensus assembly that is created from\nG5012.3.testreads.bam.\n" }, { "path": "tests/input/TestAssembleSpades/clipDb.fasta", "content": ">NuGEN\nTCTATAGTTTAGGTAACTTTGTGTTTGA\n>TruSeq3_IndexedAdapter\nAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n>TruSeq3_UniversalAdapter\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA\n>PrefixPE/1\nTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PrefixPE/2\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n>PE1_rc\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA\n>PrefixNX/1\nAGATGTGTATAAGAGACAG\n>PrefixNX/2\nAGATGTGTATAAGAGACAG\n>Trans1\nTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG\n>Trans1_rc\nCTGTCTCTTATACACATCTGACGCTGCCGACGA\n>Trans2\nGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG\n>Trans2_rc\nCTGTCTCTTATACACATCTCCGAGCCCACGAGAC\n>TruSeq2_SE\nAGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG\n>TruSeq2_PE_f\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\n>TruSeq2_PE_r\nAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG\n>PCR_Primer1_rc\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT\n>PCR_Primer2\nCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n>PCR_Primer2_rc\nAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG\n>FlowCell1\nTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC\n>FlowCell2\nTTTTTTTTTTCAAGCAGAAGACGGCATACGA\n>TruSeq Universal Adapter\t\t\t\t\t\t\nAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>TruSeq Adapter, Index 1\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 2\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 3\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 4\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 5\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 6\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 7\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 8\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 9\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 10\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 11\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 12\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG\n>Illumina Single End Adapter 1\nACACTCTTTCCCTACACGACGCTGTTCCATCT\n>Illumina Single End Adapter 2\nCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n>Illumina Paired End Adapter 2\nCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n>Illumina Paried End Sequencing Primer 1\nACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>Illumina Paired End Sequencing Primer 2\nCGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT\n>Illumina Multiplexing Adapter 1\nGATCGGAAGAGCACACGTCT\n>Illumina Multiplexing Index Sequencing Primer\nGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n>Illumina Multiplexing Read2 Sequencing Primer\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n>Illumina PCR Primer Index 1\nCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC\n>Illumina PCR Primer Index 2\nCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC\n>Illumina PCR Primer Index 3\nCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC\n>Illumina PCR Primer Index 4\nCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC\n>Illumina PCR Primer Index 5\nCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC\n>Illumina PCR Primer Index 6\nCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC\n>Illumina PCR Primer Index 7\nCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC\n>Illumina PCR Primer Index 8\nCAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC\n>Illumina PCR Primer Index 9\nCAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC\n>Illumina PCR Primer Index 10\nCAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC\n>Illumina PCR Primer Index 11\nCAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC\n>Illumina PCR Primer Index 12\nCAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC\n>RNA PCR Primer, Index 1\nCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 2\nCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 3\nCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 4\nCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 5\nCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 6\nCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 7\nCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 8\nCAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 9\nCAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 10\nCAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 11\nCAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 12\nCAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 13\nCAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 14\nCAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 15\nCAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 16\nCAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 17\nCAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 18\nCAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 19\nCAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 20\nCAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 21\nCAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 22\nCAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 23\nCAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 24\nCAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 25\nCAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 26\nCAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 27\nCAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 28\nCAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 29\nCAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 30\nCAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 31\nCAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 32\nCAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 33\nCAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 34\nCAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 35\nCAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 36\nCAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 37\nCAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 38\nCAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 39\nCAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 40\nCAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 41\nCAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 42\nCAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 43\nCAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 44\nCAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 45\nCAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 46\nCAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 47\nCAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 48\nCAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>Custom add, Illumina Paired End Adapter 2\nGATCGGAAGAGCGGTTCAGCAGGAATGC\n>Nextera S501\nAATGATACGGCGACCACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTC\n>Nextera S502\nAATGATACGGCGACCACCGAGATCTACACCTCTCTATTCGTCGGCAGCGTC\n>Nextera S503\nAATGATACGGCGACCACCGAGATCTACACTATCCTCTTCGTCGGCAGCGTC\n>Nextera S504\nAATGATACGGCGACCACCGAGATCTACACAGAGTAGATCGTCGGCAGCGTC\n>Nextera S505\nAATGATACGGCGACCACCGAGATCTACACGTAAGGAGTCGTCGGCAGCGTC\n>Nextera S506\nAATGATACGGCGACCACCGAGATCTACACACTGCATATCGTCGGCAGCGTC\n>Nextera S507\nAATGATACGGCGACCACCGAGATCTACACAAGGAGTATCGTCGGCAGCGTC\n>Nextera S508\nAATGATACGGCGACCACCGAGATCTACACCTAAGCCTTCGTCGGCAGCGTC\n>Nextera N711fw\nCAAGCAGAAGACGGCATACGAGATAAGAGGCAGTCTCGTGGGCTCGG\n>Nextera N703fw\nCAAGCAGAAGACGGCATACGAGATAGGCAGAAGTCTCGTGGGCTCGG\n>Nextera N708fw\nCAAGCAGAAGACGGCATACGAGATCAGAGAGGGTCTCGTGGGCTCGG\n>Nextera N710fw\nCAAGCAGAAGACGGCATACGAGATCGAGGCTGGTCTCGTGGGCTCGG\n>Nextera N702fw\nCAAGCAGAAGACGGCATACGAGATCGTACTAGGTCTCGTGGGCTCGG\n>Nextera N707fw\nCAAGCAGAAGACGGCATACGAGATCTCTCTACGTCTCGTGGGCTCGG\n>Nextera N709fw\nCAAGCAGAAGACGGCATACGAGATGCTACGCTGTCTCGTGGGCTCGG\n>Nextera N705fw\nCAAGCAGAAGACGGCATACGAGATGGACTCCTGTCTCGTGGGCTCGG\n>Nextera N712fw\nCAAGCAGAAGACGGCATACGAGATGTAGAGGAGTCTCGTGGGCTCGG\n>Nextera N701fw\nCAAGCAGAAGACGGCATACGAGATTAAGGCGAGTCTCGTGGGCTCGG\n>Nextera N706fw\nCAAGCAGAAGACGGCATACGAGATTAGGCATGGTCTCGTGGGCTCGG\n>Nextera N704fw\nCAAGCAGAAGACGGCATACGAGATTCCTGAGCGTCTCGTGGGCTCGG\n>Nextera N701\nCAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGG\n>Nextera N702\nCAAGCAGAAGACGGCATACGAGATCTAGTACGGTCTCGTGGGCTCGG\n>Nextera N703\nCAAGCAGAAGACGGCATACGAGATTTCTGCCTGTCTCGTGGGCTCGG\n>Nextera N704\nCAAGCAGAAGACGGCATACGAGATGCTCAGGAGTCTCGTGGGCTCGG\n>Nextera N705\nCAAGCAGAAGACGGCATACGAGATAGGAGTCCGTCTCGTGGGCTCGG\n>Nextera N706\nCAAGCAGAAGACGGCATACGAGATCATGCCTAGTCTCGTGGGCTCGG\n>Nextera N707\nCAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGG\n>Nextera N708\nCAAGCAGAAGACGGCATACGAGATCCTCTCTGGTCTCGTGGGCTCGG\n>Nextera N709\nCAAGCAGAAGACGGCATACGAGATAGCGTAGCGTCTCGTGGGCTCGG\n>Nextera N710\nCAAGCAGAAGACGGCATACGAGATCAGCCTCGGTCTCGTGGGCTCGG\n>Nextera N711\nCAAGCAGAAGACGGCATACGAGATTGCCTCTTGTCTCGTGGGCTCGG\n>Nextera N712\nCAAGCAGAAGACGGCATACGAGATTCCTCTACGTCTCGTGGGCTCGG\n>Broad Barcode tagged_57\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTAGAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_100\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACACGATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_473\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCGCGGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_373\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGATCGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_498\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTTACCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_861\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCTTGGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_23\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACGCATTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_109\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGGTATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_218\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTAAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_3\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACAATGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_163\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGTATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_220\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTCGCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_375\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGCTTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_726\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTCCAGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_880\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTGGCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_214\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGATCTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_754\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTGATGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_223\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTTATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_309\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTCTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_379\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAACATTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_500\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTAACTCGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_291\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_504\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTACCAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_534\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGCGGATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_630\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACATCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_741\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTATAACAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_367\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATAGCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_579\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACAGTAAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_938\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTACGCACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_745\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCATCTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_542\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGTAATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_655\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCGTCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_732\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAACATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_567\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAAGGAAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_584\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCTAACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_117\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACCAACTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_908\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCTCGACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_954\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCGCTGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_357\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGAGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_426\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTATGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_959\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGAATAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_438\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTTCGCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_778\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAAGCACAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_821\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATCTGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_924\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGTAATCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_868\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGCTAGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_899\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCAAGTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_934\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAATCAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_190\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCAATTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_34\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTTGACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_927\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGTCGGATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_866\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGCCTTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_38\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGACACTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_875\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGGTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_78\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATGTTCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_151\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTAAGACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_288\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTATCAAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_110\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTTGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_195\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCATGGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_222\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTGCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_236\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTGCTTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_332\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACATCCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_289\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTATGTTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_250\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGCGTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_352\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGCAAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_298\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTGTCTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_355\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGCGGTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_469\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCCTTCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_509\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTATGCGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_320\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAATAGTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_474\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCTATGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_544\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGTGGCGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_393\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAGTTAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_869\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGGAATGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_422\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTACCATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_564\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAAGAAGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_851\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCAGCAAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_559\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAACCTAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_581\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCAGGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_657\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCTAGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_747\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCACAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_583\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCGTTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_616\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATATCCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_652\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCGCAACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_960\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGAGCCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_52\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGATGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_800\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACTTAGCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_293\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCTAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_388\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAGAGCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_786\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGAACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_818\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATCCAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_910\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCTGCTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_968\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGTCTATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_878\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTGCAAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_923\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGTAACTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_944\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTATATCTATCTCGTATGCCGTCTTCTGCTTG" }, { "path": "tests/input/TestAssembleSpades/trinity_contigs.fasta", "content": ">comp0_c0_seq1 len=381 path=[0:0-380]\nTGAGACTCGGCGTCATCCAGACTTTCTGAGGACGAGAATCCATACTCGGAATTTTGTGAT\nTCCGAGCAATTTGTCTTTAAACTATTTCTAATGTTTTACCCCAGGCTTTAGGGTTGTTGA\nGTCTCCAGTCCTCTGGGTGTTCAGGTTCAAAATCAAAGTTAATTCTCAATCTTGCTTGTT\nTGACTGTGAACTAATGCTGTCCTTTAACAATAATGTTGCTATTAAGGTTGTTGGATCACC\nCTGCAGAGTTTAAGGCGGAATTTGTGATGTGATAAGGCCTAGATGTTGACAAGGGATTTT\nCAACTGAGCACACTGATGCCCTTGCCCCCTCCGGAGACCTAGGTTGTTCTCTATCTTGGT\nGATATGGCTCTGAAACAAACC\n>comp3_c0_seq1 len=348 path=[0:0-347]\nTTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTG\nAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCG\nTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAGCAGGAACAGAGCGCCGAGGACA\nATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAA\nAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGA\nATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCAC\n>comp4_c0_seq1 len=328 path=[0:0-327]\nTTTAATTTTATCATTCTGAATGGAATAGTAGCTTACTAGACAAAAATGTTAAAGTTATTA\nCACCTAATCTCTTATTTTACACAAAGATTAAGGCTATCACCATTTTTAAAATCGACAAAT\nTAAAGCAATGACAATTATAAAAAACTTAATCTTAAAGATCAGTTTTGTTTTAAGAAGTCG\nTGTTATCAACCAAAGCACTATTCCATCTGGCAAGATATTGATACAACATTACTATATCAC\nTAACAATATGAGCCCAGACCTATCGTTAAAGCTTAATTATAAAGAGTGCGGAGTTTATTA\nTGTTGCGTTAGACTCATTGCAGCAGTAA\n>comp2_c0_seq1 len=376 path=[0:0-375]\nAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATG\nACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATC\nGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGA\nCAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGA\nGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCA\nGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCA\nGGGATAGTGATAACAC\n" }, { "path": "tests/input/TestBmtagger/expected.Match.1.fastq", "content": "@from_chr1_1/1\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n@from_chr9_1\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n" }, { "path": "tests/input/TestBmtagger/expected.Match.2.fastq", "content": "@from_chr1_1/2\nAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\n+\nABABABABABABABABABABABABABABABABABABABABABABABABAB\n@from_chr9_1\nGGGGTGGATCGAGGTGGGTGGTGGCATCTGGGATCTCTGCTTGGCTTCCC\n+\nCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCD\n@from_chr1_2\nAATTCTAAGAAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTT\n+\nDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDE\n" }, { "path": "tests/input/TestBmtagger/expected.NoMatch.1.fastq", "content": "@from_ebov_1/1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n+\nEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n" }, { "path": "tests/input/TestBmtagger/expected.NoMatch.2.fastq", "content": "@from_ebov_1/2\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n@from_ebov_2\nGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\n+\nEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEF\n" }, { "path": "tests/input/TestBmtagger/humanChr1Subset.fa", "content": ">chr1\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTTCAGTGATGAATCTGGAGTGGTTCTTTTTTTATTTAATGTGGTTATTTTTTGAAGAGACTTTCAATTCCATGTCTCCTGTCAATTCTAAGAAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\n" }, { "path": "tests/input/TestBmtagger/humanChr9Subset.fa", "content": ">chr9\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGTGAAGACGGAGACTCTCTTTGGGCAAAGCGGGGCTTTCAGCACGTTCGGTGGTACAGCTCTGACCCTGGCCAATCATGGCACTGACCTATGCCACCATATGGGGGTGGATCGAGGTGGGTGGTGGCATCTGGGATCTCTGCTTGGCTTCCC\n" }, { "path": "tests/input/TestBmtagger/in1.fastq", "content": "@from_chr1_1/1\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n@from_ebov_1/1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_chr9_1\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n@from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n+\nEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n" }, { "path": "tests/input/TestBmtagger/in2.fastq", "content": "@from_chr1_1/2\nAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\n+\nABABABABABABABABABABABABABABABABABABABABABABABABAB\n@from_ebov_1/2\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n@from_chr9_1\nGGGGTGGATCGAGGTGGGTGGTGGCATCTGGGATCTCTGCTTGGCTTCCC\n+\nCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCD\n@from_chr1_2\nAATTCTAAGAAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTT\n+\nDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDE\n@from_ebov_2\nGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\n+\nEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEF\n" }, { "path": "tests/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.idx.md5", "content": "2e9748024dabadd49dc0862aae5f7180\n" }, { "path": "tests/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.imp", "content": "20\nBundibugyo_ebolavirus_complete_genome\nBundibugyo_ebolavirus_isolate_EboBund-14_2012_complete_genome\nCote_dIvoire_ebolavirus_complete_genome\nReston_ebolavirus_isolate_RESTV/M.fascicularis-tc/PHL-USA/1996/Ferlite_Philippines/Alice_TX_complete_genome\nReston_ebolavirus_isolate_RESTV/Sus-wt/PHL/2009/09A_Farm_A_complete_genome\nReston_ebolavirus_-_Reston_strain_Reston08-C_complete_genome\nReston_ebolavirus_-_Reston_strain_Reston08-E_complete_genome\nReston_Ebola_virus_strain_Pennsylvania_complete_genome\nSudan_ebolavirus_isolate_EboSud-609_2012_complete_genome\nSudan_ebolavirus_isolate_EboSud-639_complete_genome\nSudan_ebolavirus_isolate_EBOV-S-2004_from_Sudan_complete_genome\nSudan_ebolavirus_-_Nakisamata_complete_genome\nSudan_ebolavirus_strain_Gulu_complete_genome\nZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/COD/1977/Bonduni_complete_genome\nZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/COD/2007/43_Luebo_complete_genome\nZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/1Eko_complete_genome\nZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/2Nza_complete_genome\nZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/Ilembe_complete_genome\nZaire_ebolavirus_isolate_H.sapiens-wt/GIN/2014/Gueckedou-C05_complete_genome\nZaire_ebolavirus_strain_Zaire_1995_complete_genome\n" }, { "path": "tests/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.map.md5", "content": "7ecc55c01c27f9569f3926587d5b1743\n" }, { "path": "tests/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.rmp", "content": "" }, { "path": "tests/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.ss.md5", "content": "143908e3c1d360f5c3f1dae078a8f811\n" }, { "path": "tests/input/TestBmtaggerDbBuild/expected/TestBmtaggerDbBuild.srprism.ssa", "content": "R" }, { "path": "tests/input/TestDepleteBlastnBam/expected.sam", "content": "@HD\tVN:1.4\tSO:queryname\n@RG\tID:A\tPL:9.75\tLB:Alexandria\tSM:FreeSample\tCN:KareemAbdul-Jabbar\nfrom_ebov_1\t77\t*\t0\t0\t*\t*\t0\t0\tGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\t##################################################\tRG:Z:A\nfrom_ebov_1\t141\t*\t0\t0\t*\t*\t0\t0\tGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\t&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'&'\tRG:Z:A\n" }, { "path": "tests/input/TestDepleteBlastnBam/humanChr1Subset.fa", "content": ">chr1\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTTCAGTGATGAATCTGGAGTGGTTCTTTTTTTATTTAATGTGGTTATTTTTTGAAGAGACTTTCAATTCCATGTCTCCTGTCAATTCTAAGAAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\n" }, { "path": "tests/input/TestDepleteBlastnBam/humanChr9Subset.fa", "content": ">chr9\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGTGAAGACGGAGACTCTCTTTGGGCAAAGCGGGGCTTTCAGCACGTTCGGTGGTACAGCTCTGACCCTGGCCAATCATGGCACTGACCTATGCCACCATATGGGGGTGGATCGAGGTGGGTGGTGGCATCTGGGATCTCTGCTTGGCTTCCC\n" }, { "path": "tests/input/TestDepleteHuman/partial_pan-viral-9seqs-with-human-random-subset.fasta", "content": ">gi|190684443|gb|EU255973.1| Hepatitis C virus subtype 1a isolate HCV-1a/US/BID-V180/1990, complete genome\nGAGCCATGGCGTTAGTATGAGTGTCGTGCAGCCTCCAGGACCCCCCCTCCCGGGAGAGCC\nATAGTGGTCTGCGGAACCGGTGAGTACACCGGAATTGCCAGGACGACCGGGTCCTTTCTT\nGGATAAACCCGCTCAATGCCTGGAGATTTGGGCGTGCCCCCGCAAGACTGCTAGCCGAGT\nAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGG\nGAGGTCTCGTAGACCGTGCACCATGAGCACGAATCCTAAACCTCAAAGAAAAACCAAACG\nTAACACCAACCGTCGCCCACAGGACGTCAAGTTCCCGGGTGGCGGTCAGATCGTTGGTGG\nAGTTTACTTGTTGCCGCGCAGGGGCCCTAGATTGGGTGTGCGCGCGACGAGGAAGACTTC\nCGAGCGGTCGCAACCTCGAGGTAGACGTCAGCCTATCCCCAAGGCACGTCGGCCCGAGGG\nCAGGACCTGGGCTCAGCCCGGGTATCCTTGGCCCCTCTATGGCAATGAGGGTTGCGGGTG\nGGCGGGATGGCTCCTGTCTCCCCGAGGCTCTCGGCCTAGTTGGGGCCCCACAGACCCCCG\nGCGTAGGTCGCGCAATCTGGGTAAGGTCATCGATACCCTTACGTGCGGCTTCGCCGACCT\nCATGGGGTACATACCGCTCGTCGGCGCTCCTCTTGGAGGCGCTGCCAGGGCTCTGGCGCA\nTGGCGTCAGGGTTCTGGAAGACGGCGTGAACTATGCAACAGGGAACCTTCCTGGTTGCTC\nTTTCTCTATCTTCCTTCTGGCCCTACTCTCTTGCCTGACCGTGCCCGCCTCAGCCTACCA\nAGTGCGCAACTCCTCGGGGCTTTACCATGTCACCAATGATTGCCCTAACTCGAGTATTGT\nGTACGAGGCGGCCGATGCCATCCTGCACACTCCGGGGTGTGTCCCTTGCGTTCGCGAGGG\nTAACGCCTCGAGGTGTTGGGTGCCGGTGACCCCCACGGTGGCCACCAGGGACGGCAAGCT\nCCCCACAACGCAGCTTCGACGTCATATCGATCTGCTCGTCGGGGGCGCCACCCTCTGCTC\nGGCTCTCTACGTGGGGGACCTGTGCGGGTCTGTCTTTCTTGTCGGCCAGCTGTTTACCCT\nCTCTCCCAGGCGCCACTGGACGACGCAGGGCTGTAATTGTTCTATCTATCCCGGCCATAT\nAACGGGTCACCGCATGGCATGGGATATGATGATGAACTGGTCCCCTACAACGGCGTTGGT\nGGTAGCTCAGCTGCTCCGGATCCCACAAGCCATCATGGACATGATCGCTGGTGCTCACTG\nGGGAGTCCTGGCGGGCATAGCGTACTTCTCCATGGTGGGGAACTGGGCGAAGGTCCTGGT\nAGTGCTACTGCTATTTGCCGGCGTCGACGCGGAAACCCACGTCACCGGGGGAAGTGCCGG\nCCGCACCGTGGCTGGGCTTACTGGTCTCTTCGCACCAGGCGCCAGACAGAACATCCAACT\nGATCAACACCAACGGCAGTTGGCACATCAATAGCACGGCCTTGAACTGCAATGATAGCCT\nTCAAACCGGCTGGATAGCAGGCCTCTTCTATCACCACAAATTCAACTCTTCAGGCTGTTC\nCGAGAGGTTGGCCAGCTGCCGACGCCTTACTGATTTTGCCCAGGGCTGGGGCCCCATCAG\nTTATGCCAACGGAAGCGGCCCCGACGAGCGTCCCTACTGCTGGCACTACCCCCCAAGACC\nTTGTGGTATTGTGCCCGCAAGGAGCGTGTGTGGCCCGGTATATTGCTTCACTCCCAGCCC\nCGTGGTGGTGGGAACGACCGACAGGTCGGGTGCGCCTACCTACAACTGGGGTGAAAATGA\nTACGGACGTTTTCGTCCTCAACAACACCAGGCCACCGCTGGGCAATTGGTTCGGTTGCAC\nCTGGATGAACTCGACTGGATTCACCAAAGTGTGCGGAGCGCCCCCTTGTGTCATCGGAGG\nGGTGGGCAATAACACCTTGCGCTGCCCCACTGATTGCTTCCGCAAGCATCCGGAAGCCAC\nATACTCTCGGTGCGGCTCCGGTCCCTGGATTACACCCAGGTGCATGGTCGACTACCCGTA\nTAGGCTTTGGCATTACCCTTGTACCATCAACTACACCATATTCAAAGTCAGGATGTACGT\nGGGAGGGGTCGAGCACAGGCTGGAAGCTGCCTGCAACTGGACGCGGGGCGAACGCTGCGA\nTCTGGAAGACAGGGACAGGTCCGAGCTCAGCCCATTGCTGCTGTCCACCACACAGTGGCA\nGGTTCTTCCGTGTTCTTTCACGACCCTGCCAGCCTTGTCCACCGGCCTCATCCACCTCCA\nCCAGAACATCGTGGACGTGCAGTACTTGTACGGGGTAGGGTCAAGCATTGCGTCCTGGGC\nCATTAAGTGGGAGTATGTCGTTCTCCTGTTCCTTCTGCTTGCAGACGCGCGCGTCTGCTC\nCTGCTTGTGGATGATGTTACTCATATCCCAAGCGGAGGCGGCTTTGGAGAACCTCGTAAT\nACTCAATGCAGCATCCCTGGCCGGGACGCACGGTCTTGTGTCCTTCCTAGTGTTCTTCTG\nCTTTGCGTGGTATCTGAAGGGTAGGTGGGTGCCCGGAGCGGCATACGCCTTCTACGGGAT\nGTGGCCTCTCCTCCTGCTCCTGCTGGCGTTGCCTCAACGGGCATACGCACTGGACACGGA\nGGTGGCCGCGTCGTGTGGCGGCGTTGTTCTTGTCGGGTTAATGGCGCTGACTCTGTCACC\nATATTACAAGCGCCACATCGGCTGGTGCTTGTGGTGGCTTCAGTATCTTCTGACCAGAGT\nAGAAGCGCATCTGCACGTGTGGGTTCCCCCCCTCAACGTTCGAGGGAGGCGCGATGCCAT\nCATCTTGCTCATGTGTGCTGTACACCCGACTTTGGTATTTGACATCACCAAACTACTGCT\nGGCCGTCTTCGGACCCCTTTGGATTCTCCAAGCCAGTTTGCTCAAAGTCCCCTACTTCGT\nGCGCGTTCAAGGCCTCCTCCGGATCTGCGCGCTAGCGCGGAAGATGGTCGGGGGTCATTA\nCGTGCAGATGGCCATCATCAAGTTAGGGGCGCTTACTGGTACCTATGTTTACAACCACCT\nCACTCCTCTTCGGGACTGGGCGCACAACGGCCTGCAAGATCTGGCCGTGGCTGTGGAACC\nTGTCGTCTTCTCCCCAATGGAGACCAAGCTCATCACGTGGGGGGCGGACACCGCCGCGTG\nCGGCGACATCATCGACGGCTTGCCCGTCTCCGCCCGTAGGGGCCAGGAGATACTGCTTGG\nACCAGCCGACGGAATGGTCTCCAAGGGGTGGAGGTTGCTGGCGCCCATCACGGCGTACGC\nCCAGCAGACGAGAGGCCTCCTAGGGTGTATAATCACCAGCCTGACTGGCCGGGACAAGAA\nCCAAGTGGAGGGTGAGGTCCAGATCGTGTCAACCGCTGCCCAAACTTTCCTGGCAACGTG\nCATCAATGGGGTATGCTGGACTGTCTACCACGGGGCCGGAACGAGGACCATCGCATCACC\nCAAGGGTCCTGTTATCCAGATGTATACCAATGTGGACCAAGACCTCGTGGGCTGGCCCGC\nTCCTCCAGGTTCCCGCTCATTAACACCCTGCACCTGCGGCTCCTCGGACCTCTACCTGGT\nCACGAGGCACGCCGATGTCATTCCCGTGCGCCGGCGGGGTGATAGCAGGGGCAGCCTGCT\nTTCGCCCCGGCCCATCTCCTACTTGAAAGGCTCCTCGGGGGGTCCGCTGTTGTGCCCCGC\nGGGACACGCCGTGGGCATATTCAGGGCCGCGGTGTGCACCCGTGGAGTGGCTAAAGCGGT\nGGACTTTATCCCTGTGGAGAACCTAGAGACAACCATGAGATCCCCGGTGTTCACGGACAA\nCTCCTCTCCACCAGCAGTGCCCCAGAGCTTCCAGGTAGCCCACCTGCATGCTCCCACCGG\nCAGCGGTAAGAGCACCAAGGTTCCGGCTGCGTACGCAGCTCAAGGCTACAAGGTGCTGGT\nGCTCAACCCCTCTGTTGCTGCAACACTGGGCTTTGGTGCTTACATGTCCAAGGCCCATGG\nGGTCGATCCTAACATCAGGACTGGGGTGAGAACAATTACCACTGGCAGCCCCATCACGTA\nCTCCACCTACGGCAAGTTCCTTGCCGACGGCGGGTGCTCAGGGGGTGCTTATGACATAAT\nAATTTGTGACGAGTGCCACTCCACGGATGCTACATCCATCTTGGGCATCGGCACTGTCCT\nTGACCAAGCAGAGACTGCGGGGGCGAGACTGGTTGTGCTCGCCACTGCTACTCCTCCGGG\nCTCCGTCACTGTGCCCCATCCTAACATCGAGGAGGTTGCTCTGTCCACCACCGGAGAGAT\nCCCTTTTTACGGCAAGGCTATTCCCCTCGAGGTGATCAAGGGGGGAAGACATCTCATCTT\nCTGTCACTCAAAGAAGAAGTGCGATGAGCTCGCCGCAAAGCTGGTCGCGTTGGGCGTCAA\nTGCCGTGGCCTACTACCGCGGTCTCGACGTGTCTGTCATCCCGACCAGCGGCGATGTTGT\nCGTCGTGGCGACCGATGCTCTCATGACTGGCTATACCGGCGACTTCGACTCTGTGATAGA\nCTGCAACACGTGTGTCACCCAGACAGTCGATTTCAGCCTTGACCCTACCTTCACCATTGA\nGACAACCACGCTCCCCCAGGATGCTGTCTCCCGGACTCAACGTCGGGGCAGGACTGGCAG\nGGGGAAGCCAGGCATCTACAGATTTGTGGCACCGGGGGAGCGCCCCTCGGGCATGTTCGA\nCTCGTCCGTCCTCTGTGAGTGCTATGACGCGGGCTGTGCTTGGTATGAGCTCACGCCCGC\nCGAGACTACAGTTAGGCTACGAGCGTACATGAACACCCCGGGGCTTCCCGTGTGCCAGGA\nCCATCTTGAATTTTGGGAGGGCGTTTTTACGGGCCTCACTCATATAGATGCCCACTTTCT\nATCCCAGACAAAGCAGAGTGGGGAGAACTTTCCTTACCTGGTAGCGTACCAAGCCACCGT\nGTGCGCTAGGGCTCAAGCCCCGCCCCCATCGTGGGACCAGATGTGGAAGTGTTTGATCCG\nTCTCAAGCCCACCCTCCATGGGCCAACACCCCTGCTATACAGACTGGGCGCTGTTCAGAA\nTGAAGTTACCCTGACGCACCCAATCACCAAATACATCATGACATGCATGTCGGCTGACCT\nGGAGGTCGTCACGAGCACCTGGGTGCTCGTTGGCGGCGTCCTGGCTGCTTTGGCCGCGTA\nTTGCCTGTCAACAGGCTGCGTGGTCATAGTGGGCAGGATTGTCTTGTCCGGGAAGCCGGC\nAGTTATACCTGACAGGGAGGTTCTCTACCGGGAGTTCGATGAGATGGAAGAGTGCTCTCA\nGCACTTACCGTACATCGAGCAAGGGATGATGCTCGCCGAGCAGTTCAAGCAGAAGGCCCT\nCGGCCTCCTGCAGACCGCGTCCCGCCAGGCAGAGGTTATCGCCCCTGCTGTCCAGACCAA\nCTGGCAGAAACTCGAGGCCTTCTGGGCGAAGCATATGTGGAATTTCATCAGTGGGATACA\nATACTTGGCGGGCCTGTCAACGCTGCCTGGTAACCCCGCCATTGCTTCATTGATGGCTTT\nTACAGCTGCTGTCACCAGCCCACTAACCACTAGCCAAACCCTCCTCTTCAACATATTGGG\nGGGGTGGGTGGCTGCCCAGCTCGCTGCCCCCGGTGCCGCTACCGCCTTTGTGGGCGCTGG\nCTTAGCCGGCGCCGCCATCGGCAGTGTTGGGCTGGGGAAGGTCCTCGTGGACATTCTTGC\nAGGATATGGCGCGGGCGTGGCGGGAGCTCTTGTAGCATTCAAGATCATGAGCGGTGAGGT\nCCCCTCCACGGAGGACCTGGTCAATCTGCTGCCCGCCATCCTCTCGCCTGGAGCCCTTGT\nAGTCGGTGTGGTCTGCGCAGCAATACTGCGCCGGCACGTTGGCCCGGGCGAGGGGGCAGT\nGCAATGGATGAACCGGCTAATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCCACGCA\nCTACGTGCCGGAGAGCGATGCAGCCGCCCGCGTCACGGCCATACTCAGCAGCCTCACTGT\nAACCCAGCTCCTGAGGCGACTGCACCAGTGGATAAGCTCGGAGTGTACCACTCCATGCTC\nCGGTTCCTGGCTAAGAGACATCTGGGACTGGATATGCGAGGTGCTGAGCGACTTTAAGAC\nCTGGCTGAAAGCCAAGCTCATGCCACAACTGCCTGGGATTCCCTTTGTGTCCTGCCAGCG\nCGGGTATAGGGGGGTCTGGCGGGGAGACGGCATCATGCACACTCGCTGCCACTGTGGAGC\nTGAGATCACTGGACATGTCAAAAACGGGACGATGAGGATCGTCGGTCCTAGGACCTGCAG\nGAACATGTGGAGTGGGACCTTCCCCATTAACGCCTACACCACGGGCCCCTGTACCCCCCT\nTCCTGCGCCGAACTATAAGTTCGCGCTGTGGAGGGTGTCTGCAGAGGAATACGTGGAGAT\nAAGGCAGGTGGGGGACTTCCACTACGTAACGGGCATGACTACTGACAATCTTAAATGCCC\nGTGCCAGGTCCCATCGCCCGAATTCTTCACAGAATTGGACGGGGTGCGCCTACATAGGTA\nTGCGCCCCCTTGCAAGCCCTTGCTGCGGGAGGAGGTATCATTCAGAGTAGGACTCCACGA\nGTACCCGGTGGGGTCGCAACTACCTTGCGAGCCCGAACCGGACGTGGCCGTGTTGACGTC\nCATGCTCACTGATCCCTCCCACATAACAGCGGAGGCGGCCGGGAGAAGGTTGGCGAGGGG\nATCACCCCCTTCTGTGGCCAGCTCCTCGGCTAGCCAGTTGTCCGCTCCATCTCTCAAGGC\nAACTTGCACCGCCAACCATGACTCCCCTGACGCCGAGCTCATAGAGGCTAATCTCCTGTG\nGAGGCAGGAGATGGGCGGCAACATCACCAGGGTTGAGTCAGAGAACAAAGTGGTGATTCT\nGGACTCCTTCGATCCGCTTGTATCAGAGGAGGATGAGCGGGAGATCTCCGTACCCGCAGA\nAATCCTGCGGAAGTCTCGGAGATTCGCCCCGGCCCTGCCCATTTGGGCGCGGCCGGACTA\nCAACCCCCCGCTGGTAGAGACGTGGAAAAAACCTGACTACGAACCACCCGTGGTCCATGG\nCTGCCCGCTACCACCTCCACAGTCCCCTCCTGTGCCTCCGCCTCGGAAGAAGCGAACGGT\nGGTCCTCACCGAATCAACCCTATCTACTGCCTTGGCTGAGCTTGCCACCAAAAGTTTTGG\nCAGCTCCTCAACTTCCGGCATTACGGGCGACAATACGACAACATCCTCTGAGCCCGCCCC\nTTCTGGCTGCTCCCCCGACTCCGACGTTGAGTCCTATTCTTCCATGCCCCCCCTGGAGGG\nGGAGCCTGGAGATCCGGATCTCAGCGACGGGTCATGGTCGACGGTCAGTAGCGGGGCCGA\nCGCGGAGGATGTCGTGTGCTGCTCAATGTCCTATACCTGGACAGGCGCACTCGTCACCCC\nGTGCGCTGCGGAAGAACAAAAACTGCCCATCAACGCACTGAGCAACTCGTTGCTACGTCA\nTCACAATCTGGTGTATTCCACCACTTCACGCAGTGCTTGCCAAAGGCAGAAGAAAGTCAC\nATTTGACAGACTGCAAGTTCTGGACAGCCATTACCAGGACGTGCTCAAGGAGGTTAAGGC\nAGCGGCGTCAAAAGTGAAGGCTAACTTGCTATCCGTAGAGGAAGCTTGCAGCCTGACGCC\nCCCACACTCAGCCAAATCCAAGTTTGGTTATGGGGCGAAAGACGTCCGTTGCCATGCCAG\nAAAGGCCGTAGCCCACATCAACTCCGTGTGGAAAGACCTTCTGGAAGACAGTGTAACACC\nAATAGACACTACCATCATGGCTAAGAACGAGGTTTTCTGTGTTCAGCCTGAGAAGGGGGG\nTCGTAAGCCAGCTCGTCTCATCGTGTTCCCCGACCTGGGCGTGCGCGTGTGCGAGAAGAT\nGGCCCTGTACGATGTGGTTAGCAAGCTCCCCCTGGCCGTGATGGGAAGCTCCTACGGATT\nCCAATACTCACCAGGACAGCGGGTTGAATTCCTCGTGAAAGCGTGGAAGTCCAAGAAGAC\nCCCAATGGGGTTCTCATATGATACCCGCTGTTTTGACTCCACAGTCACTGAGAGCGACAT\nCCGTACGGAGGAGGCAATTTACCAATGTTGTGACCTGGACCCCCAAGCCCGCGTGGCCAT\nCAAGTCCCTCACTGAGAGGCTTTACGTTGGGGGCCCTCTTACCAATTCAAGGGGGGAGAA\nCTGCGGCTACCGCAGGTGCCGCGCGAGCGGCGTACTGACAACTAGCTGTGGTAACACCCT\nCACTTGCTACATCAAGGCCCAAGCAGCCTGTCGAGCCGCAGGGCTCCAGGACTGCACCAT\nGCTCGTGTGTGGCGACGACTTAGTCGTTATCTGTGAAAGTGCGGGGGTCCAGGAGGACGC\nGGCGAGCCTGAGAGCCTTCACGGAGGCTATGACCAGGTACTCCGCCCCCCCCGGGGACCC\nCCCACAACCAGAATACGACTTGGAGCTCATAACATCATGCTCCTCCAACGTGTCAGTCGC\nCCACGACGGCGCTGGAAAGAGGGTCTACTACCTCACCCGTGACCCTACAACCCCCCTCGC\nGAGAGCCGCGTGGGAGACAGCAAGACACACTCCAGTCAATTCCTGGCTAGGCAACATAAT\nCATGTTTGCCCCCACACTGTGGGCGAGGATGATATTGATGACCCACTTCTTTAGCGTCCT\nCATAGCCAGGGACCAGCTTGAACAGGCCCTTGATTGCGAGATCTACGGAGCCTGCTACTC\nCATAGAACCACTGGACCTACCTCCAATCATTCAAAGACTCCATGGCCTCAGCGCATTTTC\nACTCCACAGTTACTCTCCAGGTGAGATCAATAGGGTGGCCGCATGCCTCAGAAAACTTGG\nGGTCCCGCCCTTGCGAGCTTGGAGACACCGGGCCCGGAGCGTCCGCGCTAGGCTTCTGTC\nCAGAGGAGGCAGGGCTGCCATATGTGGCAAGTACCTCTTCAACTGGGCAGTAAGAACAAA\nGCTCAAACTCACTCCAATAGCGGCCGCTGGCCGGCTGGACTTGTCCGGCTGGTTCACGGC\nTGGCTACAGCGGGGGAGACATTTATCACAGCGTGTCTCATGCCCGGCCCCGCTGGTTCTG\nGTTTTGCCTACTCCTGCTCGCTGCAGGGGTAGGCATCTACCTCCTCCCCAACCGATGA\n>gi|612340474|gb|KJ207374.1| Tomato mosaic virus isolate Penghu, complete genome\nGTATTTTTACAACAATTACCAACAACAACAACAAACAACAACAACATTACATTTTACATT\nCTACAACTACAATGGCATACACACAAACAGCCACATCGTCCGCTTTGCTTGAGACCGTCC\nGAGGTAACAATACCTTGGTCAACGATCTTGCAAAGCGGCGTCTATATGACACAGCGGTCG\nATGAATTTAATGCTAGGGACCGCAGGCCTAAAGTCAATTTTTCCAAAGTAGTAAGCGAAG\nAACAGACGCTTATTGCAACCAAAGCCTACCCAGAATTCCAAATTACATTCTACAACACGC\nAGAACGCTGTGCATTCCCTTGCAGGCGGTCTCCGATCATTAGAATTGGAATATCTGATGA\nTGCAAATTCCCTACGGATCATTGACATATGATATCGGAGGTAATTTTGCATCTCATCTGT\nTCAAAGGGCGAGCATACGTTCACTGCTGTATGCCGAATCTGGATGTCCGCGACATAATGC\nGGCACGAGGGCCAAAAGGACAGTATTGAACTATACCTTTCTAGGCTCGAAAGGGGCAACA\nAACATGTCCCAAACTTCCAAAAGGAAGCTTTCGACAGATACGCTGAAATGCCAAACGAAG\nTAGTCTGTCACGATACTTTCCAAACGTGTAGGCATTCTCAAGAATGTTACACGGGAAGAG\nTGTATGCTATTGCTTTGCATAGTATATACGATATACCTGCCGACGAGTTCGGCGCGGCAC\nTGCTGAGAAAGAATGTACATGTATGTTATGCCGCTTTCCACTTTTCCGAGAATTTACTTC\nTCGAAGATTCACACGTCAACCTCGATGAGATCAATGCATGTTTCCAAAGAGATGGAGACA\nGGTTGACCTTTTCCTTTGCATCTGAGAGTACTCTTAATTATAGTCATAGTTATTCTAATA\nTTCTTAAGTATGTTTGCAAAACTTACTTCCCAGCCTCTAATAGAGAGGTTTACATGAAGG\nAGTTTTTAGTAACTAGAGTTAATACCTGGTTTTGTAAATTTTCTAGAATAGATACTTTCT\nTATTGTACAAAGGTGTAGCGCATAAGGGTGTAGATAGTGAGCAGTTTTACAAGGCTATGG\nAAGACGCATGGCACTACAAAAAGACTCTTGCGATGTGCAACAGTGAAAGAATCTTGTTAG\nAGGATTCTTCATCAGTTAATTACTGGTTTCCAAAAATGAGGGATATGGTGATAGTTCCAC\nTATTTGACATATCTCTCGAGACTAGTAAAAGAACACGCAAAGAGGTCTTAGTTTCAAAGG\nACTTTGTTTATACAGTGTTAAATCACATTCGTACGTACCAGGCAAAAGCGCTTACTTACT\nCCAACGTGTTATCTTTCGTCGAATCAATTCGTTCGAGAGTGATCATTAACGGGGTTACTG\nCTAGGTCTGAGTGGGATGTCGATAAATCATTATTACAGTCCTTGTCGATGACGTTCTTCC\nTACATACCAAGCTTGCCGTTCTGAAAGACGATCTTTTGATTAGCAAGTTTGCACTTGGTC\nCAAAAACTGTCTCACAACATGTGTGGGATGAGATTTCCCTAGCTTTCGGCAATGCTTTCC\nCATCGATCAAGGAAAGATTGATAAACCGGAAACTGATCAAAATTACGGAGAATGCGTTAG\nAGATCAGGGTGCCCGATCTTTATGTCACTTTCCATGATAGGTTAGTTTCTGAGTACAAAA\nTGTCAGTGGACATGCCGGTGCTAGACATTAGGAAAAAGATGGAAGAAACTGAGGAAATGT\nACAATGCACTGTCCGAACTGTCTGTACTTAAAAATTCAGACAAATTCGATGTTGATGTTT\nTTTCCCAGATGTGCCAATCTTTAGAAGTTGATCCAATGACTGCAGCAAAGGTAATAGTAG\nCAGTTATGAGCAACGAGAGTGGTCTTACTCTCACGTTTGAACAGCCCACCGAAGCTAATG\nTTGCGCTAGCATTGAAAGATTCTGAAAAGGCTTCTGATGGGGCGTTGGTAGTTACCTCAA\nGAGATGTTGAAGAACCGTCCATAAAGGGTTCGATGGCCCGTGGTGAGTTACAATTGGCCG\nGATTATCTGGCGACGTTCCTGAATCTTCATACACTAGGAGCGAGGAAATTGAGTCTCTCG\nAGCAGTTTCATATGGCAACAGCTAGTTCGTTAATTCACAAGCAGATGTGTTCGATCGTGT\nACACGGGCCCTCTTAAAGTTCAACAAATGAAAAACTTTATAGACAGCCTGGTAGCCTCGC\nTCTCTGCTGCGGTGTCGAATCTAGTGAAGATCCTAAAAGATACAGCTGCGATTGACCTTG\nAAACTCGTCAAAAGTTCGGAGTTCTGGATGTTGCTTCGAAAAGGTGGCTAGTTAAACCAT\nCCGCAAAGAACCATGCATGGGGGGTTGTTGAGACTCATGCGAGGAAATATCACGTCGCAT\nTACTGGAGCACGATGAATTTGGCATTATTACGTGCGATAACTGGCGACGGGTGGCTGTGA\nGTTCTGAGTCGGTAGTATATTCTGATATGGCTAAACTCAGAACTCTGAGAAGATTGCTCA\nAAGATGGAGAACCACACGTTAGTTCAGCAAAGGTGGTTTTGGTGGATGGCGTTCCAGGGT\nGCGGGAAAACAAAGGAAATTCTTTCGAGAGTTAATTTCGAAGAAGATCTAATTCTTGTCC\nCTGGTCGTCAAGCTGCCGAGATGATCAGAAGAAGAGCTAATGCGTCGGGCATAATAGTGG\nCTACAAAGGACAATGTGCGTACCGTCGATTCATTTTTGATGAATTACGGGAAAGGGGCAC\nGCTGTCAGTTCAAAAGATTGTTCATAGACGAAGGTTTGATGCTGCATACTGGTTGTGTGA\nATTTCTTGGTTGAAATGTCTCTGTGCGATATTGCATATGTTTATGGAGACACCCAACAAA\nTTCCGTACATCAACAGAGTAACTGGTTTCCCGTACCCTGCACACTTTGCAAAATTGGAGG\nTCGACGAAGTCGAAACAAGAAGAATTACTCTTCGTTGTCCGGCTGATGTCACACACTTCC\nTAAATCAAAGGTATGAAGGACACGTAATGTGCACGTCTTCTGAAAAGAAATCAGTTTCCC\nAGGAAATGGTTAGTGGGGCTGCGTCTATCAATCCTGTGTCCAAGCCGCTTAAAGGGAAAA\nTTTTGACTTTTACACAGTCTGACAAGGAGGCCCTTCTCTCAAGGGGCTATGCAGATGTCC\nATACTGTACATGAGGTACAAGGTGAGACTTATGCAGACGTATCGTTAGTTCGACTAACAC\nCTACGCCTGTATCTATCATCGCAAGAGACAGTCCGCATGTTCTGGTCTCGTTGTCAAGAC\nACACAAAATCCCTAAAGTACTACACCGTTGTGATGGATCCTTTAGTTAGTATCATTAGAG\nATTTAGAACAGGTTAGTAGTTACTTATTAGACATGTACAAAGTAGATGCAGGTACTCAAT\nAGCAATTACAGGTCGACTCTGTGTTTAAGAATTTCAATCTTTTTGTAGCAGCTCCAAAGA\nCTGGAGATATATCTGATATGCAATTTTACTATGATAAGTGTCTTCCTGGGAACAGCACGT\nTGTTGAACAACTACGACGCTGTTACCATGAAATTGACTGACATTTCTCTGAATGTCAAAG\nATTGCATATTAGATATGTCTAAGTCTGTAGCTGCTCCGAAAGATGTCAAACCAACTTTAA\nTACCGATGGTACGAACGGCGGCAGAAATGCCTCGCCAGACTGGACTGTTGGAAAATTTAG\nTTGCGATGATTAAAAGAAATTTTAATTCACCAGAGTTGTCCGGAGTAGTTGATATTGAAA\nATACTGCATCTTTAGTGGTAGATAAGTTTTTTGATAGTTATTTACTTAAGGAAAAAAGAA\nAACCAAACAAAAATTTTTCACTGTTTAGTAGAGAGTCTCTCAATAGGTGGATAGCAAAGC\nAAGAACAAGTCACAATTGGTCAGTTGGCCGATTTTGATTTTGTGGATCTTCCAGCCGTTG\nATCAGTACAGGCATATGATAAAAGCGCAACCGAAGCAGAAACTGGATCTGTCAATTCAGA\nCGGAATATCCAGCGTTGCAAACGATTGTGTATCATTCAAAGAAAATCAACGCAATATTTG\nGTCCTCTTTTCAGTGAGCTTACAAGGCAATTACTTGACAGTATTGACTCAAGCAGATTCT\nTGTTCTTTACGAGAAAGACACCGGCTCAGATCGAAGATTTCTTCGGAGATCTAGACAGTC\nATGTCCCAATGGACGTACTTGAGTTGGATATTTCAAAGTATGATAAGTCTCAAAACGAGT\nTTCATTGTGCTGTTGAGTACGAAATCTGGAGGAGACTGGGTCTGGAGGATTTCTTGGCAG\nAAGTGTGGAAACAAGGGCATAGAAAAACCACTCTGAAAGATTACACTGCTGGTATAAAAA\nCGTGTTTATGGTACCAGAGAAAGAGTGGTGATGTTACAACTTTTATCGGTAATACCGTCA\nTCATTGCTTCGTGTCTTGCATCAATGCTCCCGATGGAAAAATTGATAAAAGGAGCCTTCT\nGCGGAGATGACAGTTTGTTGTACTTTCCTAGAGGTTGTGAGTATCCCGATATACAACAAG\nCTGCTAATCTGATGTGGAATTTTGAGGCCAAACTGTTCAAGAAGCAATATGGGTACTTCT\nGCGGGAGGTACGTGATTCATCACGATAGAGGTTGCATAGTATACTACGACCCTCTGAAGC\nTGATTTCGAAACTTGGTGCTAAACACATCAAGGATTGGGATCATTTGGAGGAGTTCAGAA\nGATCCCTCTGTGATGTTGCTGAGTCGTTGAACAATTGTGCGTATTACACACAATTGGACG\nACGCTGTTGGGGAGGTTCATAAAACCGCCCCACCTGGTTCGTTTGTTTATAGGAGTTTAG\nTTAAGTATTTGTCAGATAAAGTTTTGTTTAGAAGTTTATTTCTTGATGGCTCTAGTTGTT\nAAAGGTAAGGTAAATATTAATGAGTTTATCGATCTGTCAAAGTCTGAGAAACTTCTCCCG\nTCGATGTTCACGCCTGTAAAGAGTGTTATGGTTTCAAAGGTTGATAAGATTATGGTCCAT\nGAAAATGAATCATTGTCTGAAGTAAATCTCTTAAAAGGTGTAAAACTTATAGAAGGTGGG\nTATGTTTGCTTAGTTGGTCTTGTTGTGTCCGGTGAGTGGAATTTACCAGATAATTGCCGT\nGGTGGTGTGAGTGTCTGCATGGTTGACAAGAGAATGGAAAGAGCGGACGAAGCCACACTG\nGGGTCATATTACACTGCTGCTGCTAAAAAGCGGTTTCAGTTTAAAGTGGTCCCAAATTAC\nGGTATTACTACAAAGGATGCAGAAAAGAACATATGGCAGGTCTTAGTAAATATTAAAAAT\nGTAAAAATGAGTGCGGGCTACTGCCCTTTGTCATTAGAATTTGTGTCTGTGTGTATTGTT\nTATAAAAATAATATAAAATTGGGTTTGAGGGAGAAAGTAACGAGTGTGAACGATGGAGGA\nCCCATGGAACTTTCAGAAGAAGTTGTTGATGAGTTCATGGAGAATGTTCCAATGTCGGTT\nAGACTCGCAAAGTTTCGAACCAAAACCTCAAAAAGAGGTCCGAAAAATAATAATAATTTA\nGGTAAGGGGCGTTCAGGCGGAAGGCCTAAACCAAAAAGTTTTGATGAAGTTGAAAAAGAG\nTTTGATAATTTGATTGAAGATGAAGCCGAGACGTCGGTCGCGGATTCTGATTCGTATTAA\nATATGTCTTACTCAATCACTTCTCCATCGCAATTTGTGTTTTTGTCATCTGTATGGGCTG\nACCCTATAGAATTGTTAAACGTTTGTACAAATTCGTTAGGTAACCAGTTTCAAACACAGC\nAAGCAAGAACTACTGTTCAACAGCAGTTCAGCGAGGTGTGGAAACCTTTCCCTCAGAGCA\nCCGTCAGATTTCCTGGCGATGTTTATAAGGTGTACAGGTACAATGCAGTTTTAGATCCTC\nTAATTACTGCGTTGCTGGGGGCCTTCGATACTAAGAATAGAATAATCGAAGTAGAAAACC\nAGCAGAGTCCGACAACAGCTGAAACGTTAGATGCTACCCGCAGGGTAGACGACGCTACGG\nTTGCAATCCGGTCTGCTATAAATAATTTAGTTAATGAACTAGTAAAAGGTACTGGACTGT\nACAATCAGAATACTTTTGAAAGTATGTCTGGGTTGGTCTGGACCTCTGCACCTGCATCTT\nAAATGCATAGGTGCTGAAATATAAAGTTTGTGTTTCTAAAACACACGTGGTACGTACGAT\nAACGTACAGTGTTTTTCCCTCCACTTAAATCGAAGGGTAGTGTCTTGGAGCGCGCGGAGT\nAAACATATATGGTGCATATATGTCCGTAGGCACGTAAAAAAGCGAGGGATTCGAATTCCC\nCCGGAGCACCACTGGTGGTGGCCCA\n>gi|27085398|gb|AY184220.1| Human poliovirus 2 strain Sabin 2, complete genome\nTTAAAACAGCTCTGGGGTTGTACCCACCCCAGAGGCCCACGTGGCGGCTAGCACTCCGGT\nATTACGGTACCCTTGTGCGCCTGTTTTATACTCCCCTCCCGCAACTTAGAAGCACGAAAC\nCAAGTTCAATAGAAGGGGGTACAAACCAGTACCACTACGAACAAGCACTTCTGTTTCCCC\nGGTGACATTGCATAGACTGCTCACGCGGTTGAAAGTGATCGATCCGTTACCCGCTTGTGT\nACTTCGAAAAGCCTAGTATCGCCTTGGAATCTTCGACGCGTTGCGCTCAGCACCCGACCC\nCGGGGTGTAGCTTAGGCTGATGAGTCTGGACATTCCTCACCGGTGACGGTGGTCCAGGCT\nGCGTTGGCGGCCTACCTATGGCTAACGCCATAGGACGTTAGATGTGAACAAGGTGTGAAG\nAGCCTATTGAGCTACATAAGAGTCCTCCGGCCCCTGAATGCGGCTAATCCTAACCACGGA\nACAGGCGGTCGCGAACCAGTGACTGGCTTGTCGTAACGCGCAAGTCTGTGGCGGAACCGA\nCTACTTTGGGTGTCCGTGTTTCCTGTTATTTTTATCATGGCTGCTTATGGTGACAATCAG\nAGATTGTTATCATAAAGCGAATTGGATTGGCCATCCGGTGAGTGTTGTGTCAGGTATACA\nACTGTTTGTTGGAACCACTGTGTTAGCTTTACTTCTCATTTAACCAATTAATCAAAAACA\nATACGAGGATAAAACAACAATACTACAATGGGCGCCCAAGTTTCATCACAGAAAGTTGGA\nGCCCACGAAAATTCAAACAGAGCCTATGGCGGGTCCACCATCAATTACACTACAATCAAT\nTACTATAGGGACTCTGCAAGCAATGCAGCAAGCAAGCAAGATTTTGCACAAGATCCGTCC\nAAGTTCACCGAACCCATTAAGGACGTCCTTATTAAGACCGCTCCCATGCTAAACTCCCCA\nAACATTGAGGCGTGTGGTTATAGTGACAGGGTAATGCAGCTAACTCTGGGCAATTCAACG\nATCACCACCCAAGAAGCGGCCAATTCTGTTGTTGCCTACGGTAGATGGCCTGAATACATC\nAGAGATACCGAGGCAAATCCTGTAGACCAACCAACCGAGCCCGATGTAGCCGCGTGCAGG\nTTCTACACATTAGATACCGTCACTTGGCGCAAGGAGTCCAGAGGGTGGTGGTGGAAACTA\nCCAGACGCTTTAAAAGACATGGGGTTATTTGGTCAAAACATGTTTTATCACTATCTTGGG\nAGGGCTGGCTACACAGTGCACGTACAGTGCAATGCTTCAAAGTTTCATCAAGGAGCTCTA\nGGGGTGTTTGCAGTTCCAGAAATGTGTTTAGCTGGTGATAGCACAACTCACATGTTCACA\nAAGTACGAGAATGCGAATCCAGGCGAAAAAGGAGGTGAATTCAAAGGGAGTTTCACCCTT\nGATACCAACGCCACTAACCCTGCACGGAACTTCTGCCCAGTTGATTACCTCTTCGGGAGT\nGGAGTGCTGGTAGGGAATGCATTTGTTTATCCACATCAAATAATAAACCTGCGCACTAAC\nAACTGTGCTACGCTAGTATTGCCCTATGTAAACTCACTCTCAATAGATAGCATGACAAAG\nCACAACAACTGGGGGATCGCTATCCTCCCCCTGGCGCCACTAGACTTTGCCACTGAATCT\nTCCACTGAGATACCCATTACACTGACCATTGCTCCCATGTGCTGCGAATTCAATGGTTTA\nCGCAACATCACTGTGCCAAGAACCCAAGGATTACCAGTCCTGAACACTCCAGGGAGTAAC\nCAGTACCTGACCGCAGACAATTACCAGTCTCCGTGTGCGATACCTGAGTTTGATGTCACT\nCCACCCATAGACATACCAGGGGAGGTGCGCAACATGATGGAATTGGCGGAAATAGACACC\nATGATACCCCTCAACTTGACAAGTCAACGCAAGAACACAATGGACATGTATAGAGTCGAG\nTTGAGCGACACGGCTCACTCTGACACGCCGATCTTGTGTCTCTCGTTGTCCCCCGCTTCA\nGACCCCAGATTGGCACACACTATGTTGGGTGAGATATTAAATTACTACACACACTGGGCA\nGGGTCCTTGAAATTTACCTTTCTCTTTTGCGGCTCAATGATGGCCACCGGAAAGTTATTG\nGTTTCTTACGCACCACCCGGAGCAGAGGCCCCCAAGAGTCGCAAAGAAGCAATGCTTGGG\nACACATGTGATATGGGACATTGGGTTGCAGTCTTCATGCACTATGGTGGTACCTTGGATC\nAGTAATACCACATACAGACAAACCATCAACGATAGTTTCACAGAAGGTGGCTACATTAGC\nATGTTCTATCAAACTAGGGTTGTTGTCCCGTTGTCCACACCCAGAAAGATGGACATCCTG\nGGTTTTGTGTCAGCTTGCAATGACTTCAGTGTGCGCTTACTGCGAGATACAACACACATT\nAGTCAAGAGGCTATGCCACAAGGAATTGGTGACATGATTGAGGGGGCCGTTGAAGGGATT\nACTAAAAATGCATTGGTTCCCCCGACTTCCACCAATAGCCTGCCTGACACAAAGCCGAGC\nGGTCCAGCCCACTCCAAGGAGATACCTGCATTGACAGCCGTGGAGACAGGGGCTACCAAT\nCCGTTGGTGCCTTCGGACACCGTGCAAACGCGCCATGTCATCCAGAGACGAACGCGATCA\nGAGTCCACGGTTGAGTCATTCTTTGCAAGAGGGGCTTGCGTGGCTATCATTGAGGTGGAC\nAATGATGCACCGACAAAGCGCGCCAGCAGATTGTTTTCGGTTTGGAAAATAACTTACAAA\nGATACTGTTCAACTGAGACGCAAACTGGAATTTTTCACATATTCGAGATTTGACATGGAG\nTTCACTTTTGTGGTCACCTCAAACTACATTGATGCAAATAACGGACATGCATTGAACCAA\nGTTTATCAGATAATGTATATACCACCCGGAGCACCTATCCCTGGTAAATGGAATGACTAT\nACGTGGCAGACGTCCTCTAACCCGTCGGTGTTTTACACCTATGGGGCGCCCCCAGCAAGA\nATATCAGTGCCCTACGTGGGAATTGCTAATGCGTATTCCCACTTTTATGATGGGTTTGCA\nAAAGTACCACTAGCGGGTCAAGCCTCAACTGAAGGCGATTCGTTGTACGGTGCTGCCTCA\nCTGAATGATTTTGGATCACTGGCTGTTCGCGTGGTAAATGATCACAACCCCACGCGGCTC\nACCTCCAAGATCAGAGTGTACATGAAGCCAAAGCATGTCAGAGTCTGGTGCCCACGACCT\nCCACGAGCAGTCCCATACTTCGGACCAGGTGTTGATTATAAAGATGGGCTCACCCCACTA\nCCAGAAAAGGGATTAACGACTTATGGATTTGGACACCAAAACAAAGCTGTGTACACAGCT\nGGCTACAAAATTTGCAATTACCACCTAGCTACACAAGAAGACTTGCAAAATGCCGTGAGT\nGTCATGTGGAACAGAGACCTCTTAGTGGCTGAATCAAGGGCCCTTGGCACCGACTCGATC\nGCAAGGTGCAGCTGTAACACGGGTGTGTACTACTGTGAATCCAGGAGAAAATATTATCCA\nGTTTCTTTCATTGGGCCCACCTTCCAATACATGGAAGCCAATGAATATTACCCGGCTAGA\nTATCAATCACACATGCTTATTGGTCATGGGTTTGCATCACCGGGTGATTGTGGTGGCATA\nCTTAGATGTCAACACGGGGTGATAGGAATAATCACTGCTGGTGGGGAAGGCTTGGTTGCA\nTTTTCAGACATTAGAGACCTGTATGCTTATGAGGAGGAAGCTATGGAGCAGGGCATTTCC\nAACTATATTGAGTCACTTGGTGCTGCATTTGGTAGTGGATTCACTCAACAAATTGGTGAT\nAAAGTTTCCGAGCTAACCAGCATGGTAACTAGCACCATTACAGAGAAGTTGCTTAAAAAC\nTTAATCAAAATTATCTCATCACTTGTGATCATTACCAGGAATTATGAGGACACTACCACA\nGTGCTTGCCACCCTCGCCCTCCTTGGGTGCGACATCTCACCGTGGCAGTGGCTAAAGAAG\nAAGGCATGTGACATCCTGGAAATTCCATACGCCATCAAACAAGGAGATAGTTGGTTGAAG\nAAATTCACTGAGGCATGTAATGCTGCAAAGGGACTGGAGTGGGTGTCCAATAAGATATCC\nAAATTCATTAGTTGGTTGCAGGATAAAATCATCCCACAAGCGAGAGACAAATTAGAGTTT\nGTCACTAAACTAAAGCAATTAGAAATGCTTGAAAATCAGATTTCCACCATACACCAATCT\nTGTCCAAGTCAAGAACATCAGGAGATCTTATTCAACAATGTGCGGTGGCTATCTATCCAG\nTCCAAGAGGTTTGCACCACTATATGCACATGAAGCTAAAAGGATTCAAAAGCTGGAGCAT\nACCATAAATAATTACGTACAGTTCAAGAGCAAGCACCGTATTGAGCCAGTATGTTTGTTA\nGTACATGGCAGTCCAGGGACAGGAAAATCAGTTGCAACCAATCTAATTGCTAGAGCAATA\nGCCGAGAAAGAGAACACCTCCACATACTCACTGCCACCTGATCCGTCTCACTTTGATGGC\nTACAAGCAACAGGGTGTGGTTATTATGGATGACCTAAACCAAAATCCAGACGGAGCAGAC\nATGAAACTTTTTTGTCAAATGGTGTCCACTGTGGAGTTTATTCCACCGATGGCCTCGCTA\nGAAGAGAAAGGCATTTTGTTCACATCTAATTACGTTTTAGCCTCCACCAACTCCAGTCGG\nATCACACCACCCACGGTGGCTCACAGTGATGCGCTGGCCAGGAGATTCGCATTTGACGTG\nGACATACAAGTCATGAGCGAGTACTCCAGAGACGGAAAGCTCAACATGGCAATGGCTACT\nGAAATGTGCAAAAACTGTCATCAACCAGCAAACTTCAAAAGATGTTGTCCTTTAGTGTGT\nGGCAAGGCAATTCAGTTAATGGATAAATCTTCCAGGGTTAGATACAGCATTGATCAGATC\nACTACAATGATTGTTAATGAGAGAAACAGAAGATCAAACATTGGTAATTGCATGGAAGCT\nCTATTCCAGGGACCACTGCAGTATAAAGATCTAAAAATAGATGTTAAGACCAGTCCCCCT\nCCGGAGTGTATCAACGATTTGCTCCAGGCAGTTGATTCCCAGGAAGTGAGAGATTACTGT\nGAAAAGAAAGGCTGGATTGTTAACATTACCAGTCAGGTTCAAACAGAGAGGAACATCAAC\nCGGGCGATGACTATCCTACAAGCAGTAACTACTTTCGCTGCAGTAGCCGGTGTCGTGTAC\nGTTATGTACAAGCTGTTCGCTGGGCACCAGGGTGCATACACTGGTTTGCCAAATAAACGA\nCCCAATGTACCCACTATCAGGACAGCAAAAGTGCAAGGCCCTGGGTTTGATTACGCAGTG\nGCCATGGCTAAAAGAAACATTGTTACAGCAACCACCAGCAAAGGGGAGTTTACGATGTTG\nGGAGTCTATGATAATGTGGCCATCTTGCCAACCCACGCCTCACCTGGTGAAAGCATTGCG\nATCGACGGTAAAGAGGTGGAAATTCTTGACGCCAAAGCCCTTGAAGATCAGGCAGGAACT\nAATCTTGAAATTACCATAATTACACTAAAGAGGAACGAGAAGTTCAGAGATATCAGGCCA\nCACATTCCCACCCAAATCACCGAAACAAATGATGGAGTTTTGATCGTGAACACTAGTAAG\nTACCCCAACATGTATGTTCCCGTTGGTGCTGTGACCGAACAGGGGTATCTTAATCTCGGT\nGGACGACAAACCGCTCGTACGCTAATGTACAACTTTCCAACTAGAGCAGGTCAGTGTGGT\nGGTGTCATCACGTGCACTGGTAAAGTCATTGGGATGCATGTTGGTGGGAACGGTTCACAT\nGGGTTCGCGGCGGCCCTAAAGCGGTCATACTTCACTCAGATTCAAGGTGAGATTCAATGG\nATGAAACCATCAAAAGAAGTGGGATACCCGATCATAAATGCTCCGTCCAAAACCAAACTT\nGAACCCAGCGCTTTTCACTATGTGTTTGAAGGGGTGAAGGAACCAGCAGTCCTTACCAAA\nAATGATCCCAGGCTCAGGACAGACTTTGAAGAAGCAATATTCTCTAAGTATGTAGGCAAC\nAAGATCACTGATGTGGATGAGTACATGAAAGAGGCAGTGGATCATTACGCTGGCCAACTC\nATGTCTCTAGACATCAACACAGAACAAATGTGCTTGGAGGACGCCATGTACGGCACCGAT\nGGCCTGGAAGCACTTGACTTGACCACTAGTGCTGGATACCCTTATGTAGCAATGGGAAAG\nAAAAAGAGAGACATCTTGAATAAGCAGACTAGAGACACCAAGGAAATGCGGAGACTCTTA\nGATACTTATGGAATTAACTTACCGCTTGTAACATATGTTAAAGATGAACTAAGGTCAAAA\nACTAAGGTGGAGCAGGGAAAATCCAGATTGATTGAAGCCTCCAGTTTGAATGATTCAGTG\nGCCATGAGAATGGCATTTGGAAATCTCTATGCAGCATTTCACAAAAACCCAGGAGTTGTC\nACTGGCAGTGCAGTTGGTTGTGATCCAGATCTATTTTGGAGCAAGATCCCAGTGCTAATG\nGAAGAGAAGCTCTTTGCTTTTGACTACACAGGTTATGATGCATCACTCAGCCCGGCCTGG\nTTTGAGGCACTCAAAATGGTGCTAGAGAAAATCGGATTTGGGGACAGGGTGGATTATATT\nGATTACCTCAACCATTCCCACCACCTGTACAAAAACAAAACTTATTGCGTAAAAGGCGGC\nATGCCATCTGGCTGCTCAGGCACATCAATTTTTAACTCAATGATTAACAACTTAATCATT\nAGGACACTCCTACTGAAAACCTACAAGGGCATAGATTTAGATCACCTAAAGATGATTGCC\nTATGGTGATGATGTAATTGCTTCCTACCCCCATGAGGTTGATGCTAGTCTCCTAGCCCAA\nTCAGGAAAAGACTATGGACTAACCATGACTCCAGCAGACAAGTCAGCTACCTTTGAAACA\nGTCACATGGGAGAATGTAACATTCTTGAAAAGATTCTTTAGAGCGGATGAGAAGTATCCC\nTTCCTCATACATCCAGTAATGCCAATGAAGGAGATTCATGAATCAATTAGATGGACAAAG\nGATCCCAGAAACACACAGGATCACGTGCGCTCATTGTGCCTATTGGCCTGGCACAACGGC\nGAAGAAGAATACAACAAGTTCTTAGCTAAAATCAGGAGTGTGCCAATTGGGAGAGCTTTA\nTTGCTCCCAGAGTACTCTACATTGTACCGCCGTTGGCTCGACTCTTTTTAGTAACCCTAC\nCTCAGTCGAATTGGATTGGGTCATGCTGTTGTAGGGGTAAATTTTTCTTTAATTCGGGG\n>gi|743485545|gb|KM609478.1| Coxsackievirus A8 isolate CVA8/SZ141/CHN/2012, complete genome\nTTAAAACAGCCTGTGGGTTGCACCCACTCACAGGGCCCACTGGGCGCTAGCACTCTGATT\nCTACGGAATCTTTGTGCGCCTGTTTTATAACCCCCTCCCCCAATGTAATTTAGAAGCAAT\nGCACCAATGATCAACAGCAGGCGTGGCGCACCAGCCATGTCTCGATCAAGCACTTCTGTT\nTCCCCGGACAGAGTATCAATAGACTGCTCGCGTGGTCGAAGGAGAAAACGTCCGTTACCC\nGGCTAACTACTTCGAGAAACCTAGTAGCACCAATGAAGCTGCAGAGCGTTTCGCTCAGCA\nCTTACCCCGTGTAGATCAGGCCGATGAGTCACTGCGTTCCCCACGGGCGACCGTGGCAGT\nGGCTGCGTTGGCGGCCTGCCTATGGGGTCACCCATAGGACGCTCTAATGTGGACATGGTG\nCGAAGAGTCTATTGAGCTAGTTAGTAGTCCTCCGGCCCCTGAATGCGGCTAATCCTAACT\nGCGGAGCGCATACCCTCAAACCAGGGGGTGGTGCGTCGTAACGGGTAACTCTGCAGCGGA\nACCGACTACTTTGGGTGTCCGTGTTTCCTTTTATTCTCTTAATGGCTGCTTATGGTGACA\nATTGAGGAATTGTTACCATATAGCTATTGGATTGGCCATCCGGTGTGTAACAGAGCAATT\nATCTACTTGTTTGCAGGATTTACCCCATTAACGTTCAAATCTCTTAACACACTACAGTAC\nATACTAACCTTGAATACAAGAAAATGGGAGCACAAGTTTCGACTCAAAAGTCTGGTAGCC\nACGAGACTGGCAACATAGCCACTGAAGGGTCCACCATTAACTTTACTAACATCAATTATT\nACAAGGACTCGTACGCCGCCTCGGCTAGCAAACAGGACTTCACCCAGGATCCTACTAGGT\nTTACTAGCCCTGTGCTTGATGCGCTGAGGGAAGTGGCACCTCCATTAAAGTCACCCTCAG\nTGGAAGCGTGCGGATACAGTGATAGAGTAGCGCAGTTGACTGTCGGCAATTCAACAATCA\nCCACACAAGAGGCTGCTAACATAGTCCTTGCTTACGGGGAATGGCCTGAGTACTGTCCCG\nACAAAGACGCCACCGCTGTAGATAAGCCTACACGCCCCGATGTGTCGGTTAATAGATTCT\nACACCATGTCTACGCAAATGTGGCAGGACACCTCGAAAGGGTGGTACTGGAAGTTCCCAG\nATGTTCTTACCAAGACTGGTGTCTTTGGACAAAATGCCCAGTATCACTATTTGTACAGAT\nCTGGATTTTGCATACATGTCCAATGCAACGCTAGTAAATTCCATCAAGGAGCACTGTTAG\nTGGCTGCCATCCCAGAGATGGTGTTAGGATCCAATAGCTCAGATCCCAAGCCCAACACTG\nCAAAGCACCCTGAATTCACTACAACAATGCCAGGTGCTAATGGTGGAATTTTTGAAAATC\nCCTATATCTTGGACATGGGGGTTCCCTTGAGCCAAGCTTTGGTGTTTCCACACCAATGGA\nTCAACCTGCGCACTAACAACTGTGCGACCATTATAGTGCCTTATATTAATGCTGTTCCAT\nTTGATTCAGCCATTAACCACAACAACTTCACGCTAGTCGTAATTCCGATTAGCCCGTTAA\nAATACTGCACAGGAGCGACAACAGCCATCCCTATAACAGTAACGATAGCCCCATTAAATT\nCTGAATTTTGTGGGTTGAGGCAAGCTACATCGCAGGGAATACCAGTGGAGCTAAAACCCG\nGCACCAATCAATTTTTGACAACTGATAACGAAGTCTCCGTACCAATCTTACCTGGTTTCC\nAGCCTACACCGGTTATACATATACCAGGGGAGGTGAACAACCTCCTGGAGCTCTGCCAGG\nTTGAATCTATCTTGGAGGTCAATAATGTGACTGGACAAGAAGGGATAAACCGACTCCTTA\nTCCCAGTTTCTACACAAAGTGACAAGGATACTTTGTGTGCATCACTCAGAGTCGATCCAG\nGTAGGGACGGACCGTGGCAATCTACTTTAGTTGGGCAAATATGTAGGTATTACACCCAGT\nGGTCTGGTTCATTAGAGATCACATTCATGTTTACTGGTTCATTCATGGCAACCGGTAAAA\nTGCTGATAGCTTACTCCCCGCCTGGGAGTGCGCAACCAACAACAAGAGACCTGGCAATGC\nTCGGCACGCACGTAGTGTGGGATTTTGGGTTGCAATCATCTATTACTCTTGTGATCCCAT\nGGATCAGCAACACACACTTCAGAACAGGCAAGGTGGGTGGTTACTTTGATTACTATGCGT\nCTGGTATAGTAACTATTTGGTATCAGACAAACTTCGTCGTGCCCCCCGACACGCCGAGTC\nAGGCTCATATAATAGCGTTGGGAGCTGCCCAGAAGAATTTCACGCTTAAACTGTGCAAGG\nATACAGATGAGGTAACACAACAAGCAGTGTTGCAGGGGGACCCCATTGAAGACATAATAA\nCTAGCACAGTCTCCCGCACATTGCAGCAAATTAGCACTCCAACACATAGCACTACTGCAG\nCAAACACCTCTGTGAGTAACCATAAGATAGGCACTGGAGATGTTCCAGCTCTCCAAGCTG\nCGGAGACAGGTGCTACCTCTAACGCCTCGGATGAGAACATGATCGAGACACGCTGCGTGC\nTAAATCGCAATGGAGTCGTGGAAACCAGTCTGGACCACTTCTTCTCAAGAGCAGGTCTGG\nTGGGGGTGATCAATGTGCAAGATGGTAGTACACAGAAGGGATTTGAGGTGTGGGATGTGG\nATGTGATGGGGTTTGTACAGCTCAGAAGGAAGTTGGAAATGTTTACATACATGAGATTCA\nATGCTGAGTTTACATTTGTGTCCACACTTGCAGACGGCACGACTCCCAGGGTGATGTTAC\nAGTACATGTATGTTCCACCTGGTGCCCCCAAACCTCAAGAGAGGGATTCATTCCAATGGC\nAAACAGCGACCAACCCGTCAGTGTTCTGCAAAATGAGCGATCCTCCCCCACAAGTCTCTG\nTCCCTTTCATGTCGCCAGCCAGCGCGTACCAGTGGTTCTATGATGGATATCCTACATTTG\nATGATCGACCTGCCACCTCAAATCACCCGTATGGACAGTGCCCTAATAACATGATGGGCA\nCATTTGCAGTGCGATTTGTCAGCAAGACCCCTGCTATACGGGACTTGCGTGTTAGGGTAT\nATATGCGCCTCAAACACGTGCGCGCTTGGGTACCGAGGCCCATACGATCCCAAGCATACA\nTCTTAAAGAACTATCCAAACTATGACGGGACAAATATAACACCAACATCCAAGGACAGGC\nAAAGCATCAAAACGACTGGGAAATTTGGTCAGCAGTCCGGTGCTATTTATGTGGGCAATT\nACAGAGTAGTTAACAGACACCTTGCCACACACAATGACTGGGCCAACTTAGTATGGGAAG\nACAGCTCCAGGGATCTCCTTGTGTCATCCACGACTGCTCAAGGATGTGACATCATTGCTC\nGTTGCAATTGCCAGACTGGAGTGTATTACTGTAACTCCCAAAGAAAACACTACCCAGTTA\nGCTTTTCAAAGCCTAGCCTGATCTATGTGGAAGCTAGTGAGTATTACCCAGCTAGGTATC\nAATCTCACCTTATGCTCGCACAAGGACACTCAGAACCTGGCGATTGTGGTGGTATCCTCA\nGGTGCCAACACGGCGTTGTCGGCATAGTGTCCACTGGTGGTGACGGACTCGTCGGCTTCG\nCAGATGTCAGGGATCTCCTTTGGTTAGATGAGGAGGCGATGGAGCAAGGTGTGTCTGATT\nACATCAAGGGACTCGGTGATGCATTTGGAACTGGCTTCACTGATGCTGTCTCTAGAGAAG\nTGGAGGCCCTTAAAAACCACCTAATTGGTTCTGAAGGAGCTGTTGAGAAAATCCTCAAGA\nATTTGATCAAGTTAATCTCTGCTCTTGTCATTGTGATTAGGAGTGATTATGACATGGTCA\nCCCTTACAGCAACTCTAGCTTTAATCGGGTGTCACGGTAGTCCTTGGGCATGGATTAAAA\nCAAAGACAGCATCTATTTTAGGCATCCCTATCGCTCAAAAGCAGAGCGCCTCYTGGCTTA\nAAAAGTTCAACGATATGGCCAACGCTGCCAAGGGATTGGAATGGGTTTCTAACAAGATCA\nGCAAATTCATCGATTGGCTCAAGGAAAAAATCATACCAGCAGCCAAGGAGAAGGTCGAGT\nTTTTAAATAACTTGAAACAGTTACCACTGCTAGAGAACCAAATCTCTAATCTGGAACAAT\nCTGCTGCCTCACAAGAGGACCTTGAAGTTATGTTTGGGAATGTGTCATATCTAGCTCACT\nTCTGTCGTAAGTACCAGCCACTATACGCTACAGAAGCCAAAAGAGTCTACACTCTAGAGA\nAGAGGATGAACAACTACATGCAGTTCAAGAGCAAACACCGTATTGAACCTGTATGTCTTA\nTTATCAGGGGTTCACCGGGCACTGGGAAGTCTTTAGCAACTGGCATCATTGCTCGAGCGA\nTAGCTGATAAGTATCACTCCAGTGTCTATTCACTCCCACCAGACCCAGACCACTTTGATG\nGGTACAAGCAGCAAGTGGTTACAGTCATGGATGATCTATGTCAAAATCCTGACGGCAAAG\nATATGTCACTGTTTTGCCAAATGGTGTCTACCGTGGACTTCATTCCTCCAATGGCTTCCT\nTAGAAGAGAAGGGGGTCTCTTTCACATCTAAGTTCGTCATTGCATCCACTAATGCTAGTA\nATATCATAGTGCCAACAGTATCTGATGCAGACGCCATTCGCCGCAGGTTCTATATGGATT\nGTGACATTGAAGTAACAGACTCATATAAAACAGACCTGGGTAGGTTGGATGCCGGGCGAG\nCAGCCAAATTGTGTTCTGAGAACAACACAGCAAATTTCAAGCGTTGCAGCCCATTAGTGT\nGTGGAAAGGCTATTCAATTAAGAGATAGGAAATCTAAGGTCAGATACAGCGTGGACACAG\nTGGTCTCTGAACTCATAAGAGAGCATAATAACAGATCCGCCATTGGTAACACAATTGAGG\nCTTTGTTCCAGGGCCCACCCAAATTTAGACCCATAAGGATTAGTCTTGAAGAAACGCCAG\nCTCCAGATGCTATTAGTGATCTTCTCACTAGTGTGGATAGCGAAGAGGTACGTCAATACT\nGTAGGGATCAAGGTTGGATTATTCCGGAAACCCCTACAAATGTTGAACGACACCTCAACA\nGAGCTGTGTTGATTATGCAATCCATCGCCACGGTAGTGGCGGTTGTCTCATTGGTGTACG\nTCATCTATAAACTCTTTGCTGGGTTCCAGGGCGCATATTCTGGTGCCCCCAAGCAAACGC\nTTAAGAAACCTGTTCTCCGCACAGCAACAGTGCAGGGTCCAAGCCTTGATTTTGCCCTAT\nCACTATTGAGAAGAAACATCAGGCAAGTGCAGACAGATCAAGGGCACTTCACCATGCTGG\nGTATCAGAGATCGCTTGGCTATCCTCCCGCGACATTCTCAACCTGGAAGGACTATCTGGG\nTGGAACACAAACTCGTGAACGTCCTGGATGCTATCGAGCTGGTGGATGAACAAGGGGTCA\nACTTAGAGCTGACCTTAATCACCCTCGACACCAATGAGAAATTCAGGGATATCACCAAGT\nTCATTCCAGAAACCATTAGTGGTGCCAGCGATGCCACCTTAGTGATCAATACAGAGCACA\nTGCCCTCAATGTTTGTGCCAGTAGGTGATGTTGTACAGTATGGCTTCCTAAATCTCAGCG\nGGAAACCGACTCATCGCACTATGATGTATAACTTCCCTACTAAGGCAGGACAATGTGGAG\nGGGTAGTCACATCAGTTGGAAAGATCATTGGCATTCATATAGGAGGTAATGGTAGGCAGG\nGATTCTGTGCGGGACTCAAGAGAAGCTACTTTGCTAGTGAACAGGGAGAGATCCAATGGG\nTTAAACCTAACAAAGAAACAGGAAGACTCAACATCAATGGACCAACTCGCACCAAGCTCG\nAGCCTAGTGTGTTTCATGATGTCTTTGAGGGTGACAAGGAGCCAGCAGTCTTGCATAGTA\nAGGACCCCCGCCTTGAGGTGGACTTCGAGCAAGCATTGTTCTCCAAGTACGTGGGGAACA\nCACTACACGAACCTGATGAGTATATCAGGGAGGCAGCCCTCCACTATGCGAACCAATTAA\nAGCAGCTAGACATAAATACCTCCCAGATGAGCATGGAGGAGGCCTGTTATGGCACAGAAA\nACCTTGAGGCTATTGACCTTCACACTAGTGCGGGATACCCCTATAGCGCGCTGGGAATAA\nAAAAGAGGGATATCTTAGACCCCATTACCAGAGATGTGAGCAAGATGAAGTTCTATATGG\nATAAGTACGGTCTTGACCTCCCTTACTCCACCTATGTCAAAGATGAACTTCGCTCAATAG\nATAAGATTAAGAAGGGGAAGTCTCGCTTGATTGAAGCTAGCAGCTTGAATGACTCGGTCT\nACCTTAGAATGGCCTTTGGGCACCTCTATGAAGCTTTCCATGCGAACCCTGGCACTGTGA\nCTGGCTCAGCTGTGGGGTGTAACCCAGATGTATTTTGGAGCAAGCTACCAATCCTGCTTC\nCTGGTTCCCTCTTCGCTTTTGACTACTCAGGTTACGATGCTAGCCTCAGCCCAGTTTGGT\nTCAGAGCGTTGGAATTAGTCCTTAGAGAGATAGGTTATGGTGATGAGGCAGTCTCACTCA\nTTGAAGGAATCAACCATACACACCATGTGTACCGTAACAAAACCTACTGCGTACTTGGTG\nGAATGCCCTCAGGTTGCTCAGGGACATCCATCTTCAACTCAATGATTAATAACATCATCA\nTCAGAGCACTACTTATTAAAACATTCAAGGGCATTGATCTGGATGAACTCAACATGGTTG\nCCTACGGGGACGATGTGCTCGCTAGTTACCCCTTTCCAATTGACTGCCTGGAGCTAGCAA\nAGACAGGTAAGGAGTATGGCCTAACCATGACCCCTGCAGACAAGTCCCCTTGCTTCAATG\nAAGTTAATTGGGAAAATGCAACCTTCCTCAAGAGAGGCTTCTTGCCTGATGAGCAATTCC\nCGTTTTTGATCCACCCCACCATGCCAATGAAGGAGATTCATGAATCCATTCGGTGGACCA\nAGGATGCACGCAATACTCAAGATCACGTGCGGTCTCTATGTCTGTTGGCATGGCATAACG\nGTAAGCAAGAATATGAAAAATTTGTGAGCTCAATTAGATCCGTCCCAGTAGGAAAAGCAT\nTGGCAATCCCCAACTATGAAAATCTGAGACGTAATTGGCTCGAATTGTTTTAGAGGTTGG\nACAAACGACTCAACCCCACCAGAAATCTGGTCGTGAATGTGACTGGTGGGGGTAAATTTG\nTTATAACCAGAATAGC\n" }, { "path": "tests/input/TestDifficultSampleNames/RunInfo.xml", "content": "\r\n\r\n \r\n 000000000-AEF96\r\n M04004\r\n 150821\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n" }, { "path": "tests/input/TestDifficultSampleNames/SampleSheet-inline-commas-strings.csv", "content": "[Header],,,,,,,,,\r\nIEMFileVersion,4,,,,,,,,\r\nInvestigator Name,Adrianne,,,,,,,,\r\nExperiment Name,Zika run,,,,,,,,\r\nDate,6/27/2016,,,,,,,,\r\nWorkflow,GenerateFASTQ,,,,,,,,\r\nApplication,FASTQ Only,,,,,,,,\r\nAssay,Nextera XT,,,,,,,,\r\nDescription,Samplesheet with inline commas and strings,,,,,,,,\r\nChemistry,Amplicon,,,,,,,,\r\n,,,,,,,,,\r\n[Reads],,,,,,,,,\r\n101,,,,,,,,,\r\n101,,,,,,,,,\r\n,,,,,,,,,\r\n[Settings],,,,,,,,,\r\nReverseComplement,1,,,,,,,,\r\nAdapter,CTGTCTCTTATACACATCT,,,,,,,,\r\n,,,,,,,,,\r\n[Data],,,,,,,,,\r\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\r\n\"Zika \\\"seedstock_1 (in K562, 5ng)\",,,,N705,GGACTCCT,S507 ,AAGGAGTA,,\r\n\"Zika seedstock_2 (in K562, 5ng)\",,,,N706,TAGGCATG,S507 ,AAGGAGTA,,\r\n\"Zika 'seedstock_3 (in K562, 5ng)\",,,,N707,CTCTCTAC,S507 ,AAGGAGTA,,\r\n\"Zika seedstock_4 (in K562, 5ng)\",,,,N710,CGAGGCTG,S507 ,AAGGAGTA,,\r\nK562 (5ng),,,,N714,GCTCATGA,S507 ,AAGGAGTA,,\r\nNegative control (water),,,,N715,ATCTCAGG,S507 ,AAGGAGTA,,\r\n\" Zika seedstock_7 (in K562, 10pg)\",,,,N705,GGACTCCT,S508 ,CTAAGCCT,,\r\n\"Zika seedstock_8 (in K562, 10pg)\",,,,N706,TAGGCATG,S508 ,CTAAGCCT,,\r\n\"Zika seedstock_9 (in K562, 10pg)\",,,,N707,CTCTCTAC,S508 ,CTAAGCCT,,\r\n\"Zika seedstock_10 (in K562, 10pg)\",,,,N710,CGAGGCTG,S508 ,CTAAGCCT,,\r\n\"Zika seedstock_1 (in K562, 5ng)_HS\",,,,N714,GCTCATGA,S513,TCGACTAG,,\r\n\"Zika seedstock_2 (in K562, 5ng)_HS\",,,,N714,GCTCATGA,S515,TTCTAGCT,,\r\n\"Zika seedstock_3 (in K562, 5ng)_HS\",,,,N714,GCTCATGA,S516,CCTAGAGT,,\r\n\"Zika seedstock_4 (in K562, 5ng)_HS\",,,,N714,GCTCATGA,S517,GCGTAAGA,,\r\n\"Zika seedstock_7 (in K562, 10pg)_HS\",,,,N715,ATCTCAGG,S513,TCGACTAG,,\r\n\"Zika seedstock_8 (in K562, 10pg)_HS\",,,,N715,ATCTCAGG,S515,TTCTAGCT,,\r\n\"Zika seedstock_9 (in K562, 10pg)_HS\",,,,N715,ATCTCAGG,S516,CCTAGAGT,,\r\n\"Zika seedstock_10 (in K562, 10pg)_HS\",,,,N715,ATCTCAGG,S517,GCGTAAGA,,\r\n" }, { "path": "tests/input/TestDifficultSampleNames/SampleSheet.csv", "content": "[Header],,,,,,,,,\r\nIEMFileVersion,4,,,,,,,,\r\nInvestigator Name,James,,,,,,,,\r\nExperiment Name,EBoV HS ,,,,,,,,\r\nDate,8/18/2015,,,,,,,,\r\nWorkflow,GenerateFASTQ,,,,,,,,\r\nApplication,FASTQ Only,,,,,,,,\r\nAssay,Nextera XT,,,,,,,,\r\nDescription,,,,,,,,,\r\nChemistry,Amplicon,,,,,,,,\r\n,,,,,,,,,\r\n[Reads],,,,,,,,,\r\n101,,,,,,,,,\r\n101,,,,,,,,,\r\n,,,,,,,,,\r\n[Settings],,,,,,,,,\r\nReverseComplement,0,,,,,,,,\r\n,,,,,,,,,\r\n[Data],,,,,,,,,\r\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\r\ndifficult/\\//value+for'` -〠데이터Sénégalsample_name0.6,GID/14/E021,,,N702,CGTACTAG,S502,CTCTCTAT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name0.5,GID/14/E021,,,N702,CGTACTAG,S503,TATCCTCT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name0.4,GID/14/E021,,,N702,CGTACTAG,S504,AGAGTAGA,,\r\ndifficult/\\//value+for'` -Sénégalsample_name0.3,GID/14/E021,,,N702,CGTACTAG,S505,GTAAGGAG,,\r\ndifficult/\\//value+for'` -Sénégalsample_name0.1,GID/14/E021,,,N702,CGTACTAG,S508,CTAAGCCT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name4.6,GID/14/E021,,,N703,AGGCAGAA,S502,CTCTCTAT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name4.5,GID/14/E021,,,N703,AGGCAGAA,S503,TATCCTCT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name4.4,GID/14/E021,,,N703,AGGCAGAA,S504,AGAGTAGA,,\r\ndifficult/\\//value+for'` -Sénégalsample_name4.3,GID/14/E021,,,N703,AGGCAGAA,S505,GTAAGGAG,,\r\ndifficult/\\//value+for'` -Sénégalsample_name4.1,GID/14/E021,,,N703,AGGCAGAA,S508,CTAAGCCT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name20.6,GID/14/E021,,,N704,TCCTGAGC,S502,CTCTCTAT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name20.5,GID/14/E021,,,N704,TCCTGAGC,S503,TATCCTCT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name20.4,GID/14/E021,,,N704,TCCTGAGC,S504,AGAGTAGA,,\r\ndifficult/\\//value+for'` -Sénégalsample_name20.3,GID/14/E021,,,N704,TCCTGAGC,S505,GTAAGGAG,,\r\ndifficult/\\//value+for'` -Sénégalsample_name20.1,GID/14/E021,,,N704,TCCTGAGC,S508,CTAAGCCT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name48.6,GID/14/E021,,,N705,GGACTCCT,S502,CTCTCTAT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name48.5,GID/14/E021,,,N705,GGACTCCT,S503,TATCCTCT,,\r\ndifficult/\\//value+for'` -Sénégalsample_name48.4,GID/14/E021,,,N705,GGACTCCT,S504,AGAGTAGA,,\r\ndifficult/\\//value+for'` -Sénégalsample_name48.3,GID/14/E021,,,N705,GGACTCCT,S505,GTAAGGAG,,\r\ndifficult/\\//value+for'` -Sénégalsample_name48.1,GID/14/E021,,,N705,GGACTCCT,S508,CTAAGCCT,,\r\n" }, { "path": "tests/input/TestFastaFetch/JQ610675.1.fa", "content": ">JQ610675.1 Orungo virus isolate UGMP 359 segment 1, complete sequence\nGTATAATTAGGAATGGTCATCACTGTGGAAGGTGCGTGGCTGGTGAGACGGGCGTTGCAACGTTTTTTGA\nAGTTCAGTAAAATCGACGGGGAATCAGCAGTTTATGAGTTCTATAGGTATTCAAGTAATATTCGTGAAAT\nAAGAAGGAAGCATGGGACGCGTTATAAAATGCATGATGAAGAGTTGGAGCGGAGGCGTGATTCGGGCAAA\nCTGCGTTTTAAAGGTATGCAAGTTGTGGTAGAGTCGACTTGGATGGAGATTTTAGGGAAGGGACGTACGA\nCGGACGAAATCGAGATATTCAGAAGTTCGATTTTATCGTTGGATGAACTGAATCCGGAAGAAGAATTTCT\nGCGCAATTATGCGAGTTCGGACAAGGAACATCCATCCTACTTGTTTGTTCGGGGGCGGGCGGTCAATGAG\nATGCAGATTTATGGCGACATGCCGATAAAAGCGTGGTTGAGCTTTTTAGTAGAATGTGAGGTTGAATATG\nGGTACAAACTCTTCGGAATGGAAGTTGCGAGATCGTTCGTTCAGAGCTTTGGATCTCCGTTTCACCAGAA\nCTCGCGTGATCTATCACAGATTGACGATATGGCGCCTGCTTTTACGTCACCTTTATTATTTGAAATGTGT\nTGTATGACATCAATTCTCGAAATTAATATACGCATGCGTATGCTGGAGGAGAGGGTTGCAACCCTAAAAT\nTTGGTGAGCGGGAGATCGACCCACTTGAAGTACTAAAAGAATTCTTCCGAATCTGCATTCCGCATCCGAA\nAAAGATTAATAATATGTTGAGAGCTCCATACTCATGGTTCGTCAAGCTGTGGGGCGTATCGTATCATGAG\nCCAATAGTCCTGACGGCGAGGGGCGGCGAGGATAAGAACTCGAAAGACATATTCTTTACGGGATTTCACA\nGAGTCAAGAATCCATACTCAATAATGTTGAAAAAATCGAGGTTTTTTAAGAAATCTTTAGACGAGAATAT\nCAGCAAAGTGAAAGAAGCGATAGACTATTCAAACTCGTTGACGGGGATGTCTTTAGGGCTGCCCGTATTT\nCTATCCATGCTACAGAATGTGTACGACACTGAGTTTAATCCGACTATGGTTCAACACGTGTTACTAGCGT\nCGTTCTTGTTGAGTATCCAAACAATAACTGGCTATGGACGCGCTTGGGTGAAAAATGTGTCAAGCGATAA\nCGACACTCAAATGCGCCCGGCGGAGGACAACTTCATTGATCGAGTTGCTAAGCAAACGGAGATTAATTTT\nATACAGGCGTATGAAGAGGCGTTGGGGCACGGAGAAGATATCGTTAAGCCAGAAGACATGTTTACCTCCA\nTTTTGCGTTTGGCAAGAAATACAAGTTCCGGCTTCTCTACTGCTGTTGACGTTTATAAACGATTCGGTCC\nAAAGTCGGGAGGGAGAGGAGAACGCGTTAAGATAACATCAAGAATTAAAGCATTAGTTATCTTCACAAAG\nGGCCATGAAATATTTACAGCTGAAAATCTCGCGAAAAGATATGATACGGAGGAAGATTACCAGACTAAAG\nGGTCACGGGATGTACCTATCAAAGCAACGCGGACGATTTATTCAATAAACCTCTCCATCTTGATCCCGCA\nGCTGATCCTAACTTTACCGTTGAATGAATATTTTGCCCGGTTCGGAGGATCAACTGCACCTGACTCACGT\nAGCCTAGGGGGTAAGGTGATTATCGGAGATCTAGAAGCAACGGGATCACGGACGATCGATGCGGCAGATA\nCGTTTAGAAATTCGTCCGACCCAGAAATTTTCACAATAGCGATCGATTATTCGGATTACGATCAACATTT\nGACGGTTTTTAACTTCAGGAACGGTATGCTGGAAGGAATTCGCTCTGCGATGAAGAGATATAAAGAGTTG\nAGGTATGATGGATACACGTTGAATGAATTGATTGAATTCGGGTATGGGGAGGGGAGAATTGTTAATTCGA\nAATGGAACGGAAAGAGGCGGGTCAAATCTGTACGAATGAGCGATTATATGGCATTGAGTGAAAGTCAACG\nCGCTCAGGGCACTTTCAAGCCGCCGCAGGGAGTGAGACCGGTTAGTTCAATGCAAGTGTTCGATTCAGTG\nGGTGAGGCATCTGGAGGGGATACTCTCCTCATCTCGCCCACTGACGGATCGGATTTAGCAACCGTCAACA\nCGCATTTGTCGGGTGAAAATTCAACGTTAGTTGCTAACTCTTTGCATAATATGGCTATCGGACGTATCAT\nACAAGAAGAGATCAGAAAGAACCATCGAGCGGCTTTTACCTTTGAATCTGAGCAGTACGTTGGAGATGAT\nACGTTACTTTATGCAAAGTTGAACACATTAAACCATGAAATTTTTGATAAAGCGATTGATACCATCTTCG\nATACTGTGGGAAAGTGCGGACATGTGGCATCGGCAGCGAAAACCCTTATCGCTCCTTTCTCTGTTGAAAA\nAACTCAGACTCATGCGAAGCAAGGAATTTACATTGCGCAGGATCGGATGATGATCATCTCTTCAGAGCGT\nAGAAAGGATATCGAGGACGTCCAAGGGTATATGAGATCACAAGTGTCGGTTATGGCGACAAAAGTAAGCC\nGCGGCTTTAGTCATGAACTGGCTCAGCTTGTCTTTATGATGAAGAGCAGCATCGTAGGCTTTCGTAAACT\nGAAGCGAACTGTGGTGGAGGATGGTGTATACCGTGATCGCGCGTTGGATTCGGAAGATGAGGATGGCTTC\nACTTTGATGCAGATCCGTGATCCGTTGGTCGCCTTCTACCCTGCTGAGTGGAACGGCTATGGCATGCATC\nCAGTCGCTTTGAATATCGTCATGACGGAAGACATGTTTATAGACACGAGTACCATGGTTGAGTTTCAGCA\nTGTAATGCGGCCGCTCCTTCGATTTATGGGTAGGATACCTCCAGTGTGGAATGAAACTAAAGCCGATAAA\nCGTCAGATTTCATCCATAACAAAGATGAGTTTCTTCTCCAAAATGGCTAGACCAGCGGTGAGGGCGGTTC\nTGGCGAATAGTGAACTGTCAGATCAAGTGAGAACATTGCCACTGGGCGACTTTTCGCCTTTCAATCTCTC\nCGCAACAATGATGCACTCAGCATTATTGAAAGAACCACGCGCGCGTGCCCTGCTGACGCCAGCCTACGAA\nAAAGAATTCCAGTCAGAGTTGAATTCAAACCGGGATAGCGAAGTAAATTTCGTCGGGAGGAACATGGAGA\nTCAACACTAATTATATGAAACTGTTCGATGTTGATTTGTCTACGCGAATAGTGGCCAAACAATTTAGTTT\nTCCAGATCAGAATATGTCGTTGCCTTTTTATTTTCAGAAACTCTTGATTGGACATAGACCGGTCGCGCGG\nATGAGAATGACCTATATTGACCGGATTGACCAAATCTTACGGGGAGACGTCGTGATGAGGGGTTTCATCA\nCAGCGAATACTATTATGTCCGTTTTAGAGAAGATTGGCACTGCTCACGCCGTACAGGACTTAACAACAAT\nATTTCAGTTGATGAACATTGAATCTAAGGTGGCGCATAGGCTAGCGGAGTATATCGCTTCTGAAAGGGTA\nAGATTCGACGCGCTCTCGATTGCAAAGAGGGGGATATGCGGGGATGAATTCTCCATGTCGCTGGATGTGT\nGCACGGAACGGTTTGCTGAACGGTTCATGGAACTACCAGCGCAGTTTACTAAAACTGAGAGAGATATAGC\nGATTTTATATGCCGCGCAGCTAACTATGTTGCGCTGTGCGGCTAACCTAGATCTTAGGAAAATTAAGATT\nGGGGTTTCAGCGGATCACGTTAAGAGATTTAAACAAAGACAGGCTAGATTTAAGACTCATCTACCTAAAA\nTGCGTACAGTCACGCGGCTGATAACGCCTGAACGAATCTCCGCACGCCTGGTTCAGCATCAGTTTACATG\nACGCACCACCTAATCAACTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610675.1.fasta", "content": ">JQ610675.1 Orungo virus isolate UGMP 359 segment 1, complete sequence\nGTATAATTAGGAATGGTCATCACTGTGGAAGGTGCGTGGCTGGTGAGACGGGCGTTGCAACGTTTTTTGA\nAGTTCAGTAAAATCGACGGGGAATCAGCAGTTTATGAGTTCTATAGGTATTCAAGTAATATTCGTGAAAT\nAAGAAGGAAGCATGGGACGCGTTATAAAATGCATGATGAAGAGTTGGAGCGGAGGCGTGATTCGGGCAAA\nCTGCGTTTTAAAGGTATGCAAGTTGTGGTAGAGTCGACTTGGATGGAGATTTTAGGGAAGGGACGTACGA\nCGGACGAAATCGAGATATTCAGAAGTTCGATTTTATCGTTGGATGAACTGAATCCGGAAGAAGAATTTCT\nGCGCAATTATGCGAGTTCGGACAAGGAACATCCATCCTACTTGTTTGTTCGGGGGCGGGCGGTCAATGAG\nATGCAGATTTATGGCGACATGCCGATAAAAGCGTGGTTGAGCTTTTTAGTAGAATGTGAGGTTGAATATG\nGGTACAAACTCTTCGGAATGGAAGTTGCGAGATCGTTCGTTCAGAGCTTTGGATCTCCGTTTCACCAGAA\nCTCGCGTGATCTATCACAGATTGACGATATGGCGCCTGCTTTTACGTCACCTTTATTATTTGAAATGTGT\nTGTATGACATCAATTCTCGAAATTAATATACGCATGCGTATGCTGGAGGAGAGGGTTGCAACCCTAAAAT\nTTGGTGAGCGGGAGATCGACCCACTTGAAGTACTAAAAGAATTCTTCCGAATCTGCATTCCGCATCCGAA\nAAAGATTAATAATATGTTGAGAGCTCCATACTCATGGTTCGTCAAGCTGTGGGGCGTATCGTATCATGAG\nCCAATAGTCCTGACGGCGAGGGGCGGCGAGGATAAGAACTCGAAAGACATATTCTTTACGGGATTTCACA\nGAGTCAAGAATCCATACTCAATAATGTTGAAAAAATCGAGGTTTTTTAAGAAATCTTTAGACGAGAATAT\nCAGCAAAGTGAAAGAAGCGATAGACTATTCAAACTCGTTGACGGGGATGTCTTTAGGGCTGCCCGTATTT\nCTATCCATGCTACAGAATGTGTACGACACTGAGTTTAATCCGACTATGGTTCAACACGTGTTACTAGCGT\nCGTTCTTGTTGAGTATCCAAACAATAACTGGCTATGGACGCGCTTGGGTGAAAAATGTGTCAAGCGATAA\nCGACACTCAAATGCGCCCGGCGGAGGACAACTTCATTGATCGAGTTGCTAAGCAAACGGAGATTAATTTT\nATACAGGCGTATGAAGAGGCGTTGGGGCACGGAGAAGATATCGTTAAGCCAGAAGACATGTTTACCTCCA\nTTTTGCGTTTGGCAAGAAATACAAGTTCCGGCTTCTCTACTGCTGTTGACGTTTATAAACGATTCGGTCC\nAAAGTCGGGAGGGAGAGGAGAACGCGTTAAGATAACATCAAGAATTAAAGCATTAGTTATCTTCACAAAG\nGGCCATGAAATATTTACAGCTGAAAATCTCGCGAAAAGATATGATACGGAGGAAGATTACCAGACTAAAG\nGGTCACGGGATGTACCTATCAAAGCAACGCGGACGATTTATTCAATAAACCTCTCCATCTTGATCCCGCA\nGCTGATCCTAACTTTACCGTTGAATGAATATTTTGCCCGGTTCGGAGGATCAACTGCACCTGACTCACGT\nAGCCTAGGGGGTAAGGTGATTATCGGAGATCTAGAAGCAACGGGATCACGGACGATCGATGCGGCAGATA\nCGTTTAGAAATTCGTCCGACCCAGAAATTTTCACAATAGCGATCGATTATTCGGATTACGATCAACATTT\nGACGGTTTTTAACTTCAGGAACGGTATGCTGGAAGGAATTCGCTCTGCGATGAAGAGATATAAAGAGTTG\nAGGTATGATGGATACACGTTGAATGAATTGATTGAATTCGGGTATGGGGAGGGGAGAATTGTTAATTCGA\nAATGGAACGGAAAGAGGCGGGTCAAATCTGTACGAATGAGCGATTATATGGCATTGAGTGAAAGTCAACG\nCGCTCAGGGCACTTTCAAGCCGCCGCAGGGAGTGAGACCGGTTAGTTCAATGCAAGTGTTCGATTCAGTG\nGGTGAGGCATCTGGAGGGGATACTCTCCTCATCTCGCCCACTGACGGATCGGATTTAGCAACCGTCAACA\nCGCATTTGTCGGGTGAAAATTCAACGTTAGTTGCTAACTCTTTGCATAATATGGCTATCGGACGTATCAT\nACAAGAAGAGATCAGAAAGAACCATCGAGCGGCTTTTACCTTTGAATCTGAGCAGTACGTTGGAGATGAT\nACGTTACTTTATGCAAAGTTGAACACATTAAACCATGAAATTTTTGATAAAGCGATTGATACCATCTTCG\nATACTGTGGGAAAGTGCGGACATGTGGCATCGGCAGCGAAAACCCTTATCGCTCCTTTCTCTGTTGAAAA\nAACTCAGACTCATGCGAAGCAAGGAATTTACATTGCGCAGGATCGGATGATGATCATCTCTTCAGAGCGT\nAGAAAGGATATCGAGGACGTCCAAGGGTATATGAGATCACAAGTGTCGGTTATGGCGACAAAAGTAAGCC\nGCGGCTTTAGTCATGAACTGGCTCAGCTTGTCTTTATGATGAAGAGCAGCATCGTAGGCTTTCGTAAACT\nGAAGCGAACTGTGGTGGAGGATGGTGTATACCGTGATCGCGCGTTGGATTCGGAAGATGAGGATGGCTTC\nACTTTGATGCAGATCCGTGATCCGTTGGTCGCCTTCTACCCTGCTGAGTGGAACGGCTATGGCATGCATC\nCAGTCGCTTTGAATATCGTCATGACGGAAGACATGTTTATAGACACGAGTACCATGGTTGAGTTTCAGCA\nTGTAATGCGGCCGCTCCTTCGATTTATGGGTAGGATACCTCCAGTGTGGAATGAAACTAAAGCCGATAAA\nCGTCAGATTTCATCCATAACAAAGATGAGTTTCTTCTCCAAAATGGCTAGACCAGCGGTGAGGGCGGTTC\nTGGCGAATAGTGAACTGTCAGATCAAGTGAGAACATTGCCACTGGGCGACTTTTCGCCTTTCAATCTCTC\nCGCAACAATGATGCACTCAGCATTATTGAAAGAACCACGCGCGCGTGCCCTGCTGACGCCAGCCTACGAA\nAAAGAATTCCAGTCAGAGTTGAATTCAAACCGGGATAGCGAAGTAAATTTCGTCGGGAGGAACATGGAGA\nTCAACACTAATTATATGAAACTGTTCGATGTTGATTTGTCTACGCGAATAGTGGCCAAACAATTTAGTTT\nTCCAGATCAGAATATGTCGTTGCCTTTTTATTTTCAGAAACTCTTGATTGGACATAGACCGGTCGCGCGG\nATGAGAATGACCTATATTGACCGGATTGACCAAATCTTACGGGGAGACGTCGTGATGAGGGGTTTCATCA\nCAGCGAATACTATTATGTCCGTTTTAGAGAAGATTGGCACTGCTCACGCCGTACAGGACTTAACAACAAT\nATTTCAGTTGATGAACATTGAATCTAAGGTGGCGCATAGGCTAGCGGAGTATATCGCTTCTGAAAGGGTA\nAGATTCGACGCGCTCTCGATTGCAAAGAGGGGGATATGCGGGGATGAATTCTCCATGTCGCTGGATGTGT\nGCACGGAACGGTTTGCTGAACGGTTCATGGAACTACCAGCGCAGTTTACTAAAACTGAGAGAGATATAGC\nGATTTTATATGCCGCGCAGCTAACTATGTTGCGCTGTGCGGCTAACCTAGATCTTAGGAAAATTAAGATT\nGGGGTTTCAGCGGATCACGTTAAGAGATTTAAACAAAGACAGGCTAGATTTAAGACTCATCTACCTAAAA\nTGCGTACAGTCACGCGGCTGATAACGCCTGAACGAATCTCCGCACGCCTGGTTCAGCATCAGTTTACATG\nACGCACCACCTAATCAACTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610676.1.fa", "content": ">JQ610676.1 Orungo virus isolate UGMP 359 segment 2, complete sequence\nGTATAATTGATCCGCGATGGCTTTCGAGCGTACGGTAGCCTTAACAAGAGAGTTCGCAAATGAAACAAGA\nCAGCATTTTGGGAAGTTTGATATAGTTGTAAACACGGAAAGCAGTATTGAGGACGAAGCAACGGGTGAGT\nGGGAGTTCGCACGAAGTGATGGGCGGCTTGGCATCTATGAAGAATTGCATAATAGCATCGCTTATAAACA\nTTATACGGCGATACTAAAAGGGCCGGAAAATTATTTGAATATTCCGCAGATTTTTGAGTCGAAAATCTAT\nAAGAATTTGAATAGGGATGATCTATTGGCGAGATATGATTATTCACAAATACTAAGATTCCGAGATAGTA\nAGATAGCGGGCCGATTGAGGATGCAGACGTATTTCGGGGACGTGCATGTAAGTGCGGGACTGATAGATTG\nTGTAGCGATGGTTCGTGAGCCTATTAGAAGGGAAGGGTGTCAGCATATGATGGTACGTAGTTTTGATTTG\nATGAATGCGGGCCAGTTTTTCGATGTTCATGCGCCGAAGATCCACGCGTTTGATGACACGGTGATAGTTG\nAAAGCATGGACATCGAAAACGGAGTATGGCGCGTAAAGGCGGGTGGCGTAGGTTTGAAAACGCTGCAGGA\nAAAAGCGGAAGGAATACTCGGAGATTCAGTGTTAGACTTAGTCCACAACTATCTCAGCCAAAAGTGGGAC\nGCAGGTTATGTGGCCGCGAAGTTGCTGAGGTTTGATGAGACATATAAATTTCATCCAATTCATGAGGTGG\nGAATTTTCAACACATTGATGATACGCATGGGTCAACTCGATGACGCGTATAGGGATGGGTTCTTCGATTA\nTGACGAGATTCACGCTCAATTGATGAGGGATGTGACTTTTCAGTACCCAGAAGGTAAGCCAGTCTTTCGG\nAGAGATGGCCAATTCTTTAAAAACCTAGTGCAGTATTCGGGACGGGCGAAGATTGGGTATGAGACGTATT\nTACCAGACAGGGAATTGTGGACTGAATGGCGAACGAGATCATCCGTGCAAGATGTTGTACCCAAGTATAT\nGGAATGGTTGATAGGTAGATTACAGTTGGGGAAAATGCTTAAAATAATGTCGGAATTACCAGCGGATGTT\nACGATGCCCAACTATCTTTTGAAAGCCATTACATATAAATCGAGTGTATATGTTAAGAGATTGATACTCA\nCGTACATCGCTTTACGAATGACGTTTGGACGGTGTCCAGTAAACAAAAAAGGAACGCTTGCCTCATCAGT\nCTTAGGTTTTCTACACGCGGTTATTCCGAATCTGGAGGAATTTCTGAGGAAAGCGGGAATAACGGATGAA\nCTATGTGTTAAAATGGAGTTTACGCCGAGACTTACTGTGATGGAGAGAGAGGATAGGAAGTCAGACAGAT\nACGCCGTTGTCTTGCAAGTTTATAGGGAGAGGAAGCTGGAGGTTTTTACGCCTATAGACTCAGACTTGTT\nCGAAGATCGGAAAAAGTACTATGACGAGATCTTGAAAGATAAAAGATGGCGTGGAGAAGAGACTGATTAT\nTTTTTTAAAGACTCAGGGATACACCGGTCCCAGGTGGCTGGGTTGAGCGCAGAGCAGCTCACGTTGAAAA\nAGTTAGGACGCGACTCAGATTTCAACGACCCTAAACGGTTCGTTTCATACAGATATAGATATGTATCAGT\nTAAAGCGGGAGATATCTATGCAGAAGGGGAGAGCGTTATAACGGGACCATTATTGACACTGATTCCACAT\nGCCTACGAGTTCGGACGAGTATCTTTGATTGCGGGGCAGTCTCGAGATCAATCAAAGTTGGATAATGTCC\nCAGTCTACCGTGACCACATGAAATCCTTGGAGTTAAATGGCGTCGAAGTTGGCTATGACACTTGGTGTCC\nGTCGGGGCGTGCAGTACAAGTTAACTTGGAGTTGATATCTACCATCCTGTATAACGCGTTCAAACGTCCC\nATCGTTAAGGGAGCATTATGTCACTTCGGTATGTGGGAATTTTATAACCCGAGACGTCCCGCGTATGAGT\nCAGTAGACGTGACAATCATGAATGCGATCTCGGATATCACTGGGAGCAAAAGATGGGCATATCAGGAAAT\nTCAAGATTGGTTGGCGAGATTTATTAAGGGGTCACGGGTTGACATGGTGACACACCGCTTCCACGGGGTA\nACGAAGAAGCCAACAACTCGAGGTGAGATATGGATCTGGAACCTACTACTAGTTTTGATCTCAAATCCCA\nGTCTGGTGGTATCACAAACGGATAAATTTCCCTTATGGGTTTGCGCCTCTGATGGCTTACACCTGATTAG\nTACGGGAGTGAGGCATACCGATCATTTTAGACTTTGGGAGTGGCTACCATATACCGAAAAAATTGGGAAC\nGACGATTATATGTCGGTTCTCGCCACAGATAGAGAGTTGCGGCTTTTCGAAATCGCGTTGGAATACTTCG\nAGACTATACGCATTGGATATAGGAGAGATGAATGGACGCATTTGAAATCGAACATGTTTAATACCTGGCT\nGGGGACGCATTGTGGGGGTGTAGGGGACGGGATGATATTGTTTGACCCGGTGAGATTACCATCCCCGAGC\nAGCGTCCTTTATTTGATCTGTTCGCATAACTCAACTTTAGAAGGAATGATGTATTTACTACATGATATAT\nACGGGAAGATCGTTGAAGAGAATACTGGTACTGTTTTCATAAGGGTACACGCGCGAGGTTGTAAGTGCTC\nGGTGTGCCGAGGGGGTTTACAGGGAGTTGACGTAAAGAATAGGTCAGCTATGCGTGTTCGTAGTATGCCA\nGGGAACATCGGCTTCGATTCAGTCAACCTAATTCTTTCAACATCAACGACGAGCGCGTTTGGGAACTCTT\nACATTTACTTTAAGCTTATTAATCGTTAGTGAGGTGACACTCGCTCCGCGATCACGCAGATAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610676.1.fasta", "content": ">JQ610676.1 Orungo virus isolate UGMP 359 segment 2, complete sequence\nGTATAATTGATCCGCGATGGCTTTCGAGCGTACGGTAGCCTTAACAAGAGAGTTCGCAAATGAAACAAGA\nCAGCATTTTGGGAAGTTTGATATAGTTGTAAACACGGAAAGCAGTATTGAGGACGAAGCAACGGGTGAGT\nGGGAGTTCGCACGAAGTGATGGGCGGCTTGGCATCTATGAAGAATTGCATAATAGCATCGCTTATAAACA\nTTATACGGCGATACTAAAAGGGCCGGAAAATTATTTGAATATTCCGCAGATTTTTGAGTCGAAAATCTAT\nAAGAATTTGAATAGGGATGATCTATTGGCGAGATATGATTATTCACAAATACTAAGATTCCGAGATAGTA\nAGATAGCGGGCCGATTGAGGATGCAGACGTATTTCGGGGACGTGCATGTAAGTGCGGGACTGATAGATTG\nTGTAGCGATGGTTCGTGAGCCTATTAGAAGGGAAGGGTGTCAGCATATGATGGTACGTAGTTTTGATTTG\nATGAATGCGGGCCAGTTTTTCGATGTTCATGCGCCGAAGATCCACGCGTTTGATGACACGGTGATAGTTG\nAAAGCATGGACATCGAAAACGGAGTATGGCGCGTAAAGGCGGGTGGCGTAGGTTTGAAAACGCTGCAGGA\nAAAAGCGGAAGGAATACTCGGAGATTCAGTGTTAGACTTAGTCCACAACTATCTCAGCCAAAAGTGGGAC\nGCAGGTTATGTGGCCGCGAAGTTGCTGAGGTTTGATGAGACATATAAATTTCATCCAATTCATGAGGTGG\nGAATTTTCAACACATTGATGATACGCATGGGTCAACTCGATGACGCGTATAGGGATGGGTTCTTCGATTA\nTGACGAGATTCACGCTCAATTGATGAGGGATGTGACTTTTCAGTACCCAGAAGGTAAGCCAGTCTTTCGG\nAGAGATGGCCAATTCTTTAAAAACCTAGTGCAGTATTCGGGACGGGCGAAGATTGGGTATGAGACGTATT\nTACCAGACAGGGAATTGTGGACTGAATGGCGAACGAGATCATCCGTGCAAGATGTTGTACCCAAGTATAT\nGGAATGGTTGATAGGTAGATTACAGTTGGGGAAAATGCTTAAAATAATGTCGGAATTACCAGCGGATGTT\nACGATGCCCAACTATCTTTTGAAAGCCATTACATATAAATCGAGTGTATATGTTAAGAGATTGATACTCA\nCGTACATCGCTTTACGAATGACGTTTGGACGGTGTCCAGTAAACAAAAAAGGAACGCTTGCCTCATCAGT\nCTTAGGTTTTCTACACGCGGTTATTCCGAATCTGGAGGAATTTCTGAGGAAAGCGGGAATAACGGATGAA\nCTATGTGTTAAAATGGAGTTTACGCCGAGACTTACTGTGATGGAGAGAGAGGATAGGAAGTCAGACAGAT\nACGCCGTTGTCTTGCAAGTTTATAGGGAGAGGAAGCTGGAGGTTTTTACGCCTATAGACTCAGACTTGTT\nCGAAGATCGGAAAAAGTACTATGACGAGATCTTGAAAGATAAAAGATGGCGTGGAGAAGAGACTGATTAT\nTTTTTTAAAGACTCAGGGATACACCGGTCCCAGGTGGCTGGGTTGAGCGCAGAGCAGCTCACGTTGAAAA\nAGTTAGGACGCGACTCAGATTTCAACGACCCTAAACGGTTCGTTTCATACAGATATAGATATGTATCAGT\nTAAAGCGGGAGATATCTATGCAGAAGGGGAGAGCGTTATAACGGGACCATTATTGACACTGATTCCACAT\nGCCTACGAGTTCGGACGAGTATCTTTGATTGCGGGGCAGTCTCGAGATCAATCAAAGTTGGATAATGTCC\nCAGTCTACCGTGACCACATGAAATCCTTGGAGTTAAATGGCGTCGAAGTTGGCTATGACACTTGGTGTCC\nGTCGGGGCGTGCAGTACAAGTTAACTTGGAGTTGATATCTACCATCCTGTATAACGCGTTCAAACGTCCC\nATCGTTAAGGGAGCATTATGTCACTTCGGTATGTGGGAATTTTATAACCCGAGACGTCCCGCGTATGAGT\nCAGTAGACGTGACAATCATGAATGCGATCTCGGATATCACTGGGAGCAAAAGATGGGCATATCAGGAAAT\nTCAAGATTGGTTGGCGAGATTTATTAAGGGGTCACGGGTTGACATGGTGACACACCGCTTCCACGGGGTA\nACGAAGAAGCCAACAACTCGAGGTGAGATATGGATCTGGAACCTACTACTAGTTTTGATCTCAAATCCCA\nGTCTGGTGGTATCACAAACGGATAAATTTCCCTTATGGGTTTGCGCCTCTGATGGCTTACACCTGATTAG\nTACGGGAGTGAGGCATACCGATCATTTTAGACTTTGGGAGTGGCTACCATATACCGAAAAAATTGGGAAC\nGACGATTATATGTCGGTTCTCGCCACAGATAGAGAGTTGCGGCTTTTCGAAATCGCGTTGGAATACTTCG\nAGACTATACGCATTGGATATAGGAGAGATGAATGGACGCATTTGAAATCGAACATGTTTAATACCTGGCT\nGGGGACGCATTGTGGGGGTGTAGGGGACGGGATGATATTGTTTGACCCGGTGAGATTACCATCCCCGAGC\nAGCGTCCTTTATTTGATCTGTTCGCATAACTCAACTTTAGAAGGAATGATGTATTTACTACATGATATAT\nACGGGAAGATCGTTGAAGAGAATACTGGTACTGTTTTCATAAGGGTACACGCGCGAGGTTGTAAGTGCTC\nGGTGTGCCGAGGGGGTTTACAGGGAGTTGACGTAAAGAATAGGTCAGCTATGCGTGTTCGTAGTATGCCA\nGGGAACATCGGCTTCGATTCAGTCAACCTAATTCTTTCAACATCAACGACGAGCGCGTTTGGGAACTCTT\nACATTTACTTTAAGCTTATTAATCGTTAGTGAGGTGACACTCGCTCCGCGATCACGCAGATAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610677.1.fa", "content": ">JQ610677.1 Orungo virus isolate UGMP 359 segment 3, complete sequence\nGTATATATTCCTTCGCGATGGCGCATGCGGATGCTAAAGGAAGTGATCCGGAGAGAGAGGCGTTGAGGAA\nGAACCCTTATCTAGATGGAGACGTCTTGGGAACCGCAGGCGGCCAAGTTTTGTCGGTTTTCGCATTGACC\nGAAATTTTACAAAAAGTAAGACAGACGCAAGCTGAACTGGCCGCACACGCAATCGATTTGGATGGACCAG\nTCCCTGAGATCACCGGGGTTATTAAGAAGATAGCGGAGTTAGTTGACACCGTTCCATATGAAGTGCGCGA\nTTCACCACCTATAAGCTATAAGACTTTAAGCATGCAATCGCGCGACTTTGTCATCCAGGTGGACCAGTAT\nTACGAACAGATTTCGCAAATTGGAGGAGACGTCGGGGAGGACGAGCCGATGGAGTTCTATAAAACAATGC\nTAGAAAAGGTACGCTATTTAAGGAAGAGTGGAGCATTCATTTTGAGAGGTATTAAAACACGAGACTATAG\nGGGTAATGAAGTGGCGGAACCAGAAGCTTTAGGAGTCGAATTTCGTGAAGTACTTTCTAATTTTATTGCG\nGCGGATAGACAAGTGATACAGAATGCGTTAGATGCAGCCATAGTTGAAAATGGCCAGGTGGGTGATAGGG\nCGGTCGATGTTTATATGGCTGCTGTTTCTGAGCCATGGTATCGAATATATAATAGGTTACAGGCGTATAT\nTGAAGTTACGCAACTGAGAGAATTGAGGCGCGCAATGGAGTGGCTGAATGCACTTGGTCGTCGTAAGAGA\nGTGGAGTATGATGATTCATTCTTGACCGATTTTCGAGCGAGAGATACGGTATGGGTGCAGACGCAACAGC\nTTCCCGTTAACGCTCGTGTGATCTGGGAGGTTCCGAGGTCATATATAGCTAATTTGATGATGAATATCGC\nGTTATGTCTGCCACTAGGTGATTTCATAGCCCCAAACCCGAGGATTGGGTCGATAACGATAACCCAGCGA\nATAACTATGACTACGCCTTTTGGGATGATGTCTGGGATGACCCCCACATCAATGCAGATGGACGATGTCA\nAGAAGATATATCTCGCGTTGCTCTTTCCCGGGCAGATCGTTTTGAATATTAAACCCGACCCAGCGCACTC\nCATCGATCCGGTACTGCGTATGGTTTCGGGTGTGTTGGGGCATTTGATGTTCACCTACGGTCCCAGATTT\nACTAACATAACAGCTACAACATCGCAGTTGCTAGATAGTGCCTTGAGCGACTATTTTCTGTACATGCAAA\nACAGTAGAGTTCCGGTGGTGTACGGACCAACTGGGTTACCTTTGGATTTTAGAATCGGTGGACGACAAGG\nCTATGATTGCAATAATCTGCGGGGAGACCCGCAGACTGGGAGGGGGTACAATGGATGGGGAGTCGTTGAC\nGTCGATCGAAGAGCACCCAGTCCGTACGATTTGGTTCAAAGATTTATACGTTACTGCAACATAGACTCTC\nGCGAGATCATCGACCCACGGACGTTTGGATTTAATATGAACTATCCGCTATATATGGAGATGATACGTGC\nATTAGTTGCCGGAGGAAAAGATCAGGAAGCGGCGTACCTACGACAAATGTTACCTTTTCACATGATCAGA\nTTCGCACGGATCAATCAGATAATAAACGAAGACTTACTTAGCGCGTTTTCCTTACCAGATGAGGATTTCG\nACGCATTATTTTTCAATATGCTGCGCGGCGAGTATGGAAAGGCTGAGCCGATCGTTTTAGATATCAGTTG\nGGCTTCAATTTGGTTTGCGTTCAACCGCTACTTTGACCCAGTCCAAAGGTCAGATCTATTATCAGTGGCA\nCCCATGATTGAGGCTGTCTATGCGTCAGAAATCTCCATTTTGCAATTGGATATGATCAACCTGCAGCAGT\nTGAGAGCGAGGGCACCTGATATGTTGATTAACGCAACTCCGAGTCAGTTTTGGAAAGCGGCGTTAGCATC\nCGCAGCAGAACCAGTAGTTGAGTTGATGAATCTTTCGCAGAGTTTTCGATTCATTAACGTCAGGGATATA\nATACAGTGGACTAGAACACGAGAAGTGCAACCGTCGCTGGCTCTCACTTTGGAACGAGAGGCGTGGGCGG\nTCGCAGCTGACTTCGAAGAGTTGATGCTCGTAAACCATGTCTATTTTCATAGATCGGTGGTTCCCGAACC\nACAGTTGGATGACATCGATGAATTTCGTAGGCAAGGATTCCTGTACACAAATCTATTGGAAGCGGCCCCC\nCCGCGTTTGTTAATCACCAATTATGATTACAACGTTGCGCTACTGCAGGCGAATCTTGGACAATTTAAAT\nCCGCTTTGAGGAGAATTCTGGATGACGGTGGTTGGGTGATGTTCGGGGGAATGCTGAGAAATGTTCGTTT\nGAAAATATACGATTCAAAGCCGGGAGAGGACGTCTTAAGCGAACTACCCTATCTTTACTCCGAGAAAGTG\nGAAAACGGTTTAAGGTTTGTGTCTTTGAAGTATGCGAGACGAGCAACTATTTATTTTTTAATGTATAAGG\nTTGAATATTCAAACACACCAGATGCTTTAATATCAGTCAACCCCACGTATACCATGACGAAGATTTATAC\nAAACAAGAGACTGGTCCGGAAAGTCAGGTCACCTGACGTTTTGAACATCGTTAATAAAAGAGTAGTGGCT\nTATAAAACGAAGATGCGGTTGATTGACATTACATCGGCACTGCGTCTTGGTGTTAAACTTGCAGCACCTA\nCAGTGTGAATTGACCACTCAACCTGTGGTGCTCGGTGGGGAATTCGCTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610677.1.fasta", "content": ">JQ610677.1 Orungo virus isolate UGMP 359 segment 3, complete sequence\nGTATATATTCCTTCGCGATGGCGCATGCGGATGCTAAAGGAAGTGATCCGGAGAGAGAGGCGTTGAGGAA\nGAACCCTTATCTAGATGGAGACGTCTTGGGAACCGCAGGCGGCCAAGTTTTGTCGGTTTTCGCATTGACC\nGAAATTTTACAAAAAGTAAGACAGACGCAAGCTGAACTGGCCGCACACGCAATCGATTTGGATGGACCAG\nTCCCTGAGATCACCGGGGTTATTAAGAAGATAGCGGAGTTAGTTGACACCGTTCCATATGAAGTGCGCGA\nTTCACCACCTATAAGCTATAAGACTTTAAGCATGCAATCGCGCGACTTTGTCATCCAGGTGGACCAGTAT\nTACGAACAGATTTCGCAAATTGGAGGAGACGTCGGGGAGGACGAGCCGATGGAGTTCTATAAAACAATGC\nTAGAAAAGGTACGCTATTTAAGGAAGAGTGGAGCATTCATTTTGAGAGGTATTAAAACACGAGACTATAG\nGGGTAATGAAGTGGCGGAACCAGAAGCTTTAGGAGTCGAATTTCGTGAAGTACTTTCTAATTTTATTGCG\nGCGGATAGACAAGTGATACAGAATGCGTTAGATGCAGCCATAGTTGAAAATGGCCAGGTGGGTGATAGGG\nCGGTCGATGTTTATATGGCTGCTGTTTCTGAGCCATGGTATCGAATATATAATAGGTTACAGGCGTATAT\nTGAAGTTACGCAACTGAGAGAATTGAGGCGCGCAATGGAGTGGCTGAATGCACTTGGTCGTCGTAAGAGA\nGTGGAGTATGATGATTCATTCTTGACCGATTTTCGAGCGAGAGATACGGTATGGGTGCAGACGCAACAGC\nTTCCCGTTAACGCTCGTGTGATCTGGGAGGTTCCGAGGTCATATATAGCTAATTTGATGATGAATATCGC\nGTTATGTCTGCCACTAGGTGATTTCATAGCCCCAAACCCGAGGATTGGGTCGATAACGATAACCCAGCGA\nATAACTATGACTACGCCTTTTGGGATGATGTCTGGGATGACCCCCACATCAATGCAGATGGACGATGTCA\nAGAAGATATATCTCGCGTTGCTCTTTCCCGGGCAGATCGTTTTGAATATTAAACCCGACCCAGCGCACTC\nCATCGATCCGGTACTGCGTATGGTTTCGGGTGTGTTGGGGCATTTGATGTTCACCTACGGTCCCAGATTT\nACTAACATAACAGCTACAACATCGCAGTTGCTAGATAGTGCCTTGAGCGACTATTTTCTGTACATGCAAA\nACAGTAGAGTTCCGGTGGTGTACGGACCAACTGGGTTACCTTTGGATTTTAGAATCGGTGGACGACAAGG\nCTATGATTGCAATAATCTGCGGGGAGACCCGCAGACTGGGAGGGGGTACAATGGATGGGGAGTCGTTGAC\nGTCGATCGAAGAGCACCCAGTCCGTACGATTTGGTTCAAAGATTTATACGTTACTGCAACATAGACTCTC\nGCGAGATCATCGACCCACGGACGTTTGGATTTAATATGAACTATCCGCTATATATGGAGATGATACGTGC\nATTAGTTGCCGGAGGAAAAGATCAGGAAGCGGCGTACCTACGACAAATGTTACCTTTTCACATGATCAGA\nTTCGCACGGATCAATCAGATAATAAACGAAGACTTACTTAGCGCGTTTTCCTTACCAGATGAGGATTTCG\nACGCATTATTTTTCAATATGCTGCGCGGCGAGTATGGAAAGGCTGAGCCGATCGTTTTAGATATCAGTTG\nGGCTTCAATTTGGTTTGCGTTCAACCGCTACTTTGACCCAGTCCAAAGGTCAGATCTATTATCAGTGGCA\nCCCATGATTGAGGCTGTCTATGCGTCAGAAATCTCCATTTTGCAATTGGATATGATCAACCTGCAGCAGT\nTGAGAGCGAGGGCACCTGATATGTTGATTAACGCAACTCCGAGTCAGTTTTGGAAAGCGGCGTTAGCATC\nCGCAGCAGAACCAGTAGTTGAGTTGATGAATCTTTCGCAGAGTTTTCGATTCATTAACGTCAGGGATATA\nATACAGTGGACTAGAACACGAGAAGTGCAACCGTCGCTGGCTCTCACTTTGGAACGAGAGGCGTGGGCGG\nTCGCAGCTGACTTCGAAGAGTTGATGCTCGTAAACCATGTCTATTTTCATAGATCGGTGGTTCCCGAACC\nACAGTTGGATGACATCGATGAATTTCGTAGGCAAGGATTCCTGTACACAAATCTATTGGAAGCGGCCCCC\nCCGCGTTTGTTAATCACCAATTATGATTACAACGTTGCGCTACTGCAGGCGAATCTTGGACAATTTAAAT\nCCGCTTTGAGGAGAATTCTGGATGACGGTGGTTGGGTGATGTTCGGGGGAATGCTGAGAAATGTTCGTTT\nGAAAATATACGATTCAAAGCCGGGAGAGGACGTCTTAAGCGAACTACCCTATCTTTACTCCGAGAAAGTG\nGAAAACGGTTTAAGGTTTGTGTCTTTGAAGTATGCGAGACGAGCAACTATTTATTTTTTAATGTATAAGG\nTTGAATATTCAAACACACCAGATGCTTTAATATCAGTCAACCCCACGTATACCATGACGAAGATTTATAC\nAAACAAGAGACTGGTCCGGAAAGTCAGGTCACCTGACGTTTTGAACATCGTTAATAAAAGAGTAGTGGCT\nTATAAAACGAAGATGCGGTTGATTGACATTACATCGGCACTGCGTCTTGGTGTTAAACTTGCAGCACCTA\nCAGTGTGAATTGACCACTCAACCTGTGGTGCTCGGTGGGGAATTCGCTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610678.1.fa", "content": ">JQ610678.1 Orungo virus isolate UGMP 359 segment 4, complete sequence\nGTATATTTCGAAATGGAGCCCTTTGCTGTGCTGCACCTATCAGCCAAGCTGGCACCGCTGGTGCGTGAGG\nGATTTATCCCGTATGTGGACTTGGATAATATTAAGACGTTGAATGACCTCTGGATTGAGATTGGCAAATG\nCTCATCTGATGTATATGCGGTTGGACGAATAAATAGGTGGACGATACGTCAGCTACGTGCGTATAGATTC\nATATTCGTGTCGGAGAAGAGAACAATAACGTTGAAGGATATTAAGATCACACCTGACGTGCCAATAAGAT\nGCGCGGATGGGCTAGACTTAAAGTTACTTGAGACTACAATAGGACGTAAAAGATTAGTGTTGCGAAAGAC\nGTTTGGAGACATACTGCGAAAATATGCGTTAAGCCAGTCGGTACACTTGCATGGATCTGAGGCAGAAACC\nTTGAATATGGCGGACCCTACCATACATCACGTGAAGGGGTTACCAATGATAGCGCCAAATCATTTAAATC\nCAACGAAACCATGGAGTGATCTGGACGACACAGAAACCGATGAAAAACTAGTGTCAATGCTAGATTACGC\nGATGTATAGCGCGCAAGAAGTGCATTATGTTGGCTCGGGAGACGGTAGAACGATACGGCTGTTTGCAAAG\nAGGGACAAAAAGAGATTTGATAGAGCGAAGTGGGTGTGCTATGACCCTATTATGACTGATATTGGATTGA\nCAAATGTGATAGCTGTTAAACACTATGTCAATACTTTCAGGGATATGCTACCGTATTTAAATACTGGCGA\nCCGAGTTGAGAGATTACTATTGTGGGACGTAAGTGGAGATGCGGCGAAACATGATCGGTTTTGGGAAGCT\nCAGAGGACTGAGGAGGACCGGCGGGGAGAATCAGTTGCCGTGTCTTTAACGGAGTACTTCGCCTTGGCTA\nTTATCAAACATAGAATTCCAATCTATGAGGAAAAGTATAGATGCACCACTTCGTGGATTGTACCGCAGCC\nTGGCGCGGTCCGCGAGATGTACGAGATGAGGAATATCATACTGTTGAACGGTTTTTCTAGGGTAAATCGA\nGCGCATATCCCCCAGGCAGGCGTAATGGAGATTGAGGCTGATGTGTTACGTGAGATGGTGAGGAACTTCC\nATGGAGCTGGTCGCGGTCGGCTGCTGAAGAAATCGCTTTATGAGAGTCTACATATCCATCAAGTTGATGG\nATTGGAGGATTCGGAAGACGGAGCGCGGAGCGATCTCTTTTATTTAACCAACCAACGTAATGTTAATTCA\nATACAATCAATCAGACGAGTTTTGGGAAATAGCACGGTGTCGACTTTATGGGTGTCAAGGGAACGAGTTT\nTCGAATATGATGACTTTAATTTTGACCGATCAGCGTTGATGCTCTGGCACAGGGGTAGAGAGCACTTACT\nATTTGATGGCAACGGCGCGGTTCTATATTTGATGTGGCAGCACGGAGATAGATATAGAAAGGATGTGAAC\nTATGATCCTTCGTGGGCCGAACATTTTGCAGTATTGATCCGAGAGCCACAACCTTGGCGACCAGTTCCAG\nATCTGTCCCTCTGCCGTTTTATTTCGCTAAGACGGGTGTCGACGGTTATTAGAATACGAGGCGATATTCA\nCAGGAAAAGTGATCAGGTAAAGCGTTTAGGGTTAGATTTGTCAGGACATCTGTTCGTAACGTTAATTTCT\nGGAGCGTATCTTGCCGATTTAAGATGGTGGTTCCGGATGATCATCCAATGGTCAAAGCAGCGTAGACAGG\nAAAAGATAGACGATTTGGCTAAGGTTAACGCTGAAGTGGTTGAATGGAAAGAAGAGAAAGCCGACGAACC\nGTGGCATCGCAAGGAGGACCTGATCGCTGCTTTAATCGCGGCAAAAAGTATCACCGGTGATCAGCATATA\nGATGGGTGGATTGCGGAGCTGAGGGATATGGAATGACATCCACCCGAGGGGCAATCGAACTACCTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610678.1.fasta", "content": ">JQ610678.1 Orungo virus isolate UGMP 359 segment 4, complete sequence\nGTATATTTCGAAATGGAGCCCTTTGCTGTGCTGCACCTATCAGCCAAGCTGGCACCGCTGGTGCGTGAGG\nGATTTATCCCGTATGTGGACTTGGATAATATTAAGACGTTGAATGACCTCTGGATTGAGATTGGCAAATG\nCTCATCTGATGTATATGCGGTTGGACGAATAAATAGGTGGACGATACGTCAGCTACGTGCGTATAGATTC\nATATTCGTGTCGGAGAAGAGAACAATAACGTTGAAGGATATTAAGATCACACCTGACGTGCCAATAAGAT\nGCGCGGATGGGCTAGACTTAAAGTTACTTGAGACTACAATAGGACGTAAAAGATTAGTGTTGCGAAAGAC\nGTTTGGAGACATACTGCGAAAATATGCGTTAAGCCAGTCGGTACACTTGCATGGATCTGAGGCAGAAACC\nTTGAATATGGCGGACCCTACCATACATCACGTGAAGGGGTTACCAATGATAGCGCCAAATCATTTAAATC\nCAACGAAACCATGGAGTGATCTGGACGACACAGAAACCGATGAAAAACTAGTGTCAATGCTAGATTACGC\nGATGTATAGCGCGCAAGAAGTGCATTATGTTGGCTCGGGAGACGGTAGAACGATACGGCTGTTTGCAAAG\nAGGGACAAAAAGAGATTTGATAGAGCGAAGTGGGTGTGCTATGACCCTATTATGACTGATATTGGATTGA\nCAAATGTGATAGCTGTTAAACACTATGTCAATACTTTCAGGGATATGCTACCGTATTTAAATACTGGCGA\nCCGAGTTGAGAGATTACTATTGTGGGACGTAAGTGGAGATGCGGCGAAACATGATCGGTTTTGGGAAGCT\nCAGAGGACTGAGGAGGACCGGCGGGGAGAATCAGTTGCCGTGTCTTTAACGGAGTACTTCGCCTTGGCTA\nTTATCAAACATAGAATTCCAATCTATGAGGAAAAGTATAGATGCACCACTTCGTGGATTGTACCGCAGCC\nTGGCGCGGTCCGCGAGATGTACGAGATGAGGAATATCATACTGTTGAACGGTTTTTCTAGGGTAAATCGA\nGCGCATATCCCCCAGGCAGGCGTAATGGAGATTGAGGCTGATGTGTTACGTGAGATGGTGAGGAACTTCC\nATGGAGCTGGTCGCGGTCGGCTGCTGAAGAAATCGCTTTATGAGAGTCTACATATCCATCAAGTTGATGG\nATTGGAGGATTCGGAAGACGGAGCGCGGAGCGATCTCTTTTATTTAACCAACCAACGTAATGTTAATTCA\nATACAATCAATCAGACGAGTTTTGGGAAATAGCACGGTGTCGACTTTATGGGTGTCAAGGGAACGAGTTT\nTCGAATATGATGACTTTAATTTTGACCGATCAGCGTTGATGCTCTGGCACAGGGGTAGAGAGCACTTACT\nATTTGATGGCAACGGCGCGGTTCTATATTTGATGTGGCAGCACGGAGATAGATATAGAAAGGATGTGAAC\nTATGATCCTTCGTGGGCCGAACATTTTGCAGTATTGATCCGAGAGCCACAACCTTGGCGACCAGTTCCAG\nATCTGTCCCTCTGCCGTTTTATTTCGCTAAGACGGGTGTCGACGGTTATTAGAATACGAGGCGATATTCA\nCAGGAAAAGTGATCAGGTAAAGCGTTTAGGGTTAGATTTGTCAGGACATCTGTTCGTAACGTTAATTTCT\nGGAGCGTATCTTGCCGATTTAAGATGGTGGTTCCGGATGATCATCCAATGGTCAAAGCAGCGTAGACAGG\nAAAAGATAGACGATTTGGCTAAGGTTAACGCTGAAGTGGTTGAATGGAAAGAAGAGAAAGCCGACGAACC\nGTGGCATCGCAAGGAGGACCTGATCGCTGCTTTAATCGCGGCAAAAAGTATCACCGGTGATCAGCATATA\nGATGGGTGGATTGCGGAGCTGAGGGATATGGAATGACATCCACCCGAGGGGCAATCGAACTACCTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610679.1.fa", "content": ">JQ610679.1 Orungo virus isolate UGMP 359 segment 5, complete sequence\nGTAAAAAGAATCCTCTGCGTTCACTGGGCACGAACATGGATCAATTCTTGGATTCTTTTGATGTGACTGG\nAGACGAGGCGAATGCCTTGAGATTATTGAGAGCGGTTTCACCTGAGATGACATGCTCACATTTGAGGAGA\nGATTGTTTAATTGGAGGGATATGCGCAAAACAGTTTTTCAACGAGGTGCTGATGGCCATTCTGGATTCAA\nAAGATCGTCAGGCAGCGCGTCAGCTGGTGACATTAGCTGTGATGACCAGTTACGACCGAGAGCTAATCTG\nGCTCAACGTACTAAGGTCAACTGAAGTGCTGCCGGCAAATGATTATGCACATGAAATACAGAATGTGGTT\nCTGAACTTGAAGAGGGTCTTCATAGAGAGTGGGTTGGAAGAAAAATACAAGAGTTTCAGGGCGAAGCGGC\nGTCCAAACAGATCTCCGACCGAGGATGCTTTCTCTTTTTTGCCCTTTTTCTACATACCCATGAATGAAAC\nAAAACGGGTTGGAATAAAGAAACTCACTAGAGTTCGGAACCTAGGTGTTGCTTTTGTTGATAGACGCGAA\nGTGACGCATCATTTACCGTTCACGGTGGACGCTGCTAGAAGGGACCTTATGATGCTGAGAAATTTCACGC\nTGGAGCACCAAAGAACATGTACGTTTACGGGTTCAAAGAGCTTGATACATGGGATGATATTCTGTCCTGA\nGGAGATGGAACCTCTTTTCCAGAAGAAGGAGACAGCGCTAGAAATCTACAGAATTTGTGAGCAGGATATG\nAAGTTTATCAACTCAAGAGGTACGATGTCATTTCCCCGGTTTTTGATGCAACGTTTAGCGGTGAAAAACG\nCTTCATCTGATGCGATGGACCAGGTTATGTTGGGACGAACTCCGAGCGATGGACGTTTGATGTCGGTGAC\nTGGTGCCTCTTTCTTTTTTGGAGGGGGACCTGATTGGCGCAAGTGGGCGATGCCGGCGTTGTTGGTACGT\nGCTGCAAGACTGAGAACCGTCGTGACATCATTCGTTAAGGAGTGGTTTGATTCGACTCACACATGTCAAG\nTCTGTTTCCTAGTTGAAAAAGGTGTCGCCGATTCAATTCCGATCACTGATGTTCGTTTATCGGATGTGTG\nCGGCGTAGGACCAGTCGCATATGTTAGATCTTATGCACATGATGACGGGAACGCGCCGGATGTTCGCGTA\nCTGAGAAAAGGTGAAATCTTCAGATTGATGGGCGGACATTATGTTATGCAGACAACGGCGAGTACAATGG\nAATCATTGGTCGTTGCCGCGAAGGAGATGCAGCGTTTGGTTCGCGGCGATGGTTTTTGGGACACACCGTA\nTTGGGGTTTAAGCATGGCAAACCTTTGTAAAATCATGTTTCATGAAAACCCAGCAAAGGAACAGATTCAT\nTTCATGATTAAGCTCATAACCTTTGGGATGTTTGGTGGGGTTCAAAGGCACAATGGACTGTTCACAGACT\nGGGACAATTTGGAGGAGTTCTTGAAGAGGATGTTTTCTACGGAGGAGATGGGCGTTCGTATGTATGAGTC\nAAGTTACCATGCGATACTTCGTGCGTGCATACTACATCTACAGACCACTGCGAAGCCTACCCTCGTTCAA\nCTAACTCACGCGATCGAATCACTCGACCTTGGAATAGAAGAAGTTCCTTTCAATTTTTATGTCTAAAACA\nTCATAATAAACCATAAAGAGTCTGAGTAATTGTATCCCTGAGCTCTTACTCTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610679.1.fasta", "content": ">JQ610679.1 Orungo virus isolate UGMP 359 segment 5, complete sequence\nGTAAAAAGAATCCTCTGCGTTCACTGGGCACGAACATGGATCAATTCTTGGATTCTTTTGATGTGACTGG\nAGACGAGGCGAATGCCTTGAGATTATTGAGAGCGGTTTCACCTGAGATGACATGCTCACATTTGAGGAGA\nGATTGTTTAATTGGAGGGATATGCGCAAAACAGTTTTTCAACGAGGTGCTGATGGCCATTCTGGATTCAA\nAAGATCGTCAGGCAGCGCGTCAGCTGGTGACATTAGCTGTGATGACCAGTTACGACCGAGAGCTAATCTG\nGCTCAACGTACTAAGGTCAACTGAAGTGCTGCCGGCAAATGATTATGCACATGAAATACAGAATGTGGTT\nCTGAACTTGAAGAGGGTCTTCATAGAGAGTGGGTTGGAAGAAAAATACAAGAGTTTCAGGGCGAAGCGGC\nGTCCAAACAGATCTCCGACCGAGGATGCTTTCTCTTTTTTGCCCTTTTTCTACATACCCATGAATGAAAC\nAAAACGGGTTGGAATAAAGAAACTCACTAGAGTTCGGAACCTAGGTGTTGCTTTTGTTGATAGACGCGAA\nGTGACGCATCATTTACCGTTCACGGTGGACGCTGCTAGAAGGGACCTTATGATGCTGAGAAATTTCACGC\nTGGAGCACCAAAGAACATGTACGTTTACGGGTTCAAAGAGCTTGATACATGGGATGATATTCTGTCCTGA\nGGAGATGGAACCTCTTTTCCAGAAGAAGGAGACAGCGCTAGAAATCTACAGAATTTGTGAGCAGGATATG\nAAGTTTATCAACTCAAGAGGTACGATGTCATTTCCCCGGTTTTTGATGCAACGTTTAGCGGTGAAAAACG\nCTTCATCTGATGCGATGGACCAGGTTATGTTGGGACGAACTCCGAGCGATGGACGTTTGATGTCGGTGAC\nTGGTGCCTCTTTCTTTTTTGGAGGGGGACCTGATTGGCGCAAGTGGGCGATGCCGGCGTTGTTGGTACGT\nGCTGCAAGACTGAGAACCGTCGTGACATCATTCGTTAAGGAGTGGTTTGATTCGACTCACACATGTCAAG\nTCTGTTTCCTAGTTGAAAAAGGTGTCGCCGATTCAATTCCGATCACTGATGTTCGTTTATCGGATGTGTG\nCGGCGTAGGACCAGTCGCATATGTTAGATCTTATGCACATGATGACGGGAACGCGCCGGATGTTCGCGTA\nCTGAGAAAAGGTGAAATCTTCAGATTGATGGGCGGACATTATGTTATGCAGACAACGGCGAGTACAATGG\nAATCATTGGTCGTTGCCGCGAAGGAGATGCAGCGTTTGGTTCGCGGCGATGGTTTTTGGGACACACCGTA\nTTGGGGTTTAAGCATGGCAAACCTTTGTAAAATCATGTTTCATGAAAACCCAGCAAAGGAACAGATTCAT\nTTCATGATTAAGCTCATAACCTTTGGGATGTTTGGTGGGGTTCAAAGGCACAATGGACTGTTCACAGACT\nGGGACAATTTGGAGGAGTTCTTGAAGAGGATGTTTTCTACGGAGGAGATGGGCGTTCGTATGTATGAGTC\nAAGTTACCATGCGATACTTCGTGCGTGCATACTACATCTACAGACCACTGCGAAGCCTACCCTCGTTCAA\nCTAACTCACGCGATCGAATCACTCGACCTTGGAATAGAAGAAGTTCCTTTCAATTTTTATGTCTAAAACA\nTCATAATAAACCATAAAGAGTCTGAGTAATTGTATCCCTGAGCTCTTACTCTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610680.1.fa", "content": ">JQ610680.1 Orungo virus isolate UGMP 359 segment 6, complete sequence\nGTATAAAATACCTCGGTCATCATGGGCAAATTCGTAAAGGCCCTGAAGAAAATAGGAAGGGGTACGGTGA\nAGGCACTGACGTCTGACGCTGCAAAGAAACTTTATACGACTTTAGGAAAGGCGGCGACGCGGTTTGCTGA\nAAGCGAAGTCGGCAGCGCGGCGATTGATGGATTGATACAAGGAACAGCGCAAACTTTACTGCACGGAGGC\nAGCGCGAGTGAAAATATCAAGCAAGCGGTTGTTTTAGGTGTTCTCCACAGCATGGAAACGCCGGCGGACC\nCTTTATCACCAGGAGAGCAAGGAGTATATGATAAGATTAAGGAAATTAAACGAGAAGAAAAGGAAGATCG\nGTTTTTCGAGGTTTACCAAGAAAAGATTGACGAAGAGCTTGGTTCAGATATGAAGCGAATGCGAGAAGTG\nGCAAAAGGTGATAAGCAGGCCATCAAGGAAATGGGTGGTGAAATTAAGGTTATCGAGAAAGCTTTCGATG\nGATTGATTAAAATAGATAAAATTCAAGATATGAAATTAACGCAGTTATATGGCGCGCTCGCGAAAGAGCG\nTACGGAGCGTACGCAGGACGAGATCAAAATGGTTAACGACTACACTGGAAAAATTGAAGCACTGCAATCC\nGCGATAACAGTTGAGCGGGACGCTATGCAAGAGGAGGCGTTGCAGGAGATAATAGAAATGGGAACGGATG\nTAATTGAAACCGCCTCCGAAGAGGTTCCGATATTCGGCCCTGCGGCTGCGAATGTAGTCGCAACTGGACG\nAATGGTTGAGGGCACCTTAAAGTTGAAGCAAGTAATCGAGAAATTAGCAGGGTTAGATGTTTCGCACACC\nACAAGGGACAGAATCGAGCCGAAAGTTATAAACGCTATACTAGATCACGAGGGGGGCGTCGTACCGGAAA\nAGGAACTAGCGATTGGTGTATATAATAAGCTGCAGACAGTCAGAGAACATATGGCGGAACACAGCCATCT\nAAAGGAAATGGCAATACCAAGGCTGCAAAAGCTGTACACAGAACACGGCGATGAGTGGCATCCAAAGATA\nATTACTCAAATGAAGGTAGCGAGAGAACATCAGCCGCAAATACATATATATTGCGCTCCATGGGAATCGG\nATGACGTGTTTATGTTGCGAGTGTACGCGCCGCATCATATAGGGTGTGGTCTTTTCTTAGGAGTTGATTT\nAGAGAGTGAATTCATATTTTATGAGGATTTGATAGCAGAGAACCACGTATTGCGTGGTGGCGTCATTGAA\nGTCGTTGGAAGGAACTTCAGGCAAGCAGTGCGCGAATTTCTTTTGATGGCTGCGAGCAAGATTGAGAACA\nCTATGCATGTCAAGCGGTTAGTGAGAAGCTCGGCTTCCTCACCTATCTACTTGTCAAGCATACACTATGA\nGTGTACATTTGATGAGATAAAACAGAACGTTTTACAGATCGTGCACGACGAGCAGTTACAGATGCATCTG\nTTACGTGGTCCGAAACATTTCCAAAGACGTGCTCTGATGGCGGCTGTTGTTAAGGGTGTTAAGATCTTAG\nAGGGGCCAGATACGAAGGCGCTCATGCTACAGGGTTTGTAAGTGGCTGAAAGGTATCAAGAATAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610680.1.fasta", "content": ">JQ610680.1 Orungo virus isolate UGMP 359 segment 6, complete sequence\nGTATAAAATACCTCGGTCATCATGGGCAAATTCGTAAAGGCCCTGAAGAAAATAGGAAGGGGTACGGTGA\nAGGCACTGACGTCTGACGCTGCAAAGAAACTTTATACGACTTTAGGAAAGGCGGCGACGCGGTTTGCTGA\nAAGCGAAGTCGGCAGCGCGGCGATTGATGGATTGATACAAGGAACAGCGCAAACTTTACTGCACGGAGGC\nAGCGCGAGTGAAAATATCAAGCAAGCGGTTGTTTTAGGTGTTCTCCACAGCATGGAAACGCCGGCGGACC\nCTTTATCACCAGGAGAGCAAGGAGTATATGATAAGATTAAGGAAATTAAACGAGAAGAAAAGGAAGATCG\nGTTTTTCGAGGTTTACCAAGAAAAGATTGACGAAGAGCTTGGTTCAGATATGAAGCGAATGCGAGAAGTG\nGCAAAAGGTGATAAGCAGGCCATCAAGGAAATGGGTGGTGAAATTAAGGTTATCGAGAAAGCTTTCGATG\nGATTGATTAAAATAGATAAAATTCAAGATATGAAATTAACGCAGTTATATGGCGCGCTCGCGAAAGAGCG\nTACGGAGCGTACGCAGGACGAGATCAAAATGGTTAACGACTACACTGGAAAAATTGAAGCACTGCAATCC\nGCGATAACAGTTGAGCGGGACGCTATGCAAGAGGAGGCGTTGCAGGAGATAATAGAAATGGGAACGGATG\nTAATTGAAACCGCCTCCGAAGAGGTTCCGATATTCGGCCCTGCGGCTGCGAATGTAGTCGCAACTGGACG\nAATGGTTGAGGGCACCTTAAAGTTGAAGCAAGTAATCGAGAAATTAGCAGGGTTAGATGTTTCGCACACC\nACAAGGGACAGAATCGAGCCGAAAGTTATAAACGCTATACTAGATCACGAGGGGGGCGTCGTACCGGAAA\nAGGAACTAGCGATTGGTGTATATAATAAGCTGCAGACAGTCAGAGAACATATGGCGGAACACAGCCATCT\nAAAGGAAATGGCAATACCAAGGCTGCAAAAGCTGTACACAGAACACGGCGATGAGTGGCATCCAAAGATA\nATTACTCAAATGAAGGTAGCGAGAGAACATCAGCCGCAAATACATATATATTGCGCTCCATGGGAATCGG\nATGACGTGTTTATGTTGCGAGTGTACGCGCCGCATCATATAGGGTGTGGTCTTTTCTTAGGAGTTGATTT\nAGAGAGTGAATTCATATTTTATGAGGATTTGATAGCAGAGAACCACGTATTGCGTGGTGGCGTCATTGAA\nGTCGTTGGAAGGAACTTCAGGCAAGCAGTGCGCGAATTTCTTTTGATGGCTGCGAGCAAGATTGAGAACA\nCTATGCATGTCAAGCGGTTAGTGAGAAGCTCGGCTTCCTCACCTATCTACTTGTCAAGCATACACTATGA\nGTGTACATTTGATGAGATAAAACAGAACGTTTTACAGATCGTGCACGACGAGCAGTTACAGATGCATCTG\nTTACGTGGTCCGAAACATTTCCAAAGACGTGCTCTGATGGCGGCTGTTGTTAAGGGTGTTAAGATCTTAG\nAGGGGCCAGATACGAAGGCGCTCATGCTACAGGGTTTGTAAGTGGCTGAAAGGTATCAAGAATAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610681.1.fa", "content": ">JQ610681.1 Orungo virus isolate UGMP 359 segment 7, complete sequence\nGTATAAATATCTAGAGATGGACGCCATTGCGGCACGTGCTCTGTCCGTGATCCAGGACTGCATTAGCGTT\nGGTGATGGGAGAATTAATTTAGACCCTGGGGTCATGGAGAGATTGGGAATTGCTATTAATAGATACAATG\nGGCTAACGAACAATGTGGTGACGATCAGACCAGGGACACAAGATGAGCGGAACGCGATGTTTTTTATGTG\nTCTGGATTTCGCGTTGGCGGCATTGAACATACAAATTGGGGTTATATCTAGGGAATACACGCAGGCGCTG\nGCCACTATCGGTGTGCTGGCAACGGGAGAAATCCCTTACTCGGTTGCCGCTATGGATACGATTGTACGGA\nTTAGCGGAACGATGGCGACATGGGGTCCCACCGAATATGAGTTACCGCCATATGCGCGGTCTCAGATGAT\nACAAATGAGCGGACGTTACTACGTTCCAGCGGGGGCGAATTCACATGCTGCCCATGTCGATCCCACGACG\nGTAGAGATTTCTTTAGCTGCTGGAGTAGTAGTGAATGTTACGAACGCGTTACAGCCTAGGGGCGTTGCGC\nCCACAATGATGTACATGGTATGGCATCCGTTGGCGATTTTCGCGAATCCTCAGGGTGCTACAGCTGCTTC\nGCCTCAAAATATGACTTTGGTGGTTGGTGGGCTGAATATAGCAGCTGGCACGATCATCGCTTGGGATACC\nGTCGCTCCTATACAGCTATCGAATCAGGGAGGACAAGAGGGAATGATCGCGATCCGGATACTATGGATGA\nCAACATTAGATAAATCTATGACAAGCTTGCCGGAGATGCGTGAAATAATCTCAAGATGCTATAGCTTTAT\nGCACCCTTCATGGCACGCGCTGCGAGGGACGGTCCTACATTCGCTTAATCTGCCGACTAATAATCCACCT\nATGTTTGCGCCTGCTACGCGACAGGAGGCATTGGCGTACTTAATTCTGGCAAATTTAGCGGATGCATATA\nCGTCGTTAAGGCCTGATTTCACCATACAAGGAATGCTCGCGGTTCCACAGGTCATTGACAGGCAGTTCGT\nTCAGGGTGCGTACAGGTAGAGGACGCCTTCCACAGTGGGCGTCTCATGTAGCCCCAGCGTCGGTCCCTTA\nCGTGTGCTGTAACGCGTAGGTAGAACGTCATATGATATTAAGTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610681.1.fasta", "content": ">JQ610681.1 Orungo virus isolate UGMP 359 segment 7, complete sequence\nGTATAAATATCTAGAGATGGACGCCATTGCGGCACGTGCTCTGTCCGTGATCCAGGACTGCATTAGCGTT\nGGTGATGGGAGAATTAATTTAGACCCTGGGGTCATGGAGAGATTGGGAATTGCTATTAATAGATACAATG\nGGCTAACGAACAATGTGGTGACGATCAGACCAGGGACACAAGATGAGCGGAACGCGATGTTTTTTATGTG\nTCTGGATTTCGCGTTGGCGGCATTGAACATACAAATTGGGGTTATATCTAGGGAATACACGCAGGCGCTG\nGCCACTATCGGTGTGCTGGCAACGGGAGAAATCCCTTACTCGGTTGCCGCTATGGATACGATTGTACGGA\nTTAGCGGAACGATGGCGACATGGGGTCCCACCGAATATGAGTTACCGCCATATGCGCGGTCTCAGATGAT\nACAAATGAGCGGACGTTACTACGTTCCAGCGGGGGCGAATTCACATGCTGCCCATGTCGATCCCACGACG\nGTAGAGATTTCTTTAGCTGCTGGAGTAGTAGTGAATGTTACGAACGCGTTACAGCCTAGGGGCGTTGCGC\nCCACAATGATGTACATGGTATGGCATCCGTTGGCGATTTTCGCGAATCCTCAGGGTGCTACAGCTGCTTC\nGCCTCAAAATATGACTTTGGTGGTTGGTGGGCTGAATATAGCAGCTGGCACGATCATCGCTTGGGATACC\nGTCGCTCCTATACAGCTATCGAATCAGGGAGGACAAGAGGGAATGATCGCGATCCGGATACTATGGATGA\nCAACATTAGATAAATCTATGACAAGCTTGCCGGAGATGCGTGAAATAATCTCAAGATGCTATAGCTTTAT\nGCACCCTTCATGGCACGCGCTGCGAGGGACGGTCCTACATTCGCTTAATCTGCCGACTAATAATCCACCT\nATGTTTGCGCCTGCTACGCGACAGGAGGCATTGGCGTACTTAATTCTGGCAAATTTAGCGGATGCATATA\nCGTCGTTAAGGCCTGATTTCACCATACAAGGAATGCTCGCGGTTCCACAGGTCATTGACAGGCAGTTCGT\nTCAGGGTGCGTACAGGTAGAGGACGCCTTCCACAGTGGGCGTCTCATGTAGCCCCAGCGTCGGTCCCTTA\nCGTGTGCTGTAACGCGTAGGTAGAACGTCATATGATATTAAGTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610682.1.fa", "content": ">JQ610682.1 Orungo virus isolate UGMP 359 segment 8, complete sequence\nGTAAAAAATCTCCTCTCTTTTCACGATGGCTCAAGAAGTTAAGAGAAAGTTCACTAGAACAGTGTGCATC\nTATGATCCACAAAATCGCACATTCTGTGGTCGAAGTGCCGCGATGGTGTGTAACAGTTATTATACAATTA\nAAATGGGTAGAACGACGCAGTGTGGAGTGTCGCCGGTGCCCGTACCAAAGTCATATGTGCTAGAGATACC\nGGATGTTGGCTCTTATCGCATCTTAGATGGGCAGGATTCAATCAGTGTCATCGTTACTGAGACGGGCGTC\nGAGGCAACGTCTGAGAGGTGGGAAGAGTGGAAATTCGAAGGCGTTAATTGCGTTCCGATGGTTGTTCAAA\nCGGAGATTGGGAAAGGCCTGATTGACATGGAGATCAAGTTTAGTAAGGGAATGGGGCTCGTTAAACCTTA\nTGTAAAGAATGAGGTTAGCAGAACTGAGATCCCACGGCTACCGGGTGCTTCAGTCATTGATACACCGATA\nCGCGATTACCGTCAACTTTTGAAGGATCAGAGAGATGAAAGAAGGGCGGCGCTCGATGCGATCGCATGCG\nACATATGTCCCACTCTATCAAGAATGCTAGGGGCGAATATTACAGACGGATCGCCACAAGTCGAAGAAGT\nCGCAACACGGCCAACACAACCTCCAGCTCAGCTGAAGCTGGATGTGCCTAACTGGGACCAACCGACTGAT\nTCAGATGATGAGGATGAGGAATCCAAGCGCGTGACAACGCAAAGTAATGCTGATACTGAGGAACAAGTGA\nCTTTCGAAGATTGCATTACCGATCAATACTTTTCGAAAACGGGTGAATTCGCGAAGAAGTATCCTGAAAT\nGTTAGCGGGACTTTCCGCGAAGATGCCGAGTGAAACAGGTAGGTTTACAAAAATATTGACGACGAGGAAG\nGCTCAATGGAATAACGTTCCTCTTTTCGAATTAGATCCAAACGGGTTTACATATCATTTTAGTAAGCTGG\nGTAATTCGACGAGGATCTTCTGTGTCCAACGTGATTTGAGCTACATGGTTTTACCCGCAGGGCAAGGCCT\nGAAGTAGCGGTGCATGTAGCCGGGAGAGGTACAACTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610682.1.fasta", "content": ">JQ610682.1 Orungo virus isolate UGMP 359 segment 8, complete sequence\nGTAAAAAATCTCCTCTCTTTTCACGATGGCTCAAGAAGTTAAGAGAAAGTTCACTAGAACAGTGTGCATC\nTATGATCCACAAAATCGCACATTCTGTGGTCGAAGTGCCGCGATGGTGTGTAACAGTTATTATACAATTA\nAAATGGGTAGAACGACGCAGTGTGGAGTGTCGCCGGTGCCCGTACCAAAGTCATATGTGCTAGAGATACC\nGGATGTTGGCTCTTATCGCATCTTAGATGGGCAGGATTCAATCAGTGTCATCGTTACTGAGACGGGCGTC\nGAGGCAACGTCTGAGAGGTGGGAAGAGTGGAAATTCGAAGGCGTTAATTGCGTTCCGATGGTTGTTCAAA\nCGGAGATTGGGAAAGGCCTGATTGACATGGAGATCAAGTTTAGTAAGGGAATGGGGCTCGTTAAACCTTA\nTGTAAAGAATGAGGTTAGCAGAACTGAGATCCCACGGCTACCGGGTGCTTCAGTCATTGATACACCGATA\nCGCGATTACCGTCAACTTTTGAAGGATCAGAGAGATGAAAGAAGGGCGGCGCTCGATGCGATCGCATGCG\nACATATGTCCCACTCTATCAAGAATGCTAGGGGCGAATATTACAGACGGATCGCCACAAGTCGAAGAAGT\nCGCAACACGGCCAACACAACCTCCAGCTCAGCTGAAGCTGGATGTGCCTAACTGGGACCAACCGACTGAT\nTCAGATGATGAGGATGAGGAATCCAAGCGCGTGACAACGCAAAGTAATGCTGATACTGAGGAACAAGTGA\nCTTTCGAAGATTGCATTACCGATCAATACTTTTCGAAAACGGGTGAATTCGCGAAGAAGTATCCTGAAAT\nGTTAGCGGGACTTTCCGCGAAGATGCCGAGTGAAACAGGTAGGTTTACAAAAATATTGACGACGAGGAAG\nGCTCAATGGAATAACGTTCCTCTTTTCGAATTAGATCCAAACGGGTTTACATATCATTTTAGTAAGCTGG\nGTAATTCGACGAGGATCTTCTGTGTCCAACGTGATTTGAGCTACATGGTTTTACCCGCAGGGCAAGGCCT\nGAAGTAGCGGTGCATGTAGCCGGGAGAGGTACAACTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610683.1.fa", "content": ">JQ610683.1 Orungo virus isolate UGMP 359 segment 9, complete sequence\nGTATAAAACATCCTCCCATGTCATGTTGGTGTTGGCACCGGGTGATCTCATAGACGGAGTGCGTCATCAA\nTTATCTGAAAGAGGAGTCAGGATTCGTTTACGGGAAACGAATGATGACGAGCAAAAGGATGAACCAGTGG\nATACGGGAGGCGGCAAGCCGGGTGATCGAATCGGGAAGGAAGTTGGAAATGCCGAGAGTGAACAGTCTTC\nCGATAAAGAGAAGAAGGCTGGAGGAAGTTCGGATTCAGAGCTCGGGGAAGGTGGAGATGGAAGGCGACAA\nACTGAGAAGGCTGAAGGCGGAGAGAATGGAACTAGAGATATTGGCATTCAGGATAAAGACAAACAATTTG\nATCGGCGCGCTAATCCAGATAACGCGTTGGACAGAGAAAATCGATCAGGAGATCCGCAACTTAAATATGG\nATTTGCAACCAAACGAATTGCAAACGCCGTTGAGTCAAAGTACCACTGCGGTGGATTTGAGGGGCCAGGA\nTCGGATGGATACATCAAACTAGAAATGTCAATAATGAAGGCGCTAGGTTTAAACCGAGATGACCACATCG\nAACAATTGGAGTTCCTCAAGCACCAACAGAAAGGGCCCAGCAAAATTCAAGTCAGAACGATCGCTTCCGA\nAACCAAATTAAAAGAGGTGTGTAATATAATGGACAAGCCGGTGGCTCCCACAGCGAGAAGTGCGGTGAGT\nGTAGTTAGTAACCGTGTTGAAGACGTGAAGGAAGCCCAGGTGTATTTTACAACTCCAACAGGAGATAGAG\nGCTGGAAAGAAGTAGCAAGGAAAGCGAGCCAGACACCAAACATTCGAGCGTACATTAATCCGGAGGGAGA\nTGATCCTAAAGTCTCATTTCTGCATTTAATCGATCATCTGTGAGGTCACGGTCTGAACTACGGGCATGCT\nGGGTGTTTCAGTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610683.1.fasta", "content": ">JQ610683.1 Orungo virus isolate UGMP 359 segment 9, complete sequence\nGTATAAAACATCCTCCCATGTCATGTTGGTGTTGGCACCGGGTGATCTCATAGACGGAGTGCGTCATCAA\nTTATCTGAAAGAGGAGTCAGGATTCGTTTACGGGAAACGAATGATGACGAGCAAAAGGATGAACCAGTGG\nATACGGGAGGCGGCAAGCCGGGTGATCGAATCGGGAAGGAAGTTGGAAATGCCGAGAGTGAACAGTCTTC\nCGATAAAGAGAAGAAGGCTGGAGGAAGTTCGGATTCAGAGCTCGGGGAAGGTGGAGATGGAAGGCGACAA\nACTGAGAAGGCTGAAGGCGGAGAGAATGGAACTAGAGATATTGGCATTCAGGATAAAGACAAACAATTTG\nATCGGCGCGCTAATCCAGATAACGCGTTGGACAGAGAAAATCGATCAGGAGATCCGCAACTTAAATATGG\nATTTGCAACCAAACGAATTGCAAACGCCGTTGAGTCAAAGTACCACTGCGGTGGATTTGAGGGGCCAGGA\nTCGGATGGATACATCAAACTAGAAATGTCAATAATGAAGGCGCTAGGTTTAAACCGAGATGACCACATCG\nAACAATTGGAGTTCCTCAAGCACCAACAGAAAGGGCCCAGCAAAATTCAAGTCAGAACGATCGCTTCCGA\nAACCAAATTAAAAGAGGTGTGTAATATAATGGACAAGCCGGTGGCTCCCACAGCGAGAAGTGCGGTGAGT\nGTAGTTAGTAACCGTGTTGAAGACGTGAAGGAAGCCCAGGTGTATTTTACAACTCCAACAGGAGATAGAG\nGCTGGAAAGAAGTAGCAAGGAAAGCGAGCCAGACACCAAACATTCGAGCGTACATTAATCCGGAGGGAGA\nTGATCCTAAAGTCTCATTTCTGCATTTAATCGATCATCTGTGAGGTCACGGTCTGAACTACGGGCATGCT\nGGGTGTTTCAGTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610684.1.fa", "content": ">JQ610684.1 Orungo virus isolate UGMP 359 segment 10, complete sequence\nGTATAAAATTCCGTTCGCAATGTACCGTGACTTGCTGAATATTCACACTGAAATGAGGGGCCCGCCATCT\nTATGAACCTAGTGGCTTAGCTCAAGCGACAGCACCGACTATGAGGTTTGGGGATAGAGAAGATGAGGAAG\nGCCTATTGAGGGCGCGCGAGCTTTCGCTTAATGTGTTAACGAATGCTATGACTAATACAACGGGTGCGAA\nTGAGGCGATTAAGAATGAGAAAGCGATGTTTGGGGCATATGCCGATGCACTTAGGGATACTCCGGAGATT\nAGGGTGGTGAAAAGGCGGATAAATGAACGTACGTTAGAAAAGTTGCATAAAATGCGACGTTCGCTGCACG\nGAAGACGAATGTTCGTACGAATGTTGTTGGCGATAAATGTGGGATTGGCGCTATTAACCTCGGCAGTGAA\nTGTGGTACGCCAGTCGCTAGATGATTTTGGGAAAGAAAGGTGGATAGTTGGTGGAGTGTGGTGGTTAGGT\nGAGGTCGTCGTTACGATTAATTTTGGAACGACTGTTGCTACGTTGGTATTAATGAGGATACATGGCGCAT\nTAAACGCGCAGCTTCAAACCATTAAGCGTGACATATATAAGAAAAGCTCGTATAATGAGGCCGCTGCCAT\nGCATTGGAAAGGTGAAATTAGCTTAATTGAGGAGCTAGCGGCGAGCCACGTACCTGCGGGATCGAATGTC\nTAGTCCGCGACATCGAAAAATTCACTTGTCCAGGTGAAGCCCGTAGAACGGATCGTCTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/JQ610684.1.fasta", "content": ">JQ610684.1 Orungo virus isolate UGMP 359 segment 10, complete sequence\nGTATAAAATTCCGTTCGCAATGTACCGTGACTTGCTGAATATTCACACTGAAATGAGGGGCCCGCCATCT\nTATGAACCTAGTGGCTTAGCTCAAGCGACAGCACCGACTATGAGGTTTGGGGATAGAGAAGATGAGGAAG\nGCCTATTGAGGGCGCGCGAGCTTTCGCTTAATGTGTTAACGAATGCTATGACTAATACAACGGGTGCGAA\nTGAGGCGATTAAGAATGAGAAAGCGATGTTTGGGGCATATGCCGATGCACTTAGGGATACTCCGGAGATT\nAGGGTGGTGAAAAGGCGGATAAATGAACGTACGTTAGAAAAGTTGCATAAAATGCGACGTTCGCTGCACG\nGAAGACGAATGTTCGTACGAATGTTGTTGGCGATAAATGTGGGATTGGCGCTATTAACCTCGGCAGTGAA\nTGTGGTACGCCAGTCGCTAGATGATTTTGGGAAAGAAAGGTGGATAGTTGGTGGAGTGTGGTGGTTAGGT\nGAGGTCGTCGTTACGATTAATTTTGGAACGACTGTTGCTACGTTGGTATTAATGAGGATACATGGCGCAT\nTAAACGCGCAGCTTCAAACCATTAAGCGTGACATATATAAGAAAAGCTCGTATAATGAGGCCGCTGCCAT\nGCATTGGAAAGGTGAAATTAGCTTAATTGAGGAGCTAGCGGCGAGCCACGTACCTGCGGGATCGAATGTC\nTAGTCCGCGACATCGAAAAATTCACTTGTCCAGGTGAAGCCCGTAGAACGGATCGTCTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/orungo.fa", "content": ">JQ610675.1 Orungo virus isolate UGMP 359 segment 1, complete sequence\nGTATAATTAGGAATGGTCATCACTGTGGAAGGTGCGTGGCTGGTGAGACGGGCGTTGCAACGTTTTTTGA\nAGTTCAGTAAAATCGACGGGGAATCAGCAGTTTATGAGTTCTATAGGTATTCAAGTAATATTCGTGAAAT\nAAGAAGGAAGCATGGGACGCGTTATAAAATGCATGATGAAGAGTTGGAGCGGAGGCGTGATTCGGGCAAA\nCTGCGTTTTAAAGGTATGCAAGTTGTGGTAGAGTCGACTTGGATGGAGATTTTAGGGAAGGGACGTACGA\nCGGACGAAATCGAGATATTCAGAAGTTCGATTTTATCGTTGGATGAACTGAATCCGGAAGAAGAATTTCT\nGCGCAATTATGCGAGTTCGGACAAGGAACATCCATCCTACTTGTTTGTTCGGGGGCGGGCGGTCAATGAG\nATGCAGATTTATGGCGACATGCCGATAAAAGCGTGGTTGAGCTTTTTAGTAGAATGTGAGGTTGAATATG\nGGTACAAACTCTTCGGAATGGAAGTTGCGAGATCGTTCGTTCAGAGCTTTGGATCTCCGTTTCACCAGAA\nCTCGCGTGATCTATCACAGATTGACGATATGGCGCCTGCTTTTACGTCACCTTTATTATTTGAAATGTGT\nTGTATGACATCAATTCTCGAAATTAATATACGCATGCGTATGCTGGAGGAGAGGGTTGCAACCCTAAAAT\nTTGGTGAGCGGGAGATCGACCCACTTGAAGTACTAAAAGAATTCTTCCGAATCTGCATTCCGCATCCGAA\nAAAGATTAATAATATGTTGAGAGCTCCATACTCATGGTTCGTCAAGCTGTGGGGCGTATCGTATCATGAG\nCCAATAGTCCTGACGGCGAGGGGCGGCGAGGATAAGAACTCGAAAGACATATTCTTTACGGGATTTCACA\nGAGTCAAGAATCCATACTCAATAATGTTGAAAAAATCGAGGTTTTTTAAGAAATCTTTAGACGAGAATAT\nCAGCAAAGTGAAAGAAGCGATAGACTATTCAAACTCGTTGACGGGGATGTCTTTAGGGCTGCCCGTATTT\nCTATCCATGCTACAGAATGTGTACGACACTGAGTTTAATCCGACTATGGTTCAACACGTGTTACTAGCGT\nCGTTCTTGTTGAGTATCCAAACAATAACTGGCTATGGACGCGCTTGGGTGAAAAATGTGTCAAGCGATAA\nCGACACTCAAATGCGCCCGGCGGAGGACAACTTCATTGATCGAGTTGCTAAGCAAACGGAGATTAATTTT\nATACAGGCGTATGAAGAGGCGTTGGGGCACGGAGAAGATATCGTTAAGCCAGAAGACATGTTTACCTCCA\nTTTTGCGTTTGGCAAGAAATACAAGTTCCGGCTTCTCTACTGCTGTTGACGTTTATAAACGATTCGGTCC\nAAAGTCGGGAGGGAGAGGAGAACGCGTTAAGATAACATCAAGAATTAAAGCATTAGTTATCTTCACAAAG\nGGCCATGAAATATTTACAGCTGAAAATCTCGCGAAAAGATATGATACGGAGGAAGATTACCAGACTAAAG\nGGTCACGGGATGTACCTATCAAAGCAACGCGGACGATTTATTCAATAAACCTCTCCATCTTGATCCCGCA\nGCTGATCCTAACTTTACCGTTGAATGAATATTTTGCCCGGTTCGGAGGATCAACTGCACCTGACTCACGT\nAGCCTAGGGGGTAAGGTGATTATCGGAGATCTAGAAGCAACGGGATCACGGACGATCGATGCGGCAGATA\nCGTTTAGAAATTCGTCCGACCCAGAAATTTTCACAATAGCGATCGATTATTCGGATTACGATCAACATTT\nGACGGTTTTTAACTTCAGGAACGGTATGCTGGAAGGAATTCGCTCTGCGATGAAGAGATATAAAGAGTTG\nAGGTATGATGGATACACGTTGAATGAATTGATTGAATTCGGGTATGGGGAGGGGAGAATTGTTAATTCGA\nAATGGAACGGAAAGAGGCGGGTCAAATCTGTACGAATGAGCGATTATATGGCATTGAGTGAAAGTCAACG\nCGCTCAGGGCACTTTCAAGCCGCCGCAGGGAGTGAGACCGGTTAGTTCAATGCAAGTGTTCGATTCAGTG\nGGTGAGGCATCTGGAGGGGATACTCTCCTCATCTCGCCCACTGACGGATCGGATTTAGCAACCGTCAACA\nCGCATTTGTCGGGTGAAAATTCAACGTTAGTTGCTAACTCTTTGCATAATATGGCTATCGGACGTATCAT\nACAAGAAGAGATCAGAAAGAACCATCGAGCGGCTTTTACCTTTGAATCTGAGCAGTACGTTGGAGATGAT\nACGTTACTTTATGCAAAGTTGAACACATTAAACCATGAAATTTTTGATAAAGCGATTGATACCATCTTCG\nATACTGTGGGAAAGTGCGGACATGTGGCATCGGCAGCGAAAACCCTTATCGCTCCTTTCTCTGTTGAAAA\nAACTCAGACTCATGCGAAGCAAGGAATTTACATTGCGCAGGATCGGATGATGATCATCTCTTCAGAGCGT\nAGAAAGGATATCGAGGACGTCCAAGGGTATATGAGATCACAAGTGTCGGTTATGGCGACAAAAGTAAGCC\nGCGGCTTTAGTCATGAACTGGCTCAGCTTGTCTTTATGATGAAGAGCAGCATCGTAGGCTTTCGTAAACT\nGAAGCGAACTGTGGTGGAGGATGGTGTATACCGTGATCGCGCGTTGGATTCGGAAGATGAGGATGGCTTC\nACTTTGATGCAGATCCGTGATCCGTTGGTCGCCTTCTACCCTGCTGAGTGGAACGGCTATGGCATGCATC\nCAGTCGCTTTGAATATCGTCATGACGGAAGACATGTTTATAGACACGAGTACCATGGTTGAGTTTCAGCA\nTGTAATGCGGCCGCTCCTTCGATTTATGGGTAGGATACCTCCAGTGTGGAATGAAACTAAAGCCGATAAA\nCGTCAGATTTCATCCATAACAAAGATGAGTTTCTTCTCCAAAATGGCTAGACCAGCGGTGAGGGCGGTTC\nTGGCGAATAGTGAACTGTCAGATCAAGTGAGAACATTGCCACTGGGCGACTTTTCGCCTTTCAATCTCTC\nCGCAACAATGATGCACTCAGCATTATTGAAAGAACCACGCGCGCGTGCCCTGCTGACGCCAGCCTACGAA\nAAAGAATTCCAGTCAGAGTTGAATTCAAACCGGGATAGCGAAGTAAATTTCGTCGGGAGGAACATGGAGA\nTCAACACTAATTATATGAAACTGTTCGATGTTGATTTGTCTACGCGAATAGTGGCCAAACAATTTAGTTT\nTCCAGATCAGAATATGTCGTTGCCTTTTTATTTTCAGAAACTCTTGATTGGACATAGACCGGTCGCGCGG\nATGAGAATGACCTATATTGACCGGATTGACCAAATCTTACGGGGAGACGTCGTGATGAGGGGTTTCATCA\nCAGCGAATACTATTATGTCCGTTTTAGAGAAGATTGGCACTGCTCACGCCGTACAGGACTTAACAACAAT\nATTTCAGTTGATGAACATTGAATCTAAGGTGGCGCATAGGCTAGCGGAGTATATCGCTTCTGAAAGGGTA\nAGATTCGACGCGCTCTCGATTGCAAAGAGGGGGATATGCGGGGATGAATTCTCCATGTCGCTGGATGTGT\nGCACGGAACGGTTTGCTGAACGGTTCATGGAACTACCAGCGCAGTTTACTAAAACTGAGAGAGATATAGC\nGATTTTATATGCCGCGCAGCTAACTATGTTGCGCTGTGCGGCTAACCTAGATCTTAGGAAAATTAAGATT\nGGGGTTTCAGCGGATCACGTTAAGAGATTTAAACAAAGACAGGCTAGATTTAAGACTCATCTACCTAAAA\nTGCGTACAGTCACGCGGCTGATAACGCCTGAACGAATCTCCGCACGCCTGGTTCAGCATCAGTTTACATG\nACGCACCACCTAATCAACTTAC\n\n>JQ610676.1 Orungo virus isolate UGMP 359 segment 2, complete sequence\nGTATAATTGATCCGCGATGGCTTTCGAGCGTACGGTAGCCTTAACAAGAGAGTTCGCAAATGAAACAAGA\nCAGCATTTTGGGAAGTTTGATATAGTTGTAAACACGGAAAGCAGTATTGAGGACGAAGCAACGGGTGAGT\nGGGAGTTCGCACGAAGTGATGGGCGGCTTGGCATCTATGAAGAATTGCATAATAGCATCGCTTATAAACA\nTTATACGGCGATACTAAAAGGGCCGGAAAATTATTTGAATATTCCGCAGATTTTTGAGTCGAAAATCTAT\nAAGAATTTGAATAGGGATGATCTATTGGCGAGATATGATTATTCACAAATACTAAGATTCCGAGATAGTA\nAGATAGCGGGCCGATTGAGGATGCAGACGTATTTCGGGGACGTGCATGTAAGTGCGGGACTGATAGATTG\nTGTAGCGATGGTTCGTGAGCCTATTAGAAGGGAAGGGTGTCAGCATATGATGGTACGTAGTTTTGATTTG\nATGAATGCGGGCCAGTTTTTCGATGTTCATGCGCCGAAGATCCACGCGTTTGATGACACGGTGATAGTTG\nAAAGCATGGACATCGAAAACGGAGTATGGCGCGTAAAGGCGGGTGGCGTAGGTTTGAAAACGCTGCAGGA\nAAAAGCGGAAGGAATACTCGGAGATTCAGTGTTAGACTTAGTCCACAACTATCTCAGCCAAAAGTGGGAC\nGCAGGTTATGTGGCCGCGAAGTTGCTGAGGTTTGATGAGACATATAAATTTCATCCAATTCATGAGGTGG\nGAATTTTCAACACATTGATGATACGCATGGGTCAACTCGATGACGCGTATAGGGATGGGTTCTTCGATTA\nTGACGAGATTCACGCTCAATTGATGAGGGATGTGACTTTTCAGTACCCAGAAGGTAAGCCAGTCTTTCGG\nAGAGATGGCCAATTCTTTAAAAACCTAGTGCAGTATTCGGGACGGGCGAAGATTGGGTATGAGACGTATT\nTACCAGACAGGGAATTGTGGACTGAATGGCGAACGAGATCATCCGTGCAAGATGTTGTACCCAAGTATAT\nGGAATGGTTGATAGGTAGATTACAGTTGGGGAAAATGCTTAAAATAATGTCGGAATTACCAGCGGATGTT\nACGATGCCCAACTATCTTTTGAAAGCCATTACATATAAATCGAGTGTATATGTTAAGAGATTGATACTCA\nCGTACATCGCTTTACGAATGACGTTTGGACGGTGTCCAGTAAACAAAAAAGGAACGCTTGCCTCATCAGT\nCTTAGGTTTTCTACACGCGGTTATTCCGAATCTGGAGGAATTTCTGAGGAAAGCGGGAATAACGGATGAA\nCTATGTGTTAAAATGGAGTTTACGCCGAGACTTACTGTGATGGAGAGAGAGGATAGGAAGTCAGACAGAT\nACGCCGTTGTCTTGCAAGTTTATAGGGAGAGGAAGCTGGAGGTTTTTACGCCTATAGACTCAGACTTGTT\nCGAAGATCGGAAAAAGTACTATGACGAGATCTTGAAAGATAAAAGATGGCGTGGAGAAGAGACTGATTAT\nTTTTTTAAAGACTCAGGGATACACCGGTCCCAGGTGGCTGGGTTGAGCGCAGAGCAGCTCACGTTGAAAA\nAGTTAGGACGCGACTCAGATTTCAACGACCCTAAACGGTTCGTTTCATACAGATATAGATATGTATCAGT\nTAAAGCGGGAGATATCTATGCAGAAGGGGAGAGCGTTATAACGGGACCATTATTGACACTGATTCCACAT\nGCCTACGAGTTCGGACGAGTATCTTTGATTGCGGGGCAGTCTCGAGATCAATCAAAGTTGGATAATGTCC\nCAGTCTACCGTGACCACATGAAATCCTTGGAGTTAAATGGCGTCGAAGTTGGCTATGACACTTGGTGTCC\nGTCGGGGCGTGCAGTACAAGTTAACTTGGAGTTGATATCTACCATCCTGTATAACGCGTTCAAACGTCCC\nATCGTTAAGGGAGCATTATGTCACTTCGGTATGTGGGAATTTTATAACCCGAGACGTCCCGCGTATGAGT\nCAGTAGACGTGACAATCATGAATGCGATCTCGGATATCACTGGGAGCAAAAGATGGGCATATCAGGAAAT\nTCAAGATTGGTTGGCGAGATTTATTAAGGGGTCACGGGTTGACATGGTGACACACCGCTTCCACGGGGTA\nACGAAGAAGCCAACAACTCGAGGTGAGATATGGATCTGGAACCTACTACTAGTTTTGATCTCAAATCCCA\nGTCTGGTGGTATCACAAACGGATAAATTTCCCTTATGGGTTTGCGCCTCTGATGGCTTACACCTGATTAG\nTACGGGAGTGAGGCATACCGATCATTTTAGACTTTGGGAGTGGCTACCATATACCGAAAAAATTGGGAAC\nGACGATTATATGTCGGTTCTCGCCACAGATAGAGAGTTGCGGCTTTTCGAAATCGCGTTGGAATACTTCG\nAGACTATACGCATTGGATATAGGAGAGATGAATGGACGCATTTGAAATCGAACATGTTTAATACCTGGCT\nGGGGACGCATTGTGGGGGTGTAGGGGACGGGATGATATTGTTTGACCCGGTGAGATTACCATCCCCGAGC\nAGCGTCCTTTATTTGATCTGTTCGCATAACTCAACTTTAGAAGGAATGATGTATTTACTACATGATATAT\nACGGGAAGATCGTTGAAGAGAATACTGGTACTGTTTTCATAAGGGTACACGCGCGAGGTTGTAAGTGCTC\nGGTGTGCCGAGGGGGTTTACAGGGAGTTGACGTAAAGAATAGGTCAGCTATGCGTGTTCGTAGTATGCCA\nGGGAACATCGGCTTCGATTCAGTCAACCTAATTCTTTCAACATCAACGACGAGCGCGTTTGGGAACTCTT\nACATTTACTTTAAGCTTATTAATCGTTAGTGAGGTGACACTCGCTCCGCGATCACGCAGATAC\n\n>JQ610677.1 Orungo virus isolate UGMP 359 segment 3, complete sequence\nGTATATATTCCTTCGCGATGGCGCATGCGGATGCTAAAGGAAGTGATCCGGAGAGAGAGGCGTTGAGGAA\nGAACCCTTATCTAGATGGAGACGTCTTGGGAACCGCAGGCGGCCAAGTTTTGTCGGTTTTCGCATTGACC\nGAAATTTTACAAAAAGTAAGACAGACGCAAGCTGAACTGGCCGCACACGCAATCGATTTGGATGGACCAG\nTCCCTGAGATCACCGGGGTTATTAAGAAGATAGCGGAGTTAGTTGACACCGTTCCATATGAAGTGCGCGA\nTTCACCACCTATAAGCTATAAGACTTTAAGCATGCAATCGCGCGACTTTGTCATCCAGGTGGACCAGTAT\nTACGAACAGATTTCGCAAATTGGAGGAGACGTCGGGGAGGACGAGCCGATGGAGTTCTATAAAACAATGC\nTAGAAAAGGTACGCTATTTAAGGAAGAGTGGAGCATTCATTTTGAGAGGTATTAAAACACGAGACTATAG\nGGGTAATGAAGTGGCGGAACCAGAAGCTTTAGGAGTCGAATTTCGTGAAGTACTTTCTAATTTTATTGCG\nGCGGATAGACAAGTGATACAGAATGCGTTAGATGCAGCCATAGTTGAAAATGGCCAGGTGGGTGATAGGG\nCGGTCGATGTTTATATGGCTGCTGTTTCTGAGCCATGGTATCGAATATATAATAGGTTACAGGCGTATAT\nTGAAGTTACGCAACTGAGAGAATTGAGGCGCGCAATGGAGTGGCTGAATGCACTTGGTCGTCGTAAGAGA\nGTGGAGTATGATGATTCATTCTTGACCGATTTTCGAGCGAGAGATACGGTATGGGTGCAGACGCAACAGC\nTTCCCGTTAACGCTCGTGTGATCTGGGAGGTTCCGAGGTCATATATAGCTAATTTGATGATGAATATCGC\nGTTATGTCTGCCACTAGGTGATTTCATAGCCCCAAACCCGAGGATTGGGTCGATAACGATAACCCAGCGA\nATAACTATGACTACGCCTTTTGGGATGATGTCTGGGATGACCCCCACATCAATGCAGATGGACGATGTCA\nAGAAGATATATCTCGCGTTGCTCTTTCCCGGGCAGATCGTTTTGAATATTAAACCCGACCCAGCGCACTC\nCATCGATCCGGTACTGCGTATGGTTTCGGGTGTGTTGGGGCATTTGATGTTCACCTACGGTCCCAGATTT\nACTAACATAACAGCTACAACATCGCAGTTGCTAGATAGTGCCTTGAGCGACTATTTTCTGTACATGCAAA\nACAGTAGAGTTCCGGTGGTGTACGGACCAACTGGGTTACCTTTGGATTTTAGAATCGGTGGACGACAAGG\nCTATGATTGCAATAATCTGCGGGGAGACCCGCAGACTGGGAGGGGGTACAATGGATGGGGAGTCGTTGAC\nGTCGATCGAAGAGCACCCAGTCCGTACGATTTGGTTCAAAGATTTATACGTTACTGCAACATAGACTCTC\nGCGAGATCATCGACCCACGGACGTTTGGATTTAATATGAACTATCCGCTATATATGGAGATGATACGTGC\nATTAGTTGCCGGAGGAAAAGATCAGGAAGCGGCGTACCTACGACAAATGTTACCTTTTCACATGATCAGA\nTTCGCACGGATCAATCAGATAATAAACGAAGACTTACTTAGCGCGTTTTCCTTACCAGATGAGGATTTCG\nACGCATTATTTTTCAATATGCTGCGCGGCGAGTATGGAAAGGCTGAGCCGATCGTTTTAGATATCAGTTG\nGGCTTCAATTTGGTTTGCGTTCAACCGCTACTTTGACCCAGTCCAAAGGTCAGATCTATTATCAGTGGCA\nCCCATGATTGAGGCTGTCTATGCGTCAGAAATCTCCATTTTGCAATTGGATATGATCAACCTGCAGCAGT\nTGAGAGCGAGGGCACCTGATATGTTGATTAACGCAACTCCGAGTCAGTTTTGGAAAGCGGCGTTAGCATC\nCGCAGCAGAACCAGTAGTTGAGTTGATGAATCTTTCGCAGAGTTTTCGATTCATTAACGTCAGGGATATA\nATACAGTGGACTAGAACACGAGAAGTGCAACCGTCGCTGGCTCTCACTTTGGAACGAGAGGCGTGGGCGG\nTCGCAGCTGACTTCGAAGAGTTGATGCTCGTAAACCATGTCTATTTTCATAGATCGGTGGTTCCCGAACC\nACAGTTGGATGACATCGATGAATTTCGTAGGCAAGGATTCCTGTACACAAATCTATTGGAAGCGGCCCCC\nCCGCGTTTGTTAATCACCAATTATGATTACAACGTTGCGCTACTGCAGGCGAATCTTGGACAATTTAAAT\nCCGCTTTGAGGAGAATTCTGGATGACGGTGGTTGGGTGATGTTCGGGGGAATGCTGAGAAATGTTCGTTT\nGAAAATATACGATTCAAAGCCGGGAGAGGACGTCTTAAGCGAACTACCCTATCTTTACTCCGAGAAAGTG\nGAAAACGGTTTAAGGTTTGTGTCTTTGAAGTATGCGAGACGAGCAACTATTTATTTTTTAATGTATAAGG\nTTGAATATTCAAACACACCAGATGCTTTAATATCAGTCAACCCCACGTATACCATGACGAAGATTTATAC\nAAACAAGAGACTGGTCCGGAAAGTCAGGTCACCTGACGTTTTGAACATCGTTAATAAAAGAGTAGTGGCT\nTATAAAACGAAGATGCGGTTGATTGACATTACATCGGCACTGCGTCTTGGTGTTAAACTTGCAGCACCTA\nCAGTGTGAATTGACCACTCAACCTGTGGTGCTCGGTGGGGAATTCGCTTAC\n\n>JQ610678.1 Orungo virus isolate UGMP 359 segment 4, complete sequence\nGTATATTTCGAAATGGAGCCCTTTGCTGTGCTGCACCTATCAGCCAAGCTGGCACCGCTGGTGCGTGAGG\nGATTTATCCCGTATGTGGACTTGGATAATATTAAGACGTTGAATGACCTCTGGATTGAGATTGGCAAATG\nCTCATCTGATGTATATGCGGTTGGACGAATAAATAGGTGGACGATACGTCAGCTACGTGCGTATAGATTC\nATATTCGTGTCGGAGAAGAGAACAATAACGTTGAAGGATATTAAGATCACACCTGACGTGCCAATAAGAT\nGCGCGGATGGGCTAGACTTAAAGTTACTTGAGACTACAATAGGACGTAAAAGATTAGTGTTGCGAAAGAC\nGTTTGGAGACATACTGCGAAAATATGCGTTAAGCCAGTCGGTACACTTGCATGGATCTGAGGCAGAAACC\nTTGAATATGGCGGACCCTACCATACATCACGTGAAGGGGTTACCAATGATAGCGCCAAATCATTTAAATC\nCAACGAAACCATGGAGTGATCTGGACGACACAGAAACCGATGAAAAACTAGTGTCAATGCTAGATTACGC\nGATGTATAGCGCGCAAGAAGTGCATTATGTTGGCTCGGGAGACGGTAGAACGATACGGCTGTTTGCAAAG\nAGGGACAAAAAGAGATTTGATAGAGCGAAGTGGGTGTGCTATGACCCTATTATGACTGATATTGGATTGA\nCAAATGTGATAGCTGTTAAACACTATGTCAATACTTTCAGGGATATGCTACCGTATTTAAATACTGGCGA\nCCGAGTTGAGAGATTACTATTGTGGGACGTAAGTGGAGATGCGGCGAAACATGATCGGTTTTGGGAAGCT\nCAGAGGACTGAGGAGGACCGGCGGGGAGAATCAGTTGCCGTGTCTTTAACGGAGTACTTCGCCTTGGCTA\nTTATCAAACATAGAATTCCAATCTATGAGGAAAAGTATAGATGCACCACTTCGTGGATTGTACCGCAGCC\nTGGCGCGGTCCGCGAGATGTACGAGATGAGGAATATCATACTGTTGAACGGTTTTTCTAGGGTAAATCGA\nGCGCATATCCCCCAGGCAGGCGTAATGGAGATTGAGGCTGATGTGTTACGTGAGATGGTGAGGAACTTCC\nATGGAGCTGGTCGCGGTCGGCTGCTGAAGAAATCGCTTTATGAGAGTCTACATATCCATCAAGTTGATGG\nATTGGAGGATTCGGAAGACGGAGCGCGGAGCGATCTCTTTTATTTAACCAACCAACGTAATGTTAATTCA\nATACAATCAATCAGACGAGTTTTGGGAAATAGCACGGTGTCGACTTTATGGGTGTCAAGGGAACGAGTTT\nTCGAATATGATGACTTTAATTTTGACCGATCAGCGTTGATGCTCTGGCACAGGGGTAGAGAGCACTTACT\nATTTGATGGCAACGGCGCGGTTCTATATTTGATGTGGCAGCACGGAGATAGATATAGAAAGGATGTGAAC\nTATGATCCTTCGTGGGCCGAACATTTTGCAGTATTGATCCGAGAGCCACAACCTTGGCGACCAGTTCCAG\nATCTGTCCCTCTGCCGTTTTATTTCGCTAAGACGGGTGTCGACGGTTATTAGAATACGAGGCGATATTCA\nCAGGAAAAGTGATCAGGTAAAGCGTTTAGGGTTAGATTTGTCAGGACATCTGTTCGTAACGTTAATTTCT\nGGAGCGTATCTTGCCGATTTAAGATGGTGGTTCCGGATGATCATCCAATGGTCAAAGCAGCGTAGACAGG\nAAAAGATAGACGATTTGGCTAAGGTTAACGCTGAAGTGGTTGAATGGAAAGAAGAGAAAGCCGACGAACC\nGTGGCATCGCAAGGAGGACCTGATCGCTGCTTTAATCGCGGCAAAAAGTATCACCGGTGATCAGCATATA\nGATGGGTGGATTGCGGAGCTGAGGGATATGGAATGACATCCACCCGAGGGGCAATCGAACTACCTAC\n\n>JQ610679.1 Orungo virus isolate UGMP 359 segment 5, complete sequence\nGTAAAAAGAATCCTCTGCGTTCACTGGGCACGAACATGGATCAATTCTTGGATTCTTTTGATGTGACTGG\nAGACGAGGCGAATGCCTTGAGATTATTGAGAGCGGTTTCACCTGAGATGACATGCTCACATTTGAGGAGA\nGATTGTTTAATTGGAGGGATATGCGCAAAACAGTTTTTCAACGAGGTGCTGATGGCCATTCTGGATTCAA\nAAGATCGTCAGGCAGCGCGTCAGCTGGTGACATTAGCTGTGATGACCAGTTACGACCGAGAGCTAATCTG\nGCTCAACGTACTAAGGTCAACTGAAGTGCTGCCGGCAAATGATTATGCACATGAAATACAGAATGTGGTT\nCTGAACTTGAAGAGGGTCTTCATAGAGAGTGGGTTGGAAGAAAAATACAAGAGTTTCAGGGCGAAGCGGC\nGTCCAAACAGATCTCCGACCGAGGATGCTTTCTCTTTTTTGCCCTTTTTCTACATACCCATGAATGAAAC\nAAAACGGGTTGGAATAAAGAAACTCACTAGAGTTCGGAACCTAGGTGTTGCTTTTGTTGATAGACGCGAA\nGTGACGCATCATTTACCGTTCACGGTGGACGCTGCTAGAAGGGACCTTATGATGCTGAGAAATTTCACGC\nTGGAGCACCAAAGAACATGTACGTTTACGGGTTCAAAGAGCTTGATACATGGGATGATATTCTGTCCTGA\nGGAGATGGAACCTCTTTTCCAGAAGAAGGAGACAGCGCTAGAAATCTACAGAATTTGTGAGCAGGATATG\nAAGTTTATCAACTCAAGAGGTACGATGTCATTTCCCCGGTTTTTGATGCAACGTTTAGCGGTGAAAAACG\nCTTCATCTGATGCGATGGACCAGGTTATGTTGGGACGAACTCCGAGCGATGGACGTTTGATGTCGGTGAC\nTGGTGCCTCTTTCTTTTTTGGAGGGGGACCTGATTGGCGCAAGTGGGCGATGCCGGCGTTGTTGGTACGT\nGCTGCAAGACTGAGAACCGTCGTGACATCATTCGTTAAGGAGTGGTTTGATTCGACTCACACATGTCAAG\nTCTGTTTCCTAGTTGAAAAAGGTGTCGCCGATTCAATTCCGATCACTGATGTTCGTTTATCGGATGTGTG\nCGGCGTAGGACCAGTCGCATATGTTAGATCTTATGCACATGATGACGGGAACGCGCCGGATGTTCGCGTA\nCTGAGAAAAGGTGAAATCTTCAGATTGATGGGCGGACATTATGTTATGCAGACAACGGCGAGTACAATGG\nAATCATTGGTCGTTGCCGCGAAGGAGATGCAGCGTTTGGTTCGCGGCGATGGTTTTTGGGACACACCGTA\nTTGGGGTTTAAGCATGGCAAACCTTTGTAAAATCATGTTTCATGAAAACCCAGCAAAGGAACAGATTCAT\nTTCATGATTAAGCTCATAACCTTTGGGATGTTTGGTGGGGTTCAAAGGCACAATGGACTGTTCACAGACT\nGGGACAATTTGGAGGAGTTCTTGAAGAGGATGTTTTCTACGGAGGAGATGGGCGTTCGTATGTATGAGTC\nAAGTTACCATGCGATACTTCGTGCGTGCATACTACATCTACAGACCACTGCGAAGCCTACCCTCGTTCAA\nCTAACTCACGCGATCGAATCACTCGACCTTGGAATAGAAGAAGTTCCTTTCAATTTTTATGTCTAAAACA\nTCATAATAAACCATAAAGAGTCTGAGTAATTGTATCCCTGAGCTCTTACTCTTAC\n\n>JQ610680.1 Orungo virus isolate UGMP 359 segment 6, complete sequence\nGTATAAAATACCTCGGTCATCATGGGCAAATTCGTAAAGGCCCTGAAGAAAATAGGAAGGGGTACGGTGA\nAGGCACTGACGTCTGACGCTGCAAAGAAACTTTATACGACTTTAGGAAAGGCGGCGACGCGGTTTGCTGA\nAAGCGAAGTCGGCAGCGCGGCGATTGATGGATTGATACAAGGAACAGCGCAAACTTTACTGCACGGAGGC\nAGCGCGAGTGAAAATATCAAGCAAGCGGTTGTTTTAGGTGTTCTCCACAGCATGGAAACGCCGGCGGACC\nCTTTATCACCAGGAGAGCAAGGAGTATATGATAAGATTAAGGAAATTAAACGAGAAGAAAAGGAAGATCG\nGTTTTTCGAGGTTTACCAAGAAAAGATTGACGAAGAGCTTGGTTCAGATATGAAGCGAATGCGAGAAGTG\nGCAAAAGGTGATAAGCAGGCCATCAAGGAAATGGGTGGTGAAATTAAGGTTATCGAGAAAGCTTTCGATG\nGATTGATTAAAATAGATAAAATTCAAGATATGAAATTAACGCAGTTATATGGCGCGCTCGCGAAAGAGCG\nTACGGAGCGTACGCAGGACGAGATCAAAATGGTTAACGACTACACTGGAAAAATTGAAGCACTGCAATCC\nGCGATAACAGTTGAGCGGGACGCTATGCAAGAGGAGGCGTTGCAGGAGATAATAGAAATGGGAACGGATG\nTAATTGAAACCGCCTCCGAAGAGGTTCCGATATTCGGCCCTGCGGCTGCGAATGTAGTCGCAACTGGACG\nAATGGTTGAGGGCACCTTAAAGTTGAAGCAAGTAATCGAGAAATTAGCAGGGTTAGATGTTTCGCACACC\nACAAGGGACAGAATCGAGCCGAAAGTTATAAACGCTATACTAGATCACGAGGGGGGCGTCGTACCGGAAA\nAGGAACTAGCGATTGGTGTATATAATAAGCTGCAGACAGTCAGAGAACATATGGCGGAACACAGCCATCT\nAAAGGAAATGGCAATACCAAGGCTGCAAAAGCTGTACACAGAACACGGCGATGAGTGGCATCCAAAGATA\nATTACTCAAATGAAGGTAGCGAGAGAACATCAGCCGCAAATACATATATATTGCGCTCCATGGGAATCGG\nATGACGTGTTTATGTTGCGAGTGTACGCGCCGCATCATATAGGGTGTGGTCTTTTCTTAGGAGTTGATTT\nAGAGAGTGAATTCATATTTTATGAGGATTTGATAGCAGAGAACCACGTATTGCGTGGTGGCGTCATTGAA\nGTCGTTGGAAGGAACTTCAGGCAAGCAGTGCGCGAATTTCTTTTGATGGCTGCGAGCAAGATTGAGAACA\nCTATGCATGTCAAGCGGTTAGTGAGAAGCTCGGCTTCCTCACCTATCTACTTGTCAAGCATACACTATGA\nGTGTACATTTGATGAGATAAAACAGAACGTTTTACAGATCGTGCACGACGAGCAGTTACAGATGCATCTG\nTTACGTGGTCCGAAACATTTCCAAAGACGTGCTCTGATGGCGGCTGTTGTTAAGGGTGTTAAGATCTTAG\nAGGGGCCAGATACGAAGGCGCTCATGCTACAGGGTTTGTAAGTGGCTGAAAGGTATCAAGAATAC\n\n>JQ610681.1 Orungo virus isolate UGMP 359 segment 7, complete sequence\nGTATAAATATCTAGAGATGGACGCCATTGCGGCACGTGCTCTGTCCGTGATCCAGGACTGCATTAGCGTT\nGGTGATGGGAGAATTAATTTAGACCCTGGGGTCATGGAGAGATTGGGAATTGCTATTAATAGATACAATG\nGGCTAACGAACAATGTGGTGACGATCAGACCAGGGACACAAGATGAGCGGAACGCGATGTTTTTTATGTG\nTCTGGATTTCGCGTTGGCGGCATTGAACATACAAATTGGGGTTATATCTAGGGAATACACGCAGGCGCTG\nGCCACTATCGGTGTGCTGGCAACGGGAGAAATCCCTTACTCGGTTGCCGCTATGGATACGATTGTACGGA\nTTAGCGGAACGATGGCGACATGGGGTCCCACCGAATATGAGTTACCGCCATATGCGCGGTCTCAGATGAT\nACAAATGAGCGGACGTTACTACGTTCCAGCGGGGGCGAATTCACATGCTGCCCATGTCGATCCCACGACG\nGTAGAGATTTCTTTAGCTGCTGGAGTAGTAGTGAATGTTACGAACGCGTTACAGCCTAGGGGCGTTGCGC\nCCACAATGATGTACATGGTATGGCATCCGTTGGCGATTTTCGCGAATCCTCAGGGTGCTACAGCTGCTTC\nGCCTCAAAATATGACTTTGGTGGTTGGTGGGCTGAATATAGCAGCTGGCACGATCATCGCTTGGGATACC\nGTCGCTCCTATACAGCTATCGAATCAGGGAGGACAAGAGGGAATGATCGCGATCCGGATACTATGGATGA\nCAACATTAGATAAATCTATGACAAGCTTGCCGGAGATGCGTGAAATAATCTCAAGATGCTATAGCTTTAT\nGCACCCTTCATGGCACGCGCTGCGAGGGACGGTCCTACATTCGCTTAATCTGCCGACTAATAATCCACCT\nATGTTTGCGCCTGCTACGCGACAGGAGGCATTGGCGTACTTAATTCTGGCAAATTTAGCGGATGCATATA\nCGTCGTTAAGGCCTGATTTCACCATACAAGGAATGCTCGCGGTTCCACAGGTCATTGACAGGCAGTTCGT\nTCAGGGTGCGTACAGGTAGAGGACGCCTTCCACAGTGGGCGTCTCATGTAGCCCCAGCGTCGGTCCCTTA\nCGTGTGCTGTAACGCGTAGGTAGAACGTCATATGATATTAAGTTAC\n\n>JQ610682.1 Orungo virus isolate UGMP 359 segment 8, complete sequence\nGTAAAAAATCTCCTCTCTTTTCACGATGGCTCAAGAAGTTAAGAGAAAGTTCACTAGAACAGTGTGCATC\nTATGATCCACAAAATCGCACATTCTGTGGTCGAAGTGCCGCGATGGTGTGTAACAGTTATTATACAATTA\nAAATGGGTAGAACGACGCAGTGTGGAGTGTCGCCGGTGCCCGTACCAAAGTCATATGTGCTAGAGATACC\nGGATGTTGGCTCTTATCGCATCTTAGATGGGCAGGATTCAATCAGTGTCATCGTTACTGAGACGGGCGTC\nGAGGCAACGTCTGAGAGGTGGGAAGAGTGGAAATTCGAAGGCGTTAATTGCGTTCCGATGGTTGTTCAAA\nCGGAGATTGGGAAAGGCCTGATTGACATGGAGATCAAGTTTAGTAAGGGAATGGGGCTCGTTAAACCTTA\nTGTAAAGAATGAGGTTAGCAGAACTGAGATCCCACGGCTACCGGGTGCTTCAGTCATTGATACACCGATA\nCGCGATTACCGTCAACTTTTGAAGGATCAGAGAGATGAAAGAAGGGCGGCGCTCGATGCGATCGCATGCG\nACATATGTCCCACTCTATCAAGAATGCTAGGGGCGAATATTACAGACGGATCGCCACAAGTCGAAGAAGT\nCGCAACACGGCCAACACAACCTCCAGCTCAGCTGAAGCTGGATGTGCCTAACTGGGACCAACCGACTGAT\nTCAGATGATGAGGATGAGGAATCCAAGCGCGTGACAACGCAAAGTAATGCTGATACTGAGGAACAAGTGA\nCTTTCGAAGATTGCATTACCGATCAATACTTTTCGAAAACGGGTGAATTCGCGAAGAAGTATCCTGAAAT\nGTTAGCGGGACTTTCCGCGAAGATGCCGAGTGAAACAGGTAGGTTTACAAAAATATTGACGACGAGGAAG\nGCTCAATGGAATAACGTTCCTCTTTTCGAATTAGATCCAAACGGGTTTACATATCATTTTAGTAAGCTGG\nGTAATTCGACGAGGATCTTCTGTGTCCAACGTGATTTGAGCTACATGGTTTTACCCGCAGGGCAAGGCCT\nGAAGTAGCGGTGCATGTAGCCGGGAGAGGTACAACTTAC\n\n>JQ610683.1 Orungo virus isolate UGMP 359 segment 9, complete sequence\nGTATAAAACATCCTCCCATGTCATGTTGGTGTTGGCACCGGGTGATCTCATAGACGGAGTGCGTCATCAA\nTTATCTGAAAGAGGAGTCAGGATTCGTTTACGGGAAACGAATGATGACGAGCAAAAGGATGAACCAGTGG\nATACGGGAGGCGGCAAGCCGGGTGATCGAATCGGGAAGGAAGTTGGAAATGCCGAGAGTGAACAGTCTTC\nCGATAAAGAGAAGAAGGCTGGAGGAAGTTCGGATTCAGAGCTCGGGGAAGGTGGAGATGGAAGGCGACAA\nACTGAGAAGGCTGAAGGCGGAGAGAATGGAACTAGAGATATTGGCATTCAGGATAAAGACAAACAATTTG\nATCGGCGCGCTAATCCAGATAACGCGTTGGACAGAGAAAATCGATCAGGAGATCCGCAACTTAAATATGG\nATTTGCAACCAAACGAATTGCAAACGCCGTTGAGTCAAAGTACCACTGCGGTGGATTTGAGGGGCCAGGA\nTCGGATGGATACATCAAACTAGAAATGTCAATAATGAAGGCGCTAGGTTTAAACCGAGATGACCACATCG\nAACAATTGGAGTTCCTCAAGCACCAACAGAAAGGGCCCAGCAAAATTCAAGTCAGAACGATCGCTTCCGA\nAACCAAATTAAAAGAGGTGTGTAATATAATGGACAAGCCGGTGGCTCCCACAGCGAGAAGTGCGGTGAGT\nGTAGTTAGTAACCGTGTTGAAGACGTGAAGGAAGCCCAGGTGTATTTTACAACTCCAACAGGAGATAGAG\nGCTGGAAAGAAGTAGCAAGGAAAGCGAGCCAGACACCAAACATTCGAGCGTACATTAATCCGGAGGGAGA\nTGATCCTAAAGTCTCATTTCTGCATTTAATCGATCATCTGTGAGGTCACGGTCTGAACTACGGGCATGCT\nGGGTGTTTCAGTTAC\n\n>JQ610684.1 Orungo virus isolate UGMP 359 segment 10, complete sequence\nGTATAAAATTCCGTTCGCAATGTACCGTGACTTGCTGAATATTCACACTGAAATGAGGGGCCCGCCATCT\nTATGAACCTAGTGGCTTAGCTCAAGCGACAGCACCGACTATGAGGTTTGGGGATAGAGAAGATGAGGAAG\nGCCTATTGAGGGCGCGCGAGCTTTCGCTTAATGTGTTAACGAATGCTATGACTAATACAACGGGTGCGAA\nTGAGGCGATTAAGAATGAGAAAGCGATGTTTGGGGCATATGCCGATGCACTTAGGGATACTCCGGAGATT\nAGGGTGGTGAAAAGGCGGATAAATGAACGTACGTTAGAAAAGTTGCATAAAATGCGACGTTCGCTGCACG\nGAAGACGAATGTTCGTACGAATGTTGTTGGCGATAAATGTGGGATTGGCGCTATTAACCTCGGCAGTGAA\nTGTGGTACGCCAGTCGCTAGATGATTTTGGGAAAGAAAGGTGGATAGTTGGTGGAGTGTGGTGGTTAGGT\nGAGGTCGTCGTTACGATTAATTTTGGAACGACTGTTGCTACGTTGGTATTAATGAGGATACATGGCGCAT\nTAAACGCGCAGCTTCAAACCATTAAGCGTGACATATATAAGAAAAGCTCGTATAATGAGGCCGCTGCCAT\nGCATTGGAAAGGTGAAATTAGCTTAATTGAGGAGCTAGCGGCGAGCCACGTACCTGCGGGATCGAATGTC\nTAGTCCGCGACATCGAAAAATTCACTTGTCCAGGTGAAGCCCGTAGAACGGATCGTCTTAC\n\n" }, { "path": "tests/input/TestFastaFetch/orungo.fasta", "content": ">JQ610675.1 Orungo virus isolate UGMP 359 segment 1, complete sequence\nGTATAATTAGGAATGGTCATCACTGTGGAAGGTGCGTGGCTGGTGAGACGGGCGTTGCAACGTTTTTTGA\nAGTTCAGTAAAATCGACGGGGAATCAGCAGTTTATGAGTTCTATAGGTATTCAAGTAATATTCGTGAAAT\nAAGAAGGAAGCATGGGACGCGTTATAAAATGCATGATGAAGAGTTGGAGCGGAGGCGTGATTCGGGCAAA\nCTGCGTTTTAAAGGTATGCAAGTTGTGGTAGAGTCGACTTGGATGGAGATTTTAGGGAAGGGACGTACGA\nCGGACGAAATCGAGATATTCAGAAGTTCGATTTTATCGTTGGATGAACTGAATCCGGAAGAAGAATTTCT\nGCGCAATTATGCGAGTTCGGACAAGGAACATCCATCCTACTTGTTTGTTCGGGGGCGGGCGGTCAATGAG\nATGCAGATTTATGGCGACATGCCGATAAAAGCGTGGTTGAGCTTTTTAGTAGAATGTGAGGTTGAATATG\nGGTACAAACTCTTCGGAATGGAAGTTGCGAGATCGTTCGTTCAGAGCTTTGGATCTCCGTTTCACCAGAA\nCTCGCGTGATCTATCACAGATTGACGATATGGCGCCTGCTTTTACGTCACCTTTATTATTTGAAATGTGT\nTGTATGACATCAATTCTCGAAATTAATATACGCATGCGTATGCTGGAGGAGAGGGTTGCAACCCTAAAAT\nTTGGTGAGCGGGAGATCGACCCACTTGAAGTACTAAAAGAATTCTTCCGAATCTGCATTCCGCATCCGAA\nAAAGATTAATAATATGTTGAGAGCTCCATACTCATGGTTCGTCAAGCTGTGGGGCGTATCGTATCATGAG\nCCAATAGTCCTGACGGCGAGGGGCGGCGAGGATAAGAACTCGAAAGACATATTCTTTACGGGATTTCACA\nGAGTCAAGAATCCATACTCAATAATGTTGAAAAAATCGAGGTTTTTTAAGAAATCTTTAGACGAGAATAT\nCAGCAAAGTGAAAGAAGCGATAGACTATTCAAACTCGTTGACGGGGATGTCTTTAGGGCTGCCCGTATTT\nCTATCCATGCTACAGAATGTGTACGACACTGAGTTTAATCCGACTATGGTTCAACACGTGTTACTAGCGT\nCGTTCTTGTTGAGTATCCAAACAATAACTGGCTATGGACGCGCTTGGGTGAAAAATGTGTCAAGCGATAA\nCGACACTCAAATGCGCCCGGCGGAGGACAACTTCATTGATCGAGTTGCTAAGCAAACGGAGATTAATTTT\nATACAGGCGTATGAAGAGGCGTTGGGGCACGGAGAAGATATCGTTAAGCCAGAAGACATGTTTACCTCCA\nTTTTGCGTTTGGCAAGAAATACAAGTTCCGGCTTCTCTACTGCTGTTGACGTTTATAAACGATTCGGTCC\nAAAGTCGGGAGGGAGAGGAGAACGCGTTAAGATAACATCAAGAATTAAAGCATTAGTTATCTTCACAAAG\nGGCCATGAAATATTTACAGCTGAAAATCTCGCGAAAAGATATGATACGGAGGAAGATTACCAGACTAAAG\nGGTCACGGGATGTACCTATCAAAGCAACGCGGACGATTTATTCAATAAACCTCTCCATCTTGATCCCGCA\nGCTGATCCTAACTTTACCGTTGAATGAATATTTTGCCCGGTTCGGAGGATCAACTGCACCTGACTCACGT\nAGCCTAGGGGGTAAGGTGATTATCGGAGATCTAGAAGCAACGGGATCACGGACGATCGATGCGGCAGATA\nCGTTTAGAAATTCGTCCGACCCAGAAATTTTCACAATAGCGATCGATTATTCGGATTACGATCAACATTT\nGACGGTTTTTAACTTCAGGAACGGTATGCTGGAAGGAATTCGCTCTGCGATGAAGAGATATAAAGAGTTG\nAGGTATGATGGATACACGTTGAATGAATTGATTGAATTCGGGTATGGGGAGGGGAGAATTGTTAATTCGA\nAATGGAACGGAAAGAGGCGGGTCAAATCTGTACGAATGAGCGATTATATGGCATTGAGTGAAAGTCAACG\nCGCTCAGGGCACTTTCAAGCCGCCGCAGGGAGTGAGACCGGTTAGTTCAATGCAAGTGTTCGATTCAGTG\nGGTGAGGCATCTGGAGGGGATACTCTCCTCATCTCGCCCACTGACGGATCGGATTTAGCAACCGTCAACA\nCGCATTTGTCGGGTGAAAATTCAACGTTAGTTGCTAACTCTTTGCATAATATGGCTATCGGACGTATCAT\nACAAGAAGAGATCAGAAAGAACCATCGAGCGGCTTTTACCTTTGAATCTGAGCAGTACGTTGGAGATGAT\nACGTTACTTTATGCAAAGTTGAACACATTAAACCATGAAATTTTTGATAAAGCGATTGATACCATCTTCG\nATACTGTGGGAAAGTGCGGACATGTGGCATCGGCAGCGAAAACCCTTATCGCTCCTTTCTCTGTTGAAAA\nAACTCAGACTCATGCGAAGCAAGGAATTTACATTGCGCAGGATCGGATGATGATCATCTCTTCAGAGCGT\nAGAAAGGATATCGAGGACGTCCAAGGGTATATGAGATCACAAGTGTCGGTTATGGCGACAAAAGTAAGCC\nGCGGCTTTAGTCATGAACTGGCTCAGCTTGTCTTTATGATGAAGAGCAGCATCGTAGGCTTTCGTAAACT\nGAAGCGAACTGTGGTGGAGGATGGTGTATACCGTGATCGCGCGTTGGATTCGGAAGATGAGGATGGCTTC\nACTTTGATGCAGATCCGTGATCCGTTGGTCGCCTTCTACCCTGCTGAGTGGAACGGCTATGGCATGCATC\nCAGTCGCTTTGAATATCGTCATGACGGAAGACATGTTTATAGACACGAGTACCATGGTTGAGTTTCAGCA\nTGTAATGCGGCCGCTCCTTCGATTTATGGGTAGGATACCTCCAGTGTGGAATGAAACTAAAGCCGATAAA\nCGTCAGATTTCATCCATAACAAAGATGAGTTTCTTCTCCAAAATGGCTAGACCAGCGGTGAGGGCGGTTC\nTGGCGAATAGTGAACTGTCAGATCAAGTGAGAACATTGCCACTGGGCGACTTTTCGCCTTTCAATCTCTC\nCGCAACAATGATGCACTCAGCATTATTGAAAGAACCACGCGCGCGTGCCCTGCTGACGCCAGCCTACGAA\nAAAGAATTCCAGTCAGAGTTGAATTCAAACCGGGATAGCGAAGTAAATTTCGTCGGGAGGAACATGGAGA\nTCAACACTAATTATATGAAACTGTTCGATGTTGATTTGTCTACGCGAATAGTGGCCAAACAATTTAGTTT\nTCCAGATCAGAATATGTCGTTGCCTTTTTATTTTCAGAAACTCTTGATTGGACATAGACCGGTCGCGCGG\nATGAGAATGACCTATATTGACCGGATTGACCAAATCTTACGGGGAGACGTCGTGATGAGGGGTTTCATCA\nCAGCGAATACTATTATGTCCGTTTTAGAGAAGATTGGCACTGCTCACGCCGTACAGGACTTAACAACAAT\nATTTCAGTTGATGAACATTGAATCTAAGGTGGCGCATAGGCTAGCGGAGTATATCGCTTCTGAAAGGGTA\nAGATTCGACGCGCTCTCGATTGCAAAGAGGGGGATATGCGGGGATGAATTCTCCATGTCGCTGGATGTGT\nGCACGGAACGGTTTGCTGAACGGTTCATGGAACTACCAGCGCAGTTTACTAAAACTGAGAGAGATATAGC\nGATTTTATATGCCGCGCAGCTAACTATGTTGCGCTGTGCGGCTAACCTAGATCTTAGGAAAATTAAGATT\nGGGGTTTCAGCGGATCACGTTAAGAGATTTAAACAAAGACAGGCTAGATTTAAGACTCATCTACCTAAAA\nTGCGTACAGTCACGCGGCTGATAACGCCTGAACGAATCTCCGCACGCCTGGTTCAGCATCAGTTTACATG\nACGCACCACCTAATCAACTTAC\n\n>JQ610676.1 Orungo virus isolate UGMP 359 segment 2, complete sequence\nGTATAATTGATCCGCGATGGCTTTCGAGCGTACGGTAGCCTTAACAAGAGAGTTCGCAAATGAAACAAGA\nCAGCATTTTGGGAAGTTTGATATAGTTGTAAACACGGAAAGCAGTATTGAGGACGAAGCAACGGGTGAGT\nGGGAGTTCGCACGAAGTGATGGGCGGCTTGGCATCTATGAAGAATTGCATAATAGCATCGCTTATAAACA\nTTATACGGCGATACTAAAAGGGCCGGAAAATTATTTGAATATTCCGCAGATTTTTGAGTCGAAAATCTAT\nAAGAATTTGAATAGGGATGATCTATTGGCGAGATATGATTATTCACAAATACTAAGATTCCGAGATAGTA\nAGATAGCGGGCCGATTGAGGATGCAGACGTATTTCGGGGACGTGCATGTAAGTGCGGGACTGATAGATTG\nTGTAGCGATGGTTCGTGAGCCTATTAGAAGGGAAGGGTGTCAGCATATGATGGTACGTAGTTTTGATTTG\nATGAATGCGGGCCAGTTTTTCGATGTTCATGCGCCGAAGATCCACGCGTTTGATGACACGGTGATAGTTG\nAAAGCATGGACATCGAAAACGGAGTATGGCGCGTAAAGGCGGGTGGCGTAGGTTTGAAAACGCTGCAGGA\nAAAAGCGGAAGGAATACTCGGAGATTCAGTGTTAGACTTAGTCCACAACTATCTCAGCCAAAAGTGGGAC\nGCAGGTTATGTGGCCGCGAAGTTGCTGAGGTTTGATGAGACATATAAATTTCATCCAATTCATGAGGTGG\nGAATTTTCAACACATTGATGATACGCATGGGTCAACTCGATGACGCGTATAGGGATGGGTTCTTCGATTA\nTGACGAGATTCACGCTCAATTGATGAGGGATGTGACTTTTCAGTACCCAGAAGGTAAGCCAGTCTTTCGG\nAGAGATGGCCAATTCTTTAAAAACCTAGTGCAGTATTCGGGACGGGCGAAGATTGGGTATGAGACGTATT\nTACCAGACAGGGAATTGTGGACTGAATGGCGAACGAGATCATCCGTGCAAGATGTTGTACCCAAGTATAT\nGGAATGGTTGATAGGTAGATTACAGTTGGGGAAAATGCTTAAAATAATGTCGGAATTACCAGCGGATGTT\nACGATGCCCAACTATCTTTTGAAAGCCATTACATATAAATCGAGTGTATATGTTAAGAGATTGATACTCA\nCGTACATCGCTTTACGAATGACGTTTGGACGGTGTCCAGTAAACAAAAAAGGAACGCTTGCCTCATCAGT\nCTTAGGTTTTCTACACGCGGTTATTCCGAATCTGGAGGAATTTCTGAGGAAAGCGGGAATAACGGATGAA\nCTATGTGTTAAAATGGAGTTTACGCCGAGACTTACTGTGATGGAGAGAGAGGATAGGAAGTCAGACAGAT\nACGCCGTTGTCTTGCAAGTTTATAGGGAGAGGAAGCTGGAGGTTTTTACGCCTATAGACTCAGACTTGTT\nCGAAGATCGGAAAAAGTACTATGACGAGATCTTGAAAGATAAAAGATGGCGTGGAGAAGAGACTGATTAT\nTTTTTTAAAGACTCAGGGATACACCGGTCCCAGGTGGCTGGGTTGAGCGCAGAGCAGCTCACGTTGAAAA\nAGTTAGGACGCGACTCAGATTTCAACGACCCTAAACGGTTCGTTTCATACAGATATAGATATGTATCAGT\nTAAAGCGGGAGATATCTATGCAGAAGGGGAGAGCGTTATAACGGGACCATTATTGACACTGATTCCACAT\nGCCTACGAGTTCGGACGAGTATCTTTGATTGCGGGGCAGTCTCGAGATCAATCAAAGTTGGATAATGTCC\nCAGTCTACCGTGACCACATGAAATCCTTGGAGTTAAATGGCGTCGAAGTTGGCTATGACACTTGGTGTCC\nGTCGGGGCGTGCAGTACAAGTTAACTTGGAGTTGATATCTACCATCCTGTATAACGCGTTCAAACGTCCC\nATCGTTAAGGGAGCATTATGTCACTTCGGTATGTGGGAATTTTATAACCCGAGACGTCCCGCGTATGAGT\nCAGTAGACGTGACAATCATGAATGCGATCTCGGATATCACTGGGAGCAAAAGATGGGCATATCAGGAAAT\nTCAAGATTGGTTGGCGAGATTTATTAAGGGGTCACGGGTTGACATGGTGACACACCGCTTCCACGGGGTA\nACGAAGAAGCCAACAACTCGAGGTGAGATATGGATCTGGAACCTACTACTAGTTTTGATCTCAAATCCCA\nGTCTGGTGGTATCACAAACGGATAAATTTCCCTTATGGGTTTGCGCCTCTGATGGCTTACACCTGATTAG\nTACGGGAGTGAGGCATACCGATCATTTTAGACTTTGGGAGTGGCTACCATATACCGAAAAAATTGGGAAC\nGACGATTATATGTCGGTTCTCGCCACAGATAGAGAGTTGCGGCTTTTCGAAATCGCGTTGGAATACTTCG\nAGACTATACGCATTGGATATAGGAGAGATGAATGGACGCATTTGAAATCGAACATGTTTAATACCTGGCT\nGGGGACGCATTGTGGGGGTGTAGGGGACGGGATGATATTGTTTGACCCGGTGAGATTACCATCCCCGAGC\nAGCGTCCTTTATTTGATCTGTTCGCATAACTCAACTTTAGAAGGAATGATGTATTTACTACATGATATAT\nACGGGAAGATCGTTGAAGAGAATACTGGTACTGTTTTCATAAGGGTACACGCGCGAGGTTGTAAGTGCTC\nGGTGTGCCGAGGGGGTTTACAGGGAGTTGACGTAAAGAATAGGTCAGCTATGCGTGTTCGTAGTATGCCA\nGGGAACATCGGCTTCGATTCAGTCAACCTAATTCTTTCAACATCAACGACGAGCGCGTTTGGGAACTCTT\nACATTTACTTTAAGCTTATTAATCGTTAGTGAGGTGACACTCGCTCCGCGATCACGCAGATAC\n\n>JQ610677.1 Orungo virus isolate UGMP 359 segment 3, complete sequence\nGTATATATTCCTTCGCGATGGCGCATGCGGATGCTAAAGGAAGTGATCCGGAGAGAGAGGCGTTGAGGAA\nGAACCCTTATCTAGATGGAGACGTCTTGGGAACCGCAGGCGGCCAAGTTTTGTCGGTTTTCGCATTGACC\nGAAATTTTACAAAAAGTAAGACAGACGCAAGCTGAACTGGCCGCACACGCAATCGATTTGGATGGACCAG\nTCCCTGAGATCACCGGGGTTATTAAGAAGATAGCGGAGTTAGTTGACACCGTTCCATATGAAGTGCGCGA\nTTCACCACCTATAAGCTATAAGACTTTAAGCATGCAATCGCGCGACTTTGTCATCCAGGTGGACCAGTAT\nTACGAACAGATTTCGCAAATTGGAGGAGACGTCGGGGAGGACGAGCCGATGGAGTTCTATAAAACAATGC\nTAGAAAAGGTACGCTATTTAAGGAAGAGTGGAGCATTCATTTTGAGAGGTATTAAAACACGAGACTATAG\nGGGTAATGAAGTGGCGGAACCAGAAGCTTTAGGAGTCGAATTTCGTGAAGTACTTTCTAATTTTATTGCG\nGCGGATAGACAAGTGATACAGAATGCGTTAGATGCAGCCATAGTTGAAAATGGCCAGGTGGGTGATAGGG\nCGGTCGATGTTTATATGGCTGCTGTTTCTGAGCCATGGTATCGAATATATAATAGGTTACAGGCGTATAT\nTGAAGTTACGCAACTGAGAGAATTGAGGCGCGCAATGGAGTGGCTGAATGCACTTGGTCGTCGTAAGAGA\nGTGGAGTATGATGATTCATTCTTGACCGATTTTCGAGCGAGAGATACGGTATGGGTGCAGACGCAACAGC\nTTCCCGTTAACGCTCGTGTGATCTGGGAGGTTCCGAGGTCATATATAGCTAATTTGATGATGAATATCGC\nGTTATGTCTGCCACTAGGTGATTTCATAGCCCCAAACCCGAGGATTGGGTCGATAACGATAACCCAGCGA\nATAACTATGACTACGCCTTTTGGGATGATGTCTGGGATGACCCCCACATCAATGCAGATGGACGATGTCA\nAGAAGATATATCTCGCGTTGCTCTTTCCCGGGCAGATCGTTTTGAATATTAAACCCGACCCAGCGCACTC\nCATCGATCCGGTACTGCGTATGGTTTCGGGTGTGTTGGGGCATTTGATGTTCACCTACGGTCCCAGATTT\nACTAACATAACAGCTACAACATCGCAGTTGCTAGATAGTGCCTTGAGCGACTATTTTCTGTACATGCAAA\nACAGTAGAGTTCCGGTGGTGTACGGACCAACTGGGTTACCTTTGGATTTTAGAATCGGTGGACGACAAGG\nCTATGATTGCAATAATCTGCGGGGAGACCCGCAGACTGGGAGGGGGTACAATGGATGGGGAGTCGTTGAC\nGTCGATCGAAGAGCACCCAGTCCGTACGATTTGGTTCAAAGATTTATACGTTACTGCAACATAGACTCTC\nGCGAGATCATCGACCCACGGACGTTTGGATTTAATATGAACTATCCGCTATATATGGAGATGATACGTGC\nATTAGTTGCCGGAGGAAAAGATCAGGAAGCGGCGTACCTACGACAAATGTTACCTTTTCACATGATCAGA\nTTCGCACGGATCAATCAGATAATAAACGAAGACTTACTTAGCGCGTTTTCCTTACCAGATGAGGATTTCG\nACGCATTATTTTTCAATATGCTGCGCGGCGAGTATGGAAAGGCTGAGCCGATCGTTTTAGATATCAGTTG\nGGCTTCAATTTGGTTTGCGTTCAACCGCTACTTTGACCCAGTCCAAAGGTCAGATCTATTATCAGTGGCA\nCCCATGATTGAGGCTGTCTATGCGTCAGAAATCTCCATTTTGCAATTGGATATGATCAACCTGCAGCAGT\nTGAGAGCGAGGGCACCTGATATGTTGATTAACGCAACTCCGAGTCAGTTTTGGAAAGCGGCGTTAGCATC\nCGCAGCAGAACCAGTAGTTGAGTTGATGAATCTTTCGCAGAGTTTTCGATTCATTAACGTCAGGGATATA\nATACAGTGGACTAGAACACGAGAAGTGCAACCGTCGCTGGCTCTCACTTTGGAACGAGAGGCGTGGGCGG\nTCGCAGCTGACTTCGAAGAGTTGATGCTCGTAAACCATGTCTATTTTCATAGATCGGTGGTTCCCGAACC\nACAGTTGGATGACATCGATGAATTTCGTAGGCAAGGATTCCTGTACACAAATCTATTGGAAGCGGCCCCC\nCCGCGTTTGTTAATCACCAATTATGATTACAACGTTGCGCTACTGCAGGCGAATCTTGGACAATTTAAAT\nCCGCTTTGAGGAGAATTCTGGATGACGGTGGTTGGGTGATGTTCGGGGGAATGCTGAGAAATGTTCGTTT\nGAAAATATACGATTCAAAGCCGGGAGAGGACGTCTTAAGCGAACTACCCTATCTTTACTCCGAGAAAGTG\nGAAAACGGTTTAAGGTTTGTGTCTTTGAAGTATGCGAGACGAGCAACTATTTATTTTTTAATGTATAAGG\nTTGAATATTCAAACACACCAGATGCTTTAATATCAGTCAACCCCACGTATACCATGACGAAGATTTATAC\nAAACAAGAGACTGGTCCGGAAAGTCAGGTCACCTGACGTTTTGAACATCGTTAATAAAAGAGTAGTGGCT\nTATAAAACGAAGATGCGGTTGATTGACATTACATCGGCACTGCGTCTTGGTGTTAAACTTGCAGCACCTA\nCAGTGTGAATTGACCACTCAACCTGTGGTGCTCGGTGGGGAATTCGCTTAC\n\n>JQ610678.1 Orungo virus isolate UGMP 359 segment 4, complete sequence\nGTATATTTCGAAATGGAGCCCTTTGCTGTGCTGCACCTATCAGCCAAGCTGGCACCGCTGGTGCGTGAGG\nGATTTATCCCGTATGTGGACTTGGATAATATTAAGACGTTGAATGACCTCTGGATTGAGATTGGCAAATG\nCTCATCTGATGTATATGCGGTTGGACGAATAAATAGGTGGACGATACGTCAGCTACGTGCGTATAGATTC\nATATTCGTGTCGGAGAAGAGAACAATAACGTTGAAGGATATTAAGATCACACCTGACGTGCCAATAAGAT\nGCGCGGATGGGCTAGACTTAAAGTTACTTGAGACTACAATAGGACGTAAAAGATTAGTGTTGCGAAAGAC\nGTTTGGAGACATACTGCGAAAATATGCGTTAAGCCAGTCGGTACACTTGCATGGATCTGAGGCAGAAACC\nTTGAATATGGCGGACCCTACCATACATCACGTGAAGGGGTTACCAATGATAGCGCCAAATCATTTAAATC\nCAACGAAACCATGGAGTGATCTGGACGACACAGAAACCGATGAAAAACTAGTGTCAATGCTAGATTACGC\nGATGTATAGCGCGCAAGAAGTGCATTATGTTGGCTCGGGAGACGGTAGAACGATACGGCTGTTTGCAAAG\nAGGGACAAAAAGAGATTTGATAGAGCGAAGTGGGTGTGCTATGACCCTATTATGACTGATATTGGATTGA\nCAAATGTGATAGCTGTTAAACACTATGTCAATACTTTCAGGGATATGCTACCGTATTTAAATACTGGCGA\nCCGAGTTGAGAGATTACTATTGTGGGACGTAAGTGGAGATGCGGCGAAACATGATCGGTTTTGGGAAGCT\nCAGAGGACTGAGGAGGACCGGCGGGGAGAATCAGTTGCCGTGTCTTTAACGGAGTACTTCGCCTTGGCTA\nTTATCAAACATAGAATTCCAATCTATGAGGAAAAGTATAGATGCACCACTTCGTGGATTGTACCGCAGCC\nTGGCGCGGTCCGCGAGATGTACGAGATGAGGAATATCATACTGTTGAACGGTTTTTCTAGGGTAAATCGA\nGCGCATATCCCCCAGGCAGGCGTAATGGAGATTGAGGCTGATGTGTTACGTGAGATGGTGAGGAACTTCC\nATGGAGCTGGTCGCGGTCGGCTGCTGAAGAAATCGCTTTATGAGAGTCTACATATCCATCAAGTTGATGG\nATTGGAGGATTCGGAAGACGGAGCGCGGAGCGATCTCTTTTATTTAACCAACCAACGTAATGTTAATTCA\nATACAATCAATCAGACGAGTTTTGGGAAATAGCACGGTGTCGACTTTATGGGTGTCAAGGGAACGAGTTT\nTCGAATATGATGACTTTAATTTTGACCGATCAGCGTTGATGCTCTGGCACAGGGGTAGAGAGCACTTACT\nATTTGATGGCAACGGCGCGGTTCTATATTTGATGTGGCAGCACGGAGATAGATATAGAAAGGATGTGAAC\nTATGATCCTTCGTGGGCCGAACATTTTGCAGTATTGATCCGAGAGCCACAACCTTGGCGACCAGTTCCAG\nATCTGTCCCTCTGCCGTTTTATTTCGCTAAGACGGGTGTCGACGGTTATTAGAATACGAGGCGATATTCA\nCAGGAAAAGTGATCAGGTAAAGCGTTTAGGGTTAGATTTGTCAGGACATCTGTTCGTAACGTTAATTTCT\nGGAGCGTATCTTGCCGATTTAAGATGGTGGTTCCGGATGATCATCCAATGGTCAAAGCAGCGTAGACAGG\nAAAAGATAGACGATTTGGCTAAGGTTAACGCTGAAGTGGTTGAATGGAAAGAAGAGAAAGCCGACGAACC\nGTGGCATCGCAAGGAGGACCTGATCGCTGCTTTAATCGCGGCAAAAAGTATCACCGGTGATCAGCATATA\nGATGGGTGGATTGCGGAGCTGAGGGATATGGAATGACATCCACCCGAGGGGCAATCGAACTACCTAC\n\n>JQ610679.1 Orungo virus isolate UGMP 359 segment 5, complete sequence\nGTAAAAAGAATCCTCTGCGTTCACTGGGCACGAACATGGATCAATTCTTGGATTCTTTTGATGTGACTGG\nAGACGAGGCGAATGCCTTGAGATTATTGAGAGCGGTTTCACCTGAGATGACATGCTCACATTTGAGGAGA\nGATTGTTTAATTGGAGGGATATGCGCAAAACAGTTTTTCAACGAGGTGCTGATGGCCATTCTGGATTCAA\nAAGATCGTCAGGCAGCGCGTCAGCTGGTGACATTAGCTGTGATGACCAGTTACGACCGAGAGCTAATCTG\nGCTCAACGTACTAAGGTCAACTGAAGTGCTGCCGGCAAATGATTATGCACATGAAATACAGAATGTGGTT\nCTGAACTTGAAGAGGGTCTTCATAGAGAGTGGGTTGGAAGAAAAATACAAGAGTTTCAGGGCGAAGCGGC\nGTCCAAACAGATCTCCGACCGAGGATGCTTTCTCTTTTTTGCCCTTTTTCTACATACCCATGAATGAAAC\nAAAACGGGTTGGAATAAAGAAACTCACTAGAGTTCGGAACCTAGGTGTTGCTTTTGTTGATAGACGCGAA\nGTGACGCATCATTTACCGTTCACGGTGGACGCTGCTAGAAGGGACCTTATGATGCTGAGAAATTTCACGC\nTGGAGCACCAAAGAACATGTACGTTTACGGGTTCAAAGAGCTTGATACATGGGATGATATTCTGTCCTGA\nGGAGATGGAACCTCTTTTCCAGAAGAAGGAGACAGCGCTAGAAATCTACAGAATTTGTGAGCAGGATATG\nAAGTTTATCAACTCAAGAGGTACGATGTCATTTCCCCGGTTTTTGATGCAACGTTTAGCGGTGAAAAACG\nCTTCATCTGATGCGATGGACCAGGTTATGTTGGGACGAACTCCGAGCGATGGACGTTTGATGTCGGTGAC\nTGGTGCCTCTTTCTTTTTTGGAGGGGGACCTGATTGGCGCAAGTGGGCGATGCCGGCGTTGTTGGTACGT\nGCTGCAAGACTGAGAACCGTCGTGACATCATTCGTTAAGGAGTGGTTTGATTCGACTCACACATGTCAAG\nTCTGTTTCCTAGTTGAAAAAGGTGTCGCCGATTCAATTCCGATCACTGATGTTCGTTTATCGGATGTGTG\nCGGCGTAGGACCAGTCGCATATGTTAGATCTTATGCACATGATGACGGGAACGCGCCGGATGTTCGCGTA\nCTGAGAAAAGGTGAAATCTTCAGATTGATGGGCGGACATTATGTTATGCAGACAACGGCGAGTACAATGG\nAATCATTGGTCGTTGCCGCGAAGGAGATGCAGCGTTTGGTTCGCGGCGATGGTTTTTGGGACACACCGTA\nTTGGGGTTTAAGCATGGCAAACCTTTGTAAAATCATGTTTCATGAAAACCCAGCAAAGGAACAGATTCAT\nTTCATGATTAAGCTCATAACCTTTGGGATGTTTGGTGGGGTTCAAAGGCACAATGGACTGTTCACAGACT\nGGGACAATTTGGAGGAGTTCTTGAAGAGGATGTTTTCTACGGAGGAGATGGGCGTTCGTATGTATGAGTC\nAAGTTACCATGCGATACTTCGTGCGTGCATACTACATCTACAGACCACTGCGAAGCCTACCCTCGTTCAA\nCTAACTCACGCGATCGAATCACTCGACCTTGGAATAGAAGAAGTTCCTTTCAATTTTTATGTCTAAAACA\nTCATAATAAACCATAAAGAGTCTGAGTAATTGTATCCCTGAGCTCTTACTCTTAC\n\n>JQ610680.1 Orungo virus isolate UGMP 359 segment 6, complete sequence\nGTATAAAATACCTCGGTCATCATGGGCAAATTCGTAAAGGCCCTGAAGAAAATAGGAAGGGGTACGGTGA\nAGGCACTGACGTCTGACGCTGCAAAGAAACTTTATACGACTTTAGGAAAGGCGGCGACGCGGTTTGCTGA\nAAGCGAAGTCGGCAGCGCGGCGATTGATGGATTGATACAAGGAACAGCGCAAACTTTACTGCACGGAGGC\nAGCGCGAGTGAAAATATCAAGCAAGCGGTTGTTTTAGGTGTTCTCCACAGCATGGAAACGCCGGCGGACC\nCTTTATCACCAGGAGAGCAAGGAGTATATGATAAGATTAAGGAAATTAAACGAGAAGAAAAGGAAGATCG\nGTTTTTCGAGGTTTACCAAGAAAAGATTGACGAAGAGCTTGGTTCAGATATGAAGCGAATGCGAGAAGTG\nGCAAAAGGTGATAAGCAGGCCATCAAGGAAATGGGTGGTGAAATTAAGGTTATCGAGAAAGCTTTCGATG\nGATTGATTAAAATAGATAAAATTCAAGATATGAAATTAACGCAGTTATATGGCGCGCTCGCGAAAGAGCG\nTACGGAGCGTACGCAGGACGAGATCAAAATGGTTAACGACTACACTGGAAAAATTGAAGCACTGCAATCC\nGCGATAACAGTTGAGCGGGACGCTATGCAAGAGGAGGCGTTGCAGGAGATAATAGAAATGGGAACGGATG\nTAATTGAAACCGCCTCCGAAGAGGTTCCGATATTCGGCCCTGCGGCTGCGAATGTAGTCGCAACTGGACG\nAATGGTTGAGGGCACCTTAAAGTTGAAGCAAGTAATCGAGAAATTAGCAGGGTTAGATGTTTCGCACACC\nACAAGGGACAGAATCGAGCCGAAAGTTATAAACGCTATACTAGATCACGAGGGGGGCGTCGTACCGGAAA\nAGGAACTAGCGATTGGTGTATATAATAAGCTGCAGACAGTCAGAGAACATATGGCGGAACACAGCCATCT\nAAAGGAAATGGCAATACCAAGGCTGCAAAAGCTGTACACAGAACACGGCGATGAGTGGCATCCAAAGATA\nATTACTCAAATGAAGGTAGCGAGAGAACATCAGCCGCAAATACATATATATTGCGCTCCATGGGAATCGG\nATGACGTGTTTATGTTGCGAGTGTACGCGCCGCATCATATAGGGTGTGGTCTTTTCTTAGGAGTTGATTT\nAGAGAGTGAATTCATATTTTATGAGGATTTGATAGCAGAGAACCACGTATTGCGTGGTGGCGTCATTGAA\nGTCGTTGGAAGGAACTTCAGGCAAGCAGTGCGCGAATTTCTTTTGATGGCTGCGAGCAAGATTGAGAACA\nCTATGCATGTCAAGCGGTTAGTGAGAAGCTCGGCTTCCTCACCTATCTACTTGTCAAGCATACACTATGA\nGTGTACATTTGATGAGATAAAACAGAACGTTTTACAGATCGTGCACGACGAGCAGTTACAGATGCATCTG\nTTACGTGGTCCGAAACATTTCCAAAGACGTGCTCTGATGGCGGCTGTTGTTAAGGGTGTTAAGATCTTAG\nAGGGGCCAGATACGAAGGCGCTCATGCTACAGGGTTTGTAAGTGGCTGAAAGGTATCAAGAATAC\n\n>JQ610681.1 Orungo virus isolate UGMP 359 segment 7, complete sequence\nGTATAAATATCTAGAGATGGACGCCATTGCGGCACGTGCTCTGTCCGTGATCCAGGACTGCATTAGCGTT\nGGTGATGGGAGAATTAATTTAGACCCTGGGGTCATGGAGAGATTGGGAATTGCTATTAATAGATACAATG\nGGCTAACGAACAATGTGGTGACGATCAGACCAGGGACACAAGATGAGCGGAACGCGATGTTTTTTATGTG\nTCTGGATTTCGCGTTGGCGGCATTGAACATACAAATTGGGGTTATATCTAGGGAATACACGCAGGCGCTG\nGCCACTATCGGTGTGCTGGCAACGGGAGAAATCCCTTACTCGGTTGCCGCTATGGATACGATTGTACGGA\nTTAGCGGAACGATGGCGACATGGGGTCCCACCGAATATGAGTTACCGCCATATGCGCGGTCTCAGATGAT\nACAAATGAGCGGACGTTACTACGTTCCAGCGGGGGCGAATTCACATGCTGCCCATGTCGATCCCACGACG\nGTAGAGATTTCTTTAGCTGCTGGAGTAGTAGTGAATGTTACGAACGCGTTACAGCCTAGGGGCGTTGCGC\nCCACAATGATGTACATGGTATGGCATCCGTTGGCGATTTTCGCGAATCCTCAGGGTGCTACAGCTGCTTC\nGCCTCAAAATATGACTTTGGTGGTTGGTGGGCTGAATATAGCAGCTGGCACGATCATCGCTTGGGATACC\nGTCGCTCCTATACAGCTATCGAATCAGGGAGGACAAGAGGGAATGATCGCGATCCGGATACTATGGATGA\nCAACATTAGATAAATCTATGACAAGCTTGCCGGAGATGCGTGAAATAATCTCAAGATGCTATAGCTTTAT\nGCACCCTTCATGGCACGCGCTGCGAGGGACGGTCCTACATTCGCTTAATCTGCCGACTAATAATCCACCT\nATGTTTGCGCCTGCTACGCGACAGGAGGCATTGGCGTACTTAATTCTGGCAAATTTAGCGGATGCATATA\nCGTCGTTAAGGCCTGATTTCACCATACAAGGAATGCTCGCGGTTCCACAGGTCATTGACAGGCAGTTCGT\nTCAGGGTGCGTACAGGTAGAGGACGCCTTCCACAGTGGGCGTCTCATGTAGCCCCAGCGTCGGTCCCTTA\nCGTGTGCTGTAACGCGTAGGTAGAACGTCATATGATATTAAGTTAC\n\n>JQ610682.1 Orungo virus isolate UGMP 359 segment 8, complete sequence\nGTAAAAAATCTCCTCTCTTTTCACGATGGCTCAAGAAGTTAAGAGAAAGTTCACTAGAACAGTGTGCATC\nTATGATCCACAAAATCGCACATTCTGTGGTCGAAGTGCCGCGATGGTGTGTAACAGTTATTATACAATTA\nAAATGGGTAGAACGACGCAGTGTGGAGTGTCGCCGGTGCCCGTACCAAAGTCATATGTGCTAGAGATACC\nGGATGTTGGCTCTTATCGCATCTTAGATGGGCAGGATTCAATCAGTGTCATCGTTACTGAGACGGGCGTC\nGAGGCAACGTCTGAGAGGTGGGAAGAGTGGAAATTCGAAGGCGTTAATTGCGTTCCGATGGTTGTTCAAA\nCGGAGATTGGGAAAGGCCTGATTGACATGGAGATCAAGTTTAGTAAGGGAATGGGGCTCGTTAAACCTTA\nTGTAAAGAATGAGGTTAGCAGAACTGAGATCCCACGGCTACCGGGTGCTTCAGTCATTGATACACCGATA\nCGCGATTACCGTCAACTTTTGAAGGATCAGAGAGATGAAAGAAGGGCGGCGCTCGATGCGATCGCATGCG\nACATATGTCCCACTCTATCAAGAATGCTAGGGGCGAATATTACAGACGGATCGCCACAAGTCGAAGAAGT\nCGCAACACGGCCAACACAACCTCCAGCTCAGCTGAAGCTGGATGTGCCTAACTGGGACCAACCGACTGAT\nTCAGATGATGAGGATGAGGAATCCAAGCGCGTGACAACGCAAAGTAATGCTGATACTGAGGAACAAGTGA\nCTTTCGAAGATTGCATTACCGATCAATACTTTTCGAAAACGGGTGAATTCGCGAAGAAGTATCCTGAAAT\nGTTAGCGGGACTTTCCGCGAAGATGCCGAGTGAAACAGGTAGGTTTACAAAAATATTGACGACGAGGAAG\nGCTCAATGGAATAACGTTCCTCTTTTCGAATTAGATCCAAACGGGTTTACATATCATTTTAGTAAGCTGG\nGTAATTCGACGAGGATCTTCTGTGTCCAACGTGATTTGAGCTACATGGTTTTACCCGCAGGGCAAGGCCT\nGAAGTAGCGGTGCATGTAGCCGGGAGAGGTACAACTTAC\n\n>JQ610683.1 Orungo virus isolate UGMP 359 segment 9, complete sequence\nGTATAAAACATCCTCCCATGTCATGTTGGTGTTGGCACCGGGTGATCTCATAGACGGAGTGCGTCATCAA\nTTATCTGAAAGAGGAGTCAGGATTCGTTTACGGGAAACGAATGATGACGAGCAAAAGGATGAACCAGTGG\nATACGGGAGGCGGCAAGCCGGGTGATCGAATCGGGAAGGAAGTTGGAAATGCCGAGAGTGAACAGTCTTC\nCGATAAAGAGAAGAAGGCTGGAGGAAGTTCGGATTCAGAGCTCGGGGAAGGTGGAGATGGAAGGCGACAA\nACTGAGAAGGCTGAAGGCGGAGAGAATGGAACTAGAGATATTGGCATTCAGGATAAAGACAAACAATTTG\nATCGGCGCGCTAATCCAGATAACGCGTTGGACAGAGAAAATCGATCAGGAGATCCGCAACTTAAATATGG\nATTTGCAACCAAACGAATTGCAAACGCCGTTGAGTCAAAGTACCACTGCGGTGGATTTGAGGGGCCAGGA\nTCGGATGGATACATCAAACTAGAAATGTCAATAATGAAGGCGCTAGGTTTAAACCGAGATGACCACATCG\nAACAATTGGAGTTCCTCAAGCACCAACAGAAAGGGCCCAGCAAAATTCAAGTCAGAACGATCGCTTCCGA\nAACCAAATTAAAAGAGGTGTGTAATATAATGGACAAGCCGGTGGCTCCCACAGCGAGAAGTGCGGTGAGT\nGTAGTTAGTAACCGTGTTGAAGACGTGAAGGAAGCCCAGGTGTATTTTACAACTCCAACAGGAGATAGAG\nGCTGGAAAGAAGTAGCAAGGAAAGCGAGCCAGACACCAAACATTCGAGCGTACATTAATCCGGAGGGAGA\nTGATCCTAAAGTCTCATTTCTGCATTTAATCGATCATCTGTGAGGTCACGGTCTGAACTACGGGCATGCT\nGGGTGTTTCAGTTAC\n\n>JQ610684.1 Orungo virus isolate UGMP 359 segment 10, complete sequence\nGTATAAAATTCCGTTCGCAATGTACCGTGACTTGCTGAATATTCACACTGAAATGAGGGGCCCGCCATCT\nTATGAACCTAGTGGCTTAGCTCAAGCGACAGCACCGACTATGAGGTTTGGGGATAGAGAAGATGAGGAAG\nGCCTATTGAGGGCGCGCGAGCTTTCGCTTAATGTGTTAACGAATGCTATGACTAATACAACGGGTGCGAA\nTGAGGCGATTAAGAATGAGAAAGCGATGTTTGGGGCATATGCCGATGCACTTAGGGATACTCCGGAGATT\nAGGGTGGTGAAAAGGCGGATAAATGAACGTACGTTAGAAAAGTTGCATAAAATGCGACGTTCGCTGCACG\nGAAGACGAATGTTCGTACGAATGTTGTTGGCGATAAATGTGGGATTGGCGCTATTAACCTCGGCAGTGAA\nTGTGGTACGCCAGTCGCTAGATGATTTTGGGAAAGAAAGGTGGATAGTTGGTGGAGTGTGGTGGTTAGGT\nGAGGTCGTCGTTACGATTAATTTTGGAACGACTGTTGCTACGTTGGTATTAATGAGGATACATGGCGCAT\nTAAACGCGCAGCTTCAAACCATTAAGCGTGACATATATAAGAAAAGCTCGTATAATGAGGCCGCTGCCAT\nGCATTGGAAAGGTGAAATTAGCTTAATTGAGGAGCTAGCGGCGAGCCACGTACCTGCGGGATCGAATGTC\nTAGTCCGCGACATCGAAAAATTCACTTGTCCAGGTGAAGCCCGTAGAACGGATCGTCTTAC\n\n" }, { "path": "tests/input/TestFastqBam/expected.fastq1", "content": "@myseq/1\nCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\n\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\n" }, { "path": "tests/input/TestFastqBam/expected.java1_7.sam", "content": "@HD\tVN:1.4\tSO:queryname\n@RG\tID:A\tPL:9.75\tLB:Alexandria\tSM:FreeSample\tCN:KareemAbdul-Jabbar\nmyseq\t77\t*\t0\t0\t*\t*\t0\t0\tTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\t\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\tRG:Z:A\nmyseq\t141\t*\t0\t0\t*\t*\t0\t0\tAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\t\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\tRG:Z:A\n" }, { "path": "tests/input/TestFastqBam/expected.java1_8.sam", "content": "@HD\tVN:1.4\tSO:queryname\n@RG\tID:A\tLB:Alexandria\tSM:FreeSample\tCN:KareemAbdul-Jabbar\tPL:9.75\nmyseq\t77\t*\t0\t0\t*\t*\t0\t0\tTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\t\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\tRG:Z:A\nmyseq\t141\t*\t0\t0\t*\t*\t0\t0\tAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\t\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\tRG:Z:A\n" }, { "path": "tests/input/TestFastqBam/expected.java1_8_v1.5.sam", "content": "@HD\tVN:1.5\tSO:queryname\n@RG\tID:A\tSM:FreeSample\tLB:Alexandria\tPL:9.75\tCN:KareemAbdul-Jabbar\nmyseq\t77\t*\t0\t0\t*\t*\t0\t0\tTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\t\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\tRG:Z:A\nmyseq\t141\t*\t0\t0\t*\t*\t0\t0\tAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\t\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\tRG:Z:A\n" }, { "path": "tests/input/TestFastqBam/in1.fastq", "content": "@myseq/1\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\n\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\n" }, { "path": "tests/input/TestFastqBam/in2.fastq", "content": "@myseq/2\nAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\n+\n\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\n" }, { "path": "tests/input/TestFastqBam/inHeader.txt", "content": "@HD\tVN:1.4\tSO:queryname\n@RG\tID:A\tPL:txtPlatform\tLB:txtLib\tDT:2014-11-10\tSM:txtSample\tCN:txtCenter\n" }, { "path": "tests/input/TestFeatureReader/GU481072.1.tbl", "content": ">Feature gb|GU481072.1|\n52\t1524\tgene\n\t\t\tgene_desc\tGPC\n52\t1524\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|ADU56618.1|\n3294\t1585\tgene\n\t\t\tgene_desc\tNP\n3294\t1585\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|ADU56619.1|\n\n" }, { "path": "tests/input/TestFeatureReader/GU481073.1.tbl", "content": ">Feature gb|GU481073.1|\n46\t345\tgene\n\t\t\tgene_desc\tZ\n46\t345\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|ADU56620.1|\n7116\t448\tgene\n\t\t\tgene_desc\tL\n7116\t448\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|ADU56621.1|\n\n" }, { "path": "tests/input/TestFeatureReader/KM821772.1.tbl", "content": ">Feature gb|KM821772.1|\n57\t356\tgene\n\t\t\tgene\tZ\n57\t356\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17124.1|\n7118\t456\tgene\n\t\t\tgene\tL\n7118\t456\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17125.1|\n\n" }, { "path": "tests/input/TestFeatureReader/KM821773.1.tbl", "content": ">Feature gb|KM821773.1|\n48\t1523\tgene\n\t\t\tgene\tGPC\n48\t1523\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17126.1|\n3294\t1585\tgene\n\t\t\tgene\tNP\n3294\t1585\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17127.1|\n\n" }, { "path": "tests/input/TestFeatureReader/LC889323.1.tbl", "content": ">Feature dbj|LC889323.1|\n1\t2280\tgene\n\t\t\tgene\ttest_gene\n\t\t\tlocus_tag\tTEST_gp1\n1\t2280\tCDS\n\t\t\tproduct\ttest protein\n\t\t\tprotein_id\tdbj|TEST123.1|\n\n" }, { "path": "tests/input/TestFeatureReader/NC_026438.1.tbl", "content": ">Feature ref|NC_026438.1|\n1\t2280\tgene\n\t\t\tgene\tPB2\n\t\t\tlocus_tag\tUJ99_s1gp1\n\t\t\tdb_xref\tGeneID:23308131\n1\t2280\tCDS\n\t\t\tproduct\tpolymerase PB2\n\t\t\tprotein_id\tref|YP_009118631.1|\n\n" }, { "path": "tests/input/TestFeatureReader/test1-S.tbl", "content": ">Feature gb|KM821998.1|\n59\t1531\tgene\n\t\t\tgene\tGPC\n59\t1531\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17576.1|\n3308\t1599\tgene\n\t\t\tgene\tNP\n3308\t1599\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17577.1|\n\n" }, { "path": "tests/input/TestFeatureReader/test2-L.tbl", "content": ">Feature gb|KM821997.1|\n76\t375\tgene\n\t\t\tgene\tZ\n76\t375\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17574.1|\n7132\t470\tgene\n\t\t\tgene\tL\n7132\t470\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17575.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610675.1.table", "content": ">Feature gb|JQ610675.1|\n13\t3921\tCDS\n\t\t\tproduct\tVP1\n\t\t\tprot_desc\tRNA-dependent RNA polymerase\n\t\t\tprotein_id\tgb|AFX73387.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610675.1.tbl", "content": ">Feature gb|JQ610675.1|\n13\t3921\tCDS\n\t\t\tproduct\tVP1\n\t\t\tprot_desc\tRNA-dependent RNA polymerase\n\t\t\tprotein_id\tgb|AFX73387.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610676.1.table", "content": ">Feature gb|JQ610676.1|\n17\t2899\tCDS\n\t\t\tproduct\tVP2\n\t\t\tprot_desc\tT2 protein\n\t\t\tprotein_id\tgb|AFX73388.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610676.1.tbl", "content": ">Feature gb|JQ610676.1|\n17\t2899\tCDS\n\t\t\tproduct\tVP2\n\t\t\tprot_desc\tT2 protein\n\t\t\tprotein_id\tgb|AFX73388.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610677.1.table", "content": ">Feature gb|JQ610677.1|\n18\t2738\tCDS\n\t\t\tproduct\tVP3\n\t\t\tprot_desc\touter capsid and cell attachment protein\n\t\t\tprotein_id\tgb|AFX73389.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610677.1.tbl", "content": ">Feature gb|JQ610677.1|\n18\t2738\tCDS\n\t\t\tproduct\tVP3\n\t\t\tprot_desc\touter capsid and cell attachment protein\n\t\t\tprotein_id\tgb|AFX73389.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610678.1.table", "content": ">Feature gb|JQ610678.1|\n13\t1926\tCDS\n\t\t\tproduct\tVP4\n\t\t\tprot_desc\tcapping enzyme\n\t\t\tprotein_id\tgb|AFX73390.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610678.1.tbl", "content": ">Feature gb|JQ610678.1|\n13\t1926\tCDS\n\t\t\tproduct\tVP4\n\t\t\tprot_desc\tcapping enzyme\n\t\t\tprotein_id\tgb|AFX73390.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610679.1.table", "content": ">Feature gb|JQ610679.1|\n36\t1676\tCDS\n\t\t\tproduct\tNS1\n\t\t\tprot_desc\tnon-structural protein 1\n\t\t\tprotein_id\tgb|AFX73391.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610679.1.tbl", "content": ">Feature gb|JQ610679.1|\n36\t1676\tCDS\n\t\t\tproduct\tNS1\n\t\t\tprot_desc\tnon-structural protein 1\n\t\t\tprotein_id\tgb|AFX73391.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610680.1.table", "content": ">Feature gb|JQ610680.1|\n22\t1581\tCDS\n\t\t\tproduct\tVP5\n\t\t\tprot_desc\touter capsid protein\n\t\t\tprotein_id\tgb|AFX73392.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610680.1.tbl", "content": ">Feature gb|JQ610680.1|\n22\t1581\tCDS\n\t\t\tproduct\tVP5\n\t\t\tprot_desc\touter capsid protein\n\t\t\tprotein_id\tgb|AFX73392.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610681.1.table", "content": ">Feature gb|JQ610681.1|\n17\t1069\tCDS\n\t\t\tproduct\tVP7\n\t\t\tprot_desc\tT13 protein\n\t\t\tprotein_id\tgb|AFX73393.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610681.1.tbl", "content": ">Feature gb|JQ610681.1|\n17\t1069\tCDS\n\t\t\tproduct\tVP7\n\t\t\tprot_desc\tT13 protein\n\t\t\tprotein_id\tgb|AFX73393.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610682.1.table", "content": ">Feature gb|JQ610682.1|\n26\t1057\tCDS\n\t\t\tproduct\tNS2\n\t\t\tprot_desc\tnon-structural protein 2\n\t\t\tprotein_id\tgb|AFX73394.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610682.1.tbl", "content": ">Feature gb|JQ610682.1|\n26\t1057\tCDS\n\t\t\tproduct\tNS2\n\t\t\tprot_desc\tnon-structural protein 2\n\t\t\tprotein_id\tgb|AFX73394.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610683.1.table", "content": ">Feature gb|JQ610683.1|\n23\t883\tCDS\n\t\t\tproduct\tVP6\n\t\t\tprot_desc\thelicase\n\t\t\tprotein_id\tgb|AFX73395.1|\n111\t512\tCDS\n\t\t\tproduct\tNS4\n\t\t\tprot_desc\tnon-structural protein 4\n\t\t\tprotein_id\tgb|AFX73396.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610683.1.tbl", "content": ">Feature gb|JQ610683.1|\n23\t883\tCDS\n\t\t\tproduct\tVP6\n\t\t\tprot_desc\thelicase\n\t\t\tprotein_id\tgb|AFX73395.1|\n111\t512\tCDS\n\t\t\tproduct\tNS4\n\t\t\tprot_desc\tnon-structural protein 4\n\t\t\tprotein_id\tgb|AFX73396.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610684.1.table", "content": ">Feature gb|JQ610684.1|\n20\t703\tCDS\n\t\t\tproduct\tNS3\n\t\t\tprot_desc\tnon-structural protein 3\n\t\t\tprotein_id\tgb|AFX73397.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/JQ610684.1.tbl", "content": ">Feature gb|JQ610684.1|\n20\t703\tCDS\n\t\t\tproduct\tNS3\n\t\t\tprot_desc\tnon-structural protein 3\n\t\t\tprotein_id\tgb|AFX73397.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/orungo.table", "content": ">Feature gb|JQ610675.1|\n13\t3921\tCDS\n\t\t\tproduct\tVP1\n\t\t\tprot_desc\tRNA-dependent RNA polymerase\n\t\t\tprotein_id\tgb|AFX73387.1|\n\n>Feature gb|JQ610676.1|\n17\t2899\tCDS\n\t\t\tproduct\tVP2\n\t\t\tprot_desc\tT2 protein\n\t\t\tprotein_id\tgb|AFX73388.1|\n\n>Feature gb|JQ610677.1|\n18\t2738\tCDS\n\t\t\tproduct\tVP3\n\t\t\tprot_desc\touter capsid and cell attachment protein\n\t\t\tprotein_id\tgb|AFX73389.1|\n\n>Feature gb|JQ610678.1|\n13\t1926\tCDS\n\t\t\tproduct\tVP4\n\t\t\tprot_desc\tcapping enzyme\n\t\t\tprotein_id\tgb|AFX73390.1|\n\n>Feature gb|JQ610679.1|\n36\t1676\tCDS\n\t\t\tproduct\tNS1\n\t\t\tprot_desc\tnon-structural protein 1\n\t\t\tprotein_id\tgb|AFX73391.1|\n\n>Feature gb|JQ610680.1|\n22\t1581\tCDS\n\t\t\tproduct\tVP5\n\t\t\tprot_desc\touter capsid protein\n\t\t\tprotein_id\tgb|AFX73392.1|\n\n>Feature gb|JQ610681.1|\n17\t1069\tCDS\n\t\t\tproduct\tVP7\n\t\t\tprot_desc\tT13 protein\n\t\t\tprotein_id\tgb|AFX73393.1|\n\n>Feature gb|JQ610682.1|\n26\t1057\tCDS\n\t\t\tproduct\tNS2\n\t\t\tprot_desc\tnon-structural protein 2\n\t\t\tprotein_id\tgb|AFX73394.1|\n\n>Feature gb|JQ610683.1|\n23\t883\tCDS\n\t\t\tproduct\tVP6\n\t\t\tprot_desc\thelicase\n\t\t\tprotein_id\tgb|AFX73395.1|\n111\t512\tCDS\n\t\t\tproduct\tNS4\n\t\t\tprot_desc\tnon-structural protein 4\n\t\t\tprotein_id\tgb|AFX73396.1|\n\n>Feature gb|JQ610684.1|\n20\t703\tCDS\n\t\t\tproduct\tNS3\n\t\t\tprot_desc\tnon-structural protein 3\n\t\t\tprotein_id\tgb|AFX73397.1|\n\n" }, { "path": "tests/input/TestFeatureTableFetch/orungo.tbl", "content": ">Feature gb|JQ610675.1|\n13\t3921\tCDS\n\t\t\tproduct\tVP1\n\t\t\tprot_desc\tRNA-dependent RNA polymerase\n\t\t\tprotein_id\tgb|AFX73387.1|\n\n>Feature gb|JQ610676.1|\n17\t2899\tCDS\n\t\t\tproduct\tVP2\n\t\t\tprot_desc\tT2 protein\n\t\t\tprotein_id\tgb|AFX73388.1|\n\n>Feature gb|JQ610677.1|\n18\t2738\tCDS\n\t\t\tproduct\tVP3\n\t\t\tprot_desc\touter capsid and cell attachment protein\n\t\t\tprotein_id\tgb|AFX73389.1|\n\n>Feature gb|JQ610678.1|\n13\t1926\tCDS\n\t\t\tproduct\tVP4\n\t\t\tprot_desc\tcapping enzyme\n\t\t\tprotein_id\tgb|AFX73390.1|\n\n>Feature gb|JQ610679.1|\n36\t1676\tCDS\n\t\t\tproduct\tNS1\n\t\t\tprot_desc\tnon-structural protein 1\n\t\t\tprotein_id\tgb|AFX73391.1|\n\n>Feature gb|JQ610680.1|\n22\t1581\tCDS\n\t\t\tproduct\tVP5\n\t\t\tprot_desc\touter capsid protein\n\t\t\tprotein_id\tgb|AFX73392.1|\n\n>Feature gb|JQ610681.1|\n17\t1069\tCDS\n\t\t\tproduct\tVP7\n\t\t\tprot_desc\tT13 protein\n\t\t\tprotein_id\tgb|AFX73393.1|\n\n>Feature gb|JQ610682.1|\n26\t1057\tCDS\n\t\t\tproduct\tNS2\n\t\t\tprot_desc\tnon-structural protein 2\n\t\t\tprotein_id\tgb|AFX73394.1|\n\n>Feature gb|JQ610683.1|\n23\t883\tCDS\n\t\t\tproduct\tVP6\n\t\t\tprot_desc\thelicase\n\t\t\tprotein_id\tgb|AFX73395.1|\n111\t512\tCDS\n\t\t\tproduct\tNS4\n\t\t\tprot_desc\tnon-structural protein 4\n\t\t\tprotein_id\tgb|AFX73396.1|\n\n>Feature gb|JQ610684.1|\n20\t703\tCDS\n\t\t\tproduct\tNS3\n\t\t\tprot_desc\tnon-structural protein 3\n\t\t\tprotein_id\tgb|AFX73397.1|\n\n" }, { "path": "tests/input/TestFeatureTransfer/adenovirus_truncated/expected/mapped.tbl", "content": ">Feature sample\n1740\t2010\tCDS\n2100\t2300\n\t\t\tnote\tsequencing did not capture all intervals comprising CDS\n\t\t\tproduct\tmulti-interval-protein-with-missing-middle-section\n500\t800\tCDS\n\t\t\tproduct\tcomplete-single-interval-protein\n\n" }, { "path": "tests/input/TestFeatureTransfer/adenovirus_truncated/input/aligned_1.fasta", "content": ">TEST123456.1 Synthetic adenovirus-like reference for testing\nATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\n>sample\nATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n----------------------------------------------------------------------\n--------------------------------------------------GATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\n" }, { "path": "tests/input/TestFeatureTransfer/adenovirus_truncated/input/ref.fasta", "content": ">TEST123456.1 Synthetic adenovirus-like reference for testing\nATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\nATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATC\nGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT\nCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\n" }, { "path": "tests/input/TestFeatureTransfer/adenovirus_truncated/input/ref.tbl", "content": ">Feature gb|TEST123456.1|\n1740\t2010\tCDS\n2500\t2700\n3200\t3400\n\t\t\tproduct\tmulti-interval-protein-with-missing-middle-section\n\t\t\tprotein_id\tgb|test001|\n500\t800\tCDS\n\t\t\tproduct\tcomplete-single-interval-protein\n\t\t\tprotein_id\tgb|test002|\n" }, { "path": "tests/input/TestFeatureTransfer/internal_partials/expected/mapped.tbl", "content": ">Feature sample\n\n" }, { "path": "tests/input/TestFeatureTransfer/internal_partials/input/aligned_1.fasta", "content": ">TEST_INTERNAL ref sequence for internal partials test\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\n>sample\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------ATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCGC\n" }, { "path": "tests/input/TestFeatureTransfer/internal_partials/input/ref.fasta", "content": ">TEST_INTERNAL ref sequence for internal partials test\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\n" }, { "path": "tests/input/TestFeatureTransfer/internal_partials/input/ref.tbl", "content": ">Feature gb|TEST_INTERNAL|\n500\t100\tCDS\n650\t400\n\t\t\tproduct\ttwo-interval-protein\n\t\t\tprotein_id\tgb|test_internal_001|\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0026-1.tbl", "content": ">Feature LASV_NGA_2018_0026-1\n7\t306\tgene\n\t\t\tgene\tZ\n7\t306\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n<6841\t401\tgene\n\t\t\tgene\tL\n<6841\t401\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0026-2.tbl", "content": ">Feature LASV_NGA_2018_0026-2\n13\t1485\tgene\n\t\t\tgene\tGPC\n13\t1485\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3262\t1553\tgene\n\t\t\tgene\tNP\n3262\t1553\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0097-1.tbl", "content": ">Feature LASV_NGA_2018_0097-1\n71\t370\tgene\n\t\t\tgene\tZ\n71\t370\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7127\t465\tgene\n\t\t\tgene\tL\n7127\t465\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0097-2.tbl", "content": ">Feature LASV_NGA_2018_0097-2\n56\t1528\tgene\n\t\t\tgene\tGPC\n56\t1528\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3305\t1596\tgene\n\t\t\tgene\tNP\n3305\t1596\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0541-1.tbl", "content": ">Feature LASV_NGA_2018_0541-1\n8\t307\tgene\n\t\t\tgene\tZ\n8\t307\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7064\t402\tgene\n\t\t\tgene\tL\n7064\t402\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0541-2.tbl", "content": ">Feature LASV_NGA_2018_0541-2\n<1\t1470\tgene\n\t\t\tgene\tGPC\n<1\t1470\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3247\t1538\tgene\n\t\t\tgene\tNP\n3247\t1538\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0611-1.tbl", "content": ">Feature LASV_NGA_2018_0611-1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0611-2.tbl", "content": ">Feature LASV_NGA_2018_0611-2\n52\t1524\tgene\n\t\t\tgene\tGPC\n52\t1524\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3301\t1592\tgene\n\t\t\tgene\tNP\n3301\t1592\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0664-1.tbl", "content": ">Feature LASV_NGA_2018_0664-1\n12\t311\tgene\n\t\t\tgene\tZ\n12\t311\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7068\t406\tgene\n\t\t\tgene\tL\n7068\t406\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0664-2.tbl", "content": ">Feature LASV_NGA_2018_0664-2\n37\t1509\tgene\n\t\t\tgene\tGPC\n37\t1509\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3286\t1577\tgene\n\t\t\tgene\tNP\n3286\t1577\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0959-1.tbl", "content": ">Feature LASV_NGA_2018_0959-1\n43\t342\tgene\n\t\t\tgene\tZ\n43\t342\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7099\t437\tgene\n\t\t\tgene\tL\n7099\t437\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0959-2.tbl", "content": ">Feature LASV_NGA_2018_0959-2\n52\t1524\tgene\n\t\t\tgene\tGPC\n52\t1524\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3301\t1592\tgene\n\t\t\tgene\tNP\n3301\t1592\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0998-1.tbl", "content": ">Feature LASV_NGA_2018_0998-1\n<1\t195\tgene\n\t\t\tgene\tZ\n<1\t195\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n<6915\t290\tgene\n\t\t\tgene\tL\n<6913\t290\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_0998-2.tbl", "content": ">Feature LASV_NGA_2018_0998-2\n<1\t1199\tgene\n\t\t\tgene\tGPC\n<3\t1199\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n<2580\t1267\tgene\n\t\t\tgene\tNP\n<2580\t1267\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1024-1.tbl", "content": ">Feature LASV_NGA_2018_1024-1\n<1\t274\tgene\n\t\t\tgene\tZ\n<2\t274\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7030\t368\tgene\n\t\t\tgene\tL\n7030\t368\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1024-2.tbl", "content": ">Feature LASV_NGA_2018_1024-2\n37\t1509\tgene\n\t\t\tgene\tGPC\n37\t1509\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3286\t1577\tgene\n\t\t\tgene\tNP\n3286\t1577\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1079-1.tbl", "content": ">Feature LASV_NGA_2018_1079-1\n55\t354\tgene\n\t\t\tgene\tZ\n55\t354\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7110\t448\tgene\n\t\t\tgene\tL\n7110\t448\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1079-2.tbl", "content": ">Feature LASV_NGA_2018_1079-2\n53\t1525\tgene\n\t\t\tgene\tGPC\n53\t1525\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3302\t1593\tgene\n\t\t\tgene\tNP\n3302\t1593\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1177-1.tbl", "content": ">Feature LASV_NGA_2018_1177-1\n65\t364\tgene\n\t\t\tgene\tZ\n65\t364\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7121\t459\tgene\n\t\t\tgene\tL\n7121\t459\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1177-2.tbl", "content": ">Feature LASV_NGA_2018_1177-2\n56\t1528\tgene\n\t\t\tgene\tGPC\n56\t1528\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3305\t1596\tgene\n\t\t\tgene\tNP\n3305\t1596\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1375-1.tbl", "content": ">Feature LASV_NGA_2018_1375-1\n23\t322\tgene\n\t\t\tgene\tZ\n23\t322\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7079\t417\tgene\n\t\t\tgene\tL\n7079\t417\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1375-2.tbl", "content": ">Feature LASV_NGA_2018_1375-2\n39\t1511\tgene\n\t\t\tgene\tGPC\n39\t1511\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3288\t1579\tgene\n\t\t\tgene\tNP\n3288\t1579\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1381-1.tbl", "content": ">Feature LASV_NGA_2018_1381-1\n<1\t297\tgene\n\t\t\tgene\tZ\n<1\t297\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7054\t392\tgene\n\t\t\tgene\tL\n7054\t392\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1381-2.tbl", "content": ">Feature LASV_NGA_2018_1381-2\n26\t1498\tgene\n\t\t\tgene\tGPC\n26\t1498\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3275\t1566\tgene\n\t\t\tgene\tNP\n3275\t1566\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1392-1.tbl", "content": ">Feature LASV_NGA_2018_1392-1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1392-2.tbl", "content": ">Feature LASV_NGA_2018_1392-2\n<1\t1418\tgene\n\t\t\tgene\tGPC\n<3\t1418\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n<3148\t1486\tgene\n\t\t\tgene\tNP\n<3147\t1486\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1643-1.tbl", "content": ">Feature LASV_NGA_2018_1643-1\n<1\t299\tgene\n\t\t\tgene\tZ\n<3\t299\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n7056\t394\tgene\n\t\t\tgene\tL\n7056\t394\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/LASV_NGA_2018_1643-2.tbl", "content": ">Feature LASV_NGA_2018_1643-2\n17\t1489\tgene\n\t\t\tgene\tGPC\n17\t1489\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3266\t1557\tgene\n\t\t\tgene\tNP\n3266\t1557\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/expected/test.tbl", "content": ">Feature LASV_NGA_2018_1643-2\n17\t1489\tgene\n\t\t\tgene\tGPC\n17\t1489\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n3266\t1557\tgene\n\t\t\tgene\tNP\n3266\t1557\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/input/KM821997.1.tbl", "content": ">Feature gb|KM821997.1|\n76\t375\tgene\n\t\t\tgene\tZ\n76\t375\tCDS\n\t\t\tproduct\tZ protein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17574.1|\n7132\t470\tgene\n\t\t\tgene\tL\n7132\t470\tCDS\n\t\t\tproduct\tpolymerase\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17575.1|\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/input/KM821998.1.tbl", "content": ">Feature gb|KM821998.1|\n59\t1531\tgene\n\t\t\tgene\tGPC\n59\t1531\tCDS\n\t\t\tproduct\tglycoprotein precursor\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17576.1|\n3308\t1599\tgene\n\t\t\tgene\tNP\n3308\t1599\tCDS\n\t\t\tproduct\tnucleoprotein\n\t\t\ttransl_table\t1\n\t\t\tprotein_id\tgb|AIT17577.1|\n\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/input/align_mafft-ref-lasv-ISTH2376_1.fasta", "content": ">KM821997.1 Lassa virus strain ISTH2376-NIG-2012 segment L Z protein (Z) and polymerase (L) genes, complete cds\nATCCTAGGCAATTCAGCTGGACTTCAGTGGTGAGGCTCACTTTGGTGAATTCCTGAATTA\nAAGTACCTAGTC-AAAATGGGCAACAGACAGGCCAAATCGACAAAAGTCGATGAACATCA\nAAGAGCTCATCTAGTGCCAGATGCATCCCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGGTTGGTAGAGTGCAACAATCACTACCTGTGTCTCAACTGCCTCAG\nCCTGCTCCTCAGTGTCAGCAGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAGGCT\nAAAGGCAGCGACACAGCCGAGCGCACCATCAACTGAGGCGACCCAGACCACAACACCTCC\nACCATACACCCCATGATCCCGGGATCAACACTCCCACCTCCACCGCCCACCCCNNACCCC\nCGGGGGGACCCCCCGCCGGGGGCCCCCCCGGGGGGGCAGGCGGTCCAGCTCTACTCGATG\nTCCTCAACACACTTCTCTGGCCCAAACAACTCCGAACATGTCCTTCCCTTCAGTCTTAGG\nCTACCCCCACTTGACTGTATCATCACTCTTTGCCTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATTAGCATAA\nTCCATAGGTCTCTGTTTAGTAAGGATTGAGACAATGTCCACATCCGTCCATTGAACCCTT\nTGTTTCAATCTATCAGACATCATTGATTTCAATGCACCAACCAAAAGATGCGGGGAACTA\nTCACCAATCTCCCTTACAAACATTTCCAGATCTTGATCTTGGATAGATGGTGTAAATGCA\nGCTACCCTTTTATCAGATTCCCACAGTGCTCCTCTACACACAACCAATGGCACTGGTTCG\nTTGTCAGGTCCGACCTTGGTGAAATCAAACTCACTGAACTGCAGTTTATCTGGATTAATA\nATCAGCTTCATGGGTATAACATCCCCCAACTGCTGTGTATCCTTTAAGAATTCATTTACC\nACATCTGATTCAACAAACCAGGATGATCTACCTTTGAAAGTTGGGCCCGACAAAGCAAGT\nCTCCAACAGTCAGGCAGGACACATGGGCTCACAGACCCAGAATATAGTGCCTGTATATCA\nTTCACTACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGGATAGAAAAA\nGTCTCTTTAAAACTAGCATCCTGACTCTTGATTTTATACCTAATTGTCTGGTAAAACTGA\nACAGAGTCTACTGGCATTGTGCTTAACAAATCAAAGAAATCTTCAAGGGAGTCTAACCTC\nAATTCCTCTGTCAGGCCTGAAGCAATGAGCTGGTTCAAGTTTATCTGAGCTGGTTCCATG\nTCAAAATCTATCCATGCATAGCCCATCATTAGATCAAACTTAAACATGGGTCTCTCTATC\nCCTTTGTAAATGGCTTTCTCAATGAATGAAGAGAAGGGACCCAGTCGCTGTAAACCTTCA\nCCCTCTGGTATTGAAGTTTTATGAGGAAACCAAGTGAATGACCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGACTTGTCTCATAAAGTTGTCCACTGCA\nTCAGCAGTACTAACCACCCTTTCCTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTCAGTTCAGAAGCCAATACAACATAATGTTCCTCCCTTTTCCACTTGACAATGTGTGAA\nACAAGTGAAAGTGCCTCGCAATTCACATCTAGGGCAACACAAAGGTCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTGGAAGCTAAATCACTCATAAATGGCAAGATGTGCTTC\nTCAAATAGAGACGGATATAAACGTCTCAAAGAGTGGATGATGTGGCTCATGCCAACCCTG\nTCCTCTAGCAGTTTCGAAACAGTGGGTCTCAAGGGGAAATAATCACAAGGGTTATGCTTA\nAAAAAGTCCAAGATCTGAGCTTGTTTTGGTTCCCCGAGCACCCACGCTCCAAGTTCTATA\nGCTGTAGATAGTGTTATGCACATATAATCCCATAGAAGAGGTCTTAAATAAGTGACAACA\nGTACTACCTCCATCTTTGGCTTCTGGTGAGACTTTCCATATCTGAATTCCATTGTCCCCC\nATCACTGCTTCAACACCCTGAGTCCCCAATAGTTGAGTCTGTATGGATCTAATGTAAAGA\nTTCTCCTTGTTGGGGCCTCTGACGCACTTGCTACCCAGTGTTCTGCACAACCCCACAAAC\nCCAGATGCTATAGAACTTTGGAAAGCTGATTTATTTATTGCTTCAGACAGTAGCTTCTGA\nGCTCCTCTAGTGAATGTGGATGACAACCTATTTTGCAAAGTCTTTACTATTGTAGGGACC\nCTTTCATCTTCCAGATTCACAGCGCCAGAATAGATAATCTTTTGCCGCAACACCATTCTA\nAGTGGGTGATGGGTGGCTAAGTTCAACCAATGAAACCCCAAGTCAGAATCAGACAAAGGT\nTCAATGCCTAGAAGTTTAAACAAATTCTGTAATGATGTTGTGTGTTCACCTGATAGGTAG\nTTGGTGGTGAATTCCTCATGAAGCTCACCAGTTTTTAATTTATTGAACAATATCCTAAGC\nATTGACCTCATCTTTTTGCATGCATCAGGAATTAGCCTCTCGATCTGCCTCATTATCCTA\nTAGCTACGATTCCCGTCCACCCAATCTCTTACATCAGTCTCGCAGTTCAAAAGGAATGGA\nTCAATAGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTCTGAATTTGATTGCAC\nAGATCAACTGGGACACCATTGGCCACAGACTGATCAATTATGGTATCAATTGTTTCTGCC\nAATTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCTGCAGCAACAAATTTTGTTAGC\nAGGGGCACCTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCA\nATTGCACTCTTTGGACTTACAAATTTATTTAACTGATCACTCATGTAGTAATGGAACTCT\nAACAATGTTTTGAATTCTTCTGCATCTCTTGAAAGTAATTCTGTTAAGTTCTGATCAAAT\nAATGATATCTGATCGTCACTGGACGTGTAAGCATCAATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGTAAG\nATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGGACTGTGCCAGTTTGAAAG\nTTGGAATTAAAGAAGTCTTCGGTCATTGATTGAGTTGTCTTCTTCTTCAATCCAAGTTGG\nGACTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCATGTTAATAATGTTGACAAGTAATCTTTACCTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAGATTAAGTTTTGAATTATTGTTAGAAACAAGAAAGGACACATCATA\nGGACCCCACTTACTGTGATCCATACTATATGATACATGTGCCGATGAGACATTCAGTTTC\nATTGACAAAATGGCATTATCAAACTCCTTCTCATTGTTTAGACAGCTGCCTGCTAATTGT\nGATGTGAGTGCTTCAAAGTAATCCTCAATGAGCCTTGTGAACATTTTTGTCCTTAAATCT\nCCGATGTACAACTCTCTATTGCCACCCACTTGTTCCTTGTAAGACAAAGAAAACTTTAGT\nCTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCTTGACTGTAAAAACAC\nAGGTTTTTTAGCATTGCTGTAGTACAGTTAGTTAGGGACAAGGCCTTGCTAAGTGCTTCA\nGAGTTACTCTCACGTTCACTTATCCTGACATCATCAGCCAATCTCCCTGTATCAAATTTA\nAAGTTCAGACACTTGCTCTTATAATGAGAGTATCTTCCCATCAGCTTATTCCCATTCATC\nACTAGTAAAATTGACTTAAAGCACTGAAAATATTCTTGGTCCAAAAAAGTCCTAGTCACT\nACTGCTTTTGTCAGCTCACTAATAGGACATGAATTCATTGGCCCTACATAAAAATATTTA\nCTTCTCAAAGTAGCATCATTGTAGATATTCTCACAAATTTTGATGTATTGATCTTCAGAC\nAGGATCTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATCAACCTT\nATTAAGAGTTTTTCTTCCACCACTTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCT\nGCCTGCTGCTGTCCTTTTGGTTGCTCCCTATACTGACTGACAATATTGTCAACAGTGCAC\nCTCAGTTGGTCGAAGTATTCTGATGCTCCTCCATCCAATAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCACCACTCCCTCCTTTGGACCCCAGAACAAGATTACTCATTGCTTGCTGT\nATTTTGTAATCATAATCCTGTTTATTAAGCAAGAATTTGCCTTTACGTGCAAACACCTCA\nGTTAACTGTGTGACAGCCAAAGCTGTAAGTTTATTGAAGTCATAATCCAGAATACGGGAC\nCCATCTGTATACTTATTCACAACGACGCTCTTATTGCTGGCCAGGTCCAAGGCTGTTGCA\nCAGCCGCTTGTAATAAGAGGGTCTCGCAGTGTCTTTTTTACCTCCTTTTCTTTGAACAAT\nGAACCATTGTTAAAACTGGACACAAGGAGTGAAATAAATTTCTTGGAAACACCAGGCTTT\nTTATACCTAACTTTTTCCGCATCTACACAACATTCTTTACTTAGGAATTTTCTTGCATTA\nTAAACCATTTCAACAAGCTCTTCCTCCAATGCATCATCCTTCGGGTTCACACTCACATGT\nCCAAATTCCAACTTGGGCTCAAGGAATTTTTCAAAGCATTTGATCTGGTCAGTCAGTCTG\nTCAGGTGTTTCTTTTGTAATGAAGTGACACATATAGGAGATATTTAAAACAAACTTGAAT\nCTATTGGTCATCATACTGACAACTTCTTCAGACAGAATTATCTTTAATAAGTAACGAACA\nAGTCTGTAGAGCAGATATTCTACTTCTGTGATCAAATCCTCCCTGATTTTCTCAATCAAG\nTCCTTATGATAAAAATCGGATACAAAGGCCATCACAAAATACCTGATGTTTTGTAAAAAT\nTTTTGACACCTTTTACTAGGGTGTGTCAGTATTAAAACTAAAATCATTTTAGTTAACAAT\nTTAATAGTGATCAATTGTTCAGACAACTCTGTGCACTCTTCTATCCAGCTGACCATAACA\nTCGACTACTTTCTGCAGCACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTGGGATCA\nGCATAAAAGGAACAAACCTCTCCAACTACATTATTGTTAATAGCATAACACTTTGAGCAT\nTCACCTGTTTTTTGATACAATAGTTTGAATCCCATCTTATTGATGAAGAACTCTTGGCAG\nTAGGCCTCTTTGCACCTCACAACCTGGTATCTAGAGGGTCCAAATTCATTTTGCCTTAGT\nTTCACTGTAGAAGACGTTTTCATTGAGTTAATCAAAGCCAAGCTCAATGATGATAGTCTT\nTCTAAGTCTGTTGCACCTAGAATGTCAATAACGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGGTAACTCATAGTGGGTGTGATGCCAGAGATCTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGGATTTTGAAATCAATTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCCTCAAAGCATTAGCGGCTCGAGTTAAAACTCTGTTGATGATGGCAAGGAGCTCA\nCAATTTCGTTCTTCTTTGGGTGATAGGACACCCACGTTCTTGTCTCTAGTTCTCTTCCTG\nCTATCTATCCACCGTTTTAGATCTCTTTTTGTTGATTCCAATGAAACTAATCTGTCGTTA\nACACTCACAAAACAGGAGCCCAACCAACCAGCAAGGAGCTTGTCACCATGCCTTATACAG\nTCCAGTCGGCTGGCAAGAAGGATCAGAACGTCAAAAACAAGGAGAAGTTTCCTTCTGGTG\nTTGAGGATCCTCAGAGACTTTATCTTATTTAAAAAAGATCTCCAACATTGCATCTGTTCA\nCTTTGAGAGTCAACAGCCTTTTCCTTGCTAGAATCCAAATCTGCATATAAGAATTTAAGG\nACTGGAGAGGCTCTTCGGAACTGAAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCT\nATTTTATCACAATATAGCTTTCTGAAATCCTCTAACAACTTCATCTTATCAGTCTTAACA\nAATTGACTTTCTATGTTCCCTTGCCTTAGTTTGTTCCTGAAGATTTGATACTCCTCCTCA\nATCAAACTCTTGACTTCATGAGAGGTAAGCTTGTTATTAATGCCTTGATGACAACTAGAA\nATTATTTCTTCAAAGTGTTTTGCACGCTTGTCAATTAGAACATTGATGCTTTCAATTCCT\nGAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAAAGCCTCGAATATTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAATATTTTAACAAGGTGAATAAGGTGTCCCTGAGTTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTTGTCCTGCCGTCTATGAGAGGG\nATGAGCTTGATGCCAACAGACTCCAAATCGTTCTTTAATTGTTCTAGTTTCCTGTGATCT\nTCTAAATACTTCTGTTCGAAATTGGCGGGGGATGATCTGACAAAGCACTCAAGTAAGATT\nAGAACATTGCCAGTGAGTTTGTAGCCGTCAGGCACCACAAAGCATAAAGCTGGAGTGAGA\nATCCCATGATCACTCAGAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACATCCA\nTTGGCCTTACAGGAGTCAATCTCAATGCAAAGAGATAGTAGTTTCAATCCCTCCATAAGC\nAACATTCTGGGTTCGGTTTGGACCAAAAAAGCTAATTTCTGTCTTGACAACTTCTCATTA\nTCTGCAAGGTACTTTGAGATGAGATCTTTAGCATTAGCAATGTCTTCCTCCATCGCCAAC\nTGTGGCACCTGTGTTGGGTTTGGGTTTATGCCAATATGGCTTGTGGGTCGGCTGGTGATG\nTCCTAAAGAAGCTCCTACAGAAATGAGAGACAATATGCCTAGGATC\n>LASV_NGA_2018_0026-1\n------------------------------------------------------------\n---------GCC-AAAATGGGCAACAAGCAGGCCAAATCGACAAAAGTTGATGAACATCA\nAAGAGCTCATCTAGTGCCAGATGCATCTCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGGCTGGTGGAGTGTAACAACCACTACCTGTGTCTCAACTGTCTCAG\nCCTGCTTCTCAGCGTCAGCAGCAGGTGTCCGATCTGCAAAATGCCTCTTCCCACCAGGCT\nAAAGGCAGCAACACAGCCGAGTGCACCCTCAACTGAGGCGACCCGGAACACAACACCCCC\nACCATACACCCCGTGATCCCAGGAACAACACTCCCANNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAACTCTATTCAATG\nTCTTCAATACACCTCTCTGGCCCAAACAACTCCAAACATGTTCTTCCCTTCAGTCTCAGG\nCTGCCCCTACTTGACTGAATCATAACTTTTTGCTTTGATTTACTATAGCAAAGGGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATCAGCATAA\nTCCAAAGGTCTCTGTTTNNNNNNNNNNNNNNCAATGTCCACACCCGTCCATTGAATTCTT\nTGTTTCAATCTATCAGACATCATTGATTTCAATGCACCAACTAAAAGATGTGGGGAACCA\nTCACCAATCTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATGAAATTATCCACTGCA\nTCAGCAGTACTAACCACCCTTTCCTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTCAGTTCAGAAGCCAATACAACATAATGTTCCTCCCTCTTCCACTTGACAATGTGTGAA\nACAAGTGAGAGTGCCTCGCAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTAGAAGCTAAATCACTCATAAATGGCAGTATGTGCTTC\nTCAAATAGNNNNNNNNACAAACGTCTCAAAGAATGAANNNNNNNNNNNNTGCCAACTCTG\nTCCTCTAGCAGTTTCGAAACAGTGGGTCTTAAGGGGAAGTAATCACAGGGATTGTGTNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA\nTCAATAGGATACTTGGCATAACATAACAAACTTAAAGTCCTCTTCTGAATTTGATTACAC\nAGATCAACTGGGACACCATTGGCCACAGATTGATNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCACGTTAATAATGTTGATAGGTAATCTTTGCTTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAGATTAGGTTTTGAATTACTGTTAGAAACAAGAAAGGACACATCATA\nGGGCCCCACTTACTGTGATCCATACTATATGAAACATGTGCCGATGAGACATTCAGCTTC\nATTGACAAAATGGCATTATCAAACTCCTTCTCATTGTTTAGACAGCTGCCCGCTAACTGT\nGATGTGAGCGCTTCAAAGTAATCTTCAATAAGCCTTGTGAACATCTTTGTCCTCAAATCT\nCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCTNNNTAAGACAAAGAAAATTTTAGT\nCTGCCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCCTGACTGTAAAAACAC\nAGGTTTTTCAACATTGCTGTAGTACAGTTAGTTAGNNNNNNNNCCTTGCTAAGTGCTTCA\nGAATTACTCTCACGTTCACTTATTCTGACATCCTCAGCTAATCTTCCTGTATCAAATTTA\nANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACAATATTGTCAACAGTACAC\nCTCAGTTGGTCGAAGTATTCTGATGCTCCTCCATCCAGTAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCACCACTCCCTCCTTTGGACCCCAGAACAAGATTACTCATTGCTTGCTGT\nATCTTGTAATCATAATCCTGTTTATTAAGCAAGAATTTGCCCTTACGTGCAAACACCTCG\nGTCAACTGTGTGACAGCTAAGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATCAGTCAGTCTG\nTCAGGTGTTTCCTTTGTAATGAAGTGGCACATATAAGAGACATTTAAAACAAACTTGAAC\nCTATTGGTCATCATACTGACAACTTCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNA\nAGTCTGTAGAGCAGATACTCAACTTCTGTGATCAGATCCTCCCTAATTTTCTCAATCAAA\nTCCTTATGATAAAAATCGGATACAAAGGCCATCACAAAATACCTAATGTTTTGTAAAAAT\nTTCTGACACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTGTTAATAGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATATAATAGTTTGAATCCCATCCTGTTNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNTTGCNNCTCACAACCTGATATCTAGAAGGTCCAAANNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCAAAGCCAAGCTTAATGATGATAGNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCA\nTCATAAACATCACAATCAAGAATCTTAAAATCAATTCCATAAGAGTTAGTTTCTATACCA\nACCTCCCTCAAAGCATTAGTGGCTCGAGTTAGTACTCTGTTGATGATTGCAAGGAGCTCA\nCAATTCCGTTCTTCTTTGGGTGATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNGGATCCTTAGAGACTTTATCTTATTCAGAAAAGATCTCCAACATTGCATCTGTTCA\nCTTTGAGAGTCAGCAGCCCTTTNNNNNNNAGAATCCAAGTCTGCATACAAGAACTTAAGA\nACTGGAGAGGCTCTTCGAAACTGGAATGTTAACTGTNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNCCAATCAGGTATTTGTTCATTGTAAAATGTTGTCCTGCCGTCTATGAGAGGG\nATGAGATTGATGCCAACAGACTCCAAATCATTCTTTAATTGTTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCGGGGGATGATCTAACAAAGCACTCAAGTAAGATT\nAGAACATTACCAGTGAGTTTGTAGCCGTCAGGCACCACAAAGCATAAAGCTGGAGTGAGA\nATCCCATGATC-------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n----------------------------------------------\n>LASV_NGA_2018_0097-1\n-----AGGCAATTCAGCTGGACTTCAGTGGAAAGACTCTTTTTAGTGAATCCCTGAATCA\nAAGTGCCTAATC-AAAATGGGCAACAAACAGACTAAATCGACAAAAGTGGATGAACATCA\nAAGAGCTCATCTAGTGCCAGATGCATCCCATTTAGGCCCTCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGCCTGGTGGAGTGCAACAACCACTACCTGTGTCTCAACTGCCTCAG\nCCTGCTCCTCAGCGTCAGCAGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAAGCT\nAAAGGCAGCAGCACAACCGAGCGCACCCTCAACCGAGGTGACCCAGAACACAACACCCCC\nACCGTACACCCCATGATCCCAGGATCAACACTCCCATCTCCATCACCCNNNNNNNNNNNN\nNNNNNNNACCCCCCGCCGGGGGCCCCCCCGGGGGGTGGGGCGGCCTGGCTCTACTCAATG\nTCCTCAATACACTTCTTCGGCTCGAACAGCTCTGAGCATGTCCTTCCCTTCAGTCTTAGG\nCTGCCCCCACTTGACTGAATCATAACTCTTTGCTTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGGGATTCAAGAAGTTCACTCAGTATATCCGCATAA\nTCTACAGGTCTCTGTCTTGTGAGGATTGAGACAATGTCCACACCCGTCCATTGAATTCTC\nTGTTTCAATCTATCAGACAACATTGATTTTAGTGCACCAACTAAAAGGTGCGGGGAACTA\nTCACCAATCTCCTTTACAAACATCTCCAAATCTTGATCTTGGATGGGTGGTGCAAACGTA\nGCCACCCTTGTATTAGATTCCCATAGTGCTCCCCTACATACAACCAATGGCACTGGTTCG\nTTGTCAGGTCCGACCTTGGAAAAGTCAAACTCACTGAACTGCAGTTTATCTGGATCAATT\nATCAGCCTCATAGGTATAACATCCCCTAACTGCTGTGTATCCTTTAAGAATTCATTTATC\nACATCTGATTCAACGAACCAAGCTGACCTGCCTTTGAAAGTTGGACCCGACAAAGCAAGT\nCTCCAACAGTCAGACAGAACACATGGGCTCACAGACCCAGAATATAGTGCCTGTACATCA\nTTCACTACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGGATAGAAAAA\nGTCTCTTTAAAACTAGCATCCTGACTTTTGATTTTATACCTAATTGTCTGATAAAACTGA\nACAGAGCCCACTGGCATTGTGCTTAACAAATCAAAAAAATCTTCAAGGGAGTCCAGCCTC\nAATTCCTCTGTCAGACCTGAAGCAATAAGTTGGTTCAAGTTTATCTGAGCTGGTTCTATA\nTCAAAATCTATCCATGCATAGCCCATCATTAGATCAAACTTAAACATAGGTCTCTCTATC\nCCTTTGTAAACAGCTTTCTCAATGAATGAGGAGAAGGGACCCAGTCGTTGCAGACCCTCA\nCCCTCCGGAATTGAGGTTTTATGAGGAAACCAAGTGAATGATCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGTAGTACTAACCACCCTTTCTTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTCAGTTCAGAAGCCAATACAACATAATGTTCCTCTCTTTTCCACTTAACAATGTGTGAG\nACAAGTGAAAGTGCCTCACAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTGGAAGCTAAATCACTCATAAATGGCAATATGTGCTTC\nTCAAATAGAGACGGATATAAACGTCTCAAGGAATGAATGATGTGGCTCATGCCAACTCTG\nTCCTCTAGCAGTTTCGAAACAGTGGGTCTCAAGGGAAAGTAATCACAAGGATTATGTTTA\nAAAAAGTCCAAGGTCTGAGCTTGTTTTGGTTCCCCGAGCACCCACGCTCCAAGTTCTATA\nGCTGTAGATAGTGTTATGCACATATAATCCCATAGAAGAGGTCTCAAATAAGTGATGATA\nGTGTCACTTCCATTTCTGACTTCTGGTGAAACTTTCCATATCTGGATTCCATTGTCCCCC\nATCACTGCTTCAACACCTTGAGTCCCTAGTAGCTGAGTCTGTATGGATCTAATGTAAAGA\nTTCTCCTTGTTGGGGCCCCTAACACACTTGCTACCTAGTGTTCTGCACAACCCTACAAAC\nCCAGAAGCTATAGAACTTTGGAAAGCTGATTTATTTATTGCTTCAGACAGCAGCTTCTGA\nGCCCCTCTAGTGAATGTCGATGACAACTTATTTTGCAAGGTTTTCACTATTGTAGGGACC\nTTTTCATCTTCCAGATTCACAGCACCAGAATAGATTATCTTCTGCCGCAACACCATTCTA\nAGCGGATGATGGGTGGCTAAATTCAACCAATGATACCCCAAGTCAGAATCAGACAAAGGT\nTCAATGTCTAGAAGTTTGAACAAATTCTGCAATGATGTTGTGTGTTGGCCTGATAAGTAG\nTTGGTAGTGAATTCCTCATGAAGCTCACCAGTTTTCAATTTATTGAACAGTATCCTAAGC\nATTGACCTCATCCTTTTGCATGCATCAGGAATTAGCCTCTCAATTTGCCTCATTATCCTA\nTAACTACGATTCCCGTCCACCCAATCTCTTACATCAGTCTCACAATTCAAAAGGAATGGA\nTCAATAGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTTTGAATCTGATTACAC\nAGGTCAACTGGGACACCATTAGCCACAGACTGATCAATTATGGTGTCAATTGTTTCTGCC\nAATTGATGGGGTTCTTTGCACTTTATATTATGTAAAGCTGCAGCAACAAATTTGGTTAGC\nAAGGGTACCTCGTCACCCCAAACATAGAACCTCGATTTGAACTCTGCAACAAACCTGCCA\nATTGCACTCTTTGGACTCACAAATTTATTTAGCTGATCACTCATGTAGTAATGGAATTCT\nAACAATGTTCTGAATTCCTCTGCATCTCTTGAGAGTAACTCTGTTAAGTTCTGATCAAAC\nAATGAAATCTGATCGTCACTGGACGTGTAAGCATCAATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGCAGG\nATACCCTGTCCCATATCAAGAATTGAACTAATGTGCGAGGGCACCGTGCCAATTTGAAAA\nTTGGAATTAAAAAAGTCTTCAGTCATTGACTGAGTTGTCTTCTTCTTCAGTCCAAGTTGG\nGATTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCATGTTAATAGTGTTGATAGGTAATCTTTACCTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAAATTAGGTTTTGAATTATTGTTAGAAACAAGAAGGGACACATCATG\nGGGCCCCACTTACTGTGATCCATACTATATGATACATGTGCTGATGAGACATTCAGCTTC\nATTGATAAAATGGCATTGTCAAACTCCTTCTCATTGTTTAGACAGCTGCCCGCTAATTGT\nGATGTGAGTGCTTCAAAGTAATCTTCAATGAGCCTTGTGAACATCTTTGTCCTTAAATCT\nCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCCTTATAAGACAAAGAAAATTTTAGT\nCTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGGGGTGATTCCTGACTGTAAAAACAC\nAGGTTTTTTAACATCGCTGTAGTACAGTTAGTTAGGGACAAGGCCTTGCTAAGTGCTTCA\nGAATTGCTCTCACGTTCACTTATCCTGACATCATCAGCCAATCTTCCTGTGTCAAATTTA\nAAATTTAGACACCTACTCTTATAATGAGAGTATCTCCCCATCAGCTTATTCCCATTCATT\nATTAATAAAATTGACTTGAAGCACTGGAAATATTCTTGGTCCAAGAAAGTTCTAGTCACC\nACTGCTTTTGTCAGCTCGCCAATAGGACATGAGTTCATTGGCCCTACATAAAAATATTTA\nCTCCTCAAAGCAGCATCATTGTAGATATTCTCACAAATTTTGATGTATTGATCCTCAGAC\nAGGATTTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACATTTTATCAACCTT\nATTAAGAGTTTCTCTTCCACTACCTTGTCAAGATCAGAAATCGAAGGTGCATTGTGGTCT\nGCCTGCTGCTGTCTTTCTGGTTGCTCCTTATACTGACTGACAATATTGTCAACAGTGCAC\nCTCAGTTGGTCGAAGTATTCTGATGCTCCCCCATCCAATAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCATTACTCCCCCCTTTGGACCCTAGAACAAGATTGCTCATTGCTTGCTGT\nATTTTATAATCATAATCCTGTTTATTAAGCAAGAATTTGCCTTTGCGTGCAAATACTTCA\nGTTAATTGTGTGACAGCCAAAGCTGTGAGCTTGTTGAAGTCATAATCCAGAACACGAGAT\nCCATCTGTATACTTATTCACAACAACACTCTTATTACTGGCCAAGTCCAAAGCTGTTGCA\nCAGCCGCTTGTGATAAGAGGGTCTCGCAGTGTCTTCTTTACTTCTTTTTCTTTAAACAAT\nGAGCCATTATTAAAACTAGACACAAGGAGTGAAATGAATTTTTTGGAGACACCGGGTTTT\nTTATACCTAACTTTATCCGCATCTGCACAACACTCTTTGCTAAGAAACTTTCTTGCATTG\nTAAACCATTTCAGCAAGCTCTTCTTCCGATGCATCATCCTTTGGGTTCACACTCACATGT\nCCAAATTCCAGTTTGGGCTCAAGGAATTTTTCAAAGCATTTAATCTGATCAGTCAGTCTG\nTCAGGTGTTTCTTTTGTAATGAAGTGACACATATAAGAGATATTTAAAACAAACTTGAAT\nCTATTGGTCATCATACTGACAACTTCTTCAGACAAAATTATCTTTAATAAGTGGCGAACA\nAGTCTGTAGAGCAGATATTCAACTTCTGTGATCAAATCTTCCCTGATTTTTTCAATTAAA\nTCCTTGTGATAAAAATCAGACACAAAGGCCATCACAAAATACCTAATGTTTTGTAGAAAT\nTTTTGACACCTTTTACTAGGATGTGTCAGTATCAAAACTAAAATCATCTTGGTTAACAAT\nTTAATAGTGATCAATTGTTCAGACAACTCTGTGCACTCCTCTATCCAGCTGACCATAACG\nTCAACTACTTTCTGCAATACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTAGGATCA\nGCATAAAAAGAACAAACCTCTCCAACTACATTGTTATTAATAGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATACAATAGTTTGAATCCCATTCCATTGATGAAGAACTCTTGGCAG\nTAGGCCTCTTTGCACCTCACAACCTGGTATCTAGAGGGCCCAAATTCATTTTGCCTTAGT\nTTCACTGTGGAAGACGTCTTCATTGAGTTTATCAAAGCTAAGCTCAATGATGATAGTCTT\nTCCAAGTCTGTTGCATCTAGAATGTCAATGACGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGGTAACTTATTGTGGGTGTAATACCGGAGATTTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGGATCTTGAGGTCAATTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCCTCAAAGCATTAGTGGCTCGAGTCAAAACTCTATTGATGATAGCAAGGAGCTCA\nCAATTCCGTTCTTCTTTAAGTGATGGGACACCTGCATTTCTGTCTCTAGTTCTTTTCCTA\nCTGTCCATCCACCGTTTTAAATCTCTTTTTGTTGATTCTAATGAGACCAATCTATCGTTA\nACACTCATAAAACAGGAGCCCAGCCAACCAGTAAGGAGCCTGTCACCATGCCTTATGTGG\nTCCAGCCGGCTAGCAAGGAGAATCAGAACGTCAAAAATAAGGAGAAGTTTCCTCCTGGTG\nTTGAGGATCCTCATAGATTTTATCTTATTTAGAAAAGATCTCCAACATTGCATCTGTTCA\nCTTTGAGGTTCAGCAATCCTTTCCTCACTAGAGTTCAAGTCTGCATACAAGAACTTAAGG\nACTGGAGAGGCTCTTCGGAACTGGAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCT\nATCTTGTCACTATATAGCTTTCTGAAATCCTCTAATAACTTCACTTTATCAGTCTTAACA\nAATTGACTTTCTATGTCCCCTTGCCTAAGTTTGTTCCTGAAGATTTGATACTCCTCCTCA\nATTAAACCCTTGACTTCATGAGAGGTGAGCTTGTTATTAATGCCCTGATGACAACTAGAA\nATTATTTCCTCAAAGTGTTTTGCACGCTTGTCGGTTAGAACATTGATGCTTTCAATTCCT\nGAGAGCCTCCCAGACGTTAAGGCTAAAGACTCACAAAGTCTTGAATACTCAGACTCTTCG\nAATAATGCATTACTTTCTTGTGAATATTTTAACAGGGTGAATAAGGTGTCCCTGAGCTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTGGTCCTGCCGTCTATGAGAGGG\nATGAGGTTGATGCCAACAGTCTCCAAATCATTCTTTAATTGTTCTAGTTTTTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCGGGGGATGACCTAACAAAGCACTCAAGTAAGATT\nAGAACATTACCAGTGAGTTTGTAACCGTCAGGTACCACAAAACACAAAGCTGGGGTAAGA\nATCCCATGATCACTCAGAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACATCCA\nTTAGCCTTGCAGGAGTCAATCTCAATGCAAAGAGATAACAGCTTCAACCCCTCCATAAGC\nAGCATCCTGGGTTCAGTTTGGACCAGAAAAGCTAACTTCTGTCTTGATAGCTTCTCATTG\nTCCGCAAGGTACTTTGAGATAAGATCTTTAGCATTGGCAATGTCTTCCTCCATTGCCAAT\nTGTGGCGCCTGTGTTGGGTTTGGGTTTGTGCCAGTATGGCTTGTAAGTCAGCTGGTGGTG\nCCCCACAAAAGCTCCTACAAAAATGAGAGACAATATGCCTAGGAT-\n>LASV_NGA_2018_0541-1\n------------------------------------------------------------\n--------AGTC-AAAATGGGCAACAGACAGGCCAAATCGACAAAAGTCGATGAACATCA\nAAGAGCTCATCTAGTGCCAGATGCATCTCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGGCTGGTAGAGTGCAACAATCACTACCTGTGTCTCAACTGTCTCAG\nCCTGCTCCTCAGCGTCAGCAGCAGATGCCCGATCTGCAAGATGCCTCTTCCCACCAAGCT\nAAAGGCAGCAGCACAACCGAGCGCACCATCGGCCGAGGCGACCCAGAACACAACACCTCC\nACCATATGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTCTACTCAATG\nTCCTCAATACACCTCTCCGGCCCAAACAACTCTGAACATGTCCTTCCCTTCAGTCTTAGG\nCTGCCCCCACTTGACTGAATCATGACTCTTTGCCTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGGTTCAAAAAGTTCATTCAGTACATCAACATGA\nTCCAAAGGTCTCTGTTTTGTGAGGATTGAAACAATGTCTACACTCGTCCATTGAATCCTC\nTGCTTCAATCTATCAGACATCATTGATTTTAATGCACCAACTAAGAGGTGCGGAGAACTA\nTCACCAATTTCTCTTACAAACATTTCCAAATCTTGATCTTGGATAGGTGGTGTAAACGTA\nGCCACCCTTCTATCAGATTCCCACAGTGCTCCCCTACACACAACCAATGGCACTGGCTCG\nTTGTCAGGTCCGACCTTGGAGAAGTCAAACTCACTAAACTGCAGTTTATCTGGATTAATA\nATCAGCTTCATGGGTACGACATCCCCCAGCTGCTGTGTATCTTTTAAGAATTCATTTATC\nACATCTGATTCAACAAACCAGGCTGACCTACCCTTGAAAATTGGACCCGACAGAACAAGT\nCTCCAACAGTCAGACAGAACACATGGGCTCACAGGCCCAGAATACAATGGCTGTACATCA\nCTCACTACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGGATAGAAAAA\nGTCTCTTTAAAACTGGCATCCTGACTCTTGATTTTATACCTAATTGTCTGGTAAAACTGA\nACAGAGTCCAGTGGCATTGTACTTAACAAATCAAAGAAATCTTCAAGGGAGTCTAACCTC\nAATTCTTCTGTTAGGCCTGAAGCAATAAGCTGGTTCAAGTTTATCTGAGCTGGTTCTATA\nTCAAAGTCTATCCATGCATAGCCCATCATTAGATCAAACTTAAACATAGGTCTCTCTATT\nCCTTTGTAAATTGCTTTCTCAATGAATGAAGAGAAGGGACCCAGTCGTTGCAGACCTTCA\nCCCTCTGGTATTGAGGTTTTATGAGGGAACCAAGTGAATGACCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCG\nTCAGCAGTACTAACCACCCTCTCCTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTTAGCTCAGAAGCCAACACAACATAATGTTCCTCCCTCTTCCACTTAACAATATGTGAA\nACAAGTGAAAGCGCCTCGCAATTCACATCTAAGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTAGAGGCTAAATCACTCATAAATGGCAATATGTGCTTC\nTCAAATAGAGACGGATATAAACGTCTCAAAGAGTGAATGATGTGGCTCATGCCAACCCTG\nTCCTCTAGCAGTTTCGAAACAGTGGGTCTCAAGGGGAAGTAATCACAAGGATTATGTTTA\nAAAAAGTCCAAGATCTGAGCTTGTTTTGGTTCCCCGAGCACCCATGCTCCAAGTTCTATG\nGCTGTGGATAGTGTTATGCACATATAATCCCATAGGAGAGGTCTTAAATAAGTGACAACA\nGTATTACCTCCATCTTTGATTTCTGGTGAAACTTTCCATATTTGGATTCCATTGTCCCCC\nATCACTGCTTCAACACCTTGAGTCTCTAGTAGCTGGGTCTGTATGGACCTAATGTAAAGA\nTTCTCCTTATTGGGGCCTCTGACACACTTGCTACCTAGTGTTCTGCATAACCCCACAAAC\nCCAGACGCTATAGAACTCTGGAAAGCTGATTTATTTATTGCTTCAGACAGTAGCTTCTGA\nGCTCCTCTAGTGAATGTCGATGACAACCTATTTTGCAAAGTTTTTACTATTGTAGGGACC\nTTTTCATCTTCTAAATTCACAGCACCAGAATAGATTATCTTTTGCCGCAACACCATTCTA\nAGCGGGTGATGGGTGGCTAAGTTCAACCAATGAAACCCCAAGTCAGAATCAGACAATGGT\nTCAATGCCTAGAAGTTTAAACAAATTCTGCAATGATGTTGTATGCTCACCTGACAGGTAG\nTTGGTAGTGAATTCCTCATGAAGCTCACCAGTTTTTAATTTATTGAACAATATCCTAAGC\nATTGACCTCATCTTTTTGCATGCATCAGGAATTAGCCTCTCAATCTGCCTCATTATCCTA\nTAACTACGATTCCCGTCCACCCAATCTCTCACATCAGTCTCGCAATTCAAAAGGAATGGA\nTCAATAGGATACTTAGCATAACATAACAAACTCAAGGTCCTCTTCTGAATTTGATTACAT\nAAATCAACTGGGACACCATTAGCCACAGATTGATCAATTATGGTATCAATTGTTTCTGCC\nAGTTGGTGGGGTTCTTTGCACTTTATGTTATGTAAAGCCGCAGCAACAAATTTTGTTAGC\nAGGGGCACCTCGTCACCCCAAACATAGAATCTTGATTTGAACTCTGCAACAAACCTGCCA\nATTGCACTCTTTGGACTCACAAATTTATTTAGCTGGTCACTCATGTAGTAATGGAATTCT\nAACAATGTTTTGAATTCTTCTGCATCTCTAGAGAGTAACTCTGTTAAGTTCTGATCAAAT\nAATGATATCTGATCGTCACTGGACGTGTAAGCATCGATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAAGTGTTATGCAGG\nATTCCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGGACAGTGCCAATTTGAAAG\nTTGGAATTAAAAAAGTCTTCGGTCATTGATTGAGTTGTCTTCTTCTTCAATCCAAGTTGG\nGATTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCATGTTAATAATGTTGATAGGTAATCTTTACCTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAGATTAGGTTTTGAATTATTGTTAAAAACAAGAAAGGACACATCATA\nGGGCCCCACTTGCTATGATCCATACTATATGATACATGTGCTGATGAGACATTCAGCTTC\nATTGACAGAATGGCATTATCAAACTCCTTCTCATTGTTTAGACAGCTACCTGCTAACTGT\nGATGTGAGTGCTTCAAAGTAATCCTCAATGAGCCTTGTGAACATCTTTGTCCTTAGATCT\nCCAATGTACAACTCTCTATTGCCTCCCACTTGTTCCTTGTAGGACAAAGAAAATTTTAGT\nCTACCAGTATCAGGGCCAGTTGAATTATAAGATTGAGGAGATTCTTGACTGTAAAAACAC\nAGATTCTTTAACATTGCTGTAGTGCAATTAGTCAGGGACAAGGCTTTGCTAAGTGCTTCA\nGAATTACTCTCACGTTCACTTATTCTGACATCATCAGCCAATCTTCCTGTATCAAATTTA\nAAGTTCAGGCACTTACTCTTATAATGAGAGTATCTTCCCATCAACTTATTCCCATTCATC\nACTAGCAAAATTGACTTAAAGCACTGGAAATATTCTTGGTCTAAAAAAGTCCTAGTTACC\nACTGCTTTTGTCAGCTCACTAATAGGACATGAATTCATTGGCCCCACATAAAAATATTTA\nCTCCTCAACGCAGCATCATTGTAGATATTCTCACAGATTTTGATGTATTGATCCTCAGGT\nAGGATTTCTCGATCAAAATCCTCTATCATATGGTTTGAAAGTTCACTTTTTATCAGCCTT\nATTAAGAGTTTTTCTTCTACTACCTTGTCAAGATCAGATATTGAGGGTGTATTGCAGTCT\nGTCTGTTGCTGTCTTTCTGGTTGCTCCCTATACTGACTGATAATATTGTCAACAGTGCAC\nCTCAGTTGGTCGAAGTATTCTGATGCTCCTCCATCCAGTAGTATCTCATCTAGGTCAGCA\nTTGTTGGTGTCACCACTCCCTCCTTTGGACCCTAAAACAAGATTGCTCATTGCTTGCTGT\nATTTTGTAATCATAATCCTGTTTGTTAAGCAAGAATTTACCTTTACGTGCAAACACTTCA\nGTTAACTGTGTGACAGCCAAAGCTGTGAGCTTGTTGAAGTCATAATCTAGAATGCGGGAC\nCCATCTGTATACTTATTTACAACAACACTTTTGTTACTGGCCAAGTCCAAAGCTGTTGCA\nCAGCCGCTTGTAATAAGAGGGTCTCGCAGTGTTTTCTTTACCTCCTTTTCTTTGAACAAT\nGAACCATTATTAAAACTAGACACAAGGAGTGAAATAAATTTCTTGGAAACACCAGGCTTT\nTTGTACCCAACTTTTTNNNNNNCTGCACAACATTCTTTGCTTAGAAACTTTCTTGCATTA\nTAAACCATTTCAGCAAGCTCTTCCTCCGATGCATCATCCTTCGGGTTCACACTAACATGT\nCCAAATTCCAATTTGGGTTCAAGGAATTTTTCAAAGCATTTGATTTGGTCAGTCAGTCTA\nTCAGGTGTTTCTTTTGTAATGAAATGACACATATAAGAGATATTTAAAATGAACTTGAAT\nCTATTGGTCATCATACTGACAACTTCTTCAGATAGGATTATCTTTAATAAGTGACGAATA\nAGTCTGTAGAGCAGATATTCGACTTCTGTGATCAAATCTTCCCTGATTTTCTCAATCAAA\nTCCTTGTGATAAAAATCAGACACAAAGGCCATCACAAAGTACCTGATGTTTTGCAAAAAC\nTTTTGACACCTTTTACTAGGATGTGTCAGTATCAAAACCAGGATCATTTTGGTTAACAAT\nTTAATAGTATTCACTTGTTCAGACAACTCTGTGCACTGTTCTATCCAGCTGACCATAACA\nTCGACTACTTTCTGCAACACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTGGGATCA\nGCATAAAAGGAACAAACCTCTCCAACCACATTATTGTTGATGGCATAACATTTTGAGCAT\nTCACCTGTTTTCTGATATAATAGTTTAAATCCCATCCTATTGATGAAGAACTCCTGGCAA\nTAGGCCTCTTTGCACCTCACAACTTGGTATCTAGAGGGTCCAAATTCATTTTGCCTTAGT\nTTCACTGTGGATGATGTTTTCATTGAGTTGATCAAAGCCAAACTCAATGATGATAGTCTT\nTCTAAGTCTGTTGTATCTAGAATGTCAACAGCGCCAAGAGTGTAAGGGAACATGTCTTCC\nTGAGTTTTCTGGTAACTTATAGTGGGTGTGATTCCGGAGATCTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGGATCTTGAAATCAATTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCCTCAAAGCATTAGTAGCTCGAGTTAAAACTCTGTTGATGATGGCAAGTAGCTCA\nCAATTTCGTTCTTCTTTAAGAGATAGGACACCTGCATTCCTGTCTCTGGTTTTCTTCCTG\nCTGTCTATCCACCGTTTTAGATCTCTTTTTGTTGATTCCAATGAGACTAATCTATCGTTT\nACACTCACAAAACAGGAGCCCAACCAACCAGCAAGGAGCTTGTCACCATGCCTTATGCAG\nTCCAGCCGGCTAGCAAGAAGAATCAGAACGTCAAAAATGAGGAGAAGTTTCCTCCTGGTG\nTTGAGGATCCTCAGAGACTTTATCTTATTTAGAAAAGATCTCCAACACTGCATTTGTTCA\nCTCTGAGAGTCAGCAGCCCCTTCTTTACCAGAATCCAAATCTGCATACAAGAACTTAAGG\nACTGGAGAGGCTCTTCGGAACTGGAACGTTAACTGTTCAATGTTGTCATCACAGGTGTCT\nATTTTATCACAATATAGATTTTTGAAGTCTTCTAATAACTTCATTTTATCAACCTTAACA\nAATTGACTTTCTATGTTCCCTTGTCTTAGTTTGTTCCTGAAGATTTGATACTCCTCCTCA\nATCAAACTCTTGACTTCATGAGAGGTGAGCTTGTTATTAATGCCCTGATGACAACTAAAG\nATTATTTCCTCAAAGTGCTTTGCACGCTTGTCAGTTAGAACATTGATGCTTTCAATTCCT\nGAGAGCCTCCCAGACGTTAAAGCTAAAGATTCACAAAGTCTTGAATATTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAGTATTTCAACAAAGTGAATAAGGTGTCTCTGAGTTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTTGTTCTACCATCTATGAGAGGG\nATGAGATTGATGCCAACAGATTCCAAATCATTCTTTAATTGTTCTAGTTTTTTGTGATCT\nTCTAAATACTTCTGCTCAAAATTGGCGGGAGATGATCTAACAAAACACTCAAGTAGGATT\nAGAACATTACCAGTGAGTTTGTAGCCGTCGGGTACCACAAAACATAAAGCTGGAGTAAGA\nATCCCATGATCACTCAGAATAGATTCAACCGTTTTGTTTTCAGTGTTATGTTCACATCCA\nTTGGCCTTGCAAGAGTCAATCTCAATGCAAAGAGATAGTAACTTCAATCCCTCTATAAGC\nAACATTCTGGGTTCAGTTTGGACTAAAAAGGCTAACTTCTGTCTTGACAGCTTCTCATTA\nTCTGCAAGGTACTTTGAGATGAGATCTTTAGCATTAGCAATGTCTTCCTCCATCGCCAAT\nTGTGGCACCCCTGTAGGGCTT---------------------------------------\n----------------------------------------------\n>LASV_NGA_2018_0611-1\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n----------------------------------------------------------TG\nTCACCAATTTCCCTCACAAACACTTCCAAATCCTGGTCTTGAATGGATGGNNNAAATGTA\nGCAATCCTCCTGTCAGACTCCCATAGTGCTCCCCTGCACNNNACCAACGGCACAGGCTCA\nCTATCAGGCCCGACCTTTGAGAAGTCAAACTCAGTAAACTGTAGCTTGTCTGGATCAACA\nACCAGCTTCAGGGGTGTGACATCTCCCAGTTGTTGTGTATCCCTTAAGAACTCATTTATT\nACATCTGATTCAACANACCAGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNACTCAATAAGTCAAGAAAATCCTCAAGGGACTCAAGCTTC\nAGCTCCTCTGTCAAGCCTGAGGCGATGAGTTGATTCAAGTTCATCTTGGCCGGTTCAACG\nTCAAAATCTATCCATGCATAGCCCATCATNNNNNNNNNNNNNNNNNNNNNNNNTTCTATC\nCCNNNGTGAATGGCTTTCTCAACAAATGAGGAAAAGGGACCCAGTCGCTGCAAACCTTCG\nCCCTCTGGTATTGAAGTTTTATGAGGGAACCAAGTAAATGATCCCAAAGTCCTTGTTGTT\nGCCACAAACGATCGAACATATGATTCAAAGTAAACTTGTCTCATGAAGTTGTCTACTGCA\nTCAGCAGTACTAACCACTCTTTCCTCCACCATGGGTTCATGTGTGCGGGAGTGTGAATTT\nCTCAGCTCAGATGCCAACACAACATAATGTTCCTCTCTTTTCCACTTGACAATATGTGAA\nACAAGTGAGAGTGCCTCACAGTTCACATCTAGAGCAACACAGAGGTCAAGAAACTTTATT\nCTAGGTGACCATTTCATTTTAGTAGAGGCCAAGTCACTCATGAATGGTAATATGTGTTTC\nTCAAATAGAGATGGATACAAGCGCCTCAAAGAGNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATA\nGCTGTAGACAGTGTTATGCACATATAATCCCATAGGAGGGGTCTCAGGTAAGTGACAGNN\nNNNNNNNNNNNNTCCTTGGCTTCTGGTGACACTCTCCATATCTGGATTCCATTATCCCCC\nATCACTGCCTCAACACCTTGAGTTTCCAACAACTGAGACTGTATGGATCTAATGTAAAGA\nTTCTCCCTGTTAGGACCTCTAACACACTTGCTGCCTAGTGTCCTACACAACCCCACGAAT\nCCGGATGCTATAGAGCTTTGGAAGGCAGACTTATTTATTGCTTCAGACAATAATTTCTGA\nGCCCCTCTGGTGAACGTTGATGACAATCTGTTCTGCAGAGTCTTCACTATTGTAGGGACC\nCTGTCATCCTCCAAGTTCACAGCACCAGAATAAATTATCTTTTGTCGCAACACCATCCTA\nAGTGGATAATGGGTTGCCAGGTTCAGCCAATGAAACTCTAGATCAGAATTGGACAGGGGT\nTCAATGTTCAAAAGTTTAAAAAGATTCTGCAGCGATGTCATGTGTTCACCTGACAGATAA\nTTGGTGGTAAATTCCTCATGGAGCTCACCGGTTTTTAATTTATTAAACAATATCCGAAGC\nATTGACCTCATTTTTTTACATGCATCAGGAACCAATCTCTCAATTTGCCTCATTATCCTG\nTAGCTACGATTCCCGTCCACCCAGTCTCTCACATCAGTCTCACAATTTAAGAGGAATGGG\nTCTATAGGGTACTTAGCATAACACAACAAGCTTAATGTTCTCTTTTGAATCTGATTGCAC\nAAATCAACTGGAACACCGTTTGCCACAGACTGATCAATTATTGTGTCAATTGTTTCTGCT\nAACTGATGGGGCTCCTTACACTTTATGTTGTGCAAAGCTGCAGCAACAAATTTTGTTAGT\nAAAGGCACCTCATCACCCCAGACATAAAATCGTGATTTAAACTCTGCAACAAACCTGCCA\nATGGCACTCTTTGGACTTACAAATTTGTTTAGCTGGTCACTCATATAATAGTGAAACTCT\nAACAATGTTTTGAACTCCTCTTCATCTCTTGAGAGTAATTGTGTCAAGTTCTGATCAAAT\nAAAGATATTTGGTCATCACTAGATGTGTATGCATCAATCTGTCCACCAGACACACACTTT\nATTGCAAAATTAATAAATCTTTCAGAGATCAATGCATAGAAATCTGAGGTATTGTGCAAT\nATACCTTGGCCCATATCAAGAATTGAACTAATGTGGGAAGGGACTGTGCCAGCTTGAAAG\nTTGGAGTTGAAGAAGTCTTCAGTCACTGATTGAGTGGTCTTCTTCTTCAATCCAAGTTGA\nGATTTGATGTATGATTTCATCATTGCTGACACAACATTAAAAGGAATCTCCACCATCTTG\nTGCATATGCCATGTCAGTAATGTTGACAGGTAGTCTTTGCCTTTTAGATCAGCCTGCAGG\nTCATCAGAAAGTAAAATTAGATTCTGAATGATTGTTAGGAATAGAAAGGGACACATCATT\nGGACCCCACTTACTGTGATCCATGCTATATGAAACGTGTGCTGATGAGACATTTAACTTC\nATTGATAAAATGGCATTATCGAATTCTTTCTCATTGTTTAGACAGCTGCCTGTCAACTGT\nGATGTAAGTGCCTCAAAGTAATCCTCGATGAGCCTTGTGAACATCTTTGTTCTGAGGTCT\nCCGATGTACAACTCTCGGTTGCCCCCCACCTGTTCCTTGTAGGATAAAGAGAATTTTAGC\nCTACCGGTGTCAGGACCAGTTGAATTGTAAGACTGAGGTGACTCTTGACTATAAAAACAT\nAGATTCTTTAACATTGCTGTGGTACAATTGGTCAGAGATAAAGCTTTGCTAAGTGCCTCA\nGAATTACTCTCCCGTTCACTTATTCTGACATCATCAGCCAACTTCCCTGTGTCAAACTTG\nAAATTTAGACATTTGCTTTTATAATGGGAATATTTCCCCATTAATCTGTTCCCATTCATC\nACCAACAAGATTGATTTAAAACATTGGAAATATTCCTGGTCTAAGAAAGTCCTTGTTACC\nACTGCCTTTGTCAACTCTCCTATAGGACAAGAATTCATTGGTCCTGTGTAAAAATATTTG\nTCTCTTAAAATCTCATCACTATATATGCTTTCACAGATTTTGACATATTGATCTTCAGGC\nAGGATTTCTCGATCAAAATCTTCTATCATGTGATTGGAGAGTTCACTCTTGATCAATCTT\nATGAAGAGCTTTTCCTCCACCACCTTGTCAAGGTCAGATATTGAGGGTGAATTGCAATCT\nACTTGCTGTTGTCTTCCTGGTGACTCCCTATATTGACTAATAATATTGTCAACAGTACAT\nTTTAGGTGATCAAAGTATTCTGATGCTCCTCCATCTAGTAGTATCTCATCAAGATCAGTG\nTTATCAACATCACCGCTTCCTTCTTTTGAACCTAAGACAAGATTACTCATTGCTTGTTGT\nATCTTATAATCGTAGTCCTGTTTGTTTAGCAGATATTTGCCTTTACGTGCGAACACCTCT\nGTTAATTGTGTGACAGCTAATGCTGTCAACTTGTTGAAATCATAATCTAAGACACGAGAC\nCCATCTGTATACTTATTTACGACAACACTTTTATTGCTGGCCAGATCCAAAGCTGTAGCA\nCAACCACTTGTAATAAGGGGGTCTTGCAGTGCCTTTTTTACTTCCTTTCCCTTGAATAGA\nGAGCCATTGTTAAAACTAGACACGAGAAGTGAAATGAACTTCTTGGACACACCGGGCTTC\nTTATATCTTACCTTGTCTGCATCTGCACAAGACTCTTTACTCAGGAACTTTCTCGCATTG\nTAGATCATTTCATGAAGCTCTTCTTCTGACGCATCATCCTTTGGGTTCACACTGACATGC\nCCAAAATCCAATTTGGGTTCAAGGAATTTCTCGAAGCATTTAATTTGGTCAGTCAATCTG\nTCAGGTGTTTCTTTAGTGATGAAGTGACACATGTATGAGATGTTCAAGACAAACTTGAAC\nCTATTGGTCATCATGCTGACAACCTCCTCAGATAAAATTATTCCTAATAAATGACGGACA\nAGCTTATAGAGCAGGTATTCAACCTCTGTAATTAAATCTTCTCTAATTTTGTCAATTAGA\nTCCTTGTGGTGAAAATCAGACACAAATGCCATCACAAAATACCTAATGTTTTGTAAGAAC\nTTTTGACACCTTTTACTGGGGTGTGTTAATATTAGAACCAAGATCATTTTGGTCAACAGT\nTTGATAGTGATCAGCTGTTCAGATAATTCTGAGCACTCTTCTATCCAGCTGACCATAACA\nTTGACCACTTTCTGTAGGACATCACTAGAGAAAACTGCAGGAAAGAATCGTTTGGGGTCA\nGCATAAAATGAGCAGACCTCCCCAACTACATTGTTGTTGATAGCATAACACTTTGAACAT\nTCACCTGTCTTTTGATATAACAATTTAAATCCTATCTTGTTGACAAAGAACTCTTGACAA\nTAAGCTTCCTTGCATCTAACAACCTGATATCTAGAAGGCCCAAACTCATTTTGCCTCAGC\nTTCACGGTTGAAGATGTCTTCATTGAATTGATGAGAGCCAGGCTAAGTGTTGATAGCCTT\nTCCAAGTCTGTTGTGTTTAGGATATCAACAACACCAAGGGTATAGGGGAACATGTCTTCT\nTGAGACTTTTGATAGCTCATAGTAGGTGTGATCCCAGAAACCTCAATACTCATAATTGTG\nTCATAGACATCACAATCAAGAACTTTAAGATCAATTCCATATGAATCAACCTCAATGCCA\nACCTCTTTCAGAGCATTAGTAGCTCGAGTTAAAACCTTGTTAATGATGGTTAAAAGCTCG\nTGGTTTCGTCCCTCTATGGATGATGGAAGATTTGCACTTTTATCCCTGGCTCTCCTTCTA\nCTATCTATCCACCGTTTTAGATCCCTTTTTGTTGATTCTAATGAAACTAGTCTGTCATTA\nACACTAACAAAACAAGAGCCTAGCCAACCAACGAGATACTTGTTATTATGCCCTAAACAA\nTCCAACCGGCTTGCAAGGAGGATTAGAATGTCAAAAACAAGAAGAAGTTTTCTTCTAGTG\nTTGAGAATCCTTAGTGATTTCACCTTATTCAAGAAGGATCTCCAACATTGCATCTGTCCA\nTTCTGAGGGTCAGCAGACTTTTCCTCACTGGAATTTAGACCTGCATACAAGAACTTAAGG\nACTGGAGAGGCTCTCTGAAACTGGAATGTCAATTGTTCAATACTTTCATCATTAGTGCTA\nATCTTATCATTGTATAGATTCCTGAAATCCTCCAATAACTTTATCTTGTCAGTCTTTATA\nAATTGACTTTCTATGCCTCCCTGCCTCAACTTATTTCTGAAGATTTGGTATTCTTCCTCA\nATTGAGCTTTTGACATCATGGGCAGAAAGCTTGTTGTTAATACCTTGATGGCAGCTAGAA\nATTAATTCCTCAAAGTGCTTTGCACGATTATCAATTAAAGCATTGATGCTTTCTATTCCG\nGAGAGTCTACCAGAAGTTAAAGCTAATGACTCACAGAGTCTTGAATACTCAGACTCCTCG\nAATAATGCATTGCTTTCCTGTGAATATTTCAATAAGGCAAACAAAGTATCCCTAAGTTTA\nTCATTCACCCAGTCAGGTATCTGCTCGTTGTAAAAAGTTGTTCTACCGTCTATAAGAGGG\nATGAGGTTGATGCCAACAGACTCTAGATCACCTTTCAGTTGTTCTAACTTCTTATAGTCC\nTCCAGATACTTTTGCTCAAAGTTGGCAGGAGATGATCTAACAAAACACTCAAGCAGAATC\nAAAACATTGCCAGTGAATTTATAGCCATCAGGAACCACGAAACATAGAGCAGGGGTGAGC\nACCCCATAATCATTGAGGATGGATTCAACTGTTTTGTCCTCTGTATTGTGTTCGCAGCCA\nTTAGCCTTGCAAGAGTCAATCTCAATACAGAGAGATAACAATTTCAACCCCTCCATGAGC\nAGCATTCTAGGCTCAGTCTGAACCAGAAAAGCCAGTTTCTGTCTAGAAAGCTTTTCGTTG\nTCTACAAGGTATTTTGAGATGAGA------------------------------------\n------------------------------------------------------------\n----------------------------------------------\n>LASV_NGA_2018_0664-1\n------------------------------------------------------------\n----GCCTAATC-AAAATGGGCAACAAACAGACCAAATCGACAAAAGTCGATGAACATCA\nAAGAGCTCATCTAGTGCCAGATGCTTCCCATTTAGGCCCTCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGCTTGGTGGAGTGCAACAACCACTACCTGTGTCTCAACTGCCTCAG\nTCTGCTCCTCAGCGTCAGTGGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAAGCT\nAAAGGCAGCAGCACAGCCGAGCGCACCCTCAACCGAGGCGACCCAAAACACAACACCTCC\nACCGTACACCCCATGATCCCAGGATCAACACTCCCATCTCCATCACCCNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATTCAATG\nTCCTCAATGCACTTCTTCGGCCCAAACAACTCTGAACATGTCCTTCCCTTCAGTCTTAGG\nCTACCCCCACTTGACTGAATCATAACTCTTTGCTTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGGAGTTCACTCAGTATATCCACATAA\nTCCACAGGTCTCTGTCTTGTGAGGATTGAGACAATGTCCACACCCGTCCATTGAATTTTC\nTGTTTCAATCTATCAGACAGCATTGATTTCAATGCACCAACTAAAAGGTGCGGAGAACTA\nTCACCAATCTCCTTTACAAACATCTCCAAATCTTGATCTTGGATGGGTGGTGCAAACGTA\nGCCACCCTTTTATCAGATTCCCATAGTGCTCCCCTACACACAACCAATGGCACTGGTTCG\nTTGTCAGGTCCGACCTTGAAAAAGTCAAACTCACTGAACTGCAATTTATCTGGATTAATA\nATCAGCTTCATAGGTATAACATCCCCCAACTGCTGTGTGTCCTTTAAGAATTCATTTATC\nACATCTGATTCAACGAACCAAGCTGACCTACCTTTGAAAGTTGGACCCGACAAAGCAAGT\nCTCCAACAGTCAGACAGAACACATGGGCTCACAGACCCAGAATATAGTGCCTGTACATCA\nTTTACTACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGGATAGAAAAA\nGTCTCTTTAAAACTAGCATCCTGGCTTTTGATTTTATACCTAATTGTCTGATAAAACTGA\nACAGAGCCCACTGGCATTGCGCCCAACAAATCAAAGAAATCTTCAAGGGAGTCCAACCTC\nAATTCCTCTGTCAGGCCTGAAGCAATAAGCTGGTTCAGATTTATCTGAGCTGGTTCTATA\nTCAAAATCTATCCATGCATAGCCCATCATTAGATCAAACTTAAACATAGGTCTCTCTATC\nCCTTTGTAAACAGCTTTCTCAATGAATGAGGAGAAGGGACCCAGTCGCTGCAGACCCTCA\nCCCTCTGGAATTGAGGTTTTATGAGGAAACCAAGTGAATGATCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTTTCTTCCATCATGGGCTCATGTGTGCGAGAGTGTGAATTT\nCTCAGTTCAGAAGCCAATACAACATAATGTTCCTCTCTTTTCCACTTAACAATGTGTGAG\nACAAGTGAAAGTGCCTCACAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTGGAAGCTAAATCACTCATAAATGGCAATATGTGCTTC\nTCAAATAGAGACGGATATAAACGTCTCAAGGAATGAATGATGTGGCTCATGCCAACCCTG\nTCCTCTAGCAGTTTCGAAACAGTGGGTCTCAAGGGGAAGTAATCACAAGGATTATGTTTA\nAAAAAGTCCAAGGTTTGAGCTTGTTTTGGTTCCCCTAGCACCCATGCTCCAAGTTCTATA\nGCTGTAGATAGTGTTATGCACATATAATCCCACAGAAGAGGTCTCAAATAAGTGATGATA\nGTGTCACCTCCATTTCTGACTTCTGGTGAAACTTTCCATATCTGGATTCCATTGTCCCCC\nATCACTGCCTCAACACCTTGAGTCCCTAGTAGCTGAGTCTGTATGGATCTAATGTAAAGA\nTTCTCCTTGTTGGGGCCCCTGACACACTTGCTACCTAGTGTTCTGCACAACCCTACAAAC\nCCAGAAGCTATAGAACTTTGGAAAGCTGATTTATTTATTGCTTCAGACAACAGCTTCTGA\nGCTCCTCTAGTGAATGTCGATGACAACTTATTTTGCAAGGTTTTCACTATTGTAGGGACC\nTTTTCATCTTCCAGATTCACAGCACCAGAATAGATTATCTTTTGCCGCAACACCATTCTA\nAGCGGATGATGGGTGGCCAAGTTCAACCAATGATACCCCAAATCAGAATCAGACAAAGGT\nTCAATGTCTAGAAGCTTAAACAAGTTCTGTAATGATGCTGTGTGTTCGCCTGATAAGTAG\nTTGGTAGTGAATTCCTCATGAAGCTCACCAGTTTTCAATTTATTGAACAGTATCCTAAGC\nATTGACCTCATCCTTTTGCATGCATCAGGAATTAGCCTCTCAATTTGCCTCATTATCCTA\nTAACTACGATTCCCGTCCACCCAATCTCTTACATCAGTCTCACAATTCAAAAGGAATGGA\nTCAATAGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTCTGAATCTGATTACAC\nAGGTCAACTGGGACACCATTAGCCACAGACTGATCAATTATGGTGTCAATTGTTTCTGCC\nAATTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCTGCAGCAACAAATTTGGTTAGC\nAAGGGCACCTCGTCACCCCAAACATAGAATCTTGATTTGAACTCTGCAACAAACCTGCCA\nATTGCACTCTTTGGACTCACAAATTTATTTAGCTGATCACTCATGTAGTAATGGAATTCC\nAACAATGTTCTGAATTCCTCTGCATCTCTTGAGAGTAACTCTGTTAAGTTCTGATCAAAT\nAATGAAATCTGATCGTCACTGGACGTGTAAGCATCAATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGCAGG\nATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGCACCGTGCCAATTTGAAAA\nTTGGAATTAAAAAAGTCTTCAGTCATTGATTGAGTTGTCTTCTTCTTCAGTCCAAGTTGG\nGATTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCATGTTAATAGTGTTGATAGGTAATCTTTACCTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAAATTAGGTTCTGAATTATTGTTAGAAACAAGAAGGGACACATCATG\nGGGCCCCACTTACTGTGATCCATACTATATGATACATGTGCCGATGAGACATTCAGCTTC\nATTGATAAAATGGCATTGTCAAACTCCTTCTCATTGTTTAAACAGCTGCCCGCTAATTGT\nGATGTGAGTGCCTCAAAGTAATCTTCAATGAGCCTTGTGAACATCTTTGTCCTTAAATCT\nCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCCTTATAAGACAAAGAAAATTTTAGT\nCTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCCTGACTGTAAAAACAC\nAGGTTTTTTAACATCGCTGTAGTACAGTTAGTTAGGGACAAGGCCTTGCTAAGTGCTTCA\nGAATTGCTCTCACGCTCACTTATCCTGACATCATCAGCCAATCTTCCTGTGTCAAATTTG\nAAATTCAGACACCTACTCTTATAATGAGAGTATCTCCCCATCAACTTATTCCCATTCATT\nACTAATAAAATTGACTTAAAGCACTGGAAATATTCTTGGTCCAGGAAAGTCCTAGTCACC\nACTGCTTTTGTCAGCTCGCCAATANNNNNNNNGNNNNNNNGTCCTACATAAAAATATTTA\nCTTCTCAAAGCAGCATCATTGTAGATATTCTCACAAATTTTGATGTATTGATCCTCAGAC\nAGGATTTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATTAACCTT\nATTAAGAGTTTTTCTTCCACTACCTTGTCAAGATCAGATATCGAGGGTGCATTGCAGTCT\nGCCTGCTGCTGTCTTTCCGGTTGCTCCTTATACTGACTGACAATATTGTCAACAGTGTGC\nCTCAATTGGTCGAAGTATTCTGATGCTCCCCCATCCAATAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCATCACTCCCTCCTTTGGACCCCAGAACAAGATTACTCATTGCTTGCTGT\nATTTTATAATCATAATCCTGTTTATTTAGCAAGAATTTGCCTTTACGTGCAAATACTTCA\nGTTAATTGTGTGACAGCCAAAGCTGTAAGCTTGTTGAAATCATAATCCAGAACACGAGAC\nCCATCTGTATACTTATTCACAACAACACTCTTATTACTGGCCAAGTCCAAAGCTGTTGCA\nCAGCCGCTTGTGATAAGAGGGTCTCGTAGTGTCTTCTTTACTTCTTTTTCTTTAAATAAT\nGAACCATTNNNNNNNNNNNNNNNNNNGAGTGAAATGAATTTTTTGGAGACACCAGGTTTT\nTTATACCTAACTTTATCCGCATCTGCACAACACTCTTTGCTTAGAAACTTTCTTGCATTG\nTAAACCATTTCAGCAAGCTCTTCTTCCGATGCATCATCCTTTGGGTTCACACTCACATGT\nCCAAATTCCAGTTTGGGCTCAAGGAATTTTTCAAAGCATTTGATCTGGTCAGTCAGTCTG\nTCAGGTGTTTCTTTTGTAATGAAGTGACACATATAAGAGATATTTAAAACAAACTTGAAT\nCTATTGGTCATCATACTGACAACTTCTTCAGACAGAATTATCTTTAATAAGTGGCGAACA\nAGTCTGTAGAGCAGATATTCAACTTCTGTGATCAGATCTTCCCTGATTTTCTCAATTAAA\nTCCTTGTGATAAAAATCAGACACAAAGGCCATCACAAAATACCTAATGTTTTGTAAAAAT\nTTTTGACACCTCTTACTAGGATGTGTCAGTATCAAAACTAAAATCATCTTGGTTAACAAT\nTTAATAGTGATCAATTGTTCAGACAACTCTGTGCACTCTTCTATCCAGCTGACCATAACA\nTTAACTACTTTCTGCAACACATCACTGGAGAAAACTGAAGGAAAAAACCGCTTAGGATCA\nGCATAAAAAGAACAAACCTCTCCAACTACATTGTTATTAATAGCATAACACTTTGAGCAC\nTCACCTGTCTTTTGATACAATAGTTTGAATCCCATTCCATTGATGAAGAACTCTTGGCAA\nTAGGCCTCTTTGCACCTCACAACCTGGTATCTAGAGGGCCCAAATTCATTTTGCCTTAGT\nTTCACTGTGGAAGACGTCTTCATTGAGTTTATCAGAGCTAAACTCAATGATGATAGTCTT\nTCTAAGTCTGTTGCATCTAGAATGTCAATGACGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGATAAGTTATTGTGGGTGTGATACCGGAGATTTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGGATCTTGAGATCAATTCCATAAGAGTTGATTTCTATGCCA\nACCTCCCTCAAAGCATTAGTGGCTCGAGTCAAAACTCTATTGATGATGACAAGGAGCTCA\nCAATTCCGTTCTTCTTTAAGTGATGGGACACCTGCATTTCTGTCTCTAGTTCTTTTCCTG\nCTGTCCATCCACCGTTTTAAATCTCTTTTTGTTGATTCTAATGAGACCAATCTATCGTTA\nACACTCATAAAACAGGAGCCTAGCCAGCCAGCAAGGAGCCTGTCACCATGCCTTATGTGG\nTCCAGCCGGCTAGCAAGGAGAATCAGAACGTCAAAAATAAGGAGAAGTTTCCTCCTGGTG\nTTGAGGATCCTCATAGACTTTATCTTATTTAGAAAAGATCTCCAACATTGCATCTGTTCA\nCTTTGAGATTCAGCAGTCCTTTCCTCACCAAAATTCAAATCTGCATACAAGAACTTAAGG\nACTGGAGAGGCTCTTCGGAACTGGAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCT\nATCTTATCATTATATAGCTTTCTGAAATCCTCTAACAACTTCACCTTATCAGTCTTAACA\nAATTGACTTTCTATGTCCCCTTGCCTTAGTTTGTTCCTGAAGATTTGATACTCCTCCTCA\nATTAAACCCTTGACTTCATGAGAGGTGAGCTTGTTATTAATGCCCTGATGACAACTAGAA\nATTATTTCCTCAAAGTGTTTCGCACGCTTGTCAGTTAAAACATTGATGCTTTCAATTCCT\nGAGAGCCTCCCAGACGTTAAGGCTAAAGACTCACAAAGTCTTGAATACTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAATATTTTAACAGGGTGAATAAGGTGTCCCTGAGCTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTGGTCCTGCCGTCTATGAGAGGG\nATGAGGTTGATGCCAACAGACTCCAAATCATTCTTTAATTGTTCTAGTTTTTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCGGGGGATGACCTAACAAAGCACTCAAGTAAGATT\nAGAACATTACCAGTGAGTTTGTAACCGTCAGGCACCACAAAACACAAAGCTGGGGTAAGA\nATCCCATGATCACTCAGAATAGATTCAACTGTTTTGTCTTCAGTGTTATGTTCACATCCA\nTTGGCCTTGCAAGAATCAATCTCAATGCAAAGAGATAATAGCTTCAATCCCTCCATAAGC\nAACATCCTGGGTTCCGTTTGGACCAGAAAAGCTAACTTCTGTCTTGATAGCTTTTCATTG\nTCCGCAAGGTACTTTGAGATAAGATCTTTAGCATTGGCAATGTCTTCCTCCATCGCCAGT\nTGTGGCGCCTGTGTTGGGTTTGGGTTTGTGCCGGTGTGGCTTGTGGGTCGGCTGGTGG--\n----------------------------------------------\n>LASV_NGA_2018_0959-1\n---------------------------------GGCTCATTTTAGTGAATCCCTGAATCA\nAAGTGTCCAGTT-AAAATGGGCAACAAACAGGCCAAATCGACAAAAGTCGACGAACATCA\nAAGGGCTCATCTAGTACCGGATGCATCCCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGGTTGGTAGAGTGCAACAATCACTACCTGTGTCTCAACTGTCTCAG\nCCTGCTTCTCAGTGTCAGCAGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAAGCT\nAAAGGCAGCAGCACAGCCGAGCGCACCATCAACAGAGGCGATCCAGAGCACAACACCTCC\nACCGTACACTCCATAATCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCCCAGCTCTACTCAATG\nTCCTCAACACACTTCTCCGACCCAAACAACTCTGAACATGTCCTTCCCTTCAGTCTTAGG\nCTGCCCCCACTTGACTGAATCATTACTCTTTGCTTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAATATATCAACATAA\nTCCACAGGTCTCTGTTTTGTGAGGATTGAGACAATATCCACACCTGTCCATTGAACTCTT\nTGTTTTAATCTATCAGACATCATTGATTTCAATGCACCAACTAAAAGGTGCGGGGAACTA\nTCACCAATCTCCCTTACAAACATTTCCAAATCTTGATCTTGGATAGATGGTGTAAATGTA\nGCTACTCTTCTATCAGATTCCCACAGTGCTCCCCTACACACGACCAATGGCACTGGTTCG\nTTGTCAGGTCCGACCTTGGAAAAGTCAAACTCACTGAACTGCAGTTTATCTGGACTAATA\nATCAGCTTCATGGGTATAACATCCCCTAACTGCTGTGTGTCCTTTAAGAACTCATTTATT\nACATCTGATTCAACAAACCAGGCTGATCTACCTTTGAAAGTTGGACCCGACAAAGCAAGT\nCTCCAACAGTCAGACAGAACACATGGGCTCACAGACCCAGAATATAGTGCCTGTACACCA\nTTCACTATAAACTCACCATATTGATTAACAAGTCCTATCATGTTGAGATGGATGGAAAAG\nGTCTCTTTAAAACTAGCATCCTGACTCTTGATTTTATATCTTATTGTCTGGTGAAACTGA\nACGGAGTCCACTGGCATTGTACTTAACAAATCAAAGAAATCTTCAAGGGAGTCCAACCTT\nAATTCTTCTGTCAGGCCTGAAGCTATAAGCTGGTTCAAGTTTATCTGAGCTGGTTCTATG\nTCAAAGTCTATCCATGCATAGCCCATCATTAGATCAAACTTAAACATAGGTCTCTCTATC\nCCTTTGTAAATAGCTTTCTCAATAAATGAAGAGAAGGGACCCAGTCGCTGCAGACCTTCA\nCCCTCTGGTATTGAGGTTTTGTGAGGAAACCAGGTGAATGACCCGAGTGTCCTTGTTGTT\nGCCACAAAAGAGCGAACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTTTCTTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTCAGTTCAGAAGCTAACACAACATAATGTTCCTCCCTCTTCCACTTAACAATGTGTGAA\nACAAGTGAGAGTGCCTCGCAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCACTTCATCTTTGTGGAAGCTAAGTCACTCATAAATGGCAATATGTGCTTC\nTCAAATAGAGACGGATATAACCGTCTCAAAGAATGAATGATGTGGCTCATACCAACCCTG\nTCCTCTAGCAATTTCGAAACAGTGGGTCTCAAGGGGAAGTAATCACAAGGATTATGTTTA\nAAAAAGTCCAGGATCTGAGCTTGTTTTGGTTCCCCGAGCACCCATGCTCCAAGTTCTATG\nGCTGTGGATAGCGTTATGCACATATAATCCCATAGAAGGGGTCTTAAATAAGTGACAACA\nGTATCACCTCCATCCTTGACTTCTGGTGAGACTTTCCATATTTGGATTCCATTGTCCCCC\nACCACTGCCTCAACACCTTGAATCCCTAATAGCTGAGTCTGTATAGATCTAATGTAAAGA\nTTCTCCTTATTGGGGCCTCTGACACACTTGCTTCCTAGTGTTCTGCACAACCCCACAAAC\nCCAGATGCTATGGAACTTTGAAAAGCTGATTTATTTATTGCTTCAGACAGTAGCTTCTGA\nGCTCCTCTAGTGAATGTCGATGACAACCTATTTTGCAAGGTTTTCACTATTGTAGGGACC\nTTTTCATCTTCTAGATTCACAGCACCAGAATAGATTATCTTTTGCCGCAACACCATTCTA\nAGCGGGTGATGGGTAGCTAAGTTCAACCAATGAAATCCCAAGTCAGAATCAGACAAAGGT\nTCAATGCCTAGAAGTTTGAATAAATTCTGTAATGATGTTGTATGATCACCTGATAGGTAG\nTTGGTAGTGAATTCTTCATGGAGCTCACCAGTTTTTAGTTTATTGAACAACACCCTAAGC\nATTGACCTCATCTTTTTGCATGCATCAGGGATCAGCCTCTCAATTTGCCTCATTATCCTA\nTAACTACGATTCCCATCCACCCAATCTCTTACATCAGTCTCGCAATTCAAGAGGAATGGA\nTCAATAGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTTTGAATCTGATTACAC\nAGATCAACTGGGACACCATTAGCCACAGATTGATCAATTATGGTATCAATTGTTTCTGCC\nAATTGATGGGGTTCTTTGCACTTTATGTTGTGTAAAGCCGCAGCAACAAATTTTGTTAAC\nAAAGGTACCTCATCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCA\nATCGCACTCTTTGGACTCACAAATTTATTTAGCTGATCACTCATGTAGTAGTGGAATTCT\nAACAGTGTTTTGAATTCCTCTGTATCTCTTGAGAGCAACTCTGTTAAGCTCTGATCAAAT\nAAAGATATCTGATCGTCACTGGACGTGTAAGCATCGATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATGAATCTTTCAGAAATCAATGCATAAAAGTCTGAGGTATTGTGCAAG\nATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAAGGGACTGTGCCAATTTGAAAG\nTTGGAGTTAAAAAAGTCTTCTGTCATTGATTGAGTTGTCTTCTTCTTCAATCCAAGTTGG\nGATTTAATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCATGTTAATAATGTTGATAGGTAATCTTTACCTTTCAAATCAGCTTGCAAA\nTCGTCAGAGAGTAAAATTAGGTTTTGAATTATTGTTAGAAACAAGAAAGGACACATCATA\nGGGCCCCACTTACTGTGATCCATACTATATGACACATGTGCCGATGAGACATTCAGCTTC\nATTGACAAAATGGCATTGTCAAACTCCTTCTCATTGTTTAGACAGCTGCCTGCTAACTGT\nGATGTGAGCGCTTCAAAGTAATCCTCAATGAGCCTTGTGAACATCTTTGTTCTTAAATCT\nCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCTTTGTAAGACAAAGAGAATTTTAGT\nCTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCTTGGCTGTAAAAACAC\nAAATTTTTTAACATTGCTGTAGTGCAGTTAGTTAAGGACAAGGCTTTGCTAAGTGCTTCA\nGAATTACTCTCACGTTCACTTATCCTGACATCATCAGCCAGTTTCCCTGTATCAAATTTA\nAAGTTCAGACACTTACTCTTATAATGGGAATATCTTCCCATCAGCTTATTCCCATTCATC\nACTAATAAAATTGACTTAAAGCACTGGAAATACTCTTGGTCCAAAAAGGTCCTAGTCACC\nACTGCTTTTGTCAGCTCACCAATGGGGCATGAATTCATTGGCCCTACATAAAAATACTTA\nCTTCTCAAAGTAGCATCATTGTAGACATTCTCGCAAATTTTGATGTATTGATCCTCAGAC\nAGGATTTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATCAACCTT\nATTAAGAGTTTTTCTTCCACCACCTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCT\nGCCTGCTGCTGTCTCTCTGGTTGCTCCCTATACTGACTGACAATATTGTCAACAGTACAC\nCTCAGTTGGTCGAAGTATTCTGATGCTCCTCCATCCAATAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCACCACTCCCTCCTTTGGACCCTAGAACAAGATTACTCATTGCTTGCTGT\nATCTTGTAATCATAATCCTGCTTATTGAGCAAGAATTTGCCTTTACGTGCAAACACTTCA\nGTTAATTGTGTGACAGCCAGAGCTGTAAGCTTGTTGAAGTCATAATCCAAAATACGGGAC\nCCATCTGTATACTTGTTCACAACAACACTCTTATTGCTAGCCAAGTCTAAAGCTGTTGCA\nCAGCCGCTTGTAATAAGGGGGTCTCGCAGTGTCTTCTTTACTTCCTTTTCTTTAAACAAT\nGAACCATTGTTAAAACTAGACACAAGGAGTGAAATAAACTTCTTGGAAACACCAGGCTTT\nTTATACCTAACTTTTTCCGCATCTGCACAACATTCTTTACCTAGAAACTTTCTTGCATTA\nTAAACCATTTCAGCAAGCTCTTCCTCCAATGCATCGTCCTTCGGGTTCACACTTACATGC\nCCAAATTCTAATTTAGGCTCAAGAAACTTTTCAAAGCATTTGATCTGGTCAGTCAGTCTG\nTCAGGTGTTTCTTTTGTAATGAAATGACACATATAGGAGATATTTAAAACAAACTTGAAT\nCTGTTGGTCATCATGCTGACAACTTCTTCAGACAGAATTATCTTTATTAAGTGACGAACA\nAGTCTGTAGAGCAGATATTCAACTTCTGTGATCAAATCTTCCCTGATTTTCTCAATCAAA\nTCTTTGTGATAGAAATCGGACACAAAGGCCATCACAAAATACCTAATGTTTTGCAAAAAT\nTTTTGACATCTTTTACTAGGATGTGTCAGTATCAAAACTAAAATCATTTTGGTTAACAAT\nTTTATAGTGATCAATTGTTCAGATAACTCTGTGCACTCTTCTATCCAGCTAACCATAACA\nTCGACTACTTTCTGCAACACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTAGGATCA\nGCATAAAAGGAACAAACCTCTCCAACTACATTGTTGTTAATAGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATACAATAGTTTGAATCCCATCCTATTGATGAAGAACTCTTGGCAG\nTAGGCCTCTTTGCACCTCACAACTTGGTATCTAGAGGGTCCAAATTCATTCTGTCTCAAT\nTTCACTGTGGAAGATGTTTTCATTGAGTTGATCAAAGCCAGGCTCAATGATGATAGTCTT\nTCTAGGTCTGTCGCATCTAGAATGTCAACAACGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGGTAACTTATAGTGGGTGTGATACCGGAGATCTCAATGTCCATGATGGCA\nTCATAAACGTCACAATCAAGGATCTTGAGATCAATTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCCTCAAAGCATTAGTAGCTCGAGTTAAAACTCTGTTGATGATGGCAAGGAGCTCA\nCAATTTCGTTCCTCCCTAAGTGATAGAACACCTGCATTCCTGTCTTTAGTTCTCTTCCTG\nCTGTCAATCCATCGTTTCAGATCTCTTTTTGTTGATTCCAATGAAACTAATCTATCGTTA\nACACTCACAAAACAGGAGCCCAGCCAACCAGCAAGGAGCTTGTCACCATGCCTTATGCAA\nTCCAGCCGGCTAGCAAGAAGAATCAAGACGTCAAAAATAAGGAGAAGTTTCCTCCTGGTA\nTTGAGGATCCTCAGGGACTTTATCTTATTTAGAAAAGATCTCCAACATTGCATCTGCTCA\nCTTTGAGAGTCAGCAGCCCTTTCCTTATTGGAATCTAAATCTGCATACAAGAACTTAAGG\nACTGGAGAGGCTCTTCGGAACTGGAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCT\nATTTTATCACTATATAGCTTTCTGAAATCCTCTAATAATTTCATCTTATCAGTCTTAATA\nAATTGACTTTCTATATCCCCTTGCCTTAGTTTGTTCCTAAAGATTTGATACTCCTCTTCA\nATTAGACTCTTGACTTCATGAGAAGTGAGCTTGTTATTAATGCCCTGATGACACGTAGAA\nATTATTTCCTCAAAGTGTTTTGCACGCTTGTCAGTAAGAACATTGATGCTTTCAATTCCT\nGAGAGCCTCCCAGATGTTAAGGCTAAAGATTCACAAAGTCTTGAATACTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAGTATTTTAACAAGGTGAATAGGGTGTCCCTGAGTTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTTGTCCTACCGTCTATGAGAGGG\nATAAGATTGATGCCAACAGATTCCAAATCATTCTTCAATTGTTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTAGCAGGGGATGATCTAACAAAGCACTCAAGTAAGATA\nAGTACATTACCAGTAAGTTTGTAGCCGTCAGGCACCACAAAGCATAAAGCTGGTGTGAGA\nATGCCATGATCACTCAGAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACACCCA\nTTGGCCTTGCAAGAGTCAATCTCAATGCAAAGAGATAGAAGTTTCAATCCCTCCATGAGC\nAACATTCTGGGTTCGGTTTGGACCAAGAAGGCTAACTTCTGTCTTGACAGCTTCTCATTA\nTCTGCAAGGTACTTTGAGATAAGATCTTTAGCATTAGCAATGTCTTCCTCCATCGCCAAT\nTGTGGCACCTATGCTGGGTTTGGGTTAGTGCCGGAATGGCTTGTGGG-------------\n----------------------------------------------\n>LASV_NGA_2018_0998-1\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n-TTTGAGAACAGAGGGCTGGTGGAGTGCAACAACCACTACCTGTGTCTCAACTGTCTCAG\nCCTGCTTCTCAGCGTCAGCAACAGGTGTCCGATCTGCAAAATNNNTCTTCCCACTAGGCT\nAAAGGCAGCAACACAGCCGAGCGCACCCTCAACCGAGGCAACCCNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC\nAATTCCTCTGTCAGGCCTGAGGCAATGAGCTGGTTCAAATTTATCTGGGCTGGTTCTATG\nTCAAAGTCTATCCATGCATAGCCCATCATCAAATCAAACTTAAACATAGGTCTCTCTATC\nCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGTGNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNGCTTCTGGTGAGACTTTCCATATCTGGATTCCATTGTCCCCC\nATCACTACTTCAACACCTTGAGTTCCCAGCAGCTGAGTTTGTATGGATCTAATGTAAAGA\nTTCTCCTTGTTGGGCCCTCTGACGCACTTGCTACCTAGTGTTCTGCACAACCCTACAAAC\nCCAGATGCTATAGAACTTTGGAAAGCCGATTTGTTTATTGCTTCAGACAGCAGCTTCTGA\nGCTCCTCTAGTGAATGTCGATGACAACCTATTTTGCAAGGTCTTCACTATTGTAGGGACC\nTTTTCATCTTCCAGATTCACAGCACCAGAATAAATTATCTTCTGCCGCAACACCATTCTA\nAGCGGGTGATGGGTGGCTAAGTTCAACCAATGATACCCCAAATCAGAATCAGACAAAGGT\nTCTATGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGATAGGTAG\nTTGGTGGTGAATTCCTCATGAAGCTCACCAGTTTTTAATTTATTAAACAATATCCTAAGC\nATTGACCTCATCCTTTTGCATGCATCAGGGATTAGCCTCTCAATTTGCCNNNNNNNNNNN\nNNNNTACGATTCCCGTCCACCCAATCTCTTACATNNNNNNNNNNNTTCAAAAGGAATGGA\nTCAATAGGATACTTGGCATAACATAACAAATTTAAAGTCCTCTTCNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTAAAAACAC\nAGGTTTTTCAACATTGCTGTAGTGCAGTTAGTTAGGGACAAGGCCTTGCTAAGTGCTTCA\nGAATTACTCTCACGTTCACTTATTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNCTAATAAGATTGATTTAAAGCACTGGAAATATTCCTGGTCCAAAAAAGTTCTAGTCACT\nACTGCCTTTGTCAACTCACTAATAGGACATGAGTCCATTGGCCCTACATAAAAATATTTA\nCTTCTCAAAGCAGTATCATTGTAGATGTTCTCACAAATTTTGATGTATTGATCTTCAGAC\nAGGATCTCTCGATCAAAGTCTTCTATCATATGGTTTGAAAGCTCACTTTTTATCAACCTT\nATTAAAAGTTTTTCTTCCACCACCTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCT\nGCCTGCTGCTGTCTTTCTGGTTGCTCCCTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCAGTCTG\nTCCGGTGTTTCTTTTGTAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNCTGTAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNTATGATAAAAANNNNNNNNNNNGGCCATCACAAAATACCTNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNGTGTCAGTATTNAGACTAAAATCATTTTGGTTAACAAT\nTTAATAGTGATCAGCTGTTCAGACAACTCTGTGCATTCTTCTATCCAGCTGACCATAACA\nTCGACAACTTTCTGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTGTTAATAGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATATAATAGTTTGAATCCCATCCTATTGATGAAGAACTCTTGGCAA\nTAGGCTTCTTTGCNNNNNNNNNNCTGATATCTAGAGGGTCCAAATTCATTTTGCCTTAGC\nTTCACTGTGGAAGACGTCTTCATTGAGTTGATCAAAGCCAAGCTTAATGATGATAGTCTT\nTCTAAGTCTGTTGNNNNNNNNNNNNNNNNNNCGCCAAGAGTGTAAGGGAACATGTCTTCC\nTGAGTTTTTTGGTAACTTATAGNNNGNNNNNNNNNNNNNNTCTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGAATCTTAAAATCAATTCCATAAGAGTTAGTTTCTATGCCA\nACCTCCCTCAAAGCACTAGTGGCTCGAGTTAATACTCTGTTGATGATTGCAAGGAGCTCA\nCAATTCCGTTCTTCTTTGGGTGACAGGACACTTGCATTTNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGAGGG\nATGAGATTGATGCCAACAGACTCCAAATCATTCTTTAACTGCTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCGGGGGATGANNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCACCACAAANNNNNNNNNNNNNNNNNNN\nATCCCATGATCACTCAGAATGGATTCAACCGTTTTGTCTTCAGTATTATGTTCACACCCA\nTTGGCTTTACAAGAGTCAATCTCAATACAGAGAGACAATAGCTTCAATCCCTCCATGAGT\nAACATTCTAGGTTCAGTTTGGACCAGAAAAGCTAACTTCTGTCGTGATAGCTTCTCATTA\nTCTGCAAGGTATTTTG--------------------------------------------\n------------------------------------------------------------\n----------------------------------------------\n>LASV_NGA_2018_1024-1\n------------------------------------------------------------\n------------------------------------------AAGAGTCGATGAACAACA\nAAGAGCCCATCTAGTGCCAGATGCATCCCATCTAGGCCCTCAGTTCTGTAAGAGTTGCTG\nGTTTGAGAACAGAGGGTTGGTAGAGTGCAACAACCACTACCTGTGCCTCAACTGTCTCAG\nCCTGCTCCTCAGCGTAAGCAGCAGATGCCCGATCTGCAAGATGCCCCTTCCAACCAAGCT\nGAAGGCAGCAGCACAGCCGAGCGCACCCTCAACCGAGGCGACTCAGGACACAAAACCTCC\nACCATACGCCCCATGATCCCAAGACCAACACCTCCATCTCCATCACCC-ACNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAACTCAACTCTACTCGATG\nTCCTCAATACACTTTTCTGGCCCAAACAACTCTGAACATGTCCTTCCCTTCAGTCTCAGG\nCTGCCCCCACTTGACTGAATCATGACTCTTTTCTTTGACCTACTATAGCAAAGTGCATAG\nCCTTTGAAGTCAATCCATTCTCCAAGAGATTCAAGAAGTTCACCCAGTATATCAGCATAG\nTCCATAGGTCTCTGTTTTGTGAGGATTGAGACAATGTCCACACCTGTCCATTGAATTCTT\nTGTTTCAATCTATCAGACATCATTGATTTCAATGCACCAACTAAAAGATGCGGGGAACTG\nTCACCAATCTCTCTTACAAACATTTCCAAATCTTGATCTTGGATAGATGGTGTGAATGTA\nGCTACCCTTCTATCAGACTCCCACAGTGCCCCCCTACATACAACCAATGGCACTGGTTCG\nTTGTCAGGTCCGACCTTGGAGAAGTCAAACTCACTGAACTGCAGCTTGTCTGGATCAACA\nATCAGCTTCATGGGTATGACATCCCCTAACTGCTGTGTATCTTTTAAGAATTCATTTACC\nACATCTGATTCAACAAACCAGGCTGACCTACCTTTGAAAGTTGGACCCGACAAAGCAAGT\nCTCCAACAGTCAGACAGAACACATGAGCTCACAGACCCAGAATATAATGCCTGCACATCA\nTCCACTACAAACTCACCGCGTTGGTTAACAAGACCTGTCATGTTGAGATGGATAGAAAAA\nGTCTCTTTAAAACTAGCATCTTGACTCTTAATTTTATACCTAATTGTCTGATAAAACTGA\nACAGAGCCCACTGGCATTGTACTTAACAAATCAAAGAAATCTTCAAGGGAGTCTAACCTC\nAATTCCTCTGTCAGGCCTGAAGCAATTAGCTGGTTCAAGTTTATCTGAGCTGGTTCTATG\nTCAAAGTCTATCCATGCATAGCCCATCATTAGGTCAAATTTAAACATAGGTCTCTCTATC\nCCTTTGTAAATGGCTTTCTCAATGAATGAAGAGAAGGGACCCAGTCGCTGCAGACCTTCA\nCCCTCTGGTATTGAGGTTTTGTGAGGGAACCAAGTGAATGACCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTCTCCTCCATCATAGGCTCATGTGTGCGAGAGTGTGAGTTC\nCTCAGTTCAGAAGCCAATACAACATAATGTTCCTCTCTCTTCCACTTGACAATATGTGAA\nACAAGTGAAAGTGCTTCGCAATTTACATCTAATGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTGGAAGCTAAATCACTCATAAATGGCAATATGTGCTTC\nTCAAATAGAGACGGATATAAACGTCTCAGAGAATGGATGATGTGGCTCATGCCAACCCTG\nTCCTCTAGCAATTTCGAAACAGTGGGTCTCAAGGGGAAATAATCACAAGGATTATGTTTA\nAAAAAGTCCAGGATCTGGGCTTGTTTTGGTTCCCCGAGCACCCATGCTCCAAGTTCTATA\nGCTGTAGATAGTGTTATGCACATATAATCCCATAAAAGAGGTCTTAAATAAGTGACAACA\nGTGTCACCTCTATCTTTGACTTCTGGTGAAACTTTCCATATCTGAATTCCATTATCCCCC\nATCACTGCTTCAATACCTTGAGTCCCCAGTAATTGAGTCTGTATGGATCTGATGTAAAGA\nTTCTCCTTGTTGGGGCCTCTGACACACTTGCTACCTAGTGTTCTACACAACCCTACAAAC\nCCAGATGCTATAGAACTCTGAAAAGCTGATTTATTTATTGCTTCAGACAGTAGCTTCTGA\nGCTCCCCTAGTAAATGTCGATGACAACCTATTTTGCAAGGTTTTTACTATTGTAGGGATC\nTTTTCATCTTCCAGATTTACAGCACCAGAGTAGATTATCTTCTGCCGCAATACCATTCTA\nAGCGGGTGATGGGTGGCTAAGTTCAACCAATGAAACCCCAAGTCAGAATCAGATAAAGGT\nTCAATGCCTAGAAGTTTAAACAAGTTTTGTAATGATGTTGTGTGCTCACCTGATAGGTAG\nTTTGTAGTGAATTCCTCATGGAGCTCACCAGTTTTTAATTTATTGAACAATATCCTAAGC\nATTGACCTCATTTTTTTGCACGCATCAGGAATTAGCCTCTCAATTTGTCTCATTATCCTA\nTAACTACGATTCCCGTCTACCCAGTCTCTCACATCAGTCTCGCAATTCAAAAGGAATGGG\nTCAATAGGATACTTGGCATAACACAACAAACTCAAAGTTCTCTTCTGAATTTGATTACAC\nAAATCAACTGGGACGCCATTGGCCACAGACTGATCAATTATGGTATCAATTGTTTCTGCC\nAATTGATGGGGTTCTTTGCATTTTATGTTATGCAAAGCCGCAGCAACAAATTTTGTTAGC\nAGGGGTACCTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCA\nACTGCACTCTTTGGGCTCACAAATTTATTTAGCTGATCACTCATGTAATAATGGAATTCC\nAACAATGTTCTGAATTCCTCTGTATCTCTTGAGAGTAACTCTGTCAAGTTCTGATCAAAT\nAATGATATCTGATCATCACTGGACGTATAAGCGTCGATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGCAAA\nATGCCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGGACTGTGCCAATTTGAAAG\nTTGGAATTGAAAAAGTCTTCAGTCATTGATAGAGTTGTCTTCTTCTTCAGCCCAAGTTGA\nGATTTGATGTATGACTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATGTGCCACGTTAACAATGTTGATAGGTAATCTTTACCTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAGATTAGGTTTTGGATTATTGTCAGAAACAAGAAAGGACACATCATG\nGGGCCCCACTTACTGTGATCCATACTATATGATACATGTGCTGATGAGACATTCAGCTTC\nATTGACAAAATGGCATTGTCAAACTCCTTCTCATTGTTTAGACAGCTACCCGCTAATTGT\nGATGTGAGCGCTTCAAAGTAATCTTCGATAAGCCTTGTGAACATCTTTGTCCTCAAATCT\nCCGATGTACAACTCTCTATTGCCTCCTACTTGTTCCTTGTAAGACAAAGAAAATTTTAGT\nCTACCAGTATCAGGGCCAGTTGAATTATAAGACTGAGGCGATTCCTGACTGTAAAAACAT\nAGGTTTTTTAACATTGCTGTGGTGCAGTTAGTTAGGGACAAGGCTTTGCTAAGTGCTTCA\nGAATTACTCTCACGTTCACTTATCCTGGTATCATCAGCCAATTTCCCTGTATCAAATTTA\nAAGTTCAGACATTTACTCTTATAATGAGAATATCTTCCCATCAGCTTATTCCCATTCATC\nACTAATAAAATAGATTTAAAGCACTGGAAATATTCTTGGTCCAGAAAAGTTCTAGTCACT\nACTGCTTTTGTCATCTCACTAATAGGACATGAGTTCATTGGCCCCACATAAAAGTATTTG\nCTTCTCAAAGTAGCATCATTGTAGACATTCTCACAAATTTTTATGTATTGATCCTCTGAC\nAGGATTTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATTAACCTA\nATTAAGAGTTTTTCTTCCACCACCTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCT\nGCTTGCTGCTGTCTCTCCGGTTGCTCCCTATATTGACTGATAATATTGTCAACAGTGCAT\nCTCAGTTGGTCAAAGTATTCTGATGCTCCTCCATCCAATAGTATCTCATCTAAATCAGCA\nTTATTGGTGTCACCACTCCCACTTTTGGACCCCAGAACAAGATTACTCATTGCTTGCTGT\nATCTTGTAATCATAATCCTGTTTATTAAGTAGGAATTTGCCTTTTCGTGCAAACACTTCA\nGTTAACTGTGTGACAGCTAAAGCTGTAAGCTTGTTGAAATCATAATCCAGAACACGAGAT\nCCATCTGTATACTTATTTACAACAACACTCTTATTACTGGCCAAGTCCAAAGCTGTTGCA\nCAACCGCTTGTGATAAGAGGGTCTCGCAGTGTCTTCTTTACTTCCTTTTCTTTAAACAAT\nGAACCATTATTAAAACTAGACACAAGGAGTGAAACAAATTTTTTAGAAACACCAGGCTTT\nTTGTACCTAACTTTTTCCGCATCTGCACAACATTCTTTGCTTAGAAACTTTCTTGCATTG\nTAGACCATTTCAGCAAGCTCCTCCTCCGATGCATCATCCTTTGGGTTCACACTCACATGT\nCCAAATTCCAATTTGGGCTCAAGGAATTTTTCAAAGCATTTGATCTGGTCTGTCAGTCTG\nTCAGGTGTTTCTTTTGTAATGAAATGACACATATAGGAGATATTTAAAACAAACTTGAAT\nCTATTAGTCATCATACTGACAACTTCTTCAGACAGAATTATCTTCAATAAGTGACGGACA\nAGTCTGTAGAGCAGATATTCAACTTCTGTGATCAGATCCTCCCTGATTTTCTCAATCAAA\nTCCTTGTGATAAAAATCGGATACAAAGGCCATCACAAAATACCTAATGTTTTGTAAAAGT\nTTTTGACACCTTTTACTGGGATGTGTCAGTATCAAGACTAGGATCATTTTGGTTAACAAT\nCTAATAGTGATCAATTGATCAGACAACTCTGTGCACTCTTCTATCCAGCTGACCATAACA\nTCAACTACTTTTTGCAACACATCACTGGAGAAAACCGAAGGAAAAAACCGTTTAGGATCA\nGCATAAAAGGAACAAACCTCTCCAACCACATTGTTATTAATAGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATACAATAATTTGAATCCCATCCCATTGATGAAGAACTCCTGGCAA\nTAAGCCTCTTTGCACCTCACAACCTGGTATCTGGAGGGTCCAAATTCATTTTGCCTTAGT\nTTCACTGTGGAAGACGTCTTCATTGAGTTGATCAAAGCTAAGCTTAATGATGATAGTCTT\nTCTAAGTCTGTTGCATCTAGAATGTCAATAATGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGGTAACTTATAGTGGGTGTGATACCGGAGATCTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGGATCTTGAAATCAACTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCCTCAAAGCATTGGTGGCTCGAGTTAAAACTCTGTTGATAATGGCAAGGAGCTCA\nCAATTCCGTTCTTCTTTAAGTGACAAGACACCTTCATTTCTGTCTTTAGTTCTCCTCCTG\nCTGTCTATCCACCGCTTTAAATCTCTTTTTGTTGATTCCAATGAAACTAATCTATCGTTG\nACACTCACAAAACAGGAGCCCAGCCAACCAGCAAGGAGCCTGTCACCATGCCTTATGCAG\nTCCAGCCGACTAGCAAGAAGAATCAGAACGTCAAAAATAAGGAGAAGTTTCCTCCTGGTG\nTTGAGAATCCTCAAAGACTTTATCTTATTTAGAAAAGATCTCCAACATGGCATCTGTTCA\nCTTTGAGAGTCAGCAGCCCTTTCCTTACCAGAATCCAAATCTGCATACAAGAACTTAAGG\nACTGGGGNNNNNNNNNNNNACTGGAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCC\nATTTTGTCATTGTATAGCTTTTTAAAATCCTCTAATAACTTCATCTTATCAGTCTTAACA\nAATTGACTTTCTATGTCCCCTTGCCTTAGTTTGTTCCTGAAGATTTGATACTCCTCTTCA\nATCAAACTCTTCACTTCATGAGAGGTGAGCTTATTGTTAATGCCCTGATGACAACTAGAA\nATTATTTCCTCAAAGTGTTTTGTACGCTTGTCAGTTAAAACATTGATGCTTTCAATTCCT\nGAAAGCCTTCCAGACGTCAAGGCTAAAGACTCGCAAAGTCTTGAATACTCAGACTCTTCG\nAATAATGCATTACTTTCTTGTGAATATTTTAATAAGGTGAATAAGGTGTCCCTGAGTTTA\nTCATTCACCCAATCAGGTATCTGTTCATTATAGAAAGTTGTCCTGCCGTCTATGAGGGGG\nATGAGATTGATGCCAACAGACTCTAAATCATTCTTTAATTGCTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGCTCAAAATTGGCAGGGGATGATCTAACAAAGCACTCAAGTAAGATT\nAGAACATTACCAGTGAGTTTGTAGCCATCAGGTACCACAAAGCATAAAGCTGGGGTGAGA\nATCCCATGATCACTCAAAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACATCCA\nTTAGCCTTGCAAGAGTCAATCTCAATGCAAAGAGATAGTAGTTTCAATCCCTCCATAAGT\nAACATTCTAGGTTCAGTTTGGACCAAGAAAGCTAATTTCTGTCTTGATAGCTTCTCATTA\nTCTGCAAGGTACTTTGAGATNNNNNCTTTGGCANNNNNNNNNNNNNNNNNNNNNNNNAAT\nTGTGGCACCTGTGTTGAGTTTGGGTTTATGCTAGTATGGCTTGTGGGTCAGCTGTTGGTG\nCCCCAC----------------------------------------\n>LASV_NGA_2018_1079-1\n---------------------CTTCAGTGGAAAGACTCTTCTTAGTGAATCCCTGAATCA\nAAGTGCCTAATC-AAAATGGGCAACAAACAGACCAAATCGACAAAAGTTGATGAACATCA\nAAGAGCTCATCTAGTGCCAGATGCATCCCATTTGGGCCCTCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAAAGGCTTGGTGGAGTGTAACAACCACTATTTGTGTCTCAACTGCCTCAG\nCCTGCTCCTCAGTGTCAGCAGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAAGCT\nAAAGACAGCAGCACAGCCGAGCGCACCTCCAACCGAGGCAACCCAGAACACAACACCTCC\nACCGTACACCCCATGATCCCAGGGCCAACACTCCCATCTCCATCACCC-ACCCCCCACCN\nNNNNNNNNNNNNNNNNNNNGGGGCCCCCCCGGGGGTGGGGCGGCCTGGCTCTACTCAATG\nTCCTCAATACACTTCTTCGGCCCAAACAACTCTGAACATGTCCTTCCCTTCAGTCTTAGG\nCTGCCCCCACTTGACTGAATCATAACTCTTTGCTTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGACTCAAGAAGCTCACTCAGTATATCCGCATAA\nTCCACAGGTCTCTGTCTTGTGAGGATTGAGACAATGTCCACACCCGTCCATTGAATTCTC\nTGTTTTAATCTATCAGACAACATTGATTTCAGTGCACCAACTAAAAGGTGCGGGGAACCA\nTCACCAATCTCCTTTACAAACATTTCCAAATCTTGATCTTGGATGGGTGGTGCAAACGTG\nGCCACCCTTCTATCAGATTCCCATAGTGCCCCCCTACATACAACCAATGGCACTGGTTCA\nTTGTCAGGTCCGACTTTGGAAAAGTCAAACTCACTGAACTGCAATTTATCTGGATTAACA\nATCAGCTTCATAGGTATAACATCCCCTAACTGCTGTGTGTCCTTTAAGAATTCATTTATC\nACACCTGATTCAACGAACCAGGCTGACCTACCTTTGAAAGTTGGACCTGACAAAGCAAGT\nCTCCAACAGTCAGACAGAACACATGGGCTCACAGATCCAGAATATAGTGCCTGTGCATCA\nTTCACTACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGGATGGAAAAA\nGTTTCTTTAAAACTAGCATCCTGACTTTTAATTTTATACCTAATTGTCTGATAAAACTGA\nACAGAGCCCACTGGCATTGCGCTTAACAAATCAAAGAAATCTTCAAGGGAGTCCAACCTC\nAATTCCTCTGTCAGGCCTGAAGCAATAAGCTGGTTTAAGTTTATCTGAGCTGGTTCTATA\nTCAAAATCTATCCATGCATAACCCATCATTAGGTCAAACTTAAACATAGGTCTCTCTATC\nCCTTTGTAAACAGCTTTCTCAACGAATGAGGAGAAGGGACCCAGCCGCTGCAGACCCTCA\nCCCTCTGGTATTGAGGTTTTATGAGGAAACCAGGTGAATGATCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAATTATCCACTGCA\nTCAGCAGTACTAACTACCCTTTCTTCCATCATGGGCTCATGTGTGCGGGAGTGTGAATTT\nCTCAGTTCAGAAGCCAATACAACATAATGTTCTTCTCTTTTCCACTTAACAATGTGTGAG\nACAAGTGAAAGTGCCTCACAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTGGAAGCTAAATCACTCATAAATGGTAATATGTGCTTC\nTCAAATAGAGACGGATACAAACGTCTCAAGGAATGAACGATGTGGCTCATGCCAACCCTG\nTCCTCTAACAGTTTCGAAACAGTGGGTCTCAAGGGGAAGTAATCACAAGGATTATGTTTA\nAAAAAGTCCAAGGTCTGAGCTTGTTTTGGTTCCCCGAGCACCCATGCTCCAAGTTCTATA\nGCTGTAGATAGTGTTATGCACATATAATCCCATAGAAGAGGTCTCAAATAAGTGATGATG\nGTGTCACCTCCATCTCTAACTTCTGGTGGAACTTTCCATATCTGGATTCCATTGTCCCCC\nATCACTGCTTCAACACCTTGAGTCCCTAGTAGCTGAGTCTGTATGGATCTAATGTAAAGA\nTTCTCCTTGTTAGGGCCCCTGACACACTTGCTACCTAGTGTTCTGCACAACCCTACAAAC\nCCAGAAGCTATGGAACTTTGGAAAGCTGATTTATTTATTGCTTCAGACAGTAGCTTTTGA\nGCTCCTCTAGTGAATGTCGATGACAACTTATTTTGCAAGGTTTTCACTATTGTAGGGACC\nTTTTCATCTTCCAGATTCACAGCACCAGAGTAGATTATCTTTTGCCGCAACACCATTCTA\nAGCGGATGATGGGTGGCTAAGTTCAACCAATGATACCCCAAGTCAGAATCAGACAAAGGT\nTCAATGTCTAGAAGTTTAAACAAGTTCTGTAATGATGTTGTGTGTTCGCCTGATAAGTAG\nTTAGTAGTGAATTCCTCATGAAGCTCACCAGTCTTCAACTTATTGAACAGTATCCTAAGC\nATTGACCTCATCCTTTTGCATGCATCAGGAATTAGCCTCTCAATTTGCCTCATTATCCTA\nTAACTACGATTCCCGTCCACCCAATCTCTTACATCAGTCTCACAGTTCAAAAGAAATGGA\nTCAATAGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTCTGAATCTGATTACAG\nAGGTCAACTGGGACACCATTAGCCACAGACTGATCAATTATGGTATCAATTGTTTCTGCC\nAATTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCTGCAGCAACAAATTTGGTTAGC\nAGGGGTACCTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCA\nATTGCACTCTTTGGACTCACAAATTTATTTAGCTGATCACTCATGTAGTAATGGAATTCT\nAACAATGTTCTGAATTCCTCTGTATCTCTTGAGAGTAACTCTGTTAAGTTCTGATCAAAC\nAATGAAATCTGGTCGTCACTGGACGTGTAAGCATCAATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGCAGG\nATACCCTGCCCCATATCAAGGATTGAACTAATGTGTGAGGGGACCGTGCCAATTTGAAAA\nTTGGAATTAAAAAAGTCTTCAGTCATTGATTGAGTTGTCTTCTTCTTCAGTCCAAGTTGG\nGATTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGAATCTCAACCATTTTG\nTGCATATGCCATGTTAATAGTGTTGATAGGTAATCTTTGCCTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAAATTAGGTTTTGAATTATTGTTAGGAACAAGAAGGGACACATCATG\nGGGCCCCACTTACTGTGATCCATACTATATGATACATGTGCCGATGAGACATTCAGCTTC\nATTGACAAAATGGCATTGTCAAACTCCTTCTCATTGTTTAGGCAGCTGCCCGCTAATTGT\nGATGTGAGTGCTTCAAAGTAATCTTCAATAAGCCTTGTAAACATCTTTGTCCTTAAATCT\nCCGATGTACAACTCTCTATTACCCCCCACTTGTTCCTTATAAGACAAAGAAAATTTTAGT\nCTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCCTGACTGTAAAAACAT\nAGGTTTTTTAACATCGCTGTAGTACAGTTAGTTAGGGACAAGGCCTTGCTAAGCGCTTCA\nGAATTACTCTCACGTTCACTTATCCTGACATCATCAGCCAATCTTCCCGTATCAAATTTA\nAAATTCAGACACCTACTTTTATAATGAGAGTATCTCCCCATCAGCTTATTCCCATTCATT\nACTAATAAAATTGACTTAAAGCACTGAAAATATTCTTGGTCCAAGAAAGTCCTAGTCACC\nACTGCTTTTGTCAGCTCGCCGATAGGACATGAGTTCATTGGCCCTACATAAAAATATTTA\nCTTCTCAAAGCAGCATCATTGTAGATACCCTCACAAATTTTGATGTATTGATCCTCAGGC\nAGGATTTCTCGATCAAAATCTTCTACCATATGGTTTGAAAGTTCACTTTTTATTAACCTT\nATTAAGAGTTTTTCTTCCACCACCTTGTCAAGATCAGATATCGAGGGTGCATTGCAGTCT\nGCCTGCTGCTGTCTTCCCGGTTGTTCCTTATACTGATTGACAATATTGTCAACAGTGCAC\nCTCAGTTGGTCAAAGTATTCTGATGCTCCCCCATCCAATAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCATCACTCCCTCCTTTGGACCCCAGAACAAGATTGCTCATTGCTTGCTGT\nATTTTATAATCATAATCCTGTTTATTAAGTAAGAATTTGCCTTTACGTGCAAACACTTCA\nGTTAATTGTGTGACAGCCAAAGCTGTAAGCTTGTTGAAATCATAATCCAGAACACGAGAT\nCCATCTGTATACTTATTCACAACAACACTCTTATTACTGGCCAAATCCAAAGCTGTTGCA\nCAGCCACTTGTGATAAGAGGGTCTCGCAGTGTCTTCTTTACCTCTTTTTCTTTAAACAAT\nGAACCATTATTGAAACTAGACACAAGGAGTGAAATGAATTTTTTGGAAACACCAGGCTTT\nTTATACCTGACTTTGTCCACATCTGCACAACACTCTTTGCTTAGAAACTTTCTTGCATTG\nTAAACCATCTCAGCAAGCTCCTCTTCCGATGCATCATCCTTTGGGTTCACACTCACATGT\nCCAAATTCCAGTTTGGGCTCAAGGAATTTTTCAAAGCATTTGATCTGGTCAGTTAGTCTG\nTCAGGTGTTTCTTTTGTAATAAAGTGACACATATAAGAGATATTCAAAACAAATTTGAAT\nCTATTGGTCATCATACTGACAACTTCTTCAGACAGAATTATCTTCAATAAGTAGCGAACG\nAGTCTGTAGAGCAGATATTCAACTTCTGTGATCAAATCTTCCCTGATTTTCTCAATTAAA\nTCCTTGTGGTAAAAATCGGATACAAAGGCCATCACAAAATACCTAATGTTTTGTAAAAAT\nTTCTGACACCTTTTACTAGGATGTGTCAGTATTAAAACTAAAATCATCTTGGTTAACAAT\nTTAATAGTGATCAATTGTTCAGACAACTCTGTGCACTCTTCTATCCAGCTGACCATAACA\nTCAACTACTTTCTGCAACACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTAGGATCA\nGCATAAAAAGAACAAATCTCTCCAACTACATTGTTATTAATGGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATACAATAGTTTGAATCCCATCCCATTGATGAAAAACTCTTGACAA\nTAGGCTTCTTTGCACCTCACAACTTGGTATCTAGATGGCCCAAATTCATTTTGCCTCAGT\nTTCACAGTGGAAGACGTTTTCATTGAGTTTATCAAAGCTAAGCTCAATGATGATAGTCTT\nTCTAAGTCTGTTGCATCTAGAATGTCAATGACACCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGGTAACTTATTGTGGGTGTGATACCGGAGATTTCAATGTCCATGATGACA\nTCATAAACATCACAATCAAGGATCTTGAGATCAATTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCCTCAAAGCATTAGTGGCTCGAGTTAAAACTCTATTGATGATGGCAAGGAGCTCA\nGAATTCCGTTCTTCTTTAAGTGATAGGACACCTGCATTTCTGTCTCTAGTTCTTTTCCTG\nCTGTCTATCCACCGTTTTAAATCTCTTTTTGTTGATTCCAATGAGACCAATCTATCGTTG\nACACTCACAAAACAGGAGCCCAGCCAACCAGCAAGGAGCCTGTCACCATGCCTTATGTGG\nTCCAGCCGACTAGCAAGAAGAATCAGAACGTCAAAAATAAGGAGAAGTTTCCTCCTGGTG\nTTGAGGATCCTCATAGACTTTATCTTATTTAGAAAAGATCTCCAACATTGCATCTGTTCA\nCTTTGAGAGTCAGCAGTCCTTTCTTCACCAAAATTCAAATCTGCATACAAGAACTTAAGG\nACTGGAGAGGCTCTTCGGAACTGGAATGTTAATTGTTCAATGTTGTCATCACAGGTGTCT\nATCTTATCACTATATAGCTTTCTGAAATCCTCTAATAACTTCACCTTATCGGTCTTAACA\nAATTGACTTTCTATGTCCCCTTGCCTTAGTTTGTTCCTGAAAATTTGATACTCCTCCTCG\nATTAAACCCTTGACTTCATGAGAGGTAAGCTTGTTATTAATGCCTTGATGACAACTAGAA\nATTATTTCTTCAAAGTGTTTTGCACGCTTGTCAGTTAGAGCATTGATGCTTTCAATTCCT\nGAGAGCCTCCCAGACGTTAAGGCTAAAGACTCACAAAGTCTTGAATACTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAATATTTTAACAGGGTGAATAAGGTGTCCCTGAGCTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTGGTCCTGCCGTCAATGAGAGGG\nATGAGGTTGATGCCAACAGACCCCAAATCATTCTTTAATTGTTCTAATTTTTTGTGATCT\nTCTAAATACTTCTGTTCAAAGTTGGCGGGGGATGACCTAACAAAGCATTCAAGTAAGATT\nAGAATATTACCAGTGAGTTTGTAACCGTCAGGCACCACAAAACACAAAGCTGGGGTGAGA\nATCCCATGATCACTCAGAATAGATTCAACCGTTTTGTTTTCAGTGTTATGTTCACATCCA\nTTAGCCTTGCAAGAATCAATCTCAATGCAAAGAGATAATAGCTTTAATCCCTCTATAAGC\nAACATTCTGGGTTCAGTTTGGACCAGAAAAGCTAACTTCTGTCTTGATAGCTTCTCATTG\nTCCGCAAGGTACTTTGAGATAAGATCTTTAGCATTGGCAATGTCTTCCTCCATTGCCAAT\nTGTGGCGCCTGTGTTGGGTTTGGGTTTGTACCAGTATGGCTTGTAAGTCAGCTGGTGATG\nCCCCGCAAAGGTTCCCACAAAAATGAGAGACAATATGC--------\n>LASV_NGA_2018_1177-1\n----------ATTTAGCTGGACTTCAGTGGCAAGGCTCATTTTAGTGAATCCTTGAATC-\nAAGTGCCTAGTC-GAAATGGGCAACAGACAGACCAAATCAACAAAAGTCGATGAGCATCA\nAAGAGCTCATCTAGTGCCAGATGCATCCCATCTAGGCCCCCAGTTTTGCAAAAGTTGCTG\nGTTTGAGAACAAGGGGTTGGTAGAGTGCAACAACCACTACCTGTGCCTCAACTGTCTCAG\nCCTGCTCCTCAGCGTCAGTAGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAAGCT\nGAAGGCAGCAGCACAGCCCAGCGCACCCTCAACTGAGGCAGCCCAGAACACAGCACCTCC\nACCGTATGCCCCATGATCTCAAGACCAACACCTCCATCTCCATCACCCACCCCCCACCCC\nCGGGGGNNNNNNNNNCCGGGGGCCCCCCCGGGGGGGCAGGCAGCCCAGCTCTACTCTATG\nTCCTCAACACACCTCTCCGGCTCAAACAACTCTGAACATGTCCTTCCCTTTAGTCTTAGG\nCTGCCTCCACTTGACTGAATCATAACTCTTTGCCTTGATTTACTGTAGCAAAGGGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATCAGCATGA\nTCCACAGGTCTCTGTTTTGTGAGGATTGAGACAATGTCCACACCCGTCCATTGAACTCTT\nTGTCTTAATCTATCACACATCATTGATTTCAATGCACCAACCAAAAGATGTGGGGAACTA\nTCACCAATCTCTCTTACAAACATTTCCAAATCTTGATCTTGAATAGATGGTGTAAATGTA\nGCTACCCTTCTATCAGATTCCCACAATGCTCCCCTACATACAACCAATGGCACTGGTTCA\nTTGTCAGGTCCGACCTTGGAGAAATCAAACTCACTAAACTGCAGTTTATCTGGATTGATA\nATTAGCTTCATGGGTATAACATCCCCTAACTGCTGTGTATCCTTTAAAAACTCATTCACC\nACATCTGACTCAACAAACCAGGCTGACCTACCTTTGAAAGTTGGACCCGACAGAGCAAGT\nCTCCAACAGTCAGATAGAACACATGGGCTCACAGACCCAGAATACAGTGCTTGTACATGA\nTTCACCACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGGATGGAAAAG\nGTCTCTTTAAAACTAGCATCCTGACTCTTGATTTTATACCTAATTGTCTGGTAAAACTGA\nACAGAGTCCACTGGCATTGTACTTAACAAATCAAAGAAATCTTCAAGGGAGTCTAGCCTC\nAATTCTTCTGTCAGGCCTGAAGCAATAAGCTGATTCAAATTTATCTGGGCTGGCTCTATG\nTCGAAGTCTATCCATGCATAGCCCATCATTAGATCAAACTTGAACATAGGTCTCTCTATC\nCCTTTGTAAATAGCTTTCTCGATGAATGAAGAGAAGGGACCCAGTCGTTGCAGACCTTCA\nCCCTCTGGTATTGAGGTTTTATGAGGGAACCAAGTGAATGACCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTTTCTTCCATCATCGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTCAGTTCAGAAGCCAATACAACATAGTGTTCCTCCCTCTTCCACTTAACAATGTGTGAA\nACAAGTGAAAGTGCCTCGCAATTCACATCTAGAGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTAGAAGCTAAATCACTCATAAACGGCAATATGTGCTTT\nTCAAATAGAGATGGATATAAACGTCTCAAAGAATGAATGATGTGGCTCATGCCAACCCTG\nTCCTCTAGCAGTTTCGAAACAGTGGGTCTCAAGGGGAAGTAATCACAAGGATTATGTTTA\nAAAAAGTCCAGGACCTGAGCTTGTTTTGGTTCCCCGAGCACCCACGCTCCAAGTTCTATA\nGCTGTAGATAATGTTATGCACATATAATCCCATAGAAGAGGTCTTAAATAAGTGACAACA\nGTATCACCTCCATCTTTGACTTCAGGTGAAACTTTCCATATTTGTATCCCATTGTCCCCC\nATCACTGCTTCAACACCTTGAGTCCCCAGTAGCTGAGTCTGTATGGATCTAATGTAAAGA\nTTCTCCTTGTTAGGGCCTCTGACGCACTTGCTGCCCAGTGTTCTGCACAATCCCACAAAC\nCCAGATGCTATAGAACTTTGGAAAGCTGATTTATTTATTGCTTCAGACAGTAACTTCTGA\nGCTCCTCTAGTGAATGTTGATGACAACCTATTTTGCAAGGTTTTTATTATTGTGGGGACC\nTTCTCATCTTCCAGATTCACAGCACCAGAGTAGATTATCTTTTGCCGCAACACCATTCTG\nAGCGGGTGATGGGTAGCTAAGTTCAACCAATGAAACCCCAAGTCAGAATCAGACAAAGGT\nTCAATGTTTAGAAGCTTAAATAAGTTCTGTAATGATGCTGTGTGTTCACCTGATAGGTAG\nTTGGTGGTGAATTCCTCATGAAGCTCACCAGTTTTTAATTTATTGAATAATATCCTAAGC\nATTGACCTCATCTTTTTGCATGCATCAGGAATAAGCCTCTCAATTTGCCTCATTATTCTA\nTAACTACGATTCCCGTCCACCCAATCTCTTACATCAGTCTCGCAGTTTAAGAGGAATGGA\nTCAATGGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTCTGAATTTGATTGCAC\nAGGTCAACTGGGACACCGTTAGCCACAGATTGATCAATTATGGTATCAATTGTTTCTGCC\nAATTGATGGGGTTCTTTGCACTTTATGTTATGCAGAGCTGCAGCAACAAATTTTGTTAGC\nAGAGGCACCTCATCACCCCAAACATAGAATCTTGATTTGAACTCTGCAACAAACCTGCCA\nATTGCGCTCTTTGGACTCACAAACTTATTTAGCTGGTCACTCATGTAGTAATGGAATTCT\nAACAATGTTTTGAATTCCTCTGTATCTCTTGAGAGTAACTCTGTTAAGTTCTGATCAAAT\nAATGATATCTGATCATCACTGGACGTATAAGCATCGATTTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTCTCAGAGATCAACGCATAAAAGTCTGAGGTGTTGTGCAGT\nATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGGACTGTGCCAATTTGGAAG\nTTAGAATTAAAGAAGTCTTCAGTCATTGATTGAGTTGTCTTCTTCTTCAGTCCAAGTTGG\nGATTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCATGTTAATAATGTTGATAGGTAATCTTTACCTTTTAAATCAGCCTGTAAA\nTCATCAGAAAGTAGGATTAGGTTTTGAATTATTGTTAGAAACAAGAAAGGACACATCATA\nGGGCCCCACTTACTGTGATCCATGCTGTATGACACATGTGCCGATGAGACATTCAACTTC\nATGGACAGAATGGCATTGTCAAATTCCTTCTCATTATTAAGACAGCTGCCCGCTAATTGT\nGATGTGAGTGCTTCAAAGTAATCCTCGATGAGCCTTGTGAACATTTTTGTCCTTAAATCT\nCCGATGTACAGTTCTCTATTGCCTCCCACTTGTTCCTTGTAAGACAAAGAAAATTTTAGT\nCTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCCTGACTGTAAAAACAC\nAGATTTTTTAACATTGCTGTAGTACAGTTAGTCAAGGATAAAGCCTTGCTAAGTGCTTCA\nGAATTACTCTCACGTTCACTTATTCTGACATCATCAGCTAATCTTCCTGTATCAAATTTG\nAAGTTCAGACACTTACTCTTATAATGAGAGTATCTCCCCATCAGCTTATTTCCATTCATC\nACTAATAAAATTGACTTGAAGCACTGGAAATATTCTTGGTCCAAAAAAGTCCTAGTCACC\nACTGCTTTTGTCAGCTCACTAATAGGACATGAGTTCATTGGCCCCACATAAAAGTATTTA\nTCTCTCAAGGCAGCATCATTGTAGATATTCTCACAAATTTTGATGTACTGATCCTCAGAC\nAGGATCTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATCAACCTT\nATCAGGAGCTTTTCTTCCACCACCTTGTCAAGATCAGATATTGAAGGTGCATTGCAGTCT\nGCTTGCTGCTGTCTTTCCGGTTGCTCCCTATACTGACTGACAATATTGTCAACAGTGCAC\nCTTAGTTGATCGAAGTATTCTGATGCTCCTCCATCCAATAGTATCTCATCTAGATCAGCG\nTTGTTGGTGTCACCACTCCTTCCCTTGGACCCCAGAACAAGATTGCTCATTGCTTGCTGT\nATCTTGTAATCATAATCCTGTTTATTAAGCAAAAATTTTCCTTTACGTGCAAACACCTCA\nGTCAACTGTGTGACAGCCAAGGCTGTAAGTTTGTTGAAGTCATAATCCAGGACACGAGAC\nCCATCTGTATACTTGTTCACAACAACACTCTTATTACTGGCCAGGTCCAGGGCTGTTGCA\nCAACCGCTTGTGATAAGAGGGTCCCGCAGTGTCTTCTTTACTTCCTTTTCTTTAAACAAT\nGAACCATTATTGAAGCTAGACACAAGGAGTGAGATAAACTTTTTAGAAACACCAGGCTTT\nTTATACCTAACCTTCTCCGCATCTGCACAACATTCCTTACTTAGAAACTTTCTTGCATTA\nTAAACCATTTCAGCAAGCTCTTCCTCTGATGCATCATCTTTTGGGTTCACACTCACATGT\nCCAAATTCCAATTTGGGCTCAAGGAACTTTTCGAAGCATTTGATCTGATCAGTTAGTCTG\nTCAGGCGTTTCTTTTGTAATGAAATGACACATATAAGAGATATTCAAAACAAACTTGAAT\nCTATTGGTCATCATGCTGACAACTTCTTCAGACAGAATTATCTTTAATAAGTGACGGATG\nAGCCTATAGAGCAGATATTCAACTTCTGTGATCAAATCCTCCTTAATTTTCTCAATCAAA\nTCCTTGTGATAAAAGTCGGATACAAAGGCCATCACAAAATACCTAATGTTTTGTAAAAGT\nTTTTGACACCTTTTACTAGGATGTGTTAGTATCAAAACTAAAATCATTTTGGTTAACAAT\nTTGATAGTGATCAAATGTTCAGATAACTCTGTGCACTCTTCTATCCAGCTGACCATAACA\nTTGACTACTTTTTGCAGCACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTAGGGTCA\nGCATAAAAGGAACAAACCTCTCCAACTACATTGTTGTTGATAGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATATAATAGTTTGAATCCCATCCTGTTGATGAAGAACTCCTGGCAG\nTAGGCCTCTTTGCACCTTACAACCTGGTATCTAGAGGGTCCAAATTCATTTTGCCTTAGT\nTTTACTGTGGAAGATGTTTTCATTGAGTTGATCAAAGCCAAGCTCAATGATGATAGTCTT\nTCTAAGTCTGTTGCATCAAGAATGTCAATGACGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGGTAACTTATAGTGGGTGTGATGCCGGAGATCTCAATGCCCATGATGGCA\nTCATAAACATCACAATCAAGGATTTTGAAATCAATTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCTTTAAAGCATTAGTGGCTCGAGTTAAAACTCTGTCGATGATGGTAAGGAGCTCA\nCAATTCCGTTCTCCTTTAGGTGATAGGACACTTGCATCTCTATCTTTAGTTTTCTTCCTG\nCTGTCTATCCACCGTTTTAAATCCCTTTTTGTTGATTCCAATGAAACTAATCTATCGTTA\nACACTCACAAAACAAGAGCCCAGCCAACCAGCAAGGAACCTATCACCATGCCTTATGCAG\nTCCAGCCGGCTAGCAAGAAGAATCAGAATGTCAAAAACAAGGAGAAGTTTCCTCCTGGTA\nTTGAGGATCCTCAGAGACTTTATCTTATTCAGAAAAGACCTCCAACATTGCATCTGATCA\nCTTTGAGAATCAGTAGCCCTTTCCTTACCAGAATCCAAGTCTGCATACAAGAACTTGAGG\nACTGGAGAGGCTCTTCGGAATTGGAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCT\nATTTTGTCACTATATAACTTTCTGAAATCCTCTAATAACTTCATCTTATCAGTTTTAACA\nAATTGACTTTCTATGTCCCCCTGCCTCAGTTTATTCCTGAAGATCTGGTACTCCTCCTCA\nATTAAACTCTTGACTTCGTGAGAAGTGAGTCTGTTATTAATACCCTGATGACAACTAGAA\nATTATTTCTTCGAAATGTTTTGCACGCTTGTCAGTTAGAACATTGATACTTTCAATTCCT\nGAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAAAGTCTTGAATACTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAATATTTTAACAGGGTGAATAAAGTGTCCCTGAGCTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTTGTCCTGCCGTCTATGAGAGGG\nATAAGATTGATGCCAACAGACTCCAAATCATTCTTTAACTGTTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCGGGGGATGATCTGACAAAGCACTCAAGTAGGATT\nAGAACGTTACCAGTGAGTTTGTAGCCGTCAGGTACTACAAAGCATAAAGCTGGAGTGAGA\nATTCCATGATCACTCAGAATGGATTCAACCGTTTTGTCCTCAGTGTTGTGTTCACACCCG\nTTAGCCTTGCAGGAGTCAATCTCAATGCAGAGAGACAGTAGTTTCAATCCCTCCATGAGC\nAACATTCTAGGTTCAGTTTGGACCAGAAAAGCTAACTTCTGTCTTGATAGCTTCTCATTG\nTCTGCAAGGTACTTTGAGATGAGGTCTTTAGCATTGGCAATGTCTTCCTCCAT-------\n------------------------------------------------------------\n----------------------------------------------\n>LASV_NGA_2018_1375-1\n------------------------------------------------------GAATTA\nTAGTGCCCAGCCAAAAATGGGCAACAGACATGCCAAATCGACAAAAATCAATGAACATCA\nAAGAGCTCATCTAGTGCCAGATGCATCCCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGGTTGGTAGAGTGCAACAATCACTATCTGTGTCTCAACTGTCTCAG\nCCTGCTCCTCAGTGTCAGCAGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAAGCT\nAAAGGCAGCAGCACAGCCAAGTGCACCATCGACCGAGGCAATCCAGAACACAACACCTCC\nACCATACACCCCATAATCCCAGGACCAACACTCTCACCTCCATCACCCANNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTACTCAATG\nTCCTCAATGCACTTCTCCGGCCCAAACAACTCTGAACATGTCCTTCCCTTCAGTCTTAGG\nCTGCCCCCACTTGACTGAATCATGACCCTTTGCTTTGATTTGCTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATCAGCATAA\nTCCACAGGTCTCTGTTTTGTGAGGATTGAGACAATGTCCACACCTGTCCATTGAATTCTT\nTGTTTTAATCTATCAGACATCATTGATTTCAATGCACCAAGTAAAAGGTGCGGGGGACTA\nTCACCAATCTCCCTTACAAACATATCTAAATCTTGATCTTGGATAGATGGTGTGAATGTA\nGCTACCTTTCTATCAGATTCCCACAGTGCCCCTCTACATACAACCAATGGCACTGGTTCG\nTTGTCAGGTCCAACCTTGGAGAAGTCAAACTCACTGAACTGCAGTTTATCTGGATTAATA\nATCAGCTTCATGGGTATAACATCCCCTAGCTGCTGTGTGTCCTTCAAGAATTCATTTACC\nACATCTGATTCAATAAACCAGGCTGACCTACCTTTGAAAGTTGGACCCGACAAAACAAGT\nCTCCAACAGTCAGGCAGAACACATGGGCTCACAGATCCAGAGTATAGTGCCTGCACATCA\nTTCACTGCAAACTCACCATACTGATTAACAATTCCTGTCATGTTGAGATGGATAGAAAAA\nGTCTCTTTAAAACTAGCATCCTGACTCTTGATTTTATATCTTATTGTCTGGTAAAACTGA\nACAGAGTCCACTGGCATTGTACTCAACAAATCAAAGAAATCCTCAAGAGAGTCTAACCTC\nAATTCCTCTGTCAAGCCTGAAGCAATAAGCTGGTTCAAGTTTATCTGAGCTGGCTCTATG\nTCAAAGTCTATCCATGCATAGCCCATCATTAGATCAAATTTAAACATAGGTCTCTCTATC\nCCTTTGTAAATGGCTTTCTCAATGAATGATGAGAAGGGACCTAGTCGCTGCAGACCTTCA\nCCCTCTGGTATTGAGGTTTTATGAGGGAACCAAGTAAATGACCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTTTCTTCTATCATGGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTCAGTTCAGAAGCCAATACAACATAATGTTCCTCCCTCTTCCACTTAACAATGTGTGAA\nACAAGTGAAAGTGCCTCGCAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTAGAAGCTAAGTCACTCATAAATGGCAATATATGCTTC\nTCAAATAGAGACGGATATAAACGTCTCAAAGAATGAATGATGTGGCTCATACCAATCCTA\nTCCTCTAGCAGTTTTGAGACAGTGGGTCTCAAGGGGAAGTAATCACAAGGATTGTGTTTA\nAAGAAGTCCAAAACCTGAGCTTGTTTTGGTTCCCCGAGCACCCATGCTCCAAGTTCTATG\nGCTGTGGATAGTGTTATGCACATATAATCCCAGAGAAGAGGTCTTAAATAAGTGACAACA\nGTTTCACCTCCATCTTTGACTTCTGGTGAAACTTTCCATATCTGGATTCCATTGTCCCCC\nATCACTGCTTCAACACCTTGAATCTCTAATAACTGAGTCTGTATGGATCTAATATAAAGA\nTTCTCCTTGTTGGGGCCTCTGACGCACTTGCTACCTAGTGTTCTACACAACCCTACAAAC\nCCTGATGCTATAGAGCTTTGGAAAGCTGATTTATTTATCGCTTCAGACAGTAGCTTTTGA\nGCTCCTCTAGTGAATGTCGATGACAACCTATTTTGCAAGGTTTTTACTATTGTAGGGACC\nTTTTCATCTTCCAGGTTCACAGCACCAGAATAGATTATCTTTTGCCGCAACACCATTCTA\nAGCGGGTGATGGGTGGCTAAATTCAACCAATGAAACCCCAAGTCAGAATCAGATAGAGGC\nTCAATGCCTAGAAGTTTGAACAAATTCTGTAATGATGTTGTGTGTTCACCTGATAGGTAG\nTTGGTAGTGAATTCTTCATGAAGCTCACCAGTTTTTAATTTATTGAACAATATCCTAAGC\nATCGACCTCATCTTTTTGCATGCATCAGGAATCAGCCTCTCAATTTGCCTCATTATCCTA\nTAACTACGATTCCCGTCTACCCAATCTCTTACATCAGTTTCGCAATTCAAAAGGAATGGA\nTCAATGGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTCTGAATTTGATTACAC\nAGATCAACTGGGACACCATTAGCCACAGATTGATCAATTATGGTATCAATTGTTTCTGCC\nAACTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCTGCAGCGACAAATTTTGTTAGC\nAGAGGTACCTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCA\nATTGCACTCTTTGGACTCACAAATTTATTTAACTGATCACTCATGTAGTAATGGAATTCT\nAATAATGTTTTGAATTCCTCTGTATCTCTTGAGAGCAACTCTGTTAAGTTCTGATCAAAT\nAAAGATATCTGATCGTCACTGGACGTGTAAGCATCGATTTGTCCTCCAGACACACACTTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGCAGG\nATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAAGGGACTGTGCCAGTTTGAAAG\nTTGGAATTAAAAAAGTCTTCAGTCATTGATTGAGTTGTCTTCTTCTTCAATCCAAGTTGG\nGATTTGATGTATGACTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCATGTTAATAATGTTGATAGGTAATCTTTACCTTTCAAATCAGCTTGCAAA\nTCATCAGAAAGTAAGATTAGGTTTTGAATTATTGTTAGAAATAAGAAAGGACACATCATA\nGGGCCCCACTTACTGTGATCCATACTATATGACACATGTGCCGATGAAACATTCAGCTTC\nATTGACAAAATGGCATTGTCAAACTCCTTCTCATTGTTTAGACAGCTGCCTGCTAATTGT\nGATGTGAGCGCTTCAAAGTAATCCTCAATGAGCCTTGTAAACATCTTTGTCCTTAAGTCC\nCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCCTTGTACGACAAAGAGAATTTTAGT\nCTACCAGTGTCAGGGCCAGTCGAATTATAAGATTGAGGTGATTCTTGACTGTAAAAACAC\nAGATTTTTTAACATTGCTGTAGTGCAGTTGGTTAGGGACAAGGCCTTGCTGAGTGCTTCA\nGAATTGCTCTCACGTTCACTTATTCTGACATCATCAGCCAATCTCCCTGTGTCAAATTTA\nAAGTTCAGACACTTACTCTTATAATGAGAGTATCTTCCCATCAGCTTATTCCCATTCATC\nACTAATAAAATTGACTTAAAACACTGGAAATATTCTTGGTCCAAAAAAGTCCTAGTCACC\nACTGCTTTTGTCAGCTCACTAATAGGACATGAATTCATTGGCCCCACATAAAAATACTTA\nCTTCTCAAAGTAGTATCATTGTAGATACTCTCACAAATTTTGATGTATTGATCTTCAGAC\nAGGATTTCTCGATCAAAATCCTCTATCATATGATTTGAAAGTTCACTTTTTATCAACCTT\nATTAAGAGTTTTTCTTCCACCACCTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCT\nGCCTGCTGCTGTCTTTCTGGTTGCTCCCTATACTGACTGACAATACTGTCAACAGTGCAC\nCTCAGTTGGTCAAAGTATTCCGATGCTCCTCCATCCAATAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCATCACTCCCTCCTTTGGATCCCAGAACAAGATTACTCATTGCTTGCTGT\nATCTTGTAATCATAATCCTGCTTATTAAGCAAGAACTTGCCTTTACGTGCAAATACTTCA\nGTTAACTGTGTGACAGCCAGAGCTGTAAGCTTGTTAAAGTCATAATCCAGAACACGGGAC\nCCATCTGTATACTTATTTACAACAACACTCTTATTACTGGCCAAGTCCAAAGCTGTTGCA\nCAGCCGCTTGTAATAAGAGGGTCTCGCAGTGTCTTCTTCACTTCCTTTTCTTTAAACAAT\nGAACCATTATTAAAACTAGACACAAGAAGTGAAATAAATTTCTTGGAAACACCAGGCTTT\nTTATACCTAACTTTTTCCGCATCTGCACAACATTCTTTACTTAGAAACTTCCTTGCATTA\nTAAACCATTTCAGTAAGCTCTTCCTCCAATGCATCATCCTTCGGGTTCACACTTACATGT\nCCAAACTCCAGTTTAGGCTCAAGGAATTTCTCAAAGCATTTGATCTGGTCAGTCAGCCTG\nTCAGGTGTTTCTTTTGTAATGAAATGACACATATAAGAGATATTTAAAACAAACTTGAAC\nCTGTTAGTCATCATACTGACAACTTCTTCAGACAGTATTATCTTTAGTAAGTGACGAACA\nAGTCTGTAGAGAAGATATTCAACTTCTGTGATCAAATCCTCTCTGATTTTCTCAATCAAA\nTCCTTGTGATAAAAATCGGACACAAAGGCCATCACAAAGTACCTAATGTTTTGTAAAAAT\nTTTTGACACCTTTTACTAGGATGTGTTAGTATCAAAACTAAAATCATTTTGGTTAACAAT\nTTTATAGTGATCAATTGTTCAGATAACTCTGTGCACTCTTCTATCCAGCTGACCATAACA\nTCGACTACTCTCTGCAACACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTGGGATCA\nGCATAAAAGGAACAAACCTCTCCAACCACATTGTTGTTGATAGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGATACAATAGTTTGAATCCTATCCTATTGATGAAGAACTCTTGGCAG\nTAAGCCTCTTTACACCTCACAACCTGATATCTAGAGGGTCCAAATTCATTTTGCCTTAGT\nTTCACTGTAGAAGACGTTTTCATTGAGTTGATCAAAGCCAGGCTCAGTGATGATAGTCTT\nTCCAAATCTGTCGTATCTAGAATGTCAATGACGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTCTTCTGGTAACTTATAGTTGGTGTGATACCGGAGATCTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGGATTTTGAGATCAATTCCATAAGAGTTGGTTTCTATGCCA\nACCTCCTTCAAAGCGTTAGTGGCTCGAGTTAAAACTCTGTTGATGATGGCAAGGAGCTCA\nCAATTTCGTTCTTCTTTAAGTGATAGGAAACCTGCATTCCTGTCTTTAGTTCTCTTCCTG\nCTGTCTATCCACCGTTTCAGATCTCTTTTTGTTGAATCCAATGAAACTAATCTATCGTTA\nACACTCACAAAACAGGAGCCCAGCCAGCCAGCAAGGAGCTTGTCACCATGCCTTATGCAG\nTCCAGCCGGCTAGCAAGAAGAATCAGAACGTCAAAAATAAGGAGAAGTTTCCTCCTAGTG\nTTGAGGATCCTTAGAGATTTTATCTTATTCAGAAAAGATCTCCAACACTGCATCTGTTCA\nCTTTGGGAGTCAGCAACCCTTTCCTCACCAGAATCCAGATCTGCATACAAGAACTTTAGG\nACTGGAGAGGCTCTTCGGAACTGGAATGTTAACTGTTCAATATTGTCATCACAGGTGTCT\nATTTTATCACTATATAGCTTTCTGAAATCCTCTAATAACTTCATCTTATCAGTCTTAACA\nAATTGACTTTCTATGTCCCCTTGTCTTAGTTTGTTCCTGAAGATTTGATACTCCTCTTCA\nATTAAACTTTTGACTTCATGGGAGGTGAGCTTGTTATTAATACCCTGATGACAACTAGAA\nATTATTTCCTCAAAGTGTATTGCACGCTTGTCAGTTAGAACATTGATGCTTTCTATTCCT\nGAGAGCCTCCCAGACGTTAAGGCTAAAGACTCACAAAGTCTTGAATACTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAATACTTTAACAAGGTAAATAAGGTGTCCCTGAGTTTG\nTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTTGTCCTACCATCTATGAGAGGG\nATAAGATTGATGCCAACAGATTCCAAATCATTCTTCAATTGTTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCGGGGGATGATCTGACAAAGCACTCAAGTAAGATA\nAGTACATTACCAGTGAGTTTGTAGCCATCAGGCACCACAAAGCATAAAGCTGGAGTGAGA\nATCCCATGATCACTCAGAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACATCCA\nTTGGCCTTGCAAGAATCAATCTCAATGCAAAGGGATAGTAGTTTCAATCCCTCCATGAGC\nAACATTCTGGGTTCGGTTTGGACCAAAAAAGCTAACTTTTGTCTTGATAGCTTCTCATTA\nTCTGCAAGGTACTTTGAGATAAGATCTTTAGCATTAGCAATGTCTTCCTCCATCACCAAT\nTGTGGTGCCTGTATTGGGTTTGGGTTTGTGCTAGAATGGCTTGTGGGTCAGCTG------\n----------------------------------------------\n>LASV_NGA_2018_1381-1\n------------------------------------------------------------\n-------------------GGCAACAAACAGGCCAAATCGACAAAAGTCGATGAACATCA\nAAGGGCTCATCTAGTGCCAGATGCATCCCACCTGGGCCCTCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGGTTGGTAGAGTGCAACAACCATTACCTGTGTCTCAATTGTCTCAG\nCCTGCTCCTCAGCGTCAGCAGCAGATGCCCGATATGCAAGATGCCCCTTCCCACCAAGCT\nAAAAGCAGCAGCACAGCCGAGCGCACCACCAGCCAAGGTGACCCAGGACACAACACCTCC\nACCGTACACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCGGGGGGCGGGCAGTCCAGCTCTACTCAATA\nTCCTCAACGCACTTCTCCGGTCCGAACAACTCTGAACATGTCCTTCCCTTCAGTCTTAGG\nCTGCCCCCACTTGACTGAATCATGACTCCTTGCTTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATCGGCATAA\nTCCATAGGTCTCTGTTTTGTGAGGATTGAGACAATGTCTACACCCGCCCATTGAATTCTT\nTGTTTCAGTCTATCAGACATCATCGATTTCAGCGCACCAACTAGAAGGTGCGGGGAACTA\nTCACCAATCTCCCTTACAAACATTTCTAAATCTTGATCCTGGATAGATGGTGTGAATGTA\nGCCACCCTTCTATCAGATTCCCACAGTGCCCCCCTACATACAACCAATGGCACTGGTTCG\nTTGTCAGGTCCGACCTTAGAGAAATCAAACTCACTGAACTGTAGTTTATCTGGATCAACA\nATCAGCTTCATGGGTATAACATCCCCCAATTGCTGTGTATCCNNNNNNNNNNNNNNNNNN\nNCATCTGATTCGACAAACCAGGCTGACCTACCTTTGAAAGTTGGACCCGATAGAGCAAGT\nCTCCAACAGTCAGACAGAACACACGGGCTCACAGACCCAGAATATAGTGCCTGTACATCA\nTTTACCACAAACTCACCACATTGATTAACAAGCCCTGTCATGTTGAGATGGATAGAAAAA\nGTCTCTTTAAAGCTAGCATCCTGACTCTTAATTTTATACCTAATTGTCTGATAAAACTGA\nACAGAGTCCACTGGCATTGTGCTCAGTAAATCAAAGAAATCTTCAAGGGAGTCTAACCTC\nAATTCCTCTGTCAGGCCTGAAGCAATAAGCTGGTTCAAGTTTATCTGAGCTGGTTCTATG\nTCAAAGTCTATCCATGCATAGCCCATCATTAGATNNNNNNNNNNNNNNNNNNNNNNNNNN\nNCTTTGTAGATAGCTTTTTCAACGAATGAAGAGAAGGGACCCAGTCGTTGCAGACCCTCA\nCCCTCTGGTATTGAGGTTTTATGAGGGAACCAAGNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNCACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTCTCCTCTATCATGGGCTCATGGGTGCGAGAGTGTGAGNNN\nNNNNGTTCAGAAGCTAACACAACATAATGTTCCTCCCTCTTCCACTTAACAATGTGTGAG\nACAAGTGAGAGTGCCTCGCAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTGGAAGCTAAATCACTCATAAATGGCAGTATATGTTTC\nTCAAATAGAGACGGATACAAACGTCTCAAAGAATGAATAATGTGGCTCATGCCAACCCTG\nTCTTCTAGCAGTTTCGAAACAGTAGGTCTCAAGGGGAAGTAATCACAAGGATTATGTTTA\nAAAAAGTCCAAGATCTGAGCTTGTTTTGGTTCCCCGAGCACCCATGCTCCAAGTTCTATA\nGCTGTAGATAGTGTTATGCACATATAATCCCATAGAAGGGGTCTTAAATAAGCGACAACA\nGTATCACCTCCACCTTTGGCTTCTGGTGAAACCTTCCATATCTGGATTCCATTGTCCCCC\nATCACCACCTCAACACCTTGAGTCCCTAGTAACTGAGTCTGTATGGATCTAATGTAAAGA\nTTCTCCTTGTTAGGCCCTCTGACGCACTTGCTACCTAGTGTTCTGCACAATCCTACAAAC\nCCAGATGCTATGGAGCTCTGGAAAGCTGACTTGTTTATTGCTTCGGACAGTAGCTTTTGA\nGCTCCTCTAGTGAATGTTGATGACAACCTATTTTGCAAGGTTTTCACTATTGTAGGGNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGCCTCATTATCCTA\nTAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNAATTTATTTAGCNGGTCACTCATGTAATAATGGAATTCT\nAACAATGTTTTGAATTCCTCTGTATCTCTTGAGAGTAACTCTGTTAAGTTCTGATCAAAT\nAACGATATCTGATCGTCACTGGACGTGTAAGCATCGATTTGTCCTCCAGACACACACCTC\nACCGCAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNTAGGATTGAGCTAATGTGTGAGGGGACTGTGCCAGTTTGAAAG\nTTGGAATTGAAAAAGTCTTCAGTCATTGACTGAGTTGTCTTCTTCTTCAGTCCAAGTTGG\nGATTTGATATATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCNNNNNN\nNNNNNNNNNNNTGTCAATAATGTTGATAAGTAATCTTTNCCTTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAGATTAGGTTTTGAATTATTGTTAAAAACAAGAAAGGACNCATNNNN\nNNNNNNCACTTACTGTGATCCATACTATATGATACGTGTGCCGATGAAACATTCAGCTTC\nATTGACAAAATGGCATTGTCAAACTCCTTCTCGTTGTTCAGACAGCTGCCTGCTAATTGT\nGATGTGANNNNNNNNNNNNNATCCTCAATGAGCCTTGTGAACATCTTTGTCCTTAAATCT\nCCAATGTACAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAAAATACTTA\nCTTCTCAAAGCAGCATCATTGTAGATATTCTCACAAATTTTGATGTACTGATCCTCNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCTAGATCAGCA\nTTGTTGGTGTCACCACTCCCTCCTTTGGACCCCAGAACAAGATTACTCATTGCTTGCTGT\nATCTTGTAATCATAATCCTGTTTATTAAGCAAGAATTTGCCTTTACGTGCAAATACTTCA\nGTTAACTGTGTGACAGCCAAAGCTGTGAGCTTGTTGAAGTCATAATCCAGAATGCGAGAC\nCCATCTGTATATTTATTCACAACAACACTCTTATTACTGGCCNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGT\nTTGATAGTGATCAATTGTTCAGATAACTCTGTGCACTCTTCTATCCAGCTGACCATAACA\nTCGACTACTTTCTGTAATACATCACTGGAGAAAATTGAAGGAAAAAATCGTTTAGGGTCA\nGCATAAAAGGAACAAACCTCTCCAACCACATTGTTGTTAATAGCATAACACTTTGAGCAC\nTCTCCTGTCTTTTGATATAATAGTTTGAACCCCATCCTGTTGATAAAGAACTCTTGGCAA\nTAGGCCTCTTTGCACCTCACAACTTGGTATCTAGNNNNNNNNNNNNNNNNNNNNNNTAGT\nTTCACTGTGGAAGACGTTTTCATTGAGTTGATCAAAGCTAAACTCAGTGATGATAATCTT\nTCTAAGTCTGTTGCATCTAGAATGTCAATGATGCCAAGAGTATAAGGGAACATGTCTTCC\nTGAGTTTTCTGATAACTTATAGTGGGTGTGATACCGGAGGTCTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGGATCTTGAAATCAATTCCATAAGAGCTGGTTTCTATGCCA\nACCTCCCTCAAAGCACTAGTGGCTCGGGTTAAAACTCNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTCCTGGTG\nTTGAGGATCCTCAGAGACTTTATCTTATTTAGAAAGGATCTCCAACATTGCATCTGTTCA\nCTTTGAGAGTCAGCAGCCCTTTCCTCACCAGAATCCAAATCTGCATACAGGAACTTAAGG\nACTGGAGAGGCTCTTCGGAACTGGAATGTTAACTGTTCAATGTNNNNNNNNNNNNNNNNN\nNNNNNNNNNCTATATAGCTTTCTGAAATCCTCTAATAACTTCATCTTATCTGTTTTGACA\nAATTGACTTTCTATATCCCCTTGCCTTAGTTTGTTTCTGAAGATTTGATACTCCTCTTCA\nATCATACTCTTGACTTCATGAGTGGTGAGCTTATTATTAATGCCCTGATGACAACTAGAA\nATTATTTCCTCAAAGTGTTTTNCACGCTTGTCAGTTAGAACATTGANNNNNNNNNNTCCT\nGAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAGAGTCTTGAATACTCAGACTCTTCG\nAACAATGCATTACTTTCTTGTGAATACTTTAATAGGGTGAATAAGGNNNNNNNNNNNNNN\nTCATTCACCCAATCAGGTATTTGCTCATTGTAAAATGTTGTTCTGCCGTCTATGAGAGGG\nATGAGATTGATGCNNNNNNNNNNNNNNNNNTTCTTTAATTGTTCTAGTTTCTTGTGATCT\nTCTAAATACTTTTGTTCAAAATTAGCGGGGGACGATCTAACAAAGCACTCAAGTAAGATT\nAGAACATTACCGGTAAGTTTATAGCCGTCAGGCACCACAAAGCATAAAGCTGGAGTGAGT\nATCCCATGATCATTCAGAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACATCCA\nTTAGCCTTGCAAGAATCAATCTCAATGCAAAGAGACAGTAGTTTCAACCCCTCCATGAGC\nAACATTCTAGGTTCAGTTTGGACCAGAAAGGCTAGCTTCTGTCTTGACAGCCTCTCATTG\nTCTGCAAGGTACTTTGAGACAAGATCTTTAGCATTGGCAATGTCTTCCTCCATCGCCAAT\nTGTGGCACCTATGTTGGGTTCGGG------------------------------------\n----------------------------------------------\n>LASV_NGA_2018_1392-1\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n--------------CTGAATCATAACTCTTTGCTTTGATTTACTATAGCAAAGAGCATAG\nCCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATCAGCATAA\nTCCACAGGTCTCTGTTTTGTGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNCTTACAAACATTTCTAAATCTTGATCTTGGATAGATGGTGTAAATGTA\nGCTACCCTTCTANNNNNNNNNNNNNATGCTCCCCTACACACAACCAATGGCACTGGTTCA\nTTGTCAGGTCCGACCTTGGAGAAGTCAAATTCATTGAACTGCAGTTTATCTGGATTGATA\nATCAGCNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNCAACAAACCAGGCTGACCTACCTTTGAAGGTTGGACCCGACANNNNNNNN\nNNCCAACAGTCAGACAGAACACATGGGCTCACAGACCCAGAATATAGTGCCNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAGACCTTCA\nCCCTCTGGGATTGAGGTTTTATGAGGAAACCAAGTGAATGACCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAGCGGACATATGATTCAAAGTAGATTTGTCTCATAAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTTTCTTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTC\nCTCAGTTCAGAAGCCAATACAACATAATGTTCCTCCCNNNNNNACTTAACANNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNCTTTGTGGAGGCTAAGTCACTCATAAATGGCAATATGTGCTTT\nTCAAATAGGGACGGATATAAACGTCTCAAAGAANNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNTTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGCAAG\nATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAAGGGACTGTGCCAATTTGAAAG\nTTGGAATTAAAAAAGTCTTCAGTCATTGATTGAGTTGTCTTCTTCTTCNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCTTTACCCTTTAAATCAGCTTGTAAA\nTCATCAGAAAGTAAGATTAGGTTTTGAATTATTGTCAGAAACAAGAAAGGACACATCATA\nGGACCCCACTTACTGTGATCCATACTATATGATACATGTGCCGATGAGACATTCAGCTTC\nATTGACAAAATGGCATTGTCAAACTCCTTCTCATTGTTTAGACAGCTGCCTGCTAACTGT\nGATGTGAGCGCTTCAAAGTAATCCTCAATGAGCCTTGTGAACATCTTTGTCCTCAAATCT\nCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCCTTGTAAGACAAAGAGAATTTTAGT\nCTACCAGTGTCAGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATTTA\nAAGTTCAGACACTTACTCTTATAATGAGAGTACCTTCCCATCAATTTATTCCCATTCATC\nACCAACAAAATTGACTTAAAGCACTGGAAATATTCTTGNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNGGATGTGTCAGTATCAAAACTAAAATCATTTTGGTTAACAAN\nNNNNNNGTGATCAATNNNNNNNNNNNNNNNNNNNNNNCTTCTATCCAACTGACCATAACN\nNNNNNNNNNNNCTGCAAAACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTGGGATCA\nGCATAAAAGGAACAGACCTCTCCAATTTCATTGTTGTTGATAGCATAGCACTTTGAGCAT\nTCACCTGTCTTTTGATATAATAATTTGAATCCCATCCTATTAATGAAGAACTCTTGGCAG\nTAGGCCTCTTTGCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNTCTAGAATGTCAACAGCGCCAAGAGTATAAGGGAACATGTCCTCC\nTGAGTTTTCTGGTAAGTTATAGTGGGTGTGATGCCGGAGATCTCAATGTCCATAATNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTAGAACATTGATGCTCTCAATTCCT\nGAGAGCCTCCCAGATGTTAAGGCTAATGATTCACAAAGTCTTGAATACTCAGACTCTTCA\nAACAATGCATTGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGG\nATAAGATTGATGCCAACAGATTCCAAATCATTCTTTAATTGTTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCAGGAGATGATCTANNNAAGCACTCAAGTAAAATA\nAGTACATTACCAGTGAGTTTGTAGCCGTCAGGCACCACAAAGCATAAAGCTGGAGTGAGA\nATCCCATGATCACTCAGAATGGATTCAACCGTTTTGTCCTCAGTGTTATGTTCACATCCA\nTTGGCCTTACAA------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n----------------------------------------------\n>LASV_NGA_2018_1643-1\n------------------------------------------------------------\n-----------------TGGGCAACAAACAGGCCAAAACGACAAAAGTCGATGAACATCA\nAAGAGCTCATATAGTGCCAGATGCATCTCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTG\nGTTTGAGAACAGAGGGCTGGTAGAGTGCAACAACCACTACCTGTGTCTCAACTGTCTCAG\nTCTGCTACTCAGCGTCAGCAGTAGGTGTCCGATCTGTAAAATGCCCCTCCCCACCAGGCT\nAAAGGCAGCAACACAGCCAAGCGCACCCTCAACCGAGGCGACCCAGAACNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNCTTCAATACACCTCTCCGGCCCAAACAACTCTGAACATGTTCTTCCCTTCAGTCTCAAG\nCTGCCCCCACTTGACTGTATCATAACTTTTTGCTTTGATTTACTATAGCAAAGGGCATAG\nCCTTTGAAATCAATCCATTCCCCAAGAGATTCAAGAAGTTCACTCAGTATATCAGCATGA\nTCCAAAGGTCTCTGTTTTGTTAAGATTGAGACAATGTCCACACCCGTCCATTGAATTCTT\nTGTTTCAATCTATCAGACATCATTGATTTCAATGCACCAACTAAAAGATGTGGGAGACTG\nTCACCAACCTCCCTTACAAACATCTCTAAATCTTGATCTTGGATAGATGGTGAAAATGTG\nGCTACTCTCCTATCAGATTCCCACAGTGCTCCCCTACATACAACCAATGGCACTGGTTCG\nTTGTCAGGACCGACCTTGGTGAAGTCAAACTCACTGAACTGCAGTTTATCTGGATTGATA\nATCAGCTTCATGGGTATAACATCCCCTAACTGCTGTGTATCCTTTAAGAACTCATTTACT\nACACCTGATTCAACAAACCAGGCTGACCTACCTTTGAAAGTTGGACCCGACAAAGCAAGT\nCTCCAACAGTCAGACAGAACACATGGGCTCACAGACCCAGAATATAGTGCCTGTACATCA\nTTCACTACAAATTCACCACATTGGTTAACAAGCCCTGTCATATTGAGATGGATAGAAAAA\nGTCTCTTTAAAGCTAGCATCCTGACTCTTGATTTTATACCTGATTGTCTGGTAAAACTGA\nACAGAGTCCATTGGCATTGTACTCAACAAATCAAAGAAATCTTCAAGAGAGTCCAACCTT\nAATTCCTCTGTCAGACCTGAGGCAATAAGCTGGTTCAAATTTATCTGGGCTGGTTCTATG\nTCAAAGTCTATCCATGCATAGCCCATCATTAAATCAAACTTAAACATAGGTCTCTCTATC\nCCTTTGTAAATGGCCTTTTCAATAAATGAGGAGAAGGGACCTAGTCGCTGCAGACCTTCA\nCCCTCTGGTATTGAGGTTTTGTGAGGGAACCAAGTGAAAGACCCAAGTGTCCTTGTTGTT\nGCTACAAAAGAACGGACATATGATTCAAAGTAGATTTGTCTCATGAAGTTATCCACTGCA\nTCAGCAGTACTAACCACCCTTTCTTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTT\nCTCAGCTCAGAAGCCAACACAACATAATGTTCCTCCCTCTTCCACTTGACAATATGTGAA\nACAAGTGAGAGTGCCTCGCAATTCACATCTAGGGCAACACAAAGATCAAGGAACTTTATT\nCTAGGTGACCATTTCATCTTTGTAGAAGCTAAATCACTCATAAACGGCAGTATGTGCTTC\nTCAAATAGAGACGGATATAAACGTCTCAAAGAATGAATGATGTGGCTCATGCCAACCCTG\nTCCTCTAGCAGTTTCGAAACAGTGGGTCTTAAGGGGAAGTAATCACAAGGATTGTGTTTA\nAAAAAGTCCAAGATCTGGGCTTGTTTTGGTTCCCCGAGTACCCATGCCCCAAGTTCTATA\nGCTGTAGATAGTGTTATGCACATATAATCCCATAGAAGAGGTCTTAAATAAGCAACAACA\nGCATCACCTCCATCTTTGACTTCTGGTGAGACTTTCCATATCTGGATTCCATTGTCCCCC\nATCACTACTTCAACACCTTGAGTCCCCAACAGCTGAGTCTGTATGGATCTAATGTAAAGA\nTTCTCTTTATTAGGCCCTCTGACGCACTTGCTACCTAGTGTTCTGCACAACCCTACAAAC\nCCAGATGCTATAGAACTTTGGAAAGCCGATTTATTTATTGCTTCAGACAGCAGCTTCTGA\nGCTCCTCTAGTGAATGTCGATGACAACCTATTTTGCAGGGTCTTTACTATTGTAGGGACC\nTTTTCATCTTCCAAATTCACAGCACCAGAATAAATTATCTTTTGCCGCAACACCATTCTA\nAGCGGGTGATGGGTGGCTAAGTTTAACCAATGATACCCCAAATCAGAATCAGACAAAGGT\nTCAATGCCTAGAAGCTTAAACAAATTCTGTAATGATGTTGTGTGTTCACCTGATAGGTAG\nTTGGTGGTGAATTCCTCATGAAGCTCACCAGTTTTTAATTTATTAAACAATATCCTAAGC\nATTGACCTCATTTTTTTGCATGCATCAGGAATTAGCCTCTCAATTTGCCTCATTATCCTA\nTAGCTACGATTCCCGTCCACCCAATCCCTTACATCAGTCTCGCAATTCAAAAGGAATGGA\nTCAATAGGATACTTAGCATAACATAACAAATTTAAAGTCCTCTTTTGAATTTGATTACAC\nAGATCAACTGGGACACCATTGGCCACAGATTGATCAATTATGGTATCAATTGTTTCTGCC\nAATTGATGGGGTTCCTTGCACTTTATGTTATGTAAAGCCGCAGCAACAAATTTTGTTAAC\nAGAGGTACCTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAATCTGCCA\nATTGCACTCTTTGGACTCACAAATTTATTTAGCTGATCACTCATGTAGTAGTGGAATTCT\nAACAGTGTTTTGAATTCCTCTGTATCTCTTGAGAGTAACTCTGTTAAGTTCTGATCAAAC\nAATGATATCTGATCGTCACTGGACGTGTAAGCATCGATCTGTCCTCCAGACACACACCTC\nACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAAGTGTTGTGCAGA\nATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGGACTGTGCCAATTTGAAAG\nTTGGAATTGAAAAAGTCTTCAGTCACTGATTGAGTTGTCTTCTTCTTCAATCCAAGTTGG\nGATTTGATGTATGATTTCATCATTGCTGACACAACATTAAATGGGATCTCAACCATTTTG\nTGCATATGCCACGTTAATAATGTTGACAGGTAATCTTTACCTTTCAAATCAGCTTGTAAA\nTCATCAGAAAGTAAGATTAGGTTTTGAATTATTGTTAGAAACAAGAAAGGACACATCATG\nGGGCCCCACTTACTGTGATCCATACTATATGATACATGTGCCGATGAGACATTCAGCTTC\nATTGACAAAATGGCATTATCAAACTCCTTCTCATTGTTTAGACAGCTGCCTGCTAACTGT\nGATGTAAGTGCTTCAAAGTAATCTTCAATAAGCCTTGTGAACATCTTTGTCCTCAAATCT\nCCGATGTACAACTCTCTATTACCTCCCACTTGTTCCTTGTAAGACAAAGAAAATTTCAAT\nCTGCCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCCTGACTGTAAAAACAC\nAGGTTTTTTAACATTGCTGTAGTACAGTTAGTTAGGGATAAGGCCTTGCTAAGTGCTTCA\nGAATTACTCTCACGTTCACTTATTCTGACATCCTCAGCTAATCTTCCTGTGTCAAATTTA\nAAGTTCAGACACTTACTCTTATAATGAGAGTATCTTCCCATTAGCTTATTTCCATTCATC\nACCAATAGGATTGACTTAAAGCACTGAAAATATTCCTGGTCCAAAAAAGTCCTGGTTACT\nACTGCCTTTGTCAGTTCACTAATAGGACATGAGTTCATTGGCCCTTCATAAAAATATTTA\nCTTCTCAAAGCAGCATCATTGTAGATGTTCTCACAAATTTTGATGTATTGATCTTCAGAC\nAGGATTTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATCAACCTT\nATTAAAAGTTTTTCTTCCACCACCTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCT\nGCCTGCTGCTGTCTTTCTGGTTGCTCCTTATACTGACTGACAATATTGTCAACAGTACAC\nCTCAGTTGGTCGAAGTATTCTGATGCTCCTCCATCCAGTAGTATCTCATCTAGATCAGCA\nTTGTTGGTGTCACCACCCCCTCCTTTGGACCCCAGAACAAGATTACTCATTGCTTGCTGT\nATCTTGTAATCATAATCCTGTTTATTAAGCAAGAATTTACCCTTACGTGCAAACACCTCA\nGTCAACTGTGTGACAGCCAAAGCTGTAAGCTTATTGAAGTCATAATCCAGAATGCGAGAC\nCCATCTGTATATTTATTCACAACAACACTCTTATTGCTGGCTAAGTCCAAAGCTGTTGCA\nCAGCCACTTGTGATAAGAGGGTCTCGCAGTGTCCTCTTTACTTCCTTTTCTTTAAATAGT\nGAACCATTATTGAAACTAGACACAAGGAGTGAGATAAATTTTTTGGAAACACCAGGCTTT\nTTATACCTAATTTTTTCTGCGTCTGCACAACATTCTTTACTTAAAAACCTTCTTGCATTA\nTAAACCATTTCAGCAAGCTCTTCCTCCGATGCATCATCCTTCGGGTTCACACTCACATGT\nCCGAATTCCAATTTGGGTTCAAGGAATTTTTCAAAGCATTTGATCTGATCAGTCAGTCTG\nTCAGGTGTTTCTTTTGTAATGAAATGGCACATATAAGAGACATTTAAAACAAACTTGAAT\nCTATTGGTCATCATACTGACAACTTCTTCAGACAGAATTATTTTTAATAAATGACGAACA\nAGTCTGTAGAGCAGATATTCAACTTCTGTGATCAGATCCTCCTTAATTTTCTCAATCAAA\nTCTTTGTGATAAAAATCGGATACAAAGGCCATCACAAAATACCTAATGTTTTGTAAAAAC\nTTTTGACACCTTTTACTAGGATGTGTCAATATCAAAACTAAAATCATTTTGGTTAACAAT\nTTAATAGTGATCAATTGTTCAGACAACTCTGTGCATTCTTCTATCCAGCTGACCATAACA\nTCGACCACCTTCTGCAACACATCACTAGAGAAAACTGAAGGAAAGAACCGTTTAGGATCA\nGCATAAAAGGAACAAACCTCTCCAACTACATTGTTGTTGATGGCATAACACTTTGAGCAT\nTCACCTGTCTTTTGGTATAATAGTTTGAATCCCATCCTATTAATGAAGAACTCTTGGCAA\nTAGGCTTCTTTGCACCTTACAACCTGATATCTAGAGGGTCCAAATTCATTTTGCCTTAGT\nTTCACTGTGGAAGATGTCTTCATTGAGTTGATCAAAGCCAAGCTCAATGATGATAGTCTT\nTCTAAGTCTGTTGCATCTAGAATGTCAATGACGCCAAGAGTGTAAGGGAACATGTCTTCC\nTGAATTTTCTGGTAACTTATAGTGGGTGTGATACCGGAAATCTCAATGTCCATGATGGCA\nTCATAAACATCACAATCAAGAATCTTAAAATCAATTCCATAAGAGTTAGTTTCTATGCCA\nACCTCCCTCAAAGCATTAGTGGCTCGAGTTAGTACTCTGTTGATGATAGCAAGGAGCTCA\nCAATTCCGTTCTTCTTTGGGTGATAGGACACCTGCATTTTTGTCCCTAGTTCTCTTTCTG\nCTGTCTATCCACCGTTTTAAATCTCTTTTTGTTGATTCCAATGAAACTAATCTATCGTTG\nACACTCACAAAACAAGAGCCCAGCCAACCAGCAAGGAGCCCGTCATCATGCTTTATGCGG\nTCCAACCGGCTAGCAAGAAGAATGAGAACATCAAAAATAAGGAGAAGTTTCCTCCTGGTG\nTTAAGGATCCTTAGAGACTTTATCTTATTCAGAAAAGATCTCCAACATTGCATCTGTCCA\nCTTTGAGAGTCAGCAGCCCTTTCTTCACCAGAATCCAAGTCTGCATACAAGAACTTAAGA\nACTGGAGAGGCTCTTCGGAACTGGAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCT\nATTTTATCACTATACAGCTTTTTGAAATCCTCCAATAACTTCACCTTATCAGTCTTAACA\nAATTGATTTTCTATGTCCCCTTGCCTTAGTTTGTTCCTGAAGATTTGATATTCCTCCTCA\nATTAAACTCTTGACTTCATGAGAGGTAAGCTTGTTATTAATGCCCTGATGACAACTAGAA\nATTATTTCCTCAAAGTGTTTTGCACGCTTATCAGTTAGAACATTGATGCTTTCGATTCCT\nGAGAGCCTACCAGACGTTAAGGCTAAAGACTCACAAAGTCTTGAATACTCAGACTCTTCA\nAACAATGCATTACTTTCTTGTGAATATTTTAACAGGGTGAACAAGGTGTCCCTGAGTTTG\nTCATTTACCCAATCAGGTATTTGTTCATTATAAAATGTTGTCCTGCCGTCTATGAGGGGG\nATGAGATTGATGCCAACAGACTCCAAATCATTCTTTAATTGTTCTAGTTTCTTGTGATCT\nTCTAAATACTTCTGTTCAAAATTGGCGGGGGATGATCTAACAAAGCACTCAAGTAAGATT\nAGAACATTACCAGTGAGTTTGTAGCCGTCAGGTACTACAAAGCATAAAGCTGGAGTGAGA\nATCCCATGATCACTCAGAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACACCCA\nTTAGCCTTACAAGAATCAATCTCAATACAGAGAGACAATAGCTTCAATCCCTCCATGAGC\nAACATTCTAGGTTCAGTTTGGACCAGAAAAGCTAACTTCTGTCTTGATAGCTTCTCATTA\nTCTGCAAGGTATTTTGAGATAAGATCTTTAGCATTGGCAATGTCTTCCTCCATCGCCAAT\nTATGGCACCTG-------------------------------------------------\n----------------------------------------------\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/input/align_mafft-ref-lasv-ISTH2376_2.fasta", "content": ">KM821998.1 Lassa virus strain ISTH2376-NIG-2012 segment S glycoprotein precursor (GPC) and nucleoprotein (NP) genes, complete cds\nCCTAGGCATTTAGGATTGCGCTTTTAGAGATCTTTGTGTGAGTGAGCTTCATCAAGCCAT\nGGGGCAAATTATAACATTTTTCCAAGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTCAGCCTTCTGGCAATTCTGAAAGGGATCTACAATGTTGCTACATG\nTGGCCTTTTTGGACTGGTGTCTTTTCTCCTCTTATGTGGAAGATCATGCTCAACAACTTA\nCAAGGGTGTTTATGAGCTACAGACTCTAGAGCTAGACATGGCTAGCCTTAACATGACAAT\nGCCCTTATCTTGCACGAAGAACAACTCCCACCATTACATCATGGTCGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATTATCAACCACAAGTTTTGCAACCTCTCTGA\nTGCACATAAGAAGAATCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTCCACTT\nATCCATTCCCAACTTTAATCAATATGAAGCGATGAGCTGTGACTTCAATGGGGGGAAGAT\nAAGTGTGCAGTACAACCTCAGCCACACTTACGCTGTGGATGCGGCTAACCACTGTGGGAC\nCATTGCCAATGGCGTTCTTCAGACTTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAAGGGGAATTGGGATTGCATAATGACTTCCTACCAATATTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGTCCATCCCCCATCGGTTATCT\nGGGGCTACTGTCACAAAGGACCAGGGACATTTATATCAGTCGAAGACTTCTTGGGACTTT\nCACTTGGACTCTCTCTGATTCCGAAGGTAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGCTGATTGAGGCCGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCAAAATGTAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGC\nTATAAGTAGGCTGAAGACAGAAGCACAGATGAGTATCCAACTGATAAACAAAGCAGTAAA\nTGCACTGATCAATGACCAGCTGATTATGAAGAATCATTTGAGAGATATCATGGGAATTCC\nTTATTGCAATTACAGCAAATATTGGTATCTAAATCACACTGTAACAGGGAAGACATCGTT\nGCCAAGATGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAAACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAAATGTTGCAAAAGGAGTACATAGATAG\nGCAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGTTTTTACCT\nTATTAGCATCTTCCTCCACCTGGTTAAAATCCCAACCCACAGACACATCACAGGGAAACC\nCTGCCCCAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTATACAAACA\nTCCTGGTGTGCCAGTCAAGTGGAAAAGATAGAAGATAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCC\nCCTGACACAGCTGCATCATACATTATGCAGTCCATCAAAGCACAGTGCGGGGTAATTTCT\nTCTTTACCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTATGCATATGGCACAGATCC\nCTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTACTCAGTGCAATG\nTCAATAAGCTTTATGTCCCTCCTTCCCTGAGAGTCCAAGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTCAGTACCATGTTGCGAGGAAGGGCTTCAATAACTGCACTGGTCAGGCCA\nGGTTGAGCAGGGAAAAGATCTGCCACATCAATCCCGTGAGAATACTTGGCATCTTGCTTG\nAACTGTTTTAAATCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGACATGGGTTGG\nTAAAGAGCTATTTCCACAGGATCTTCTGGACGACCTTCAATGTCTATCCATGTTTTGGCA\nCTTGGGTCAAGTTGCATCATTGAGTCCTTAAGTGTCATCAACTGAGAATAGGTCAGCCCC\nGTTGGAAACCCCGCTGACTGTAAAGACTTGTTGGACCCAGCAGCACCCACTTTTTGTGGT\nTTTCCATCTGACTCGAGATCCACAGTAGTATTCTCCCAAGCTCTACCCGCAATAGAAGTC\nCTTGAAGCTATGTAAGGCCAGCCGTCACCGGAAAGACAGATCTTATAAAGTATGTTCTCG\nTAAGGGTTCCTCTCACCAGGTGTGTCTGAAACAAACATTCCCAAGGATCTTTTTACCTTT\nAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCTCCTAAACTGAAGTTATAA\nCCAGAAATGTTCAAGGAGCTCTTCTTGGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAGAGTCTGTCCAGGTCGGAGCTATTTGGATACTTAGCTGTGTATATTAGACCCAGGTCT\nGTCAGTGCTAAGACGGCATCATTCAAATCAACTTGACCTTGTTTGGTGAGACATGCTAAT\nGTCAGACTAGGCATGGTGCCGAACTGGTTGTTCAGAAGATCCGGGTTCTTAACATCCCAC\nACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAATGCTCTTCTTTGCTCAAGCTGCTGTGTACTTAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAACGTCAACAGGTCATCTGAGGTCAGGGTCCCAACTCTCAAGATGCTCTTTTGTTGC\nGTCGATTTGAGTTCTACAAGATTGTTGACAGCCTGATTCAAATCTCTAAGACGTTTCAGA\nTCACTATCATCCCTTTTTTGTTTGCGCATTAAGCGTTGCACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGTTTTATGCTGGAGCAA\nTAACCTGAAAGCTCCCTCCTCAATGACTGTGTCCAGAGAAATGACTTCACTTCCTTGGAA\nGCACTCATCTTAGTCTGGACACCTAGGGATTGACTGGTCAAAAGTTTCACTCAGTAAGTC\nAATGAAAGGCGCAATCCAGTAGCCTAGGATCCACTG\n>LASV_NGA_2018_0026-2\n----------------------------------------------TTTCATTAAGCCAT\nGGGGCAAATCATAACATTTTTCCAGGAAGTGCCTCATGTCATTGAGGAGGTGATGAACAT\nTGTCTTGATTGCTCTCAGCCTTCTAGCAGTGCTAAAAGGGATTTATAATGTTGCTACTTG\nTGGCCTCTTTGGGTTGGTGTCCTTTCTTCTCTTATGTGGAAGGTCATGCTCAACAACTTA\nCAAGGGTGTTTATGAGCTTCAAACTCTGGAGCTGGATATGGCAAGCCTTAACATGACAAT\nGCCCTTATCCTGCACGAAGAACAACAGCCACCACTACATCATGGTTGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAACACAAGTATCATCAACCACAAGTTCTGCAACCTTTCTGA\nTGCACATAAAAAGAATCTCTATGACCATGCTTTGATGAGCATCATCTCAACCTTCCACCT\nATCCATCCCTAATTTTAATCAGTATGAAGCAATGAGTTGTGACTTCAATGGAGGAAAGAT\nAAGTGTTCAGTATAACCTCAGCCATGCTTATGCTGTGGATGCAGCCAACCATTGTGGGAC\nCATTGCCAATGGTGTCCTTCAAACTTTTATGAGGATGGCCTGGGGTGGCAGTTACATAGC\nACTTGATTCTGGAAAGGGGAGTTGGGATTGTATAATGACGTCCTACCAATATTTGATAAT\nCCAAAACACCAGTTGGGAAGATCACTGCCAGTTTTCTCGCCCGTCCCCCATCGGTTATCT\nGGGGCTACTGTCACAAAGAACCAGGGACATTTACATCAGCCGAAGGCTCCTTGGAACTTT\nTACCTGGACTCTCTCTGACTCTGAGGGCAATGAAACACCAGGTGGATATTGTTTGACAAG\nATGGATGTTGATTGAGGCCGAATTAAAGTGCTTTGGGAACACAGCAGTTGCGAAATGCAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTGAGGCTGTTTGACTTTAACAAACAGGC\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAATAAAGCAGTGAA\nCGCATTAATCAATGACCAGCTCATTATGAAGAATCATTTAAGAGATATCATGGGAATTCC\nTTACTGCAATTACAGCAAGTATTGGTACTTAAACCACACTGTAACAGGGAAGACATCGTT\nGCCAAGATGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAAACATATTTTTCTGATGA\nCATTGAGCAACAAGCAGACAACATGATAACAGAATTGTTACAGAAGGAGTACATTGACAG\nGCAAGGGAGAACACCCTTAGGGTTGGTGGATCTTTTTGTCTTCAGCACTAGCTTCTACCT\nTATTAGCATCTTCCTCCACCTGGTCAAAATCCCAACCCACAGACATGTCATAGGGAAACC\nCTGCCCCAAGCCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTGTACAAACA\nTCCTGGTGTACCAGTCAAGTGGAAAAGATAGGAGACAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGATGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTCAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAATCCATTAGAGCACAGTNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCCAGTATNNNNNNNNNNNNNNNNN\nNNNNNNNGATCCCAAACAGCATTCTCAAACCTCCTAGAGTCAGCCCTGCTCAGTGCAATG\nTCAATAAGTTTTATGTCCCTTCTTCCTTGTGAATCTAAGAGTTTCTTGATATCGTCTGAA\nCCCTGACAGGTCAGTACCATATTGCGAGGAAGGGCTTCAATGACTGCACTGGTCAAGCCA\nGGCTGAGCAGGGAAAAGATCTGCCACATCAATCCCATGAGAATATTTGGCATCTTGCTTG\nAACTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGATATAGGTTGG\nTAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGT\nTTTCCATCTGACTCGAGATCTACAGTGGTGTTCTCCCAAGCTCTACCCACAATGGAAGTT\nCTTGAAGCTATGTAGGGCCAACCGTCCCCAGAAAGACAGATCTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTCTCACCAGGTGCATCTGAAACAAACATTCCCAAAGATCTCTTTACCTTT\nAAGATAGATTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAGGCTCCAGCTTTCACTGCAGCTCCTAAACTGAAGTTGTAA\nCCAGAAATATTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATGGCTTTGA\nGAAAGTCTGTCCAAGTCGGAGCTGTTTGGGTACTTAGCTGTGTATATTAGACCCAGGTCT\nGTTAGTGCTAAGACGGCATCATTTAGATCAACTTGTCCTTGTTTGGTGAGACATGCTAAT\nGTCAGACTAGGCATGGTGCCGAATTGGTTGTTCAAAAGATCCGGATTCTTGACATCCCAA\nACCCTAACAACTCCGTCCCTTCCAGGTTGGGTACCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAATGCTCTTCTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNGAGTTCCACAAGATTGTTGACAGCTTGGTTCAGATCTCTGAGACGTTTCAGA\nTCACTGTCGTCCCTTTTTTGTTTGCGCATCAAGCGCTGAACATTGCTGACCTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGCTTTATGCTGGAGCAG\nAAACCTGAGAGCTCCCTCCTCAATGACTGTGTCCAAAGGAATGATTTTACTTCCTTGGAA\nGCACTCATCCTGATCTAGACAATCA-----------------------------------\n------------------------------------\n>LASV_NGA_2018_0097-2\n---AGGCATTTAGGATTGCGCTTTTAGAGATCTTTGTGTGAGTGGGCTTCATCAAGCCAT\nGGGACAAATCATAACATTTTTCCAGGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTTAGCCTTCTGGCAATATTGAAAGGGATCTACAATGTTGCTACCTG\nTGGCCTCTTTGGATTGGTGTCCTTTCTCCTCTTGTGCGGAAGATCATGCTCGACAACCTA\nCAAGGGCGTTTATGAGCTACAAACCCTAGAGCTAGACATGGCTAGCCTTAATATGACAAT\nGCCTTTATCTTGCACGAAGAACAACAGCCATCATTACATCATGGTCGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATCATCAACCACAAGTTTTGTAACCTTTCTGA\nTGCACATAAAAAGAATCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTCCACTT\nATCCATTCCCAACTTTAATCAGTATGAAGCAATGAGTTGTGACTTCAATGGAGGAAAGAT\nAAGTGTTCAGTACAACCTCAGCCACACTTATGCTGTAGATGCAGCTAACCACTGTGGAAC\nCATTGCCAATGGTGTTCTTCAGACTTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAAGGGGAGTTGGGACTGCATAATGACTTCCTACCAATATTTGATAAT\nCCAAAACACCACTTGGGAAGATCATTGCCAATTTTCTCGCCCATCCCCTATCGGTTATCT\nGGGGCTACTGTCACAAAGGACCAGGGATATTTACATCAGCCGAAGGCTTCTTGGAACCTT\nTACTTGGACTCTCTCTGATTCTGAAGGTAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGTTGATTGAGGCCGAGCTGAAATGCTTTGGGAACACAGCAGTTGCGAAGTGCAA\nTGAGAAACACGATGAGGAGTTTTGTGACATGTTAAGGTTGTTTGACTTTAACAAACAAGC\nTATAAGGAGGCTGAAGACGGAAGCACAGATGAGCATTCAACTGATAAACAAAGCAGTAAA\nCGCACTAATCAATGACCAACTGATCATGAAGAATCATTTGAGAGATATCATGGGAATTCC\nCTACTGCAATTACAGCAAATACTGGTATCTAAATCATACTGTGACAGGGAGGACATCACT\nGCCAAGATGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAACTGTTGCAAAAGGAGTACATAGAGAG\nGCAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACTAGCTTTTATCT\nCATTAGCATCTTCCTCCACCTGATTAAAATCCCAACCCATAGACATGTCATAGGGAAACC\nCTGCCCTAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTATACAAACA\nTCCTGGTGTACCAGTTAAGTGGAAAAGATAGAAGACAGACCCACTCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTAAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAATCCATTAAAGCACAGTGCGGGGTAATTTCT\nTCTTTGCCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTATGCATATGGCATAGATCT\nTTGCATTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTGCTCAGTGAAATG\nTCAATAAGTTTTATGTCTCTTCTCCCTTGGGAGTCTAAGAGTCTCTTAATGTCATCTGAG\nCCTTGACAGGTCAGTACCATATTGCGAGGGAGAGCTTCTATGACTGCACTAGTCAAACCA\nGGTTGAGCAGGGAAAAGATCTGCTACATCAATCCCATGAGAATATTTGGCATCCTGCTTG\nAATTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCTGACATAGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTCTTGGCA\nCTTGGGTCAAGCTGCATCATTGAGTCTTTGAGTGTCATCAACTGAGAATAGGTCAGCCCT\nGTTGGGAACCCTGCTGACTGTAAAGACTTGTTGGACCCAGCTGTGCCCACTTTTTGTGGT\nTTTCCATCTGACTCGAGATCCACAGTGGTATTCTCCCAAGCTCTACCCACAATGGAAGTC\nCTTGAAGCTATGTAGGGCCAGCCGTCACCAGAAAGACAGATTTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTCTCACCAGGTGTATCTGAAACAAACATTCCTAAGGATTTTTTCACCTTT\nAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTTCCCCCATCAAGCATACAAGCTCCGGCTTTCACTGCAGCTCCTAAGCTGAAGTTGTAA\nCCAGAAATGTTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAAAGTCTGTCTAGGTCAGAGCTATTTGGGTATTTGGCTGTGTATATCAGACCTAGGTCT\nGTTAGTGCCAGGACGGCATCATTCAGATCAACTTGACCTTGTTTGGTGAGACATGCTAAT\nGTCAAACTAGGCATGGTGCCGAACTGGTTGTTCAAAAGATCCGGATTCTTAACATCCCAC\nACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGTCCCGCCAACCATGCCTATC\nATGTTCAGCAATGCTCTTCTTTGCTCAAGCTGTTGTGTACTCAAATTCCCCATGTAAACA\nCCTGAGCTCAGTGGCCTTTCTGTCCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAATGTCAGCAGGTCATCTGAAGTCAAGGTCCCAACTCTCAGGATACTCTTCTGTTGT\nGTTGACTTGAGTTCAACAAGATTGTTGACAGCCTGATTTAGATCTCTGAGACGTTTCAGA\nTCACTATCATCCCTTTTTTGTTTGCGCATTAAACGCTGCACATTGCTGACTTCAGAAAAA\nTCAAGACCATGAAGGAGAGCCTGAGCATCTTTAACAACCTGAAGCTTTATACTGGAACAA\nTAACCTGAAAGTTCCCTCCTTAATGATTGTGTCCAGAGAAATGACTTCACTTCCTTGGAA\nGCACTCATCTTGGTCTGGACACCTAGAGATTTACTGGTTGAAAGTATTACAAAGTAAGTC\nAATGAAAAGCGCAATCCAATAGCCTAGGATCCA---\n>LASV_NGA_2018_0541-2\n------------------------------------------------------------\n-GGACAAATCATAACATTCTTCCAGGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTCAGCCTTCTGGCAATACTGAAAGGGATCTACAATGTTGCTACCTG\nTGGCCTCTTTGGATTGGTGTCCTTTCTCCTCTTATGTGGTAGATCATGCTCAACAACTTA\nCAAGGGTGTTTATGAGTTACAAACTCTAGAGCTAGACATGGCAAGCCTTAATATGACAAT\nGCCCTTGTCTTGCACGAAGAACAACTCCCACCATTACATCATGGTTGGAAATGAGACTGG\nCCTGGAGCTGACTCTAACAAATACAAGCATTATCAACCACAAGTTTTGTAACCTTTCTGA\nTGCACATAAAAAGAATCTCTACGACCATGCTCTAATGAGTATCATCTCAACCTTCCACTT\nATCCATTCCCAACTTTAATCAATATGAAGCGATGAGTTGTGACTTCAATGGGGGTAAGAT\nAAGTGTCCAGTACAACCTTAGCCACACTTATGCTGTCGATGCAGCTAACCACTGTGGGAC\nCATTGCCAATGGCGTTCTTCAGACTTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAAGGGGAGCTGGGATTGCATAATGACTTCCTATCAATACTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGCCCGTCCCCCATCGGTTATCT\nGGGGCTGCTGTCACAAAGGACCAGGGACATTTACATCAGTCGGAGACTTCTTGGGACTTT\nTACTTGGACTCTCTCTGACTCTGAAGGCAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGCTGATTGAGGCCGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCAAAATGCAA\nTGAAAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGC\nCATAAGGAGGTTGAAGACAGAAGCACAGATGAGTATTCAACTGATAAACAAAGCAGTGAA\nCGCACTGATCAATGACCAGCTAATTATGAAGAATCATTTGAGAGACATCATGGGAATTCC\nTTACTGCAATTACAGCAAGTATTGGTACCTGAATCACACTGTAACAGGGAAGACATCGTT\nGCCAAGATGCTGGCTTGTGTCAAATGGTTCCTACTTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAACTGTTGCAAAAGGAGTACATAGAAAG\nACAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nTATTAGCATCTTCCTCCACCTGGTTAAAATCCCAACCCACAGACATATCACAGGAAAACC\nCTGCCCTAAACCACACAGACTCAACCATATGGGCATATGCTCATGTGGTCTGTACAAACA\nTCCTGGTGTGCCAGTCAAGTGGAAAAGATAGAAGACAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGCCCT\nCCTGACACAGCTGCATCATACATTATGCAGTCCATTAAAGCACAGTGCGGGGTAATTTCC\nTCCTTGCCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTGTGCATATGGCATAGATCT\nTTGCACTGATCCCAAACAGCATTCTCAAATCTCCTAGAGTCAGCCTTGCTCAGTGCAATG\nTCAATAAGCTTTATGTCCCTTCTTCCTTGGGAGTCCAAGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTCAGCACCATATTGCGAGGGAGGGCTTCAATGACTGCACTGGTCAAACCA\nGGTTGAGCAGGGAAGAGATCTGCCACATCAATCCCATGAGAAAATTTGGCATCTTGCTTG\nAACTGTTTCAAATCTGTTGGTTCTCTGAAGAAATGTATGTAACAGCCCGACATAGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTCTTGGCA\nCTTGGGTCAAGCTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAGGTCAGCCCT\nGTTGGAAACCCTGCTGACTGTAAAGACTTGTTGGACCCGGCAACACCTACTTTTTGTGGT\nTTCCCATCTGACTCGAGATCCACCGTAGTGTTCTCCCAAGCTCTACCCACAATAGAAGTC\nCTTGAAGCTATGTAAGGCCAGCCGTCACCGGAAAGGCAGATCTTGTAAAGTATGTTCTCG\nTAAGGGTTCCTCTCACCAGGTGTATCTGAAACAAACATTCCCAAAGATCTCTTCACCTTT\nAAAATAGACTTCAAGATACCATCCATTGTCTGGGGTGTAACCTTTATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAGGCTCCAGCTTTCACTGCAGCACCTAAGCTGAAATTATAA\nCCAGAAATGTTCAAAGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAAAGTCTGTCCAGGTCGGAGCTATTTGGGTACTTAGCTGTGTATATTAGACCCAGGTCT\nGTTAGTGCTAAGACAGCATCATTCAAATCAACTTGACCTTGTTTGGTGAGACATGCTAAT\nGTCAGACTAGGCATAGTGCCAAACTGATTGTTCAAAAGATCCGGGTTCTTGACGTCCCAT\nACCCTAACAACCCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAGTGCTCTTCTTTGCTCAAGTTGCTGTGTGCTCAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAATGTCAGCAAGTCATCTGAGGTTAAAGTCCCAACTCTCAAGATGCTCTTTTGTTGT\nGTCGATTTGAGTTCTACAAGATTGTTGACAGCCTGATTTAAATCTCTGAGACGTTTCAGG\nTCACTATCATCCCTCTTTTGTTTGCGCATTAAGCGTTGCACATTACTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGTTTTATGCTGGAGCAA\nTAACCTGAAAGCTCCCTCCTCAATGACTGTGTCCAGAGAAATGACTTCACTTCCTTAGAA\nGCACTCATCTTGGTCTGGACACTTAGGGATTTACTG------------------------\n------------------------------------\n>LASV_NGA_2018_0611-2\n-------ATTTAGGATTGCGCTTTAAGAGATCTTTGTGTGACTGAGCTTCATCAAGCCAT\nGGGACAAATAATAACATTCTTTCAGGAAGTTCCTCATGTCATAGAAGAGGTGATGAATAT\nTGTCCTGATTGCTCTCAGCCTCCTGGCGATACTGAAGGGGATTTACAATATTGCCACTTG\nTGGTCTTTTTGGGCTGATCTCCTTTCTTCTTTTGTGTGGAAGATCATGCTCAACAACCTA\nCAAAGGTGTCTATGAGCTACAAACCCTGGAACTGGATATGGCAAACCTCAACATGACCAT\nGCCTCTATCTTGTACAAAAAACAACAGCCATCATTATATTATGGTTGGGAATGAGACGGG\nCCTAGAACTGACCTTGACAAACACAAGCATAATCAACCACAAGTTCTGCAACCTTTCTGA\nTGCACACAAAAGGAATCTTTATGATCATGCCTTGATGAGCATCATTTCAACTTTCCACTT\nATCCATTCCGAACTTCAATCAGTATGAAGCAATGAGTTGTGACTTTAATGGAGGGAAAAT\nAAGTGTGCAATACAATCTCAGTCATAGTTATGCTATAGATGCAGCCGGCCACTGTGGGAC\nCATTGCCAACGGTGTCCTACAGACTTTCATGAGAATGGCTTGGGGCGGCAGTTACATAGC\nGCTTGATTCTGGGAAAGGGAACTGGGATTGCATAATGACTTCCTATCAGTACTTGATTAT\nTCAAAACACCACCTGGGAAGATCACTGTCAATTTTCCCGCCCATCCCCTATTGGATACCT\nAGGACTGCTGTCACAAAGAACTAGAGATATTTACATTAGTCGGAGACTTCTTGGAACTTT\nCACCTGGACTCTCTCTGACTCTGAGGGCAATGAAGCACCAGGTGGATACTGCCTTACTAG\nGTGGATGCTAATTGAAGCTGAATTGAAGTGCTTTGGGAACACAGCCATTGCAAAGTGCAA\nTGAGAAGCACGATGAGGAATTCTGTGATATGTTGAGACTTTTTGACTTCAACAAACAAGC\nCATAAGTAGGCTAAAAGCAGAAGCACAGATGAGCATCCAGTTGATAAATAAAGCAGTAAA\nTGCACTAATCAATGACCAGTTGATCATGAAGAACCACTTGAGGGATATCATGGGAATTCC\nTTATTGCAATTACAGCAAGTACTGGTATCTAAACCACACTGTGACAGGGAAGACATCATT\nGCCAAAGTGTTGGCTTGTTTCAAATGGTTCTTACCTAAATGAGACACATTTCTCCGATGA\nTATCGAACAGCAAGCAGATAACATGATAACAGAACTGTTGCAAAAGGAGTATATGGACAG\nGCAGGGGAAAACACCCTTAGGGTTGGTGGATCTTTTTGTTTTTAGCACTAGCTTTTATCT\nCATAAGTATTTTCCTCCACCTGGTCAAAATTCCGACCCATAGACACATTGTGGGGAAACC\nCTGCCCCAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTTNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNGCGTCAAACATTATGCAATCCATTAAAGCACAATGTGGAGTGATCTCC\nTCTTTACCTCCTCTCTTCTTTTTCTCAACGACCACTCCGGTGTGCATGTGACACAAATCT\nTTGCACTGATCCCAGACAGCATTTTCAAATCTCCTAGAATCAGCCTTACTTAATGAGATA\nTCGATGAGCTTGATGTCCCTTCTCCCCTGAGAATCAAAGAGTTTTTTAATGTCGTCTGAA\nCCTTGACACGTTAACACCATGTTACGGGGGAGAGCCTCAATGACTGCACTGGTTAGACCA\nGGCTGAGCAGAAAAGAGATCTGTCACATCAATCCCATGAGAATATTTGGCATCTTGTTTG\nAACTGTTTTAAATCCGTTGGTTCTCTGAAGAAATGTATATAACAGCCTGACATAGGCTGG\nTAAAGAGCTATCTCAACAGGGTCTTCTGGACGACCCTCAATGTCTATCCAAGTTTTGGCG\nCTTGGGTCAAGTTGCATCATTGAATCTTTGAGTGTCATCAGTTGGGAATAAGTTAGCCCT\nGTTGGGAACCCTGCAGATTGCAGAGATTTGTTGGATCCAGCAGTGCCCACTTTCTGTGGT\nTTCCCATCTGACTCAAGGTCTACAGTGGTATTCTCCCAAGCTCTACCCACAATGGAGGTT\nCTTGAAGCTATGTAGGGCCAACCGTCCCCAGAGAGACAAATTTTGTAAAGTATGTTTTCA\nTAGGGGTTTCTTTCACCAGGTGTGTCTGAAACAAACATTCCCAGGGACCTTTTCACCTTT\nAGAATGGACTTCAGAATGCCATCCATTGTCTGAGGCGTTACCTTGATAGTTTCCAACATG\nTTACCCCCATCGAGCATGCAAGCTCCAGCCTTCACTGCAGCTCCCAAACTAAAATTGTAG\nCCAGAAATATTTAGGGAGCTCTTCTTGGTGTCTACCATGTTCAATATAGGATGGCTCTGG\nGAAAGTCTGTCCAGGTCAGAACTATTGGGGTATTTAGCTGTGTATATTAACCCCAAGTCT\nGTTAGCGCCAAGACGGCGTCATTTAAATCAACTTGACCCTGTTTAGTGAGACATGCTAGT\nGTTAAACTAGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCACCGACCATGCCTATC\nATACTCAACAACGCCTTCCTCTGCTCAAGTTGTTGTGTGCTCAAGTTTCCCATATACACG\nCCTGAACTTAGTGGCCTCTCTGTCCTAATGACCTTTGACTTCAATTTCTCTAGATCAGCT\nGCTAAAATCAGCAAGTCGTCTGAGGTCAGTGTTCCAACTCTCAGAACACTCTTTTGTTGT\nGTTGACTTGAGCTCAACAAGATTGTTAACTGCCTGATTTAGGTCTCTAAGACGTTTTAGG\nTCACCGTCATCTCTTTTCTGTTTGCGCATCAAGCGCTGGACATTGCTGACCTCAGAGAAG\nTCGAGGCCATGCAGAAGGGCCTGAGCATCCTTAACCACCTGGAGTTTTATATTAGAGCAG\nTAGCCTGAAAGCTCTCTCCTCAGTGATTGTGTCCAAAGGAATGATTTCACTTCCTTGGAA\nGCACTCAT----------------------------------------------------\n------------------------------------\n>LASV_NGA_2018_0664-2\n----------------------TTTAGAGATCTTTGTGTGAGTGGGCTTCATCAAGCCAT\nGGGACAAATCATAACATTTTTCCAGGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTCAGCCTTTTGGCAATACTGAAAGGGATCTACAATGTTGCCACCTG\nTGGCCTCTTTGGATTGGTGTCCTTTCTCCTCTTGTGTGGAAGATCATGCTCGACAACCTA\nTAAGGGTGTTTATGAGTTACAAACCCTAGAGCTAGACATGGCAAGCCTTAATATGACAAT\nGCCTTTATCTTGCACGAAGAACAACAGCCATCATTACATCATGGTCGGGAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATCATCAACCACAAGTTTTGTAACCTTTCTGA\nTGCACATAAAAAGAATCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTCCACTT\nATCCATTCCCAACTTTAATCAGTATGAAGCAATGAGTTGTGACTTCAATGGAGGAAAGAT\nAAGTGTTCAGTACAACCTTAGCCACACTTATGCTGTGGATGCAGCTAACCACTGTGGAAC\nCATTGCCAATGGCGTTCTTCAGACTTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAAGGGGAGTTGGGACTGCATAATGACTTCCTACCAATACTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAATTTTCTCGCCCATCCCCTATCGGTTATCT\nGGGGCTACTGTCACAAAGGACCAGGGATATTTACATCAGCCGAAGGCTTCTTGGAACTTT\nTACTTGGACTCTCTCTGATTCTGAAGGTAATGAGACACCGGGTGGGTATTGTCTAACAAG\nATGGATGTTGATTGAGGCCGAGCTGAAGTGCTTTGGGAACACAGCAGTTGCGAAGTGCAA\nTGAGAAACACGATGAGGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGC\nTATAAGGAGGCTGAAGACGGAAGCACAGATGAGTATCCAACTGATAAACAAAGCAGTAAA\nCGCACTAATCAATGACCAGCTGATCATGAAGAATCATTTGAGAGATATCATGGGAATTCC\nCTACTGCAATTACAGTAAATACTGGTATCTAAATCATACTGTGACAGGGAGGACATCACT\nGCCAAGATGCTGGCTTGTGTCAAATGGCTCCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAACTGTTGCAAAAGGAGTACATAGACAG\nGCAAGGGAAAACACCCTTAGGGTTGGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nCATTAGCATCTTCCTCCACCTGATTAAAATCCCAACCCATAGACATGTCATAGGGAAACC\nCTGCCCTAAACCACATAGACTCAACCACATGGGAATATGCTCATGTGGTCTGTACAAACA\nTCCTGGTGTACCAGTTAAATGGAAAAGATAAGAGACAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAATCCATTAAAGCACAGTGCGGGGTAATTTCT\nTCTTTGCCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTGTGCATATGGCATAGATCT\nTTGCATTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTGCTCAGTGAAATG\nTCAATAAGCTTTATGTCTCTTCTTCCTTGGGAGTCTAAGAGTCTCTTAATGTCATCTGAA\nCCTTGACAGGTCAGTACCATATTGCGAGGGAGGGCTTCAATAACTGCACTAGTCAAACCA\nGGTTGAGCAGGGAAAAGATCTGCTACATCAATCCCATGAGAATATTTGGCATCCTGCTTG\nAATTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGACATAGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTCTTGGCA\nCTTGGGTCAAGCTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAGGTCAGCCCT\nGTTGGGAACCCTGCTGACTGTAAAGACTTGTTGGACCCAACTGTGCCCACTTTTTGTAGT\nTTTCCATCTGGCTCGAGATCCACAGTGGTATTCTCCCAAGCTCTACCCACAATGGAAGTC\nCTTGAAGCTATGTAGGGCCAGCCGTCACCAGAAAGACAGATCTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTCTCACCAGGTGTATCTGAAACAAACATCCCTAGGGATTTTTTCACCTTT\nAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAGGCTCCAGCTTTCACTGCAGCTCCTAAGCTGAAGTTGTAA\nCCAGAAATGTTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAAAGTCTGTCTAGGTCAGAGCTATTTGGGTACTTAGCTGTGTATATTAGACCCAGGTCT\nGTTAGTGCCAGGACGGCATCATTTAGATCAACTTGACCTTGTTTGGTGAGACATGCTAGT\nGTCAAACTAGGCATGGTACCGAACTGATTGTTCAAAAGATCCGGATTCTTAACATCCCAC\nACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCTTGAGTCCCGCCAACCATGCCTATC\nATGTTCAGCAATGCTCTTCTTTGCTCAAGCTGCTGTGTACTCAAATTCCCCATGTAGACA\nCCTGAACTCAGTGGCCTTTCTGTCCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAATGTCAGCAGGTCATCTGAAGTCAAGGTCCCAACTCTCAGGATACTTTTTTGTTGT\nGTTGATTTGAGTTCAACAAGATTGTTGACAGCCTGATTCAGATCTCTGAGACGTTTCAGA\nTCACTATCATCCCTCTTTTGTTTGCGCATTAAACGCTGCACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGGGCCTGAGCATCTTTAACAACCTGAAGCTTTATACTGGAGCAA\nTAACCTGAAAGTTCCCTCCTTAATGATTGTGTCCAGAGAAATGACTTCACTTCCTTGGAA\nGCGCTCATCTTGATCTGAACACCTAGAGATTTACTGGTTGAAAGTATTACACAGTAAG--\n------------------------------------\n>LASV_NGA_2018_0959-2\n-------ATTTAGGATTGCGCTTTTAGAGATCTTTGTGTGAGTGGGCTTCATCAAGCCAT\nGGGACAAATCATAACATTTTTCCAGGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTCAGCCTTTTGGCAATACTGAAGGGGATCTACAATGTTGTTACCTG\nTGGCCTCTTTGGATTGGTGTCCTTCCTCCTCTTATGTGGAAGATCATGTTCAACAACTTA\nCAAGGGTGTTTATGAGCTACAAACTCTGGAGCTGGACATGGCAAGCCTTAATATGACAAT\nGCCCTTATCTTGCACGAAGAACAACAGCCACCATTACATCATGGTCGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATCATCAACCATAAATTTTGTAACCTCTCTGA\nTGCACATAAAAAGAATCTTTATGATCATGCTTTAATGAGTATCATTTCAACCTTCCACTT\nATCCATTCCAAACTTTAATCAGTATGAAGCAATGAGCTGTGACTTCAATGGGGGAAAGAT\nAAGTGTTCAGTACAACCTTAGCCACGCCTATGCTATAGATGCAGCCAACCACTGCGGGAC\nTATTGCCAATGGCGTTCTTCAAACTTTTATGAGGATGGCTTGGGGTGGCAGCTATATAGC\nACTTGATTCCGGAAAGGGGAGTTGGGACTGTATAATGACTTCCTACCAGTATTTGATAAT\nCCAAAACACCACTTGGGAAGATCATTGTCAGTTTTCTCGCCCATCCCCTATCGGTTACCT\nAGGGCTACTGTCACAAAGGACCAGGGACATTTACATCAGTCGAAGACTTCTTGGGACTTT\nTACTTGGACTCTCTCTGATTCTGAAGGTAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGCTGATTGAGGCCGAGTTGAAATGCTTTGGGAACACAGCAGTTGCGAAATGCAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGC\nTATAAGGAGGCTAAAGACAGAAGCACAGATGAGTATCCAGCTGATAAACAAAGCAGTGAA\nCGCACTGATCAATGACCAGCTGATTATGAAAAATCATTTGAGAGATATCATGGGGATTCC\nTTACTGCAATTACAGCAAGTACTGGTATCTAAATCATACTGTAACAGGGAAGACATCGTT\nGCCAAGGTGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAATATGATAACAGAACTGCTGCAAAAGGAGTACATAGACAG\nGCAAGGGAAAACACCTTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nCATTAGCATCTTCCTCCACCTGGTTAAAATCCCAACCCACAGACATGTCATAGGAAAACC\nCTGCCCTAAACCACACAGACTTAATCACATGGGCATATGTTCATGTGGTCTATACAAACA\nTCCTGGTGTGCCAGTCAAGTGGAAAAGATAGGAGACAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGACTT\nGAGGTTCTAAACACCATGTCCCTGGGGAGAACTGCCCTTAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAGTCCATTAAAGCACAGTGCGGGGTGATCTCT\nTCTTTGCCTCCTCTCTTCTTCTTTTCGACAACCACTCCAGTGTGCATATGGCATAGATCC\nTTACACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGTCTTGCTCAGTGCAATG\nTCAATAAGCTTTATATCCTTTCTTCCTTGGGAGTCTAAGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTTAGCACCATATTGCGAGGGAGGGCTTCAATGACTGCGCTGGTCAAACCA\nGGTTGAGCAGGGAAAAGATCTGCCACATCAATCCCATGAGAATATTTGGCATCTTGCTTG\nAATTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCTGACATAGGTTGG\nTAGAGGGCTATCTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTCTTGGCA\nCTTGGGTCAAGCTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAAGTCAGCCCT\nGTTGGGAACCCCGCTGACTGTAAAGACTTGTTGGACCCAGCAGTGCCTACTTTATGCGGT\nTTTCCATCTGACTCGAGATCCACAGTGGTATTCTCCCAAGCCCTACCCACAATGGAAGTC\nCTTGAAGCTATATAGGGCCATCCGTCACCGGAAAGACAGATCTTGTAAAGTATATTCTCA\nTAAGGGTTCCTCTCACCAGGTGTGTCCGAAACAAACATTCCCAAAGATTTTTTTACCTTT\nAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCTAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTTACTGCAGCTCCTAAGCTGAAGTTGAAA\nCCAGAAATGTTCAAAGAGCTCTTCTTTGTGTCCACCATATTCAGTATAGGATGGCTCTGG\nGAAAGTCTGTCCAGGTCGGAGCTATTTGGGTACTTGGCTGTGTATATTAGGCCCAGGTCT\nGTCAGTGCTAAGACGACATCATTCAAATCAACTTGACCTTGTTTGGTGAGACATGCCAAT\nGTCAGACTAGGCATGGTGCCGAACTGGTTGTTCAGAAGGTCCGGATTCTTAACATCCCAA\nACCCTAACAACTCCGTCTCTTCCAGGCTGGGTGCCCTGAGCCCCACCAACCATGCCTATC\nAAGTTCAGCAATGCCCTTCTCTGCTCAAGCTGCTGTGTACTCAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAGTGTCAGCAGGTCATCTGAGGTCAGGGTCCCAACTCTCAAGATGCTCTTTTGTTGT\nGTCGATTTAAGTTCTACAAGATTGTTGACAGCCTGATTCAAATCTCTGAGACGCTTCAGA\nTCACTATCATCCCTCTTTTGTTTGCGCATTAAGCGCTGCACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGTTTTATATTGGAGCAA\nTAACCTGAAAGCTCCCTCCTCAAAGACTGTGTCCAGAGAAATGACTTCACTTCCTTAGAA\nGCACTCATCTTGGTCTGGACACTTGGAGACTTACTGGTTGAAAGTATCACTCAGTAAGTC\nAATGAAAAGCGCAATCCAATAG--------------\n>LASV_NGA_2018_0998-2\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n--------------------------------ACTACATCATGGTTGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAACACAAGTATCATCAACCACAAGTTCTNNNACCTTTCTGA\nTGCACATAAAAAGNNNNNNNNNGACNNNNNNNNNNNNAGCATCATCTCAACCTTCCACCT\nATCCATCCCTAACTTTAATCAGTATGAAGCANNGAGTTGTGACTTCAATGGAGGAAAGAT\nAAGNGTTCAGTATAACCTCAGCCATGCTTATGCTGTGGATGCAGCTAACCATTGTGGGAC\nCATTGCCAATGGAGTCCTTCAAACTTTCATGAGGATGGCCTGGGGTGGCAGTTACATNNN\nNNNNNNNNNNNGAAAGGGGAGTTGGGATTGTATAATGACGTCCTACCAATATTTGATAAT\nCCAAAACATCAGTTGGGAAGATCACTGCCAGTTTTCTCGCCCATCCCCTATCGGTTATCT\nGGGGCTACTGTCACAAAGAACCAGGGACATTTACATCAGCCGAAGGCTCCTTGGAACTTT\nTACTTGGACTCTCTCTGACTCTGAGGGCAATGAAACACCGGGTGGGTATTGTTTAACAAG\nNNNNNNNNNNNNNNNNNNNNNNNNNNAGTGCTTTGGGAACACAGCAGTTGCGAAATGCAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGGTTGTTTGACTTTAACAAACAGGC\nTATAAGGAGGCTAAAGACAGAAGCACAGATGAGTATCCAACTAATAAATAAAGCAGTGAA\nCGCATTGATCAATGACCAGCTCATTATGAAGAATCATTTAAGAGATATCATGGGAATTCC\nTTACTGCAATTACAGCAAGTATTGGTACTTAAACCACACTGTAACAGGGAAGACATCGTT\nGCCAAGATGCTGGCTTGTATCAAATGGTTCCTACCTAAATGAAACACATTTTTCTGATGA\nCATTGAGCAACAAGCAGACAACATGATAACAGAATTGTTACAGAAAGAGTACATTGACAG\nGCAAGGGAAAACACCCTTAGGGTTGGTGGATCTTTTTGTCTTCAGCACTAGCTTCTACCT\nTATTAGCATCTTCCTCCACCTAGTCAAAATCCCTACCCACAGACATGTCATAGGGAAGCC\nCTGCCCCAAGCCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTGTACAAACA\nTCCTGGTGTACCAGTCAAGTGGAAAAGATAGGAGATAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGATGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTCAAAGTTGGAATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAATCCATTAGAGCACAGTGTGGGGTGATTTCT\nTCTTTACCTCCTCTTTTCTTCTTTTCAACAACCACCCCAGTGTGCATATGGCATAGATCC\nTTGCATTGATCCCAGACAGCATTCTCAAACCTCCTAGAGTCAGCCTTGCTCAGTGCAATG\nTCAATAAGCTTTATGTCCCTTCTTCCTTGTGAATCTAAGAGTTTCTTGATGTCGTCTGAA\nCCCTGACAGGTCAGTACCATATTGCGAGGAAGGGCTTCAATGACTGCACTGGTCAAGCCA\nGGTTGAGCAGGGAAAAGATCTGCCACATCAATCCCATGAGAATATTTGGCATCTTGCTTG\nAACTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAGCAGCCCGACATAGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCTATGTCTATCCAGGTTTTGGCA\nCTTGGATCAAGCTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAGTAGGTCAACCCT\nGTTGGAAACCCCGCTGACTGTAAAGACTTGTTGGACCCAGCAGTGCCCATCTTTTGTGGT\nTTTCCATCTGACTCGAGATCCACAGTGGTGTTCTCCCAAGCTCTACCCACAATGGAAGTT\nCTTGAAGCTATGTAGGGCCAACCGTCCCCAGAAAGACAGATCTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTCTCACCAGGTGCATCTGAAACGAACATTCCCAAAGATCTNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNTATTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCCCAC\nACCCTAACAACTCCGTCCCTTCCAGGTTGGGTGCCCTGAGCCCCGCCAACCATACCTATC\nATGTTCAGCAATGCTCTTCTTTGCTCAAGTTG----------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------------\n>LASV_NGA_2018_1024-2\n----------------------TTTAGAGATCTTTGTGTGAGTGGGCTTAATTAAGCCAT\nGGGACAAATCATAACATTTTTCCAGGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTTTTGATTGCTCTCAGCCTTCTGGCAATACTGAAAGGGGTCTACAATGTTGCTACCTG\nTGGCCTCTTTGGATTGGTGTCTTTTCTTCTCTTATGTGGAAGATCATGCTCAACAACTTA\nCAAGGGCGTTTATGAGTTGCAAACTCTAGAGCTAGACATGGCAAACCTTAACATGACAAT\nGCCCTTATCTTGCACGAAGAATAACAGCCACCATTACATCAGGGTCGGAAATGAGACTGG\nTCTGGAGCTGACTTTAACAAACACGAGCATCATCAACCACAAGTTTTGTAACCTTTCTGA\nTGCACATAAAAATAATCTTTATGACCATGCTTTAATGAGTATCATCTCAACTTTCCACTT\nATCCATTCCTAACTTTAATCAGTATGAGGCAATGAGTTGTGACTTCAATGGGGGGAAGAT\nAAGTGTTCAGTACAACCTCAGCCACGCTTATGCTGTGGATGCAGCTAACCATTGTGGGAC\nCATTGCCAATGGCGTTCTTCAAACTTTTATGAGAATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAGGGGGAGTTGGGATTGTATAATGACTTCCTACCAATACTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGTCCATCCCCTATCGGTTATCT\nGGGGCTACTGTCACAGAGGACCAGGGACATTTACATCAGTCGGAGGCTTCTTGGGACTTT\nTACTTGGACTCTCTCTGATTCTGAAGGTAATGAAACACCGGGTGGATATTGTCTAACAAG\nGTGGATGCTGATTGAGGCTGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCAAAATGCAA\nCGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGC\nTATAAGGAGGCTGAAAACAGAAGCACAAATGAGTATCCAACTGATAAACAAAGCAGTGAA\nCGCACTGATTAATGACCAGCTGATCATGAAGAATCATTTAAGAGATATCATGGGAATTCC\nTTATTGCAATTACAGCAAGTATTGGTACTTAAATCACACTGTAACAGGGAAGACATCGTT\nGCCAAGATGCTGGCTTGTATCAAATGGTACCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAATATGATAACAGAACTGTTGCAGAAGGAGTACATGGACAG\nGCAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nCATTAGCATCTTCCTCCATCTGGTTAAGATCCCAACCCACAGACATGTCATAGGGAAACC\nCTGCCCTAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTATACAAACA\nTCCTGGTGTACCAGTCAAGTGGAAGAGATAGGAGACAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTGAACACCATGTCTCTAGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAGTCCATTAAAGCACAATGTGGGGTGATTTCT\nTCTTTGCCCCCTCTTTTCTTCTTTTCGACAACCACCCCAGTGTGCATGTGGCACAGATCT\nTTGCATTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTGCTCAGTGCAATG\nTCAATAAGCTTTATGTCCCTTCTTCCTTGGGAATCCAAGAGTCTCTTGATATCATCTGAA\nCCTTGACAGGTCAGTACCATATTGCGAGGGAGGGCTTCAATAACTGCACTGGTCAAGCCA\nGGTTGAGCAGGGAAAAGATCTACTACATCAATCCCATGGGAGTATTTGGCATCTTGTTTG\nAATTGTTTTAAGTCTGTTGGTTCTCTGAAGAAGTGTATATAACAGCCCGACATAGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTTTTGGCA\nCTTGGGTCAAGCTGCATCATTGAATCCTTAAGTGTCATCAGCTGAGAGTAGGTCAGCCCT\nGTTGGAAACCCCGCTGACTGCAAAGACTTGTTAGACCCAGCAGTGCCCACCTTTTGTGGT\nTTTCCATCTGATTCGAGATCCACAGTAGTATTCTCCCAAGCTCTACCCACAATAGAAGTC\nCTGGAAGCTATGTAGGGCCAGCCGTCACCGGAAAGACAGATCTTATAAAGTATGTTCTCA\nTAAGGGTTTCTCTCACCAGGCGTATCTGAGACAAACATTCCCAAGGATTTTTTCACCTTT\nAAAATAGACTTCAGGATACCATCTATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCTCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCTCCTAAACTGAAGTTGTAA\nCCAGAAATATTCAAAGAGCTTTTCTTGGTGTCCACCATGTTCAGTATGGGATGACTTTGG\nGAAAGTCTATCCAGGTCGGAGCTATTTGGGTACTTGGCTGTGTATATTAAACCCAGGTCT\nGTTAGTGCTAAAACGGCATCATTTAAATCAACTTGACCTTGTTTAGTGAGACATGCTAAT\nGTCAGACTGGGCATGGTGCCAAACTGGTTGTTCAAGAGATCCGGATTTTTAACATCCCAC\nACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAATGCTCTCCTTTGCTCAAGTTGCTGTGTACTCAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTGATGACCTTTGACTTTAGCTTCTCTAAATCAGCT\nGCTAATGTCAGCAGGTCATCTGAGGATAAGGTCCCAACTCTTAAGACACTCTTTTGTTGT\nGTTGATTTGAGTTCCACAAGATTGTTGACAGCCTGATTCAGATCTCTAAGACGCTTCAGA\nTCACTATCATCCCTTTTCTGCTTACGCATTAAGCGTTGCACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGTGCATCTTTAACAACTTGAAGCTTTATGCTGGAGCAA\nTAACCTGAAAGCTCCCTTCTCAATGACTGTGTCCAGAGGAATGATTTTACTTCCTTAGAA\nGCACTCATCCTGGTCTGAACACTTAGGGACTTGCTGGTTGAATGTATCACTC--------\n------------------------------------\n>LASV_NGA_2018_1079-2\n------CATTTAGGATTGCGCTTTTAGAGATCTTTGTGTGAGTGAGCTTCATCAAGCCAT\nGGGACAAATCATAACATTTTTCCAGGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTTAGCCTTCTGGCAATACTGAAAGGGATCTACAATGTTGCCACCTG\nTGGCCTCTTTGGATTGGTGGCCTTTCTCCTCTTGTGTGGGAGATCATGCTCGACAACCTA\nCAAGGGTGTTTATGAGCTACAAACCCTAGAGCTAGACATGGCAAGCCTCAATATGACAAT\nGCCTTTATCTTGCACGAAGAACAACAGCCATCATTACATCATGGTCGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATTATTAACCACAAGTTTTGTAACCTTTCTGA\nTGCACATAAAAAGAATCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTTCACTT\nATCCATTCCCAACTTTAATCAGTATGAAGCGATGAGTTGTGACTTCAATGGAGGAAAGAT\nAAGTGTTCAGTACAACCTTAGCCACACTTATGCTGTAGATGCAGCTAACCACTGTGGAAC\nCATTGCCAATGGTGTTCTTCAGACTTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAAGGGGAGCTGGGACTGCATAATGACTTCCTACCAATATTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAATTTTCTCGCCCATCCCCTATCGGTTACCT\nGGGGCTACTGTCACAAAGGACCAGGGATATTTACATCAGCCGAAGGCTTCTTGGGACTTT\nTACCTGGACTCTCTCTGACTCTGAAGGTAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGCTGATTGAGGCCGAGCTGAAGTGCTTTGGGAACACAGCAGTTGCGAAGTGCAA\nTGAGAAACACGATGAAGAGTTTTGTGACATGTTAAGGTTGTTTGACTTTAACAAACAAGC\nTATAAGGAGGCTGAAAACGGAAGCACAGATGAGCATCCAACTGATAAACAAAGCAGTGAA\nCGCACTAATCAATGACCAGCTGATCATGAAGAATCATTTAAGAGATATCATGGGAATTCC\nCTACTGCAATTACAGCAAATACTGGTATCTAAATCATACTGTGACAGGGAGAACATCACT\nGCCAAGGTGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAGACACATTTCTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAACTGTTGCAAAAGGAGTACATGGACAG\nGCAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nCATTAGCATCTTCCTCCACCTGATTAAAATCCCAACCCATAGACATGTCATAGGGAAACC\nCTGCCCTAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTGTACAAACA\nTCCTGGTGTACCAGTTAAGTGGAAAAGATAGGAGATAGACCCACCCACGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAATCCATTAAAGCACAGTGCGGGGTAATTTCT\nTCTTTACCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTATGCATATGGCATAGATCT\nTTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTGCTCAGTGAAATG\nTCAATGAGCTTTATGTCTCTTCTTCCTTGGGAGTCTAAGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTCAGTACCATATTGCGAGGGAGGGCTTCGATGACTGCACTAGTCAAACCA\nGGTTGAGCAGGGAAAAGATCTGCTACATCAATCCCATGAGAATATTTGGCATCCTGCTTG\nAATTGTTTTAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGATATGGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTTTTGGCA\nCTTGGGTCAAGCTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAGGTCAGCCCT\nGTTGGAAACCCTGCTGACTGTAAAGACTTGTTGGACCCAGCTGTGCCCACTTTTTGTGGT\nTTTCCATCTGACTCGAGATCCACAGTGGTATTCTCCCAAGCTCTACCTACAATGGAAGTC\nCTTGAAGCTATATAGGGCCAGCCGTCACCAGAAAGACAGATCTTGTAAAGTATATTCTCA\nTAAGGGTTCCTCTCACCAGGTGTATCTGAAACAAACATTCCTAAGGATTTTTTCACCTTT\nAAAATAGACTTCAGGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCTCCTAAGCTGAAGTTGTAA\nCCAGAAATGTTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAAAGTCTGTCTAGGTCAGAGCTATTTGGGTACTTAGCTGTGTATATCAGACCTAGGTCT\nGTTAGTGCCAGGACGGCATCATTTAGATCAACTTGACCTTGTTTGGTGAGACATGCTAAT\nGTCAAACTAGGCATGGTGCCGAACTGGTTGTTCAGAAGATCCGGATTCTTAACATCCCAC\nACCCTGACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGGGTTCCACCAACCATGCCTATC\nATGTTCAGCAATGCTCTTCTTTGCTCAAGCTGTTGTGTGCTCAAATTCCCCATATAAACA\nCCTGAGCTCAATGGCCTTTCTGTCCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAATGTCAGCAGATCATCTGAAGTCAAGGTCCCAACTCTCAGGATACTCTTTTGTTGT\nGTTGATTTGAGTTCAACAAGATTGTTGACAGCCTGATTCAGATCTCTGAGACGTTTCAGA\nTCACTGTCATCCCTTTTTTGTTTGCGCATTAAACGCTGCACATTGCTGACTTCAGAAAAG\nTCAAGGCCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGCTTTATATTGGAGCAA\nTAACCTGAAAGTTCCCTCCTTAATGACTGTGTCCAGAGAAATGACTTCACTTCCTTGGAA\nGCACTCATCTTGGTCTGGACGCTTAGAGATTCACTGGTTGAAAATATTACCCAGTAAGTC\nAATGAAAAGCGCAATCCAATAGCC------------\n>LASV_NGA_2018_1177-2\n---AGGCATTTAGGATTGCGCTTTTAGAGATCTTTGTGTGAGTGGGCTTTATTAAGCCAT\nGGGACAAATTATAACATTTTTCCAGGAAGTACCTCATGTTATAGAAGAAGTGATGAACAT\nTGTCCTGATTGCCCTCAGCCTTCTGGCAATATTGAAAGGGATCTACAATGTTGCTACCTG\nTGGCCTCTTTGGATTGGTGTCCTTCCTTCTCTTATGTGGAAGATCATGCTCAACAACTTA\nCAAAGGTGTTTATGAGCTGCAAACTCTAGAGCTGGACATGGCAAGCCTTAACATGACAAT\nGCCCTTATCCTGCACAAAAAATAACAGCCACCATTACATCAGGGTTGGAAATGAGACTGG\nCTTAGAGTTGACTTTAACAAATACAAGTATCATCGACCACAAGTTCTGTAACCTTTCTGA\nTGCACATAAAAAGAACCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTCCACTT\nATCCATTCCTAACTTTAATCAGTATGAAGCAATGAGTTGTGACTTCAATGGGGGGAAGAT\nAAGTGTTCAGTACAACCTTAGCCACACTTACGCTGTAGATGCAGCTAACCACTGTGGGAC\nTATTGCTAATGGCGTTCTCCAGACTTTCATGAGGATGGCTTGGGGTGGTAGTTACATAGC\nACTTGATTCCGGAAAAGGAAGCTGGGATTGCATAATGACTTCCTACCAATATTTGATAAT\nCCAGAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGCCCATCCCCTATCGGTTATCT\nGGGGCTGCTGTCACAAAGGACCAGGGACATTTACATCAGTCGAAGACTCCTTGGGACTTT\nTACTTGGACCCTCTCTGATTCTGAAGGCAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGCTGATTGAGGCCGAATTGAAGTGCTTTGGAAACACAGCAGTTGCGAAATGCAA\nTGAGAAACATGATGAGGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGC\nTATAAGGAGGCTGAAGACAGAAGCACAGATGAGTATCCAACTGATAAACAAAGCAGTGAA\nCGCACTGATCAATGACCAGCTGATTATGAAGAATCATTTAAGAGATATCATGGGAATTCC\nTTACTGCAATTACAGCAAGTACTGGTATTTAAATCACACTATAACAGGGAGGACATCGTT\nACCAAGATGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAACTGTTGCAGAAGGAGTACATGGATAG\nGCAAGGGAAAACACCCTTGGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGTTTTTATCT\nCATTAGCATCTTTCTCCACCTAGTTAAAATCCCAACTCACAGACATGTTATAGGAAAACC\nCTGCCCTAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTGTACAAACA\nTCCTGGTGTACCAGTCAAATGGAAAAGATAGGAGACGGACCCATCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTAAACACCATGTCCCTGGGGAGGACTGCTCTCAGAACTGGTATATTAAGACCT\nCCTGACACAGCTGCATCATACATTATGCAGTCCATTAGAGCACAGTGTGGGGTAATTTCT\nTCTTTGCCTCCTCTTTTCTTCTTTTCGACGACCACTCCAGTGTGCATATGGCATAGATCT\nTTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTGTTCAGTGCAATG\nTCAATAAGTTTTATGTCCCTTCTTCCTTGGGAATCCAAGAGTCGCTTAATATCATCTGAA\nCCTTGACAGGTCAGTACCATATTGCGAGGGAGAGCTTCAATGACTGCACTGGTTAATCCA\nGGTTGAGCAGAGAAAAGATCTGTTACATCAATCCCATGAGAATATTTGGCATCTTGCTTG\nAACTGTTTTAAGTCTGTTGGTTCTCTGAAGAAGTGTATATAGCAGCCCGACATAGGCTGG\nTAAAGAGCTATCTCCACAGGGTCTTCTGGACGACCCTCAATGTCTATCCAGGTTTTGGCA\nCTTGGGTCAAGTTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAAGTCAGCCCT\nGTTGGAAACCCCGCTGACTGTAAAGACTTGTTGGATCCAGCAGTTCCCACTTTTTGTGGT\nTTTCCATCTGACTCAAGATCTACAGTAGTATTTTCCCAAGCTCTACCTACAATAGAAGTC\nCTTGAAGCGATGTAGGGCCAGCCGTCACCGGAAAGACAGATCTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTTTCACCAGGTGTATCTGAAACAAACATTCCTAAGGATTTTTTTACCTTT\nAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTTTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCCCCTAAACTAAAGTTGTAA\nCCAGAGATGTTCAAAGAGCTCTTCTTAGTGTCCACCATATTCAATATAGGATGGCTTTGG\nGAAAGTCTGTCCAGGTCAGAGCTATTAGGATACTTAGCTGTGTATATTAGACCCAGGTCT\nGTCAGTGCTAAGACGGCATCATTCAAATCAACCTGACCCTGTTTAGTGAGACATGCTAAT\nGTCAAACTGGGCATGGTGCCGAATTGGTTGTTCAAAAGATCTGGATTCTTAACATCCCAC\nACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAATGCCCTTCTTTGCTCAAGTTGCTGTGTACTCAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTGATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAATGTCAGCAGGTCATCTGAGGTCAAAGTCCCAACTCTCAAGATACTCTTTTGTTGT\nGTTGATTTGAGTTCTACAAGATTGTTGACAGCCTGATTCAGATCTCTGAGACGTTTCAGA\nTCACCATCATCCCTCTTTTGTTTGCGCATCAAGCGCTGCACATTGCTAACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCTTGAGCATCCTTAACAACTTGAAGCTTTATGTTGGAGCAA\nTAACCTGAAAGCTCCCTCCTCAATGACTGTGTCCAGAGAAATGACTTCACTTCCTTAGAA\nGCACTCATCTTGATCTGGACACTTTGAGGTTTGCTGGCTGAAAGTATCACTCAGTGAGTC\nAAAGAAAAGCGCAATCCAATAGCCTAGGATCC----\n>LASV_NGA_2018_1375-2\n--------------------CTTTTAGAGATCTTTGTGTGAGTGAGCTTCATTAAGCCAT\nGGGACAAATCATAACATTTTTCCAGGAAGTACCTCATGTTATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTCAGCCTTCTGGCAATACTGAAGGGGATCTACAATATTGCTACCTG\nTGGCCTCTTTGGATTGGTGTCCTTTCTCCTCTTATGTGGAAGATCATGTTCAACAACTTA\nCAAGGGTGTTTATGAGCTACAAACTCTGGAGCTAGACATGGCAAGCCTTAATATGACAAT\nGCCCTTATCTTGCACGAAGAACAACAGCCACCATTACATCATGGTCGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATCATCAACCACAGGTTTTGTAATCTCTCTGA\nTGCACATAAAAAGAATCTTTATGATCATGCTTTAATGAGTATCATTTCAACCTTCCACTT\nATCCATTCCTAACTTTAATCAGTATGAAGCAATGAGCTGTGACTTCAATGGGGGAAAGAT\nAAGTGTTCAGTACAACCTTAGCCACGCTTATGCTGTAGATGCAGCCAACCACTGTGGGAC\nCATCGCCAATGGCGTTCTTCAGACTTTTATGAGGATGGCTTGGGGTGGCAGTTATATAGC\nACTTGATTCCGGAAAGGGGAGTTGGGACTGTATAATGACTTCCTACCAATATTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGCCCATCCCCTATCGGTTACCT\nGGGGCTATTGTCACAGAGGACCAGGGACATTTACATCAGTCGAAGGCTCCTTGGGACTTT\nTACTTGGACTCTCTCTGATTCTGAAGGTAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGCTGATTGAGGCCGAGTTGAAATGCTTTGGGAACACAGCAGTTGCGAAATGCAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAATAAACAAGC\nTATAAGGAGGCTGAAGACGGAAGCACAGATGAGTATCCAGCTGATAAACAAAGCAGTGAA\nCGCACTGATCAATGACCAGCTGATTATGAAGAATCATTTGAGAGATATCATGGGGATTCC\nTTACTGCAATTACAGCAAGTACTGGTATCTAAATCATACTGTAACAGGGAAGACATCGTT\nGCCAAGGTGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAATATGATAACAGAACTGCTGCAAAAGGAGTACATAGACAG\nGCAAGGAAAAACACCTTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nCATTAGCATCTTCCTCCACCTGGTCAAAATCCCAACCCACAGACATGTCATAGGAAAACC\nCTGCCCTAAACCACACAGACTTAACCACATGGGCATATGTTCATGTGGTCTATACAAACA\nTCCTGGTGTGCCAGTCAAGTGGAAAAGATAGGAGACGGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGACTT\nGAGGTTCTGAACACCATGTCCCTGGGGAGAACTGCCCTTAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAGTCCATTAAAGCACAGTGTGGGGTGATTTCT\nTCTTTGCCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTGTGCATATGGCATAGATCT\nTTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTGCTCAGTGCAATG\nTCAATAAGCTTTATATCCCTTCTTCCTTGGGAGTCCAAGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTTAGCACCATATTGCGAGGGAGGGCTTCAATGACTGCGCTGGTCAATCCA\nGGTTGAGCAGGGAAAAGATCTGCCACATCAATCCCATGAGAATATTTGGCATCTTGCTTG\nAACTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATATAACAGCCTGACATAGGTTGG\nTAAAGGGCTATCTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTTTTGGCA\nCTTGGGTCAAGCTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAAGTCAGCCCT\nGTTGGGAACCCCGCTGACTGTAAAGACTTGTTGGACCCAGCAGTGCCCACTTTATGCGGT\nTTTCCATCTGACTCGAGATCCACAGTGGTATTCTCCCAAGCCCTACCCACAATAGAAGTC\nCTTGAAGCTATGTAGGGCCATCCGTCACCGGAAAGACAGATCTTGTAAAGTATATTCTCA\nTAAGGGTTCCTCTCACCAGGTGTGTCCGAAACAAACATTCCCAAAGATTTTTTTACCTTT\nAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTGATCCTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCTCCTAAGCTGAAGTTGAAA\nCCAGAAATATTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAAAGTCTGTCCAGGTCGGAGCTATTTGGGTACTTGGCTGTGTATATTAGGCCCAGGTCT\nGTCAGTGCTAAGACAGCATCATTCAAATCGACTTGGCCTTGTTTGGTGAGACATGCCAAT\nGTCAGACTAGGCATGGTGCCGAACTGGTTGTTCAAAAGGTCTGGATTCTTAACATCCCAA\nACCCTGACAACTCCGTCTCTCCCAGGTTGAGTGCCCTGAGCCCCACCAACCATGCCTATC\nAAGTTCAGCAATGCTCTTCTCTGCTCAAGCTGCTGTGTGCTCAAGTTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGATTTCAGTTTCTCTAAGTCAGCT\nGCCAATATCAGCAGGTCATCTGAGGTCAAGGTCCCAACTCTCAAGATACTCTTTTGTTGT\nGTCGATTTAAGTTCTACAAGATTGTTGACAGCTTGATTCAAATCTCTGAGACGTTTCAGA\nTCACTGTCATCCCTCTTTTGTTTGCGCATTAAGCGCTGCACATTGCTAACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGTTTTATGTTGGAGCAA\nTAGCCTGAAAGCTCCCTCCTCAAGGACTGTGTCCAGAGAAATGACTTCACTTCCTTAGAA\nGCACTCATCTTGGTCTGGACACTTGGGAATTTACTGGTTGAAAGTATCACTCAGTAAGTC\n------------------------------------\n>LASV_NGA_2018_1381-2\n---------------------------------TTATGTGAGTGGGCTTCATCAAGCCAT\nGGGACAAATTGTAACATTTTTCCAGGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCTTGATTGCTCTCAGCCTTCTGGCAATACTGAAAGGGATCTACAATGTTGCTACCTG\nTGGCCTCTTTGGATTGGTATCCTTTCTTCTCTTGTGTGGAAGATCATGCTCAACAACTTA\nCAAGGGTGTTTATGAGCTACAAACTCTAGAGCTAGACATGGCAAGCCTTAATATGACAAT\nGCCCTTATCTTGCACGAAGAACAACAGCCACCATTACATCATGGTCGGAAATGAGACTGG\nCTTAGAGCTGACCTTAACAAATACAAGTATTATCAACCACAAGTTTTGCAACCTTTCTGA\nTGCACATAAAAAGAACCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTCCACTT\nATCCATTCCCAACTTTAATCAGTATGAAGCAATGAGTTGTGACTTCAATGGGGGGAAGAT\nAAGTGTTCAGTACAACCTTAGCCACACTTATGCTGTAGATGCAGCCAACCACTGTGGGAC\nTATCGCCAATGGCGTCCTTCAGACCTTTATGAGGATGGCTTGGGGAGGCAGCTACATAGC\nACTTGATTCCGGAAAGGGGAGTTGGGACTGTATAATGACTTCCTACCAATATTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGCCCATCCCCTATCGGTTACCT\nGGGGTTGTTGTCACAAAGGACCAGGGACATTTACATCAGTCGAAGACTTCTTGGGACTTT\nTACTTGGACTCTTTCTGATTCTGAAGGCAATGAGACACCGGGTGGGTATTGTCTAACAAG\nGTGGATGCTGATTGAGGCCGAATTGAAGTGCTTTGGGAACACAGCGGTTGCGAAATGCAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGACTGTTTGACTTTAACAAACAAGC\nCATAAGGAGGCTGAAGACGGAAGCACAGATGAGTATCCAACTAATAAACAAAGCAGTGAA\nCGCACTGATCAATGACCAGTTGATCATGAAAAATCATTTAAGAGATATCATGGGAATTCC\nTTACTGCAATTACAGCAAGTACTGGTATCTAAATCACACTGTAACAGGGAAGACATCGCT\nGCCAAGATGTTGGCTTGTGTCAAATGGTTCCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAGCAAGCAGACAACATGATAACAGAACTGTTGCAAAAGGAGTACATGGACAG\nGCAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nCATCAGTATCTTCCTCCACTTGGTTAAAATTCCAACCCACAGACATGTTGTAGGGAAGCC\nTTGCCCTAAACCACACAGACTTAATCACATGGGTATATGCTCATGTGGTCTGTACAAACA\nTCCTGGTGTACCAGTCAGATGGAAAAGATAAGAGATAGACCCATCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTA\nGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAGTCCATTAAAGCACAGTGCGGGGTAATTTCT\nTCTTTACCTCCTCTTTTCTTCTTCTCGACAACCACTCCAGTGTGCATATGGCACAGGTCT\nTTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTGCTCAGTGCAATG\nTCAATAAGCTTTATGTCTCTTCTTCCTTGGGATTCAAGGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTCAGTACCATATTGCGAGGGAGGGCTTCAATGACTGCACTGGTCAAACCA\nGGTTGAGCAGGGAAAAGATCTGCTACATCAATTCCATGAGAATATTTGGCATCTTGCTTA\nAACTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGACATAGGCTGG\nTAAAGAGCTATTTCTACGGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTTTTGGCA\nCTTGGGTCAAGCTGCATCATTGAATCCTTAAGTGTCATCAACTGAGAATAGGTCAGCCCT\nGTTGGAAACCCCGCTGACTGTAGAGACTTGTTGGACCCAGTATTGCCTATCTTTTGTGGC\nTTTCCATCTGACTCGAGATCCACAGTGGTATTCTCCCAAGCTCTACCCACAATGGAAGTC\nCTTGAAGCTATGTAGGGCCAGCCGTCACCGGAAAGACAGATCTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTCTCACCAGGTGTATCTGAAACAAACATTCCCAAGGATCTTTTTACCTTC\nAAAATAGACTTCAGGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCCCCTAAGCTGAAGTTGTAA\nCCAGAAATGTTCAAGGAGCTCTTCTTAGTGTCTACCATATTTAGTATGGGATGACTTTGG\nGAAAGCCTGTCTAGGTCGGAGCTATTTGGGTACTTAGCTGTGTATATTAGACCCAGGTCT\nGTTAGTGCTAAGACAGCATCATTCAAATCAACTTGACCTTGTTTGGTGAGACATGCTAAT\nGTCAGACTAGGCATGGTGCCAAACTGATTGTTCAAAAGATCCGGATTCTTAACATCCCAC\nACCCTAACAACTCCATCTCTTCCAGGCTGGGTGCCCTGGGCCCCACCAGCCATGCCTATC\nATGTTCAGCAATGCTCTTCTTTGCTCAAGTTGCTGTGTACTCAGGTTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAATGTCAACAGGTCATCTGAGGTTAGAGTCCCAACTCTCAAGATGCTCTTTTGTTGT\nGTTGATTTGAGTTCTACAAGATTGTTGACAGCCTGATTCAGATCTCTGAGACGTTTCAGA\nTCACTATCATCTCTTTTTTGCTTGCGCATTAAGCGCTGCACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGCTTTATGCTGGAGCAA\nTAACCTGAAAGTTCCCTCCTCAGTGACTGTGTCCAGAGAAATGACTTCACTTCCTTGGAA\nACACTCATCTTGGTCTGGAAACCCAGAGATCCACTGGTTGAAAGTATCACAC--------\n------------------------------------\n>LASV_NGA_2018_1392-2\n------------------------------------------------------------\n-----------------------------------------------------TGAACAT\nTGTTCTGATTGCTCTCAGCCTTCTGGCAATACTGAAAGGAATCTACAATGTTGCCACCTG\nTGGCCTCTTTGGATTGGTATCCTTTCTCTTCTTGNNNNNNAGATCATGCTCAACAACTTA\nCAAGGGTGTCTATGAGCTACAAACTCTAGAGTTAGACATGGCAAACCTTAACATGACAAT\nGCCCTTATCTTGCACGAAGAACAACAGCCACCATTATATCATGGTCGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATTATCAACCACAAGTTCTGTAACCTTTCTGA\nTGCACATAAAAAGAATCTTTATGACCATGCCTTAATGAGTATCATCTCAACCTTCCACTT\nATCCATCCCTAACTTTAATCAGTATGAAGCAATGAGTTGTGACTTCAATGGGGGAAAGAT\nAAGTGTTCAGTACAACCTTAGCCACACTTATGCTGTAGATGCAGCCAATCACTGTGGGAC\nTATCGCCAATGGCGTTCTCCAGACCTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAAAGGGAGTTGGGATTGTATAATGACTTCCTACCAGTATTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGTCCATCCCCTATCGGCTATCT\nGGGGCTACTGTCACAAAGGACCAAGGACATTTACATCAGTCGAAGACTTCTAGGGACTTT\nTACTTGGACTCTCTCTGATTCTGAAGGTAATGAAACACCGGGTGGGTATTGTTTAACAAG\nATGGATGTTGATTGAGGCCGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCGAAATGCAA\nTGAGAAACATGATGAAGAGTTTTGTGATATGTTGAGATTGTTTGACTTTAACAAACAAGC\nTATAAGGAGGCTAAAGACAGAAGCACAGATGAGTATCCAACTGATAAACAAAGCAGTGAA\nCGCACTGATCAATGACCAGCTGATCATGAAGAATCATTTGAGAGACATCATGGGAATTCC\nTTACTGCAACTACAGCAAGTACTGGTATCTGAATCACACTGTAACAGGGAAGACATCGTT\nGCCAAGGTGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAGACACATTTTTCTGATGA\nCATTGAACAACAAGCGGACAACATGATAACAGAACTGTTGCAAAAGGAGTACATGGACAG\nACAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGCTTTTATCT\nCATTAGCATCTTCCTCCACCTGGTAAAAATCCCAACCCACAGACATGTCATAGGGAAACC\nTTGCCCTAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTATATAAACA\nTCCTGGTGTGCCAGTGAAGTGGAAAAGATAGGAGACAAACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATNNNNNNNNNGANNNNNNNNNNN\nNNNNNNNNNNNNACCATGTCCCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCT\nCCTGACACAGCTGCATCATACATTATGCAATCCATCAAAGCACAGTGTGGGGTAATCTCT\nTCTTTGCCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTGTGCATATGGCATAGATCT\nTTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGTCTTGCTCAGTGCAATG\nTCAATAAGTTTTATGTCCCTTCTTCCTTGGGAATCTAAGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTCAGTACCATATTGCGAGGGAGGGCTTCAATGACTGCGCTGGTCNNNCCA\nGGTTGAGCAGGGAAAAGGTCTGCCACATCAATTCCATGAGAATACTTGGCATCTTGCTTG\nAACTGTTTCAAGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGACACAGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCAATGTCTATCCAGGTTTTGGCA\nCTTGGGTCAAGCTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAGGTCAGCCCT\nGTTGGGAACCCCGCTGACTGTAAAGACTTGTTGGACCCAGCAGTGCCCACTTTTTGTGGT\nTTTCCATCTGACTCGAGATCCACAGTAGTATTCTCCCAAGCTCTACCCACAATAGAAGTT\nCTTGAAGCTATGTAGGGCCAGCCGTCACCAGAAAGACAGATCTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTCTCACCAGGCGTATCTGAAACAAACATTCCCAAAGATTTTTTTACCTTC\nAAAATGGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCCTTTACTGCAGCTCCCAAGCTGAAGTTGTAA\nCCAGAAATGTTCAAGGAGCTTTTCTTAGTGTCCACCATGTTCAGTATAGGATGGCTTTGG\nGAAAGTCTATCCAAGTCGGAGCTGTTTGGGTACTTAGCTGTGTATATTAGACCCAGGTCC\nGTTAGTGCTAAGACAGCATCATTCAAATCAACTTGACCTTGTTTGGTAAGACATGCTAAA\nGTCAGACTAGGCATGGTGCCGAACTGGTTGTTCAGAAGATCCGGATTCTTAACATCCCAC\nACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAATGCTCTTCTCTGCTCAAGCTGTTGTGTACTCAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTAGACTTTAGTTTCTCCAAGTCAGCT\nGCCAGTGTCAGCAGGTCATCTGAGGTCAAGGTGCCAACTCTCAAGATACTCTTCTGTTGT\nGTCGATTTAAGTTCTACAAGATTGTTGACAGCCTGATTCAAATCTCTGAGACGTTTCAGA\nTCACTGTCATCCCTCTTTTGTTTGCGCATTAAGCGCTGTACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGGGCCTGAGCATCCNTTACAACTTGAAGTTTTATGTTTGAGCAA\nTAACCTGAAAGCTCCCTCCTC---------------------------------------\n------------------------------------------------------------\n------------------------------------\n>LASV_NGA_2018_1643-2\n------------------------------------------TGGGTTTCATTAAGCCAT\nGGGGCAAATCATAACATTTTTCCAGGAAGTGCCTCATGTCATTGAGGAGGTGATGAACAT\nTGTCTTAATTGCTCTCAGCCTTCTAGCAATACTAAAAGGGATTTACAATGTTGCTACCTG\nTGGCCTCTTTGGGTTGGTGTCCTTTCTTCTCTTATGTGGAAGGTCATGCTCAACAACTTA\nCAAGGGTGTTTATGAGCTTCAAACTCTGGAGCTGGATATGGCAAGCCTTAATATGACAAT\nGCCCTTATCCTGCACGAAGAACAACAGCCACCACTACATCATGGTTGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAACACAAGTATCATCAACCACAAGTTTTGCAACCTTTCTGA\nTGCACATAAAAAGAATCTCTATGACCATGCTTTAATGAGCATCATCTCAACCTTCCACCT\nATCCATCCCTAACTTTAATCAGTATGAAGCAATGAGTTGTGATTTCAATGGGGGAAAGAT\nAAGTGTTCAGTACAACCTCAGCCATACTTATGCTGTGGATGCAGCTAACCATTGTGGGAC\nCATTGCCAATGGAGTCCTTCAAACTTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCTGGAAAAGGGAGTTGGGATTGTATAATGACATCCTACCAATATTTGATAAT\nCCAAAACACCAGTTGGGAAGATCACTGCCAGTTTTCTCGCCCGTCCCCTATCGGTTATCT\nGGGACTACTTTCACAAAGAACCAGAGACATTTACATCAGCCGAAGACTCCTTGGGACTTT\nTACTTGGACTCTCTCTGATTCTGAGGGCAATGAAACACCGGGTGGGTATTGTTTAACAAG\nATGGATGCTGATTGAAGCCGAATTGAAGTGCTTTGGGAACACAGCAGTTGCGAAATGCAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGGTTGTTTGACTTTAATAAACAGGC\nTATAAGGAGGCTAAAGACAGAAGCACAGATGAGTATCCAACTAATAAACAAAGCAGTGAA\nTGCATTGATCAATGACCAGCTCATTATGAAGAATCATTTAAGAGATATCATGGGAATTCC\nTTACTGCAATTACAGCAAGTATTGGTACTTAAACCACACTGTAACAGGGAAGACGTCGTT\nGCCAAGGTGTTGGCTTGTATCAAATGGTACCTACCTGAATGAAACACATTTTTCTGATGA\nCATTGAGCAACAAGCAGACAACATGATAACAGAATTGTTACAGAAAGAGTACATTGATAG\nGCAAGGGAAAACACCCTTAGGGTTGGTGGATCTTTTTGTCTTCAGCACTAGCTTCTACCT\nTATTAGCATCTTCCTCCACCTGGTTAAAATCCCAACCCACAGACATGTCATAGGGAAACC\nCTGCCCCAAGCCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTGTATAAACA\nTCCTGGTGTACCAGTCAAGTGGAAAAGATAAGAGACAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGATGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTCAAAACTGGTATATTGAGTCCT\nCCTGACACAGCCGCATCATACATTATGCAATCCATTAGAGCACAGTGTGGGGTAATTTCT\nTCTTTACCTCCTCTTTTCTTCTTTTCAACAACCACCCCAGTATGCATATGGCATAGATCC\nTTGCATTGATCCCAAACAGCATTCTCAAACCTCCTAGAGTCAGCCTTGCTCAGTGCAATG\nTCAATAAGCTTTATGTCCCTTCTTCCTTGGGAGTCTAAGAGTTTCTTAATATCATCTGAA\nCCCTGACAGGTCAGTACCATATTGCGAGGAAGGGCTTCAATGACTGCACTGGTCAAGCCA\nGGTTGAGCAGGGAAAAGATCTGCTACATCAATCCCATGAGAATATTTGGCATCTTGCTTG\nAACTGTTTCAAATCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGACATAGGTTGG\nTAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCAATATCTATCCAGGTTTTAGCA\nCTTGGGTCAAGTTGCATCATTGAGTCTTTAAGTGTCATCAACTGAGAATAGGTCAACCCT\nGTTGGAAACCCTGCTGACTGTAAAGACTTGTTGGACCCAGCAGTGCCCACCTTTTGTGGC\nTTTCCATCTGACTCGAGATCCACAGTGGTATTCTCCCAAGCTCTACCTACAATGGAAGTT\nCTTGAAGCTATGTAGGGCCAACCGTCCCCAGAAAGACAGATCTTGTAAAGTATGTTCTCA\nTAAGGGTTCCTCTCACCAGGTGCATCTGAAACAAACATTCCTAAAGATCTTTTTACCTTT\nAAGATAGATTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCTCCATCAAGCATACAGGCTCCAGCTTTCACTGCAGCTCCTAAACTGAAGTTGTAA\nCCAGAAATATTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAAAGTCTGTCCAGGTCGGAGCTGTTTGGGTACTTAGCTGTGTATATTAGACCCAGGTCT\nGTTAGTGCTAAGACGGCATCATTTAAATCAACTTGACCTTGTTTGGTGAGACATGCTAAT\nGTCAGACTAGGCATGGTGCCGAATTGGTTGTTCAAAAGATCCGGATTCTTGACATCCCAC\nACCCTAACAACTCCGTCCCTTCCAGGTTGGGTACCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAATGCCCTTCTTTGCTCAAGTTGCTGTGTACTCAAATTTCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTGATGACCTTCGACTTCAGTTTCTCCAAGTCAGCA\nGCCAATGTCAGCAGGTCATCTGAAGTCAAGGTCCCAACTCTCAGGATACTCTTTTGTTGT\nGTTGATTTGAGTTCTACAAGATTGTTGACAGCCTGGTTCAGATCTCTGAGACGTTTCAGA\nTCACTGTCGTCCCTTTTTTGTTTGCGCATCAAGCGTTGAACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACCTGAAGCTTTATGCTGGAGCAG\nTAACCTGAGAGCTCCCTCCTCAATGACTGTGTCCAAAGGAATGACTTTACTTCCTTGGAA\nGCACTCATCCTGATCTAGACACTCAGGAACTCACTGGTTGAAAGTATCACTCAGTAAGTC\nAGTGA-------------------------------\n" }, { "path": "tests/input/TestFeatureTransfer/lasv/input/ref-lasv-ISTH2376.fasta", "content": ">KM821997.1 Lassa virus strain ISTH2376-NIG-2012 segment L Z protein (Z) and polymerase (L) genes, complete cds\nATCCTAGGCAATTCAGCTGGACTTCAGTGGTGAGGCTCACTTTGGTGAATTCCTGAATTAAAGTACCTAG\nTCAAAATGGGCAACAGACAGGCCAAATCGACAAAAGTCGATGAACATCAAAGAGCTCATCTAGTGCCAGA\nTGCATCCCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTGGTTTGAGAACAGAGGGTTGGTAGAGTGCAAC\nAATCACTACCTGTGTCTCAACTGCCTCAGCCTGCTCCTCAGTGTCAGCAGCAGATGCCCGATCTGCAAGA\nTGCCCCTTCCCACCAGGCTAAAGGCAGCGACACAGCCGAGCGCACCATCAACTGAGGCGACCCAGACCAC\nAACACCTCCACCATACACCCCATGATCCCGGGATCAACACTCCCACCTCCACCGCCCACCCCNNACCCCC\nGGGGGGACCCCCCGCCGGGGGCCCCCCCGGGGGGGCAGGCGGTCCAGCTCTACTCGATGTCCTCAACACA\nCTTCTCTGGCCCAAACAACTCCGAACATGTCCTTCCCTTCAGTCTTAGGCTACCCCCACTTGACTGTATC\nATCACTCTTTGCCTTGATTTACTATAGCAAAGAGCATAGCCTTTGAAATCAATCCATTCTCCAAGAGATT\nCAAGAAGTTCACTCAGTATATTAGCATAATCCATAGGTCTCTGTTTAGTAAGGATTGAGACAATGTCCAC\nATCCGTCCATTGAACCCTTTGTTTCAATCTATCAGACATCATTGATTTCAATGCACCAACCAAAAGATGC\nGGGGAACTATCACCAATCTCCCTTACAAACATTTCCAGATCTTGATCTTGGATAGATGGTGTAAATGCAG\nCTACCCTTTTATCAGATTCCCACAGTGCTCCTCTACACACAACCAATGGCACTGGTTCGTTGTCAGGTCC\nGACCTTGGTGAAATCAAACTCACTGAACTGCAGTTTATCTGGATTAATAATCAGCTTCATGGGTATAACA\nTCCCCCAACTGCTGTGTATCCTTTAAGAATTCATTTACCACATCTGATTCAACAAACCAGGATGATCTAC\nCTTTGAAAGTTGGGCCCGACAAAGCAAGTCTCCAACAGTCAGGCAGGACACATGGGCTCACAGACCCAGA\nATATAGTGCCTGTATATCATTCACTACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGG\nATAGAAAAAGTCTCTTTAAAACTAGCATCCTGACTCTTGATTTTATACCTAATTGTCTGGTAAAACTGAA\nCAGAGTCTACTGGCATTGTGCTTAACAAATCAAAGAAATCTTCAAGGGAGTCTAACCTCAATTCCTCTGT\nCAGGCCTGAAGCAATGAGCTGGTTCAAGTTTATCTGAGCTGGTTCCATGTCAAAATCTATCCATGCATAG\nCCCATCATTAGATCAAACTTAAACATGGGTCTCTCTATCCCTTTGTAAATGGCTTTCTCAATGAATGAAG\nAGAAGGGACCCAGTCGCTGTAAACCTTCACCCTCTGGTATTGAAGTTTTATGAGGAAACCAAGTGAATGA\nCCCAAGTGTCCTTGTTGTTGCTACAAAAGAGCGGACATATGATTCAAAGTAGACTTGTCTCATAAAGTTG\nTCCACTGCATCAGCAGTACTAACCACCCTTTCCTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTTC\nTCAGTTCAGAAGCCAATACAACATAATGTTCCTCCCTTTTCCACTTGACAATGTGTGAAACAAGTGAAAG\nTGCCTCGCAATTCACATCTAGGGCAACACAAAGGTCAAGGAACTTTATTCTAGGTGACCATTTCATCTTT\nGTGGAAGCTAAATCACTCATAAATGGCAAGATGTGCTTCTCAAATAGAGACGGATATAAACGTCTCAAAG\nAGTGGATGATGTGGCTCATGCCAACCCTGTCCTCTAGCAGTTTCGAAACAGTGGGTCTCAAGGGGAAATA\nATCACAAGGGTTATGCTTAAAAAAGTCCAAGATCTGAGCTTGTTTTGGTTCCCCGAGCACCCACGCTCCA\nAGTTCTATAGCTGTAGATAGTGTTATGCACATATAATCCCATAGAAGAGGTCTTAAATAAGTGACAACAG\nTACTACCTCCATCTTTGGCTTCTGGTGAGACTTTCCATATCTGAATTCCATTGTCCCCCATCACTGCTTC\nAACACCCTGAGTCCCCAATAGTTGAGTCTGTATGGATCTAATGTAAAGATTCTCCTTGTTGGGGCCTCTG\nACGCACTTGCTACCCAGTGTTCTGCACAACCCCACAAACCCAGATGCTATAGAACTTTGGAAAGCTGATT\nTATTTATTGCTTCAGACAGTAGCTTCTGAGCTCCTCTAGTGAATGTGGATGACAACCTATTTTGCAAAGT\nCTTTACTATTGTAGGGACCCTTTCATCTTCCAGATTCACAGCGCCAGAATAGATAATCTTTTGCCGCAAC\nACCATTCTAAGTGGGTGATGGGTGGCTAAGTTCAACCAATGAAACCCCAAGTCAGAATCAGACAAAGGTT\nCAATGCCTAGAAGTTTAAACAAATTCTGTAATGATGTTGTGTGTTCACCTGATAGGTAGTTGGTGGTGAA\nTTCCTCATGAAGCTCACCAGTTTTTAATTTATTGAACAATATCCTAAGCATTGACCTCATCTTTTTGCAT\nGCATCAGGAATTAGCCTCTCGATCTGCCTCATTATCCTATAGCTACGATTCCCGTCCACCCAATCTCTTA\nCATCAGTCTCGCAGTTCAAAAGGAATGGATCAATAGGATACTTGGCATAACATAACAAACTCAAAGTCCT\nCTTCTGAATTTGATTGCACAGATCAACTGGGACACCATTGGCCACAGACTGATCAATTATGGTATCAATT\nGTTTCTGCCAATTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCTGCAGCAACAAATTTTGTTAGCA\nGGGGCACCTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCAATTGCACTCTT\nTGGACTTACAAATTTATTTAACTGATCACTCATGTAGTAATGGAACTCTAACAATGTTTTGAATTCTTCT\nGCATCTCTTGAAAGTAATTCTGTTAAGTTCTGATCAAATAATGATATCTGATCGTCACTGGACGTGTAAG\nCATCAATTTGTCCTCCAGACACACACCTCACCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAA\nGTCTGAGGTGTTGTGTAAGATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGGACTGTGCCA\nGTTTGAAAGTTGGAATTAAAGAAGTCTTCGGTCATTGATTGAGTTGTCTTCTTCTTCAATCCAAGTTGGG\nACTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTGTGCATATGCCA\nTGTTAATAATGTTGACAAGTAATCTTTACCTTTTAAATCAGCTTGTAAATCATCAGAAAGTAAGATTAAG\nTTTTGAATTATTGTTAGAAACAAGAAAGGACACATCATAGGACCCCACTTACTGTGATCCATACTATATG\nATACATGTGCCGATGAGACATTCAGTTTCATTGACAAAATGGCATTATCAAACTCCTTCTCATTGTTTAG\nACAGCTGCCTGCTAATTGTGATGTGAGTGCTTCAAAGTAATCCTCAATGAGCCTTGTGAACATTTTTGTC\nCTTAAATCTCCGATGTACAACTCTCTATTGCCACCCACTTGTTCCTTGTAAGACAAAGAAAACTTTAGTC\nTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCTTGACTGTAAAAACACAGGTTTTTTAG\nCATTGCTGTAGTACAGTTAGTTAGGGACAAGGCCTTGCTAAGTGCTTCAGAGTTACTCTCACGTTCACTT\nATCCTGACATCATCAGCCAATCTCCCTGTATCAAATTTAAAGTTCAGACACTTGCTCTTATAATGAGAGT\nATCTTCCCATCAGCTTATTCCCATTCATCACTAGTAAAATTGACTTAAAGCACTGAAAATATTCTTGGTC\nCAAAAAAGTCCTAGTCACTACTGCTTTTGTCAGCTCACTAATAGGACATGAATTCATTGGCCCTACATAA\nAAATATTTACTTCTCAAAGTAGCATCATTGTAGATATTCTCACAAATTTTGATGTATTGATCTTCAGACA\nGGATCTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATCAACCTTATTAAGAGTTT\nTTCTTCCACCACTTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCTGCCTGCTGCTGTCCTTTTGGT\nTGCTCCCTATACTGACTGACAATATTGTCAACAGTGCACCTCAGTTGGTCGAAGTATTCTGATGCTCCTC\nCATCCAATAGTATCTCATCTAGATCAGCATTGTTGGTGTCACCACTCCCTCCTTTGGACCCCAGAACAAG\nATTACTCATTGCTTGCTGTATTTTGTAATCATAATCCTGTTTATTAAGCAAGAATTTGCCTTTACGTGCA\nAACACCTCAGTTAACTGTGTGACAGCCAAAGCTGTAAGTTTATTGAAGTCATAATCCAGAATACGGGACC\nCATCTGTATACTTATTCACAACGACGCTCTTATTGCTGGCCAGGTCCAAGGCTGTTGCACAGCCGCTTGT\nAATAAGAGGGTCTCGCAGTGTCTTTTTTACCTCCTTTTCTTTGAACAATGAACCATTGTTAAAACTGGAC\nACAAGGAGTGAAATAAATTTCTTGGAAACACCAGGCTTTTTATACCTAACTTTTTCCGCATCTACACAAC\nATTCTTTACTTAGGAATTTTCTTGCATTATAAACCATTTCAACAAGCTCTTCCTCCAATGCATCATCCTT\nCGGGTTCACACTCACATGTCCAAATTCCAACTTGGGCTCAAGGAATTTTTCAAAGCATTTGATCTGGTCA\nGTCAGTCTGTCAGGTGTTTCTTTTGTAATGAAGTGACACATATAGGAGATATTTAAAACAAACTTGAATC\nTATTGGTCATCATACTGACAACTTCTTCAGACAGAATTATCTTTAATAAGTAACGAACAAGTCTGTAGAG\nCAGATATTCTACTTCTGTGATCAAATCCTCCCTGATTTTCTCAATCAAGTCCTTATGATAAAAATCGGAT\nACAAAGGCCATCACAAAATACCTGATGTTTTGTAAAAATTTTTGACACCTTTTACTAGGGTGTGTCAGTA\nTTAAAACTAAAATCATTTTAGTTAACAATTTAATAGTGATCAATTGTTCAGACAACTCTGTGCACTCTTC\nTATCCAGCTGACCATAACATCGACTACTTTCTGCAGCACATCACTGGAGAAAACTGAAGGAAAAAACCGT\nTTGGGATCAGCATAAAAGGAACAAACCTCTCCAACTACATTATTGTTAATAGCATAACACTTTGAGCATT\nCACCTGTTTTTTGATACAATAGTTTGAATCCCATCTTATTGATGAAGAACTCTTGGCAGTAGGCCTCTTT\nGCACCTCACAACCTGGTATCTAGAGGGTCCAAATTCATTTTGCCTTAGTTTCACTGTAGAAGACGTTTTC\nATTGAGTTAATCAAAGCCAAGCTCAATGATGATAGTCTTTCTAAGTCTGTTGCACCTAGAATGTCAATAA\nCGCCAAGAGTATAAGGGAACATGTCTTCCTGAGTTTTCTGGTAACTCATAGTGGGTGTGATGCCAGAGAT\nCTCAATGTCCATGATGGCATCATAAACATCACAATCAAGGATTTTGAAATCAATTCCATAAGAGTTGGTT\nTCTATGCCAACCTCCCTCAAAGCATTAGCGGCTCGAGTTAAAACTCTGTTGATGATGGCAAGGAGCTCAC\nAATTTCGTTCTTCTTTGGGTGATAGGACACCCACGTTCTTGTCTCTAGTTCTCTTCCTGCTATCTATCCA\nCCGTTTTAGATCTCTTTTTGTTGATTCCAATGAAACTAATCTGTCGTTAACACTCACAAAACAGGAGCCC\nAACCAACCAGCAAGGAGCTTGTCACCATGCCTTATACAGTCCAGTCGGCTGGCAAGAAGGATCAGAACGT\nCAAAAACAAGGAGAAGTTTCCTTCTGGTGTTGAGGATCCTCAGAGACTTTATCTTATTTAAAAAAGATCT\nCCAACATTGCATCTGTTCACTTTGAGAGTCAACAGCCTTTTCCTTGCTAGAATCCAAATCTGCATATAAG\nAATTTAAGGACTGGAGAGGCTCTTCGGAACTGAAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCTA\nTTTTATCACAATATAGCTTTCTGAAATCCTCTAACAACTTCATCTTATCAGTCTTAACAAATTGACTTTC\nTATGTTCCCTTGCCTTAGTTTGTTCCTGAAGATTTGATACTCCTCCTCAATCAAACTCTTGACTTCATGA\nGAGGTAAGCTTGTTATTAATGCCTTGATGACAACTAGAAATTATTTCTTCAAAGTGTTTTGCACGCTTGT\nCAATTAGAACATTGATGCTTTCAATTCCTGAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAAAGCCT\nCGAATATTCAGACTCTTCGAACAATGCATTACTTTCTTGTGAATATTTTAACAAGGTGAATAAGGTGTCC\nCTGAGTTTGTCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTTGTCCTGCCGTCTATGAGAGGGA\nTGAGCTTGATGCCAACAGACTCCAAATCGTTCTTTAATTGTTCTAGTTTCCTGTGATCTTCTAAATACTT\nCTGTTCGAAATTGGCGGGGGATGATCTGACAAAGCACTCAAGTAAGATTAGAACATTGCCAGTGAGTTTG\nTAGCCGTCAGGCACCACAAAGCATAAAGCTGGAGTGAGAATCCCATGATCACTCAGAATGGATTCAACCG\nTTTTGTCTTCAGTGTTATGTTCACATCCATTGGCCTTACAGGAGTCAATCTCAATGCAAAGAGATAGTAG\nTTTCAATCCCTCCATAAGCAACATTCTGGGTTCGGTTTGGACCAAAAAAGCTAATTTCTGTCTTGACAAC\nTTCTCATTATCTGCAAGGTACTTTGAGATGAGATCTTTAGCATTAGCAATGTCTTCCTCCATCGCCAACT\nGTGGCACCTGTGTTGGGTTTGGGTTTATGCCAATATGGCTTGTGGGTCGGCTGGTGATGTCCTAAAGAAG\nCTCCTACAGAAATGAGAGACAATATGCCTAGGATC\n\n>KM821998.1 Lassa virus strain ISTH2376-NIG-2012 segment S glycoprotein precursor (GPC) and nucleoprotein (NP) genes, complete cds\nCCTAGGCATTTAGGATTGCGCTTTTAGAGATCTTTGTGTGAGTGAGCTTCATCAAGCCATGGGGCAAATT\nATAACATTTTTCCAAGAAGTACCTCATGTCATAGAGGAAGTGATGAACATTGTCCTGATTGCTCTCAGCC\nTTCTGGCAATTCTGAAAGGGATCTACAATGTTGCTACATGTGGCCTTTTTGGACTGGTGTCTTTTCTCCT\nCTTATGTGGAAGATCATGCTCAACAACTTACAAGGGTGTTTATGAGCTACAGACTCTAGAGCTAGACATG\nGCTAGCCTTAACATGACAATGCCCTTATCTTGCACGAAGAACAACTCCCACCATTACATCATGGTCGGAA\nATGAGACTGGCTTGGAGCTGACTTTAACAAATACAAGTATTATCAACCACAAGTTTTGCAACCTCTCTGA\nTGCACATAAGAAGAATCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTCCACTTATCCATTCCC\nAACTTTAATCAATATGAAGCGATGAGCTGTGACTTCAATGGGGGGAAGATAAGTGTGCAGTACAACCTCA\nGCCACACTTACGCTGTGGATGCGGCTAACCACTGTGGGACCATTGCCAATGGCGTTCTTCAGACTTTTAT\nGAGGATGGCTTGGGGTGGCAGTTACATAGCACTTGATTCCGGAAAGGGGAATTGGGATTGCATAATGACT\nTCCTACCAATATTTGATAATCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGTCCATCCCCCA\nTCGGTTATCTGGGGCTACTGTCACAAAGGACCAGGGACATTTATATCAGTCGAAGACTTCTTGGGACTTT\nCACTTGGACTCTCTCTGATTCCGAAGGTAATGAAACACCGGGTGGGTATTGTCTAACAAGATGGATGCTG\nATTGAGGCCGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCAAAATGTAATGAGAAACATGATGAAGAGT\nTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGCTATAAGTAGGCTGAAGACAGAAGCACAGAT\nGAGTATCCAACTGATAAACAAAGCAGTAAATGCACTGATCAATGACCAGCTGATTATGAAGAATCATTTG\nAGAGATATCATGGGAATTCCTTATTGCAATTACAGCAAATATTGGTATCTAAATCACACTGTAACAGGGA\nAGACATCGTTGCCAAGATGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAAACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAAATGTTGCAAAAGGAGTACATAGATAGGCAAGGGAAA\nACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGTTTTTACCTTATTAGCATCTTCCTCCACC\nTGGTTAAAATCCCAACCCACAGACACATCACAGGGAAACCCTGCCCCAAACCACACAGACTCAACCACAT\nGGGCATATGCTCATGTGGTCTATACAAACATCCTGGTGTGCCAGTCAAGTGGAAAAGATAGAAGATAGAC\nCCACCCATGGGCCCCCGTGACCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGAC\nCTTGGGGCTTGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCC\nCCTGACACAGCTGCATCATACATTATGCAGTCCATCAAAGCACAGTGCGGGGTAATTTCTTCTTTACCTC\nCTCTTTTCTTCTTTTCGACAACCACTCCAGTATGCATATGGCACAGATCCCTGCACTGATCCCAAACAGC\nATTTTCAAATCTCCTAGAGTCAGCCTTACTCAGTGCAATGTCAATAAGCTTTATGTCCCTCCTTCCCTGA\nGAGTCCAAGAGTCTCTTAATATCATCTGAACCTTGACAGGTCAGTACCATGTTGCGAGGAAGGGCTTCAA\nTAACTGCACTGGTCAGGCCAGGTTGAGCAGGGAAAAGATCTGCCACATCAATCCCGTGAGAATACTTGGC\nATCTTGCTTGAACTGTTTTAAATCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGACATGGGTTGG\nTAAAGAGCTATTTCCACAGGATCTTCTGGACGACCTTCAATGTCTATCCATGTTTTGGCACTTGGGTCAA\nGTTGCATCATTGAGTCCTTAAGTGTCATCAACTGAGAATAGGTCAGCCCCGTTGGAAACCCCGCTGACTG\nTAAAGACTTGTTGGACCCAGCAGCACCCACTTTTTGTGGTTTTCCATCTGACTCGAGATCCACAGTAGTA\nTTCTCCCAAGCTCTACCCGCAATAGAAGTCCTTGAAGCTATGTAAGGCCAGCCGTCACCGGAAAGACAGA\nTCTTATAAAGTATGTTCTCGTAAGGGTTCCTCTCACCAGGTGTGTCTGAAACAAACATTCCCAAGGATCT\nTTTTACCTTTAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCTCCTAAACTGAAGTTATAACCAGAAATGT\nTCAAGGAGCTCTTCTTGGTGTCCACCATATTCAGTATAGGATGGCTTTGGGAGAGTCTGTCCAGGTCGGA\nGCTATTTGGATACTTAGCTGTGTATATTAGACCCAGGTCTGTCAGTGCTAAGACGGCATCATTCAAATCA\nACTTGACCTTGTTTGGTGAGACATGCTAATGTCAGACTAGGCATGGTGCCGAACTGGTTGTTCAGAAGAT\nCCGGGTTCTTAACATCCCACACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAAC\nCATGCCTATCATGTTCAGCAATGCTCTTCTTTGCTCAAGCTGCTGTGTACTTAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCTGCCAACGTCA\nACAGGTCATCTGAGGTCAGGGTCCCAACTCTCAAGATGCTCTTTTGTTGCGTCGATTTGAGTTCTACAAG\nATTGTTGACAGCCTGATTCAAATCTCTAAGACGTTTCAGATCACTATCATCCCTTTTTTGTTTGCGCATT\nAAGCGTTGCACATTGCTGACTTCAGAAAAGTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTT\nGAAGTTTTATGCTGGAGCAATAACCTGAAAGCTCCCTCCTCAATGACTGTGTCCAGAGAAATGACTTCAC\nTTCCTTGGAAGCACTCATCTTAGTCTGGACACCTAGGGATTGACTGGTCAAAAGTTTCACTCAGTAAGTC\nAATGAAAGGCGCAATCCAGTAGCCTAGGATCCACTG\n\n" }, { "path": "tests/input/TestFeatureTransfer/negative_strand_partial/expected/mapped.tbl", "content": ">Feature sample\n550\t>1\tCDS\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\tnegative-strand-protein\n\n" }, { "path": "tests/input/TestFeatureTransfer/negative_strand_partial/input/aligned_1.fasta", "content": ">TEST123.1 Synthetic test sequence for negative strand partial\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\n>sample\n------------------------------------------------------------\n------------------------------------------------------------\n------------------------------ATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT\nGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCGC\n" }, { "path": "tests/input/TestFeatureTransfer/negative_strand_partial/input/ref.fasta", "content": ">TEST123.1 Synthetic test sequence for negative strand partial\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\nATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC\n" }, { "path": "tests/input/TestFeatureTransfer/negative_strand_partial/input/ref.tbl", "content": ">Feature gb|TEST123.1|\n700\t100\tCDS\n\t\t\tproduct\tnegative-strand-protein\n\t\t\tprotein_id\tgb|test001|\n" }, { "path": "tests/input/TestFeatureTransfer/synthetic/expected/mapped.tbl", "content": ">Feature sample\n<1\t99\tCDS\n\t\t\tproduct\tshould-be-output-if-not-ignore_ambig_feature_edge\n<1508\t2740\tCDS\n\t\t\tproduct\tshould-output-with-fuzzy-lt-start-if-not-ignore_ambig_feature_edge\n225\t1703\tCDS\n\t\t\tproduct\tone-complete-range-should-be-included\n2740\t>1508\tgene\n\t\t\tgene\tneg-strand-should-be-present-fuzzy-gt-end\n4000\t4027\tCDS\n7000\t7034\n7500\t7578\n\t\t\tproduct\tthree-ranges-all-output-sorted\n4000\t4027\tCDS\n\t\t\tnote\tsequencing did not capture all intervals comprising CDS\n\t\t\tproduct\ttwo-ranges-with-second-truncated-downstream\n5379\t5454\tCDS\n\t\t\tnote\tsequencing did not capture all intervals comprising CDS\n\t\t\tproduct\tonly-5379-range-should-output\n200\t212\tCDS\n\t\t\tproduct\tafter-offset-should-be_200-212\n\n" }, { "path": "tests/input/TestFeatureTransfer/synthetic/input/aligned_1.fasta", "content": ">AY772699.1 HIV-1 isolate 04ZASK146B1 from South Africa, complete genome\nTACT-GTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA\n>sample\nT-CTGGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA" }, { "path": "tests/input/TestFeatureTransfer/synthetic/input/ref.fasta", "content": ">AY772699.1 HIV-1 isolate 04ZASK146B1 from South Africa, complete genome\nTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA\n\n" }, { "path": "tests/input/TestFeatureTransfer/synthetic/input/ref.tbl", "content": ">Feature gb|AY772699.1|\n<1\t99\tCDS\n\t\t\tproduct\tshould-be-output-if-not-ignore_ambig_feature_edge\n<1508\t2740\tCDS\n\t\t\tproduct\tshould-output-with-fuzzy-lt-start-if-not-ignore_ambig_feature_edge\n225\t1703\tCDS\n\t\t\tproduct\tone-complete-range-should-be-included\n2740\t>1508\tgene\n\t\t\tgene\tneg-strand-should-be-present-fuzzy-gt-end\n4000\t4027\tCDS\n7500\t7578\n7000\t7034\n\t\t\tproduct\tthree-ranges-all-output-sorted\n4000\t4027\tCDS\n7000\t10000\n\t\t\tproduct\ttwo-ranges-with-second-truncated-downstream\n5379\t5454\tCDS\n12000\t12001\n\t\t\tproduct\tonly-5379-range-should-output\n\t\t\tprotein_id\tgb|should-not-appear|\n12002\t12500\tgene\n\t\t\tgene\tshould-not-output\n[offset=100]\n100\t112\tCDS\n\t\t\tproduct\tafter-offset-should-be_200-212" }, { "path": "tests/input/TestFeatureTransfer/synthetic_ignore_ambig_edges/expected/mapped.tbl", "content": ">Feature sample\n1\t99\tCDS\n\t\t\tproduct\tshould-be-output-if-not-ignore_ambig_feature_edge\n1508\t2740\tCDS\n\t\t\tproduct\tshould-output-with-fuzzy-lt-start-if-not-ignore_ambig_feature_edge\n225\t1703\tCDS\n\t\t\tproduct\tone-complete-range-should-be-included\n2740\t1508\tgene\n\t\t\tgene\tneg-strand-should-be-present-fuzzy-gt-end\n4000\t4027\tCDS\n7000\t7034\n7500\t7578\n\t\t\tproduct\tthree-ranges-all-output-sorted\n4000\t4027\tCDS\n\t\t\tnote\tsequencing did not capture all intervals comprising CDS\n\t\t\tproduct\ttwo-ranges-with-second-truncated-downstream\n5379\t5454\tCDS\n\t\t\tnote\tsequencing did not capture all intervals comprising CDS\n\t\t\tproduct\tonly-5379-range-should-output\n200\t212\tCDS\n\t\t\tproduct\tafter-offset-should-be_200-212\n\n" }, { "path": "tests/input/TestFeatureTransfer/synthetic_ignore_ambig_edges/input/aligned_1.fasta", "content": ">AY772699.1 HIV-1 isolate 04ZASK146B1 from South Africa, complete genome\nTACT-GTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA\n>sample\nT-CTGGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA" }, { "path": "tests/input/TestFeatureTransfer/synthetic_ignore_ambig_edges/input/ref.fasta", "content": ">AY772699.1 HIV-1 isolate 04ZASK146B1 from South Africa, complete genome\nTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA\n\n" }, { "path": "tests/input/TestFeatureTransfer/synthetic_ignore_ambig_edges/input/ref.tbl", "content": ">Feature gb|AY772699.1|\n<1\t99\tCDS\n\t\t\tproduct\tshould-be-output-if-not-ignore_ambig_feature_edge\n<1508\t2740\tCDS\n\t\t\tproduct\tshould-output-with-fuzzy-lt-start-if-not-ignore_ambig_feature_edge\n225\t1703\tCDS\n\t\t\tproduct\tone-complete-range-should-be-included\n2740\t>1508\tgene\n\t\t\tgene\tneg-strand-should-be-present-fuzzy-gt-end\n4000\t4027\tCDS\n7500\t7578\n7000\t7034\n\t\t\tproduct\tthree-ranges-all-output-sorted\n4000\t4027\tCDS\n7000\t10000\n\t\t\tproduct\ttwo-ranges-with-second-truncated-downstream\n5379\t5454\tCDS\n12000\t12001\n\t\t\tproduct\tonly-5379-range-should-output\n\t\t\tprotein_id\tgb|should-not-appear|\n12002\t12500\tgene\n\t\t\tgene\tshould-not-output\n[offset=100]\n100\t112\tCDS\n\t\t\tproduct\tafter-offset-should-be_200-212" }, { "path": "tests/input/TestFeatureTransfer/synthetic_oob_clip/expected/mapped.tbl", "content": ">Feature sample\n<1\t99\tCDS\n\t\t\tproduct\tshould-be-output-if-not-ignore_ambig_feature_edge\n<1508\t2740\tCDS\n\t\t\tproduct\tshould-output-with-fuzzy-lt-start-if-not-ignore_ambig_feature_edge\n225\t1703\tCDS\n\t\t\tproduct\tone-complete-range-should-be-included\n2740\t>1508\tgene\n\t\t\tgene\tneg-strand-should-be-present-fuzzy-gt-end\n4000\t4027\tCDS\n7000\t7034\n7500\t7578\n\t\t\tproduct\tthree-ranges-all-output-sorted\n4000\t4027\tCDS\n7000\t>9012\n\t\t\tnote\tsequencing did not capture complete CDS\n\t\t\tproduct\ttwo-ranges-with-second-truncated-downstream\n5379\t5454\tCDS\n\t\t\tnote\tsequencing did not capture all intervals comprising CDS\n\t\t\tproduct\tonly-5379-range-should-output\n200\t212\tCDS\n\t\t\tproduct\tafter-offset-should-be_200-212\n\n" }, { "path": "tests/input/TestFeatureTransfer/synthetic_oob_clip/input/aligned_1.fasta", "content": ">AY772699.1 HIV-1 isolate 04ZASK146B1 from South Africa, complete genome\nTACT-GTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA\n>sample\nT-CTGGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA" }, { "path": "tests/input/TestFeatureTransfer/synthetic_oob_clip/input/ref.fasta", "content": ">AY772699.1 HIV-1 isolate 04ZASK146B1 from South Africa, complete genome\nTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA\n\n" }, { "path": "tests/input/TestFeatureTransfer/synthetic_oob_clip/input/ref.tbl", "content": ">Feature gb|AY772699.1|\n<1\t99\tCDS\n\t\t\tproduct\tshould-be-output-if-not-ignore_ambig_feature_edge\n<1508\t2740\tCDS\n\t\t\tproduct\tshould-output-with-fuzzy-lt-start-if-not-ignore_ambig_feature_edge\n225\t1703\tCDS\n\t\t\tproduct\tone-complete-range-should-be-included\n2740\t>1508\tgene\n\t\t\tgene\tneg-strand-should-be-present-fuzzy-gt-end\n4000\t4027\tCDS\n7500\t7578\n7000\t7034\n\t\t\tproduct\tthree-ranges-all-output-sorted\n4000\t4027\tCDS\n7000\t10000\n\t\t\tproduct\ttwo-ranges-with-second-truncated-downstream\n5379\t5454\tCDS\n12000\t12001\n\t\t\tproduct\tonly-5379-range-should-output\n\t\t\tprotein_id\tgb|should-not-appear|\n12002\t12500\tgene\n\t\t\tgene\tshould-not-output\n[offset=100]\n100\t112\tCDS\n\t\t\tproduct\tafter-offset-should-be_200-212" }, { "path": "tests/input/TestFilterLastal/expected.fastq", "content": "@ebola:1000-1067\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGA\n+ebola:1000-1067\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n@ebola:2000-2067_with_insertion_deletion_N_and_SNP\nAGCCAAAAGGGCCAGCATATAGAGGGCAGAAGACACAATCCCAGGCCAATTCAAAATGTCCCANGCCC\n+ebola:2000-2067_with_insertion_deletion_N_and_SNP\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n@ebola:1000-1066_with_description XXX length=101\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTG\n+ebola:1000-1066_with_description XXX length=101\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD\n" }, { "path": "tests/input/TestFilterLastal/in.fastq", "content": "@ebola:1000-1067\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGA\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n@human:chr19:1000000-1000067\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n@ebola:2000-2067_with_insertion_deletion_N_and_SNP\nAGCCAAAAGGGCCAGCATATAGAGGGCAGAAGACACAATCCCAGGCCAATTCAAAATGTCCCANGCCC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n@ebola:1000-1066_with_description XXX length=101\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTG\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD\n" }, { "path": "tests/input/TestGap2Seq/expected.ebov.doublehit.gapfill.fasta", "content": ">KJ660346.2_contigs_ordered_and_oriented\nCTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTC\nTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCC\nTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAA\nCATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACTT\nTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAA\nAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTC\nTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAA\nGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGT\nGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGG\nTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTA\nCCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGG\nGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGC\nAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGAC\nTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGT\nAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGG\nACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTT\nGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGC\nCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGG\nTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCG\nTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGC\nACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTC\nTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGT\nCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCT\nCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACT\nTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAA\nGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGC\nCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGA\nTGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGA\nTGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGATGA\nTGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTT\nGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGAC\nCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACA\nATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCC\nACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGAC\nCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCC\nGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCAC\nTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGA\nTGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCA\nGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGA\nTGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGG\nTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAA\nAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCC\nAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCAT\nGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAAC\nAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTT\nTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAA\nTGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCG\nATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATT\nTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCC\nTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCT\nGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAA\nACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAA\nGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCAT\nCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACC\nCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTG\nTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATG\nGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTG\nAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTG\nCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATG\nAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTA\nGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAAC\nCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAA\nCTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGG\nACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCC\nTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACA\nTCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCAT\nCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTG\nGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTT\nCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGA\nTAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAA\nGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACC\nCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCAT\nTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGC\nCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTG\nCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTC\nCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAG\nGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAG\nTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACA\nGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCA\nAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCC\nTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCC\nAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGC\nCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAA\nTTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGA\nACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACT\nTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTC\nTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTG\nTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAA\nTCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGT\nAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACAT\nCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGC\nTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATA\nCCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTA\nCTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTT\nATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGAT\nGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTC\nTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCT\nCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCA\nAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATAT\nTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTT\nTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTG\nATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTG\nGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGG\nGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAA\nACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAG\nACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCAT\nGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTT\nCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGC\nCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGG\nAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAA\nCTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAA\nGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGA\nGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGG\nAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTC\nTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTC\nTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTC\nCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAAC\nCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAG\nCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACA\nTCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGC\nCGGACCCTTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGC\nCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCA\nAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGC\nTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGC\nTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAAT\nCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCT\nAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCA\nAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCG\nTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGA\nCTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTAT\nTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGG\nATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGC\nTTTATTCTGTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAAC\nTCAACCTCAAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTAC\nTTGACAAATGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCC\nTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAA\nTGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCC\nTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAG\nTTGTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCA\nTTGGTAAAAAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCT\nTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCAC\nCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGG\nAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACA\nGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGT\nAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTA\nATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGAC\nTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCCAAAATTACC\nTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGAG\nGATTCCAAATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAA\nTCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAG\nGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAA\nGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTG\nAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACA\nTTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCT\nGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACA\nATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCA\nGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAA\nGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCAAT\nATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACT\nCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATG\nATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGG\nAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATAT\nTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAAT\nGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCA\nTCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCTGT\nATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACAC\nATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAG\nTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTA\nCAACGAACATTACTTTGAGCACCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATC\nGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAG\nACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATA\nTCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTT\nAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCAC\nAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATG\nACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTG\nTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTG\nATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACT\nAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCG\nTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAAC\nTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACT\nCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGC\nAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACA\nCAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATC\nTAACTAAGATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACT\nTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTT\nGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCT\nTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATT\nGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTG\nTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCA\nTACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAA\nACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATAT\nTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTG\nGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATCCG\nCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTT\nACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATT\nCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTC\nTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAA\nAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCA\nATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACT\nCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATTTA\nATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCA\nCTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAA\nGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATG\nTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTT\nGAGGACCCAGTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGC\nGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAA\nCCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGATTC\nTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCA\nCTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAG\nATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTG\nCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTA\nCGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTAT\nTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTT\nAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTATGG\nGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGT\nATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAG\nCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAA\nTTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAG\nTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTA\nGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCT\nCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGT\nGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGT\nGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCA\nTTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAG\nAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTAT\nTATAATCCACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGT\nTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATT\nTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTG\nATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGC\nGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTT\nACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATC\nTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCT\nACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGT\nATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATA\nACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTT\nAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATA\nTCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAA\nTGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTAT\nCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAAC\nTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGAC\nTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAA\nCTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGTGG\nCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCG\nAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCT\nAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTG\nCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCT\nTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCA\nCATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTC\nAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACCT\nGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAAT\nGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAA\nGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCC\nATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTA\nATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACC\nCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCT\nTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTTA\nGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTT\nATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATC\nCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAG\nTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATTG\nATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCA\nTTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTA\nTCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCG\nTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTAT\nCCCAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACA\nATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATT\nCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTT\nATGTCACGATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGT\nGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTT\nACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATAT\nCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTG\nCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACAT\nCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCA\nTTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCT\nTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACC\nACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATA\nAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCTA\nAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAAT\nGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACAT\nCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAAT\nGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGAT\nACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAG\nGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCT\nGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGCT\nACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTA\nCCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGC\nCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGG\nCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTG\nTACGAAGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTG\nGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCC\nCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAG\nTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCAT\nCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATAC\nTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTT\nGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGA\nGGTCCACTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTG\nACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACT\nGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACAA\nGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGT\nGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAA\nACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGG\nCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATT\nTTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCT\nCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTA\nCATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAGC\nATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTT\nATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTAT\nCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACT\nGATCTTTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGG\nTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGT\nCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAA\nTCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAAT\nTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCC\nTGGAAAAATGGTCACACACAAAAAAGAAGAAATAGATTTATTTTTAAATTTTTGTGTG\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610675.1.gb", "content": "LOCUS JQ610675 3942 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 1, complete sequence.\nACCESSION JQ610675\nVERSION JQ610675.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 3942)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 3942)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..3942\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"1\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..3921\n /note=\"RNA-dependent RNA polymerase\"\n /codon_start=1\n /product=\"VP1\"\n /protein_id=\"AFX73387.1\"\n /translation=\"MVITVEGAWLVRRALQRFLKFSKIDGESAVYEFYRYSSNIREIR\n RKHGTRYKMHDEELERRRDSGKLRFKGMQVVVESTWMEILGKGRTTDEIEIFRSSILS\n LDELNPEEEFLRNYASSDKEHPSYLFVRGRAVNEMQIYGDMPIKAWLSFLVECEVEYG\n YKLFGMEVARSFVQSFGSPFHQNSRDLSQIDDMAPAFTSPLLFEMCCMTSILEINIRM\n RMLEERVATLKFGEREIDPLEVLKEFFRICIPHPKKINNMLRAPYSWFVKLWGVSYHE\n PIVLTARGGEDKNSKDIFFTGFHRVKNPYSIMLKKSRFFKKSLDENISKVKEAIDYSN\n SLTGMSLGLPVFLSMLQNVYDTEFNPTMVQHVLLASFLLSIQTITGYGRAWVKNVSSD\n NDTQMRPAEDNFIDRVAKQTEINFIQAYEEALGHGEDIVKPEDMFTSILRLARNTSSG\n FSTAVDVYKRFGPKSGGRGERVKITSRIKALVIFTKGHEIFTAENLAKRYDTEEDYQT\n KGSRDVPIKATRTIYSINLSILIPQLILTLPLNEYFARFGGSTAPDSRSLGGKVIIGD\n LEATGSRTIDAADTFRNSSDPEIFTIAIDYSDYDQHLTVFNFRNGMLEGIRSAMKRYK\n ELRYDGYTLNELIEFGYGEGRIVNSKWNGKRRVKSVRMSDYMALSESQRAQGTFKPPQ\n GVRPVSSMQVFDSVGEASGGDTLLISPTDGSDLATVNTHLSGENSTLVANSLHNMAIG\n RIIQEEIRKNHRAAFTFESEQYVGDDTLLYAKLNTLNHEIFDKAIDTIFDTVGKCGHV\n ASAAKTLIAPFSVEKTQTHAKQGIYIAQDRMMIISSERRKDIEDVQGYMRSQVSVMAT\n KVSRGFSHELAQLVFMMKSSIVGFRKLKRTVVEDGVYRDRALDSEDEDGFTLMQIRDP\n LVAFYPAEWNGYGMHPVALNIVMTEDMFIDTSTMVEFQHVMRPLLRFMGRIPPVWNET\n KADKRQISSITKMSFFSKMARPAVRAVLANSELSDQVRTLPLGDFSPFNLSATMMHSA\n LLKEPRARALLTPAYEKEFQSELNSNRDSEVNFVGRNMEINTNYMKLFDVDLSTRIVA\n KQFSFPDQNMSLPFYFQKLLIGHRPVARMRMTYIDRIDQILRGDVVMRGFITANTIMS\n VLEKIGTAHAVQDLTTIFQLMNIESKVAHRLAEYIASERVRFDALSIAKRGICGDEFS\n MSLDVCTERFAERFMELPAQFTKTERDIAILYAAQLTMLRCAANLDLRKIKIGVSADH\n VKRFKQRQARFKTHLPKMRTVTRLITPERISARLVQHQFT\"\nORIGIN \n 1 gtataattag gaatggtcat cactgtggaa ggtgcgtggc tggtgagacg ggcgttgcaa\n 61 cgttttttga agttcagtaa aatcgacggg gaatcagcag tttatgagtt ctataggtat\n 121 tcaagtaata ttcgtgaaat aagaaggaag catgggacgc gttataaaat gcatgatgaa\n 181 gagttggagc ggaggcgtga ttcgggcaaa ctgcgtttta aaggtatgca agttgtggta\n 241 gagtcgactt ggatggagat tttagggaag ggacgtacga cggacgaaat cgagatattc\n 301 agaagttcga ttttatcgtt ggatgaactg aatccggaag aagaatttct gcgcaattat\n 361 gcgagttcgg acaaggaaca tccatcctac ttgtttgttc gggggcgggc ggtcaatgag\n 421 atgcagattt atggcgacat gccgataaaa gcgtggttga gctttttagt agaatgtgag\n 481 gttgaatatg ggtacaaact cttcggaatg gaagttgcga gatcgttcgt tcagagcttt\n 541 ggatctccgt ttcaccagaa ctcgcgtgat ctatcacaga ttgacgatat ggcgcctgct\n 601 tttacgtcac ctttattatt tgaaatgtgt tgtatgacat caattctcga aattaatata\n 661 cgcatgcgta tgctggagga gagggttgca accctaaaat ttggtgagcg ggagatcgac\n 721 ccacttgaag tactaaaaga attcttccga atctgcattc cgcatccgaa aaagattaat\n 781 aatatgttga gagctccata ctcatggttc gtcaagctgt ggggcgtatc gtatcatgag\n 841 ccaatagtcc tgacggcgag gggcggcgag gataagaact cgaaagacat attctttacg\n 901 ggatttcaca gagtcaagaa tccatactca ataatgttga aaaaatcgag gttttttaag\n 961 aaatctttag acgagaatat cagcaaagtg aaagaagcga tagactattc aaactcgttg\n 1021 acggggatgt ctttagggct gcccgtattt ctatccatgc tacagaatgt gtacgacact\n 1081 gagtttaatc cgactatggt tcaacacgtg ttactagcgt cgttcttgtt gagtatccaa\n 1141 acaataactg gctatggacg cgcttgggtg aaaaatgtgt caagcgataa cgacactcaa\n 1201 atgcgcccgg cggaggacaa cttcattgat cgagttgcta agcaaacgga gattaatttt\n 1261 atacaggcgt atgaagaggc gttggggcac ggagaagata tcgttaagcc agaagacatg\n 1321 tttacctcca ttttgcgttt ggcaagaaat acaagttccg gcttctctac tgctgttgac\n 1381 gtttataaac gattcggtcc aaagtcggga gggagaggag aacgcgttaa gataacatca\n 1441 agaattaaag cattagttat cttcacaaag ggccatgaaa tatttacagc tgaaaatctc\n 1501 gcgaaaagat atgatacgga ggaagattac cagactaaag ggtcacggga tgtacctatc\n 1561 aaagcaacgc ggacgattta ttcaataaac ctctccatct tgatcccgca gctgatccta\n 1621 actttaccgt tgaatgaata ttttgcccgg ttcggaggat caactgcacc tgactcacgt\n 1681 agcctagggg gtaaggtgat tatcggagat ctagaagcaa cgggatcacg gacgatcgat\n 1741 gcggcagata cgtttagaaa ttcgtccgac ccagaaattt tcacaatagc gatcgattat\n 1801 tcggattacg atcaacattt gacggttttt aacttcagga acggtatgct ggaaggaatt\n 1861 cgctctgcga tgaagagata taaagagttg aggtatgatg gatacacgtt gaatgaattg\n 1921 attgaattcg ggtatgggga ggggagaatt gttaattcga aatggaacgg aaagaggcgg\n 1981 gtcaaatctg tacgaatgag cgattatatg gcattgagtg aaagtcaacg cgctcagggc\n 2041 actttcaagc cgccgcaggg agtgagaccg gttagttcaa tgcaagtgtt cgattcagtg\n 2101 ggtgaggcat ctggagggga tactctcctc atctcgccca ctgacggatc ggatttagca\n 2161 accgtcaaca cgcatttgtc gggtgaaaat tcaacgttag ttgctaactc tttgcataat\n 2221 atggctatcg gacgtatcat acaagaagag atcagaaaga accatcgagc ggcttttacc\n 2281 tttgaatctg agcagtacgt tggagatgat acgttacttt atgcaaagtt gaacacatta\n 2341 aaccatgaaa tttttgataa agcgattgat accatcttcg atactgtggg aaagtgcgga\n 2401 catgtggcat cggcagcgaa aacccttatc gctcctttct ctgttgaaaa aactcagact\n 2461 catgcgaagc aaggaattta cattgcgcag gatcggatga tgatcatctc ttcagagcgt\n 2521 agaaaggata tcgaggacgt ccaagggtat atgagatcac aagtgtcggt tatggcgaca\n 2581 aaagtaagcc gcggctttag tcatgaactg gctcagcttg tctttatgat gaagagcagc\n 2641 atcgtaggct ttcgtaaact gaagcgaact gtggtggagg atggtgtata ccgtgatcgc\n 2701 gcgttggatt cggaagatga ggatggcttc actttgatgc agatccgtga tccgttggtc\n 2761 gccttctacc ctgctgagtg gaacggctat ggcatgcatc cagtcgcttt gaatatcgtc\n 2821 atgacggaag acatgtttat agacacgagt accatggttg agtttcagca tgtaatgcgg\n 2881 ccgctccttc gatttatggg taggatacct ccagtgtgga atgaaactaa agccgataaa\n 2941 cgtcagattt catccataac aaagatgagt ttcttctcca aaatggctag accagcggtg\n 3001 agggcggttc tggcgaatag tgaactgtca gatcaagtga gaacattgcc actgggcgac\n 3061 ttttcgcctt tcaatctctc cgcaacaatg atgcactcag cattattgaa agaaccacgc\n 3121 gcgcgtgccc tgctgacgcc agcctacgaa aaagaattcc agtcagagtt gaattcaaac\n 3181 cgggatagcg aagtaaattt cgtcgggagg aacatggaga tcaacactaa ttatatgaaa\n 3241 ctgttcgatg ttgatttgtc tacgcgaata gtggccaaac aatttagttt tccagatcag\n 3301 aatatgtcgt tgccttttta ttttcagaaa ctcttgattg gacatagacc ggtcgcgcgg\n 3361 atgagaatga cctatattga ccggattgac caaatcttac ggggagacgt cgtgatgagg\n 3421 ggtttcatca cagcgaatac tattatgtcc gttttagaga agattggcac tgctcacgcc\n 3481 gtacaggact taacaacaat atttcagttg atgaacattg aatctaaggt ggcgcatagg\n 3541 ctagcggagt atatcgcttc tgaaagggta agattcgacg cgctctcgat tgcaaagagg\n 3601 gggatatgcg gggatgaatt ctccatgtcg ctggatgtgt gcacggaacg gtttgctgaa\n 3661 cggttcatgg aactaccagc gcagtttact aaaactgaga gagatatagc gattttatat\n 3721 gccgcgcagc taactatgtt gcgctgtgcg gctaacctag atcttaggaa aattaagatt\n 3781 ggggtttcag cggatcacgt taagagattt aaacaaagac aggctagatt taagactcat\n 3841 ctacctaaaa tgcgtacagt cacgcggctg ataacgcctg aacgaatctc cgcacgcctg\n 3901 gttcagcatc agtttacatg acgcaccacc taatcaactt ac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610675.1.gbk", "content": "LOCUS JQ610675 3942 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 1, complete sequence.\nACCESSION JQ610675\nVERSION JQ610675.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 3942)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 3942)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..3942\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"1\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..3921\n /note=\"RNA-dependent RNA polymerase\"\n /codon_start=1\n /product=\"VP1\"\n /protein_id=\"AFX73387.1\"\n /translation=\"MVITVEGAWLVRRALQRFLKFSKIDGESAVYEFYRYSSNIREIR\n RKHGTRYKMHDEELERRRDSGKLRFKGMQVVVESTWMEILGKGRTTDEIEIFRSSILS\n LDELNPEEEFLRNYASSDKEHPSYLFVRGRAVNEMQIYGDMPIKAWLSFLVECEVEYG\n YKLFGMEVARSFVQSFGSPFHQNSRDLSQIDDMAPAFTSPLLFEMCCMTSILEINIRM\n RMLEERVATLKFGEREIDPLEVLKEFFRICIPHPKKINNMLRAPYSWFVKLWGVSYHE\n PIVLTARGGEDKNSKDIFFTGFHRVKNPYSIMLKKSRFFKKSLDENISKVKEAIDYSN\n SLTGMSLGLPVFLSMLQNVYDTEFNPTMVQHVLLASFLLSIQTITGYGRAWVKNVSSD\n NDTQMRPAEDNFIDRVAKQTEINFIQAYEEALGHGEDIVKPEDMFTSILRLARNTSSG\n FSTAVDVYKRFGPKSGGRGERVKITSRIKALVIFTKGHEIFTAENLAKRYDTEEDYQT\n KGSRDVPIKATRTIYSINLSILIPQLILTLPLNEYFARFGGSTAPDSRSLGGKVIIGD\n LEATGSRTIDAADTFRNSSDPEIFTIAIDYSDYDQHLTVFNFRNGMLEGIRSAMKRYK\n ELRYDGYTLNELIEFGYGEGRIVNSKWNGKRRVKSVRMSDYMALSESQRAQGTFKPPQ\n GVRPVSSMQVFDSVGEASGGDTLLISPTDGSDLATVNTHLSGENSTLVANSLHNMAIG\n RIIQEEIRKNHRAAFTFESEQYVGDDTLLYAKLNTLNHEIFDKAIDTIFDTVGKCGHV\n ASAAKTLIAPFSVEKTQTHAKQGIYIAQDRMMIISSERRKDIEDVQGYMRSQVSVMAT\n KVSRGFSHELAQLVFMMKSSIVGFRKLKRTVVEDGVYRDRALDSEDEDGFTLMQIRDP\n LVAFYPAEWNGYGMHPVALNIVMTEDMFIDTSTMVEFQHVMRPLLRFMGRIPPVWNET\n KADKRQISSITKMSFFSKMARPAVRAVLANSELSDQVRTLPLGDFSPFNLSATMMHSA\n LLKEPRARALLTPAYEKEFQSELNSNRDSEVNFVGRNMEINTNYMKLFDVDLSTRIVA\n KQFSFPDQNMSLPFYFQKLLIGHRPVARMRMTYIDRIDQILRGDVVMRGFITANTIMS\n VLEKIGTAHAVQDLTTIFQLMNIESKVAHRLAEYIASERVRFDALSIAKRGICGDEFS\n MSLDVCTERFAERFMELPAQFTKTERDIAILYAAQLTMLRCAANLDLRKIKIGVSADH\n VKRFKQRQARFKTHLPKMRTVTRLITPERISARLVQHQFT\"\nORIGIN \n 1 gtataattag gaatggtcat cactgtggaa ggtgcgtggc tggtgagacg ggcgttgcaa\n 61 cgttttttga agttcagtaa aatcgacggg gaatcagcag tttatgagtt ctataggtat\n 121 tcaagtaata ttcgtgaaat aagaaggaag catgggacgc gttataaaat gcatgatgaa\n 181 gagttggagc ggaggcgtga ttcgggcaaa ctgcgtttta aaggtatgca agttgtggta\n 241 gagtcgactt ggatggagat tttagggaag ggacgtacga cggacgaaat cgagatattc\n 301 agaagttcga ttttatcgtt ggatgaactg aatccggaag aagaatttct gcgcaattat\n 361 gcgagttcgg acaaggaaca tccatcctac ttgtttgttc gggggcgggc ggtcaatgag\n 421 atgcagattt atggcgacat gccgataaaa gcgtggttga gctttttagt agaatgtgag\n 481 gttgaatatg ggtacaaact cttcggaatg gaagttgcga gatcgttcgt tcagagcttt\n 541 ggatctccgt ttcaccagaa ctcgcgtgat ctatcacaga ttgacgatat ggcgcctgct\n 601 tttacgtcac ctttattatt tgaaatgtgt tgtatgacat caattctcga aattaatata\n 661 cgcatgcgta tgctggagga gagggttgca accctaaaat ttggtgagcg ggagatcgac\n 721 ccacttgaag tactaaaaga attcttccga atctgcattc cgcatccgaa aaagattaat\n 781 aatatgttga gagctccata ctcatggttc gtcaagctgt ggggcgtatc gtatcatgag\n 841 ccaatagtcc tgacggcgag gggcggcgag gataagaact cgaaagacat attctttacg\n 901 ggatttcaca gagtcaagaa tccatactca ataatgttga aaaaatcgag gttttttaag\n 961 aaatctttag acgagaatat cagcaaagtg aaagaagcga tagactattc aaactcgttg\n 1021 acggggatgt ctttagggct gcccgtattt ctatccatgc tacagaatgt gtacgacact\n 1081 gagtttaatc cgactatggt tcaacacgtg ttactagcgt cgttcttgtt gagtatccaa\n 1141 acaataactg gctatggacg cgcttgggtg aaaaatgtgt caagcgataa cgacactcaa\n 1201 atgcgcccgg cggaggacaa cttcattgat cgagttgcta agcaaacgga gattaatttt\n 1261 atacaggcgt atgaagaggc gttggggcac ggagaagata tcgttaagcc agaagacatg\n 1321 tttacctcca ttttgcgttt ggcaagaaat acaagttccg gcttctctac tgctgttgac\n 1381 gtttataaac gattcggtcc aaagtcggga gggagaggag aacgcgttaa gataacatca\n 1441 agaattaaag cattagttat cttcacaaag ggccatgaaa tatttacagc tgaaaatctc\n 1501 gcgaaaagat atgatacgga ggaagattac cagactaaag ggtcacggga tgtacctatc\n 1561 aaagcaacgc ggacgattta ttcaataaac ctctccatct tgatcccgca gctgatccta\n 1621 actttaccgt tgaatgaata ttttgcccgg ttcggaggat caactgcacc tgactcacgt\n 1681 agcctagggg gtaaggtgat tatcggagat ctagaagcaa cgggatcacg gacgatcgat\n 1741 gcggcagata cgtttagaaa ttcgtccgac ccagaaattt tcacaatagc gatcgattat\n 1801 tcggattacg atcaacattt gacggttttt aacttcagga acggtatgct ggaaggaatt\n 1861 cgctctgcga tgaagagata taaagagttg aggtatgatg gatacacgtt gaatgaattg\n 1921 attgaattcg ggtatgggga ggggagaatt gttaattcga aatggaacgg aaagaggcgg\n 1981 gtcaaatctg tacgaatgag cgattatatg gcattgagtg aaagtcaacg cgctcagggc\n 2041 actttcaagc cgccgcaggg agtgagaccg gttagttcaa tgcaagtgtt cgattcagtg\n 2101 ggtgaggcat ctggagggga tactctcctc atctcgccca ctgacggatc ggatttagca\n 2161 accgtcaaca cgcatttgtc gggtgaaaat tcaacgttag ttgctaactc tttgcataat\n 2221 atggctatcg gacgtatcat acaagaagag atcagaaaga accatcgagc ggcttttacc\n 2281 tttgaatctg agcagtacgt tggagatgat acgttacttt atgcaaagtt gaacacatta\n 2341 aaccatgaaa tttttgataa agcgattgat accatcttcg atactgtggg aaagtgcgga\n 2401 catgtggcat cggcagcgaa aacccttatc gctcctttct ctgttgaaaa aactcagact\n 2461 catgcgaagc aaggaattta cattgcgcag gatcggatga tgatcatctc ttcagagcgt\n 2521 agaaaggata tcgaggacgt ccaagggtat atgagatcac aagtgtcggt tatggcgaca\n 2581 aaagtaagcc gcggctttag tcatgaactg gctcagcttg tctttatgat gaagagcagc\n 2641 atcgtaggct ttcgtaaact gaagcgaact gtggtggagg atggtgtata ccgtgatcgc\n 2701 gcgttggatt cggaagatga ggatggcttc actttgatgc agatccgtga tccgttggtc\n 2761 gccttctacc ctgctgagtg gaacggctat ggcatgcatc cagtcgcttt gaatatcgtc\n 2821 atgacggaag acatgtttat agacacgagt accatggttg agtttcagca tgtaatgcgg\n 2881 ccgctccttc gatttatggg taggatacct ccagtgtgga atgaaactaa agccgataaa\n 2941 cgtcagattt catccataac aaagatgagt ttcttctcca aaatggctag accagcggtg\n 3001 agggcggttc tggcgaatag tgaactgtca gatcaagtga gaacattgcc actgggcgac\n 3061 ttttcgcctt tcaatctctc cgcaacaatg atgcactcag cattattgaa agaaccacgc\n 3121 gcgcgtgccc tgctgacgcc agcctacgaa aaagaattcc agtcagagtt gaattcaaac\n 3181 cgggatagcg aagtaaattt cgtcgggagg aacatggaga tcaacactaa ttatatgaaa\n 3241 ctgttcgatg ttgatttgtc tacgcgaata gtggccaaac aatttagttt tccagatcag\n 3301 aatatgtcgt tgccttttta ttttcagaaa ctcttgattg gacatagacc ggtcgcgcgg\n 3361 atgagaatga cctatattga ccggattgac caaatcttac ggggagacgt cgtgatgagg\n 3421 ggtttcatca cagcgaatac tattatgtcc gttttagaga agattggcac tgctcacgcc\n 3481 gtacaggact taacaacaat atttcagttg atgaacattg aatctaaggt ggcgcatagg\n 3541 ctagcggagt atatcgcttc tgaaagggta agattcgacg cgctctcgat tgcaaagagg\n 3601 gggatatgcg gggatgaatt ctccatgtcg ctggatgtgt gcacggaacg gtttgctgaa\n 3661 cggttcatgg aactaccagc gcagtttact aaaactgaga gagatatagc gattttatat\n 3721 gccgcgcagc taactatgtt gcgctgtgcg gctaacctag atcttaggaa aattaagatt\n 3781 ggggtttcag cggatcacgt taagagattt aaacaaagac aggctagatt taagactcat\n 3841 ctacctaaaa tgcgtacagt cacgcggctg ataacgcctg aacgaatctc cgcacgcctg\n 3901 gttcagcatc agtttacatg acgcaccacc taatcaactt ac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610676.1.gb", "content": "LOCUS JQ610676 2933 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 2, complete sequence.\nACCESSION JQ610676\nVERSION JQ610676.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2933)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2933)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2933\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"2\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..2899\n /note=\"T2 protein\"\n /codon_start=1\n /product=\"VP2\"\n /protein_id=\"AFX73388.1\"\n /translation=\"MAFERTVALTREFANETRQHFGKFDIVVNTESSIEDEATGEWEF\n ARSDGRLGIYEELHNSIAYKHYTAILKGPENYLNIPQIFESKIYKNLNRDDLLARYDY\n SQILRFRDSKIAGRLRMQTYFGDVHVSAGLIDCVAMVREPIRREGCQHMMVRSFDLMN\n AGQFFDVHAPKIHAFDDTVIVESMDIENGVWRVKAGGVGLKTLQEKAEGILGDSVLDL\n VHNYLSQKWDAGYVAAKLLRFDETYKFHPIHEVGIFNTLMIRMGQLDDAYRDGFFDYD\n EIHAQLMRDVTFQYPEGKPVFRRDGQFFKNLVQYSGRAKIGYETYLPDRELWTEWRTR\n SSVQDVVPKYMEWLIGRLQLGKMLKIMSELPADVTMPNYLLKAITYKSSVYVKRLILT\n YIALRMTFGRCPVNKKGTLASSVLGFLHAVIPNLEEFLRKAGITDELCVKMEFTPRLT\n VMEREDRKSDRYAVVLQVYRERKLEVFTPIDSDLFEDRKKYYDEILKDKRWRGEETDY\n FFKDSGIHRSQVAGLSAEQLTLKKLGRDSDFNDPKRFVSYRYRYVSVKAGDIYAEGES\n VITGPLLTLIPHAYEFGRVSLIAGQSRDQSKLDNVPVYRDHMKSLELNGVEVGYDTWC\n PSGRAVQVNLELISTILYNAFKRPIVKGALCHFGMWEFYNPRRPAYESVDVTIMNAIS\n DITGSKRWAYQEIQDWLARFIKGSRVDMVTHRFHGVTKKPTTRGEIWIWNLLLVLISN\n PSLVVSQTDKFPLWVCASDGLHLISTGVRHTDHFRLWEWLPYTEKIGNDDYMSVLATD\n RELRLFEIALEYFETIRIGYRRDEWTHLKSNMFNTWLGTHCGGVGDGMILFDPVRLPS\n PSSVLYLICSHNSTLEGMMYLLHDIYGKIVEENTGTVFIRVHARGCKCSVCRGGLQGV\n DVKNRSAMRVRSMPGNIGFDSVNLILSTSTTSAFGNSYIYFKLINR\"\nORIGIN \n 1 gtataattga tccgcgatgg ctttcgagcg tacggtagcc ttaacaagag agttcgcaaa\n 61 tgaaacaaga cagcattttg ggaagtttga tatagttgta aacacggaaa gcagtattga\n 121 ggacgaagca acgggtgagt gggagttcgc acgaagtgat gggcggcttg gcatctatga\n 181 agaattgcat aatagcatcg cttataaaca ttatacggcg atactaaaag ggccggaaaa\n 241 ttatttgaat attccgcaga tttttgagtc gaaaatctat aagaatttga atagggatga\n 301 tctattggcg agatatgatt attcacaaat actaagattc cgagatagta agatagcggg\n 361 ccgattgagg atgcagacgt atttcgggga cgtgcatgta agtgcgggac tgatagattg\n 421 tgtagcgatg gttcgtgagc ctattagaag ggaagggtgt cagcatatga tggtacgtag\n 481 ttttgatttg atgaatgcgg gccagttttt cgatgttcat gcgccgaaga tccacgcgtt\n 541 tgatgacacg gtgatagttg aaagcatgga catcgaaaac ggagtatggc gcgtaaaggc\n 601 gggtggcgta ggtttgaaaa cgctgcagga aaaagcggaa ggaatactcg gagattcagt\n 661 gttagactta gtccacaact atctcagcca aaagtgggac gcaggttatg tggccgcgaa\n 721 gttgctgagg tttgatgaga catataaatt tcatccaatt catgaggtgg gaattttcaa\n 781 cacattgatg atacgcatgg gtcaactcga tgacgcgtat agggatgggt tcttcgatta\n 841 tgacgagatt cacgctcaat tgatgaggga tgtgactttt cagtacccag aaggtaagcc\n 901 agtctttcgg agagatggcc aattctttaa aaacctagtg cagtattcgg gacgggcgaa\n 961 gattgggtat gagacgtatt taccagacag ggaattgtgg actgaatggc gaacgagatc\n 1021 atccgtgcaa gatgttgtac ccaagtatat ggaatggttg ataggtagat tacagttggg\n 1081 gaaaatgctt aaaataatgt cggaattacc agcggatgtt acgatgccca actatctttt\n 1141 gaaagccatt acatataaat cgagtgtata tgttaagaga ttgatactca cgtacatcgc\n 1201 tttacgaatg acgtttggac ggtgtccagt aaacaaaaaa ggaacgcttg cctcatcagt\n 1261 cttaggtttt ctacacgcgg ttattccgaa tctggaggaa tttctgagga aagcgggaat\n 1321 aacggatgaa ctatgtgtta aaatggagtt tacgccgaga cttactgtga tggagagaga\n 1381 ggataggaag tcagacagat acgccgttgt cttgcaagtt tatagggaga ggaagctgga\n 1441 ggtttttacg cctatagact cagacttgtt cgaagatcgg aaaaagtact atgacgagat\n 1501 cttgaaagat aaaagatggc gtggagaaga gactgattat ttttttaaag actcagggat\n 1561 acaccggtcc caggtggctg ggttgagcgc agagcagctc acgttgaaaa agttaggacg\n 1621 cgactcagat ttcaacgacc ctaaacggtt cgtttcatac agatatagat atgtatcagt\n 1681 taaagcggga gatatctatg cagaagggga gagcgttata acgggaccat tattgacact\n 1741 gattccacat gcctacgagt tcggacgagt atctttgatt gcggggcagt ctcgagatca\n 1801 atcaaagttg gataatgtcc cagtctaccg tgaccacatg aaatccttgg agttaaatgg\n 1861 cgtcgaagtt ggctatgaca cttggtgtcc gtcggggcgt gcagtacaag ttaacttgga\n 1921 gttgatatct accatcctgt ataacgcgtt caaacgtccc atcgttaagg gagcattatg\n 1981 tcacttcggt atgtgggaat tttataaccc gagacgtccc gcgtatgagt cagtagacgt\n 2041 gacaatcatg aatgcgatct cggatatcac tgggagcaaa agatgggcat atcaggaaat\n 2101 tcaagattgg ttggcgagat ttattaaggg gtcacgggtt gacatggtga cacaccgctt\n 2161 ccacggggta acgaagaagc caacaactcg aggtgagata tggatctgga acctactact\n 2221 agttttgatc tcaaatccca gtctggtggt atcacaaacg gataaatttc ccttatgggt\n 2281 ttgcgcctct gatggcttac acctgattag tacgggagtg aggcataccg atcattttag\n 2341 actttgggag tggctaccat ataccgaaaa aattgggaac gacgattata tgtcggttct\n 2401 cgccacagat agagagttgc ggcttttcga aatcgcgttg gaatacttcg agactatacg\n 2461 cattggatat aggagagatg aatggacgca tttgaaatcg aacatgttta atacctggct\n 2521 ggggacgcat tgtgggggtg taggggacgg gatgatattg tttgacccgg tgagattacc\n 2581 atccccgagc agcgtccttt atttgatctg ttcgcataac tcaactttag aaggaatgat\n 2641 gtatttacta catgatatat acgggaagat cgttgaagag aatactggta ctgttttcat\n 2701 aagggtacac gcgcgaggtt gtaagtgctc ggtgtgccga gggggtttac agggagttga\n 2761 cgtaaagaat aggtcagcta tgcgtgttcg tagtatgcca gggaacatcg gcttcgattc\n 2821 agtcaaccta attctttcaa catcaacgac gagcgcgttt gggaactctt acatttactt\n 2881 taagcttatt aatcgttagt gaggtgacac tcgctccgcg atcacgcaga tac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610676.1.gbk", "content": "LOCUS JQ610676 2933 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 2, complete sequence.\nACCESSION JQ610676\nVERSION JQ610676.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2933)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2933)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2933\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"2\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..2899\n /note=\"T2 protein\"\n /codon_start=1\n /product=\"VP2\"\n /protein_id=\"AFX73388.1\"\n /translation=\"MAFERTVALTREFANETRQHFGKFDIVVNTESSIEDEATGEWEF\n ARSDGRLGIYEELHNSIAYKHYTAILKGPENYLNIPQIFESKIYKNLNRDDLLARYDY\n SQILRFRDSKIAGRLRMQTYFGDVHVSAGLIDCVAMVREPIRREGCQHMMVRSFDLMN\n AGQFFDVHAPKIHAFDDTVIVESMDIENGVWRVKAGGVGLKTLQEKAEGILGDSVLDL\n VHNYLSQKWDAGYVAAKLLRFDETYKFHPIHEVGIFNTLMIRMGQLDDAYRDGFFDYD\n EIHAQLMRDVTFQYPEGKPVFRRDGQFFKNLVQYSGRAKIGYETYLPDRELWTEWRTR\n SSVQDVVPKYMEWLIGRLQLGKMLKIMSELPADVTMPNYLLKAITYKSSVYVKRLILT\n YIALRMTFGRCPVNKKGTLASSVLGFLHAVIPNLEEFLRKAGITDELCVKMEFTPRLT\n VMEREDRKSDRYAVVLQVYRERKLEVFTPIDSDLFEDRKKYYDEILKDKRWRGEETDY\n FFKDSGIHRSQVAGLSAEQLTLKKLGRDSDFNDPKRFVSYRYRYVSVKAGDIYAEGES\n VITGPLLTLIPHAYEFGRVSLIAGQSRDQSKLDNVPVYRDHMKSLELNGVEVGYDTWC\n PSGRAVQVNLELISTILYNAFKRPIVKGALCHFGMWEFYNPRRPAYESVDVTIMNAIS\n DITGSKRWAYQEIQDWLARFIKGSRVDMVTHRFHGVTKKPTTRGEIWIWNLLLVLISN\n PSLVVSQTDKFPLWVCASDGLHLISTGVRHTDHFRLWEWLPYTEKIGNDDYMSVLATD\n RELRLFEIALEYFETIRIGYRRDEWTHLKSNMFNTWLGTHCGGVGDGMILFDPVRLPS\n PSSVLYLICSHNSTLEGMMYLLHDIYGKIVEENTGTVFIRVHARGCKCSVCRGGLQGV\n DVKNRSAMRVRSMPGNIGFDSVNLILSTSTTSAFGNSYIYFKLINR\"\nORIGIN \n 1 gtataattga tccgcgatgg ctttcgagcg tacggtagcc ttaacaagag agttcgcaaa\n 61 tgaaacaaga cagcattttg ggaagtttga tatagttgta aacacggaaa gcagtattga\n 121 ggacgaagca acgggtgagt gggagttcgc acgaagtgat gggcggcttg gcatctatga\n 181 agaattgcat aatagcatcg cttataaaca ttatacggcg atactaaaag ggccggaaaa\n 241 ttatttgaat attccgcaga tttttgagtc gaaaatctat aagaatttga atagggatga\n 301 tctattggcg agatatgatt attcacaaat actaagattc cgagatagta agatagcggg\n 361 ccgattgagg atgcagacgt atttcgggga cgtgcatgta agtgcgggac tgatagattg\n 421 tgtagcgatg gttcgtgagc ctattagaag ggaagggtgt cagcatatga tggtacgtag\n 481 ttttgatttg atgaatgcgg gccagttttt cgatgttcat gcgccgaaga tccacgcgtt\n 541 tgatgacacg gtgatagttg aaagcatgga catcgaaaac ggagtatggc gcgtaaaggc\n 601 gggtggcgta ggtttgaaaa cgctgcagga aaaagcggaa ggaatactcg gagattcagt\n 661 gttagactta gtccacaact atctcagcca aaagtgggac gcaggttatg tggccgcgaa\n 721 gttgctgagg tttgatgaga catataaatt tcatccaatt catgaggtgg gaattttcaa\n 781 cacattgatg atacgcatgg gtcaactcga tgacgcgtat agggatgggt tcttcgatta\n 841 tgacgagatt cacgctcaat tgatgaggga tgtgactttt cagtacccag aaggtaagcc\n 901 agtctttcgg agagatggcc aattctttaa aaacctagtg cagtattcgg gacgggcgaa\n 961 gattgggtat gagacgtatt taccagacag ggaattgtgg actgaatggc gaacgagatc\n 1021 atccgtgcaa gatgttgtac ccaagtatat ggaatggttg ataggtagat tacagttggg\n 1081 gaaaatgctt aaaataatgt cggaattacc agcggatgtt acgatgccca actatctttt\n 1141 gaaagccatt acatataaat cgagtgtata tgttaagaga ttgatactca cgtacatcgc\n 1201 tttacgaatg acgtttggac ggtgtccagt aaacaaaaaa ggaacgcttg cctcatcagt\n 1261 cttaggtttt ctacacgcgg ttattccgaa tctggaggaa tttctgagga aagcgggaat\n 1321 aacggatgaa ctatgtgtta aaatggagtt tacgccgaga cttactgtga tggagagaga\n 1381 ggataggaag tcagacagat acgccgttgt cttgcaagtt tatagggaga ggaagctgga\n 1441 ggtttttacg cctatagact cagacttgtt cgaagatcgg aaaaagtact atgacgagat\n 1501 cttgaaagat aaaagatggc gtggagaaga gactgattat ttttttaaag actcagggat\n 1561 acaccggtcc caggtggctg ggttgagcgc agagcagctc acgttgaaaa agttaggacg\n 1621 cgactcagat ttcaacgacc ctaaacggtt cgtttcatac agatatagat atgtatcagt\n 1681 taaagcggga gatatctatg cagaagggga gagcgttata acgggaccat tattgacact\n 1741 gattccacat gcctacgagt tcggacgagt atctttgatt gcggggcagt ctcgagatca\n 1801 atcaaagttg gataatgtcc cagtctaccg tgaccacatg aaatccttgg agttaaatgg\n 1861 cgtcgaagtt ggctatgaca cttggtgtcc gtcggggcgt gcagtacaag ttaacttgga\n 1921 gttgatatct accatcctgt ataacgcgtt caaacgtccc atcgttaagg gagcattatg\n 1981 tcacttcggt atgtgggaat tttataaccc gagacgtccc gcgtatgagt cagtagacgt\n 2041 gacaatcatg aatgcgatct cggatatcac tgggagcaaa agatgggcat atcaggaaat\n 2101 tcaagattgg ttggcgagat ttattaaggg gtcacgggtt gacatggtga cacaccgctt\n 2161 ccacggggta acgaagaagc caacaactcg aggtgagata tggatctgga acctactact\n 2221 agttttgatc tcaaatccca gtctggtggt atcacaaacg gataaatttc ccttatgggt\n 2281 ttgcgcctct gatggcttac acctgattag tacgggagtg aggcataccg atcattttag\n 2341 actttgggag tggctaccat ataccgaaaa aattgggaac gacgattata tgtcggttct\n 2401 cgccacagat agagagttgc ggcttttcga aatcgcgttg gaatacttcg agactatacg\n 2461 cattggatat aggagagatg aatggacgca tttgaaatcg aacatgttta atacctggct\n 2521 ggggacgcat tgtgggggtg taggggacgg gatgatattg tttgacccgg tgagattacc\n 2581 atccccgagc agcgtccttt atttgatctg ttcgcataac tcaactttag aaggaatgat\n 2641 gtatttacta catgatatat acgggaagat cgttgaagag aatactggta ctgttttcat\n 2701 aagggtacac gcgcgaggtt gtaagtgctc ggtgtgccga gggggtttac agggagttga\n 2761 cgtaaagaat aggtcagcta tgcgtgttcg tagtatgcca gggaacatcg gcttcgattc\n 2821 agtcaaccta attctttcaa catcaacgac gagcgcgttt gggaactctt acatttactt\n 2881 taagcttatt aatcgttagt gaggtgacac tcgctccgcg atcacgcaga tac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610677.1.gb", "content": "LOCUS JQ610677 2781 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 3, complete sequence.\nACCESSION JQ610677\nVERSION JQ610677.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2781)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2781)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2781\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"3\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 18..2738\n /note=\"outer capsid and cell attachment protein\"\n /codon_start=1\n /product=\"VP3\"\n /protein_id=\"AFX73389.1\"\n /translation=\"MAHADAKGSDPEREALRKNPYLDGDVLGTAGGQVLSVFALTEIL\n QKVRQTQAELAAHAIDLDGPVPEITGVIKKIAELVDTVPYEVRDSPPISYKTLSMQSR\n DFVIQVDQYYEQISQIGGDVGEDEPMEFYKTMLEKVRYLRKSGAFILRGIKTRDYRGN\n EVAEPEALGVEFREVLSNFIAADRQVIQNALDAAIVENGQVGDRAVDVYMAAVSEPWY\n RIYNRLQAYIEVTQLRELRRAMEWLNALGRRKRVEYDDSFLTDFRARDTVWVQTQQLP\n VNARVIWEVPRSYIANLMMNIALCLPLGDFIAPNPRIGSITITQRITMTTPFGMMSGM\n TPTSMQMDDVKKIYLALLFPGQIVLNIKPDPAHSIDPVLRMVSGVLGHLMFTYGPRFT\n NITATTSQLLDSALSDYFLYMQNSRVPVVYGPTGLPLDFRIGGRQGYDCNNLRGDPQT\n GRGYNGWGVVDVDRRAPSPYDLVQRFIRYCNIDSREIIDPRTFGFNMNYPLYMEMIRA\n LVAGGKDQEAAYLRQMLPFHMIRFARINQIINEDLLSAFSLPDEDFDALFFNMLRGEY\n GKAEPIVLDISWASIWFAFNRYFDPVQRSDLLSVAPMIEAVYASEISILQLDMINLQQ\n LRARAPDMLINATPSQFWKAALASAAEPVVELMNLSQSFRFINVRDIIQWTRTREVQP\n SLALTLEREAWAVAADFEELMLVNHVYFHRSVVPEPQLDDIDEFRRQGFLYTNLLEAA\n PPRLLITNYDYNVALLQANLGQFKSALRRILDDGGWVMFGGMLRNVRLKIYDSKPGED\n VLSELPYLYSEKVENGLRFVSLKYARRATIYFLMYKVEYSNTPDALISVNPTYTMTKI\n YTNKRLVRKVRSPDVLNIVNKRVVAYKTKMRLIDITSALRLGVKLAAPTV\"\nORIGIN \n 1 gtatatattc cttcgcgatg gcgcatgcgg atgctaaagg aagtgatccg gagagagagg\n 61 cgttgaggaa gaacccttat ctagatggag acgtcttggg aaccgcaggc ggccaagttt\n 121 tgtcggtttt cgcattgacc gaaattttac aaaaagtaag acagacgcaa gctgaactgg\n 181 ccgcacacgc aatcgatttg gatggaccag tccctgagat caccggggtt attaagaaga\n 241 tagcggagtt agttgacacc gttccatatg aagtgcgcga ttcaccacct ataagctata\n 301 agactttaag catgcaatcg cgcgactttg tcatccaggt ggaccagtat tacgaacaga\n 361 tttcgcaaat tggaggagac gtcggggagg acgagccgat ggagttctat aaaacaatgc\n 421 tagaaaaggt acgctattta aggaagagtg gagcattcat tttgagaggt attaaaacac\n 481 gagactatag gggtaatgaa gtggcggaac cagaagcttt aggagtcgaa tttcgtgaag\n 541 tactttctaa ttttattgcg gcggatagac aagtgataca gaatgcgtta gatgcagcca\n 601 tagttgaaaa tggccaggtg ggtgataggg cggtcgatgt ttatatggct gctgtttctg\n 661 agccatggta tcgaatatat aataggttac aggcgtatat tgaagttacg caactgagag\n 721 aattgaggcg cgcaatggag tggctgaatg cacttggtcg tcgtaagaga gtggagtatg\n 781 atgattcatt cttgaccgat tttcgagcga gagatacggt atgggtgcag acgcaacagc\n 841 ttcccgttaa cgctcgtgtg atctgggagg ttccgaggtc atatatagct aatttgatga\n 901 tgaatatcgc gttatgtctg ccactaggtg atttcatagc cccaaacccg aggattgggt\n 961 cgataacgat aacccagcga ataactatga ctacgccttt tgggatgatg tctgggatga\n 1021 cccccacatc aatgcagatg gacgatgtca agaagatata tctcgcgttg ctctttcccg\n 1081 ggcagatcgt tttgaatatt aaacccgacc cagcgcactc catcgatccg gtactgcgta\n 1141 tggtttcggg tgtgttgggg catttgatgt tcacctacgg tcccagattt actaacataa\n 1201 cagctacaac atcgcagttg ctagatagtg ccttgagcga ctattttctg tacatgcaaa\n 1261 acagtagagt tccggtggtg tacggaccaa ctgggttacc tttggatttt agaatcggtg\n 1321 gacgacaagg ctatgattgc aataatctgc ggggagaccc gcagactggg agggggtaca\n 1381 atggatgggg agtcgttgac gtcgatcgaa gagcacccag tccgtacgat ttggttcaaa\n 1441 gatttatacg ttactgcaac atagactctc gcgagatcat cgacccacgg acgtttggat\n 1501 ttaatatgaa ctatccgcta tatatggaga tgatacgtgc attagttgcc ggaggaaaag\n 1561 atcaggaagc ggcgtaccta cgacaaatgt taccttttca catgatcaga ttcgcacgga\n 1621 tcaatcagat aataaacgaa gacttactta gcgcgttttc cttaccagat gaggatttcg\n 1681 acgcattatt tttcaatatg ctgcgcggcg agtatggaaa ggctgagccg atcgttttag\n 1741 atatcagttg ggcttcaatt tggtttgcgt tcaaccgcta ctttgaccca gtccaaaggt\n 1801 cagatctatt atcagtggca cccatgattg aggctgtcta tgcgtcagaa atctccattt\n 1861 tgcaattgga tatgatcaac ctgcagcagt tgagagcgag ggcacctgat atgttgatta\n 1921 acgcaactcc gagtcagttt tggaaagcgg cgttagcatc cgcagcagaa ccagtagttg\n 1981 agttgatgaa tctttcgcag agttttcgat tcattaacgt cagggatata atacagtgga\n 2041 ctagaacacg agaagtgcaa ccgtcgctgg ctctcacttt ggaacgagag gcgtgggcgg\n 2101 tcgcagctga cttcgaagag ttgatgctcg taaaccatgt ctattttcat agatcggtgg\n 2161 ttcccgaacc acagttggat gacatcgatg aatttcgtag gcaaggattc ctgtacacaa\n 2221 atctattgga agcggccccc ccgcgtttgt taatcaccaa ttatgattac aacgttgcgc\n 2281 tactgcaggc gaatcttgga caatttaaat ccgctttgag gagaattctg gatgacggtg\n 2341 gttgggtgat gttcggggga atgctgagaa atgttcgttt gaaaatatac gattcaaagc\n 2401 cgggagagga cgtcttaagc gaactaccct atctttactc cgagaaagtg gaaaacggtt\n 2461 taaggtttgt gtctttgaag tatgcgagac gagcaactat ttatttttta atgtataagg\n 2521 ttgaatattc aaacacacca gatgctttaa tatcagtcaa ccccacgtat accatgacga\n 2581 agatttatac aaacaagaga ctggtccgga aagtcaggtc acctgacgtt ttgaacatcg\n 2641 ttaataaaag agtagtggct tataaaacga agatgcggtt gattgacatt acatcggcac\n 2701 tgcgtcttgg tgttaaactt gcagcaccta cagtgtgaat tgaccactca acctgtggtg\n 2761 ctcggtgggg aattcgctta c\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610677.1.gbk", "content": "LOCUS JQ610677 2781 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 3, complete sequence.\nACCESSION JQ610677\nVERSION JQ610677.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2781)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2781)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2781\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"3\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 18..2738\n /note=\"outer capsid and cell attachment protein\"\n /codon_start=1\n /product=\"VP3\"\n /protein_id=\"AFX73389.1\"\n /translation=\"MAHADAKGSDPEREALRKNPYLDGDVLGTAGGQVLSVFALTEIL\n QKVRQTQAELAAHAIDLDGPVPEITGVIKKIAELVDTVPYEVRDSPPISYKTLSMQSR\n DFVIQVDQYYEQISQIGGDVGEDEPMEFYKTMLEKVRYLRKSGAFILRGIKTRDYRGN\n EVAEPEALGVEFREVLSNFIAADRQVIQNALDAAIVENGQVGDRAVDVYMAAVSEPWY\n RIYNRLQAYIEVTQLRELRRAMEWLNALGRRKRVEYDDSFLTDFRARDTVWVQTQQLP\n VNARVIWEVPRSYIANLMMNIALCLPLGDFIAPNPRIGSITITQRITMTTPFGMMSGM\n TPTSMQMDDVKKIYLALLFPGQIVLNIKPDPAHSIDPVLRMVSGVLGHLMFTYGPRFT\n NITATTSQLLDSALSDYFLYMQNSRVPVVYGPTGLPLDFRIGGRQGYDCNNLRGDPQT\n GRGYNGWGVVDVDRRAPSPYDLVQRFIRYCNIDSREIIDPRTFGFNMNYPLYMEMIRA\n LVAGGKDQEAAYLRQMLPFHMIRFARINQIINEDLLSAFSLPDEDFDALFFNMLRGEY\n GKAEPIVLDISWASIWFAFNRYFDPVQRSDLLSVAPMIEAVYASEISILQLDMINLQQ\n LRARAPDMLINATPSQFWKAALASAAEPVVELMNLSQSFRFINVRDIIQWTRTREVQP\n SLALTLEREAWAVAADFEELMLVNHVYFHRSVVPEPQLDDIDEFRRQGFLYTNLLEAA\n PPRLLITNYDYNVALLQANLGQFKSALRRILDDGGWVMFGGMLRNVRLKIYDSKPGED\n VLSELPYLYSEKVENGLRFVSLKYARRATIYFLMYKVEYSNTPDALISVNPTYTMTKI\n YTNKRLVRKVRSPDVLNIVNKRVVAYKTKMRLIDITSALRLGVKLAAPTV\"\nORIGIN \n 1 gtatatattc cttcgcgatg gcgcatgcgg atgctaaagg aagtgatccg gagagagagg\n 61 cgttgaggaa gaacccttat ctagatggag acgtcttggg aaccgcaggc ggccaagttt\n 121 tgtcggtttt cgcattgacc gaaattttac aaaaagtaag acagacgcaa gctgaactgg\n 181 ccgcacacgc aatcgatttg gatggaccag tccctgagat caccggggtt attaagaaga\n 241 tagcggagtt agttgacacc gttccatatg aagtgcgcga ttcaccacct ataagctata\n 301 agactttaag catgcaatcg cgcgactttg tcatccaggt ggaccagtat tacgaacaga\n 361 tttcgcaaat tggaggagac gtcggggagg acgagccgat ggagttctat aaaacaatgc\n 421 tagaaaaggt acgctattta aggaagagtg gagcattcat tttgagaggt attaaaacac\n 481 gagactatag gggtaatgaa gtggcggaac cagaagcttt aggagtcgaa tttcgtgaag\n 541 tactttctaa ttttattgcg gcggatagac aagtgataca gaatgcgtta gatgcagcca\n 601 tagttgaaaa tggccaggtg ggtgataggg cggtcgatgt ttatatggct gctgtttctg\n 661 agccatggta tcgaatatat aataggttac aggcgtatat tgaagttacg caactgagag\n 721 aattgaggcg cgcaatggag tggctgaatg cacttggtcg tcgtaagaga gtggagtatg\n 781 atgattcatt cttgaccgat tttcgagcga gagatacggt atgggtgcag acgcaacagc\n 841 ttcccgttaa cgctcgtgtg atctgggagg ttccgaggtc atatatagct aatttgatga\n 901 tgaatatcgc gttatgtctg ccactaggtg atttcatagc cccaaacccg aggattgggt\n 961 cgataacgat aacccagcga ataactatga ctacgccttt tgggatgatg tctgggatga\n 1021 cccccacatc aatgcagatg gacgatgtca agaagatata tctcgcgttg ctctttcccg\n 1081 ggcagatcgt tttgaatatt aaacccgacc cagcgcactc catcgatccg gtactgcgta\n 1141 tggtttcggg tgtgttgggg catttgatgt tcacctacgg tcccagattt actaacataa\n 1201 cagctacaac atcgcagttg ctagatagtg ccttgagcga ctattttctg tacatgcaaa\n 1261 acagtagagt tccggtggtg tacggaccaa ctgggttacc tttggatttt agaatcggtg\n 1321 gacgacaagg ctatgattgc aataatctgc ggggagaccc gcagactggg agggggtaca\n 1381 atggatgggg agtcgttgac gtcgatcgaa gagcacccag tccgtacgat ttggttcaaa\n 1441 gatttatacg ttactgcaac atagactctc gcgagatcat cgacccacgg acgtttggat\n 1501 ttaatatgaa ctatccgcta tatatggaga tgatacgtgc attagttgcc ggaggaaaag\n 1561 atcaggaagc ggcgtaccta cgacaaatgt taccttttca catgatcaga ttcgcacgga\n 1621 tcaatcagat aataaacgaa gacttactta gcgcgttttc cttaccagat gaggatttcg\n 1681 acgcattatt tttcaatatg ctgcgcggcg agtatggaaa ggctgagccg atcgttttag\n 1741 atatcagttg ggcttcaatt tggtttgcgt tcaaccgcta ctttgaccca gtccaaaggt\n 1801 cagatctatt atcagtggca cccatgattg aggctgtcta tgcgtcagaa atctccattt\n 1861 tgcaattgga tatgatcaac ctgcagcagt tgagagcgag ggcacctgat atgttgatta\n 1921 acgcaactcc gagtcagttt tggaaagcgg cgttagcatc cgcagcagaa ccagtagttg\n 1981 agttgatgaa tctttcgcag agttttcgat tcattaacgt cagggatata atacagtgga\n 2041 ctagaacacg agaagtgcaa ccgtcgctgg ctctcacttt ggaacgagag gcgtgggcgg\n 2101 tcgcagctga cttcgaagag ttgatgctcg taaaccatgt ctattttcat agatcggtgg\n 2161 ttcccgaacc acagttggat gacatcgatg aatttcgtag gcaaggattc ctgtacacaa\n 2221 atctattgga agcggccccc ccgcgtttgt taatcaccaa ttatgattac aacgttgcgc\n 2281 tactgcaggc gaatcttgga caatttaaat ccgctttgag gagaattctg gatgacggtg\n 2341 gttgggtgat gttcggggga atgctgagaa atgttcgttt gaaaatatac gattcaaagc\n 2401 cgggagagga cgtcttaagc gaactaccct atctttactc cgagaaagtg gaaaacggtt\n 2461 taaggtttgt gtctttgaag tatgcgagac gagcaactat ttatttttta atgtataagg\n 2521 ttgaatattc aaacacacca gatgctttaa tatcagtcaa ccccacgtat accatgacga\n 2581 agatttatac aaacaagaga ctggtccgga aagtcaggtc acctgacgtt ttgaacatcg\n 2641 ttaataaaag agtagtggct tataaaacga agatgcggtt gattgacatt acatcggcac\n 2701 tgcgtcttgg tgttaaactt gcagcaccta cagtgtgaat tgaccactca acctgtggtg\n 2761 ctcggtgggg aattcgctta c\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610678.1.gb", "content": "LOCUS JQ610678 1957 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 4, complete sequence.\nACCESSION JQ610678\nVERSION JQ610678.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1957)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1957)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1957\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"4\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..1926\n /note=\"capping enzyme\"\n /codon_start=1\n /product=\"VP4\"\n /protein_id=\"AFX73390.1\"\n /translation=\"MEPFAVLHLSAKLAPLVREGFIPYVDLDNIKTLNDLWIEIGKCS\n SDVYAVGRINRWTIRQLRAYRFIFVSEKRTITLKDIKITPDVPIRCADGLDLKLLETT\n IGRKRLVLRKTFGDILRKYALSQSVHLHGSEAETLNMADPTIHHVKGLPMIAPNHLNP\n TKPWSDLDDTETDEKLVSMLDYAMYSAQEVHYVGSGDGRTIRLFAKRDKKRFDRAKWV\n CYDPIMTDIGLTNVIAVKHYVNTFRDMLPYLNTGDRVERLLLWDVSGDAAKHDRFWEA\n QRTEEDRRGESVAVSLTEYFALAIIKHRIPIYEEKYRCTTSWIVPQPGAVREMYEMRN\n IILLNGFSRVNRAHIPQAGVMEIEADVLREMVRNFHGAGRGRLLKKSLYESLHIHQVD\n GLEDSEDGARSDLFYLTNQRNVNSIQSIRRVLGNSTVSTLWVSRERVFEYDDFNFDRS\n ALMLWHRGREHLLFDGNGAVLYLMWQHGDRYRKDVNYDPSWAEHFAVLIREPQPWRPV\n PDLSLCRFISLRRVSTVIRIRGDIHRKSDQVKRLGLDLSGHLFVTLISGAYLADLRWW\n FRMIIQWSKQRRQEKIDDLAKVNAEVVEWKEEKADEPWHRKEDLIAALIAAKSITGDQ\n HIDGWIAELRDME\"\nORIGIN \n 1 gtatatttcg aaatggagcc ctttgctgtg ctgcacctat cagccaagct ggcaccgctg\n 61 gtgcgtgagg gatttatccc gtatgtggac ttggataata ttaagacgtt gaatgacctc\n 121 tggattgaga ttggcaaatg ctcatctgat gtatatgcgg ttggacgaat aaataggtgg\n 181 acgatacgtc agctacgtgc gtatagattc atattcgtgt cggagaagag aacaataacg\n 241 ttgaaggata ttaagatcac acctgacgtg ccaataagat gcgcggatgg gctagactta\n 301 aagttacttg agactacaat aggacgtaaa agattagtgt tgcgaaagac gtttggagac\n 361 atactgcgaa aatatgcgtt aagccagtcg gtacacttgc atggatctga ggcagaaacc\n 421 ttgaatatgg cggaccctac catacatcac gtgaaggggt taccaatgat agcgccaaat\n 481 catttaaatc caacgaaacc atggagtgat ctggacgaca cagaaaccga tgaaaaacta\n 541 gtgtcaatgc tagattacgc gatgtatagc gcgcaagaag tgcattatgt tggctcggga\n 601 gacggtagaa cgatacggct gtttgcaaag agggacaaaa agagatttga tagagcgaag\n 661 tgggtgtgct atgaccctat tatgactgat attggattga caaatgtgat agctgttaaa\n 721 cactatgtca atactttcag ggatatgcta ccgtatttaa atactggcga ccgagttgag\n 781 agattactat tgtgggacgt aagtggagat gcggcgaaac atgatcggtt ttgggaagct\n 841 cagaggactg aggaggaccg gcggggagaa tcagttgccg tgtctttaac ggagtacttc\n 901 gccttggcta ttatcaaaca tagaattcca atctatgagg aaaagtatag atgcaccact\n 961 tcgtggattg taccgcagcc tggcgcggtc cgcgagatgt acgagatgag gaatatcata\n 1021 ctgttgaacg gtttttctag ggtaaatcga gcgcatatcc cccaggcagg cgtaatggag\n 1081 attgaggctg atgtgttacg tgagatggtg aggaacttcc atggagctgg tcgcggtcgg\n 1141 ctgctgaaga aatcgcttta tgagagtcta catatccatc aagttgatgg attggaggat\n 1201 tcggaagacg gagcgcggag cgatctcttt tatttaacca accaacgtaa tgttaattca\n 1261 atacaatcaa tcagacgagt tttgggaaat agcacggtgt cgactttatg ggtgtcaagg\n 1321 gaacgagttt tcgaatatga tgactttaat tttgaccgat cagcgttgat gctctggcac\n 1381 aggggtagag agcacttact atttgatggc aacggcgcgg ttctatattt gatgtggcag\n 1441 cacggagata gatatagaaa ggatgtgaac tatgatcctt cgtgggccga acattttgca\n 1501 gtattgatcc gagagccaca accttggcga ccagttccag atctgtccct ctgccgtttt\n 1561 atttcgctaa gacgggtgtc gacggttatt agaatacgag gcgatattca caggaaaagt\n 1621 gatcaggtaa agcgtttagg gttagatttg tcaggacatc tgttcgtaac gttaatttct\n 1681 ggagcgtatc ttgccgattt aagatggtgg ttccggatga tcatccaatg gtcaaagcag\n 1741 cgtagacagg aaaagataga cgatttggct aaggttaacg ctgaagtggt tgaatggaaa\n 1801 gaagagaaag ccgacgaacc gtggcatcgc aaggaggacc tgatcgctgc tttaatcgcg\n 1861 gcaaaaagta tcaccggtga tcagcatata gatgggtgga ttgcggagct gagggatatg\n 1921 gaatgacatc cacccgaggg gcaatcgaac tacctac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610678.1.gbk", "content": "LOCUS JQ610678 1957 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 4, complete sequence.\nACCESSION JQ610678\nVERSION JQ610678.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1957)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1957)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1957\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"4\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..1926\n /note=\"capping enzyme\"\n /codon_start=1\n /product=\"VP4\"\n /protein_id=\"AFX73390.1\"\n /translation=\"MEPFAVLHLSAKLAPLVREGFIPYVDLDNIKTLNDLWIEIGKCS\n SDVYAVGRINRWTIRQLRAYRFIFVSEKRTITLKDIKITPDVPIRCADGLDLKLLETT\n IGRKRLVLRKTFGDILRKYALSQSVHLHGSEAETLNMADPTIHHVKGLPMIAPNHLNP\n TKPWSDLDDTETDEKLVSMLDYAMYSAQEVHYVGSGDGRTIRLFAKRDKKRFDRAKWV\n CYDPIMTDIGLTNVIAVKHYVNTFRDMLPYLNTGDRVERLLLWDVSGDAAKHDRFWEA\n QRTEEDRRGESVAVSLTEYFALAIIKHRIPIYEEKYRCTTSWIVPQPGAVREMYEMRN\n IILLNGFSRVNRAHIPQAGVMEIEADVLREMVRNFHGAGRGRLLKKSLYESLHIHQVD\n GLEDSEDGARSDLFYLTNQRNVNSIQSIRRVLGNSTVSTLWVSRERVFEYDDFNFDRS\n ALMLWHRGREHLLFDGNGAVLYLMWQHGDRYRKDVNYDPSWAEHFAVLIREPQPWRPV\n PDLSLCRFISLRRVSTVIRIRGDIHRKSDQVKRLGLDLSGHLFVTLISGAYLADLRWW\n FRMIIQWSKQRRQEKIDDLAKVNAEVVEWKEEKADEPWHRKEDLIAALIAAKSITGDQ\n HIDGWIAELRDME\"\nORIGIN \n 1 gtatatttcg aaatggagcc ctttgctgtg ctgcacctat cagccaagct ggcaccgctg\n 61 gtgcgtgagg gatttatccc gtatgtggac ttggataata ttaagacgtt gaatgacctc\n 121 tggattgaga ttggcaaatg ctcatctgat gtatatgcgg ttggacgaat aaataggtgg\n 181 acgatacgtc agctacgtgc gtatagattc atattcgtgt cggagaagag aacaataacg\n 241 ttgaaggata ttaagatcac acctgacgtg ccaataagat gcgcggatgg gctagactta\n 301 aagttacttg agactacaat aggacgtaaa agattagtgt tgcgaaagac gtttggagac\n 361 atactgcgaa aatatgcgtt aagccagtcg gtacacttgc atggatctga ggcagaaacc\n 421 ttgaatatgg cggaccctac catacatcac gtgaaggggt taccaatgat agcgccaaat\n 481 catttaaatc caacgaaacc atggagtgat ctggacgaca cagaaaccga tgaaaaacta\n 541 gtgtcaatgc tagattacgc gatgtatagc gcgcaagaag tgcattatgt tggctcggga\n 601 gacggtagaa cgatacggct gtttgcaaag agggacaaaa agagatttga tagagcgaag\n 661 tgggtgtgct atgaccctat tatgactgat attggattga caaatgtgat agctgttaaa\n 721 cactatgtca atactttcag ggatatgcta ccgtatttaa atactggcga ccgagttgag\n 781 agattactat tgtgggacgt aagtggagat gcggcgaaac atgatcggtt ttgggaagct\n 841 cagaggactg aggaggaccg gcggggagaa tcagttgccg tgtctttaac ggagtacttc\n 901 gccttggcta ttatcaaaca tagaattcca atctatgagg aaaagtatag atgcaccact\n 961 tcgtggattg taccgcagcc tggcgcggtc cgcgagatgt acgagatgag gaatatcata\n 1021 ctgttgaacg gtttttctag ggtaaatcga gcgcatatcc cccaggcagg cgtaatggag\n 1081 attgaggctg atgtgttacg tgagatggtg aggaacttcc atggagctgg tcgcggtcgg\n 1141 ctgctgaaga aatcgcttta tgagagtcta catatccatc aagttgatgg attggaggat\n 1201 tcggaagacg gagcgcggag cgatctcttt tatttaacca accaacgtaa tgttaattca\n 1261 atacaatcaa tcagacgagt tttgggaaat agcacggtgt cgactttatg ggtgtcaagg\n 1321 gaacgagttt tcgaatatga tgactttaat tttgaccgat cagcgttgat gctctggcac\n 1381 aggggtagag agcacttact atttgatggc aacggcgcgg ttctatattt gatgtggcag\n 1441 cacggagata gatatagaaa ggatgtgaac tatgatcctt cgtgggccga acattttgca\n 1501 gtattgatcc gagagccaca accttggcga ccagttccag atctgtccct ctgccgtttt\n 1561 atttcgctaa gacgggtgtc gacggttatt agaatacgag gcgatattca caggaaaagt\n 1621 gatcaggtaa agcgtttagg gttagatttg tcaggacatc tgttcgtaac gttaatttct\n 1681 ggagcgtatc ttgccgattt aagatggtgg ttccggatga tcatccaatg gtcaaagcag\n 1741 cgtagacagg aaaagataga cgatttggct aaggttaacg ctgaagtggt tgaatggaaa\n 1801 gaagagaaag ccgacgaacc gtggcatcgc aaggaggacc tgatcgctgc tttaatcgcg\n 1861 gcaaaaagta tcaccggtga tcagcatata gatgggtgga ttgcggagct gagggatatg\n 1921 gaatgacatc cacccgaggg gcaatcgaac tacctac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610679.1.gb", "content": "LOCUS JQ610679 1735 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 5, complete sequence.\nACCESSION JQ610679\nVERSION JQ610679.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1735)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1735)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1735\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"5\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 36..1676\n /note=\"non-structural protein 1\"\n /codon_start=1\n /product=\"NS1\"\n /protein_id=\"AFX73391.1\"\n /translation=\"MDQFLDSFDVTGDEANALRLLRAVSPEMTCSHLRRDCLIGGICA\n KQFFNEVLMAILDSKDRQAARQLVTLAVMTSYDRELIWLNVLRSTEVLPANDYAHEIQ\n NVVLNLKRVFIESGLEEKYKSFRAKRRPNRSPTEDAFSFLPFFYIPMNETKRVGIKKL\n TRVRNLGVAFVDRREVTHHLPFTVDAARRDLMMLRNFTLEHQRTCTFTGSKSLIHGMI\n FCPEEMEPLFQKKETALEIYRICEQDMKFINSRGTMSFPRFLMQRLAVKNASSDAMDQ\n VMLGRTPSDGRLMSVTGASFFFGGGPDWRKWAMPALLVRAARLRTVVTSFVKEWFDST\n HTCQVCFLVEKGVADSIPITDVRLSDVCGVGPVAYVRSYAHDDGNAPDVRVLRKGEIF\n RLMGGHYVMQTTASTMESLVVAAKEMQRLVRGDGFWDTPYWGLSMANLCKIMFHENPA\n KEQIHFMIKLITFGMFGGVQRHNGLFTDWDNLEEFLKRMFSTEEMGVRMYESSYHAIL\n RACILHLQTTAKPTLVQLTHAIESLDLGIEEVPFNFYV\"\nORIGIN \n 1 gtaaaaagaa tcctctgcgt tcactgggca cgaacatgga tcaattcttg gattcttttg\n 61 atgtgactgg agacgaggcg aatgccttga gattattgag agcggtttca cctgagatga\n 121 catgctcaca tttgaggaga gattgtttaa ttggagggat atgcgcaaaa cagtttttca\n 181 acgaggtgct gatggccatt ctggattcaa aagatcgtca ggcagcgcgt cagctggtga\n 241 cattagctgt gatgaccagt tacgaccgag agctaatctg gctcaacgta ctaaggtcaa\n 301 ctgaagtgct gccggcaaat gattatgcac atgaaataca gaatgtggtt ctgaacttga\n 361 agagggtctt catagagagt gggttggaag aaaaatacaa gagtttcagg gcgaagcggc\n 421 gtccaaacag atctccgacc gaggatgctt tctctttttt gccctttttc tacataccca\n 481 tgaatgaaac aaaacgggtt ggaataaaga aactcactag agttcggaac ctaggtgttg\n 541 cttttgttga tagacgcgaa gtgacgcatc atttaccgtt cacggtggac gctgctagaa\n 601 gggaccttat gatgctgaga aatttcacgc tggagcacca aagaacatgt acgtttacgg\n 661 gttcaaagag cttgatacat gggatgatat tctgtcctga ggagatggaa cctcttttcc\n 721 agaagaagga gacagcgcta gaaatctaca gaatttgtga gcaggatatg aagtttatca\n 781 actcaagagg tacgatgtca tttccccggt ttttgatgca acgtttagcg gtgaaaaacg\n 841 cttcatctga tgcgatggac caggttatgt tgggacgaac tccgagcgat ggacgtttga\n 901 tgtcggtgac tggtgcctct ttcttttttg gagggggacc tgattggcgc aagtgggcga\n 961 tgccggcgtt gttggtacgt gctgcaagac tgagaaccgt cgtgacatca ttcgttaagg\n 1021 agtggtttga ttcgactcac acatgtcaag tctgtttcct agttgaaaaa ggtgtcgccg\n 1081 attcaattcc gatcactgat gttcgtttat cggatgtgtg cggcgtagga ccagtcgcat\n 1141 atgttagatc ttatgcacat gatgacggga acgcgccgga tgttcgcgta ctgagaaaag\n 1201 gtgaaatctt cagattgatg ggcggacatt atgttatgca gacaacggcg agtacaatgg\n 1261 aatcattggt cgttgccgcg aaggagatgc agcgtttggt tcgcggcgat ggtttttggg\n 1321 acacaccgta ttggggttta agcatggcaa acctttgtaa aatcatgttt catgaaaacc\n 1381 cagcaaagga acagattcat ttcatgatta agctcataac ctttgggatg tttggtgggg\n 1441 ttcaaaggca caatggactg ttcacagact gggacaattt ggaggagttc ttgaagagga\n 1501 tgttttctac ggaggagatg ggcgttcgta tgtatgagtc aagttaccat gcgatacttc\n 1561 gtgcgtgcat actacatcta cagaccactg cgaagcctac cctcgttcaa ctaactcacg\n 1621 cgatcgaatc actcgacctt ggaatagaag aagttccttt caatttttat gtctaaaaca\n 1681 tcataataaa ccataaagag tctgagtaat tgtatccctg agctcttact cttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610679.1.gbk", "content": "LOCUS JQ610679 1735 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 5, complete sequence.\nACCESSION JQ610679\nVERSION JQ610679.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1735)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1735)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1735\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"5\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 36..1676\n /note=\"non-structural protein 1\"\n /codon_start=1\n /product=\"NS1\"\n /protein_id=\"AFX73391.1\"\n /translation=\"MDQFLDSFDVTGDEANALRLLRAVSPEMTCSHLRRDCLIGGICA\n KQFFNEVLMAILDSKDRQAARQLVTLAVMTSYDRELIWLNVLRSTEVLPANDYAHEIQ\n NVVLNLKRVFIESGLEEKYKSFRAKRRPNRSPTEDAFSFLPFFYIPMNETKRVGIKKL\n TRVRNLGVAFVDRREVTHHLPFTVDAARRDLMMLRNFTLEHQRTCTFTGSKSLIHGMI\n FCPEEMEPLFQKKETALEIYRICEQDMKFINSRGTMSFPRFLMQRLAVKNASSDAMDQ\n VMLGRTPSDGRLMSVTGASFFFGGGPDWRKWAMPALLVRAARLRTVVTSFVKEWFDST\n HTCQVCFLVEKGVADSIPITDVRLSDVCGVGPVAYVRSYAHDDGNAPDVRVLRKGEIF\n RLMGGHYVMQTTASTMESLVVAAKEMQRLVRGDGFWDTPYWGLSMANLCKIMFHENPA\n KEQIHFMIKLITFGMFGGVQRHNGLFTDWDNLEEFLKRMFSTEEMGVRMYESSYHAIL\n RACILHLQTTAKPTLVQLTHAIESLDLGIEEVPFNFYV\"\nORIGIN \n 1 gtaaaaagaa tcctctgcgt tcactgggca cgaacatgga tcaattcttg gattcttttg\n 61 atgtgactgg agacgaggcg aatgccttga gattattgag agcggtttca cctgagatga\n 121 catgctcaca tttgaggaga gattgtttaa ttggagggat atgcgcaaaa cagtttttca\n 181 acgaggtgct gatggccatt ctggattcaa aagatcgtca ggcagcgcgt cagctggtga\n 241 cattagctgt gatgaccagt tacgaccgag agctaatctg gctcaacgta ctaaggtcaa\n 301 ctgaagtgct gccggcaaat gattatgcac atgaaataca gaatgtggtt ctgaacttga\n 361 agagggtctt catagagagt gggttggaag aaaaatacaa gagtttcagg gcgaagcggc\n 421 gtccaaacag atctccgacc gaggatgctt tctctttttt gccctttttc tacataccca\n 481 tgaatgaaac aaaacgggtt ggaataaaga aactcactag agttcggaac ctaggtgttg\n 541 cttttgttga tagacgcgaa gtgacgcatc atttaccgtt cacggtggac gctgctagaa\n 601 gggaccttat gatgctgaga aatttcacgc tggagcacca aagaacatgt acgtttacgg\n 661 gttcaaagag cttgatacat gggatgatat tctgtcctga ggagatggaa cctcttttcc\n 721 agaagaagga gacagcgcta gaaatctaca gaatttgtga gcaggatatg aagtttatca\n 781 actcaagagg tacgatgtca tttccccggt ttttgatgca acgtttagcg gtgaaaaacg\n 841 cttcatctga tgcgatggac caggttatgt tgggacgaac tccgagcgat ggacgtttga\n 901 tgtcggtgac tggtgcctct ttcttttttg gagggggacc tgattggcgc aagtgggcga\n 961 tgccggcgtt gttggtacgt gctgcaagac tgagaaccgt cgtgacatca ttcgttaagg\n 1021 agtggtttga ttcgactcac acatgtcaag tctgtttcct agttgaaaaa ggtgtcgccg\n 1081 attcaattcc gatcactgat gttcgtttat cggatgtgtg cggcgtagga ccagtcgcat\n 1141 atgttagatc ttatgcacat gatgacggga acgcgccgga tgttcgcgta ctgagaaaag\n 1201 gtgaaatctt cagattgatg ggcggacatt atgttatgca gacaacggcg agtacaatgg\n 1261 aatcattggt cgttgccgcg aaggagatgc agcgtttggt tcgcggcgat ggtttttggg\n 1321 acacaccgta ttggggttta agcatggcaa acctttgtaa aatcatgttt catgaaaacc\n 1381 cagcaaagga acagattcat ttcatgatta agctcataac ctttgggatg tttggtgggg\n 1441 ttcaaaggca caatggactg ttcacagact gggacaattt ggaggagttc ttgaagagga\n 1501 tgttttctac ggaggagatg ggcgttcgta tgtatgagtc aagttaccat gcgatacttc\n 1561 gtgcgtgcat actacatcta cagaccactg cgaagcctac cctcgttcaa ctaactcacg\n 1621 cgatcgaatc actcgacctt ggaatagaag aagttccttt caatttttat gtctaaaaca\n 1681 tcataataaa ccataaagag tctgagtaat tgtatccctg agctcttact cttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610680.1.gb", "content": "LOCUS JQ610680 1605 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 6, complete sequence.\nACCESSION JQ610680\nVERSION JQ610680.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1605)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1605)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1605\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"6\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 22..1581\n /note=\"outer capsid protein\"\n /codon_start=1\n /product=\"VP5\"\n /protein_id=\"AFX73392.1\"\n /translation=\"MGKFVKALKKIGRGTVKALTSDAAKKLYTTLGKAATRFAESEVG\n SAAIDGLIQGTAQTLLHGGSASENIKQAVVLGVLHSMETPADPLSPGEQGVYDKIKEI\n KREEKEDRFFEVYQEKIDEELGSDMKRMREVAKGDKQAIKEMGGEIKVIEKAFDGLIK\n IDKIQDMKLTQLYGALAKERTERTQDEIKMVNDYTGKIEALQSAITVERDAMQEEALQ\n EIIEMGTDVIETASEEVPIFGPAAANVVATGRMVEGTLKLKQVIEKLAGLDVSHTTRD\n RIEPKVINAILDHEGGVVPEKELAIGVYNKLQTVREHMAEHSHLKEMAIPRLQKLYTE\n HGDEWHPKIITQMKVAREHQPQIHIYCAPWESDDVFMLRVYAPHHIGCGLFLGVDLES\n EFIFYEDLIAENHVLRGGVIEVVGRNFRQAVREFLLMAASKIENTMHVKRLVRSSASS\n PIYLSSIHYECTFDEIKQNVLQIVHDEQLQMHLLRGPKHFQRRALMAAVVKGVKILEG\n PDTKALMLQGL\"\nORIGIN \n 1 gtataaaata cctcggtcat catgggcaaa ttcgtaaagg ccctgaagaa aataggaagg\n 61 ggtacggtga aggcactgac gtctgacgct gcaaagaaac tttatacgac tttaggaaag\n 121 gcggcgacgc ggtttgctga aagcgaagtc ggcagcgcgg cgattgatgg attgatacaa\n 181 ggaacagcgc aaactttact gcacggaggc agcgcgagtg aaaatatcaa gcaagcggtt\n 241 gttttaggtg ttctccacag catggaaacg ccggcggacc ctttatcacc aggagagcaa\n 301 ggagtatatg ataagattaa ggaaattaaa cgagaagaaa aggaagatcg gtttttcgag\n 361 gtttaccaag aaaagattga cgaagagctt ggttcagata tgaagcgaat gcgagaagtg\n 421 gcaaaaggtg ataagcaggc catcaaggaa atgggtggtg aaattaaggt tatcgagaaa\n 481 gctttcgatg gattgattaa aatagataaa attcaagata tgaaattaac gcagttatat\n 541 ggcgcgctcg cgaaagagcg tacggagcgt acgcaggacg agatcaaaat ggttaacgac\n 601 tacactggaa aaattgaagc actgcaatcc gcgataacag ttgagcggga cgctatgcaa\n 661 gaggaggcgt tgcaggagat aatagaaatg ggaacggatg taattgaaac cgcctccgaa\n 721 gaggttccga tattcggccc tgcggctgcg aatgtagtcg caactggacg aatggttgag\n 781 ggcaccttaa agttgaagca agtaatcgag aaattagcag ggttagatgt ttcgcacacc\n 841 acaagggaca gaatcgagcc gaaagttata aacgctatac tagatcacga ggggggcgtc\n 901 gtaccggaaa aggaactagc gattggtgta tataataagc tgcagacagt cagagaacat\n 961 atggcggaac acagccatct aaaggaaatg gcaataccaa ggctgcaaaa gctgtacaca\n 1021 gaacacggcg atgagtggca tccaaagata attactcaaa tgaaggtagc gagagaacat\n 1081 cagccgcaaa tacatatata ttgcgctcca tgggaatcgg atgacgtgtt tatgttgcga\n 1141 gtgtacgcgc cgcatcatat agggtgtggt cttttcttag gagttgattt agagagtgaa\n 1201 ttcatatttt atgaggattt gatagcagag aaccacgtat tgcgtggtgg cgtcattgaa\n 1261 gtcgttggaa ggaacttcag gcaagcagtg cgcgaatttc ttttgatggc tgcgagcaag\n 1321 attgagaaca ctatgcatgt caagcggtta gtgagaagct cggcttcctc acctatctac\n 1381 ttgtcaagca tacactatga gtgtacattt gatgagataa aacagaacgt tttacagatc\n 1441 gtgcacgacg agcagttaca gatgcatctg ttacgtggtc cgaaacattt ccaaagacgt\n 1501 gctctgatgg cggctgttgt taagggtgtt aagatcttag aggggccaga tacgaaggcg\n 1561 ctcatgctac agggtttgta agtggctgaa aggtatcaag aatac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610680.1.gbk", "content": "LOCUS JQ610680 1605 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 6, complete sequence.\nACCESSION JQ610680\nVERSION JQ610680.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1605)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1605)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1605\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"6\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 22..1581\n /note=\"outer capsid protein\"\n /codon_start=1\n /product=\"VP5\"\n /protein_id=\"AFX73392.1\"\n /translation=\"MGKFVKALKKIGRGTVKALTSDAAKKLYTTLGKAATRFAESEVG\n SAAIDGLIQGTAQTLLHGGSASENIKQAVVLGVLHSMETPADPLSPGEQGVYDKIKEI\n KREEKEDRFFEVYQEKIDEELGSDMKRMREVAKGDKQAIKEMGGEIKVIEKAFDGLIK\n IDKIQDMKLTQLYGALAKERTERTQDEIKMVNDYTGKIEALQSAITVERDAMQEEALQ\n EIIEMGTDVIETASEEVPIFGPAAANVVATGRMVEGTLKLKQVIEKLAGLDVSHTTRD\n RIEPKVINAILDHEGGVVPEKELAIGVYNKLQTVREHMAEHSHLKEMAIPRLQKLYTE\n HGDEWHPKIITQMKVAREHQPQIHIYCAPWESDDVFMLRVYAPHHIGCGLFLGVDLES\n EFIFYEDLIAENHVLRGGVIEVVGRNFRQAVREFLLMAASKIENTMHVKRLVRSSASS\n PIYLSSIHYECTFDEIKQNVLQIVHDEQLQMHLLRGPKHFQRRALMAAVVKGVKILEG\n PDTKALMLQGL\"\nORIGIN \n 1 gtataaaata cctcggtcat catgggcaaa ttcgtaaagg ccctgaagaa aataggaagg\n 61 ggtacggtga aggcactgac gtctgacgct gcaaagaaac tttatacgac tttaggaaag\n 121 gcggcgacgc ggtttgctga aagcgaagtc ggcagcgcgg cgattgatgg attgatacaa\n 181 ggaacagcgc aaactttact gcacggaggc agcgcgagtg aaaatatcaa gcaagcggtt\n 241 gttttaggtg ttctccacag catggaaacg ccggcggacc ctttatcacc aggagagcaa\n 301 ggagtatatg ataagattaa ggaaattaaa cgagaagaaa aggaagatcg gtttttcgag\n 361 gtttaccaag aaaagattga cgaagagctt ggttcagata tgaagcgaat gcgagaagtg\n 421 gcaaaaggtg ataagcaggc catcaaggaa atgggtggtg aaattaaggt tatcgagaaa\n 481 gctttcgatg gattgattaa aatagataaa attcaagata tgaaattaac gcagttatat\n 541 ggcgcgctcg cgaaagagcg tacggagcgt acgcaggacg agatcaaaat ggttaacgac\n 601 tacactggaa aaattgaagc actgcaatcc gcgataacag ttgagcggga cgctatgcaa\n 661 gaggaggcgt tgcaggagat aatagaaatg ggaacggatg taattgaaac cgcctccgaa\n 721 gaggttccga tattcggccc tgcggctgcg aatgtagtcg caactggacg aatggttgag\n 781 ggcaccttaa agttgaagca agtaatcgag aaattagcag ggttagatgt ttcgcacacc\n 841 acaagggaca gaatcgagcc gaaagttata aacgctatac tagatcacga ggggggcgtc\n 901 gtaccggaaa aggaactagc gattggtgta tataataagc tgcagacagt cagagaacat\n 961 atggcggaac acagccatct aaaggaaatg gcaataccaa ggctgcaaaa gctgtacaca\n 1021 gaacacggcg atgagtggca tccaaagata attactcaaa tgaaggtagc gagagaacat\n 1081 cagccgcaaa tacatatata ttgcgctcca tgggaatcgg atgacgtgtt tatgttgcga\n 1141 gtgtacgcgc cgcatcatat agggtgtggt cttttcttag gagttgattt agagagtgaa\n 1201 ttcatatttt atgaggattt gatagcagag aaccacgtat tgcgtggtgg cgtcattgaa\n 1261 gtcgttggaa ggaacttcag gcaagcagtg cgcgaatttc ttttgatggc tgcgagcaag\n 1321 attgagaaca ctatgcatgt caagcggtta gtgagaagct cggcttcctc acctatctac\n 1381 ttgtcaagca tacactatga gtgtacattt gatgagataa aacagaacgt tttacagatc\n 1441 gtgcacgacg agcagttaca gatgcatctg ttacgtggtc cgaaacattt ccaaagacgt\n 1501 gctctgatgg cggctgttgt taagggtgtt aagatcttag aggggccaga tacgaaggcg\n 1561 ctcatgctac agggtttgta agtggctgaa aggtatcaag aatac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610681.1.gb", "content": "LOCUS JQ610681 1166 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 7, complete sequence.\nACCESSION JQ610681\nVERSION JQ610681.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1166)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1166)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1166\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"7\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..1069\n /note=\"T13 protein\"\n /codon_start=1\n /product=\"VP7\"\n /protein_id=\"AFX73393.1\"\n /translation=\"MDAIAARALSVIQDCISVGDGRINLDPGVMERLGIAINRYNGLT\n NNVVTIRPGTQDERNAMFFMCLDFALAALNIQIGVISREYTQALATIGVLATGEIPYS\n VAAMDTIVRISGTMATWGPTEYELPPYARSQMIQMSGRYYVPAGANSHAAHVDPTTVE\n ISLAAGVVVNVTNALQPRGVAPTMMYMVWHPLAIFANPQGATAASPQNMTLVVGGLNI\n AAGTIIAWDTVAPIQLSNQGGQEGMIAIRILWMTTLDKSMTSLPEMREIISRCYSFMH\n PSWHALRGTVLHSLNLPTNNPPMFAPATRQEALAYLILANLADAYTSLRPDFTIQGML\n AVPQVIDRQFVQGAYR\"\nORIGIN \n 1 gtataaatat ctagagatgg acgccattgc ggcacgtgct ctgtccgtga tccaggactg\n 61 cattagcgtt ggtgatggga gaattaattt agaccctggg gtcatggaga gattgggaat\n 121 tgctattaat agatacaatg ggctaacgaa caatgtggtg acgatcagac cagggacaca\n 181 agatgagcgg aacgcgatgt tttttatgtg tctggatttc gcgttggcgg cattgaacat\n 241 acaaattggg gttatatcta gggaatacac gcaggcgctg gccactatcg gtgtgctggc\n 301 aacgggagaa atcccttact cggttgccgc tatggatacg attgtacgga ttagcggaac\n 361 gatggcgaca tggggtccca ccgaatatga gttaccgcca tatgcgcggt ctcagatgat\n 421 acaaatgagc ggacgttact acgttccagc gggggcgaat tcacatgctg cccatgtcga\n 481 tcccacgacg gtagagattt ctttagctgc tggagtagta gtgaatgtta cgaacgcgtt\n 541 acagcctagg ggcgttgcgc ccacaatgat gtacatggta tggcatccgt tggcgatttt\n 601 cgcgaatcct cagggtgcta cagctgcttc gcctcaaaat atgactttgg tggttggtgg\n 661 gctgaatata gcagctggca cgatcatcgc ttgggatacc gtcgctccta tacagctatc\n 721 gaatcaggga ggacaagagg gaatgatcgc gatccggata ctatggatga caacattaga\n 781 taaatctatg acaagcttgc cggagatgcg tgaaataatc tcaagatgct atagctttat\n 841 gcacccttca tggcacgcgc tgcgagggac ggtcctacat tcgcttaatc tgccgactaa\n 901 taatccacct atgtttgcgc ctgctacgcg acaggaggca ttggcgtact taattctggc\n 961 aaatttagcg gatgcatata cgtcgttaag gcctgatttc accatacaag gaatgctcgc\n 1021 ggttccacag gtcattgaca ggcagttcgt tcagggtgcg tacaggtaga ggacgccttc\n 1081 cacagtgggc gtctcatgta gccccagcgt cggtccctta cgtgtgctgt aacgcgtagg\n 1141 tagaacgtca tatgatatta agttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610681.1.gbk", "content": "LOCUS JQ610681 1166 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 7, complete sequence.\nACCESSION JQ610681\nVERSION JQ610681.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1166)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1166)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1166\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"7\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..1069\n /note=\"T13 protein\"\n /codon_start=1\n /product=\"VP7\"\n /protein_id=\"AFX73393.1\"\n /translation=\"MDAIAARALSVIQDCISVGDGRINLDPGVMERLGIAINRYNGLT\n NNVVTIRPGTQDERNAMFFMCLDFALAALNIQIGVISREYTQALATIGVLATGEIPYS\n VAAMDTIVRISGTMATWGPTEYELPPYARSQMIQMSGRYYVPAGANSHAAHVDPTTVE\n ISLAAGVVVNVTNALQPRGVAPTMMYMVWHPLAIFANPQGATAASPQNMTLVVGGLNI\n AAGTIIAWDTVAPIQLSNQGGQEGMIAIRILWMTTLDKSMTSLPEMREIISRCYSFMH\n PSWHALRGTVLHSLNLPTNNPPMFAPATRQEALAYLILANLADAYTSLRPDFTIQGML\n AVPQVIDRQFVQGAYR\"\nORIGIN \n 1 gtataaatat ctagagatgg acgccattgc ggcacgtgct ctgtccgtga tccaggactg\n 61 cattagcgtt ggtgatggga gaattaattt agaccctggg gtcatggaga gattgggaat\n 121 tgctattaat agatacaatg ggctaacgaa caatgtggtg acgatcagac cagggacaca\n 181 agatgagcgg aacgcgatgt tttttatgtg tctggatttc gcgttggcgg cattgaacat\n 241 acaaattggg gttatatcta gggaatacac gcaggcgctg gccactatcg gtgtgctggc\n 301 aacgggagaa atcccttact cggttgccgc tatggatacg attgtacgga ttagcggaac\n 361 gatggcgaca tggggtccca ccgaatatga gttaccgcca tatgcgcggt ctcagatgat\n 421 acaaatgagc ggacgttact acgttccagc gggggcgaat tcacatgctg cccatgtcga\n 481 tcccacgacg gtagagattt ctttagctgc tggagtagta gtgaatgtta cgaacgcgtt\n 541 acagcctagg ggcgttgcgc ccacaatgat gtacatggta tggcatccgt tggcgatttt\n 601 cgcgaatcct cagggtgcta cagctgcttc gcctcaaaat atgactttgg tggttggtgg\n 661 gctgaatata gcagctggca cgatcatcgc ttgggatacc gtcgctccta tacagctatc\n 721 gaatcaggga ggacaagagg gaatgatcgc gatccggata ctatggatga caacattaga\n 781 taaatctatg acaagcttgc cggagatgcg tgaaataatc tcaagatgct atagctttat\n 841 gcacccttca tggcacgcgc tgcgagggac ggtcctacat tcgcttaatc tgccgactaa\n 901 taatccacct atgtttgcgc ctgctacgcg acaggaggca ttggcgtact taattctggc\n 961 aaatttagcg gatgcatata cgtcgttaag gcctgatttc accatacaag gaatgctcgc\n 1021 ggttccacag gtcattgaca ggcagttcgt tcagggtgcg tacaggtaga ggacgccttc\n 1081 cacagtgggc gtctcatgta gccccagcgt cggtccctta cgtgtgctgt aacgcgtagg\n 1141 tagaacgtca tatgatatta agttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610682.1.gb", "content": "LOCUS JQ610682 1089 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 8, complete sequence.\nACCESSION JQ610682\nVERSION JQ610682.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1089)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1089)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1089\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"8\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 26..1057\n /note=\"non-structural protein 2\"\n /codon_start=1\n /product=\"NS2\"\n /protein_id=\"AFX73394.1\"\n /translation=\"MAQEVKRKFTRTVCIYDPQNRTFCGRSAAMVCNSYYTIKMGRTT\n QCGVSPVPVPKSYVLEIPDVGSYRILDGQDSISVIVTETGVEATSERWEEWKFEGVNC\n VPMVVQTEIGKGLIDMEIKFSKGMGLVKPYVKNEVSRTEIPRLPGASVIDTPIRDYRQ\n LLKDQRDERRAALDAIACDICPTLSRMLGANITDGSPQVEEVATRPTQPPAQLKLDVP\n NWDQPTDSDDEDEESKRVTTQSNADTEEQVTFEDCITDQYFSKTGEFAKKYPEMLAGL\n SAKMPSETGRFTKILTTRKAQWNNVPLFELDPNGFTYHFSKLGNSTRIFCVQRDLSYM\n VLPAGQGLK\"\nORIGIN \n 1 gtaaaaaatc tcctctcttt tcacgatggc tcaagaagtt aagagaaagt tcactagaac\n 61 agtgtgcatc tatgatccac aaaatcgcac attctgtggt cgaagtgccg cgatggtgtg\n 121 taacagttat tatacaatta aaatgggtag aacgacgcag tgtggagtgt cgccggtgcc\n 181 cgtaccaaag tcatatgtgc tagagatacc ggatgttggc tcttatcgca tcttagatgg\n 241 gcaggattca atcagtgtca tcgttactga gacgggcgtc gaggcaacgt ctgagaggtg\n 301 ggaagagtgg aaattcgaag gcgttaattg cgttccgatg gttgttcaaa cggagattgg\n 361 gaaaggcctg attgacatgg agatcaagtt tagtaaggga atggggctcg ttaaacctta\n 421 tgtaaagaat gaggttagca gaactgagat cccacggcta ccgggtgctt cagtcattga\n 481 tacaccgata cgcgattacc gtcaactttt gaaggatcag agagatgaaa gaagggcggc\n 541 gctcgatgcg atcgcatgcg acatatgtcc cactctatca agaatgctag gggcgaatat\n 601 tacagacgga tcgccacaag tcgaagaagt cgcaacacgg ccaacacaac ctccagctca\n 661 gctgaagctg gatgtgccta actgggacca accgactgat tcagatgatg aggatgagga\n 721 atccaagcgc gtgacaacgc aaagtaatgc tgatactgag gaacaagtga ctttcgaaga\n 781 ttgcattacc gatcaatact tttcgaaaac gggtgaattc gcgaagaagt atcctgaaat\n 841 gttagcggga ctttccgcga agatgccgag tgaaacaggt aggtttacaa aaatattgac\n 901 gacgaggaag gctcaatgga ataacgttcc tcttttcgaa ttagatccaa acgggtttac\n 961 atatcatttt agtaagctgg gtaattcgac gaggatcttc tgtgtccaac gtgatttgag\n 1021 ctacatggtt ttacccgcag ggcaaggcct gaagtagcgg tgcatgtagc cgggagaggt\n 1081 acaacttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610682.1.gbk", "content": "LOCUS JQ610682 1089 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 8, complete sequence.\nACCESSION JQ610682\nVERSION JQ610682.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1089)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1089)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1089\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"8\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 26..1057\n /note=\"non-structural protein 2\"\n /codon_start=1\n /product=\"NS2\"\n /protein_id=\"AFX73394.1\"\n /translation=\"MAQEVKRKFTRTVCIYDPQNRTFCGRSAAMVCNSYYTIKMGRTT\n QCGVSPVPVPKSYVLEIPDVGSYRILDGQDSISVIVTETGVEATSERWEEWKFEGVNC\n VPMVVQTEIGKGLIDMEIKFSKGMGLVKPYVKNEVSRTEIPRLPGASVIDTPIRDYRQ\n LLKDQRDERRAALDAIACDICPTLSRMLGANITDGSPQVEEVATRPTQPPAQLKLDVP\n NWDQPTDSDDEDEESKRVTTQSNADTEEQVTFEDCITDQYFSKTGEFAKKYPEMLAGL\n SAKMPSETGRFTKILTTRKAQWNNVPLFELDPNGFTYHFSKLGNSTRIFCVQRDLSYM\n VLPAGQGLK\"\nORIGIN \n 1 gtaaaaaatc tcctctcttt tcacgatggc tcaagaagtt aagagaaagt tcactagaac\n 61 agtgtgcatc tatgatccac aaaatcgcac attctgtggt cgaagtgccg cgatggtgtg\n 121 taacagttat tatacaatta aaatgggtag aacgacgcag tgtggagtgt cgccggtgcc\n 181 cgtaccaaag tcatatgtgc tagagatacc ggatgttggc tcttatcgca tcttagatgg\n 241 gcaggattca atcagtgtca tcgttactga gacgggcgtc gaggcaacgt ctgagaggtg\n 301 ggaagagtgg aaattcgaag gcgttaattg cgttccgatg gttgttcaaa cggagattgg\n 361 gaaaggcctg attgacatgg agatcaagtt tagtaaggga atggggctcg ttaaacctta\n 421 tgtaaagaat gaggttagca gaactgagat cccacggcta ccgggtgctt cagtcattga\n 481 tacaccgata cgcgattacc gtcaactttt gaaggatcag agagatgaaa gaagggcggc\n 541 gctcgatgcg atcgcatgcg acatatgtcc cactctatca agaatgctag gggcgaatat\n 601 tacagacgga tcgccacaag tcgaagaagt cgcaacacgg ccaacacaac ctccagctca\n 661 gctgaagctg gatgtgccta actgggacca accgactgat tcagatgatg aggatgagga\n 721 atccaagcgc gtgacaacgc aaagtaatgc tgatactgag gaacaagtga ctttcgaaga\n 781 ttgcattacc gatcaatact tttcgaaaac gggtgaattc gcgaagaagt atcctgaaat\n 841 gttagcggga ctttccgcga agatgccgag tgaaacaggt aggtttacaa aaatattgac\n 901 gacgaggaag gctcaatgga ataacgttcc tcttttcgaa ttagatccaa acgggtttac\n 961 atatcatttt agtaagctgg gtaattcgac gaggatcttc tgtgtccaac gtgatttgag\n 1021 ctacatggtt ttacccgcag ggcaaggcct gaagtagcgg tgcatgtagc cgggagaggt\n 1081 acaacttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610683.1.gb", "content": "LOCUS JQ610683 925 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 9, complete sequence.\nACCESSION JQ610683\nVERSION JQ610683.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 925)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 925)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..925\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"9\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 23..883\n /note=\"helicase\"\n /codon_start=1\n /product=\"VP6\"\n /protein_id=\"AFX73395.1\"\n /translation=\"MLVLAPGDLIDGVRHQLSERGVRIRLRETNDDEQKDEPVDTGGG\n KPGDRIGKEVGNAESEQSSDKEKKAGGSSDSELGEGGDGRRQTEKAEGGENGTRDIGI\n QDKDKQFDRRANPDNALDRENRSGDPQLKYGFATKRIANAVESKYHCGGFEGPGSDGY\n IKLEMSIMKALGLNRDDHIEQLEFLKHQQKGPSKIQVRTIASETKLKEVCNIMDKPVA\n PTARSAVSVVSNRVEDVKEAQVYFTTPTGDRGWKEVARKASQTPNIRAYINPEGDDPK\n VSFLHLIDHL\"\n CDS 111..512\n /note=\"non-structural protein 4\"\n /codon_start=1\n /product=\"NS4\"\n /protein_id=\"AFX73396.1\"\n /translation=\"MMTSKRMNQWIREAASRVIESGRKLEMPRVNSLPIKRRRLEEVR\n IQSSGKVEMEGDKLRRLKAERMELEILAFRIKTNNLIGALIQITRWTEKIDQEIRNLN\n MDLQPNELQTPLSQSTTAVDLRGQDRMDTSN\"\nORIGIN \n 1 gtataaaaca tcctcccatg tcatgttggt gttggcaccg ggtgatctca tagacggagt\n 61 gcgtcatcaa ttatctgaaa gaggagtcag gattcgttta cgggaaacga atgatgacga\n 121 gcaaaaggat gaaccagtgg atacgggagg cggcaagccg ggtgatcgaa tcgggaagga\n 181 agttggaaat gccgagagtg aacagtcttc cgataaagag aagaaggctg gaggaagttc\n 241 ggattcagag ctcggggaag gtggagatgg aaggcgacaa actgagaagg ctgaaggcgg\n 301 agagaatgga actagagata ttggcattca ggataaagac aaacaatttg atcggcgcgc\n 361 taatccagat aacgcgttgg acagagaaaa tcgatcagga gatccgcaac ttaaatatgg\n 421 atttgcaacc aaacgaattg caaacgccgt tgagtcaaag taccactgcg gtggatttga\n 481 ggggccagga tcggatggat acatcaaact agaaatgtca ataatgaagg cgctaggttt\n 541 aaaccgagat gaccacatcg aacaattgga gttcctcaag caccaacaga aagggcccag\n 601 caaaattcaa gtcagaacga tcgcttccga aaccaaatta aaagaggtgt gtaatataat\n 661 ggacaagccg gtggctccca cagcgagaag tgcggtgagt gtagttagta accgtgttga\n 721 agacgtgaag gaagcccagg tgtattttac aactccaaca ggagatagag gctggaaaga\n 781 agtagcaagg aaagcgagcc agacaccaaa cattcgagcg tacattaatc cggagggaga\n 841 tgatcctaaa gtctcatttc tgcatttaat cgatcatctg tgaggtcacg gtctgaacta\n 901 cgggcatgct gggtgtttca gttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610683.1.gbk", "content": "LOCUS JQ610683 925 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 9, complete sequence.\nACCESSION JQ610683\nVERSION JQ610683.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 925)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 925)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..925\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"9\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 23..883\n /note=\"helicase\"\n /codon_start=1\n /product=\"VP6\"\n /protein_id=\"AFX73395.1\"\n /translation=\"MLVLAPGDLIDGVRHQLSERGVRIRLRETNDDEQKDEPVDTGGG\n KPGDRIGKEVGNAESEQSSDKEKKAGGSSDSELGEGGDGRRQTEKAEGGENGTRDIGI\n QDKDKQFDRRANPDNALDRENRSGDPQLKYGFATKRIANAVESKYHCGGFEGPGSDGY\n IKLEMSIMKALGLNRDDHIEQLEFLKHQQKGPSKIQVRTIASETKLKEVCNIMDKPVA\n PTARSAVSVVSNRVEDVKEAQVYFTTPTGDRGWKEVARKASQTPNIRAYINPEGDDPK\n VSFLHLIDHL\"\n CDS 111..512\n /note=\"non-structural protein 4\"\n /codon_start=1\n /product=\"NS4\"\n /protein_id=\"AFX73396.1\"\n /translation=\"MMTSKRMNQWIREAASRVIESGRKLEMPRVNSLPIKRRRLEEVR\n IQSSGKVEMEGDKLRRLKAERMELEILAFRIKTNNLIGALIQITRWTEKIDQEIRNLN\n MDLQPNELQTPLSQSTTAVDLRGQDRMDTSN\"\nORIGIN \n 1 gtataaaaca tcctcccatg tcatgttggt gttggcaccg ggtgatctca tagacggagt\n 61 gcgtcatcaa ttatctgaaa gaggagtcag gattcgttta cgggaaacga atgatgacga\n 121 gcaaaaggat gaaccagtgg atacgggagg cggcaagccg ggtgatcgaa tcgggaagga\n 181 agttggaaat gccgagagtg aacagtcttc cgataaagag aagaaggctg gaggaagttc\n 241 ggattcagag ctcggggaag gtggagatgg aaggcgacaa actgagaagg ctgaaggcgg\n 301 agagaatgga actagagata ttggcattca ggataaagac aaacaatttg atcggcgcgc\n 361 taatccagat aacgcgttgg acagagaaaa tcgatcagga gatccgcaac ttaaatatgg\n 421 atttgcaacc aaacgaattg caaacgccgt tgagtcaaag taccactgcg gtggatttga\n 481 ggggccagga tcggatggat acatcaaact agaaatgtca ataatgaagg cgctaggttt\n 541 aaaccgagat gaccacatcg aacaattgga gttcctcaag caccaacaga aagggcccag\n 601 caaaattcaa gtcagaacga tcgcttccga aaccaaatta aaagaggtgt gtaatataat\n 661 ggacaagccg gtggctccca cagcgagaag tgcggtgagt gtagttagta accgtgttga\n 721 agacgtgaag gaagcccagg tgtattttac aactccaaca ggagatagag gctggaaaga\n 781 agtagcaagg aaagcgagcc agacaccaaa cattcgagcg tacattaatc cggagggaga\n 841 tgatcctaaa gtctcatttc tgcatttaat cgatcatctg tgaggtcacg gtctgaacta\n 901 cgggcatgct gggtgtttca gttac\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610684.1.gb", "content": "LOCUS JQ610684 761 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 10, complete sequence.\nACCESSION JQ610684\nVERSION JQ610684.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 761)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 761)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..761\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"10\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 20..703\n /note=\"non-structural protein 3\"\n /codon_start=1\n /product=\"NS3\"\n /protein_id=\"AFX73397.1\"\n /translation=\"MYRDLLNIHTEMRGPPSYEPSGLAQATAPTMRFGDREDEEGLLR\n ARELSLNVLTNAMTNTTGANEAIKNEKAMFGAYADALRDTPEIRVVKRRINERTLEKL\n HKMRRSLHGRRMFVRMLLAINVGLALLTSAVNVVRQSLDDFGKERWIVGGVWWLGEVV\n VTINFGTTVATLVLMRIHGALNAQLQTIKRDIYKKSSYNEAAAMHWKGEISLIEELAA\n SHVPAGSNV\"\nORIGIN \n 1 gtataaaatt ccgttcgcaa tgtaccgtga cttgctgaat attcacactg aaatgagggg\n 61 cccgccatct tatgaaccta gtggcttagc tcaagcgaca gcaccgacta tgaggtttgg\n 121 ggatagagaa gatgaggaag gcctattgag ggcgcgcgag ctttcgctta atgtgttaac\n 181 gaatgctatg actaatacaa cgggtgcgaa tgaggcgatt aagaatgaga aagcgatgtt\n 241 tggggcatat gccgatgcac ttagggatac tccggagatt agggtggtga aaaggcggat\n 301 aaatgaacgt acgttagaaa agttgcataa aatgcgacgt tcgctgcacg gaagacgaat\n 361 gttcgtacga atgttgttgg cgataaatgt gggattggcg ctattaacct cggcagtgaa\n 421 tgtggtacgc cagtcgctag atgattttgg gaaagaaagg tggatagttg gtggagtgtg\n 481 gtggttaggt gaggtcgtcg ttacgattaa ttttggaacg actgttgcta cgttggtatt\n 541 aatgaggata catggcgcat taaacgcgca gcttcaaacc attaagcgtg acatatataa\n 601 gaaaagctcg tataatgagg ccgctgccat gcattggaaa ggtgaaatta gcttaattga\n 661 ggagctagcg gcgagccacg tacctgcggg atcgaatgtc tagtccgcga catcgaaaaa\n 721 ttcacttgtc caggtgaagc ccgtagaacg gatcgtctta c\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/JQ610684.1.gbk", "content": "LOCUS JQ610684 761 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 10, complete sequence.\nACCESSION JQ610684\nVERSION JQ610684.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 761)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 761)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..761\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"10\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 20..703\n /note=\"non-structural protein 3\"\n /codon_start=1\n /product=\"NS3\"\n /protein_id=\"AFX73397.1\"\n /translation=\"MYRDLLNIHTEMRGPPSYEPSGLAQATAPTMRFGDREDEEGLLR\n ARELSLNVLTNAMTNTTGANEAIKNEKAMFGAYADALRDTPEIRVVKRRINERTLEKL\n HKMRRSLHGRRMFVRMLLAINVGLALLTSAVNVVRQSLDDFGKERWIVGGVWWLGEVV\n VTINFGTTVATLVLMRIHGALNAQLQTIKRDIYKKSSYNEAAAMHWKGEISLIEELAA\n SHVPAGSNV\"\nORIGIN \n 1 gtataaaatt ccgttcgcaa tgtaccgtga cttgctgaat attcacactg aaatgagggg\n 61 cccgccatct tatgaaccta gtggcttagc tcaagcgaca gcaccgacta tgaggtttgg\n 121 ggatagagaa gatgaggaag gcctattgag ggcgcgcgag ctttcgctta atgtgttaac\n 181 gaatgctatg actaatacaa cgggtgcgaa tgaggcgatt aagaatgaga aagcgatgtt\n 241 tggggcatat gccgatgcac ttagggatac tccggagatt agggtggtga aaaggcggat\n 301 aaatgaacgt acgttagaaa agttgcataa aatgcgacgt tcgctgcacg gaagacgaat\n 361 gttcgtacga atgttgttgg cgataaatgt gggattggcg ctattaacct cggcagtgaa\n 421 tgtggtacgc cagtcgctag atgattttgg gaaagaaagg tggatagttg gtggagtgtg\n 481 gtggttaggt gaggtcgtcg ttacgattaa ttttggaacg actgttgcta cgttggtatt\n 541 aatgaggata catggcgcat taaacgcgca gcttcaaacc attaagcgtg acatatataa\n 601 gaaaagctcg tataatgagg ccgctgccat gcattggaaa ggtgaaatta gcttaattga\n 661 ggagctagcg gcgagccacg tacctgcggg atcgaatgtc tagtccgcga catcgaaaaa\n 721 ttcacttgtc caggtgaagc ccgtagaacg gatcgtctta c\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/orungo.gb", "content": "LOCUS JQ610675 3942 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 1, complete sequence.\nACCESSION JQ610675\nVERSION JQ610675.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 3942)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 3942)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..3942\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"1\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..3921\n /note=\"RNA-dependent RNA polymerase\"\n /codon_start=1\n /product=\"VP1\"\n /protein_id=\"AFX73387.1\"\n /translation=\"MVITVEGAWLVRRALQRFLKFSKIDGESAVYEFYRYSSNIREIR\n RKHGTRYKMHDEELERRRDSGKLRFKGMQVVVESTWMEILGKGRTTDEIEIFRSSILS\n LDELNPEEEFLRNYASSDKEHPSYLFVRGRAVNEMQIYGDMPIKAWLSFLVECEVEYG\n YKLFGMEVARSFVQSFGSPFHQNSRDLSQIDDMAPAFTSPLLFEMCCMTSILEINIRM\n RMLEERVATLKFGEREIDPLEVLKEFFRICIPHPKKINNMLRAPYSWFVKLWGVSYHE\n PIVLTARGGEDKNSKDIFFTGFHRVKNPYSIMLKKSRFFKKSLDENISKVKEAIDYSN\n SLTGMSLGLPVFLSMLQNVYDTEFNPTMVQHVLLASFLLSIQTITGYGRAWVKNVSSD\n NDTQMRPAEDNFIDRVAKQTEINFIQAYEEALGHGEDIVKPEDMFTSILRLARNTSSG\n FSTAVDVYKRFGPKSGGRGERVKITSRIKALVIFTKGHEIFTAENLAKRYDTEEDYQT\n KGSRDVPIKATRTIYSINLSILIPQLILTLPLNEYFARFGGSTAPDSRSLGGKVIIGD\n LEATGSRTIDAADTFRNSSDPEIFTIAIDYSDYDQHLTVFNFRNGMLEGIRSAMKRYK\n ELRYDGYTLNELIEFGYGEGRIVNSKWNGKRRVKSVRMSDYMALSESQRAQGTFKPPQ\n GVRPVSSMQVFDSVGEASGGDTLLISPTDGSDLATVNTHLSGENSTLVANSLHNMAIG\n RIIQEEIRKNHRAAFTFESEQYVGDDTLLYAKLNTLNHEIFDKAIDTIFDTVGKCGHV\n ASAAKTLIAPFSVEKTQTHAKQGIYIAQDRMMIISSERRKDIEDVQGYMRSQVSVMAT\n KVSRGFSHELAQLVFMMKSSIVGFRKLKRTVVEDGVYRDRALDSEDEDGFTLMQIRDP\n LVAFYPAEWNGYGMHPVALNIVMTEDMFIDTSTMVEFQHVMRPLLRFMGRIPPVWNET\n KADKRQISSITKMSFFSKMARPAVRAVLANSELSDQVRTLPLGDFSPFNLSATMMHSA\n LLKEPRARALLTPAYEKEFQSELNSNRDSEVNFVGRNMEINTNYMKLFDVDLSTRIVA\n KQFSFPDQNMSLPFYFQKLLIGHRPVARMRMTYIDRIDQILRGDVVMRGFITANTIMS\n VLEKIGTAHAVQDLTTIFQLMNIESKVAHRLAEYIASERVRFDALSIAKRGICGDEFS\n MSLDVCTERFAERFMELPAQFTKTERDIAILYAAQLTMLRCAANLDLRKIKIGVSADH\n VKRFKQRQARFKTHLPKMRTVTRLITPERISARLVQHQFT\"\nORIGIN \n 1 gtataattag gaatggtcat cactgtggaa ggtgcgtggc tggtgagacg ggcgttgcaa\n 61 cgttttttga agttcagtaa aatcgacggg gaatcagcag tttatgagtt ctataggtat\n 121 tcaagtaata ttcgtgaaat aagaaggaag catgggacgc gttataaaat gcatgatgaa\n 181 gagttggagc ggaggcgtga ttcgggcaaa ctgcgtttta aaggtatgca agttgtggta\n 241 gagtcgactt ggatggagat tttagggaag ggacgtacga cggacgaaat cgagatattc\n 301 agaagttcga ttttatcgtt ggatgaactg aatccggaag aagaatttct gcgcaattat\n 361 gcgagttcgg acaaggaaca tccatcctac ttgtttgttc gggggcgggc ggtcaatgag\n 421 atgcagattt atggcgacat gccgataaaa gcgtggttga gctttttagt agaatgtgag\n 481 gttgaatatg ggtacaaact cttcggaatg gaagttgcga gatcgttcgt tcagagcttt\n 541 ggatctccgt ttcaccagaa ctcgcgtgat ctatcacaga ttgacgatat ggcgcctgct\n 601 tttacgtcac ctttattatt tgaaatgtgt tgtatgacat caattctcga aattaatata\n 661 cgcatgcgta tgctggagga gagggttgca accctaaaat ttggtgagcg ggagatcgac\n 721 ccacttgaag tactaaaaga attcttccga atctgcattc cgcatccgaa aaagattaat\n 781 aatatgttga gagctccata ctcatggttc gtcaagctgt ggggcgtatc gtatcatgag\n 841 ccaatagtcc tgacggcgag gggcggcgag gataagaact cgaaagacat attctttacg\n 901 ggatttcaca gagtcaagaa tccatactca ataatgttga aaaaatcgag gttttttaag\n 961 aaatctttag acgagaatat cagcaaagtg aaagaagcga tagactattc aaactcgttg\n 1021 acggggatgt ctttagggct gcccgtattt ctatccatgc tacagaatgt gtacgacact\n 1081 gagtttaatc cgactatggt tcaacacgtg ttactagcgt cgttcttgtt gagtatccaa\n 1141 acaataactg gctatggacg cgcttgggtg aaaaatgtgt caagcgataa cgacactcaa\n 1201 atgcgcccgg cggaggacaa cttcattgat cgagttgcta agcaaacgga gattaatttt\n 1261 atacaggcgt atgaagaggc gttggggcac ggagaagata tcgttaagcc agaagacatg\n 1321 tttacctcca ttttgcgttt ggcaagaaat acaagttccg gcttctctac tgctgttgac\n 1381 gtttataaac gattcggtcc aaagtcggga gggagaggag aacgcgttaa gataacatca\n 1441 agaattaaag cattagttat cttcacaaag ggccatgaaa tatttacagc tgaaaatctc\n 1501 gcgaaaagat atgatacgga ggaagattac cagactaaag ggtcacggga tgtacctatc\n 1561 aaagcaacgc ggacgattta ttcaataaac ctctccatct tgatcccgca gctgatccta\n 1621 actttaccgt tgaatgaata ttttgcccgg ttcggaggat caactgcacc tgactcacgt\n 1681 agcctagggg gtaaggtgat tatcggagat ctagaagcaa cgggatcacg gacgatcgat\n 1741 gcggcagata cgtttagaaa ttcgtccgac ccagaaattt tcacaatagc gatcgattat\n 1801 tcggattacg atcaacattt gacggttttt aacttcagga acggtatgct ggaaggaatt\n 1861 cgctctgcga tgaagagata taaagagttg aggtatgatg gatacacgtt gaatgaattg\n 1921 attgaattcg ggtatgggga ggggagaatt gttaattcga aatggaacgg aaagaggcgg\n 1981 gtcaaatctg tacgaatgag cgattatatg gcattgagtg aaagtcaacg cgctcagggc\n 2041 actttcaagc cgccgcaggg agtgagaccg gttagttcaa tgcaagtgtt cgattcagtg\n 2101 ggtgaggcat ctggagggga tactctcctc atctcgccca ctgacggatc ggatttagca\n 2161 accgtcaaca cgcatttgtc gggtgaaaat tcaacgttag ttgctaactc tttgcataat\n 2221 atggctatcg gacgtatcat acaagaagag atcagaaaga accatcgagc ggcttttacc\n 2281 tttgaatctg agcagtacgt tggagatgat acgttacttt atgcaaagtt gaacacatta\n 2341 aaccatgaaa tttttgataa agcgattgat accatcttcg atactgtggg aaagtgcgga\n 2401 catgtggcat cggcagcgaa aacccttatc gctcctttct ctgttgaaaa aactcagact\n 2461 catgcgaagc aaggaattta cattgcgcag gatcggatga tgatcatctc ttcagagcgt\n 2521 agaaaggata tcgaggacgt ccaagggtat atgagatcac aagtgtcggt tatggcgaca\n 2581 aaagtaagcc gcggctttag tcatgaactg gctcagcttg tctttatgat gaagagcagc\n 2641 atcgtaggct ttcgtaaact gaagcgaact gtggtggagg atggtgtata ccgtgatcgc\n 2701 gcgttggatt cggaagatga ggatggcttc actttgatgc agatccgtga tccgttggtc\n 2761 gccttctacc ctgctgagtg gaacggctat ggcatgcatc cagtcgcttt gaatatcgtc\n 2821 atgacggaag acatgtttat agacacgagt accatggttg agtttcagca tgtaatgcgg\n 2881 ccgctccttc gatttatggg taggatacct ccagtgtgga atgaaactaa agccgataaa\n 2941 cgtcagattt catccataac aaagatgagt ttcttctcca aaatggctag accagcggtg\n 3001 agggcggttc tggcgaatag tgaactgtca gatcaagtga gaacattgcc actgggcgac\n 3061 ttttcgcctt tcaatctctc cgcaacaatg atgcactcag cattattgaa agaaccacgc\n 3121 gcgcgtgccc tgctgacgcc agcctacgaa aaagaattcc agtcagagtt gaattcaaac\n 3181 cgggatagcg aagtaaattt cgtcgggagg aacatggaga tcaacactaa ttatatgaaa\n 3241 ctgttcgatg ttgatttgtc tacgcgaata gtggccaaac aatttagttt tccagatcag\n 3301 aatatgtcgt tgccttttta ttttcagaaa ctcttgattg gacatagacc ggtcgcgcgg\n 3361 atgagaatga cctatattga ccggattgac caaatcttac ggggagacgt cgtgatgagg\n 3421 ggtttcatca cagcgaatac tattatgtcc gttttagaga agattggcac tgctcacgcc\n 3481 gtacaggact taacaacaat atttcagttg atgaacattg aatctaaggt ggcgcatagg\n 3541 ctagcggagt atatcgcttc tgaaagggta agattcgacg cgctctcgat tgcaaagagg\n 3601 gggatatgcg gggatgaatt ctccatgtcg ctggatgtgt gcacggaacg gtttgctgaa\n 3661 cggttcatgg aactaccagc gcagtttact aaaactgaga gagatatagc gattttatat\n 3721 gccgcgcagc taactatgtt gcgctgtgcg gctaacctag atcttaggaa aattaagatt\n 3781 ggggtttcag cggatcacgt taagagattt aaacaaagac aggctagatt taagactcat\n 3841 ctacctaaaa tgcgtacagt cacgcggctg ataacgcctg aacgaatctc cgcacgcctg\n 3901 gttcagcatc agtttacatg acgcaccacc taatcaactt ac\n//\n\nLOCUS JQ610676 2933 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 2, complete sequence.\nACCESSION JQ610676\nVERSION JQ610676.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2933)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2933)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2933\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"2\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..2899\n /note=\"T2 protein\"\n /codon_start=1\n /product=\"VP2\"\n /protein_id=\"AFX73388.1\"\n /translation=\"MAFERTVALTREFANETRQHFGKFDIVVNTESSIEDEATGEWEF\n ARSDGRLGIYEELHNSIAYKHYTAILKGPENYLNIPQIFESKIYKNLNRDDLLARYDY\n SQILRFRDSKIAGRLRMQTYFGDVHVSAGLIDCVAMVREPIRREGCQHMMVRSFDLMN\n AGQFFDVHAPKIHAFDDTVIVESMDIENGVWRVKAGGVGLKTLQEKAEGILGDSVLDL\n VHNYLSQKWDAGYVAAKLLRFDETYKFHPIHEVGIFNTLMIRMGQLDDAYRDGFFDYD\n EIHAQLMRDVTFQYPEGKPVFRRDGQFFKNLVQYSGRAKIGYETYLPDRELWTEWRTR\n SSVQDVVPKYMEWLIGRLQLGKMLKIMSELPADVTMPNYLLKAITYKSSVYVKRLILT\n YIALRMTFGRCPVNKKGTLASSVLGFLHAVIPNLEEFLRKAGITDELCVKMEFTPRLT\n VMEREDRKSDRYAVVLQVYRERKLEVFTPIDSDLFEDRKKYYDEILKDKRWRGEETDY\n FFKDSGIHRSQVAGLSAEQLTLKKLGRDSDFNDPKRFVSYRYRYVSVKAGDIYAEGES\n VITGPLLTLIPHAYEFGRVSLIAGQSRDQSKLDNVPVYRDHMKSLELNGVEVGYDTWC\n PSGRAVQVNLELISTILYNAFKRPIVKGALCHFGMWEFYNPRRPAYESVDVTIMNAIS\n DITGSKRWAYQEIQDWLARFIKGSRVDMVTHRFHGVTKKPTTRGEIWIWNLLLVLISN\n PSLVVSQTDKFPLWVCASDGLHLISTGVRHTDHFRLWEWLPYTEKIGNDDYMSVLATD\n RELRLFEIALEYFETIRIGYRRDEWTHLKSNMFNTWLGTHCGGVGDGMILFDPVRLPS\n PSSVLYLICSHNSTLEGMMYLLHDIYGKIVEENTGTVFIRVHARGCKCSVCRGGLQGV\n DVKNRSAMRVRSMPGNIGFDSVNLILSTSTTSAFGNSYIYFKLINR\"\nORIGIN \n 1 gtataattga tccgcgatgg ctttcgagcg tacggtagcc ttaacaagag agttcgcaaa\n 61 tgaaacaaga cagcattttg ggaagtttga tatagttgta aacacggaaa gcagtattga\n 121 ggacgaagca acgggtgagt gggagttcgc acgaagtgat gggcggcttg gcatctatga\n 181 agaattgcat aatagcatcg cttataaaca ttatacggcg atactaaaag ggccggaaaa\n 241 ttatttgaat attccgcaga tttttgagtc gaaaatctat aagaatttga atagggatga\n 301 tctattggcg agatatgatt attcacaaat actaagattc cgagatagta agatagcggg\n 361 ccgattgagg atgcagacgt atttcgggga cgtgcatgta agtgcgggac tgatagattg\n 421 tgtagcgatg gttcgtgagc ctattagaag ggaagggtgt cagcatatga tggtacgtag\n 481 ttttgatttg atgaatgcgg gccagttttt cgatgttcat gcgccgaaga tccacgcgtt\n 541 tgatgacacg gtgatagttg aaagcatgga catcgaaaac ggagtatggc gcgtaaaggc\n 601 gggtggcgta ggtttgaaaa cgctgcagga aaaagcggaa ggaatactcg gagattcagt\n 661 gttagactta gtccacaact atctcagcca aaagtgggac gcaggttatg tggccgcgaa\n 721 gttgctgagg tttgatgaga catataaatt tcatccaatt catgaggtgg gaattttcaa\n 781 cacattgatg atacgcatgg gtcaactcga tgacgcgtat agggatgggt tcttcgatta\n 841 tgacgagatt cacgctcaat tgatgaggga tgtgactttt cagtacccag aaggtaagcc\n 901 agtctttcgg agagatggcc aattctttaa aaacctagtg cagtattcgg gacgggcgaa\n 961 gattgggtat gagacgtatt taccagacag ggaattgtgg actgaatggc gaacgagatc\n 1021 atccgtgcaa gatgttgtac ccaagtatat ggaatggttg ataggtagat tacagttggg\n 1081 gaaaatgctt aaaataatgt cggaattacc agcggatgtt acgatgccca actatctttt\n 1141 gaaagccatt acatataaat cgagtgtata tgttaagaga ttgatactca cgtacatcgc\n 1201 tttacgaatg acgtttggac ggtgtccagt aaacaaaaaa ggaacgcttg cctcatcagt\n 1261 cttaggtttt ctacacgcgg ttattccgaa tctggaggaa tttctgagga aagcgggaat\n 1321 aacggatgaa ctatgtgtta aaatggagtt tacgccgaga cttactgtga tggagagaga\n 1381 ggataggaag tcagacagat acgccgttgt cttgcaagtt tatagggaga ggaagctgga\n 1441 ggtttttacg cctatagact cagacttgtt cgaagatcgg aaaaagtact atgacgagat\n 1501 cttgaaagat aaaagatggc gtggagaaga gactgattat ttttttaaag actcagggat\n 1561 acaccggtcc caggtggctg ggttgagcgc agagcagctc acgttgaaaa agttaggacg\n 1621 cgactcagat ttcaacgacc ctaaacggtt cgtttcatac agatatagat atgtatcagt\n 1681 taaagcggga gatatctatg cagaagggga gagcgttata acgggaccat tattgacact\n 1741 gattccacat gcctacgagt tcggacgagt atctttgatt gcggggcagt ctcgagatca\n 1801 atcaaagttg gataatgtcc cagtctaccg tgaccacatg aaatccttgg agttaaatgg\n 1861 cgtcgaagtt ggctatgaca cttggtgtcc gtcggggcgt gcagtacaag ttaacttgga\n 1921 gttgatatct accatcctgt ataacgcgtt caaacgtccc atcgttaagg gagcattatg\n 1981 tcacttcggt atgtgggaat tttataaccc gagacgtccc gcgtatgagt cagtagacgt\n 2041 gacaatcatg aatgcgatct cggatatcac tgggagcaaa agatgggcat atcaggaaat\n 2101 tcaagattgg ttggcgagat ttattaaggg gtcacgggtt gacatggtga cacaccgctt\n 2161 ccacggggta acgaagaagc caacaactcg aggtgagata tggatctgga acctactact\n 2221 agttttgatc tcaaatccca gtctggtggt atcacaaacg gataaatttc ccttatgggt\n 2281 ttgcgcctct gatggcttac acctgattag tacgggagtg aggcataccg atcattttag\n 2341 actttgggag tggctaccat ataccgaaaa aattgggaac gacgattata tgtcggttct\n 2401 cgccacagat agagagttgc ggcttttcga aatcgcgttg gaatacttcg agactatacg\n 2461 cattggatat aggagagatg aatggacgca tttgaaatcg aacatgttta atacctggct\n 2521 ggggacgcat tgtgggggtg taggggacgg gatgatattg tttgacccgg tgagattacc\n 2581 atccccgagc agcgtccttt atttgatctg ttcgcataac tcaactttag aaggaatgat\n 2641 gtatttacta catgatatat acgggaagat cgttgaagag aatactggta ctgttttcat\n 2701 aagggtacac gcgcgaggtt gtaagtgctc ggtgtgccga gggggtttac agggagttga\n 2761 cgtaaagaat aggtcagcta tgcgtgttcg tagtatgcca gggaacatcg gcttcgattc\n 2821 agtcaaccta attctttcaa catcaacgac gagcgcgttt gggaactctt acatttactt\n 2881 taagcttatt aatcgttagt gaggtgacac tcgctccgcg atcacgcaga tac\n//\n\nLOCUS JQ610677 2781 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 3, complete sequence.\nACCESSION JQ610677\nVERSION JQ610677.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2781)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2781)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2781\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"3\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 18..2738\n /note=\"outer capsid and cell attachment protein\"\n /codon_start=1\n /product=\"VP3\"\n /protein_id=\"AFX73389.1\"\n /translation=\"MAHADAKGSDPEREALRKNPYLDGDVLGTAGGQVLSVFALTEIL\n QKVRQTQAELAAHAIDLDGPVPEITGVIKKIAELVDTVPYEVRDSPPISYKTLSMQSR\n DFVIQVDQYYEQISQIGGDVGEDEPMEFYKTMLEKVRYLRKSGAFILRGIKTRDYRGN\n EVAEPEALGVEFREVLSNFIAADRQVIQNALDAAIVENGQVGDRAVDVYMAAVSEPWY\n RIYNRLQAYIEVTQLRELRRAMEWLNALGRRKRVEYDDSFLTDFRARDTVWVQTQQLP\n VNARVIWEVPRSYIANLMMNIALCLPLGDFIAPNPRIGSITITQRITMTTPFGMMSGM\n TPTSMQMDDVKKIYLALLFPGQIVLNIKPDPAHSIDPVLRMVSGVLGHLMFTYGPRFT\n NITATTSQLLDSALSDYFLYMQNSRVPVVYGPTGLPLDFRIGGRQGYDCNNLRGDPQT\n GRGYNGWGVVDVDRRAPSPYDLVQRFIRYCNIDSREIIDPRTFGFNMNYPLYMEMIRA\n LVAGGKDQEAAYLRQMLPFHMIRFARINQIINEDLLSAFSLPDEDFDALFFNMLRGEY\n GKAEPIVLDISWASIWFAFNRYFDPVQRSDLLSVAPMIEAVYASEISILQLDMINLQQ\n LRARAPDMLINATPSQFWKAALASAAEPVVELMNLSQSFRFINVRDIIQWTRTREVQP\n SLALTLEREAWAVAADFEELMLVNHVYFHRSVVPEPQLDDIDEFRRQGFLYTNLLEAA\n PPRLLITNYDYNVALLQANLGQFKSALRRILDDGGWVMFGGMLRNVRLKIYDSKPGED\n VLSELPYLYSEKVENGLRFVSLKYARRATIYFLMYKVEYSNTPDALISVNPTYTMTKI\n YTNKRLVRKVRSPDVLNIVNKRVVAYKTKMRLIDITSALRLGVKLAAPTV\"\nORIGIN \n 1 gtatatattc cttcgcgatg gcgcatgcgg atgctaaagg aagtgatccg gagagagagg\n 61 cgttgaggaa gaacccttat ctagatggag acgtcttggg aaccgcaggc ggccaagttt\n 121 tgtcggtttt cgcattgacc gaaattttac aaaaagtaag acagacgcaa gctgaactgg\n 181 ccgcacacgc aatcgatttg gatggaccag tccctgagat caccggggtt attaagaaga\n 241 tagcggagtt agttgacacc gttccatatg aagtgcgcga ttcaccacct ataagctata\n 301 agactttaag catgcaatcg cgcgactttg tcatccaggt ggaccagtat tacgaacaga\n 361 tttcgcaaat tggaggagac gtcggggagg acgagccgat ggagttctat aaaacaatgc\n 421 tagaaaaggt acgctattta aggaagagtg gagcattcat tttgagaggt attaaaacac\n 481 gagactatag gggtaatgaa gtggcggaac cagaagcttt aggagtcgaa tttcgtgaag\n 541 tactttctaa ttttattgcg gcggatagac aagtgataca gaatgcgtta gatgcagcca\n 601 tagttgaaaa tggccaggtg ggtgataggg cggtcgatgt ttatatggct gctgtttctg\n 661 agccatggta tcgaatatat aataggttac aggcgtatat tgaagttacg caactgagag\n 721 aattgaggcg cgcaatggag tggctgaatg cacttggtcg tcgtaagaga gtggagtatg\n 781 atgattcatt cttgaccgat tttcgagcga gagatacggt atgggtgcag acgcaacagc\n 841 ttcccgttaa cgctcgtgtg atctgggagg ttccgaggtc atatatagct aatttgatga\n 901 tgaatatcgc gttatgtctg ccactaggtg atttcatagc cccaaacccg aggattgggt\n 961 cgataacgat aacccagcga ataactatga ctacgccttt tgggatgatg tctgggatga\n 1021 cccccacatc aatgcagatg gacgatgtca agaagatata tctcgcgttg ctctttcccg\n 1081 ggcagatcgt tttgaatatt aaacccgacc cagcgcactc catcgatccg gtactgcgta\n 1141 tggtttcggg tgtgttgggg catttgatgt tcacctacgg tcccagattt actaacataa\n 1201 cagctacaac atcgcagttg ctagatagtg ccttgagcga ctattttctg tacatgcaaa\n 1261 acagtagagt tccggtggtg tacggaccaa ctgggttacc tttggatttt agaatcggtg\n 1321 gacgacaagg ctatgattgc aataatctgc ggggagaccc gcagactggg agggggtaca\n 1381 atggatgggg agtcgttgac gtcgatcgaa gagcacccag tccgtacgat ttggttcaaa\n 1441 gatttatacg ttactgcaac atagactctc gcgagatcat cgacccacgg acgtttggat\n 1501 ttaatatgaa ctatccgcta tatatggaga tgatacgtgc attagttgcc ggaggaaaag\n 1561 atcaggaagc ggcgtaccta cgacaaatgt taccttttca catgatcaga ttcgcacgga\n 1621 tcaatcagat aataaacgaa gacttactta gcgcgttttc cttaccagat gaggatttcg\n 1681 acgcattatt tttcaatatg ctgcgcggcg agtatggaaa ggctgagccg atcgttttag\n 1741 atatcagttg ggcttcaatt tggtttgcgt tcaaccgcta ctttgaccca gtccaaaggt\n 1801 cagatctatt atcagtggca cccatgattg aggctgtcta tgcgtcagaa atctccattt\n 1861 tgcaattgga tatgatcaac ctgcagcagt tgagagcgag ggcacctgat atgttgatta\n 1921 acgcaactcc gagtcagttt tggaaagcgg cgttagcatc cgcagcagaa ccagtagttg\n 1981 agttgatgaa tctttcgcag agttttcgat tcattaacgt cagggatata atacagtgga\n 2041 ctagaacacg agaagtgcaa ccgtcgctgg ctctcacttt ggaacgagag gcgtgggcgg\n 2101 tcgcagctga cttcgaagag ttgatgctcg taaaccatgt ctattttcat agatcggtgg\n 2161 ttcccgaacc acagttggat gacatcgatg aatttcgtag gcaaggattc ctgtacacaa\n 2221 atctattgga agcggccccc ccgcgtttgt taatcaccaa ttatgattac aacgttgcgc\n 2281 tactgcaggc gaatcttgga caatttaaat ccgctttgag gagaattctg gatgacggtg\n 2341 gttgggtgat gttcggggga atgctgagaa atgttcgttt gaaaatatac gattcaaagc\n 2401 cgggagagga cgtcttaagc gaactaccct atctttactc cgagaaagtg gaaaacggtt\n 2461 taaggtttgt gtctttgaag tatgcgagac gagcaactat ttatttttta atgtataagg\n 2521 ttgaatattc aaacacacca gatgctttaa tatcagtcaa ccccacgtat accatgacga\n 2581 agatttatac aaacaagaga ctggtccgga aagtcaggtc acctgacgtt ttgaacatcg\n 2641 ttaataaaag agtagtggct tataaaacga agatgcggtt gattgacatt acatcggcac\n 2701 tgcgtcttgg tgttaaactt gcagcaccta cagtgtgaat tgaccactca acctgtggtg\n 2761 ctcggtgggg aattcgctta c\n//\n\nLOCUS JQ610678 1957 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 4, complete sequence.\nACCESSION JQ610678\nVERSION JQ610678.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1957)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1957)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1957\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"4\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..1926\n /note=\"capping enzyme\"\n /codon_start=1\n /product=\"VP4\"\n /protein_id=\"AFX73390.1\"\n /translation=\"MEPFAVLHLSAKLAPLVREGFIPYVDLDNIKTLNDLWIEIGKCS\n SDVYAVGRINRWTIRQLRAYRFIFVSEKRTITLKDIKITPDVPIRCADGLDLKLLETT\n IGRKRLVLRKTFGDILRKYALSQSVHLHGSEAETLNMADPTIHHVKGLPMIAPNHLNP\n TKPWSDLDDTETDEKLVSMLDYAMYSAQEVHYVGSGDGRTIRLFAKRDKKRFDRAKWV\n CYDPIMTDIGLTNVIAVKHYVNTFRDMLPYLNTGDRVERLLLWDVSGDAAKHDRFWEA\n QRTEEDRRGESVAVSLTEYFALAIIKHRIPIYEEKYRCTTSWIVPQPGAVREMYEMRN\n IILLNGFSRVNRAHIPQAGVMEIEADVLREMVRNFHGAGRGRLLKKSLYESLHIHQVD\n GLEDSEDGARSDLFYLTNQRNVNSIQSIRRVLGNSTVSTLWVSRERVFEYDDFNFDRS\n ALMLWHRGREHLLFDGNGAVLYLMWQHGDRYRKDVNYDPSWAEHFAVLIREPQPWRPV\n PDLSLCRFISLRRVSTVIRIRGDIHRKSDQVKRLGLDLSGHLFVTLISGAYLADLRWW\n FRMIIQWSKQRRQEKIDDLAKVNAEVVEWKEEKADEPWHRKEDLIAALIAAKSITGDQ\n HIDGWIAELRDME\"\nORIGIN \n 1 gtatatttcg aaatggagcc ctttgctgtg ctgcacctat cagccaagct ggcaccgctg\n 61 gtgcgtgagg gatttatccc gtatgtggac ttggataata ttaagacgtt gaatgacctc\n 121 tggattgaga ttggcaaatg ctcatctgat gtatatgcgg ttggacgaat aaataggtgg\n 181 acgatacgtc agctacgtgc gtatagattc atattcgtgt cggagaagag aacaataacg\n 241 ttgaaggata ttaagatcac acctgacgtg ccaataagat gcgcggatgg gctagactta\n 301 aagttacttg agactacaat aggacgtaaa agattagtgt tgcgaaagac gtttggagac\n 361 atactgcgaa aatatgcgtt aagccagtcg gtacacttgc atggatctga ggcagaaacc\n 421 ttgaatatgg cggaccctac catacatcac gtgaaggggt taccaatgat agcgccaaat\n 481 catttaaatc caacgaaacc atggagtgat ctggacgaca cagaaaccga tgaaaaacta\n 541 gtgtcaatgc tagattacgc gatgtatagc gcgcaagaag tgcattatgt tggctcggga\n 601 gacggtagaa cgatacggct gtttgcaaag agggacaaaa agagatttga tagagcgaag\n 661 tgggtgtgct atgaccctat tatgactgat attggattga caaatgtgat agctgttaaa\n 721 cactatgtca atactttcag ggatatgcta ccgtatttaa atactggcga ccgagttgag\n 781 agattactat tgtgggacgt aagtggagat gcggcgaaac atgatcggtt ttgggaagct\n 841 cagaggactg aggaggaccg gcggggagaa tcagttgccg tgtctttaac ggagtacttc\n 901 gccttggcta ttatcaaaca tagaattcca atctatgagg aaaagtatag atgcaccact\n 961 tcgtggattg taccgcagcc tggcgcggtc cgcgagatgt acgagatgag gaatatcata\n 1021 ctgttgaacg gtttttctag ggtaaatcga gcgcatatcc cccaggcagg cgtaatggag\n 1081 attgaggctg atgtgttacg tgagatggtg aggaacttcc atggagctgg tcgcggtcgg\n 1141 ctgctgaaga aatcgcttta tgagagtcta catatccatc aagttgatgg attggaggat\n 1201 tcggaagacg gagcgcggag cgatctcttt tatttaacca accaacgtaa tgttaattca\n 1261 atacaatcaa tcagacgagt tttgggaaat agcacggtgt cgactttatg ggtgtcaagg\n 1321 gaacgagttt tcgaatatga tgactttaat tttgaccgat cagcgttgat gctctggcac\n 1381 aggggtagag agcacttact atttgatggc aacggcgcgg ttctatattt gatgtggcag\n 1441 cacggagata gatatagaaa ggatgtgaac tatgatcctt cgtgggccga acattttgca\n 1501 gtattgatcc gagagccaca accttggcga ccagttccag atctgtccct ctgccgtttt\n 1561 atttcgctaa gacgggtgtc gacggttatt agaatacgag gcgatattca caggaaaagt\n 1621 gatcaggtaa agcgtttagg gttagatttg tcaggacatc tgttcgtaac gttaatttct\n 1681 ggagcgtatc ttgccgattt aagatggtgg ttccggatga tcatccaatg gtcaaagcag\n 1741 cgtagacagg aaaagataga cgatttggct aaggttaacg ctgaagtggt tgaatggaaa\n 1801 gaagagaaag ccgacgaacc gtggcatcgc aaggaggacc tgatcgctgc tttaatcgcg\n 1861 gcaaaaagta tcaccggtga tcagcatata gatgggtgga ttgcggagct gagggatatg\n 1921 gaatgacatc cacccgaggg gcaatcgaac tacctac\n//\n\nLOCUS JQ610679 1735 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 5, complete sequence.\nACCESSION JQ610679\nVERSION JQ610679.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1735)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1735)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1735\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"5\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 36..1676\n /note=\"non-structural protein 1\"\n /codon_start=1\n /product=\"NS1\"\n /protein_id=\"AFX73391.1\"\n /translation=\"MDQFLDSFDVTGDEANALRLLRAVSPEMTCSHLRRDCLIGGICA\n KQFFNEVLMAILDSKDRQAARQLVTLAVMTSYDRELIWLNVLRSTEVLPANDYAHEIQ\n NVVLNLKRVFIESGLEEKYKSFRAKRRPNRSPTEDAFSFLPFFYIPMNETKRVGIKKL\n TRVRNLGVAFVDRREVTHHLPFTVDAARRDLMMLRNFTLEHQRTCTFTGSKSLIHGMI\n FCPEEMEPLFQKKETALEIYRICEQDMKFINSRGTMSFPRFLMQRLAVKNASSDAMDQ\n VMLGRTPSDGRLMSVTGASFFFGGGPDWRKWAMPALLVRAARLRTVVTSFVKEWFDST\n HTCQVCFLVEKGVADSIPITDVRLSDVCGVGPVAYVRSYAHDDGNAPDVRVLRKGEIF\n RLMGGHYVMQTTASTMESLVVAAKEMQRLVRGDGFWDTPYWGLSMANLCKIMFHENPA\n KEQIHFMIKLITFGMFGGVQRHNGLFTDWDNLEEFLKRMFSTEEMGVRMYESSYHAIL\n RACILHLQTTAKPTLVQLTHAIESLDLGIEEVPFNFYV\"\nORIGIN \n 1 gtaaaaagaa tcctctgcgt tcactgggca cgaacatgga tcaattcttg gattcttttg\n 61 atgtgactgg agacgaggcg aatgccttga gattattgag agcggtttca cctgagatga\n 121 catgctcaca tttgaggaga gattgtttaa ttggagggat atgcgcaaaa cagtttttca\n 181 acgaggtgct gatggccatt ctggattcaa aagatcgtca ggcagcgcgt cagctggtga\n 241 cattagctgt gatgaccagt tacgaccgag agctaatctg gctcaacgta ctaaggtcaa\n 301 ctgaagtgct gccggcaaat gattatgcac atgaaataca gaatgtggtt ctgaacttga\n 361 agagggtctt catagagagt gggttggaag aaaaatacaa gagtttcagg gcgaagcggc\n 421 gtccaaacag atctccgacc gaggatgctt tctctttttt gccctttttc tacataccca\n 481 tgaatgaaac aaaacgggtt ggaataaaga aactcactag agttcggaac ctaggtgttg\n 541 cttttgttga tagacgcgaa gtgacgcatc atttaccgtt cacggtggac gctgctagaa\n 601 gggaccttat gatgctgaga aatttcacgc tggagcacca aagaacatgt acgtttacgg\n 661 gttcaaagag cttgatacat gggatgatat tctgtcctga ggagatggaa cctcttttcc\n 721 agaagaagga gacagcgcta gaaatctaca gaatttgtga gcaggatatg aagtttatca\n 781 actcaagagg tacgatgtca tttccccggt ttttgatgca acgtttagcg gtgaaaaacg\n 841 cttcatctga tgcgatggac caggttatgt tgggacgaac tccgagcgat ggacgtttga\n 901 tgtcggtgac tggtgcctct ttcttttttg gagggggacc tgattggcgc aagtgggcga\n 961 tgccggcgtt gttggtacgt gctgcaagac tgagaaccgt cgtgacatca ttcgttaagg\n 1021 agtggtttga ttcgactcac acatgtcaag tctgtttcct agttgaaaaa ggtgtcgccg\n 1081 attcaattcc gatcactgat gttcgtttat cggatgtgtg cggcgtagga ccagtcgcat\n 1141 atgttagatc ttatgcacat gatgacggga acgcgccgga tgttcgcgta ctgagaaaag\n 1201 gtgaaatctt cagattgatg ggcggacatt atgttatgca gacaacggcg agtacaatgg\n 1261 aatcattggt cgttgccgcg aaggagatgc agcgtttggt tcgcggcgat ggtttttggg\n 1321 acacaccgta ttggggttta agcatggcaa acctttgtaa aatcatgttt catgaaaacc\n 1381 cagcaaagga acagattcat ttcatgatta agctcataac ctttgggatg tttggtgggg\n 1441 ttcaaaggca caatggactg ttcacagact gggacaattt ggaggagttc ttgaagagga\n 1501 tgttttctac ggaggagatg ggcgttcgta tgtatgagtc aagttaccat gcgatacttc\n 1561 gtgcgtgcat actacatcta cagaccactg cgaagcctac cctcgttcaa ctaactcacg\n 1621 cgatcgaatc actcgacctt ggaatagaag aagttccttt caatttttat gtctaaaaca\n 1681 tcataataaa ccataaagag tctgagtaat tgtatccctg agctcttact cttac\n//\n\nLOCUS JQ610680 1605 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 6, complete sequence.\nACCESSION JQ610680\nVERSION JQ610680.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1605)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1605)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1605\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"6\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 22..1581\n /note=\"outer capsid protein\"\n /codon_start=1\n /product=\"VP5\"\n /protein_id=\"AFX73392.1\"\n /translation=\"MGKFVKALKKIGRGTVKALTSDAAKKLYTTLGKAATRFAESEVG\n SAAIDGLIQGTAQTLLHGGSASENIKQAVVLGVLHSMETPADPLSPGEQGVYDKIKEI\n KREEKEDRFFEVYQEKIDEELGSDMKRMREVAKGDKQAIKEMGGEIKVIEKAFDGLIK\n IDKIQDMKLTQLYGALAKERTERTQDEIKMVNDYTGKIEALQSAITVERDAMQEEALQ\n EIIEMGTDVIETASEEVPIFGPAAANVVATGRMVEGTLKLKQVIEKLAGLDVSHTTRD\n RIEPKVINAILDHEGGVVPEKELAIGVYNKLQTVREHMAEHSHLKEMAIPRLQKLYTE\n HGDEWHPKIITQMKVAREHQPQIHIYCAPWESDDVFMLRVYAPHHIGCGLFLGVDLES\n EFIFYEDLIAENHVLRGGVIEVVGRNFRQAVREFLLMAASKIENTMHVKRLVRSSASS\n PIYLSSIHYECTFDEIKQNVLQIVHDEQLQMHLLRGPKHFQRRALMAAVVKGVKILEG\n PDTKALMLQGL\"\nORIGIN \n 1 gtataaaata cctcggtcat catgggcaaa ttcgtaaagg ccctgaagaa aataggaagg\n 61 ggtacggtga aggcactgac gtctgacgct gcaaagaaac tttatacgac tttaggaaag\n 121 gcggcgacgc ggtttgctga aagcgaagtc ggcagcgcgg cgattgatgg attgatacaa\n 181 ggaacagcgc aaactttact gcacggaggc agcgcgagtg aaaatatcaa gcaagcggtt\n 241 gttttaggtg ttctccacag catggaaacg ccggcggacc ctttatcacc aggagagcaa\n 301 ggagtatatg ataagattaa ggaaattaaa cgagaagaaa aggaagatcg gtttttcgag\n 361 gtttaccaag aaaagattga cgaagagctt ggttcagata tgaagcgaat gcgagaagtg\n 421 gcaaaaggtg ataagcaggc catcaaggaa atgggtggtg aaattaaggt tatcgagaaa\n 481 gctttcgatg gattgattaa aatagataaa attcaagata tgaaattaac gcagttatat\n 541 ggcgcgctcg cgaaagagcg tacggagcgt acgcaggacg agatcaaaat ggttaacgac\n 601 tacactggaa aaattgaagc actgcaatcc gcgataacag ttgagcggga cgctatgcaa\n 661 gaggaggcgt tgcaggagat aatagaaatg ggaacggatg taattgaaac cgcctccgaa\n 721 gaggttccga tattcggccc tgcggctgcg aatgtagtcg caactggacg aatggttgag\n 781 ggcaccttaa agttgaagca agtaatcgag aaattagcag ggttagatgt ttcgcacacc\n 841 acaagggaca gaatcgagcc gaaagttata aacgctatac tagatcacga ggggggcgtc\n 901 gtaccggaaa aggaactagc gattggtgta tataataagc tgcagacagt cagagaacat\n 961 atggcggaac acagccatct aaaggaaatg gcaataccaa ggctgcaaaa gctgtacaca\n 1021 gaacacggcg atgagtggca tccaaagata attactcaaa tgaaggtagc gagagaacat\n 1081 cagccgcaaa tacatatata ttgcgctcca tgggaatcgg atgacgtgtt tatgttgcga\n 1141 gtgtacgcgc cgcatcatat agggtgtggt cttttcttag gagttgattt agagagtgaa\n 1201 ttcatatttt atgaggattt gatagcagag aaccacgtat tgcgtggtgg cgtcattgaa\n 1261 gtcgttggaa ggaacttcag gcaagcagtg cgcgaatttc ttttgatggc tgcgagcaag\n 1321 attgagaaca ctatgcatgt caagcggtta gtgagaagct cggcttcctc acctatctac\n 1381 ttgtcaagca tacactatga gtgtacattt gatgagataa aacagaacgt tttacagatc\n 1441 gtgcacgacg agcagttaca gatgcatctg ttacgtggtc cgaaacattt ccaaagacgt\n 1501 gctctgatgg cggctgttgt taagggtgtt aagatcttag aggggccaga tacgaaggcg\n 1561 ctcatgctac agggtttgta agtggctgaa aggtatcaag aatac\n//\n\nLOCUS JQ610681 1166 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 7, complete sequence.\nACCESSION JQ610681\nVERSION JQ610681.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1166)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1166)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1166\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"7\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..1069\n /note=\"T13 protein\"\n /codon_start=1\n /product=\"VP7\"\n /protein_id=\"AFX73393.1\"\n /translation=\"MDAIAARALSVIQDCISVGDGRINLDPGVMERLGIAINRYNGLT\n NNVVTIRPGTQDERNAMFFMCLDFALAALNIQIGVISREYTQALATIGVLATGEIPYS\n VAAMDTIVRISGTMATWGPTEYELPPYARSQMIQMSGRYYVPAGANSHAAHVDPTTVE\n ISLAAGVVVNVTNALQPRGVAPTMMYMVWHPLAIFANPQGATAASPQNMTLVVGGLNI\n AAGTIIAWDTVAPIQLSNQGGQEGMIAIRILWMTTLDKSMTSLPEMREIISRCYSFMH\n PSWHALRGTVLHSLNLPTNNPPMFAPATRQEALAYLILANLADAYTSLRPDFTIQGML\n AVPQVIDRQFVQGAYR\"\nORIGIN \n 1 gtataaatat ctagagatgg acgccattgc ggcacgtgct ctgtccgtga tccaggactg\n 61 cattagcgtt ggtgatggga gaattaattt agaccctggg gtcatggaga gattgggaat\n 121 tgctattaat agatacaatg ggctaacgaa caatgtggtg acgatcagac cagggacaca\n 181 agatgagcgg aacgcgatgt tttttatgtg tctggatttc gcgttggcgg cattgaacat\n 241 acaaattggg gttatatcta gggaatacac gcaggcgctg gccactatcg gtgtgctggc\n 301 aacgggagaa atcccttact cggttgccgc tatggatacg attgtacgga ttagcggaac\n 361 gatggcgaca tggggtccca ccgaatatga gttaccgcca tatgcgcggt ctcagatgat\n 421 acaaatgagc ggacgttact acgttccagc gggggcgaat tcacatgctg cccatgtcga\n 481 tcccacgacg gtagagattt ctttagctgc tggagtagta gtgaatgtta cgaacgcgtt\n 541 acagcctagg ggcgttgcgc ccacaatgat gtacatggta tggcatccgt tggcgatttt\n 601 cgcgaatcct cagggtgcta cagctgcttc gcctcaaaat atgactttgg tggttggtgg\n 661 gctgaatata gcagctggca cgatcatcgc ttgggatacc gtcgctccta tacagctatc\n 721 gaatcaggga ggacaagagg gaatgatcgc gatccggata ctatggatga caacattaga\n 781 taaatctatg acaagcttgc cggagatgcg tgaaataatc tcaagatgct atagctttat\n 841 gcacccttca tggcacgcgc tgcgagggac ggtcctacat tcgcttaatc tgccgactaa\n 901 taatccacct atgtttgcgc ctgctacgcg acaggaggca ttggcgtact taattctggc\n 961 aaatttagcg gatgcatata cgtcgttaag gcctgatttc accatacaag gaatgctcgc\n 1021 ggttccacag gtcattgaca ggcagttcgt tcagggtgcg tacaggtaga ggacgccttc\n 1081 cacagtgggc gtctcatgta gccccagcgt cggtccctta cgtgtgctgt aacgcgtagg\n 1141 tagaacgtca tatgatatta agttac\n//\n\nLOCUS JQ610682 1089 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 8, complete sequence.\nACCESSION JQ610682\nVERSION JQ610682.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1089)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1089)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1089\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"8\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 26..1057\n /note=\"non-structural protein 2\"\n /codon_start=1\n /product=\"NS2\"\n /protein_id=\"AFX73394.1\"\n /translation=\"MAQEVKRKFTRTVCIYDPQNRTFCGRSAAMVCNSYYTIKMGRTT\n QCGVSPVPVPKSYVLEIPDVGSYRILDGQDSISVIVTETGVEATSERWEEWKFEGVNC\n VPMVVQTEIGKGLIDMEIKFSKGMGLVKPYVKNEVSRTEIPRLPGASVIDTPIRDYRQ\n LLKDQRDERRAALDAIACDICPTLSRMLGANITDGSPQVEEVATRPTQPPAQLKLDVP\n NWDQPTDSDDEDEESKRVTTQSNADTEEQVTFEDCITDQYFSKTGEFAKKYPEMLAGL\n SAKMPSETGRFTKILTTRKAQWNNVPLFELDPNGFTYHFSKLGNSTRIFCVQRDLSYM\n VLPAGQGLK\"\nORIGIN \n 1 gtaaaaaatc tcctctcttt tcacgatggc tcaagaagtt aagagaaagt tcactagaac\n 61 agtgtgcatc tatgatccac aaaatcgcac attctgtggt cgaagtgccg cgatggtgtg\n 121 taacagttat tatacaatta aaatgggtag aacgacgcag tgtggagtgt cgccggtgcc\n 181 cgtaccaaag tcatatgtgc tagagatacc ggatgttggc tcttatcgca tcttagatgg\n 241 gcaggattca atcagtgtca tcgttactga gacgggcgtc gaggcaacgt ctgagaggtg\n 301 ggaagagtgg aaattcgaag gcgttaattg cgttccgatg gttgttcaaa cggagattgg\n 361 gaaaggcctg attgacatgg agatcaagtt tagtaaggga atggggctcg ttaaacctta\n 421 tgtaaagaat gaggttagca gaactgagat cccacggcta ccgggtgctt cagtcattga\n 481 tacaccgata cgcgattacc gtcaactttt gaaggatcag agagatgaaa gaagggcggc\n 541 gctcgatgcg atcgcatgcg acatatgtcc cactctatca agaatgctag gggcgaatat\n 601 tacagacgga tcgccacaag tcgaagaagt cgcaacacgg ccaacacaac ctccagctca\n 661 gctgaagctg gatgtgccta actgggacca accgactgat tcagatgatg aggatgagga\n 721 atccaagcgc gtgacaacgc aaagtaatgc tgatactgag gaacaagtga ctttcgaaga\n 781 ttgcattacc gatcaatact tttcgaaaac gggtgaattc gcgaagaagt atcctgaaat\n 841 gttagcggga ctttccgcga agatgccgag tgaaacaggt aggtttacaa aaatattgac\n 901 gacgaggaag gctcaatgga ataacgttcc tcttttcgaa ttagatccaa acgggtttac\n 961 atatcatttt agtaagctgg gtaattcgac gaggatcttc tgtgtccaac gtgatttgag\n 1021 ctacatggtt ttacccgcag ggcaaggcct gaagtagcgg tgcatgtagc cgggagaggt\n 1081 acaacttac\n//\n\nLOCUS JQ610683 925 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 9, complete sequence.\nACCESSION JQ610683\nVERSION JQ610683.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 925)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 925)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..925\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"9\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 23..883\n /note=\"helicase\"\n /codon_start=1\n /product=\"VP6\"\n /protein_id=\"AFX73395.1\"\n /translation=\"MLVLAPGDLIDGVRHQLSERGVRIRLRETNDDEQKDEPVDTGGG\n KPGDRIGKEVGNAESEQSSDKEKKAGGSSDSELGEGGDGRRQTEKAEGGENGTRDIGI\n QDKDKQFDRRANPDNALDRENRSGDPQLKYGFATKRIANAVESKYHCGGFEGPGSDGY\n IKLEMSIMKALGLNRDDHIEQLEFLKHQQKGPSKIQVRTIASETKLKEVCNIMDKPVA\n PTARSAVSVVSNRVEDVKEAQVYFTTPTGDRGWKEVARKASQTPNIRAYINPEGDDPK\n VSFLHLIDHL\"\n CDS 111..512\n /note=\"non-structural protein 4\"\n /codon_start=1\n /product=\"NS4\"\n /protein_id=\"AFX73396.1\"\n /translation=\"MMTSKRMNQWIREAASRVIESGRKLEMPRVNSLPIKRRRLEEVR\n IQSSGKVEMEGDKLRRLKAERMELEILAFRIKTNNLIGALIQITRWTEKIDQEIRNLN\n MDLQPNELQTPLSQSTTAVDLRGQDRMDTSN\"\nORIGIN \n 1 gtataaaaca tcctcccatg tcatgttggt gttggcaccg ggtgatctca tagacggagt\n 61 gcgtcatcaa ttatctgaaa gaggagtcag gattcgttta cgggaaacga atgatgacga\n 121 gcaaaaggat gaaccagtgg atacgggagg cggcaagccg ggtgatcgaa tcgggaagga\n 181 agttggaaat gccgagagtg aacagtcttc cgataaagag aagaaggctg gaggaagttc\n 241 ggattcagag ctcggggaag gtggagatgg aaggcgacaa actgagaagg ctgaaggcgg\n 301 agagaatgga actagagata ttggcattca ggataaagac aaacaatttg atcggcgcgc\n 361 taatccagat aacgcgttgg acagagaaaa tcgatcagga gatccgcaac ttaaatatgg\n 421 atttgcaacc aaacgaattg caaacgccgt tgagtcaaag taccactgcg gtggatttga\n 481 ggggccagga tcggatggat acatcaaact agaaatgtca ataatgaagg cgctaggttt\n 541 aaaccgagat gaccacatcg aacaattgga gttcctcaag caccaacaga aagggcccag\n 601 caaaattcaa gtcagaacga tcgcttccga aaccaaatta aaagaggtgt gtaatataat\n 661 ggacaagccg gtggctccca cagcgagaag tgcggtgagt gtagttagta accgtgttga\n 721 agacgtgaag gaagcccagg tgtattttac aactccaaca ggagatagag gctggaaaga\n 781 agtagcaagg aaagcgagcc agacaccaaa cattcgagcg tacattaatc cggagggaga\n 841 tgatcctaaa gtctcatttc tgcatttaat cgatcatctg tgaggtcacg gtctgaacta\n 901 cgggcatgct gggtgtttca gttac\n//\n\nLOCUS JQ610684 761 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 10, complete sequence.\nACCESSION JQ610684\nVERSION JQ610684.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 761)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 761)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..761\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"10\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 20..703\n /note=\"non-structural protein 3\"\n /codon_start=1\n /product=\"NS3\"\n /protein_id=\"AFX73397.1\"\n /translation=\"MYRDLLNIHTEMRGPPSYEPSGLAQATAPTMRFGDREDEEGLLR\n ARELSLNVLTNAMTNTTGANEAIKNEKAMFGAYADALRDTPEIRVVKRRINERTLEKL\n HKMRRSLHGRRMFVRMLLAINVGLALLTSAVNVVRQSLDDFGKERWIVGGVWWLGEVV\n VTINFGTTVATLVLMRIHGALNAQLQTIKRDIYKKSSYNEAAAMHWKGEISLIEELAA\n SHVPAGSNV\"\nORIGIN \n 1 gtataaaatt ccgttcgcaa tgtaccgtga cttgctgaat attcacactg aaatgagggg\n 61 cccgccatct tatgaaccta gtggcttagc tcaagcgaca gcaccgacta tgaggtttgg\n 121 ggatagagaa gatgaggaag gcctattgag ggcgcgcgag ctttcgctta atgtgttaac\n 181 gaatgctatg actaatacaa cgggtgcgaa tgaggcgatt aagaatgaga aagcgatgtt\n 241 tggggcatat gccgatgcac ttagggatac tccggagatt agggtggtga aaaggcggat\n 301 aaatgaacgt acgttagaaa agttgcataa aatgcgacgt tcgctgcacg gaagacgaat\n 361 gttcgtacga atgttgttgg cgataaatgt gggattggcg ctattaacct cggcagtgaa\n 421 tgtggtacgc cagtcgctag atgattttgg gaaagaaagg tggatagttg gtggagtgtg\n 481 gtggttaggt gaggtcgtcg ttacgattaa ttttggaacg actgttgcta cgttggtatt\n 541 aatgaggata catggcgcat taaacgcgca gcttcaaacc attaagcgtg acatatataa\n 601 gaaaagctcg tataatgagg ccgctgccat gcattggaaa ggtgaaatta gcttaattga\n 661 ggagctagcg gcgagccacg tacctgcggg atcgaatgtc tagtccgcga catcgaaaaa\n 721 ttcacttgtc caggtgaagc ccgtagaacg gatcgtctta c\n//\n\n" }, { "path": "tests/input/TestGenbankRecordFetch/orungo.gbk", "content": "LOCUS JQ610675 3942 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 1, complete sequence.\nACCESSION JQ610675\nVERSION JQ610675.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 3942)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 3942)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..3942\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"1\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..3921\n /note=\"RNA-dependent RNA polymerase\"\n /codon_start=1\n /product=\"VP1\"\n /protein_id=\"AFX73387.1\"\n /translation=\"MVITVEGAWLVRRALQRFLKFSKIDGESAVYEFYRYSSNIREIR\n RKHGTRYKMHDEELERRRDSGKLRFKGMQVVVESTWMEILGKGRTTDEIEIFRSSILS\n LDELNPEEEFLRNYASSDKEHPSYLFVRGRAVNEMQIYGDMPIKAWLSFLVECEVEYG\n YKLFGMEVARSFVQSFGSPFHQNSRDLSQIDDMAPAFTSPLLFEMCCMTSILEINIRM\n RMLEERVATLKFGEREIDPLEVLKEFFRICIPHPKKINNMLRAPYSWFVKLWGVSYHE\n PIVLTARGGEDKNSKDIFFTGFHRVKNPYSIMLKKSRFFKKSLDENISKVKEAIDYSN\n SLTGMSLGLPVFLSMLQNVYDTEFNPTMVQHVLLASFLLSIQTITGYGRAWVKNVSSD\n NDTQMRPAEDNFIDRVAKQTEINFIQAYEEALGHGEDIVKPEDMFTSILRLARNTSSG\n FSTAVDVYKRFGPKSGGRGERVKITSRIKALVIFTKGHEIFTAENLAKRYDTEEDYQT\n KGSRDVPIKATRTIYSINLSILIPQLILTLPLNEYFARFGGSTAPDSRSLGGKVIIGD\n LEATGSRTIDAADTFRNSSDPEIFTIAIDYSDYDQHLTVFNFRNGMLEGIRSAMKRYK\n ELRYDGYTLNELIEFGYGEGRIVNSKWNGKRRVKSVRMSDYMALSESQRAQGTFKPPQ\n GVRPVSSMQVFDSVGEASGGDTLLISPTDGSDLATVNTHLSGENSTLVANSLHNMAIG\n RIIQEEIRKNHRAAFTFESEQYVGDDTLLYAKLNTLNHEIFDKAIDTIFDTVGKCGHV\n ASAAKTLIAPFSVEKTQTHAKQGIYIAQDRMMIISSERRKDIEDVQGYMRSQVSVMAT\n KVSRGFSHELAQLVFMMKSSIVGFRKLKRTVVEDGVYRDRALDSEDEDGFTLMQIRDP\n LVAFYPAEWNGYGMHPVALNIVMTEDMFIDTSTMVEFQHVMRPLLRFMGRIPPVWNET\n KADKRQISSITKMSFFSKMARPAVRAVLANSELSDQVRTLPLGDFSPFNLSATMMHSA\n LLKEPRARALLTPAYEKEFQSELNSNRDSEVNFVGRNMEINTNYMKLFDVDLSTRIVA\n KQFSFPDQNMSLPFYFQKLLIGHRPVARMRMTYIDRIDQILRGDVVMRGFITANTIMS\n VLEKIGTAHAVQDLTTIFQLMNIESKVAHRLAEYIASERVRFDALSIAKRGICGDEFS\n MSLDVCTERFAERFMELPAQFTKTERDIAILYAAQLTMLRCAANLDLRKIKIGVSADH\n VKRFKQRQARFKTHLPKMRTVTRLITPERISARLVQHQFT\"\nORIGIN \n 1 gtataattag gaatggtcat cactgtggaa ggtgcgtggc tggtgagacg ggcgttgcaa\n 61 cgttttttga agttcagtaa aatcgacggg gaatcagcag tttatgagtt ctataggtat\n 121 tcaagtaata ttcgtgaaat aagaaggaag catgggacgc gttataaaat gcatgatgaa\n 181 gagttggagc ggaggcgtga ttcgggcaaa ctgcgtttta aaggtatgca agttgtggta\n 241 gagtcgactt ggatggagat tttagggaag ggacgtacga cggacgaaat cgagatattc\n 301 agaagttcga ttttatcgtt ggatgaactg aatccggaag aagaatttct gcgcaattat\n 361 gcgagttcgg acaaggaaca tccatcctac ttgtttgttc gggggcgggc ggtcaatgag\n 421 atgcagattt atggcgacat gccgataaaa gcgtggttga gctttttagt agaatgtgag\n 481 gttgaatatg ggtacaaact cttcggaatg gaagttgcga gatcgttcgt tcagagcttt\n 541 ggatctccgt ttcaccagaa ctcgcgtgat ctatcacaga ttgacgatat ggcgcctgct\n 601 tttacgtcac ctttattatt tgaaatgtgt tgtatgacat caattctcga aattaatata\n 661 cgcatgcgta tgctggagga gagggttgca accctaaaat ttggtgagcg ggagatcgac\n 721 ccacttgaag tactaaaaga attcttccga atctgcattc cgcatccgaa aaagattaat\n 781 aatatgttga gagctccata ctcatggttc gtcaagctgt ggggcgtatc gtatcatgag\n 841 ccaatagtcc tgacggcgag gggcggcgag gataagaact cgaaagacat attctttacg\n 901 ggatttcaca gagtcaagaa tccatactca ataatgttga aaaaatcgag gttttttaag\n 961 aaatctttag acgagaatat cagcaaagtg aaagaagcga tagactattc aaactcgttg\n 1021 acggggatgt ctttagggct gcccgtattt ctatccatgc tacagaatgt gtacgacact\n 1081 gagtttaatc cgactatggt tcaacacgtg ttactagcgt cgttcttgtt gagtatccaa\n 1141 acaataactg gctatggacg cgcttgggtg aaaaatgtgt caagcgataa cgacactcaa\n 1201 atgcgcccgg cggaggacaa cttcattgat cgagttgcta agcaaacgga gattaatttt\n 1261 atacaggcgt atgaagaggc gttggggcac ggagaagata tcgttaagcc agaagacatg\n 1321 tttacctcca ttttgcgttt ggcaagaaat acaagttccg gcttctctac tgctgttgac\n 1381 gtttataaac gattcggtcc aaagtcggga gggagaggag aacgcgttaa gataacatca\n 1441 agaattaaag cattagttat cttcacaaag ggccatgaaa tatttacagc tgaaaatctc\n 1501 gcgaaaagat atgatacgga ggaagattac cagactaaag ggtcacggga tgtacctatc\n 1561 aaagcaacgc ggacgattta ttcaataaac ctctccatct tgatcccgca gctgatccta\n 1621 actttaccgt tgaatgaata ttttgcccgg ttcggaggat caactgcacc tgactcacgt\n 1681 agcctagggg gtaaggtgat tatcggagat ctagaagcaa cgggatcacg gacgatcgat\n 1741 gcggcagata cgtttagaaa ttcgtccgac ccagaaattt tcacaatagc gatcgattat\n 1801 tcggattacg atcaacattt gacggttttt aacttcagga acggtatgct ggaaggaatt\n 1861 cgctctgcga tgaagagata taaagagttg aggtatgatg gatacacgtt gaatgaattg\n 1921 attgaattcg ggtatgggga ggggagaatt gttaattcga aatggaacgg aaagaggcgg\n 1981 gtcaaatctg tacgaatgag cgattatatg gcattgagtg aaagtcaacg cgctcagggc\n 2041 actttcaagc cgccgcaggg agtgagaccg gttagttcaa tgcaagtgtt cgattcagtg\n 2101 ggtgaggcat ctggagggga tactctcctc atctcgccca ctgacggatc ggatttagca\n 2161 accgtcaaca cgcatttgtc gggtgaaaat tcaacgttag ttgctaactc tttgcataat\n 2221 atggctatcg gacgtatcat acaagaagag atcagaaaga accatcgagc ggcttttacc\n 2281 tttgaatctg agcagtacgt tggagatgat acgttacttt atgcaaagtt gaacacatta\n 2341 aaccatgaaa tttttgataa agcgattgat accatcttcg atactgtggg aaagtgcgga\n 2401 catgtggcat cggcagcgaa aacccttatc gctcctttct ctgttgaaaa aactcagact\n 2461 catgcgaagc aaggaattta cattgcgcag gatcggatga tgatcatctc ttcagagcgt\n 2521 agaaaggata tcgaggacgt ccaagggtat atgagatcac aagtgtcggt tatggcgaca\n 2581 aaagtaagcc gcggctttag tcatgaactg gctcagcttg tctttatgat gaagagcagc\n 2641 atcgtaggct ttcgtaaact gaagcgaact gtggtggagg atggtgtata ccgtgatcgc\n 2701 gcgttggatt cggaagatga ggatggcttc actttgatgc agatccgtga tccgttggtc\n 2761 gccttctacc ctgctgagtg gaacggctat ggcatgcatc cagtcgcttt gaatatcgtc\n 2821 atgacggaag acatgtttat agacacgagt accatggttg agtttcagca tgtaatgcgg\n 2881 ccgctccttc gatttatggg taggatacct ccagtgtgga atgaaactaa agccgataaa\n 2941 cgtcagattt catccataac aaagatgagt ttcttctcca aaatggctag accagcggtg\n 3001 agggcggttc tggcgaatag tgaactgtca gatcaagtga gaacattgcc actgggcgac\n 3061 ttttcgcctt tcaatctctc cgcaacaatg atgcactcag cattattgaa agaaccacgc\n 3121 gcgcgtgccc tgctgacgcc agcctacgaa aaagaattcc agtcagagtt gaattcaaac\n 3181 cgggatagcg aagtaaattt cgtcgggagg aacatggaga tcaacactaa ttatatgaaa\n 3241 ctgttcgatg ttgatttgtc tacgcgaata gtggccaaac aatttagttt tccagatcag\n 3301 aatatgtcgt tgccttttta ttttcagaaa ctcttgattg gacatagacc ggtcgcgcgg\n 3361 atgagaatga cctatattga ccggattgac caaatcttac ggggagacgt cgtgatgagg\n 3421 ggtttcatca cagcgaatac tattatgtcc gttttagaga agattggcac tgctcacgcc\n 3481 gtacaggact taacaacaat atttcagttg atgaacattg aatctaaggt ggcgcatagg\n 3541 ctagcggagt atatcgcttc tgaaagggta agattcgacg cgctctcgat tgcaaagagg\n 3601 gggatatgcg gggatgaatt ctccatgtcg ctggatgtgt gcacggaacg gtttgctgaa\n 3661 cggttcatgg aactaccagc gcagtttact aaaactgaga gagatatagc gattttatat\n 3721 gccgcgcagc taactatgtt gcgctgtgcg gctaacctag atcttaggaa aattaagatt\n 3781 ggggtttcag cggatcacgt taagagattt aaacaaagac aggctagatt taagactcat\n 3841 ctacctaaaa tgcgtacagt cacgcggctg ataacgcctg aacgaatctc cgcacgcctg\n 3901 gttcagcatc agtttacatg acgcaccacc taatcaactt ac\n//\n\nLOCUS JQ610676 2933 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 2, complete sequence.\nACCESSION JQ610676\nVERSION JQ610676.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2933)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2933)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2933\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"2\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..2899\n /note=\"T2 protein\"\n /codon_start=1\n /product=\"VP2\"\n /protein_id=\"AFX73388.1\"\n /translation=\"MAFERTVALTREFANETRQHFGKFDIVVNTESSIEDEATGEWEF\n ARSDGRLGIYEELHNSIAYKHYTAILKGPENYLNIPQIFESKIYKNLNRDDLLARYDY\n SQILRFRDSKIAGRLRMQTYFGDVHVSAGLIDCVAMVREPIRREGCQHMMVRSFDLMN\n AGQFFDVHAPKIHAFDDTVIVESMDIENGVWRVKAGGVGLKTLQEKAEGILGDSVLDL\n VHNYLSQKWDAGYVAAKLLRFDETYKFHPIHEVGIFNTLMIRMGQLDDAYRDGFFDYD\n EIHAQLMRDVTFQYPEGKPVFRRDGQFFKNLVQYSGRAKIGYETYLPDRELWTEWRTR\n SSVQDVVPKYMEWLIGRLQLGKMLKIMSELPADVTMPNYLLKAITYKSSVYVKRLILT\n YIALRMTFGRCPVNKKGTLASSVLGFLHAVIPNLEEFLRKAGITDELCVKMEFTPRLT\n VMEREDRKSDRYAVVLQVYRERKLEVFTPIDSDLFEDRKKYYDEILKDKRWRGEETDY\n FFKDSGIHRSQVAGLSAEQLTLKKLGRDSDFNDPKRFVSYRYRYVSVKAGDIYAEGES\n VITGPLLTLIPHAYEFGRVSLIAGQSRDQSKLDNVPVYRDHMKSLELNGVEVGYDTWC\n PSGRAVQVNLELISTILYNAFKRPIVKGALCHFGMWEFYNPRRPAYESVDVTIMNAIS\n DITGSKRWAYQEIQDWLARFIKGSRVDMVTHRFHGVTKKPTTRGEIWIWNLLLVLISN\n PSLVVSQTDKFPLWVCASDGLHLISTGVRHTDHFRLWEWLPYTEKIGNDDYMSVLATD\n RELRLFEIALEYFETIRIGYRRDEWTHLKSNMFNTWLGTHCGGVGDGMILFDPVRLPS\n PSSVLYLICSHNSTLEGMMYLLHDIYGKIVEENTGTVFIRVHARGCKCSVCRGGLQGV\n DVKNRSAMRVRSMPGNIGFDSVNLILSTSTTSAFGNSYIYFKLINR\"\nORIGIN \n 1 gtataattga tccgcgatgg ctttcgagcg tacggtagcc ttaacaagag agttcgcaaa\n 61 tgaaacaaga cagcattttg ggaagtttga tatagttgta aacacggaaa gcagtattga\n 121 ggacgaagca acgggtgagt gggagttcgc acgaagtgat gggcggcttg gcatctatga\n 181 agaattgcat aatagcatcg cttataaaca ttatacggcg atactaaaag ggccggaaaa\n 241 ttatttgaat attccgcaga tttttgagtc gaaaatctat aagaatttga atagggatga\n 301 tctattggcg agatatgatt attcacaaat actaagattc cgagatagta agatagcggg\n 361 ccgattgagg atgcagacgt atttcgggga cgtgcatgta agtgcgggac tgatagattg\n 421 tgtagcgatg gttcgtgagc ctattagaag ggaagggtgt cagcatatga tggtacgtag\n 481 ttttgatttg atgaatgcgg gccagttttt cgatgttcat gcgccgaaga tccacgcgtt\n 541 tgatgacacg gtgatagttg aaagcatgga catcgaaaac ggagtatggc gcgtaaaggc\n 601 gggtggcgta ggtttgaaaa cgctgcagga aaaagcggaa ggaatactcg gagattcagt\n 661 gttagactta gtccacaact atctcagcca aaagtgggac gcaggttatg tggccgcgaa\n 721 gttgctgagg tttgatgaga catataaatt tcatccaatt catgaggtgg gaattttcaa\n 781 cacattgatg atacgcatgg gtcaactcga tgacgcgtat agggatgggt tcttcgatta\n 841 tgacgagatt cacgctcaat tgatgaggga tgtgactttt cagtacccag aaggtaagcc\n 901 agtctttcgg agagatggcc aattctttaa aaacctagtg cagtattcgg gacgggcgaa\n 961 gattgggtat gagacgtatt taccagacag ggaattgtgg actgaatggc gaacgagatc\n 1021 atccgtgcaa gatgttgtac ccaagtatat ggaatggttg ataggtagat tacagttggg\n 1081 gaaaatgctt aaaataatgt cggaattacc agcggatgtt acgatgccca actatctttt\n 1141 gaaagccatt acatataaat cgagtgtata tgttaagaga ttgatactca cgtacatcgc\n 1201 tttacgaatg acgtttggac ggtgtccagt aaacaaaaaa ggaacgcttg cctcatcagt\n 1261 cttaggtttt ctacacgcgg ttattccgaa tctggaggaa tttctgagga aagcgggaat\n 1321 aacggatgaa ctatgtgtta aaatggagtt tacgccgaga cttactgtga tggagagaga\n 1381 ggataggaag tcagacagat acgccgttgt cttgcaagtt tatagggaga ggaagctgga\n 1441 ggtttttacg cctatagact cagacttgtt cgaagatcgg aaaaagtact atgacgagat\n 1501 cttgaaagat aaaagatggc gtggagaaga gactgattat ttttttaaag actcagggat\n 1561 acaccggtcc caggtggctg ggttgagcgc agagcagctc acgttgaaaa agttaggacg\n 1621 cgactcagat ttcaacgacc ctaaacggtt cgtttcatac agatatagat atgtatcagt\n 1681 taaagcggga gatatctatg cagaagggga gagcgttata acgggaccat tattgacact\n 1741 gattccacat gcctacgagt tcggacgagt atctttgatt gcggggcagt ctcgagatca\n 1801 atcaaagttg gataatgtcc cagtctaccg tgaccacatg aaatccttgg agttaaatgg\n 1861 cgtcgaagtt ggctatgaca cttggtgtcc gtcggggcgt gcagtacaag ttaacttgga\n 1921 gttgatatct accatcctgt ataacgcgtt caaacgtccc atcgttaagg gagcattatg\n 1981 tcacttcggt atgtgggaat tttataaccc gagacgtccc gcgtatgagt cagtagacgt\n 2041 gacaatcatg aatgcgatct cggatatcac tgggagcaaa agatgggcat atcaggaaat\n 2101 tcaagattgg ttggcgagat ttattaaggg gtcacgggtt gacatggtga cacaccgctt\n 2161 ccacggggta acgaagaagc caacaactcg aggtgagata tggatctgga acctactact\n 2221 agttttgatc tcaaatccca gtctggtggt atcacaaacg gataaatttc ccttatgggt\n 2281 ttgcgcctct gatggcttac acctgattag tacgggagtg aggcataccg atcattttag\n 2341 actttgggag tggctaccat ataccgaaaa aattgggaac gacgattata tgtcggttct\n 2401 cgccacagat agagagttgc ggcttttcga aatcgcgttg gaatacttcg agactatacg\n 2461 cattggatat aggagagatg aatggacgca tttgaaatcg aacatgttta atacctggct\n 2521 ggggacgcat tgtgggggtg taggggacgg gatgatattg tttgacccgg tgagattacc\n 2581 atccccgagc agcgtccttt atttgatctg ttcgcataac tcaactttag aaggaatgat\n 2641 gtatttacta catgatatat acgggaagat cgttgaagag aatactggta ctgttttcat\n 2701 aagggtacac gcgcgaggtt gtaagtgctc ggtgtgccga gggggtttac agggagttga\n 2761 cgtaaagaat aggtcagcta tgcgtgttcg tagtatgcca gggaacatcg gcttcgattc\n 2821 agtcaaccta attctttcaa catcaacgac gagcgcgttt gggaactctt acatttactt\n 2881 taagcttatt aatcgttagt gaggtgacac tcgctccgcg atcacgcaga tac\n//\n\nLOCUS JQ610677 2781 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 3, complete sequence.\nACCESSION JQ610677\nVERSION JQ610677.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 2781)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 2781)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..2781\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"3\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 18..2738\n /note=\"outer capsid and cell attachment protein\"\n /codon_start=1\n /product=\"VP3\"\n /protein_id=\"AFX73389.1\"\n /translation=\"MAHADAKGSDPEREALRKNPYLDGDVLGTAGGQVLSVFALTEIL\n QKVRQTQAELAAHAIDLDGPVPEITGVIKKIAELVDTVPYEVRDSPPISYKTLSMQSR\n DFVIQVDQYYEQISQIGGDVGEDEPMEFYKTMLEKVRYLRKSGAFILRGIKTRDYRGN\n EVAEPEALGVEFREVLSNFIAADRQVIQNALDAAIVENGQVGDRAVDVYMAAVSEPWY\n RIYNRLQAYIEVTQLRELRRAMEWLNALGRRKRVEYDDSFLTDFRARDTVWVQTQQLP\n VNARVIWEVPRSYIANLMMNIALCLPLGDFIAPNPRIGSITITQRITMTTPFGMMSGM\n TPTSMQMDDVKKIYLALLFPGQIVLNIKPDPAHSIDPVLRMVSGVLGHLMFTYGPRFT\n NITATTSQLLDSALSDYFLYMQNSRVPVVYGPTGLPLDFRIGGRQGYDCNNLRGDPQT\n GRGYNGWGVVDVDRRAPSPYDLVQRFIRYCNIDSREIIDPRTFGFNMNYPLYMEMIRA\n LVAGGKDQEAAYLRQMLPFHMIRFARINQIINEDLLSAFSLPDEDFDALFFNMLRGEY\n GKAEPIVLDISWASIWFAFNRYFDPVQRSDLLSVAPMIEAVYASEISILQLDMINLQQ\n LRARAPDMLINATPSQFWKAALASAAEPVVELMNLSQSFRFINVRDIIQWTRTREVQP\n SLALTLEREAWAVAADFEELMLVNHVYFHRSVVPEPQLDDIDEFRRQGFLYTNLLEAA\n PPRLLITNYDYNVALLQANLGQFKSALRRILDDGGWVMFGGMLRNVRLKIYDSKPGED\n VLSELPYLYSEKVENGLRFVSLKYARRATIYFLMYKVEYSNTPDALISVNPTYTMTKI\n YTNKRLVRKVRSPDVLNIVNKRVVAYKTKMRLIDITSALRLGVKLAAPTV\"\nORIGIN \n 1 gtatatattc cttcgcgatg gcgcatgcgg atgctaaagg aagtgatccg gagagagagg\n 61 cgttgaggaa gaacccttat ctagatggag acgtcttggg aaccgcaggc ggccaagttt\n 121 tgtcggtttt cgcattgacc gaaattttac aaaaagtaag acagacgcaa gctgaactgg\n 181 ccgcacacgc aatcgatttg gatggaccag tccctgagat caccggggtt attaagaaga\n 241 tagcggagtt agttgacacc gttccatatg aagtgcgcga ttcaccacct ataagctata\n 301 agactttaag catgcaatcg cgcgactttg tcatccaggt ggaccagtat tacgaacaga\n 361 tttcgcaaat tggaggagac gtcggggagg acgagccgat ggagttctat aaaacaatgc\n 421 tagaaaaggt acgctattta aggaagagtg gagcattcat tttgagaggt attaaaacac\n 481 gagactatag gggtaatgaa gtggcggaac cagaagcttt aggagtcgaa tttcgtgaag\n 541 tactttctaa ttttattgcg gcggatagac aagtgataca gaatgcgtta gatgcagcca\n 601 tagttgaaaa tggccaggtg ggtgataggg cggtcgatgt ttatatggct gctgtttctg\n 661 agccatggta tcgaatatat aataggttac aggcgtatat tgaagttacg caactgagag\n 721 aattgaggcg cgcaatggag tggctgaatg cacttggtcg tcgtaagaga gtggagtatg\n 781 atgattcatt cttgaccgat tttcgagcga gagatacggt atgggtgcag acgcaacagc\n 841 ttcccgttaa cgctcgtgtg atctgggagg ttccgaggtc atatatagct aatttgatga\n 901 tgaatatcgc gttatgtctg ccactaggtg atttcatagc cccaaacccg aggattgggt\n 961 cgataacgat aacccagcga ataactatga ctacgccttt tgggatgatg tctgggatga\n 1021 cccccacatc aatgcagatg gacgatgtca agaagatata tctcgcgttg ctctttcccg\n 1081 ggcagatcgt tttgaatatt aaacccgacc cagcgcactc catcgatccg gtactgcgta\n 1141 tggtttcggg tgtgttgggg catttgatgt tcacctacgg tcccagattt actaacataa\n 1201 cagctacaac atcgcagttg ctagatagtg ccttgagcga ctattttctg tacatgcaaa\n 1261 acagtagagt tccggtggtg tacggaccaa ctgggttacc tttggatttt agaatcggtg\n 1321 gacgacaagg ctatgattgc aataatctgc ggggagaccc gcagactggg agggggtaca\n 1381 atggatgggg agtcgttgac gtcgatcgaa gagcacccag tccgtacgat ttggttcaaa\n 1441 gatttatacg ttactgcaac atagactctc gcgagatcat cgacccacgg acgtttggat\n 1501 ttaatatgaa ctatccgcta tatatggaga tgatacgtgc attagttgcc ggaggaaaag\n 1561 atcaggaagc ggcgtaccta cgacaaatgt taccttttca catgatcaga ttcgcacgga\n 1621 tcaatcagat aataaacgaa gacttactta gcgcgttttc cttaccagat gaggatttcg\n 1681 acgcattatt tttcaatatg ctgcgcggcg agtatggaaa ggctgagccg atcgttttag\n 1741 atatcagttg ggcttcaatt tggtttgcgt tcaaccgcta ctttgaccca gtccaaaggt\n 1801 cagatctatt atcagtggca cccatgattg aggctgtcta tgcgtcagaa atctccattt\n 1861 tgcaattgga tatgatcaac ctgcagcagt tgagagcgag ggcacctgat atgttgatta\n 1921 acgcaactcc gagtcagttt tggaaagcgg cgttagcatc cgcagcagaa ccagtagttg\n 1981 agttgatgaa tctttcgcag agttttcgat tcattaacgt cagggatata atacagtgga\n 2041 ctagaacacg agaagtgcaa ccgtcgctgg ctctcacttt ggaacgagag gcgtgggcgg\n 2101 tcgcagctga cttcgaagag ttgatgctcg taaaccatgt ctattttcat agatcggtgg\n 2161 ttcccgaacc acagttggat gacatcgatg aatttcgtag gcaaggattc ctgtacacaa\n 2221 atctattgga agcggccccc ccgcgtttgt taatcaccaa ttatgattac aacgttgcgc\n 2281 tactgcaggc gaatcttgga caatttaaat ccgctttgag gagaattctg gatgacggtg\n 2341 gttgggtgat gttcggggga atgctgagaa atgttcgttt gaaaatatac gattcaaagc\n 2401 cgggagagga cgtcttaagc gaactaccct atctttactc cgagaaagtg gaaaacggtt\n 2461 taaggtttgt gtctttgaag tatgcgagac gagcaactat ttatttttta atgtataagg\n 2521 ttgaatattc aaacacacca gatgctttaa tatcagtcaa ccccacgtat accatgacga\n 2581 agatttatac aaacaagaga ctggtccgga aagtcaggtc acctgacgtt ttgaacatcg\n 2641 ttaataaaag agtagtggct tataaaacga agatgcggtt gattgacatt acatcggcac\n 2701 tgcgtcttgg tgttaaactt gcagcaccta cagtgtgaat tgaccactca acctgtggtg\n 2761 ctcggtgggg aattcgctta c\n//\n\nLOCUS JQ610678 1957 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 4, complete sequence.\nACCESSION JQ610678\nVERSION JQ610678.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1957)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1957)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1957\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"4\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 13..1926\n /note=\"capping enzyme\"\n /codon_start=1\n /product=\"VP4\"\n /protein_id=\"AFX73390.1\"\n /translation=\"MEPFAVLHLSAKLAPLVREGFIPYVDLDNIKTLNDLWIEIGKCS\n SDVYAVGRINRWTIRQLRAYRFIFVSEKRTITLKDIKITPDVPIRCADGLDLKLLETT\n IGRKRLVLRKTFGDILRKYALSQSVHLHGSEAETLNMADPTIHHVKGLPMIAPNHLNP\n TKPWSDLDDTETDEKLVSMLDYAMYSAQEVHYVGSGDGRTIRLFAKRDKKRFDRAKWV\n CYDPIMTDIGLTNVIAVKHYVNTFRDMLPYLNTGDRVERLLLWDVSGDAAKHDRFWEA\n QRTEEDRRGESVAVSLTEYFALAIIKHRIPIYEEKYRCTTSWIVPQPGAVREMYEMRN\n IILLNGFSRVNRAHIPQAGVMEIEADVLREMVRNFHGAGRGRLLKKSLYESLHIHQVD\n GLEDSEDGARSDLFYLTNQRNVNSIQSIRRVLGNSTVSTLWVSRERVFEYDDFNFDRS\n ALMLWHRGREHLLFDGNGAVLYLMWQHGDRYRKDVNYDPSWAEHFAVLIREPQPWRPV\n PDLSLCRFISLRRVSTVIRIRGDIHRKSDQVKRLGLDLSGHLFVTLISGAYLADLRWW\n FRMIIQWSKQRRQEKIDDLAKVNAEVVEWKEEKADEPWHRKEDLIAALIAAKSITGDQ\n HIDGWIAELRDME\"\nORIGIN \n 1 gtatatttcg aaatggagcc ctttgctgtg ctgcacctat cagccaagct ggcaccgctg\n 61 gtgcgtgagg gatttatccc gtatgtggac ttggataata ttaagacgtt gaatgacctc\n 121 tggattgaga ttggcaaatg ctcatctgat gtatatgcgg ttggacgaat aaataggtgg\n 181 acgatacgtc agctacgtgc gtatagattc atattcgtgt cggagaagag aacaataacg\n 241 ttgaaggata ttaagatcac acctgacgtg ccaataagat gcgcggatgg gctagactta\n 301 aagttacttg agactacaat aggacgtaaa agattagtgt tgcgaaagac gtttggagac\n 361 atactgcgaa aatatgcgtt aagccagtcg gtacacttgc atggatctga ggcagaaacc\n 421 ttgaatatgg cggaccctac catacatcac gtgaaggggt taccaatgat agcgccaaat\n 481 catttaaatc caacgaaacc atggagtgat ctggacgaca cagaaaccga tgaaaaacta\n 541 gtgtcaatgc tagattacgc gatgtatagc gcgcaagaag tgcattatgt tggctcggga\n 601 gacggtagaa cgatacggct gtttgcaaag agggacaaaa agagatttga tagagcgaag\n 661 tgggtgtgct atgaccctat tatgactgat attggattga caaatgtgat agctgttaaa\n 721 cactatgtca atactttcag ggatatgcta ccgtatttaa atactggcga ccgagttgag\n 781 agattactat tgtgggacgt aagtggagat gcggcgaaac atgatcggtt ttgggaagct\n 841 cagaggactg aggaggaccg gcggggagaa tcagttgccg tgtctttaac ggagtacttc\n 901 gccttggcta ttatcaaaca tagaattcca atctatgagg aaaagtatag atgcaccact\n 961 tcgtggattg taccgcagcc tggcgcggtc cgcgagatgt acgagatgag gaatatcata\n 1021 ctgttgaacg gtttttctag ggtaaatcga gcgcatatcc cccaggcagg cgtaatggag\n 1081 attgaggctg atgtgttacg tgagatggtg aggaacttcc atggagctgg tcgcggtcgg\n 1141 ctgctgaaga aatcgcttta tgagagtcta catatccatc aagttgatgg attggaggat\n 1201 tcggaagacg gagcgcggag cgatctcttt tatttaacca accaacgtaa tgttaattca\n 1261 atacaatcaa tcagacgagt tttgggaaat agcacggtgt cgactttatg ggtgtcaagg\n 1321 gaacgagttt tcgaatatga tgactttaat tttgaccgat cagcgttgat gctctggcac\n 1381 aggggtagag agcacttact atttgatggc aacggcgcgg ttctatattt gatgtggcag\n 1441 cacggagata gatatagaaa ggatgtgaac tatgatcctt cgtgggccga acattttgca\n 1501 gtattgatcc gagagccaca accttggcga ccagttccag atctgtccct ctgccgtttt\n 1561 atttcgctaa gacgggtgtc gacggttatt agaatacgag gcgatattca caggaaaagt\n 1621 gatcaggtaa agcgtttagg gttagatttg tcaggacatc tgttcgtaac gttaatttct\n 1681 ggagcgtatc ttgccgattt aagatggtgg ttccggatga tcatccaatg gtcaaagcag\n 1741 cgtagacagg aaaagataga cgatttggct aaggttaacg ctgaagtggt tgaatggaaa\n 1801 gaagagaaag ccgacgaacc gtggcatcgc aaggaggacc tgatcgctgc tttaatcgcg\n 1861 gcaaaaagta tcaccggtga tcagcatata gatgggtgga ttgcggagct gagggatatg\n 1921 gaatgacatc cacccgaggg gcaatcgaac tacctac\n//\n\nLOCUS JQ610679 1735 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 5, complete sequence.\nACCESSION JQ610679\nVERSION JQ610679.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1735)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1735)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1735\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"5\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 36..1676\n /note=\"non-structural protein 1\"\n /codon_start=1\n /product=\"NS1\"\n /protein_id=\"AFX73391.1\"\n /translation=\"MDQFLDSFDVTGDEANALRLLRAVSPEMTCSHLRRDCLIGGICA\n KQFFNEVLMAILDSKDRQAARQLVTLAVMTSYDRELIWLNVLRSTEVLPANDYAHEIQ\n NVVLNLKRVFIESGLEEKYKSFRAKRRPNRSPTEDAFSFLPFFYIPMNETKRVGIKKL\n TRVRNLGVAFVDRREVTHHLPFTVDAARRDLMMLRNFTLEHQRTCTFTGSKSLIHGMI\n FCPEEMEPLFQKKETALEIYRICEQDMKFINSRGTMSFPRFLMQRLAVKNASSDAMDQ\n VMLGRTPSDGRLMSVTGASFFFGGGPDWRKWAMPALLVRAARLRTVVTSFVKEWFDST\n HTCQVCFLVEKGVADSIPITDVRLSDVCGVGPVAYVRSYAHDDGNAPDVRVLRKGEIF\n RLMGGHYVMQTTASTMESLVVAAKEMQRLVRGDGFWDTPYWGLSMANLCKIMFHENPA\n KEQIHFMIKLITFGMFGGVQRHNGLFTDWDNLEEFLKRMFSTEEMGVRMYESSYHAIL\n RACILHLQTTAKPTLVQLTHAIESLDLGIEEVPFNFYV\"\nORIGIN \n 1 gtaaaaagaa tcctctgcgt tcactgggca cgaacatgga tcaattcttg gattcttttg\n 61 atgtgactgg agacgaggcg aatgccttga gattattgag agcggtttca cctgagatga\n 121 catgctcaca tttgaggaga gattgtttaa ttggagggat atgcgcaaaa cagtttttca\n 181 acgaggtgct gatggccatt ctggattcaa aagatcgtca ggcagcgcgt cagctggtga\n 241 cattagctgt gatgaccagt tacgaccgag agctaatctg gctcaacgta ctaaggtcaa\n 301 ctgaagtgct gccggcaaat gattatgcac atgaaataca gaatgtggtt ctgaacttga\n 361 agagggtctt catagagagt gggttggaag aaaaatacaa gagtttcagg gcgaagcggc\n 421 gtccaaacag atctccgacc gaggatgctt tctctttttt gccctttttc tacataccca\n 481 tgaatgaaac aaaacgggtt ggaataaaga aactcactag agttcggaac ctaggtgttg\n 541 cttttgttga tagacgcgaa gtgacgcatc atttaccgtt cacggtggac gctgctagaa\n 601 gggaccttat gatgctgaga aatttcacgc tggagcacca aagaacatgt acgtttacgg\n 661 gttcaaagag cttgatacat gggatgatat tctgtcctga ggagatggaa cctcttttcc\n 721 agaagaagga gacagcgcta gaaatctaca gaatttgtga gcaggatatg aagtttatca\n 781 actcaagagg tacgatgtca tttccccggt ttttgatgca acgtttagcg gtgaaaaacg\n 841 cttcatctga tgcgatggac caggttatgt tgggacgaac tccgagcgat ggacgtttga\n 901 tgtcggtgac tggtgcctct ttcttttttg gagggggacc tgattggcgc aagtgggcga\n 961 tgccggcgtt gttggtacgt gctgcaagac tgagaaccgt cgtgacatca ttcgttaagg\n 1021 agtggtttga ttcgactcac acatgtcaag tctgtttcct agttgaaaaa ggtgtcgccg\n 1081 attcaattcc gatcactgat gttcgtttat cggatgtgtg cggcgtagga ccagtcgcat\n 1141 atgttagatc ttatgcacat gatgacggga acgcgccgga tgttcgcgta ctgagaaaag\n 1201 gtgaaatctt cagattgatg ggcggacatt atgttatgca gacaacggcg agtacaatgg\n 1261 aatcattggt cgttgccgcg aaggagatgc agcgtttggt tcgcggcgat ggtttttggg\n 1321 acacaccgta ttggggttta agcatggcaa acctttgtaa aatcatgttt catgaaaacc\n 1381 cagcaaagga acagattcat ttcatgatta agctcataac ctttgggatg tttggtgggg\n 1441 ttcaaaggca caatggactg ttcacagact gggacaattt ggaggagttc ttgaagagga\n 1501 tgttttctac ggaggagatg ggcgttcgta tgtatgagtc aagttaccat gcgatacttc\n 1561 gtgcgtgcat actacatcta cagaccactg cgaagcctac cctcgttcaa ctaactcacg\n 1621 cgatcgaatc actcgacctt ggaatagaag aagttccttt caatttttat gtctaaaaca\n 1681 tcataataaa ccataaagag tctgagtaat tgtatccctg agctcttact cttac\n//\n\nLOCUS JQ610680 1605 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 6, complete sequence.\nACCESSION JQ610680\nVERSION JQ610680.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1605)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1605)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1605\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"6\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 22..1581\n /note=\"outer capsid protein\"\n /codon_start=1\n /product=\"VP5\"\n /protein_id=\"AFX73392.1\"\n /translation=\"MGKFVKALKKIGRGTVKALTSDAAKKLYTTLGKAATRFAESEVG\n SAAIDGLIQGTAQTLLHGGSASENIKQAVVLGVLHSMETPADPLSPGEQGVYDKIKEI\n KREEKEDRFFEVYQEKIDEELGSDMKRMREVAKGDKQAIKEMGGEIKVIEKAFDGLIK\n IDKIQDMKLTQLYGALAKERTERTQDEIKMVNDYTGKIEALQSAITVERDAMQEEALQ\n EIIEMGTDVIETASEEVPIFGPAAANVVATGRMVEGTLKLKQVIEKLAGLDVSHTTRD\n RIEPKVINAILDHEGGVVPEKELAIGVYNKLQTVREHMAEHSHLKEMAIPRLQKLYTE\n HGDEWHPKIITQMKVAREHQPQIHIYCAPWESDDVFMLRVYAPHHIGCGLFLGVDLES\n EFIFYEDLIAENHVLRGGVIEVVGRNFRQAVREFLLMAASKIENTMHVKRLVRSSASS\n PIYLSSIHYECTFDEIKQNVLQIVHDEQLQMHLLRGPKHFQRRALMAAVVKGVKILEG\n PDTKALMLQGL\"\nORIGIN \n 1 gtataaaata cctcggtcat catgggcaaa ttcgtaaagg ccctgaagaa aataggaagg\n 61 ggtacggtga aggcactgac gtctgacgct gcaaagaaac tttatacgac tttaggaaag\n 121 gcggcgacgc ggtttgctga aagcgaagtc ggcagcgcgg cgattgatgg attgatacaa\n 181 ggaacagcgc aaactttact gcacggaggc agcgcgagtg aaaatatcaa gcaagcggtt\n 241 gttttaggtg ttctccacag catggaaacg ccggcggacc ctttatcacc aggagagcaa\n 301 ggagtatatg ataagattaa ggaaattaaa cgagaagaaa aggaagatcg gtttttcgag\n 361 gtttaccaag aaaagattga cgaagagctt ggttcagata tgaagcgaat gcgagaagtg\n 421 gcaaaaggtg ataagcaggc catcaaggaa atgggtggtg aaattaaggt tatcgagaaa\n 481 gctttcgatg gattgattaa aatagataaa attcaagata tgaaattaac gcagttatat\n 541 ggcgcgctcg cgaaagagcg tacggagcgt acgcaggacg agatcaaaat ggttaacgac\n 601 tacactggaa aaattgaagc actgcaatcc gcgataacag ttgagcggga cgctatgcaa\n 661 gaggaggcgt tgcaggagat aatagaaatg ggaacggatg taattgaaac cgcctccgaa\n 721 gaggttccga tattcggccc tgcggctgcg aatgtagtcg caactggacg aatggttgag\n 781 ggcaccttaa agttgaagca agtaatcgag aaattagcag ggttagatgt ttcgcacacc\n 841 acaagggaca gaatcgagcc gaaagttata aacgctatac tagatcacga ggggggcgtc\n 901 gtaccggaaa aggaactagc gattggtgta tataataagc tgcagacagt cagagaacat\n 961 atggcggaac acagccatct aaaggaaatg gcaataccaa ggctgcaaaa gctgtacaca\n 1021 gaacacggcg atgagtggca tccaaagata attactcaaa tgaaggtagc gagagaacat\n 1081 cagccgcaaa tacatatata ttgcgctcca tgggaatcgg atgacgtgtt tatgttgcga\n 1141 gtgtacgcgc cgcatcatat agggtgtggt cttttcttag gagttgattt agagagtgaa\n 1201 ttcatatttt atgaggattt gatagcagag aaccacgtat tgcgtggtgg cgtcattgaa\n 1261 gtcgttggaa ggaacttcag gcaagcagtg cgcgaatttc ttttgatggc tgcgagcaag\n 1321 attgagaaca ctatgcatgt caagcggtta gtgagaagct cggcttcctc acctatctac\n 1381 ttgtcaagca tacactatga gtgtacattt gatgagataa aacagaacgt tttacagatc\n 1441 gtgcacgacg agcagttaca gatgcatctg ttacgtggtc cgaaacattt ccaaagacgt\n 1501 gctctgatgg cggctgttgt taagggtgtt aagatcttag aggggccaga tacgaaggcg\n 1561 ctcatgctac agggtttgta agtggctgaa aggtatcaag aatac\n//\n\nLOCUS JQ610681 1166 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 7, complete sequence.\nACCESSION JQ610681\nVERSION JQ610681.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1166)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1166)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1166\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"7\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 17..1069\n /note=\"T13 protein\"\n /codon_start=1\n /product=\"VP7\"\n /protein_id=\"AFX73393.1\"\n /translation=\"MDAIAARALSVIQDCISVGDGRINLDPGVMERLGIAINRYNGLT\n NNVVTIRPGTQDERNAMFFMCLDFALAALNIQIGVISREYTQALATIGVLATGEIPYS\n VAAMDTIVRISGTMATWGPTEYELPPYARSQMIQMSGRYYVPAGANSHAAHVDPTTVE\n ISLAAGVVVNVTNALQPRGVAPTMMYMVWHPLAIFANPQGATAASPQNMTLVVGGLNI\n AAGTIIAWDTVAPIQLSNQGGQEGMIAIRILWMTTLDKSMTSLPEMREIISRCYSFMH\n PSWHALRGTVLHSLNLPTNNPPMFAPATRQEALAYLILANLADAYTSLRPDFTIQGML\n AVPQVIDRQFVQGAYR\"\nORIGIN \n 1 gtataaatat ctagagatgg acgccattgc ggcacgtgct ctgtccgtga tccaggactg\n 61 cattagcgtt ggtgatggga gaattaattt agaccctggg gtcatggaga gattgggaat\n 121 tgctattaat agatacaatg ggctaacgaa caatgtggtg acgatcagac cagggacaca\n 181 agatgagcgg aacgcgatgt tttttatgtg tctggatttc gcgttggcgg cattgaacat\n 241 acaaattggg gttatatcta gggaatacac gcaggcgctg gccactatcg gtgtgctggc\n 301 aacgggagaa atcccttact cggttgccgc tatggatacg attgtacgga ttagcggaac\n 361 gatggcgaca tggggtccca ccgaatatga gttaccgcca tatgcgcggt ctcagatgat\n 421 acaaatgagc ggacgttact acgttccagc gggggcgaat tcacatgctg cccatgtcga\n 481 tcccacgacg gtagagattt ctttagctgc tggagtagta gtgaatgtta cgaacgcgtt\n 541 acagcctagg ggcgttgcgc ccacaatgat gtacatggta tggcatccgt tggcgatttt\n 601 cgcgaatcct cagggtgcta cagctgcttc gcctcaaaat atgactttgg tggttggtgg\n 661 gctgaatata gcagctggca cgatcatcgc ttgggatacc gtcgctccta tacagctatc\n 721 gaatcaggga ggacaagagg gaatgatcgc gatccggata ctatggatga caacattaga\n 781 taaatctatg acaagcttgc cggagatgcg tgaaataatc tcaagatgct atagctttat\n 841 gcacccttca tggcacgcgc tgcgagggac ggtcctacat tcgcttaatc tgccgactaa\n 901 taatccacct atgtttgcgc ctgctacgcg acaggaggca ttggcgtact taattctggc\n 961 aaatttagcg gatgcatata cgtcgttaag gcctgatttc accatacaag gaatgctcgc\n 1021 ggttccacag gtcattgaca ggcagttcgt tcagggtgcg tacaggtaga ggacgccttc\n 1081 cacagtgggc gtctcatgta gccccagcgt cggtccctta cgtgtgctgt aacgcgtagg\n 1141 tagaacgtca tatgatatta agttac\n//\n\nLOCUS JQ610682 1089 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 8, complete sequence.\nACCESSION JQ610682\nVERSION JQ610682.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 1089)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 1089)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..1089\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"8\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 26..1057\n /note=\"non-structural protein 2\"\n /codon_start=1\n /product=\"NS2\"\n /protein_id=\"AFX73394.1\"\n /translation=\"MAQEVKRKFTRTVCIYDPQNRTFCGRSAAMVCNSYYTIKMGRTT\n QCGVSPVPVPKSYVLEIPDVGSYRILDGQDSISVIVTETGVEATSERWEEWKFEGVNC\n VPMVVQTEIGKGLIDMEIKFSKGMGLVKPYVKNEVSRTEIPRLPGASVIDTPIRDYRQ\n LLKDQRDERRAALDAIACDICPTLSRMLGANITDGSPQVEEVATRPTQPPAQLKLDVP\n NWDQPTDSDDEDEESKRVTTQSNADTEEQVTFEDCITDQYFSKTGEFAKKYPEMLAGL\n SAKMPSETGRFTKILTTRKAQWNNVPLFELDPNGFTYHFSKLGNSTRIFCVQRDLSYM\n VLPAGQGLK\"\nORIGIN \n 1 gtaaaaaatc tcctctcttt tcacgatggc tcaagaagtt aagagaaagt tcactagaac\n 61 agtgtgcatc tatgatccac aaaatcgcac attctgtggt cgaagtgccg cgatggtgtg\n 121 taacagttat tatacaatta aaatgggtag aacgacgcag tgtggagtgt cgccggtgcc\n 181 cgtaccaaag tcatatgtgc tagagatacc ggatgttggc tcttatcgca tcttagatgg\n 241 gcaggattca atcagtgtca tcgttactga gacgggcgtc gaggcaacgt ctgagaggtg\n 301 ggaagagtgg aaattcgaag gcgttaattg cgttccgatg gttgttcaaa cggagattgg\n 361 gaaaggcctg attgacatgg agatcaagtt tagtaaggga atggggctcg ttaaacctta\n 421 tgtaaagaat gaggttagca gaactgagat cccacggcta ccgggtgctt cagtcattga\n 481 tacaccgata cgcgattacc gtcaactttt gaaggatcag agagatgaaa gaagggcggc\n 541 gctcgatgcg atcgcatgcg acatatgtcc cactctatca agaatgctag gggcgaatat\n 601 tacagacgga tcgccacaag tcgaagaagt cgcaacacgg ccaacacaac ctccagctca\n 661 gctgaagctg gatgtgccta actgggacca accgactgat tcagatgatg aggatgagga\n 721 atccaagcgc gtgacaacgc aaagtaatgc tgatactgag gaacaagtga ctttcgaaga\n 781 ttgcattacc gatcaatact tttcgaaaac gggtgaattc gcgaagaagt atcctgaaat\n 841 gttagcggga ctttccgcga agatgccgag tgaaacaggt aggtttacaa aaatattgac\n 901 gacgaggaag gctcaatgga ataacgttcc tcttttcgaa ttagatccaa acgggtttac\n 961 atatcatttt agtaagctgg gtaattcgac gaggatcttc tgtgtccaac gtgatttgag\n 1021 ctacatggtt ttacccgcag ggcaaggcct gaagtagcgg tgcatgtagc cgggagaggt\n 1081 acaacttac\n//\n\nLOCUS JQ610683 925 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 9, complete sequence.\nACCESSION JQ610683\nVERSION JQ610683.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 925)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 925)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..925\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"9\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 23..883\n /note=\"helicase\"\n /codon_start=1\n /product=\"VP6\"\n /protein_id=\"AFX73395.1\"\n /translation=\"MLVLAPGDLIDGVRHQLSERGVRIRLRETNDDEQKDEPVDTGGG\n KPGDRIGKEVGNAESEQSSDKEKKAGGSSDSELGEGGDGRRQTEKAEGGENGTRDIGI\n QDKDKQFDRRANPDNALDRENRSGDPQLKYGFATKRIANAVESKYHCGGFEGPGSDGY\n IKLEMSIMKALGLNRDDHIEQLEFLKHQQKGPSKIQVRTIASETKLKEVCNIMDKPVA\n PTARSAVSVVSNRVEDVKEAQVYFTTPTGDRGWKEVARKASQTPNIRAYINPEGDDPK\n VSFLHLIDHL\"\n CDS 111..512\n /note=\"non-structural protein 4\"\n /codon_start=1\n /product=\"NS4\"\n /protein_id=\"AFX73396.1\"\n /translation=\"MMTSKRMNQWIREAASRVIESGRKLEMPRVNSLPIKRRRLEEVR\n IQSSGKVEMEGDKLRRLKAERMELEILAFRIKTNNLIGALIQITRWTEKIDQEIRNLN\n MDLQPNELQTPLSQSTTAVDLRGQDRMDTSN\"\nORIGIN \n 1 gtataaaaca tcctcccatg tcatgttggt gttggcaccg ggtgatctca tagacggagt\n 61 gcgtcatcaa ttatctgaaa gaggagtcag gattcgttta cgggaaacga atgatgacga\n 121 gcaaaaggat gaaccagtgg atacgggagg cggcaagccg ggtgatcgaa tcgggaagga\n 181 agttggaaat gccgagagtg aacagtcttc cgataaagag aagaaggctg gaggaagttc\n 241 ggattcagag ctcggggaag gtggagatgg aaggcgacaa actgagaagg ctgaaggcgg\n 301 agagaatgga actagagata ttggcattca ggataaagac aaacaatttg atcggcgcgc\n 361 taatccagat aacgcgttgg acagagaaaa tcgatcagga gatccgcaac ttaaatatgg\n 421 atttgcaacc aaacgaattg caaacgccgt tgagtcaaag taccactgcg gtggatttga\n 481 ggggccagga tcggatggat acatcaaact agaaatgtca ataatgaagg cgctaggttt\n 541 aaaccgagat gaccacatcg aacaattgga gttcctcaag caccaacaga aagggcccag\n 601 caaaattcaa gtcagaacga tcgcttccga aaccaaatta aaagaggtgt gtaatataat\n 661 ggacaagccg gtggctccca cagcgagaag tgcggtgagt gtagttagta accgtgttga\n 721 agacgtgaag gaagcccagg tgtattttac aactccaaca ggagatagag gctggaaaga\n 781 agtagcaagg aaagcgagcc agacaccaaa cattcgagcg tacattaatc cggagggaga\n 841 tgatcctaaa gtctcatttc tgcatttaat cgatcatctg tgaggtcacg gtctgaacta\n 901 cgggcatgct gggtgtttca gttac\n//\n\nLOCUS JQ610684 761 bp RNA linear VRL 31-JAN-2014\nDEFINITION Orungo virus isolate UGMP 359 segment 10, complete sequence.\nACCESSION JQ610684\nVERSION JQ610684.1\nKEYWORDS .\nSOURCE Orungo virus (ORUV)\n ORGANISM Orungo virus\n Viruses; dsRNA viruses; Reoviridae; Sedoreovirinae; Orbivirus.\nREFERENCE 1 (bases 1 to 761)\n AUTHORS Mohd Jaafar,F., Belhouchet,M., Belaganahalli,M., Tesh,R.B.,\n Mertens,P.P. and Attoui,H.\n TITLE Full-genome characterisation of orungo, lebombo and changuinola\n viruses provides evidence for co-evolution of orbiviruses with\n their arthropod vectors\n JOURNAL PLoS ONE 9 (1), E86392 (2014)\n PUBMED 24475112\n REMARK Publication Status: Online-Only\nREFERENCE 2 (bases 1 to 761)\n AUTHORS Attoui,H., Mohd Jaafar,F., Mertens,P.P.C. and Belhouchet,M.\n TITLE Direct Submission\n JOURNAL Submitted (01-FEB-2012) Vector-Borne Diseases, Institute for Animal\n Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United\n Kingdom\nCOMMENT GenBank Accession Numbers JQ610675-JQ610684 represent sequences\n from the 10 segments of Orungo virus.\n \n ##Assembly-Data-START##\n Assembly Method :: manually v. manually\n Sequencing Technology :: Sanger dideoxy sequencing\n ##Assembly-Data-END##\nFEATURES Location/Qualifiers\n source 1..761\n /organism=\"Orungo virus\"\n /mol_type=\"genomic RNA\"\n /isolate=\"UGMP 359\"\n /isolation_source=\"Anopheles funestus\"\n /host=\"Homo sapiens\"\n /db_xref=\"taxon:40058\"\n /segment=\"10\"\n /country=\"Uganda\"\n /collection_date=\"Sep-1959\"\n /note=\"acronym: ORUV\"\n CDS 20..703\n /note=\"non-structural protein 3\"\n /codon_start=1\n /product=\"NS3\"\n /protein_id=\"AFX73397.1\"\n /translation=\"MYRDLLNIHTEMRGPPSYEPSGLAQATAPTMRFGDREDEEGLLR\n ARELSLNVLTNAMTNTTGANEAIKNEKAMFGAYADALRDTPEIRVVKRRINERTLEKL\n HKMRRSLHGRRMFVRMLLAINVGLALLTSAVNVVRQSLDDFGKERWIVGGVWWLGEVV\n VTINFGTTVATLVLMRIHGALNAQLQTIKRDIYKKSSYNEAAAMHWKGEISLIEELAA\n SHVPAGSNV\"\nORIGIN \n 1 gtataaaatt ccgttcgcaa tgtaccgtga cttgctgaat attcacactg aaatgagggg\n 61 cccgccatct tatgaaccta gtggcttagc tcaagcgaca gcaccgacta tgaggtttgg\n 121 ggatagagaa gatgaggaag gcctattgag ggcgcgcgag ctttcgctta atgtgttaac\n 181 gaatgctatg actaatacaa cgggtgcgaa tgaggcgatt aagaatgaga aagcgatgtt\n 241 tggggcatat gccgatgcac ttagggatac tccggagatt agggtggtga aaaggcggat\n 301 aaatgaacgt acgttagaaa agttgcataa aatgcgacgt tcgctgcacg gaagacgaat\n 361 gttcgtacga atgttgttgg cgataaatgt gggattggcg ctattaacct cggcagtgaa\n 421 tgtggtacgc cagtcgctag atgattttgg gaaagaaagg tggatagttg gtggagtgtg\n 481 gtggttaggt gaggtcgtcg ttacgattaa ttttggaacg actgttgcta cgttggtatt\n 541 aatgaggata catggcgcat taaacgcgca gcttcaaacc attaagcgtg acatatataa\n 601 gaaaagctcg tataatgagg ccgctgccat gcattggaaa ggtgaaatta gcttaattga\n 661 ggagctagcg gcgagccacg tacctgcggg atcgaatgtc tagtccgcga catcgaaaaa\n 721 ttcacttgtc caggtgaagc ccgtagaacg gatcgtctta c\n//\n\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/ambiguous/barcodes.txt", "content": "Barcode1\tLikely_Index_Names1\tBarcode2\tLikely_Index_Names2\tCount\r\nCTCTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t40324834\r\nGGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t12067922\r\nCTCTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t9352602\r\nTAAGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t9213648\r\nGGACTCCT\tN705\tAAGGCTAT\tS520\t6391634\r\nTCCTGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t4891900\r\nCTCTCTAC\tN707\tTCGACTAG\tS513\t4242203\r\nTAAGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t4160867\r\nCTCTCTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t1831895\r\nGGACTCCT\tN705\tGAGCCTTA\tS521\t1418032\r\nCGTACTAG\tN702\tAAGGCTAT\tS520\t1021205\r\nCGTACTAG\tN702\tGAGCCTTA\tS521\t652596\r\nTAGGCATG\tN706\tTAGATCGC\t[N|S|E]501\t455611\r\nTAGGCATG\tN706\tGAGCCTTA\tS521\t418837\r\nTCCTGAGC\tN704\tTCGTAAGA\tE517,S517,[N|S|E]517\t175892\r\nCTCTCTAC\tN707\tAGGAGTAT\tUnknown\t145075\r\nCAGAGAGG\tN708\tGCGTAAGA\tE517,S517,[N|S|E]517\t118186\r\nCTCTCTAC\tN707\tAAGAGTAT\tUnknown\t79895\r\nTCTCTACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t74461\r\nCTCTCTAC\tN707\tTCGTAAGA\tE517,S517,[N|S|E]517\t71672\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tAAGGAGTA\tS507,[N|S|E]507\t71100\r\nCTCTCACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t66418\r\nCGTACTAG\tN702\tTCGACTAG\tS513\t61974\r\nCTCCTACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t60633\r\nGGACTCCT\tN705\tTAGCCTTA\tS521\t56252\r\nCTCTCTAC\tN707\tAAGGAGTT\tS507,[N|S|E]507\t56036\r\nCTCTTACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t48032\r\nCTCTCTCA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t46157\r\nCTCTCTAC\tN707\tAATGAGTA\tS507,[N|S|E]507\t45196\r\nCTCTCTAT\tE502,S502,[N|S|E]502\tAAGGAGTA\tS507,[N|S|E]507\t41520\r\nCTTCTACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t38556\r\nCTCTCTAC\tN707\tAAGGATAT\tS520\t38371\r\nGGGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t37779\r\nCTCTCTAC\tN707\tAAGGGTAT\tS520\t37348\r\nCTCTCTAC\tN707\tAAGTAGTA\tS507,[N|S|E]507\t33737\r\nCTCGCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t31828\r\nCTCTCTAC\tN707\tAAGGCGTA\tS507,[N|S|E]507\t29290\r\nTAAGGCGA\tN701\tTCTCTATT\tUnknown\t27529\r\nCCTCTACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t27185\r\nCGTACTAG\tN702\tTAGCCTTA\tS521\t27026\r\nCTCTCTAC\tN707\tACGGAGTA\tS507,[N|S|E]507\t26688\r\nCTCTCTAC\tN707\tATGGAGTA\tS507,[N|S|E]507\t25576\r\nCTCTCTAC\tN707\tTCTCTATT\tUnknown\t24747\r\nCTCTCTAC\tN707\tGGAGTATC\tUnknown\t24158\r\nGGACTCCT\tN705\tAGGCTATT\tD501\t23435\r\nCTCTCTAC\tN707\tGAGGAGTA\tS507,[N|S|E]507\t23353\r\nCTCTCTAC\tN707\tAAGGAGAA\tS507,[N|S|E]507\t22625\r\nGGACTCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t21208\r\nGACTCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t19930\r\nCTCCCTAC\tE505,N707,S505,[N|S|E]505\tAAGGAGTA\tS507,[N|S|E]507\t19487\r\nGGACTCCT\tN705\tATCCTCTT\tUnknown\t18705\r\nCTCTCTAC\tN707\tAAGGAGTC\tS507,[N|S|E]507\t18162\r\nTCTCTACA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t18065\r\nGGACTCCT\tN705\tTATCTCTT\tUnknown\t17988\r\nCTCTCTAC\tN707\tAAGGAGCA\tS507,[N|S|E]507\t17930\r\nCTCTCTAC\tN707\tAAAGAGTA\tS507,[N|S|E]507\t17907\r\nCTCTCTAC\tN707\tTAGGAGTA\tS507,[N|S|E]507\t17665\r\nTAGGCATG\tN706\tTAGCCTTA\tS521\t16651\r\nCTCTCACA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t16525\r\nCTCTCTAC\tN707\tAAGGATTA\tS507,[N|S|E]507\t16149\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tCTCTCTAT\tE502,S502,[N|S|E]502\t15992\r\nGGACTCCT\tN705\tGATCCTCT\tE503,S503,[N|S|E]503\t14680\r\nCTCTCTAC\tN707\tAAGGAGTG\tS507,[N|S|E]507\t14393\r\nCTCCTACA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t14390\r\nGGGCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t14330\r\nCTCTCTAC\tN707\tAAGGTGTA\tS507,[N|S|E]507\t14229\r\nCTCTACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t13739\r\nCTCTCTTC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t13735\r\nCTCTCTAC\tN707\tTCGACTAT\tS513\t13710\r\nGGACTCCT\tN705\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t13370\r\nGGACTCCT\tN705\tTAGCCTCT\tE503,S503,[N|S|E]503\t13355\r\nGGACTCCT\tN705\tTATCCTTT\tE503,S503,[N|S|E]503\t13243\r\nTAAGGCGA\tN701\tCTCTCTTT\tE502,S502,[N|S|E]502\t13112\r\nCTCTCTAC\tN707\tAGGGAGTA\tS507,[N|S|E]507\t13046\r\nGGACTCCT\tN705\tTATCATCT\tE503,S503,[N|S|E]503\t12648\r\nCTCTCTAC\tN707\tAAGCAGTA\tS507,[N|S|E]507\t12637\r\nCTCTCTAC\tN707\tCAGGAGTA\tS507,[N|S|E]507\t12237\r\nCTCTCTAC\tN707\tCTATCTAT\tE502,S502,[N|S|E]502\t12226\r\nCTCTCTGC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t12207\r\nCTCTCTAC\tN707\tCTCTCTTT\tE502,S502,[N|S|E]502\t12085\r\nTAAGGCGA\tN701\tCTATCTAT\tE502,S502,[N|S|E]502\t11989\r\nCTCTCTAC\tN707\tAAGGGGTA\tS507,[N|S|E]507\t11970\r\nCTCACTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t11821\r\nCTCTCTCA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t11693\r\nTTCTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t11666\r\nCCTCTCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t11534\r\nTCCTGAGC\tN704\tACGTAAGA\tE517,S517,[N|S|E]517\t11394\r\nTAAGGCGA\tN701\tAGGAGTAT\tUnknown\t11322\r\nTAGGCGAA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t11123\r\nCTCTTACA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t11028\r\nCTCTCTAC\tN707\tAACGAGTA\tS507,[N|S|E]507\t10914\r\nTAAGGCGA\tN701\tCTCTTATT\tUnknown\t10736\r\nGGACTCTA\tUnknown\tAAGGCTAT\tS520\t10618\r\nGGACTCAT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t10411\r\nTAAGCGAA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t10332\r\nCTCTCTAC\tN707\tAAGAAGTA\tS507,[N|S|E]507\t10232\r\nGACTCCTA\tUnknown\tAAGGCTAT\tS520\t10048\r\nGGCTCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t9937\r\nGGACTCCT\tN705\tTTCCTCTT\tUnknown\t9867\r\nCTCTCCAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t9819\r\nGGACCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t9587\r\nCTCTCTAC\tN707\tCTCTTATT\tUnknown\t9492\r\nTCCTGAGC\tN704\tGCGTACGA\tE517,S517,[N|S|E]517\t9445\r\nTCTCTACA\tUnknown\tTCGACTAG\tS513\t9358\r\nCTCTCTAC\tN707\tAAGGACTA\tS507,[N|S|E]507\t9350\r\nGGATCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t9282\r\nTCCTGAGC\tN704\tGCGTAAGT\tE517,S517,[N|S|E]517\t9139\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tTCGACTAG\tS513\t8975\r\nTCCTGAGC\tN704\tGGTAAGAT\tUnknown\t8968\r\nTAAGGCGA\tN701\tCTTCTATT\tUnknown\t8774\r\nGGACTCCT\tN705\tTACCTCTT\tUnknown\t8701\r\nGGACTCCT\tN705\tAATGCTAT\tS520\t8635\r\nGGAGTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t8631\r\nCTCTCTAC\tN707\tCCCTCTAT\tD502,E502,S502,[N|S|E]502\t8628\r\nCTCTCTAT\tE502,S502,[N|S|E]502\tCTCTCTAT\tE502,S502,[N|S|E]502\t8559\r\nTAAGGCGA\tN701\tCTCTCATT\tD703\t8510\r\nCTCTCACA\tUnknown\tTCGACTAG\tS513\t8391\r\nGGACTCCT\tN705\tTATCCTAT\tE503,S503,[N|S|E]503\t8333\r\nGGACTCCT\tN705\tTATCCCTT\tUnknown\t8264\r\nAAGGCGAA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t8114\r\nCTTCTACA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t8053\r\nGGATTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t7982\r\nATCTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t7964\r\nTCCTGAGC\tN704\tGCATAAGA\tE517,S517,[N|S|E]517\t7945\r\nCCCTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t7945\r\nCTCTCTAC\tN707\tAAAGGAGT\tUnknown\t7821\r\nCTCTCTAC\tN707\tAAGGAATA\tS507,[N|S|E]507\t7779\r\nGGACTCCC\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t7719\r\nCTCTCTAC\tN707\tCGACTAGT\tUnknown\t7704\r\nTCTGAGCA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t7665\r\nTAAGGCGA\tN701\tCCTCTATT\tUnknown\t7645\r\nCTCCTACA\tUnknown\tTCGACTAG\tS513\t7612\r\nCTCTCTAC\tN707\tCTTCTATT\tUnknown\t7540\r\nCTCTCTAC\tN707\tAAGGAGGA\tS507,[N|S|E]507\t7391\r\nCTCTCTAC\tN707\tTGACTAGT\tUnknown\t7378\r\nTCCTGAGC\tN704\tGCTAAGAT\tUnknown\t7331\r\nCTCGCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t7323\r\nGGACTCCT\tN705\tAAGCTATT\tUnknown\t7288\r\nTCCTGAGC\tN704\tCGTAAGAT\tUnknown\t7249\r\nCTATCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t7247\r\nGGGCTCCT\tN705\tAAGGCTAT\tS520\t7231\r\nCTCTCTAC\tN707\tCTCTATTC\tUnknown\t7200\r\nTAAGGCGA\tN701\tCTCCTATT\tUnknown\t7191\r\nCTCTCTAC\tN707\tCTCCTATT\tUnknown\t7109\r\nTCCTGAGC\tN704\tCCGTAAGA\tE517,S517,[N|S|E]517\t7032\r\nGGACTCCT\tN705\tAATCCTCT\tE503,S503,[N|S|E]503\t7013\r\nCTCTCTAC\tN707\tAAGGTATC\tUnknown\t6989\r\nTCCTGAGC\tN704\tGCGTAAAT\tUnknown\t6962\r\nTCCTGAGC\tN704\tGCGTAGAT\tUnknown\t6932\r\nTAAGGCGA\tN701\tCTCTATTC\tUnknown\t6905\r\nCTCTCTAC\tN707\tAAGGGAGT\tUnknown\t6885\r\nCTCTCTAC\tN707\tATCTCTAT\tE502,S502,[N|S|E]502\t6875\r\nCTCTCTAC\tN707\tAAGGAGAT\tUnknown\t6826\r\nCTCTTACA\tUnknown\tTCGACTAG\tS513\t6699\r\nCTCTATAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t6682\r\nGGACTCCT\tN705\tTATCCTCC\tE503,S503,[N|S|E]503\t6682\r\nTAAGGCAA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t6590\r\nCTCTCTAC\tN707\tCCTCTATT\tUnknown\t6533\r\nTAATGCGA\tD708,N701,S522\tCTCTCTAT\tE502,S502,[N|S|E]502\t6491\r\nGGACTCCT\tN705\tAAGGCTTT\tS520\t6466\r\nCTCTCTAC\tN707\tCTCTCATT\tD703\t6451\r\nCTCTCTAC\tN707\tCTCTATAT\tE502,S502,[N|S|E]502\t6442\r\nTAAGGCGA\tN701\tATCTCTAT\tE502,S502,[N|S|E]502\t6427\r\nCACTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t6395\r\nCTCTCTAC\tN707\tCACTCTAT\tE502,S502,[N|S|E]502\t6380\r\nTAAGGCGA\tN701\tCTCTATAT\tE502,S502,[N|S|E]502\t6258\r\nGGACTCCT\tN705\tAAGTCTAT\tS520\t6243\r\nCCTCTACA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t6111\r\nCTCTTTAC\tE505,N707,S505,[N|S|E]505\tAAGGAGTA\tS507,[N|S|E]507\t6040\r\nTAAGGCGA\tN701\tCACTCTAT\tE502,S502,[N|S|E]502\t5961\r\nGGACTCCT\tN705\tTATCCTGT\tE503,S503,[N|S|E]503\t5957\r\nGGATCCTA\tUnknown\tAAGGCTAT\tS520\t5949\r\nCTCTCTCA\tUnknown\tTCGACTAG\tS513\t5756\r\nCTTTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t5708\r\nGGACTCCT\tN705\tAAGGTATT\tUnknown\t5669\r\nCTCTCTAC\tN707\tTCAACTAG\tS513\t5607\r\nCTCTCTCC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t5598\r\nTCCTGAGA\tD702,N704\tGCGTAAGA\tE517,S517,[N|S|E]517\t5572\r\nTAAGGCGA\tN701\tCTCTCTGT\tE502,S502,[N|S|E]502\t5528\r\nTAAGGCGA\tN701\tCCCTCTAT\tD502,E502,S502,[N|S|E]502\t5509\r\nTAGGCGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t5496\r\nCTCTCTAC\tN707\tGTCTCTAT\tD502,E502,S502,[N|S|E]502\t5448\r\nTAAGGCGA\tN701\tGTCTCTAT\tD502,E502,S502,[N|S|E]502\t5431\r\nGGACTCAT\tN705\tAAGGCTAT\tS520\t5365\r\nGGACTCCA\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t5354\r\nCTCTCTAC\tN707\tCTCTCTGT\tE502,S502,[N|S|E]502\t5343\r\nGGACTCCT\tN705\tCATCCTCT\tE503,S503,[N|S|E]503\t5276\r\nCTCTCTAC\tN707\tTCTACTAG\tS513\t5241\r\nTAAGGCGA\tN701\tCTCTCTAC\tN707\t5233\r\nGGACTCCT\tN705\tTTTCCTCT\tE503,S503,[N|S|E]503\t5212\r\nCTCTCTAC\tN707\tCAAGGAGT\tUnknown\t5153\r\nTCCTGAGC\tN704\tGTAAGATC\tUnknown\t5146\r\nGGGGGGGG\tUnknown\tGGGGGCGG\tUnknown\t5132\r\nCTCTCTAC\tN707\tAAGGCGTT\tUnknown\t5073\r\nCTCTCTAC\tN707\tAAGTATCG\tUnknown\t5052\r\nGGACTCCT\tN705\tTCCTCTTC\tUnknown\t5043\r\nCTCTCTAC\tN707\tCTCTCTAC\tN707\t5041\r\nCTCCCTAC\tE505,N707,S505,[N|S|E]505\tCTCTCTAT\tE502,S502,[N|S|E]502\t5038\r\nCTCTCTAC\tN707\tTCGACTGT\tUnknown\t4961\r\nTGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t4959\r\nGGACTCCT\tN705\tTATCCTTC\tUnknown\t4952\r\nCTCTCTAC\tN707\tGCGACTAG\tS513\t4938\r\nTAAGGCGA\tN701\tAAGGAGTT\tS507,[N|S|E]507\t4936\r\nCTTCTACA\tUnknown\tTCGACTAG\tS513\t4916\r\nGGACTCCT\tN705\tACGGCTAT\tS520\t4889\r\nTCCTGAGC\tN704\tGCGAAGAT\tUnknown\t4876\r\nTCCGAGCA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t4874\r\nCTCTCTAC\tN707\tTTCTCTAT\tE502,S502,[N|S|E]502\t4857\r\nTAAGGCGA\tN701\tAAGAGTAT\tUnknown\t4830\r\nCTCTCTAC\tN707\tCTGTCTAT\tE502,S502,[N|S|E]502\t4827\r\nGGGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t4812\r\nGGACCCTA\tUnknown\tAAGGCTAT\tS520\t4777\r\nCTCTCTAC\tN707\tACGTAAGA\tE517,S517,[N|S|E]517\t4763\r\nGGACTCCC\tN705\tAAGGCTAT\tS520\t4686\r\nCTCTCTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4684\r\nGGACTCCT\tN705\tTATCGTCT\tE503,S503,[N|S|E]503\t4653\r\nGGACTCCT\tN705\tAAGGATAT\tS520\t4578\r\nGGAGTCCT\tN705\tAAGGCTAT\tS520\t4553\r\nTCCTAGCA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t4550\r\nTAAGGCGA\tN701\tCTGTCTAT\tE502,S502,[N|S|E]502\t4549\r\nTAAGGCGA\tN701\tTTCTCTAT\tE502,S502,[N|S|E]502\t4547\r\nTCCGGAGC\tD702,N704\tGCGTAAGA\tE517,S517,[N|S|E]517\t4533\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tGCGTAAGA\tE517,S517,[N|S|E]517\t4479\r\nCGTACTAG\tN702\tAGGCTATT\tD501\t4459\r\nGGACTCCT\tN705\tAAGACTAT\tS520\t4432\r\nTAAGGGAA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t4425\r\nTAACGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t4413\r\nGGCTCCTA\tUnknown\tAAGGCTAT\tS520\t4393\r\nCTCTCTAT\tE502,S502,[N|S|E]502\tTCGACTAG\tS513\t4386\r\nGGCCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t4380\r\nCTTCTCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4366\r\nTCCTGGCA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t4357\r\nGGACTCCT\tN705\tTAACCTCT\tE503,S503,[N|S|E]503\t4341\r\nTCCTGAGC\tN704\tGCTTAAGA\tE517,S517,[N|S|E]517\t4323\r\nGGACTCCT\tN705\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t4322\r\nCTCTCTAC\tN707\tAGAGTATC\tUnknown\t4319\r\nTCTCTACA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t4309\r\nTAAGGCGA\tN701\tAATGAGTA\tS507,[N|S|E]507\t4291\r\nGGACTCCT\tN705\tATGGCTAT\tS520\t4262\r\nTCCTGAGC\tN704\tGCGTAATA\tE517,N719,S517,[N|S|E]517\t4234\r\nGGACTCCT\tN705\tTATCCCCT\tE503,S503,[N|S|E]503\t4204\r\nGGATTCCT\tN705\tAAGGCTAT\tS520\t4192\r\nGGGGGGGG\tUnknown\tGGTGGGGG\tUnknown\t4115\r\nTAAGCGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4041\r\nCTCTCTAC\tN707\tGCGTACGA\tE517,S517,[N|S|E]517\t4022\r\nTCCTGAGC\tN704\tGCGTCAGA\tE517,S517,[N|S|E]517\t4018\r\nCAGAGAGG\tN708\tTCGTAAGA\tE517,S517,[N|S|E]517\t4003\r\nCCTGAGCA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t3997\r\nTAAGGCGA\tN701\tTCTATTCG\tUnknown\t3950\r\nTCCTGACA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t3946\r\nAAGGCGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3923\r\nTTCTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t3911\r\nCTCTCTAC\tN707\tAAGGATCG\tUnknown\t3887\r\nGGACTCCT\tN705\tGAGGCTAT\tS520\t3878\r\nGGACTCCT\tN705\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t3806\r\nGGACTCCT\tN705\tAAAGCTAT\tS520\t3771\r\nCCTCTACA\tUnknown\tTCGACTAG\tS513\t3762\r\nCTCTTCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3734\r\nGGAATCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t3728\r\nCTCTCTAC\tN707\tAAGGAAGT\tUnknown\t3721\r\nTCCTGAGC\tN704\tGAGTAAGA\tE517,S517,[N|S|E]517\t3696\r\nCTCTCTAC\tN707\tTCACTAGT\tUnknown\t3651\r\nCTCTCTAC\tN707\tGCGTAAGT\tE517,S517,[N|S|E]517\t3592\r\nGGGGGGGG\tUnknown\tGGGCGGGG\tUnknown\t3580\r\nCTCTCTAC\tN707\tAAGGCGTC\tUnknown\t3563\r\nCTCTCTAC\tN707\tGCGTAAAT\tUnknown\t3524\r\nGTACTAGA\tUnknown\tAAGGCTAT\tS520\t3511\r\nTAAGGCGA\tN701\tAAGTAGTA\tS507,[N|S|E]507\t3509\r\nCTCTCTAC\tN707\tAAGGAATC\tUnknown\t3494\r\nTAAGGCAA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t3461\r\nCTCTCTAC\tN707\tCGTAAGAT\tUnknown\t3444\r\nCTCTCTAC\tN707\tCTCGCTAT\tE502,S502,[N|S|E]502\t3443\r\nGGACTCCT\tN705\tAAGGCTGT\tS520\t3442\r\nCTCTCACA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t3435\r\nCTCTCAAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t3428\r\nCTCTCTAC\tN707\tCCGTAAGA\tE517,S517,[N|S|E]517\t3425\r\nCTCTCCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3419\r\nCTCTCTAC\tN707\tCTCTCTAA\tE502,N707,S502,[N|S|E]502\t3406\r\nCTCTCTAC\tN707\tACGACTAG\tS513\t3377\r\nGGACTCCT\tN705\tTATGCTCT\tE503,S503,[N|S|E]503\t3350\r\nCTCGCTAC\tN707\tTCGACTAG\tS513\t3334\r\nCTCTCTAC\tN707\tCTCACTAT\tE502,S502,[N|S|E]502\t3333\r\nGGACTCCT\tN705\tTATCCTCG\tE503,S503,[N|S|E]503\t3326\r\nCTCTCTAC\tN707\tTCTATTCG\tUnknown\t3324\r\nGGACTCCT\tN705\tTACCCTCT\tE503,S503,[N|S|E]503\t3323\r\nCTCTCTCA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t3321\r\nGGACTCCT\tN705\tAAGCCTTA\tS521\t3320\r\nTAAGGCGA\tN701\tCTCACTAT\tE502,S502,[N|S|E]502\t3313\r\nTAAGGCTA\tN701,S521\tCTCTCTAT\tE502,S502,[N|S|E]502\t3296\r\nCTCTCTAC\tN707\tCTCTGTAT\tE502,S502,[N|S|E]502\t3294\r\nCTCTCTAC\tN707\tAAGGAGCG\tUnknown\t3290\r\nTAAGGCGA\tN701\tCTCTCTTC\tN707\t3278\r\nGGGGGGGG\tUnknown\tGGAGGGGG\tUnknown\t3275\r\nCTCTCTAC\tN707\tTAGACTAG\tS513\t3265\r\nCCTCTCTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3228\r\nAGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t3214\r\nCTCTCTAC\tN707\tCTCCCTAT\tE502,S502,[N|S|E]502\t3195\r\nCTCTCTAC\tN707\tCTCTCCAT\tE502,S502,[N|S|E]502\t3189\r\nCTCTCTAC\tN707\tTCGATAGT\tUnknown\t3189\r\nGGACTCCT\tN705\tCCTCTTCG\tUnknown\t3183\r\nTCCTATCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t3180\r\nCTCCTACA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t3148\r\nCTCCTCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3146\r\nTAAGGCGA\tN701\tCTCTGTAT\tE502,S502,[N|S|E]502\t3144\r\nCTCTCTAC\tN707\tGCTAAGAT\tUnknown\t3143\r\nGGACTCCT\tN705\tAAGGCATT\tUnknown\t3098\r\nTAAGGAGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t3098\r\nTAAGGCGA\tN701\tCTCTCCAT\tE502,S502,[N|S|E]502\t3096\r\nTAAGGCGA\tN701\tCTCTCTCT\tE502,S502,[N|S|E]502\t3088\r\nTAAGGCGA\tN701\tCTCGCTAT\tE502,S502,[N|S|E]502\t3082\r\nCTCTCTAC\tN707\tTCGACTAA\tS513\t3079\r\nTCCTGAGC\tN704\tGCGTGAGA\tE517,S517,[N|S|E]517\t3065\r\nTCCTGAGC\tN704\tGTGTAAGA\tE517,S517,[N|S|E]517\t3043\r\nTCCCGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t3023\r\nCTCTCTGC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t3017\r\nGGGGGGGG\tUnknown\tGGCCGCGG\tUnknown\t3013\r\nCTCACTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t3002\r\nTAATGCGA\tD708,N701,S522\tAAGGAGTA\tS507,[N|S|E]507\t2995\r\nCTCTCTAC\tN707\tGCATAAGA\tE517,S517,[N|S|E]517\t2984\r\nTAAGGCGA\tN701\tCTCCCTAT\tE502,S502,[N|S|E]502\t2947\r\nTAAGGCGA\tN701\tCTCTCTAA\tE502,N707,S502,[N|S|E]502\t2913\r\nCTCTTACA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t2912\r\nCTCTCTAC\tN707\tCTCTCTCT\tE502,S502,[N|S|E]502\t2910\r\nCTCTCTAC\tN707\tAAGGAGGT\tUnknown\t2849\r\nTAAGGTGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t2849\r\nGGACTCCT\tN705\tGAGCTTAT\tUnknown\t2819\r\nCTCTACAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t2808\r\nGCGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t2796\r\nCTCTCTAC\tN707\tGAGTATCG\tUnknown\t2789\r\nGGACTCCT\tN705\tTAGGCTAT\tS520\t2736\r\nCTCTATCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t2727\r\nCTCTCTAC\tN707\tAAGTATTA\tUnknown\t2720\r\nGGACTCCT\tN705\tGGCTATTC\tUnknown\t2716\r\nGTACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t2710\r\nCTCTCTAC\tN707\tGGTAAGAT\tUnknown\t2682\r\nGGACTTCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t2670\r\nGGGGGGGG\tUnknown\tGGACGCGG\tUnknown\t2666\r\nCTCTCTAC\tN707\tTCGCTAGT\tUnknown\t2633\r\nGGACTCCT\tN705\tAAGGCTAC\tS520\t2627\r\nTAAGGCGA\tN701\tAAGGATAT\tS520\t2614\r\nTCCTGAGC\tN704\tGCGTAAGG\tE517,S517,[N|S|E]517\t2606\r\nCTCTCTTC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t2604\r\nCTCTCTAC\tN707\tGCGTAGAT\tUnknown\t2603\r\nTAGGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t2588\r\nCTCTCTAC\tN707\tTCGACTGG\tS513\t2586\r\nGGACTCCT\tN705\tAACGCTAT\tS520\t2580\r\nGGACTCCT\tN705\tAAGGCTAA\tS520\t2574\r\nCCCTCTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t2574\r\nGGACTCTT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t2562\r\nTAAGGCGA\tN701\tAAGGCGTA\tS507,[N|S|E]507\t2534\r\nGGACCTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t2533\r\nCTCTCTAC\tN707\tCTCTCTTC\tN707\t2531\r\nCTCTCTAC\tN707\tAAAGTATC\tUnknown\t2524\r\nTAAGGCGA\tN701\tATGGAGTA\tS507,[N|S|E]507\t2490\r\nGGACTACT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t2483\r\nGGCCTCCT\tN705\tAAGGCTAT\tS520\t2468\r\nTAAGGCGA\tN701\tGAGGAGTA\tS507,[N|S|E]507\t2435\r\nGGGGGGGG\tUnknown\tGGCGGCGG\tUnknown\t2434\r\nGGACTCTA\tUnknown\tGAGCCTTA\tS521\t2429\r\nCTCTCCAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t2426\r\nGGACTCCT\tN705\tAAGGCCAT\tS520\t2422\r\nTAAGGCGA\tN701\tAAGGGTAT\tS520\t2405\r\nCTCTCATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t2397\r\nTCCTGCGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t2381\r\nTAAGGCGA\tN701\tAAGGAGAA\tS507,[N|S|E]507\t2361\r\nCTTCTACA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t2355\r\nGGACTCCT\tN705\tGAGCCTTT\tS521\t2351\r\nGGACTCCA\tN705\tAAGGCTAT\tS520\t2348\r\nGGACTCCT\tN705\tCAGGCTAT\tS520\t2343\r\nGGACTCCT\tN705\tAGGGCTAT\tS520\t2336\r\nGGACTCCT\tN705\tTATCTTCG\tUnknown\t2333\r\nGGACTCCT\tN705\tTATCCGCT\tE503,S503,[N|S|E]503\t2313\r\nCCCTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t2269\r\nCTCTCTAC\tN707\tAGTATCGT\tUnknown\t2263\r\nCTCTCTAC\tN707\tAAGGACGT\tD507\t2253\r\nTAAGGCGA\tN701\tCGCTCTAT\tE502,S502,[N|S|E]502\t2250\r\nCTCTCCAT\tE502,S502,[N|S|E]502\tAAGGAGTA\tS507,[N|S|E]507\t2234\r\nCTCTCTAC\tN707\tGCGAAGAT\tUnknown\t2223\r\nGGACTCCT\tN705\tCTCTTCGT\tUnknown\t2221\r\nGGACCCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t2209\r\nCTCTCTAC\tN707\tCGCTCTAT\tE502,S502,[N|S|E]502\t2195\r\nGGACTCCT\tN705\tTACTCTTC\tUnknown\t2191\r\nGGGGGGGG\tUnknown\tGGGCGCGG\tUnknown\t2188\r\nCTCTCTAC\tN707\tAAGGTGTT\tUnknown\t2169\r\nCTCTCTAC\tN707\tAAGGGGTG\tUnknown\t2145\r\nCTCTCTAC\tN707\tGACTAGTC\tUnknown\t2136\r\nTAAGGCGA\tN701\tGGAGTATC\tUnknown\t2112\r\nGGACTCCT\tN705\tTATCATCA\tUnknown\t2112\r\nTAAGTCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t2109\r\nGGACTCCT\tN705\tGAGCCTAT\tUnknown\t2105\r\nCCTCTCTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t2102\r\nTAAGGGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t2102\r\nCTCTCTAC\tN707\tGTAAGATC\tUnknown\t2102\r\nTAAGGCGA\tN701\tACGGAGTA\tS507,[N|S|E]507\t2091\r\nATCTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t2088\r\nCTCTCTAC\tN707\tCTCTCTCG\tUnknown\t2080\r\nTGACTCCT\tN705\tAAGGCTAT\tS520\t2078\r\nTAAGGCGA\tN701\tAAGGAGTC\tS507,[N|S|E]507\t2070\r\nGGACTCGT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t2058\r\nCTCCCTAC\tE505,N707,S505,[N|S|E]505\tTCGACTAG\tS513\t2057\r\nGGACTCCT\tN705\tTATCCTCA\tE503,S503,[N|S|E]503\t2051\r\nCCCCCCCC\tUnknown\tCCCCCCCC\tUnknown\t2044\r\nGGTCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t2038\r\nTCCTGAGC\tN704\tGCGCAAGA\tE517,S517,[N|S|E]517\t2036\r\nTCCTGATC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t2023\r\nTCCTGAGC\tN704\tGCGTAGGA\tE517,N719,S517,[N|S|E]517\t2020\r\nGGGGGGGG\tUnknown\tGGGTGGGG\tUnknown\t2018\r\nCTCTACAT\tUnknown\tTCGACTAG\tS513\t2007\r\nTCCTGAGC\tN704\tGCGTAAAA\tE517,S517,[N|S|E]517\t1979\r\nCTCTCTAC\tN707\tTTGACTAG\tS513\t1976\r\nCTCTCTAC\tN707\tGCGTCAGA\tE517,S517,[N|S|E]517\t1975\r\nTAACGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t1967\r\nGACTCCTA\tUnknown\tGAGCCTTA\tS521\t1960\r\nGGACTCCT\tN705\tAAGGCTCT\tS520\t1944\r\nTAAGGCGA\tN701\tAAAGAGTA\tS507,[N|S|E]507\t1936\r\nGGAATCCT\tN705\tAAGGCTAT\tS520\t1925\r\nGGACTCCT\tN705\tTCTTCGTC\tUnknown\t1922\r\nCTCTCTAC\tN707\tCCGACTAG\tS513\t1917\r\nCTCTCTAC\tN707\tTCGCCTAG\tS513\t1913\r\nCTGAGCAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t1897\r\nCTCTCTCC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t1880\r\nTAAGGCGA\tN701\tCTCTCTCG\tUnknown\t1876\r\nCTATCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t1868\r\nCCTTCTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1849\r\nGGGGGGGG\tUnknown\tGGCAGCGG\tUnknown\t1844\r\nTAAGGCGC\tD708,N701,S521\tCTCTCTAT\tE502,S502,[N|S|E]502\t1840\r\nCTCTCTAC\tN707\tCTCTCGAT\tE502,S502,[N|S|E]502\t1834\r\nTACGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1818\r\nTAAGGCGG\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1815\r\nTAAGGCGA\tN701\tAAGGAGCA\tS507,[N|S|E]507\t1814\r\nTCCTGAGC\tN704\tGCGTATGA\tE517,S517,[N|S|E]517\t1807\r\nCTCTCTAC\tN707\tGCTTAAGA\tE517,S517,[N|S|E]517\t1799\r\nTAAGGCGA\tN701\tCTCTCGAT\tE502,S502,[N|S|E]502\t1798\r\nGGACTCCT\tN705\tAGCCTTAT\tUnknown\t1797\r\nTCCTGAGG\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t1793\r\nCGTACTAG\tN702\tAAGCCTTA\tS521\t1790\r\nCTCTCTAC\tN707\tTCGAATAG\tA505,S513\t1759\r\nTAAGGGGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1758\r\nTCTACATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1751\r\nGGACTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1747\r\nGGGGGGGG\tUnknown\tGGGAGGGG\tUnknown\t1736\r\nCTCTCTAC\tN707\tTCCACTAG\tS513\t1730\r\nCTTTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t1725\r\nCTCTCTAC\tN707\tATCGTCGG\tUnknown\t1722\r\nTAAGGCGA\tN701\tTAGGAGTA\tS507,[N|S|E]507\t1703\r\nTGAGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1693\r\nGGACTCCT\tN705\tTATCTTCT\tE503,S503,[N|S|E]503\t1686\r\nCTCTCTAC\tN707\tCTCTATAA\tUnknown\t1681\r\nGGGGGGGG\tUnknown\tGGAAGCGG\tUnknown\t1677\r\nGGACTCCT\tN705\tAAGGCGAT\tS520\t1671\r\nTCCCGAGG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t1651\r\nTATGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1626\r\nGGGGGGGG\tUnknown\tGGACGAGG\tUnknown\t1626\r\nGGACTCCT\tN705\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t1622\r\nGGGCTCCT\tN705\tGAGCCTTA\tS521\t1620\r\nGGTCCTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1619\r\nGTCTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t1619\r\nTAAGGCGA\tN701\tAAGGAGTG\tS507,[N|S|E]507\t1613\r\nGGACTCCT\tN705\tTATCGTCA\tUnknown\t1612\r\nGGGGGGGG\tUnknown\tGGGGGAGG\tUnknown\t1609\r\nTAAGGCGA\tN701\tAAGGTGTA\tS507,[N|S|E]507\t1605\r\nTAAAGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1602\r\nCTCTCTAT\tE502,S502,[N|S|E]502\tGCGTAAGA\tE517,S517,[N|S|E]517\t1594\r\nTAAGGCGA\tN701\tCTATTCGT\tUnknown\t1590\r\nCTCTCTAC\tN707\tGCGTAATA\tE517,N719,S517,[N|S|E]517\t1581\r\nCTTTCTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1581\r\nGTACTAGA\tUnknown\tGAGCCTTA\tS521\t1572\r\nAGACTCCT\tN705\tAAGGCTAT\tS520\t1568\r\nGGGGGGGG\tUnknown\tGGTCGCGG\tUnknown\t1563\r\nCTCTATAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t1562\r\nACGAAATG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1560\r\nTCCTTAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t1559\r\nTCCCAACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1557\r\nCCTCTACA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t1536\r\nGGACTCCT\tN705\tCAGCCTTA\tS521\t1531\r\nTAAGGCGA\tN701\tCCTCTCTA\tUnknown\t1527\r\nTAAGGCGA\tN701\tCTCTATAA\tUnknown\t1522\r\nTAAGGCGA\tN701\tAAGGATTA\tS507,[N|S|E]507\t1520\r\nGGACTTCT\tN705\tAAGGCTAT\tS520\t1520\r\nGGCTCCTA\tUnknown\tGAGCCTTA\tS521\t1518\r\nGGACTCCT\tN705\tGATCCTTA\tS521\t1516\r\nCTCTCTAC\tN707\tTCGACAGT\tUnknown\t1514\r\nTCCTATCT\tUnknown\tAAGGCTAT\tS520\t1514\r\nGGACTCCT\tN705\tTATCATCC\tUnknown\t1512\r\nTTCTCTAC\tN707\tTCGACTAG\tS513\t1499\r\nGGGGGGGG\tUnknown\tGGAGGCGG\tUnknown\t1498\r\nTAAGGAAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t1494\r\nCTCTCTAC\tN707\tAAGGTGTC\tUnknown\t1491\r\nGGGGGGCG\tUnknown\tGGGGGGGG\tUnknown\t1482\r\nTAAGGCGA\tN701\tTATTCGTC\tUnknown\t1479\r\nCTCTCTAC\tN707\tAAGGGGTT\tUnknown\t1477\r\nCGTACTAA\tN702\tAAGGCTAT\tS520\t1469\r\nGGGCTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1464\r\nCTCTCTAC\tN707\tCTATTCGT\tUnknown\t1461\r\nCTCGCTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t1456\r\nTAAGGAGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t1456\r\nTAAGGCGA\tN701\tCTCTCTAG\tE502,N707,S502,[N|S|E]502\t1436\r\nCTCTCTAC\tN707\tTCGAGTAG\tA505,S513\t1425\r\nGGGGGGGG\tUnknown\tTGGGGGGG\tUnknown\t1413\r\nGTACTCCT\tN705\tAAGGCTAT\tS520\t1413\r\nTCCAGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t1409\r\nCTCTCTAC\tN707\tAATCGTCG\tUnknown\t1407\r\nCTCTTTAC\tE505,N707,S505,[N|S|E]505\tCTCTCTAT\tE502,S502,[N|S|E]502\t1403\r\nGGATCCTA\tUnknown\tGAGCCTTA\tS521\t1403\r\nCTCTCTAC\tN707\tTCGTCTAG\tS513\t1401\r\nCACTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t1384\r\nCTGTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t1380\r\nCTCTCTAC\tN707\tAAGGCGTG\tUnknown\t1377\r\nTAAAGGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t1369\r\nGGGGGGGG\tUnknown\tGGAAGAGG\tUnknown\t1368\r\nTAAGGCGA\tN701\tAGGGAGTA\tS507,[N|S|E]507\t1362\r\nGAACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t1358\r\nCTCTCTAC\tN707\tCGTCGGCA\tUnknown\t1350\r\nCCTCTCTA\tUnknown\tTCGACTAG\tS513\t1343\r\nGGGGGGGG\tUnknown\tGGCCGGGG\tUnknown\t1342\r\nTAAGGCGA\tN701\tAAGCAGTA\tS507,[N|S|E]507\t1339\r\nCTCTCTAC\tN707\tAATATCGT\tUnknown\t1337\r\nCGACTAGA\tUnknown\tAAGGCTAT\tS520\t1332\r\nCTCTGTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t1327\r\nTAAGGCTA\tN701,S521\tAAGGAGTA\tS507,[N|S|E]507\t1324\r\nTCCTGAGC\tN704\tGCGTAAGC\tE517,S517,[N|S|E]517\t1323\r\nTCATGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t1316\r\nTCCTGAGC\tN704\tGCGTAACA\tE517,S517,[N|S|E]517\t1309\r\nCTCTCTAC\tN707\tAAGGGGTC\tUnknown\t1303\r\nGGGGGGGG\tUnknown\tGGGGGTGG\tUnknown\t1301\r\nCTCTCTAC\tN707\tCCTCTCTA\tUnknown\t1300\r\nCGTACTAG\tN702\tAATGCTAT\tS520\t1300\r\nCTCTCTGC\tN707\tTCGACTAG\tS513\t1299\r\nCGTACTAT\tN702\tAAGGCTAT\tS520\t1297\r\nACGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t1290\r\nCTCTCTTC\tN707\tTCGACTAG\tS513\t1287\r\nGGACCCCT\tN705\tAAGGCTAT\tS520\t1285\r\nACGAAGTG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1281\r\nTAAAAGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t1276\r\nCTCTCTAC\tN707\tTCGACTCG\tS513\t1268\r\nTAAGGCGA\tN701\tAACGAGTA\tS507,[N|S|E]507\t1264\r\nGGACTCTT\tN705\tAAGGCTAT\tS520\t1261\r\nCTCTCTAC\tN707\tGAGTAAGA\tE517,S517,[N|S|E]517\t1259\r\nCTCTCTAC\tN707\tCTCTCTAG\tE502,N707,S502,[N|S|E]502\t1254\r\nCTCTCTAC\tN707\tGTGTAAGA\tE517,S517,[N|S|E]517\t1253\r\nGGGGGGGG\tUnknown\tGGACGGGG\tUnknown\t1247\r\nGGACCTAT\tUnknown\tAAGGCTAT\tS520\t1244\r\nGGACTCCT\tN705\tAAGGGCTA\tUnknown\t1244\r\nGGACTCCT\tN705\tGAGCATTA\tS521\t1236\r\nATCTCGTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1231\r\nGGACTCCT\tN705\tGCGCCTTA\tS521\t1227\r\nGGACTCCT\tN705\tAAGGATAA\tUnknown\t1220\r\nGGGGGGGG\tUnknown\tGGCAGAGG\tUnknown\t1213\r\nTCCTAACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1206\r\nTCCTGAGC\tN704\tCGCGTAAG\tUnknown\t1205\r\nCTCACTAC\tN707\tTCGACTAG\tS513\t1201\r\nCTCTCTAC\tN707\tGGGGGGGG\tUnknown\t1198\r\nGGACTCCT\tN705\tTCTCTTCG\tS511\t1193\r\nCCTCTCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1191\r\nGGACTCCT\tN705\tTATCGTCG\tUnknown\t1189\r\nCTCTCTAC\tN707\tTATCGTCG\tUnknown\t1177\r\nGGACTCAT\tN705\tGAGCCTTA\tS521\t1169\r\nGGGGGGGG\tUnknown\tGGCCGAGG\tUnknown\t1162\r\nTAAGGCGA\tN701\tAAGGGGTA\tS507,[N|S|E]507\t1159\r\nCTCTCTAC\tN707\tTATTCGTC\tUnknown\t1159\r\nGGACTCCT\tN705\tAAGCCTAT\tS520\t1159\r\nTCCTGAGC\tN704\tGCGTAAAG\tUnknown\t1158\r\nGGGGGGGG\tUnknown\tGGTGGCGG\tUnknown\t1157\r\nCTCTCTAC\tN707\tTCGGCTAG\tS513\t1155\r\nCTCTCTAC\tN707\tCTCTTCGT\tUnknown\t1151\r\nTCCTGAGT\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t1147\r\nGGACTCCT\tN705\tAAGGCTTC\tUnknown\t1147\r\nTAAGGCGA\tN701\tCTCTGTAA\tUnknown\t1145\r\nCTCTCTAC\tN707\tGCGTAGGA\tE517,N719,S517,[N|S|E]517\t1142\r\nCTCTCTAC\tN707\tGTATCGTC\tUnknown\t1139\r\nTAAGGCGA\tN701\tCAGGAGTA\tS507,[N|S|E]507\t1138\r\nTAAGACGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1138\r\nCTCTCTAC\tN707\tGTCGGCAG\tUnknown\t1134\r\nGGGCTACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1128\r\nCTCTCTAG\tE502,N707,S502,[N|S|E]502\tAAGGAGTA\tS507,[N|S|E]507\t1127\r\nCTCTCTAC\tN707\tGCGTGAGA\tE517,S517,[N|S|E]517\t1126\r\nCTCTCTAC\tN707\tCTCTGTAA\tUnknown\t1125\r\nGGACTCCT\tN705\tTATCGTCC\tUnknown\t1112\r\nCTCTCTAC\tN707\tCTCTTTCG\tUnknown\t1112\r\nTAAGGTGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t1111\r\nCATGCTCA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1107\r\nCTCTCTAC\tN707\tTCGACCAG\tS513\t1106\r\nTAGGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t1101\r\nCAAGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1097\r\nGGACTATC\tUnknown\tAAGGCTAT\tS520\t1089\r\nTCCTGAGC\tN704\tGCGTAATC\tUnknown\t1088\r\nCCTCTCCT\tD503\tAAGGAGTA\tS507,[N|S|E]507\t1085\r\nTTCTGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t1083\r\nCCTCTTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1081\r\nGGACTCGT\tN705\tAAGGCTAT\tS520\t1080\r\nGGGGGGTG\tUnknown\tGGGGGGGG\tUnknown\t1072\r\nCTCTCCAC\tN707\tTCGACTAG\tS513\t1068\r\nCTCTCTAC\tN707\tTCGTCGGC\tUnknown\t1061\r\nCGTACTAG\tN702\tGAGCCTTT\tS521\t1058\r\nGGGGGGGG\tUnknown\tGGGAGCGG\tUnknown\t1057\r\nCTCTCTAC\tN707\tGCGTAAGG\tE517,S517,[N|S|E]517\t1055\r\nCGTACTAG\tN702\tACGGCTAT\tS520\t1054\r\nTGGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t1054\r\nGGACTCCT\tN705\tCTATCCTC\tUnknown\t1052\r\nGGGACTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1050\r\nTAGCATGA\tUnknown\tTAGATCGC\t[N|S|E]501\t1040\r\nCTCTCTAC\tN707\tAAGGGGGG\tUnknown\t1036\r\nTAAGGCGA\tN701\tCTCTTCGT\tUnknown\t1035\r\nCGTACTAG\tN702\tAAGGCTTT\tS520\t1035\r\nGGACTTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1027\r\nACTAAATG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t1021\r\nGGGGGGGG\tUnknown\tGGTCGGGG\tUnknown\t1019\r\nCTCTCTAC\tN707\tATATCGTC\tUnknown\t1014\r\nGGAGTCCT\tN705\tGAGCCTTA\tS521\t1013\r\nTCCTGTGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t1012\r\nCTCTCTAC\tN707\tAGGGTATC\tUnknown\t1010\r\nTAAGGCGA\tN701\tAAGAAGTA\tS507,[N|S|E]507\t1010\r\nGGACTCCT\tN705\tAAGGTTAT\tS520\t1009\r\nTAAGGCGA\tN701\tCTTTCTAT\tE502,S502,[N|S|E]502\t1007\r\nTTCTCTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t1006\r\nCTCTCTAC\tN707\tAATGATTA\tUnknown\t1001\r\nGGACTCCT\tN705\tTATTCTTC\tUnknown\t1000\r\nCGGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t997\r\nGGACTCCT\tN705\tCAAGGCTA\tUnknown\t992\r\nGGATTCCT\tN705\tGAGCCTTA\tS521\t992\r\nGGGGGGGG\tUnknown\tGGTAGCGG\tUnknown\t991\r\nCTCTCTAC\tN707\tAAGTCGTC\tUnknown\t991\r\nCTATCTCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t991\r\nTCCTGAAC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t990\r\nCTCTCTAC\tN707\tTGAGTATC\tUnknown\t988\r\nGGACTCCC\tN705\tGAGCCTTA\tS521\t982\r\nCGTCTAGA\tUnknown\tAAGGCTAT\tS520\t973\r\nCTCTCTAC\tN707\tAACGCGTA\tUnknown\t972\r\nCGTACTAG\tN702\tAAGGTATT\tUnknown\t972\r\nCTCTCTAC\tN707\tTCGACTTG\tS513\t970\r\nCTCTCTAC\tN707\tAAGGTGTG\tUnknown\t967\r\nCTCTCTAC\tN707\tACGGCGTA\tUnknown\t966\r\nTAGGCATG\tN706\tAAGCCTTA\tS521\t966\r\nCGTACTAG\tN702\tGAGCCTAT\tUnknown\t964\r\nCGTACTAG\tN702\tAGCCTTAT\tUnknown\t952\r\nGGGGGGGG\tUnknown\tGGGGTGGG\tUnknown\t951\r\nATCTCTAC\tN707\tTCGACTAG\tS513\t947\r\nGAGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t944\r\nTAAGGCGA\tN701\tCTCTCGTC\tUnknown\t943\r\nCTAAGGCG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t943\r\nTAGGCATG\tN706\tGAGATCGC\t[N|S|E]501\t941\r\nCTCTCTAC\tN707\tAAGGCTTA\tUnknown\t941\r\nCTCTCTAC\tN707\tTCGACTAC\tS513\t939\r\nTCTTGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t938\r\nTAAGGCGT\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t937\r\nGGACTCCT\tN705\tTATCATCG\tUnknown\t937\r\nCTCTCTAC\tN707\tAATTAGTA\tUnknown\t933\r\nTACGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t932\r\nGGGCGGGG\tUnknown\tGGGGGGGG\tUnknown\t931\r\nCCGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t927\r\nTAAGGGGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t924\r\nCTCTACAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t924\r\nGGACTCCT\tN705\tGGCCTTAT\tUnknown\t924\r\nCTCTCTAC\tN707\tGCGCAAGA\tE517,S517,[N|S|E]517\t923\r\nCCCTGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t922\r\nTAAGGCGA\tN701\tAAGGAATA\tS507,[N|S|E]507\t918\r\nCTCTCTAC\tN707\tCTCTATAC\tN707\t913\r\nTCCTGGGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t913\r\nCCCTCTAC\tN707\tTCGACTAG\tS513\t910\r\nCTTCTCTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t909\r\nCTCTCTAC\tN707\tAGGGGGGG\tUnknown\t906\r\nGGACCCTA\tUnknown\tGAGCCTTA\tS521\t904\r\nGGACTCCT\tN705\tTATCCACT\tE503,S503,[N|S|E]503\t903\r\nTAAGGCGA\tN701\tCTCTGTAC\tN707\t896\r\nTCCTGCAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t895\r\nCTCTCAAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t893\r\nTAAAGGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t892\r\nCTCTCTTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t888\r\nGGTCTCCT\tN705\tAAGGCTAT\tS520\t887\r\nCTCCCTAC\tE505,N707,S505,[N|S|E]505\tGCGTAAGA\tE517,S517,[N|S|E]517\t886\r\nGGACACCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t884\r\nCTCTCTAC\tN707\tCTCTCGTC\tUnknown\t884\r\nGGACTCCT\tN705\tGAGCCTAA\tS521\t876\r\nGGGCACCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t875\r\nCTCTCTAC\tN707\tCTTTCTAT\tE502,S502,[N|S|E]502\t874\r\nCTCTCTAC\tN707\tCTCTGTAC\tN707\t873\r\nTAAGGCGA\tN701\tAAGGACTA\tS507,[N|S|E]507\t873\r\nCGTACTAG\tN702\tGAGCTTAT\tUnknown\t872\r\nCGTACTAG\tN702\tAAGGATAT\tS520\t872\r\nTAAGGCGA\tN701\tCCTATTCG\tUnknown\t872\r\nCGTACTAG\tN702\tAAGTCTAT\tS520\t868\r\nCTCTATCT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t868\r\nCTCCACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t865\r\nCGTACTAG\tN702\tAAAGCTAT\tS520\t858\r\nGCTCCTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t857\r\nTAAGGCGC\tD708,N701,S521\tAAGGAGTA\tS507,[N|S|E]507\t856\r\nCTCTTTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t851\r\nTCTCAACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t849\r\nTAAGGCCG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t848\r\nCTCTTCTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t848\r\nGGACTCCT\tN705\tGTGCCTTA\tA504,S521\t845\r\nTAGCATGA\tUnknown\tGAGCCTTA\tS521\t843\r\nCTCTCTAC\tN707\tCTCTTTAT\tE502,S502,[N|S|E]502\t841\r\nTAAGGCGA\tN701\tAAGGGAGT\tUnknown\t840\r\nCTCTCTGC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t840\r\nCTCTCTAC\tN707\tAACGTCGG\tUnknown\t835\r\nCTCTCTAC\tN707\tAAGCGTCG\tUnknown\t835\r\nCACTCTAC\tN707\tTCGACTAG\tS513\t835\r\nTAGGCATG\tN706\tAGATCGCT\tUnknown\t833\r\nGGACCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t832\r\nACTAAATG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t825\r\nGGGATCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t813\r\nCGTACTAG\tN702\tCAGCCTTA\tS521\t813\r\nTAAAAGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t812\r\nTAAGGCGA\tN701\tCTCTCAAT\tE502,S502,[N|S|E]502\t812\r\nCTCTCTAC\tN707\tACGTAGTA\tN719\t812\r\nCTCTCTAC\tN707\tAAGGCTAT\tS520\t811\r\nGGTCCTAT\tUnknown\tAAGGCTAT\tS520\t811\r\nCGTGCTAG\tN702\tAAGGCTAT\tS520\t810\r\nGGGGGGGG\tUnknown\tGGCTGCGG\tUnknown\t810\r\nTAAGGCGA\tN701\tCTCTATAC\tN707\t808\r\nCTCTCAAT\tE502,S502,[N|S|E]502\tAAGGAGTA\tS507,[N|S|E]507\t806\r\nGGACTCCT\tN705\tAAAGGCTA\tUnknown\t801\r\nTCCTGAGC\tN704\tGCCTAAGA\tE517,S517,[N|S|E]517\t801\r\nCTCTATAC\tN707\tTCGACTAG\tS513\t799\r\nGGACTCCT\tN705\tAAGGCTAG\tS520\t797\r\nTAAGGCCA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t794\r\nTAAGGCGA\tN701\tAAGGAGGA\tS507,[N|S|E]507\t789\r\nCATACTAG\tN702\tAAGGCTAT\tS520\t788\r\nTAAGTCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t782\r\nGGACTCCT\tN705\tTTCGTCGG\tUnknown\t777\r\nGGGGGGGG\tUnknown\tGGTCGAGG\tUnknown\t777\r\nGGGGGGGG\tUnknown\tGGAGGAGG\tUnknown\t774\r\nTAAAGGCG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t773\r\nGGACTCCT\tN705\tAAGGGTAT\tS520\t772\r\nTCCTGAGC\tN704\tGCGTGAGG\tUnknown\t771\r\nCTCTCTAC\tN707\tGCGGAGTA\tN719\t769\r\nTAGGCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t768\r\nCTCTCTAC\tN707\tAAGGAGGG\tUnknown\t768\r\nCGTACTGA\tUnknown\tAAGGCTAT\tS520\t767\r\nCTCTCTAC\tN707\tGCGTAAAA\tE517,S517,[N|S|E]517\t767\r\nTAAGGCGA\tN701\tGATGGCAC\tUnknown\t766\r\nCTCTCTAC\tN707\tCTCTCAAT\tE502,S502,[N|S|E]502\t765\r\nACTAAGTG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t765\r\nGGACTACT\tN705\tAAGGCTAT\tS520\t765\r\nTAGGCATG\tN706\tTGATCGCT\tUnknown\t765\r\nCGTACTAG\tN702\tGATCCTTA\tS521\t764\r\nGCTCCTAT\tUnknown\tAAGGCTAT\tS520\t764\r\nGCGGGGGG\tUnknown\tGGCCGCGG\tUnknown\t763\r\nTCGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t758\r\nTCCCTAGG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t758\r\nGGGGGGGG\tUnknown\tGGTAGAGG\tUnknown\t756\r\nCCTTTTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t755\r\nTTAAGGCG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t755\r\nGGGGGGGG\tUnknown\tGGCAGGGG\tUnknown\t753\r\nCTCTCTAC\tN707\tGCGTATGA\tE517,S517,[N|S|E]517\t751\r\nAAGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t748\r\nTCCTGAGC\tN704\tGCGAAAGA\tE517,S517,[N|S|E]517\t746\r\nGGGGTCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t745\r\nTACTGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t741\r\nCTCTCTAC\tN707\tAAGTCGGC\tUnknown\t740\r\nGGGCAACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t737\r\nTAAGGCGA\tN701\tCTCTTTAT\tE502,S502,[N|S|E]502\t735\r\nCTCTCGAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t728\r\nGGGGGGGG\tUnknown\tCGGGGGGG\tUnknown\t725\r\nCTCCTCTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t725\r\nGGGGGGGG\tUnknown\tGGGCGAGG\tUnknown\t724\r\nTGAGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t722\r\nCGTACTAG\tN702\tATGGCTAT\tS520\t720\r\nGGGCTCCC\tUnknown\tAAGGCTAT\tS520\t716\r\nCGTCTAGA\tUnknown\tGAGCCTTA\tS521\t714\r\nCTCTCTAC\tN707\tAAGGTCGT\tUnknown\t709\r\nCTCTTTAC\tE505,N707,S505,[N|S|E]505\tTCGACTAG\tS513\t703\r\nCTCTCTAC\tN707\tAAATCGTC\tUnknown\t700\r\nGGCCTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t699\r\nGGGGGGGG\tUnknown\tGGAAGGGG\tUnknown\t697\r\nCATGCTCA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t696\r\nCTCTCTAC\tN707\tTCGACGAG\tS513\t695\r\nGCGGGGGG\tUnknown\tGGGGGCGG\tUnknown\t694\r\nTAAGGCAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t693\r\nTAAAGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t692\r\nTAAGGCGA\tN701\tCTCTCCGT\tUnknown\t692\r\nTAGGCATG\tN706\tTATATCGC\t[N|S|E]501\t691\r\nGGGGGGGG\tUnknown\tGGGAGAGG\tUnknown\t690\r\nCTCTCTAC\tN707\tTCGATTAG\tA505\t690\r\nCTCTCTCC\tN707\tTCGACTAG\tS513\t689\r\nGGGCTGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t688\r\nGCGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t687\r\nTAGGCATG\tN706\tGAGCTTAT\tUnknown\t687\r\nGGGGGGGG\tUnknown\tGGCGGAGG\tUnknown\t685\r\nCTCTCATC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t681\r\nCTCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t681\r\nCTAAGGCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t680\r\nCGCTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t676\r\nCGGACTCC\tUnknown\tAAGGCTAT\tS520\t676\r\nCGTACTAG\tN702\tAAGCTATT\tUnknown\t673\r\nGGACTCCT\tN705\tCTCTCTAT\tE502,S502,[N|S|E]502\t672\r\nGGACTCCT\tN705\tGAGCCCTA\tS521\t672\r\nTAAGGGCG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t672\r\nCCTCTTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t671\r\nCGGACTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t670\r\nCTCTCTAC\tN707\tGAGGGGGG\tUnknown\t664\r\nCTCTCTAC\tN707\tCTCTGTAG\tUnknown\t661\r\nGGACTCCT\tN705\tGAGCCTGA\tS521\t661\r\nTAAGGCGG\tN701\tAAGGAGTA\tS507,[N|S|E]507\t659\r\nGGACTCCT\tN705\tGAGCCTTC\tS521\t659\r\nACGAAATG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t657\r\nACTAAATG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t655\r\nCTCACTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t655\r\nGGTGGGGG\tUnknown\tGGGGGGGG\tUnknown\t654\r\nAGGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t653\r\nCGTACTAG\tN702\tGCGCCTTA\tS521\t650\r\nCTCTCTAC\tN707\tGAGCCTTA\tS521\t648\r\nGTGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t647\r\nCGTACAGA\tUnknown\tAAGGCTAT\tS520\t646\r\nTAGGCATG\tN706\tTAATCGCT\tUnknown\t646\r\nGGGGCGGG\tUnknown\tGGGGGGGG\tUnknown\t642\r\nTCCCTGAG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t642\r\nGGCCTTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t639\r\nGAACTCCT\tN705\tAAGGCTAT\tS520\t636\r\nCTCACATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t636\r\nTATGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t635\r\nCTCTCTAC\tN707\tTCGAATAT\tUnknown\t635\r\nTAGGCATG\tN706\tGAGCCTTT\tS521\t631\r\nCGACTAGA\tUnknown\tGAGCCTTA\tS521\t630\r\nGGACTCCT\tN705\tGAGCCTCA\tS521\t627\r\nGGACTCCT\tN705\tAAGGATAC\tUnknown\t625\r\nTAAGGCGA\tN701\tAAGGAGAT\tUnknown\t624\r\nCGTACTAG\tN702\tGAGCATTA\tS521\t619\r\nCTCTCTAC\tN707\tAGGAGTAC\tUnknown\t618\r\nTCCTGAGC\tN704\tGCGTCAGT\tUnknown\t618\r\nGGACTCCT\tN705\tTAATCCTC\tUnknown\t618\r\nCTCTCTAC\tN707\tAGGAGTTC\tUnknown\t617\r\nCTCTCTAC\tN707\tCTCTATAG\tUnknown\t617\r\nCTCTCTCT\tE502,S502,[N|S|E]502\tAAGGAGTA\tS507,[N|S|E]507\t617\r\nGGGGGGGG\tUnknown\tGGGTGCGG\tUnknown\t615\r\nTCCTGAGC\tN704\tTCGTACGA\tUnknown\t615\r\nCTCTCACC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t614\r\nGTCTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t614\r\nCGTACTAG\tN702\tGAGGCTAT\tS520\t612\r\nCTCTCTAC\tN707\tACGTCGGC\tUnknown\t610\r\nCTCTCTAC\tN707\tAGGATATC\tUnknown\t609\r\nGGACTCCT\tN705\tGAACCTTA\tS521\t607\r\nGGACTGCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t606\r\nCTCTCCTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t605\r\nTAAGGCGA\tN701\tCTCTGTAG\tUnknown\t605\r\nCCTTCTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t604\r\nCGTACTAG\tN702\tAAGACTAT\tS520\t603\r\nGGACTCCT\tN705\tGACCTTAT\tUnknown\t602\r\nTCCCAACT\tUnknown\tAAGGCTAT\tS520\t599\r\nGGACTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t599\r\nCTCTCTAC\tN707\tCCTATTCG\tUnknown\t598\r\nTAGGCATG\tN706\tGAGCCTAT\tUnknown\t598\r\nCTCTCTAC\tN707\tAAGGGGGA\tUnknown\t596\r\nCTCTCTAC\tN707\tGCGTAAGC\tE517,S517,[N|S|E]517\t596\r\nCCTCTCTT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t595\r\nCTCTCTAC\tN707\tTGGACTAG\tS513\t595\r\nTAGGCATG\tN706\tTAGATCAC\t[N|S|E]501\t594\r\nCGTACTAG\tN702\tAAGGCTGT\tS520\t594\r\nCTCCTAAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t593\r\nTCCTAAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t593\r\nCTTTCTAC\tN707\tTCGACTAG\tS513\t592\r\nTAGGCATG\tN706\tTAGTCGCT\tUnknown\t591\r\nGGGGGGGG\tUnknown\tGGCTGGGG\tUnknown\t591\r\nCCCCCTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t590\r\nTCCTGAGC\tN704\tGCGGAAGA\tE517,S517,[N|S|E]517\t588\r\nCGTCCTAG\tN702\tAAGGCTAT\tS520\t585\r\nCCTACATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t581\r\nCTCTCTTC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t581\r\nTAAGGCGA\tN701\tAAGGCGTT\tUnknown\t579\r\nTAGCGAAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t578\r\nTTAGGCGA\tN701,S522\tCTCTCTAT\tE502,S502,[N|S|E]502\t577\r\nGGAGGGGG\tUnknown\tGGGGGGGG\tUnknown\t576\r\nCCTCCTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t576\r\nGGGGGGGG\tUnknown\tGGTAGGGG\tUnknown\t576\r\nTAAGGCGA\tN701\tCTCATTCG\tUnknown\t576\r\nCTCTCTAC\tN707\tAAGGACGG\tUnknown\t576\r\nGCACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t574\r\nGGGGTGGG\tUnknown\tGGGGGGGG\tUnknown\t574\r\nCCTCTTTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t574\r\nGGGGGGGG\tUnknown\tGGATGCGG\tUnknown\t572\r\nGGACTCCA\tN705\tGAGCCTTA\tS521\t572\r\nTCCTGCGC\tN704\tTCGTAAGA\tE517,S517,[N|S|E]517\t572\r\nCTCTCTAC\tN707\tAAGGAGGC\tUnknown\t568\r\nCGTACTAG\tN702\tGGCCTTAT\tUnknown\t566\r\nTAAGCCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t564\r\nCTCTCTAC\tN707\tTCGAATAA\tS522\t564\r\nACCTGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t561\r\nCGTATAGA\tUnknown\tAAGGCTAT\tS520\t560\r\nTAAGGCGA\tN701\tCTCTATAG\tUnknown\t558\r\nTCCTGAGC\tN704\tTCTTAAGA\tUnknown\t555\r\nTAGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t551\r\nCTCTCTAC\tN707\tTTTTTTTT\tUnknown\t551\r\nCGTACTAA\tN702\tGAGCCTTA\tS521\t548\r\nGGGGACCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t546\r\nCTCCCTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t545\r\nCTCTCTAC\tN707\tTCGAGTAA\tUnknown\t544\r\nCGTACTAG\tN702\tAACGCTAT\tS520\t543\r\nCTATCTAC\tN707\tTCGACTAG\tS513\t543\r\nCTCTCTAC\tN707\tTCGAGTAT\tUnknown\t543\r\nTTAAAGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t543\r\nGGGGGGGG\tUnknown\tGGTGGAGG\tUnknown\t542\r\nCTCTCTAC\tN707\tAAGGCGAA\tUnknown\t542\r\nCGTACTAG\tN702\tAAGGCTAA\tS520\t541\r\nACGGGGGG\tUnknown\tGGCAGCGG\tUnknown\t537\r\nTAGGCATG\tN706\tTAGATCTC\t[N|S|E]501\t537\r\nAGGCATGA\tUnknown\tGAGCCTTA\tS521\t535\r\nGGACTTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t534\r\nTGACTCCT\tN705\tGAGCCTTA\tS521\t534\r\nTAGGCAGA\tUnknown\tTAGATCGC\t[N|S|E]501\t533\r\nTAAGGCGA\tN701\tCTTATTCG\tUnknown\t531\r\nCCCTTTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t530\r\nAAAAAATA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t528\r\nGCGGGGGG\tUnknown\tGGCAGCGG\tUnknown\t526\r\nAATAAATA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t525\r\nTCCTGAAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t525\r\nCGTGCTAG\tN702\tGAGCCTTA\tS521\t522\r\nAAGAAGTG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t521\r\nTAGGCATC\tN706\tTAGATCGC\t[N|S|E]501\t520\r\nCTCTCCCC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t520\r\nTAAGGCGA\tN701\tCAAGGAGT\tUnknown\t520\r\nCTCTCTAC\tN707\tCGCGTAAG\tUnknown\t519\r\nCGCACTAG\tN702\tAAGGCTAT\tS520\t518\r\nTAAGGCGA\tN701\tCTTCGTCG\tUnknown\t518\r\nCCTCTCTA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t517\r\nCTCTCTAC\tN707\tGAGGAGGA\tUnknown\t514\r\nGGACTCCG\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t514\r\nGGACTCCT\tN705\tTACTTCGT\tUnknown\t514\r\nCTCTCTAC\tN707\tCTCTCCTA\tUnknown\t513\r\nTATGCATG\tN706\tTAGATCGC\t[N|S|E]501\t511\r\nCTCTCTAC\tN707\tCTCTCCGT\tUnknown\t510\r\nCTCTTAAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t510\r\nGCGGGGGG\tUnknown\tGGACGCGG\tUnknown\t510\r\nGGCGGGGG\tUnknown\tGGGGGGGG\tUnknown\t510\r\nAAAAAAGA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t508\r\nTAGGCTGA\tUnknown\tTAGATCGC\t[N|S|E]501\t506\r\nCGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t506\r\nCTCTCTAC\tN707\tGCGTAACA\tE517,S517,[N|S|E]517\t505\r\nTAAGGCGA\tN701\tCGTCGGCA\tUnknown\t503\r\nCTCTCTAC\tN707\tCTCGACTA\tUnknown\t502\r\nGGGCACCT\tUnknown\tAAGGCTAT\tS520\t502\r\nGGGGGGCG\tUnknown\tGGCCGCGG\tUnknown\t501\r\nCGTACTAG\tN702\tCAGGCTAT\tS520\t500\r\nGGACTCCT\tN705\tGAGACTTA\tS521\t499\r\nCAAGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t499\r\nGGACTCCT\tN705\tGCTCCTCT\tUnknown\t498\r\nTCCTGAGC\tN704\tGGCGTAAG\tUnknown\t496\r\nCTTCCTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t495\r\nTACGGCGC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t493\r\nCTCTCTTA\tUnknown\tTCGACTAG\tS513\t493\r\nTAAGGCGA\tN701\tCTTTCGTC\tUnknown\t493\r\nTCCTGAGC\tN704\tGCGTGAGC\tUnknown\t492\r\nGGACTCCT\tN705\tGAGTCTTA\tA504,S521\t492\r\nTAGGCATG\tN706\tAGCCTTAT\tUnknown\t492\r\nTAAGGAAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t492\r\nCTCTCTAC\tN707\tGCGTAAAG\tUnknown\t490\r\nGGACTCCT\tN705\tTTATCCTC\tUnknown\t487\r\nCGTACTAG\tN702\tAAGGCCAT\tS520\t486\r\nGGACTCCT\tN705\tTATTTCGT\tUnknown\t486\r\nTCCTGAGC\tN704\tGCGTGAGT\tUnknown\t485\r\nTCCTGAGC\tN704\tGCGTATCG\tUnknown\t484\r\nTAGGCATG\tN706\tTAGAACGC\t[N|S|E]501\t484\r\nCTCTCTAC\tN707\tCTTCGTCG\tUnknown\t484\r\nTAAGGATC\tS521\tCTCTCTAT\tE502,S502,[N|S|E]502\t483\r\nTCCTATCT\tUnknown\tGAGCCTTA\tS521\t483\r\nGGATCTCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t483\r\nTTTAAGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t482\r\nCTCTCTAC\tN707\tCTCTTCTA\tUnknown\t481\r\nAAAGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t480\r\nGGGCGGCG\tUnknown\tGGGGGGGG\tUnknown\t480\r\nGGGGGGGG\tUnknown\tGGGGGGTG\tUnknown\t479\r\nCTACATCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t478\r\nTAAGGCGA\tN701\tCTCTTTCG\tUnknown\t476\r\nGGCGAATC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t472\r\nTAGGCAGA\tUnknown\tGAGCCTTA\tS521\t471\r\nTTAAGGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t471\r\nGCGGGGGG\tUnknown\tGGAGGGGG\tUnknown\t471\r\nCGTTCTAG\tA506,N702\tAAGGCTAT\tS520\t471\r\nTAGGCATG\tN706\tGATCCTTA\tS521\t470\r\nCGTATAGA\tUnknown\tGAGCCTTA\tS521\t470\r\nCTCCTCAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t470\r\nGGACTCCT\tN705\tTATCCCTC\tUnknown\t468\r\nGGGGGGGG\tUnknown\tGGCCGCGC\tUnknown\t467\r\nACGGGGGG\tUnknown\tGGAAGCGG\tUnknown\t467\r\nGGACTCCT\tN705\tGACCCTTA\tS521\t465\r\nGGCCTCCT\tN705\tGAGCCTTA\tS521\t463\r\nTCTCGAGG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t462\r\nCGTACTAG\tN702\tGACCTTAT\tUnknown\t461\r\nCGTACTAG\tN702\tGTGCCTTA\tA504,S521\t461\r\nCGTACTAG\tN702\tAGGGCTAT\tS520\t459\r\nTCCTGAGC\tN704\tGCGAGATC\tUnknown\t458\r\nGGACTCCT\tN705\tGAGCGTTA\tS521\t458\r\nGGGGGGCG\tUnknown\tGGACGCGG\tUnknown\t457\r\nGGACTCCT\tN705\tTATTCGTC\tUnknown\t455\r\nTAAGGCGA\tN701\tGTCGGCAG\tUnknown\t455\r\nGCGGGGGG\tUnknown\tGGCGGCGG\tUnknown\t454\r\nTATGCATG\tN706\tGAGCCTTA\tS521\t452\r\nTATAAGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t452\r\nTAGGCATG\tN706\tCAGCCTTA\tS521\t451\r\nCGTACTAG\tN702\tAAGGCTAC\tS520\t450\r\nGGGGGGGG\tUnknown\tGGATGAGG\tUnknown\t449\r\nGGACTCCT\tN705\tAAGGCAAT\tS520\t448\r\nCTCTCTAC\tN707\tCAGGCGTA\tUnknown\t448\r\nTAGGCATG\tN706\tTAGATGCT\tUnknown\t447\r\nTTCTCTGC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t447\r\nGGGGGGGG\tUnknown\tGGCTGAGG\tUnknown\t446\r\nTAAGGCGT\tN701\tAAGGAGTA\tS507,[N|S|E]507\t445\r\nTAGGCATG\tN706\tTAGATCGT\t[N|S|E]501\t445\r\nCTCATCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t445\r\nGGGCTACT\tUnknown\tAAGGCTAT\tS520\t445\r\nAGAGAGGA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t442\r\nCATCTCGT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t442\r\nTCCTACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t442\r\nCTCTCTAC\tN707\tCTCTCTTA\tUnknown\t441\r\nCTCTCCAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t440\r\nCATACTAG\tN702\tGAGCCTTA\tS521\t440\r\nCTCTCTAC\tN707\tACGGAGTG\tUnknown\t438\r\nTCCTAACT\tUnknown\tAAGGCTAT\tS520\t438\r\nGGAATCCT\tN705\tGAGCCTTA\tS521\t433\r\nGGGCCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t432\r\nGGGAGGGG\tUnknown\tGGGGGGGG\tUnknown\t432\r\nCTCTCTAC\tN707\tTCGACCTA\tA508\t431\r\nACGAAATG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t427\r\nTCCCAATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t427\r\nTAGGCATC\tN706\tGAGCCTTA\tS521\t426\r\nTAGGCATG\tN706\tTAGATCCT\tUnknown\t426\r\nCGTACTAG\tN702\tTAGGCTAT\tS520\t426\r\nGGGGTCCT\tUnknown\tAAGGCTAT\tS520\t425\r\nCTCTCTCC\tN707\tAAGGCGTA\tS507,[N|S|E]507\t424\r\nCTCCTCTA\tUnknown\tTCGACTAG\tS513\t424\r\nCTCTCTAC\tN707\tAAGAGTTC\tUnknown\t423\r\nTAGGCATA\tN706\tTAGATCGC\t[N|S|E]501\t423\r\nCTTCTCTA\tUnknown\tTCGACTAG\tS513\t423\r\nCGTACTTG\tN702\tAAGGCTAT\tS520\t423\r\nAGGCATGA\tUnknown\tTAGATCGC\t[N|S|E]501\t423\r\nCGTACTAT\tN702\tGAGCCTTA\tS521\t423\r\nGCGGGGGG\tUnknown\tGGAAGCGG\tUnknown\t421\r\nCGTAATAG\tN702,S518\tAAGGCTAT\tS520\t421\r\nTAAGGCGA\tN701\tAAAGGAGT\tUnknown\t421\r\nCTCTCTAC\tN707\tAAGATCGT\tUnknown\t421\r\nTCCTCAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t420\r\nTAAGGCGA\tN701\tTCGTCGGC\tUnknown\t420\r\nGGACTCCT\tN705\tGAGCCGTA\tS521\t419\r\nGGGCAGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t418\r\nCTCTTCAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t418\r\nGGACTCCT\tN705\tCGTCGGCA\tUnknown\t418\r\nGTCCTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t417\r\nCCCTCTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t417\r\nCTCTCTAC\tN707\tAGGGGGTG\tUnknown\t417\r\nTGAGCATC\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t417\r\nGCGGGGGG\tUnknown\tGGGCGGGG\tUnknown\t416\r\nCTTTACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t415\r\nCTCTCTAC\tN707\tACGGAGGA\tUnknown\t413\r\nGGGGGGGG\tUnknown\tGTGGGGGG\tUnknown\t412\r\nCTCTCCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t409\r\nCTCTCTAC\tN707\tGATGGCAC\tUnknown\t409\r\nAAGAAGTA\tS507,[N|S|E]507\tAAGGAGTA\tS507,[N|S|E]507\t408\r\nTCCTTGAG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t408\r\nGGCGAATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t407\r\nGGACTCCT\tN705\tAAGGATAG\tUnknown\t406\r\nCTCTCTAC\tN707\tAATTATTA\tUnknown\t404\r\nCTCTCTAC\tN707\tGCGGGGGG\tUnknown\t402\r\nCTCTCTAC\tN707\tCTCCGTCG\tUnknown\t402\r\nGGGGGGGG\tUnknown\tGGATGGGG\tUnknown\t400\r\nGGGTGGGG\tUnknown\tGGGGGGGG\tUnknown\t400\r\nGGGGGGGG\tUnknown\tGGGGGGGC\tUnknown\t400\r\nGGACTTCT\tN705\tGAGCCTTA\tS521\t397\r\nCTCTCTAC\tN707\tAAGAGTAC\tUnknown\t397\r\nAGGCGAAT\tD505\tCTCTCTAT\tE502,S502,[N|S|E]502\t394\r\nACGGGGGG\tUnknown\tGGAAGAGG\tUnknown\t393\r\nTCGAGCAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t393\r\nTCCTGACC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t392\r\nTAGGCTGA\tUnknown\tGAGCCTTA\tS521\t392\r\nCTCTCCCA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t392\r\nTAGGCATG\tN706\tGAGCATTA\tS521\t391\r\nGGGGGGGG\tUnknown\tGGGTGAGG\tUnknown\t391\r\nCGTACTGA\tUnknown\tGAGCCTTA\tS521\t390\r\nTAAGGCGA\tN701\tTTCGTCGG\tUnknown\t388\r\nCGTCCTAG\tN702\tGAGCCTTA\tS521\t388\r\nGGACACCT\tN705\tAAGGCTAT\tS520\t387\r\nCTCTCTAC\tN707\tTACTAGTC\tUnknown\t387\r\nACGGGGGG\tUnknown\tGGAGGGGG\tUnknown\t387\r\nCTCTACAC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t386\r\nCTCCCTCC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t386\r\nCTCCTGAG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t386\r\nCTTTTTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t385\r\nCCGAAATG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t385\r\nCTTCACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t385\r\nTCCCTACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t384\r\nCTCTCTAC\tN707\tAAGGCGGC\tUnknown\t384\r\nGGGGAGGG\tUnknown\tGGGGGGGG\tUnknown\t384\r\nACGAAGTG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t384\r\nCGTACTAG\tN702\tAAGGCGAT\tS520\t383\r\nTAGGCATG\tN706\tGCGCCTTA\tS521\t382\r\nTCCTGAGC\tN704\tTCGTCAGA\tUnknown\t382\r\nTAAAGGCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t382\r\nCTCTCTAC\tN707\tCACGAGTA\tUnknown\t381\r\nGGGGGGGG\tUnknown\tGCGGGGGG\tUnknown\t381\r\nTAAGGCGA\tN701\tCTCTTCGG\tUnknown\t381\r\nCGTACTAG\tN702\tGAGCCCTA\tS521\t380\r\nTAGGCATG\tN706\tGGCCTTAT\tUnknown\t377\r\nACGAAATG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t377\r\nTAAGGCCA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t376\r\nCTCTCTAC\tN707\tCTTCTCTA\tUnknown\t375\r\nAGACTCCT\tN705\tGAGCCTTA\tS521\t374\r\nTAAGGCGA\tN701\tAAGGCGTC\tUnknown\t373\r\nTTAAAGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t372\r\nGGGATCCT\tUnknown\tAAGGCTAT\tS520\t372\r\nAAGGAGTA\tS507,[N|S|E]507\tAAGGAGTA\tS507,[N|S|E]507\t371\r\nTAGGCATG\tN706\tAAGATCGC\t[N|S|E]501\t371\r\nCGTACTAG\tN702\tGAGCCTAA\tS521\t370\r\nAGGCGAAA\tD505\tCTCTCTAT\tE502,S502,[N|S|E]502\t370\r\nTAAGGCCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t370\r\nCTCTCTAC\tN707\tCTCGTCGG\tUnknown\t370\r\nGGACTCCT\tN705\tGCTATTCG\tUnknown\t368\r\nTAAGACGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t367\r\nGGACTACT\tN705\tGAGCCTTA\tS521\t367\r\nGGGGGGGG\tUnknown\tGGGGGGCG\tUnknown\t367\r\nCCCCTTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t366\r\nCGTACTAG\tN702\tGAGCCTTC\tS521\t366\r\nTGTACTAG\tA506,N702\tAAGGCTAT\tS520\t366\r\nTACGAATC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t365\r\nTAAGCCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t364\r\nTCTCTACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t364\r\nCCCCTCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t364\r\nCTCTCTAC\tN707\tGGGGAGTA\tUnknown\t363\r\nTAAGGGCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t361\r\nGGCCTTCT\tUnknown\tAAGGCTAT\tS520\t361\r\nCGTACTAG\tN702\tGGCTATTC\tUnknown\t359\r\nCGTACTAG\tN702\tGAGCCTCA\tS521\t359\r\nACGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t358\r\nCCCCTCTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t358\r\nGGCCTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t357\r\nCTCTCTAC\tN707\tACGTAGGA\tUnknown\t357\r\nTCCTGAGC\tN704\tTGTAAGAT\tUnknown\t356\r\nACGGGGGG\tUnknown\tGGGAGGGG\tUnknown\t356\r\nCTCTCTAC\tN707\tCTCTCGGC\tUnknown\t356\r\nCTCTCTAC\tN707\tCATTCGTC\tUnknown\t355\r\nTCTTACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t355\r\nCTCTCTAC\tN707\tAAGGTCGG\tUnknown\t354\r\nAAGAAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t354\r\nTCTCTAAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t353\r\nGGGGGCGG\tUnknown\tGGGGGGGG\tUnknown\t353\r\nTCCCATCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t352\r\nTCCTGAGC\tN704\tTCGTAAGT\tUnknown\t350\r\nGGACTCCT\tN705\tGAGCCTTG\tS521\t350\r\nAAGAAATA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t349\r\nTAGGCATA\tN706\tGAGCCTTA\tS521\t349\r\nCTTTCTTC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t349\r\nGGACTCCT\tN705\tAGCTATTC\tUnknown\t349\r\nACTAAGTG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t349\r\nTCTCAATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t348\r\nCGTACTAG\tN702\tAAGGGCTA\tUnknown\t347\r\nTCCCACCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t347\r\nCTCTGTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t346\r\nTGGCATGA\tUnknown\tGAGCCTTA\tS521\t345\r\nCTCTCTAC\tN707\tCGGCAGCG\tUnknown\t345\r\nGGGGGGGG\tUnknown\tCGCCGCGG\tUnknown\t345\r\nTAAGGCGA\tN701\tCTCCTCTA\tUnknown\t344\r\nAAGAAATG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t344\r\nTAAGGCGA\tN701\tAACAAATG\tUnknown\t344\r\nCTCTCTAC\tN707\tGCGAAAGA\tE517,S517,[N|S|E]517\t343\r\nTCCTGAGC\tN704\tACGTAATA\tUnknown\t343\r\nGGGCAACT\tUnknown\tAAGGCTAT\tS520\t343\r\nACGAAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t342\r\nCGTACTGG\tN702\tAAGGCTAT\tS520\t341\r\nGGGGGGCG\tUnknown\tGGGGGCGG\tUnknown\t340\r\nTCCTGAGC\tN704\tGGGTAAGA\tE517,S517,[N|S|E]517\t340\r\nGGACTCCT\tN705\tTTTCGTCG\tUnknown\t339\r\nGGGGGGGG\tUnknown\tGGTTGGGG\tUnknown\t338\r\nTAGTCATG\tN706\tTAGATCGC\t[N|S|E]501\t337\r\nTAGGCATG\tN706\tTAGCTCGC\t[N|S|E]501\t336\r\nTAAAGGGA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t336\r\nCCCCTCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t336\r\nCTCTCTAC\tN707\tCTTATTCG\tUnknown\t335\r\nTCCAGCAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t334\r\nTAAGGCGA\tN701\tCTCTTCTA\tUnknown\t334\r\nCTCTCTAC\tN707\tAATGAGTT\tUnknown\t334\r\nTAGGCATG\tN706\tTCGATCGC\t[N|S|E]501\t333\r\nCTCTCTAC\tN707\tAAGGATTT\tUnknown\t333\r\nTCTCACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t332\r\nTAGGCATG\tN706\tTAGACGCT\tUnknown\t332\r\nCTCTCTAC\tN707\tAATGCGTA\tUnknown\t332\r\nGGGGACCT\tUnknown\tAAGGCTAT\tS520\t331\r\nCTCTCTAC\tN707\tAAGGCTTT\tS520\t331\r\nCTCTCTAC\tN707\tGCCTAAGA\tE517,S517,[N|S|E]517\t331\r\nACTCCTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t331\r\nCTCTCTAC\tN707\tTCGAGTAC\tUnknown\t330\r\nCGTACAGA\tUnknown\tGAGCCTTA\tS521\t330\r\nTACGCATG\tN706\tTAGATCGC\t[N|S|E]501\t329\r\nCTCTCTAC\tN707\tGGGGGGTG\tUnknown\t329\r\nCTCTCTGC\tN707\tAAGCAGTA\tS507,[N|S|E]507\t329\r\nTCCTGAGC\tN704\tGCGTCAGC\tUnknown\t328\r\nCTCTCTAC\tN707\tGAGGAGTG\tUnknown\t328\r\nCTCTCTAC\tN707\tTAGTCGTC\tUnknown\t327\r\nGGGACTCC\tUnknown\tAAGGCTAT\tS520\t327\r\nTACGGCGC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t327\r\nTAAGGGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t327\r\nTTAAGGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t327\r\nCTCTCTAC\tN707\tGCGTAGTA\tN719\t327\r\nGGGGGGGG\tUnknown\tCGCGGGGG\tUnknown\t327\r\nCTCTCTAC\tN707\tCCCATATG\tUnknown\t326\r\nGGACTGCT\tN705\tAAGGCTAT\tS520\t326\r\nATCTCTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t325\r\nGGACTCCT\tN705\tGGGCCTTA\tS521\t325\r\nCGTTCTAG\tA506,N702\tGAGCCTTA\tS521\t325\r\nGGGGGGCG\tUnknown\tGGCGGGGG\tUnknown\t325\r\nCTCTTTAC\tE505,N707,S505,[N|S|E]505\tGCGTAAGA\tE517,S517,[N|S|E]517\t324\r\nCTGTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t323\r\nTAGTCATG\tN706\tGAGCCTTA\tS521\t323\r\nTGGCGAAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t323\r\nCTTCTTTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t323\r\nCCCTCTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t322\r\nCTTCCTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t321\r\nCTCTCTAC\tN707\tGCGTGAGG\tUnknown\t321\r\nGGGCTGCG\tUnknown\tGGGGGGGG\tUnknown\t321\r\nACGGGGGG\tUnknown\tGGCAGAGG\tUnknown\t319\r\nGTACTCCT\tN705\tGAGCCTTA\tS521\t319\r\nCTCTCTAC\tN707\tCTCCTCTA\tUnknown\t318\r\nAAGGGGGG\tUnknown\tGGAAGCGG\tUnknown\t318\r\nCTCTATCT\tUnknown\tTCGACTAG\tS513\t317\r\nCCTTTTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t317\r\nGGGGGGGG\tUnknown\tGGCCGTGG\tUnknown\t317\r\nGGACTCCT\tN705\tTTCTTCGT\tUnknown\t316\r\nCAGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t316\r\nACGGGGGG\tUnknown\tGGCCGCGG\tUnknown\t316\r\nCTCCATCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t315\r\nGGACTTCC\tUnknown\tAAGGCTAT\tS520\t314\r\nGGACTCCT\tN705\tAAGGGTAA\tUnknown\t314\r\nCGTACTAG\tN702\tGAGCCTGA\tS521\t314\r\nAATAAAGA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t314\r\nTAAGGCGA\tN701\tCTCTCCTA\tUnknown\t314\r\nCTCTCTAC\tN707\tTCGCCTAT\tUnknown\t313\r\nCTCTCTAC\tN707\tGCGGAAGA\tE517,S517,[N|S|E]517\t313\r\nTTAGGCGA\tN701,S522\tAAGGAGTA\tS507,[N|S|E]507\t312\r\nAAGGGGGG\tUnknown\tGGAAGAGG\tUnknown\t311\r\nCTTTCTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t311\r\nCTCTCTAC\tN707\tTCTACTAT\tE504,[N|S|E]504\t311\r\nACGAAACG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t311\r\nTAAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t311\r\nGCGGGGGG\tUnknown\tGGAAGAGG\tUnknown\t310\r\nGGGGGGGG\tUnknown\tGGCGGTGG\tUnknown\t310\r\nGCGGGGGG\tUnknown\tGGGCGCGG\tUnknown\t309\r\nTAGGCATG\tN706\tTAAATCGC\t[N|S|E]501\t309\r\nTAGCGAAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t309\r\nCCTCCCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t308\r\nTTTAAGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t308\r\nGGGGGGGG\tUnknown\tGGACGTGG\tUnknown\t308\r\nCGTACTAG\tN702\tAAGGCTCT\tS520\t306\r\nGATCTCGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t306\r\nGGGCTGCT\tUnknown\tAAGGCTAT\tS520\t306\r\nAATAAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t305\r\nGGGGGGGG\tUnknown\tGGACGCGC\tUnknown\t304\r\nCTCTCTAC\tN707\tGCGGAGGA\tUnknown\t304\r\nCTCTCTAC\tN707\tTCGACTTC\tN729\t304\r\nACTAAATG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t304\r\nTATAAGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t304\r\nCTCTCTAC\tN707\tAGGGAGGG\tUnknown\t303\r\nTTCTACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t302\r\nCTATCTCG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t302\r\nCTACATCT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t301\r\nAATAAGTG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t301\r\nACGGGGGG\tUnknown\tGGACGCGG\tUnknown\t301\r\nCTCTCTAC\tN707\tCTCATTCG\tUnknown\t301\r\nCTCTCGAC\tN707\tGGGGGGGG\tUnknown\t300\r\nGGGGGGGG\tUnknown\tGGTGGTGG\tUnknown\t300\r\nCTCTCTAC\tN707\tAGGGAGGA\tUnknown\t300\r\nATCTCGTA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t299\r\nTCTACATC\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t298\r\nGGACTCCT\tN705\tAAGTATTC\tUnknown\t297\r\nCTCTCTAC\tN707\tAAGGATTC\tUnknown\t297\r\nACTAAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t297\r\nTCCTGGAG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t297\r\nCGTACCAG\tN702\tAAGGCTAT\tS520\t296\r\nTGGCGAAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t296\r\nGGTCTACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t296\r\nGCGGGGGG\tUnknown\tGGCAGAGG\tUnknown\t295\r\nCTCTCTAC\tN707\tTCGTACGA\tUnknown\t294\r\nTAAGGCGA\tN701\tAAGGATCG\tUnknown\t293\r\nGGGGGGGG\tUnknown\tGGCGGGGC\tUnknown\t292\r\nCCGAAGTG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t292\r\nGCGGGGGG\tUnknown\tGGGAGGGG\tUnknown\t292\r\nAATAAGTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t291\r\nGGACTCCT\tN705\tTATCTCGT\tUnknown\t291\r\nAATAAGTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t291\r\nAAAAAAAA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t290\r\nTCCTGAGC\tN704\tGCAAGATC\tUnknown\t290\r\nCTATCTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t290\r\nCTCCTATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t290\r\nCCTCTGTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t290\r\nGGACTCCT\tN705\tTATCCCGT\tUnknown\t290\r\nGGGGGGGG\tUnknown\tGGGCGTGG\tUnknown\t289\r\nCTTACATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t289\r\nCGTAACTG\tUnknown\tAAGGCTAT\tS520\t288\r\nCCTCTATT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t288\r\nGGGGGGGG\tUnknown\tGGGGAGGG\tUnknown\t288\r\nAAGAAAGA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t288\r\nCTCTCTAC\tN707\tTCTTAAGA\tUnknown\t287\r\nGGACCTCC\tUnknown\tAAGGCTAT\tS520\t287\r\nAATAAATG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t286\r\nTAAGGCGA\tN701\tCTCGTCGG\tUnknown\t286\r\nCTCTCTAC\tN707\tTTCGACTA\tUnknown\t286\r\nCGCACTAG\tN702\tGAGCCTTA\tS521\t285\r\nGGACTCCT\tN705\tAGGCTTTC\tUnknown\t285\r\nGGGGGGGG\tUnknown\tGGCAGTGG\tUnknown\t284\r\nCCCTCTTC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t284\r\nGGGGGGGG\tUnknown\tGGTTGCGG\tUnknown\t283\r\nGGGATCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t283\r\nGGACTCTT\tN705\tGAGCCTTA\tS521\t283\r\nTCCTGAGC\tN704\tCCGTCAGA\tUnknown\t283\r\nGGTCTGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t282\r\nACTCTCTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t282\r\nCTCTTAAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t281\r\nCTCTCTAC\tN707\tAGGGAGTG\tUnknown\t281\r\nGGGGGGGC\tUnknown\tGGGGGGGG\tUnknown\t281\r\nTCCTGAGC\tN704\tGCGTTAAG\tUnknown\t281\r\nTAGGAATG\tN706\tTAGATCGC\t[N|S|E]501\t281\r\nGGACTTAT\tUnknown\tAAGGCTAT\tS520\t279\r\nTAGGATGA\tUnknown\tGAGCCTTA\tS521\t278\r\nCTCTCAAC\tN707\tTCGACTAG\tS513\t278\r\nTAAGGCGA\tN701\tAAGGTATC\tUnknown\t278\r\nTCCTGAGC\tN704\tTCTAAGAT\tUnknown\t278\r\nCTCTCTAC\tN707\tTCGAATAC\tUnknown\t278\r\nCTTCTAAT\tS510\tAAGGAGTA\tS507,[N|S|E]507\t278\r\nCAGAGAGG\tN708\tACGTAAGA\tE517,S517,[N|S|E]517\t278\r\nTCCTAATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t278\r\nCTCTCTTT\tE502,S502,[N|S|E]502\tAAGGAGTA\tS507,[N|S|E]507\t278\r\nCCTTCTTC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t278\r\nCGTACTAG\tN702\tGAACCTTA\tS521\t278\r\nGGCCTATC\tUnknown\tAAGGCTAT\tS520\t277\r\nACGGGGGG\tUnknown\tGGGGGCGG\tUnknown\t277\r\nGGACTCCT\tN705\tTATCCTTA\tUnknown\t276\r\nCTCTCTAC\tN707\tGGGGAGGG\tUnknown\t276\r\nCTCTCTAC\tN707\tATGAGTAT\tUnknown\t275\r\nGGGGGCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t275\r\nAATAAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t275\r\nGGGGGGCG\tUnknown\tGGGCGGGG\tUnknown\t275\r\nCTCTCTAC\tN707\tCTTTCGTC\tUnknown\t275\r\nGGACTCCT\tN705\tTATCGGCA\tUnknown\t274\r\nGGGCCCCC\tUnknown\tAAGGCTAT\tS520\t273\r\nCCCCCCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t273\r\nACGGGGGG\tUnknown\tGGAAGGGG\tUnknown\t273\r\nCGCTAGAT\tUnknown\tGAGCCTTA\tS521\t273\r\nCTGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t272\r\nGGACTCCT\tN705\tAAGGGTAG\tUnknown\t272\r\nCCTCCCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t272\r\nGGGGGGGG\tUnknown\tGGGGCGGG\tUnknown\t272\r\nCTCTCTAC\tN707\tCGGGGGGG\tUnknown\t272\r\nTACGCATG\tN706\tGAGCCTTA\tS521\t271\r\nGGGGGGGT\tUnknown\tGGGGGGGG\tUnknown\t271\r\nCTCTCTAC\tN707\tTTCGTCGG\tUnknown\t271\r\nTCCTGAGC\tN704\tACGTAGGA\tUnknown\t271\r\nTCTAAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t271\r\nTTCCTGAG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t270\r\nGGACTCCT\tN705\tGAGCATTT\tUnknown\t270\r\nTAGCCATG\tN706\tTAGATCGC\t[N|S|E]501\t270\r\nAAGGAGTG\tS507,[N|S|E]507\tAAGGAGTA\tS507,[N|S|E]507\t270\r\nGGGGGGCG\tUnknown\tGGTCGCGG\tUnknown\t270\r\nAAGGGGGG\tUnknown\tGGCAGCGG\tUnknown\t270\r\nGGGCTTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t269\r\nCTCCTTTC\tE505,S505,[N|S|E]505\tAAGGAGTA\tS507,[N|S|E]507\t269\r\nGGACTCCT\tN705\tAAGGTTCG\tA501\t269\r\nGGGAACCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t268\r\nGGGGGGCG\tUnknown\tGGAGGGGG\tUnknown\t268\r\nCTCTCTAC\tN707\tGAGGGGTG\tUnknown\t268\r\nCTCTCTAC\tN707\tAAGATATC\tUnknown\t268\r\nTAAGGCAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t268\r\nCCTGGGGG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t268\r\nTTCTCTAC\tN707\tAAGGCGTA\tS507,[N|S|E]507\t267\r\nTAAGGCGA\tN701\tCTCTCGGC\tUnknown\t267\r\nTCTGAGCA\tUnknown\tTCGTAAGA\tE517,S517,[N|S|E]517\t267\r\nCCTAAATG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t267\r\nTCCCTCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t267\r\nTAGGCATG\tN706\tTATCGCTC\tN723\t266\r\nGGACGCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t266\r\nGGACTCCT\tN705\tATATTCGT\tUnknown\t265\r\nCCTCTGCG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t265\r\nCGTACTAG\tN702\tGAGCCGTA\tS521\t265\r\nGGACTCCT\tN705\tGAGCCATA\tS521\t265\r\nTCTCAACT\tUnknown\tAAGGCTAT\tS520\t264\r\nAAGAAAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t264\r\nCTCTCTAC\tN707\tAACGCGTT\tUnknown\t263\r\nGGGGGGCG\tUnknown\tGGGCGCGG\tUnknown\t263\r\nTAGGCATG\tN706\tCAGATCGC\t[N|S|E]501\t263\r\nGCGGGGGG\tUnknown\tGGAGGCGG\tUnknown\t263\r\nTATAGGGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t263\r\nCTCTCTAC\tN707\tGGCGTAAG\tUnknown\t263\r\nCTGTCTAC\tN707\tTCGACTAG\tS513\t263\r\nACTAAACG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t262\r\nTAGGGATG\tN706\tTAGATCGC\t[N|S|E]501\t262\r\nCTCTCTAC\tN707\tAAGGCTAA\tS520\t262\r\nCCTCCTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t262\r\nCCGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t262\r\nGGGGGGCG\tUnknown\tGGCAGCGG\tUnknown\t261\r\nTAGGCATG\tN706\tGATCGCTC\tUnknown\t261\r\nGCGGGGGG\tUnknown\tGGTGGGGG\tUnknown\t261\r\nGGACTCCT\tN705\tGATGGCAC\tUnknown\t260\r\nGGACTCCT\tN705\tAAGGGTAC\tUnknown\t260\r\nACTAAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t260\r\nTAAGGCGA\tN701\tAAGGAATC\tUnknown\t260\r\nCTCTCTAC\tN707\tGCGTAATC\tUnknown\t259\r\nCTCTCTAC\tN707\tTAGAGGCC\tUnknown\t259\r\nCGTACTTG\tN702\tGAGCCTTA\tS521\t259\r\nCTCTCCTA\tUnknown\tTCGACTAG\tS513\t259\r\nGGACCCCT\tN705\tGAGCCTTA\tS521\t258\r\nCTCTCTAC\tN707\tTCGACAAG\tS513\t257\r\nTTCGCTAC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t256\r\nGGACTCCT\tN705\tTATCCGTC\tUnknown\t256\r\nGGGCAGCG\tUnknown\tGGGGGGGG\tUnknown\t255\r\nGGGAAACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t255\r\nCTCTCTAC\tN707\tCCCCTATT\tUnknown\t255\r\nCTCTTATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t254\r\nGGACTCCT\tN705\tTTCCTCTC\tUnknown\t254\r\nTAAGTCTA\tA508\tCTCTCTAT\tE502,S502,[N|S|E]502\t254\r\nGCGGGGGG\tUnknown\tGGCCGGGG\tUnknown\t253\r\nGGACATCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t253\r\nGGGGGGAG\tUnknown\tGGGGGGGG\tUnknown\t253\r\nCGTACTAG\tN702\tGAGTCTTA\tA504,S521\t253\r\nTCCTGAGC\tN704\tTCGTAAAT\tUnknown\t252\r\nGGGGGGCG\tUnknown\tGGACGAGG\tUnknown\t252\r\nCTCTCTAC\tN707\tTCCTAGTC\tUnknown\t252\r\nACGAAGTG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t252\r\nCTCTCTAC\tN707\tTCGAACTA\tUnknown\t252\r\nCTCTCTAC\tN707\tAAGGCAGC\tUnknown\t251\r\nGGGCGGGG\tUnknown\tGGGGGCGG\tUnknown\t251\r\nTCCTGAGC\tN704\tGCGTTAGA\tE517,S517,[N|S|E]517\t251\r\nCTCTCACA\tUnknown\tAGGAGTAT\tUnknown\t251\r\nAAAAAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t251\r\nTAGGCCTG\tN706\tTAGATCGC\t[N|S|E]501\t250\r\nCTCTCGAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t250\r\nTCCTGAGC\tN704\tTTAAGATC\tUnknown\t249\r\nCTCTCTAC\tN707\tCTCGCGAT\tUnknown\t249\r\nCCTCTACT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t249\r\nGGACTCCT\tN705\tCGAGCCTT\tUnknown\t249\r\nACGGGGGG\tUnknown\tGGCGGCGG\tUnknown\t248\r\nACGGGGGG\tUnknown\tGGCAGGGG\tUnknown\t248\r\nCAGAGAGG\tN708\tGCGTACGA\tE517,S517,[N|S|E]517\t248\r\nCTCTCTAG\tE502,N707,S502,[N|S|E]502\tCTCTCTAT\tE502,S502,[N|S|E]502\t247\r\nTAAGGCGA\tN701\tAAGGGGTG\tUnknown\t247\r\nTATCTCGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t247\r\nGCGGGGGG\tUnknown\tGGACGAGG\tUnknown\t247\r\nTTGAGCAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t246\r\nACTAAATA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t246\r\nCTCTCTAC\tN707\tACGGCGTG\tUnknown\t246\r\nAAAAAAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t245\r\nCTTTCTAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t245\r\nCTCTTCTA\tUnknown\tTCGACTAG\tS513\t245\r\nCCTCTCTT\tUnknown\tTCGACTAG\tS513\t245\r\nAAGGGGGG\tUnknown\tGGAGGGGG\tUnknown\t245\r\nGGGGGGCG\tUnknown\tGGAAGCGG\tUnknown\t244\r\nCTTCTTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t244\r\nTCCTGAGC\tN704\tGCGTCAGG\tUnknown\t244\r\nTCTACATC\tUnknown\tTCGACTAG\tS513\t244\r\nCTCTCTCC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t243\r\nGGGACCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t243\r\nTAAGGCGA\tN701\tCATTCGTC\tUnknown\t243\r\nTCTCTACA\tUnknown\tAGGAGTAT\tUnknown\t242\r\nTAGGCATG\tN706\tGAGCCTAA\tS521\t242\r\nTCTCACCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t242\r\nCTCGCTAC\tN707\tGGGGGGGG\tUnknown\t241\r\nGGACCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t240\r\nAAGGGGGG\tUnknown\tGGCAGAGG\tUnknown\t240\r\nAATAAGTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t240\r\nAAAAAACA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t240\r\nGGGGGGGG\tUnknown\tGGGTGTGG\tUnknown\t240\r\nGGACTCCT\tN705\tAATTCTAT\tUnknown\t240\r\nGGACTCGT\tN705\tGAGCCTTA\tS521\t239\r\nTAGGTATG\tN706\tTAGATCGC\t[N|S|E]501\t239\r\nTAGGATGA\tUnknown\tTAGATCGC\t[N|S|E]501\t239\r\nCGCTCTAC\tN707\tGGGGGGGG\tUnknown\t238\r\nGCGGGGGG\tUnknown\tGGCTGCGG\tUnknown\t238\r\nCTCTCACT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t238\r\nCTCTTCAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t238\r\nGGGGGGCG\tUnknown\tGGTGGGGG\tUnknown\t237\r\nCTCTCTAC\tN707\tAGTCGGCA\tUnknown\t236\r\nTCCTGAGC\tN704\tTCGTAGAT\tUnknown\t235\r\nTAGGCATG\tN706\tGTGCCTTA\tA504,S521\t235\r\nGCGGGGGG\tUnknown\tGGACGGGG\tUnknown\t235\r\nGGGCAGCT\tUnknown\tAAGGCTAT\tS520\t235\r\nCCTAAGTG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t234\r\nTAAGGCGA\tN701\tCTCTCTTA\tUnknown\t234\r\nTAAGGCGA\tN701\tAAGTATTA\tUnknown\t234\r\nAAGAAATG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t234\r\nATCTCGTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t233\r\nTAAGGCGA\tN701\tCTCTCCGG\tUnknown\t233\r\nTAGCCATG\tN706\tGAGCCTTA\tS521\t233\r\nCTCCTACC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t233\r\nCTCTCTAC\tN707\tCACGCGTA\tUnknown\t232\r\nTAAGGCGA\tN701\tATTCGTCG\tUnknown\t232\r\nCGTACTCG\tN702\tAAGGCTAT\tS520\t232\r\nCGTACTAG\tN702\tAAGGATAA\tUnknown\t231\r\nCTCTCGCC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t231\r\nCTCTCTAC\tN707\tAAGGAGAC\tUnknown\t231\r\nACGAAGTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t231\r\nCCTCTCCA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t230\r\nCTCTCTGC\tN707\tAAGAAGTA\tS507,[N|S|E]507\t230\r\nAGGCGAAT\tD505\tAAGGAGTA\tS507,[N|S|E]507\t230\r\nGGCCTCCC\tUnknown\tAAGGCTAT\tS520\t230\r\nGGGGGGGG\tUnknown\tAGGGGGGG\tUnknown\t230\r\nGGGGGGGG\tUnknown\tGGAAGTGG\tUnknown\t229\r\nCTCTCTAC\tN707\tACAGAGTA\tUnknown\t229\r\nACTAAATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t229\r\nGGGGGGTG\tUnknown\tGGTGGGGG\tUnknown\t228\r\nCTCTCTAC\tN707\tGAGGAGGG\tUnknown\t228\r\nCTCTCTAC\tN707\tCCGGAGTA\tUnknown\t228\r\nCTCTCTAC\tN707\tACGGGGGG\tUnknown\t228\r\nGGACTCCT\tN705\tAAGGATTC\tUnknown\t227\r\nCTCTCTAC\tN707\tTCGACTTA\tUnknown\t227\r\nCTCCTATC\tUnknown\tAAGGCTAT\tS520\t227\r\nCTCTCTAC\tN707\tAAGGCGAT\tS520\t226\r\nTAGGCATG\tN706\tTACATCGC\t[N|S|E]501\t226\r\nGCGGGGGG\tUnknown\tGGGTGGGG\tUnknown\t226\r\nGAGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t226\r\nAATAAATG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t225\r\nTAAGGCGA\tN701\tCTCGGCAG\tUnknown\t225\r\nCCGCTCTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t225\r\nTCGTGAGC\tN704\tGCGTAAGA\tE517,S517,[N|S|E]517\t224\r\nAAGAAGTA\tS507,[N|S|E]507\tCTCTCTAT\tE502,S502,[N|S|E]502\t224\r\nACGAAGCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t223\r\nGGGCGCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t223\r\nTAAGGCGA\tN701\tCCCCTATT\tUnknown\t222\r\nTCCTGAGC\tN704\tAACAAATG\tUnknown\t222\r\nGGACTCCG\tN705\tAAGGCTAT\tS520\t222\r\nCGTACTGG\tN702\tGAGCCTTA\tS521\t222\r\nCCTCACTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t221\r\nAAGAAGTG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t221\r\nTCCTGAGC\tN704\tGCGTAACG\tUnknown\t221\r\nGAGGGGGG\tUnknown\tGGAGGGGG\tUnknown\t221\r\nACGAAGTG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t221\r\nGGGGGGGG\tUnknown\tGGCGGCGC\tUnknown\t221\r\nCGTACTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t220\r\nGGGGGGGG\tUnknown\tTGGGGCGG\tUnknown\t220\r\nTCTCTAGG\tS516\tGCGTAAGA\tE517,S517,[N|S|E]517\t220\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tAGGAGTAT\tUnknown\t220\r\nGGACTCCT\tN705\tACTATTCG\tUnknown\t220\r\nCTCTCCAT\tE502,S502,[N|S|E]502\tTCGACTAG\tS513\t219\r\nGGGGGGGG\tUnknown\tGGTCGTGG\tUnknown\t219\r\nCGTACTAG\tN702\tGACCCTTA\tS521\t219\r\nCTCTCTAC\tN707\tAGGGGGTA\tUnknown\t219\r\nGGACTCCT\tN705\tCTTCGTCG\tUnknown\t219\r\nGCGGGGGG\tUnknown\tGGCCGCGC\tUnknown\t219\r\nACTAAGTG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t219\r\nTCCTGCGC\tN704\tGCGTATGA\tE517,S517,[N|S|E]517\t218\r\nTGGCATGA\tUnknown\tTAGATCGC\t[N|S|E]501\t218\r\nCGTACTAG\tN702\tAAGGCATT\tUnknown\t218\r\nACGAAATG\tUnknown\tAAGGCTAT\tS520\t218\r\nCTCTCTAC\tN707\tGGCAGCGT\tUnknown\t217\r\nCTCTCTAC\tN707\tCTTCGGCA\tUnknown\t217\r\nGGACTAGA\tUnknown\tAAGGCTAT\tS520\t217\r\nGGGGGGTG\tUnknown\tGGAGGGGG\tUnknown\t217\r\nCTCTCTAC\tN707\tACGGCTAG\tUnknown\t216\r\nGGACTCCT\tN705\tAAGGCCTA\tUnknown\t216\r\nCTCTCTAC\tN707\tATCGCTAT\tUnknown\t216\r\nTAGGCATG\tN706\tGAGCCCTA\tS521\t216\r\nGGGGGGGG\tUnknown\tGGTTGAGG\tUnknown\t216\r\nCGTTACTA\tUnknown\tAAGGCTAT\tS520\t216\r\nACTAAATG\tUnknown\tAAGGCTAT\tS520\t215\r\nGGGGGGGG\tUnknown\tGGTGTGGG\tUnknown\t215\r\nTTCTCTGC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t215\r\nCTCTCTAC\tN707\tAACAAATG\tUnknown\t215\r\nGCGGGGGG\tUnknown\tGGCCGAGG\tUnknown\t214\r\nTCCTTAGC\tN704\tTCGTAAGA\tE517,S517,[N|S|E]517\t214\r\nCGCTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t214\r\nCAGAGAGG\tN708\tGGTAAGAT\tUnknown\t214\r\nCTCTCTAC\tN707\tCTCTGTCG\tUnknown\t214\r\nCTCTCTAC\tN707\tTCGACGTC\tN729\t214\r\nCCTTTCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t214\r\nGTACTAGA\tUnknown\tTCGACTAG\tS513\t213\r\nCCCCTCCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t213\r\nCTCTCTAC\tN707\tAAGGGTTC\tUnknown\t213\r\nCTCTCTAC\tN707\tATTCGTCG\tUnknown\t213\r\nGCACTCCT\tN705\tAAGGCTAT\tS520\t213\r\nTCCTGAGC\tN704\tGCGTAGTC\tN719\t213\r\nGGGCTCCC\tUnknown\tGAGCCTTA\tS521\t212\r\nGGACTCCT\tN705\tAATGCTCT\tUnknown\t212\r\nTCCTTAGG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t212\r\nGGACTCCT\tN705\tAAGGCTCG\tUnknown\t212\r\nCAGAGAGG\tN708\tGCGTAAGT\tE517,S517,[N|S|E]517\t211\r\nTAGGCATG\tN706\tGAGCCTGA\tS521\t211\r\nACTCTCCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t211\r\nCTCTCTAC\tN707\tAGGGGGGA\tUnknown\t211\r\nCTCTCTAC\tN707\tGCGTTAGA\tE517,S517,[N|S|E]517\t210\r\nGGACTCCT\tN705\tGCCTTATC\tUnknown\t210\r\nCGTAAATG\tUnknown\tAAGGCTAT\tS520\t210\r\nGCGGGGGG\tUnknown\tGGTCGCGG\tUnknown\t210\r\nCGTAATTG\tUnknown\tAAGGCTAT\tS520\t209\r\nCTCTTACA\tUnknown\tAGGAGTAT\tUnknown\t209\r\nCTCTCAAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t209\r\nTTAAGGCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t209\r\nGGGCCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t209\r\nACTAAGTG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t208\r\nTCCTGATC\tN704\tTCGTAAGA\tE517,S517,[N|S|E]517\t208\r\nCTCTCCCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t208\r\nCTCTCTAC\tN707\tATCGAGTA\tUnknown\t208\r\nGAGGGGGG\tUnknown\tGGAAGCGG\tUnknown\t207\r\nACTCCTAT\tUnknown\tAAGGCTAT\tS520\t207\r\nTAAAGGGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t206\r\nTAAGGCGA\tN701\tCTTCTCTA\tUnknown\t206\r\nGGGGGGGG\tUnknown\tGGAGGGGC\tUnknown\t206\r\nGGGATACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t206\r\nGCGGGGGG\tUnknown\tGGGAGCGG\tUnknown\t206\r\nTAAGGCGA\tN701\tAAGGTGTT\tUnknown\t206\r\nTGTACTAG\tA506,N702\tGAGCCTTA\tS521\t205\r\nACTAAGTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t205\r\nCTCTCCAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t205\r\nTAAAAAGG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t205\r\nGAGGGGGG\tUnknown\tGGAAGAGG\tUnknown\t205\r\nAAGGGGGG\tUnknown\tGGGAGGGG\tUnknown\t204\r\nGGGGGGCG\tUnknown\tGGCGGCGG\tUnknown\t204\r\nTAAGGCGA\tN701\tTCTCTATC\tUnknown\t204\r\nTAGGCATG\tN706\tTTGATCGC\t[N|S|E]501\t204\r\nGGGAAGTG\tUnknown\tGGGGGGGG\tUnknown\t203\r\nGGGGGGTG\tUnknown\tGGACGCGG\tUnknown\t203\r\nCTCTCTAC\tN707\tTCGTCAGA\tUnknown\t203\r\nTAAGCGAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t203\r\nGGGAAGCG\tUnknown\tGGGGGGGG\tUnknown\t203\r\nCTCTCTAC\tN707\tGAGGGGGA\tUnknown\t203\r\nCTCCACAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t202\r\nAGTACTAG\tN702\tAAGGCTAT\tS520\t202\r\nTAAGGCGA\tN701\tAAGGAGCG\tUnknown\t202\r\nCGTACTAG\tN702\tGAGACTTA\tS521\t202\r\nCTCTCTAC\tN707\tAATCGGCA\tUnknown\t202\r\nCAGAGAGG\tN708\tCCGTAAGA\tE517,S517,[N|S|E]517\t202\r\nCGTAATAG\tN702,S518\tGAGCCTTA\tS521\t202\r\nGGGGAACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t202\r\nACGAAAGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t202\r\nTACATCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t202\r\nCTCTCTAC\tN707\tAGAAGTAT\tUnknown\t201\r\nCGGGCGGG\tUnknown\tGGGGGGGG\tUnknown\t201\r\nGGACTCCT\tN705\tATCCTCTC\tUnknown\t201\r\nGGTCTCCT\tN705\tGAGCCTTA\tS521\t201\r\nCGTACTAG\tN702\tGGGCCTTA\tS521\t201\r\nGGGGGGGG\tUnknown\tGGAGGTGG\tUnknown\t201\r\nTAAGGCGA\tN701\tAAGGCTAT\tS520\t201\r\nCTCTCTAC\tN707\tCCCCCTAT\tUnknown\t200\r\nTACGAATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t200\r\nGCGGGGGG\tUnknown\tGGGGGAGG\tUnknown\t200\r\nGGACTCCT\tN705\tTAGCCTTT\tUnknown\t200\r\nCTCCTACA\tUnknown\tAGGAGTAT\tUnknown\t199\r\nCCTTTCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t199\r\nGGGGGGGG\tUnknown\tCGCGGCGG\tUnknown\t199\r\nACGGGGGG\tUnknown\tGGCTGCGG\tUnknown\t198\r\nTAAGGGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t198\r\nTCCTGAGA\tD702,N704\tTCGTAAGA\tE517,S517,[N|S|E]517\t198\r\nGGGGGTGG\tUnknown\tGGGGGGGG\tUnknown\t198\r\nGGGGGGGG\tUnknown\tCGACGCGG\tUnknown\t198\r\nGGGCGGGG\tUnknown\tGGCCGCGG\tUnknown\t198\r\nGGACTCCT\tN705\tGCGTAAGA\tE517,S517,[N|S|E]517\t198\r\nTCAGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t197\r\nCTCTCTAC\tN707\tGCGTCAGT\tUnknown\t197\r\nGGGGGGGG\tUnknown\tGGCCGCCG\tUnknown\t197\r\nGTCTCTCC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t196\r\nGGACTCCT\tN705\tGTCGGCAG\tUnknown\t196\r\nGGGGGGGG\tUnknown\tCGGGGCGG\tUnknown\t196\r\nCTCTCTAC\tN707\tAGTAGTAT\tUnknown\t196\r\nCTCCCCAC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t196\r\nGGACTCCT\tN705\tGAGGCCTT\tUnknown\t196\r\nCAGAGAGG\tN708\tAAGGAGTA\tS507,[N|S|E]507\t196\r\nCTCTTCTA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t196\r\nCTTACTAG\tN702,S518\tAAGGCTAT\tS520\t196\r\nCTCTCTAC\tN707\tAAGCGGCA\tN711\t195\r\nTAAGGCGA\tN701\tAACTCTAT\tUnknown\t195\r\nTCGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t195\r\nCCTCTGCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t195\r\nTAGGCATG\tN706\tTGGATCGC\t[N|S|E]501\t194\r\nCTCTCATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t194\r\nCTCTCTAC\tN707\tCCGTCAGA\tUnknown\t193\r\nGGGGGGCG\tUnknown\tGGAAGAGG\tUnknown\t193\r\nTAAGGCGA\tN701\tCGGCAGCG\tUnknown\t193\r\nCTCTCTAC\tN707\tAAGGGTCG\tUnknown\t193\r\nTCCTGAGC\tN704\tACGCGTAA\tUnknown\t193\r\nCTCTCTAC\tN707\tAAGGATAC\tUnknown\t192\r\nACGAAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t192\r\nGGACTCCT\tN705\tGGTCCTCT\tUnknown\t192\r\nAGGCGGAA\tN703\tCTCTCTAT\tE502,S502,[N|S|E]502\t191\r\nTAAGGCGA\tN701\tCATGGCAC\tUnknown\t191\r\nTCCGGAGC\tD702,N704\tTCGTAAGA\tE517,S517,[N|S|E]517\t191\r\nGGGGGGGG\tUnknown\tTGTGGGGG\tUnknown\t191\r\nCTCTTCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t191\r\nTCCCAATT\tUnknown\tAAGGCTAT\tS520\t191\r\nCGTACTAG\tN702\tAAGCCTAT\tS520\t189\r\nCTCTCTAC\tN707\tTAGGGGCC\tUnknown\t189\r\nGGGCGCCT\tUnknown\tAAGGCTAT\tS520\t189\r\nGGCCTTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t189\r\nCTCCCTCC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t189\r\nACGGGGGG\tUnknown\tGGAGGCGG\tUnknown\t189\r\nCTCTCTAC\tN707\tACGTAATA\tUnknown\t189\r\nCGTACTAG\tN702\tAAGGCTTC\tUnknown\t189\r\nGGACTCCT\tN705\tGAGGCTTA\tS521\t189\r\nAATAAAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t189\r\nGAGGGGGG\tUnknown\tGGCAGCGG\tUnknown\t188\r\nGGGGGGGG\tUnknown\tGGTAGTGG\tUnknown\t188\r\nACTAAATT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t188\r\nCGTACTAG\tN702\tTCGACTAT\tS513\t188\r\nCTCTCTAC\tN707\tGAGGCGTA\tUnknown\t188\r\nCAGAGAGG\tN708\tGCGTAGAT\tUnknown\t188\r\nAATAAGTG\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t188\r\nCCCTACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t187\r\nCTCTCTAC\tN707\tGCGGTAAG\tUnknown\t187\r\nGGGCTTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t187\r\nCCGGGGGG\tUnknown\tGGGGGCGG\tUnknown\t187\r\nCTCTCTAC\tN707\tGAGTAGTA\tN719\t187\r\nGGGGGGGG\tUnknown\tGGACGAGC\tUnknown\t186\r\nCTCTCTAC\tN707\tGGGGAGTG\tUnknown\t186\r\nCTCTCTAC\tN707\tACGGCGAA\tUnknown\t186\r\nCCTAAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t186\r\nCCCTCTTC\tUnknown\tTCGACTAG\tS513\t186\r\nTAAGGCGA\tN701\tCTCGCGAT\tUnknown\t185\r\nTCTACATC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t185\r\nAAAAAGTA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t185\r\nCTCTCTAC\tN707\tCTGGAGTA\tUnknown\t185\r\nTCGGAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t185\r\nCGACTCCT\tN705\tAAGGCTAT\tS520\t185\r\nGGACTCCT\tN705\tTATCTTCA\tUnknown\t184\r\nGAACTCCT\tN705\tGAGCCTTA\tS521\t184\r\nCTCTCTAC\tN707\tACGGATTA\tUnknown\t184\r\nCTCTCTAC\tN707\tCTCTCCAC\tN707\t183\r\nGGGGGGGG\tUnknown\tGGGAGTGG\tA712\t183\r\nTCCTGAGC\tN704\tTCGTATGA\tUnknown\t183\r\nCTCTCTAC\tN707\tAACTCTAT\tUnknown\t183\r\nTCCTGAGC\tN704\tTCGAAGAT\tUnknown\t183\r\nTAGGCATG\tN706\tGAGCCTCA\tS521\t183\r\nGGGCTCTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t183\r\nGTCTCTAC\tN707\tTCGACTAG\tS513\t183\r\nGGACTCCT\tN705\tAAGGCTTA\tUnknown\t182\r\nGCGGGGGG\tUnknown\tGGCAGGGG\tUnknown\t182\r\nTAGACATG\tN706\tTAGATCGC\t[N|S|E]501\t182\r\nACGGAATA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t182\r\nGGGGGGCG\tUnknown\tGGCCGCGC\tUnknown\t182\r\nGGGGTGCG\tUnknown\tGGGGGGGG\tUnknown\t182\r\nGGGGGGTG\tUnknown\tGGGGGCGG\tUnknown\t181\r\nCTTCACAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t181\r\nCTCTCTAC\tN707\tAAGGGATC\tUnknown\t181\r\nACGGGGGG\tUnknown\tGGACGGGG\tUnknown\t181\r\nAAGGGGGG\tUnknown\tGGAAGGGG\tUnknown\t181\r\nGGACATCT\tUnknown\tAAGGCTAT\tS520\t181\r\nCTCTCTAC\tN707\tATCGGCAG\tUnknown\t181\r\nGGACTCCT\tN705\tTTTTTTTT\tUnknown\t181\r\nCTCTAATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t181\r\nTCTAAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t180\r\nGGGGGCCT\tUnknown\tAAGGCTAT\tS520\t180\r\nCTCTCTAC\tN707\tCCCACTAT\tUnknown\t180\r\nCATGCTCA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t180\r\nACTAAATT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t180\r\nTAGACATG\tN706\tGAGCCTTA\tS521\t180\r\nCTCTCTGC\tN707\tGGGGGGGG\tUnknown\t179\r\nCGTACTAG\tN702\tGAGCGTTA\tS521\t179\r\nCTCTCTAC\tN707\tGGGGAGGA\tUnknown\t179\r\nCTCTCTAC\tN707\tAGGAATAT\tUnknown\t178\r\nAAGAAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t178\r\nCTCTCTAC\tN707\tATGGCGTA\tUnknown\t178\r\nCTCTCTAC\tN707\tCACGCTAT\tUnknown\t178\r\nCGGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t178\r\nGGACTTAT\tUnknown\tGAGCCTTA\tS521\t177\r\nTAGGAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t177\r\nCAGAGAGG\tN708\tGCTAAGAT\tUnknown\t177\r\nCCTCACAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t177\r\nACGGGGGG\tUnknown\tGGACGAGG\tUnknown\t177\r\nCTCTCTAC\tN707\tTCTTATTC\tUnknown\t177\r\nCTCTCTAC\tN707\tAACGGCAG\tUnknown\t177\r\nTAGGCATG\tN706\tATCGCTCG\tUnknown\t177\r\nTAGGCATG\tN706\tGAGACTTA\tS521\t176\r\nTCGGGGGG\tUnknown\tGGCAGCGG\tUnknown\t176\r\nGGGGGGGG\tUnknown\tGCACGCGG\tUnknown\t176\r\nTAGGGGGA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t176\r\nTAGGAATG\tN706\tGAGCCTTA\tS521\t176\r\nGGACTCCT\tN705\tCACGCTAT\tUnknown\t176\r\nGGGCCGCG\tUnknown\tGGGGGGGG\tUnknown\t176\r\nTAAGGCGA\tN701\tAGTATCGT\tUnknown\t176\r\nCTCTCTAC\tN707\tGCGTGAGT\tUnknown\t175\r\nTAGGCCTG\tN706\tGAGCCTTA\tS521\t175\r\nTCCTGAGC\tN704\tGCAGATCG\tUnknown\t175\r\nACGGGGGG\tUnknown\tGGATGCGG\tUnknown\t175\r\nTAAGGCGA\tN701\tCTCCGTCG\tUnknown\t175\r\nTAAGAATC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t175\r\nTAAGGCGA\tN701\tTCGGCAGC\tUnknown\t175\r\nCTCCTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t174\r\nCTCTCATT\tD703\tAAGGAGTA\tS507,[N|S|E]507\t174\r\nTTATCTAC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t174\r\nTCCCGAGC\tN704\tTCGTAAGA\tE517,S517,[N|S|E]517\t174\r\nCAGAGAGG\tN708\tGCATAAGA\tE517,S517,[N|S|E]517\t174\r\nGGACTCCT\tN705\tCGAACTGA\tUnknown\t174\r\nCTACATCT\tUnknown\tTCGACTAG\tS513\t174\r\nCTCTCTAC\tN707\tTCGGACTA\tUnknown\t174\r\nCCCTTCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t173\r\nGGGCGGGG\tUnknown\tGGGCGGGG\tUnknown\t173\r\nGGGCTATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t173\r\nCTCTCTAC\tN707\tAAGTCGTA\tUnknown\t173\r\nGTCCTATC\tUnknown\tAAGGCTAT\tS520\t172\r\nGGGAAGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t172\r\nTCCCACCT\tUnknown\tAAGGCTAT\tS520\t172\r\nCTCTCTAC\tN707\tGCGGCTAG\tUnknown\t172\r\nCTCTCTAC\tN707\tGCGTGAGC\tUnknown\t172\r\nAAGGAATA\tS507,[N|S|E]507\tAAGGAGTA\tS507,[N|S|E]507\t172\r\nCTCTCTAC\tN707\tAACGAGTT\tUnknown\t171\r\nCTCCACAT\tUnknown\tTCGACTAG\tS513\t171\r\nGGACTCCT\tN705\tTACGTCGG\tUnknown\t171\r\nGGACTCCT\tN705\tGGAGCCTT\tUnknown\t171\r\nCCACTCCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t171\r\nCCTCCCTT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t171\r\nTAGGCATG\tN706\tGACCTTAT\tUnknown\t171\r\nACGAAGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t171\r\nCAGAGAGG\tN708\tGCGTAAAT\tUnknown\t171\r\nTATAAATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t170\r\nCTCTCTAC\tN707\tGGGGGGGA\tUnknown\t170\r\nCTCTTTCC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t170\r\nCTCTCTGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t170\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tTCGTAAGA\tE517,S517,[N|S|E]517\t170\r\nCGTACTAG\tN702\tGCCTTATC\tUnknown\t170\r\nGGACTCCT\tN705\tAGGTATTC\tUnknown\t170\r\nGGACTCCT\tN705\tATCTCTTC\tUnknown\t169\r\nCTTCCTAC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t169\r\nTCCTATTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t169\r\nCTCTCTGC\tN707\tAAGGACTA\tS507,[N|S|E]507\t169\r\nTAAGGCGA\tN701\tAAGGGGTT\tUnknown\t169\r\nTAAGGCGA\tN701\tGGGGGGGG\tUnknown\t169\r\nTTCTCTAC\tN707\tAACGAGTA\tS507,[N|S|E]507\t169\r\nCTGTCTAC\tN707\tGGGGGGGG\tUnknown\t169\r\nCTCCTCTA\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t168\r\nGCTCTCCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t168\r\nGCGGGGGG\tUnknown\tGGAAGGGG\tUnknown\t168\r\nAAGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t168\r\nAGGGGGGG\tUnknown\tGGAGGGGG\tUnknown\t168\r\nACGGAGTA\tS507,[N|S|E]507\tAAGGAGTA\tS507,[N|S|E]507\t167\r\nTGGGGGGG\tUnknown\tGGCGGGGG\tUnknown\t167\r\nCTCTCAGC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t167\r\nTATAGGGG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t167\r\nGGAACTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t167\r\nGGGGGGGG\tUnknown\tGGCTGTGG\tUnknown\t167\r\nCTCTCTAC\tN707\tACGGCTAA\tUnknown\t166\r\nTAACGAAT\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t166\r\nGAGGGGGG\tUnknown\tGGGGGCGG\tUnknown\t166\r\nCAGAGAGG\tN708\tCGTAAGAT\tUnknown\t166\r\nTCCCTACT\tUnknown\tAAGGCTAT\tS520\t166\r\nGGACTCAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t166\r\nGGGCAATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t166\r\nGGACCTAT\tUnknown\tGAGCCTTA\tS521\t166\r\nCCGTACTA\tUnknown\tAAGGCTAT\tS520\t166\r\nGGACGCCT\tN705\tAAGGCTAT\tS520\t166\r\nCCTCAATT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t166\r\nAGGGGGGG\tUnknown\tGGAAGCGG\tUnknown\t165\r\nCTCTCTAC\tN707\tAGGCGTAT\tUnknown\t165\r\nCTCTTTTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t165\r\nTAAGGCGA\tN701\tCTCTCCAC\tN707\t165\r\nACTAAGGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t165\r\nTAAGGCGA\tN701\tCTCTGCAC\tUnknown\t165\r\nCTCTCTAC\tN707\tCGACTGTC\tUnknown\t165\r\nACGGGGGG\tUnknown\tGGGAGCGG\tUnknown\t165\r\nGGACTCCT\tN705\tCCTCCTCT\tUnknown\t165\r\nACGAAATA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t164\r\nCTCTCAAC\tN707\tGCGTAAGA\tE517,S517,[N|S|E]517\t164\r\nTCCTAGCA\tUnknown\tTCGTAAGA\tE517,S517,[N|S|E]517\t164\r\nTAGGCATG\tN706\tTAGAGCGC\t[N|S|E]501\t163\r\nCTCCTCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t163\r\nCTCTCTAC\tN707\tTGGGAGTA\tUnknown\t163\r\nGGGCCCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t163\r\nGGAATCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t163\r\nCTCTCTAC\tN707\tAAGGGTAC\tUnknown\t163\r\nCTCTCTAC\tN707\tAAGGATAA\tUnknown\t163\r\nTAAAAAGA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t163\r\nAAGAAGTA\tS507,[N|S|E]507\tTATCCTCT\tE503,S503,[N|S|E]503\t163\r\nTCTCTCAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t163\r\nTAAGGCGA\tN701\tAAGGTGTC\tUnknown\t163\r\nTAGGCATG\tN706\tGAACCTTA\tS521\t163\r\nCCTCGGGG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t162\r\nCTCTCTAC\tN707\tAAGAGATC\tUnknown\t162\r\nCTCTGTAC\tN707\tTCGACTAG\tS513\t162\r\nGGGCAGCG\tUnknown\tGGACGCGG\tUnknown\t162\r\nGGCCCCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t162\r\nCTCGCTAC\tN707\tAGGGGGGG\tUnknown\t162\r\nCTCTCTAC\tN707\tCCGTCTAT\tUnknown\t162\r\nGGGGGGGG\tUnknown\tGGGGGGGT\tUnknown\t162\r\nCTCTCTAC\tN707\tTCGTAAGT\tUnknown\t162\r\nTAAGGCGA\tN701\tGTATCGTC\tUnknown\t162\r\nCATCTCGT\tUnknown\tAAGGCTAT\tS520\t161\r\nTCCTGAGC\tN704\tTCGTAATA\tUnknown\t161\r\nGGACCTCC\tUnknown\tGAGCCTTA\tS521\t161\r\nTCCTATCT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t161\r\nGGGGGGTG\tUnknown\tGGAAGCGG\tUnknown\t160\r\nCGTACTAG\tN702\tGAGCCTTG\tS521\t160\r\nCCCTCCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t160\r\nTCCGAGCA\tUnknown\tTCGTAAGA\tE517,S517,[N|S|E]517\t160\r\nGAGGGGGG\tUnknown\tGGACGCGG\tUnknown\t160\r\nCGGGGGGG\tUnknown\tGGGGGCGG\tUnknown\t160\r\nTAGGGATG\tN706\tGAGCCTTA\tS521\t160\r\nCCTCTCAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t160\r\nCCATCTCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t160\r\nCCGCTCCT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t160\r\nTAGGCGTG\tN706\tTAGATCGC\t[N|S|E]501\t160\r\nCTATCTCG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t159\r\nGGGAAATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t159\r\nCTCTCTAC\tN707\tCGGGAGTA\tUnknown\t159\r\nCTCCTTAC\tE505,S505,[N|S|E]505\tAAGGAGTA\tS507,[N|S|E]507\t159\r\nGGGCGGCG\tUnknown\tGGGGGCGG\tUnknown\t159\r\nGGGGGGGG\tUnknown\tGGACGCCG\tUnknown\t159\r\nCTCTCTAC\tN707\tCCCACTAG\tUnknown\t159\r\nTTCTCCAC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t159\r\nTAAGCGAA\tUnknown\tTCTCTATT\tUnknown\t159\r\nCTACTAGA\tUnknown\tAAGGCTAT\tS520\t158\r\nGAGGGGGG\tUnknown\tGGGAGGGG\tUnknown\t158\r\nTCGGGGGG\tUnknown\tGGAAGCGG\tUnknown\t158\r\nGGGGCGCG\tUnknown\tGGGGGGGG\tUnknown\t158\r\nGGACTCCT\tN705\tGATCCTTT\tUnknown\t158\r\nCTTTCTTC\tUnknown\tTCGACTAG\tS513\t158\r\nCCTTTTTC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t158\r\nCTCCCTAC\tE505,N707,S505,[N|S|E]505\tAAGGCGTA\tS507,[N|S|E]507\t158\r\nGGACTCCT\tN705\tTACCTTTC\tUnknown\t158\r\nGGGGGGGG\tUnknown\tCGCAGCGG\tUnknown\t157\r\nACGAAAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t157\r\nGGCCCCCT\tUnknown\tAAGGCTAT\tS520\t157\r\nTCCCTGGG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t157\r\nCTCTTTTC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t156\r\nTTAGGCGC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t156\r\nCGTACTAG\tN702\tAAGGCTAG\tS520\t156\r\nAAGGGGGG\tUnknown\tGGGGGCGG\tUnknown\t156\r\nTAGGCATG\tN706\tTAGAATCG\tUnknown\t156\r\nGGACTCCT\tN705\tACGTCTAT\tUnknown\t156\r\nTCTCTACA\tUnknown\tAAGAGTAT\tUnknown\t156\r\nGGGGAGCG\tUnknown\tGGGGGGGG\tUnknown\t155\r\nTAAGGCGA\tN701\tAAGGGGTC\tUnknown\t155\r\nGGGGGGCG\tUnknown\tGGAGGCGG\tUnknown\t155\r\nGGACTCCT\tN705\tGAGCATTC\tUnknown\t155\r\nCGTAATCT\tUnknown\tAAGGCTAT\tS520\t155\r\nTAAGGCGA\tN701\tTCTTATTC\tUnknown\t155\r\nTAAGAAGA\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t155\r\nCTCTCTAC\tN707\tACGGCTTA\tUnknown\t155\r\nTCCTGTGC\tN704\tGCGTAGGA\tE517,N719,S517,[N|S|E]517\t155\r\nCTCTCTAC\tN707\tCCCTCTCT\tUnknown\t155\r\nGGACTCCT\tN705\tAAGATTCG\tUnknown\t155\r\nTCCTGAGC\tN704\tGCGTAGAC\tUnknown\t155\r\nATCTCGTA\tUnknown\tTCGACTAG\tS513\t155\r\nCTCTCTAC\tN707\tGTGGAGTA\tUnknown\t155\r\nGGGGGGCG\tUnknown\tGGCCGGGG\tUnknown\t155\r\nGGGGGGGG\tUnknown\tGGCGGGCG\tUnknown\t155\r\nCTCATCTC\tUnknown\tTCGACTAG\tS513\t155\r\nAGGAAGTG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t154\r\nCGTACTAG\tN702\tAAGGGTAT\tS520\t154\r\nGGATCTCG\tUnknown\tAAGGCTAT\tS520\t154\r\nCTCCTCCC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t154\r\nCCTCTCTC\tUnknown\tCTCTCTAT\tE502,S502,[N|S|E]502\t154\r\nGCGGGGGG\tUnknown\tGGATGCGG\tUnknown\t154\r\nAAAAAACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t154\r\nCGTACTAG\tN702\tAAGGTTAT\tS520\t154\r\nGGGCGGCG\tUnknown\tGGACGCGG\tUnknown\t154\r\nTCCCAACT\tUnknown\tGAGCCTTA\tS521\t154\r\nGGACTCCT\tN705\tGAGCTTTA\tS521\t154\r\nGGACTCCT\tN705\tAATCCTAT\tUnknown\t153\r\nAATGAGTA\tS507,[N|S|E]507\tAAGGAGTA\tS507,[N|S|E]507\t153\r\nTCCTGAAG\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t153\r\nGGGGGGTG\tUnknown\tGGGCGGGG\tUnknown\t153\r\nGGGGGGCG\tUnknown\tGGCCGAGG\tUnknown\t153\r\nTAACGAAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t152\r\nGGGGACTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t152\r\nCTTACTAG\tN702,S518\tGAGCCTTA\tS521\t152\r\nGGGGGGGG\tUnknown\tGCGGGCGG\tUnknown\t152\r\nGGGGGGTG\tUnknown\tGGCGGGGG\tUnknown\t152\r\nACGGGGGG\tUnknown\tGGGTGGGG\tUnknown\t152\r\nTCTCTACA\tUnknown\tTCGTAAGA\tE517,S517,[N|S|E]517\t152\r\nGGACCCCC\tUnknown\tAAGGCTAT\tS520\t152\r\nCTCTCTAC\tN707\tACGGAGAA\tUnknown\t152\r\nCTCTTAAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t152\r\nAAGGGGGG\tUnknown\tGGCAGGGG\tUnknown\t152\r\nCTCTCTAC\tN707\tTCTCTTTC\tUnknown\t151\r\nAGGGGGGG\tUnknown\tGGAAGAGG\tUnknown\t151\r\nGGGGAGGG\tUnknown\tGGACGCGG\tUnknown\t151\r\nACGGGGGG\tUnknown\tGGATGAGG\tUnknown\t151\r\nCGTACATC\tUnknown\tAAGGCTAT\tS520\t151\r\nGGGGGGGG\tUnknown\tGGCAGCGC\tUnknown\t151\r\nTCCTACAT\tUnknown\tGCGTAAGA\tE517,S517,[N|S|E]517\t151\r\nGGGGCGAG\tUnknown\tGGGGGGGG\tUnknown\t151\r\nCCTCTCCT\tD503\tCTCTCTAT\tE502,S502,[N|S|E]502\t150\r\nGGGGGGGG\tUnknown\tGGCGTGGG\tUnknown\t150\r\nCTCTCTAC\tN707\tCGAACTGA\tUnknown\t150\r\nCTCTCTAC\tN707\tCCGTCGGC\tUnknown\t150\r\nCTCCCCCC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t150\r\nCTCTCTAC\tN707\tTCGGCAGC\tUnknown\t149\r\nCCTTCCTC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t149\r\nTCGGGGGG\tUnknown\tGGGAGGGG\tUnknown\t149\r\nTCTCTCCT\tS511\tTATCCTCT\tE503,S503,[N|S|E]503\t149\r\nACGGGGGG\tUnknown\tGGCCGGGG\tUnknown\t149\r\nGGGCTGGG\tUnknown\tGGGGGGGG\tUnknown\t149\r\nTCTCTATC\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t149\r\nTCCTGACA\tUnknown\tTCGTAAGA\tE517,S517,[N|S|E]517\t149\r\nACTAAATG\tUnknown\tGAGCCTTA\tS521\t149\r\nGTCCTCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t149\r\nGGGCGGGG\tUnknown\tGGGCGCGG\tUnknown\t149\r\nGGAATCTC\tUnknown\tAAGGCTAT\tS520\t148\r\nTCGGGGGG\tUnknown\tGGAGGGGG\tUnknown\t148\r\nTCCTGAGC\tN704\tGCGGTAAG\tUnknown\t148\r\nCGTACTAG\tN702\tGAGCATTT\tUnknown\t148\r\nGGGGGGGG\tUnknown\tGGCCGGGC\tUnknown\t148\r\nTCCTGAGC\tN704\tTCGTAAGG\tUnknown\t147\r\nCTCTCTAC\tN707\tAAGGGCAG\tUnknown\t147\r\nGGGGGGGG\tUnknown\tGGCCGAGC\tUnknown\t147\r\nAAGGGGGG\tUnknown\tGGACGCGG\tUnknown\t147\r\nGGGCCCCT\tUnknown\tAAGGCTAT\tS520\t147\r\nGACCCTAT\tUnknown\tAAGGCTAT\tS520\t147\r\nCTTCTCAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t147\r\nACGAAGTG\tUnknown\tAAGGCTAT\tS520\t147\r\nCTCTCTAC\tN707\tTCGTAAAT\tUnknown\t146\r\nCGTACTAG\tN702\tGAGGCTTA\tS521\t146\r\nCTCTCTAC\tN707\tGAGGGGTA\tUnknown\t146\r\nACGAAGTG\tUnknown\tGGAAGCGG\tUnknown\t146\r\nCGAACTAG\tN702\tAAGGCTAT\tS520\t146\r\nCGTATTAG\tN702\tAAGGCTAT\tS520\t146\r\nAAGGCGAT\tS520\tAAGGAGTA\tS507,[N|S|E]507\t146\r\nGGACTCCT\tN705\tACAGCTAT\tUnknown\t145\r\nTAAGGATC\tS521\tAAGGAGTA\tS507,[N|S|E]507\t145\r\nGGCCTCCT\tN705\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t145\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/ambiguous/expected.txt", "content": "sample_name\texpected_barcode_1\texpected_barcode_2\texpected_barcode_1_name\texpected_barcode_2_name\texpected_barcodes_read_count\tguessed_barcode_1\tguessed_barcode_2\tguessed_barcode_1_name\tguessed_barcode_2_name\tguessed_barcodes_read_count\tmatch_type\r\nG4509.1_180615\tTAGGCATG\tGAGCCTTA\tBI7H12,N706\tS521\t447585\t\t\t\t\t\talternative_indices_uncertain\r\nG4439.1_180615\tCGTACTAG\tGAGCCTTA\tBI7H07,N702\tS521\t698370\t\t\t\t\t\talternative_indices_uncertain\r\nG4438.1_180615\tCAGAGAGG\tGCGTAAGA\tBI7A06,N708\tE517,S517,[N|S|E]517\t125735\t\t\t\t\t\talternative_indices_uncertain\r\nG4762.2_180615\tCGTACTAG\tTCGACTAG\tBI7H07,N702\tS513\t63465\t\t\t\t\t\talternative_indices_uncertain\r\nG5748.1_180615\tTAGGCATG\tTAGATCGC\tBI7H12,N706\tBI5A06,[N|S|E]501\t469572\t\t\t\t\t\talternative_indices_uncertain\r\nG5413.1_180615\tTAGGCATG\tAGAGTAGA\tBI7H12,N706\tBI5G06,E504,[N|S|E]504\t0\t\t\t\t\t\talternative_indices_uncertain\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/ambiguous/metrics.txt", "content": "## htsjdk.samtools.metrics.StringHeader\n# ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/tmp.BlCr1Hi364/Data/Intensities/BaseCalls OUTPUT_DIR=/tmp/tmp-illumina-illumina_demux-s_l2zlkg/extracted_barcodes-7e8qlzo5 LANE=2 READ_STRUCTURE=101T8B8B101T BARCODE_FILE=/tmp/tmp-illumina-illumina_demux-s_l2zlkg/barcodeData.HHK7CBCX2.28b1b6msw.txt METRICS_FILE=metrics.txt MAX_MISMATCHES=1 MINIMUM_BASE_QUALITY=10 MINIMUM_QUALITY=10 NUM_PROCESSORS=0 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\n## htsjdk.samtools.metrics.StringHeader\n# Started on: Thu Sep 06 15:00:30 UTC 2018\n\n## METRICS CLASS\tpicard.illumina.ExtractIlluminaBarcodes$BarcodeMetric\nBARCODE\tBARCODE_WITHOUT_DELIMITER\tBARCODE_NAME\tLIBRARY_NAME\tREADS\tPF_READS\tPERFECT_MATCHES\tPF_PERFECT_MATCHES\tONE_MISMATCH_MATCHES\tPF_ONE_MISMATCH_MATCHES\tPCT_MATCHES\tRATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_PCT_MATCHES\tPF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_NORMALIZED_MATCHES\nGGACTCCT-GAGCCTTA\tGGACTCCTGAGCCTTA\tG4508.1_180615\tG4508.1_180615\t1513398\t1500642\t1426282\t1416509\t87116\t84133\t0.014648\t0.036633\t0.014782\t0.036663\t0.259294\nTAGGCATG-GAGCCTTA\tTAGGCATGGAGCCTTA\tG4509.1_180615\tG4509.1_180615\t447585\t443680\t421320\t418341\t26265\t25339\t0.004332\t0.010834\t0.004371\t0.01084\t0.076663\nCGTACTAG-GAGCCTTA\tCGTACTAGGAGCCTTA\tG4439.1_180615\tG4439.1_180615\t698370\t691798\t656466\t651475\t41904\t40323\t0.006759\t0.016905\t0.006815\t0.016901\t0.119535\nGGACTCCT-AAGGCTAT\tGGACTCCTAAGGCTAT\tG4489.1_180615\tG4489.1_180615\t6551371\t6490595\t6430062\t6377484\t121309\t113111\t0.063409\t0.158582\t0.063936\t0.158573\t1.121502\nCGTACTAG-AAGGCTAT\tCGTACTAGAAGGCTAT\tG4482.1_180615\tG4482.1_180615\t1049237\t1039060\t1027266\t1018608\t21971\t20452\t0.010155\t0.025398\t0.010235\t0.025386\t0.179538\nTCCTGAGC-GCGTAAGA\tTCCTGAGCGCGTAAGA\tG3773.1_180615\tG3773.1_180615\t5209877\t5161381\t4920943\t4882130\t288934\t279251\t0.050425\t0.12611\t0.050843\t0.126099\t0.891828\nCAGAGAGG-GCGTAAGA\tCAGAGAGGGCGTAAGA\tG4438.1_180615\tG4438.1_180615\t125735\t124542\t118849\t117921\t6886\t6621\t0.001217\t0.003044\t0.001227\t0.003043\t0.021519\nCTCTCTAC-GCGTAAGA\tCTCTCTACGCGTAAGA\tG4121.1_180615\tG4121.1_180615\t1962258\t1943116\t1842708\t1828048\t119550\t115068\t0.018992\t0.047498\t0.019141\t0.047473\t0.335748\nCTCTCTAC-TCGACTAG\tCTCTCTACTCGACTAG\tG4323.1_180615\tG4323.1_180615\t4342192\t4303172\t4252523\t4219208\t89669\t83964\t0.042027\t0.105106\t0.042389\t0.105132\t0.74354\nCGTACTAG-TCGACTAG\tCGTACTAGTCGACTAG\tG4762.2_180615\tG4762.2_180615\t63465\t62876\t62097\t61604\t1368\t1272\t0.000614\t0.001536\t0.000619\t0.001536\t0.010864\nTAAGGCGA-AAGGAGTA\tTAAGGCGAAAGGAGTA\tG5208.2_180615\tG5208.2_180615\t4224502\t4194555\t4149242\t4123682\t75260\t70873\t0.040888\t0.102258\t0.041319\t0.102478\t0.724772\nCTCTCTAC-AAGGAGTA\tCTCTCTACAAGGAGTA\tG4220.1_180615\tG4220.1_180615\t41312326\t40931185\t40566981\t40221276\t745345\t709909\t0.399852\t1\t0.403197\t1\t7.072446\nTAGGCATG-AGAGTAGA\tTAGGCATGAGAGTAGA\tG5413.1_180615\tG5413.1_180615\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\nGGACTCCT-TATCCTCT\tGGACTCCTTATCCTCT\tG5585.1_180615\tG5585.1_180615\t12380244\t12269547\t12141046\t12045590\t239198\t223957\t0.119825\t0.299674\t0.120862\t0.29976\t2.120039\nCTCTCTAC-CTCTCTAT\tCTCTCTACCTCTCTAT\tG5784.1_180615\tG5784.1_180615\t9587474\t9490089\t9408832\t9323748\t178642\t166341\t0.092795\t0.232073\t0.093483\t0.231855\t1.63978\nTAAGGCGA-CTCTCTAT\tTAAGGCGACTCTCTAT\tG5767.1_180615\tG5767.1_180615\t9349304\t9277016\t9173332\t9112595\t175972\t164421\t0.09049\t0.226308\t0.091384\t0.226649\t1.602964\nTAGGCATG-TAGATCGC\tTAGGCATGTAGATCGC\tG5748.1_180615\tG5748.1_180615\t469572\t462806\t458368\t452686\t11204\t10120\t0.004545\t0.011366\t0.004559\t0.011307\t0.079968\nNNNNNNNN-NNNNNNNN\tNNNNNNNNNNNNNNNN\t\t\t4032103\t3130582\t0\t0\t0\t0\t0.039026\t0.0976\t0.030838\t0.076484\t0\n\n\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/few_assigned/barcodes.txt", "content": "Barcode1\tLikely_Index_Names1\tBarcode2\tLikely_Index_Names2\tCount\r\nGTAGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t18969580\r\nAGGCAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t12459537\r\nTCCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t10788903\r\nTAAGGCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t10436673\r\nGGACTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t9941054\r\nGGACTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t8851019\r\nAAGAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t8677012\r\nAGGCAGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t8554648\r\nTAAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t8294319\r\nTAAGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t7919201\r\nCGTACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t7741249\r\nTAGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t7054916\r\nTAGGCATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t7046412\r\nTCCTGAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t6941251\r\nCTCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t6872843\r\nTCCTGAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t6445936\r\nTAGGCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t6293965\r\nCGAGGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t6259554\r\nGGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t6067309\r\nCGTACTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t6064383\r\nGTAGAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t5889232\r\nAAGAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t5812472\r\nCGTACTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t5613671\r\nGCTACGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t5383537\r\nCAGAGAGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t4563539\r\nCGAGGCTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t4398418\r\nCTCTCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t4355047\r\nCAGAGAGG\tN708\tCTAAGCCT\tS508,[N|S|E]508\t2772738\r\nCAGAGAGG\tN708\tAGAGTAGA\tE504,[N|S|E]504\t1638249\r\nCTCTCTAC\tN707\tCTAAGCCT\tS508,[N|S|E]508\t1456663\r\nGCTACGCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t1331747\r\nAGGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t1232119\r\nGCTACGCT\tN709\tAGAGTAGA\tE504,[N|S|E]504\t873181\r\nGTAGAGGA\tN712\tAGAGTAGG\tE504,[N|S|E]504\t626046\r\nCGAGGCTG\tN710\tCTAAGCCT\tS508,[N|S|E]508\t557897\r\nAAGAGGCA\tN711\tACTGCATT\tE506,S506,[N|S|E]506\t386797\r\nCTCTCTAC\tN707\tACTGCATT\tE506,S506,[N|S|E]506\t360546\r\nCGAGGCTG\tN710\tAGAGTAGG\tE504,[N|S|E]504\t270716\r\nCGAGGCTG\tN710\tACTGCATT\tE506,S506,[N|S|E]506\t266888\r\nGTAGAGGA\tN712\tACTGCATT\tE506,S506,[N|S|E]506\t238172\r\nGTAGAGGA\tN712\tAGCGTAGA\tE504,[N|S|E]504\t233638\r\nGGACTCCT\tN705\tGTACGGAG\tE505,S505,[N|S|E]505\t225387\r\nAAGAGGCA\tN711\tACTGCATC\tE506,S506,[N|S|E]506\t221657\r\nGGACTCCT\tN705\tAAGGAGTT\tS507,[N|S|E]507\t217573\r\nGTAGAGGA\tN712\tCGAGTAGA\tE504,[N|S|E]504\t214926\r\nTAAGGCGA\tN701\tGTACGGAG\tE505,S505,[N|S|E]505\t213686\r\nGTAGAGGA\tN712\tAGAGTAGC\tE504,[N|S|E]504\t208128\r\nGCTACGCT\tN709\tACTGCATT\tE506,S506,[N|S|E]506\t205385\r\nTAAGGCGA\tN701\tAAGGAGTT\tS507,[N|S|E]507\t191687\r\nAAGAGGCA\tN711\tAGAGTAGG\tE504,[N|S|E]504\t190290\r\nAGGCAGAA\tN703\tAAGGAGTT\tS507,[N|S|E]507\t190116\r\nAGGCAGAA\tN703\tGTACGGAG\tE505,S505,[N|S|E]505\t186013\r\nCAGAGAGG\tN708\tCTAAGCCC\tS508,[N|S|E]508\t184597\r\nGGACTCCT\tN705\tGTCAGGAG\tE505,S505,[N|S|E]505\t180173\r\nTAGGCATG\tN706\tAAGGAGTT\tS507,[N|S|E]507\t175949\r\nCAGAGAGG\tN708\tACTGCATT\tE506,S506,[N|S|E]506\t168260\r\nAGGCAGAA\tN703\tAAGGAGTC\tS507,[N|S|E]507\t165041\r\nCTCTCTAC\tN707\tAGAGTAGG\tE504,[N|S|E]504\t164593\r\nCGTACTAG\tN702\tAAGGAGTT\tS507,[N|S|E]507\t163864\r\nTCCTGAGC\tN704\tAAGGAGTT\tS507,[N|S|E]507\t163482\r\nCTCTCTAC\tN707\tACTGCATC\tE506,S506,[N|S|E]506\t148474\r\nGTAGAGGA\tN712\tAGAGTAGT\tE504,[N|S|E]504\t148334\r\nTAAGGCGA\tN701\tAAGGAGTC\tS507,[N|S|E]507\t140453\r\nTAAGGCGA\tN701\tGTCAGGAG\tE505,S505,[N|S|E]505\t140291\r\nGGACTCCT\tN705\tCAGGAGTA\tS507,[N|S|E]507\t136568\r\nGTAGAGGA\tN712\tAGAGTCGA\tE504,[N|S|E]504\t131858\r\nAGGCAGAA\tN703\tGTCAGGAG\tE505,S505,[N|S|E]505\t124584\r\nAGGCAGAA\tN703\tAAGGAGTG\tS507,[N|S|E]507\t123558\r\nTCCTGAGC\tN704\tGTACGGAG\tE505,S505,[N|S|E]505\t122660\r\nTAGGCATG\tN706\tGTACGGAG\tE505,S505,[N|S|E]505\t119478\r\nGGACTCCT\tN705\tAAGGAGTC\tS507,[N|S|E]507\t115875\r\nAAGAGGCA\tN711\tCCTGCATA\tE506,S506,[N|S|E]506\t113851\r\nGTAGAGGA\tN712\tAGTGTAGA\tE504,[N|S|E]504\t107267\r\nTCCTGAGC\tN704\tTATCCTCC\tE503,S503,[N|S|E]503\t106563\r\nCTCTCTAC\tN707\tAGCGTAGA\tE504,[N|S|E]504\t103472\r\nTCCTGAGC\tN704\tAAGGAGTC\tS507,[N|S|E]507\t102685\r\nCTCTCTAC\tN707\tAGAGTAGC\tE504,[N|S|E]504\t102497\r\nCGTACTAG\tN702\tGTACGGAG\tE505,S505,[N|S|E]505\t101557\r\nTAAGGCGA\tN701\tCAGGAGTA\tS507,[N|S|E]507\t99162\r\nTAAGGCGA\tN701\tTATCCTCC\tE503,S503,[N|S|E]503\t97311\r\nCTCTCTAC\tN707\tCGAGTAGA\tE504,[N|S|E]504\t92600\r\nCAGAGAGG\tN708\tAGAGTAGG\tE504,[N|S|E]504\t91279\r\nGTAGAGGA\tN712\tAGGGTAGA\tE504,[N|S|E]504\t89196\r\nAAGAGGCA\tN711\tCGAGTAGA\tE504,[N|S|E]504\t81433\r\nGTAGAGGA\tN712\tACTGCATC\tE506,S506,[N|S|E]506\t80169\r\nCGTACTAG\tN702\tAAGGAGTC\tS507,[N|S|E]507\t79728\r\nTAAGGCGA\tN701\tAAGGAGTG\tS507,[N|S|E]507\t79659\r\nCGTACTAG\tN702\tTATCCTCC\tE503,S503,[N|S|E]503\t79474\r\nCGAGGCTG\tN710\tCGAGTAGA\tE504,[N|S|E]504\t78976\r\nGTAGAGGA\tN712\tGGAGTAGA\tE504,[N|S|E]504\t78931\r\nTAGGCATG\tN706\tAAGGAGTC\tS507,[N|S|E]507\t73651\r\nAAGAGGCA\tN711\tAATGCATA\tE506,S506,[N|S|E]506\t71902\r\nCTCTCTAC\tN707\tCTAAGCCC\tS508,[N|S|E]508\t71801\r\nTAGGCATG\tN706\tGTCAGGAG\tE505,S505,[N|S|E]505\t71626\r\nCAGAGAGG\tN708\tACTGCATC\tE506,S506,[N|S|E]506\t71328\r\nTAGGCATG\tN706\tCAGGAGTA\tS507,[N|S|E]507\t69881\r\nTCCTGAGC\tN704\tCAGGAGTA\tS507,[N|S|E]507\t68954\r\nAAGAGGCA\tN711\tTGCATATC\tUnknown\t67736\r\nCTCTCTAC\tN707\tAGAGTAGT\tE504,[N|S|E]504\t66829\r\nAGGCAGAA\tN703\tAAGAAGTA\tS507,[N|S|E]507\t66820\r\nAGGCAGAA\tN703\tCAGGAGTA\tS507,[N|S|E]507\t65181\r\nAGGCAGAA\tN703\tGTAAGTAG\tE505,S505,[N|S|E]505\t64589\r\nCGTACTAG\tN702\tAAGGAGTG\tS507,[N|S|E]507\t63621\r\nGCTACGCT\tN709\tCTAAGCCC\tS508,[N|S|E]508\t62214\r\nAAGAGGCA\tN711\tACTGCCTA\tE506,S506,[N|S|E]506\t62182\r\nGGACTCCT\tN705\tACGGAGTA\tS507,[N|S|E]507\t61738\r\nTCCTGAGC\tN704\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t61391\r\nAGGCAGAA\tN703\tGTAAGGCG\tE505,S505,[N|S|E]505\t59196\r\nCGAGGCTG\tN710\tAGCGTAGA\tE504,[N|S|E]504\t58458\r\nGTAGAGGA\tN712\tAGAGTAAT\tUnknown\t58274\r\nGTAGAGGA\tN712\tCGAGTAGG\tUnknown\t57584\r\nCTCTCTAC\tN707\tAGAGTCGA\tE504,[N|S|E]504\t57488\r\nCGTACTAG\tN702\tCAGGAGTA\tS507,[N|S|E]507\t57112\r\nGTAGAGGA\tN712\tGGAGTAGG\tUnknown\t55826\r\nCTCTCTAC\tN707\tACTGCCTA\tE506,S506,[N|S|E]506\t55678\r\nTCCTGAGC\tN704\tGTCAGGAG\tE505,S505,[N|S|E]505\t55015\r\nAGGCAGAA\tN703\tGTAAGAGT\tUnknown\t54491\r\nGGACTCCT\tN705\tAAGGAGTG\tS507,[N|S|E]507\t54355\r\nTCCTGAGC\tN704\tAAGGAGTG\tS507,[N|S|E]507\t53682\r\nTAAGGCGA\tN701\tTATCATCT\tE503,S503,[N|S|E]503\t52580\r\nCGAGGCTG\tN710\tACTGCATC\tE506,S506,[N|S|E]506\t51416\r\nGGACTCCT\tN705\tGTAAGAGT\tUnknown\t51103\r\nCGAGGCTG\tN710\tAGAGTAGC\tE504,[N|S|E]504\t50988\r\nGTAGAGAA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t49686\r\nTAGGCATG\tN706\tAAGGAGTG\tS507,[N|S|E]507\t49422\r\nTCCTGAGC\tN704\tTATCATCT\tE503,S503,[N|S|E]503\t49332\r\nTAAGGCGA\tN701\tGTAAGGCG\tE505,S505,[N|S|E]505\t49172\r\nTAGGCATG\tN706\tTATCCTCC\tE503,S503,[N|S|E]503\t49098\r\nCGAGGCTG\tN710\tAGAGTAGT\tE504,[N|S|E]504\t48714\r\nGTAGAGGA\tN712\tTGCATATC\tUnknown\t47742\r\nGGACTCCT\tN705\tGTAGGAGT\tUnknown\t47536\r\nGTAGAGGA\tN712\tAGAGTGAT\tUnknown\t46566\r\nAGGCAGAA\tN703\tGTAAGCAG\tE505,S505,[N|S|E]505\t46306\r\nAAGAGGCA\tN711\tAGAGTAGC\tE504,[N|S|E]504\t46260\r\nGTAGAGGA\tN712\tGGAGTAGC\tUnknown\t45845\r\nTAAGGCGA\tN701\tACGGAGTA\tS507,[N|S|E]507\t45180\r\nCCCCCCCC\tUnknown\tCCCCCCCC\tUnknown\t45134\r\nGGACTCCT\tN705\tTATCCTCC\tE503,S503,[N|S|E]503\t44982\r\nAGGCAGAA\tN703\tGTAGGAGT\tUnknown\t44194\r\nCTCTCTAC\tN707\tCCTGCATA\tE506,S506,[N|S|E]506\t43488\r\nAGGCAGAA\tN703\tAAGCAGTA\tS507,[N|S|E]507\t43031\r\nAGGCAGAA\tN703\tAAGGAGAA\tS507,[N|S|E]507\t42493\r\nTAAGGCGA\tN701\tAAGGAGAA\tS507,[N|S|E]507\t42345\r\nTAGGCATG\tN706\tGTAAGAGT\tUnknown\t41389\r\nGTAGAGGA\tN712\tACTGCCTA\tE506,S506,[N|S|E]506\t41032\r\nTAAGGCGA\tN701\tGTAAGAGT\tUnknown\t40888\r\nCGTACTAA\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t40388\r\nTAAGGCGA\tN701\tGTGAGGAG\tE505,S505,[N|S|E]505\t40159\r\nGGACTCCT\tN705\tGTGAGGAG\tE505,S505,[N|S|E]505\t40099\r\nGCTACGCT\tN709\tACTGCATC\tE506,S506,[N|S|E]506\t40023\r\nGTAGAGGA\tN712\tAGAGTGGA\tE504,[N|S|E]504\t39767\r\nTAAGGCGA\tN701\tGTAAGCAG\tE505,S505,[N|S|E]505\t39438\r\nGTAGAGGA\tN712\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t39359\r\nAAGAGGCA\tN711\tAGCGTAGA\tE504,[N|S|E]504\t39049\r\nCAGAGAGG\tN708\tCTACGCCT\tD505,S508,[N|S|E]508\t38988\r\nAGGCAGAA\tN703\tGAAAGGAG\tE505,S505,[N|S|E]505\t38945\r\nCGAGGCTG\tN710\tAGTGTAGA\tE504,[N|S|E]504\t38937\r\nGCTACGCT\tN709\tACTGCCTA\tE506,S506,[N|S|E]506\t38829\r\nTAGGCATG\tN706\tGTAGGAGT\tUnknown\t38596\r\nGGACTCCT\tN705\tGTAAGCAG\tE505,S505,[N|S|E]505\t38592\r\nCGAGGCTG\tN710\tCCTGCATA\tE506,S506,[N|S|E]506\t38398\r\nTAAGGCGA\tN701\tTATCCTAT\tE503,S503,[N|S|E]503\t38309\r\nTCCTGAGC\tN704\tGTAAGAGT\tUnknown\t38210\r\nTAGGCATG\tN706\tTATCATCT\tE503,S503,[N|S|E]503\t37995\r\nCGAGGCTG\tN710\tCTAAGCCC\tS508,[N|S|E]508\t37293\r\nCTCTCTAC\tN707\tTGCATATC\tUnknown\t37154\r\nAGGCAGAA\tN703\tAGGAGTAT\tUnknown\t36847\r\nCGAGGCTG\tN710\tAGAGTCGA\tE504,[N|S|E]504\t36812\r\nAAGAGGCA\tN711\tAGAGTAGT\tE504,[N|S|E]504\t36682\r\nTCCTGAGC\tN704\tTATCCTTT\tE503,S503,[N|S|E]503\t36459\r\nCGTACTAG\tN702\tACGGAGTA\tS507,[N|S|E]507\t36349\r\nTCCTGAGC\tN704\tACGGAGTA\tS507,[N|S|E]507\t35782\r\nCAGAGAGG\tN708\tTGCATATC\tUnknown\t35732\r\nTCCTGAGC\tN704\tTATCGTCT\tE503,S503,[N|S|E]503\t35647\r\nGGACTCCT\tN705\tAGGAGTAT\tUnknown\t35638\r\nAGGCAGAA\tN703\tACTGCATA\tE506,S506,[N|S|E]506\t35587\r\nGTAGAGGA\tN712\tGGAGTCGC\tUnknown\t35485\r\nCGTACTAG\tN702\tTATCATCT\tE503,S503,[N|S|E]503\t35424\r\nGTAGAGGA\tN712\tAGAGAGAT\tUnknown\t35137\r\nGTAGAGGA\tN712\tGAGTAGAT\tUnknown\t35081\r\nTAAGGCGA\tN701\tAAGGAGGA\tS507,[N|S|E]507\t35067\r\nCGTACTAG\tN702\tGTAAGGCG\tE505,S505,[N|S|E]505\t35057\r\nTCCTGAGC\tN704\tTATCCTAT\tE503,S503,[N|S|E]503\t34844\r\nCGTACTAG\tN702\tAAGGCGTA\tS507,[N|S|E]507\t34794\r\nTAGGCATG\tN706\tACGGAGTA\tS507,[N|S|E]507\t34623\r\nAGGCAGAA\tN703\tTATCCTCC\tE503,S503,[N|S|E]503\t34596\r\nGGACTCCT\tN705\tGTAAGGCG\tE505,S505,[N|S|E]505\t34132\r\nCTCTCTAC\tN707\tAGTGTAGA\tE504,[N|S|E]504\t33760\r\nCGAGGCTG\tN710\tTGCATATC\tUnknown\t33629\r\nGTAGAGGA\tN712\tAATGCATA\tE506,S506,[N|S|E]506\t33576\r\nCAGAGAGG\tN708\tACTGCCTA\tE506,S506,[N|S|E]506\t33456\r\nCGAGGCTG\tN710\tAGGGTAGA\tE504,[N|S|E]504\t33103\r\nGCTACGCT\tN709\tCCTGCATA\tE506,S506,[N|S|E]506\t33022\r\nTAAGGCGA\tN701\tGTAAGTAG\tE505,S505,[N|S|E]505\t32937\r\nTAAGGCGA\tN701\tACTGCATA\tE506,S506,[N|S|E]506\t32801\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tAGAGTAGA\tE504,[N|S|E]504\t32716\r\nTAAGGCGA\tN701\tGTAGGAGT\tUnknown\t32667\r\nGGACTCCT\tN705\tACTGCATA\tE506,S506,[N|S|E]506\t32505\r\nCGAGGCTG\tN710\tACTGCCTA\tE506,S506,[N|S|E]506\t32291\r\nTCCTGAGC\tN704\tGTAGGAGT\tUnknown\t32277\r\nCTCTCTAC\tN707\tCTACGCCT\tD505,S508,[N|S|E]508\t32275\r\nAGGCAGAA\tN703\tGTAAGAAG\tE505,S505,[N|S|E]505\t32224\r\nAAGAGGCA\tN711\tGCTGCATC\tUnknown\t32059\r\nCGTACTAA\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t32053\r\nTAGGCATG\tN706\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t31411\r\nGGACTCCT\tN705\tAAGCAGTA\tS507,[N|S|E]507\t31403\r\nTAAGGCGA\tN701\tAGGAGTAT\tUnknown\t31326\r\nGGACTCCT\tN705\tTATCATCT\tE503,S503,[N|S|E]503\t31093\r\nTAAGGCGA\tN701\tAAGAAGTA\tS507,[N|S|E]507\t30686\r\nTAAGGCGA\tN701\tTATCGTCT\tE503,S503,[N|S|E]503\t30656\r\nGCTACGCT\tN709\tTGCATATC\tUnknown\t30626\r\nAGGCAGAA\tN703\tAAGTAGTA\tS507,[N|S|E]507\t30487\r\nGAAGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t30364\r\nGTAGAGGA\tN712\tAGAGTCGC\tUnknown\t30349\r\nAGGCAGAA\tN703\tACGGAGTA\tS507,[N|S|E]507\t30341\r\nGTAGAGGA\tN712\tAGAGTTGA\tE504,[N|S|E]504\t30263\r\nGGACTCCT\tN705\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t30088\r\nGTAGAGGA\tN712\tCCTGCATA\tE506,S506,[N|S|E]506\t29975\r\nCAGAGAGG\tN708\tAATGCATA\tE506,S506,[N|S|E]506\t29941\r\nCGTACTAG\tN702\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t29873\r\nGCTACGCT\tN709\tAATGCATA\tE506,S506,[N|S|E]506\t29683\r\nAGGCAGAA\tN703\tGTGAGGAG\tE505,S505,[N|S|E]505\t29595\r\nCGTACTAA\tN702\tAAGGAGTA\tS507,[N|S|E]507\t29329\r\nCGTACTAG\tN702\tGTCAGGAG\tE505,S505,[N|S|E]505\t29326\r\nGTAGAGGA\tN712\tAGAGCAGA\tE504,[N|S|E]504\t29282\r\nTAAGGCGA\tN701\tGTAGGGAG\tE505,S505,[N|S|E]505\t29224\r\nTAGGCGAA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t29182\r\nGTAGAGGA\tN712\tAGAGTAAA\tE504,[N|S|E]504\t29170\r\nCGTACTAG\tN702\tGTAAGTAG\tE505,S505,[N|S|E]505\t29097\r\nTAAGGCGA\tN701\tTATCCTTT\tE503,S503,[N|S|E]503\t29073\r\nAGGCAGAA\tN703\tAAGGAGGA\tS507,[N|S|E]507\t29072\r\nTAAGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t28950\r\nGTAGAGGA\tN712\tAGACTAGA\tE504,[N|S|E]504\t28821\r\nTAAGGCGA\tN701\tAAGGCGTA\tS507,[N|S|E]507\t28634\r\nTAGGCATG\tN706\tGTGAGGAG\tE505,S505,[N|S|E]505\t28267\r\nTCCTGAGC\tN704\tGTAAGGCG\tE505,S505,[N|S|E]505\t27857\r\nTAAGGCGA\tN701\tGAGGAGTA\tS507,[N|S|E]507\t27820\r\nTAGGCATG\tN706\tAGGAGTAT\tUnknown\t27796\r\nAAGAGGCA\tN711\tACTGCATG\tE506,S506,[N|S|E]506\t27778\r\nTCCTGAGC\tN704\tACTGCATA\tE506,S506,[N|S|E]506\t27715\r\nGTAGAGGA\tN712\tAAAGTAGA\tE504,[N|S|E]504\t27686\r\nGGACTCCT\tN705\tAAGAAGTA\tS507,[N|S|E]507\t27650\r\nTAAGGCGA\tN701\tAAGCAGTA\tS507,[N|S|E]507\t27572\r\nTCCTGAGC\tN704\tAAGGCGTA\tS507,[N|S|E]507\t27248\r\nGTACTAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t27095\r\nCGTACTAG\tN702\tGTAAGAGT\tUnknown\t27094\r\nAGGCAGAA\tN703\tGTAGGAGG\tUnknown\t27092\r\nTAGGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t27026\r\nAGGCAGAA\tN703\tAAGGCGTA\tS507,[N|S|E]507\t26912\r\nTAAGGCGA\tN701\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t26873\r\nTAAGCGAA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t26791\r\nAAGAGGCA\tN711\tGCTGCATA\tE506,S506,[N|S|E]506\t26770\r\nCGTACTAG\tN702\tTATCCTTT\tE503,S503,[N|S|E]503\t26756\r\nAAGAGGCA\tN711\tCCTGCATC\tUnknown\t26751\r\nTAAGGCGA\tN701\tGATCCTCT\tE503,S503,[N|S|E]503\t26615\r\nTAAGGCGA\tN701\tGAGGAGTC\tUnknown\t26457\r\nCTCTCTAC\tN707\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t26053\r\nAGGCAGAA\tN703\tGTAAGGAT\tE505,S505,[N|S|E]505\t25976\r\nGTAGAGGA\tN712\tCTGCGGCG\tUnknown\t25765\r\nTCCTGAGC\tN704\tAATCCTCT\tE503,S503,[N|S|E]503\t25735\r\nGGACTCCT\tN705\tAAGGCGTA\tS507,[N|S|E]507\t25638\r\nAAGAGGCA\tN711\tAGTGTAGA\tE504,[N|S|E]504\t25628\r\nGGACTCCT\tN705\tGTAAGTAG\tE505,S505,[N|S|E]505\t25481\r\nTAGGCATG\tN706\tTATCCTTT\tE503,S503,[N|S|E]503\t25330\r\nGGACTCCT\tN705\tGTAAGGAT\tE505,S505,[N|S|E]505\t25329\r\nGGACTCCT\tN705\tGTAGGGAG\tE505,S505,[N|S|E]505\t25312\r\nAAGAGGCA\tN711\tCTGCATAT\tUnknown\t25157\r\nCGTACTAG\tN702\tAATCCTCT\tE503,S503,[N|S|E]503\t25047\r\nGGACTCCT\tN705\tGTAAGGAA\tE505,S505,[N|S|E]505\t24977\r\nGTAAGGAA\tE505,S505,[N|S|E]505\tAGAGTAGA\tE504,[N|S|E]504\t24751\r\nTAAGCGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t24487\r\nGTAGAGGA\tN712\tAGAATAGA\tE504,[N|S|E]504\t24396\r\nGTAGAGGA\tN712\tAGATAGAT\tUnknown\t24096\r\nTAGGCATG\tN706\tTATCCTAT\tE503,S503,[N|S|E]503\t24090\r\nTTAGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t23962\r\nTAGGCGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t23915\r\nCGTACTAG\tN702\tAGGAGTAT\tUnknown\t23839\r\nGTAGAGGA\tN712\tAGAGAAGA\tA503,E504,[N|S|E]504\t23611\r\nCGTACTAG\tN702\tTATCCTAT\tE503,S503,[N|S|E]503\t23584\r\nAGAGGCAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t23573\r\nTAAGGCGA\tN701\tGTTAGGAG\tE505,S505,[N|S|E]505\t23568\r\nAAGAGGCA\tN711\tAGAGCAGA\tE504,[N|S|E]504\t23442\r\nCGTACTAG\tN702\tACTGCATA\tE506,S506,[N|S|E]506\t23354\r\nTAAGGCGA\tN701\tGTAGGAGG\tUnknown\t23286\r\nAGGCAGAA\tN703\tGAGGAGTC\tUnknown\t23219\r\nGGACTCCT\tN705\tAAGGAGAA\tS507,[N|S|E]507\t23130\r\nTGACTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t22989\r\nTAGGCATG\tN706\tTATCGTCT\tE503,S503,[N|S|E]503\t22948\r\nTCCTGAGC\tN704\tAGGAGTAT\tUnknown\t22925\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tACTGCATA\tE506,S506,[N|S|E]506\t22830\r\nTAAGGCGA\tN701\tGTACGGCG\tUnknown\t22825\r\nTAGGCATG\tN706\tGTAAGTAG\tE505,S505,[N|S|E]505\t22800\r\nCGAGGCTG\tN710\tAATGCATA\tE506,S506,[N|S|E]506\t22797\r\nTAAGGCGA\tN701\tGTAAGAAG\tE505,S505,[N|S|E]505\t22773\r\nGTAGAGGA\tN712\tAGCGTAGC\tUnknown\t22769\r\nTGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t22711\r\nTCCTGAGC\tN704\tTATCTCTT\tUnknown\t22682\r\nTCCTGAGC\tN704\tTTTCCTCT\tE503,S503,[N|S|E]503\t22581\r\nCGTACTAG\tN702\tAAGGAGAA\tS507,[N|S|E]507\t22544\r\nCGTACTAG\tN702\tTATCGTCT\tE503,S503,[N|S|E]503\t22414\r\nTAGGCATG\tN706\tGTAAGGCG\tE505,S505,[N|S|E]505\t22225\r\nCGTACTAG\tN702\tGTAGGAGT\tUnknown\t22223\r\nGGACTCCT\tN705\tGTTAGGAG\tE505,S505,[N|S|E]505\t22216\r\nAGGCAGAA\tN703\tGTAGGGAG\tE505,S505,[N|S|E]505\t22150\r\nTAAGGCGA\tN701\tCTGCGGCG\tUnknown\t22140\r\nTAGGCATG\tN706\tAAGAAGTA\tS507,[N|S|E]507\t22125\r\nGAGGCTGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t22096\r\nAAGAGGCA\tN711\tACAGCATA\tE506,S506,[N|S|E]506\t21851\r\nGGACTCCT\tN705\tGAGGAGTA\tS507,[N|S|E]507\t21766\r\nTAAGGCGA\tN701\tGTAAGGAT\tE505,S505,[N|S|E]505\t21736\r\nAAGAGGCA\tN711\tACTGAATA\tE506,S506,[N|S|E]506\t21736\r\nAGGCAGAA\tN703\tGTAAAGAG\tE505,S505,[N|S|E]505\t21724\r\nAGGCAGAA\tN703\tAAGGAGCA\tS507,[N|S|E]507\t21722\r\nAAGAGGCA\tN711\tACTACATA\tE506,S506,[N|S|E]506\t21654\r\nTACTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t21626\r\nGTACTAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t21557\r\nTCCTGAGC\tN704\tAAGCAGTA\tS507,[N|S|E]507\t21400\r\nAGGCAGAA\tN703\tAAGAGTAT\tUnknown\t21384\r\nGTAGAGAA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t21331\r\nAGGCAGAA\tN703\tGTAAGGAA\tE505,S505,[N|S|E]505\t21291\r\nAAGAGGCA\tN711\tAGAGTCGA\tE504,[N|S|E]504\t21287\r\nAAGAGGCA\tN711\tAAAGTAGA\tE504,[N|S|E]504\t21204\r\nTCCTGAGC\tN704\tATCCTCTT\tUnknown\t21089\r\nGTAGAGGA\tN712\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t21061\r\nCAGAGAGG\tN708\tAGCGTAGA\tE504,[N|S|E]504\t21056\r\nTAGGCATG\tN706\tGTAAGGAA\tE505,S505,[N|S|E]505\t21041\r\nGTAGAGGA\tN712\tCGAGTAGC\tUnknown\t20938\r\nTCCTGAGC\tN704\tGATCCTCT\tE503,S503,[N|S|E]503\t20858\r\nTAGGCATG\tN706\tGTAAGGAT\tE505,S505,[N|S|E]505\t20691\r\nCTCTCTAC\tN707\tACAGTAGA\tE504,[N|S|E]504\t20655\r\nTCCTGACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t20451\r\nTAGGCATG\tN706\tGTTAGGAG\tE505,S505,[N|S|E]505\t20392\r\nAGGCAGAA\tN703\tGTAAGAGG\tUnknown\t20386\r\nAGGCAAAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t20341\r\nAAGAGGCA\tN711\tCCTGCATT\tUnknown\t20234\r\nGGACTCCT\tN705\tGAGGAGTC\tUnknown\t20189\r\nGTACTAGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t20155\r\nGGACTCCT\tN705\tTATCCTTT\tE503,S503,[N|S|E]503\t20133\r\nTCCTGAGC\tN704\tCATCCTCT\tE503,S503,[N|S|E]503\t20104\r\nTCCTGAGC\tN704\tAAGGAGGA\tS507,[N|S|E]507\t20063\r\nCTCTCTAC\tN707\tAGAGTAAT\tUnknown\t20048\r\nTAAGGCGA\tN701\tGTAAGGAA\tE505,S505,[N|S|E]505\t20010\r\nTCCTGAGC\tN704\tAAGGAGAA\tS507,[N|S|E]507\t20001\r\nGGACTCCT\tN705\tAAGAGTAT\tUnknown\t19999\r\nTAAGGCGA\tN701\tAATCCTCT\tE503,S503,[N|S|E]503\t19969\r\nTCCTGAGC\tN704\tGTAAGGAT\tE505,S505,[N|S|E]505\t19949\r\nCAGAGAGG\tN708\tCTAAGCAT\tS508,[N|S|E]508\t19842\r\nGGACTCCT\tN705\tTATCGTCT\tE503,S503,[N|S|E]503\t19830\r\nAGGCAGAA\tN703\tGAGGAGTA\tS507,[N|S|E]507\t19688\r\nAGGCAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t19681\r\nTAGGCATG\tN706\tAATCCTCT\tE503,S503,[N|S|E]503\t19667\r\nTAAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t19660\r\nTAGCATGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t19626\r\nGGACTCCT\tN705\tTATCCTAT\tE503,S503,[N|S|E]503\t19615\r\nTAAGGCGA\tN701\tCTAAGCCT\tS508,[N|S|E]508\t19414\r\nTAGGCATG\tN706\tGTAAGCAG\tE505,S505,[N|S|E]505\t19406\r\nTAGGCATG\tN706\tAAGCAGTA\tS507,[N|S|E]507\t19388\r\nAGCAGAAA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t19293\r\nTCCTGAGC\tN704\tGTAAGTAG\tE505,S505,[N|S|E]505\t19285\r\nAAGAGGCA\tN711\tAGGGTAGA\tE504,[N|S|E]504\t19234\r\nTAGGCATG\tN706\tAAGGCGTA\tS507,[N|S|E]507\t19212\r\nCGAGGCTG\tN710\tGGAGTAGG\tUnknown\t19097\r\nAGGCAGAA\tN703\tGTTAGGAG\tE505,S505,[N|S|E]505\t19084\r\nTAGCATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t19082\r\nGGACTCCT\tN705\tCAGGAGTC\tUnknown\t19059\r\nAGGCAGAA\tN703\tGTACGGCG\tUnknown\t18965\r\nAGGCAGAA\tN703\tAAGGAATA\tS507,[N|S|E]507\t18824\r\nTAGGCATG\tN706\tGTAGGGAG\tE505,S505,[N|S|E]505\t18816\r\nGGACTCCT\tN705\tCTAAGCCT\tS508,[N|S|E]508\t18740\r\nGTAGAGGA\tN712\tAGGTAGAT\tUnknown\t18733\r\nTAGGCATG\tN706\tACTGCATA\tE506,S506,[N|S|E]506\t18715\r\nAGGCAGAA\tN703\tCTAAGCCT\tS508,[N|S|E]508\t18675\r\nTCCTGAGC\tN704\tAAGAGTAT\tUnknown\t18613\r\nAAGCAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t18573\r\nGGACTCCT\tN705\tAGAGTAGA\tE504,[N|S|E]504\t18437\r\nGTAGAGGA\tN712\tGGAGTCGA\tUnknown\t18398\r\nGTAGAGGA\tN712\tAGAGTATC\tUnknown\t18350\r\nTCCTGAGC\tN704\tGTGAGGAG\tE505,S505,[N|S|E]505\t18128\r\nGTAGAGGA\tN712\tATAGTAGA\tE504,[N|S|E]504\t18052\r\nGGACTCCT\tN705\tAAGGAGGA\tS507,[N|S|E]507\t18009\r\nGTAGAGGA\tN712\tCGAGTCGA\tS513\t18003\r\nGTAGAGGA\tN712\tGCTGCATA\tE506,S506,[N|S|E]506\t17980\r\nCGAGGCTG\tN710\tCGAGTAGG\tUnknown\t17942\r\nAGGCAGAA\tN703\tAAAGAGTA\tS507,[N|S|E]507\t17934\r\nAGGCAAAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t17843\r\nAAGAGGCA\tN711\tGCTGCCTC\tUnknown\t17839\r\nTCTCTACA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t17830\r\nGTAGAGGA\tN712\tCTGCATAT\tUnknown\t17763\r\nTAAGGCGA\tN701\tTATCTCTT\tUnknown\t17752\r\nTCCTGAGC\tN704\tCTAAGCCT\tS508,[N|S|E]508\t17733\r\nAAGAGGCA\tN711\tCGAGTAGG\tUnknown\t17700\r\nAAGAGGCA\tN711\tACTGCGTA\tE506,S506,[N|S|E]506\t17693\r\nTCCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t17655\r\nCAGAGAGA\tN708,S511\tACTGCATA\tE506,S506,[N|S|E]506\t17653\r\nCTCTCTAC\tN707\tATAGTAGA\tE504,[N|S|E]504\t17579\r\nCGTACTAG\tN702\tGTAGGGAG\tE505,S505,[N|S|E]505\t17561\r\nTAAGGCGA\tN701\tAAGAGTAT\tUnknown\t17545\r\nGCTACGCT\tN709\tACTGCGTA\tE506,S506,[N|S|E]506\t17498\r\nCGAGGCTG\tN710\tAGAGTGGA\tE504,[N|S|E]504\t17464\r\nCGTACTAG\tN702\tAAGGAGGA\tS507,[N|S|E]507\t17427\r\nGGACTCCT\tN705\tGTACGGCG\tUnknown\t17318\r\nTAGGCATG\tN706\tAAGGAGAA\tS507,[N|S|E]507\t17250\r\nGTAGAGGA\tN712\tACTGCGTA\tE506,S506,[N|S|E]506\t17154\r\nTCCTGAGC\tN704\tAAGAAGTA\tS507,[N|S|E]507\t17153\r\nGAACTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t17126\r\nTCCTGAGA\tD702,N704\tTATCCTCT\tE503,S503,[N|S|E]503\t17106\r\nGTAGAGGA\tN712\tAGAGTGGG\tUnknown\t17068\r\nAAGAGCAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t17057\r\nTCCTGAGC\tN704\tGTAGGAGG\tUnknown\t17025\r\nCGTACTAG\tN702\tAAGAAGTA\tS507,[N|S|E]507\t17011\r\nAAGAGGCA\tN711\tGGAGTAGA\tE504,[N|S|E]504\t17007\r\nTAGCATGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t16950\r\nAAGAGGCA\tN711\tAGAGAAGA\tA503,E504,[N|S|E]504\t16908\r\nCGAGGCTG\tN710\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t16857\r\nGAGGCTGA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t16832\r\nGGACTCCT\tN705\tAAGTAGTA\tS507,[N|S|E]507\t16817\r\nGGACTCCT\tN705\tATGGAGTA\tS507,[N|S|E]507\t16770\r\nTAAGGCGA\tN701\tGTAAGAGG\tUnknown\t16763\r\nAGGCAGAA\tN703\tGTATGGAG\tE505,S505,[N|S|E]505\t16711\r\nAGAGGCAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t16682\r\nCGTACTAG\tN702\tTTTCCTCT\tE503,S503,[N|S|E]503\t16630\r\nAAGAGGCA\tN711\tACTGATAT\tUnknown\t16609\r\nTAGGCATG\tN706\tTTTCCTCT\tE503,S503,[N|S|E]503\t16576\r\nGGACTCCT\tN705\tCTGCGGCG\tUnknown\t16565\r\nTAAGGCGA\tN701\tATCCTCTT\tUnknown\t16483\r\nGGACTCCT\tN705\tGTAAGAAG\tE505,S505,[N|S|E]505\t16442\r\nGTAGAGGG\tN712\tAGAGTAGA\tE504,[N|S|E]504\t16434\r\nTCCTGAGC\tN704\tGTAAGCAG\tE505,S505,[N|S|E]505\t16408\r\nCAGAGAGG\tN708\tGTAAGCCT\tS508,[N|S|E]508\t16384\r\nAGCAGAAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t16371\r\nCGTACTAG\tN702\tCTGCGGCG\tUnknown\t16354\r\nTAAGGCGA\tN701\tCAGGAGTC\tUnknown\t16292\r\nGTAGAGCA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t16236\r\nGAACTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t16233\r\nGCTACGAT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t16222\r\nCGAGGCTG\tN710\tACTGCGTA\tE506,S506,[N|S|E]506\t16202\r\nCGAGGCTG\tN710\tAGAGTAAT\tUnknown\t16171\r\nGCTACGCT\tN709\tCTACGCCT\tD505,S508,[N|S|E]508\t16134\r\nTAAGGCGA\tN701\tAAGTAGTA\tS507,[N|S|E]507\t16132\r\nTAAGGCGA\tN701\tAAGGAATA\tS507,[N|S|E]507\t16132\r\nCAGAGAGG\tN708\tCCTGCATA\tE506,S506,[N|S|E]506\t16088\r\nGTAGAGGA\tN712\tACAGTAGA\tE504,[N|S|E]504\t16008\r\nTCCTGAGC\tN704\tCTGCGGCG\tUnknown\t15992\r\nTAGGCATG\tN706\tTATCTCTT\tUnknown\t15978\r\nCGTACTAG\tN702\tCTAAGCCT\tS508,[N|S|E]508\t15970\r\nGTAGAGGA\tN712\tAGAGTCGG\tUnknown\t15925\r\nGCTACGCA\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t15925\r\nAAGAGGCA\tN711\tAGAGTAAT\tUnknown\t15913\r\nAGAGAGGA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t15844\r\nAGGCAGAA\tN703\tATAAGGAG\tE505,S505,[N|S|E]505\t15843\r\nTCCTGAGC\tN704\tGATCCTCC\tUnknown\t15825\r\nTGACTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t15766\r\nCAGAGAGG\tN708\tACTGCGTA\tE506,S506,[N|S|E]506\t15716\r\nCGAGGCTG\tN710\tGGAGTAGA\tE504,[N|S|E]504\t15682\r\nAAGAGGCA\tN711\tACTGCCTC\tUnknown\t15665\r\nCTCTCTAC\tN707\tAGAGTGAT\tUnknown\t15663\r\nTCCTGAGC\tN704\tGTAGGGAG\tE505,S505,[N|S|E]505\t15635\r\nGTAGAGGA\tN712\tAAGTAGAT\tUnknown\t15621\r\nTAGGCATG\tN706\tAAGAGTAT\tUnknown\t15600\r\nCGTACTAG\tN702\tGTAGGAGG\tUnknown\t15552\r\nAAGAGGCA\tN711\tGGAGTAGG\tUnknown\t15544\r\nTCCTGCGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t15518\r\nAGGCAGAA\tN703\tCTGCGGCG\tUnknown\t15506\r\nTAGGCATG\tN706\tGAGGAGTA\tS507,[N|S|E]507\t15494\r\nGGACTCCT\tN705\tGTAGGAGG\tUnknown\t15476\r\nAGGCAGAA\tN703\tAAGCAGTT\tUnknown\t15407\r\nCTCTCTAC\tN707\tAGGGTAGA\tE504,[N|S|E]504\t15407\r\nCGTATAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t15379\r\nCGTACTAG\tN702\tAAGCAGTA\tS507,[N|S|E]507\t15272\r\nGTAGAGGA\tN712\tCGCGTAGA\tUnknown\t15203\r\nGTAGAGGA\tN712\tAGTGTATA\tUnknown\t15167\r\nCGTACTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t15152\r\nCGTACTAG\tN702\tTATCTCTT\tUnknown\t14984\r\nCGAGCTGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t14974\r\nCGTACTAG\tN702\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t14973\r\nCAGAGAGG\tN708\tACTGCATG\tE506,S506,[N|S|E]506\t14885\r\nCATACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t14876\r\nTGTACTAG\tA506,N702\tTATCCTCT\tE503,S503,[N|S|E]503\t14844\r\nGTAGAGGA\tN712\tACTGAATA\tE506,S506,[N|S|E]506\t14802\r\nCTCTCTAC\tN707\tCTCAGCCT\tS508,[N|S|E]508\t14775\r\nGGACTCCT\tN705\tCAGGAGTT\tUnknown\t14760\r\nCTCTCTAC\tN707\tAGAGTTGA\tE504,[N|S|E]504\t14665\r\nTACTGAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t14660\r\nGGAGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t14636\r\nGTAGAGGA\tN712\tAGCGTAGG\tUnknown\t14610\r\nTAGGCATG\tN706\tGAGGAGTC\tUnknown\t14610\r\nTCCTGAGA\tD702,N704\tGTAAGGAG\tE505,S505,[N|S|E]505\t14585\r\nCGTACTAG\tN702\tGTAAGGAT\tE505,S505,[N|S|E]505\t14517\r\nTAGGCATG\tN706\tATCCTCTT\tUnknown\t14511\r\nAAGCAGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t14502\r\nTAAGGCGA\tN701\tGTAAAGAG\tE505,S505,[N|S|E]505\t14422\r\nCGTACTAG\tN702\tATCCTCTT\tUnknown\t14412\r\nCGTACTAG\tN702\tGTGAGGAG\tE505,S505,[N|S|E]505\t14376\r\nCGTACTAG\tN702\tGTACGGCG\tUnknown\t14365\r\nGTAGAGGA\tN712\tAGATTAGA\tE504,[N|S|E]504\t14347\r\nGGACTCCT\tN705\tGTATGGAG\tE505,S505,[N|S|E]505\t14283\r\nTAGGCATG\tN706\tAAGGAGGA\tS507,[N|S|E]507\t14264\r\nAAGAGGCA\tN711\tATGCATAT\tUnknown\t14249\r\nGATACGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t14238\r\nGGACTCCT\tN705\tGTAAGGAC\tE505,S505,[N|S|E]505\t14201\r\nCAGAGAGG\tN708\tATAAGCCT\tS508,[N|S|E]508\t14193\r\nGGACTCCT\tN705\tTTTCCTCT\tE503,S503,[N|S|E]503\t14176\r\nCGTACTAG\tN702\tATAAGGAG\tE505,S505,[N|S|E]505\t14146\r\nCGAGGCTG\tN710\tAGAGTGAT\tUnknown\t14037\r\nAAGAGGCA\tN711\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t14022\r\nTCCTGAGC\tN704\tGAGGAGTC\tUnknown\t13999\r\nCTCTCTAC\tN707\tAGACTAGA\tE504,[N|S|E]504\t13986\r\nTAGGCATA\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t13985\r\nTAAGGCGA\tN701\tGATCCTCC\tUnknown\t13959\r\nAAAGGCAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t13935\r\nTAGGCAGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t13916\r\nCGAGGCTG\tN710\tAGAGTTGA\tE504,[N|S|E]504\t13885\r\nTAAGGCGA\tN701\tAAGGAGCA\tS507,[N|S|E]507\t13873\r\nTCCTGAGC\tN704\tGTTAGGAG\tE505,S505,[N|S|E]505\t13873\r\nCTCTCTAC\tN707\tACTGCCTT\tUnknown\t13866\r\nAAGAGGCA\tN711\tACGCATAT\tUnknown\t13849\r\nCTCTCTAC\tN707\tGAGTAGAT\tUnknown\t13834\r\nCTCTCTAC\tN707\tCCTGCATT\tUnknown\t13828\r\nTAGGCATG\tN706\tCTGCGGCG\tUnknown\t13810\r\nAAGAGGCA\tN711\tACTGCAAT\tUnknown\t13752\r\nCTCTCTAC\tN707\tCTGCATAT\tUnknown\t13719\r\nTAGGCAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t13688\r\nTAAGGCGA\tN701\tGTATGGAG\tE505,S505,[N|S|E]505\t13685\r\nGTAGAGGA\tN712\tGGCGTCGC\tUnknown\t13675\r\nGGACTCCT\tN705\tTATCTCTT\tUnknown\t13656\r\nCGTACTAG\tN702\tAAGGAGCA\tS507,[N|S|E]507\t13631\r\nTCCTGACA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t13544\r\nTCTACGCT\tE504,N709,[N|S|E]504\tACTGCATA\tE506,S506,[N|S|E]506\t13540\r\nTAAGGCGA\tN701\tCATCCTCT\tE503,S503,[N|S|E]503\t13529\r\nCAGAGAGG\tN708\tAGAGTAGC\tE504,[N|S|E]504\t13529\r\nGGACTCCT\tN705\tGTGCGGAG\tUnknown\t13523\r\nTAAGGCGA\tN701\tGTAAGGGG\tE505,S505,[N|S|E]505\t13477\r\nGTAGAGGC\tD502,N712\tAGAGTAGA\tE504,[N|S|E]504\t13420\r\nGTAGAGGA\tN712\tAGTGTAGT\tUnknown\t13410\r\nGAACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t13399\r\nCAGAGAGG\tN708\tCGAGTAGA\tE504,[N|S|E]504\t13384\r\nTGAGGCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t13361\r\nGCAGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t13319\r\nTGGCAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t13274\r\nTCCTGAGC\tN704\tGTACGGCG\tUnknown\t13262\r\nGGGCTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t13240\r\nTAGGCATG\tN706\tGTAAGAAG\tE505,S505,[N|S|E]505\t13220\r\nCGAGGCTA\tN710\tAGAGTAGA\tE504,[N|S|E]504\t13204\r\nAGGCAGAA\tN703\tAAGCAGTG\tUnknown\t13130\r\nCAGAGAGG\tN708\tCTGCATAT\tUnknown\t13113\r\nAAGAGGCA\tN711\tACTCCATA\tE506,S506,[N|S|E]506\t13089\r\nAAGAGGCA\tN711\tACTGCTTT\tUnknown\t13073\r\nGTAGGGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t13007\r\nGGACTCCT\tN705\tATCCTCTT\tUnknown\t12990\r\nCAAGGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t12962\r\nGGACTCCT\tN705\tAAGGAATA\tS507,[N|S|E]507\t12960\r\nTACTGAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t12923\r\nCGAGGCTG\tN710\tGAGTAGAT\tUnknown\t12922\r\nTCCTGAGC\tN704\tGTAAGGAA\tE505,S505,[N|S|E]505\t12876\r\nGGCAGAAA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t12854\r\nCGTACTAG\tN702\tAAGAGTAT\tUnknown\t12844\r\nCTCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t12789\r\nCAGAGAGG\tN708\tGCTGCATA\tE506,S506,[N|S|E]506\t12766\r\nAAGAGGCA\tN711\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t12763\r\nCGAGGCTG\tN710\tCTGCATAT\tUnknown\t12703\r\nAAGAGCAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t12688\r\nAAGAGGCA\tN711\tAATGCATT\tUnknown\t12683\r\nCTCTCTAC\tN707\tACTGCTTT\tUnknown\t12660\r\nCTCTCTAC\tN707\tAGAGTAAA\tE504,[N|S|E]504\t12643\r\nGGACTCCT\tN705\tAAGCAGTT\tUnknown\t12634\r\nCTCTCTAC\tN707\tAATGCATA\tE506,S506,[N|S|E]506\t12629\r\nTAAGGCGA\tN701\tTATCTTCT\tE503,S503,[N|S|E]503\t12588\r\nGTAGAGGA\tN712\tAGTGCATA\tE506,S506,[N|S|E]506\t12578\r\nGCTAAGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t12523\r\nAGGCAGAA\tN703\tCAGGAGTC\tUnknown\t12509\r\nTCCTGCGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t12509\r\nTAGGCATG\tN706\tCATCCTCT\tE503,S503,[N|S|E]503\t12460\r\nCGTACTAG\tN702\tGTTAGGAG\tE505,S505,[N|S|E]505\t12454\r\nAGGCAGAA\tN703\tTAAGGAGT\tUnknown\t12430\r\nTAAGGCGA\tN701\tGTGCGGAG\tUnknown\t12425\r\nCTCTCTAC\tN707\tAAAGTAGA\tE504,[N|S|E]504\t12423\r\nGGACTCCT\tN705\tTAAGGAGT\tUnknown\t12418\r\nGTAGCGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t12406\r\nCGTACTAG\tN702\tGTAAGCAG\tE505,S505,[N|S|E]505\t12317\r\nTAAGGCGA\tN701\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t12307\r\nAGGCAGCA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t12258\r\nTCTCTACA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t12257\r\nGTAGAGGA\tN712\tACTGATAT\tUnknown\t12255\r\nTAAGGCGA\tN701\tGTGCGGCG\tUnknown\t12245\r\nCAGAGAGG\tN708\tCTAAGCTT\tS508,[N|S|E]508\t12184\r\nTAGGCATA\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t12178\r\nAAGAGGCA\tN711\tAGAGTGAT\tUnknown\t12168\r\nAGGCAGAA\tN703\tGTAAGGAC\tE505,S505,[N|S|E]505\t12157\r\nTAGGCAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t12153\r\nTAGGCATG\tN706\tGTAGGAGG\tUnknown\t12145\r\nCTCTCTAC\tN707\tCCTGCATC\tUnknown\t12135\r\nAAGAAGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t12118\r\nCTCTCTAC\tN707\tCGAGTAGG\tUnknown\t12115\r\nAAGAGGAA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t12099\r\nTAAGGCGA\tN701\tGTAAGGAC\tE505,S505,[N|S|E]505\t12091\r\nAAGAGGCA\tN711\tACTCATAT\tUnknown\t12069\r\nTCCTGAGC\tN704\tGAGGAGTA\tS507,[N|S|E]507\t12068\r\nGTAGAGGA\tN712\tTGAGTAGA\tE504,[N|S|E]504\t12038\r\nAAGAAGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t12030\r\nTCCTGAGC\tN704\tTATCTTCT\tE503,S503,[N|S|E]503\t12020\r\nCGAGGCTG\tN710\tACTGCATG\tE506,S506,[N|S|E]506\t12002\r\nCGTACTAG\tN702\tAAGTAGTA\tS507,[N|S|E]507\t12000\r\nCAGAGAGG\tN708\tAGAGTCGA\tE504,[N|S|E]504\t11981\r\nAAGAGGCA\tN711\tGAGTAGAT\tUnknown\t11966\r\nGTAGACGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t11961\r\nGTAGAGGA\tN712\tCGACTAGG\tUnknown\t11930\r\nTAGGCATG\tN706\tGATCCTCT\tE503,S503,[N|S|E]503\t11915\r\nGCTACGCT\tN709\tCTAAGCAT\tS508,[N|S|E]508\t11906\r\nCGTATAGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t11900\r\nTAAGGCGA\tN701\tGTAAGGTG\tE505,S505,[N|S|E]505\t11846\r\nAAGAGGCA\tN711\tAGAGTAAA\tE504,[N|S|E]504\t11815\r\nGTAGAGGA\tN712\tAGAGTACA\tA503,E504,[N|S|E]504\t11746\r\nCTCTCTAC\tN707\tACTGCGTA\tE506,S506,[N|S|E]506\t11711\r\nCAGAGAGG\tN708\tAGTGCATA\tE506,S506,[N|S|E]506\t11691\r\nAAGAGGCA\tN711\tACTGCCTT\tUnknown\t11684\r\nTAGGCATG\tN706\tAGAGTAGA\tE504,[N|S|E]504\t11653\r\nTAAGGCGA\tN701\tGAGGAGTG\tUnknown\t11639\r\nAGGCAGAA\tN703\tAAGGACTA\tS507,[N|S|E]507\t11623\r\nTAAGGCGA\tN701\tTTTCCTCT\tE503,S503,[N|S|E]503\t11605\r\nAGGCAGAA\tN703\tGGCTCCAC\tUnknown\t11604\r\nGTAGAGGA\tN712\tCTAAGCCT\tS508,[N|S|E]508\t11558\r\nCTCTCTAC\tN707\tAGAGAGAT\tUnknown\t11519\r\nTAAGGCGA\tN701\tCAGGAGTT\tUnknown\t11519\r\nAGGAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t11517\r\nTAGGCATG\tN706\tCTAAGCCT\tS508,[N|S|E]508\t11510\r\nGCTACGCT\tN709\tACTGAATA\tE506,S506,[N|S|E]506\t11492\r\nAGGCAGAA\tN703\tGTAAGGGG\tE505,S505,[N|S|E]505\t11473\r\nGCTACGCT\tN709\tCTGCATAT\tUnknown\t11467\r\nCGTACTAG\tN702\tTAACCTCT\tE503,S503,[N|S|E]503\t11419\r\nGTAGAGGA\tN712\tAGTGCAGA\tUnknown\t11418\r\nGTAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t11417\r\nTAAGGCGA\tN701\tAAGCAGTT\tUnknown\t11410\r\nTCCTGAGC\tN704\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t11396\r\nCGTACTAG\tN702\tATGGAGTA\tS507,[N|S|E]507\t11380\r\nCTCTCTAC\tN707\tACTGCCTC\tUnknown\t11322\r\nCTCTCTAC\tN707\tAGATTAGA\tE504,[N|S|E]504\t11262\r\nAGGCAGCA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t11232\r\nCAGAGAGA\tN708,S511\tCTAAGCCT\tS508,[N|S|E]508\t11215\r\nCGTATAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t11190\r\nCGTACTAG\tN702\tCATCCTCT\tE503,S503,[N|S|E]503\t11183\r\nGGCAGAAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t11162\r\nCAGAGAGG\tN708\tCTCAGCCT\tS508,[N|S|E]508\t11154\r\nCGTACTAG\tN702\tGAGGAGTC\tUnknown\t11145\r\nGGATCCTA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t11141\r\nTCCTGAGC\tN704\tGTAAGAGG\tUnknown\t11133\r\nAAGAGGAA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t11130\r\nAGGCAGAA\tN703\tAATCCTCT\tE503,S503,[N|S|E]503\t11112\r\nAAGAGGCA\tN711\tACTCCATT\tUnknown\t11089\r\nGGCCTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t11080\r\nCTCTCTAC\tN707\tCGAGTAGC\tUnknown\t11080\r\nTGAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t11049\r\nCATACTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t11038\r\nGTAAAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t11023\r\nCAGAGAGG\tN708\tACTGAATA\tE506,S506,[N|S|E]506\t11015\r\nTAGGCATG\tN706\tAAGGAATA\tS507,[N|S|E]507\t10976\r\nGTAGAGGA\tN712\tAGAGTCGT\tUnknown\t10959\r\nTAGGCATG\tN706\tATGGAGTA\tS507,[N|S|E]507\t10934\r\nTCCTGAGC\tN704\tTTCCTCTT\tUnknown\t10932\r\nTAAGGCAA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t10924\r\nGTAGAGGA\tN712\tACTGCATG\tE506,S506,[N|S|E]506\t10922\r\nCATACTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t10914\r\nAGGCAGAA\tN703\tGTAACGAG\tE505,S505,[N|S|E]505\t10900\r\nTAGGCATA\tN706\tAAGGAGTA\tS507,[N|S|E]507\t10887\r\nGGCCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t10875\r\nCGAGGCTG\tN710\tACTGCTTT\tUnknown\t10866\r\nGTAGAGGA\tN712\tGCTGCATC\tUnknown\t10864\r\nCGAGGCTA\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t10863\r\nGTATAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t10862\r\nGCTACGAT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t10845\r\nGTAGAGGA\tN712\tATGCATAT\tUnknown\t10827\r\nGAAGAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t10816\r\nCGAGGCTG\tN710\tAGAGAGAT\tUnknown\t10783\r\nTCCTGACA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t10754\r\nGTAGAGGA\tN712\tAGTAGATC\tUnknown\t10751\r\nAAGAGGCA\tN711\tCTGCGGCG\tUnknown\t10735\r\nTAGGCATG\tN706\tAAGTAGTA\tS507,[N|S|E]507\t10732\r\nCTCTCTAC\tN707\tAGCGTAGC\tUnknown\t10724\r\nCGAGGCTG\tN710\tACTGAATA\tE506,S506,[N|S|E]506\t10708\r\nCGAGCTGA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t10705\r\nGTAGGGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t10688\r\nTCCTGAGC\tN704\tCAGGAGTC\tUnknown\t10672\r\nCGTACTAT\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t10649\r\nCTCTCTAC\tN707\tAGAGTCGC\tUnknown\t10633\r\nCAAGGCTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t10624\r\nCGAGGCTG\tN710\tAGAGCAGA\tE504,[N|S|E]504\t10602\r\nTAGTCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t10586\r\nCAGAGAGG\tN708\tCTAGGCCT\tS508,[N|S|E]508\t10569\r\nCTCTCTAC\tN707\tAGAATAGA\tE504,[N|S|E]504\t10565\r\nAAAGGCAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t10535\r\nTAGGCATG\tN706\tAAGCAGTT\tUnknown\t10534\r\nAGGCAGAA\tN703\tAAGGATAT\tS520\t10522\r\nTAGGCATG\tN706\tGTACGGCG\tUnknown\t10478\r\nTAAGGCGG\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t10476\r\nCGTACTAG\tN702\tGTAAGGTG\tE505,S505,[N|S|E]505\t10451\r\nGTAGAGGA\tN712\tAGAGGAGG\tUnknown\t10449\r\nTGCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t10438\r\nCGTACTAG\tN702\tGTAAGAGG\tUnknown\t10427\r\nAGAGAGGA\tUnknown\tCTAAGCCT\tS508,[N|S|E]508\t10418\r\nTAGGCATG\tN706\tTAAGGAGT\tUnknown\t10394\r\nGGATCCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t10362\r\nGTAGAGGA\tN712\tACTGCAAT\tUnknown\t10347\r\nCACTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t10264\r\nTAAGGCAA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t10242\r\nTAAGGCGA\tN701\tATAAGGAG\tE505,S505,[N|S|E]505\t10237\r\nTAGGCATG\tN706\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t10220\r\nTAAGGCGA\tN701\tAAGGACTA\tS507,[N|S|E]507\t10213\r\nGGACTCCT\tN705\tAAGGACTA\tS507,[N|S|E]507\t10208\r\nTGTACTAG\tA506,N702\tGTAAGGAG\tE505,S505,[N|S|E]505\t10180\r\nGTAGAGGA\tN712\tACGCATAT\tUnknown\t10179\r\nAAGGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t10172\r\nTAATGCGA\tD708,N701,S522\tTATCCTCT\tE503,S503,[N|S|E]503\t10160\r\nAGGCAGAA\tN703\tAATGAGTA\tS507,[N|S|E]507\t10156\r\nCGTACTAG\tN702\tGAGGAGTA\tS507,[N|S|E]507\t10149\r\nGGGCTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t10146\r\nTAGGCATG\tN706\tCAGGAGTT\tUnknown\t10140\r\nTAAGACGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t10139\r\nGGACTCCT\tN705\tGTAAAGAG\tE505,S505,[N|S|E]505\t10110\r\nAGGCAGAA\tN703\tAAGGGTAT\tS520\t10106\r\nCTCTCTAC\tN707\tACTGCATG\tE506,S506,[N|S|E]506\t10100\r\nGTAGAGGA\tN712\tAGACTAGG\tUnknown\t10092\r\nGGACTCCT\tN705\tGTAAGAGG\tUnknown\t10085\r\nAGGCAGAA\tN703\tGTAAGGTG\tE505,S505,[N|S|E]505\t10083\r\nTCCTGAGC\tN704\tAAGTAGTA\tS507,[N|S|E]507\t10047\r\nTCCTGAGC\tN704\tAAGCAGTT\tUnknown\t10023\r\nTCCTTAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t10022\r\nCGTACTAG\tN702\tGATCCTCT\tE503,S503,[N|S|E]503\t9979\r\nAGGCAGGA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t9950\r\nGGGCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t9949\r\nGTAGAGTA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t9944\r\nGCTACGCT\tN709\tCGAGTAGA\tE504,[N|S|E]504\t9937\r\nGCTACGCA\tN709\tCTAAGCCT\tS508,[N|S|E]508\t9934\r\nAAGAGGCA\tN711\tGGAGTAGC\tUnknown\t9929\r\nCTCTCTAC\tN707\tAGAGTGGA\tE504,[N|S|E]504\t9929\r\nTCCTGAGC\tN704\tGTAAGGTG\tE505,S505,[N|S|E]505\t9902\r\nCGTACTAG\tN702\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t9887\r\nTCCTGAGC\tN704\tTAGCCTCT\tE503,S503,[N|S|E]503\t9886\r\nAGGCAGAA\tN703\tGTGCGGAG\tUnknown\t9876\r\nTAGGCATG\tN706\tCAGGAGTC\tUnknown\t9870\r\nGGACTCCT\tN705\tAAGGATAT\tS520\t9847\r\nGTAGAGGA\tN712\tACTACATA\tE506,S506,[N|S|E]506\t9813\r\nTCTACGCT\tE504,N709,[N|S|E]504\tCTAAGCCT\tS508,[N|S|E]508\t9807\r\nGGACTCAT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t9764\r\nTAGGCATG\tN706\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t9748\r\nAGGCAGAA\tN703\tAAGGATTA\tS507,[N|S|E]507\t9743\r\nAGACAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t9740\r\nAAGAGGCA\tN711\tAGTGCATA\tE506,S506,[N|S|E]506\t9739\r\nCAGAGAGG\tN708\tAGAGTAGT\tE504,[N|S|E]504\t9732\r\nGGACTCCT\tN705\tAAGGGTAT\tS520\t9725\r\nGTAGAGGA\tN712\tAGAGTAAG\tUnknown\t9707\r\nCTCTCTAC\tN707\tACTGATAT\tUnknown\t9705\r\nGTAGAGGA\tN712\tACTGTATA\tE506,S506,[N|S|E]506\t9697\r\nAGGCAGAA\tN703\tTATCATCT\tE503,S503,[N|S|E]503\t9694\r\nCAGAGAGG\tN708\tACTGCTTT\tUnknown\t9694\r\nCTCTCTAC\tN707\tACTACATA\tE506,S506,[N|S|E]506\t9687\r\nTGAGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t9686\r\nAGGCAGAA\tN703\tAAGCAGTC\tUnknown\t9681\r\nCGTACTAG\tN702\tGTAAGAAG\tE505,S505,[N|S|E]505\t9670\r\nTCCTGAGA\tD702,N704\tAAGGAGTA\tS507,[N|S|E]507\t9661\r\nTAAGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t9654\r\nGGACTCCT\tN705\tGTGCGGCG\tUnknown\t9636\r\nTAAGGCGA\tN701\tATGGAGTA\tS507,[N|S|E]507\t9633\r\nTCCTGAGC\tN704\tAAGGATAT\tS520\t9621\r\nGAGAGGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t9612\r\nGTAGAGGA\tN712\tGGCGTAGC\tUnknown\t9593\r\nAAGGCGAA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t9550\r\nAGTCAGAA\tD705,N703\tGTAAGGAG\tE505,S505,[N|S|E]505\t9541\r\nGTAGAGGA\tN712\tAGAGTTGT\tUnknown\t9538\r\nCGTACTAG\tN702\tGTATGGAG\tE505,S505,[N|S|E]505\t9509\r\nTCCTGAGC\tN704\tTATCCCTT\tUnknown\t9493\r\nTAGGCATG\tN706\tGTATGGAG\tE505,S505,[N|S|E]505\t9482\r\nGTAGAGGA\tN712\tACAGCATA\tE506,S506,[N|S|E]506\t9469\r\nACGCAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t9463\r\nTAGGCATG\tN706\tTATCTTCT\tE503,S503,[N|S|E]503\t9463\r\nAAGAGGCA\tN711\tACTGCTAT\tUnknown\t9449\r\nGTAGAGGA\tN712\tACTGCTTT\tUnknown\t9448\r\nAAGAGGCA\tN711\tAGAGAGAT\tUnknown\t9448\r\nGGACTCCT\tN705\tGTAAGGGG\tE505,S505,[N|S|E]505\t9426\r\nTAAGGCGA\tN701\tGAAAGGAG\tE505,S505,[N|S|E]505\t9408\r\nTCCTGAGC\tN704\tGTAAGAAG\tE505,S505,[N|S|E]505\t9398\r\nTAGACATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t9396\r\nTCCTGAGC\tN704\tAAGGGTAT\tS520\t9323\r\nTCCTGAGC\tN704\tTACCTCTT\tUnknown\t9306\r\nGCTACACT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t9304\r\nGTAGAGGA\tN712\tACTCATAT\tUnknown\t9300\r\nACGAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t9284\r\nCGAGGCTG\tN710\tCTACGCCT\tD505,S508,[N|S|E]508\t9207\r\nTAGAGGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t9190\r\nCTCTCTAC\tN707\tAGAGCAGA\tE504,[N|S|E]504\t9159\r\nCAGAGAGG\tN708\tTAAGCCTT\tUnknown\t9157\r\nAAGAGGCA\tN711\tCCTGCATG\tUnknown\t9141\r\nGCTACTCT\tE504,N709,[N|S|E]504\tACTGCATA\tE506,S506,[N|S|E]506\t9118\r\nGTAAGGAA\tE505,S505,[N|S|E]505\tACTGCATA\tE506,S506,[N|S|E]506\t9117\r\nCGAGGCTG\tN710\tAGTGCATA\tE506,S506,[N|S|E]506\t9113\r\nCTCTCTAC\tN707\tAGATAGAT\tUnknown\t9106\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tCTAAGCCT\tS508,[N|S|E]508\t9066\r\nGTAGATGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t9055\r\nTCCTGATC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t9030\r\nGGACTCCT\tN705\tAATCCTCT\tE503,S503,[N|S|E]503\t9014\r\nCGTACTAG\tN702\tAAGGAATA\tS507,[N|S|E]507\t9006\r\nTCTGAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t9000\r\nTCATGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t8999\r\nGACTCCTA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t8981\r\nCGACTCCT\tN705\tACTGCATA\tE506,S506,[N|S|E]506\t8976\r\nCAGAGAGG\tN708\tACTGATAT\tUnknown\t8974\r\nTAAGGCGA\tN701\tTAAGGAGT\tUnknown\t8967\r\nTAAGGCGA\tN701\tAATGAGTA\tS507,[N|S|E]507\t8940\r\nTCCTGAGC\tN704\tCAGGAGTT\tUnknown\t8939\r\nAAGGCGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t8917\r\nTAAGGAGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t8876\r\nGTAGAGGA\tN712\tAGCGTCGA\tUnknown\t8872\r\nAAAAAAAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t8866\r\nAAGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t8854\r\nGCACTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t8844\r\nTAAGGCGA\tN701\tAAGCAGTG\tUnknown\t8844\r\nGCTACGCT\tN709\tAGTGTAGA\tE504,[N|S|E]504\t8843\r\nGACTCCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t8837\r\nTCCTGAGC\tN704\tAATGAGTA\tS507,[N|S|E]507\t8830\r\nCGTACTAG\tN702\tGATCCTCC\tUnknown\t8821\r\nCTCTCTAC\tN707\tAGAGTACA\tA503,E504,[N|S|E]504\t8821\r\nCTCTCTAC\tN707\tGCTGCATC\tUnknown\t8820\r\nAGACAGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t8815\r\nTAAGGCGG\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t8811\r\nTCCTGAAC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t8794\r\nCGAGGCTG\tN710\tAGATAGAT\tUnknown\t8784\r\nGGACTCCT\tN705\tATAAGGAG\tE505,S505,[N|S|E]505\t8781\r\nTCCTGAGC\tN704\tTAAGGAGT\tUnknown\t8772\r\nAGGCAGAA\tN703\tCAGCAGTG\tUnknown\t8759\r\nTCCTAAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t8757\r\nTCCTGAGC\tN704\tAAGGAATA\tS507,[N|S|E]507\t8752\r\nTAAGGCGA\tN701\tTTCCTCTT\tUnknown\t8747\r\nGTAGAGGA\tN712\tAGAGTACG\tUnknown\t8743\r\nCGAGGCTG\tN710\tACTGATAT\tUnknown\t8729\r\nTAGGCATG\tN706\tGTAAGGAC\tE505,S505,[N|S|E]505\t8720\r\nAAGAGGCA\tN711\tAGAGTTGA\tE504,[N|S|E]504\t8703\r\nCGAGGCTG\tN710\tAGAGTAAA\tE504,[N|S|E]504\t8691\r\nGTGGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t8689\r\nCGTCCTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t8684\r\nAGGCAGAA\tN703\tGGAGTATC\tUnknown\t8681\r\nGGTCTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t8660\r\nTAAGGCGA\tN701\tAAGGATAT\tS520\t8660\r\nCGAGGCTG\tN710\tCCTGCATT\tUnknown\t8657\r\nCAGAGAGG\tN708\tGCTGCATC\tUnknown\t8648\r\nGTAGAGGA\tN712\tAAGGTAGA\tUnknown\t8644\r\nTGGCAGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t8612\r\nGGCCTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t8586\r\nTAAGGCGA\tN701\tGTAACGAG\tE505,S505,[N|S|E]505\t8586\r\nCAGAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t8585\r\nCAGAGAGG\tN708\tAGGGTAGA\tE504,[N|S|E]504\t8579\r\nTAAGGCAA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t8574\r\nGGACTCAT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t8551\r\nTAGGCCTG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t8549\r\nAGGCAGAA\tN703\tAAGAAGAA\tUnknown\t8546\r\nTAATGCGA\tD708,N701,S522\tGTAAGGAG\tE505,S505,[N|S|E]505\t8541\r\nGGACTCCT\tN705\tGTAAGGTG\tE505,S505,[N|S|E]505\t8537\r\nGTAGAGGA\tN712\tAGGGTGGA\tUnknown\t8509\r\nTCCTGAGC\tN704\tATAAGGAG\tE505,S505,[N|S|E]505\t8486\r\nGTAGAAGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t8474\r\nCAGAGCGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t8469\r\nCGTACTAG\tN702\tAAGGAGCT\tUnknown\t8460\r\nAGGCAGAA\tN703\tAAGGAGAG\tUnknown\t8443\r\nTAAGACGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t8438\r\nGGACTCTA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t8435\r\nCGTACTAG\tN702\tCAGGAGTC\tUnknown\t8411\r\nTCAGGCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t8405\r\nGGTCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t8392\r\nCTCTCTAC\tN707\tGTAAGGAG\tE505,S505,[N|S|E]505\t8389\r\nAAGAGGCA\tN711\tACTTCATA\tE506,S506,[N|S|E]506\t8380\r\nAGGCAGAA\tN703\tGAGGAGTG\tUnknown\t8367\r\nTATGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t8344\r\nCGAGGCTG\tN710\tGGAGTAGC\tUnknown\t8339\r\nTTCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t8337\r\nATAGAGGA\tD502,N712\tAGAGTAGA\tE504,[N|S|E]504\t8335\r\nGGATCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t8304\r\nCTCTCTAC\tN707\tCTAAGCAT\tS508,[N|S|E]508\t8298\r\nCTATCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t8290\r\nTAAGGCGA\tN701\tAAGGGTAT\tS520\t8268\r\nCTCTCTAC\tN707\tGGAGTAGA\tE504,[N|S|E]504\t8266\r\nCTCTCTAC\tN707\tATGCATAT\tUnknown\t8252\r\nGGACTCAT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t8246\r\nCGTACTAG\tN702\tGTAAGGAA\tE505,S505,[N|S|E]505\t8236\r\nGGACTCCT\tN705\tGGAGTATC\tUnknown\t8229\r\nGCTAAGCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t8198\r\nTAGGCATG\tN706\tGTAAAGAG\tE505,S505,[N|S|E]505\t8192\r\nCGTACTAG\tN702\tCAGGAGTT\tUnknown\t8188\r\nAGGCAGGA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t8182\r\nTCCTCAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t8172\r\nCAGAGAGG\tN708\tAGTGTAGA\tE504,[N|S|E]504\t8168\r\nTCCTGAGC\tN704\tAAGGAGCA\tS507,[N|S|E]507\t8161\r\nAGGAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t8152\r\nTGGGCATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t8150\r\nCGTACTAG\tN702\tTATCTTCT\tE503,S503,[N|S|E]503\t8143\r\nAGGCAGAA\tN703\tAAGGAGCT\tUnknown\t8122\r\nTGGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t8097\r\nTAGGCATG\tN706\tAAGGATAT\tS520\t8091\r\nAAGAGGCA\tN711\tAGATAGAT\tUnknown\t8046\r\nAAGGGCAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t8041\r\nAAGAGGCA\tN711\tCTAAGCCT\tS508,[N|S|E]508\t8027\r\nGTAGAGCA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t8024\r\nTCCTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t8013\r\nCTCTCTAC\tN707\tTGAGTAGA\tE504,[N|S|E]504\t8009\r\nTAGGCATG\tN706\tGTAAGAGG\tUnknown\t8004\r\nCAGAGAGG\tN708\tATGCATAT\tUnknown\t7997\r\nGCACTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t7996\r\nAGGCAGAA\tN703\tGTACGCAG\tUnknown\t7993\r\nGCTACGCT\tN709\tACTACATA\tE506,S506,[N|S|E]506\t7993\r\nCTCTCTAC\tN707\tACTCCATT\tUnknown\t7964\r\nCTCTCTAC\tN707\tACTGCAAT\tUnknown\t7964\r\nGGACTCCT\tN705\tTATCTTCT\tE503,S503,[N|S|E]503\t7957\r\nGCTACGCT\tN709\tCTTAGCCT\tD505,S508,[N|S|E]508\t7955\r\nAGGCAGAA\tN703\tCAGGAGTT\tUnknown\t7937\r\nAGGCAGAA\tN703\tGTGCGGCG\tUnknown\t7929\r\nAGGCAGAA\tN703\tGTACGTAG\tUnknown\t7915\r\nTAGGCATG\tN706\tATAAGGAG\tE505,S505,[N|S|E]505\t7909\r\nATGCAGAA\tD705,N703\tGTAAGGAG\tE505,S505,[N|S|E]505\t7908\r\nCTCTCTAC\tN707\tACGCATAT\tUnknown\t7904\r\nTCCTGAGC\tN704\tGTAAAGAG\tE505,S505,[N|S|E]505\t7891\r\nCGTACTAG\tN702\tAAGCAGTT\tUnknown\t7885\r\nTAAGGCGA\tN701\tTATCCCTT\tUnknown\t7884\r\nTCAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t7878\r\nGGACTCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t7854\r\nAAGAGGCA\tN711\tAGAGTGGA\tE504,[N|S|E]504\t7849\r\nAGGCAGAA\tN703\tAAGAAGTG\tUnknown\t7844\r\nAGGCAGAA\tN703\tGCAAGGAG\tE505,S505,[N|S|E]505\t7844\r\nTCCTGAGC\tN704\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t7840\r\nCGTCCTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t7833\r\nGGACTCCT\tN705\tAATGAGTA\tS507,[N|S|E]507\t7832\r\nGTACAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t7814\r\nGTAGAGGA\tN712\tCGCGTAGC\tUnknown\t7809\r\nGCTACGCC\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t7803\r\nCTAGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t7800\r\nGTAGAGGA\tN712\tGTAAGGAG\tE505,S505,[N|S|E]505\t7791\r\nTCCTGAGC\tN704\tGTAAGGGG\tE505,S505,[N|S|E]505\t7788\r\nGGACTCCC\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t7784\r\nTCCTGAGC\tN704\tACTGCATT\tE506,S506,[N|S|E]506\t7776\r\nCGTACTAG\tN702\tAGGGAGTA\tS507,[N|S|E]507\t7764\r\nCTCTCTAC\tN707\tACTGAATA\tE506,S506,[N|S|E]506\t7757\r\nTCCTAAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t7744\r\nCGAGGCTG\tN710\tACTGCCTT\tUnknown\t7740\r\nCGAGGCTG\tN710\tATGCATAT\tUnknown\t7736\r\nTAAGGCGA\tN701\tAAGGAGCT\tUnknown\t7734\r\nAGGCAGAA\tN703\tAAGGATTT\tUnknown\t7732\r\nTCCTGAGC\tN704\tTAACCTCT\tE503,S503,[N|S|E]503\t7723\r\nTCCTGAGC\tN704\tATGGAGTA\tS507,[N|S|E]507\t7697\r\nTAGGCATG\tN706\tTTCCTCTT\tUnknown\t7696\r\nGTAGAGGA\tN712\tAGAATAGG\tD503\t7688\r\nAAGAGGCA\tN711\tAGAATAGA\tE504,[N|S|E]504\t7684\r\nAGGCAGAA\tN703\tGACTCCAC\tUnknown\t7672\r\nCAGAGAGG\tN708\tCTACGCCC\tUnknown\t7671\r\nTAGGCATG\tN706\tAAGGGTAT\tS520\t7671\r\nCGTACTAG\tN702\tTTCCTCTT\tUnknown\t7670\r\nTAAGGCGC\tD708,N701,S521\tTATCCTCT\tE503,S503,[N|S|E]503\t7653\r\nTAAGGCGA\tN701\tGTACGTAG\tUnknown\t7649\r\nTAAGGCGA\tN701\tGTACGCAG\tUnknown\t7647\r\nTTAGAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t7645\r\nTAGTCATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t7639\r\nCTCTCTAC\tN707\tCGAGTCGA\tS513\t7612\r\nGTAGAGGA\tN712\tCGAGTCGC\tUnknown\t7609\r\nGTAGAGGA\tN712\tACTGCCTT\tUnknown\t7609\r\nGGACTCCT\tN705\tAGGGAGTA\tS507,[N|S|E]507\t7603\r\nCGTACTAT\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t7590\r\nTCCTGAGC\tN704\tGTAAGGAC\tE505,S505,[N|S|E]505\t7590\r\nGTAGAGGA\tN712\tAAGGAGTA\tS507,[N|S|E]507\t7588\r\nCTCTCTAC\tN707\tACTCCATA\tE506,S506,[N|S|E]506\t7585\r\nACGCAGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t7585\r\nTAAGGCGA\tN701\tTACCTCTT\tUnknown\t7584\r\nGCTACGCT\tN709\tACTGCTTT\tUnknown\t7581\r\nTAGACATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t7566\r\nGCTACGCT\tN709\tCCTGCATT\tUnknown\t7547\r\nCTCTATAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t7539\r\nCCCTGAGC\tN704\tACTGCATA\tE506,S506,[N|S|E]506\t7539\r\nCGTACTAG\tN702\tTAGCCTCT\tE503,S503,[N|S|E]503\t7536\r\nTAGGAATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t7522\r\nCTAGAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t7518\r\nTAAGACGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t7500\r\nCAGAGAGG\tN708\tGGAGTAGG\tUnknown\t7496\r\nTAAGCATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t7489\r\nAATAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t7480\r\nTGGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t7465\r\nGTACTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t7462\r\nCGGCAGAA\tN703\tACTGCATA\tE506,S506,[N|S|E]506\t7454\r\nTAAGGAGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t7454\r\nGCTACCCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t7447\r\nCAGAGAGG\tN708\tACTGCAAT\tUnknown\t7446\r\nTAGGCATG\tN706\tAATGAGTA\tS507,[N|S|E]507\t7446\r\nCGAGGCTG\tN710\tGCTGCATA\tE506,S506,[N|S|E]506\t7443\r\nCAGAGAGG\tN708\tACAGCATA\tE506,S506,[N|S|E]506\t7442\r\nTCGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t7422\r\nGGACTCCT\tN705\tGAAGGAGT\tUnknown\t7412\r\nTAGGCCTG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t7411\r\nCGAGGCTG\tN710\tACTGCAAT\tUnknown\t7411\r\nGATACGCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t7395\r\nCGAGGCTG\tN710\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t7395\r\nGTAGAGGA\tN712\tCTGCTGCG\tUnknown\t7392\r\nTAAGGCGA\tN701\tTAACCTCT\tE503,S503,[N|S|E]503\t7381\r\nAAGAGGCA\tN711\tAGACTAGA\tE504,[N|S|E]504\t7375\r\nGGACTCCT\tN705\tGTACGCAG\tUnknown\t7364\r\nACCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t7363\r\nAGGCAGAA\tN703\tGTAATGAG\tE505,S505,[N|S|E]505\t7358\r\nGCTACGCT\tN709\tACTGTATA\tE506,S506,[N|S|E]506\t7348\r\nGTAGAGGA\tN712\tCCTGCATT\tUnknown\t7347\r\nAGTCAGAA\tD705,N703\tAAGGAGTA\tS507,[N|S|E]507\t7337\r\nTGTACTAG\tA506,N702\tAAGGAGTA\tS507,[N|S|E]507\t7329\r\nTAGGAATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t7325\r\nAGGCAGAA\tN703\tTATCCTAT\tE503,S503,[N|S|E]503\t7324\r\nCAGAGAGG\tN708\tACGCATAT\tUnknown\t7322\r\nGCTACGCA\tN709\tAGAGTAGA\tE504,[N|S|E]504\t7311\r\nCGTACTAG\tN702\tAAGGATTT\tUnknown\t7307\r\nTAGGCATG\tN706\tGTGCGGAG\tUnknown\t7305\r\nCACTCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t7278\r\nTGCTGAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t7275\r\nGCTACGCT\tN709\tAGAGTAGG\tE504,[N|S|E]504\t7269\r\nCTCTCTAC\tN707\tAGGTAGAT\tUnknown\t7256\r\nTCCTGAGC\tN704\tGTATGGAG\tE505,S505,[N|S|E]505\t7254\r\nGGACTCCA\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t7248\r\nCTCTCTAC\tN707\tACTCATAT\tUnknown\t7233\r\nCGTACTAG\tN702\tGTAAGGGG\tE505,S505,[N|S|E]505\t7222\r\nCTCTCTAC\tN707\tGGAGTAGG\tUnknown\t7206\r\nTAAGGCGA\tN701\tTATCCACC\tUnknown\t7192\r\nGTAGAGGA\tN712\tCGAGTAGT\tUnknown\t7160\r\nCGAGGCTG\tN710\tACGCATAT\tUnknown\t7142\r\nCGAGGCTG\tN710\tCGAGTAGC\tUnknown\t7140\r\nGTACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t7138\r\nTAGGCATC\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t7128\r\nGGACTCCT\tN705\tAAGGAGCA\tS507,[N|S|E]507\t7126\r\nTCCTGAAC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t7115\r\nGCACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t7108\r\nCGTACTAG\tN702\tGTAAAGAG\tE505,S505,[N|S|E]505\t7088\r\nTCATGAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t7076\r\nTAGGCATG\tN706\tGATCCTCC\tUnknown\t7072\r\nGTAGAGGA\tN712\tAATGCATT\tUnknown\t7061\r\nTAAGGCGG\tN701\tAAGGAGTA\tS507,[N|S|E]507\t7061\r\nAGGCAGAA\tN703\tTACCCTCC\tUnknown\t7059\r\nTAAGGCGC\tD708,N701,S521\tGTAAGGAG\tE505,S505,[N|S|E]505\t7055\r\nGGACTCCT\tN705\tGTCCGGAG\tUnknown\t7046\r\nTAAGGCGA\tN701\tCTAAGGAG\tE505,S505,[N|S|E]505\t7044\r\nCGACTCCT\tN705\tCTAAGCCT\tS508,[N|S|E]508\t7043\r\nGGACTCCT\tN705\tCTAAGGAG\tE505,S505,[N|S|E]505\t7043\r\nCTCTCTAC\tN707\tAGTGTATA\tUnknown\t7042\r\nTAAGGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t7039\r\nCCCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t7028\r\nGCTACGCT\tN709\tACTGATAT\tUnknown\t7027\r\nAGGCAGAA\tN703\tAAGGAGCC\tUnknown\t7018\r\nATGCAGAA\tD705,N703\tAAGGAGTA\tS507,[N|S|E]507\t7005\r\nTCCTGAGC\tN704\tAAGCAGTG\tUnknown\t7004\r\nTAGACATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t7000\r\nAAGAGACA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t6989\r\nAGGCAGAA\tN703\tATGGAGTA\tS507,[N|S|E]507\t6983\r\nCTCTCTAC\tN707\tACTGTATA\tE506,S506,[N|S|E]506\t6975\r\nCTCTCTAC\tN707\tAAGGAGTA\tS507,[N|S|E]507\t6973\r\nTAAGCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t6971\r\nCGTACTAG\tN702\tAAGGCGTT\tUnknown\t6971\r\nCGTACTAT\tN702\tAAGGAGTA\tS507,[N|S|E]507\t6965\r\nGGACTCCT\tN705\tGTAACGAG\tE505,S505,[N|S|E]505\t6941\r\nCTCTCTAC\tN707\tCTAAGCTT\tS508,[N|S|E]508\t6938\r\nTCCTGCGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t6934\r\nGGTCTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t6931\r\nTAAGGCGA\tN701\tGGAGTATC\tUnknown\t6916\r\nTAAAGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t6914\r\nGTAGAGGA\tN712\tACTGCTAT\tUnknown\t6914\r\nGGACTCCT\tN705\tCATCCTCT\tE503,S503,[N|S|E]503\t6911\r\nGCTACGCT\tN709\tACTGCAAT\tUnknown\t6911\r\nCGAGGCTG\tN710\tAGTGTATA\tUnknown\t6908\r\nCGAGGCTG\tN710\tAGAGTGGG\tUnknown\t6904\r\nAAAAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t6893\r\nTAGGCATG\tN706\tGTAAGGTG\tE505,S505,[N|S|E]505\t6883\r\nCAAGGCGA\tN701\tACTGCATA\tE506,S506,[N|S|E]506\t6875\r\nTCCTGAGC\tN704\tGCATCTCG\tUnknown\t6874\r\nGCTACGCT\tN709\tACTGCCTT\tUnknown\t6873\r\nGCTACGAT\tN709\tAGAGTAGA\tE504,[N|S|E]504\t6862\r\nTAAGGCGA\tN701\tACTGCATT\tE506,S506,[N|S|E]506\t6854\r\nTGGGCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t6847\r\nCGAGGCTG\tN710\tAGGTAGAT\tUnknown\t6847\r\nTAGGCATG\tN706\tGTAAGGGG\tE505,S505,[N|S|E]505\t6843\r\nTAAGGCGA\tN701\tTAGCCTCT\tE503,S503,[N|S|E]503\t6831\r\nAAGAGGCA\tN711\tACGGCATA\tE506,S506,[N|S|E]506\t6808\r\nAGGCAGAA\tN703\tTAAGGAGG\tUnknown\t6800\r\nCAGAGAGG\tN708\tACTCATAT\tUnknown\t6793\r\nTAAGGCGA\tN701\tCAGCAGTG\tUnknown\t6791\r\nAAGAGGCA\tN711\tCGAGTAGC\tUnknown\t6786\r\nCGTACTAG\tN702\tAAGGATTA\tS507,[N|S|E]507\t6776\r\nGACTCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t6773\r\nAAAAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t6767\r\nAGGCAGAA\tN703\tGAAGGAGT\tUnknown\t6746\r\nCTATCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t6744\r\nCGAGGCTG\tN710\tACTCATAT\tUnknown\t6727\r\nGGACTCCT\tN705\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t6713\r\nAAGAGGCA\tN711\tACTGCTTA\tE506,S506,[N|S|E]506\t6710\r\nAAGACGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t6704\r\nTAGGCATG\tN706\tGGAGTATC\tUnknown\t6694\r\nTAAGGCGA\tN701\tCAGGAGTG\tUnknown\t6692\r\nGTAGAGGA\tN712\tACTGCCTC\tUnknown\t6673\r\nCGAGGCTG\tN710\tGGAGTCGC\tUnknown\t6670\r\nTCTGAGCA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t6664\r\nGGACTCCT\tN705\tAAGCAGTG\tUnknown\t6661\r\nCTCTCTAC\tN707\tGGAGTAGC\tUnknown\t6658\r\nGCTACTCT\tE504,N709,[N|S|E]504\tCTAAGCCT\tS508,[N|S|E]508\t6658\r\nGGACTCCC\tN705\tAAGGAGTA\tS507,[N|S|E]507\t6652\r\nGGACTCCT\tN705\tGATCCTCT\tE503,S503,[N|S|E]503\t6651\r\nGTAGAGGA\tN712\tAGCGTCGC\tUnknown\t6641\r\nTAGTCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t6633\r\nGGACTCCT\tN705\tAAGGATTT\tUnknown\t6627\r\nTAAGGCGA\tN701\tGTAATGAG\tE505,S505,[N|S|E]505\t6625\r\nCTCTCTAC\tN707\tAGAGTATC\tUnknown\t6619\r\nTCCTTAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t6605\r\nCGTACTAG\tN702\tAATGAGTA\tS507,[N|S|E]507\t6604\r\nCAGAGAGG\tN708\tCTAAGCCG\tS508,[N|S|E]508\t6596\r\nAAGAGGCC\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t6588\r\nGGACTACT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t6583\r\nCGTACTAG\tN702\tTATCCCTT\tUnknown\t6574\r\nCGAGGCTG\tN710\tAGACTAGA\tE504,[N|S|E]504\t6570\r\nGGACTCCT\tN705\tGAGGAGTG\tUnknown\t6567\r\nGCTACACT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t6567\r\nGTACTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t6565\r\nGGACTCCT\tN705\tTTCCTCTT\tUnknown\t6564\r\nTAGGGATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t6561\r\nGGACTACT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t6557\r\nGTAGAGGA\tN712\tGCTGCCTC\tUnknown\t6557\r\nGTAGAGGT\tN712\tAGAGTAGA\tE504,[N|S|E]504\t6550\r\nGTAGAAGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t6548\r\nCGAGGCTG\tN710\tACTACATA\tE506,S506,[N|S|E]506\t6543\r\nTAAGGCGA\tN701\tAAGGATTT\tUnknown\t6540\r\nCGCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t6537\r\nTAGGCATG\tN706\tTACCTCTT\tUnknown\t6535\r\nTAGGCATG\tN706\tTATCCCTT\tUnknown\t6528\r\nTCAGGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t6523\r\nTGAGGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t6515\r\nCAGAGAGA\tN708,S511\tAGAGTAGA\tE504,[N|S|E]504\t6500\r\nGTAGACGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t6500\r\nCTCTCTAC\tN707\tGCTGCCTC\tUnknown\t6496\r\nTAAGGCTA\tN701,S521\tTATCCTCT\tE503,S503,[N|S|E]503\t6477\r\nTAAGTCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t6476\r\nCGTACTCG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t6469\r\nAGGCAGAA\tN703\tGGAAGGAG\tE505,S505,[N|S|E]505\t6466\r\nGCTACGCT\tN709\tAATGCATT\tUnknown\t6459\r\nCGTACTAG\tN702\tAAGGGTAT\tS520\t6438\r\nCGTACTAG\tN702\tAAGGATAT\tS520\t6435\r\nCGGCAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t6434\r\nGCTACGCT\tN709\tATGCATAT\tUnknown\t6434\r\nCGAGGCTG\tN710\tAGAGAAGA\tA503,E504,[N|S|E]504\t6414\r\nAAGAGGCA\tN711\tAGAGTACA\tA503,E504,[N|S|E]504\t6410\r\nGGACTCCT\tN705\tGTAATGAG\tE505,S505,[N|S|E]505\t6407\r\nAGGCATGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t6401\r\nACGAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t6396\r\nCAGAGAGG\tN708\tCTAGCCTT\tS520\t6390\r\nCGAGGCTG\tN710\tAGAGTCGC\tUnknown\t6387\r\nGTAAAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t6381\r\nTTCTCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t6379\r\nCTCTCTAC\tN707\tGCTGCATA\tE506,S506,[N|S|E]506\t6376\r\nGCTACGCT\tN709\tACGCATAT\tUnknown\t6374\r\nCGTACTAG\tN702\tTAAGGAGT\tUnknown\t6371\r\nTAGGCATG\tN706\tTAGCCTCT\tE503,S503,[N|S|E]503\t6369\r\nAAGAGGCA\tN711\tAGGTAGAT\tUnknown\t6365\r\nTCCTGAGC\tN704\tAAGGACTA\tS507,[N|S|E]507\t6363\r\nCGTACTAG\tN702\tTACCTCTT\tUnknown\t6362\r\nCGTACTAG\tN702\tACTGCATT\tE506,S506,[N|S|E]506\t6351\r\nTAATGCGA\tD708,N701,S522\tAAGGAGTA\tS507,[N|S|E]507\t6349\r\nTCCTGAGC\tN704\tCATCCTCC\tUnknown\t6349\r\nAAGAGACA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t6335\r\nGTAGAGGA\tN712\tATAGTAGG\tUnknown\t6329\r\nCTCTCTAC\tN707\tAAGTAGAT\tUnknown\t6323\r\nCAGAGCGG\tN708\tCTAAGCCT\tS508,[N|S|E]508\t6322\r\nCGTACTAG\tN702\tGTAACGAG\tE505,S505,[N|S|E]505\t6320\r\nCTCTATAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t6313\r\nAAGCGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t6313\r\nTAAGTCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t6311\r\nGCTAGGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t6310\r\nCCCTGAGC\tN704\tCTAAGCCT\tS508,[N|S|E]508\t6310\r\nGTAGAGGA\tN712\tCCTGCATC\tUnknown\t6308\r\nTCCTGAGC\tN704\tTATGCTCT\tE503,S503,[N|S|E]503\t6302\r\nTCCTGAGC\tN704\tGTAACGAG\tE505,S505,[N|S|E]505\t6293\r\nTCCTGACC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t6292\r\nCGAGGCTG\tN710\tCCTGCATC\tUnknown\t6287\r\nGTAGGAAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t6285\r\nAGGCAGAA\tN703\tCTGCAGCG\tUnknown\t6285\r\nTCCTGAGC\tN704\tTATCCTTC\tUnknown\t6282\r\nTAGGCATG\tN706\tTAACCTCT\tE503,S503,[N|S|E]503\t6277\r\nGGACTCCT\tN705\tGTAAGGGT\tUnknown\t6272\r\nCCTGAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t6270\r\nTCCTGAGC\tN704\tTACCCTCT\tE503,S503,[N|S|E]503\t6269\r\nAGGCATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t6266\r\nTCGGCATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t6264\r\nCGAGGCTG\tN710\tCGAGTCGA\tS513\t6256\r\nGCTCCGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t6250\r\nCCTACGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t6245\r\nCAGAGAGG\tN708\tAATGCATT\tUnknown\t6210\r\nTAAGGCGA\tN701\tAAGGAGAG\tUnknown\t6205\r\nTAAGGCGA\tN701\tAAGGATTA\tS507,[N|S|E]507\t6202\r\nTAAGGAGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t6199\r\nAGGCAGAA\tN703\tCTAAGGAG\tE505,S505,[N|S|E]505\t6198\r\nTAAGCCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t6192\r\nTAGGAATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t6190\r\nCGAGGCTG\tN710\tTGAGTAGA\tE504,[N|S|E]504\t6190\r\nAAAAAAAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t6188\r\nGTAGAGGG\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t6187\r\nAAGAGGCA\tN711\tGGAGTCGC\tUnknown\t6181\r\nTAGGCATG\tN706\tAGGGAGTA\tS507,[N|S|E]507\t6181\r\nGGACTCCA\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t6179\r\nGGACTCCT\tN705\tGTCCGCCC\tUnknown\t6177\r\nCGAGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t6173\r\nTAGGCATT\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t6159\r\nTAGGCATC\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t6141\r\nGCTACGCT\tN709\tCTAAGCTT\tS508,[N|S|E]508\t6135\r\nGGACTCCT\tN705\tGTACGTAG\tUnknown\t6131\r\nGGACTCCT\tN705\tCAGCAGTG\tUnknown\t6129\r\nACCTGAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t6128\r\nTAAGGGAA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t6122\r\nGGACTCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t6117\r\nTGCTGAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t6116\r\nCGTACTAG\tN702\tGTACGTAG\tUnknown\t6109\r\nAAGAGGCA\tN711\tCCTGCCTA\tUnknown\t6098\r\nTCCAGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t6088\r\nAAGAGGCA\tN711\tACCGCATA\tE506,S506,[N|S|E]506\t6086\r\nCGAGGCTG\tN710\tAGAATAGA\tE504,[N|S|E]504\t6084\r\nAAGAGGCA\tN711\tAAGGAGTA\tS507,[N|S|E]507\t6078\r\nCAGAGAAG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t6076\r\nGTAGAGGA\tN712\tGGAGTGGG\tUnknown\t6068\r\nCAGAGAGG\tN708\tACTACATA\tE506,S506,[N|S|E]506\t6065\r\nCGAGGCTG\tN710\tAAGTAGAT\tUnknown\t6058\r\nCGTACTGG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t6037\r\nCGAGGCTG\tN710\tTCTGCATT\tUnknown\t6035\r\nCGAACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t6023\r\nTCCTGATC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t6007\r\nGGACTACT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t6001\r\nCGTAATAG\tN702,S518\tGTAAGGAG\tE505,S505,[N|S|E]505\t5995\r\nTAGGCATG\tN706\tAAGGATTT\tUnknown\t5994\r\nTAAGGCGA\tN701\tAGGGAGTA\tS507,[N|S|E]507\t5993\r\nTAGGCATG\tN706\tGAAGGAGT\tUnknown\t5990\r\nAAGAGGCA\tN711\tAGAGGAGG\tUnknown\t5959\r\nCAGAGAGG\tN708\tCTAAGACT\tS508,[N|S|E]508\t5955\r\nTATGCATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t5943\r\nTCTGAGCA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t5941\r\nGTAGAGGA\tN712\tGGAGGAGG\tUnknown\t5939\r\nACTACGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t5938\r\nCAGAGAGG\tN708\tACTGCCTT\tUnknown\t5928\r\nTAGGCATG\tN706\tGTGCGGCG\tUnknown\t5908\r\nTAAGGCGA\tN701\tAAGCAGTC\tUnknown\t5907\r\nCTCTCTAC\tN707\tCGCGTAGA\tUnknown\t5877\r\nCGAGGCTG\tN710\tAAAGTAGA\tE504,[N|S|E]504\t5873\r\nTTCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t5865\r\nCGTAATAG\tN702,S518\tTATCCTCT\tE503,S503,[N|S|E]503\t5864\r\nGGACTCCA\tN705\tAAGGAGTA\tS507,[N|S|E]507\t5862\r\nGCTACGCT\tN709\tGCTGCATA\tE506,S506,[N|S|E]506\t5862\r\nTCCTGAGC\tN704\tGGAGTATC\tUnknown\t5856\r\nAAGAGGCA\tN711\tAGTGCAGA\tUnknown\t5856\r\nGGACTCCT\tN705\tGAAAGGAG\tE505,S505,[N|S|E]505\t5851\r\nTAAGGCGA\tN701\tTATGCTCT\tE503,S503,[N|S|E]503\t5850\r\nGGACTCCT\tN705\tCAGGAGTG\tUnknown\t5846\r\nGCTAGCTA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t5839\r\nTAAGGGAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t5838\r\nTCCTGGGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t5831\r\nAGGCAGAA\tN703\tGTAAGTCG\tUnknown\t5823\r\nCTCTCTAC\tN707\tAGAGAAGA\tA503,E504,[N|S|E]504\t5811\r\nGGACTCCT\tN705\tAAGGTGTA\tS507,[N|S|E]507\t5807\r\nCTCTCTAC\tN707\tGGAGTCGC\tUnknown\t5799\r\nTAACGCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t5796\r\nTAGGGATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t5795\r\nCTCTCTAC\tN707\tACAGCATA\tE506,S506,[N|S|E]506\t5794\r\nGTAGAGGA\tN712\tAGGGTAGG\tD503\t5792\r\nCTCTCTAC\tN707\tAGAGTCGG\tUnknown\t5788\r\nGCTACCCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t5787\r\nGTAGAGGA\tN712\tAGAGTTCG\tUnknown\t5773\r\nTCGGCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t5771\r\nCGACTAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t5769\r\nTCCTCAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t5766\r\nAAGAGGCA\tN711\tCCTGCCTC\tUnknown\t5763\r\nGCTAAGCT\tN709\tAGAGTAGA\tE504,[N|S|E]504\t5749\r\nAGGCATGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t5743\r\nGCTACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t5742\r\nAAGAGGCA\tN711\tGTAAGGAG\tE505,S505,[N|S|E]505\t5742\r\nTAGGCATG\tN706\tAAGGACTA\tS507,[N|S|E]507\t5731\r\nGCTACGCT\tN709\tCTCAGCCT\tS508,[N|S|E]508\t5722\r\nTCCTGAGC\tN704\tAAGGCGTT\tUnknown\t5721\r\nCAGAGAGG\tN708\tACTGCCTC\tUnknown\t5721\r\nAGGAAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t5719\r\nAAGGGCAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t5702\r\nGCTCCGCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t5699\r\nTAGGCCTG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t5698\r\nAGGCAGAA\tN703\tCAGCAGCG\tUnknown\t5689\r\nGTGAGGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t5687\r\nCTCTCTAC\tN707\tAGAGTTGT\tUnknown\t5687\r\nTCCTGAGC\tN704\tAAGGTGTA\tS507,[N|S|E]507\t5673\r\nTCCTGAGC\tN704\tTCCTCTTC\tUnknown\t5658\r\nAGGCAGAA\tN703\tGTAGAGTC\tUnknown\t5656\r\nGGACTCCT\tN705\tAAGCAGTC\tUnknown\t5655\r\nAAGAGGCA\tN711\tACTGTATA\tE506,S506,[N|S|E]506\t5653\r\nGCTATGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t5652\r\nGGTACGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t5648\r\nTAGCCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t5638\r\nCTTACTAG\tN702,S518\tTATCCTCT\tE503,S503,[N|S|E]503\t5634\r\nCAGAGAGG\tN708\tCTGAGCCT\tN720,S508,[N|S|E]508\t5631\r\nTTAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t5624\r\nTAAAGCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t5615\r\nTAAGGCGA\tN701\tAAAGAGTA\tS507,[N|S|E]507\t5614\r\nTAGGCATC\tN706\tAAGGAGTA\tS507,[N|S|E]507\t5612\r\nGGACTCCT\tN705\tTACCTCTT\tUnknown\t5612\r\nGGACTCCT\tN705\tGTACGGAC\tD508\t5611\r\nGTAGAGGA\tN712\tACTCCATA\tE506,S506,[N|S|E]506\t5611\r\nCCGTACTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t5610\r\nAAGACGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t5608\r\nTAAGGCTA\tN701,S521\tGTAAGGAG\tE505,S505,[N|S|E]505\t5582\r\nCAGAGGGA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t5573\r\nCGTACTAG\tN702\tAAAGAGTA\tS507,[N|S|E]507\t5572\r\nAGGCAGAA\tN703\tAAGGAGAT\tUnknown\t5569\r\nCGAGGCGG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t5565\r\nCTCTCTAC\tN707\tATAGTAGG\tUnknown\t5562\r\nCTCTCTAC\tN707\tACTTCATA\tE506,S506,[N|S|E]506\t5551\r\nCTCTCTAT\tE502,S502,[N|S|E]502\tAGAGTAGA\tE504,[N|S|E]504\t5550\r\nTCCTGAGC\tN704\tCTAAGGAG\tE505,S505,[N|S|E]505\t5548\r\nAAGAGGCA\tN711\tAAGTAGAT\tUnknown\t5544\r\nTAAGGCGA\tN701\tAAGGCGTT\tUnknown\t5539\r\nCAGCGAGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t5537\r\nCGTACTAG\tN702\tGTGCGGCG\tUnknown\t5533\r\nTAAGCCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t5521\r\nAGGCAGAA\tN703\tGTCCGCCC\tUnknown\t5520\r\nGGACTCCT\tN705\tTATCCCTT\tUnknown\t5520\r\nCGGGCTGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t5517\r\nACCTGAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t5515\r\nAGGCAGAA\tN703\tCAGGAGTG\tUnknown\t5512\r\nAGGCGGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t5488\r\nCGGCAGAA\tN703\tCTAAGCCT\tS508,[N|S|E]508\t5484\r\nGGACTCCT\tN705\tAAGGATTA\tS507,[N|S|E]507\t5482\r\nTAAGGCGA\tN701\tCTGCAGCG\tUnknown\t5482\r\nTAAGGCGA\tN701\tTAAGGAGG\tUnknown\t5481\r\nTAAGGCGA\tN701\tGTCCGCCC\tUnknown\t5481\r\nGCTACGCT\tN709\tATTGCATA\tE506,S506,[N|S|E]506\t5478\r\nAGGCAGAT\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t5471\r\nCTCTCTAC\tN707\tAGTGTAGT\tUnknown\t5471\r\nAAGAGGGA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t5471\r\nCTCACTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t5448\r\nTATGCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t5427\r\nTCCTGAGC\tN704\tAAGGGGTA\tS507,[N|S|E]507\t5425\r\nTAGCCATG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t5412\r\nTAGGCAAG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t5411\r\nGTAGAGGA\tN712\tAGACTAGT\tUnknown\t5408\r\nCGAGGCTG\tN710\tATAGTAGA\tE504,[N|S|E]504\t5408\r\nCTCTCTAC\tN707\tACTGCTAT\tUnknown\t5405\r\nTCCTGAGC\tN704\tAAGGAGCT\tUnknown\t5394\r\nCAGAGAGG\tN708\tTATCCTCT\tE503,S503,[N|S|E]503\t5393\r\nTCCTGGCA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t5377\r\nTCCTAAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t5377\r\nAAGAGGCA\tN711\tATAGTAGA\tE504,[N|S|E]504\t5376\r\nTCCTGAGC\tN704\tGAAAGGAG\tE505,S505,[N|S|E]505\t5366\r\nCGTACTAG\tN702\tGGAGTATC\tUnknown\t5362\r\nCGTGCTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t5357\r\nAGGCATAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t5357\r\nCGAGGCTG\tN710\tAATGCATT\tUnknown\t5353\r\nAAGAGGCA\tN711\tATTGCATA\tE506,S506,[N|S|E]506\t5353\r\nCGAGGCTG\tN710\tACTGTATA\tE506,S506,[N|S|E]506\t5352\r\nAAGCGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t5351\r\nGGACTCCT\tN705\tGTACGCAC\tUnknown\t5349\r\nAGAGAGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t5346\r\nAGGCAGAA\tN703\tAAGGCGTC\tUnknown\t5345\r\nATGAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t5322\r\nCGAGGCTG\tN710\tAGTGTAGT\tUnknown\t5316\r\nTAGGCATG\tN706\tAAGGAGCA\tS507,[N|S|E]507\t5310\r\nAAGAGCCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t5309\r\nCGAGGCTG\tN710\tAGCGTAGC\tUnknown\t5299\r\nGGACTCCT\tN705\tTAGCCTCT\tE503,S503,[N|S|E]503\t5297\r\nTCTACGCT\tE504,N709,[N|S|E]504\tAGAGTAGA\tE504,[N|S|E]504\t5297\r\nGGACTCCC\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t5294\r\nTAGGCATG\tN706\tGAGGAGTG\tUnknown\t5294\r\nTAGGCAGG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t5293\r\nCAAGGCGA\tN701\tCTAAGCCT\tS508,[N|S|E]508\t5285\r\nGGACTCCT\tN705\tAAGGCGTT\tUnknown\t5278\r\nTCATGAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t5278\r\nTCCTGAGC\tN704\tAAAGAGTA\tS507,[N|S|E]507\t5274\r\nTAAGGCGA\tN701\tGTCAGGCG\tUnknown\t5272\r\nCGAGGCAG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t5271\r\nGGACTCCT\tN705\tCAGCAGTA\tUnknown\t5256\r\nAGGAAGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t5255\r\nCGTACTAG\tN702\tTATGCTCT\tE503,S503,[N|S|E]503\t5250\r\nGGACTCCT\tN705\tGTAGAGTC\tUnknown\t5249\r\nTAAGGCGA\tN701\tAAGAAGAA\tUnknown\t5247\r\nGCTACGCT\tN709\tACTCATAT\tUnknown\t5232\r\nCTCTCTAC\tN707\tACTGCTTA\tE506,S506,[N|S|E]506\t5217\r\nCCTACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t5214\r\nTAGGGATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t5212\r\nAAGAGGCA\tN711\tAGAGTATC\tUnknown\t5209\r\nAAGAGTCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t5175\r\nAAGAGGGA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t5170\r\nTAGGCATG\tN706\tGTAACGAG\tE505,S505,[N|S|E]505\t5170\r\nTCCTGAGC\tN704\tAAGGATTT\tUnknown\t5169\r\nCAGAGAGG\tN708\tACTGCTTA\tE506,S506,[N|S|E]506\t5167\r\nTAAGGCGA\tN701\tTATCCACT\tE503,S503,[N|S|E]503\t5157\r\nGTAGAGGA\tN712\tATTGCATA\tE506,S506,[N|S|E]506\t5153\r\nCTAGGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t5153\r\nAGGCAGAA\tN703\tGTCAGGCG\tUnknown\t5152\r\nCGAGGATG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t5145\r\nTAAGGCGA\tN701\tGTCCGGAG\tUnknown\t5140\r\nTAAGGCGA\tN701\tTATCCTTC\tUnknown\t5138\r\nTAAGGCGC\tD708,N701,S521\tAAGGAGTA\tS507,[N|S|E]507\t5137\r\nCAGCGAGG\tN708\tCTAAGCCT\tS508,[N|S|E]508\t5128\r\nTAAGGCGA\tN701\tGTACGCAC\tUnknown\t5113\r\nGATACGCT\tN709\tAGAGTAGA\tE504,[N|S|E]504\t5111\r\nCAGAGAGG\tN708\tACTGCTAT\tUnknown\t5107\r\nCGTACTAG\tN702\tAAGGGGTA\tS507,[N|S|E]507\t5104\r\nTAAGGCGA\tN701\tAAGGGGTA\tS507,[N|S|E]507\t5102\r\nCGAGACTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t5100\r\nTCCCTGAG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t5097\r\nTAGGCATG\tN706\tAAGCAGTG\tUnknown\t5094\r\nCGTCCTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t5091\r\nCTCTCTAC\tN707\tAGAGTCGT\tUnknown\t5088\r\nCGAGACTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t5084\r\nGTAGAGGA\tN712\tACTCCATT\tUnknown\t5075\r\nCGACTCCT\tN705\tAGAGTAGA\tE504,[N|S|E]504\t5074\r\nTAGGCATT\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t5073\r\nCGAGGCTG\tN710\tACTGCTAT\tUnknown\t5072\r\nCAGAGAGG\tN708\tAGAGCAGA\tE504,[N|S|E]504\t5072\r\nGGACTCCT\tN705\tAAGGGGTA\tS507,[N|S|E]507\t5065\r\nAAGAGGCA\tN711\tCCTCCATG\tUnknown\t5058\r\nTAAGGCGA\tN701\tGTACGGAC\tD508\t5057\r\nAGGCAGAA\tN703\tGAAGGAGG\tUnknown\t5055\r\nCGAGGCTG\tN710\tAGAGTCGG\tUnknown\t5052\r\nGTAGCGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t5043\r\nGGAGAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t5042\r\nTAAAGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t5039\r\nTCCTGAGC\tN704\tAAGGAGAT\tUnknown\t5028\r\nCGGAGAGG\tN708,S511\tACTGCATA\tE506,S506,[N|S|E]506\t5021\r\nTCCTGAAC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t5019\r\nAAGATGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t5015\r\nCGAGGCTG\tN710\tAGAGTACA\tA503,E504,[N|S|E]504\t5014\r\nAAGAGGCG\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t5007\r\nCGTACTAG\tN702\tACGGCGTA\tUnknown\t5007\r\nAAGAGGCA\tN711\tACTGGATA\tE506,S506,[N|S|E]506\t5006\r\nCGAGGCTG\tN710\tAGAGTATC\tUnknown\t5004\r\nCTCACTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t4999\r\nAAGAGGCA\tN711\tGCTGCATG\tUnknown\t4997\r\nCGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t4987\r\nTAGGCATG\tN706\tGTAAGGGT\tUnknown\t4985\r\nCAGAGAGG\tN708\tCTTAGCCT\tD505,S508,[N|S|E]508\t4979\r\nAGACTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t4976\r\nGCTACGCT\tN709\tAGCGTAGA\tE504,[N|S|E]504\t4966\r\nTAGGCAAG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t4966\r\nTAAGGCCA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t4959\r\nAGGCAGAA\tN703\tGTAAGGGT\tUnknown\t4957\r\nGTACGCTA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t4954\r\nTCCTGAGC\tN704\tCAGCAGTG\tUnknown\t4950\r\nCGAGGCTG\tN710\tCTGCGGCG\tUnknown\t4950\r\nTAAGGCGA\tN701\tAAGGTGTA\tS507,[N|S|E]507\t4947\r\nCAGAGAGG\tN708\tGCTGCCTC\tUnknown\t4938\r\nTCCTGAGC\tN704\tGTAATGAG\tE505,S505,[N|S|E]505\t4936\r\nCGAGGCTG\tN710\tAGTGCAGA\tUnknown\t4924\r\nTAGGCATG\tN706\tGTACGTAG\tUnknown\t4923\r\nTAAGGCGA\tN701\tCATCCTCC\tUnknown\t4919\r\nGCTACGCT\tN709\tACTCCATT\tUnknown\t4913\r\nCGTACTAG\tN702\tAAGGAGAG\tUnknown\t4908\r\nAGGCAGAA\tN703\tTAACCTCT\tE503,S503,[N|S|E]503\t4907\r\nGCTACGTA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t4898\r\nTAACTCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t4896\r\nCGTACTAG\tN702\tAAGGACTA\tS507,[N|S|E]507\t4890\r\nGGACTCCT\tN705\tGTCAGCAG\tUnknown\t4890\r\nTAGGCATG\tN706\tACTGCATT\tE506,S506,[N|S|E]506\t4889\r\nAGGCAGAA\tN703\tAAGTAGTC\tUnknown\t4880\r\nCAGAGAGG\tN708\tGGAGTAGA\tE504,[N|S|E]504\t4874\r\nCGTACTAG\tN702\tCTAAGGAG\tE505,S505,[N|S|E]505\t4871\r\nGGACTCCT\tN705\tAAGGAGAT\tUnknown\t4870\r\nAAGAGGCA\tN711\tACAGTAGA\tE504,[N|S|E]504\t4861\r\nCGACTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t4847\r\nCTCTCTAC\tN707\tAGAGTACG\tUnknown\t4844\r\nGTAGAGGA\tN712\tCTGCGACG\tUnknown\t4842\r\nCTCTCTAC\tN707\tACAGTATA\tUnknown\t4836\r\nCGTACTCG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t4836\r\nAGGCAGAA\tN703\tAAGGACTC\tUnknown\t4832\r\nAAGAGGCC\tN711\tAGAGTAGA\tE504,[N|S|E]504\t4827\r\nGTAGAGGA\tN712\tAGGGAAGA\tUnknown\t4826\r\nTAGGCATG\tN706\tCTAAGGAG\tE505,S505,[N|S|E]505\t4826\r\nTCCTAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t4826\r\nCCCTGAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t4821\r\nCAGAGAGG\tN708\tCTCAGCCC\tUnknown\t4820\r\nGGACTCCT\tN705\tGATCCTCC\tUnknown\t4810\r\nAAGAGCCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t4804\r\nTCCTTAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t4797\r\nCGAGGCTG\tN710\tAGAGTTGT\tUnknown\t4796\r\nGCAGAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t4795\r\nTCCTGAGC\tN704\tGTACGTAG\tUnknown\t4793\r\nCGTACTAG\tN702\tAAGGTGTA\tS507,[N|S|E]507\t4793\r\nATCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t4792\r\nGTTACGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t4782\r\nCGTACTAG\tN702\tGTAAGTCG\tUnknown\t4775\r\nGGCTCCTA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t4762\r\nGCTACGCT\tN709\tACTGCTAT\tUnknown\t4762\r\nTAAGGCGA\tN701\tGCAAGGAG\tE505,S505,[N|S|E]505\t4762\r\nAGGCACAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t4761\r\nTCCTGAGC\tN704\tGAAGGAGT\tUnknown\t4761\r\nGGACTCCT\tN705\tTAGGAGTA\tS507,[N|S|E]507\t4760\r\nGCACGCTA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t4760\r\nCAGAGGGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t4760\r\nTAGGCATG\tN706\tGTAATGAG\tE505,S505,[N|S|E]505\t4756\r\nCGAACTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t4754\r\nCTCTCTAC\tN707\tTAAGCCTT\tUnknown\t4752\r\nTAGGCATG\tN706\tAAGGCGTT\tUnknown\t4752\r\nGGACTCCT\tN705\tGTAAGCAC\tUnknown\t4751\r\nTAGGCATG\tN706\tAAGGAGAT\tUnknown\t4751\r\nTAAGGCGA\tN701\tCAGCAGCG\tUnknown\t4750\r\nCGTAGTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t4747\r\nTAGGCATG\tN706\tAAAGAGTA\tS507,[N|S|E]507\t4743\r\nGGACTGCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t4742\r\nGTAGAGGA\tN712\tACTGGATA\tE506,S506,[N|S|E]506\t4741\r\nGCTACGCT\tN709\tCCTGCATC\tUnknown\t4730\r\nAGGCAGAG\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t4727\r\nCGCTCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t4726\r\nTAAGGCGA\tN701\tAAGGAGCC\tUnknown\t4720\r\nCGAAGCTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t4708\r\nTAACGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t4701\r\nGCTACGCT\tN709\tACTGGATA\tE506,S506,[N|S|E]506\t4692\r\nTAGGCAGG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t4691\r\nGGACTCGT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t4689\r\nTCCTGGCA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4689\r\nCGTACTAG\tN702\tGTAAGGAC\tE505,S505,[N|S|E]505\t4683\r\nTAGGCATG\tN706\tTATGCTCT\tE503,S503,[N|S|E]503\t4679\r\nAGGCAAAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t4678\r\nCCTCTCTA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t4677\r\nTAAGGCGA\tN701\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t4671\r\nAATAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t4666\r\nTCCTGATC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t4663\r\nGTAGAGTA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t4659\r\nTCCGGAGC\tD702,N704\tTATCCTCT\tE503,S503,[N|S|E]503\t4658\r\nGTAGGGAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t4642\r\nCAGAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t4635\r\nCGTAGAGG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t4632\r\nCGAGGCTG\tN710\tCTAAGCAT\tS508,[N|S|E]508\t4632\r\nCGAAGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t4632\r\nCGAGGCTG\tN710\tAGAGGAGG\tUnknown\t4630\r\nTAGGCATG\tN706\tAAGGATTA\tS507,[N|S|E]507\t4623\r\nGGACTCCT\tN705\tACTGCATT\tE506,S506,[N|S|E]506\t4620\r\nTCCTGGGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t4603\r\nCGAGGCTG\tN710\tTGAGCTCG\tUnknown\t4602\r\nGTAGAGGC\tD502,N712\tACTGCATA\tE506,S506,[N|S|E]506\t4592\r\nTAGGCGTG\tN706\tGTAAGGAG\tE505,S505,[N|S|E]505\t4586\r\nCAGAGAGG\tN708\tCTAAGTCT\tS508,[N|S|E]508\t4583\r\nAAGAGGCA\tN711\tAGTGTATA\tUnknown\t4580\r\nTAAGGCGA\tN701\tGAATCTCG\tUnknown\t4574\r\nTCCTGAGC\tN704\tAATCCTTT\tUnknown\t4574\r\nGGACTCCT\tN705\tCTGCAGTG\tUnknown\t4574\r\nTCCTGAGC\tN704\tGTAAGGGT\tUnknown\t4570\r\nTCCTGAGC\tN704\tGTGCGGCG\tUnknown\t4569\r\nTAAGGCGA\tN701\tGAAGGAGT\tUnknown\t4560\r\nCGAGGCTG\tN710\tACTGCTTA\tE506,S506,[N|S|E]506\t4556\r\nTAAGGCGA\tN701\tTAGGAGTA\tS507,[N|S|E]507\t4554\r\nTAAGGCGA\tN701\tAAGGCGTC\tUnknown\t4553\r\nGTAGAGGA\tN712\tAGAGATCG\tUnknown\t4552\r\nCTCTCAAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t4552\r\nCTCTCTAC\tN707\tCTATGCCT\tS508,[N|S|E]508\t4545\r\nAAGAGGCA\tN711\tAGAGTCGC\tUnknown\t4544\r\nCGTACTAG\tN702\tAAGCAGTG\tUnknown\t4538\r\nCTAAGGCG\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t4536\r\nCAGAGACG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t4536\r\nTAGGCATG\tN706\tCAGCAGTG\tUnknown\t4534\r\nCGAGGCTG\tN710\tACAGCATA\tE506,S506,[N|S|E]506\t4532\r\nCAGAGAAG\tN708\tCTAAGCCT\tS508,[N|S|E]508\t4531\r\nGCTACGGT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t4530\r\nAGGCAGAA\tN703\tGTAAGCAC\tUnknown\t4524\r\nTAAGTCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t4524\r\nAGGCAGAA\tN703\tGACTCTAC\tUnknown\t4523\r\nGGACTCCT\tN705\tAAAGAGTA\tS507,[N|S|E]507\t4521\r\nTAAGGCGA\tN701\tTCCTCTTC\tUnknown\t4519\r\nGTAGAGGA\tN712\tAGACTAGC\tUnknown\t4516\r\nTCCGAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t4515\r\nCTCTCTAC\tN707\tCTTAGCCT\tD505,S508,[N|S|E]508\t4514\r\nCAGGGAGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t4510\r\nAGACTCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t4505\r\nCGAGGCTG\tN710\tACTTCATA\tE506,S506,[N|S|E]506\t4505\r\nTCCTGAGC\tN704\tTTTCGTCT\tUnknown\t4504\r\nTAAGGCGA\tN701\tGTAAGCAC\tUnknown\t4495\r\nTCCTGAGC\tN704\tTCTCCTCC\tUnknown\t4488\r\nGGACTCCT\tN705\tGTCAGGAC\tD508\t4488\r\nAGGCAGAA\tN703\tGTCAGCAG\tUnknown\t4486\r\nAGGCAGAA\tN703\tAGGGAGTA\tS507,[N|S|E]507\t4485\r\nGGACTCCT\tN705\tTAACCTCT\tE503,S503,[N|S|E]503\t4484\r\nAGGCAGAA\tN703\tAAGGAGCG\tUnknown\t4483\r\nGGACTCCT\tN705\tGTCCGCAC\tUnknown\t4482\r\nCTCTCTCC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t4473\r\nCTCTCTAC\tN707\tTCTGCATT\tUnknown\t4473\r\nTCCTGAGC\tN704\tTAAGGAGG\tUnknown\t4470\r\nGGACTCCT\tN705\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t4465\r\nTCCTGAGC\tN704\tTATCCGCT\tE503,S503,[N|S|E]503\t4456\r\nTAAGGCGA\tN701\tGTCAGCAG\tUnknown\t4446\r\nTAGGCATG\tN706\tTATCCTTC\tUnknown\t4444\r\nTAAGGCCA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t4444\r\nTAGGCATT\tN706\tAAGGAGTA\tS507,[N|S|E]507\t4435\r\nTCCTGAGC\tN704\tGTGCGGAG\tUnknown\t4433\r\nGTAGGGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t4431\r\nCGAACTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t4429\r\nCGGCAGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t4428\r\nAGGCAGAA\tN703\tAAGGTGTA\tS507,[N|S|E]507\t4421\r\nGGACTCCT\tN705\tAAGGAGCT\tUnknown\t4421\r\nCCCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t4420\r\nGCTACGCT\tN709\tACTCCATA\tE506,S506,[N|S|E]506\t4419\r\nGGACTCCT\tN705\tACGGCGTA\tUnknown\t4418\r\nTAGGCATG\tN706\tGTAGAGTC\tUnknown\t4417\r\nCAGAGAGG\tN708\tACGGCATA\tE506,S506,[N|S|E]506\t4412\r\nAAGAGGCA\tN711\tACTGCAAA\tE506,S506,[N|S|E]506\t4409\r\nTCCTGAGC\tN704\tAAGCAGTC\tUnknown\t4409\r\nTAAGGGGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t4406\r\nTCCTGAGC\tN704\tGCACCTCG\tUnknown\t4404\r\nTAGGCGTG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t4395\r\nTAGGCAAG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t4394\r\nTAGGCATG\tN706\tAAGGGGTA\tS507,[N|S|E]507\t4392\r\nCAGAGAGG\tN708\tACTGGATA\tE506,S506,[N|S|E]506\t4385\r\nAGGCAGAA\tN703\tGTACGCAC\tUnknown\t4385\r\nGGACTCCT\tN705\tACGGAGTC\tUnknown\t4382\r\nTAGAGAGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t4370\r\nTAAGACGA\tN701\tACTGCATA\tE506,S506,[N|S|E]506\t4368\r\nCGTACAAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t4366\r\nTAGGCATG\tN706\tAAGGTGTA\tS507,[N|S|E]507\t4361\r\nCCCTGAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t4359\r\nCTCTCTAC\tN707\tAGTGCATA\tE506,S506,[N|S|E]506\t4358\r\nGCTAGGCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t4358\r\nCGTACTGG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t4353\r\nAAGGGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t4351\r\nTCCTGAGC\tN704\tGAGGAGTG\tUnknown\t4347\r\nCGAGGCTG\tN710\tAGCGTAGG\tUnknown\t4344\r\nCCCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t4343\r\nTAAGGCGA\tN701\tAAGGAGAT\tUnknown\t4340\r\nAGGCAGAA\tN703\tGAGAGGAG\tUnknown\t4337\r\nAGGCGGAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t4337\r\nCGAGGCTG\tN710\tGTAAGGAG\tE505,S505,[N|S|E]505\t4336\r\nCGTACTAG\tN702\tGTGCGGAG\tUnknown\t4336\r\nCCGTACTA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t4335\r\nTAGGCATG\tN706\tGAAAGGAG\tE505,S505,[N|S|E]505\t4332\r\nTCCTGAGC\tN704\tGTAGAGTC\tUnknown\t4329\r\nCGAGGCTA\tN710\tCTAAGCCT\tS508,[N|S|E]508\t4328\r\nCTCTCTAC\tN707\tATAAGCCT\tS508,[N|S|E]508\t4328\r\nGGACTCCT\tN705\tTAGGAGTT\tUnknown\t4326\r\nTGAGGCTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t4322\r\nTAAGGCGA\tN701\tGAGGCGTC\tUnknown\t4321\r\nGCTACGCT\tN709\tAGTGCATA\tE506,S506,[N|S|E]506\t4318\r\nCTCTCTAC\tN707\tAGTAGATC\tUnknown\t4315\r\nCGTTCTAG\tA506,N702\tTATCCTCT\tE503,S503,[N|S|E]503\t4308\r\nCGTACTAG\tN702\tAGATCTCG\tUnknown\t4301\r\nGCTACGCT\tN709\tAGAGTAGT\tE504,[N|S|E]504\t4298\r\nCGAGGATG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t4296\r\nTAAGGCGA\tN701\tACGGCGTA\tUnknown\t4295\r\nTCCTCAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t4295\r\nTAAGGGGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t4294\r\nGGACTCCT\tN705\tGTCAGGCG\tUnknown\t4289\r\nCTCTACAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t4288\r\nGGAATCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t4287\r\nCGACTAGA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4284\r\nTAAGGCGA\tN701\tGAGGAGCC\tUnknown\t4283\r\nCGATGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t4282\r\nCTAGGCTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t4281\r\nCGAGGCTG\tN710\tATTGCATA\tE506,S506,[N|S|E]506\t4277\r\nTCCTGAGC\tN704\tCAGGAGTG\tUnknown\t4273\r\nTCCAGAGC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t4273\r\nGTATAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t4268\r\nAGGCAGAA\tN703\tTATCCTTT\tE503,S503,[N|S|E]503\t4265\r\nTAAGGCCG\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t4263\r\nGGACTCCT\tN705\tCTGCAGCG\tUnknown\t4256\r\nCGTGCTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t4255\r\nCCTACGCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t4255\r\nCGACTAGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t4255\r\nCGTAATAG\tN702,S518\tAAGGAGTA\tS507,[N|S|E]507\t4251\r\nAGGCGAAA\tD505\tGTAAGGAG\tE505,S505,[N|S|E]505\t4250\r\nGCTATGCT\tN709\tCTAAGCCT\tS508,[N|S|E]508\t4249\r\nGGCTCCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4245\r\nGGACTCCT\tN705\tGCAAGGAG\tE505,S505,[N|S|E]505\t4241\r\nCGTACTAG\tN702\tTATCCTTC\tUnknown\t4240\r\nCGTACAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t4240\r\nAAGAGGCA\tN711\tCATGCATA\tUnknown\t4233\r\nAGGCAGAA\tN703\tCAGCAGTA\tUnknown\t4232\r\nCGTACTCG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t4227\r\nGCTACCTA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t4226\r\nGTAGAGGA\tN712\tGGCGTCGA\tUnknown\t4216\r\nTCCTGAGC\tN704\tAAGGATTA\tS507,[N|S|E]507\t4216\r\nCAGGCATG\tN706\tACTGCATA\tE506,S506,[N|S|E]506\t4212\r\nCTCTATAC\tN707\tCTAAGCCT\tS508,[N|S|E]508\t4212\r\nAAGAGGCA\tN711\tCGAGTCGA\tS513\t4198\r\nTCCTGACC\tN704\tGTAAGGAG\tE505,S505,[N|S|E]505\t4197\r\nATCTCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t4194\r\nTCCTGAGG\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t4193\r\nGTAGAGGA\tN712\tGGCGTAGA\tUnknown\t4184\r\nGAGAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t4183\r\nAGGCAGAT\tN703\tAAGGAGTA\tS507,[N|S|E]507\t4175\r\nAGGCAGAA\tN703\tGTACGCCC\tUnknown\t4171\r\nGTAGAGGA\tN712\tAGTGTAGC\tUnknown\t4171\r\nTAGAGGCA\tN711\tACTGCATA\tE506,S506,[N|S|E]506\t4170\r\nGTCGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t4159\r\nAGGCAGAA\tN703\tAAGGCGTT\tUnknown\t4156\r\nTAAGGCGA\tN701\tGTACGCCC\tUnknown\t4154\r\nATGAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t4150\r\nATAGAGGA\tD502,N712\tACTGCATA\tE506,S506,[N|S|E]506\t4148\r\nTAGCCATG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t4146\r\nTAAGGCTA\tN701,S521\tAAGGAGTA\tS507,[N|S|E]507\t4142\r\nCCGTACTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4139\r\nCGTACTAG\tN702\tTAAGGAGG\tUnknown\t4139\r\nGGAATCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t4138\r\nCAGAGAGG\tN708\tCCTGCATT\tUnknown\t4134\r\nAGTACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t4133\r\nCGTACTGG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t4130\r\nTAGGGCGA\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t4123\r\nGCTACGCC\tN709\tCTAAGCCT\tS508,[N|S|E]508\t4120\r\nGTAGAGGA\tN712\tAGTGTTGT\tUnknown\t4116\r\nGCTACGCT\tN709\tGTAAGGAG\tE505,S505,[N|S|E]505\t4115\r\nCCCTCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t4108\r\nGCTACGCT\tN709\tAAGGAGTA\tS507,[N|S|E]507\t4108\r\nGTAGAGGA\tN712\tACTGCTTA\tE506,S506,[N|S|E]506\t4106\r\nCGAGGCTG\tN710\tAGGGTGGA\tUnknown\t4104\r\nCTCTCTAT\tE502,S502,[N|S|E]502\tACTGCATA\tE506,S506,[N|S|E]506\t4104\r\nGGACTGCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t4101\r\nTAGGCAGG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t4098\r\nTCCTGAGC\tN704\tAAGGCGTC\tUnknown\t4098\r\nGTACAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t4097\r\nGTAGAGGA\tN712\tAGAGCATA\tE503,S503,[N|S|E]503\t4095\r\nCCTGAGCA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t4095\r\nCGAGGCTG\tN710\tAGTAGATC\tUnknown\t4094\r\nCAGAAAGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t4094\r\nCTCTCTGC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t4087\r\nTAAGGCGA\tN701\tGTAGAGTC\tUnknown\t4085\r\nAGGCAGAA\tN703\tGTACGGAC\tD508\t4083\r\nTCCTGAGC\tN704\tTATCCTCG\tE503,S503,[N|S|E]503\t4080\r\nCGTACTAG\tN702\tGAGGAGTG\tUnknown\t4073\r\nGTTGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t4053\r\nCAGAGAGG\tN708\tGTAAGGAG\tE505,S505,[N|S|E]505\t4050\r\nCGTACTAG\tN702\tCAGGAGTG\tUnknown\t4048\r\nAGGCAGAG\tN703\tAAGGAGTA\tS507,[N|S|E]507\t4046\r\nCTTTCTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t4039\r\nCGTACTAG\tN702\tAAGGCGTC\tUnknown\t4036\r\nAAGAGGCA\tN711\tACTCCATC\tUnknown\t4035\r\nTAGGCATG\tN706\tTCCTCTTC\tUnknown\t4027\r\nTAACTCCT\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t4027\r\nAGGCAGAA\tN703\tAAGCAGCT\tUnknown\t4025\r\nCGTAGTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t4024\r\nAGGCAGAA\tN703\tAACGAGTA\tS507,[N|S|E]507\t4022\r\nAAGAGGCA\tN711\tACTCCTTT\tUnknown\t4019\r\nTAAGGCCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t4018\r\nTAAGGCGA\tN701\tGAAGGAGG\tUnknown\t4017\r\nCGGGCTGA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t4015\r\nAGGCAGAA\tN703\tGTCCGGAG\tUnknown\t4015\r\nCAGAGAGG\tN708\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t4014\r\nGGACTCGT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t4011\r\nCTTTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t4011\r\nCAGAAGGA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t4010\r\nAAGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t4009\r\nTAAGCCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t4005\r\nAGGCAGAA\tN703\tAAGAAGTT\tUnknown\t4002\r\nAAGATGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t3993\r\nTAGAGAGG\tN708\tCTAAGCCT\tS508,[N|S|E]508\t3992\r\nGCTACGCT\tN709\tACTGCCTC\tUnknown\t3992\r\nCGTACTAC\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t3988\r\nAGGCAGAA\tN703\tAAGAAGAG\tUnknown\t3987\r\nGGACTCGT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t3987\r\nGCTACGCT\tN709\tACTGCATG\tE506,S506,[N|S|E]506\t3984\r\nTAAGGCGA\tN701\tTACCCTCT\tE503,S503,[N|S|E]503\t3983\r\nGGAATCCT\tN705\tAAGGAGTA\tS507,[N|S|E]507\t3983\r\nCGTCTAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t3972\r\nCTCTCTAC\tN707\tCCTGCCTA\tUnknown\t3968\r\nCGTACTAG\tN702\tAATCCTTT\tUnknown\t3966\r\nCCTGAGCA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3962\r\nCGAGCCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t3958\r\nGGACTCCT\tN705\tATGGAGTG\tUnknown\t3953\r\nCGAGGCTG\tN710\tACAGTAGA\tE504,[N|S|E]504\t3948\r\nCGTACTAG\tN702\tCATCCTCC\tUnknown\t3945\r\nCGTACTAG\tN702\tAAGGAGAT\tUnknown\t3940\r\nCAAGAGGA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t3939\r\nGTAGAGGA\tN712\tGTAGTAGG\tUnknown\t3937\r\nAAGCAGAA\tN703\tACTGCATA\tE506,S506,[N|S|E]506\t3935\r\nGCTAAGCA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t3923\r\nCGAGGCTG\tN710\tCGCGTAGA\tUnknown\t3921\r\nAAGAGGCA\tN711\tGCTGCCTA\tUnknown\t3918\r\nCTAAGGCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t3916\r\nGCTACACT\tN709\tAGAGTAGA\tE504,[N|S|E]504\t3916\r\nAAGGGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t3914\r\nCTCTCTCC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t3911\r\nGTAGAGGA\tN712\tCTGCTACG\tUnknown\t3904\r\nTAAGGCGT\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t3904\r\nCGAGGCAG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t3903\r\nGTAGAGGA\tN712\tCGAGTGGG\tUnknown\t3902\r\nCAAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t3896\r\nCCGAGGCT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t3882\r\nCTTACTAG\tN702,S518\tGTAAGGAG\tE505,S505,[N|S|E]505\t3878\r\nCTCTCAAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t3877\r\nAAGAGTCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t3877\r\nCAGAGAGG\tN708\tCCTGCATC\tUnknown\t3876\r\nTAGGCATG\tN706\tAAGGAGCT\tUnknown\t3874\r\nCAGAGAGG\tN708\tAGAGAAGA\tA503,E504,[N|S|E]504\t3873\r\nTCCTGAGC\tN704\tTATCCTGT\tE503,S503,[N|S|E]503\t3873\r\nTCCTGAGC\tN704\tACGGCGTA\tUnknown\t3871\r\nGTAGAGGA\tN712\tACAGTATA\tUnknown\t3869\r\nAAGAGGCA\tN711\tAGAGTAAG\tUnknown\t3857\r\nCTCTGTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t3851\r\nCGTACTAG\tN702\tGTAATGAG\tE505,S505,[N|S|E]505\t3851\r\nTCCTGAGC\tN704\tCATCGTCT\tUnknown\t3848\r\nCGTACTAG\tN702\tTACCCTCT\tE503,S503,[N|S|E]503\t3847\r\nCTCTCTAC\tN707\tCTGCGGCG\tUnknown\t3847\r\nCAGGCAGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3847\r\nAGACAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t3847\r\nTCCAGAGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t3844\r\nGGACTCCT\tN705\tTATCCTTC\tUnknown\t3842\r\nTCCTGAGC\tN704\tTATCCCCT\tE503,S503,[N|S|E]503\t3840\r\nAGGCAGAA\tN703\tAAGTATCG\tUnknown\t3833\r\nTCCTGAGC\tN704\tAAGGAGAG\tUnknown\t3831\r\nCGAGGTGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t3831\r\nCAGAGAGG\tN708\tGAGTAGAT\tUnknown\t3826\r\nAAGAGGCA\tN711\tAGTAGATC\tUnknown\t3826\r\nTAGGCGTG\tN706\tAAGGAGTA\tS507,[N|S|E]507\t3825\r\nCGAGGCTG\tN710\tAAGGAGTA\tS507,[N|S|E]507\t3825\r\nTAAGGCGA\tN701\tCAGCAGTA\tUnknown\t3811\r\nCGTACTAG\tN702\tATGGAGTG\tUnknown\t3810\r\nTTCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t3809\r\nCGGACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t3805\r\nAAGAGGCA\tN711\tAATGAATA\tUnknown\t3804\r\nGCAACGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t3803\r\nGTAGATGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t3803\r\nTAGGCATG\tN706\tCAGGAGTG\tUnknown\t3792\r\nAGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t3791\r\nCGTACTAG\tN702\tCTGCAGCG\tUnknown\t3789\r\nAGGCAGAA\tN703\tAAGCAGCA\tUnknown\t3787\r\nAGGCAGAA\tN703\tGAGGAGCC\tUnknown\t3784\r\nCGAGGCTG\tN710\tACTCCATT\tUnknown\t3779\r\nGGACACCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t3774\r\nTCCTGAGC\tN704\tCTGCAGCG\tUnknown\t3774\r\nTAAGGCGA\tN701\tTATCCTGT\tE503,S503,[N|S|E]503\t3771\r\nTCCTGAGC\tN704\tAGGGAGTA\tS507,[N|S|E]507\t3765\r\nCGGACTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t3763\r\nCGTACTAG\tN702\tTATCCTCG\tE503,S503,[N|S|E]503\t3761\r\nGGACTCCT\tN705\tAAGGCGTC\tUnknown\t3758\r\nAGGCATAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t3753\r\nCGTACTAG\tN702\tAAGGAGCC\tUnknown\t3751\r\nTAAGGCGT\tN701\tGTAAGGAG\tE505,S505,[N|S|E]505\t3746\r\nCAGAGAGG\tN708\tACTCCATA\tE506,S506,[N|S|E]506\t3739\r\nCCTACTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t3738\r\nCGTACTAG\tN702\tTCCTCTTC\tUnknown\t3738\r\nGCTCGCTA\tN716\tACTGCATA\tE506,S506,[N|S|E]506\t3738\r\nTAAGGGGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t3737\r\nAGGCCAGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3736\r\nCGAGGCTT\tN710\tAGAGTAGA\tE504,[N|S|E]504\t3735\r\nTAAGGCGA\tN701\tGTAAGGGT\tUnknown\t3733\r\nTTCTCTAC\tN707\tCTAAGCCT\tS508,[N|S|E]508\t3731\r\nCCTACTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t3726\r\nTAGGCATG\tN706\tCATCCTCC\tUnknown\t3726\r\nTAAGGCGA\tN701\tACGGAGTC\tUnknown\t3723\r\nAGGCAGCA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t3717\r\nAAAAAAAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t3713\r\nTAGGCATG\tN706\tTAGGAGTA\tS507,[N|S|E]507\t3712\r\nCGAGGCTG\tN710\tGGAGTCGA\tUnknown\t3712\r\nTAAGGCGA\tN701\tGTAAGTCG\tUnknown\t3712\r\nCAGAGAGG\tN708\tAGAGTGGA\tE504,[N|S|E]504\t3709\r\nAAGAGGCG\tN711\tAGAGTAGA\tE504,[N|S|E]504\t3709\r\nTCTTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t3704\r\nAAAAAAAA\tUnknown\tCTAAGCCT\tS508,[N|S|E]508\t3704\r\nTCTCTACA\tUnknown\tCTAAGCCT\tS508,[N|S|E]508\t3700\r\nTAAGGCCA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t3697\r\nTTCTCTAC\tN707\tGTAAGGAG\tE505,S505,[N|S|E]505\t3697\r\nGGACTGCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t3694\r\nGGGCAGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t3691\r\nGTAGAGGA\tN712\tCGACTAGA\tUnknown\t3690\r\nTAAAAAAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t3684\r\nAAGAGGCA\tN711\tAGCGTAGC\tUnknown\t3680\r\nGTAGAGGA\tN712\tACTGCAGA\tE506,S506,[N|S|E]506\t3680\r\nTAGGATGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3679\r\nCTAGAGGA\tN712\tCTAAGCCT\tS508,[N|S|E]508\t3678\r\nCTTACTAG\tN702,S518\tAAGGAGTA\tS507,[N|S|E]507\t3677\r\nCGAGGCGG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t3668\r\nAGGCCGAA\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t3668\r\nTTAGAGGA\tN712\tGTAAGGAG\tE505,S505,[N|S|E]505\t3660\r\nGCTACGCT\tN709\tCTAAGACT\tS508,[N|S|E]508\t3658\r\nCTCTCTAC\tN707\tACTCCTTT\tUnknown\t3656\r\nCTCTCTAC\tN707\tCTCAGCCC\tUnknown\t3651\r\nTCCTGAGC\tN704\tTCTCCTTT\tUnknown\t3647\r\nGCTACTCT\tE504,N709,[N|S|E]504\tAGAGTAGA\tE504,[N|S|E]504\t3643\r\nTAGGCATG\tN706\tGTACGCAG\tUnknown\t3643\r\nGGACTCCT\tN705\tTATGCTCT\tE503,S503,[N|S|E]503\t3641\r\nTAGGCCAT\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3641\r\nGCTACGCT\tN709\tGCTGCATC\tUnknown\t3640\r\nTAGGCCAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t3639\r\nTCCTGGGC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t3636\r\nTAAGGCGA\tN701\tAATCCTTT\tUnknown\t3636\r\nTAAGGCGA\tN701\tTAGGAGTT\tUnknown\t3635\r\nGTAGAGGA\tN712\tACGGCATA\tE506,S506,[N|S|E]506\t3628\r\nCTCTCTAC\tN707\tAGCGTCGA\tUnknown\t3627\r\nGTAGAGGA\tN712\tCGCGTCGC\tUnknown\t3626\r\nCAGGCATG\tN706\tCTAAGCCT\tS508,[N|S|E]508\t3626\r\nCTCTGTAC\tN707\tACTGCATA\tE506,S506,[N|S|E]506\t3626\r\nGTAGAGGA\tN712\tAGAGTTGG\tUnknown\t3611\r\nCCGAGAGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t3606\r\nAGTACTAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t3604\r\nCTAAGGCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3604\r\nCGGGGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t3601\r\nCCAGGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t3601\r\nAGGAGAAA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3595\r\nGTAGAGGA\tN712\tTGAGTAGT\tUnknown\t3591\r\nGGAGTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t3590\r\nAGGCAGAA\tN703\tCTGCAGTG\tUnknown\t3588\r\nTAGGATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t3588\r\nCGATGCTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t3587\r\nTCCCTGAG\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3586\r\nGTCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t3582\r\nCGAGGCTG\tN710\tACTGGATA\tE506,S506,[N|S|E]506\t3565\r\nCTCTCTAC\tN707\tCTAACCCT\tS508,[N|S|E]508\t3562\r\nCGAGGCTG\tN710\tAGAGTAAG\tUnknown\t3560\r\nCGTGCTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t3555\r\nGGACTCCT\tN705\tTAAGGAGG\tUnknown\t3554\r\nTAGAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t3552\r\nCAGAGATG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t3552\r\nCTCTCTAC\tN707\tAGAGTAAG\tUnknown\t3550\r\nTCCTGACC\tN704\tAAGGAGTA\tS507,[N|S|E]507\t3550\r\nGCTACGCT\tN709\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t3545\r\nGTAGAGGA\tN712\tAGATCGTC\tUnknown\t3544\r\nCGTACAAG\tN702\tGTAAGGAG\tE505,S505,[N|S|E]505\t3541\r\nGGACCCTA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3539\r\nGGAGTCCT\tN705\tGTAAGGAG\tE505,S505,[N|S|E]505\t3538\r\nCTCTCACA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t3535\r\nTCGTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t3532\r\nCTCTCTAC\tN707\tAGCGTAGG\tUnknown\t3530\r\nCAGAGAGG\tN708\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t3526\r\nAAGAGGCA\tN711\tAGAGCATA\tE503,S503,[N|S|E]503\t3525\r\nCAGAGAGG\tN708\tATTGCATA\tE506,S506,[N|S|E]506\t3520\r\nGTAGAGGA\tN712\tCGACTACG\tUnknown\t3509\r\nCTCTCTAC\tN707\tAATGCATT\tUnknown\t3509\r\nCTCTCTAC\tN707\tCTAGCCTT\tS520\t3508\r\nCGCGGCTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t3507\r\nTAAGGCGA\tN701\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t3504\r\nCGAGCCTG\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t3495\r\nTAGGCATG\tN706\tAAGCAGTC\tUnknown\t3492\r\nCAAAGAGG\tN708\tACTGCATA\tE506,S506,[N|S|E]506\t3484\r\nAGTACTAG\tN702\tAAGGAGTA\tS507,[N|S|E]507\t3482\r\nGTAGAGGA\tN712\tACTTCATA\tE506,S506,[N|S|E]506\t3481\r\nAGGCAGAC\tN703\tGTAAGGAG\tE505,S505,[N|S|E]505\t3479\r\nCAGAGAGG\tN708\tCTGCGGCG\tUnknown\t3477\r\nTAAGGCGA\tN701\tAATGCATA\tE506,S506,[N|S|E]506\t3475\r\nCTCTCTAC\tN707\tCGAGTAGT\tUnknown\t3475\r\nCTCTCTAC\tN707\tCGCGTAGC\tUnknown\t3473\r\nTAACGCGA\tN701\tAAGGAGTA\tS507,[N|S|E]507\t3467\r\nTAAGGCCG\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3465\r\nGCTGCGCT\tN709\tACTGCATA\tE506,S506,[N|S|E]506\t3462\r\nAGGCAGAA\tN703\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t3462\r\nTAGGCATG\tN706\tTAGGAGTT\tUnknown\t3462\r\nCGAGGCTG\tN710\tACTCCATA\tE506,S506,[N|S|E]506\t3459\r\nCGGACTCC\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3459\r\nCGTACCAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t3453\r\nAGGCAGAA\tN703\tAAGTAGTG\tUnknown\t3453\r\nCGTACTAG\tN702\tCAGCAGTG\tUnknown\t3452\r\nAGGCAGAA\tN703\tTTAAGGAG\tE505,S505,[N|S|E]505\t3450\r\nAAGAGGCA\tN711\tAAAGAAGA\tUnknown\t3444\r\nGTAGAGGA\tN712\tAGAGAGGA\tUnknown\t3442\r\nTAAGGCGA\tN701\tTATCCTCG\tE503,S503,[N|S|E]503\t3439\r\nCTCTCTAC\tN707\tAGAGTGGG\tUnknown\t3438\r\nAGGCACAA\tN703\tAAGGAGTA\tS507,[N|S|E]507\t3432\r\nTAGGCATG\tN706\tTGATCTCG\tUnknown\t3426\r\nCAAAAAAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t3425\r\nAGGCAGAA\tN703\tGTAAGCCG\tUnknown\t3423\r\nCAGAGAGG\tN708\tCTAAACCT\tS508,[N|S|E]508\t3418\r\nCGTACAGA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3416\r\nGGACTCCT\tN705\tAAGAAGAA\tUnknown\t3412\r\nCGGCAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t3412\r\nCAAGAGGC\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t3406\r\nCTCTCTAC\tN707\tCCTGCCTT\tUnknown\t3403\r\nATGCAGAA\tD705,N703\tACTGCATA\tE506,S506,[N|S|E]506\t3402\r\nCGAGGCTG\tN710\tAGAGTCGT\tUnknown\t3398\r\nTAAGGCGA\tN701\tTATCCGCT\tE503,S503,[N|S|E]503\t3394\r\nAGGCAGAA\tN703\tGAGGCGTC\tUnknown\t3391\r\nCTACGCTA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t3391\r\nCGAGGCTG\tN710\tAGATTAGA\tE504,[N|S|E]504\t3390\r\nGCTACGCT\tN709\tATAAGCCT\tS508,[N|S|E]508\t3386\r\nTAAGGCGA\tN701\tGAGTATCG\tUnknown\t3385\r\nCTCTCTAC\tN707\tAGACTAGT\tUnknown\t3381\r\nAAGAAGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t3378\r\nGTGGAGGA\tN712\tACTGCATA\tE506,S506,[N|S|E]506\t3377\r\nCAGAGAGG\tN708\tAGAGTTGA\tE504,[N|S|E]504\t3376\r\nAAGAGGCA\tN711\tAGAGTACG\tUnknown\t3376\r\nCGTACTAG\tN702\tGAAGGAGT\tUnknown\t3376\r\nGGACTCCT\tN705\tTCCTCTTC\tUnknown\t3374\r\nGGACTCCT\tN705\tAAGGAGAG\tUnknown\t3373\r\nTAAGGCGA\tN701\tGTCAGGAC\tD508\t3371\r\nTAGAGGAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t3370\r\nCGAGGGTG\tN710\tAGAGTAGA\tE504,[N|S|E]504\t3369\r\nCTCTCTAC\tN707\tCTACGCCC\tUnknown\t3368\r\nTCCTGAGC\tN704\tAATCATCT\tUnknown\t3364\r\nCGAGGCTG\tN710\tACTGCCTC\tUnknown\t3362\r\nTCCTAAAC\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3362\r\nAAGAGGCA\tN711\tAGATTAGA\tE504,[N|S|E]504\t3359\r\nCGAGGCTT\tN710\tACTGCATA\tE506,S506,[N|S|E]506\t3358\r\nGTACTCCT\tN705\tACTGCATA\tE506,S506,[N|S|E]506\t3356\r\nGGACCCTA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3353\r\nAAGAGGCA\tN711\tACTGCACA\tE506,S506,[N|S|E]506\t3353\r\nTCCTGAGC\tN704\tGAAGGAGG\tUnknown\t3352\r\nTAGGCCAT\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3352\r\nCAGAGAGG\tN708\tCGAGTAGG\tUnknown\t3351\r\nAAGAGGCA\tN711\tGGAGTCGA\tUnknown\t3345\r\nCTCTCTCA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t3345\r\nTAAGGCGA\tN701\tATGGAGTG\tUnknown\t3344\r\nCAGAGCGG\tN708\tAGAGTAGA\tE504,[N|S|E]504\t3341\r\nAGCCAGAA\tN703,S515\tGTAAGGAG\tE505,S505,[N|S|E]505\t3340\r\nAGGCAGAA\tN703\tGGCTCTAC\tUnknown\t3340\r\nGTAGAGGA\tN712\tAGAGGATC\tE503,S503,[N|S|E]503\t3339\r\nAGGAGAAA\tUnknown\tAAGGAGTA\tS507,[N|S|E]507\t3337\r\nGGACTCCT\tN705\tGAGGCGTC\tUnknown\t3331\r\nCAGAGAGG\tN708\tCTAAGGCT\tS508,[N|S|E]508\t3328\r\nGCACTCCT\tN705\tACTGCATA\tE506,S506,[N|S|E]506\t3327\r\nCGTACTAG\tN702\tAGTCCTCG\tUnknown\t3323\r\nTAGGCATG\tN706\tTACCCTCT\tE503,S503,[N|S|E]503\t3323\r\nAAGAGGCA\tN711\tCCTGCCTT\tUnknown\t3321\r\nGAGAGGAA\tUnknown\tACTGCATA\tE506,S506,[N|S|E]506\t3317\r\nAAGAGGCA\tN711\tAAGGTAGA\tUnknown\t3311\r\nTAGGCATG\tN706\tTTTCGTCT\tUnknown\t3311\r\nCGTACTAG\tN702\tGTAAGGGT\tUnknown\t3309\r\nTCCTAGCA\tUnknown\tGTAAGGAG\tE505,S505,[N|S|E]505\t3308\r\nGGACTCCT\tN705\tGTACGCCC\tUnknown\t3306\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/few_assigned/metrics.txt", "content": "## htsjdk.samtools.metrics.StringHeader\n# ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/tmp.4ca6mVHJzT/seq/illumina/proc/SL-HAK/171013_SL-HAK_0510_ACBMYCANXX/Data/Intensities/BaseCalls OUTPUT_DIR=/tmp/tmp-illumina-illumina_demux-xr2r0084/extracted_barcodes-yji4jkcr LANE=6 READ_STRUCTURE=100T8B8B100T BARCODE_FILE=/tmp/tmp-illumina-illumina_demux-xr2r0084/barcodeData.CBMYCANXX.6jrypqot6.txt METRICS_FILE=metrics.txt MAX_MISMATCHES=1 MINIMUM_BASE_QUALITY=10 MINIMUM_QUALITY=10 NUM_PROCESSORS=0 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\n## htsjdk.samtools.metrics.StringHeader\n# Started on: Thu Sep 06 02:50:46 UTC 2018\n\n## METRICS CLASS\tpicard.illumina.ExtractIlluminaBarcodes$BarcodeMetric\nBARCODE\tBARCODE_WITHOUT_DELIMITER\tBARCODE_NAME\tLIBRARY_NAME\tREADS\tPF_READS\tPERFECT_MATCHES\tPF_PERFECT_MATCHES\tONE_MISMATCH_MATCHES\tPF_ONE_MISMATCH_MATCHES\tPCT_MATCHES\tRATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_PCT_MATCHES\tPF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_NORMALIZED_MATCHES\nCGTACTAG-GCGTAAGA\tCGTACTAGGCGTAAGA\tMumps_5_171013\tMumps_5_171013\t1\t1\t0\t0\t1\t1\t0\t0\t0\t0\t0.000001\nAGGCAGAA-CCTAGAGT\tAGGCAGAACCTAGAGT\tG4225.1_171013\tG4225.1_171013\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\nGGACTCCT-GCGTAAGA\tGGACTCCTGCGTAAGA\tG3911.1_171013\tG3911.1_171013\t1\t1\t0\t0\t1\t1\t0\t0\t0\t0\t0.000001\nTAGGCATG-AAGGCTAT\tTAGGCATGAAGGCTAT\tG4490.1_171013\tG4490.1_171013\t11221\t11034\t7\t7\t11214\t11027\t0.000041\t0.001812\t0.000044\t0.001821\t0.010601\nTAAGGCGA-CTCTCTAT\tTAAGGCGACTCTCTAT\tG5767.1_171013\tG5767.1_171013\t10\t10\t9\t9\t1\t1\t0\t0.000002\t0\t0.000002\t0.00001\nGGACTCCT-CTAAGCCT\tGGACTCCTCTAAGCCT\tG4137.1_171013\tG4137.1_171013\t2359\t2107\t776\t692\t1583\t1415\t0.000009\t0.000381\t0.000008\t0.000348\t0.002024\nTAGGCATG-CTAAGCCT\tTAGGCATGCTAAGCCT\tG4947.1_171013\tG4947.1_171013\t1216\t1041\t365\t307\t851\t734\t0.000004\t0.000196\t0.000004\t0.000172\t0.001\nCAGAGAGG-AGAGTAGA\tCAGAGAGGAGAGTAGA\tG5416.1_171013\tG5416.1_171013\t1184996\t1159869\t577516\t564073\t607480\t595796\t0.004359\t0.191384\t0.004625\t0.191393\t1.114383\nCGTACTAG-TATCCTCT\tCGTACTAGTATCCTCT\tG5787.1_171013\tG5787.1_171013\t6191732\t6060133\t3613555\t3532430\t2578177\t2527703\t0.022774\t1\t0.024164\t1\t5.822478\nTCCTGAGC-AGAGTAGA\tTCCTGAGCAGAGTAGA\tG5619.1_171013\tG5619.1_171013\t2308\t2228\t950\t919\t1358\t1309\t0.000008\t0.000373\t0.000009\t0.000368\t0.002141\nCTCTCTAC-AGAGTAGA\tCTCTCTACAGAGTAGA\tG5415.1_171013\tG5415.1_171013\t4853952\t4780289\t3211496\t3163679\t1642456\t1616610\t0.017854\t0.783941\t0.019061\t0.788809\t4.592825\nAGGCAGAA-AAGGCTAT\tAGGCAGAAAAGGCTAT\tG4483.1_171013\tG4483.1_171013\t13772\t13536\t10\t10\t13762\t13526\t0.000051\t0.002224\t0.000054\t0.002234\t0.013005\nGGACTCCT-AGAGTAGA\tGGACTCCTAGAGTAGA\tG5621.1_171013\tG5621.1_171013\t2468\t2383\t881\t844\t1587\t1539\t0.000009\t0.000399\t0.00001\t0.000393\t0.00229\nGGACTCCT-TATCCTCT\tGGACTCCTTATCCTCT\tG5585.1_171013\tG5585.1_171013\t4897225\t4764847\t3192388\t3102458\t1704837\t1662389\t0.018013\t0.79093\t0.018999\t0.786261\t4.577988\nTAGGCATG-CCTAGAGT\tTAGGCATGCCTAGAGT\tWater_4_171013\tWater_4_171013\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\nCAGAGAGG-CTAAGCCT\tCAGAGAGGCTAAGCCT\tG4880.1_171013\tG4880.1_171013\t1963811\t1923084\t646734\t630354\t1317077\t1292730\t0.007223\t0.317167\t0.007668\t0.317334\t1.847668\nTAAGGCGA-AAGGCTAT\tTAAGGCGAAAGGCTAT\tG4439.1_171013\tG4439.1_171013\t11783\t11581\t11\t9\t11772\t11572\t0.000043\t0.001903\t0.000046\t0.001911\t0.011127\nAGGCAGAA-CTAAGCCT\tAGGCAGAACTAAGCCT\tG4715.2_171013\tG4715.2_171013\t2848\t2558\t919\t831\t1929\t1727\t0.00001\t0.00046\t0.00001\t0.000422\t0.002458\nNNNNNNNN-NNNNNNNN\tNNNNNNNNNNNNNNNN\t\t\t252733991\t232055835\t0\t0\t0\t0\t0.929601\t40.81798\t0.925297\t38.292202\t0\n\n\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/one_correction/barcodes.txt", "content": "Barcode1\tLikely_Index_Names1\tBarcode2\tLikely_Index_Names2\tCount\r\nGTAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t3025191\r\nCTCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t2816035\r\nTAAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t2545155\r\nAAGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t2123013\r\nGCTACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t1533037\r\nTCCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t1366847\r\nTAAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t849939\r\nTAGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t712147\r\nAGGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t556637\r\nAGGCAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t420657\r\nCGAGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t390503\r\nTCCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t355304\r\nCGTACTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t321177\r\nGGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t231310\r\nCGTACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t123272\r\nTAGGCATT\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t41442\r\nTAAGGCGA\tN701\tAGAGCAGA\tE504,[N|S|E]504\t28449\r\nCGAGGCTT\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t25596\r\nTAAGGCGA\tN701\tTGTGCTGT\tUnknown\t24710\r\nTAAGGCGA\tN701\tAGAGTAGT\tE504,[N|S|E]504\t17272\r\nCGTACTAT\tN702\tAGAGTAGA\tE504,[N|S|E]504\t16583\r\nTCCTGAGC\tN704\tAGAGCAGA\tE504,[N|S|E]504\t14075\r\nGTAGGGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t11484\r\nTAAGGCGA\tN701\tTGAGTAGA\tE504,[N|S|E]504\t11368\r\nTAAGGCGA\tN701\tAGTGCTGT\tUnknown\t10313\r\nTAAGGCGA\tN701\tTGGGGAGA\tUnknown\t9596\r\nTCCTGAGC\tN704\tTGTGCTGT\tUnknown\t9324\r\nGTAGCGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t8899\r\nTAAGGCGA\tN701\tAGTGCAGT\tUnknown\t7839\r\nTCCTGAGC\tN704\tAGAGTAGT\tE504,[N|S|E]504\t7775\r\nTAAGGCGA\tN701\tTAGAGACA\tUnknown\t7575\r\nTAAGGCGA\tN701\tAGTGTAGA\tE504,[N|S|E]504\t7458\r\nCGTACTAT\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t7315\r\nTAAGGCGA\tN701\tAGAGCAGT\tUnknown\t6548\r\nAGGCAGAA\tN703\tAGAGCAGA\tE504,[N|S|E]504\t6534\r\nTCCTGAGC\tN704\tTGAGTAGA\tE504,[N|S|E]504\t5207\r\nTAAGGCGA\tN701\tAGAGTAAT\tUnknown\t5075\r\nTAAGGCGA\tN701\tAGTGCAGA\tUnknown\t5062\r\nTAAGGCGA\tN701\tTGTGCAGT\tE506,S506,[N|S|E]506\t5049\r\nTTCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t4968\r\nTAAGGCGA\tN701\tAGGGGAGA\tUnknown\t4903\r\nTAAGGCGA\tN701\tAGTGTAGT\tUnknown\t4844\r\nTAAGGCGA\tN701\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t4726\r\nGTTACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t4721\r\nTCCTGAGC\tN704\tAGTGCTGT\tUnknown\t4604\r\nTCTACGCT\tE504,N709,[N|S|E]504\tTATCCTCT\tE503,S503,[N|S|E]503\t4271\r\nGCTAGCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t4235\r\nTAAGGCGA\tN701\tAGAGTAGG\tE504,[N|S|E]504\t4230\r\nTTAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t4221\r\nTCCTGAGC\tN704\tAGTGTAGA\tE504,[N|S|E]504\t4079\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\tTATCCTCT\tE503,S503,[N|S|E]503\t4046\r\nAAGAGGCA\tN711\tGCGTAAGA\tE517,S517,[N|S|E]517\t4024\r\nCTCTCTAC\tN707\tTAGGGGCA\tUnknown\t3923\r\nGCTAGGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t3893\r\nGCAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t3875\r\nTAAGGCGA\tN701\tAGTGTTGT\tUnknown\t3754\r\nAGGCAGAA\tN703\tTGTGCTGT\tUnknown\t3701\r\nCTCTCTCC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t3669\r\nTAAGGCGA\tN701\tAGAGTTGA\tE504,[N|S|E]504\t3528\r\nTAAGGCGA\tN701\tAGAGTGAT\tUnknown\t3470\r\nTAGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t3448\r\nCGTACTAG\tN702\tAGAGCAGA\tE504,[N|S|E]504\t3274\r\nTCCTGAGC\tN704\tAGTGCAGT\tUnknown\t3261\r\nCTCTCTAC\tN707\tTATGCTCT\tE503,S503,[N|S|E]503\t3260\r\nAGGCAGAA\tN703\tAGAGTAGT\tE504,[N|S|E]504\t3086\r\nCTCTGTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t3040\r\nTAAGGCGA\tN701\tAGAGAGAT\tUnknown\t3020\r\nTAAGGCGA\tN701\tTGTGCTCT\tA503\t2970\r\nGCTACGCA\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t2967\r\nGTAGAGGA\tN712\tTATCTCTT\tUnknown\t2940\r\nATGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t2885\r\nGTAGAGAA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t2838\r\nCTCTCTAC\tN707\tTTTCCTCT\tE503,S503,[N|S|E]503\t2772\r\nTAGGCATA\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t2751\r\nCTCTCTAC\tN707\tTAGGGGCT\tUnknown\t2730\r\nGTAGAGGA\tN712\tATCCTCTT\tUnknown\t2686\r\nTCCTGAGC\tN704\tAGAGCAGT\tUnknown\t2673\r\nCTCTCTAC\tN707\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t2662\r\nTAAGGCGA\tN701\tTGTGTAGT\tUnknown\t2613\r\nGAAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t2572\r\nGCTACGCC\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t2570\r\nTAAGGCGA\tN701\tTGTGTTGT\tUnknown\t2564\r\nCTCTCTAC\tN707\tTATCTCTT\tUnknown\t2552\r\nTAGGCGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t2523\r\nTCCTGAGC\tN704\tAGTGCAGA\tUnknown\t2491\r\nCTCTCTAC\tN707\tATCCTCTT\tUnknown\t2414\r\nTCCTGAGC\tN704\tAGAGTAAT\tUnknown\t2322\r\nAAGAGGCA\tN711\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t2276\r\nGGAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t2263\r\nGTAGAGGA\tN712\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t2258\r\nTAAGGCGA\tN701\tAGATAGAT\tUnknown\t2208\r\nTCCTGAGC\tN704\tAGTGTAGT\tUnknown\t2194\r\nCGTACTAG\tN702\tTGTGCTGT\tUnknown\t2177\r\nTCCTGAGC\tN704\tAGAGTTGA\tE504,[N|S|E]504\t2135\r\nGTAGAGGA\tN712\tTATCCCTT\tUnknown\t2133\r\nTCCTGAGC\tN704\tAGAGTAGG\tE504,[N|S|E]504\t2131\r\nGTAGAGGG\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t2074\r\nTAAGGCGA\tN701\tAGAGCTGT\tUnknown\t2070\r\nTAGGCATC\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t2040\r\nTCTCTACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t2024\r\nTCCTGAGC\tN704\tAGTGTTGT\tUnknown\t2024\r\nAAGAGGCA\tN711\tTATCTCTT\tUnknown\t2016\r\nGCTACGAT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t1996\r\nTAAGGCGA\tN701\tTGAGTAGT\tUnknown\t1958\r\nCTCTCTAT\tE502,S502,[N|S|E]502\tTATCCTCT\tE503,S503,[N|S|E]503\t1930\r\nTTAGGCGA\tN701,S522\tTGTGCTGT\tUnknown\t1906\r\nCGAGGCTA\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t1897\r\nGTAGAGGA\tN712\tTATCCTTT\tE503,S503,[N|S|E]503\t1897\r\nCGTACTAA\tN702\tAGAGTAGA\tE504,[N|S|E]504\t1858\r\nTCCTGAGC\tN704\tTGTGCAGT\tE506,S506,[N|S|E]506\t1837\r\nAAGAGGCA\tN711\tATCCTCTT\tUnknown\t1823\r\nTAAGCGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t1807\r\nAAGAGGCA\tN711\tTATGCTCT\tE503,S503,[N|S|E]503\t1801\r\nTAAGGCGA\tN701\tTGAGCAGA\tUnknown\t1795\r\nCTCTCTAC\tN707\tTATCCCTT\tUnknown\t1757\r\nCCTCTCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1740\r\nGTCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t1739\r\nTAAGGCGA\tN701\tAGAGCTGA\tUnknown\t1691\r\nTAAGGCGA\tN701\tTGAGCAGT\tUnknown\t1689\r\nTAAGGCGA\tN701\tTGAGGAGA\tUnknown\t1666\r\nCTCTCTAC\tN707\tTATCCTTT\tE503,S503,[N|S|E]503\t1652\r\nCTCTCTAC\tN707\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t1642\r\nGCTACGGT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t1640\r\nTCCTGAGC\tN704\tAGAGTGAT\tUnknown\t1634\r\nCAGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t1624\r\nTCCTGAGA\tD702,N704\tAGAGTAGA\tE504,[N|S|E]504\t1599\r\nTAAGGCGA\tN701\tTAGGGACA\tUnknown\t1570\r\nTTCTGAGC\tN704\tTGTGCTGT\tUnknown\t1562\r\nCTCTCTAC\tN707\tTACCTCTT\tUnknown\t1556\r\nAAGAGGCA\tN711\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t1551\r\nGCTACCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1535\r\nTTCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t1533\r\nCTCTCTAC\tN707\tTTCCTCTT\tUnknown\t1528\r\nTAAGGCGA\tN701\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t1522\r\nTAAGGCCG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t1511\r\nAGGCAGAA\tN703\tAGAGCAGT\tUnknown\t1495\r\nGTACGCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1482\r\nCTAAGGCG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t1481\r\nCGTACTAG\tN702\tAGAGTAGT\tE504,[N|S|E]504\t1472\r\nAGGCAGAA\tN703\tAGTGCAGT\tUnknown\t1444\r\nTAAGGCGA\tN701\tCTCTCTAT\tE502,S502,[N|S|E]502\t1442\r\nGTAGAGGA\tN712\tTTCCTCTT\tUnknown\t1441\r\nTCCTGAGC\tN704\tAGAGAGAT\tUnknown\t1437\r\nCTCTCTGC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t1435\r\nGCTACGTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1427\r\nTTAGGCGA\tN701,S522\tTATCCTCT\tE503,S503,[N|S|E]503\t1423\r\nTCCTGCGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t1419\r\nCTCTCCAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t1415\r\nTAAGGGGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t1405\r\nTAAGGCGA\tN701\tCGAGTAGA\tE504,[N|S|E]504\t1405\r\nAGAGGCAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1404\r\nTAAGGCGA\tN701\tGAGTAGAT\tUnknown\t1401\r\nAGGCGGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t1401\r\nGCTACGCT\tN709\tGCGTAAGA\tE517,S517,[N|S|E]517\t1385\r\nCTCTCTAC\tN707\tTGTGCTCT\tA503\t1383\r\nGTAGGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1382\r\nTAAGGGGA\tN701\tTGTGCTGT\tUnknown\t1372\r\nAAGAGGCA\tN711\tTTTCCTCT\tE503,S503,[N|S|E]503\t1368\r\nGCTCGCTA\tN716\tTATCCTCT\tE503,S503,[N|S|E]503\t1365\r\nTAAGGCGA\tN701\tTGGGGACA\tUnknown\t1363\r\nTAAGGCGA\tN701\tTGTGTAGA\tUnknown\t1361\r\nTCCTGAGC\tN704\tTGTGTTGT\tUnknown\t1359\r\nGCTAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1346\r\nGTAGAGGA\tN712\tTTTCCTCT\tE503,S503,[N|S|E]503\t1343\r\nGCACGCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1335\r\nTAAGGCGA\tN701\tTGTGCAGA\tUnknown\t1330\r\nCTCTCTAC\tN707\tTGTGCTGT\tUnknown\t1312\r\nTAAGGAGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t1311\r\nAAGAGGCA\tN711\tTATCCTTT\tE503,S503,[N|S|E]503\t1308\r\nAAGAGGCA\tN711\tTATCCCTT\tUnknown\t1298\r\nGTAGAGGC\tD502,N712\tTATCCTCT\tE503,S503,[N|S|E]503\t1297\r\nTAAGGAGA\tN701\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t1291\r\nAGGCAGAA\tN703\tTGAGTAGA\tE504,[N|S|E]504\t1289\r\nAGGCAGAA\tN703\tAGTGCTGT\tUnknown\t1287\r\nGTAGAGGA\tN712\tTACCTCTT\tUnknown\t1283\r\nCAGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t1281\r\nGAAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t1263\r\nCTCTCGAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t1257\r\nCTCGCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t1257\r\nAGGCGGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t1246\r\nTAAGGCGG\tN701\tAGAGTAGA\tE504,[N|S|E]504\t1237\r\nGTAAGGAA\tE505,S505,[N|S|E]505\tTATCCTCT\tE503,S503,[N|S|E]503\t1236\r\nTAAGGCGA\tN701\tAGAGTATC\tUnknown\t1235\r\nGAGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t1222\r\nGCTACGCT\tN709\tTATCTCTT\tUnknown\t1222\r\nGCTACGCT\tN709\tATCCTCTT\tUnknown\t1219\r\nTAAGGCGA\tN701\tAGTGCTGA\tUnknown\t1210\r\nTAAGGCGA\tN701\tTATGCTCT\tE503,S503,[N|S|E]503\t1204\r\nAAGAGGCA\tN711\tTTCCTCTT\tUnknown\t1189\r\nAAGAGGCA\tN711\tTGTGCTGT\tUnknown\t1188\r\nCGTAGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1182\r\nCTCTCTAC\tN707\tTATGGTCT\tUnknown\t1179\r\nCGAGGCTC\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t1172\r\nAAGGGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t1166\r\nAAGGCGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t1155\r\nTGGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t1150\r\nTCCTGAGC\tN704\tTGTGTAGT\tUnknown\t1141\r\nCTCTCTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1139\r\nAAGAGGCA\tN711\tTGTGCTCT\tA503\t1135\r\nCGTACTAG\tN702\tTGAGTAGA\tE504,[N|S|E]504\t1130\r\nTCCTGAGC\tN704\tAGATAGAT\tUnknown\t1126\r\nGTAGCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1121\r\nCTCTCTAC\tN707\tTATCGTCT\tE503,S503,[N|S|E]503\t1120\r\nAAGAGGCA\tN711\tTACCTCTT\tUnknown\t1118\r\nGAGAGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1109\r\nTAAGGCGA\tN701\tAGAGTTGT\tUnknown\t1105\r\nTAAGGCGA\tN701\tTGAGCTGT\tUnknown\t1091\r\nACGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t1087\r\nGCTACGCT\tN709\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t1085\r\nTAAGGCGA\tN701\tAGAGTAGC\tE504,[N|S|E]504\t1084\r\nAGGCAGCA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t1074\r\nTAAGGCGC\tD708,N701,S521\tAGAGTAGA\tE504,[N|S|E]504\t1068\r\nAGGCAGAA\tN703\tAGAGTAAT\tUnknown\t1066\r\nTCCCTGAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t1057\r\nGTAGAGGA\tN712\tTATGCTCT\tE503,S503,[N|S|E]503\t1055\r\nTCCTGAGC\tN704\tTGTGCTCT\tA503\t1055\r\nTAGAGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1053\r\nATGCAGAA\tD705,N703\tTATCCTCT\tE503,S503,[N|S|E]503\t1050\r\nAGGCAGAA\tN703\tTGTGCAGT\tE506,S506,[N|S|E]506\t1050\r\nCTACGCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t1047\r\nCAAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t1045\r\nAGGCAGAA\tN703\tAAACCGTC\tUnknown\t1038\r\nCTCTCTAC\tN707\tCTCTCTAT\tE502,S502,[N|S|E]502\t1035\r\nGCTACGCG\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t1035\r\nAAAAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t1029\r\nCGTACTAC\tN702\tAGAGTAGA\tE504,[N|S|E]504\t1027\r\nCTCTCTCC\tN707\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t1020\r\nTCCTGAGC\tN704\tCGAGTAGA\tE504,[N|S|E]504\t1014\r\nAAGAGGGA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t1012\r\nGCTACGCT\tN709\tTATCCCTT\tUnknown\t1010\r\nTCCTGAGC\tN704\tAGAGCTGT\tUnknown\t997\r\nGCTACGCT\tN709\tTATGCTCT\tE503,S503,[N|S|E]503\t984\r\nCTATCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t983\r\nTAAGGCGA\tN701\tAGAGTAAG\tUnknown\t973\r\nCTCTCACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t972\r\nGAAGGCGA\tN701\tTGTGCTGT\tUnknown\t967\r\nTAGGGATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t959\r\nTTCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t953\r\nAGGCAGAA\tN703\tAGAGTAGG\tE504,[N|S|E]504\t948\r\nGAAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t947\r\nGTAGAGGA\tN712\tTATCCTTC\tUnknown\t944\r\nGTAGAGGA\tN712\tTATCCTCC\tE503,S503,[N|S|E]503\t940\r\nTCAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t938\r\nGCAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t937\r\nCTCTCTAC\tN707\tTAGCGGCT\tUnknown\t934\r\nCGTACTAG\tN702\tAGTGTAGA\tE504,[N|S|E]504\t926\r\nGCTACGCT\tN709\tTTTCCTCT\tE503,S503,[N|S|E]503\t924\r\nCGTACTAG\tN702\tAGTGCTGT\tUnknown\t922\r\nCTCCTACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t910\r\nTAAGGCGA\tN701\tTAGAGAGA\tUnknown\t907\r\nCAGAGAGG\tN708\tCTCTCTAT\tE502,S502,[N|S|E]502\t905\r\nTCCTGAGC\tN704\tAGAGCTGA\tUnknown\t896\r\nGCAGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t894\r\nTGAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t893\r\nTAAGGCAA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t892\r\nTCCGGAGC\tD702,N704\tAGAGTAGA\tE504,[N|S|E]504\t892\r\nTAGGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t890\r\nCCCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t890\r\nGGACTCCT\tN705\tCTCTCTAT\tE502,S502,[N|S|E]502\t878\r\nAAGAGCAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t876\r\nCTCTCTAC\tN707\tTATCCTCC\tE503,S503,[N|S|E]503\t874\r\nGCTACGCT\tN709\tTATCCTTT\tE503,S503,[N|S|E]503\t866\r\nGTGGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t858\r\nCCTCTACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t843\r\nTCCTGAGC\tN704\tTGAGTAGT\tUnknown\t842\r\nGCAACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t835\r\nAAGAGGCA\tN711\tCATCCTCT\tE503,S503,[N|S|E]503\t834\r\nCTCTCTAC\tN707\tCATCCTCT\tE503,S503,[N|S|E]503\t830\r\nTAAGGCGA\tN701\tTAGGGAGA\tUnknown\t830\r\nCCTACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t828\r\nTAAGGCGA\tN701\tTATCTCTT\tUnknown\t819\r\nGAAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t814\r\nATCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t810\r\nCTCCTCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t805\r\nTAAGGCGA\tN701\tTGGAGAGA\tS511\t804\r\nTCATGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t804\r\nTAAGGCGA\tN701\tAGGTAGAT\tUnknown\t804\r\nTAAGGCGA\tN701\tAGGGTAGA\tE504,[N|S|E]504\t804\r\nAGGCAGAA\tN703\tAGTGTAGA\tE504,[N|S|E]504\t802\r\nTCTGAGCA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t796\r\nGTAGAGGA\tN712\tAATCCTCT\tE503,S503,[N|S|E]503\t794\r\nCTCTCTAC\tN707\tTATCCTTC\tUnknown\t792\r\nTGAGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t790\r\nTGGCAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t790\r\nCTCTCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t786\r\nAGGCAGAA\tN703\tAGTGCAGA\tUnknown\t782\r\nGTAGGGGA\tN712\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t780\r\nGTAGAGGA\tN712\tCATCCTCT\tE503,S503,[N|S|E]503\t777\r\nAAGAGGAA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t767\r\nGCTACGCT\tN709\tTTCCTCTT\tUnknown\t757\r\nTAAGGCGA\tN701\tATCCTCTT\tUnknown\t747\r\nAAGAGGCC\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t744\r\nCGTACTAA\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t742\r\nTCCTGAGC\tN704\tAGTGCTGA\tUnknown\t733\r\nTAAGGGGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t732\r\nAGGCAGGA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t727\r\nGTAGAGGA\tN712\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t727\r\nTAAGGCGA\tN701\tAGAGTGGA\tE504,[N|S|E]504\t725\r\nGCTGCGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t724\r\nAAGAGGCA\tN711\tTATCCTCC\tE503,S503,[N|S|E]503\t721\r\nGTGAGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t716\r\nGCTACGCT\tN709\tTACCTCTT\tUnknown\t715\r\nTCCTGAGC\tN704\tTGAGCAGA\tUnknown\t714\r\nGAGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t699\r\nGTAGGGGA\tN712\tTGTGCTCT\tA503\t699\r\nGTAGGGGA\tN712\tTGTGCTGT\tUnknown\t695\r\nTCCTGCGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t695\r\nTAAGGCGA\tN701\tAGTGTTGA\tUnknown\t692\r\nGTTAGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t688\r\nTAAGGGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t683\r\nTCCTGAGC\tN704\tTGTGTAGA\tUnknown\t679\r\nTCCTGAGC\tN704\tGAGTAGAT\tUnknown\t679\r\nTCCTTCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t678\r\nTCCTGAGC\tN704\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t676\r\nGCCACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t675\r\nAGGCAGAA\tN703\tAGAGTGAT\tUnknown\t674\r\nGTAGAGGA\tN712\tGATCCTCT\tE503,S503,[N|S|E]503\t673\r\nTTAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t669\r\nTCCTGAGC\tN704\tTGAGCAGT\tUnknown\t667\r\nGAAGGGGA\tUnknown\tTGTGCTGT\tUnknown\t665\r\nGTAGAGCA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t664\r\nTAATGCGA\tD708,N701,S522\tAGAGTAGA\tE504,[N|S|E]504\t664\r\nGTCACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t664\r\nCGTACTAG\tN702\tAGAGTAGG\tE504,[N|S|E]504\t660\r\nTGTACTAG\tA506,N702\tAGAGTAGA\tE504,[N|S|E]504\t659\r\nCGTACTAG\tN702\tAGTGCAGA\tUnknown\t658\r\nCTCTTACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t653\r\nCTCCCTAC\tE505,N707,S505,[N|S|E]505\tTATCCTCT\tE503,S503,[N|S|E]503\t652\r\nGTAGAGGA\tN712\tCTATCCTC\tUnknown\t650\r\nTAGGCATG\tN706\tTATCTCTT\tUnknown\t648\r\nTCAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t647\r\nAGGCAGAA\tN703\tCTCTCTAT\tE502,S502,[N|S|E]502\t645\r\nTTAGGCGA\tN701,S522\tAGAGTAGA\tE504,[N|S|E]504\t644\r\nAGGCAGAA\tN703\tAGTGTAGT\tUnknown\t634\r\nGCTACCCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t634\r\nAAAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t633\r\nGTAGAGGA\tN712\tTATCCCTC\tUnknown\t633\r\nTAGGCATG\tN706\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t619\r\nTAGGCATG\tN706\tATCCTCTT\tUnknown\t619\r\nCGTAGTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t617\r\nCTCTCTAC\tN707\tCTATCCTC\tUnknown\t617\r\nGTAGAGGT\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t613\r\nGTTACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t611\r\nAAGCGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t610\r\nTAAGGCGA\tN701\tAAGTAGAT\tUnknown\t605\r\nAAGAGGCA\tN711\tTATCCTTC\tUnknown\t598\r\nTAAGGCGA\tN701\tGGAGTAGA\tE504,[N|S|E]504\t597\r\nTGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t596\r\nGTAGAGGA\tN712\tTGTGCTCT\tA503\t595\r\nCGTACTAG\tN702\tAGTGCAGT\tUnknown\t587\r\nCTTCTACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t585\r\nTAAGGGCG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t585\r\nCTCTCTAC\tN707\tTATCCGCT\tE503,S503,[N|S|E]503\t583\r\nCTCCTGAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t583\r\nATAGAGGA\tD502,N712\tTATCCTCT\tE503,S503,[N|S|E]503\t583\r\nCTCTCTAC\tN707\tTATCCCTC\tUnknown\t581\r\nTCCTGGCA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t574\r\nCCTGAGCA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t574\r\nAGGCAGAA\tN703\tTATGCTCT\tE503,S503,[N|S|E]503\t572\r\nTAAGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t572\r\nAGGAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t571\r\nCGTACTAG\tN702\tAGAGTAAT\tUnknown\t570\r\nTAAGGCGA\tN701\tTATCCCTT\tUnknown\t569\r\nACTACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t568\r\nTAAGGCGA\tN701\tAGTAGATC\tUnknown\t567\r\nTTCTCCAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t566\r\nTCCTGAGC\tN704\tAGAGTTGT\tUnknown\t563\r\nCTTTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t563\r\nGCTCCGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t563\r\nCTCACTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t563\r\nTAAGGCGG\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t561\r\nGTATAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t560\r\nCTCTACAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t557\r\nAGGCAGAA\tN703\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t556\r\nGTCTCGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t556\r\nGCCACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t555\r\nAAGGGCAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t553\r\nCGTACTAG\tN702\tCTCTCTAT\tE502,S502,[N|S|E]502\t552\r\nTTCTGAGC\tN704\tAGTGCTGT\tUnknown\t550\r\nAGGCCGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t550\r\nCTCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t549\r\nAGGCAGGA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t547\r\nGCTACGCT\tN709\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t544\r\nTAAGGCGA\tN701\tTGTGCTGA\tUnknown\t542\r\nTAAGGCGA\tN701\tAGGAGTAG\tA712\t542\r\nCTCTCAAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t538\r\nCAAGGCGA\tN701\tTGTGCTGT\tUnknown\t537\r\nCTCTCTAC\tN707\tTAGCCTCT\tE503,S503,[N|S|E]503\t535\r\nAGGCAGAA\tN703\tATCCTCTT\tUnknown\t534\r\nGCCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t533\r\nAAGAGGCA\tN711\tAATCCTCT\tE503,S503,[N|S|E]503\t532\r\nTAAGGCCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t531\r\nCTCTCTAC\tN707\tTCCTCTTC\tUnknown\t530\r\nGCTACGCT\tN709\tTATCCTCC\tE503,S503,[N|S|E]503\t530\r\nGTAGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t529\r\nGTAGGAAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t527\r\nTAGGCACG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t527\r\nGTAGAGGA\tN712\tTACCCTCT\tE503,S503,[N|S|E]503\t526\r\nTAAGGCGA\tN701\tTGGAGACA\tUnknown\t526\r\nTAAGGCGA\tN701\tTATCCTTT\tE503,S503,[N|S|E]503\t521\r\nAGGCAGAA\tN703\tTGTGCTCT\tA503\t521\r\nGTAGAGGA\tN712\tTCCTCTTC\tUnknown\t518\r\nTTAGGCGA\tN701,S522\tTGTGCTCT\tA503\t516\r\nAAGAGACA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t513\r\nAAAGGCAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t510\r\nTCCTGAGC\tN704\tTGTGCAGA\tUnknown\t510\r\nCTCTCTTC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t510\r\nTTAAGGCG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t507\r\nGCTACTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t506\r\nAGGCAGAA\tN703\tTATCTCTT\tUnknown\t506\r\nAGGCGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t505\r\nGCTACGTT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t502\r\nTAGGCATG\tN706\tTATGCTCT\tE503,S503,[N|S|E]503\t500\r\nTAAGGCGC\tD708,N701,S521\tTATCCTCT\tE503,S503,[N|S|E]503\t499\r\nGTACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t498\r\nTACTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t496\r\nCTAGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t495\r\nTAGGCCAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t494\r\nCTCTCTAC\tN707\tTATGGGCT\tUnknown\t494\r\nTAAGGGGA\tN701\tTGTGCTCT\tA503\t494\r\nGTCTCTTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t494\r\nTGGCAGAA\tN703\tTGAGTAGA\tE504,[N|S|E]504\t493\r\nTCCTGAGC\tN704\tAGAGTAGC\tE504,[N|S|E]504\t489\r\nCGGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t488\r\nAGGCAGAA\tN703\tAGAGAGAT\tUnknown\t486\r\nTCCTGGGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t486\r\nTAAGGCGA\tN701\tTTTCCTCT\tE503,S503,[N|S|E]503\t486\r\nGTAGGCGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t486\r\nGCCTACGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t485\r\nCGAGGCTG\tN710\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t484\r\nAGCAGAAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t482\r\nTTGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t482\r\nGAGGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t480\r\nAATAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t480\r\nCTAGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t473\r\nAAGAGGCA\tN711\tCTATCCTC\tUnknown\t470\r\nTACGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t469\r\nCAAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t468\r\nGCCTGAGC\tN704\tTGTGCTGT\tUnknown\t468\r\nGTCGCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t467\r\nCTCTCTAG\tE502,N707,S502,[N|S|E]502\tTATCCTCT\tE503,S503,[N|S|E]503\t464\r\nTAGGCATG\tN706\tTATCCCTT\tUnknown\t463\r\nTCCTGAGC\tN704\tTGAGCTGT\tUnknown\t463\r\nCTCTCTAC\tN707\tTAGGGTCT\tUnknown\t461\r\nTCCTGAGG\tN704\tAGAGTAGA\tE504,[N|S|E]504\t461\r\nCTAAGGCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t460\r\nTCCTGAGC\tN704\tAGTGTTGA\tUnknown\t459\r\nTAGGCAGG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t458\r\nTCCGAGCA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t457\r\nGTAGAGGA\tN712\tTGTGCTGT\tUnknown\t455\r\nGCTACACT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t455\r\nCTCTCTAC\tN707\tAATCCTCT\tE503,S503,[N|S|E]503\t454\r\nTAAGGCGA\tN701\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t453\r\nTAAGGCGA\tN701\tAGAGGTAG\tUnknown\t452\r\nCTCTCTAC\tN707\tTACCCTCT\tE503,S503,[N|S|E]503\t452\r\nCGTACTAG\tN702\tAGAGCAGT\tUnknown\t452\r\nAGGCAGAA\tN703\tAGAGTTGA\tE504,[N|S|E]504\t452\r\nTTAGGCGA\tN701,S522\tAGTGCTGT\tUnknown\t451\r\nAAGAGGCA\tN711\tTATCCCTC\tUnknown\t451\r\nGCTACGCT\tN709\tTATCCTTC\tUnknown\t450\r\nTAAGGCGA\tN701\tTTCCTCTT\tUnknown\t447\r\nGTAGAGGA\tN712\tTAATCCTC\tUnknown\t445\r\nAAGAGGCA\tN711\tAAACCGTC\tUnknown\t445\r\nCTCTGAGC\tUnknown\tTGTGCTGT\tUnknown\t445\r\nTCCTGAGC\tN704\tAGAGTAAG\tUnknown\t445\r\nAAGTGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t444\r\nAGGCAGAA\tN703\tTGAGCAGT\tUnknown\t443\r\nAAGGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t442\r\nCGTACTAG\tN702\tAGAGTTGA\tE504,[N|S|E]504\t441\r\nAAGAGGCG\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t441\r\nTAGCATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t439\r\nTAAGGCGA\tN701\tAGAGGATC\tE503,S503,[N|S|E]503\t437\r\nCTCTATAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t437\r\nTAAGGCGA\tN701\tTACCTCTT\tUnknown\t436\r\nTCCTGAGC\tN704\tAGAGTATC\tUnknown\t434\r\nTCCTGACA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t434\r\nCTCTGTGC\tUnknown\tTGTGCTGT\tUnknown\t433\r\nGTACTAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t432\r\nAAGAGCCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t432\r\nTCCTGAGA\tD702,N704\tTATCCTCT\tE503,S503,[N|S|E]503\t430\r\nTAGGCATG\tN706\tTATCCTTT\tE503,S503,[N|S|E]503\t429\r\nGGTAGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t429\r\nTTCTGAGC\tN704\tAGAGCAGA\tE504,[N|S|E]504\t428\r\nTAAGGCGA\tN701\tTATGCTGT\tE506,S506,[N|S|E]506\t426\r\nAGGCAGAA\tN703\tAGTGTTGT\tUnknown\t425\r\nTAAAGGCG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t425\r\nGTAGACGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t425\r\nCGAGGCCG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t424\r\nTCCTTCTC\tUnknown\tATCTTCTC\tUnknown\t423\r\nCTCTTCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t423\r\nTCCTGAGC\tN704\tAGGTAGAT\tUnknown\t423\r\nAAGAGGCA\tN711\tGATCCTCT\tE503,S503,[N|S|E]503\t422\r\nCGTACTAC\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t422\r\nTAAGGCGA\tN701\tAGAGTCGA\tE504,[N|S|E]504\t419\r\nGTAGAAGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t419\r\nCTCTCTAC\tN707\tTATGCTGT\tE506,S506,[N|S|E]506\t418\r\nCTCTCTTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t417\r\nAAGAGGCA\tN711\tTAGAGGCC\tUnknown\t417\r\nAAGAGGCA\tN711\tTCCTCTTC\tUnknown\t417\r\nTCCTGAGC\tN704\tAGAGTGGA\tE504,[N|S|E]504\t417\r\nCGTACTAG\tN702\tTGTGCAGT\tE506,S506,[N|S|E]506\t416\r\nTAAGGCGA\tN701\tCAGAGTAG\tUnknown\t416\r\nCGCACTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t415\r\nAAGGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t411\r\nTAAGGCGA\tN701\tTGAGTTGT\tUnknown\t410\r\nGCTACGCT\tN709\tAATCCTCT\tE503,S503,[N|S|E]503\t408\r\nAAGAGGCA\tN711\tTATGCTGT\tE506,S506,[N|S|E]506\t407\r\nTGAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t407\r\nGGAGAGGA\tN712\tTAGAAGAG\tUnknown\t405\r\nCTCTCTAC\tN707\tTAATCCTC\tUnknown\t402\r\nCGTACTAG\tN702\tAGAGTGAT\tUnknown\t401\r\nGAAGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t401\r\nCGTACTAG\tN702\tAGTGTAGT\tUnknown\t400\r\nTAAGGTGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t400\r\nCTTCTCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t399\r\nCGCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t398\r\nTCCTGAGC\tN704\tCTCTCTAT\tE502,S502,[N|S|E]502\t396\r\nTCCTGAGC\tN704\tTATGCTCT\tE503,S503,[N|S|E]503\t394\r\nCCCTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t394\r\nTAAGGGGA\tN701\tAGTGCTGT\tUnknown\t391\r\nCGAGGCGG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t391\r\nGAAGGAGA\tUnknown\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t389\r\nCTCTGTAC\tN707\tTGTGCTGT\tUnknown\t389\r\nTAGGCATG\tN706\tTACCTCTT\tUnknown\t388\r\nGCTACGCT\tN709\tTGTGCTCT\tA503\t388\r\nGTAGAGGA\tN712\tTATCTTCT\tE503,S503,[N|S|E]503\t387\r\nGGAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t387\r\nCGCTACGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t385\r\nTCCTGAGA\tD702,N704\tTGTGCTGT\tUnknown\t385\r\nTAAGGCGA\tN701\tAGAGTAAA\tE504,[N|S|E]504\t384\r\nAGGCAGAA\tN703\tAGATAGAT\tUnknown\t375\r\nGTAAAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t375\r\nGATACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t375\r\nAAGAGGCA\tN711\tTACCCTCT\tE503,S503,[N|S|E]503\t372\r\nGCTACGCT\tN709\tCATCCTCT\tE503,S503,[N|S|E]503\t372\r\nGATAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t371\r\nTACGCTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t370\r\nAGGCCAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t370\r\nAGGCAGAA\tN703\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t369\r\nAGGCAGAA\tN703\tTGAGCAGA\tUnknown\t369\r\nTAAGGAGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t368\r\nCCGTACTA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t368\r\nAGGCAGAA\tN703\tTATCCTTT\tE503,S503,[N|S|E]503\t368\r\nTCCTAGCA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t368\r\nGAAGGGGA\tUnknown\tTGTGCTCT\tA503\t367\r\nGTCACGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t366\r\nGGACGCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t366\r\nTCCCGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t365\r\nCCGAGGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t364\r\nTAGGCATG\tN706\tTTTCCTCT\tE503,S503,[N|S|E]503\t364\r\nGCTATCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t363\r\nGTAGAGGA\tN712\tTATCCCCT\tE503,S503,[N|S|E]503\t363\r\nCGAGGCTG\tN710\tTATCTCTT\tUnknown\t362\r\nCAAGAGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t361\r\nAAGAGGCA\tN711\tTATCCTGT\tE503,S503,[N|S|E]503\t360\r\nGTAGGGGA\tN712\tTATGCTCT\tE503,S503,[N|S|E]503\t359\r\nCTCTGTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t357\r\nTCTTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t356\r\nGAAAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t356\r\nTACGGCGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t356\r\nGCTGCGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t356\r\nTAGGCATG\tN706\tTTCCTCTT\tUnknown\t356\r\nAGCAGAAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t354\r\nCTCTCTAC\tN707\tTAGCGTCT\tUnknown\t354\r\nAGGCAGAA\tN703\tTTTCCTCT\tE503,S503,[N|S|E]503\t354\r\nTAGGCAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t353\r\nAAGAGGAA\tN711\tTAGAAGAG\tUnknown\t352\r\nCTCTCTCC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t351\r\nTCCTGAGC\tN704\tAAGTAGAT\tUnknown\t351\r\nGCAACGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t350\r\nTAAGGCGA\tN701\tAGAGTACA\tA503,E504,[N|S|E]504\t349\r\nGGGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t347\r\nAAAGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t347\r\nGGGGGGGG\tUnknown\tGGGGGGGG\tUnknown\t347\r\nACTAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t346\r\nGCTACGCT\tN709\tCTATCCTC\tUnknown\t346\r\nGCAGCGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t346\r\nTTCTGTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t343\r\nCGCGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t342\r\nCTCTCTAC\tN707\tTATCTTCT\tE503,S503,[N|S|E]503\t341\r\nTAGGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t341\r\nCGAGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t340\r\nCCCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t340\r\nTAAGGCGA\tN701\tAGAGTACG\tUnknown\t340\r\nTCCTGAGC\tN704\tTATCTCTT\tUnknown\t339\r\nGGTACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t338\r\nTAAGGCAA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t337\r\nAAAGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t332\r\nGCTACGCT\tN709\tTATCCCTC\tUnknown\t332\r\nCCCTGAGC\tN704\tTGTGCTGT\tUnknown\t332\r\nTCTAGGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t328\r\nCGTACTAG\tN702\tAGAGAGAT\tUnknown\t326\r\nTAGGCATG\tN706\tTGTGCTCT\tA503\t325\r\nAGGCAGAA\tN703\tTGAGTAGT\tUnknown\t325\r\nTAAGGAGA\tN701\tGGAGGAGA\tUnknown\t324\r\nTAAGGCGA\tN701\tCATCCTCT\tE503,S503,[N|S|E]503\t324\r\nAAGAGGTA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t322\r\nGCCTCGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t321\r\nTAAGGCGA\tN701\tAGAGATCG\tUnknown\t321\r\nTACTGCGC\tD708\tAGAGTAGA\tE504,[N|S|E]504\t320\r\nGTCTCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t319\r\nAGGCAGAA\tN703\tTGTGTAGT\tUnknown\t319\r\nAGGCAGAA\tN703\tTATCCCTT\tUnknown\t318\r\nACCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t316\r\nGCAACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t316\r\nGCTACTCT\tE504,N709,[N|S|E]504\tTATCCTCT\tE503,S503,[N|S|E]503\t315\r\nTTCTGAGC\tN704\tTGTGCTCT\tA503\t314\r\nAAGAGGCA\tN711\tTAATCCTC\tUnknown\t314\r\nTAAGGCGA\tN701\tAGAATAGA\tE504,[N|S|E]504\t313\r\nATGCAGAA\tD705,N703\tTGTGCTGT\tUnknown\t313\r\nCTCACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t313\r\nGCTATGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t313\r\nAAGAGGCA\tN711\tTATCCGCT\tE503,S503,[N|S|E]503\t313\r\nACTCTTCC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t312\r\nCACGAGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t311\r\nGCTAGGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t309\r\nCTCTGTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t308\r\nGCCTCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t308\r\nGCCTTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t307\r\nCGTACTAG\tN702\tAGTGTTGT\tUnknown\t307\r\nGCTACGCT\tN709\tTGTGCTGT\tUnknown\t307\r\nTAAAGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t306\r\nTAAGGCGA\tN701\tAGAGTCGT\tUnknown\t306\r\nCAGGCAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t306\r\nTCCTGAGC\tN704\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t306\r\nGACGCTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t305\r\nTCCTGAGC\tN704\tTGTGCTGA\tUnknown\t304\r\nGCTACGCT\tN709\tGATCCTCT\tE503,S503,[N|S|E]503\t304\r\nTAAGGCGA\tN701\tAGAGTTAG\tUnknown\t303\r\nGCCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t303\r\nCTCTCTAC\tN707\tTATCCCCT\tE503,S503,[N|S|E]503\t302\r\nAAAGGGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t301\r\nAGGCAGCA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t301\r\nAAGAGGCA\tN711\tTATCTTCT\tE503,S503,[N|S|E]503\t300\r\nGTAGATGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t299\r\nCTCTCTAC\tN707\tTAGCCGCT\tUnknown\t299\r\nTCCTGAGC\tN704\tTTTCCTCT\tE503,S503,[N|S|E]503\t298\r\nCGAGGCGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t298\r\nAGGCAGAA\tN703\tTTCCTCTT\tUnknown\t297\r\nAGGCAGAA\tN703\tTACCTCTT\tUnknown\t296\r\nTCCTGAGT\tN704\tAGAGTAGA\tE504,[N|S|E]504\t295\r\nTAAGGCCA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t295\r\nAAGAGGCA\tN711\tTATCGTCT\tE503,S503,[N|S|E]503\t293\r\nAGGCAGAA\tN703\tTATCCGCT\tE503,S503,[N|S|E]503\t293\r\nTCCTGAGC\tN704\tATCCTCTT\tUnknown\t292\r\nAGGCAGAA\tN703\tAGAGCTGT\tUnknown\t291\r\nTCCTGAGC\tN704\tGGAGTAGA\tE504,[N|S|E]504\t291\r\nTAAGGCGA\tN701\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t291\r\nCGAGGCTG\tN710\tTATGCTCT\tE503,S503,[N|S|E]503\t290\r\nTAAGGCGA\tN701\tTATCCTCC\tE503,S503,[N|S|E]503\t290\r\nTAAGGCGA\tN701\tGGAGTAGG\tUnknown\t290\r\nTCCTGGGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t290\r\nGCTACCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t289\r\nTAGGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t287\r\nTAGGCATG\tN706\tTGTGCTGT\tUnknown\t287\r\nGTAGGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t287\r\nGCAACGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t287\r\nTAAGGGGA\tN701\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t286\r\nAGGCAGAA\tN703\tTAGAGGCT\tUnknown\t286\r\nCGAGGCTG\tN710\tATCCTCTT\tUnknown\t285\r\nTCCCTGAG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t284\r\nGTAGAGGA\tN712\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t283\r\nTAAGGCGA\tN701\tAAGAGTAG\tUnknown\t283\r\nTCCTGAGC\tN704\tAGTAGATC\tUnknown\t282\r\nTCAGGAGA\tD702\tAGAGTAGA\tE504,[N|S|E]504\t282\r\nCCTCTTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t280\r\nGCTCCTCT\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t279\r\nGCCGCTAT\tD502\tTATCCTCT\tE503,S503,[N|S|E]503\t279\r\nGCTAAGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t279\r\nGTACAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t278\r\nTAAGGCGA\tN701\tATAGTAGA\tE504,[N|S|E]504\t278\r\nCGAGGCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t277\r\nGCGAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t277\r\nTAAGGCCA\tN701\tTGTGCTGT\tUnknown\t274\r\nGTAGAAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t273\r\nCTCTCTAC\tN707\tGATCCTCT\tE503,S503,[N|S|E]503\t273\r\nAAGAGGCA\tN711\tTATCCCCT\tE503,S503,[N|S|E]503\t273\r\nTAGGGATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t272\r\nAGGCAAAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t272\r\nCTCTCTAC\tN707\tTATCGGCT\tUnknown\t272\r\nTCCTGACC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t271\r\nCTGTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t270\r\nGTAGCGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t270\r\nTCATGAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t269\r\nTCATGAGC\tN704\tTGTGCTGT\tUnknown\t269\r\nTAAGGCGA\tN701\tAGAAGTAG\tUnknown\t269\r\nAAGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t268\r\nTCCGGAGC\tD702,N704\tTATCCTCT\tE503,S503,[N|S|E]503\t268\r\nAAGAGGCA\tN711\tTAGCCTCT\tE503,S503,[N|S|E]503\t268\r\nTGGCATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t267\r\nTAAGGCGT\tN701\tAGAGTAGA\tE504,[N|S|E]504\t267\r\nCTCGCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t266\r\nAGGCAGAA\tN703\tAGAGTATC\tUnknown\t266\r\nCTCTTTAC\tE505,N707,S505,[N|S|E]505\tTATCCTCT\tE503,S503,[N|S|E]503\t265\r\nGGACCCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t264\r\nCTCACTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t262\r\nCTCTCTAC\tN707\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t262\r\nGCGACGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t261\r\nAAGAGTCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t261\r\nAAGAAGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t260\r\nCGAGGCTG\tN710\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t260\r\nGTAGTGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t260\r\nGCTACGCT\tN709\tTCCTCTTC\tUnknown\t260\r\nGCCCTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t260\r\nGTCTCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t259\r\nTCAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t259\r\nTTCTGTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t259\r\nTACGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t258\r\nGTAGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t258\r\nGGCCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t257\r\nCGAGGGTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t257\r\nTAAGGCGA\tN701\tTAGAGCTG\tUnknown\t256\r\nAGGCAGAA\tN703\tCATCCTCT\tE503,S503,[N|S|E]503\t256\r\nATGCAGAA\tD705,N703\tAGAGTAGA\tE504,[N|S|E]504\t256\r\nTCCTGAGC\tN704\tAGCGTAGA\tE504,[N|S|E]504\t256\r\nGTAGAGTA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t256\r\nGTAGGCGA\tUnknown\tTGTGCTGT\tUnknown\t255\r\nATGTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t255\r\nTAAGGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t254\r\nCTCTGTAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t252\r\nTAAGGGGA\tN701\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t252\r\nGAAGGGGA\tUnknown\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t251\r\nCTCCCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t251\r\nGAGCCCAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t251\r\nGCTCCTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t251\r\nCGTACCAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t249\r\nTAGGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t249\r\nTCTGAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t249\r\nGGAGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t249\r\nCAGGCAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t249\r\nAGGCGGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t249\r\nCTCTGAGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t248\r\nAAGAGGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t248\r\nTAAGGCGA\tN701\tTATCCTTC\tUnknown\t248\r\nTGCTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t248\r\nGCTACGCT\tN709\tTACCCTCT\tE503,S503,[N|S|E]503\t248\r\nAGGCAGAA\tN703\tGAGTAGAT\tUnknown\t247\r\nCTCTCTAC\tN707\tTATCCTGT\tE503,S503,[N|S|E]503\t246\r\nTCTACCCT\tE504,[N|S|E]504\tTATCCTCT\tE503,S503,[N|S|E]503\t246\r\nCGTACTAG\tN702\tAGATAGAT\tUnknown\t246\r\nTTAGGGGA\tUnknown\tTGTGCTGT\tUnknown\t245\r\nAGGCCAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t244\r\nTTAGGCGA\tN701,S522\tTGTGTTGT\tUnknown\t244\r\nTCCTTCTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t243\r\nCTGAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t243\r\nTCCTGAGC\tN704\tTATCCCTT\tUnknown\t243\r\nTCCTGAGC\tN704\tTATCCTTT\tE503,S503,[N|S|E]503\t242\r\nCGAGGCTG\tN710\tTATCCCTT\tUnknown\t242\r\nCTCTCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t242\r\nGGACTCCT\tN705\tTATCTCTT\tUnknown\t240\r\nTTCTGAGC\tN704\tAGTGCAGT\tUnknown\t240\r\nGGACTCCT\tN705\tATCCTCTT\tUnknown\t240\r\nTAAAGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t240\r\nCGTACTAG\tN702\tTGTGCTCT\tA503\t239\r\nTAAGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t239\r\nTCCTGAGC\tN704\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t238\r\nCGTACCTA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t238\r\nAAGAGGCA\tN711\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t237\r\nCTCTCTAC\tN707\tTATGGTCA\tUnknown\t236\r\nTAAGGCGA\tN701\tAGATTAGA\tE504,[N|S|E]504\t236\r\nAGGCATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t235\r\nAGGCAGAA\tN703\tTGTGTTGT\tUnknown\t233\r\nCTTACGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t232\r\nCTCTCTTC\tN707\tTTTCCTCT\tE503,S503,[N|S|E]503\t232\r\nCGTACTAG\tN702\tTGTGTAGT\tUnknown\t231\r\nAGGCAGCA\tN703\tTGTGCTGT\tUnknown\t231\r\nCTCTCTAC\tN707\tCTGTCTCT\tUnknown\t230\r\nTTAGGCGA\tN701,S522\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t230\r\nTAAGGCGA\tN701\tAGTGCTCT\tUnknown\t230\r\nTTCTCTAC\tN707\tTTTCCTCT\tE503,S503,[N|S|E]503\t230\r\nTAGGCCTG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t230\r\nCGAGGCTG\tN710\tGCGTAAGA\tE517,S517,[N|S|E]517\t229\r\nGTCGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t229\r\nGCTACGCT\tN709\tTAATCCTC\tUnknown\t229\r\nGGAGAGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t229\r\nCTCTCTCT\tE502,S502,[N|S|E]502\tTATCCTCT\tE503,S503,[N|S|E]503\t227\r\nCCCTCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t227\r\nAGGCAGAA\tN703\tAGAGCTGA\tUnknown\t226\r\nCGTACTAG\tN702\tTGTGTTGT\tUnknown\t226\r\nTAAGGCGA\tN701\tTGAGCTGA\tUnknown\t225\r\nCCTCCTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t224\r\nTAAGGCGA\tN701\tAGAGTTCG\tUnknown\t224\r\nCTAGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t224\r\nGGAGGAAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t223\r\nTAGGCATG\tN706\tCATCCTCT\tE503,S503,[N|S|E]503\t223\r\nTAGAGCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t223\r\nGTCTCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t223\r\nTAAGGCGT\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t222\r\nGTAGAGGA\tN712\tTTATCCTC\tUnknown\t222\r\nCTCTCGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t222\r\nTTAGGTGA\tUnknown\tTGTGCTGT\tUnknown\t222\r\nCTCTGAGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t221\r\nGTAAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t221\r\nGTGAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t221\r\nAGGCAGAA\tN703\tTATCCTCC\tE503,S503,[N|S|E]503\t219\r\nCGGGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t219\r\nGCTACGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t219\r\nCGTACTAG\tN702\tAGAGCTGA\tUnknown\t219\r\nCGGCAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t219\r\nCTAGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t219\r\nCTAGGCGA\tS513\tTGTGCTGT\tUnknown\t219\r\nTCCTGAGC\tN704\tCAGAGTAG\tUnknown\t218\r\nTCATGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t218\r\nCGAACTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t218\r\nTAGGCATG\tN706\tTATCCTCC\tE503,S503,[N|S|E]503\t217\r\nCGTACTAG\tN702\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t217\r\nGCGCTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t217\r\nAGGCGAAA\tD505\tTATCCTCT\tE503,S503,[N|S|E]503\t217\r\nGAAGGAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t217\r\nAGGCAGAA\tN703\tAGAGTAGC\tE504,[N|S|E]504\t217\r\nCGTACTAA\tN702\tTGTGCTGT\tUnknown\t216\r\nCTCTCTAC\tN707\tCCTCTTCG\tUnknown\t216\r\nTCCTGATC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t216\r\nGTCGCGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t216\r\nTCCTGCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t216\r\nCGAGGCTG\tN710\tTATCCTTT\tE503,S503,[N|S|E]503\t215\r\nTAGGCATG\tN706\tCTCTCTAT\tE502,S502,[N|S|E]502\t214\r\nTTCTCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t214\r\nTTCCTGAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t213\r\nTAGGCGTG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t213\r\nTAGGCATG\tN706\tTATCCTTC\tUnknown\t213\r\nTAATGCGA\tD708,N701,S522\tTATCCTCT\tE503,S503,[N|S|E]503\t213\r\nCTCTCTAC\tN707\tTATCCTCG\tE503,S503,[N|S|E]503\t212\r\nAAAGAGGC\tD502\tTATCCTCT\tE503,S503,[N|S|E]503\t212\r\nAGGAAGAA\tN703\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t212\r\nAGACAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t211\r\nCTCTCTAC\tN707\tTACTCTTC\tUnknown\t211\r\nCGAGGCTG\tN710\tTTTCCTCT\tE503,S503,[N|S|E]503\t211\r\nCGAGGCTG\tN710\tTACCTCTT\tUnknown\t210\r\nGTTACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t210\r\nAGGCGGAA\tN703\tTGTGCTGT\tUnknown\t210\r\nGTAAGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t210\r\nTCAGGCGA\tN701\tTGTGCTGT\tUnknown\t210\r\nTAAGGCGA\tN701\tAAAGTAGA\tE504,[N|S|E]504\t210\r\nTCCAGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t209\r\nGAAGGCGA\tN701\tTGTGCTCT\tA503\t208\r\nTAAGGGCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t208\r\nGTCTCGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t208\r\nAAAGGCGA\tN701\tTGTGCTGT\tUnknown\t207\r\nCTCTGCAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t206\r\nCGAGGCTG\tN710\tTTCCTCTT\tUnknown\t206\r\nTTCTCTTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t205\r\nCTAGGTGA\tUnknown\tTGTGCTGT\tUnknown\t205\r\nGTACTAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t204\r\nGTCGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t204\r\nAGGCAGAA\tN703\tTGAGCTGT\tUnknown\t203\r\nCGTACTAG\tN702\tTGAGCAGA\tUnknown\t203\r\nCTATCTAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t203\r\nGTAGCGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t202\r\nCGTACAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t202\r\nGTAGAGGA\tN712\tTATCCTCG\tE503,S503,[N|S|E]503\t202\r\nTCCTGAGC\tN704\tTGAGTTGT\tUnknown\t202\r\nGTAGAGGA\tN712\tCCTCTTCG\tUnknown\t201\r\nCTCTCTAC\tN707\tTATTCCTC\tUnknown\t201\r\nTCCTGAGC\tN704\tAGAGGTAG\tUnknown\t201\r\nTCCTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t200\r\nTCCTGAGC\tN704\tAGGGTAGA\tE504,[N|S|E]504\t200\r\nCTAGGCAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t199\r\nTCCGGCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t199\r\nTACGGCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t199\r\nGTAACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t199\r\nAGGCAAAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t198\r\nAGGCAGAA\tN703\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t198\r\nGTAGAGGA\tN712\tTATCCTGT\tE503,S503,[N|S|E]503\t198\r\nTCCTGAGC\tN704\tAGAGGATC\tE503,S503,[N|S|E]503\t198\r\nGTCACGAC\tA701\tTATCCTCT\tE503,S503,[N|S|E]503\t197\r\nAGGCCGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t197\r\nCGCACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t197\r\nTCGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t197\r\nTCCTGAGC\tN704\tAGAGTCGA\tE504,[N|S|E]504\t197\r\nGTAACGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t197\r\nGCCCCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t196\r\nTAGGCATG\tN706\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t196\r\nTCAGGCGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t196\r\nGTTACGAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t196\r\nAGGGAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t196\r\nCGTACTGG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t196\r\nGCTACGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t196\r\nGGAGTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t195\r\nGTAGAGGA\tN712\tTATTCCTC\tUnknown\t195\r\nTCCGGAGC\tD702,N704\tTGTGCTGT\tUnknown\t195\r\nTCCTGAGC\tN704\tTACCTCTT\tUnknown\t194\r\nCGTACTAG\tN702\tGAGTAGAT\tUnknown\t194\r\nTTCTGTGC\tUnknown\tTGTGCTGT\tUnknown\t193\r\nTCCTGAGC\tN704\tAGAGTAAA\tE504,[N|S|E]504\t193\r\nCACTCTAC\tN707\tTATCCTCT\tE503,S503,[N|S|E]503\t193\r\nCGTACTGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t192\r\nGTAACGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t192\r\nCCTACTCT\tE504,[N|S|E]504\tTATCCTCT\tE503,S503,[N|S|E]503\t192\r\nGGACTCCC\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t191\r\nCGTACTAT\tN702\tAGAGCAGA\tE504,[N|S|E]504\t191\r\nGCTGCTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t190\r\nTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\tTATCCTCT\tE503,S503,[N|S|E]503\t190\r\nCTAGCTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t190\r\nAGGCAGAA\tN703\tTGTGCAGA\tUnknown\t190\r\nAAAGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t189\r\nGAAGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t188\r\nTAAGGCGA\tN701\tAGACTAGA\tE504,[N|S|E]504\t188\r\nTCATGCGA\tS522\tAGAGTAGA\tE504,[N|S|E]504\t188\r\nTTCTGCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t188\r\nGTAGAGGA\tN712\tTACTCTTC\tUnknown\t187\r\nCAAGGCGA\tN701\tAGAGCAGA\tE504,[N|S|E]504\t186\r\nCTCGCGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t186\r\nCTCTCTAC\tN707\tTTATCCTC\tUnknown\t186\r\nCTAGGCGA\tS513\tTATCCTCT\tE503,S503,[N|S|E]503\t186\r\nTCCGGCGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t185\r\nGTAGAGGA\tN712\tAGAGTAGA\tE504,[N|S|E]504\t185\r\nCGTACTAG\tN702\tCGAGTAGA\tE504,[N|S|E]504\t184\r\nTCCTGAGC\tN704\tAGAATAGA\tE504,[N|S|E]504\t183\r\nTAAGGCGA\tN701\tCTATCCTC\tUnknown\t183\r\nTTTCTTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t183\r\nAAGAGGAA\tN711\tGAGAAGAG\tUnknown\t183\r\nAAAAGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t183\r\nGGACAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t182\r\nCTCTGGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t182\r\nCTGGCATG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t181\r\nTAAGGCTA\tN701,S521\tTATCCTCT\tE503,S503,[N|S|E]503\t181\r\nTCAGGAGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t181\r\nTCCTGAGC\tN704\tAGAGTTAG\tUnknown\t180\r\nGTAGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t180\r\nAGGTAGAA\tN703,S515\tAGAGTAGA\tE504,[N|S|E]504\t180\r\nATCTCTAC\tN707\tGATCCTCT\tE503,S503,[N|S|E]503\t180\r\nTAAGGAGA\tN701\tTGTGCTGT\tUnknown\t180\r\nTGTACTAG\tA506,N702\tTATCCTCT\tE503,S503,[N|S|E]503\t179\r\nATCTCTAC\tN707\tAATCCTCT\tE503,S503,[N|S|E]503\t179\r\nGTCGCTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t179\r\nTAAGGCGA\tN701\tAGCGTAGA\tE504,[N|S|E]504\t179\r\nAACAGGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t179\r\nTAAGGCGA\tN701\tTGTGTTGA\tUnknown\t179\r\nTAGAGGCA\tN711\tTTTCCTCT\tE503,S503,[N|S|E]503\t178\r\nAGGCAGAT\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t177\r\nTTAGGGGA\tUnknown\tTGTGCTCT\tA503\t177\r\nAAGAGGCA\tN711\tAGAGTAGA\tE504,[N|S|E]504\t177\r\nGTATCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t176\r\nTAGGGCAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t176\r\nGGACTCCT\tN705\tTATCCCTT\tUnknown\t176\r\nTAAGAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t175\r\nTTCTGCAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t175\r\nTTAAGGCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t175\r\nAAGGCAAT\tS520\tTATCCTCT\tE503,S503,[N|S|E]503\t174\r\nTAAGGCGA\tN701\tTGGGTAGA\tUnknown\t174\r\nCGACTAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t174\r\nGGACTCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t174\r\nCGTACTAG\tN702\tAGTGCTGA\tUnknown\t173\r\nAGGCAGAA\tN703\tAATCCTCT\tE503,S503,[N|S|E]503\t173\r\nCTCTGTAC\tN707\tTGTGCTCT\tA503\t173\r\nGCTACGCT\tN709\tTATGCTGT\tE506,S506,[N|S|E]506\t172\r\nAGGCGAAA\tD505\tAGAGTAGA\tE504,[N|S|E]504\t172\r\nTAAGGCGA\tN701\tTATCCCTC\tUnknown\t172\r\nAGGCAGAA\tN703\tCGAGTAGA\tE504,[N|S|E]504\t172\r\nTCCTGAGC\tN704\tAGGAGTAG\tA712\t172\r\nGCTCCCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t171\r\nTAAGACGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t171\r\nTGGCGGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t171\r\nTCGTGAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t171\r\nAAGAGGCA\tN711\tTAGCGGCT\tUnknown\t171\r\nTCCTGCGC\tN704\tTGTGCTGT\tUnknown\t171\r\nGTAGCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t170\r\nTTAAGGGG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t170\r\nCTCTCTAC\tN707\tTATCTTCG\tUnknown\t169\r\nCGTACTAG\tN702\tAGAGCTGT\tUnknown\t169\r\nGTAGAGGA\tN712\tTATCTTCG\tUnknown\t168\r\nTAAGGCGA\tN701\tTGAGTTGA\tUnknown\t167\r\nAGGCAGAA\tN703\tAGAGTGGA\tE504,[N|S|E]504\t167\r\nAAGAGGCA\tN711\tTATCCTCG\tE503,S503,[N|S|E]503\t167\r\nGGAGAGGA\tN712\tGAGAAGAG\tUnknown\t167\r\nGCTACGCT\tN709\tTATCCCCT\tE503,S503,[N|S|E]503\t167\r\nGTAGCGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t167\r\nGGAGGGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t166\r\nTCCTGAGC\tN704\tTTCCTCTT\tUnknown\t166\r\nGTCGAGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t166\r\nTAGGATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t166\r\nTCCTGGGC\tN704\tTGTGCTGT\tUnknown\t166\r\nTCCTGAGC\tN704\tAAGAGTAG\tUnknown\t165\r\nTCTTCCTT\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t165\r\nTCTAGGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t165\r\nGACTCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t165\r\nGGCAGAAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t165\r\nTACTGAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t164\r\nTTCTGAGC\tN704\tTGTGCAGT\tE506,S506,[N|S|E]506\t164\r\nCGTACTCG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t164\r\nAGGAGAAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t164\r\nGTAGGGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t164\r\nGTAGAGGA\tN712\tTATCCGCT\tE503,S503,[N|S|E]503\t164\r\nTTAGGCGA\tN701,S522\tAGTGTTGT\tUnknown\t163\r\nTCCTCCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t163\r\nTAAGGCGA\tN701\tTAGCCTCT\tE503,S503,[N|S|E]503\t163\r\nAGGCAGAA\tN703\tAGAGTAAG\tUnknown\t163\r\nGGACTCGT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t162\r\nAAGACGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t162\r\nAAGAGGCT\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t162\r\nCCGTACTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t162\r\nAGGCAGAA\tN703\tTATGCTGT\tE506,S506,[N|S|E]506\t161\r\nAGGCCGAA\tN703\tTGTGCTGT\tUnknown\t161\r\nCTTACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t161\r\nCCTACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t161\r\nAAGAGGCA\tN711\tCCTCTTCG\tUnknown\t160\r\nAGGGAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t160\r\nCTCTCTAC\tN707\tTATGGGCA\tUnknown\t160\r\nTAGGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t160\r\nTAGGAATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t159\r\nCGTAGTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t159\r\nCGTAGTAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t159\r\nCTCTCTAC\tN707\tTAGGGTCG\tUnknown\t158\r\nGGGCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t158\r\nCGCACTAC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t158\r\nGCTAGGCT\tN709\tTGTGCTGT\tUnknown\t158\r\nTCCTGAGC\tN704\tATAGTAGA\tE504,[N|S|E]504\t157\r\nCGTCTAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t157\r\nGTAGCGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t157\r\nAGGCAGAA\tN703\tTATCCTTC\tUnknown\t157\r\nCCTCCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t157\r\nCCCCCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t157\r\nCGTACTAT\tN702\tTGTGCTGT\tUnknown\t156\r\nGCTACGCT\tN709\tTATCGTCT\tE503,S503,[N|S|E]503\t156\r\nGAGGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t156\r\nGCTACGCT\tN709\tTATCTTCT\tE503,S503,[N|S|E]503\t155\r\nTCCTAAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t155\r\nTTCTCTTC\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t155\r\nCTAGGCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t155\r\nTGGGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t155\r\nCGAGGCTG\tN710\tCATCCTCT\tE503,S503,[N|S|E]503\t155\r\nGGACTCCT\tN705\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t154\r\nTCCTGAGC\tN704\tAGAGTACA\tA503,E504,[N|S|E]504\t154\r\nAGGCAGAA\tN703\tAGGTAGAT\tUnknown\t154\r\nTAGGCATG\tN706\tCTATCCTC\tUnknown\t154\r\nTCCTGAGC\tN704\tAGAGATCG\tUnknown\t154\r\nCTCTCTAC\tN707\tTAGGGCTG\tUnknown\t153\r\nGCTTCGCT\tN709\tTATCCTCT\tE503,S503,[N|S|E]503\t153\r\nGCTACGCT\tN709\tTATCCGCT\tE503,S503,[N|S|E]503\t153\r\nTAGGCATT\tN706\tTTTCCTCT\tE503,S503,[N|S|E]503\t153\r\nTTAGGCGA\tN701,S522\tTGTGCAGT\tE506,S506,[N|S|E]506\t153\r\nTCCTGAGG\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t152\r\nAGGCGGCA\tUnknown\tTGTGCTGT\tUnknown\t152\r\nTTAGGCGA\tN701,S522\tAGTGCAGT\tUnknown\t152\r\nGTCTGAGC\tUnknown\tTGTGCTGT\tUnknown\t152\r\nTCCTGACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t152\r\nCGTACTAG\tN702\tTGTGCAGA\tUnknown\t152\r\nTAAGGCGA\tN701\tTGTCCTGT\tUnknown\t152\r\nCGGGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t152\r\nCTCTGTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t151\r\nTTAGTGGA\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t151\r\nCTCTCTAC\tN707\tCTGCCTCT\tUnknown\t151\r\nGGGCAGAA\tN703\tTGTGCTGT\tUnknown\t151\r\nGTATCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t150\r\nGGACTCCT\tN705\tTTCCTCTT\tUnknown\t150\r\nTCCTGAAC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t150\r\nTAAGGCGA\tN701\tAGGGGAGG\tUnknown\t150\r\nCTTACTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t150\r\nCTTACTAG\tN702,S518\tTATCCTCT\tE503,S503,[N|S|E]503\t150\r\nTAGGCATG\tN706\tTCCTCTTC\tUnknown\t149\r\nCCCCCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t149\r\nGCCTCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t149\r\nTCCTGAGC\tN704\tAGATTAGA\tE504,[N|S|E]504\t149\r\nTAAGGCGT\tN701\tTGTGCTGT\tUnknown\t149\r\nCCACGAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t149\r\nCGTACTAG\tN702\tTGAGTAGT\tUnknown\t148\r\nTCCTGAGC\tN704\tAGAGTCGT\tUnknown\t148\r\nAAGAGGCA\tN711\tTAGAGGCT\tUnknown\t148\r\nTAAAGGCG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t148\r\nTAAGGCGG\tN701\tTGTGCTGT\tUnknown\t147\r\nCGTACTAG\tN702\tTGTGTAGA\tUnknown\t147\r\nCTATCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t147\r\nTCCTGACC\tN704\tTGTGCTGT\tUnknown\t147\r\nCCCTGAGC\tN704\tAGAGCAGA\tE504,[N|S|E]504\t147\r\nGCTACGCT\tN709\tTATCCTGT\tE503,S503,[N|S|E]503\t147\r\nGTATCTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t147\r\nTAAGGCGA\tN701\tGATCCTCT\tE503,S503,[N|S|E]503\t147\r\nTACTGCGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t147\r\nGGAGAGGA\tN712\tTGTGCTGT\tUnknown\t147\r\nGATAGGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t146\r\nTAGAGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t146\r\nAGGCGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t146\r\nTCCTGCGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t146\r\nTCCTTGAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t146\r\nGCAGGGGA\tUnknown\tTGTGCTGT\tUnknown\t146\r\nGTAGAGAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t146\r\nTAAGGCGA\tN701\tTACCCTCT\tE503,S503,[N|S|E]503\t146\r\nTCATGCGC\tD708\tAGAGTAGA\tE504,[N|S|E]504\t146\r\nAAGAGGCA\tN711\tTATTCCTC\tUnknown\t146\r\nGGACTGCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t146\r\nTACTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t146\r\nTTCGGCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t145\r\nCGTAATAG\tN702,S518\tAGAGTAGA\tE504,[N|S|E]504\t145\r\nTCCTGAGC\tN704\tAGAAGTAG\tUnknown\t145\r\nCTTTCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t145\r\nTTAGGGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t145\r\nCTCTCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t145\r\nAGTACTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t145\r\nTCCTGAGC\tN704\tAGAGTATA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t145\r\nTAAGGCGA\tN701\tTGGGGAGC\tUnknown\t145\r\nATCAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t145\r\nTAGGCATG\tN706\tTATCCCTC\tUnknown\t145\r\nTAAGGCGA\tN701\tAATCCTCT\tE503,S503,[N|S|E]503\t145\r\nTGTACCAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t145\r\nTAAGGCGA\tN701\tTATGGACA\tUnknown\t145\r\nGGTCTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t144\r\nGCTAGGCT\tN709\tTATGCTCT\tE503,S503,[N|S|E]503\t144\r\nTCCTGAGC\tN704\tCATCCTCT\tE503,S503,[N|S|E]503\t143\r\nTCCTGAGC\tN704\tTATCCTCC\tE503,S503,[N|S|E]503\t143\r\nTAAGGCGA\tN701\tAGAGTCGG\tUnknown\t143\r\nTCCTGAGC\tN704\tTATGCTGT\tE506,S506,[N|S|E]506\t143\r\nCGAGGTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t143\r\nTCTCCCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t143\r\nTAACGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t142\r\nGAGGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t142\r\nCTAGCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t142\r\nGGACTCCT\tN705\tTTTCCTCT\tE503,S503,[N|S|E]503\t142\r\nAGGCAGAA\tN703\tCTATCCTC\tUnknown\t142\r\nTCCTTCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t142\r\nCGAGGCTG\tN710\tTGTGCTGT\tUnknown\t142\r\nGCTACGCT\tN709\tTAGCCTCT\tE503,S503,[N|S|E]503\t142\r\nCCTGAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t142\r\nTAAGGAGA\tN701\tTAGAAGAG\tUnknown\t142\r\nGAAGGCGA\tN701\tAGTGCTGT\tUnknown\t141\r\nTCCCGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t141\r\nTATGGCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t141\r\nAAGAGGCA\tN711\tTAGCGGCC\tUnknown\t141\r\nTAGGGCGA\tN701\tTGTGCTGT\tUnknown\t140\r\nGCAGAGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t140\r\nGTAGAGGA\tN712\tCTCTTCGT\tUnknown\t140\r\nTCCTGAGC\tN704\tAGAGTACG\tUnknown\t140\r\nCGTGCTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t139\r\nTCCTTCTC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t139\r\nTAAGGCTG\tS521\tTATCCTCT\tE503,S503,[N|S|E]503\t139\r\nACTACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t139\r\nGGACTCCT\tN705\tTATCCTTT\tE503,S503,[N|S|E]503\t139\r\nTAATGCGC\tD708\tAGAGTAGA\tE504,[N|S|E]504\t139\r\nGGACTCCT\tN705\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t139\r\nTAAGGCGA\tN701\tTATCCTGT\tE503,S503,[N|S|E]503\t138\r\nGTAGAATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t138\r\nTAGGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t138\r\nTAAGGCGA\tN701\tAATGCTGT\tUnknown\t138\r\nGTATCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t138\r\nAGACAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t138\r\nTTCTCAAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t138\r\nAAGAGGCA\tN711\tTTATCCTC\tUnknown\t137\r\nTAAGGCGA\tN701\tTATCTTCT\tE503,S503,[N|S|E]503\t137\r\nTAAGGCGA\tN701\tTCCTCTTC\tUnknown\t137\r\nTAAGGCGA\tN701\tCTGTCTCT\tUnknown\t137\r\nATAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t137\r\nCTGAGCAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t137\r\nCAAGGTGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t136\r\nTAAGCCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t136\r\nCGAACTAG\tN702\tTGTGCTGT\tUnknown\t135\r\nCGTACTAT\tN702\tAGTGTTGT\tUnknown\t135\r\nAGGAAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t135\r\nTAAGGTGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t135\r\nGCAGCGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t135\r\nGTTACTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t135\r\nTCCTTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t135\r\nTAGACATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t135\r\nAGGCAGAA\tN703\tAGTGCTGA\tUnknown\t135\r\nAAAAGACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t135\r\nTAAGGCGA\tN701\tAGAAGATC\tUnknown\t135\r\nTTAGGCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t134\r\nTCCTGTGC\tN704\tTGTGTTGT\tUnknown\t134\r\nGTCGCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t134\r\nAAGAGGCA\tN711\tTATCTTCG\tUnknown\t134\r\nTAAGACGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t134\r\nCTTCCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t134\r\nGGAGTCGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t133\r\nCGAGGCTG\tN710\tTGTGCTCT\tA503\t133\r\nTCCTGAGC\tN704\tGGAGTAGG\tUnknown\t133\r\nCCCTTCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t132\r\nAAGAGGCA\tN711\tTACTCTTC\tUnknown\t132\r\nGTAGAGGA\tN712\tGCGTAAGA\tE517,S517,[N|S|E]517\t131\r\nGCTACGCT\tN709\tTATTCCTC\tUnknown\t131\r\nGTAGGCGA\tUnknown\tTGTGCTCT\tA503\t131\r\nAGAGAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t130\r\nTCATGAGA\tUnknown\tTGTGCTGT\tUnknown\t130\r\nTTCTCTTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t130\r\nCTTACTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t130\r\nGGACTCCA\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t130\r\nGTAGAGGA\tN712\tTATGCTGT\tE506,S506,[N|S|E]506\t130\r\nTAAGGCGC\tD708,N701,S521\tTGTGCTGT\tUnknown\t130\r\nTTAGGGGA\tUnknown\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t129\r\nGCTAGGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t129\r\nTTAGGCAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t129\r\nCCCCTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t129\r\nTAAGGCGA\tN701\tTAATCCTC\tUnknown\t129\r\nGTAGAGGA\tN712\tTATTCTTC\tUnknown\t128\r\nCGTATAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t128\r\nTTCTGAGC\tN704\tAGAGCAGT\tUnknown\t128\r\nAGGCAGAA\tN703\tTGTGTAGA\tUnknown\t128\r\nAGGCAGAG\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t128\r\nTCCGAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t128\r\nCGTACTAG\tN702\tTGAGCAGT\tUnknown\t128\r\nTTCTGAGC\tN704\tAGTGCAGA\tUnknown\t128\r\nTCAGGAGA\tD702\tTGTGCTGT\tUnknown\t128\r\nCTCTGAGC\tUnknown\tAGAGCAGA\tE504,[N|S|E]504\t128\r\nTAAGGCGA\tN701\tCGGGCTGT\tUnknown\t128\r\nTTCTCTAC\tN707\tTATGCTCT\tE503,S503,[N|S|E]503\t128\r\nTAGGCATG\tN706\tTACCCTCT\tE503,S503,[N|S|E]503\t128\r\nCCTCTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t128\r\nAGGAGAAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t127\r\nTCCTGAGC\tN704\tTGAGCTGA\tUnknown\t127\r\nGTCTAGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t127\r\nTAGGGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t127\r\nCGTACTAG\tN702\tAGAGTAGC\tE504,[N|S|E]504\t126\r\nTAAGCCGA\tN701\tTGTGCTGT\tUnknown\t126\r\nATCTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t126\r\nTCTAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t125\r\nCTTACTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t125\r\nCAAGGTGA\tUnknown\tTGTGCTGT\tUnknown\t125\r\nTAAGGCGA\tN701\tACAGTAGA\tE504,[N|S|E]504\t125\r\nTCCTGAGC\tN704\tTGTGTTGA\tUnknown\t125\r\nAAGAGGCA\tN711\tTAGCGTCT\tUnknown\t125\r\nTTCTGAGC\tN704\tAGTGTAGA\tE504,[N|S|E]504\t125\r\nGGACTCCT\tN705\tTACCTCTT\tUnknown\t125\r\nATGCCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t125\r\nGGAGGCGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t125\r\nCGAGGCTG\tN710\tTATCCTCC\tE503,S503,[N|S|E]503\t124\r\nATGAGTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t124\r\nCTCGCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t124\r\nTCTACGCT\tE504,N709,[N|S|E]504\tTTTCCTCT\tE503,S503,[N|S|E]503\t124\r\nTCCTGAGA\tD702,N704\tAGAGCAGA\tE504,[N|S|E]504\t124\r\nTTCTGCGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t124\r\nTTCTGTAC\tUnknown\tTGTGCTGT\tUnknown\t124\r\nGTTGAGGA\tN712\tTATCCTCT\tE503,S503,[N|S|E]503\t124\r\nAAGAGGCA\tN711\tTGTCCTGT\tUnknown\t124\r\nTAGAGGCA\tN711\tTGTGCTGT\tUnknown\t123\r\nGCTAGGCT\tN709\tTGTGCTCT\tA503\t123\r\nTTCTCTAC\tN707\tTGTGCTGT\tUnknown\t123\r\nGCTTACGC\tE517,S517,[N|S|E]517\tTATCCTCT\tE503,S503,[N|S|E]503\t123\r\nTTCTGAGC\tN704\tAGAGTAGT\tE504,[N|S|E]504\t123\r\nTCAGAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t122\r\nTAGGCATG\tN706\tTATGCTGT\tE506,S506,[N|S|E]506\t122\r\nCGAACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t122\r\nACCTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t122\r\nCTCTCTGC\tN707\tTGTGCTGT\tUnknown\t122\r\nGGTGGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t122\r\nTCCCTCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t122\r\nTAAGGTGA\tN701\tTGTGCTGT\tUnknown\t122\r\nTTAGACGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t121\r\nCGAGAGAA\tUnknown\tTAGAAGAG\tUnknown\t121\r\nTCCTGAGC\tN704\tCGCGTAGA\tUnknown\t121\r\nTTCTCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t121\r\nAAGAGGCA\tN711\tAGTGCTGT\tUnknown\t121\r\nGTATAGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t121\r\nTTAGGCGA\tN701,S522\tAGAGCAGA\tE504,[N|S|E]504\t121\r\nAGGCAGGA\tN703\tTGTGCTGT\tUnknown\t120\r\nCGAGGATG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t120\r\nAGGCAGAA\tN703\tGATCCTCT\tE503,S503,[N|S|E]503\t120\r\nAGGGAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t120\r\nCTCTGTAC\tN707\tTATGCTCT\tE503,S503,[N|S|E]503\t119\r\nAGGCAGAA\tN703\tAAACCGCC\tUnknown\t119\r\nCTCACGAC\tA701\tTATCCTCT\tE503,S503,[N|S|E]503\t119\r\nTTTCTTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t119\r\nCTCCTGAG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t119\r\nTAAGGCGA\tN701\tTGTGGAGA\tUnknown\t119\r\nCTCGGTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t119\r\nTCCTGATC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t119\r\nATGAGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t119\r\nGGGGGGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t119\r\nGGCAGAAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t119\r\nCGTACTAG\tN702\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t118\r\nCGAGGGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t118\r\nTGGCGGAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t118\r\nTCAGGCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t118\r\nTACTGCGC\tD708\tTATCCTCT\tE503,S503,[N|S|E]503\t118\r\nAGGGCAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t118\r\nCGTACTAG\tN702\tAGAGTGGA\tE504,[N|S|E]504\t118\r\nCTCTCTAC\tN707\tCTCTTCGT\tUnknown\t117\r\nTCCTGAGC\tN704\tTGAGTTGA\tUnknown\t117\r\nCTTTCTAT\tE502,S502,[N|S|E]502\tTATCCTCT\tE503,S503,[N|S|E]503\t117\r\nCTCTCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t117\r\nTCCTGAGC\tN704\tAGACTAGA\tE504,[N|S|E]504\t117\r\nTCCGGAGC\tD702,N704\tAGTGCTGT\tUnknown\t117\r\nGGACTCAT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t117\r\nCGTACTAG\tN702\tATCCTCTT\tUnknown\t117\r\nTCCTTAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t116\r\nCGTACTAG\tN702\tAGAGTAAG\tUnknown\t116\r\nGATACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t116\r\nAAGGGGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t116\r\nTCCTGAGA\tD702,N704\tAGTGCTGT\tUnknown\t116\r\nAAGCGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t115\r\nAGGCAGAA\tN703\tAAGTAGAT\tUnknown\t115\r\nCTCTCTAC\tN707\tTATTCTTC\tUnknown\t115\r\nCAGGCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t115\r\nGTAGGGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t115\r\nACTAGGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t115\r\nGTAAGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t115\r\nTGAGGCGA\tN701\tTGTGCTGT\tUnknown\t115\r\nAGAGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t115\r\nTAGTCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t115\r\nCGTACTAG\tN702\tAGAGTATC\tUnknown\t114\r\nGCAGAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t114\r\nCTCTCCAT\tE502,S502,[N|S|E]502\tTATCCTCT\tE503,S503,[N|S|E]503\t114\r\nTTAGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t114\r\nTAAGGCGA\tN701\tAGATCGTC\tUnknown\t114\r\nGTAGAGGA\tN712\tTAGCCTCT\tE503,S503,[N|S|E]503\t114\r\nGTAGAGGA\tN712\tTCTTCGTC\tUnknown\t113\r\nAGCCAGAA\tN703,S515\tTATCCTCT\tE503,S503,[N|S|E]503\t113\r\nGGGGGAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t113\r\nGTCTGGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t113\r\nGCAGCGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t113\r\nCACGAGAC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t113\r\nTCCTTAGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t113\r\nTTTTTTTT\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t113\r\nAGGAAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t113\r\nCAAGGCGA\tN701\tTGTGCAGT\tE506,S506,[N|S|E]506\t113\r\nAGGCAGAC\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t113\r\nGAAGGCGA\tN701\tTGTGCAGT\tE506,S506,[N|S|E]506\t113\r\nCGCACTAG\tN702\tTGTGCTGT\tUnknown\t113\r\nGCTACCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t113\r\nCTCTGGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t112\r\nTCCTTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t112\r\nTAAGGCGA\tN701\tAGAGGAGG\tUnknown\t112\r\nCTCTCTAC\tN707\tTCTTCGTC\tUnknown\t112\r\nCTATCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t112\r\nTCAGGGGA\tUnknown\tTGTGCTGT\tUnknown\t112\r\nCGAGGCTG\tN710\tTATCCTTC\tUnknown\t111\r\nAGGTAGAA\tN703,S515\tTATCCTCT\tE503,S503,[N|S|E]503\t111\r\nCTCTCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t111\r\nACGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t111\r\nTCCTGAGA\tD702,N704\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t111\r\nTTAGGCGA\tN701,S522\tAGAGCAGT\tUnknown\t111\r\nGCTCTCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t111\r\nTAAGGCGA\tN701\tAGAGAAGA\tA503,E504,[N|S|E]504\t111\r\nGCTACGCT\tN709\tTATCCTCG\tE503,S503,[N|S|E]503\t111\r\nAGACAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t111\r\nTAGGCAAG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t110\r\nTAAGGCAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t110\r\nGTATCTGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t110\r\nGAAAGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t110\r\nTAGGCATG\tN706\tTATCTTCT\tE503,S503,[N|S|E]503\t110\r\nTCCGGCGA\tD702\tTATCCTCT\tE503,S503,[N|S|E]503\t109\r\nAGGCAGAA\tN703\tAGAGTTGT\tUnknown\t109\r\nAGGCGAAT\tD505\tAGAGTAGA\tE504,[N|S|E]504\t109\r\nGCTACGCT\tN709\tTACTCTTC\tUnknown\t109\r\nCTCTGTAC\tN707\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t109\r\nCGTACTAT\tN702\tAGAGTAGT\tE504,[N|S|E]504\t109\r\nTTGGCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t108\r\nGAAGGCGA\tN701\tAGAGCAGA\tE504,[N|S|E]504\t108\r\nTCCTCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t108\r\nTTAGAGGA\tN712\tTTTCCTCT\tE503,S503,[N|S|E]503\t108\r\nTAAAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t108\r\nAGAGGAAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t108\r\nTAAGGCGA\tN701\tTATCGTCT\tE503,S503,[N|S|E]503\t108\r\nGTGGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t108\r\nATGAGGCA\tN711\tTTTCCTCT\tE503,S503,[N|S|E]503\t107\r\nGTAGAGGA\tN712\tTAACCTCT\tE503,S503,[N|S|E]503\t107\r\nTCCTGACC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t107\r\nGTTACGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t107\r\nCGAGGCAG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t107\r\nGCCCTCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t107\r\nAAAGGGGA\tUnknown\tTGTGCTGT\tUnknown\t107\r\nGCTACGCT\tN709\tAGAGTAGA\tE504,[N|S|E]504\t107\r\nTAGGGAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t106\r\nTAAGGCGA\tN701\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t106\r\nGTAGAAAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t106\r\nTAATGAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t106\r\nTTAGGTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t106\r\nTCCTGAGC\tN704\tAGTGCTCT\tUnknown\t106\r\nCGAGCCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t106\r\nGTATATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t105\r\nGGACTCCT\tN705\tTATGCTCT\tE503,S503,[N|S|E]503\t105\r\nCTAGGTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t105\r\nCTAGCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t105\r\nTAAGGCGA\tN701\tTGTGCACA\tUnknown\t105\r\nCGTACTAA\tN702\tAGAGCAGA\tE504,[N|S|E]504\t105\r\nAGGCAGTA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t105\r\nAAGGAGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t105\r\nCTAGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t105\r\nCGTACTAG\tN702\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t104\r\nAATAGGCC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t104\r\nTCCGGAGA\tD702\tAGAGTAGA\tE504,[N|S|E]504\t104\r\nTAAGCAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t104\r\nTAAGGCCA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t104\r\nTAGGCATG\tN706\tAATCCTCT\tE503,S503,[N|S|E]503\t104\r\nCCCTCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t104\r\nTAGGCATG\tN706\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t103\r\nGCAGGGGA\tUnknown\tTGTGCTCT\tA503\t103\r\nCGTACTAG\tN702\tTATGCTCT\tE503,S503,[N|S|E]503\t103\r\nCTCTCTAC\tN707\tTAGGGTCA\tUnknown\t103\r\nTAAGGCGA\tN701\tAGAGCGTC\tUnknown\t103\r\nCTCTCTGC\tN707\tTGTGCTCT\tA503\t103\r\nAGGCAGAA\tN703\tTCCTCTTC\tUnknown\t103\r\nTCTTCCTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t103\r\nTTCTGAGC\tN704\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t103\r\nTTCGCTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t102\r\nCAAGGCGA\tN701\tTGTGCTCT\tA503\t102\r\nTAAGGCGA\tN701\tTATGCACA\tUnknown\t102\r\nTCCTGGAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t102\r\nTCAGGAGA\tD702\tTATCCTCT\tE503,S503,[N|S|E]503\t102\r\nGAAGGGGA\tUnknown\tTATGCTCT\tE503,S503,[N|S|E]503\t102\r\nCGTACTAG\tN702\tTGAGCTGT\tUnknown\t101\r\nTCCTGAAC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t101\r\nCTCTGTGC\tUnknown\tTGTGCTCT\tA503\t101\r\nCTAGCTAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t101\r\nACTCTTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t101\r\nCGTACTAG\tN702\tAAGTAGAT\tUnknown\t101\r\nCGCGGCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t101\r\nTAAGGCGA\tN701\tTATCCGCT\tE503,S503,[N|S|E]503\t101\r\nTAGGGCTG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t101\r\nGAAGGCGA\tN701\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t100\r\nGAAGGGGA\tUnknown\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t100\r\nCGACTAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t100\r\nTCTCCGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t100\r\nATAAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t100\r\nCCCCTCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t100\r\nTCCTCAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t100\r\nAGGCAGAA\tN703\tGGAGTAGA\tE504,[N|S|E]504\t100\r\nCTCTGAGC\tUnknown\tAGTGCTGT\tUnknown\t100\r\nTAAGGCGA\tN701\tTATCCCCT\tE503,S503,[N|S|E]503\t100\r\nCTCTCTAC\tN707\tAGTGCTGT\tUnknown\t100\r\nTAGGCAAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t100\r\nAGGCAGAA\tN703\tAGTAGATC\tUnknown\t99\r\nCTCGGTGC\tUnknown\tTGTGCTGT\tUnknown\t99\r\nTTCTGAGC\tN704\tTGTGTTGT\tUnknown\t99\r\nTCCTGCAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t99\r\nCGGCAGAA\tN703\tCGAGTAGA\tE504,[N|S|E]504\t99\r\nTCTTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t99\r\nAGGCAGAA\tN703\tTATCGTCT\tE503,S503,[N|S|E]503\t99\r\nCGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t98\r\nTCCTGAGC\tN704\tTATCCTTC\tUnknown\t98\r\nGTAGCGTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t98\r\nGTATGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t98\r\nGCTACGCT\tN709\tTAGAGGCT\tUnknown\t98\r\nTCCTGAGC\tN704\tTATCCCTC\tUnknown\t98\r\nTTAGTGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t98\r\nTTAGGCGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t98\r\nCGTACTAC\tN702\tTGTGCTGT\tUnknown\t97\r\nCTCTCCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nCGCACTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nCAAGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nTAAGGAAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t97\r\nTAACGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nAGGCAGAA\tN703\tAGGAGTAG\tA712\t97\r\nTTAGGCGA\tN701,S522\tAGAGTAGT\tE504,[N|S|E]504\t97\r\nGCTGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nGTTGCGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nGTCTCTGA\tD504\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nGCCCACGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nGCCTGGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t97\r\nGCTACGCT\tN709\tTTATCCTC\tUnknown\t97\r\nCTCTCTAC\tN707\tTATGCGCT\tUnknown\t97\r\nTAAGGAGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t96\r\nAAGAGGCA\tN711\tTATACTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t96\r\nTACTGAGC\tN704\tTGTGCTGT\tUnknown\t96\r\nTCCTTCTC\tUnknown\tCTCTTCTC\tUnknown\t96\r\nTCCTCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t96\r\nGCAGGGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t96\r\nTATGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t96\r\nAAGAGGCA\tN711\tTAGCCGCT\tUnknown\t96\r\nGTTGAGTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t96\r\nCGTACTAG\tN702\tTATCTCTT\tUnknown\t96\r\nGGGGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t95\r\nGGCTCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t95\r\nTAGGCACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t95\r\nTAAGGCGA\tN701\tTAGGGCTG\tUnknown\t95\r\nAAGAGGGA\tN711\tTGTGCTGT\tUnknown\t95\r\nTTAAGGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t95\r\nAGTCAGAA\tD705,N703\tTATCCTCT\tE503,S503,[N|S|E]503\t94\r\nTCTTGAGC\tN704\tTGTGCTGT\tUnknown\t94\r\nGCTAAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t94\r\nGCTAGGGT\tUnknown\tTGTGCTGT\tUnknown\t94\r\nGAGACGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t94\r\nGCTACGCT\tN709\tTAGAGGCC\tUnknown\t94\r\nGTAGAGTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t94\r\nATCTGTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t94\r\nAGGCGGCA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t94\r\nCGTGGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t94\r\nGCAAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t93\r\nAGGCAGAA\tN703\tAAATCGTC\tUnknown\t93\r\nGCTTCTCT\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t93\r\nTGAGGCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t93\r\nGCGACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t93\r\nTCCGGCGA\tD702\tAGAGTAGA\tE504,[N|S|E]504\t93\r\nTAAGGCGA\tN701\tTGGGGAGG\tUnknown\t93\r\nGTCTGAGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t93\r\nCGAGGCTG\tN710\tCTATCCTC\tUnknown\t93\r\nCGCTCTAC\tN707\tAGAGTAGA\tE504,[N|S|E]504\t93\r\nGCTACGCT\tN709\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t93\r\nTCCTGAGT\tN704\tTGTGCTGT\tUnknown\t92\r\nATCTGTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t92\r\nTAAAGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t92\r\nTTCTCTAC\tN707\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t92\r\nGTAGGGGA\tN712\tTATGCTGT\tE506,S506,[N|S|E]506\t92\r\nTAAGGCGA\tN701\tTAGCGTCT\tUnknown\t92\r\nTAAGGCCA\tN701\tTGTGCTCT\tA503\t92\r\nAACTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t92\r\nTCTCTTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t92\r\nCGAGGCTG\tN710\tTATCCCTC\tUnknown\t92\r\nTTCTCTAC\tN707\tTGTGCTCT\tA503\t92\r\nTATGGCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t92\r\nCCCCCCCC\tUnknown\tCCCCCCCC\tUnknown\t92\r\nCGAGGGTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t92\r\nGGTGAAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t92\r\nCTCTATCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t91\r\nATTCCTCC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t91\r\nTAAAGCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t91\r\nTAAGGCGA\tN701\tTGGGGCTG\tUnknown\t91\r\nAAGAGGCA\tN711\tTAACCTCT\tE503,S503,[N|S|E]503\t91\r\nTAAGGCGA\tN701\tTGTGGACA\tUnknown\t91\r\nCTCTCTCC\tN707\tTTTCCTCT\tE503,S503,[N|S|E]503\t91\r\nCGTACTAG\tN702\tAGGTAGAT\tUnknown\t91\r\nAGGCAGAT\tN703\tAGAGTAGA\tE504,[N|S|E]504\t91\r\nCCTCTCTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t91\r\nGCATGAGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t91\r\nTCTTCTCT\tA503,E504,[N|S|E]504\tTTTCCTCT\tE503,S503,[N|S|E]503\t91\r\nTAAGGGGA\tN701\tAGTGCAGT\tUnknown\t90\r\nTTAGGCGC\tUnknown\tTGTGCTGT\tUnknown\t90\r\nGCTACGCT\tN709\tCCTCTTCG\tUnknown\t90\r\nTAAAGGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t90\r\nGATCTCGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t90\r\nGCCTGAGC\tN704\tAGTGCTGT\tUnknown\t90\r\nGCCTCACC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t90\r\nGTAGAGGA\tN712\tTAGAAGAG\tUnknown\t90\r\nTTAAGGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t90\r\nTAAGGCGA\tN701\tTAGAGACC\tUnknown\t90\r\nCGAGGCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t90\r\nGGAGAGGA\tN712\tTGTGCTCT\tA503\t90\r\nCGAACTAA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t90\r\nCGTACTAG\tN702\tTGTGCTGA\tUnknown\t90\r\nTAAGGGCA\tUnknown\tTGTGCTGT\tUnknown\t90\r\nGTAGAGGA\tN712\tTATCGTCT\tE503,S503,[N|S|E]503\t89\r\nGCCTTCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t89\r\nATCTGTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t89\r\nAAGAGGCA\tN711\tTCTTCGTC\tUnknown\t89\r\nGGGCAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t89\r\nCTTTCTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t89\r\nCTAGGTGC\tUnknown\tTGTGCTGT\tUnknown\t89\r\nCGTACTAC\tN702\tAGAGCAGA\tE504,[N|S|E]504\t89\r\nGCTATATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t89\r\nCTCTCTAC\tN707\tTGTCCTGT\tUnknown\t89\r\nTGAGGCGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t88\r\nATCTCTAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t88\r\nGAGGCATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t88\r\nAGGCAGAA\tN703\tTATCTTCT\tE503,S503,[N|S|E]503\t88\r\nGTAGTGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t88\r\nCGGACTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t88\r\nGCTACGCT\tN709\tTATCTTCG\tUnknown\t88\r\nTAGGGATG\tN706\tTGTGCTGT\tUnknown\t87\r\nCTTACTAT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t87\r\nGCCTGAGC\tN704\tTGTGCTCT\tA503\t87\r\nCCTCTCCT\tD503\tTATCCTCT\tE503,S503,[N|S|E]503\t87\r\nTAGGCACT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t87\r\nTAGGCGTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t87\r\nCTCTGAGC\tUnknown\tTGTGCTCT\tA503\t87\r\nGGTACTAG\tN702\tTGTGCTGT\tUnknown\t87\r\nGTAGCGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t87\r\nAGGCAGAA\tN703\tTATCCCTC\tUnknown\t87\r\nTCAGGAGC\tUnknown\tTGTGCTGT\tUnknown\t87\r\nATCTGGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nCGTACCAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nGAGGAATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nTCATGAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nTAAGGGGA\tN701\tTATGCTCT\tE503,S503,[N|S|E]503\t86\r\nGCTCTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nGTCTCTAC\tN707\tAATCCTCT\tE503,S503,[N|S|E]503\t86\r\nGTAGAGTT\tUnknown\tTCTTCTCT\tA503,E504,[N|S|E]504\t86\r\nAGGCAGAG\tN703\tAGAGTAGA\tE504,[N|S|E]504\t86\r\nGCGAGGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nTAAGCAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nTTATGCGA\tS522\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nTCCTAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nGTTGCGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t86\r\nAGGCAGCA\tN703\tAGAGCAGA\tE504,[N|S|E]504\t86\r\nTCATGAGC\tN704\tAGTGCTGT\tUnknown\t85\r\nACGAGGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t85\r\nTCTACGTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t85\r\nGTAGAGAG\tE502,S502,[N|S|E]502\tTATCCTCT\tE503,S503,[N|S|E]503\t85\r\nGCTAGGCT\tN709\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t85\r\nCCCCTTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t85\r\nTATAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t85\r\nGGACTCCT\tN705\tTATCCTCC\tE503,S503,[N|S|E]503\t85\r\nAAGAAGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t85\r\nGGTACTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t85\r\nTCTAGCCT\tD501\tTATCCTCT\tE503,S503,[N|S|E]503\t85\r\nTACGCATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t84\r\nCTCTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t84\r\nTAGGCATG\tN706\tTAATCCTC\tUnknown\t84\r\nAAAAGAAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t84\r\nCGTACTAG\tN702\tTATCCCTT\tUnknown\t84\r\nGCTTCGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t84\r\nCTGCAGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t84\r\nCGTTACTA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t84\r\nTTCTGAGC\tN704\tTGAGTAGA\tE504,[N|S|E]504\t84\r\nTCCTCTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t84\r\nCTCTCTAC\tN707\tTCTCTTCG\tS511\t84\r\nCTCTCTAC\tN707\tTAGGCTCT\tUnknown\t84\r\nGTAGTGGT\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t84\r\nTCCTGAAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t83\r\nTCCTGAGC\tN704\tACAGTAGA\tE504,[N|S|E]504\t83\r\nTTCTGTGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t83\r\nTCCTGAGC\tN704\tAAAGTAGA\tE504,[N|S|E]504\t83\r\nTGTACTAG\tA506,N702\tTGAGTAGA\tE504,[N|S|E]504\t83\r\nATGTGTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t83\r\nTAAGGCGA\tN701\tTGGGGCGG\tUnknown\t83\r\nTCCTGAGT\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t83\r\nTACGGAGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t83\r\nATCTCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t83\r\nTAGGGCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t83\r\nAGGCAGAA\tN703\tTATCCTGT\tE503,S503,[N|S|E]503\t83\r\nATGCAGAA\tD705,N703\tTGTGCTCT\tA503\t83\r\nTTCTGAGC\tN704\tAGTGTTGT\tUnknown\t82\r\nATGCAGAA\tD705,N703\tAGTGCTGT\tUnknown\t82\r\nGCTAATCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t82\r\nTAAGGCGA\tN701\tTATTCCTC\tUnknown\t82\r\nGGGCAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t82\r\nTTCTGAGC\tN704\tAGTGTAGT\tUnknown\t82\r\nTAAGGCCA\tN701\tAGTGCTGT\tUnknown\t82\r\nTAAGGCGA\tN701\tTGAGGACA\tUnknown\t82\r\nCTCTTCTT\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t82\r\nTAGGCATG\tN706\tTATCCTGT\tE503,S503,[N|S|E]503\t82\r\nCTCTCTAC\tN707\tTAACCTCT\tE503,S503,[N|S|E]503\t82\r\nTAGAGGCA\tN711\tTGTGCTCT\tA503\t81\r\nGGACTCCT\tN705\tCATCCTCT\tE503,S503,[N|S|E]503\t81\r\nCGTACTAG\tN702\tAGTGTTGA\tUnknown\t81\r\nCTGGCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t81\r\nTAAGGCGT\tN701\tAGTGTTGT\tUnknown\t81\r\nCTTCCTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t81\r\nAAGATGCA\tN711\tTATCCTCT\tE503,S503,[N|S|E]503\t81\r\nCTCTCTAC\tN707\tTAGGGGCC\tUnknown\t81\r\nGTAGAGGA\tN712\tTCTCTTCG\tS511\t81\r\nAAGAGGCA\tN711\tCTGTCTCT\tUnknown\t81\r\nGGGGAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t81\r\nTCTACGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t81\r\nAGCCAGAA\tN703,S515\tAGAGTAGA\tE504,[N|S|E]504\t80\r\nTCTCTTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t80\r\nGCAAAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t80\r\nACGCAGAA\tN703\tAGAGTAGA\tE504,[N|S|E]504\t80\r\nGCCCTACC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t80\r\nGTAGGCGA\tUnknown\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t80\r\nTCCTGAGC\tN704\tCTATCCTC\tUnknown\t80\r\nCGTACCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t80\r\nTTAGGCGA\tN701,S522\tAGTGTAGT\tUnknown\t80\r\nTCCTGGGA\tUnknown\tTGTGCTGT\tUnknown\t80\r\nCTAGGCGA\tS513\tAGAGTAGA\tE504,[N|S|E]504\t80\r\nGCTAGCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t80\r\nTCCTGAGC\tN704\tAGAGTTCG\tUnknown\t80\r\nGAAGAGGA\tN712\tTAGAAGAG\tUnknown\t80\r\nTCGTGAGC\tN704\tTGTGCTGT\tUnknown\t80\r\nGGAGAGGA\tN712\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t79\r\nCTCTGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t79\r\nGAAGGCGA\tN701\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t79\r\nAGGGCAGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t79\r\nCCTCTTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t79\r\nCTTACTAG\tN702,S518\tAGAGTAGA\tE504,[N|S|E]504\t79\r\nTCTACGCT\tE504,N709,[N|S|E]504\tTATGCTCT\tE503,S503,[N|S|E]503\t79\r\nTCGAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t79\r\nAAAGGCCA\tUnknown\tTGTGCTGT\tUnknown\t79\r\nGGAGAGGA\tN712\tGATAAGAT\tUnknown\t79\r\nTAGGCATG\tN706\tTATCCCCT\tE503,S503,[N|S|E]503\t79\r\nAGGCAGCA\tN703\tAGTGCTGT\tUnknown\t79\r\nCGTACTGG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t79\r\nAGGCAGAA\tN703\tAGAGGTAG\tUnknown\t79\r\nTTCTCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t79\r\nTCCTGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t79\r\nCTTACTAG\tN702,S518\tTGTGCTGT\tUnknown\t78\r\nTTAGGCGA\tN701,S522\tAGTGTAGA\tE504,[N|S|E]504\t78\r\nTCTGGCGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nGCTACGCT\tN709\tTAGCCGCT\tUnknown\t78\r\nGTCGGGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nTCGTGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nGTAGCTAC\tN718\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nCCCACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nTCCGTCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nAAGAGGCA\tN711\tTATTCTTC\tUnknown\t78\r\nAAGGCACG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nCGGCCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nCGTACTCG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t78\r\nGTGGCATG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t78\r\nGCTCCCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t77\r\nTCCTGCGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t77\r\nCGTACTAG\tN702\tTACCTCTT\tUnknown\t77\r\nAACTGGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t77\r\nTTAGGCGA\tN701,S522\tTGTGTAGT\tUnknown\t77\r\nAGGCAGAA\tN703\tAATCCGCT\tUnknown\t77\r\nCTTTCTCC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t77\r\nTGTAGTAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t77\r\nCGTACTAG\tN702\tAGAGTTGT\tUnknown\t77\r\nACGAGGCA\tN711\tTGTGCTGT\tUnknown\t77\r\nAGGGAGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t77\r\nCAGGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t77\r\nGCAGGGGA\tUnknown\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t77\r\nCTCTCTGC\tN707\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t77\r\nAAGAGGCA\tN711\tCTCTTCGT\tUnknown\t77\r\nCCCTGAGC\tN704\tTGTGCAGT\tE506,S506,[N|S|E]506\t76\r\nTCTACTCT\tE504,[N|S|E]504\tTATCCTCT\tE503,S503,[N|S|E]503\t76\r\nTCAGGAGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t76\r\nCGTACTAA\tN702\tAGTGCTGT\tUnknown\t76\r\nTAAGGCCT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t76\r\nTAGGTATG\tN706\tTATCCTCT\tE503,S503,[N|S|E]503\t76\r\nTATGGCTC\tS521\tATCTTCTC\tUnknown\t76\r\nCCTCCCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t76\r\nCGCACTAG\tN702\tAGAGCAGA\tE504,[N|S|E]504\t76\r\nCTGTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t76\r\nATGTGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t76\r\nAGGCAGAA\tN703\tTACCCTCT\tE503,S503,[N|S|E]503\t75\r\nGCTACGCT\tN709\tCTCCTATG\tUnknown\t75\r\nCCTCTTCC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t75\r\nTGGCAGAA\tN703\tTGTGCTGT\tUnknown\t75\r\nTAATGCGA\tD708,N701,S522\tTGTGCTGT\tUnknown\t75\r\nTAAGGGGA\tN701\tGGAGGAGA\tUnknown\t75\r\nGGCTCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t75\r\nGAGGCATG\tN706\tAATCCTCT\tE503,S503,[N|S|E]503\t75\r\nCGAGGCTG\tN710\tTCCTCTTC\tUnknown\t75\r\nGCAGAGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t75\r\nATAGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t75\r\nAAGGGGCA\tN711\tTGTGCTGT\tUnknown\t74\r\nGCTACATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t74\r\nGTAGTGGA\tN712\tTTTCCTCT\tE503,S503,[N|S|E]503\t74\r\nTCCTTCTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t74\r\nCAAGGCGA\tN701\tAGTGCAGT\tUnknown\t74\r\nGTAGAGGA\tN712\tTATCCACT\tE503,S503,[N|S|E]503\t74\r\nCTCTCTAC\tN707\tTAGGCGCT\tUnknown\t74\r\nTAGGCATG\tN706\tGATCCTCT\tE503,S503,[N|S|E]503\t74\r\nAAGGGGGA\tUnknown\tTGTGCTGT\tUnknown\t74\r\nAGGCAGAA\tN703\tTATTCTCT\tA503,E503,S503,[N|S|E]503\t74\r\nTCCTGCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t74\r\nTGAGGCGG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t74\r\nTTAGTGGT\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t74\r\nCGTACTAG\tN702\tAGGAGTAG\tA712\t73\r\nACGCGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t73\r\nGCTCTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t73\r\nTAAAGCGG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t73\r\nTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t73\r\nAGGGAGAA\tN703\tAGAGGAGA\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t73\r\nGTAACGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t73\r\nTTAGCCGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t73\r\nTTCGGCGC\tUnknown\tTGTGCTGT\tUnknown\t73\r\nAGGCAGAA\tN703\tTATCCCCT\tE503,S503,[N|S|E]503\t73\r\nCGAGGCTG\tN710\tAATCCTCT\tE503,S503,[N|S|E]503\t73\r\nGCTACGTG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t73\r\nTAAGGCGA\tN701\tCCTCTTCG\tUnknown\t73\r\nTGAGAGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t73\r\nCGTACTAG\tN702\tAGGGTAGA\tE504,[N|S|E]504\t73\r\nAAAGGGCA\tUnknown\tTGTGCTGT\tUnknown\t73\r\nCAAGGCGA\tN701\tAGTGCTGT\tUnknown\t72\r\nCGGCAGAA\tN703\tTGTGCTGT\tUnknown\t72\r\nGTCTCTAC\tN707\tGATCCTCT\tE503,S503,[N|S|E]503\t72\r\nCGTGCTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t72\r\nAGGCAGAA\tN703\tTAATCCTC\tUnknown\t72\r\nGCCTGGGC\tUnknown\tTGTGCTGT\tUnknown\t72\r\nTCCTGAGC\tN704\tCGCGTAGC\tUnknown\t72\r\nTAAGGCTA\tN701,S521\tAGAGTAGA\tE504,[N|S|E]504\t72\r\nTAGGCATG\tN706\tTATCCGCT\tE503,S503,[N|S|E]503\t72\r\nGAAGGGGA\tUnknown\tAGTGCTGT\tUnknown\t72\r\nAAGCGGCA\tN711\tTGTGCTGT\tUnknown\t71\r\nTCTAGCGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t71\r\nTAAAGGGG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t71\r\nCGTACTAG\tN702\tTTTCCTCT\tE503,S503,[N|S|E]503\t71\r\nTAAGGGGA\tN701\tTGTGCAGT\tE506,S506,[N|S|E]506\t71\r\nCTCTCTCC\tN707\tTCTGCTCT\tE504,[N|S|E]504\t71\r\nAGGCAGAA\tN703\tAGGGTAGA\tE504,[N|S|E]504\t71\r\nGCTAACGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t71\r\nCGTACTAG\tN702\tGGAGTAGA\tE504,[N|S|E]504\t71\r\nTAGCGAAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t71\r\nTCTTGAGT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t71\r\nAAGCAGAA\tN703\tTATCCTCT\tE503,S503,[N|S|E]503\t71\r\nTCCTGAGC\tN704\tAGAGCAGG\tUnknown\t71\r\nTAAGGCGT\tN701\tTGTGTTGT\tUnknown\t71\r\nCGTAGTAG\tN702\tTGTGCTGT\tUnknown\t71\r\nCTCTCTAC\tN707\tTGTGTTGT\tUnknown\t70\r\nTCTTGAGT\tUnknown\tTGTGCTGT\tUnknown\t70\r\nCGTCTAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nCGAGGTTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nAGGAAGAA\tN703\tTAGAAGAG\tUnknown\t70\r\nTAAGGCGC\tD708,N701,S521\tAGAGCAGA\tE504,[N|S|E]504\t70\r\nTACTCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nTAAGTCGA\tN701\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nGTTTCGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nTCCCTCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nCGTACTAG\tN702\tAGTAGATC\tUnknown\t70\r\nAGGCGGAA\tN703\tAGTGCTGT\tUnknown\t70\r\nGAGGCATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nTAAGGCGA\tN701\tAGGGGCGG\tUnknown\t70\r\nATGACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nGCCTTACC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t70\r\nGCACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t69\r\nCGTACTAG\tN702\tTATCCTTT\tE503,S503,[N|S|E]503\t69\r\nGCCCCACC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t69\r\nTAGTGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t69\r\nGAAGGCGA\tN701\tAATCCTCT\tE503,S503,[N|S|E]503\t69\r\nAGGCGGAA\tN703\tTGTGCTCT\tA503\t69\r\nAGGCAGAA\tN703\tAGAGTAAA\tE504,[N|S|E]504\t69\r\nGTCGGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t69\r\nTCCTGAGA\tD702,N704\tAGTGCAGT\tUnknown\t69\r\nTGGCAGAA\tN703\tTGTGTAGT\tUnknown\t69\r\nCGATGCTG\tN710\tTATCCTCT\tE503,S503,[N|S|E]503\t69\r\nCTCTCTAC\tN707\tTAGAGGCC\tUnknown\t69\r\nCTATATGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t69\r\nAAGAGGCA\tN711\tTGTGTTGT\tUnknown\t69\r\nTAGAGGCA\tN711\tTATGCTCT\tE503,S503,[N|S|E]503\t69\r\nACCTGAGC\tN704\tTGTGCTGT\tUnknown\t68\r\nATGAGGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nGCTACGAG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nGCCACCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nTGGCAGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t68\r\nTTCTGTGC\tUnknown\tTGTGTTGT\tUnknown\t68\r\nCTCTGAGC\tUnknown\tTGTGCAGT\tE506,S506,[N|S|E]506\t68\r\nTAAGGCGA\tN701\tTAGAGAGC\tUnknown\t68\r\nGTAGTCGA\tS513\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nCGTACAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nTTCGGCGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nTCAGGCGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nGGTGGGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t68\r\nAGGCAGAA\tN703\tAGAGTCGA\tE504,[N|S|E]504\t68\r\nATGCAGAA\tD705,N703\tAGAGCAGA\tE504,[N|S|E]504\t68\r\nGCTACGCT\tN709\tTAGCGTCT\tUnknown\t68\r\nAGGCAGAA\tN703\tCAGAGTAG\tUnknown\t68\r\nGGACAGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t67\r\nTTTTCTTT\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t67\r\nAGGCGGAA\tN703\tAGAGCAGA\tE504,[N|S|E]504\t67\r\nTCCTGACC\tN704\tAGTGCTGT\tUnknown\t67\r\nCGTACTTA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t67\r\nTAGGCATG\tN706\tTATCGTCT\tE503,S503,[N|S|E]503\t67\r\nCGAGGCTT\tN710\tTTTCCTCT\tE503,S503,[N|S|E]503\t67\r\nTGGCGAAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t67\r\nTAAGCATA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t67\r\nCGTACAAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t67\r\nCGAGGCTG\tN710\tGATCCTCT\tE503,S503,[N|S|E]503\t66\r\nGGACCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nCTAAGGCT\tS508,[N|S|E]508\tAGAGTAGA\tE504,[N|S|E]504\t66\r\nAGGCAGAA\tN703\tAGTGTTGA\tUnknown\t66\r\nAAAGGCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nAGGCAGAA\tN703\tTAGCCTCT\tE503,S503,[N|S|E]503\t66\r\nCTCTGCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nGGAGGGTG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nGTCGATTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t66\r\nTAGGCCTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nGTAGAGGT\tN712\tTTTCCTCT\tE503,S503,[N|S|E]503\t66\r\nTCCTAAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nCAAGGCGA\tN701\tAGAGCAGT\tUnknown\t66\r\nAAAAGCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nACGACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t66\r\nAGGCGGGA\tUnknown\tTGTGCTGT\tUnknown\t66\r\nGAAGGCGA\tN701\tTGTGTTGT\tUnknown\t66\r\nTCCTGAGC\tN704\tTATCCGCT\tE503,S503,[N|S|E]503\t65\r\nGCTGGGGT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t65\r\nGCATGAGC\tUnknown\tTGTGCTGT\tUnknown\t65\r\nGTTACGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t65\r\nAAGAGGCA\tN711\tTCTCTTCG\tS511\t65\r\nCGTACTAT\tN702\tTGAGTAGA\tE504,[N|S|E]504\t65\r\nTCCTGAGC\tN704\tAGAGAAGA\tA503,E504,[N|S|E]504\t65\r\nTTCTGCGC\tUnknown\tTGTGCTGT\tUnknown\t65\r\nTACGGCGA\tN701\tTGTGCTGT\tUnknown\t65\r\nACGCTATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t65\r\nGGACTCCG\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t65\r\nTAGGGACG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t65\r\nTAAGTCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t65\r\nTCCTGTGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nGGACTCCT\tN705\tTATCCTTC\tUnknown\t64\r\nGCAAAGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nTTCGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nCTCGGCAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nAGGCGGAA\tN703\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t64\r\nGTCTAGTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t64\r\nATCTCGTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nCCTCTACC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nTAGGGAGG\tUnknown\tTGTGCTGT\tUnknown\t64\r\nCAGAGTCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nAGGCAGAA\tN703\tAGAGGATC\tE503,S503,[N|S|E]503\t64\r\nGCCTCGGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t64\r\nAGGCAGAA\tN703\tAGAGATCG\tUnknown\t64\r\nTTCTGTGC\tUnknown\tTGTGCTCT\tA503\t63\r\nTACTGCGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nTACGGCTC\tS521\tATCTTCTC\tUnknown\t63\r\nTCTAGGCT\tUnknown\tTGTGCTGT\tUnknown\t63\r\nGTGGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nCGTACTAT\tN702\tAGTGCTGT\tUnknown\t63\r\nCGTACTAG\tN702\tTTCCTCTT\tUnknown\t63\r\nAAGAGGCA\tN711\tAAACCGCC\tUnknown\t63\r\nGGAGGCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nTAGGCATG\tN706\tTAGAGGCC\tUnknown\t63\r\nCCCTCCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nGTGCAGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nGTCGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nTCCTGAGG\tN704\tTGTGCTGT\tUnknown\t63\r\nAAGGGACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nTTCTGAGC\tN704\tAGTGCTGA\tUnknown\t63\r\nTACTGCGC\tD708\tTGTGCTGT\tUnknown\t63\r\nTCTTCGCT\tUnknown\tTTTCCTCT\tE503,S503,[N|S|E]503\t63\r\nGGATTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nGTCCTCCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nCGTACTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nCCCTGAGC\tN704\tAGTGCTGT\tUnknown\t63\r\nAAGGGCCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nTTCCTGAG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nAGACAGGA\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t63\r\nGAAGAAGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t63\r\nGGACAGGA\tUnknown\tTGTGCTGT\tUnknown\t62\r\nGCTACGCT\tN709\tTATTCTTC\tUnknown\t62\r\nGCTACGCT\tN709\tTAGCGGCT\tUnknown\t62\r\nTAAGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nAGGCGAAT\tD505\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nGTAGAGTC\tUnknown\tTCTGCTCT\tE504,[N|S|E]504\t62\r\nGCTGCGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nTCTACGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nTTCTCCGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nCTCTCTAC\tN707\tTATCCACT\tE503,S503,[N|S|E]503\t62\r\nATCCAGAA\tD705\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nTCATGCGC\tD708\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nGGATCCTA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nGTCTCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nTCTCTCCT\tS511\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nTAGGGACA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nTTTTTTTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nTAGGAAGG\tUnknown\tTAGAAGAG\tUnknown\t62\r\nTCCAGAGC\tN704\tTATCCTCT\tE503,S503,[N|S|E]503\t62\r\nGCCATCCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t61\r\nGTAGAGGA\tN712\tTATCATCT\tE503,S503,[N|S|E]503\t61\r\nTAGGGATT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t61\r\nCAAGGCGA\tN701\tTGAGTAGA\tE504,[N|S|E]504\t61\r\nGTATCGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t61\r\nGTATCTAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t61\r\nGGTGAGGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t61\r\nGAAGGCGA\tN701\tAGTGCAGT\tUnknown\t61\r\nCCTCTTCC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t61\r\nCGAGGCTG\tN710\tTACCCTCT\tE503,S503,[N|S|E]503\t61\r\nTCCTGTGC\tN704\tAGAGTAGA\tE504,[N|S|E]504\t61\r\nAGGCAGAA\tN703\tAGAGTACA\tA503,E504,[N|S|E]504\t61\r\nCAGAGAGT\tN708\tCTCTCTAT\tE502,S502,[N|S|E]502\t61\r\nCTCAGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t61\r\nTTAGGCGA\tN701,S522\tAGAGCTGT\tUnknown\t61\r\nTTCTCCTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nTCCTTCGC\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t60\r\nTAAGCCGA\tN701\tTGTGCTCT\tA503\t60\r\nGTCTATTC\tUnknown\tTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t60\r\nCTAGCGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nCGTAGCAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t60\r\nGTAGAGGA\tN712\tTATCCTAT\tE503,S503,[N|S|E]503\t60\r\nTAAGGCGA\tN701\tTTATCCTC\tUnknown\t60\r\nTCCTGAGC\tN704\tTAGAGGCC\tUnknown\t60\r\nTGTAGCAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t60\r\nTAAGGGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nCGCTCTAG\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t60\r\nTGGCGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nAGGCAGCA\tN703\tAGAGCAGT\tUnknown\t60\r\nAGGCCGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nTAAGGAGA\tN701\tAGAGAAGA\tA503,E504,[N|S|E]504\t60\r\nTCCTGGGC\tN704\tTGTGCTCT\tA503\t60\r\nTAAGGCGA\tN701\tTACTCTTC\tUnknown\t60\r\nCCCCTCTT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nGTCTCTTC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nTCATGAGC\tN704\tAGAGCAGA\tE504,[N|S|E]504\t60\r\nGAGGCATG\tN706\tGATCCTCT\tE503,S503,[N|S|E]503\t60\r\nCATACTAG\tN702\tAGAGTAGA\tE504,[N|S|E]504\t60\r\nCGTACTCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nCGTACTCG\tN702\tTGTGCTGT\tUnknown\t60\r\nGTAGAGGA\tN712\tTATCTCCT\tUnknown\t60\r\nGGACCTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nAGACTCCT\tN705\tTATCCTCT\tE503,S503,[N|S|E]503\t60\r\nGAGGCGTG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nGTCTCTAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTCCTGAGA\tD702,N704\tTGTGCTCT\tA503\t59\r\nCGCACTAC\tUnknown\tTGTGCTGT\tUnknown\t59\r\nTAAGGCTT\tS521\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nGTACAGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nCTCACGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTCCTGAGC\tN704\tTAATCCTC\tUnknown\t59\r\nTACGGAGA\tD702\tAGAGTAGA\tE504,[N|S|E]504\t59\r\nTCTTCGCT\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTTAGCTGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTAAGCCGA\tN701\tAGAGTAGA\tE504,[N|S|E]504\t59\r\nGCAGGGGA\tUnknown\tTATGCTCT\tE503,S503,[N|S|E]503\t59\r\nGTCTGAGC\tUnknown\tTGTGCTCT\tA503\t59\r\nTCAGGCGA\tN701\tTGTGCTCT\tA503\t59\r\nTCTACACT\tE504,[N|S|E]504\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nGGTACTAG\tN702\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTTCTGAGC\tN704\tAGAGCTGT\tUnknown\t59\r\nCCCTCGCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTTAGGCGA\tN701,S522\tTTTCCTCT\tE503,S503,[N|S|E]503\t59\r\nCTCTGAGC\tUnknown\tAGTGCAGT\tUnknown\t59\r\nTCCTTCTC\tUnknown\tATCTTATC\tUnknown\t59\r\nGCTACGCT\tN709\tTAACCTCT\tE503,S503,[N|S|E]503\t59\r\nGAGGCGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nGCTACGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTACGCATC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTCCTGAGC\tN704\tTCCTCTTC\tUnknown\t59\r\nGCTATCCT\tD503\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTCCTCACC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTAGGCATG\tN706\tTATTCCTC\tUnknown\t59\r\nGGCTACGC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nCGCCCTAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTCCCTGAT\tUnknown\tAGAGTAGA\tE504,[N|S|E]504\t59\r\nTCTACGCA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t59\r\nTCATGGGA\tUnknown\tTGTGCTGT\tUnknown\t58\r\nTAAGGCGA\tN701\tAGGGCAGA\tUnknown\t58\r\nGCTACGCT\tN709\tCTCTTCGT\tUnknown\t58\r\nTGGCGGGA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nTAAGGCGA\tN701\tTATCCTCG\tE503,S503,[N|S|E]503\t58\r\nCTCCCGAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nGGGGGGAA\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nGAGGCAGG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nTCTCTCCC\tS511\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nCGCTCTAC\tN707\tTGTGCTGT\tUnknown\t58\r\nCTCGCCAC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nTAGAGGCA\tN711\tTGTCCTCT\tA503,E503,S503,[N|S|E]503\t58\r\nGTCACTCC\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nCTCTCTAC\tN707\tTATCTCCT\tUnknown\t58\r\nTAAGGCGA\tN701\tAGAGCAGG\tUnknown\t58\r\nTACGGCGC\tUnknown\tTGTGCTGT\tUnknown\t58\r\nTAGGGGGA\tUnknown\tTGTGCTGT\tUnknown\t58\r\nGTAGCGTG\tUnknown\tTATCCTCT\tE503,S503,[N|S|E]503\t58\r\nCGTACTAT\tN702\tAGTGTAGA\tE504,[N|S|E]504\t58\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/one_correction/expected.txt", "content": "sample_name\texpected_barcode_1\texpected_barcode_2\texpected_barcode_1_name\texpected_barcode_2_name\texpected_barcodes_read_count\tguessed_barcode_1\tguessed_barcode_2\tguessed_barcode_1_name\tguessed_barcode_2_name\tguessed_barcodes_read_count\tmatch_type\r\nG5767.1_171025\tCAGAGAGG\tTATCCTCT\tBI7A06,N708\tBI5G02,E503,S503,[N|S|E]503\t69\tTAGGCATT\tTATCCTCT\tN706\tE503,S503,[N|S|E]503\t41442\tone_barcode_match\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/one_correction/metrics.txt", "content": "## htsjdk.samtools.metrics.StringHeader\n# ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/tmp.MFbcoiGo6L/Data/Intensities/BaseCalls OUTPUT_DIR=/tmp/tmp-illumina-illumina_demux-6rg4yi1t/extracted_barcodes-bdo5m9xj LANE=1 READ_STRUCTURE=101T8B8B101T BARCODE_FILE=/tmp/tmp-illumina-illumina_demux-6rg4yi1t/barcodeData.AYAC2.1po0amae6.txt METRICS_FILE=metrics.txt MAX_MISMATCHES=1 MINIMUM_BASE_QUALITY=10 MINIMUM_QUALITY=10 NUM_PROCESSORS=0 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\n## htsjdk.samtools.metrics.StringHeader\n# Started on: Wed Sep 05 21:57:07 UTC 2018\n\n## METRICS CLASS\tpicard.illumina.ExtractIlluminaBarcodes$BarcodeMetric\nBARCODE\tBARCODE_WITHOUT_DELIMITER\tBARCODE_NAME\tLIBRARY_NAME\tREADS\tPF_READS\tPERFECT_MATCHES\tPF_PERFECT_MATCHES\tONE_MISMATCH_MATCHES\tPF_ONE_MISMATCH_MATCHES\tPCT_MATCHES\tRATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_PCT_MATCHES\tPF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_NORMALIZED_MATCHES\nTAAGGCGA-TATCCTCT\tTAAGGCGATATCCTCT\tG4220.1_171025\tG4220.1_171025\t865707\t803364\t849939\t796393\t15768\t6971\t0.046287\t0.280799\t0.046622\t0.287287\t0.766694\nCGTACTAG-TATCCTCT\tCGTACTAGTATCCTCT\tG4324.1_171025\tG4324.1_171025\t134239\t126862\t123272\t117996\t10967\t8866\t0.007177\t0.043542\t0.007362\t0.045366\t0.121071\nAGGCAGAA-TATCCTCT\tAGGCAGAATATCCTCT\tG4468.2_171025\tG4468.2_171025\t569363\t538190\t556637\t531720\t12726\t6470\t0.030442\t0.184678\t0.031233\t0.192459\t0.513624\nTCCTGAGC-TATCCTCT\tTCCTGAGCTATCCTCT\tG5135.1_171025\tG5135.1_171025\t363423\t339128\t355304\t334983\t8119\t4145\t0.019431\t0.117879\t0.019681\t0.121274\t0.323648\nGGACTCCT-TATCCTCT\tGGACTCCTTATCCTCT\tG5395.1_171025\tG5395.1_171025\t236368\t220798\t231310\t218284\t5058\t2514\t0.012638\t0.076668\t0.012814\t0.078958\t0.21072\nTAGGCATG-TATCCTCT\tTAGGCATGTATCCTCT\tG5413.1_171025\tG5413.1_171025\t768484\t721458\t712147\t675201\t56337\t46257\t0.041088\t0.249264\t0.041869\t0.257997\t0.688527\nCTCTCTAC-TATCCTCT\tCTCTCTACTATCCTCT\tG5754.1_171025\tG5754.1_171025\t2866604\t2692792\t2816035\t2663917\t50569\t28875\t0.153268\t0.929807\t0.156272\t0.962955\t2.569879\nCAGAGAGG-TATCCTCT\tCAGAGAGGTATCCTCT\tG5767.1_171025\tG5767.1_171025\t69\t66\t4\t3\t65\t63\t0.000004\t0.000022\t0.000004\t0.000024\t0.000063\nGCTACGCT-TATCCTCT\tGCTACGCTTATCCTCT\tG5787.1_171025\tG5787.1_171025\t1571414\t1502484\t1533037\t1479389\t38377\t23095\t0.084019\t0.509701\t0.087195\t0.537295\t1.433903\nCGAGGCTG-TATCCTCT\tCGAGGCTGTATCCTCT\tG3773.1_171025\tG3773.1_171025\t425490\t400469\t390503\t371648\t34987\t28821\t0.02275\t0.138011\t0.023241\t0.14321\t0.382189\nAAGAGGCA-TATCCTCT\tAAGAGGCATATCCTCT\tG4121.1_171025\tG4121.1_171025\t2156674\t2003380\t2123013\t1986343\t33661\t17037\t0.115311\t0.699535\t0.116263\t0.716418\t1.911935\nGTAGAGGA-TATCCTCT\tGTAGAGGATATCCTCT\tG4441.1_171025\tG4441.1_171025\t3083011\t2796383\t3025191\t2770962\t57820\t25421\t0.164839\t1\t0.162284\t1\t2.668741\nTAAGGCGA-AGAGTAGA\tTAAGGCGAAGAGTAGA\tG4494.1_171025\tG4494.1_171025\t2643139\t2507469\t2545155\t2434742\t97984\t72727\t0.14132\t0.857324\t0.145517\t0.896683\t2.393015\nCGTACTAG-AGAGTAGA\tCGTACTAGAGAGTAGA\tG4489.1_171025\tG4489.1_171025\t353013\t339894\t321177\t312249\t31836\t27645\t0.018875\t0.114503\t0.019725\t0.121548\t0.324379\nAGGCAGAA-AGAGTAGA\tAGGCAGAAAGAGTAGA\tWater_2_171025\tWater_2_171025\t440262\t424432\t420657\t409246\t19605\t15186\t0.023539\t0.142803\t0.024631\t0.151779\t0.405059\nTCCTGAGC-AGAGTAGA\tTCCTGAGCAGAGTAGA\tK562_2_171025\tK562_2_171025\t1418503\t1348085\t1366847\t1310862\t51656\t37223\t0.075843\t0.460103\t0.078234\t0.482082\t1.286551\nNNNNNNNN-NNNNNNNN\tNNNNNNNNNNNNNNNN\t\t\t807391\t466153\t0\t0\t0\t0\t0.043169\t0.261884\t0.027053\t0.166699\t0\n\n\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/single_index/barcodes.txt", "content": "Barcode1\tLikely_Index_Names1\tBarcode2\tLikely_Index_Names2\tCount\r\nCAGAGAGG\tN708\t\tUnknown\t2236892\r\nGGACTCCT\tN705\t\tUnknown\t1481969\r\nTAGGCATG\tN706\t\tUnknown\t1388954\r\nCAGGCGAT\tUnknown\t\tUnknown\t1375668\r\nGCTACGCT\tN709\t\tUnknown\t1370424\r\nCTCTCTAC\tN707\t\tUnknown\t1181498\r\nGTAGAGGA\tN712\t\tUnknown\t1144504\r\nCGAGGCTG\tN710\t\tUnknown\t1078586\r\nAAGAGGCA\tN711\t\tUnknown\t910195\r\nTACAGCAT\tUnknown\t\tUnknown\t670800\r\nCATTTTAT\tUnknown\t\tUnknown\t627525\r\nTCATTCAT\tUnknown\t\tUnknown\t624071\r\nACTGATAT\tUnknown\t\tUnknown\t613337\r\nATTCCTAT\tUnknown\t\tUnknown\t578494\r\nCGGAATAT\tUnknown\t\tUnknown\t564153\r\nGACGACAT\tUnknown\t\tUnknown\t555371\r\nTATAATAT\tUnknown\t\tUnknown\t545928\r\nCATGGCAT\tUnknown\t\tUnknown\t455796\r\nATGAGCAT\tUnknown\t\tUnknown\t449580\r\nCCAACAAT\tUnknown\t\tUnknown\t446825\r\nTAATCGAT\tUnknown\t\tUnknown\t409191\r\nCAACTAAT\tUnknown\t\tUnknown\t402513\r\nTCCCGAAT\tUnknown\t\tUnknown\t340067\r\nCAAAAGAT\tUnknown\t\tUnknown\t305712\r\nCTAGCTAT\tUnknown\t\tUnknown\t298921\r\nCACCGGAT\tUnknown\t\tUnknown\t217902\r\nGAAGAGGA\tN712\t\tUnknown\t8740\r\nAGAGAGGA\tUnknown\t\tUnknown\t8486\r\nGCTACGAT\tN709\t\tUnknown\t6491\r\nGGACTCAT\tN705\t\tUnknown\t5693\r\nAAGAGAGG\tN708\t\tUnknown\t5249\r\nCAGGCATG\tN706\t\tUnknown\t5051\r\nCAGGGAGG\tN708\t\tUnknown\t4417\r\nCAGAGAGA\tN708,S511\t\tUnknown\t4238\r\nCAGAGAGT\tN708\t\tUnknown\t4217\r\nGTAGAGGT\tN712\t\tUnknown\t4012\r\nTAATTCAT\tUnknown\t\tUnknown\t4012\r\nGATACGCT\tN709\t\tUnknown\t3956\r\nCTTCCTAT\tUnknown\t\tUnknown\t3741\r\nGGAGAGGA\tN712\t\tUnknown\t3650\r\nCTCTCTAA\tE502,N707,S502,[N|S|E]502\t\tUnknown\t3421\r\nCAGGCGAG\tUnknown\t\tUnknown\t3409\r\nAAGAGGAA\tN711\t\tUnknown\t3380\r\nCAGACGAT\tUnknown\t\tUnknown\t3260\r\nGTAGAGAA\tN712\t\tUnknown\t3247\r\nCAGAGAAG\tN708\t\tUnknown\t3185\r\nACTGATCT\tUnknown\t\tUnknown\t3119\r\nCATTTATC\tUnknown\t\tUnknown\t3101\r\nTATAATCT\tUnknown\t\tUnknown\t2948\r\nGCAACGCT\tN709\t\tUnknown\t2912\r\nCGAGGCTA\tN710\t\tUnknown\t2893\r\nTAGAGAGG\tN708\t\tUnknown\t2785\r\nCAGAGCGG\tN708\t\tUnknown\t2785\r\nGGACTCTA\tUnknown\t\tUnknown\t2749\r\nCAGAGGGG\tN708\t\tUnknown\t2693\r\nTAGGCAAG\tN706\t\tUnknown\t2675\r\nCAAGAGGA\tUnknown\t\tUnknown\t2615\r\nATCTCTAC\tN707\t\tUnknown\t2608\r\nCGAGGCTT\tN710\t\tUnknown\t2566\r\nAAGGCGAT\tS520\t\tUnknown\t2561\r\nCTACGCTA\tUnknown\t\tUnknown\t2553\r\nTAGGCATT\tN706\t\tUnknown\t2541\r\nGGACTACT\tN705\t\tUnknown\t2499\r\nCCAACATC\tUnknown\t\tUnknown\t2479\r\nGGAATCCT\tN705\t\tUnknown\t2477\r\nCAGGAGAT\tUnknown\t\tUnknown\t2476\r\nTATAAATC\tUnknown\t\tUnknown\t2454\r\nGAGAGAGG\tN708\t\tUnknown\t2441\r\nCAAGCGAT\tUnknown\t\tUnknown\t2437\r\nTATATATC\tUnknown\t\tUnknown\t2436\r\nCTCTCTAT\tE502,S502,[N|S|E]502\t\tUnknown\t2419\r\nCAGGCGCT\tUnknown\t\tUnknown\t2404\r\nATTTTATC\tUnknown\t\tUnknown\t2402\r\nGCACGCTA\tUnknown\t\tUnknown\t2320\r\nCAGAGGCA\tN711\t\tUnknown\t2304\r\nCAAAGATC\tUnknown\t\tUnknown\t2268\r\nGCTACCTA\tUnknown\t\tUnknown\t2250\r\nCAGAGGGA\tUnknown\t\tUnknown\t2217\r\nTAGGCGAT\tUnknown\t\tUnknown\t2190\r\nCGAGGCAG\tN710\t\tUnknown\t2168\r\nTCATCATC\tUnknown\t\tUnknown\t2148\r\nGAGGCTGA\tUnknown\t\tUnknown\t2128\r\nGAGGCATG\tN706\t\tUnknown\t2123\r\nCTCTCACA\tUnknown\t\tUnknown\t2080\r\nGGGCTCCT\tN705\t\tUnknown\t2028\r\nGCTCGCTA\tN716\t\tUnknown\t2027\r\nCGGAATCT\tUnknown\t\tUnknown\t2024\r\nCTATCTAC\tN707\t\tUnknown\t2014\r\nTAGCATGA\tUnknown\t\tUnknown\t2003\r\nGCTAGCTA\tUnknown\t\tUnknown\t1985\r\nTAAATATC\tUnknown\t\tUnknown\t1983\r\nGCTACGTA\tUnknown\t\tUnknown\t1964\r\nCCTCTCTT\tUnknown\t\tUnknown\t1964\r\nAGAGGCTG\tN710\t\tUnknown\t1937\r\nCAGGCGAA\tUnknown\t\tUnknown\t1922\r\nCAGAGGAT\tUnknown\t\tUnknown\t1888\r\nCTCTCTCC\tN707\t\tUnknown\t1872\r\nTCCCGATC\tUnknown\t\tUnknown\t1863\r\nCAGCGAGG\tN708\t\tUnknown\t1857\r\nCAGAGAAT\tUnknown\t\tUnknown\t1837\r\nCAGAAGGA\tUnknown\t\tUnknown\t1786\r\nTAGGAATG\tN706\t\tUnknown\t1757\r\nAATGATAT\tUnknown\t\tUnknown\t1745\r\nCGAGGATG\tN710\t\tUnknown\t1740\r\nCTCCTACA\tUnknown\t\tUnknown\t1725\r\nCAACAATC\tUnknown\t\tUnknown\t1723\r\nGCAGAGGA\tN712\t\tUnknown\t1702\r\nTAAGCATG\tN706\t\tUnknown\t1689\r\nTTCTCTAC\tN707\t\tUnknown\t1664\r\nGCGACGCT\tN709\t\tUnknown\t1664\r\nGTACGCTA\tUnknown\t\tUnknown\t1663\r\nGTAGAGGC\tD502,N712\t\tUnknown\t1646\r\nCAGGCAAT\tUnknown\t\tUnknown\t1641\r\nCAGGGGAT\tUnknown\t\tUnknown\t1625\r\nAAGAGGCT\tN711\t\tUnknown\t1612\r\nCAAACAAT\tUnknown\t\tUnknown\t1596\r\nAGGCGATC\tUnknown\t\tUnknown\t1596\r\nCAGGCATC\tUnknown\t\tUnknown\t1590\r\nCCTGATAT\tUnknown\t\tUnknown\t1582\r\nTAGACATG\tN706\t\tUnknown\t1572\r\nGCTAAGCT\tN709\t\tUnknown\t1567\r\nGAACTCCT\tN705\t\tUnknown\t1567\r\nCAACTATC\tUnknown\t\tUnknown\t1565\r\nCGAGGCGA\tUnknown\t\tUnknown\t1553\r\nAGGCATGA\tUnknown\t\tUnknown\t1526\r\nCCTTCTCT\tUnknown\t\tUnknown\t1522\r\nCGAGCTGA\tUnknown\t\tUnknown\t1519\r\nCATGCGAT\tUnknown\t\tUnknown\t1508\r\nTGACTCCT\tN705\t\tUnknown\t1498\r\nCAGGAGGA\tUnknown\t\tUnknown\t1498\r\nGTCTCTAC\tN707\t\tUnknown\t1487\r\nTACAGCAG\tUnknown\t\tUnknown\t1474\r\nCTCTTACA\tUnknown\t\tUnknown\t1469\r\nAAGGCATG\tN706\t\tUnknown\t1463\r\nGTAGCGGA\tN712\t\tUnknown\t1442\r\nCGAGAGGA\tUnknown\t\tUnknown\t1433\r\nGAGGCGAT\tUnknown\t\tUnknown\t1421\r\nTCTCTACA\tUnknown\t\tUnknown\t1413\r\nCCTACGCT\tN709\t\tUnknown\t1402\r\nTACAGAAT\tUnknown\t\tUnknown\t1395\r\nCATAATAT\tUnknown\t\tUnknown\t1373\r\nTCTACGCT\tE504,N709,[N|S|E]504\t\tUnknown\t1364\r\nCGACTCCT\tN705\t\tUnknown\t1364\r\nATGGCATC\tUnknown\t\tUnknown\t1352\r\nTCTCCTCT\tE503,E504,S503,[N|S|E]503,[N|S|E]504\t\tUnknown\t1346\r\nGGAGGCTG\tN710\t\tUnknown\t1335\r\nCTGAGCAT\tUnknown\t\tUnknown\t1325\r\nCTCTCTCA\tUnknown\t\tUnknown\t1312\r\nCAAAGAGG\tN708\t\tUnknown\t1302\r\nGGTCTCCT\tN705\t\tUnknown\t1292\r\nGGCTCCTA\tUnknown\t\tUnknown\t1285\r\nCGGGATAT\tUnknown\t\tUnknown\t1284\r\nGTACTCCT\tN705\t\tUnknown\t1278\r\nCTCACTAC\tN707\t\tUnknown\t1278\r\nCAGCGATC\tUnknown\t\tUnknown\t1275\r\nTAGGCATA\tN706\t\tUnknown\t1273\r\nTAAGCATC\tUnknown\t\tUnknown\t1272\r\nCGGAGAGG\tN708,S511\t\tUnknown\t1266\r\nAGGAATAT\tUnknown\t\tUnknown\t1261\r\nTAGGCGTG\tN706\t\tUnknown\t1259\r\nCAAGGCAT\tUnknown\t\tUnknown\t1257\r\nACTGAATC\tUnknown\t\tUnknown\t1250\r\nCAGGCTAT\tS520\t\tUnknown\t1241\r\nCAGGCAAG\tUnknown\t\tUnknown\t1241\r\nCAGACAGG\tN708\t\tUnknown\t1234\r\nGGACCCTA\tUnknown\t\tUnknown\t1234\r\nTACCGAAT\tUnknown\t\tUnknown\t1233\r\nAATTTTAT\tUnknown\t\tUnknown\t1232\r\nTCTTCCTT\tUnknown\t\tUnknown\t1225\r\nCACTCTAC\tN707\t\tUnknown\t1223\r\nCGGAAATC\tUnknown\t\tUnknown\t1222\r\nCACAGCAT\tUnknown\t\tUnknown\t1220\r\nAAAAGGCA\tN711\t\tUnknown\t1214\r\nACTGCTAT\tUnknown\t\tUnknown\t1209\r\nCATAGCAT\tUnknown\t\tUnknown\t1205\r\nACTGAGAT\tUnknown\t\tUnknown\t1203\r\nCTTCTACA\tUnknown\t\tUnknown\t1200\r\nGAAGACAT\tUnknown\t\tUnknown\t1199\r\nGGACTGCT\tN705\t\tUnknown\t1198\r\nGACTCCTA\tUnknown\t\tUnknown\t1197\r\nTAAAGCAT\tUnknown\t\tUnknown\t1196\r\nTAGGGATG\tN706\t\tUnknown\t1187\r\nCCAAAATC\tUnknown\t\tUnknown\t1168\r\nTGAGGCTG\tN710\t\tUnknown\t1160\r\nGGACTCCA\tN705\t\tUnknown\t1148\r\nATTACTAT\tUnknown\t\tUnknown\t1147\r\nCGGATATC\tUnknown\t\tUnknown\t1135\r\nGGATCCTA\tUnknown\t\tUnknown\t1133\r\nGTAGAGGG\tN712\t\tUnknown\t1123\r\nGCTACACT\tN709\t\tUnknown\t1122\r\nAGAGGCAA\tUnknown\t\tUnknown\t1122\r\nTAGGCAGA\tUnknown\t\tUnknown\t1120\r\nCAGTCGAT\tUnknown\t\tUnknown\t1120\r\nCGAGGGTG\tN710\t\tUnknown\t1119\r\nAAGAGGCC\tN711\t\tUnknown\t1109\r\nATTCATAT\tUnknown\t\tUnknown\t1101\r\nGGACCCCT\tN705\t\tUnknown\t1100\r\nTCCCGCAT\tUnknown\t\tUnknown\t1095\r\nCATTCTAT\tUnknown\t\tUnknown\t1092\r\nAAGACGCA\tN711\t\tUnknown\t1086\r\nCAGAATAT\tUnknown\t\tUnknown\t1070\r\nAAGAGCAA\tUnknown\t\tUnknown\t1068\r\nAAGAGACA\tN711\t\tUnknown\t1065\r\nGTAAGGAA\tE505,S505,[N|S|E]505\t\tUnknown\t1062\r\nCCACAATC\tUnknown\t\tUnknown\t1061\r\nCAGGGCAT\tUnknown\t\tUnknown\t1057\r\nTACAGCAA\tUnknown\t\tUnknown\t1052\r\nCAGGTGAT\tUnknown\t\tUnknown\t1037\r\nTCCCTCCT\tUnknown\t\tUnknown\t1034\r\nTACACATC\tUnknown\t\tUnknown\t1033\r\nACTGACAT\tUnknown\t\tUnknown\t1032\r\nTAGAGGAA\tUnknown\t\tUnknown\t1030\r\nCTCGCTAC\tN707\t\tUnknown\t1029\r\nGCTACTCT\tE504,N709,[N|S|E]504\t\tUnknown\t1027\r\nGGAGTCCT\tN705\t\tUnknown\t1025\r\nGGCCTCCT\tN705\t\tUnknown\t1022\r\nGCTACGCA\tN709\t\tUnknown\t1014\r\nCAATCGAT\tUnknown\t\tUnknown\t1009\r\nCAGAGATG\tN708\t\tUnknown\t1002\r\nCAAGGCTG\tN710\t\tUnknown\t999\r\nCGGGGCTG\tN710\t\tUnknown\t999\r\nTAAACGAT\tUnknown\t\tUnknown\t989\r\nTATACTAT\tUnknown\t\tUnknown\t987\r\nTCACGAAT\tUnknown\t\tUnknown\t977\r\nCAAAAATC\tUnknown\t\tUnknown\t977\r\nGCTGCGCT\tN709\t\tUnknown\t976\r\nTATCGATC\tUnknown\t\tUnknown\t971\r\nGGAATATC\tUnknown\t\tUnknown\t969\r\nCCGGCGAT\tUnknown\t\tUnknown\t964\r\nAAGGGGCA\tN711\t\tUnknown\t956\r\nTTATTCAT\tUnknown\t\tUnknown\t956\r\nCACGACAT\tUnknown\t\tUnknown\t950\r\nTAGGCCTG\tN706\t\tUnknown\t949\r\nTATAAGAT\tUnknown\t\tUnknown\t943\r\nCTTCCTCT\tUnknown\t\tUnknown\t942\r\nGACAACAT\tUnknown\t\tUnknown\t942\r\nCAAGAGAT\tUnknown\t\tUnknown\t941\r\nTCATTAAT\tUnknown\t\tUnknown\t937\r\nTATGATAT\tUnknown\t\tUnknown\t932\r\nCGGGCTGA\tUnknown\t\tUnknown\t932\r\nAAGAGCAT\tUnknown\t\tUnknown\t931\r\nGACGACAG\tUnknown\t\tUnknown\t928\r\nGAGAGGAA\tUnknown\t\tUnknown\t927\r\nCATATTAT\tUnknown\t\tUnknown\t926\r\nGGCGACAT\tUnknown\t\tUnknown\t925\r\nTAGGCTGA\tUnknown\t\tUnknown\t924\r\nCGAGCCTG\tN710\t\tUnknown\t923\r\nCAAACGAT\tUnknown\t\tUnknown\t922\r\nCCGAGAGG\tN708\t\tUnknown\t918\r\nCAGGGATG\tUnknown\t\tUnknown\t917\r\nTCATTCAG\tUnknown\t\tUnknown\t907\r\nTAGGCATC\tN706\t\tUnknown\t903\r\nTACGACAT\tUnknown\t\tUnknown\t900\r\nCTCTTCTT\tUnknown\t\tUnknown\t900\r\nTAATCGAG\tUnknown\t\tUnknown\t898\r\nCCTTTTAT\tUnknown\t\tUnknown\t897\r\nTATGCATG\tN706\t\tUnknown\t896\r\nGGACACCT\tN705\t\tUnknown\t896\r\nATGAGAAT\tUnknown\t\tUnknown\t885\r\nCGGAAGAT\tUnknown\t\tUnknown\t878\r\nCAGAGTGG\tN708\t\tUnknown\t875\r\nATTCCTCT\tUnknown\t\tUnknown\t872\r\nGACGACAA\tUnknown\t\tUnknown\t872\r\nGACGAAAT\tUnknown\t\tUnknown\t871\r\nCATTTCAT\tUnknown\t\tUnknown\t869\r\nTACAACAT\tUnknown\t\tUnknown\t869\r\nTTCCTCCT\tUnknown\t\tUnknown\t869\r\nCGAGGCAT\tUnknown\t\tUnknown\t861\r\nCTCTATAC\tN707\t\tUnknown\t860\r\nCAGGCCAT\tUnknown\t\tUnknown\t859\r\nATGAGCAG\tN722\t\tUnknown\t858\r\nCGGACTAT\tUnknown\t\tUnknown\t854\r\nTATAACAT\tUnknown\t\tUnknown\t849\r\nTTTCCTAT\tUnknown\t\tUnknown\t849\r\nACTACGCT\tN709\t\tUnknown\t848\r\nAATGGCAT\tUnknown\t\tUnknown\t848\r\nTCAATCAT\tUnknown\t\tUnknown\t845\r\nGACGCCAT\tUnknown\t\tUnknown\t843\r\nTGGCATGA\tUnknown\t\tUnknown\t843\r\nGAGACATC\tUnknown\t\tUnknown\t842\r\nCTACTATC\tUnknown\t\tUnknown\t836\r\nGCTACGCG\tN709\t\tUnknown\t833\r\nCATGGCAG\tUnknown\t\tUnknown\t832\r\nTAATAGAT\tUnknown\t\tUnknown\t831\r\nACAACAAT\tUnknown\t\tUnknown\t830\r\nTAACGATC\tUnknown\t\tUnknown\t825\r\nATGATATC\tUnknown\t\tUnknown\t825\r\nCAGAAGAT\tUnknown\t\tUnknown\t816\r\nAAACTAAT\tUnknown\t\tUnknown\t815\r\nTAGGCAGG\tN706\t\tUnknown\t813\r\nGACGAATC\tUnknown\t\tUnknown\t813\r\nCTGGCGAT\tUnknown\t\tUnknown\t812\r\nCCAGGCGA\tUnknown\t\tUnknown\t811\r\nCAGAGCAT\tUnknown\t\tUnknown\t808\r\nTAGGCAAT\tUnknown\t\tUnknown\t802\r\nTATAAAAT\tUnknown\t\tUnknown\t800\r\nGATACGAT\tUnknown\t\tUnknown\t798\r\nCATTTTAG\tUnknown\t\tUnknown\t798\r\nTATTTTAT\tUnknown\t\tUnknown\t797\r\nCGGGCGAT\tUnknown\t\tUnknown\t792\r\nGCTAGGCT\tN709\t\tUnknown\t790\r\nCGAAATAT\tUnknown\t\tUnknown\t789\r\nTGATTCAT\tUnknown\t\tUnknown\t788\r\nTACACCAT\tUnknown\t\tUnknown\t788\r\nGTTCCTAT\tUnknown\t\tUnknown\t786\r\nTCTAATAT\tUnknown\t\tUnknown\t785\r\nTGGAATAT\tUnknown\t\tUnknown\t782\r\nCAACTCAT\tUnknown\t\tUnknown\t774\r\nTCCTTCCT\tUnknown\t\tUnknown\t773\r\nGGACGCCT\tN705\t\tUnknown\t773\r\nTGGGCATG\tN706\t\tUnknown\t770\r\nCCTCTACA\tUnknown\t\tUnknown\t770\r\nCCTTTTCT\tUnknown\t\tUnknown\t765\r\nCAGCCGAT\tUnknown\t\tUnknown\t763\r\nAAAAGATC\tUnknown\t\tUnknown\t761\r\nTACAGCCT\tD501\t\tUnknown\t761\r\nCAAATAAT\tUnknown\t\tUnknown\t759\r\nCAGGCGGT\tUnknown\t\tUnknown\t758\r\nATTCCGAT\tUnknown\t\tUnknown\t757\r\nTACGGCAT\tUnknown\t\tUnknown\t755\r\nTCATTCAA\tUnknown\t\tUnknown\t754\r\nCTGAGAGG\tN708\t\tUnknown\t753\r\nTCAACAAT\tUnknown\t\tUnknown\t753\r\nGCTACCCT\tN709\t\tUnknown\t752\r\nGCCACGCT\tN709\t\tUnknown\t750\r\nACTGAAAT\tUnknown\t\tUnknown\t749\r\nCATTTGAT\tUnknown\t\tUnknown\t747\r\nCTCTCAAC\tN707\t\tUnknown\t743\r\nGCTATGCT\tN709\t\tUnknown\t737\r\nAACTAATC\tUnknown\t\tUnknown\t736\r\nGCTACTAT\tUnknown\t\tUnknown\t736\r\nCTGTCTAC\tN707\t\tUnknown\t736\r\nGTCGACAT\tUnknown\t\tUnknown\t735\r\nTAATCGCT\tUnknown\t\tUnknown\t734\r\nTAGGATGA\tUnknown\t\tUnknown\t732\r\nAGACTCCT\tN705\t\tUnknown\t731\r\nTATAATAG\tUnknown\t\tUnknown\t730\r\nCATTTAAT\tUnknown\t\tUnknown\t726\r\nCATGCCAT\tUnknown\t\tUnknown\t726\r\nCAGAAAGG\tN708\t\tUnknown\t726\r\nTATAGCAT\tD501\t\tUnknown\t723\r\nTATGGCAT\tUnknown\t\tUnknown\t722\r\nGAGACGCT\tUnknown\t\tUnknown\t721\r\nAAGAGGAT\tUnknown\t\tUnknown\t718\r\nGGACTCCG\tN705\t\tUnknown\t718\r\nATGAGCAA\tUnknown\t\tUnknown\t717\r\nTCGGCATG\tN706\t\tUnknown\t716\r\nGACGAGAT\tUnknown\t\tUnknown\t716\r\nGTAGAGAT\tUnknown\t\tUnknown\t716\r\nAAGAGGGA\tN711\t\tUnknown\t713\r\nCGGAAAAT\tUnknown\t\tUnknown\t711\r\nCCATTCAT\tUnknown\t\tUnknown\t707\r\nACCGGATC\tUnknown\t\tUnknown\t704\r\nTAGCTATC\tUnknown\t\tUnknown\t703\r\nATCCTATC\tUnknown\t\tUnknown\t701\r\nCATGGAAT\tUnknown\t\tUnknown\t701\r\nTAAAAGAT\tUnknown\t\tUnknown\t700\r\nACTAATAT\tUnknown\t\tUnknown\t697\r\nGCCGACAT\tUnknown\t\tUnknown\t692\r\nTAGAGCAT\tUnknown\t\tUnknown\t691\r\nCATGACAT\tUnknown\t\tUnknown\t690\r\nTACAGGAT\tUnknown\t\tUnknown\t688\r\nACTGATAG\tUnknown\t\tUnknown\t688\r\nCGAGGTGA\tUnknown\t\tUnknown\t687\r\nTGTAATAT\tUnknown\t\tUnknown\t685\r\nCGTTTTAT\tUnknown\t\tUnknown\t685\r\nCCCCCCCC\tUnknown\t\tUnknown\t684\r\nGCTCCGCT\tN709\t\tUnknown\t684\r\nTAAGCGAT\tUnknown\t\tUnknown\t678\r\nCGAAGCTG\tN710\t\tUnknown\t676\r\nCGGCATAT\tUnknown\t\tUnknown\t673\r\nTATAGTAT\tUnknown\t\tUnknown\t669\r\nGGTACGCT\tN709\t\tUnknown\t666\r\nGACGACCT\tUnknown\t\tUnknown\t664\r\nAAAAAAAA\tUnknown\t\tUnknown\t664\r\nCAGGGGGG\tUnknown\t\tUnknown\t661\r\nCAGGCGTT\tUnknown\t\tUnknown\t659\r\nTCATTCCT\tUnknown\t\tUnknown\t659\r\nCGGAATAG\tUnknown\t\tUnknown\t658\r\nCAGTGAGG\tN708\t\tUnknown\t657\r\nCATAGAGG\tN708\t\tUnknown\t656\r\nGACAGCAT\tUnknown\t\tUnknown\t655\r\nGTAAAGGA\tN712\t\tUnknown\t653\r\nTATAATAA\tUnknown\t\tUnknown\t652\r\nAAAAAGAT\tUnknown\t\tUnknown\t651\r\nATAAGCAT\tUnknown\t\tUnknown\t651\r\nTAACTAAT\tUnknown\t\tUnknown\t651\r\nCTAGCGAT\tUnknown\t\tUnknown\t650\r\nCGGAACAT\tUnknown\t\tUnknown\t649\r\nGTTACGCT\tN709\t\tUnknown\t647\r\nGAAGAGAT\tUnknown\t\tUnknown\t646\r\nTAATCGAA\tUnknown\t\tUnknown\t645\r\nCAACTGAT\tUnknown\t\tUnknown\t645\r\nAAGGAGAT\tUnknown\t\tUnknown\t642\r\nCCAACGAT\tUnknown\t\tUnknown\t640\r\nATTCCCAT\tUnknown\t\tUnknown\t635\r\nACAGATAT\tUnknown\t\tUnknown\t635\r\nGAAGAGAA\tUnknown\t\tUnknown\t635\r\nGGACTTCT\tN705\t\tUnknown\t634\r\nTACATCAT\tUnknown\t\tUnknown\t634\r\nCAGGCGAC\tUnknown\t\tUnknown\t632\r\nATTCCTAG\tUnknown\t\tUnknown\t632\r\nTCAGTCAT\tUnknown\t\tUnknown\t628\r\nAAGAAGCA\tN711\t\tUnknown\t625\r\nGTAGGGAA\tUnknown\t\tUnknown\t624\r\nCAATTTAT\tUnknown\t\tUnknown\t623\r\nAATCCTAT\tUnknown\t\tUnknown\t623\r\nCAGGCAGG\tUnknown\t\tUnknown\t623\r\nCATGTTAT\tUnknown\t\tUnknown\t621\r\nCATTATAT\tUnknown\t\tUnknown\t621\r\nAATAATAT\tUnknown\t\tUnknown\t620\r\nTAATTGAT\tUnknown\t\tUnknown\t620\r\nCGAGGCGG\tN710\t\tUnknown\t620\r\nCCCCCCCT\tUnknown\t\tUnknown\t618\r\nTAAAATAT\tUnknown\t\tUnknown\t617\r\nTAGGTATG\tN706\t\tUnknown\t611\r\nCTCTCGAC\tN707\t\tUnknown\t609\r\nCACGGATC\tUnknown\t\tUnknown\t604\r\nGTCCTCCT\tUnknown\t\tUnknown\t604\r\nTTTAATAT\tUnknown\t\tUnknown\t603\r\nATTCCTAA\tUnknown\t\tUnknown\t598\r\nCGCGGCTG\tN710\t\tUnknown\t595\r\nCTCTCCAC\tN707\t\tUnknown\t595\r\nGGACTCTT\tN705\t\tUnknown\t593\r\nTAGGCACG\tN706\t\tUnknown\t591\r\nCACGGCAT\tUnknown\t\tUnknown\t590\r\nCAGATAGG\tN708\t\tUnknown\t590\r\nGAGAGGCA\tN711\t\tUnknown\t589\r\nATTCCAAT\tUnknown\t\tUnknown\t589\r\nCAAAAAAT\tUnknown\t\tUnknown\t589\r\nGCTCCTCT\tUnknown\t\tUnknown\t589\r\nCATTTTCT\tUnknown\t\tUnknown\t588\r\nGATGACAT\tUnknown\t\tUnknown\t588\r\nCCACTAAT\tUnknown\t\tUnknown\t585\r\nCACTAATC\tUnknown\t\tUnknown\t585\r\nAATAGGCA\tN711\t\tUnknown\t585\r\nAAGAGGCG\tN711\t\tUnknown\t585\r\nGCACTCCT\tN705\t\tUnknown\t584\r\nCCCCTCCT\tUnknown\t\tUnknown\t583\r\nTTCTCTTC\tUnknown\t\tUnknown\t581\r\nGGACTCCC\tN705\t\tUnknown\t581\r\nCAGGGATC\tUnknown\t\tUnknown\t580\r\nTCGTTCAT\tUnknown\t\tUnknown\t578\r\nCCAACAAG\tUnknown\t\tUnknown\t577\r\nTTGGCATG\tN706\t\tUnknown\t577\r\nCTATCTAT\tE502,S502,[N|S|E]502\t\tUnknown\t576\r\nCGTAATAT\tUnknown\t\tUnknown\t574\r\nCCAACACT\tUnknown\t\tUnknown\t573\r\nAAGGGCAA\tUnknown\t\tUnknown\t570\r\nGGGAATAT\tUnknown\t\tUnknown\t569\r\nACTGATAA\tUnknown\t\tUnknown\t569\r\nGCTACGCC\tN709\t\tUnknown\t568\r\nGAAGAGGT\tUnknown\t\tUnknown\t567\r\nCATTTTAA\tUnknown\t\tUnknown\t566\r\nTCTTTCAT\tUnknown\t\tUnknown\t561\r\nTCACTCAT\tUnknown\t\tUnknown\t561\r\nTAGTCATG\tN706\t\tUnknown\t559\r\nATGGGCAT\tUnknown\t\tUnknown\t557\r\nGTAGATGA\tN712\t\tUnknown\t557\r\nCTTTCTAC\tN707\t\tUnknown\t556\r\nAGGAGGCA\tN711\t\tUnknown\t551\r\nGCATTCAT\tUnknown\t\tUnknown\t550\r\nATTCGTAT\tUnknown\t\tUnknown\t550\r\nCGAATATC\tUnknown\t\tUnknown\t549\r\nCAACTACT\tUnknown\t\tUnknown\t549\r\nATAGCTAT\tUnknown\t\tUnknown\t547\r\nCAGGCGTG\tUnknown\t\tUnknown\t543\r\nCTAACTAT\tUnknown\t\tUnknown\t543\r\nCTTTTTAT\tUnknown\t\tUnknown\t542\r\nTCCAGAAT\tUnknown\t\tUnknown\t541\r\nTTAGAGGA\tN712\t\tUnknown\t541\r\nTCATCGAT\tUnknown\t\tUnknown\t540\r\nCAACTAAG\tUnknown\t\tUnknown\t538\r\nCATGCTAT\tUnknown\t\tUnknown\t537\r\nAAGAGCCA\tN711\t\tUnknown\t536\r\nCAAAAGAG\tUnknown\t\tUnknown\t536\r\nGTGAGGAA\tUnknown\t\tUnknown\t534\r\nATTGATAT\tUnknown\t\tUnknown\t533\r\nCATGGCAA\tUnknown\t\tUnknown\t533\r\nTACCGCAT\tUnknown\t\tUnknown\t533\r\nTAGTCGAT\tUnknown\t\tUnknown\t531\r\nCGAGACTG\tN710\t\tUnknown\t531\r\nCAGGGAAG\tUnknown\t\tUnknown\t531\r\nCTCCCTAC\tE505,N707,S505,[N|S|E]505\t\tUnknown\t531\r\nCGACTAAT\tS510\t\tUnknown\t530\r\nTCCCGACT\tUnknown\t\tUnknown\t529\r\nACGAGGCA\tN711\t\tUnknown\t526\r\nCAGAGACG\tN708\t\tUnknown\t525\r\nTCCTTCAT\tUnknown\t\tUnknown\t524\r\nCGGCGATC\tUnknown\t\tUnknown\t524\r\nATACCTAT\tUnknown\t\tUnknown\t523\r\nCCGCGCGG\tUnknown\t\tUnknown\t523\r\nCATGATAT\tUnknown\t\tUnknown\t521\r\nCCAACCAT\tUnknown\t\tUnknown\t521\r\nCACAGGAT\tUnknown\t\tUnknown\t520\r\nCAATAATC\tUnknown\t\tUnknown\t519\r\nCTAGATAT\tUnknown\t\tUnknown\t516\r\nCAGACAAT\tUnknown\t\tUnknown\t515\r\nATTGCTAT\tUnknown\t\tUnknown\t515\r\nCCATTTTA\tUnknown\t\tUnknown\t511\r\nCAAGCTAT\tUnknown\t\tUnknown\t509\r\nAACGACAT\tUnknown\t\tUnknown\t508\r\nTCCCGGAT\tUnknown\t\tUnknown\t506\r\nATGAGCCT\tUnknown\t\tUnknown\t505\r\nTTCAGCAT\tUnknown\t\tUnknown\t504\r\nCAACCAAT\tUnknown\t\tUnknown\t502\r\nCCAAAAAT\tUnknown\t\tUnknown\t500\r\nAACAGCAT\tUnknown\t\tUnknown\t500\r\nTACAGATC\tUnknown\t\tUnknown\t499\r\nGGATTCCT\tN705\t\tUnknown\t499\r\nCGCTCTAC\tN707\t\tUnknown\t497\r\nGATAAGAT\tUnknown\t\tUnknown\t496\r\nGTAGGGGA\tN712\t\tUnknown\t493\r\nTCCCGAAG\tUnknown\t\tUnknown\t493\r\nCATGCATC\tUnknown\t\tUnknown\t490\r\nCTAACAAT\tUnknown\t\tUnknown\t490\r\nTCCAGCAT\tUnknown\t\tUnknown\t486\r\nAAGCGGCA\tN711\t\tUnknown\t485\r\nCTAGCTAG\tUnknown\t\tUnknown\t485\r\nCATGGTAT\tUnknown\t\tUnknown\t484\r\nACTGGTAT\tUnknown\t\tUnknown\t482\r\nTCATTGAT\tUnknown\t\tUnknown\t481\r\nATGACATC\tUnknown\t\tUnknown\t480\r\nGCTATCTC\tUnknown\t\tUnknown\t479\r\nATTAGCAT\tUnknown\t\tUnknown\t477\r\nCAAAGAAT\tUnknown\t\tUnknown\t476\r\nATTCTATC\tUnknown\t\tUnknown\t475\r\nCGAGGCCG\tN710\t\tUnknown\t475\r\nGGAGAGGT\tUnknown\t\tUnknown\t474\r\nTATCATAT\tUnknown\t\tUnknown\t472\r\nGACGGCAT\tUnknown\t\tUnknown\t472\r\nTGCAGCAT\tUnknown\t\tUnknown\t472\r\nTACCGGAT\tUnknown\t\tUnknown\t471\r\nGATAATAT\tUnknown\t\tUnknown\t471\r\nCTAGGCTG\tN710\t\tUnknown\t470\r\nCTAGCAAT\tUnknown\t\tUnknown\t468\r\nCATCTTAT\tUnknown\t\tUnknown\t467\r\nCCAGCAAT\tUnknown\t\tUnknown\t467\r\nCAACGGAT\tUnknown\t\tUnknown\t465\r\nCAAAAGCT\tUnknown\t\tUnknown\t465\r\nCACGCGAT\tUnknown\t\tUnknown\t464\r\nATGAGGAT\tUnknown\t\tUnknown\t464\r\nCATGTCAT\tUnknown\t\tUnknown\t463\r\nGTGGAGGA\tN712\t\tUnknown\t463\r\nCCCCGAAT\tUnknown\t\tUnknown\t461\r\nTAATCAAT\tUnknown\t\tUnknown\t459\r\nGAAAAGAT\tUnknown\t\tUnknown\t457\r\nTACAGTAT\tUnknown\t\tUnknown\t456\r\nAAGATGCA\tN711\t\tUnknown\t456\r\nCAGGCGGG\tUnknown\t\tUnknown\t456\r\nGTAGAAGA\tN712\t\tUnknown\t455\r\nAAAGGCAA\tUnknown\t\tUnknown\t455\r\nATTCTTAT\tUnknown\t\tUnknown\t454\r\nCATACGAT\tUnknown\t\tUnknown\t454\r\nCCCAACAA\tUnknown\t\tUnknown\t453\r\nATGAGGCA\tN711\t\tUnknown\t452\r\nCGAGTCTG\tN710\t\tUnknown\t451\r\nCTCTGTAC\tN707\t\tUnknown\t449\r\nCCTCTTCC\tUnknown\t\tUnknown\t449\r\nATTCCCTA\tUnknown\t\tUnknown\t447\r\nGCAACAAT\tUnknown\t\tUnknown\t447\r\nCTAGCCAT\tUnknown\t\tUnknown\t444\r\nCAGGGGAG\tUnknown\t\tUnknown\t443\r\nCACCGAAT\tUnknown\t\tUnknown\t442\r\nATGACCAT\tUnknown\t\tUnknown\t438\r\nAACCGGAT\tUnknown\t\tUnknown\t437\r\nCAGAGCGT\tUnknown\t\tUnknown\t435\r\nCTGGCTAT\tUnknown\t\tUnknown\t434\r\nAGAGCATC\tUnknown\t\tUnknown\t434\r\nCCTACGAT\tUnknown\t\tUnknown\t434\r\nTCTGATAT\tUnknown\t\tUnknown\t434\r\nGAGGCGCT\tUnknown\t\tUnknown\t430\r\nTCCCGAAA\tUnknown\t\tUnknown\t429\r\nCACCGGAG\tUnknown\t\tUnknown\t429\r\nGCTACGTT\tN709\t\tUnknown\t429\r\nCATTGTAT\tUnknown\t\tUnknown\t429\r\nCGGAATAA\tUnknown\t\tUnknown\t428\r\nCTCTACAT\tUnknown\t\tUnknown\t428\r\nCAGACGCT\tUnknown\t\tUnknown\t427\r\nTAATTAAT\tUnknown\t\tUnknown\t424\r\nCCAACAAA\tUnknown\t\tUnknown\t420\r\nATAGAGGA\tD502,N712\t\tUnknown\t420\r\nAAGAGTCA\tN711\t\tUnknown\t417\r\nGTAGACGA\tN712\t\tUnknown\t414\r\nCATGGGAT\tUnknown\t\tUnknown\t414\r\nTCATTATC\tUnknown\t\tUnknown\t413\r\nCGGAGTAT\tUnknown\t\tUnknown\t412\r\nTAGAATAT\tUnknown\t\tUnknown\t412\r\nCAAAGGAT\tUnknown\t\tUnknown\t412\r\nGAAAAGGA\tUnknown\t\tUnknown\t411\r\nGCAGAGGT\tUnknown\t\tUnknown\t411\r\nCTACTAAT\tUnknown\t\tUnknown\t411\r\nGGACTCGT\tN705\t\tUnknown\t411\r\nCAGGGCGG\tUnknown\t\tUnknown\t409\r\nGAACTAAT\tUnknown\t\tUnknown\t408\r\nTAATCCAT\tUnknown\t\tUnknown\t408\r\nCGTGGCTG\tN710\t\tUnknown\t407\r\nCCTTTCCT\tD503\t\tUnknown\t406\r\nTCCGAATC\tUnknown\t\tUnknown\t405\r\nCGACTCAT\tUnknown\t\tUnknown\t404\r\nCACCGGCT\tUnknown\t\tUnknown\t402\r\nTCTCGAAT\tUnknown\t\tUnknown\t401\r\nGAAGAGGG\tUnknown\t\tUnknown\t398\r\nCTCTCTGC\tN707\t\tUnknown\t397\r\nGCTGATAT\tUnknown\t\tUnknown\t396\r\nCAGACAAG\tUnknown\t\tUnknown\t396\r\nGATGGCAT\tUnknown\t\tUnknown\t395\r\nCGGTATAT\tUnknown\t\tUnknown\t394\r\nGTATAGGA\tN712\t\tUnknown\t394\r\nCAACTAAA\tUnknown\t\tUnknown\t393\r\nCCTGGCAT\tUnknown\t\tUnknown\t393\r\nCATACGCT\tUnknown\t\tUnknown\t392\r\nCTGAATAT\tUnknown\t\tUnknown\t391\r\nGATTTTAT\tUnknown\t\tUnknown\t390\r\nCATTTTTA\tUnknown\t\tUnknown\t390\r\nTACGCATG\tN706\t\tUnknown\t387\r\nTCATCCAT\tUnknown\t\tUnknown\t387\r\nTCCTCTCT\tUnknown\t\tUnknown\t387\r\nTAATGGAT\tUnknown\t\tUnknown\t387\r\nCAATTCAT\tUnknown\t\tUnknown\t386\r\nCTTTCTAT\tE502,S502,[N|S|E]502\t\tUnknown\t386\r\nCAGCTAAT\tUnknown\t\tUnknown\t386\r\nGCTACGGT\tN709\t\tUnknown\t385\r\nCATGGCCT\tUnknown\t\tUnknown\t383\r\nCAGGATCT\tUnknown\t\tUnknown\t383\r\nGAGGACAT\tUnknown\t\tUnknown\t382\r\nAAGAGAGA\tUnknown\t\tUnknown\t382\r\nGAGGAGAT\tUnknown\t\tUnknown\t382\r\nCAAAAGAA\tUnknown\t\tUnknown\t381\r\nATGAACAT\tUnknown\t\tUnknown\t380\r\nCCAAGAAT\tUnknown\t\tUnknown\t379\r\nTCATTTAT\tUnknown\t\tUnknown\t379\r\nGAGCTCCT\tUnknown\t\tUnknown\t378\r\nCCAATAAT\tUnknown\t\tUnknown\t377\r\nTAGAGAAG\tUnknown\t\tUnknown\t375\r\nGACGATAT\tUnknown\t\tUnknown\t375\r\nCGTGGCAT\tUnknown\t\tUnknown\t375\r\nGAGGAGGA\tUnknown\t\tUnknown\t375\r\nCCAACTAA\tUnknown\t\tUnknown\t374\r\nGTAGAGTA\tN712\t\tUnknown\t371\r\nCTCTTTAC\tE505,N707,S505,[N|S|E]505\t\tUnknown\t371\r\nGCAACGAT\tUnknown\t\tUnknown\t369\r\nATGAGTAT\tUnknown\t\tUnknown\t368\r\nACAGCATC\tUnknown\t\tUnknown\t366\r\nCAGAGGGT\tUnknown\t\tUnknown\t366\r\nCAAAATAT\tUnknown\t\tUnknown\t365\r\nTAAAGAAT\tUnknown\t\tUnknown\t365\r\nCAGGCTGA\tUnknown\t\tUnknown\t363\r\nGAACTCAT\tUnknown\t\tUnknown\t363\r\nGACGCTAT\tUnknown\t\tUnknown\t357\r\nTAATCTAT\tUnknown\t\tUnknown\t355\r\nCATTGCAT\tUnknown\t\tUnknown\t355\r\nCAACAGAT\tUnknown\t\tUnknown\t354\r\nGGAATCAT\tUnknown\t\tUnknown\t353\r\nACTTATAT\tUnknown\t\tUnknown\t352\r\nCCCCCTCT\tUnknown\t\tUnknown\t352\r\nGAATCGAT\tUnknown\t\tUnknown\t351\r\nAAATCGAT\tUnknown\t\tUnknown\t351\r\nCATTATCT\tUnknown\t\tUnknown\t349\r\nCAGAGATC\tUnknown\t\tUnknown\t348\r\nCAGGGCTG\tUnknown\t\tUnknown\t348\r\nTAGAGGCA\tN711\t\tUnknown\t347\r\nCAGGGCGA\tUnknown\t\tUnknown\t347\r\nTCCTCCCT\tUnknown\t\tUnknown\t346\r\nCCGACAAT\tUnknown\t\tUnknown\t345\r\nGAAGGGGA\tUnknown\t\tUnknown\t345\r\nCAGAGGAA\tUnknown\t\tUnknown\t345\r\nGTAGAGCA\tN712\t\tUnknown\t345\r\nTACGCTAT\tUnknown\t\tUnknown\t344\r\nGCTAAGAT\tUnknown\t\tUnknown\t343\r\nCGAGGTTG\tN710\t\tUnknown\t342\r\nGTCTCTTC\tUnknown\t\tUnknown\t342\r\nTAGAGATG\tUnknown\t\tUnknown\t341\r\nTTATCGAT\tUnknown\t\tUnknown\t341\r\nTACGCATC\tUnknown\t\tUnknown\t341\r\nTCCCGTAT\tUnknown\t\tUnknown\t341\r\nCATTCATC\tUnknown\t\tUnknown\t339\r\nTGATCGAT\tUnknown\t\tUnknown\t339\r\nCAGAGTAG\tUnknown\t\tUnknown\t337\r\nCAACGAAT\tUnknown\t\tUnknown\t337\r\nCACCGATC\tUnknown\t\tUnknown\t337\r\nATGCGCAT\tN722\t\tUnknown\t336\r\nCATCTCGT\tUnknown\t\tUnknown\t334\r\nCATGGATC\tUnknown\t\tUnknown\t334\r\nCAGGGAAT\tUnknown\t\tUnknown\t333\r\nCGAAAGAT\tUnknown\t\tUnknown\t333\r\nATTCCATC\tUnknown\t\tUnknown\t333\r\nCACCCGAT\tUnknown\t\tUnknown\t332\r\nGGACCTAT\tUnknown\t\tUnknown\t332\r\nCATAGTAT\tUnknown\t\tUnknown\t332\r\nACATTCAT\tUnknown\t\tUnknown\t331\r\nACTCTTCC\tUnknown\t\tUnknown\t331\r\nCTACCTAT\tUnknown\t\tUnknown\t329\r\nGAAGCGGA\tUnknown\t\tUnknown\t329\r\nCAAGCAAT\tUnknown\t\tUnknown\t328\r\nCACCGCAT\tUnknown\t\tUnknown\t328\r\nCAGACATG\tUnknown\t\tUnknown\t327\r\nTCCCCGAA\tD710\t\tUnknown\t326\r\nGGAATGCT\tUnknown\t\tUnknown\t325\r\nAAGAGGTA\tN711\t\tUnknown\t325\r\nTAATCATC\tUnknown\t\tUnknown\t325\r\nCCTGCTAT\tUnknown\t\tUnknown\t325\r\nCTCTCTCT\tE502,S502,[N|S|E]502\t\tUnknown\t323\r\nGAGAGGGG\tUnknown\t\tUnknown\t322\r\nCTAGCTAA\tUnknown\t\tUnknown\t322\r\nACTGTATC\tUnknown\t\tUnknown\t322\r\nATTTCTAT\tUnknown\t\tUnknown\t321\r\nCAAGTAAT\tUnknown\t\tUnknown\t320\r\nCAGAGGAG\tUnknown\t\tUnknown\t319\r\nATGAGCCA\tUnknown\t\tUnknown\t318\r\nTAGGCCAT\tUnknown\t\tUnknown\t318\r\nACTCCTAT\tUnknown\t\tUnknown\t318\r\nATTAATAT\tUnknown\t\tUnknown\t316\r\nCTAGAGGA\tN712\t\tUnknown\t316\r\nATGAGATC\tUnknown\t\tUnknown\t316\r\nCCGGAATA\tUnknown\t\tUnknown\t315\r\nCATAAGAT\tUnknown\t\tUnknown\t315\r\nATTCATCT\tUnknown\t\tUnknown\t315\r\nCAGGCGGA\tUnknown\t\tUnknown\t313\r\nTAGCCATG\tN706\t\tUnknown\t312\r\nCAGCGAGT\tUnknown\t\tUnknown\t311\r\nCAGCGGAT\tUnknown\t\tUnknown\t310\r\nCTAGCTAC\tUnknown\t\tUnknown\t309\r\nTAAATCAT\tUnknown\t\tUnknown\t308\r\nGCCGCTAT\tD502\t\tUnknown\t307\r\nTAACCGAT\tUnknown\t\tUnknown\t307\r\nTACAGCCA\tUnknown\t\tUnknown\t307\r\nCAGGCCGA\tUnknown\t\tUnknown\t306\r\nCTTGCTAT\tUnknown\t\tUnknown\t304\r\nGATAGGCT\tUnknown\t\tUnknown\t304\r\nTCGGCCTG\tUnknown\t\tUnknown\t302\r\nCAGATCTC\tUnknown\t\tUnknown\t302\r\nGAGGGAGG\tUnknown\t\tUnknown\t301\r\nCAGAGTAT\tUnknown\t\tUnknown\t301\r\nTATGCATT\tE506,S506,[N|S|E]506\t\tUnknown\t300\r\nAAGAGACG\tUnknown\t\tUnknown\t299\r\nTAGTTCAT\tUnknown\t\tUnknown\t297\r\nCCTCCTCT\tUnknown\t\tUnknown\t297\r\nTAGGGAGG\tUnknown\t\tUnknown\t296\r\nATGATCAT\tUnknown\t\tUnknown\t296\r\nAGAGGATG\tE503,S503,[N|S|E]503\t\tUnknown\t294\r\nACTATATC\tUnknown\t\tUnknown\t292\r\nTACAATAT\tUnknown\t\tUnknown\t292\r\nCATCCTAT\tUnknown\t\tUnknown\t291\r\nCGAGTCTT\tUnknown\t\tUnknown\t291\r\nGCCCGAAT\tUnknown\t\tUnknown\t291\r\nCCAACTAT\tUnknown\t\tUnknown\t290\r\nTACAGAAG\tUnknown\t\tUnknown\t290\r\nCATAGAGT\tS516\t\tUnknown\t289\r\nGACTACAT\tUnknown\t\tUnknown\t288\r\nGACGCATC\tUnknown\t\tUnknown\t288\r\nTTGAGCAT\tUnknown\t\tUnknown\t287\r\nGTGAGCAT\tUnknown\t\tUnknown\t285\r\nTCCCCAAT\tUnknown\t\tUnknown\t285\r\nTAGGAAAG\tUnknown\t\tUnknown\t284\r\nTCATACAT\tUnknown\t\tUnknown\t284\r\nCAAAACAT\tUnknown\t\tUnknown\t283\r\nGGCCTCAT\tUnknown\t\tUnknown\t282\r\nCAGAGCAG\tUnknown\t\tUnknown\t282\r\nTAGAGAAT\tUnknown\t\tUnknown\t281\r\nTCTTCATC\tUnknown\t\tUnknown\t280\r\nCATACTAT\tUnknown\t\tUnknown\t280\r\nGGAATAAT\tUnknown\t\tUnknown\t279\r\nACGATATC\tUnknown\t\tUnknown\t278\r\nTCCCGATA\tUnknown\t\tUnknown\t277\r\nAAGAGAAG\tUnknown\t\tUnknown\t277\r\nAGTCCTAT\tUnknown\t\tUnknown\t276\r\nGTAGCGGT\tUnknown\t\tUnknown\t276\r\nGACCACAT\tUnknown\t\tUnknown\t276\r\nCCAAAGAT\tUnknown\t\tUnknown\t275\r\nGTAGCTAT\tUnknown\t\tUnknown\t274\r\nAGTGATAT\tUnknown\t\tUnknown\t273\r\nCTTTTATC\tUnknown\t\tUnknown\t273\r\nTATTCGAT\tUnknown\t\tUnknown\t273\r\nGGACTAAT\tUnknown\t\tUnknown\t273\r\nCACCGGAA\tUnknown\t\tUnknown\t272\r\nGAAGAAGA\tUnknown\t\tUnknown\t272\r\nCCATGGCA\tUnknown\t\tUnknown\t271\r\nTCATTCCA\tUnknown\t\tUnknown\t271\r\nTTAGCTAT\tUnknown\t\tUnknown\t270\r\nTATACGAT\tUnknown\t\tUnknown\t270\r\nCATCTAAT\tS510\t\tUnknown\t269\r\nCATCGCAT\tUnknown\t\tUnknown\t268\r\nGGAATACT\tUnknown\t\tUnknown\t268\r\nAAGGCAAT\tS520\t\tUnknown\t267\r\nATTTCCTA\tUnknown\t\tUnknown\t267\r\nATGCCTAT\tUnknown\t\tUnknown\t267\r\nTCTCCGCT\tUnknown\t\tUnknown\t267\r\nCAGGAGAG\tUnknown\t\tUnknown\t266\r\nGCTGCTAT\tUnknown\t\tUnknown\t265\r\nTCGCGAAT\tUnknown\t\tUnknown\t265\r\nATCTCGTA\tUnknown\t\tUnknown\t265\r\nGAGGAAGG\tUnknown\t\tUnknown\t264\r\nGGACTTAT\tUnknown\t\tUnknown\t264\r\nTATATTAT\tUnknown\t\tUnknown\t263\r\nTTCCTATC\tUnknown\t\tUnknown\t262\r\nCAAGCATG\tUnknown\t\tUnknown\t261\r\nCAACTCCT\tUnknown\t\tUnknown\t260\r\nCTTCTCCT\tD505\t\tUnknown\t260\r\nAAGGCGCA\tUnknown\t\tUnknown\t259\r\nCCACCAAT\tUnknown\t\tUnknown\t259\r\nCCAAAAGA\tUnknown\t\tUnknown\t258\r\nGCGACATC\tUnknown\t\tUnknown\t257\r\nCAGAAAAT\tUnknown\t\tUnknown\t256\r\nCATAGAAT\tUnknown\t\tUnknown\t256\r\nATCAGCAT\tUnknown\t\tUnknown\t256\r\nAGGAGCAT\tUnknown\t\tUnknown\t256\r\nCGGGGATG\tUnknown\t\tUnknown\t256\r\nTACAGCAC\tUnknown\t\tUnknown\t255\r\nCGAACAAT\tUnknown\t\tUnknown\t254\r\nACGGATAT\tUnknown\t\tUnknown\t254\r\nCGATGCTG\tN710\t\tUnknown\t253\r\nCAGTCTAT\tUnknown\t\tUnknown\t252\r\nCTAGCTCT\tUnknown\t\tUnknown\t251\r\nCTTGGCAT\tUnknown\t\tUnknown\t251\r\nTAGAGGAT\tUnknown\t\tUnknown\t251\r\nCAAAGCAT\tUnknown\t\tUnknown\t251\r\nCTCGCTAT\tE502,S502,[N|S|E]502\t\tUnknown\t250\r\nCCGGCGCT\tUnknown\t\tUnknown\t250\r\nGCGCTATC\tUnknown\t\tUnknown\t249\r\nAAGAGAAT\tUnknown\t\tUnknown\t248\r\nCACAGAGG\tN708\t\tUnknown\t247\r\nTATTATAT\tUnknown\t\tUnknown\t247\r\nTCCCAAAT\tUnknown\t\tUnknown\t247\r\nCTCTCTTC\tN707\t\tUnknown\t246\r\nCATTCCTA\tUnknown\t\tUnknown\t246\r\nGGAGTCAT\tUnknown\t\tUnknown\t245\r\nGGAGACAT\tUnknown\t\tUnknown\t245\r\nCAATTAAT\tUnknown\t\tUnknown\t244\r\nCTATAATA\tUnknown\t\tUnknown\t243\r\nATTCCTAC\tUnknown\t\tUnknown\t243\r\nGATCTCGT\tUnknown\t\tUnknown\t242\r\nGAGAGGAT\tUnknown\t\tUnknown\t242\r\nTAGGCGTT\tUnknown\t\tUnknown\t241\r\nCATTCGAT\tUnknown\t\tUnknown\t241\r\nCACCGTAT\tUnknown\t\tUnknown\t241\r\nAAGGCGAA\tUnknown\t\tUnknown\t241\r\nCAACAAAT\tUnknown\t\tUnknown\t241\r\nCTAGGTAT\tUnknown\t\tUnknown\t240\r\nCAAGGAGG\tUnknown\t\tUnknown\t240\r\nTAGACGAT\tUnknown\t\tUnknown\t240\r\nCGAGGATC\tUnknown\t\tUnknown\t239\r\nGAGAGGCT\tUnknown\t\tUnknown\t238\r\nGAAGCGAT\tUnknown\t\tUnknown\t238\r\nTGACTCAT\tUnknown\t\tUnknown\t238\r\nTAGGCTTG\tN706\t\tUnknown\t237\r\nGGGATCCT\tUnknown\t\tUnknown\t237\r\nTACAGCGT\tUnknown\t\tUnknown\t237\r\nCGGGAGAT\tUnknown\t\tUnknown\t237\r\nTCCCTAAT\tUnknown\t\tUnknown\t236\r\nCAGAGAGC\tN708\t\tUnknown\t236\r\nTACTCGAT\tUnknown\t\tUnknown\t236\r\nCAGGGCAG\tUnknown\t\tUnknown\t236\r\nCTCACTAT\tE502,S502,[N|S|E]502\t\tUnknown\t236\r\nGCCACGAT\tUnknown\t\tUnknown\t236\r\nGGAGACCT\tUnknown\t\tUnknown\t236\r\nGACCGGAT\tUnknown\t\tUnknown\t235\r\nTAGACAGG\tUnknown\t\tUnknown\t235\r\nCCCTCTAC\tN707\t\tUnknown\t235\r\nTACTTCAT\tUnknown\t\tUnknown\t234\r\nCAAAGAAG\tUnknown\t\tUnknown\t234\r\nGTAGGAAT\tUnknown\t\tUnknown\t234\r\nCAGAGGCG\tUnknown\t\tUnknown\t234\r\nCACTCTAT\tE502,S502,[N|S|E]502\t\tUnknown\t233\r\nTATTCATC\tUnknown\t\tUnknown\t233\r\nTCATTTCA\tUnknown\t\tUnknown\t233\r\nGAAGAAAT\tUnknown\t\tUnknown\t233\r\nAACAGGCA\tN711\t\tUnknown\t233\r\nCGAGGAGG\tUnknown\t\tUnknown\t232\r\nGGATTCAT\tUnknown\t\tUnknown\t232\r\nGGAGAGGG\tUnknown\t\tUnknown\t231\r\nCAGTTTAT\tUnknown\t\tUnknown\t231\r\nATATATAA\tUnknown\t\tUnknown\t231\r\nCCCGAATC\tUnknown\t\tUnknown\t230\r\nCAGGAGAA\tUnknown\t\tUnknown\t229\r\nTCCTATCT\tUnknown\t\tUnknown\t228\r\nCAGGCGCA\tUnknown\t\tUnknown\t228\r\nGGAACGCT\tUnknown\t\tUnknown\t227\r\nTAACTCAT\tUnknown\t\tUnknown\t227\r\nGACGTCAT\tUnknown\t\tUnknown\t227\r\nTATCTCGT\tUnknown\t\tUnknown\t226\r\nTCATGCAT\tUnknown\t\tUnknown\t226\r\nCAGAAAAG\tUnknown\t\tUnknown\t225\r\nATTCTCCT\tUnknown\t\tUnknown\t225\r\nATAATATC\tUnknown\t\tUnknown\t225\r\nCAGAGACA\tUnknown\t\tUnknown\t225\r\nGCGACGCG\tUnknown\t\tUnknown\t225\r\nCAGAGGCT\tUnknown\t\tUnknown\t224\r\nACGACATC\tUnknown\t\tUnknown\t224\r\nCAGGATAT\tUnknown\t\tUnknown\t224\r\nAAGACGCT\tUnknown\t\tUnknown\t224\r\nACTTCTCT\tUnknown\t\tUnknown\t224\r\nTACACGAT\tUnknown\t\tUnknown\t223\r\nCACGCCAT\tUnknown\t\tUnknown\t223\r\nCAAGGCAG\tUnknown\t\tUnknown\t222\r\nGAGGCATT\tUnknown\t\tUnknown\t220\r\nCTCATTCA\tUnknown\t\tUnknown\t220\r\nTAATCGGT\tUnknown\t\tUnknown\t220\r\nTCAGCATC\tUnknown\t\tUnknown\t219\r\nCAGTCTAC\tUnknown\t\tUnknown\t219\r\nACTGTTAT\tUnknown\t\tUnknown\t219\r\nACCCGAAT\tUnknown\t\tUnknown\t219\r\nTAAAGGAT\tUnknown\t\tUnknown\t219\r\nGGAGGCTT\tUnknown\t\tUnknown\t218\r\nCTTACTAT\tUnknown\t\tUnknown\t217\r\nCACGGGAT\tUnknown\t\tUnknown\t217\r\nCTACAGCA\tUnknown\t\tUnknown\t216\r\nGAAGCATG\tUnknown\t\tUnknown\t215\r\nTAGGCCTT\tUnknown\t\tUnknown\t215\r\nGAACTACT\tUnknown\t\tUnknown\t214\r\nCAGGCATT\tUnknown\t\tUnknown\t214\r\nCAACTAGT\tUnknown\t\tUnknown\t214\r\nGACGACCA\tUnknown\t\tUnknown\t213\r\nCCTACAAT\tUnknown\t\tUnknown\t213\r\nCTGATATC\tUnknown\t\tUnknown\t213\r\nTATTTCAT\tUnknown\t\tUnknown\t212\r\nATCCCTAT\tUnknown\t\tUnknown\t212\r\nTAAGCATT\tUnknown\t\tUnknown\t211\r\nCAGCGAAT\tUnknown\t\tUnknown\t210\r\nTTCCGAAT\tUnknown\t\tUnknown\t210\r\nACCGATAT\tUnknown\t\tUnknown\t210\r\nGACGACGT\tUnknown\t\tUnknown\t210\r\nCAGACGGT\tUnknown\t\tUnknown\t209\r\nCAACCGAT\tUnknown\t\tUnknown\t209\r\nTCCATTCA\tUnknown\t\tUnknown\t208\r\nGTAGCGAA\tUnknown\t\tUnknown\t208\r\nTATAATGT\tUnknown\t\tUnknown\t208\r\nCTCCCTAT\tE502,S502,[N|S|E]502\t\tUnknown\t207\r\nGCAAAGCT\tUnknown\t\tUnknown\t207\r\nGACGAAAG\tUnknown\t\tUnknown\t206\r\nCAAGCCAT\tUnknown\t\tUnknown\t206\r\nTAATCGAC\tUnknown\t\tUnknown\t205\r\nGGAGACGA\tUnknown\t\tUnknown\t205\r\nCAGATAGT\tUnknown\t\tUnknown\t205\r\nCCTAGCTA\tUnknown\t\tUnknown\t205\r\nCATGGCCA\tUnknown\t\tUnknown\t205\r\nCATTTTTT\tUnknown\t\tUnknown\t204\r\nCCAGCGAT\tUnknown\t\tUnknown\t204\r\nCCTACTAT\tUnknown\t\tUnknown\t204\r\nGCAACACT\tUnknown\t\tUnknown\t203\r\nACTCATAT\tUnknown\t\tUnknown\t202\r\nGTAGATAA\tUnknown\t\tUnknown\t202\r\nGATGATAT\tUnknown\t\tUnknown\t202\r\nCATGAGAT\tUnknown\t\tUnknown\t202\r\nGACACATC\tUnknown\t\tUnknown\t202\r\nTGAGCATC\tUnknown\t\tUnknown\t201\r\nCCGACGCT\tUnknown\t\tUnknown\t201\r\nGTACAGGA\tN712\t\tUnknown\t200\r\nCGAGGCCT\tUnknown\t\tUnknown\t200\r\nGTAGTGGA\tN712\t\tUnknown\t200\r\nCAAGTCAT\tUnknown\t\tUnknown\t200\r\nCTCTCTAG\tE502,N707,S502,[N|S|E]502\t\tUnknown\t200\r\nTAGGTGAT\tUnknown\t\tUnknown\t200\r\nGAGAGAGT\tUnknown\t\tUnknown\t199\r\nGCAGCGCT\tUnknown\t\tUnknown\t198\r\nAGGCGATA\tD501\t\tUnknown\t198\r\nCCCCTTCT\tUnknown\t\tUnknown\t198\r\nCATCGGAT\tUnknown\t\tUnknown\t197\r\nCTAGTTAT\tUnknown\t\tUnknown\t197\r\nTAATCGTT\tUnknown\t\tUnknown\t196\r\nTATACGCT\tUnknown\t\tUnknown\t196\r\nGGTCCTAT\tUnknown\t\tUnknown\t195\r\nTAAACAAT\tUnknown\t\tUnknown\t195\r\nGCTCCTAT\tUnknown\t\tUnknown\t195\r\nGGAAGCCT\tUnknown\t\tUnknown\t195\r\nCGACGCTG\tN710\t\tUnknown\t195\r\nTAAGTCAT\tUnknown\t\tUnknown\t194\r\nTATAAATA\tUnknown\t\tUnknown\t194\r\nCATTTTAC\tUnknown\t\tUnknown\t193\r\nCTAATCGA\tA505\t\tUnknown\t193\r\nGTTACGAT\tUnknown\t\tUnknown\t193\r\nCACTGATA\tUnknown\t\tUnknown\t193\r\nTCCTGAAT\tUnknown\t\tUnknown\t193\r\nCAACTTAT\tUnknown\t\tUnknown\t192\r\nCACAGAAT\tUnknown\t\tUnknown\t192\r\nGGACTATC\tUnknown\t\tUnknown\t192\r\nCATGAGCA\tUnknown\t\tUnknown\t192\r\nCGGATCTC\tUnknown\t\tUnknown\t192\r\nCTAGTATC\tUnknown\t\tUnknown\t192\r\nATAGCATC\tUnknown\t\tUnknown\t192\r\nGCCTCCCT\tUnknown\t\tUnknown\t192\r\nGTACTCAT\tUnknown\t\tUnknown\t191\r\nACCTGATA\tUnknown\t\tUnknown\t191\r\nGAGGAATG\tUnknown\t\tUnknown\t191\r\nTAAGGCAT\tUnknown\t\tUnknown\t191\r\nCACCAGAT\tUnknown\t\tUnknown\t190\r\nTAATATCT\tUnknown\t\tUnknown\t189\r\nCCAACGCT\tUnknown\t\tUnknown\t188\r\nCACTTTAT\tUnknown\t\tUnknown\t187\r\nATCTCTAA\tUnknown\t\tUnknown\t187\r\nGGGCTACT\tUnknown\t\tUnknown\t187\r\nTCTACGAT\tUnknown\t\tUnknown\t186\r\nGTCTCTAT\tD502,E502,S502,[N|S|E]502\t\tUnknown\t186\r\nATGAGCAC\tUnknown\t\tUnknown\t186\r\nTCATTCAC\tUnknown\t\tUnknown\t185\r\nCGAGCTAT\tUnknown\t\tUnknown\t185\r\nTATGCTAT\tUnknown\t\tUnknown\t185\r\nTACTGCAT\tUnknown\t\tUnknown\t185\r\nCGAGGAAG\tUnknown\t\tUnknown\t185\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/single_index/expected.txt", "content": "sample_name\texpected_barcode_1\texpected_barcode_1_name\texpected_barcodes_read_count\tguessed_barcode_1\tguessed_barcode_1_name\tguessed_barcodes_read_count\tmatch_type\r\nEBOV-VP24UTR_G10218A-C10220U.DMSO\tCAAAAGAT\tRPI28\t264750\t\t\t\talternative_indices_uncertain\r\nEBOV-VP24UTR_G10218A-C10242U.DMSO\tCACCGGAT\tRPI30\t187070\t\t\t\talternative_indices_uncertain\r\nEBOV-VP24UTR_G10218A-C10242U.NMIA\tCTAGCTAT\tRPI38\t268529\t\t\t\talternative_indices_uncertain\r\nEBOV-VP24UTR_G10218A-C10242U.DENAT\tTCCCGAAT\tRPI46\t287559\t\t\t\talternative_indices_uncertain\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/single_index/metrics.txt", "content": "## htsjdk.samtools.metrics.StringHeader\n# ExtractIlluminaBarcodes BASECALLS_DIR=tmp/00_flowcells/171110_M04004_0212_000000000-BDTT8/Data/Intensities/BaseCalls OUTPUT_DIR=/tmp/8574290.1.broad/tmp-illumina-illumina_demux-8574290-0-5ctjr6gn/extracted_barcodes-qt71mddp LANE=1 READ_STRUCTURE=150T8B150T BARCODE_FILE=/tmp/8574290.1.broad/tmp-illumina-illumina_demux-8574290-0-5ctjr6gn/barcodeData.BDTT8.1x4fc_7rw.txt METRICS_FILE=/idi/sabeti-scratch/alin/software/viral-ngs-etc/projects/190206-LCMV-C2c2/reports/barcodes/barcodes-metrics-BDTT8.1.txt MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=20 NUM_PROCESSORS=0 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\n## htsjdk.samtools.metrics.StringHeader\n# Started on: Sat Feb 16 00:09:44 EST 2019\n\n## METRICS CLASS\tpicard.illumina.ExtractIlluminaBarcodes$BarcodeMetric\nBARCODE\tBARCODE_WITHOUT_DELIMITER\tBARCODE_NAME\tLIBRARY_NAME\tREADS\tPF_READS\tPERFECT_MATCHES\tPF_PERFECT_MATCHES\tONE_MISMATCH_MATCHES\tPF_ONE_MISMATCH_MATCHES\tPCT_MATCHES\tRATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_PCT_MATCHES\tPF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_NORMALIZED_MATCHES\nGGACTCCT\tGGACTCCT\tpTOPO-LCMV-Arm-emGFP-S-NoEnds_P3-IC-170825-cloned_171103\tpTOPO-LCMV-Arm-emGFP-S-NoEnds_P3-IC-170825-cloned_171103.l1\t1282976\t1239382\t1282976\t1239382\t0\t0\t0.060095\t0.655219\t0.065356\t0.652624\t1.904065\nTAGGCATG\tTAGGCATG\tpcDNA34-MGC-ADAR2-V5\tpcDNA34-MGC-ADAR2-V5.l1\t1192766\t1159442\t1192766\t1159442\t0\t0\t0.055869\t0.609149\t0.06114\t0.61053\t1.781253\nCTCTCTAC\tCTCTCTAC\tpT7CFE-MGC-ADAR2\tpT7CFE-MGC-ADAR2.l1\t1051975\t1009354\t1051975\t1009354\t0\t0\t0.049275\t0.537247\t0.053226\t0.531497\t1.550672\nCAGAGAGG\tCAGAGAGG\tp20_3E5E_fLuc2\tp20_3E5E_fLuc2.l1\t1958086\t1899076\t1958086\t1899076\t0\t0\t0.091717\t1\t0.100143\t1\t2.917554\nGCTACGCT\tGCTACGCT\tp20_3E5E_rLuc-fLuc2_6\tp20_3E5E_rLuc-fLuc2_6.l1\t1184157\t1158385\t1184157\t1158385\t0\t0\t0.055466\t0.604752\t0.061084\t0.609973\t1.779629\nCGAGGCTG\tCGAGGCTG\tp20_3E5E_rLuc-fLuc2_5\tp20_3E5E_rLuc-fLuc2_5.l1\t941504\t917972\t941504\t917972\t0\t0\t0.0441\t0.480829\t0.048407\t0.483378\t1.410282\nAAGAGGCA\tAAGAGGCA\tp20_3E5E_rLuc-fLuc2_7\tp20_3E5E_rLuc-fLuc2_7.l1\t765762\t744083\t765762\t744083\t0\t0\t0.035868\t0.391077\t0.039237\t0.391813\t1.143136\nGTAGAGGA\tGTAGAGGA\tp20_3E5E_rLuc-fLuc2_8\tp20_3E5E_rLuc-fLuc2_8.l1\t940017\t917850\t940017\t917850\t0\t0\t0.044031\t0.480069\t0.0484\t0.483314\t1.410095\nACTGATAT\tACTGATAT\tEBOV-VP24UTR_G10218.DMSO\tEBOV-VP24UTR_G10218.DMSO.l1\t538711\t517696\t538711\t517696\t0\t0\t0.025233\t0.275121\t0.027299\t0.272604\t0.795337\nATGAGCAT\tATGAGCAT\tEBOV-VP24UTR_G10218A.DMSO\tEBOV-VP24UTR_G10218A.DMSO.l1\t382966\t366987\t382966\t366987\t0\t0\t0.017938\t0.195582\t0.019352\t0.193245\t0.563803\nATTCCTAT\tATTCCTAT\tEBOV-VP24UTR_G10218A-A10232G.DMSO\tEBOV-VP24UTR_G10218A-A10232G.DMSO.l1\t490275\t472589\t490275\t472589\t0\t0\t0.022965\t0.250385\t0.024921\t0.248852\t0.726039\nCAAAAGAT\tCAAAAGAT\tEBOV-VP24UTR_G10218A-C10220U.DMSO\tEBOV-VP24UTR_G10218A-C10220U.DMSO.l1\t264750\t255281\t264750\t255281\t0\t0\t0.012401\t0.135209\t0.013462\t0.134424\t0.392189\nCAACTAAT\tCAACTAAT\tEBOV-VP24UTR_G10218A-A10240G.DMSO\tEBOV-VP24UTR_G10218A-A10240G.DMSO.l1\t353697\t337630\t353697\t337630\t0\t0\t0.016567\t0.180634\t0.017804\t0.177786\t0.518702\nCACCGGAT\tCACCGGAT\tEBOV-VP24UTR_G10218A-C10242U.DMSO\tEBOV-VP24UTR_G10218A-C10242U.DMSO.l1\t187070\t179344\t187070\t179344\t0\t0\t0.008762\t0.095537\t0.009457\t0.094438\t0.275526\nCAGGCGAT\tCAGGCGAT\tEBOV-VP24UTR_G10218.NMIA\tEBOV-VP24UTR_G10218.NMIA.l1\t1179793\t1125673\t1179793\t1125673\t0\t0\t0.055262\t0.602524\t0.059359\t0.592748\t1.729373\nCATGGCAT\tCATGGCAT\tEBOV-VP24UTR_G10218A.NMIA\tEBOV-VP24UTR_G10218A.NMIA.l1\t386930\t371948\t386930\t371948\t0\t0\t0.018124\t0.197606\t0.019614\t0.195857\t0.571424\nCATTTTAT\tCATTTTAT\tEBOV-VP24UTR_G10218A-A10232G.NMIA\tEBOV-VP24UTR_G10218A-A10232G.NMIA.l1\t561855\t537740\t561855\t537740\t0\t0\t0.026317\t0.286941\t0.028356\t0.283159\t0.826131\nCCAACAAT\tCCAACAAT\tEBOV-VP24UTR_G10218A-C10220U.NMIA\tEBOV-VP24UTR_G10218A-C10220U.NMIA.l1\t395259\t379142\t395259\t379142\t0\t0\t0.018514\t0.20186\t0.019993\t0.199646\t0.582477\nCGGAATAT\tCGGAATAT\tEBOV-VP24UTR_G10218A-A10240G.NMIA\tEBOV-VP24UTR_G10218A-A10240G.NMIA.l1\t487124\t470904\t487124\t470904\t0\t0\t0.022817\t0.248776\t0.024832\t0.247965\t0.723451\nCTAGCTAT\tCTAGCTAT\tEBOV-VP24UTR_G10218A-C10242U.NMIA\tEBOV-VP24UTR_G10218A-C10242U.NMIA.l1\t268529\t257633\t268529\t257633\t0\t0\t0.012578\t0.137139\t0.013586\t0.135662\t0.395802\nGACGACAT\tGACGACAT\tEBOV-VP24UTR_G10218.DENAT\tEBOV-VP24UTR_G10218.DENAT.l1\t471442\t454685\t471442\t454685\t0\t0\t0.022082\t0.240767\t0.023977\t0.239424\t0.698533\nTAATCGAT\tTAATCGAT\tEBOV-VP24UTR_G10218A.DENAT\tEBOV-VP24UTR_G10218A.DENAT.l1\t349709\t334453\t349709\t334453\t0\t0\t0.01638\t0.178597\t0.017637\t0.176114\t0.513821\nTACAGCAT\tTACAGCAT\tEBOV-VP24UTR_G10218A-A10232G.DENAT\tEBOV-VP24UTR_G10218A-A10232G.DENAT.l1\t588492\t559195\t588492\t559195\t0\t0\t0.027565\t0.300545\t0.029488\t0.294456\t0.859092\nTATAATAT\tTATAATAT\tEBOV-VP24UTR_G10218A-C10220U.DENAT\tEBOV-VP24UTR_G10218A-C10220U.DENAT.l1\t482453\t460095\t482453\t460095\t0\t0\t0.022598\t0.24639\t0.024262\t0.242273\t0.706845\nTCATTCAT\tTCATTCAT\tEBOV-VP24UTR_G10218A-A10240G.DENAT\tEBOV-VP24UTR_G10218A-A10240G.DENAT.l1\t541051\t519095\t541051\t519095\t0\t0\t0.025343\t0.276316\t0.027373\t0.273341\t0.797487\nTCCCGAAT\tTCCCGAAT\tEBOV-VP24UTR_G10218A-C10242U.DENAT\tEBOV-VP24UTR_G10218A-C10242U.DENAT.l1\t287559\t278125\t287559\t278125\t0\t0\t0.013469\t0.146857\t0.014666\t0.146453\t0.427284\nNNNNNNNN\tNNNNNNNN\t\t\t3814272\t2039896\t0\t0\t0\t0\t0.178661\t1.947959\t0.107569\t1.074152\t0\n\n\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/single_index_i5_only/barcodes.txt", "content": "Barcode1\tLikely_Index_Names1\tBarcode2\tLikely_Index_Names2\tCount\r\nGACGGTTA\tBI5B07\t\tUnknown\t232258\r\nGAACTTCG\tBI5B06\t\tUnknown\t226749\r\nTTAGCCAG\tBI5B05\t\tUnknown\t176648\r\nTCTTTCCC\tUnknown\t\tUnknown\t100792\r\nCAAGCTTA\tBI5B08\t\tUnknown\t21771\r\nTCCTTTTC\tUnknown\t\tUnknown\t662\r\nTCCCTTCT\tUnknown\t\tUnknown\t630\r\nTTCTCCCT\tUnknown\t\tUnknown\t626\r\nTACGGTTA\tBI5B07,X5135,X7346\t\tUnknown\t596\r\nTAACTTCG\tBI5B06,X5016,X5355,X7126\t\tUnknown\t535\r\nGTACTTCG\tBI5B06,X5337\t\tUnknown\t319\r\nGTCGGTTA\tBI5B07,X5188,X7293\t\tUnknown\t183\r\nTTAGCCTG\tBI5B05\t\tUnknown\t155\r\nGCCTTTTC\tUnknown\t\tUnknown\t151\r\nGCCCTTCT\tX5312,X7169\t\tUnknown\t143\r\nGACCTTCG\tBI5B06\t\tUnknown\t137\r\nTTAGCCAA\tBI5B05\t\tUnknown\t137\r\nGACGTTTA\tBI5B07\t\tUnknown\t135\r\nTCTTTTCC\tUnknown\t\tUnknown\t133\r\nGAAAGGAG\tBI5H02,E505,S505,[N|S|E]505\t\tUnknown\t129\r\nGACGGTTT\tBI5B07\t\tUnknown\t126\r\nTCTTTCCT\tUnknown\t\tUnknown\t119\r\nGAACTTCA\tBI5B06\t\tUnknown\t117\r\nGAAGGGGA\tBI5F04\t\tUnknown\t112\r\nTAGCCAGA\tUnknown\t\tUnknown\t111\r\nGACGGCTA\tBI5B07\t\tUnknown\t100\r\nGAACTTTG\tBI5B06\t\tUnknown\t98\r\nGAGGGGGA\tUnknown\t\tUnknown\t97\r\nGCACTTCG\tBI5B06,X5258,X7223\t\tUnknown\t97\r\nTCTTTCTC\tUnknown\t\tUnknown\t96\r\nGACGGTAA\tBI5B07,BI7C04,X5188,X7293\t\tUnknown\t85\r\nATAGCCAG\tBI5E07\t\tUnknown\t84\r\nGAACTTCT\tBI5B06\t\tUnknown\t79\r\nTCTTCCCT\tUnknown\t\tUnknown\t78\r\nAACGGTTA\tBI5B07,X5004,X5204,X7277\t\tUnknown\t76\r\nTTAGCTAG\tBI5B05,X5094,X7003\t\tUnknown\t76\r\nCCCTCTTC\tX5140\t\tUnknown\t75\r\nTTACTTCG\tX5355,X7126\t\tUnknown\t73\r\nTTAGCCAT\tBI5B05,RPI3,X5373\t\tUnknown\t73\r\nTTAGTCAG\tBI5B05,BI7D11\t\tUnknown\t71\r\nCGACGGTT\tUnknown\t\tUnknown\t70\r\nGAAACTTC\tX5359\t\tUnknown\t70\r\nTTTTTCCC\tUnknown\t\tUnknown\t68\r\nGAACTCGA\tUnknown\t\tUnknown\t67\r\nGAAAAAAG\tUnknown\t\tUnknown\t65\r\nGATGGTTA\tBI5B07\t\tUnknown\t65\r\nTTATCCAG\tBI5B05\t\tUnknown\t65\r\nAAACTTCG\tBI5B06\t\tUnknown\t64\r\nGGAGAAAG\tUnknown\t\tUnknown\t64\r\nACGGTTAA\tUnknown\t\tUnknown\t62\r\nGACTTCGA\tX5282\t\tUnknown\t62\r\nGTAGCCAG\tBI5B05,BI5E07\t\tUnknown\t61\r\nCGAACTTC\tBI5D12\t\tUnknown\t60\r\nTTAACCAG\tBI5B05,BI7D11\t\tUnknown\t60\r\nGAACTTCC\tBI5B06\t\tUnknown\t59\r\nGAAGGAAA\tBI7C10,X5057,X7040\t\tUnknown\t57\r\nGACCGTTA\tBI5B07,BI7G10,X5031\t\tUnknown\t56\r\nCCCCCCCC\tUnknown\t\tUnknown\t55\r\nGACGGTTG\tBI5B07,BI7G10,X5135,X7346\t\tUnknown\t55\r\nGACGTTAA\tBI5E12\t\tUnknown\t55\r\nGACGGGTT\tUnknown\t\tUnknown\t54\r\nGATCTTCG\tBI5B06,X5337\t\tUnknown\t54\r\nGAACGGTT\tX5003\t\tUnknown\t52\r\nGAACTTGA\tX5225\t\tUnknown\t52\r\nGACGGTCA\tBI5B07,X5204,X7277\t\tUnknown\t52\r\nGAAGGTTA\tBI5B07,X5359,X7122\t\tUnknown\t51\r\nGACAGTTA\tBI5B07,BI7C04\t\tUnknown\t51\r\nAACTTCGA\tX5187\t\tUnknown\t48\r\nGACTGTTA\tBI5B07\t\tUnknown\t48\r\nACTTTCCC\tUnknown\t\tUnknown\t47\r\nGAATTTCG\tBI5B06,BI5D12\t\tUnknown\t47\r\nGACCTTTA\tUnknown\t\tUnknown\t46\r\nCTTAGCCA\tUnknown\t\tUnknown\t45\r\nGAAAAGAG\tX5230,X7251\t\tUnknown\t45\r\nGCCGGTTA\tBI5B07,X5004\t\tUnknown\t45\r\nGCTTTCCC\tUnknown\t\tUnknown\t44\r\nGAACCTCG\tBI5B06,X5005,X7092\t\tUnknown\t43\r\nAGAGAAAG\tUnknown\t\tUnknown\t42\r\nGACGATTA\tBI5B07\t\tUnknown\t41\r\nTGAGAAAG\tUnknown\t\tUnknown\t41\r\nTTTGCCAG\tBI5B05\t\tUnknown\t41\r\nGACGGATA\tBI5B07,X5031\t\tUnknown\t40\r\nTTAGCCCG\tBI5B05\t\tUnknown\t40\r\nGGAACTTC\tA507,BI5D12\t\tUnknown\t39\r\nGGTTAACA\tUnknown\t\tUnknown\t39\r\nTAACTTCT\tUnknown\t\tUnknown\t39\r\nTTAGCAGA\tUnknown\t\tUnknown\t39\r\nTTAGCCGG\tBI5B05\t\tUnknown\t38\r\nTTCGGTTA\tX5268\t\tUnknown\t38\r\nTTCGCCTG\tUnknown\t\tUnknown\t37\r\nCTTTCCCT\tUnknown\t\tUnknown\t36\r\nTTAAGCCA\tUnknown\t\tUnknown\t36\r\nAAAAAAAA\tUnknown\t\tUnknown\t35\r\nGAACTTTC\tX5359\t\tUnknown\t35\r\nGAGGTTAA\tUnknown\t\tUnknown\t35\r\nTAAGCTTA\tBI5B08,D506\t\tUnknown\t34\r\nTTCGGCTA\tX5268\t\tUnknown\t34\r\nTTGCCAGA\tX5179\t\tUnknown\t34\r\nGAAAGAAG\tBI7C10,X5057,X5288,X7040\t\tUnknown\t33\r\nGAGCTTCG\tBI5B06\t\tUnknown\t33\r\nTCTTTCAC\tUnknown\t\tUnknown\t33\r\nTTAGCCAC\tBI5B05\t\tUnknown\t33\r\nTTAGGCCA\tUnknown\t\tUnknown\t33\r\nGACTTTTA\tUnknown\t\tUnknown\t32\r\nGGACGGTT\tX5003\t\tUnknown\t32\r\nGGCGGTTA\tBI5B07\t\tUnknown\t31\r\nTCCTTCCC\tUnknown\t\tUnknown\t31\r\nTTAGCCCA\tUnknown\t\tUnknown\t31\r\nTTAGCCGA\tUnknown\t\tUnknown\t31\r\nTTATCCAT\tUnknown\t\tUnknown\t31\r\nAAAGAAAG\tUnknown\t\tUnknown\t30\r\nGGACTTCG\tBI5B06,X5355,X7126\t\tUnknown\t30\r\nGACGGTTC\tBI5B07,X5359,X7122\t\tUnknown\t29\r\nGCGGTTAA\tUnknown\t\tUnknown\t29\r\nTCAGCCAG\tBI5B05\t\tUnknown\t29\r\nGAATTCGA\tD706,X5076,X7021\t\tUnknown\t28\r\nTCTCTCCC\tS511\t\tUnknown\t28\r\nTTCGCCAG\tBI5B05,X5373\t\tUnknown\t28\r\nTTTCCCTA\tUnknown\t\tUnknown\t28\r\nCACGGTTA\tBI5B07\t\tUnknown\t27\r\nCTAGCCAG\tBI5B05,BI5E07\t\tUnknown\t27\r\nCACGCTTA\tBI5B08,BI7B02\t\tUnknown\t26\r\nTTCGCCTA\tX5268\t\tUnknown\t26\r\nTTTAGCCA\tUnknown\t\tUnknown\t26\r\nCCTTTCCC\tUnknown\t\tUnknown\t25\r\nGAAGAAAG\tBI7C10,X5057,X7040\t\tUnknown\t25\r\nGAAGGAAG\tBI7C10,X5057,X7040\t\tUnknown\t25\r\nGAAGGAGA\tUnknown\t\tUnknown\t25\r\nTACTTTTA\tUnknown\t\tUnknown\t25\r\nTTTTCCCT\tUnknown\t\tUnknown\t25\r\nGTCGGCTA\tX5268\t\tUnknown\t24\r\nGAACTTAG\tBI5B06\t\tUnknown\t23\r\nTACGGCTA\tX5268\t\tUnknown\t23\r\nCTCTTTCC\tUnknown\t\tUnknown\t22\r\nGACCGGTT\tX5003\t\tUnknown\t22\r\nTCTTCCCC\tUnknown\t\tUnknown\t22\r\nTAAGCCAG\tBI5B05\t\tUnknown\t21\r\nTCTCTTCC\tUnknown\t\tUnknown\t21\r\nTTACCAGA\tUnknown\t\tUnknown\t21\r\nTTACCCAG\tBI5B05,X5156,X7325\t\tUnknown\t21\r\nTTGGCCAG\tBI5B05\t\tUnknown\t21\r\nAAGCTTAA\tUnknown\t\tUnknown\t20\r\nGAACTCCG\tBI5B06\t\tUnknown\t20\r\nGACCTTTG\tBI7G10\t\tUnknown\t20\r\nTTCTCCCC\tUnknown\t\tUnknown\t20\r\nCTAGCTTA\tBI5B08,X5094\t\tUnknown\t19\r\nGCTCTTCG\tX5337\t\tUnknown\t19\r\nTCCCTTCC\tUnknown\t\tUnknown\t19\r\nGAAGGGAG\tBI7C10,X5057,X7040\t\tUnknown\t18\r\nTTAGCAAG\tBI5B05\t\tUnknown\t18\r\nGAAGGGAA\tUnknown\t\tUnknown\t17\r\nTGTTTCCC\tUnknown\t\tUnknown\t17\r\nTTACTTAG\tUnknown\t\tUnknown\t17\r\nTTTTTCAC\tUnknown\t\tUnknown\t17\r\nGAGGGAAA\tUnknown\t\tUnknown\t17\r\nCAACTTCG\tBI5B06,X5150\t\tUnknown\t16\r\nGACCTTCA\tUnknown\t\tUnknown\t16\r\nGACGCTTA\tBI5B07\t\tUnknown\t16\r\nTAGGGAAA\tUnknown\t\tUnknown\t16\r\nTCCCTTTC\tUnknown\t\tUnknown\t16\r\nAAAGAGGA\tUnknown\t\tUnknown\t16\r\nGAGGGAGA\tUnknown\t\tUnknown\t15\r\nAAAGCTTA\tBI5B08\t\tUnknown\t13\r\nCAACCCCC\tUnknown\t\tUnknown\t13\r\nGCTCTTCC\tUnknown\t\tUnknown\t13\r\nTAAGAAAG\tUnknown\t\tUnknown\t13\r\nTTACTCCG\tUnknown\t\tUnknown\t13\r\nTTAGCCTA\tUnknown\t\tUnknown\t13\r\nAAGGGAAA\tUnknown\t\tUnknown\t13\r\nGAACCTTC\tX5359\t\tUnknown\t12\r\nGACGGGGA\tUnknown\t\tUnknown\t12\r\nTCCTTTCC\tUnknown\t\tUnknown\t12\r\nTTAGACAG\tBI5B05\t\tUnknown\t12\r\nCAAGCTTT\tBI5B08\t\tUnknown\t11\r\nCAAGTTTA\tBI5B08\t\tUnknown\t11\r\nGAACTACG\tBI5B06\t\tUnknown\t11\r\nNACGGTTA\tBI5B07\t\tUnknown\t11\r\nTTAGTCCG\tUnknown\t\tUnknown\t11\r\nTTAGTTAG\tBI5H08\t\tUnknown\t11\r\nGAAGGTTG\tBI5E01,X5359,X7122\t\tUnknown\t10\r\nGAAGTTCG\tBI5D12\t\tUnknown\t10\r\nCAATCTTA\tBI5B08,D506\t\tUnknown\t9\r\nCCACCCAC\tUnknown\t\tUnknown\t9\r\nGAACGTCG\tBI5B06,X5005,X5016,X7092\t\tUnknown\t9\r\nGCACTTCC\tUnknown\t\tUnknown\t9\r\nGCCGGTTC\tUnknown\t\tUnknown\t9\r\nNAACTTCG\tBI5B06\t\tUnknown\t9\r\nTCACTTCG\tX5355,X7126\t\tUnknown\t9\r\nTCTTTCCA\tUnknown\t\tUnknown\t9\r\nCAAGCTAA\tBI5B08\t\tUnknown\t8\r\nGAAATTCG\tBI5B06,BI5D12,X5258,X7223\t\tUnknown\t8\r\nGAAGAGAG\tUnknown\t\tUnknown\t8\r\nGACCTTCT\tBI5C11,X5312,X7169\t\tUnknown\t8\r\nGACGGGTA\tBI5B07\t\tUnknown\t8\r\nTCACTTCT\tRP3-v4\t\tUnknown\t8\r\nTCTTACCC\tE517,S517,[N|S|E]517\t\tUnknown\t8\r\nTTACTCAG\tBI7D11\t\tUnknown\t8\r\nTTAGGCAG\tBI5B05,RPI3\t\tUnknown\t8\r\nTTCCCCCT\tX5138\t\tUnknown\t8\r\nTTCTCCCG\tX5207,X7274\t\tUnknown\t8\r\nTTCTTTCC\tUnknown\t\tUnknown\t8\r\nAAGAGAAA\tUnknown\t\tUnknown\t8\r\nCACCCCCC\tUnknown\t\tUnknown\t7\r\nGACGCTCT\tX5080,X7017\t\tUnknown\t7\r\nGCCTCTTC\tX5140\t\tUnknown\t7\r\nGCCTGTTA\tUnknown\t\tUnknown\t7\r\nGTCGCCTA\tUnknown\t\tUnknown\t7\r\nTGAGCCAG\tBI5B05,X5094,X7003\t\tUnknown\t7\r\nTTAGCGAG\tBI5B05,X5156,X7325\t\tUnknown\t7\r\nTTATCCCT\tUnknown\t\tUnknown\t7\r\nTTCGGCTG\tX5268\t\tUnknown\t7\r\nGAGAGAAA\tUnknown\t\tUnknown\t7\r\nACTTCGAC\tX5071\t\tUnknown\t6\r\nCAGCTTAA\tUnknown\t\tUnknown\t6\r\nCCAAGCTT\tX5252\t\tUnknown\t6\r\nCCCTTTTC\tUnknown\t\tUnknown\t6\r\nGAAATGAG\tX5109\t\tUnknown\t6\r\nGAACATCG\tX5005,X7092\t\tUnknown\t6\r\nGAACCCCG\tUnknown\t\tUnknown\t6\r\nGAACTTTA\tUnknown\t\tUnknown\t6\r\nGACGTTTG\tUnknown\t\tUnknown\t6\r\nGATCTTCC\tX5086\t\tUnknown\t6\r\nGTAGTTAG\tUnknown\t\tUnknown\t6\r\nTAAGGCAA\tN701\t\tUnknown\t6\r\nTATTTCCC\tUnknown\t\tUnknown\t6\r\nTCATTCCC\tUnknown\t\tUnknown\t6\r\nTCCTTTTA\tUnknown\t\tUnknown\t6\r\nTCTTTAAC\tUnknown\t\tUnknown\t6\r\nTCTTTACC\tUnknown\t\tUnknown\t6\r\nCACCCCTA\tX5277,X7204\t\tUnknown\t6\r\nACTCTTTC\tUnknown\t\tUnknown\t5\r\nCAAAGCTT\tUnknown\t\tUnknown\t5\r\nCAAGCCTA\tBI5B08\t\tUnknown\t5\r\nCAAGTTAA\tUnknown\t\tUnknown\t5\r\nCAGGCTTA\tBI5B08,BI7B02\t\tUnknown\t5\r\nCATGCTTA\tBI7B02\t\tUnknown\t5\r\nCCAGCTTA\tBI5B08\t\tUnknown\t5\r\nCCTCCCCC\tUnknown\t\tUnknown\t5\r\nGAAACTCG\tUnknown\t\tUnknown\t5\r\nGAAAGGCG\tUnknown\t\tUnknown\t5\r\nGAAAGGGA\tUnknown\t\tUnknown\t5\r\nGAAAGTCG\tBI5F09\t\tUnknown\t5\r\nGAACGTTA\tBI5C09,X5225\t\tUnknown\t5\r\nGAACTTGG\tBI5B06,X5041,X5150,X7056\t\tUnknown\t5\r\nGAAGCTTA\tBI5B08\t\tUnknown\t5\r\nGACACTCT\tUnknown\t\tUnknown\t5\r\nGACCGTCA\tUnknown\t\tUnknown\t5\r\nGACGGAAC\tUnknown\t\tUnknown\t5\r\nGCCCCTCT\tUnknown\t\tUnknown\t5\r\nGCCCTTCC\tUnknown\t\tUnknown\t5\r\nGCCTGTTC\tUnknown\t\tUnknown\t5\r\nNTAGCCAG\tBI5B05,BI5E07\t\tUnknown\t5\r\nTATCTTCG\tUnknown\t\tUnknown\t5\r\nTCACTTCC\tUnknown\t\tUnknown\t5\r\nTCCTCTTC\tBI5F04,X5140\t\tUnknown\t5\r\nTCTATCCC\tUnknown\t\tUnknown\t5\r\nTCTCTTCG\tS511\t\tUnknown\t5\r\nTCTTTCGC\tE517,S517,[N|S|E]517\t\tUnknown\t5\r\nTTATCCAC\tX5290\t\tUnknown\t5\r\nTTATCCCG\tUnknown\t\tUnknown\t5\r\nTTTGTCAG\tX5169\t\tUnknown\t5\r\nCAAGAAAA\tUnknown\t\tUnknown\t4\r\nCAAGGTTA\tBI5B08\t\tUnknown\t4\r\nCACCCCCA\tUnknown\t\tUnknown\t4\r\nCCACCCCC\tUnknown\t\tUnknown\t4\r\nCCCCTTCC\tBI7F07\t\tUnknown\t4\r\nCTACCCAC\tX5290\t\tUnknown\t4\r\nGAACGGCG\tUnknown\t\tUnknown\t4\r\nGACGGCAA\tUnknown\t\tUnknown\t4\r\nGAGGGTTA\tBI5B07\t\tUnknown\t4\r\nGCAAGGAG\tBI5H02,E505,S505,X5109,[N|S|E]505\t\tUnknown\t4\r\nGCCGGCTC\tUnknown\t\tUnknown\t4\r\nGCTGGTTA\tUnknown\t\tUnknown\t4\r\nGGGGGGGG\tUnknown\t\tUnknown\t4\r\nGGGTTAAC\tBI5H03\t\tUnknown\t4\r\nGTACTTAG\tUnknown\t\tUnknown\t4\r\nGTAGTTCG\tBI5D12,X5056,X7041\t\tUnknown\t4\r\nGTCGCTTA\tUnknown\t\tUnknown\t4\r\nTAAGCCAA\tUnknown\t\tUnknown\t4\r\nTACCTTCT\tUnknown\t\tUnknown\t4\r\nTAGAGAAA\tUnknown\t\tUnknown\t4\r\nTCCGGTTC\tUnknown\t\tUnknown\t4\r\nTCCTCCCT\tX5374,X7107\t\tUnknown\t4\r\nTTACCCCG\tUnknown\t\tUnknown\t4\r\nTTAGCTCG\tX5222,X7259\t\tUnknown\t4\r\nTTCGCCAA\tX5373\t\tUnknown\t4\r\nTTCTCCAT\tX5373\t\tUnknown\t4\r\nTTGCCCGA\tUnknown\t\tUnknown\t4\r\nTTTTCCCC\tUnknown\t\tUnknown\t4\r\nAAAGGAAA\tUnknown\t\tUnknown\t4\r\nCAAACTTA\tBI5B08\t\tUnknown\t4\r\nCAAGCTTG\tBI5B08\t\tUnknown\t4\r\nGATGTTTA\tUnknown\t\tUnknown\t4\r\nGGAGGAAG\tBI7C10,X5057,X7040\t\tUnknown\t4\r\nAATACCAT\tBI5A09\t\tUnknown\t3\r\nAGGGGGCA\tUnknown\t\tUnknown\t3\r\nCAACTTCC\tUnknown\t\tUnknown\t3\r\nCAAGAGGA\tUnknown\t\tUnknown\t3\r\nCAAGCTCA\tBI5B08,X5094\t\tUnknown\t3\r\nCAAGGCTT\tUnknown\t\tUnknown\t3\r\nCACGGCTA\tX5063,X5367,X7034\t\tUnknown\t3\r\nCCCCCCTC\tUnknown\t\tUnknown\t3\r\nCCCCTTCT\tUnknown\t\tUnknown\t3\r\nCCTCTCCC\tUnknown\t\tUnknown\t3\r\nCCTTCTTC\tUnknown\t\tUnknown\t3\r\nCCTTTTTC\tUnknown\t\tUnknown\t3\r\nCTACCCCC\tUnknown\t\tUnknown\t3\r\nGAAACACT\tUnknown\t\tUnknown\t3\r\nGAAAGGGG\tUnknown\t\tUnknown\t3\r\nGAAGGCTA\tBI5C09\t\tUnknown\t3\r\nGAAGGTAA\tUnknown\t\tUnknown\t3\r\nGAAGTTAG\tBI5D12,X5041,X7056\t\tUnknown\t3\r\nGAAGTTTA\tUnknown\t\tUnknown\t3\r\nGAAGTTTG\tBI5D12,X5041,X7056\t\tUnknown\t3\r\nGACGGTAC\tUnknown\t\tUnknown\t3\r\nGACTCTTT\tUnknown\t\tUnknown\t3\r\nGCCCTTTC\tUnknown\t\tUnknown\t3\r\nGCTAGCAG\tBI5B01\t\tUnknown\t3\r\nGCTTAACA\tX5116\t\tUnknown\t3\r\nGCTTTCTC\tUnknown\t\tUnknown\t3\r\nGTAGCTAG\tUnknown\t\tUnknown\t3\r\nTAAGCTAG\tBI5B08,X5094,X7003\t\tUnknown\t3\r\nTAAGGAAA\tUnknown\t\tUnknown\t3\r\nTAAGGAAG\tBI7C10,X5057,X7040\t\tUnknown\t3\r\nTACGCTTA\tUnknown\t\tUnknown\t3\r\nTACGTTTA\tUnknown\t\tUnknown\t3\r\nTAGGTAAA\tUnknown\t\tUnknown\t3\r\nTAGTGAAA\tUnknown\t\tUnknown\t3\r\nTATGGCTA\tX5063,X7034\t\tUnknown\t3\r\nTATTTCTA\tUnknown\t\tUnknown\t3\r\nTCCCCCCC\tUnknown\t\tUnknown\t3\r\nTCCGGTTA\tX5004\t\tUnknown\t3\r\nTCGGGAAC\tUnknown\t\tUnknown\t3\r\nTCTGTCCC\tUnknown\t\tUnknown\t3\r\nTCTTTCCG\tS511\t\tUnknown\t3\r\nTTACCTCG\tUnknown\t\tUnknown\t3\r\nTTAGCGAC\tX5188\t\tUnknown\t3\r\nTTAGTTCG\tBI5H08,X5222,X7259\t\tUnknown\t3\r\nTTCAGACA\tUnknown\t\tUnknown\t3\r\nTTCGACAC\tUnknown\t\tUnknown\t3\r\nTTCGCTTG\tUnknown\t\tUnknown\t3\r\nAAAGAAAA\tUnknown\t\tUnknown\t3\r\nAAGTGAAA\tUnknown\t\tUnknown\t3\r\nAAGTTAAA\tUnknown\t\tUnknown\t3\r\nAGGGGAAA\tUnknown\t\tUnknown\t3\r\nGAACGACA\tUnknown\t\tUnknown\t3\r\nGAACTTAC\tUnknown\t\tUnknown\t3\r\nGACGGGCA\tUnknown\t\tUnknown\t3\r\nGACGTTCA\tUnknown\t\tUnknown\t3\r\nGAGGGGAA\tUnknown\t\tUnknown\t3\r\nGCCTTCTC\tX5193,X7288\t\tUnknown\t3\r\nGTAGGTTA\tUnknown\t\tUnknown\t3\r\nNCTTTCCC\tUnknown\t\tUnknown\t3\r\nTTAGCTTA\tUnknown\t\tUnknown\t3\r\nTTCGCTTA\tBI7D01\t\tUnknown\t3\r\nAACGGATA\tUnknown\t\tUnknown\t2\r\nACACTCTT\tUnknown\t\tUnknown\t2\r\nAGCCAGAC\tUnknown\t\tUnknown\t2\r\nAGGGGGAG\tUnknown\t\tUnknown\t2\r\nATCCTTAA\tBI5A12\t\tUnknown\t2\r\nCAACCTTA\tBI5B08,X5135\t\tUnknown\t2\r\nCAACTTCA\tX5183\t\tUnknown\t2\r\nCAAGCCTT\tUnknown\t\tUnknown\t2\r\nCACCCCTC\tA706\t\tUnknown\t2\r\nCACGGTTC\tBI5F05,X5111\t\tUnknown\t2\r\nCACTCTTT\tUnknown\t\tUnknown\t2\r\nCAGACACT\tBI7E05\t\tUnknown\t2\r\nCCATCTTC\tX5041\t\tUnknown\t2\r\nCCCCCTCC\tUnknown\t\tUnknown\t2\r\nCCCGGTTA\tX5004\t\tUnknown\t2\r\nCCGGGGCA\tUnknown\t\tUnknown\t2\r\nCGGGGGAG\tUnknown\t\tUnknown\t2\r\nCGGTTAAC\tX5299,X7182\t\tUnknown\t2\r\nGAAAAGCG\tUnknown\t\tUnknown\t2\r\nGAAAATCG\tX5005,X7092\t\tUnknown\t2\r\nGAACCGAC\tBI5D05\t\tUnknown\t2\r\nGAACCTAG\tX5168,X7313\t\tUnknown\t2\r\nGAACGTCA\tX5225\t\tUnknown\t2\r\nGAACGTTG\tBI7G10\t\tUnknown\t2\r\nGAACTACA\tUnknown\t\tUnknown\t2\r\nGAACTGCG\tBI5B06\t\tUnknown\t2\r\nGAAGGACA\tUnknown\t\tUnknown\t2\r\nGAAGGTCA\tUnknown\t\tUnknown\t2\r\nGAAGGTCG\tBI5D12\t\tUnknown\t2\r\nGAATCGAC\tBI5D05\t\tUnknown\t2\r\nGACAACAC\tUnknown\t\tUnknown\t2\r\nGACCGTCG\tBI7G10\t\tUnknown\t2\r\nGACCTTTC\tUnknown\t\tUnknown\t2\r\nGACGCCTA\tUnknown\t\tUnknown\t2\r\nGACGGACA\tUnknown\t\tUnknown\t2\r\nGACGGCAC\tUnknown\t\tUnknown\t2\r\nGACGTTCG\tBI5D12\t\tUnknown\t2\r\nGACGTTCT\tX5080,X7017\t\tUnknown\t2\r\nGACTTCTA\tUnknown\t\tUnknown\t2\r\nGATGGCTA\tX5063,X7034\t\tUnknown\t2\r\nGATTTTTC\tUnknown\t\tUnknown\t2\r\nGCACTGAG\tX5109\t\tUnknown\t2\r\nGCACTTCT\tBI7C01\t\tUnknown\t2\r\nGCCCGTTC\tUnknown\t\tUnknown\t2\r\nGCCCTTCG\tUnknown\t\tUnknown\t2\r\nGCCGGCTA\tUnknown\t\tUnknown\t2\r\nGCCTTCCC\tUnknown\t\tUnknown\t2\r\nGCCTTTTA\tUnknown\t\tUnknown\t2\r\nGTACCTAG\tUnknown\t\tUnknown\t2\r\nGTAGCCTA\tX5084\t\tUnknown\t2\r\nGTAGCTCG\tUnknown\t\tUnknown\t2\r\nGTCGACAC\tUnknown\t\tUnknown\t2\r\nTAACCTCG\tX5016\t\tUnknown\t2\r\nTAACTTCC\tA507\t\tUnknown\t2\r\nTAAGACAG\tA504\t\tUnknown\t2\r\nTAAGGCTA\tN701,S521\t\tUnknown\t2\r\nTAAGGTTA\tD506\t\tUnknown\t2\r\nTATCTTCC\tBI7D07\t\tUnknown\t2\r\nTATGTTTA\tUnknown\t\tUnknown\t2\r\nTATTTTCG\tUnknown\t\tUnknown\t2\r\nTATTTTTA\tUnknown\t\tUnknown\t2\r\nTCAGCCAC\tX5356\t\tUnknown\t2\r\nTCCGGCTA\tX5268\t\tUnknown\t2\r\nTCCGGCTC\tUnknown\t\tUnknown\t2\r\nTCCTCCCC\tUnknown\t\tUnknown\t2\r\nTCCTCCTC\tUnknown\t\tUnknown\t2\r\nTCCTTCTC\tX5193,X7288\t\tUnknown\t2\r\nTCTCCCTC\tUnknown\t\tUnknown\t2\r\nTCTGTCAC\tUnknown\t\tUnknown\t2\r\nTCTTTTTA\tUnknown\t\tUnknown\t2\r\nTGAGACAG\tUnknown\t\tUnknown\t2\r\nTGGGGGGG\tUnknown\t\tUnknown\t2\r\nTTACAGAC\tX5027,X5188,X7070\t\tUnknown\t2\r\nTTACCAAA\tUnknown\t\tUnknown\t2\r\nTTACCCAC\tBI7C05,X5188\t\tUnknown\t2\r\nTTACCCGG\tUnknown\t\tUnknown\t2\r\nTTAGCAAA\tUnknown\t\tUnknown\t2\r\nTTAGCCTT\tS520,X5216\t\tUnknown\t2\r\nTTAGCTGA\tBI7D01\t\tUnknown\t2\r\nTTAGCTTG\tBI5B08\t\tUnknown\t2\r\nTTAGGCAA\tRPI3\t\tUnknown\t2\r\nTTATTCAG\tBI7D11\t\tUnknown\t2\r\nTTATTCAT\tBI5A10,RPI45\t\tUnknown\t2\r\nTTCCCCAC\tUnknown\t\tUnknown\t2\r\nTTCCCCCC\tUnknown\t\tUnknown\t2\r\nTTCCCTAC\tUnknown\t\tUnknown\t2\r\nTTCGCTAA\tBI7D01\t\tUnknown\t2\r\nTTCGGTTG\tX5135,X7346\t\tUnknown\t2\r\nTTCTCCTC\tUnknown\t\tUnknown\t2\r\nTTCTCTTC\tUnknown\t\tUnknown\t2\r\nAAAAAATA\tUnknown\t\tUnknown\t2\r\nAAGAAAAA\tUnknown\t\tUnknown\t2\r\nAAGGTAAA\tBI5F12\t\tUnknown\t2\r\nAGAGAGAG\tBI5D03,E502,S502,[N|S|E]502\t\tUnknown\t2\r\nAGGGGGGG\tUnknown\t\tUnknown\t2\r\nCCACTTCC\tUnknown\t\tUnknown\t2\r\nCCCGGTTC\tUnknown\t\tUnknown\t2\r\nCTGCTCCT\tBI5A05\t\tUnknown\t2\r\nGAAAGAAA\tUnknown\t\tUnknown\t2\r\nGAAGAAAA\tUnknown\t\tUnknown\t2\r\nGAAGCCAG\tUnknown\t\tUnknown\t2\r\nGAAGGATA\tUnknown\t\tUnknown\t2\r\nGAAGGGGG\tUnknown\t\tUnknown\t2\r\nGACGACAC\tRPI41\t\tUnknown\t2\r\nGAGTGAAA\tUnknown\t\tUnknown\t2\r\nGATCTTTC\tX5086\t\tUnknown\t2\r\nGCAAAGAG\tX5109\t\tUnknown\t2\r\nGCCAGACA\tUnknown\t\tUnknown\t2\r\nGCCTTTCC\tUnknown\t\tUnknown\t2\r\nGGGGGGGA\tUnknown\t\tUnknown\t2\r\nGTAGCCTG\tUnknown\t\tUnknown\t2\r\nTACCTTCG\tUnknown\t\tUnknown\t2\r\nTACTTTTC\tUnknown\t\tUnknown\t2\r\nTATTTCCA\tUnknown\t\tUnknown\t2\r\nTATTTCTC\tUnknown\t\tUnknown\t2\r\nTCTGGCTC\tUnknown\t\tUnknown\t2\r\nTCTTCCTC\tUnknown\t\tUnknown\t2\r\nTCTTGCCC\tUnknown\t\tUnknown\t2\r\nTCTTTTTC\tUnknown\t\tUnknown\t2\r\nTTAACTCT\tUnknown\t\tUnknown\t2\r\nTTAGACAC\tA504,X5356\t\tUnknown\t2\r\nTTAGCCTC\tUnknown\t\tUnknown\t2\r\nTTGCCCGG\tUnknown\t\tUnknown\t2\r\nTTGGCCGG\tUnknown\t\tUnknown\t2\r\nTTTGCCAC\tUnknown\t\tUnknown\t2\r\nTTTTTTTT\tUnknown\t\tUnknown\t2\r\nAAAAGAAA\tUnknown\t\tUnknown\t1\r\nAAAGCCAG\tBI5E07\t\tUnknown\t1\r\nAACACTCT\tX5051\t\tUnknown\t1\r\nAACCTCTT\tBI5A03\t\tUnknown\t1\r\nAACCTTCA\tUnknown\t\tUnknown\t1\r\nAACTGAGC\tX5079,X7018\t\tUnknown\t1\r\nAACTTCCA\tUnknown\t\tUnknown\t1\r\nAAGGGGGG\tUnknown\t\tUnknown\t1\r\nAATTCAAC\tBI5C02\t\tUnknown\t1\r\nACCGGTTC\tX5004\t\tUnknown\t1\r\nACGGAACA\tX5089,X7008\t\tUnknown\t1\r\nACGGGGAG\tUnknown\t\tUnknown\t1\r\nACGGGGAT\tUnknown\t\tUnknown\t1\r\nACGTGAAG\tX5118,X7363\t\tUnknown\t1\r\nAGGGGATG\tUnknown\t\tUnknown\t1\r\nATGACGTC\tX5040,X7057\t\tUnknown\t1\r\nCAACCCCG\tUnknown\t\tUnknown\t1\r\nCAACCTCC\tBI5E01,X5292\t\tUnknown\t1\r\nCAACGCCG\tUnknown\t\tUnknown\t1\r\nCAACTCCC\tBI7B08,X5183\t\tUnknown\t1\r\nCAAGAAGA\tX5257\t\tUnknown\t1\r\nCAAGAGAA\tX5207\t\tUnknown\t1\r\nCAAGCAAC\tUnknown\t\tUnknown\t1\r\nCAAGCTAG\tX5168,X7313\t\tUnknown\t1\r\nCAAGCTTC\tBI5B08\t\tUnknown\t1\r\nCAAGGGGG\tUnknown\t\tUnknown\t1\r\nCACCGCCC\tUnknown\t\tUnknown\t1\r\nCACCGTTC\tX5003,X7094\t\tUnknown\t1\r\nCAGGGGGG\tUnknown\t\tUnknown\t1\r\nCAGGGGTG\tUnknown\t\tUnknown\t1\r\nCATACCAC\tX5042,X7055\t\tUnknown\t1\r\nCATCCCCC\tUnknown\t\tUnknown\t1\r\nCATTTTCA\tUnknown\t\tUnknown\t1\r\nCCAGACAC\tX5356\t\tUnknown\t1\r\nCCCCCTTC\tUnknown\t\tUnknown\t1\r\nCCCCGTTC\tUnknown\t\tUnknown\t1\r\nCCCCTCCC\tUnknown\t\tUnknown\t1\r\nCCCGCCCC\tUnknown\t\tUnknown\t1\r\nCCCGGGTA\tUnknown\t\tUnknown\t1\r\nCCCTTCCC\tUnknown\t\tUnknown\t1\r\nCCGGGGAA\tUnknown\t\tUnknown\t1\r\nCCTGCTTC\tUnknown\t\tUnknown\t1\r\nCCTGGCCC\tUnknown\t\tUnknown\t1\r\nCCTTCCTC\tX5248,X7233\t\tUnknown\t1\r\nCCTTTCAC\tUnknown\t\tUnknown\t1\r\nCGAAACTT\tUnknown\t\tUnknown\t1\r\nCGAACTTG\tBI5D12\t\tUnknown\t1\r\nCGAGCTTA\tBI5B08\t\tUnknown\t1\r\nCGAGGGTT\tUnknown\t\tUnknown\t1\r\nCGCAGATC\tUnknown\t\tUnknown\t1\r\nCGGCTTCT\tX5112,X7369\t\tUnknown\t1\r\nCGGGGATA\tUnknown\t\tUnknown\t1\r\nCGGGGCGG\tUnknown\t\tUnknown\t1\r\nCGGGGGGG\tUnknown\t\tUnknown\t1\r\nCGGTTCTT\tBI5A02\t\tUnknown\t1\r\nCTAGCCAC\tX5290\t\tUnknown\t1\r\nCTAGCCCC\tUnknown\t\tUnknown\t1\r\nCTATTAGC\tBI5C07\t\tUnknown\t1\r\nCTCCCTAC\tBI5H02,BI7G02,E505,N707,S505,[N|S|E]505\t\tUnknown\t1\r\nCTGGGGGG\tUnknown\t\tUnknown\t1\r\nCTTCGACA\tX5011,X7086\t\tUnknown\t1\r\nGAAAAAGA\tUnknown\t\tUnknown\t1\r\nGAAACTCT\tUnknown\t\tUnknown\t1\r\nGAACACTC\tUnknown\t\tUnknown\t1\r\nGAACCTTG\tX5359\t\tUnknown\t1\r\nGAACTAAG\tX5288\t\tUnknown\t1\r\nGAACTCCC\tUnknown\t\tUnknown\t1\r\nGAACTCCT\tBI7D03,N705\t\tUnknown\t1\r\nGAACTCTT\tX5132,X7349\t\tUnknown\t1\r\nGAACTGAC\tD508,X5120\t\tUnknown\t1\r\nGAAGCTAG\tUnknown\t\tUnknown\t1\r\nGAAGTTCA\tBI5D12\t\tUnknown\t1\r\nGAATTTCC\tUnknown\t\tUnknown\t1\r\nGACCGTTG\tBI7G10\t\tUnknown\t1\r\nGACCTACA\tUnknown\t\tUnknown\t1\r\nGACGAACA\tX5047\t\tUnknown\t1\r\nGACGGACT\tX5047\t\tUnknown\t1\r\nGACGGCTT\tUnknown\t\tUnknown\t1\r\nGACGGGAA\tUnknown\t\tUnknown\t1\r\nGACGGTCG\tUnknown\t\tUnknown\t1\r\nGACGGTCT\tX5080,X7017\t\tUnknown\t1\r\nGACGTCCC\tUnknown\t\tUnknown\t1\r\nGACTCCTA\tUnknown\t\tUnknown\t1\r\nGACTGACA\tX5283,X7198\t\tUnknown\t1\r\nGACTGTTC\tUnknown\t\tUnknown\t1\r\nGAGGGGTA\tUnknown\t\tUnknown\t1\r\nGAGTGACA\tUnknown\t\tUnknown\t1\r\nGATGTTCA\tUnknown\t\tUnknown\t1\r\nGATGTTCG\tBI5D12,X5056,X7041\t\tUnknown\t1\r\nGATTAACA\tUnknown\t\tUnknown\t1\r\nGATTTCCA\tBI7G11\t\tUnknown\t1\r\nGATTTCGA\tX5262\t\tUnknown\t1\r\nGCACAGAG\tUnknown\t\tUnknown\t1\r\nGCACCTCC\tUnknown\t\tUnknown\t1\r\nGCACCTTC\tX5359\t\tUnknown\t1\r\nGCACGTTC\tX5225,X7256\t\tUnknown\t1\r\nGCAGCCAG\tUnknown\t\tUnknown\t1\r\nGCCCTCCC\tUnknown\t\tUnknown\t1\r\nGCCTGCTC\tUnknown\t\tUnknown\t1\r\nGCCTTTCT\tUnknown\t\tUnknown\t1\r\nGCGGGAAA\tUnknown\t\tUnknown\t1\r\nGCGTGTTC\tUnknown\t\tUnknown\t1\r\nGCTCTCTT\tBI5E02\t\tUnknown\t1\r\nGCTCTTTC\tUnknown\t\tUnknown\t1\r\nGCTGGTTC\tBI5C05\t\tUnknown\t1\r\nGCTTGTTC\tUnknown\t\tUnknown\t1\r\nGCTTTCCG\tUnknown\t\tUnknown\t1\r\nGCTTTTTC\tUnknown\t\tUnknown\t1\r\nGGCCTGCC\tUnknown\t\tUnknown\t1\r\nGGCTGATA\tX5202\t\tUnknown\t1\r\nGGGAGAAT\tUnknown\t\tUnknown\t1\r\nGGGCTACG\tUnknown\t\tUnknown\t1\r\nGGGGGGAG\tUnknown\t\tUnknown\t1\r\nGGGGGGGT\tUnknown\t\tUnknown\t1\r\nGTACCTCG\tUnknown\t\tUnknown\t1\r\nGTACTCCG\tX5255\t\tUnknown\t1\r\nGTACTTCT\tX5312,X7169\t\tUnknown\t1\r\nGTAGCCAA\tUnknown\t\tUnknown\t1\r\nGTAGCCGG\tUnknown\t\tUnknown\t1\r\nGTAGCTTG\tUnknown\t\tUnknown\t1\r\nGTAGGCAG\tUnknown\t\tUnknown\t1\r\nGTAGGCTA\tUnknown\t\tUnknown\t1\r\nGTAGTCCG\tX5255\t\tUnknown\t1\r\nGTCGCCTG\tUnknown\t\tUnknown\t1\r\nGTGGGGAG\tUnknown\t\tUnknown\t1\r\nGTGGGGGA\tUnknown\t\tUnknown\t1\r\nGTTCCCTA\tUnknown\t\tUnknown\t1\r\nTAACCCGA\tUnknown\t\tUnknown\t1\r\nTAACCTAG\tX5168,X5191,X7313\t\tUnknown\t1\r\nTAAGAAGA\tUnknown\t\tUnknown\t1\r\nTAAGCAGA\tBI7D08\t\tUnknown\t1\r\nTAAGCTTG\tBI5B08\t\tUnknown\t1\r\nTAAGGAAC\tBI7H05\t\tUnknown\t1\r\nTAAGGGAG\tUnknown\t\tUnknown\t1\r\nTAAGTCCG\tUnknown\t\tUnknown\t1\r\nTAAGTTAG\tUnknown\t\tUnknown\t1\r\nTAATTTCC\tA507\t\tUnknown\t1\r\nTACCCAGA\tUnknown\t\tUnknown\t1\r\nTACCTTTA\tUnknown\t\tUnknown\t1\r\nTACGGCAA\tUnknown\t\tUnknown\t1\r\nTACGGTTG\tX5135,X7346\t\tUnknown\t1\r\nTACTTCGA\tUnknown\t\tUnknown\t1\r\nTACTTCTA\tUnknown\t\tUnknown\t1\r\nTAGATAAA\tUnknown\t\tUnknown\t1\r\nTAGCCTGA\tBI5B09,X5007\t\tUnknown\t1\r\nTAGGGCCA\tUnknown\t\tUnknown\t1\r\nTAGGGGGG\tUnknown\t\tUnknown\t1\r\nTAGTAAAA\tUnknown\t\tUnknown\t1\r\nTAGTAAAC\tUnknown\t\tUnknown\t1\r\nTAGTCCGA\tUnknown\t\tUnknown\t1\r\nTATCCCCC\tUnknown\t\tUnknown\t1\r\nTATCGCCG\tUnknown\t\tUnknown\t1\r\nTATCTCCA\tBI5G04\t\tUnknown\t1\r\nTATGTCCC\tUnknown\t\tUnknown\t1\r\nTATTGCTA\tUnknown\t\tUnknown\t1\r\nTATTTTCC\tUnknown\t\tUnknown\t1\r\nTCAGCCAT\tX5216\t\tUnknown\t1\r\nTCAGGTTC\tX5225,X7256\t\tUnknown\t1\r\nTCAGTCAG\tUnknown\t\tUnknown\t1\r\nTCAGTCCG\tX5174\t\tUnknown\t1\r\nTCATTTCG\tUnknown\t\tUnknown\t1\r\nTCCCTCCC\tUnknown\t\tUnknown\t1\r\nTCCCTCTC\tUnknown\t\tUnknown\t1\r\nTCCGTTTC\tUnknown\t\tUnknown\t1\r\nTCTCTCCG\tS511\t\tUnknown\t1\r\nTCTCTTCT\tUnknown\t\tUnknown\t1\r\nTCTGCCGC\tUnknown\t\tUnknown\t1\r\nTCTGTCTC\tUnknown\t\tUnknown\t1\r\nTCTTGCTA\tUnknown\t\tUnknown\t1\r\nTGAGAGAG\tUnknown\t\tUnknown\t1\r\nTGCCTGGT\tUnknown\t\tUnknown\t1\r\nTGGGGCAA\tUnknown\t\tUnknown\t1\r\nTGGGGGCG\tUnknown\t\tUnknown\t1\r\nTTAAAAAG\tUnknown\t\tUnknown\t1\r\nTTAAGAAG\tUnknown\t\tUnknown\t1\r\nTTAAGCCC\tUnknown\t\tUnknown\t1\r\nTTACAAAG\tUnknown\t\tUnknown\t1\r\nTTACCCAA\tUnknown\t\tUnknown\t1\r\nTTACCCAT\tUnknown\t\tUnknown\t1\r\nTTACCTAG\tX5156,X5191,X7325\t\tUnknown\t1\r\nTTAGAAAG\tUnknown\t\tUnknown\t1\r\nTTAGAGAG\tBI5D03,E502,S502,[N|S|E]502\t\tUnknown\t1\r\nTTAGCACT\tBI5H01\t\tUnknown\t1\r\nTTAGCAGG\tUnknown\t\tUnknown\t1\r\nTTAGCCCT\tBI5H01\t\tUnknown\t1\r\nTTAGGCTA\tX5268\t\tUnknown\t1\r\nTTAGTCAC\tBI5E11\t\tUnknown\t1\r\nTTAGTCTG\tBI5F03\t\tUnknown\t1\r\nTTATCCAA\tUnknown\t\tUnknown\t1\r\nTTCACTCT\tUnknown\t\tUnknown\t1\r\nTTCCAGCT\tBI5F01\t\tUnknown\t1\r\nTTCCCAGA\tBI5D02\t\tUnknown\t1\r\nTTCCCCTT\tBI5F12\t\tUnknown\t1\r\nTTCCTTCT\tX5138,X5312,X7169\t\tUnknown\t1\r\nTTCGCCAT\tX5373\t\tUnknown\t1\r\nTTCGCCTT\tBI5F12,X5015,X5373,X7082\t\tUnknown\t1\r\nTTCGCTTC\tUnknown\t\tUnknown\t1\r\nTTCGTTTT\tUnknown\t\tUnknown\t1\r\nTTCTAAGG\tX5091,X7006\t\tUnknown\t1\r\nTTCTTCTA\tUnknown\t\tUnknown\t1\r\nTTCTTGGC\tBI5B12\t\tUnknown\t1\r\nTTCTTTAT\tUnknown\t\tUnknown\t1\r\nTTGGCAAG\tUnknown\t\tUnknown\t1\r\nTTGGCCTG\tBI5F03,X5028\t\tUnknown\t1\r\nTTTCCAGA\tX5273,X7208\t\tUnknown\t1\r\nTTTTCCAG\tUnknown\t\tUnknown\t1\r\nAAAAATTA\tUnknown\t\tUnknown\t1\r\nAAAATAAA\tUnknown\t\tUnknown\t1\r\nAAAATAAG\tUnknown\t\tUnknown\t1\r\nAAAGAGAG\tBI5D03,E502,S502,[N|S|E]502\t\tUnknown\t1\r\nAAAGGGAG\tUnknown\t\tUnknown\t1\r\nAAAGTTTA\tUnknown\t\tUnknown\t1\r\nAACAGCCA\tX5075,X5245,X7236\t\tUnknown\t1\r\nAACGCTTA\tUnknown\t\tUnknown\t1\r\nAAGATAAA\tUnknown\t\tUnknown\t1\r\nAAGATAAG\tUnknown\t\tUnknown\t1\r\nAAGATTAA\tUnknown\t\tUnknown\t1\r\nAATAAAAA\tUnknown\t\tUnknown\t1\r\nAATTCGAC\tBI5C02\t\tUnknown\t1\r\nAATTTCCA\tBI5G04\t\tUnknown\t1\r\nACAGCCAG\tBI5E07,X5148\t\tUnknown\t1\r\nACGGGGCA\tUnknown\t\tUnknown\t1\r\nACGGGGGA\tUnknown\t\tUnknown\t1\r\nACTCCATC\tX5025,X7072\t\tUnknown\t1\r\nAGACACTC\tUnknown\t\tUnknown\t1\r\nAGAGACAG\tUnknown\t\tUnknown\t1\r\nAGAGGAAG\tUnknown\t\tUnknown\t1\r\nAGCGCTAA\tBI5H01\t\tUnknown\t1\r\nAGGAAAGA\tUnknown\t\tUnknown\t1\r\nAGGAGAAG\tBI5A05,D505\t\tUnknown\t1\r\nAGGGGCAG\tBI5A05\t\tUnknown\t1\r\nAGTGTCCA\tX5083\t\tUnknown\t1\r\nAGTTTCCA\tUnknown\t\tUnknown\t1\r\nATCTTCTC\tBI5E10\t\tUnknown\t1\r\nATGAATTA\tBI5A10\t\tUnknown\t1\r\nATGGGGCA\tUnknown\t\tUnknown\t1\r\nATTAAAAA\tUnknown\t\tUnknown\t1\r\nCAAAAAAA\tUnknown\t\tUnknown\t1\r\nCAAACTCC\tUnknown\t\tUnknown\t1\r\nCAACCCCA\tX5183\t\tUnknown\t1\r\nCAACTTAA\tUnknown\t\tUnknown\t1\r\nCAACTTTG\tX5150\t\tUnknown\t1\r\nCAAGCTAC\tUnknown\t\tUnknown\t1\r\nCAAGCTGA\tBI5B08\t\tUnknown\t1\r\nCAAGTTCC\tA507\t\tUnknown\t1\r\nCACCCTTA\tUnknown\t\tUnknown\t1\r\nCACCGCTA\tX5277,X7204\t\tUnknown\t1\r\nCACGATTC\tBI5F05,X5111\t\tUnknown\t1\r\nCACTCTTA\tUnknown\t\tUnknown\t1\r\nCACTGTTC\tUnknown\t\tUnknown\t1\r\nCAGCTGCG\tUnknown\t\tUnknown\t1\r\nCAGCTTCG\tUnknown\t\tUnknown\t1\r\nCAGCTTTA\tUnknown\t\tUnknown\t1\r\nCCACTTCG\tUnknown\t\tUnknown\t1\r\nCCAGCTTC\tX5041\t\tUnknown\t1\r\nCCAGGCTT\tBI5B09,X5007,X7090\t\tUnknown\t1\r\nCCCCCCAC\tUnknown\t\tUnknown\t1\r\nCCCCCCCT\tUnknown\t\tUnknown\t1\r\nCCCCCTTA\tUnknown\t\tUnknown\t1\r\nCCCCGCTC\tUnknown\t\tUnknown\t1\r\nCCCGCCCT\tUnknown\t\tUnknown\t1\r\nCCCGCCTA\tUnknown\t\tUnknown\t1\r\nCCCGGCCC\tUnknown\t\tUnknown\t1\r\nCCCTACAC\tUnknown\t\tUnknown\t1\r\nCCCTCCCC\tUnknown\t\tUnknown\t1\r\nCCCTTCTC\tX5193,X7288\t\tUnknown\t1\r\nCCGGGGAC\tUnknown\t\tUnknown\t1\r\nCCTGCTTA\tBI7B02\t\tUnknown\t1\r\nCCTTTTCC\tUnknown\t\tUnknown\t1\r\nCGACACTC\tBI5F09\t\tUnknown\t1\r\nCGAGCCAG\tUnknown\t\tUnknown\t1\r\nCGCCGGTT\tUnknown\t\tUnknown\t1\r\nCGGGGCAG\tUnknown\t\tUnknown\t1\r\nCGGGGGGA\tUnknown\t\tUnknown\t1\r\nCGGGGGTA\tUnknown\t\tUnknown\t1\r\nCTACATTG\tBI5B03\t\tUnknown\t1\r\nCTACCCTC\tUnknown\t\tUnknown\t1\r\nCTACGGTT\tX5233\t\tUnknown\t1\r\nCTCCGTCA\tUnknown\t\tUnknown\t1\r\nCTCTCCCC\tUnknown\t\tUnknown\t1\r\nGAAAAAAA\tUnknown\t\tUnknown\t1\r\nGAAAAACG\tUnknown\t\tUnknown\t1\r\nGAAAACCG\tUnknown\t\tUnknown\t1\r\nGAAAGACG\tUnknown\t\tUnknown\t1\r\nGAAAGAGG\tUnknown\t\tUnknown\t1\r\nGAAAGGAA\tUnknown\t\tUnknown\t1\r\nGAAATTTG\tUnknown\t\tUnknown\t1\r\nGAACAACG\tX5005,X7092\t\tUnknown\t1\r\nGAACACAC\tUnknown\t\tUnknown\t1\r\nGAACAGAG\tUnknown\t\tUnknown\t1\r\nGAACGACG\tX5288\t\tUnknown\t1\r\nGAACGCCG\tUnknown\t\tUnknown\t1\r\nGAACGGAG\tX5288\t\tUnknown\t1\r\nGAACTCAC\tUnknown\t\tUnknown\t1\r\nGAACTCAG\tX5289\t\tUnknown\t1\r\nGAACTTTT\tUnknown\t\tUnknown\t1\r\nGAAGAAGA\tBI7G04\t\tUnknown\t1\r\nGAAGAGGA\tBI5F04,N712,X5140,X7341\t\tUnknown\t1\r\nGAAGCTCG\tBI5D12\t\tUnknown\t1\r\nGAAGGCAA\tUnknown\t\tUnknown\t1\r\nGAAGGCCG\tUnknown\t\tUnknown\t1\r\nGAAGGGCA\tX5147\t\tUnknown\t1\r\nGAAGGGCG\tUnknown\t\tUnknown\t1\r\nGAATATCA\tUnknown\t\tUnknown\t1\r\nGAATGAAG\tBI7C10,X5057,X5288,X7040\t\tUnknown\t1\r\nGAATTCCG\tX5255\t\tUnknown\t1\r\nGAATTCGC\tD706\t\tUnknown\t1\r\nGACCCCCA\tUnknown\t\tUnknown\t1\r\nGACCTTAG\tUnknown\t\tUnknown\t1\r\nGACGAAAA\tUnknown\t\tUnknown\t1\r\nGACGGGCT\tUnknown\t\tUnknown\t1\r\nGACGTTTC\tUnknown\t\tUnknown\t1\r\nGACTGATA\tX5031\t\tUnknown\t1\r\nGACTTTTC\tUnknown\t\tUnknown\t1\r\nGAGAAAAA\tUnknown\t\tUnknown\t1\r\nGAGCCAGA\tUnknown\t\tUnknown\t1\r\nGAGGGATA\tUnknown\t\tUnknown\t1\r\nGAGGTTAC\tUnknown\t\tUnknown\t1\r\nGATACTTC\tUnknown\t\tUnknown\t1\r\nGATCGACA\tUnknown\t\tUnknown\t1\r\nGATGGTTC\tX5359,X7122\t\tUnknown\t1\r\nGATTCCCT\tUnknown\t\tUnknown\t1\r\nGATTTTCC\tUnknown\t\tUnknown\t1\r\nGCAGAAAG\tUnknown\t\tUnknown\t1\r\nGCAGAGAG\tUnknown\t\tUnknown\t1\r\nGCCCTCCT\tUnknown\t\tUnknown\t1\r\nGCCGTTTC\tUnknown\t\tUnknown\t1\r\nGCCTTGTC\tX5123,X7358\t\tUnknown\t1\r\nGCGCGCCC\tUnknown\t\tUnknown\t1\r\nGCGCTTCG\tUnknown\t\tUnknown\t1\r\nGCGGGAAG\tUnknown\t\tUnknown\t1\r\nGCGGGCCC\tUnknown\t\tUnknown\t1\r\nGCGGTAAC\tUnknown\t\tUnknown\t1\r\nGCTCTCCC\tUnknown\t\tUnknown\t1\r\nGCTGGCCC\tUnknown\t\tUnknown\t1\r\nGCTGGCTC\tUnknown\t\tUnknown\t1\r\nGCTTACCA\tBI5G11\t\tUnknown\t1\r\nGCTTTTCC\tUnknown\t\tUnknown\t1\r\nGGAGAGAG\tUnknown\t\tUnknown\t1\r\nGGAGCCAG\tUnknown\t\tUnknown\t1\r\nGGCGGTTG\tUnknown\t\tUnknown\t1\r\nGGCTAACA\tUnknown\t\tUnknown\t1\r\nGGGGGAAA\tUnknown\t\tUnknown\t1\r\nGGGGGACT\tUnknown\t\tUnknown\t1\r\nGGGGGAGG\tUnknown\t\tUnknown\t1\r\nGGGGGCAG\tUnknown\t\tUnknown\t1\r\nGGGGGGAC\tUnknown\t\tUnknown\t1\r\nGGGGGGCG\tUnknown\t\tUnknown\t1\r\nGGGGGGTA\tUnknown\t\tUnknown\t1\r\nGGGGGTGG\tUnknown\t\tUnknown\t1\r\nGGGGTCAA\tA711\t\tUnknown\t1\r\nGGGGTGGA\tUnknown\t\tUnknown\t1\r\nGTAGGCTG\tX5106,X7375\t\tUnknown\t1\r\nGTAGTCAG\tUnknown\t\tUnknown\t1\r\nGTAGTTTG\tUnknown\t\tUnknown\t1\r\nGTCCTTCT\tX5312,X7169\t\tUnknown\t1\r\nGTCGTTTA\tUnknown\t\tUnknown\t1\r\nGTCTCTCT\tUnknown\t\tUnknown\t1\r\nGTTAACAC\tUnknown\t\tUnknown\t1\r\nGTTCTTCG\tX5337\t\tUnknown\t1\r\nTAAAGGAG\tUnknown\t\tUnknown\t1\r\nTAACTCCG\tUnknown\t\tUnknown\t1\r\nTAACTTTA\tUnknown\t\tUnknown\t1\r\nTAAGAAAA\tUnknown\t\tUnknown\t1\r\nTAAGCTCG\tBI5B08\t\tUnknown\t1\r\nTAAGCTTC\tBI5B08\t\tUnknown\t1\r\nTAAGTCAG\tUnknown\t\tUnknown\t1\r\nTAATGAAA\tBI7H05\t\tUnknown\t1\r\nTAATTCCC\tUnknown\t\tUnknown\t1\r\nTAATTTCG\tUnknown\t\tUnknown\t1\r\nTACAGTTA\tUnknown\t\tUnknown\t1\r\nTACGCCTA\tX5015,X7082\t\tUnknown\t1\r\nTACGGCCA\tUnknown\t\tUnknown\t1\r\nTACGGGAA\tUnknown\t\tUnknown\t1\r\nTACTGTTA\tUnknown\t\tUnknown\t1\r\nTAGAGCCA\tX5245,X7236\t\tUnknown\t1\r\nTAGCCAGG\tBI7H08,X5063\t\tUnknown\t1\r\nTAGGGACA\tUnknown\t\tUnknown\t1\r\nTAGGTCCA\tA508\t\tUnknown\t1\r\nTATCTTCT\tBI5G02,E503,S503,[N|S|E]503\t\tUnknown\t1\r\nTATGGTGA\tUnknown\t\tUnknown\t1\r\nTCACCCAC\tUnknown\t\tUnknown\t1\r\nTCACCCAG\tX5191\t\tUnknown\t1\r\nTCACCCCC\tUnknown\t\tUnknown\t1\r\nTCACTCCC\tUnknown\t\tUnknown\t1\r\nTCAGAAAG\tUnknown\t\tUnknown\t1\r\nTCATCCAC\tUnknown\t\tUnknown\t1\r\nTCCGTCTA\tUnknown\t\tUnknown\t1\r\nTCCTGTTC\tUnknown\t\tUnknown\t1\r\nTCGGGGAA\tUnknown\t\tUnknown\t1\r\nTCGTTCCC\tUnknown\t\tUnknown\t1\r\nTCTCCCTA\tUnknown\t\tUnknown\t1\r\nTCTGCTTA\tUnknown\t\tUnknown\t1\r\nTCTTAAAC\tUnknown\t\tUnknown\t1\r\nTCTTCCGC\tE517,S517,[N|S|E]517\t\tUnknown\t1\r\nTCTTTCTA\tUnknown\t\tUnknown\t1\r\nTCTTTGAC\tX5071\t\tUnknown\t1\r\nTCTTTGCC\tUnknown\t\tUnknown\t1\r\nTCTTTTCG\tUnknown\t\tUnknown\t1\r\nTGCCAGAC\tUnknown\t\tUnknown\t1\r\nTGCTATTA\tBI5G09\t\tUnknown\t1\r\nTGCTTCAC\tBI5A11\t\tUnknown\t1\r\nTGGAAAGA\tUnknown\t\tUnknown\t1\r\nTGGGGCAG\tUnknown\t\tUnknown\t1\r\nTTAAAAAA\tUnknown\t\tUnknown\t1\r\nTTAAGACA\tUnknown\t\tUnknown\t1\r\nTTACAGAG\tX5156,X7325\t\tUnknown\t1\r\nTTACTCTT\tUnknown\t\tUnknown\t1\r\nTTACTTGG\tBI5F02,BI5H08,X5376,X7105\t\tUnknown\t1\r\nTTAGCTAA\tUnknown\t\tUnknown\t1\r\nTTAGTTTG\tBI5H08\t\tUnknown\t1\r\nTTATTCAC\tBI5E11\t\tUnknown\t1\r\nTTATTCCC\tUnknown\t\tUnknown\t1\r\nTTATTCCG\tX5255\t\tUnknown\t1\r\nTTATTTCG\tUnknown\t\tUnknown\t1\r\nTTCCCCAT\tX5373\t\tUnknown\t1\r\nTTCGCCCG\tUnknown\t\tUnknown\t1\r\nTTCGGCAA\tX5268\t\tUnknown\t1\r\nTTCGGTTT\tUnknown\t\tUnknown\t1\r\nTTCGTTTA\tUnknown\t\tUnknown\t1\r\nTTCTCCTT\tBI5F12,BI5H07,S507,X5176,X7305,[N|S|E]507\t\tUnknown\t1\r\nTTGACACT\tUnknown\t\tUnknown\t1\r\nTTGGCAGA\tUnknown\t\tUnknown\t1\r\nTTGGCCGA\tUnknown\t\tUnknown\t1\r\nTTGGGGAT\tUnknown\t\tUnknown\t1\r\nTTGGTCTG\tBI5F03\t\tUnknown\t1\r\nTTTGCCAT\tX5373\t\tUnknown\t1\r\nTTTTAATT\tUnknown\t\tUnknown\t1\r\nTTTTCCAC\tUnknown\t\tUnknown\t1\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/single_index_i5_only/expected.txt", "content": "sample_name\texpected_barcode_1\texpected_barcode_1_name\texpected_barcodes_read_count\tguessed_barcode_1\tguessed_barcode_1_name\tguessed_barcodes_read_count\tmatch_type\r\nAmm_RNA-Tag\tCAAGCTTA\tBI5B08\t21771\t\t\t\talternatives_have_lower_read_counts\r\n" }, { "path": "tests/input/TestIlluminaBarcodeHelper/single_index_i5_only/metrics.txt", "content": "## htsjdk.samtools.metrics.StringHeader\n# ExtractIlluminaBarcodes BASECALLS_DIR=/2022-08-12/220729_M04004_0626_000000000-DGV59/Data/Intensities/BaseCalls OUTPUT_DIR=/tmp/tmp-illumina-illumina_demux-wfkcl506/extracted_barcodes-ohj84p5l LANE=1 READ_STRUCTURE=150T3S8B150T BARCODE_FILE=/tmp/tmp-illumina-illumina_demux-wfkcl506/barcodeData.DGV59.11s52n5o4.txt METRICS_FILE=metrics.txt MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=10 NUM_PROCESSORS=0 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false\n## htsjdk.samtools.metrics.StringHeader\n# Started on: Fri Aug 12 19:08:48 UTC 2022\n\n## METRICS CLASS\tpicard.illumina.ExtractIlluminaBarcodes$BarcodeMetric\nBARCODE\tBARCODE_WITHOUT_DELIMITER\tBARCODE_NAME\tLIBRARY_NAME\tREADS\tPF_READS\tPERFECT_MATCHES\tPF_PERFECT_MATCHES\tONE_MISMATCH_MATCHES\tPF_ONE_MISMATCH_MATCHES\tPCT_MATCHES\tRATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_PCT_MATCHES\tPF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\tPF_NORMALIZED_MATCHES\nTTAGCCAG\tTTAGCCAG\tCtrl_RNA-Tag\tCtrl_RNA-Tag.lCtrl_RNA-Tag\t176653\t153671\t176653\t153671\t0\t0\t0.229165\t0.760557\t0.22364\t0.745784\t1.13097\nGAACTTCG\tGAACTTCG\tLowMgCl2_RNA-Tag\tLowMgCl2_RNA-Tag.lLowMgCl2_RNA-Tag\t226758\t206053\t226758\t206053\t0\t0\t0.294165\t0.976277\t0.299872\t1\t1.516485\nGACGGTTA\tGACGGTTA\tForm_RNA-Tag\tForm_RNA-Tag.lForm_RNA-Tag\t232268\t200616\t232268\t200616\t0\t0\t0.301313\t1\t0.29196\t0.973614\t1.47647\nCAAGCTTA\tCAAGCTTA\tAmm_RNA-Tag\tAmm_RNA-Tag.lAmm_RNA-Tag\t21771\t19346\t21771\t19346\t0\t0\t0.028243\t0.093732\t0.028155\t0.093888\t0.14238\nTCTTTCCC\tTCTTTCCC\tmisc_barcode\tmisc_barcode.lmisc_barcode\t100795\t99691\t100795\t99691\t0\t0\t0.130758\t0.43396\t0.145082\t0.483812\t0.733694\nNNNNNNNN\tNNNNNNNN\t\t\t12609\t7759\t0\t0\t0\t0\t0.016357\t0.054286\t0.011292\t0.037655\t0\n\n\n" }, { "path": "tests/input/TestIlluminaDir/empty_dir/Data/Intensities/BaseCalls/README", "content": "This is an empty mock directory just for testing\n" }, { "path": "tests/input/TestImputeFromReference/contigs.sub.ebov.fasta", "content": ">c1_with_snp\nCTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGG\nCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAA\nACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCA\nGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACC\nATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTG\nCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATA\nCTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGC\nAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTT\nTTGGAACTAATGAG\n>c2_with_6bp_ins_and_tail_snps\nGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGG\nCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAG\nGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACT\nTAGTAG\nCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGAC\nTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAG\nCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTG\nAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCAGAATTGA\nG\n>c3_doesnt_map\nTGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGA\nGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACA\nGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAG\nTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTAC\nTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAG\nGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCCAAAAT\nTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGA\n>c4_too_short\nCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATT\nGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACC\n>c5_overlap_end_revcomp\nTGATCAATTTTGTCTGTTATGTTCTTGGTCCAATCATGTGGTTCGATACAGCAGTCCGG\nTCCCAAAATGTGGCATGTGCCACCCCATCGCTGCAGCAGGAAGTCAATTGCCTTACGGT\nTGAGGATTGAAAAGGTTCGCAGCTCAGTTGTGGCTCTCAGGAACAGCTGGAGAGATTG\n" }, { "path": "tests/input/TestImputeFromReference/expected.hhv3.mummer.fasta", "content": ">HHV3-test-1\nAGGCCAGCCCTCTCGCGGCCCCCTCGAGAGAGAAAAAAAAAAGCGACCCCACCTCCCCGC\nGCGTTTGCGGGGCGACCATCGGGGGGGATGGGATTTTTTGCCGGGAAACCCCCCCCCGCC\nAGCCTTTAACAAAACCCGCGCCTTTTGCGTCCACCCCTCGTTTACTGCTCGGATGGCGAC\nCGTGCACTACTCCCGCCGACCTGGGACCCCGCCGGTCACCCTCACGTCGTCCCCCAGCAT\nGGATGACGTTGCGACCCCCATCCCCTACCTACCCACATACGCCGAGGCCGTGGCAGACGC\nGCCCCCCCCTTACAGAAGCCGCGAGAGTCTGGTGTTCTCCCCGCCTCTTTTTCCTCACGT\nGGAGAACGGCACCACCCAACAGTCTTACGATTGCCTAGACTGCGCTTATGATGGAATCCA\nCAGACTTCAGCTGGCTTTTCTAAGAATTCGCAAATGCTGTGTACCGGCTTTTTTAATTCT\nTTTTGGTATTCTCACCCTTACTGCTGTCGTGGTCGCCATTGTTGCCGTTTTTCCCGAGGA\nACCTCCCAACTCAACTACATGAAACTACTGTCCGGAAGGGGAAGGTATTTATTCTCGCTT\nGCAGCTTGTCGCGCGTGTATGCACAACAAAAGCTATATATGTCACCAAAGCCAACGTCGC\nCATCTGGAGTACTACACCCAGTACGTTGCATAACCTGTCCATTTGCATTTTCAGTTGCGC\nGGACGCCTTTCTCCGGGATCGTGGCCTTGGGACATCAACCAGTGGAATAAGAACCGCCGG\nTGGTCTTGCCCGAACGACGAGTGGCGACGCGTTGTTCTGCATAAGCTCTGTATGCTGATA\nCATAAACACAGAGTCTGTATCGCTATCAGATTCCCGAACACCTTCCGGTACCCCATACTC\nCGATACCCTGGACATTGCGGATCCCAAAAATATAATATTAACAGGATTTGCTTATACTTT\nGCTACAGCTTATATAAATTTATGTGCGATACATCTTAAGTGCATCCGTACGTTATTTATA\nCATTGCCGGTCACGTGAAAAGACTGTGTTACCCAATAAAGGTTCTACAAAAAATGCTTTA\nTTGGGTGTTTGTTTAATAGCTATTATCGTAACCCACCCCCGTAAAATCATAAAATGCATG\nTAATTTCTGAGACACTTGCATATGGGCATGTTCCCGCATTTATTATGGGCTCCACTCTGG\nTGCGTCCCAGTTTAAACGCCACCGCCGAGGAAAATCCCGCGTCAGAAACGCGATGTTTAT\nTACGAGTGCTTGCGGGGAGAACTGTAGACCTGCCAGGCGGAGGAACGTTACACATTACCT\nGTACCAAAACCTATGTAATTATTGGCAAATATAGCAAACCCGGCGAACGTCTTAGCCTTG\nCCCGTCTAATAGGGCGTGCAATGACGCCTGGAGGTGCAAGGACATTTATTATTTTGGCGA\nTGAAGGAAAAGCGATCCACAACGCTTGGGTATGAATGTGGTACGGGCTTGCATTTACTGG\nCTCCATCTATGGGTACATTTCTCCGCACACACGGTTTAAGTAACAGAGATCTCTGTTTAT\nGGCGGGGTAATATTTATGATATGCATATGCAACGTCTTATGTTTTGGGAGAATATCGCGC\nAAAATACCACTGAAACACCTTGTATAACGTCGACGTTAACATGCAACTTGACAGAAGACT\nCTGGTGAAGCCGCACTTACCACGTCAGACCGACCCACTCTCCCAACCCTAACAGCCCAAG\nGAAGACCAACAGTTTCCAACATTCGTGGAATATTGAAAGGATCCCCCCGTCAACAGCCGG\nTCTGTCACCGGGTTAGATTTGCCGAACCTACGGAGGGCGTATTGATGTAATCACTAAATA\nAAATACACCTTTTTTCGATTGTACGTATTTTTATTTAAATGTGTAGTTCATAGTCCGCCG\nACAGCCGCTCGGGCTTTTCCCCCACATACAACATGATCGTATGCCTCGGATGCACCGGTC\nCAACACTCCGCCGAGAAGGGGGATTTACAATGACAGTGATACCCAATAGCCGCCAGATGT\nACACCCAGCTGTCCGGACTCCAGCATCATCTGCTGAGTTGCGGCGCTGAAGGGTGCATCG\nCATAGGGTGTTATAATTAGCCATTTCCGGTAACAGTCGTTGGGAATTTAGGAGGCTGCAA\nAACGGCTGTAGGTCAACATACATTGGGGATTCAGATGGTTTATCTCGACGTCCAAGTCCA\nATCAAAAAAGCGTGTAAATCATCAGCCCGGCCGCATGTTGCTCGAAGAGCACATAACCTC\nTTAACACCGTACAGAGGGGATGGCGTCGGTGCATGTGAGTTGGCAGGGCATGTCCACGTT\nGTTTCCAACGCCAGTGGCGGTATAACTTGTGTAAACGACGCCAACGGGTCAGGTTTAAGA\nTTCACTCGGATGGGTTGACTGCTTTCGGAAGCTCCCGTTGTATCCATTAATTAAACGTTC\nGGTACACGTCTGGTGTGTGTTTTACCCGAATCAGAGACGGAATTGCAAAGATATTGGTTT\nGAAAGCAATGTAATCCCGCCCATATATCCCCAACGTCGCCTTAAAAACTCCCACAATATT\nACATTTTTATTAGTCTTTTATTAATATAGAATCACATAAACAATTGATAAAATCAAGGGG\nTGGTGTATAATGATTAAAAATATAAATTGATATGTTTTACAAGCATGAAATAGGTATTTA\nCTATTCTAACAGGTAAATATGCTTAATGATTAAAAATACAAATTAGTATGTTTTGACAAG\nCATGAAAAAGGTATTTTTTATTTTAGCAGTTAAAGGTACTACACTTAAAATATTTACCGT\nATGGACGGGCGTCAGAAAGATGCCCGGCCCAAGTTGAGAGGGTACATTCAACACGACCAC\nACTCGCGTTGGTGGGTGATTAGGGCCTCTAAAACACCGGCCAGACATGACCCGGGTGTAT\nATTCTTGTAACACTTGAACGTTACAACTGATATCATCATATTCCACAAATTTAGAGCCAC\nGGACAACTATATTAGCAATGCGGGCAATCATAACAAACATATAAGTAGTAATACACGTGA\nTATCACTAAAACGTTGCTGGCGCAACAGTTCGGGGAGAGTACGAGACCCCAAATCGTTGT\nCCCTGTTTAGAAGAAGACATCTTACAAAAGGCCCCAGCTTTAACTTTAAATTCTCCAAAA\nGTGACTTCGAGGTTGCAACAATGGGATTATTTGTGTAGATGGGCAAGTTTTTTGCCGCTA\nACATTTTAATCCACGTTAACAGTTCATCCGCAGACTCCAACGCTTCAATCAAAGATTCTC\nCACGTATGACTCTCTCACGCAACGCGCGGGCAATACGTGAGTCCATTTTATATGACTCAA\nAGGTACGATAAAGTTCATGTCCGTACAACATCAACTCCGGCCAAGATGTGTTTTGTTTTA\nTCCCCGGAAAACATCCACCGGAAGCCCATGAATCACCCTCTTGTATTGTGGCATATCGGA\nCTACCAGTTTTTCAATTGTTTCATCTAAATGGCGTACCGAGTCAATGGTCACGCTGGCTC\nCCGCGGTGGAGACGACTTCAATAGCACGGCCCGTAATTCGATCGACCGGGATATCATACT\nCTTTTCGAATACGCTCTCGGCGGGCGTCTCTCTTGGAAAATCGCAACCTGTACGATTCGT\nCATGTGTCTGATCATTTCTTTCTCCCGTGGTCATTGCAGGAGGCGTTGTAGGACGCCGTC\nTTCGATTTGACAGGGATCGATCACGGTGTTTTCTTGAACTTTGGGTGTTATAAGATCTGG\nATGATCGTCGATGTCCCCGTTCGATGCGTGCATATCCAGTCTCCACGTCTCTTCCTCCAT\nGATGGTTTGAATCGGGTAATACAACAACCAAAGTTTTCGGGCGATTGTGGTGGTAGCTTT\nCACGCCTTCCGTGCCTTCGTTTGGAATACCGTGGATTATATGCTGTATCTGCAGTACGCT\nCCACATACACAGTTCTAGACGTTGTGGAGTCCTCGCCTGGAGTGGAGCCAATAGCTTCAT\nCATTTGCCCAATCGGTGACTTCCAATGCAAAGTCATCCGAAGGTTCGTCTGGTAGCAAAT\nTCATAAAGTCTTCACAAATAGTAGACACGTCTGGGTCGGTTGGAATTGAAGCAGAGGCCA\nTGGCTGCAAAATATCTGACAATTGCGTGTTTGCAGTTGCCTGTATCTTCCGCCAATGTTG\nTAGAATTTATAGGCTCACCCAACCCCGCAATGGGCGTGTTTAGTCACATGATTAATGTTT\nCTGGGAGTTTTCACTTTCCCCAAACAAGCTTACCTGCACCCTTTGTTCGTAATGCATAAA\nAATAACCACTGCTATAGCAAATATGACGATATAAAAACATTTTATAGCAAGGCCGGACAT\nTACTGTAGCACAACATGTTGTGCATATACCACGTATTCCCCCCGTATTGATATGATTTAA\nATGATTATCCTTGGTTGGTTTTGGTCTAACATAAGATATAAGCTCTACTATAGCGAGCGT\nGCATACAACAACCCAGGCCAGAATCCGAATGTATGTGGGGTATAATAACGCGCATGGTGT\nATATGCAACGCCAAGCGTTAAAAGCACAATACATCCAGATGATATATGAGCGATAACCTC\nCAAAAGCATCAATAACGTAACACCTTTATGCATATATAAAAAACTTATAGGGTCAGCATT\nAAATACTTTACTCATACCATCCCGTCGCATGGAAACATCACATAACAACCTTGCCAACTT\nTGTATATGGGTAACCAAGAAGAATGTTCGAAATAACCCGTGTTACGTAATTCAGTGAATA\nTGATGTGGGGGATATTAACTCACAGGATGATCGGAATGGCCCAAACATACGACGTATTCG\nTCGAAATTGTAAATACATACCATATACAAACCATGCAAAAAAAATCATTTTTAGCTGCAC\nGCACCAAAAATAAGCGTGACAATTACGTGTTCCCAGAACAATTCGAATTTTGTCATGCAA\nAGGTGTAGAAATAGCGGTTTTTACCATAGTATCTCCTGATAATAGATTTTCCCGGCAGCT\nGTAATCGTATCCAGATAGGCCATCCAAAAACGTTGAGTGGTTTACAAACGTTACATATAT\nAAGAGAGTTGTTATAAGACCCCCATACAACCGGTCCACCATTAATCACCGTGGTTGCATA\nCACACACTCATGTTCAAACTTTACACGAGCGGTATACCATAGGGTAAAAACAGCATGTCC\nGCTAAGTAGACACATAATTATAAAATGTTCTGTCTTGATTCCTAAAGCCTGCATGACCCG\nTGGAAGATGGCAATTCAAGCACGATGTAGTATCACACGGTTGGTGTTAACTCGAAGTTAA\nATTTGGATAATTAGGTACTTCTAGAGTAAAGATTGTATGCATGCGATTGCTATCGCACTT\nTGTAGCAAAACATTGTTGTGCAAGCGAAATACACAAACGGTTGTGATGATCCACTCGCAG\nAGACACAAATGTCCGGGGAGCCGTTCTTCCTCCGCGATGGGGATATCGAAGACAAGTGAA\nCCCTTTTGTTCCGCATATGAGCTGAAATAACACCCAGTCCCTTTTGATGGCGATACACTT\nTGATGATGTTAAGGTATATTCGCGATCACGCCCGGGGAAATGAACAGCAATATGCTCCAC\nAATAGATTCTAATATTGTGCTGTCGACAAAGGCCTCCAGTGTAAATGCGTCCAGACAAGT\nTACCCCGCGCTCTTTTAGAGCCTTTGTTAAAGATATTTGCGGGGAGCTAAATATTTGTTT\nATTACGCGCAACCTTACGTTCAAAAAACTCTGCGTATTCCCCCCCAAGGTTATGTAAAAT\nAAATTGCACTGGAACATTCGACTGCGGTCTTGAATGAAAATGAAAGTTTGCCGGGTTTCT\nATGTGATGTCACAAACGCTAATATATCAATACACTGCTCAGGTACAACATAAAATGGGAG\nTAGTTGTCCAACCGCCGTCCCTGTGGTTGTTACTTTGGAGAAAAAAGGCAGTCTTAAACT\nATGTCCGTGGCTATAAACACCAGTATCTATAAACGAAAAGTCCCGTAAATACGGACCAAT\nATATTCAACAAATTCCCGTTCCAGCAACACCGCTTGTTGTAATATTTGTGCAAACCCCTT\nTAAAGTGGAAGACCCCACTAACGCATAGGGATTTGGGATTGGTACGCATACCCTGAAACC\nTATTTTCTCTTTACAGTTACAGGGTAGAGTTTCATGCAAGTTTTCATTGTTTGATACATC\nGGCGTGTGTATGGACTTCAGACGTTGTCTGTGTATCAAAAAACCATACATCCTCTGTATA\nATTCTCTTCTACACACGTGTATAATTCGCCATTTTCTATGTAAAAATCGATGTCAGAATG\nGCTGGTTATATCCAATAAATTATCATCATCCAACACCTCAACGGTAGGTTCAGGACATGC\nAGTTTTATAAAAATAACATGGGTCTTTGTTAGGGTTTACCACGGCCTTTGGAAAAAGTAA\nTTGCATGGCCGTTAAAATACCATGACGAAATGCTCGCATGCCGGCATGTAAAATACCCAA\nTGGGATGGGTTTTCTTATATGAAAGTCTACATCAAGTATGAGGTTTGTGATTATAAGATT\nTGTATTAAATAGCTCATTCCTGTTTATATAAAGCTGATCTTTGGGTATGTTAGATGAAAT\nTTTAGAAACGTTTTTAACAGACGTAGATAATAGTAAAGTCAACTGCATATCTCGTAGTGA\nAGCGGCAACAAAATTACATGGATTAATTTGTTTAAGGTCCTCCGCAATTAATCGAGCCTC\nGTGCGGTAAAGTGTAACGGTTTGTTATTGATGACCACGTATCATTAGCAATAACAGCAAA\nTGCTTGGGCACCTTGAGGCAAGGCTACCCGATATACAGGCATTGGTCCAGTTACCTCAGA\nATGGCCGATGAGGGCTTCTAATGGAGTTTTATAACTCAGGATGGATACATCATGTGTGGC\nTATCCCAGTGGCAGCAGAGAAAAACAGTAATAGTTTTGTAATCCCCGGGCTCGTATCAAA\nACCAGTACGACCACTTTGGTTAGGTGTATCGTTTGCAAAGTTGGCTGCTCGTAACGCCTC\nCGCGGAAACAACCGAATCCTCAAAATTAGACAATTCGTCAAAACCGGGTGGATTTGAGGG\nAATAGTGGAGGACCATCCATATGGACTAAATTGTTTTTCAATGTTTTCCACACGACGAGT\nTAGCGTTGTAGCTAGGTCACATACGCCTATAAACTTGCTAGGTTTTGCGGCATACGTAAG\nACTTAAAGTATATGTTTTAGTAATTGTATATTTATGTCCAATCTCAGGTCCAAGTTCAGT\nGACATCACAAATTACGTTCTTTTTTATATAGTCACGCATGTTGAGACGAGAACGTACATG\nATTAAAAAAATTAGCAGTAGCTCTTTTTCCCAGGTTGGATGATTTTAAGAGGACCGGTTT\nATTCACAAAATCTGAGTATGTAACCGCTTGTAGGTGGTCTGCGATCTGTTTCCGATTGAA\nACATTCAAAATGTGCCAGATAAATATAATCAACAAATTCACGGTCTGGAACTTTAAGGCC\nTTTTCTATCGTTGGTAATATACTCCGATACTGCGTGTATTTCCGTTGTGTCTGTATGTAT\nTCGCTGTAAAATGTACGATAGAGCATTTTTGGCTGTCAAACCTCGTGTATATGTTGAGGA\nACAACAAAACATGGAAAGTTTATCAAAAGACAACAAGTCCGAAATATTGTACCCACTACA\nATTAGGTAATGCCGGGACTTGGTAAGTTAAAAACAAATCTTTAATTGCCTGTAAGTCATA\nTAAGGGGGTTTCCAACGTATTGTAACTTGTGTCCGTTTGTAACAAGTAATAGCGTGTAGC\nCAACACTAGCGTTTTTTCAGAGGGTCCAAATCGAACAATATACCAAAACGGCGAGCATCC\nATACCCCCAGTAGAGTCGTCGATATGCAGCCAATACTTGACGTTCGTAATGGGCATATAA\nTGATGTTAGCTCCTGACGACCAACGGATTTTTTAACTAACTTGCAGAGTGTTGCCTCTGT\nGATGCATAGGCCGTTGTCCGATAATCCCTTTCGGTTTAAATGGTGTGTTGTTACCATCAG\nAGTTTGTATAACTTCCGAGTGAATGTCAAACGTCTCCGATATACATAGGGTATCAGATAT\nTATATGCGGATTTAGGGGTGCTCCATACCATAACGCCTTATATAAAGCTTTAAAATCAGT\nTTGGGTTTTAAAACAACAAAAAAATATAGGCCAGACCCGGGATCGTACATCTCCAGTTGA\nAAATCCACCAATTAAATAAAAAATAACGTTGACGTCCCTACTACAAAATAAATGCATTAT\nTTGGTTTTCTTCATCGTTTTCAGTTACTTCACGTGGGCGTTTAGTTGGGATTACTTGCGT\nGATCTCTTCCCTCCCATTTTTGACAAAGACGTCATCTAAGTCGGGAGTCCAAGTATAACT\nCACCACATACAGAGGTTCTGTGCTTATCTGCCCGGTAAGCAACAACAGCGAGTGGGAGAT\nTGCACATCCCTTTGTGGCAAATAATAACCGAATCGTCGGTTTGGAGGATTTATCCATAGT\nTCAATACGTTGGAAAGCCAGTCAATCATGCAGACGGTGTGTGCCAGCTTATGTGGATATG\nCTCGAATACCAACTGAAGAGCCATCTTATGAAGAGGTGCGTGTAAACACGCACCCCCAAG\nGAGCCGCCCTGCTCCGCCTCCAAGAGGCTTTAACCGCTGTGAATGGATTATTGCCTGCAC\nCTCTAACGTTAGAAGACGTAGTCGCTTCTGCAGATAATACCCGTCGTTTGGTCCGCGCCC\nAGGCTTTGGCGCGAACTTACGCTGCATGTTCTCGTAACATTGAATGTTTAAAACAGCACC\nATTTTACTGAAGATAACCCCGGTCTTAACGCCGTGGTCCGTTCACACATGGAAAACTCAA\nAACGGCTTGCTGATATGTGTTTAGCTGCAATTACCCATTTGTATTTATCGGTTGGCGCGG\nTGGATGTTACTACGGATGATATTGTCGATCAAACCCTGAGAATGACCGCTGAAAGTGAAG\nTGGTCATGTCTGATGTTGTTCTTTTGGAAAAAACTCTTGGGGTCGTTGCTAAACCTCAGG\nCATCGTTTGATGTTTCCCACAACCATGAATTATCTATAGCTAAAGGGGAAAATGTGGGTT\nTAAAAACATCACCTATTAAATCGGAGGCGACACAATTATCTGAAATTAAACCCCCACTTA\nTAGAAGTATCGGATAATAACACATCTAACCTAACAAAAAAAACGTATCCGACAGAAACTC\nTTCAGCCCGTGTTGACCCCAAAACAGACGCAAGATGTACAACGCACAACCCCCGCGATCA\nAGAAATCCCATGTTATGCTTGTATAAATATTGAAATAAAAACTAAAAACGTTTCTGGTGT\nATGTTTTTATTTTGTATATAAAATTAAAACATTGCTGGCTGGCGTGGTTATTACATTTAA\nTGTTTTAGTAGAAAATCGACATCGTTTGTTTCTTTATCAGTTGAACCAAATCCACGCGTT\nCCCCGTTCGCTGGGTGTGGCTATTAGATCTAACGTTTTAGTAAAATACCATTGTACACCC\nGGTATGCCACATTTACCGCGGATAGCATAAGGAAATGCAATATTACTTAAAACGTTGTGT\nTTTAAGTGTATTTGGGTGTTGTGATCTATTAACAGGACCTGTGCAAGACGATCTCCCGTT\nTTTATACGTATGTCATCACCCGTGAGATTATATACGTAGAATTTACAGTGTTCTCCTGCA\nGGCCATGCCGTTGGACACACGATAATGCCTGATCGGCTTTTCGATGATCTTCCAAAAATA\nTAAGCGTTTATACTCGGATGTTGTAAGTCCCAGTCTCTTATAATCGGTAAGACAATTTTT\nATAAATTCATTCCTTTTTAAATATAGGTTATATGGTACACAAATATCATATCCCGCGTCT\nTCTTGGCGTTTTGGATTGATGATATGTTTGTAGGTTAAGGGAACATCGATATGGTATTCT\nGCAGAATCCCTATGTAAAGGTTGCCCCTGCTGTACCGTGGAAATATCAGCAAATTCAGGT\nATAACGGGTTTTTCATAATTTGACGGCGAGTTTGATAAGGGTTGAACTTGTATCGATTTA\nAAAATTGGATCCAGATGTTTAAGAACGTTTTTTGGGAGAAGGCGACTTTGTCTTAATTTT\nACCGGGAACAAGTAGATTGTTAAATGTCCGGGTAAAATAACGGTTACTCCTGGCCGGTAA\nTACAAAAGGGCTGAAATTACTCCTCTGTAACCCGCATCAATAACTCCGTTGGCGACAAAA\nAAATTGTCTTCATCAGCAAGGGCAGTATCTTTGCATTGAATTAACAACAGTGCGTATTCA\nTTGGGAGGCGCCGACTTAACCAACAGCTCCAACTGCTGCATATAAAAACCGCCCCGTGTT\nACAGATTTTTCAGATGGCAGTTCGAGTTTCTTGTGGTTCCGGAGTAACAACGGTTGATGT\nCGACTTACTTTATCGTCTAACACGCATTGCAGCGTATCTGCACATTCAGGTTGAACTTCT\nATTAAAATTGTATCTTTTAAACACCGATTCGGAATAGTTTGGCTACAAAACATATCACCT\nGTATTTACTGCCGTTTCCAAGATGGGATCAATTACCGCTTCGTTCATATTAATAACGATG\nCAAATTTTATTTTTTTGTGAAGACAGCAGTGGGGAGCCAAACTTTGCAGAACGGAATTTT\nTGGCATGCCAGCTGTTCGGCTCGTGGAGTTTATATCGACGGATCAATGATCACCACCCTT\nTTCTTCTACGCATCCCTGTTGGGGGTGTGTGTAGCCCTTATTTCGTTAGCTTATCATGCG\nTGTTTCCGGTTATTTACTCGTTCTGTATTACGCAGCACGTGGTAAACCCGTTTGCCTATA\nAAAGGGGCAGGCGTGTATAAGAGGGTCCCTGTTTAATACGCGGTCTGCCGTGTTTGGATA\nTTTCACGACCCTATCGTTTATTTACGTAATGGCATCTTCCGACGGTGACAGACTTTGTCG\nCTCTAATGCAGTGCGTCGTAAAACAACGCCTAGTTATTCCGGACAATATCGAACCGCGCG\nGCGAAGTGTGGTCGTAGGACCCCCCGATGATTCAGACGACTCGTTGGGTTACATTACCAC\nAGTTGGGGCCGATTCTCCTTCTCCAGTGTACGCGGATCTTTATTTTGAACATAAAAATAC\nGACCCCTCGCGTACATCAACCAAACGACTCCAGCGGATCGGAAGATGACTTTGAAGACAT\nCGATGAAGTAGTGGCCGCCTTTCGGGAGGCCCGTTTGAGACATGAACTGGTTGAAGATGC\nTGTATATGAAAACCCGCTAAGTGTAGAAAAACCATCTAGATCTTTTACTAAAAATGCGGC\nGGTTAAACCTAAATTAGAGGATTCACCGAAGCGAGCTCCCCCGGGAGCGGGCGCAATTGC\nCAGCGGGAGACCAATTTCCTTCAGCACTGCACCAAAAACCGCAACAAGCTCGTGGTGCGG\nTCCTACGCCATCATATAACAAACGCGTCTTTTGTGAAGCGGTCCGGCGCGTAGCCGCCAT\nGCAGGCACAAAAGGCTGCCGAAGCGGCTTGGAATAGTAATCCCCCAAGGAATAACGCCGA\nATTAGACCGTTTGTTAACCGGAGCCGTTATTCGTATTACGGTGCATGAGGGTTTAAATTT\nAATACAAGCCGCTAATGAAGCAGAACTAGGTGAAGGAGCATCGGTATCCAAACGTGGACA\nTAATCGAAAAACTGGAGATTTACAGGGGGGCATGGGTAATGAACCTATGTACGCACAAGT\nTCGTAAGCCAAAAAGTCGAACGGATACACAAACGACTGGGCGTATAACTAATCGAAGTAG\nGGCCCGTTCGGCATCAAGAACTGATGCGCGAAAATAGGGATATAATTACGCAGTAACGGT\nTTACCCGGTATTATGTATAATAAATAAACGTATAAAAGACAGTCGTGGTTTGTGTTTATT\nATAAATGTGTATTATATGTCACATATTATAAACTGTTTAAATAGTACCACGTGGTATTAT\nGAACAGTTTATAATCAGTTGCTACCAAACAAACCCCATTAGACGGCGGGTTTTGATAAAG\nGGAATCGCTTATTTAAACTAAAGATTTTACTCTATAAGTATGGAGTGTAATTTAGGAACC\nGAACATCATAGTACAGATACGTGGAATCGTAGTAAAACGGAACAAGCGGTTGTGGACGCA\nTTTGATGAATCGTTGTTTGGTGATGTAGCATCGGATATTGGATCCGAAACGTCGTTATAT\nTCACATGCAGTTAAAACTGCTCCGTCTCCGCCTTGGGTAGCTAGCCCTAAAATTTTATAT\nCAACAGTTAATACGGGATCTTGATTTTTCAGAAGGGCCGCGTTTACTATCATGTCTTGAA\nACCTGGAACGAGGATTTATTCTCATGTTTTCCTATTAATGAGGACCTATATTCCGATATG\nATGGTTTTATCCCCGGATCCAGATGACGTTATCTCAACCGTTTCAACCAAAGACCATGTT\nGAAATGTTTAATTTAACAACCCGGGGTTCCGTTCGATTGCCTAGTCCACCAAAGCAACCG\nACGGGGCTTCCAGCTTACGTTCAGGAGGTCCAGGATTCGTTTACCGTAGAACTACGCGCC\nCGGGAAGAAGCATACACAAAACTACTAGTTACTTATTGTAAATCGATTATACGTTATCTC\nCAAGGAACGGCGAAAAGGACGACAATAGGTCTTAATATACAAAACCCTGACCAGAAAGCT\nTACACGCAACTCAGGCAAAGTATTCTACTTAGATATTATCGTGAGGTGGCAAGTTTGGCG\nCGTCTTTTGTACCTACATTTATATTTAACCGTAACGCGTGAATTTTCCTGGCGTTTGTAC\nGCCAGTCAATCTGCACACCCGGACGTGTTTGCGGCTTTAAAATTCACCTGGACCGAACGT\nCGACAGTTCACGTGTGCGTTTCATCCTGTATTATGCAACCACGGCATTGTGTTATTAGAA\nGGGAAACCACTAACAGCGTCTGCCTTGAGGGAAATAAATTACCGCCGCCGAGAACTGGGA\nCTGCCTCTAGTTAGATGTGGTCTTGTTGAAGAAAACAAATCTCCGTTGGTTCAACAACCC\nTCATTTTCGGTTCATTTACCACGGTCGGTGGGTTTTCTTACCCACCACATTAAGCGTAAG\nTTAGACGCATATGCGGTCAAACATCCTCAAGAACCGAGACATGTACGAGCGGATCATCCT\nTACGCAAAAGTTGTTGAAAATAGAAACTACGGTAGTAGCATCGAAGCTATGATTTTAGCA\nCCTCCGTCCCCATCCGAGATCCTGCCGGGGGACCCACCACGCCCACCCACGTGTGGGTTT\nTTAACGCGTTAAACGTCATTGGGGTAGAGGGTGTAAATAAATTACGAAAACGTGCATGCG\nTTTTTTATTTTTACAATGCGCCGTATATGGTATGTCTGTCATGTGCTCTAAAGTCCCATA\nTATAAAAGAAGCCCCAACGAGTGTATGCGTATTGCGTACCGCGACCCTGGGATGTTTTAC\nAGGCGCGTTTGTTTGTCTCGGTTATAAGTATGCAGTCGGGTCATTATAACCGGAGGCAAT\nCCCGCCGACAGCGGATATCGTCTAATACCACAGACTCCCCCCGTCACACACACGGAACAC\nGTTATCGGTCAACCAATTGGTATACACACCCACCCCAGATATTGTCCAATTCAGAAACAT\nTAGTTGCGGTTCAAGAACTACTGAACTCCGAGATGGATCAGGACAGCAGTTCTGACGCAT\nCGGATGATTTTCCGGGATACGCCTTACATCATTCTACATATAATGGATCCGAACAAAATA\nCATCAACTTCCAGACATGAAAATCGCATATTTAAATTAACGGAGAGGGAAGCTAATGAGG\nAAATCAACATCAATACGGACGCGATCGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGG\nAGGAGGACGCGATCGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGACGCGA\nTTGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGACGCGATTGACGACGAGG\nGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGG\nACGCGATCGACGACGAGGGAGAGGCGGAGGAGGACGCGGCGGAGGAGGACGCGATCGACG\nACGAGGGAGAGGCGGAGGAGGATTATTTTTCTGTAAGTCAAGTTTGCAGTCGAGACGCGG\nATGAGGTTTATTTTACGTTAGACCCGGAAATAAGTTACAGTACCGATCTTCGCATTGCAA\nAGGTTATGGAGCCTGCGGTATCAAAGGAACTTAATGTATCAAAACGTTGCGTTGAACCTG\nTTACCCTAACAGGCTCTATGTTAGCGCATAATGGGTTTGATGAGTCCTGGTTTGCTATGC\nGCGAATGTACCCGTCGCGAATATATTACGGTCCAAGGATTATACGACCCAATTCATTTAC\nGGTATCAGTTTGATACTTCCCGGATGACACCCCCACAGATTTTGAGAACTATACCAGCCC\nTTCCTAACATGACACTTGGTGAACTTTTATTGATTTTTCCTATTGAATTTATGGCCCAGC\nCAATTTCTATAGAACGTATTTTAGTTGAAGATGTATTTTTAGATAGGCGGGCTTCCAGTA\nAAACACATAAATACGGCCCGCGTTGGAATTCCGTCTACGCACTTCCATATAATGCGGGTA\nAAATGTATGTACAACACATTCCTGGGTTTTATGACGTGTCCTTACGTGCTGTGGGCCAAG\nGAACGGCCATTTGGCATCACATGATATTATCCACAGCAGCATGCGCTATTTCTAATCGCA\nTTTCACATGGAGATGGATTAGGATTTTTGTTAGACGCGGCAATTCGTATTAGCGCAAACT\nGTATTTTTTTGGGACGTAACGATAATTTTGGCGTGGGGGATCCATGTTGGTTAGAAGACC\nATCTTGCCGGATTACCACGAGAAGCCGTACCCGACGTACTCCAAGTGACACAGTTGGTTT\nTGCCAAATCGGGGTCCAACGGTTGCCATTATGCGTGGTTTTTTTGGGGCGTTGGCATATT\nGGCCCGAACTAAGAATTGCTATAAGTGAACCATCTACATCTTTGGTGCGATATGCTACCG\nGTCACATGGAACTTGCCGAATGGTTTTTATTTTCACGTACACATAGTTTAAAGCCACAAT\nTTACCCCAACGGAACGGGAAATGTTAGCGTCATTTTTTACGTTGTATGTTACTCTTGGTG\nGAGGAATGTTGAACTGGATCTGTAGAGCAACTGCAATGTATTTAGCTGCTCCTTACCATT\nCCCGTTCGGCTTACATCGCGGTCTGTGAATCTCTGCCCTATTACTATATCCCGGTTAATA\nGTGACCTGTTATGTGATTTAGAGGTATTACTGTTAGGCGAGGTCGACCTCCCAACTGTTT\nGTGAATCCTACGCAACTATTGCACACGAATTAACCGGATATGAGGCTGTTCGCACAGCAG\nCCACAAATTTTATGATAGAGTTTGCCGATTGTTATAAGGAAAGTGAGACCGATTTAATGG\nTAAGCGCGTACCTGGGGGCCGTTTTATTGTTACAACGGGTGTTGGGTCATGCAAATCTTC\nTTTTGTTGCTTCTCTCCGGTGCTGCGTTGTACGGAGGATGTTCAATTTACATCCCCCGAG\nGTATTTTAGATGCATATAATACTTTAATGTTGGCAGCAAGTCCTCTTTACGCTCACCAAA\nCTTTAACATCCTTTTGGAAAGACCGCGATGATGCAATGCAAACTTTGGGGATTCGACCGA\nCAACGGACGTTTTACCCAAAGAGCAAGACAGGATAGTTCAGGCATCACCTATAGAGATGA\nACTTCCGTTTTGTGGGATTGGAGACCATCTATCCCCGAGAACAGCCCATTCCCTCCGTGG\nACCTAGCCGAAAATCTTATGCAATACAGGAATGAAATTCTGGGTTTGGATTGGAAAAGCG\nTAGCCATGCATTTACTACGAAAATATTAAGGGTTGTGATTTTTTTCATTAGGATGAAAAG\nAACGTTTCCTAGCCACACCCACAAAGGAGTTTGTAAAATAAAATCTCTGTTTAGACCTTA\nAAATTTGTTGTGTGTGTTGTGTGGGGGGTCCGTGAGGATCGACCTTTACAAGATATAATT\nTGTCCATATCGCAATGTTTTCTCGGTTTGCGCGTTCCTTTTCCAGCGATGATAGAACGCG\nTAAATCTTATGATGGTAGTTACCAAAGTTTTAATGCCGGCGAACGTGATTTGCCCACACC\nTACCCGGGACTGGTGTTCTATTTCCCAACGCATAACCAGCGAGCGCGTGAGGGATGGATG\nTCTTATTCCAACGCCCGGCGAGGCTTTGGAGACGGCGGTAAAGGCTTTATCTGAAAAGAC\nCGACAGCCTAACATCGCCGGTTTTACAAAGTACCGAAAGACACAGTGTTCTGCTTGGATT\nACACCATAATAATGTTCCTGAATCGTTGGTGGTCTCGTGTATGTCTAACGATGTTCATGA\nCGGGTTTATGCAGCGTTATATGGAAACAATTCAAAGATGTTTGGATGACCTGAAACTTTC\nTGGGGATGGACTTTGGTGGGTTTATGAAAATACATATTGGCAGTATCTCAAATACACCAC\nAGGAGCCGAGGTACCGGTGACTTCAGAGAAGGTAAATAAAAAGTCTAAATCCACGGTTTT\nGTTGTTTTCATCCGTAGTTGCCAATAAACCAATATCCAGACATCCTTTTAAATCTAAAGT\nTATAAATTCGGATTACCGGGGAATATGTCAGGAGCTACGTGAGGCGTTAGGAGCTGTGCA\nAAAGTATATGTATTTTATGCGTCCAGATGATCCTACAAACCCCAGCCCGGATACAAGAAT\nACGTGTACAAGAAATTGCGGCTTACACGGCTACTGGCTACGGGTGGATGTTATGGTTCTT\nGGACGTTGTGGACGCCAGGGTATGTCGCCATCTCAAACTTCAATTTCGACGGATTCGAGG\nGCCGCGCGCGTCTGTTATTCCAGATGATTTGCTTAGACGACATTTAAAAACGGGTCCTGC\nGGTCTCAGCGGGCACAGGAGTTGCGTTTATTTTAGCAGCAACAACTGCCAGCGCTCTTAC\nTGCGCTTTTGCGTATTAGTGTATTATGGCGAAAGGAAGAGTGGCGGGATGGTTTAAATGG\nAACCGCAGCTGCAATTGTTGCGGCGGTTGAACTTATTACGCTTTTGCACCACCATTTTCA\nATACTTAATTAATATGATGCTTATTGGATATGCATGTTGGGGGGATGGGGGATTAAACGA\nTCCTTATATATTAAAGGCGCTACGCGCCCAGGGACGGTTTTTATATTTTGCGGGTCAGTT\nGGTTAGAACAATGTCAACACACAGTTGGGTTGTGTTAGAGACCAGCACCCATATGTGGTT\nTTCCCGGGCCGTGGCGCAGAGTATTTTAGCACATGGGGGTAAACCCACAAAGTATTATGC\nTCAGGTTCTTGCCGCCAGTAAACGGTATACTCCGTTACATTTAAGACGTATATCCGAACC\nATCGAGTGTGTCTGATCAGCCGTATATTCGTTTTAATCGACTGGGATCTCCAATAGGGAC\nAGGTATAGGGAATTTGGAATGTGTCTGTTTAACGGGAAATTATTTATCTGACGACGTAAA\nTGCAAGTTCGCATGTAATTAATACGGAAGCACCGTTAAACAGTATAGCACCCGATACAAA\nTAGACAGCGGACTTCTCGCGTTTTAGTTCGTCCAGACACGGGTTTGGATGTAACTGTCCG\nAAAAAACCACTGTCTGGACATAGGCCATACGGACGGTAGTCCAGTTGACCCAACGTATCC\nTGATCATTACACCCGGATAAAGGCGGAATATGAAGGTCCGGTTCGGGATGAATCAAACAC\nAATGTTTGACCAAAGATCGGATTTACGTCACATAGAAACCCAAGCATCTTTAAATGATCA\nCGTATATGAAAATATACCACCCAAGGAAGTGGGTTTTAACTCATCTTCAGACCCGGATGT\nGGATAGCCTTAACGGGTACACCTCCGGAGACATGCATACAGACGATGACTTATCACCAGA\nTTTTATACCCAACGACGTTCCCGTTAGATGTAAAACCACGGTTACGTTTAGGAAAAATAC\nGCCTAAGAGTCATCATTAAGTACAGCGGTTAATAGATAGTTATGGACTAGGCACTTTGGC\nGGTCATTTCCACAACCAGGTTAAAATTGGGGGATTTGGGAGAAAATAGTCTATTGCGTAT\nTTTCTGTTCAATAATTGGACTGCGTTATTTAAAGGTCTGATTGGTTGATTGGGTTATAAA\nAGGAATTACTCCTTTAAATTTTACTTAATGTACCCACAATATCAAGTGGTCGTTTGTATT\nTAACGATTATTACCGGTACCATGGGAGACTTGTCATGTTGGACAAAAGTGCCGGGTTTTA\nCGTTAACCGGCGAACTTCAGTACTTAAAACAAGTGGATGATATTTTAAGGTATGGAGTTC\nGGAAACGCGATCGAACAGGAATCGGAACGTTATCTTTATTTGGAATGCAAGCTCGATACA\nATTTGCGAAATGAATTTCCTCTTTTAACTACAAAGCGTGTTTTTTGGAGGGCCGTCGTGG\nAAGAGTTGTTATGGTTTATCCGCGGGTCAACCGATTCCAAAGAACTCGCCGCTAAAGATA\nTACACATATGGGATATATACGGATCGAGCAAATTTCTAAATAGGAATGGCTTCCATAAAA\nGACACACGGGGGACCTTGGCCCCATTTACGGCTTCCAGTGGAGACATTTTGGAGCGGAAT\nATAAAGACTGTCAATCAAACTATTTACAGCAAGGAATCGATCAGCTGCAAACTGTTATAG\nATACAATTAAAACAAACCCAGAAAGCCGACGAATGATTATATCGTCTTGGAATCCAAAGG\nATATCCCCTTAATGGTACTACCTCCATGTCACACGTTATGTCAGTTTTACGTTGCAAACG\nGTGAATTATCCTGCCAAGTATACCAGAGATCGGGGGATATGGGCCTTGGGGTACCGTTCA\nACATTGCTGGATATGCACTTCTTACCTACATAGTAGCGCATGTTACAGGACTTAAAACCG\nGAGATTTAATTCATACAATGGGGGATGCACATATTTACTTGAATCATATAGATGCTTTAA\nAAGTGCAGCTAGCTCGATCCCCAAAACCTTTTCCTTGCCTTAAAATTATTCGAAATGTAA\nCAGATATAAACGACTTTAAATGGGACGATTTTCAGCTTGATGGATATAATCCACACCCCC\nCCCTAAAAATGGAAATGGCTCTTTAATGGATTTTTAAATGTTGTCAAGACAGTAGATGTG\nTTGCGAATGTAATAAAATGATATACACAGACGCGTTTGGTTGGTTTCTGTTTATGAACAG\nCAACGGATGCATAGGGTTGCGATAACTGCGATAAGACCCAATGTCCCAAGGATAGATATC\nACACCAATTATAACTGCTACAACGGAAAATGTAGTGGCGTAGGTAGATGCATCGTAGGTA\nTAAACGGCCGAAAACGGAGGGAATTTTTTAGGGTAACCATCTAGATGACACGAATAGGTG\nATAGGTCCGTCGAGTTCCGATGTTGGACAAGAACTTTGCATGTTTACAAACCGTTTGTTT\nTGATCACACACCCCAGTAATCTCACTGTTTTCGTGGTTAATGGGAGAATCGTTAACCCAC\nCATACGAAATGTACAACGCCACGTGGCACACATTTTGCCGTACATACTATGTGTCCATCA\nATAATACCTATAGACACGTTGGGAAATGGATAGACGTCAGGGGTAACGACAGCAGAATAT\nTTCATATTAGAGACGCCATCCCGAATCCATAAAACATTACATTGGATGGCTGGGGGTGGG\nTAATCCATTTGTTTTTGCTGTGGAATTCGTACCGCCGAAACATAACTAAATAATCCATTG\nGCATATTCTTGTATTGCATCGGTTATAAAATTTTTTCCGATGTTACCAAACCTTGAAGTC\nCACCGAACACGTACCGAGTGCGGTGGATAATACTTTGATACGTTACAGTAGGCTGTGTAT\nGTCTGTCCGGTTAAGACTGGATCGCCGACAACGGTAATATTTGGACGATAATACGTTGTA\nACTGTAATACTGTGTTCCGATATGACGTTCTTAGTTTTTGTATTAACGACTCGCCAAATA\nTACGTTCCCTCCGTGGTAGCATCCATAGATAAAATTGTTACAGAAAAATCAGACGTTGTT\nTTAACATCTGGTATTACATAATTTTCCTTAGCGTGTGTAAATATCTCAGGGTTGTTTATT\nAAGTTTAAATCGGCACTGTTGCTATATAACATAACCGGTAAATCTGGCATGCGTATTAAC\nGCATTGCCCAGTTGACGGTGCGGATCTATAAGGTGACGCGTAAACCAAACTTCAATATGA\nAGATCGGGGCGTATAAGCGACTTCCACCTTGTTATATTTGAACCTTCCGGATCTAAAGAA\nTATTGTTCATATGTTTTTTGTTGCTGCTTAAAGGCCGCCTGTTGTCCGGTCGTTAGACGC\nATGTAACAAGGCATGATAAATGTGTGAAAATAGGGTATGGATTGTATTCCGCCGTGAACG\nCATTGTATATTTTCATATAGAAAAGGTGGTTGTGAATGTTGGGTGTTGGCTGCGGGATCG\nGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGTAGCGGCC\nGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGACGGCG\nGGATCGGGCTTTCGGGTAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGAA\nGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCG\nACGGCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTT\nCGGGTAGCGGCCGAGGTATATAATTCAGTTATACTTACGGGTGTGGGTTGAGATTCAGTC\nGATAATTGTATACACGCGATCGTTAAAATTAAATTTATTTGTATCCGCTTCATCCTGGTT\nTTTATTGACACATCCACGCTCCCCTTAAATAAAAGATTAAAACACCCACCGCGGAATTTA\nAATGATGGAAACGTTTTTTTCGACATTGGGAATAATAAAAACGGCTTTTGCAACTTTAAA\nAACTTTATTTATCTCGATTACGATACATATGTACCACATAGATAGCATAGATTTATTATA\nATATAAACACACACGTGATATACTTTAGTGATATGAGATGCCATAAAACAGTCAATAGGT\nTTAACGCTTAGTCTCATCATCTGAATACACGTCAAACCCGCCGCAACTGTTGATGTTAGA\nATTATAATAGCTCCCCATGAAATGCCGGCAAATGTTACAGCTATACCCGTCACCGAGGTC\nGTTGTATATAATACAATTACCCATAGGTTTTTTTTTTCTTGATATAAAACGGCAAAACCC\nTGTAACCCAAATGCTATAATATGACCTCCTATTGAAACTGCTAACGTTACTTGTGTAAGT\nTTGATAAAATGATTTAATTTAATTATATGTGAGATTGCCCACATTAATGGGGTAACTATA\nTATAACACCGGGGGTATAACAGACATTATACGAATTCCTTTAAACACGCGTTTAAGGGTC\nCGGGAACTTTCTCGATGGTCACATACTCTCCCGCGGTCATTTTGTGTATATACAACGGCA\nAAACCTAAATCTGTATAAGTGTTTAATTGCTTATGGCGATTTTTACGATATATACACGTA\nTCTTGCAAATCGGTGGCGGCATCGACAATTGAAACTAGTGTGACAATAGATATACACAAT\nCCAATAAGAACCTCATATTTACTGACATACATATATAAAATAACGGTTAGTAAACCTCCC\nAACCCAGTTCCCAACATCATAACATAAAAATAAATATGCGGTCCATTGAATGTCGTAACA\nAAGTTGTAGTAATGGATATGCACAGCAGCCACTGTTCCGGTAATCGCGGATATGGAAATT\nCCCAGTAATTCTACAAATGGAAGATCCCGGGATATTGGGCAACCAACCGCCCATAACACA\nGCAAAACCCAACACGACCACCGTCTGCAAACATCGTCCCAATTTTGCTAATGTGCGTAGA\nAATTTCACGGATGTTGGCCATAACCCCGAAACGACGATCAACCCCATAATAGTTGCATTG\nACGGCAGCTTCGCAGACGTGATATTGTAAAATTAACCCGGACGTGATAACACTTGCTTGT\nAGTCCCACGAGAAACAACCGCGATGCTGAGGTTATTGCACACGAATTACATTCTTGAGGG\nTTTCCGACACATCCTTGGATTGATTGAGCGCGGATTAATTCTCTGTCTAACACACCCAGG\nTTTTCATCATGGACAGCTCTTTCACCATTCACGGCCATGTCTTAAGTTTAATAATTCAAA\nACAAATAAAAATGTGTTCATCTATGGTACACACAAGTTTGTATGTAAAATATAAGCAAAA\nGTTGCACTTATTTAACTGTACATATTACGTCAGATTCACGTGATAATTCAGAATAATCCA\nGGGTTCCTGCAGGGTCCACTGGAGGAGCCACACAATATTCGCGAATTCCGATTCCCTCCT\nGCCATGTGGTTTCGGGGAGTTTCCCCCCCATTTTATTTCCGGTATTTTTTTCGTTTCTTT\nTTGTTAATAAATTGCGTCTTTTTTTTAATGGTGGTTCATCCTTCACAGATTCCATGTTCG\nCAAATAATTGCATCGAGGTTAATTTTTCTTTAAGGTCTTTGGGACTTAAGAACGTTGCAT\nAAAAAAAAGAATGCACGGGTGCGGAACGTTGGATATACAATCCAACCATGGGGGAGTTAG\nTTAAGGCGAGATAAAAATTAATATAACACGTCTCATCCCGTGTTAACTTAAGATTTTGTA\nCGGCAGAACGGAATCCACTGTGTGTTTCCAATAATACTCCAAATTCACGCATACTCCCGC\nTGCCATAAACAACATTATTAAGGATCCTTTTTGAATTTGTGATTGAGCGTATTAAATTAT\nATGGTGTAGGCTTGCTTCCGTTTATATCCAAGGAAACATTAAATGAGATAAAACCACCCC\nCGGCGGTCTGGATGTACATATCCGTGGCTGTTAGAATGAAGCATGTTGTAAACCCAAAAG\nTTTTAAGTAGTCGCTGTAAACGGGTGAATTGATCGCGTTTTAAGCAAATGCTTATATCTG\nGAGTTAGATTTGGGAACATCATTGTATAACAAGCGAGTTCACGTTTTACAACTTGTTTGT\nAACATTGTACTTGATCATCTGGACCACAATCACCCGGGCGTTGCCATACCATCGTTTGGA\nTAATACTCCGCTCGGGGGGTTGTCCGGTGAATTTAAAATATAACCGTGTTGGGGTCGACG\nGATCTTTTGTATGGCGAAACGCGTCAATAAGCGAGGACCGTCCCTCCGTTGCCGCGAGTA\nCAACCATTCTCGGCCCAGTCCAATTATACTGGTCAAACATATTTGCCGGTATAGGAATAT\nACAGTTGTTCTGTTTCCAAACTACAGTGAATAATTAATCCTTCGTCGCTGAATATTAAAA\nTAGAATCCCTTAGTCTATTAACCAGAGGTGATATAGACGAAATTAAACCAGTAAGCGTTT\nTTTCCGTTAAAACAGCTCTGGCGATTTCTGGGGCGTCAAAACCCGCATGCAATTCCATGT\nCCAAAGCATCGTCTGTACGCGACCTCAAATCCATAATTTACTACTTAAAATGTTTACTAT\nAGAAAAAGTAATCATATGTAAACACACGAGTTTCGTTAATATGTTTGTTTAACCCGATCC\nGGTGACTTAAGTACATAAACAGGCATGATATTTGAATAGTACGGCCCATGGGAGGGAACA\nTTTCCACGTGTTCCAATACAGGGGGTGTTCCTTAATAGGGACTGTGCAATAAAATACGTA\nAGAAGTTACCAGATTTGATGTAATGTTTGTCATAAAAAATATGTACATCATTATATACGT\nCTGTAATTAACACAAGATCACATCGAAGAATTACTGAAGCCGCTGTGAAACCTTTCACAA\nGACGATATAAACTTGGTTAAGTGTATTGATGGGGCTCTTTGGACTGACACGCTTTATCCA\nTGAACATAAACTGGTTAAACCCAGCATCATTTCAACGCCACCCGGAGTTTTAACCCCCGT\nGGCGGTAGACGTATGGAACGTCATGTACACATTGTTGGAACGTTTATACCCTGTGGGTAA\nACGCGAGAATTTACACGGACCATCTGTAACGATACATTGTCTTGGAGTCTTATTGCGGCT\nATTAACACAACGGTCATACTATCCGATATTTGTATTGGAACGTTGTACAGACGGCCCATT\nATCACGTGGAGCCAAGGCAATTATGTCACGGGCCATGAACCACGATGAAAGGGGAACCTC\nGGACTTAACCCGTGTTCTACTATCATCCAACACATCATGTTCTATCAAGTATAACAAAAC\nATCGGAAACATATGACAGTGTGTTTCGAAACTCTTCCGCGAGTTGTATTCCTAGCGAAGA\nAAACAAATCCCAGGATATGTTTTTGGACGGTTGTCCACGACAAACTGACAAGATGATCTG\nCCTGCGCGACCAAAACGTATGCAGTCTTACCTCTACAATGCCATCCCGAGGACATCCTAA\nCCATCGATTATATCACAAATTGTGTGCAAGTCTTATTAGATGGATGGGGTATGCATACGT\nCGAGGCGGTTGACATTGAGGCGGACGAGGCATGTGCAAACTTATTTCATACGCGTACAGT\nGGCTTTGGTTTATACGACAGATACTGATTTACTCTTCATGGGCTGTGATATTTTGTTAGA\nTGCAATTCCTATGTTTGCTCCAGTAGTACGATGTCGCGATTTGCTTCAATATTTAGGAAT\nTACATACCCTGAATTTTTGGTTGCCTTTGTTCGCTGTCAGACCGATTTGCATACAAGTGA\nCAACCTAAAATCTGTTCAGCAAGTTATTCAGGATACCGGCCTGAAAATTCCACATCAAAT\nGGACACTTCAACGCGCTCCCCCACTTACGACTCGTGGAGACATGGCGAGGTTTTCAAAAG\nTCTTACCGTAGCCACGTCGGGTAAAACAGAAAACGGAGTGTCCGTTTCCAAATATGCATC\nTAACCGATCGGAGGTGACAGTAGACGCCAGTTGGGCTTTAAACCTTCTGCCACCCTCATC\nCTCCCCATTGGATAATTTGGAACGCGCATTTGTTGAACATATAATCGCCGTGGTAACTCC\nATTGACCCGCGGTCGCCTAAAGTTAATGAAACGTGTAAATATTATGCAAAATACGGCAGA\nCCCATATATGGTTATTAACACCTTATATCATAACTTAAAGGGGGAAAAAATGGCTCGCCA\nATACGCACGTATTTTTAAACAGTTTATTCCTACTCCACTCCCACTAAACACTGTATTAAC\nAAAATATTGGAATTAAAACACACATAAGAGCGACTTAATGGTTCATTGTTTTATTTTGCT\nCGTATATACATGTTATAAATCGTTTATCACTGTGCCCGCATAAGATGTACTGTGTCTCTC\nAAAAAAATTTGTGTTTTTATCTGCAATCATAAATGCAAGTGGAAAGTCCGAATCTGGAGG\nTGGGGTGTTAAATAGTTTTGGTACATTAATCGCTGATAAAAGCCTGTCCGCGCTGAATTT\nCACGTATTGTGTAATTGCATCGACGTTCACCAAACGGGTTTTGGGTGCATGGGATTTTAA\nAAACGCACACTCGATTTCAACGGCTTCCGAAAACAGTTGATGTATTCTGGTGATAGCGGG\nTTTTTCGGGTACATAGTTATTGTATATACAACACGATGCGCTGGTATGTATGGCTTCATC\nTCGGCTTATAAGGTCGTTAAATTGACAAGTTACAACAAATAGTCCGTTATTGCGTAAATA\nTGCAATAGCCGCGAACGATGATACAAAAAAAATGCCCTCTATAAGAATCATTAGTATATA\nTTTTTCTGCAACGGATGGGTTGTCCCGTACCTTTTCTTCCAACCATTGTACTTTTTGTTG\nGATCGACGGATTATTAATAGTGACATTTACGTATTGTACCCGCAACGATTCATCCCCTCT\nGAACAACATTAGTTGAATTTGACTATAGACACGCGCGTGGACAACCTCGATGCACTCTTG\nTTCAATGTAGTAATGGTGAATATCCTTTTGGGAAAAGAGTTGGGTTAGAGAGCCCAAATT\nAACATTTACCAGATCATCTGCCGCCGATAAAAATGTAAAAATAAATCTGTAGAATATTAG\nTTCATCTTCCGTTAAACAGTCCAAGTATTGATAATCATCTTCAATGATAAAATCGCTTTC\nTAACCAACGATTCGAAATGCTCAGGGCACGTAAATTGTTTATATCTGGACACTCCGGCCT\nGTAAAAAAAATGACTGCAATCTTTCTGATCCATTTTGGAATAGTTTCCCGTGTAAATTTA\nTAAAGCACAACTGGTACAGGTTAATTCGCCTCCCGCAAACAGTCCGCTGTTTGTAGCTTT\nACGAATTTTACAGTAGTACATACCCGTTTTAAGGCCGGCTTTATAGGCACGTATAAGCAA\nATTCATTATTTTGGAGGCGGGAATTGTCCCGTCTGGGCGTTCCTCAATAAATAAAGTCAT\nTGATTGACTTTGGTCAATAAATGGCGCCCTTTCTGCACACATATCAACGAGATCCTCTTG\nCTCATATTCAAACGCTGTTTTATATTTTAAGAGTGGGTGACTATTAGATAAACAGCCAAA\nCGAACGTATTACTGACCATTGGTTTTTCTCAAGTATGTTTATAACTTCCAGTCGTTTTTC\nTTCACATGAATACATATCTCTTAGTTCGTCCATAAGGTCTAAGTTGGGTCTAAGTAACTC\nACCCGAGGTGGTGACCTTACTAAACATATTATTATAAATTGGAGAGAAACCCTCACTGCA\nCTCCGTTACCTGTGCAGATGAAACTGTGGGCATTAACGCTAAGAACTGCGAGTTGTATAA\nCCCATAAGCGCAAATATCATCTCGCAGGGTACACCATGGTAAATCTAAATAACTTATCGT\nAGAAAACCCATCTTGGTGTAACCATCCCTTAGCATATTTACTTTCGGTAAAACCCTTAAA\nCGGGGCTAAGCCGCCAATCTTACACATTTCCATGCTTGTTTTCATTGTCTCATACAACAT\nTAACTCCGCTATTTGTACATTTAACCGTCTAGCTGGTTGGGAAGTTAAATCAAATCCTAA\nGCGGAGACAAGTTGTATGTAACCCTTGTATGCCAATGCCAAGTGATCGGTTGTTTTTTAC\nACCTTTACATGATTTTTTACATGGAAAGTTCCCAGCCGCCAGGACCCCGTTTAAAAAAAT\nAACAGTCGTTCTTGCTGTCAATTGAAGGTCGTTTAAATTAAATGACACTGGGCCTTTGGA\nTAAGCACGTTGTAAGATTTATGCTGGCAAGATTACATACGCCATGTTGATGAGCGTCTGC\nCTTTTGAACAATTTCCGTACACAAATTTGACCCCGTGATAGCATTTCCTTGGGTATTCAT\nATGATAATTACGATTACAGGCATCTTTGAACATTAAAAAGGGGCTTCCTGTTACAGCAGC\nACTGCGTATGATTGTGAATGCGATATCTTGAATGGGAACAGAAGAAACGCCTAATCCTTC\nTCTCTCTAAACGTAAATAGGTTGAAGTGAATGCCTCCCCGTGTAATGTTCGAAGGATATC\nGGCTCTGTTATCAAAAAGAGTCCACTGAACATTACTAGCCCCTTTTAGATAGCTTAGGTA\nTCTTTCAAAAAATAAATCTGGGGTCCATAAACAACAAAATATGTTATCACATCGAAATAT\nTTCATCACGAACCAACATTCCACGTGTGGCCAAAACAGTTTGTAGATCGACGTGCCATGG\nTTCTATGTAAACACAAACTCCAGTTGGTCGTTCACAATCACTGTTAATTGCCATAACCAT\nGCAATCTAAAAGTTTTAAAACTGCAAGAAGACCTTTCGTTTGATTTTCCGTAGGTATTAA\nATTCAGACTCTGTAGAGAAATTCCCACTCCGCCTCGACTTTGTAATACCGTTCCCACATC\nGCCTGTGATAGCTCGAACAGCTCTCCCAACAGTGATGGATTCCGGGTCCATTAAATAACA\nACTGGCCGTTGCCCCGGTCTCTCGACCTAAAAACATCATAACCGGTGTAGCCGGGACAAT\nTTTCTGACATGCCAACGCTGTGAAAAATACCCGACAGACATCAGTCCATGTATAACCATC\nATTTATTCCGGGAATAAGAGTTGCGATTTTAGGCAGGTTTACGATTTCTGTTGTCACGGT\nGGCCGCCAGTCTTAAAAAGAATTGGCAAAGCGACTCTAATTTACCTTCCTCTAACTTAGT\nTAAATAAAAGTCTTCGTACTTTAAAGCAGACTGTAGTCCAAGGGTAGCTAAAGCGGGGTA\nTTGATCTTTCAAAAACGGTTCTAATATAGCCCGACGAATTTCGTCCCTCCGCCCTTCAAT\nTGCTTGGCGGACTCGGGGAGTTAAACAGAGAATTGGGGAAGTCAACCACGTTTCCATGGA\nAACGGATCGTAGGTTAATACGGCAATGGATAAGTTCTCCACAACATCGGTACACTCGCTC\nATCTTGTCGCGTCACCGCCTTAAGTTTTGAGACGATAGTGCTAATATACTCCATTAATTC\nCACCGGTGTGGTTGATTCGGGCGGAATGATGTATTCCTTGTAGCCATGTTGACATAATCG\nGTTTATAATGTCATGAACCGATTAAAAATTCTTTTGAACTCCATAACGGATAACGTATTT\nAGGCTCCGGAATAAACCTTTAAACCCTAAACTCACAGCTGAGTTAGTTCTACAATATTGT\nAGACTCCCTTATATATGGTTACGTACAGCCTGCCCCTCCCCAGTATATAATATCACGCAA\nAACCCACGCTATGTTAAATTCAGTTTATTTTACATACATGCTTTAATAATAACATTCGTT\nCCATGTATTTGTACCCCCCCACACAACCCCCTCTAACCAAATAGTTGGCACGTTATAACC\nTCCGAACCGTTCCATGCGTCTTGTATAACGCACAGACTCTGATGGAATTGTTCCAATTAA\nCGTATATGCCGCATACATGCAGGATAATTGTGTGGGAAGTCCCCGAAAATCGCCGGTCCA\nTTGATACAATCGCTGTCTAGCCAAGTTCCAATTTACTCCTGTAATTTCGCCAATACTACA\nTCGAGGGCTTGTCGGGTCATTGGATAACTGCACAAGCGGCAACGCCCTTGTGTTATATGG\nCTGGTGGGTATTTGCAACCCCTTCAGTCCCCCAGGCGGCATTTTCAGCTCGTATGCGTCC\nTAACAGGAAGCCAATACCACGACCAAAACATTGTTCGTTTAGTTGGCTTAATGCAAGATG\nCAGTCTTACACCTTCTCGTTGGCGTCGCTGTGTATATACAAAAACCAAGAACACATGCTT\nCAGTCCGTCCGCGGAAAGATGTAAGTCTTTGTCAACGTCCCAAAATACGCAGGCCGGGAT\nGTTGGCTGTGACCCTGCGAGTTGAAGTTTTGTCTGTACGTGCAGCTTCTTGGGGACCTTT\nGGCCACGGCGGTTATATTGCATAAATTATCCTGAATGGTATATTCCAGCAGGGACCCAAA\nAAAACTTATAAATCGATGTGGAAATACATGACATTGTACCATCGCACGTAAACACTCCGA\nAAACCTTATGAGCCGCGTTTCCATACGACTGCATCCATAGGCAGAAACAATTGCTGTTCT\nGTTGGCATCTGCTGCCTGTTTATCCGTATATTCTTCTGCCCGGCATGCGGCGATGAAACT\nTAATGACGTTACATATGCTCTAAGCCCCCCACCTTCTCCAACGGTCCAAGGAGCCGTGCA\nGGCATTGAATAGGTTTCGTAAACCCTCTAGTATTACATCGGGGTCACGTCCAGCCTGTGT\nAAGTGTATTAGCTTCTCCAATCATGTCAGATGGATGACGAAGGATTAAGACGATTGACCC\nAGCATGCTCAATGTCCGGACGAAAAAAATCGGTTAATGACACTTGTTGGATTAGCTGTGT\nCGTTGATTTAAAATTATTTAACGGGAGTCTAATGGTAACTTGCGGGTTACCAATTGAAGT\nTGGATTTATTTGAATGTTGTTCATGCGATTAATAACAATTGAACGGGGGGTTACTTGAAT\nAGACGCGGTTTCTGTACGTTTTGGTGGTCCATGTATCGGTTGTTTGTTCAGACCTCCAAA\nGCGAGGGCCAATTGTTAAATCGCGACTCCAATTTCCGAAGAAGCCCGGAGCATAAGTCAT\nATGAAGCCCGTTCCCTATTTGAATAAAACGGTTATTTCCTAAAAGACTGATATTAGTTCC\nACATAGCGTTTGTTCGTTTAAAGTAAAATGCGAGTTGGTTGGTTGACTCCCCATAGCTGA\nGGGGGTAAATTCACACAATGCAATCGTGACGTGGTACTATCTGAAATGTTGCCTGGGGTA\nTGTGTACACATTATACAGTCGTAGTACCGTTTATATAATGTTAGGTAGGAGGAGCCTATA\nAAAATATTTTGATTGGCGTTAAAAGGTTCTTCAACTTACCGTGACGTCCTTTTTATTAAC\nATGCGTTTTTATTGATGTTACATTTATGTCTTTTCATTCCGGACGGATGTAGCTTTTTCA\nTATCACGTTATAAAGTTAAGTCAGCGTAGAATATACCATGGAAGAACCAATTTGTTATGA\nTACACAAAAACTTTTGGATGATTTAAGTAACTTGAAAGTACAAGAAGCGGACAACGAAAG\nACCATGGTCACCAGAGAAAACAGAAATCGCCAGAGTTAAGGTAGTTAAGTTTTTACGATC\nTACCCAGAAAATTCCAGCTAAACATTTTATTCAGATATGGGAACCCCTGCATTCTAATAT\nCTGTTTTGTATATTCCAATACATTTTTGGCGGAGGCTGCTTTCACGGCCGAAAATTTACC\nCGGACTGTTGTTTTGGAGACTAGATCTAGACTGGACGATAGAGGAGCCAGGTAATAGCTT\nAAAAATTTTAACCCAGCTATCAAGTGTAGTACAAGATTCCGAGACGTTACATCGTTTATC\nGGCCAATAAATTACGAACCTCGTCTAAATTTGGACCCGTTTCGATACACTTCATTATAAC\nGGACTGGATAAATATGTACGAGGTCGCCTTAAAGGATGCAACAACAGCCATTGAATCACC\nATTCACTCACGCTCGTATTGGAATGTTGGAAAGCGCCATTGCAGCTTTAACACAACATAA\nATTTGCGATCATTTACGATATGCCATTTGTTCAAGAGGGGATTCGTGTTTTAACACAATA\nTGCAGGATGGCTTCTTCCGTTTAATGTTATGTGGAATCAGATTCAAAATAGCTCACTCAC\nTCCTCTAACACGAGCCCTTTTTATAATCTGTATGATTGATGAATATCTCACGGAAACGCC\nAGTACATAGCATATCAGAATTATTTGCAGATACTGTAAATTTAATTAAAGATGAGGCGTT\nCGTATCCATCGAAGAAGCGGTAACGAATCCACGAACGGTGCACGAGTCACGAATTTCTTC\nAGCTCTGGCTTATCGAGACCCTTATGTTTTTGAGACATCCCCGGGAATGCTTGCTAGGAG\nACTTAGATTAGACAATGGTATATGGGAAAGCAACCTCTTATCGTTGTCCACCCCCGGAAT\nTCATATTGAGGCGCTGTTACATTTACTAAACTCCGACCCGGAAGCGGAAACCACATCTGG\nAAGTAATGTAGCAGAACACACCCGTGGCATTTGGGAAAAGGTTCAGGCTAGTACATCGCC\nTAGTATGTTAATAAGCACCCTTGCCGAATCCGGGTTTACAAGATTTTCATGCAAATTGCT\nACGTCGGTTTATTGCTCACCACACACTCGCCGGTTTTATTCACGGAAGCGTTGTAGCAGA\nCGAGCATATTACAGATTTCCAACAAACACTAGGATGTCTCGCTTTAGTGGGTGGACTGGC\nATACCAATTAGTGGAAACGTACGCTCCTACTACCGAGTATGTGTTAACATATACACGGAC\nAGTAAACGAGACCGAAAAACGGTATGAAACGCTATTACCCGCCTTAGGATTACCACCGGG\nAGGCCTGGGACAAATTATGCGGCGCTGTTTTGCTCCACGACCCCTTATTGAAAGTATACA\nAGCGACACGCGTAATACTACTTAATGAAATTTCTCATGCAGAAGCTAGAGAGACAACATA\nTTTTAAGCAAACACATAATCAATCCTCAGGTGCGTTATTACCACAAGCAGGACAAAGTGC\nCGTACGCGAAGCCGTACTAACCTGGTTTGACCTACGTATGGATTCAAGATGGGGTATTAC\nTCCCCCGGTGGATGTGGGTATGACACCTCCTATTTGTGTTGATCCACCGGCTACAGGGTT\nGGAAGCTGTCATGATAACAGAAGCACTAAAGATTGCATATCCTACCGAATATAATCGCTC\nTAGCGTGTTTGTGGAACCGTCGTTTGTGCCTTATATTATTGCAACAAGCACGCTTGATGC\nCCTTTCGGCAACAATAGCTTTGTCTTTTGATACACGGGGAATACAGCAAGCCTTGTCTAT\nTCTTCAGTGGGCTCGCGATTATGGATCCGGAACCGTGCCCAATGCAGATGGATATCGCAC\nAAAACTATCTGCTCTTATAACAATATTAGAACCTTTTACCCGTACACACCCCCCAGTACT\nTTTACCATCTCACGTTTCTACTATAGATTCCCTTATATGCGAACTTCATCGGACTGTTGG\nCATTGCCGTTGACCTGCTTCCCCAGCACGTCCGTCCTTTGGTTCCTGACCGTCCTTCTAT\nTACAAATAGCGTTTTTTTAGCAACTCTCTATTATGATGAACTTTACGGTCGTTGGACCCG\nACTGGATAAAACATCGCAGGCGTTGGTTGAAAATTTTACATCCAACGCGTTAGTGGTTTC\nTCGGTACATGTTAATGTTACAAAAATTTTTTGCGTGTCGTTTTTATCCAACGCCAGATCT\nTCAGGCCGTTGGTATCTGTAACCCAAAGGTTGAACGCGATGAACAATTTGGGGTATGGCG\nTTTAAACGATCTTGCTGATGCGGTTGGTCATATTGTTGGGACAATACAAGGAATCCGAAC\nGCAAATGAGAGTGGGAATATCCAGCCTGCGCACAATTATGGCCGATGCTTCCTCAGCCCT\nTAGGGAATGTGAAAATTTAATGACTAAAACCTCCACTTCTGCTATTGGGCCTCTTTTTTC\nAACGATGGCTTCCCGGTATGCACGGTTTACACAGGATCAAATGGACATTTTAATGCGTGT\nTGACAAACTAACAACAGGAGAAAATATACCCGGTCTTGCAAATGTAGAGATTTTTTTAAA\nTAGGTGGGAACGAATAGCAACAGCTTGTAGGCATGCCACGGCAGTCCCGTCTGCCGAATC\nTATTGCAACCGTGTGTAATGAATTGAGGCGCGGTTTAAAAAATATACAAGAGGATCGTGT\nAAATGCCCCAACCTCATATATGAGTCACGCCCGAAATCTGGAAGATCACAAGGCAGCAGT\nTTCATTCGTTATGGACTCCAGGCAACAGTTTATTGTGGATTCTGGACCTCAGATGGGCGC\nGGTTTTAACTTCACAATGTAATATAGGAACATGGGAGAATGTAAATGCAACGTTTTTACA\nCGACAACGTTAAAATAACGACAACGGTCAGAGACGTAATTTCAGAGGCTCCGACGCTGAT\nAATAGGACAAAGATGGCTTCGTCCAGATGAGATTTTATCTAATGTAGATTTGCGTCTTGG\nCGTACCCGGGAATACAAGTGGGAGTGACCCTTAATATAAAACAGGCGTGTTTATGTACAT\nTAAAGTATTTGTGGTTTTTATTGACTGGGCGTTTCGTTTGTATAACGCTGTTGTTGCTAG\nTATTTTCATAACCTCCTAGGTTTTTGGAGCTACACGTGCTTATTCAACGCTCTTTGGGAT\nTTGAATCATCGTAAACGTAGCGTCCCTACCAGTTGAGCGCGTAATTTTCGTAAGCAATAA\nAATGGATATAATTCCGCCTATAGCTGTCACTGTTGCGGGAGTGGGAAGCCGTAATCAATT\nTGACGGTGCCCTGGGACCGGCGTCAGGTCTGTCATGTTTAAGAACATCTTTATCGTTTTT\nGCATATGACATATGCGCATGGAATTAATGCAACCCTGTCATCAGACATGATTGATGGATG\nTTTACAAGAGGGTGCAGCATGGACTACGGATCTGTCTAATATGGGGAGGGGTGTCCCAGA\nTATGTGTGCTCTTGTTGATCTCCCCAATCGAATTTCATATATTAAACTGGGGGACACTAC\nCAGTACGTGCTGCGTTTTGTCTAGAATATACGGCGATAGCCATTTTTTTACCGTTCCAGA\nCGAGGGTTTTATGTGCACACAAATTCCCGCTAGAGCGTTTTTCGATGATGTGTGGATGGG\nACGTGAAGAGTCGTATACAATTATAACTGTAGACTCAACGGGAATGGCCATCTATCGTCA\nGGGAAACATATCTTTTATTTTTGATCCACATGGCCATGGGACTATAGGACAGGCTGTAGT\nTGTTCGGGTGAATACCACGGATGTGTACTCTTATATCGCATCGGAGTATACCCACCGCCC\nCGATAACGTAGAATCCCAATGGGCCGCTGCATTAGTTTTTTTTGTCACCGCAAACGACGG\nTCCCGTAAGCGAAGAAGCGCTATCTTCGGCAGTAACGCTTATATACGGAAGCTGTGATAC\nATATTTTACAGATGAACAATATTGCGAAAAACTGGTTACAGCTCAACATCCGTTGCTTCT\nTTCACCTCCTAATTCCACGACAATTGTGCTTAATAAATCGTCTATAGTACCTCTTCACCA\nAAACGTTGGTGAAAGTGTATCCTTGGAAGCAACCCTACATTCAACGTTAACCAACACGGT\nTGCACTGGACCCTAGATGTAGTTACAGCGAGGTTGATCCTTGGCATGCGGTTCTAGAAAC\nAACCTCGACTGGGTCTGGCGTTTTGGATTGTCGTCGTAGACGCCGTCCTTCATGGACTCC\nTCCTTCAAGCGAGGAAAATTTAGCTTGTATCGACGATGGCTTGGTAAATAATACACATTC\nCACGGATAATTTACATAAACCCGCTAAAAAGGTTCTCAAATTTAAACCAACTGTAGACGT\nGCCGGATAAAACACAAGTGGCACATGTATTACCCCGCCTACGAGAAGTTGCTAACACCCC\nAGACGTTGTGTTAAATGTATCCAATGTAGATACGCCTGAATCCAGTCCCACTTTTTCACG\nGAACATGAATGTAGGAAGCAGTTTGAAAGATCGGAAGCCATTTCTATTTGAACAGAGTGG\nTGATGTCAACATGGTTGTCGAAAAACTACTACAACATGGGCATGAAATTAGCAATGGATA\nCGTACAAAATGCGGTGGGTACGTTGGATACTGTTATTACCGGTCATACAAATGTTCCCAT\nTTGGGTAACAAGGCCCTTGGTCATGCCAGACGAAAAGGATCCATTGGAGCTTTTTATTAA\nCCTCACCATTTTGCGTTTAACGGGATTTGTGGTGGAAAATGGAACACGTACACATCATGG\nTGCTACAAGCGTTGTATCAGACTTTATAGGTCCCCTTGGGGAAATTTTAACAGGATTTCC\nCTCCGCCGCGGAACTTATACGCGTTACAAGTTTGATATTAACAAACATGCCGGGGGCGGA\nATATGCTATTAAAACTGTTCTCCGGAAAAAATGTACAATTGGCATGCTCATTATCGCTAA\nGTTTGGTCTAGTTGCCATGCGGGTTCAGGATACAACCGGCGCTTTACATGCCGAACTAGA\nTGTGTTAGAAGCGGATCTAGGAGGTTCGTCGCCCATAGACCTCTATTCTAGACTGTCGAC\nAGGTCTTATAAGTATACTAAATTCGCCTATTATTTCTCATCCCGGACTTTTTGCCGAGCT\nTATTCCAACCCGTACAGGGTCCCTGTCTGAACGAATACGTCTTCTTTGTGAATTAGTCTC\nGGCCCGGGAGACACGCTATATGCGTGAACACACCGCGCTTGTTTCTAGTGTAAAGGCTTT\nAGAGAATGCATTACGGTCTACCCGCAATAAAATTGATGCCATTCAAATACCAGAAGTTCC\nCCAGGAACCCCCGGAAGAAACCGACATTCCACCCGAAGAGTTAATTCGGCGTGTATATGA\nGATACGATCCGAAGTTACAATGCTATTGACCTCGGCTGTTACAGAATACTTCACCCGCGG\nAGTGTTATATAGCACACGGGCCTTGATCGCTGAACAATCCCCTAGGCGTTTTCGGGTCGC\nGACCGCAAGTACGGCACCCATTCAACGGCTTTTAGATTCTCTTCCGGAATTCGACGCTAA\nATTAACGGCAATCATATCGTCCCTGTCTATACACCCTCCTCCTGAGACTATACAAAATCT\nCCCCGTCGTATCTCTGTTAAAAGAGCTTATTAAAGAAGGGGAAGATTTAAACACAGACAC\nGGCTCTCGTATCGTGGTTATCTGTAGTCGGGGAAGCTCAAACCGCAGGTTACTTATCCAG\nACGAGAGTTCGATGAATTATCACGTACAATTAAAACCATTAATACACGCGCAACGCAACG\nGGCTTCCGCGGAAGCAGAGTTGTCTTGCTTTAATACGCTAAGCGCGGCCGTAGACCAAGC\nCGTAAAGGACTATGAAACATATAACAATGGTGAGGTCAAGTATCCTGAAATAACACGGGA\nTGATTTATTAGCAACAATTGTACGTGCTACAGACGATTTGGTGCGACAGATAAAAATTTT\nAAGTGATCCAATGATCCAATCCGGTTTACAACCTTCGATTAAAAGACGATTGGAAACAAG\nGCTTAAAGAGGTTCAGACGTATGCAAACGAGGCCCGAACCACACAGGACACAATAAAGAG\nTCGAAAACAGGCGGCATATAATAAACTCGGGGGGTTACTTCGCCCGGTAACCGGTTTTGT\nGGGACTTAGGGCTGCAGTAGATTTATTACCGGAACTTGCTTCTGAGTTAGATGTCCAAGG\nAGCCCTGGTAAATCTCAGGACCAAAGTCTTAGAGGCGCCGGTAGAGATCCGTTCTCAACT\nTACGGGTGATTTCTGGGCGTTATTTAACCAATATCGAGACATTTTAGAACATCCCGGAAA\nCGCACGCACATCTGTCTTAGGAGGACTGGGAGCTTGTTTTACAGCTATTATCGAAATTGT\nGCCGATACCTACGGAGTATAGACCATCATTGCTTGCGTTTTTTGGTGACGTGGCAGATGT\nGCTTGCATCCGACATCGCGACCGTATCTACTAACCCGGAAAGTGAGTCCGCCATAAACGC\nTGTTGTTGCAACTCTTAGTAAAGCGACGTTAGTTTCATCTACAGTGCCAGCCTTATCCTT\nTGTGTTGTCGTTATATAAAAAATATCAGGCTTTACAACAAGAAATTACGAATACCCATAA\nGTTGACTGAATTACAAAAACGACTTGGAGATGACTTCTCCACCCTAGCTGTCTCATCTGG\nACACTTGAAGTTTATATCATCTTCAAATGTAGATGATTATGAAATAAACGATGCGATATT\nATCAATACAAACAAATGTGCACGCCCTAATGGATACGGTTAAACTTGTTGAAGTTGAACT\nGCAAAAGCTACCCCCCCATTGTATTGCTGGGACATCTACCTTATCTCGAGTAGTAAAGGA\nTCTTCATAAACTCGTCACAATGGCACATGAGAAGAAGGAACAGGCAAAAGTGTTAATTAC\nCGATTGTGAACGTGCACATAAACAACAAACGACTCGGGTTTTGTATGAGCGTTGGACACG\nTGATATTATAGCATGTCTGGAGGCAATGGAAACGCGCCATATATTTAACGGGACAGAACT\nGGCACGGTTGCGAGATATGGCCGCTGCGGGAGGGTTTGATATACACGCAGTTTACCCACA\nAGCACGTCAGGTTGTAGCGGCATGTGAAACTACAGCCGTTACGGCATTAGATACTGTGTT\nTCGCCACAATCCATATACCCCCGAAAATACAAATATTCCCCCACCTTTGGCTTTGTTAAG\nAGGGTTAACATGGTTTGATGATTTTTCGATTACGGCTCCCGTATTCACCGTTATGTTTCC\nAGGTGTTAGTATTGAGGGACTCCTTCTGCTTATGCGTATTCGCGCGGTTGTGTTATTATC\nCGCCGATACGTCTATTAATGGAATACCTAACTACAGAGATATGATATTACGAACCTCGGG\nGGATCTATTACAAATACCCGCATTGGCTGGGTATGTTGATTTTTACACACGGTCTTATGA\nTCAGTTTATAACCGAAAGTGTAACGTTAAGTGAACTTAGAGCAGACATCAGACAGGCTGC\nCGGGGCTAAACTTACAGAAGCAAATAAGGCTTTGGAGGAAGTAACTCATGTTCGGGCACA\nCGAAACGGCTAAACTTGCACTTAAAGAAGGTGTCTTCATTACATTACCAAGCGAAGGTTT\nATTGATTCGGGCTATAGAGTATTTTACAACTTTCGATCATAAACGATTTATAGGAACGGC\nATATGAAAGAGTTTTACAAACAATGGTAGACCGCGATCTAAAGGAGGCCAACGCAGAGCT\nTGCACAGTTTCGTATGGTGTGTCAGGCAACAAAGAACCGTGCAATACAAATTTTACAAAA\nCATTGTTGATACTGCCAATGCCACTGAGCAACAAGAAGACGTGGATTTCACTAACCTGAA\nGACGTTATTAAAACTAACCCCCCCTCCCAAAACAATTGCATTGGCCATTGATAGATCTAC\nTTCCGTTCAGGACATTGTCACGCAGTTTGCATTGCTGTTAGGGCGTCTGGAAGAAGAAAC\nTGGTACGTTGGACATTCAGGCGGTTGACTGGATGTACCAAGCTCGCAATATTATTGACTC\nCCATCCACTAAGTGTGCGTATAGACGGTACCGGCCCCCTGCATACTTATAAAGATAGGGT\nGGATAAACTTTATGCGTTACGAACTAAATTAGATCTCCTACGACGACGAATAGAAACCGG\nTGAGGTTACGTGGGACGATGCATGGACAACATTTAAAAGAGAAACGGGGGATATGTTGGC\nATCGGGGGACACGTACGCTACTTCCGTAGATAGTATAAAGGCACTCCAGGCATCGGCGTC\nTGTGGTTGACATGCTTTGTTCCGAACCCGAATTTTTTTTATTGCCTGTGGAAACGAAAAA\nCCGTTTCCACAAAAAGCAACAGGAACGTAAAACGGCGTTGGATGTTGTGTTGCAAAAACA\nAAGACAGTTTGAAGAGACCGCGTCTCGCTTACGAGCTTTAATTGAACGTATTCCAACGGA\nGAGTGACCATGACGTTCTTCGTATGTTATTACATGATTTCGATCAATTTACACATTTGCC\nTATATGGATAAAAACACAGTATATGACATTTCGAAATTTACTCATGGTACGGTTAGGCTT\nGTATGCAAGTTATGCTGAGATTTTTCCACCCGCGTCTCCAAACGGAGTGTTTGCTCCTAT\nTCCCGCCATGTCGGGTGTATGTCTAGAAGACCAATCCCGATGCATTCGCGCGCGGGTGGC\nCGCGTTTATGGGGGAGGCGTCTGTGGTGCAAACGTTTAGGGAAGCCAGATCTTCTATAGA\nCGCTTTGTTTGGAAAAAATTTAACCTTTTACTTGGATACTGATGGGGTTCCACTTCGATA\nTAGAGTGTGTTATAAATCAGTTGGGGTTAAACTTGGAACCATGCTATGCAGGCAGGGTGG\nATTATCTTTACGACCGGCACTTCCCGATGAAGGTATTGTGGAAGAAACTACACTATCGGC\nATTACGCGTGGCCAATGAGGTCAATGAGCTACGCATTGAATACGAATCCGCTATAAAATC\nCGGGTTTTCTGCCTTTTCCACCTTTGTTAGGCATCGCCACGCCGAATGGGGTAAAACCAA\nCGCACGCAGAGCCATTGCAGAGATATACGCCGGCCTTATAACAACAACATTGACACGACA\nATACGGGGTTCATTGGGACAAGCTTATTTATTCTTTTGAAAAACACCACCTAACTTCTGT\nAATGGGCAATGGACTAACTAAACCAATCCAGAGAAGGGGTGATGTACGCGTATTAGAGTT\nAACCCTATCTGATATTGTAACTATTTTGGTTGCCACAACCCCGGTACATCTTCTCAATTT\nTGCTAGATTGGATTTAATTAAACAGCATGAGTATATGGCCCGTACCCTCAGACCCGTAAT\nCGAGGCCGCATTTAGAGGTCGTTTACTCGTTCGCTCATTGGATGGAGACCCGAAAGGCAA\nTGCCCGGGCCTTTTTTAATGCCGCCCCATCCAAACATAAACTCCCGTTAGCTCTTGGATC\nAAACCAAGATCCTACCGGCGGGAGAATATTTGCATTTCGGATGGCAGATTGGAAACTTGT\nTAAAATGCCACAGAAAATAACGGATCCTTTTGCGCCATGGCAACTTTCCCCCCCCCCCGG\nGGTAAAGGCCAATGTCGATGCAGTTACCCGTATAATGGCAACAGATCGTCTTGCGACCAT\nTACTGTACTTGGGCGCATGTGTCTCCCGCCAATTTCCTTAGTGTCAATGTGGAATACGCT\nGCAACCGGAGGAATTCGCATACAGAACACAAGATGATGTGGACATTATAGTTGATGCGAG\nACTGGATTTGTCATCCACGCTTAATGCAAGATTTGATACCGCTCCCAGCAATACCACGTT\nAGAGTGGAATACAGACCGTAAAGTAATTACAGATGCTTATATTCAAACCGGGGCAACGAC\nAGTTTTTACAGTAACGGGGGCGGCACCAACTCACGTTTCTAATGTAACAGCGTTTGACAT\nAGCAACTACGGCTATTTTATTTGGGGCTCCTTTGGTTATTGCCATGGAACTTACATCCGT\nTTTTTCACAAAATTCCGGACTTACTTTGGGGTTAAAATTATTCGATTCCCGGCATATGGC\nTACAGATTCGGGTATATCCTCAGCCGTATCTCCCGATATTGTTTCTTGGGGGTTACGTTT\nACTGCATATGGATCCTCACCCAACTGAAAATGCATGTTTAACTGTCCAACTAGAAAAACT\nGTCCGCGCTCATTGCAAACAAACCTCTTACAAACAATCCCCCGTGTTTACTGCTATTGGA\nCGAACATATGAATCCCTCTTATGTTTTATGGGAACGAAAAGACTCGATTCCAGCTCCGGA\nTTATGTGGTCTTTTGGGGGCCAGAATCTCTTATTGATTTGCCGTACATCGACTCCGATGA\nGGACTCTTTCCCCTCGTGTCCCGATGATCCATTTTACTCGCAAATTATTGCCGGTTATGC\nGCCCCAAGGCCCCCCAAACCTCGACACAACTGATTTTTACCCAACGGAGCCACTATTTAA\nGTCTCCCGTTCAAGTTGTTAGAAGTTCCAAATGTAAAAAAATGCCCGTCCGGCCCGCGCA\nGCCCGCGCAGCCCGCGCAGCCCGCGCAGCCCGCGCAGACCGTCCAGCCCGCGCAGCCCAT\nAGAACCGGGCACACAAATAGTGGTACAAAATTTTAAGAAACCCCAAAGCGTAAAAACAAC\nCCTTAGCCAAAAAGATATTCCCTTGTATGTGGAAACCGAATCAGAAACGGCTGTGCTTAT\nACCTAAGCAATTAACCACCTCCATTAAAACAACCGTTTGTAAAAGTATTACCCCACCAAA\nTAACCAATTGTCGGATTGGAAAAATAATCCACAGCAAAACCAAACGTTAAACCAAGCGTT\nCAGTAAACCAATACTTGAGATTACCTCCATTCCGACAGATGACTCGATATCTTACCGGAC\nTTGGATTGAAAAATCAAATCAAACACAAAAACGGCATCAAAATGACCCTCGAATGTATAA\nCTCCAAAACAGTATTCCACCCTGTAAATAACCAATTACCTTCTTGGGTTGACACGGCAGC\nCGATGCCCCCCAAACGGACCTATTGACAAACTATAAAACAAGACAGCCGTCGCCAAACTT\nTCCGCGGGACGTACACACATGGGGCGTATCTTCTAACCCGTTTAACTCACCGAACAGAGA\nCCTATATGAAAGTGATTTTAGTGAACCTTCTGACGGCTATAGCAGTGAGAGTGAAAATTC\nTATCGTACTAAGTCTCGACGAACATCGGTCATGTCGCGTTCCTAGGCACGTACGCGTTGT\nTAATGCCGATGTAGTCACCGGTCGACGTTATGTCCGAGGGACCGCCTTGGGAGCACTGGC\nCCTGTTAAGCCAGGCATGTCGGCGTATGATCGACAACGTTAGATATACACGTAAACTTTT\nAATGGACCACACGGAAGATATATTTCAAGGCCTGGGGTATGTTAAATTGTTATTAGATGG\nAACATATATATAAAGTAGCGCCTATTAAAGAAAAAAAAAAAACAACGATTATTTTCTGTG\nTATTTTTATTTACACCCTACGACTTCTTGAAGCGTTTCCAGATTGTCCCGTGTGTGACAA\nGGTCTGTCCCTTACCCCCCTGGGGGGTATTTTGGGTTGGGGGCGGGGTAGACTGTGGCAC\nGCCTTGGGCCGCGGGCGGTGATCCGGTTGTTGGCTGGACAGTGCTTGACTGTGCTCCCTG\nTTGCGGTTGTTGTCCAGAAGACCCCGACACCACGTGTTGCTGTTGTCCAACGGATGCCGA\nCGTCGTTTGAGGTGGGGGGTGTTGCGGGGATGATCCCGAAAACGCCAACGCGGCGGGCTG\nTTGTAAAGCAGACTGATCGGCGCTCTGTGTTTTTTGCGGCAATATAGTAGGCCCCGAGAT\nTCCCAAACTCATGGATGGATTTGGGGGTTGTGGTCGTATAATACGCGGGTTAAACGTACG\nTTTTAAGCCAACCGTTGGTCTTAACCATGTCATAGGGTCAGTCTCGGCAAACATGGCCGT\nTCGGCGTATCGTATTTGCATTATGGTTAGCGCGTGCACGCGCGGCACTGGCCGCGGCTCC\nCACGGTGTAAATGCTTCTGGCATCAGCGATGTCCACACGGTGACCAGGTTGCAAAGGTCC\nACTGGCGTTTAAAAGTCGTATTAAAGCAACGGGGGTGTAAGCCGCAATTGCTTCCACCGA\nAAATGTGGTGGGGTTGCTGGGATCAAAGACTACACGAGACGATGCGGGTTGTGTCATCGT\nTTATTAGTTTACGGGACAATCGATAACAGCATACACGTACATCTGCGCAGGATATGTACG\nGAAAGGCAATTTATTTCCAGAAAAGCACCGCCCCTAATACAACTACCAGTACAATTACAA\nCGAACAGGGCATATGTCACGTTAGCTACGGGTAGAGCAAGTTTCCAGACACGCGTAGTTT\nGGGTATCGGGTAACGCAGGTTTAATGTCACTTTGCATTTGAACAGACGTGTTTGGACTTC\nCGTTCTCGGGTGGGGATCTGAATGAAGGCCGCCAGCGTATATATTCATCCAAATTATTGC\nCAGTTTCCTTATACATGTATGCATCCGTGGCGCGGGCCATAAGTTTAATGGTGCGAGATG\nGATCTTCCGGTCCCATAAAACGAAAGGATAACTGAACATATGGCATTCGCACAAAGCAGT\nTCACCCACATTAAAGCCTGGAGAGGTCGGCGGTCAATACCCCCACCTCGTTTAATTGATT\nCCAAAGCAGATAGGTTGATACCGGTACTTAACGTTGAACTAAGAATCACGTTATTACTGT\nCAATGGACACTTCAGCCACTGGTGCGTTAGTCGGACGAAAAAAAAAACCTTGAAATAGCA\nCAGACACCCCCGTATTTTGAATTTTTATGTAAGGGTCACAATCTACTTGCGCCCAATTCG\nCCATTAAACGCATAATATACTCTACCGGAAAGGCTTCGGATACGTTGTCTTCGCCGTTAA\nACTGAAAAACACAACGGGCGGGGGGGCGTTGTGGATCAAATATTGGAAGATCCCCATCGC\nAACATTGAAGAGCGCTTGGTACCACCAACCGAATACGTTGTAAAAGATTATCTCCGCAAC\nCCCTCCTGCGTTCACTCCGTACATACGTTCTCCGTGACATATTGATCTAAGGTTGCAAAC\nCAAGGCACACGCGTGAAGTATTTAGACCATTTATCGTGGGATATAGGAGGAGTTTGGAGT\nGATCCACCCCCTGACGACTTATTAATGCGTTTATTTTCCCCATGTATTAAGCATCCTTCA\nATATTTCATGCAAATCTAGAAATTTGGCCATGACTCCCGCAAAGCGTTCACGGCGACGGG\nTCACGCTGGCACTATGTTCACATGGAACAACATAAGCAGATTTTTCTGAATCGTTACTTT\nCTTTATGTTTTAAAACGGACGCCAGGCGACTGGTAAATGATATATAATTTAATTGAGCGT\nCAGTTGTAGGTAGAATTGCTTCTATTTCCGGGGGAATTAAATTTTCAAACCAAACGGAAA\nGAGTAAAGGTGCTATCAGCAGGAAAATACTTTGACTCCAGTGCATCGATATTTAATAGAT\nTAACATCGGTGTCTGTAATTAAATCGCGGGCCCTCATCCCAGAGATGGATCGGGTAGAAT\nCAGAAGAACCCATGGATGGATTCGAATCGCCCGTATTCTCCGAAAATACATCTTCTAATT\nCCGGATGGTGTTCCGACGCATTTTCCGATTCGTACATCGCTTATAATCCAGCCCTTCTGC\nTAAAAAACGATTTGTTATTTTCAGAATTGTTATTTGCCTCCCACTTAATAAATGTTCCCC\nGTGCAATAGAAAACAACGTCACTTATGAGGCCTCTTCGGCGGTAGGTGTGGATAATGAAA\nTGACCTCAAGTACCACTGAATTTATAGAAGAAATTGGAGACGTTTTGGCGTTAGACAGAG\nCCTGTTTGGTCTGTAGAACGCTTGATTTGTATAAACGTAAATTTGGACTGACACCGGAAT\nGGGTTGCGGACTACGCCATGTTATGTATGAAAAGTCTGGCATCCCCGCCCTGTGCAGTTG\nTCACTTTTAGCGCTGCCTTTGAATTTGTGTATCTTATGGATCGTTACTACCTGTGCCGTT\nATAACGTTACTTTGGTTGGGTCCTTTGCCAGGCGCACGCTTTCCCTGTTAGATATACAAA\nGACATTTTTTTTTGCATGTATGTTTTCGTACCGATGGAGGGTTACCAGGTATACGACCGC\nCCCCCGGTAAGGAAATGGCCAACAAAGTAAGATATTCCAATTACTCCTTTTTTGTACAGG\nCGGTAGTTAGGGCTGCATTACTATCGATCAGCACGTCTCGTTTAGACGAAACCGAAACGC\nGTAAGTCATTTTACTTTAATCAGGACGGACTGACTGGAGGCCCTCAACCTTTAGCGGCCG\nCCTTGGCTAATTGGAAAGATTGCGCGCGGATGGTTGACTGTTCATCATCGGAACATCGCA\nCAAGTGGGATGATTACCTGCGCGGAACGTGCATTAAAAGAGGATATAGAGTTTGAAGATA\nTATTAATAGACAAACTTAAAAAATCGTCTTACGTAGAAGCAGCTTGGGGTTACGCAGACT\nTGGCTTTATTATTACTGAGTGGGGTTGCTACTTGGAATGTAGACGAGCGTACAAATTGTG\nCTATAGAAACTCGCGTTGGATGTGTTAAATCATACTGGCAGGCGAACCGGATTGAAAACT\nCCAGGGACGTTCCAAAACAATTTTCCAAATTTACGAGCGAGGATGCCTGTCCCGAAGTAG\nCATTTGGGCCTATTTTGTTAACTACCTTAAAAAACGCAAAGTGCCGTGGTCGCACGAATA\nCCGAATGCATGTTATGTTGTTTATTAACCATAGGGCACTATTGGATCGCTTTGCGGCAGT\nTTAAAAGGGATATATTAGCATACTCAGCAAATAACACAAGTTTATTTGACTGTATCGAAC\nCTGTAATCAATGCATGGAGCCTAGATAACCCCATTAAACTTAAATTTCCATTTAATGATG\nAGGGTCGATTCATAACCATTGTAAAAGCAGCAGGTTCCGAGGCCGTATATAAACATTTAT\nTTTGCGATCTCCTATGCGCTCTCTCGGAATTACAGACAAACCCTAAAATTTTATTTGCCC\nATCCTACAACCGCGGATAAGGAAGTGTTGGAGTTATATAAAGCCCAACTGGCTGCACAAA\nACAGATTTGAAGGTCGTGTATGTGCTGGCCTGTGGACATTGGCGTATGCATTTAAAGCCT\nACCAGATTTTTCCACGCAAACCAACCGCCAATGCCGCATTCATACGAGATGGAGGACTTA\nTGCTTCGACGACATGCAATATCGCTGGTCTCCCTCGAACACACCCTATCGAAGTATGTCT\nAGGCGATATAAATCCGTATCTCGGAGCGGGCCTTCGATGCGTGTACGCTCCAGAACGCCA\nTGCCGCCGTCAAACCATTCGAGGAAAACTTATGTCAAAGGAGCGGTCTGTGTACCGCCAT\nTATTTTAATTACATCGCAAGGTCCCCCCCAGAAGAACTAGCTACCGTTAGAGGCTTAATC\nGTGCCAATTATTAAGACGACCCCTGTCACCCTTCCGTTTAACTTGGGTCAGACAGTGGCG\nGATAACTGCCTGTCGTTATCCGGAATGGGTTATCATTTAGGTCTCGGAGGTTATTGTCCG\nACATGCACTGCATCTGGAGAACCGCGTCTATGTCGAACCGATCGGGCGGCTCTGATACTA\nGCATATGTTCAGCAGCTTAACAACATATACGAATATCGTGTGTTTCTTGCATCCATTTTG\nGCGCTATCAGACCGAGCCAACATGCAAGCAGCGTCCGCTGAACCCCTATTGTCGAGCGTA\nTTGGCACAACCGGAATTATTTTTTATGTATCATATTATGAGGGAGGGGGGCATGCGAGAT\nATACGCGTACTTTTTTATCGTGATGGAGATGCCGGAGGGTTTATGATGTATGTTATATTT\nCCGGGGAAATCTGTTCACCTCCATTACAGACTAATCGATCATATACAGGCCGCGTGTCGG\nGGGTATAAAATAGTCGCACACGTTTGGCAGACAACATTTTTACTGTCGGTATGTCGCAAC\nCCAGAACAACAAACAGAGACTGTGGTGCCATCCATTGGAACATCGGACGTTTACTGTAAA\nATGTGTGACCTTAACTTTGATGGAGAATTGCTTTTGGAATACAAAAGACTCTACGCATTA\nTTTGATGACTTTGTTCCTCCTCGGTGATTTCAGCTTCAGTGTTCATTTTATTATCCCAGC\nACGGGGCGTGTATACAAACAAAGCCTGCCGCCTGCAAGCGGTTTAGCATTTTAACGTTAA\nCAACTCGTGTCTCTGGAATAAAACGTTTTAAAAGCCGTTCTGTGAGTTTAGTGTCGTTTC\nCAAATAACGCCTTAAAAGTTACACTCGCCGTCCCAATGAGATGAGAAAAATAATAGTCAA\nTGTTTAAAGACAGCCCGTGTGATGTTACGTGAATGGGATCTTCCGCTAAGTCAGATATTA\nTTAACTTACGCTTTGCTTCCCCACACCGTTTACCTGCGGTATTCTGTAAAGGATCTCCAC\nGTAGCAAAGCTACACTTTTTGCATCAGCCTCCACTTCGTCTGTGGGGGCCACAATAACAT\nAAGGGATGCGTTCTCGAACGTTTGGGATTTGACCCTGTCTCATTACTAATTTATAATATA\nCTGTTAAGTGAGCCAAGCGACGGTTTATGTAGGCGGATGGTGGACGACTAAGCTCGGCCG\nTCATAACAAACTTATTAATATCCAATTTGGGTGATGTAATCTGGCGATGTGCATCTGCAA\nTTATGCGTCCAAACCCGGCCATCCCAGACGGCATGGCCCGTCTATTCCATTCAGCAATGG\nAAACACACGACGCCTCCGCCGCAGCACGCGAGACGGTGTCGTCATATAACAACAGTTCTA\nCAAGTTTGCGGGCATAATCGTTAATAAATTGACAGTTGTTTTTTCTAACCAAGTCGACTC\nCCTTCATTAAAACCTTTCCGCCGTAAATTACCCCAATGTACTTTTTCTTTGTTATAAGCA\nAAAGTTTTATAAAAGTTTTTTCACACTCCAACTTTATAGGAGGACAAAACAGAGCCGTTG\nAAATTATATGTGCCATTTTCTCGCCGATTTTAGCTATCCCCTCAACACCAACACCCTTGA\nATCGGATAAACACAGAATCCGTATCTCCATATATAACCTTTACCTCGTACGCTTTTTGGG\nAGAGAACGCTACTTTCAATGTCTGGAAACGCTGTAATAAAACGTTCAAATGCGGCCCAGT\nTATTATGAATATAATCTCTGGTACTTAATAACATTTGACGGCCAATTGTAGTGACAGTGG\nCCGCTACGTATAAACATGGCAGAAATCCCTGCGCAACTCCAGTAAAACCGTACACGGAAT\nTACAAACTACTTTTATCGCGGCTTGTTGTTTGTCTAATAACACTGCTTCATCTGAAGAAC\nTTCCGGGTATGCGCGCTCTAATAGCCTTGCGCATAGCCAACCAGTCTTTTAAAAGAACAC\nCCAGCAGACTTTCTCGAACGTTAGAGCGCACAAAAAAAAGACGTTTTCCTCCAACTGTAA\nAGGTGGCATAATCGGATGGATTCAAACGTTTAACCGTCTCAAAATTTAACGTTAGCGTGG\nTAAAACATAAGTTATGGGCCTGAATTATACTTGGATATAAACTTGCAAAATCCAATACGA\nCCACCGGATCGATATAAAATCCCGTATCAGGGTCAAAAACCCTGGCTCCTTTATATCCTA\nCATTTCGCCCACTTGACGTACCAGTGGGAGAAACGCTCTCGTCTTCATCCATCTCTTCCT\nCAACATCCCCGACATCGGGAATAACATCCTTATATTCAAAAGTAGCTGGGTATCCCCCAT\nCGGGTAAAATAAATCCTCGAGACGAAGCCAGTCCTAATAAACAGGTGTAAATCCTAACCT\nGCTGTCCGTCGTAAATAGCCTTGGTTAAAGTAATTCTAGCTAGCCTTGCAACCGCGGATA\nACTCAAGGTGTGGTAAATATTTAAAAAACAGTTTCCCCACAAGAGCCGAGTCTTGTATAC\nAATATTCACCAATAATTCCTCGTGTATTCGGTCCACTAGCGTAGTATCCCGGAATGTCTT\nTGTAGGGCAAATCTCTCTTGGACTCATTTAGAGCTTCACGTGCAACCGAATCTAATTTAT\nAACTCGAGAGTTTTAATTTTTCAGTTGCAATTGCATACATATCCAGAGATATGAGACCGT\nTGATCTTTACCTTGCTTCGTCGCTGAAATCCGGATTTGCCAACATCCCATATCTTAAACA\nGACCCCCACGGTTTATACTGCCATAACCATCAAGCTTGAGACTGTATATAGAATTAAGTT\nTCTCCATAATAAACGCCCAATCAAAATTAACAATGTTATAACCTGTGGCAAACTCGGGAG\nCGTACTGTTTTACGAGGGTCATAAATGCAATTAATAGCTCGAATTCACTATCAAACTCCA\nGCACAGTCGGCTCCGGTAACCCCGCGTCCTTCATTTCTTGTACATACCTTTGTGGTAAGT\nCACAAGAGCCAAGGGAAAACAGTAAAATGTGTTCTAAAGACTGTCGAGGGATTGAATATA\nATAGACAAGAAATTTGGATTACAAGATCCTCCAGATGTGTTGCATCGGGAAACGCCAGCT\nCATTAGATCCTCCTGATTTACATTCAATATCGAAACATAACAACTTGTAGTCAGGCCATG\nAGTCATCGTTTGGTATAGCCTGCAGATTATCCGACATGCAGTCAATTTCAACGTCGCTTA\nACGTTAATTGGCGACTTGCCGGTCGAACTCGAACACGTTCCCCATCAACTCCAGGTTTTA\nGTTGATACCAACCAAAACTAACAAAGCCGGGATTATCCATTAGAAAACGAGTGGTAGCGT\nCTACCCGACCTTCATACTTTTTCAACTCCGGGTGAAAGTTATCACAAAGATAATTTGTAA\nATTTAGATGAGGGAGAATACACCCTGTAAAACGCACATGGCTGTGTATCGTAGTAATAAA\nCATCTGTGCGCTCAATAACCTCAACGCGAAAGCTTTCTGGAGATGCGCTTTTAAACGAGG\nTACCATGAAAAGCGTTCTTGTCTCCATTTAACGTTGCATCATTTTGTGTTATCATAGAAC\nTGCGTAAACACTCGGCAAGTAATACAGATAACTCGCTACCGGAACGTATGCCACAAGCGG\nTATCCACCTCGGCTTTGTTTATATAAAAATATTGACAGATGCCGTATACATGAACTGCCA\nCCCTTTTTCCACATCGGGACATGCCAAGTAAAGTAATAACGGTACCAAGCGGTCGTGTTG\nCAGTTGCAAACCGGGATACATCTCCATTAGACGCGGCTTCTGTTGTTTCGACAATATCAT\nATACATGGAATGTGTTAAAGCGGGGGTCAAACTTATCCCCACGAAAGTCGATTTCCCCCC\nAAATATTCACGCGTCTAGGCCAGGGGCTGGAACAACGAAAATCCAGAATCGGAACTTCTT\nTTCCATTACAGTAAACTTTAGGCGGTCGACTAAGTGTACCGACGTGAACCCCCTTTCGTT\nCTTCCATGGGCACATCTTCATCTAAACATTTAGGGGCCAAAAATTGAAACGATGACATGG\nTAGTTTTGTAACTATGAAGAAATTCTCTGTTACTACCGCGCCCGGTTCTTGGGTTATATG\nTAATCCCTGATGCTTGGGTTAAAAAGGGATTACAAAACCCCGTTCTGATCGCCATTTTAT\nGTTAACGATTGATAATCTTGTAAAAAGCCAGTGTTACTGAGTAACACAACCCCACGCCCT\nTCTAATACATAAAGTGTAATCACGTGATTTGTTGTGGTTTCCGCATATGTAATACCCGTT\nTAAAAGCCTCTCTTCTTAATGTATCGACAGACTGGGTTTTGGGTGGTCATTTGACCCTGC\nCAACAACCCCCCATTATTACGAGTACTTCACCAAAATGGAAAATACTCAGAAGACTGTGA\nCAGTGCCCACGGGGCCCCTGGGTTACGTTTATGCGTGCCGGGTTGAAGATTTGGATCTGG\nAGGAAATTTCATTTTTGGCCGCTCGTAGCACGGACTCTGATTTGGCTTTATTACCTTTGA\nTGCGTAATTTGACCGTGGAAAAAACTTTTACATCCAGCCTGGCGGTGGTTTCTGGAGCAC\nGCACTACGGGTCTTGCCGGAGCTGGTATTACCTTAAAACTCACTACCAGTCATTTCTATC\nCATCTGTCTTTGTCTTTCACGGAGGCAAACACGTTTTACCCAGCTCCGCGGCCCCAAATC\nTCACACGCGCGTGTAACGCGGCTCGAGAACGGTTTGGGTTTTCACGCTGCCAAGGGCCTC\nCTGTTGACGGTGCTGTTGAGACGACCGGCGCTGAGATATGCACCCGCCTTGGATTAGAGC\nCAGAAAATACAATATTATACTTGGTGGTCACGGCATTGTTTAAGGAAGCCGTATTTATGT\nGCAACGTGTTTCTGCATTATGGAGGACTCGATATTGTTCATATTAACCATGGGGATGTTA\nTACGTATACCGTTATTTCCGGTACAACTTTTCATGCCCGATGTTAACCGTCTGGTACCCG\nACCCATTCAACACTCATCACAGGTCTATCGGAGAGGGTTTTGTATACCCAACACCCTTTT\nATAACACCGGGTTGTGCCATTTAATACATGACTGTGTTAAATGGCACAACCCGGTGTTAT\nTGCTCCCATGGCCGTTGCCTTGCGCGTCAGAAATGTAACTGCCGTCGCCCGAGGAGCGGC\nCCACCTTGCTTTTGATGAAAATCACGAGGGGGCAGTACTCCCCCCTGACATTACGTACAC\nGTATTTTCAGTCCTCTTCAAGTGGAACCACTACCGCCCGTGGAGCGCGTCGAAACGATGT\nCAACTCCACGTCTAAGCCTAGCCCATCGGGGGGGTTTGAAAGACGGTTGGCGTCTATTAT\nGGCCGCTGACACAGCCTTGCACGCAGAAGTTATATTCAACACTGGAATTTACGAAGAAAC\nTCCAACAGATATCAAAGAATGGCCAATGTTTATAGGCATGGAGGGCACTTTGCCAAGGCT\nAAACGCTCTGGGGTCATATACCGCTCGTGTGGCCGGGGTCATTGGTGCGATGGTTTTCAG\nCCCAAATTCTGCGTTGTATCTAACTGAGGTGGAGGATAGCGGGATGACCGAAGCCAAGGA\nTGGGGGACCGGGTCCATCATTTAATCGATTTTACCAGTTTGCCGGACCTCATTTAGCTGC\nGAATCCCCAAACAGATCGAGATGGCCACGTTCTATCCAGTCAGTCTACGGGTTCATCAAA\nCACAGAGTTTAGCGTGGATTATTTGGCACTCATTTGTGGATTTGGAGCACCCCTGTTGGC\nGCGACTGCTTTTTTATCTAGAACGCTGTGACGCTGGTGCGTTTACAGGGGGTCACGGGGA\nTGCGTTAAAATATGTTACGGGGACCTTTGACTCTGAAATTCCATGTAGTTTATGTGAAAA\nACATACGCGGCCGGTATGCGCTCACACAACAGTACACCGACTTAGACAACGCATGCCGCG\nATTTGGACAAGCCACCCGTCAACCTATTGGGGTGTTTGGAACAATGAACAGCCAATATAG\nCGACTGCGATCCTCTAGGAAACTATGCTCCATATTTAATCCTTCGAAAACCCGGGGATCA\nAACGGAAGCAGCAAAGGCAACCATGCAGGACACTTATAGGGCTACACTAGAACGCTTGTT\nTATCGATCTAGAACAAGAGCGACTACTGGATCGCGGTGCCCCATGTTCTTCCGAGGGACT\nATCGTCTGTCATTGTGGATCATCCAACGTTTCGTCGCATATTAGACACACTGCGTGCGCG\nTATAGAACAGACAACAACACAATTTATGAAAGTGTTGGTTGAGACCCGCGATTATAAGAT\nCCGTGAAGGATTATCCGAAGCCACCCATTCAATGGCGTTAACGTTTGATCCATACTCAGG\nAGCATTTTGTCCCATTACCAATTTTTTAGTTAAACGAACACACCTAGCCGTGGTACAAGA\nCTTAGCATTAAGCCAGTGTCATTGTGTATTTTACGGACAGCAAGTTGAGGGGCGGAACTT\nTCGTAACCAATTCCAGCCTGTTTTGCGGCGGCGTTTTGTTGACCTGTTTAATGGGGGGTT\nTATATCAACACGCTCTATAACCGTAACATTATCTGAAGGTCCTGTATCCGCCCCAAATCC\nGACATTGGGACAAGACGCGCCCGCGGGGCGTACCTTTGATGGGGATTTAGCGCGCGTAAG\nCGTGGAAGTTATTCGGGATATACGAGTTAAAAATAGGGTCGTTTTTTCAGGTAACTGTAC\nAAATCTCTCTGAGGCAGCCCGGGCAAGGCTTGTAGGCCTTGCAAGTGCGTACCAACGCCA\nAGAAAAAAGAGTGGATATGTTACACGGGGCCCTAGGGTTTTTGCTTAAACAGTTTCACGG\nCCTGTTATTTCCTCGGGGTATGCCACCAAACAGTAAATCCCCCAACCCGCAGTGGTTTTG\nGACCCTGTTACAACGCAACCAGATGCCGGCAGATAAACTTACACACGAAGAGATTACCAC\nTATTGCAGCTGTTAAACGGTTTACCGAGGAATATGCAGCAATAAACTTTATTAATCTACC\nCCCAACCTGCATAGGAGAATTAGCCCAGTTTTATATGGCAAATCTTATTCTTAAATACTG\nCGATCATTCACAGTACCTTATAAATACCTTAACTTCTATAATTACGGGTGCCAGGCGCCC\nGCGTGACCCATCATCCGTTTTGCATTGGATTCGTAAAGATGTCACGTCCGCCGCGGACAT\nAGAAACCCAAGCAAAGGCGCTTCTTGAAAAAACGGAAAACTTACCGGAATTATGGACTAC\nGGCTTTTACTTCAACTCATTTAGTCCGCGCGGCCATGAATCAACGTCCCATGGTCGTTTT\nAGGAATAAGCATTAGTAAATATCACGGAGCGGCAGGAAACAACCGCGTCTTTCAGGCAGG\nGAATTGGAGCGGTTTAAACGGGGGTAAAAATGTATGCCCGCTATTTACATTTGATCGCAC\nTCGCCGTTTTATAATAGCATGTCCTAGAGGAGGTTTTATCTGCCCCGTAACAGGTCCCTC\nGTCGGGAAATCGAGAAACCACCCTATCCGACCAAGTTCGCGGTATAATTGTCAGTGGCGG\nGGCCATGGTTCAATTAGCCATATACGCCACGGTTGTGCGTGCAGTGGGCGCTCGAGCACA\nACATATGGCATTTGACGACTGGTTAAGTCTTACAGACGATGAGTTTTTAGCCAGAGACTT\nGGAGGAGTTACACGACCAGATTATCCAAACCCTGGAAACGCCCTGGACCGTAGAAGGCGC\nTCTAGAAGCCGTAAAGATTCTAGATGAAAAAACGACAGCGGGAGATGGGGAAACCCCCAC\nAAACCTAGCATTTAATTTTGATTCTTGTGAACCAAGCCATGACACCACATCTAACGTATT\nAAACATTTCAGGGTCAACTGTCCCTGGTCTTAAACGACCCCCCGAAGATGACGAACTCTT\nTGATCTTAGTGGTATTCCCATAAAACATGGGAACATTACAATGGAAATGATTTAACCTCC\nCTCTTTATCCAATTAAAGCCCACACGCGGGTGAGTGTACGTAATAAACAAGTCAATATTA\nCATATTCTGTTGTGTTTTCTTTTTTGCGTGTAGTCCTTACCCATATGACCTGTAATATAG\nTGTGTCTCCAACCATTCAGCTTACAGTCCAGTGGACAGTAACAGCCCGATAACATGGAAT\nTGGATATTAATCGAACATTGTTGGTTCTACTGGGTCAAGTTTATACGTACATCTTTCAGG\nTTGAACTGCTACGTCGCTGTGATCCAAGGGTGGCGTGTCGCTTTTTATATCGGTTAGCGG\nCTAACTGTTTGACAGTTCGTTATTTATTAAAGCTGTTTCTCCGGGGATTTAATACCCAGC\nTAAAATTTGGAAACACTCCCACGGTTTGTGCACTGCATTGGGCATTATGTTATGTAAAGG\nGAGAAGGTGAGCGTTTGTTTGAGTTGCTACAACATTTTAAAACGCGTTTTGTTTATGGTG\nAGACCAAAGACTCAAACTGTATCAAAGATTACTTTGTCTCAGCGTTTAACTTAAAAACCT\nGCCAATATCACCATGAGCTGTCGTTAACAACATACGGAGGTTACGTATCGAGTGAAATTC\nAGTTTTTACACGACATTGAGAATTTTTTAAAACAGCTTAATTACTGCTATATTATCACGT\nCTTCTCGTGAGGCGCTAAACACATTGGAAACCGTGACGCGGTTTATGACAGATACTATAG\nGAAGCGGTCTAATACCACCCGTGGAGTTGTTTGATCCGGCGCATCCATGTGCTATATGTT\nTTGAAGAATTATGTATAACAGCTAACCAAGGTGAGACCTTACATCGTAGATTATTAGGAT\nGTATCTGCGATCACGTTACTAAGCAAGTTCGGGTTAACGTGGATGTTGACGATATTATTC\nGGTGTTTACCATATATCCCTGATGTACCGGATATCAAACGTCAATCCGCCGTTGAAGCGT\nTACGAACACTTCAAACCAAGACGGTAGTCAATCCCATGGGAGCAAAGAACGATACGTTTG\nACCAAACATACGAAATTGCGAGCACCATGCTTGATTCTTATAATGTTTTTAAACCTGCCC\nCTCGGTGTATGTACGCCATCAGCGAGCTTAAATTCTGGTTAACGTCTAATTCCACTGAAG\nGACCCCAACGTACTTTAGACGTGTTTGTTGATAATTTGGATGTATTAAACGAACATGAAA\nAACACGCAGAACTTACAGCCGTAACGGTTGAGTTGGCGTTATTTGGAAAAACTCCCATAC\nACTTTGATAGGGCGTTTTCTGAAGAACTCGGATCTCTGGATGCAATTGATAGTATTTTGG\nTTGGCAATCGCTCATCCTCACCAGACAGTCAGATAGAAGCATTAATTAAAGCCTGTTATG\nCCCATCATCTATCGTCGCCTCTCATGCGTCACATTTCTAACCCGAGTCATGATAACGAAG\nCCGCCTTACGCCAACTTTTAGAAAGAGTTGGGTGTGAGGATGATTTAACCAAAGAGGCGA\nGTGACAGCGCTACAGCATCCGAATGTGATCTGAACGATGATAGTAGCATAACTTTTGCTG\nTTCATGGATGGGAAAACCTGTTATCCAAAGCAAAAATTGACGCTGCGGAAAGAAAACGAG\nTATATCTTGAACATCTGTCTAAGCGCTCTCTAACCAGCCTCGGTAGATGTATCCGCGAAC\nAGCGCCAAGAGCTAGAAAAAACACTCAGGGTAAACGTTTATGGAGAGGCCTTATTGCAGA\nCATTTGTTTCGATGCAAAATGGGTTTGGGGCACGAAACGTGTTTTTAGCTAAGGTTTCCC\nAGGCAGGGTGTATTATCGACAATCGCATTCAGGAAGCGGCCTTTGATGCACATAGATTTA\nTAAGGAATACCTTAGTTCGACATACAGTAGATGCGGCTATGTTACCTGCACTTACACATA\nAATTTTTTGAGTTGGTCAACGGCCCATTGTTTAATCACGATGAACACCGTTTTGCACAAC\nCCCCTAACACCGCCTTATTTTTTACCGTGGAAAACGTTGGCCTATTTCCGCACTTAAAAG\nAGGAATTGGCAAAGTTTATGGGCGGTGTCGTTGGTTCCAACTGGCTTCTCAGTCCATTTA\nGGGGCTTTTATTGCTTTTCTGGGGTAGAAGGCGTTACTTTTGCACAGAGACTTGCCTGGA\nAATATATTAGGGAGCTTGTGTTTGCAACCACACTATTCACCTCTGTTTTCCATTGTGGGG\nAGGTGCGGTTATGTCGCGTTGACCGTCTAGGTAAGGATCCACGCGGGTGCACGTCTCAAC\nCTAAAGGTATAGGCAGTTCCCACGGACCCTTAGACGGCATTTATTTAACGTACGAAGAAA\nCATGTCCCCTTGTGGCTATTATTCAAAGTGGAGAAACAGGGATCGACCAGAATACCGTCG\nTAATCTACGATTCAGACGTTTTTTCTCTTCTATACACCCTAATGCAGCGGCTGGCTCCGG\nATTCAACGGACCCGGCGTTTTCATAACCTCCGTTACGGGGGTGTGGTTATGCTTTTTATG\nCATATTTTCTATGTTTGTTACGGCGGTTGTGTCGGTCTCTCCAAGCTCGTTTTATGAGAG\nTTTACAAGTAGAGCCCACACAATCAGAAGATATAACCCGGTCTGCTCATCTGGGCGATGG\nTGATGAAATCAGAGAAGCTATACACAAGTCCCAGGACGCCGAAACAAAACCCACGTTTTA\nCGTCTGCCCACCGCCAACAGGCTCCACAATCGTACGATTAGAACCAACTCGGACATGTCC\nGGATTATCACCTTGGTAAAAACTTTACAGAGGGTATTGCTGTTGTTTATAAAGAAAACAT\nTGCCGCGTACAAGTTTAAGGCGACGGTATATTACAAAGATGTTATCGTTAGCACGGCGTG\nGGCCGGAAGTTCTTATACGCAAATTACTAATAGATATGCGGATAGGGTACCAATTCCCGT\nTTCAGAGATCACGGACACCATTGATAAGTTTGGCAAGTGTTCTTCTAAAGCAACGTACGT\nACGAAATAACCACAAAGTTGAAGCCTTTAATGAGGATAAAAATCCACAGGATATGCCTCT\nAATCGCATCAAAATATAATTCTGTGGGATCCAAAGCATGGCATACTACCAATGACACGTA\nCATGGTTGCCGGAACCCCCGGAACATATAGGACGGGCACGTCGGTGAATTGCATCATTGA\nGGAAGTTGAAGCCAGATCAATATTCCCTTATGATAGTTTTGGACTTTCCACGGGAGATAT\nAATATACATGTCCCCGTTTTTTGGCCTACGGGATGGTGCATACAGAGAACATTCCAATTA\nTGCAATGGATCGTTTTCACCAGTTTGAGGGTTATAGACAAAGGGATCTTGACACTAGAGC\nATTACTGGAACCTGCAGCGCGGAACTTTTTAGTCACGCCTCATTTAACGGTTGGTTGGAA\nCTGGAAGCCAAAACGAACGGAAGTTTGTTCGCTTGTCAAGTGGCGTGAGGTTGAAGATGT\nAGTTCGCGATGAGTATGCACACAATTTTCGCTTTACAATGAAAACACTTTCTACCACGTT\nTATAAGTGAAACAAACGAGTTTAATCTTAACCAAATCCATCTCAGTCAATGTGTAAAGGA\nGGAAGCCCGGGCTATTATTAACCGGATCTATACAACCAGATACAACTCATCTCATGTTAG\nAACCGGGGATATCCAGACCTACCTTGCCAGAGGGGGGTTTGTTGTGGTGTTTCAACCCCT\nGCTGAGCAATTCCCTCGCCCGTCTCTATCTCCAAGAATTGGTCCGTGAAAACACTAATCA\nTTCACCACAAAAACACCCGACTCGAAATACCAGATCCCGACGAAGCGTGCCAGTTGAGTT\nGCGTGCCAATAGAACAATAACAACCACCTCATCGGTGGAATTTGCTATGCTCCAGTTTAC\nATATGACCACATTCAAGAGCATGTTAATGAAATGTTGGCACGTATCTCCTCGTCGTGGTG\nCCAGCTACAAAATCGCGAACGCGCCCTTTGGAGCGGACTATTTCCAATTAACCCAAGTGC\nTTTAGCGAGCACCATTTTGGATCAACGTGTTAAAGCTCGTATTCTCGGCGACGTTATCTC\nCGTTTCTAATTGTCCAGAACTGGGATCAGATACACGCATTATACTTCAAAACTCTATGAG\nGGTATCTGGTAGTACTACGCGTTGTTATAGCCGTCCTTTAATTTCAATAGTTAGTTTAAA\nTGGGTCCGGGACGGTGGAGGGCCAGCTTGGAACAGATAACGAGTTAATTATGTCCAGAGA\nTCTGTTAGAACCATGCGTGGCTAATCACAAGCGATATTTTCTATTTGGGCATCACTACGT\nATATTATGAGGATTATCGTTACGTCCGTGAAATCGCAGTCCATGATGTGGGAATGATTAG\nCACTTACGTAGATTTAAACTTAACACTTCTTAAAGATAGAGAGTTTATGCCGCTGCAAGT\nATATACAAGAGACGAGCTGCGGGATACAGGGTTACTAGACTACAGTGAAATTCAACGCCG\nAAATCAAATGCATTCGCTGCGTTTTTATGACATAGACAAGGTTGTGCAATATGATAGCGG\nAACGGCCATTATGCAGGGCATGGCTCAGTTTTTCCAGGGACTTGGGACCGCGGGCCAGGC\nCGTTGGACATGTGGTTCTTGGGGCCACGGGAGCGCTGCTTTCCACCGTACACGGATTTAC\nCACGTTTTTATCTAACCCATTTGGGGCATTGGCCGTGGGATTATTGGTTTTGGCGGGACT\nGGTAGCGGCCTTTTTTGCGTACCGGTACGTGCTTAAACTTAAAACAAGCCCGATGAAGGC\nATTATATCCACTCACAACCAAGGGGTTAAAACAGTTACCGGAAGGAATGGATCCCTTTGC\nCGAGAAACCCAACGCTACTGATACCCCAATAGAAGAAATTGGCGACTCACAAAACACTGA\nACCGTCGGTAAATAGCGGGTTTGATCCCGATAAATTTCGAGAAGCCCAGGAAATGATTAA\nATATATGACGTTAGTATCTGCGGCTGAGCGCCAAGAATCTAAAGCCCGCAAAAAAAATAA\nGACTAGCGCCCTTTTAACTTCACGTCTTACCGGCCTTGCTTTACGAAATCGCCGAGGATA\nCTCCCGTGTTCGCACCGAGAATGTAACGGGGGTGTAAATAGCCAGGGGGTTTGTTTTAAT\nTTATTAATAAAAATGTGTATTACGTTACTCATGTGTCTCCATTACGCATCACAGGGGGTA\nTTTATACCCGATAATATACAAAACGCGTTTTGTACCTCTACCGCACCCGATATCTTAACG\nGGGTTATTATGGAATCGTCTAACATTAACGCGCTACAACAACCGTCGTCTATCGCACATC\nATCCGTCCAAACAGTGCGCTTCAAGTCTCAATGAAACAGTAAAAGATTCTCCCCCCGCGA\nTTTATGAAGATAGGTTAGAACACACGCCGGTACAATTACCCCGCGACGGTACACCCCGAG\nACGTATGTTCTGTGGGACAGCTAACCTGTCGAGCATGTGCAACGAAACCTTTTCGCCTTA\nACCGCGACAGCCAATACGACTACTTAAACACATGTCCAGGGGGCCGTCATATTTCACTGG\nCACTGGAGATTATAACGGGTCGATGGGTTTGCATCCCGCGTGTGTTTCCGGATACCCCAG\nAGGAAAAATGGATGGCGCCATATATTATTCCAGACCGAGAACAACCATCATCAGGGGATG\nAAGATTCTGACACCGATTAAATTTAACTTAAATAAAACCTTACCACCCATAAAAACGCCT\nTCTGTTTGTTTAACACGACACCGCTTAACAAAAAAAAAAAAACCAAACACGCCTTTTATG\nAATGTAATACTTTTATTTGTTGGTTAACACCGCCCCACCATCATCTGATTTGCAAACATA\nTCGGCGTCGTCTGCCGTGGACCCCTGTATTAAAGGGGCCTTGGAACTAGCCTCCACTGCA\nTTTACATCTTGTCCAACTGTATCTGTATGTGGGGTGCTTGTTGTATTTTGGGATGAGCAT\nAGACCCGAAACGCTTTGAAGCTGTTTTAATAAAATCGATATTCGAGGATCCCGTGTCCCC\nTCTGGTATATTTGTATGGTGCGACAAAGGCATTTGTGTCCCATTTTGTGATTTTAGCTCT\nGTAACCTCCTGTTGCAGTTTTGCCACAACCCCAGCAAGCTCTTCGTGCTGACCATTAGAA\nACTCTGTGTCTCCTCTGCCAATATGATGGAGAAACTCGACGTCTCCGATGCGTTATATAC\nGTTGGTTCACCGGGAAAATATATATTTGAGGGAAACTCTCCGTCCATTTGAGACTCCCCA\nCTAGAAAAAGAATCCAATTCCCTTTGATCCATGCTCTTGAAATCCCGTTTTCCTGGACGA\nCGGACATCGGTTTTGTCTGGAAAATTTACACACGGGGTCTGCAAGTCAATACCCCGTTCG\nGCGGCCAATGCGTTCATAAATGCGGACATTTGCATTTCCAAACGATTGGGTGGTGGATAT\nCCCGGAAACCCGTACGGTCCCCCGAAGTGTCCCGGAGGGCAACCATAACCCCCTGTATTA\nGGTGGGAAGGCAGGCGGGTGTGGAGATCCATATGGCCCGACGATATACTGTCCGTTATTT\nGGAGCTCCAATTGATACCTGCGGATTTTTAGTCTGCCCGGTTAACAGCTGTGAATAATAC\nGCGGTAGGTATCAGTACAAATTCCCCTCCGGTTGGAACGCCCGACGGGGGCTGTGGTGAG\nATACCACTAGCGTTACCTGCTACAGAAGCCATATCGCTGTCGTTCCTACACAACTGCGTA\nACCTTTAAATGCGGAACAGTCTTTTCACAATCTTCATTTGATTCCCCAACACCCAACGCG\nAGATCGTATATGGGCCCGCCGGGGTGGAATGTGGCGTTTATAACACCCGCGTTGGGTAAT\nTTAGACTCCACCCCATTAACGTTGGTTATCCGAGCAAGTCCATATCCGGTGCTAGCCTGA\nAGATAAACGTGACCCATAATTCCGGCTTCGCGTCTACGTTTTGCAACCACGTCCCATCTA\nTCTCTTAAAAGCATATTGTTCACGGCTGTGGATAATAACACCTTGGCGAGTTTATCTTCG\nCTAACCTTCCATACTTTATTTAAACCCGCGTAGTCTTTAACCAGCGACAATAACCGCGCT\nTTACTTTCCATCGATAAAACCCGGAATGGTTCAATTGAAGATTCCGGGGTACAGTCATAA\nTTGACCACTGTTCCAACGCGTCTTCCAACAACACATAACGCAACATGGGTAAAAAAATTA\nCCGTCTGGTATCTCATTCGGGGACAATCGTTTTGAAGACAGGGATACGGAGGGTAAGTAA\nTTTGTGACCAAGTATAACGCACGTTCTAGCGGAGATAATACAGAATCTCTATTTCCAAAA\nAAATTCGAATGGGCCGCTTCAAACAGCACCGCATGTAGTTGAGGGCATCTAACGATACCC\nAAAAAAAAAGGTCCGCGTATGTCCTCAATGATTGCGATTACTTCACCCACGACACAGTCT\nTTTCGATGATCGATGTTTATTGGTATTTTACTAGTAGGCGGCAAAGCGGACCGCACAATC\nTCTGGGGTAATATTTAATTCCCCTTCGTCCTTTGAATATAAGGCTAAATACCCAGCCACG\nTATAACGCTTCACAGTTCTCTTCGTCAGCTTCAGCAGCCATTATAAACACCCCACGGACC\nGGATAGTGAATACTCACGGTGTGGAGGCAAACTGAGGAATGACACCCAAACAGACAAAAT\nATAGAAGATCATAGTCACTGTTAACGTTGAACTGCGCAAGGCGGCGACTTTCTTCCAATG\nCCGCCCTTACACGCGGTTGGTGCATTAACATTCCAAGTCCCCGTTCATATTGCAACATAA\nCACTGTCATGTATTGATACCACGGCGGCTATGGGTAGGGATGTAACATTTTGTCGGCGGT\nGTTCTAATTCCAATGCAATTAAGCTTATGAGCCGATCTTGGTACTGTCCAGAAGAAATAT\nCTATTACGGTTCTTCCTAAACTTCCACGACTAAGCTGGGTATGCGCGTCTAAACAAAGAG\nCAACTAATCCAGGAAACATTTCAGTCAGCTCTGTGGTCCGATTTAACGTATACAGTGGTG\nCTATATATCGTTCACATAAAAATTGAAAGTTATTATTACCGCTTTTAAACTTCCCATCAA\nACCCCGTCGCTCCGCGCAAGATTACATTGTTGGTAGGGGTTCCTGTTGCTTCTGACACAA\nTCAAACCCAGTTGAAAATTATTTTTTAGTTTATCTCCGTATACGTTCCCGTTCCATAATA\nAGCGCCTTAATAATAATAACGCCGTAATCGTGTCAATTGTTAACCTTAATAGAGTTTGGT\nCTTCCATAAGAAACACGTTTTGGGCCCGTTCTAAATACGCCGCGGCCGCCTGTTGAATCT\nTGTCCACATATGCGGTATGATTGCGATCAATAATGTCATTAACCCCAGGATTAAACTGTC\nCAGGTGCAGGCGGTAGGACCTGCAACCGTATAAGCGCATCCATAACAGAATGTGACGTTA\nAGGCGCCTTGATCATACCGCCCCCCACGAGCATGAAACTGGTCGCGTGGTAGACGATCAT\nAGCAAAATTGATAACTGTTTTTATTTTCGTGTGTTGTCATATAATTCACAAATGTCTCAG\nTATATTCCGGTAGGTGCTCTATAAGGTTCCCGAAGGACGAAACTTGAGGTTCGTGGACAC\nTATTAGATGTCCTATACATTAAATATAAACATAATACCGCACACTCGAACGCGGAGTACG\nCTCTATCTCCAACATACATTCTCCCGGCGGACTGTAGACATGTTACCGTTGTGTTCATAA\nACGTACGGGAAATGCGCCCGTCTTTACAATCAACTCCGCGTGCAGCTACGGGCCTATCTA\nACACAAGCCGTTCCTGCAGAGTACGATACCATGGCCCGAAAACAATCCCTGGAGAGTTAT\nTGCCCCTTGCCCTTCCCAAGTACACCAGGGTGATAAAATCCACTTGAAAGTTTGTATCGT\nACTGCAACGGTGCATCATTTTTGGCAATCTGTACCTCGGGGTGTATAGACTCATTGCGTA\nTTATTTCTGTACGTGTACATTCCTCAGATTGTGCATCTGCTTCTTCCGCCTCGGCAGCAG\nCCGTCTCCAGGGAATCCAAAACCTTGGCCATGCGCGTTAGTTGGTCTTCGAGGGGCTTTA\nAACGACGATCTATTTCCGTTGGTAACGTAATCGTTTCCCCGCGAAGGTTGTCTAATGCGG\nCAACGGCCGCCGCATTTTTTAACGTTAACGTATTTTTTTCCAAATCGGGATTCATACGCC\nCTCTTAACTCAAACGCGGGAGCCGTCCAGTAGTGTATGGGGAAGTTGGGGGCTATAAAGT\nTCTTAGTGGTAGACAAAAATATCCCACATTTATTCGGAAACGAGATAGATCCGAACCCAT\nATCTCGCCGTCATGGTGTCTGCAGCAAACAAAGTCAACTGGCGTGAATATAAACCGGTAC\nTGCTTTAAAAGCTGTTTTCTTACCCATGGGAAAACATCCCGGTTATACTTTGTAAAATTC\nCACCACAAGCACCTAAAGAAGGCCTTCTAAGGGGTAAATCCACCCCACAAGCTGCATTTT\nCTTCAAACTTTGTTAAAGCGGAACGATGGCATGATTTCGCACGCTTTTTCGCAAGAGAAC\nATACGTGAATTTTCTTTTTGCATAGACGTCTTCGCTCTCTAACGGACCTTATCGGGGGGG\nTATATTCCGCTACATTCTCCAAATGCGACGCTAGCATAACAAGGTTTCCATGAATCACCT\nTTGGGGGTAACCGAGTTACCTGTAACAGGTTCAGACCCCGTTGAGATACAAACACAAGGA\nGGGGGGTCACCATTATTTCATCAGATCCCGTGGGTGTGGTTTCCTTTATTAAAGCCACGG\nTATCCCTCAGCTGGCGCATACCCTCGCAAAACTGGTGATACTTAGTAGGGGTATGTATAT\nTAGCGCTAAAACGGCAAGATTTTAATTCCACTATAAAACAAACGGTCTTTCCGGCACCAC\nTGGATTCCGTTTGTATAATACAAATACAATCGGGGCGTCGGCGTCCCAAATTTACTTCAA\nACGACATTGATATGCGTACAGCCCTTTGAACATCCACGTGGGATAACGGCGACAGGAGTT\nTTGCCAGCCTCGGGTTGAACGCGTCCGCGAAACCTCGACGTACGTTATCAATATCCTTTT\nTGAGTACATCGTAAAAACGAGTGTGACAACGTTGTCCCAAACGAAAACACTTGGCCCGAA\nTTTGACTAGCGGACATATTTGAAGTTCCGTCCCAGAAGATAACCTAAGACGCGTTTGTCT\nACAATAAACATGTCAACGGATAAAACCGATGTAAAAATGGGCGTTTTGCGTATTTATTTG\nGACGGGGCGTATGGAATTGGAAAAACAACCGCCGCCGAAGAATTTTTACACCACTTTGCA\nATAACACCAAACCGGATCTTACTCATTGGGGAGCCCCTGTCGTATTGGCGTAACCTTGCA\nGGGGAGGACGCCATTTGCGGAATTTACGGAACACAAACTCGCCGTCTTAATGGAGACGTT\nTCGCCTGAAGACGCACAACGCCTCACGGCTCATTTTCAGAGCCTGTTCTGTTCTCCGCAT\nGCAATTATGCATGCGAAAATCTCGGCATTGATGGACACAAGTACATCGGATCTCGTACAA\nGTAAATAAGGAGCCGTATAAAATTATGTTATCCGACCGACACCCAATCGCCTCAACTATA\nTGTTTTCCCTTGTCCAGATACTTAGTGGGAGATATGTCCCCAGCGGCGCTTCCTGGGTTA\nTTGTTTACGCTTCCCGCTGAACCCCCCGGGACCAACTTGGTAGTTTGTACCGTTTCACTC\nCCCAGTCATTTATCCAGAGTAAGCAAACGGGCCAGACCGGGAGAAACGGTTAATCTGCCG\nTTTGTTATGGTTCTGAGAAATGTATATATAATGCTTATTAATACAATTATATTTCTTAAA\nACTAACAACTGGCACGCGGGCTGGAACACACTGTCATTTTGTAATGATGTATTTAAACAG\nAAATTACAAAAATCCGAGTGTATAAAACTACGCGAAGTACCTGGGATTGAAGACACGTTA\nTTCGCCGTGCTTAAACTTCCGGAGCTTTGCGGAGAGTTTGGAAATATTCTGCCGTTATGG\nGCATGGGGAATGGAGACCCTTTCAAACTGCTTACGAAGCATGTCTCCGTTCGTATTATCG\nTTAGAACAGACACCCCAGCATGCGGCACAAGAACTAAAAACTCTGCTACCCCAGATGACC\nCCGGCAAACATGTCCTCCGGTGCATGGAATATATTGAAAGAGCTTGTTAATGCCGTTCAG\nGACAACACTTCCTAAATATACCTAGTATTTACGTATGTACCAGTAAAAAGATGATACACA\nTTGTCATACTCGCGTGTACGTGTTTTTCTTTTTTATATATGCGTCATTTATTACCACATC\nCTTTAATCCCGCCTTTATCTCCCTAAAACGGAGTGGTAATATTAAAAGCCGCCAAGCCTG\nTTGGTGGGTGAGGAGGGGTAAAGGCACGCTGTGTGCATAACGTTGCGGTGATATTGTAGC\nGCAAGTAACAGCGACTATGTTTGCGCTAGTTTTAGCGGTGGTAATTCTTCCTCTTTGGAC\nCACGGCTAATAAATCTTACGTAACACCAACCCCTGCGACTCGCTCTATCGGACATATGTC\nTGCTCTTCTACGAGAATATTCCGACCGTAATATGTCTCTGAAATTAGAAGCCTTTTATCC\nTACTGGTTTCGATGAAGAACTCATTAAATCACTTCACTGGGGAAATGATAGAAAACACGT\nTTTCTTGGTTATTGTTAAGGTTAACCCTACAACACACGAAGGAGACGTCGGGCTGGTTAT\nATTTCCAAAATACTTGTTATCGCCATACCATTTCAAAGCAGAACATCGAGCACCGTTTCC\nTGCTGGACGTTTTGGATTTCTTAGTCACCCTGTGACACCCGACGTGAGCTTCTTTGACAG\nTTCGTTTGCGCCGTATTTAACTACGCAACATCTTGTTGCGTTTACTACGTTCCCACCAAA\nCCCCCTTGTATGGCATTTGGAAAGAGCTGAGACCGCAGCAACTGCAGAAAGGCCGTTTGG\nGGTAAGTCTTTTACCCGCTCGCCCAACAGTCCCCAAGAATACTATTCTGGAACATAAAGC\nGCATTTTGCTACATGGGATGCCCTTGCCCGACATACTTTTTTTTCTGCCGAAGCAATTAT\nCACCAACTCAACGTTGAGAATACACGTTCCCCTTTTTGGGTCGGTATGGCCAATTCGATA\nCTGGGCCACCGGTTCGGTGCTTCTCACAAGCGACTCGGGTCGTGTGGAAGTAAATATTGG\nTGTAGGATTTATGAGCTCGCTCATTTCTTTATCCTCTGGACTACCGATAGAATTAATTGT\nTGTACCACATACAGTAAAACTGAACGCGGTTACAAGCGACACCACATGGTTCCAGCTAAA\nTCCACCGGGTCCGGATCCGGGGCCATCTTATCGAGTTTATTTACTTGGACGTGGGTTGGA\nTATGAATTTTTCAAAGCATGCTACGGTCGATATATGCGCATATCCCGAAGAGAGTTTGGA\nTTACCGCTATCATTTATCCATGGCCCACACGGAGGCTCTGCGGATGACAACGAAGGCGGA\nTCAACATGACATAAACGAGGAAAGCTATTACCATATCGCCGCAAGAATAGCCACATCAAT\nTTTTGCGTTGTCGGAAATGGGCCGTACCACAGAATATTTTCTGTTAGATGAGATCGTAGA\nTGTTCAGTATCAATTAAAATTCCTTAATTACATTTTAATGCGGATAGGAGCAGGAGCTCA\nTCCCAACACTATATCCGGAACCTCGGATCTGATCTTTGCCGATCCATCGCAGCTTCATGA\nCGAACTTTCACTTCTTTTTGGTCAGGTAAAACCCGCAAATGTCGATTATTTTATTTCATA\nTGATGAAGCCCGTGATCAACTAAAGACCGCATACGCGCTTTCCCGTGGTCAAGACCATGT\nGAATGCACTTTCTCTCGCCAGGCGTGTTATAATGAGCATATACAAGGGGCTGCTTGTGAA\nGCAAAATTTAAATGCTACAGAGAGGCAGGCTTTATTTTTTGCCTCAATGATTTTATTAAA\nTTTCCGCGAAGGACTAGAAAATTCATCTCGGGTATTAGACGGTCGCACAACTTTGCTTTT\nAATGACATCCATGTGTACGGCAGCTCACGCCACGCAAGCAGCACTTAACATACAAGAAGG\nCCTGGCATACTTAAATCCTTCAAAACACATGTTTACAATACCAAACGTATACAGTCCTTG\nTATGGGTTCCCTTCGTACAGACCTCACGGAAGAGATTCATGTTATGAATCTCCTGTCGGC\nAATACCAACACGCCCAGGACTTAACGAGGTATTGCATACCCAACTAGACGAATCTGAAAT\nATTCGACGCGGCATTTAAAACCATGATGATTTTTACCACATGGACTGCCAAAGATTTGCA\nTATACTCCACACCCATGTACCAGAAGTATTTACGTGTCAAGATGCAGCCGCGCGTAACGG\nAGAATATGTGCTCATTCTTCCAGCTGTCCAGGGACACAGTTATGTGATTACACGAAACAA\nACCTCAAAGGGGTTTGGTATATTCCCTGGCAGATGTGGATGTATATAACCCCATATCCGT\nTGTTTATTTAAGCAAGGATACTTGCGTGTCTGAACATGGTGTCATAGAGACGGTCGCACT\nGCCCCATCCGGACAATTTAAAAGAATGTTTGTATTGCGGAAGTGTTTTTCTTAGGTATCT\nAACCACGGGGGCGATTATGGATATAATTATTATTGACAGCAAAGATACAGAACGACAACT\nAGCCGCTATGGGAAACTCCACAATTCCACCCTTTAATCCAGACATGCACGGGGATGACTC\nTAAGGCTGTGTTGTTGTTTCCAAACGGAACTGTGGTAACGCTTCTAGGATTCGAACGACG\nACAAGCCATACGAATGTCGGGACAATACCTTGGGGCCTCTTTAGGAGGGGCGTTTCTGGC\nGGTAGTGGGGTTTGGTATTATCGGATGGATGTTATGTGGAAATTCCCGCCTTCGAGAATA\nTAATAAAATACCTCTGACATAAAAAACATGTATAATAAAAAGTCACTATAAACGTATTCT\nCTACAATACTTTATTCGCGAATAATACACACTACCTTTGGGTTTTTTTCCCGTCCCCAAA\nTGGTGTTTGGTGCACTCTACCAAAAAATAGAGCGCCTAAATATGCTATATAACGCCTCCC\nAGCAAAATACGGTTCAAAGGCATTACCCGATATTGTATTGTAGTACAGGGCAATGGGAAT\nTGATGATCCCAATAAACGGCATAGACGCACAGCGCCGTTATAGCAGGGGTCTCCAGAGTA\nCAGGGTATCTAAGTACCGGGATATCTCATACTCATGCCTTTCCGTGACAGAAACATCAAC\nCGGAACAGTATCCGATAAACCAACTCCTGTTTTTGCAAGGCGTAAAATTCGCACACCTTC\nCTTTTTTGCAAGATGTGACGTTTCCTTGTAACAGGGAAGCTGGGGGAGTGGTAAGAACAA\nCAAAGTTTCAGCCAACGTGCCAATAAAGCCCACTTCCCTCAAGAGGCTGTTTGCTGTATC\nCACAATGGTCCGTATTAAATCTTGAGCAACTTGATCCGTGTCATCATCACTGGGTAACGC\nGTTAACATAACTACGCGTTAAATCTTCAATAACGGCATAACAATTAAACGCTTCCCACCG\nAGACAGTATATATTGAACAATCACGAACCGTTGACAGGACGTCAGATCACGTCCGTAAGC\nATGCCCGAAAAATGGAAGTTCCCCCCGTTCGCCATATACCGCAACAACTGCAGTATATAT\nCGTCTCACGGGCTTCATTAAGTTCATCTTCAAGTCCAGGCCATTTTCTGGCTTTAAATAT\nAACCTCGTCCGCAAAAAAAACCGCACATGATAACGCGCGGATACAATGAGTAGTGGCTTT\nATGGCGAGGATCCCAAATGTCCATTACCCGGGGGATGGTCCTAATCTGTACAAAGTTACT\nTAGTGTAATATGATCGGACTTCTTACGCCGTCTAGGCTGTTTCTCAGAATACGGTTCACC\nCGAAATCGGCACATCATCTGCTTTTACGTCTTCCGTAACCACATCAGCAGCGCGCCGACT\nAACAATTATACTTGTTTTTTCATCGTCGTTACTTCCGTTAAGCGCGTCTCGTATCTCGGG\nCGTCCCGTCGAATAATCCACTCACTAGCTCCTGCAAACCTTCTGGTAACTCCAACATACG\nCATATACACCAATGAAAAACTGGCTTCGTTTGGTACGTACATAAAGCCATTTGTGGTATT\nAATGGCGGTGGGTGTTGGAGACAATTTTAGCTTATTCTCGCGCGTAACATCTACCCCCGC\nCACCAATGTTAAATGCGTCACGGGGAGGGACACGAGATAATCTGCGAGCGTAGGGTCCTC\nCACTTCAACATCAAATGTTCCGCAAAGGTCGCGATCCACCGCCCCCGATCCCGCTGCAAG\nTAAGGCCACTCGATCCAAAAACACGCAGTTATTATTGGATGATACCGCCCATGTCTTCCC\nGGTGCGATTGAGCTCACTTCGAACGTAACTGGCAACAGATCTGTCACCGGGTCCGACCCC\nGCGAACAACATGTCCAAATTTTGCGATCTCGCCTCCATGTTTGCGGGGTATGGAAATTAA\nGCATCCCCCGCATATAAAATACGCCCTGGTAGCACGCTCGTTAAAATAAAACGTTACGCC\nGTTATAAGATACGGTTGAATGATATGGAAATTCCATATTAAAGCGTTTATCGGAACATTA\nACCTCGAACTTGCCGTCCCGTGATCGTGTGATCGCCAACCTTAGGTCCACACCGAATATG\nAGAAATATATAACTACACGCAAACATTCAAAACACCGTGGTATCATTAACGTCATATGAA\nAAGATCCAATCAATCCAATCAACCACACCTCCTACCGTTTAGCACGTCAGCTATGTGACA\nTGCTCCAAACATACGTAAACATTTAGAGAGGGTGTTATAACAGTCTGTCAGGCGGGGTAT\nATTCTACATAATACAAGGATCGGCTTTAACTTTGTCAACATTTTTACTTTGGACTATAAA\nCTGCGACTGAACGTTATGAACCCACCCCAAGCCCGCGTCTCGGAACAGACAAAGGACTTG\nCTTAGCGTTATGGTTAACCAGCACCCCGAAGAGGACGCAAAAGTGTGTAAATCCAGTGAT\nAATTCACCGCTTTATAACACCATGGTTATGTTATCGTATGGGGGTGATACGGACTTACTA\nTTAAGCTCTGCATGTACCCGCACATCTACCGTAAACAGGTCGGCGTTTACGCAACACTCC\nGTGTTTTATATTATATCCACGGTGTTGATTCAACCAATATGTTGTATCTTCTTTTTTTTT\nTACTATAAAGCGACACGCTGTATGCTCTTATTCACAGCCGGGTTACTTCTGACGATTCTA\nCATCACTTTCGACTTATTATTATGTTATTGTGTGTCTACAGAAATATACGATCAGACCTG\nCTACCCTTATCTACATCCCAGCAACTGCTGCTTGGAATTATTGTTGTGACTCGAACAATG\nCTATTTTGTATTACGGCGTATTATACTCTTTTTATAGACACCCGGGTGTTCTTTTTGATT\nACCGGACACTTGCAAAGTGAGGTTATTTTTCCAGATAGCGTTTCAAAAATACTTCCTGTG\nTCGTGGGGTCCAAGTCCAGCCGTGTTACTGGTAATGGCGGCAGTTATTTACGCTATGGAC\nTGTTTGGTGGACACGGTATCCTTTATTGGGCCAAGGGTGTGGGTCCGTGTTATGTTAAAA\nACATCTATTTCGTTTTAGTCCATTTCAATAAATGTACTATAATTGTTCAGTCTAAAAATA\nATGTTGGGTATTTATAATTACCGCCCCCGTGTTACTTGGAAACACCCATACATATGTTCC\nACTCTACATCAAACTTCTCGCAGTTTTCTTGTTCCCGCACACGTTTACACGTCCGGATTC\nAAGTCGCAACGCTGCTGACAAAATGACAACGGTTTCATGTCCCGCTAACGTGATTACTAC\nAACGGAATCTGATCGTATTGCTGGGTTATTTAACATCCCAGCGGGGATCATTCCAACTGG\nAAATGTGCTGTCAACCATAGAGGTGTGTGCACACCGTTGCATTTTTGATTTTTTTAAACA\nAATACGATCAGATGATAACAGCCTTTACTCGGCTCAATTCGATATTCTTTTGGGGACATA\nCTGCAATACATTAAACTTTGTGCGTTTTCTAGAACTTGGACTGTCTGTCGCTTGCATCTG\nTACTAAATTTCCGGAGCTGGCTTACGTGCGAGATGGCGTTATTCAATTTGAGGTACAACA\nACCCATGATAGCACGTGATGGCCCACATCCCGTCGATCAGCCTGTTCATAATTATATGGT\nTAAGCGGATACACAAGCGTTCGTTAAGCGCTGCGTTTGCAATTGCATCGGAAGCGTTGAG\nTTTGTTAAGTAACACATATGTCGATGGGACAGAGATTGACTCATCGTTACGTATAAGAGC\nTATCCAACAGATGGCTCGTAATTTACGCACCGTTTTGGACTCATTTGAACGAGGCACTGC\nCGATCAACTTCTTGGTGTTCTATTGGAGAAAGCCCCACCGCTATCGCTGCTTTCACCAAT\nTAATAAATTCCAACCCGAGGGACATCTAAATCGTGTTGCACGCGCGGCCCTACTTTCGGA\nCCTCAAACGTAGAGTCTGTGCGGATATGTTTTTTATGACCCGACACGCCAGGGAACCTAG\nGCTGATCTCTGCGTATCTGTCGGATATGGTTTCGTGCACCCAACCATCGGTGATGGTATC\nACGAATAACTCATACAAACACTCGCGGACGGCAGGTTGACGGTGTGTTGGTAACAACAGC\nAACCTTAAAACGGCAACTATTACAGGGAATTTTACAAATTGACGACACCGCCGCTGACGT\nACCAGTAACATATGGCGAAATGGTTCTACAGGGGACAAACTTGGTAACCGCCCTTGTGAT\nGGGAAAGGCCGTCCGCGGAATGGATGATGTAGCCCGCCATCTCCTTGATATAACCGACCC\nTAACACGTTAAACATACCGTCTATACCCCCACAATCCAACTCCGATTCAACGACAGCTGG\nGCTTCCGGTTAACGCCCGTGTTCCTGCGGATTTAGTGATTGTTGGGGATAAACTTGTATT\nCTTAGAAGCATTAGAACGGCGGGTCTACCAAGCTACGCGCGTTGCCTACCCTCTTATTGG\nAAATATAGATATTACGTTTATCATGCCAATGGGAGTGTTTCAGGCAAACTCCATGGACAG\nATATACACGACACGCCGGCGATTTTTCAACTGTATCCGAACAGGATCCACGTCAATTTCC\nACCCCAAGAGATTTTTTTTTATAATAAAGATGGGATATTAACACAGTTGACTCTTCGTGA\nTGCAATGGGTACCATCTGCCACAGTTCATTGCTTGATGTTGAGGCCACACTTGTTGCCCT\nCCGCCAACAACATTTAGATCGTCAGTGTTATTTTGGTGTATACGTGGCCGAGGGTACAGA\nGGACACATTGGATGTTCAAATGGGGAGGTTTATGGAAACGTGGGCAGATATGATGCCTCA\nTCACCCTCATTGGGTAAACGAACATTTAACAATTCTACAGTTTATAGCTCCGAGCAACCC\nGCGTCTAAGGTTTGAATTAAACCCCGCCTTTGATTTTTTTGTTGCACCGGGGGACGTAGA\nCCTTCCCGGACCGCAGCGTCCCCCGGAAGCCATGCCAACCGTTAACGCAACATTACGGAT\nTATCAACGGAAACATTCCCGTGCCTCTATGTCCCATTTCATTTCGAGACTGTCGCGGAAC\nCCAACTCGGTTTGGGAAGACATACAATGACCCCGGCAACCATTAAAGCCGTAAAGGATAC\nATTTGAAGACCGCGCATACCCAACTATTTTCTACATGCTAGAGGCTGTTATTCATGGAAA\nCGAAAGAAACTTCTGTGCGTTACTGCGACTGTTAACACAGTGTATTCGCGGGTATTGGGA\nGCAATCCCACAGGGTGGCATTTGTAAATAACTTTCACATGTTAATGTACATAACTACATA\nTCTCGGAAACGGTGAGCTTCCCGAAGTCTGTATTAATATATATCGGGATTTACTGCAGCA\nTGTAAGAGCATTACGCCAAACTATAACCGATTTTACAATACAAGGAGAGGGCCATAACGG\nCGAGACCTCGGAAGCGCTAAATAACATCCTTACGGATGACACGTTTATTGCACCTATTCT\nATGGGATTGTGATGCGTTAATATACCGTGATGAAGCCGCCCGAGACCGACTCCCCGCAAT\nTCGTGTAAGCGGGCGAAACGGATACCAAGCCCTTCACTTTGTGGATATGGCCGGGCATAA\nCTTCCAACGACGCGATAATGTGTTAATCCACGGGAGACCCGTTCGGGGAGACACGGGTCA\nGGGTATTCCCATTACCCCACACCATGACCGTGAATGGGGTATTCTCTCCAAGATTTACTA\nCTATATTGTCATTCCTGCATTTTCCCGCGGTTCCTGTTGTACAATGGGCGTGCGTTATGA\nTCGCCTATACCCTGCGTTACAGGCAGTTATCGTTCCGGAAATTCCCGCTGATGAAGAAGC\nCCCAACTACCCCAGAAGATCCAAGACACCCTCTTCACGCACACCAACTCGTTCCGAACTC\nTCTTAACGTTTACTTCCATAATGCACACCTAACCGTTGATGGTGATGCATTGCTCACACT\nACAAGAGTTAATGGGAGATATGGCTGAACGAACGACGGCCATTTTAGTATCAAGCGCCCC\nCGATGCGGGAGCCGCCACGGCAACAACCAGAAATATGAGAATATATGACGGAGCGCTTTA\nCCATGGCCTTATTATGATGGCATATCAGGCGTACGATGAAACCATTGCAACGGGTACTTT\nTTTTTATCCCGTTCCGGTCAACCCTCTGTTTGCATGTCCGGAACATTTGGCATCATTGCG\nTGGAATGACAAATGCTAGGCGGGTTTTGGCAAAAATGGTACCACCAATCCCTCCTTTTCT\nGGGAGCCAACCACCACGCAACTATACGCCAACCCGTTGCCTACCATGTAACGCATAGTAA\nGTCGGATTTTAATACTCTTACATATTCTCTTCTTGGAGGGTATTTTAAGTTTACACCAAT\nAGCTCTTACACATCAACTACGAACGGGATTTCACCCCGGGATTGCCTTTACCGTAGTGCG\nCCAGGATCGCTTTGCCACAGAGCAACTTTTATATGCCGAGCGTGCTTCTGAATCGTACTT\nTGTCGGACAAATCCAAGTACACCATCATGATGCTATTGGGGGGGTAAACTTTACCCTAAC\nCCAACCCAGAGCTCACGTGGACCTGGGAGTTGGGTATACAGCTGTATGTGCCACAGCAGC\nCCTGCGATGCCCTCTCACGGATATGGGCAATACTGCCCAAAATCTTTTTTTTTCACGAGG\nAGGAGTGCCAATGTTACATGATAACGTTACCGAATCGTTGCGTCGTATAACAGCATCGGG\nGGGTCGCTTAAATCCCACCGAACCCCTACCCATCTTCGGCGGACTGCGTCCTGCTACATC\nGGCAGGAATTGCACGAGGGCAAGCCTCTGTGTGTGAGTTTGTGGCCATGCCGGTGTCCAC\nTGACCTACAATATTTTAGAACTGCATGCAATCCTAGAGGTCGAGCATCTGGAATGTTATA\nTATGGGTGACCGTGACGCCGACATAGAGGCTATAATGTTTGATCACACACAATCGGATGT\nTGCTTATACAGATCGAGCAACTCTTAACCCATGGGCATCACAAAAACATTCATACGGTGA\nCAGGCTATACAACGGAACATACAACCTTACAGGCGCTTCTCCTATCTACAGCCCATGCTT\nTAAGTTTTTTACACCAGCGGAGGTTAACACTAATTGTAATACACTGGATCGGCTTCTAAT\nGGAGGCAAAGGCTGTGGCGTCGCAAAGCTCCACCGACACTGAATATCAATTTAAACGCCC\nTCCCGGTTCTACCGAAATGACACAGGATCCGTGTGGCCTTTTTCAAGAAGCATATCCACC\nACTATGCTCAAGCGATGCGGCCATGTTACGAACGGCTCACGCGGGAGAAACCGGGGCAGA\nTGAAGTTCACTTAGCCCAATATCTGATTCGAGACGCGTCGCCCCTTAGGGGATGTCTTCC\nTCTTCCGCGATAATTTCACCACGCCCACATACCCACTCCCAATAAAAGCCCTGTAGAGCG\nCATTGGCATCTTACTTGAGATTTGGATACGCTCGGCCGACTTGGTCTGTTTCACGCTTCC\nTTAAACAACATGGCTATGCCATTTGAGATAGAGGTATTGTTACCAGGAGACCTATCCCCG\nGCGGAAACATCTGCATTACAGAAATGTGAGGGAAAAATTATTACCTTCTCAACCCTGCGT\nCATCGAGCTTCACTGGTGGATATAGCGCTGTCGTCATATTACATTAACGGTGCTCCACCA\nGACACGCTCTCGCTGTTAGAGGCATACCGAATGCGATTCGCGGCAGTTATAACACGGGTC\nATCCCGGGAAAGTTGTTGGCGCATGCCATTGGCGTGGGTACTCCTACACCCGGGTTGTTT\nATTCAAAATACATCCCCCGTTGATCTTTGTAATGGCGATTACATCTGCTTACTTCCTCCG\nGTTTTCGGGTCCGCAGACTCAATTCGCTTGGACTCTGTAGGACTGGAAATTGTTTTCCCT\nTTAACCATCCCCCAGACCTTAATGCGAGAAATCATCGCCAAAGTGGTTGCACGGGCCGTT\nGAGCGCACGGCCGCGGGTGCTCAAATTTTACCCCACGAAGTTCTACGAGGCGCGGATGTC\nATTTGTTACAATGGAAGGCGTTATGAACTCGAAACAAATTTACAACATCGGGACGGATCG\nGATGCGGCTATTCGCACATTGGTTTTAAATCTAATGTTTTCCATAAACGAGGGATGTCTG\nCTTTTATTGGCGCTGATTCCAACTTTGTTAGTCCAAGGAGCACACGACGGTTATGTAAAT\nTTATTGATACAAACGGCCAATTGCGTTAGAGAAACCGGCCAGTTAATTAATATACCGCCA\nATGCCGCGGATTCAAGACGGCCATCGCCGATTTCCCATATATGAAACTATTTCATCTTGG\nATATCAACATCATCTAGACTGGGGGATACCTTGGGAACTCGCGCAATTTTACGCGTCTGT\nGTGTTTGATGGACCCTCTACTGTTCATCCGGGAGACCGCACAGCCGTGATTCAAGTGTAA\nACAGGTGTTAATAAAAACACAACCAGTCTAGTTACATTTCACGCGTCTTGTTTTTATTTA\nATAGGCATAAACACGGAATCCGGTATACATGAACTGCCAATATACACGGACATAATTAAT\nGCAACCATCAGATCATCTGACATTGTTCCCGTGGTACCTTTACCCGTGTAAGTTTTTGTG\nTCTAGATGACCCATACCGCCTTTAATTACCTCTGTCAGGTTATCCAACTGTTTACATAGA\nTACTCCACGGGGTCTACACCTAACTTTACTGTTAGGGATACAAGCTCCTGTGAGGCTATT\nATATTTCCGGAGTTAAATCGTTTAACAAAATAGTCTACGGCCGGCGTTTTTTGTTTTTGT\nAATAAAAAAAAAGGGTACGCCACGCTACATCCGGGAGGTATGGAATGATAAAACAGTAAC\nACTGGAGCGGAAGATAGCACGTTTCCCTTTTCGAGGACAGCAAACTGTTGTGCTATAGCC\nAACGATATGGCAACTGCAGAATCCTGGCTGCTGTTTCCCTCTATAGAAACGTGTACGTTT\nGTAAATGTATTGGGGTGTAAAGCGAGTATGTGGCCTAAGCATTGAGTAACGCAACGCCCT\nATCTCACTGGAAGACGTGCCAGTTAAAGCTCTAAGAAAAAAGTGCTCCAATCCAAATATA\nATCCAATCCGACTTATAACGACCAACAATCGCTACACCAGTACCAGACGCTCCTGCATTT\nGAGGTAAATGCAGGGTCTACGTAAACGTACAACACTGACGATAATATAGCACAATTCGCA\nACGGTTGACGGCCGATATAAAATAAACCTCTCACGGGCAGTTTTTGTAAATAATGGCCGG\nTCAAACCCCACACCCCCAGAATTCTGTTTACGCCCACCTACAATTTCCTGCACGAAGGAG\nTCGGCCATAAATAAATCTGCAGTGCGCCGCATGGCTCCATCCATTGTGATGAAAACCGGC\nTTATTTAATACATAACACGAACAAGCTGTGACATCGCTATGTGCTAAAACACGCGGCATG\nTGATCGTCGCATACATATGTAACAACGTTTAACAACTGATCCGACGATCCACGTAAGTTA\nTACAAAAAACTTGTACTTGCTTTTCCGGTATTTGTTGATGAAACAAAAATAATTTTACAA\nTTGGTTTGATTTAAAAATCCGACTATAGTTTGTACAGCATCAGGTCGAATAAAATTAGCT\nTCATCCACAAACAGAAGATTAAAATCTTGACCTCGGATACCCTGGAACGATAGAAAGATA\nTATAGTTACCCCACCAAAGTTTAAATGTATCCTTAAATACCACGTACGTAAAAAATGTTT\nGAATACGTACATATTTCTTTTTTTTTTTTCCAGTACAACCATATCCGGTGTATAATGGAA\nGCCCATTTGGCAAATGAAACCAAACATGCACTTTGGCATAATGATCACACAAAAGGATTA\nCTACACGTTGTGATACCTAACGCGGGGCTTATTGCGGCCGGAATAGATCCCGCATTACTG\nATTTTAAAGAAACCCGGACAACGCTTCAAGGTTGAAGTACAAACAAGATATCATGCTACA\nGGTCAATGCGAACCGTGGTGTCAAGTTTTCGCCGCGTACATTCCCGATAACGCCTTAACA\nAATCTCTTAATACCAAAAACGGAACCATTTGTTTCACACGTTTTTTCGGCCACGCATAAT\nTCAGGGGGATTGATTTTATCATTGCCTGTTTATCTTAGCCCCGGTTTATTCTTTGATGCA\nTTTAACGTTGTAGCGATACGAATAAATACTGGAAACCGCAAGCACCGTGATATTTGTATT\nATGTATGCAGAACTAATCCCAAACGGAACGCGTTATTTTGCTGATGGACAACGGGTACTT\nTTATTATGCAAACAGCTGATTGCGTATATCCGATGCACCCCTCGTCTTGCATCGTCTATA\nAAAATATACGCAGAGCATATGGTGGCAGCCATGGGTGAATCACACACGTCAAATGGGGAC\nAATATTGGACCCGTTTCATCCATAATCGATCTTGATCGACAGTTAACTTCTGGAGGTATT\nGATGACTCCCCTGCTGAAACACGCATACAGGAAAATAATCGGGACGTCCTTGAGCTAATA\nAAACGGGCCGTAAACATTGTTAACTCCAGGCACCCCGTCCGACCTTCTAGTTCCCGCGTT\nGCATCTGGGTTGCTTCAAAGTGCAAAGGGCCACGGAGCGCAAACTTCCAACACAGATCCG\nATCAATAACGGTTCCTTTGATGGCGTCCTTGAGCCGCCTGGACAAGGGCGATTTACGGGA\nAAGAAAAACAATTCGTCCGCCAGCATCCCACCTTTACAAGACGTTCTATTGTTTACCCCA\nGCTTCGACAGAACCCCAAAGTCTTATGGAATGGTTCGACATCTGTTATGCCCAATTAGTT\nAGCGGGGACACTCCAGCAGATTTCTGGAAACGGCGTCCCCTATCAATTGTACCGCGACAT\nTACGCAGAATCCCCCAGTCCGTTGATTGTAGTATCTTACAACGGATCCTCTGCCTGGGGA\nGGACGTATTACCGGAAGTCCAATTTTATATCACTCTGCACAGGCTATTATTGATGCTGCG\nTGTATAAATGCCCGGGTTGACAATCCCCAAAGCCTACATGTGACAGCTCGCCAAGAGCTA\nGTCGCGCGTTTACCGTTTTTGGCTAACGTCCTAAATAATCAAACCCCCTTACCCGCCTTT\nAAACCAGGCGCCGAAATGTTTTTAAACCAGGTATTTAAACAAGCGTGTGTGACATCGCTA\nACCCAAGGTCTTATAACGGAGTTACAAACGAACCCGACTCTACAACAACTCATGGAATAT\nGATATTGCAGATTCTTCCCAAACGGTTATTGATGAAATTGTAGCCCGCACACCAGACCTG\nATTCAGACTATAGTTTCGGTGTTAACGGAAATGTCAATGGATGCGTTTTATAACAGCTCC\nTTGATGTATGCGGTTTTGGCGTATCTGTCATCTGTATATACACGACCACAAGGTGGGGGG\nTATATACCCTACCTTCACGCTTCCTTCCCATGCTGGTTAGGTAATCGTTCTATATATTTA\nTTTGACTATTATAATTCAGGAGGGGAAATACTTAAGCTTTCCAAGGTCCCCGTTCCCGTA\nGCCTTAGAAAAGGTTGGTATTGGTAATTCCACACAACTGAGGGGTAAATTTATACGCAGC\nGCGGATATTGTTGATATTGAAATTTGTTCTAAGTATTTACCCGGTCAATGTTACGCGTAC\nATTTGTCTAGGATTTAACCAGCAATTACAATCCATTTTAGTTTTACCGGGGGGATTTGCG\nGCATGTTTTTGTATTACCGATACCCTACAGGCAGCACTACCTGCATCGTTAATCGGACCT\nATTCTAGACAGATTCTGCTTCTCTATTCCCAACCCCCATAAATAAATTAGTGTCACTATA\nAAAACATAACACCAGAATCTCTTCATATTTAATTTTACGTCATTTCTCCCGTTTCCACCC\nCCTCTTAAAATATAAAATAACCGGGTGGGTGGCATTAAACCCACAAGTACCCGGGCGGCA\nATCCGCTAGACTGTTTTTCTGCTCATGGAATTACAACGCATATTTCCGCTGTACACCGCT\nACGGGTGCAGCGCGCAAATTAACCCCCGAGGCAGTTCAGAGACTCTGCGATGCATTAACG\nCTGGATATGGGATTATGGAAGTCCATCCTGACCGATCCCCGGGTGAAAATAATGCGATCA\nACTGCTTTTATAACTTTAAGGATCGCTCCGTTTATCCCCCTTCAAACGGATACTACTAAT\nATTGCCGTTGTTGTAGCCACAATTTACATCACGCGCCCACGTCAGATGAACTTACCTCCG\nAAGACTTTTCATGTAATTGTAAATTTTAATTACGAGGTCTCGTACGCAATGACGGCGACT\nTTAAGAATTTATCCGGTTGAAAACATAGACCATGTTTTTGGAGCAACGTTTAAGAACCCG\nATCGCGTACCCCCTTCCAACATCTATTCCGGATCCTCGAGCAGATCCCACCCCCGCAGAT\nCTTACACCAACGCCAAACTTAAGCGACTACTTACAACCCCCGCGGCTTCCGAAAAATCCA\nTACGCATGTAAAGTTATTTCTCCGGGAGTGTGGTGGTCAGACGAACGAAGGCGTTTATAT\nGTACTGGCTATGGAACCTAATTTAATAGGGCTATGTCCCGCCGGATGGCATGCTCGGATA\nCTTGGCTCTGTATTAAATCGACTCCTCAGCCATGCGGACGGATGTGATGAATGTAATCAT\nAGAGTTCACGTGGGGGCACTGTATGCGTTACCCCATGTCACAAATCATGCGGAAGGTTGT\nGTGTGTTGGGCTCCGTGTATGTGGAGAAAGGCCGGTCAGCGGGAATTAAAAGTGGAGGTA\nGACATTGGCGCCACGCAGGTTCTTTTTGTAGATGTCACCACCTGCATTCGAATTACGAGT\nACTAAAAATCCTCGCATTACCGCAAATCTTGGCGACGTTATAGCGGGAACCAACGCCAGT\nGGTCTCTCTGTACCAGTAAATTCATCTGGGTGGCAGCTTTATATGTTTGGAGAAACATTA\nAGCCGGGCTATTATTAACGGCTGTGGTCTGCTTCAGCGAATTTGCTTCCCCGAGACACAA\nAGATTATCGGGTGAACCGGAACCTACAACCACCTAGTATACCTTAACTCAACCGCCGTTG\nTGGAAAGGTATATGTCAACATTTACAGTAATATATTAAAGGTTAAATTTATAAAACACTC\nACGTTTGTGTTGTGACTTGACGCGAACACCGCTGTGCTGTAAGACCCGTCGGTAAATGAA\nAACGTAATAGATTCGCCTTTTACATGATCCACGTAATTTGCCCCAAACCACTGTTCCAGG\nCGAGACTTGATACCCTCAAACACGGGTTCCGTTGCTTTGCGTATATGAGCCGTATAACCC\nACTTTAATTCCTCTAAACGTGGCCATTACTAAAGCTATTAATGGTACAAGAAACCATGTT\nTTCCCATGTCTACGTGGTACCAAAAACACAGTTGATTTTTGTTTGAAGTGTTCTAAAACA\nCTGTCAGAAACACTTGGCGTGTTAAACACTGTACGCAGAAAGCAGTCAACTCTGTCGGCA\nTGATCGCCCAATAGCACCGATGAAATAAAATGCGTGGTGTGCATGAGGATCATTTTTTGA\nAACAGTTCCAACGTCCCCTTATATCTGCCATAGATTGGAACGTCAACCTTTGCGCGTTTG\nCCATGACTTCCACACTCTTCAATACTCTCAAAAGATGTTTCCACAAGGTACGAAAACCGT\nTGTGTAAAGGTAGACAACTGACAGAAACTATCCGACAGAGAAAACGCGCGAAATGTGTTC\nATAACCCCGCTATACGCATTTCGATGAGGTGCTGCTTCTTCCGGTGAATATTCATAAAAC\nTGTACACTACTGACAGCCTTTTTTAATTCAGGGCTTACGTTTGCATTTACCGAATATCGC\nCATGGTTTCAAAACTACATTGGGGGTACAGTTGTACCCTGTTGACGATAGAAACGCGCCA\nAACATTGCCCGTCGAGCAGTAGCCGAGAACAGTGGAATATATTCACAACAGTTGTGAAGC\nGTTCCAATTCCGGGAATAACGGCCTGATGACGTCGGGTTACATCTATAGCAAAATTCAGA\nAACGGGATTTGGGTTGCGTTTCCCAGAGACCCTTGCCGCGTGGAACACGGGGTAGGGGAC\nTCCAACGTCTAAAGCGTTCATCCCTACGACGCTTTAGACGTTCAAAATATCTTACAGATT\nCTTCACCAAGCGTACGACCAAACATTATCAATGACATTTAACATCAATTCACGGAATCCG\nCCTCATCTCTTGTAAGCAGTAAAACAGGAAGCCGCGTCATCTTACGTACTCGTTACGTAT\nATATCATAAACATTTTCAGGGCCGCATTCATTCACTTTGGTCATGTCAGGCCACACTCCA\nACCTACGCTTCTCATAGGCGTAACCGTGTCAAACTAGTTGAGGCGCATAACCGCGCGGGG\nTTATTTAAAGAACGGACCCTCGATCTAATCCGTGGGGGTGCGAGTGTACAAGATCCAGCA\nTTTGTGTATGCCTTTACTGCTGCCAAAGAGGCCTGCGCCGATTTAAATAACCAGCTCCGC\nTCTGCAGCTCGCATAGCTTCAGTTGAACAGAAGATTCGTGATATACAATCCAAGGTTGAG\nGAACAAACAAGTATTCAACAGATTTTAAATACAAACAGACGCTATATAGCACCCGATTTT\nATTCGCGGTTTGGATAAAACAGAAGACGATAATACCGATAATATAGACAGACTGGAAGAC\nGCGGTAGGACCGAACATCGAACACGAAAATCATACTTGGTTTGGAGAAGACGACGAAGCG\nTTACTTACACAATGGATGCTGACGACACACCCCCCAACCTCCAAATATCTCCAACTGCAG\nGACCTTTGCGTTCCCACCACAATACCGACGGACATGAACCAAATGCAACCACAGCCGATC\nAGCAAGAACGAGAATCCACCAACCCCACACACGGATGTGTAAATCATCCATGGGCCAATC\nCGTCAACTGCAACATGCATGGAATCACCAGAACGATCACAACAGACAAGCTTATTTTTAT\nTAAAGCACGGCTTAACGAGAGATCCAATACATCAACGCGAAAGGGTGGACGTTTTTCCAC\nAATTTAACAAACCCCCATGGGTTTTTAGAATTTCCAAATTATCCCGTTTAATTGTACCCA\nTCTTCACGCTCAATGAACAGTTATGTTTTTCTAAATTACAGATTCGAGATAGACCCAGGT\nTTGCGGGACGGGGAACGTATGGGCGTGTTCATATATACCCATCGTCAAAAATAGCTGTAA\nAAACCATGGACAGTCGTGTTTTTAATAGAGAGTTAATTAACGCGATTTTAGCGAGTGAGG\nGTTCTATACGAGCAGGGGAAAGGCTAGGTATTTCTAGCATAGTTTGCCTTTTAGGTTTTT\nCGTTACAAACCAAACAGCTACTGTTTCCGGCATACGACATGGATATGGATGAATACATTG\nTTCGCCTGTCCAGACGGTTGACAATACCTGATCACATAGACAGAAAAATTGCCCATGTAT\nTTTTAGATTTGGCTCAAGCGTTGACGTTTTTAAATCGAACGTGCGGCCTGACCCACCTAG\nATGTGAAATGTGGCAATATTTTTCTTAACGTCGACAACTTTGCCTCGTTGGAAATAACCA\nCAGCAGTAATCGGAGACTATAGCCTAGTAACATTAAATACGTATTCCCTTTGTACTCGAG\nCGATATTTGAAGTTGGAAATCCATCCCACCCGGAGCACGTACTACGCGTACCCCGGGATG\nCATCGCAGATGTCATTTCGTTTGGTGTTGAGTCATGGAACAAACCAACCCCCTGAAATCT\nTGCTTGATTATATTAATGGAACGGGCCTTACTAAATATACTGGAACCTTGCCCCAAAGAG\nTTGGACTTGCGATTGATCTTTATGCATTGGGCCAAGCACTCTTAGAAGTTATCCTGCTAG\nGACGTCTTCCCGGACAACTGCCCATTTCAGTACATCGGACCCCGCATTATCACTACTACG\nGTCATAAGTTATCACCAGATTTGGCGCTTGATACGCTGGCATATCGATGTGTCCTGGCGC\nCATATATACTCCCATCTGACATCCCCGGGGACTTAAATTATAATCCCTTTATACACGCCG\nGAGAGCTGAACACCCGTATTTCCCGGAATTCTTTACGCCGGATATTCCAGTGTCACGCAG\nTGCGTTACGGCGTAACGCACTCAAAGCTTTTCGAAGGCATACGCATTCCGGCCTCATTAT\nACCCAGCCACTGTTGTTACGTCGTTGTTGTGTCACGATAATTCAGAAATACGCTCGGATC\nACCCTTTATTATGGCACGATCGGGATTGGATAGGATCGACATAAGCCCCCAGCCAGCCAA\nAAAAATTGCCCGTGTGGGAGGTCTACAGCACCCTTTTGTAAAAACGGATATTAACACGAT\nTAACGTTGAACACCATTTTATAGACACGCTACAGAAGACATCACCGAACATGGACTGTCG\nCGGGATGACAGCGGGTATTTTTATTCGTTTATCCCACATGTATAAAATTCTAACAACTCT\nGGAGTCTCCAAATGATGTAACCTACACAACACCCGGTTCTACCAACGCACTGTTCTTTAA\nGACGTCCACACAGCCTCAGGAGCCGCATCCGGAAGAGTTAGCATCCAAATTAACCCAAGA\nCGACATTAAACGTATTCTATTAACGATAGAATCGGAGACTCGTGGTCAGGGCGACAATGC\nCATTTGGACACTACTCAGACGAAATTTAATCACCGCATCAACTCTTAAATGGAGTGTATC\nTGGACCCGTCATTCCACCTCAGTGGTTTTACCACCATAACACTACAGACACATACGGTGA\nTGCGGCGGCAATGGCGTTTGGAAAAACCAACGAACCGGCGGCACGAGCGATAGTTGAAGC\nATTGTTTATAGATCCGGCTGATATCCGTACTCCTGATCATTTAACGCCAGAAGCTACAAC\nTAAGTTTTTTAATTTTGACATGCTCAATACCAAATCTCCAAGTCTCCTTGTGGGTACACC\nAAGAATCGGAACGTATGAATGTGGACTTTTAATCGACGTTCGAACGGGACTTATAGGCGC\nGTCGTTGGACGTTCTTGTATGTGACAGGGACCCTTTAACTGGCACCCTAAATCCCCACCC\nTGCAGAAACCGACATTTCATTTTTTGAAATTAAATGTCGTGCTAAATACCTCTTTGATCC\nAGATGACAAAAATAACCCGCTCGGTCGGACGTACACCACGTTAATAAATAGACCTACAAT\nGGCAAATCTACGGGACTTTTTATATACTATAAAAAACCCATGTGTAAGCTTCTTTGGACC\nCTCAGCAAACCCAAGTACACGCGAGGCCTTAATAACGGATCACGTTGAATGGAAACGTTT\nAGGATTTAAAGGTGGGAGGGCCCTTACAGAACTCGACGCCCATCATTTGGGCCTCAATCG\nGACAATCTCATCCCGAGTGTGGGTATTTAATGATCCGGACATACAAAAGGGGACAATTAC\nAACCATTGCATGGGCCACTGGAGATACGGCTCTTCAAATTCCTGTATTTGCCAATCCGCG\nGCACGCTAACTTTAAACAAATTGCCGTACAAACCTATGTATTATCCGGTTACTTTCCAGC\nGCTAAAACTACGGCCCTTCCTTGTCACCTTTATAGGACGTGTGCGCCGACCACACGAGGT\nGGGAGTCCCATTGCGCGTCGATACACAAGCGGCTGCCATTTACGAATATAACTGGCCGAC\nTATCCCACCCCACTGTGCGGTTCCGGTTATAGCCGTTCTAACGCCTATCGAAGTTGATGT\nGCCTAGAGTGACACAAATACTTAAAGACACAGGAAACAACGCGATTACATCAGCATTGCG\nGTCATTGCGATGGGACAATCTTCATCCAGCGGTCGAGGAGGAATCTGTGGATTGTGCAAA\nCGGTACAACGAGCTTGTTACGTGCAACGGAGAAACCGTTGCTTTGAACTCAGAGTTCTTT\nGAAGACTTTGACTTTGATGAGAATGTAACAGAGGACGCCGATAAATCCACACAACGCCGC\nCCACGAGTGATCGATGTAACACCAAAACGAAAACCTTCGGGAAAGAGCTCCCATTCCAAA\nTGCGCAAAATGTTAAACCCTGATAAACCCTGATAAACGTTCTAATAAAAACATCAAATCA\nTGGTTGGTTACTGTGAATGTTTGTTTTATTGCTTGGGGGTTTACAAGTACAACCCACGCT\nACTCCCACCCACTGTTTGATCGCTCGTATAACAGCTCATCCTCACGGTCCGTTTCATATG\nTTGAGTCATTTTCATAGACGTAGCCGTAGCCTTGTGATGGGTAATTTGTGCGGCGAGAAT\nTTCTATGTGCAGGTTTTACTTTTCGTATGTATCCCCGTACCCGCTCGGGTACTCTTCTTA\nCGGCACCGTAGAACCGACTGCGTTTCTGTCGATGATACACATATGCACGCATCAATCTGA\nGAAGCAACATGACAACGGAAAACACGGCCAGGCAAGCCAAGGTTCCCCGAGTTGTGGGAA\nTTAACCGTGGAGATTGAACCGATATAGGGTCATATAATCGGTCCATATACGAGTGCGCGG\nCGGTTCCCAACGTAGCACAGGCCACGAGCGTTCCCAGGGACGGTCCTATTAACACGTGTA\nTATAATGCGCCAAAATTAATTCTGATACTATAAGATATACAACTGACAATGTACTAAATG\nTAGACATGGCCACGGACACCGATGACCACAGTCCCGTATGTAGATGATTCGCCACCACAA\nGTTCCAGCATTAATGATACAAATAGGATACATATCGCCATCAACGCAGCCATCAAATTCA\nCGAACACTGCGCGCGTAGGCCCCGCAAGGCGATATAAAAAGACGCTCTGCTGTCGTAAAT\nTTGCGACCGCTTTTATGTTCGTTTCGTCCAATTTTCCGCGTCCACAAAAATACGTTGTAA\nATATTACACTTGTCGCAAAATGTCCAAGATATAATGTAGCAGCCACGCCGATTTGCTTGT\nAAGCTAATAATAACACAACGGCGTTTAATAACCACAATGACAAAAGACCCCAAAAAAGTG\nTTGTGGGATCTACAACTAACCATGCAACACCGGAGCTTTGCCGGACACGTTGATTTTTCG\nTTTCTCGGTGTATAATCGCGGCCGTGATCAGTGTATATACCGCCATGGCCATTGCCGTTA\nAAGCCGTGTAGTAAGTAAATGCCACAACGCTATGTGGTTCCAAAAACAAAACCGGGGCGC\nTGTATCCACCTCTATTTCCGGACCATACCCCCCCATCTAGGGTGGCGTTAAATAACTCAT\nAATCAACTACGGCAGCATAAAAACAAGGGATCCCGGTATATTCAGAAGAGGCGGCAATTA\nACGTAGCCAGGAGCATTACCGCACCCAAAGTGAACATCATCACCTGAATTATCCAAATTC\nGCCAATTAAGCGTATCCATTTGATGATCTAACGCTTCCACCTCGGGTGTCGTGGTGTCGT\nACGGTGAGACTTTTTCAGAACGCGGCCCCTTCTTTTGAGTTCCCATGTCTCCCAACACCG\nGGGAGAGCAACGCCGCCGTCTATGCGTCCAGTACACAGCTCGCGCGGGCGTTATATGGAG\nGGGATCTGGTTTCGTGGATTAAACACACCCACCCGGGAATTAGCCTGGAACTGCAATTGG\nATGTTCCAGTAAAACTAATAAAACCTGGTATGTCACAAACTCGCCCGGTAACCGTCGTAC\nGTGCCCCTATGGGCTCTGGTAAAACAACAGCCTTGCTTGAGTGGCTTCAACACGCGTTAA\nAGGCAGATATTAGCGTACTGGTTGTCTCATGTCGCCGTAGCTTTACCCAGACGTTGATTC\nAACGGTTTAACGATGCAGGCCTCTCCGGATTCGTAACATATTTGACATCCGAGACATATA\nTTATGGGTTTTAAACGTTTGATTGTGCAACTTGAAAGCCTACACCGCGTATCCAGCGAAG\nCTATCGACAGCTACGACGTATTAATACTGGATGAGGTAATGTCAGTGATTGGACAATTAT\nACTCCCCCACAATGAGACGTCTTTCCGCGGTTGATAGCCTATTATATCGTCTTTTAAATC\nGCTGTTCTCAAATTATCGCGATGGATGCTACAGTAAACTCTCAGTTTATTGATTTAATCT\nCCGGATTGCGTGGAGATGAAAACATACACACAATTGTGTGTACATACGCGGGAGTTGGGT\nTCTCCGGAAGAACTTGCACGATCCTGCGTGATATGGGCATCGACACGCTTGTGCGAGTCA\nTTAAACGATCTCCTGAACACGAGGATGTACGTACCATACACCAACTACGTGGAACATTTT\nTTGACGAACTAGCACTACGATTACAATGTGGGCATAACATCTGTATATTTTCATCAACTT\nTATCGTTTTCGGAGCTAGTTGCTCAGTTTTGTGCAATATTTACAGACTCTATTCTTATTT\nTAAACTCAACTCGGCCCCTATGTAATGTAAACGAATGGAAACATTTTCGCGTGTTGGTGT\nACACTACCGTCGTGACCGTTGGATTGAGTTTTGACATGGCTCATTTTCATAGCATGTTTG\nCTTACATAAAGCCAATGTCATATGGGCCGGATATGGTATCGGTCTACCAATCATTAGGGC\nGTGTACGGTTATTGCTACTTAATGAAGTTTTGATGTACGTCGATGGCTCAAGGACCAGAT\nGCGGACCCCTGTTCTCGCCAATGTTACTAAACTTTACCATCGCAAATAAATTTCAATGGT\nTTCCTACACACACCCAAATAACTAACAAACTGTGCTGTGCATTTAGGCAACGATGTGCAA\nATGCATTTACACGCTCGAACACCCATCTCTTCTCAAGATTTAAATACAAACACCTTTTCG\nAGAGATGCTCTCTTTGGAGTTTAGCCGATAGCATTAATATCTTACAAACTCTTTTGGCCT\nCTAACCAAATTTTGGTTGTATTGGATGGCATGGGTCCAATAACGGACGTTTCCCCAGTTC\nAATTTTGTGCATTTATACACGATCTCAGACATAGCGCTAACGCCGTAGCTTCCTGTATGC\nGTTCTCTTAGACAGGACAATGACAGCTGCTTGACCGATTTTGGCCCTTCCGGATTTATGG\nCCGATAACATTACCGCGTTTATGGAAAAGTATCTTATGGAGTCAATTAATACCGAAGAAC\nAAATTAAAGTATTTAAAGCCCTTGCATGTCCAATAGAACAGCCTAGACTAGTCAATACGG\nCAATATTGGGGGCGTGTATACGAATACCTGAAGCGTTGGAAGCATTTGACGTATTTCAAA\nAAATATACACGCACTACGCTTCCGGTTGGTTTCCCGTCCTGGACAAAACCGGGGAATTTA\nGCATCGCGACTATAACTACCGCCCCAAATTTAACCACACATTGGGAGCTGTTTCGCCGTT\nGTGCCTATATTGCAAAAACACTCAAGTGGAATCCGTCCACCGAAGGCTGTGTAACACAAG\nTTTTGGATACGGACATTAATACACTTTTCAATCAACACGGGGATTCGCTGGCTCAACTAA\nTATTTGAGGTTATGCGCTGTAACGTTACCGACGCTAAGATTATATTAAACCGCCCGGTTT\nGGCGAACAACCGGATTCTTAGATGGATGCCATAATCAATGCTTCCGTCCAATCCCTACAA\nAACACGAATATAACATTGCTCTATTTCGTTTAATTTGGGAACAATTATTTGGCGCCCGCG\nTAACTAAAAGTACCCAGACCTTTCCGGGAAGTACTCGTGTGAAAAACCTAAAAAAAAAAG\nATCTAGAAACTTTACTTGATTCAATTAACGTGGATCGTTCTGCATGTCGTACCTACCGCC\nAGTTGTATAACCTGCTTATGAGCCATCGCCATTCGTTCTCCCAACAGCGTTACAAAATTA\nCTGCCCCCGCTTGGGCACGCCACGTGTATTTTCAAGCACATCAAATGCACTTGGCCCCGC\nATGCCGAAGCCATGCTACAATTAGCGCTATCGGAACTGTCCCCGGGATCGTGGCCGCGGA\nTAAACGGGGCGGTAAATTTTGAAAGTTTATAACCCATTAATACCATATATGGACATCCAT\nAGGGGGGGTTACATAAATACTAAGCCTCTGTACAACACAAAGGGCCTCTAACAATGCACT\nGAACCACAACCAAGCTATGGACGCAACGCAGATTACCTTGGTTAGAGAAAGCGGACACAT\nTTGTGCCGCAAGCATATACACATCCTGGACACAGTCCGGACAATTAACACAGAACGGTCT\nTTCCGTGTTATACTACTTATTATGCAAAAACTCATGTGGGAAATACGTCCCTAAGTTTGC\nCGAAATTACCGTACAACAAGAGGATTTATGTCGCTACTCCAGGCATGGGGGGAGTGTTTC\nTGCGGCAACGTTTGCGTCTATCTGCAGGGCGGCGTCCTCGGCTGCGTTAGACGCCTGGCC\nCCTTGAACCACTGGGTAACGCAGACACCTGGCGGTGTCTCCATGGCACTGCCCTGGCCAC\nTTTACGGCGCGTATTAGGGTTTAAATCGTTTTATTCGCCAGTAACATTCGAGACTGATAC\nGAATACAGGTCTTCTGTTAAAAACAATCCCCGATGAACACGCGTTGAATAATGACAACAC\nGCCATCTACCGGAGTATTGAGGGCTAATTTTCCCGTGGCCATTGATGTTTCAGCAGTCAG\nCGCATGTAACGCCCACACGCAAGGTACGTCGCTAGCCTACGCCCGCCTGACCGCACTTAA\nATCTAACGGTGACACCCAGCAACAAACACCTTTAGACGTGGAGGTAATTACACCAAAGGC\nCTACATACGTCGGAAATATAAGTCTACGTTTTCCCCCCCTATAGAGCGGGAAGGCCAAAC\nCTCCGATTTGTTTAACCTTGAAGAACGCCGCTTGGTTCTTAGTGGCAATCGCGCAATTGT\nGGTAAGGGTACTCTTACCGTGTTATTTTGACTGTTTAACAACGGATTCCACCGTTGCATC\nTTCCCTTTCAATATTAGCGGCATGTGGACTGTGGTACGCGGCGGCGTTTGGAAAACCCGG\nGGTTGTCCGTCCAATCTTTGCGTATTTAGGCCCGGAACTCAATCCGAAGGGTGAAGACAG\nAGACTACTTTTGTACTGTCGGATTTCCCGGATGGACCACTCTTCGGACACAAACTCCAGC\nCGTCGAATCTATTCGCACGGCTACGGAGATGTACATGGAAACGGATGGGTTGTGGCCAGT\nAACCGGTATTCAGGCCTTTCATTATCTAGCCCCCTGGGGACAGCATCCCCCCTTACCTCC\nGCGGGTGCAGGATCTTATTGGGCAAATCCCTCAAGATACTGGACATGCAGATGCAACTGT\nCAATTGGGACGCGGGCCGGATATCTACCGTCTTCAAACAGCCTGTACAACTACAAGATCG\nTTGGATGGCAAAGTTTGATTTCAGCGCCTTTTTTCCCACGATATACTGCGCTATGTTCCC\nCATGCATTTTAGATTAGGCAAAATCGTCCTGGCTAGAATGCGTCGAGGAATGGGGTGCCT\nAAAACCCGCGTTGGTGTCTTTTTTTGGGGGGTTACGGCACATACTCCCGAGTATATACAA\nAGCTATTATTTTTATAGCCAATGAAATTAGCCTTTGCGTCGAACAAACGGCCTTGGAACA\nGGGCTTTGCTATATGTACTTATATAAAAGATGGATTTTGGGGAATCTTCACCGATTTACA\nTACGCGCAATGTATGTTCAGATCAGGCACGTTGTTCGGCCTTAAATTTAGCGGCCACCTG\nCGAAAGAGCAGTCACGGGCTTATTACGAATTCAACTAGGTCTTAACTTTACACCCGCCAT\nGGAACCGGTACTCCGGGTCGAGGGTGTGTACACTCACGCATTTACCTGGTGTACCACGGG\nAAGCTGGCTGTGGAATTTACAAACAAACACGCCTCCGGATTTAGTTGGCGTGCCATGGCG\nAAGTCAGGCGGCGCGAGATTTAAAGGAGCGTCTTTCAGGACTCCTATGTACCGCAACAAA\nAATTCGAGAACAGATACAGGAAAATTGCATATGGGACCATGTCCTATACGACATATGGGC\nCGGACAAGTTGTGGAGGCTGCCAGAAAAACATACGTCGATTTTTTTGAACATGTTTTTGA\nTCGCCGTTATACTCCGGTATACTGGAGTCTTCAGGAGCAAAATTCGGAAACAAAAGCAAT\nACCGGCATCTTATCTGACATACGGACACATGCAAGATAAGGATTATAAACCAAGACAGAT\nAATTATGGTTCGTAATCCCAACCCACATGGACCTCCTACTGTTGTTTACTGGGAATTGCT\nACCATCGTGTGCCTGTATTCCCCCCATAGACTGCGCTGCTCATCTCAAGCCCCTTATACA\nCACGTTTGTCACTATTATTAACCATCTTCTAGATGCTCATAATGATTTTTCAAGTCCATC\nATTGAAATTTACTGACGATCCCCTTGCTTCATATAACTTCTTGTTTTTATGACAAAAAAA\nCACGCCGCAACAACCCATCCTTAAAATAAAAGGTTTATTTACTTTACAACCCGTGGTGAA\nTTTTTATACGTTTCAAATAACTGAACATTTTTCGGTGTTACCATGGTGCGATTTAACCAC\nCAAAAATATACGCTCTTCTGATATTCCGAATCTCGTAAAGGTCCATTTAACAATCCCGGG\nGGCACTTGCACCACACCATCTGGACAGGGGGGGGTTCCGTGGGGCAGGTCAAAACGCTGA\nCCCACCCCACATGAATATATAGCCTTTATAATATTGGGGGCCGTTCCAGGCTGAGGGTTC\nAGTAACTTAACAAACATATAATGCGGCAATACGCGGGTTTTTGTAAAGGGGTTGTTATCA\nACGACATACATTAGAGTGTTTAACAACCATAAAACTCCCTCATATAAAAACCGACGCATT\nTTTTCCAAAGGTCCTATTTGACACTCAACGCGTCTAAGATATACAGACAATTGTACAAAC\nAGCGATGGAGATGCCCCGGAGGGCCCAATGCCTTCCAGATACATTAAAATAACACATAAG\nGTAAAATCTAAAACATTATCCGGGCGGAATAGAGTCATCCGATAGATTAACAGGCGCGGA\nGGCACCCCCACCGTATACACCCTATCTTCAACCGCAGTTAATACGGAAAAAATAAATCCG\nCGGAACGCTGGTTGAGTAACACACTCCATGTAGTAACGATCACAGGACACCTCACTTGAA\nTCACCATTCAACACTACTAAAACGGTCTCTTGGTGTTCCGGTTTTACGCGCAGTGATACA\nACAGAGTTTGCCAAAAAGCGTGGCTTCAAACCGGTTACCTCCCGCGCCTCGCATACGAAT\nCTTGGTATTGCTTGTATTCTAAGATCTTCGATCACGTCGCTCACATCCAACCCCTCTTCG\nGCTCGTGTTAGTAAGTTGTCGATCGTTACGCTGCAACCTAAAATGCTGGGTATATTTATT\nCCGGACATCCCATCGGCCATCCCCGCGCCTCCGGTTTGCTCGAATTTTATCCAGTAAGGT\nCGAATCCGCTGCATTTACCTTGTGTACCCGTAACCTCTCAGGGGGGTGTCCTTTCATAAA\nATGGGATAGGTTTTTATATCCAACATGCATGTATTGGTTATTTATTTTATTGGGTTCCGG\nGATTCTTTCGTCATCTTCTGTAGGGTCAGGCAAACCCCAGGAAGGACTTGGCGTTCTCCG\nTGGGCCCCGTTTTATTACCTCTGCGCGAACCTGCATTTCATATAATATTCGGATTTGGGA\nTAAATAGGACTCTGTTCTCGCCTTTTTAAAAATAGCCTGGCATAACTCTTCCTCTGACCT\nATGTACCTCGCTTTGAGTTACCAAGAATCCTAATCGGGTGGCCCGTAATATGAATGAAAA\nATACGGCGCAACTAGTAATGAGATTGACGCATTTGAATATGATACAGAAATTTCCTGGCC\nTTGATTATTGTTTACCCGGTGAAGCTTAAAACAGCGAACAAGTTCCTGTTTCCATAGCTC\nAGACAAACGTGTTATATCATCTCCATAAGGGGGGATATAACGAGATTGAAAACTATTGGC\nAATATATGCATCATCCCCTATTATGCCGGTAAGATCTATAACCTCGTGATTTAAATCGGC\nAATACGTGTTTCTTCTGCCATTGTAATATGTGACCCTTTAGATGGCTTTATTTTTACCCT\nCTCTTCCCGTAACCGTTTCAGCTCTCCTTCTTTGAACTGGAGCCTTTCGGTCAGATCGCT\nGTTCACATCCTTGAGACCCTCAATGGTTTTGAATAAATTATTCACATAACCCTCGAGCAT\nGCCGTTGATACTGTTAACCACCGATGTTTTAAACGCACTTTGAACGTTTGTTGTTCCGGA\nCATTGCCCCCCCGTTAAAGGATTGGTTGGCCTTGCCAAACCCCGGTTGTGATGTGTCCAC\nCGATCCACTTCCTTCCAGAATGTGATTGCCCGTTTCTTCTAGATAGGAACGTACGGTTTC\nGGTAATATCTCCAACATGTCTCATGTTTTTTAAGTTAACTATTAGCTTTACAAGTCTAGA\nCGCGGCCGATCCAGCCCGTGTTGTATCGTTCTCGCCCATTATACGATCAACCGCACGTGT\nGCTGTGAGATCTATCATCTTCATTCCGGCGACCTATTAACACGCGCAAAGGGGCTGTATT\nTAAAACTTGGCAGACGCGAGCATGTTCACGTAATGCATAACAGGCCAACACCTCCCCAGA\nAAGCCGCTGTAAGGGTGAGTCAAATACTACACCCTCCCCACATACAACGGGCGGCCACAC\nGACCAAACACTCTCCCTTCATGCCCGTTACATCATCCTTTGCCATAATTAATCTTCGGTT\nATAATTATAATAAAGACGCGTCCTATCATAATCCATAATAGCAACATTTTGCATACACTC\nAACTAGGCTTGTGACAACCGCCGCCCCTCTGGCCAACGTTGCATCGGCAACTTTTAACAT\nCTGGGACAGTTCTGCCGCTTGACTCATATACGTATTTAATGGTGCAGGGGTTCCATCCTG\nTTCTGATCGTACCTTTCTTACAACGGGCACAATACCTACACAGGCTATCCAGTCCACGTA\nTTTGGCAAAACCGACCCTTCCATTTAAACCACTGGTATAGAGACAACCGGTTATTCCACG\nCAGAAACTCAAGTAACGATGACTGTAATGTTTGACGCCAGGTTTCAAAAACCTGATGTGC\nAAGCCGTACGGCTTCTGATTCTCCACATAACCCATAACGTTCCGCTAGAGCCCCGGCATG\nCAGGTTACATTGTTGGATGTGGTGTTCCCAATCTGCTGCTAGGTCCTCATACCGAGTTGC\nATCCAACGCGTTCATCAAAACGGTTGCCTGAACTTGGCGAATTACAGTTTCCGTAGACCG\nTACAGCGCTATATATGCCTTGTCCATCGGTATATCCAAAGTCACCGGCTAGGATTTTTCG\nAAACAACATACTTTGCGTGGTTGGGTGTATTAACATCCAGCCATCTTCCTCCGGAAATGT\nACAAAACCCTATATCCGGGGCGTACTCATTCCAGTATATATCGAACATGTTCTTGTATTG\nGTCATTTGGGTTACTTCCATTCAAGCCCTGGTCAATAGAAACAGAACTTGCTATCCTTTT\nTTCTTCACTACCGGAACTGTTATTAAAAAGAGACGTTATTTCGGCCATTGAAAACCACGA\nTGAAAAGATCAATTTCTGTAGACAGTTCTTCACCCAAAAACGTTTTTAATCCAGAGACGC\nCCAATGGATTTGATGACAGTGTATATTTAAACTTCACCTCTATGCATAGCATTCAACCTA\nTCCTCTCACGGATTCGAGAACTTGCCGCAATTACGATTCCAAAAGAACGTGTTCCGCGGT\nTGTGTTGGTTTAAACAGTTACTCGAACTGCAAGCGCCTCCTGAAATGCAGAGGAATGAGC\nTCCCCTTCTCCGTTTATTTAATTAGCGGAAATGCCGGCTCCGGAAAAAGCACGTGTATCC\nAAACGCTTAACGAAGCTATCGATTGCATTATTACCGGATCCACCAGGGTTGCTGCCCAAA\nATGTTCATGCTAAGTTATCAACGGCTTATGCGAGTCGTCCGATAAACACAATCTTTCATG\nAATTTGGTTTTCGCGGAAATCACATTCAGGCTCAGCTGGGCCGTTACGCATATAACTGGA\nCTACGACCCCCCCTTCTATTGAGGACCTGCAAAAAAGAGATATTGTATACTACTGGGAAG\nTTTTAATTGATATAACAAAACGAGTGTTTCAAATGGGGGACGACGGTCGCGGAGGAACAT\nCGACATTTAAAACCCTGTGGGCAATTGAACGTTTGCTTAATAAACCTACAGGCTCAATGT\nCCGGAACCGCGTTTATCGCATGCGGTTCCCTTCCGGCTTTTACCCGGAGCAACGTTATTG\nTTATTGATGAAGCAGGATTGCTAGGGCGTCATATTCTCACGGCCGTTGTTTACTGTTGGT\nGGCTTTTGAATGCTATATATCAAAGCCCTCAGTACATAAACGGTCGAAAACCGGTCATAG\nTATGCGTCGGTTCGCCCACCCAAACTGACTCGTTAGAATCTCATTTTCAACATGACATGC\nAGCGTTCACACGTAACTCCTAGTGAAAATATACTCACGTATATAATCTGCAATCAAACTC\nTGCGTCAATATACTAACATCTCACATAACTGGGCAATCTTTATTAATAACAAACGATGTC\nAAGAGGACGATTTTGGAAATCTTTTAAAAACGCTTGAGTACGGGCTACCTATTACCGAAG\nCACATGCGCGTCTGGTCGATACATTTGTTGTACCTGCATCCTATATTAACAATCCTGCTA\nATCTTCCCGGATGGACGCGTCTGTATTCGTCGCATAAGGAGGTGAGCGCGTATATGAGTA\nAGTTACACGCGCATTTAAAACTATCGAAAAATGACCATTTTTCTGTGTTTGCCTTACCGA\nCTTATACATTCATCCGGCTAACGGCATTTGATGAATACCGCAAATTAACGGGACAACCCG\nGACTTTCTGTTGAACATTGGATACGGGCAAACTCCGGTCGTTTGCACAATTATTCCCAAA\nGCCGAGATCATGACATGGGAACAGTTAAATACGAAACACATTCAAATCGCGACTTAATTG\nTAGCCCGTACAGACATCACTTACGTGCTAAATAGTCTCGTAGTTGTAACCACAAGACTAC\nGTAAGTTAGTTATTGGATTCAGTGGTACATTTCAATCGTTTGCAAAGGTTTTACGTGACG\nACTCCTTTGTGAAGGCTCGAGGAGAGACATCCATCGAATATGCTTACCGGTTTCTGTCAA\nACCTAATCTTTGGAGGCTTGATTAACTTTTACAATTTTTTGTTAAATAAAAACCTACATC\nCCGATAAGGTATCGTTAGCATACAAACGGTTAGCTGCCTTAACCCTGGAGTTATTGTCTG\nGAACAAACAAAGCCCCCTTACACGAAGCAGCGGTTAATGGGGCGGGTGCCGGGATTGACT\nGTGATGGTGCAGCTACTTCTGCCGATAAAGCCTTCTGCTTTACCAGAGCCCCCGAGTCCA\nAAGTAACGGCCTCCATACCCGAAGACCCGGATGATGTAATTTTTACGGCACTTAACGACG\nAGGTTATTGACTTGGTATACTGCCAGTACGAATTTTCCTATCCCAAATCATCCAATGAGG\nTCCATGCTCAGTTTCTGTTAATGAAAGCTATTTACGATGGTCGATATGCCATATTAGCAG\nAGCTTTTCGAAAGCAGCTTTACAACCGCCCCCTTTAGCGCGTATGTCGATAATGTTAATT\nTCAACGGAAGCGAGCTTTTGATCGGCAATGTGCGGGGGGGGCTGTTATCTTTGGCATTAC\nAAACAGATACGTATACCCTTTTGGGGTATACTTTTGCACCCGTGCCAGTCTTTGTAGAGG\nAACTGACCCGAAAAAAGCTGTACCGCGAAACTACCGAAATGTTATATGCTCTACACGTAC\nCTCTTATGGTCTTACAGGATCAACATGGGTTTGTGTCCATCGTAAACGCTAACGTATGTG\nAATTTACCGAGTCTATAGAGGATGCAGAATTGGCAATGGCCACCACGGTGGACTATGGCC\nTTAGTTCTAAACTAGCCATGACAATTGCACGCTCACAGGGTCTGAGTTTAGAGAAGGTAG\nCTATCTGTTTTACGGCGGATAAACTGCGCCTAAATAGTGTGTATGTTGCCATGTCGCGTA\nCGGTCTCCTCTAGGTTCTTAAAAATGAATCTAAACCCTCTACGGGAACGATATGAAAAAT\nCCGCAGAAATTAGCGATCACATTCTTGCCGCTCTACGTGATCCCAACGTACACGTTGTGT\nATTAAAGCATTGTATAAAAACACGCATGCGGGCTTGCTGTTCTCATTTCTAGGTTTTGTC\nTTAAATACACCCGCCATGAGCATCTCTGGACCCCCAACGACGTTTATTTTATATAGGTTA\nCATGGGGTTAGGCGGGTTCTTCACTGGACTTTACCGGATCATGAACAAACACTCTACGCA\nTTTACGGGCGGGTCAAGATCAATGGCGGTGAAGACGGACGCTCGATGTGATACAATGAGC\nGGTGGTATGATCGTCCTTCAACACACCCATACAGTGACCCTGCTAACCATAGACTGTTCT\nACTGACTTTTCATCATACGCATTTACGCACCGGGATTTCCACTTACAGGACAAACCCCAC\nGCAACATTTGCGATGCCGTTTATGTCCTGGGTCGGTTCTGACCCAACATCTCAGCTGTAC\nAGTAATGTGGGGGGGGTACTATCCGTAATAACGGAAGATGACCTATCCATGTGTATCTCA\nATTGTTATATACGGTTTACGGGTAAACAGACCTGACGATCAGACCACACCAACACCAACC\nCCGCACCAGTATACATCGCAAAGGCGGCAGCCTGAAACCAACTGTCCTTCTTCACCACAA\nCCGGCCTTTTTCACATCAGACGACGACGTTCTTTCGTTAATATTACGGGACGCCGCAAAC\nGCGTAAAGACAGATTCAAGACTAACATTTATCCCAACTGATTACATTTCATACGCGAATA\nAACGACACAAAAAATTTATATTTAACGGCTTTTAATTTGAAGACACCTATCCTCTTAACG\nTTGATGAGCCTTGCAGGTTGGGTGCCGCGCTTCACCGGTATTATACATAACCGATTTACC\nGTGTTTACGGCAGTCTGACCATTTACCAGTGTATGTCTGTAATACGACGTTGTTGTGTCC\nCGACAAAATTAACTCGCGTACAAATTTCTGATGTTCCCCCGGCGTGGCAACGCTGGCATT\nTCCAAACACATTACGTTCTCGTACGTCCATGACCGCTATTTTCAGTATTAATTGGTTGGT\nCGGTCAAAGTATTTTCCTTATGTAAAAGGACACGATCTAAAGCCGTAAACTCGTACACAA\nACACTGGTACCAACGGACGCGATTTTCCGTCCGTTGAGCGGGTGTAATATCGGCGAGGTC\nTTCTTGCACGAATACTCTCGTACAGTAGGTTTCTGACACGGGGTGCATGGGTTTTTTGAC\nACAACACAAACATTTGCAGGCTCTTATGACTGGATGGATTGAATTTATTTTTAGATAGGG\nTCACGTGTTTTTGTCGTGACACGCCTCGACCAGAAAAGGCTGCGGTTTTCGTACACGCGA\nCCGTTATTTCACAGGCGTTCATAACCAAGCTGCGGCGGATGGTGTCGGTTAATTGTCTCC\nGCCCAAGTTCGTCAATAGATGATACCATGAACAACGTATCAAATGGTACATAGTCGTCTT\nTGGTTTTCTCAATACAGCCCGCGTGCCCAATCGGAAAATTTTCATTTGCATCAACGCTAT\nTTTCTGTAAAATCGTTCTGAACACTGTGTTGGCTGGCTACCTGTTTAAAATTTGGGATCG\nAACACGGTCCACGATGCAATCCCCAACCCCATTGAAGCAATGCCGTCGGTACGGAAGGAG\nGCAACTCCGAAAACATTATGGTACGCAAGAGGGTCGATTGGAGTGTTATATAACACTCCA\nATCGATCTCGGGTTCGCCTTTACGCGTAAAATACTCATTGGCTTGAACGAAATGTCGACA\nATTCCGAAATGGAACACGGGACAATGGCGACGGATGCGCGTGTGTTAGCACCAGATGACA\nTCTTGAATTCGGTTGGGTTGTCTTCTGTGCATGCGCACCCCACAGCATAAAAACTAACCC\nTGTACGGTTCTCGCATAACCTCTGTAGCACGCGTTGCACCAGCCGCCCCCAGCCTAAGTA\nTACATGCGACCCCGGAGTCCCGCGACGAACCGTAAGCGTGGTATTCAGCAATAACACCCC\nCTGCCTTGCCCAACTCTCCAGGCATCCGTGAGTGGGCGGAGTCATATTTGGGTATGATTC\nCATGAGGGCCGCAAAAATATTTTTAAGACTAGACGGTGGTGTTATGCCACGTTTTACACT\nAAACGCTAGCCCATGTGCATGTCCCGCGGTAGGGTATGGATCTTGACCAATAATTACAAC\nGCGAATGCTCTGGGGTCCGCAAAATCGCGTCCATGCAAAAATATCGCCTGTAGATGGAAG\nTATTTCTTCCCCTGAATTTAAAAGACGATTGTATTCTAAAAAAATACCTTTCGCGTACGG\nCTCTTTAAGTTCGTCCGACAACAGGTCATACCACTCAGGGGAAATGTTAAACTTGCTGAA\nAACTTCAACCGAATCCAGTTGCGAAGAGACGGGGGTGAACGTTTCCGTGTCGTAATGATG\nTGACATGTTATTTAACTTGAAGGTTGGGGGGTCTAGCTTAACCCCCAAAGGCAGCCCGCG\nGGGTCGCTTGCGGGTTTTTTTGGTAACCGGATGGGCCAAAACATAAATGTCCTTTGAATC\nCGATAGTTTCATTTCATTGGCATACGCGTTGGAACAAACGGTCGGCTCCCCAGACACATC\nCATTTTCCGGGATATTTGTGGAAGATGGAGTAGAGTCTACCCATACACCGGAAAGGGCAT\nCCAACAAAGCATCGCGTATGTCCCCGCTTTTATGTTCTTCACCAACAGATTGTGCCAGCC\nCCTTTAAGGTGACGTATGGATTTGTCCAGTACGCCATTTGTTTGTCTTTAAACCAAAGTA\nTAACTTCCGGTACTGGACATTTTGTCTTAACCACGATTCCCGATAGCGCCTCGCTGAGGT\nTTGATACAGGGGGTGCCGCATAGTCCCACGCCTCATATACCGATGACACGCACGGTTCCG\nTTATAATCAAACTCACATCCGATAGCGGTTTGGCTCCAAAAAACAACGGAGTGTCGTCTT\nGGAGATGAAGACAATACGCGATTGTGATAGTTTTTAAAAAAACTATCTGCAGTAACCATT\nTATGTGATGCCATGACGCTTGTGTTTTCCCTTCACTACGACGTTGTCGTATCCTTTGAAA\nAACTTGACCACTCTAATGGAAGCATGGACAAGTATGAGTTTTATATATACAGTTGGCCTT\nTAGTTAAACTCTTGGTGTCATATCTCATTTTCCTAAAAAGGGCGATCTTAATATGTCAAA\nCGTCACGGCGTGCCGACAAAGCGAATTTCCATGCAAGATTTGGATGTAGTATTTATACAC\nCCAATCACATGTCACGTATTAAGCTTTACAGTCCCCCGTTATCTGATATAATCACTTTTC\nTTAACACGTCATCGGGAAAACAGATGTTTATATTATACCTCTCGCGGTCATTTATGGCAA\nATACTTAGACCGTTTTCAAGCGGACTGAAAACGCTCAAATTGCCTTTTGGAGGCCTGCCC\nAACGGCCATTATCCCTTGGATCTGAGATTGATTTGCGGTAACGTTTGCCAATCAAGCTTT\nAAAAACGTACCCCAAACTGAAAACGCTCAAATTGCCTTTTGGAGGCCTGCCCAACGGCCA\nTTATCCCTTGGATCTGAGATTGATTTGCGGTAACGTTTGCCAAACCCACGCATTTCAGTT\nTAAATATTTCTAAGCATTCTTAGTGCGTACTTGGCAGCGTGCTTAAAATATCAACCAATA\nTCCATTATGCTACACGTTTCCTTCTATCCGTTTCAATCCATTAAAAGTCCATTAACAAAA\nATGATGCATCATACCTAATTCACCTAAAAACCTGACTCATTGCAGCAGCGTTTCCTCCTT\nGCAGACTATCCAGTTGGCATTTTAAACGGGTCCGGCTGCCTAAACCGAAAACACCGTTGC\nCTTTACTGTAAGTACAAAACTAAAATTTATATTTGCGTGCGTATTTTGTAACATATATGC\nCTTTTATCCCCCCGCAAGTTTGCTTTACCCTCGCCTTCACCACCCCCGCCACCTTCCGGC\nCATTTTAATAACTTTAATTGCTATAAGACATACCCAAACCGGATGATTTTTGCCGCTGGA\nAAAACAGCTTCTAATTTTCCCGTCTCAACTCGGCCTTGGTTGCATCTCCAAGTATACCTT\nTAGTTTGCTCCCGTAGAGGTGTATAAATACAAACGGTGACAAGTATTGAGCGTAATCTCA\nAATTTTTGTAATTTAGGGCGGAGCGCTTACGACAGCACATGCGTACTGTTAGACTGTTAT\nGTTTATTGTATTTGCAGAGCAGGATGCCCCGGTTACTCCGAGACCGGATTGCGGGCATTC\nCGAATCGTGTACGGACTTACCAGGGGGCAGTATTTACACCTTGGGTTCCAGATATACCAA\nCCCTTACGACCAATAGCAACACTCAGGTATTTTTAAAATGCACGTTTAATGATCATAATT\nTACATACAGTTGGTAATAAAGCAGACTGTGGATGTTTAAGGCATTTCCTTCCCCCTCCCA\nACAAACTAGGACTTCTTCATCTTGTTTGGAATACCTTTACCCGCTTTACCGGCAGAGCTT\nTTTTTGGTAAGGTGTTTCAGTGAACCTGATGTTGATCCGGAGGTGGAGGGGGTATTGGAC\nTCCCCCTGTGGAGAGGCAACTTTGCGGGTTTTACTTCCCTTACATGCCGAATCAGACTCA\nGATGTCAGGTCTATTGTTAAGCATCGTTTAACGTCTCTGCCGGTATGAAATAAACGGCGC\nTTAGCACCCCTTGCGCTTCCCGGTTTAATCCCCGGTAACACAGAAAAAAGCCTGACTTTT\nTGGGGTGTATTTACCAATCGGGTATCCCTTTCATCGCCACGAGAGGTCTCCCCGGTTGAG\nGTGGTTTCTGGTCTTACAATTGGACCTGTAATTAGTTGGATGGCTGTATCTTTCCAGGTC\nCAGGTTTGCATGGTTAGGCGGGTTGGATCGGTACATCGATCCAACAAGAATAACATGTTT\nGTTACAAACGGTCCTGTTGAATCATGCAAAAGACAACGCAGGGATGTTTTTAATCCCGCC\nTCATCACGCCCGTAAATACCTATATAGTTTAATATCAACATTTTTGTAGGCTCTACAATT\nTCGGGTTGATACAGTTCCGCAAGTTGATCATCAAGCCATCCGAGTAAAGGTTGCATGTAA\nCACGGGAATCTCGCGTTTCCCTCTGTTCCTCTATCCGTGGCTCGAAAAGGCAGTCTGTCC\nATGGTTCGTGGGTCTTGATTAATTCCCACAGATACTGGACGATCACGGTAGTCCTGCCCC\nCCGGTCCGGGGTTGCTGTGCAGATTCAATCGAGCCATACACCACCGGGGTCGCCGATCGA\nACAGCAGGTTGGTCTTTAAAAAATACCTTCCGTAAAAATGATGCGGTAGAGCATGTTTTG\nGTTACACCAGGGCTCGAGTCTCGGGTCGGTGGTTGTATAGAATCCTGTTGAGAGTCACTT\nGGTGACTCTGCTGTGGGCTCTCTAGCCGACGATTGAAGGGGCCCAGGGTTTGGTGATTGA\nATGGGCTCCCGACTCGATCTTGATGTTGGCTGTTGGATGGACTCCCGACTCGGTCCTGGG\nCTTGGTGGCAGAAGATCTATGACATCTCCCGGTAGGATGTCGATGGAATCTTCAAATGAC\nGGCTCAGAAAAACCATCGTCGTCGGATGGGTGCACTTCATATTCCTTGTAACTTGTATCA\nCTTACGATCTTATGCAGGATGGATTGCACTGGACACCGGCAGAGAGGACACTGGACGCTG\nGTGGAGGTCCATGCCCGAATACAAACAAAGCAGAAGTCGTGCAAACACGGCATGGTTTTT\nCCGAGATCGGAAACGGTGCTCATGCATATGGTGCAGGTATTATCCGAAGCGTCGGAGGTG\nCCGCTACCGCCCGCTAATATGGTATCCATGGTAACAACTGGCTGTATTCTAATGTCCGGG\nCATCCAAACACGTAGCAGAACTGCCATGCGTTCTAAATTGTGAGTTGTGGCGAGTACATT\nTTTATAATTGGTACCAACGAAGACACACCCCTATATCCCTCCACCCATTTCTTTTAAGTC\nCCACCCACTAAAACGTGGGTATAAAATGTGTATTGGGGTAGGCGGACAGTCCCAACAAAC\nAGGGAAGTTGATTGGTATAACCTTGGGCCGGGTATACAGCTAAGTGACATTTTAGATTCT\nGTCTTTATTTAGATAAAGAGCGATACGAAGACATTTCTCCACCCCCCTGTAATACCCGTA\nAATAAAGGTAAGTCCACAAACAAAAGCACTGTATATAGGAAGTCGGGTGTATTGGGACAG\nTTACTCCATTAGAGGCGTACAAACAATACTGGGATAGGGTAATGCAAGTCCCCCCCGATG\nGTCGCCCCGCAAACGCGCGGGGAGGTGGGGTCGCTTTTTTTTTTCTCTCTCGAGGGGGCC\nGCGAGAGGGCTGGCCTCCTCTCCCGGGGTCCGCCGGGCGCCCAGAAACCGGGGGGGGGTT\nATTTTCGGGGGGGGGTCCGACCAGCCCGCCCGTCGCCCGCCCGCACAGACAGACAGACAC\nTTTTTTCATAAAAACCGTTCCGCTTTTATTAACAACAAACAGTCCGCGCGCCAGTGGCGC\nTCACGAGAAAAGGAGGGGACTCCGTCACCCCCGACTCTGCGGGGGGCTCCTCCCCCCGCG\nCCCTCCCCACACATCGTCCTCGTCCTCGGAGGACGAGGACGAGGACAACAGCTCCACCTT\nGACCGCCGGGCGCAAACCCACCCGGCGGTCTCGCAGCACACCCGGGGCCACCGACACGAT\nGCTCACCCCAAAGGATGACCCCGGTGCGTCCCCGTCGTCCCCGCCCCCCTCCTCGCTGTC\nCCACGCGTCTTCACACCCCACCTCCCAATCGTCCAGCTCCAAAGCGTGTTCTCTGTCGTC\nTGCGGTGCGCCGCTGTCGCCCCGCCTGGGTTTCTGACGGCCGTTCCGAGCCCCCGTGGTG\nTCCGAACACGAACCGTGTTCCGTCGCTCCCCTCCAACACCGTCTCCGCGGCCCCAAAACC\nGGGCGGCCACATTACTCTGGGAATCGGGGGGAGGGCATTCCGAGCCTCGTCCGCCGACGC\nATACAGCGCCACCGACCGACCGGCCACGGGTGGAAGCACGAGTGGTTCTGCGGCAGGGTC\nGGGTTCCAGCAGGGCGTGGCGGCAAAACACCCTCGCCCAGGTGGGTACGTCGCCGGCCTC\nCGGCCCGGCGGCCCCCGGTCTCCGTCCCTCGGGAAGGAAGACGGGTCGAAGCGCGGCACC\nCAGGCCCCATCGGTTTGCTGCGCGGTGGCTATGTGCCGCCTCGTCCACAAAGTCGGCTGC\nCCCGAGCCCCAGACCCCGAGACTGTCGCGCGAGGTCCTTGCAACCGTCAAAACCCGGCAG\nCACGTACTGCCGGTATTCACGGGGCGACAGGGGGACGCGGGTCTTGGGGCCCGCGCGGGT\nACACACGGTGTATGCGACGTTCCCACCGCGGCACAAACACAGGGGTTGTTCGCCCGGGTA\nCAGGTTGGCAAACGCAGTCTCGATACGAGCAAAACTCGCTGGCCCAAAGGTGCGCGACGA\nTGCAAACACGGCCCGGGCGAGTCCTTCTGTGACCGCCGAGTCTGGCCATCGGACGACGGC\nCTGGGCGTCCGGTCGCGCCGGGGCCCGGACGTACACGTGATACTGAGACAAAGCGGGTCC\nATCCCTGGGCCACCTCTCGAGGGCCACCGCGTCCAACACCAGCAACCGGCGCCGGGCAGA\nGGCCAACCGCGAGCCTAGATACTCGACGGCCCCGGCAAAGGCCAGGTCTCGGGTCGACAG\nTAATAAAACGCCCCGGGCGTTCAAAGCGGACACGTCCGGCGGGCCGGTCCAGTTCCCGGC\nCCAGGCATGAGTGCTCGGCAGGCACAACCGGTTACTCAGGGCTGCCAGGACCACAGACAG\nTCCCCCTCGGGATGGACTCCATGACGGTCCCGGATCTGTCGCGAGGGTGCTCTCGAGGGG\nGCCGTTGATGTCCTCTCCGGGCAACGGATCGTAGATGATCAGAAGCCTCACATCCTCCGG\nGTCTGGGATCTGCCGCATCCAGGCGCACCTCCGTCGCAGCGCCTCCACTCCGCTGGGTGG\nACCAAACCGTCGGTCTCCTCCGCCCGGACGCCGAGCGGCGATTTCCGCCAAGGCGCCGGG\nATCAAAGCTTAGCGCAGGGCGCCAGGCCGTGGGAAACAATGGGTCGTCGACCAGACGGGC\nGATGGTTTCGGGGGTACAGTACGCCTTGCGAGCCTGGTCCGACGGGACCGGGGTATGCAG\nGGCCCCCCGGGGAATACGCCGAAATCCCCCGTTTGGGGCCGGTCCGTCAAGTGGCATCGT\nTATTACGGCGGGGGGATCCACCACAGGGCCCGAGGTGATGGTCACGGGCTCGGATACCCG\nCCTCTTGGCCTTGGAAACCACATGATCGTCTGCAACCCGGGCGTCCGCGACGGGTGTCTC\nCCTAATCTTGTCGAGGAGGCTTCTGCTCTCGACTGGCTGGGACTTGCGCTTGCGCGGAGT\nTCGTAAACGATCATCCGGTGGACACACAGAAAGAGAGCGTGCGGCGGCCGACGGCTGAGG\nGTCGGGAGCCTGTGTGGCCGGGGTTGTTGGAGAAGGGTGACCGCGGGAGATCCGCGCCGC\nCGGACTGGAGCCCGTTGCCTCGGGGTATGCCATGCTGGCAAAGGCTCTGCGGAGACTCTG\nTAGGATAAAGTGTTTTTGGGCCCGGTCGTATCGACGGCTCATAGCCACGGCCGCGGCCGC\nGTGGGGGAGAGCCCAGAGGGCCTCCCCCGTGGCCATGGCTTCGCCTACATGCGGAACGGG\nAGACGCTACGCTCCCCGTAACGGCGGTACCCGCCCGTCCCGGTGGCAACAGCTTTTGGTA\nGAACTGGTTCAGGGCCGAGTTGACACCGGTCAGCTTGGGGTTCTGGAGCCATGCTATAGG\nGTCTCTGTCTGGACAGTAGATCAGGTTAATCAGCGCGCGGTACTGTCTAGCCGGATCTCC\nCAACTCCGGCACGTAAAGCGGCACGGGTTCCGTTGAGGCCTCGTAACGAGCCCGCGCCGC\nTCTCACAGCCTCATCCTCCCAGTGACCCTCTCTGGTCTCCCCGGACGGTCCAAACCGCAC\nCCTGTTGGATGGGAGGGGTGCCGATCCGGGCCAAGGGCTTCCGTCGGGCATCATGAGCGG\nCCCCGACACCGGGGGAATTATCGGGGTTCTGGATCGCGGCAGGGAAAATGATTTCTGTCT\nCTGGCGCCCCGGTTCCCCCGCAAGACGTTTGGTCTTACGAATCCTCGGATCGGGACCGCT\nGATGGATCGATATCCCGGTTGGATATTTTGTTTCGTCGACCCACCATCATTTGAGTCCGA\nATCATCCGAATTTGACGGGGAAGGGGCGTGTTCGCGTCCGGACCTGCTGCCTGTAGTTTC\nACTTCCCACCGAAACGCGCCGGGGTTCATCGTCTTCATCCTCCGATGACGATCCCCACGA\nCGAGGAAGAGGATGAAGACGAAACAAACTCACGACTCTTTGGCTTTTTCTCCACTGGGCT\nGTCATCCTCAATCGGGTCTGGTGCGTGGGATCTTCCCGGCAGGGCCAAAAACGCTCTAGG\nTTTGCCCCCCGACGAACGTCCAGGGACGCGAGGTGTTATACCCCGGGCATCATGTTTCCT\nTGGGCGGGTATCATCGGTCTCAAACGGCAGGTCCGCCTTTGCCCCCTTAGCGGGAACGCT\nGTCCGAAAGGACGTGGTACAATTGCTCAACCGGGCCGGGTACAGGTCCACCGGGTTTCCG\nCGCCGGGAGTGGGACCTTAACCTTCAAAGTCTTTTTCTTCGGGCTCTTTCCCTGAGCGGG\nCCGTTGAGTTTTCTGGAGAACTACTCCGTCCCCCGATGCATGCGCATGACCCGCTTGCTC\nATCGCCCGGCTTTTTACCCGAGATGGACTGAGTTTGTCTGTCTCGATGGACCACCGACGG\nCAAACCTGGTGAATTTCCTCTCGTCGTTTGTCGGGGTATAGACCGCTGGTCTTCCCGTTG\nATCGTTCCCGGCGGCGTCTCCAACAGGAGACGCGGGGGATACAGGGGAGAAGGCCTGCGG\nGAACGGAGGGGTCGTACCTCTGCCCGTTTCCCCATCGTTCATCGGTGGTTTTGGAGACCT\nAGCAAGCTTCGTTCCGAGAGAGACTGTCTCAAGGGAGCGATCGGCTCCTGTTGGTTCTCG\nCGCGCCGGCCTCCGAGAATCGGGTGTGGAAGACCTCGGCCAGCGGGATTACAGGCGAGCC\nCATTAGATCCTGACCGTCCTCGCATACGTAGTCGTCTTGTGTTAGCTCTTCGCCAACATC\nTTCCGTTCTGGGTTCTGGTTGAAGTCCCGATACGGAGGGAATTGAAACGATCTCGTGTTC\nCCGTCCCACCATGACCCCGTTCTCTCCAAATAGTAGATCGTCAGGCTGACTCGAGGTGAC\nCACCCGGGCCCTGTGTTCGGCGGCCGCCGCGGCCGCGTCCAACAGGTCCATTAACTCCAA\nAGTATCAGGCGACCCCGCGCGTTGGGGTGTAGAGCGCTGCATCGGCGGCGTATCCATCGC\nACTGGGGTGAATTTAGACGTACCCGAGTTTTCCAAACGCTCTCGCAGCCTTCAAAGGATT\nGCGATTGCGGTTGGTGAGGGAGTTCCAACAGTACTTAAAACGTGTTGTGCCCCCCCCTCG\nACCGCATATTTCCTCCCCGTGTCGTCACCGTGTAAATATTCTTAATGATAAGACGATGTA\nGTGATTGGACGAGACTCGAGGCGGGAAGTTCATGGACCATAGTATGCGTTTAAGGAGAGA\nCCGCTGGTTGGCGATGTACGCCCGGTGTCTATTTCCGCATACCTTACAACATCATAACAA\nGGGATACCAGACATGTGAATTTCATTTACATATGTTTAAATAACAACCAATCATCGTGTG\nTCTACAGACGATATATAATATACATAAACACAATTGGGGTTGTCTCACATGCAAAACATC\nTTATATAACACGGGTTGTTTCCACCCATCCGGCATCTAGTTAATCAAATGCACGTCGACG\nGTGTGTTTGGGTCCCTCTCCGTCGTCATTACGTTCGCGCAATCAACAAGCGTATACACCA\nCCACCCCTCCCAACGATTATGTCAGGCGGCACGAAGCCCGCGATAACCCATAAAATACAC\nACGGGGTTGTGGTGTTCACGTAACCCCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCG\nATGGGGAGGGGGCGCGGTACCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCGATGGGG\nAGGGGGCGCGGTACCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCGATGTTTATAACC\nATAATTCTCTAAACCGTTGTAGAAAATCACAAAAAAATTTATTCAAAAACAAGTCGAAGA\nACTTCATATCTGAGGCATGTAAACCCGTTCGCACTTCCTGGGGTGGAATGGGGTGGGGTG\nGGGGGGTGAAAAAGGGGGGGGGTTAAATTGGGCGTCCGCATGTCTGTGGTGTACGCCAAT\nCGGATACACTCTTTTGATCTGCATTCGCACTTCCCGTTTTTTCACTGTATGGGTTTTCAT\nGTTTTGGCATGTGTCCAACCACCGTTCGCACTTTCTTTCTATATATATATATATATATAT\nATATATATATAGAGAAAGAGAGAGAGTTTCTTGTTCGCGCGTGTTCCCGCGATGTCGCGG\nTTTTATGGGGTGTGGGCGGGCTTTTCACAGAATATATATATTCCAAATGGAGCGGCAGGC\nTTTTTAAAATCGATTTGACGTGATAAAAAAAAACACACGGGGCCCCCCCCTTTTTTTGGT\nGTTATAAAGGCAACCCAATCGAAGGTCTCCCGCCCCGGAATCCCCCATTGCCATTTTACC\nCAAGTAGCCTTATTCATAGATGTAAACGTTTGGGTGTGTGTTTTGTTGTGCAGGGTTCGT\nCCGATTCATAACGCGACAGCGTCGAGTCGGTTTTAAGGGAAAAGGTTACTACGGCCCCAA\nGGACATGTTTTGCACCTCACCGGCTACGCGGGGCGACTCGTCCGAGTCAAAACCCGGGGC\nATCGGTTGATGTTAACGGAAAGATGGAATATGGATCTGCACCAGGACCCCTGAACGGCCG\nGGATACGTCGCGGGGCCCCGGCGCGTTTTGTACTCCGGGTTGGGAGATCCACCCGGCCAG\nGCTCGTTGAGGACATCAACCGTGTTTTTTTATGTATTGCACAGTCGTCGGGACGCGTCAC\nGCGAGATTCACGAAGATTGCGGCGCATATGCCTCGACTTTTATCTAATGGGTCGCACCAG\nACAGCGTCCCACGTTAGCGTGCTGGGAGGAATTGTTACAGCTTCAACCCACCCAGACGCA\nGTGCTTACGCGCTACTTTAATGGAAGTGTCCCATCGACCCCCTCGGGGGGAAGACGGGTT\nCATTGAGGCGCCGAATGTTCCTTTGCATAGGAGCGCACTGGAATGTGACGTATCTGATGA\nTGGTGGTGAAGACGATAGCGACGATGATGGGTCTACGCCATCGGATGTAATTGAATTTCG\nGGATTCCGACGCGGAATCATCGGACGGGGAAGACTTTATAGTGGAAGAAGAATCAGAGGA\nGAGCACCGATTCTTGTGAACCAGACGGGGTACCCGGCGATTGTTATCGAGACGGGGATGG\nGTGCAACACCCCGTCCCCAAAGAGACCCCAGCGTGCCATCGAGCGATACGCGGGTGCAGA\nAACCGCGGAATATACAGCCGCGAAAGCGCTCACCGCGTTGGGCGAGGGGGGTGTAGATTG\nGAAGCGACGTCGACACGAAGCCCCGCGCCGGCATGATATACCGCCCCCCCATGGCGTGTA\nGTCTTTATAAATAAATACAATGGTTTGGCTCGTGTCTTTTTTTGATGTCTGTCTGTGGGG\nGAGTGGGGTGTTGTGGATATTAGAGGGTAGAGGGTGCTGGTTTGAACGTCTCCATTAACC\nCACGGGGTCCCCACACGGGCCGTGTGGTATGAATCTCTGCGGATCCCGCGGTGAGCACCC\nGGGCGGTGAATATGCCGGACTTTACTGCACACGACACGATACCCCCGCGCACCAGGCTCT\nCATGAACGACGCCGAACGGTACTTCGCCGCCGCGCTATGCGCCATATCTACCGAGGCCTA\nCGAGGCTTTTATACACAGCCCCTCCGAGAGACCGTGCGCGAGTTTGTGGGGGAGGGCAAA\nGGACGCCTTCGGACGGATGTGCGGGGAGCTCGCAGCGGATAGACAACGTCCACCCTCGGT\nTCCGCCGATCCGCAGAGCGGTGTTATCGTTATTACGCGAGCAATGCATGCCGGATCCACA\nATCGCATCTGGAGCTCAGCGAGCGGCTGATATTGATGGCATATTGGTGCTGTTTGGGACA\nCGCCGGACTTCCGACTATTGGATTGTCGCCCGATAATAAATGCATCCGCGCCGAATTATA\nTGACCGCCCCGGGGGAATTTGTCACAGGCTTTTTGACGCGTACCTGGGCTGCGGGTCCCT\nTGGAGTCCCAAGAACCTACGAGAGATCCTGACACCCCATCCCTTTATATAGAAAAAAAAA\nATAAATTTAAAACATACACCGGATAAAAGCGTACTGTTTTTTATTTAAATTTACACGCTC\nGGCGTTGCCCCGGTTCGGTGATCACCGGGTCTTATCTATATACACCGTGTAACTCGAACC\nCCCGTGACTCCCTCCAATCGCGTTACCAAACTCTTCTTCCGTATCCGTAGATTCCGAGTC\nCTCGAAATCGTCCACTTATCCAACAAATTGTGACGTTATATATCCCAAGGCAAAGGCCGC\nTCCCGTCATAGCAAATACAAAGACAATTATTAGCGTAATATAACAGAATTTTTTACGATG\nATATATTTTATGTTGATATTTTCCAATTCGACGCAAAAATTCATCTGCCGTTTCATTTTC\nGCTATCACTATAATAACACTTTTCAGCCGAACGGCTCGGTTGTATGGCTGTTATCGTTGT\nATTATTTGGTTGCGCTCGCGGGGTTACCACCGCTTCCATCAGTAAGGCCACGGCCTCACC\nCTCCATGGTGTTTTGTCCGGCCATAGAAATCCAGATTGTAAGGCCAGCAGGCTAGTTTAA\nAAGTGTTTAATACCACACCTTTTGATATTTATATACATGCAAGATTCTAGATTATTCATC\nAATAGGTCGTTTAAAGCGCGTTTTCATAAACGTTGTCAGCTATACCGACATTCTCACAAA\nGAGGTAAAGTTACCTTACGTTATTATTAAATAAAACATGTAGACATTATTAATAATCCTA\nGGAACAATCAAATCCATATTTGTAAGTTATGTTTAACCCCTCCCCTTTTTGTCATTATCT\nCCGCCCTCTTATAATCGGATCACTTTATAAGTGTGTCGGTGAGTATATTTTGTACAGTTG\nTTGGACAACAGGTTTTTGGTTCATTAACACTATCAACATAAGTCGGGGTATACAAGTATA\nATGAACGACGTTGATGCAACAGACACCTTTGTTGGACAAGGAAAGTTCCGTGGCGCCATC\nTCAACATCACCGTCACATATTATGCAAACATGTGGGTTTATACAACAGATGTTTCCAGTT\nGAAATGTCGCCCGGCATAGAATCTGAGGATGATCCCAATTATGACGTTAACATGGATATA\nCAGTCTTTTAATATATTTGATGGTGTCCACGAAACTGAAGCCGAAGCCTCTGTGGCATTG\nTGTGCAGAAGCACGCGTTGGAATTAATAAAGCGGGATTTGTAATATTAAAAACGTTTACA\nCCAGGGGCGGAAGGTTTTGCGTTTGCGTGTATGGACAGTAAAACATGTGAACATGTGGTC\nATTAAAGCGGGTCAACGTCAAGGAACGGCCACCGAGGCAACCGTGTTAAGAGCGTTAACC\nCACCCATCCGTTATACAGCTTAAAGGAACGTTTACGTATAACAAAATGACATGTCTTATA\nTTACCACGTTACCGAACAGATTTATACTGCTATCTAGCTGCAAAGCGCAACCTCCCCATA\nTGTGACATTTTAGCAATTCAGCGATCTGTATTACGCGCGTTACAGTATCTTCATAATAAC\nAGTATTATTCACCGTGATATAAAATCTGAAAATATATTTATTAACCACCCAGGTGATGTT\nTGTGTGGGAGACTTTGGAGCAGCGTGTTTCCCCGTGGATATTAATGCCAACAGGTATTAT\nGGCTGGGCTGGAACAATCGCCACAAACTCTCCTGAGTTATTGGCTAGAGATCCATATGGA\nCCTGCCGTGGACATATGGAGTGCCGGGATTGTATTATTTGAAATGGCTACAGGACAGAAC\nTCGTTATTTGAACGAGACGGTTTAGATGGCAATTGTGACAGTGAGCGTCAAATTAAACTT\nATTATACGACGATCTGGAACTCATCCCAATGAATTTCCCATTAACCCTACATCAAATCTT\nCGTCGACAATACATTGGTTTGGCAAAACGGTCTTCTCGAAAACCCGGATCCAGGCCATTG\nTGGACAAATCTATATGAGTTGCCAATTGATTTGGAGTATTTGATATGTAAGATGTTATCG\nTTTGACGCACGTCATCGACCATCGGCAGAGGTGTTGCTTAACCACTCTGTTTTCCAAACT\nCTTCCCGATCCATATCCAAATCCAATGGAAGTTGGAGATTAAAATTCATTAAGCCTGTTA\nATAAAATATTGTATAAATTGTGTTTATAACGTATAACCCGTTAAGGCAAATAGGGTACAA\nACGCGCAATGTTTTGAAATACTAATATAAATAACATAACCAATAGAAACTTAATACAGAG\nTCACGCCCCATTACAACAAGGATAAAACACGGGATCATTTTCTTAACATTGTAGTAGCGC\nTGAAAAGCGTCCCCTCCCCCGGCTCACAGAGCTGCTCTTCGGTGTAGTTGGGTATACTGG\nTGCGCCTCATTTAATCGCGATGTTTTTAATCCAATGTTTGATATCGGCCGTTATATTTTA\nCATACAAGTGACCAACGCTTTGATCTTCAAGGGCGACCACGTGAGCTTGCAAGTTAACAG\nCAGTCTCACGTCTATCCTTATTCCCATGCAAAATGATAATTATACAGAGATAAAAGGACA\nGCTTGTCTTTATTGGAGAGCAACTACCTACCGGGACAAACTATAGCGGAACACTGGAACT\nGTTATACGCGGATACGGTGGCGTTTTGTTTCCGGTCAGTACAAGTAATAAGATACGACGG\nATGTCCCCGGATTAGAACGAGCGCTTTTATTTCGTGTAGGTACAAACATTCGTGGCATTA\nTGGTAACTCAACGGATCGGATATCAACAGAGCCGGATGCTGGTGTAATGTTGAAAATTAC\nCAAACCGGGAATAAATGATGCTGGTGTGTATGTACTTCTTGTTCGGTTAGACCATAGCAG\nATCCACCGATGGTTTTATTCTTGGTGTAAATGTATATACAGCGGGCTCGCATCACAACAT\nTCACGGGGTTATCTACACTTCTCCGTCTCTACAGAATGGATATTCTACAAGAGCCCTTTT\nTCAACAAGCTCGTTTGTGTGATTTACCCGCGACACCCAAAGGGTCCGGTACCTCCCTGTT\nTCAACATATGCTTGATCTTCGTGCCGGTAAATCGTTAGAGGATAACCCTTGGTTACATGA\nGGACGTTGTTACGACAGAAACTAAGTCCGTTGTTAAGGAGGGGATAGAAAATCACGTATA\nTCCAACGGATATGTCCACGTTACCCGAAAAGTCCCTTAATGATCCTCCAGAAAATCTACT\nTATAATTATTCCTATAGTAGCGTCTGTCATGATCCTCACCGCCATGGTTATTGTTATTGT\nAATAAGCGTTAAGCGACGTAGAATTAAAAAACATCCAATTTATCGCCCAAATACAAAAAC\nAAGAAGGGGCATACAAAATGCGACACCAGAATCCGATGTGATGTTGGAGGCCGCCATTGC\nACAACTAGCAACGATTCGCGAAGAATCCCCCCCACATTCCGTTGTAAACCCGTTTGTTAA\nATAGAACTAATTATCCCGGATTTTATATTAAATAAACTATATGCGTTTTATTTAGCGTTT\nTGATTACGCGTTGTGATATGAGGGGAAGGATTAAGAATCTCCTAACTATAAGTTAACACG\nCCCACATTTGGGCGGGGATGTTTTATGAAGCCTTAAAGGCCGAGCTGGTATACACGAGAG\nCAGTCCATGGTTTTAGACCTCGGGCGAATTGCGTGGTTTTAAGTGACTATATTCCGAGGG\nTCGCCTGTAATATGGGGACAGTTAATAAACCTGTGGTGGGGGTATTGATGGGGTTCGGAA\nTTATCACGGGAACGTTGCGTATAACGAATCCGGTCAGAGCATCCGTCTTGCGATACGATG\nATTTTCACATCGATGAAGACAAACTGGATACAAACTCCGTATATGAGCCTTACTACCATT\nCAGATCATGCGGAGTCTTCATGGGTAAATCGGGGAGAGTCTTCGCGAAAAGCGTACGATC\nATAACTCACCTTATATATGGCCACGTAATGATTATGATGGATTTTTAGAGAACGCACACG\nAACACCATGGGGTGTATAATCAGGGCCGTGGTATCGATAGCGGGGAACGGTTAATGCAAC\nCCACACAAATGTCTGCACAGGAGGATCTTGGGGACGATACGGGCATCCACGTTATCCCTA\nCGTTAAACGGCGATGACAGACATAAAATTGTAAATGTGGACCAACGTCAATACGGTGACG\nTGTTTAAAGGAGATCTTAATCCAAAACCCCAAGGCCAAAGACTCATTGAGGTGTCAGTGG\nAAGAAAATCACCCGTTTACTTTACGCGCACCGATTCAGCGGATTTATGGAGTCCGGTACA\nCCGAGACTTGGAGCTTTTTGCCGTCATTAACCTGTACGGGAGACGCAGCGCCCGCCATCC\nAGCATATATGCTTAAAACATACAACATGCTTTCAAGACGTGGTGGTGGATGTGGATTGCG\nCGGAAAATACTAAAGAGGATCAGTTGGCCGAAATCAGTTACCGTTTTCAAGGTAAGAAGG\nAAGCGGACCAACCGTGGATTGTTGTAAACACGAGCACACTGTTTGATGAACTCGAATTAG\nACCCCCCCGAGATTGAACCGGGTGTCTTGAAAGTACTTCGGACAGAAAAACAATACTTGG\nGTGTGTACATTTGGAACATGCGCGGCTCCGATGGTACGTCTACCTACGCCACGTTTTTGG\nTCACCTGGAAAGGGGATGAAAAAACAAGAAACCCTACGCCCGCAGTAACTCCTCAACCAA\nGAGGGGCTGAGTTTCATATGTGGAATTACCACTCGCATGTATTTTCAGTTGGGGATACGT\nTTAGCTTGGCAATGCATCTTCAGTATAAGATACATGAAGCGCCATTTGATTTGCTGTTAG\nAGTGGTTGTATGTCCCCATCGATCCTACATGTCAACCAATGCGGTTATATTCTACGTGTT\nTGTATCATCCCAACGCACCCCAATGCCTCTCTCATATGAATTCCGGTTGTACATTTACCT\nCGCCACATTTAGCCCAGCGTGTTGCAAGCACAGTGTATCAAAATTGTGAACATGCAGATA\nACTACACCGCATATTGTCTGGGAATATCTCATATGGAGCCTAGCTTTGGTCTAATCTTAC\nACGACGGGGGCACCACGTTAAAGTTTGTAGATACACCCGAGAGTTTGTCGGGATTATACG\nTTTTTGTGGTGTATTTTAACGGGCATGTTGAAGCCGTAGCATACACTGTTGTATCCACAG\nTAGATCATTTTGTAAACGCAATTGAAGAGCGTGGATTTCCGCCAACGGCCGGTCAGCCAC\nCGGCGACTACTAAACCCAAGGAAATTACCCCCGTAAACCCCGGAACGTCACCACTTCTAC\nGATATGCCGCATGGACCGGAGGGCTTGCAGCAGTAGTACTTTTATGTCTCGTAATATTTT\nTAATCTGTACGGCTAAACGAATGAGGGTTAAAGCCTATAGGGTAGACAAGTCCCCGTATA\nACCAAAGCATGTATTACGCTGGCCTTCCAGTGGACGATTTCGAGGACTCGGAATCTACGG\nATACGGAAGAAGAGTTTGGTAACGCGATTGGAGGGAGTCACGGGGGTTCGAGTTACACGG\nTGTATATAGATAAGACCCGGTGATCACCGAACCGGGGCAACGTCGAGCGTGTAAATTTAA\nATAAAAAACAGTACGCTTTTATCCGGTGTATGTTTTAAATTTATTTTTTTTTTCTATATA\nAAGGGATGGGGTGTCAGGATCTCTCGTAGGTTCTTGGGACTCCAAGGGACCCGCAGCCCA\nGGTACGCGTCAAAAAGCCTGTGACAAATTCCCCCGGGGCGGTCATATAATTCGGCGCGGA\nTGCATTTATTATCGGGCGACAATCCAATAGTCGGAAGTCCGGCGTGTCCCAAACAGCACC\nAATATGCCATCAATATCAGCCGCTCGCTGAGCTCCAGATGCGATTGTGGATCCGGCATGC\nATTGCTCGCGTAATAACGATAACACCGCTCTGCGGATCGGCGGAACCGAGGGTGGACGTT\nGTCTATCCGCTGCGAGCTCCCCGCACATCCGTCCGAAGGCGTCCTTTGCCCTCCCCCACA\nAACTCGCGCACGGTCTCTCGGAGGGGCTGTGTATAAAAGCCTCGTAGGCCTCGGTAGATA\nTGGCGCATAGCGCGGCGGCGAAGTACCGTTCGGCGTCGTTCATGAGAGCCTGGTGCGCGG\nGGGTATCGTGTCGTGTGCAGTAAAGTCCGGCATATTCACCGCCCGGGTGCTCACCGCGGG\nATCCGCAGAGATTCATACCACACGGCCCGTGTGGGGACCCCGTGGGTTAATGGAGACGTT\nCAAACCAGCACCCTCTACCCTCTAATATCCACAACACCCCACTCCCCCACAGACAGACAT\nCAAAAAAAGACACGAGCCAAACCATTGTATTTATTTATAAAGACTACACGCCATGGGGGG\nGCGGTATATCATGCCGGCGCGGGGCTTCGTGTCGACGTCGCTTCCAATCTACACCCCCCT\nCGCCCAACGCGGTGAGCGCTTTCGCGGCTGTATATTCCGCGGTTTCTGCACCCGCGTATC\nGCTCGATGGCACGCTGGGGTCTCTTTGGGGACGGGGTGTTGCACCCATCCCCGTCTCGAT\nAACAATCGCCGGGTACCCCGTCTGGTTCACAAGAATCGGTGCTCTCCTCTGATTCTTCTT\nCCACTATAAAGTCTTCCCCGTCCGATGATTCCGCGTCGGAATCCCGAAATTCAATTACAT\nCCGATGGCGTAGACCCATCATCGTCGCTATCGTCTTCACCACCATCATCAGATACGTCAC\nATTCCAGTGCGCTCCTATGCAAAGGAACATTCGGCGCCTCAATGAACCCGTCTTCCCCCC\nGAGGGGGTCGATGGGACACTTCCATTAAAGTAGCGCGTAAGCACTGCGTCTGGGTGGGTT\nGAAGCTGTAACAATTCCTCCCAGCACGCTAACGTGGGACGCTGTCTGGTGCGACCCATTA\nGATAAAAGTCGAGGCATATGCGCCGCAATCTTCGTGAATCTCGCGTGACGCGTCCCGACG\nACTGTGCAATACATAAAAAAACACGGTTGATGTCCTCAACGAGCCTGGCCGGGTGGATCT\nCCCAACCCGGAGTACAAAACGCGCCGGGGCCCCGCGACGTATCCCGGCCGTTCAGGGGTC\nCTGGTGCAGATCCATATTCCATCTTTCCGTTAACATCAACCGATGCCCCGGGTTTTGACT\nCGGACGAGTCGCCCCGCGTAGCCGGTGAGGTGCAAAACATGTCCTTGGGGCCGTAGTAAC\nCTTTTCCCTTAAAACCGACTCGACGCTGTCGCGTTATGAATCGGACGAACCCTGCACAAC\nAAAACACACACCCAAACGTTTACATCTATGAATAAGGCTACTTGGGTAAAATGGCAATGG\nGGGATTCCGGGGCGGGAGACCTTCGATTGGGTTGCCTTTATAACACCAAAAAAAGGGGGG\nGGCCCCGTGTGTTTTTTTTTATCACGTCAAATCGATTTTAAAAAGCCTGCCGCTCCATTT\nGGAATATATATATTCTGTGAAAAGCCCGCCCACACCCCATAAAACCGCGACATCGCGGGA\nACACGCGCGAACAAGAAACTCTCTCTCTTTCTCTATATATATATATATATATATATATAT\nATATAGAAAGAAAGTGCGAACGGTGGTTGGACACATGCCAAAACATGAAAACCCATACAG\nTGAAAAAACGGGAAGTGCGAATGCAGATCAAAAGAGTGTATCCGATTGGCGTACACCACA\nGACATGCGGACGCCCAATTTAACCCCCCCCCTTTTTCACCCCCCCACCCCACCCCATTCC\nACCCCAGGAAGTGCGAACGGGTTTACATGCCTCAGATATGAAGTTCTTCGACTTGTTTTT\nGAATAAATTTTTTTGTGATTTTCTACAACGGTTTAGAGAATTATGGTTATAAACATCGGC\nGGGGTACCGCGCCCCCTCCCCATCGGCGGGGTACCGCGCCCCCTCCCCATCGGCGGGGTA\nCCGCGCCCCCTCCCCATCGGCGGGGTACCGCGCCCCCTCCCCATCGGCGGGGTACCGCGC\nCCCCTCCCCATCGGCGGGGGGTTACGTGAACACCACAACCCCGTGTGTATTTTATGGGTT\nATCGCGGGCTTCGTGCCGCCTGACATAATCGTTGGGAGGGGTGGTGGTGTATACGCTTGT\nTGATTGCGCGAACGTAATGACGACGGAGAGGGACCCAAACACACCGTCGACGTGCATTTG\nATTAACTAGATGCCGGATGGGTGGAAACAACCCGTGTTATATAAGATGTTTTGCATGTGA\nGACAACCCCAATTGTGTTTATGTATATTATATATCGTCTGTAGACACACGATGATTGGTT\nGTTATTTAAACATATGTAAATGAAATTCACATGTCTGGTATCCCTTGTTATGATGTTGTA\nAGGTATGCGGAAATAGACACCGGGCGTACATCGCCAACCAGCGGTCTCTCCTTAAACGCA\nTACTATGGTCCATGAACTTCCCGCCTCGAGTCTCGTCCAATCACTACATCGTCTTATCAT\nTAAGAATATTTACACGGTGACGACACGGGGAGGAAATATGCGGTCGAGGGGGGGGCACAA\nCACGTTTTAAGTACTGTTGGAACTCCCTCACCAACCGCAATCGCAATCCTTTGAAGGCTG\nCGAGAGCGTTTGGAAAACTCGGGTACGTCTAAATTCACCCCAGTGCGATGGATACGCCGC\nCGATGCAGCGCTCTACACCCCAACGCGCGGGGTCGCCTGATACTTTGGAGTTAATGGACC\nTGTTGGACGCGGCCGCGGCGGCCGCCGAACACAGGGCCCGGGTGGTCACCTCGAGTCAGC\nCTGACGATCTACTATTTGGAGAGAACGGGGTCATGGTGGGACGGGAACACGAGATCGTTT\nCAATTCCCTCCGTATCGGGACTTCAACCAGAACCCAGAACGGAAGATGTTGGCGAAGAGC\nTAACACAAGACGACTACGTATGCGAGGACGGTCAGGATCTAATGGGCTCGCCTGTAATCC\nCGCTGGCCGAGGTCTTCCACACCCGATTCTCGGAGGCCGGCGCGCGAGAACCAACAGGAG\nCCGATCGCTCCCTTGAGACAGTCTCTCTCGGAACGAAGCTTGCTAGGTCTCCAAAACCAC\nCGATGAACGATGGGGAAACGGGCAGAGGTACGACCCCTCCGTTCCCGCAGGCCTTCTCCC\nCTGTATCCCCCGCGTCTCCTGTTGGAGACGCCGCCGGGAACGATCAACGGGAAGACCAGC\nGGTCTATACCCCGACAAACGACGAGAGGAAATTCACCAGGTTTGCCGTCGGTGGTCCATC\nGAGACAGACAAACTCAGTCCATCTCGGGTAAAAAGCCGGGCGATGAGCAAGCGGGTCATG\nCGCATGCATCGGGGGACGGAGTAGTTCTCCAGAAAACTCAACGGCCCGCTCAGGGAAAGA\nGCCCGAAGAAAAAGACTTTGAAGGTTAAGGTCCCACTCCCGGCGCGGAAACCCGGTGGAC\nCTGTACCCGGCCCGGTTGAGCAATTGTACCACGTCCTTTCGGACAGCGTTCCCGCTAAGG\nGGGCAAAGGCGGACCTGCCGTTTGAGACCGATGATACCCGCCCAAGGAAACATGATGCCC\nGGGGTATAACACCTCGCGTCCCTGGACGTTCGTCGGGGGGCAAACCTAGAGCGTTTTTGG\nCCCTGCCGGGAAGATCCCACGCACCAGACCCGATTGAGGATGACAGCCCAGTGGAGAAAA\nAGCCAAAGAGTCGTGAGTTTGTTTCGTCTTCATCCTCTTCCTCGTCGTGGGGATCGTCAT\nCGGAGGATGAAGACGATGAACCCCGGCGCGTTTCGGTGGGAAGTGAAACTACAGGCAGCA\nGGTCCGGACGCGAACACGCCCCTTCCCCGTCAAATTCGGATGATTCGGACTCAAATGATG\nGTGGGTCGACGAAACAAAATATCCAACCGGGATATCGATCCATCAGCGGTCCCGATCCGA\nGGATTCGTAAGACCAAACGTCTTGCGGGGGAACCGGGGCGCCAGAGACAGAAATCATTTT\nCCCTGCCGCGATCCAGAACCCCGATAATTCCCCCGGTGTCGGGGCCGCTCATGATGCCCG\nACGGAAGCCCTTGGCCCGGATCGGCACCCCTCCCATCCAACAGGGTGCGGTTTGGACCGT\nCCGGGGAGACCAGAGAGGGTCACTGGGAGGATGAGGCTGTGAGAGCGGCGCGGGCTCGTT\nACGAGGCCTCAACGGAACCCGTGCCGCTTTACGTGCCGGAGTTGGGAGATCCGGCTAGAC\nAGTACCGCGCGCTGATTAACCTGATCTACTGTCCAGACAGAGACCCTATAGCATGGCTCC\nAGAACCCCAAGCTGACCGGTGTCAACTCGGCCCTGAACCAGTTCTACCAAAAGCTGTTGA\nCACCGGGACGGGCGGGTACCGCCGTTACGGGGAGCGTAGCGTCTCCCGTTCCGCATGTAG\nGCGAAGCCATGGCCACGGGGGAGGCCCTCTGGGCTCTCCCCCACGCGGCCGCGGCCGTGG\nCTATGAGCCGTCGGTACGACCGGGCCCAAAAACACTTTATCCTACAGAGTCTCCGCAGAG\nCCTTTGCCAGCATGGCATACCCCGAGGCAACGGGCTCCAGTCCGGCGGCGCGGATCTCCC\nGCGGTCACCCTTCTCCAACAACCCCGGCCACACAGACTCCCGACCCTCAGCCGTCGGCCG\nCCGCACGCTCTCTTTCTGTGTGTCCACCGGATGATCGTTTACGAACTCCGCGCAAGCGCA\nAGTCCCAGCCAGTCGAGAGCAGAAGCCTCCTCGACAAGATTAGGGAGACACCCGTCGCGG\nACGCCCGGGTTGCAGACGATCATGTGGTTTCCAAGGCCAAGAGGCGGGTATCCGAGCCCG\nTGACCATCACCTCGGGCCCTGTGGTGGATCCCCCCGCCGTAATAACGATGCCACTTGACG\nGACCGGCCCCAAACGGGGGATTTCGGCGTATTCCCCGGGGGGCCCTGCATACCCCGGTCC\nCGTCGGACCAGGCTCGCAAGGCGTACTGTACCCCCGAAACCATCGCCCGTCTGGTCGACG\nACCCATTGTTTCCCACGGCCTGGCGCCCTGCGCTAAGCTTTGATCCCGGCGCCTTGGCGG\nAAATCGCCGCTCGGCGTCCGGGCGGAGGAGACCGACGGTTTGGTCCACCCAGCGGAGTGG\nAGGCGCTGCGACGGAGGTGCGCCTGGATGCGGCAGATCCCAGACCCGGAGGATGTGAGGC\nTTCTGATCATCTACGATCCGTTGCCCGGAGAAGACATCAACGGCCCCCTCGAGAGCACCC\nTCGCGACAGATCCGGGACCGTCATGGAGTCCATCCCGAGGGGGACTGTCTGTGGTCCTGG\nCAGCCCTGAGTAACCGGTTGTGCCTGCCGAGCACTCATGCCTGGGCCGGGAACTGGACCG\nGCCCGCCGGACGTGTCCGCTTTGAACGCCCGGGGCGTTTTATTACTGTCGACCCGAGACC\nTGGCCTTTGCCGGGGCCGTCGAGTATCTAGGCTCGCGGTTGGCCTCTGCCCGGCGCCGGT\nTGCTGGTGTTGGACGCGGTGGCCCTCGAGAGGTGGCCCAGGGATGGACCCGCTTTGTCTC\nAGTATCACGTGTACGTCCGGGCCCCGGCGCGACCGGACGCCCAGGCCGTCGTCCGATGGC\nCAGACTCGGCGGTCACAGAAGGACTCGCCCGGGCCGTGTTTGCATCGTCGCGCACCTTTG\nGGCCAGCGAGTTTTGCTCGTATCGAGACTGCGTTTGCCAACCTGTACCCGGGCGAACAAC\nCCCTGTGTTTGTGCCGCGGTGGGAACGTCGCATACACCGTGTGTACCCGCGCGGGCCCCA\nAGACCCGCGTCCCCCTGTCGCCCCGTGAATACCGGCAGTACGTGCTGCCGGGTTTTGACG\nGTTGCAAGGACCTCGCGCGACAGTCTCGGGGTCTGGGGCTCGGGGCAGCCGACTTTGTGG\nACGAGGCGGCACATAGCCACCGCGCAGCAAACCGATGGGGCCTGGGTGCCGCGCTTCGAC\nCCGTCTTCCTTCCCGAGGGACGGAGACCGGGGGCCGCCGGGCCGGAGGCCGGCGACGTAC\nCCACCTGGGCGAGGGTGTTTTGCCGCCACGCCCTGCTGGAACCCGACCCTGCCGCAGAAC\nCACTCGTGCTTCCACCCGTGGCCGGTCGGTCGGTGGCGCTGTATGCGTCGGCGGACGAGG\nCTCGGAATGCCCTCCCCCCGATTCCCAGAGTAATGTGGCCGCCCGGTTTTGGGGCCGCGG\nAGACGGTGTTGGAGGGGAGCGACGGAACACGGTTCGTGTTCGGACACCACGGGGGCTCGG\nAACGGCCGTCAGAAACCCAGGCGGGGCGACAGCGGCGCACCGCAGACGACAGAGAACACG\nCTTTGGAGCTGGACGATTGGGAGGTGGGGTGTGAAGACGCGTGGGACAGCGAGGAGGGGG\nGCGGGGACGACGGGGACGCACCGGGGTCATCCTTTGGGGTGAGCATCGTGTCGGTGGCCC\nCGGGTGTGCTGCGAGACCGCCGGGTGGGTTTGCGCCCGGCGGTCAAGGTGGAGCTGTTGT\nCCTCGTCCTCGTCCTCCGAGGACGAGGACGATGTGTGGGGAGGGCGCGGGGGGAGGAGCC\nCCCCGCAGAGTCGGGGGTGACGGAGTCCCCTCCTTTTCTCGTGAGCGCCACTGGCGCGCG\nGACTGTTTGTTGTTAATAAAAGCGGAACGGTTTTTATGAAAAAAGTGTCTGTCTGTCTGT\nGCGGGCGGGCGACGGGCGGGCTGGTCGGACCCCCCCCCGAAAATAACCCCCCCCCGGTTT\nCTGGGCGCCCGGCGGACCCCGGGAGAGG\n" }, { "path": "tests/input/TestImputeFromReference/expected.hhv3.muscle.fasta", "content": ">HHV3-test-1\nAGGCCAGCCCTCTCGCGGCCCCCTCGAGAGAGAAAAAAAAAAGCGACCCCACCTCCCCGC\nGCGTTTGCGGGGCGACCATCGGGGGGGATGGGATTTTTTGCCGGGAAACCCCCCCCCGCC\nAGCCTTTAACAAAACCCGCGCCTTTTGCGTCCACCCCTCGTTTACTGCTCGGATGGCGAC\nCGTGCACTACTCCCGCCGACCTGGGACCCCGCCGGTCACCCTCACGTCGTCCCCCAGCAT\nGGATGACGTTGCGACCCCCATCCCCTACCTACCCACATACGCCGAGGCCGTGGCAGACGC\nGCCCCCCCCTTACAGAAGCCGCGAGAGTCTGGTGTTCTCCCCGCCTCTTTTTCCTCACGT\nGGAGAACGGCACCACCCAACAGTCTTACGATTGCCTAGACTGCGCTTATGATGGAATCCA\nCAGACTTCAGCTGGCTTTTCTAAGAATTCGCAAATGCTGTGTACCGGCTTTTTTAATTCT\nTTTTGGTATTCTCACCCTTACTGCTGTCGTGGTCGCCATTGTTGCCGTTTTTCCCGAGGA\nACCTCCCAACTCAACTACATGAAACTACTGTCCGGAAGGGGAAGGTATTTATTCTCGCTT\nGCAGCTTGTCGCGCGTGTATGCACAACAAAAGCTATATATGTCACCAAAGCCAACGTCGC\nCATCTGGAGTACTACACCCAGTACGTTGCATAACCTGTCCATTTGCATTTTCAGTTGCGC\nGGACGCCTTTCTCCGGGATCGTGGCCTTGGGACATCAACCAGTGGAATAAGAACCGCCGG\nTGGTCTTGCCCGAACGACGAGTGGCGACGCGTTGTTCTGCATAAGCTCTGTATGCTGATA\nCATAAACACAGAGTCTGTATCGCTATCAGATTCCCGAACACCTTCCGGTACCCCATACTC\nCGATACCCTGGACATTGCGGATCCCAAAAATATAATATTAACAGGATTTGCTTATACTTT\nGCTACAGCTTATATAAATTTATGTGCGATACATCTTAAGTGCATCCGTACGTTATTTATA\nCATTGCCGGTCACGTGAAAAGACTGTGTTACCCAATAAAGGTTCTACAAAAAATGCTTTA\nTTGGGTGTTTGTTTAATAGCTATTATCGTAACCCACCCCCGTAAAATCATAAAATGCATG\nTAATTTCTGAGACACTTGCATATGGGCATGTTCCCGCATTTATTATGGGCTCCACTCTGG\nTGCGTCCCAGTTTAAACGCCACCGCCGAGGAAAATCCCGCGTCAGAAACGCGATGTTTAT\nTACGAGTGCTTGCGGGGAGAACTGTAGACCTGCCAGGCGGAGGAACGTTACACATTACCT\nGTACCAAAACCTATGTAATTATTGGCAAATATAGCAAACCCGGCGAACGTCTTAGCCTTG\nCCCGTCTAATAGGGCGTGCAATGACGCCTGGAGGTGCAAGGACATTTATTATTTTGGCGA\nTGAAGGAAAAGCGATCCACAACGCTTGGGTATGAATGTGGTACGGGCTTGCATTTACTGG\nCTCCATCTATGGGTACATTTCTCCGCACACACGGTTTAAGTAACAGAGATCTCTGTTTAT\nGGCGGGGTAATATTTATGATATGCATATGCAACGTCTTATGTTTTGGGAGAATATCGCGC\nAAAATACCACTGAAACACCTTGTATAACGTCGACGTTAACATGCAACTTGACAGAAGACT\nCTGGTGAAGCCGCACTTACCACGTCAGACCGACCCACTCTCCCAACCCTAACAGCCCAAG\nGAAGACCAACAGTTTCCAACATTCGTGGAATATTGAAAGGATCCCCCCGTCAACAGCCGG\nTCTGTCACCGGGTTAGATTTGCCGAACCTACGGAGGGCGTATTGATGTAATCACTAAATA\nAAATACACCTTTTTTCGATTGTACGTATTTTTATTTAAATGTGTAGTTCATAGTCCGCCG\nACAGCCGCTCGGGCTTTTCCCCCACATACAACATGATCGTATGCCTCGGATGCACCGGTC\nCAACACTCCGCCGAGAAGGGGGATTTACAATGACAGTGATACCCAATAGCCGCCAGATGT\nACACCCAGCTGTCCGGACTCCAGCATCATCTGCTGAGTTGCGGCGCTGAAGGGTGCATCG\nCATAGGGTGTTATAATTAGCCATTTCCGGTAACAGTCGTTGGGAATTTAGGAGGCTGCAA\nAACGGCTGTAGGTCAACATACATTGGGGATTCAGATGGTTTATCTCGACGTCCAAGTCCA\nATCAAAAAAGCGTGTAAATCATCAGCCCGGCCGCATGTTGCTCGAAGAGCACATAACCTC\nTTAACACCGTACAGAGGGGATGGCGTCGGTGCATGTGAGTTGGCAGGGCATGTCCACGTT\nGTTTCCAACGCCAGTGGCGGTATAACTTGTGTAAACGACGCCAACGGGTCAGGTTTAAGA\nTTCACTCGGATGGGTTGACTGCTTTCGGAAGCTCCCGTTGTATCCATTAATTAAACGTTC\nGGTACACGTCTGGTGTGTGTTTTACCCGAATCAGAGACGGAATTGCAAAGATATTGGTTT\nGAAAGCAATGTAATCCCGCCCATATATCCCCAACGTCGCCTTAAAAACTCCCACAATATT\nACATTTTTATTAGTCTTTTATTAATATAGAATCACATAAACAATTGATAAAATCAAGGGG\nTGGTGTATAATGATTAAAAATATAAATTGATATGTTTTACAAGCATGAAATAGGTATTTA\nCTATTCTAACAGGTAAATATGCTTAATGATTAAAAATACAAATTAGTATGTTTTGACAAG\nCATGAAAAAGGTATTTTTTATTTTAGCAGTTAAAGGTACTACACTTAAAATATTTACCGT\nATGGACGGGCGTCAGAAAGATGCCCGGCCCAAGTTGAGAGGGTACATTCAACACGACCAC\nACTCGCGTTGGTGGGTGATTAGGGCCTCTAAAACACCGGCCAGACATGACCCGGGTGTAT\nATTCTTGTAACACTTGAACGTTACAACTGATATCATCATATTCCACAAATTTAGAGCCAC\nGGACAACTATATTAGCAATGCGGGCAATCATAACAAACATATAAGTAGTAATACACGTGA\nTATCACTAAAACGTTGCTGGCGCAACAGTTCGGGGAGAGTACGAGACCCCAAATCGTTGT\nCCCTGTTTAGAAGAAGACATCTTACAAAAGGCCCCAGCTTTAACTTTAAATTCTCCAAAA\nGTGACTTCGAGGTTGCAACAATGGGATTATTTGTGTAGATGGGCAAGTTTTTTGCCGCTA\nACATTTTAATCCACGTTAACAGTTCATCCGCAGACTCCAACGCTTCAATCAAAGATTCTC\nCACGTATGACTCTCTCACGCAACGCGCGGGCAATACGTGAGTCCATTTTATATGACTCAA\nAGGTACGATAAAGTTCATGTCCGTACAACATCAACTCCGGCCAAGATGTGTTTTGTTTTA\nTCCCCGGAAAACATCCACCGGAAGCCCATGAATCACCCTCTTGTATTGTGGCATATCGGA\nCTACCAGTTTTTCAATTGTTTCATCTAAATGGCGTACCGAGTCAATGGTCACGCTGGCTC\nCCGCGGTGGAGACGACTTCAATAGCACGGCCCGTAATTCGATCGACCGGGATATCATACT\nCTTTTCGAATACGCTCTCGGCGGGCGTCTCTCTTGGAAAATCGCAACCTGTACGATTCGT\nCATGTGTCTGATCATTTCTTTCTCCCGTGGTCATTGCAGGAGGCGTTGTAGGACGCCGTC\nTTCGATTTGACAGGGATCGATCACGGTGTTTTCTTGAACTTTGGGTGTTATAAGATCTGG\nATGATCGTCGATGTCCCCGTTCGATGCGTGCATATCCAGTCTCCACGTCTCTTCCTCCAT\nGATGGTTTGAATCGGGTAATACAACAACCAAAGTTTTCGGGCGATTGTGGTGGTAGCTTT\nCACGCCTTCCGTGCCTTCGTTTGGAATACCGTGGATTATATGCTGTATCTGCAGTACGCT\nCCACATACACAGTTCTAGACGTTGTGGAGTCCTCGCCTGGAGTGGAGCCAATAGCTTCAT\nCATTTGCCCAATCGGTGACTTCCAATGCAAAGTCATCCGAAGGTTCGTCTGGTAGCAAAT\nTCATAAAGTCTTCACAAATAGTAGACACGTCTGGGTCGGTTGGAATTGAAGCAGAGGCCA\nTGGCTGCAAAATATCTGACAATTGCGTGTTTGCAGTTGCCTGTATCTTCCGCCAATGTTG\nTAGAATTTATAGGCTCACCCAACCCCGCAATGGGCGTGTTTAGTCACATGATTAATGTTT\nCTGGGAGTTTTCACTTTCCCCAAACAAGCTTACCTGCACCCTTTGTTCGTAATGCATAAA\nAATAACCACTGCTATAGCAAATATGACGATATAAAAACATTTTATAGCAAGGCCGGACAT\nTACTGTAGCACAACATGTTGTGCATATACCACGTATTCCCCCCGTATTGATATGATTTAA\nATGATTATCCTTGGTTGGTTTTGGTCTAACATAAGATATAAGCTCTACTATAGCGAGCGT\nGCATACAACAACCCAGGCCAGAATCCGAATGTATGTGGGGTATAATAACGCGCATGGTGT\nATATGCAACGCCAAGCGTTAAAAGCACAATACATCCAGATGATATATGAGCGATAACCTC\nCAAAAGCATCAATAACGTAACACCTTTATGCATATATAAAAAACTTATAGGGTCAGCATT\nAAATACTTTACTCATACCATCCCGTCGCATGGAAACATCACATAACAACCTTGCCAACTT\nTGTATATGGGTAACCAAGAAGAATGTTCGAAATAACCCGTGTTACGTAATTCAGTGAATA\nTGATGTGGGGGATATTAACTCACAGGATGATCGGAATGGCCCAAACATACGACGTATTCG\nTCGAAATTGTAAATACATACCATATACAAACCATGCAAAAAAAATCATTTTTAGCTGCAC\nGCACCAAAAATAAGCGTGACAATTACGTGTTCCCAGAACAATTCGAATTTTGTCATGCAA\nAGGTGTAGAAATAGCGGTTTTTACCATAGTATCTCCTGATAATAGATTTTCCCGGCAGCT\nGTAATCGTATCCAGATAGGCCATCCAAAAACGTTGAGTGGTTTACAAACGTTACATATAT\nAAGAGAGTTGTTATAAGACCCCCATACAACCGGTCCACCATTAATCACCGTGGTTGCATA\nCACACACTCATGTTCAAACTTTACACGAGCGGTATACCATAGGGTAAAAACAGCATGTCC\nGCTAAGTAGACACATAATTATAAAATGTTCTGTCTTGATTCCTAAAGCCTGCATGACCCG\nTGGAAGATGGCAATTCAAGCACGATGTAGTATCACACGGTTGGTGTTAACTCGAAGTTAA\nATTTGGATAATTAGGTACTTCTAGAGTAAAGATTGTATGCATGCGATTGCTATCGCACTT\nTGTAGCAAAACATTGTTGTGCAAGCGAAATACACAAACGGTTGTGATGATCCACTCGCAG\nAGACACAAATGTCCGGGGAGCCGTTCTTCCTCCGCGATGGGGATATCGAAGACAAGTGAA\nCCCTTTTGTTCCGCATATGAGCTGAAATAACACCCAGTCCCTTTTGATGGCGATACACTT\nTGATGATGTTAAGGTATATTCGCGATCACGCCCGGGGAAATGAACAGCAATATGCTCCAC\nAATAGATTCTAATATTGTGCTGTCGACAAAGGCCTCCAGTGTAAATGCGTCCAGACAAGT\nTACCCCGCGCTCTTTTAGAGCCTTTGTTAAAGATATTTGCGGGGAGCTAAATATTTGTTT\nATTACGCGCAACCTTACGTTCAAAAAACTCTGCGTATTCCCCCCCAAGGTTATGTAAAAT\nAAATTGCACTGGAACATTCGACTGCGGTCTTGAATGAAAATGAAAGTTTGCCGGGTTTCT\nATGTGATGTCACAAACGCTAATATATCAATACACTGCTCAGGTACAACATAAAATGGGAG\nTAGTTGTCCAACCGCCGTCCCTGTGGTTGTTACTTTGGAGAAAAAAGGCAGTCTTAAACT\nATGTCCGTGGCTATAAACACCAGTATCTATAAACGAAAAGTCCCGTAAATACGGACCAAT\nATATTCAACAAATTCCCGTTCCAGCAACACCGCTTGTTGTAATATTTGTGCAAACCCCTT\nTAAAGTGGAAGACCCCACTAACGCATAGGGATTTGGGATTGGTACGCATACCCTGAAACC\nTATTTTCTCTTTACAGTTACAGGGTAGAGTTTCATGCAAGTTTTCATTGTTTGATACATC\nGGCGTGTGTATGGACTTCAGACGTTGTCTGTGTATCAAAAAACCATACATCCTCTGTATA\nATTCTCTTCTACACACGTGTATAATTCGCCATTTTCTATGTAAAAATCGATGTCAGAATG\nGCTGGTTATATCCAATAAATTATCATCATCCAACACCTCAACGGTAGGTTCAGGACATGC\nAGTTTTATAAAAATAACATGGGTCTTTGTTAGGGTTTACCACGGCCTTTGGAAAAAGTAA\nTTGCATGGCCGTTAAAATACCATGACGAAATGCTCGCATGCCGGCATGTAAAATACCCAA\nTGGGATGGGTTTTCTTATATGAAAGTCTACATCAAGTATGAGGTTTGTGATTATAAGATT\nTGTATTAAATAGCTCATTCCTGTTTATATAAAGCTGATCTTTGGGTATGTTAGATGAAAT\nTTTAGAAACGTTTTTAACAGACGTAGATAATAGTAAAGTCAACTGCATATCTCGTAGTGA\nAGCGGCAACAAAATTACATGGATTAATTTGTTTAAGGTCCTCCGCAATTAATCGAGCCTC\nGTGCGGTAAAGTGTAACGGTTTGTTATTGATGACCACGTATCATTAGCAATAACAGCAAA\nTGCTTGGGCACCTTGAGGCAAGGCTACCCGATATACAGGCATTGGTCCAGTTACCTCAGA\nATGGCCGATGAGGGCTTCTAATGGAGTTTTATAACTCAGGATGGATACATCATGTGTGGC\nTATCCCAGTGGCAGCAGAGAAAAACAATTTAATCCATATGGATTACGACCACTTTGGTTA\nGGTGTATCGTTTGCAAAGTTGGCTGCTCGTAACGCCTCCGCGGAAACAACCGAATCCTCA\nAAATTAGACAATTCGTCAAAACCGGGTGGATTTGAGGGAATAGTGGAGGACCATCCATAT\nGGACTAAATTGTTTTTCAATGTTTTCCACACGACGAGTTAGCGTTGTAGCTAGGTCACAT\nACGCCTATAAACTTGCTAGGTTTTGCGGCATACGTAAGACTTAAAGTATATGTTTTAGTA\nATTGTATATTTATGTCCAATCTCAGGTCCAAGTTCAGTGACATCACAAATTACGTTCTTT\nTTTATATAGTCACGCATGTTGAGACGAGAACGTACATGATTAAAAAAATTAGCAGTAGCT\nCTTTTTCCCAGGTTGGATGATTTTAAGAGGACCGGTTTATTCACAAAATCTGAGTATGTA\nACCGCTTGTAGGTGGTCTGCGATCTGTTTCCGATTGAAACATTCAAAATGTGCCAGATAA\nATATAATCAACAAATTCACGGTCTGGAACTTTAAGGCCTTTTCTATCGTTGGTAATATAC\nTCCGATACTGCGTGTATTTCCGTTGTGTCTGTATGTATTCGCTGTAAAATGTACGATAGA\nGCATTTTTGGCTGTCAAACCTCGTGTATATGTTGAGGAACAACAAAACATGGAAAGTTTA\nTCAAAAGACAACAAGTCCGAAATATTGTACCCACTACAATTAGGTAATGCCGGGACTTGG\nTTGCCTGTAAGTCATATAAGGGGGTTTCCAACGTATTGTAACTTGTGTCCGTTTGTAACA\nAGTAATAGCGTGTAGCCAACACTAGCGTTTTTTCAGAGGGTCCAAATCGAACAATATACC\nAAAACGGCGAGCATCCATACCCCCAGTAGAGTCGTCGATATGCAGCCAATACTTGACGTT\nCGTAATGGGCATATAATGATGTTAGCTCCTGACGACCAACGGATTTTTTAACTAACTTGC\nAGAGTGTTGCCTCTGTGATGCATAGGCCGTTGTCCGATAATCCCTTTCGGTTTAAATGGT\nGTGTTGTTACCATCAGAGTTTGTATAACTTCCGAGTGAATGTCAAACGTCTCCGATATAC\nATAGGGTATCAGATATTATATGCGGATTTAGGGGTGCTCCATACCATAACGCCTTATATA\nAAGCTTTAAAATCAGTTTGGGTTTTAAAACAACAAAAAAATATAGGCCAGACCCGGGATC\nGTACATCTCCAGTTGAAAATCCACCAATTAAATAAAAAATAACGTTGACGTCCCTACTAC\nAAAATAAATGCATTATTTGGTTTTCTTCATCGTTTTCAGTTACTTCACGTGGGCGTTTAG\nTTGGGATTACTTGCGTGATCTCTTCCCTCCCAAGTCGGGAGTCCAAGTATAACTCACCAC\nATACAGAGGTTCTGTGCTTATCTGCCCGGTAAGCAACAACAGCGAGTGGGAGATTGCACA\nTCCCTTTGTGGCAAATAATAACCGAATCGTCGGTTTGGAGGATTTATCCATAGTTCAATA\nCGTTGGAAAGCCAGTCAATCATGCAGACGGTGTGTGCCAGCTTATGTGGATATGCTCGAA\nTACCAACTGAAGAGCCATCTTATGAAGAGGTGCGTGTAAACACGCACCCCCAAGGAGCCG\nCCCTGCTCCGCCTCCAAGAGGCTTTAACCGCTGTGAATGGATTATTGCCTGCACCTCTAA\nCGTTAGAAGACGTAGTCGCTTCTGCAGATAATACCCGTCGTTTGGTCCGCGCCCAGGCTT\nTGGCGCGAACTTACGCTGCATGTTCTCGTAACATTGAATGTTTAAAACAGCACCATTTTA\nCTGAAGATAACCCCGGTCTTAACGCCGTGGTCCGTTCACACATGGAAAACTCAAAACGGC\nTTGCTGATATGTGTTTAGCTGCAATTACCCATTTGTATTTATCGGTTGGCGCGGTGGATG\nTTACTACGGATGATATTGTCGATCAAACCCTGAGAATGACCGCTGAAAGTGAAGTGGTCA\nTGTCTGATGTTGTTCTTTTGGAAAAAACTCTTGGGGTCGTTGCTAAACCTCAGGCATCGT\nTTGATGTTTCCCACAACCATGAATTATCTATAGCTAAAGGGGAAAATGTGGGTTTAAAAA\nCATCACCTATTAAATCGGAGGCGACACAATTATCTGAAATTAAACCCCCACTTATAGAAG\nTATCGGATAATAACACATCTAACCTAACAATCTTCAGCCCGTGTTGACCCCAAAACAGAC\nGCAAGATGTACAACGCACAACCCCCGCGATCAAGAAATCCCATGTTATGCTTGTATAAAT\nATTGAAATAAAAACTAAAAACGTTTCTGGTGTATGTTTTTATTTTGTATATAAAATTAAA\nACATTGCTGGCTGGCGTGGTTATTACATTTAATGTTTTAGTAGAAAATCGACATCGTTTG\nTTTCTTTATCAGTTGAACCAAATCCACGCGTTCCCCGTTCGCTGGGTGTGGCTATTAGAT\nCTAACGTTTTAGTAAAATACCATTGTACACCCGGTATGCCACATTTACCGCGGATAGCAT\nAAGGAAATGCAATATTACTTAAAACGTTGTGTTTTAAGTGTATTTGGGTGTTGTGATCTA\nTTAACAGGACCTGTGCAAGACGATCTCCCGTTTTTATACGTATGTCATCACCCGTGAGAT\nTATATACGTAGAATTTACAGTGTTCTCCTGCAGGCCATGCCGTTGGACACACGATAATGC\nCTGATCGGCTTTTCGATGATCTTCCAAAAATATAAGCGTTTATACTCGGATGTTGTAAGT\nCCCAGTCTCTTATAATCGGTAAGACAATTTTTATAAATTCATTCCTTTTTAAATATAGGT\nTATATGGTACACAAATATCATATCCCGCGTCTTCTTGGCGTTTTGGATTGATGATATGTT\nTGTAGGTTAAGGGAACATCGATATGGTATTCTGCAGAATCCCTATGTAAAGGTTGCCCCT\nGCTGTACCGTGGAAATATCAGCAAATTCAGGTATAACGGGTTTTTCATAATTTGACGGCG\nAGTTTGATAAGGGTTGAACTTGTATCGATTTAAAAATTGGATCCAGATGTTTAAGAACGT\nTTTTTGGGAGAAGGCGACTTTGTCTTAATTTTACCGGGAACAAGTAGATTGTTAAATGTC\nCGGGTAAAATAACGGTTACTCCTGGCCGGTAATACAAAAGGGCTGAAATTACTCCTCTGT\nAACCCGCATCAATAACTCCGTTGGCGACAAAAAAATTGTCTTCATCAGCAAGGGCAGTAT\nCTTTGCATTGAATTAACAACAGTGCGTATTCATTGGGAGGCGCCGACTTAACCAACAGCT\nCCAACTGCTGCATATAAAAACCGCCCCGTGTTACAGATTTTTCAGATGGCAGTTCGAGTT\nTCTTGTGGTTCCGGAGTAACAACGGTTGATGTCGACTTACTTTATCGTCTAACACGCATT\nGCAGCGTATCTGCACATTCAGGTTGAACTTCTATTAAAATTGTATCTTTTAAACACCGAT\nTCGGAATAGTTTGGCTACAAAACATATCACCTGTATTTACTGCCGTTTCCAAGATGGGAT\nCAATTACCGCTTCGTTCATATTAATAACGATGCAAATTTTATTTTTTTGTGAAGACAGCA\nGTGGGGAGCCAAACTTTGCAGAACGGAATTTTTGGCATGCCAGCTGTTCGGCTCGTGGAG\nTTTATATCGACGGATCAATGATCACCACCCTTTTCTTCTACGCATCCCTGTTGGGGGTGT\nGTGTAGCCCTTATTTCGTTAGCTTATCATGCGTGTTTCCGGTTATTTACTCGTTCTGTAT\nTACGCAGCACGTGGTAAACCCGTTTGCCTATAAAAGGGGCAGGCGTGTATAAGAGGGTCC\nCTGTTTAATACGCGGTCTGCCGTGTTTGGATATTTCACGACCCTATCGTTTATTTACGTA\nATGGCATCTTCCGACGGTGACAGACTTTGTCGCTCTAATGCAGTGCGTCGTAAAACAACG\nCCTAGTTATTCCGGACAATATCGAACCGCGCGGCGAAGTGTGGTCGTAGGACCCCCCGAT\nGATTCAGACGACTCGTTGGGTTACATTACCACAGTTGGGGCCGATTCTCCTTCTCCAGTG\nTACGCGGATCTTTATTTTGAACATAAAAATACGACCCCTCGCGTACATCAACCAAACGAC\nTCCAGCGGATCGGAAGATGACTTTGAAGACATCGATGAAGTAGTGGCCGCCTTTCGGGAG\nGCCCGTTTGAGACATGAACTGGTTGAAGATGCTGTATATGAAAACCCGCTAAGTGTAGAA\nAAACCATCTAGATCTTTTACTAAAAATGCGGCGGTTAAACCTAAATTAGAGGATTCACCG\nAAGCGAGCTCCCCCGGGAGCGGGCGCAATTGCCAGCGGGAGACCAATTTCCTTCAGCACT\nGCACCAAAAACCGCAACAAGCTCGTGGTGCGGTCCTACGCCATCATATAACAAACGCGTC\nTTTTGTGAAGCGGTCCGGCGCGTAGCCGCCATGCAGGCACAAAAGGCTGCCGAAGCGGCT\nTGGAATAGTAATCCCCCAAGGAATAACGCCGAATTAGACCGTTTGTTAACCGGAGCCGTT\nATTCGTATTACGGTGCATGAGGGTTTAAATTTAATACAAGCCGCTAATGAAGCAGAACTA\nGGTGAAGGAGCATCGGTATCCAAACGTGGACATAATCGAAAAACTGGAGATTTACAGGGG\nGGCATGGGTAATGAACCTATGTACGCACAAGTTCGTAAGCCAAAAAGTCGAACGGATACA\nCAAACGACTGGGCGTATAACTAATCGAAGTAGGGCCCGTTCGGCATCAAGAACTGATGCG\nCGAAAATAGGGATATAATTACGCAGTAACGGTTTACCCGGTATTATGTATAATAAATAAA\nCGTATAAAAGACAGTCGTGGTTTGTGTTTATTATAAATGTGTATTATATGTCACATATTA\nTAAACTGTTTAAATAGTACCACGTGGTATTATGAACAGTTTATAATCAGTTGCTACCAAA\nCAAACCCCATTAGACGGCGGGTTTTGATAAAGGGAATCGCTTATTTAAACTAAAGATTTT\nACTCTATAAGTATGGAGTGTAATTTAGGAACCGAACATCATAGTACAGATACGTGGAATC\nGTAGTAAAACGGAACAAGCGGTTGTGGACGCATTTGATGAATCGTTGTTTGGTGATGTAG\nCATCGGATATTGGATCCGAAACGTCGTTATATTCACATGCAGTTAAAACTGCTCCGTCTC\nCGCCTTGGGTAGCTAGCCCTAAAATTTTATATCAACAGTTAATACGGGATCTTGATTTTT\nCAGAAGGGCCGCGTTTACTATCATGTCTTGAAACCTGGAACGAGGATTTATTCTCATGTT\nTTCCTATTAATGAGGACCTATATTCCGATATGATGGTTTTATCCCCGGATCCAGATGACG\nTTATCTCAACCGTTTCAACCAAAGACCATGTTGAAATGTTTAATTTAACAACCCGGGGTT\nCCGTTCGATTGCCTAGTCCACCAAAGCAACCGACGGGGCTTCCAGCTTACGTTCAGGAGG\nTCCAGGATTCGTTTACCGTAGAACTACGCGCCCGGGAAGAAGCATACACAAAACTACTAG\nTTACTTATTGTAAATCGATTATACGTTATCTCCAAGGAACGGCGAAAAGGACGACAATAG\nGTCTTAATATACAAAACCCTGACCAGAAAGCTTACACGCAACTCAGGCAAAGTATTCTAC\nTTAGATATTATCGTGAGGTGGCAAGTTTGGCGCGTCTTTTGTACCTACATTTATATTTAA\nCCGTAACGCGTGAATTTTCCTGGCGTTTGTACGCCAGTCAATCTGCACACCCGGACGTGT\nTTGCGGCTTTAAAATTCACCTGGACCGAACGTCGACAGTTCACGTGTGCGTTTCATCCTG\nTATTATGCAACCACGGCATTGTGTTATTAGAAGGGAAACCACTAACAGCGTCTGCCTTGA\nGGGAAATAAATTACCGCCGCCGAGAACTGGGACTGCCTCTAGTTAGATGTGGTCTTGTTG\nAAGAAAACAAATCTCCGTTGGTTCAACAACCCTCATTTTCGGTTCATTTACCACGGTCGG\nTGGGTTTTCTTACCCACCACATTAAGCGTAAGTTAGACGCATATGCGGTCAAACATCCTC\nAAGAACCGAGACATGTACGAGCGGATCATCCTTACGCAAAAGTTGTTGAAAATAGAAACT\nACGGTAGTAGCATCGAAGCTATGATTTTAGCACCTCCGTCCCCATCCGAGATCCTGCCGG\nGGGACGGTTTTTAACGCGTTAAACGTCATTGGGGTAGAGGGTGTAAATAAATTACGAAAA\nCGTGCATGCGTTTTTTATTTTTACAATGCGCCGTATATGGTATGTCTGTCATGTGCTCTA\nAAGTCCCATATATAAAAGAAGCCCCAACGAGTGTATGCGTATTGCGTACCGCGACCCTGG\nGATGTTTTACAGGCGCGTTTGTTTGTCTCGGTTATAAGTATGCAGTCGGGTCATTATAAC\nCGGAGGCAATCCCGCCGACAGCGGATATCGTCTAATACCACAGACTCCCCCCGTCACACA\nCACGGAACACGTTATCGGTCAACCAATTGGTATACACACCCACCCCAGATATTGTCCAAT\nTCAGAAACATTAGTTGCGGTTCAAGAACTACTGAACTCCGAGATGGATCAGGACAGCAGT\nTCTGACGCATCGGATGATTTTCCGGGATACGCCTTACATCATTCTACATATAATGGATCC\nGAACAAAATACATCAACTTCCAGACATGAAAATCGCATATTTAAATTAACGGAGAGGGAA\nGCTAATGAGGAAATCAACATCAATACGGACGCGATCGACGACGAGGGAGAGGCGGAGGAG\nGGAGAGGCGGAGGAGGACGCGATCGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGGAG\nGAGGACGCGATTGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGACGCGATT\nGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGGAGAG\nGCGGAGGAGGACGCGATCGACGACGAGGGAGAGGCGGAGGAGGACGCGGCGGAGGAGGAC\nGCGATCGACGACGAGGGAGAGGCGGAGGAGGTTGCAGTCGAGACGCGGATGAGGTTTATT\nTTACGTTAGACCCGGAAATAAGTTACAGTACCGATCTTCGCATTGCAAAGGTTATGGAGC\nCTGCGGTATCAAAGGAACTTAATGTATCAAAACGTTGCGTTGAACCTGTTACCCTAACAG\nGCTCTATGTTAGCGCATAATGGGTTTGATGAGTCCTGGTTTGCTATGCGCGAATGTACCC\nGTCGCGAATATATTACGGTCCAAGGATTATACGACCCAATTCATTTACGGTATCAGTTTG\nATACTTCCCGGATGACACCCCCACAGATTTTGAGAACTATACCAGCCCTTCCTAACATGA\nCACTTGGTGAACTTTTATTGATTTTTCCTATTGAATTTATGGCCCAGCCAATTTCTATAG\nAACGTATTTTAGTTGAAGATGTATTTTTAGATAGGCGGGCTTCCAGTAAAACACATAAAT\nACGGCCCGCGTTGGAATTCCGTCTACGCACTTCCATATAATGCGGGTAAAATGTATGTAC\nAACACATTCCTGGGTTTTATGACGTGTCCTTACGTGCTGTGGGCCAAGGAACGGCCATTT\nGGCATCACATGATATTATCCACAGCAGCATGCGCTATTTCTAATCGCATTTCACATGGAG\nATGGATTAGGATTTTTGTTAGACGCGGCAATTCGTATTAGCGCAAACTGTATTTTTTTGG\nGACGTAACGATAATTTTGGCGTGGGGGATCCATGTTGGTTAGAAGACCATCTTGCCGGAT\nTACCACGAGAAGCCGTACCCGACGTACTCCAAGTGACACAGTTGGTTTTGCCAAATCGGG\nGTCCAACGGTTGCCATTATGCGTGGTTTTTTTGGGGCGTTGGCATATTGGCCCGAACTAA\nGAATTGCTATAAGTGAACCATCTACATCTTTGGTGCGATATGCTACCGGTCACATGGAAC\nTTGCCGAATGGTTTTTATTTTCACGTACACATAGTTTAAAGCCACAATTTACCCCAACGG\nAACGGGAAATGTTAGCGTCATTTTTTACGTTGTATGTTACTCTTGGTGGAGGAATGTTGA\nACTGGATCTGTAGAGCAACTGCAATGTATTTAGCTGCTCCTTACCATTCCCGTTCGGCTT\nACATCGCGGTCTGTGAATCTCTGCCCTATTACTATATCCCGGTTAATAGTGACCTGTTAT\nGTGATTTAGAGGTATTACTGTTAGGCGAGGTCGACCTCCCAACTGTTTGTGAATCCTACG\nCAACTATTGCACACGAATTAACCGGATATGAGGCTGTTCGCACAGCAGCCACAAATTTTA\nTGATAGAGTTTGCCGATTGTTATAAGGAAAGTGAGACCGATTTAATGGTAAGCGCGTACC\nTGGGGGCCGTTTTATTGTTACAACGGGTGTTGGGTCATGCAAATCTTCTTTTGTTGCTTC\nTCTCCGGTGCTGCGTTGTACGGAGGATGTTCAATTTACATCCCCCGAGGTATTTTAGATG\nCATATAATACTTTAATGTTGGCAGCAAGTCCTCTTTACGCTCACCAAACTTTAACATCCT\nTTTGGAAAGACCGCGATGATGCAATGCAAACTTTGGGGATTCGACCGACAACGGACGTTT\nTACCCAAAGAGCAAGACAGGATAGTTCAGGCATCACCTATAGAGATGAACTTCCGTTTTG\nTGGGATTGGAGACCATCTATCCCCGAGAACAGCCCATTCCCTCCGTGGACCTAGCCGAAA\nATCTTATGCAATACAGGAATGAAATTCTGGGTTTGGATTGGAAAAGCGTAGCCATGCATT\nTACTACGAAAATATTAAGGGTTGTGATTTTTTTCATTAGGATGAAAAGAACGTTTCCTAG\nCCACACCCACAAAGGAGTTTGTAAAATAAAATCTCGTGTGTGTTGTGTGGGGGGTCCGTG\nAGGATCGACCTTTACAAGATATAATTTGTCCATATCGCAATGTTTTCTCGGTTTGCGCGT\nTCCTTTTCCAGCGATGATAGAACGCGTAAATCTTATGATGGTAGTTACCAAAGTTTTAAT\nGCCGGCGAACGTGATTTGCCCACACCTACCCGGGACTGGTGTTCTATTTCCCAACGCATA\nACCAGCGAGCGCGTGAGGGATGGATGTCTTATTCCAACGCCCGGCGAGGCTTTGGAGACG\nGCGGTAAAGGCTTTATCTGAAAAGACCGACAGCCTAACATCGCCGGTTTTACAAAGTACC\nGAAAGACACAGTGTTCTGCTTGGATTACACCATAATAATGTTCCTGAATCGTTGGTGGTC\nTCGTGTATGTCTAACGATGTTCATGACGGGTTTATGCAGCGTTATATGGAAACAATTCAA\nAGATGTTTGGATGACCTGAAACTTTCTGGGGATGGACTTTGGTGGGTTTATGAAAATACA\nTATTGGCAGTATCTCAAATACACCACAGGAGCCGAGGTACCGGTGACTTCAGAGAAGGTA\nAATAAAAAGTCTAAATCCACGGTTTTGTTGTTTTCATCCGTAGTTGCCAATAAACCAATA\nTCCAGACATCCTTTTAAATCTAAAGTTATAAATTCGGATTACCGGGGAATATGTCAGGAG\nCTACGTGAGGCGTTAGGAGCTGTGCAAAAGTATATGTATTTTATGCGTCCAGATGATCCT\nACAAACCCCAGCCCGGATACAAGAATACGTGTACAAGAAATTGCGGCTTACACGGCTACT\nGGCTACGGGTGGATGTTATGGTTCTTGGACGTTGTGGACGCCAGGGTATGTCGCCATCTC\nAAACTTCAATTTCGACGGATTCGAGGGCCGCGCGCGTCTGTTATTCCAGATGATTTGCTT\nAGACGACATTTAAAAACGGGTCCTGCGGTCTCAGCGGGCACAGGAGTTGCGTTTATTTTA\nGCAGCAACAACTGCCAGCGCTCTTACTGCGCTTTTGCGTATTAGTGTATTATGGCGAAAG\nGAAGAGTGGCGGGATGGTTTAAATGGAACCGCAGCTGCAATTGTTGCGGCGGTTGAACTT\nATTACGCTTTTGCACCACCATTTTCAATACTTAATTAATATGATGCTTATTGGATATGCA\nTGTTGGGGGGATGGGGGATTAAACGATCCTTATATATTAAAGGCGCTACGCGCCCAGGGA\nCGGTTTTTATATTTTGCGGGTCAGTTGGTTAGAACAATGTCAACACACAGTTGGGTTGTG\nTTAGAGACCAGCACCCATATGTGGTTTTCCCGGGCCGTGGCGCAGAGTATTTTAGCACAT\nGGGGGTAAACCCACAAAGTATTATGCTCAGGTTCTTGCCGCCAGTAAACGGTATACTCCG\nTTACATTTAAGACGTATATCCGAACCATCGAGTGTGTCTGATCAGCCGTATATTCGTTTT\nAATCGACTGGGATCTCCAATAGGGACAGGTATAGGGAATTTGGAATGTGTCTGTTTAACG\nGGAAATTATTTATCTGACGACGTAAATGCAAGTTCGCATGTAATTAATACGGAAGCACCG\nTTAAACAGTATAGCACCCGATACAAATAGACAGCGGACTTCTCGCGTTTTAGTTCGTCCA\nGACACGGGTTTGGATGTAACTGTCCGAAAAAACCACTGTCTGGACATAGGCCATACGGAC\nGGTAGTCCAGTTGACCCAACGTATCCTGATCATTACACCCGGATAAAGGCGGAATATGAA\nGGTCCGGTTCGGGATGAATCAAACACAATGTTTGACCAAAGATCGGATTTACGTCACATA\nGAAACCCAAGCATCTTTAAATGATCACGTATATGAAAATATACCACCCAAGGAAGTGGGT\nTTTAACTCATCTTCAGACCCGGATGTGGATAGCCTTAACGGGTACACCTCCGGAGACATG\nCATACAGACGATGACTTATCACCAGATTTTATACCCAACGACGTTCCCGTTAGATGTAAA\nACCACGGTTACGTTTAGGAAAAATACGCCTAAGAGTCATCATTAAGTACAGCGGTTAATA\nGATAGTTATGGACTAGGCACTTTGGCGGTCATTTCCACAACCAGGTTAAAATTGGGGGAT\nTTGGGAGAAAATAGTCTATTGCGTATTTTCTGTTCAATAATTGGACTGCGTTATTTAAAG\nGTCTGATTGGTTGATTGGGTTATAAAAGGAATTACTCCTTTAAATTTTACTTAATGTACC\nCACAATATCAAGTGGTCGTTTGTATTTAACGATTATTACCGGTACCATGGGAGACTTGTC\nATGTTGGACAAAAGTGCCGGGTTTTACGTTAACCGGCGAACTTCAGTACTTAAAACAAGT\nGGATGATATTTTAAGGTATGGAGTTCGGAAACGCGATCGAACAGGAATCGGAACGTTATC\nTTTATTTGGAATGCAAGCTCGATACAATTTGCGAAATGAATTTCCTCTTTTAACTACAAA\nGCGTGTTTTTTGGAGGGCCGTCGTGGAAGAGTTGTTATGGTTTATCCGCGGGTCAACCGA\nTTCCAAAGAACTCGCCGCTAAAGATATACACATATGGGATATATACGGATCGAGCAAATT\nTCTAAATAGGAATGGCTTCCATAAAAGACACACGGGGGACCTTGGCCCCATTTACGGCTT\nCCAGTGGAGACATTTTGGAGCGGAATATAAAGACTGTCAATCAAACTATTTACAGCAAGG\nAATCGATCAGCTGCAAACTGTTATAGATACAATTAAAACAAACCCAGAAAGCCGACGAAT\nGATTATATCGTCTTGGAATCCAAAGGATATCCCCTTAATGGTACTACCTCCATGTCACAC\nGTTATGTCAGTTTTACGTTGCAAACGGTGAATTATCCTGCCAAGTATACCAGAGATCGGG\nGGATATGGGCCTTGGGGTACCGTTCAACATTGCTGGATATGCACTTCTTACCTACATAGT\nAGCGCATGTTACAGGACTTAAAACCGGAGATTTAATTCATACAATGGGGGATGCACATAT\nTTACTTGAATCATATAGATGCTTTAAAAGTGCAGCTAGCTCGATCCCCAAAACCTTTTCC\nTTGCCTTAAAATTATTCGAAATGTAACAGATATAAACGACTTTAAATGGGACGATTTTCA\nGCTTGATGGATATAATCCACACCCCCCCCTAAAAATGGAAATGGCTCTTTAATGGATTTT\nTAAATGTTGTCAAGACAGTAGATGTGTTGCCAGACGCGTTTGGTTGGTTTCTGTTTATGA\nACAGCAACGGATGCATAGGGTTGCGATAACTGCGATAAGACCCAATGTCCCAAGGATAGA\nTATCACACCAATTATAACTGCTACAACGGAAAATGTAGTGGCGTAGGTAGATGCATCGTA\nGGTATAAACGGCCGAAAACGGAGGGAATTTTTTAGGGTAACCATCTAGATGACACGAATA\nGGTGATAGGTCCGTCGAGTTCCGATGTTGGACAAGAACTTTGCATGTTTACAAACCGTTT\nGTTTTGATCACACACCCCAGTAATCTCACTGTTTTCGTGGTTAATGGGAGAATCGTTAAC\nCCACCATACGAAATGTACAACGCCACGTGGCACACATTTTGCCGTACATACTATGTGTCC\nATCAATAATACCTATAGACACGTTGGGAAATGGATAGACGTCAGGGGTAACGACAGCAGA\nATATTTCATATTAGAGACGCCATCCCGAATCCATAAAACATTACATTGGATGGCTGGGGG\nTGGGTAATCCATTTGTTTTTGCTGTGGAATTCGTACCGCCGAAACATAACTAAATAATCC\nATTGGCATATTCTTGTATTGCATCGGTTATAAAATTTTTTCCGATGTTACCAAACCTTGA\nAGTCCACCGAACACGTACCGAGTGCGGTGGATAATACTTTGATACGTTACAGTAGGCTGT\nGTATGTCTGTCCGGTTAAGACTGGATCGCCGACAACGGTAATATTTGGACGATAATACGT\nTGTAACTGTAATACTGTGTTCCGATATGACGTTCTTAGTTTTTGTATTAACGACTCGCCA\nAATATACGTTCCCTCCGTGGTAGCATCCATAGATAAAATTGTTACAGAAAAATCAGACGT\nTGTTTTAACATCTGGTATTACATAATTTTCCTTAGCGTGTGTAAATATCTCAGGGTTGTT\nTATTAAGTTTAAATCGGCACTGTTGCTATATAACATAACCGGTAAATCTGGCATGCGTAT\nTAACGCATTGCCCAGTTGACGGTGCGGATCTATAAGGTGACGCGTAAACCAAACTTCAAT\nATGAAGATCGGGGCGTATAAGCGACTTCCACCTTGTTATATTTGAACCTTCCGGATCTAA\nAGAATATTGTTCATATGTTTTTTGTTGCTGCTTAAAGGCCGCCTGTTGTCCGGTCGTTAG\nACGCATGTAACAAGGCATGATAAATGTGTGAAAATAGGGTATGGATTGTATTCCGCCGTG\nAACGCATTGTATATTTTCATATAGAAAAGGTGGTTGTGAATGTTGGGTGTTGGCTGCGGG\nATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGTAGC\nGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGAC\nGGCGGGATCGGGCTTTCGGGTAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCG\nGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGG\nCGCGACGGCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGG\nCTTTCGGGTAGCGGCCGAGGTATATAATTCAGTTATACTTACGGGTGTGGGTTGAGATTC\nAGTCGATAATTGTATACACGCGATCGCCGCTTCATCCTGGTTTTTATTGACACATCCACG\nCTCCCCTTAAATAAAAGATTAAAACACCCACCGCGGAATTTAAATGATGGAAACGTTTTT\nTTCGACATTGGGAATAATAAAAACGGCTTTTGCAACTTTAAAAACTTTATTTATCTCGAT\nTACGATACATATGTACCACATAGATAGCATAGATTTATTATAATATAAACACACACGTGA\nTATACTTTAGTGATATGAGATGCCATAAAACAGTCAATAGGTTTAACGCTTAGTCTCATC\nATCTGAATACACGTCAAACCCGCCGCAACTGTTGATGTTAGAATTATAATAGCTCCCCAT\nGAAATGCCGGCAAATGTTACAGCTATACCCGTCACCGAGGTCGTTGTATATAATACAATT\nACCCATAGGTTTTTTTTTTCTTGATATAAAACGGCAAAACCCTGTAACCCAAATGCTATA\nATATGACCTCCTATTGAAACTGCTAACGTTACTTGTGTAAGTTTGATAAAATGATTTAAT\nTTAATTATATGTGAGATTGCCCACATTAATGGGGTAACTATATATAACACCGGGGGTATA\nACAGACATTATACGAATTCCTTTAAACACGCGTTTAAGGGTCCGGGAACTTTCTCGATGG\nTCACATACTCTCCCGCGGTCATTTTGTGTATATACAACGGCAAAACCTAAATCTGTATAA\nGTGTTTAATTGCTTATGGCGATTTTTACGATATATACACGTATCTTGCAAATCGGTGGCG\nGCATCGACAATTGAAACTAGTGTGACAATAGATATACACAATCCAATAAGAACCTCATAT\nTTACTGACATACATATATAAAATAACGGTTAGTAAACCTCCCAACCCAGTTCCCAACATC\nATAACATAAAAATAAATATGCGGTCCATTGAATGTCGTAACAAAGTTGTAGTAATGGATA\nTGCACAGCAGCCACTGTTCCGGTAATCGCGGATATGGAAATTCCCAGTAATTCTACAAAT\nGGAAGATCCCGGGATATTGGGCAACCAACCGCCCATAACACAGCAAAACCCAACACGACC\nACCGTCTGCAAACATCGTCCCAATTTTGCTAATGTGCGTAGAAATTTCACGGATGTTGGC\nCATAACCCCGAAACGACGATCAACCCCATAATAGTTGCATTGACGGCAGCTTCGCAGACG\nTGATATTGTAAAATTAACCCGGACGTGATAACACTTGCTTGTAGTCCCACGAGAAACAAC\nCGCGATGCTGAGGTTATTGCACACGAATTACATTCTTGAGGGTTTCCGACACATCCTTGG\nATTGATTGAGCGCGGATTAATTCTCTGTCTAACACACCCAGGTTTTCATCATGGACAGCT\nCTTTCACCATTCACGGCCATGTCTTAAGTTTAATAATTCAAAACAAATAAAAATGTGTTC\nATCTATGGTACACACAAGTTTGTATGTAAAATATAAGCAAAAGTTGCACTTATTTAACTG\nTACATATTACGTCAGATTCACGTGATAATTCAGAATAATCCAGGGTTCCTGCAGGGTCCA\nCTGGAGGAGCCACACAATATTCGCGAATTCCGATTCCCTCCTGCCATGTGGTTTCGGAAT\nTCGCGAATATTGTGTTCTTTTTGTTAATAAATTGCGTCTTTTTTTTAATGGTGGTTCATC\nCTTCACAGATTCCATGTTCGCAAATAATTGCATCGAGGTTAATTTTTCTTTAAGGTCTTT\nGGGACTTAAGAACGTTGCATAAAAAAAAGAATGCACGGGTGCGGAACGTTGGATATACAA\nTCCAACCATGGGGGAGTTAGTTAAGGCGAGATAAAAATTAATATAACACGTCTCATCCCG\nTGTTAACTTAAGATTTTGTACGGCAGAACGGAATCCACTGTGTGTTTCCAATAATACTCC\nAAATTCACGCATACTCCCGCTGCCATAAACAACATTATTAAGGATCCTTTTTGAATTTGT\nGATTGAGCGTATTAAATTATATGGTGTAGGCTTGCTTCCGTTTATATCCAAGGAAACATT\nAAATGAGATAAAACCACCCCCGGCGGTCTGGATGTACATATCCGTGGCTGTTAGAATGAA\nGCATGTTGTAAACCCAAAAGTTTTAAGTAGTCGCTGTAAACGGGTGAATTGATCGCGTTT\nTAAGCAAATGCTTATATCTGGAGTTAGATTTGGGAACATCATTGTATAACAAGCGAGTTC\nACGTTTTACAACTTGTTTGTAACATTGTACTTGATCATCTGGACCACAATCACCCGGGCG\nTTGCCATACCATCGTTTGGATAATACTCCGCTCGGGGGGTTGTCCGGTGAATTTAAAATA\nTAACCGTGTTGGGGTCGACGGATCTTTTGTATGGCGAAACGCGTCAATAAGCGAGGACCG\nTCCCTCCGTTGCCGCGAGTACAACCATTCTCGGCCCAGTCCAATTATACTGGTCAAACAT\nATTTGCCGGTATAGGAATATACAGTTGTTCTGTTTCCAAACTACAGTGAATAATTAATCC\nTTCGTCGCTGAATATTAAAATAGAATCCCTTAGTCTATTAACCAGAGGTGATATAGACGA\nAATTAAACCAGTAAGCGTTTTTTCCGTTAAAACAGCTCTGGCGATTTCTGGGGCGTCAAA\nACCCGCATGCAATTCCATGTCCAAAGCATCGTCTGTACGCGACCTCAAATCCATAATTTA\nCTACTTAAAATGTTTACTATAGAAAAAGTAATCATATGTAAACACACGAGTTTCGTTAAT\nATGTTTGTTTAACCCGATCCGGTGACTTAAGTACATAAACAGGCATGATATTTGAATAGT\nACGGCCCATGGGAGGGAACATTTCCACGTGTTCCAATACAGGGGGTGTTCCTTAATAGGG\nACTGTGCAATAAAATACGTAAGAAGTTACCAGATTTGATGGTACATCATTATATACGTCT\nGTAATTAACACAAGATCACATCGAAGAATTACTGAAGCCGCTGTGAAACCTTTCACAAGA\nCGATATAAACTTGGTTAAGTGTATTGATGGGGCTCTTTGGACTGACACGCTTTATCCATG\nAACATAAACTGGTTAAACCCAGCATCATTTCAACGCCACCCGGAGTTTTAACCCCCGTGG\nCGGTAGACGTATGGAACGTCATGTACACATTGTTGGAACGTTTATACCCTGTGGGTAAAC\nGCGAGAATTTACACGGACCATCTGTAACGATACATTGTCTTGGAGTCTTATTGCGGCTAT\nTAACACAACGGTCATACTATCCGATATTTGTATTGGAACGTTGTACAGACGGCCCATTAT\nCACGTGGAGCCAAGGCAATTATGTCACGGGCCATGAACCACGATGAAAGGGGAACCTCGG\nACTTAACCCGTGTTCTACTATCATCCAACACATCATGTTCTATCAAGTATAACAAAACAT\nCGGAAACATATGACAGTGTGTTTCGAAACTCTTCCGCGAGTTGTATTCCTAGCGAAGAAA\nACAAATCCCAGGATATGTTTTTGGACGGTTGTCCACGACAAACTGACAAGATGATCTGCC\nTGCGCGACCAAAACGTATGCAGTCTTACCTCTACAATGCCATCCCGAGGACATCCTAACC\nATCGATTATATCACAAATTGTGTGCAAGTCTTATTAGATGGATGGGGTATGCATACGTCG\nAGGCGGTTGACATTGAGGCGGACGAGGCATGTGCAAACTTATTTCATACGCGTACAGTGG\nCTTTGGTTTATACGACAGATACTGATTTACTCTTCATGGGCTGTGATATTTTGTTAGATG\nCAATTCCTATGTTTGCTCCAGTAGTACGATGTCGCGATTTGCTTCAATATTTAGGAATTA\nCATACCCTGAATTTTTGGTTGCCTTTGTTCGCTGTCAGACCGATTTGCATACAAGTGACA\nACCTAAAATCTGTTCAGCAAGTTATTCAGGATACCGGCCTGAAAATTCCACATCAAATGG\nACACTTCAACGCGCTCCCCCACTTACGACTCGTGGAGACATGGCGAGGTTTTCAAAAGTC\nTTACCGTAGCCACGTCGGGTAAAACAGAAAACGGAGTGTCCGTTTCCAAATATGCATCTA\nACCGATCGGAGGTGACAGTAGACGCCAGTTGGGCTTTAAACCTTCTGCCACCCTCATCCT\nCCCCATTGGATAATTTGGAACGCGCATTTGTTGAACATATAATCGCCGTGGTAACTCCAT\nTGACCCGCGGTCGCCTAAAGTTAATGAAACGTGTAAATATTATGCAAAATACGGCAGACC\nCATATATGGTTATTAACACCTTATATCATAACTTAAAGGGGGAAAAAATGGCTCGCCAAT\nACGCACGTATTTTTAAACAGTTTATTCCTACTCCACTCCCACTAAACACTGAAACACACA\nTAAGAGCGACTTAATGGTTCATTGTTTTATTTTGCTCGTATATACATGTTATAAATCGTT\nTATCACTGTGCCCGCATAAGATGTACTGTGTCTCTCAAAAAAATTTGTGTTTTTATCTGC\nAATCATAAATGCAAGTGGAAAGTCCGAATCTGGAGGTGGGGTGTTAAATAGTTTTGGTAC\nATTAATCGCTGATAAAAGCCTGTCCGCGCTGAATTTCACGTATTGTGTAATTGCATCGAC\nGTTCACCAAACGGGTTTTGGGTGCATGGGATTTTAAAAACGCACACTCGATTTCAACGGC\nTTCCGAAAACAGTTGATGTATTCTGGTGATAGCGGGTTTTTCGGGTACATAGTTATTGTA\nTATACAACACGATGCGCTGGTATGTATGGCTTCATCTCGGCTTATAAGGTCGTTAAATTG\nACAAGTTACAACAAATAGTCCGTTATTGCGTAAATATGCAATAGCCGCGAACGATGATAC\nAAAAAAAATGCCCTCTATAAGAATCATTAGTATATATTTTTCTGCAACGGATGGGTTGTC\nCCGTACCTTTTCTTCCAACCATTGTACTTTTTGTTGGATCGACGGATTATTAATAGTGAC\nATTTACGTATTGTACCCGCAACGATTCATCCCCTCTGAACAACATTAGTTGAATTTGACT\nATAGACACGCGCGTGGACAACCTCGATGCACTCTTGTTCAATGTAGTAATGGTGAATATC\nCTTTTGGGAAAAGAGTTGGGTTAGAGAGCCCAAATTAACATTTACCAGATCATCTGCCGC\nCGATAAAAATGTAAAAATAAATCTGTAGAATATTAGTTCATCTTCCGTTAAACAGTCCAA\nGTATTGATAATCATCTTCAATGATAAAATCGCTTTCTAACCAACGATTCGAAATGCTCAG\nGGCACGTAAATTGTTTATATCTGGACACTCCGGCCTGTAAAAAAAATGACTGCAATCTTT\nCTGATCCATTTTGGAATAGTTTCCCGTGTAAATTTATAAAGCACAACTGGTACAGGTTAA\nTTCGCCTCCCGCAAACAGTCCGCTGTTTGTAGCTTTACGAATTTTACAGTAGTACATACC\nCGTTTTAAGGCCGGCTTTATAGGCACGTATAAGCAAATTCATTATTTTGGAGGCGGGAAT\nTGTCCCGTCTGGGCGTTCCTCAATAAATAAAGTCATTGATTGACTTTGGTCAATAAATGG\nCGCCCTTTCTGCACACATATCAACGAGATCCTCTTGCTCATATTCAAACGCTGTTTTATA\nTTTTAAGAGTGGGTGACTATTAGATAAACAGCCAAACGAACGTATTACTGACCATTGGTT\nTTTCTCAAGTATGTTTATAACTTCCAGTCGTTTTTCTTCACATGAATACATATCTCTTAG\nTTCGTCCATAAGGTCTAAGTTGGGTCTAAGTAACTCACCCGAGGTGGTGACCTTACTAAA\nCATATTATTATAAATTGGAGAGAAACCCTCACTGCACTCCGTTACCTGTGCAGATGAAAC\nTGTGGGCATTAACGCTAAGAACTGCGAGTTGTATAACCCATAAGCGCAAATATCATCTCG\nCAGGGTACACCATGGTAAATCTAAATAACTTATCGTAGAAAACCCATCTTGGTGTAACCA\nTCCCTTAGCATATTTACTTTCGGTAAAACCCTTAAACGGGGCTAAGCCGCCAATCTTACA\nCATTTCCATGCTTGTTTTCATTGTCTCATACAACATTAACTCCGCTATTTGTACATTTAA\nCCGTCTAGCTGGTTGGGAAGTTAAATCAAATCCTAAGCGGAGACAAGTTGTATGTAACCC\nTTGTATGCCAATGCCAAGTGATCGGTTGTTTTTTACACCTTTACATGATTTTTTACATGG\nAAAGTTCCCAGCCGCCAGGACCCCGTTTAAAAAAATAACAGTCGTTCTTGCTGTCAATTG\nAAGGTCGTTTAAATTAAATGACACTGGGCCTTTGGATAAGCACGTTGTAAGATTTATGCT\nGGCAAGATTACATACGCCATGTTGATGAGCGTCTGCCTTTTGAACAATTTCCGTACACAA\nATTTGACCCCGTGATAGCATTTCCTTGGGTATTCATATGATAATTACGATTACAGGCATC\nTTTGAACATTAAAAAGGGGCTTCCTGTTACAGCAGCACTGCGTATGATTGTGAATGCGAT\nATCTTGAATGGGAACAGAAGAAACGCCTAATCCTTCTCTCTCTAAACGTAAATAGGTTGA\nAGTGAATGCCTCCCCGTGTAATGTTCGAAGGATATCGGCTCTGTTATCAAAAAGAGTCCA\nCTGAACATTACTAGCCCCTTTTAGATAGCTTAGGTATCTTTCAAAAAATAAATCTGGGGT\nCCATAAACAACAAAATATGTTATCACATCGAAATATTTCATCACGAACCAACATTCCACG\nTGTGGCCAAAACAGTTTGTAGATCGACGTGCCATGGTTCTATGTAAACACAAACTCCAGT\nTGGTCGTTCACAATCACTGTTAATTGCCATAACCATGCAATCTAAAAGTTTTAAAACTGC\nAAGAAGACCTTTCGTTTGATTTTCCGTAGGTATTAAATTCAGACTCTGTAGAGAAATTCC\nCACTCCGCCTCGACTTTGTAATACCGTTCCCACATCGCCTGTGATAGCTCGAACAGCTCT\nCCCAACAGTGATGGATTCCGGGTCCATTAAATAACAACTGGCCGTTGCCCCGGTCTCTCG\nACCTAAAAACATCATAACCGGTGTAGCCGGGACAATTTTCTGACATGCCAACGCTGTGAA\nAAATACCCGACAGACATCAGTCCATGTATAACCATCATTTATTCCGGGAATAAGAGTTGC\nGATTTTAGGCAGGTTTACGATTTCTGTTGTCACGGTGGCCGCCAGTCTTAAAAAGAATTG\nGCAAAGCGACTCTAATTTACCTTCCTCTAACTTAGTTAAATAAAAGTCTTCGTACTTTAA\nAGCAGACTGTAGTCCAAGGGTAGCTAAAGCGGGGTATTGATCTTTCAAAAACGGTTCTAA\nTATAGCCCGACGAATTTCGTCCCTCCGCCCTTCAATTGCTTGGCGGACTCGGGGAGTTAA\nACAGAGAATTGGGGAAGTCAACCACGTTTCCATGGAAACGGATCGTAGGTTAATACGGCA\nATGGATAAGTTCTCCACAACATCGGTACACTCGCTCATCTTGTCGCGTCACCGCCTTAAG\nTTTTGAGACGATAGTGCTAATATACTCCATTAATTCCACCGGTGTGGTTGATTCGGGCGG\nAATGATGTATTCCTTGTAGCCATGTTGACATAATCGGTTTATAATGTCATGAACCGATTA\nTGTCAACATGGCTACGTACAGCCTGCCCCTCCCCAGTATATAATATCACGCAAAACCCAC\nGCTATGTTAAATTCAGTTTATTTTACATACATGCTTTAATAATAACATTCGTTCCATGTA\nTTTGTACCCCCCCACACAACCCCCTCTAACCAAATAGTTGGCACGTTATAACCTCCGAAC\nCGTTCCATGCGTCTTGTATAACGCACAGACTCTGATGGAATTGTTCCAATTAACGTATAT\nGCCGCATACATGCAGGATAATTGTGTGGGAAGTCCCCGAAAATCGCCGGTCCATTGATAC\nAATCGCTGTCTAGCCAAGTTCCAATTTACTCCTGTAATTTCGCCAATACTACATCGAGGG\nCTTGTCGGGTCATTGGATAACTGCACAAGCGGCAACGCCCTTGTGTTATATGGCTGGTGG\nGTATTTGCAACCCCTTCAGTCCCCCAGGCGGCATTTTCAGCTCGTATGCGTCCTAACAGG\nAAGCCAATACCACGACCAAAACATTGTTCGTTTAGTTGGCTTAATGCAAGATGCAGTCTT\nACACCTTCTCGTTGGCGTCGCTGTGTATATACAAAAACCAAGAACACATGCTTCAGTCCG\nTCCGCGGAAAGATGTAAGTCTTTGTCAACGTCCCAAAATACGCAGGCCGGGATGTTGGCT\nGTGACCCTGCGAGTTGAAGTTTTGTCTGTACGTGCAGCTTCTTGGGGACCTTTGGCCACG\nGCGGTTATATTGCATAAATTATCCTGAATGGTATATTCCAGCAGGGACCCAAAAAAACTT\nATAAATCGATGTGGAAATACATGACATTGTACCATCGCACGTAAACACTCCGAAAACCTT\nATGAGCCGCGTTTCCATACGACTGCATCCATAGGCAGAAACAATTGCTGTTCTGTTGGCA\nTCTGCTGCCTGTTTATCCGTATATTCTTCTGCCCGGCATGCGGCGATGAAACTTAATGAC\nGTTACATATGCTCTAAGCCCCCCACCTTCTCCAACGGTCCAAGGAGCCGTGCAGGCATTG\nAATAGGTTTCGTAAACCCTCTAGTATTACATCGGGGTCACGTCCAGCCTGTGTAAGTGTA\nTTAGCTTCTCCAATCATGTCAGATGGATGACGAAGGATTAAGACGATTGACCCAGCATGC\nTCAATGTCCGGACGAAAAAAATCGGTTAATGACACTTGTTGGATTAGCTGTGTCGTTGAT\nTTAAAATTATTTAACGGGAGTCTAATGGTAACTTGCGGGTTACCAATTGAAGTTGGATTT\nATTTGAATGTTGTTCATGCGATTAATAACAATTGAACGGGGGGTTACTTGAATAGACGCG\nGTTTCTGTACGTTTTGGTGGTCCATGTATCGGTTGTTTGTTCAGACCTCCAAAGCGAGGG\nCCAATTGTTAAATCGCGACTCCAATTTCCGAAGAAGCCCGGAGCATAAGTCATATGAAGC\nCCGTTCCCTATTTGAATAAAACGGTTATTTCCTAAAAGACTGATATTAGTTCCACATAGC\nGTTTGTTCGTTTAAAGTAAAATGCGAGTTGGTTGGTTGACTCCCCATAGCTGAGGGGGTA\nAATTCACACAATGCAATCGTGACGTGGTACTATCTGAAATGTTGCCTGGGGTATGTGTAC\nACATTATACAGTCGTAGTACCGTTTATATAATGTTAGGTAGGAGGAGCCTATAAAAATAT\nTTTGATTGGCGTTAAAAGGTTCTTCAACTTACCGTGACGTCCTTTTTATTAACATGCGGT\nCTTTTCATTCCGGACGGATGTAGCTTTTTCATATCACGTTATAAAGTTAAGTCAGCGTAG\nAATATACCATGGAAGAACCAATTTGTTATGATACACAAAAACTTTTGGATGATTTAAGTA\nACTTGAAAGTACAAGAAGCGGACAACGAAAGACCATGGTCACCAGAGAAAACAGAAATCG\nCCAGAGTTAAGGTAGTTAAGTTTTTACGATCTACCCAGAAAATTCCAGCTAAACATTTTA\nTTCAGATATGGGAACCCCTGCATTCTAATATCTGTTTTGTATATTCCAATACATTTTTGG\nCGGAGGCTGCTTTCACGGCCGAAAATTTACCCGGACTGTTGTTTTGGAGACTAGATCTAG\nACTGGACGATAGAGGAGCCAGGTAATAGCTTAAAAATTTTAACCCAGCTATCAAGTGTAG\nTACAAGATTCCGAGACGTTACATCGTTTATCGGCCAATAAATTACGAACCTCGTCTAAAT\nTTGGACCCGTTTCGATACACTTCATTATAACGGACTGGATAAATATGTACGAGGTCGCCT\nTAAAGGATGCAACAACAGCCATTGAATCACCATTCACTCACGCTCGTATTGGAATGTTGG\nAAAGCGCCATTGCAGCTTTAACACAACATAAATTTGCGATCATTTACGATATGCCATTTG\nTTCAAGAGGGGATTCGTGTTTTAACACAATATGCAGGATGGCTTCTTCCGTTTAATGTTA\nTGTGGAATCAGATTCAAAATAGCTCACTCACTCCTCTAACACGAGCCCTTTTTATAATCT\nGTATGATTGATGAATATCTCACGGAAACGCCAGTACATAGCATATCAGAATTATTTGCAG\nATACTGTAAATTTAATTAAAGATGAGGCGTTCGTATCCATCGAAGAAGCGGTAACGAATC\nCACGAACGGTGCACGAGTCACGAATTTCTTCAGCTCTGGCTTATCGAGACCCTTATGTTT\nTTGAGACATCCCCGGGAATGCTTGCTAGGAGACTTAGATTAGACAATGGTATATGGGAAA\nGCAACCTCTTATCGTTGTCCACCCCCGGAATTCATATTGAGGCGCTGTTACATTTACTAA\nACTCCGACCCGGAAGCGGAAACCACATCTGGAAGTAATGTAGCAGAACACACCCGTGGCA\nTTTGGGAAAAGGTTCAGGCTAGTACATCGCCTAGTATGTTAATAAGCACCCTTGCCGAAT\nCCGGGTTTACAAGATTTTCATGCAAATTGCTACGTCGGTTTATTGCTCACCACACACTCG\nCCGGTTTTATTCACGGAAGCGTTGTAGCAGACGAGCATATTACAGATTTCCAACAAACAC\nTAGGATGTCTCGCTTTAGTGGGTGGACTGGCATACCAATTAGTGGAAACGTACGCTCCTA\nCTACCGAGTATGTGTTAACATATACACGGACAGTAAACGAGACCGAAAAACGGTATGAAA\nCGCTATTACCCGCCTTAGGATTACCACCGGGAGGCCTGGGACAAATTATGCGGCGCTGTT\nTTGCTCCACGACCCCTTATTGAAAGTATACAAGCGACACGCGTAATACTACTTAATGAAA\nTTTCTCATGCAGAAGCTAGAGAGACAACATATTTTAAGCAAACACATAATCAATCCTCAG\nGTGCGTTATTACCACAAGCAGGTCAAACCAGGTTAGTACGGCTTCGCGTACGGCACTTTG\nTCCTGCTTGTGGATTCAAGATGGGGTATTACTCCCCCGGTGGATGTGGGTATGACACCTC\nCTATTTGTGTTGATCCACCGGCTACAGGGTTGGAAGCTGTCATGATAACAGAAGCACTAA\nAGATTGCATATCCTACCGAATATAATCGCTCTAGCGTGTTTGTGGAACCGTCGTTTGTGC\nCTTATATTATTGCAACAAGCACGCTTGATGCCCTTTCGGCAACAATAGCTTTGTCTTTTG\nATACACGGGGAATACAGCAAGCCTTGTCTATTCTTCAGTGGGCTCGCGATTATGGATCCG\nGAACCGTGCCCAATGCAGATGGATATCGCACAAAACTATCTGCTCTTATAACAATATTAG\nAACCTTTTACCCGTACACACCCCCCAGTACTTTTACCATCTCACGTTTCTACTATAGATT\nCCCTTATATGCGAACTTCATCGGACTGTTGGCATTGCCGTTGACCTGCTTCCCCAGCACG\nTCCGTCCTTTGGTTCCTGACCGTCCTTCTATTACAAATAGCGTTTTTTTAGCAACTCTCT\nATTATGATGAACTTTACGGTCGTTGGACCCGACTGGATAAAACATCGCAGGCGTTGGTTG\nAAAATTTTACATCCAACGCGTTAGTGGTTTCTCGGTACATGTTAATGTTACAAAAATTTT\nTTGCGTGTCGTTTTTATCCAACGCCAGATCTTCAGGCCGTTGGTATCTGTAACCCAAAGG\nTTGAACGCGATGAACAATTTGGGGTATGGCGTTTAAACGATCTTGCTGATGCGGTTGGTC\nATATTGTTGGGACAATACAAGGAATCCGAACGCAAATGAGAGTGGGAATATCCAGCCTGC\nGCACAATTATGGCCGATGCTTCCTCAGCCCTTAGGGAATGTGAAAATTTAATGACTAAAA\nCCTCCACTTCTGCTATTGGGCCTCTTTTTTCAACGATGGCTTCCCGGTATGCACGGTTTA\nCACAGGATCAAATGGACATTTTAATGCGTGTTGACAAACTAACAACAGGAGAAAATATAC\nCCGGTCTTGCAAATGTAGAGATTTTTTTAAATAGGTGGGAACGAATAGCAACAGCTTGTA\nGGCATGCCACGGCAGTCCCGTCTGCCGAATCTATTGCAACCGTGTGTAATGAATTGAGGC\nGCGGTTTAAAAAATATACAAGAGGATCGTGTAAATGCCCCAACCTCATATATGAGTCACG\nCCCGAAATCTGGAAGATCACAAGGCAGCAGTTTCATTCGTTATGGACTCCAGGCAACAGT\nTTATTGTGGATTCTGGACCTCAGATGGGCGCGGTTTTAACTTCACAATGTAATATAGGAA\nCATGGGAGAATGTAAATGCAACGTTTTTACACGACAACGTTAAAATAACGACAACGGTCA\nGAGACGTAATTTCAGAGGCTCCGACGCTGATAATAGGACAAAGATGGCTTCGTCCAGATG\nAGATTTTATCTAATGTAGATTTGCGTCTTGGCGTACCCGGGAATACAAGTGGGAGTGACC\nCTTAATATAAAACAGGCGTGTTTATGTACATTAAAGTATTTGTGGTTTTTATTGACTGGG\nCGTTTCGTTTGTATAACGCTGTTGTTGCTAGTATTTTCATAACCTCCTAGGTTTTTGGAG\nCTACACGTGCTTATTCAACGCTCTTTGGGATTTGAATCATCGTAAACGTAGCGTCCCTAC\nCAGTTGAGCGCGTAATTTTCGTAAGCAATAAAATGGATATAATTCCGCCTATAGCTGTCA\nCTGTTGCGGGAGTGGGAAGCCGTAATCAATTTGACGGTGCCCTGGGACCGGCGTCAGGTC\nTGTCATGTTTAAGAACATCTTTATCGTTTTTGCATATGACATATGCGCATGGAATTAATG\nCAACCCTGTCATCAGACATGATTGATGGATGTTTACAAGAGGGTGCAGCATGGACTACGG\nATCTGTCTAATATGGGGAGGGGTGTCCCAGATATGTGTGCTCTTGTTGATCTCCCCAATC\nGAATTTCATATATTAAACTGGGGGACACTACCAGTACGTGCTGCGTTTTGTCTAGAATAT\nACGGCGATAGCCATTTTTTTACCGTTCCAGACGAGGGTTTTATGTGCACACAAATTCCCG\nCTAGAGCGTTTTTCGATGATGTGTGGATGGGACGTGAAGAGTCGTATACAATTATAACTG\nTAGACTCAACGGGAATGGCCATCTATCGTCAGGGAAACATATCTTTTATTTTTGATCCAC\nATGGCCATGGGACTATAGGACAGGCTGTAGTTGTTCGGGTGAATACCACGGATGTGTACT\nCTTATATCGCATCGGAGTATACCCACCGCCCCGATAACGTAGAATCCCAATGGGCCGCTG\nCATTAGTTTTTTTTGTCACCGCAAACGACGGTCCCGTAAGCGAAGAAGCGCTATCTTCGG\nCAGTAACGCTTATATACGGAAGCTGTGATACATATTTTACAGATGAACAATATTGCGAAA\nAACTGGTTACAGCTCAACATCCGTTGCTTCTTTCACCTCCTAATTCCACGACAATTGTGC\nTTAATAAATCGTCTATAGTACCTCTTCACCAAAACGTTGGTGAAAGTGTATCCTTGGAAG\nCAACCCTACATTCAACGTTAACCAACACGGTTGCACTGGACCCTAGATGTAGTTACAGCG\nAGGTTGATCCTTGGCATGCGGTTCTAGAAACAACCTCGACTGGGTCTGGCGTTTTGGATT\nGTCGTCGTAGACGCCGTCCTTCATGGACTCCTCCTTCAAGCGAGGAAAATTTAGCTTGTA\nTCGACGATGGCTTGGTAAATAATACACATTCCACGGATAATTTACATAAACCCGCTAAAA\nAGGTTCTCAAATTTAAACCAACTGTAGACGTGCCGGATAAAACACAAGTGGCACATGTAT\nTACCCCGCCTACGAGAAGTTGCTAACACCCCAGACGTTGTGTTAAATGTATCCAATGTAG\nATACGCCTGAATCCAGTCCCACTTTTTCACGGAACATGAATGTAGGAAGCAGTTTGAAAG\nATCGGAAGCCATTTCTATTTGAACAGAGTGGTGATGTCAACATGGTTGTCGAAAAACTAC\nTACAACATGGGCATGAAATTAGCAATGGATACGTACAAAATGCGGTGGGTACGTTGGATA\nCTGTTATTACCGGTCATACAAATGTTCCCATTTGGGTAACAAGGCCCTTGGTCATGCCAG\nACGAAAAGGATCCATTGGAGCTTTTTATTAACCTCACCATTTTGCGTTTAACGGGATTTG\nTGGTGGAAAATGGAACACGTACACATCATGGTGCTACAAGCGTTTATAGGTCCCCTTGGG\nGAAATTTTAACAGGATTTCCCTCCGCCGCGGAACTTATACGCGTTACAAGTTTGATATTA\nACAAACATGCCGGGGGCGGAATATGCTATTAAAACTGTTCTCCGGAAAAAATGTACAATT\nGGCATGCTCATTATCGCTAAGTTTGGTCTAGTTGCCATGCGGGTTCAGGATACAACCGGC\nGCTTTACATGCCGAACTAGATGTGTTAGAAGCGGATCTAGGAGGTTCGTCGCCCATAGAC\nCTCTATTCTAGACTGTCGACAGGTCTTATAAGTATACTAAATTCGCCTATTATTTCTCAT\nCCCGGACTTTTTGCCGAGCTTATTCCAACCCGTACAGGGTCCCTGTCTGAACGAATACGT\nCTTCTTTGTGAATTAGTCTCGGCCCGGGAGACACGCTATATGCGTGAACACACCGCGCTT\nGTTTCTAGTGTAAAGGCTTTAGAGAATGCATTACGGTCTACCCGCAATAAAATTGATGCC\nATTCAAATACCAGAAGTTCCCCAGGAACCCCCGGAAGAAACCGACATTCCACCCGAAGAG\nTTAATTCGGCGTGTATATGAGATACGATCCGAAGTTACAATGCTATTGACCTCGGCTGTT\nACAGAATACTTCACCCGCGGAGTGTTATATAGCACACGGGCCTTGATCGCTGAACAATCC\nCCTAGGCGTTTTCGGGTCGCGACCGCAAGTACGGCACCCATTCAACGGCTTTTAGATTCT\nCTTCCGGAATTCGACGCTAAATTAACGGCAATCATATCGTCCCTGTCTATACACCCTCCT\nCCTGAGACTATACAAAATCTCCCCGTCGTATCTCTGTTAAAAGAGCTTATTAAAGAAGGG\nGAAGATTTAAACACAGACACGGCTCTCGTATCGTGGTTATCTGTAGTCGGGGAAGCTCAA\nACCGCAGGTTACTTATCCAGACGAGAGTTCGATGAATTATCACGTACAATTAAAACCATT\nAATACACGCGCAACGCAACGGGCTTCCGCGGAAGCAGAGTTGTCTTGCTTTAATACGCTA\nAGCGCGGCCGTAGACCAAGCCGTAAAGGACTATGAAACATATAACAATGGTGAGGTCAAG\nTATCCTGAAATAACACGGGATGATTTATTAGCAACAATTGTACGTGCTACAGACGATTTG\nGTGCGACAGATAAAAATCAATGATCCAATCCGGTTTACAACCTTCGATTAAAAGACGATT\nGGAAACAAGGCTTAAAGAGGTTCAGACGTATGCAAACGAGGCCCGAACCACACAGGACAC\nAATAAAGAGTCGAAAACAGGCGGCATATAATAAACTCGGGGGGTTACTTCGCCCGGTAAC\nCGGTTTTGTGGGACTTAGGGCTGCAGTAGATTTATTACCGGAACTTGCTTCTGAGTTAGA\nTGTCCAAGGAGCCCTGGTAAATCTCAGGACCAAAGTCTTAGAGGCGCCGGTAGAGATCCG\nTTCTCAACTTACGGGTGATTTCTGGGCGTTATTTAACCAATATCGAGACATTTTAGAACA\nTCCCGGAAACGCACGCACATCTGTCTTAGGAGGACTGGGAGCTTGTTTTACAGCTATTAT\nCGAAATTGTGCCGATACCTACGGAGTATAGACCATCATTGCTTGCGTTTTTTGGTGACGT\nGGCAGATGTGCTTGCATCCGACATCGCGACCGTATCTACTAACCCGGAAAGTGAGTCCGC\nCATAAACGCTGTTGTTGCAACTCTTAGTAAAGCGACGTTAGTTTCATCTACAGTGCCAGC\nCTTATCCTTTGTGTTGTCGTTATATAAAAAATATCAGGCTTTACAACAAGAAATTACGAA\nTACCCATAAGTTGACTGAATTACAAAAACGACTTGGAGATGACTTCTCCACCCTAGCTGT\nCTCATCTGGACACTTGAAGTTTATATCATCTTCAAATGTAGATGATTATGAAATAAACGA\nTGCGATATTATCAATACAAACAAATGTGCACGCCCTAATGGATACGGTTAAACTTGTTGA\nAGTTGAACTGCAAAAGCTACCCCCCCATTGTATTGCTGGGACATCTACCTTATCTCGAGT\nAGTAAAGGATCTTCATAAACTCGTCACAATGGCACATGAGAAGAAGGAACAGGCAAAAGT\nGTTAATTACCGATTGTGAACGTGCACATAAACAACAAACGACTCGGGTTTTGTATGAGCG\nTTGGACACGTGATATTATAGCATGTCTGGAGGCAATGGAAACGCGCCATATATTTAACGG\nGACAGAACTGGCACGGTTGCGAGATATGGCCGCTGCGGGAGGGTTTGATATACACGCAGT\nTTACCCACAAGCACGTCAGGTTGTAGCGGCATGTGAAACTACAGCCGTTACGGCATTAGA\nTACTGTGTTTCGCCACAATCCATATACCCCCGAAAATACAAATATTCCCCCACCTTTGGC\nTTTGTTAAGAGGGTTAACATGGTTTGATGATTTTTCGATTACGGCTCCCGTATTCACCGT\nTATGTTTCCAGGTGTTAGTATTGAGGGACTCCTTCTGCTTATGCGTATTCGCGCGGTTGT\nGTTATTATCCGCCGATACGTCTATTAATGGAATACCTAACTACAGAGATATGATATTACG\nAACCTCGGGGGATCTATTACAAATACCCGCATTGGCTGGGTATGTTGATTTTTACACACG\nGTCTTATGATCAGTTTATAACCGAAAGTGTAACGTTAAGTGAACTTAGAGCAGACATCAG\nACAGGCTGCCGGGGCTAAACTTACAGAAGCAAATAAGGCTTTGGAGGAAGTAACTCATGT\nTCGGGCACACGAAACGGCTAAACTTGCACTTAAAGAAGGTGTCTTCATTACATTACCAAG\nCGAAGGTTTATTGATTCGGGCTATAGAGTATTTTACAACTTTCGATCATAAACGATTTAT\nAGGAACGGCATATGAAAGAGTTTTACAAACAATGGTAGACCGCGATCTAAAGGAGGCCAA\nCGCAGAGCTTGCACAGTTTCGTATGGTGTGTCAGGCAACAAAGAACCGTGCAATACAAAT\nTTTACAAAACATTGTTGATACTGCCAATGCCACTGAGCAACAAGAAGACGTGGATTTCAC\nTAACCTGAAGACGTTATTAAAACTAACCCCCCCTCCCAAAACAATTGCATTGGCCATTGA\nTAGATCTACTTCCGTTCAGGACATTGTCACGCAGTTTGCATTGCTGTTAGGGCGTCTGGA\nAGAAGAAACTGGTACGTTGGACATTCAGGCGGTTGACTGGATGTACCAAGCTCGCAATAT\nTATTGACTCCCATCCACTAAGTGTGCGTATAGACGGTACCGGCCCCCTGCATACTTATAA\nAGATAGGGTGGATAAACTTTATGCGTTACGAACTAAATTAGATCTCCTACGACGACGAAT\nAGAAACCGGTGAGGTTACGTGGGACGATGCATGGACAACATTTAAAAGAGAAACGGGGGA\nTATGTTGGCATCGGGGGACACGTACGCTACTTCCGTAGATAGTATAAAGGCACTCCAGGC\nATCGGCGTCTGTGGTTGACATGCTTTGTTCCGAACCCGAATTTTTTTTATTGCCTGTGGA\nAACGAAAAACCGTCTCCAAAAAAAGCAACAGGAACGTAAAACGGCGTTGGATGTTGTGTT\nGCAAAAACAAAGACAGTTTGAAGAGACCGCGTCTCGCTTACGAGCTTTAATTGAACGTAT\nTCCAACGGAGAGTGACCATGACGTTCTTCGTATGTTATTACGTGATTTCGATCAATTTAC\nACATTTGCCTATATGGATAAAAACACAGTATATGACATTTCGAAATTTACTCATGGTACG\nGTTAGGCTTGTATGCAAGTTATGCTGAGATTTTTCCACCCGCGTCTCCAAACGGAGTATT\nTGCTCCTATTCCCGCCATGTCGGGTGTATGTCTAGAAGACCAATCCCGATGCATTCGCGC\nGCGGGTGGCCGCGTTTATGGGGGAGGCGTCTGTGGTGCAAACGTTTAGGGAAGCCAGATC\nTTCTATAGACGCTTTGCTTGGATACTGATGGGGTTCCACTTCGATATAGAGTGTGTTATA\nAATCAGTTGGGGTTAAACTTGGAACCATGCTATGCAGTCAGGGTGGATTATCTTTACGAC\nCGGCACTTCCCGATGAAGGTATTGTGGAAGAAACTACACTATCGGCATTACGCGTGGCCA\nATGAGGTCAATGAGCTACGCATTGAATACGAATCCGCTATAAAATCCGGGTTTTCTGCCT\nTTTCCACCTTTGTTAGGCATCGCCACGCCGAATGGGGTAAAACCAACGCACGCAGAGCCA\nTTGCAGAGATATACGCCGGCCTTATAACAACAACATTGACACGACAATACGGGGTTCATT\nGGGACAAGCTTATTTATTCTTTTGAAAAACACCACCTAACTTCTGTAATGGGCAATGGAC\nTAACTAAACCAATCCAGAGAAGGGGTGATGTACGCGTATTAGAGTTAACCCTATCTGATA\nTTGTAACTATTTTGGTTGCCACAACCCCGGTACATCTTCTCAATTTTGCTAGATTGGATT\nTAATTAAACAGCATGAGTATATGGCCCGTACCCTCAGACCCGTAATCGAGGCCGCATTTA\nGAGGTCGTTTACTCGTTCGCTCATTGGATGGAGACCCGAAAGGCAATGCCCGGGCCTTTT\nTTAATGCCGCCCCATCCAAACATAAACTCCCGTTAGCTCTTGGATCAAACCAAGATCCTA\nCCGGCGGGAGAATATTTGCATTTCGGATGGCAGATTGGAAACTTGTTAAAATGCCACAGA\nAAATAACGGATCCTTTTGCGCCATGGCAACTTTCCCCCCCCCCCGGGGTAAAGGCCAATG\nTCGATGCAGTTACCCGTATAATGGCAACAGATCGTCTTGCGACCATTACTGTACTTGGGC\nGCATGTGTCTCCCGCCAATTTCCTTAGTGTCAATGTGGAATACGCTGCAACCGGAGGAAT\nTCGCATACAGAACACAAGATGATGTGGACATTATAGTTGATGCGAGACTGGATTTGTCAT\nCCACGCTTAATGCAAGATTTGATACCGCTCCCAGCAATACCACGTTAGAGTGGAATACAG\nACCGTAAAGTAATTACAGATGCTTATATTCAAACCGGGGCAACGACAGTTTTTACAGTAA\nCGGGGGCGGCACCAACTCACGTTTCTAATGTAACAGCGTTTGACATAGCAACTACGGCTA\nTTTTATTTGGGGCTCCTTTGGTTATTGCCATGGAACTTACATCCGTTTTTTCACAAAATT\nCCGGACTTACTTTGGGGTTAAAATTATTCGATTCCCGGCATATGGCTACAGATTCGGGTA\nTATCCTCAGCCGTATCTCCCGATATTGTTTCTTGGGGGTTACGTTTACTGCATATGGATC\nCTCACCCAACTGAAAATGCATGTTTAACTGTCCAACTAGAAAAACTGTCCGCGCTCATTG\nCAAACAAACCTCTTACAAACAATCCCCCGTGTTTACTGCTATTGGACGAACATATGAATC\nCCTCTTATGTTTTATGGGAACGAAAAGACTCGATTCCAGCTCCGGATTATGTGGTCTTTT\nGGGGGCCAGAATCTCTTATTGATTTGCCGTACATCGACTCCGATGAGGACTCTTTCCCCT\nCGTGTCCCGATGATCCATTTTACTCGCAAATTATTGCCGGTTATGCGCCCCAAGGCCCCC\nCAAACCTCGACACAACTGATTTTTACCCAACGGAGCCACTATTTAAGTCTCCCGTTCAAG\nTTGTTAGAAGTTCCAAATGTAAAAAAATGCCCGTCCGGCCCGCGCAGCCCGCGCAGCCCG\nCGCAGCCCGCGCAGCCCGCGCAGACCGTCCAGCCCGCGCAGCCCATAGAACCGGGCACAC\nAAATAGTGGTACAAAATTTTAAGAAACCCCAAAGCGTAAAAACAACCCTTAGCCAAAAAG\nATATTCCCTTGTATGTGGAAACCGAATCAGAAACGGCTGTGCTTATACCTAAGCAATTAA\nCCACCTCCATTAAAACAACCGTTTGTAAAAGTATTACCCCACCAAATAACCAATTGTCGG\nATTGGAAAAATAATCCACAGCAAAACCAAACGTTAAACCAAGCGTTCAGTAAACCAATAC\nTTGAGATTACCTCCATTCCGACAGATGACTCGATATCTTACCGGACTTGGATTGCGGCAT\nCAAAATGACCCTCGAATGTATAACTCCAAAACAGTATTCCACCCTGTAAATAACCAATTA\nCCTTCTTGGGTTGACACGGCAGCCGATGCCCCCCAAACGGACCTATTGACAAACTATAAA\nACAAGACAGCCGTCGCCAAACTTTCCGCGGGACGTACACACATGGGGCGTATCTTCTAAC\nCCGTTTAACTCACCGAACAGAGACCTATATGAAAGTGATTTTAGTGAACCTTCTGACGGC\nTATAGCAGTGAGAGTGAAAATTCTATCGTACTAAGTCTCGACGAACATCGGTCATGTCGC\nGTTCCTAGGCACGTACGCGTTGTTAATGCCGATGTAGTCACCGGTCGACGTTATGTCCGA\nGGGACCGCCTTGGGAGCACTGGCCCTGTTAAGCCAGGCATGTCGGCGTATGATCGACAAC\nGTTAGATATACACGTAAACTTTTAATGGACCACACGGAAGATATATTTCAAGGCCTGGGG\nTATGTTAAATTGTTATTAGATGGAACATATATATAAAGTAGCGCCCGATTATTTTCTGTG\nTATTTTTATTTACACCCTACGACTTCTTGAAGCGTTTCCAGATTGTCCCGTGTGTGACAA\nGGTCTGTCCCTTACCCCCCTGGGGGGTATTTTGGGTTGGGGGCGGGGTAGACTGTGGCAC\nGCCTTGGGCCGCGGGCGGTGATCCGGTTGTTGGCTGGACAGTGCTTGACTGTGCTCCCTG\nTTGCGGTTGTTGTCCAGAAGACCCCGACACCACGTGTTGCTGTTGTCCAACGGATGCCGA\nCGTCGTTTGAGGTGGGGGGTGTTGCGGGGATGATCCCGAAAACGCCAACGCGGCGGGCTG\nTTGTAAAGCAGACTGATCGGCGCTCTGTGTTTTTTGCGGCAATATAGTAGGCCCCGAGAT\nTCCCAAACTCATGGATGGATTTGGGGGTTGTGGTCGTATAATACGCGGGTTAAACGTACG\nTTTTAAGCCAACCGTTGGTCTTAACCATGTCATAGGGTCAGTCTCGGCAAACATGGCCGT\nTCGGCGTATCGTATTTGCATTATGGTTAGCGCGTGCACGCGCGGCACTGGCCGCGGCTCC\nCACGGTGTAAATGCTTCTGGCATCAGCGATGTCCACACGGTGACCAGGTTGCAAAGGTCC\nACTGGCGTTTAAAAGTCGTATTAAAGCAACGGGGGTGTAAGCCGCAATTGCTTCCACCGA\nAAATGTGGTGGGGTTGCTGGGATCAAAGACTACACGAGACGATGCGGGTTGTGTCATCGT\nTTATTAGTTTACGGGACAATCGATAACAGCATACACGTACATCTGCGCAGGATATGTACG\nGAAAGGCAATTTATTTCCAGAAAAGCACCGCCCCTAATACAACTACCAGTACAATTACAA\nCGAACAGGGCATATGTCACGTTAGCTACGGGTAGAGCAAGTTTCCAGACACGCGTAGTTT\nGGGTATCGGGTAACGCAGGTTTAATGTCACTTTGCATTTGAACAGACGTGTTTGGACTTC\nCGTTCTCGGGTGGGGATCTGAATGAAGGCCGCCAGCGTATATATTCATCCAAATTATTGC\nCAGTTTCCTTATACATGTATGCATCCGTGGCGCGGGCCATAAGTTTAATGGTGCGAGATG\nGATCTTCCGGTCCCATAAAACGAAAGGATAACTGAACATATGGCATTCGCACAAAGCAGT\nTCACCCACATTAAAGCCTGGAGAGGTCGGCGGTCAATACCCCCACCTCGTTTAATTGATT\nCCAAAGCAGATAGGTTGATACCGGTACTTAACGTTGAACTAAGAATCACGTTATTACTGT\nCAATGGACACTTCAGCCACTGGTGCGTTAGTCGGACGAAAAAAAAAACCTTGAAATAGCA\nCAGACACCCCCGTATTTTGAATTTTTATGTAAGGGTCACAATCTACTTGCGCCCAATTCG\nCCATTAAACGCATAATATACTCTACCGGAAAGGCTTCGGATACGTTGTCTTCGCCGTTAA\nACTGAAAAACACAACGGGCGGGGGGGCGTTGTGGATCAAATATTGGAAGATCCCCATCGC\nAACATTGAAGAGCGCTTGGTACCACCAACCGAATACGTTGTAAAAGATTATCTCCGCAAC\nCCCTCCTGCGTTCACTCCGTACATACGTTCTCCGTGACATATTGATCTAAGGTTGCAAAC\nCAAGGCACACGCGTGAAGTATTTAGACCATTTATCGTGGGATATAGGAGGAGTTTGGAGT\nGATCCACCCCCTGACGACTTATTAATGCGTTTATTTTCCCCATGTATTAAGCATCCTTCA\nATATTTCATGCAAATCTAGAAATTTGGCCATGACTCCCGCAAAGCGTTCACGGCGACGGG\nTCACGCTGGCACTATGTTCACATGGAACAACATAAGCAGATTTTTCTGAATCGTTACTTT\nCTTTATGTTTTAAAACGGACGCCAGGCGACTGGTAAATGATATATAATTTAATTGAGCGT\nCAGTTGTAGGTAGAATTGCTTCTATTTCCGGGGGAATTAAATTTTCAAACCAAACGGAAA\nGAGTAAAGGTGCTATCAGCAGGAAAATACTTTGACTCCAGTGCATCGATATTTAATAGAT\nTAACATCGGTGTCTGTAATTAAATCGCGGGCCCTCATCCCAGAGATGGATCGGGTAGAAT\nCAGAAGAACCCATGGATGGATTCGAATCGCCCGTATTCTCCGAAAATACATCTTCTAATT\nCCGGATGGTGTTCCGACGCATTTTCCGATTCGTACATCGCTTATAATCCAGCCCTTCTGC\nTAAAAAACGATTTGTTATTTTCAGAATTGTTATTTGCCTCCCACTTAATAAATGTTCCCC\nGTGCAATAGAAAACAACGTCACTTATGAGGCCTCTTCGGCGGTAGGTGTGGATAATGAAA\nTGACCTCAAGTACCACTGAATTTATAGAAGAAATTGGAGACGTTTTGGCGTTAGACAGAG\nCCTGTTTGGTCTGTAGAACGCTTGATTTGTATAAACGTAAATTTGGACTGACACCGGAAT\nGGGTTGCGGACTACGCCATGTTATGTATGAACAGTTGTCACTTTTAGCGCTGCCTTTGAA\nTTTGTGTATCTTATGGATCGTTACTACCTGTGCCGTTATAACGTTACTTTGGTTGGGTCC\nTTTGCCAGGCGCACGCTTTCCCTGTTAGATATACAAAGACATTTTTTTTTGCATGTATGT\nTTTCGTACCGATGGAGGGTTACCAGGTATACGACCGCCCCCCGGTAAGGAAATGGCCAAC\nAAAGTAAGATATTCCAATTACTCCTTTTTTGTACAGGCGGTAGTTAGGGCTGCATTACTA\nTCGATCAGCACGTCTCGTTTAGACGAAACCGAAACGCGTAAGTCATTTTACTTTAATCAG\nGACGGACTGACTGGAGGCCCTCAACCTTTAGCGGCCGCCTTGGCTAATTGGAAAGATTGC\nGCGCGGATGGTTGACTGTTCATCATCGGAACATCGCACAAGTGGGATGATTACCTGCGCG\nGAACGTGCATTAAAAGAGGATATAGAGTTTGAAGATATATTAATAGACAAACTTAAAAAA\nTCGTCTTACGTAGAAGCAGCTTGGGGTTACGCAGACTTGGCTTTATTATTACTGAGTGGG\nGTTGCTACTTGGAATGTAGACGAGCGTACAAATTGTGCTATAGAAACTCGCGTTGGATGT\nGTTAAATCATACTGGCAGGCGAACCGGATTGAAAACTCCAGGGACGTTCCAAAACAATTT\nTCCAAATTTACGAGCGAGGATGCCTGTCCCGAAGTAGCATTTGGGCCTATTTTGTTAACT\nACCTTAAAAAACGCAAAGTGCCGTGGTCGCACGAATACCGAATGCATGTTATGTTGTTTA\nTTAACCATAGGGCACTATTGGATCGCTTTGCGGCAGTTTAAAAGGGATATATTAGCATAC\nTCAGCAAATAACACAAGTTTATTTGACTGTATCGAACCTGTAATCAATGCATGGAGCCTA\nGATAACCCCATTAAACTTAAATTTCCATTTAATGATGAGGGTCGATTCATAACCATTGTA\nAAAGCAGCAGGTTCCGAGGCCGTATATAAACATTTGCAAAATAAATGTTTATATACGGCC\nTCGGAATTACAGACAAACCCTAAAATTTTATTTGCCCATCCTACAACCGCGGATAAGGAA\nGTGTTGGAGTTATATAAAGCCCAACTGGCTGCACAAAACAGATTTGAAGGTCGTGTATGT\nGCTGGCCTGTGGACATTGGCGTATGCATTTAAAGCCTACCAGATTTTTCCACGCAAACCA\nACCGCCAATGCCGCATTCATACGAGATGGAGGACTTATGCTTCGACGACATGCAATATCG\nCTGGTCTCCCTCGAACACACCCTATCGAAGTATGTCTAGGCGATATAAATCCGTATCTCG\nGAGCGGGCCTTCGATGCGTGTACGCTCCAGAACGCCATGCCGCCGTCAAACCATTCGAGG\nAAAACTTATGTCAAAGGAGCGGTCTGTGTACCGCCATTATTTTAATTACATCGCAAGGTC\nCCCCCCAGAAGAACTAGCTACCGTTAGAGGCTTAATCGTGCCAATTATTAAGACGACCCC\nTGTCACCCTTCCGTTTAACTTGGGTCAGACAGTGGCGGATAACTGCCTGTCGTTATCCGG\nAATGGGTTATCATTTAGGTCTCGGAGGTTATTGTCCGACATGCACTGCATCTGGAGAACC\nGCGTCTATGTCGAACCGATCGGGCGGCTCTGATACTAGCATATGTTCAGCAGCTTAACAA\nCATATACGAATATCGTGTGTTTCTTGCATCCATTTTGGCGCTATCAGACCGAGCCAACAT\nGCAAGCAGCGTCCGCTGAACCCCTATTGTCGAGCGTATTGGCACAACCGGAATTATTTTT\nTATGTATCATATTATGAGGGAGGGGGGCATGCGAGATATACGCGTACTTTTTTATCGTGA\nTGGAGATGCCGGAGGGTTTATGATGTATGTTATATTTCCGGGGAAATCTGTTCACCTCCA\nTTACAGACTAATCGATCATATACAGGCCGCGTGTCGGGGGTATAAAATAGTCGCACACGT\nTTGGCAGACAACATTTTTACTGTCGGTATGTCGCAACCCAGAACAACAAACAGAGACTGT\nGGTGCCATCCATTGGAACATCGGACGTTTACTGTAAAATGTGTGACCTTAACTTTGATGG\nAGAATTGCTTTTGGAATACAAAAGACTCTACGCATTATTTGATGACTTTGTTCCTCCTCG\nGTGATTTCAGCTTCAGTGTTCATTTTATTATCCCAGCACGGGGCGTGTATACAAACAAAG\nCCTGCCGCCTGCAAGCGGTTTAGCATTTTAACGTTAACAACTCGTGTCTCTGGAATAAAA\nCGTTTTAAAAGCCGTTCTGTGAGTTTAGTGTCGTTTCCAAATAACGCCTTAAAAGTTACA\nCTCGCCGTCCCAATGAGATGAGAAAAATAATAGTCAATGTTTAAAGACAGCCCGTGTGAT\nGTTACGTGAATGGGATCTTCCGCTAAGTCAGATATTATTAACTTACGCTTTGCTTCCCCA\nCACCGTTTACCTGCGGTATTCTGTAAAGGATCTCCACGTAGCAAAGCTACACTTTTTGCA\nTCAGCCTCCACTTCGTCTGTGGGGGCCACAATAACATAAGGGATGCGTTCTCGAACGTTT\nGGGATTTGACCCTGTCTCATTACTAATTTATAATATACTGTTAAGTGAGCCAAGCGACGG\nTTTATGTAGGCGGATGGTGGACGACTAAGCTCGGCCGTCATAACAAACTTATTAATATCC\nAATTTGGGTGATGTAATCTGGCGATGTGCATCTGCAATTATGCGTCCAAACCCGGCCATC\nCCAGACGGCATGGCCCGTCTATTCCATTCAGCAATGGAAACACACGACGCCTCCGCCGCA\nGCACGCGAGACGGTGTCGTCATATAACAACAGTTCTACAAGTTTGCGGGCATAATCGTTA\nATAAATTGACAGTTGTTTTTTCTAACCAAGTCGACTCCCTTCATTAAAACCTTTCCGCCG\nTAAATTACCCCAATGTACTTTTTCTTTGTTATAAGCAAAAGTTTTATAAAAGTTTTTTCA\nCACTCCAACTTTATAGGAGGACAAAACAGAGCCGTTGAAATTATATGTGCCATTTTCTCG\nCCGATTTTAGCTATCCCCTCAACACCAACACCCTTGAATCGGATAAACACAGAATCCGTA\nTCTCCATATATAACCTTTACCTCGTACGCTTTTTGGGAGAGAACGCTACTTTCAATGTCT\nGGAAACGCTGTAATAAAACGTTCAAATGCGGCCCAGTTATTATGAATATAATCTCTGGTA\nCTTAATAACATTTGACGGCCAATTGTAGTGACAGTGGCCGCTACGTATAAACATGGCAGA\nAATCCCTGCGCAACTCCAGTAAAACCGTACACGGAATTACAAACTACTTTTATCGCGGCT\nTGTTGTTTGTCTAATAACACTGCTTCATCTGAAGAACTTCCGGGTATGCGCGCTCTAATA\nGCCTTGCGCATAGCCAACCAGTCTTTTAAAAGAACACCCAGCAGACTTTCTCGAACGTTA\nGAGCGCACAAAAAAAAGACGTTTTCCTCCAACTGTAAAGGTGGCATAATCGGATGGATTC\nAAACGTTTAACCGTCTCAAAATTTAACGTTAGCGTGGTAAAACATAAGTTATGGGCCTGA\nATTATACTTATACGACCACCGGATCGATATAAAATCCCGTATCAGGGTCAAAAACCCTGG\nCTCCTTTATATCCTACATTTCGCCCACTTGACGTACCAGTGGGAGAAACGCTCTCGTCTT\nCATCCATCTCTTCCTCAACATCCCCGACATCGGGAATAACATCCTTATATTCAAAAGTAG\nCTGGGTATCCCCCATCGGGTAAAATAAATCCTCGAGACGAAGCCAGTCCTAATAAACAGG\nTGTAAATCCTAACCTGCTGTCCGTCGTAAATAGCCTTGGTTAAAGTAATTCTAGCTAGCC\nTTGCAACCGCGGATAACTCAAGGTGTGGTAAATATTTAAAAAACAGTTTCCCCACAAGAG\nCCGAGTCTTGTATACAATATTCACCAATAATTCCTCGTGTATTCGGTCCACTAGCGTAGT\nATCCCGGAATGTCTTTGTAGGGCAAATCTCTCTTGGACTCATTTAGAGCTTCACGTGCAA\nCCGAATCTAATTTATAACTCGAGAGTTTTAATTTTTCAGTTGCAATTGCATACATATCCA\nGAGATATGAGACCGTTGATCTTTACCTTGCTTCGTCGCTGAAATCCGGATTTGCCAACAT\nCCCATATCTTAAACAGACCCCCACGGTTTATACTGCCATAACCATCAAGCTTGAGACTGT\nATATAGAATTAAGTTTCTCCATAATAAACGCCCAATCAAAATTAACAATGTTATAACCTG\nTGGCAAACTCGGGAGCGTACTGTTTTACGAGGGTCATAAATGCAATTAATAGCTCGAATT\nCACTATCAAACTCCAGCACAGTCGGCTCCGGTAACCCCGCGTCCTTCATTTCTTGTACAT\nACCTTTGTGGTAAGTCACAAGAGCCAAGGGAAAACAGTAAAATGTGTTCTAAAGACTGTC\nGAGGGATTGAATATAATAGACAAGAAATTTGGATTACAAGATCCTCCAGATGTGTTGCAT\nCGGGAAACGCCAGCTCATTAGATCCTCCTGATTTACATTCAATATCGAAACATAACAACT\nTGTAGTCAGGCCATGAGTCATCGTTTGGTATAGCCTGCAGATTATCCGACATGCAGTCAA\nTTTCAACGTCGCTTAACGTTAATTGGCGACTTGCCGGTCGAACTCGAACACGTTCCCCAT\nCAACTCCAGGTTTTAGTTGATACCAACCAAAACTAACAAAGCCGGGATTATCCATTAGAA\nAACGAGTGGTAGCGTCTACCCGACCTTCATACTTTTTCAACTCCGGGTGAAAGTTATCAC\nAAAGATAATTTGTAAATTTAGATGAGGGAGAATACACCCTGTAAAACGCACATGGCTGTG\nTATCGTAGTAATAAACATCTGTGCGCTCAATAACCTCAACGCGAAAGCTTTCTGGAGATG\nCGCTTTTAAACGAGGTACCATGAAAAGCGTTCTTGTCTCCATTTAACGTTGCATCATTTT\nGTGTTATCATAGAACTGCGTAAACACTCGGCAAGTAATACAGATAACTCGCTACCGGAAC\nGTATGCCACAAGCGGTATCCACCTCGGCTTTGTTTATATAAAAATATTGACAGATGCCGT\nATACATGAACTGCCACCCTTTTTCCACATCGGGACATGCCAAGTAAAGTAATAACGGTAC\nCAAGCGGTCGTGTTGCAGTTGCAAACCGGGATACATCTCCATTAGACGCGGCTTCTGTTG\nTTTCGACAATATCATATACATGGAATGTGTTAAAGCGGGGGTCAAACTTATCCCCACGAA\nAGTCGATTTCCCCCCAAATATTCACGCGTCTAGGCCAGGGGCTGGAACAACGAAAATCCA\nGAATCGGAACTTCTTTTCCATTACAGTAAACTTTAGGCGGTCGACTAAGTGTACCGACGT\nGAACCCCCTTTCGTTCTTCCATGGGCACATCTTCATCTAAACATTTAGGGGCCAAAAATT\nGAAACGATGACATGGTAGTTTTGTAACTATGAAGAAATTCTCTGTTACTACCGCGCCCGG\nTTCTTGGGTTATATGTAATCCCTTTTTAACCCAAGCATCAGGGATTAAATATAACCCAAG\nAACCGGGCGCGGTTTCCGCATATGTAATACCCGTTTAAAAGCCTCTCTTCTTAATGTATC\nGACAGACTGGGTTTTGGGTGGTCATTTGACCCTGCCAACAACCCCCCATTATTACGAGTA\nCTTCACCAAAATGGAAAATACTCAGAAGACTGTGACAGTGCCCACGGGGCCCCTGGGTTA\nCGTTTATGCGTGCCGGGTTGAAGATTTGGATCTGGAGGAAATTTCATTTTTGGCCGCTCG\nTAGCACGGACTCTGATTTGGCTTTATTACCTTTGATGCGTAATTTGACCGTGGAAAAAAC\nTTTTACATCCAGCCTGGCGGTGGTTTCTGGAGCACGCACTACGGGTCTTGCCGGAGCTGG\nTATTACCTTAAAACTCACTACCAGTCATTTCTATCCATCTGTCTTTGTCTTTCACGGAGG\nCAAACACGTTTTACCCAGCTCCGCGGCCCCAAATCTCACACGCGCGTGTAACGCGGCTCG\nAGAACGGTTTGGGTTTTCACGCTGCCAAGGGCCTCCTGTTGACGGTGCTGTTGAGACGAC\nCGGCGCTGAGATATGCACCCGCCTTGGATTAGAGCCAGAAAATACAATATTATACTTGGT\nGGTCACGGCATTGTTTAAGGAAGCCGTATTTATGTGCAACGTGTTTCTGCATTATGGAGG\nACTCGATATTGTTCATATTAACCATGGGGATGTTATACGTATACCGTTATTTCCGGTACA\nACTTTTCATGCCCGATGTTAACCGTCTGGTACCCGACCCATTCAACACTCATCACAGGTC\nTATCGGAGAGGGTTTTGTATACCCAACACCCTTTTATAACACCGGGTTGTGCCATTTAAT\nACATGACTGTGTTAAATGGCACAACCCGGTGTTATTGCTCCCATGGCCGTTGCCTTGCGC\nGTCAGAAATGTAACTGCCGTCGCCCGAGGAGCGGCCCACCTTGCTTTTGATGAAAATCAC\nGAGGGGGCAGTACTCCCCCCTGACATTACGTACACGTATTTTCAGTCCTCTTCAAGTGGA\nACCACTACCGCCCGTGGAGCGCGTCGAAACGATGTCAACTCCACGTCTAAGCCTAGCCCA\nTCGGGGGGGTTTGAAAGACGGTTGGCGTCTATTATGGCCGCTGACACAGCCTTGCACGCA\nGAAGTTATATTCAACACTGGAATTTACGAAGAAACTCCAACAGATATCAAAGAATGGCCA\nATGTTTATAGGCATGGAGGGCACTTTGCCAAGGCTAAACGCTCTGGGGTCATATACCGCT\nCGTGTGGCCGGGGTCATTGGTGCGATGGTTTTCAGCCCAAATTCTGCGTTGTATCTAACT\nGAGGTGGAGGATAGCGGGATGACCGAAGCCAAGGATGGGGGACCGGGTCCATCATTTAAT\nCGATTTTACCAGTTTGCCGGACCTCATTTAGCTGCGAATCCCCAAACAGATCGAGATGGC\nCACGTTCTATCCAGTCAGTCTACGGGTTCATCAAACACAGAGTTTAGCGTGGATTATTTG\nGCACTCATTTGTGGATTTGGAGCACCCCTGTTGGCGCGACTGCTTTTTTATCTAGAACGC\nTGTGACGCTGGTGCGTTTACAGGGGGTCACGGGGATGCGTTAAAATATGTTACGGGGACC\nTTTGACTCTGAAATTCCATGTAGTTTATGTGAAAAACATACGCGGCCGGTATGCGCTCAC\nACAACAGTACACCGACTTAGACAACGCATGCCGCGATTTGGACAAGCCACCCGTCAACCT\nATTGGGGTGTTTGGAACAATGAACAGCCAATATAGCGACTGCGATCCTCTAGGAAACTAT\nGCTCCATATTTAATCCTTCGAAAACCCGGGGATCAAACGGAAGCAGCAAAGGCAACCATG\nCAGGACACTTATAGGGCTACACTAGAACGCTTGTTTATCGATCTAGAACAAGAGCGACTA\nCTGGATCGCGGTGCCCCATGTTCTTCCGAGGGACTATCGTCTGTCATTGTGGATCATCCA\nACGTTTCGTCGCATATTAGACACACTGCGTGCGCGTATAGAACAGACAACAACACAATTT\nATGAAAGTGTTGGTTGAGACCCGCGATTATAAGATCCGTGAAGGATTATCCGAAGCCACC\nCATTCAATGGCGTTAACGTTTGATCCATACTCAGGAGCATTTTGTCCCATTACCAATTTT\nTTAGTTAAACGAACACACCTAGCCGTGGTACAAGACTTAGCATTAAGCCAGTGTCATTGT\nGTATTTTACGGACAGCAAGTTGAGGGGCGGAACTTTCGTAACCAATTCCAGCCTGTTTTG\nCGGCGGCGTTTTGTTGACCTGTTTAATGGGGGGTTTATATCAACACGCTCTATAACCGTA\nACATTATCTGAAGGTCCTGTACGTACCTTTGATGGGGATTTAGCGCGCGTAAGCGTGGAA\nGTTATTCGGGATATACGAGTTAAAAATAGGGTCGTTTTTTCAGGTAACTGTACAAATCTC\nTCTGAGGCAGCCCGGGCAAGGCTTGTAGGCCTTGCAAGTGCGTACCAACGCCAAGAAAAA\nAGAGTGGATATGTTACACGGGGCCCTAGGGTTTTTGCTTAAACAGTTTCACGGCCTGTTA\nTTTCCTCGGGGTATGCCACCAAACAGTAAATCCCCCAACCCGCAGTGGTTTTGGACCCTG\nTTACAACGCAACCAGATGCCGGCAGATAAACTTACACACGAAGAGATTACCACTATTGCA\nGCTGTTAAACGGTTTACCGAGGAATATGCAGCAATAAACTTTATTAATCTACCCCCAACC\nTGCATAGGAGAATTAGCCCAGTTTTATATGGCAAATCTTATTCTTAAATACTGCGATCAT\nTCACAGTACCTTATAAATACCTTAACTTCTATAATTACGGGTGCCAGGCGCCCGCGTGAC\nCCATCATCCGTTTTGCATTGGATTCGTAAAGATGTCACGTCCGCCGCGGACATAGAAACC\nCAAGCAAAGGCGCTTCTTGAAAAAACGGAAAACTTACCGGAATTATGGACTACGGCTTTT\nACTTCAACTCATTTAGTCCGCGCGGCCATGAATCAACGTCCCATGGTCGTTTTAGGAATA\nAGCATTAGTAAATATCACGGAGCGGCAGGAAACAACCGCGTCTTTCAGGCAGGGAATTGG\nAGCGGTTTAAACGGGGGTAAAAATGTATGCCCGCTATTTACATTTGATCGCACTCGCCGT\nTTTATAATAGCATGTCCTAGAGGAGGTTTTATCTGCCCCGTAACAGGTCCCTCGTCGGGA\nAATCGAGAAACCACCCTATCCGACCAAGTTCGCGGTATAATTGTCAGTGGCGGGGCCATG\nGTTCAATTAGCCATATACGCCACGGTTGTGCGTGCAGTGGGCGCTCGAGCACAACATATG\nGCATTTGACGACTGGTTAAGTCTTACAGACGATGAGTTTTTAGCCAGAGACTTGGAGGAG\nTTACACGACCAGATTATCCAAACCCTGGAAACGCCCTGGACCGTAGAAGGCGCTCTAGAA\nGCCGTAAAGATTCTAGATGAAAAAACGACAGCGGGAGATGGGGAAACCCCCACAAACCTA\nGCATTTAATTTTGATTCTTGTGAACCAAGCCATGACACCACATCTAACGTATTAAACATT\nTCAGGGTCAACTGTCCCTGGTCTTAAACGACCCCCCGAAGATGACGAACTCTTTGATCTT\nAGTGGTATTCCCATAAAACATGGGAACATTACAATGGAAATGATTTAACCTCCCTCTTTA\nTCCAATTAAAGCCCACACGCGGGTGAGTGTACGTAATAAACAAGTCAATATTACATATTC\nTGTTGTGTTTTCTTTTTTGCGTGTAGTCCTTACCCATATGACCTGTAATATAGTGTGTCT\nATTCAGCTTACAGTCCAGTGGACAGTAACAGCCCGATAACATGGAATTGGATATTAATCG\nAACATTGTTGGTTCTACTGGGTCAAGTTTATACGTACATCTTTCAGGTTGAACTGCTACG\nTCGCTGTGATCCAAGGGTGGCGTGTCGCTTTTTATATCGGTTAGCGGCTAACTGTTTGAC\nAGTTCGTTATTTATTAAAGCTGTTTCTCCGGGGATTTAATACCCAGCTAAAATTTGGAAA\nCACTCCCACGGTTTGTGCACTGCATTGGGCATTATGTTATGTAAAGGGAGAAGGTGAGCG\nTTTGTTTGAGTTGCTACAACATTTTAAAACGCGTTTTGTTTATGGTGAGACCAAAGACTC\nAAACTGTATCAAAGATTACTTTGTCTCAGCGTTTAACTTAAAAACCTGCCAATATCACCA\nTGAGCTGTCGTTAACAACATACGGAGGTTACGTATCGAGTGAAATTCAGTTTTTACACGA\nCATTGAGAATTTTTTAAAACAGCTTAATTACTGCTATATTATCACGTCTTCTCGTGAGGC\nGCTAAACACATTGGAAACCGTGACGCGGTTTATGACAGATACTATAGGAAGCGGTCTAAT\nACCACCCGTGGAGTTGTTTGATCCGGCGCATCCATGTGCTATATGTTTTGAAGAATTATG\nTATAACAGCTAACCAAGGTGAGACCTTACATCGTAGATTATTAGGATGTATCTGCGATCA\nCGTTACTAAGCAAGTTCGGGTTAACGTGGATGTTGACGATATTATTCGGTGTTTACCATA\nTATCCCTGATGTACCGGATATCAAACGTCAATCCGCCGTTGAAGCGTTACGAACACTTCA\nAACCAAGACGGTAGTCAATCCCATGGGAGCAAAGAACGATACGTTTGACCAAACATACGA\nAATTGCGAGCACCATGCTTGATTCTTATAATGTTTTTAAACCTGCCCCTCGGTGTATGTA\nCGCCATCAGCGAGCTTAAATTCTGGTTAACGTCTAATTCCACTGAAGGACCCCAACGTAC\nTTTAGACGTGTTTGTTGATAATTTGGATGTATTAAACGAACATGAAAAACACGCAGAACT\nTACAGCCGTAACGGTTGAGTTGGCGTTATTTGGAAAAACTCCCATACACTTTGATAGGGC\nGTTTTCTGAAGAACTCGGATCTCTGGATGCAATTGATAGTATTTTGGTTGGCAATCGCTC\nATCCTCACCAGACAGTCAGATAGAAGCATTAATTAAAGCCTGTTATGCCCATCATCTATC\nGTCGCCTCTCATGCGTCACATTTCTAACCCGAGTCATGATAACGAAGCCGCCTTACGCCA\nACTTTTAGAAAGAGTTGGGTGTGAGGATGATTTAACCAAAGAGGCGAGTGACAGCGCTAC\nAGCATCCGAATGTGATCTGAACGATGATAGTAGCATAACTTTTGCTGTTCATGGATGGGA\nAAACCTGTTATCCAAAGCAAAAATTGACGCTGCGGAAAGAAAACGAGTATATCTTGAACA\nTCTGTCTAAGCGCTCTCTAACCAGCCTCGGTAGATGTATCCGCGAACAGCGCCAAGAGCT\nAGAAAAAACACTCAGGGTAAACGTTTATGGAGAGGCCTTATTGCAGACATTTGTTTCGAT\nGCAAAATGGGTTTGGGGCACGAAACGTGTTTTTAGCTAAGGTTTCCCAGGCAGGGTGTAT\nTATCGACAATCGCATTCAGGAAGCGGCCTTTGATGCACATAGATTTATAAGGAATACCTT\nAGTTCGACATACAGTAAGTGCAGGTAACATAGCCCATTGTTTAATCACGATGAACACCGT\nTTTGCACAACCCCCTAACACCGCCTTATTTTTTACCGTGGAAAACGTTGGCCTATTTCCG\nCACTTAAAAGAGGAATTGGCAAAGTTTATGGGCGGTGTCGTTGGTTCCAACTGGCTTCTC\nAGTCCATTTAGGGGCTTTTATTGCTTTTCTGGGGTAGAAGGCGTTACTTTTGCACAGAGA\nCTTGCCTGGAAATATATTAGGGAGCTTGTGTTTGCAACCACACTATTCACCTCTGTTTTC\nCATTGTGGGGAGGTGCGGTTATGTCGCGTTGACCGTCTAGGTAAGGATCCACGCGGGTGC\nACGTCTCAACCTAAAGGTATAGGCAGTTCCCACGGACCCTTAGACGGCATTTATTTAACG\nTACGAAGAAACATGTCCCCTTGTGGCTATTATTCAAAGTGGAGAAACAGGGATCGACCAG\nAATACCGTCGTAATCTACGATTCAGACGTTTTTTCTCTTCTATACACCCTAATGCAGCGG\nCTGGCTCCGGATTCAACGGACCCGGCGTTTTCATAACCTCCGTTACGGGGGTGTGGTTAT\nGCTTTTTATGCATATTTTCTATGTTTGTTACGGCGGTTGTGTCGGTCTCTCCAAGCTCGT\nTTTATGAGAGTTTACAAGTAGAGCCCACACAATCAGAAGATATAACCCGGTCTGCTCATC\nTGGGCGATGGTGATGAAATCAGAGAAGCTATACACAAGTCCCAGGACGCCGAAACAAAAC\nCCACGTTTTACGTCTGCCCACCGCCAACAGGCTCCACAATCGTACGATTAGAACCAACTC\nGGACATGTCCGGATTATCACCTTGGTAAAAACTTTACAGAGGGTATTGCTGTTGTTTATA\nAAGAAAACATTGCCGCGTACAAGTTTAAGGCGACGGTATATTACAAAGATGTTATCGTTA\nGCACGGCGTGGGCCGGAAGTTCTTATACGCAAATTACTAATAGATATGCGGATAGGGTAC\nCAATTCCCGTTTCAGAGATCACGGACACCATTGATAAGTTTGGCAAGTGTTCTTCTAAAG\nCAACGTACGTACGAAATAACCACAAAGTTGAAGCCTTTAATGAGGATAAAAATCCACAGG\nATATGCCTCTAATCGCATCAAAATATAATTCTGTGGGATCCAAAGCATGGCATACTACCA\nATGACACGTACATGGTTGCCGGAACCCCCGGAACATATAGGACGGGCACGTCGGTGAATT\nGCATCATTGAGGAAGTTGAAGCCAGATCAATATTCCCTTATGATAGTTTTGGACTTTCCA\nCGGGAGATATAATATACATGTCCCCGTTTTTTGGCCTACGGGATGGTGCATACAGAGAAC\nATTCCAATTATGCAATGGATCGTTTTCACCAGTTTGAGGGTTATAGACAAAGGGATCTTG\nACACTAGAGCATTACTGGAACCTGCAGCGCGGAACTTTTTAGTCACGCCTCATTTAACGG\nTTGGTTGGAACTGGAAGCCAAAACGAACGGAAGTTTGTTCGCTTGTCAAGTGGCGTGAGG\nTTGAAGATGTAGTTCGCGATGAGTATGCACACAATTTTCGCTTTACAATGAAAACACTTT\nCTACCACGTTTATAAGTGAAACAAACGAGTTTAATCTTAACCAAATCCATCTCAGTCAAT\nGTGTAAAGGAGGAAGCCCGGGCTATTATTAACCGGATCTATACAACCAGATACAACTCAT\nCTCATGTTAGAACCGGGGATATCCAGACCTACCTTGCCAGAGGGGGGTTTGTTGTGGTGT\nTTCAACCCCTGCTGAGCAATTCCCTCGCCCGTCTCTATCTCCAAGAATTGGTCCGTGAAA\nACACTAATCATTCACCACAAAAACACCCGACTCGAAATACCAGATCCCGACGAAGCGTGC\nCAGTTGAGTTGCGTGCCAATAGAACAATAACAACCACCTCATCGGTGGAATTTGCTATGC\nTCCAGTTTACATATGACCACATTCAAGAGCATGTTAATGAAATGTTGGCACGTATCTCCT\nCGTCGTGGTGCCAGCTACAAAATCGCGAACGCGCCCTTTGGAGCGGACTATTTCCAATTA\nACCCAAGTGCTTTAGCGAGCACCATTTTGGATCAACGTGTTAAAGCTCGTATTCTCGGCG\nACGTTATCTCCGTTTCTAATTGTCCAGAACTGGGATCAGATACACGCATTATACTTCAAA\nACTCTATGAGGGTATCTGGTAGTACTACGCGTTGTTATAGCCGTCCTTTAATTTCAATAG\nTTAGTTTAAATGGGTCCGGGACGGTGGAGGGCCAGCTTGGAACAGATAACGAGTTAATTA\nTGTCCAGAGATCTGTTAGAACCATGCGTGGCTAATCACAAGCGATATTTTCTATTTGGGC\nATCACTACGTATATTATGAGGATTATCGTTACGTCCGTGAAATCGCAGTCCATGATGTGG\nGAATGATTAGCACTTACGTAGATTTAAACTTAACACTTCTTAAAGATAGAGAGTTTATGC\nCGCTGCAAGTATATACAAGAGACGAGCTGCGGGATACAGGGTTACTAGACTACAGTGAAA\nTTCAACGCCGAAATCAAATGCATTCGCTGCGTTTTTATGACATAGACAAGGTTGTGCAAT\nATGATAGCGGAACGGCCATTATGCAGGGCATGGCTCAGTTTTTCCAGGGACTTGGGACCG\nCGGGCCAGGCCGTTGGACATGTGGTTCTTGGGGCCACGGGAGCGCTGCTTTCCACCGTAC\nACGGATTTACCACGTTTTTATCTAACCCATTTGGGGCATTGGCCGTGGGATTATTGGTTT\nTGGCGGGACTGGTAGCGGCCTTTTTTGCGTACCGGTACGTGCTTAAACTTAAAACAAGCC\nCGATGAAGGCATTATATCCACTCACAACCAAGGGGGTTGGGTTTCTCGGCAAAGGAATGG\nATCCCTTTGCCGAGAAACCCAACGCTACTGATACCCCAATAGAAGAAATTGGCGACTCAC\nAAAACACTGAACCGTCGGTAAATAGCGGGTTTGATCCCGATAAATTTCGAGAAGCCCAGG\nAAATGATTAAATATATGACGTTAGTATCTGCGGCTGAGCGCCAAGAATCTAAAGCCCGCA\nAAAAAAATAAGACTAGCGCCCTTTTAACTTCACGTCTTACCGGCCTTGCTTTACGAAATC\nGCCGAGGATACTCCCGTGTTCGCACCGAGAATGTAACGGGGGTGTAAATAGCCAGGGGGT\nTTGTTTTAATTTATTAATAAAAATGTGTATTACGTTACTCATGTGTCTCCATTACGCATC\nACAGGGGGTATTTATACCCGATAATATACAAAACGCGTTTTGTACCTCTACCGCACCCGA\nTATCTTAACGGGGTTATTATGGAATCGTCTAACATTAACGCGCTACAACAACCGTCGTCT\nATCGCACATCATCCGTCCAAACAGTGCGCTTCAAGTCTCAATGAAACAGTAAAAGATTCT\nCCCCCCGCGATTTATGAAGATAGGTTAGAACACACGCCGGTACAATTACCCCGCGACGGT\nACACCCCGAGACGTATGTTCTGTGGGACAGCTAACCTGTCGAGCATGTGCAACGAAACCT\nTTTCGCCTTAACCGCGACAGCCAATACGACTACTTAAACACATGTCCAGGGGGCCGTCAT\nATTTCACTGGCACTGGAGATTATAACGGGTCGATGGGTTTGCATCCCGCGTGTGTTTCCG\nGATACCCCAGAGGAAAAATGGATGGCGCCATATATTATTCCAGACCGAGAACAACCATCA\nTCAGGGGATGAAGATTCTGACACCGATTAAATTTAACTTAAATAAAACCTTACCACCCAT\nAAAAACGCCTTCTGTTTGACACGACACCGCTTAACAAAAAAAAAAAAACCAAACACGCCT\nTTTATGAATGTAATACTTTTATTTGTTGGTTAACACCGCCCCACCATCATCTGATTTGCA\nAACATATCGGCGTCGTCTGCCGTGGACCCCTGTATTAAAGGGGCCTTGGAACTAGCCTCC\nACTGCATTTACATCTTGTCCAACTGTATCTGTATGTGGGGTGCTTGTTGTATTTTGGGAT\nGAGCATAGACCCGAAACGCTTTGAAGCTGTTTTAATAAAATCGATATTCGAGGATCCCGT\nGTCCCCTCTGGTATATTTGTATGGTGCGACAAAGGCATTTGTGTCCCATTTTGTGATTTT\nAGCTCTGTAACCTCCTGTTGCAGTTTTGCCACAACCCCAGCAAGCTCTTCGTGCTGACCA\nTTAGAAACTCTGTGTCTCCTCTGCCAATATGATGGAGAAACTCGACGTCTCCGATGCGTT\nATATACGTTGGTTCACCGGGAAAATATATATTTGAGGGAAACTCTCCGTCCATTTGAGAC\nTCCCCACTAGAAAAAGAATCCAATTCCCTTTGATCCATGCTCTTGAAATCCCGTTTTCCT\nGGACGACGGACATCGGTTTTGTCTGGAAAATTTACACACGGGGTCTGCAAGTCAATACCC\nCGTTCGGCGGCCAATGCGTTCATAAATGCGGACATTTGCATTTCCAAACGATTGGGTGGT\nGGATATCCCGGAAACCCGTACGGTCCCCCGAAGTGTCCCGGAGGGCAACCATAACCCCCT\nGTATTAGGTGGGAAGGCAGGCGGGTGTGGAGATCCATATGGCCCGACGATATACTGTCCG\nTTATTTGGAGCTCCAATTGATACCTGCGGATTTTTAGTCTGCCCGGTTAACAGCTGTGAA\nTAATACGCGGTAGGTATCAGTACAAATTCCCCTCCGGTTGGAACGCCCGACGGGGGCTGT\nGGTGAGATACCACTAGCGTTACCTGCTACAGAAGCCATATCGCTGTCGTTCCTACACAAC\nTGCGTAACCTTTAAATGCGGAACAGTCTTTTCACAATCTTCATTTGATTCCCCAACACCC\nAACGCGAGATCATGGGCCCGCCGGGGTGGAATGTGGCGTTTATAACACCCGCGTTGGGTA\nATTTAGACTCCACCCCATTAACGTTGGTTATCCGAGCAAGTCCATATCCGGTGCTAGCCT\nGAAGATAAACGTGACCCATAATTCCGGCTTCGCGTCTACGTTTTGCAACCACGTCCCATC\nTATCTCTTAAAAGCATATTGTTCACGGCTGTGGATAATAACACCTTGGCGAGTTTATCTT\nCGCTAACCTTCCATACTTTATTTAAACCCGCGTAGTCTTTAACCAGCGACAATAACCGCG\nCTTTACTTTCCATCGATAAAACCCGGAATGGTTCAATTGAAGATTCCGGGGTACAGTCAT\nAATTGACCACTGTTCCAACGCGTCTTCCAACAACACATAACGCAACATGGGTAAAAAAAT\nTACCGTCTGGTATCTCATTCGGGGACAATCGTTTTGAAGACAGGGATACGGAGGGTAAGT\nAATTTGTGACCAAGTATAACGCACGTTCTAGCGGAGATAATACAGAATCTCTATTTCCAA\nAAAAATTCGAATGGGCCGCTTCAAACAGCACCGCATGTAGTTGAGGGCATCTAACGATAC\nCCAAAAAAAAAGGTCCGCGTATGTCCTCAATGATTGCGATTACTTCACCCACGACACAGT\nCTTTTCGATGATCGATGTTTATTGGTATTTTACTAGTAGGCGGCAAAGCGGACCGCACAA\nTCTCTGGGGTAATATTTAATTCCCCTTCGTCCTTTGAATATAAGGCTAAATACCCAGCCA\nCGTATAACGCTTCACAGTTCTCTTCGTCAGCTTCAGCAGCCATTATAAACACCCCACGGA\nCCGGATAGTGAATACTCACGGTGTGGAGGCAAACTGAGGAATGACACCCAAACAGACAAA\nATATAGAAGATCATAGTCACTGTTAACGTTGAACTGCGCAAGGCGGCGACTTTCTTCCAA\nTGCCGCCCTTACACGCGGTTGGTGCATTAACATTCCAAGTCCCCGTTCATATTGCAACAT\nAACACTGTCATGTATTGATACCACGGCGGCTATGGGTAGGGATGTAACATTTTGTCGGCG\nGTGTTCTAATTCCAATGCAATTAAGCTTATGAGCCGATCTTGGTACTGTCCAGAAGAAAT\nATCTATTACGGTTCTTCCTAAACTTCCACGACTAAGCTGGGTATGCGCGTCTAAACAAAG\nAGCAACTAATCCAGGAAACATTTCAGTCAGCTCTGTGGTCCGATTTAACGTATACAGTGG\nTGCTATATATCGTTCACATAAAAATTGAAAGTTATTATTACCGCTTTTAAACTTCCCATC\nAAACCCCGTCGCTCCGCGCAAGATTACATTGTTGGTAGGGGTTCCTGTTGCTTCTGACAC\nAATCAAACCCAGCTTAGTCGTGGAAGTTTATCTCCGTATACGTTCCCGTTCCATAATAAG\nCGCCTTAATAATAATAACGCCGTAATCGTGTCAATTGTTAACCTTAATAGAGTTTGGTCT\nTCCATAAGAAACACGTTTTGGGCCCGTTCTAAATACGCCGCGGCCGCCTGTTGAATCTTG\nTCCACATATGCGGTATGATTGCGATCAATAATGTCATTAACCCCAGGATTAAACTGTCCA\nGGTGCAGGCGGTAGGACCTGCAACCGTATAAGCGCATCCATAACAGAATGTGACGTTAAG\nGCGCCTTGATCATACCGCCCCCCACGAGCATGAAACTGGTCGCGTGGTAGACGATCATAG\nCAAAATTGATAACTGTTTTTATTTTCGTGTGTTGTCATATAATTCACAAATGTCTCAGTA\nTATTCCGGTAGGTGCTCTATAAGGTTCCCGAAGGACGAAACTTGAGGTTCGTGGACACTA\nTTAGATGTCCTATACATTAAATATAAACATAATACCGCACACTCGAACGCGGAGTACGCT\nCTATCTCCAACATACATTCTCCCGGCGGACTGTAGACATGTTACCGTTGTGTTCATAAAC\nGTACGGGAAATGCGCCCGTCTTTACAATCAACTCCGCGTGCAGCTACGGGCCTATCTAAC\nACAAGCCGTTCCTGCAGAGTACGATACCATGGCCCGAAAACAATCCCTGGAGAGTTATTG\nCCCCTTGCCCTTCCCAAGTACACCAGGGTGATAAAATCCACTTGAAAGTTTGTATCGTAC\nTGCAACGGTGCATCATTTTTGGCAATCTGTACCTCGGGGTGTATAGACTCATTGCGTATT\nATTTCTGTACGTGTACATTCCTCAGATTGTGCATCTGCTTCTTCCGCCTCGGCAGCAGCC\nGTCTCCAGGGAATCCAAAACCTTGGCCATGCGCGTTAGTTGGTCTTCGAGGGGCTTTAAA\nCGACGATCTATTTCCGTTGGTAACGTAATCGTTTCCCCGCGAAGGTTGTCTAATGCGGCA\nACGGCCGCCGCATTAGACAACCTTCGCGGGAGCCGTCCAGTAGTGTATGGGGAAGTTGGG\nGGCTATAAAGTTCTTAGTGGTAGACAAAAATATCCCACATTTATTCGGAAACGAGATAGA\nTCCGAACCCATATCTCGCCGTCATGGTGTCTGCAGCAAACAAAGTCAACTGGCGTGAATA\nTAAACCGGGATGTTTTGTAAAATTCCACCACAAGCACCTAAAGAAGGCCTTCTAAGGGGT\nAAATCCACCCCACAAGCTGCATTTTCTTCAAACTTTGTTAAAGCGGAACGATGGCATGAT\nTTCGCACGCTTTTTCGCAAGAGAACATACGTGAATTTTCTTTTTGCATAGACGTCTTCGC\nTCTCTAACGGACCTTATCGGGGGGGTATATTCCGCTACATTCTCCAAATGCGACGCTAGC\nATAACAAGGTTTCCATGAATCACCTTTGGGGGTAACCGAGTTACCTGTAACAGGTTCAGA\nCCCCGTTGAGATACAAACACAAGGAGGGGGGTCACCATTATTTCATCAGATCCCGTGGGT\nGTGGTTTCCTTTATTAAAGCCACGGTATCCCTCAGCTGGCGCATACCCTCGCAAAACTGG\nTGATACTTAGTAGGGGTATGTATATTAGCGCTAAAACGGCAAGATTTTAATTCCACTATA\nAAACAAACGGTCTTTCCGGCACCACTGGATTCCGTTTGTATAATACAAATACAATCGGGG\nCGTCGGCGTCCCAAATTTACTTCAAACGACATTGATATGCGTACAGCCCTTTGAACATCC\nACGTGGGATAACGGCGACAGGAGTTTTGCCAGCCTCGGGTTGAACGCGTCCGCGAAACCT\nCGACGTACGTTATCAATATCCTTTTTGAGTACATCGTAAAAACGAGTGTGACAACGTTGT\nCCCAAACGAAAACACTTGGCCCGAATTTGACTAGCGGACATATTTGAAGTTCCGTCCCAG\nAAGATAACCTAAGACGCGTTTGTCTACAATAAACATGTCAACGGATAAAACCGATGTAAA\nAATGGGCGTTTTGCGTATTTATTTGGACGGGGCGTATGGAATTGGAAAAACAACCGCCGC\nCGAAGAATTTTTACACCACTTTGCAATAACACCAAACCGGATCTTACTCATTGGGGAGCC\nCCTGTCGTATTGGCGTAACCTTGCAGGGGAGGACGCCATTTGCGGAATTTACGGAACACA\nAACTCGCCGTCTTAATGGAGACGTTTCGCCTGAAGACGCACAACGCCTCACGGCTCATTT\nTCAGAGCCTGTTCTGTTCTCCGCATGCAATTATGCATGCGAAAATCTCGGCATTGATGGA\nCACAAGTACATCGGATCTCGTACAAGTAAATAAGGAGCCGTATAAAATTATGTTATCCGA\nCCGACACCCAATCGCCTCAACTATATGTTTTCCCTTGTCCAGATACTTAGTGGGAGATAT\nGTCCCCAGCGGCGCTTCCTGGGTTATTGTTTACGCTTCCCGCTGAACCCCCCGGGACCAA\nCTTGGTAGTTTGTACCGTTTCACTCCCCAGTCATTTATCCAGAGTAAGCAAACGGGCCAG\nACCGGGAGAAACGGTTAATCTGCCGTTTGTTATGGTTCTGAGAAATGTATATATAATGCT\nTATTAATACAATTATATTTCTTAAAACTAACAACTGGCACGCGGGCTGGAACACACTGTC\nATTTTGTAATGATGTATTTAAACAGAAATTACAAAAATCCGAGTGTATAAAACTACGCGA\nAGTACCTGGGATTGAAGACACGTTATTCGCCGTGCTTAAACTTCCGGAGCTTTGCGGAGA\nGTTTGGAAATATTCTGCCGTTATGGGCATGGGGAATGGAGACCCTTTCAAACTGCTTACG\nAAGCATGTCTCCGTTCGTATTATCGTTAGAACAGACACCCCAGCATGCGGCACAAGAACT\nAAAAACTCTGCTACCCCAGATGACCCCGGCAAACATGTCCTCCGGTGCATGGAATATATT\nGAAAGAGCTTGTTAATGCCGTTCAGGACAACACTTCCTAAATATACCTAGTATTTACGTA\nTGTACCAGTAAAAAGATGATACACATTGTCATACTCGCGTGTACGTGTTTTTCTTTTTTA\nTATATGCGTCATTTATTACCACATCCTTTAATCCCGCCTTTATCTCCCTAAAACGGAGTG\nGTAATATTAAAAGCCGCCAAGCCTGTTGGTGGGTGAGGAGGGGTAAAGGCACGCTGTGTG\nCATAACGTTGCGGTGATATTGTAGCGCAAGTAACAGCGACTATGTTTGCGCTAGTTTTAG\nCGGTGGTAATTCTTCCTCTTTGGACCACGGCTAATAAATCTTACGTAACACCAACCCCTG\nCGACTCGCTCTATCGGACATATGTCTGCTCTTCTACGAGAATATTCCGACCGTAATATGT\nCTCTGAAATTAGAAGCCTTTTATCCTACTGGTTTCGATGAAGAACTCATTAAATCACTTC\nACTGGGGAAATGATAGAAAACACGTTTTCTTGGTTATTGTTAAGGTTAACCCTACAACAC\nACGAAGGAGACGTCGGGCTGGTTATATTTCCAAAATACTTGTTATCGCCATACCATTTCA\nAAGCAGAACATCGAGCACCGTTTCCTGCTGGACGTTTTGGATTTCTTAGTCACCCTGTGA\nCACCCGACGTGAGCTTCTTTGACAGTTCGTTTGCGCCGTATTTAACTACGCAACATCTTG\nTTGCGTTTACTACGTTCCCACCAAACCCCCTTGTATGGCATTTGGAAAGAGCTGAGACCG\nCAGCAACTGCAGAAAGGCCGTTTGGGGTAAGTCTTTTACCCGCTCGCCCAACAGTCCCCA\nAGAATACTATTCTGGAACATAAAGCGCATTTTGCTACATGGGATGCCCTTGCCCGACATA\nCTTTTTTTTCTGCCGAAGCAATTATCACCAACTCAACGTTGAGAATACACGTTCCCCTTT\nTTGGGTCGGTATGGCCAATTCGATACTGGGCCACCGGTTCGGTGCTTCTCACAAGCGACT\nCGGGTCGTGTGGAAGTAAATATTGGTGTAGGATTTATGAGCTCGCTCATTTCTTTATCCT\nCTGGACTACCGATAGAATTAATTGTTGTACCACATACAGTAAAACTGAACGCGGTTACAA\nGCGACACCACATGGTTCCAGCTAAATCCACCGGGTCCGGATCCGGGGCCATCTTATCGAG\nTTTATTTACTTGGACGTGGGTTGGATATGAATTTTTCAAAGCATGCTACGGTCGATATAT\nGCGCATATCCCGAAGAGAGTTTGGATTACCGCTATCATTTATCCATGGCCCACACGGAGG\nCTCTGCGGATGACAACGAAGGCGGATCAACATGACATAAACGAGGAAAGCTATTACCATA\nTCGCCGCAAGAATAGCCACATCAATTTTTGCGTTGTCGGAAATGGGCCGTACCACAGAAT\nATTTTCTGTTAGATGAGATCGTAGATGTTCAGTATCAATTAAAATTCCTTAATTACATTT\nTAATGCGGATAGGAGCAGGAGCTCATCCCAACACTATATCCGGAACCTCGGATCTGATCT\nTTGCCGATCCATCGCAGCTTCATGACGAACTTTCACTTCTTTTTGGTCAGGTAAAACCCG\nCAAATGTCGATTATTTTATTTCATATGATGAAGCCCGTGATCAACTAAAGACCGCATACG\nCGCTTTCCCGTGGTCAAGACCATGTGAATGCACTTTCTCTCGCCAGGCGTGTTATAATGA\nGCATATACAAGGGGCTGCTTGTGAAGCAAAATTTAAATGCTACAGAGAGGCAGGCTTTAT\nTTTTTGCCTCAATGATTTTATTAAATTTCCGCGAAGGACTAGAAAATTCATCTCGGGTAT\nTAGACGGTCGCACAACTTTGCTTTTAATGACATCCATGTGTACGGCAGCTCACGCCACGC\nAAGCAGCACTTAACATACAAGAAGGCCTGGCATACTTAAATCCTTCAAAACACATGTTTA\nCAATACCAAACGTATACAGTCCTTGTATGGGTTCCCTTCGTACAGACCTCACGGAAGAGA\nTTCATGTTATGAATCTCCTGTCGGCAATACCAACACGCCCAGGACTTAACGAGGTATTGC\nATACCCAACTAGACGAATCTGAAATATTCGACGCGGCATTTAAAACCATGATGATTTTTA\nCCACATGGACTGCCAAAGATTTGCATATACTCCACACCCATGTACCAGAAGTATTTACGT\nGTCAAGATGCAGCCGCGCGTAACGGAGAATATGTGCTCATTCTTCCAGCTGTCCAGGGAC\nACAGTTATGTGATTACACGAAACAAACCTCAAAGGGGTTTGGTATATTCCCTGGCAGATG\nTGGATGTATATAACCCCATATCCGTTGTTTATTTAAGCAAGGATACTTGCGTGTCTGAAC\nATGGTGTCATAGAGACGGTCGCACTGCCCCATCCGGACAATTTAAAAGAATGTTTGTATT\nGCGGAAGTGTTTTTCTTAGGTATCTAACCACGGGGGCGATTATGGATATAATTATTATTG\nACAGCAAAGATACAGAACGACAACTAGCCGCTATGGGAAACTCCACAATTCCACCCTTTA\nATCCAGACATGCACGGGGATGACTCTAAGGCTGTGTTGTTGTTTCCAAACGGAACTGTGG\nTAACGCTTCTAGGATTCGAACGACGACAAGCCATACGAATGTCGGGACAATACCTTGGGG\nCCTCTTTAGGAGGGGCGTTTCTGGCGGTAGTGGGGTTTGGTATTATCGGATGGATGTTAT\nGTGGAAATTCCCGCCTTCGAGAATATAATAAAATACCTCTGACATAAAAAACATGTATAA\nTAAAAAGTCACTATAAACGTATTAATAATACACACTACCTTTGGGTTTTTTTCCCGTCCC\nCAAATGGTGTTTGGTGCACTCTACCAAAAAATAGAGCGCCTAAATATGCTATATAACGCC\nTCCCAGCAAAATACGGTTCAAAGGCATTACCCGATATTGTATTGTAGTACAGGGCAATGG\nGAATTGATGATCCCAATAAACGGCATAGACGCACAGCGCCGTTATAGCAGGGGTCTCCAG\nAGTACAGGGTATCTAAGTACCGGGATATCTCATACTCATGCCTTTCCGTGACAGAAACAT\nCAACCGGAACAGTATCCGATAAACCAACTCCTGTTTTTGCAAGGCGTAAAATTCGCACAC\nCTTCCTTTTTTGCAAGATGTGACGTTTCCTTGTAACAGGGAAGCTGGGGGAGTGGTAAGA\nACAACAAAGTTTCAGCCAACGTGCCAATAAAGCCCACTTCCCTCAAGAGGCTGTTTGCTG\nTATCCACAATGGTCCGTATTAAATCTTGAGCAACTTGATCCGTGTCATCATCACTGGGTA\nACGCGTTAACATAACTACGCGTTAAATCTTCAATAACGGCATAACAATTAAACGCTTCCC\nACCGAGACAGTATATATTGAACAATCACGAACCGTTGACAGGACGTCAGATCACGTCCGT\nAAGCATGCCCGAAAAATGGAAGTTCCCCCCGTTCGCCATATACCGCAACAACTGCAGTAT\nATATCGTCTCACGGGCTTCATTAAGTTCATCTTCAAGTCCAGGCCATTTTCTGGCTTTAA\nATATAACCTCGTCCGCAAAAAAAACCGCACATGATAACGCGCGGATACAATGAGTAGTGG\nCTTTATGGCGAGGATCCCAAATGTCCATTACCCGGGGGATGGTCCTAATCTGTACAAAGT\nTACTTAGTGTAATATGATCGGACTTCTTACGCCGTCTAGGCTGTTTCTCAGAATACGGTT\nCACCCGAAATCGGCACATCATCTGCTTTTACGTCTTCCGTAACCACATCAGCAGCGCGCC\nGACTAACAATTATACTTGTTTTTTCATCGTCGTTACTTCCGTTAAGCGCGTCTCGTATCT\nCGGGCGTCCCGTCGAATAATCCACTCACTAGCTCCTGCAAACCTTCTGGTAACTCCAACA\nTACGCATATACACCAATGAAAAACTGGCTTCGTTTGGTACGTACATAAAGCCATTTGTGG\nTATACAATTTTAGCTTATTCTCGCGCGTAACATCTACCCCCGCCACCAATGTTAAATGCG\nTCACGGGGAGGGACACGAGATAATCTGCGAGCGTAGGGTCCTCCACTTCAACATCAAATG\nTTCCGCAAAGGTCGCGATCCACCGCCCCCGATCCCGCTGCAAGTAAGGCCACTCGATCCA\nAAAACACGCAGTTATTATTGGATGATACCGCCCATGTCTTCCCGGTGCGATTGAGCTCAC\nTTCGAACGTAACTGGCAACAGATCTGTCACCGGGTCCGACCCCGCGAACAACATGTCCAA\nATTTTGCGATCTCGCCTCCATGTTTGCGGGGTATGGAAATTAAGCATCCCCCGCATATAA\nAATACGCCCTGGTAGCACGCTCGTTAAAATAAAACGTTACGCCGTTATAAGATACGGTTG\nAATGATATGGAAATTCCATATTAAAGCGTTTATCGGAACATTAACCTCGAACTTGCCGTC\nCCGTGATCGTGTGATCGCCATGAGAAATATATAACTACACGCAAACATTCAAAACACCGT\nGGTATCATTAACGTCATATGAAAAGATCCAATCAATCCAATCAACCACACCTCCTACCGT\nTTAGCACGTCAGCTATGTGACATGCTCCAAACATACGTAAACATTTAGAGAGGGTGTTAT\nAACAGTCTGTCAGGCGGGGTATATTCTACATAATACAAGGATCGGCTTTAACTTTGTCAA\nCATTTTTACTTTGGACTATAAACTGCGACTGAACGTTATGAACCCACCCCAAGCCCGCGT\nCTCGGAACAGACAAAGGACTTGCTTAGCGTTATGGTTAACCAGCACCCCGAAGAGGACGC\nAAAAGTGTGTAAATCCAGTGATAATTCACCGCTTTATAACACCATGGTTATGTTATCGTA\nTGGGGGTGATACGGACTTACTATTAAGCTCTGCATGTACCCGCACATCTACCGTAAACAG\nGTCGGCGTTTACGCAACACTCCGTGTTTTATATTATATCCACGGTGTTGATTCAACCAAT\nATGTTGTATCTTCTTTTTTTTTTACTATAAAGCGACACGCTGTATGCTCTTATTCACAGC\nCGGGTTACTTCTGACGATTCTACATCACTTTCGACTTATTATTATGTTATTGTGTGTCTA\nCAGAAATATACGATCAGACCTGCTACCCTTATCTACATCCCAGCAACTGCTGCTTGGAAT\nTATTGTTGTGACTCGAACAATGCTATTTTGTATTACGGCGTATTATACTCTTTTTATAGA\nCACCCGGGTGTTCTTTTTGATTACCGGACACTTGCAAAGTGAGGTTATTTTTCCAGATAG\nCGTTTCAAAAATACTTCCTGTGTCGTGGGGTCCAAGTCCAGCCGTGTTACTGGTAATGGC\nGGCAGTTATTTACGCTATGGACTGTTTGGTGGACACGGTATCCTTTATTGGGCCAAGGGT\nGTGGGTCCGTGTTATGTTAAAAACATCTATTTCGTTTTAGTCCATTTCAATAAATGTACT\nATAATTGTTCAGTCTAAAAATAATGTTGGGTATTTATAATTACCGCCCCCGTGTTACTTG\nGAAACACCCATACATATGTTCCACTCTACATCAAACTTCTCGCAGTTTTCTTGTTCCCGC\nACACGTTTACACGTCCGGATTCAAGTCGCAACGCTGCTGACAAAATGACAACGGTTTCAT\nGTCCCGCTAACGTGATTACTACAACGGAATCTGATCGTATTGCTGGGTTATTTAACATCC\nCAGCGGGGATCATTCCAACTGGAAATGTGCTGTCAACCATAGAGGTGTGTGCACACCGTT\nGCATTTTTGATTTTTTTAAACAAATACGATCAGATGATAACAGCCTTTACTCGGCTCAAT\nTCGATATTCTTTTGGGGACATACTGCAATACATTAAACTTTGTGCGTTTTCTAGAACTTG\nGACTGTCTGTCGCTTGCATCTGTACTAAATTTCCGGAGCTGGCTTACGTGCGAGATGGCG\nTTATTCAATTTGAGGTACAACAACCCATGATAGCACGTGATGGCCCACATCCCGTCGATC\nAGCCTGTTCATAATTATATGGTTAAGCGGATACACAAGCGTTCGTTAAGCGCTGCGTTTG\nCAATTGCATCGGAAGCGTTGAGTTTGTTAAGTAACACATATGTCGATGGGACAGAGATTG\nACTCATCGTTACGTATAAGAGCTATCCAACAGATGGCTCGTAATTTACGCACCGTTTTGG\nACTCATTTGAACGAGGCACTGCCGATCAACTTCTTGGTGTTCTATTGGAGAAAGCCCCAC\nCGCTATCGCTGCTTTCACCAATTAATAAATTCCAACCCGAGGGACATCTAAATCGTGTTG\nCACGCGCGGCCCTACTTTCGGACCTCAAACGTAGAGTCTGTGCGGATATGTTTTTTATGA\nCCCGACACGCCAGGGAACCTAGGCTGATCTCTGCGTATCTGTCGGATATGGTTTCGTGCA\nCCCAACCATCGGTGATGGTATCACGAATAACTCATACAAACACTCGCGGACGGCAGGTTG\nACGGTGTGTTGGTAACAACAGCAACCTTAAAACGGCAACTATTACAGGGAATTTTACAAA\nTTGACGACACCGCCGCTGACGTACCAGTAACATATGGCGAAATGGTTCTACAGGGGACAA\nACTTGGTAACCGCCCTTGTGATGGGAAAGGCCGTCCGCGGAATGGATGATGTAGCCCGCC\nATCTCCTTGATATAACCGACCCTAACACGTTAAACATACCGTCTATACCCCCACAATCCA\nACTCCGATTCAACGACAGCTGGGCTTCCGGTTAACGCCCGTGTTCCTGCGGATTTAGTGA\nTTGTTGGGGATAAACTTGTATTCTTAGAAGCATTAGAACGGCGGGTCTACCAAGCTACGC\nGCGTTGCCTACCCTCTTATTGGAAATATAGATATTACGTTTATCATGCCAATGGGAGTGT\nTTCAGGCAAACTCCATGGACAGATATACACGACACGCCGGCGATTTTTCAACTGTATCCG\nAACAGGATCCACGTCAATTTCCACCCCAAGAGATTTTTTTTTATAATAAAGATGGGATAT\nTAACACAGTTGACTCTTCGTGATGCAATGGGTACCATCTGCCACAGTTCATTGCTTGATG\nTTGAGGCCACACTTGTTGCCCTCCGCCAACAACATTTAGATCGTCAGTGTTATTTTGGTG\nTATACGTGGCCGAGGGTACAGAGGACACATTGGATGTTCAAATGGGGAGGTTTATGGAAA\nCGTGGGCAGATATGATGCCTCATCACCCTCATTGGGTAAACGAACATTTAACAATTCTAC\nAGTTTATAGCTCCGAGCAACCCGCGTCTAAGGTTTGAATTAAACCCCGCCTTTGATTTTT\nTTGTTGCACCGGGGGACGTAGACCTTCCCGGACCGCAGCGTCCCCCGGAAGCCATGCCAA\nCCGTTAACGCAACATTACGGATTATCAACGGAAACATTCCCGTGCCTCTATGTCCCATTT\nCATTTCGAGACTGTCGCGGAACCCAACTCGGTTTGGGAAGACATACAATGACCCCGGCAA\nCCATTAAAGCCGTAAAGGATACATTTGAAGACCGCGCATACCCAACTATTTTCTACATGC\nTAGAGGCTGTTATTCATGGAAACGAAAGAAACTTCTGTGCGTTACTGCGACTGTTAACAC\nAGTGTATTCGCGGGTATTGGGAGCAATCCCACAGGGTGGCATTTGTAAATAACTTTCACA\nTGTTAATGTACATAACTACATATCTCGGAAACGGTGAGCTTCCCGAAGTCTGTATTAATA\nTATATCGGGATTTACTGCAGCATGTAAGAGCATTACGCCAAACTATAACCGATTTTACAA\nTACAAGGAGAGGGCCATAACGGCGAGACCTCGGAAGCGCTAAATAACATCCTTACGGATG\nACACGTTTATTGCACCTATTCTATGGGATTGTGATGCGTTAATATACCGTGATGAAGCCG\nCCCGAGACCGACTCCCCGCAATTCGTGTAAGCGGGCGAAACGGATACCAAGCCCTTCACT\nTTGTGGATATGGCCGGGCATAACTTCCAACGACGCGATAATGTGTTAATCCACGGGAGAC\nCCGTTCGGGGAGACACGGGTCAGGGTATTCCCATTACCCCACACCATGACCGTGAATGGG\nGTATTCTCTCCAAGATTTACTACTATATTGTCATTCCTGCATTTTCCCGCGGTTCCTGTT\nGTACAATGGGCGTGCGTTATGATCGCCTATACCCTGCGTTACAGGCAGTTATCGTTCCGG\nAAATTCCCGCTGATGAAGAAGCCCCAACTACCCCAGAAGATCCAAGACACCCTCTTCACG\nCACACCAACTCGTTCCGAACTCTCTTAACGTTTACTTCCATAATGCACACCTAACCGTTG\nATGGTGATGCATTGCTCACACTACAAGAGTTAATGGGAGATATGGCTGAACGAACGACGG\nCCATTTTAGTATCAAGCGCCCCCGATGCGGGAGCCGCCACGGCAACAACCAGAAATATGA\nGAATATATGACGGAGCGCTTTACCATGGCCTTATTATGATGGCATATCAGGCGTACGATG\nAAACCATTGCAACGGGTACTTTTTTTTATCCCGTTCCGGTCAACCCTCTGTTTGCATGTC\nCGGAACATTTGGCATCATTGCGTGGAATGACAAATGCTAGGCGGGTTTTGGCAAAAATGG\nTACCACCAATCCCTCCTTTTCTGGGAGCCAACCACCACGCAACTATACGCCAACCCGTTG\nCCTACCATGTAACGCATAGTAAGTCGGATTTTAATACTCTTACATATTCTCTTCTTGGAG\nGGTATTTTAAGTTTACACCAATAGCTCTTACACATCAACTACGAACGGGATTTCACCCCG\nGGATTGCCTTTACCGTAGTGCGCCAGGATCGCTTTGCCACAGAGCAACTTTTATATGCCG\nAGCGTGCTTCTGAATCGTACTTTGTCGGACAAATCCAAGTACACCATCATGATGCTATTG\nGGGGGGTAAACTTTACCCTAACCCAACCCAGAGCTCACGTGGACCTGGGAGTTGGGTATA\nCAGCTGTATGTGCCACAGCAGCCCTGCGATGCCCTCTCACGGATATGGGCAATACTGCCC\nAAAATCTTTTTTTTTCACGAGGAGGAGTGCCAATGTTACATGATAACGTTACCGAATCGT\nTGCGTCGTATAACAGCATCGGGGGGTCGCTTAAATCCCACCGAACCCCTACCCATCTTCG\nGCGGACTGCGTCCTGCTACATCGGCAGGAATTGCACGAGGGCAAGCCTCTGTGTGTGAGT\nTTGTGGCCATGCCGGTGTCCACTGACCTACAATATTTTAGAACTGCATGCAATCCTAGAG\nGTCGAGCATCTGGAATGTTATATATGGGTGACCGTGACGCCGACATAGAGGCTATAATGT\nTTGATCACACACAATCGGATGTTGCTTATACAGATCGAGCAACTCTTAACCCATGGGCAT\nCACAAAAACATTCATACGGTGACAGGCTATACAACGGAACATACAACCTTACAGGCGCTT\nCTCCTATCTACAGCCCATGCTTTAAGTTTTTTACACCAGCGGAGGTTAACACTAATTGTA\nATACACTGGATCGGCTTCTAATGGAGGCAAAGGCTGTGGCGTCGCAAAGCTCCACCGACA\nCTGAATATCAATTTAAACGCCCTCCCGGTTCTACCGAAATGACACAGGATCCGTGTGGCC\nTTTTTCAAGAAGCATATCCACCACTATGCTCAAGCGATGCGGCCATGTTACGAACGGCTC\nACGCGGGAGAAACCGGGGCAGATGAAGTTCACTTAGCCCAATATCTGATTCGAGACGCGT\nCGCCCCTTAGGGGATGTCTTCCTCTTCCGCGATAATTTCACCACGCCCACATACCCACTC\nCCAATAAAAGCCCTGTAGAGCGCATTGGCATCTTACTTGAGATTTGGATACGCTCGGCCG\nACTTGGTCTGTTTCACGCTTCCTTAAACAACATGGCTATGCCATTTGAGATAGAGGTATT\nGTTACCAGGAGACCTATCCCCGGCGGAAACATCTGCATTACAGAAATGTGAGGGAAAAAT\nTATTACCTTCTCAACCCTGCGTCATCGAGCTTCACTGGTGGATATAGCGCTGTCGTCATA\nTTACATTAACGGTGCTCCACCAGACACGCTCTCGCTGTTAGAGGCATACCGAATGCGATT\nCGCGGCAGTTATAACACGGGTCATCCCGGGAAAGTTGTTGGCGCATGCCATTGGCGTGGG\nTACTCCTACACCCGGGTTGTTTATTCAAAATACATCCCCCGTTGATCTTTGTAATGGCGA\nTTACATCTGCTTACTTCCTCCGGTTTTCGGGTCCGCAGACTCAATTCGCTTGGACTCTGT\nAGGACTGGAAATTGTTTTCCCTTTAACCATCCCCCAGACCTTAATGCGAGAAATCATCGC\nCAAAGTGGTTGCACGGGCCGTTGAGCGCACGGCCGCGGGTGCTCAAATTTTACCCCACGA\nAGTTCTACGAGGCGCGGATGTCATTTGTTACAATGGAAGGCGTTATGAACTCGAAACAAA\nTTTACAACATCGGGACGGATCGGATGCGGCTATTCGCACATTGGTTTTAAATCTAATGTT\nTTCCATAAACGAGGGATGTCTGCTTTTATTGGCGCTGATTCCAACTTTGTTAGTCCAAGG\nAGCACACGACGGTTATGTAAATTTATTGATACAAACGGCCAATTGCGTTAGAGAAACCGG\nCCAGTTAATTAATATACCGCCAATGCCGCGGATTCAAGACGGCCATCGCCGATTTCCCAT\nATATGAAACTATTTCATCTTGGATATCAACATCATCTAGACTGGGGGATACCTTGGGAAC\nTCGCGCAATTTTACGCGTCTGTGTGTTTGATGGACCCTCTACTGTTCATCCGGGAGACCG\nCACAGCCGTGATTCAAGTGTAAACAGGTGTTAATAAAAACACAACCAGTCTAGTTACATT\nTCACGCGTCTTGTTTTTATTTAATAGGCATAAACACGGAATCCGGTATACATGAACTGCC\nAATATACACGGACATAATTAATGCAACCATCAGATCATCTGACATTGTTCCCGTGGTACC\nTTTACCCGTGTAAGTTTTTGTGTCTAGATGACCCATACCGCCTTTAATTACCTCTGTCAG\nGTTATCCAACTGTTTACATAGATACTCCACGGGGTCTACACCTAACTTTACTGTTAGGGA\nTACAAGCTCCTGTGAGGCTATTATATTTCCGGAGTTAAATCGTTTAACAAAATAGTCTAC\nGGCCGGCGTTTTTTGTTTTTGTAATAAAAAAAAAGGGTACGCCACGCTACATCCGGGAGG\nTATGGAATGATAAAACAGTAACACTGGAGCGGAAGATAGCACGTTTCCCTTTTCGAGGAC\nAGCAAACTGTTGTGCTATAGCCAACGATATGGCAACTGCAGAATCCTGGCTGCTGTTTCC\nCTCTATAGAAACGTGTACGTTTGTAAATGTATTGGGGTGTAAAGCGAGTATGTGGCCTAA\nGCATTGAGTAACGCAACGCCCTATCTCACTGGAAGACGTGCCAGTTAAAGCTCTAAGAAA\nAAAGTGCTCCAATCCAAATATAATCCAATCCGACTTATAACGACCAACAATCGCTACACC\nAGTACCAGACGCTCCTGCATTTACCTCAAATACACGAGCGTCTGGTACTGGTGTAGCGAC\nAACGGTTGACGGCCGATATAAAATAAACCTCTCACGGGCAGTTTTTGTAAATAATGGCCG\nGTCAAACCCCACACCCCCAGAATTCTGTTTACGCCCACCTACAATTTCCTGCACGAAGGA\nGTCGGCCATAAATAAATCTGCAGTGCGCCGCATGGCTCCATCCATTGTGATGAAAACCGG\nCTTATTTAATACATAACACGAACAAGCTGTGACATCGCTATGTGCTAAAACACGCGGCAT\nGTGATCGTCGCATACATATGTAACAACGTTTAACAACTGATCCGACGATCCACGTAAGTT\nATACAAAAAACTTGTACTTGCTTTTCCGGTATTTGTTGATGAAACAAAAATAATTTTACA\nATTGGTTTGATTTAAAAATCCGACTATAGTTTGTACAGCATCAGGTCGAATAAAATTAGC\nTTCATCCACAAACAGAAGATTAAAATCTTGACCTCGGATACCCTGGAACGATAGAAAGAT\nATATAGTTACCCCACCAAAGTTTAAATGTATCCTTAAATACCACGTACGTAAAAAATGTT\nTGAATACGTACATATTTCTTTTTTTTTTTTCCAGTACAACCATATCCGGTGTATAATGGA\nAGCCCATTTGGCAAATGAAACCAAACATGCACTTTGGCATAATGATCACACAAAAGGATT\nACTACACGTTGTGATACCTAACGCGGGGCTTATTGCGGCCGGAATAGATCCCGCATTACT\nGATTTTAAAGAAACCCGGACAACGCTTCAAGGTTGAAGTACAAACAAGATATCATGCTAC\nAGGTCAATGCGAACCGTGGTGTCAAGTTTTCGCCGCGTACATTCCCGATAACGCCTTAAC\nAAATCTCTTAATACCAAAAACGGAACCATTTGTTTCACACGTTTTTTCGGCCACGCATAA\nTTCAGGGGGATTGATTTTATCATTGCCTGTTTATCTTAGCCCCGGTTTATTCTTTGATGC\nATTTAACGTTGTAGCGATACGAATAAATACTGGAAACCGCAAGCACCGTGATATTTGTAT\nTATGTATGCAGAACTAATCCCAAACGGAACGCGTTATTTTGCTGATGGACAACGGGTACT\nTTTATTATGCAAACAGCTGATTGCGTATATCCGATGCACCCCTCGTCTTGCATCGTCTAT\nAAAAATATACGCAGAGCATATGGTGGCAGCCATGGGTGAATCACACACGTCAAATGGGGA\nCAATATTGGACCCGTTTCATCCATAATCGATCTTGATCGACAGTTAACTTCTGGAGGTAT\nTGATGACTCCCCTGCTGAAACACGCATACAGGAAAATAATCGGGACGTCCTTGAGCTAAT\nAAAACGGGCCGTAAACATTGTTAACTCCAGGCACCCCGTCCGACCTTCTAGTTCCCGCGT\nTGCATCTGGGTTGCTTCAAAGTGCAAAGGGCCACGGAGCGCAAACTTCCAACACAGATCC\nGATCAATAACGGTTCCTTTGATGGCGTCCTTGAGCCGCCTGGACAAGGGCGATTTACGGG\nAAAGAAAAACAATTCGTCCGCCAGCATCCCACCTTTACAAGACGTTCTATTGTTTACCCC\nAGCTTCGACAGAACCCCAAAGTCTTATGGAATGGTTCGACATCTGTTATGCCCAATTAGT\nTAGCGGGGACACTCCAGCAGATTTCTGGAAACGGCGTCCCCTATCAATTGTACCGCGACA\nTTACGCAGAATCCCCCAGTCCGTTGATTGTAGTATCTTACAACGGATCCTCTGCCTGGGG\nAGGACGTATTACCGGAAGTCCAATTTTATATCACTCTGCACAGGCTATTATTGATGCTGC\nGTGTATAAATGCCCGGGTTGACAATCCCCAAAGCCTACATGTGACAGCTCGCCAAGAGCT\nAGTCGCGCGTTTACCGTTTTTGGCTAACGTCCTAAATAATCAAACCCCCTTACCCGCCTT\nTAAACCAGGCGCCGAAATGTTTTTAAACCAGGTATTTAAACAAGCGTGTGTGACATCGCT\nAACCCAAGGTCTTATAACGGAGTTACAAACGAACCCGACTCTACAACAACTCATGGAATA\nTGATATTGCAGATTCTTCCCAAACGGTTATTGATGAAATTGTAGCCCGCACACCAGACCT\nGATTCAGACTATAGTTTCGGTGTTAACGGAAATGTCAATGGATGCGTTTTATAACAGCTC\nCTTGATGTATGCGGTTTTGGCGTATCTGTCATCTGTATATACACGACCACAAGGTGGGGG\nGTATATACCCTACCTTCACGCTTCCTTCCCATGCTGGTTAGGTAATCGTTCTATATATTT\nATTTGACTATTATAATTCAGGAGGGGAAATACTTAAGCTTTCCAAGGTCCCCGTTCCCGT\nAGCCTTAGAAAAGGTTGGTATTGGTAATTCCACACAACTGAGGGGTAAATTTATACGCAG\nCGCGGATATTGTTGATATTGAAATTTGTTCTAAGTATTTACCCGGTCAATGTTACGCGTA\nCATTTGTCTAGGATTTAACCAGCAATTACAATCCATTTTAGTTTTACCGGGGGGATTTGC\nGGCATGTTTTTGTATTACCGATACCCTACAGGCAGCACTACCTGCATCGTTAATCGGACC\nTATTCTAGACAGATTCTGCTTCTCTATTCCCAACCCCCATAAATAAATTAGTGTCACTAT\nAAAAACATAACACCAGAATCTCTTCATATTTAATTTTACGTCATTTCTCCCGTTTCCACC\nGGGTGGGTGGCATTAAACCCACAAGTACCCGGGCGGCAATCCGCTAGACTGTTTTTCTGC\nTCATGGAATTACAACGCATATTTCCGCTGTACACCGCTACGGGTGCAGCGCGCAAATTAA\nCCCCCGAGGCAGTTCAGAGACTCTGCGATGCATTAACGCTGGATATGGGATTATGGAAGT\nCCATCCTGACCGATCCCCGGGTGAAAATAATGCGATCAACTGCTTTTATAACTTTAAGGA\nTCGCTCCGTTTATCCCCCTTCAAACGGATACTACTAATATTGCCGTTGTTGTAGCCACAA\nTTTACATCACGCGCCCACGTCAGATGAACTTACCTCCGAAGACTTTTCATGTAATTGTAA\nATTTTAATTACGAGGTCTCGTACGCAATGACGGCGACTTTAAGAATTTATCCGGTTGAAA\nACATAGACCATGTTTTTGGAGCAACGTTTAAGAACCCGATCGCGTACCCCCTTCCAACAT\nCTATTCCGGATCCTCGAGCAGATCCCACCCCCGCAGATCTTACACCAACGCCAAACTTAA\nGCGACTACTTACAACCCCCGCGGCTTCCGAAAAATCCATACGCATGTAAAGTTATTTCTC\nCGGGAGTGTGGTGGTCAGACGAACGAAGGCGTTTATATGTACTGGCTATGGAACCTAATT\nTAATAGGGCTATGTCCCGCCGGATGGCATGCTCGGATACTTGGCTCTGTATTAAATCGAC\nTCCTCAGCCATGCGGACGGATGTGATGAATGTAATCATAGAGTTCACGTGGGGGCACTGT\nATGCGTTACCCCATGTCACAAATCATGCGGAAGGTTGTGTGTGTTGGGCTCCGTGTATGT\nGGAGAAAGGCCGGTCAGCGGGAATTAAAAGTGGAGGTAGACATTGGCGCCACGCAGGTTC\nTTTTTGTAGATGTCACCACCTGCATTCGAATTACGAGTACTAAAAATCCTCGCATTACCG\nCAAATCTTGGCGACGTTATAGCGGGAACCAACGCCAGTGGTCTCTCTGTACCAGTAAATT\nCATCTGGGTGGCAGCTTTATATGTTTGGAGAAACATTAAGCCGGGCTATTATTAACGGCT\nGTGGTCTGCTTCAGCGAATTTGCTTCCCCGAGACACAAAGATTATCGGGTGAACCGGAAC\nCTACAACCACCTAGTATACCTTAACTATATGTCAACATTTACAGTAATATATTAAAGGTT\nAAATTTATAAAACACTCACGTTTGTGTTGTGACTTGACGCGAACACCGCTGTGCTGTAAG\nACCCGTCGGTAAATGAAAACGTAATAGATTCGCCTTTTACATGATCCACGTAATTTGCCC\nCAAACCACTGTTCCAGGCGAGACTTGATACCCTCAAACACGGGTTCCGTTGCTTTGCGTA\nTATGAGCCGTATAACCCACTTTAATTCCTCTAAACGTGGCCATTACTAAAGCTATTAATG\nGTACAAGAAACCATGTTTTCCCATGTCTACGTGGTACCAAAAACACAGTTGATTTTTGTT\nTGAAGTGTTCTAAAACACTGTCAGAAACACTTGGCGTGTTAAACACTGTACGCAGAAAGC\nAGTCAACTCTGTCGGCATGATCGCCCAATAGCACCGATGAAATAAAATGCGTGGTGTGCA\nTGAGGATCATTTTTTGAAACAGTTCCAACGTCCCCTTATATCTGCCATAGATTGGAACGT\nCAACCTTTGCGCGTTTGCCATGACTTCCACACTCTTCAATACTCTCAAAAGATGTTTCCA\nCAAGGTACGAAAACCGTTGTGTAAAGGTAGACAACTGACAGAAACTATCCGACAGAGAAA\nACGCGCGAAATGTGTTCATAACCCCGCTATACGCATTTCGATGAGGTGCTGCTTCTTCCG\nGTGAATATTCATAAAACTGTACACTACTGACAGCCTTTTTTAATTCAGGGCTTACGTTTG\nCATTTACCGAATATCGCCATGGTTTCAAAACTACATTGGGGGTACAGTTGTACCCTGTTG\nACGATAGAAACGCGCCAAACATTGCCCGTCGAGCAGTAGCCGAGAACAGTGGAATATATT\nCACAACAGTTGTGAAGCGTTCCAATTCCGGGAATAACGGCCTGATGACGTCGGGTTACAT\nCTATAGCAAAATTCAGAAACGGGATTTGGGTTGCGTTTCCCAGAGACCCTTGCCGCGTGG\nAACACGGGGTAGGGGACTCCAACGTCTAAAGCGTCGTAGGGATGAACGCTTTGGGACGTT\nGGAGTCCCCTACCCCGTGTAAGCAGTAAAACAGGAAGCCGCGTCATCTTACGTACTCGTT\nACGTATATATCATAAACATTTTCAGGGCCGCATTCATTCACTTTGGTCATGTCAGGCCAC\nACTCCAACCTACGCTTCTCATAGGCGTAACCGTGTCAAACTAGTTGAGGCGCATAACCGC\nGCGGGGTTATTTAAAGAACGGACCCTCGATCTAATCCGTGGGGGTGCGAGTGTACAAGAT\nCCAGCATTTGTGTATGCCTTTACTGCTGCCAAAGAGGCCTGCGCCGATTTAAATAACCAG\nCTCCGCTCTGCAGCTCGCATAGCTTCAGTTGAACAGAAGATTCGTGATATACAATCCAAG\nGTTGAGGAACAAACAAGTATTCAACAGATTTTAAATACAAACAGACGCTATATAGCACCC\nGATTTTATTCGCGGTTTGGATAAAACAGAAGACGATAATACCGATAATATAGACAGACTG\nGAAGACGCGGTAGGACCGAACATCGAACACGAAAATCATACTTGGTTTGGAGAAGACGAC\nGAAGCGTTACTTACACAATGGATGCTGACGACACACCCCCCAACCTCCAAATATCTCCAA\nCTGCAGGACCTTTGCGTTCCCACCACAATACCGACGGACATGAACCAAATGCAACCACAG\nCCGATCAGCAAGAACGAGAATCCACCAACCCCACACACGGATGTGTAAATCATCCATGGG\nCCAATCCGTCAACTGCAACATGCATGGAATCACCAGAACGATCACAACAGACAAGCTTAT\nTTTTATTAAAGCACGGCTTAACGAGAGATCCAATACATCAACGCGAAAGGGTGGACGTTT\nTTCCACAATTTAACAAACCCCCATGGGTTTTTAGAATTTCCAAATTATCCCGTTTAATTG\nTACCCATCTTCACGCTCAATGAACAGTTATGTTTTTCTAAATTACAGATTCGAGATAGAC\nCCAGGTTTGCGGGACGGGGAACGTATGGGCGTGTTCATATATACCCATCGTCAAAAATAG\nCTGTAAAAACCATGGACAGTCGTGTTTTTAATAGAGAGTTAATTAACGCGATTTTAGCGA\nGTGAGGGTTCTATACGAGCAGGGGAAAGGCTAGGTATTTCTAGCATAGTTTGCCTTTTAG\nGTTTTTCGTTACAAACCAAACAGCTACTGTTTCCGGCATACGACATGGATATGGATGAAT\nACATTGTTCGCCTGTCCAGACGGTTGACAATACCTGATCACATAGACAGAAAAATTGCCC\nATGTATTTTTAGATTTGGCTCAAGCGTTGACGTTTTTAAATCGAACGTGCGGCCTGACCC\nACCTAGATGTGAAATGTGGCAATATTTTTCTTAACGTCGACAACTTTGCCTCGTTGGAAA\nTAACCACAGCAGTAATCGGAGACTATAGCCTAGTAACATTAAATACGTATTCCCTTTGTA\nCTCGAGCGATATTTGAAGTTGGAAATCCATCCCACCCGGAGCACGTACTACGCGTACCCC\nGGGATGCATCGCAGATGTCATTTCGTTTGGTGTTGAGTCATGGAACAAACCAACCCCCTG\nAAATCTTGCTTGATTATATTAATGGAACGGGCCTTACTAAATATACTGGAACCTTGCCCC\nAAAGAGTTGGACTTGCGATTGATCTTTATGCATTGGGCCAAGCACTCTTAGAAGTTATCC\nTGCTAGGACGTCTTCCCGGACAACTGCCCATTTCAGTACATCGGACCCCGCATTATCACT\nACTACGGTCATAAGTTATCACCAGATTTGGCGCTTGATACGCTGGCATATCGATGTGTCC\nTGGCGCCATATATACTCCCATCTGACATCCCCGGGGACTTAAATTATAATCCCTTTATAC\nACGCCGGAGAGCTGAACACCCGTATTTCCCGGAATTCTTTACGCCGGATATTCCAGTGTC\nACGCAGTGCGTTACGGCGTAACGCACTCAAAGCTTTTCGAAGGCATACGCATTCCGGCCT\nCATTATACCCAGCCACTGTTGTTACGTCGTTGTTGTGTCACGATAATTCAGAAATACGCT\nCGGATCACCCTTTATTATGGCACGATCGGGATTGGATAGGATCGACATAAGCCCCCAGCC\nAGCCAAAAAAATTGCCCGTGTGGGAGGTCTACAGCACCCTTTTGTAAAAACGGATATTAA\nCACGATTAACGTTGAACACCATTTTATAGACACGCTACAGAAGACATCACCGAACATGGA\nCTGTCGCGGGATGACAGCGGGTATTTTTATTCGTTTATCCCACATGTATAAAATTCTAAC\nAACTCTGGAGTCTCCAAATGATGTAACCTACACAACACCCGGTTCTACCAACGCACTGTT\nCTTTAAGACGTCCACACAGCCTCAGGAGCCGCATCCGGAAGAGTTAGCATCCAAATTAAC\nCCAAGACGACATTAAACGTATTCTATTAACGATAGAATCGGAGACTCGTGGTCAGGGCGA\nCAATGCCATTTGGACACTACTCAGACGAAATTTAATCACCGCATCAACTCTTAAATGGAG\nTGTATCTGGACCCGTCATTCCACCTCAGTGGTTTTACCACCATAACACTACAGACACATA\nCGGTGATGCGGCGGCAATGGCGTTTGGAAAAACCAACGAACCGGCGGCACGAGCGATAGT\nTGAAGCATTGTTTATAGATCCGGCTGATATCCGTACTCCTGATCATTTAACGCCAGAAGC\nTACAACTAAGTTTTTTAATTTTGACATGCTCAATACCAAATCTCCAAGTCTCCTTGTGGG\nTACACCAAGAATCGGAACGTATGAATGTGGACTTTTAATCGACGTTCGAACGGGACTTAT\nAGGCGCGTCGTTGGACGTTCTTGTATGTGACAGGGACCCTTTAACTGGCACCCTAAATCC\nCCACCCTGCAGAAACCGACATTTCATTTTTTGAAATTAAATGTCGTGCTAAATACCTCTT\nTGATCCAGATGACAAAAATAACCCGCTCGGTCGGACGTACACCACGTTAATAAATAGACC\nTACAATGGCAAATCTACGGGACTTTTTATATACTATAAAAAACCCATGTGTAAGCTTCTT\nTGGACCCTCAGCAAACCCAAGTACACGCGAGGCCTTAATAACGGATCACGTTGAATGGAA\nACGTTTAGGATTTAAAGGTGGGAGGGCCCTTACAGAACTCGACGCCCATCATTTGGGCCT\nCAATCGGACAATCTCATCCCGAGTGTGGGTATTTAATGATCCGGACATACAAAAGGGGAC\nAATTACAACCATTGCATGGGCCACTGGAGATACGGCTCTTCAAATTCCTGTATTTGCCAA\nTCCGCGGCACGCTAACTTTAAACAAATTGCCGTACAAACCTATGTATTATCCGGTTACTT\nTCCAGCGCTAAAACTACGGCCCTTCCTTGTCACCTTTATAGGACGTGTGCGCCGACCACA\nCGAGGTGGGAGTCCCATTGCGCGTCGATACACAAGCGGCTGCCATTTACGAATATAACTG\nGCCGACTATCCCACCCCACTGTGCGGTTCCGGTTATAGCCGTTCTAACGCCTATCGAAGT\nTGATGTGCCTAGAGTGACACAAATACTTAAAGACACAGGAAACAACGCGATTACATCAGC\nATTGCGGTCATTGCGATGGGACAATCTTCATCCAGCGGTCGAGGAGGAATCTGTGGATTG\nTGCAAACGGTACAACGAGCTTGTTACGTGCAACGGAGAAACCGTTGCTTTGAACTCAGAG\nTTCTTTGAAGACTTTGACTTTGATGAGAATGTAACAGAGGACGCCGATAAATCCACACAA\nCGCCGCCCACGAGTGATCGATGTAACACCAAAACGAAAACCTTCGGGAAAGAGCTCCCAT\nTCCAAATGCGCAAAATGTTAAACCCTGATAAACCCTGATAAACGTTCTAATAAAAACATC\nAAATCATGGTTGGTTACTGTGAATGTTTGTTTTATTGCTTGGGGGTTTACAAGTACAACC\nCACGCTACTCCCACCCACTGTTTGATCGCTCGTATAACAGCTCATCCTCACGGTCCGTTT\nCATATGTTGAGTCATTTTCATAGACGTAGCCGTAGCCTTGTGATGGGTAATTTGTGCGGC\nGAGAATTTCTATGTGCAGGTTTTACTTTTCGTATGTATCCCCGTACCCGCTCGGGTACTC\nTTCTTACGGCACCGTAGAACCGACTGCGTTTCTGTCGATGATACACATATGCACGCATCA\nATCTGAGAAGCAACATGACAACGGAAAACACGGCCAGGCAAGCCAAGGTTCCCCGAGTTG\nTGGGAATTAACCGTGGAGATTGAACCGATATAGGGTCATATAATCGGTCCATATACGAGT\nGCGCGGCGGTTCCCAACGTAGCACAGGCCACGAGCGTTCCCAGGGACGGTCCTATTAACA\nCGTGTATATAATGCGCCAAAATTAATTCTGATACTATAAGATATACAACTGACAATGTAC\nTAAATGTAGACATGGCCACGGACACCGATGACCACAGTCCCGTATGTAGATGATTCGCCA\nCCACAAGTTCCAGCATTAATGATACAAATAGGATACATATCGCCATCAACGCAGCCATCA\nAATTCACGAACACTGCGCGCGTAGGCCCCGCAAGGCGATATAAAAAGACGCTCTGCTGTC\nGTAAATTTGCGACCGCTTTTATGTTCGTTTCGTCCAATTTTCCGCGTCCACAAAAATACG\nTTGTAAATATTACACTTGTCGCAAAATGTCCAAGATATAATGTAGCAGCCACGCCGATTT\nGCTTGTAAGCTAATAATAACACAACGGCGTTTAATAACCACAATGACAAAAGACCCCAAA\nAAAGTGTTGTGGGATCTACAACTAACCATGCAACACCGGAGCTTTGCCGGACACGTTGAT\nTTTTCGTTTCTCGGTGTATAATCGCGGCCGTGATCAGTGTATATACCGCCATGGCCATTG\nCCGTTAAAGCCGTGTAGTAAGTAAATGCCACAACGCTATGTGGTTCCAAAAACAAAACCG\nGGGCGCTGTATCCACCTCTATTTCCGGACCATACCCCCCCATCTAGGGTGGCGTTAAATA\nACTCATAATCAACTACGGCAGCATAAAAACAAGGGATCCCGGTATATTCAGAAGAGGCGG\nCAATTAACGTAGCCAGGAGCATTACCGCACCCAAAGTGAACATCATCACCTGAATTATCC\nAAATTCGCCAATTAAGCGTATCCATTTGATGATCTAACGCTTCCACCTCGGGTGTCGTGG\nTGTCGTACGGTGAGACTTTTTCAGAACGCGGCCCCTTCTTTTGAGTTCCCATGTCTCCCA\nACACCGGGGAGAGCAACGCCGCCGTCTATGCGTCCAGTACACAGCTCGCGCGGGCTTCGT\nGGATTAAACACACCCACCCGGGAATTAGCCTGGAACTGCAATTGGATGTTCCAGTAAAAC\nTAATAAAACCTGGTATGTCACAAACTCGCCCGGTAACCGTCGTACGTGCCCCTATGGGCT\nCTGGTAAAACAACAGCCTTGCTTGAGTGGCTTCAACACGCGTTAAAGGCAGATATTAGCG\nTACTGGTTGTCTCATGTCGCCGTAGCTTTACCCAGACGTTGATTCAACGGTTTAACGATG\nCAGGCCTCTCCGGATTCGTAACATATTTGACATCCGAGACATATATTATGGGTTTTAAAC\nGTTTGATTGTGCAACTTGAAAGCCTACACCGCGTATCCAGCGAAGCTATCGACAGCTACG\nACGTATTAATACTGGATGAGGTAATGTCAGTGATTGGACAATTATACTCCCCCACAATGA\nGACGTCTTTCCGCGGTTGATAGCCTATTATATCGTCTTTTAAATCGCTGTTCTCAAATTA\nTCGCGATGGATGCTACAGTAAACTCTCAGTTTATTGATTTAATCTCCGGATTGCGTGGAG\nATGAAAACATACACACAATTGTGTGTACATACGCGGGAGTTGGGTTCTCCGGAAGAACTT\nGCACGATCCTGCGTGATATGGGCATCGACACGCTTGTGCGAGTCATTAAACGATCTCCTG\nAACACGAGGATGTACGTACCATACACCAACTACGTGGAACATTTTTTGACGAACTAGCAC\nTACGATTACAATGTGGGCATAACATCTGTATATTTTCATCAACTTTATCGTTTTCGGAGC\nTAGTTGCTCAGTTTTGTGCAATATTTACAGACTCTATTCTTATTTTAAACTCAACTCGGC\nCCCTATGTAATGTAAACGAATGGAAACATTTTCGCGTGTTGGTGTACACTACCGTCGTGA\nCCGTTGGATTGAGTTTTGACATGGCTCATTTTCATAGCATGTTTGCTTACATAAAGCCAA\nTGTCATATGGGCCGGATATGGTATCGGTCTACCAATCATTAGGGCGTGTACGGTTATTGC\nTACTTAATGAAGTTTTGATGTACGTCGATGGCTCAAGGACCAGATGCGGACCCCTGTTCT\nCGCCAATGTTACTAAACTTTACCATCGCAAATAAATTTCAATGGTTTCCTACACACACCC\nAAATAACTAACAAACTGTGCTGTGCATTTAGGCAACGATGTGCAAATGCATTTACACGCT\nCGAACACCCATCTCTTCTCAAGATTTAAATACAAACACCTTTTCGAGAGATGCTCTCTTT\nGGAGTTTAGCCGATAGCATTAATATCTTACAAACTCTTTTGGCCTCTAACCAAATTTTGG\nTTGTATTGGATGGCATGGGTCCAATAACGGACGTTTCCCCAGTTCAATTTTGTGCATTTA\nTACACGATCTCAGACATAGCGCTAACGCCGTAGCTTCCTGTATGCGTTCTCTTAGACAGG\nACAATGACAGCTGCTTGACCGATTTTGGCCCTTCCGGATTTATGGCCGATAACATTACCG\nCGTTTATGGAAAAGTATCTTATGGAGTCAATTAATACCGAAGAACAAATTAAAGTATTTA\nAAGCCCTTGCATGTCCAATAGAACAGCCTAGACTAGTCAATACGGCAATATTGGGGGCGT\nGTATACGAATACCTGAAGCGTTGGAAGCATTTGACGTATTTCAAAAAATATACACGCACT\nACGCTTCCGGTTGGTTTCCCGTCCTGGACAAAACCGGGGAATTTAGCATCGCGACTATAA\nCTACCGCCCCAAATTTAACCACACATTGGGAGCTGTTTCGCCGTTGTGCCTATATTGCAA\nAAACACTCAAGTGGAATCCGTCCACCGAAGGCTGTGTAACACAAGTTTTGGATACGGACA\nTTAATACACTTTTCAATCAACACGGGGATTCGCTGGCTCAACTAATATTTGAGGTTATGC\nGCTGTAACGTTACCGACGCTAAGATTATGGCATCCATCTAAGAATCCGGTTGTTCGCCAA\nACCGGGCGGTTTAATATAATCTTCCAATCCCTACAAAACACGAATATAACATTGCTCTAT\nTTCGTTTAATTTGGGAACAATTATTTGGCGCCCGCGTAACTAAAAGTACCCAGACCTTTC\nCGGGAAGTACTCGTGTGAAAAACCTAAAAAAAAAAGATCTAGAAACTTTACTTGATTCAA\nTTAACGTGGATCGTTCTGCATGTCGTACCTACCGCCAGTTGTATAACCTGCTTATGAGCC\nATCGCCATTCGTTCTCCCAACAGCGTTACAAAATTACTGCCCCCGCTTGGGCACGCCACG\nTGTATTTTCAAGCACATCAAATGCACTTGGCCCCGCATGCCGAAGCCATGCTACAATTAG\nCGCTATCGGAACTGTCCCCGGGATCGTGGCCGCGGATAAACGGGGCGGTAAATTTTGAAA\nGTTTATAACCCATTAATACCATATATGGACATCCATAGGGGGGGTTACATAAATACTAAG\nCCTCTGTACAACACAAAGGGCCTCTAACAATGCACTGAACCACAACCAAGCTATGGACGC\nAACGCAGATTACCTTGGTTAGAGAAAGCGGACACATTTGTGCCGCAAGCATATACACATC\nCTGGACACAGTCCGGACAATTAACACAGAACGGTCTTTCCGTGTTATACTACTTATTATG\nCAAAAACTCATGTGGGAAATACGTCCCTAAGTTTGCCGAAATTACCGTACAACAAGAGGA\nTTTATGTCGCTACTCCAGGCATGGGGGGAGTGTTTCTGCGGCAACGTTTGCGTCTATCTG\nCAGGGCGGCGTCCTCGGCTGCGTTAGACGCCTGGCCCCTTGAACCACTGGGTAACGCAGA\nCACCTGGCGGTGTCTCCATGGCACTGCCCTGGCCACTTTACGGCGCTTTAAATCGTTTTA\nTTCGCCAGTAACATTCGAGACTGATACGAATACAGGTCTTCTGTTAAAAACAATCCCCGA\nTGAACACGCGTTGAATAATGACAACACGCCATCTACCGGAGTATTGAGGGCTAATTTTCC\nCGTGGCCATTGATGTTTCAGCAGTCAGCGCATGTAACGCCCACACGCAAGGTACGTCGCT\nAGCCTACGCCCGCCTGACCGCACTTAAATCTAACGGTGACACCCAGCAACAAACACCTTT\nAGACGTGGAGGTAATTACACCAAAGGCCTACATACGTCGGAAATATAAGTCTACGTTTTC\nCCCCCCTATAGAGCGGGAAGGCCAAACCTCCGATTTGTTTAACCTTGAAGAACGCCGCTT\nGGTTCTTAGTGGCAATCGCGCAATTGTGGTAAGGGTACTCTTACCGTGTTATTTTGACTG\nTTTAACAACGGATTCCACCGTTACATCTTCCCTTTCAATATTAGCGGCATGTGGACTGTG\nGTACGCGGCGGCGTTTGGAAAACCCGGGGTTGTCCGTCCAATCTTTGCGTATTTAGGCCC\nGGAACTCAATCCGAAGGGTGAAGACAGAGACTACTTTTGTACTGTCGGATTTCCCGGATG\nGACCACTCTTCGGACACAAACTCCAGCCGTCGAATCTATTCGCACGGCTACGGAGATGTA\nCATGGAAACGGATGGGTTGTGGCCAGTAACCGGTATTCAGGCCTTTCATTATCTAGCCCC\nCTGGGGACAGCATCCCCCCTTACCTCCGCGGGTGCAGGATCTTATTGGGCAAATCCCTCA\nAGATACTGGACATGCAGATGCAACTGTCAATTGGGACGCGGGCCGGATATCTACCGTCTT\nCAAACAGCCTGTACAACTACAAGATCCAAAGTTTGATTTCAGCGCCTTTTTTCCCACGAT\nATACTGCGCTATGTTCCCCATGCATTTTAGATTAGGCAAAATCGTCCTGGCTAGAATGCG\nTCGAGGAATGGGGTGCCTAAAACCCGCGTTGGTGTCTTTTTTTGGGGGGTTACGGCACAT\nACTCCCGAGTATATACAAAGCTATTATTTTTATAGCCAATGAAATTAGCCTTTGCGTCGA\nACAAACGGCCTTGGAACAGGGCTTTGCTATATGTACTTATATAAAAGATGGATTTTGGGG\nAATCTTCACCGATTTACATACGCGCAATGTATGTTCAGATCAGGCACGTTGTTCGGCCTT\nAAATTTAGCGGCCACCTGCGAAAGAGCAGTCACGGGCTTATTACGAATTCAACTAGGTCT\nTAACTTTACACCCGCCATGGAACCGGTACTCCGGGTCGAGGGTGTGTACACTCACGCATT\nTACCTGGTGTACCACGGGAAGCTGGCTGTGGAATTTACAAACAAACACGCCTCCGGATTT\nAGTTGGCGTGCCATGGCGAAGTCAGGCGGCGCGAGATTTAAAGGAGCGTCTTTCAGGACT\nCCTATGTACCGCAACAAAAATTCGAGAACAGATACAGGAAAATTGCATATGGGACCATGT\nCCTATACGACATATGGGCCGGACAAGTTGTGGAGGCTGCCAGAAAAACATACGTCGATTT\nTTTTGAACATGTTTTTGATCGCCGTTATACTCCGGTATACTGGAGTCTTCAGGAGCAAAA\nTTCGGAAACAAAAGCAATACCGGCATCTTATCTGACATACGGACACATGCAAGATAAGGA\nTTATAAACCAAGACAGATAATTATGGTTCGTAATCCCAACCCACATGGACCTCCTACTGT\nTGTTTACTGGGAATTGCTACCATCGTGTGCCTGTATTCCCCCCATAGACTGCGCTGCTCA\nTCTCAAGCCCCTTATACACACGTTTGTCACTATTATTAACCATCTTCTAGATGCTCATAA\nTGATTTTTCAAGTCCATCATTGAAATTTACTGACGATCCCCTTGCTTCATATAACTTCTT\nGTTTTTATGACAAAAAAACACGCCGCAACAACCCATCCTTAAAATAAAAGGTTTATTTCC\nCGTGGTGAATTTTTATACGTTTCAAATAACTGAACATTTTTCGGTGTTACCATGGTGCGA\nTTTAACCACCAAAAATATACGCTCTTCTGATATTCCGAATCTCGTAAAGGTCCATTTAAC\nAATCCCGGGGGCACTTGCACCACACCATCTGGACAGGGGGGGGTTCCGTGGGGCAGGTCA\nAAACGCTGACCCACCCCACATGAATATATAGCCTTTATAATATTGGGGGCCGTTCCAGGC\nTGAGGGTTCAGTAACTTAACAAACATATAATGCGGCAATACGCGGGTTTTTGTAAAGGGG\nTTGTTATCAACGACATACATTAGAGTGTTTAACAACCATAAAACTCCCTCATATAAAAAC\nCGACGCATTTTTTCCAAAGGTCCTATTTGACACTCAACGCGTCTAAGATATACAGACAAT\nTGTACAAACAGCGATGGAGATGCCCCGGAGGGCCCAATGCCTTCCAGATACATTAAAATA\nACACATAAGGTAAAATCTAAAACATTATCCGGGCGGAATAGAGTCATCCGATAGATTAAC\nAGGCGCGGAGGCACCCCCACCGTATACACCCTATCTTCAACCGCAGTTAATACGGAAAAA\nATAAATCCGCGGAACGCTGGTTGAGTAACACACTCCATGTAGTAACGATCACAGGACACC\nTCACTTGAATCACCATTCAACACTACTAAAACGGTCTCTTGGTGTTCCGGTTTTACGCGC\nAGTGATACAACAGAGTTTGCCAAAAAGCGTGGCTTCAAACCGGTTACCTCCCGCGCCTCG\nCATACGAATCTTGGTATTGCTTGTATTCTAAGATCTTCGATCACGTCGCTCACATCCAAC\nCCCTCTTCGGCTCGTGTTAGTAAGTTGTCGATCGTTACGCTGCAACCTAAAATGCTGGGT\nATATTTATTCCGGACATCCCATCGGCCATCCCCGCGCCTCCGGTTTGCTCGAATTTTATC\nCAGTAAGGTCGAATCCGCTGCATTTACCTTGTGTACCCGTAACCTCTCAGGGGGGTGTCC\nTTTCATAAAATGGGATAGGTTTTTATATCCAACATGCATGTATTGGTTATTTATTTTATT\nGGGTTCCGGGATTCTTTCGTCATCTTCTGTAGGGTCAGGCAAACCCCAGGAAGGACTTGG\nCGTTCTCCGTGGGCCCCGTTTTATTACCTCTGCGCGAACCTATTTATCCCAAATCCGAAT\nATTATATGAAATGCAGGTTCGCGCAGAGGTAATAAAACTGACGCATTTGAATATGATACA\nGAAATTTCCTGGCCTTGATTATTGTTTACCCGGTGAAGCTTAAAACAGCGAACAAGTTCC\nTGTTTCCATAGCTCAGACAAACGTTTTATATCATCTCCATAAGGGGGGATATAACGAGAT\nTGAAAACTATTGGCAATATATGCATCATCCCCTATTATGCCGGTAAGATCTATAACCTCG\nTGATTTAAATCGGCAATACGTGTTTCTTCTGCCATTGTAATATGTGACCCTTTAGATGGC\nTTTATTTTTACCCTCTCTTCCCGTAACCGTTTCAGCTCTCCTTCTTTGAACTGGAGCCTT\nTCGGTCAGATCGCTGTTCACATCCTTGAGACCCTCAATGGTTTTGAATAAATTATTCACA\nTAACCCTCGAGCATGCCGTTGATACTGTTAACCACCGATGTTTTAAACGCACTTTGAACG\nTTTGTTGTTCCGGACATTGCCCCCCCGTTAAAGGATTGGTTGGCCTTGCCAAACCCCGGT\nTGTGATGTGTCCACCGCTTCCAGAATGTGATTGCCCGTTTCTTCTAGATAGGAACGTACG\nGTTTCGGTAATATCTCCAACATGTCTCATGTTTTTTAAGTTAACTATTAGCTTTACAAGT\nCTAGACGCGGCCGATCCAGCCCGTGTTGTATCGTTCTCGCCCATTATACGATCAACCGCA\nCGTGTGCTGTGAGATCTATCATCTTCATTCCGGCGACCTATTAACACGCGCAAAGGGGCT\nGTATTTAAAACTTGGCAGACGCGAGCATGTTCACGTAATGCATAACAGGCCAACACCTCC\nCCAGAAAGCCGCTGTAAGGGTGAGTCAAATACTACACCCTCCCCACATACAACGGGCGGC\nCACACGACCAAACACTCTCCCTTCATGCCCGTTACATCATCCTTTGCCATAATTAATCTT\nCGGTTATAATTATAATAAAGACGCGTCCTATCATAATCCATAATAGCAACATTTTGCATA\nCACTCAACTAGGCTTGTGACAACCGCCGCCCCTCTGGCCAACGTTGCATCGGCAACTTTT\nAACATCTGGGACAGTTCTGCCGCTTGACTCATATACGTATTTAATGGTGCAGGGGTTCCA\nTCCTGTTCTGATCGTACCTTTCTTACAACGGGCACAATACCTACACAGGCTATCCAGTCC\nACGTATTTGGCAAAACCGACCCTTCCATTTAAACCACTGGTATAGAGACAACCGGTTATT\nCCACGCAGAAACTCAAGTAACGATGACTGTAATGTTTGACGCCAGGTTTCAAAAACCTGA\nTGTGCAAGCCGTACGGCTTCTGATTCTCCACATAACCCATAACGTTCCGCTAGAGCCCCG\nGCATGCAGGTTACATTGTTGGATGTGGTGTTCCCAATCTGCTGCTAGGTCCTCATACCGA\nGTTGCATCCAACGCGTTCATCAAAACGGTTGCCTGAACTTGGCGAATTACAGTTTCCGTA\nGACCGTACAGCGCTATATATGCCTTGTCCATCGGTATATCCAAAGTCACCGGCTAGGATT\nTTTCGAAACAACATACTTTGCGTGGTTGGGTGTATTAACATCCAGCCATCTTCCTCCGGA\nAATGTACAAAACCCTATATCCGGGGCGTACTCATTCCAGTATATATCGAACATGTTCTTG\nTATTGGTCATTTGGGTTACTTCCATTCAAGCCCTGGTCAATAGAAACAGAACTTGCTATC\nCTTTTTTCTTCACTACCGGAACTGTTATTAAAAAGAGACGTTATTTCGGCCATTGAAAAC\nCACGATGAAAAGATCAATTTCTGTAGACAGTTCTTCACCCAAAAACGTTTTTAATCCAGA\nGACGCCCAATGGATTTGATGACAGTGTATATTTAAACTTCACCTCTATGCATAGCATTCA\nACCTATCCTCTCACGGATTCGAGAACTTGCCGCAATTACGATTCCAAAAGAACGTGTTCC\nGCGGTTGTGTTGGTTTAAACAGTTACTCGAACTGCAAGCGCCTCCTGAAATGCAGAGGAA\nTGAGCTCCCCTTCTCCGTTTATTTAATTAGCGGAAATGCCGGCTCCGGAAAAAGCACGTG\nTATCCAAACGCTTAACGAAGCTATCGATTGCATTATTACCGGATCCACCAGGGTTGCTGC\nCCAAAATGTTCATGCTAAGTTATCAACGGCTTATGCGAGTCGTCCGATAAACACAATCTT\nTCATGAATTTGGTTTTCGCGGAAATCACATTCAGGCTCAGCTGGGCCGTTACGCATATAA\nCTGGACTACGACCCCCCCTTCTATTGAGGACCTGCAAAAAAGAGATATTGTATACTACTG\nGGAAGTTTTAATTGATATAACAAAACGAGTGTTTCAAATGGGGGACGACGGTCGCGGAGG\nAACATCGACATTTAAAACCCTGTGGGCAATTGAACGTTTGCTTAATAAACCTACAGGCTC\nAATGTCCGGAACCGCGTTTATCGCATGCGGTTCCCTTCCGGCTTTTACCCGGAGCAACGT\nTATTGTTATTGATGAAGCAGGATTGCTAGGGCGTCATATTCTCACGGCCGTTGTTTACTG\nTTGGTGGCTTTTGAATGCTATATATCAAAGCCCTCAGTACATAAACGGTCGAAAACCGGT\nCATAGTATGCGTCGGTTCGCCCACCCAAACTGACTCGTTAGAATCTCATTTTCAACATGA\nCATGCAGCGTTCACACGTAACTCCTAGTGAAAATATACTCACGTATATAATCTGCAATCA\nAACTCTGCGTCAATATACTAACATCTCACATAACTGGGCAATCTTTATTAATAACAAACG\nATGTCAAGAGGACGATTTTGGAAATCTTTTAAAAACGCTTGAGTACGGGCTACCTATTAC\nCGAAGCACATGCGCGTCTGGTCGATACATTTGTTGTACCTGCATCCTATATTAACAATCC\nTGCTAATCTTCCCGGATGGACGCGTCTGTATTCGTCGCATAAGGAGGTGAGCGCGTATAT\nGAGTAAGTTACACGCGCATTTAAAACTATCGAAAAATGACCATTTTTCTGTGTTTGCCTT\nACCGACTTATACATTCATCCGGCTAACGGCATTTGATGAATACCGCAAATTAACGGGACA\nACCCGGACTTTCTGTTGAACATTGGATACGGGCAAACTCCGGTCGTTTGCACAATTATTC\nCCAAAGCCGAGATCATGACATGGGAACAGTTAAATACGAAACACATTCAAATCGCGACTT\nAATTGTAGCCCGTACAGACATCACTTACGTGCTAAATAGTCTCGTAGTTGTAACCACAAG\nACTACGTAAGTTAGTTATTGGATTCAGTGGTACATTTCAATCGTTTGCAAAGGTTTTACG\nTGACGACTCCTTTGTGAAGGCTCGAGGAGAGACATCCATCGAATATGCTTACCGGTTTCT\nGTCAAACCTAATCTTTGGAGGCTTGATTAACTTTTACAATTTTTTGTTAAATAAAAACCT\nACATCCCGATAAGGTATCGTTAGCATACAAACGGTTAGCTGCCTTAACCCTGGAGTTATT\nGTCTGGAACAAACAAAGCCCCCTTACACGAAGCAGCGGTTAATGGGGCGGGTGCCGGGAT\nTGACTACTTCTGCCGATAAAGCCTTCTGCTTTACCAGAGCCCCCGAGTCCAAAGTAACGG\nCCTCCATACCCGAAGACCCGGATGATGTAATTTTTACGGCACTTAACGACGAGGTTATTG\nACTTGGTATACTGCCAGTACGAATTTTCCTATCCCAAATCATCCAATGAGGTCCATGCTC\nAGTTTCTGTTAATGAAAGCTATTTACGATGGTCGATATGCCATATTAGCAGAGCTTTTCG\nAAAGCAGCTTTACAACCGCCCCCTTTAGCGCGTATGTCGATAATGTTAATTTCAACGGAA\nGCGAGCTTTTGATCGGCAATGTGCGGGGGGGGCTGTTATCTTTGGCATTACAAACAGATA\nCGTATACCCTTTTGGGGTATACTTTTGCACCCGTGCCAGTCTTTGTAGAGGAACTGACCC\nGAAAAAAGCTGTACCGCGAAACTACCGAAATGTTATATGCTCTACACGTACCTCTTATGG\nTCTTACAGGATCAACATGGGTTTGTGTCCATCGTAAACGCTAACGTATGTGAATTTACCG\nAGTCTATAGAGGATGCAGAATTGGCAATGGCCACCACGGTGGACTATGGCCTTAGTTCTA\nAACTAGCCATGACAATTGCACGCTCACAGGGTCTGAGTTTAGAGAAGGTAGCTATCTGTT\nTTACGGCGGATAAACTGCGCCTAAATAGTGTGTATGTTGCCATGTCGCGTACGGTCTCCT\nCTAGGTTCTTAAAAATGAATCTAAACCCTCTACGGGAACGATATGAAAAATCCGCAGAAA\nTTAGCGATCACATTCTTGCCGCTCTACGTGATCCCAACGTACACGTTGTGTATTAAAGCA\nTTGTATAAAAACACGCATGCGGGCTTGCTGTTCTCATTTCTAGGTTTTGTCTTAAATACA\nCCCGCCATGAGCATCTCTGGACCCCCAACGACGTTTATTTTATATAGGTTACATGGGGTT\nAGGCGGGTTCTTCACTGGACTTTACCGGATCATGAACAAACACTCTACGCATTTACGGGC\nGGGTCAAGATCAATGGCGGTGAAGACGGACGCTCGATGTGATACAATGAGCGGTGGTATG\nATCGTCCTTCAACACACCCATACAGTGACCCTGCTAACCATAGACTGTTCTACTGACTTT\nTCATCATACGCATTTACGCACCGGGATTTCCACTTACAGGACAAACCCCACGCAACATTT\nGCGATGCCGTTTATGTCCTGGGTCGGTTCTGACCCAACATCTCAGCTGTACAGTAATGTG\nGGGGGGGTACTATCCGTAATAACGGAAGATGACCTATCCATGTGTATCTCAATTGTTATA\nTACGGTTTACGGGTAAACAGACCTGACGATCAGACCACACCAACACCAACCCCGCACCAG\nTATACATCGCAAAGGCGGCAGCCTGAAACCAACTGTCCTTCTTCACCACAACCGGCCTTT\nTTCACATCAGACGACGACGTTCTTTCGTTAATATTACGGGACGCCGCAAACGCGTAAAGA\nCAGATTCAAGACTAACATTTATCCCAACTGATTACATTTCATACGCGAATAAACGACACA\nAAAAATTTATATTTAACGGCTTTTAATTTGAAGACACCTATCCTCTTAACGTTGATGAGC\nCTTGCAGGTTGGGTGCCGCGCTTCACCGGTATTATACATAACCGATTTACCGTGTTTACG\nGCAGTCTGACCATTTACCAGTGTATGTCTGTAATACGACGTTGTTGTGTCCCGACAAAAT\nTAACTCGCGTACAAATTTCTGATGTTCCCCCGGCGTGGCAACGCTGGCATTTCCAAACAC\nATTACGTTCTCGTACGTCCATGACCGCTATTTTCAGTATTAATTGGTTGGTCGGTCAAAG\nTATTTTCCTTATGTAAAAGGACACGATCTAAAGCCGTAAACTCGTACACAAACACTGGTA\nCCAACGGACGCGATTTTCCGTCCGTTGAGCGGGTGTAATATCGGCGAGGTCTTCTTGCAC\nGAATACTCTCGTACAGTAGGTTTCTGACACGGGGTGCATGGGTTTTTTGACACAACACAA\nACATTTGCAGGCTCTTATGACTGGATGGATTGAATTTATTTTTAGATAGGGTCACGTGTT\nTTTGTCGTGACACGCCTCGACCAGAAAAGGCTGCGGTTTTCGTACACGCGACCGTTATTT\nCACAGGCGTTCATAACCAAGCTGCGGCGGATGGTGTCGGTTAATTGTCTCCGCCCAAGTT\nCGTCAATAGATGATACCATGAACAACGTATCAAATGGTACATAGTCGTCTTTGGTTTTCT\nCAATACAGCCCGCGTGCCCAATCGGAAAATTTTCATTTGCATCAACGCTATTTTCTGTAA\nAATCGTTCTGAACACTGTGTTGGCTGGCTACCTGTTTAAAATTTGGGATCGAACACGGTC\nCACGATGCAATCCCCAACCCCATTGAAGCAATGCCGTCGGTACGGAAGGAGGCAACTCCG\nAAAACATTATGGTACGCAAGAGGGTCGATTGGCCAATCGATCTCGGGTTCGCCTTTACGC\nGTAAAATACTCATTGGCTTGAACGAAATGTCGACAATTCCGAAATGGAACACGGGACAAT\nGGCGACGGATGCGCGTGTGTTAGCACCAGATGACATCTTGAATTCGGTTGGGTTGTCTTC\nTGTGCATGCGCACCCCACAGCATAAAAACTAACCCTGTACGGTTCTCGCATAACCTCTGT\nAGCACGCGTTGCACCAGCCGCCCCCAGCCTAAGTATACATGCGACCCCGGAGTCCCGCGA\nCGAACCGTAAGCGTGGTATTCAGCAATAACACCCCCTGCCTTGCCCAACTCTCCAGGCAT\nCCGTGAGTGGGCGGAGTCATATTTGGGTATGATTCCATGAGGGCCGCAAAAATATTTTTA\nAGACTAGACGGTGGTGTTATGCCACGTTTTACACTAAACGCTAGCCCATGTGCATGTCCC\nGCGGTAGGGTATGGATCTTGACCAATAATTACAACGCGAATGCTCTGGGGTCCGCAAAAT\nCGCGTCCATGCAAAAATATCGCCTGTAGATGGAAGTATTTCTTCCCCTGAATTTAAAAGA\nCGATTGTATTCTAAAAAAATACCTTTCGCGTACGGCTCTTTAAGTTCGTCCGACAACAGG\nTCATACCACTCAGGGGAAATGTTAAACTTGCTGAAAACTTCAACCGAATCCAGTTGCGAA\nGAGACGGGGGTGAACGTTTCCGTGTCGTAATGATGTGACATGTTATTTAACTTGAAGGTT\nGGGGGGTCTAGCTTAACCCCCAAAGGCAGCCCGCGGGGTCGCTTGCGGGTTTTTTTGGTA\nACCGGATGGGCCAAAACATAAATGTCCTTTGAATCCGATAGTTTCATTTCATTGGCATAC\nGCGTTGGAACAAACGGTCGGCTCCCCAGACACATCCATTTTCCGGGATATTTGTGGAAGA\nTGGAGTAGAGTCTACCCATACACCGGAAAGGGCATCCAACAAAGCATCGCGTATGTCCCC\nGCTTTTATGTTCTTCACCAACAGATTGTGCCAGCCCCTTTAAGGTGACGTATGGATTTGT\nCCAGTACGCCATTTGTTTGTCTTTAAACCAAAGTATAACTTCCGGTACTGGACATTTTGT\nCTTAACCACGATTCCCGATAGCGCCTCGCTGAGGTTTGATACAGGGGGTGCCGCATAGTC\nCCACGCCTCATATACCGATGACACGCACGGTTCCGTTATAATCAAACTCACATCCGATAG\nCGGTTTGGCTCCAAAAAACAACGGAGTGTCGTCTTGGAGATGAAGACAATACGCGATTGT\nGATAGTTTTTAAAAAAACTATCTGCAGTAACCATTTATGTGATGCCATGACGCTATCGGA\nTGTGAGTTTGATTAATATACAGTTGGCCTTTAGTTAAACTCTTGGTGTCATATCTCATTT\nTCCTAAAAAGGGCGATCTTAATATGTCAAACGTCACGGCGTGCCGACAAAGCGAATTTCC\nATGCAAGATTTGGATGTAGTATTTATACACCCAATCACATGTCACGTATTAAGCTTTACA\nGTCCCCCGTTATCTGATATAATCACTTTTCTTAACACGTCATCGGGAAAACAGATGTTTA\nTATTATACCTCTCGCGGTCATTTATGGCAAATACTTAGACCGTTTTCAAGCGGACTGAAA\nACGCTCAAATTGCCTTTTGGAGGCCTGCCCAACGGCCATTATCCCTTGGATCTGAGATTG\nATTTGCGGTAACGTTTGCCAAACCCACGCATTTCAGTTTAAATATTTCTAAGCATTCTTA\nGTGCGTACTTGGCAGCGTGCTTAAAATATCAACCAATATCCATTATGCTACACGTTTCCT\nTCTATCCGTTTCAATCCATTAAAAGTCCATTAACAAAAATGATGCATCATACCTAATTCA\nCCTAAAAACCTGACTCATTGCAGCAGCGTTTCCTCCTTGCAGACTATCCAGTTGGCAAGG\nAGGAAACGCTGCTGCCTTTACTGTAAGTACAAAACTAAAATTTATATTTGCGTGCGTATT\nTTGTAACATATATGCCTTTTATCCCCCCGCAAGTTTGCTTTACCCTCGCCTTCACCACCC\nCCGCCACCTTCCGGCCATTTTAATAACTTTAATTGCTATAAGACATACCCAAACCGGATG\nATTTTTGCCGCTGGAAAAACAGCTTCTAATTTTCCCGTCTCAACTCGGCCTTGGTTGCAT\nCTCCAAGTATACCTTTAGTTTGCTCCCGTAGAGGTGTATAAATACAAACGGTGACAAGTA\nTTGAGCGTAATCTCAAATTTTTGTAATTTAGGGCGGAGCGCTTACGACAGCACATGCGTA\nCTGTTAGACTGTTATGTTTATTGTATTTGCAGAGCAGGATGCCCCGGTTACTCCGAGACC\nGGATTGCGGGCATTCCGAATCGTGTACGGACTTACCAGGGGGCAGTATTTACACCTTGGG\nTTCCAGATATACCAACCCTTACGACCAATAGCAACACTCAGGTATTTTTAAAATGCACGT\nTTAATGATCATAATTTACATACAGTTGGTAATAAAGCAGACTGTGGATGTTTAAGGCATT\nTCCTTCCCCCTCCCAACAAACTAGGACTTCTTCATCTTGTTTGGAATACCTTTACCCGCT\nTTACCGGCAGAGCTTTTTTTGGTAAGGTGTTTCAGTGAACCTGATGTTGATCCGGAGGTG\nGAGGGGGTATTGGACTCCCCCTGTGGAGAGGCAACTTTGCGGGTTTTACTTCCCTTACAT\nGCCGAATCAGACTCAGATGTCAGGTCTATTGTTAAGCATCGTTTAACGTCTCTGCCGGTA\nTGAAATAAACGGCGCTTAGCACCCCTTGCGCTTCCCGGTTTAATCCCCGGTAACACAGAA\nAAAAGCCTGACTTTTTGGGGTGTATTTACCAATCGGGTATCCCTTTCATCGCCACGAGAG\nGTCTCCCCGGTTGAGGTGGTTTCTGGTCTTACAATTGGACCTGTAATTAGTTGGATGGCT\nGTATCTTTCCAGGTCCAGGTTTGCATGGTTAGGCGGGTTGGATCGGTACATCGATCCAAC\nAAGAATAACATGTTTGTTACAAACGGTCCTGTTGAATCATGCAAAAGACAACGCAGGGAT\nGTTTTTAATCCCGCCTCATCACGCCCGTAAATACCTATATAGTTTAATATCAACATTTTT\nGTAGGCTCTACAATTTCGGGTTGATACAGTTCCGCAAGTTGATCATCAAGCCATCCGAGT\nAAAGGTTGCATGTAACACGGGAATCTCGCGTTTCCCTCTGTTCCTCTATCCGTGGCTCGA\nAAAGGCAGTCTGTCCATGGTTCGTGGGTCTTGATTAATTCCCACAGATACTGGACGATCA\nCGGTAGTCCTGCCCCCCGGTCCGGGGTTGCTGTGCAGATTCAATCGAGCCATACACCACC\nGGGGTCGCCGATCGAACAGCAGGTTGGTCTTTAAAAAATACCTTCCGTAAAAATGATGCG\nGTAGAGCATGTTTTGGTTACACCAGGGCTCGAGTCTCGGGTCGGTGGTTGTATAGAATCC\nTGTTGAGAGTCACTTGGTGACTCTGCTGTGGGCTCTCTAGCCGACGATTGAAGGGGCCCA\nGGGTTTGGTGATTGAATGGGCTCCCGACTCGATCTTGATGTTGGCTGTTGGATGGACTCC\nCGACTCGGTCCTGGGCTTGGTGGCAGAAGATCTATGACATCTCCCGGTAGGATGTCGATG\nGAATCTTCAAATGACGGCTCAGAAAAACCATCGTCGTCGGATGGGTGCACTTCATATTCC\nTTGTAACTTGTATCACTTACGATCTTATGCAGGATGGATTGCACTGGACACCGGCAGAGA\nGGACACTGGACGCTGGTGGAGGTCCATGCCCGAATACAAACAAAGCAGAAGTCGTGCAAA\nCACGGCATGGTTTTTCCGAGATCGGAAACGGTGCTCATGCATATGGTGCAGGTATTATCC\nGAAGCGTCGGAGGTGCCGCTACCGCCCGCTAATATGGTATCCATGGTAACAACTGGCTGT\nATTCTAATGTCCGGGCATCCAAACACGTAGCAGAACTGCCATGCGTTTGGATGCCCGGAC\nATTAGAATTGGTACCAACGAAGACACACCCCTATATCCCTCCACCCATTTCTTTTAAGTC\nCCACCCACTAAAACGTGGGTATAAAATGTGTATTGGGGTAGGCGGACAGTCCCAACAAAC\nAGGGAAGTTGATTGGTATAACCTTGGGCCGGGTATACAGCTAAGTGACATTTTAGATTCT\nGTCTTTATTTAGATAAAGAGCGATACGAAGACATTTCTCCACCCCCCTGTAATACCCGTA\nAATAAAGGTAAGTCCACAAACAAAAGCACTGTATATAGGAAGTCGGGTGTATTGGGACAG\nTTACTCCATTAGAGGCGTACAAACAATACTGGGATAGGGTAATGCAAGTCCCCCCCGATG\nGTCGCCCCGCAAACGCGCGGGGAGGTGGGGTCGCTTTTTTTTTTCTCTCTCGAGGGGGCC\nGCGAGAGGGCTGGCCTCCTCTCCCGGGGTCCGCCGGGCGCCCAGAAACCGGGGGGGGGTT\nATTTTCGGGGGGGGGTCCGACCAGCCCGCCCGTCGCCCGCCCGCACAGACAGACAGACAC\nTTTTTTCATAAAAACCGTTCCGCTTTTATTAACAACAAACAGTCCGCGCGCCAGTGGCGC\nTCACGAGAAAAGGAGGGGACTCCGTCACCCCCGACTCTGCGGGGGGCTCCTCCCCCCGCG\nCCCTCCCCACACATCGTCCTCGTCCTCGGAGGACGAGGACGAGGACAACAGCTCCACCTT\nGACCGCCGGGCGCAAACCCACCCGGCGGTCTCGCAGCACACCCGGGGCCACCGACACGAT\nGCTCACCCCAAAGGATGACCCCGGTGCGTCCCCGTCGTCCCCGCCCCCCTCCTCGCTGTC\nCCACGCGTCTTCACACCCCACCTCCCAATCGTCCAGCTCCAAAGCGTGTTCTCTGTCGTC\nTGCGGTGCGCCGCTGTCGCCCCGCCTGGGTTTCTGACGGCCGTTCCGAGCCCCCGTGGTG\nTCCGAACACGAACCGTGTTCCGTCGCTCCCCTCCAACACCGTCTCCGCGGCCCCAAAACC\nGGGCGGCCACATTACTCTGGGAATCGGGGGGAGGGCATTCCGAGCCTCGTCCGCCGACGC\nATACAGCGCCACCGACCGACCGGCCACGGGTGGAAGCACGAGTGGTTCTGCGGCAGGGTC\nGGGTTCCAGCAGGGCGTGGCGGCAAAACACCCTCGCCCAGGTGGGTACGTCGCCGGCCTC\nCGGCCCGGCGGCCCCCGGTCTCCGTCCCTCGGGAAGGAAGACGGGTCGAAGCGCGGCACC\nCAGGCCCCATCGGTTTGCTGCGCGGTGGCTATGTGCCGCCTCGTCCACAAAGTCGGCTGC\nCCCGAGCCCCAGACCCCGAGACTGTCGCGCGAGGTCCTTGCAACCGTCAAAACCCGGCAG\nCACGTACTGCCGGTATTCACGGGGCGACAGGGGGACGCGGGTCTTGGGGCCCGCGCGGGT\nACACACGGTGTATGCGACGTTCCCACCGCGGCACAAACACAGGGGTTGTTCGCCCGGGTA\nCAGGTTGGCAAACGCAGTCTCGATACGAGCAAAACTCGCTGGCCCAAAGGTGCGCGACGA\nTGCAAACACGGCCCGGGCGAGTCCTTCTGTGACCGCCGAGTCTGGCCATCGGACGACGGC\nCTGGGCGTCCGGTCGCGCCGGGGCCCGGACGTACACGTGATACTGAGACAAAGCGGGTCC\nATCCCTGGGCCACCTCTCGAGGGCCACCGCGTCCAACACCAGCAACCGGCGCCGGGCAGA\nGGCCAACCGCGAGCCTAGATACTCGACGGCCCCGGCAAAGGCCAGGTCTCGGGTCGACAG\nTAATAAAACGCCCCGGGCGTTCAAAGCGGACACGTCCGGCGGGCCGGTCCAGTTCCCGGC\nCCAGGCATGAGTGCTCGGCAGGCACAACCGGTTACTCAGGGCTGCCAGGACCACAGACAG\nTCCCCCTCGGGATGGACTCCATGACGGTCCCGGATCTGTCGCGAGGGTGCTCTCGAGGGG\nGCCGTTGATGTCCTCTCCGGGCAACGGATCGTAGATGATCAGAAGCCTCACATCCTCCGG\nGTCTGGGATCTGCCGCATCCAGGCGCACCTCCGTCGCAGCGCCTCCACTCCGCTGGGTGG\nACCAAACCGTCGGTCTCCTCCGCCCGGACGCCGAGCGGCGATTTCCGCCAAGGCGCCGGG\nATCAAAGCTTAGCGCAGGGCGCCAGGCCGTGGGAAACAATGGGTCGTCGACCAGACGGGC\nGATGGTTTCGGGGGTACAGTACGCCTTGCGAGCCTGGTCCGACGGGACCGGGGTATGCAG\nGGCCCCCCGGGGAATACGCCGAAATCCCCCGTTTGGGGCCGGTCCGTCAAGTGGCATCGT\nTATTACGGCGGGGGGATCCACCACAGGGCCCGAGGTGATGGTCACGGGCTCGGATACCCG\nCCTCTTGGCCTTGGAAACCACATGATCGTCTGCAACCCGGGCGTCCGCGACGGGTGTCTC\nCCTAATCTTGTCGAGGAGGCTTCTGCTCTCGACTGGCTGGGACTTGCGCTTGCGCGGAGT\nTCGTAAACGATCATCCGGTGGACACACAGAAAGAGAGCGTGCGGCGGCCGACGGCTGAGG\nGTCGGGAGCCTGTGTGGCCGGGGTTGTTGGAGAAGGGTGACCGCGGGAGATCCGCGCCGC\nCGGACTGGAGCCCGTTGCCTCGGGGTATGCCATGCTGGCAAAGGCTCTGCGGAGACTCTG\nTAGGATAAAGTGTTTTTGGGCCCGGTCGTATCGACGGCTCATAGCCACGGCCGCGGCCGC\nGTGGGGGAGAGCCCAGAGGGCCTCCCCCGTGGCCATGGCTTCGCCTACATGCGGAACGGG\nAGACGCTACGCTCCCCGTAACGGCGGTACCCGCCCGTCCCGGTGGCAACAGCTTTTGGTA\nGAACTGGTTCAGGGCCGAGTTGACACCGGTCAGCTTGGGGTTCTGGAGCCATGCTATAGG\nGTCTCTGTCTGGACAGTAGATCAGGTTAATCAGCGCGCGGTACTGTCTAGCCGGATCTCC\nCAACTCCGGCACGTAAAGCGGCACGGGTTCCGTTGAGGCCTCGTAACGAGCCCGCGCCGC\nTCTCACAGCCTCATCCTCCCAGTGACCCTCTCTGGTCTCCCCGGACGGTCCAAACCGCAC\nCCTGTTGGATGGGAGGGGTGCCGATCCGGGCCAAGGGCTTCCGTCGGGCATCATGAGCGG\nCCCCGACACCGGGGGAATTATCGGGGTTCTGGATCGCGGCAGGGAAAATGATTTCTGTCT\nCTGGCGCCCCGGTTCCCCCGCAAGACGTTTGGTCTTACGAATCCTCGGATCGGGACCGCT\nGATGGATCGATATCCCGGTTGGATATTTTGTTTCGTCGACCCACCATCATTTGAGTCCGA\nATCATCCGAATTTGACGGGGAAGGGGCGTGTTCGCGTCCGGACCTGCTGCCTGTAGTTTC\nACTTCCCACCGAAACGCGCCGGGGTTCATCGTCTTCATCCTCCGATGACGATCCCCACGA\nCGAGGAAGAGGATGAAGACGAAACAAACTCACGACTCTTTGGCTTTTTCTCCACTGGGCT\nGTCATCCTCAATCGGGTCTGGTGCGTGGGATCTTCCCGGCAGGGCCAAAAACGCTCTAGG\nTTTGCCCCCCGACGAACGTCCAGGGACGCGAGGTGTTATACCCCGGGCATCATGTTTCCT\nTGGGCGGGTATCATCGGTCTCAAACGGCAGGTCCGCCTTTGCCCCCTTAGCGGGAACGCT\nGTCCGAAAGGACGTGGTACAATTGCTCAACCGGGCCGGGTACAGGTCCACCGGGTTTCCG\nCGCCGGGAGTGGGACCTTAACCTTCAAAGTCTTTTTCTTCGGGCTCTTTCCCTGAGCGGG\nCCGTTGAGTTTTCTGGAGAACTACTCCGTCCCCCGATGCATGCGCATGACCCGCTTGCTC\nATCGCCCGGCTTTTTACCCGAGATGGACTGAGTTTGTCTGTCTCGATGGACCACCGACGG\nCAAACCTGGTGAATTTCCTCTCGTCGTTTGTCGGGGTATAGACCGCTGGTCTTCCCGTTG\nATCGTTCCCGGCGGCGTCTCCAACAGGAGACGCGGGGGATACAGGGGAGAAGGCCTGCGG\nGAACGGAGGGGTCGTACCTCTGCCCGTTTCCCCATCGTTCATCGGTGGTTTTGGAGACCT\nAGCAAGCTTCGTTCCGAGAGAGACTGTCTCAAGGGAGCGATCGGCTCCTGTTGGTTCTCG\nCGCGCCGGCCTCCGAGAATCGGGTGTGGAAGACCTCGGCCAGCGGGATTACAGGCGAGCC\nCATTAGATCCTGACCGTCCTCGCATACGTAGTCGTCTTGTGTTAGCTCTTCGCCAACATC\nTTCCGTTCTGGGTTCTGGTTGAAGTCCCGATACGGAGGGAATTGAAACGATCTCGTGTTC\nCCGTCCCACCATGACCCCGTTCTCTCCAAATAGTAGATCGTCAGGCTGACTCGAGGTGAC\nCACCCGGGCCCTGTGTTCGGCGGCCGCCGCGGCCGCGTCCAACAGGTCCATTAACTCCAA\nAGTATCAGGCGACCCCGCGCGTTGGGGTGTAGAGCGCTGCATCGGCGGCGTATCCATCGC\nACTGGGGTGAATTTAGACGTACCCGAGTTTTCCAAACGCTCTCGCAGCCTTCAAAGGATT\nGCGATTGCGGTTGGTGAGGGAGTTCCAACAGTACTTAAAACGTGTTGTGCCCCCCCCTCG\nACCGCATATTTCCTCCCCGTGTCGTCACCGTGTAAATATTCTTAATGATAAGACGATGTA\nGTGATTGGACGAGACTCGAGGCGGGAAGTTCATGGACCATAGTATGCGTTTAAGGAGAGA\nCCGCTGGTTGGCGATGTACGCCCGGTGTCTATTTCCGCATACCTTACAACATCATAACAA\nGGGATACCAGACATGTGAATTTCATTTACATATGTTTAAATAACAACCAATCATCGTGTG\nTCTACAGACGATATATAATATACATAAACACAATTGGGGTTGTCTCACATGCAAAACATC\nTTATATAACACGGGTTGTTTCCACCCATCCGGCATCTAGTTAATCAAATGCACGTCGACG\nGTGTGTTTGGGTCCCTCTCCGTCGTCATTACGTTCGCGCAATCAACAAGCGTATACACCA\nCCACCCCTCCCAACGATTATGTCAGGCGGCACGAAGCCCGCGATAACCCATAAAATACAC\nACGGGGTTGTGGTGTTCACGTAACCCCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCG\nATGGGGAGGGGGCGCGGTACCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCGATGGGG\nAGGGGGCGCGGTACCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCGATGTTTATAACC\nATAATTCTCTAAACCGTTGTAGAAAATCACAAAAAAATTTATTCAAAAACAAGTCGAAGA\nACTTCATATCTGAGGCATGTAAACCCGTTCGCACTTCCTGGGGTGGAATGGGGTGGGGTG\nGGGGGGTGAAAAAGGGGGGGGGTTAAATTGGGCGTCCGCATGTCTGTGGTGTACGCCAAT\nCGGATACACTCTTTTGATCTGCATTCGCACTTCCCGTTTTTTCACTGTATGGGTTTTCAT\nGTTTTGGCATGTGTCCAACCACCGTTCGCACTTTCTTTCTATATATATATATATATATAT\nATATATATATAGAGAAAGAGAGAGAGTTTCTTGTTCGCGCGTGTTCCCGCGATGTCGCGG\nTTTTATGGGGTGTGGGCGGGCTTTTCACAGAATATATATATTCCAAATGGAGCGGCAGGC\nTTTTTAAAATCGATTTGACGTGATAAAAAAAAACACACGGGGCCCCCCCCTTTTTTTGGT\nGTTATAAAGGCAACCCAATCGAAGGTCTCCCGCCCCGGAATCCCCCATTGCCATTTTACC\nCAAGTAGCCTTATTCATAGATGTAAACGTTTGGGTGTGTGTTTTGTTGTGCAGGGTTCGT\nCCGATTCATAACGCGACAGCGTCGAGTCGGTTTTAAGGGAAAAGGTTACTACGGCCCCAA\nGGACATGTTTTGCACCTCACCGGCTACGCGGGGCGACTCGTCCGAGTCAAAACCCGGGGC\nATCGGTTGATGTTAACGGAAAGATGGAATATGGATCTGCACCAGGACCCCTGAACGGCCG\nGGATACGTCGCGGGGCCCCGGCGCGTTTTGTACTCCGGGTTGGGAGATCCACCCGGCCAG\nGCTCGTTGAGGACATCAACCGTGTTTTTTTATGTATTGCACAGTCGTCGGGACGCGTCAC\nGCGAGATTCACGAAGATTGCGGCGCATATGCCTCGACTTTTATCTAATGGGTCGCACCAG\nACAGCGTCCCACGTTAGCGTGCTGGGAGGAATTGTTACAGCTTCAACCCACCCAGACGCA\nGTGCTTACGCGCTACTTTAATGGAAGTGTCCCATCGACCCCCTCGGGGGGAAGACGGGTT\nCATTGAGGCGCCGAATGTTCCTTTGCATAGGAGCGCACTGGAATGTGACGTATCTGATGA\nTGGTGGTGAAGACGATAGCGACGATGATGGGTCTACGCCATCGGATGTAATTGAATTTCG\nGGATTCCGACGCGGAATCATCGGACGGGGAAGACTTTATAGTGGAAGAAGAATCAGAGGA\nGAGCACCGATTCTTGTGAACCAGACGGGGTACCCGGCGATTGTTATCGAGACGGGGATGG\nGTGCAACACCCCGTCCCCAAAGAGACCCCAGCGTGCCATCGAGCGATACGCGGGTGCAGA\nAACCGCGGAATATACAGCCGCGAAAGCGCTCACCGCGTTGGGCGAGGGGGGTGTAGATTG\nGAAGCGACGTCGACACGAAGCCCCGCGCCGGCATGATATACCGCCCCCCCATGGCGTGTA\nGTCTTTATAAATAAATACAATGGTTTGGCTCGTGTCTTTTTTTGATGTCTGTCTGTGGGG\nGAGTGGGGTGTTGTGGATATTAGAGGGTAGAGGGTGCTGGTTTGAACGTCTCCATTAACC\nCACGGGGTCCCCACACGGGCCGTGTGGTATGAATCTCTGCGGATCCCGCGGTGAGCACCC\nGGGCGGTGAATATGCCGGACTTTACTGCACACGACACGATACCCCCGCGCACCAGGCTCT\nCATGAACGACGCCGAACGGTACTTCGCCGCCGCGCTATGCGCCATATCTACCGAGGCCTA\nCGAGGCTTTTATACACAGCCCCTCCGAGAGACCGTGCGCGAGTTTGTGGGGGAGGGCAAA\nGGACGCCTTCGGACGGATGTGCGGGGAGCTCGCAGCGGATAGACAACGTCCACCCTCGGT\nTCCGCCGATCCGCAGAGCGGTGTTATCGTTATTACGCGAGCAATGCATGCCGGATCCACA\nATCGCATCTGGAGCTCAGCGAGCGGCTGATATTGATGGCATATTGGTGCTGTTTGGGACA\nCGCCGGACTTCCGACTATTGGATTGTCGCCCGATAATAAATGCATCCGCGCCGAATTATA\nTGACCGCCCCGGGGGAATTTGTCACAGGCTTTTTGACGCGTACCTGGGCTGCGGGTCCCT\nTGGAGTCCCAAGAACCTACGAGAGATCCTGACACCCCATCCCTTTATATAGAAAAAAAAA\nATAAATTTAAAACATACACCGGATAAAAGCGTACTGTTTTTTATTTAAATTTACACGCTC\nGGCGTTGCCCCGGTTCGGTGATCACCGGGTCTTATCTATATACACCGTGTAACTCGAACC\nCCCGTGACTCCCTCCAATCGCGTTACCAAACTCTTCTTCCGTATCCGTAGATTCCGAGTC\nCTCGAAATCGTCCACTTATCCAACAAATTGTGACGTTATATATCCCAAGGCAAAGGCCGC\nTCCCGTCATAGCAAATACAAAGACAATTATTAGCGTAATATAACAGAATTTTTTACGATG\nATATATTTTATGTTGATATTTTCCAATTCGACGCAAAAATTCATCTGCCGTTTCATTTTC\nGCTATCACTATAATAACACTTTTCAGCCGAACGGCTCGGTTGTATGGCTGTTATCGTTGT\nATTATTTGGTTGCGCTCGCGGGGTTACCACCGCTTCCATCAGTAAGGCCACGGCCTCACC\nCTCCATGGTGTTTTGTCCGGCCATAGAAATCCAGATTGTAAGGCCAGCAGGCTAGTTTAA\nAAGTGTTTAATACCACACCTTTTGATATTTATATACATGCAAGATTCTAGATTATTCATC\nAATAGGTCGTTTAAAGCGCGTTTTCATAAACGTTGTCAGCTATACCGACATTCTCACAAA\nGAGGTAAAGTTACCTTACGTTATTATTAAATAAAACATGTAGACATTATTAATAATCCTA\nGGAACAATCAAATCCATATTTGTAAGTTATGTTTAACCCCTCCCCTTTTTGTCATTATCT\nCCGCCCTCTTATAATCGGATCACTTTATAAGTGTGTCGGTGAGTATATTTTGTATAGTGT\nTTTTGGTTCATTAACACTATCAACATAAGTCGGGGTATACAAGTATAATGAACGACGTTG\nATGCAACAGACACCTTTGTTGGACAAGGAAAGTTCCGTGGCGCCATCTCAACATCACCGT\nCACATATTATGCAAACATGTGGGTTTATACAACAGATGTTTCCAGTTGAAATGTCGCCCG\nGCATAGAATCTGAGGATGATCCCAATTATGACGTTAACATGGATATACAGTCTTTTAATA\nTATTTGATGGTGTCCACGAAACTGAAGCCGAAGCCTCTGTGGCATTGTGTGCAGAAGCAC\nGCGTTGGAATTAATAAAGCGGGATTTGTAATATTAAAAACGTTTACACCAGGGGCGGAAG\nGTTTTGCGTTTGCGTGTATGGACAGTAAAACATGTGAACATGTGGTCATTAAAGCGGGTC\nAACGTCAAGGAACGGCCACCGAGGCAACCGTGTTAAGAGCGTTAACCCACCCATCCGTTA\nTACAGCTTAAAGGAACGTTTACGTATAACAAAATGACATGTCTTATATTACCACGTTACC\nGAACAGATTTATACTGCTATCTAGCTGCAAAGCGCAACCTCCCCATATGTGACATTTTAG\nCAATTCAGCGATCTGTATTACGCGCGTTACAGTATCTTCATAATAACAGTATTATTCACC\nGTGATATAAAATCTGAAAATATATTTATTAACCACCCAGGTGATGTTTGTGTGGGAGACT\nTTGGAGCAGCGTGTTTCCCCGTGGATATTAATGCCAACAGGTATTATGGCTGGGCTGGAA\nCAATCGCCACAAACTCTCCTGAGTTATTGGCTAGAGATCCATATGGACCTGCCGTGGACA\nTATGGAGTGCCGGGATTGTATTATTTGAAATGGCTACAGGACAGAACTCGTTATTTGAAC\nGAGACGGTTTAGATGGCAATTGTGACAGTGAGCGTCAAATTAAACTTATTATACGACGAT\nCTGGAACTCATCCCAATGAATTTCCCATTAACCCTACATCAAATCTTCGTCGACAATACA\nTTGGTTTGGCAAAACGGTCTTCTCGAAAACCCGGATCCAGGCCATTGTGGACAAATCTAT\nATGAGTTGCCAATTGATTTGGAGTATTTGATATGTAAGATGTTATCGTTTGACGCACGTC\nATCGACCATCGGCAGAGGTGTTGCTTAACCACTCTGTTTTCCAAACTCTTCCCGATCCAT\nATCCAAATCCAATGGAAGTTGGAGATTAAAATTCATTAAGCCTGTTAATAAAATATTGTA\nTAAATTGTGTTTATAACGTATAACCCGTTAAGGCAAATAGGGTACAAACGCGCAATGTTT\nTGAAATACTAATATAAATAACATAACCAATAGAAACTTAATACAGAGTCACGCCCCATTA\nCAACAAGGATAAAACACGGGATCATTTTCTTAACATTGTAGTAGCGCTGAAAAGCGTCCC\nCTCCCCCGGCTCACAGAGCTGCTCTTCGGTGTAGTTGGGTATACTGGTGCGCCTCATTTA\nATCGCGATGTTTTTAATCCAATGTTTGATATCGGCCGTTATATTTTACATACAAGTGACC\nAACGCTTTGATCTTCAAGGGCGACCACGTGAGCTTGCAAGTTAACAGCAGTCTCACGTCT\nATCCTTATTCCCATGCAAAATGATAATTATACAGAGATAAAAGGACAGCTTGTCTTTATT\nGGAGAGCAACTACCTACCGGGACAAACTATAGCGGAACACTGGAACTGTTATACGCGGAT\nACGGTGGCGTTTTGTTTCCGGTCAGTACAAGTAATAAGATACGACGGATGTCCCCGGATT\nAGAACGAGCGCTTTTATTTCGTGTAGGTACAAACATTCGTGGCATTATGGTAACTCAACG\nGATCGGATATCAACAGAGCCGGATGCTGGTGTAATGTTGAAAATTACCAAACCGGGAATA\nAATGATGCTGGTGTGTATGTACTTCTTGTTCGGTTAGACCATAGCAGATCCACCGATGGT\nTTTATTCTTGGTGTAAATGTATATACAGCGGGCTCGCATCACAACATTCACGGGGTTATC\nTACACTTCTCCGTCTCTACAGAATGGATATTCTACAAGAGCCCTTTTTCAACAAGCTCGT\nTTGTGTGATTTACCCGCGACACCCAAAGGGTCCGGTACCTCCCTGTTTCAACATATGCTT\nGATCTTCGTGCCGGTAAATCGTTAGAGGATAACCCTTGGTTACATGAGGACGTTGTTACG\nACAGAAACTAAGTCCGTTGTTAAGGAGGGGATAGAAAATCACGTATATCCAACGGATATG\nTCCACGTTACCCGAAAAGTCCCTTAATGATCCTCCAGAAAATCTACTTATAATTATTCCT\nATAGTAGCGTCTGTCATGATCCTCACCGCCATGGTTATTGTTATTGTAATAAGCGTTAAG\nCGACGTAGAATTAAAAAACATCCAATTTATCGCCCAAATACAAAAACAAGAAGGGGCATA\nCAAAATGCGACACCAGAATCCGATGTGATGTTGGAGGCCGCCATTGCACAACTAGCAACG\nATTCGCGAAGAATCCCCCCCACATTCCGTTGTAAACCCGTTTGTTAAATAGAACTAATTA\nTCCCGGATTTTATATTAAATAAACTATATGCGTTTTATTTAGCGTTTTGATTACGCGTTG\nTGATATGAGGGGAAGGATTAAGAATCTCCTAACTATAAGTTAACACGCCCACATTTGGGC\nGGGGATGTTTTATGAAGCCTTAAAGGCCGAGCTGGTATACACGAGAGCAGTCCATGGTTT\nTAGACCTCGGGCGAATTGCGTGGTTTTAAGTGACTATATTCCGAGGGTCGCCTGTAATAT\nGGGGACAGTTAATAAACCTGTGGTGGGGGTATTGATGGGGTTCGGAATTATCACGGGAAC\nGTTGCGTATAACGAATCCGGTCAGAGCATCCGTCTTGCGATACGATGATTTTCACATCGA\nTGAAGACAAACTGGATACAAACTCCGTATATGAGCCTTACTACCATTCAGATCATGCGGA\nGTCTTCATGGGTAAATCGGGGAGAGTCTTCGCGAAAAGCGTACGATCATAACTCACCTTA\nTATATGGCCACGTAATGATTATGATGGATTTTTAGAGAACGCACACGAACACCATGGGGT\nGTATAATCAGGGCCGTGGTATCGATAGCGGGGAACGGTTAATGCAACCCACACAAATGTC\nTGCACAGGAGGATCTTGGGGACGATACGGGCATCCACGTTATCCCTACGTTAAACGGCGA\nTGACAGACATAAAATTGTAAATGTGGACCAACGTCAATACGGTGACGTGTTTAAAGGAGA\nTCTTAATCCAAAACCCCAAGGCCAAAGACTCATTGAGGTGTCAGTGGAAGAAAATCACCC\nGTTTACTTTACGCGCACCGATTCAGCGGATTTATGGAGTCCGGTACACCGAGACTTGGAG\nCTTTTTGCCGTCATTAACCTGTACGGGAGACGCAGCGCCCGCCATCCAGCATATATGCTT\nAAAACATACAACATGCTTTCAAGACGTGGTGGTGGATGTGGATTGCGCGGAAAATACTAA\nAGAGGATCAGTTGGCCGAAATCAGTTACCGTTTTCAAGGTAAGAAGGAAGCGGACCAACC\nGTGGATTGTTGTAAACACGAGCACACTGTTTGATGAACTCGAATTAGACCCCCCCGAGAT\nTGAACCGGGTGTCTTGAAAGTACTTCGGACAGAAAAACAATACTTGGGTGTGTACATTTG\nGAACATGCGCGGCTCCGATGGTACGTCTACCTACGCCACGTTTTTGGTCACCTGGAAAGG\nGGATGAAAAAACAAGAAACCCTACGCCCGCAGTAACTCCTCAACCAAGAGGGGCTGAGTT\nTCATATGTGGAATTACCACTCGCATGTATTTTCAGTTGGGGATACGTTTAGCTTGGCAAT\nGCATCTTCAGTATAAGATACATGAAGCGCCATTTGATTTGCTGTTAGAGTGGTTGTATGT\nCCCCATCGATCCTACATGTCAACCAATGCGGTTATATTCTACGTGTTTGTATCATCCCAA\nCGCACCCCAATGCCTCTCTCATATGAATTCCGGTTGTACATTTACCTCGCCACATTTAGC\nCCAGCGTGTTGCAAGCACAGTGTATCAAAATTGTGAACATGCAGATAACTACACCGCATA\nTTGTCTGGGAATATCTCATATGGAGCCTAGCTTTGGTCTAATCTTACACGACGGGGGCAC\nCACGTTAAAGTTTGTAGATACACCCGAGAGTTTGTCGGGATTATACGTTTTTGTGGTGTA\nTTTTAACGGGCATGTTGAAGCCGTAGCATACACTGTTGTATCCACAGTAGATCATTTTGT\nAAACGCAATTGAAGAGCGTGGATTTCCGCCAACGGCCGGTCAGCCACCGGCGACTACTAA\nACCCAAGGAAATTACCCCCGTAAACCCCGGAACGTCACCACTTCTACGATATGCCGCATG\nGACCGGAGGGCTTGCAGCAGTAGTACTTTTATGTCTCGTAATATTTTTAATCTGTACGGC\nTAAACGAATGAGGGTTAAAGCCTATAGGGTAGACAAGTCCCCGTATAACCAAAGCATGTA\nTTACGCTGGCCTTCCAGTGGACGATTTCGAGGACTCGGAATCTACGGATACGGAAGAAGA\nGTTTGGTAACGCGATTGGAGGGAGTCACGGGGGTTCGAGTTACACGGTGTATATAGATAA\nGACCCGGTGATCACCGAACCGGGGCAACGTCGAGCGTGTAAATTTAAATAAAAAACAGTA\nCGCTTTTATCCGGTGTATGTTTTTCTATATAAAGGGATGGGGTGTCAGGATCTCTCGTAG\nGTTCTTGGGACTCCAAGGGACCCGCAGCCCAGGTACGCGTCAAAAAGCCTGTGACAAATT\nCCCCCGGGGCGGTCATATAATTCGGCGCGGATGCATTTATTATCGGGCGACAATCCAATA\nGTCGGAAGTCCGGCGTGTCCCAAACAGCACCAATATGCCATCAATATCAGCCGCTCGCTG\nAGCTCCAGATGCGATTGTGGATCCGGCATGCATTGCTCGCGTAATAACGATAACACCGCT\nCTGCGGATCGGCGGAACCGAGGGTGGACGTTGTCTATCCGCTGCGAGCTCCCCGCACATC\nCGTCCGAAGGCGTCCTTTGCCCTCCCCCACAAACTCGCGCACGGTCTCTCGGAGGGGCTG\nTGTATAAAAGCCTCGTAGGCCTCGGTAGATATGGCGCATAGCGCGGCGGCGAAGTACCGT\nTCGGCGTCGTTCATGAGAGCCTGGTGCGCGGGGGTATCGTGTCGTGTGCAGTAAAGTCCG\nGCATATTCACCGCCCGGGTGCTCACCGCGGGATCCGCAGAGATTCATACCACACGGCCCG\nTGTGGGGACCCCGTGGGTTAATGGAGACGTTCAAACCAGCACCCTCTACCCTCTAATATC\nCACAACACCCCACTCCCCCACAGACAGACATCAAAAAAAGACACGAGCCAAACCATTGTA\nTTTATTTATAAAGACTACACGCCATGGGGGGGCGGTATATCATGCCGGCGCGGGGCTTCG\nTGTCGACGTCGCTTCCAATCTACACCCCCCTCGCCCAACGCGGTGAGCGCTTTCGCGGCT\nGTATATTCCGCGGTTTCTGCACCCGCGTATCGCTCGATGGCACGCTGGGGTCTCTTTGGG\nGACGGGGTGTTGCACCCATCCCCGTCTCGATAACAATCGCCGGGTACCCCGTCTGGTTCA\nCAAGAATCGGTGCTCTCCTCTGATTCTTCTTCCACTATAAAGTCTTCCCCGTCCGATGAT\nTCCGCGTCGGAATCCCGAAATTCAATTACATCCGATGGCGTAGACCCATCATCGTCGCTA\nTCGTCTTCACCACCATCATCAGATACGTCACATTCCAGTGCGCTCCTATGCAAAGGAACA\nTTCGGCGCCTCAATGAACCCGTCTTCCCCCCGAGGGGGTCGATGGGACACTTCCATTAAA\nGTAGCGCGTAAGCACTGCGTCTGGGTGGGTTGAAGCTGTAACAATTCCTCCCAGCACGCT\nAACGTGGGACGCTGTCTGGTGCGACCCATTAGATAAAAGTCGAGGCATATGCGCCGCAAT\nCTTCGTGAATCTCGCGTGACGCGTCCCGACGACTGTGCAATACATAAAAAAACACGGTTG\nATGTCCTCAACGAGCCTGGCCGGGTGGATCTCCCAACCCGGAGTACAAAACGCGCCGGGG\nCCCCGCGACGTATCCCGGCCGTTCAGGGGTCCTGGTGCAGATCCATATTCCATCTTTCCG\nTTAACATCAACCGATGCCCCGGGTTTTGACTCGGACGAGTCGCCCCGCGTAGCCGGTGAG\nGTGCAAAACATGTCCTTGGGGCCGTAGTAACCTTTTCCCTTAAAACCGACTCGACGCTGT\nCGCGTTATGAATCGGACGAACCCTGCACAACAAAACACACACCCAAACGTTTACATCTAT\nGAATAAGGCTACTTGGGTAAAATGGCAATGGGGGATTCCGGGGCGGGAGACCTTCGATTG\nGGTTGCCTTTATAACACCAAAAAAAGGGGGGGGCCCCGTGTGTTTTTTTTTATCACGTCA\nAATCGATTTTAAAAAGCCTGCCGCTCCATTTGGAATATATATATTCTGTGAAAAGCCCGC\nCCACACCCCATAAAACCGCGACATCGCGGGAACACGCGCGAACAAGAAACTCTCTCTCTT\nTCTCTATATATATATATATATATATATATATATATAGAAAGAAAGTGCGAACGGTGGTTG\nGACACATGCCAAAACATGAAAACCCATACAGTGAAAAAACGGGAAGTGCGAATGCAGATC\nAAAAGAGTGTATCCGATTGGCGTACACCACAGACATGCGGACGCCCAATTTAACCCCCCC\nCCTTTTTCACCCCCCCACCCCACCCCATTCCACCCCAGGAAGTGCGAACGGGTTTACATG\nCCTCAGATATGAAGTTCTTCGACTTGTTTTTGAATAAATTTTTTTGTGATTTTCTACAAC\nGGTTTAGAGAATTATGGTTATAAACATCGGCGGGGTACCGCGCCCCCTCCCCATCGGCGG\nGGTACCGCGCCCCCTCCCCATCGGCGGGGTACCGCGCCCCCTCCCCATCGGCGGGGTACC\nGCGCCCCCTCCCCATCGGCGGGGTACCGCGCCCCCTCCCCATCGGCGGGGGGTTACGTGA\nACACCACAACCCCGTGTGTATTTTATGGGTTATCGCGGGCTTCGTGCCGCCTGACATAAT\nCGTTGGGAGGGGTGGTGGTGTATACGCTTGTTGATTGCGCGAACGTAATGACGACGGAGA\nGGGACCCAAACACACCGTCGACGTGCATTTGATTAACTAGATGCCGGATGGGTGGAAACA\nACCCGTGTTATATAAGATGTTTTGCATGTGAGACAACCCCAATTGTGTTTATGTATATTA\nTATATCGTCTGTAGACACACGATGATTGGTTGTTATTTAAACATATGTAAATGAAATTCA\nCATGTCTGGTATCCCTTGTTATGATGTTGTAAGGTATGCGGAAATAGACACCGGGCGTAC\nATCGCCAACCAGCGGTCTCTCCTTAAACGCATACTATGGTCCATGAACTTCCCGCCTCGA\nGTCTCGTCCAATCACTACATCGTCTTATCATTAAGAATATTTACACGGTGACGACACGGG\nGAGGAAATATGCGGTCGAGGGGGGGGCACAACACGTTTTAAGTACTGTTGGAACTCCCTC\nACCAACCGCAATCGCAATCCTTTGAAGGCTGCGAGAGCGTTTGGAAAACTCGGGTACGTC\nTAAATTCACCCCAGTGCGATGGATACGCCGCCGATGCAGCGCTCTACACCCCAACGCGCG\nGGGTCGCCTGATACTTTGGAGTTAATGGACCTGTTGGACGCGGCCGCGGCGGCCGCCGAA\nCACAGGGCCCGGGTGGTCACCTCGAGTCAGCCTGACGATCTACTATTTGGAGAGAACGGG\nGTCATGGTGGGACGGGAACACGAGATCGTTTCAATTCCCTCCGTATCGGGACTTCAACCA\nGAACCCAGAACGGAAGATGTTGGCGAAGAGCTAACACAAGACGACTACGTATGCGAGGAC\nGGTCAGGATCTAATGGGCTCGCCTGTAATCCCGCTGGCCGAGGTCTTCCACACCCGATTC\nTCGGAGGCCGGCGCGCGAGAACCAACAGGAGCCGATCGCTCCCTTGAGACAGTCTCTCTC\nGGAACGAAGCTTGCTAGGTCTCCAAAACCACCGATGAACGATGGGGAAACGGGCAGAGGT\nACGACCCCTCCGTTCCCGCAGGCCTTCTCCCCTGTATCCCCCGCGTCTCCTGTTGGAGAC\nGCCGCCGGGAACGATCAACGGGAAGACCAGCGGTCTATACCCCGACAAACGACGAGAGGA\nAATTCACCAGGTTTGCCGTCGGTGGTCCATCGAGACAGACAAACTCAGTCCATCTCGGGT\nAAAAAGCCGGGCGATGAGCAAGCGGGTCATGCGCATGCATCGGGGGACGGAGTAGTTCTC\nCAGAAAACTCAACGGCCCGCTCAGGGAAAGAGCCCGAAGAAAAAGACTTTGAAGGTTAAG\nGTCCCACTCCCGGCGCGGAAACCCGGTGGACCTGTACCCGGCCCGGTTGAGCAATTGTAC\nCACGTCCTTTCGGACAGCGTTCCCGCTAAGGGGGCAAAGGCGGACCTGCCGTTTGAGACC\nGATGATACCCGCCCAAGGAAACATGATGCCCGGGGTATAACACCTCGCGTCCCTGGACGT\nTCGTCGGGGGGCAAACCTAGAGCGTTTTTGGCCCTGCCGGGAAGATCCCACGCACCAGAC\nCCGATTGAGGATGACAGCCCAGTGGAGAAAAAGCCAAAGAGTCGTGAGTTTGTTTCGTCT\nTCATCCTCTTCCTCGTCGTGGGGATCGTCATCGGAGGATGAAGACGATGAACCCCGGCGC\nGTTTCGGTGGGAAGTGAAACTACAGGCAGCAGGTCCGGACGCGAACACGCCCCTTCCCCG\nTCAAATTCGGATGATTCGGACTCAAATGATGGTGGGTCGACGAAACAAAATATCCAACCG\nGGATATCGATCCATCAGCGGTCCCGATCCGAGGATTCGTAAGACCAAACGTCTTGCGGGG\nGAACCGGGGCGCCAGAGACAGAAATCATTTTCCCTGCCGCGATCCAGAACCCCGATAATT\nCCCCCGGTGTCGGGGCCGCTCATGATGCCCGACGGAAGCCCTTGGCCCGGATCGGCACCC\nCTCCCATCCAACAGGGTGCGGTTTGGACCGTCCGGGGAGACCAGAGAGGGTCACTGGGAG\nGATGAGGCTGTGAGAGCGGCGCGGGCTCGTTACGAGGCCTCAACGGAACCCGTGCCGCTT\nTACGTGCCGGAGTTGGGAGATCCGGCTAGACAGTACCGCGCGCTGATTAACCTGATCTAC\nTGTCCAGACAGAGACCCTATAGCATGGCTCCAGAACCCCAAGCTGACCGGTGTCAACTCG\nGCCCTGAACCAGTTCTACCAAAAGCTGTTGACACCGGGACGGGCGGGTACCGCCGTTACG\nGGGAGCGTAGCGTCTCCCGTTCCGCATGTAGGCGAAGCCATGGCCACGGGGGAGGCCCTC\nTGGGCTCTCCCCCACGCGGCCGCGGCCGTGGCTATGAGCCGTCGGTACGACCGGGCCCAA\nAAACACTTTATCCTACAGAGTCTCCGCAGAGCCTTTGCCAGCATGGCATACCCCGAGGCA\nACGGGCTCCAGTCCGGCGGCGCGGATCTCCCGCGGTCACCCTTCTCCAACAACCCCGGCC\nACACAGACTCCCGACCCTCAGCCGTCGGCCGCCGCACGCTCTCTTTCTGTGTGTCCACCG\nGATGATCGTTTACGAACTCCGCGCAAGCGCAAGTCCCAGCCAGTCGAGAGCAGAAGCCTC\nCTCGACAAGATTAGGGAGACACCCGTCGCGGACGCCCGGGTTGCAGACGATCATGTGGTT\nTCCAAGGCCAAGAGGCGGGTATCCGAGCCCGTGACCATCACCTCGGGCCCTGTGGTGGAT\nCCCCCCGCCGTAATAACGATGCCACTTGACGGACCGGCCCCAAACGGGGGATTTCGGCGT\nATTCCCCGGGGGGCCCTGCATACCCCGGTCCCGTCGGACCAGGCTCGCAAGGCGTACTGT\nACCCCCGAAACCATCGCCCGTCTGGTCGACGACCCATTGTTTCCCACGGCCTGGCGCCCT\nGCGCTAAGCTTTGATCCCGGCGCCTTGGCGGAAATCGCCGCTCGGCGTCCGGGCGGAGGA\nGACCGACGGTTTGGTCCACCCAGCGGAGTGGAGGCGCTGCGACGGAGGTGCGCCTGGATG\nCGGCAGATCCCAGACCCGGAGGATGTGAGGCTTCTGATCATCTACGATCCGTTGCCCGGA\nGAAGACATCAACGGCCCCCTCGAGAGCACCCTCGCGACAGATCCGGGACCGTCATGGAGT\nCCATCCCGAGGGGGACTGTCTGTGGTCCTGGCAGCCCTGAGTAACCGGTTGTGCCTGCCG\nAGCACTCATGCCTGGGCCGGGAACTGGACCGGCCCGCCGGACGTGTCCGCTTTGAACGCC\nCGGGGCGTTTTATTACTGTCGACCCGAGACCTGGCCTTTGCCGGGGCCGTCGAGTATCTA\nGGCTCGCGGTTGGCCTCTGCCCGGCGCCGGTTGCTGGTGTTGGACGCGGTGGCCCTCGAG\nAGGTGGCCCAGGGATGGACCCGCTTTGTCTCAGTATCACGTGTACGTCCGGGCCCCGGCG\nCGACCGGACGCCCAGGCCGTCGTCCGATGGCCAGACTCGGCGGTCACAGAAGGACTCGCC\nCGGGCCGTGTTTGCATCGTCGCGCACCTTTGGGCCAGCGAGTTTTGCTCGTATCGAGACT\nGCGTTTGCCAACCTGTACCCGGGCGAACAACCCCTGTGTTTGTGCCGCGGTGGGAACGTC\nGCATACACCGTGTGTACCCGCGCGGGCCCCAAGACCCGCGTCCCCCTGTCGCCCCGTGAA\nTACCGGCAGTACGTGCTGCCGGGTTTTGACGGTTGCAAGGACCTCGCGCGACAGTCTCGG\nGGTCTGGGGCTCGGGGCAGCCGACTTTGTGGACGAGGCGGCACATAGCCACCGCGCAGCA\nAACCGATGGGGCCTGGGTGCCGCGCTTCGACCCGTCTTCCTTCCCGAGGGACGGAGACCG\nGGGGCCGCCGGGCCGGAGGCCGGCGACGTACCCACCTGGGCGAGGGTGTTTTGCCGCCAC\nGCCCTGCTGGAACCCGACCCTGCCGCAGAACCACTCGTGCTTCCACCCGTGGCCGGTCGG\nTCGGTGGCGCTGTATGCGTCGGCGGACGAGGCTCGGAATGCCCTCCCCCCGATTCCCAGA\nGTAATGTGGCCGCCCGGTTTTGGGGCCGCGGAGACGGTGTTGGAGGGGAGCGACGGAACA\nCGGTTCGTGTTCGGACACCACGGGGGCTCGGAACGGCCGTCAGAAACCCAGGCGGGGCGA\nCAGCGGCGCACCGCAGACGACAGAGAACACGCTTTGGAGCTGGACGATTGGGAGGTGGGG\nTGTGAAGACGCGTGGGACAGCGAGGAGGGGGGCGGGGACGACGGGGACGCACCGGGGTCA\nTCCTTTGGGGTGAGCATCGTGTCGGTGGCCCCGGGTGTGCTGCGAGACCGCCGGGTGGGT\nTTGCGCCCGGCGGTCAAGGTGGAGCTGTTGTCCTCGTCCTCGTCCTCCGAGGACGAGGAC\nGATGTGTGGGGAGGGCGCGGGGGGAGGAGCCCCCCGCAGAGTCGGGGGTGACGGAGTCCC\nCTCCTTTTCTCGTGAGCGCCACTGGCGCGCGGACTGTTTGTTGTTAATAAAAGCGGAACG\nGTTTTTATGAAAAAAGTGTCTGTCTGTCTGTGCGGGCGGGCGACGGGCGGGCTGGTCGGA\nCCCCCCCCCGAAAATAACCCCCCCCCGGTTTCTGGGCGCCCGGCGGACCCCGGGAGAGG\n" }, { "path": "tests/input/TestImputeFromReference/expected.sub.ebov.impute.fasta", "content": ">test_sub-EBOV.genome-1\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAA\nTGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCC\nACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAAT\nCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCC\nCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTT\nCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGG\nAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT\nCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTA\nTTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTT\nGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCT\nGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACT\nAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAAC\nTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAAC\nGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC\nACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTG\nCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACG\nAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACACCCGTG\nTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAAC\nGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAG\nAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAA\nAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT\nGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATC\nACAGGCGGGAGAAGGACTTAGTAGCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGC\nAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGG\nATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAA\nGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAACAATCTCTCCAGCTGTTCCTG\nAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTG\nCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT\nGATTGGACCAAGAACAT\n" }, { "path": "tests/input/TestImputeFromReference/ref.sub.ebov.fasta", "content": ">test_ref\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGA\nATGGAGTGGCAACTGACGTGCCATCTGCGACTAAAAGATGGGGCTTCAGGTCCGGTGTC\nCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGA\nAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCT\nTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTT\nGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTA\nCCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGA\nAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCG\nAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGAC\nAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACAC\nCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACC\nACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGC\nCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCAC\nAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCG\nACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCT\nGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCT\nTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCA\nCCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACAT\nCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGC\nCGGACCCTTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCG\nCCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCAC\nCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTAT\nTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCA\nATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCT\nGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGA\nGGGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAA\nCGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATC\nCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTT\nGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACAT\n" }, { "path": "tests/input/TestImputeFromReference/test.pseudo.fasta", "content": ">pseudo_used_test_ref\nCTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGC\nTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAAC\nTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGAC\nGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGT\nGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCC\nACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCC\nCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAG\nGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACT\nAATGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTGACTCCCTGGACCTCGCCA\nCCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAG\nATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTG\nGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTTAGTAGCGAAGAGAAGTAATTGTCA\nATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTG\nCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGG\nGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAACAAT\nCTCTCCAGCTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTA\nAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACT\nGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCA\n" }, { "path": "tests/input/TestKMA/ref.fasta", "content": ">NC_045512.2_Wuhan-Hu-1_partial\nATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAA\n>NC_002645.1_SARS-CoV_partial\nATATTAGGTTTTTACCTACCCAGGAAAAGCCAACCAACCTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTAGCTGTCGCTCGGCTGCATGCCTAGTGCACCTACGCAGTATAAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAA\n>MN908947.3_SARS-CoV-2_partial\nGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCG\n" }, { "path": "tests/input/TestKbPython/palmdb_clustered_t2g.txt", "content": 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848\tu117848\nu117854\tu117854\nu117856\tu117856\nu117861\tu117861\nu117868\tu117868\nu117870\tu117870\nu117871\tu117871\nu117874\tu117874\nu117881\tu117874\nu118010\tu117874\nu2490\tu117874\nu270854\tu117874\nu2911\tu117874\nu296602\tu117874\nu64608\tu117874\nu117875\tu117875\nu117877\tu117877\nu117879\tu117879\nu117891\tu117891\nu117893\tu117893\nu117896\tu117896\nu117900\tu117900\nu117903\tu117903\nu117905\tu117905\nu117906\tu117906\nu117907\tu117907\nu117910\tu117910\nu117911\tu117911\nu117912\tu117912\nu117916\tu117916\nu117921\tu117921\nu117922\tu117922\nu117923\tu117923\nu117925\tu117925\nu117926\tu117926\nu117930\tu117930\nu117934\tu117934\nu117938\tu117938\nu117942\tu117942\nu117944\tu117944\nu117947\tu117947\nu117949\tu117949\nu117950\tu117950\nu117951\tu117951\nu117952\tu117952\nu117954\tu117954\nu117956\tu117956\nu117959\tu117959\nu117960\tu117960\nu117961\tu117961\nu117962\tu117962\nu117966\tu117966\nu117969\tu117969\nu117971\tu117971\nu117973\tu117973\nu117974\tu117974\nu117975\tu117975\nu117977\tu117977\nu117986\tu117986\nu117987\tu117987\nu117990\tu117990\nu117994\tu117994\nu117996\tu117996\nu117997\tu117997\nu117998\tu117998\nu117999\tu117999\nu118000\tu118000\nu118005\tu118005\nu118006\tu118006\nu118007\tu118007\nu118011\tu118011\nu118012\tu118012\nu118015\tu118015\nu118016\tu118016\nu118017\tu118017\nu118018\tu118018\nu118020\tu118020\nu118021\tu118021\nu118023\tu118023\nu118027\tu118027\nu118030\tu118030\nu159996\tu118030\nu187418\tu118030\nu279770\tu118030\nu296237\tu118030\nu32823\tu118030\nu64696\tu118030\nu118032\tu118032\nu118033\tu118033\nu118035\tu118035\nu118036\tu118036\nu118040\tu118040\nu118043\tu118043\nu118044\tu118044\nu118048\tu118048\nu118049\tu118049\nu118051\tu118051\nu118053\tu118053\nu118055\tu118055\nu118057\tu118057\nu118059\tu118059\nu118060\tu118060\nu118062\tu118062\nu118064\tu118064\nu118066\tu118066\nu118067\tu118067\nu118069\tu118069\nu118073\tu118073\nu118074\tu118074\nu118080\tu118080\nu118082\tu118082\nu118089\tu118089\nu118091\tu118091\nu118093\tu118093\nu118097\tu118097\nu118104\tu118104\nu118107\tu118107\nu118110\tu118110\nu118114\tu118114\nu118116\tu118116\nu118118\tu118118\nu118119\tu118119\nu118121\tu118121\nu118122\tu118122\nu118123\tu118123\nu118126\tu118126\nu118131\tu118131\nu118134\tu118134\nu118136\tu118136\nu118138\tu118138\nu118143\tu118143\nu118147\tu118147\nu118148\tu118148\nu118150\tu118150\nu118154\tu118154\nu118156\tu118156\nu15257\tu118156\nu16234\tu118156\nu269778\tu118156\nu54187\tu118156\nu118162\tu118162\nu118165\tu118165\nu118169\tu118169\nu118172\tu118172\nu118173\tu118173\nu118174\tu118174\nu118176\tu118176\nu118181\tu118181\nu118183\tu118183\nu118184\tu118184\nu118185\tu118185\nu118186\tu118186\nu118187\tu118187\nu118188\tu118188\nu118189\tu118189\nu118192\tu118192\nu118196\tu118196\nu118197\tu118197\nu118201\tu118201\nu118205\tu118205\nu118209\tu118209\nu118210\tu118210\nu118214\tu118214\nu118215\tu118215\nu118216\tu118216\nu118219\tu118219\nu118227\tu118227\nu118232\tu118232\nu118240\tu118240\nu118241\tu118241\nu118243\tu118243\nu118245\tu118245\nu125874\tu118245\nu135062\tu118245\nu14602\tu118245\nu212809\tu118245\nu2144\tu118245\nu239531\tu118245\nu278315\tu118245\nu280483\tu118245\nu9102\tu118245\nu9644\tu118245\nu118253\tu118253\nu118260\tu118260\nu118261\tu118261\nu118262\tu118262\nu118265\tu118265\nu118267\tu118267\nu118272\tu118272\nu118273\tu118273\nu118274\tu118274\nu118276\tu118276\nu118286\tu118286\nu118289\tu118289\nu118293\tu118293\nu118297\tu118297\nu118298\tu118298\nu118301\tu118301\nu118302\tu118302\nu118304\tu118304\nu118307\tu118307\nu118308\tu118308\nu118315\tu118315\nu118318\tu118318\nu118320\tu118320\nu118324\tu118324\nu118338\tu118338\nu118342\tu118342\nu118343\tu118343\nu118345\tu118345\nu118347\tu118347\nu118348\tu118348\nu118350\tu118350\nu118351\tu118351\nu118355\tu118355\nu118359\tu118359\nu118364\tu118364\nu118367\tu118367\nu118369\tu118369\nu118370\tu118370\nu118381\tu118381\nu118384\tu118384\nu118387\tu118387\nu126171\tu118387\nu277224\tu118387\nu280465\tu118387\nu118388\tu118388\nu118390\tu118390\nu118391\tu118391\nu118392\tu118392\nu118393\tu118393\nu118401\tu118401\nu118403\tu118403\nu118404\tu118404\nu118405\tu118405\nu118407\tu118407\nu118408\tu118408\nu118410\tu118410\nu118411\tu118411\nu1341\tu118411\nu209291\tu118411\nu25888\tu118411\nu269326\tu118411\nu5167\tu118411\nu53123\tu118411\nu63809\tu118411\nu118413\tu118413\nu118416\tu118416\nu118418\tu118418\nu118420\tu118420\nu118425\tu118425\nu118428\tu118428\nu118435\tu118435\nu118437\tu118437\nu118439\tu118439\nu118443\tu118443\nu118460\tu118460\nu118461\tu118461\nu118467\tu118467\nu118469\tu118469\nu118473\tu118473\nu118476\tu118476\nu118477\tu118477\nu118478\tu118478\nu118479\tu118479\nu118484\tu118484\nu118485\tu118485\nu118488\tu118488\nu118499\tu118499\nu118507\tu118507\nu118509\tu118509\nu118520\tu118520\nu118523\tu118523\nu3442\tu118523\nu3917\tu118523\nu51658\tu118523\nu61946\tu118523\nu73506\tu118523\nu80233\tu118523\nu118524\tu1185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140992\tu140992\nu140993\tu140993\nu141004\tu141004\nu141008\tu141008\nu141011\tu141011\nu141012\tu141012\nu141023\tu141023\nu141027\tu141027\nu141031\tu141031\nu141032\tu141032\nu141036\tu141036\nu141040\tu141040\nu141043\tu141043\nu141044\tu141044\nu141046\tu141046\nu141049\tu141049\nu141052\tu141052\nu141056\tu141056\nu141064\tu141064\nu141066\tu141066\nu141067\tu141067\nu141068\tu141068\nu141070\tu141070\nu141075\tu141075\nu141078\tu141078\nu141079\tu141079\nu141083\tu141083\nu141085\tu141085\nu141086\tu141086\nu141087\tu141087\nu141089\tu141089\nu141091\tu141091\nu141095\tu141095\nu141098\tu141098\nu141102\tu141102\nu141105\tu141105\nu16175\tu141105\nu20385\tu141105\nu24939\tu141105\nu141107\tu141107\nu141108\tu141108\nu141114\tu141114\nu141116\tu141116\nu141120\tu141120\nu141122\tu141122\nu141123\tu141123\nu141125\tu141125\nu141130\tu141130\nu141131\tu141131\nu141133\tu141133\nu141137\tu141137\nu141140\tu141140\nu141141\tu141141\nu141151\tu141151\nu141157\tu141157\nu141164\tu141164\nu141165\tu141165\nu141172\tu141172\nu141174\tu141174\nu141175\tu141175\nu141176\tu141176\nu141178\tu141178\nu141181\tu141181\nu141182\tu141182\nu141187\tu141187\nu141188\tu141188\nu141191\tu141191\nu141193\tu141193\nu141194\tu141194\nu141202\tu141202\nu141203\tu141203\nu141204\tu141204\nu141207\tu141207\nu141209\tu141209\nu141212\tu141212\nu141213\tu141213\nu141214\tu141214\nu141217\tu141217\nu141220\tu141220\nu141223\tu141223\nu141224\tu141224\nu141227\tu141227\nu141231\tu141231\nu141232\tu141232\nu141240\tu141240\nu141241\tu141241\nu141242\tu141242\nu141244\tu141244\nu141246\tu141246\nu141247\tu141247\nu141255\tu141255\nu141256\tu141256\nu141258\tu141258\nu141261\tu141261\nu141262\tu141262\nu141264\tu141264\nu141266\tu141266\nu141268\tu141268\nu141273\tu141273\nu141275\tu141275\nu141276\tu141276\nu1557\tu141276\nu141277\tu141277\nu141282\tu141282\nu141283\tu141283\nu141285\tu141285\nu141286\tu141286\nu141287\tu141287\nu141288\tu141288\nu141289\tu141289\nu141291\tu141291\nu141294\tu141294\nu141295\tu141295\nu141300\tu141300\nu141303\tu141303\nu141304\tu141304\nu141306\tu141306\nu141309\tu141309\nu141310\tu141310\nu141846\tu141310\nu146225\tu141310\nu157211\tu141310\nu157886\tu141310\nu198302\tu141310\nu240550\tu141310\nu240559\tu141310\nu275792\tu141310\nu276280\tu141310\nu276457\tu141310\nu282473\tu141310\nu283443\tu141310\nu283557\tu141310\nu30371\tu141310\nu36308\tu141310\nu796\tu141310\nu141311\tu141311\nu141314\tu141314\nu141316\tu141316\nu141317\tu141317\nu141321\tu141321\nu141323\tu141323\nu141330\tu141330\nu141333\tu141333\nu141334\tu141334\nu141335\tu141335\nu141339\tu141339\nu141341\tu141341\nu141343\tu141343\nu141344\tu141344\nu141345\tu141345\nu141347\tu141347\nu141350\tu141350\nu141351\tu141351\nu141353\tu141353\nu141357\tu141357\nu141359\tu141359\nu141360\tu141360\nu141361\tu141361\nu141363\tu141363\nu141364\tu141364\nu141365\tu141365\nu141370\tu141370\nu141371\tu141371\nu141374\tu141374\nu141376\tu141376\nu141380\tu141380\nu141391\tu141391\nu141392\tu141392\nu141395\tu141395\nu141396\tu141396\nu141397\tu141397\nu141398\tu141398\nu141400\tu141400\nu141402\tu141402\nu141408\tu141408\nu141411\tu141411\nu141412\tu141412\nu141414\tu141414\nu141416\tu141416\nu141417\tu141417\nu141424\tu141424\nu141440\tu141440\nu141445\tu141445\nu141446\tu141446\nu141449\tu141449\nu141457\tu141457\nu141461\tu141461\nu141466\tu141466\nu141468\tu141468\nu141470\tu141470\nu141472\tu141472\nu141473\tu141473\nu141476\tu141476\nu141477\tu141477\nu141479\tu141479\nu141482\tu141482\nu141489\tu141489\nu141490\tu141490\nu141492\tu141492\nu141495\tu141495\nu141496\tu141496\nu141499\tu141499\nu141501\tu141501\nu141504\tu141504\nu141505\tu141505\nu141507\tu141507\nu141508\tu141508\nu141510\tu141510\nu141516\tu141516\nu165943\tu141516\nu168957\tu141516\nu173084\tu141516\nu206798\tu141516\nu214663\tu141516\nu229820\tu141516\nu235551\tu141516\nu271271\tu141516\nu277358\tu141516\nu81680\tu141516\nu141517\tu141517\nu141519\tu141519\nu141520\tu141520\nu141523\tu141523\nu141524\tu141524\nu141525\tu141525\nu141526\tu141526\nu141534\tu141534\nu141535\tu141535\nu141542\tu141542\nu141544\tu141544\nu141545\tu141545\nu141547\tu141547\nu141548\tu141548\nu141549\tu141549\nu141550\tu141550\nu141551\tu141551\nu141555\tu141555\nu141559\tu141559\nu141564\tu141564\nu141567\tu141567\nu141572\tu141572\nu141576\tu141576\nu141577\tu141577\nu141578\tu141578\nu141581\tu141581\nu141582\tu141582\nu141583\tu141583\nu141586\tu141586\nu141592\tu141592\nu141599\tu141599\nu141600\tu141600\nu141602\tu141602\nu141605\tu141605\nu141615\tu141615\nu141624\tu141624\nu141631\tu141631\nu141635\tu141635\nu141637\tu141637\nu141639\tu141639\nu141640\tu141640\nu141643\tu141643\nu141644\tu141644\nu141646\tu141646\nu141647\tu141647\nu141648\tu141648\nu141650\tu141650\nu141651\tu141651\nu141657\tu141657\nu141659\tu141659\nu141661\tu141661\nu141663\tu141663\nu141665\tu141665\nu141671\tu141671\nu141672\tu141672\nu141673\tu141673\nu141675\tu141675\nu141687\tu141687\nu141688\tu141688\nu141692\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3152\tu143152\nu143156\tu143156\nu143157\tu143157\nu143161\tu143161\nu143163\tu143163\nu143164\tu143164\nu143170\tu143170\nu143174\tu143174\nu143175\tu143175\nu143177\tu143177\nu143179\tu143179\nu143185\tu143185\nu143186\tu143186\nu143187\tu143187\nu143188\tu143188\nu143190\tu143190\nu143193\tu143193\nu143195\tu143195\nu143198\tu143198\nu143202\tu143202\nu143211\tu143211\nu143215\tu143215\nu143227\tu143227\nu143229\tu143229\nu143232\tu143232\nu143234\tu143234\nu143239\tu143239\nu143241\tu143241\nu143243\tu143243\nu143249\tu143249\nu164391\tu143249\nu19751\tu143249\nu200097\tu143249\nu206845\tu143249\nu210905\tu143249\nu217980\tu143249\nu242746\tu143249\nu243280\tu143249\nu25423\tu143249\nu41334\tu143249\nu52406\tu143249\nu53357\tu143249\nu5966\tu143249\nu6330\tu143249\nu94580\tu143249\nu95100\tu143249\nu143250\tu143250\nu143255\tu143255\nu143257\tu143257\nu143260\tu143260\nu1556\tu143260\nu157217\tu143260\nu171724\tu143260\nu200104\tu143260\nu235866\tu143260\nu240912\tu143260\nu258150\tu143260\nu292118\tu143260\nu8431\tu143260\nu143262\tu143262\nu143263\tu143263\nu143264\tu143264\nu143265\tu143265\nu143269\tu143269\nu145218\tu143269\nu270660\tu143269\nu2836\tu143269\nu4870\tu143269\nu61143\tu143269\nu6166\tu143269\nu90296\tu143269\nu143270\tu143270\nu143274\tu143274\nu143276\tu143276\nu143277\tu143277\nu143280\tu143280\nu143287\tu143287\nu143290\tu143290\nu143291\tu143291\nu143294\tu143294\nu143296\tu143296\nu143297\tu143297\nu143299\tu143299\nu143301\tu143301\nu143302\tu143302\nu143307\tu143307\nu143309\tu143309\nu143312\tu143312\nu143314\tu143314\nu143315\tu143315\nu143317\tu143317\nu143319\tu143319\nu143320\tu143320\nu143324\tu143324\nu143326\tu143326\nu143327\tu143327\nu143330\tu143330\nu143332\tu143332\nu143333\tu143333\nu143335\tu143335\nu143338\tu143338\nu143339\tu143339\nu143341\tu143341\nu143343\tu143343\nu143345\tu143345\nu143346\tu143346\nu143348\tu143348\nu143349\tu143349\nu143350\tu143350\nu143354\tu143354\nu143357\tu143357\nu143358\tu143358\nu143359\tu143359\nu143360\tu143360\nu143361\tu143361\nu143362\tu143362\nu143366\tu143366\nu143368\tu143368\nu143375\tu143375\nu143378\tu143378\nu143379\tu143379\nu143380\tu143380\nu143385\tu143385\nu143386\tu143386\nu143396\tu143396\nu143397\tu143397\nu143401\tu143401\nu143404\tu143404\nu143405\tu143405\nu143408\tu143408\nu143412\tu143412\nu143414\tu143414\nu143417\tu143417\nu143419\tu143419\nu143421\tu143421\nu143426\tu143426\nu143428\tu143428\nu143429\tu143429\nu143430\tu143430\nu143434\tu143434\nu143435\tu143435\nu143436\tu143436\nu143437\tu143437\nu143443\tu143443\nu143445\tu143445\nu143447\tu143447\nu143449\tu143449\nu143451\tu143451\nu143454\tu143454\nu143455\tu143455\nu143457\tu143457\nu143460\tu143460\nu143461\tu143461\nu143464\tu143464\nu143473\tu143473\nu143475\tu143475\nu143488\tu143488\nu143492\tu143492\nu143493\tu143493\nu143494\tu143494\nu143496\tu143496\nu143499\tu143499\nu143506\tu143506\nu143511\tu143511\nu143513\tu143513\nu143518\tu143518\nu143527\tu143527\nu143528\tu143528\nu143529\tu143529\nu143530\tu143530\nu143531\tu143531\nu143535\tu143535\nu143542\tu143542\nu143543\tu143543\nu143552\tu143552\nu143555\tu143555\nu143557\tu143557\nu143558\tu143558\nu143564\tu143564\nu143565\tu143565\nu143574\tu143574\nu143578\tu143578\nu143579\tu143579\nu143589\tu143589\nu143596\tu143596\nu143600\tu143600\nu143602\tu143602\nu143604\tu143604\nu143608\tu143608\nu143610\tu143610\nu143611\tu143611\nu143613\tu143613\nu143614\tu143614\nu143615\tu143615\nu143617\tu143617\nu143618\tu143618\nu143624\tu143624\nu143625\tu143625\nu143629\tu143629\nu143637\tu143637\nu143639\tu143639\nu143641\tu143641\nu143643\tu143643\nu143645\tu143645\nu143653\tu143653\nu143655\tu143655\nu143658\tu143658\nu143659\tu143659\nu143660\tu143660\nu143663\tu143663\nu143664\tu143664\nu143666\tu143666\nu143669\tu143669\nu143670\tu143670\nu143675\tu143675\nu143680\tu143680\nu143682\tu143682\nu143684\tu143684\nu143685\tu143685\nu143686\tu143686\nu143690\tu143690\nu143691\tu143691\nu143693\tu143693\nu143697\tu143697\nu143699\tu143699\nu143701\tu143701\nu143702\tu143702\nu143703\tu143703\nu143708\tu143708\nu143711\tu143711\nu143717\tu143717\nu143718\tu143718\nu143719\tu143719\nu143721\tu143721\nu143723\tu143723\nu143727\tu143727\nu143729\tu143729\nu143737\tu143737\nu143738\tu143738\nu143740\tu143740\nu152775\tu143740\nu156671\tu143740\nu166694\tu143740\nu167759\tu143740\nu170332\tu143740\nu172231\tu143740\nu172950\tu143740\nu173663\tu143740\nu178514\tu143740\nu181988\tu143740\nu18309\tu143740\nu186933\tu143740\nu186938\tu143740\nu216946\tu143740\nu218378\tu143740\nu22149\tu143740\nu235656\tu143740\nu238612\tu143740\nu250280\tu143740\nu257188\tu143740\nu268217\tu143740\nu268303\tu143740\nu277796\tu143740\nu294591\tu143740\nu45825\tu143740\nu47854\tu143740\nu54120\tu143740\nu54339\tu143740\nu76829\tu143740\nu78201\tu143740\nu81851\tu143740\nu8457\tu143740\nu99992\tu143740\nu143746\tu143746\nu143747\tu143747\nu143749\tu143749\nu143751\tu143751\nu143755\tu143755\nu143756\tu143756\nu143757\tu143757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5\nu147397\tu147397\nu147398\tu147398\nu147400\tu147400\nu147402\tu147402\nu147403\tu147403\nu147407\tu147407\nu147408\tu147408\nu147409\tu147409\nu147410\tu147410\nu147413\tu147413\nu147416\tu147416\nu147420\tu147420\nu147423\tu147423\nu147426\tu147426\nu147428\tu147428\nu147429\tu147429\nu147430\tu147430\nu147431\tu147431\nu147433\tu147433\nu147434\tu147434\nu147438\tu147438\nu147442\tu147442\nu147443\tu147443\nu147446\tu147446\nu147448\tu147448\nu147450\tu147450\nu147451\tu147451\nu147455\tu147455\nu147456\tu147456\nu147460\tu147460\nu147461\tu147461\nu147464\tu147464\nu147467\tu147467\nu147468\tu147468\nu147470\tu147470\nu147471\tu147471\nu147476\tu147476\nu147481\tu147481\nu147483\tu147483\nu147484\tu147484\nu147485\tu147485\nu147486\tu147486\nu147487\tu147487\nu147491\tu147491\nu147496\tu147496\nu147502\tu147502\nu147504\tu147504\nu147505\tu147505\nu147506\tu147506\nu147514\tu147514\nu147515\tu147515\nu147518\tu147518\nu147520\tu147520\nu147523\tu147523\nu147528\tu147528\nu147531\tu147531\nu147535\tu147535\nu147539\tu147539\nu147540\tu147540\nu147543\tu147543\nu147551\tu147551\nu147552\tu147552\nu147553\tu147553\nu147558\tu147558\nu147560\tu147560\nu147564\tu147564\nu147568\tu147568\nu147578\tu147578\nu147579\tu147579\nu147583\tu147583\nu147588\tu147588\nu147589\tu147589\nu147591\tu147591\nu147599\tu147599\nu147601\tu147601\nu147604\tu147604\nu147606\tu147606\nu147608\tu147608\nu147609\tu147609\nu147611\tu147611\nu147612\tu147612\nu147613\tu147613\nu147619\tu147619\nu147620\tu147620\nu147621\tu147621\nu147625\tu147625\nu147626\tu147626\nu147627\tu147627\nu147631\tu147631\nu147633\tu147633\nu147634\tu147634\nu147636\tu147636\nu147641\tu147641\nu147644\tu147644\nu147645\tu147645\nu147648\tu147648\nu147654\tu147654\nu147655\tu147655\nu147656\tu147656\nu147658\tu147658\nu147660\tu147660\nu147663\tu147663\nu147664\tu147664\nu147665\tu147665\nu147666\tu147666\nu147669\tu147669\nu147673\tu147673\nu147675\tu147675\nu147679\tu147679\nu147682\tu147682\nu147685\tu147685\nu147687\tu147687\nu147690\tu147690\nu147696\tu147696\nu147697\tu147697\nu147703\tu147703\nu147706\tu147706\nu147707\tu147707\nu147712\tu147712\nu147718\tu147718\nu147719\tu147719\nu147721\tu147721\nu147723\tu147723\nu147724\tu147724\nu147725\tu147725\nu147729\tu147729\nu147731\tu147731\nu147732\tu147732\nu147737\tu147737\nu147741\tu147741\nu147742\tu147742\nu147743\tu147743\nu147747\tu147747\nu147749\tu147749\nu147751\tu147751\nu147753\tu147753\nu147754\tu147754\nu147758\tu147758\nu147761\tu147761\nu147765\tu147765\nu147766\tu147766\nu147772\tu147772\nu147773\tu147773\nu147774\tu147774\nu147775\tu147775\nu147776\tu147776\nu147782\tu147782\nu147791\tu147791\nu147793\tu147793\nu147794\tu147794\nu147795\tu147795\nu147796\tu147796\nu147807\tu147807\nu147811\tu147811\nu147812\tu147812\nu147814\tu147814\nu147818\tu147818\nu147819\tu147819\nu147820\tu147820\nu147821\tu147821\nu147822\tu147822\nu147823\tu147823\nu147828\tu147828\nu147832\tu147832\nu147840\tu147840\nu147844\tu147844\nu147845\tu147845\nu147846\tu147846\nu147847\tu147847\nu147848\tu147848\nu147850\tu147850\nu147853\tu147853\nu147854\tu147854\nu147855\tu147855\nu147861\tu147861\nu147863\tu147863\nu147866\tu147866\nu147869\tu147869\nu147873\tu147873\nu147874\tu147874\nu147875\tu147875\nu147876\tu147876\nu147880\tu147880\nu147883\tu147883\nu147884\tu147884\nu147888\tu147888\nu147889\tu147889\nu147891\tu147891\nu147893\tu147893\nu147897\tu147897\nu147899\tu147899\nu147902\tu147902\nu147903\tu147903\nu147905\tu147905\nu147907\tu147907\nu147918\tu147918\nu147922\tu147922\nu147923\tu147923\nu147924\tu147924\nu147925\tu147925\nu147933\tu147933\nu147936\tu147936\nu147938\tu147938\nu147945\tu147945\nu147946\tu147946\nu147947\tu147947\nu147949\tu147949\nu147954\tu147954\nu147955\tu147955\nu147964\tu147964\nu147968\tu147968\nu147977\tu147977\nu147980\tu147980\nu147983\tu147983\nu147999\tu147999\nu148001\tu148001\nu148017\tu148017\nu148019\tu148019\nu148027\tu148027\nu148033\tu148033\nu148038\tu148038\nu148039\tu148039\nu148042\tu148042\nu148043\tu148043\nu148046\tu148046\nu148047\tu148047\nu148054\tu148054\nu148059\tu148059\nu148061\tu148061\nu148062\tu148062\nu148065\tu148065\nu148069\tu148069\nu148070\tu148070\nu148072\tu148072\nu148073\tu148073\nu148074\tu148074\nu148078\tu148078\nu148079\tu148079\nu148081\tu148081\nu148086\tu148086\nu148087\tu148087\nu148088\tu148088\nu148089\tu148089\nu148090\tu148090\nu148091\tu148091\nu148093\tu148093\nu148094\tu148094\nu148096\tu148096\nu148097\tu148097\nu148099\tu148099\nu148100\tu148100\nu148103\tu148103\nu148109\tu148109\nu148115\tu148115\nu148116\tu148116\nu148117\tu148117\nu148122\tu148122\nu148124\tu148124\nu148125\tu148125\nu148133\tu148133\nu148137\tu148137\nu148146\tu148146\nu148151\tu148151\nu148154\tu148154\nu148155\tu148155\nu148159\tu148159\nu148162\tu148162\nu148163\tu148163\nu148165\tu148165\nu148168\tu148168\nu148169\tu148169\nu148170\tu148170\nu148171\tu148171\nu148174\tu148174\nu148175\tu148175\nu148177\tu148177\nu148180\tu148180\nu148184\tu148184\nu148185\tu148185\nu148186\tu148186\nu148189\tu148189\nu148191\tu148191\nu148197\tu148197\nu148198\tu148198\nu148199\tu148199\nu148200\tu148200\nu148201\tu148201\nu148206\tu148206\nu148209\tu148209\nu148211\tu148211\nu148213\tu148213\nu148214\tu148214\nu148215\tu148215\nu148216\tu148216\nu148217\tu148217\nu148221\tu148221\nu148224\tu148224\nu148227\tu148227\nu148231\tu148231\nu148234\tu148234\nu148235\tu148235\nu148236\tu148236\nu148239\tu148239\nu148240\tu148240\nu148241\tu148241\nu148246\tu148246\nu148248\tu148248\nu148251\tu148251\nu148252\tu148252\nu148255\tu148255\nu148256\tu148256\nu148264\tu148264\nu148272\tu148272\nu148276\tu148276\nu148278\tu148278\nu148283\tu148283\nu148284\tu148284\nu148287\tu148287\nu148290\tu148290\nu148291\tu148291\nu148292\tu148292\nu148297\tu148297\nu148298\tu148298\nu148301\tu148301\nu148303\tu148303\nu148304\tu148304\nu148307\tu148307\nu148309\tu148309\nu148312\tu148312\nu148314\tu148314\nu148315\tu148315\nu148319\tu148319\nu148320\tu148320\nu148325\tu148325\nu148326\tu148326\nu148334\tu148334\nu148335\tu148335\nu148343\tu148343\nu148347\tu148347\nu148348\tu148348\nu148350\tu148350\nu148351\tu148351\nu148354\tu148354\nu148355\tu148355\nu148360\tu148360\nu148361\tu148361\nu148363\tu148363\nu148364\tu148364\nu148371\tu148371\nu15266\tu148371\nu15847\tu148371\nu17005\tu148371\nu17527\tu148371\nu2010\tu148371\nu2022\tu148371\nu20700\tu148371\nu22070\tu148371\nu23979\tu148371\nu4094\tu148371\nu5336\tu148371\nu56429\tu148371\nu6517\tu148371\nu75593\tu148371\nu80564\tu148371\nu9264\tu148371\nu9504\tu148371\nu148372\tu148372\nu148374\tu148374\nu148376\tu148376\nu148381\tu148381\nu148384\tu148384\nu148385\tu148385\nu148387\tu148387\nu148397\tu148397\nu148400\tu148400\nu148401\tu148401\nu148409\tu148409\nu148410\tu148410\nu148416\tu148416\nu148419\tu148419\nu148420\tu148420\nu148421\tu148421\nu148422\tu148422\nu148426\tu148426\nu148430\tu148430\nu148433\tu148433\nu148436\tu148436\nu148437\tu148437\nu148438\tu148438\nu148442\tu148442\nu148443\tu148443\nu148446\tu148446\nu148448\tu148448\nu148449\tu148449\nu148453\tu148453\nu148454\tu148454\nu148456\tu148456\nu148457\tu148457\nu148458\tu148458\nu148459\tu148459\nu148461\tu148461\nu148462\tu148462\nu148466\tu148466\nu148468\tu148468\nu148475\tu148475\nu148479\tu148479\nu148480\tu148480\nu148483\tu148483\nu148484\tu148484\nu148485\tu148485\nu148486\tu148486\nu148488\tu148488\nu148489\tu148489\nu148497\tu148497\nu148498\tu148498\nu148501\tu148501\nu148504\tu148504\nu148507\tu148507\nu148510\tu148510\nu148516\tu148516\nu148517\tu148517\nu148520\tu148520\nu148522\tu148522\nu148523\tu148523\nu148527\tu148527\nu148529\tu148529\nu148530\tu148530\nu148532\tu148532\nu148533\tu148533\nu148536\tu148536\nu148539\tu148539\nu148545\tu148545\nu148546\tu148546\nu148550\tu148550\nu148551\tu148551\nu148554\tu148554\nu148555\tu148555\nu148560\tu148560\nu148561\tu148561\nu148562\tu148562\nu148564\tu148564\nu148565\tu148565\nu148570\tu148570\nu148571\tu148571\nu148572\tu148572\nu148573\tu148573\nu148578\tu148578\nu148581\tu148581\nu148584\tu148584\nu148585\tu148585\nu148593\tu148593\nu148598\tu148598\nu148600\tu148600\nu148602\tu148602\nu148603\tu148603\nu148605\tu148605\nu148606\tu148606\nu148607\tu148607\nu148610\tu148610\nu148612\tu148612\nu148613\tu148613\nu148615\tu148615\nu148617\tu148617\nu148619\tu148619\nu148622\tu148622\nu148623\tu148623\nu148629\tu148629\nu148631\tu148631\nu148632\tu148632\nu148638\tu148638\nu148639\tu148639\nu148640\tu148640\nu148642\tu148642\nu148644\tu148644\nu148651\tu148651\nu148654\tu148654\nu148655\tu148655\nu148657\tu148657\nu148658\tu148658\nu148660\tu148660\nu148664\tu148664\nu148668\tu148668\nu148671\tu148671\nu148673\tu148673\nu148676\tu148676\nu148679\tu148679\nu148681\tu148681\nu148682\tu148682\nu148683\tu148683\nu148686\tu148686\nu148689\tu148689\nu148690\tu148690\nu148696\tu148696\nu148700\tu148700\nu148703\tu148703\nu148704\tu148704\nu148708\tu148708\nu148709\tu148709\nu148715\tu148715\nu148722\tu148722\nu15507\tu148722\nu18709\tu148722\nu148723\tu148723\nu148729\tu148729\nu148731\tu148731\nu148733\tu148733\nu148740\tu148740\nu148749\tu148749\nu148750\tu148750\nu148752\tu148752\nu148753\tu148753\nu148754\tu148754\nu148757\tu148757\nu148758\tu148758\nu148761\tu148761\nu148763\tu148763\nu148765\tu148765\nu148768\tu148768\nu148771\tu148771\nu148772\tu148772\nu148773\tu148773\nu148775\tu148775\nu148778\tu148778\nu148782\tu148782\nu148788\tu148788\nu148789\tu148789\nu148792\tu148792\nu148798\tu148798\nu148800\tu148800\nu148803\tu148803\nu148804\tu148804\nu148806\tu148806\nu148810\tu148810\nu148811\tu148811\nu148813\tu148813\nu148815\tu148815\nu148820\tu148820\nu148825\tu148825\nu148827\tu148827\nu148829\tu148829\nu148832\tu148832\nu148833\tu148833\nu148834\tu148834\nu148843\tu148843\nu148845\tu148845\nu148848\tu148848\nu148849\tu148849\nu148853\tu148853\nu148855\tu148855\nu148857\tu148857\nu148864\tu148864\nu148867\tu148867\nu148870\tu148870\nu148878\tu148878\nu148887\tu148887\nu148892\tu148892\nu148896\tu14889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1181\tu161181\nu161184\tu161184\nu161187\tu161187\nu161190\tu161190\nu161196\tu161196\nu161197\tu161197\nu161202\tu161202\nu161204\tu161204\nu161205\tu161205\nu161208\tu161208\nu161210\tu161210\nu161211\tu161211\nu161214\tu161214\nu161218\tu161218\nu161223\tu161223\nu161224\tu161224\nu161251\tu161251\nu161266\tu161266\nu161273\tu161273\nu161276\tu161276\nu161280\tu161280\nu161281\tu161281\nu161282\tu161282\nu161288\tu161288\nu161291\tu161291\nu161292\tu161292\nu161297\tu161297\nu161299\tu161299\nu161301\tu161301\nu161305\tu161305\nu161306\tu161306\nu161307\tu161307\nu161309\tu161309\nu161317\tu161317\nu161318\tu161318\nu161325\tu161325\nu161326\tu161326\nu161327\tu161327\nu161332\tu161332\nu161333\tu161333\nu161334\tu161334\nu161336\tu161336\nu161339\tu161339\nu161343\tu161343\nu161346\tu161346\nu161347\tu161347\nu161348\tu161348\nu161351\tu161351\nu161352\tu161352\nu161353\tu161353\nu161354\tu161354\nu161358\tu161358\nu161362\tu161362\nu161365\tu161365\nu161373\tu161373\nu161374\tu161374\nu161382\tu161382\nu161383\tu161383\nu161387\tu161387\nu161389\tu161389\nu161390\tu161390\nu161393\tu161393\nu161404\tu161404\nu161405\tu161405\nu161407\tu161407\nu161408\tu161408\nu161410\tu161410\nu161411\tu161411\nu161414\tu161414\nu161417\tu161417\nu161418\tu161418\nu161423\tu161423\nu161426\tu161426\nu161434\tu161434\nu161436\tu161436\nu161437\tu161437\nu161439\tu161439\nu161440\tu161440\nu161441\tu161441\nu161442\tu161442\nu161443\tu161443\nu161444\tu161444\nu161450\tu161450\nu161452\tu161452\nu161454\tu161454\nu161457\tu161457\nu161459\tu161459\nu161460\tu161460\nu161461\tu161461\nu161462\tu161462\nu161463\tu161463\nu161464\tu161464\nu161465\tu161465\nu161466\tu161466\nu161468\tu161468\nu161470\tu161470\nu161473\tu161473\nu161475\tu161475\nu161476\tu161476\nu161477\tu161477\nu161478\tu161478\nu161479\tu161479\nu161486\tu161486\nu161490\tu161490\nu161508\tu161508\nu161511\tu161511\nu161515\tu161515\nu161517\tu161517\nu161527\tu161527\nu161529\tu161529\nu161537\tu161537\nu161541\tu161541\nu161542\tu161542\nu161546\tu161546\nu161551\tu161551\nu161554\tu161554\nu161557\tu161557\nu161560\tu161560\nu161561\tu161561\nu161562\tu161562\nu161563\tu161563\nu161564\tu161564\nu161566\tu161566\nu161568\tu161568\nu161571\tu161571\nu161578\tu161578\nu161579\tu161579\nu161581\tu161581\nu161583\tu161583\nu161584\tu161584\nu161591\tu161591\nu161593\tu161593\nu161596\tu161596\nu161597\tu161597\nu161600\tu161600\nu161601\tu161601\nu161602\tu161602\nu161603\tu161603\nu161610\tu161610\nu161615\tu161615\nu161620\tu161620\nu161623\tu161623\nu161629\tu161629\nu161632\tu161632\nu161635\tu161635\nu161639\tu161639\nu161640\tu161640\nu161641\tu161641\nu161644\tu161644\nu161645\tu161645\nu161646\tu161646\nu161648\tu161648\nu161649\tu161649\nu161652\tu161652\nu161653\tu161653\nu161656\tu161656\nu161658\tu161658\nu161659\tu161659\nu161660\tu161660\nu161661\tu161661\nu161662\tu161662\nu161663\tu161663\nu161665\tu161665\nu161667\tu161667\nu161671\tu161671\nu161673\tu161673\nu161681\tu161681\nu161685\tu161685\nu161689\tu161689\nu161690\tu161690\nu161692\tu161692\nu161694\tu161694\nu161695\tu161695\nu161703\tu161703\nu161704\tu161704\nu161710\tu161710\nu161712\tu161712\nu161731\tu161731\nu161733\tu161733\nu161734\tu161734\nu161736\tu161736\nu161737\tu161737\nu161738\tu161738\nu161746\tu161746\nu161748\tu161748\nu161750\tu161750\nu161753\tu161753\nu161755\tu161755\nu161757\tu161757\nu161758\tu161758\nu161760\tu161760\nu161763\tu161763\nu161766\tu161766\nu161767\tu161767\nu161769\tu161769\nu161772\tu161772\nu161773\tu161773\nu161774\tu161774\nu161781\tu161781\nu161783\tu161783\nu161784\tu161784\nu161785\tu161785\nu161787\tu161787\nu161789\tu161789\nu161791\tu161791\nu161793\tu161793\nu161797\tu161797\nu161802\tu161802\nu161809\tu161809\nu161810\tu161810\nu161814\tu161814\nu161815\tu161815\nu161820\tu161820\nu161821\tu161821\nu161823\tu161823\nu161826\tu161826\nu161831\tu161831\nu161836\tu161836\nu161838\tu161838\nu161842\tu161842\nu161843\tu161843\nu161844\tu161844\nu161847\tu161847\nu161853\tu161853\nu161856\tu161856\nu161858\tu161858\nu161859\tu161859\nu161862\tu161862\nu161869\tu161869\nu161870\tu161870\nu161874\tu161874\nu161877\tu161877\nu161880\tu161880\nu161882\tu161882\nu161883\tu161883\nu161885\tu161885\nu161887\tu161887\nu161889\tu161889\nu161899\tu161899\nu161902\tu161902\nu161906\tu161906\nu161907\tu161907\nu161909\tu161909\nu161911\tu161911\nu161915\tu161915\nu161916\tu161916\nu161920\tu161920\nu161924\tu161924\nu161928\tu161928\nu161935\tu161935\nu161940\tu161940\nu161945\tu161945\nu161949\tu161949\nu161952\tu161952\nu161953\tu161953\nu161955\tu161955\nu161958\tu161958\nu161961\tu161961\nu161963\tu161963\nu161964\tu161964\nu161968\tu161968\nu161969\tu161969\nu161970\tu161970\nu161973\tu161973\nu161974\tu161974\nu161976\tu161976\nu161982\tu161982\nu161983\tu161983\nu161986\tu161986\nu161989\tu161989\nu161994\tu161994\nu162000\tu162000\nu162002\tu162002\nu162003\tu162003\nu162005\tu162005\nu162006\tu162006\nu162007\tu162007\nu162008\tu162008\nu162009\tu162009\nu162010\tu162010\nu162012\tu162012\nu162014\tu162014\nu162015\tu162015\nu162016\tu162016\nu162018\tu162018\nu162022\tu162022\nu162026\tu162026\nu162027\tu162027\nu162028\tu162028\nu162030\tu162030\nu162031\tu162031\nu162034\tu162034\nu162036\tu162036\nu162038\tu162038\nu162041\tu162041\nu162043\tu162043\nu162049\tu162049\nu162050\tu162050\nu162051\tu162051\nu162056\tu162056\nu162060\tu162060\nu162061\tu162061\nu162071\tu162071\nu162078\tu162078\nu162083\tu162083\nu162088\tu162088\nu162090\tu162090\nu162091\tu162091\nu162092\tu162092\nu162097\tu162097\nu162099\tu162099\nu162100\tu162100\nu162102\tu162102\nu162103\tu162103\nu162106\tu162106\nu162113\tu162113\nu162117\tu162117\nu162118\tu162118\nu162121\tu162121\nu162123\tu162123\nu162129\tu162129\nu162132\tu162132\nu162133\tu162133\nu162134\tu162134\nu162135\tu162135\nu162136\tu162136\nu162137\tu162137\nu162142\tu162142\nu162143\tu162143\nu162155\tu162155\nu162158\tu162158\nu162159\tu162159\nu162166\tu162166\nu162167\tu162167\nu162168\tu162168\nu162170\tu162170\nu162174\tu162174\nu162180\tu162180\nu162182\tu162182\nu162183\tu162183\nu162186\tu162186\nu162191\tu162191\nu162198\tu162198\nu162199\tu162199\nu162204\tu162204\nu162205\tu162205\nu162208\tu162208\nu162210\tu162210\nu162214\tu162214\nu162215\tu162215\nu162217\tu162217\nu162218\tu162218\nu162219\tu162219\nu162223\tu162223\nu162225\tu162225\nu162228\tu162228\nu162237\tu162237\nu162239\tu162239\nu162247\tu162247\nu162248\tu162248\nu162255\tu162255\nu162256\tu162256\nu162257\tu162257\nu162258\tu162258\nu162261\tu162261\nu162262\tu162262\nu162266\tu162266\nu162269\tu162269\nu162270\tu162270\nu162271\tu162271\nu162272\tu162272\nu162273\tu162273\nu162274\tu162274\nu162275\tu162275\nu162276\tu162276\nu162277\tu162277\nu162280\tu162280\nu162281\tu162281\nu162285\tu162285\nu162288\tu162288\nu162290\tu162290\nu162291\tu162291\nu162295\tu162295\nu162300\tu162300\nu162301\tu162301\nu162303\tu162303\nu162305\tu162305\nu162307\tu162307\nu162308\tu162308\nu162309\tu162309\nu162318\tu162318\nu162326\tu162326\nu162328\tu162328\nu162329\tu162329\nu162335\tu162335\nu162336\tu162336\nu162337\tu162337\nu162340\tu162340\nu162343\tu162343\nu162344\tu162344\nu162350\tu162350\nu162351\tu162351\nu162354\tu162354\nu162355\tu162355\nu162359\tu162359\nu162362\tu162362\nu162375\tu162375\nu162376\tu162376\nu162379\tu162379\nu162383\tu162383\nu162384\tu162384\nu162386\tu162386\nu162387\tu162387\nu162389\tu162389\nu162393\tu162393\nu162400\tu162400\nu162402\tu162402\nu162404\tu162404\nu162414\tu162414\nu162417\tu162417\nu162424\tu162424\nu162428\tu162428\nu162434\tu162434\nu162442\tu162442\nu162446\tu162446\nu162450\tu162450\nu162455\tu162455\nu162457\tu162457\nu162461\tu162461\nu162462\tu162462\nu162465\tu162465\nu162468\tu162468\nu162472\tu162472\nu162474\tu162474\nu162475\tu162475\nu162477\tu162477\nu162479\tu162479\nu162480\tu162480\nu162482\tu162482\nu162484\tu162484\nu162488\tu162488\nu162489\tu162489\nu162492\tu162492\nu162498\tu162498\nu162499\tu162499\nu162500\tu162500\nu162501\tu162501\nu162505\tu162505\nu162506\tu162506\nu162507\tu162507\nu162508\tu162508\nu162514\tu162514\nu162517\tu162517\nu162519\tu162519\nu162522\tu162522\nu162525\tu162525\nu162526\tu162526\nu162527\tu162527\nu162528\tu162528\nu162532\tu162532\nu162534\tu162534\nu162536\tu162536\nu162537\tu162537\nu162538\tu162538\nu162541\tu162541\nu162549\tu162549\nu162552\tu162552\nu162553\tu162553\nu162554\tu162554\nu162556\tu162556\nu162558\tu162558\nu162560\tu162560\nu162564\tu162564\nu162567\tu162567\nu162569\tu162569\nu162574\tu162574\nu162577\tu162577\nu162578\tu162578\nu162580\tu162580\nu162583\tu162583\nu162589\tu162589\nu162590\tu162590\nu162591\tu162591\nu162595\tu162595\nu162596\tu162596\nu162598\tu162598\nu162603\tu162603\nu162608\tu162608\nu162615\tu162615\nu162616\tu162616\nu162622\tu162622\nu162623\tu162623\nu162634\tu162634\nu162638\tu162638\nu162639\tu162639\nu162647\tu162647\nu162649\tu162649\nu162652\tu162652\nu162656\tu162656\nu162665\tu162665\nu162668\tu162668\nu162669\tu162669\nu162674\tu162674\nu162675\tu162675\nu162678\tu162678\nu162680\tu162680\nu162688\tu162688\nu162689\tu162689\nu162690\tu162690\nu162692\tu162692\nu162694\tu162694\nu162695\tu162695\nu162696\tu162696\nu162697\tu162697\nu162698\tu162698\nu162705\tu162705\nu162706\tu162706\nu162710\tu162710\nu162711\tu162711\nu162713\tu162713\nu162716\tu162716\nu162719\tu162719\nu162723\tu162723\nu162725\tu162725\nu162727\tu162727\nu162728\tu162728\nu162732\tu162732\nu162734\tu162734\nu162735\tu162735\nu162738\tu162738\nu162740\tu162740\nu162741\tu162741\nu162746\tu162746\nu162747\tu162747\nu162751\tu162751\nu162753\tu162753\nu162758\tu162758\nu162759\tu162759\nu162763\tu162763\nu162764\tu162764\nu162765\tu162765\nu162768\tu162768\nu162771\tu162771\nu162772\tu162772\nu162773\tu162773\nu162777\tu162777\nu162780\tu162780\nu162782\tu162782\nu162784\tu162784\nu162785\tu162785\nu162787\tu162787\nu162792\tu162792\nu162795\tu162795\nu162799\tu162799\nu162802\tu162802\nu162814\tu162814\nu162817\tu162817\nu162819\tu162819\nu162820\tu162820\nu162822\tu162822\nu162824\tu162824\nu162825\tu162825\nu162828\tu162828\nu162832\tu162832\nu162835\tu162835\nu162837\tu162837\nu162838\tu162838\nu162844\tu162844\nu162845\tu162845\nu162846\tu162846\nu162847\tu162847\nu162850\tu162850\nu162851\tu162851\nu162855\tu162855\nu162856\tu162856\nu162860\tu162860\nu162861\tu162861\nu162862\tu162862\nu162863\tu162863\nu162866\tu162866\nu162868\tu162868\nu162870\tu162870\nu162872\tu162872\nu162875\tu162875\nu162879\tu162879\nu162881\tu162881\nu162882\tu162882\nu162885\tu162885\nu162886\tu162886\nu162887\tu162887\nu162888\tu162888\nu162890\tu162890\nu162894\tu162894\nu162898\tu162898\nu162899\tu162899\nu162903\tu162903\nu162904\tu162904\nu162905\tu162905\nu162906\tu162906\nu162909\tu162909\nu162911\tu162911\nu162912\tu162912\nu162915\tu162915\nu162916\tu162916\nu162917\tu162917\nu162922\tu162922\nu162923\tu162923\nu162926\tu162926\nu162930\tu162930\nu162932\tu162932\nu162936\tu162936\nu162937\tu162937\nu162940\tu162940\nu162941\tu162941\nu162944\tu162944\nu162947\tu162947\nu162949\tu162949\nu162952\tu162952\nu162956\tu162956\nu162957\tu162957\nu162959\tu162959\nu162960\tu162960\nu162962\tu162962\nu162972\tu162972\nu162980\tu162980\nu162981\tu162981\nu162982\tu162982\nu162988\tu162988\nu162989\tu162989\nu162990\tu162990\nu162993\tu162993\nu162994\tu162994\nu162997\tu162997\nu163000\tu163000\nu163004\tu163004\nu163005\tu163005\nu163006\tu163006\nu163007\tu163007\nu163015\tu163015\nu163017\tu163017\nu163027\tu163027\nu163030\tu163030\nu163033\tu163033\nu163034\tu163034\nu163035\tu163035\nu163041\tu163041\nu163043\tu163043\nu163050\tu163050\nu163051\tu163051\nu163055\tu163055\nu163056\tu163056\nu163058\tu163058\nu163068\tu163068\nu163073\tu163073\nu163074\tu163074\nu163076\tu163076\nu163077\tu163077\nu163078\tu163078\nu163082\tu163082\nu163085\tu163085\nu163093\tu163093\nu163100\tu163100\nu163102\tu163102\nu163105\tu163105\nu188614\tu163105\nu212015\tu163105\nu227109\tu163105\nu271430\tu163105\nu290596\tu163105\nu3052\tu163105\nu45964\tu163105\nu48735\tu163105\nu51342\tu163105\nu58286\tu163105\nu75977\tu163105\nu7792\tu163105\nu84133\tu163105\nu87420\tu163105\nu163109\tu163109\nu163112\tu163112\nu163113\tu163113\nu163115\tu163115\nu163116\tu163116\nu163117\tu163117\nu163120\tu163120\nu163125\tu163125\nu163126\tu163126\nu163128\tu163128\nu163129\tu163129\nu163130\tu163130\nu163131\tu163131\nu163135\tu163135\nu163137\tu163137\nu163138\tu163138\nu163141\tu163141\nu163143\tu163143\nu163150\tu163150\nu163152\tu163152\nu163155\tu163155\nu163157\tu163157\nu163160\tu163160\nu163169\tu163169\nu163174\tu163174\nu163187\tu163187\nu163191\tu163191\nu163197\tu163197\nu163199\tu163199\nu163200\tu163200\nu163201\tu163201\nu163205\tu163205\nu163208\tu163208\nu163215\tu163215\nu163218\tu163218\nu163222\tu163222\nu163227\tu163227\nu163238\tu163238\nu163240\tu163240\nu163245\tu163245\nu163247\tu163247\nu163249\tu163249\nu163256\tu163256\nu163261\tu163261\nu163262\tu163262\nu163266\tu163266\nu163268\tu163268\nu163269\tu163269\nu163274\tu163274\nu163277\tu163277\nu163286\tu163286\nu163289\tu163289\nu19283\tu163289\nu233699\tu163289\nu6125\tu163289\nu68298\tu163289\nu6852\tu163289\nu163293\tu163293\nu163294\tu163294\nu163297\tu163297\nu163299\tu163299\nu163305\tu163305\nu163307\tu163307\nu163309\tu163309\nu163311\tu163311\nu163318\tu163318\nu163322\tu163322\nu163323\tu163323\nu163325\tu163325\nu163327\tu163327\nu163328\tu163328\nu163330\tu163330\nu163332\tu163332\nu163334\tu163334\nu163336\tu163336\nu163337\tu163337\nu163348\tu163348\nu163351\tu163351\nu163358\tu163358\nu163362\tu163362\nu163366\tu163366\nu163368\tu163368\nu163369\tu163369\nu163370\tu163370\nu163373\tu163373\nu163374\tu163374\nu163383\tu163383\nu163384\tu163384\nu163385\tu163385\nu163387\tu163387\nu163389\tu163389\nu163392\tu163392\nu163394\tu163394\nu163399\tu163399\nu163403\tu163403\nu163406\tu163406\nu163407\tu163407\nu163408\tu163408\nu163410\tu163410\nu163415\tu163415\nu163417\tu163417\nu163420\tu163420\nu163421\tu163421\nu163422\tu163422\nu163423\tu163423\nu163425\tu163425\nu163430\tu163430\nu163431\tu163431\nu163434\tu163434\nu163440\tu163440\nu163441\tu163441\nu169441\tu163441\nu1792\tu163441\nu235332\tu163441\nu52847\tu163441\nu93501\tu163441\nu163446\tu163446\nu163447\tu163447\nu163448\tu163448\nu163449\tu163449\nu163453\tu163453\nu163456\tu163456\nu163458\tu163458\nu163459\tu163459\nu163460\tu163460\nu163462\tu163462\nu163464\tu163464\nu163465\tu163465\nu163468\tu163468\nu163471\tu163471\nu163473\tu163473\nu163474\tu163474\nu163481\tu163481\nu163484\tu163484\nu163485\tu163485\nu163490\tu163490\nu163492\tu163492\nu163493\tu163493\nu163494\tu163494\nu163496\tu163496\nu18758\tu163496\nu18875\tu163496\nu238803\tu163496\nu272229\tu163496\nu51740\tu163496\nu5457\tu163496\nu5598\tu163496\nu73706\tu163496\nu163501\tu163501\nu163502\tu163502\nu163504\tu163504\nu163505\tu163505\nu163509\tu163509\nu163515\tu163515\nu163519\tu163519\nu163523\tu163523\nu163524\tu163524\nu163526\tu163526\nu163528\tu163528\nu163531\tu163531\nu163532\tu163532\nu163533\tu163533\nu163537\tu163537\nu163538\tu163538\nu163541\tu163541\nu163542\tu163542\nu163544\tu163544\nu163545\tu163545\nu163546\tu163546\nu163548\tu163548\nu163549\tu163549\nu163553\tu163553\nu163558\tu163558\nu163560\tu163560\nu163562\tu163562\nu163565\tu163565\nu163566\tu163566\nu163569\tu163569\nu163583\tu163583\nu163586\tu163586\nu163589\tu163589\nu163590\tu163590\nu163593\tu163593\nu163594\tu163594\nu163597\tu163597\nu163600\tu163600\nu163602\tu163602\nu163606\tu163606\nu163607\tu163607\nu163616\tu163616\nu163619\tu163619\nu163620\tu163620\nu163623\tu163623\nu163632\tu163632\nu163635\tu163635\nu163637\tu163637\nu163639\tu163639\nu163641\tu163641\nu163643\tu163643\nu163647\tu163647\nu163648\tu163648\nu163650\tu163650\nu163656\tu163656\nu163657\tu163657\nu163658\tu163658\nu163664\tu163664\nu163666\tu163666\nu163667\tu163667\nu163669\tu163669\nu163670\tu163670\nu163676\tu163676\nu163682\tu163682\nu163683\tu163683\nu163694\tu163694\nu163696\tu163696\nu163699\tu163699\nu163701\tu163701\nu163704\tu163704\nu163705\tu163705\nu163707\tu163707\nu163721\tu163721\nu163726\tu163726\nu163730\tu163730\nu163737\tu163737\nu163738\tu163738\nu163741\tu163741\nu163744\tu163744\nu163745\tu163745\nu163748\tu163748\nu163751\tu163751\nu163752\tu163752\nu163756\tu163756\nu163760\tu163760\nu163762\tu163762\nu163763\tu163763\nu163771\tu163771\nu163775\tu163775\nu163776\tu163776\nu163778\tu163778\nu163779\tu163779\nu163786\tu163786\nu163787\tu163787\nu163790\tu163790\nu163799\tu163799\nu163801\tu163801\nu163802\tu163802\nu163805\tu163805\nu163806\tu163806\nu163808\tu163808\nu163809\tu163809\nu163814\tu163814\nu163817\tu163817\nu163819\tu163819\nu163831\tu163831\nu163833\tu163833\nu163846\tu163846\nu163848\tu163848\nu163849\tu163849\nu163850\tu163850\nu163857\tu163857\nu163874\tu163874\nu163875\tu163875\nu163876\tu163876\nu163881\tu163881\nu163884\tu163884\nu163885\tu163885\nu163898\tu163898\nu163901\tu163901\nu163903\tu163903\nu163907\tu163907\nu163908\tu163908\nu163910\tu163910\nu163915\tu163915\nu163917\tu163917\nu163924\tu163924\nu163926\tu163926\nu163927\tu163927\nu163929\tu163929\nu163937\tu163937\nu163941\tu163941\nu163942\tu163942\nu163944\tu163944\nu163948\tu163948\nu163949\tu163949\nu163953\tu163953\nu163971\tu163971\nu163975\tu163975\nu163977\tu163977\nu163985\tu163985\nu163986\tu163986\nu163987\tu163987\nu163988\tu163988\nu163989\tu163989\nu163993\tu163993\nu163994\tu163994\nu163995\tu163995\nu163997\tu163997\nu164000\tu164000\nu164007\tu164007\nu164009\tu164009\nu164013\tu164013\nu164015\tu164015\nu164017\tu164017\nu164018\tu164018\nu164020\tu164020\nu164023\tu164023\nu164024\tu164024\nu164027\tu164027\nu164033\tu164033\nu164037\tu164037\nu164040\tu164040\nu164042\tu164042\nu164048\tu164048\nu164050\tu164050\nu164054\tu164054\nu164055\tu164055\nu164056\tu164056\nu164059\tu164059\nu164062\tu164062\nu164065\tu164065\nu164069\tu164069\nu164075\tu164075\nu164076\tu164076\nu164081\tu164081\nu164082\tu164082\nu164084\tu164084\nu164088\tu164088\nu164090\tu164090\nu164093\tu164093\nu164096\tu164096\nu164101\tu164101\nu164102\tu164102\nu164111\tu164111\nu164121\tu164121\nu164133\tu164133\nu164134\tu164134\nu164136\tu164136\nu164140\tu164140\nu164142\tu164142\nu164147\tu164147\nu164148\tu164148\nu164153\tu164153\nu164158\tu164158\nu164163\tu164163\nu164170\tu164170\nu164171\tu164171\nu164172\tu164172\nu164184\tu164184\nu164188\tu164188\nu164194\tu164194\nu175178\tu164194\nu3722\tu164194\nu56952\tu164194\nu164206\tu164206\nu164207\tu164207\nu164210\tu164210\nu164211\tu164211\nu164217\tu164217\nu164223\tu164223\nu164224\tu164224\nu164232\tu164232\nu164234\tu164234\nu164236\tu164236\nu164237\tu164237\nu164240\tu164240\nu164241\tu164241\nu164242\tu164242\nu164245\tu164245\nu164248\tu164248\nu164250\tu164250\nu164252\tu164252\nu164253\tu164253\nu164254\tu164254\nu164255\tu164255\nu164263\tu164263\nu164269\tu164269\nu164271\tu164271\nu164272\tu164272\nu164281\tu164281\nu164287\tu164287\nu164291\tu164291\nu173301\tu164291\nu18460\tu164291\nu23504\tu164291\nu6357\tu164291\nu69736\tu164291\nu71774\tu164291\nu164293\tu164293\nu164294\tu164294\nu164296\tu164296\nu164299\tu164299\nu164301\tu164301\nu164304\tu164304\nu164307\tu164307\nu164314\tu164314\nu164323\tu164323\nu164327\tu164327\nu164331\tu164331\nu164334\tu164334\nu164337\tu164337\nu164341\tu164341\nu164344\tu164344\nu164347\tu164347\nu164348\tu164348\nu164350\tu164350\nu164353\tu164353\nu164355\tu164355\nu164357\tu164357\nu164361\tu164361\nu164362\tu164362\nu164365\tu164365\nu164370\tu164370\nu164372\tu164372\nu164384\tu164384\nu164385\tu164385\nu164388\tu164388\nu164394\tu164394\nu164395\tu164395\nu164397\tu164397\nu164398\tu164398\nu164403\tu164403\nu164404\tu164404\nu164405\tu164405\nu164406\tu164406\nu164408\tu164408\nu164409\tu164409\nu164410\tu164410\nu164411\tu164411\nu164414\tu164414\nu164415\tu164415\nu164419\tu164419\nu164422\tu164422\nu164423\tu164423\nu164429\tu164429\nu164431\tu164431\nu164433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403\nu169410\tu169410\nu169412\tu169412\nu169413\tu169413\nu169415\tu169415\nu169416\tu169416\nu169418\tu169418\nu169419\tu169419\nu169420\tu169420\nu169426\tu169426\nu169432\tu169432\nu169439\tu169439\nu169442\tu169442\nu169443\tu169443\nu169447\tu169447\nu169457\tu169457\nu169472\tu169472\nu169475\tu169475\nu169479\tu169479\nu169482\tu169482\nu169484\tu169484\nu169489\tu169489\nu169496\tu169496\nu169498\tu169498\nu182109\tu169498\nu189564\tu169498\nu58497\tu169498\nu6712\tu169498\nu8115\tu169498\nu169509\tu169509\nu174661\tu169509\nu190085\tu169509\nu20788\tu169509\nu20802\tu169509\nu21815\tu169509\nu218979\tu169509\nu23882\tu169509\nu252056\tu169509\nu284997\tu169509\nu35420\tu169509\nu37227\tu169509\nu41847\tu169509\nu5589\tu169509\nu169511\tu169511\nu169514\tu169514\nu169518\tu169518\nu169520\tu169520\nu169521\tu169521\nu169522\tu169522\nu169523\tu169523\nu169524\tu169524\nu169525\tu169525\nu169529\tu169529\nu169530\tu169530\nu169531\tu169531\nu169533\tu169533\nu169543\tu169543\nu169552\tu169552\nu169560\tu169560\nu169564\tu169564\nu169568\tu169568\nu169570\tu169570\nu169575\tu169575\nu169581\tu169581\nu169583\tu169583\nu169588\tu169588\nu169591\tu169591\nu169598\tu169598\nu169604\tu169604\nu169608\tu169608\nu169611\tu169611\nu169622\tu169622\nu169629\tu169629\nu169640\tu169640\nu169641\tu169641\nu169647\tu169647\nu169649\tu169649\nu169652\tu169652\nu169653\tu169653\nu169654\tu169654\nu169659\tu169659\nu169662\tu169662\nu169674\tu169674\nu169677\tu169677\nu169682\tu169682\nu169688\tu169688\nu169692\tu169692\nu169694\tu169694\nu169695\tu169695\nu169696\tu169696\nu169700\tu169700\nu169701\tu169701\nu169704\tu169704\nu169709\tu169709\nu169712\tu169712\nu169715\tu169715\nu169726\tu169726\nu169727\tu169727\nu169730\tu169730\nu169734\tu169734\nu169739\tu169739\nu169742\tu169742\nu169743\tu169743\nu169748\tu169748\nu169757\tu169757\nu7723\tu169757\nu9173\tu169757\nu169763\tu169763\nu169764\tu169764\nu169765\tu169765\nu169770\tu169770\nu169773\tu169773\nu169774\tu169774\nu169778\tu169778\nu169784\tu169784\nu169787\tu169787\nu169789\tu169789\nu169792\tu169792\nu169797\tu169797\nu169798\tu169798\nu169799\tu169799\nu169800\tu169800\nu169805\tu169805\nu169815\tu169815\nu169816\tu169816\nu169820\tu169820\nu169828\tu169828\nu169829\tu169829\nu169831\tu169831\nu169833\tu169833\nu169835\tu169835\nu169836\tu169836\nu169837\tu169837\nu169838\tu169838\nu169842\tu169842\nu169865\tu169865\nu169870\tu169870\nu169873\tu169873\nu169874\tu169874\nu169876\tu169876\nu169879\tu169879\nu169881\tu169881\nu169882\tu169882\nu169885\tu169885\nu169887\tu169887\nu169891\tu169891\nu169910\tu169910\nu169917\tu169917\nu169918\tu169918\nu169920\tu169920\nu169921\tu169921\nu169925\tu169925\nu169928\tu169928\nu169929\tu169929\nu169930\tu169930\nu169932\tu169932\nu169933\tu169933\nu169937\tu169937\nu169939\tu169939\nu169940\tu169940\nu169941\tu169941\nu169944\tu169944\nu169947\tu169947\nu169948\tu169948\nu169952\tu169952\nu169955\tu169955\nu169956\tu169956\nu169957\tu169957\nu169958\tu169958\nu169959\tu169959\nu169963\tu169963\nu178449\tu169963\nu169965\tu169965\nu169966\tu169966\nu169967\tu169967\nu169968\tu169968\nu169971\tu169971\nu169972\tu169972\nu169976\tu169976\nu169980\tu169980\nu169987\tu169987\nu169989\tu169989\nu169990\tu169990\nu169991\tu169991\nu169993\tu169993\nu169994\tu169994\nu169997\tu169997\nu169998\tu169998\nu169999\tu169999\nu170001\tu170001\nu170005\tu170005\nu170008\tu170008\nu170009\tu170009\nu170011\tu170011\nu170013\tu170013\nu170020\tu170020\nu170022\tu170022\nu170026\tu170026\nu170027\tu170027\nu170028\tu170028\nu170030\tu170030\nu170034\tu170034\nu170036\tu170036\nu170038\tu170038\nu170045\tu170045\nu170046\tu170046\nu170047\tu170047\nu170050\tu170050\nu170051\tu170051\nu170052\tu170052\nu170055\tu170055\nu170056\tu170056\nu170059\tu170059\nu170062\tu170062\nu170063\tu170063\nu170064\tu170064\nu170069\tu170069\nu170070\tu170070\nu170075\tu170075\nu170077\tu170077\nu170079\tu170079\nu170080\tu170080\nu170083\tu170083\nu170088\tu170088\nu170089\tu170089\nu170092\tu170092\nu170096\tu170096\nu170097\tu170097\nu170102\tu170102\nu170109\tu170109\nu170110\tu170110\nu170111\tu170111\nu170112\tu170112\nu170117\tu170117\nu170119\tu170119\nu170121\tu170121\nu170123\tu170123\nu170125\tu170125\nu170126\tu170126\nu170130\tu170130\nu170131\tu170131\nu170133\tu170133\nu170136\tu170136\nu170137\tu170137\nu170140\tu170140\nu170141\tu170141\nu170142\tu170142\nu170143\tu170143\nu170144\tu170144\nu170147\tu170147\nu170148\tu170148\nu170150\tu170150\nu170153\tu170153\nu170155\tu170155\nu170158\tu170158\nu170162\tu170162\nu170164\tu170164\nu170166\tu170166\nu170167\tu170167\nu170169\tu170169\nu170171\tu170171\nu170172\tu170172\nu170179\tu170179\nu170186\tu170186\nu170190\tu170190\nu170196\tu170196\nu170198\tu170198\nu170201\tu170201\nu170202\tu170202\nu170203\tu170203\nu170204\tu170204\nu170209\tu170209\nu170210\tu170210\nu170212\tu170212\nu170213\tu170213\nu170215\tu170215\nu170216\tu170216\nu170221\tu170221\nu170222\tu170222\nu170225\t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6064\nu176066\tu176066\nu176069\tu176069\nu176070\tu176070\nu176072\tu176072\nu176075\tu176075\nu176078\tu176078\nu176083\tu176083\nu176086\tu176086\nu176092\tu176092\nu176094\tu176094\nu176097\tu176097\nu176103\tu176103\nu176104\tu176104\nu176105\tu176105\nu176109\tu176109\nu176111\tu176111\nu176112\tu176112\nu176115\tu176115\nu176117\tu176117\nu176118\tu176118\nu176120\tu176120\nu176123\tu176123\nu176127\tu176127\nu176128\tu176128\nu176129\tu176129\nu176133\tu176133\nu176134\tu176134\nu176136\tu176136\nu176138\tu176138\nu176141\tu176141\nu176142\tu176142\nu176145\tu176145\nu176146\tu176146\nu176147\tu176147\nu176148\tu176148\nu176149\tu176149\nu176153\tu176153\nu176154\tu176154\nu176156\tu176156\nu176157\tu176157\nu176159\tu176159\nu176161\tu176161\nu176162\tu176162\nu176165\tu176165\nu176166\tu176166\nu176168\tu176168\nu176170\tu176170\nu176173\tu176173\nu176177\tu176177\nu176178\tu176178\nu176179\tu176179\nu176180\tu176180\nu176182\tu176182\nu176183\tu176183\nu176185\tu176185\nu176188\tu176188\nu176190\tu176190\nu176193\tu176193\nu176195\tu176195\nu176199\tu176199\nu176200\tu176200\nu176203\tu176203\nu176204\tu176204\nu176205\tu176205\nu176206\tu176206\nu176207\tu176207\nu176210\tu176210\nu176212\tu176212\nu176216\tu176216\nu176218\tu176218\nu176220\tu176220\nu176221\tu176221\nu176223\tu176223\nu176224\tu176224\nu176225\tu176225\nu176227\tu176227\nu176229\tu176229\nu176233\tu176233\nu176234\tu176234\nu176236\tu176236\nu176239\tu176239\nu176241\tu176241\nu176242\tu176242\nu176243\tu176243\nu176247\tu176247\nu176249\tu176249\nu176255\tu176255\nu176256\tu176256\nu176257\tu176257\nu176259\tu176259\nu176264\tu176264\nu176265\tu176265\nu176266\tu176266\nu176267\tu176267\nu176268\tu176268\nu176271\tu176271\nu176275\tu176275\nu176276\tu176276\nu176277\tu176277\nu176280\tu176280\nu176283\tu176283\nu176284\tu176284\nu176286\tu176286\nu176288\tu176288\nu176291\tu176291\nu176293\tu176293\nu176294\tu176294\nu176295\tu176295\nu176296\tu176296\nu176297\tu176297\nu176298\tu176298\nu176301\tu176301\nu176302\tu176302\nu176304\tu176304\nu176305\tu176305\nu176308\tu176308\nu176310\tu176310\nu176311\tu176311\nu176312\tu176312\nu176313\tu176313\nu176314\tu176314\nu176315\tu176315\nu176317\tu176317\nu176319\tu176319\nu176323\tu176323\nu176324\tu176324\nu176327\tu176327\nu176328\tu176328\nu176329\tu176329\nu176330\tu176330\nu176331\tu176331\nu176334\tu176334\nu176337\tu176337\nu176338\tu176338\nu176345\tu176345\nu176346\tu176346\nu176347\tu176347\nu176348\tu176348\nu176349\tu176349\nu176350\tu176350\nu176356\tu176356\nu176357\tu176357\nu176358\tu176358\nu176359\tu176359\nu176360\tu176360\nu176361\tu176361\nu176362\tu176362\nu22279\tu176362\nu176365\tu176365\nu176367\tu176367\nu176368\tu176368\nu176371\tu176371\nu176374\tu176374\nu176375\tu176375\nu176378\tu176378\nu176379\tu176379\nu176380\tu176380\nu176381\tu176381\nu176382\tu176382\nu176383\tu176383\nu176386\tu176386\nu176389\tu176389\nu176394\tu176394\nu176395\tu176395\nu176399\tu176399\nu176401\tu176401\nu176402\tu176402\nu176405\tu176405\nu176406\tu176406\nu176410\tu176410\nu176412\tu176412\nu176413\tu176413\nu176415\tu176415\nu176419\tu176419\nu176423\tu176423\nu176424\tu176424\nu176426\tu176426\nu176428\tu176428\nu176429\tu176429\nu176430\tu176430\nu176432\tu176432\nu176434\tu176434\nu176440\tu176440\nu176442\tu176442\nu176444\tu176444\nu176445\tu176445\nu176447\tu176447\nu176448\tu176448\nu176450\tu176450\nu176455\tu176455\nu176461\tu176461\nu176463\tu176463\nu176464\tu176464\nu176466\tu176466\nu176467\tu176467\nu176470\tu176470\nu176471\tu176471\nu176473\tu176473\nu176474\tu176474\nu176475\tu176475\nu176479\tu176479\nu176480\tu176480\nu176485\tu176485\nu176487\tu176487\nu176488\tu176488\nu176491\tu176491\nu176493\tu176493\nu176494\tu176494\nu176495\tu176495\nu176496\tu176496\nu176497\tu176497\nu176498\tu176498\nu176499\tu176499\nu176500\tu176500\nu176501\tu176501\nu176503\tu176503\nu176504\tu176504\nu176506\tu176506\nu176507\tu176507\nu176509\tu176509\nu176510\tu176510\nu176511\tu176511\nu176514\tu176514\nu176516\tu176516\nu176523\tu176523\nu176525\tu176525\nu176527\tu176527\nu176532\tu176532\nu176533\tu176533\nu176535\tu176535\nu176540\tu176540\nu176541\tu176541\nu176542\tu176542\nu176543\tu176543\nu176545\tu176545\nu176549\tu176549\nu176555\tu176555\nu176559\tu176559\nu176562\tu176562\nu176563\tu176563\nu176564\tu176564\nu176565\tu176565\nu176568\tu176568\nu176571\tu176571\nu176575\tu176575\nu176579\tu176579\nu176581\tu176581\nu176582\tu176582\nu176583\tu176583\nu176584\tu176584\nu176588\tu176588\nu176590\tu176590\nu176591\tu176591\nu176597\tu176597\nu176598\tu176598\nu176602\tu176602\nu176604\tu176604\nu176606\tu176606\nu176609\tu176609\nu176617\tu176617\nu176618\tu176618\nu176620\tu176620\nu176622\tu176622\nu176624\tu176624\nu176625\tu176625\nu176629\tu176629\nu176634\tu176634\nu176639\tu176639\nu176645\tu176645\nu176647\tu176647\nu176651\tu176651\nu176652\tu176652\nu176654\tu176654\nu176655\tu176655\nu176657\tu176657\nu176658\tu176658\nu176660\tu176660\nu176667\t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3626\tu183626\nu183628\tu183628\nu183629\tu183629\nu183635\tu183635\nu183636\tu183636\nu183637\tu183637\nu183641\tu183641\nu183644\tu183644\nu183646\tu183646\nu183648\tu183648\nu183649\tu183649\nu183652\tu183652\nu183654\tu183654\nu183656\tu183656\nu183659\tu183659\nu183660\tu183660\nu183662\tu183662\nu183669\tu183669\nu183671\tu183671\nu183673\tu183673\nu183676\tu183676\nu183677\tu183677\nu183678\tu183678\nu183684\tu183684\nu183691\tu183691\nu183693\tu183693\nu183696\tu183696\nu183698\tu183698\nu183699\tu183699\nu183701\tu183701\nu183705\tu183705\nu183707\tu183707\nu183712\tu183712\nu183718\tu183718\nu183723\tu183723\nu183724\tu183724\nu183725\tu183725\nu183727\tu183727\nu183729\tu183729\nu183730\tu183730\nu183731\tu183731\nu183734\tu183734\nu183737\tu183737\nu183738\tu183738\nu183741\tu183741\nu183742\tu183742\nu183745\tu183745\nu183747\tu183747\nu183749\tu183749\nu183751\tu183751\nu183756\tu183756\nu183758\tu183758\nu183759\tu183759\nu183767\tu183767\nu183776\tu183776\nu183781\tu183781\nu183783\tu183783\nu183786\tu183786\nu183788\tu183788\nu183789\tu183789\nu183797\tu183797\nu183798\tu183798\nu183808\tu183808\nu183809\tu183809\nu183811\tu183811\nu183812\tu183812\nu183814\tu183814\nu183817\tu183817\nu183819\tu183819\nu183821\tu183821\nu183822\tu183822\nu183827\tu183827\nu183828\tu183828\nu183829\tu183829\nu183831\tu183831\nu183833\tu183833\nu183834\tu183834\nu183836\tu183836\nu183837\tu183837\nu183840\tu183840\nu183845\tu183845\nu183846\tu183846\nu183848\tu183848\nu183849\tu183849\nu183852\tu183852\nu183857\tu183857\nu183862\tu183862\nu183871\tu183871\nu183873\tu183873\nu183875\tu183875\nu183877\tu183877\nu183879\tu183879\nu183882\tu183882\nu183883\tu183883\nu183885\tu183885\nu183888\tu183888\nu183891\tu183891\nu183897\tu183897\nu183898\tu183898\nu183899\tu183899\nu183900\tu183900\nu183905\tu183905\nu183906\tu183906\nu183909\tu183909\nu183913\tu183913\nu183916\tu183916\nu183920\tu183920\nu183924\tu183924\nu183925\tu183925\nu183926\tu183926\nu183927\tu183927\nu183929\tu183929\nu183930\tu183930\nu183932\tu183932\nu183937\tu183937\nu183940\tu183940\nu183943\tu183943\nu183945\tu183945\nu183946\tu183946\nu183947\tu183947\nu183950\tu183950\nu183951\tu183951\nu183952\tu183952\nu183953\tu183953\nu183957\tu183957\nu183959\tu183959\nu183960\tu183960\nu183961\tu183961\nu183963\tu183963\nu183964\tu183964\nu183969\tu183969\nu183970\tu183970\nu183976\tu183976\nu183979\tu183979\nu183981\tu183981\nu183982\tu183982\nu183987\tu183987\nu183989\tu183989\nu183994\tu183994\nu183995\tu183995\nu183996\tu183996\nu184001\tu184001\nu184002\tu184002\nu184003\tu184003\nu184008\tu184008\nu184010\tu184010\nu184014\tu184014\nu184017\tu184017\nu184025\tu184025\nu184026\tu184026\nu184029\tu184029\nu184032\tu184032\nu184037\tu184037\nu184041\tu184041\nu184042\tu184042\nu184044\tu184044\nu184046\tu184046\nu184047\tu184047\nu184048\tu184048\nu184050\tu184050\nu184051\tu184051\nu184057\tu184057\nu184059\tu184059\nu184062\tu184062\nu184063\tu184063\nu184069\tu184069\nu184070\tu184070\nu184071\tu184071\nu184075\tu184075\nu184078\tu184078\nu184082\tu184082\nu184083\tu184083\nu184084\tu184084\nu184085\tu184085\nu184087\tu184087\nu184088\tu184088\nu184097\tu184097\nu184099\tu184099\nu184106\tu184106\nu184111\tu184111\nu184113\tu184113\nu184117\tu184117\nu184121\tu184121\nu184137\tu184137\nu184141\tu184141\nu184142\tu184142\nu184149\tu184149\nu184151\tu184151\nu184153\tu184153\nu184154\tu184154\nu184155\tu184155\nu184156\tu184156\nu184166\tu184166\nu184169\tu184169\nu184170\tu184170\nu184172\tu184172\nu184176\tu184176\nu184182\tu184182\nu184183\tu184183\nu184185\tu184185\nu184188\tu184188\nu184201\tu184201\nu184202\tu184202\nu184204\tu184204\nu184209\tu184209\nu184215\tu184215\nu184217\tu184217\nu184218\tu184218\nu184220\tu184220\nu184221\tu184221\nu184227\tu184227\nu184237\tu184237\nu184238\tu184238\nu184242\tu184242\nu184245\tu184245\nu184248\tu184248\nu184251\tu184251\nu184253\tu184253\nu184255\tu184255\nu184258\tu184258\nu184261\tu184261\nu184267\tu184267\nu184268\tu184268\nu184271\tu184271\nu184279\tu184279\nu184281\tu184281\nu184282\tu184282\nu184284\tu184284\nu184285\tu184285\nu184290\tu184290\nu184299\tu184299\nu184306\tu184306\nu184309\tu184309\nu184318\tu184318\nu184320\tu184320\nu184321\tu184321\nu184322\tu184322\nu184327\tu184327\nu184334\tu184334\nu184336\tu184336\nu184344\tu184344\nu184349\tu184349\nu184350\tu184350\nu184359\tu184359\nu184364\tu184364\nu184367\tu184367\nu184370\tu184370\nu184371\tu184371\nu184373\tu184373\nu184374\tu184374\nu184375\tu184375\nu184377\tu184377\nu184379\tu184379\nu184380\tu184380\nu184385\tu184385\nu184399\tu184399\nu184405\tu184405\nu184419\tu184419\nu184424\tu184424\nu184426\tu184426\nu184428\tu184428\nu184429\tu184429\nu184430\tu184430\nu184431\tu184431\nu184435\tu184435\nu184436\tu184436\nu184440\tu184440\nu184446\tu184446\nu184455\tu184455\nu184456\tu184456\nu184464\tu184464\nu184466\tu184466\nu184475\tu184475\nu184480\tu184480\nu184481\tu184481\nu184482\tu184482\nu184486\tu184486\nu184488\tu184488\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292\tu186292\nu186293\tu186293\nu186296\tu186296\nu186307\tu186307\nu186308\tu186308\nu186309\tu186309\nu186311\tu186311\nu186312\tu186312\nu186313\tu186313\nu186319\tu186319\nu186327\tu186327\nu186329\tu186329\nu186330\tu186330\nu186331\tu186331\nu186332\tu186332\nu186333\tu186333\nu186334\tu186334\nu186336\tu186336\nu186338\tu186338\nu186339\tu186339\nu186340\tu186340\nu186343\tu186343\nu186345\tu186345\nu186346\tu186346\nu186348\tu186348\nu186353\tu186353\nu186357\tu186357\nu186361\tu186361\nu186365\tu186365\nu186366\tu186366\nu186368\tu186368\nu186369\tu186369\nu186373\tu186373\nu186375\tu186375\nu186376\tu186376\nu186380\tu186380\nu186381\tu186381\nu186385\tu186385\nu186386\tu186386\nu186387\tu186387\nu186391\tu186391\nu186392\tu186392\nu186393\tu186393\nu186396\tu186396\nu186401\tu186401\nu186406\tu186406\nu186407\tu186407\nu186408\tu186408\nu186409\tu186409\nu186416\tu186416\nu186417\tu186417\nu186422\tu186422\nu186424\tu186424\nu186425\tu186425\nu186428\tu186428\nu186430\tu186430\nu186432\tu186432\nu186433\tu186433\nu186435\tu186435\nu186437\tu186437\nu186440\tu186440\nu186441\tu186441\nu186443\tu186443\nu186445\tu186445\nu186446\tu186446\nu186456\tu186456\nu186457\tu186457\nu186463\tu186463\nu186472\tu186472\nu186478\tu186478\nu186480\tu186480\nu186482\tu186482\nu186485\tu186485\nu186487\tu186487\nu186489\tu186489\nu186497\tu186497\nu186499\tu186499\nu186501\tu186501\nu186507\tu186507\nu186508\tu186508\nu186509\tu186509\nu186518\tu186518\nu186520\tu186520\nu186522\tu186522\nu186526\tu186526\nu186531\tu186531\nu186532\tu186532\nu186533\tu186533\nu186534\tu186534\nu186538\tu186538\nu186542\tu186542\nu186545\tu186545\nu186546\tu186546\nu186548\tu186548\nu186553\tu186553\nu186554\tu186554\nu186555\tu186555\nu186563\tu186563\nu186568\tu186568\nu186573\tu186573\nu186581\tu186581\nu186586\tu186586\nu186588\tu186588\nu186589\tu186589\nu186597\tu186597\nu186599\tu186599\nu186605\tu186605\nu186606\tu186606\nu186609\tu186609\nu186613\tu186613\nu186615\tu186615\nu186616\tu186616\nu186619\tu186619\nu186624\tu186624\nu186625\tu186625\nu186632\tu186632\nu186634\tu186634\nu186639\tu186639\nu186649\tu186649\nu186655\tu186655\nu186661\tu186661\nu186664\tu186664\nu186666\tu186666\nu186673\tu186673\nu186681\tu186681\nu186683\tu186683\nu186692\tu186692\nu186694\tu186694\nu186695\tu186695\nu186699\tu186699\nu186706\tu186706\nu186709\tu186709\nu186711\tu186711\nu186713\tu186713\nu186715\tu186715\nu186720\tu186720\nu186726\tu186726\nu186727\tu186727\nu186739\tu186739\nu186744\tu186744\nu186752\tu186752\nu186757\tu186757\nu186758\tu186758\nu186759\tu186759\nu186761\tu186761\nu186762\tu186762\nu186769\tu186769\nu186776\tu186776\nu186779\tu186779\nu186786\tu186786\nu186787\tu186787\nu186788\tu186788\nu186795\tu186795\nu186796\tu186796\nu186798\tu186798\nu186800\tu186800\nu186802\tu186802\nu186809\tu186809\nu186818\tu186818\nu186822\tu186822\nu186830\tu186830\nu186832\tu186832\nu186835\tu186835\nu186837\tu186837\nu186851\tu186851\nu186854\tu186854\nu186855\tu186855\nu186860\tu186860\nu186861\tu186861\nu186862\tu186862\nu186863\tu186863\nu186869\tu186869\nu186874\tu186874\nu186878\tu186878\nu186880\tu186880\nu186882\tu186882\nu186883\tu186883\nu186888\tu186888\nu186889\tu186889\nu186890\tu186890\nu186893\tu186893\nu186895\tu186895\nu186896\tu186896\nu186899\tu186899\nu186907\tu186907\nu186914\tu186914\nu186917\tu186917\nu186923\tu186923\nu186936\tu186936\nu186943\tu186943\nu186950\tu186950\nu186951\tu186951\nu186953\tu186953\nu186959\tu186959\nu186961\tu186961\nu186962\tu186962\nu186966\tu186966\nu186972\tu186972\nu186975\tu186975\nu186976\tu186976\nu186978\tu186978\nu186980\tu186980\nu186983\tu186983\nu186989\tu186989\nu186992\tu186992\nu186993\tu186993\nu186994\tu186994\nu186995\tu186995\nu187006\tu187006\nu187019\tu187019\nu187024\tu187024\nu187026\tu187026\nu187028\tu187028\nu187029\tu187029\nu187031\tu187031\nu187033\tu187033\nu187034\tu187034\nu187035\tu187035\nu187038\tu187038\nu187053\tu187053\nu187054\tu187054\nu187060\tu187060\nu187071\tu187071\nu187077\tu187077\nu187079\tu187079\nu187083\tu187083\nu187085\tu187085\nu187088\tu187088\nu187090\tu187090\nu187092\tu187092\nu187093\tu187093\nu187096\tu187096\nu187098\tu187098\nu187100\tu187100\nu187101\tu187101\nu187103\tu187103\nu187106\tu187106\nu187112\tu187112\nu187114\tu187114\nu187116\tu187116\nu187117\tu187117\nu187119\tu187119\nu187124\tu187124\nu187127\tu187127\nu187129\tu187129\nu187131\tu187131\nu187133\tu187133\nu187136\tu187136\nu187137\tu187137\nu187138\tu187138\nu187140\tu187140\nu187142\tu187142\nu187144\tu187144\nu187145\tu187145\nu187147\tu187147\nu187154\tu187154\nu187157\tu187157\nu187159\tu187159\nu187160\tu187160\nu187161\tu187161\nu187162\tu187162\nu187164\tu187164\nu187165\tu187165\nu187169\tu187169\nu187172\tu187172\nu187175\tu187175\nu187176\tu187176\nu187180\tu187180\nu187183\tu187183\nu187184\tu187184\nu187188\tu187188\nu187191\tu187191\nu187193\tu187193\nu187194\tu187194\nu187195\tu187195\nu187200\tu187200\nu187201\tu187201\nu187202\tu187202\n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921\tu187921\nu187924\tu187924\nu187927\tu187927\nu187931\tu187931\nu187935\tu187935\nu187936\tu187936\nu187941\tu187941\nu187949\tu187949\nu187954\tu187954\nu187961\tu187961\nu187962\tu187962\nu187966\tu187966\nu187967\tu187967\nu187972\tu187972\nu187986\tu187986\nu187992\tu187992\nu187993\tu187993\nu187994\tu187994\nu187996\tu187996\nu187998\tu187998\nu188000\tu188000\nu188005\tu188005\nu188006\tu188006\nu188007\tu188007\nu188008\tu188008\nu188010\tu188010\nu188012\tu188012\nu188013\tu188013\nu188021\tu188021\nu3848\tu188021\nu188026\tu188026\nu188028\tu188028\nu188029\tu188029\nu188031\tu188031\nu188033\tu188033\nu188036\tu188036\nu188037\tu188037\nu188038\tu188038\nu188040\tu188040\nu188044\tu188044\nu188047\tu188047\nu188051\tu188051\nu188052\tu188052\nu188054\tu188054\nu188055\tu188055\nu188058\tu188058\nu188060\tu188060\nu188063\tu188063\nu188064\tu188064\nu188065\tu188065\nu188066\tu188066\nu188067\tu188067\nu188068\tu188068\nu188071\tu188071\nu188074\tu188074\nu188075\tu188075\nu188081\tu188081\nu188082\tu188082\nu188088\tu188088\nu188094\tu188094\nu188095\tu188095\nu188096\tu188096\nu188099\tu188099\nu188100\tu188100\nu188101\tu188101\nu188102\tu188102\nu188109\tu188109\nu188110\tu188110\nu188115\tu188115\nu188116\tu188116\nu188119\tu188119\nu188120\tu188120\nu188122\tu188122\nu188125\tu188125\nu188126\tu188126\nu188129\tu188129\nu188133\tu188133\nu188138\tu188138\nu188147\tu188147\nu188150\tu188150\nu188155\tu188155\nu188158\tu188158\nu188162\tu188162\nu188163\tu188163\nu188164\tu188164\nu188166\tu188166\nu188169\tu188169\nu188170\tu188170\nu188173\tu188173\nu188177\tu188177\nu188184\tu188184\nu188187\tu188187\nu23106\tu188187\nu272302\tu188187\nu273363\tu188187\nu40130\tu188187\nu4457\tu188187\nu188192\tu188192\nu188193\tu188193\nu188194\tu188194\nu188195\tu188195\nu188196\tu188196\nu188197\tu188197\nu188199\tu188199\nu188201\tu188201\nu188204\tu188204\nu188206\tu188206\nu188209\tu188209\nu188211\tu188211\nu188214\tu188214\nu188216\tu188216\nu188221\tu188221\nu188224\tu188224\nu188228\tu188228\nu188230\tu188230\nu188231\tu188231\nu188232\tu188232\nu188233\tu188233\nu188234\tu188234\nu188236\tu188236\nu188238\tu188238\nu188239\tu188239\nu188241\tu188241\nu188242\tu188242\nu188248\tu188248\nu188250\tu188250\nu188253\tu188253\nu188254\tu188254\nu188257\tu188257\nu188258\tu188258\nu188264\tu188264\nu188274\tu188274\nu188277\tu188277\nu188281\tu188281\nu188282\tu188282\nu188285\tu188285\nu188300\tu188300\nu188305\tu188305\nu188306\tu188306\nu188310\tu188310\nu188313\tu188313\nu280954\tu188313\nu28157\tu188313\nu28631\tu188313\nu34990\tu188313\nu43579\tu188313\nu188316\tu188316\nu188317\tu188317\nu188324\tu188324\nu188328\tu188328\nu188329\tu188329\nu188331\tu188331\nu188334\tu188334\nu188336\tu188336\nu188337\tu188337\nu188338\tu188338\nu188339\tu188339\nu188347\tu188347\nu188353\tu188353\nu188356\tu188356\nu188357\tu188357\nu25589\tu188357\nu188362\tu188362\nu188365\tu188365\nu188369\tu188369\nu188370\tu188370\nu188371\tu188371\nu188373\tu188373\nu188376\tu188376\nu188380\tu188380\nu188381\tu188381\nu188382\tu188382\nu188385\tu188385\nu188386\tu188386\nu188388\tu188388\nu188392\tu188392\nu188394\tu188394\nu188395\tu188395\nu188398\tu188398\nu188401\tu188401\nu188406\tu188406\nu188410\tu188410\nu188411\tu188411\nu188413\tu188413\nu188420\tu188420\nu188424\tu188424\nu188425\tu188425\nu188429\tu188429\nu188431\tu188431\nu188433\tu188433\nu188439\tu188439\nu188450\tu188450\nu188469\tu188469\nu188472\tu188472\nu188473\tu188473\nu188474\tu188474\nu188480\tu188480\nu188483\tu188483\nu188489\tu188489\nu188491\tu188491\nu188497\tu188497\nu188501\tu188501\nu188502\tu188502\nu188505\tu188505\nu188509\tu188509\nu188510\tu188510\nu188511\tu188511\nu188514\tu188514\nu188523\tu188523\nu188525\tu188525\nu188527\tu188527\nu188529\tu188529\nu188530\tu188530\nu188534\tu188534\nu188537\tu188537\nu188546\tu188546\nu188547\tu188547\nu188548\tu188548\nu188552\tu188552\nu188560\tu188560\nu188561\tu188561\nu188563\tu188563\nu188566\tu188566\nu188570\tu188570\nu188572\tu188572\nu188574\tu188574\nu188576\tu188576\nu188577\tu188577\nu188578\tu188578\nu188580\tu188580\nu188583\tu188583\nu188584\tu188584\nu188586\tu188586\nu188587\tu188587\nu188588\tu188588\nu188590\tu188590\nu188593\tu188593\nu188595\tu188595\nu188601\tu188601\nu188604\tu188604\nu188607\tu188607\nu188618\tu188618\nu188620\tu188620\nu188621\tu188621\nu188622\tu188622\nu188629\tu188629\nu188630\tu188630\nu188642\tu188642\nu188644\tu188644\nu188648\tu188648\nu188652\tu188652\nu188653\tu188653\nu188657\tu188657\nu188659\tu188659\nu1923\tu188659\nu232438\tu188659\nu263466\tu188659\nu57387\tu188659\nu60483\tu188659\nu62734\tu188659\nu76439\tu188659\nu81435\tu188659\nu85081\tu188659\nu98153\tu188659\nu188667\tu188667\nu188668\tu188668\nu188669\tu188669\nu188676\tu188676\nu188689\tu188689\nu188693\tu188693\nu188699\tu188699\nu188702\tu188702\nu188716\tu188716\nu188721\tu188721\nu188728\tu188728\nu188731\tu188731\nu188733\tu188733\nu188742\tu188742\nu188747\tu188747\nu188748\tu188748\nu188749\tu188749\nu188755\tu188755\nu188767\tu188767\nu188772\tu188772\nu188774\tu188774\nu188776\tu188776\nu188778\tu188778\nu188786\tu188786\nu188788\tu188788\nu188790\tu188790\nu188794\tu188794\nu188798\tu188798\nu188799\tu188799\nu188800\tu188800\nu188801\tu188801\nu188802\tu188802\nu188810\tu188810\nu188812\tu188812\nu188819\tu188819\nu188826\tu188826\nu188831\tu188831\nu188837\tu188837\nu188840\tu188840\nu188846\tu188846\nu188847\tu188847\nu188849\tu188849\nu188860\tu188860\nu188863\tu188863\nu188864\tu188864\nu188866\tu188866\nu188867\tu188867\nu188868\tu188868\nu188869\tu188869\nu188871\tu188871\nu188872\tu188872\nu188874\tu188874\nu188882\tu188882\nu188883\tu188883\nu188885\tu188885\nu188886\tu188886\nu188887\tu188887\nu188889\tu188889\nu188893\tu188893\nu188896\tu188896\nu188900\tu188900\nu188903\tu188903\nu188904\tu188904\nu188907\tu188907\nu188910\tu188910\nu188914\tu188914\nu188918\tu188918\nu188923\tu188923\nu188928\tu188928\nu188938\tu188938\nu188940\tu188940\nu188943\tu188943\nu188944\tu188944\nu188946\tu188946\nu188948\tu188948\nu188954\tu188954\nu188959\tu188959\nu188961\tu188961\nu188971\tu188971\nu188972\tu188972\nu188973\tu188973\nu188974\tu188974\nu188976\tu188976\nu188979\tu188979\nu188985\tu188985\nu188988\tu188988\nu188989\tu188989\nu188992\tu188992\nu188995\tu188995\nu188997\tu188997\nu189000\tu189000\nu189003\tu189003\nu268981\tu189003\nu43525\tu189003\nu189007\tu189007\nu189008\tu189008\nu189010\tu189010\nu189011\tu189011\nu189017\tu189017\nu189020\tu189020\nu189024\tu189024\nu189026\tu189026\nu189028\tu189028\nu189030\tu189030\nu189032\tu189032\nu189038\tu189038\nu189039\tu189039\nu189048\tu189048\nu189051\tu189051\nu189052\tu189052\nu189054\tu189054\nu189056\tu189056\nu189062\tu189062\nu189065\tu189065\nu189067\tu189067\nu189075\tu189075\nu189079\tu189079\nu189089\tu189089\nu189090\tu189090\nu189091\tu189091\nu189094\tu189094\nu189095\tu189095\nu189099\tu189099\nu189103\tu189103\nu189104\tu189104\nu189105\tu189105\nu189106\tu189106\nu189108\tu189108\nu189117\tu189117\nu189118\tu189118\nu189122\tu189122\nu189124\tu189124\nu189125\tu189125\nu189126\tu189126\nu189128\tu189128\nu189133\tu189133\nu189135\tu189135\nu189139\tu189139\nu189141\tu189141\nu189143\tu189143\nu189144\tu189144\nu189146\tu189146\nu189151\tu189151\nu189154\tu189154\nu189157\tu189157\nu189163\tu189163\nu189165\tu189165\nu189166\tu189166\nu189169\tu189169\nu189172\tu189172\nu189174\tu189174\nu189177\tu189177\nu189181\tu189181\nu189183\tu189183\nu189185\tu189185\nu189187\tu189187\nu189190\tu189190\nu189192\tu189192\nu189194\tu189194\nu189195\tu189195\nu189212\tu189212\nu189215\tu189215\nu189216\tu189216\nu189220\tu189220\nu189225\tu189225\nu189232\tu189232\nu189233\tu189233\nu189234\tu189234\nu189237\tu189237\nu189239\tu189239\nu189242\tu189242\nu189244\tu189244\nu189248\tu189248\nu189249\tu189249\nu189253\tu189253\nu189258\tu189258\nu189260\tu189260\nu189262\tu189262\nu189273\tu189273\nu189276\tu189276\nu189278\tu189278\nu189283\tu189283\nu189286\tu189286\nu189288\tu189288\nu189291\tu189291\nu189294\tu189294\nu189296\tu189296\nu189301\tu189301\nu189302\tu189302\nu189304\tu189304\nu189305\tu189305\nu189306\tu189306\nu189311\tu189311\nu189320\tu189320\nu189321\tu189321\nu189322\tu189322\nu189323\tu189323\nu189324\tu189324\nu189325\tu189325\nu189326\tu189326\nu189330\tu189330\nu189331\tu189331\nu189336\tu189336\nu189339\tu189339\nu189343\tu189343\nu189348\tu189348\nu189350\tu189350\nu189351\tu189351\nu189352\tu189352\nu189355\tu189355\nu189362\tu189362\nu189364\tu189364\nu189369\tu189369\nu189371\tu189371\nu189374\tu189374\nu189377\tu189377\nu189378\tu189378\nu189380\tu189380\nu189383\tu189383\nu189386\tu189386\nu189387\tu189387\nu189388\tu189388\nu189389\tu189389\nu189390\tu189390\nu189391\tu189391\nu189394\tu189394\nu189395\tu189395\nu189396\tu189396\nu189399\tu189399\nu189400\tu189400\nu189407\tu189407\nu189408\tu189408\nu189410\tu189410\nu189411\tu189411\nu189414\tu189414\nu189417\tu189417\nu189422\tu189422\nu189424\tu189424\nu189425\tu189425\nu189426\tu189426\nu189430\tu189430\nu189442\tu189442\nu189443\tu189443\nu189444\tu189444\nu189445\tu189445\nu189446\tu189446\nu189447\tu189447\nu189448\tu189448\nu189460\tu189460\nu189462\tu189462\nu189463\tu189463\nu189464\tu189464\nu189468\tu189468\nu189469\tu189469\nu189472\tu189472\nu189475\tu189475\nu189479\tu189479\nu189480\tu189480\nu189483\tu189483\nu189485\tu189485\nu189486\tu189486\nu189488\tu189488\nu189491\tu189491\nu189492\tu189492\nu189496\tu189496\nu189497\tu189497\nu189499\tu189499\nu189500\tu189500\nu189503\tu189503\nu189506\tu189506\nu189509\tu189509\nu189510\tu189510\nu189512\tu189512\nu189513\tu189513\nu189516\tu189516\nu189522\tu189522\nu189524\tu189524\nu189528\tu189528\nu189530\tu189530\nu189532\tu189532\nu1949\tu189532\nu2663\tu189532\nu287778\tu189532\nu51529\tu189532\nu7983\tu189532\nu929\tu189532\nu9436\tu189532\nu189533\tu189533\nu189537\tu189537\nu189544\tu189544\nu189545\tu189545\nu189549\tu189549\nu189551\tu189551\nu189552\tu1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5628\tu195628\nu195632\tu195632\nu195634\tu195634\nu195639\tu195639\nu195640\tu195640\nu195642\tu195642\nu195643\tu195643\nu195652\tu195652\nu195653\tu195653\nu195656\tu195656\nu195657\tu195657\nu195664\tu195664\nu195667\tu195667\nu195676\tu195676\nu195682\tu195682\nu195684\tu195684\nu195685\tu195685\nu195691\tu195691\nu195697\tu195697\nu23496\tu195697\nu23678\tu195697\nu245187\tu195697\nu6557\tu195697\nu773\tu195697\nu195701\tu195701\nu195703\tu195703\nu195711\tu195711\nu195712\tu195712\nu195723\tu195723\nu195728\tu195728\nu195737\tu195737\nu195739\tu195739\nu195748\tu195748\nu195749\tu195749\nu195751\tu195751\nu195752\tu195752\nu195754\tu195754\nu195756\tu195756\nu195758\tu195758\nu195762\tu195762\nu195764\tu195764\nu195765\tu195765\nu195770\tu195770\nu195772\tu195772\nu195773\tu195773\nu195777\tu195777\nu195778\tu195778\nu195781\tu195781\nu195783\tu195783\nu195785\tu195785\nu195787\tu195787\nu195789\tu195789\nu195790\tu195790\nu195794\tu195794\nu195795\tu195795\nu195796\tu195796\nu195798\tu195798\nu195800\tu195800\nu195808\tu195808\nu195812\tu195812\nu195818\tu195818\nu195819\tu195819\nu195820\tu195820\nu195825\tu195825\nu195828\tu195828\nu195829\tu195829\nu195831\tu195831\nu195832\tu195832\nu195835\tu195835\nu195838\tu195838\nu195839\tu195839\nu195841\tu195841\nu195842\tu195842\nu195843\tu195843\nu195845\tu195845\nu195847\tu195847\nu195850\tu195850\nu195853\tu195853\nu195856\tu195856\nu195857\tu195857\nu195858\tu195858\nu195860\tu195860\nu195861\tu195861\nu195862\tu195862\nu195864\tu195864\nu195867\tu195867\nu195868\tu195868\nu195870\tu195870\nu195871\tu195871\nu195877\tu195877\nu195878\tu195878\nu195879\tu195879\nu195880\tu195880\nu195881\tu195881\nu195882\tu195882\nu195885\tu195885\nu195886\tu195886\nu195887\tu195887\nu195888\tu195888\nu195890\tu195890\nu195892\tu195892\nu195893\tu195893\nu195897\tu195897\nu195905\tu195905\nu195906\tu195906\nu195908\tu195908\nu195910\tu195910\nu195915\tu195915\nu195919\tu195919\nu195925\tu195925\nu195940\tu195940\nu195943\tu195943\nu195944\tu195944\nu195945\tu195945\nu195949\tu195949\nu195950\tu195950\nu195953\tu195953\nu195955\tu195955\nu195956\tu195956\nu195957\tu195957\nu195959\tu195959\nu195961\tu195961\nu195964\tu195964\nu195965\tu195965\nu195968\tu195968\nu195979\tu195979\nu195980\tu195980\nu195989\tu195989\nu195994\tu195994\nu195997\tu195997\nu196000\tu196000\nu196010\tu196010\nu196012\tu196012\nu196013\tu196013\nu196016\tu196016\nu196017\tu196017\nu196021\tu196021\nu196026\tu196026\nu196028\tu196028\nu196029\tu196029\nu196030\tu196030\nu196031\tu196031\nu196032\tu196032\nu196033\tu196033\nu196036\tu196036\nu196040\tu196040\nu196041\tu196041\nu196048\tu196048\nu196049\tu196049\nu196056\tu196056\nu196061\tu196061\nu196062\tu196062\nu196063\tu196063\nu268464\tu196063\nu271367\tu196063\nu4164\tu196063\nu78348\tu196063\nu196066\tu196066\nu196069\tu196069\nu196072\tu196072\nu196074\tu196074\nu196075\tu196075\nu196078\tu196078\nu196081\tu196081\nu196087\tu196087\nu196094\tu196094\nu196100\tu196100\nu196112\tu196112\nu196116\tu196116\nu196125\tu196125\nu196127\tu196127\nu196128\tu196128\nu196131\tu196131\nu196134\tu196134\nu196137\tu196137\nu196139\tu196139\nu196142\tu196142\nu196145\tu196145\nu196148\tu196148\nu196149\tu196149\nu196155\tu196155\nu196159\tu196159\nu196160\tu196160\nu196163\tu196163\nu196167\tu196167\nu196168\tu196168\nu196172\tu196172\nu196174\tu196174\nu196178\tu196178\nu196181\tu196181\nu196182\tu196182\nu196184\tu196184\nu196185\tu196185\nu196190\tu196190\nu196191\tu196191\nu196192\tu196192\nu196193\tu196193\nu196196\tu196196\nu196203\tu196203\nu196204\tu196204\nu196206\tu196206\nu196212\tu196212\nu196219\tu196219\nu196224\tu196224\nu196225\tu196225\nu196226\tu196226\nu196228\tu196228\nu196231\tu196231\nu196232\tu196232\nu196234\tu196234\nu196242\tu196242\nu196243\tu196243\nu196244\tu196244\nu196245\tu196245\nu196248\tu196248\nu196252\tu196252\nu196255\tu196255\nu196259\tu196259\nu196260\tu196260\nu196263\tu196263\nu196264\tu196264\nu196265\tu196265\nu196266\tu196266\nu196271\tu196271\nu196272\tu196272\nu196276\tu196276\nu196280\tu196280\nu196281\tu196281\nu196284\tu196284\nu196286\tu196286\nu196291\tu196291\nu196292\tu196292\nu196297\tu196297\nu196299\tu196299\nu196300\tu196300\nu196302\tu196302\nu196307\tu196307\nu196311\tu196311\nu196319\tu196319\nu196322\tu196322\nu196327\tu196327\nu196331\tu196331\nu196335\tu196335\nu196351\tu196351\nu196353\tu196353\nu22085\tu196353\nu22943\tu196353\nu196356\tu196356\nu196360\tu196360\nu196374\tu196374\nu196376\tu196376\nu196377\tu196377\nu196380\tu196380\nu196381\tu196381\nu196383\tu196383\nu196384\tu196384\nu196387\tu196387\nu196389\tu196389\nu196392\tu196392\nu196393\tu196393\nu196401\tu196401\nu196411\tu196411\nu196419\tu196419\nu196421\tu196421\nu196428\tu196428\nu196429\tu196429\nu196433\tu196433\nu196437\tu196437\nu196441\tu196441\nu196454\tu196454\nu196455\tu196455\nu196456\tu196456\nu196459\tu196459\nu196462\tu196462\nu196463\tu196463\nu196465\tu196465\nu196468\tu196468\nu196470\tu196470\nu196473\tu196473\nu196477\tu196477\nu196481\tu196481\nu196484\tu196484\nu196485\tu196485\nu196488\tu196488\nu196490\tu196490\nu196494\tu196494\nu196495\tu196495\nu196496\tu196496\nu196502\tu196502\nu196504\tu196504\nu196507\tu196507\nu196508\tu196508\nu196509\tu196509\nu196510\tu196510\nu196511\tu196511\nu196512\tu196512\nu196514\tu196514\nu196515\tu196515\nu196517\tu196517\nu196518\tu196518\nu196529\tu196529\nu196531\tu196531\nu196532\tu196532\nu196533\tu196533\nu196534\tu196534\nu196537\tu196537\nu196538\tu196538\nu196543\tu196543\nu196547\tu196547\nu196549\tu196549\nu196550\tu196550\nu196554\tu196554\nu196556\tu196556\nu196559\tu196559\nu196560\tu196560\nu196561\tu196561\nu196562\tu196562\nu196565\tu196565\nu196566\tu196566\nu196569\tu196569\nu196570\tu196570\nu196571\tu196571\nu196575\tu196575\nu196577\tu196577\nu196579\tu196579\nu196580\tu196580\nu196583\tu196583\nu196587\tu196587\nu196589\tu196589\nu196592\tu196592\nu196593\tu196593\nu196594\tu196594\nu196600\tu196600\nu196602\tu196602\nu196603\tu196603\nu196605\tu196605\nu196609\tu196609\nu196611\tu196611\nu196612\tu196612\nu196614\tu196614\nu196615\tu196615\nu196618\tu196618\nu196621\tu196621\nu196623\tu196623\nu196624\tu196624\nu196625\tu196625\nu196629\tu196629\nu196630\tu196630\nu196634\tu196634\nu196637\tu196637\nu196639\tu196639\nu196641\tu196641\nu196647\tu196647\nu196648\tu196648\nu196649\tu196649\nu196652\tu196652\nu196654\tu196654\nu196656\tu196656\nu196657\tu196657\nu196658\tu196658\nu196659\tu196659\nu196661\tu196661\nu196665\tu196665\nu196666\tu196666\nu196667\tu196667\nu196668\tu196668\nu196670\tu196670\nu196671\tu196671\nu196676\tu196676\nu196677\tu196677\nu196678\tu196678\nu196679\tu196679\nu196681\tu196681\nu196683\tu196683\nu196684\tu196684\nu196690\tu196690\nu196693\tu196693\nu196695\tu196695\nu196696\tu196696\nu196697\tu196697\nu196699\tu196699\nu196700\tu196700\nu196709\tu196709\nu196710\tu196710\nu196720\tu196720\nu196721\tu196721\nu196723\tu196723\nu196724\tu196724\nu196725\tu196725\nu196738\tu196738\nu196741\tu196741\nu196742\tu196742\nu196745\tu196745\nu196750\tu196750\nu196751\tu196751\nu196752\tu196752\nu196756\tu196756\nu196757\tu196757\nu196761\tu196761\nu196764\tu196764\nu196765\tu196765\nu196772\tu196772\nu196774\tu196774\nu196776\tu196776\nu196778\tu196778\nu196779\tu196779\nu196784\tu196784\nu196789\tu196789\nu196790\tu196790\nu196794\tu196794\nu196798\tu196798\nu196799\tu196799\nu196809\tu196809\nu196810\tu196810\nu196811\tu196811\nu196812\tu196812\nu196815\tu196815\nu196821\tu196821\nu196822\tu196822\nu196826\tu196826\nu196828\tu196828\nu196830\tu196830\nu196832\tu196832\nu196834\tu196834\nu196837\tu196837\nu196840\tu196840\nu196842\tu196842\nu196843\tu196843\nu196845\tu196845\nu196847\tu196847\nu196850\tu196850\nu196853\tu196853\nu196854\tu196854\nu196856\tu196856\nu196864\tu196864\nu196866\tu196866\nu196867\tu196867\nu196871\tu196871\nu196872\tu196872\nu196874\tu196874\nu196879\tu196879\nu196881\tu196881\nu196886\tu196886\nu196888\tu196888\nu196889\tu196889\nu196892\tu196892\nu196893\tu196893\nu196894\tu196894\nu196895\tu196895\nu196900\tu196900\nu196903\tu196903\nu196906\tu196906\nu196907\tu196907\nu196910\tu196910\nu196913\tu196913\nu196915\tu196915\nu196917\tu196917\nu196918\tu196918\nu196920\tu196920\nu196922\tu196922\nu196924\tu196924\nu196925\tu196925\nu196927\tu196927\nu196929\tu196929\nu196930\tu196930\nu196941\tu196941\nu196945\tu196945\nu196947\tu196947\nu196948\tu196948\nu196950\tu196950\nu196951\tu196951\nu196952\tu196952\nu196953\tu196953\nu196954\tu196954\nu196957\tu196957\nu196960\tu196960\nu196961\tu196961\nu196962\tu196962\nu196966\tu196966\nu196967\tu196967\nu196968\tu196968\nu196972\tu196972\nu196973\tu196973\nu196974\tu196974\nu196975\tu196975\nu196976\tu196976\nu196977\tu196977\nu196979\tu196979\nu196981\tu196981\nu196982\tu196982\nu196983\tu196983\nu196985\tu196985\nu196988\tu196988\nu196992\tu196992\nu196993\tu196993\nu196995\tu196995\nu196997\tu196997\nu196998\tu196998\nu196999\tu196999\nu197000\tu197000\nu197002\tu197002\nu197006\tu197006\nu197007\tu197007\nu197010\tu197010\nu197011\tu197011\nu197012\tu197012\nu197013\tu197013\nu197014\tu197014\nu197015\tu197015\nu197018\tu197018\nu197019\tu197019\nu197021\tu197021\nu197022\tu197022\nu197024\tu197024\nu197025\tu197025\nu197026\tu197026\nu197027\tu197027\nu197031\tu197031\nu197032\tu197032\nu197033\tu197033\nu197036\tu197036\nu197038\tu197038\nu197043\tu197043\nu197044\tu197044\nu197045\tu197045\nu197047\tu197047\nu197051\tu197051\nu197052\tu197052\nu197055\tu197055\nu197057\tu197057\nu197062\tu197062\nu197065\tu197065\nu197070\tu197070\nu197072\tu197072\nu197075\tu197075\nu197077\tu197077\nu197078\tu197078\nu197081\tu197081\nu197083\tu197083\nu197087\tu197087\nu197090\tu197090\nu197092\tu197092\nu197098\tu197098\nu197104\tu197104\nu197117\tu197117\nu197120\tu197120\nu197121\tu197121\nu197124\tu197124\nu197132\tu197132\nu197137\tu197137\nu197145\tu197145\nu197146\tu197146\nu197148\tu197148\nu197152\tu197152\nu197156\tu197156\nu197157\tu197157\nu197158\tu197158\nu197161\tu197161\nu197162\tu197162\nu197163\tu197163\nu197164\tu197164\nu197165\tu197165\nu197166\tu197166\nu197168\tu197168\nu197173\tu197173\nu197177\tu197177\nu197178\tu197178\nu197183\tu197183\nu197187\tu197187\nu197188\tu197188\nu197189\tu197189\nu197190\tu197190\nu197191\tu197191\nu197197\tu197197\nu197198\tu197198\nu197199\tu197199\nu197200\tu197200\nu197201\tu197201\nu197204\tu197204\nu197210\tu197210\nu197214\tu197214\nu197217\tu197217\nu197218\tu197218\nu197219\tu197219\nu197222\tu197222\nu197227\tu197227\nu197230\tu197230\nu197238\tu197238\nu197245\tu197245\nu197254\tu197254\nu197256\tu197256\nu197258\tu197258\nu197260\tu197260\nu197263\tu197263\nu197265\tu197265\nu197268\tu197268\nu197272\tu197272\nu197274\tu197274\nu197277\tu197277\nu197284\tu197284\nu197285\tu197285\nu197292\tu197292\nu197296\tu197296\nu197298\tu197298\nu197303\tu197303\nu197318\tu197318\nu197321\tu197321\nu197325\tu197325\nu197331\tu197331\nu197334\tu197334\nu197335\tu197335\nu197336\tu197336\nu197342\tu197342\nu197343\tu197343\nu197350\tu197350\nu197354\tu197354\nu197357\tu197357\nu197364\tu197364\nu197368\tu197368\nu197369\tu197369\nu197377\tu197377\nu197385\tu197385\nu197388\tu197388\nu197395\tu197395\nu197396\tu197396\nu197402\tu197402\nu197405\tu197405\nu197408\tu197408\nu197413\tu197413\nu197421\tu197421\nu197424\tu197424\nu197425\tu197425\nu197427\tu197427\nu197429\tu197429\nu197430\tu197430\nu197431\tu197431\nu197432\tu197432\nu197433\tu197433\nu197434\tu197434\nu197436\tu197436\nu197438\tu197438\nu197439\tu197439\nu197440\tu197440\nu197443\tu197443\nu197446\tu197446\nu197448\tu197448\nu197450\tu197450\nu197453\tu197453\nu197456\tu197456\nu197460\tu197460\nu197463\tu197463\nu197469\tu197469\nu197471\tu197471\nu197474\tu197474\nu197479\tu197479\nu197481\tu197481\nu197483\tu197483\nu197484\tu197484\nu197486\tu197486\nu197487\tu197487\nu197488\tu197488\nu197491\tu197491\nu197492\tu197492\nu197495\tu197495\nu197496\tu197496\nu197498\tu197498\nu197503\tu197503\nu197506\tu197506\nu197508\tu197508\nu197516\tu197516\nu197517\tu197517\nu197520\tu197520\nu197521\tu197521\nu197522\tu197522\nu197523\tu197523\nu197524\tu197524\nu197529\tu197529\nu197530\tu197530\nu197532\tu197532\nu197534\tu197534\nu197539\tu197539\nu197544\tu197544\nu197556\tu197556\nu197559\tu197559\nu197560\tu197560\nu197561\tu197561\nu197573\tu197573\nu197575\tu197575\nu197576\tu197576\nu197577\tu197577\nu197578\tu197578\nu197579\tu197579\nu197582\tu197582\nu197589\tu197589\nu197592\tu197592\nu197594\tu197594\nu197598\tu197598\nu197604\tu197604\nu197606\tu197606\nu197615\tu197615\nu197616\tu197616\nu197623\tu197623\nu197626\tu197626\nu197627\tu197627\nu197628\tu197628\nu197636\tu197636\nu197637\tu197637\nu197643\tu197643\nu197644\tu197644\nu197645\tu197645\nu197646\tu197646\nu197649\tu197649\nu197650\tu197650\nu197651\tu197651\nu197652\tu197652\nu197653\tu197653\nu197654\tu197654\nu197659\tu197659\nu197662\tu197662\nu197665\tu197665\nu197667\tu197667\nu197668\tu197668\nu197674\tu197674\nu197680\tu197680\nu197684\tu197684\nu197686\tu197686\nu197687\tu197687\nu197688\tu197688\nu197693\tu197693\nu197695\tu197695\nu197696\tu197696\nu197697\tu197697\nu197702\tu197702\nu197704\tu197704\nu197706\tu197706\nu197709\tu197709\nu197714\tu197714\nu197716\tu197716\nu197719\tu197719\nu197720\tu197720\nu197730\tu197730\nu197733\tu197733\nu197737\tu197737\nu197743\tu197743\nu197762\tu197762\nu197765\tu197765\nu197770\tu197770\nu197772\tu197772\nu197777\tu197777\nu197778\tu197778\nu197798\tu197798\nu197810\tu197810\nu197811\tu197811\nu197812\tu197812\nu197817\tu197817\nu197819\tu197819\nu197824\tu197824\nu197826\tu197826\nu197829\tu197829\nu197836\tu197836\nu197837\tu197837\nu197848\tu197848\nu197850\tu197850\nu197851\tu197851\nu197852\tu197852\nu197857\tu197857\nu197859\tu197859\nu197865\tu197865\nu197866\tu197866\nu197869\tu197869\nu197873\tu197873\nu197875\tu197875\nu197878\tu197878\nu197880\tu197880\nu197881\tu197881\nu197883\tu197883\nu197886\tu197886\nu197888\tu197888\nu197889\tu197889\nu197890\tu197890\nu197893\tu197893\nu197894\tu197894\nu197895\tu197895\nu197896\tu197896\nu197899\tu197899\nu197902\tu197902\nu197908\tu197908\nu197909\tu197909\nu197912\tu197912\nu197913\tu197913\nu197915\tu197915\nu197917\tu197917\nu197919\tu197919\nu197921\tu197921\nu197923\tu197923\nu197924\tu197924\nu197925\tu197925\nu197937\tu197937\nu197949\tu197949\nu197951\tu197951\nu197952\tu197952\nu197953\tu197953\nu197954\tu197954\nu197958\tu197958\nu197960\tu197960\nu197968\tu197968\nu197969\tu197969\nu197974\tu197974\nu197975\tu197975\nu197978\tu197978\nu197979\tu197979\nu197982\tu197982\nu197984\tu197984\nu197986\tu197986\nu197990\tu197990\nu197996\tu197996\nu198000\tu198000\nu198001\tu198001\nu198002\tu198002\nu198003\tu198003\nu198006\tu198006\nu198010\tu198010\nu198013\tu198013\nu198014\tu198014\nu198022\tu198022\nu198023\tu198023\nu198029\tu198029\nu198033\tu198033\nu198041\tu198041\nu198061\tu198061\nu198066\tu198066\nu198067\tu198067\nu198068\tu198068\nu198077\tu198077\nu198080\tu198080\nu198086\tu198086\nu198092\tu198092\nu198094\tu198094\nu198095\tu198095\nu198096\tu198096\nu198097\tu198097\nu198106\tu198106\nu198108\tu198108\nu198109\tu198109\nu198112\tu198112\nu198115\tu198115\nu198116\tu198116\nu198119\tu198119\nu198120\tu198120\nu198122\tu198122\nu198123\tu198123\nu198124\tu198124\nu198125\tu198125\nu198129\tu198129\nu198135\tu198135\nu198136\tu198136\nu198138\tu198138\nu198141\tu198141\nu198143\tu198143\nu198146\tu198146\nu198151\tu198151\nu198152\tu198152\nu198162\tu198162\nu198163\tu198163\nu198168\tu198168\nu198169\tu198169\nu198172\tu198172\nu198175\tu198175\nu198178\tu198178\nu198181\tu198181\nu198182\tu198182\nu198183\tu198183\nu198189\tu198189\nu198190\tu198190\nu198202\tu198202\nu198204\tu198204\nu198206\tu198206\nu198218\tu198218\nu198219\tu198219\nu198222\tu198222\nu198223\tu198223\nu198227\tu198227\nu198228\tu198228\nu198231\tu198231\nu198233\tu198233\nu198241\tu198241\nu198246\tu198246\nu198248\tu198248\nu198256\tu198256\nu198260\tu198260\nu198271\tu198271\nu198278\tu198278\nu198283\tu198283\nu198285\tu198285\nu198293\tu198293\nu198294\tu198294\nu198299\tu198299\nu198303\tu198303\nu198304\tu198304\nu198306\tu198306\nu198310\tu198310\nu198311\tu198311\nu198312\tu198312\nu198318\tu198318\nu198319\tu198319\nu198321\tu198321\nu198322\tu198322\nu198325\tu198325\nu198327\tu198327\nu198330\tu198330\nu198331\tu198331\nu198335\tu198335\nu198336\tu198336\nu198345\tu198345\nu198348\tu198348\nu198349\tu198349\nu198350\tu198350\nu198352\tu198352\nu198354\tu198354\nu198361\tu198361\nu198362\tu198362\nu198364\tu198364\nu198365\tu198365\nu198366\tu198366\nu198368\tu198368\nu198371\tu198371\nu198376\tu198376\nu198377\tu198377\nu198378\tu198378\nu198380\tu198380\nu198385\tu198385\nu198389\tu198389\nu198392\tu198392\nu198393\tu198393\nu198397\tu198397\nu198399\tu198399\nu198403\tu198403\nu198404\tu198404\nu198406\tu198406\nu198411\tu198411\nu198415\tu198415\nu198416\tu198416\nu198418\tu198418\nu198422\tu198422\nu198423\tu198423\nu198424\tu198424\nu198425\tu198425\nu198426\tu198426\nu198427\tu198427\nu198429\tu198429\nu198431\tu198431\nu198433\tu198433\nu198436\tu198436\nu198437\tu198437\nu198440\tu198440\nu198445\tu198445\nu198453\tu198453\nu198457\tu198457\nu198458\tu198458\nu198460\tu198460\nu198462\tu198462\nu198468\tu198468\nu198469\tu198469\nu198470\tu198470\nu198475\tu198475\nu198478\tu198478\nu198479\tu198479\nu198482\tu198482\nu198483\tu198483\nu198486\tu198486\nu198488\tu198488\nu198492\tu198492\nu198497\tu198497\nu198498\tu198498\nu198503\tu198503\nu198504\tu198504\nu198506\tu198506\nu198510\tu198510\nu198513\tu198513\nu198514\tu198514\nu198517\tu198517\nu198518\tu198518\nu198520\tu198520\nu198522\tu198522\nu198523\tu198523\nu198524\tu198524\nu198525\tu198525\nu198528\tu198528\nu198532\tu198532\nu198533\tu198533\nu198534\tu198534\nu198541\tu198541\nu198545\tu198545\nu198547\tu198547\nu198551\tu198551\nu198556\tu198556\nu198560\tu198560\nu198562\tu198562\nu198564\tu198564\nu198566\tu198566\nu198567\tu198567\nu198575\tu198575\nu198576\tu198576\nu198577\tu198577\nu198581\tu198581\nu198582\tu198582\nu198586\tu198586\nu198591\tu198591\nu198592\tu198592\nu198598\tu198598\nu198599\tu198599\nu198601\tu198601\nu198605\tu198605\nu198607\tu198607\nu198608\tu198608\nu198609\tu198609\nu198616\tu198616\nu198618\tu198618\nu198619\tu198619\nu198622\tu198622\nu198623\tu198623\nu198624\tu198624\nu198625\tu198625\nu198627\tu198627\nu198632\tu198632\nu198634\tu198634\nu198637\tu198637\nu198638\tu198638\nu198642\tu198642\nu198644\tu198644\nu198646\tu198646\nu198647\tu198647\nu198648\tu198648\nu198651\tu198651\nu198652\tu198652\nu198653\tu198653\nu198657\tu198657\nu198659\tu198659\nu198664\tu198664\nu198666\tu198666\nu198667\tu198667\nu198669\tu198669\nu198670\tu198670\nu198671\tu198671\nu198672\tu198672\nu198673\tu198673\nu198676\tu198676\nu198678\tu198678\nu198679\tu198679\nu198680\tu198680\nu198686\tu198686\nu198689\tu198689\nu198690\tu198690\nu198691\tu198691\nu198692\tu198692\nu198698\tu198698\nu198700\tu198700\nu198705\tu198705\nu198706\tu198706\nu198707\tu198707\nu198710\tu198710\nu198715\tu198715\nu198717\tu198717\nu198719\tu198719\nu198720\tu198720\nu198721\tu198721\nu198723\tu198723\nu198728\tu198728\nu198732\tu198732\nu198735\tu198735\nu198736\tu198736\nu198740\tu198740\nu198741\tu198741\nu198742\tu198742\nu198744\tu198744\nu198746\tu198746\nu198748\tu198748\nu198749\tu198749\nu198750\tu198750\nu198751\tu198751\nu198752\tu198752\nu198754\tu198754\nu198755\tu198755\nu198756\tu198756\nu198759\tu198759\nu198760\tu198760\nu198765\tu198765\nu198766\tu198766\nu198767\tu198767\nu198769\tu198769\nu198774\tu198774\nu198777\tu198777\nu198784\tu198784\nu198788\tu198788\nu198791\tu198791\nu198792\tu198792\nu198794\tu198794\nu198801\tu198801\nu198807\tu198807\nu198810\tu198810\nu198812\tu198812\nu198813\tu198813\nu198815\tu198815\nu198819\tu198819\nu198820\tu198820\nu198823\tu198823\nu198824\tu198824\nu198825\tu198825\nu198826\tu198826\nu198830\tu198830\nu198834\tu198834\nu198837\tu198837\nu198840\tu198840\nu198842\tu198842\nu198843\tu198843\nu198847\tu198847\nu198851\tu198851\nu198856\tu198856\nu198860\tu198860\nu198865\tu198865\nu198868\tu198868\nu198870\tu198870\nu198874\tu198874\nu198878\tu198878\nu198879\tu198879\nu198880\tu198880\nu198881\tu198881\nu198883\tu198883\nu198885\tu198885\nu198887\tu198887\nu198891\tu198891\nu198892\tu198892\nu198893\tu198893\nu198895\tu198895\nu198896\tu198896\nu198897\tu198897\nu198905\tu198905\nu198906\tu198906\nu198907\tu198907\nu198909\tu198909\nu198910\tu198910\nu198912\tu198912\nu198913\tu198913\nu198916\tu198916\nu198918\tu198918\nu198923\tu198923\nu198927\tu198927\nu198929\tu198929\nu198935\tu198935\nu198936\tu198936\nu198939\tu198939\nu198941\tu198941\nu198943\tu198943\nu198945\tu198945\nu198946\tu198946\nu198951\tu198951\nu198953\tu198953\nu198954\tu198954\nu198956\tu198956\nu198957\tu198957\nu198958\tu198958\nu198959\tu198959\nu198960\tu198960\nu198962\tu198962\nu198966\tu198966\nu198967\tu198967\nu198968\tu198968\nu198971\tu198971\nu198976\tu198976\nu198980\tu198980\nu198981\tu198981\nu198982\tu198982\nu198989\tu198989\nu198992\tu198992\nu198995\tu198995\nu198998\tu198998\nu198999\tu198999\nu199010\tu199010\nu199011\tu199011\nu199015\tu199015\nu199019\tu199019\nu199020\tu199020\nu199022\tu199022\nu199023\tu199023\nu199024\tu199024\nu199025\tu199025\nu199026\tu199026\nu199028\tu199028\nu199030\tu199030\nu199032\tu199032\nu199033\tu199033\nu199035\tu199035\nu199036\tu199036\nu199038\tu199038\nu199040\tu199040\nu199042\tu199042\nu199045\tu199045\nu199049\tu199049\nu199051\tu199051\nu199053\tu199053\nu199056\tu199056\nu199058\tu199058\nu199061\tu199061\nu199062\tu199062\nu199064\tu199064\nu199065\tu199065\nu199067\tu199067\nu199069\tu199069\nu199073\tu199073\nu199076\tu199076\nu199078\tu199078\nu199080\tu199080\nu199081\tu199081\nu199082\tu199082\nu199085\tu199085\nu199088\tu199088\nu199090\tu199090\nu199091\tu199091\nu199093\tu199093\nu199094\tu199094\nu199095\tu199095\nu199097\tu199097\nu199100\tu199100\nu199101\tu199101\nu199104\tu199104\nu199105\tu199105\nu199107\tu199107\nu199108\tu199108\nu199109\tu199109\nu199110\tu199110\nu199111\tu199111\nu199116\tu199116\nu199117\tu199117\nu199118\tu199118\nu199120\tu199120\nu199122\tu199122\nu199124\tu199124\nu199125\tu199125\nu199127\tu199127\nu199131\tu199131\nu199133\tu199133\nu199134\tu199134\nu199139\tu199139\nu199140\tu199140\nu199142\tu199142\nu199148\tu199148\nu199149\tu199149\nu199150\tu199150\nu199154\tu199154\nu199156\tu199156\nu199158\tu199158\nu199160\tu199160\nu199162\tu199162\nu199163\tu199163\nu199171\tu199171\nu199173\tu199173\nu199179\tu199179\nu199182\tu199182\nu199188\tu199188\nu199190\tu199190\nu199191\tu199191\nu199195\tu199195\nu199196\tu199196\nu199201\tu199201\nu199202\tu199202\nu199208\tu199208\nu199210\tu199210\nu199212\tu199212\nu199215\tu199215\nu199216\tu199216\nu199217\tu199217\nu199222\tu199222\nu199226\tu199226\nu199228\tu199228\nu199232\tu199232\nu199237\tu199237\nu199242\tu199242\nu199245\tu199245\nu199246\tu199246\nu199252\tu199252\nu199262\tu199262\nu199264\tu199264\nu199265\tu199265\nu199272\tu199272\nu199273\tu199273\nu199274\tu199274\nu199276\tu199276\nu199280\tu199280\nu199282\tu199282\nu199285\tu199285\nu199291\tu199291\nu199292\tu199292\nu199294\tu199294\nu199296\tu199296\nu199300\tu199300\nu199301\tu199301\nu199306\tu199306\nu199307\tu199307\nu199309\tu199309\nu199311\tu199311\nu199314\tu199314\nu199315\tu199315\nu199318\tu199318\nu199320\tu199320\nu199322\tu199322\nu199324\tu199324\nu199325\tu199325\nu199328\tu199328\nu199329\tu199329\nu199330\tu199330\nu199334\tu199334\nu199337\tu199337\nu199339\tu199339\nu199342\tu199342\nu199343\tu199343\nu199344\tu199344\nu199353\tu199353\nu199354\tu199354\nu199357\tu199357\nu199362\tu199362\nu199366\tu199366\nu199376\tu199376\nu199378\tu199378\nu199380\tu199380\nu199384\tu199384\nu199387\tu199387\nu199388\tu199388\nu199396\tu199396\nu199397\tu199397\nu199399\tu199399\nu199401\tu199401\nu199403\tu199403\nu199406\tu199406\nu199407\tu199407\nu199409\tu199409\nu199414\tu199414\nu199416\tu199416\nu199421\tu199421\nu199423\tu199423\nu199430\tu199430\nu199432\tu199432\nu199433\tu199433\nu199436\tu199436\nu199439\tu199439\nu199440\tu199440\nu199441\tu199441\nu199445\tu199445\nu199446\tu199446\nu199448\tu199448\nu199450\tu199450\nu199452\tu199452\nu199454\tu199454\nu199455\tu199455\nu199456\tu199456\nu199457\tu199457\nu199458\tu199458\nu199459\tu199459\nu199460\tu199460\nu199463\tu199463\nu199464\tu199464\nu199465\tu199465\nu199467\tu199467\nu199470\tu199470\nu199471\tu199471\nu199479\tu199479\nu199482\tu199482\nu199483\tu199483\nu199485\tu199485\nu199486\tu199486\nu199494\tu199494\nu199495\tu199495\nu199498\tu199498\nu199500\tu199500\nu199501\tu199501\nu199503\tu199503\nu199504\tu199504\nu199506\tu199506\nu199508\tu199508\nu199509\tu199509\nu199512\tu199512\nu199514\tu199514\nu199515\tu199515\nu199517\tu199517\nu199518\tu199518\nu199519\tu199519\nu199522\tu199522\nu199525\tu199525\nu199526\tu199526\nu199530\tu199530\nu199531\tu199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765\tu214765\nu214766\tu214766\nu214768\tu214768\nu214772\tu214772\nu214776\tu214776\nu214779\tu214779\nu214783\tu214783\nu214785\tu214785\nu214786\tu214786\nu214790\tu214790\nu214792\tu214792\nu214793\tu214793\nu214796\tu214796\nu214797\tu214797\nu214800\tu214800\nu214801\tu214801\nu214805\tu214805\nu214810\tu214810\nu214815\tu214815\nu214820\tu214820\nu214831\tu214831\nu214836\tu214836\nu214841\tu214841\nu214847\tu214847\nu214850\tu214850\nu214852\tu214852\nu214854\tu214854\nu214857\tu214857\nu214858\tu214858\nu214865\tu214865\nu214866\tu214866\nu214867\tu214867\nu214869\tu214869\nu214870\tu214870\nu214871\tu214871\nu214873\tu214873\nu214878\tu214878\nu214879\tu214879\nu214886\tu214886\nu214888\tu214888\nu214889\tu214889\nu214890\tu214890\nu214891\tu214891\nu214892\tu214892\nu214894\tu214894\nu214895\tu214895\nu214896\tu214896\nu214899\tu214899\nu214901\tu214901\nu214907\tu214907\nu214909\tu214909\nu214912\tu214912\nu214913\tu214913\nu214917\tu214917\nu214918\tu214918\nu214921\tu214921\nu214923\tu214923\nu214925\tu214925\nu214931\tu214931\nu214933\tu214933\nu214934\tu214934\nu217766\tu214934\nu243261\tu214934\nu3454\tu214934\nu214940\tu214940\nu214942\tu214942\nu214944\tu214944\nu214945\tu214945\nu214946\tu214946\nu214948\tu214948\nu214955\tu214955\nu214956\tu214956\nu214960\tu214960\nu214962\tu214962\nu214964\tu214964\nu214966\tu214966\nu214967\tu214967\nu214968\tu214968\nu214970\tu214970\nu214974\tu214974\nu214976\tu214976\nu214979\tu214979\nu214982\tu214982\nu214984\tu214984\nu214986\tu214986\nu214993\tu214993\nu214994\tu214994\nu214995\tu214995\nu214999\tu214999\nu215006\tu215006\nu215009\tu215009\nu215011\tu215011\nu215014\tu215014\nu215015\tu215015\nu215019\tu215019\nu215020\tu215020\nu215026\tu215026\nu215027\tu215027\nu215029\tu215029\nu215033\tu215033\nu215035\tu215035\nu215037\tu215037\nu215040\tu215040\nu215041\tu215041\nu215044\tu215044\nu215046\tu215046\nu215050\tu215050\nu215052\tu215052\nu215053\tu215053\nu215054\tu215054\nu215055\tu215055\nu215057\tu215057\nu215060\tu215060\nu215061\tu215061\nu215063\tu215063\nu215065\tu215065\nu215067\tu215067\nu215069\tu215069\nu215070\tu215070\nu215071\tu215071\nu215072\tu215072\nu215074\tu215074\nu215075\tu215075\nu215076\tu215076\nu215080\tu215080\nu215081\tu215081\nu215083\tu215083\nu215089\tu215089\nu215090\tu215090\nu215091\tu215091\nu215093\tu215093\nu215094\tu215094\nu215098\tu215098\nu215100\tu215100\nu215101\tu215101\nu215103\tu215103\nu215104\tu215104\nu215106\tu215106\nu215109\tu215109\nu215110\tu215110\nu215113\tu215113\nu215115\tu215115\nu215117\tu215117\nu215118\tu215118\nu215119\tu215119\nu215120\tu215120\nu215124\tu215124\nu215127\tu215127\nu215131\tu215131\nu215137\tu215137\nu215148\tu215148\nu215149\tu215149\nu215150\tu215150\nu215151\tu215151\nu215155\tu215155\nu215156\tu215156\nu215158\tu215158\nu215167\tu215167\nu215168\tu215168\nu215182\tu215182\nu215196\tu215196\nu215200\tu215200\nu215203\tu215203\nu215206\tu215206\nu215207\tu215207\nu215208\tu215208\nu215209\tu215209\nu215213\tu215213\nu215214\tu215214\nu215217\tu215217\nu215220\tu215220\nu215224\tu215224\nu215228\tu215228\nu215230\tu215230\nu215232\tu215232\nu215233\tu215233\nu215235\tu215235\nu215236\tu215236\nu215239\tu215239\nu215241\tu215241\nu215243\tu215243\nu215245\tu215245\nu215246\tu215246\nu215247\tu215247\nu215252\tu215252\nu215256\tu215256\nu215260\tu215260\nu215261\tu215261\nu215265\tu215265\nu215266\tu215266\nu215271\tu215271\nu215273\tu215273\nu215278\tu215278\nu215281\tu215281\nu215282\tu215282\nu215284\tu215284\nu215288\tu215288\nu215293\tu215293\nu215294\tu215294\nu215295\tu215295\nu215301\tu215301\nu215302\tu215302\nu215304\tu215304\nu215305\tu215305\nu215308\tu215308\nu215309\tu215309\nu215313\tu215313\nu215315\tu215315\nu215317\tu215317\nu215321\tu215321\nu215324\tu215324\nu215327\tu215327\nu215336\tu215336\nu215342\tu215342\nu215345\tu215345\nu215349\tu215349\nu215351\tu215351\nu215352\tu215352\nu215354\tu215354\nu215356\tu215356\nu215357\tu215357\nu215358\tu215358\nu215359\tu215359\nu215362\tu215362\nu215365\tu215365\nu215366\tu215366\nu215368\tu215368\nu215369\tu215369\nu215375\tu215375\nu215376\tu215376\nu215377\tu215377\nu215380\tu215380\nu215381\tu215381\nu215383\tu215383\nu215384\tu215384\nu215385\tu215385\nu215386\tu215386\nu215387\tu215387\nu215391\tu215391\nu215394\tu215394\nu215395\tu215395\nu215396\tu215396\nu215397\tu215397\nu215398\tu215398\nu215399\tu215399\nu215401\tu215401\nu215402\tu215402\nu215407\tu215407\nu215412\tu215412\nu215426\tu215426\nu215427\tu215427\nu215428\tu215428\nu215432\tu215432\nu215434\tu215434\nu215436\tu215436\nu215437\tu215437\nu215440\tu215440\nu215442\tu215442\nu215445\tu215445\nu215449\tu215449\nu215453\tu215453\nu215460\tu215460\nu215461\tu215461\nu215463\tu215463\nu215465\tu215465\nu215467\tu215467\nu215468\tu215468\nu215472\tu215472\nu215473\tu215473\nu215475\tu215475\nu215478\tu215478\nu215480\tu215480\nu215482\tu215482\nu215483\tu215483\nu215484\tu215484\nu215488\tu215488\nu215489\tu215489\nu215490\tu215490\nu2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1851\nu251852\tu251852\nu251854\tu251854\nu251857\tu251857\nu251859\tu251859\nu251861\tu251861\nu251864\tu251864\nu251865\tu251865\nu251869\tu251869\nu251872\tu251872\nu251877\tu251877\nu251878\tu251878\nu251879\tu251879\nu251881\tu251881\nu251883\tu251883\nu251884\tu251884\nu251885\tu251885\nu251886\tu251886\nu251892\tu251892\nu251895\tu251895\nu251897\tu251897\nu251907\tu251907\nu251911\tu251911\nu251913\tu251913\nu251915\tu251915\nu251920\tu251920\nu251925\tu251925\nu251930\tu251930\nu251931\tu251931\nu251935\tu251935\nu251940\tu251940\nu251941\tu251941\nu251942\tu251942\nu251946\tu251946\nu251947\tu251947\nu251948\tu251948\nu251951\tu251951\nu251952\tu251952\nu251953\tu251953\nu251956\tu251956\nu251957\tu251957\nu251959\tu251959\nu251960\tu251960\nu251964\tu251964\nu251966\tu251966\nu251967\tu251967\nu251968\tu251968\nu251970\tu251970\nu251971\tu251971\nu251973\tu251973\nu251975\tu251975\nu251976\tu251976\nu251977\tu251977\nu251979\tu251979\nu251981\tu251981\nu251984\tu251984\nu251986\tu251986\nu251987\tu251987\nu251989\tu251989\nu251990\tu251990\nu251991\tu251991\nu251994\tu251994\nu251996\tu251996\nu251998\tu251998\nu252001\tu252001\nu252004\tu252004\nu252008\tu252008\nu252013\tu252013\nu252016\tu252016\nu252019\tu252019\nu252021\tu252021\nu252022\tu252022\nu252025\tu252025\nu252027\tu252027\nu252028\tu252028\nu252029\tu252029\nu252030\tu252030\nu252031\tu252031\nu252034\tu252034\nu252035\tu252035\nu252036\tu252036\nu252037\tu252037\nu252038\tu252038\nu252039\tu252039\nu252043\tu252043\nu252044\tu252044\nu252055\tu252055\nu252058\tu252058\nu252059\tu252059\nu252061\tu252061\nu252064\tu252064\nu252065\tu252065\nu252068\tu252068\nu252069\tu252069\nu252071\tu252071\nu252074\tu252074\nu252075\tu252075\nu252076\tu252076\nu252078\tu252078\nu252081\tu252081\nu252083\tu252083\nu252084\tu252084\nu252088\tu252088\nu252089\tu252089\nu252091\tu252091\nu252095\tu252095\nu252096\tu252096\nu252098\tu252098\nu252101\tu252101\nu252102\tu252102\nu252106\tu252106\nu252108\tu252108\nu252114\tu252114\nu252116\tu252116\nu252117\tu252117\nu252121\tu252121\nu252124\tu252124\nu252130\tu252130\nu252132\tu252132\nu252133\tu252133\nu252135\tu252135\nu252136\tu252136\nu252139\tu252139\nu252140\tu252140\nu252145\tu252145\nu252146\tu252146\nu252147\tu252147\nu252149\tu252149\nu252150\tu252150\nu252153\tu252153\nu252154\tu252154\nu252155\tu252155\nu252158\tu252158\nu252165\tu252165\nu252174\tu252174\nu252176\tu252176\nu252177\tu252177\nu252188\tu252188\nu252189\tu252189\nu252191\tu252191\nu252195\tu252195\nu252204\tu252204\nu252205\tu252205\nu252208\tu252208\nu252209\tu252209\nu252212\tu252212\nu252213\tu252213\nu252217\tu252217\nu252219\tu252219\nu252221\tu252221\nu252225\tu252225\nu252229\tu252229\nu252231\tu252231\nu252232\tu252232\nu252235\tu252235\nu252240\tu252240\nu252242\tu252242\nu252243\tu252243\nu252244\tu252244\nu252245\tu252245\nu252249\tu252249\nu252251\tu252251\nu252252\tu252252\nu252255\tu252255\nu252257\tu252257\nu252260\tu252260\nu252263\tu252263\nu252266\tu252266\nu252267\tu252267\nu252271\tu252271\nu252272\tu252272\nu252275\tu252275\nu252276\tu252276\nu252281\tu252281\nu252283\tu252283\nu252285\tu252285\nu252287\tu252287\nu252290\tu252290\nu252292\tu252292\nu252297\tu252297\nu252303\tu252303\nu252304\tu252304\nu252312\tu252312\nu252320\tu252320\nu252321\tu252321\nu252322\tu252322\nu252324\tu252324\nu252325\tu252325\nu252327\tu252327\nu252328\tu252328\nu252331\tu252331\nu252336\tu252336\nu252338\tu252338\nu252340\tu252340\nu252345\tu252345\nu252350\tu252350\nu252351\tu252351\nu252352\tu252352\nu252353\tu252353\nu252356\tu252356\nu252364\tu252364\nu252365\tu252365\nu252367\tu252367\nu252368\tu252368\nu252372\tu252372\nu252373\tu252373\nu252374\tu252374\nu252375\tu252375\nu252377\tu252377\nu252378\tu252378\nu252379\tu252379\nu252380\tu252380\nu252382\tu252382\nu252388\tu252388\nu252392\tu252392\nu252396\tu252396\nu252398\tu252398\nu252399\tu252399\nu252400\tu252400\nu252401\tu252401\nu252402\tu252402\nu252404\tu252404\nu252406\tu252406\nu252408\tu252408\nu252410\tu252410\nu252411\tu252411\nu252414\tu252414\nu252422\tu252422\nu252424\tu252424\nu252425\tu252425\nu252428\tu252428\nu252430\tu252430\nu252432\tu252432\nu252434\tu252434\nu252435\tu252435\nu252436\tu252436\nu252440\tu252440\nu252441\tu252441\nu252444\tu252444\nu252445\tu252445\nu252448\tu252448\nu252449\tu252449\nu252453\tu252453\nu252454\tu252454\nu252457\tu252457\nu252462\tu252462\nu252465\tu252465\nu252468\tu252468\nu252472\tu252472\nu252473\tu252473\nu252479\tu252479\nu252481\tu252481\nu252489\tu252489\nu252491\tu252491\nu252493\tu252493\nu252494\tu252494\nu252498\tu252498\nu252500\tu252500\nu252505\tu252505\nu252508\tu252508\nu252513\tu252513\nu252516\tu252516\nu252519\tu252519\nu252521\tu252521\nu252525\tu252525\nu252527\tu252527\nu252530\tu252530\nu252531\tu252531\nu252532\tu252532\nu252534\tu252534\nu252535\tu252535\nu252536\tu252536\nu252539\tu252539\nu252546\tu252546\nu252547\tu252547\nu252551\tu252551\nu252552\tu252552\nu252554\tu252554\nu252562\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253971\tu253971\nu253972\tu253972\nu253973\tu253973\nu253977\tu253977\nu253978\tu253978\nu253981\tu253981\nu253982\tu253982\nu253983\tu253983\nu253984\tu253984\nu253989\tu253989\nu253991\tu253991\nu253992\tu253992\nu28744\tu253992\nu253994\tu253994\nu253997\tu253997\nu253999\tu253999\nu254001\tu254001\nu254007\tu254007\nu254010\tu254010\nu254012\tu254012\nu254014\tu254014\nu254015\tu254015\nu254018\tu254018\nu254027\tu254027\nu254028\tu254028\nu254030\tu254030\nu254031\tu254031\nu254034\tu254034\nu254038\tu254038\nu254040\tu254040\nu254041\tu254041\nu254042\tu254042\nu254043\tu254043\nu254044\tu254044\nu254045\tu254045\nu254046\tu254046\nu254047\tu254047\nu254049\tu254049\nu254051\tu254051\nu254055\tu254055\nu254058\tu254058\nu254059\tu254059\nu254060\tu254060\nu254061\tu254061\nu254064\tu254064\nu254069\tu254069\nu254072\tu254072\nu254074\tu254074\nu254076\tu254076\nu254078\tu254078\nu254080\tu254080\nu254081\tu254081\nu254082\tu254082\nu254083\tu254083\nu254084\tu254084\nu254086\tu254086\nu254091\tu254091\nu254093\tu254093\nu254094\tu254094\nu254097\tu254097\nu254106\tu254106\nu254107\tu254107\nu254112\tu254112\nu254115\tu254115\nu254116\tu254116\nu254118\tu254118\nu254119\tu254119\nu254121\tu254121\nu254122\tu254122\nu254125\tu254125\nu254129\tu254129\nu254130\tu254130\nu254131\tu254131\nu254133\tu254133\nu254134\tu254134\nu254135\tu254135\nu254136\tu254136\nu254137\tu254137\nu254139\tu254139\nu254140\tu254140\nu254147\tu254147\nu254148\tu254148\nu254150\tu254150\nu254152\tu254152\nu254153\tu254153\nu254154\tu254154\nu254158\tu254158\nu254159\tu254159\nu254160\tu254160\nu254161\tu254161\nu254163\tu254163\nu254164\tu254164\nu254166\tu254166\nu254167\tu254167\nu254168\tu254168\nu254171\tu254171\nu254173\tu254173\nu254174\tu254174\nu254176\tu254176\nu254177\tu254177\nu254179\tu254179\nu254180\tu254180\nu254182\tu254182\nu254185\tu254185\nu254186\tu254186\nu254192\tu254192\nu254196\tu254196\nu254197\tu254197\nu254201\tu254201\nu254202\tu254202\nu254210\tu254210\nu254212\tu254212\nu254215\tu254215\nu254219\tu254219\nu254220\tu254220\nu254221\tu254221\nu254223\tu254223\nu254227\tu254227\nu254228\tu254228\nu254229\tu254229\nu254230\tu254230\nu254233\tu254233\nu254234\tu254234\nu254235\tu254235\nu254236\tu254236\nu254238\tu254238\nu254241\tu254241\nu254245\tu254245\nu254246\tu254246\nu254249\tu254249\nu254251\tu254251\nu254260\tu254260\nu254266\tu254266\nu254267\tu254267\nu254268\tu254268\nu254269\tu254269\nu254270\tu254270\nu254273\tu254273\nu254275\tu254275\nu254277\tu254277\nu254278\tu254278\nu254279\tu254279\nu254282\tu254282\nu254284\tu254284\nu254287\tu254287\nu254288\tu254288\nu254290\tu254290\nu254292\tu254292\nu254293\tu254293\nu254295\tu254295\nu254296\tu254296\nu254301\tu254301\nu254303\tu254303\nu254304\tu254304\nu254310\tu254310\nu254311\tu254311\nu254313\tu254313\nu254318\tu254318\nu254326\tu254326\nu254327\tu254327\nu254328\tu254328\nu254329\tu254329\nu254331\tu254331\nu254332\tu254332\nu254333\tu254333\nu254335\tu254335\nu254337\tu254337\nu254340\tu254340\nu254343\tu254343\nu254345\tu254345\nu254346\tu254346\nu254347\tu254347\nu254348\tu254348\nu254350\tu254350\nu254351\tu254351\nu254353\tu254353\nu254354\tu254354\nu254359\tu254359\nu254363\tu254363\nu254364\tu254364\nu254366\tu254366\nu254367\tu254367\nu254368\tu254368\nu254370\tu254370\nu254374\tu254374\nu254376\tu254376\nu254377\tu254377\nu254378\tu254378\nu254379\tu254379\nu254381\tu254381\nu254383\tu254383\nu254384\tu254384\nu254385\tu254385\nu254388\tu254388\nu254390\tu254390\nu254392\tu254392\nu254393\tu254393\nu254394\tu254394\nu254397\tu254397\nu254398\tu254398\nu254400\tu254400\nu254402\tu254402\nu254403\tu254403\nu254404\tu254404\nu254405\tu254405\nu254406\tu254406\nu254407\tu254407\nu254408\tu254408\nu254409\tu254409\nu254411\tu254411\nu254412\tu254412\nu254413\tu254413\nu254414\tu254414\nu254415\tu254415\nu254418\tu254418\nu254421\tu254421\nu254423\tu254423\nu254425\tu254425\nu254427\tu254427\nu254433\tu254433\nu254434\tu254434\nu254437\tu254437\nu254438\tu254438\nu254442\tu254442\nu254449\tu254449\nu254450\tu254450\nu254451\tu254451\nu254452\tu254452\nu254454\tu254454\nu254460\tu254460\nu254464\tu254464\nu254467\tu254467\nu254468\tu254468\nu254471\tu254471\nu254473\tu254473\nu254474\tu254474\nu254476\tu254476\nu254483\tu254483\nu254484\tu254484\nu254485\tu254485\nu254486\tu254486\nu254487\tu254487\nu254488\tu254488\nu254494\tu254494\nu254495\tu254495\nu254498\tu254498\nu254500\tu254500\nu254503\tu254503\nu254505\tu254505\nu254506\tu254506\nu254507\tu254507\nu254508\tu254508\nu254509\tu254509\nu254510\tu254510\nu254513\tu254513\nu254515\tu254515\nu254517\tu254517\nu254518\tu254518\nu254521\tu254521\nu254522\tu254522\nu254527\tu254527\nu254529\tu254529\nu254532\tu254532\nu254537\tu254537\nu254539\tu254539\nu254540\tu254540\nu254541\tu254541\nu254542\tu254542\nu254543\tu254543\nu254545\tu254545\nu254546\tu254546\nu254549\tu254549\nu254550\tu254550\nu254551\tu254551\nu254552\tu254552\nu254553\tu254553\nu254554\tu254554\nu254557\tu254557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259154\nu259159\tu259159\nu259163\tu259163\nu259165\tu259165\nu259170\tu259170\nu259178\tu259178\nu259181\tu259181\nu259185\tu259185\nu259186\tu259186\nu259187\tu259187\nu259195\tu259195\nu259198\tu259198\nu259202\tu259202\nu259203\tu259203\nu259205\tu259205\nu259206\tu259206\nu259210\tu259210\nu259212\tu259212\nu259213\tu259213\nu259221\tu259221\nu259224\tu259224\nu259225\tu259225\nu259236\tu259236\nu259238\tu259238\nu259241\tu259241\nu259242\tu259242\nu259245\tu259245\nu259248\tu259248\nu259251\tu259251\nu259253\tu259253\nu259254\tu259254\nu259255\tu259255\nu259257\tu259257\nu259258\tu259258\nu259259\tu259259\nu259260\tu259260\nu259261\tu259261\nu259266\tu259266\nu259267\tu259267\nu259269\tu259269\nu259270\tu259270\nu259271\tu259271\nu259273\tu259273\nu259274\tu259274\nu259275\tu259275\nu259279\tu259279\nu259280\tu259280\nu259281\tu259281\nu259286\tu259286\nu259291\tu259291\nu259295\tu259295\nu259296\tu259296\nu259297\tu259297\nu259300\tu259300\nu259301\tu259301\nu259303\tu259303\nu259304\tu259304\nu259306\tu259306\nu259307\tu259307\nu259309\tu259309\nu259310\tu259310\nu259311\tu259311\nu259315\tu259315\nu259316\tu259316\nu259320\tu259320\nu259321\tu259321\nu259324\tu259324\nu259326\tu259326\nu259328\tu259328\nu259335\tu259335\nu259338\tu259338\nu259341\tu259341\nu259346\tu259346\nu259349\tu259349\nu259351\tu259351\nu259357\tu259357\nu259360\tu259360\nu259364\tu259364\nu259365\tu259365\nu259368\tu259368\nu259370\tu259370\nu259376\tu259376\nu259380\tu259380\nu259383\tu259383\nu259385\tu259385\nu259388\tu259388\nu259390\tu259390\nu259392\tu259392\nu259393\tu259393\nu259398\tu259398\nu259400\tu259400\nu259402\tu259402\nu259403\tu259403\nu259404\tu259404\nu259405\tu259405\nu259407\tu259407\nu259413\tu259413\nu259415\tu259415\nu259418\tu259418\nu259419\tu259419\nu259424\tu259424\nu259431\tu259431\nu259443\tu259443\nu259459\tu259459\nu259471\tu259471\nu259475\tu259475\nu259485\tu259485\nu259488\tu259488\nu259504\tu259504\nu259509\tu259509\nu259510\tu259510\nu259518\tu259518\nu259519\tu259519\nu259520\tu259520\nu259524\tu259524\nu259536\tu259536\nu259537\tu259537\nu259543\tu259543\nu259546\tu259546\nu259548\tu259548\nu259558\tu259558\nu259560\tu259560\nu259571\tu259571\nu259572\tu259572\nu259574\tu259574\nu259575\tu259575\nu259578\tu259578\nu259581\tu259581\nu259585\tu259585\nu259586\tu259586\nu259588\tu259588\nu259591\tu259591\nu259599\tu259599\nu259600\tu259600\nu259604\tu259604\nu259606\tu259606\nu259609\tu259609\nu259611\tu259611\nu259614\tu259614\nu259618\tu259618\nu259619\tu259619\nu259620\tu259620\nu259621\tu259621\nu259623\tu259623\nu259626\tu259626\nu259634\tu259634\nu259643\tu259643\nu259644\tu259644\nu259645\tu259645\nu259648\tu259648\nu259650\tu259650\nu259652\tu259652\nu259653\tu259653\nu259654\tu259654\nu259663\tu259663\nu259668\tu259668\nu259671\tu259671\nu259677\tu259677\nu259684\tu259684\nu259688\tu259688\nu259689\tu259689\nu259692\tu259692\nu259694\tu259694\nu259695\tu259695\nu259700\tu259700\nu259704\tu259704\nu259705\tu259705\nu259707\tu259707\nu259709\tu259709\nu259711\tu259711\nu259714\tu259714\nu259718\tu259718\nu259720\tu259720\nu259722\tu259722\nu259726\tu259726\nu259727\tu259727\nu259730\tu259730\nu259733\tu259733\nu259735\tu259735\nu259739\tu259739\nu259741\tu259741\nu259748\tu259748\nu259749\tu259749\nu259752\tu259752\nu259763\tu259763\nu259764\tu259764\nu259766\tu259766\nu259773\tu259773\nu259776\tu259776\nu259790\tu259790\nu259794\tu259794\nu259797\tu259797\nu259799\tu259799\nu259802\tu259802\nu259803\tu259803\nu259808\tu259808\nu259809\tu259809\nu259810\tu259810\nu259812\tu259812\nu259814\tu259814\nu259817\tu259817\nu259818\tu259818\nu259820\tu259820\nu259823\tu259823\nu259827\tu259827\nu259828\tu259828\nu259829\tu259829\nu259833\tu259833\nu259835\tu259835\nu259837\tu259837\nu259839\tu259839\nu259842\tu259842\nu259843\tu259843\nu259845\tu259845\nu259849\tu259849\nu259851\tu259851\nu259852\tu259852\nu259853\tu259853\nu259856\tu259856\nu259858\tu259858\nu259862\tu259862\nu259863\tu259863\nu259868\tu259868\nu259873\tu259873\nu259874\tu259874\nu259875\tu259875\nu259877\tu259877\nu259878\tu259878\nu259879\tu259879\nu259880\tu259880\nu259881\tu259881\nu259885\tu259885\nu259886\tu259886\nu259889\tu259889\nu259893\tu259893\nu259894\tu259894\nu259895\tu259895\nu259902\tu259902\nu259903\tu259903\nu259907\tu259907\nu259908\tu259908\nu259918\tu259918\nu259922\tu259922\nu259925\tu259925\nu259926\tu259926\nu259927\tu259927\nu259928\tu259928\nu259930\tu259930\nu259931\tu259931\nu259932\tu259932\nu259936\tu259936\nu259940\tu259940\nu259943\tu259943\nu259945\tu259945\nu259951\tu259951\nu259952\tu259952\nu259956\tu259956\nu259957\tu259957\nu259967\tu259967\nu259970\tu259970\nu259973\tu259973\nu259974\tu259974\nu259980\tu259980\nu259982\tu259982\nu259983\tu259983\nu259984\tu259984\nu259994\tu259994\nu259995\tu259995\nu259998\tu259998\nu260000\tu260000\nu260003\tu260003\nu260005\tu260005\nu260006\tu260006\nu260009\tu260009\nu260014\tu260014\nu260022\tu260022\nu260024\tu260024\nu260025\tu260025\nu260026\tu260026\nu260028\tu260028\nu260029\tu260029\nu260033\tu260033\nu260039\tu260039\nu260042\tu260042\nu260043\tu260043\nu260044\tu260044\nu260045\tu260045\nu260056\tu260056\nu260057\tu260057\nu260059\tu260059\nu260060\tu260060\nu260061\tu260061\nu260063\tu260063\nu260067\tu260067\nu260068\tu260068\nu260078\tu260078\nu260080\tu260080\nu260081\tu260081\nu260085\tu260085\nu260086\tu260086\nu260087\tu260087\nu260090\tu260090\nu260091\tu260091\nu260094\tu260094\nu260097\tu260097\nu260099\tu260099\nu260100\tu260100\nu260102\tu260102\nu260105\tu260105\nu260107\tu260107\nu260110\tu260110\nu260112\tu260112\nu260116\tu260116\nu260120\tu260120\nu260121\tu260121\nu260122\tu260122\nu260125\tu260125\nu260128\tu260128\nu260129\tu260129\nu260130\tu260130\nu260131\tu260131\nu260133\tu260133\nu260134\tu260134\nu260136\tu260136\nu260140\tu260140\nu260141\tu260141\nu260142\tu260142\nu260147\tu260147\nu260148\tu260148\nu260157\tu260157\nu260160\tu260160\nu260162\tu260162\nu260163\tu260163\nu260166\tu260166\nu260168\tu260168\nu260169\tu260169\nu260172\tu260172\nu260173\tu260173\nu260174\tu260174\nu260178\tu260178\nu260182\tu260182\nu260183\tu260183\nu260184\tu260184\nu260186\tu260186\nu260188\tu260188\nu260190\tu260190\nu260191\tu260191\nu260194\tu260194\nu260197\tu260197\nu260200\tu260200\nu260203\tu260203\nu260204\tu260204\nu260205\tu260205\nu260209\tu260209\nu260212\tu260212\nu260215\tu260215\nu260217\tu260217\nu260218\tu260218\nu260221\tu260221\nu260222\tu260222\nu260223\tu260223\nu260230\tu260230\nu260233\tu260233\nu260237\tu260237\nu260238\tu260238\nu260239\tu260239\nu260242\tu260242\nu260244\tu260244\nu260245\tu260245\nu260249\tu260249\nu260250\tu260250\nu260251\tu260251\nu260253\tu260253\nu260255\tu260255\nu260257\tu260257\nu260265\tu260265\nu260266\tu260266\nu260269\tu260269\nu260272\tu260272\nu260273\tu260273\nu260274\tu260274\nu260276\tu260276\nu260277\tu260277\nu260279\tu260279\nu260285\tu260285\nu260286\tu260286\nu260288\tu260288\nu260289\tu260289\nu260291\tu260291\nu260293\tu260293\nu260295\tu260295\nu260297\tu260297\nu260299\tu260299\nu260300\tu260300\nu260305\tu260305\nu260306\tu260306\nu260308\tu260308\nu260313\tu260313\nu260314\tu260314\nu260315\tu260315\nu260318\tu260318\nu260320\tu260320\nu260324\tu260324\nu260331\tu260331\nu260333\tu260333\nu260334\tu260334\nu260337\tu260337\nu260342\tu260342\nu260346\tu260346\nu260351\tu260351\nu260366\tu260366\nu260370\tu260370\nu260373\tu260373\nu260378\tu260378\nu260380\tu260380\nu260381\tu260381\nu260383\tu260383\nu260385\tu260385\nu260390\tu260390\nu260396\tu260396\nu260402\tu260402\nu260406\tu260406\nu260408\tu260408\nu260411\tu260411\nu260412\tu260412\nu260415\tu260415\nu260418\tu260418\nu260425\tu260425\nu260429\tu260429\nu260434\tu260434\nu260436\tu260436\nu260438\tu260438\nu260439\tu260439\nu260444\tu260444\nu260447\tu260447\nu260452\tu260452\nu260453\tu260453\nu260454\tu260454\nu260455\tu260455\nu260456\tu260456\nu260457\tu260457\nu260458\tu260458\nu260460\tu260460\nu260464\tu260464\nu260466\tu260466\nu260468\tu260468\nu260471\tu260471\nu260472\tu260472\nu260473\tu260473\nu260474\tu260474\nu260478\tu260478\nu260481\tu260481\nu260484\tu260484\nu260487\tu260487\nu260488\tu260488\nu260489\tu260489\nu260490\tu260490\nu260492\tu260492\nu260494\tu260494\nu260495\tu260495\nu260503\tu260503\nu260510\tu260510\nu260513\tu260513\nu260515\tu260515\nu260521\tu260521\nu260522\tu260522\nu260523\tu260523\nu260524\tu260524\nu260526\tu260526\nu260530\tu260530\nu260531\tu260531\nu260532\tu260532\nu260534\tu260534\nu260535\tu260535\nu260536\tu260536\nu260538\tu260538\nu260539\tu260539\nu260540\tu260540\nu260542\tu260542\nu260543\tu260543\nu260544\tu260544\nu260547\tu260547\nu260549\tu260549\nu260551\tu260551\nu260552\tu260552\nu260553\tu260553\nu260555\tu260555\nu260556\tu260556\nu260560\tu260560\nu260564\tu260564\nu260568\tu260568\nu260570\tu260570\nu260576\tu260576\nu260577\tu260577\nu260578\tu260578\nu260584\tu260584\nu260586\tu260586\nu260587\tu260587\nu260591\tu260591\nu260595\tu260595\nu260596\tu260596\nu260598\tu260598\nu260599\tu260599\nu260608\tu260608\nu260609\tu260609\nu260610\tu260610\nu260611\tu260611\nu260614\tu260614\nu260615\tu260615\nu260616\tu260616\nu260617\tu260617\nu260619\tu260619\nu260624\tu260624\nu260626\tu260626\nu260627\tu260627\nu260628\tu260628\nu260631\tu260631\nu260635\tu260635\nu260637\tu260637\nu260639\tu260639\nu260644\tu260644\nu260646\tu260646\nu260648\tu260648\nu260649\tu260649\nu260654\tu260654\nu260655\tu260655\nu260656\tu260656\nu260657\tu260657\nu260659\tu260659\nu260660\tu260660\nu260662\tu260662\nu260663\tu260663\nu260666\tu260666\nu260667\tu260667\nu260674\tu260674\nu260675\tu260675\nu260680\tu260680\nu260683\tu260683\nu260692\tu260692\nu260693\tu260693\nu260700\tu260700\nu260708\tu260708\nu260710\tu260710\nu260724\tu260724\nu260726\tu260726\nu260733\tu260733\nu260738\tu260738\nu260741\tu260741\nu260752\tu260752\nu260754\tu260754\nu260756\tu260756\nu260758\tu260758\nu260759\tu260759\nu260766\tu260766\nu260773\tu260773\nu260781\tu260781\nu260782\tu260782\nu260784\tu260784\nu260791\tu260791\nu260794\tu260794\nu260796\tu260796\nu260800\tu260800\nu260802\tu260802\nu260808\tu260808\nu260810\tu260810\nu260812\tu260812\nu260813\tu260813\nu260814\tu260814\nu260815\tu260815\nu260816\tu260816\nu260817\tu260817\nu260820\tu260820\nu260821\tu260821\nu260824\tu260824\nu260825\tu260825\nu260829\tu260829\nu260831\tu260831\nu260835\tu260835\nu260845\tu260845\nu260846\tu260846\nu260848\tu260848\nu260851\tu260851\nu260854\tu260854\nu260855\tu260855\nu260856\tu260856\nu260857\tu260857\nu260858\tu260858\nu260860\tu260860\nu260862\tu260862\nu260865\tu260865\nu260867\tu260867\nu260868\tu260868\nu260872\tu260872\nu260873\tu260873\nu260878\tu260878\nu260880\tu260880\nu260883\tu260883\nu260884\tu260884\nu260885\tu260885\nu260887\tu260887\nu260888\tu260888\nu260890\tu260890\nu260891\tu260891\nu260892\tu260892\nu260893\tu260893\nu260894\tu260894\nu260898\tu260898\nu260899\tu260899\nu260903\tu260903\nu260904\tu260904\nu260905\tu260905\nu260906\tu260906\nu260909\tu260909\nu260917\tu260917\nu260918\tu260918\nu260921\tu260921\nu260927\tu260927\nu260928\tu260928\nu260935\tu260935\nu260936\tu260936\nu260937\tu260937\nu260946\tu260946\nu260947\tu260947\nu260950\tu260950\nu260957\tu260957\nu260958\tu260958\nu260963\tu260963\nu260964\tu260964\nu260967\tu260967\nu260968\tu260968\nu260969\tu260969\nu260977\tu260977\nu260980\tu260980\nu260982\tu260982\nu260985\tu260985\nu260989\tu260989\nu260992\tu260992\nu260993\tu260993\nu260996\tu260996\nu260998\tu260998\nu260999\tu260999\nu261001\tu261001\nu261003\tu261003\nu261007\tu261007\nu261008\tu261008\nu261009\tu261009\nu261012\tu261012\nu261013\tu261013\nu261017\tu261017\nu261018\tu261018\nu261022\tu261022\nu261025\tu261025\nu261026\tu261026\nu261028\tu261028\nu261032\tu261032\nu261036\tu261036\nu261037\tu261037\nu261039\tu261039\nu261040\tu261040\nu261042\tu261042\nu261044\tu261044\nu261046\tu261046\nu261050\tu261050\nu261057\tu261057\nu261059\tu261059\nu261061\tu261061\nu261064\tu261064\nu261071\tu261071\nu261076\tu261076\nu261080\tu261080\nu261084\tu261084\nu261085\tu261085\nu261093\tu261093\nu261095\tu261095\nu261098\tu261098\nu261103\tu261103\nu261105\tu261105\nu261108\tu261108\nu261109\tu261109\nu261117\tu261117\nu261118\tu261118\nu261120\tu261120\nu261124\tu261124\nu261126\tu261126\nu261127\tu261127\nu261129\tu261129\nu261135\tu261135\nu261136\tu261136\nu261142\tu261142\nu261145\tu261145\nu261146\tu261146\nu261148\tu261148\nu261151\tu261151\nu261158\tu261158\nu261161\tu261161\nu261165\tu261165\nu261171\tu261171\nu261179\tu261179\nu261181\tu261181\nu261182\tu261182\nu261183\tu261183\nu261187\tu261187\nu261190\tu261190\nu261194\tu261194\nu261199\tu261199\nu261215\tu261215\nu261220\tu261220\nu261221\tu261221\nu261223\tu261223\nu261229\tu261229\nu261232\tu261232\nu261235\tu261235\nu261236\tu261236\nu261240\tu261240\nu261242\tu261242\nu261244\tu261244\nu261257\tu261257\nu261262\tu261262\nu261278\tu261278\nu261279\tu261279\nu261282\tu261282\nu261284\tu261284\nu261286\tu261286\nu261287\tu261287\nu261291\tu261291\nu261296\tu261296\nu261297\tu261297\nu261300\tu261300\nu261302\tu261302\nu261305\tu261305\nu261307\tu261307\nu261311\tu261311\nu261312\tu261312\nu261313\tu261313\nu261317\tu261317\nu261321\tu261321\nu261323\tu261323\nu261331\tu261331\nu261332\tu261332\nu261334\tu261334\nu261335\tu261335\nu261337\tu261337\nu261338\tu261338\nu261339\tu261339\nu261340\tu261340\nu261341\tu261341\nu261343\tu261343\nu261344\tu261344\nu261346\tu261346\nu261347\tu261347\nu261348\tu261348\nu261353\tu261353\nu261354\tu261354\nu261359\tu261359\nu261360\tu261360\nu261365\tu261365\nu261367\tu261367\nu261369\tu261369\nu261371\tu261371\nu261373\tu261373\nu261374\tu261374\nu261375\tu261375\nu261378\tu261378\nu261381\tu261381\nu261385\tu261385\nu261386\tu261386\nu261387\tu261387\nu261388\tu261388\nu261393\tu261393\nu261396\tu261396\nu261398\tu261398\nu261401\tu261401\nu261402\tu261402\nu261403\tu261403\nu261404\tu261404\nu261407\tu261407\nu261410\tu261410\nu261411\tu261411\nu261413\tu261413\nu261417\tu261417\nu261418\tu261418\nu261419\tu261419\nu261421\tu261421\nu261422\tu261422\nu261423\tu261423\nu261425\tu261425\nu261427\tu261427\nu261428\tu261428\nu261432\tu261432\nu261433\tu261433\nu261436\tu261436\nu261444\tu261444\nu261446\tu261446\nu261448\tu261448\nu261451\tu261451\nu261454\tu261454\nu261456\tu261456\nu261457\tu261457\nu261461\tu261461\nu261462\tu261462\nu261466\tu261466\nu261468\tu261468\nu261475\tu261475\nu261481\tu261481\nu261482\tu261482\nu261485\tu261485\nu261487\tu261487\nu261488\tu261488\nu261497\tu261497\nu261500\tu261500\nu261509\tu261509\nu261512\tu261512\nu261519\tu261519\nu261521\tu261521\nu261523\tu261523\nu261526\tu261526\nu261530\tu261530\nu261532\tu261532\nu261537\tu261537\nu261540\tu261540\nu261541\tu261541\nu261545\tu261545\nu261547\tu261547\nu261551\tu261551\nu261552\tu261552\nu261554\tu261554\nu261556\tu261556\nu261557\tu261557\nu261558\tu261558\nu261560\tu261560\nu261561\tu261561\nu261562\tu261562\nu261563\tu261563\nu261565\tu261565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272485\nu272490\tu272490\nu272492\tu272492\nu272494\tu272494\nu272496\tu272496\nu272498\tu272498\nu272502\tu272502\nu272504\tu272504\nu272507\tu272507\nu272511\tu272511\nu272512\tu272512\nu272513\tu272513\nu272514\tu272514\nu272515\tu272515\nu272518\tu272518\nu272519\tu272519\nu272521\tu272521\nu272522\tu272522\nu272525\tu272525\nu272527\tu272527\nu272529\tu272529\nu272534\tu272534\nu272535\tu272535\nu272536\tu272536\nu272537\tu272537\nu272539\tu272539\nu272540\tu272540\nu272547\tu272547\nu272552\tu272552\nu272553\tu272553\nu272556\tu272556\nu272567\tu272567\nu272569\tu272569\nu272572\tu272572\nu272583\tu272583\nu272586\tu272586\nu272587\tu272587\nu272589\tu272589\nu272590\tu272590\nu272594\tu272594\nu272595\tu272595\nu272604\tu272604\nu272611\tu272611\nu272612\tu272612\nu272613\tu272613\nu272615\tu272615\nu272616\tu272616\nu272621\tu272621\nu272622\tu272622\nu272624\tu272624\nu272625\tu272625\nu272634\tu272634\nu272636\tu272636\nu272653\tu272653\nu272662\tu272662\nu272674\tu272674\nu272680\tu272680\nu272683\tu272683\nu272686\tu272686\nu272690\tu272690\nu272696\tu272696\nu272715\tu272715\nu272716\tu272716\nu272717\tu272717\nu272719\tu272719\nu272722\tu272722\nu272726\tu272726\nu272729\tu272729\nu272730\tu272730\nu272736\tu272736\nu272737\tu272737\nu272752\tu272752\nu272754\tu272754\nu272760\tu272760\nu272761\tu272761\nu272767\tu272767\nu272774\tu272774\nu272784\tu272784\nu272787\tu272787\nu272788\tu272788\nu272794\tu272794\nu272798\tu272798\nu272806\tu272806\nu272807\tu272807\nu272808\tu272808\nu272818\tu272818\nu272819\tu272819\nu272820\tu272820\nu272821\tu272821\nu272823\tu272823\nu272824\tu272824\nu272828\tu272828\nu272830\tu272830\nu272833\tu272833\nu272838\tu272838\nu272843\tu272843\nu272844\tu272844\nu272848\tu272848\nu272849\tu272849\nu272851\tu272851\nu272853\tu272853\nu272854\tu272854\nu272855\tu272855\nu272857\tu272857\nu272862\tu272862\nu272865\tu272865\nu272868\tu272868\nu272872\tu272872\nu272874\tu272874\nu272875\tu272875\nu272876\tu272876\nu272877\tu272877\nu272878\tu272878\nu272880\tu272880\nu272881\tu272881\nu272884\tu272884\nu272885\tu272885\nu272886\tu272886\nu272888\tu272888\nu272892\tu272892\nu272895\tu272895\nu272897\tu272897\nu272898\tu272898\nu272899\tu272899\nu272901\tu272901\nu272902\tu272902\nu272907\tu272907\nu272913\tu272913\nu272915\tu272915\nu272919\tu272919\nu272920\tu272920\nu272922\tu272922\nu272924\tu272924\nu272925\tu272925\nu272928\tu272928\nu272929\tu272929\nu272939\tu272939\nu272940\tu272940\nu272941\tu272941\nu272942\tu272942\nu272944\tu272944\nu272951\tu272951\nu272958\tu272958\nu272960\tu272960\nu272965\tu272965\nu272979\tu272979\nu272986\tu272986\nu272987\tu272987\nu272990\tu272990\nu272999\tu272999\nu273001\tu273001\nu273002\tu273002\nu273006\tu273006\nu273011\tu273011\nu273012\tu273012\nu273013\tu273013\nu273014\tu273014\nu273015\tu273015\nu273018\tu273018\nu273019\tu273019\nu273020\tu273020\nu273023\tu273023\nu273025\tu273025\nu273026\tu273026\nu273031\tu273031\nu273032\tu273032\nu273033\tu273033\nu273034\tu273034\nu273035\tu273035\nu273043\tu273043\nu273044\tu273044\nu273045\tu273045\nu273046\tu273046\nu273048\tu273048\nu273049\tu273049\nu273052\tu273052\nu273054\tu273054\nu273055\tu273055\nu273056\tu273056\nu273057\tu273057\nu273058\tu273058\nu273059\tu273059\nu273061\tu273061\nu273062\tu273062\nu273064\tu273064\nu273065\tu273065\nu273066\tu273066\nu273068\tu273068\nu273071\tu273071\nu273085\tu273085\nu273087\tu273087\nu273090\tu273090\nu273091\tu273091\nu273092\tu273092\nu273093\tu273093\nu273096\tu273096\nu273097\tu273097\nu273099\tu273099\nu273100\tu273100\nu273101\tu273101\nu273103\tu273103\nu273107\tu273107\nu273111\tu273111\nu273117\tu273117\nu273124\tu273124\nu273125\tu273125\nu273126\tu273126\nu273128\tu273128\nu273134\tu273134\nu273135\tu273135\nu273139\tu273139\nu273140\tu273140\nu273143\tu273143\nu273145\tu273145\nu273151\tu273151\nu273153\tu273153\nu273154\tu273154\nu273155\tu273155\nu273157\tu273157\nu273160\tu273160\nu273164\tu273164\nu273166\tu273166\nu273169\tu273169\nu273174\tu273174\nu273175\tu273175\nu273178\tu273178\nu273179\tu273179\nu273180\tu273180\nu273183\tu273183\nu273187\tu273187\nu273189\tu273189\nu273190\tu273190\nu273191\tu273191\nu273192\tu273192\nu273193\tu273193\nu273194\tu273194\nu273195\tu273195\nu273197\tu273197\nu273198\tu273198\nu273199\tu273199\nu273201\tu273201\nu273203\tu273203\nu273212\tu273212\nu273215\tu273215\nu273219\tu273219\nu273222\tu273222\nu273227\tu273227\nu273228\tu273228\nu273230\tu273230\nu273238\tu273238\nu273240\tu273240\nu273242\tu273242\nu273248\tu273248\nu273249\tu273249\nu273250\tu273250\nu273251\tu273251\nu273252\tu273252\nu273253\tu273253\nu273254\tu273254\nu273258\tu273258\nu273260\tu273260\nu273265\tu273265\nu273271\tu273271\nu273272\tu273272\nu273273\tu273273\nu273282\tu273282\nu273283\tu273283\nu273284\tu273284\nu273287\tu273287\nu273288\tu273288\nu273290\tu273290\nu273294\tu273294\nu273297\tu273297\nu273298\tu273298\nu273299\tu273299\nu273300\tu273300\nu273304\tu273304\nu273306\tu273306\nu27330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0130\nu280133\tu280133\nu280142\tu280142\nu280143\tu280143\nu280145\tu280145\nu280149\tu280149\nu280150\tu280150\nu280151\tu280151\nu280155\tu280155\nu280156\tu280156\nu280158\tu280158\nu280160\tu280160\nu280161\tu280161\nu280165\tu280165\nu280166\tu280166\nu280170\tu280170\nu280179\tu280179\nu280181\tu280181\nu280182\tu280182\nu280184\tu280184\nu280185\tu280185\nu280186\tu280186\nu280188\tu280188\nu280189\tu280189\nu280190\tu280190\nu280192\tu280192\nu280195\tu280195\nu280197\tu280197\nu280199\tu280199\nu280203\tu280203\nu280204\tu280204\nu280209\tu280209\nu280212\tu280212\nu280214\tu280214\nu280216\tu280216\nu280218\tu280218\nu280219\tu280219\nu280226\tu280226\nu280231\tu280231\nu280242\tu280242\nu280243\tu280243\nu280246\tu280246\nu280251\tu280251\nu280253\tu280253\nu280256\tu280256\nu280257\tu280257\nu280263\tu280263\nu280264\tu280264\nu280267\tu280267\nu280268\tu280268\nu280269\tu280269\nu280270\tu280270\nu280273\tu280273\nu280274\tu280274\nu280275\tu280275\nu280277\tu280277\nu280279\tu280279\nu280282\tu280282\nu280285\tu280285\nu280290\tu280290\nu280291\tu280291\nu280293\tu280293\nu280295\tu280295\nu280297\tu280297\nu280301\tu280301\nu280302\tu280302\nu280304\tu280304\nu280310\tu280310\nu280320\tu280320\nu280324\tu280324\nu280332\tu280332\nu280338\tu280338\nu280351\tu280351\nu280355\tu280355\nu280363\tu280363\nu280368\tu280368\nu280371\tu280371\nu280376\tu280376\nu280377\tu280377\nu280380\tu280380\nu280383\tu280383\nu280394\tu280394\nu280398\tu280398\nu280399\tu280399\nu280400\tu280400\nu280402\tu280402\nu280406\tu280406\nu280417\tu280417\nu280419\tu280419\nu280423\tu280423\nu280428\tu280428\nu280429\tu280429\nu280431\tu280431\nu280433\tu280433\nu280434\tu280434\nu280437\tu280437\nu280440\tu280440\nu280441\tu280441\nu280442\tu280442\nu280446\tu280446\nu280447\tu280447\nu280470\tu280470\nu280473\tu280473\nu280482\tu280482\nu280497\tu280497\nu280500\tu280500\nu280501\tu280501\nu280506\tu280506\nu280508\tu280508\nu280517\tu280517\nu280519\tu280519\nu280522\tu280522\nu280523\tu280523\nu280527\tu280527\nu280529\tu280529\nu280531\tu280531\nu280534\tu280534\nu280535\tu280535\nu280537\tu280537\nu280541\tu280541\nu280543\tu280543\nu280547\tu280547\nu280564\tu280564\nu280570\tu280570\nu280574\tu280574\nu280576\tu280576\nu280580\tu280580\nu280584\tu280584\nu280594\tu280594\nu280595\tu280595\nu280606\tu280606\nu280611\tu280611\nu280612\tu280612\nu280613\tu280613\nu280614\tu280614\nu280616\tu280616\nu280618\tu280618\nu280620\tu280620\nu280621\tu280621\nu280623\tu280623\nu280625\tu280625\nu280626\tu280626\nu280629\tu280629\nu280634\tu280634\nu280637\tu280637\nu280646\tu280646\nu280647\tu280647\nu280648\tu280648\nu280651\tu280651\nu280654\tu280654\nu280655\tu280655\nu280659\tu280659\nu280662\tu280662\nu280667\tu280667\nu280668\tu280668\nu280673\tu280673\nu280674\tu280674\nu280675\tu280675\nu280680\tu280680\nu280683\tu280683\nu280690\tu280690\nu280693\tu280693\nu280694\tu280694\nu280695\tu280695\nu280697\tu280697\nu280698\tu280698\nu280702\tu280702\nu280703\tu280703\nu280705\tu280705\nu280708\tu280708\nu280710\tu280710\nu280713\tu280713\nu280721\tu280721\nu280722\tu280722\nu280725\tu280725\nu280730\tu280730\nu280732\tu280732\nu280735\tu280735\nu280738\tu280738\nu280739\tu280739\nu280740\tu280740\nu280743\tu280743\nu280746\tu280746\nu280752\tu280752\nu280753\tu280753\nu280754\tu280754\nu280755\tu280755\nu280756\tu280756\nu280761\tu280761\nu280762\tu280762\nu280768\tu280768\nu280770\tu280770\nu280772\tu280772\nu280774\tu280774\nu280784\tu280784\nu280787\tu280787\nu280789\tu280789\nu280790\tu280790\nu280792\tu280792\nu280793\tu280793\nu280796\tu280796\nu280803\tu280803\nu280805\tu280805\nu280806\tu280806\nu280811\tu280811\nu280813\tu280813\nu280815\tu280815\nu280819\tu280819\nu280826\tu280826\nu280827\tu280827\nu280828\tu280828\nu280831\tu280831\nu280834\tu280834\nu280836\tu280836\nu280849\tu280849\nu280850\tu280850\nu280852\tu280852\nu280855\tu280855\nu280858\tu280858\nu280866\tu280866\nu280873\tu280873\nu280875\tu280875\nu280876\tu280876\nu280878\tu280878\nu280880\tu280880\nu280886\tu280886\nu280887\tu280887\nu280888\tu280888\nu280889\tu280889\nu280893\tu280893\nu280897\tu280897\nu280908\tu280908\nu280918\tu280918\nu280923\tu280923\nu280930\tu280930\nu280931\tu280931\nu280934\tu280934\nu280938\tu280938\nu280946\tu280946\nu280952\tu280952\nu280953\tu280953\nu280968\tu280968\nu280970\tu280970\nu280971\tu280971\nu280977\tu280977\nu280980\tu280980\nu280982\tu280982\nu280985\tu280985\nu280997\tu280997\nu280998\tu280998\nu281002\tu281002\nu281004\tu281004\nu281010\tu281010\nu281014\tu281014\nu281018\tu281018\nu281023\tu281023\nu281029\tu281029\nu281036\tu281036\nu281038\tu281038\nu281047\tu281047\nu281063\tu281063\nu281066\tu281066\nu281069\tu281069\nu281075\tu281075\nu281081\tu281081\nu281086\tu281086\nu281088\tu281088\nu281090\tu281090\nu281093\tu281093\nu281094\tu281094\nu281098\tu281098\nu281099\tu281099\nu281103\tu281103\nu281107\tu281107\nu281110\tu281110\nu281111\tu281111\nu281114\tu281114\nu281115\tu281115\nu281118\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81827\nu281832\tu281832\nu281836\tu281836\nu281838\tu281838\nu281839\tu281839\nu281840\tu281840\nu281843\tu281843\nu281844\tu281844\nu281845\tu281845\nu281847\tu281847\nu281858\tu281858\nu281860\tu281860\nu281864\tu281864\nu281867\tu281867\nu281868\tu281868\nu281871\tu281871\nu281873\tu281873\nu281874\tu281874\nu281875\tu281875\nu281877\tu281877\nu281878\tu281878\nu281880\tu281880\nu281882\tu281882\nu281883\tu281883\nu281890\tu281890\nu281893\tu281893\nu281894\tu281894\nu281895\tu281895\nu281896\tu281896\nu281897\tu281897\nu281898\tu281898\nu281903\tu281903\nu281910\tu281910\nu281911\tu281911\nu281914\tu281914\nu281915\tu281915\nu281918\tu281918\nu281919\tu281919\nu281923\tu281923\nu281924\tu281924\nu281926\tu281926\nu281928\tu281928\nu281929\tu281929\nu281930\tu281930\nu281935\tu281935\nu281936\tu281936\nu281937\tu281937\nu281940\tu281940\nu281941\tu281941\nu281944\tu281944\nu281945\tu281945\nu281950\tu281950\nu281951\tu281951\nu281953\tu281953\nu281955\tu281955\nu281956\tu281956\nu281959\tu281959\nu281960\tu281960\nu281961\tu281961\nu281963\tu281963\nu281964\tu281964\nu281965\tu281965\nu281966\tu281966\nu281967\tu281967\nu281971\tu281971\nu281972\tu281972\nu281978\tu281978\nu281980\tu281980\nu281981\tu281981\nu281982\tu281982\nu281988\tu281988\nu281990\tu281990\nu281991\tu281991\nu281992\tu281992\nu281993\tu281993\nu281994\tu281994\nu281995\tu281995\nu281998\tu281998\nu282000\tu282000\nu282009\tu282009\nu282013\tu282013\nu282016\tu282016\nu282018\tu282018\nu282022\tu282022\nu282023\tu282023\nu282025\tu282025\nu282027\tu282027\nu282028\tu282028\nu282032\tu282032\nu282037\tu282037\nu282038\tu282038\nu282041\tu282041\nu282043\tu282043\nu282044\tu282044\nu282046\tu282046\nu282048\tu282048\nu282049\tu282049\nu282050\tu282050\nu282051\tu282051\nu282055\tu282055\nu282060\tu282060\nu282062\tu282062\nu282065\tu282065\nu282066\tu282066\nu282069\tu282069\nu282075\tu282075\nu282078\tu282078\nu282081\tu282081\nu282082\tu282082\nu282084\tu282084\nu282086\tu282086\nu282092\tu282092\nu282093\tu282093\nu282099\tu282099\nu282100\tu282100\nu282102\tu282102\nu282106\tu282106\nu282109\tu282109\nu282112\tu282112\nu282121\tu282121\nu282132\tu282132\nu282134\tu282134\nu282135\tu282135\nu282139\tu282139\nu282150\tu282150\nu282158\tu282158\nu282160\tu282160\nu282162\tu282162\nu282165\tu282165\nu282166\tu282166\nu282167\tu282167\nu282168\tu282168\nu282169\tu282169\nu282173\tu282173\nu282175\tu282175\nu282177\tu282177\nu282180\tu282180\nu282181\tu282181\nu282183\tu282183\nu282184\tu282184\nu282186\tu282186\nu282188\tu282188\nu282189\tu282189\nu282191\tu282191\nu282194\tu282194\nu282196\tu282196\nu282198\tu282198\nu282199\tu282199\nu282200\tu282200\nu282202\tu282202\nu282205\tu282205\nu282206\tu282206\nu282215\tu282215\nu282217\tu282217\nu282219\tu282219\nu282220\tu282220\nu282222\tu282222\nu282225\tu282225\nu282227\tu282227\nu282229\tu282229\nu282231\tu282231\nu282235\tu282235\nu282236\tu282236\nu282237\tu282237\nu282239\tu282239\nu282242\tu282242\nu282244\tu282244\nu282245\tu282245\nu282249\tu282249\nu282250\tu282250\nu282252\tu282252\nu282254\tu282254\nu282255\tu282255\nu282259\tu282259\nu282263\tu282263\nu282264\tu282264\nu282265\tu282265\nu282266\tu282266\nu282267\tu282267\nu282268\tu282268\nu282270\tu282270\nu282271\tu282271\nu282276\tu282276\nu282282\tu282282\nu282284\tu282284\nu282285\tu282285\nu282286\tu282286\nu282287\tu282287\nu282288\tu282288\nu282290\tu282290\nu282292\tu282292\nu282293\tu282293\nu282294\tu282294\nu282295\tu282295\nu282296\tu282296\nu282297\tu282297\nu282300\tu282300\nu282306\tu282306\nu282310\tu282310\nu282319\tu282319\nu282320\tu282320\nu282323\tu282323\nu282325\tu282325\nu282329\tu282329\nu282335\tu282335\nu282342\tu282342\nu282343\tu282343\nu282344\tu282344\nu282345\tu282345\nu282346\tu282346\nu282349\tu282349\nu282350\tu282350\nu282351\tu282351\nu282353\tu282353\nu282354\tu282354\nu282362\tu282362\nu282364\tu282364\nu282366\tu282366\nu282369\tu282369\nu282376\tu282376\nu282380\tu282380\nu282381\tu282381\nu282383\tu282383\nu282387\tu282387\nu282388\tu282388\nu282389\tu282389\nu282393\tu282393\nu282394\tu282394\nu282395\tu282395\nu282398\tu282398\nu282401\tu282401\nu282408\tu282408\nu282411\tu282411\nu282412\tu282412\nu282415\tu282415\nu282420\tu282420\nu282423\tu282423\nu282426\tu282426\nu282427\tu282427\nu282431\tu282431\nu282434\tu282434\nu282437\tu282437\nu282440\tu282440\nu282446\tu282446\nu282447\tu282447\nu282448\tu282448\nu282449\tu282449\nu282450\tu282450\nu282451\tu282451\nu282456\tu282456\nu282458\tu282458\nu282459\tu282459\nu282461\tu282461\nu282465\tu282465\nu282468\tu282468\nu282471\tu282471\nu282476\tu282476\nu282479\tu282479\nu282482\tu282482\nu282488\tu282488\nu282489\tu282489\nu282490\tu282490\nu282493\tu282493\nu282495\tu282495\nu282501\tu282501\nu282504\tu282504\nu282506\tu282506\nu282508\tu282508\nu282509\tu282509\nu282511\tu282511\nu282512\tu282512\nu282515\tu282515\nu282519\tu282519\nu282522\tu282522\nu282523\tu282523\nu282524\tu282524\nu282525\tu282525\nu282527\tu282527\nu282528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3240\tu283240\nu283255\tu283255\nu283259\tu283259\nu283264\tu283264\nu283265\tu283265\nu283268\tu283268\nu283270\tu283270\nu283279\tu283279\nu283288\tu283288\nu283289\tu283289\nu283290\tu283290\nu283292\tu283292\nu283297\tu283297\nu283301\tu283301\nu283305\tu283305\nu283311\tu283311\nu283319\tu283319\nu283320\tu283320\nu283332\tu283332\nu283333\tu283333\nu283334\tu283334\nu283339\tu283339\nu283341\tu283341\nu283350\tu283350\nu283351\tu283351\nu283353\tu283353\nu283354\tu283354\nu283355\tu283355\nu283358\tu283358\nu283360\tu283360\nu283361\tu283361\nu283367\tu283367\nu283368\tu283368\nu283371\tu283371\nu283374\tu283374\nu283376\tu283376\nu283380\tu283380\nu283382\tu283382\nu283383\tu283383\nu283386\tu283386\nu283387\tu283387\nu283391\tu283391\nu283392\tu283392\nu283396\tu283396\nu283397\tu283397\nu283400\tu283400\nu283403\tu283403\nu283410\tu283410\nu283415\tu283415\nu283416\tu283416\nu283417\tu283417\nu283420\tu283420\nu283421\tu283421\nu283427\tu283427\nu283431\tu283431\nu283432\tu283432\nu283433\tu283433\nu283436\tu283436\nu283437\tu283437\nu283438\tu283438\nu283440\tu283440\nu283444\tu283444\nu283445\tu283445\nu283446\tu283446\nu283448\tu283448\nu283449\tu283449\nu283464\tu283464\nu283465\tu283465\nu283466\tu283466\nu283467\tu283467\nu283472\tu283472\nu283474\tu283474\nu283479\tu283479\nu283480\tu283480\nu283484\tu283484\nu283486\tu283486\nu283489\tu283489\nu283490\tu283490\nu283494\tu283494\nu283495\tu283495\nu283499\tu283499\nu283508\tu283508\nu283528\tu283528\nu283532\tu283532\nu283535\tu283535\nu283537\tu283537\nu283538\tu283538\nu283541\tu283541\nu283543\tu283543\nu283549\tu283549\nu283551\tu283551\nu283552\tu283552\nu283553\tu283553\nu283554\tu283554\nu283555\tu283555\nu283558\tu283558\nu283562\tu283562\nu283564\tu283564\nu283566\tu283566\nu283570\tu283570\nu283571\tu283571\nu283574\tu283574\nu283575\tu283575\nu283579\tu283579\nu283580\tu283580\nu283582\tu283582\nu283583\tu283583\nu283587\tu283587\nu283588\tu283588\nu283589\tu283589\nu283590\tu283590\nu283591\tu283591\nu283593\tu283593\nu283595\tu283595\nu283598\tu283598\nu283599\tu283599\nu283603\tu283603\nu283605\tu283605\nu283615\tu283615\nu283616\tu283616\nu283617\tu283617\nu283618\tu283618\nu283619\tu283619\nu283620\tu283620\nu283621\tu283621\nu283622\tu283622\nu283625\tu283625\nu283627\tu283627\nu283632\tu283632\nu283642\tu283642\nu283645\tu283645\nu283651\tu283651\nu283656\tu283656\nu283661\tu283661\nu283664\tu283664\nu283666\tu283666\nu283667\tu283667\nu283670\tu283670\nu283671\tu283671\nu283672\tu283672\nu283673\tu283673\nu283674\tu283674\nu283682\tu283682\nu283684\tu283684\nu283687\tu283687\nu283688\tu283688\nu283693\tu283693\nu283694\tu283694\nu283696\tu283696\nu283698\tu283698\nu283699\tu283699\nu283701\tu283701\nu283702\tu283702\nu283703\tu283703\nu283707\tu283707\nu283709\tu283709\nu283710\tu283710\nu283713\tu283713\nu283714\tu283714\nu283715\tu283715\nu283717\tu283717\nu283718\tu283718\nu283719\tu283719\nu283721\tu283721\nu283724\tu283724\nu283725\tu283725\nu283729\tu283729\nu283733\tu283733\nu283734\tu283734\nu283735\tu283735\nu283743\tu283743\nu283744\tu283744\nu283745\tu283745\nu283748\tu283748\nu283749\tu283749\nu283750\tu283750\nu283755\tu283755\nu283756\tu283756\nu283757\tu283757\nu283761\tu283761\nu283764\tu283764\nu283765\tu283765\nu283769\tu283769\nu283775\tu283775\nu283776\tu283776\nu283777\tu283777\nu283781\tu283781\nu283782\tu283782\nu283783\tu283783\nu283789\tu283789\nu283790\tu283790\nu283791\tu283791\nu283792\tu283792\nu283796\tu283796\nu283797\tu283797\nu283798\tu283798\nu283802\tu283802\nu283806\tu283806\nu283808\tu283808\nu283809\tu283809\nu283814\tu283814\nu283815\tu283815\nu283833\tu283833\nu283834\tu283834\nu283835\tu283835\nu283837\tu283837\nu283838\tu283838\nu283841\tu283841\nu283849\tu283849\nu283850\tu283850\nu283855\tu283855\nu283857\tu283857\nu283876\tu283876\nu283877\tu283877\nu283881\tu283881\nu283882\tu283882\nu283883\tu283883\nu283888\tu283888\nu283894\tu283894\nu283899\tu283899\nu283900\tu283900\nu283903\tu283903\nu283904\tu283904\nu283906\tu283906\nu283907\tu283907\nu283908\tu283908\nu283909\tu283909\nu283910\tu283910\nu283919\tu283919\nu283920\tu283920\nu283921\tu283921\nu283922\tu283922\nu283923\tu283923\nu283924\tu283924\nu283926\tu283926\nu283929\tu283929\nu283930\tu283930\nu283931\tu283931\nu283935\tu283935\nu283936\tu283936\nu283940\tu283940\nu283945\tu283945\nu283946\tu283946\nu283948\tu283948\nu283949\tu283949\nu283952\tu283952\nu283953\tu283953\nu283961\tu283961\nu283962\tu283962\nu283965\tu283965\nu283971\tu283971\nu283973\tu283973\nu283974\tu283974\nu283979\tu283979\nu283982\tu283982\nu283983\tu283983\nu283995\tu283995\nu284000\tu284000\nu284003\tu284003\nu284004\tu284004\nu284007\tu284007\nu284008\tu284008\nu284015\tu284015\nu284021\tu284021\nu284024\tu284024\nu284025\tu284025\nu284026\tu284026\nu284029\tu284029\nu284032\tu284032\nu284034\tu284034\nu284035\tu284035\nu284036\tu284036\nu284037\tu284037\nu284040\tu284040\nu284041\tu284041\nu284042\tu284042\nu284043\tu284043\nu284044\tu284044\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7753\tu287753\nu287758\tu287758\nu287760\tu287760\nu287761\tu287761\nu287763\tu287763\nu287768\tu287768\nu287773\tu287773\nu287776\tu287776\nu287782\tu287782\nu287786\tu287786\nu287791\tu287791\nu287796\tu287796\nu287799\tu287799\nu287803\tu287803\nu287806\tu287806\nu287807\tu287807\nu287809\tu287809\nu287812\tu287812\nu287815\tu287815\nu287817\tu287817\nu287825\tu287825\nu287826\tu287826\nu287829\tu287829\nu287830\tu287830\nu287836\tu287836\nu287838\tu287838\nu287842\tu287842\nu287844\tu287844\nu287848\tu287848\nu287850\tu287850\nu287853\tu287853\nu287855\tu287855\nu287861\tu287861\nu287862\tu287862\nu287864\tu287864\nu287865\tu287865\nu287877\tu287877\nu287879\tu287879\nu287880\tu287880\nu287881\tu287881\nu287883\tu287883\nu287885\tu287885\nu287886\tu287886\nu287892\tu287892\nu287895\tu287895\nu287906\tu287906\nu287908\tu287908\nu287912\tu287912\nu287913\tu287913\nu287920\tu287920\nu287922\tu287922\nu287927\tu287927\nu287931\tu287931\nu287932\tu287932\nu287933\tu287933\nu287935\tu287935\nu287936\tu287936\nu287942\tu287942\nu287943\tu287943\nu287944\tu287944\nu287946\tu287946\nu287948\tu287948\nu287951\tu287951\nu287953\tu287953\nu287956\tu287956\nu287957\tu287957\nu287958\tu287958\nu287959\tu287959\nu287970\tu287970\nu287971\tu287971\nu287977\tu287977\nu287983\tu287983\nu287984\tu287984\nu287986\tu287986\nu287988\tu287988\nu288002\tu288002\nu288003\tu288003\nu288005\tu288005\nu288011\tu288011\nu288019\tu288019\nu288025\tu288025\nu288027\tu288027\nu288031\tu288031\nu288039\tu288039\nu288041\tu288041\nu288042\tu288042\nu288045\tu288045\nu288046\tu288046\nu288051\tu288051\nu288052\tu288052\nu288057\tu288057\nu288058\tu288058\nu288066\tu288066\nu288069\tu288069\nu288070\tu288070\nu288071\tu288071\nu288077\tu288077\nu288078\tu288078\nu288079\tu288079\nu288081\tu288081\nu288082\tu288082\nu288084\tu288084\nu288085\tu288085\nu288087\tu288087\nu288088\tu288088\nu288090\tu288090\nu288092\tu288092\nu288096\tu288096\nu288102\tu288102\nu288105\tu288105\nu288114\tu288114\nu288115\tu288115\nu288116\tu288116\nu288118\tu288118\nu288121\tu288121\nu288122\tu288122\nu288123\tu288123\nu288126\tu288126\nu288130\tu288130\nu288131\tu288131\nu288135\tu288135\nu288136\tu288136\nu288138\tu288138\nu288139\tu288139\nu288141\tu288141\nu288142\tu288142\nu288143\tu288143\nu288146\tu288146\nu288148\tu288148\nu288150\tu288150\nu288152\tu288152\nu288156\tu288156\nu288162\tu288162\nu288169\tu288169\nu288174\tu288174\nu288175\tu288175\nu288183\tu288183\nu288187\tu288187\nu288188\tu288188\nu288190\tu288190\nu288191\tu288191\nu288192\tu288192\nu288202\tu288202\nu288206\tu288206\nu288207\tu288207\nu288208\tu288208\nu288209\tu288209\nu288212\tu288212\nu288213\tu288213\nu288214\tu288214\nu288216\tu288216\nu288218\tu288218\nu288220\tu288220\nu288221\tu288221\nu288223\tu288223\nu288225\tu288225\nu288226\tu288226\nu288228\tu288228\nu288229\tu288229\nu288232\tu288232\nu288233\tu288233\nu288234\tu288234\nu288235\tu288235\nu288237\tu288237\nu288238\tu288238\nu288241\tu288241\nu288242\tu288242\nu288243\tu288243\nu288246\tu288246\nu288248\tu288248\nu288250\tu288250\nu288251\tu288251\nu288254\tu288254\nu288255\tu288255\nu288256\tu288256\nu288257\tu288257\nu288259\tu288259\nu288260\tu288260\nu288266\tu288266\nu288268\tu288268\nu288270\tu288270\nu288271\tu288271\nu288280\tu288280\nu288284\tu288284\nu288288\tu288288\nu288293\tu288293\nu288296\tu288296\nu288298\tu288298\nu288300\tu288300\nu288301\tu288301\nu288306\tu288306\nu288309\tu288309\nu288311\tu288311\nu288312\tu288312\nu288314\tu288314\nu288321\tu288321\nu288324\tu288324\nu288325\tu288325\nu288328\tu288328\nu288329\tu288329\nu288332\tu288332\nu288333\tu288333\nu288340\tu288340\nu288349\tu288349\nu288350\tu288350\nu288351\tu288351\nu288358\tu288358\nu288364\tu288364\nu288366\tu288366\nu288367\tu288367\nu288369\tu288369\nu288370\tu288370\nu288373\tu288373\nu288377\tu288377\nu288380\tu288380\nu288384\tu288384\nu288386\tu288386\nu288389\tu288389\nu288391\tu288391\nu288396\tu288396\nu288397\tu288397\nu288403\tu288403\nu288405\tu288405\nu288406\tu288406\nu288412\tu288412\nu288413\tu288413\nu288414\tu288414\nu288418\tu288418\nu288424\tu288424\nu288425\tu288425\nu288427\tu288427\nu288429\tu288429\nu288432\tu288432\nu288439\tu288439\nu288442\tu288442\nu288443\tu288443\nu288447\tu288447\nu288450\tu288450\nu288458\tu288458\nu288459\tu288459\nu288460\tu288460\nu288473\tu288473\nu288474\tu288474\nu288484\tu288484\nu288488\tu288488\nu288492\tu288492\nu288501\tu288501\nu288504\tu288504\nu288505\tu288505\nu288513\tu288513\nu288515\tu288515\nu288516\tu288516\nu288519\tu288519\nu288526\tu288526\nu288530\tu288530\nu288532\tu288532\nu288534\tu288534\nu288535\tu288535\nu288542\tu288542\nu288543\tu288543\nu288546\tu288546\nu288548\tu288548\nu288549\tu288549\nu288555\tu288555\nu288558\tu288558\nu288568\tu288568\nu288576\tu288576\nu288585\tu288585\nu288587\tu288587\nu288588\tu288588\nu288589\tu288589\nu288595\tu288595\nu288598\tu288598\nu288600\tu288600\nu288601\tu288601\nu288604\tu288604\nu288606\tu288606\nu288607\tu288607\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91831\nu291833\tu291833\nu291835\tu291835\nu291851\tu291851\nu291853\tu291853\nu291859\tu291859\nu291869\tu291869\nu291870\tu291870\nu291872\tu291872\nu291875\tu291875\nu291876\tu291876\nu291878\tu291878\nu291881\tu291881\nu291884\tu291884\nu291892\tu291892\nu291893\tu291893\nu291894\tu291894\nu291897\tu291897\nu291899\tu291899\nu291900\tu291900\nu291901\tu291901\nu291908\tu291908\nu291912\tu291912\nu291915\tu291915\nu291916\tu291916\nu291924\tu291924\nu291926\tu291926\nu291930\tu291930\nu291933\tu291933\nu291934\tu291934\nu291935\tu291935\nu291939\tu291939\nu291942\tu291942\nu291944\tu291944\nu291946\tu291946\nu291956\tu291956\nu291957\tu291957\nu291963\tu291963\nu291966\tu291966\nu291969\tu291969\nu291972\tu291972\nu291973\tu291973\nu291976\tu291976\nu291981\tu291981\nu291994\tu291994\nu291996\tu291996\nu291997\tu291997\nu292003\tu292003\nu292004\tu292004\nu292005\tu292005\nu292007\tu292007\nu292015\tu292015\nu292019\tu292019\nu292020\tu292020\nu292022\tu292022\nu292023\tu292023\nu292024\tu292024\nu292025\tu292025\nu292033\tu292033\nu292034\tu292034\nu292039\tu292039\nu292041\tu292041\nu292049\tu292049\nu292054\tu292054\nu292058\tu292058\nu292059\tu292059\nu292062\tu292062\nu292065\tu292065\nu292066\tu292066\nu292069\tu292069\nu292072\tu292072\nu292077\tu292077\nu292086\tu292086\nu292087\tu292087\nu292090\tu292090\nu292092\tu292092\nu292093\tu292093\nu292094\tu292094\nu292096\tu292096\nu292100\tu292100\nu292102\tu292102\nu292104\tu292104\nu292106\tu292106\nu292108\tu292108\nu292113\tu292113\nu292114\tu292114\nu292119\tu292119\nu292122\tu292122\nu292123\tu292123\nu292125\tu292125\nu292126\tu292126\nu292128\tu292128\nu292129\tu292129\nu292134\tu292134\nu292135\tu292135\nu292139\tu292139\nu292141\tu292141\nu292144\tu292144\nu292145\tu292145\nu292147\tu292147\nu292159\tu292159\nu292161\tu292161\nu292163\tu292163\nu292177\tu292177\nu292194\tu292194\nu292197\tu292197\nu292200\tu292200\nu292201\tu292201\nu292206\tu292206\nu292207\tu292207\nu292208\tu292208\nu292210\tu292210\nu292213\tu292213\nu292229\tu292229\nu292231\tu292231\nu292232\tu292232\nu292233\tu292233\nu292234\tu292234\nu292239\tu292239\nu292249\tu292249\nu292256\tu292256\nu292258\tu292258\nu292260\tu292260\nu292261\tu292261\nu292263\tu292263\nu292264\tu292264\nu85725\tu292264\nu85775\tu292264\nu292269\tu292269\nu292270\tu292270\nu292271\tu292271\nu292272\tu292272\nu292276\tu292276\nu292279\tu292279\nu292283\tu292283\nu292285\tu292285\nu292288\tu292288\nu292289\tu292289\nu292293\tu292293\nu292305\tu292305\nu292307\tu292307\nu292308\tu292308\nu292309\tu292309\nu292310\tu292310\nu292312\tu292312\nu292316\tu292316\nu292317\tu292317\nu292321\tu292321\nu292322\tu292322\nu292323\tu292323\nu292325\tu292325\nu292326\tu292326\nu292334\tu292334\nu292335\tu292335\nu292337\tu292337\nu292340\tu292340\nu292346\tu292346\nu292349\tu292349\nu292350\tu292350\nu292354\tu292354\nu292357\tu292357\nu292361\tu292361\nu292365\tu292365\nu292366\tu292366\nu292367\tu292367\nu292369\tu292369\nu292371\tu292371\nu292374\tu292374\nu292375\tu292375\nu292380\tu292380\nu292387\tu292387\nu292388\tu292388\nu292396\tu292396\nu292400\tu292400\nu292404\tu292404\nu292413\tu292413\nu292414\tu292414\nu292416\tu292416\nu292426\tu292426\nu292427\tu292427\nu292439\tu292439\nu292441\tu292441\nu292442\tu292442\nu292448\tu292448\nu292449\tu292449\nu292455\tu292455\nu292459\tu292459\nu292465\tu292465\nu292466\tu292466\nu292477\tu292477\nu292478\tu292478\nu292482\tu292482\nu292486\tu292486\nu292487\tu292487\nu292491\tu292491\nu292492\tu292492\nu292497\tu292497\nu292499\tu292499\nu292500\tu292500\nu292503\tu292503\nu292507\tu292507\nu292508\tu292508\nu292509\tu292509\nu292513\tu292513\nu292517\tu292517\nu292520\tu292520\nu292521\tu292521\nu292522\tu292522\nu292523\tu292523\nu292524\tu292524\nu292528\tu292528\nu292529\tu292529\nu292532\tu292532\nu292533\tu292533\nu292536\tu292536\nu292537\tu292537\nu292540\tu292540\nu292541\tu292541\nu292545\tu292545\nu292548\tu292548\nu292552\tu292552\nu292557\tu292557\nu292561\tu292561\nu292564\tu292564\nu292565\tu292565\nu292567\tu292567\nu292571\tu292571\nu292578\tu292578\nu292581\tu292581\nu292582\tu292582\nu292584\tu292584\nu292585\tu292585\nu292586\tu292586\nu292588\tu292588\nu292589\tu292589\nu292590\tu292590\nu292591\tu292591\nu292594\tu292594\nu292597\tu292597\nu292599\tu292599\nu292603\tu292603\nu292608\tu292608\nu292611\tu292611\nu292612\tu292612\nu292614\tu292614\nu292615\tu292615\nu292617\tu292617\nu292618\tu292618\nu292619\tu292619\nu292621\tu292621\nu292624\tu292624\nu292626\tu292626\nu292631\tu292631\nu292633\tu292633\nu292637\tu292637\nu292638\tu292638\nu292643\tu292643\nu292645\tu292645\nu292648\tu292648\nu292649\tu292649\nu292650\tu292650\nu292651\tu292651\nu292655\tu292655\nu292658\tu292658\nu292661\tu292661\nu292662\tu292662\nu292663\tu292663\nu292667\tu292667\nu292678\tu292678\nu292679\tu292679\nu292682\tu292682\nu292683\tu292683\nu292684\tu292684\nu292691\tu292691\nu292692\tu292692\nu292695\tu292695\nu292697\tu292697\nu292698\tu292698\nu292702\t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}, { "path": "tests/input/TestKbPython/palmdb_rdrp_seqs.corona.fa", "content": ">u4907\nIETDISKMDKSQGAVHQYIQDMMFHVLGLDLEIIQMWSDAHGRCQIRDSDCGFSFATLWQ\nRRTGDACTLLGNTIVTAVVNHYVLDFTKFEAVGVIGDDFTG\n>u5166\nAIADAKSFDSQQSPLTLEIERQFMKRLGANMPSLEQYYQIRNPMEFRXFNLFSGKTRGEK\nGSGFPDTLLGNTILQTCLSTYVFEGMGPMVVAAKGDDHLR\n>u9210\nTCNDFSEWDASFRQAFVKLTSWLLIAAGCPRALVEEYEKFRESWVMQYRTMWGNASLHGE\nEKQFSGNPFTICENTIGNMALCFTLFEYKGFQFAYFKGDDSAV\n>u10985\nLELDLSKQDRQTSKEILSKHFTFMQALGLTDGHNALYQELLLTWSFNSRTKIRGNLPPMH\nMSGGTFTGLGNELRNLYILSDINAMYPIDYSWSLGDDSIS\n>u11438\nSTNDYTAFDQSQTGEALSFELMMLRAFGIPDGVISYYTELKLELTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPSDTAIAVAGDDLAM\n>u11684\nYECDMSAFDKSLERTMFSGVLELYRSFGLSDADCELWEILHRLTLSRSRAGISFYTSYQT\nKSGDPATALGNTLATMIALARVMHAVSPQLSLFMGDDSLL\n>u11814\nKESDIRKFDKSQQEKVLRAEQKVLMLFGFPPQLAELWLRVHEDTILIDRGLGIMFRVRWH\nRKSGDASTFLGNSLVLLMVLCSTYDLTKAVMVVFPGDDFYI\n>u12665\nCESDLEACDAGQDETTMLFERKMMELFDVPQIAIDFLFFIRKNWKLSARDLASVDNEGKK\nHSGAPDTLDGNTIVNAAIVARMFKITRLILAMFKGDDTFI\n>u12968\nSWNDFTAFDQGQDASFLAMEVNLMEKLSIPASEIAFYIHLKTNTFSNLGSFSIMRFTGEV\nFTFIFNSLANMAISNLRFVLDRSGKPICFGGDDSCF\n>u15124\nYEFDVPKFDKSQDMMCFNLILEVMSILGISQEFIQYWRRASYEGTIFNSAFSMVFTLFYG\nNRSGSGGTLAVNCICLLFAFYTEFANLSIVAALIKGDDSII\n>u15127\nSENDFEAFDSTQNEEFLTAQVALMHALQLPVPLIQDYINWVTHLSIFAGELGIMIASGYK\nPTWLFNTFDNMCIAALSFGLTPHTSVLGDLPYHNPLPATRSVARAFSGDDSAH\n>u16744\nIEIDISQMDKSQMELHQLIQDKVFLRLGADPEFIFKWKEAHRLCHMAEASVGFAFTTSWQ\nRRTGDAATLLGNSVVTLVVNNYVLGFKNFVAVGCVGDDFSG\n>u17082\nIENDFSDYDRSQDALALAIERWVDYYCGFDGEYCDAWFNAHVFTNNRNHVTGLSAFLLYQ\nRKSGDVSTSYGNTVVGMVVVAWGYKLPSFVFCIFLGDDSIF\n>u17899\nFAADATEFDSSQNYTALLFLSKFINYLLGLTNSKLVNNFICMNQVANLVGPKFTTRVCYN\nRHSGEPFTIFCNTLFNMGLAATFLEGRIDFVGFKGDDMII\n>u18032\nLAADVTEFDSVHSQVTKEVEKILMQKCELPQPIIDLYMHMRNKWKLSTYSVGYLHGEHKQ\nHSGQPATLFSNTFLAMMIMIIGLDEEEMEKGNYMMMAKGDDTVL\n>u18851\nYEDDYTGFDGTQNEDFLAFQVLLMGWYGIPTNIIETYVLWVTHLRDALGECGVWIASGFI\nPTWLFNTADNMAFQALKHALTTHTWSPSDVARSFSGDDSTH\n>u18993\nIQVDISEYDKSQESRTRHLEDLIFRELGMLDDYIDLWSYSHIDTTIRVLGMGIKMVVAYQ\nRKSGDATTALGNVMLNMMASAYVFGKPTVSISQGDDGLI\n>u19711\nWEMDFSKQDRQTDQNAMEFEFHLYEKLGMDQETLELWKSCHATWISRSSHTKGKREWMRK\nTGDASTALGNAINNFRAILRLAEDPRFRGALILGDDSHV\n>u20466\nLTCDFSEFDSSQEKQGILSSCMILKMMGFDGDLVNFYMAKRKDWTLINQDENFNMPLRTM\nLDGEYMQHSGQPFTLDGNTMFNMSCMGMCFEFVNMIFASFKGDDSYI\n>u20478\nLENDFKAYDKTQDNIALEIELHFLKLLGVPEDMIEMWRSGHVYTRATCRETGFLLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFQNHNDAKHKLRCAFFLGDDSLF\n>u22346\nTINDFTAFGSSQGGESVTMDLCWFRWCSMPESLCDLYVGFKTKLLALGAIKVICRDDGEP\nGTYLFNSLYDIGNTAAKFSPMALWLGYWLFGGDDMAT\n>u24448\nTWCDYTGWDSGVNESFTLLYTDVLRSYGVPSAVAARFASDRHSLRSFLGPMPAMQASGDR\nYTWLANTLGNMALTGISFDLPADVPACFSGDDMIL\n>u25128\nTACDYTGWDSGVDESFTLLYSNVMRAFGIPDSVVDRFCSDRNNLRSFLGPMPAMQASGDR\nYTWLANTIGNMAVTGVSFDVGPKTAACFSGDDMIM\n>u26309\nLSNDFTEFDSAQNNVEKHLIRIILTEIGCPAHVINHYENLRSRRLVYGSAARFVLHDKRD\nSGEPFTLIGNTAFNAAVVLRLVLGDVRFAIFKGDDSYV\n>u26790\nYANDYTSFDQSQTGEVLASELLYMWHAGIPEVIINCYESNKVDMFCAFGHLQTMRFSGEP\nATYAFNCRCNLAVLNLQFPLDRNLNVPIFVSGDDGGL\n>u27314\nIENDFSAYDKSQDDACLELEMLFLRRLGFPPDLLDMWETGHIFTRIRAFDSGFTLWTMYQ\nRKSGDVTTSFGNTILNMIAVAWCYFKSAVDCWNDVIFAWFLGDDSTL\n>u27647\nVQNDLQKQDKQTVMQIIQIQMLIYKYLGMQNNLVDFWRLMHIDWQLRSKYSTTMATAQRL\nTGQATTAIGNVITNLIVHTDFIKYNMSQLKLMLVLGDDFVA\n>u28806\nISLDGSAFDSSQFECLMRLVDDKFWRGMRPFIRRVIQHNWDGMVNTPANSVDKITEQLMK\nALLKSQNLVFVHLPGVKSPSWPPQVRKQFFRDVEQAGQWKNGDPEEDWIYLELNGTTFSG\nHSTKTTLGNTLRTLCYAWFYIMKAGISQTPWNSNKVFAIASGDDCVI\n>u30539\nTASDYNAFDSSQRGDSLGLEYKLMEYLHISNNWSLAFELFRSEAATLPDLYLNWKLDTVS\nNLGFVKRSGRDTGEPGTYDFNTYFNMAVYRLMYGALPGLPACFGGDDLAA\n>u30705\nIMNDFGGYDAAQGRALSLECDLMEALNWPKEIINSYIWHKTNARARNLKNGAYLAPMRFT\nGEVWTYVFNTLFNIVIINIKYEIGSRSVLISGDDSAI\n>u31688\nYEGDAEMYDQSQSFGPLNFEREVLRVFGVKDFAVRLFRTLAENEYLVMSRDRESKLLIDK\nGERALRDTGGANTSFGNGVIMALSWTAVILRTGLNCVSILISGDDSLV\n>u32186\nVDVDANRFDASFNELCRKLERLIYVKYGLHLDIIRMLEKQDRINGTSFVGCRVFETVKSG\nKRRSGEQNTSIGNSLVNGSLVLAYLRKIGVVGHCLVLGDDLVI\n>u32205\nVDNDFSSFDSTQSKHALGLVYDFYEMCGMDTDIVNLMRKDTIKGCRIFTNCGVKLHARNI\nRISGRGDTLIGNTVLNCLIMNHAAGGWLRKMIIKGDDSVL\n>u32590\nYEGDASMFDQSQSTGPLDFEYRCLHVLGVDPGVTNCLRQLSKAKYIYSSIDGVGKLSVDK\nTLRPMRDTGGADTSIGNSINMAHAWVYALGSVVHIIVSGDDSLV\n>u32831\nVESDFSEFDSGQNDLTLRCEEMIMRKFHVPESAIFLYVSMRKKWKLSARDVATLYGAYKQ\nHSGQPATLFGNSLVTLLIIAEVCDVTDALVLVKGDDCCI\n>u33284\nFEADARNFDCTESHGPLEWERSVLLRLGIPFQICQALYASASNTLRAMPHRREGDQVAFE\nIDCKERPMRRTGDADTYLGNTIVMISAWYFVLQMITYEKHCPWDDPGVAILACGDDSVV\n>u33295\nVEGDFSTYDQTQTTSIINKFETEIYNCDAETHQFFNDMTRTDLELRVRFSHYTFRIRRPD\nGKRNSGGYNTSTGNSLVTGCAWVNALVHTDYLRDNTIVIIVVGDDSLV\n>u33693\nEEDDYTAFDQSQDAAFLEFELLLMRHLGIPDHLVQEYEQHKRCTKCQIGVRDLAILRFSG\nEFGTFILNCTANIAYTNLKYNIPRNAIQLYAGDDLVV\n>u34022\nLENDMSRFDSTQTPEALHLVHLFYSLAGLPITAIECLQSDLSDVKVSTSVGINCHVKGFR\nLSGRSDTLVGNTILNLLIMYHAFPSLKRVIVKGDDSVM\n>u34211\nSADDFEAFDQSLDENFAEAERHLALNVYHIPPELVEQVVEFKVTMRWMGRELAHMILSGF\nPGTWFANTTNNIAYQATKYALDRGVAAAYSGDDSGY\n>u34481\nIECDMTQFDQSQGPETLSREVYHMRHYSVPENLIDLYIWQKTHLRHQFGTSDVMRFTGEP\nATYYFNTCMNEAYLHCRYHLNGVAYAISGDDSLI\n>u34954\nGDADGSKFDKLQQEFALLCELYLYKLLGWRGFDFDKWFEAVDHKSMLSYRAKLRLQLAFQ\nRSSGNRNTALGNSIVMLLAVFSKVNIEYDQLLCAINLGDDITF\n>u35481\nIEMDMKKQDRQTDQGEIENEELIMIKLGFPKFMMEKWHSYNSDWRYVSGSGIRARRNWFR\nKTGDEMTSLGNAIKNLSGLAAPFIKFGAERVLVLGDDSIA\n>u35664\nKAIDFAEFDSRVVDAGPRLNALLMFYMFCPSYLCQEYTQQRSNWVLDTGIIKLLGFDKMH\nSGEPWTLMGNTLYNMAVIGCVYLIDGLVVAGFKGDDSGI\n>u35682\nVSTDWSEYDSTHNKVAMYVFAEVLRWVGTPEPLVKYFQARCGRRNLVSDAGTVTVNWMLD\nSGAVWTLAKNTVYSAGFLFAATLGVRMGFFKGDDALL\n>u35840\nFEADARMFDQSQSFGPLQAEYFALQCYGVPSHICDMLFAVASNRYVVRPSDKDKHLEPLY\nLDKKARPIRDTGGADTYLGNTLVMAMAWFLVLTEPDQNYSLGFAILVCGDDSVV\n>u35853\nLEGDASMYDQSQSYGPLNLENHVLVKCGLSYEASRILTLLSANTYALRYKETHTKTHIKR\nTERPIRDSGGVNTSIGNSIVMAHLWCYSLLTKACFILVSGDDSLV\n>u36358\nLATDFTQHDTSHSYIIKLWMLKDFLDMGFDACAMAEFFHAYEDWMQTARIDDELIASVHN\nFFIQHSGSPDTLHGNTKLTMAANGMAYRFRNLRFGSFKGDDSLI\n>u36827\nFESDLSKQDRQTDAHSLAFEYMLYEKLGVPIHINNFYKLQHKNTRLTHSNFRTQTKPKRH\nTGQTTVGFGNIINNMRTYAQLFNDKEFDFVCLLGDDLLA\n>u37152\nLENDFSSFEASVSDAIMDIVECEAFRFFFKKVLTKERLAELIADVKTSVFGYKTFTGVVR\nGRRKSGDLWTSTGNGFTNLVVLLVAAHMSSTKIVAAKVEGDDSLV\n>u37183\nIELDLSMCETTMRGPFLVLESMIYKALGLSLYDIDYLLNHDKSHGKSMKGNLRFNMTFCR\nESGTANTTPGNTVVFMAVLWATLLKHGMTENDFVCLIGGDDAAI\n>u37789\nTTNDYEAYDQSQNAECLIFEVMLLEYFNIPDDLIEFYKFLKVSANTQFGNLEIMRLTGEW\nCTFLFNTYVNIAYSTFKFQELRLPRKLKPASAFGGDDLVI\n>u37921\nSTCDFTAYDQSCRAETLSFELCLFDFFSLSSEFPDAVFLYFFIKTHMFTQFGPSAIMRFT\nGEFGTYDFNTWYNIAYMSFRFLLDERSPDEASAFSGDDSIF\n>u38952\nLELDLSKQDRQTDAPIIEAEMDFLCALGMHPEVMDSFRNILKPSFVKTADNLSFHLPVMQ\nWTGGELTAFGNTFRNLLFIADLWDECDFDYAMVLGDDSLI\n>u40536\nFEGDASMYDQSQSFGPLSYEYRFLQILGVPPEVIEILVTLSQNVYELRTKDPQYHGIIDK\nYKRPMRDTGGTDTSLGNSLIMAVAWIFVALRKDVAIIVSGDDSLV\n>u40538\nVEGDASMFDQSQSHGPLSFERKILARLGLDPETCDMIERLARATYVIRTPSGAIRIHRAD\nRPFRDTGGGETTLGNSLVMGVGWLYTWQALAAMTLWPATGIHIGISGDDSVC\n>u40718\nMDNDFSSFDCTQNKRALSLLNKFYKMCGIPGKVIGQFAKFQMGARMRAKYLSTFVTKGHR\nVSGTADTLVGNTILNFIISNHVQPKLLKVIAKGDDSVV\n>u40733\nGENDYEAFDATQHVACRLLIIEMLVEHFGMAPEVARLMRAAAKEKFGHTMNGTYVSMEGT\nMASGHPDTYLTNTMMNILLQWYASECCGVHQPPIAAAGDDSVI\n>u41736\nTESDYSGFDATQKGDSVGFEVGLMRHVGLDDAWTALFADFSGYAETMPELYEFWKTHIVS\nTVIGPKDLGRDTGEPGTFDFNTYFNLALVILMYDPPRTLPICVGGDDMSA\n>u42095\nAVYDVSEFDSKQSADTQFLEDIEYELFCDKSLLWFYRQLRLSAPQASKVVRLRKFGVKDS\nGESATLQSNTSVIKWLMLIATRVTCPKIEAFKGDDVFI\n>u42152\nFEGDASMYDQSESFGPLSLGWMACRRLGVDSGTIKLLSELASNSYLVCAKDSTDQNYFRI\nNKRNRPLRDTGGADTSLGNSLVMGCAWYYVIKKCFKSSFNFAAIVVSGDDSFV\n>u42218\nLVNDFKQFDSAQDETSILAFASFLKMLRMPEVCIKLYTKLRLRWVMALRGSNLQQDTITL\nLRGVFKKHSGEPATLDGNTWFNRAVTCMCIKWKNPYIAGFKGDDSII\n>u43280\nISLDGSAFDSSXFECLMRLVDDKFWRGMRPFIRRVIXHNWDGMVNTPANSVDKITEQLMK\nALLKSXNLVFVHLPGVKSPSWPPXVRKQFFRDVEXAGQWKNGDPEEDWIYLELNGTTFSG\nHSTKTTLGNTLRTLCYAWFYIMKAGISXTPWNSNKVFAIASGDDCVI\n>u43947\nLEIDQSRYDGTLCEHAIALEHAFYQRFMVYRQTGAVGDQFRECIKAMKSTNVYLVNGVKA\nHYHAGRQSGDANTSVGNSYINAVVISYALWEAGIRFGSYRMLVLGDDNLV\n>u44041\nLEADIEAFDKSWQTLHLDFLTELLVIMGFPAFSVNLFQKHMYGSTYRSRDCGISTFVGVQ\nQKSGMFMTYLGNTIITMAVFAAAGNITKFKLGIFGGDDSVV\n>u44289\nLENDFSSMDRTQGVHALEAEARILQTLGIPEEKTKILFDTMLKNPVYKAEKLGVKIKLQM\nPPQRATGAPDTTIGNTIINIMSVIYALNECRRMACIVAGDDFYA\n>u44293\nWEGDFSMFDQSQSKGPLNLEYEVLQSLGVPKFVTDRMRRLSYASYVLHTKDKEGAERAII\nSRADRPMRDTGGSDTTIGNSIVTAHAIAHVMKKFCRKGNAIFFIVAGDDSLV\n>u44807\nIEGDAGMFDASESKGPLKDEEENNRKLGVDEETLEILCELSSNTYVARSRKDTQVLMIIK\nTHCWKRDTGGPNTSTGNSNVMGNSWFYTVLETWHCKMISIIVCGDDSLL\n>u45995\nLEGDWTEFDSSQNNVEHELLMMQLEAIGCPAELRDLFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDHVLFKGDDSLM\n>u46005\nLEIDFSKFDKSQARMCHLFEMFFWEQLGMDQYLNGLWRAGHYTTSALDFSTGVKAFFLYQ\nRKSGDAATAFGNTLVAMASLARAADVSGFATAMFVGDDSLL\n>u46307\nLEGDWTEFDSSQNNVEHELFMMQLEAIGCPEELRDLFMLMMLKRGVHSSFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETISHVLFKGDDSLM\n>u46786\nTWCDYTGWDSGVNESFTLLYTDVLRSYGVPSAVAARFASDRHSLRSFLGPMPAMQASGDR\nYTWLANTLGNMALTGISFDLPPDVPACFSGDDMIL\n>u47256\nLEYDASKFDKSQGYLALEVEIEIMRRFGFPEIVLSKWKEAHEQSYIKDYGTGMKVKLNYQ\nRKSGDSMTLLGNTIITMSTLSMVYDLDDAVFGLFVGDDSLI\n>u47560\nAENDMKEYDTSQNEITIENEIKWLKRMGCNELFIRLFKKHRIEWKANYPGYCQLIGYAKK\nHSGEPFTIDFNTLLCMALNGLLFPLEHFVFAAFKGDDSEI\n>u48052\nVACDISEQDTTKTEATHLVFRWLFEAIGVPSHTYDIVQQACIRWTGFGLDFSINNVETFQ\nSGINWTYLNNTVDSMARIGASFEIEGLRLAMFKGDDAYV\n>u48136\nLEGDWTEFDSSQNNVEHELLMMQLEAIGCPAELRELFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDHVLFKGDDSLM\n>u48145\nVSGDDSLVIVWSETSNISVYEGDFGMFDQSQSVGPLTFEYAVLKRLGVPHDIVERMEGLA\nHATYLFRTRDKRSSAEVRVDLTRRPMRHTGGTDTTFGNTVVN\n>u48846\nTCNDFSEWDSSFRSCFAKVTSRLLIMIGCPEKLAQWFENFRESWRMEYRHEFGKTVLSGF\nEKQFSGNPFTICENTIGNMALCFISFEYKGLDFAMFKGDDSAV\n>u48950\nTTSDYTAYDSSQKGDSLGLEHLLMYHFGLDKCWTLLFADYVKAFKTVPELYLHWKTHIES\nTVIGSKETGRDTGEPGTYDFNTYFNLALISLMYKPRRGIPIAVGGDDMAT\n>u49101\nSWNDFTAYDQGQDASFLRMELTLMERLCLPQDVIDYYSWLKTSTFSRLGSFAIMRFTGEV\nFTFIFNSLANIAVSSMRYYFAPGRACMFGGDDSCF\n>u49200\nSTNDYTAFDQSQTGEALSFELMMLRAFGIPDGVIAYYTELKLELTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPSDTAIAVAGDDLAM\n>u49619\nCSGDDSIVAEFYPTHMVFWEGDASMFDSSQSKGPLKFQYLMMHCLGVDASITLSLYKVAH\nATLVVRPKKNDYDFDILRVDRSQRPHRDTGGADTYIGNTLVM\n>u49874\nVEVDYSKFDKSQGEAILLFECLLFNWLGMPQQFIEHHYRSHSESFVRCSTTGFSATTQYQ\nRKSGDPWTFHGNSIVTLATIVHALAGYSVVGVVAYGDDSIV\n>u49885\nLEMDMGKFDKSQGLTALLFECEVFRKAGMDTWMVNLWFLSHFLIRVKGFGTSIRLSIPHQ\nRRSGDPWTYGGNTFFLLAILLKMCGNRLRYLMVSGDDSLA\n>u49925\nVAGDDFFAIVREKDEIFYLENDFAKFDRTQGVHAQDAEAKVLKLLGMSERISYILFTTMN\nLQPRYENKRLDHQAIYHMPAQRATGAPDTTIGNTINN\n>u50292\nGTNDYSAFDQSQTGEALSLEVVKMRVFNIPEHVIHYYEELKLTLTCQFGSLAVMRFTGEG\nPTLLFNSDFNTALIGCQYEMPPDTPLMVAGDDSAI\n>u50293\nLENDFAKFDKSQLEVVYWFEYYLFKSFGMDEYLLEIYLNANRTSRFYDAKHGVSANVNYQ\nRKSGGATTWLGNSLFTLCVLLCVYDIEDIIAMLVAGDDSFV\n>u51315\nTTCDYTRYDFGCRGPTLNFELCLFEWGNLPGVLGQIYVDIKLTMMTQFGHVAIMRFTGEF\nGTYDFNTWWNMAFQALKFHLGDVRFSKIKACMFSGDDSLF\n>u51320\nLEIDFSKFDKSQTEICFEIEMAFWSLLGMDEALHDLWKIGHFNVSAMDFQAGIKAYLQYQ\nRKSGDSATAFGNTIISMASVAYAFTAPEVTAAYFIGDDSLI\n>u51336\nLEIDFSKFDKSQTEICFEIEMAFWSLLGMDEALHDLWKIGHFNVSAMDFQAGIKAYLQYQ\nRKSGDSATAFGNTIISMASVAYAFTGPEVTAAYFIGDDSLI\n>u51666\nMSIDLSQQDSSHVNVHRFFIGKVLAFLGFDDTVVSLYLMTRAKRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSTGTSVCTFDFSKFELFIGKGDDNTV\n>u51885\nLESDFANNDGSQSVEFRRREAMFYAKHGAPAWFVREFARNTSVRVWTRYGIEATVYGQRW\nSGETTTTTGNSYVGSVLLLASALLAGIKKSTHIHGGDDFMG\n>u52027\nTTNDYTAFDQSQTGEALALEQIILKVFRVPEHVISYYITLKLELTCQFGELAVMRFTGEG\nPTLCFNSWMNDAIIGVQYVIERDTPTAVCGDDAAI\n>u52034\nIESDAKNNDGSQSKEFRKYEAMFYRKLGAPDWFVREFARTLKVRVWTRYGICAEVSGERW\nSGETTTTTGNSYVHMALIQAAHERAEIKNSTNIHGGDDYLG\n>u52061\nMSIDLSQQDSSHVNVHRFFIGKVLAFLGFDDTVVSLYLMTRAKRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSTGTSVCTFDFSKFDLFIGKGDDNTV\n>u52073\nTINDYSNFDATQGGESVVLELAVLQWSGLPDYIVQGYAHWKTHIVTSFIGLKQTSRDSGE\nPGTWDGNTWYNIANCALKFGYQALRRGTWLFSGDDMAC\n>u52086\nIEVDISKFDKSLLMWAFWYLRLLMIQFGVPEWIADLYYSVHLLTTMVDVQTGVKLETFCQ\nMKSGDPITFPGNSFITLGTLLYCLSDIDDIQLMMFGGDDSLI\n>u52094\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELMALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKVARAFAGDDSLF\n>u52280\nTESDFTLFDSSQNGRGVAFEELKMEYFRLPTVDIDFYVELKLTSESFLGTLPVMRFSGDV\nNTLLGNSDFTIAVMNLRFRIGCCIRLGRNVLHCGDDFAC\n>u52508\nSTCDFTKYDMSCKAETLSFELCLFSYFGLDVIFPDLVNDYFFIKTHMYTQLGTSGIMRFT\nGEFGTYDFNSWYNIAYMAFRFKLNPLDTRGSAFSGDDSIF\n>u52700\nMSIDLSQQDSSHVNVHRFFIGKVLAFLGFDDTIVSLYLMTRAKRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSTGTSVCTFDFSKFELFIGKGDDNTV\n>u53148\nFELDVSKYDKSQEAVWLDAQCIVFKLLGMCDQMIDLWRVLHEMCILTAPKFGATYRVGYQ\nRRSGDALTWFGNTLVLLMMMAYLYPIEEAHMVLLGGDDNVT\n>u53181\nTCNDFSEWDASWRGCFTEFTCTLLRYMGCPKPLVEDYKLFRDDWIMTYMTAFGNVTLSGR\nEKQFSGNPFTICENTLGNMALCFSIFEVRDMQYAMFKGDDSVI\n>u53329\nLEIDMAKFDKSQGERILEMTCEIMRLFRVPEAYIQEWKNCHIINRLVFHKIGVSLKVKYQ\nRRSGDVSTFIGNTIVTMIILSYVYDLKSPECKGGVFGGDDSLI\n>u53415\nTTNDFTAFDQSQSADALALELMLLRYLNVPESMISLYTEIKLETKSFLGVLAIMRFTGEW\nCTFLFNTLFNIAYTSLMYNLDPLTPCAFAGDDSII\n>u53442\nCENDYTQYDKCQNGEFLNFEIYLMKHYCIPSYLLDFYVNNKIGLHSFVGHHATQRGTGEG\nPTFDANTDCNIAIDSLKFEIPKGTPAAYAGDDMGR\n>u53621\nASGDDSIMASGGLDGTRDYIEGDQSMFDQSQDEAPLSFTAEIFRECGIPEDFIDLFWYCC\nKQGYTVRKGRLEVKGSPGTQMPTGVVVTTLTNSMNT\n>u53921\nSTNDYTAFDQSQTGEAVSLELTNLRAHHIPDEVIEYYIDLKLNLCCQFGELAVMRFTGEG\nPTLKFNSDFNAALIGVQYDFPDDMARAVAGDDMAL\n>u54033\nSTNDYTAFDQSQTGEALSFELMMLRAFGLPDGVISYYTELKLELTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPADTAVAVAGDDLAM\n>u54862\nLEIDFAKFDKSQQDFCLKTELKIMKEYGISQDLINAWELYHWISVATDYNTGIKARMIRQ\nRRTGDSFTCLGNSLISMQSIAACIDLRRLICAAFVGDDSLL\n>u55046\nTYCDYSGWDTGVDESFTLAYASIMRSYGLSESVVERFVRDRHNRVSFLGPMPAMQASGDR\nYTWLNNTIGNMCLTGHSFKRVAGAPIAFSGDDMIA\n>u55214\nLTADFSEFDSSQEMQGILAGATYFKLCGVPDHIVEMYLSQRRRWLMLAVDKDDSTIMRAM\nLEGVWKQHSGQPDTLNGNTTFNMAAMGACYNITDLQFASFKGDDSII\n>u55265\nVDNDYTAFDQSQDATALFLEIELMRHFNVPSDMIELYYWLKTETRSWLGPFGIMRFTGEW\nSTFLFNTLFSIAYSHTKYSFPPGMLQCYGGDDSSF\n>u55305\nVENDFSRFDSSVHDLAIQLEEEIYTACGLTGDALKMFQHQRFTSGYTSHNIHYGVPATRK\nSGDPNTTLGNSIINMLMSKYVFQCITGEHWSKIPILVGGDDSVI\n>u55634\nCSGDDSIVAEFYPTHMVFWEGDASMFDSSQSKGPLKFQYLMMHCLGVDASITLALYKVAH\nATLVVRPKKNDYDFDILRVDRSQRPHRDTGGADTYIGNTLVM\n>u55770\nIEMDLKKQDRQTDMHELENEFILMTALGFPSYLMPLWRQYNESWRYKASDGTTSQQTGKR\nKTGDEMTSLGNTFKNMSGLVEPFNKYKTERILILSDDMIA\n>u56161\nLEIDQEKFDKSQTRECFEVEMYFLEKLGLDKELLAVWGDGHESSTAINFANGIKCYFVYQ\nRKTGDAMTCFGNTLISMAAMATVFDLKGSEASYFVGDDSFI\n>u56398\nVCNDFSEWDSTFRSPFVNMMSDLILACGCPKMIVDIFVGLRIKWVMRFNKNGEKTKLYGN\nEKQFSGNPFTICENTICNMALTNALLDIKDEQMALFKGDDSAI\n>u56924\nLMADFSEFDSSQEKQGIMGNAILLSEMGCHHSITDLYIEMREKWLLCGQSEQDHVPIRMM\nLAGKYKQHSGQPDTLDGNTRFNMAVMGMCYDYKNICFAAFKGDDSFI\n>u57146\nTESDFEGFDSTQRGDSLGLELKLMAQFGLKDAWMSLFEQFSFGFLDMPELYAWWKTHIIS\nTVIGPKQTGRDTGEPGTYDFNTYFNLAVTCLMYELPRGVPLCIGGDDMSA\n>u57466\nTTNDYTAFDQSQTGEALALESAKLTAFHIPDHVLAYYLELKLNLSCQFGDLAVMRFTGEG\nPTLLFNSDFNAALLGCQYAQIASYAVAVAGDDCAI\n>u57496\nLENDFGKFDKSQGEFAYIFLAFVLVQLGMDDELIDRWIDSNERATLKSVVLGILLIIRYQ\nNKSGGPATSFVNGVLNMASTATAYAGTVVYWATYMGDDSLL\n>u57667\nTWCDYTGWDSGVNESFTLLYTDVLRSYGVPSAVAARFASDRHSLRSFLGPMPAMQASGDR\nYTWLANTLGNMALTGISFDLPSDVPACFSGDDMIL\n>u57774\nVACDISEQDTTKTEATHLVFRWLFEAIGVPSHTYDLVQQACIQWTGYGLDFSINNVETFQ\nSGINWTYLNNTVDSMARIGASFEIEGLRLAMFKGDDAYI\n>u58072\nVAGDDFFAIVREKDEIFYLENDFAKFDRTQGVHAQDAEAKILKLLGMSERISYILFTTMN\nLQPRYENKRLDHQAIYHMPAQRATGAPDTTIGNTINN\n>u58260\nMSIDLSQQDSSHVNVHRFFIGKVLAFLGFDDTIVTLYLMTRAKRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSTGTSVCTFDFSKFELFIGKGDDNTV\n>u58441\nIENDFSDYDRSQDALALAIERWVDYYCGFDGEYCDAWFNAHVFTNNRNHVTGLSAFLLYQ\nRKSGDVSTSYGNTVVNMVVVAWGYKLPSFVFCIFLGDDSIF\n>u58796\nLEMDMGKFDKSQGLTALLFECEVFRKAGMDTWMVNLWFLSHFLIRVKGFGTSLRLSIPHQ\nRRSGDPWTYGGNTFFLLAILLKMCGNRLRYLMVSGDDSLA\n>u58991\nLECDFSKFDCSQGKGAYLFEKYVYQKIGKLNKHPDAYRTFQAQAMTRGRCAQGTTYRVRY\nGRKSGDPNTSCGNSLLNGVTCAISLENLGLRFKVIVMGDDMLA\n>u59347\nLENDYSKYDKSQSEMCVRLEQFVNDQLGFDINMMERWYRGHEHSRIHSVQHALTLFIDWQ\nRRSGGSNTAFGNVVVNLLTTSYVYKGSEVIAAAYIGDDSLI\n>u59553\nMMCDFTEFDSSQNEKAMIASVMMLKAMGLPSHILDHYLHRRKEWVLYVKNNTGAVDLTVY\nLDGVWNQHSGQPFTLGGNTQYNMSAIGMCYNFKDFQFAAFKGDDSVV\n>u60032\nTETDYTAWDSSIDGPFIKFDAWLFTAIGIDPEYVELYLNECCNTRYWGGNLRLMQHSGNR\nYTFILNTLRNLALTNATYNLGTTPQAYGGDDSLI\n>u60673\nLEIDMSKYDKSQGERVLEITCAIMRRFKVPEEYISYWKDCHIINRLVFHKTGVSFKVKYQ\nRRSGDIATFIGNTIVTMVILSFVYDLKQKPCIGGIFGGDDSLI\n>u60838\nVENDFSNYDKSLDDFGMEVEACFLQMIGLDPELAELWNQGHNYTSIKNHDVGFVLHTLFQ\nRKSGDVTTSFGNTFINMMTVSWCYFRNPADFDTKALFAMFLGDDSII\n>u62415\nLENDYSKFDKSQDRFTFIVMRLILDDLGFDEEMLDRWVDANDRCVLRSFALGIMFVVFYG\nNKSGGPATAFQNAVMNMISVAYAYKGTDAVWAVFMGDDSLV\n>u62546\nLELDISKFDKSQEGTMLEAQCDILKLFGVSELVIDLWRSFHELVKLSSPKFGVSYMVKYQ\nRRSGDAITWLGNTMVLIMIVAYLYPIEKAIMVLLAGDDNLL\n>u62595\nFTNDFTAYDQSCTGEAVQFEMAMMRYFGFPEELVGYYFWQKTTLTTNFGPSAVMRFTGEP\nGTYIFNSLFNLAYMLLKYQCEDVPSIYSGDDSLL\n>u63276\nSAFDKSQQEASHFIKLHFYRMLGMPEALLRLWDYGHRAAICQARGCGVAFQMPFQHKSGD\nASTAIGNTIVNMASMAVVFEPRCFDYAAFLGDDNFL\n>u64339\nLAADVTEFDSVHSQVTKEVEKILMQKCDLPQPIIDLYMHMRNKWKLSTYSVGYLHGEHKQ\nHSGQPATLFSNTFLAMMIMIIGLDEEEMEKGNYMMMAKGDDTVL\n>u64395\nTANDYTSWDSGVDKVFAHFDEWYFRLHGLPEEFIERYLDLKYNSYFYGGPLEPMQFSGDR\nFTWLLNSVRNAALTGASLDLPQHAPSLSPVTMEQMSARRSRGTPAAFSGDDSIV\n>u64638\nVAGDDSLVGVWENGALRWYEADAGMFDQSESYGPLLSEYRALHKLGVPGRTTDLLFHLAH\nASYRVAGREHQWHATIDRSHRPMRDTGGADTSIGNSIVM\n>u64688\nWESDLTLQDMSMTGAYVTLLECMMRHFEIPEHLVEGYSKYKKTLILNKVLTGIMTFSGEI\nLTWIKNTFGNMARVSLKYDLRPGEPSKWSGDDSLV\n>u64793\nVENDYTAYDQSQREECLYFERKVMRHFRIPEELIEQYVYQKVHCKHKYGDAAIMRFSGEP\nSTYTFNTWVNVAVLHCKFDLNGMPYGVSGDDSII\n>u65293\nIESDAKNNDGSQPKELRKYEAMFYLKLGAPEWFVREFARTTKVRVWTRYGICAPIVGQRW\nSGETTTTTGNSYTHMALMQAALECASIKDSTNVHGGDDYLG\n>u66398\nEMCDIEGFDSSIRGADVTLEQDLMRFFHVPEDHISEYVEDKMDFHTRTIHFGIMRFSGEI\nFTWLFNTMHTLARECLKYDHQPGDPIAVSGDDVLK\n>u66963\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPTSLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u67520\nTTNDFTAYDQSQSADALALELLILEFFSIPASIIELYREIKVNTQTFLGVLSIMRFTGEW\nCTFLFNTVFNIAYTFTMYNLKPTDPCAFAGDDSVI\n>u67838\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELMALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPNPEVARAFAGDDSLF\n>u68399\nFEDDLSKQDRQTDDDILKVEMCVYQLLGIDKHILRWWSIVHDRWRFKQQHMWGWNRSKRQ\nTGSVTTAIGNVVTNLQVRRDLYQRNKDRIEMMLMLGDDNAM\n>u68450\nVSGDDSMAVKRGGWQQKGRAFLRFGEGDFSAYDQSQRAHCLTAHAVWMTALGLPKLLIDL\nILWVCSMPYRARGKRVKVKGKAGCQLATGIDWTTVINSMSN\n>u68966\nTCNDFSEWDASFRTPFVKLTSWLLIASGCPRNLVNTYEKFRESWTMQYRTIWGFASLDGF\nEKQFSGNPFTICENTIGNMALCFSLFEYKDFQFAYFKGDDSAV\n>u69269\nVENDFTEYDSSQSELTIYFESDILFLACHNPELVELYREHRTNWSTSTPGLVHMRGYAKK\nHSGEPFTIDFNTILNIAICGAIYDIDDLCCALFKGDDSLI\n>u69339\nQENDFSKFDGTHGFPSRELEERYLLRLFHPSYAARALKLHKSTHFRRCGNNDTHYERLSG\nGFDTSIFNTLVAAFVDYLALRRSGFDSHKAYSMIGLHGGDDSLT\n>u69595\nVESDAKNNDGSQPKELRKYEAMFYRKLGAPVWFVRDFARTTKIRVWTRYGVAGDVDGERW\nSGETTTTTGNSYTHMALMQVAAERASIEESTNVHGGDDYLG\n>u69689\nTINDFSNFDSTQGGESVRLDMAVPIWAGVPEEWMLLYKHWKTHMVSDKIGVKKTSRDSGE\nPGTFDGNTWYSIANTALKYGWRALWCGTWLFGGDDMAC\n>u70092\nGTCDYSAFDQSQDISVLLFELKVYEYMGVPRTLLERFKRWKMNLICQYGSLEVMRFTGES\nGTILGNTLANMALSNLERDLAGPRGVHFPCAFIGDDSVF\n>u70867\nTTNDYTAYDASQNGDILDFEVKKQRYIFSIPEEFIQDYIYFKLHLSTKDLIFAIIRFTGE\nPGTFNFNTDASIAFVALRFKKVKGSKIAFAGDDMVC\n>u70938\nSTNDYTAFDQSQTGEALSFELMMLRAFGLPDGVISYYTELKLELTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPLDTAIAVAGDDLAM\n>u71159\nTVNDFTKFGATQGGDSLQMDLQWFQWAGMSDASVELYRRIKLSLQALGGTKKTCRDDGEP\nGTYLFNCFYDLGITAERFGVEALWRGFWLIGGDDEAA\n>u71552\nFENDFEKFDKSQLEECFESEMFFYDVLGLEQWLQALWALGLIKTEARNFILGILIYLIFQ\nRKTGTVTTSLGNLIINMIATAIAYKLLETGFIAVYYVGDDSFL\n>u72286\nLENDFSKFDKSQDRFTFILMRLILDDLGFDEDMLNRWVDSNERCVLRSLLLGVLIVVSYG\nNKSGGPATAFQNAVMNMAAVCTAYAGTDIAWAVFMGDDSLV\n>u72622\nFANDFSEFDSAQDEISILAFAAFLSMLGFNEKCIKLYVNLRLKWVMALRGSSLQHDTITT\nLKGVFKKHSGEPATLCGNTWFNRAVTCLCVTFLNPYICAFKGDDSLI\n>u73925\nTTNDYTAYDASQNGDILDFEVKKQRYIFSIPEEFIQDYIYFKLHLSTKDLIFAIIRFTGE\nPGTFNFNTDASIAFVALRFKNVKGSKIAFAGDDMVC\n>u74362\nFTCDFTAYDQSCTEETLSFELAFMAYCKIPQSLIDLYSWIKLNMRTQFGFTAVMRFTGEF\nGTYDFNTFWNMAYMELRYAPSPSIPACYSGDDSLF\n>u74639\nTGTDYTSWDTGCDEAFLGFDRWLMGIASLPSSFVAHYVNRKLSLNSFAGPMPVMQCSGDR\nWTWLLNTHRNIAFSNNKFAIPFGTPQCYSGDDMLL\n>u75059\nYANDYTAYDQSQRGEVLASEKMYFWQASIPDFIVDMYVQNKTEMTCSLGNLQTMRFSGEP\nPTYDFNGRCNLAVMNMQFPIAERKDVAAFVSGDDGGL\n>u75067\nVENDFKSYDKTQDDVALDIEMRFLEMIGFDKDLLELWESGHVYTKAFAHDTGFMILTAFQ\nRKSGDVTTSFGNTLINMLAVAWTYFTDIPSARRHIKFGWFLGDDSII\n>u75135\nTTNDFTAYDQSQSADALALELLILEFFSIPASIIDLYREIKVNTQTFLGVLSIMRFTGEW\nCTFLFNTVFNIAYTFTMYNLKPTDPCAFAGDDSVI\n>u75186\nMSIDLSQQDSSHINVHRFFIGKVLAFLGFDDTIVTLYLMTRAKRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSTGTSVCTFDFSKFELFIGKGDDNTV\n>u75224\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPVSLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRDLACAFSGDDSLF\n>u75414\nVENDFSSYDKSQHIETWILEREVYRLLGCDEDLLQHWEDGHWFTKIRSPSVGFTMYTLFQ\nRKSGDVTTSFGNTLVNMITMIYSYRYVDIEYGLFLGDDSLI\n>u75466\nTVNDFSAFDSTQGGESVRLETSMMHLFGVPEETITAYVYWKTHIRSNVVGEKKTARDSGE\nPGTFDANTWYSMAITFLKFGWPAARRGCWLFGGDDMAA\n>u75659\nTCNDFSEWDASWRGCFTEFTCTLLRYMGCPKPLVEDYKRFRDDWIMTYMTAFGNVTLSGR\nEKQFSGNPFTICENTLGNMALCFSIFEVRDMQYAMFKGDDSVI\n>u75870\nLETDLEACDAGQDETTMLFESKLMRQFQVPDIVIDFLMFIRKEWKLSARDLASVENEGKK\nHSGAPDTLDGNTIVTAAIISRLFRFKNLKLALFKGDDGAI\n>u76057\nVENDFSAYDKSQDDACLELEMLFLRRLGVPADLIDMWETGHIFTRIRAYDSGFTLWTMYQ\nRKSGDVTTSFGNTLINMIAVACSYFPTPQSCWDDIIYAWFLGDDSTI\n>u76243\nTDDDFEQFDSSQNGQILAFELRLLQYFNVPAHLIELYRQAKINAHCFVGPLAILRLTGEW\nSTFLFNTLANIAFKNLKYIIRPGTPQVYAGDDSSI\n>u76559\nGVTDFEMYDSQQDKFSQDLERAFYEALQLDEQFLEHYFSFRSKQKLLVPGFSGVLGTEKT\nSGEPLTLTGNSVVSMLLANWLLRGEGPFLMAFKGDDGFK\n>u76580\nAYCDYTGWDTNVDEAFTLLYTGVMRSYGFPEDVAERYAFERHNSRAFIGKMPPMQFSGDR\nYTWLLNTVGNMALTGISFKLAPDQPACFSGDDMIL\n>u77068\nEMCDIEGFDSSIRGGDVTLEQELMRFFGVPEDHITEYVEDKLDFHTRTIHFGIMRFSGEI\nFTWLFNTIHTLARECLKFGHEPGDSIAVSGDDVLK\n>u77578\nVENDFSEYDASQNESTIQFDSDHIRDMGATEECVQLYREQRSEWVTVYPGFMVLIGKFKK\nQSGEPFTIDFNTTICMGAIGHMLDINNLVCAQFKGDDSWI\n>u77678\nIENDFTEYDTSQNEATIEWEMSVLRDLGVTDQCVVLYGEHKKKWKATYPGKCSLNGVMKK\nHSGEPFTLDFNTVLNMSICGAIYDIEELTCALFKGDDSCV\n>u77731\nVELDISKYDKSQSLLALLVEYKLMRTFGFSKLDCDVWFNMRHYCRFSSTATGIKFDVLYQ\nMKSGVASTFISNTLHQMCVLFSEWHPSPDSFSLFCGDDSLL\n>u77902\nAANDFAEFDASQNNLELSFNMSIMRDFGVPPDVVEFYGLYRTEWVQIKHGLMKLHGHNKK\nHSGEPATLLFNTTFNMAVTLQLMKPTGLTFAGFKGDDSIV\n>u78038\nVLNDFKQFDCTQQRTGAEAVFFAYKVLGMNYKVREYMWDMRRKWTLEMYEPGKKGNLKST\nLNGQWEQHSGQPHTLRSNSLYNMAAMGAGVEWTTVHAAGFKGDDSQV\n>u78171\nTYCDYTGWDSGVNESFTLLYEKIMRSYGVPHSIVAKWKRERHSLTSFLGPLPAMQASGDR\nYTWLHNTIGNMALSAISFNLKPSTVAAFSGDDMIV\n>u78278\nVSGDDSLVAVWNGETWDWYEGDATMYDQSESLGPLLSEYAALRALGVPENVITVLYQLAH\nARYMVRGDGWTLTIDRSERPMRDTGGADTSAGNSIVM\n>u78336\nGVTDYKMFDAQQDEFTQQIEKEFFHMLGFSERFTTEYYRLRKNYNMQAGPISGKARTEKT\nSGEPATLLGNSVLGGVVMNYIFRGEGPCAMAIKGDDGFK\n>u78545\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPASLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRSLACAFSGDDSLF\n>u78594\nRTNDYTAFDQGQTAEALYLEIRLMEMFNIPKHFRDDYFQSKVSAFSWLGSFAIMRFTGEF\nGTFLFNTLFNMAYSNLKYNMVGRVALFGGDDSAF\n>u78925\nIEIDFSKFDKSQLQLCHETEMHVWRILGMDQYLHSLWKLGHFDTTAIDYLNGVIATLMFQ\nRRSGDAATCFGNTLISMLALARCTDLRTVASGYFVGDDSIM\n>u79367\nIENDMEEYDTSQSEITIGNEIKWLRRMGCNELFIAMFKKHRTQWTANYPGYVSMRGYAKK\nHSGEPFTLDFNTLLCLCLNGLMFPLENFVFAAFKGDDSEI\n>u79517\nYEGDLSKQDRQTDESLLGVEMYLYVLLGLELNIAEWWSATHGLWKFKTKFFSGYRKAMRQ\nTGTPTTALGNVFTNFQVHKPLVKNMWENIVLFLGLGDDNAM\n>u79633\nFTCDFTAYDQSCTEETLSFEICFMDYCKIPTELIDLYRWIKLNMRTQFGFTAIMRFTGEF\nGTYDFNTFWNMAYMTLRYKPRKDMACCYSGDDSLF\n>u80493\nVSGDDSLVYISLNGERYCFEGDASMYDQSQSVGPLTVGWRAYKRLGVDSETIKLLRALAY\nNKYVVEGRDRSNLPTFYTIDKRHRPMRDTGGADTSLGNSVLM\n>u80730\nLEIDESKFDKSQLEFIFAIEQMFWEMFGLNSESAQIWAEGHSSTTLRSWLHGFTVQILFQ\nRKSGDVTTCFGNTIINMMALADCFDLTDAAALYFVGDDSFL\n>u80928\nAENDMEEYDTSQNEITIENEVKWLKRMGCNEFFVKIFKQHRVEWRTNYPGYCQLIGYGKK\nHSGEPFTLDFNTLLCMALNGLLFPLEHFVFAAFKGDDSEL\n>u80990\nLINDYTAFDQGQSGAALYLELRLMKYCGVPRRYRDEYFESKVSAFSWLGHLAIMRFTGEF\nGTFLFNTLYNMAYANLKYDLTGIVCCFGGDDSAF\n>u81136\nGTNDYSAFDQSQTGEALSLEVVKMRVFNIPDHVIHYYEELKLTLTCQFGSLAVMRFTGEG\nPTLLFNSDFNTALIGCQYEMPPDTPLMVAGDDSAI\n>u81155\nMSIDLSQQDSSHVNVHRFFIGKVLTFLGFDDTIVSLYLMTRAKRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSTGTSVCTFDFSKFDLFIGKGDDNTV\n>u81272\nLEVDFSKFDKSQERMILMIVLALFRRFNIPEEFIENWDKCHQLTKLIFHIIGIMLIASHQ\nRRSGDVGTFILNTVVAMVAMSMSYSLSLAIGGIFGGDDMII\n>u81332\nIENDFSKFDKSQLGVCWAVEGYAYKQLGLAPELLEHWMDSNVTGEVRSATAGLRYWVAFQ\nRKSGTATTSLGNTIVNMAAVAYSYALAGENIVYAVFLGDDSLI\n>u81433\nTTNDYTSFDQSQTGETLSFERSLLDFFNIPEWLKDWYTESKMDLVCQYGHLQTMRFTGEG\nPTWLFNTLFNFALIYCQYEMRPSQPVAVSGDDMAI\n>u81443\nISIDGSAFDSSQFQVLMSLVDDLFWRRIRPFIRVIVQHNWQCRILTPHNTVDQITDRLMG\nALLKSQNLVFVHLPGVNSPXWPXPIRKXFFLDIDESKKWRETGPEXDWIYIEINGTTFSG\nHSTKTTLGNTLRTLCYSWYYILKSGVSMTPWNSDKVFSIASGDDCVI\n>u81850\nTTNDYTSFDQSQTGETLAFERSLLDFFNIPEWLKDWYTESKMDLVCQYGHLQTMRFTGEG\nPTWLFNTLFNFALIFCQYEMGVAQPVAVSGDDMAI\n>u81856\nTGNDVTGWDAGCEAEFLYGIDVPLMELLGFPQQYIDTYLHRRLNSFTHLGSFPIMQASGD\nRYTWLLNTYRNIAITTLYFNLPKGTVMAFSGDDAII\n>u81905\nTTNDFSEFDQSQTGDALSLELKVMEYASIPQPLVDYYFHLKTNMTSSLGDLAIMRHTGEG\nPTWFFNTLFNLAVTGLRYENAHLYPRCFAGDDSAI\n>u81994\nTCNDFSEWDSCVRKAFYEFTCYLMKLMGAPDHIIDFYRRFRDEWTMKFDTQYGSAFLKGT\nEKQLSGNPFTICENTIWNMSLCFVIFEYKNLKFAAFKGDDSAV\n>u82100\nTVNDYTAFDSTQQGESVVLDNCLLAWVGCPIEVREAYAYWKTHIVSDQLGVTPVQTHRAT\nGESGTWLGNTLYNIACVALLYGPKALHHGAWLFGGDDMAT\n>u82557\nVSGDDSVVGWGAFNPEIPFSEADQSKFDHTQDEGPLSLSLHWMKELGAPDWFLDAVCFCC\nRAPYTMQKHFMRARGHAGTQMPTGITLTTLLNSMAT\n>u82909\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELQALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKVARAFAGDDSLF\n>u82941\nAENDMEEYDTSQNEITIENEINWLKRMGCNDFFIRLFKQHRIEWRTNYPGYCQLIGYGKK\nHSGEPFTLDFNTLLCMALNGLLFPLEQFVFAAFKGDDSEL\n>u83094\nAENDMEEYDTSQNEITIENECRMLKRLGSNDLFVSLYKKHRTEWSTNYNGYCKFFGYAKK\nHSGEPFTLDFNTWLCMCLNGLMFPLDDFVFAGFKGDDSEI\n>u83596\nTYSDYTGWDSGTDESFTLFYSDVMRMFGVPPNIAARFRSDRHGRRSFLGPMPAMQASGDR\nYTWLNNTIGNMALTGISFDLTHVPAASFSGDDMIL\n>u83954\nLELDISKFDKSQDATLLEAQCRIFKLFNMADWAIDLWIAFHELCKLTFPKWGVRFTVGFQ\nRRSGDALTWFGNTLVMLMIMAYLYEVEKSVFTILGGDDNTT\n>u83986\nLEIDESKFDKSQLEFIFAIEQMFWEMFGLNSESAQIWAEGHSSTTLRSWLHGFTVQILFQ\nRKSGDVTTCFGNTIINMMALADCFELTDAAALYFVGDDSFL\n>u84009\nTINDYSAYDLSQRGEALSFELQQLKWFSMPEDIIQYYYELKIAITCQFGDLATLRHTGEG\nPTWKFNSDFNTAVVGLQYEGAESVALAISGDDMAA\n>u84054\nIENDFSDYDRSQDALALAIERWVDYYCGFDGEYCDAWFNAHVFTNNRNHVTGLSAFLLYQ\nRKSGDVSTSYGNTIVNMVVVAWGYKLPSFVFCIFLGDDSIF\n>u84080\nTGNDVTGWDAGCEAEFLYGVDLYLMELCGFPQHYIDSYLHRRLNSYTHLGKFPIMQASGD\nRYTWLLNTYRNIAITTLYFTIPRGTVMAFSGDDAIV\n>u84109\nSTNDYTAFDQSQTGEAVSLELTNLRAHHIPDDVIEYYIDLKLNLCCQFGELAVMRFTGEG\nPTLKFNSDFNAALIGVQYDLPSGMARAVAGDDMAL\n>u84268\nTCNDFSEWDASFRIPFVKLTSWLLIASGCPRNLVNTYEKFRESWTMQYRTIWGFASLDGF\nEKQFSGNPFTICENTIGNMALCFSLFEYKDFQFAYFKGDDSAV\n>u84680\nLENDYTRFDQSQKAEFVNFQIHILKMFNTPENLINKFMDIKLNCFNDISVLDFMILSGDW\nATLLFNTLDNAAYANLQYNIPPGTAQLYVGDDSAI\n>u84756\nGVTDGADFDSMQNKFTQQIEKRHSHHLLVPKVLIDSYYQYRNDYRMVENGLFSGRARSEK\nTSGEPGTLLYNSQLGGTVCNFSLRGIGQSTMEIQGDDAKK\n>u85114\nFEADISQFDKSQTELSLAVEMAVYRKLGLDPEWAMRWEGAMFETRNVCHAVGITIYLMHQ\nRKSGSVTTSIGNTIVNMVACAYPDTLTAECIIAALFLGDDSLI\n>u85498\nAENDMEEYDTSQNEITIENECRMLKRLGCNDLFVMLYRKHRLEWSTSYAGYCKFIGYAKK\nHSGEPFTLDFNTWLCMCLNGLMFPLNDFVYAGFKGDDSDI\n>u85501\nDERDGKNWDSTMQCETLTAEALVYEMLKLPVLAPFIVRSSKCWGRVRCQGFPPVKYITSW\nKRLSGDWNTSVGNTLISMIICATTIRALPDHLRPASVEAYFMGDDYLG\n>u85540\nVENDFTEYDTSQNAVTIEFECGFLRAMQLSEEFVVLYKEHRSEWCANYPGFVKMYGKYKK\nHSGEPFTICFNTILNAAVCGAIYDFDNFVGGIVKGDDSHF\n>u85833\nFTCDFTAYDQSCKAETLAFELVLMDWANIPFDLQDLYFNIKIGMFLDRQSYKIHSSIMRF\nTGEFCTYDFNTFWNICYMATRYNLQPTERCAFSGDDSLF\n>u86024\nTSNDFSEFDQSQTGDALSLEMVMMSAYDIPDSITDYYFSLKTRLRTSLGPLATMRHTGEG\nPTWFFNTMFNCAVTGLRYGYLGDKARCFAGDDSCI\n>u86128\nVEIDFSKFDKSQNAFILNIQLILMAKLGIEPHFIEFWSKNHEKTTLDFRNHGFKINVDHQ\nRKSGDAFTFLGNTIVTMMVLNYVLDLDKAICALFGGDDSFI\n>u86241\nFTCDFTAYDQSCKTETLAFELVLMDWAHIPLPLIDLYYDIKVSMYLDRGWYKIPSAVMRF\nTGEFCTYDFNTFWNICYMATRYQIRDDTACCFSGDDSLF\n>u86298\nREIDFSKYDKSQGELHLLMEMLIFDILGLPPFYLLLWYRMHFLTQVKDKSMGFTAWLFYQ\nRKTGDAATFIGNTVVCICMLLLLYDFTGILFAIFAGDDSIL\n>u86313\nGIADGEEFDSWQNSVTLHAEKEFRRLQGACSESIAAYYQIRGPQEFTMFGCFRGRTNFEK\nGSGFLDTLLGNTTLAVIAGHQMFKGVGPKVVASKGDDYMH\n>u86647\nLSLDIKGFDGTQRGAALELERQWMTCFNVPEDLVDAYVHDKLDAHTKTIHLGLMRLSGEI\nFTFFFNTVFMSARTVTKYRIEAGDPMAGSGDDIEL\n>u86666\nVENDFSEYDSSQNEATICWEASILSYFVLNPEIVQLYIEHRKNWRTCCPGLVSFKGFVKK\nHSGEPFTIDFNTILNIAICGSIYDINNMHFALFKGDDSLI\n>u87045\nVENDFSSFDSTQSKYALGMVYDFYAMCGMPDDVIALLKLDLEYANVSTRVGLRFKAGGFR\nFSGRGDTLGGNGVLNYIVMYHAYMCMILRMIFKGDDSVI\n>u87195\nLENDFSEYDSTQGKGAHELELMFYRSFNPTQPVLNALEAQSKTEGFGSFYKYRVAYTRKS\nGDQNTSIGNTVINAVVHMEAMSRAGVADYRLICLGDDMVL\n>u87259\nESLDWTMFDSCQGNVEHELTRLSLNKIGCPHILTQLFVAVVYNRKITGKIASLNVRNKKD\nSGRIDTLLSNSQFNAAVIIFMIDWERSYLDHLFIKGDDSLL\n>u87382\nGENDYEAFDATQHVDCRLLIIEMLVEHFGMSASVARYMRAAAKEKFGHTLNGTYVSMEGT\nMASGHPDTYLTNTMMNILLQWYASACCGVFKPPIAAAGDDSVI\n>u87396\nTANDYTAFDASQGYDSVLLECHVMRLAGLPDALVDNYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLHCLALFGGDDSAI\n>u87732\nTSIDYTAWDSSLDEPFLRLNAHILEFVGVPDPYVQVFLDERLNTRSFLGPMPLMQFSGDR\nYTWLFNTLSNVSLAHAAFENAATTTMGVSGDDIVL\n>u87741\nTETDYTSWDSSIDGPFIEFDCWLLTQIGAPSHYIETYRHEACNTRYFGGNLRLMQHSGNR\nYTFLLNTLRNLALTNASYAGISKTPQAFGGDDSLI\n>u87829\nLSTDFTQHDTSHSHVVKLWFLKDFLDAGFDPEAMITQFNTYSDWVQKAKIGEDVQFDVHN\nFFIQHSGSPDTLHGNTKLTMAANGLAYDFKNLVFAAFKGDDSML\n>u88085\nIENDFSKFDKSQQWAALRLEWRMYQALGLDCQMAEIWEVGHISCSMSSYAAGIKVWSMLQ\nRLSGDAATALGNSIVSLVTVATCYDIPKFEYAMGLGDDSVI\n>u88646\nVSGDDFYGLVNEFGSVWVAENDFTKMDRTQGAHALETEFQLLLFLGVPRSVCRRLFLAML\nSTAKYENKSLGVKMKCPMPYQRATGAPDTTIGNTLIN\n>u88691\nSTNDYTAFDQSQTGEALSFELMMLRAFGLPDGVISYYTELKLELTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPSDTAIAVAGDDLAM\n>u88746\nVSGDDMIGFFQEKGLVQAFENDYKRFDRTQGRCAQESEFRILRKLGVTERKISILRQALG\nAKTVFESRRYEEQIKIDLPLQRNTGGADTTLGNCITN\n>u89229\nVSGDDSLVIYRDCHGLTTYFEGDASMFDQSQSKGPLNFEYKCLERLGVSKVFCRDLRVLS\nSNRYIATCRGLRQHRITVDRTIRPMRDTGGADTSLGNSINM\n>u89865\nTINDYSNFDATQGGESVVLELAVLQWSGLPDFIVQGYAHWKTHIVTSFIGLKQTSRDSGE\nPGTWDGNTWYNIANCALKFGYQALRRGTWLFSGDDMAC\n>u89949\nTVNDYTAFDSTQQGESVVLDNCLLAWVGCPLDVREAYAYWKTHIVSDQLGGTPVQTHRAT\nGESGTWLGNTLYNIACVALLYGPKALHHGAWLFGGDDMAT\n>u90344\nLENDFSKFDKSQQEICLFLEMELYRLLGVDVDFIQNWYRTSEYSRIKSTTAGLKLFSVWQ\nRKSGEGTTAMGNSIVNMLVLCCFYDIDPADLLYSVFMGDDSLL\n>u90904\nLENDFSSFDSTQNQCALGMVYDYYEMCGMPTQVVNMMRNDTFNGCKITTSVGISFHQRNS\nRISGRGDTLFGNTILSFVAVNHSTGGKVKKIIAKGDDSVM\n>u91052\nIESDGRRWDARMQRMHHDFKIRLYRVVDAELASSVEQGFACVGVVVLPDDRLVYRVHGTV\nKSGHNDTTLGNSLINAAVAYETCVSMGLKASIIVAGDDLLI\n>u91056\nTEVDFAKYDKSQTHNIYLLEEKILIALGMPKELIPLWRYANCHSRLINFKNKFRGSVNWQ\nRKSGTAFTYFGNTILCMAMLAYSMNLKDVIVLFSGDDSLI\n>u91192\nLENDFSSFDSTQNQCALGMVYDYYEMCGMPTNVVDMMRRDTFNGCKITTSVGISFHQRNS\nRISGRGDTLFGNTILSFVAMNYSTAGKVKRIIAKGDDSVM\n>u91513\nVEIDFSKFDKSQESIALETQLVIMKMFGIPDRVIDEWYSCHILGYYIDPRTSIAFRVCYQ\nRRSGDSFTYTGNTLVTMCAMCHTMDLTRAVGGMFSGDDSLI\n>u92120\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPEELMALYEEIKIDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKVARAFAGDDSLF\n>u92280\nEMCDIEGFDSSIRGGDVTLEQCMMRHFGVPEQHIDEYTEDKMDFHTRTIHFGIMRFSGEI\nFTWLFNTMHTLARECLKYDHIPGDQIACSGDDVLK\n>u92384\nVESDAKNNDGSQPKELRKYEAMFYRKLGAPVWFVQEFARTTKITVWTRYGIAAQVEGERW\nSGETTTTTGNSYVHMAMIQAALERASIEESTNVHGGDDYLG\n>u92391\nVAIDISAFDSSQRGADCQLASRLFRLIGMPEELIQEYLDDKYDFHTATIHFGLMRFSGEV\nWTWCLNTTFQTARTVTKYAVPKGAPIKVAGDDILM\n>u92418\nVELDISKYDKSQSLLALLVEYKLMRTFGFSKLDCDVWFNMRHYCHFSSTATGIKFDVLYQ\nMKSGVASTFISNTLHQMCVLFSEWHPSPDSFSLFCGDDSLL\n>u92467\nTETDYTSWDSSVDGPFIKFDCWLLHQMGAPAEYIAAYQEEACSTRFFRGNLRLMQHSGNR\nYTFLLNTLRVLALTHATYHRIKYTPQAYGGDDSLL\n>u93013\nMDGDMSKFDKSQGELVLRTQLEILKRFGMCEEILLEWEYNHIINILDFPLFGLRFKCLYQ\nRRSGNIFTYLGNTILTMTVFSYFYDLETCICAIFSGDDSTI\n>u93097\nLEGDFTAFDQSEDAAFVDFERRLMEDCSFPEHIIADYLQLKASLSSRFGHLAVMRFTGEV\nWTFIFNTVANFAYTHLKYDIPPGTPQCYGGDDKVI\n>u93158\nTVNDYTAFDSTQQGESVVLDNCLLAWVGCPLEVREAYAYWKTHIVSDQLGVTPVQTHRAT\nGESGTWLGNTLYNIACVALLYGPKALHHGAWLFGGDDMAT\n>u93200\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPTSLVELYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u93479\nGVTDFTMYDSQQDAFTQAIERRFLFKMGMTTEAIADYFSFRNDYKIISASASGRGKTEKT\nSGEPGTLLFNTVINAVVMNWLLRGVGPVAMAFKGDDGYK\n>u93805\nDEDDCVALDQSMREEFIAFESYLCAYAGWPQDIIDEYVSHKLTLFCFLGNLSPARFTGEP\nPTFLFNTLGLIAYKHLKYRIPPGCPQLYAGDDSAT\n>u94031\nLMADFTEFDTSQDEKAVVSSCIILKSLGFNKNLVDYYQHKRKEWTMIAHAETDHMPITIT\nLNGKWNQHSGQPFTLDGNTLFNMSAMGMCYNFKELILASFKGDDSFI\n>u94293\nGIMDFTEFDSQQNDVTLAIEKEVCRLMGVPVQWSEEYYAYRSKGLKVSFPGLFKLKMNQE\nKPSGFLDTKSGNTILSCALATWLFDYKGPRVHAAKGDDTLF\n>u94591\nAENDFSKFEGCQTPELLKDTELKIFLALYPKCYHQEIKLLFKHKLQKKIFSREGMKADLI\nGCRGSGDMDTGLGNTIVNLIACKYNYKRNKISGNQIVDGDDGVL\n>u94699\nMVADFSEFDSSQEMQGILAGAMFMRLCNVPYHIVDMYLKQRQHWVMVACDKSDGGGVMRA\nVLEGAWKQHSGQPDTLNGNTTFNMMAMGACYVYTDIQFASFKGDDSII\n>u94711\nVENDFSDYDKSQDARVYSIEARIVALLGVDVELAGDWYAAHIVTHNYCRSVALTLTVCYQ\nRKSGDVTTSFGNTLTNMVAIVVGYRFLEDAGENLRFMIFLGDDSLI\n>u95209\nTTNDFTGFDSTQKGDSHGFEMHLLEWAHLPLAWTRHFVDLGRGRDMSLLYSWWKTNIVSD\nVIGPKELGRDTGEPGTYDFNTYFNIAVTSRMYIIPPNTSLAFGGDDFAA\n>u95328\nYGSDVTRWDVGCDAAMVNFDVHVMRQLHFPSWYIDAYVERRVSPFSQHGPMRTMQNSGDR\nYTWILNSVRRAVVTSIVCQIKPEDTVAINGDDAAV\n>u95755\nMENDFSKYDGTISLAARELEIRLFTRHFDTSVIAQALQVHDNLHHRTTTTGDHTEYERLS\nGGFDTSLLNTTVAAFADYLGLRRANHNPEEAYSLIGLHGGDDSLT\n>u95764\nLECDFSQFDKSQQWFILRLEWILYQLLGLDPNILVAWKEGNIINDTRGRCGIYLVLILQR\nRSGTATTALGNTVCNMIAVATVYKLDGFAYAMFIGDDSII\n>u95963\nVENDYTRFDQSQKAEFVNFQIKILQMFNVPTELIDLFVDLKIRCYTDVDVLDFMILTGDW\nATLLFNTLDNATFANLQYNIPPGTPQLYIGDDSVI\n>u96140\nLSNDYSAWDSGCDKVFAEFDAWVIGQAGLPEHVSTRYLEWKYNIRTVIGPLRVMQNSGDR\nWTWLLNTVRNVSLLTAQYECDKLPMAVSGDDCSI\n>u96253\nFTCDFTAYDQSCTGETLWFEIKLLRHIGVPEELVSLYWEQKINLQTTFGHSAVMRFTGEP\nWTFVFNTAFNMAYMWTRYDLANDQSCPPQCFAGDDSLF\n>u96374\nLEGDFTAFDQSEDAAFVDFERRIMEDCSFPEHIISDYLNLKASLSSRFGHLAVMRFTGEV\nWTFIYNTLANFAFTHLKYCIPPGTPQCYGGDDKVI\n>u97119\nTESDYEGYDASQRGDSIQFEYQLMRHFGLSDAWVELFLDFRADFPTMTDLYVWWKLNIIS\nDVIGPKQSGRDTGEPGTYDFNTYFNLALIQLMYAPARTVPIAVGGDDMSA\n>u97367\nASDDFSKNDLTTDGPHIDLEMLIYKYLGGEPNTIDLWATCHRHWRYLGANGLMGKSDWKR\nLTGQATTALGNFIVNMNVHKHWLLDSLTKIKLMLVLGDDCTV\n>u97604\nAENDMEEYDTSQNEITIENEVNWLRRMGCNEVFIRLFKQHRIEWRTNYPGYCQLIGYGKK\nHSGEPFTLDFNTLLCMALNGLLFPVEHFVFAAFKGDDSEL\n>u97726\nFANDFSEFDSAQDEISILAFASFLTMLGFSDKCVKFYIKLRIKWVMALRGSSLQEDTITL\nLKGIFKKHSGEPATLCGNTWFNRAVTCLCVVIVNPYICGFKGDDSII\n>u97861\nEMLDLTALDTSVRGGAVLVMSKLMRRFSIPEDLIEAYIADKMDFHTRNLTFAIMTFSGEI\nFTWLGNTIDVASRECAMFDMPPGWPMASSGDDIWR\n>u98398\nSTCDFTQYDMSCTAETLSFELCLFSYFCLDLVFPEAYQLYYFIKTEMYTQLGTSAIMRFT\nGEFGTYDFNTWYNIAYMALRYHFDETNPDEGCAFSGDDSIF\n>u99134\nYANDYTAYDQSQTGEVLASEIAYLRHAGIPEHYVAMYEENKTDMSMFLGHLQTMRFSGEP\nATYEFNCRCNIAVMNLQFPLDQHPEIPIFISGDDGGL\n>u99290\nLENDFKAYDKTQDNVALEIELSFLALLGVPLDLLEMWRSGHVYTRATCRETGFMLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFAKPEDARTKIRCAFFLGDDSLF\n>u99753\nTDNDYTAFDQSQDAAALYMELQLMVHFGIPQHYIDFYYWLKTETRSWLGPFAIMRFTGEW\nSTFLFNTLFSIAYSFSKYDFPADALLCFGGDDSSF\n>u99805\nYEFDVPKFDKSQDMMCFTLILEVMSVLGVSSEFIEYWRRASYEGTIFNSAFSMVFTLFYG\nNRSGSGGTLAVNCICLLFAFYTEFSNLTIVAALIKGDDSVI\n>u100031\nVSGDDSFVVVSWEGQLFTFEGDATMYDQSESFGPLGVAWKACRRLGVDSSTIKLLSELAH\nNSYTVRSKDPTDQATLRINKRNRPIRDTGGADTSLGNSLVM\n>u100065\nMAGDDFFGLVNSQGLKAYENDFSKMDRTQGVHALGVEFVILRAFGVRHFTLCRLFDAMLS\nNPRYESVKYDIRVKLPMQPQRATGAPDTTIGNTLIN\n>u100279\nGVTDYKMFDAQQDEFTQQIEKEFFHMLGFSERFTDEYYRLRRNYDMQAGPISGKARTEKT\nSGEPATLLGNSVLGGVVMNYIFRGEGRCAMAIKGDDGFK\n>u100615\nVEDDASKQDRQTDQDTLRIEMLIYEGLGLHPQLLNLWSTIHHRWYFWNRHIKGYNSSKRQ\nTGSATTALGNFIVNLLIHLKMFKDNWNKLLVAYLLGDDNSS\n>u100617\nIEMDLSKQDRQTDAQMNAIELAIYEMLGMDKQLVRMWAHLHEKWRYFGADVSGFWQNMRH\nSGAATTAIGNVITNITLLSEAIKRESDKFVFCLMLGDDNLS\n>u100719\nGVTDFEMYDSQQDEFSQELEKGLLSLMGVDQGFIDHYFSFRKGGKLLANGLSGRLGTEKT\nSGEPMTLLGNSIISMVLANWILRGDGPFVMAVKGDDGFK\n>u100758\nTTNDFSEFDQSQTGDALSLELKVMEYASIPQSLVDYYFHLKTNMTSSLGDLAIMRHTGEG\nPTWFFNTLFNLAVTGLRYENAHLYPRCFAGDDSAI\n>u100858\nTDNDFSEMDSSHAESSVKLEMLLYKLVGMPENMLNMYLSMRKRWMMSYMNNDGITKLWND\nWLQHSGQPLTLAGNTLLNMAAVGAFIELGEVLYAMFKGDDSHI\n>u100900\nIENDFSKYDKSQKGLCMAIEFEIYRLIGMNPVTIEIWEEGNRVGIVFSFDTGIKFTIVWQ\nRHSGGVTTSLGNTIVNIVTIAYAYKRLRFFYYAIFLGDDSLI\n>u101247\nLELDLSKQDRQTDLPILNTEIEFMGDLGVTEDCLDSFANITKHAYVQSSDKISLMLPPMQ\nWTGGEMTAFGNSFRNLLIMADLKRKYHLKFVAILGDDSLI\n>u101506\nIMMDASKFEQSVSAECIDFESELYGAYYPGDKLFKYMMRKQRKYKGKARCQDGKLSFTIE\nGVRASGMNNTALGNCVISAGFLWDVQGKLASKDKTFEMRGHVDGDDVVV\n>u101709\nGVTDGKDFDSMQNKFTQEIERRHSYHLRVPKEVIEAYYTYRNDYPMIQNGLFKATARSEK\nTSGEPGTLLFNSQLGGSVNNYVLRGMGPSAMAIQGDDAKK\n>u102045\nVDNDFTEYDASQNSSTIEFETLILEDLGVVTEVIELYQERRSKWKTYYPGYASLEGRDKK\nHSGESFTIDFNTSLNMAICGYIYEFDLLVVAQFKGDDSNI\n>u102456\nLTADFSEFDSSQEMQGILAGATYFRLCGVPEHVIDMYLDQRRKWLMVAVDKDDSTMMRAM\nLEGAWKQHSGQPDTLNGNTTFNMAAMGACYDVENLQFASFKGDDSII\n>u102994\nRCSDWTEFDSSQNNVEHELLMMQLEAIGCPAELRDLFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDHVLFKGDDSLM\n>u103697\nSCNDFSEWDASFRTPFSKVTSQLMTYMGIPNEVVQEFEAYREKWSMMFQHDLGTTTLRGS\nEKQFSGNPFTICENTIGNMALCFSIFDYRNFQMALFKGDDSAV\n>u103938\nLELDLAKFDKSQRRLALMIEVHFMLVFGYPIDFVIAWIIKHNVSVLRSIKAMVKLVIEMQ\nRRSGDAWTYIGNTIHNGCVLAHCFGPMLLRQCIVLISGDDSVV\n>u104223\nYENDLHKQDRQTNEAILDTEKELYIKIGLAPLTAEFWFICHRHWTFRSRMYKGVFDKMRL\nTGQVTTALGNFITNLIVHVDMVLSNIDNIKLMLLLGDDNLA\n>u104269\nLENDFVEYDSSQQAMHVGFLGELLKFVGVPDHIVTSWKELRSERMMVARGVIAGRIEEKQ\nDSGEPFTLGGNTELARALIALLVQFDGLALCLSKGDDIYL\n>u104447\nVENDFTEYDSSQSELTIYFESDILFLACHNPELVELYKEHRTNWSTSTPGLVHMRGYAKK\nHSGEPFTIDFNTILNIAICGAIYDIDDLCCALFKGDDSLI\n>u104580\nLEVDFSKYDKSQDYNCYIVEEMLLVALGFPVELLGCWRYACFVSKLVNIKTKISGKIIYQ\nRKSGTAVTYFGNTLVCMSSLCTVADLSNAACLFSGDDSLI\n>u104622\nLENDWSEFDSSQNNLEHALFMQAMRDLGCPSVLMEFFLQMMEMRFVTSGNHSVLVQDKKD\nSGRVDTLVGNTLFNAAVVLSLINYEDVVLAAFKGDDSVI\n>u105165\nYEDDYTGFDGTQNEEFLYFQTLFMRQFGIPEDLISEFVIWATHLSSTIGPLGIMIPSGFK\nPTWFFNTIDSMAYQALKHKLTPHSSKRVARAFSGDDTLH\n>u105334\nSTCDFTAYDQSCQGETLSLEVLLMRHLNFPKWFVDWYVELKVDLKTSFGHSAIARFTGEF\nCTYTFNTFYNIAYMHLRFEIPRDMAKAFSGDDSIF\n>u105337\nMEQDFDNFDRSQGESVVSIELELYRRFGLDLVEWYNWAEHSEYVTVASIKTGLEFVMRWM\nRRTGSPTTAMGNTLVDMVSVARVYRFPSDFYYAMFLGDDSLI\n>u105397\nTDNDFERYDNSQDEGPLSFELNLMLCLNIDAELVELYKWLKLNAKCFLGNMAVARLTGEF\nSTFLFNTYVNVAYTHLRYDIPANTARAFAGDDSSI\n>u106422\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPSSLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u106521\nTCNDFSEWDASFRQAFVKLTSWLLIAAGCPRALVEEYEKFRESWVMQYRTMWGNASLHGE\nEKQFSGNPFTICENTISNMALCFTLFEYKGFQFAYFKGDDSAV\n>u106578\nSSDLLAKFDKSQRRLALMIEVHFMLVFGYPIDFVIAWIIKHNVSVLRSIKAMVKLVIEMQ\nRRSGDAWTYIGNTIHNGCVLAHCFGPMLLRQCIVLISGDDSVV\n>u106759\nRENDYSKYDKGEGYNVLPLERGFYLEFGMDIDEANTWFAGQDIGVIRAVSFLFKLHLELQ\nRRTGQLTTLLGNTIVCMLTIWFVYRIKREDVNWALIKGDDSII\n>u107324\nMSGDDSLVVIWDHCGNMHIFEGDFSMFDQSQSFGPLAHQYKFMRALGLTAEYEALFRKLA\nRTQYVLKTRDAKAVNRIKVDLRDRPIRHTGGADTSLGNSIVT\n>u107566\nHEVDISGFDSTVRGGSITNNVRVMQHFSIPQDLINDYVEDKLDFHTSTMHFGIMTFSGEI\nFTWLFNTIHEHSREALKYDLTDEPIMVSGDDILR\n>u107616\nFECDFTSFDSSQNEISVMLEVEIFQRMCPELIGTELIEMYQKLRMDWIASNEYVKWHGSG\nVKCSGEPATLLGNTMVNMLIIISSFIFEGVKFCLFKGDDSLI\n>u107687\nTTNDFTGFDSTQKGDSHGFEMHLLEWAHLPLAWTRHFVDLGRGRDMSLLYSWWKTNIVSD\nVIGPKELGRDTGEPGTYDFNTYFNIAVTSRMYVIPPNTSLAFGGDDFAA\n>u107707\nWESDLEQQEKSMSGAYVTLFSKVLEHFGVPRDIIEAYIDDKLDKKTARMHLGLMTFSGEI\nFTFLANTLGNMARIAAKYDLKPAERGKFGGDDSLC\n>u107828\nVETDYTAWDSSVDGAFITFDCWLMAQVGIPDWYISTYRSEMEGTLSRLGNLRTMQHSGNR\nWTFLLNTLRNVALTQHVYAGIHNTPQAFGGDDSLI\n>u107941\nGTTDVAEMDAMQDYFTQLVERLILEHLGFDDEFLDYYYQFRSNYPMVGRDVFKCRGGTEK\nTSGEPGTLLLNSILSGVFSYFIMEGRGPFVIIIKGDDNGR\n>u108081\nREIDFSKYDKSQGELHLLMEMLIFDILGLPPFYLLLWYRIHFLTQVKDKSMGFTAWLFYQ\nRKTGDAATFIGNTVVCICMLLLLYDFTGILFAIFAGDDSIL\n>u108116\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELMALYEEIKIDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPNVARAFAGDDSLF\n>u108182\nVENDFTEYDASQNTLTVQFESDILLLVSQNVELAELYREHRTHWTTVMPGVVVMKGYAKK\nHSGEPFTLDFNTLLNIAICGMIYEFDELVVALFKGDDSLI\n>u108371\nTANDYTAFDASQGYDSVLLECHVMRLAGLPDALVDSYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLSCMALFGGDDSAI\n>u108429\nLETDFSKFDGTLSSDVRFCEKKIMCNMMLPQHRRKLKELFDAEINCPSKTSLGYRYKVGT\nSRLSGSANTTLGNTLVNAFAAYVGLRLAGLTTQESFANLGPKYGDDSIT\n>u108447\nTINDYSAFDSTQGGESLNMEVVLMQRYSIPTVLIQHYLDWKLHQRSLSIGEKKLARDTGE\nPGTFLFNTLYSIANCTLKYGKITCMALFGGDDMAA\n>u108709\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELMALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPTIARAFAGDDSLF\n>u108946\nLTADFSEFDSSQEMQGILAGATYFKLCGVPDHIVEMYLSQRRRWLMLAVDKDDSTIMRAM\nLEGVWKQHSGQPDTLNGNTTFNMAAMGACYNIIDLQFASFKGDDSII\n>u109228\nRENDYSKYDKGEGYNVMPLERAFYLMFGMEIHEADLWFSGQDIGVIRAVSFLFKLHLELQ\nRRSGQLSTLLGNTVVCMLTVWFVYRIKRKDVNWALIKGDDSIV\n>u109315\nCTTDVAEMDSIQDIFTQAIEREVLLRLGFDDGFIAYYYQFRSNYPIIIQGVAKATGGTEK\nTSGEPGTLLFNSVLSAVFSYFIIDGKGRFFIVIKGDDNAR\n>u109609\nYEDDFEAYDASQGEGAWGCENGVYDDFHPPASVKHGLEQQRQTIGTGKYYFYSCPFTRKS\nGDQNTSIGNTIINFAAHALVMSRLGLSDFYMLGLGDDNLI\n>u109713\nLELDISKFDKSQDATLLEAQCRIFKLFNMADWAIDLWIAFHELCKLTFPKWGVRFTVGFQ\nRRSGDALTWFGNTLVMLMIMAYLYEIEKSVFTILGGDDNTT\n>u109953\nMVNDFSDFDSTQGGNSVWLEVLVMRYCGIPDELVDAYTHWKTHLRSDRIGPKKTSRDTGE\nPGTYFGNTIYSIAVTFARFGWEASRKGMWVFGGDDMAT\n>u110281\nVELDISKYDKSQGLVALLFEIKLLRYFGVDERILDVIYGSNVSTILKSFNSGLKMKIPLQ\nRKSGEARTLFGNTVFNMAVAACAYDMTKARFAVFQGDDSVI\n>u110299\nVQSDFSQFDSTQHERCLRLINRLMRLCGMPEEVVKLMDLDMESIKVTHRKGFKYLCKNLR\nLSGRSETLLGNTMLTLMTFLHCCGPNLCAILVKGDDVLL\n>u110451\nFSGDWTEFDSSQNNVTAALQQRIFREIGVPEHYARLFGDMVKKRTVACTTGSLQVESKKD\nSGRVDTLVDNTVFNAAVLLSVVANPDDICL\n>u110472\nIELDISKYDKSQGEAALIFECNVMRLLGVEERFVDHWQAFHKYALLTAKSEGLLEVKYSV\nNYQRKSGEANTFIGNTLLTLALLLYVYDYNEIYFLTVAGDDSVI\n>u110524\nVGGDDSLVGVHLDDGKVRWLETDFSQFDQSQSTGPLDIECIYLGRLGLSPSDVCYVQEMH\nKATWVFRGKGDVKFRIKHQHRPERATGGPNTTSGNSSVN\n>u110562\nLETDFSKFDKSQEHFCLKVQKYIMQYLGMPIDIIKEWVNCHLINKLIFNGGVYLETFNQR\nRSGDVFTFIGNTIINMAAMAYVYNLKEEIGGVFAGDDSII\n>u110758\nDCSDVNEWDTKFRTVFQQLTSTLVCAIGCPTWLASWFTQFRSKWKMVIMTKSIRTVLIGD\nEKQFSGNPFTICENTIGNMAMTYAIKRFVSEYISLFKGDDSAI\n>u110915\nIEIDFEKFDKSQLQMCHEMEMAVWEVLGMDAFLLSIWKLGHFDTSATDFIAGIKSRRSGD\nASTCFANTLISMMAIAHSVELQKMICAYFVGDDSDV\n>u111000\nVESDFSKFESTQQMDLLVHIELGVWKRLLNLGDYHIVERLFWLKMVKQGHCTHGVKFCFL\nFCRGSGDMDTGLFNTIINWIATRYFEDINGMFKGQFLVDGDDNVM\n>u111835\nQANDMSKFDKQQTEDHLNVERAIYEWFGVEPEFLNFYYDFHFNWILTSAQTQMYLNAMRI\nSGEPTTALGNAIVNLIIHSKLVVNNISKLTWLLVVGDDIII\n>u111857\nFCADYSEWDSRFRHIFVEIMGEFLVAAGCEEALVEEYIQFRKKWVMTANNYRSAGNTKLY\nGEEKKFSGDPFTICENTIMNMILTFSAFDFDGIALALFKGDDSAI\n>u112018\nVCGDDSVVARWYNGKLTFKEGDARMFDQSQSFGPLCAEYQALQHFGVPREITGRLGEVAA\nNTYVVRPYRKDRDQAVFQLGRKSRPMRDTGGADTYIGNTLVM\n>u112368\nGVTDFTMFDAQQDEFTQAIEKEFLRRVGASEEFIAHYYSMRKGYKISAGPLSGTAGTEKT\nSGEPGTLLFNSIVNCMMMNFLLRGEGPSAVAIKGDDGFK\n>u112406\nWCYDMLGVDTNISQFYYXLHKNWPFXTQLQXGXGNNXRLTGEPATAVGNFLINTIVNXEL\nLGNNYNXLXLSLMLGDDCIS\n>u113300\nATNDFSEWDSTFRTPLANVTTQLIRYMGCPEWLADWFSLYRKEWTMHYASKVGNTKLSGH\nEKQFSGNPFTICENTILNFALTHLVYDFKEPILQLFKGDDSAI\n>u113620\nTETDYTSWDSSVDGPFIKFDCWLLHQMGAPAEYIASYQEEACSTRFFRGNLRLMQHSGNR\nYTFLLNTLRVLALTQATYQRLRFVPQAYGGDDSLI\n>u113685\nLEGDWTEFDSSQNNVEHELLMMQLEAIGCPAELRDLFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDYVLFKGDDSLM\n>u113850\nLEMDMGKFDKSQGLTSLLFECEMFVRAGMPRWMVNLWFLSHALARVKGFGTSLRTRLPHQ\nRRSGDPWTFGGNTFFLLSILKYYCKDSINFLMVSGDDSLV\n>u113927\nLENDFKAYDKTQDNIALEIELYFLSLLGVPEDMIEMWRSGHVYTRATCRETGFLLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFQNHNDAKHKLRCAFFLGDDSLF\n>u114016\nTTNDYTSFDKGQAGEVLGFELMRLAQADIPREIIDSYKRDKLSLTSQLGDLATLRFTGEA\nATWKFNTDMNYAMIGLMYDVPPTMALMVSGDDSLI\n>u114079\nLIVDAQQFDSQQNAVTVEIERRFCEMAGASPIALEEYYQIRQAGVPWSLLGRAQGKMNGE\nKGSGFPDTKLGNTVLQLCVASHKYKGRGPKVVAAKGDDYLR\n>u114132\nFANDFAEFDSSQFILSPYANAIIMIHLGCPWNLVESYIEMRRCWITSDDTVKLRGHQKMH\nSGEPFTLVGNTFFGMLIIAHCVEFDLLCYAVFKGDDSAI\n>u114366\nTDLDISALDSSERGDSLQLEINILKHFSIPDEFIEDYTEDKYDFHTATIHFGLMRFSGEI\nYTFLFNTMFMLARTVTKYSILRGRPIKVAGDDVLI\n>u114385\nLENDLSKQDRQTTKESIQVEMGVYHDLGVTADTLRMWYEAHNHWKASDKVTTIILDGMRQ\nTGQATTALGNLITQLTVHSRHVERNLKTLKLMLMLGDDHLS\n>u114561\nSCNDFSEWDASFRKPFQSLTGKLIQFLGCPEELARWFVAYRENWTMLYRNKFGTTSLRGQ\nEKQFSGNPFTIAENTIGNMALCFALFDYKNMRMALFKGDDSAV\n>u114642\nLELDIGKFDKSQDETMLDAQCKLFEAFGMETWMIELWRTYHELCKLSSPKWGASYWVGFQ\nRRSGDPLTWFGNTLVLLMILAYLYDIEKAYLVLVGGDDNVC\n>u114741\nFSNDFTAYDQSQDQKVLAFEVRLLNYFNIPRELIDEYVWIKLNSHAFPGPLQTMRFTGEW\nCTLIFNTFMNMAYMNLKYHIPKGMPQCYAGDDSIF\n>u114773\nGVTDYKMFDAQQDEFTQQIEKEFFHMLGFSERFTDEYYRLRRNYDMQAGPISGKARTEKT\nSGEPATLLGNSVLGGVVMNYIFRGEGKCAMAIKGDDGFK\n>u114920\nTGNDVTGWDAGCEAEFLYGIDLYLMELCGFPQHYIDSYLHRRLNSYTHLGKFPIMQASGD\nRYTWLLNTYRNIAITTLYFTIPRGTVMAFSGDDAIV\n>u114991\nQANDFTAFDQGQDGSFLYQEVSIMESLCIPQADIDYYVWLKTHMQSRYGHLSIMRFTGEV\nFTFLFNSLANLAVTNLRFFICGRPTLIGGDDSAI\n>u115093\nITSDGTRYEQGFSRGSGEMGTSVWNTIINLFMIFYAKYMEVTDFDAAWAFLQSSAIAGGD\nDSVV\n>u115134\nVAGDDMLLLNHEKSRYIEGDASMFDQSQATGPLEVEHLLLAKLGLDQETIEVSLQASKAN\nYVGYSGDKTGKLLLTVDKKGVATRASGHCDTTVGNSIVM\n>u115171\nSNNDFEEWDSSYNEFLIEFDCLLITALGANEYVVNCYRFFRKHWVLSYGYADFPIKLVGE\nMKQHSGQPFTLVCNSAGNMALTASLIDFTDIYYALFKGDDGCV\n>u115421\nVEDDLSKQDRQTDWELLNIEKLIYLYCGLDESICEMYMKMHKNWTWIGHGVRGKCDAGRL\nTGEPTTSLGNAIVNLIVHIIFIYDNWNDILAVYILGDDNMI\n>u115465\nTGNDVTGWDAGCEAEFLYGIDVTLMELLGFPQQYIDTYLHRRLNSFTHLGSFPIMQASGD\nRYTWLLNTYRNIAITTLYFNLPKGTVMAFSGDDAII\n>u115790\nTVNDYTAFDSTQQGESVVLDNCLLAWVGCPLEVREAYAYWKTHIVSDQLGVTPVQTHRAT\nGESGTWLGNTLYNIACVALLYGPKALHRGAWLFGGDDMAT\n>u116058\nTCNDFSEWDASFRTAFVKLTSWLLIAAGCPRDLVLDYENFRSSWIMQYRSMWGSASLRGR\nEKQFSGNPFTICENTIGNMALCFSIFDYEGFQFAMFKGDDSAV\n>u116237\nYENDLEKQDRQTDSHIITIELSLYKALGVHDDVLYLWQTMHRIWRFRSNFNWGFCKEMRL\nTGQSTTSIGNWITDMITHTDLLITQIDDIVYMIMLGDDNNI\n>u116338\nTYCDYTGWDTGVNESFTLLYRSIMHSYGIPDHVLDRWQRERHSLVSFLGPMPAMQASGDR\nYTWLHNTIGNMALTGISFSVDGSEPIAFSGDDMII\n>u116935\nIENDWTEFDSSQNNLEHSLFVSCMRRLGCPEQLVLFFLEMMQMRYVSSGDHSVLVQDKKD\nSGRVDTLVGNTIFNAAIVLSLIDYKNVEFAAFKGDDSVI\n>u117228\nVAGDDSLVGVWENGVLRWYEADAGMFDQSESYGPLLSEYRALHKLGVPGRTTDLLFHLAH\nASYRVAGREHQWHATIDRSHRPMRDTGGADTSIGNSIVM\n>u117240\nVENDFTEYDTSQNSVTIEFECCFLRSMQLTNEFVQLYKEHRSEWVANYPGFVSMQGRFKK\nHSGEPFTICFNTILNAAVCGAIYDFRGFVGGIVKGDDSHF\n>u117284\nLELDISKYDKSQEGTMLDAQCMILKRFGVDKTVIEMWRQYHEICKLSSPNYGLSYSIKYQ\nRRSGDALTWLGNTMVLLMIVAYLYPIEKAYMVLLAGDDNSM\n>u117375\nMVADFSEFDSSQEMQGILAGAMFMRLCNVPYHIVDMYLKQRQHWVMIACDKSDGGGVMRA\nVLEGAWKQHSGQPDTLNGNTTFNMMAMGACYVYTDIQFASFKGDDSII\n>u117408\nMMADFSEFDCSQEEKGIVASTVVLRMMGCNQKILGYYLKLRSEWTLSSIANDGPNSITAY\nLDGVWKQHSGQPFTLDGNTMFNMMAMGMCYDWTYLDAAAFKGDDTGL\n>u118224\nLEIDFSKFDKSQEGMLLLIVTKILVVFLDMPIDMAKRYVEDHVINTLAFRSLGVHLRTRF\nQRRSGDILTLLGNTLVSMVVIAFAYDLGNSYGGVFVGDDSLV\n>u118475\nLLNDFSEFDCSQEKRGIEAIFEMYRICGMNKFTMDFMFRMRSQWTLTLKSTTKHIPIQAF\nLEGQWQQHSGQVHTLGSNTLYNMGAMGMCYDFTNMYFAAFKGDDSFI\n>u118578\nVGADFSEFDSSQEMQGILAGLMFYRLCGVPEEICQLYLQQRAKWALIAADKNSVSSMMMR\nAILYGLWKQHSGQPATLDGNTTFNMMAMGACYEFIELVFASFKGDDSDA\n>u118867\nLENDFSKFDKSQQEICLFLEMEMYRLLGVDVDFIQNWYRTSEYSRIKSTTAGLKLFSVWQ\nRKSGEGTTAMGNSIVNMLVLCCFYDIDPSDLLYSVFMGDDSLL\n>u119230\nQESDFSKFDASLGPFWLWFNRLFIYSLFPDHKDELDELLGDSEFQEVSTTLRQKFSYGCG\nRFSGVNETALFNTLDQAFVQYVSFREHGLSHKSAVARLEQCLLGGDDGIV\n>u119394\nLEADSSMYDKSQSLLALMIEVEFLKRLGISCEVTEQLKQSFIGRVSTRNAGLSFVIAMQR\nKSGHVDTMIGNLIFNFVSLGKSVGYEKIYGMIGKGDDNVA\n>u119420\nFTCDFTAYDQSCTEETLAFELAFMDYCGLPSELIELYTWIKLTMHTQYGTTAVMRFTGEF\nGTYDFNTFWNMAYMTLRYDPDPSIASCFSGDDSLF\n>u119710\nGENDYEAFDATQHVSCRMLIIEMLVEHFGMAPDVARYMRAAAKEKFGHTLNGTFVSMEGT\nMASGHPDTYLTNTMMNILLQWYASACCGVFKPPIAAAGDDSVI\n>u119854\nSENDYTQFDRSQKAEFVLFQIELMKFFNVPQVLIDTFLDLKLNAHTDDGLLDFMILTGEW\nCTFLFNTFDNAAFTVTKYDIPKGTPCLFGGDDSVV\n>u119923\nVAGDDSLVIEWWNGTLRVVEGDASMFDQSQSFGPLEFEYQCQRRLGLSELAIQLMRKLNA\nAPYVAISRDKQRLGKLTIDRSQRPIRDTGGGNTSVGNSLVM\n>u119935\nFTCDFTSYDQSCTAETLAFELTLFEWAGIPQDLSDLYSFIKINVYTQLGHLQIMRLTGEF\nGTYDFNSWWNICYMRVRYGFDSDQPCCFSGDDSLF\n>u120015\nAEVDMSKYDKSQPQLSLELECRLFSRMGMPAELVKYWRLFHLNVRLSDRHTGLTFSTGPQ\nRRSGDPATYLGNTFYNMIAVDALQDLRTIRLAMFSGDDSLL\n>u120287\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPDSLVELYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u120457\nLEIDESKFDKSQLEFIFQVEQMFWEMFGLNGESADIWAKGHSSTTLRSWLHGFTVQIMFQ\nRKSGDVTTCFGNTIINMMALADCFDLKDAAAMYFVGDDSFL\n>u120661\nMVADFSEFDSSQEKQGIMSSILILKFCGFSTKITNFYMEMRQKWTLSARTEGDVMMNMTL\nCGEFMQHSGQPFTLDGNTLFNMACMGMCYNIKQMCFAAFKGDDSII\n>u120796\nVAGDDSIAIIWDEDGNMWIIEGDFGMFDQSQSFGPLRLEWANLLRYGVSYGTVGALERLS\nHASYVFRSGTKYSKEKIVVSREERPFRDTGGANTSLGNSLVT\n>u120869\nLELDISKFDKSQDDMALDLQCRIFVQFGMPSGLVNRYRQEHVKNKIKFRALGLTLTTFFQ\nRRSGDVFTLLGNTLVTMFSAAYCYDLKNAVGGVFVGDDSLI\n>u120914\nFCSDLQKQDMMTTHTELDAEFLMYEWLGVDPSLNRVYRESHNNWRFKSNTFRGVSDAMRW\nTGQVTTALGNVLVNMMVHSQLMKDNSKSVKHCFMLGDDNLM\n>u120925\nLLLDFSKFDSRNKTEVMTRLYRIYKKHLSTELYHWLEQTFHKFGKTSQGIKFSVEATVAS\nGRIDTSLGNTWIVFMLAYAIMYLLDPKYLPDLFISALGDDNNI\n>u120949\nMMCDFTEFDSSQNEKAMVASVMMLKSMGLPSHILDHYLNRRKEWVLYVKNNTGTVDLTVY\nLDGVWNQHSGQPFTLGGNTQYNMSAIGMCYNFKDFQFAAFKGDDSVV\n>u121524\nFAGDDFFALVHVGSEVFALENDFSKFDRTQGVHALGAECRVLVELGMSRKQARLLFQTQL\nASPRYQVERYEIKRRLPMPPQRATGGPDTTIGNTLTN\n>u122029\nWESDLEQQEKSMSGAYVTLFSKVLEHFGVPRDIIEAYIDDKLDKKTARMHLGIMTFSGEI\nFTFLANTLGNMARIAAKYDLKPAERGKFGGDDSLC\n>u122090\nTCNDFSEWDASFRKPFVKLTSWLLIASGCPRNLVNTYEKFRESWTMQYRTIWGFASLDGF\nEKQFSGNPFTICENTIGNMALCFSLFEYKDFQFAYFKGDDSAV\n>u122140\nFSCDFTAYDQSCTEETLSFELAFMEYCGIPVSLVELYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u122281\nASGDDSVVSFGGLHPEFDFGEADQSAFDHTQDDGPNKIFQGYVQRALGFPREFTELAYEA\nCSSGYTSRKGRFFARGECGTQMPTGITTTTTYNSLAT\n>u122633\nTTADATFYDYHQGAPGLLFEQMLFETFSMPQPLLSEYMRTKVDTQCFLGHMAIMRLTGEW\nFTLDGNTYYNIADFLLRHPQCLSSLMAPLHSPISRCLLVVGDDRCY\n>u122634\nLVNDYEAFDQKQDGCALYLELKLFERFSLPKWFTTMYFESKVGAFSWLGHLAIMRFTGEF\nGTYLFNTLFNMAYANLKFDLSVMISLFGGDDSAF\n>u122826\nLEADMSQYDKSQLEMAMRMEIYWYEHVGLNKEFINCWLVAARQASLTAKVGMRLLIEYQR\nKSGHSNTTLGNTVLTMLVMAYCYDLGRPWASMFVGDDSTI\n>u123451\nSCNDFSEWDASFRKCFAKLTTNLILWMGCPQSLADFFEHYRSRWTMIYRHEYGTTSLKGE\nEKQFSGNPFTICENTIGNMALCYSLFQYEGVKLALFKGDDSAV\n>u123597\nVSGDDSLVLTKREGRMRIYEGDASMYDQSQSFGPLRYQYDVLERLGVPVEVTNILADLAG\nNNYVLHTRDPTYHGIINKKNRPIRDTGGTDTSIGNSLIM\n>u123915\nLEIDFSKFDKSQDDLTLEMNILLMRKFGMPEHVLTEWEKCHVNTKLVFQSFGIKISIMFQ\nRKSGDVFTFMGNTITSMLALGFVYNLNHAVMAVFGGDDSLI\n>u124222\nAILDAKTFDAQQNEVTLEIERQMLLLLGHKIPAVHEFYKIRGSLPYRMFGAFEGKTDGSK\nGSGFLDTKSGNTILETALAGMLFEGKGPKLIAAKGDDLTR\n>u124229\nSTNDYTAFDQSQTGEAVALEMVNLRAHHIPDPIIEYYIELKLNLQCQFGALAIMRFTGEG\nPTLRFNSDFNAALMGVQYVVEEETARAVAGDDMAI\n>u124844\nVENDFSSYDKSQHIETWILEREVYRLLGCDEDLLQHWEDGHWFTKIRSPAVGFTMYTLFQ\nRKSGDVTTSFGNTLVNMITMIYSYRYVDIEYGLFLGDDSLI\n>u124877\nAILDSEEFDSKQGPVTLYLERCFLGKLGFDFEDIDEFQQARQPNRFRAPGQFKGKHKGEK\nPSGALDTKSGNTTLEMVLASQMFVGKGPEVEAGKGDDYLK\n>u124963\nVDNDFTEYDASQNSSTIEFETCILEDLGLTDECIDLYRNHRSQWKTYYPSYASFEGVDKK\nHSGEPFTIDFNTSLNMAICGYIYDFDDLVV\n>u125351\nITTDVVEMDSIQDVFTQEIERQVLARLGFTDKFVEYYYSYRRNYPLFCQGVFSAKGGTEK\nTSGEPGTLLFNSVLSSVFACYIIRFDGDFVMAIKGDDNTI\n>u125405\nLETDFSKFDGTLSSDVRFCEKKIMCNMMLPQHRRKLKELFDAEINCPSKTSLGYRYKVGT\nSRLSGSANTTLGNTLVNAFAAYVGLRLAGLTTQDSFANLGPKYGDDSIT\n>u125490\nFENDVKRMDVNVDSYVLNDEYKFLEILGLDLNIINLIKEIHKSFYFRGCNTKGYSKDKRL\nTGEMTTALGNVILNMIIHSKFVLNNMKNYKASFFLGDDSLI\n>u125543\nLENDYTKFDQSQKAEFVHFQIQLLEYLNIPKYLIKMFIELKLGYHDDKSLIDFMILTGAF\nYTYIFNTLDNMAFAATKYAIPIDTPQCYSGDDSVI\n>u125778\nYECDYTNFDATQNDVSMTVERMVYETVFPGIGSLMEVYFDARAKWRADTGFFAWDAQFIK\nTSGEPATLLGNTIVNMFVMYSAFTFGGQEFALFKGDDSLI\n>u125855\nMVNDFSDFDSTQGGNSVWLEVLVMRYCGIPDELVDAYTHWKTHLRSDRIGPKKTSRDTGE\nPGTYFGNTVYSIAVTFARFGWEASRKGMWVFGGDDMAT\n>u126262\nMTADFSEFDTAQEEIGTLSSAVILRSAGIPENLVGWYLARRKEWTLLNRDSVFDLSVLTT\nVPGTWKQHSGQPFTLTGNAIFNMSAMGMVYNYKNLKLAAFKGDDSII\n>u126687\nFEADISKFDKSQGELHLDIECALFEFLGMQKRVVEFWRHCHTVTYLKDFINKIRVQIYHQ\nRKSGDASTWFGNTIVTMAAIAVALYGYMEEVLVGMFSGDDSGL\n>u126926\nLELEVGKFDKSQDENMLEAQCRAFKILGMHDWQIELWRVFHELNILVAPKFGARMTVGFQ\nRRSGDSITWFGNTLVLLMMLGYLYPIENSIACVLGGDDNYT\n>u127036\nYEDDYTAFDGTQNEDFLVFQVMLMSECITLDQLIDEYIEHMTEVKVHGKRSRPFIASGYK\nFTWLINTLDNMAYQSVKHRLTPHTPEERVARAFSGDDSIH\n>u127367\nTINDYSAFDSTQGGESLNMEVVLMQRFSIPTVLIQHYLDWKLHQRSLSVGEKKLARDTGE\nPGTFLFNTLYSIANCTLKYGKITCMALFGGDDMAA\n>u127771\nTENDYERYDQSQGAECLWFEIYLMRFLNVPTEYIEFYIFLKLNAETQFGLLDIMRLTGEW\nATFLFNTLVNMAYTFLKYKDFRRKLEDKPAAAFGGDDMVV\n>u127835\nAENDMEEYDTSQSEITIENECNWLKRMGCNEFFVWLFKQHRTEWRTNYTGYVSMVGFAKK\nHSGEPFTLDFNTLLCMCLNGLMFPLDHFVFAAFKGDDSEI\n>u128463\nYENDLSKQDRQTDKAHLDLAAALYAYLGIEATTLALWRRCDTMWRFKGNNSLRGVLPHMR\nKTGEAPTALGNIITNLNIHKSWVLHNFDNLNLFLGLGDDMAA\n>u128704\nVAADITEFDSSQEAKGIYSSALLLRSYGFNQKVIDGYLSMRNSWSLYMSGKTVNESFYCI\nLGGVFKQHSGQPFTLDGNTIFNMGLIGACYDLGHIFFASFKGDDSFL\n>u128982\nLELDIGKFDKSQDEAMLHAQCKMFKIFGMDDVYIDLWRVYHELCRLTSPKWGARYTVGHQ\nRRSGDPLTWFGNTLVLLMILCYLYDIDKCSLAVLGGDDNLC\n>u128993\nTADDCVALDQSMREEFLAMECLLMANYGIPAHVIEEYVLVKLTTYCFLGPLAVMRFTGEW\nCTFLFNTVGVIGHKHLKYLIPRGTPQVFAGDDSAI\n>u129117\nWESDLEQQEKSMSGAYVTLFSCIMRHFGVPEDIIDAYVEDKLDKQTARMHFGLMTFSGEI\nFTFLANTLGNIARFVAKYDVTPGERGKFGGDDLLM\n>u129183\nTELDITALDSSERGGSLQLEVEIMEHFCTPAELVRDYVEDKFNFHTDTIHFGLMRFSGEI\nFTFLFNTMFMLARTVTKYAIPRGSPIKVAGDDILL\n>u129188\nLENDYTKFDQSQKAEFVHFQIHLLEYLNIPKYLIKMFVELKLGYHDDKSTIDFMILTGAF\nYTYIFNTLDNMAFAATKYSIPIETPQCYSGDDSVI\n>u129224\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELMALYEDIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKVARAFAGDDSLF\n>u129344\nLMVDISKYDKSQDEFDITLQVEFFRWFGLSDYDAELLLATYRETKLISKDLKVQAELAFQ\nQKSGGPFTWLGNTILLLVCVATVLDLRRANLVVLGGDDSII\n>u130145\nLECDWTEFDSSQNNLEHHLLMANLAALKCPEVLRDNFLAMMRIRNVQSRVGTVRVENKKD\nSGRVDTLIGNTLFNAAILLSCIDRTEMKYLLVKGDDGLV\n>u130390\nLEGDWTEFDSSQNNFXHELLMMQLEAIGCPAELRDLFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDHVLFKGDDSLM\n>u130493\nVSGDDSLVAVWNGETWDWYEGDATMYDQSESLGPLLSEYAALRALGVPENVITILYQLAH\nARYMVRGDGWTLTIDRSERPMRDTGGADTSAGNSIVM\n>u130611\nTEDDYTAFDSTQGGEFLNFDRLIMLDAGIPEKDILDYLYFMTHLETWMGRMGLMMPSGCK\nFTLLFNTTRSAAYQALKYDIKRNTPIALTGDDTAC\n>u130978\nFACDFTEYDSSQYDLSPLINAIFMLSMGAPVKLVDFYINMRANWVLSDDVMKLYGHDKMH\nSGEPFTLVGNTLFGMFVIAHAVAFDHWAYAAFKGDDSAI\n>u131060\nIDTDFTEFDTSHCRASLEAEITIFKKMGIPANIESLYRNQRMKWTLFYVNNYGLSKLSNV\nFMQHSGQPNTLTGNTLFNMMAIGSCYKFENLIVAAFKGDDFHG\n>u131064\nTGTDYTSWDTGCNAPFLVFDVWLFRWLGLPEAFIDHYVHRKLNVRCFMGTMPIMQCSGDR\nWTWFLNSIRNIAFTHNKFSIPWGTPQCYSGDDMLL\n>u131172\nGEGDWTEFDSSQNNVEHELLMMQLEAIGCPAELRDLFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDHVLFKGDDSLM\n>u131344\nLENDFSKYDKTQSETTYECEYIIYELLGIDRQFLNYWKDGHCVTKLVSRTVGIALVIIFQ\nRKSGDATTSIGNTLVNMLTIAAVYNIVDFKCALFLGDDSLL\n>u131662\nLENDFSKFDKSQQEICLFLEMEMYRLLGVDVDFIQNWYRTSEYSRIKSTTAGLKLFSVWQ\nRKSGEGTTAMGNSIVNMLVLCCFYDIDPADLLYSVFMGDDSLL\n>u131743\nIENDLEKXDRETNLFGLEVEIXLYEEFGLDKEVCDVLRDVHKHWXWATDTIXGKHSGVRL\nTGQPTTALGNFITNLRCHLLLRMREKNNIRNMLVCGDDNLL\n>u132104\nEMCDIEGFDSSIRGADVTLECELMRHFGVPADHVHEYVEDKMDFHTRTIHFGIMRFSGEI\nFTWLFNTMHTLARECLKFNHQPGDPIAVSGDDILK\n>u132257\nFACDFTQFDQSCVGETLHFELLWLRYFKVPEEIIQLYLMIKLDLQHTFGHSAIMRFTGEA\nSTFAFNTAYNMAVIASKYEIDQGTPCAFSGDDSII\n>u132323\nLELDISKYDKSQEGTMLDAQCMILRRFGVDKTVIEMWRQYHEICKLSSPNYGLSYSIKYQ\nRRSGDALTWLGNTMVLLMIVAYLYPIEKAYMVLLAGDDNSM\n>u132630\nLENDFSKYDKTQSETTYECEYIIYELLGIDRQFLNYWKDGHCITKLVSRTVGIALVIIFQ\nRKSGDATTSIGNTLVNMLTIAAVYNITDFKCALFLGDDSLL\n>u132702\nLEIDQEKFDKSQTRECFEVEMYFLEKLGLDKELLAIWGDGHESSTAINFANGIKCYFVYQ\nRKTGDAMTCFGNTLISMAAMATVFDLKGSEASYFVGDDSFI\n>u132853\nNAGDDVLVVVNTGFTYEIIEADVSKCDHSMRLPMLRAEYSLLAHAGLKEDTLDFLRVNAA\nAALVVCRRTRKDFGQKVVYRQAERNTGGTDTSIGNSLVI\n>u132860\nFTCDFTAYDQSCKAETLAFELVLMDWAHIPRELSELYYDIKVGMYLDRGWYKIPSAIMRF\nTGEFCTYDFNTFWNICYMATRYNIRNDTACCFSGDDSLF\n>u133004\nFEADQSKFDKSQDHVSLELERLVYTMLGLDPSVLTTWVQACEYGEVASVSAGFRAFVAYQ\nRKTGTGTTTLGNTLVNVFSTITAFKFKIEDVAYAIFLGDDSLV\n>u133324\nLESDFKSNDATQNGAWRKHEAMFYMKLGAPQWFVRAFAKQTTVRVWTRVGLEATVQGQRW\nSGEATTTTGNTYVGACQIQSALSQAGVEDSMNIHGGDDYLG\n>u133380\nANNDFSEWDASYRQPFTTLMWDLMVASGCPTPLADEFKQFRAKWKAIAHTKHGNIVLQGN\nEKQFSGNPFTICENTIGNMAMCFAVFTYDHPTVALFKGDDSSV\n>u133460\nQWSDKTAFDSAQDHSALHMEIRAMEFFNVPQSLIDIYVKDKLDTRTWVGHMAILRFTGEL\nFTWLFNTWHVIGRTQCQYLIPWGVPQMYSGDDEAH\n>u133473\nLEIDYSKFDKSQTERCAMIEMFIYSMLGLDKDFLIYWYESLEESSVYNYHDLIKAFIEWQ\nRRTGTATTALGNTLITMVTVCYVLFPDHPEDDMDGPFELAAYLGDDSSV\n>u133489\nTTNDFTAYDEANRGPSLHLECDIMRTFSIPSHYIDEYIFLKMNVISWMGNLATMRFSGEF\nATFDFNSYTGVAVINLALVIPRGVAQLFGGDDSAI\n>u133626\nTANDFSEFDQSQTGDALSLELKLMELLSIPDHLLSHYLHLKTNMSCSLGPLATMRHTGEG\nPTWFFNTLFNMAVTGARYRNASEYSRCFAGDDSAV\n>u133707\nIELDISKYDKSQGEAALIFECNVMRLLGVEERFVDHWQKFHKYALLTAKSEGLLEVKYSV\nNYQRKSGEANTFIGNTLLTLALILYVYDYDEIYFLTVAGDDSVI\n>u133828\nTEDDYTTFDSTQGGEFLNFDALLMRAMGIPEFEIEQYLNFMCSLCCWMGKMGYMMPSGCK\nFTLAFNTTRSGGYQSTKYIIPKKMPICLTGDDVAC\n>u133954\nSTNDYTAFDQSQTGEALSFELMMLRAFGLPDGVISYYTELKLELTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPSDTAVAVAGDDLAM\n>u134001\nTVNDYTAFDSTQQGESVVLDNCLLAWVGCPIEVREAYAYWKTHIVSDQLGVTPVQTHRAT\nGESGTWLGNTLYNIACVALLYGPKALHRGAWLFGGDDMAT\n>u134015\nIMMDASKFEQSVSAECIDFESELYGAYYPGDRLFKYMMRKQRKYKGKARCQDGKLSFTIE\nGVRASGMNNTALGNCVISAGFLWDVQGKLASKDKTFEMRGHVDGDDVVV\n>u134048\nMSIDLKQQDSSHVNVHRFFIAKVLAFLGFDDTICTLYLMSRARRFCKGLTMMGLLFEVIE\nRLFSGEPGTALFNFLMSTGTSVCTYDFAKFEVFLAKGDDNTV\n>u134218\nTSIYSRKYDFTVRTDSXRKSGDPATFLFNTLVTLCLFCNCYNLHSPRIVCAVFGGDDSLI\n>u134257\nLENDYTRFDQSQKAEFVNFQVHILKMFNTPEHLINKYMDIKLNCFNDISVLDFMILSGDW\nATLLFNTLDNAAYANLQYNIPPGTAQLYVGDDSAI\n>u134489\nVELDLSKQDRQTDKPILEAELDFLAKLGITNDCMASFRNIVDDKSYIRTADNLTFKIGPM\nQWTGGELTAFGNTYRNLLVVSDFYNHNKYEHVFVLGDDSLF\n>u135239\nTTSDYTAFDSTQRGDSLGLETMLMRHFCLDEAWVSLFSDYRHLAADIPELYTWWKLNITS\nDVIGPKRTGRDTGEPGTYDFNTYFNLALIQLMYSPPRGTPIAVGGDDMAA\n>u136589\nFDDDIEGFDGGQNEDFSHFQTLVAHFYSVPPPMWAEYQRFTAHILVLGKRSRFWIPSGLK\nPTWLFNTIDNMANQALKYDLTPHPPWTGCSAGRSRGVARGFSGDDATH\n>u137026\nMCADITEFDSTHSEATIDFEVRLMGLMGIPDSVTEIYRALRQTWTLNTFAGHRLAGKNKQ\nHSGQPSTLFANSLVCLLVNISMLNREQILAGDYAIAIKGDDSFI\n>u137458\nIEDDLEKQDMQTDLPQLNVEAAIYKLLGVQDEVLQFWMTCHRFWTFKGNQGLFGHDDLKR\nLTGQATTALGNVITRMNNTKDSIISMGNSMSFAVFLGDDLNI\n>u137757\nSTCDFTQYDMSCKAETLSFEMCLFSYFELDVQFPDLTELYLFIKTHMYTQFGPSAIMRFT\nGEFGTYDFNTWYNIAYMAFRYELDVRAPTGGAAFSGDDSIM\n>u137825\nLAADVTEFDSVHSQVTKEVEKILMQKCELPQPIIDLYMHMRNKWKLSTYSVGYLHGEHKQ\nHSGQPATLFSNTFLAMMIMIIGLNEEEMEKGNYMMMAKGDDTVL\n>u138371\nFMADISEFDSSQEEKAVLASAIMLKSIGISTKVIDFYTEQRKKWVMINKTSTSFETLSTV\nLAGNWKQHSGQPFTLDGNTLYNMSLIGICYDFKNIAFASFKGDDSYI\n>u138530\nLEDDLEKQDRQTDKPTIEVELELYRLVGMPDYLVKVWERVHEKWRLKGKFSQLWCQYMRL\nTGQASTSIGNLINNMTCHAHWVSQNLDRIQLILMMGDDFTA\n>u138629\nQANDMSKFDKQQTEDHLNVEKAIYKWFGVDPEFLEFYYDFHFNWILSSAQTQMYLNAMRI\nSGEPTTALGNAIVNLVIHSKLVVNNISKLTWLLVVGDDIII\n>u138904\nLGADFSEFDSSQEMQGILAGLMFKRMCNVPENICQLYMEQRRKWMLLATDKNNVTHMMMR\nAILHGFWKQHSGQPETLDGNTTFNMMAMGACYNVEQLAFASFKGDDSEI\n>u139213\nVCGDDSVVARWFNGKLTFKEGDARMFDQSQSFGPLCAEYQALQHFGVPREITGRLGEVAA\nNTYVVRPYRKDRDQAVFQLGRKSRPMRDTGGADTYIGNTLVM\n>u139985\nLENDYSKFDKSQSELCVRLEMFQNEQLGMDLDLLANWFQGHERSRIRCIQHALVLMISWQ\nRRSGGGNTSYGNVTLNILSTAYVYRHSEVACGVYIGDDSLL\n>u139994\nFECDLEQQDTQTDSEMIKVEQGLYELVGMDKEVSKIWFLVHEDWMLRSSLISHKNRSKRL\nTGQATTSLGCFINNIKTLSSVFQKSKHIINFLIFLGDDNVA\n>u141152\nAEVDMSKYDKSQPQLSLELECRLFARMGMPAKLVQYWRLFHLNVRLSDRHTGLTFSTGPQ\nRRSGDPATYLGNTFYNMIAVDALQDLRTIRLAMFSGDDSLL\n>u141218\nFTCDFTAYDQSCTGNTLSFELCLCRWAGVPEIVLDAYFRQKTTMYTQFGPSAIMRFTGEG\nPTYDFNTYYNVAYMSLRYDAGDMARCFSGDDSLL\n>u141324\nFTCDFTAYDQSCTSGVLGFELAFMDYCGIPQELMALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKVARAFAGDDSLF\n>u141383\nGTTDVKEMDSIQDLFTQEIERCMLRDLGEDEAFCNEYYSYRVNYPIMCRGVFTAKGQGEK\nTSGEPGTLLFNSVLAAVFTNFILIGVGIAILLFKGDDVIK\n>u142823\nVAGDDSVVYSLGKWFRADASAFDKSQSFGPLYFQRNMLVDLGMPRDIADLLNAVSAWPYF\nYRDHSGCLLITRKQRPMRDTGGPDTSLGNTIVM\n>u143741\nFEGDISQFDKSQTELALAIEMAVYRKLGLDPEWALRWESAMFETRNVCHAAGITIYLMHQ\nRKSGSVTTSIGNTIVNMVANAYPDTLQIDNVKAALFLGDDSLV\n>u143851\nTTNDYTAFDQSQTGEALALELSILRLFNVPEHVIEFYLTLKMQLTCAFGELAVMRFTGEG\nPTLKFNSDFNAALLGCQYDFDYSHAVAVAGDDSAI\n>u143897\nIENDFAKYDKSQLEMVYWFEYFLYRALGMDPYLLEIYMNAHRRSKYFDSKHGLSATIEFQ\nRRSGGSTTWLGNTLFALGILLCVYDIDEIVLLLAGGDDSFI\n>u144223\nYEDDFSSYDATQGEGAHECEMALYKLFMPDHAVYNALERQKLTEGYGKYHKYTCPYTRKS\nGDQNTSIGNTFINFSVHCWALDQLNVSDFYMLALGDDNLL\n>u144422\nVAGDDSLVAINRGDGVWFEEMDASMFDQSQSTGPLQAEYVILKRLGVPVYVTRMLWRLAH\nARYVACGKYVKIKIDRARRPMRDTGGADTTLGNTITM\n>u144474\nGYTDASEFDSRQNVVTQYLEYDFFRRMGVPEFFLKDYYSKRSNAKMIAHGIFKVQMGYEK\nSSGEPGTLLTNSLVAKVTAFYQMEGTGPFLMGYKGDDTFK\n>u144513\nIENDWTEFDSSQNNLEHALFIECMRNLGCPEQVVRFFLEMMQLRFVSSGDHAVLVQDKKD\nSGRVDTLVGNTLFNAAVVLSLIEYKDVELAAFKGDDSVI\n>u144652\nVDNDFTEYDASQNSSTIEFETLILEDLGVVTEVIELYRERRSKWKTYYPGYASLEGRDKK\nHSGESFTIDFNTSLNMAICGYIYEFDLLVVAQFKGDDSNI\n>u144655\nYSSDLKQQDRQTDHPLLDIENAIEIEFGLDPALAKLWRSVHYAWKARGVHIGGKFDAMRL\nSGQATTALGNGITNLIVNWRRCSGFGSTLVYYLFLGDDTNC\n>u144766\nLCADFSEFDSSQERRGIMSSLIMLSMCGYNQKILQFYLDKRTSWTLFSRSEHCEMPIKLF\nLDGHDMQHSGQPFTLDGNTLFNMSSIGMCYKFDDLAVAAFKGDDSFI\n>u144778\nCANDFTEFDSCQNNVSLEFECYLLRKTGIPEFCVQLFKEQRSKWSITSPGNVQLNGMWKK\nHSGAPDTLSFNCYFNMSVMGYVCEWDELVFAAFKGDDSLL\n>u144905\nLMIDFTEFDTSQESKSVISSCILMKSLGFNNNVVDFYMSRRRSWTMMTQAELNHERVVAM\nLDGEWNQHSGQPFTLDGNTLFNMCAVGMCYDMKGMILSAFKGDDSLI\n>u145726\nMLNDFSEFDSSQGGESVGLEINVFNHFSIPPRLIAFYRWWKLHIRSNVVGEKKTSRDTGE\nPNTFDGNTWYAAAITFLKYGWRTAYKAVWVFGGDDMAA\n>u145883\nTCNDFSEWDASFRTPFVKLTSWLLIASGCPRPLVNTYEKFRESWTMQYRTIWGFASLDGF\nEKQFSGNPFTICENTIGNMALCFSLFEYKDFQFAYFKGDDSAV\n>u146196\nACNDFSEWDASFRTPFAQLTHTLICYMGCPPELADYFLLYREKWTMTFRHAYGITKLVGR\nEKQFSGNPFTICENTIGNMALCFAIFDFRGYQMCLFKGDDSAV\n>u146554\nGTNDYSAFDQSQTGEALSLEVVKMRVFNIPEHIIHYYEELKLTLTCQFGSLAVMRFTGEG\nPTLLFNSDFNTALIGCQYEMPPDTPLMVAGDDSAI\n>u146617\nGVTDFEMYDSQQDEFSQEIEKEILKLLGVDQSFLDHYFSFRKGGKLLASGISGRLGTEKT\nSGEPMTLLGNSVISMVLANWILRGDGPFVMAVKGDDGFK\n>u146936\nKTNDYSAYDQSQTGEALAFESVKCRAFGIPDIVLEYYLELKLRLTCQFGELAVMRFTGEG\nPTLLFNSDFNAALVGCQYQFGPDMAIAIAGDDLAI\n>u147151\nIECDESRYDAHQGEGAYTNQMNVYKKFGIDEYNQAAKSMESMIRIKGYSQKGVAYRVPYT\nMTSGSATTSVGNTINNAATLTFAITSIMPKLKYKMIVHGDDSLV\n>u147152\nFENDFEKFDKSQMIAAFCTEMNFFWILGLDALLLALWAAGATITEAANLLLAIKILLYFQ\nRKTGTVTTSFGNLWINMASAAWVYKLGDVLFFAVYFVGDDSWL\n>u148158\nLENDYSKFDSTQTSPALKCIIMFLELCGMPKDLAGRMLLDTEAMTVRGPYKLKYVARGFR\nASGRSETLIGNTILNIVVTYHIFGKDCVGFIVKGDDSII\n>u148450\nMEDDLEAQDRQTPVDIIDVEMYLLKYFGVNQALVNLWRVTHENWRFKGRFSSGTRNAMRW\nTGQVTTALGNYIVNMLVRANWVLRNASYITFTLKLGDDFLA\n>u148525\nVDNDFTEYDASQNSSTIEFETLILEDLGVVSEVIELYRERRSKWKTYYQSYASFEGFDKK\nHSGEPFTIDFNTSLNMAICGYIYDFDDLVVAQFKGDDSNI\n>u148634\nTMNDWSAWDSGIDGAFLSFDMYVLRWLGLPADYLRFFVAMRIGSFNFLGNVKLMQLSGDR\nYTFLLNTLRNLCLCAAIFLLTLAHYLMVAGDDVLL\n>u149151\nLEVDFSKFDKSQERMILMIVLALFRRFNIPEEFIENWDKCHQLTKLIFHIIGIMLIASHQ\nRRSGDVGTFILNTVVAMVAMSMSYCLLLAIGGIFGGDDMII\n>u149426\nVENDFTEYDSSQSELTIYFESDILLLACHNPELVELYKEHRTNWSTSTPGLVHMRGYAKK\nHSGEPFTIDFNTILNIAICGAIYDIDDLCCALFKGDDSLI\n>u149466\nLEIDESKFDKSQLEFIFAIEQMFWEMFGLNSESAQIWAEGHSSTTLRSWLHGFTVQILFQ\nRKSGDVTTCFGNTIINMMALADCFELTDAAALYFVGDESFL\n>u149839\nEMCDIEGFDSSIRGADITLEKSFMLHFNVPLDHISAYVEDKLDFHTRTIHFGIMRFSGEI\nFTWLFNSVHTLARECLKFDHVPGDSIAVSGDDVLK\n>u149916\nFENDVSAWDASMHELLGELEVWLAQKMGARPAVIQLMHANIDTHGVTNSGIKYSVKGTRK\nSGDPYTSCFNSVINGLMHLFCIFKGGVPVESLQSVVRMLVQGDDNAM\n>u149992\nLEIDQEKFDKSQTRECFEVEMYFLERLGLDKELLAIWGDGHESSTAINFANGIKCYFVYQ\nRKTGDAMTCFGNTLISMAAMATVFDLKGSEASYFVGDDSFI\n>u149996\nTANDYTAFDASQGYDSVLLECHVMRLAGLPDALVDRYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLSCLALFGGDDSAI\n>u150066\nLEMDISKFDKSQNDYILEVQMEILRQLGFQEEVLKLYEKYHSFNKLNFRSFGVILDVAYQ\nRRSGDVFTFIGNTLVTMFTTLTSMDMNDVYGGIFCGDDNIM\n>u150100\nTVNDFTKFRATQGGDSLQMDLQWFQWAGMSDASVELYRRIKLSLQALGGTKKTCRDDGEP\nGTYLFNCFYDLGITAERFGVEALWRDFWLIGGDDEAA\n>u150245\nVSGDDSMAVKRRGWQRKGQAFLRFGEGDFSAYDQSQRAHCLTAHAVWMTALGLPKLLIDL\nILWVCSMPYRARGKRVKVKGKAGCQLATGIDWTTVINSMSN\n>u150546\nLEIDFSKFDKSXEEDLLLAXCYLMERFGIPRDIILSWFKCHIYTILNFXXVGLKFSVAFX\nRKSGDVFTFIGNTIVSMLILCNTYEIXDIIGGIFAGDDSLX\n>u150571\nGVTDGTEFDSMQNRFTQEIERRHCAHLQVPQVVIDAYYEYRNDYNMIQQGLFRATAGSEK\nTSGEPGTLLFNSMLGGSICNYVLRGIGPSTLCVQGDDAKK\n>u150843\nLEIDFGKYDKSQDDVMLEFQCRVFERFGMEPWLIDAWRYFHELCILTAPKYGVSYAVGYQ\nRRSGDALTWVGNTMVLVAAIAYLYPIERAHMVVVGGDDNLA\n>u151036\nFTNDFTAYDQSCTGEAIWFIIKPLQWRGYPDEFVQLFFRLKTDLSTSFGHSAVMMFTGEP\nGTYIINSLYNLAYMSMKYELKGMTLAVSGDDSIF\n>u151172\nVEIDFSKFDKSXDEVSLLILTEIFDCFGISSEFMSMWTKSHISNKLIFAKLGIWIYTQFQ\nRRSGDVCTFIGNTIVTMASLAYVYPMEHCLGAGMGGDDSYM\n>u151381\nTACDYTGWDTGVDEAFSVLYRDVMCSFGVPRRVADAFFDTRHERRSFLGPMPAMQASGDR\nYTWLCNTIGNMAVTCANFDFPSSTPACFSGDDMIL\n>u151474\nSANDYTQFDQSQGAEALHFEILRMKWYNIPSLFIDLYRWQKLHLHHQLWTSAIMRFTGEP\nGTYKFNTDFGEAYYYLQYDLKPSDPIVHSGDDTLC\n>u151535\nIESDAKNNDGSQSKEFRKYEAMFYRKLGAPDWFVREFARTLKIRVWTRYGICAEVVGERW\nSGETTTTTGNSYVHMALIQAAHELAGIKESTNIHGGDDYLG\n>u151610\nTACDYTGWDTGVDESFSLLYKEVFIALGVPAHVAAELVVNRHSRRPFLGDFPAMQASGDR\nYTWLCNTIGNMALTSLSFDVPAGTPACFSGDDMLL\n>u151939\nMELDISKYDKSQDSVMLDAQCLLFKEFGLTPTIIELWRQFHELCQLTAPGYGVTYRVGYQ\nRRSGDSLTWVGNTIVLIMLLAYLYPIEKAYLVLVGGDDNSC\n>u152157\nSCNDFSEWDASFRKPFSVLTSRLLQYMGMPDELNDWFLRCREEWTMVYRSAGGITKLHGK\nEKQFSGNPFTICENTLGNMALCFALFDYGQFDFAAFKGDDSIV\n>u152625\nGENDYEAFDATQHVSCRMLIIEMLVEHFGMAPDVARYMRAAAKEKFGHTLNGTFVSMEGT\nMASGHPDTYLTNTMMNVLLQWYASACCGVFKPPIAAAGDDSVI\n>u153012\nTENDFTAYDQSQRGVVLGFELLVLRFYGIPEPLIELYLAMKLYLRRTRVPFAEAELGTMR\nFSGEPATWSFNSRFNLVVSHTKFDLRGLPVLISGDDFLC\n>u153162\nLVADFGEFDSSQEMQGILAGAMFMRLCNVPTHIIEMYLSQRQHWVMVACDKWDGNGVMRA\nILEGAWKQHSGQPDTLNGNTTFNMMAMGACYKYVETQFASFKGDDSII\n>u153292\nICTDLKKQDRQTDLELLEVEMNIFLLFGVAPHVVKLWSMMHYNWRWLARQCVGWRHMFRH\nTGSVTTALGNLITDLQCNTVTMEMLDGEFNFAILLGDDNTI\n>u153455\nFEDDLEMQDCRTEHNLLYLEKKIYQLMNVDDNILNMWFTTHDIWRVKGKTIRAVNKLMRL\nTGQATTALGNAVVNLIVHLEIVINSPKLNLYLFLGDDALL\n>u153847\nFGDDYQMWDGGQGAEFIMAQVLLMRALGVPEFWINLYILWMTALDALGKILGLSLFSGFQ\nPTWTFNTFDDLCFQALKHALTPHVPKSSFNLSITPPGAAHVARAVSGDDCTH\n>u154303\nLELDIGKFDKSQDETMLDAQCALFRIFGMEEDLIELWRAYHELCKLVSPKWGAHFWVSYQ\nRRSGDPLTWFGNTLVLMMILAYLYDLEKAYLVLVGGDDNFC\n>u154448\nVSGDDSLVYISLNGERYCFEGDASMYDQSQSVGPLTVGWRAYKRLGVDSETIKLLRALAY\nNKYVVEGRDRSNLPTFYTIDKRRRPMRDTGGADTSLGNSVLM\n>u154487\nVENDFSSFDSTEGRRALLMVYRFYNMCGVPKEITDLMERDLDDTKISTSVGITFNCKGFR\nFSGRSDTLLGNTVLNVIIMYHVFKSSLQKMIVKGDDSVI\n>u154663\nVSGDDSLVVVWDVYSNIPNCIENDFSQFDRSQGVHALEAQHKVMRAAGCSHEEEQLFAQM\nYNEPVLVQDRTSQTEFVFPIPVQRRTGGPDTTLGNTLNN\n>u154681\nTQIDISKQDTSHTLLTLLVFCHLLRHFGVPAELVDIYLVHSHKFRFKSLIPGLYAGEATD\nNLGSGDPFTLIRNIFQVATKIVAAFVIQESKDACWIIKGDDVET\n>u154696\nYYSDLKKQDRQTDQTMLEVEMNIFLLLGVHPSIVKLWSAMHFNWRWLARQSHGYRHMMRH\nTGAVTTSFGNFLTDMQVNTELLIELHSNFNGVIMLGDDNLL\n>u155190\nTENDYTAWDSSIDGPFVKFDLWLLRQIGVPEEYLATWAEERCSTTCFMGNLRLMQHSGDR\nYTFLLNTVRNLAITNAQYAGMAGRPQAYGGDDSLV\n>u155295\nVENDFTEYDSYQNALTIEFESDILLLACHNQELVNLYKEHRTHWKTLQPGVLTMHGYAKK\nHSGEPFTLDFNTILNIAICGCIYDIDDLACAAFKGDDSFI\n>u156249\nVENDFSKYDKSQQWTCLRMEWEVYALLGMDPEMLADWRAGHVECNASSISAGVKIFSLLQ\nRRSGDATTALGNTIVNMLTVAATYSLRGYHYAMFLGDDSVV\n>u156259\nLSDDLSKNDLTTDKPQLNIEMLMYKYLGGEPELIDLWATCHRHWTYLGANGLMGKSDLKR\nLTGQATTALGNFIVNMNCHKEWWLDLTVKAKLTLALGDDNTT\n>u157159\nMCADFSEFDSSQEKQGIMSSLLILRSCGINQDVLDYYLSMRQHWYMSCRGNGELETFNVS\nMNVMWKQCSGQPFTLSGNTLFNMSAIGMCYNIQDMAFASFKGDDSFI\n>u157450\nTKNDFKQFDQSQRGEAVCAEVLHLDYWGIPVHLVDLYERQKVSLKHQFGTSAIMRFTGEP\nGTYKFNSFFSEGLCGLQYQFTPGYPRAHSGDDTLF\n>u157660\nIELDLSKQDRQTDNDILELETYMVYALTGNRNLSNYLDEARTGFTVKTQSKHLFHRPGMR\nWTGGEITALGNNIRNWLCIGDIARHYDVAYVITLGDDSLI\n>u157840\nLEDDIGKFDASVCEDWCKLEVWMARAFGAPRAVLDLMRANINTHGYTSQGFKYSVPGTRK\nSGDPYTSLFNSVLNGLMHLFIFCEHFGVTVEQARHLLRMLVQGDDNLI\n>u157850\nFSTDAKKFDRQXNHWLLDFEYMIYDILGMDVKVQQLLRNSHNNWKWSSGEMXGIMDSMRL\nTGQSTTALGNLIVNMCIHSIFLNKNXXITTFVIMLGDDNVI\n>u158136\nLEDDISAYDASICEELCKLEVWMSKRFGLRGVGLQLMHANIKTHGWTTHGIKYSCVGTRK\nSGDPFTSLYNSILNGLMHLYIFCKARHLEVHVALGLIKMVVMGDDNLL\n>u158556\nCITDGQMFDANQDEFTQMLERETYIRLGASAAWVEWYMSHRRDYPLITPYAYGVAGYEKT\nSGEPFTLLGNTIVAACMSNYLYRGHGPAILAVKGDDGWK\n>u158707\nFENDFEKFDKSQLEECFSAEMKLYEILGLHWLLHALWAFGLIKTEARNFILGILIYLMFQ\nRKTGTVTTSFGNLIINMIATAVAYNLLEVGFEAVYYVGDDSYL\n>u159528\nTYTDYTGWDTGVNESFSLFYAKVMMEYGIPHAIAKKFIHDRHSRQSFMGHMPAMQASGDR\nYTWLNNTIGNMGLTGISFSGLDGLAVCFSGDDMII\n>u159582\nLENDFSKFDKSQEYIALMVEYEVYRRLGFDELLLEAWKDGHFDTRLTDYNAGFRAFISFQ\nRKSGEATTLLGNTIVQMVAIAYAYKDLNFDMAAFVGDDSAI\n>u159598\nTETDYTAWDSGIDAPFFKFDAWLMTQVGIPQWYIDVYLEEACTTTSFRGNLGLSQKSGNR\nYTFLFNSLRNLALTNHTYSNLRRVPQAYGGDDSLI\n>u159708\nYDNDLSKQDRQTTPELLEIEHYLYSKLGVADEFISVYIKCFDNWRFKSKFGLGMLNAMRL\nTGQASTAIGNMVVNMITSWRTVLKCKARLTLLCGDDHLS\n>u159784\nFTCDFTQYDQSCTEETLSFELCLMDWAGIPDDLISLYRWIKLNMRTQFGYTAVMRFTGEF\nGTYDFNTFWNMAYMCIRYDIPSDMACCYSGDDSLF\n>u159811\nFTCDFTAYDQSCTEETLSFELAFMAYCKIPQSLIDLYSWIKLNMRTQFGFTAVMRFTGEF\nGTYDFNTFWNMAYMELRYAPSSSIPACYSGDDSLF\n>u159836\nVDNDFTEYDASQNSSTIEFETLILEDLGVVTEMIELYQERRSKWKTYYPGYASLEGRDKK\nHSGESFTIDFNTSLNMAICGYIYEFDLLVVAQFKGDDSNI\n>u159867\nVESDMKNNDGTQPAECRKYEAMFYKKLGAPDWFVREFAKNTQVRVWTRFGISARINGQRW\nSGESTTTTGNSYVSMCIMLAALDSAGVQRSLNVHGGDDYLG\n>u160017\nYGSDVTRWDVGCDAAMVNFDVHVMRSLCFPTWYIDAYIERRVSSFSQHGPMKTMQNSGDR\nYTWILNSIRRAVVTSLVCAITPADTAAINGDDAAV\n>u160459\nMEIDFSKFDKSQESFCLEIQLHILKFLYMPEHIINLWWNCHRTNKLVFNNGITLITHNQR\nRSGDIFTFMGNTIINMAALNFVYNLKNSYGGCFAGDDSLI\n>u160593\nVAGDDSLCYYRGFGYEGDASSFDQCQSFGPLEYEARALRRLGLPEWADDILRNVHSATCV\nNDERAGFKIKRDNRPFRNSGAPDTTIGNSIVM\n>u160903\nTENDYERYDQSQGAECLWFEVYLMRHLNIPEDFIEFYIFLKLNAETQFGLLDIMRLTGEW\nATFLFNTFVNMAYTFLKYKDFRRKIEDRPAAAFGGDDMVV\n>u161278\nVDNDFTEYDASQNSSTIEFETLILEDLGVVSEVIELYQERRSRWKTYYPGYASFEGVEKK\nHSGEPFTIDFNTSLNMAICGYIYDFDDLVVAQFKGDDSNI\n>u161413\nQEIDFSKFDKCQEEFILSLTSEVLRRFRFPEYIIREWEDCHRVNKLIFHKQGVSLQVRYQ\nRRSGDIFTFIGNTLVAMIVMSYAYDLKSCIGGLFGGDDSLI\n>u162029\nVSGDDSLIVLKKSGSYLLYEADASMFDQSQSEGPLFSEYAVLRQLGVPNEITEVLYHCAT\nAPYYYYSKMKGKMRVNHKHRPMRPTGGADTSLGNSIVM\n>u162184\nTATDYVAWDGGCDGKFLGLDVKIMRHVGLSEEFIDAYIDRKLHTRYFGGPLPIMQFSGDR\nWTWLLNTLRNIALTHVKYDIPPGTPQAYSGDDMIV\n>u162242\nFTNDFTAFDQSCTGESVWAIIKLLRWRHYPEWFINLFFQIKVDLETSFGHSAVMMYTGEP\nGTYIINCLINVMYMASKYDLRSVTFAVSGDDSIF\n>u162432\nTCDDFESYDQSQDGTCVNLEIFLFDWLKIPRDLLNLYLHVKCHALTFVGFLELMRLTGEW\nATFLFNTLNNIAYHHTDKKIKDGTPQMYGGDDLTI\n>u162752\nTEVDYAKFDKSQGEVCHKVENKIFSLLGFDATMHELWKHGHLFSRVTDYLTGVRLFLYYQ\nRRSGDATTCFGNTLIAMSSLAYCLELEGKIQAAYFIGDDSSI\n>u163182\nFENDLHRQDRQTEEDLLYLEMLIYIYVLGVPYKIISAWYIIHKYWRYHTSDIKGDFSGMR\nLSGQASTALGNFLVNLLITSNIMYKQPTNLVCMLGLGDDNLM\n>u163228\nLSLDIKGFDGTQRGAALELERQWMTCFNVPEELMDAYVHDKLDAHTKTIHLGLMRLSGEI\nFTFFFNTVFMSARTVTKYRIEPGDPMASSGDDIEL\n>u163237\nGVTDYAKFDAQQGHFTKLLERFALFDLGATHEFLDHYYSFRKDYKIKSKEVSCTGADEKT\nSGEPGTLFLNTLINAIIGDYVLEGIGPCVIVFKGDDGFK\n>u163442\nITSDGTRYEQGFSRGSGEMGTAVWNTIINLFMIFYAKYMEATDFDVSWSFLQSSAIAGGD\nDSVV\n>u163499\nTINDFSDFDSTQKGESVWLEVSVMRCFGVPTELIDSYVWWKLHVVSDKIGVKATSRDTGE\nGGTFDGNTWYSTANTALKYGVAALWIGLWLFGGDDMAT\n>u163625\nTVNDYSAFDSTQGGESVQMELAWLRWAGAPGEVVDMYSWWKTHIFNSVVGEKKTSRDTGD\nPGTFLFNTLYSIGNTALKYGTACFETTTFLFGGDDMAA\n>u163665\nLEGDWTEFDSSQNNVEHELLMMQLEAIGCPAELRDLFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDHVLFKGDDSLS\n>u163732\nLELDFSKFDKSQHRAFKLFELKIYEFMGVEPEILAIWFQGEMHAIGTTNDKSISYDFGVQ\nRRTGSANTWLGNTLVTSGILSYYMHEKNALFLVSGDDSLL\n>u163736\nISGDDSLVVVRFQGLTTCYEGDAEMYDQSQSFGPLNFEREVLRVFGVKDSAVRLFRTLAE\nNEYLVMSRDRESKLLIDKSERALRDTGGANTSFGNGVIM\n>u163853\nYSNDYTSFDQSQTGEVLASELLYMWHAGIPESIISMYEENKVDMVCAFGHLQTMRFSGEP\nATYAFNCRCNLAVLNLQFPLDQNGDVPIFVSGDDGGL\n>u164528\nFTADFSEFDSAQEQKGIMSSIVVLKSLGFNNDMLDFYLNMRSSWTLASNTKDSCGSYIFY\nLNNSWMQHSGQPFTLDGNTLFNMSSIGACYELKDLICASFKGDDSII\n>u165253\nIQVDISEYDKSQESRTRALEDLIFTELGMSASMMDNWSHSHKDTVIRCLALGIKLSVAYQ\nRKSGDATTALGNVMLNMMATAYAFACPVVSISQGDDGLV\n>u165281\nLVADFSEFDSSQEMQGILAGAMFMRLCNVPYHIVDMYLKQRQHWVMVACDKSDGGGVMRA\nVLEGAWKQHSGQPDTLNGNTTFNMMAMGACYVYTDIQFASFKGDDSII\n>u165410\nFTSDMTGFDAGQDENPLAMELLVMEFFNVPQDLRDFYERTKLDTTLGRHVLAIARDSGEL\nFTWLFNTLHTIARRYLKWVIPKGAIAMFGGDDENL\n>u165418\nTMFDSSQGNVEHELTRLSLNKIGCPHILTQLFVAVVYNRKITGKIASLNVRNKKDSGRID\nTLLSNSQFNAAVIIFMIDWERSYLDHLFIKGDDSLL\n>u165425\nVSGDDALAVGEMNGTHYVIEGDASMYDQSQSIGPLSMGWRVCKKLGADDETIDLLSTLSY\nNTYTVEPRQREDASFFKINKRDRPLRDTGGADTSVGNSIVI\n>u165738\nAIVDAEKFDSQQNEVTVYAEKLFFEKLGANVSSLEEYYKIRQKGIPWSLLGRIYGEMNGE\nKGSGFPDTKIGNTVLSGILANQQYVGKGVKVEAGKGDDWLR\n>u166125\nFDSDLEKQDRQTTHSLIDIEFGVDENVLSLWRQVHNHWRLKGRFVRGKRDAMRQSGMATT\nAIGNACVNLIVNNDIGLKRRREITCFMFLGDDSIM\n>u166157\nIELDISKYDKSQGEAALIFECNVMKLLGVEERFVDHWQNFHKYALLTAKSEGLLEVKYSV\nNYQRKSGEANTFIGNTLLTLALLLYVYDYNEIYFLTVAGDDSVI\n>u166255\nFEDDFSAYDASQGFGAHWVENHVFKRLGLDAAACEAFDRQVWSKGFGRWFTYTVPFTRKS\nGDQNTSLGNSIINALAHMWCMLQLGITDFKMIVMGDDNLL\n>u166438\nLSTDFTEHDTSHSMVVKMWFCYDMIHFGFDKRLIAKYWNAYVHWSQHTTTDTPITVDNVF\nMQHSGSPDTIHGNTKLTMGANGACYVFDRLHFSSFKGDDTLI\n>u166458\nFTNDYTSYDKNQKHATTRFEILMMKFFDVPEEEANFYLNLKHETVCYLGTLDHLRTSGEG\nPTFDFNTRMNIAYNHAKFNIPLDTTELYAGDHLAQ\n>u166546\nFENDLHRQDRQTDIDLLYLEMLIYIYILGVPYKIVSAWYTIHRFWRFHTNEIKGSFEGMR\nLSGQASTALGNFLVNLLITSNILHKQPDNLVCMLGLGDDNLM\n>u166547\nLEIDFSKFDKSQTEVCFEIEMAIWSLLGMDKFLHDLWKIGHFSVSATDFTAGIKAYFQYQ\nRKSGDSATAFGNSLISMASLAYAATFPSVEAAYFVGDDSLI\n>u166568\nYGDDYTGFDGTQNEDFLAFHVQLMRFYGIPEPYIEDHAVWSTHLRCMLGPMAVVIPSGYK\nPTWLLNTMDSMAFQAIKFALTPGVARAFSGDDTLH\n>u166640\nVCGDDSVVAYCGTDGKFLFMEGDASMFDQSESFGPLLSEYRVLEHLGVSKSHTTALYKTA\nRNSYRVRPKKPQSDQEFFLMSRQNRPMRDTGGADTYLGNTIVM\n>u166754\nVTIDYTAYDQSCTHVTLCFEECLMGWCDIPIELQLVYIDIKLNMRTQFGPSAIMRFTGEA\nFTYDFNTYWNIAYSATRYQLSGHFICAFSGDDSLF\n>u166766\nTTNDYTAFDQSQTGEALALEACKMRCFGIPDHVMAYYMDLKLNLTCQFGALAVMCFTGEG\nPTLHFNSDFNAALIGCQYLGVDKLPVAVAGDDCAI\n>u166867\nTTNDFEAYDKSLRGEFINFNILLLNWFNIPQNLIDCFVELKTNAHTFLGILQLMTLTGEW\nATYLLNTLDNIAFTHTKFNIEKKTPQCYSGDDLAV\n>u166871\nAETDLAECDAGQDETTARFERKLMELFGVPEIAIDFLFFIRKTWVLSARDLAKVENHGKK\nHSGAPDTLDGNTIVSAGQIARVFKFTNLKLALFKGDDGCM\n>u166887\nTTNDYTSFDKGQAGEVLGFELMRLAQADIPREIIDSYRSDKLSLTCQLGNLATLRFTGEA\nATWKFNTDMNYAMIGLMYDVPPEMALMVSGDDSLI\n>u166955\nTCNDYTKYDQSQNEQFLSFERKLMEFLNIPRELIDLYTTIKMNTQYFGGILDIMRITGEK\nFTFLFNTYANIAHTELKYSTNNLKLAEVYGGDDMAI\n>u167177\nTCNDFSEWDASWRGCFTEFTCTLLRYMGCPKQLVEDYKRFRDDWIMTYMTAFGNVTLSGR\nEKQFSGNPFTICENTLGNMALCFSIFEVRDMQYAMFKGDDSVI\n>u167276\nLAADVTEFDSVHSQVTKEVEKILMQKCELPQPIIDLYMHMRNKWKLSTYSVGYLHGEHKQ\nHSGQPATLFSNTFLAMMIMIIGLDEEEMGKGNYMMMAKGDDTVL\n>u167659\nHESDATAFDQSQRGEALQLEKLVFWHYSIPDELVDMYIEDKLTFRCQMFTIATQRLTGEA\nFTWLFNTLFNIAYTYTRYDVTPEDPQAYGGDDQAI\n>u168009\nTVNDFSAFGASQGGDSLKMDLLFFAWCGMPDSLMALYFKLKTQLIALSKVKKTCRDDGEP\nGTFLFNCLYDIGVCAMRFGWGAFWYGYWLIGGDDMAC\n>u168122\nAIGDAEEFDSNQDYYTVAVEEENRRLLGASVEWAKVFYDTRGPSPLRAFGLFKGETKGEK\nGSGFLDTLLGNTTSAGTLADTRISGSGPAVKAVKGDDFLR\n>u168185\nVENDYTQYDQSQREECLYFEVLLMKHFSVPEGLIDRYVFNKTHCKHKYGDAAIMRFSGEP\nGTYTFNTWVNIAVLCCKFRIDGYAFAVSGDDSLI\n>u168211\nVSIDFSKFDSSQKREILEMLIIFYRHIYQGPQKEILMKYIKMCCGKKKSFSNTRDDDRMF\nIIEFDSTRGSGDSDTTCSNTLLAILLTHYICRDFRDDIWDYFWSFNAGDDILL\n>u168783\nLQVDISRQDSSHTAALLYVFLMVLRDCGANEDDLQFYFKYCSQYKVRSRGSDAARMRISF\nNLGSGDPFTLIRNDVMEATVLACRFEHAAKALWVFKGDDTHS\n>u168979\nTESDFTAFDQSQKGESVAFEALVMRHFSIPEEIIEAYEIDKTSYRCQFFEIAIQRLTGEA\nFTWLYNTMFNFVYTQIRYDISLDDPQMYGGDDMTV\n>u168989\nTDVDFTEMDTSHGESIIKLEMLLFGIAQMPLFIRSMYENARTNWMMMYNNGNGVSKMWGM\nYCQHSGQPFTLGGNTILNMAAIGAFIDFGTVLYAAFKGDDSHI\n>u169359\nFENDSSRQDRQTSEEAIAFEMSVYKLLGVPSELIDIWFTFHKNWKFKSSLLSGEYEWQRL\nSGLITTAIGNFIVHLLVNMKLILLYTTSFKMYIGVGDDSLM\n>u169776\nLELDLEKQDKQTDHDILEFEFSMYEALGIDSELLSVWKTVHNKWKWEGGHMRNYADAMRL\nTGQATTALGNVITNIYVNASLMLKTNQRWEWMLMLGDDMIA\n>u169809\nTCNDYTKYDQSQNEQFLSFERKLMEFLNIPRELIDLYTTIKMNTQYFGGILDIMRITGEK\nFTFLFNTYANIAHTELKYSTRTLKLAEVYGGDDMAI\n>u170085\nAENDMEEYDTSQSEITIENECRWLKRMGCNDFFIWMYKMHRTEWRTTYIGYVSMMGFAKK\nHSGEPFTLDFNTLLCMCLNGLMFPLDKFIFASFKGDDSDI\n>u170941\nAEADLEKQDRQTDDNVIKAELSVYHALGVADEVLATYQTLHETWRFKSKFSWGLHKSMRL\nSGQPTTASGNGLTTLQTTARNIAELGDDLSFFVFIGDDNTF\n>u171096\nLQVDVSKQDSSHTAAFLYAFILVARDCGLPEDRLCFYLQYCRKYAFLSRGADACRGQLSY\nNLGSGDPFTLIRNDIMEMMVIAARYEAADKAILVEKGDDVHA\n>u171220\nTTNDFTQFDCSQGAETLRREVHAMQLFSIPQWLIDLYVWQKLSLDHQFWTSAIIRFTGEP\nGTYRFNTDFSAAQLSLQYDPPEKTAMVISGDDILI\n>u171404\nVELDMSSFDKSQQELAHLVKMAWYKLLGMPPYLLELWDRFHRVTFNRGISSGITFWTSYQ\nHKSGDASTAFGNTLMTMTALADIVAPQGFDSAFFIGDDVIV\n>u171409\nIENDYTAYDQSQGAEALQMEIRLMHHYNIPQKFVDMYVQMKTHSFHQFGVSRIMRFSGEP\nSTYAFNTLFNIAVAGAQYWILDRPFCVSGDDLLI\n>u171445\nTASDYTGFDSTQKGDSLGLELRILLHCGLDLAWIDLMSQFLHIAQTLPEMYRWWKLHIES\nTVIGVKDTGRDTGEPGTYDFNTYFNLALIQLMYAPPKGTPIAVGGDDMVA\n>u171466\nTTNDYTSFDQSQTGETLAFERSLLDFFNIPEWLKDWYTESKMDLVCQYGHLQTMRFTGEG\nPTWLFNTLFNFALIFCQYEMGVAQPVAVSGDDTAI\n>u171713\nAENDMEEYDTSQNEITIENECRMLKRLGCNDLFVMLYKKHRIDWSTTYSGYCKFIGYAKK\nHSGEPFTLNFNTWLCMCLNGLMFPLDDFVYAGFKGDDSDI\n>u171784\nCMGDDKLIFGMGDFTEFDSTQNELMPELCTAYVQLFTGMPDSILATYVNQLSAWVVTVEG\nVLKIKNQNQKHSGAAATLLFNTIWN\n>u172164\nLEGDFTAFDQSEDAAFVDFERRIMEDCSFPEHIISDYLNLKASLSSRFGHLAVMRFTGEV\nWTFIYNTLANFAFTHLKYCIPPGTPQCYGGDDTVI\n>u172201\nVEGDFSEFDSTQNELMPIICCEVLEMFTGIDPQLTATYKQHLAEWKVEIPSLMTIAGKNQ\nKHSGEAATLLFNTIWNAAWVSALFDTKDVVATCFKGDDSLI\n>u172465\nLENDFKAYDKTQDNVALEIELSFLALLGVPLDLLEMWRSGHVYTRATCRETGFMLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFSKPEDARIKIRCAFFLGDDSLF\n>u172468\nLENDFKAYDKTQDNVALEIELSFLALLGVPLELLEMWRSGHVYTRATCRETGFMLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFAKPEDARTKIRCAFFLGDDSLF\n>u172471\nLECDLEQQDAQTDEFIINVEKEMYIELGMDPALADFWFLVHEDWYLRSRMIKYGSRSKRH\nTGQASTALGNLITNLLTMGRWHEQNQRAVCFGLFLGDDSVI\n>u172474\nVENDMSMYDSQQTLEQHEIEAGVYKALGGDSGMIDFYMSFHEDWYMRNSTLLMRLSGGRV\nTGEAATALGNAVVNMIIHIGLIERYGQDLVFCLIVGDDIVL\n>u172478\nYFNDYSRQDRQTLDDLLLAEMVVYNRLGLSKSITDIWYWFCHKLWRLKTNTSSAWLKFMR\nLSGQATTALGNTVVNLIMTARIVNISHTKLNWGIVMGDDSLF\n>u172491\nFDCDLEQQDAQTDENIIAIEKELYIQFGMDREVADIWFLVHEDWAVRSSLNKLYNRAKRL\nTGQASTSLGCFLNNINTLARTFEREGDNVKWAMMLGDDNTG\n>u172627\nIEYDLSAQDCQTTRELIDVEFKLYELLGLDYVTAQFYKNCHNMWRWKGKGIRGMMDAMRL\nTGQVTTALGNAIVNLIVYNRFTMRNANNISCTLILGDDYLC\n>u172880\nLENDFSKFDASQNLFTQKFEQWLLESLFPGYSGVLEHYYSLRRSWYARNGYVSWHSKYIK\nTSGEPGTLFLNCVVTMLITSLTIKCSGVRFFAVKGDDSIL\n>u172985\nQENDFSKYDKSEGENILPLEKLIYEELGMKLSRSDEWFDGQHMGVVKAVSFLFTIHLELQ\nRRSGQLTTLLGNTIICMMTVWYVYQVKRDNVNWSFFKGDDSIV\n>u173031\nSENDYTAYDQSQNEEFLNFERNLMEYLNIPQKIIQFYVENKLSLRSFMGTHQVMRGTGEG\nPTFDFNTYCNIAYDSMKFRNKRIPSLYAGDDMAK\n>u173144\nTETDFTLFDSSQNGRGVAFEELKMEYFRLPCADIDFYVELKLTSESFLGTLPVMRFSGDV\nNTLLGNSDFTIAVMNLRFRIGCRLRAGRNVLHCGDDFAA\n>u173260\nGISDAEEFDAQQNESTVEVEKEFTRLQGAVSADIEQYYLVRGRLPARMFGFFSGTTNGAK\nGSGFLDTLLGNSKLSLCCSRRLFRGSGPKIEAVKGDDYLR\n>u173283\nVMADFSEFDSSQERQGIMATCVILRKMGMPYGYIQEYYERRAKWVVACKTTTDSMKITGH\nFSQHSGQPFTLAGNTMFNMMVMGAVYVYKTVVCASFKGDDSFI\n>u173311\nVENDFSKYDKSQQWATHVREWILYEMLGFNFDQSLQWRYGHIITVANSLTAGIKMFTLLQ\nRKSGDATTAIGNTIVNVIAVMKVYNIRPENMAFALFLGDDSVI\n>u173413\nSTCDYESYDKTQNEDFLQFQITLMEHLNIPKELIALAMAYKLSVNFNGKHLQVAIYSGEK\nWTFDFNTLDNIAFTYLKFGFRGPYPSTRPIELYGGDDNAL\n>u173668\nTATDYTAWDTGCDESFLSFDCWLLDRVGLPQWYVSEYARGKVSTRCYAGHIPTMQFSGDR\nWTWLLNTYRNIAITSVRYKVRRGTPCAFSGDDMIM\n>u173674\nAIVDARSFDSQQSQVTLEIERQFLKLLGAKMEVLERYYEFRKPMPYSCFGRFSGHTNGEK\nGSGFPDTLLGNTILQTCLATYALEGKGPMCVASKGDDHLR\n>u174113\nMEGDYTAFDSTQDASFGTMEVLLMERLNLQSYAREYKAHKNTLVCMFGQLAVMRFTGEVF\nTWIFNTLGNIAYTHTKYNIPPNTPQMYAGDDKAI\n>u174287\nYANDYTAYDQSQRGEVLASERMYFWQASIPEFIVDMYVTNKTEMYCSLGSLQTMRFSGEP\nPTYDFNGRCNLAVMNLQFPICENPDVAVFASGDDGGL\n>u174659\nTTNDYAGFDATQRGDSLGMEMRAMRHWGLDCAWIALFAQYARMADTIPELYEWWKLARVS\nDVIGPQRTARDTGEPGTYDFNTWFNLGILGLMYDIQPDTAVAVGGDDSAI\n>u174760\nTCNDFSEWDSCVRKAFYEFTCYLMKLMGAPDHIIDFYCRFRDEWTMKFDTQYGSAFLKGT\nEKQLSGNPFTICENTIWNMSLCFVIFEYKNLKFAAFKGDDSAV\n>u174847\nFTCDFTAYDQSCTEETLSFELAFMEYCGVPTSLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRSLACAFSGDDSLF\n>u175093\nVCGDDSLVVTNYFGQWMVFEGDASMFDQSESFGPLNFVNGIYLRLGVDLDVCLILQTLAS\nNSYIVRSRKEHHCLSINKKNRPLRDTGGADTSLGNSLVM\n>u175153\nAENDFSKFEGCQTPELLKDTELKIFLALYPKCYHQEIKLLFKHKLQKKIFSREGMKADLI\nGCRGSGDMDTGLGNTIVNLIACKYNYKRNKISGDQIVDGDDGVL\n>u175194\nVENDYTAYDQSQREECLYFERKVMRHFRVPDELIEQYVYQKVHCRHKYGDAAIMRFSGEP\nSTYTFNTWVNVAVLHCKFDLNGMAYGVSGDDSII\n>u175196\nTTSDYTAFDSSQKGDSLGLEYQLMLHFGLDWAWVELFGMFSEGLHHIPELYLFWKTHLES\nTVIGPKATGRDTGEPGTYDFNTYFNLALIQLMYEPLTGTPIAVGGDDMAA\n>u175416\nKNTDVNEFDSSNTDAQAEYDALNLERCRVPEVLIQMYKAQRHVWKLNCPDTIMVEGEQKQ\nHSGQPFTLIFNTATNMSWIGAMYDWDTIIAGGFKGDDSTL\n>u175827\nSAFDKSQQEASHFIKLHFYRMLGMPEALLRVWDYGHRAAICQARGCGVAFQMPFQHKSGD\nASTAIGNTIVNMASMAVVFEPRCFDYAAFLGDDNFL\n>u175994\nCMGDDKLIFGMGDFTEFDSTQNELMPELCTAYVQLFTGMPDSILATYVNQLSAWVVTVEG\nVLKIKNQNQKHSGEAATLLFNTIWN\n>u176211\nVGADFSEFDSSQEMQGILAGLMFYRLCGVPEEICQLYLQQRAKWALIAADKNTVSSMMMR\nAILYGLWKQHSGQPATLDGNTTFNMMAMGACYEFIGLVFASFKGDDSDA\n>u176306\nLEVDFSKFDKSQQRFCLETELYFMRKLGIHPALVDLWREIHTITSATCHANGIRARFLYQ\nRKTGDSYTCMGNTIISMHALAATFDLSDMICASFVGDDSLL\n>u176453\nLMADIQEFDSSQNSKALIATVLIMRALGMNEKIIRYYYKRRAEWIMHVKDNTSIVDIFAV\nLEGIFNQHSGQPFTLGGNTQYNMMIIGMCYRSEGLKCEAFKGDDSFI\n>u176492\nIEVDISKFDKSLLMWAFWYLRLLMIQFGVPEWIADLYYSVHLLTTMVDVQTGVKLETFCQ\nMKSGDPITFPGNSFITLGTLLYCLSDINDIHLMLFGGDDSLI\n>u176515\nIANDLKKQDKQTDENILEVEKLLYKELGVSSEIVEAYMGFHEQWRWYNPKVKGMGKYQRQ\nSGQVTTALGNLITNYQVNSDFVYKNRHDIILSLFLGDDSLF\n>u176934\nLEGDWTEFDSSQNNVEHELLMTQLEAIGCPAELRDLFMQMMLKRGVHCPFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETIDHVLFKGDDSLM\n>u176963\nLEGDWTEFDSSQNNVEHELLMMQLEAIGCPEELRDLFMLMMLKRGVHSSFASLQVQSKKD\nSGRVDTLIGNTSFNAGVMLTLVDLETISHVLFKGDDSLM\n>u176968\nCSGDDSIVAEFHPTHMVFWEGDASMFDSSQSKGPLKFQYLMMHCLGVDASITLSLYKVAH\nATLVVRPKKNDYDFDILRVDRSQRPHRDTGGADTYIGNTLVM\n>u177068\nARGDWETMDACQNRFTQQIERRLLHLAGFSHAFIEHYYWYRSGYTIAAGAVFAKGDTEKT\nSGEPGTLLFNTMINGAIGLWLVRGEGPMAVVLKGDDSMK\n>u177240\nSANDYTSWDSGCDEVFLTAFVVLLERLGVPAEYIDKLLVEETLLMAGSREFPIMQQSGNR\nWTWIRNTVWNAMLTGASLLVPRGTPAAFSGDDSAL\n>u178068\nVESDFSKFESTQQMDLLVHIELGVWKRLLNLEEYHIVERLFWLKMVKQGHCTHGVKFCFL\nFCRGSGDMDTGLFNTIINWIATRYFEYVNGMFKGQFLVDGDDNVM\n>u178116\nVACDISEQDTTKTEATHLVFRWLFEAIGVPSHTYDIVQQACIRWTGFGLDFSINNVETFQ\nSGINWTYLNNTVDSMARIGASFEVEGLRLAMFKGDDAYV\n>u178152\nLELDIGKFDKSQDETMLDAQCRLFKVFGMDEWAVELWRAFHELCKLSAPTWGVRFNVGFQ\nRRSGDPLTWLGNTLVLLIIVCQLYEIDKAYMVLLAGDDNVC\n>u178471\nMAGDDSLVFIYQSGRLAVIWEGDFSMYDQSQSWGPLFAEMAVLKALGVSEEARDLLLRSS\nLAKIVAKGKRGDKVAIRHLHRPMRVTGGADTTVGNTITG\n>u179034\nVENDFTEYDSSQNALTIEFESDILLLACHNQELVNLYKEHRTHWKTLQPGVLTMHGYAKK\nHSGEPFTLDFNTILNIAICGCIYDIDDLACAAFKGDDSFI\n>u179493\nTETDYTAFDQSQHAEYLHLQLNLMRHYEMPNHIIEFYFWLKTHSSCFLGVLNITLFTGED\nPTFLFNTITNIATQPVLFNFDPLAAQVYAGDDSAI\n>u179636\nTINDFSAFDSTQGGESLNMEIAMARHFSIPEELIHYYALWKSRQRSARIGVKAIARDTGE\nPGTFFFNTCYNVAVNTLKYGKITQPALFGGDDMAV\n>u179658\nLELDLSKFDKSQDLLCLLLDCKLMLLFGIDEFYVKFWYHIHVSTRLYNLRYSLVQYIPFQ\nRKSGDPSTYIGNTFITMCTVALYTDASQFDIALFSGDDSLC\n>u179866\nTQIDISKQDTSHTLLTLLVFCHILRYFGVPENLIDIYRVHSHRFRFKSLVPGLYGGEVTD\nNLGSGDPFTLIRNIFQVATKIVAAFDLNEAKASYWIIKGDDVET\n>u180021\nSTNDYTAFDQSQTGEALSFELMMLRAFGIPDGVIAYYTELKLELTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPSDTAIAIAGDDLAM\n>u180073\nAENDMKEYDTSQNEITIENEIKWLKRMGCNELFIKLFKKHRIEWKTNYPGYCQLIGYAKK\nHSGEPFTIDFNTLLCMALNGLLFPLEYFVFAAFKGDDSEI\n>u180321\nIEVDLSAFDKSQQEICHLLKESWYRLLGMPEHLLALWSKYHRVTHNKGIQSGITFVSTYQ\nHKSGDASTAFGNSLVTLTSLADCVDLGDFSTLFFIGDDVVV\n>u180382\nYENDLTKQDRQTRMFNIDCEYGMYKFLGCDEKILSVFKRTHDLWKFQYDAGSGICKEQRL\nTGQATTAIGNAINNLLAHWEFISSNWSTMEWMLFLGDDMLC\n>u181387\nVAGDDSLVLSGHTWYESDFSAFDQSQSTGPLEFEMAVLRRLGVPREIRTLLLATAKQPYI\nAKDKQRHWSMVVNHPKRPMRVTGGADTTIGNSIIT\n>u181462\nLELDIGKFDKSQDETMLDVQCKFFMLFGMEKWAVELWRVYHELCKLSSPTWGVRFNVGFQ\nRRSGDPLTWLGNTLVLLIILCQLYDLNKAHLVVLAGDDNLS\n>u181728\nTINDFSAFDSTQGGESLNMEIAMARHFSVPEELIHYYALWKSRQRSARIGVKAIARDTGE\nPGTFFFNTCYNVAVNTLKYGKITQPALFGGDDMAV\n>u181843\nLEVDFSKFDKSQQRFCLLTECFLMRKFGVAEELVRMWEIFHHASVATDYTAGIRARFIYQ\nRKTGDSYTCLGNTLMSMMALASVFQMEDLICASFIGDDSLL\n>u182030\nCMIDIRKQDSSHTISHVLLQTMLMEYVGMPADLVELYFSMRSHYRVRSKGSKLYQGTVSF\nNLPSGDPFTLIANCVQALASIVTRYDIAGRSMIMKGDDFIC\n>u182055\nSWNDFSAFDQGQDASFLAMEVRLMEQLSIPASEIAFYIHLKTHTFSNLGSFSIMRFTGEV\nFTFIFNTLANMAISNLRFVLDRSSKPLCFGGDDSCF\n>u182488\nHCTDVSEWDTKFRKIFTQLTDTLIRALGCPDWLATWFTLFRSKWRMYFLTKDGRVWLEGS\nEKQFSGNPFTICENTLGNMALFYTIFDIQKETAALFKGDDSAV\n>u182708\nFELDLSMCETTMRGPHLVLEGDVYRKLGVKKEDVDFLLTHKTSYGTSTKKNLKFTMPFCR\nESGTANTTPGNTTVFAVELWASLISVGLTEHDFVALIGGDDSAL\n>u182783\nVMIDIEKQDSSHSSVTLYTFYLFLVWFGVPEYVARCYLLLSSGYDVKSLNPRLYRAYVEF\nNLGSGDAFTLIRNIFQVLTTVVDRYEIEDDSIWIVKGDDVET\n>u182826\nCVTDGKMFDANQDEFTQMLEREVYLRLGASKPWVEWYMSHRADYPLITPYAYGKATTEKT\nSGEPFTLLGNTIVAALMSNYIYRGVGQCMLAIKGDDGWK\n>u182985\nAEGDFSEFDSTQNELMPEICVMVLQEFTGINSPLAHTYINHLKKWRVDIKGVGEIFGKHQ\nKHSGEAATLLFNTLWNAAWCSALFSVRGARVCAFKGDDSLI\n>u183619\nLINDYTAFDQGQNAQALYLEIRLMKRFGIPASFVNEYFESKVSAYSWLGSLAIMRFTGEF\nGTFLFNSLFNMAYANLKYDLAGVVCLFGGDDSAY\n>u184413\nTTNDFSAFDSTQQGDSVGLEWRVMRHFGLDEAWLQLFETYRGACATLPELYVQWKMTVES\nDLIGPKEVGRDTGEPGTYDFNCWFNAAVSHLKYAVPSGVAACIGGDDSAF\n>u184472\nLNNDYTQFDRSERGDALMFEIYLMHHFCLPIELINKYYELKCSFELFTIDNRRIGNLCTL\nRLSGEPSTFHFNSYYNLAVILTAYKIKSTKHVVMIAGDDSNI\n>u184537\nHCTDVSEWDTKFRKIFTQLTDTLITALGCPDWLATWFTLFRSKWRMYFLTKDGRVWLEGS\nEKQFSGNPFTICENTLGNMALFYTIFDIQKETAALFKGDDSAV\n>u185295\nHESDAKAFDQSQRGESLCFEARLMRRFSIPTEIIDAYVRDKTTYRCQFMLIATQRLTGEA\nFTWLFNTLFNIAYTYVRYDIRPTDPQAYGGDDNTV\n>u185386\nLESDFANNDGSQSVEFRRREAMFYAKHGAPAWFVREFARNTSVRVWTRYGIEPTVNGQRW\nSGETTTTTGNSYVGSVLLLACALLAGIEKSTHIHGGDDFMG\n>u185481\nTANDYTGWDTGVDLAFHHFHAWLLRRVGLGHRVDAYFHQAFNARTHLGPFPIQMPSGSAW\nTWDFNTADDFALTGASTNFPVGTPIAVAGDDSAV\n>u185563\nTANDYSAWDTSMDRVFLAFDCWLMEQYGLPPWYVDEYRFSRVMSRTFAGPYPIMQPSGDR\nWTLFLNSMRNLAVTGASVNFPAGTPIAVCGDDSVI\n>u185696\nTENDYTAWDSGVDGPFVRFLAWLMEQLSFPASYIAEWKEEKAATRFFGGNLQLMQHSGDR\nYTYLANTVCNLALSNAVYGGLGRVGQVYGGDDSLI\n>u185729\nFNSDFKEFDSHQSGGALSMEMLLMERFQIPQRYREMYLDLKLTMRGFVGEIAIMRFTGEF\nSTYLFNTIYNIAYCHMSFLILPGTPQLYSGDDSCL\n>u185987\nMMCDFTEFDSSQNEKAMIATVMMLKAMGLPSHILDHYLHRRKEWVLYVKNNTGVVDLTVY\nLDGIWNQHSGQPFTLGGNTQYNMSAIGMCYNFKDFQFAAFKGDDSVV\n>u186037\nYENDMTQIDRQTNEGLIETEFEIYNMLGVNPAILLIWKDIHRHWIARGKTVTGQFDWMRL\nTGQATTALGNVIVNMICHRFFINRNYGLLRKAFFLGDDSLF\n>u186070\nVENDFSEYDSSQNEATICWEASILSYFVVNPEIVQLYIEHRKQWRTNSPEIATFKGFVKK\nHSGEPFTIDFNTILNIAICGSIYDIDSMYFALFKGDDSLI\n>u186085\nVDNDYTAFDQSQDATALFLEIELMRHFNVPSDMIELYYWLKTESRSWLGPFGIMRFTGEW\nSTFLFNTLFSIAYSHTKYSFSPGMLQCYGGDDSSF\n>u186567\nLEIDFSKFDKSQARMCHLFEMFFWEQLGMDQYLNGLWRAGHYTTSALDFSTGVKAFFLYQ\nRKSGDAATAFGNTLVAMASLARAADVSGFATAMIVGDDSLL\n>u186732\nTASDYTGFDSTQKGDSLGLELRILLHCGLDLAWIDLMSQFLHIAQSLPEMYRWWKLHIES\nTVIGIKDTGRDTGEPGTYDFNTYFNLALIQLMYAPPKGTPIAVGGDDMVA\n>u186750\nTTNDYTAFDQSQTGEALALEQIILKVFRVPEHVISYYINLKLELTCQFGELAVMRFTGEG\nPTLCFNSWMNDAIIGVQYVIERDTPTAVCGDDAAI\n>u186944\nTENDYTAFDQSQKAEFVLFQVRIMEYFDIPSELIETFMKLKIEGHVDTGLLDFMILTGEW\nCTFLFNTLDNMAFTSLKYNVDPETPMAFGGDDSAI\n>u186998\nLENDFSKFDKSQNAFAYKLFCFIMEKLGFTQELLDIWIDANTDCTLKSMQLGVLLVSHYQ\nNKSGGPATALMNGVLNMCAVAYCYNGTQVEWATFMGDDSLI\n>u187051\nTCSDYTAFDTSQKGDSLGLEVLCMRQVGLGLASTELYADYHRLYGDEFTGILGLYTGWKV\nHVTSSVIGQKELGRDTGEPGTYDFNTIYNLALVELMYAPPPGTPIAVGGDDMAA\n>u187181\nVGIDWSGFDSCQNNAEHALSTWVMAEAGVPSFLSELFQNFRFKWTMISRNKFSVRGTSKK\nHSGEPGTLIFNTIFNMCVCDSMMQVDGFVFAAFRGDDSIL\n>u187380\nTINDYTQYDRSQRGETLAFEVQLMKFFSIPEGIIDFYVNLKCNIKTFIGTLRLLRNTGED\nGTFDFNTYMNIAYTETKFAPSEKNVAQIYGGDDMAI\n>u187403\nTENDYEAYDQSQTEEALDFELRLMRYFNIPEELLEFYVFLKTNAITNLGQLSIMRLTGEW\nCTFLFNTYYNIAYTALKFYDYHGKPEDMPPSAFGGDDMVV\n>u187422\nLENDFSKFDKSQDRFSYMLMQFIMTKLGFDDELLDRWIDANERCVLKLMALGILLVSRWQ\nNKSGGAATALMNVVVNVCATVTCYAGTDMVWAAFMGDDSIV\n>u187512\nIELDISKYDKSQGEAALIFECNVMRLLGVEERFVDHWQNFHKYALLTAKSEGLLEVKYSV\nNYQRKSGEANTFIGNTLLTLALLLYVYDYNEIYFLTVAGDDSVI\n>u187745\nLEGDFTAFDQSEDAAFVDFERRIMEDCSFPQHIIDDYLTLKASLSSRFGHLAVMRFTGEV\nWTFIFNTLANFSYTHLKYCIPPGTPQCYGGDDKVI\n>u187849\nSENDYTAYDQSQNEEFLNFERNLMEYLNIPRKIIQFYVENKLSLRSFMGTHQVMRGTGEG\nPTFDFNTYCNIAYDSMKFRNKKLPSLYAGDDMAK\n>u187934\nLEADVSKFDKSQEALCLMFFRTLAKRMGIHDQILDDWDSAHIHSKIVFPNLGIRANTMYQ\nRKSGDILTFIGNTIIVMMVTSLIVQKDEPEFYMFAGDDSLI\n>u187943\nTESDFTAFDQSQKGESVAFEALVMRHFSIPEEIIEAYEYDKTHYRCQFFEIAIQRLTGEA\nFTWLYNTMFNFVYTHIRYEITLDDPQMYGGDDMTV\n>u187953\nTTNDYTAFDQSQTGEALALEQIILQQFGIPDNVLEYYLSLKLNLTCQFGELAVMRFTGEG\nPTLKFNSDFNAAIVGCQYVFSPDTAIAVAGDDMAA\n>u187955\nTLNDFESFDTTQGAEFANLHVAIMRLFNIPERVIQFYLDLKVNCYTFLGPQAVTLFTGEP\nPTFLFNTLTNLAFLATFYNIKGTTIIVAGDDSAI\n>u188050\nVSGDDSLVAVRNGVDWDWYEADATMYDQSESIGPLLSEYRALRALGVTSDVVAILHQLAH\nARYVVRGEGWSLNIDRTARPMRDTGGADTSMGNSIVM\n>u188077\nYANDYTSFDQSQTGEVLDSELLYMWHAGIPESIVNVYRENKMNMSSFLGHLQTMRFSGEP\nATYAFNCRCNLAVLNLQFPLDQRKNVAVMVSGDDGGL\n>u188128\nAILDAEEFDSQQGPVTVYLERRFLEKLGFDAQDILDFQEVRRPERVVCPGQFKGRHNGEK\nGSGFLDTLSGNTTDILVLANGMFDGVGPKVVAAKGDDYLL\n>u188307\nLTCDFSEFDSSQEKQGILSSCIILKSMGFNDNIINFYYHKRASWTLINHDSEHNMPYHTI\nLNGVFMQHSGQPFTLDGNTMFNMSCIGMCYEFVNLIFASFKGDDSYV\n>u188712\nTDNDFERYDNSQDEGPLSFELNLMLCLNIDAELVELYKWLKLNAKCFLGNMAVARLTGEF\nSTFLFNTYVNVAYTHLRYDIPANVARAFAGDDSSI\n>u188730\nTYCDYSGWDTGVDESFTLAYASIMRSYGLSESVVERFIRDRHNRVSFLGPMPAMQASGDR\nYTWLNNTIGNMCLTGHSFKRVAGAPIAFSGDDMIA\n>u188809\nIEVDFSKFDKSQLMIALHLECYFMTKLGVPPVFIQIWRQMHEVKWLRSLVTEFRAKVVLQ\nRNSGDAFTFTGNTCVSMFALIYILLLIFGKKTLKYILRFAAFAGDDSIL\n>u188817\nVENDFSKFDKSQGWQSLYLVWGLYQLLGVNVPDLMRWVSGHQVTVACDLKVGLQVLLNLQ\nQKSGDVTTALGNSILNILTVADVYEFRDFLYAIFLGDDSIV\n>u188880\nLEGDFTAFDQSEDSSFLRFEEQLLRDCGFPEQLITDYRNDKQQLRCRLGPLATMRFTGEV\nWTFIFNTLANVAYTHCKYDIPSSSAQMFGGDDKVI\n>u188957\nVEIDHSKYDKSQQWTALRIEWFMYKKLGLDMDLCDVWKAGAVDCVMQSTQLGIKLWSILQ\nRRSGTATTALGNSMVTLFTLGASTDFPHGFYYVLFLGDDSLV\n>u189006\nSTCDFTEYYQSCTSSTLSFELLLLRWCGLPESLLAAYWEQKVSMRTQFGHSAIMRFTGEG\nPTYDFNTFFNIAYMALRYGLTSKDACCFSGDDSLV\n>u189080\nMSIDLSQQDSSHINVHRFFIAKVLAFLGFDDTVVTLYLMSRARRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSSGTTACTFDFAKFILFVGKGDDNTT\n>u189132\nQANDMSKFDKQQTEDHLNVERAIYEWFGVEPEFLNFYYDFHFNWILSSAQTQMYLNAMRI\nSGEPTTALGNAIVNLIIHSKLVVNNVSKLTWLLVVGDDIII\n>u189523\nFEIDFSKFDKSQLALCYEFENQMYQLLGMDPYLDNIWKMGHRKTSAMDFQTGIKALLFYQ\nRKSGDAATAFGNTLVSMASIARSTDIRGYVCAYFVGDDSLI\n>u189933\nLENDFAKFDKSQLEVVYWFEYYLFKSFGMDEDLLEIYLNANRTSRFYDAKHGVSANVNYQ\nRKSGGATTWLGNSLFTLCVLLCVYDIEDIIAMLVAGDDSFV\n>u189949\nFENDFTQFDSGQDECFLSMERCLMEWAQFPPELIDEYVSLKLHMNCFLGPVGTMRTTGEA\nFTYLFNTLANIAYTHLRYQIPPGTAQAYSGDDSGL\n>u190132\nCALPISAYDQSQRANVLAFEVLLLRYYNIPEFYLDLYVEMKLHLSRTGASFEEAELGTMR\nFSGEPATWAFNTRVNLAIAANKYFLLGRPIMLSGDDFLA\n>u190139\nQEGDFTAYDQSQKHEFLVFDAWLFRHLGVPERLVNDYLWFMTNLYTHLGELGCMMPSGCK\nMTLIMNSMRTLAYLTLRYQVKPGTPLMVSGDDSAI\n>u190154\nFTCDFTAYDQSCTEETLSFELAFMSYCGIPIDLIEIYKWIKLNMRTQFGFTAVMRFTGEF\nGTYDFNTFWNMAYMTLRYRFNPNMACCFSGDGSLF\n>u190214\nGTCDYSAFDQSQDISVLLFELKVYEAMGVPRALLERFKRWKMNLICQYGSLEVMRFTGES\nGTILGNTLANMALSNLERDLAGLRGVHSPCAFIGDDSVF\n>u190286\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELIALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKVARAFAGDDSLF\n>u190470\nVAGDDSLVGVWENGALRWYEADAGMFDQFESYGPLLSEYRALHKLGVPGRTTDLLFHLAH\nASYRVAGREHQWHATIDRSHRPMRDTGGADTSIGNSIVM\n>u190852\nVSTDWTEYDSTHNKVAALVFAEMLRKVGTPEWLIDYFMQRCGKRKLTSNSCTLTVNWMLD\nSGAVWTLAKNTLCSIGFLLATTMGVEYAFAKGDDSLL\n>u191019\nLSNDFTEFDSAQNNVEKHLIRIILTEIGCPAHVINHYENLRSRRLVCGSAARFVLHDKRD\nSGEPFTLIGNTAFNAAVVLRLVLGDVRFAIFKGDDSYV\n>u191031\nSEDDLSKQDKQTDQNLINCEFRVYQWLGADPSMLKMWRNVHNEWRGRGKHLTIYGDGMRL\nTGQATTSLGNAIINMLIHSQLVITLDSRLRVMLILGDDNLF\n>u191197\nLTADFSEFDSSQEMQGILAGATYFRLCGVPEHVIDMYLDQRRRWLMVAVDKDDSTMMRAM\nLEGAWKQHSGQPDTLNGNTTFNMAAMGACYNVENLQFASFKGDDSII\n>u191586\nLTADFSEFDSSQEMQGILAGATYFRMCGVPEHVIDMYLDQRRKWLMVAVDKDDSTMMRAM\nLEGAWKQHSGQPDTLNGNTTFNMAAMGACYDVENLQFASFKGDDSII\n>u191814\nTINDFSGFGASQKGESLHMDLLWLRWAHLPDAFVSKYIKLKTALHVSHTEVKDICRDDGE\nPGTFWFNCLFNLGVCVIRFGPDCFSRGLVLIAGDDMAC\n>u191820\nTYCDYSGWDTGVDESFTLAYAQIMRSYGLSDSVVERFIRDRHNRVSFLGPMPAMQASGDR\nYTWLNNTIGNMCLTGHSFKRVEGAPIAFSGDDMIA\n>u191953\nYSNDYTSFDQSQTGEVLASELLYMWHAGIPENVISIYENNKIDMFCAFGHLQTMRFSGEP\nATYAFNCRCNLAVLNLQFPLDVYSEVAVMVSGDDGGI\n>u192124\nYEDDYTGFDGTQNEDFLAFQVLLMRAFSIPEDLIFDYTNWVTHLSCMVGPLGIMIASGFK\nPTWFFNTVDSMAYQALKHELTPHREGSPRIARAFSGDDTLH\n>u192127\nTTNDYSEFDLSQRGEALSFEDHLLHHFSIPEDVIEYYLDLKVKLKCQYGDLAVLRHTGEG\nPTWAFNSFFNMAVCGLQYDMHANTPVAVSGDDLAI\n>u192151\nVEIDIRKYDKSQGEEALLFETELLIKFGVPLFFADLWYKCHAGVKVTDPTTGFGAELDVM\nRLSGDGGTYKGNTYFLMAVIAYLYCQVKQPIRAGVFSGDDSNL\n>u192210\nRTNDYTAFDQSQTGEALALEVKLCSAFGIPAEVLDYYLDLKLNLTCQFGDLAVMRFTGEG\nPTLLFNSVFNMALIGLQYELEVDTAIAVAGDDCAI\n>u192215\nCTTDVAEMDAMQCIVTQXVEKEMLRHLGFDEGFIAYYYQFRSDYPMTGKGTFSCKGGTEK\nTSGEPGTLLFNTIVSAVFSYFVIDGKGAFCMLMKGDDNAR\n>u192383\nVSGDDSVVITHNFGRPGMVIYEGDATMYDQSQSTGPLYYSREGQRSLGMDKETCKRLQKL\nSAAKYVAVSRDKQQPRRFIIYKDLRPMRDTGGSDTSLGNSTVM\n>u192388\nVSGDDSLVVFQDEAGVHILEGDASMYDQSQSLGPLHTEYAVLSLLGVSQHYLEMLSTLSA\nNTYNVRTKELLHKGFINRQHRPMRDSGGTDTSLGNSVIM\n>u192847\nIEVDISKFDKSLLMWAFWYLRLLMIQFGVPEWIADLYYSVHLLTTMVDVQTGVKLETFCQ\nMKSGDPITFPGNSFITLGTLLYCLSDIDDIRLMMFGGDDSLI\n>u192886\nFTADFSEFDSAQEQKGIMSSVVVLKSLGFNNDMLDFYLNMRSSWTLASNTKDSYGSYIFY\nLNNSWMQHSGQPFTLDGNTLFNMSSIGACYELKDLICASFKGDDSII\n>u193126\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELQALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u193306\nVGADFSEFDSSQEMQGILAGLMFYRLCGVPEEICQLYLQQRAKWALIAADKNAVSSMMMR\nAILYGLWKQHSGQPATLDGNTTFNMMAMGACYDFIGLVFASFKGDDSDA\n>u193329\nTCNDFSEWDASFRTPFAELTRRLLEYMGCTKAMNDWFFANRKNWTMSFVKGSERTTLKGF\nEKQFSGNPFTICENTLGNMALCFAIFEFIDMDFALFKGDDSCV\n>u193553\nMEIDFSKFDKSQEEIVLNSVCLLMLRLGVAKNEVDEWRRTHIINILVFSGVGMKITTQFQ\nRRSGDVLTFLGNVLVAMMAISYLHDLSSAIGGIFGGDDSLI\n>u193555\nFQADLSKQDSSHSAPLVLAFCAIAADAGCDASLMGLYAIHRSRFSFRSRTDDRTRGAATW\nSLPSGDPFTLIANDVMELCVIGCSLEDAPLMHIVEKGDDVHA\n>u193660\nGVTDFKMYDSQQDDFSQALERAFLRELGVGDEFLDHYFSFRKDGKLITGGIAGRLGTEKT\nSGEPMTLLGNSVISMLLANWLLRGEGEYVMAVKGDDGFK\n>u193765\nLENDFSKFDKSQMQECLLLEKVLYEFVGLAPNLLEYWIDSNVSGEVRSVAAGLRYWLSLQ\nRKSGTATTSIGNTLVNMATVALAYDLRPQDYVYAVFLGDDSLV\n>u193841\nVSGDDSLVIVWSETSNISVYEGDFGMFDQSQSVGPLTFEYAVLKRLGVPHDIVERMEGLA\nHATYLFRTRDKRSSAEVRVNLTRRPMRHTGGTDTTFGNTVVN\n>u193957\nTDNDYTAFDQSQDAAALFMEIQLMTHFNIPQHFIDFYFWLKTETYSWLGPFSIMRFTGEW\nSTFLFNTLFSIAYSFSKYDFPKDALLCFGGDDSSF\n>u194215\nIESDAKNNDGSQSKEFRKYEALWYRRHGAPLWFVQEFARNTSVTVWTRYGVQARVDGQRW\nSGESTTTTGNSYVHMALMLAAAEKASVVDSVHIHGGDDFLG\n>u194563\nASGIDSAALANKLYSLSASYVEDDISVWDSSLGEEFCKFELRVCKYFKVPRAVYQLCKAN\nIATHGISRFGHKYSVPGTRKSGDPYTSLFNTMIN\n>u194643\nVENDFSTFDATQKYEALNMIIDCFELANFPREIIHLMRQDIKYCKVTSRLGVSYAIGGAR\nLSGVTETLVGNTLLSLIVMYHVFEDSINGGIYKGDDSVI\n>u194702\nVENDYTQYDQSQREECLYFEVLLMKHFSVPEGLIDRYVHNKTHCRHKYGEAAIMRFSGEP\nGTYTFNTWVNIAVLCCKFRIDGFAFAVSGDDSLI\n>u194723\nVENDYTAYDQSQREECLYFERKVMRHFRIPEELIEQYVYQKVHCRHKYGDAAIMRFSGEP\nSTYTFNTWVNVAVLHCKFDLNGMPYGVSGDDSII\n>u194854\nFECDFTSFDSSQNEISVMLEIEIFERMCPELAGTELIEMYRQMRLNWVASNEYVKWHGSG\nVKCSGEPATLLGNTMVNMLIIISSFVFEGVRFCLFKGDDSLI\n>u194896\nTESDFTAFDQSQKGESVAFEALVMRHFSIPEEIIEAYEIDKTSYRCQFFEIAIQRLTGEA\nFTWLYNTMFNFVYTQIRYDISLEDPQMYGGDDMTV\n>u194958\nTVNDYTAYDQSQVGEALAFEICLLGFFGFPQDVIDYYVELKLALECQYGPLQTMRFTGEG\nPTWLFNSLFNAAVLGLQYELEPDQAVAISGDDMAI\n>u195134\nSWNDFTAYDQGQDASFLAMEVTLMEQLNIPRSEIDFYIWLKSNTFSRLGSFSIMRFTGEV\nFTFIFNTLANMAISNLRYHLDSSPAALCFGGDDSCF\n>u195175\nAVTDGADFDSMQNRFTQEIEREHSRFLGVPERFLDAYYELRNDYRMTQQGLFTAQCRSEK\nTSGEPGTLLYNSQLGGTVTDNAVQGIGPMTLDMQGDDAKK\n>u195398\nGENDYEAFDATQHVACRMLIIEMLVEHFGMAPEVARLMRAAAKEKFGHTLNGTFVSMEGT\nMASGHPDTYLTNTMMNILLQWYASACCGVFKPPIAAAGDDSVI\n>u195633\nLENDFSKYDKSQGEFATRLKGYLYQQLGFGPELVKRWMDAQESSVLVSMVLAIRLEIVDQ\nQKSGDGATAFANGALNVMSVSWAYKGTQVDAAVFVGDDSGV\n>u195675\nTGNDYTSWDQGCDTTILKLDEHIFRRCGLPDSFIASYLDRKLHSRSFPGLLAVMQNSGDR\nFTWPMNSLRNAVVTLTNLGYRPDVQYWFNGDDFVA\n>u196209\nLTADFSEFDSSQEMQGILAGATYFKLCGVPDHIVDMYLSQRRRWLMLAVDKDDSTIMRAM\nLEGVWKQHSGQPDTLNGNTTFNMAAMGACYNITDLQFASFKGDDSII\n>u196326\nSWNDFTAFDQGQDASFLAMEVRLMEQLSIPASEIAFYIHLKTHTFSNLGSFSIMRFTGEV\nFTFIFNTLANMAISNLRFVLDRSSKPLCFGGDDSCF\n>u196404\nVEVDYSKFDKSQGEAILLFECLLFNWLGMPQQFIEHHYRSHSESFVRCSTTGFSATTQYQ\nRKSGDPWTFHGNSIVTLATIVHALAGYSAVGVVAYGDDSIV\n>u197053\nLMLDFEQFDTSQNEKATMSSCIMLKNVGMPPHIVNYYLQRRSEWVLQVKDNTSADVDLIA\nFLEGEWNQHSGQPFTLSGNTQYNMSAIGMCYKIEDLVCAAFKGDDSFI\n>u197257\nFAGDDTFFMVNKRGHNYYGEIDFSKYDRTQGHHALCSAIRIENLLGIQANVCEAMFISYS\nSSSKYEEKSLNLKDKISMPIQRATGGPDTTIGNTINN\n>u198009\nLQIDLTRQDSTHRPSHVLAYAMFLEFCNVPREICDLYIMLRSMAYVKSLAEGLYKAIIKW\nNLGSGDPFTLNANCFMMKSTLAVRYTGLRYCAGIQKGDDFTC\n>u198111\nAVMDHKAYDATQNLFTQEIEKEVLRTMGVSEKYIQWYYHLRASYKLIGGCFIARVNFKKT\nSGEPGTLLYNSVLNAVLCNYIVRGSGPFILFIQGDDGSK\n>u198272\nLENDLEKQDRQTESQIINAEFALYYLLGADESMLAAYKKTHDYWKFTTDYSVGVGYEMRL\nSGEATTALGNAIVDLIIQTNEINDIQWMIFLGDDSVI\n>u198557\nSCNDFSEWDASFRKCFAKLTTNLILWMGCPQSLADFFEHYRSRWTMIYRHEYGTTSLKGE\nEKQFSGNPFTICENTIGNMALCYSLFKYEGVKLALFKGDDSAV\n>u199059\nYEDDLSKQDRQTDKQNIEFQQQMLILLGVHPQVVRLWSYTYSLWRFKSKQTWGWQMYQRA\nTGSALTALGNVLTNINVHADLIANNMANIRLVLCLGDDHCT\n>u199235\nLELDISKYDKSQEGVWLDAQCEVFKLLGMSDDMIELWRVFHEVCILTAPKFGVSYRVGFQ\nRRSGDALTWFGNTLVLLMLMAYLYPIENAIMVLLGGDDNLT\n>u199355\nLELDISKFDKSQDETMLDAQCKLFKLFGMQDWMIELWRSHHELCKLTSPTWGARYSVGFQ\nRRSGDPLTWFGNTLVLLMIMAYLYPIEKYHMTLLGGDDNLC\n>u199408\nLEIDLSKYDKSQQDNCFAVEMKIYNLLGFSDELFLQWKKGHELSFVKAFAGGIMFMLRLQ\nRRSGDAATWLGNTIVNMAAVCTAIDCRDVYFGLFSGDDSLL\n>u199607\nLENDFAKFDKSQLEVVYWFEYYLFKSFGMYEYLLEIYLNANRTSRFYDAKHGVSANVNYQ\nRKSGGATTWLGNSLFTLCVLLCVYDIEDIIAMLVAGDDSFV\n>u199853\nVEGDFSRYDGRQTTWCVDLNTRLMLRAYGPEEAETIRELRYKLSHALFTTGYGVKYDSAD\nSQKSGSATTSIDNTVTHAFCQFSHFRNIGYEPDQAYQAVGLCAGDDGLL\n>u199906\nTEFDTTQGEGAVVANAVTFRLFAMEESFIQEYFKMRAKWFMATVTPGARMILTGKFMQHS\nGQPATLDGNTLFDMQAVGACYEIKDLRFAAFKGDDSLV\n>u200266\nTTNDFTGFDSTQRGDSVGLEYRAMRHFNLQEAWVALFDWYRDQCQTVPDLYLDWKLTVES\nDLIGPKETGRDTGEPGTYDFNTWFNAAITQGKYDLPRTVASALGGDDGAQ\n>u200536\nLEIDLSKFDKSQGELALELELLFMQHFGVSELFLDIWRAQHTHTTLHSRSGRWSTNITYQ\nRKSGDGLTFWGNTIFSMCITAYLYRNSDIKVAMFAGDDSLI\n>u200537\nTESDFTLFDSSQNGRGVAFEELKMEYFRLPTVDIDFYVELKLTSESFLGTLPVMRFSGDV\nNTLLGNSDFTIAVMNLRFRIGCCIRLGRNVLHCGDDFAW\n>u201028\nVEIDHSKYDKSQQWTALRIEWFLYKKLGLDMDLCEVWKAGAVDCVMRSTQLGIKLWSILQ\nRRSGTATTALGNSMVTLFTLGASTDFPHGFYYVLFLGDDSLV\n>u201130\nHANDFTAYDQGQDGPFLFMETKLMEALSIPREYIDYYIWLKTHLNVRYGDVGIMRFTGEV\nFTFLFNSLANIAITNLRFVLGTSVCCFAGDDMAC\n>u201371\nVACDISEQDTTKSEATHLVFRWLFEAIGVPSHTYDIVQQACIRWTGFGLDFSINNVETFQ\nSGINWTYLNNTVDSMARIGASFEIEGLRLAMFKGDDAYV\n>u201383\nGENDYEAFDATQHVDCRLLIIEMLVEHFGMSVSVARYMRAAAKEKFGHTLNGTYVSMEGT\nMASGHPDTYLTNTMMNILLQWYASACCGVFKPPIAAAGDDSVI\n>u202287\nLENDFSKYDKSQSEMCVRLEQFVNDQLGFDINMMERWYKGHERSRIHSVQNALTLFIDWQ\nRRSGGGNTAFGNVTVNILTTAYVYKGSEVIAATYIGDDSLI\n>u202349\nYENDLEKXDRQTTKYITDVEMEIYKLCGMDWELVDFWSXVHDTFIIKGRFCRTIAKEMRT\nTGQATTSIGNFITNLXVHSDMILRNQDKLIIGLFLGDDMLL\n>u202366\nFCVDDCARKRLSKPLAMLNNLERDQDPSLRDNHTVLNFLKGQLINKLDTLTKFSESENIS\nVPTVKPAQMITTYTEEINAFFGPITRYLATKLRLSLPDDHVLFYGGYSLSDLDEWSRRHI\nPANLSQSFANDYTAYDKSCRGDSLQFEVCVMRFFNVPERYIDLHVDLTCHLNSALGHLGI\nMRTSGQWCTYLFNSWFN\n>u202733\nTINDFSAFGASQGGDSLAMDEKWFEWLGVLESMIQLHHRLKCNMQIGAFVKKICRDDGEP\nGTFFFNSVFNIGNCVCKFARAALWRGKWYFAGDDMAC\n>u203050\nLENDFSRFDSTQTPELLEMFYAFSERCGVPSDVADLMRQDLEGCKVKVKHNVTYVVRGCL\nLSGRSQTLLSNTIINMCVMIWALEDAFRMMVVKGDDSVV\n>u203051\nIEDDFSSFDATQSLGAHEAEMSFYRLFNPSKTVLTALQAQKRTVGVSKYYTYMCPYTRKS\nGDQNTSIGNTLINFVVHNYVIRKHYPGMRFWMMALGDDNLL\n>u203804\nFELDVSKYDKSQEAVWLEAQCIVFKLLGMCNQMIDLWRVLHEMCILTAPKFGATYRVGYQ\nRRSGDALTWFGNTLVLLMMMAYLYPIEEAIMVLLGGDDNVT\n>u204910\nTETDYTAWDSSIDAPFFRFDAWLMEQLGVPQWYIDLYLEEACRTKFFRGNMGLSQKSGNR\nYTFLFNSLRNLALTNHTYAGLTHVPQAYGGDDSLL\n>u205365\nIELDLSMCETTMRGPFLVLEGDIYRAFGLNLEDISYLLDHKTSFGKSGKKDLTFKMPFCR\nESGTANTTPGNTVVFAAMLYATLLLAGLGSSYFCLIGGDDACI\n>u205425\nGTNDYSAFDQSQTGEALSLEVVKMRVFNIPDHVIHYYEELKLTLTCQFGSLAVMRFTGEG\nPTLLFNSDFNTALIGCQYEMPPDTPLMVAGDDSAD\n>u205428\nTVNDFTKFGATQGGDSLQMDLQWFQWAGMSDASVELYRRIKLSLQALGGTKKTCRDDGEP\nGTYLFNCFYDLGITAERFGVEALWIGFWLIGGDDEAA\n>u205887\nVEDDLEKQDKQTDHWLLYLERLIYLICGLDPSVADWWFNMHNIWKCMSKKNYGLRILSRL\nTGQATTALGNLVVNTIVHSDLVLELGNRCLLMIMLGDDNLA\n>u206074\nYGSDVTRWDVGCDVAMVNFDVHVMRSLCFPTWYIDAYIERRVSSFSQHGTMKTMQNSGDR\nYTWILNSIRRAVVTSLVCAITPADTAAINGDDAAV\n>u206482\nLANDFSEFDSTQGVVTTKLEQKLWRHCGLPAHLVSLYGVLRASWRIKVPGVASVQNGDMR\nHSGEPFTLLGNTAVNMAVSGVIMQCQGFSFAGFKGDDSIV\n>u206583\nLQIDLTRQDSTHRPAHVLAYAMFLEFCNVPQEVCNLYVMMRSMAYVKSLAEGLYKAIIKW\nNLGSGDPFTLNANCFTMKSTMAVRYTGLEYCAGIQKGDDFIC\n>u206623\nEMCDIEGFDSSIRGADVTLERLLMTHFGVPTDHIDAYCEDKMDFHTRTIHFGIMRFSGEI\nFTWLFNTMHTLARECLKFGHKPGDPIAVSGDDILK\n>u206703\nTMSDCTGWDRGRGKPFLALDIHIMRQTGLPEGYVELYKDEKYGTSCYLGPLPVMQFSGDR\nWTFLFNSFSCLAFSMALFDCPDDAPIIVGGDDVII\n>u206971\nFTCDFTAYDQSCTEETLSFELCFMNFCGIPEDLIDLYRWIKLSMRTQFGFSAVMRFTGEF\nGTYDFNTFWNMAYMETRYHIPLNTACAFSGDDSLF\n>u207095\nGTCDYSAFDQSQDISVLLFELKVYEAMGVPRALLDRFKRWKMNLICQYGSLEVMRFTGES\nGTILGNTLANMALSNLERDLAGPRGVHSPCAFIGDDSVF\n>u207167\nTTNDYTSFDQSQTGETLSFERSLLDFFCIPGWLKDWYTESKMDLFCQYGHLQTMRFTGEG\nPTWLFNTLFNFALIFCQYNMSPSQPLAVSGDDMAI\n>u207186\nVMSDVSGFDSSVRGASVTNELRFMEHFGVPQDLRDAYKEDKMDFKTATIHFGIMRFSGEI\nFTFLFNTTHTMSREALKYRLMPGERMMGAGDDLLR\n>u207597\nIANDFTRFDSTQTNPLLNLIIECFELTNMPPEVIELLRRDVDVGTSVSTKFLDYVVRGVR\nMSGRGETLSGNTIANLIIVIYAFDDLIRMAIFKGDDAVL\n>u207755\nTACDMTGWDTGVDESFSLLYRRVFASFGVPESVCDAFVEARHSRRSFMGPMGAMQASGDR\nFTWLCNTIGNMAVTSLTFKLNPLQASSFSGDDMLL\n>u207921\nVRLDAAEMDSKQNEFTHYINRCFIERLCVSCEFLDLYFSMLEDYYVVNPEMKLHLRWVKP\nSGEPWTLLGNSFLMTALCLWLIIGDGPMALFTQGDDVDR\n>u208087\nAWNDFSAYDQGQDASFLAMETQLMECLGIPASEVSFYVWLKTNTFSRLGSFAIMRFTGEV\nFTFIFNSLANIAISNLRFVLTGERRAMAFGGDDSCF\n>u208109\nFTNDFTAYDQSCTGEAIWFIVKLLQWRGYPDEFVQLFFRLKTDLSTSFGHSAVMMFTGEP\nGTYIINSLYNLAYMSMKYELKGITLAVSGDDSIF\n>u208129\nLENDLSKQDRQTEDNTLKLEMEIYRQLGVNETILKWWSSVHMKWRYKYRTVKGWDESKRQ\nSGAVTTAIGNLITNLIVNKQMVSSAKMHNKFICGVLLGDDGLF\n>u208608\nVAGDDSLVAINSTKLQLLIEGDASMFDQSQSFPLLHDLWGLYEALGGTDEVISIFRRQAR\nATYQCRGLKVSRSKRSNRETGGADTTLGNTIVM\n>u208988\nTACDYTGWDTGVNESFSLLYREVFIRLGVPVHVADAFVETRHSRRSFLGPMPAMQASGDR\nYTWLCNTIGNMALTSASFNFPPDTPCCFSGDDMIL\n>u209007\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELMALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKIARAFAGDDSLF\n>u209248\nMMADFTEFDSSQEEKGILASNMVLKMCGFDEDILNFYMSMRSEWKLLSNASNDVSKMIII\nLEGEWMQHSGQPNTLDGNTQFNMAAIGMCYDFSEPDLSSFKGDDSLL\n>u209342\nVDNDFTEYDASQNSSTIEFETLILEDLGVVTEVIELYKERRSKWKTYYPGYASLEGRDKK\nHSGESFTIDFNTSLNMAICGYIYEFDLLVVAQFKGDDSNI\n>u209428\nVSGDDSMAVKRGGWQQKGRAFLRFGEGDFSAYDQSQRAHCLTAHAVWMTALGLPKLLIDL\nILWVCAMPYRARGKRVKVKGKAGCQLATGIDWTTVINSMSN\n>u209748\nGIVDGEEFDAGQTQGTLFAEMIHRRMSKISEKFIETYYKIREPGTFVYGGICSGQTRYEK\nGSGFPDTLLGNTTLEEIIGHNAIVGEGPRVLGVKGDDFFK\n>u210032\nWESDLEQQEKSMSGAYVTLFSKVLEHFGVPRDIIEAYIDDKLDKRTARMHLGLMTFSGEI\nFTFLANTLGNMARIAAKYDLKPAERGKFGGDDSLC\n>u210280\nMEIDFSKFDKSQEEIVLNSVCLLMLRLGVSKKDVDEWRRTHIINILVFSGVGIKITTQFQ\nRRSGDVLTFLGNVLVAMMAISYLHDLSSAIGGIFGGDDSLI\n>u210345\nLEVDFSKYDKSQELFCLKLFLEILRRFDVPEKYLVDWERYHISNVIKFKREGVKTKVEYQ\nRRSGDVFTFIGNTLVAMCCIVWSYKDIISQAAGGVFGGDDSLV\n>u210412\nSTCDFTEYDQSCTSSTLSFELLLLRWCGLPESLLAAYWEQKVSMRTQFGHSAIMRFTGEG\nPTYDFNTFFNMAYMALRYGLTSKDACCFSGDDSLV\n>u210621\nYTCDFTAYDQSCTAETVTFELALFHWAGITQEDPRLAEAYLDIKMTMHTQIGPSAVMRFT\nGEFGTYDFNTFWNIAYMSLRFVLRPSRAAAFSGDDSLF\n>u210673\nTCNDYSKYDQSQNEQFLAFEILLMKFLHIPEPLISLYANIKMNTKYFAGILDIMRITGEK\nFTFLFNTYANIAHTELKYNTSHLSIPEVYGGDDMAI\n>u210693\nFSNDFKAYDQSQDQKVLAFEVRLMKFLDIPKEIIDEYVYIKLNSKAFTGPLQTMRFTGEW\nCTLIFNTFMNMAYMNLKYKIPKGMPCAFAGDDSIF\n>u210796\nLEVDFSKFDKSQTEVCFEIEMAFWELLGMDEALLQLWRLGHFSVSATDFRAGIKAFLHYQ\nRKSGDSATAFGNTIISMSSLAYAACFSEVEAAYFVGDDSLV\n>u210806\nTEDDYTAYDQSQDESFLHLDVLMMTRLGMPQHFIDDHVWLMTHCTSWAGPCAVGGKSGEQ\nLTWARNTHHSLAYQALKYRIVPGTPIMASGDDVAL\n>u210854\nTDADHTQFDCTQGNGLARLQEAVYNRMGFPRRTTAWLLAMRAKYHASALDASTMAYCTFD\nFMWQMTSGALYTLTWNTVANMAITGACYHFGDIALAAFKGDDVHI\n>u211157\nIESDMKNNDGSQSVEYRRYEAMFYKKLGAPTWFVKEFAKNKEVRIWTRFGIEAKVVGQRW\nSGESTTTTGNSFVSMCIMLAALHASGVKESLNVHGGDDYLG\n>u211251\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELLALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPQVARAFAGDDSLF\n>u211275\nLELDMSKFDKSQGSMHLKTECMILKHFGMSDELLDLYYLSTLVTKNVDPISGITLLMGPI\nRKTGGWDTFDGNTIVTMAAIAHRTHGIGQADLLYFGGDDSTI\n>u211298\nTANDYTAFDASQGYDSVLLECHVMRLAGLPDHLVDSYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLNCLALFGGDDSAI\n>u211533\nVSGDDSLVIKNHNGALTIFEADASAFDQSQSTGPLNFENEALTSLGAEPVLLECLDALSH\nAPYLVKFKQGARKILHNKRPMRITGGADTSLGNSAIM\n>u211707\nVENGYTAYDQSQREECLYFERKVMRHFRIPDELIEQYVYQKVHCKHKYGDAAIMRFSGEP\nSTYTFNTWVNVAVLHCKFDLNGMAYGVSGDDSII\n>u211785\nTVNDYTAYDQSQTGEALAFELALNNMFGLPHHVSQYYFELKVDLSCAFGHLAVMRFTGEG\nPTLRANSDFNAAVIGLQYVFGPDLAIAVAGDDSAI\n>u211832\nTENDYEAYDQSQTEEALDFELRLMRYFNIPEEYLEYYVFLKSNAITNLGQLSIMRLTGEW\nCTFLFNTYYNIAYTALKFLEFQGDSSEI\n>u211846\nMSIDLSQQDSSHINVHRYFIAKVLAFLGFDDTIVTLYLMSRARRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNFLMSTGTTASTFDLSKFVVFLGKGDDNTI\n>u211852\nGTTDVKEMDSIQDLFTQEIEKEMLRELGCSELFIAEYYSYRSKYPIVCRGVFSGKGEGEK\nTSGEPGTLLFNSVLAAVFTNAIFRGIGISVLLFKGDDVIK\n>u211955\nTETDYTSWDSGVDAPFFKFDAWLMSQLGVPQWYIDTYLDEACTTDSFRGVLALGQRSGNR\nYTFLFNTLRNLALTNHTYSGLSRVAQAYGGDDSLL\n>u212002\nTTNDYTAFDQSQTGEALALEQIILKVFKVPEHVISYYITLKLELTCQFGELAVMRFTGEG\nPTLCFNSWMNDAIIGVQYVIERDTPTAVCGDDAAI\n>u212089\nYSNDYTSFDQSQTGEVLSSELLYMWHSGIPESIIKIYEENKVDMNCAFGHLQTMRFSGEP\nATYAFNCRCNLAILNLQFPLDRNSDVAVFVSGDDGGI\n>u212094\nTYCDYSGWDTGVDESFTLAYASIMRSYGLSQSVVERFVRDRHNRVSFLGPMPAMQASGDR\nYTWLNNTIGNMCLTGHSFKRVAGAPIAFSGDDMIA\n>u212257\nTYTDYTGWDTGVDESFTILYSETMIRFGIPAHVAKKFAQDRHSRRSFMGPMPAMQASGDR\nYTWLNNTIGNMALTGISFDIRPDTVAAFSGDDMIL\n>u212328\nVENDFTEYDSSQTELSINFEADILKFAVHNEEIVELYKEHRTNWKTNTPGLLTMKGYAKK\nHSGEPFTIDFNTILNIAICGSIYNIDNLSCALFKGDDSLI\n>u212329\nIFNDYSKFESAQQPELLCDIELTLWGELLSGTHLDIIKSIFSIKMEKKGTTPHGVGFSFT\nGCRGSGDADTGLGNSLVNYVACRYFEIINGLGTEDFVVDGDDSVI\n>u212387\nLENDFSKFDKSQNAFAYKLFCFIMEKLGFTQELLDIWTDANTDCTLKSMQLGVLLVSHYQ\nNKSGGPATALMNGVLNMCAVAYCYNGTQVEWATFMGDDSLI\n>u212416\nTSNDFSEFDQSQTGDALSLEMVMMDAYHIPEPLRDYYFSLKTHLRCSLGPLATMRHTGEG\nPTWFFNTMFNCAVTGLRYGPCADKARCFAGDDSSI\n>u212444\nFESDISGFDSGQDHNPLRMELELMHFFNVPKKLIDFYEKTKISTTLGKHILAIARDSGEL\nFTWLFNTMHTIARRHCKSLVPRGTPQGYGGDDEVH\n>u212493\nLEMDMGKFDKSQGLTSLLFECKLFSYAGLPDWLVRLWYISHFHAKVHGFGTSLRTQLPHQ\nRRSGDPWTYGGNTFFLLAILSEVCASNGRFYMVSGDDSLV\n>u212630\nTSNDFSEFDQSQTGDALSLEMVMMSAYDIPDSITDYYFSLKTRLRTSLGPLATMRHTGEG\nPTWFFNTMFNCAVTGLRYGHLGDKARCFAGDDSCI\n>u212639\nTSNDFSEFDQSQTGDALSLEMVMMSAYDIPDSITDYYFSLKTRLRTSLGPLATMRHTGEG\nPTSFFNTMFNCAVTGLRYGHLGDKARCFAGDDSCI\n>u212706\nSWNDFTAFDQGQDGAFLSMEVQLMRALNIPVKEIDFYIWLKTNTWSRLGSFSIMRFTGEV\nFTFIFNTLANISISFLRYHIRLIPCCFGGDDSCF\n>u212812\nVSGDDSMAVKRGGCQQKGRAFLRFGEGDFSAYDQSQRAHCLTAHAVWMTALGLPKLLIDL\nILWVCSMPYRARGKRVKVKGKAGCQLATGIDWTTVINSMSN\n>u212890\nYVSDMTKFDSSQRGEWVAMELALMRLMNFDKSVLEEYSWLKTHTAAFPGWLRIMRFTGEA\nFTFIFNTLVTISHGALKYHLDPSVARCNAGDDEAY\n>u213106\nTESDFTAFDQSQKGESVAFETLVMRHFSIPEEIIEAYEIDKTSYRCQFFEIAIQRLTGEA\nFTWLYNTMFNFVYTQIRYDISLDDPQMYGGDDMTV\n>u213363\nIANDYTAFDASQGYDSVLLECHVMRLAGLPDHLVDRYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLPCLALFGGDDSAI\n>u213480\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPTSLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYRIPRDLACAFSGDDSLF\n>u213944\nLENDFSKFDKSQQWTIIMIEYLLYQMLGLDVLDEDLWESGHIITEGTAFAAGLKVFILLQ\nRKSGDVTTATGNTISNEITVCVIYVLPDGFFYSCSLGDDIVI\n>u213996\nLELDMGKFDKSQGLTALLFDCELFVRAGMPRWMVNLWFLSHIIARVKGFGTSLRTVIPHQ\nRRSGDPWTYGGNTFFLLAVLKYYCGDRINYIMVSGDDSLV\n>u214122\nSTCDFTQYDMSCKAETLSFEMCLFSYFELDVQFPDLTELYLFIKTHMYTQFGPSAIMRFT\nGEFGTYDFNTWYNIAYMAFRYELDVRAPTDGAAFSGDDSIM\n>u214219\nQEIDFSKYDKSQEEVILDIQCQIMRRMKVPEETVQAWFDMHTSNTLVFHRYGLAIRTKFQ\nRRSGDALTFIGNTIVTMAVLAYTNNFNDAYGGVFGGDDALT\n>u214237\nFTCDFTAYDQSCTGETVIFELSWMRSCGVPEWVLDLYVKIKVDLTHNFGHSAVMRFTGEA\nSTFAFNTAFNMAYMRLRFVIGETSPCCFSGDDSAF\n>u214318\nFTCDFTAYDQSCTSEVLGFELAFMDYCRIPQELMALYEEIKIDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPNVARAFAGDDSLF\n>u214416\nYENDFKSYDKSQHTACLALELEVYRSLGVPYRVVELWDEAHSKTTGTVRNEQLGIKIELE\nTQKRSGEVTTALGNTIVNLLSVNAVYDFKDAIFQAALGDDHIA\n>u214682\nTATDYTMWDKGCDASFLHFDVLLMERAGLPTWFRDQYVERKLGTHIGRRTLPIMQISGDR\nWTWLLNTLRNLAFTNLRFRDLSECAQAYSGDDSAI\n>u214719\nMIGDFPMYDSSQNGFTQQIERALWRSGGVSDLFLDAYFDHREKYTIQSDCVRGDIKYIKG\nSGFSDTLTGNSGLTAVLNNYIARGAGPCTIVIKGDDFNK\n>u214762\nTCEDFENFDQSQRAEIVAMEILLLKFYNLPQEYIDFYLTFKTHFETYIGNMATSRFTGEP\nPTFDFNTYATIAYTHTKFHMPPNTPQCYGGDDSAR\n>u215002\nTELDITALDSSERGGSLQLEVEIMEHFTTDPNLVRDYVDDKFSFHTDTIHFGLMRFSGEI\nFTFLFNTLFMLARTLCKYAIPRGTPMKVAGDDILL\n>u215152\nSWNDFSKFDKGQNAAVLAAEIRFMECIDLPREEIEFYTWLKTHVFSRLGSFAIMRFTGEL\nFTFIFNTLFNIMVAELAFGISRFKFAMFFAGDDSCF\n>u215181\nGITDYTMYDSQQDDFTQCIEKEFLRRLKISDEYIDIYYRYRKNYKIISDNIYGKCGTEKT\nSGEPATLLMNSIIAMVITNYIFRGEGPSVMAAKGDDGFK\n>u215610\nMEIDFKKFDKCQHSLLFKFEIELYRRFGMPEWMIDIWIASHEQTRLKSYATGVKVSVNYQ\nRKSGDPATLLGNTLVSMGMVCLMYDFDFGMFVGDDVSL\n>u216443\nVECDFSKFDKTQTPVILEMEYAVYEMLGLDTRIIDEWRKCHEYTTARNVATGVKLTTVGQ\nRKTGDVATALGNTIANMCTLAMVLPMQRMVAGLFSGDDSAF\n>u216491\nTSIDYTAWDSSLDEPFLRLNAHILEFVGVPSPYIEKFLDERLNTRSFLGPMPLMQFSGDR\nYTWLFNTLSNVSLAHAAFENASTTTLGVSGDDIIL\n>u216530\nLELDISKFDKSQDETMLDAQCKIFKIFGMDEWLIELWRAFHELSKLTFPTWGARFTVGYQ\nRRSGDALTWFGNTLVLLMILAYLYPIEKSYMSILGGDDNIT\n>u216980\nTTNDYTAFDLSQRGEAMAVEVLYLKYEDFPDWIVEYYVYLKTNMSCQYGDLAVLRHTGEG\nPTWFFNCVFNISVSGLQYELGPDQPMAISGDDEAI\n>u217251\nIEIDFSKFDKSQQLFCHNLEMGFLGLLGFDQEWLDLWKFAHQDTTAQDFKCGVRIRTQYQ\nRKTGDSATAFSNTLISVFSIARCMNLSDLCAAYFVGDDSLI\n>u217567\nIEMDFSKFDKSCTPYTVLLEEKWMERLKAPKEYIDAWRKTHTNTKLKSREYGFKIDGGSX\nRKSGDPATFLFNTMVTMITLAGSYDLKQFKCGLFGGDDSLL\n>u218054\nLCLRVGKYDKSQEAVWLDAQCIVFKLLGMCDQMIDLWRVLHEMCILTAPKFGATYRVGYQ\nRRSGDALTWFGNTLVLLMMMAYLYPIEKAHMVLLGGDDNVT\n>u218155\nTETDFTEFDCNQDSLTLEAECYMMTIYGLPPAVVWLYRQMRTCWRLSARNCAQVFGQYGQ\nHSGQPATLHGNSFVSMFLISNVVDVDRDSVMLFKGDDCLI\n>u218731\nVSGDDSLVAVWNGADWDWYEADATMYDQSESLGPLLSEYRALAALGVTSDVVAILHQLAH\nAKYVVRGEGWSLNIDRTARPMRDTGGADTSMGNSIVM\n>u219003\nPXRDWTEFDSSQNNIEHLLFAKCMRALGCPQRLLLRFVDMMRSRYVQSRYGSVNVRNKKD\nSGRVDTLIGNTIFNATVLLSCFELDSLTAVFFKGDDSLL\n>u219062\nLSSIYSEGDTSISTFLDGIWKQHSGQPFTLDGNTMFNMMAIGMCYDWIQLDAASFKGDDS\nAL\n>u219257\nTACDYTGWDTGVDEGFTLLYADVFRAFGVPWSIVDDFKDARHGRRSFLGPMPAMQASGDR\nYTWLCNTIGNMALTAATFDLTPTTPCCFSGDDMIL\n>u219348\nFENDYEKFDKQTDEVDVELEFELYKRLGLSDNIINVWRAIYKNIKIISHQFSMKLPTMRL\nSGAPDTALGNTIVNFFAMIYMCKTYKNSLNRLYTMGDDMTS\n>u219445\nVDNDFTEYDASQNSSTIEFETCILEDLGLTDECIDLYRNHRSQWKTYYPSYASFEGVEKK\nHSGEPFTIDFNTSLNMAICGYIYDFDDLVV\n>u219456\nFACDFAEYDSSQYAMSPMANAVFMSLLGAHRNIIDLYIDMRTNWRLNDDMMKLYGNQKMH\nSGEPFTLVGNTLFNMLIIANCVEFDHLVFASFKGDDSAI\n>u219596\nSEQDTTKTEATHLVFRWLFEAIGVPSHTYDIVQQACIRWTGFGLDFSINNVETFQSGINW\nTYLNNTVDSMARIGASFEIEGLRLAMFKGDDAYV\n>u220044\nFENDWAEFDSSQNNLEHELFCCVMLQLGCPPRLVSLFKAMMYQRYVAANIGALSVLNKKD\nSGRVDTLIGNTLFNSSVLLSMIPNWRELLVVVKGDDSVI\n>u220357\nCEDDFSKQDRQTSDDTLRIELNTWALLGLHPDLVRWLSTLHSKWFYKFKEMWGFEKGKRK\nTGSVFTALGNWHTNLLVHADYYKKYRYVINFVLFLGDDYLV\n>u220572\nGENDYEAFDATQHVACRLLIIEMLVTHFGMRPEVARLMRAAAEEKFGHTTNGTYVSMEGT\nMASGHPDTYLTNTMMNILLQWYASECCGVLMPPIAAAGDDSVI\n>u220598\nSWNDFTAYDQGQDASFLRLELTLMERLCLPQDVIDYYSWLKTSTFSRLGSFAIMRFTGEV\nFTFIFNSLANIAVSSMRYYFAPGRACMFGGDDSCF\n>u221597\nTCNDFSEWDASWRGCFTEFTCTLLLYMGCPKPLVEDYKRFRDDWIMTYMTAFGNVTLSGR\nEKQFSGNPFTICENTLGNMALCFSIFEVRDMQYAMFKGDDSVI\n>u221605\nIENDFEKYDKSQHITAVKLKNYVYKRFGLNDIDHDTWEYGSELTHAIAFDTGISFTYCFQ\nMRSGMSDTAIGNTVINAISVAYSYKIKVYIFAVFLGDDSII\n>u221695\nLELDISKFDKSQDETMLDAKCKLFKLFGMQDWMIELWRSHHELCKLTSPKWGARYSVGFQ\nRRSGDPLTWFGNTLVLLMIMAYLYPIEKYYMTLLGGDDNLC\n>u221738\nTETDYTSWDSSVDGPFIKFDCWLLHQMGAPAEYIASYQEEACSTRLFRGNLRLMQHSGNR\nYTFLLNTLRVLALTQATYQRLRFVPQAYGGDDSLI\n>u221746\nSTCDFTQYDMSCKAETLSFEMCLFSYFELDIQFPDLTELYLFIKTHMYTQFGPSAIMRFT\nGEFGTYDFNTWYNIAYMAFRYELDVRAPTGGAAFSGDDSIM\n>u221905\nMCADFSEFDLSQEAQGILSSIIILKICGYKTPIIDFYLAMRAKWTLFARSTNNNEILTMY\nLSGHNMQHSGQPFTLDGNTIFNMACMGMCYIYDDLICAAFKGDDSFI\n>u222360\nYEDDFSAYDSSQGAGAHAAEMAVYKLFGPDEVVLNALSNQQRTVGYGKYHRYKAKYTRKS\nGDQNTSIGNTIINMMAHVWAISKYNVGRKQKVEFKMLALGDDNLL\n>u222473\nGVTDFTMYDSQQDEFTQLIEKTYLRKIGVDEGFIEHYFSFRRDYQIICGGIKGKAGTEKT\nSGEPGTLFFNSIINAVCLNYILVGEGPFAMAFKGDDGYK\n>u222732\nVSGDDSLVVDHRFGHSRFFEGDASMYDQSLSIGPLESEYMALAKLGVPCETLEQLRTIAR\nAPFILYDKKRTRYLKITKVGHPIRDTGGADTSVGNSYVM\n>u223687\nLENDFSSFDATQNQCALGMVYDYYEMCGMPTNVVDMMRRDTFNGCKITTSVGISFHQRNS\nRISGRGDTLFGNTILSFVAMNYSTAGKVKRIIAKGDDSVM\n>u223759\nTTNDFTQFDCSQGAEALWREIHVMRLFSIPEWLIALYVHQKLTFTHQFWISLIIRFTGEP\nGTYRFNTDFSAAQLQLQYNLPPGTACVISGDDILI\n>u224100\nAENDCTEFDASQNNVSIAFDSIMLSSTGVSQLFIDLYVSHRTDWSTIYQSYAKFYGTCKK\nHSGEPATIDFNSALVLAINGALYDFQELVTAGFKGDDIYI\n>u224337\nSTCDFTKYDMSCKAETLSFELCLFSYFGLDVIFPDLVNDYFFIKTHMYTQLGTSGIMRFT\nGEFGTYDFNSWYNIAYMAFRFKLNPLDTRGSAFSGDDRSE\n>u224567\nYFSDDSCFSFLHKGVVHRYNVDISKCDASHGPGIFEALECITPTEHRDDMHILTEQCKLP\nIRIVSTFDKSQKVVGRFKGARLYSGSTITTIINNLAN\n>u224669\nSTNDYTAFDQSQTGEAVALEMVALRARNIPDHVIEYYINLKLELSCQFGELAIMRFTGEG\nPTLKFNSDFNAALIGVQYIVEPDDARCVAGDDMAI\n>u224706\nQEDDFTAFDQSQTAEFLAMETLLMQHLNIPEEYITFYTWLKTHCKCQYGDLAIMRFTGEW\nCTFLFNTLANIAYQHTKYVIPPNTAQVYGGDDSAI\n>u225135\nVENDFTEWDRFNTEPNIRFGAHLLSYVGLPPEFEDFYVQHRMYWKTKCVNVITLHGEVKQ\nHSGQSLTLLDNTNNNMALSGILFEIVKLYVAGFKGDDDSI\n>u225565\nVGGDDSLVVLDFPGQPLLLVEGDASMHDQSQSMGPLLHEMKLLRFLGVTSEVIRVLMQNT\nFAAYKLRYPTCEGGVRIEHPSRPMRPTGGPETSLGNSITM\n>u225698\nLENDFSKFDKSQDEFSFKVFMYIMQNLGFDQELLDRWVESNRDVTMRSMILGIILKASWG\nNKSGGPATALQNVALNLAAVCTCYPGTQIVWAVFMGDDSIV\n>u226007\nVDGDATSFDSRQNHLVIAAEFLIYTMLGIDHGALALYKTCHDHWYLKGKGVTGTFNAMRI\nSGQATTALGNVIVNMLIHADFVIANRSALSLGMFVGDDNLF\n>u226057\nATTDVKEMDSIQDLFTQEIERCMLRALGCSDLFIEEYFTYRSKYPILCRGVFAAFGEAEK\nTSGEPGTLLFNSTLSAVFTNFIIRGVGLCILLFKGDDVIK\n>u226064\nIQMDVKKQDSSHCCSHVVALCILSEYCGVPKATIDTYFEMRSCLTVKSQVPNLYRGTISW\nNLPSGDPFTLLANCFQALCTLALKYREMPIVCGIQKGDDVLL\n>u226068\nFEADISQFDKSQDQLALAIEMAVYRKLGLDPEWAMRWEGAMFETRNICHAVGITIYLMHQ\nRKSGSVTTSIGNTIVSMVACAYPNSLDADNVKAAMFLGDDSLI\n>u226071\nLELDCSKFDKSQGKVLLMFQELLWRKLGLDPHMGGIWNEAHRLTFISDFLNGVMFSVNYQ\nRKSGDATTYMGNTLVTMAMIAYLYPIERALFSVFGGDDSLV\n>u226084\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELMALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPRVARAFAGDDSLF\n>u226568\nMERDLEKQDRQTDKQDLNIEYILYDLLGVHKTTLSLYRKTHSNWRMKSGPLRAFGDGMRM\nTGQATTALGNVEVNLMVHSRWAERNLHQLHRVYILGDDFIG\n>u226854\nVENDFSKYDKSQQWTCLRMEWEVYALLGMDPEMLTDWRAGHVECNASSISAGVKIFSLLQ\nRRSGDATTALGNTIVNMLTVAATYSLRGYHYAMFLGDDSVV\n>u227008\nTCNDFSEWDASFRTPFVKLTSWLLIASGCPRPLVNTYEKFRENWTMQYRTIWGFASLDGF\nEKQFSGNPFTICENTIGNMALCFSLFEYKDFQFAYFKGDDSAV\n>u227331\nLTCDFSEFDSSQEKQGILSSCMILKFMGFEKDTINFYMARRSNWTLINQDESNNIPVKTL\nLDGKFMQHSGQPFTLDGNTMFNMSCMGMCFEITDLVFASFKGDDSYI\n>u227354\nDLNDFSEFDTSQEQKTVVSSCITLRMMGANPSVLDYYRDLRSKWVLSSYNEVDNMDIMQT\nLEGVWLQHSGQPFTLDGNTQFNMSAIGMCYDIKGMILASFKGDDSAI\n>u227494\nTATDFTAFDQGQTCDFLAFELKLLQFFGIPRAFIDFYEHLKLQSFCYAGALPVMRFTGEA\nGTFLFNTLGNMAYHALMYNWPLSAACAFTGDDSAI\n>u227794\nRVREHPKFDKSQDEVILEFNCHLMTMLGVPEHVVVEWRRCHMNTSLVFHKFGVRVKTLYQ\nRKSGDVFTFMGNTVTAMAVLAYTYSLDESLVGVFGGDDSLI\n>u228563\nSCNDFSEWDASFRTPFSKITSMLLEFMGAPNDIIRDFEEYRKSWSMIYRNKHGLTKLRGH\nEKQFSGNPFTICENTICNMALCFTIFDYKDMKMALFKGDDSAV\n>u228737\nLEIDLSKFDKSQGPMFLEFELMVYKYFGVSEEFIDLWRNARTETKLIDRLHKLIAFIMFQ\nRKSGAADTYIGNTIVTMGIIAALYIVEQCALAMFAGDDSGL\n>u228762\nLENDFSSYDKTQTDTTFQIEYALWRTLGVDPGLLQYWIDGHIDTYVVSSTLGVRIMLQYQ\nRKSGDVTTSLGNTVVNMMTVCAVYDVIMFKYAVFSGDDSLI\n>u228785\nTCNDFSEWDASFRKPFAGITQTLLEFMGAPRDLVEYYGKFRANWVMRYQYAHGSASLRGT\nEKQFSGNPFTIAENTICNMAMCYTMFDYRGLELAMFKGDDSAI\n>u229127\nLENDYTKFDQSQKAEFVHFQIHLLEYLNIPKYLIKMFVELKLGYHDDKSTIDFMILTGAF\nYTYIFNTLDNMAFAATKYAIPIETPQCYSGDDSVI\n>u229338\nAITDMTAFDSLQNRFTQQIERNILSAMGITPNFIEHYYSFRNEYRIISGYSVHKAKSEKT\nSGEPGTLPLNTLLSSALTHYIIEGEGDFVLVGKGDDGFK\n>u229459\nTACDYTGWDTGVDEAFSVFYRELFIRFGVPVHIADDFLADRHARRSFLGPMPAMQASGDR\nYTWLNNTIGNMALTALVFNPPAHAPACFSGDDMLL\n>u229604\nVETDYSAWDSSIDAPFIKFDCWLMQQVGFPPSYISTYHQEACCTMSMKGNLRLMQHSGNR\nYTFLLNTLRNLALTQHTYQNIAHIPQAYGGDDSLL\n>u229683\nVALDHSKYDKSQGRVAKYCEMRFYCDYLGLCPDLVDEWFTGQYGAELSSSAVGVRLFIEL\nQRRTGDATTALGNTILNFISFVTLFDGWHENVLFDGFMGDDMIR\n>u229776\nLEGDFTAFDQSEDSSFLRFEEKLMRDCGFPDTVVTDYRQRKLDLKCRLGHLATMRFTGEV\nWTFLFNTTANIGFSHLKYDIPKHFSQMYGGDDKVV\n>u229813\nTENDYTAWDSGIDQDFLRFDAWLLTSLGVSQEYVTQFVHERCSTRFFGGTLGLMQLSGDR\nYTFLLNTIRNMALTNAQYDSMIGRAQIYGGDDSLI\n>u230255\nLSADFSEFDSSQEMQGVLAGNLVLKMCGVPENILKMYLEQRKNWILQSVDKSPNGGIMRA\nVLEGAWKQHSGQPATLVGNTIFNMMAMGACFKFEDFQFASFKGDDSLI\n>u230354\nTINDFTAFGSSQGGESVTMDLCWFRWCGMPESLCDLYVGFKTKLLALGAIKVICRDDGEP\nGTYLFNSLYDIGNTAAKFSPMALWLGYWLFGGDDMAT\n>u230659\nTCNDFSEWDASFRQAFVKLTSWLLIAAGCPRALVEEYEKFRESWVMQYRTMWGNASLHGQ\nEKQFSGNPFTICENTIGNMALCFTLFEYKGFQFAYFKGDDSAV\n>u230803\nGENDYEAFDATQHVACRLLIIEMLVAHFGMPSEVARIMRAAAREKFGHTANGTYVSMEGT\nMASGHPDTYLTNTMMNILLQWYASECCGVRMPPIAAAGDDSVI\n>u231057\nMMCDFTEFDSSQNEKAMIASVMMLKAMGLPSHILDQYLHRRKEWVLYVKNNTGAVDLTVY\nLDGVWNQHSGQPFTLGGNTQYNMSAIGMCYNFKDFQFAAFKGDDSVV\n>u231106\nTEMDISSFDKSQLESAHIAKMTFYRMMGLHPTIAEIWDKSHVSSKARNIQTGVSIDTVFQ\nHKSGDATTLLGNTLMNLFVYSVAYRKIPKFMIAIGDDSLF\n>u231558\nLENDFSQFDKSQLWTCHRLEMDFYGALGLNSEDLEKWDHGHLRAHGWSMVTLVSIWIWLQ\nRRTGDAATALGNTIINMLTVGYIYDITVFVCCAFIGDDSIV\n>u231666\nVEVDFSTYDGTQSLESHLFERDELIRAGIADFPSALDVFDHQKNMRGYTGDGLVYYVPNG\nRNSGDPNTSCGNSLMTGATAEFVLYRVFGSTDGVHIAVMGDDNTS\n>u231736\nLQADISKQDSSHTASLLYAFILIAKDAGCDDETLQFYLAYCRRYKFRSRGADSVTSNVSF\nNLGSGDPFTLIRNDIMELCIISCLYQHADSMVTVAKGDDIHG\n>u232459\nAAGDDSIVYTGNAWYCCDASAYDQSQSFGPLKHAYKVYQLLGVPKIVIDLLEKVSKLPYR\nYDAKEYGSFKVDRKLRPIRDTGGPDTTLGNTINM\n>u232564\nVSGDDSMAVKRGGWQQKGRAFLRFGEGDFSAYDQSQRAHCLTAHAVWMTALGLPKLLIDL\nILWVCSMPYRARGKRVKVKGKAGCXLATGIDWTTVINSMSN\n>u232624\nVVNDFSEFDSAQDEVSILAFAFYLRKLNFPDKIIRFYVKLRLRWNMALRSSCLGVQTITI\nLKGTEKKHSGEPATLDGNTWFNKAVIGVCVNIVNPYFLGFKGDDCIM\n>u232832\nFAGDDFFALVHRDQRIGALENDFAKFDRTQGVHALGSEYRVLRALGMSPFQCKRLFKTML\nSSPRYESKKYELRMNLPMPPQRATGGPDTTIGNTLTN\n>u232842\nFCADYSEWDSRFRHIFVEIMGELLIAAGCEEALVEEYVQFRKKWVMTANNYRTAGNTKLY\nGEEKKFSGDPFTICENTIMNMMLTFSAFEFDEIALALFKGDDSAI\n>u233153\nMENDVSAWDSSVSVEWCQMEVRLAKWFGAPRAVIDLMTANINTHGYTTNGYKYKVPGTRK\nSGDPYTSLFNSVLNGCMHVFVYCLNTGKTVKEIKSSYKMLVQGDDSAI\n>u233284\nFAGDDFFAIYWDGSKYWYYENDFSKFDRTEGVHALQSELVYMHTQGVPPTVTEAILDSLQ\nVKSTYQNRKMEIKYSCPMPQQRLTGGPNTTTGNSIVN\n>u233332\nFDYYLRKQDRQTTHDLLSIEMMMYETLGVDQDVLTMWKQVHNHWNFRGKYVKGNLDAMRL\nTGQATTSLGNAIVNLITHWRFIKENYNKWVFTLICGDDHLT\n>u233397\nTANDYTGWDTGVDLAFHHFHAWLLRRVGLGHRVDAYFKQAFNARTHLGPFPIQMPSGSAW\nTWDFNTADDFALTGASTAFPTGTPIAVAGDDSAV\n>u233828\nRTNDFTAYDQSCVGETLNFEINLMRWLGFDEELIHNYVWLKLHTDTTFGHSAIARFTGEP\nGTYILNTLFNIAYTFLQYGITWGMACIFSGDDSLI\n>u234073\nSAFDKSQLESAHMFKMMMYQDFGLHPVILELWDRSHILTLNKHFNSGTTFKFLYQHKSGD\nATTLIGNTIYNAAVHAVAYRCVPEFISLVGDDSIF\n>u234103\nVEVDFSKFDKSQGRMAFLVEREIWRILGVDEDFLQFWWETNEYSRLMDYKHGTSANVNFQ\nRKSGAGDTLMGNTIYGSSVLSVFKPAKIFSVFIGDDSFF\n>u234331\nVDNDYTAFDQSQDATALFLEIELMRHFNVPSDMIELYYWLKTETRSWLGPFGIMRFTGEW\nSTFLFNTLFSIAYSHTKYSFPPGMLQCYGGDDSRS\n>u234352\nAWNDFSAYDQGQDASFLAMETQLMERLGIPAPEVSFYIWLKTNTFSRLGSFAIVRFTGEV\nFTFIFNSLANMAISNLRFNLTGERRAMAFGGDDSVF\n>u234438\nFKSDGTSFDQGCRGGSMAFEVSLLHFFEIPSELIDFYVEDKIDQATKSFIIGLMRLTGEI\nFTFIFNLLFQIARTYVRYHVPRGTPRMFAGDDVDI\n>u234462\nTETDYTAWDSSIDGPFIKFDCWLMGQLSFPEEYIATYRSEACSTTARGKNLRLMQHSGNR\nYTFLFNSIRNLALTQATYADIANVPQAFGGDDSII\n>u234818\nLENDFTAFDQSQNAEFLWFEIFKMRHFNYPESEISLYVETKLNTVLYLGVLKIMRLTGEG\nPTFDFNSDGGKAATALKYDLGPDAVLGNSGDDTVL\n>u234842\nIESDAKNNDGSQSKEFRKYEALWYRRHGAPLWFVQEFARNTSVTVWTRYGVQARVDGQRW\nSGESTTTTGNSYVHMALMLAAAERASVVDSVHIHGGDDFLG\n>u234926\nTEIDMKKYDKSQDEICLYFECLMFSYFGMDPELVTMWYEIHKTSVLYDRANKIKTFCVCQ\nRKSGDAATFFGNTMVLMMLIMTVYDIENCELAMFAGDDSII\n>u235061\nYELDISQYDKNQQHTALLFDCKVFAELGVPRELVSLWYSAHVVTWIVNKSIKLKKLVYFQ\nRKSGDAYTFMGNTMYNLGALCNHLKRDFIHFPLVLVAGDDSLI\n>u235136\nRSNDFTAFDASQTAQVLLFEVYMLRAFSIPEAEIEYYVELKLDAYCRYGHLAVMRFSGEF\nSTFLFNSTMNMAYLACHYNLTDEPLVVAGDDSSI\n>u235287\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPTSLVALYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u235314\nQIIDFSTFDSQQNQVTLEIEKQLALLMGMNPGQVEAYYTVRDNHKVKMNRVFKGRMNGEK\nGSGFLDTKSGNTSLSTSLAAHVLRGKGPEVLAAKGDDILY\n>u235343\nAIADAKSFDSQQSPLTLEIERQFMKRLGANMPSLEQYYQIRNPMEFRAFNLFSGKTRGEK\nGSGFPDTLLGNTILQTCLSTYVFEGMGPMVVAAKGDDHLR\n>u235393\nTDNDMKEYDTSQSEITIENEIKWLRRMGCNELFVKLFKQHRIEWKTSYPGYCQLIGYAKK\nHSGEPFTIDFNALLCMALNGLLFPLEHFVFAAFKGDDSEI\n>u235543\nFSNDFKAYDQSQDQKVLAFEVRLMKFLDIPKELIDEYVFIKLNSKAFVGPLQTMRFTGEW\nCTLIFNTFMNMAYMNLKYKIPRGMPCAFAGDDSIF\n>u235790\nTINDFTAFGSSQGGESVTMDLCWFRWCSMPESLCDLYVGFKTTLLALGAIKAICRDDGEP\nGTYLFNSLYDIGNTAAKFSPMALWLGYWLFGGDDMAT\n>u235914\nSTNDYTAFDQSQTGEALSFELMMLRAFGLPDGVISYYTELKLDLTCQFGELAVMRFTGEG\nPTLWFNGCFNTALVGVQYDFPADTAVAVAGDDLAM\n>u235961\nGVTDYKMFDAQQDEFTQQIEKEFFHMLGFSERFTTEYYRLRKNYNMQAGPMSGKARTEKT\nSGEPATLLGNSVLGGVVMNYIFRGEGPCAMAIKGDDGFK\n>u236017\nVECDFSKFDKSQSVLAVWCTVAILKRFKASDAVINKWLNSHLNNVVTSYAHGFRATLGSQ\nRPSGDVFTFLANSIYTICALTYATKGKYVGLMVGGDDSVM\n>u236076\nFENDFTKFDSSQGGAFVSLETHVMAHYGVPREWIEEYVYLKSHTLSAHGWLSIMRFTGEA\nTTFDFNTLACIAFTHLKYEVPHGVAEAHAGDDLAL\n>u236579\nFENDLSKQDAYTDGHMLKIEMFIYKKLGLNEILVDTWSKMHDKWLWRSNKSKGFNNYKRL\nTGQATTALGNVIVNMIIHVSLFNKFNIVPTFYLMLGDDALV\n>u236590\nVETDFSKFDKSQQEFCLRTELMMMTALGLAPSLVQAWRHFHAITSATDYGVGIRARFIYQ\nRKTGDSYTCFGNTIINMSAIASCLDLSHLICASFVGDDSLM\n>u236636\nKELDFSKYDKSQDAAMLEFECNFMSFFGVASWLVETWRTAHRRGRFRDYNNGIRADVEYQ\nRRSGDAATYLGNTIFLMAVIAAVVDVDDMEF\n>u236775\nHTSDVTRWDYGCDAGVLNFDEHIMLRCGFPGDYVQAYVDRRLETRTQHGVVQTTQPSGDR\nYTWTLNSIRRAVVASILHKIRPEDTVAINGDDEAM\n>u236863\nAECDWTQMDSVQNKFTQEIERQFLVLMGVDQAFLDHYYRFRCGPRIIAAGVYGRGGTEKT\nSGEPGTLLLNTVLALCITLWALDWEGPVVGAFKGDDSVI\n>u237294\nFANDYTAWDSGRNEAFLLLDLHIMRFCGVPRTYRDTYTHEKLHTRSYLGPVGVMQHSGDR\nYTKLFNTYSNIALTHLSRLIPLGTPQAFCGDDSIL\n>u237628\nMENDFSKYDKSQQWRALYTEWGLYELLGLHIVDLDRWCRGHRIRTVVSPELGLLIIALLQ\nRCSGDATTTLGNTVVNMISVADVYEIDRFYLAFFIGDDSVL\n>u238299\nFTNDFTAYDQSCTGEAMQFELAMMRYFGFPEEIVSYYFWQKTTLTTNFGPSAIMRFTGEP\nGTYIFNSLFNLAYMLLKYQCEATPSIYSGDDSLL\n>u238550\nTENDYEAYDQSQTEECLDFELRLLREFNIPEELIEFYVFLKTHAFTNLGQLDIMRLTGEW\nCTFLFNTYNNIAYTSLKFVEFQGPVEERPASAFGGDDMIV\n>u238562\nIESDAKNNDGSQSKEFRKYEAMFYLKLGAPEWFVREFARTTKVRVWTRYGVAATVEGQRW\nSGETTTTTGNSYVHMALMQASMEEAQVKESTNIHGGDDYLG\n>u238565\nFECDFTSFDSSQNEISVMLEIEIFERMCPELIGTELIEMYRQMRLNWVASNEYVKWHGSG\nVKCSGEPATLLGNTMVNMLIIISSFVFEGVKFCLFKGDDSLI\n>u238584\nTTNDYTAFDQSQTGEALAFEIVKLTAFGVPGPVIAYYIDLKLNLTCQFGELAVMRFTGEG\nPTLLANSDFNAAVLGCQYDNIALFAVAVAGDDCAI\n>u238777\nTENDYEAYDQSQTEEALDFELRLMRFFNIPNEFLEFYVFLKTNAITNLGQLSIMRLTGEW\nCTFLFNTYYNIAYTALKFYDYHGKPEDMPPSAFGGDDMVV\n>u238862\nTSSDYVAYDTTQDESNLHMELALMQHLGFPAKVLDGYRDMKLYMQHRVGNLAVMRFTGEV\nFTFIFNTLGNIAYTHLKYTIPPGTLQCYGGDDKII\n>u238930\nYEDDYTGFDGTQNEDFLAFQVLFMRALDIPGPIIADYVNWVTHLRCMLGPLGVMIASGFK\nPTWFFNTLDSMAYQALKHDLTPHRTPGIKPVARSFSGDDTLH\n>u238979\nTTSDYTGFDRSQRGESIGLEVRLMQHFQLDQSWLLAFDSWRGQHDSVVDLYLDWKLNTVS\nNLVGRKRAGRDTGEPGTYDFNTYFNLALIQLMYDPPPGLPIAVGGDDMAA\n>u238980\nMSIDLSQQDSSHVNVHRFFIAKVLTFLGFDDTIVSLYLMSRARRFCKGLTMLGLLFEVIE\nRLFSGEPGTALFNYLMSTGTSVCTFDFSKFILFLGKGDDNSI\n>u239092\nAENDFSQFDSMQCHTTVEMMCRLYALCGMPKELLTIYRHMRAKWVMNTRSAGIKMEGEAK\nKHSGAPDTLLENTVLNMALNNYVLDMRELSIAFYQGDDFMA\n>u239418\nTEDDLEKQDRQTDHPLLSCERLISRAMGVDESVLETWALIHELWTYKGNDRLQSTLHAMR\nLSGQATTAYGNAITNLVLHSRLVERHYSQIELILLLGDDFLM\n>u239494\nLEIDQEKFDKSQTRECFEVEMYFLEKLGLDKELLTIWGDGHESSTAINFANGIKCYFVYQ\nRKTGDAMTCFGNTLISMAAMATVFDLKGSEASYFVGDDSFI\n>u239533\nQEDDLTKXDRQTTMEHIEIEMKIYEDLGADPDFIRFWMTMHXKWRFYSCEARGKLNGMRI\nTGQATTAIGNAIVNFIVHMKFIQDNRYNINWMIVVGDDNLI\n>u239534\nFENDFTAFDQSQNSDFLWFEIFLMQQYSVPERVIQFYKKTKLKLSVKKRNIRTGRGTGEG\nPTFTFNSFASYAFTALKYNTTPADLLVVSGDDTLA\n>u239549\nFESDMTGFDSAQDENPLAMELLFMEHLGVPPQLRTFYERTKLDTKLGRHVLAIARDSGEI\nFTWLFNTLHTIARRHLKSFIPPKTPQAYGGDDEAH\n>u239563\nSTNVYTAFDQSQTGEAVSLELTNLRAHHIPDEVIEYYIDLKLNLCCQFGELAVMRFTGEG\nPTLKFNSDFNAALIGVQYDFPDDMARAVAGDDMAL\n>u239613\nIEVDFSAFDKSQQEVCHDIKILMYRMLGLPARLCDLWDRFHRITRSYGYLAGVSFDTFFQ\nQKSGDASTALGNTIVSLVATADSLKFKRCAVAAFLGDDSIV\n>u239747\nGTNDYSAFDQSQTGEALSLEVVKMRVFNIPEHVIHYYEELKLILTCQFGSLAVMRFTGEG\nPTLLFNSDFNTALIGCQYEMPPDTPLMVAGDDSAI\n>u239855\nVSGDDSLIIRMNADGSIDFVEGDASMFDQSQGTGPLMFELKMLYLLGVDQETISILSESF\nGSTYVAKSRDRARSVKIKRKGVRYMRDTGGPTTSFGNSVVM\n>u240037\nLELDIGKFDKSQDETMLEAQLALFRIFGMEEWMIGLWRVFHQLCRLSVPKWGLRYKVGFQ\nRRSGDPLTWFGNTLVLLMILAYLYDLEDAFMVLLGGDDNIC\n>u240628\nLEIDMSQYDKSQQRMCYLLEMAFYLHLGLCPLFMEKWTSACLRANLRADSISLFLDYQRR\nSGNAPTTLGNTAISMLTVADSYDLHLADIVQAMFVGDDSAI\n>u240794\nLEVDFSKFDKSQERMILMIVLALFRRFNIPEEFIENWDKCHQLTKLIFHIIGIMLIASHQ\nRRSGDVGTFILNTVVAMVAMSMSYSLILAIGGIFGGDDMII\n>u241498\nTENDFGEFDSTQNELMPIVCTEYVQSVCGTADSILHTYINHLMEWKVVIDGLLTILNKNQ\nKHSGEAATLLFNTIWNAAWCGVIMNVDELVVALFKGDDSLV\n>u241657\nVCGDDSLMVIRTESGTVIYEGDASMFDQSQSFGPLNESYDIYTLLGVSMEVLVLLMKLAS\nNDYVAYSKFHPEQRLKINKSGRAMRDTGGSDTTLGNSVVM\n>u241943\nLQIDLTRQDSTHRPAHVLAYAMFLEFCNVPQEVCNLYVMMRSMAYVKSLAEGLYKAIIKW\nNLGSGDPFTLNANCFMMKSTMAVRYTGLEYCAGIQKGDDFIC\n>u243395\nLEIDFSKFDKSXEEDLLLAXCYIMXRCDIPLDIIXQWFKCHIYTILNFQRIGLKFDIAFX\nRKSGDVFTFIGNTIVSMLILCNTYNIXDIIGGIFAGDDSLX\n>u243539\nVDNDFTEYDASQNSSTIEFETLILEDLGVVSEVIELYQERRSKWKTYYPGYASFEGVEKK\nHSGEPFTIDFNTSLNMAICGYIYDFDDLVVAQFKGDDSNI\n>u243715\nGENDYEAFDATQHVACRLLIIEMLVTHFGMRPEVARLMRAAAEEKFGHTTNGTFVSMEGT\nMASGHPDTYLTNTMMNILLQWYASECCGVLMPPIAAAGDDSVI\n>u243762\nRSSDLAQQDRQTDDYLIATELELYNRMGMMKETLDLWRKTHEDWFYKGLSVKGRRNHMRL\nSGQASTSIGNTITNLIVHSRMMLANKDNVQLAMLLGDDIIV\n>u244039\nVENDFSAYDKSQDDACLELEMLFLRRLGVPADLIDMWETGHIFTRIRAYDSGFTLWTMYQ\nRKSGDVTTSFGNTLINMIAVACSYFPTPQSCWDDIIYAWFLGDDSTR\n>u244079\nTINDYTAFGASQGGESLQMDTMWYAWCGMPESLIARYVELKTQLRVGGGVKVISRDDGEA\nDTYNGNCRYNIALCAARFGVEAMWRGCWWVAGDDMVV\n>u244888\nIELDLSKQDRQTDNDILEFETYMVYALTGNRNFSNYLDEARTGFTVKTQSKHLFHRPGMR\nWTGGEITALGNNIRNWLCIGDIAKHYDISYVITLGDDSLI\n>u244953\nLELDISKFDKSQDGTMLEAQCKILLIFGVSQSVVDLWRAFHQICKLSAPRYGVSYSVKYQ\nRRSGDALTWLGNTMVLLMIVAYLYPIEKSFMTLLAGDDNLM\n>u245159\nYENDLAKQDRQTEDALISFELYFYEKMGVSKQMIDWWASVHGVWKFKSSTSSGVRKSMRH\nTGSVTTALGNLITNMRSNIDFLRDNDSTLELVLMLGDDHLS\n>u245179\nIECDESRYDAHQGEGAYTNQMNVYRKFGIDEYNQAAKSMESMIRIKGYSQKGVAYRVPYT\nMTSGSATTSVGNTINNATTLTFAITSIMPKLKYKMIVHGDDSLV\n>u245242\nLTADFSEFDSSQEMQGILAGATYFRLCGVPEHVIDRYLDQRRKWLMVAVDKDDSTMMRAM\nLEGAWKQHSGQPDTLNGNTTFNMAAMGACYDVENLQFASFKGDDSII\n>u245847\nVENDFSKFDKSQLWVALRMEWYVYAQLGLDPCLLKLWAGGHMTTTAASVAAGVKIVLELQ\nRKSGDATTALGNTIVNMLSVADTYDIDEFYYAMFIGDDSVI\n>u245938\nLEIDFSKFDKSQDELTLEANIELMRMFGVPKTILEEWEACHTSTKLVFQRWGIKLETAFQ\nRKSGDVFTFTGNTITSMQALAFVYDLTEIVMGVFGGDDSII\n>u246161\nSTCDFTKYDMSCKAETLSFELCLFSYFGLDVIFPDLVNDYFYIKTHMYTQLGTSGIMRFT\nGEFGTYDFNSWYNIAYMAFRFKLNPLDTRGSAFSGDDSIF\n>u247937\nTEDDLEQQDKQTDGEDIALEMLWYSHIGVSKVVLDSWLRVHRSWRAKGKFLTFMGDFMRL\nTGQATTALGNFIINAFIHAELVKTLGSRAKLVMFLGDDNLI\n>u248031\nLEGDWTEFDSSQNNVEHQLFMLQLEAIGCPQELRDMFLAMMTRRTVHAPYASLNVESKKD\nSGRVDTLIGNTTFNAAVMLTLVDPETVDHVFFKGDDSLI\n>u248486\nLELDISKYDKSQEGTVLDAQCKVLKAFGLDDTVVEMWRQFHEVCKLSSPNYGLSYSIKYQ\nRRSGDALTWLGNTMVLLMIVAYLYPIEKAYMVLLAGDDNSM\n>u248585\nIEMDLKKQDRQTDMHELENEFILMTALGFPSYLMPLWRQYNKSWRYKASDGTTSQQTGKR\nKTGDEMTSLGNTFKNMSGLVEPFNKYKTERILILSDDMIA\n>u248786\nLMNDFSSFDGTQSIRALALVYKFYELCGVPIDVVDIMRRDLHDIEVKTSQGIEFVAGGFR\nFSGRSDTLLGNTILNIIIMHHACGGHLTKFIVKGDDSVI\n>u248964\nVACDFSEFDTTQEFNGVYTCATFQAMGWFNPKAVGLMMKQRSAWTMKLMVGNEEVTSYAF\nLNGEWQQHSGQVATLESNGFYNMAALGLVMKITDLKFASFKGDDSLI\n>u249150\nLESDLSKQDRQVDEYMLGLHFNIYLLFGVDRSIINLWSAMHKNWSFRGVDVMGYLSGYQH\nTGGSNTGIGNLLTNLIVHADLANDLGPQLEYCIMLGDDNNM\n>u249541\nLELDISKFDKSQDETMLDAQCKIFKIFGMDEWLVELWRAFHELSKLTFPTWGARFTVGYQ\nRRSGDALTWFGNTLVLLMILAYLYPIEKSYMSILGGDDNIT\n>u249567\nYEDDLSKQDRQTDKQNIEFQQQMLILLGVHPQVVRLWSYTYSLWRFKSKQTWGWQMYQRA\nTGSALTALGNVLTNINVHADLIADNMPNIRLVLCLGDDHCT\n>u249769\nLEMDMGKFDKSQGLTSLIFECEMFRRAGMPVWMINLWFLPHLLIRVKGFGTSIRFTLPHQ\nRRSGDPWTFGGNTFFLLAILLDLCKGRINYLMVSGDDSVV\n>u249937\nLENDFSKFDKSQQWTTFHIEMRFYELLGLHPVLLDMWKRGHVATTVTSFSGGLHGDIPYQ\nRKSGDATTSLGNTLVNMVTVSYVYDLPVFDYAMFLGDDSLV\n>u250025\nLEIDFSKFDKSQARMCHLFEMFFWEQLGMDQYLNGLWRAGHYTTSALDFSTGVKAFFLYQ\nRKSGDAATAFGNTLVAMVSLARAADVSGFATAMFVGDDSLL\n>u250167\nQEVDVSKFDKSQEQLSLEIQTEIMKRFGSPDYLLNMWFHCHTMTTLVIQSHGIKVKTRYQ\nRKSGDVTTFIGNTIVTMAALAYVYDYTKAYGGLFGGDDSLV\n>u250272\nTYTDYTGWDTGVDESFTILYSETMIRFGIPARIAKKFAEDRHSRRSFMGPMPAMQASGDR\nYTWLNNTIGNMALTGISFDIDSSTVAAFSGDDMIL\n>u250374\nVEVDYSKFDKSQGEAILLFECLLFNWLGMPQQFIEHYYRSHSESFVRCSTTGFSATTQYQ\nRKSGDPWTFHGNSIVTLATIVHALAGYSVVGVVAYGDDSIV\n>u250696\nLEIDFSKFDKSXEEDLLLAXCYLMERFGIPRDIILSWFKCHIYTILNFXXVGLKFSVAFX\nRKSGDVFTFIGNTIVSMLILCNTYEIXDIIGGIFAGADSLX\n>u250964\nADCDTSHFDSSARGEAVVLTERWLRRYGIPEHLILEYRNDKLSFHTKQLWIGIMTLSGEI\nFTWLTNTLKNWGVEALKYDMKPGQPLASNGDDKLR\n>u252452\nAENDMEEYDTSQNEITIENECRMLKRLGCNDLYIALFKKHRTSWTTTYNGYCSFTGYAKK\nHSGEPFTLDFNTWLCMCLNGLLFPLEDFVYAGFKGDDSDI\n>u252501\nTTNDFTQFDCSQGAEALWREIHAMRLFSIPEWLIALYVHQKLTLTHQFWVSLIIRFTGEP\nGTYRFNTDFSAAQLQLQYNLPPGTPCVISGDDILI\n>u252579\nTEIDLSAFDKSQLEAAHTFKMNLYADLGMDCRLLEAWSEGHKYTTNRHKNSGASFGILYQ\nHKSGDATTLFGNTLVNLAMYAVSHDVTPDFMVAVGDDSLF\n>u252841\nYELDIEKQDSSHRAVHVLVAAEFLRMAADKLGLDTIATEIRTMRSVKMMNGPFSFILALA\nLASGDPWTLIINKIMAISCLVSVAKLKDVRMQQSGDDVTL\n>u253006\nVENDMSSFDSSQSQFALSQVYKFYRDCGVPDEVVEYLEKDLEPTEVETSVGIKFKGKNFR\nFSGRGDTLLGNTVLNLLIMSNAYPHVRKMIVKGDDSVV\n>u253216\nTESDYTLFDSSQNGRGVAFEELKMEYFRLPCADIDFYVELKLTSESFLGTLPVMRFSGDV\nNTLLGNSDFTIAIMNLRFRIGCCLRLGRNVLHCGDDFAC\n>u253489\nAISDAKSFDSQQSEVTLEIEKQFLMKLGVNADILAQYHEIRKPQVFRSINYFSGHTNGEK\nGSGFPDTLLGNTILQTCLSSYIFEGVGPMVIAAKGDDHLR\n>u253525\nTEVDFAKYDKSQTHNIYLLEEKILLALGMPKELIPLWRYANCHSRLINFKNKFRGSVNWQ\nRKSGTAFTYFGNTILCMAMLAYSMNLKDVIVLFSGDDSLI\n>u253700\nGENDFTEFDSTQNQLMPAVCTEILQYYSGISHALSNTYTQQLAKRMIDIPGVMKILVEWM\nKDSGEVATLLFNTTWNTIWVSFILDIKGILLGAFKGDDSAI\n>u254109\nLEIDYSRFDRSQGVGCLCIELEMFERLGLDQVILDMWEYAHRRTDLMSYKNGIRAFIAFQ\nRKTGDAATAFGNSLISMAAMAAAVRAKERSQLVCASFLGDDSLA\n>u254183\nFEDDAEKQDRQTTQELIDIEYLIYNMLGLSDKCAMMFRETHNNWKAYSSTFRIYGDAMRN\nTGSATTALGNVVVNMITHCDLISAHLSCLKLCTFLGDDHHG\n>u254355\nTATDYVAWDVGCDAPFQLFDESLMRRVGLPEGFIAHYRHRKLHSRTFKGPLPIMQCSGDR\nWTWVLNTYRNVALTHVRYVVPPGSAEMYSGDDMAV\n>u254610\nVEVDYSKFDKSQGEAILLFECLLFNWLGMPQQFIEHHYRSHSESFVRCSTTGFSATTQYQ\nRKSGDPWTFHGNSIVTLATIVHALAGYSVVGVVAYGDASIV\n>u254650\nVAGDDSLIVINHNHTVEYIEGDASMFDQSQSRGPLEYEYKVLSILGVSTRGIDVLRQITR\nAPYRISYKTCKGHIDRSHRPTRDTGGPDTSLGNSIVM\n>u255625\nFSDDLSKQDRQTDDDIIKVELVMYELLGMNSSLLKWWCTVHDKWRWKSDVVRGWQHSKRQ\nSGSVTTALGNVITNMQVRHRLYKRNKNKIEMMLMLGDDNIM\n>u255661\nTVCDYTGWDSGVNESFSLLYHRVMTTFGVPIEVADRFVHERHSLRSFMGPIPAMQASGDR\nFTWLHNTIGNMAITGFFYPSAGSVSACFSGDDMVL\n>u255930\nTATDYTAWDTGCDEAFLGFDCWLMKRCGLPLWFVSEYARGKVSTRCFAGEIPTMQFSGDR\nWTWLLNTHRNIAITAVRYRPRPLTPCAFSGDDMIL\n>u255962\nFVFDVSKYDKSQEAVWLDAQCIVFKLLGMCDQMIDLWRVLHEMCILTAPKFGATYRVGYQ\nRRSGDALTWFGNTLVLLMMMAYLYPIEEAHMVLLGGDDNVT\n>u256054\nLEIDFSKFDKSQDDLTLEMNCELMKRFGVPEHIINEWEECHVSTTLVFQNFGIKVETLFQ\nRKSGDVFTFMGNTVTAMIALAYVYDLTEVYLAVFGGDDSII\n>u256489\nFESDMTGFDAAQDENPLAMELEFMKFFGVPADLVHFYEQSKLNTTMGKLVLAIARDSGEI\nFTWLFNTLHTIARRHTKSEVPRSAPQGYGGDDEVH\n>u256973\nIESDISKQDMSTKLQLIRVEFEIYHALGIDSNVLSTYFDLHELWQYRGRTSRGWLEGQRK\nTGEPTTALGNVIVAMIAGRRCIQSQMRLGLFIFNARIGDDSID\n>u257009\nIEMDLKKQDRQTDMHELENEFVLMTALGFPSYLMPLWRAYNESWRYKASDMTESWQVGKR\nKTGDEMTSLGNTFKNMSGIAEPFVKYNTERVLILSDDMIA\n>u257086\nWESDMSYFDSSQNGEWVAAEMAMMEFMNFPKEVRDEYAWLKTNTSCFKGWLRIMRFTGEA\nFTFIFNTCATIAHGAVKYNLDVNVPRCNAGDDEAY\n>u257726\nFSTDAKKFDRQXNHWLLDFEYMIYDILGMDVKVQQLLRNSHNNWKWSSGEMXGIMDSMRL\nTGQSTTALGNLIVNMCIHSIFLNKNXXITTCVIMLGDDNVI\n>u257876\nLLTDFAEFDTSQEMMSVLAAEIILRSVGFNQDILAFYRQKRSEWTMINHGEEFGVPLMIL\nLSGVWNQHSGQPFTLSGNTLFNMAAIGMCYNIEEMACAAFKGDDAIV\n>u257920\nLELDIGKFDKSQDETMLDAQCALFQVFGMDVGLIELWRAYHELCKLSSPKWGASFWVAHQ\nRRSGDPLTWFGNTLVLLMILAYLYPIDEAYLVLVGGDDNFC\n>u257952\nVQMDVSAQDSSHTPALIDAMCKLAVFFGVPKDTMDLYYESRSYIKIKSMAPGLYTGFQCD\nNLPSGDPFTLIANMFQMLMTVACNFTGLDKAIVLQKGDDLAT\n>u258267\nMMADFTEFDSSQEEKGILSSAVAFKNLGFDEKIIDFYVKMRKEWTLYNVADSGGMHYSFK\nLQGEWMQHSGQPMTLDGNTLFNMSAIGLCYNFKDLVMAAFKGDDSFI\n>u258287\nLENDYSSFEATVSTAALALEFYVYRKFMGLSKKEERVFRKQFHQRIFSKYGHKASRKGGR\nASGVGNTSCGNTVINVCLTLIAMEHCLDEKKPLGEQIFLLALGDDSLL\n>u258310\nLMCDFSEFDSSQEEVGILASTVILRSIGIPDKQLGFYTDLRRKWKLASIDSNLNSTIMTT\nLTGKWMQHSGQPFTLDGNTMFNMCAIGMCYDIEDLVFAGFKGDDSII\n>u258938\nFEADLEKQDRQTNDSIFDVECEIYKRLGMNGETLTLWRSMKSNWYLKSQHVRTTLNIKRC\nTGEPTTALGNMINNLLVNWRFIRDNETFLDINLFLGDDFLA\n>u259352\nTCNDFSEWDASFRTPFSKVTSYLLKCMGAPKALIDNFETYRKSWSMTYQNKIGRATLKGF\nEKQFSGNPFTICENTIGNMALCFAIFDYKNFKFAMFKGDDSAV\n>u259785\nLELDISKFDKSQDDMALDLQCRIFVQFGMPSGLVNRYRQEHVKNKIKFRALGLTLTTFFQ\nRRSGDVFTLLGNTLVTMFSAAYCYDLKNAAGGVFVGDESLI\n>u259958\nSTCDYESYDKTQNEDFLNFQIQLMEHLNFPKELIDLAIAYKLTVNFDGKHLQVAIYSGEK\nWTFDFNTMDNIAFTYLKFGFRGPYPKDRPLELYGGDDNAL\n>u260062\nGVTDFEMYDSQQDEFSQQIEKETLKLLGVDQSFLDHYFSFRQGGKLLASGISGRLGTEKT\nSGEPMTLLGNSVISMVLANWILRGDGPFVMAVKGDDGFK\n>u260093\nVAGDDFFCIYIESEVNVVNFVENDFSSFDRTQGVHALEAKALCYTALGVSACKRDFLFEA\nILTDPIYENSRFELKEKIRMPPQCATGGPDTTLGNTVLN\n>u260165\nLEVDFSKYDKSQMFETYSLEEELFRRLGFDSYYAFIWIEGYILSTAASFTLGVRIILFFQ\nRESGTQTTSFGNTIVSMITVVWTFKLGDEQWIAMAFIGDDSIL\n>u260450\nYEDDYTGFDGTQNEEFLTFQVLVYQACGIPDSIIEDYVKWDTHITTAMGDLGVVIPSGLK\nQTWLNNTLDNMAFQALKHNLTPHTELKRVARAFSGDDSAH\n>u260459\nGISDAVMFDASQDEFTQAIEKIHLSKLGMSPEAIAIYYSFREKYRVYAEGFSGDVEYSKT\nSGEPGTLLNNSLVASSTTNYVFRGRGPAAIALKGDDGYK\n>u260475\nTINDFSAFDSTQGGESVQLELCVLKWARVPESIVDGYPAWKSTIVTQWAGIKTVSRDSGE\nPGTFDGNTWYSMANCALKFGPIALQRGCWCFGGDDMAT\n>u260678\nCENDYTQYDRCQNGEFLNFEICLMKHYCIPSYLLDFYVNNKIGLHSFVGHHATQRGTGEG\nPTFDANTDCNIAIDSLKFEIPKGTPAAYAGDDMGR\n>u260684\nAENDFSQFEGSQRIELFDEVQFECFIQLMEPWLLEIDPLYEEKLHKHGWTLRGLWYYLYA\nLMASGDFETGAFNTIFNMVSCRYFEIVHGFGNFNFIVDGDDSVI\n>u260763\nVENDFTEYDASQNTLTVQFESDILLLVCQNPELAELYREHRTHWTTIMPGVVVMKGYAKK\nHSGEPFTLDFNTLLNIAICGMIYDIDELVVALFKGDDSLI\n>u260966\nVAGDDFFAIIHDKNGIRFFENDFSKYDRTQGVHAQDAERQILLLLGMSEYVAFTLFSTAN\nLQPRYESKRLDFHQIMKMPPQRATGAPDTTIGNTINN\n>u261210\nTACDYTGWDTGVDESFTLFYADLFARFGVPKDVAERFISDRHNRRTFLGPLPAMQASGDR\nYTWLCNTIGNMALTSLSFGIKRGQPCAFSGDDMIL\n>u261259\nIANDFTRFDSTQTTPLLNLIIECFELTNMPPEVIELLRRDVDVGTSVSTKFLDYVVRGVR\nMSGRGETLSGNTIANLIIVIYAFDDLIRMAIFKGDDAVL\n>u261280\nIESDMKNNDGSQSAEFRRPEAMFYRKLGAPDWFVREFAKTTSIRVWTRYGVTAQVDGERW\nSGETSTTTGNSYVSMALMQQALSVAGVEKSTNIHGGDDYLG\n>u261469\nTATDYTGWDTGVDEAFTEFYRKVFVQFGVPPSVARKFAEVRHSRRTFLGPLPAMQASGDR\nYTWLCNTMGNIAVTYLTHDIPASTPACFSGDDMIL\n>u261673\nVAGDDVLACVKRPRHKAIWIENDATMFDQSQSIGPLLYEGDFLRLLGVPDNVVDLLWHSY\nHSKLVAKHPKTEYSLSVNRSKRPIRDTGGPMTTLGNGIVM\n>u261783\nTANDYTAFDASQGYDSVLLECHVMRLAGLPDALVDNYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKIDCLALFGGDDSAI\n>u261983\nTANDYTAFDASQGYDSVLLECHVMRLAGLPDSLVDSYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLSCMALFGGDDSAI\n>u262068\nFTCDFTAYDQSCTEETLSFEICFMDYCKIPTDLIDLYRWIKLNMRTQFGFTAIMRFTGEF\nGTYDFNTFWNMAYMTLRYKPRKDMACCYSGDDSLF\n>u262139\nTENDYEAFDQSQVEEQLAFECRILKNFSIPEELIEFYVFLKLNAKVEDKLLDIMRLTGEW\nCTFLFNTLSNLAYLGVRFNEFRKPNHNIPLAVGGDDMVA\n>u262197\nVSGDDSVVVVRYKGLTSCYEGDASMYDQSQSFGPLAFERKVLKAFGVDDSVLLLLKTLSE\nNDYLLLNRNRDSRILIDKMNRALRDTGGSNTSFGNGVVM\n>u262445\nTEIDLSKQDRQTDKPILEEHIHMLRDVGMPENMINIIKSLAEPVNILTANKIMSHRPPFH\nLSGGEMTSLGNELRNLYLLAEIASNYKTRMIYTLGDDSII\n>u262449\nITSDLKKQDRQTDKEILEVEMNLFLLMGISPEVIIIWSMMHEDWRWVARQSTGYRHVMRH\nTGAPTTAIGNAITDLQVNTLVVEELMGDINWAVFLGDDNDI\n>u262560\nKETDYERYDQSQREEFLRAEVMLMQLFNLPKEDVDLYLESKFNARVFLGELDIMRLSGEW\nCTFLFNTLGNIAYQHLRYKIPPGTAQIYAGDDSCI\n>u262714\nVSSDLKKQDRQTDSYMLEVEMNLMLLLGVNPWVVKLWSSMHSNWRWMSKQCKGWRNMMRQ\nTGSVTTAIGNLITDLQVNCETIESLSEVKFVIMLGDDNTM\n>u263110\nLELDCSKFDKSQGKVLLMFQELLWRKLGLDPHMGGIWNEAHRLTFISDFLNGVMFTVNYQ\nRKSGDATTYMGNTLVTMAMIAYLYPIEKALFSVFGGDDSLV\n>u263172\nTEIDYTAWDKGVDGKFLTFDLWMMRWFGFPTYYISFFLYCRLNSSYFGGTIGLMQLSGDR\nFTFLFNTLHNMLLTFLLYVLPLTVFIMFAGDDVLI\n>u263215\nVSGDDSLIVGNYKGKLYVFEGDASMYDQSESTGPLTVGWMMCQRFGANKETIEILSTLAH\nNTYIVEPKKREDGEYYRINKKKRPLRDTGGADTSVGNSIVM\n>u263328\nTCNDFSEWDASFRKAFAKLTSFINRAMGMPEHAVDWFERNRENWTMIYRNALGATILKGK\nEKQFSGNPYTIAENTVCNMALCFALFEFKGMSIAMFKGDDSAV\n>u263334\nFTCDFTAYDQSCTSEVLGFELAFMDYCGIPQELLALYEEIKVDMFTEFGHSAVMRFTGEF\nGTFDFNTFWNMAYMELRYRPDPKIARAFAGDDSLF\n>u263758\nFENDFGKFDKSQFDETYSIEEQVFKMLGLDALIAHMWANSYTEKQIRVVEHAIKLVLYYQ\nRNSGTVTTGLGNLIVNLFCTVFAACIKRNDYRAIYAVGDDSLF\n>u263862\nTCNDFSECDASFRTPFVKLTSWLLIASGCPRNLVNTYEKFRESWTMQYRTIWGFASLDGF\nEKQFSGNPFTICENTIGNMALCFSLFEYKDFQFAYFKGDDSAV\n>u263889\nVEIDHSKYDKSQQWTALRIEWFLYQKLGLDMDLCDVWKAGAVDCVMQSTQLGIKLWSILQ\nRRSGTATTALGNSMVTLFTLGASTDFPHGFYYVLFLGDDSLV\n>u264125\nLEIDYSKFDKSQDDLILETNCLLMSKLGVPEHVVEEWRDCHISTQLSFLDWGIKINTLYQ\nRKSGDVFTFMGNTVTSMLTLSYVYDLSQCIMCIFGGDDSLI\n>u264276\nVENDFSKYDKSQQEFCLMLEWAFYELLGFGLEELEMWRRGNMDSSVIDMSLGLAFYLMWQ\nRRSGAQPTLLGNILVNMFSVADTYDIEPELMEAAAFVGDDSII\n>u264637\nTEIDMKKYDKSQDELVLKFEIEMFRYLGLDDYLCDLWYDMHKTSRLYDRSNKIRVECVCQ\nRKSGDAATFFGNTMFLMVVLMTVIKMEDVILAMFAGDDSIV\n>u264797\nIMADFSEFDSSQEEQGTMASIVMMKQLGMPQNIMDKYQEMRHKWKLRSITDESYIMLSGE\nWKQHSGQVFTLAGNTLFNMLIMGAVYQYDHIVVAAFKGDDSLI\n>u265075\nLEVDFSKFDKSQERMILMIVLALFRRFNIPEEFIENWDKCHQLTKLIFHIIGIMLIASHQ\nRRSGDVGTFILNTVVAMVAMSMSYSLLLAIGGIFGGDDMII\n>u265382\nVSGDDSLVAVWNGAEWDWYEADATMYDQSESLGPLLSEYRALRALGVTSDVVAILHQLAH\nAKYVVRGEGWSLNIDRTARPMRDTGGADTSMGNSIVM\n>u265402\nFANDFSEFDSAQDEISILAFAAFLSMLGFNEKCIKLYVNLRLKWVMALRGSSLQHETITT\nLKGVFKKHSGEPATLCGNTWFNRAVTCLCVTFLNPYICAFKGDDSLI\n>u266106\nIEVDFSKFDKSQHRTALFLETLLMQDLGLPADWAALWYRMHTQSVCCGLRHGIKFYCMFQ\nRRSGDAMTMLGNTFINMAALAHSIPQKGFVCGAYSGDDSFE\n>u266174\nVENDFSEFDSSQNNLEHENFLATMRLLGCPEILLEPFSAMMKQRVVTDGPNTVVVKSKKD\nSGRVDTLVGNTLFNLCVLLSLLDEVKSDVRAVFVKGDDSLL\n>u266488\nLTCDFSEFDSSQEKQGILSSCMILKMMGFNKDTISFYMDKRSKWTLLNQDQIDNMPVRTV\nLDGEYMQHSGQPFTLDGNTMFNMSCMGMCFEFQDLIFASFKGDDSYI\n>u266551\nVAGDDFYALAVRNGKIVALENDFSSMDRTQGVHALEAEARILQTLGIPEEKTKILFDTML\nKNPVYKAEKLGVKIKLQMPPQRATGAPDTTIGNTIIN\n>u266625\nYESDMSKYDRQQDMNLISIEMAIYKLLGADEHLINWYSKVHVRWMYKSQYSKGYLKAMRL\nTGQPTTALGNAVVNMILFYTIFRFEKNIINMLIIMGDDNVA\n>u266878\nGTNDYSAFDQSQTGEALSLEVVKLRVFNIPEHVIHYYEELKLTLTCQFGSLAVMRFTGEG\nPTLLFNSDFNTALIGCQYEMPPDTPLMVAGDDSAI\n>u266891\nFEGDWTEFDSSQNNVEHALFCLQLRAIGCPKSLVHRFASMMDRRGVSCPLASVIVENKKD\nSGRVDTLVGNTTFNAAVLLNLIQGDILHTLWKGDDSLI\n>u266961\nLENDFSKFDKSQDRFSYLVFAHVMRMLGFDDELLDRWLEGNARCTLRSMTLGILLIIRYQ\nNKSGGPATTLMNVVMNACATAVCYRGTVIVYALFMGDDSLV\n>u267308\nLENDFSKFDKSQGRFCTDLKMHFYAALGMDESLLARWESAQRESEFVSLAERVRVHVRDQ\nQKSGDGATTLANTIVNICSVVYAYRGTQVDFAVFIGDDSLV\n>u267354\nTTNDFTAFDQSQTADALALELQVLRFLQIPESFISLYVEIKVETRSFLGVLAIMRFTGEW\nCTFLFNTLFNMAYTSLMYELGPDTACAFAGDDSII\n>u267358\nVCGDDSLVVTNISGKWEVWEGDASMFDQSESFGPLLLCWEIYKILGVDSHTIALLQTLAS\nNTYTVRSRKSHEVLFISKKLRPLRDTGGADTSLGNSIVM\n>u267649\nTGNDVTGWDAGCEAEFLYGIDLFLMELCGFPQHYIDSYLHRRLNSYTHLGPFPIMQASGD\nRYTWLLNTYRNIAITTLYFSLPRGTVMAFSGDDAII\n>u267766\nLENDYTKFDQSQKAEFVHFQIQLLEYLNIPKYLIKMFVELKLGYHDDKSAIDFMILTGAF\nYTYIYNTLDNMAFAATKYEIPVNTPQCYSGDDSVI\n>u267874\nVENDFTEYDSSQSELTIYFXSDILFLACHNPELVELYREHRTNWSTSTPGLVHMRGYAKK\nHSGEPFTIDFNTILNIAICGAIYDIDDLCCALFKGDDSLI\n>u267924\nFANDFTEYDSSQYELSPYANSIVMLAMGAPSLLVDVYLQMRADWVLSDDMMKLYGHQKMH\nSGEPFTLTGNTFFGMLVIASAIEFDDLAYAIFKGDDSAI\n>u267964\nMMCDFTEFDSSQNEKAMIASVMMLKAMGLPSHILDHYLHRRKEWVLYVKNNTGVVDLTVY\nLDGIWNQHSGQPFTLGGNTQYNMSAIGMCYNFKDFQFAAFKGDDSVV\n>u268162\nTCNDFSEWDSCVRKAFYEFTCYLMKLMGAPDHIIDFYRRFRDEWTMKFDTQYGSAFLKGT\nEKQLSGNPFTICENTIWNMSLCFVIFEYKNLKFAAFKGDDSAG\n>u268341\nLEGDYTAFDQSEDAAFAVFETLIMERLGFPQAIINGYHDCKNRLRSSVENHAIMRFTGEV\nWTFIFNTMGNIGYTALKYDIPPKTKFLFGGDDKLA\n>u268342\nTTNDYTAFDQSQTGEALALEQIVLQAFGIPDNVLSYYLELKLNLTCQFGDLAVMRFTGEG\nPTLKFNSDFNAAIVGCQYEFDSDTAIAVAGDDMAA\n>u268356\nTINDFTAFGSSQGGESVTMDLCWFRWCSMPESLCDLYVGFKTKLLALGAIKAICRDDGEP\nGTYLFNSLYDIGNTAAKFSPMALWLGYWLFGGDDMAT\n>u268408\nFSNDFKAYDQSQDQKVLAFEVRLMKFLDIPKELIDEYVFIKLNSKAFVGPLQTMRFTGEW\nCTLIFNTFMNMAYMNLKYKIPKGMPCAFAGDDSIF\n>u268486\nYESDASKQDRQTDEFDLKVEYILYARLGVHESINNCLKQIHDMWRFKTNLVRGHMDNDRH\nTGSLTTAIGNVIVNLQVLWRTIKRYNDQLELVLILGDDNLL\n>u268597\nLENDFSKFDKTQSETTYEAEYIIYELLGIDKSFIQYWKEGHFITRLISRTAGIALTIIFQ\nRKSGDATTSLGNTLVNMLTIAAVYNITDFKYAMFLGDDSLI\n>u268680\nGVTDFEMFDSQQDGFTQLLEKEVLKALGTSEEFIEHYFSFRRNGKLLGPGIAGTCTTEKT\nSGEPMTLLGNSLISMFLGNWLLRGEGPFVSAYKGDDGFK\n>u268761\nYENDFEAFDSTQNEEFLGAQVMLMHAVQIPPPIIADYINWVTHLKIFAGELGIMIASGYK\nPTWLFNTFDNMCIAATQFQLTPHVSVLGHLPYHNALPASHPVARAFSGDDSAH\n>u268818\nTVNDYSAFDSTQGGESVQMELAWLRWAHAPGEIVDMYSWWKTHIFNSVVGEKKTSRDTGE\nPGTFLFNTLYSIGNTALKYGTECFEHTTFLFGGDDMAA\n>u268930\nYEDDYTGFDGTQNEDFLAFQTFYMRALQIPEPIISDYLTWVTHLTCLLGPTGIFIASGFK\nPTWFFNTLDSMAYQALKHDLTPHRLPGKAPVARAFSGDDTLH\n>u268973\nTTNDFTAYDQSQSADALALELIILQFFSIPTSLIELYREIKLNTQTFLGVLSIMRFTGEW\nCTFLFNTVFNIAYTYAMYSLTPETPMAFAGDDSVI\n>u269072\nTSNDFSEFDQSQTGDALSLEMVMMSAYNLPDAITDYYFSLKTRLRTSLGPLATMRHTGEG\nPTWFFNTMFNCAVTGLRYGYLGDKARCFAGDDSCI\n>u269418\nIEVDISKFDKSLLMWAFWYLRLLMIQFGVPEWIADLYYSVHLLTTMVDVQTGVKLETFCQ\nMKSGDPITFPGNSFITLGTLLYCLSDINDIQLMMFGGDDSLI\n>u269856\nFENDWAEFDSSQNNLEHELFCCVMLQLGCPPRLVTLFKAMMYQRYVAANIGALSVLNKKD\nSGRVDTLIGNTLFNSSVLLSMIPNWRELLVVVKGDDSVI\n>u269898\nVSGDDSIVIVKYKGELFCFEGDASMYDQSQSFGPLGVGWRSCRHLGVDKSTIKLLSELAR\nNTYVVRSRIKDDPGLFRINKRNRPLRDTGGADTSLGNSLVM\n>u269940\nVGGDDSLVALNQKGKTTFFEGDASMFDQSQSFGPLGFERRVLKHLGVQKDELDLITKMAA\nCPYVVPFSNGEKLTVDRSHRPLRDTGGPDTTIGNTTVM\n>u270105\nVEIDISKMDKSQNEIHQLIQDKMFSFLGVDKEFIEMWHNCHVKSVMSEIGVGFQFTTLWQ\nRRTGDACTLLGNTIVTAVVNNYILDFSKFAAVGVVGDDFTG\n>u270398\nTETDFTEFDCNQDSLTLEAECYMMTIYGLPPAVVWLYRQMRTCWRLSARNCAQVFGQYGQ\nHSGQPATLHGNSFVSMFLISNVVDVDRNSVMLFKGDDCLI\n>u270401\nCSGDDSIVAEFHPGHIVLWEGDASMFDSSQSRGPLKWQYKLMHMLGVDASVTMALYKVAH\nATLVVRPRTGDYDMDVFRVDLSDRPHRDTGGADTYLGNTLVM\n>u270727\nTTSDYTGYDSTQKGDSLGFEHLLMLHWGLPQAYVALFAEFQVIQRSLPELYVWWKTHIIS\nDIIGPKSTGRDTGEPGTFDFNTYFNLALIFTMYIVPLGTVMAVGGDDFAA\n>u270752\nTASDYTRYDQSQNEAMLYFEYLLLQHLNIPADYVDMYIHMKTHCVHQFSKAPLQAAVMRF\nSGEPGTYTFNTWVNIAVLNVQYDLTGLSYCASGDDSLI\n>u270778\nSWNDFTAFDQGQDASFLAMEVRLMEQLSLPASEIAFYIHLKTHTFSNLGSFSIMRFTGEV\nFTFIFNTLANMAISNLRFCLDKSNKPLCFGGDDSCF\n>u271084\nLEIDFSKFDKSQEDVILSFSAKILLKLGMPDPIVQEWVNCHKTNRLIFYNIGLSIKTKFQ\nRKSGDIFTFIGNTIVTMAVLAYVYDLDKAEGGIFGGDDSII\n>u271310\nLSNDFTDFDSAQNNVEKHLIRIILTEIGCPAHVINHYENLRSRRLVCGSAARFVLHDKRD\nSGEPFTLIGNTAFNAAVVLRLVLGDVRFAIFKGDDSYV\n>u271379\nFTCDFTAYDQSCTEETLSFELAFIEYCGIPTSLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u271380\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPVSLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRNLACAFSGDDSLF\n>u271449\nFENDFEEFDSSQGGAFVALECSLMRAFAIPEDLIEYYANIKTHTRARAGYLSIMRFTGEA\nFTFDFNTLACIAYTHLKYCIPPKTPEAHAGDDLAL\n>u271574\nFTCDFTAYDQSCTEETLSFELCFMSYCNIPQPLIDLYSWIKLNMRTQFGFTAVMRFTGEF\nGTYDFNTFWNMAYMELRYSPNRDIAACYSGDDSLF\n>u271636\nTATDYTAWDTGRDMSFLHFDDALFARLSLPKAFREEYLDRKLHTRSFVGAMPVMQFSGDR\nWTWLLNTLSNVAFTHHRYRVPPGAPCCFSGDDMLG\n>u271763\nTENDYTAYDQSQRGPTLELERLLFIHIGIPQDIVDLYVWQKTRMRHQFGISAIARFSGEA\nGTYDLNTLFNAAILCIQYEDMDKLAFAVSGDDSMI\n>u271858\nSTCDFTAFDQSQQAETLAFEMCLFEYFSFTKVMFDLVALYYFIKVAMFTQFGEMGIMRFT\nGEFGTYDFNTWMSIAYMSWRFGLWRAEYCSLGAAFSGDDSIF\n>u271950\nYSNDYTSFDQSQTGEVLASELLYMWHAGIPENVISIYENNKIDMFCAFGHLQTMRFSGEP\nATYAFNCRCNLAVLNLQFPLDVYSEVAVMVSGDDGVI\n>u272117\nCETDYTAWDSSIDAPFIKFDCWIMRQLGIPESYIDTYVNEVSATRSFRGNLRIMQHSGNR\nYTFLFNTIRNLALTHAAYKNLHKVPQAYGGDDSLL\n>u272189\nLENDFKAYDKTQDNIALEIELSFLALLGVPFDFLEMWRSGHVYTRATCRETGFMLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFPKPEDANTKIRCAFFLGDDSLF\n>u272220\nTENDYTLYDQSQNAEFLNFQILLMRYMNMPPFFIDYYYHYKTHLFSQHGPLDIMVFSGEP\nPTFQFNSEDNLAFCATQYDIPDGTPILIAGDDSAI\n>u272322\nSCNDFSEWDASFRKCFSSMTCDLLRMMNAPEGLVSWFEQYRENWTMLYQHQYGTTTLSGH\nEKQFSGNPFTICENTIGNLALCFSIFEYRKLRLALFKGDDSAV\n>u272332\nSTCDFTQYDMSCTAETLSFELCLFSYFCLDLVFPEAYQLYYFIKTEMYTQLGTSAIMRFT\nGEFGTYDFNTWYNIAYMALRYHFDETNPNEGCAFSGDDSIF\n>u272472\nISGDDSLVVTNYNGVLEAFEGDASMYDQSESFGPLSVGWKACKRLGADSRTIKLLSTLAH\nNTYHVRSRVSTEFFRINKRDRPLRDTGGADTSLGNSLVM\n>u272499\nFENDWAEFDSSQNNLEHELFCCVMLQLGCPPRLVTLFKAMMYQRYVAANIGALSVLNKKD\nSGRVDTLIGNTLFNSSVLLSMISNWRELLVVVKGDDSVI\n>u272574\nGVTDFTMFDAQQDEFTQEVEKQVLYRLGASESFVHHYYSNRKNYRILAGPLSGRAGTEKT\nSGEPGTLLFNSIVNVVIMNFLLRGAGPVAMAVKGDDGFK\n>u272596\nSCKDVKEWDSVYTSLFIDFFSSLMEMLGCPMQIVQWWRLYRKKWRMVHRKSGTSLYGTNK\nEMSGSPFTICENTIMNMILIFTLYDFKDLVLGCFKGDDSSV\n>u272742\nLEMDFGKFDKSQGIDCFEVEMKMYELLGMDDLLNQLWRMGHFRTSAYDFRTSIKAYFFYQ\nRKTGDVSTAFGNSMITFMALAKCVAVDRRFSCFAAMGDDSIM\n>u272745\nTCNDYSKYDQSQNEQFLAFEILLMKFLHLPEPLISLYANIKMNTKYFAGILDIMRITGEK\nFTFLFNTYANIAHTELKYNTSHLQIPEVYGGDDMAI\n>u272900\nGVTDGADFDSMQNKFTQQIEKRHSHHLLVPKVLIDSYYQYRNDYRMVENGLFSGRARSEK\nTSGEPGTLLYNSQLGGTVCNFSLRGIGQSTMEIQGDDARS\n>u273130\nIEDDLEKQDRQTDRWLLKCEEILSDELGVDSAVTLVWQSMHEMWRYYGGDRLRGVLKEMR\nLSGQATTAYGNAITNLVLHRKMVEKHYDSIARVLILGDDFLM\n>u273208\nAIADAKSFDSQQSPLTLEIERQFMKRLGANMPSLEQYYQIRNPMEFRSFNLFSGKTRGEK\nGSGFPDTLLGNTILQTCLSTYVFEGMGPMVVAAKGDDHLR\n>u273499\nSEDDYTAFDQSQGMEFLQFDNYLMQACGIPEIVRHDYLSFMTHLRTWLGPMGVMMPSGCK\nFTLLFNTTRSAAYQQLKYTIPRNTPMCATGDDVAL\n>u273556\nLVSDYTAFDANQDGSFLRFEQRLMAMYGVPEDVIDNYTELKLTLVSFLGPLAISRFSGET\nFTWFFNTMANVAYTHLKYDIPPAIAQMYSGDDRAI\n>u273571\nYEDDYTGFDGTQNEDFLAFQVMYMRACSVPEPLIADYVQWVTHLIVLGRESGVFIASGFK\nPTWFFNTIDSMAYQALKHELTPHRRTGIRPVARAFSGDDTLH\n>u273716\nTTNDYTAFDQSQTGEALSLELTKLHAFGLPDEIINYYFHLKLHLVCQFGELAVMRFTGEG\nPTLAFNSDFNAALLGLQYLRIENTAVAVAGDDCAL\n>u273955\nLSNDFTEFDSAQNNVEKHLIRIILTEIGCPAHVINHYENLRSRRLVYGSAARFVLHDKRD\nSGKPFTLIGNTAFNAAVVLRLVLGDVRFAIFKGDDSYV\n>u274297\nVSGDDSVVGWGTFNSTVSFSEADQSKFDHTQDDGPLSLSLSWMRKLGAPDWFLDLVVFCC\nRSPYTMRKHEMRARGVAGVQMPTGITLTTLLNSMAT\n>u274467\nLELDIGKFDKSQDETMLDVQCKFFILFGMEKWAVELWRVYHELCKLSSPTWGVRFNVGFQ\nRRSGDPLTWLGNTLVLLIILCQLYDLNKAHLVVLAGDDNLS\n>u274601\nLCTDFSEHDTSHSLIVLLWKCEDYIQMGFDQTLVANYFNAYMHWRQTAKQDGENVTVYND\nLMQHSGSSDTIHGNSKLTMGANGACFDFRGLKFAAFKGDDTYI\n>u274703\nMEIDVSKYDKSQEKFCLDIQMEIWRRLGVQEEAIKLWYDCHTNTTLTFVNYGLRLPVSFQ\nRKSGDTFTFLGNTLLLMAMIAYSYDIDACNGAIFGGDDSII\n>u274884\nREIDFSKYDKSQGELHLLMEMLIFDILGLPPFYLLLWYRMHFLTQVKDKSMGFTAWLFYQ\nRKTGDAATFIGNTVVCICMLLLLYDFSGILFAIFAGDDSIL\n>u275159\nLENDFSKFDKSQDRFSYMLMQFMMTKLGFDDELLDRWIDANERCVLMTMALGILLVSRWQ\nNKSGGAATALMNVVVNMCATVTCYAGTDMVWAAFMGDDSIV\n>u275164\nFANDFEAFDSGIQGEFVWFFTLLMKHLNIPEHFIEFYLNQSTNAQTFLGALQLMNLTGTW\nCTWILNTFSNIAYTHTKYVIKNNTPQGYSGDDLTI\n>u275255\nVAGDDFFAIVREKNEIFYLENDFAKFDRTQGVHAQDAEAKVLKLLGMSERISYILFTTMN\nLQPRYENKRLDHQAIYHMPAQRATGAPDTTIGNTINN\n>u275343\nASGDDSVVSWGEFARGRVSPFVEADQSKFDHTQDEGPLSLSIYWMRLLGAPEWFLDLVFY\nCCREGYTSRKHEFSSRGTSGTQMPTGITLTTLLNSMAT\n>u275394\nIQIDLSEYDKSQESRTREFEDIALQDLGMGLLDVQRWSDGQTIKLVKSLQLGIKAVVAFQ\nRSSGIVTTAFGNVLWALGLESHIIDGPPIVSSNRGDDGYA\n>u275609\nAIVDAESFDSQQNEVTVYAEKVFLELLGASKRSLDEYYEVRKVGIPWALIGRAYGKLNGE\nKGSGFPDTKTGNTVLQGILANHQFDGVGPKVEAGKGDDWLR\n>u276232\nLEVDFSKFDKSQQRFCLLTECYLMRKFGVAEELVRMWEIFHHASVATDFTSGIRAFFTYQ\nRKTGDSYTCLGNTLMSMMALVSVFTMDDLICASFIGDDSLL\n>u276528\nLENYFSKFDKSQQEICLFLEMELYRLLGVDVDFIQNWYRTSEYSRIKSTTAGLKLFSVWQ\nRKSGEGTTAMGNSIVNMLVLCCFYDIDPADLLYSVFMGDDSLL\n>u276611\nATTDVKEMDSIQDLFTQEIEKEMLRELGCSELFIAEYYSYRSKYPIVCRGVFSGKGEGEK\nTSGEPGTLLFNSVLAAVFTNAIFRGIGISVLLFKGDDVIK\n>u276726\nYEFDVPKFDKSQDETCFALILEVMRIVGISEEFINYWERASFSGSVFNAQFSMVFTLFYG\nNRSGSGGTLAVNCICLLFAFLSEFSNLNIIAALIKGDDSVI\n>u276740\nTVNDYTAYDQSQTAETLAFELSLNDLFHVPDHITAYYAELKLSLTCAFGGLAVMRFTGEG\nPTLRANSDFNAAIIGLQYDFSSSQPICVAGDDSAM\n>u276834\nLEVDFSKFDKSQQRFCLLTECYIMKKFGMAPELVRMWEIFHHASVATDFTAGIRAKFTYQ\nRKTGDSYTCLGNTLMSMMALASVFDLSDLLCASFIGDDSLL\n>u276987\nIENDYTAFDQSQRGEFLNLHIKIMEYFNIPKDFIETFIKAKTEASTFIGILMIMILTGEW\nCTFLFNTFSNQAMAVTKYDFDPEVAQVYGGDDSVI\n>u277155\nVENDMEKFDKSQQWTALRLEWFLYTLLGLSVVESHMWQQGHIGCVMTSILAGLKVFSLLQ\nRRSGDATTALGNTIVNILSVVATYDISGFLYAMFLGDDSLI\n>u277349\nFMADFSEFDSSQEKQGVISSLMILRMMGANTKVMSLYLQMRKQWILTSTNHTDHMSIYHT\nLNGVWKQHSGQPFTLDGNTMFNMSAIGMCYDIKNLAFASFKGDDSAI\n>u277455\nTENDFTAYDQSQRGVVLGFEIHLLRFYSIPEPLIELYVEMKLHLRRSGVPFVESELGTMR\nFSGEPATWSFNSRFNLVVSHAKFDLRGVPVLISGDDFLA\n>u277553\nLSSDLSQQDSSHTNVHRFFIAKVMAFLGFNDTIVTLYLISRARRFCSGLTILGLMFEVIE\nRLFSGEPGTAFFNWLMSGGTAACTLDLVTRPPRLMIGKGDDFSV\n>u277626\nEMCDIEGFDSSIRGADVTLERLLMTHFGVPADHIDAYCEDKMDFHTRTIHFGIMRFSGEI\nFTWLFNTMHTLARECLKFGHKPGDPIAVSGDDVLK\n>u277643\nTSNDFSEFDQSQTGDALSLEMVMMSAYNLPDAITDYYFSLKTQLRTSMGPLATMRHTGEG\nPTWFFNTMFNCAVTGLRYGYLGDKARCFAGDDSCI\n>u277715\nLEIDFSKFDKSQTDICYELEMNFWGMLGMDTVLEQLWRIGHYKCTAIDFISGIKLYIAYQ\nRKSGDSATAFGNTLISMLTIAYCQLPVTLSCAYFVGDDSLF\n>u278127\nYEDDYTGFDGTQNEDFLSFQMFILRALHLPEALIEDYLEWVTDLRGMGKPFGIFIASGFK\nPTWLFNTLDSMAYQALKHKLQRHLPGTKHVARAFSGDDTLH\n>u278324\nQEDDFTKFDQSQTAEVLHFEILFMKHLSLPQDLIDFYFWTKTHCKSQLGPLAIMRFTGEK\nFTFFFNTLLNMAFQMTKYVIIKKTPQVYGGDDSAI\n>u278487\nLEIDMGKFDKSQGLTALLFECEYFKRAGMPIWMVNLWFISHFLIKVKGFGTSLKFSLPHQ\nRRSGDPWTYGGNTMYLLAIMLNLCGNRINYIMVSGDDSLI\n>u278496\nFSTDYSRFESSFKFDIMLALELAYYKPMVPEDIYEAMCKCHKYFRSRNIFVTMDYDNGIR\nASGDGDTSLSNTLSNICLTSYIFDTLQIPWDGLFEGDDGLI\n>u278545\nLENDFKAYDKTQDNVALEIELSFLALLGVPLDLLEMWRSGHVYTRATCRETGFMLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFPKPEDARTKIRCAFFLGDDSLF\n>u278634\nYSNDYTSFDQSQTGEVLASELLYMWHAGIPESIIRIYEQNKTDMFCAFGHLQTMRFSGEP\nATYAFNCRCNLAVLNLQFPLDRNESLAVMVSGDDGGI\n>u278638\nTENDYTLYDQSQSEEFLHFQSLLMRYHNLPTFIIDYYILYKTSLVSQHGPLDIMVFSGEP\nPTFQFNSDDNIAFAHTQYDIDPTTPLLIAGDDSVI\n>u278659\nTVNDYSAFDSTQGGESVQMELAWLRWAGAPGEVVDMYSWWKTHIFNSVVGEKKTSRDTGE\nPGTFLFNTLYSIGNTALKYGTACFETTTFLFGGDDMAA\n>u278691\nLEIDFSKFDKSQMQTCFEVEMTIYELLGFDQYLLNLWKIGHIETTITDFVNDFKAFIMYQ\nRKSGDISTAFGNSLISMIAIAMTTNFKEGVTCAMFLGDDSLI\n>u278895\nFEDDLSKQDRQTDKHLLDTEYAIYDILGLSEEVSSSFRKIHDLWKMKAREIKGIGTEQRN\nTGVATTALGNALVNLIAHRPFIESHWSQIKITTILGDDHHG\n>u278921\nFENDFSAYDKSQHIETWIVEKTVYEMLGLDVGLLDVWEDAHWFTKVRSPAVGLTMHLLFQ\nRKSGDVTTSFGNTLVNMICLTYCYRIREFTYGLFLGDDSLI\n>u279067\nIANDWTAWDSGCNKTTVLAVAHYFTSLGLPQSYVDTYVHDRLNVTSYLGTHRTKQESGDR\nWTWLVNTIVNMMISGATIACPAATPAGFSGDDSII\n>u279286\nVCGDDSITVIKHQNVMYFVENDFSRYDTTIGPEAIAFELTFYDKLGYFDGDARFVLEQQK\nMTKGYTRVGVSYSFPGERKSGDPNTSTGNSMIT\n>u279450\nSCNDFSEWDSCFRECFAMLTCKLLTFMGCPRALVNWFGKYRQEWEMHYHSVFGMVSLKGH\nEKQFSGNPFTICENTIGNLALCFSIFEYKNLKFAMFKGDDSAV\n>u279454\nTEDDYTAFDSTQGGEFLNFDQHLLLAAGVPQVDIEAYLYFMTNLETWMGRMGLMMPSGCK\nFTLLFNTTRSAAYQALKYDIPRNTPIALTGDDTAC\n>u279460\nVESDMKNNDGTQQAECRKYEAMFYKKLGAPDWFVREFAKNTQVRVWTRFGISARINGQRW\nSGESTTTTGNSYVSMCIMLAALDSAGVQRSLNVHGGDDYLG\n>u279475\nTANDYTGWDTGVDLAFHHFHAWLLRRVGLGHRVDAYFHQAFNARTHLGPFPIQMPSWSAW\nTWDFNTADDFALTGASTNFPVGTPIAVAGDDSAV\n>u279632\nTTSDYTAYDSSQKGDSLGLEHLLMYHFGLEKSWTLLFADYTKAFKTIPELYLHWKTHIES\nTVIGSKETGRDTGEPGTYDFNTYFNLALISLMYRPAGNVPIAVGGDDMAA\n>u279772\nRENDFRMFDKSQLQKTVELELAFYERLGHCKYLNAVWAEGITTSLVKSLLLAVKVIINYQ\nRRSGACTTAFGNTAINMITNAWELKLLNNFFAVYFISDDSSL\n>u279808\nLELDCSKFDKSQGKVLLMFQELLWRKLGLDPHMGGIWNEAHRLTFISDFLNGVMFSVNYQ\nRKSGDATTYMGNTLVTMAMIAYLYPIEKALFSVFGGDDSLV\n>u279878\nVDNDYTAFDQSQDATALFLEIELMRHFNVPSDMIELYYWLKTETRSWLGPFGIMRFTGEW\nSTFLFNNLFSIAYSHTKYSFPPGMLQCYGGDDSSF\n>u279903\nTANDYTAFDASQGYDSVMLECHVMRLAGLPDALVDSYEQWKISIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLHCLALFGGDDSAI\n>u279930\nTANDYTAFDASQGYDSVLLECHVMRLAGIPDHLVDSYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLQCMALFGGDDSAI\n>u280499\nDENDYTAYDQSQDGGVTGFKRRIMETFSIPEHYIKENEERCMTLRAFMGELGHQMFSGSW\nDTHFINTTLNVAMNHTKYNINPRTPQMYAGDDSAT\n>u280505\nFEADISQFDKSQTELSLAVEMAVYRKLGLDPEWAMRWEGAMFETRNVCHAVGITIYLMHQ\nRKSGSVTTSIGNTIVNMVACAYPDTLTAECIIAAMFLGDDSLI\n>u280615\nFANDFTEYDSSQYELSPYANSIVMLAMGAPSLLVDVYLQMRADWVLSDDMMKLYGHQKMH\nSGEPFTLTGNTFFGMLVIAFAIEFDDLAYAIFKGDDSAI\n>u280979\nTANDYTAFDASQGYDSVLLECHVMRLAGLPDALVDNYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSVAVSSLKYGKLRCLALFGGDDSAI\n>u281095\nFTCDFTAYDQSCTEETLSFELAFMEYCGIPISLVDLYRWIKLSMRTQFGFSAIMRFTGEF\nGTYDFNTFWNMAYMETRYHIPRTLACAFSGDDSLF\n>u281100\nTANDYTAFDASQGYDSVLLECQVMRLAGLPDQLVDNYEQWKVSIRSNLIGPKDVSRDTGE\nPGTFDFNTLFSIAVSSLKYGKLHCLALFGGDDSAI\n>u281105\nFENDFSTFDATQSDRALEIIVNALSLTNMSKQALDLMLLDVQGCRISNSVGSYTAKGVRF\nSGRSETLVGNTILNLVVMCHAFKGKLSAMIIKGDDSVV\n>u281161\nIEDDFSAYDSTQSKGCHYAEKWFYDKFEGFAVAKNIVSFQAKTVGEGRFHRYEVEYTRKS\nGDQNTSIGNTIINFLAHAYAIAMYEKKYETKVKYYMIGLGDDNLL\n>u281283\nAIVDAKEFDSQQSDVTVYAEKCFLELLGANPRSLEEYYKVRDAGVPWGLIGRAYGLMGGK\nKGSGFPDTKMGNTVLQGILANQQFKGLGPKVEAGKGDDWLR\n>u281359\nEMCDIEGFDSSIRGADVTLEKELMAFFGVPQTHIDAYVEDKMDFHTRTIHFGIMRFSGEI\nFTWLFNTMHTLARECLKFGHQPGDPIACSGDDVLK\n>u281901\nFENDFEKFDKSQLEETFAVEMLIYKRLGLDLKLLDLWAFGQTLKTATSLLLGVRVQLLFQ\nRTSGTVVTAFGNVLVNMAATAWAYKLRDTKFHAAYYVGDDSFV\n>u282014\nLETDFSKFDGTLSSDVRFCEKKIMCNMMLPQHRRKLKELFDAEINCPSKTSLGHRYKVGT\nSRLSGSANTTLGNTLVNAFAAYVGLRLAGLTTQESFANLGPKYGDDSIT\n>u282903\nVENDLKKQDRQTKMDLIXVEFGLYEKLGMNKNLLDFYKQVHTLWHWFNKQVNGMGTEMRL\nTGFPNTSLGNVIVNLIVNTNLIQQLGPKLTMFIVLGDDGLM\n>u283000\nVENDLKKQDRQTKMDLIXVEFGLYEKLGMNKNLLDFYKQVHTLWHWFNKQVNGMGTEMRL\nTGFPNTSLGNVIVNLIVNTNLIKQLGPKLTMFIVLGDDGLM\n>u283393\nGTNDFTAFDQGQDGATLQMEVRLMEAFNTPRPMINYYIWLKMNVYSWLGPFSIMRFTGEF\nCTFLFNTLSNMAFSNLRFFLVGVVCLFGGDDSAF\n>u283498\nFENDMSKFDRQTDTQLINIELAIYKLLGCDSTTLKHWRKMHGKWKWRSKHANGTREAMRL\nSGQATTALGNAITNMVCHTDYFYDNKLSITGALFLGDDMLV\n>u284330\nVDNDFTEYDASQNSSTIEFETCILEDLGLTDECIDLYRNHRSQWKTYYPSYASFEGVDKK\nHSGEPFTIDFNTSLNMAICGYIYDFDDLVVAQFKGDDSNI\n>u284512\nFENDFEKFDKSQLEETFAVEMGIYRKLGLDIRLLDLWAYGQVFKTATSLLLGVRIELLFQ\nRTSGTVVTAFGNVLINMAAMAWAYKLRVIKFFAAYFVGDDSYV\n>u284580\nTENDYTAWDSSIDGPFVKFDLWLLRQIGVPEDYLSTWAEERCSTTCFMGNLRLMQHSGDR\nYTFLLNTVRNLAITNAQYAGMAGRAQAYGGDDSLV\n>u284777\nMAGDDFFGLVNSQGLRAYENDFSKMDRTQGVHALGVEFVILRAFGVRHFTLCRLFDAMLS\nNPRYESVKYDIRVKLPMQPQRATGAPDTTIGNTLIN\n>u284912\nVSGDDSVCSRAMTNFQGRARNVSTYVEGDFSAFDQAQREECLRAHGLWMKMIGVSPYVID\nLILHACSMPYKALCKRLRVDGDCGYEMATGIDWTTVINSMSN\n>u284977\nSEADHAKFDKSLDDVFLELEIIFLDSFRMPARVVRLWREMHEYCRLLSMQHAIAYDLPLQ\nRKSGDPATWIFNTLATLCMLCYAYRKVDLLLVSGDDSLI\n>u285023\nAANDFSEFDSSQNNVGHLLLKNILIKIGCPIEMAELFAARMHQRVVTADVGSLNVENKKD\nSGRVDTLIDNTLFGAAVVLYLLDPSSKLTHAFFKGDDSLL\n>u285318\nMEADISKFDKSQNEFCLLLELELMKRLGVPTCVISAWDYVHTXTKLNFRKEGLIVDTGVX\nRKSGDPGTFLFNTFVTMAMLNYCLDLHHPNIKCAIFGGDDSLI\n>u285388\nFENDFEKFDKSQLIEALRLEFRAYQILGVDKFLENLWYYGVTLTEARNLLLGVRIYLLFQ\nRKTGSVTTSFGNVLVNMISTCWAYKLGDTGFVALYYVGDDSYI\n>u285591\nTINDFSEFDSTQGAESVYMEVAMMRHYSIPEELVELYLHWKLFQTSKLIPEKKTARDTGE\nPGTFDFNTIYNIANCTLKYGKICDFALFGGDDTAI\n>u286183\nGTCDYSAFDQSQDISVLLFELKVYEAMGVPRALLERFKRWKMNLICQYGSLEVMRFTGES\nGTILGNTLANMALSNLERDLAGPRGVHSPCAFIGDDSVF\n>u286275\nWESDLEQQEKSMSGAYVTLFSCIMRHFGVPDDIIDAYVEDKLDKQTARMHFGLMTFSGEI\nFTFLANTLGNIARFVAKYDVTPGERGKFGGDDLLM\n>u286454\nYECDMSKFDKSQGQAVLEMEIHVLKHFGVPDYLVTVWRMAHTHTIVKDRSHQITFKIDYE\nRKSGDPATFAGNTLNQMASHAQVYPVNKFVYGMFAGDDSLI\n>u286457\nVDADANKQDRQTNKHLRMIEMQVYKILGIPASIAESWISNFETRLLQSRTTRVSGTPWQR\nASGEPTTALGNYIVNLVVHGKVIRTNIKSLVLSMGLGDDHLS\n>u286550\nFMADFSEFDCSQEQQGVISSTIILSMMGCNHKVLDLYIQMRKQWTLTSVNELEGIKMMTK\nLKGVWKQHSGQPFTLDXNTMFNMSAIGMCYDIKNLIFASFKGDDSVL\n>u286809\nEEMDISQFDKSEGENCVEGIEKPLVLDLGLDPEVAALWYEPNEEARIASVAFNFKIFLQV\nQRRSGQLSTLLGNSMVTAGAVCLTMALDRVPFLWFFFQGDDSLI\n>u287179\nLEVDFSKYDKSQDYNCYIVEEMLLVALGFPVELLGAWRYACFVSKLVNIKTKISGKIIYQ\nRKSGTAVTYFGNTLVCMSSLCTVADLSNAACLFSGDDSLI\n>u287316\nMANDYTEYDQSQTGEALAFEVSRLRAHRVPEFLVQYYEELKLSLRCQYGHLQTLRHTGEG\nPTWKFNSDFNAAVAGCQYVFSAGQARAISGDDSAF\n>u287411\nAVIDFDSYDATQNRFTQQIERRIMEKLGISEYVIDIYYSFRENYPLVTKILKANGGYTKT\nSGEPGTLLFNTLLAMALTNYIIRGFLKIVMLGQGDDVIK\n>u287427\nTYCDYTGWDSGVDESFTLLYSDLQRSYGVPIDIVERFIDERHNSRSFMGPMPAMQFSGDR\nYTWLNNTVGNMALTGLSFHIDADTRAAFSGDDMIL\n>u287863\nTVNDFTKFGATQGGEALQMDMQWFRWAGCSEAVVYRYRELKLSMIALGSTKKTCRDDGEP\nGTYCFNCLYAIGVTALRFGVAALWRGMWWFGGDDEAC\n>u288181\nVCGDDSLVVTNISGSWRVFEGDASMYDQSESKGPLGTAWAVYMKLGVTAYVIQILTTLAE\nNTYTVRSRKSHEVLFINKKDRPLRDTGGADTSLGNSIVM\n>u288663\nLENDFKAYDKTQDNVALEIELSFLALLGVPLDLLEMWRSGHVYTRATCRETGFMLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFEKPEDARTKIRCAFFLGDDSLF\n>u288945\nFSGFDEVLKGKNYSQRGEIFKKKYITKFLLENDYSKFESSQRPEVLKLIELELFKKIIDP\nQYLDEFLKIYEYKLHKPIKTIQGISAYVYGCRGSGDMDTGLGNTIVN\n>u289188\nYADDYVAFDEKQGLAFLWLHVFIMLGPNGIKLPSGFKFTWLFNTLDNMAYQAIKYWLTPR\nNIKPVARSFSGDDSGH\n>u289228\nSCNDFTAFDQGQDASFLAMEVRLMEQLSLPASEIAFYIHLKTHTFSNLGSFSLMCFTGDV\nFTFILNTLANMAISNLRFCLDKSNKPLCFGGDDSCF\n>u289527\nTINDYSAFDSTQGAESLWMEIVLMRHYNLPADLIQAYQDWKCHQRSSIIGLKTLSRDTGE\nPGTVLFNTFYSVANCTLKYGKINAFSLFGGDDMAS\n>u289867\nTINDYTKFGATQGGDSLKMDMLWFQWAGVPDSLVELYFHYKTRLETNGFVKTISRDDGEN\nGTWLFNTLYNLGNIALRFGVSALHSGMWLLSGDDGEN\n>u290151\nVACDISEQDTTKTEATHLVFRWLFEAIGVPSHTYDIVQQACIRWIGFGLDFSINNVETFQ\nSGINWTYLNNTVDSMARIGASFEIEGLRLAMFKGDDAYV\n>u290693\nVEDDLEKQDGQTTHLVIETEMLIYAHLGVDPGTLELYSWIHKRWAWKSQGLSGVWDAMRL\nTGQPTTALGNAITNLLVHVRFFIKNRSDIIVMYVLGDDNAI\n>u290833\nCSGDDSIVAEFHPGHIVFWEGDASMFDSSQSRGPLKWQYKLMHMLGVDASVTMALYKVAH\nATLVVRPRTGDYDMDVFRVDLSDRPHRDTGGADTYLGNTLVM\n>u291244\nLENDFKAYDKTQDNVALEIELSFLALLGVPLDLLEMWRSGHVYTRATCRETGFMLLTTFQ\nRKSGDVTTSFGNTLINMVGTAQAYFVKPEDARTKIRCAFFLGDDSLF\n>u292259\nLENDFSKFDKSQDRFSYMLMQFIMAKLGFDDELLDRWVDANERCTLKSMALGILLVTRYQ\nNKSGGPATALMNVTVNLCATVTCYAGTDVVWAAFMGDDSIV\n>u292454\nYERDGKNWDSTMQRPHIDLRKHAYACAGEKFLEFVEAGYRVKGRDPCGALKYILQGTVKS\nGHNDTTLGNSLVNGLLAATALKRCGLRGDIIVAGDDLLC\n>u292732\nFELDVSKYDKSQEAVWLDAQCIVFKLLGMCDQMIDLWRALHEMCILTAPKFGATYRVGYQ\nRRSGDALTWFGNTLVLLMMMAYLYPIEEAHMVLLGGDDNVT\n>u292858\nYFDDASKFESSQRENLLRDVELSLWQQILLPSDFELLKRCFEVKMVKHGYTNLGMEFIFY\nALRCSGEVDTWLGNTIMNWVAHRYFXIKNGFPKYNFIVTGDDGVG\n>u293202\nVEMDYSKFDKNQDETMMMYQLFLFEYLGLKDKVIIDYLLTHLNCELMFRDAGIKVRVSAQ\nRRTGDAFTFFGNTLMTMMMAIYAFREEDIVLGVFGGDDSII\n>u293475\nDCSDVNEWDTKFRTVFQQLTSTLVCAIGCPTWLASWFTRFRSKWKMVIMTKSIRTVLIGD\nEKQFSGNPFTICENTIGNMAMTYAIKRFISEYMSLFKGDDSAI\n>u294390\nIENDLSRNDSTQTTWMRKYEAMFYHKLGATKWWVREFVKNTSVDVWTRFGISAHIEGQRW\nSGEVPTTPGNGHTNXAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAISPKLGXLSRFQ\nXYTVKHKSVNVWTRFGISATIEGQRWSGEVPTTPGNGHTNACHILSYLPEVGVTESVSVV\nYGDDRSE\n>u294466\nAEDDLGKFDTSIREEWCWYEWWLCKTFGAPKALLDLLEANIQTHGYTMHGMKYKVLSTRK\nSGDPFTSMFNSNINGVAHAFVFCMHPRSRQMPLRRARKILKMLLQGDDNAI\n>u295080\nLENDFSKFDKSQDEFSFKVFMYIMQNLGFDQELLDRWVESNRDVTMRSMILGILLKASWG\nNKSGGPATALQNVALNLAAVCTCYPGTQIVWAVFMGDDSIV\n>u295996\nIAVDAGKLDQVLPSFISEFSIGHRLGNAFHSCMRLTGEPGTYDDNTDYNIAVLFLRYDLR\nPYHNVLVSGDDSAI\n>u296007\nLENDFGKFDKSQDSFSYAIMIRVCEECGFNQELLDRWRDANDKCTLHSTLLTIVLVVHDQ\nNKSGGPATAFMNAVSNMSAVAVCYAGTVIVWAAFMGDDSLA\n>u296316\nSTNDYSAFDQSQTGEALSLEITLLRAFSIPDHVISYYEQVKLYLTCQFGALAVMRHTGEG\nPTLFFNSVFNAALVGVQYDLPAGTAIAVAGDDLPI\n" }, { "path": "tests/input/TestKmers/ambig_bases.fasta", "content": ">seq_with_Ns\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGTGTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCTAATCT\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGGACACACAAAAAGAATGAAGGATTTTGAANNNNTCTTTATTGTGTGCGAGTAACTAGAAATTGAGATTCTAATCT\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGTGTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCTAATCT\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGTGTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCTAATCT\n>seq_with_ambig_bases\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGTGTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCTAATCT\nMRWSCGGACACACAAAAAGAATGAAGGATTTTGAANNNNTCTTTATTGTGTGCGAGTAACTAGAAATTGAGATTCTAATCTTTGAAATTGAAATTGAGATTCTAATCT\nCGGACACACAAAAAGAATGAAGYKVTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCTAATCTAATTGAGATTCTAATCT\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGHDBHDBHDBCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCT\n" }, { "path": "tests/input/TestKmers/filt.fasta", "content": ">seq1\nAAAAAAAAAAAAAAAAAAAA\n>seq2\nAAAAAAAAAAAATCGATCGAAAAAAAAAAAAAAAAAA\n" }, { "path": "tests/input/TestKmers/palindromic_kmers.fasta", "content": ">seq_with_reverse_complement_palindromic_kmers\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n" }, { "path": "tests/input/TestKmers/simple.fasta", "content": ">test_seq\nTCGATCGATCGATCGA\n" }, { "path": "tests/input/TestKmers/simple.fasta.kmers.k4.txt", "content": "ATCG\t6\nGATC\t3\nTCGA\t4\n" }, { "path": "tests/input/TestKmers/tcgaattt.fasta", "content": ">rec1\nTCGATCGATCGA\n>rec2\nATTTATTTATTTATTTATTT\n>rec3\nAAAAAAAATTTTTTTT\n" }, { "path": "tests/input/TestLastalDbBuild/expected/TestLastalDbBuild.des", "content": "Bundibugyo_ebolavirus,_complete_genomeBundibugyo_ebolavirus_isolate_EboBund-14_2012,_complete_genomeCote_d'Ivoire_ebolavirus,_complete_genomeReston_ebolavirus_isolate_RESTV/M.fascicularis-tc/PHL-USA/1996/Ferlite,_Philippines/Alice,_TX,_complete_genomeReston_ebolavirus_isolate_RESTV/Sus-wt/PHL/2009/09A_Farm_A,_complete_genomeReston_ebolavirus_-_Reston_strain_Reston08-C,_complete_genomeReston_ebolavirus_-_Reston_strain_Reston08-E,_complete_genomeReston_Ebola_virus_strain_Pennsylvania,_complete_genomeSudan_ebolavirus_isolate_EboSud-609_2012,_complete_genomeSudan_ebolavirus_isolate_EboSud-639,_complete_genomeSudan_ebolavirus_isolate_EBOV-S-2004_from_Sudan,_complete_genomeSudan_ebolavirus_-_Nakisamata,_complete_genomeSudan_ebolavirus_strain_Gulu,_complete_genomeZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/COD/1977/Bonduni,_complete_genomeZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/COD/2007/43_Luebo,_complete_genomeZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/1Eko,_complete_genomeZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/2Nza,_complete_genomeZaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/Ilembe,_complete_genomeZaire_ebolavirus_isolate_H.sapiens-wt/GIN/2014/Gueckedou-C05,_complete_genomeZaire_ebolavirus_strain_Zaire_1995,_complete_genome" }, { "path": "tests/input/TestLastalDbBuild/expected/TestLastalDbBuild.prj", "content": "version=876\nalphabet=ACGT\nnumofsequences=20\nnumofletters=378200\nletterfreqs=119533 81197 74635 102835\nmaxunsortedinterval=0\nkeeplowercase=1\nmasklowercase=0\nnumofindexes=1\nintegersize=32\ntotallength=378222\nspecialcharacters=22\nprefixlength=13\nsubsetseed=A C G T\nsubsetseed=AG CT\nsubsetseed=A C G T\nsubsetseed=ACGT\nsubsetseed=ACGT\nsubsetseed=A C G T\nsubsetseed=A C G T\nsubsetseed=ACGT\nsubsetseed=ACGT\nsubsetseed=A C G T\nsubsetseed=ACGT\nsubsetseed=A C G T\n" }, { "path": "tests/input/TestLastalDbBuild/expected/TestLastalDbBuild.suf.md5", "content": "38fa84aa28cd468b7dd789906a6db721\n" }, { "path": "tests/input/TestManualSnpCaller/output.fasta", "content": ">EBOV_2014_G6060.1\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACAT\nGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGAT\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Bundibugyo_ebolavirus/GCF_000889155.1_ViralProj51245_genomic.fna", "content": ">NC_014373.1 Bundibugyo ebolavirus isolate Bundibugyo virus/H.sapiens-tc/UGA/2007/Butalya-811250, complete genome\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGTGTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTC\nATTGAAATTGAAATTGAGATTCTAATCTCGACGGATCGATCCCCAATACCAACACTGAGAATTGGCCTGAAGAAGTCATC\nTGCTCCTTGGCAAAACCAAGAGCAGGCCCAAAGGGCCATTAGGCCACATCTGCTGAGCCTGCAGAACACGCAGGACTTAC\nTTAGCAGAAGAGAGCGCGTGCCGAAACCAGCCAACAAATTGACACAGCTGCTCACTCTGACCCTGAATTCATAAACAATA\nTTAAGTTGACAACAGAGATACTAATCCAATATTTGGATCAAGAATCAAAATAGTGAAACGACTGACTATCCCTCCTTAGA\nATTAGCAAAGATCCTTTTGTAGACTATTGTGCTACATTCTCTATCCAAGACCTCAAAATGGATCCTCGTCCAATCAGAAC\nCTGGATGATGCATAACACATCTGAAGTTGAAGCAGACTACCATAAGATTCTAACTGCCGGATTGTCCGTCCAGCAAGGCA\nTTGTGAGACAAAGAATCATTCCTGTTTACCAAATCTCAAACCTGGAGGAAGTATGTCAACTCATCATACAGGCATTCGAG\nGCTGGCGTCGACTTCCAGGATAGTGCAGATAGCTTTTTGTTAATGCTATGTCTGCATCATGCCTATCAAGGGGATTATAA\nACAATTTTTGGAAAGTAATGCGGTAAAATACCTTGAAGGTCATGGATTCCGTTTTGAGATGAAGAAAAAGGAAGGTGTCA\nAGCGCCTGGAGGAACTACTCCCTGCTGCCTCGAGTGGAAAGAACATCAAGAGAACATTGGCTGCAATGCCCGAGGAGGAA\nACAACAGAAGCAAATGCTGGACAATTTCTTTCATTTGCTAGTCTGTTTCTCCCAAAATTGGTTGTCGGAGAAAAGGCCTG\nTCTGGAGAAGGTTCAACGACAAATCCAAGTGCACGCAGAACAAGGTCTGATTCAATACCCGACATCTTGGCAATCGGTGG\nGACATATGATGGTCATCTTCAGACTAATGCGAACCAACTTCCTGATTAAGTTCCTCCTAATACATCAAGGAATGCATATG\nGTTGCAGGGCATGATGCTAATGATGCCGTCATTGCCAACTCTGTAGCTCAAGCTCGTTTCTCCGGATTGTTGATAGTCAA\nAACAGTGCTTGATCATATCCTCCAAAAAACAGAGCACGGAGTTCGCCTGCATCCCTTGGCGCGAACAGCCAAAGTCAAAA\nATGAGGTGAGCTCTTTTAAGGCCGCTTTAGCCTCACTAGCACAACATGGAGAATATGCCCCGTTTGCTCGTCTGCTGAAT\nCTATCTGGGGTTAATAATCTTGAGCATGGGCTTTTCCCTCAACTTTCTGCAATTGCTTTGGGAGTAGCAACTGCACATGG\nGAGCACTCTGGCTGGAGTCAATGTAGGAGAGCAATACCAACAACTGCGAGAAGCAGCCACTGAGGCCGAAAAGCAGTTGC\nAGAAATATGCTGAATCTCGTGAACTTGATCACCTAGGTCTTGATGATCAGGAAAAGAAAATCCTAAAAGACTTCCATCAG\nAAAAAGAATGAGATCAGCTTCCAGCAGACGACAGCCATGGTCACACTGCGGAAAGAGAGATTGGCCAAATTGACCGAAGC\nTATTACTTCCACCTCTATCCTCAAAACAGGAAGGCGGTATGATGATGACAATGACATACCCTTTCCAGGGCCAATCAATG\nATAACGAGAACTCTGGTCAGAACGATGACGATCCAACAGACTCCCAGGATACCACAATCCCGGATGTAATAATCGATCCA\nAACGATGGTGGGTATAATAATTACAGCGATTATGCAAATGATGCTGCAAGTGCTCCTGATGACCTAGTTCTTTTTGACCT\nTGAGGACGAGGATGATGCTGATAACCCGGCTCAAAACACGCCAGAAAAAAATGATAGACCAGCAACAACAAAGCTGAGAA\nATGGACAGGACCAGGATGGAAACCAAGGCGAAACTGCATCCCCACGGGTAGCCCCCAACCAATACAGAGACAAGCCAATG\nCCACAAGTACAGGACAGATCCGAAAATCATGACCAAACCCTTCAAACACAGTCCAGGGTTTTGACTCCTATCAGCGAGGA\nAGCAGACCCCAGCGACCACAACGATGGTGACAATGAAAGCATTCCTCCCCTGGAATCAGACGACGAGGGTAGCACTGATA\nCTACTGCAGCAGAAACAAAGCCTGCCACTGCACCTCCCGCTCCCGTCTACCGAAGTATCTCCGTAGATGATTCTGTCCCC\nTCAGAGAACATTCCCGCACAGTCCAATCAAACGAACAATGAGGACAATGTCAGGAACAATGCTCAGTCGGAGCAATCCAT\nTGCAGAAATGTATCAACATATCTTGAAAACACAAGGACCTTTTGATGCCATCCTTTACTACCATATGATGAAAGAAGAGC\nCCATCATTTTCAGCACTAGTGATGGGAAGGAGTATACATATCCAGACTCTCTTGAAGATGAGTATCCACCCTGGCTCAGC\nGAGAAGGAAGCCATGAACGAAGACAATAGATTCATAACCATGGATGGTCAGCAGTTTTACTGGCCTGTGATGAATCATAG\nAAATAAATTCATGGCAATCCTCCAGCATCACAGGTGATCCGACCTCTAAAACTGAGCTCCTAACTACAAGCTACCCCATC\nACTCTGCCGGAATGCCAGAACCTCCCTCCAAAACAGCTCCACATCGAGAACCTCCGACGCGGTACACAGGCAAGACAGGC\nAACCTAATGATGTTCCTGTTCACCCACAACCGCAACCAACACTTGATCGACTTCCAAGACAACTACAACCCCCTTAGCCA\nACTCCACCACAGAAGCACCACCCCATAACAACAACCCCAAACCAACAACACTGCATGTAAGTATTGTCTCACCCCAAGAT\nGATCCCTGGACACCAACAACCCCCTAACCTCCCCAAGTTGTCATTAAGAAAAAATATATGATGAAGATTAAAACCTTCAT\nCAGAGCTATTTCTTCTACGCTTGGTTAGGACCAGTATTCACAAACTATTTTACAATCCCTACCCAATATGACCTCTAACA\nGAGCAAGGGTGACTTACAACCCACCACCAACAACCACAGGCACACGATCGTGTGGGCCGGAACTTTCCGGGTGGATCTCT\nGAGCAATTGATGACAGGCAAGATTCCGATTACCGATATCTTCAATGAAATTGAAACCTTACCTAGTATAAGTCCCTCGAT\nCCACTCCAAAATCAAAACCCCAAGTGTTCAAACACGCAGTGTCCAGACCCAAACTGACCCAAATTGTAATCATGATTTTG\nCAGAGGTTGTGAAAATGCTAACATCTCTAACCCTTGTCGTACAAAAACAAACCCTTGCAACTGAATCACTTGAGCAACGC\nATTACTGACCTGGAAGGTAGCCTGAAACCAGTGTCTGAGATCACCAAGATTGTTTCTGCACTAAATAGATCCTGTGCAGA\nGATGGTGGCCAAATATGATCTTCTAGTAATGACGACTGGTCGTGCAACTGCCACTGCTGCAGCTACTGAAGCATACTGGG\nCAGAACATGGACGTCCTCCACCGGGGCCCTCATTGTACGAGGAGGATGCAATCAGGACTAAAATTGGAAAACAAGGGGAT\nATGGTACCCAAGGAAGTGCAAGAGGCCTTCCGTAATCTGGATAGTACTGCCCTTCTAACGGAAGAGAATTTTGGGAAACC\nAGACATATCCGCAAAAGACTTGCGCAATATCATGTATGATCACCTCCCAGGTTTTGGCACAGCATTTCATCAACTAGTGC\nAAGTTATCTGCAAGTTAGGGAAGGACAATTCCTCACTTGATGTAATTCATGCAGAATTTCAGGCCAGCCTTGCTGAAGGA\nGACTCTCCTCAGTGTGCCCTGATTCAGATAACCAAACGGATTCCTATTTTCCAAGATGCAGCACCACCCGTAATCCATAT\nTCGGTCACGCGGTGATATACCAAAGGCGTGTCAAAAGAGCCTCCGCCCTGTTCCACCATCACCAAAGATTGATAGGGGTT\nGGGTATGCATATTCCAGCTACAAGACGGAAAAACACTCGGACTCAAAATCTAAGGTGAACAATTGCGCAACCTCCACAGT\nCGCCTATATTGCTTCCTTCCGGAATCAGGGTATGATCGCGTAAAAAATAAGCTTCCAACATATTGATACACGATCCATAT\nCCATAATGCCATCTCCAGGAATATGAGAACGCAAGGCCATATCAGGACCCGATCTCAATTCCAATGCAACCTACTGTTAA\nGAATAAAATAACCAATGTCCTCTAGCCTTATATGTTCTCAAAAATACAAGTGATGAAGATTAAGAAAAAGCATCCTTTAC\nTTGAGAGGAGCTAATTCTTTATACTTCATCTAATCTTTAAGTAAGTTGATCACTACCACCATGAGGAGGGCAATTCTACC\nTACTGCACCGCCAGAATACATAGAGGCTGTCTACCCAATGAGAACGGTTAGTACTAGTATCAACAGTACTGCCAGTGGTC\nCGAACTTTCCAGCACCGGATGTAATGATGAGTGATACACCCTCCAACTCACTCCGACCAATTGCTGATGATAACATCGAT\nCATCCAAGTCATACACCAACCAGTGTTTCATCAGCCTTTATACTCGAGGCAATGGTGAATGTGATATCGGGGCCGAAGGT\nACTAATGAAGCAAATTCCTATATGGCTCCCCTTGGGTGTTGCTGATCAAAAAACATATAGTTTTGACTCAACTACAGCTG\nCAATTATGCTCGCATCGTACACCATCACTCACTTTGGCAAAACCTCCAATCCGCTTGTGAGAATCAATCGACTTGGTCCT\nGGGATCCCCGATCACCCGTTGCGGCTTCTAAGAATAGGAAATCAAGCCTTCTTGCAAGAGTTTGTGCTGCCTCCAGTTCA\nATTGCCGCAGTATTTCACTTTTGACCTGACGGCTCTAAAGCTGATCACTCAACCTCTCCCGGCAGCAACCTGGACGGATG\nATACTCCGACCGGTCCTACAGGAATACTTCGTCCTGGAATTTCCTTTCATCCCAAACTGAGACCTATCCTATTGCCAGGG\nAAGACCGGGAAAAGAGGATCCAGCTCCGATCTTACTTCTCCTGATAAAATACAAGCAATAATGAACTTTCTCCAAGACCT\nCAAACTCGTGCCGATTGATCCAGCCAAGAACATTATGGGTATTGAAGTGCCGGAACTCTTGGTCCACAGACTAACTGGAA\nAGAAAATCACAACAAAAAATGGTCAACCAATAATTCCTATTCTTCTACCAAAGTATATTGGCATGGATCCCATTTCTCAG\nGGAGACCTCACAATGGTCATCACTCAAGACTGTGACACTTGCCATTCTCCTGCTAGTCTTCCTCCAGTCAGCGAGAAATG\nAGCATGAAGTCCGAGGCTGCCCGGCCCACACGACCCCCAGGGCCTTCGTCCGGCTACCGAACCAACCATCCGACCTTCAT\nCAAAACCAAAAAATACCGCCACGCGAAAGCTAAAATGCAGGACCACAATCCAACCAGCAACACCATCCATACACAGGTAT\nCAATTGGGCTGCCGCAGCATATAGACCCAATAGCAAGCTGCTGTCCAGAAAATAGTTCCGGAAAGTAACTCAACCATCGC\nAAGCCCAATGCAGCTTTCAGAAATCCGCCAGCAACCCAACTCCACTGTACCCCCAATATTAACCTGAATCGACTAACCGC\nACTTTAATTTGAAGTACATTTGTTCAATGGGTTCATTATTAACAGTGTTGCTTTTAGATTGTACCTTTGCTCACAGATAG\nTAAATTGTTATGGTATCAAATCTTATTAAGAAAAAGAACACGATGAAGATTAACGCGACCTAGAGCGCTGCCTTCATCTC\nATCAATTTAACTTGTCAATAGAGCAACCTAGTTTGTGATTACTCATCTTCCGTAGTTGACAAACACTTTGCTGGTTAATT\nGTAAATATACCACAGTCATCATGGTTACATCAGGAATTCTACAATTGCCCCGTGAACGCTTCAGAAAAACATCATTTTTT\nGTTTGGGTAATAATCCTATTTCACAAAGTTTTCCCTATCCCATTGGGCGTAGTTCACAACAACACTCTCCAGGTAAGTGA\nTATAGATAAATTGGTGTGCCGGGATAAACTTTCCTCCACAAGTCAGCTGAAATCGGTCGGGCTTAATCTAGAAGGTAATG\nGAGTTGCCACAGATGTACCAACAGCAACGAAGAGATGGGGATTCCGAGCTGGTGTTCCACCCAAAGTGGTGAACTACGAA\nGCTGGGGAGTGGGCTGAAAACTGCTACAACCTGGACATCAAGAAAGCAGATGGTAGCGAATGCCTACCTGAAGCCCCTGA\nGGGTGTAAGAGGCTTCCCTCGCTGCCGTTATGTGCACAAGGTTTCTGGAACAGGGCCGTGCCCTGAAGGTTACGCTTTCC\nACAAAGAAGGCGCTTTCTTCCTGTATGATCGACTGGCATCAACAATCATCTATCGAAGCACCACGTTTTCAGAAGGTGTT\nGTGGCTTTCTTGATCCTCCCCGAAACTAAAAAGGACTTTTTCCAATCGCCACCACTACATGAACCGGCCAATATGACAAC\nAGACCCATCCAGCTACTACCACACAGTCACACTTAATTATGTGGCTGACAATTTTGGGACCAATATGACTAACTTTCTGT\nTTCAAGTGGATCATCTAACTTATGTGCAACTTGAACCAAGATTCACACCACAATTTCTTGTCCAACTCAATGAGACCATT\nTATACTAATGGGCGTCGCAGCAACACCACAGGAACACTAATTTGGAAAGTAAATCCTACTGTTGACACCGGCGTAGGTGA\nATGGGCCTTCTGGGAAAATAAAAAAACTTCACAAAAACCCTTTCAAGTGAAGAGCTGTCTGTCATATTTGTACCAAGAGC\nCCAGGATCCAGGCAGCAACCAGAAGACGAAGGTCACTCCCACCAGCTTCGCCAACAACCAAACCTCCAAGAACCACGAAG\nACTTGGTTCCAGAGGATCCCGCTTCAGTGGTTCAAGTGCGAGACCTCCAGAGGGAAAACACAGTGCCGACCCCACCCCCA\nGACACAGTCCCCACAACTCTGATCCCCGACACAATGGAGGAACAAACCACCAGCCACTACGAACCACCAAACATTTCCAG\nAAACCATCAAGAGAGGAACAACACCGCACACCCCGAAACTCTCGCCAACAATCCCCCAGACAACACAACCCCGTCGACAC\nCACCTCAAGACGGTGAGCGGACAAGTTCCCACACAACACCCTCCCCCCGCCCAGTCCCAACCAGCACAATCCATCCCACC\nACACGAGAGACTCACATTCCCACCACAATGACAACAAGCCATGACACCGACAGCAATCGACCCAACCCAATTGACATCAG\nCGAGTCTACAGAGCCAGGACCACTCACCAACACCACAAGAGGGGCTGCAAATCTGCTGACAGGCTCAAGAAGAACCCGAA\nGGGAAATCACCCTGAGAACACAAGCCAAATGCAACCCAAACCTACACTATTGGACAACCCAAGATGAAGGGGCTGCCATT\nGGTTTAGCCTGGATACCTTACTTCGGGCCCGCAGCAGAGGGAATTTATACGGAAGGGATAATGCACAATCAAAATGGGCT\nAATTTGCGGGTTGAGGCAGCTAGCAAATGAGACGACTCAAGCCCTACAGTTATTCTTGCGTGCTACCACGGAATTGCGCA\nCTTTCTCTATATTGAATCGAAAAGCCATCGACTTTTTACTCCAAAGATGGGGAGGAACGTGCCACATCTTAGGCCCAGAT\nTGCTGTATTGAGCCCCATGATTGGACTAAGAACATTACTGACAAAATAGATCAAATCATTCATGATTTCATTGATAAACC\nTCTACCAGATCAAACAGATAATGACAATTGGTGGACAGGGTGGAGGCAATGGGTTCCTGCCGGGATCGGGATCACGGGGG\nTAATAATCGCAGTTATAGCACTGCTGTGTATTTGCAAATTTCTACTCTAATCTAGTCCGACTCTGTACCAGCATAATGGC\nCTCTAAAATAAGCTTTTGCTTCTGCTTCCTATAGTTAATACATTTCAGCAAAAATCAACTATTAAGTCAAAAGAAGATCC\nCTCTAATAATCCTAATTACCTTCAAAAATCTAGAACTTTATTAATTCTCAGGGTATTTAGAACAGCCAGATGACTTGACT\nAAGTTTGTACTGTAATAAAAAGATACTTGATGAAGATTAAGAAAAAGACAGTCTTGTGATTGTCACTAATCTTCATCTCA\nAAACATATTATTTTACCAGAAGCTACTATAGCCTACCTCCTTGACACATAGCAAACCTTACTCATGTTGATAATTGTTTG\nCCTGCTATTTACATATTTACTAACTTACAAAATTATCTTGGGGATTTCTCTGAACATATAATCAGAATTGGCATTTAAAA\nCACAAGTTAGTCCTAATGGACTCATTTCATGAGAGAGGGCGTAGCAGAACTATTCGACAGAGTGCAAGAGATGGGCCGAG\nTCATCAAGTAAGAACAAGATCATCCTCCAGAGACAGCCACCGCAGCGAATATCATACACCTAGGAGCTCTTCCCAAGTTC\nGAGTCCCGACTGTGTTTCATCGGAAGCGTACTGATTCTTTGACAGTTCCACCAGCACCAAAGGACATATGTCCTACCTTA\nAGGAAAGGATTTTTGTGTGACAGCAATTTTTGTAAAAAGGACCATCAACTAGAAAGTTTAACAGATAGGGAGCTGCTTTT\nGCTGATTGCACGGAAAACCTGCGGCTCCCTTGAACAACAATTGAACATCACTGCTCCTAAAGATACACGATTAGCAAATC\nCAATTGCAGATGATTTCCAACAAAAAGACGGCCCAAAAATTACACTATTGACACTTTTGGAGACTGCGGAGTATTGGTCA\nAAACAAGATATCAAGGGCATTGATGACTCAAGACTAAGAGCATTACTAACCCTTTGTGCCGTCATGACGAGGAAATTCTC\nAAAATCCCAGCTTAGTCTATTGTGTGAGAGTCATCTACGACGAGAAGGGCTAGGACAGGATCAATCAGAATCTGTTCTTG\nAAGTGTATCAGCGCTTACATAGCGACAAAGGCGGAAATTTTGAGGCAGCCCTATGGCAACAATGGGACCGACAGTCCTTG\nATCATGTTTATAACAGCATTTCTTAATATTGCTTTACAATTACCCTGTGAAAGTTCATCTGTTGTTATTTCAGGATTAAG\nGCTGCTAGTGCCTCAATCAGAAGATACCGAGACCTCAACCTACACCGAGACACGTGCATGGTCAGAGGAAGGTGGCCCCC\nATTAACATCTTCCACAGTCGAATCTACCATAATTTCCCTATTCAACGCAGATAAGAATCAGTACTAAACCACAAGTGCAA\nAAATTAACAAAACACCAGCATAAGTGAAATCCTGTCTGTGATTAGCAACACGAATGATCTTCAATCCTGTTGCAATTCGC\nCAGTGATAATTGTATTCACATTGTGGCCACAATATACTGTCTTTTCCCATTGAAAAATAAGGCTGAATCTATTACGCTAC\nACAAACTTACAGGATTAGCACCACGACGGCTCAATACTATACCTATTGGTCACGGCTCGATGTGTTAATCACTTATATTG\nTATTCATTTGAAATTACTCATTAGGCAAATACTTTGATTAAGAAAAAATAATTGGAAAACCAGAAAATCCCTAGGTATTT\nAAATTCCTATCTCCGGAGATCCGAGATAATTAATCAAGCAATGAGGGAACAATGGTGAACAACAACATATTGTTGCCCCC\nTTTAGATTGGTCAGTTCCAAAAACAAGTGATGAAGATTAATGCAGATGTCCAAGGAACACATATTTGTGATTTAAACGTT\nCCAGTTAGACTCTGTTCAAGGATCTTCATCTTTTGTAGCTCCACTCTGAGTCACAACATAATTGAGTTTTTGCTCAGAAC\nAGTTATCAGGATTAAATTCTCTCAAATAACTGAAACTACTAGCATCACTCTCAATTTCATTACTTACGACAATCATTATC\nTTAATAATATTTCTCTAAATTACTGACTTAATTAGCTTGTAATCAGATAATATCGAAACCAATTTATCATAAGGCATAAT\nTTGTATAAGTGATTTAGGATTTACCCCAGAAGTGAAATAATTCTTAGAATAAAAGACCGACTAGAATATCCTTAAGGCTG\nTCTAACGTGCCACACAGCTAGGGTTAGCCTGACATCTGGAACAAGATCGATACTAATATAGGGATTTGTTTCATACTAGC\nTCTCTGCAAACACAATGGCTAAGGCAACAGGTAGGTACAACTTGGTTTCACCTAAAAAGGACCTCGAGAGGGGGCTTGTT\nTTGAGTGATTTGTGCACGTTTTTAGTTGATCAGACTATCCAGGGGTGGCGGGTGACTTGGGTTGGGATTGAATTTGACAT\nCGCCCAGAAAGGGATGGCTCTACTGCATCGGTTAAAAACTGCTGACTTCGCTCCTGCATGGTCGATGACAAGGAATTTAT\nTTCCTCATTTATTTCAAAATTCAAATTCTACTATTGAGTCTCCCCTCTGGGCATTACGAGTGATTCTGGCAGCTGGTATT\nCAAGACCAGTTAATTGACCAATCCTTGGTAGAACCGTTGGCCGGAGCCCTGAGCTTAGTCTCCGATTGGCTTCTTACAAC\nAAACACAAACCATTTTCAAATGCGCACGCAGCACGCTAAAGAGCAACTGAGCTTGAAGATGCTATCATTAGTGCGCTCTA\nATATCTTGAAATTCATCAGTCAATTGGACGCACTACATGTCGTGAACTACAATGGACTCTTGAGCAGTATCGAAATTGGC\nACTAGAAATCATACCATTATCATCACAAGAACCAACATGGGTTTCCTGGTAGAATTACAGGAGCCTGATAAATCTGCCAT\nGAATCAAAAGAAACCAGGACCAGTCAAGTTCTCCCTCCTGCATGAATCAACCTTCAAGGCTCTAATCAAAAAACCCGCAA\nCTAAGATGCAGGCCTTGATTCTGGAATTTAACAGCTCCCTGGCAATATAGTCCAACGCTACCAACCATCATTTTTTGTAA\nCTGCATCTCTTTTATTTCCTTTCTAACTTGATACAATTATAATCAAGATCCCTAATCCCTTTTGACGAAGTGGGCTAATT\nTTTGCTCATTCTAATAATAAATCATAACCTGAATAAAAGACACCACAATATTATAACCCAATAACACCTAGAGAATTTCT\nGAATTGCTAAAGATTATATACTCGCACTAAGAGACAAGTTAATCAATCTTTACTTAATAATATACTAAATGCTAGATAGC\nTCTGGCTAACTAACCTGAGTTGTGGATTACTCCTTTTAAAAGTCTATCAATTTAAGCTTATCACTAATATTAAGGAGGAC\nTTTTTAAATAAGAGCAAGTGTTATGTAGTCTTACTAAGAATGATTTGAGGAAGATTAAGAAAAAGTGCTTGTGGGGTCTT\nTCCGTTGTAGAGGACACACGAGCAAACTTCTTCCTCTAATTTTAATATGGCAACTCAACATACACAATATCCAGATGCAA\nGATTATCTTCACCCATTGTCTTAGATCAATGTGATCTTGTCACCCGTGCTTGCGGTCTGTATTCTTCATACTCATTAAAT\nCCTCAGTTGAAAAATTGTAGACTACCAAAACATATTTACCGCCTCAAATTTGATGCTACGGTTACAAAATTTTTAAGCGA\nTGTTCCAATAGTTACATTGCCGATAGATTACTTGACCCCTTTACTTTTACGAACTTTATCCGGGGAGGGCTTATGCCCTG\nTCGAACCAAAGTGCAGCCAATTCTTAGATGAAATAGTAAGTTATGTTTTGCAGGATGCACGTTTTTTAAGATACTATTTT\nAGGCATGTTGGAGTACACGATGACAATGTTGGAAAAAATTTTGAGCCAAAGATTAAGGCTTTGATTTATGATAATGAATT\nTCTGCAACAATTGTTTTATTGGTACGATTTAGCAATCCTAACGCGTAGAGGGCGCCTGAATCGAGGGAATAACCGTTCAA\nCATGGTTTGCAAATGACGATTTAATAGACATTCTCGGGTACGGTGATTATATTTTCTGGAAAATACCGTTGTCATTGTTG\nTCACTCAACACAGAGGGGATTCCTCATGCAGCTAAGGACTGGTATCACGCATCAATCTTCAAAGAAGCGGTTCAAGGTCA\nCACACATATCGTGTCAGTTTCCACTGCAGATGTTTTAATTATGTGTAAGGACATCATAACCTGTCGTTTCAATACCACAC\nTCATTGCAGCATTGGCAAATTTAGAAGATTCTATCTGTTCTGACTATCCACAACCTGAAACAATCTCTAATCTGTATAAG\nGCAGGGGATTACTTAATCTCGATACTGGGTTCAGAAGGTTATAAGGTCATAAAGTTTTTAGAACCACTATGTTTAGCTAA\nGATCCAATTGTGCTCAAATTACACTGAGAGGAAAGGGAGATTCCTTACTCAAATGCATTTGGCCGTTAATCACACACTTG\nAAGAACTTATTGAGGGCCGGGGATTGAAGTCACAACAAGACTGGAAGATGAGGGAATTTCACCGAATCTTAGTAAATTTA\nAAGTCAACACCACAACAACTCTGTGAATTGTTTTCAGTGCAAAAGCATTGGGGGCATCCTGTGCTACATAGCGAGAAGGC\nTATTCAGAAAGTAAAGAAACATGCAACCGTAATAAAAGCATTGCGTCCCGTAATCATCTTTGAGACATATTGTGTGTTCA\nAGTACAGCATTGCCAAACATTATTTTGATAGCCAAGGGTCATGGTATAGTGTAATCTCAGATAAACATCTAACACCAGGT\nTTACACTCTTACATTAAGAGGAACCAATTTCCGCCACTGCCTATGATTAAAGACTTATTGTGGGAATTCTATCACCTTGA\nTCATCCTCCCTTATTTTCCACCAAGATTATTAGTGACTTGAGTATTTTCATTAAGGATCGCGCTACCGCAGTGGAAAAAA\nCATGTTGGGATGCAGTTTTCGAGCCTAATGTTCTTGGATATAGTCCTCCAAACAAGTTCTCAACTAAGAGGGTTCCTGAA\nCAGTTTCTTGAACAAGAAAATTTCTCGATTGATAGTGTTCTCACTTATGCCCAGCGCCTGGATTATCTACTTCCACAATA\nCCGGAATTTTTCTTTCTCACTTAAGGAAAAAGAATTAAATGTAGGACGAGCTTTTGGTAAGCTACCTTATCCTACACGTA\nATGTTCAAACTTTATGTGAAGCCTTATTGGCAGATGGATTAGCTAAAGCCTTTCCTAGTAACATGATGGTTGTAACAGAG\nCGTGAGCAGAAGGAAAGCCTCTTGCACCAGGCGTCGTGGCACCACACAAGTGACGATTTCGGTGAGAATGCCACTGTTAG\nAGGCAGCAGTTTTGTTACCGACCTAGAAAAATACAACTTGGCATTTAGATATGAGTTTACAGCTCCATTTATTGAATACT\nGTAATCGATGTTATGGTGTAAAAAATTTATTCAATTGGATGCATTATACGATACCGCAATGTTATATACATGTAAGTGAT\nTATTATAATCCCCCTCATGGAGTTTCGCTAGAAAATCGGGAAGATCCCCCGGAAGGCCCTAGCTCTTACCGTGGTCATCT\nTGGGGGAATTGAGGGACTCCAACAGAAACTCTGGACCAGCATTTCATGTGCACAAATCTCATTAGTTGAGATCAAGACTG\nGTTTCAAATTGAGATCTGCGGTAATGGGTGATAATCAATGCATCACAGTTCTTTCCGTATTTCCTCTAGAGACAGATTCC\nAATGAGCAAGAGCATAGCTCCGAGGACAATGCTGCTCGCGTAGCAGCCAGTTTAGCCAAAGTCACGAGTGCCTGTGGCAT\nCTTCCTAAAACCAGATGAGACTTTTGTGCATTCAGGCTTTATTTATTTCGGTAAGAAGCAATATTTAAATGGCGTTCAAT\nTGCCACAATCACTCAAGACTGCTACCAGGATTGCTCCCTTGTCAGATGCAATCTTTGATGACCTTCAGGGAACTCTGGCT\nAGTATAGGAACGGCATTTGAGAGATCTATATCCGAGACTAGACATGTATACCCTTGCCGGGTGGTTGCCGCATTCCATAC\nATTCTTCTCCGTTAGGATCCTCCAATACCACCACCTTGGTTTCAACAAAGGAACCGATCTAGGTCAACTATCACTAAGCA\nAACCGTTGGATTTCGGAACTATCACTCTTGCTTTAGCGGTACCTCAAGTTCTAGGAGGTTTATCGTTTTTAAACCCAGAG\nAAATGTTTTTATCGCAACCTTGGAGACCCCGTGACCTCCGGCCTATTCCAACTTAGGACTTACCTGCAAATGATCAACAT\nGGACGACTTATTTCTACCTTTAATTGCCAAGAACCCCGGGAACTGTAGTGCAATTGACTTTGTACTCAACCCAAGCGGAT\nTGAATGTCCCTGGGTCACAAGACCTAACATCTTTTTTACGTCAGATAGTGCGTAGAACAATCACATTGAGTGCAAAAAAT\nAAGCTAATAAACACATTGTTTCACTCCTCAGCCGATTTAGAAGATGAGATGGTATGTAAATGGCTACTTTCTTCAACACC\nTGTAATGAGTCGGTTTGCTGCTGATATATTCTCTCGTACTCCGAGTGGGAAGCGCTTGCAGATCCTAGGTTATTTAGAAG\nGGACTAGAACCTTGCTAGCCTCCAAAGTCATCAATAACAATGCAGAGACTCCTATTTTAGATAGGTTGAGGAAAATCACA\nCTGCAGAGATGGAGTTTGTGGTTTAGCTACCTAGACCACTGTGATCAGGTTCTAGCAGATGCTTTAATAAAAGTTTCTTG\nTACAGTTGATTTGGCGCAAATTTTACGTGAATATACCTGGGCACACATACTAGAGGGAAGACAGCTCATTGGTGCAACAC\nTTCCTTGCATGTTAGAACAATTTAATGTGTTTTGGCTCAAATCGTACGAACAATGCCCTAAATGTGCAAAATCTAGAAAT\nCCAAAAGGAGAGCCATTTGTGTCAATTGCAATTAAGAAACAAGTTGTGAGTGCATGGCCGAATCAGTCACGGTTAAATTG\nGACCATTGGGGACGGTGTACCTTACATCGGGTCTCGAACAGAGGACAAGATTGGGCAGCCAGCAATCAAGCCTAAGTGTC\nCCTCTGCTGCCTTACGTGAAGCAATAGAGTTGACATCTAGACTAACATGGGTTACCCAAGGTGGTGCCAATAGTGATTTG\nCTAGTTAAACCTTTTGTAGAGGCACGAGTAAACCTGAGTGTGCAGGAGATCCTTCAAATGACGCCTTCTCATTATTCAGG\nGAACATCGTACATCGGTATAATGACCAATACAGCCCTCATTCTTTCATGGCAAATAGAATGAGTAATTCCGCGACGAGAT\nTGGTGGTGTCGACAAATACTCTCGGGGAGTTCTCAGGTGGGGGGCAATCAGCAAGGGACAGCAATATCATCTTTCAAAAT\nGTAATCAATTTTTCGGTTGCCCTATTTGATTTACGATTTCGGAACACCGAAACATCCTCCATTCAGCATAATCGTGCCCA\nTCTCCATCTTTCACAGTGTTGCACACGGGAAGTCCCAGCTCAATACCTAACCTACACGTCTACGCTTTCCTTGGATCTCA\nCAAGGTACCGAGAGAATGAGTTAATTTATGATAACAATCCGTTAAAAGGTGGACTTAATTGCAACCTATCCTTTGATAAT\nCCACTTTTCAAGGGCCAAAGGCTCAATATCATAGAGGAGGATTTGATTAGATTTCCTCATCTATCTGGGTGGGAACTTGC\nGAAAACCATCATTCAGTCCATTATCTCAGACAGCAATAACTCATCCACAGACCCCATTAGCAGTGGAGAAACACGATCAT\nTCACAACTCACTTTCTCACATATCCTAAGGTTGGGCTCCTCTATAGTTTCGGCGCCATCGTGAGTTATTACTTAGGGAAT\nACCATTATTAGGACCAAAAAGCTAGACCTCAGTCATTTTATGTATTACTTAACAACTCAAATCCATAATTTGCCACATCG\nCTCGTTGAGGATACTTAAGCCCACCTTTAAACATGTTAGTGTGATATCAAGACTAATGAGTATTGATCCTCATTTTTCAA\nTCTACATCGGGGGTACGGCAGGTGATCGAGGGCTTTCGGATGCTACCAGACTATTCCTTCGAGTGGCCATTTCTTCCTTC\nCTTCAATTTATCAAAAAATGGATCGTGGAATACAAGACAGCTATTCCTCTGTGGGTTATATACCCTTTGGAGGGACAAAA\nTCCAGATCCAATTAATAGCTTTCTACATCTGATTATAGCCTTACTGCAAAATGAATCCCCTCAAAACAACATCCAATTCC\nAAGAAGACAGAAATAATCAACAGTTGTCCGATAATCTAGTTTACATGTGCAAGAGCACTGCCAGTAATTTCTTCCATGCA\nTCACTTGCCTATTGGAGGAGCCGGCACAAAGGACGGCCCAAAAATCGATCGACCGAAGAACAGACAGTTAAACCCATACC\nATATGATAATTTTCATTCTGTTAAATGTGCCTCAAACCCACCAAGCATCCCCAAATCTAAGTCAGGAACTCAAGGTTCAA\nGCGCATTTTTTGAGAAACTTGAATATGATAAAGAAAGAGAATTGCCAACAGCTTCCACACCAGCCGAACAATCCAAGACC\nTATATCAAGGCCCTATCCAGCCGAATTTATCATGGTAAAACACCATCCAATGCCGCAAAAGATGATTCAACAACCTCCAA\nGGGCTGCGATTCCAAAGAAGAAAATGCCGTTCAAGCTTCACACCGAATTGTCCTACCATTTTTTACATTGTCACAGAACG\nACTACAGAACTCCCTCAGCTAAAAAGTCAGAGTATATAACTGAAATCACCAAACTAATTCGACAATTAAAGGCAATTCCA\nGATACCACTGTATACTGTCGCTTTACAGGGGTTGTATCTTCAATGCATTATAAGCTTGATGAGGTTCTCTGGGAATTCGA\nTAGTTTCAAAACTGCTGTGACTCTAGCTGAAGGAGAAGGGTCAGGTGCCTTATTACTACTACAAAAATATAAGGTCAGAA\nCAATCTTTTTTAACACTTTAGCTACAGAGCATAGCATCGAGGCAGAAATAGTTTCTGGGACAACCACACCTCGAATGCTC\nCTTCCTGTAATGGCCAAACTTCATGATGATCAAATAAATGTAATATTAAACAATTCTGCTAGCCAGGTTACTGATATCAC\nTAACCCTGCATGGTTCACTGACCAGAAATCTAGAATCCCCACACAAGTTGAGATTATGACTATGGATGCTGAAACGACAG\nAAAATATTAATCGGTCAAAATTATATGAGGCTATTCAGCAATTAATTGTTTCACACATTGATACAAGGGTGCTAAAGATT\nGTTATTATAAAGGTTTTTTTAAGTGATATTGAAGGTCTCCTGTGGCTTAATGACCATCTTGCCCCTTTATTCGGATCCGG\nCTATTTAATTAAACCTATTACTTCGAGTCCAAAGTCAAGCGAATGGTACTTATGTCTTTCAAATTTCCTTTCAGCCTCTC\nGACGACGGCCTCATCAGGGTCATGCTACCTGTATGCAAGTCATCCAAACAGCGCTACGACTCCAAGTTCAAAGGAGTTCA\nTACTGGCTTAGCCATTTAGTGCAATATGCTGATATTAATTTGCACTTGAGTTATGTTAATTTGGGTTTCCCTTCATTGGA\nAAAGGTTCTTTACCATCGATATAACCTAGTTGATTCACGGAAGGGTCCACTGGTCTCGATCCTTTACCATTTAACACACT\nTGCAAGCAGAGATTAGAGAATTAGTGTGTGACTATAATCAGCAACGACAAAGTCGAACCCAAACATACCACTTCATCAAA\nACGACAAAGGGCCGGATTACAAAATTAGTCAATGACTACCTTAAATTTTATCTCGTAGTGCAAGCACTGAAGCATAATTG\nTCTTTGGCAGGAAGAACTCAGAACACTTCCTGACTTAATCAATGTTTGCAATCGATTTTACCATATAAGGGACTGCTCAT\nGTGAAGATCGATTTTTAATTCAAACTCTTTACTTAACCCGTATGCAAGACTCAGAAGCAAAATTAATGGAGAGATTAACC\nGGGTTTCTAGGATTGTATCCTAATGGTATTAACGCTTAAGATCCCCTTAGAGGCATCGCAATATGACTCCAAACATTAAA\nTGATATTGCTGTCAATACATCTACCTGACCGAGAGCAAGGTTTATTATAAAAAACCTATACACATGACTGCAATGCGTAA\nTTTATACCGAAACACAGTGAGGGCTGCACATGCAGGTTCCTGTTGAGCTTTAAAAGATCATGCAATATAAAATGATATTT\nGTATACTAATCATGTTAGTACTAACTAACAGTACTCACTGCATATACTCTATCAATTAAGAAAAATTACTGTGGTTTATG\nCATTTAAATGACATCACAGATGGATATAATATAGTTAATTCTTACCTAAATGTTGAGTTATAGTAATTTGAAGTTATAAT\nTATGATTAGTGCTTATACTATAAATAATAGCTATACCAAGTATACACAAGAAGTTATGATTTTGTATTCAAATTATATTC\nACAGGAACTTGTGATTAATAATAAAAGTCTCAGTTGTTGGTTGTTGAGTTGTAAAACTCCCGTTAAAAATTTATTTTCCA\nCTTATAACTAATAATAATCATAGATCAGTATGAGTTGAGGCTATTCAAACCTTAGAAAAATTGTGCGATGTTTTTTACCA\nTGTCAATCTTGATTTCAATGATATTGGAGGGCTTGTCGATAAATTCAGTAATTAACATTAAGTCAGTGTGGAACCTCATT\nGGATATTTGATCGTACACAAAATATCTTTACAAAATTGTTTTCTCTTTTTTGTGTGTCCA\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Bundibugyo_ebolavirus/GCF_000889155.1_ViralProj51245_protein.faa", "content": ">YP_003815432.1 nucleoprotein [Bundibugyo virus]\nMDPRPIRTWMMHNTSEVEADYHKILTAGLSVQQGIVRQRIIPVYQISNLEEVCQLIIQAFEAGVDFQDSADSFLLMLCLH\nHAYQGDYKQFLESNAVKYLEGHGFRFEMKKKEGVKRLEELLPAASSGKNIKRTLAAMPEEETTEANAGQFLSFASLFLPK\nLVVGEKACLEKVQRQIQVHAEQGLIQYPTSWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDAVIANSVAQAR\nFSGLLIVKTVLDHILQKTEHGVRLHPLARTAKVKNEVSSFKAALASLAQHGEYAPFARLLNLSGVNNLEHGLFPQLSAIA\nLGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQKYAESRELDHLGLDDQEKKILKDFHQKKNEISFQQTTAMVTLRKE\nRLAKLTEAITSTSILKTGRRYDDDNDIPFPGPINDNENSGQNDDDPTDSQDTTIPDVIIDPNDGGYNNYSDYANDAASAP\nDDLVLFDLEDEDDADNPAQNTPEKNDRPATTKLRNGQDQDGNQGETASPRVAPNQYRDKPMPQVQDRSENHDQTLQTQSR\nVLTPISEEADPSDHNDGDNESIPPLESDDEGSTDTTAAETKPATAPPAPVYRSISVDDSVPSENIPAQSNQTNNEDNVRN\nNAQSEQSIAEMYQHILKTQGPFDAILYYHMMKEEPIIFSTSDGKEYTYPDSLEDEYPPWLSEKEAMNEDNRFITMDGQQF\nYWPVMNHRNKFMAILQHHR\n>YP_003815433.1 polymerase complex protein [Bundibugyo virus]\nMTSNRARVTYNPPPTTTGTRSCGPELSGWISEQLMTGKIPITDIFNEIETLPSISPSIHSKIKTPSVQTRSVQTQTDPNC\nNHDFAEVVKMLTSLTLVVQKQTLATESLEQRITDLEGSLKPVSEITKIVSALNRSCAEMVAKYDLLVMTTGRATATAAAT\nEAYWAEHGRPPPGPSLYEEDAIRTKIGKQGDMVPKEVQEAFRNLDSTALLTEENFGKPDISAKDLRNIMYDHLPGFGTAF\nHQLVQVICKLGKDNSSLDVIHAEFQASLAEGDSPQCALIQITKRIPIFQDAAPPVIHIRSRGDIPKACQKSLRPVPPSPK\nIDRGWVCIFQLQDGKTLGLKI\n>YP_003815434.1 matrix protein [Bundibugyo virus]\nMRRAILPTAPPEYIEAVYPMRTVSTSINSTASGPNFPAPDVMMSDTPSNSLRPIADDNIDHPSHTPTSVSSAFILEAMVN\nVISGPKVLMKQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKTSNPLVRINRLGPGIPDHPLRLLRIGNQAFLQE\nFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDDTPTGPTGILRPGISFHPKLRPILLPGKTGKRGSSSDLTSPDKIQAI\nMNFLQDLKLVPIDPAKNIMGIEVPELLVHRLTGKKITTKNGQPIIPILLPKYIGMDPISQGDLTMVITQDCDTCHSPASL\nPPVSEK\n>YP_003815435.1 spike glycoprotein [Bundibugyo virus]\nMVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVP\nTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGYAFHKEGAFF\nLYDRLASTIIYRSTTFSEGVVAFLILPETKKDFFQSPPLHEPANMTTDPSSYYHTVTLNYVADNFGTNMTNFLFQVDHLT\nYVQLEPRFTPQFLVQLNETIYTNGRRSNTTGTLIWKVNPTVDTGVGEWAFWENKKNFTKTLSSEELSVIFVPRAQDPGSN\nQKTKVTPTSFANNQTSKNHEDLVPEDPASVVQVRDLQRENTVPTPPPDTVPTTLIPDTMEEQTTSHYEPPNISRNHQERN\nNTAHPETLANNPPDNTTPSTPPQDGERTSSHTTPSPRPVPTSTIHPTTRETHIPTTMTTSHDTDSNRPNPIDISESTEPG\nPLTNTTRGAANLLTGSRRTRREITLRTQAKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGIMHNQNGLICGLRQ\nLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFIDKPLPDQTD\nNDNWWTGWRQWVPAGIGITGVIIAVIALLCICKFLL\n>YP_003815436.1 small secreted glycoprotein [Bundibugyo virus]\nMVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVP\nTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGYAFHKEGAFF\nLYDRLASTIIYRSTTFSEGVVAFLILPETKKDFFQSPPLHEPANMTTDPSSYYHTVTLNYVADNFGTNMTNFLFQVDHLT\nYVQLEPRFTPQFLVQLNETIYTNGRRSNTTGTLIWKVNPTVDTGVGEWAFWENKKTSQKPFQVKSCLSYLYQEPRIQAAT\nRRRRSLPPASPTTKPPRTTKTWFQRIPLQWFKCETSRGKTQCRPHPQTQSPQL\n>YP_003815437.1 second secreted glycoprotein [Bundibugyo virus]\nMVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVP\nTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGYAFHKEGAFF\nLYDRLASTIIYRSTTFSEGVVAFLILPETKKDFFQSPPLHEPANMTTDPSSYYHTVTLNYVADNFGTNMTNFLFQVDHLT\nYVQLEPRFTPQFLVQLNETIYTNGRRSNTTGTLIWKVNPTVDTGVGEWAFWENKKLHKNPFK\n>YP_003815438.1 minor nucleoprotein [Bundibugyo virus]\nMDSFHERGRSRTIRQSARDGPSHQVRTRSSSRDSHRSEYHTPRSSSQVRVPTVFHRKRTDSLTVPPAPKDICPTLRKGFL\nCDSNFCKKDHQLESLTDRELLLLIARKTCGSLEQQLNITAPKDTRLANPIADDFQQKDGPKITLLTLLETAEYWSKQDIK\nGIDDSRLRALLTLCAVMTRKFSKSQLSLLCESHLRREGLGQDQSESVLEVYQRLHSDKGGNFEAALWQQWDRQSLIMFIT\nAFLNIALQLPCESSSVVISGLRLLVPQSEDTETSTYTETRAWSEEGGPH\n>YP_003815439.1 membrane-associated protein [Bundibugyo virus]\nMAKATGRYNLVSPKKDLERGLVLSDLCTFLVDQTIQGWRVTWVGIEFDIAQKGMALLHRLKTADFAPAWSMTRNLFPHLF\nQNSNSTIESPLWALRVILAAGIQDQLIDQSLVEPLAGALSLVSDWLLTTNTNHFQMRTQHAKEQLSLKMLSLVRSNILKF\nISQLDALHVVNYNGLLSSIEIGTRNHTIIITRTNMGFLVELQEPDKSAMNQKKPGPVKFSLLHESTFKALIKKPATKMQA\nLILEFNSSLAI\n>YP_003815440.1 RNA-dependent RNA polymerase [Bundibugyo virus]\nMATQHTQYPDARLSSPIVLDQCDLVTRACGLYSSYSLNPQLKNCRLPKHIYRLKFDATVTKFLSDVPIVTLPIDYLTPLL\nLRTLSGEGLCPVEPKCSQFLDEIVSYVLQDARFLRYYFRHVGVHDDNVGKNFEPKIKALIYDNEFLQQLFYWYDLAILTR\nRGRLNRGNNRSTWFANDDLIDILGYGDYIFWKIPLSLLSLNTEGIPHAAKDWYHASIFKEAVQGHTHIVSVSTADVLIMC\nKDIITCRFNTTLIAALANLEDSICSDYPQPETISNLYKAGDYLISILGSEGYKVIKFLEPLCLAKIQLCSNYTERKGRFL\nTQMHLAVNHTLEELIEGRGLKSQQDWKMREFHRILVNLKSTPQQLCELFSVQKHWGHPVLHSEKAIQKVKKHATVIKALR\nPVIIFETYCVFKYSIAKHYFDSQGSWYSVISDKHLTPGLHSYIKRNQFPPLPMIKDLLWEFYHLDHPPLFSTKIISDLSI\nFIKDRATAVEKTCWDAVFEPNVLGYSPPNKFSTKRVPEQFLEQENFSIDSVLTYAQRLDYLLPQYRNFSFSLKEKELNVG\nRAFGKLPYPTRNVQTLCEALLADGLAKAFPSNMMVVTEREQKESLLHQASWHHTSDDFGENATVRGSSFVTDLEKYNLAF\nRYEFTAPFIEYCNRCYGVKNLFNWMHYTIPQCYIHVSDYYNPPHGVSLENREDPPEGPSSYRGHLGGIEGLQQKLWTSIS\nCAQISLVEIKTGFKLRSAVMGDNQCITVLSVFPLETDSNEQEHSSEDNAARVAASLAKVTSACGIFLKPDETFVHSGFIY\nFGKKQYLNGVQLPQSLKTATRIAPLSDAIFDDLQGTLASIGTAFERSISETRHVYPCRVVAAFHTFFSVRILQYHHLGFN\nKGTDLGQLSLSKPLDFGTITLALAVPQVLGGLSFLNPEKCFYRNLGDPVTSGLFQLRTYLQMINMDDLFLPLIAKNPGNC\nSAIDFVLNPSGLNVPGSQDLTSFLRQIVRRTITLSAKNKLINTLFHSSADLEDEMVCKWLLSSTPVMSRFAADIFSRTPS\nGKRLQILGYLEGTRTLLASKVINNNAETPILDRLRKITLQRWSLWFSYLDHCDQVLADALIKVSCTVDLAQILREYTWAH\nILEGRQLIGATLPCMLEQFNVFWLKSYEQCPKCAKSRNPKGEPFVSIAIKKQVVSAWPNQSRLNWTIGDGVPYIGSRTED\nKIGQPAIKPKCPSAALREAIELTSRLTWVTQGGANSDLLVKPFVEARVNLSVQEILQMTPSHYSGNIVHRYNDQYSPHSF\nMANRMSNSATRLVVSTNTLGEFSGGGQSARDSNIIFQNVINFSVALFDLRFRNTETSSIQHNRAHLHLSQCCTREVPAQY\nLTYTSTLSLDLTRYRENELIYDNNPLKGGLNCNLSFDNPLFKGQRLNIIEEDLIRFPHLSGWELAKTIIQSIISDSNNSS\nTDPISSGETRSFTTHFLTYPKVGLLYSFGAIVSYYLGNTIIRTKKLDLSHFMYYLTTQIHNLPHRSLRILKPTFKHVSVI\nSRLMSIDPHFSIYIGGTAGDRGLSDATRLFLRVAISSFLQFIKKWIVEYKTAIPLWVIYPLEGQNPDPINSFLHLIIALL\nQNESPQNNIQFQEDRNNQQLSDNLVYMCKSTASNFFHASLAYWRSRHKGRPKNRSTEEQTVKPIPYDNFHSVKCASNPPS\nIPKSKSGTQGSSAFFEKLEYDKERELPTASTPAEQSKTYIKALSSRIYHGKTPSNAAKDDSTTSKGCDSKEENAVQASHR\nIVLPFFTLSQNDYRTPSAKKSEYITEITKLIRQLKAIPDTTVYCRFTGVVSSMHYKLDEVLWEFDSFKTAVTLAEGEGSG\nALLLLQKYKVRTIFFNTLATEHSIEAEIVSGTTTPRMLLPVMAKLHDDQINVILNNSASQVTDITNPAWFTDQKSRIPTQ\nVEIMTMDAETTENINRSKLYEAIQQLIVSHIDTRVLKIVIIKVFLSDIEGLLWLNDHLAPLFGSGYLIKPITSSPKSSEW\nYLCLSNFLSASRRRPHQGHATCMQVIQTALRLQVQRSSYWLSHLVQYADINLHLSYVNLGFPSLEKVLYHRYNLVDSRKG\nPLVSILYHLTHLQAEIRELVCDYNQQRQSRTQTYHFIKTTKGRITKLVNDYLKFYLVVQALKHNCLWQEELRTLPDLINV\nCNRFYHIRDCSCEDRFLIQTLYLTRMQDSEAKLMERLTGFLGLYPNGINA\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Reston_ebolavirus/GCF_000854085.1_ViralProj15006_genomic.fna", "content": ">NC_004161.1 Reston ebolavirus isolate Reston virus/M.fascicularis-tc/USA/1989/Philippines89-Pennsylvania, complete genome\nCGGACACACAAAAAGAAAAAAGGTTTTTTAAGACTTTTTGTGTGCGAGTAACTATGAGGAAGATTAACAGTTTTCCTCAG\nTTTAAGATATACACTGAAATTGAGATTGAGATTCTCCTCTTTGCTATTCTGTAACTTTCCCTGGTTGTGACAATTGAATC\nAGTTTTATCTATTACCAATTACCATCAACATGGTATGTCTAGTGATCTTGGGACTCTTCTTCATCTGGTTTTTCCTAGAG\nCTCTGAATCCATTTTGCGAGAAGTTCATCCAAACGACCCAGTGTCTGAAAATACAAAAGGTTCCCCTTTCCGTCAAGTTT\nAAGGGGTTGTTTTGATTGTGTGTAGATTTTATAATCCTAGAGTGCCAAGGAGTTGCGTGTCATCATTGATTGGGAAGATC\nAAGGAAACAATTTGTTCCAATAATATCGTACATCTTGACTAAGTCGAACAAGGGGAAGTCGATATGGATCGTGGGACCAG\nAAGAATCTGGGTGTCGCAAAATCAAGGTGATACTGATTTAGATTATCATAAAATTTTGACAGCTGGCCTTACTGTTCAAC\nAGGGAATTGTCAGGCAGAAAATAATTTCTGTATATCTTGTTGATAACTTGGAGGCTATGTGTCAATTGGTAATACAAGCC\nTTTGAGGCCGGAATTGATTTCCAAGAAAATGCCGACAGCTTCCTTCTGATGCTTTGCCTACATCATGCTTACCAAGGTGA\nCTATAAATTGTTCTTGGAGAGCAATGCTGTACAGTATTTGGAAGGTCATGGATTCAAATTTGAGCTCCGGAAGAAGGACG\nGTGTCAATCGGCTCGAGGAATTGCTTCCTGCTGCAACGAGTGGAAAAAACATCAGGCGTACGTTGGCCGCACTGCCTGAA\nGAGGAGACTACAGAAGCAAATGCAGGGCAATTTCTCTCATTTGCGAGTTTGTTTCTTCCCAAACTGGTTGTGGGAGAGAA\nGGCTTGCTTGGAAAAAGTCCAGCGACAAATTCAGGTTCATGCAGAACAGGGTTTAATTCAATATCCCACTGCATGGCAAT\nCAGTTGGACACATGATGGTAATCTTCAGATTGATGAGGACTAATTTCTTGATTAAATATTTACTGATCCACCAGGGTATG\nCATATGGTAGCTGGCCACGATGCCAATGATGCTGTCATTGCTAATTCAGTTGCTCAGGCTCGCTTTTCAGGACTCCTAAT\nTGTCAAAACCGTTCTTGATCATATTCTGCAAAAAACCGACCAAGGAGTAAGACTTCACCCTTTGGCCCGAACAGCCAAAG\nTGCGTAATGAGGTTAATGCATTTAAGGCCGCCCTAAGCTCACTTGCTAAGCATGGGGAATATGCCCCTTTTGCTCGCCTT\nCTCAATCTCTCGGGAGTTAACAACCTAGAACATGGTCTCTACCCACAGTTATCAGCAATTGCTCTTGGAGTTGCCACAGC\nACATGGTAGCACCCTTGCAGGAGTTAATGTTGGTGAGCAGTATCAGCAGCTTAGAGAGGCTGCCACTGAAGCTGAGAAGC\nAACTCCAACAATATGCTGAGTCCAGAGAACTCGACAGCCTAGGCCTGGACGATCAGGAAAGAAGAATACTAATGAACTTC\nCATCAGAAGAAAAACGAAATTAGTTTCCAGCAGACCAATGCAATGGTAACCCTTAGGAAAGAGCGACTGGCTAAATTAAC\nAGAAGCTATAACGCTGGCCTCAAGACCTAACCTCGGGTCTAGACAAGACGACGGCAATGAAATACCGTTCCCTGGGCCTA\nTAAGCAACAACCCAGACCAAGATCATCTGGAGGATGATCCTAGAGACTCCAGAGACACCATCATTCCTAATGGTGCAATT\nGACCCCGAGGATGGTGATTTTGAAAATTACAATGGCTATCATGATGATGAAGTTGGGACGGCAGGTGACTTGGTCCTGTT\nCGATCTTGACGATCATGAGGATGACAATAAAGCTTTTGAGCCACAGGACAGCTCGCCACAATCCCAAAGGGAAATAGAGA\nGAGAAAGATTAATTCATCCACCCCCAGGCAACAACAAGGACGACAATCGAGCCTCAGACAACAATCAACAATCAGCAGAT\nTCTGAGGAACAAGGAGGTCAATACAACTGGCACCGAGGCCCAGAACGTACGACCGCCAATCGAAGACTCTCACCAGTGCA\nCGAAGAGGACACCCTTATGGATCAAGGTGATGATGATCCCTCAAGCTTACCTCCGCTGGAATCTGATGATGACGATGCAT\nCAAGTAGCCAACAAGATCCCGATTATACAGCTGTTGCCCCTCCTGCTCCTGTATACCGCAGTGCAGAAGCCCACGAGCCT\nCCCCACAAATCCTCGAACGAGCCAGCTGAAACATCACAATTGAATGAAGACCCTGATATCGGTCAATCAAAGTCTATGCA\nAAAATTAGAAGAGACATATCACCATCTGCTGAGAACTCAAGGTCCATTTGAAGCCATCAATTATTATCACATGATGAAGG\nATGAGCCGGTAATATTTAGCACTGATGATGGGAAGGAATACACCTACCCGGATTCACTTGAGGAAGCCTATCCTCCATGG\nCTCACCGAGAAAGAACGACTGGACAAAGAGAATCGCTACATTTACATAAATAATCAACAGTTCTTCTGGCCTGTCATGAG\nTCCCAGAGACAAATTTCTTGCAATCTTGCAGCACCATCAGTAACCACAGCACAAAGCGCGGTCCACTTCGTAAAGCTAAA\nTACACTTAAGACTTGACCGATTCATCTACAAAAACTAATCCATTATAACTTATTAGTGCTACTTTTCTATAAGTGATTCT\nTAATCTAAGGCCATTAAGAGTTTAAGTAATATACATATACACTTACACCGGTCTATCCAAGATGTGGCTCAATGTTCTTG\nATTTGAACATAGTCATAAGGGGATAAATAATACTTTATATTTCTGATTGTGGATTGACCCATTCTGCTTAAAATGCTTCG\nCCCATTGAAAATGTGATCTAATAGATAGCCCTGACTAGACAAATTAAGAAAAACATTTGATGAAGATTAAAACCTTCATC\nGCCAGTAAATGATTATATTGTCTGTAGGCAGGTGTTTACTCCACCTTAAATTTGGAAATATCCTACCTTAGGACCATTGT\nCAAGAGGTGCATAGGCATTACCACCCTTGAGAACATGTACAATAATAAATTGAAGGTATGTTCAGGCCCAGAAACGACTG\nGATGGATTTCTGAGCAACTTATGACAGGTAAGATTCCAGTAACTGATATATTCATTGATATTGATAACAAGCCAGATCAA\nATGGAAGTCCGACTCAAACCATCATCAAGGAGCTCAACAAGAACTTGTACAAGTAGCAGTCAGACGGAGGTCAACTATGT\nACCTCTCCTTAAAAAGGTTGAGGATACATTAACTATGCTAGTGAATGCCACCAGTCGTCAGAATGCTGCAATCGAGGCCC\nTTGAAAACCGCCTCAGCACACTTGAGAGTAGCTTAAAGCCAATCCAAGACATGGGTAAAGTGATTTCATCATTGAATCGC\nAGTTGTGCCGAAATGGTTGCAAAATATGATCTTCTAGTTATGACAACTGGACGGGCTACTTCAACTGCAGCTGCAGTAGA\nTGCGTATTGGAAAGAGCACAAACAGCCACCACCAGGGCCAGCGTTGTATGAAGAGAATGCGCTTAAAGGAAAAATCGATG\nATCCAAACAGCTATGTACCAGATGCTGTGCAAGAGGCTTACAAGAACCTTGACAGTACATCGACCCTGACCGAGGAAAAT\nTTTGGGAAACCTTATATATCTGCTAAAGACCTGAAGGAGATCATGTATGATCATCTACCTGGTTTTGGGACTGCCTTTCA\nCCAACTTGTTCAAGTGATTTGTAAAATAGGAAAGGATAACAACCTTTTGGACACAATCCATGCTGAGTTCCAGGCAAGTC\nTAGCAGATGGTGACTCTCCCCAATGTGCACTCATACAGATAACCAAAAGGGTCCCAATCTTTCAGGATGTGCCGCCCCCG\nATAATCCATATTAGATCCCGTGGTGACATCCCACGAGCATGCCAAAAGAGTCTCCGACCAGCACCACCATCACCCAAAAT\nTGATCGTGGTTGGGTTTGTTTGTTTAAGATGCAAGATGGTAAAACGCTTGGACTTAAGATCTAAGAATCAAGATTTATTT\nAACAAGGCAAGCCACAACCTTAGATGGAACCTCAGCCAGACTATTGAACTATTGACGCTGTTGATGATAATATATAATTA\nATGGTCTTATTTGAATATGACAACATCTTGCTTCTTGTTCTGCCTTGTAGCTCTTTGAATTGGAAGATCATTCCAAACTT\nACAAACATGCACAAGATGTTATGGTTTAGCAAAGAATTGATAGGAGTACTGGTATATAATGTAAATATAACAAGTGATGA\nAGATTAAGAAAAACCAGTCGGTATTTTCCAGACTTGGCATTTCTTATCTTCATCTTCTAAAGTGAGATATTTTATCATCA\nAAAAATGAGGCGCGGAGTGTTACCAACGGCTCCTCCAGCATATAATGATATTGCATACCCTATGAGCATACTCCCAACCC\nGACCAAGTGTCATAGTCAATGAGACCAAATCAGATGTACTGGCAGTGCCAGGGGCAGATGTTCCATCAAACTCCATGAGA\nCCAGTGGCTGATGATAACATTGATCACTCAAGCCATACTCCAAGCGGAGTAGCTTCTGCCTTTATATTGGAAGCTACAGT\nGAATGTAATTTCGGGAACAAAAGTCCTGATGAAGCAAATACCTATTTGGCTTCCACTGGGTGTAGCTGATCAGAAGATAT\nACAGCTTTGATTCAACAACAGCCGCAATTATGTTGGCTTCCTACACAGTGACACACTTCGGGAAGATATCTAACCCGCTG\nGTACGTGTCAACAGGCTAGGCCCAGGAATACCCGATCATCCGCTACGACTCCTAAGGTTGGGCAATCAGGCATTCCTTCA\nAGAGTTTGTTCTTCCACCAGTCCAGCTTCCCCAGTATTTCACATTTGATCTAACAGCTCTAAAGCTCATCACTCAACCAT\nTGCCAGCTGCAACCTGGACAGACGAAACTCCAGCAGGAGCAGTCAATGCTCTTCGTCCTGGGCTCTCACTCCATCCCAAG\nCTTCGTCCAATTCTCCTGCCGGGGAAGACAGGAAAGAAAGGACATGCTTCAGACTTAACATCACCTGACAAGATTCAAAC\nAATCATGAATGCAATACCGGACCTCAAAATTGTCCCGATTGATCCAACCAAGAACATAGTTGGAATTGAGGTTCCAGAAT\nTACTAGTTCAAAGGCTGACCGGCAAAAAACCACAACCCAAAAATGGCCAACCAATTATTCCAGTTCTTCTTCCGAAATAT\nGTTGGACTTGATCCTATATCGCCAGGGGACTTAACTATGGTTATCACCCAGGATTGTGATTCATGCCACTCTCCAGCCAG\nCCATCCGTATCACATGGACAAGCAGAATAGTTACCAATAATTTAAATTCCATTCGAGCTATTATTCTGCTAGTAATTCCG\nACGGGATCAATAGACTAAAAATCTGATTGTATAGAATTATAAAAGAATCAAGCAGAGGCAACAGACTCACAGCTTACGCC\nTAGATAACTAATATTAAGGAGTTTTTTAATCTAATTTTCCAGTCTTGAGTAATAATCATTTCTTTTGTAATTAATTATGC\nATTTGTTAACTTATCGGTGCGAGATTTCCTTGAGAACCCGGCGGAGCTTCTACTATCTGCAGTAACCAGAAGAGAAGTTC\nAACCCAGTCAAAACTAAACCAAGCAATATTCTGAATGCTCTATAGTCTATTCTAATCAGAGGTATAACAATGGCTAAGAT\nTTCAATGACTCGTTAACAATCGCTAGTAATTTTAATCTCCAGATTAAGAAAAAGATATACGATGAAGATTAAGGCGACAA\nCGAGCCGAAACTTCATCTCTTTTAAAGATCTAACATTATCTGTTCCAAAGTCATACAAGGACACATTCAAATCAGGGATT\nGTAAGCTGCTATTTCTTACCTCCCCAAATTACCTATACAACATGGGGTCAGGATATCAACTTCTCCAATTGCCTCGGGAA\nCGTTTTCGTAAAACTTCGTTCTTAGTATGGGTAATCATCCTCTTCCAGCGAGCAATCTCCATGCCGCTTGGTATAGTGAC\nAAATAGCACTCTCAAAGCAACAGAAATTGATCAATTGGTTTGTCGGGACAAACTGTCATCAACCAGTCAGCTCAAGTCTG\nTGGGGCTGAATCTGGAAGGAAATGGAATTGCAACCGATGTCCCATCAGCAACAAAACGCTGGGGATTTCGTTCAGGTGTG\nCCTCCCAAGGTGGTCAGCTATGAAGCCGGAGAATGGGCAGAAAATTGCTACAATCTGGAGATCAAAAAGTCAGACGGAAG\nTGAATGCCTCCCTCTCCCTCCCGACGGTGTACGAGGATTCCCTAGATGTCGCTATGTCCACAAAGTTCAAGGAACAGGTC\nCTTGTCCTGGTGACTTAGCTTTCCATAAAAATGGGGCTTTTTTCTTGTATGATAGATTGGCCTCAACTGTCATCTACCGA\nGGGACAACTTTTGCTGAAGGTGTCGTAGCTTTTTTAATTCTGTCAGAGCCCAAGAAGCATTTTTGGAAGGCTACACCAGC\nTCATGAACCGGTGAACACAACAGATGATTCCACAAGCTACTACATGACCCTGACACTCAGCTACGAGATGTCAAATTTTG\nGGGGCAATGAAAGCAACACCCTTTTTAAGGTAGACAACCACACATATGTGCAACTAGATCGTCCACACACTCCGCAGTTC\nCTTGTTCAGCTCAATGAAACACTTCGAAGAAATAATCGCCTTAGCAACAGTACAGGGAGATTGACTTGGACATTGGATCC\nTAAAATTGAACCAGATGTTGGTGAGTGGGCCTTCTGGGAAACTAAAAAAACTTTTCCCAACAACTTCATGGAGAAAACTT\nGCATTTCCAAATTCCATCAACCCACACCAACAACTCCTCAGATCAGAGCCCGGCGGGAACTGTCCAAGGAAAAATTAGCT\nACCACCCACCCGCCAACAACTCCGAGCTGGTTCCAACGGATTCCCCTCCAGTGGTTTCAGTGCTCACTGCAGGACGGACA\nGAGGAAATGTCGACCCAAGGTCTAACCAACGGAGAGACAATCACAGGTTTCACCGCGAACCCAATGACAACCACCATTGC\nCCCAAGTCCAACCATGACAAGCGAGGTTGATAACAATGTACCAAGTGAACAGCCGAACAACACAGCATCCATTGAAGACT\nCCCCCCCATCGGCAAGCAACGAGACAATTTACCACTCCGAGATGGATCCGATCCAAGGCTCGAACAACTCCGCCCAGAGC\nCCACAGACCAAGACCACGCCAGCACCCACAACATCCCCGATGACCCAGGACCCGCAAGAGACGGCCAACAGCAGCAAACC\nAGGAACCAGCCCAGGAAGCGCAGCCGGACCAAGTCAGCCCGGACTCACTATAAATACAGTAAGTAAGGTAGCTGATTCAC\nTGAGTCCCACCAGGAAACAAAAGCGATCGGTTCGACAAAACACCGCTAATAAATGTAACCCAGATCTTTACTATTGGACA\nGCTGTTGATGAGGGGGCAGCAGTAGGATTGGCATGGATTCCATATTTCGGACCTGCAGCAGAAGGCATCTACATTGAGGG\nTGTAATGCATAATCAGAATGGGCTTATTTGCGGGCTACGTCAGCTAGCCAATGAAACTACCCAGGCTCTTCAATTATTTC\nTGCGGGCCACAACAGAACTGAGGACTTACTCACTTCTTAACAGAAAAGCTATTGATTTTCTTCTTCAACGATGGGGAGGT\nACCTGTCGAATCCTAGGACCATCTTGTTGCATTGAGCCACATGATTGGACAAAAAATATTACTGATGAAATTAACCAAAT\nTAAACATGACTTTATTGACAATCCCCTACCAGACCACGGAGATGATCTTAATCTATGGACAGGTTGGAGACAATGGATCC\nCGGCTGGAATTGGGATTATTGGAGTTATAATTGCTATAATAGCCCTACTTTGTATATGTAAGATTTTGTGTTGATTTATT\nCTGAGATCTGAGAGAGAAAAATCTCAGGGTTACTCTAAGGAGAAATATTATTTTTAAAATTTACTTGAATGCTGACCACT\nTATCTTAAATGAGCAATTAATAATATGTTTTTCTGCTTCTTTGCTTGATTTACAATATGATATTTCTCTTAATAATGATT\nAATATATTAAGAAAAACTTATGACGAAGATTAAAGGAGAGGATCGTTAACGGGAAAACCTCCCATCTCGTTCGTCGAAGC\nCACGTTGGTGGTGCTTGCAGCTGAGAACAACTCCAGAGATTGTAGGTAGAAAGGACCAACATTTATAGGTAGGGGTCAGA\nAAGCAACAATAACCATAAAAGGAGAGCCTGACATTGCTATTTAATATCCTAGAACCTGATTTCTAGGTTCTAGCTTTAAA\nATCCGGATGATGGAGCATTCAAGAGAACGGGGTAGATCTAGCAACATGCGACATAATAGCCGGGAACCATACGAAAATCC\nATCAAGGTCTCGCTCATTATCTCGGGACCCTAATCAGGTTGATCGTAGACAGCCTCGAAGTGCATCCCAAATTCGTGTTC\nCGAATCTGTTCCATCGGAAAAAGACTGATGCACTCATAGTTCCTCCGGCTCCTAAAGATATATGCCCAACACTCAAAAAA\nGGATTCCTCTGCGATAGCAAATTTTGCAAAAAAGATCACCAATTGGATAGCTTAAATGATCATGAATTACTACTGCTAAT\nTGCAAGAAGAACATGTGGAATTATCGAGAGCAATTCGCAGATTACATCCCCAAAAGATATGCGGTTAGCGAATCCAACAG\nCTGAAGACTTCTCACAAGGTAATAGTCCTAAATTAACACTTGCAGTCCTTCTTCAAATTGCTGAACATTGGGCAACCAGA\nGACCTAAGGCAAATTGAGGACTCTAAACTTAGAGCTCTTTTAACCCTTTGTGCCGTATTAACAAGGAAATTTTCTAAATC\nCCAACTGGGTCTTCTATGTGAGACCCACCTACGGCATGAGGGCCTCGGACAGGACCAAGCTGATTCTGTATTAGAGGTCT\nACCAAAGACTCCACAGTGATAAAGGAGGGAATTTTGAGGCTGCCCTGTGGCAACAATGGGACCGACAGTCATTAATAATG\nTTCATCTCTGCTTTTCTCAACATTGCTCTCCAGATACCTTGTGAAAGTTCTAGTGTCGTAGTCTCAGGTCTTGCCACATT\nGTACCCAGCACAAGACAATTCTACACCATCCGAGGCAACTAATGATACCACCTGGTCAAGTACAGTTGAATAGAAAACCA\nCTGGAGCTATTTTTCCACGATTGCTCTCAGTCAATAAATTAATATAGATATAATACGACTTCGGTGTGCAATTGTCAAGA\nGTTCCATTTAGTAATAATGATTCTTAAAACAATCTACTATCGCAATTATCGATGGATCTACCCTATTTGACGGTACATGA\nCTTGAATGTAATAAGGTAAGTTGGTATCTGAGGTATTTTGTCTAGAGTATACTCAAAATCGTATGTCTAGCAAATTATCA\nATAGCAAAGTTAAATTCTCCTAACCTCATATTTTGATCAAGTAATCATGATTTTATGATAATTCTTTTCAGATTATCGGT\nTTAATCTTTATTAAGAAAAAATCATGATTGTAGACAATTTACTGGTAGTCCTTGGGTATCCAAGTTTATGAATAGAGCTA\nGAGAGAATTTGCTACTTCCGAGGTATAACTTTATTATTTGCTACTTCGAATGCCTAAAACCAGTAATGCAGGATGAAGAT\nTAATTGCGGAGGAATCAGGAATTCAACTTTAGTTCCTTAAGGCCTCGTCCGAATCTTCATCAGTTCGTAAGTTCTTTTAT\nAGAAGTCATTAGCTTCTAAGGTGATTATATTTTAGTATTAAATTTTGCTAATTGCTTGCTATAAAGTTGAAATGTCTAAT\nGCTTAAATGAACACTTTTTTGAAGCTGACATACGAATACATCATATCATATGAAAACATCGCAATTAGAGCGTCCTTGAA\nGTCTGGCATTGACAGTCACCAGGCTGTTCTCAGTAGTCTGTCCTTGGAAGCTCTTGGGGAGACAAAAAGAGGTCCCAGAG\nAGTCCCAACAGGTTGGCATAAGGTCATTAACACCAGCATAGTCGGCTCGACCAAGACTGTAAGCGAGTCGATTTCAACTA\nAAAAGATTATTTCTTGTTGTTTAAACAAATTCCTTTTGTGTGAGACATCCTCAAGGCACAAGATGGCTAAAGCCACAGGC\nCGATACAATCTCGTGCCCCCAAAGAAAGATATGGAAAAGGGAGTGATTTTTAGTGATCTTTGTAATTTCTTGATTACTCA\nAACCCTGCAAGGTTGGAAGGTTTATTGGGCAGGAATTGAGTTTGATGTAAGTCAAAAAGGCATGGCTCTTCTGACAAGAC\nTCAAAACAAATGACTTTGCTCCTGCCTGGGCGATGACAAGAAATCTTTTCCCACATCTGTTCCAGAACCCAAATTCGGTT\nATTCAATCTCCCATCTGGGCTTTGAGGGTAATTTTGGCAGCCGGATTGCAGGATCAGTTGTTAGACCATTCATTGGTTGA\nGCCATTGACAGGGGCTCTCGGTCTAATTTCTGATTGGCTCCTAACTACAACGTCAACACATTTCAATCTTCGTACTAGAA\nGCGTAAAGGACCAGCTTAGTCTTCGTATGTTATCTTTGATCAGGTCAAACATCTTGCAGTTCATCAACAAGCTTGACGCC\nCTGCATGTTGTCAATTACAATGGTTTACTCAGTAGTATTGAGATCGGGACTTCTACACACACAATCATTATAACTCGTAC\nAAATATGGGTTTTCTCGTGGAAGTTCAAGAGCCTGACAAATCAGCTATGAATTCTAAGCGCCCAGGACCAGTCAAGTTCT\nCATTACTTCATGAGTCTGCCTTCAAACCTTTCACTCGTGTTCCACAATCTGGGATGCAATCATTAATAATGGAGTTCAAC\nAGTTTGTTGGCAATTTAACAAGGTAATCTTAAAATAAGTACATGAATGAGAATTAGTTGTGGGTCTTATCTAGCATTGTT\nGAGTTAACTATCTAATCTATTTTCGCTAATTGCATTGAGCACTGCTAATAGGTTTGTATCACGTTAAAGATTTAGAGTGT\nATGAATTGTGCAGATTTAAACTTGGGTTTTGCCTTATGCTTCATAGGTGGTCTTTTTGAAATGGAGATTATCAGCATTTC\nTTAAATGGGAGGAGTTAGCAATCAGAAATTGGAGATAAATGGACATCGGGATAGAACAATGCCTAACTATTGGGCGGCTT\nCCATTTTTACATGTGTATATAACCAATCTTTTCCTATCTTTGCTTATATTGGTGTAACTTTATTTTAATAACATGTCAAT\nGCTATACTGTTAAGAGAAGGTCTGAGGAAGATTAAGAAAAAGGCCTCGTGTTCACTTGGTTGCCGTCAAGTATCCTGTGG\nTTTTTTTCTACCTAACTTCCTCATGCCATATGGCTACCCAGCATACCCAGTACCCGGATGCACGTTTATCCTCACCTATA\nGTCCTGGATCAATGTGATTTGGTAACTCGAGCATGTGGGTTATATTCATCTTATTCTCTAAATCCTCAACTAAGGCAATG\nTAAATTACCAAAACATATATATCGACTTAAGTTCGACACAATAGTATCCAAATTCCTAAGTGATACACCTGTAGCAACAC\nTGCCGATAGACTATTTAGTACCAATTCTCCTGCGTTCCCTAACGGGGCACGGTGATAGGCCATTGACCCCGACTTGCAAT\nCAATTCCTTGATGAAATTATTAATTACACTCTTCATGATGCAGCCTTTCTTGATTACTATCTCAAGGCAACAGGTGCACA\nGGACCATTTGACAAACATTGCAACTAGAGAGAAGCTTAAAAACGAAATTCTAAACAATGATTATGTCCATCAATTGTTCT\nTCTGGCATGACCTTTCTATTTTGGCTCGACGTGGGCGTCTGAATCGCGGGAACAACCGTTCAACCTGGTTTGTTCATGAT\nGAATTCATTGATATTTTAGGATATGGCGATTATATTTTTTGGAAAATACCTTTATCATTATTACCAGTTACTATAGACGG\nGGTCCCACACGCAGCAACTGACTGGTATCAACCGACTCTTTTTAAAGAATCCATCCTAGGGCATAGCCAAATCCTATCTG\nTGTCAACAGCTGAAATACTAATTATGTGTAAAGATATTATCACCTGTAGGTTTAATACATCACTGATTGCATCCATTGCA\nAAATTAGAGGATGTAGATGTGTCTGATTATCCTGACCCGAGTGATATTCTTAAGATATACAATGCTGGAGACTATGTAAT\nATCTATTCTTGGCTCAGAGGGTTATAAGATAATAAAGTACCTTGAACCACTTTGTTTGGCCAAAATCCAACTTTGCTCTA\nAATTCACAGAAAGAAAAGGTCGTTTCCTCACACAGATGCATTTATCAGTAATAAATGATCTTCGGGAGTTGATTTCTAAC\nCGCAGGTTAAAGGACTATCAGCAAGAGAAGATTAGAGATTTTCACAAAATATTATTACAATTGCAATTATCTCCTCAACA\nGTTTTGTGAATTATTCTCTGTTCAAAAACATTGGGGGCATCCAATTTTACATAGTGAGAAAGCTATACAAAAAGTAAAAC\nGGCATGCAACCATCCTTAAGGCTCTCAGACCTAATGTCATCTTTGAGACATATTGTGTATTCAAGTACAATATTGCCAAG\nCACTATTTCGACAGCCAAGGAACTTGGTACAGTGTAATCTCAGACAGGAATTTAACTCCAGGACTCAACTCCTTCATAAA\nACGTAATCACTTTCCTTCACTACCCATGATTAAGGATCTTCTATGGGAATTCTATCATCTTAATCACCCTCCGTTATTCT\nCTACAAAGGTGATTAGTGACTTAAGTATTTTCATCAAAGATAGGGCCACAGCTGTTGAACAGACATGTTGGGATGCAGTC\nTTTGAACCCAATGTGCTAGGTTACAATCCTCCAAACAAATTCTCCACTAAAAGGGTGCCGGAACAATTTCTAGAACAAGA\nGGATTTTTCAATCGAAAGTGTCCTGAATTATGCACAGGAATTACATTATTTATTACCACAGAATAGGAATTTTTCCTTTT\nCTCTCAAAGAAAAGGAATTAAATATTGGACGAACATTTGGGAAGCTACCATATCTCACACGGAATGTCCAAACTTTATGT\nGAGGCTCTGTTAGCAGATGGACTGGCCAAGGCCTTCCCCAGTAACATGATGGTAGTAACTGAACGTGAACAAAAAGAGAG\nCCTTCTTCATCAGGCATCATGGCACCACACCAGTGATGATTTTGGAGAGAATGCTACCGTTCGAGGGAGTAGTTTTGTAA\nCTGATTTAGAGAAGTACAATCTTGCATTTCGCTATGAGTTCACTGCACCATTTATTGAGTACTGCAACCATTGCTATGGT\nGTGCGTAATGTCTTTAATTGGATGCATTATTTAATCCCGCAGTGTTACATGCATGTAAGTGATTATTATAATCCGCCTCA\nCAATGTTAATCTTAGCAATCGAGAATATCCTCCTGAAGGCCCGAGTTCGTACCGAGGGCACTTAGGAGGCATAGAGGGAT\nTACAACAAAAACTGTGGACGAGTATATCCTGTGCACAAATCTCCTTAGTGGAAATTAAAACTGGTTTTAAGTTACGATCA\nGCGGTCATGGGAGACAATCAGTGTATAACCGTATTGTCTGTTTTTCCACTTAAAACAGACCCTGAAGAGCAGGAGCAAAG\nCGCCGAAGACAATGCTGCAAGAGTAGCAGCAAGTCTTGCAAAAGTAACCAGTGCATGTGGGATCTTTCTTAAACCAGATG\nAGACATTTGTACACTCAGGTTTCATTTATTTCGGAAAAAAACAATATCTCAATGGTGTACAATTACCGCAATCACTCAAA\nACAGCAGCAAGAATGGCACCACTCTCTGATGCTATATTCGATGATCTACAAGGAACACTTGCCAGTATTGGAACTGCCTT\nCGAACGTGCTATATCGGAAACGCGACATATCCTCCCATGTCGTATTGTAGCAGCTTTCCATACGTATTTCGCCGTTCGGA\nTTTTACAATATCACCATCTTGGATTTAATAAAGGCATCGATTTAGGACAGTTGTCACTTAGTAAACCATTAGACTATGGG\nACTATTACTCTAACATTGGCGGTTCCACAAGTCCTTGGGGGATTGTCTTTTCTAAATCCAGAAAAGTGTTTTTATCGAAA\nCTTCGGAGATCCTGTGACTTCTGGACTTTTCCAGCTACGGGTGTACCTAGAAATGGTTAACATGAAAGACCTATTTTGTC\nCATTAATATCGAAAAATCCAGGAAATTGTAGTGCCATTGATTTTGTCTTAAATCCATCCGGATTAAATGTTCCAGGATCA\nCAAGACTTGACATCCTTTTTGCGACAAATCGTTAGGCGTAGTATTACCCTAACTGCTAGAAATAAGTTAATTAACACTCT\nCTTCCATGCCTCTGCTGATTTGGAAGATGAGATGGTTTGTAAGTGGCTCCTTTCATCAAACCCTGTCATGAGTCGCTTTG\nCAGCGGATATTTTTTCCAGGACACCGAGTGGTAAACGTCTCCAAATATTAGGTTATCTTGAAGGGACCAGGACTCTATTG\nGCCTCCAAAATCATAAACAACAACAGTGAGACACCTGTACTTGATAAGCTGAGGAAGATCACCCTACAAAGATGGAATCT\nGTGGTTCAGTTATTTGGACCATTGTGACCAATTACTAGCAGATGCTCTACAGAAAATTAGTTGCACGGTGGATTTGGCCC\nAGATTTTGCGTGAGTATACATGGTCACACATCTTAGAGGGTAGATCATTGATCGGAGCGACATTACCATGTATGGTGGAG\nCAATTCAAAGTTAAGTGGCTAGGACAATATGAACCTTGTCCAGAATGTCTCAACAAAAAAGGCTCAAATGCTTATGTCTC\nAGTTGCAGTCAAAGATCAAGTGGTCAGTGCTTGGCCTAATACTTCTCGAATAAGTTGGACAATAGGGAGTGGTGTCCCCT\nATATAGGGTCAAGAACCGAGGATAAAATCGGACAGCCTGCTATCAAGCCGCGATGCCCTTCATCTGCCCTCAAGGAGGCT\nATAGAATTAGCATCAAGGCTCACTTGGGTTACACAAGGAGGTTCTAATAGTGAACAATTAATCCGGCCTTTCTTGGAAGC\nGAGAGTCAACCTTAGTGTCAGTGAAGTCCTGCAAATGACACCATCACATTATTCAGGAAATATTGTCCATCGATATAACG\nACCAATACAGCCCGCACTCATTTATGGCGAATCGCATGAGCAATACTGCGACCCGTCTCATAGTGTCAACTAATACACTT\nGGAGAATTTTCAGGTGGAGGGCAGGCCGCCAGGGATAGCAATATAATTTTCCAGAATGTTATAAATTTAGCAGTTGCCCT\nTTATGATATTAGATTCCGGAATACAAACACCTCTGATATAAGGCATAATAGGGCTCATCTTCACCTGACAGAGTGCTGTA\nCTAAAGAGGTCCCGGCCCAGTATTTGACATATACAAGTGCACTTAATCTGGATTTAAGCCGTTATCGTGATAATGAACTA\nATATATGACTCAAATCCACTGAAGGGAGGATTGAACTGCAATTTAACAATAGATAGTCCTTTAGTGAAGGGTCCTAGGCT\nTAACATGATTGAAGATGATCTTCTCCGCTTTCCACACCTTTCTGGATGGGAGTTAGCGAAAACGGTGGTACAATCCATCA\nTCTCAGACAATAGCAACTCATCAACAGATCCAATCAGTAGCGGAGAAACACGCTCTTTCACAACTCATTTTCTCACTTAC\nCCTCAGATTGGCCTTCTTTACAGTTTCGGAGCAGTATTATGCTTTTATCTAGGCAATACTATCCTATGGACTAAAAAACT\nTGATTACGAACAGTTTCTATATTATTTGCATAACCAGCTGCACAACTTACCTCATCGAGCACTCCGTGTTTTTAAACCAA\nCATTTAAGCATGCCAGTGTGATGTCCCGATTAATGGAAATTGATTCTAACTTCTCAATTTATATTGGCGGGACATCTGGA\nGATCGAGGGCTGTCTGATGCTGCTCGACTGTTTCTTCGGACAGCAATCGCGAGTTTTTTACAATTTCTTAAAAGCTGGAT\nCATCGATCGCCAAAAGACAATTCCTTTATGGATAGTATATCCGCTTGAAGGTCAACAGCCGGAATCCATCAATGAATTTC\nTACATAAAATTTTGGGTCTGCTCAAACAAGGCCCCAAAAGTATTCCAAAGGAGGTCAGCATCCAAAATGATGGACATTTG\nGATTTGGCAGAAAATAATTATGTTTACAATAGTAAGAGCACTGCTAGTAATTTCTTCCATGCATCCTTAGCTTACTGGAG\nAAGTAGGAAATCTCGGAAAACTCAAGACCATAATGATTTCTCAAGAGGGGATGGAACACTTACAGAACCCGTGCGTAAGT\nTTTCAAGCAATCATCAGTCAGATGAAAAGTACTACAATGTGACATGTGGAAAGTCACCGAAGCCGCAAGAACGCAAAGAC\nTTCTCGCAATACAGACTCAGCAATAACGGGCAAACAATGAGTAATCATCGTAAGAAAGGGAAGTTCCACAAGTGGAATCC\nCTGCAAAATGTTAATGGAGAGTCAAAGGGGAACTGTTCTAACAGAGGGTGACTACTTTCAAAACAATACTCCACCAACAG\nATGATGTATCAAGTCCTCACCGACTCATTCTACCATTTTTTAAATTGGGAAATCACAACCATGCACATGATCAAGATGCC\nCAAGAATTGATGAATCAAAATATTAAACAGTACCTACATCAGCTAAGGTCTATGTTGGACACCACTATATATTGTAGATT\nCACAGGGATTGTCTCATCCATGCATTACAAATTGGACGAAGTTCTTCTAGAATACAATAGTTTCGATTCAGCTATCACAT\nTAGCTGAAGGTGAGGGGTCAGGGGCTCTATTACTTTTGCAAAAATATAGTACAAGGTTATTATTTTTGAACACATTGGCA\nACAGAACACAGTATAGAATCAGAAGTTGTATCAGGTTTTTCTACTCCGAGAATGTTGTTACCAATAATGCAAAAGGTTCA\nTGAAGGACAAGTCACTGTTATCTTAAATAATTCAGCAAGTCAGATAACTGACATAACTAGCTCAATGTGGTTAAGTAATC\nAAAAATATAATCTACCTTGTCAAGTTGAAATCATTATGATGGATGCTGAAACAACAGAGAACTTAAACAGGTCCCAACTC\nTACCGAGCAGTATATAACTTAATACTTGATCACATTGATCCGCAGTATCTCAAGGTGGTGGTACTCAAAGTATTTCTGAG\nTGATATAGAAGGAATATTATGGATTAATGATTACTTGGCTCCATTATTCGGGGCTGGTTACTTGATTAAACCGATTACAT\nCAAGTGCCCGGTCAAGTGAATGGTACCTTTGCTTATCAAATTTGATATCTACTAACAGGAGATCGGCCCATCAGACTCAC\nAAGGCATGTCTTGGTGTTATCAGAGATGCTTTGCAAGCACAAGTCCAGCGAGGCGTGTACTGGTTGAGTCACATCGCACA\nGTATGCTACAAAGAATCTCCATTGTGAATACATAGGCCTTGGTTTCCCATCTCTAGAAAAGGTCCTATATCACAGGTATA\nATCTAGTTGATACTGGACTCGGTCCATTGTCGTCAGTTATTAGACATTTAACTAACCTCCAGGCAGAGATACGAGACTTA\nGTATTAGATTATAACCTGATGAGGGAGAGTCGCACTCAAACGTACCATTTTATTAAGACTGCAAAAGGCAGAATCACAAA\nGTTAGTCAATGACTTTCTGAAGTTTTCTTTAATTGTCCAGGCACTCAAAAATAATTCTTCTTGGTATACTGAGCTTAAAA\nAATTACCTGAGGTTATTAATGTGTGTAATCGATTTTATCATACTCACAATTGCGAATGTCAGGAAAAATTCTTTGTCCAG\nACGCTTTATTTACAACGCCTACGCGATGCAGAAATCAAGCTAATTGAACGCCTTACCGGGTTAATGCGATTTTATCCAGA\nAGGGTTAATATATTCCAATCACACATAGGTACTAAATCATCATAGTATGAGGAATAAGATAATGATAATTCCTGACGACA\nGTTTTAGTTCCGATTCTAAGTATATCGGAAGAGAGTATGCCAATCTTAATTGTTAGAGGTAACAAGCTATTAGTTATTAC\nTTATTGATAAGAATACACTTTATCATAGCGTAACACATCATAACTTTATAACGATTTTGCATTTCTAATCCTAGTATTTA\nTTAGAATGTACTACCAGAGAAATGACCCCAGTTCCTATCTTTAAATAATGATTGTGTGTATTAAATTATTAGTTTATTAG\nGTTTATGAGTTGGTTACACAGTGAGTATTAGTAATTGAGGATTATGTAGATAGGTAATCTAACACTGAATCACCCATCTG\nATGTCACCATATCCAAATGTTGTGCTAGTCGCATTTAAACATGCTATCTTCAGTTAAGTAACATAGACTGAAAATGCTAA\nGAAGAGATTGGAGTAAAAGTATAAAATAAATTTAATTAAACTTCAAAGTGATTAAATGATAATGATCTTGGGAACTCGAT\nATGACCTCAAGTCAAAAATAATGTCAATATAATTGTTTAGTAATATGAGTGATAATGTAAATTTTGATAACTAACTAGCT\nTTAGTAGTTAAGATCAAATGCAAACATTATAAGAATGTTAAGCGCACACAAAAACATTATAAAAAACCAATTTTTTCCTT\nTTTGTGTGTCC\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Reston_ebolavirus/GCF_000854085.1_ViralProj15006_protein.faa", "content": ">NP_690580.1 nucleoprotein [Reston ebolavirus]\nMDRGTRRIWVSQNQGDTDLDYHKILTAGLTVQQGIVRQKIISVYLVDNLEAMCQLVIQAFEAGIDFQENADSFLLMLCLH\nHAYQGDYKLFLESNAVQYLEGHGFKFELRKKDGVNRLEELLPAATSGKNIRRTLAALPEEETTEANAGQFLSFASLFLPK\nLVVGEKACLEKVQRQIQVHAEQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKYLLIHQGMHMVAGHDANDAVIANSVAQAR\nFSGLLIVKTVLDHILQKTDQGVRLHPLARTAKVRNEVNAFKAALSSLAKHGEYAPFARLLNLSGVNNLEHGLYPQLSAIA\nLGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQQYAESRELDSLGLDDQERRILMNFHQKKNEISFQQTNAMVTLRKE\nRLAKLTEAITLASRPNLGSRQDDGNEIPFPGPISNNPDQDHLEDDPRDSRDTIIPNGAIDPEDGDFENYNGYHDDEVGTA\nGDLVLFDLDDHEDDNKAFEPQDSSPQSQREIERERLIHPPPGNNKDDNRASDNNQQSADSEEQGGQYNWHRGPERTTANR\nRLSPVHEEDTLMDQGDDDPSSLPPLESDDDDASSSQQDPDYTAVAPPAPVYRSAEAHEPPHKSSNEPAETSQLNEDPDIG\nQSKSMQKLEETYHHLLRTQGPFEAINYYHMMKDEPVIFSTDDGKEYTYPDSLEEAYPPWLTEKERLDKENRYIYINNQQF\nFWPVMSPRDKFLAILQHHQ\n>NP_690581.1 polymerase complex protein [Reston ebolavirus]\nMYNNKLKVCSGPETTGWISEQLMTGKIPVTDIFIDIDNKPDQMEVRLKPSSRSSTRTCTSSSQTEVNYVPLLKKVEDTLT\nMLVNATSRQNAAIEALENRLSTLESSLKPIQDMGKVISSLNRSCAEMVAKYDLLVMTTGRATSTAAAVDAYWKEHKQPPP\nGPALYEENALKGKIDDPNSYVPDAVQEAYKNLDSTSTLTEENFGKPYISAKDLKEIMYDHLPGFGTAFHQLVQVICKIGK\nDNNLLDTIHAEFQASLADGDSPQCALIQITKRVPIFQDVPPPIIHIRSRGDIPRACQKSLRPAPPSPKIDRGWVCLFKMQ\nDGKTLGLKI\n>NP_690582.1 matrix protein [Reston ebolavirus]\nMRRGVLPTAPPAYNDIAYPMSILPTRPSVIVNETKSDVLAVPGADVPSNSMRPVADDNIDHSSHTPSGVASAFILEATVN\nVISGTKVLMKQIPIWLPLGVADQKIYSFDSTTAAIMLASYTVTHFGKISNPLVRVNRLGPGIPDHPLRLLRLGNQAFLQE\nFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDETPAGAVNALRPGLSLHPKLRPILLPGKTGKKGHASDLTSPDKIQTI\nMNAIPDLKIVPIDPTKNIVGIEVPELLVQRLTGKKPQPKNGQPIIPVLLPKYVGLDPISPGDLTMVITQDCDSCHSPASH\nPYHMDKQNSYQ\n>NP_690583.1 spike glycoprotein [Reston ebolavirus]\nMGSGYQLLQLPRERFRKTSFLVWVIILFQRAISMPLGIVTNSTLKATEIDQLVCRDKLSSTSQLKSVGLNLEGNGIATDV\nPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKSDGSECLPLPPDGVRGFPRCRYVHKVQGTGPCPGDLAFHKNGAF\nFLYDRLASTVIYRGTTFAEGVVAFLILSEPKKHFWKATPAHEPVNTTDDSTSYYMTLTLSYEMSNFGGNESNTLFKVDNH\nTYVQLDRPHTPQFLVQLNETLRRNNRLSNSTGRLTWTLDPKIEPDVGEWAFWETKKNFSQQLHGENLHFQIPSTHTNNSS\nDQSPAGTVQGKISYHPPANNSELVPTDSPPVVSVLTAGRTEEMSTQGLTNGETITGFTANPMTTTIAPSPTMTSEVDNNV\nPSEQPNNTASIEDSPPSASNETIYHSEMDPIQGSNNSAQSPQTKTTPAPTTSPMTQDPQETANSSKPGTSPGSAAGPSQP\nGLTINTVSKVADSLSPTRKQKRSVRQNTANKCNPDLYYWTAVDEGAAVGLAWIPYFGPAAEGIYIEGVMHNQNGLICGLR\nQLANETTQALQLFLRATTELRTYSLLNRKAIDFLLQRWGGTCRILGPSCCIEPHDWTKNITDEINQIKHDFIDNPLPDHG\nDDLNLWTGWRQWIPAGIGIIGVIIAIIALLCICKILC\n>NP_690584.1 small secreted glycoprotein [Reston ebolavirus]\nMGSGYQLLQLPRERFRKTSFLVWVIILFQRAISMPLGIVTNSTLKATEIDQLVCRDKLSSTSQLKSVGLNLEGNGIATDV\nPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKSDGSECLPLPPDGVRGFPRCRYVHKVQGTGPCPGDLAFHKNGAF\nFLYDRLASTVIYRGTTFAEGVVAFLILSEPKKHFWKATPAHEPVNTTDDSTSYYMTLTLSYEMSNFGGNESNTLFKVDNH\nTYVQLDRPHTPQFLVQLNETLRRNNRLSNSTGRLTWTLDPKIEPDVGEWAFWETKKTFPNNFMEKTCISKFHQPTPTTPQ\nIRARRELSKEKLATTHPPTTPSWFQRIPLQWFQCSLQDGQRKCRPKV\n>NP_690585.1 minor nucleoprotein [Reston ebolavirus]\nMEHSRERGRSSNMRHNSREPYENPSRSRSLSRDPNQVDRRQPRSASQIRVPNLFHRKKTDALIVPPAPKDICPTLKKGFL\nCDSKFCKKDHQLDSLNDHELLLLIARRTCGIIESNSQITSPKDMRLANPTAEDFSQGNSPKLTLAVLLQIAEHWATRDLR\nQIEDSKLRALLTLCAVLTRKFSKSQLGLLCETHLRHEGLGQDQADSVLEVYQRLHSDKGGNFEAALWQQWDRQSLIMFIS\nAFLNIALQIPCESSSVVVSGLATLYPAQDNSTPSEATNDTTWSSTVE\n>NP_690586.1 membrane-associated protein [Reston ebolavirus]\nMAKATGRYNLVPPKKDMEKGVIFSDLCNFLITQTLQGWKVYWAGIEFDVSQKGMALLTRLKTNDFAPAWAMTRNLFPHLF\nQNPNSVIQSPIWALRVILAAGLQDQLLDHSLVEPLTGALGLISDWLLTTTSTHFNLRTRSVKDQLSLRMLSLIRSNILQF\nINKLDALHVVNYNGLLSSIEIGTSTHTIIITRTNMGFLVEVQEPDKSAMNSKRPGPVKFSLLHESAFKPFTRVPQSGMQS\nLIMEFNSLLAI\n>NP_690587.1 RNA-dependent RNA polymerase [Reston ebolavirus]\nMATQHTQYPDARLSSPIVLDQCDLVTRACGLYSSYSLNPQLRQCKLPKHIYRLKFDTIVSKFLSDTPVATLPIDYLVPIL\nLRSLTGHGDRPLTPTCNQFLDEIINYTLHDAAFLDYYLKATGAQDHLTNIATREKLKNEILNNDYVHQLFFWHDLSILAR\nRGRLNRGNNRSTWFVHDEFIDILGYGDYIFWKIPLSLLPVTIDGVPHAATDWYQPTLFKESILGHSQILSVSTAEILIMC\nKDIITCRFNTSLIASIAKLEDVDVSDYPDPSDILKIYNAGDYVISILGSEGYKIIKYLEPLCLAKIQLCSKFTERKGRFL\nTQMHLSVINDLRELISNRRLKDYQQEKIRDFHKILLQLQLSPQQFCELFSVQKHWGHPILHSEKAIQKVKRHATILKALR\nPNVIFETYCVFKYNIAKHYFDSQGTWYSVISDRNLTPGLNSFIKRNHFPSLPMIKDLLWEFYHLNHPPLFSTKVISDLSI\nFIKDRATAVEQTCWDAVFEPNVLGYNPPNKFSTKRVPEQFLEQEDFSIESVLNYAQELHYLLPQNRNFSFSLKEKELNIG\nRTFGKLPYLTRNVQTLCEALLADGLAKAFPSNMMVVTEREQKESLLHQASWHHTSDDFGENATVRGSSFVTDLEKYNLAF\nRYEFTAPFIEYCNHCYGVRNVFNWMHYLIPQCYMHVSDYYNPPHNVNLSNREYPPEGPSSYRGHLGGIEGLQQKLWTSIS\nCAQISLVEIKTGFKLRSAVMGDNQCITVLSVFPLKTDPEEQEQSAEDNAARVAASLAKVTSACGIFLKPDETFVHSGFIY\nFGKKQYLNGVQLPQSLKTAARMAPLSDAIFDDLQGTLASIGTAFERAISETRHILPCRIVAAFHTYFAVRILQYHHLGFN\nKGIDLGQLSLSKPLDYGTITLTLAVPQVLGGLSFLNPEKCFYRNFGDPVTSGLFQLRVYLEMVNMKDLFCPLISKNPGNC\nSAIDFVLNPSGLNVPGSQDLTSFLRQIVRRSITLTARNKLINTLFHASADLEDEMVCKWLLSSNPVMSRFAADIFSRTPS\nGKRLQILGYLEGTRTLLASKIINNNSETPVLDKLRKITLQRWNLWFSYLDHCDQLLADALQKISCTVDLAQILREYTWSH\nILEGRSLIGATLPCMVEQFKVKWLGQYEPCPECLNKKGSNAYVSVAVKDQVVSAWPNTSRISWTIGSGVPYIGSRTEDKI\nGQPAIKPRCPSSALKEAIELASRLTWVTQGGSNSEQLIRPFLEARVNLSVSEVLQMTPSHYSGNIVHRYNDQYSPHSFMA\nNRMSNTATRLIVSTNTLGEFSGGGQAARDSNIIFQNVINLAVALYDIRFRNTNTSDIRHNRAHLHLTECCTKEVPAQYLT\nYTSALNLDLSRYRDNELIYDSNPLKGGLNCNLTIDSPLVKGPRLNMIEDDLLRFPHLSGWELAKTVVQSIISDNSNSSTD\nPISSGETRSFTTHFLTYPQIGLLYSFGAVLCFYLGNTILWTKKLDYEQFLYYLHNQLHNLPHRALRVFKPTFKHASVMSR\nLMEIDSNFSIYIGGTSGDRGLSDAARLFLRTAIASFLQFLKSWIIDRQKTIPLWIVYPLEGQQPESINEFLHKILGLLKQ\nGPKSIPKEVSIQNDGHLDLAENNYVYNSKSTASNFFHASLAYWRSRKSRKTQDHNDFSRGDGTLTEPVRKFSSNHQSDEK\nYYNVTCGKSPKPQERKDFSQYRLSNNGQTMSNHRKKGKFHKWNPCKMLMESQRGTVLTEGDYFQNNTPPTDDVSSPHRLI\nLPFFKLGNHNHAHDQDAQELMNQNIKQYLHQLRSMLDTTIYCRFTGIVSSMHYKLDEVLLEYNSFDSAITLAEGEGSGAL\nLLLQKYSTRLLFLNTLATEHSIESEVVSGFSTPRMLLPIMQKVHEGQVTVILNNSASQITDITSSMWLSNQKYNLPCQVE\nIIMMDAETTENLNRSQLYRAVYNLILDHIDPQYLKVVVLKVFLSDIEGILWINDYLAPLFGAGYLIKPITSSARSSEWYL\nCLSNLISTNRRSAHQTHKACLGVIRDALQAQVQRGVYWLSHIAQYATKNLHCEYIGLGFPSLEKVLYHRYNLVDTGLGPL\nSSVIRHLTNLQAEIRDLVLDYNLMRESRTQTYHFIKTAKGRITKLVNDFLKFSLIVQALKNNSSWYTELKKLPEVINVCN\nRFYHTHNCECQEKFFVQTLYLQRLRDAEIKLIERLTGLMRFYPEGLIYSNHT\n>YP_009246340.1 second secreted glycoprotein [Reston ebolavirus]\nMGSGYQLLQLPRERFRKTSFLVWVIILFQRAISMPLGIVTNSTLKATEIDQLVCRDKLSSTSQLKSVGLNLEGNGIATDV\nPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKSDGSECLPLPPDGVRGFPRCRYVHKVQGTGPCPGDLAFHKNGAF\nFLYDRLASTVIYRGTTFAEGVVAFLILSEPKKHFWKATPAHEPVNTTDDSTSYYMTLTLSYEMSNFGGNESNTLFKVDNH\nTYVQLDRPHTPQFLVQLNETLRRNNRLSNSTGRLTWTLDPKIEPDVGEWAFWETKKLFPTTSWRKLAFPNSINPHQQLLR\nSEPGGNCPRKN\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Sudan_ebolavirus/GCF_000855585.1_ViralProj15012_genomic.fna", "content": ">NC_006432.1 Sudan ebolavirus isolate Sudan virus/H.sapiens-tc/UGA/2000/Gulu-808892, complete genome\nCGGACACACAAAAAGAAAGAAAAGTTTTTTATACTTTTTGTGTGCGAATAACTATGAGGAAGATTAATCATTTTCCTCAA\nACTCAAACTAATATTAACATTGAGATTGATCTCATCATTTACCAATTGGAGACAATTTAACTAGTCAATCCCCCATTTGG\nGGGCATTCCTAAAGTGTTGCAAAGGTATGTGGGTCGTATTGCTTTGCCTTTTCCTAACCTGGCTCCTCCTACAATTCTAA\nCCTGCTTGATAAGTGTGATTACCTGAGTAATAGACTAATTTCGTCCTGGTAATTAGCATTTTCTAGTAAAACCAATACTA\nTCTCAAGTCCTAAGAGAAGGTGAGAAGAGGGTCCCGAGGTATCCCTCCAGTCCACAAAATCTAGCTAATTTTAGCTGAGT\nGGACTGATTACTCTCATCACACGCTAACTACTAAGGGTTTACCTGAGAGCCTACAACATGGATAAACGGGTGAGAGGTTC\nATGGGCCCTGGGAGGACAATCTGAAGTTGATCTTGACTACCACAAAATATTAACAGCCGGGCTTTCGGTCCAACAAGGGA\nTTGTGCGACAAAGAGTCATCCCGGTATATGTTGTGAGTGATCTTGAGGGTATTTGTCAACATATCATTCAGGCCTTTGAA\nGCAGGCGTAGATTTCCAAGATAATGCTGACAGCTTCCTTTTACTTTTATGTTTACATCATGCTTACCAAGGAGATCATAG\nGCTCTTCCTCAAAAGTGATGCAGTTCAATACTTAGAGGGCCATGGTTTCAGGTTTGAGGTCCGAGAAAAGGAGAATGTGC\nACCGTCTGGATGAATTGTTGCCCAATGTCACCGGTGGAAAAAATCTTAGGAGAACATTGGCTGCAATGCCTGAAGAGGAG\nACAACAGAAGCTAATGCTGGTCAGTTTTTATCCTTTGCCAGTTTGTTTCTACCCAAACTTGTCGTTGGGGAGAAAGCGTG\nTCTGGAAAAAGTACAAAGGCAGATTCAGGTCCATGCAGAACAAGGGCTCATTCAATATCCAACTTCCTGGCAATCAGTTG\nGACACATGATGGTGATCTTCCGTTTGATGAGAACAAACTTTTTAATCAAGTTCCTACTAATACATCAGGGGATGCACATG\nGTCGCAGGCCATGATGCGAATGACACAGTAATATCTAATTCTGTTGCCCAAGCAAGGTTCTCTGGTCTTCTGATTGTAAA\nGACTGTTCTGGACCACATCCTACAAAAAACAGATCTTGGAGTACGACTTCATCCACTGGCCAGGACAGCAAAAGTCAAGA\nATGAGGTCAGTTCATTCAAGGCAGCTCTTGGCTCACTTGCCAAGCATGGAGAATATGCTCCATTTGCACGTCTCCTCAAT\nCTTTCTGGAGTCAACAACTTGGAACATGGGCTTTATCCACAACTCTCAGCCATTGCTTTGGGTGTTGCAACTGCCCACGG\nGAGCACGCTGGCTGGTGTTAATGTAGGGGAGCAATATCAGCAACTGCGTGAGGCTGCTACTGAAGCTGAAAAGCAACTCC\nAACAATATGCTGAAACACGTGAGTTGGACAACCTTGGGCTTGATGAACAGGAAAAGAAGATTCTCATGAGCTTCCACCAG\nAAGAAGAATGAGATCAGCTTCCAGCAAACTAACGCAATGGTAACCCTGAGGAAAGAGCGGCTGGCCAAACTGACCGAAGC\nCATCACGACTGCATCAAAGATCAAGGTTGGAGATCGTTATCCTGATGACAATGATATTCCATTTCCCGGGCCGATCTATG\nATGAAACCCACCCCAACCCTTCTGATGATAATCCTGATGATTCACGTGATACAACTATCCCAGGTGGTGTTGTTGACCCG\nTATGATGATGAGAGTAATAATTATCCTGACTACGAGGATTCGGCTGAAGGCACCACAGGAGATCTTGATCTCTTCAATTT\nGGACGACGACGATGACGACAGCCAACCAGGACCACCAGACAGGGGGCAGAGCAAGGAAAGAGCGGCTCGGACACATGGCC\nTCCAAGATCCGACCTTGGACGGAGCGAAAAAGGTGCCGGAGTTGACCCCAGGTTCCCACCAACCAGGCAACCTCCACATC\nACCAAGCCGGGTTCAAACACCAACCAACCACAAGGCAATATGTCATCTACTCTCCAGAGTATGACCCCTATACAGGAAGA\nATCAGAGCCCGATGATCAGAAAGATGATGATGACGAGAGTCTCACATCCCTTGACTCTGAAGGTGACGAAGATGTTGAGA\nGCGTATCAGGGGAGAACAACCCAACTGTAGCTCCACCAGCACCAGTCTACAAAGATACTGGAGTAGACACTAATCAGCAA\nAATGGACCAAGCAATGCTGTAGATGGTCAAGGTTCTGAAAGTGAAGCTCTCCCAATCAACCCCGAAAAGGGATCTGCACT\nGGAAGAAACATATTATCATCTCCTAAAAACACAGGGTCCATTTGAGGCAATCAATTATTATCACCTAATGAGTGATGAGC\nCCATTGCTTTTAGCACTGAAAGTGGCAAGGAATATATCTTCCCAGATTCTCTTGAAGAAGCCTACCCGCCTTGGTTGAGT\nGAGAAGGAGGCCTTAGAGAAAGAAAATCGTTATCTGGTCATTGATGGCCAGCAATTCCTCTGGCCAGTAATGAGCCTACA\nGGACAAGTTCCTTGCTGTTCTTCAACATGACTGAGGACCCATGATTAGTAGATTTTGTTTATTCTGAGCTTGATTATAAT\nTGTTTTGATAATTCAAGTATGAGCAACCAACCCGAAATATAAACCCTATTTTAGTTATGAGGAAATTAAATAAATAATCT\nGTAAGTTGTAGGACTATGAAGAGCTGCTTGTGTCAATTTATCACGGGCTAATACCCATACCGCAAGAATAATTATTTAGT\nAATTTTGATCAGCTTATGATATGTACCAATAGGAAAACATTATAGCATTAAAACATAAAGTATCCTTCGATGAGCTTAGG\nAGGATAATATCCTGATGAATTCTATAGAACTTAGGATTAAGAAAAAATTCATGATGAAGATTAAAACCTTCATCATCCTT\nTAAAAAGAGAGCTATTCTTTATCTGAATGTCCTTATTAATGTCTAAGAGCTATTATTTTGTACCCTCTTAGCCTAGACAC\nTGCCCAGCATATAAGCCATGCAGCAGGATAGGACTTATAGACATCATGGACCCGAAGTGTCTGGCTGGTTTTCTGAGCAA\nTTAATGACCGGCAAAATACCGCTAACAGAGGTGTTTGTTGATGTTGAAAACAAACCAAGTCCTGCCCCGATAACCATTAT\nTAGTAAGAATCCCAAGACAACACGTAAAAGTGATAAGCAAGTCCAAACAGATGATGCCAGTAGCTTATTGACAGAAGAAG\nTCAAGGCTGCCATAAATTCGGTGATATCAGCTGTGCGTCGGCAAACCAATGCTATTGAATCACTAGAAGGTCGAGTAACA\nACTCTTGAGGCCAGCTTAAAACCCGTTCAAGACATGGCAAAGACCATATCATCCCTGAATCGCAGCTGTGCCGAAATGGT\nTGCAAAATACGACCTACTGGTGATGACCACTGGGCGAGCAACTGCCACTGCTGCAGCAACAGAAGCATATTGGAATGAAC\nATGGACAAGCACCTCCAGGCCCATCATTGTACGAGGATGATGCTATTAAGGCTAAATTGAAAGATCCGAACGGGAAGGTT\nCCAGAAAGTGTCAAACAGGCCTACATAAATCTAGATAGCACAAGTGCCCTCAATGAGGAAAATTTCGGGCGACCTTACAT\nTTCAGCAAAAGATCTCAAGGAAATCATCTATGACCATCTCCCAGGATTTGGGACAGCTTTTCATCAGTTGGTGCAGGTTA\nTCTGCAAAATTGGTAAGGATAATAATATCCTAGACATAATTCATGCAGAATTCCAAGCAAGCTTGGCTGAGGGAGACTCC\nCCCCAGTGTGCATTAATCCAGATAACAAAACGGATCCCTGCTTTCCAAGATGCCTCTCCTCCAATTGTGCATATCAAGTC\nTCGAGGAGATATACCCAAAGCCTGTCAGAAAAGCCTCCGGCCGGTCCCACCGTCACCAAAGATCGATAGAGGTTGGGTCT\nGTATTTTTCAATTCCAAGACGGGAAGGCCCTTGGGCTAAAAATATGATACAGAAGCAAGGTAAGCTCATTTTGCGATGGC\nCAAATGATACTTATGACTGTTTAAAATCAAGTTAGACTAATAGTCTATTGTGTCATAAGCTTATAAGTCAGTTTTAAATT\nTCCCCTCTATCCTAATCAATTGATAATGCTGTCAATAGGGAAATTCCCCTGTATTGTAATAAGACCTCATTAACATATTT\nCCCCTGCTTAGTACTATGCAGAAACCCCCGAGCAAATTAAAATTGATGAAGATTAAGAAAAAGAGGGATTTTCTCAGGAA\nAAATCTTTTTTCTTACCTTCATCTCATTTAAACAAATTTAGGACTCAGGAAAAATGAGAAGGGTCACTGTGCCGACTGCA\nCCACCTGCCTATGCTGACATTGGCTATCCTATGAGCATGCTTCCCATCAAGTCAAGCAGGGCTGTGAGTGGAATTCAACA\nGAAACAAGAGGTCCTTCCTGGAATGGATACACCATCAAATTCTATGAGACCTGTTGCTGATGATAACATTGATCATACAA\nGTCATACCCCGAACGGAGTGGCCTCAGCATTCATCTTGGAGGCAACTGTCAATGTGATCTCGGGGCCCAAAGTCCTCATG\nAAACAAATCCCTATTTGGTTGCCACTCGGAATTGCTGACCAAAAAACGTACAGTTTTGACTCAACAACAGCAGCAATTAT\nGCTCGCATCTTATACGATCACCCATTTTGGAAAGGCCAACAACCCCCTCGTTAGAGTGAATCGACTTGGTCAGGGAATAC\nCGGATCACCCACTCAGATTGCTCAGGATGGGGAACCAGGCTTTCCTTCAAGAGTTTGTGCTACCACCAGTTCAACTGCCG\nCAATATTTCACTTTTGATCTGACTGCACTCAAACTAGTGACACAGCCTCTCCCTGCTGCAACATGGACAGATGAGACTCC\nGAGCAACCTTTCAGGAGCCCTTCGTCCCGGGCTTTCATTTCACCCAAAGCTGAGACCCGTTCTACTTCCAGGCAAGACGG\nGAAAGAAAGGGCATGTTTCTGATCTGACTGCCCCAGACAAAATTCAGACAATTGTGAACCTGATGCAAGATTTCAAAATC\nGTGCCAATTGATCCAGCTAAGAGTATCATTGGGATCGAGGTTCCAGAATTGCTGGTCCACAAGCTCACTGGGAAGAAAAT\nGAGTCAGAAGAATGGACAGCCTATAATTCCTGTCTTACTCCCAAAATACATTGGGCTAGATCCAATCTCACCTGGAGACC\nTGACTATGGTCATAACACCAGATTATGATGATTGTCATTCACCTGCCAGTTGCTCTTATCTCAGTGAAAAGTGATTCTCA\nCAAAGTGAGAGAAACACCTCCAGTAAAGAAATCAAATCTTATCTATAGCAACTCAATCGACTTTTAGGAAGCTAGCAGTC\nCATATACTATGGGACAACTCAACCCTCTTGTTAAAATGTACTAATCGGGTCAAGGAACTCTCACTGATCAAGCCTGAATC\nCAAGATAGAACCAGCCCAAAGGGCCTCCCCAGAGTCTCTTACAAGCTTAGCCAATCAATTAACATGCATAAGCGATCCAT\nACTTCGCCCAATCAGTGTCCGATGTTCACCCCTTCAAGCCTCCTTCCTAGCAAATTGACCTAGCTGTACCAAGAGATTCC\nCTCAGCCTCCTTCTCAAATAACCTGATCCTCGAGGGTTACACCTTCACCACTCTATGCTCATTTCACCCAAACATAAAAT\nGAAATGTCTTAACATGATTGCACCATTAAGAAAAACAAATCTGATGAAGATTAAGCCTGATGAAGGCCCAACCTTCATCT\nTTTTACCATAATCTTGTTCTCAGTACCATTTGATAAGGGTACACTTGCCAATACGCCCCCATCCTAAGGGTCTCGCAATG\nGGGGGTCTTAGCCTACTCCAATTGCCCAGGGACAAATTTCGGAAAAGCTCTTTCTTTGTTTGGGTCATCATCTTATTCCA\nAAAGGCCTTTTCCATGCCTTTGGGTGTTGTGACTAACAGCACTTTAGAAGTAACAGAGATTGACCAGCTAGTCTGCAAGG\nATCATCTTGCATCTACTGACCAGCTGAAATCAGTTGGTCTCAACCTCGAGGGGAGCGGAGTATCTACTGATATCCCATCT\nGCAACAAAGCGTTGGGGCTTCAGATCTGGTGTTCCTCCCAAGGTGGTCAGCTATGAAGCGGGAGAATGGGCTGAAAATTG\nCTACAATCTTGAAATAAAGAAGCCGGACGGGAGCGAATGCTTACCCCCACCGCCAGATGGTGTCAGAGGCTTTCCAAGGT\nGCCGCTATGTTCACAAAGCCCAAGGAACCGGGCCCTGCCCAGGTGACTACGCCTTTCACAAGGATGGAGCTTTCTTCCTC\nTATGACAGGCTGGCTTCAACTGTAATTTACAGAGGAGTCAATTTTGCTGAGGGGGTAATTGCATTCTTGATATTGGCTAA\nACCAAAAGAAACGTTCCTTCAGTCACCCCCCATTCGAGAGGCAGTAAACTACACTGAAAATACATCAAGTTATTATGCCA\nCATCCTACTTGGAGTATGAAATCGAAAATTTTGGTGCTCAACACTCCACGACCCTTTTCAAAATTGACAATAATACTTTT\nGTTCGTCTGGACAGGCCCCACACGCCTCAGTTCCTTTTCCAGCTGAATGATACCATTCACCTTCACCAACAGTTGAGTAA\nTACAACTGGGAGACTAATTTGGACACTAGATGCTAATATCAATGCTGATATTGGTGAATGGGCTTTTTGGGAAAATAAAA\nAAATCTCTCCGAACAACTACGTGGAGAAGAGCTGTCTTTCGAAGCTTTATCGCTCAACGAGACAGAAGACGATGATGCGG\nCATCGTCGAGAATTACAAAGGGAAGAATCTCCGACCGGGCCACCAGGAAGTATTCGGACCTGGTTCCAAAGAATTCCCCT\nGGGATGGTTCCATTGCACATACCAGAAGGGGAAACAACATTGCCGTCTCAGAATTCGACAGAAGGTCGAAGAGTAGGTGT\nGAACACTCAGGAGACCATTACAGAGACAGCTGCAACAATTATAGGCACTAACGGCAACCATATGCAGATCTCCACCATCG\nGGATAAGACCGAGCTCCAGCCAAATCCCGAGTTCCTCACCGACCACGGCACCAAGCCCTGAGGCTCAGACCCCCACAACC\nCACACATCAGGTCCATCAGTGATGGCCACCGAGGAACCAACAACACCACCGGGAAGCTCCCCCGGCCCAACAACAGAAGC\nACCCACTCTCACCACCCCAGAAAATATAACAACAGCGGTTAAAACTGTCCTGCCACAGGAGTCCACAAGCAACGGTCTAA\nTAACTTCAACAGTAACAGGGATTCTTGGGAGTCTTGGGCTTCGAAAACGCAGCAGAAGACAAACTAACACCAAAGCCACG\nGGTAAGTGCAATCCCAACTTACACTACTGGACTGCACAAGAACAACATAATGCTGCTGGGATTGCCTGGATCCCGTACTT\nTGGACCGGGTGCGGAAGGCATATACACTGAAGGCCTGATGCATAACCAAAATGCCTTAGTCTGTGGACTTAGGCAACTTG\nCAAATGAAACAACTCAAGCTCTGCAGCTTTTCTTAAGAGCCACAACGGAGCTGCGGACATATACCATACTCAATAGGAAG\nGCCATAGATTTCCTTCTGCGACGATGGGGCGGGACATGCAGGATCCTGGGACCAGATTGTTGCATTGAGCCACATGATTG\nGACAAAAAACATCACTGATAAAATCAACCAAATCATCCATGATTTCATCGACAACCCCTTACCTAATCAGGATAATGATG\nATAATTGGTGGACGGGCTGGAGACAGTGGATCCCTGCAGGAATAGGCATTACTGGAATTATTATTGCAATTATTGCTCTT\nCTTTGCGTTTGCAAGCTGCTTTGCTGAATATCAATTTGAATCATCAATTTAAGCTTGATACATTTCTAGCATTTTAAATT\nATAAACCGATACTGATACTTGAAAATCAGGCTAATGCCAAGTTCTGTGCAAAACTTGAAAGTAGGTTTACAAAAATCCTT\nTGGACTGGAATGCTTTGATACTCTTTCTCAATACTATATAAGTTCCTTCCCAAGAATAATATTGATGAAGATTAAGAAAA\nAGTGACATTGTGCCCACTTTTGTAATCTTCATCCACCTACACATTCATATTCAGGAATCTTTGAATTAACCCTCACACTT\nGCTTAGGAAAGAGCCTATCCTCTACAAGAATCCCGAGGCGGCAATTCAGTTAATTTCATATCAAGATAACATCCATTTCC\nAAGACCACAGATAACTATATTATTAATCTTTACCACAAATATGGAGAGGGGTCGTGAGCGCGGGAGATCAAGGAATTCAC\nGTGCCGACCAGCAAAATTCAACAGGTCCTCAATTTAGGACAAGATCCATTTCCCGGGATAAGACAACAACAGACTACCGT\nAGTAGTCGAAGTACTTCGCAAGTTAGAGTCCCTACGGTTTTCCATAAGAAAGGTACTGGGACCCTTACTGTCCCTCCAGC\nACCTAAGGATGTTTGTCCTACTCTCAGAAAAGGATTTCTATGTGATAGTAATTTCTGTAAAAAGGACCATCAACTTGAAA\nGCCTAACCGACCGGGAGCTCCTACTTCTTATAGCACGGAAGACCTGTGGATCAACTGATTCATCGCTTAATATAGCTGCT\nCCTAAAGACCTAAGACTAGCAAATCCTACGGCTGATGACTTCAAGCAAGACGGCAGTCCAAAATTAACCCTAAAATTACT\nAGTCGAGACTGCTGAGTTTTGGGCCAATCAGAATATTAATGAAGTAGATGATGCAAAACTCCGTGCTCTCTTGACGTTGA\nGTGCTGTCTTAGTGCGGAAATTCTCTAAGTCACAGCTTAGTCAATTATGTGAGAGTCATCTTAGGAGGGAAAACTTAGGA\nCAAGACCAAGCTGAATCAGTTCTCGAGGTTTATCAACGTTTACATAGTGACAAAGGAGGTGCTTTTGAGGCAGCACTATG\nGCAACAGTGGGATAGACAATCATTAACTATGTTTATATCTGCTTTCCTCCATGTAGCATTGCAACTTTCCTGTGAGAGCT\nCCACTGTAGTGATATCAGGCCTACGCTTACTTGCCCCCCCAAGCGTTAATGAAGGGCTCCCTCCTGCACCAGGGGAATAT\nACTTGGTCAGAAGATAGTACAACTTAGCCTGTAGGGAGGACAAGTAAAACAAGATGCCCTTATCCTCTATAGATGGTATT\nTTTAGAGAGGGGGACAGGATAGGAATAAAGATAATGACTAAAGCCAATATAAAGATACGAACACAAGTAGAAATTAAAAT\nAGAAATCAAAACAATCTCCCCTTATTCAATATGAAATATAATAGTGAGTATTTGTTTCATGATGTCAATCATTTATTGTT\nAAAAATAAACAAAGTCAGTAAGAGTGTTAGGATCGTTATATTGCAAGGATCCTCCCTAGAAGCGTTGAATCATCTCAAGT\nAGCCTAGAACAAGAACAGCAGAGCATTAAATTGAAATAGATAATAAGGATATTGCTTGTTTTTAAGATAGTTTTAGGAAG\nTTTAAAATTAAGAAAAAGAACCCATGGACACACTCTAGCATTGAGGATGGGGTTCCCTTGATGATAGTATAGTCTTAGGT\nATAGGGTAGTCCTACACGTACTATATTATACAGTCTAAACTTGTAAAATTAAACTACAAGAACATGATGAAAATTAATGA\nGAAGGTTCCAAGATTGACTTCAATCCAAACACCTTGCTCTGCCAATTTTCATCTCCTTAAGATATATGATTTTGTTCCTG\nCGAGATAAGGTTATCAAATAGGGTGTGTATCTCTTTTACATATTTGGGCTCCCACTAGGCTAGGGTTTATAGTTAAGGAA\nGACTCATCACATTTTTTATTGAACTAGTCTACTCGCAGAATCCTACCGGGAATAGAAATTAGAACATTTGTGATACTTTG\nACTATAGGAAATAATTTTCAACACTACCTGAGATCAGGTTATTCTTCCAACTTATTCTGCAAGTAATTGTTTAGCATCAT\nAACAACAACGTTATAATTTAAGAATCAAGTCTTGTAACAGAAATAAAGATAACAGAAAGAACCTTTATTATACGGGTCCA\nTTAATTTTATAGGAGAAGCTCCTTTTACAAGCCTAAGATTCCATTAGAGATAACCAGAATGGCTAAAGCCACAGGCCGGT\nACAACTTGGTAACACCAAAACGGGAGCTAGAGCAAGGAGTTGTGTTTAGCGACCTATGCAACTTCCTAGTGACTCCAACT\nGTGCAAGGATGGAAGGTTTACTGGGCTGGACTTGAGTTTGATGTCAACCAAAAGGGTATTACCCTGTTAAATCGTCTTAA\nAGTGAATGATTTTGCTCCTGCATGGGCGATGACCCGGAACCTCTTCCCACACTTGTTCAAAAACCAACAGTCTGAAGTCC\nAAACTCCCATTTGGGCCTTGAGGGTAATTCTTGCCGCCGGGATTCTTGACCAATTAATGGATCATTCCCTCATTGAGCCG\nCTATCAGGGGCCCTGAACCTAATTGCTGATTGGTTACTAACAACATCTACTAATCACTTCAACATGAGAACTCAACGAGT\nAAAGGACCAACTGAGCATGAGGATGTTATCTCTTATAAGGTCAAATATTATTAACTTTATAAATAAGCTCGAGACTCTTC\nATGTCGTTAATTACAAGGGACTTCTAAGCAGTGTTGAGATAGGAACACCAAGCTATGCAATCATCATTACCAGGACTAAT\nATGGGTTATCTTGTCGAGGTTCAGGAACCAGATAAATCTGCGATGGATATACGACACCCTGGTCCTGTCAAATTCTCCTT\nACTACATGAATCGACACTTAAACCTGTTGCCACTCCTAAACCATCAAGCATTACTTCATTGATCATGGAGTTCAACAGTT\nCTTTGGCAATTTAATTGCCGTAATAAAAATTGTACGATAGGGCTAACATTGATTCCATAATCCATCGTAGGACAGAATCA\nTTTTCCTGTATGATCTTAGTTTAATCTCTCTTTATACAATGATTAATAAGGAGCCTGTTTAAAATGTTACAAAAGTATAC\nTGTTTGAACCCCTAGTATCCCTGTAAATATCCTCATTCAATTTTTTGCTTTTACATGTGTAGTCACCTGTATAGCATGAC\nCCTAGTCATGCCTTTAATTAATACTTAATCTAACAGTTAATATAATGTATAACTTTCCATGTTCAAAGAGTAGTCAAAAC\nAATGTGAGATCCAGTTTCACTCACAGCATCTATTCACTATTTACAGTATGATGAGCCCAAATTAACACGGTAGAGGTCTA\nGATTTATTAATAGAACGAGGAAGATTAAGAAAAAGTCCATAATGCTGGGGAGGCAATCCTTGCCACCATAGGACTTTTTC\nAATTCCTCTATTTTATGATGGCTACCCAACATACACAATATCCTGATGCAAGATTGTCTTCCCCAATTGTCTTAGACCAA\nTGTGACCTAGTGACAAGAGCATGTGGACTTTACTCTGAGTATTCGCTGAACCCTAAACTAAAGACATGCCGTTTACCGAA\nACATATCTATAGATTAAAATATGACACTATTGTTTTACGATTTATTAGTGATGTCCCTGTAGCTACAATCCCAATAGACT\nACATTGCTCCGATGTTAATAAATGTTCTGGCAGATAGTAAAAATGTACCATTGGAACCTCCCTGCTTGAGTTTCTTGGAT\nGAAATAGTCAATTATACCGTGCAGGATGCAGCCTTCCTTAATTATTACATGAATCAGATTAAAACACAGGAAGGAGTAAT\nTACAGATCAATTAAAACAGAACATTCGTAGGGTCATTCACAAAAACAGATATCTATCTGCTCTATTCTTCTGGCATGATC\nTTGCCATCCTCACCCGTCGAGGGAGAATGAACCGAGGAAATGTGCGCTCCACTTGGTTTGTAACGAATGAGGTTGTTGAC\nATTCTAGGATATGGTGATTATATCTTCTGGAAGATCCCTATTGCTCTATTACCAATGAACACAGCTAATGTTCCACATGC\nATCAACTGACTGGTACCAACCTAATATCTTCAAGGAGGCTATTCAAGGACACACACATATTATTTCAGTCTCTACAGCCG\nAGGTCCTTATTATGTGTAAGGATCTTGTCACAAGTCGTTTTAATACCCTTCTGATTGCTGAGTTAGCCAGGTTGGAAGAT\nCCAGTGTCTGCTGATTATCCACTAGTAGATAATATTCAATCTCTGTATAACGCAGGAGACTACCTGTTGTCCATATTGGG\nATCAGAGGGGTACAAAATAATCAAATATCTCGAACCTCTGTGTTTGGCTAAGATTCAACTATGTTCCCAATATACAGAAC\nGAAAAGGGCGGTTTTTAACCCAGATGCATCTTGCAGTTATTCAGACATTGCGTGAACTCCTCCTTAATAGAGGGTTGAAA\nAAATCACAATTGTCTAAAATCCGCGAGTTTCACCAACTGTTGCTCAGACTCCGATCTACACCACAACAATTATGTGAATT\nATTTTCAATCCAAAAACACTGGGGCCACCCAGTTCTGCATAGTGAAAAGGCCATCCAAAAGGTTAAAAATCATGCAACAG\nTTCTAAAGGCATTGCGGCCGATTATCATCTTTGAAACGTATTGTGTATTCAAGTATAGTGTTGCAAAACATTTCTTTGAT\nAGTCAAGGCACTTGGTACAGTGTGATATCAGACCGATGTTTAACGCCGGGATTGAATTCCTACATTAGGCGAAATCAATT\nCCCTCCACTTCCAATGATCAAAGATCTTTTATGGGAATTTTACCATTTGGATCATCCTCCATTATTCTCCACGAAGATCA\nTTAGTGACCTCAGCATTTTCATTAAAGACCGCGCAACAGCAGTTGAACAAACCTGTTGGGATGCAGTTTTTGAGCCTAAC\nGTTTTGGGCTACAGTCCACCTTATCGATTCAATACCAAACGTGTACCTGAACAATTCCTGGAGCAAGAGGATTTTTCTAT\nTGAGAGTGTCTTACAATACGCCCAAGAACTTAGGTACTTATTGCCCCAGAATCGAAATTTTTCTTTTTCATTGAAGGAAA\nAAGAATTAAATGTTGGTAGGACATTTGGAAAATTGCCTTATTTAACCAGGAATGTCCAAACCCTCTGCGAAGCATTACTT\nGCAGATGGTTTGGCTAAAGCCTTTCCAAGCAATATGATGGTTGTCACAGAGAGGGAACAAAAGGAGAGCCTCCTTCACCA\nAGCATCCTGGCACCATACAAGTGATGATTTCGGAGAGCATGCCACAGTTCGTGGAAGTAGTTTTGTCACAGACCTGGAAA\nAATACAATCTGGCCTTCAGGTATGAATTCACAGCTCCCTTCATCAAATATTGCAACCAATGCTATGGGGTTCGCAATGTC\nTTTGATTGGATGCACTTCCTAATTCCGCAATGTTACATGCATGTTAGTGATTATTATAACCCACCACATAATGTAACCTT\nAGAGAATAGGGAATATCCCCCCGAAGGACCAAGTGCTTATAGAGGCCACCTTGGCGGTATTGAGGGGCTTCAACAAAAGT\nTATGGACTAGTATCTCATGTGCTCAAATCTCATTGGTAGAGATCAAGACCGGGTTCAAATTGCGATCAGCAGTCATGGGG\nGATAATCAATGTATTACAGTATTATCAGTCTTTCCACTAGAATCTAGTCCGAATGAGCAGGAGAGATGCGCAGAAGACAA\nTGCAGCCAGAGTGGCTGCTAGCTTGGCCAAAGTCACAAGTGCCTGTGGGATATTCCTCAAGCCTGATGAGACTTTCGTAC\nACTCAGGCTTTATCTATTTTGGCAAAAAGCAATACTTGAACGGAATTCAATTACCTCAATCACTCAAGACAGCAGCTAGG\nATGGCCCCTCTCTCAGATGCAATTTTTGATGACTTGCAAGGTACACTTGCCAGTATAGGAACTGCCTTTGAGCGATCAAT\nCTCCGAAACTAGACATATTTTACCATGCCGTGTTGCAGCTGCCTTTCATACATATTTCTCTGTTCGGATCTTACAACATC\nATCACCTTGGTTTCCATAAGGGTTCAGACCTTGGACAATTGGCAATCAATAAACCTCTTGATTTCGGGACCATTGCACTA\nTCCTTAGCAGTTCCTCAGGTATTGGGTGGATTATCCTTCCTAAATCCAGAAAAGTGCCTTTATCGCAACTTGGGTGATCC\nTGTAACTTCAGGCCTATTTCAGTTGAAGCATTATCTGTCAATGGTGGGTATGAGTGATATCTTTCATGCACTTATTGCAA\nAAAGCCCAGGGAATTGTAGCGCAATTGACTTTGTTCTAAACCCAGGCGGGTTAAATGTCCCTGGATCACAGGATTTAACA\nTCTTTCCTTCGTCAGATTGTCAGAAGGAGTATCACACTTTCGGCAAGGAACAAGTTAATCAACACGTTATTTCACGCTTC\nTGCAGATCTTGAAGACGAATTAGTATGTAAATGGTTACTTTCTTCAACGCCCGTGATGAGCCGTTTTGCAGCCGATATTT\nTCTCACGAACACCAAGCGGGAAAAGATTACAAATCTTGGGATACCTCGAGGGAACCAGAACTTTATTAGCATCCAAAATG\nATAAGCAATAATGCAGAGACACCAATCTTGGAGAGGCTCAGAAAAATAACACTTCAAAGATGGAATCTATGGTTTAGTTA\nCCTAGACCATTGTGACCCAGCTTTAATGGAAGCAATTCAACCAATTAAGTGTACTGTTGATATTGCTCAAATTCTTAGAG\nAATACTCCTGGGCTCATATCCTTGATGGTAGACAGTTAATAGGGGCAACACTGCCATGTATACCTGAGCAGTTCCAAACC\nACATGGTTAAAACCTTACGAGCAATGTGTGGAATGTTCATCCACAAACAATTCTAGTCCATATGTATCAGTTGCATTAAA\nAAGGAACGTGGTTAGTGCTTGGCCTGATGCATCTAGATTGGGGTGGACGATTGGTGATGGGATTCCCTACATAGGCTCAA\nGAACTGAGGACAAAATAGGTCAGCCCGCTATTAAGCCGAGGTGCCCATCAGCTGCATTAAGAGAAGCTATTGAATTGACC\nTCTAGGTTGACCTGGGTCACTCAAGGTAGTGCAAACAGCGATCAGTTAATTCGCCCTTTTCTTGAGGCAAGAGTAAACTT\nGAGTGTACAAGAGATTCTTCAAATGACCCCCTCACATTACTCCGGTAATATTGTGCATCGGTATAATGATCAGTATAGCC\nCTCACTCCTTTATGGCTAACCGCATGAGTAACACAGCAACGCGCTTGATGGTATCTACCAACACACTAGGAGAGTTTTCC\nGGAGGGGGTCAGGCTGCACGTGATAGCAACATTATATTTCAAAATGTGATTAACTTTGCAGTGGCCTTGTATGACATTAG\nGTTTCGGAACACTTGTACATCTTCTATTCAATATCACAGGGCCCATATTCACCTGACGAATTGTTGTACGAGGGAAGTAC\nCGGCCCAATACTTAACATACACAACCACGCTAAATCTAGATTTGAGTAAGTACCGTAATAATGAACTGATTTATGATTCA\nGATCCACTAAGAGGAGGTCTCAACTGCAACTTATCGATTGACAGTCCTTTGATGAAGGGCCCACGTTTAAATATTATTGA\nGGATGACTTAATACGGTTGCCACATTTATCCGGCTGGGAATTAGCAAAAACAGTCTTGCAATCAATAATCTCTGATAGTA\nGCAATTCATCAACAGATCCCATTAGCAGCGGTGAAACAAGATCCTTCACAACCCACTTCTTAACGTATCCCAAAATAGGG\nCTTCTATACAGTTTTGGAGCCCTCATAAGTTTTTATTTGGGTAATACTATTCTATGCACGAAAAAGATCGGACTCACAGA\nATTTCTATACTATCTCCAGAATCAGATCCACAACTTATCACATAGATCCCTTCGAATCTTCAAACCGACATTTAGACACT\nCAAGTGTCATGTCCAGGTTGATGGATATAGACCCCAACTTCTCAATATATATTGGTGGGACTGCAGGTGACCGTGGATTA\nTCGGACGCTGCAAGATTATTTCTCCGAATTGCAATTTCAACTTTCTTGAGCTTTGTTGAGGAGTGGGTTATCTTTAGGAA\nGGCAAACATCCCACTATGGGTTATCTATCCTCTCGAAGGCCAACGCTCTGATCCTCCTGGCGAATTTTTGAACCGAGTAA\nAATCTCTAATTGTTGGGACTGAAGATGATAAAAATAAAGGCTCTATACTTTCAAGATCTGGAGAGAAATGCTCTTCAAAT\nCTAGTTTATAATTGCAAGAGTACAGCAAGCAATTTTTTCCATGCATCATTGGCTTACTGGAGAGGTCGACATAGACCTAA\nGAAGACTATAGGTGCAACTAACGCGACAACAGCTCCACATATCATTTTGCCACTGGGAAATTCTGATCGACCGCCTGGCC\nTAGACCTTAATAGGAACAATGATACTTTCATTCCTACCAGAATTAAACAGATAGTCCAAGGAGACTCTAGAAACGACAGA\nACGACCACCACGAGATTTCCACCCAAAAGTAGGTCCACTCCAACATCAGCAACCGAGCCTCCTACAAAAATGTATGAGGG\nTTCGACAACCCACCAAGGGAAATTAACAGATACACATTTGGATGAGGATCACAATGCCAAAGAGTTCCCATCCAATCCGC\nATCGTTTAGTAGTACCATTCTTTAAATTAACAAAAGATGGGGAATACAGCATCGAACCTTCTCCTGAAGAAAGCCGCAGT\nAATATAAAAGGGTTACTTCAACATTTAAGAACCATGGTTGATACTACCATATATTGTCGCTTCACTGGAATTGTTTCATC\nAATGCATTATAAGTTAGATGAAGTACTATGGGAATATAATAAATTTGAATCAGCTGTAACCCTAGCAGAAGGGGAGGGTT\nCAGGTGCCTTACTACTGATCCAAAAATACGGCGTTAAGAAGTTATTTTTGAATACACTTGCTACTGAACATAGTATTGAG\nAGTGAAGTGATATCAGGTTACACCACTCCAAGGATGCTACTCCCAATTATGCCTAAAACACATCGTGGTGAGCTAGAGGT\nCATATTAAATAACTCAGCTAGTCAAATAACTGATATTACACATCGAGATTGGTTTTCAAATCAAAAAAATAGGATTCCAA\nATGATGCTGATATTATTACCATGGATGCTGAAACTACAGAAAACTTAGATCGTTCCAGATTATATGAAGCAGTATATACG\nATTATTTGTAATCATATCAATCCTAAAACTTTGAAAGTGGTCATCTTAAAAGTCTTCCTCAGCGATTTGGATGGGATGTG\nCTGGATTAACAATTATCTTGCTCCTATGTTTGGATCAGGATATTTAATCAAACCTATAACATCAAGTGCAAAGTCAAGTG\nAGTGGTATTTATGCTTATCTAATCTACTTTCAACCTTGAGAACTACTCAGCATCAAACCCAGGCAAACTGTCTCCATGTC\nGTACAATGTGCTCTTCAACAGCAAGTACAAAGAGGGTCATATTGGCTAAGTCATCTTACCAAATACACCACAAGTAGATT\nGCACAATAGTTATATTGCATTTGGTTTTCCTTCATTAGAGAAGGTCCTATATCATAGGTATAACCTTGTTGATTCGAGAA\nATGGACCATTAGTTTCTATAACGAGACACCTTGCCCTCCTCCAAACTGAGATCCGGGAGTTGGTAACTGATTATAATCAG\nCTGCGACAAAGTCGAACCCAGACTTATCATTTCATAAAAACATCCAAGGGACGGATAACTAAACTAGTGAATGATTATCT\nAAGATTTGAGTTGGTTATACGGGCTCTTAAAAATAATTCTACATGGCACCATGAGTTATACTTGCTACCAGAACTTATAG\nGTGTTTGCCATCGATTTAATCATACACGTAACTGTACATGCAGTGAAAGGTTCCTGGTTCAAACTTTATATCTACACCGA\nATGAGTGATGCTGAGATAAAACTTATGGACCGGCTCACCAGCCTAGTCAATATGTTTCCTGAAGGTTTCAGGTCTAGTTC\nAGTCTAATTCTAACTGCACCAAAGGCTCTAAAAATATTTTAAATAACCAGGTGTATATCAAAGTCAATACAAGTGTAAAA\nACAATATGCAAGGGACCACATTTAGGATCAGTTTATTGACTCTTCCAATACACAGAGTTGGAAGCACCGATTCAAGGTTT\nCTAAGACGCCCTATCGATTATGTTGATAATGTAAATAATAGCTTTTCCTGTCTATTATGACTTAAATAATCATATCTATA\nACGACCATCACAGCTAAGTCGTTGCCCTAGTTCATATATTAAATTAAAATTTAGAAGCTAGGTTGACTCTAATTACATAA\nGTATTAAGAAAAAATTACTAAGACTAATACTCTCATGCCAAGAACTAGTAATGTGTTTCACATGACAGATTATTTCTAAC\nACTAAATTGCAATTTCAATTTTAAAGCTAAGTTTAACACCTATACAGCCAAAATATTTCATAGGGCCGATGGGAATAACA\nTAAGAGGAACATGATCAATGAACCCTTTATTCCAACTAGGCAGTTGATTGATAATCTACAAATTCCATAAGATGTTCTTA\nCGATATTCTTTTGTTTTTAATCTCAATGTCAATGATTTAATAAGTAATAATAAAAAAATCACATTAAAGATGCAGGAAGA\nTCTTGACCTCGCCAGGAAAATTAAGCGCACACAAATAAATTAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCCA\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Sudan_ebolavirus/GCF_000855585.1_ViralProj15012_protein.faa", "content": ">YP_009246341.1 second secreted glycoprotein [Sudan ebolavirus]\nMGGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIP\nSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTGPCPGDYAFHKDGAFF\nLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIREAVNYTENTSSYYATSYLEYEIENFGAQHSTTLFKIDNNT\nFVRLDRPHTPQFLFQLNDTIHLHQQLSNTTGRLIWTLDANINADIGEWAFWENKKSLRTTTWRRAVFRSFIAQRDRRR\n>YP_138520.1 nucleoprotein [Sudan ebolavirus]\nMDKRVRGSWALGGQSEVDLDYHKILTAGLSVQQGIVRQRVIPVYVVSDLEGICQHIIQAFEAGVDFQDNADSFLLLLCLH\nHAYQGDHRLFLKSDAVQYLEGHGFRFEVREKENVHRLDELLPNVTGGKNLRRTLAAMPEEETTEANAGQFLSFASLFLPK\nLVVGEKACLEKVQRQIQVHAEQGLIQYPTSWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDTVISNSVAQAR\nFSGLLIVKTVLDHILQKTDLGVRLHPLARTAKVKNEVSSFKAALGSLAKHGEYAPFARLLNLSGVNNLEHGLYPQLSAIA\nLGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQQYAETRELDNLGLDEQEKKILMSFHQKKNEISFQQTNAMVTLRKE\nRLAKLTEAITTASKIKVGDRYPDDNDIPFPGPIYDETHPNPSDDNPDDSRDTTIPGGVVDPYDDESNNYPDYEDSAEGTT\nGDLDLFNLDDDDDDSQPGPPDRGQSKERAARTHGLQDPTLDGAKKVPELTPGSHQPGNLHITKPGSNTNQPQGNMSSTLQ\nSMTPIQEESEPDDQKDDDDESLTSLDSEGDEDVESVSGENNPTVAPPAPVYKDTGVDTNQQNGPSNAVDGQGSESEALPI\nNPEKGSALEETYYHLLKTQGPFEAINYYHLMSDEPIAFSTESGKEYIFPDSLEEAYPPWLSEKEALEKENRYLVIDGQQF\nLWPVMSLQDKFLAVLQHD\n>YP_138521.1 polymerase complex protein [Sudan ebolavirus]\nMQQDRTYRHHGPEVSGWFSEQLMTGKIPLTEVFVDVENKPSPAPITIISKNPKTTRKSDKQVQTDDASSLLTEEVKAAIN\nSVISAVRRQTNAIESLEGRVTTLEASLKPVQDMAKTISSLNRSCAEMVAKYDLLVMTTGRATATAAATEAYWNEHGQAPP\nGPSLYEDDAIKAKLKDPNGKVPESVKQAYINLDSTSALNEENFGRPYISAKDLKEIIYDHLPGFGTAFHQLVQVICKIGK\nDNNILDIIHAEFQASLAEGDSPQCALIQITKRIPAFQDASPPIVHIKSRGDIPKACQKSLRPVPPSPKIDRGWVCIFQFQ\nDGKALGLKI\n>YP_138522.1 matrix protein [Sudan ebolavirus]\nMRRVTVPTAPPAYADIGYPMSMLPIKSSRAVSGIQQKQEVLPGMDTPSNSMRPVADDNIDHTSHTPNGVASAFILEATVN\nVISGPKVLMKQIPIWLPLGIADQKTYSFDSTTAAIMLASYTITHFGKANNPLVRVNRLGQGIPDHPLRLLRMGNQAFLQE\nFVLPPVQLPQYFTFDLTALKLVTQPLPAATWTDETPSNLSGALRPGLSFHPKLRPVLLPGKTGKKGHVSDLTAPDKIQTI\nVNLMQDFKIVPIDPAKSIIGIEVPELLVHKLTGKKMSQKNGQPIIPVLLPKYIGLDPISPGDLTMVITPDYDDCHSPASC\nSYLSEK\n>YP_138523.1 spike glycoprotein [Sudan ebolavirus]\nMGGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIP\nSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTGPCPGDYAFHKDGAFF\nLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIREAVNYTENTSSYYATSYLEYEIENFGAQHSTTLFKIDNNT\nFVRLDRPHTPQFLFQLNDTIHLHQQLSNTTGRLIWTLDANINADIGEWAFWENKKNLSEQLRGEELSFEALSLNETEDDD\nAASSRITKGRISDRATRKYSDLVPKNSPGMVPLHIPEGETTLPSQNSTEGRRVGVNTQETITETAATIIGTNGNHMQIST\nIGIRPSSSQIPSSSPTTAPSPEAQTPTTHTSGPSVMATEEPTTPPGSSPGPTTEAPTLTTPENITTAVKTVLPQESTSNG\nLITSTVTGILGSLGLRKRSRRQTNTKATGKCNPNLHYWTAQEQHNAAGIAWIPYFGPGAEGIYTEGLMHNQNALVCGLRQ\nLANETTQALQLFLRATTELRTYTILNRKAIDFLLRRWGGTCRILGPDCCIEPHDWTKNITDKINQIIHDFIDNPLPNQDN\nDDNWWTGWRQWIPAGIGITGIIIAIIALLCVCKLLC\n>YP_138524.1 small secreted glycoprotein [Sudan ebolavirus]\nMGGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIP\nSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTGPCPGDYAFHKDGAFF\nLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIREAVNYTENTSSYYATSYLEYEIENFGAQHSTTLFKIDNNT\nFVRLDRPHTPQFLFQLNDTIHLHQQLSNTTGRLIWTLDANINADIGEWAFWENKKISPNNYVEKSCLSKLYRSTRQKTMM\nRHRRELQREESPTGPPGSIRTWFQRIPLGWFHCTYQKGKQHCRLRIRQKVEE\n>YP_138525.1 minor nucleoprotein [Sudan ebolavirus]\nMERGRERGRSRNSRADQQNSTGPQFRTRSISRDKTTTDYRSSRSTSQVRVPTVFHKKGTGTLTVPPAPKDVCPTLRKGFL\nCDSNFCKKDHQLESLTDRELLLLIARKTCGSTDSSLNIAAPKDLRLANPTADDFKQDGSPKLTLKLLVETAEFWANQNIN\nEVDDAKLRALLTLSAVLVRKFSKSQLSQLCESHLRRENLGQDQAESVLEVYQRLHSDKGGAFEAALWQQWDRQSLTMFIS\nAFLHVALQLSCESSTVVISGLRLLAPPSVNEGLPPAPGEYTWSEDSTT\n>YP_138526.1 membrane-associated protein [Sudan ebolavirus]\nMAKATGRYNLVTPKRELEQGVVFSDLCNFLVTPTVQGWKVYWAGLEFDVNQKGITLLNRLKVNDFAPAWAMTRNLFPHLF\nKNQQSEVQTPIWALRVILAAGILDQLMDHSLIEPLSGALNLIADWLLTTSTNHFNMRTQRVKDQLSMRMLSLIRSNIINF\nINKLETLHVVNYKGLLSSVEIGTPSYAIIITRTNMGYLVEVQEPDKSAMDIRHPGPVKFSLLHESTLKPVATPKPSSITS\nLIMEFNSSLAI\n>YP_138527.1 RNA-dependent RNA polymerase [Sudan ebolavirus]\nMMATQHTQYPDARLSSPIVLDQCDLVTRACGLYSEYSLNPKLKTCRLPKHIYRLKYDTIVLRFISDVPVATIPIDYIAPM\nLINVLADSKNVPLEPPCLSFLDEIVNYTVQDAAFLNYYMNQIKTQEGVITDQLKQNIRRVIHKNRYLSALFFWHDLAILT\nRRGRMNRGNVRSTWFVTNEVVDILGYGDYIFWKIPIALLPMNTANVPHASTDWYQPNIFKEAIQGHTHIISVSTAEVLIM\nCKDLVTSRFNTLLIAELARLEDPVSADYPLVDNIQSLYNAGDYLLSILGSEGYKIIKYLEPLCLAKIQLCSQYTERKGRF\nLTQMHLAVIQTLRELLLNRGLKKSQLSKIREFHQLLLRLRSTPQQLCELFSIQKHWGHPVLHSEKAIQKVKNHATVLKAL\nRPIIIFETYCVFKYSVAKHFFDSQGTWYSVISDRCLTPGLNSYIRRNQFPPLPMIKDLLWEFYHLDHPPLFSTKIISDLS\nIFIKDRATAVEQTCWDAVFEPNVLGYSPPYRFNTKRVPEQFLEQEDFSIESVLQYAQELRYLLPQNRNFSFSLKEKELNV\nGRTFGKLPYLTRNVQTLCEALLADGLAKAFPSNMMVVTEREQKESLLHQASWHHTSDDFGEHATVRGSSFVTDLEKYNLA\nFRYEFTAPFIKYCNQCYGVRNVFDWMHFLIPQCYMHVSDYYNPPHNVTLENREYPPEGPSAYRGHLGGIEGLQQKLWTSI\nSCAQISLVEIKTGFKLRSAVMGDNQCITVLSVFPLESSPNEQERCAEDNAARVAASLAKVTSACGIFLKPDETFVHSGFI\nYFGKKQYLNGIQLPQSLKTAARMAPLSDAIFDDLQGTLASIGTAFERSISETRHILPCRVAAAFHTYFSVRILQHHHLGF\nHKGSDLGQLAINKPLDFGTIALSLAVPQVLGGLSFLNPEKCLYRNLGDPVTSGLFQLKHYLSMVGMSDIFHALIAKSPGN\nCSAIDFVLNPGGLNVPGSQDLTSFLRQIVRRSITLSARNKLINTLFHASADLEDELVCKWLLSSTPVMSRFAADIFSRTP\nSGKRLQILGYLEGTRTLLASKMISNNAETPILERLRKITLQRWNLWFSYLDHCDPALMEAIQPIKCTVDIAQILREYSWA\nHILDGRQLIGATLPCIPEQFQTTWLKPYEQCVECSSTNNSSPYVSVALKRNVVSAWPDASRLGWTIGDGIPYIGSRTEDK\nIGQPAIKPRCPSAALREAIELTSRLTWVTQGSANSDQLIRPFLEARVNLSVQEILQMTPSHYSGNIVHRYNDQYSPHSFM\nANRMSNTATRLMVSTNTLGEFSGGGQAARDSNIIFQNVINFAVALYDIRFRNTCTSSIQYHRAHIHLTNCCTREVPAQYL\nTYTTTLNLDLSKYRNNELIYDSDPLRGGLNCNLSIDSPLMKGPRLNIIEDDLIRLPHLSGWELAKTVLQSIISDSSNSST\nDPISSGETRSFTTHFLTYPKIGLLYSFGALISFYLGNTILCTKKIGLTEFLYYLQNQIHNLSHRSLRIFKPTFRHSSVMS\nRLMDIDPNFSIYIGGTAGDRGLSDAARLFLRIAISTFLSFVEEWVIFRKANIPLWVIYPLEGQRSDPPGEFLNRVKSLIV\nGTEDDKNKGSILSRSGEKCSSNLVYNCKSTASNFFHASLAYWRGRHRPKKTIGATNATTAPHIILPLGNSDRPPGLDLNR\nNNDTFIPTRIKQIVQGDSRNDRTTTTRFPPKSRSTPTSATEPPTKMYEGSTTHQGKLTDTHLDEDHNAKEFPSNPHRLVV\nPFFKLTKDGEYSIEPSPEESRSNIKGLLQHLRTMVDTTIYCRFTGIVSSMHYKLDEVLWEYNKFESAVTLAEGEGSGALL\nLIQKYGVKKLFLNTLATEHSIESEVISGYTTPRMLLPIMPKTHRGELEVILNNSASQITDITHRDWFSNQKNRIPNDADI\nITMDAETTENLDRSRLYEAVYTIICNHINPKTLKVVILKVFLSDLDGMCWINNYLAPMFGSGYLIKPITSSAKSSEWYLC\nLSNLLSTLRTTQHQTQANCLHVVQCALQQQVQRGSYWLSHLTKYTTSRLHNSYIAFGFPSLEKVLYHRYNLVDSRNGPLV\nSITRHLALLQTEIRELVTDYNQLRQSRTQTYHFIKTSKGRITKLVNDYLRFELVIRALKNNSTWHHELYLLPELIGVCHR\nFNHTRNCTCSERFLVQTLYLHRMSDAEIKLMDRLTSLVNMFPEGFRSSSV\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Tai_Forest_ebolavirus/GCF_000888475.1_ViralProj51257_genomic.fna", "content": ">NC_014372.1 Tai Forest ebolavirus isolate Tai Forest virus/H.sapiens-tc/CIV/1994/Pauleoula-CI, complete genome\nCGGACACACAAAAAGAAAGAAGGTTTTTTGATCTTTATTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTC\nATTGACACTTACATTAAGATTAAGATTCTCATTGATCTGTTACTTACTCTGAGGATAATAATTGGTGTTCAGAAGTACCC\nCATTCCCCAGTGGGGGCAAAGACAGTCCAAAAGACTCAACTTGTCCTATTCAACTAATCTGTTTTGTCTCAGTAGTTCAC\nATATTGATCATACCCAGGAGTTGGACCTAATTCCAAAGCTTAGAGTGGGACCTAGTGTATCCTCGGGGCTGTAATATAAT\nCAGCCATTTAACACATAACAAGCCCTACTGTTTTCTTGTTTTGCCGTGCATTTAGAATAAGAGACAACTTAAACCTCCGA\nTTCGGCAACACAGGGAATAATCTCACCAGACCCGGCAGTGTCTTCAGGCTTCATAGCCCCAAGATGGAGAGTCGGGCCCA\nCAAAGCATGGATGACGCACACCGCATCAGGTTTCGAAACAGATTACCATAAGATTTTAACAGCAGGATTGTCAGTCCAAC\nAAGGCATTGTGAGACAACGGGTCATTCAAGTCCACCAGGTTACAAACCTAGAAGAAATATGCCAATTGATCATTCAAGCC\nTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCAGACAGTTTCTTGCTGATGCTATGTTTACATCATGCTTATCAGGGTGA\nCTACAAGCAATTCTTGGAAAGCAATGCAGTCAAGTACCTTGAGGGTCATGGCTTTCGCTTTGAGGTCAGGAAAAAGGAAG\nGAGTCAAGCGACTCGAAGAATTGCTTCCTGCTGCATCCAGTGGCAAGAGCATCAGGAGAACACTGGCTGCAATGCCTGAA\nGAGGAGACAACAGAAGCAAATGCCGGACAGTTCCTCTCTTTTGCTAGCTTATTTCTTCCTAAGCTAGTTGTCGGAGAAAA\nAGCCTGTCTAGAAAAGGTGCAGCGGCAAATTCAAGTTCATTCTGAGCAGGGATTGATCCAATACCCCACAGCCTGGCAGT\nCAGTTGGACACATGATGGTCATTTTCAGACTGATGAGAACAAATTTTCTAATTAAGTTCCTCCTTATACATCAAGGGATG\nCATATGGTAGCAGGACACGATGCTAACGATGCTGTCATCGCAAACTCTGTAGCTCAAGCACGTTTTTCAGGATTATTGAT\nCGTTAAAACAGTGCTAGATCACATCCTTCAGAAAACAGAGCACGGAGTGCGTCTTCATCCTTTGGCAAGAACTGCTAAGG\nTCAAGAACGAAGTAAATTCCTTTAAGGCTGCCCTTAGCTCGCTAGCACAACATGGAGAGTATGCTCCTTTTGCTCGCTTG\nCTGAATCTTTCTGGAGTCAACAATCTCGAGCACGGACTGTTTCCTCAGCTTTCTGCAATTGCCCTAGGTGTCGCAACGGC\nACACGGCAGTACCCTGGCAGGAGTAAATGTGGGGGAACAGTATCAGCAACTACGAGAAGCAGCCACTGAGGCAGAAAAAC\nAATTGCAGAAATACGCTGAATCTCGCGAGCTTGACCATCTAGGTCTCGATGATCAAGAGAAGAAGATCTTGAAAGACTTC\nCATCAGAAGAAAAATGAAATCAGCTTCCAGCAGACAACAGCCATGGTCACACTACGGAAGGAAAGGCTAGCCAAGCTCAC\nTGAGGCAATCACCTCCACATCCCTTCTCAAGACAGGAAAACAGTATGATGATGACAACGATATCCCCTTTCCTGGGCCCA\nTCAATGATAACGAAAACTCAGAACAGCAAGACGATGATCCAACAGATTCTCAGGACACTACCATCCCTGATATCATTGTT\nGACCCGGATGATGGCAGATACAACAATTATGGAGACTATCCTAGTGAGACGGCGAATGCCCCTGAAGACCTTGTTCTTTT\nTGACCTTGAAGATGGTGACGAGGATGATCACCGACCGTCAAGTTCATCAGAGAACAACAACAAACACAGTCTTACAGGAA\nCTGACAGTAACAAAACAAGTAACTGGAATCGAAACCCGACTAATATGCCAAAGAAAGACTCCACACAAAACAATGACAAT\nCCTGCACAGCGGGCTCAAGAATACGCCAGGGATAACATCCAGGATACACCAACACCCCATCGAGCTCTAACTCCCATCAG\nCGAAGAAACCGGCTCCAATGGTCACAATGAAGATGACATTGATAGCATCCCTCCTTTGGAATCAGACGAAGAAAACAACA\nCTGAGACAACCATTACCACCACAAAAAATACCACTGCTCCACCAGCACCTGTTTATCGGAGTAATTCAGAAAAGGAGCCC\nCTCCCGCAAGAAAAATCCCAGAAGCAACCAAACCAAGTGAGTGGTAGTGAGAATACCGACAATAAACCTCACTCAGAGCA\nATCAGTGGAAGAAATGTATCGACACATCCTCCAAACACAAGGACCATTTGATGCCATCCTATACTATTACATGATGACGG\nAGGAGCCGATTGTCTTTAGCACTAGTGATGGGAAAGAATACGTATACCCTGATTCTCTTGAAGGGGAGCATCCACCGTGG\nCTCAGTGAAAAAGAGGCCTTGAATGAGGACAATAGGTTTATCACAATGGATGATCAACAATTCTACTGGCCTGTAATGAA\nTCACAGGAACAAATTCATGGCTATCCTTCAGCACCACAAGTAATTTCTTCATAATGACAGATCATTGTAAGGTTATTACC\nACCATCCCTGCAACAAAGCATGAAAACCACACTCAACAACGCCCTACCACAGGATACCTTGGAGACCATACACCAAGATC\nAGCAGCTGTGCAACCACCCCCATGCGAATCCACCACCACAACCACCAAACAATAATCCCAAGACCAAACCGCACACATCC\nAGATCAACCCAAACCCTCAAACACCACCCCACTCCGCGATCCCAGACCAAACTCCGCCCCAGACAAGCACCCCACCCATC\nCCAGAAACCGCACGGCCGAGAATCGATCCCCAGCATTCAAAATGCGTTATTAAGAAAAAACATATGATGAAGATTAAAAC\nCTTCATCAACATTGCACAGACTTTGATCCTTAGGAGTTTATTCTAGCTATCTACAAAACGGGTCCAAAACGGAATGATTT\nCCACTAGGGCTGCAGCAATCAATGATCCTTCATTACCAATCAGAAACCAGTGTACACGTGGCCCTGAACTATCAGGATGG\nATCTCCGAACAATTAATGACAGGCAAAATTCCGGTACATGAAATCTTCAACGACACTGAGCCCCACATAAGCTCAGGGTC\nCGACTGCCTTCCCAGACCCAAAAACACGGCCCCCCGGACTCGCAACACCCAGACACAGACCGATCCGGTTTGCAATCACA\nATTTTGAAGACGTTACACAAGCACTAACATCATTAACCAATGTCATACAAAAACAGGCTCTTAACTTAGAGTCTCTCGAA\nCAACGCATCATAGATCTAGAGAATGGCTTAAAGCCAATGTATGACATGGCTAAAGTCATTTCTGCATTGAATAGATCTTG\nTGCTGAGATGGTAGCAAAATATGATCTCCTGGTGATGACAACTGGCCGCGCAACCGCCACCGCCGCTGCAACTGAGGCTT\nATTGGGAGGAACATGGACAACCACCACCTGGACCATCACTTTATGAAGAGAGTGCGATTAGAGGCAAGATTAACAAGCAA\nGAGGATAAAGTACCTAAGGAAGTTCAAGAAGCTTTTCGTAATCTGGACAGTACCAGCTCACTAACAGAAGAGAACTTTGG\nCAAGCCAGATATATCTGCAAAGGACCTACGAGACATCATGTATGACCACCTACCAGGCTTCGGTACGGCTTTTCACCAAC\nTGGTCCAGGTAATTTGCAAGCTAGGAAAAGACAATTCTGCATTGGACATTATTCATGCTGAGTTCCAAGCCAGCCTTGCT\nGAAGGTGATTCTCCCCAATGTGCCCTGATCCAAATAACAAAACGGATCCCCATCTTCCAGGATGCCACTCCGCCCACAAT\nTCACATCCGCTCTCGTGGTGACATCCCACGTGCCTGCCAAAAAAGTCTCCGTCCAGTTCCTCCATCACCAAAAATAGACA\nGAGGTTGGGTTTGCATTTTCCAATTGCAGGACGGGAAGACACTTGGGCTCAAGATATAGGGTCCCCCAGTCAAAGACACG\nTGCGGTCCCATCCTCCCTCACCTTCAGACATCAACGCATGGCAGTCCCAAACACCGGTGAGGGAGGCGCCCGGCGACAAC\nACATGATGATAGGCTGATCTTCGGGATAAGAGACATGAAAAACCAAAAAGCCGTTTACATCCAGATCCAAGATCAAGAGT\nGGCTTGGAAATAAGGGGCACTTGTTCTTTGTCTCAAAGGACTTACAAAAACAAGGGTGATGAAGATTAAGAAAAAGCCTC\nCTTCAGTTGCAAGGAGCTAATTCTTAAAACTTCATCTAGACTAAGGATAAATCGATTCCAATCACGATGAGGAGAATCAT\nCCTACCCACGGCACCACCTGAATACATGGAGGCTGTTTACCCAATGAGAACAATGAATTCTGGTGCAGACAACACTGCCA\nGTGGCCCTAATTACACAACAACTGGTGTGATGACAAATGATACTCCCTCTAATTCACTCCGACCAGTTGCAGATGATAAT\nATTGATCATCCGAGCCACACGCCTAACAGTGTTGCCTCTGCATTTATATTGGAAGCTATGGTGAATGTAATATCTGGCCC\nGAAAGTGCTGATGAAGCAAATCCCAATCTGGCTTCCTCTGGGTGTCTCTGACCAGAAGACATATAGCTTTGATTCAACCA\nCTGCTGCCATTATGCTAGCATCATATACCATCACTCATTTTGGCAAAACCTCAAATCCCCTTGTGAGAATCAACCGACTT\nGGTCCTGGCATACCTGATCACCCACTACGACTCCTAAGAATAGGAAATCAAGCCTTCCTACAAGAGTTTGTGCTACCTCC\nTGTACAACTGCCACAATACTTCACTTTTGATCTGACAGCGCTGAAGCTGATCACCCAGCCACTCCCAGCGGCAACCTGGA\nCAGATGAAACTCCAGCTGTGTCAACTGGCACGCTCCGCCCAGGGATCTCATTCCATCCCAAATTAAGGCCTATCCTGCTA\nCCAGGAAGAGCTGGAAAGAAGGGCTCCAACTCCGATCTAACATCTCCTGACAAAATCCAGGCTATAATGAATTTCCTACA\nAGACCTCAAAATTGTACCAATCGATCCAACCAAGAATATCATGGGTATTGAAGTGCCAGAACTCCTGGTTCACAGGCTGA\nCTGGGAAGAAGACAACTACCAAGAATGGTCAACCAATCATTCCAATTCTGCTACCAAAGTACATTGGTCTTGATCCTCTA\nTCTCAAGGTGATCTCACAATGGTGATCACTCAGGACTGTGATTCCTGCCACTCCCCGGCCAGTCTTCCCCCAGTCAATGA\nAAAATGACCATGAGACTCAACATCACACTGCCAGAGCACCTCACCGCAAGTCTATACAACAATCAACCCCGGCATCTACA\nACCTGCAAAAACCAGCCCATCTGATACTCCTGGCATCGGGGGCAAGACAAGGCAGCCAAGCAGCAGCCCCCGAGCCGAGC\nCCAAACCCATTACACCCGAGCCCAACACCCATCCAGCAACCCACAACCGTCAAACGCACAGATGGACAAGCAAAGAACAT\nCAAGCCAGGAGCAACACAGACCCCAAGTCTAAGCTGATCAACCCCTCCCGCAATCCCACCAACGCCAGCAAAAATCCCCC\nAACTCGATACCAACCCCAAGCAAATCAGCTCAAACCGTCTATCTCTCCCCGCTTCACTCCACACCCCAGATTCAGCAAAC\nGATCAACGCACTTCTTATGCCACAGCTTATATTAAGAAAAAGAACTTGATGAAGATTAAGGCAACCAGTGGTGCTATCTT\nCATCTCTTTGATTTGAGTCTTAAGTGAATACACAGGTTCTAATACTGTTCTTCTGTCCAACGGTATAATTCAGCCAGGCC\nTAAGACAGTAGCTAATCACAGTCATCATGGGAGCGTCAGGGATTCTGCAATTGCCCCGTGAGCGCTTCAGGAAAACATCT\nTTCTTTGTTTGGGTAATAATCCTATTCCATAAAGTCTTTTCAATCCCGTTGGGGGTTGTACACAACAATACCCTACAAGT\nGAGTGATATTGACAAGTTTGTGTGCCGAGACAAACTCTCTTCAACTAGCCAATTGAAGTCAGTCGGGTTGAACTTGGAGG\nGCAATGGAGTAGCAACTGATGTACCAACGGCAACCAAAAGATGGGGTTTTCGAGCTGGTGTTCCACCAAAGGTGGTAAAT\nTGCGAAGCTGGAGAATGGGCTGAGAACTGTTATAACCTGGCTATAAAGAAAGTTGATGGTAGTGAGTGCCTACCAGAAGC\nCCCTGAGGGAGTGAGGGATTTTCCCCGTTGCCGCTATGTACACAAAGTCTCAGGAACTGGACCATGCCCAGGAGGACTCG\nCCTTTCACAAAGAAGGAGCCTTCTTCCTGTATGACCGACTCGCATCAACAATCATTTATCGGGGTACAACCTTTGCCGAA\nGGAGTTATTGCATTTCTGATCTTGCCTAAGGCGCGAAAGGATTTTTTCCAGTCTCCTCCATTGCATGAGCCTGCCAACAT\nGACCACGGATCCCTCCAGTTACTATCACACGACAACAATAAACTACGTGGTTGATAATTTTGGAACCAACACCACAGAGT\nTTCTGTTCCAAGTCGATCATTTGACGTATGTGCAGCTCGAGGCAAGATTCACACCACAATTCCTTGTCCTCCTAAATGAA\nACCATCTACTCTGATAACCGCAGAAGTAACACAACAGGAAAACTAATCTGGAAAATAAATCCCACTGTTGATACCAGCAT\nGGGTGAGTGGGCTTTCTGGGAAAATAAAAAAACTTCACAAAAACCCTTTCAAGTGAAGAGTTGTCTTTCGTACCTGTACC\nAGAAACCCAGAACCAGGTCCTTGACACGACAGCGACGGTCTCTCCTCCCATCTCCGCCCACAACCACGCAGCCGAAGACC\nACAAAGAATTGGTTTCAGAGGATTCCACTCCAGTGGTTCAGATGCAAAACATCAAGGGAAAGGACACAATGCCAACCACA\nGTGACGGGTGTACCAACAACCACACCCTCTCCATTTCCAATCAATGCTCGCAACACTGATCATACCAAATCATTTATCGG\nCCTGGAGGGGCCCCAAGAAGACCACAGCACCACACAGCCTGCCAAGACCACCAGCCAACCAACCAACAGCACAGAATCGA\nCGACACTAAACCCAACATCAGAGCCCTCCAGTAGAGGCACGGGACCATCCAGCCCCACGGTCCCCAACACCACAGAAAGC\nCACGCCGAACTTGGCAAGACAACCCCAACCACACTCCCAGAACAGCACACTGCCGCCAGTGCCATTCCAAGAGCCGTGCA\nCCCCGACGAACTCAGTGGACCTGGCTTCCTGACGAACACAATACGGGGGGTTACAAATCTCCTGACAGGATCCAGAAGAA\nAGCGAAGGGATGTCACTCCCAATACACAACCCAAATGCAACCCAAACCTGCACTATTGGACAGCCTTGGATGAGGGTGCT\nGCCATAGGTTTAGCCTGGATACCATACTTCGGGCCAGCAGCTGAGGGAATTTACACTGAAGGCATAATGGAGAATCAAAA\nTGGATTGATCTGTGGATTGAGGCAGCTGGCCAACGAAACGACACAAGCTCTTCAATTGTTCTTAAGGGCAACTACTGAGT\nTGCGTACATTCTCTATACTAAATCGGAAAGCAATAGACTTCTTGCTCCAAAGATGGGGAGGAACATGTCACATTCTAGGG\nCCTGATTGTTGCATTGAACCCCAAGATTGGACCAAAAATATCACTGATAAAATTGATCAAATAATCCATGACTTTGTCGA\nTAATAATCTTCCAAATCAGAATGATGGCAGCAACTGGTGGACTGGATGGAAACAATGGGTTCCTGCTGGAATAGGAATCA\nCAGGAGTAATCATTGCTATTATTGCTTTGCTGTGCATTTGCAAATTCATGCTTTGAACTAATATAGCATCATACTTTCTA\nATATTCCCCCAATATGAATTTTTGTTTTCGATTTTATTTAATGATATATCCTCTGTATACCTCACTAATGTACTCGAGCA\nTAATTTCCCTGATAGACTTGATTGTATTTGATGATTAAGGACCTCACAAAATTCCTGGGGATTGAAAAGAACTGGATAAC\nTCAATAAATTTTATGCTAGGACCACAAATACACTTGATGAAGATTAAGAAAAAGATAATCTTATGATTATCATTGATCTT\nCATCTATACCTTAAATACTCTATTCAAGGAGAGTATGACAAAACCAAGTAGTATTGGATAAACTTGTCCTGCATTCAAAT\nCTGAAGACATACGGCTTATCTATTCACTATTGTATTAGAAAATCTAGGGAATATCATTTGAAACTAATTAGTGACTAAAA\nCACACAACTCAAGTCGGCCAGAATGGAAGTTGTTCATGAAAGAGGTCGCTCCAGGATCTCCCGACAAAACACAAGGGATG\nGACCTAGTCATTTAGTACGGGCGAGATCATCCTCTCGAGCTAGTTATCGAAGTGAATACCATACACCAAGGAGTGCCTCG\nCAGATCCGTGTCCCCACTGTCTTTCATCGGAAAAAGACAGATTTATTGACAGTTCCACCAGCACCTAAAGATGTATGCCC\nGACTTTAAAGAAAGGGTTTCTATGTGACAGCAATTTCTGTAAAAAGGATCACCAACTTGAAAGCTTAACAGATAGAGAGT\nTACTCTTGCTGATTGCACGCAAGACATGTGGATCCACGGAACAACAACTAAGCATAGTTGCTCCAAAAGATTCACGTCTG\nGCTAATCCTATTGCTGAGGATTTCCAACAAAAAGATGGGCCTAAGGTAACACTGTCGATGCTTATAGAGACAGCAGAGTA\nTTGGTCCAAACAGGACATTAAGAACATCGATGATTCAAGATTAAGAGCTTTATTGACCCTTTGTGCTGTTATGACGCGCA\nAATTTTCAAAATCTCAACTTAGCTTGCTATGTGAAAGCCACTTACGGCGAGAAGGACTTGGTCAAGACCAATCAGAGTCA\nGTTCTGGAGGTATATCAACGCTTACACAGCGATAAAGGTGGGAATTTCGAGGCAGCACTATGGCAGCAGTGGGATCGGCA\nATCATTGATAATGTTCATAACAGCATTTTTAAATATTGCATTACAATTACCATGTGAGAGTTCATCTGTTGTTATTTCAG\nGTTTGAGAATGCTGATACCCCAGTCGGAAGCCACTGAGGTTGTAACCCCCTCCGAAACCTGCACATGGTCAGAAGGAGGA\nAGTTCCCATTGAAGCCCCAAATCACAAGGCGAGCTAAAAAATCCCTTTTGAACATGCATAACATCACATACAATTTCAAA\nGGCATTGGAATAAATGGTGATTTCAGGAAGATTAGTGTTTGCCCTCAAAATCAGATCCGAGCAATAATCATCTACTCTAC\nAGCCAGTTAATTTCTAATATAAAGGTTAAAAAAATGCTGCAGGCCAGCTATTGTTCCACAGGTCCCAATTCTTCTTGTTA\nAATTGTAGGAGCTAGCACAAGTGATGCAATTAAATGATACTAGTATATACAATGCCACCAACTTAATTCTAAGATTTTGT\nATATCTCGGAAATTCAAAATTAAATGCTACGTTATTGATTCAATTAAGAAAAAGACAATGGACCATCAAAATTAGTTCAA\nTACCTGAACTAATGCACTTATAGAAACAGGAGAACCAGCCAGACAGCAGACAAATAACAATGAACCACAATATGTTACTG\nCTATAATGAAGTTCGTTAATTCAAAAACAAATGATGAAGATTAATGCAGATGTCTAAAGGATAAACACTCCATGCATCAG\nTGTTATAATTGGGCTCTGTAGAAAATCTTCATCTCCTCCAACCTACCTCAAAGAAGGATTTTACCGCGATTGGGAGTTAT\nAACGACAATAGGGACAACCACCTTTGACACTAGCCAAGCTTGTCGTGGGCACACAGCATTTTATCTTGCAACGTCGACAT\nTCCCATCAATCTGAGGAGTAACAGCTATCAAAACAACGCATATGTAGACATTGTCGGTAATAGTACTGCCTAAGACAACT\nATTTATAATAACAGTTGGAATTCATTTTTTCACCCAAGCTATTCTCAAGTTAACAGTTGAAACAGGACTCGACCCAGGAC\nAACTCCGGATACGTAACATAAGAAAAGAACAACCCTTGACCCAGAGTGAACAAGCTCATACTATCAAGGCTAATCCTCGG\nGCCTGCCTGGAGTCCACAATGGCCAAGGCTACTGGGAGGTACAACCTTATCTCCCCAAAGAAAGATCTTGAAAAAGGGCT\nGGTTCTGAATGACCTTTGCACTCTCTCAGTGGCCCAGACGGTCCAGGGATGGAAGGTTACCTGGGCTGGGATTGAATTTG\nATGTTACACAGAAAGGGATGGCCTTATTGCACAGGCTCAAGACCAGTGATTTTGCTCCAGCCTGGTCAATGACCAGGAAC\nTTATTTCCACATCTCTTTCAAAACCCGAACTCTACAATTGAGTCGCCACTTTGGGCACTGCGGGTCATACTAGCAGCAGG\nTATTCAAGATCAGCTAATTGATCAATCGTTGATCGAACCCTTGGCAGGAGCGCTAGGCTTAATTGCTGATTGGCTTCTTA\nCTACTGGAACAAACCACTTTCAAATGCGCACACAACAGGCTAAGGAGCAACTAAGTCTAAAAATGTTGTCCCTGGTGCGA\nTCAAACATCCTAAAGTTCATCAACCAACTAGATGCACTACATGTTGTGAATTACAATGGACTTCTCAGTAGCATTGAAAT\nTGGCACCAAAAGCCATACAATTATAATTACCCGGACAAATATGGGTTTTTTGGTAGAGTTGCAAGAGCCTGACAAATCAG\nCCATGAACACCAGAAAACCAGGACCAGTCAAATTCTCCCTCCTCCATGAATCAACCTTGAAGACACTTGCTAAAAAACCT\nGCGACCCAGATGCAAGCACTAATCTTAGAATTCAATAGTTCTCTCGCTATTTAACTCAACTCATCAAAATGCTAACTTGT\nGATCCTTAAGCTGCACCTTAGACTTTTGATAAGAATACTAACTATTGATGATTGTCTTTGACATGAGGATAAGAACACTG\nCCCATTAGATAGATGGGGTTCACCATTAATACACAATTACCCAATCATGTTAACAGCAGTTAGATCCCTCAAGTATATCA\nAGTTCATTCTACCCTTTGCATTGTCACTCTAATTAAATCACCTGATACAATTATGTTAATTAGCTAGATTCTCTCATTTT\nTAGACTTGTTTGCTAGAATAATTGATCATCCACTTGATTACACATCCAACTAGGGTCTAGTTCATAGATTGCTAATAATC\nTTTAGTTCAATACTAATGACAAAGAGATTAGATTAGCTATAGCTTGAGGAAGATTAAGAAAAAGTGTCTGTGGGGTCTTT\nCCGTGTAGAAGGGCACACAGCCATAATTCTTCCTCTTTATACAACATGGCTACACAACATACGCAATATCCAGACGCAAG\nGTTATCATCACCTATAGTTTTAGATCAGTGTGATCTTGTCACTCGTGCTTGTGGATTGTATTCCGCATACTCCTTAAATC\nCCCAACTAAAGAACTGTAGACTACCGAAACATATATACCGACTAAAATATGACACCACTGTTACAGAGTTTTTGAGTGAT\nGTGCCGGTAGCAACATTGCCAGCGGATTTTTTAGTACCTACATTTCTTAGGACTCTATCAGGAAATGGTTCTTGTCCAAT\nTGATCCAAAATGCAGTCAATTTTTAGAAGAAATTGTCAATTATACTCTACAAGATATTCGCTTCCTAAACTATTACCTCA\nATCGAGCCGGAGTGCATAACGATCATGTGGATAGGGATTTTGGACAAAAAATTCGCAATCTAATTTGCGACAATGAGGTT\nTTACATCAAATGTTTCACTGGTATGATCTTGCAATTCTAGCACGTAGAGGGCGACTAAATAGAGGGAATAATCGCTCAAC\nATGGTTTGCAAGTGATAATTTGGTAGATATCCTAGGTTATGGAGATTATATTTTTTGGAAAATACCATTATCACTACTAC\nCAGTGGATACACAAGGCCTCCCACATGCAGCCAAGGACTGGTATCATGAATCGGTTTTCAAGGAGGCTATTCAAGGCCAT\nACACACATCGTGTCCATCTCTACAGCAGATGTCTTAATCATGTGTAAGGACATAATCACCTGTCGATTTAATACTTTACT\nGATTGCTGCTGTGGCAAATCTAGAGGATTCAGTTCATTCAGATTACCCTTTACCAGAAACAGTGTCTGACCTATACAAAG\nCAGGAGATTATTTAATCTCATTGCTAGGATCAGAAGGTTACAAAGTCATAAAATTCCTTGAGCCGTTATGCTTAGCAAAG\nATCCAACTCTGCTCAAATTACACTGAGAGGAAAGGAAGATTCCTCACTCAAATGCATTTAGCTGTAAATCATACACTTGA\nGGAACTTACAGGGTCCCGAGAATTAAGGCCACAACAGATTCGGAAGGTAAGGGAATTCCATCAAATGCTGATAAACCTTA\nAGGCAACTCCTCAACAACTCTGTGAGTTGTTTTCAGTGCAAAAGCATTGGGGGCACCCTGTCTTGCATAGCGAAAAGGCT\nATCCAAAAAGTAAAGAAGCATGCAACAGTGATAAAAGCATTGCGCCCAATAATAATCTTTGAAACATATTGTGTGTTTAA\nATACAGCATTGCAAAACATTATTTTGATAGTCAGGGTACGTGGTACAGTGTGACTTCTGACAGATGCTTAACACCAGGCC\nTTTCCTCTTACATCAAAAGAAACCAATTTCCTCCACTACCTATGATCAAAGAACTTTTGTGGGAATTTTATCACTTAGAT\nCATCCTCCGTTATTCTCCACCAAAGTGATTAGTGATTTGAGTATCTTTATTAAAGATCGTGCTACTGCAGTCGAGAAAAC\nATGCTGGGACGCAGTTTTTGAACCCAATGTTCTTGGTTATAACCCACCGAATAAATTTGCTACAAAAAGGGTACCTGAGC\nAATTCCTTGAACAGGAGAATTTCTCAATAGAGAGTGTCCTACATTATGCTCAACGTCTGGAATATCTTCTCCCGGAGTAC\nCGGAACTTCTCTTTTTCACTCAAGGAGAAGGAGTTAAACATTGGACGAGCTTTTGGGAAATTGCCATATCCAACACGCAA\nTGTTCAAACTCTGTGCGAAGCTTTGTTAGCAGATGGTTTGGCGAAAGCATTCCCAAGCAATATGATGGTTGTGACAGAGC\nGCGAGCAAAAAGAAAGCCTTTTGCATCAAGCGTCTTGGCATCACACAAGTGATGATTTTGGTGAGAATGCTACTGTTAGA\nGGCAGTAGTTTTGTAACAGACTTGGAAAAATACAATTTAGCATTCCGATATGAGTTTACAGCTCCTTTTATTGAATACTG\nTAATCGTTGTTACGGTGTAAGAAATTTGTTTAATTGGATGCACTACACTATACCACAGTGTTATATACATGTGAGTGATT\nATTATAACCCCCCACATGGAGTCTCTCTCGAAAACCGAGAAAATCCACCAGAAGGTCCAAGCTCTTACCGTGGTCATCTA\nGGCGGGATTGAGGGACTTCAACAAAAACTCTGGACAAGCATCTCATGTGCACAGATTTCATTAGTTGAAATCAAAACCGG\nTTTTAAACTGCGATCTGCGGTAATGGGTGACAATCAATGTATAACTGTACTCTCTGTATTTCCCCTCGAAACTGAGTCTA\nGTGAGCAAGAATTAAGTTCTGAAGATAATGCCGCTAGAGTAGCTGCTAGCTTAGCAAAAGTCACAAGTGCCTGCGGCATC\nTTTTTAAAACCTGATGAAACTTTTGTTCACTCAGGTTTCATTTATTTTGGCAAAAAACAATATTTGAATGGAGTACAATT\nACCTCAATCACTGAAAACTGCTACTAGAATTGCACCCTTGTCAGATGCTATCTTTGATGATCTTCAAGGGACACTAGCTA\nGCATAGGCACGGCTTTTGAAAGATCTATCTCCGAAACTAGGCACGTAGTCCCTTGTAGAGTAGCAGCTGCATTCCATACC\nTTTTTTTCCGTAAGAATCTTACAATATCATCATCTTGGCTTCAACAAGGGAACAGACCTGGGTCAATTGTCATTAAGCAA\nGCCATTAGATTTTGGAACTATAACTTTGGCCTTGGCAGTACCACAAGTCTTGGGTGGCTTATCATTCCTAAATCCAGAAA\nAATGTTTTTATAGAAATCTGGGTGATCCTGTTACTTCAGGGCTGTTTCAGCTCAAGACATATCTTCAAATGATCCACATG\nGATGATTTGTTTTTACCTTTGATCGCAAAGAACCCAGGGAACTGTAGCGCAATTGACTTTGTGTTAAACCCTAGTGGGTT\nAAACGTACCGGGGTCACAGGATTTGACATCCTTCCTACGTCAGATAGTGCGCCGAACAATTACTCTAAGTGCTAAAAATA\nAATTAATAAACACTTTGTTCCATTCTTCTGCTGATTTAGAAGATGAAATGGTTTGCAAATGGTTGCTTTCTTCTACACCA\nGTCATGAGTAGGTTTGCCGCCGATATATTTTCTCGCACTCCCAGTGGGAAACGTTTACAGATCTTAGGTTACCTTGAAGG\nGACTAGAACATTGTTAGCCTCTAAAATTATAAATCATAATACTGAGACACCTATCCTAGATCGATTGAGGAAAATTACGC\nTGCAAAGGTGGAGCCTGTGGTTTAGTTATCTCGACCACTGTGATCAAGTTCTGGCTGATGCCCTAACTCAGATAACCTGC\nACTGTGGACTTAGCACAGATTCTTCGCGAGTACACCTGGGCACACATACTAGAGGGAAGGCAGCTCATTGGAGCAACACT\nTCCTTGTATACTAGAACAACTAAATGTCATCTGGCTCAAACCATATGAGCATTGCCCTAAATGTGCAAAGTCAGCAAACC\nCTAAAGGGGAACCTTTTGTTTCTATTGCAATTAAAAAACATGTAGTAAGTGCTTGGCCTGATCAATCACGACTTAGTTGG\nACAATTGGAGATGGCATCCCTTATATCGGATCTCGAACAGAGGATAAGATTGGGCAGCCAGCCATCAAACCAAAATGCCC\nTTCAGCAGCCTTACGTGAAGCAATTGAGTTGACATCAAGATTGACTTGGGTTACTCAAGGTGGAGCAAACAGCGACTTAC\nTAGTTAAACCCTTCATAGAAGCACGAGTAAATTTAAGCGTACAGGAAATTCTCCAAATGACACCTTCTCATTACTCCGGC\nAACATTGTGCATCGATATAATGATCAATATAGTCCACACTCATTTATGGCAAATAGGATGAGTAATTCTGCTACTAGGTT\nAGTTGTTTCGACAAACACTCTTGGAGAATTTTCAGGAGGAGGTCAGTCAGCAAGAGATAGTAATATTATCTTCCAGAATG\nTCATTAATTTTGCTGTTGCACTTTTTGATCTACGATTTAGGAACGTGGCTACTTCTTCTATACAACATCATCGGGCTCAT\nCTTCATTTGTCAAAGTGTTGCACGCGAGAGGTTCCAGCCCAATATTTAGTTTATACATCAACATTGCCATTGGACCTTAC\nACGGTATCGGGATAATGAGTTGATTTACGATGACAATCCATTAAGAGGTGGTTTAAATTGCAATCTTTCTTTTGATAATC\nCGCTTTTCAAGGGCCAGAGACTTAACATAATTGAAGAAGACTTGATTAGACTACCTTACTTATCAGGATGGGAGCTAGCT\nAAAACTGTTATCCAATCTATAATTTCTGACAGCAACAATTCATCAACGGATCCAATCAGTAGTGGGGAAACACGATCATT\nCACCACTCACTTCTTGACATATCCTAAGATTGGACTACTATATAGTTTTGGTGCACTCATCAGTTATTATCTAGGCAACA\nCCATTATTAGAACCAAAAAATTGACTCTTAACAACTTCATATATTACCTAGCTACTCAAATACATAATTTACCTCATCGC\nTCGTTGAGAATCCTTAAACCTACTTTGAAACACGCTAGTGTTATCTCGAGATTAATAAGTATTGACTCTCACTTCTCAAT\nTTATATTGGAGGAACTGCTGGTGATCGAGGACTTTCCGATGCGGCAAGATTGTTTCTTAGAACTGCCATTACTGTCTTCC\nTTCAATTCGTTAGAAAGTGGATAGTTGAACGCAAGACAGCTATTCCACTGTGGGTCATCTACCCTCTAGAAGGTCAAAGT\nCCTAGTCCGATCAACAGTTTTCTACACCACGTCATCGCATTGTTGCAACATGAGTCCTCCCACGATCATGTTTGTGCTGC\nAGAAGCCCACAGTCGAGTGGAGACATTTGATAATTTAGTTTATATGTGTAAAAGCACAGCAAGTAACTTCTTTCATGCTT\nCATTAGCATACTGGAGAAGTCGATCTAAAAATCAAGACAAAAGAGAGATGACAAAGATATTATCTTTGACGCAAACGGAA\nAAGAAAAATTCATTCGGCTATACAGCACATCCAGAAAGCACTGCTGTTCTTGGTTCCCTCCAGACCAGCCTTGCTCCACC\nTCCATCTGCTGACGAGGCTACATATGATAGGAAAAACAAAGTTTTGAAAGCTTCCAGACCTGGCAAGTATTCCCAGAATA\nCAACCAAAGCCCCACCCAACCAAACCAGTTGTCGCGATGTATCTCCCAATATCACAGGCACAGATGGGTGCCCTTCTGCC\nAATGAGGGTTCTAACAGCAATAACAATAATTTAGTCTCGCACAGAATTGTACTGCCGTTTTTTACATTGTCTCATAATTA\nTAACGAAAGACCCTCTATCAGAAAGTCTGAGGGGACAACAGAGATTGTAAGGCTTACTCGGCAGCTGAGGGCAATACCAG\nACACCACAATATATTGCCGCTTCACGGGAATAGTTTCTTCAATGCACTATAAGCTCGATGAAGTCCTTTGGGAATTTGAT\nAATTTTAAGTCTGCTATAACACTTGCCGAAGGTGAAGGTTCGGGTGCATTACTCTTATTACAAAAATATAAAGTAGAAAC\nCTTGTTTTTTAATACACTAGCCACAGAACACAGCATTGAAGCAGAAATTATTTCTGGAATAACTACACCAAGAATGCTTC\nTCCCTATTATGTCTAGGTTCCATGGTGGACAAATAAAAGTCACTTTAAACAATTCTGCAAGCCAGATTACCGATATTACT\nAATCCAAGTTGGTTGGCAGACCAAAAATCTAGGATCCCTAAGCAAGTAGAGATTATAACCATGGATGCTGAAACAACAGA\nAAACATTAATCGGTCAAAATTGTACGAAGCAGTCCAACAGCTGATTGTCTCACATATTGATCCGAATGCACTCAAAGTTG\nTGGTTCTTAAAGTTTTCTTAAGTGACATTGATGGAATCCTATGGCTGAATGATAACCTTACCCCTTTGTTTGGGCTGGGT\nTACTTGATCAAGCCGATCACCTCTAGCCCAAAATCTAGTGAGTGGTACCTATGTCTCTCAAACCTTCTTTCAACTTCAAG\nACGATTACCTCATCAGAGTCATACTACTTGCATGCATGTTATTCAAACAGCACTCCAGCTACAAATTCAGAGGAGCTCAT\nATTGGCTTAGCCACCTTGTCCAGTATGCCAATCATAATTTGCATTTAGATTATATTAATCTCGGTTTCCCTTCATTGGAG\nAGGGTTTTATACCATAGATACAATTTAGTCGATTCTCAGAAAGGCCCTTTGACTTCCATTGTCCAACATCTAGCGCACCT\nGCAGACCGAGATTAGGGAGTTGGTTAATGACTATAATCAACAAAGACAAAGTCGAACCCAAACATATCATTTCATTAAAA\nCAATAAAAGGTCGTATTACAAAATTGGTAAATGATTACCTTAAGTTCTTTCTAATAATACAAGCCTTAAAGCACAATTGC\nACATGGCAAGAGGAACTAAGAGCTCTTCCAGATCTAATTAGTGTCTGCACTCGATTCTATCATACTCGAAACTGTTCATG\nTGAAAACCGGTTCCTAGTACAGACTTTATACTTATCACGCATGCAGGATTCGGAAATCAAACTAATAGATAGATTGACCG\nGCCTTCTTAGTCTATGTCCAAATGGTTTTTTTCGGTAAGGACTCTTGACGTACAAACTCCACATAGTTATACAATGGTAC\nCAGGACACTATATGTAAATTGACCCTAAGAAAGAGTAATTCGACACACAGAGTTCTCAAGTGAAACCCCTCATCTCAGAT\nTATCTGTGGTTGCAATTCTAATATCCGATTGTTACCCCGTGAGTATAACTCCAGATTAATATAAGAAAATACCTTTTGTC\nCTGCAAATTTATCTTAAATTCAAGTACATACGCTCCAAATCGTATAAAATATTAAGAAAAAGTTAATCTGCTTGCTTTAA\nTTATAACTTTAATATTCGACAAATAGTTAACGGTCTCATCACTCAAAAATTTCATTAACAAAAGAAGTACTCTGAGTATA\nTTCACATATCATATGTGATTAACATATAAGCAACGCATGATGCGCCTTCCTCTTACTTATTGTGTTGTCACGCAGTCGTT\nGTACTACCTCGAAAATTCCAAACAATAAATCGTGTCTATCCCGCATTTAGTGTCTTTAATTTAAGATCTCAAATCCAAAA\nAACTGGGTTTATGTTGATGTAAATCAATAATACCGAAATTGCTTGATATTAAAATAAAGCTTAAAGGATTTTTCCTTAAA\nCGGTGATGTTAGGTATATAGGAAAGCTCGATCACGATGTCCCTTACTCAGAAAAAGAAAAACGGAAGCCCTATTGGCCAT\nTTAATCGTACACAAAAATATCTTTACCAAATTGTTTTCTCTTTTTTGTGTGTCCA\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Tai_Forest_ebolavirus/GCF_000888475.1_ViralProj51257_protein.faa", "content": ">YP_003815423.1 nucleoprotein [Tai Forest ebolavirus]\nMESRAHKAWMTHTASGFETDYHKILTAGLSVQQGIVRQRVIQVHQVTNLEEICQLIIQAFEAGVDFQESADSFLLMLCLH\nHAYQGDYKQFLESNAVKYLEGHGFRFEVRKKEGVKRLEELLPAASSGKSIRRTLAAMPEEETTEANAGQFLSFASLFLPK\nLVVGEKACLEKVQRQIQVHSEQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDAVIANSVAQAR\nFSGLLIVKTVLDHILQKTEHGVRLHPLARTAKVKNEVNSFKAALSSLAQHGEYAPFARLLNLSGVNNLEHGLFPQLSAIA\nLGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQKYAESRELDHLGLDDQEKKILKDFHQKKNEISFQQTTAMVTLRKE\nRLAKLTEAITSTSLLKTGKQYDDDNDIPFPGPINDNENSEQQDDDPTDSQDTTIPDIIVDPDDGRYNNYGDYPSETANAP\nEDLVLFDLEDGDEDDHRPSSSSENNNKHSLTGTDSNKTSNWNRNPTNMPKKDSTQNNDNPAQRAQEYARDNIQDTPTPHR\nALTPISEETGSNGHNEDDIDSIPPLESDEENNTETTITTTKNTTAPPAPVYRSNSEKEPLPQEKSQKQPNQVSGSENTDN\nKPHSEQSVEEMYRHILQTQGPFDAILYYYMMTEEPIVFSTSDGKEYVYPDSLEGEHPPWLSEKEALNEDNRFITMDDQQF\nYWPVMNHRNKFMAILQHHK\n>YP_003815424.1 polymerase complex protein [Tai Forest ebolavirus]\nMISTRAAAINDPSLPIRNQCTRGPELSGWISEQLMTGKIPVHEIFNDTEPHISSGSDCLPRPKNTAPRTRNTQTQTDPVC\nNHNFEDVTQALTSLTNVIQKQALNLESLEQRIIDLENGLKPMYDMAKVISALNRSCAEMVAKYDLLVMTTGRATATAAAT\nEAYWEEHGQPPPGPSLYEESAIRGKINKQEDKVPKEVQEAFRNLDSTSSLTEENFGKPDISAKDLRDIMYDHLPGFGTAF\nHQLVQVICKLGKDNSALDIIHAEFQASLAEGDSPQCALIQITKRIPIFQDATPPTIHIRSRGDIPRACQKSLRPVPPSPK\nIDRGWVCIFQLQDGKTLGLKI\n>YP_003815425.1 matrix protein [Tai Forest ebolavirus]\nMRRIILPTAPPEYMEAVYPMRTMNSGADNTASGPNYTTTGVMTNDTPSNSLRPVADDNIDHPSHTPNSVASAFILEAMVN\nVISGPKVLMKQIPIWLPLGVSDQKTYSFDSTTAAIMLASYTITHFGKTSNPLVRINRLGPGIPDHPLRLLRIGNQAFLQE\nFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDETPAVSTGTLRPGISFHPKLRPILLPGRAGKKGSNSDLTSPDKIQAI\nMNFLQDLKIVPIDPTKNIMGIEVPELLVHRLTGKKTTTKNGQPIIPILLPKYIGLDPLSQGDLTMVITQDCDSCHSPASL\nPPVNEK\n>YP_003815426.1 spike glycoprotein [Tai Forest ebolavirus]\nMGASGILQLPRERFRKTSFFVWVIILFHKVFSIPLGVVHNNTLQVSDIDKFVCRDKLSSTSQLKSVGLNLEGNGVATDVP\nTATKRWGFRAGVPPKVVNCEAGEWAENCYNLAIKKVDGSECLPEAPEGVRDFPRCRYVHKVSGTGPCPGGLAFHKEGAFF\nLYDRLASTIIYRGTTFAEGVIAFLILPKARKDFFQSPPLHEPANMTTDPSSYYHTTTINYVVDNFGTNTTEFLFQVDHLT\nYVQLEARFTPQFLVLLNETIYSDNRRSNTTGKLIWKINPTVDTSMGEWAFWENKKNFTKTLSSEELSFVPVPETQNQVLD\nTTATVSPPISAHNHAAEDHKELVSEDSTPVVQMQNIKGKDTMPTTVTGVPTTTPSPFPINARNTDHTKSFIGLEGPQEDH\nSTTQPAKTTSQPTNSTESTTLNPTSEPSSRGTGPSSPTVPNTTESHAELGKTTPTTLPEQHTAASAIPRAVHPDELSGPG\nFLTNTIRGVTNLLTGSRRKRRDVTPNTQPKCNPNLHYWTALDEGAAIGLAWIPYFGPAAEGIYTEGIMENQNGLICGLRQ\nLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPQDWTKNITDKIDQIIHDFVDNNLPNQND\nGSNWWTGWKQWVPAGIGITGVIIAIIALLCICKFML\n>YP_003815427.1 small secreted glycoprotein [Tai Forest ebolavirus]\nMGASGILQLPRERFRKTSFFVWVIILFHKVFSIPLGVVHNNTLQVSDIDKFVCRDKLSSTSQLKSVGLNLEGNGVATDVP\nTATKRWGFRAGVPPKVVNCEAGEWAENCYNLAIKKVDGSECLPEAPEGVRDFPRCRYVHKVSGTGPCPGGLAFHKEGAFF\nLYDRLASTIIYRGTTFAEGVIAFLILPKARKDFFQSPPLHEPANMTTDPSSYYHTTTINYVVDNFGTNTTEFLFQVDHLT\nYVQLEARFTPQFLVLLNETIYSDNRRSNTTGKLIWKINPTVDTSMGEWAFWENKKTSQKPFQVKSCLSYLYQKPRTRSLT\nRQRRSLLPSPPTTTQPKTTKNWFQRIPLQWFRCKTSRERTQCQPQ\n>YP_003815428.1 second secreted glycoprotein [Tai Forest ebolavirus]\nMGASGILQLPRERFRKTSFFVWVIILFHKVFSIPLGVVHNNTLQVSDIDKFVCRDKLSSTSQLKSVGLNLEGNGVATDVP\nTATKRWGFRAGVPPKVVNCEAGEWAENCYNLAIKKVDGSECLPEAPEGVRDFPRCRYVHKVSGTGPCPGGLAFHKEGAFF\nLYDRLASTIIYRGTTFAEGVIAFLILPKARKDFFQSPPLHEPANMTTDPSSYYHTTTINYVVDNFGTNTTEFLFQVDHLT\nYVQLEARFTPQFLVLLNETIYSDNRRSNTTGKLIWKINPTVDTSMGEWAFWENKKLHKNPFK\n>YP_003815429.1 minor nucleoprotein [Tai Forest ebolavirus]\nMEVVHERGRSRISRQNTRDGPSHLVRARSSSRASYRSEYHTPRSASQIRVPTVFHRKKTDLLTVPPAPKDVCPTLKKGFL\nCDSNFCKKDHQLESLTDRELLLLIARKTCGSTEQQLSIVAPKDSRLANPIAEDFQQKDGPKVTLSMLIETAEYWSKQDIK\nNIDDSRLRALLTLCAVMTRKFSKSQLSLLCESHLRREGLGQDQSESVLEVYQRLHSDKGGNFEAALWQQWDRQSLIMFIT\nAFLNIALQLPCESSSVVISGLRMLIPQSEATEVVTPSETCTWSEGGSSH\n>YP_003815430.1 membrane-associated protein [Tai Forest ebolavirus]\nMAKATGRYNLISPKKDLEKGLVLNDLCTLSVAQTVQGWKVTWAGIEFDVTQKGMALLHRLKTSDFAPAWSMTRNLFPHLF\nQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALGLIADWLLTTGTNHFQMRTQQAKEQLSLKMLSLVRSNILKF\nINQLDALHVVNYNGLLSSIEIGTKSHTIIITRTNMGFLVELQEPDKSAMNTRKPGPVKFSLLHESTLKTLAKKPATQMQA\nLILEFNSSLAI\n>YP_003815431.1 RNA-dependent RNA polymerase [Tai Forest ebolavirus]\nMATQHTQYPDARLSSPIVLDQCDLVTRACGLYSAYSLNPQLKNCRLPKHIYRLKYDTTVTEFLSDVPVATLPADFLVPTF\nLRTLSGNGSCPIDPKCSQFLEEIVNYTLQDIRFLNYYLNRAGVHNDHVDRDFGQKIRNLICDNEVLHQMFHWYDLAILAR\nRGRLNRGNNRSTWFASDNLVDILGYGDYIFWKIPLSLLPVDTQGLPHAAKDWYHESVFKEAIQGHTHIVSISTADVLIMC\nKDIITCRFNTLLIAAVANLEDSVHSDYPLPETVSDLYKAGDYLISLLGSEGYKVIKFLEPLCLAKIQLCSNYTERKGRFL\nTQMHLAVNHTLEELTGSRELRPQQIRKVREFHQMLINLKATPQQLCELFSVQKHWGHPVLHSEKAIQKVKKHATVIKALR\nPIIIFETYCVFKYSIAKHYFDSQGTWYSVTSDRCLTPGLSSYIKRNQFPPLPMIKELLWEFYHLDHPPLFSTKVISDLSI\nFIKDRATAVEKTCWDAVFEPNVLGYNPPNKFATKRVPEQFLEQENFSIESVLHYAQRLEYLLPEYRNFSFSLKEKELNIG\nRAFGKLPYPTRNVQTLCEALLADGLAKAFPSNMMVVTEREQKESLLHQASWHHTSDDFGENATVRGSSFVTDLEKYNLAF\nRYEFTAPFIEYCNRCYGVRNLFNWMHYTIPQCYIHVSDYYNPPHGVSLENRENPPEGPSSYRGHLGGIEGLQQKLWTSIS\nCAQISLVEIKTGFKLRSAVMGDNQCITVLSVFPLETESSEQELSSEDNAARVAASLAKVTSACGIFLKPDETFVHSGFIY\nFGKKQYLNGVQLPQSLKTATRIAPLSDAIFDDLQGTLASIGTAFERSISETRHVVPCRVAAAFHTFFSVRILQYHHLGFN\nKGTDLGQLSLSKPLDFGTITLALAVPQVLGGLSFLNPEKCFYRNLGDPVTSGLFQLKTYLQMIHMDDLFLPLIAKNPGNC\nSAIDFVLNPSGLNVPGSQDLTSFLRQIVRRTITLSAKNKLINTLFHSSADLEDEMVCKWLLSSTPVMSRFAADIFSRTPS\nGKRLQILGYLEGTRTLLASKIINHNTETPILDRLRKITLQRWSLWFSYLDHCDQVLADALTQITCTVDLAQILREYTWAH\nILEGRQLIGATLPCILEQLNVIWLKPYEHCPKCAKSANPKGEPFVSIAIKKHVVSAWPDQSRLSWTIGDGIPYIGSRTED\nKIGQPAIKPKCPSAALREAIELTSRLTWVTQGGANSDLLVKPFIEARVNLSVQEILQMTPSHYSGNIVHRYNDQYSPHSF\nMANRMSNSATRLVVSTNTLGEFSGGGQSARDSNIIFQNVINFAVALFDLRFRNVATSSIQHHRAHLHLSKCCTREVPAQY\nLVYTSTLPLDLTRYRDNELIYDDNPLRGGLNCNLSFDNPLFKGQRLNIIEEDLIRLPYLSGWELAKTVIQSIISDSNNSS\nTDPISSGETRSFTTHFLTYPKIGLLYSFGALISYYLGNTIIRTKKLTLNNFIYYLATQIHNLPHRSLRILKPTLKHASVI\nSRLISIDSHFSIYIGGTAGDRGLSDAARLFLRTAITVFLQFVRKWIVERKTAIPLWVIYPLEGQSPSPINSFLHHVIALL\nQHESSHDHVCAAEAHSRVETFDNLVYMCKSTASNFFHASLAYWRSRSKNQDKREMTKILSLTQTEKKNSFGYTAHPESTA\nVLGSLQTSLAPPPSADEATYDRKNKVLKASRPGKYSQNTTKAPPNQTSCRDVSPNITGTDGCPSANEGSNSNNNNLVSHR\nIVLPFFTLSHNYNERPSIRKSEGTTEIVRLTRQLRAIPDTTIYCRFTGIVSSMHYKLDEVLWEFDNFKSAITLAEGEGSG\nALLLLQKYKVETLFFNTLATEHSIEAEIISGITTPRMLLPIMSRFHGGQIKVTLNNSASQITDITNPSWLADQKSRIPKQ\nVEIITMDAETTENINRSKLYEAVQQLIVSHIDPNALKVVVLKVFLSDIDGILWLNDNLTPLFGLGYLIKPITSSPKSSEW\nYLCLSNLLSTSRRLPHQSHTTCMHVIQTALQLQIQRSSYWLSHLVQYANHNLHLDYINLGFPSLERVLYHRYNLVDSQKG\nPLTSIVQHLAHLQTEIRELVNDYNQQRQSRTQTYHFIKTIKGRITKLVNDYLKFFLIIQALKHNCTWQEELRALPDLISV\nCTRFYHTRNCSCENRFLVQTLYLSRMQDSEIKLIDRLTGLLSLCPNGFFR\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Zaire_ebolavirus/GCF_000848505.1_ViralProj14703_genomic.fna", "content": ">NC_002549.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1976/Yambuku-Mayinga, complete genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTC\nATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGAT\nAGAGAACAACCTAGGTCTCCGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTA\nTCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCCAACAACCTTAATAGAAACATTATTGTTAAAGGACAGCATT\nAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGGTTTTGAACTTGAACACTTAGGGGATTGAAGATTCAACAAC\nCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCG\nTCCTCAGAAAATCTGGATGGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG\nTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAAGAAATTTGCCAACTTATCATA\nCAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCA\nGGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGC\nGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATG\nCCGGAAGAGGAGACAACTGAAGCTAATGCCGGTCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGG\nAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTT\nGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTCTGATCAAATTTCTCCTAATACACCAA\nGGGATGCACATGGTTGCCGGGCATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGCTT\nATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCG\nCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCC\nCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTATCGGCAATTGCACTCGGAGTCGC\nCACAGCACACGGGAGTACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAACTCAGAGAGGCTGCCACTGAGGCTG\nAGAAGCAACTCCAACAATATGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATG\nAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGAGCGCCTGGCCAA\nGCTGACAGAAGCTATCACTGCTGCGTCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAG\nGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTG\nGTGGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGAAAACGGCATGAATGCACCAGATGACTTGGT\nCCTATTCGATCTAGACGAGGACGACGAGGACACTAAGCCAGTGCCTAATAGATCGACCAAGGGTGGACAACAGAAGAACA\nGTCAAAAGGGCCAGCATATAGAGGGCAGACAGACACAATCCAGGCCAATTCAAAATGTCCCAGGCCCTCACAGAACAATC\nCACCACGCCAGTGCGCCACTCACGGACAATGACAGAAGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACC\nAATTAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTGGAGTCAGATGATGAAG\nAGCAGGACAGGGACGGAACTTCCAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAAAG\nAAAGAACTCCCGCAAGACGAGCAACAAGATCAGGACCACACTCAAGAGGCCAGGAACCAGGACAGTGACAACACCCAGTC\nAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCTGTTTTGTATTATCATATGA\nTGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAAAGAGTACACGTATCCAGACTCCCTTGAAGAGGAATATCCA\nCCATGGCTCACTGAAAAAGAGGCTATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGT\nGATGAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAACAATGGGATGATTCAACCG\nACAAATAGCTAACATTAAGTAGTCAAGGAACGAAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAAT\nAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGC\nAAATAGGCGTTAAGCCACAGTTATAGCCATAATTGTAACTCAATATTCTAACTAGCGATTTATCTAAATTAAATTACATT\nATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGAT\nTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGT\nCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGCGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAG\nCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCC\nAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGACGCGCAACAGTCAAACCCAAACGGACCCAA\nTTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCA\nGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATT\nGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGG\nCAACTGAGGCTTATTGGGCCGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAG\nATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAAACAGTACCACTTCACTAACTGA\nGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTG\nCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAG\nGCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGC\nTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAGCTTGCGTCCAGTCCCACCATCGC\nCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTC\nCCTTCCCTCCGAAAGAGGCGAATAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTACGTTACATTAATGATACACTTG\nTGAGTATCAGCCCTGGATAATATAAGTCAATTAAACGACCAAGATAAAATTGTTCATATCTCGCTAGCAGCTTAAAATAT\nAAATGTAATAGGAGCTATATCTCTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAACCAAAAGTGATGAAGATTA\nAGAAAAACCTACCTCGGCTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATAT\nGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTA\nGAGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCATCGAATCCACTCAGGCCAATT\nGCCGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTTGAAGCTATGGTGAATGT\nCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCT\nTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATACACTATCACCCATTTCGGCAAGGCAACCAATCCACTTGTCAGA\nGTCAATCGGCTGGGTCCTGGAATCCCGGATCATCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTT\nCGTTCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTG\nCTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGC\nCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAAT\nGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGAATCGAAGTGCCAGAAACTCTGG\nTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGG\nTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCC\nAGCTGTGATTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTATAGAATCTTCTCAGGGATAGTGATAACATCTA\nTTTAGTAATCCGTCCATTAGAGGAGACACTTTTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTTTTTTCTC\nTCCTAAATGTAGAACTTAACAAAAGACTCATAATATACTTGTTTTTAAAGGATTGATTGATGAAAGATCATAACTAATAA\nCATTACAAATAATCCTACTATAATCAATACGGTGATTCAAATGTTAATCTTTCTCATTGCACATACTTTTTGCCCTTATC\nCTCAAATTGCCTGCATGCTTACATCTGAGGATAGCCAGTGTGACTTGGATTGGAAATGTGGAGAAAAAATCGGGACCCAT\nTTCTAGGTTGTTCACAATCCAAGTACAGACATTGCCCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGT\nGAGCGTAATCTTCATCTCTCTTAGATTATTTGTTTTCCAGAGTAGGGGTCGTCAGGTCCTTTTCAATCGTGTAACCAAAA\nTAAACTCCACTAGAAGGATATTGTGGGGCAACAACACAATGGGCGTTACAGGAATATTGCAGTTACCTCGTGATCGATTC\nAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAG\nCACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGAC\nTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCA\nAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTG\nTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCGTGTG\nCCGGAGACTTTGCCTTCCATAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACG\nACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGA\nGCCGGTCAATGCAACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACCA\nATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTC\nCAGCTGAATGAGACAATATATACAAGTGGGAAAAGGAGCAATACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAAT\nTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTT\nCACAGTTGTATCAAACGGAGCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGGGACCAACACAA\nCAACTGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCA\nGTGTCGCATCTAACAACCCTTGCCACAATCTCCACGAGTCCCCAATCCCTCACAACCAAACCAGGTCCGGACAACAGCAC\nCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGACA\nGCACAGCCTCCGACACTCCCTCTGCCACGACCGCAGCCGGACCCCCAAAAGCAGAGAACACCAACACGAGCAAGAGCACT\nGACTTCCTGGACCCCGCCACCACAACAAGTCCCCAAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGA\nTACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTCGCAGGACTGATCACAG\nGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAACCCTAATTTACATTACTGGACTACTCAG\nGATGAAGGTGCTGCAATCGGACTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACATAGAGGGGCTAAT\nGCACAATCAAGATGGTTTAATCTGTGGGTTGAGACAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTGTTCCTGAGAG\nCCACAACTGAGCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGC\nCACATTCTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCA\nTGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAG\nGTATTGGAGTTACAGGCGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGA\nTTGCTTCATGGAAAAGCTCAGCCTCAAATCAATGAAACCAGGATTTAATTATATGGATTACTTGAATCTAAGATTACTTG\nACAAATGATAATATAATACACTGGAGCTTTAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAA\nACAAGGTTTGACATCAATCTAGTTATCTCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATT\nATCTTTAATCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTG\nTAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGGTCAAAAAGTCAATAGAAAT\nTTAAACAGTGAGTGGAGACAACTTTTAAATGGAAGCTTCATATGAGAGAGGACGCCCACGAGCTGCCAGACAGCATTCAA\nGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGC\nGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACAT\nATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAGAGTTTAACTGATA\nGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCG\nCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGC\nAGAACACTGGGCGAGACAAGACATCAGAACCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCTGTGATGA\nCGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGCGAGGGGCTTGGGCAAGATCAGGCA\nGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGA\nCCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATTGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTG\nTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGAT\nGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCAT\nATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATGTGCATGA\nTTGCCCTAATATATGAAGAGGTATGATACAACCCTAACAGTGATCAAAGAAAATCATAATCTCGTATCGCTCGTAATATA\nACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACTCTACAGGAGGTAGCAACGATCCA\nTCCCATCAAAAAATAAGTATTTCATGACTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTT\nTATGCTTCAAGCTGTGGAGGAGGTGTTTGGTATTGGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGT\nTCTTGTTTCAAGAGGTAGATTGTGACCGGAAATGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAAC\nCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTG\nGCACGTCTTTTAGCTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTCTCTAAGCTAAATTGGTCTGTACACATC\nCCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCTGGGCTAACACCA\nCCAGGTCAACTCCATTGGCTGAAAAGAAGCTTACCTACAACGAACATCACTTTGAGCGCCCTCACAATTAAAAAATAGGA\nACGTCGTTCCAACAATCGAGCGCAAGGTTTCAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATTGATACTCCAGACA\nCCAAGCAAGACCTGAGAAAAAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAA\nAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGCCAAACTATTCAGGGGTGGAAGGTTTATTGGGCTGGTATTG\nAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACA\nAGGAATCTCTTTCCTCATTTATTTCAAAATCCGAATTCCACAATTGAATCACCGCTGTGGGCATTGAGAGTCATCCTTGC\nAGCAGGGATACAGGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGC\nTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTG\nATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAACGGATTGTTGAGCAGTAT\nTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACA\nAATCGGCAATGAACCGCATGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAA\nGGATCCTCGACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGGTAGAATACTTCATA\nTTGAGCTAACTCATATATGCTGACTCAATAGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAAT\nAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTAC\nAAAAACCAGGACTCAGAATCCCTCAAACAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATGAATAAGCATT\nTTATCACCAGAAATCCTATATACTAAATGGTTAATTGTAACTGAACCCGCAGGTCACATGTGTTAGGTTTCACAGATTCT\nATATATTACTAACTCTATACTCGTAATTAACATTAGATAAGTAGATTAAGAAAAAAGCCTGAGGAAGATTAAGAAAAACT\nGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGAAATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCA\nATACCCAGACGCTAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCAT\nCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACC\nAAGTTCTTGAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAGTTCTTCTCAAGGCACTGTCAGGCAA\nTGGATTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATCATTAAGTACACAATGCAAGATGCTCTCTTCT\nTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAACACTTTCAAGAGAAAATCTTATCTTCAATT\nCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGATCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGG\nAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCC\nCAATTTCAATGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGACTGGTATCAGGCATCAGTATTCAAAGAA\nGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCG\nATTCAACACAACTCTAATCTCAAAAATAGCAGAGATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTGTGT\nCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATTATTAAGTTCCTCGAACCA\nTTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACTGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGT\nAAATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTAAAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAA\nCATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTA\nCATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGAC\nATACTGTGTTTTTAAATATAGTATTGCCAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACTTCAGATAGGA\nATCTAACACCGGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTACTATGGGAA\nTTTTACCACCTTGACCACCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTAC\nCGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTTAGTACTA\nAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCACAAAAACTCGAGTAT\nCTACTACCACAATATCGGAACTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACCTTCGGAAAATTGCC\nTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGA\nTGGTAGTTACGGAACGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAA\nCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACC\nTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATA\nTGCATGTCAGTGATTATTATAATCCACCACATAACCTCACACTGGAGAATCGAGACAACCCCCCCGAAGGGCCTAGTTCA\nTACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGT\nTGAAATTAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGGTGACAATCAGTGCATTACTGTTTTATCAGTCTTCCCCT\nTAGAGACTGACGCAGACGAGCAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACA\nAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTT\nGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTC\nAAGGGACCCTGGCTAGTATAGGCACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGGATAACC\nGCAGCTTTCCATACGTTTTTTTCGGTGAGAATCTTGCAATATCATCATCTCGGGTTCAATAAAGGTTTTGACCTTGGACA\nGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCT\nTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGCTTATTCCAGTTAAAAACTTATCTC\nCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCT\nAAATCCTAGCGGATTAAATGTCCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGCAGGACCATCACCC\nTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTGTAAATGGCTA\nTTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGATATCTTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCT\nAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACACCGGTTTTGGACAGAC\nTGAGGAAAATAACATTGCAAAGGTGGAGCCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTA\nACCCAAATAACTTGCACAGTTGATTTAGCACAGATTCTGAGGGAATATTCATGGGCTCATATTTTAGAGGGAAGACCTCT\nTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGTTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTT\nCAAATGCAAAGCAACCAGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCA\nTCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGACAACCTGCTAT\nTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTT\nCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCT\nTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAA\nTTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATA\nTTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAA\nTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTATTTAACATACACATCTACATT\nGGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAGTAATCCTCTAAAAGGAGGACTCAATTGCAATA\nTCTCATTCGATAATCCATTTTTCCAAGGTAAACGGCTGAACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCT\nGGATGGGAGCTAGCCAAGACCATCATGCAATCAATTATTTCAGATAGCAACAATTCATCTACAGACCCAATTAGCAGTGG\nAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTT\nATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACTCAAATTCAT\nAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGA\nTCCTCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGT\nCCATTTCATCTTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCG\nCTAGAGGGTCAAAACCCAACACCTGTGAATAATTTTCTCTATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACA\nACAGGCTTTTAAAACTACCATAAGTGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCA\nATTTCTTCCATGCATCATTGGCGTACTGGAGGAGCAGACACAGAAACAGCAACCGAAAATACTTGGCAAGAGACTCTTCA\nACTGGATCAAGCACAAACAACAGTGATGGTCATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCAC\nTGAACGGAATCTAGTCCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAACACGCACCAGGGTCCGT\nCGTTCCAGTCCTTTCTAAGTGACTCTGCTTGTGGTACAGCAAATCCAAAACTAAATTTCGATCGATCGAGACACAATGTG\nAAATTTCAGGATCATAACTCGGCATCCAAGAGGGAAGGTCATCAAATAATCTCACACCGTCTAGTCCTACCTTTCTTTAC\nATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGACGAGATATCAAAGTACTTACGGCAAT\nTGAGATCCGTCATTGATACCACAGTTTATTGTAGATTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTC\nCTTTGGGAAATAGAGAGTTTCAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAA\nATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTA\nCTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAA\nATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAAGCAAGTCGAGGTTATAACCATGGA\nTGCAGAGACAACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAATTGATCTTACACCATATTGATCCTA\nGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGTTATGGCTAAATGATAATTTAGCCCCG\nTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATCTAGTGAGTGGTATCTTTGTCTGACGAACTT\nCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAA\nTTCAACGAAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGTGAGTTACATTTAAGTTATATCCGCCTTGGT\nTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCCACTAGTCTCTATCACTCA\nGCACTTAGCACATCTTAGAGCAGAGATTCGAGAATTAACTAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACAT\nATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCA\nTTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTACCATAT\nTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTA\nTCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCGGATGGTCTCTACAGGTTTGATTGAATTACCGTGCATAGTATCCTG\nATACTTGCAAAGGTTGGTTATTAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCTAATCT\nCAATAAACAACTATTTAAATAACGAAAGGAGTCCCTATATTATATACTATATTTAGCCTCTCTCCCTGCGTGATAATCAA\nAAAATTCACAATGCAGCATGTGTGACATATTACTGCCGCAATGAATTTAACGCAACATAATAAACTCTGCACTCTTTATA\nATTAAGCTTTAACGAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTGTATCAATATCCTGTCAGATGGAATAG\nTGTTTTGGTTGATAACACAACTTCTTAAAACAAAATTGATCTTTAAGATTAAGTTTTTTATAATTATCATTACTTTAATT\nTGTCGTTTTAAAAACGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACCTTAACATTTTTGTCTA\nGTAAGCTACTATTTCATACAGAATGATAAAATTAAAAGAAAAGGCAGGACTGTAAAATCAGAAATACCTTCTTTACAATA\nTAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGACATTGACCACGCTCATCAGAAGGCTCGCCAGAATAAAC\nGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/Viruses/Zaire_ebolavirus/GCF_000848505.1_ViralProj14703_protein.faa", "content": ">NP_066243.1 nucleoprotein [Zaire ebolavirus]\nMDSRPQKIWMAPSLTESDMDYHKILTAGLSVQQGIVRQRVIPVYQVNNLEEICQLIIQAFEAGVDFQESADSFLLMLCLH\nHAYQGDYKLFLESGAVKYLEGHGFRFEVKKRDGVKRLEELLPAVSSGKNIKRTLAAMPEEETTEANAGQFLSFASLFLPK\nLVVGEKACLEKVQRQIQVHAEQGLIQYPTAWQSVGHMMVIFRLMRTNFLIKFLLIHQGMHMVAGHDANDAVISNSVAQAR\nFSGLLIVKTVLDHILQKTERGVRLHPLARTAKVKNEVNSFKAALSSLAKHGEYAPFARLLNLSGVNNLEHGLFPQLSAIA\nLGVATAHGSTLAGVNVGEQYQQLREAATEAEKQLQQYAESRELDHLGLDDQEKKILMNFHQKKNEISFQQTNAMVTLRKE\nRLAKLTEAITAASLPKTSGHYDDDDDIPFPGPINDDDNPGHQDDDPTDSQDTTIPDVVVDPDDGSYGEYQSYSENGMNAP\nDDLVLFDLDEDDEDTKPVPNRSTKGGQQKNSQKGQHIEGRQTQSRPIQNVPGPHRTIHHASAPLTDNDRRNEPSGSTSPR\nMLTPINEEADPLDDADDETSSLPPLESDDEEQDRDGTSNRTPTVAPPAPVYRDHSEKKELPQDEQQDQDHTQEARNQDSD\nNTQSEHSFEEMYRHILRSQGPFDAVLYYHMMKDEPVVFSTSDGKEYTYPDSLEEEYPPWLTEKEAMNEENRFVTLDGQQF\nYWPVMNHKNKFMAILQHHQ\n>NP_066244.1 polymerase complex protein [Zaire ebolavirus]\nMTTRTKGRGHTAATTQNDRMPGPELSGWISEQLMTGRIPVSDIFCDIENNPGLCYASQMQQTKPNPKTRNSQTQTDPICN\nHSFEEVVQTLASLATVVQQQTIASESLEQRITSLENGLKPVYDMAKTISSLNRVCAEMVAKYDLLVMTTGRATATAAATE\nAYWAEHGQPPPGPSLYEESAIRGKIESRDETVPQSVREAFNNLNSTTSLTEENFGKPDISAKDLRNIMYDHLPGFGTAFH\nQLVQVICKLGKDSNSLDIIHAEFQASLAEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKI\nDRGWVCVFQLQDGKTLGLKI\n>NP_066245.1 matrix protein [Zaire ebolavirus]\nMRRVILPTAPPEYMEAIYPVRSNSTIARGGNSNTGFLTPESVNGDTPSNPLRPIADDTIDHASHTPGSVSSAFILEAMVN\nVISGPKVLMKQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKATNPLVRVNRLGPGIPDHPLRLLRIGNQAFLQE\nFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDDTPTGSNGALRPGISFHPKLRPILLPNKSGKKGNSADLTSPEKIQAI\nMTSLQDFKIVPIDPTKNIMGIEVPETLVHKLTGKKVTSKNGQPIIPVLLPKYIGLDPVAPGDLTMVITQDCDTCHSPASL\nPAVIEK\n>NP_066246.1 spike glycoprotein [Zaire ebolavirus]\nMGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVP\nSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFF\nLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLT\nYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVSNGAKNISG\nQSPARTSSDPGTNTTTEDHKIMASENSSAMVQVHSQGREAAVSHLTTLATISTSPQSLTTKPGPDNSTHNTPVYKLDISE\nATQVEQHHRRTDNDSTASDTPSATTAAGPPKAENTNTSKSTDFLDPATTTSPQNHSETAGNNNTHHQDTGEESASSGKLG\nLITNTIAGVAGLITGGRRTRREAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQ\nLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDKTLPDQGD\nNDNWWTGWRQWIPAGIGVTGVIIAVIALFCICKFVF\n>NP_066247.1 small secreted glycoprotein [Zaire ebolavirus]\nMGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVP\nSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFF\nLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLT\nYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKTSLEKFAVKSCLSQLYQTEPKTSVV\nRVRRELLPTQGPTQQLKTTKSWLQKIPLQWFKCTVKEGKLQCRI\n>NP_066248.1 second secreted glycoprotein [Zaire ebolavirus]\nMGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVP\nSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFF\nLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLT\nYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKPH\n>NP_066249.1 minor nucleoprotein [Zaire ebolavirus]\nMEASYERGRPRAARQHSRDGHDHHVRARSSSRENYRGEYRQSRSASQVRVPTVFHKKRVEPLTVPPAPKDICPTLKKGFL\nCDSSFCKKDHQLESLTDRELLLLIARKTCGSVEQQLNITAPKDSRLANPTADDFQQEEGPKITLLTLIKTAEHWARQDIR\nTIEDSKLRALLTLCAVMTRKFSKSQLSLLCETHLRREGLGQDQAEPVLEVYQRLHSDKGGSFEAALWQQWDRQSLIMFIT\nAFLNIALQLPCESSAVVVSGLRTLVPQSDNEEASTNPGTCSWSDEGTP\n>NP_066250.1 membrane-associated protein [Zaire ebolavirus]\nMAKATGRYNLISPKKDLEKGVVLSDLCNFLVSQTIQGWKVYWAGIEFDVTHKGMALLHRLKTNDFAPAWSMTRNLFPHLF\nQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALGLISDWLLTTNTNHFNMRTQRVKEQLSLKMLSLIRSNILKF\nINKLDALHVVNYNGLLSSIEIGTQNHTIIITRTNMGFLVELQEPDKSAMNRMKPGPAKFSLLHESTLKAFTQGSSTRMQS\nLILEFNSSLAI\n>NP_066251.1 RNA-dependent RNA polymerase [Zaire ebolavirus]\nMATQHTQYPDARLSSPIVLDQCDLVTRACGLYSSYSLNPQLRNCKLPKHIYRLKYDVTVTKFLSDVPVATLPIDFIVPVL\nLKALSGNGFCPVEPRCQQFLDEIIKYTMQDALFLKYYLKNVGAQEDCVDEHFQEKILSSIQGNEFLHQMFFWYDLAILTR\nRGRLNRGNSRSTWFVHDDLIDILGYGDYVFWKIPISMLPLNTQGIPHAAMDWYQASVFKEAVQGHTHIVSVSTADVLIMC\nKDLITCRFNTTLISKIAEIEDPVCSDYPNFKIVSMLYQSGDYLLSILGSDGYKIIKFLEPLCLAKIQLCSKYTERKGRFL\nTQMHLAVNHTLEEITEMRALKPSQAQKIREFHRTLIRLEMTPQQLCELFSIQKHWGHPVLHSETAIQKVKKHATVLKALR\nPIVIFETYCVFKYSIAKHYFDSQGSWYSVTSDRNLTPGLNSYIKRNQFPPLPMIKELLWEFYHLDHPPLFSTKIISDLSI\nFIKDRATAVERTCWDAVFEPNVLGYNPPHKFSTKRVPEQFLEQENFSIENVLSYAQKLEYLLPQYRNFSFSLKEKELNVG\nRTFGKLPYPTRNVQTLCEALLADGLAKAFPSNMMVVTEREQKESLLHQASWHHTSDDFGEHATVRGSSFVTDLEKYNLAF\nRYEFTAPFIEYCNRCYGVKNVFNWMHYTIPQCYMHVSDYYNPPHNLTLENRDNPPEGPSSYRGHMGGIEGLQQKLWTSIS\nCAQISLVEIKTGFKLRSAVMGDNQCITVLSVFPLETDADEQEQSAEDNAARVAASLAKVTSACGIFLKPDETFVHSGFIY\nFGKKQYLNGVQLPQSLKTATRMAPLSDAIFDDLQGTLASIGTAFERSISETRHIFPCRITAAFHTFFSVRILQYHHLGFN\nKGFDLGQLTLGKPLDFGTISLALAVPQVLGGLSFLNPEKCFYRNLGDPVTSGLFQLKTYLRMIEMDDLFLPLIAKNPGNC\nTAIDFVLNPSGLNVPGSQDLTSFLRQIVRRTITLSAKNKLINTLFHASADFEDEMVCKWLLSSTPVMSRFAADIFSRTPS\nGKRLQILGYLEGTRTLLASKIINNNTETPVLDRLRKITLQRWSLWFSYLDHCDNILAEALTQITCTVDLAQILREYSWAH\nILEGRPLIGATLPCMIEQFKVFWLKPYEQCPQCSNAKQPGGKPFVSVAVKKHIVSAWPNASRISWTIGDGIPYIGSRTED\nKIGQPAIKPKCPSAALREAIELASRLTWVTQGSSNSDLLIKPFLEARVNLSVQEILQMTPSHYSGNIVHRYNDQYSPHSF\nMANRMSNSATRLIVSTNTLGEFSGGGQSARDSNIIFQNVINYAVALFDIKFRNTEATDIQYNRAHLHLTKCCTREVPAQY\nLTYTSTLDLDLTRYRENELIYDSNPLKGGLNCNISFDNPFFQGKRLNIIEDDLIRLPHLSGWELAKTIMQSIISDSNNSS\nTDPISSGETRSFTTHFLTYPKIGLLYSFGAFVSYYLGNTILRTKKLTLDNFLYYLTTQIHNLPHRSLRILKPTFKHASVM\nSRLMSIDPHFSIYIGGAAGDRGLSDAARLFLRTSISSFLTFVKEWIINRGTIVPLWIVYPLEGQNPTPVNNFLYQIVELL\nVHDSSRQQAFKTTISDHVHPHDNLVYTCKSTASNFFHASLAYWRSRHRNSNRKYLARDSSTGSSTNNSDGHIERSQEQTT\nRDPHDGTERNLVLQMSHEIKRTTIPQENTHQGPSFQSFLSDSACGTANPKLNFDRSRHNVKFQDHNSASKREGHQIISHR\nLVLPFFTLSQGTRQLTSSNESQTQDEISKYLRQLRSVIDTTVYCRFTGIVSSMHYKLDEVLWEIESFKSAVTLAEGEGAG\nALLLIQKYQVKTLFFNTLATESSIESEIVSGMTTPRMLLPVMSKFHNDQIEIILNNSASQITDITNPTWFKDQRARLPKQ\nVEVITMDAETTENINRSKLYEAVYKLILHHIDPSVLKAVVLKVFLSDTEGMLWLNDNLAPFFATGYLIKPITSSARSSEW\nYLCLTNFLSTTRKMPHQNHLSCKQVILTALQLQIQRSPYWLSHLTQYADCELHLSYIRLGFPSLEKVLYHRYNLVDSKRG\nPLVSITQHLAHLRAEIRELTNDYNQQRQSRTQTYHFIRTAKGRITKLVNDYLKFFLIVQALKHNGTWQAEFKKLPELISV\nCNRFYHIRDCNCEERFLVQTLYLHRMQDSEVKLIERLTGLLSLFPDGLYRFD\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/library/prelim_map.txt", "content": "ACCNUM\tNC_014373.1\tNC_014373\nACCNUM\tNC_002549.1\tNC_002549\nACCNUM\tNC_004161.1\tNC_004161\nACCNUM\tNC_014372.1\tNC_014372\nACCNUM\tNC_006432.1\tNC_006432\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/accession2taxid/nucl_est.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/accession2taxid/nucl_gb.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\nNC_002549\tNC_002549.1\t186538\t10313991\nNC_004161\tNC_004161.1\t186539\t22789222\nNC_006432\tNC_006432.1\t186540\t55770807\nNC_014373\tNC_014373.1\t565995\t302371213\nNC_014372\tNC_014372.1\t186541\t302315369\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/accession2taxid/nucl_gss.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/accession2taxid/nucl_wgs.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/accession2taxid/pdb.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n5HQL_A\t5HQL_A\t1\t1134776119\n5HQL_B\t5HQL_B\t1\t1134776120\n5HQL_C\t5HQL_C\t1\t1134776121\n5HQL_D\t5HQL_D\t1\t1134776122\n5HQL_E\t5HQL_E\t1\t1134776123\n5HQL_F\t5HQL_F\t1\t1134776124\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/accession2taxid/prot.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\nNP_066244\tNP_066244.1\t186538\t10313992\nNP_066245\tNP_066245.1\t186538\t10313993\nNP_066247\tNP_066247.1\t186538\t10313994\nNP_066246\tNP_066246.1\t186538\t10313995\nNP_066248\tNP_066248.1\t186538\t10313996\nNP_066249\tNP_066249.1\t186538\t10313997\nNP_066250\tNP_066250.1\t186538\t10313998\nNP_066251\tNP_066251.1\t186538\t10313999\nNP_066243\tNP_066243.1\t186538\t10314000\nNP_690580\tNP_690580.1\t186539\t22789223\nNP_690581\tNP_690581.1\t186539\t22789224\nNP_690582\tNP_690582.1\t186539\t22789225\nNP_690584\tNP_690584.1\t186539\t22789226\nNP_690585\tNP_690585.1\t186539\t22789227\nNP_690586\tNP_690586.1\t186539\t22789228\nNP_690587\tNP_690587.1\t186539\t22789229\nNP_690583\tNP_690583.1\t186539\t22789230\nYP_138520\tYP_138520.1\t186540\t55770808\nYP_138521\tYP_138521.1\t186540\t55770809\nYP_138522\tYP_138522.1\t186540\t55770810\nYP_138524\tYP_138524.1\t186540\t55770811\nYP_138523\tYP_138523.1\t186540\t55770812\nYP_138525\tYP_138525.1\t186540\t55770813\nYP_138526\tYP_138526.1\t186540\t55770814\nYP_138527\tYP_138527.1\t186540\t55770815\nYP_003815432\tYP_003815432.1\t565995\t302371214\nYP_003815433\tYP_003815433.1\t565995\t302371215\nYP_003815434\tYP_003815434.1\t565995\t302371216\nYP_003815436\tYP_003815436.1\t565995\t302371217\nYP_003815435\tYP_003815435.1\t565995\t302371218\nYP_003815438\tYP_003815438.1\t565995\t302371219\nYP_003815439\tYP_003815439.1\t565995\t302371220\nYP_003815440\tYP_003815440.1\t565995\t302371221\nYP_003815437\tYP_003815437.1\t565995\t302371222\nYP_003815423\tYP_003815423.1\t186541\t302315370\nYP_003815424\tYP_003815424.1\t186541\t302315371\nYP_003815425\tYP_003815425.1\t186541\t302315372\nYP_003815426\tYP_003815426.1\t186541\t302315373\nYP_003815427\tYP_003815427.1\t186541\t302315374\nYP_003815429\tYP_003815429.1\t186541\t302315375\nYP_003815430\tYP_003815430.1\t186541\t302315376\nYP_003815431\tYP_003815431.1\t186541\t302315377\nYP_003815428\tYP_003815428.1\t186541\t302315378\nYP_009246340\tYP_009246340.1\t186539\t1021000625\nYP_009246341\tYP_009246341.1\t186540\t1021000626\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/delnodes.dmp", "content": "" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/gi_taxid_nucl.dmp", "content": "" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/gi_taxid_prot.dmp", "content": "1134776119\t1\n1134776120\t1\n1134776121\t1\n1134776122\t1\n1134776123\t1\n1134776124\t1\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/merged.dmp", "content": "" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/names.dmp", "content": "1\t|\tall\t|\t\t|\tsynonym\t|\n1\t|\troot\t|\t\t|\tscientific name\t|\n10239\t|\tVira\t|\t\t|\tsynonym\t|\n10239\t|\tViridae\t|\t\t|\tsynonym\t|\n10239\t|\tViruses\t|\t\t|\tscientific name\t|\n10239\t|\tviruses\t|\tviruses\t|\tblast name\t|\n11157\t|\tMononegavirales\t|\t\t|\tscientific name\t|\n11157\t|\tnegative-sense genome single-stranded RNA viruses\t|\t\t|\tgenbank common name\t|\n11266\t|\tFiloviridae\t|\t\t|\tscientific name\t|\n11266\t|\tFilovirus\t|\t\t|\tsynonym\t|\n35301\t|\tssRNA negative-strand viruses\t|\t\t|\tscientific name\t|\n186536\t|\tEbola-like viruses\t|\t\t|\tsynonym\t|\n186536\t|\tEbolavirus\t|\t\t|\tscientific name\t|\n186538\t|\tZEBOV\t|\t\t|\tacronym\t|\n186538\t|\tZaire Ebola virus\t|\t\t|\tsynonym\t|\n186538\t|\tZaire ebolavirus\t|\t\t|\tscientific name\t|\n186539\t|\tEbola virus Reston\t|\t\t|\tsynonym\t|\n186539\t|\tREBOV\t|\t\t|\tacronym\t|\n186539\t|\tRESTV\t|\t\t|\tacronym\t|\n186539\t|\tReston Ebola virus\t|\t\t|\tsynonym\t|\n186539\t|\tReston ebolavirus\t|\t\t|\tscientific name\t|\n186540\t|\tEbolavirus Sudan\t|\t\t|\tsynonym\t|\n186540\t|\tSEBOV\t|\t\t|\tacronym\t|\n186540\t|\tSUDV\t|\t\t|\tacronym\t|\n186540\t|\tSudan Ebola virus\t|\t\t|\tsynonym\t|\n186540\t|\tSudan ebolavirus\t|\t\t|\tscientific name\t|\n186541\t|\tCIEBOV\t|\t\t|\tacronym\t|\n186541\t|\tCote d'Ivoire Ebola virus\t|\t\t|\tsynonym\t|\n186541\t|\tCote d'Ivoire ebolavirus\t|\t\t|\tsynonym\t|\n186541\t|\tIvory Coast ebolavirus\t|\t\t|\tsynonym\t|\n186541\t|\tTAFV\t|\t\t|\tacronym\t|\n186541\t|\tTai Forest ebolavirus\t|\t\t|\tscientific name\t|\n186541\t|\tTai Forest virus\t|\t\t|\tsynonym\t|\n439488\t|\tssRNA viruses\t|\t\t|\tscientific name\t|\n565995\t|\tBDBV\t|\t\t|\tacronym\t|\n565995\t|\tBundibugyo ebolavirus\t|\t\t|\tscientific name\t|\n565995\t|\tBundibugyo virus\t|\t\t|\tsynonym\t|\n565995\t|\tEbolavirus bundibugyo\t|\t\t|\tsynonym\t|\n" }, { "path": "tests/input/TestMetagenomicsSimple/db/taxonomy/nodes.dmp", "content": "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|\n10239\t|\t1\t|\tsuperkingdom\t|\t\t|\t9\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|\n11157\t|\t35301\t|\torder\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n11266\t|\t11157\t|\tfamily\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n35301\t|\t439488\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n186536\t|\t11266\t|\tgenus\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n186538\t|\t186536\t|\tspecies\t|\tZE\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n186539\t|\t186536\t|\tspecies\t|\tRE\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n186540\t|\t186536\t|\tspecies\t|\tSE\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n186541\t|\t186536\t|\tspecies\t|\tTF\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n439488\t|\t10239\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n565995\t|\t186536\t|\tspecies\t|\tBE\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n" }, { "path": "tests/input/TestMetagenomicsSimple/zaire_ebola.1.fastq", "content": "@gi|10313991|ref|NC_002549.1|_10362_10852_0:0:0_5:0:0_0/1\nCGACATGTAGAGCATCCAAATTTTTAATAAACTTGAGACTATTGGATCGAATCAACGACCGCATTTTTAGGCTCAATTGTACCTTGACACGTTGTGTTCGCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15762_16228_1:0:1_1:0:0_1/1\nCTCATTCGATAATCCATTTTTCCAAGGTAAACGGCTGAACATTATAGAATAGATGATCTTATTCGCCTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11931_12413_0:0:0_0:0:0_2/1\nTCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAACACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4003_4599_1:0:0_2:0:0_3/1\nCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAACGCTTGCGTCCAGTCCCACCATCGCCCAAGATTGATCGAGGTTGGGTAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14754_15169_1:0:0_0:0:0_4/1\nTTGATCCAATGTATGGGATTCCATCCCCGATAGTCCAGCTTATTCGGGATGCGTTCGGCCATGCACTAACAATATGTTTCTTGACTGCCACTGACACGAATG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13715_14227_2:0:0_2:0:0_5/1\nAACCTTTATTGAACCCGAGATGATGATATTGCAAGATTCTCACCGAAAAAAACGTATGGAACGCTGCGGTTATCCTGCAATGAAAGATATGTCGTGTCTCAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4686_5203_2:0:0_0:0:0_6/1\nGTCATTATTGCTTGGATTTTCTCCGGAGATGTTAGATCGGCACTGTTCCCCTTCTTCCCACTTTTGTTGGGTAAAAGAATGGGGCGAAGTTTTGGATGAAAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15756_16318_1:0:1_0:0:0_7/1\nGATATACTATCCATAAAGGGACAATTGTTCCGCGATTAATTATCCATTCTTTTACAAATGTAAGAAAAGATGAAATGGACGTTCTCAAAAATAACCTGGCCG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10034_10501_2:0:0_2:0:0_8/1\nAGATACGCCACACAAGTGTCTCTAAGCTAAATTGGTCTGTACACATCCCATACATTGTATTAGGGGCAATAATATCTAATTGCACTTAGCCGTTTAAAATTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5357_5868_2:0:0_4:0:0_9/1\nTGGGTAGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGAGATTGAGAAGTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7324_7712_4:0:0_0:0:0_a/1\nGCCAAAAGCAGAGAACACCAACACGAGCAAGCGCACTGACTTCCTGGACGCCGCCACCACAACAAGTCCCCAAAACGACAGCGAGACCGCTGGCAACAACAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14867_15301_1:0:0_1:0:0_b/1\nTTATTAGCAAGTCACTGTTCGAACTGCCTTGAGTTACCCATGTTAAACGGGACGCCAATTCAATGGCCTCTCTTAAGGCTGGGGAAGGACATTTTGGTTTAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2491_3004_4:0:0_5:1:0_c/1\nGCCTGTAGTTTACAGTACCAGTTATGGCAAAGAGTACACGTATCCAGACTCCCTTGAAGAGGAATATCCACCCTGGCTCACTGACAAAGAGGCTATGAATGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11709_12286_2:0:0_3:0:0_d/1\nCGTCGGCAGTAGAAACAGAAACAAAGTGTGTATGCCCTTGAACCGCTTCTTAGAATACTGATTCCTGATACCAGTCCATAGCAGCATGGGGGATTCCTTGTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12245_12709_3:0:0_1:0:0_e/1\nGCCCCCAGTGTTTTTGAATGGAAAATAGCTCACAAAGTTGTTGTGGCGTCATCTCCAGCCTTATCAATGTTCTATGGAATTCACGGATCTTTTGATCCTGTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10110_10593_2:0:0_3:0:0_f/1\nCGGATTTTGAAATAAATGAGGAAAGAGATTCCTTGTCATTGACCATGCAGGGGCAAAGTCATTAGTTTTCAGTCAATGCCATAGGTCCATTCCTTTGTGAGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5082_5545_2:0:0_2:0:0_10/1\nCTCCTCTAATGGACGGATTACTAAATAGATGTTATCACTATCCCTGAGACGATTCTATAAAACTGGATCTTAGTCAATTATTGCAATTACTTCTCAATCACA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17955_18488_1:1:0_5:0:0_11/1\nAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATACTGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTAATTAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7196_7578_0:0:0_4:0:2_12/1\nTTAGGGTTGCAATTGGGTTGAGCATTGACAATTTCTTCTCTTCGAGTTCTTCTCCCGCCTGTGATCACCTGCGACTGCAGCAATAGTATTGGTCATTAAGCC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6892_7455_3:0:0_2:0:0_13/1\nTCGGGGAGATGTCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGTTGTATCAAACGGAGCCAAAAACATCAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10430_10922_1:0:0_1:0:0_14/1\nGTTCGAGTTATGATGATTGTATGATTTTGAGTTCCAATTTCAATACTGCTCAACAATCCGTTGTAGTTCACGACATGTAGAGCATCCCATTTGTTAATAAAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13242_13711_2:1:0_2:0:0_15/1\nGAAAGAGTTGAATGTAGGTAGAACCTTCGGAAAATTGCGTTATCCGACTCGCAATGTTCAAACACTTTGTGAACCTCTGATAGCTGATGGTCTTGCTAAAGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11689_12287_0:0:0_2:0:0_16/1\nCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACCAAGTTCTTGAGTGATGTACCAGTGGCGACA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11181_11646_2:0:0_5:0:0_17/1\nACATTGGTCCAATACAATTGGTGAAGATAACCTCGCTTCTGGGTATTGGGTATGTTGTGTAGCCATTTAAAATCAAGAGTAAGAATTTCAACTGCTTCATCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17689_18218_2:0:0_5:0:0_18/1\nATCCCATACTGGCTAAGTGATTTAACTCAGTATGCTGACTGTGAGTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6823_7340_1:0:0_4:0:0_19/1\nCAAGTGGGAAAAGGAGCAATACCACGGGAAAACTCATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9594_10146_2:0:0_2:0:0_1a/1\nATTTATGCACTAAATTTTAAACGGCTAAGTTCAATTAGATATTATTGCCCCTAATACAATGTATGTGATGTGTACAGACCAATTTAGCTTAGAGAGACTTTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14066_14537_3:0:0_2:0:0_1b/1\nTGGCGCAGAAATGAAGTTAAGTCTTTCGACCCAGGGACATTTAATCCGCTAGGATTTAGCCCAAAGTCAATGGCAGTGCAGTTCCCAGGGTTCTTCGCAATT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10897_11452_2:0:0_2:0:0_1c/1\nTTCGTAATATATAGAATCTGTGAAACGTAACACATGTGACCTGCGGGTTCAGTTACAATTAACCATTTAGTATATAGGATTTCTGGTGATAAAATGCTTATT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16074_16594_4:0:0_1:0:0_1d/1\nTATGACCATCACTGTTGTTTGTGCTTGATGCAGTTGAAGAGTCTCTTGCCAAGTATTTTCGGTTGCTGTTTCTGTGTCTGCTCCTCCAGTACGCCAATGATG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12408_12931_0:0:0_2:0:0_1e/1\nTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14051_14574_0:0:0_1:0:0_1f/1\nCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGCACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_1538_2036_3:0:0_1:0:0_20/1\nAATGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCATGAAAAGAAAATTCTTATTAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14954_15496_1:0:0_2:0:0_21/1\nCACCTCCTGAAAACTCACCTAAAGTGTTTGTAGAAACAATCAATCGCGTTGCTGAATTACTCATACGAATGGCCCTGAAAGAATGAGGACTGTATTGATCGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15843_16395_4:0:0_1:0:0_22/1\nTGATGAAACATGCACCAGCAGTTCTACGATCTGATAGAGAAAATTATTCACAGGTGTTGGGTTTTGACCCTCTAGCGGATATACTATCCATAAAGGGACAAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_112_638_0:0:0_1:0:0_23/1\nTTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGATAGAGAACAACCTAGGTCTCCGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7088_7662_0:0:0_2:0:0_24/1\nAATCCCTCGGCTGCTGGCCCGAAATATGGTATCCAGGCCAGTCCGATTGCAGCACCTTCATCCTGAGTAGTCCAGAAATGTAAATTAGGGTTGCATTTGGGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15221_15694_2:0:0_2:0:0_25/1\nCATCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACATTGACTTGCTAATAAAACCATTTTTGGAAGCACGAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9871_10361_2:0:0_0:0:0_26/1\nAATGCTAAAGTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCCCCCAGAGGCATTCTTCATCTCCTTTTAGCAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9314_9818_2:0:1_1:0:0_27/1\nATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCAAGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTAAATAACCTCTCTACTTGATC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6318_6789_0:0:0_1:0:0_28/1\nCCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17500_17934_3:0:0_3:0:0_29/1\nACGAATCCAGTGATATGTTTGAGTCCGACTTTGTCGCTGTTGATTATAATCATTCGTTAATTCTCGAATCTCTGCTCTAAGATGTGCTAAGTGCTGAGTGAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_1309_1873_5:0:0_2:1:0_2a/1\nTTCGCCGTAGCTTCCATCATCGGTATCAACCACCACATCGGGAATGGTCGTATCCTGTGAGTAAGTCGGATCATCATGTTGATGGCCAGGATTGTCGTCATC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15542_16049_4:0:0_1:0:0_2b/1\nATTATGCCGTTGCACTGTTCGATAAAAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTGCTCAGCTTCATCTAACTAAGTGTTGCACCCGGG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16649_17083_3:0:0_1:0:0_2c/1\nCTGCTAGCGTCACAGCCGACTTGAAACTCTCTATTTCCCAACGGACCTCATCAAGTTTGTAATGCATGGACGAGACTATACCGGTAAATCTACAATAAACTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14204_14547_4:1:0_1:0:0_2d/1\nGCGTACAATCTGGCGCAGAAATGAAGTTAAGTCTTGCGACCCAGGGACATTTAATCCGCTAGGATTTAGCACAAAGTCAATGGCAGTGCAGTTCGCAGGGTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13818_14306_2:0:0_0:1:0_2e/1\nTACTGTTTTATCAGTCTTCCCCTTAGAGACTGACGCATACGCGCAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5740_6258_4:0:0_3:0:0_2f/1\nCACATAGTTTTTGCCCTTATCCTGAAATTGCCTGCCTGCTTACATCTGAGGATAGCCAGTGTGACTTGGATTTGAAATGTGGAGAAAAAATCGGGACCCATT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7037_7561_1:0:0_4:0:0_30/1\nACAACAACTGAAGACCACAAAAACATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTAACAACC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13166_13606_1:0:0_3:0:0_31/1\nAGAATGTTCTTTCCTACGCACAAAAACTCGAGTATCTACTACCACAATATCGGAACTTTTGTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6612_7154_2:0:0_2:0:0_32/1\nGACTTCATCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCCACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGTTTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13034_13513_2:0:0_1:0:0_33/1\nTAAACTCATATCTAAATGCAAGATTGTATTTCTCTAAATCAGTTACAAAGCTACTCCCTCTAACTGTGGCATGTACACCAAAATCATCACTTGTGTGGTGCC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17102_17518_1:0:0_1:0:0_34/1\nCCTTACTAATGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15980_16409_2:0:0_4:0:0_35/1\nAAAGCCTGTTGTCTTGATTAATCATGCACCAGCAGTTCTCCGATCTTAAAGAGAAAATTATTCACAGGTGTTGGGTTTTGACCCTCTAGCGGATATACTATC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5718_6211_3:0:0_2:0:0_36/1\nGACAGTTTGTCACGACAAACTAGTTTGTGGACATCACTAACCTGTAATGTGCTATTGTGGATGACTCCAAGTGGGATGGAAAAAGTTCTTTGGAAAAGGATA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4507_5067_2:0:0_2:0:0_37/1\nTTGGAGTGTCATCGGTCCATGTTGCAGCAGGCAGTGGTTGGGTGATCAGTTTGAGTGCTGTCAAATCAAAGGTGAAATACTGGGGTAGTTGGACTTGCGGCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13979_14474_2:0:0_3:0:0_38/1\nATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTAAAAAGGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15468_15909_0:0:0_3:0:1_39/1\nTGGTTCTGTAGATGAATTGTTGCTATCTGAAATAATTGATTGCATGATGGTCTTGGCTAGCTCCCATCCAGATAAGTGAGGCAGTCGCATAAGCTCATCTAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17365_17889_2:0:0_1:0:0_3a/1\nTAGACAACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAATTGATCTTACACCATATTTATCCTAGCGTATTGAAAGCAGTGGTCCTTAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4529_5011_0:0:0_3:0:0_3b/1\nGCTGTCAAATCAAAGGTGAAATACTGGGGTAGTTGGACTGGCGGAAGAACGAACTCCTGGATGAAAGCCTGGTTACCACTTCGCAGGAGCCTGAGGGGATGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9252_9780_0:0:0_2:0:0_3c/1\nGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3703_4201_6:0:0_1:0:0_3d/1\nTCCCTCAAAGTGATAGGGAGGCAATCAACAATCTAAACAGTACCACATCACTAACTGAGGAAACTTTTGGGAAACCTGCCATTTCGGCAAAGTATTTGAGAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13584_14067_2:0:0_3:0:0_3e/1\nAATTGCATCAGACAATGTTGCCATTCTTGTAGCCGTTTTAAGGGCCTGAGGCAATTGGACCCCATTCACATATTGTTTTTTTCCAAAATAGATAAAACCTGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11303_11748_2:0:0_2:0:0_3f/1\nATCGAATTTCAAACGGTAGATATGTTTCGGGAGTTTACAGTTGCGTAGTTGCGGATTAAGGGAGTCTGATGAATATAACCCGCAAGCTCTAGTGACTAGGTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3848_4203_3:0:0_0:0:0_40/1\nCCAATTAGTACAAGTGATTTGTAAATTGGTAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACACTCGTCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18346_18839_3:0:0_2:0:0_41/1\nAAGGAGTCCCTATATTATATACTATATTTAGCCTCTCTCCCTGCGTGATACTCAAAAAATTCACAATGCAGCATGTGTGACATATTACTGCCGGAATGCATT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3761_4298_3:0:0_1:0:0_42/1\nGGAAAATTTTGTGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCGACCAATTAGTACACGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14140_14694_2:0:0_3:1:0_43/1\nATCTTTCCTTGCAGGATAACCGCATCTTTCCATACGTTTTTTTCGGTGAGAATCTTGCAATATCATCATCTCGGGTTCAATAAAGGTTTTGACCTTGGACAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9952_10439_3:0:0_3:0:0_44/1\nTCTTCATCTCCTATTAGCAAAGTACTATTTCAGGGTCGTCGAATTAGTGGCACGTCTTTTAGCTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16744_17246_1:0:0_4:0:0_45/1\nTGGTCATTATGGAATTTTGACATAACAGGTATAAGCATCCTAGGAGAAGTCATTCCTGATACTATTTCTGACTCTATACTTGACTCAGTCGCTAGCGTGTTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3643_4087_2:0:0_0:0:0_46/1\nGACCAACACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGTGAGGCATTCAACAATCTAAACAGTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_8369_8867_1:0:0_1:0:0_47/1\nTGACAAGGGAAAGAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGGTCAAAAATT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6226_6670_1:0:0_2:0:0_48/1\nTGAGATCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCGCACCAAAGGTGG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7389_7891_0:0:0_3:0:0_49/1\nGTCCCCAAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2456_2976_1:0:0_0:0:0_4a/1\nTAAGTTATAAAAGCATAATGTAATTTAATTTAGATAAATCGCTAGTTAGAATATTGAGTTACAATTATGGCTATAACTGTGGCTTAACGCCTATTTGCATTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_8060_8538_1:0:0_2:0:0_4b/1\nTGGGCGTCCTCTCTCATATGAAGCATCCATTTAAAAGTTGTCACCACTCACTGTTTAAATTTCTATTGACTTTTTGACCAATGCTTTATGTGTGTTAGGTTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18004_18473_0:0:0_1:0:0_4c/1\nAGTGCAGAGTTTATTATGTTGCGTTACATTCATTGCGGCAGTAATATGTCACACATGCTGCATTGTGAATTTTTTGATTATCACGCAGGGAGAGAGGCTAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_913_1414_1:0:0_1:0:0_4d/1\nTCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAAATCAAGTACATGCAGAGCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9100_9692_2:0:0_2:0:0_4e/1\nGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCATTTTTGAATCTGCACTATGGCAACAATGGGAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9248_9710_3:0:0_1:0:0_4f/1\nTCCATTTAGCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCATATAATGAGGAAGCTTCAACCAACCCGGGGACATGCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18001_18506_2:1:0_1:0:0_50/1\nGCCCAGACCTTTCGTTAAAGCTAAATTATAAAGAGTGCAGAGTTTATTATGTTGCGTTAAATTCATTGCGGCAGTAATATGTCACACATGCTGCATTGTGAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2800_3284_1:0:0_1:0:0_51/1\nTCCTGGATTGTTCTCAATATCACAGAAGATGTCGCTTCCAGGAATTCTTCCGGTCATTAGCTGCTCAGAGATCCAGCCCGAAAGCTCAGGGCCTGGCATTCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10425_10979_3:0:0_2:0:0_52/1\nTAACTTCTTAGTTAGCCAAACTATTCAGGGGTGGACGGTTTATTGGGCTGGTATTGAGTATGATGTGACTCACAAAGGACTGGCCCTATTGCATAGACTGAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12355_12840_3:0:0_1:0:0_53/1\nAAAATAATGTTTGGCAATACTATATTTAAAAACACAGTATGTCTCGAAAATCACTATAGGGCGTAATGCTTTTAGCACCGTAGCATGTTTTTTACCTTTTTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16177_16756_2:0:0_4:0:0_54/1\nAACCACAAGCAGAGTCACTTAGAAAGGACTGGAACGACGGACCCTGGTGCGTGTTTTCATGTGGAATTTTCGTTCTTTTTATTTCATGGCTCCTTTGTAGGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10689_11116_1:0:0_1:0:0_55/1\nAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAAGACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7751_8212_4:0:0_0:0:0_56/1\nTTCCTGAGAGCCACAACTGATCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATATCTTGGTGCAGCGATGGGGCGGCACATGGCACATTCTGGGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12563_13167_0:0:0_2:0:0_57/1\nCTCACTAGAAAAGATTTCTTGCTCTAAAAATTGTTCCGGTACACGTTTAGTACTAAATTTGTGAGGTGGATTATATCCTAGAACATTAGGCTCGAATACTGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6554_7043_3:0:0_1:0:0_58/1\nAGGAACGACTTTCGCTGAAGGTGTCGATGCATTACTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCATGAGAGAGCCGGTCAATGCAAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16027_16579_2:0:0_4:0:0_59/1\nTGTTTGTGCTTGATCCAGATGAAGAGTCTCTTGCCAAGTATTTTCGGTTGCTGTTTCAGTGTCTGCTGCTCCAGTACGCCAATGATGCATGGAAGAAAATGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2878_3350_5:0:0_2:0:0_5a/1\nTGCAAATAGGCGTTAAGCCCCAGTTATAGCCATAATTGTAACTCAAAATTCTAACTAGCGATTAATCTCAATTAAATTACATTCTGCTTTTATAACTTACCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13608_14037_4:0:0_0:0:0_5b/1\nAGCCGTTTTAAGGGACTGAGGCAATTGGACCCCATTCAAATATTGTTTTTTTCCAAAATAGATAAAACCTGAATGTACAAATGTTTCATCAGGTTTTAAAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11348_11900_4:0:0_2:0:0_5c/1\nGTGTACTTAATGATTTCATCTAAGACCTGTTGGCACCGCGGCTCAAGAGGACAGAATCCATTGCCTGACAGTGCCTTGAGAAGAACTGGGACTATGAAATCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_1455_2087_2:0:0_3:0:0_5d/1\nGTACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAAGAACTCAGAGAGGCTGCCACTGAGGCTGAGCAGCAACTCCAACAATATGCAGAGTCTCGCGAAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6969_7495_4:0:0_2:0:0_5e/1\nAATAGTATTGGTAATTAAGCCTAGGTTCCCGCTGCTGGCACTCTCTTCTCCGGTATCTTGGTGATGAGTGTTGTTGTTGCCAGCGGTCTCGCTGTGTTTTTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4103_4480_6:0:0_6:0:0_5f/1\nAAATTTTTAACAATTTTGCTCAACGATTACAAGATGAAGGTTAATGCAAAAACACTCTCACAGCCGAGGTAGGTTTTTCTTAATGTTCATCACTATTGGTTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18236_18768_1:0:0_0:0:0_60/1\nCCTGCCTTTTCTTTTAATTTTATCATTCTGTATGAAATAGTAGCTTACTAGACAAAAATGTTAAGGTTATTACACCTAATCTCTTATTTTACACAAAGATTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9854_10419_4:0:0_0:0:0_61/1\nGTCGCTTAAGACAACCCCTTTCTCCAGGTCCTTTTTGGGCGATATTAGATTGTATCGTCCCGTAGCTTTAGCCATGGTTTTTTCTCAGGTCTTGCTTGGTGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12604_13104_2:0:0_2:0:0_62/1\nAGGTGGATTATATCCTAGACCATTAGGCTCGAATACTTCATCCCAGCATGTCCTTTCTACTGCGGTAGCTCTGTCTTTTATAAAAATACTTAAGTCACTAAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4144_4676_5:0:0_2:0:0_63/1\nTGGTGTGTGGCTGGCATGGTCGATGGTGTCATCGGCAATTGTCCTGAGTGGATTCGATGGAGAGTCCCCATTGACTGACTCCGGTGTCAGGAAGCCTGTATT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n" }, { "path": "tests/input/TestMetagenomicsSimple/zaire_ebola.2.fastq", "content": "@gi|10313991|ref|NC_002549.1|_10362_10852_0:0:0_5:0:0_0/2\nACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGCCAAACTATTCAGGGGTGGAAGGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15762_16228_1:0:1_1:0:0_1/2\nATAACCTGGCCGCATCTGAGAGTCCTCTGTCACCTGCAGCAGCGCCTATGTAAATAGAAAAATGAGGATCAATACTCATTAACCGTGACATAACGCTTGCAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11931_12413_0:0:0_0:0:0_2/2\nTGGTAAAGCATAGACACAATCTTAAAATTGGGATAATCAGAACAAACTGGATCCTCAATCTCTGCTATTTTTGAGATTAGAGTTGTGTTGAATCGACATGTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4003_4599_1:0:0_2:0:0_3/2\nACTCCGGTGTCAGGAAGCCTGTAATGCTGTTGCCACCTCTAGCAATTGTTGAATTTGACCTGACAGGGAATATGGCCTCCATATATTCAGGAGGAGCAGTAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14754_15169_1:0:0_0:0:0_4/2\nCTCTAAGATCATCAACAATAATACAGAGACACCGGTTTTGGACAGACTGATGAAAATAACATTGCAAAGGTGGAGCCTATGGTTTAGTTATCTTGATCATTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13715_14227_2:0:0_2:0:0_5/2\nAACAAACACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGTTGACAATCAGTGCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4686_5203_2:0:0_0:0:0_6/2\nTCATCAGCATTCATCCTTGACGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATATGGCTTCCTCTAGGTGTCGCTGATCAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15756_16318_1:0:1_0:0:0_7/2\nCAATATCTCATTCGATAATCCATTTTTCCAAGGTAAACGGCTGAACATTATAGAATAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTCGCC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10034_10501_2:0:0_2:0:0_8/2\nGTTTGTGAGTCACATCAAACTCAATACCAGCCCAATACACCTTCCACCCCTGAATAGTTTGGCTAACTAAGAAGTTACAGAGGTCGCTTAAGACAACCCCTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5357_5868_2:0:0_4:0:0_9/2\nCTGTACTTGGATTGTGAACAACCTAGAAATGGGTCCCGATTTTTTCTCCACATTTCCAATGCAAGTCACACTGGCTCTCCTCCGATTTAAGCATGCAGGCAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7324_7712_4:0:0_0:0:0_a/2\nTCAACCCACAGATTAAACCATCTTGATTGTGCATTAGCCCCTCTATGTAAATTCCCTCGGCTGCTGGCCCGAAATATGGTATCCAGGCCAGTCCGATTGCAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14867_15301_1:0:0_1:0:0_b/2\nTGGCGGAGGCTTTAACCCAACTAACTTGCACAGTTGATTTAGCACAGATTCTGAGGGAATATTCATGGGCTCATATTTTAGAGGGAAGACCTCTTATTGGAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2491_3004_4:0:0_5:1:0_c/2\nTCTTGTAAATGTTGGGCAGGCTAGTAGGTAAGTTATAAAAGCCTAATGTAATTTAATTTCGATAAATCGCTAGTTAGAATAATGAGTTACAATTATGGCCAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11709_12286_2:0:0_3:0:0_d/2\nCTGTAAACTCCGGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACCAAGTTCTTGCGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12245_12709_3:0:0_1:0:0_e/2\nTTCAATGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACAGAACTGTAATCTCAAAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10110_10593_2:0:0_3:0:0_f/2\nTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCAGGGCTAACACCACCAGGTCAACTCCATTGGCTGAAACGAAGCTTACCTACAACGAACATCACT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5082_5545_2:0:0_2:0:0_10/2\nGCGTTGGGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCACCAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17955_18488_1:1:0_5:0:0_11/2\nAGCTTAATTATAAAGAGTTCAGAGTTTATTATGTTGCGTTAAATTCATTGCGGCAGTAAACTGTGACACATGCTGCATTGTGAATTTTTTGAATATCACGCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7196_7578_0:0:0_4:0:2_12/2\nAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGACAGCACAGCCTCCGACACT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6892_7455_3:0:0_2:0:0_13/2\nCTCTCTTCTCCGGTATCTTGGTGATGAGTGTTGTTGTAGCCAGCGGTCTCGCTGTTGTTTTGGGGACTTGTTGTGGTGGCGGGGTCCAGGAAGTCAGTGCTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10430_10922_1:0:0_1:0:0_14/2\nTCTTAGTTAGCCAAACTATTCAGGGGTGGAAGGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGACTGGCCCTATTGCATAGACTGAAAACTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13242_13711_2:1:0_2:0:0_15/2\nGTCCTTCAATCCCTCCCATATGACCCCTGTATGAACTAGGCCCTTCGGGGGGGTTGTCTCGATTCTCCAGTGTGAGGTTATGAGTTGGATTATAATAATCAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11689_12287_0:0:0_2:0:0_16/2\nACGTCGGCAGTAGAAACAGACACCATGTGTGTATGCCCTTGAACCGCTTCTTTGAATACTGATGCCTGATACCAGTCCATAGCAGCATGGGGGATTCCTTGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11181_11646_2:0:0_5:0:0_17/2\nGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTATAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTAGACACCCTTACAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17689_18218_2:0:0_5:0:0_18/2\nCAATCAAACCTGTAGAGACCATCGGGAAATAAACTCAGAAGCCCTGTCAGCCTATCGATAAGCTTAACTTCAGAAACGTGCCTTCTATGTAAATATAAGGTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6823_7340_1:0:0_4:0:0_19/2\nTTTTCTCTGCTTTTGGGGGTCCGGCTGCGGTGGTGGCAGAGGGAGTGACGGAGGCTGTGCAGTCGTTGTCTGTTCTGCGGTGATGTTGTTCAACTTGAGTTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9594_10146_2:0:0_2:0:0_1a/2\nTAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACTCAACAGGAGGTAGCAACGATCCAACCCATCAAAAAATA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14066_14537_3:0:0_2:0:0_1b/2\nTTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGCACTGCTATTGAGCGATCCATCTCTGAGACACGACCTATCTTTCGTTGCAGGATAACCGCAGCTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10897_11452_2:0:0_2:0:0_1c/2\nCATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTTGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCATGAAGCCTGGGCCGGCGAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16074_16594_4:0:0_1:0:0_1d/2\nAATTCATAATCTACCACATGGGTCATTGCGAATACTTAAGCGAACATTCAAACATGCAAGCGTTATGACACGGTTAATGAGTATTGATCCTCATTTTTCTAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12408_12931_0:0:0_2:0:0_1e/2\nACGGAGGGAATTGATTTCTTTTGATAAAAGAATTAAGACCCGGTGTTAGATTCCTATCTGAAGTAACCCTGTACCAAGATCCTTGACTATCAAAATAATGTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14051_14574_0:0:0_1:0:0_1f/2\nGTTTTTCGCACTTAGGGTGAAGGTCCTGCGTACAATCTGGCGCAGAAATGAAGTTAAGTCTTGCGACCCAGGGACATTTAATCCGCTAGGATTTAGCACAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_1538_2036_3:0:0_1:0:0_20/2\nGTGTCTGTCTGCCGTCTATATGCTGGCCCTTTTGACTGTTCTTCTGTTGTCCACCCTTGGTCGATCTATTAGGCACTGGCTTAGTGTCCTCGTCGTCCTCGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14954_15496_1:0:0_2:0:0_21/2\nGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGTTTTGGCTGAACCCCTACGAACAATGTCCGCAGTGTTCAAATGCAAAGCAAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15843_16395_4:0:0_1:0:0_22/2\nATGGGAGCTAGCCAAGACCATCATGCAAACAATTATTTCAGATAGCAACAATTCATCTACAGACCCACTTAGCAGTGGAGAAACAAGATCATTCACTAGCGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_112_638_0:0:0_1:0:0_23/2\nTGATAAGTTGGCAAATTTCTTCAAGATTGTTTACTTGATACACTGGGATGACTCTTTGGCGAACAATCCCCTGTTGAACGGACAGACCTGCTGTCAAGATCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7088_7662_0:0:0_2:0:0_24/2\nGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTAACAACCCTTGCCACAATCTCCACGAGTCCCCAATCCCTCACAACCAAACCAGGTCCG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15221_15694_2:0:0_2:0:0_25/2\nTTAAATCTAAATCCAATGTAGATGTGTATGTTAAATACTGAGCAGGTACTTGCCGGGTGCAACACTTAGTTAGATGAAGGTGAGCACGATTATATTGGATAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9871_10361_2:0:0_0:0:0_26/2\nCCCGTAGCTTTAGCCATGGTTTTTTCTCAGGTCTTGCTTGGTGTCTGGAGTATCAATATTTTGTTGTCTAGACACTCTCAGTTCAACCTTGAAACCTTGCGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9314_9818_2:0:1_1:0:0_27/2\nATTGATTGTAATATAACAATAGCCAATACCAAACACCTCCTCCACAGCTTTAAGCATAAAGAATTTATGTTCCGTCAGTTTTTCTTAATATTTTAAGAGATC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6318_6789_0:0:0_1:0:0_28/2\nGTGGTGTGAATCTTGATTCAAGTTGGACGTAGGTCAAATTGTCAACCTCGAACAAGTACTCTGTCTCATTGGTTCCAAACCCGGTAGCCTGATATCTAATTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17500_17934_3:0:0_3:0:0_29/2\nCTAAATGATAATTTAGCCCCGTTTTTAGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGGTAGATCTAGTGAGAGGTATCTTTGTCTGACGAACTTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_1309_1873_5:0:0_2:1:0_2a/2\nTAAGTCTGCACTCATCTCCCTGGCCAAGGATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTATGCC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15542_16049_4:0:0_1:0:0_2b/2\nTTGTCAAGTGTTAATTTCTTAGTCCGAAGAATTGTATTGCCAAGATAATAACTTACAAAGGCCCCAAAACTGTACAGAAGTCCTATGTTGGGATAAGTTAAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16649_17083_3:0:0_1:0:0_2c/2\nATCTAGTCCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACACGAAAACACGCACCAGGGTCCGTCGTTCGCGTCCTTTCTAAGTGACTCTGCTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14204_14547_4:1:0_1:0:0_2d/2\nATCATCTCGTGTTGAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAAGCACTGGATTTCGGAACAATATCATTGGCACTAGCGGTCCCGCAGGTGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13818_14306_2:0:0_0:1:0_2e/2\nAGCACCTGCGGGACCGCTAGTGCCAATGATATTGTTCCGAAATCCAGAGGTTTGCCGAGTGTTAACTGTCCAAGGTCAAAACCTTTATTGAACCCGAGATGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5740_6258_4:0:0_3:0:0_2f/2\nCATTCCCTTCGAGATTCAGTCCCACTGATCTCAATTGAATTGTGGATGACAGTTTGTCACGACACACTAGTTTGTCGACATCACTAACCTGTAATGTGCTAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7037_7561_1:0:0_4:0:0_30/2\nTTGAGCATTGACAAATGCTTCTCTTCGAGTTCTTCTCCCGCCTGTGATCAGTCCTGCGACTCCAGCAATAGTATTGGTAATTAAGCCTCGCTAGCCGCTGCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13166_13606_1:0:0_3:0:0_31/2\nCATGCATATAACACTGTGGGATTGTATAATTCATCCAATTAAAAAGATTCTTAACACCATAGCAACGGTTGCACTATTCTATAAAAGGTGCTGTAAACTCAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6612_7154_2:0:0_2:0:0_32/2\nTGGAGATTGTGGCAAGGGTTGTTAGATGCGACACTGCAGCTTCCCTTCCATGACTGTGCACTTGAACCATTGCAGAGGCATTTTCTGAAGCCATGATTTTGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13034_13513_2:0:0_1:0:0_33/2\nGCGCTACCGCAGTAGAAAGGACATGCTGGGATGCAGTATACGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTTAGTACTAAACGTGTACCGGAAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17102_17518_1:0:0_1:0:0_34/2\nGGGCTAAATTATCATTTAGCCATAACATACCCTCAGTATCACTTAGAAAGACTTTAAGGACCACTGCTATCAATACGCTAGGATCAATATGGTGTAAGATCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15980_16409_2:0:0_4:0:0_35/2\nGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACACTTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACTCAAATACATA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_5718_6211_3:0:0_2:0:0_36/2\nCAAATGTTAATCTTTCTCATTGCACATACTTTTTGCCCTTATCCTCAACTTGCCTGCATGCTTACATCTGAGGATAGCCAGTGTGACTTTGATTGTAAATGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4507_5067_2:0:0_2:0:0_37/2\nCTCCTGAAAATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGAGGTGGCAACAGCAATACAGGCTTGCTGACACCGGAGTCAGTCAATG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13979_14474_2:0:0_3:0:0_38/2\nAAGTCAATGGCAGTGCAGTTCCCAGGGTTCTTCGCAATTAAAGGTAATAATAACTCATCCATCTCAATCATTCGGAGATAAGTTTTTAACTGGAATCAGCCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_15468_15909_0:0:0_3:0:1_39/2\nAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_17365_17889_2:0:0_1:0:0_3a/2\nATAATCATTAGTTAATTCTCGAATCTCTGCTCTAAGATGTGCTAAGTGCTGAGTGATAGAGACTCGTGGACCTCTTTTTGAATCGACGAGGTTATACCTGTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4529_5011_0:0:0_3:0:0_3b/2\nATACCCTGTCAGGTCAAATTCAACAATTGCTAGAGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCATCGAATCCACT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9252_9780_0:0:0_2:0:0_3c/2\nCCTCCACAGCTTGAAGCATAAAGAATTTATGTTCCGTCAGTTTTTCTTAATATTTTACGAGATCATTAGTAAGTCATGAAATACTTAATTTTTGATGGGATG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3703_4201_6:0:0_1:0:0_3d/2\nGTTGAAGCCTCTGCTATTATTCGCCTCTTTCGGAGGGAAGGGAGATTGGCTCAAATTTTGAGTCCAAGTGTTTTAGCATCTTGAAGCTGAAAAACACATACC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13584_14067_2:0:0_3:0:0_3e/2\nAATCCCACAGTGTTATATGCATGTCAGTGATTATTATACTCCACCACATAACCTCACACTGGAGAATCGAGACAACCCCCCCGCAGGGCCTAGTTCATACAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11303_11748_2:0:0_2:0:0_3f/2\nTCAAACAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATGAATAAGCATTTTATCACCAGACATCCTATATACAAAATGGTTAATTGTAACTGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3848_4203_3:0:0_0:0:0_40/2\nCAGTTGAAGCCTCTGCTATTATTCGCCTCTTTCGGAGGGAAGGGAGATTGGCTCAAATTTTGAGTCCAAGTGTTTTACCATCTTGAAGCTGAAAAACACATA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18346_18839_3:0:0_2:0:0_41/2\nTAATTATCATTAACACGAAGATTATTAACTAGTCTGCTATATTGTAAAGAAGGTATTTCTGATTTTACAGTCCTGCGTTTTCTTTTAATTTTATCATTCTGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3761_4298_3:0:0_1:0:0_42/2\nTATGAACAATTTTATCTTGGTCGTTTAATTGACTTATAATATCCAGGGCTGATACTCACAAGTGTATCATTAATGTAACGTACCCTATAGTTCAGCAGTTGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_14140_14694_2:0:0_3:1:0_43/2\nCGTGCGTGAAAAGAAATCGGCCGCAAAACGACTCATAACAGGAGTTGATGATAATCTCCATTTACAAACCATTTCGTCTTCGAAGTCAGCTGACGCATCAAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9952_10439_3:0:0_3:0:0_44/2\nCTAACTAAGAAGTTACCGAGGTCGCTTAAGACAACCCCTTTCTCCAGGTCCTTTTTGGGCGATATTAGATTGTATGGTCCCGTAGCTTTATCCATGGTTTTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16744_17246_1:0:0_4:0:0_45/2\nTCTGCTTGTGGTACAGCAAATCCAAAACTAAATTTCGATCGATCGAGACACAATGTGAAATTTCAGGATCATAACTCTGCATCCAAGAGGGAAGGTCATCAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_3643_4087_2:0:0_0:0:0_46/2\nATCTTGGGCGATGGTGGGACTGGACGCAAGCTTTTCTGGCAAGCTCGGGGAATGTCACCTCGAGAGCGGATGTGGATGACAGGTGGAGCAGCATCTTGGAAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_8369_8867_1:0:0_1:0:0_47/2\nGCAGTTATAATTAATTGTTGTTCTACTGATCCACAAGTCTTACGGGCGATTAGTAGGAGTAATTCCCTATCAGTTAAACTCTCCAACTGGTGATCTTTTTTG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6226_6670_1:0:0_2:0:0_48/2\nCTAGACGGGTCCTCCGTTGCATTGACCGGCTCTCTCAAGGGGTGTGAGCTGAAGAAGTCCTTCATAGCTTGGGTCAGTATCAGAAATGCAACGACACCTTCA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7389_7891_0:0:0_3:0:0_49/2\nGTTCTTGGTCCAATCATGTGGTTCTATACAGCAGTCCGGTCCCAGAATGTGGCATGTGCCTCCCCCTCGCTGCAGCAAGAAATCAATTGCCTTACGGTTGAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2456_2976_1:0:0_0:0:0_4a/2\nGATGCTGTTTTGTATTATCATATGATGCAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAAAGAGTACACGTATCCAGACTCCCTTGAAGAGGAATAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_8060_8538_1:0:0_2:0:0_4b/2\nGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGAAAAGCTCAGCCTCAAATCAATGACACCAGGATTTAATTATATGGATTACTTGAATCTAAGATTACTTGA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18004_18473_0:0:0_1:0:0_4c/2\nAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTACCATATTAGAGATTGCAATTGTGAAGAACGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_913_1414_1:0:0_1:0:0_4d/2\nTTGAGGGAAAAGACCATGCTCAAGATTATTTACTCCAGAAAGGTTGAAAAGTCGGGCGAAAGGAGCATACTCTCCATGCTTGGCCAGGGAGCTGAGTGCAGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9100_9692_2:0:0_2:0:0_4e/2\nTTTTTGATGGGATGGATCGTTGCTACCTCCTGTAGAGTAAAACATTATTTTTGTACAAGAATCACTTTGTGCAAGAGGTATGCTTGGCAGGTTATATTACTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9248_9710_3:0:0_1:0:0_4f/2\nAAGTCATGAAATACTTATTTTTTGATGGGATGGATCGTTGCTACCTCCTGTAGAGTAAAACCTTATTTGTGTACAAGAATCACTTTGTGCAAGAGGTATGCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18001_18506_2:1:0_1:0:0_50/2\nTTAAAACATAATGGGACATGGCCAGCTGAGTTTAAGAAATTACCAGAGTTAATTAGTGTGTGCAATAGGTTCTACCATATTAGATATTGCAATTGTGAAGAA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2800_3284_1:0:0_1:0:0_51/2\nTAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATTCAAATAGGCGTTAAGCCACAGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10425_10979_3:0:0_2:0:0_52/2\nATGCGGTTCATTGCCGATTTGTCGGGTTCTTGGAGCTCCACCCGAAAACCCATGTTAGTTCGAGTTATGATGATTGTATGATTTTGAGTTGCAATTTCAATA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12355_12840_3:0:0_1:0:0_53/2\nATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTTTGTCTATGCTTTACCAGAGCGGAGATTACATACTCTCCCTATTAGGGTCTGATGGGTAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16177_16756_2:0:0_4:0:0_54/2\nTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCGAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAAGCATGGATA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_10689_11116_1:0:0_1:0:0_55/2\nAAGTATTCTACCTTAGTTAGCTAGCAAGAGAGCTATTAAATTCAAGAATCAAACTTTGCATTCGTGTCGAGGATCCTTGTGTAAATGCTTTCAGTGTGGACT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_7751_8212_4:0:0_0:0:0_56/2\nTAGAATCACATTGGCTATGTTTAAAGCTCCAGTGTATTATATTATCATTTGTCAAGTAATCTTAGATTCAAGTAATCCATATAATTAAATCCTGGTTTCATT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12563_13167_0:0:0_2:0:0_57/2\nATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTAAAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6554_7043_3:0:0_1:0:0_58/2\nTTGTTGTGTTGGTCCCTGGGTCGGAAGAAGTTCGCGCCGGACTCTGACCACTGATGTTTTTGGCTCCGTTAGATACAACTGTGAAAGACAACTCTTCACTGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_16027_16579_2:0:0_4:0:0_59/2\nACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACAACTCAAATTCATAATCTAGCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACAT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_2878_3350_5:0:0_2:0:0_5a/2\nTTGGGTTTGACTGTTGCGCGTCTTCGGGTTTGGCTTCGTTTGTTGCATTTGGGATGCGTAGCATAATCCTGGATTGTTGTCAATATCACAGAAGCTGTCGCT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_13608_14037_4:0:0_0:0:0_5b/2\nCAGTGATTATTATAATCCACCACATAACCTCACACTGGAGAATCGAGACAAGCCCCCCGACGGTCCTAGTTCATCCAGGGGTCATATGGGAGGGATTGAAGG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_11348_11900_4:0:0_2:0:0_5c/2\nATGAATAAGCATTTTATCACCAGAACACCTATATACTCAATGGTTAATTGTAACTGAACCCGCAGGTCACATGTGTTAGGTTTCACAGATACTATATATTAC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_1455_2087_2:0:0_3:0:0_5d/2\nCGTGGTGGATTGTTCTGTTAGGTCCTGGGACATTTTGAATTGGCCTGGATTGTGTCTGTCTGCCGTCTATATGCTGGCCCTTTTGACTGTTCTTCTGTTGTC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_6969_7495_4:0:0_2:0:0_5e/2\nTATCAAACGGAGCCAAAAAGATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGTGACCAACCCAACAACTGAAGACCACAAAATCATGTCTTCAG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4103_4480_6:0:0_6:0:0_5f/2\nATGAGTTTTTCAGCTTGAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCCCTTCCGTCGGAACGAGGCGAATAATAGGAGAGGCTTCAACTGC\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_18236_18768_1:0:0_0:0:0_60/2\nTCCTGATACTTGCAAAGGTTGGTTATTAACCTACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCTAATCTCAATAAACAACTATTTA\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_9854_10419_4:0:0_0:0:0_61/2\nGGTAGATTGTGACCGGAAATGCTAAACTAATGATGAAGATTAATGCGGAGGACAGAAAAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTGTT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_12604_13104_2:0:0_2:0:0_62/2\nCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAATGCTGGAGATGACGGCACAACAACTTTGTGAGCTATTTTCCATTCAAAAACACTGG\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n@gi|10313991|ref|NC_002549.1|_4144_4676_5:0:0_2:0:0_63/2\nAAATTTGAGCCAATCTCCCTTCCCTCCGAAAGAGGCGAATAATAGCAGAGTCTTCAACTGCTGAACAATAGGGTACGTTCCATTACTGATACACTTGTGCGT\n+\n222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/Viruses/Enterovirus_C/GCF_000861165.1_ViralProj15288_genomic.fna", "content": ">NC_002058.3 Poliovirus, complete genome\nTTAAAACAGCTCTGGGGTTGTACCCACCCCAGAGGCCCACGTGGCGGCTAGTACTCCGGTATTGCGGTACCCTTGTACGC\nCTGTTTTATACTCCCTTCCCGTAACTTAGACGCACAAAACCAAGTTCAATAGAAGGGGGTACAAACCAGTACCACCACGA\nACAAGCACTTCTGTTTCCCCGGTGATGTCGTATAGACTGCTTGCGTGGTTGAAAGCGACGGATCCGTTATCCGCTTATGT\nACTTCGAGAAGCCCAGTACCACCTCGGAATCTTCGATGCGTTGCGCTCAGCACTCAACCCCAGAGTGTAGCTTAGGCTGA\nTGAGTCTGGACATCCCTCACCGGTGACGGTGGTCCAGGCTGCGTTGGCGGCCTACCTATGGCTAACGCCATGGGACGCTA\nGTTGTGAACAAGGTGTGAAGAGCCTATTGAGCTACATAAGAATCCTCCGGCCCCTGAATGCGGCTAATCCCAACCTCGGA\nGCAGGTGGTCACAAACCAGTGATTGGCCTGTCGTAACGCGCAAGTCCGTGGCGGAACCGACTACTTTGGGTGTCCGTGTT\nTCCTTTTATTTTATTGTGGCTGCTTATGGTGACAATCACAGATTGTTATCATAAAGCGAATTGGATTGGCCATCCGGTGA\nAAGTGAGACTCATTATCTATCTGTTTGCTGGATCCGCTCCATTGAGTGTGTTTACTCTAAGTACAATTTCAACAGTTATT\nTCAATCAGACAATTGTATCATAATGGGTGCTCAGGTTTCATCACAGAAAGTGGGCGCACATGAAAACTCAAATAGAGCGT\nATGGTGGTTCTACCATTAATTACACCACCATTAATTATTATAGAGATTCAGCTAGTAACGCGGCTTCGAAACAGGACTTC\nTCTCAAGACCCTTCCAAGTTCACCGAGCCCATCAAGGATGTCCTGATAAAAACAGCCCCAATGCTAAACTCGCCAAACAT\nAGAGGCTTGCGGGTATAGCGATAGAGTACTGCAATTAACACTGGGAAACTCCACTATAACCACACAGGAGGCGGCTAATT\nCAGTAGTCGCTTATGGGCGTTGGCCTGAATATCTGAGGGACAGCGAAGCCAATCCAGTGGACCAGCCGACAGAACCAGAC\nGTCGCTGCATGCAGGTTTTATACGCTAGACACCGTGTCTTGGACGAAAGAGTCGCGAGGGTGGTGGTGGAAGTTGCCTGA\nTGCACTGAGGGACATGGGACTCTTTGGGCAAAATATGTACTACCACTACCTAGGTAGGTCCGGGTACACCGTGCATGTAC\nAGTGTAACGCCTCCAAATTCCACCAGGGGGCACTAGGGGTATTCGCCGTACCAGAGATGTGTCTGGCCGGGGATAGCAAC\nACCACTACCATGCACACCAGCTATCAAAATGCCAATCCTGGCGAGAAAGGAGGCACTTTCACGGGTACGTTCACTCCTGA\nCAACAACCAGACATCACCTGCCCGCAGGTTCTGCCCGGTGGATTACCTCCTTGGAAATGGCACGTTGTTGGGGAATGCCT\nTTGTGTTCCCGCACCAGATAATAAACCTACGGACCAACAACTGTGCTACACTGGTACTCCCTTACGTGAACTCCCTCTCG\nATAGATAGTATGGTAAAGCACAATAATTGGGGAATTGCAATATTACCATTGGCCCCATTAAATTTTGCTAGTGAGTCCTC\nCCCAGAGATTCCAATCACCTTGACCATAGCCCCTATGTGCTGTGAGTTCAATGGATTAAGAAACATCACCCTGCCACGCT\nTACAGGGCCTGCCGGTCATGAACACCCCTGGTAGCAATCAATATCTTACTGCAGACAACTTCCAGTCACCGTGTGCGCTG\nCCTGAATTTGATGTGACCCCACCTATTGACATACCCGGTGAAGTAAAGAACATGATGGAATTGGCAGAAATCGACACCAT\nGATTCCCTTTGACTTAAGTGCCACAAAAAAGAACACCATGGAAATGTATAGGGTTCGGTTAAGTGACAAACCACATACAG\nACGATCCCATACTCTGCCTGTCACTCTCTCCAGCTTCAGATCCTAGGTTGTCACATACTATGCTTGGAGAAATCCTAAAT\nTACTACACACACTGGGCAGGATCCCTGAAGTTCACGTTTCTGTTCTGTGGATTCATGATGGCAACTGGCAAACTGTTGGT\nGTCATACGCGCCTCCTGGAGCCGACCCACCAAAGAAGCGTAAGGAGGCGATGTTGGGAACACATGTGATCTGGGACATAG\nGACTGCAGTCCTCATGTACTATGGTAGTGCCATGGATTAGCAACACCACGTATCGGCAAACCATAGATGATAGTTTCACC\nGAAGGCGGATACATCAGCGTCTTCTACCAAACTAGAATAGTCGTCCCTCTTTCGACACCCAGAGAGATGGACATCCTTGG\nTTTTGTGTCAGCGTGTAATGACTTCAGCGTGCGCTTGTTGCGAGATACCACACATATAGAGCAAAAAGCGCTAGCACAGG\nGGTTAGGTCAGATGCTTGAAAGCATGATTGACAACACAGTCCGTGAAACGGTGGGGGCGGCAACATCTAGAGACGCTCTC\nCCAAACACTGAAGCCAGTGGACCAACACACTCCAAGGAAATTCCGGCACTCACCGCAGTGGAAACTGGGGCCACAAATCC\nACTAGTCCCTTCTGATACAGTGCAAACCAGACATGTTGTACAACATAGGTCAAGGTCAGAGTCTAGCATAGAGTCTTTCT\nTCGCGCGGGGTGCATGCGTGACCATTATGACCGTGGATAACCCAGCTTCCACCACGAATAAGGATAAGCTATTTGCAGTG\nTGGAAGATCACTTATAAAGATACTGTCCAGTTACGGAGGAAATTGGAGTTCTTCACCTATTCTAGATTTGATATGGAACT\nTACCTTTGTGGTTACTGCAAATTTCACTGAGACTAACAATGGGCATGCCTTAAATCAAGTGTACCAAATTATGTACGTAC\nCACCAGGCGCTCCAGTGCCCGAGAAATGGGACGACTACACATGGCAAACCTCATCAAATCCATCAATCTTTTACACCTAC\nGGAACAGCTCCAGCCCGGATCTCGGTACCGTATGTTGGTATTTCGAACGCCTATTCACACTTTTACGACGGTTTTTCCAA\nAGTACCACTGAAGGACCAGTCGGCAGCACTAGGTGACTCCCTTTATGGTGCAGCATCTCTAAATGACTTCGGTATTTTGG\nCTGTTAGAGTAGTCAATGATCACAACCCGACCAAGGTCACCTCCAAAATCAGAGTGTATCTAAAACCCAAACACATCAGA\nGTCTGGTGCCCGCGTCCACCGAGGGCAGTGGCGTACTACGGCCCTGGAGTGGATTACAAGGATGGTACGCTTACACCCCT\nCTCCACCAAGGATCTGACCACATATGGATTCGGACACCAAAACAAAGCGGTGTACACTGCAGGTTACAAAATTTGCAACT\nACCACTTGGCCACTCAGGATGATTTGCAAAACGCAGTGAACGTCATGTGGAGTAGAGACCTCTTAGTCACAGAATCAAGA\nGCCCAGGGCACCGATTCAATCGCAAGGTGCAATTGCAACGCAGGGGTGTACTACTGCGAGTCTAGAAGGAAATACTACCC\nAGTATCCTTCGTTGGCCCAACGTTCCAGTACATGGAGGCTAATAACTATTACCCAGCTAGGTACCAGTCCCATATGCTCA\nTTGGCCATGGATTCGCATCTCCAGGGGATTGTGGTGGCATACTCAGATGTCACCACGGGGTGATAGGGATCATTACTGCT\nGGTGGCGAAGGGTTGGTTGCATTTTCAGACATTAGAGACTTGTATGCCTACGAAGAAGAAGCCATGGAACAAGGCATCAC\nCAATTACATAGAGTCACTTGGGGCCGCATTTGGAAGTGGATTTACTCAGCAGATTAGCGACAAAATAACAGAGTTGACCA\nATATGGTGACCAGTACCATCACTGAAAAGCTACTTAAGAACTTGATCAAGATCATATCCTCACTAGTTATTATAACTAGG\nAACTATGAAGACACCACAACAGTGCTCGCTACCCTGGCCCTTCTTGGGTGTGATGCTTCACCATGGCAGTGGCTTAGAAA\nGAAAGCATGCGATGTTCTGGAGATACCTTATGTCATCAAGCAAGGTGACAGTTGGTTGAAGAAGTTTACTGAAGCATGCA\nACGCAGCTAAGGGACTGGAGTGGGTGTCAAACAAAATCTCAAAATTCATTGATTGGCTCAAGGAGAAAATTATCCCACAA\nGCTAGAGATAAGTTGGAATTTGTAACAAAACTTAGACAACTAGAAATGCTGGAAAACCAAATCTCAACTATACACCAATC\nATGCCCTAGTCAGGAACACCAGGAAATTCTATTCAATAATGTCAGATGGTTATCCATCCAGTCTAAGAGGTTTGCCCCTC\nTTTACGCAGTGGAAGCCAAAAGAATACAGAAACTAGAGCATACTATTAACAACTACATACAGTTCAAGAGCAAACACCGT\nATTGAACCAGTATGTTTGCTAGTACATGGCAGCCCCGGAACAGGTAAATCTGTAGCAACCAACCTGATTGCTAGAGCCAT\nAGCTGAAAGAGAAAACACGTCCACGTACTCGCTACCCCCGGATCCATCACACTTCGACGGATACAAACAACAGGGAGTGG\nTGATTATGGACGACCTGAATCAAAACCCAGATGGTGCGGACATGAAGCTGTTCTGTCAGATGGTATCAACAGTGGAGTTT\nATACCACCCATGGCATCCCTGGAGGAGAAAGGAATCCTGTTTACTTCAAATTACGTTCTAGCATCCACAAACTCAAGCAG\nAATTTCCCCCCCCACTGTGGCACACAGTGATGCATTAGCCAGGCGCTTTGCGTTCGACATGGACATTCAGGTCATGAATG\nAGTATTCTAGAGATGGGAAATTGAACATGGCCATGGCTACTGAAATGTGTAAGAACTGTCACCAACCAGCAAACTTTAAG\nAGATGCTGTCCTTTAGTGTGTGGTAAGGCAATTCAATTAATGGACAAATCTTCCAGAGTTAGATACAGTATTGACCAGAT\nCACTACAATGATTATCAATGAGAGAAACAGAAGATCCAACATTGGCAATTGTATGGAGGCTTTGTTTCAAGGACCACTCC\nAGTATAAAGACTTGAAAATTGACATCAAGACGAGTCCCCCTCCTGAATGTATCAATGACTTGCTCCAAGCAGTTGACTCC\nCAGGAGGTGAGAGATTACTGTGAGAAGAAGGGTTGGATAGTCAACATCACCAGCCAGGTTCAAACAGAAAGGAACATCAA\nCAGGGCAATGACAATTCTACAAGCGGTGACAACCTTCGCCGCAGTGGCTGGAGTTGTCTATGTCATGTATAAACTGTTTG\nCTGGACACCAGGGAGCATACACTGGTTTACCAAACAAAAAACCCAACGTGCCCACCATTCGGACAGCAAAGGTACAAGGA\nCCAGGGTTCGATTACGCAGTGGCTATGGCTAAAAGAAACATTGTTACAGCAACTACTAGCAAGGGAGAGTTCACTATGTT\nAGGAGTCCACGACAACGTGGCTATTTTACCAACCCACGCTTCACCTGGTGAAAGCATTGTGATCGATGGCAAAGAAGTGG\nAGATCTTGGATGCCAAAGCGCTCGAAGATCAAGCAGGAACCAATCTTGAAATCACTATAATCACTCTAAAGAGAAATGAA\nAAGTTCAGAGACATTAGACCACATATACCTACTCAAATCACTGAGACAAATGATGGAGTCTTGATCGTGAACACTAGCAA\nGTACCCCAATATGTATGTTCCTGTCGGTGCTGTGACTGAACAGGGATATCTAAATCTCGGTGGGCGCCAAACTGCTCGTA\nCTCTAATGTACAACTTTCCAACCAGAGCAGGACAGTGTGGTGGAGTCATCACATGTACTGGGAAAGTCATCGGGATGCAT\nGTTGGTGGGAACGGTTCACACGGGTTTGCAGCGGCCCTGAAGCGATCATACTTCACTCAGAGTCAAGGTGAAATCCAGTG\nGATGAGACCTTCGAAGGAAGTGGGATATCCAATCATAAATGCCCCGTCCAAAACCAAGCTTGAACCCAGTGCTTTCCACT\nATGTGTTTGAAGGGGTGAAGGAACCAGCAGTCCTCACTAAAAACGATCCCAGGCTTAAGACAGACTTTGAGGAGGCAATT\nTTCTCCAAGTACGTGGGTAACAAAATTACTGAAGTGGATGAGTACATGAAAGAGGCAGTAGACCACTATGCTGGCCAGCT\nCATGTCACTAGACATCAACACAGAACAAATGTGCTTGGAGGATGCCATGTATGGCACTGATGGTCTAGAAGCACTTGATT\nTGTCCACCAGTGCTGGCTACCCTTATGTAGCAATGGGAAAGAAGAAGAGAGACATCTTGAACAAACAAACCAGAGACACT\nAAGGAAATGCAAAAACTGCTCGACACATATGGAATCAACCTCCCACTGGTGACTTATGTAAAGGATGAACTTAGATCCAA\nAACAAAGGTTGAGCAGGGGAAATCCAGATTAATTGAAGCTTCTAGTTTGAATGACTCAGTGGCAATGAGAATGGCTTTTG\nGGAACCTATATGCTGCTTTTCACAAAAACCCAGGAGTGATAACAGGTTCAGCAGTGGGGTGCGATCCAGATTTGTTTTGG\nAGCAAAATTCCGGTATTGATGGAAGAGAAGCTGTTTGCTTTTGACTACACAGGGTATGATGCATCTCTCAGCCCTGCTTG\nGTTCGAGGCACTAAAGATGGTGCTTGAGAAAATCGGATTCGGAGACAGAGTTGACTACATCGACTACCTAAACCACTCAC\nACCACCTGTACAAGAATAAAACATACTGTGTCAAGGGCGGTATGCCATCTGGCTGCTCAGGCACTTCAATTTTTAACTCA\nATGATTAACAACTTGATTATCAGGACACTCTTACTGAAAACCTACAAGGGCATAGATTTAGACCACCTAAAAATGATTGC\nCTATGGTGATGATGTAATTGCTTCCTACCCCCATGAAGTTGACGCTAGTCTCCTAGCCCAATCAGGAAAAGACTATGGAC\nTAACTATGACTCCAGCTGACAAATCAGCTACATTTGAAACAGTCACATGGGAGAATGTAACATTCTTGAAGAGATTCTTC\nAGGGCAGACGAGAAATACCCATTTCTTATTCATCCAGTAATGCCAATGAAGGAAATTCATGAATCAATTAGATGGACTAA\nAGATCCTAGGAACACTCAGGATCACGTTCGCTCTCTGTGCCTTTTAGCTTGGCACAATGGCGAAGAAGAATATAACAAAT\nTCCTAGCTAAAATCAGGAGTGTGCCAATTGGAAGAGCTTTATTGCTCCCAGAGTACTCAACATTGTACCGCCGTTGGCTT\nGACTCATTTTAGTAACCCTACCTCAGTCGAATTGGATTGGGTCATACTGTTGTAGGGGTAAATTTTTCTTTAATTCGGAG\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/Viruses/Enterovirus_C/GCF_000861165.1_ViralProj15288_protein.faa", "content": ">NP_041277.1 genome polyprotein [Enterovirus C]\nMGAQVSSQKVGAHENSNRAYGGSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVLIKTAPMLNSPNIEACGYSD\nRVLQLTLGNSTITTQEAANSVVAYGRWPEYLRDSEANPVDQPTEPDVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGL\nFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGTFTPDNNQTSPA\nRRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITL\nTIAPMCCEFNGLRNITLPRLQGLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSA\nTKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFLFCGFMMATGKLLVSYAPPGA\nDPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACND\nFSVRLLRDTTHIEQKALAQGLGQMLESMIDNTVRETVGAATSRDALPNTEASGPTHSKEIPALTAVETGATNPLVPSDTV\nQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTAN\nFTETNNGHALNQVYQIMYVPPGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKDQS\nAALGDSLYGAASLNDFGILAVRVVNDHNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTT\nYGFGHQNKAVYTAGYKICNYHLATQDDLQNAVNVMWSRDLLVTESRAQGTDSIARCNCNAGVYYCESRRKYYPVSFVGPT\nFQYMEANNYYPARYQSHMLIGHGFASPGDCGGILRCHHGVIGIITAGGEGLVAFSDIRDLYAYEEEAMEQGITNYIESLG\nAAFGSGFTQQISDKITELTNMVTSTITEKLLKNLIKIISSLVIITRNYEDTTTVLATLALLGCDASPWQWLRKKACDVLE\nIPYVIKQGDSWLKKFTEACNAAKGLEWVSNKISKFIDWLKEKIIPQARDKLEFVTKLRQLEMLENQISTIHQSCPSQEHQ\nEILFNNVRWLSIQSKRFAPLYAVEAKRIQKLEHTINNYIQFKSKHRIEPVCLLVHGSPGTGKSVATNLIARAIAERENTS\nTYSLPPDPSHFDGYKQQGVVIMDDLNQNPDGADMKLFCQMVSTVEFIPPMASLEEKGILFTSNYVLASTNSSRISPPTVA\nHSDALARRFAFDMDIQVMNEYSRDGKLNMAMATEMCKNCHQPANFKRCCPLVCGKAIQLMDKSSRVRYSIDQITTMIINE\nRNRRSNIGNCMEALFQGPLQYKDLKIDIKTSPPPECINDLLQAVDSQEVRDYCEKKGWIVNITSQVQTERNINRAMTILQ\nAVTTFAAVAGVVYVMYKLFAGHQGAYTGLPNKKPNVPTIRTAKVQGPGFDYAVAMAKRNIVTATTSKGEFTMLGVHDNVA\nILPTHASPGESIVIDGKEVEILDAKALEDQAGTNLEITIITLKRNEKFRDIRPHIPTQITETNDGVLIVNTSKYPNMYVP\nVGAVTEQGYLNLGGRQTARTLMYNFPTRAGQCGGVITCTGKVIGMHVGGNGSHGFAAALKRSYFTQSQGEIQWMRPSKEV\nGYPIINAPSKTKLEPSAFHYVFEGVKEPAVLTKNDPRLKTDFEEAIFSKYVGNKITEVDEYMKEAVDHYAGQLMSLDINT\nEQMCLEDAMYGTDGLEALDLSTSAGYPYVAMGKKKRDILNKQTRDTKEMQKLLDTYGINLPLVTYVKDELRSKTKVEQGK\nSRLIEASSLNDSVAMRMAFGNLYAAFHKNPGVITGSAVGCDPDLFWSKIPVLMEEKLFAFDYTGYDASLSPAWFEALKMV\nLEKIGFGDRVDYIDYLNHSHHLYKNKTYCVKGGMPSGCSGTSIFNSMINNLIIRTLLLKTYKGIDLDHLKMIAYGDDVIA\nSYPHEVDASLLAQSGKDYGLTMTPADKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQD\nHVRSLCLLAWHNGEEEYNKFLAKIRSVPIGRALLLPEYSTLYRRWLDSF\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/Viruses/Hepatitis_C_virus/GCF_000861845.1_ViralProj15432_genomic.fna", "content": ">NC_004102.1 Hepatitis C virus genotype 1, complete genome\nGCCAGCCCCCTGATGGGGGCGACACTCCACCATGAATCACTCCCCTGTGAGGAACTACTGTCTTCACGCAGAAAGCGTCT\nAGCCATGGCGTTAGTATGAGTGTCGTGCAGCCTCCAGGACCCCCCCTCCCGGGAGAGCCATAGTGGTCTGCGGAACCGGT\nGAGTACACCGGAATTGCCAGGACGACCGGGTCCTTTCTTGGATAAACCCGCTCAATGCCTGGAGATTTGGGCGTGCCCCC\nGCAAGACTGCTAGCCGAGTAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGGG\nAGGTCTCGTAGACCGTGCACCATGAGCACGAATCCTAAACCTCAAAGAAAAACCAAACGTAACACCAACCGTCGCCCACA\nGGACGTCAAGTTCCCGGGTGGCGGTCAGATCGTTGGTGGAGTTTACTTGTTGCCGCGCAGGGGCCCTAGATTGGGTGTGC\nGCGCGACGAGGAAGACTTCCGAGCGGTCGCAACCTCGAGGTAGACGTCAGCCTATCCCCAAGGCACGTCGGCCCGAGGGC\nAGGACCTGGGCTCAGCCCGGGTACCCTTGGCCCCTCTATGGCAATGAGGGTTGCGGGTGGGCGGGATGGCTCCTGTCTCC\nCCGTGGCTCTCGGCCTAGCTGGGGCCCCACAGACCCCCGGCGTAGGTCGCGCAATTTGGGTAAGGTCATCGATACCCTTA\nCGTGCGGCTTCGCCGACCTCATGGGGTACATACCGCTCGTCGGCGCCCCTCTTGGAGGCGCTGCCAGGGCCCTGGCGCAT\nGGCGTCCGGGTTCTGGAAGACGGCGTGAACTATGCAACAGGGAACCTTCCTGGTTGCTCTTTCTCTATCTTCCTTCTGGC\nCCTGCTCTCTTGCCTGACTGTGCCCGCTTCAGCCTACCAAGTGCGCAATTCCTCGGGGCTTTACCATGTCACCAATGATT\nGCCCTAACTCGAGTATTGTGTACGAGGCGGCCGATGCCATCCTGCACACTCCGGGGTGTGTCCCTTGCGTTCGCGAGGGT\nAACGCCTCGAGGTGTTGGGTGGCGGTGACCCCCACGGTGGCCACCAGGGACGGCAAACTCCCCACAACGCAGCTTCGACG\nTCATATCGATCTGCTTGTCGGGAGCGCCACCCTCTGCTCGGCCCTCTACGTGGGGGACCTGTGCGGGTCTGTCTTTCTTG\nTTGGTCAACTGTTTACCTTCTCTCCCAGGCGCCACTGGACGACGCAAGACTGCAATTGTTCTATCTATCCCGGCCATATA\nACGGGTCATCGCATGGCATGGGATATGATGATGAACTGGTCCCCTACGGCAGCGTTGGTGGTAGCTCAGCTGCTCCGGAT\nCCCACAAGCCATCATGGACATGATCGCTGGTGCTCACTGGGGAGTCCTGGCGGGCATAGCGTATTTCTCCATGGTGGGGA\nACTGGGCGAAGGTCCTGGTAGTGCTGCTGCTATTTGCCGGCGTCGACGCGGAAACCCACGTCACCGGGGGAAGTGCCGGC\nCGCACCACGGCTGGGCTTGTTGGTCTCCTTACACCAGGCGCCAAGCAGAACATCCAACTGATCAACACCAACGGCAGTTG\nGCACATCAATAGCACGGCCTTGAACTGCAATGAAAGCCTTAACACCGGCTGGTTAGCAGGGCTCTTCTATCAGCACAAAT\nTCAACTCTTCAGGCTGTCCTGAGAGGTTGGCCAGCTGCCGACGCCTTACCGATTTTGCCCAGGGCTGGGGTCCTATCAGT\nTATGCCAACGGAAGCGGCCTCGACGAACGCCCCTACTGCTGGCACTACCCTCCAAGACCTTGTGGCATTGTGCCCGCAAA\nGAGCGTGTGTGGCCCGGTATATTGCTTCACTCCCAGCCCCGTGGTGGTGGGAACGACCGACAGGTCGGGCGCGCCTACCT\nACAGCTGGGGTGCAAATGATACGGATGTCTTCGTCCTTAACAACACCAGGCCACCGCTGGGCAATTGGTTCGGTTGTACC\nTGGATGAACTCAACTGGATTCACCAAAGTGTGCGGAGCGCCCCCTTGTGTCATCGGAGGGGTGGGCAACAACACCTTGCT\nCTGCCCCACTGATTGTTTCCGCAAGCATCCGGAAGCCACATACTCTCGGTGCGGCTCCGGTCCCTGGATTACACCCAGGT\nGCATGGTCGACTACCCGTATAGGCTTTGGCACTATCCTTGTACCATCAATTACACCATATTCAAAGTCAGGATGTACGTG\nGGAGGGGTCGAGCACAGGCTGGAAGCGGCCTGCAACTGGACGCGGGGCGAACGCTGTGATCTGGAAGACAGGGACAGGTC\nCGAGCTCAGCCCATTGCTGCTGTCCACCACACAGTGGCAGGTCCTTCCGTGTTCTTTCACGACCCTGCCAGCCTTGTCCA\nCCGGCCTCATCCACCTCCACCAGAACATTGTGGACGTGCAGTACTTGTACGGGGTAGGGTCAAGCATCGCGTCCTGGGCC\nATTAAGTGGGAGTACGTCGTTCTCCTGTTCCTCCTGCTTGCAGACGCGCGCGTCTGCTCCTGCTTGTGGATGATGTTACT\nCATATCCCAAGCGGAGGCGGCTTTGGAGAACCTCGTAATACTCAATGCAGCATCCCTGGCCGGGACGCACGGTCTTGTGT\nCCTTCCTCGTGTTCTTCTGCTTTGCGTGGTATCTGAAGGGTAGGTGGGTGCCCGGAGCGGTCTACGCCTTCTACGGGATG\nTGGCCTCTCCTCCTGCTCCTGCTGGCGTTGCCTCAGCGGGCATACGCACTGGACACGGAGGTGGCCGCGTCGTGTGGCGG\nCGTTGTTCTTGTCGGGTTAATGGCGCTGACTCTGTCGCCATATTACAAGCGCTACATCAGCTGGTGCATGTGGTGGCTTC\nAGTATTTTCTGACCAGAGTAGAAGCGCAACTGCACGTGTGGGTTCCCCCCCTCAACGTCCGGGGGGGGCGCGATGCCGTC\nATCTTACTCATGTGTGTTGTACACCCGACTCTGGTATTTGACATCACCAAACTACTCCTGGCCATCTTCGGACCCCTTTG\nGATTCTTCAAGCCAGTTTGCTTAAAGTCCCCTACTTCGTGCGCGTTCAAGGCCTTCTCCGGATCTGCGCGCTAGCGCGGA\nAGATAGCCGGAGGTCATTACGTGCAAATGGCCATCATCAAGTTAGGGGCGCTTACTGGCACCTATGTGTATAACCATCTC\nACCCCTCTTCGAGACTGGGCGCACAACGGCCTGCGAGATCTGGCCGTGGCTGTGGAACCAGTCGTCTTCTCCCGAATGGA\nGACCAAGCTCATCACGTGGGGGGCAGATACCGCCGCGTGCGGTGACATCATCAACGGCTTGCCCGTCTCTGCCCGTAGGG\nGCCAGGAGATACTGCTTGGGCCAGCCGACGGAATGGTCTCCAAGGGGTGGAGGTTGCTGGCGCCCATCACGGCGTACGCC\nCAGCAGACGAGAGGCCTCCTAGGGTGTATAATCACCAGCCTGACTGGCCGGGACAAAAACCAAGTGGAGGGTGAGGTCCA\nGATCGTGTCAACTGCTACCCAAACCTTCCTGGCAACGTGCATCAATGGGGTATGCTGGACTGTCTACCACGGGGCCGGAA\nCGAGGACCATCGCATCACCCAAGGGTCCTGTCATCCAGATGTATACCAATGTGGACCAAGACCTTGTGGGCTGGCCCGCT\nCCTCAAGGTTCCCGCTCATTGACACCCTGCACCTGCGGCTCCTCGGACCTTTACCTGGTCACGAGGCACGCCGATGTCAT\nTCCCGTGCGCCGGCGAGGTGATAGCAGGGGTAGCCTGCTTTCGCCCCGGCCCATTTCCTACTTGAAAGGCTCCTCGGGGG\nGTCCGCTGTTGTGCCCCGCGGGACACGCCGTGGGCCTATTCAGGGCCGCGGTGTGCACCCGTGGAGTGGCTAAGGCGGTG\nGACTTTATCCCTGTGGAGAACCTAGAGACAACCATGAGATCCCCGGTGTTCACGGACAACTCCTCTCCACCAGCAGTGCC\nCCAGAGCTTCCAGGTGGCCCACCTGCATGCTCCCACCGGCAGCGGTAAGAGCACCAAGGTCCCGGCTGCGTACGCAGCCC\nAGGGCTACAAGGTGTTGGTGCTCAACCCCTCTGTTGCTGCAACGCTGGGCTTTGGTGCTTACATGTCCAAGGCCCATGGG\nGTTGATCCTAATATCAGGACCGGGGTGAGAACAATTACCACTGGCAGCCCCATCACGTACTCCACCTACGGCAAGTTCCT\nTGCCGACGGCGGGTGCTCAGGAGGTGCTTATGACATAATAATTTGTGACGAGTGCCACTCCACGGATGCCACATCCATCT\nTGGGCATCGGCACTGTCCTTGACCAAGCAGAGACTGCGGGGGCGAGACTGGTTGTGCTCGCCACTGCTACCCCTCCGGGC\nTCCGTCACTGTGTCCCATCCTAACATCGAGGAGGTTGCTCTGTCCACCACCGGAGAGATCCCTTTTTACGGCAAGGCTAT\nCCCCCTCGAGGTGATCAAGGGGGGAAGACATCTCATCTTCTGCCACTCAAAGAAGAAGTGCGACGAGCTCGCCGCGAAGC\nTGGTCGCATTGGGCATCAATGCCGTGGCCTACTACCGCGGTCTTGACGTGTCTGTCATCCCGACCAGCGGCGATGTTGTC\nGTCGTGTCGACCGATGCTCTCATGACTGGCTTTACCGGCGACTTCGACTCTGTGATAGACTGCAACACGTGTGTCACTCA\nGACAGTCGATTTCAGCCTTGACCCTACCTTTACCATTGAGACAACCACGCTCCCCCAGGATGCTGTCTCCAGGACTCAAC\nGCCGGGGCAGGACTGGCAGGGGGAAGCCAGGCATCTACAGATTTGTGGCACCGGGGGAGCGCCCCTCCGGCATGTTCGAC\nTCGTCCGTCCTCTGTGAGTGCTATGACGCGGGCTGTGCTTGGTATGAGCTCACGCCCGCCGAGACTACAGTTAGGCTACG\nAGCGTACATGAACACCCCGGGGCTTCCCGTGTGCCAGGACCATCTTGAATTTTGGGAGGGCGTCTTTACGGGCCTCACTC\nATATAGATGCCCACTTTCTATCCCAGACAAAGCAGAGTGGGGAGAACTTTCCTTACCTGGTAGCGTACCAAGCCACCGTG\nTGCGCTAGGGCTCAAGCCCCTCCCCCATCGTGGGACCAGATGTGGAAGTGTTTGATCCGCCTTAAACCCACCCTCCATGG\nGCCAACACCCCTGCTATACAGACTGGGCGCTGTTCAGAATGAAGTCACCCTGACGCACCCAATCACCAAATACATCATGA\nCATGCATGTCGGCCGACCTGGAGGTCGTCACGAGCACCTGGGTGCTCGTTGGCGGCGTCCTGGCTGCTCTGGCCGCGTAT\nTGCCTGTCAACAGGCTGCGTGGTCATAGTGGGCAGGATTGTCTTGTCCGGGAAGCCGGCAATTATACCTGACAGGGAGGT\nTCTCTACCAGGAGTTCGATGAGATGGAAGAGTGCTCTCAGCACTTACCGTACATCGAGCAAGGGATGATGCTCGCTGAGC\nAGTTCAAGCAGAAGGCCCTCGGCCTCCTGCAGACCGCGTCCCGCCAAGCAGAGGTTATCACCCCTGCTGTCCAGACCAAC\nTGGCAGAAACTCGAGGTCTTCTGGGCGAAGCACATGTGGAATTTCATCAGTGGGATACAATACTTGGCGGGCCTGTCAAC\nGCTGCCTGGTAACCCCGCCATTGCTTCATTGATGGCTTTTACAGCTGCCGTCACCAGCCCACTAACCACTGGCCAAACCC\nTCCTCTTCAACATATTGGGGGGGTGGGTGGCTGCCCAGCTCGCCGCCCCCGGTGCCGCTACCGCCTTTGTGGGCGCTGGC\nTTAGCTGGCGCCGCCATCGGCAGCGTTGGACTGGGGAAGGTCCTCGTGGACATTCTTGCAGGGTATGGCGCGGGCGTGGC\nGGGAGCTCTTGTAGCATTCAAGATCATGAGCGGTGAGGTCCCCTCCACGGAGGACCTGGTCAATCTGCTGCCCGCCATCC\nTCTCGCCTGGAGCCCTTGTAGTCGGTGTGGTCTGCGCAGCAATACTGCGCCGGCACGTTGGCCCGGGCGAGGGGGCAGTG\nCAATGGATGAACCGGCTAATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCCACGCACTACGTGCCGGAGAGCGATGC\nAGCCGCCCGCGTCACTGCCATACTCAGCAGCCTCACTGTAACCCAGCTCCTGAGGCGACTGCATCAGTGGATAAGCTCGG\nAGTGTACCACTCCATGCTCCGGTTCCTGGCTAAGGGACATCTGGGACTGGATATGCGAGGTGCTGAGCGACTTTAAGACC\nTGGCTGAAAGCCAAGCTCATGCCACAACTGCCTGGGATTCCCTTTGTGTCCTGCCAGCGCGGGTATAGGGGGGTCTGGCG\nAGGAGACGGCATTATGCACACTCGCTGCCACTGTGGAGCTGAGATCACTGGACATGTCAAAAACGGGACGATGAGGATCG\nTCGGTCCTAGGACCTGCAGGAACATGTGGAGTGGGACGTTCCCCATTAACGCCTACACCACGGGCCCCTGTACTCCCCTT\nCCTGCGCCGAACTATAAGTTCGCGCTGTGGAGGGTGTCTGCAGAGGAATACGTGGAGATAAGGCGGGTGGGGGACTTCCA\nCTACGTATCGGGTATGACTACTGACAATCTTAAATGCCCGTGCCAGATCCCATCGCCCGAATTTTTCACAGAATTGGACG\nGGGTGCGCCTACATAGGTTTGCGCCCCCTTGCAAGCCCTTGCTGCGGGAGGAGGTATCATTCAGAGTAGGACTCCACGAG\nTACCCGGTGGGGTCGCAATTACCTTGCGAGCCCGAACCGGACGTAGCCGTGTTGACGTCCATGCTCACTGATCCCTCCCA\nTATAACAGCAGAGGCGGCCGGGAGAAGGTTGGCGAGAGGGTCACCCCCTTCTATGGCCAGCTCCTCGGCCAGCCAGCTGT\nCCGCTCCATCTCTCAAGGCAACTTGCACCGCCAACCATGACTCCCCTGACGCCGAGCTCATAGAGGCTAACCTCCTGTGG\nAGGCAGGAGATGGGCGGCAACATCACCAGGGTTGAGTCAGAGAACAAAGTGGTGATTCTGGACTCCTTCGATCCGCTTGT\nGGCAGAGGAGGATGAGCGGGAGGTCTCCGTACCCGCAGAAATTCTGCGGAAGTCTCGGAGATTCGCCCGGGCCCTGCCCG\nTTTGGGCGCGGCCGGACTACAACCCCCCGCTAGTAGAGACGTGGAAAAAGCCTGACTACGAACCACCTGTGGTCCATGGC\nTGCCCGCTACCACCTCCACGGTCCCCTCCTGTGCCTCCGCCTCGGAAAAAGCGTACGGTGGTCCTCACCGAATCAACCCT\nATCTACTGCCTTGGCCGAGCTTGCCACCAAAAGTTTTGGCAGCTCCTCAACTTCCGGCATTACGGGCGACAATACGACAA\nCATCCTCTGAGCCCGCCCCTTCTGGCTGCCCCCCCGACTCCGACGTTGAGTCCTATTCTTCCATGCCCCCCCTGGAGGGG\nGAGCCTGGGGATCCGGATCTCAGCGACGGGTCATGGTCGACGGTCAGTAGTGGGGCCGACACGGAAGATGTCGTGTGCTG\nCTCAATGTCTTATTCCTGGACAGGCGCACTCGTCACCCCGTGCGCTGCGGAAGAACAAAAACTGCCCATCAACGCACTGA\nGCAACTCGTTGCTACGCCATCACAATCTGGTGTATTCCACCACTTCACGCAGTGCTTGCCAAAGGCAGAAGAAAGTCACA\nTTTGACAGACTGCAAGTTCTGGACAGCCATTACCAGGACGTGCTCAAGGAGGTCAAAGCAGCGGCGTCAAAAGTGAAGGC\nTAACTTGCTATCCGTAGAGGAAGCTTGCAGCCTGACGCCCCCACATTCAGCCAAATCCAAGTTTGGCTATGGGGCAAAAG\nACGTCCGTTGCCATGCCAGAAAGGCCGTAGCCCACATCAACTCCGTGTGGAAAGACCTTCTGGAAGACAGTGTAACACCA\nATAGACACTACCATCATGGCCAAGAACGAGGTTTTCTGCGTTCAGCCTGAGAAGGGGGGTCGTAAGCCAGCTCGTCTCAT\nCGTGTTCCCCGACCTGGGCGTGCGCGTGTGCGAGAAGATGGCCCTGTACGACGTGGTTAGCAAGCTCCCCCTGGCCGTGA\nTGGGAAGCTCCTACGGATTCCAATACTCACCAGGACAGCGGGTTGAATTCCTCGTGCAAGCGTGGAAGTCCAAGAAGACC\nCCGATGGGGTTCTCGTATGATACCCGCTGTTTTGACTCCACAGTCACTGAGAGCGACATCCGTACGGAGGAGGCAATTTA\nCCAATGTTGTGACCTGGACCCCCAAGCCCGCGTGGCCATCAAGTCCCTCACTGAGAGGCTTTATGTTGGGGGCCCTCTTA\nCCAATTCAAGGGGGGAAAACTGCGGCTACCGCAGGTGCCGCGCGAGCGGCGTACTGACAACTAGCTGTGGTAACACCCTC\nACTTGCTACATCAAGGCCCGGGCAGCCTGTCGAGCCGCAGGGCTCCAGGACTGCACCATGCTCGTGTGTGGCGACGACTT\nAGTCGTTATCTGTGAAAGTGCGGGGGTCCAGGAGGACGCGGCGAGCCTGAGAGCCTTCACGGAGGCTATGACCAGGTACT\nCCGCCCCCCCCGGGGACCCCCCACAACCAGAATACGACTTGGAGCTTATAACATCATGCTCCTCCAACGTGTCAGTCGCC\nCACGACGGCGCTGGAAAGAGGGTCTACTACCTTACCCGTGACCCTACAACCCCCCTCGCGAGAGCCGCGTGGGAGACAGC\nAAGACACACTCCAGTCAATTCCTGGCTAGGCAACATAATCATGTTTGCCCCCACACTGTGGGCGAGGATGATACTGATGA\nCCCATTTCTTTAGCGTCCTCATAGCCAGGGATCAGCTTGAACAGGCTCTTAACTGTGAGATCTACGGAGCCTGCTACTCC\nATAGAACCACTGGATCTACCTCCAATCATTCAAAGACTCCATGGCCTCAGCGCATTTTCACTCCACAGTTACTCTCCAGG\nTGAAATCAATAGGGTGGCCGCATGCCTCAGAAAACTTGGGGTCCCGCCCTTGCGAGCTTGGAGACACCGGGCCCGGAGCG\nTCCGCGCTAGGCTTCTGTCCAGAGGAGGCAGGGCTGCCATATGTGGCAAGTACCTCTTCAACTGGGCAGTAAGAACAAAG\nCTCAAACTCACTCCAATAGCGGCCGCTGGCCGGCTGGACTTGTCCGGTTGGTTCACGGCTGGCTACAGCGGGGGAGACAT\nTTATCACAGCGTGTCTCATGCCCGGCCCCGCTGGTTCTGGTTTTGCCTACTCCTGCTCGCTGCAGGGGTAGGCATCTACC\nTCCTCCCCAACCGATGAAGGTTGGGGTAAACACTCCGGCCTCTTAGGCCATTTCCTGTTTTTTTTTTTTTTTTTTTTTTT\nTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTCTTTCCTTCTTT\nTTTCCTTTCTTTTCCTTCCTTCTTTAATGGTGGCTCCATCTTAGCCCTAGTCACGGCTAGCTGTGAAAGGTCCGTGAGCC\nGCATGACTGCAGAGAGTGCTGATACTGGCCTCTCTGCAGATCATGT\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/Viruses/Hepatitis_C_virus/GCF_000861845.1_ViralProj15432_protein.faa", "content": ">NP_671491.1 polyprotein [Hepatitis C virus]\nMSTNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRTWAQPG\nYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIPLVGAPLGGAARALAHGVRVLED\nGVNYATGNLPGCSFSIFLLALLSCLTVPASAYQVRNSSGLYHVTNDCPNSSIVYEAADAILHTPGCVPCVREGNASRCWV\nAVTPTVATRDGKLPTTQLRRHIDLLVGSATLCSALYVGDLCGSVFLVGQLFTFSPRRHWTTQDCNCSIYPGHITGHRMAW\nDMMMNWSPTAALVVAQLLRIPQAIMDMIAGAHWGVLAGIAYFSMVGNWAKVLVVLLLFAGVDAETHVTGGSAGRTTAGLV\nGLLTPGAKQNIQLINTNGSWHINSTALNCNESLNTGWLAGLFYQHKFNSSGCPERLASCRRLTDFAQGWGPISYANGSGL\nDERPYCWHYPPRPCGIVPAKSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGANDTDVFVLNNTRPPLGNWFGCTWMNSTGF\nTKVCGAPPCVIGGVGNNTLLCPTDCFRKHPEATYSRCGSGPWITPRCMVDYPYRLWHYPCTINYTIFKVRMYVGGVEHRL\nEAACNWTRGERCDLEDRDRSELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGVGSSIASWAIKWEYVV\nLLFLLLADARVCSCLWMMLLISQAEAALENLVILNAASLAGTHGLVSFLVFFCFAWYLKGRWVPGAVYAFYGMWPLLLLL\nLALPQRAYALDTEVAASCGGVVLVGLMALTLSPYYKRYISWCMWWLQYFLTRVEAQLHVWVPPLNVRGGRDAVILLMCVV\nHPTLVFDITKLLLAIFGPLWILQASLLKVPYFVRVQGLLRICALARKIAGGHYVQMAIIKLGALTGTYVYNHLTPLRDWA\nHNGLRDLAVAVEPVVFSRMETKLITWGADTAACGDIINGLPVSARRGQEILLGPADGMVSKGWRLLAPITAYAQQTRGLL\nGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSL\nTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVEN\nLETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGVDPNIRT\nGVRTITTGSPITYSTYGKFLADGGCSGGAYDIIICDECHSTDATSILGIGTVLDQAETAGARLVVLATATPPGSVTVSHP\nNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVSTDAL\nMTGFTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTLPQDAVSRTQRRGRTGRGKPGIYRFVAPGERPSGMFDSSVLCEC\nYDAGCAWYELTPAETTVRLRAYMNTPGLPVCQDHLEFWEGVFTGLTHIDAHFLSQTKQSGENFPYLVAYQATVCARAQAP\nPPSWDQMWKCLIRLKPTLHGPTPLLYRLGAVQNEVTLTHPITKYIMTCMSADLEVVTSTWVLVGGVLAALAAYCLSTGCV\nVIVGRIVLSGKPAIIPDREVLYQEFDEMEECSQHLPYIEQGMMLAEQFKQKALGLLQTASRQAEVITPAVQTNWQKLEVF\nWAKHMWNFISGIQYLAGLSTLPGNPAIASLMAFTAAVTSPLTTGQTLLFNILGGWVAAQLAAPGAATAFVGAGLAGAAIG\nSVGLGKVLVDILAGYGAGVAGALVAFKIMSGEVPSTEDLVNLLPAILSPGALVVGVVCAAILRRHVGPGEGAVQWMNRLI\nAFASRGNHVSPTHYVPESDAAARVTAILSSLTVTQLLRRLHQWISSECTTPCSGSWLRDIWDWICEVLSDFKTWLKAKLM\nPQLPGIPFVSCQRGYRGVWRGDGIMHTRCHCGAEITGHVKNGTMRIVGPRTCRNMWSGTFPINAYTTGPCTPLPAPNYKF\nALWRVSAEEYVEIRRVGDFHYVSGMTTDNLKCPCQIPSPEFFTELDGVRLHRFAPPCKPLLREEVSFRVGLHEYPVGSQL\nPCEPEPDVAVLTSMLTDPSHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGN\nITRVESENKVVILDSFDPLVAEEDEREVSVPAEILRKSRRFARALPVWARPDYNPPLVETWKKPDYEPPVVHGCPLPPPR\nSPPVPPPRKKRTVVLTESTLSTALAELATKSFGSSSTSGITGDNTTTSSEPAPSGCPPDSDVESYSSMPPLEGEPGDPDL\nSDGSWSTVSSGADTEDVVCCSMSYSWTGALVTPCAAEEQKLPINALSNSLLRHHNLVYSTTSRSACQRQKKVTFDRLQVL\nDSHYQDVLKEVKAAASKVKANLLSVEEACSLTPPHSAKSKFGYGAKDVRCHARKAVAHINSVWKDLLEDSVTPIDTTIMA\nKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSKLPLAVMGSSYGFQYSPGQRVEFLVQAWKSKKTPMGFSYD\nTRCFDSTVTESDIRTEEAIYQCCDLDPQARVAIKSLTERLYVGGPLTNSRGENCGYRRCRASGVLTTSCGNTLTCYIKAR\nAACRAAGLQDCTMLVCGDDLVVICESAGVQEDAASLRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDGAGKR\nVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMFAPTLWARMILMTHFFSVLIARDQLEQALNCEIYGACYSIEPLDLP\nPIIQRLHGLSAFSLHSYSPGEINRVAACLRKLGVPPLRAWRHRARSVRARLLSRGGRAAICGKYLFNWAVRTKLKLTPIA\nAAGRLDLSGWFTAGYSGGDIYHSVSHARPRWFWFCLLLLAAGVGIYLLPNR\n>NP_803170.1 protein F [Hepatitis C virus]\nMSTNPKPQRKPNVTPTVAHRTSSSRVAVRSLVEFTCCRAGALDWVCARRGRLPSGRNLEVDVSLSPRHVGPRAGPGLSPG\nTLGPSMAMRVAGGRDGSCLPVALGLAGAPQTPGVGRAIWVRSSIPLRAASPTSWGTYRSSAPLLEALPGPWRMASGFWKT\nA\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/Viruses/Tomato_mosaic_virus/GCF_000853705.1_ViralProj14926_genomic.fna", "content": ">NC_002692.1 Tomato mosaic virus, complete genome\nGTATTTTTACAACAATTACCAACAACAACAACAAACAACAACAACATTACATTTTACATTCTACAACTACAATGGCATAC\nACACAAACAGCCACATCGTCCGCTTTGCTTGAGACCGTCCGAGGTAACAATACCTTGGTCAACGATCTTGCAAAGCGGCG\nTCTATATGACACAGCGGTAGATGAATTTAATGCTAGGGACCGCAGGCCTAAAGTCAATTTTTCCAAAGTAGTAAGCGAAG\nAACAGACGCTTATTGCAACCAAAGCCTACCCAGAATTCCAAATTACATTCTACAACACGCAGAATGCTGTGCATTCCCTT\nGCAGGCGGTCTCCGATCATTAGAATTGGAATATCTGATGATGCAAATTCCCTACGGATCATTGACATATGATATCGGAGG\nTAATTTTGCATCTCATCTGTTCAAAGGGCGAGCATACGTTCACTGCTGTATGCCGAATCTAGATGTCCGCGACATAATGC\nGGCACGAGGGCCAAAAGGACAGTATTGAACTATACCTTTCTAGGCTCGAGAGGGGCAACAAACATGTCCCAAACTTCCAA\nAAGGAAGCTTTCGACAGATACGCTGAAATGCCAAACGAAGTAGTCTGTCACGATACTTTCCAAACGTGTAGGCATTCTCA\nAGAATGTTACACGGGAAGAGTGTATGCTATTGCTTTGCATAGTATATACGATATACCTGCCGACGAGTTCGGCGCGGCAC\nTGCTGAGAAAGAATGTACATGTATGTTATGCCGCTTTCCACTTTTCCGAGAATTTACTTCTCGAAGATTCACACGTCAAC\nCTCGATGAGATCAATGCATGTTTCCAAAGAGATGGAGACAGGTTGACTTTTTCCTTTGCATCTGAGAGTACTCTTAATTA\nTAGTCATAGTTATTCTAATATTCTTAAGTATGTTTGCAAAACTTACTTCCCAGCCTCTAATAGAGAGGTTTACATGAAGG\nAGTTTTTAGTAACTAGAGTTAATACCTGGTTTTGTAAATTTTCTAGAATAGATACTTTCTTATTGTACAAAGGTGTAGCG\nCATAAGGGTGTAGATAGTGAGCAGTTTTACAAGGCTATGGAAGACGCATGGCACTACAAAAAGACTCTTGCGATGTGCAA\nCAGTGAAAGAATCTTGTTAGAGGATTCTTCATCAGTTAATTACTGGTTTCCAAAAATGAGGGATATGGTGATAGTTCCAC\nTATTTGACATATCTCTCGAGACTAGTAAAAGAACACGCAAAGAGGTCTTAGTTTCAAAGGACTTTGTTTATACAGTGTTA\nAATCACATTCGTACGTACCAGGCCAAAGCGCTTACTTACTCCAACGTGTTATCTTTCGTCGAATCAATTCGTTCGAGAGT\nGATCATTAACGGGGTTACTGCCAGGTCTGAGTGGGATGTCGATAAATCATTATTACAGTCCTTGTCGATGACGTTCTTCC\nTACATACCAAGCTTGCCGTTCTGAAAGACGATCTTTTGATTAGCAAGTTTGCACTTGGACCAAAAACTGTCTCACAACAT\nGTGTGGGATGAGATTTCCCTAGCTTTCGGCAATGCTTTCCCATCGATCAAGGAAAGATTGATAAACCGGAAACTGATCAA\nAATTACGGAGAATGCGTTAGAGATCAGGGTGCCCGATCTTTATGTCACTTTCCATGATAGGTTAGTTTCTGAGTACAAAA\nTGTCAGTGGACATGCCGGTGCTAGACATTAGGAAAAAGATGGAAGAAACTGAGGAAATGTACAATGCACTGTCCGAACTG\nTCTGTACTTAAAAATTCAGACAAGTTCGATGTTGATGTTTTTTCCCAGATGTGCCAATCTTTAGAAGTTGATCCAATGAC\nTGCAGCAAAGGTAATAGTAGCAGTTATGAGCAACGAGAGTGGTCTTACTCTCACGTTTGAACAGCCCACCGAAGCTAATG\nTTGCGCTAGCATTGCAAGATTCTGAAAAGGCTTCTGATGGGGCGTTGGTAGTTACCTCAAGAGATGTTGAGGAACCGTCC\nATAAAGGGTTCGATGGCCCGTGGTGAGTTACAATTGGCCGGATTATCTGGCGACGTTCCTGAATCTTCATACACTAGGAG\nCGAGGAGATTGAGTCTCTCGAGCAGTTTCATATGGCAACAGCTAGTTCGTTAATTCATAAGCAGATGTGTTCGATCGTGT\nACACGGGCCCTCTTAAAGTTCAACAAATGAAAAACTTTATAGACAGCCTGGTAGCCTCGCTCTCTGCTGCGGTGTCGAAT\nCTAGTGAAGATCCTAAAAGATACAGCCGCGATTGACCTTGAAACTCGTCAAAAGTTCGGAGTTCTGGATGTTGCTTCGAA\nAAGGTGGCTAGTTAAACCATCCGCAAAGAACCATGCATGGGGGGTTGTTGAGACTCATGCGAGGAAATATCACGTCGCAT\nTACTGGAGCACGATGAATTTGGCATTATTACGTGCGATAACTGGCGACGGGTGGCTGTGAGTTCTGAGTCGGTAGTATAT\nTCTGATATGGCTAAACTCAGGACTCTGAGAAGATTGCTCAAAGATGGAGAACCACACGTTAGTTCAGCAAAGGTGGTTTT\nGGTGGATGGCGTTCCAGGGTGCGGGAAGACAAAGGAAATTCTTTCGAGAGTTAATTTCGAAGAAGATCTAATTCTTGTCC\nCTGGTCGTCAAGCTGCCGAGATGATCAGAAGAAGAGCTAATGCGTCGGGCATAATAGTGGCTACAAAGGATAATGTGCGC\nACCGTCGATTCATTTTTGATGAATTACGGGAAAGGGGCACGCTGTCAGTTCAAAAGATTGTTCATAGACGAAGGTTTGAT\nGCTGCATACTGGTTGTGTGAATTTCTTGGTTGAAATGTCTCTGTGCGATATTGCATATGTTTATGGAGACACCCAACAAA\nTTCCGTACATCAACAGAGTAACTGGTTTCCCGTACCCTGCGCACTTTGCAAAATTGGAGGTCGACGAAGTCGAAACAAGA\nAGAACTACTCTTCGCTGTCCGGCTGATGTCACACACTTCCTAAATCAAAGGTATGAAGGACACGTAATGTGCACGTCTTC\nTGAAAAGAAATCAGTTTCCCAGGAAATGGTTAGTGGGGCTGCGTCTATCAATCCTGTGTCCAAGCCGCTTAAAGGGAAAA\nTTTTGACTTTCACACAGTCTGACAAGGAGGCCCTTCTCTCAAGGGGCTACGCAGATGTCCATACTGTACATGAGGTACAA\nGGTGAGACTTATGCAGACGTATCGTTAGTTCGACTAACACCTACGCCTGTATCTATCATCGCAAGAGACAGTCCGCATGT\nTCTGGTCTCGTTGTCAAGACACACAAAATCCCTAAAGTACTACACCGTTGTGATGGATCCTTTAGTTAGTATCATTAGAG\nATTTAGAACGGGTTAGTAGTTACTTATTAGACATGTACAAAGTAGATGCAGGTACTCAATAGCAATTACAGGTCGACTCT\nGTGTTTAAAAATTTCAATCTTTTTGTAGCAGCTCCAAAGACTGGAGATATATCTGATATGCAATTTTACTATGATAAGTG\nTCTTCCTGGGAACAGCACGTTGTTGAACAACTACGACGCTGTTACCATGAAATTGACTGACATTTCTCTGAATGTCAAAG\nATTGCATATTAGATATGTCTAAGTCTGTAGCTGCTCCGAAAGATGTCAAACCAACTTTAATACCGATGGTACGAACGGCG\nGCAGAAATGCCTCGCCAGACTGGACTGTTGGAAAATCTAGTTGCGATGATTAAAAGAAATTTTAATTCACCAGAGTTGTC\nCGGAGTAGTTGATATTGAAAATACTGCATCTTTAGTGGTAGATAAGTTTTTTGATAGTTATTTACTTAAGGAAAAAAGAA\nAACCAAACAAAAATTTTTCACTGTTTAGTAGAGAGTCTCTCAATAGGTGGATAGCAAAGCAAGAACAAGTCACAATTGGT\nCAGTTGGCCGATTTTGATTTTGTGGATCTTCCAGCCGTTGATCAGTACAGGCATATGATTAAAGCGCAACCGAAGCAGAA\nACTGGATCTGTCAATTCAGACAGAATATCCAGCGTTGCAAACGATTGTGTATCATTCAAAGAAAATCAACGCAATATTTG\nGTCCTCTTTTCAGTGAGCTTACAAGGCAATTACTTGACAGTATTGACTCAAGCAGATTCTTGTTCTTTACGAGAAAGACA\nCCGGCTCAGATCGAAGATTTCTTCGGAGATCTAGACAGTCATGTCCCAATGGACGTACTTGAGTTGGATGTTTCGAAGTA\nTGATAAGTCTCAAAACGAGTTTCATTGTGCTGTTGAGTACGAAATCTGGAGGAGACTGGGTCTGGAGGATTTCTTGGCAG\nAAGTGTGGAAACAAGGGCATAGAAAAACCACCCTGAAAGATTACACTGCTGGTATAAAAACGTGTTTATGGTACCAGAGA\nAAGAGTGGTGATGTTACAACTTTTATCGGTAATACCGTCATCATTGCTTCGTGTCTTGCATCAATGCTCCCGATGGAAAA\nATTGATAAAAGGAGCCTTCTGCGGAGATGACAGTTTGTTGTACTTTCCTAAGGGTTGTGAGTATCCCGATATACAACAAG\nCTGCCAATCTAATGTGGAATTTTGAGGCCAAACTGTTCAAGAAGCAATATGGGTACTTCTGCGGGAGGTACGTGATTCAT\nCACGATAGAGGTTGCATAGTATACTACGACCCTTTGAAGCTGATTTCGAAACTTGGTGCTAAACACATCAAGGATTGGGA\nTCATTTGGAGGAGTTCAGAAGATCCCTCTGTGATGTTGCTGAGTCGTTGAACAATTGCGCGTATTACACACAATTGGACG\nACGCTGTTGGGGAGGTTCATAAAACCGCCCCACCTGGTTCGTTTGTTTATAAGAGTTTAGTTAAGTATTTGTCAGATAAA\nGTTTTGTTTAGAAGTTTATTTCTTGATGGCTCTAGTTGTTAAAGGTAAGGTAAATATTAATGAGTTTATCGATCTGTCAA\nAGTCTGAGAAACTTCTCCCGTCGATGTTCACGCCTGTAAAGAGTGTTATGGTTTCAAAGGTTGATAAGATTATGGTCCAT\nGAAAATGAATCATTGTCTGAAGTAAATCTCTTAAAAGGTGTAAAACTTATAGAAGGTGGGTATGTTTGCTTAGTCGGTCT\nTGTTGTGTCCGGTGAGTGGAATTTACCAGATAATTGCCGTGGTGGTGTGAGTGTCTGCATGGTTGACAAGAGAATGGAAA\nGAGCGGACGAAGCCACACTGGGGTCATATTACACTGCTGCTGCTAAAAAGCGGTTTCAGTTTAAAGTGGTCCCAAATTAC\nGGTATTACAACAAAGGATGCAGAAAAGAACATATGGCAGGTCTTAGTAAATATTAAAAATGTAAAAATGAGTGCGGGCTA\nCTGCCCTTTGTCATTAGAATTTGTGTCTGTGTGTATTGTTTATAAAAATAATATAAAATTGGGTTTGAGGGAGAAAGTAA\nCGAGTGTGAACGATGGAGGACCCATGGAACTTTCAGAAGAAGTTGTTGATGAGTTCATGGAGAATGTTCCAATGTCGGTT\nAGACTCGCAAAGTTTCGAACCAAATCCTCAAAAAGAGGTCCGAAAAATAATAATAATTTAGGTAAGGGGCGTTCAGGCGG\nAAGGTCTAAACCAAAAAGTTTTGATGAAGTTGAAAAAGAGTTTGATAATTTGATTGAAGATGAAGCCGAGACGTCGGTCG\nCGGATTCTGATTCGTATTAAATATGTCTTACTCAATCACTTCTCCATCGCAATTTGTGTTTTTGTCATCTGTATGGGCTG\nACCCTATAGAATTGTTAAACGTTTGTACAAATTCGTTAGGTAACCAGTTTCAAACACAGCAAGCAAGAACTACTGTTCAA\nCAGCAGTTCAGCGAGGTGTGGAAACCTTTCCCTCAGAGCACCGTCAGATTTCCTGGCGATGTTTATAAGGTGTACAGGTA\nCAATGCAGTTTTAGATCCTCTAATTACTGCGTTGCTGGGGGCTTTCGATACTAGGAATAGAATAATCGAAGTAGAAAACC\nAGCAGAGTCCGACAACAGCTGAAACGTTAGATGCTACCCGCAGGGTAGACGACGCTACGGTTGCAATTCGGTCTGCTATA\nAATAATTTAGTTAATGAACTAGTAAGAGGTACTGGACTGTACAATCAGAATACTTTTGAAAGTATGTCTGGGTTGGTCTG\nGACCTCTGCACCTGCATCTTAAATGCATAGGTGCTGAAATATAAATTTTGTGTTTCTAAAACACACGTGGTACGTACGAT\nAACGTACAGTGTTTTTCCCTCCACTTAAATCGAAGGGTAGTGTCTTGGAGCGCGCGGAGTAAACATATATGGTTCATATA\nTGTCCGTAGGCACGTAAAAAAGCGAGGGATTCGAATTCCCCCGGAACCCCCGGTTGGGGCCCA\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/Viruses/Tomato_mosaic_virus/GCF_000853705.1_ViralProj14926_protein.faa", "content": ">NP_078446.1 unnamed protein product [Tomato mosaic virus]\nMAYTQTATSSALLETVRGNNTLVNDLAKRRLYDTAVDEFNARDRRPKVNFSKVVSEEQTLIATKAYPEFQITFYNTQNAV\nHSLAGGLRSLELEYLMMQIPYGSLTYDIGGNFASHLFKGRAYVHCCMPNLDVRDIMRHEGQKDSIELYLSRLERGNKHVP\nNFQKEAFDRYAEMPNEVVCHDTFQTCRHSQECYTGRVYAIALHSIYDIPADEFGAALLRKNVHVCYAAFHFSENLLLEDS\nHVNLDEINACFQRDGDRLTFSFASESTLNYSHSYSNILKYVCKTYFPASNREVYMKEFLVTRVNTWFCKFSRIDTFLLYK\nGVAHKGVDSEQFYKAMEDAWHYKKTLAMCNSERILLEDSSSVNYWFPKMRDMVIVPLFDISLETSKRTRKEVLVSKDFVY\nTVLNHIRTYQAKALTYSNVLSFVESIRSRVIINGVTARSEWDVDKSLLQSLSMTFFLHTKLAVLKDDLLISKFALGPKTV\nSQHVWDEISLAFGNAFPSIKERLINRKLIKITENALEIRVPDLYVTFHDRLVSEYKMSVDMPVLDIRKKMEETEEMYNAL\nSELSVLKNSDKFDVDVFSQMCQSLEVDPMTAAKVIVAVMSNESGLTLTFEQPTEANVALALQDSEKASDGALVVTSRDVE\nEPSIKGSMARGELQLAGLSGDVPESSYTRSEEIESLEQFHMATASSLIHKQMCSIVYTGPLKVQQMKNFIDSLVASLSAA\nVSNLVKILKDTAAIDLETRQKFGVLDVASKRWLVKPSAKNHAWGVVETHARKYHVALLEHDEFGIITCDNWRRVAVSSES\nVVYSDMAKLRTLRRLLKDGEPHVSSAKVVLVDGVPGCGKTKEILSRVNFEEDLILVPGRQAAEMIRRRANASGIIVATKD\nNVRTVDSFLMNYGKGARCQFKRLFIDEGLMLHTGCVNFLVEMSLCDIAYVYGDTQQIPYINRVTGFPYPAHFAKLEVDEV\nETRRTTLRCPADVTHFLNQRYEGHVMCTSSEKKSVSQEMVSGAASINPVSKPLKGKILTFTQSDKEALLSRGYADVHTVH\nEVQGETYADVSLVRLTPTPVSIIARDSPHVLVSLSRHTKSLKYYTVVMDPLVSIIRDLERVSSYLLDMYKVDAGTQXQLQ\nVDSVFKNFNLFVAAPKTGDISDMQFYYDKCLPGNSTLLNNYDAVTMKLTDISLNVKDCILDMSKSVAAPKDVKPTLIPMV\nRTAAEMPRQTGLLENLVAMIKRNFNSPELSGVVDIENTASLVVDKFFDSYLLKEKRKPNKNFSLFSRESLNRWIAKQEQV\nTIGQLADFDFVDLPAVDQYRHMIKAQPKQKLDLSIQTEYPALQTIVYHSKKINAIFGPLFSELTRQLLDSIDSSRFLFFT\nRKTPAQIEDFFGDLDSHVPMDVLELDVSKYDKSQNEFHCAVEYEIWRRLGLEDFLAEVWKQGHRKTTLKDYTAGIKTCLW\nYQRKSGDVTTFIGNTVIIASCLASMLPMEKLIKGAFCGDDSLLYFPKGCEYPDIQQAANLMWNFEAKLFKKQYGYFCGRY\nVIHHDRGCIVYYDPLKLISKLGAKHIKDWDHLEEFRRSLCDVAESLNNCAYYTQLDDAVGEVHKTAPPGSFVYKSLVKYL\nSDKVLFRSLFLDGSSC\n>NP_078447.1 unnamed protein product [Tomato mosaic virus]\nMAYTQTATSSALLETVRGNNTLVNDLAKRRLYDTAVDEFNARDRRPKVNFSKVVSEEQTLIATKAYPEFQITFYNTQNAV\nHSLAGGLRSLELEYLMMQIPYGSLTYDIGGNFASHLFKGRAYVHCCMPNLDVRDIMRHEGQKDSIELYLSRLERGNKHVP\nNFQKEAFDRYAEMPNEVVCHDTFQTCRHSQECYTGRVYAIALHSIYDIPADEFGAALLRKNVHVCYAAFHFSENLLLEDS\nHVNLDEINACFQRDGDRLTFSFASESTLNYSHSYSNILKYVCKTYFPASNREVYMKEFLVTRVNTWFCKFSRIDTFLLYK\nGVAHKGVDSEQFYKAMEDAWHYKKTLAMCNSERILLEDSSSVNYWFPKMRDMVIVPLFDISLETSKRTRKEVLVSKDFVY\nTVLNHIRTYQAKALTYSNVLSFVESIRSRVIINGVTARSEWDVDKSLLQSLSMTFFLHTKLAVLKDDLLISKFALGPKTV\nSQHVWDEISLAFGNAFPSIKERLINRKLIKITENALEIRVPDLYVTFHDRLVSEYKMSVDMPVLDIRKKMEETEEMYNAL\nSELSVLKNSDKFDVDVFSQMCQSLEVDPMTAAKVIVAVMSNESGLTLTFEQPTEANVALALQDSEKASDGALVVTSRDVE\nEPSIKGSMARGELQLAGLSGDVPESSYTRSEEIESLEQFHMATASSLIHKQMCSIVYTGPLKVQQMKNFIDSLVASLSAA\nVSNLVKILKDTAAIDLETRQKFGVLDVASKRWLVKPSAKNHAWGVVETHARKYHVALLEHDEFGIITCDNWRRVAVSSES\nVVYSDMAKLRTLRRLLKDGEPHVSSAKVVLVDGVPGCGKTKEILSRVNFEEDLILVPGRQAAEMIRRRANASGIIVATKD\nNVRTVDSFLMNYGKGARCQFKRLFIDEGLMLHTGCVNFLVEMSLCDIAYVYGDTQQIPYINRVTGFPYPAHFAKLEVDEV\nETRRTTLRCPADVTHFLNQRYEGHVMCTSSEKKSVSQEMVSGAASINPVSKPLKGKILTFTQSDKEALLSRGYADVHTVH\nEVQGETYADVSLVRLTPTPVSIIARDSPHVLVSLSRHTKSLKYYTVVMDPLVSIIRDLERVSSYLLDMYKVDAGTQ\n>NP_078448.1 unnamed protein product [Tomato mosaic virus]\nMALVVKGKVNINEFIDLSKSEKLLPSMFTPVKSVMVSKVDKIMVHENESLSEVNLLKGVKLIEGGYVCLVGLVVSGEWNL\nPDNCRGGVSVCMVDKRMERADEATLGSYYTAAAKKRFQFKVVPNYGITTKDAEKNIWQVLVNIKNVKMSAGYCPLSLEFV\nSVCIVYKNNIKLGLREKVTSVNDGGPMELSEEVVDEFMENVPMSVRLAKFRTKSSKRGPKNNNNLGKGRSGGRSKPKSFD\nEVEKEFDNLIEDEAETSVADSDSY\n>NP_078449.1 unnamed protein product [Tomato mosaic virus]\nMSYSITSPSQFVFLSSVWADPIELLNVCTNSLGNQFQTQQARTTVQQQFSEVWKPFPQSTVRFPGDVYKVYRYNAVLDPL\nITALLGAFDTRNRIIEVENQQSPTTAETLDATRRVDDATVAIRSAINNLVNELVRGTGLYNQNTFESMSGLVWTSAPAS\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/Viruses/partial_pan-viral-9seqs-with-human-random-subset.fna", "content": ">EU255973.1 Hepatitis C virus subtype 1a isolate HCV-1a/US/BID-V180/1990, complete genome\nGAGCCATGGCGTTAGTATGAGTGTCGTGCAGCCTCCAGGACCCCCCCTCCCGGGAGAGCC\nATAGTGGTCTGCGGAACCGGTGAGTACACCGGAATTGCCAGGACGACCGGGTCCTTTCTT\nGGATAAACCCGCTCAATGCCTGGAGATTTGGGCGTGCCCCCGCAAGACTGCTAGCCGAGT\nAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGG\nGAGGTCTCGTAGACCGTGCACCATGAGCACGAATCCTAAACCTCAAAGAAAAACCAAACG\nTAACACCAACCGTCGCCCACAGGACGTCAAGTTCCCGGGTGGCGGTCAGATCGTTGGTGG\nAGTTTACTTGTTGCCGCGCAGGGGCCCTAGATTGGGTGTGCGCGCGACGAGGAAGACTTC\nCGAGCGGTCGCAACCTCGAGGTAGACGTCAGCCTATCCCCAAGGCACGTCGGCCCGAGGG\nCAGGACCTGGGCTCAGCCCGGGTATCCTTGGCCCCTCTATGGCAATGAGGGTTGCGGGTG\nGGCGGGATGGCTCCTGTCTCCCCGAGGCTCTCGGCCTAGTTGGGGCCCCACAGACCCCCG\nGCGTAGGTCGCGCAATCTGGGTAAGGTCATCGATACCCTTACGTGCGGCTTCGCCGACCT\nCATGGGGTACATACCGCTCGTCGGCGCTCCTCTTGGAGGCGCTGCCAGGGCTCTGGCGCA\nTGGCGTCAGGGTTCTGGAAGACGGCGTGAACTATGCAACAGGGAACCTTCCTGGTTGCTC\nTTTCTCTATCTTCCTTCTGGCCCTACTCTCTTGCCTGACCGTGCCCGCCTCAGCCTACCA\nAGTGCGCAACTCCTCGGGGCTTTACCATGTCACCAATGATTGCCCTAACTCGAGTATTGT\nGTACGAGGCGGCCGATGCCATCCTGCACACTCCGGGGTGTGTCCCTTGCGTTCGCGAGGG\nTAACGCCTCGAGGTGTTGGGTGCCGGTGACCCCCACGGTGGCCACCAGGGACGGCAAGCT\nCCCCACAACGCAGCTTCGACGTCATATCGATCTGCTCGTCGGGGGCGCCACCCTCTGCTC\nGGCTCTCTACGTGGGGGACCTGTGCGGGTCTGTCTTTCTTGTCGGCCAGCTGTTTACCCT\nCTCTCCCAGGCGCCACTGGACGACGCAGGGCTGTAATTGTTCTATCTATCCCGGCCATAT\nAACGGGTCACCGCATGGCATGGGATATGATGATGAACTGGTCCCCTACAACGGCGTTGGT\nGGTAGCTCAGCTGCTCCGGATCCCACAAGCCATCATGGACATGATCGCTGGTGCTCACTG\nGGGAGTCCTGGCGGGCATAGCGTACTTCTCCATGGTGGGGAACTGGGCGAAGGTCCTGGT\nAGTGCTACTGCTATTTGCCGGCGTCGACGCGGAAACCCACGTCACCGGGGGAAGTGCCGG\nCCGCACCGTGGCTGGGCTTACTGGTCTCTTCGCACCAGGCGCCAGACAGAACATCCAACT\nGATCAACACCAACGGCAGTTGGCACATCAATAGCACGGCCTTGAACTGCAATGATAGCCT\nTCAAACCGGCTGGATAGCAGGCCTCTTCTATCACCACAAATTCAACTCTTCAGGCTGTTC\nCGAGAGGTTGGCCAGCTGCCGACGCCTTACTGATTTTGCCCAGGGCTGGGGCCCCATCAG\nTTATGCCAACGGAAGCGGCCCCGACGAGCGTCCCTACTGCTGGCACTACCCCCCAAGACC\nTTGTGGTATTGTGCCCGCAAGGAGCGTGTGTGGCCCGGTATATTGCTTCACTCCCAGCCC\nCGTGGTGGTGGGAACGACCGACAGGTCGGGTGCGCCTACCTACAACTGGGGTGAAAATGA\nTACGGACGTTTTCGTCCTCAACAACACCAGGCCACCGCTGGGCAATTGGTTCGGTTGCAC\nCTGGATGAACTCGACTGGATTCACCAAAGTGTGCGGAGCGCCCCCTTGTGTCATCGGAGG\nGGTGGGCAATAACACCTTGCGCTGCCCCACTGATTGCTTCCGCAAGCATCCGGAAGCCAC\nATACTCTCGGTGCGGCTCCGGTCCCTGGATTACACCCAGGTGCATGGTCGACTACCCGTA\nTAGGCTTTGGCATTACCCTTGTACCATCAACTACACCATATTCAAAGTCAGGATGTACGT\nGGGAGGGGTCGAGCACAGGCTGGAAGCTGCCTGCAACTGGACGCGGGGCGAACGCTGCGA\nTCTGGAAGACAGGGACAGGTCCGAGCTCAGCCCATTGCTGCTGTCCACCACACAGTGGCA\nGGTTCTTCCGTGTTCTTTCACGACCCTGCCAGCCTTGTCCACCGGCCTCATCCACCTCCA\nCCAGAACATCGTGGACGTGCAGTACTTGTACGGGGTAGGGTCAAGCATTGCGTCCTGGGC\nCATTAAGTGGGAGTATGTCGTTCTCCTGTTCCTTCTGCTTGCAGACGCGCGCGTCTGCTC\nCTGCTTGTGGATGATGTTACTCATATCCCAAGCGGAGGCGGCTTTGGAGAACCTCGTAAT\nACTCAATGCAGCATCCCTGGCCGGGACGCACGGTCTTGTGTCCTTCCTAGTGTTCTTCTG\nCTTTGCGTGGTATCTGAAGGGTAGGTGGGTGCCCGGAGCGGCATACGCCTTCTACGGGAT\nGTGGCCTCTCCTCCTGCTCCTGCTGGCGTTGCCTCAACGGGCATACGCACTGGACACGGA\nGGTGGCCGCGTCGTGTGGCGGCGTTGTTCTTGTCGGGTTAATGGCGCTGACTCTGTCACC\nATATTACAAGCGCCACATCGGCTGGTGCTTGTGGTGGCTTCAGTATCTTCTGACCAGAGT\nAGAAGCGCATCTGCACGTGTGGGTTCCCCCCCTCAACGTTCGAGGGAGGCGCGATGCCAT\nCATCTTGCTCATGTGTGCTGTACACCCGACTTTGGTATTTGACATCACCAAACTACTGCT\nGGCCGTCTTCGGACCCCTTTGGATTCTCCAAGCCAGTTTGCTCAAAGTCCCCTACTTCGT\nGCGCGTTCAAGGCCTCCTCCGGATCTGCGCGCTAGCGCGGAAGATGGTCGGGGGTCATTA\nCGTGCAGATGGCCATCATCAAGTTAGGGGCGCTTACTGGTACCTATGTTTACAACCACCT\nCACTCCTCTTCGGGACTGGGCGCACAACGGCCTGCAAGATCTGGCCGTGGCTGTGGAACC\nTGTCGTCTTCTCCCCAATGGAGACCAAGCTCATCACGTGGGGGGCGGACACCGCCGCGTG\nCGGCGACATCATCGACGGCTTGCCCGTCTCCGCCCGTAGGGGCCAGGAGATACTGCTTGG\nACCAGCCGACGGAATGGTCTCCAAGGGGTGGAGGTTGCTGGCGCCCATCACGGCGTACGC\nCCAGCAGACGAGAGGCCTCCTAGGGTGTATAATCACCAGCCTGACTGGCCGGGACAAGAA\nCCAAGTGGAGGGTGAGGTCCAGATCGTGTCAACCGCTGCCCAAACTTTCCTGGCAACGTG\nCATCAATGGGGTATGCTGGACTGTCTACCACGGGGCCGGAACGAGGACCATCGCATCACC\nCAAGGGTCCTGTTATCCAGATGTATACCAATGTGGACCAAGACCTCGTGGGCTGGCCCGC\nTCCTCCAGGTTCCCGCTCATTAACACCCTGCACCTGCGGCTCCTCGGACCTCTACCTGGT\nCACGAGGCACGCCGATGTCATTCCCGTGCGCCGGCGGGGTGATAGCAGGGGCAGCCTGCT\nTTCGCCCCGGCCCATCTCCTACTTGAAAGGCTCCTCGGGGGGTCCGCTGTTGTGCCCCGC\nGGGACACGCCGTGGGCATATTCAGGGCCGCGGTGTGCACCCGTGGAGTGGCTAAAGCGGT\nGGACTTTATCCCTGTGGAGAACCTAGAGACAACCATGAGATCCCCGGTGTTCACGGACAA\nCTCCTCTCCACCAGCAGTGCCCCAGAGCTTCCAGGTAGCCCACCTGCATGCTCCCACCGG\nCAGCGGTAAGAGCACCAAGGTTCCGGCTGCGTACGCAGCTCAAGGCTACAAGGTGCTGGT\nGCTCAACCCCTCTGTTGCTGCAACACTGGGCTTTGGTGCTTACATGTCCAAGGCCCATGG\nGGTCGATCCTAACATCAGGACTGGGGTGAGAACAATTACCACTGGCAGCCCCATCACGTA\nCTCCACCTACGGCAAGTTCCTTGCCGACGGCGGGTGCTCAGGGGGTGCTTATGACATAAT\nAATTTGTGACGAGTGCCACTCCACGGATGCTACATCCATCTTGGGCATCGGCACTGTCCT\nTGACCAAGCAGAGACTGCGGGGGCGAGACTGGTTGTGCTCGCCACTGCTACTCCTCCGGG\nCTCCGTCACTGTGCCCCATCCTAACATCGAGGAGGTTGCTCTGTCCACCACCGGAGAGAT\nCCCTTTTTACGGCAAGGCTATTCCCCTCGAGGTGATCAAGGGGGGAAGACATCTCATCTT\nCTGTCACTCAAAGAAGAAGTGCGATGAGCTCGCCGCAAAGCTGGTCGCGTTGGGCGTCAA\nTGCCGTGGCCTACTACCGCGGTCTCGACGTGTCTGTCATCCCGACCAGCGGCGATGTTGT\nCGTCGTGGCGACCGATGCTCTCATGACTGGCTATACCGGCGACTTCGACTCTGTGATAGA\nCTGCAACACGTGTGTCACCCAGACAGTCGATTTCAGCCTTGACCCTACCTTCACCATTGA\nGACAACCACGCTCCCCCAGGATGCTGTCTCCCGGACTCAACGTCGGGGCAGGACTGGCAG\nGGGGAAGCCAGGCATCTACAGATTTGTGGCACCGGGGGAGCGCCCCTCGGGCATGTTCGA\nCTCGTCCGTCCTCTGTGAGTGCTATGACGCGGGCTGTGCTTGGTATGAGCTCACGCCCGC\nCGAGACTACAGTTAGGCTACGAGCGTACATGAACACCCCGGGGCTTCCCGTGTGCCAGGA\nCCATCTTGAATTTTGGGAGGGCGTTTTTACGGGCCTCACTCATATAGATGCCCACTTTCT\nATCCCAGACAAAGCAGAGTGGGGAGAACTTTCCTTACCTGGTAGCGTACCAAGCCACCGT\nGTGCGCTAGGGCTCAAGCCCCGCCCCCATCGTGGGACCAGATGTGGAAGTGTTTGATCCG\nTCTCAAGCCCACCCTCCATGGGCCAACACCCCTGCTATACAGACTGGGCGCTGTTCAGAA\nTGAAGTTACCCTGACGCACCCAATCACCAAATACATCATGACATGCATGTCGGCTGACCT\nGGAGGTCGTCACGAGCACCTGGGTGCTCGTTGGCGGCGTCCTGGCTGCTTTGGCCGCGTA\nTTGCCTGTCAACAGGCTGCGTGGTCATAGTGGGCAGGATTGTCTTGTCCGGGAAGCCGGC\nAGTTATACCTGACAGGGAGGTTCTCTACCGGGAGTTCGATGAGATGGAAGAGTGCTCTCA\nGCACTTACCGTACATCGAGCAAGGGATGATGCTCGCCGAGCAGTTCAAGCAGAAGGCCCT\nCGGCCTCCTGCAGACCGCGTCCCGCCAGGCAGAGGTTATCGCCCCTGCTGTCCAGACCAA\nCTGGCAGAAACTCGAGGCCTTCTGGGCGAAGCATATGTGGAATTTCATCAGTGGGATACA\nATACTTGGCGGGCCTGTCAACGCTGCCTGGTAACCCCGCCATTGCTTCATTGATGGCTTT\nTACAGCTGCTGTCACCAGCCCACTAACCACTAGCCAAACCCTCCTCTTCAACATATTGGG\nGGGGTGGGTGGCTGCCCAGCTCGCTGCCCCCGGTGCCGCTACCGCCTTTGTGGGCGCTGG\nCTTAGCCGGCGCCGCCATCGGCAGTGTTGGGCTGGGGAAGGTCCTCGTGGACATTCTTGC\nAGGATATGGCGCGGGCGTGGCGGGAGCTCTTGTAGCATTCAAGATCATGAGCGGTGAGGT\nCCCCTCCACGGAGGACCTGGTCAATCTGCTGCCCGCCATCCTCTCGCCTGGAGCCCTTGT\nAGTCGGTGTGGTCTGCGCAGCAATACTGCGCCGGCACGTTGGCCCGGGCGAGGGGGCAGT\nGCAATGGATGAACCGGCTAATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCCACGCA\nCTACGTGCCGGAGAGCGATGCAGCCGCCCGCGTCACGGCCATACTCAGCAGCCTCACTGT\nAACCCAGCTCCTGAGGCGACTGCACCAGTGGATAAGCTCGGAGTGTACCACTCCATGCTC\nCGGTTCCTGGCTAAGAGACATCTGGGACTGGATATGCGAGGTGCTGAGCGACTTTAAGAC\nCTGGCTGAAAGCCAAGCTCATGCCACAACTGCCTGGGATTCCCTTTGTGTCCTGCCAGCG\nCGGGTATAGGGGGGTCTGGCGGGGAGACGGCATCATGCACACTCGCTGCCACTGTGGAGC\nTGAGATCACTGGACATGTCAAAAACGGGACGATGAGGATCGTCGGTCCTAGGACCTGCAG\nGAACATGTGGAGTGGGACCTTCCCCATTAACGCCTACACCACGGGCCCCTGTACCCCCCT\nTCCTGCGCCGAACTATAAGTTCGCGCTGTGGAGGGTGTCTGCAGAGGAATACGTGGAGAT\nAAGGCAGGTGGGGGACTTCCACTACGTAACGGGCATGACTACTGACAATCTTAAATGCCC\nGTGCCAGGTCCCATCGCCCGAATTCTTCACAGAATTGGACGGGGTGCGCCTACATAGGTA\nTGCGCCCCCTTGCAAGCCCTTGCTGCGGGAGGAGGTATCATTCAGAGTAGGACTCCACGA\nGTACCCGGTGGGGTCGCAACTACCTTGCGAGCCCGAACCGGACGTGGCCGTGTTGACGTC\nCATGCTCACTGATCCCTCCCACATAACAGCGGAGGCGGCCGGGAGAAGGTTGGCGAGGGG\nATCACCCCCTTCTGTGGCCAGCTCCTCGGCTAGCCAGTTGTCCGCTCCATCTCTCAAGGC\nAACTTGCACCGCCAACCATGACTCCCCTGACGCCGAGCTCATAGAGGCTAATCTCCTGTG\nGAGGCAGGAGATGGGCGGCAACATCACCAGGGTTGAGTCAGAGAACAAAGTGGTGATTCT\nGGACTCCTTCGATCCGCTTGTATCAGAGGAGGATGAGCGGGAGATCTCCGTACCCGCAGA\nAATCCTGCGGAAGTCTCGGAGATTCGCCCCGGCCCTGCCCATTTGGGCGCGGCCGGACTA\nCAACCCCCCGCTGGTAGAGACGTGGAAAAAACCTGACTACGAACCACCCGTGGTCCATGG\nCTGCCCGCTACCACCTCCACAGTCCCCTCCTGTGCCTCCGCCTCGGAAGAAGCGAACGGT\nGGTCCTCACCGAATCAACCCTATCTACTGCCTTGGCTGAGCTTGCCACCAAAAGTTTTGG\nCAGCTCCTCAACTTCCGGCATTACGGGCGACAATACGACAACATCCTCTGAGCCCGCCCC\nTTCTGGCTGCTCCCCCGACTCCGACGTTGAGTCCTATTCTTCCATGCCCCCCCTGGAGGG\nGGAGCCTGGAGATCCGGATCTCAGCGACGGGTCATGGTCGACGGTCAGTAGCGGGGCCGA\nCGCGGAGGATGTCGTGTGCTGCTCAATGTCCTATACCTGGACAGGCGCACTCGTCACCCC\nGTGCGCTGCGGAAGAACAAAAACTGCCCATCAACGCACTGAGCAACTCGTTGCTACGTCA\nTCACAATCTGGTGTATTCCACCACTTCACGCAGTGCTTGCCAAAGGCAGAAGAAAGTCAC\nATTTGACAGACTGCAAGTTCTGGACAGCCATTACCAGGACGTGCTCAAGGAGGTTAAGGC\nAGCGGCGTCAAAAGTGAAGGCTAACTTGCTATCCGTAGAGGAAGCTTGCAGCCTGACGCC\nCCCACACTCAGCCAAATCCAAGTTTGGTTATGGGGCGAAAGACGTCCGTTGCCATGCCAG\nAAAGGCCGTAGCCCACATCAACTCCGTGTGGAAAGACCTTCTGGAAGACAGTGTAACACC\nAATAGACACTACCATCATGGCTAAGAACGAGGTTTTCTGTGTTCAGCCTGAGAAGGGGGG\nTCGTAAGCCAGCTCGTCTCATCGTGTTCCCCGACCTGGGCGTGCGCGTGTGCGAGAAGAT\nGGCCCTGTACGATGTGGTTAGCAAGCTCCCCCTGGCCGTGATGGGAAGCTCCTACGGATT\nCCAATACTCACCAGGACAGCGGGTTGAATTCCTCGTGAAAGCGTGGAAGTCCAAGAAGAC\nCCCAATGGGGTTCTCATATGATACCCGCTGTTTTGACTCCACAGTCACTGAGAGCGACAT\nCCGTACGGAGGAGGCAATTTACCAATGTTGTGACCTGGACCCCCAAGCCCGCGTGGCCAT\nCAAGTCCCTCACTGAGAGGCTTTACGTTGGGGGCCCTCTTACCAATTCAAGGGGGGAGAA\nCTGCGGCTACCGCAGGTGCCGCGCGAGCGGCGTACTGACAACTAGCTGTGGTAACACCCT\nCACTTGCTACATCAAGGCCCAAGCAGCCTGTCGAGCCGCAGGGCTCCAGGACTGCACCAT\nGCTCGTGTGTGGCGACGACTTAGTCGTTATCTGTGAAAGTGCGGGGGTCCAGGAGGACGC\nGGCGAGCCTGAGAGCCTTCACGGAGGCTATGACCAGGTACTCCGCCCCCCCCGGGGACCC\nCCCACAACCAGAATACGACTTGGAGCTCATAACATCATGCTCCTCCAACGTGTCAGTCGC\nCCACGACGGCGCTGGAAAGAGGGTCTACTACCTCACCCGTGACCCTACAACCCCCCTCGC\nGAGAGCCGCGTGGGAGACAGCAAGACACACTCCAGTCAATTCCTGGCTAGGCAACATAAT\nCATGTTTGCCCCCACACTGTGGGCGAGGATGATATTGATGACCCACTTCTTTAGCGTCCT\nCATAGCCAGGGACCAGCTTGAACAGGCCCTTGATTGCGAGATCTACGGAGCCTGCTACTC\nCATAGAACCACTGGACCTACCTCCAATCATTCAAAGACTCCATGGCCTCAGCGCATTTTC\nACTCCACAGTTACTCTCCAGGTGAGATCAATAGGGTGGCCGCATGCCTCAGAAAACTTGG\nGGTCCCGCCCTTGCGAGCTTGGAGACACCGGGCCCGGAGCGTCCGCGCTAGGCTTCTGTC\nCAGAGGAGGCAGGGCTGCCATATGTGGCAAGTACCTCTTCAACTGGGCAGTAAGAACAAA\nGCTCAAACTCACTCCAATAGCGGCCGCTGGCCGGCTGGACTTGTCCGGCTGGTTCACGGC\nTGGCTACAGCGGGGGAGACATTTATCACAGCGTGTCTCATGCCCGGCCCCGCTGGTTCTG\nGTTTTGCCTACTCCTGCTCGCTGCAGGGGTAGGCATCTACCTCCTCCCCAACCGATGA\n>KJ207374.1 Tomato mosaic virus isolate Penghu, complete genome\nGTATTTTTACAACAATTACCAACAACAACAACAAACAACAACAACATTACATTTTACATT\nCTACAACTACAATGGCATACACACAAACAGCCACATCGTCCGCTTTGCTTGAGACCGTCC\nGAGGTAACAATACCTTGGTCAACGATCTTGCAAAGCGGCGTCTATATGACACAGCGGTCG\nATGAATTTAATGCTAGGGACCGCAGGCCTAAAGTCAATTTTTCCAAAGTAGTAAGCGAAG\nAACAGACGCTTATTGCAACCAAAGCCTACCCAGAATTCCAAATTACATTCTACAACACGC\nAGAACGCTGTGCATTCCCTTGCAGGCGGTCTCCGATCATTAGAATTGGAATATCTGATGA\nTGCAAATTCCCTACGGATCATTGACATATGATATCGGAGGTAATTTTGCATCTCATCTGT\nTCAAAGGGCGAGCATACGTTCACTGCTGTATGCCGAATCTGGATGTCCGCGACATAATGC\nGGCACGAGGGCCAAAAGGACAGTATTGAACTATACCTTTCTAGGCTCGAAAGGGGCAACA\nAACATGTCCCAAACTTCCAAAAGGAAGCTTTCGACAGATACGCTGAAATGCCAAACGAAG\nTAGTCTGTCACGATACTTTCCAAACGTGTAGGCATTCTCAAGAATGTTACACGGGAAGAG\nTGTATGCTATTGCTTTGCATAGTATATACGATATACCTGCCGACGAGTTCGGCGCGGCAC\nTGCTGAGAAAGAATGTACATGTATGTTATGCCGCTTTCCACTTTTCCGAGAATTTACTTC\nTCGAAGATTCACACGTCAACCTCGATGAGATCAATGCATGTTTCCAAAGAGATGGAGACA\nGGTTGACCTTTTCCTTTGCATCTGAGAGTACTCTTAATTATAGTCATAGTTATTCTAATA\nTTCTTAAGTATGTTTGCAAAACTTACTTCCCAGCCTCTAATAGAGAGGTTTACATGAAGG\nAGTTTTTAGTAACTAGAGTTAATACCTGGTTTTGTAAATTTTCTAGAATAGATACTTTCT\nTATTGTACAAAGGTGTAGCGCATAAGGGTGTAGATAGTGAGCAGTTTTACAAGGCTATGG\nAAGACGCATGGCACTACAAAAAGACTCTTGCGATGTGCAACAGTGAAAGAATCTTGTTAG\nAGGATTCTTCATCAGTTAATTACTGGTTTCCAAAAATGAGGGATATGGTGATAGTTCCAC\nTATTTGACATATCTCTCGAGACTAGTAAAAGAACACGCAAAGAGGTCTTAGTTTCAAAGG\nACTTTGTTTATACAGTGTTAAATCACATTCGTACGTACCAGGCAAAAGCGCTTACTTACT\nCCAACGTGTTATCTTTCGTCGAATCAATTCGTTCGAGAGTGATCATTAACGGGGTTACTG\nCTAGGTCTGAGTGGGATGTCGATAAATCATTATTACAGTCCTTGTCGATGACGTTCTTCC\nTACATACCAAGCTTGCCGTTCTGAAAGACGATCTTTTGATTAGCAAGTTTGCACTTGGTC\nCAAAAACTGTCTCACAACATGTGTGGGATGAGATTTCCCTAGCTTTCGGCAATGCTTTCC\nCATCGATCAAGGAAAGATTGATAAACCGGAAACTGATCAAAATTACGGAGAATGCGTTAG\nAGATCAGGGTGCCCGATCTTTATGTCACTTTCCATGATAGGTTAGTTTCTGAGTACAAAA\nTGTCAGTGGACATGCCGGTGCTAGACATTAGGAAAAAGATGGAAGAAACTGAGGAAATGT\nACAATGCACTGTCCGAACTGTCTGTACTTAAAAATTCAGACAAATTCGATGTTGATGTTT\nTTTCCCAGATGTGCCAATCTTTAGAAGTTGATCCAATGACTGCAGCAAAGGTAATAGTAG\nCAGTTATGAGCAACGAGAGTGGTCTTACTCTCACGTTTGAACAGCCCACCGAAGCTAATG\nTTGCGCTAGCATTGAAAGATTCTGAAAAGGCTTCTGATGGGGCGTTGGTAGTTACCTCAA\nGAGATGTTGAAGAACCGTCCATAAAGGGTTCGATGGCCCGTGGTGAGTTACAATTGGCCG\nGATTATCTGGCGACGTTCCTGAATCTTCATACACTAGGAGCGAGGAAATTGAGTCTCTCG\nAGCAGTTTCATATGGCAACAGCTAGTTCGTTAATTCACAAGCAGATGTGTTCGATCGTGT\nACACGGGCCCTCTTAAAGTTCAACAAATGAAAAACTTTATAGACAGCCTGGTAGCCTCGC\nTCTCTGCTGCGGTGTCGAATCTAGTGAAGATCCTAAAAGATACAGCTGCGATTGACCTTG\nAAACTCGTCAAAAGTTCGGAGTTCTGGATGTTGCTTCGAAAAGGTGGCTAGTTAAACCAT\nCCGCAAAGAACCATGCATGGGGGGTTGTTGAGACTCATGCGAGGAAATATCACGTCGCAT\nTACTGGAGCACGATGAATTTGGCATTATTACGTGCGATAACTGGCGACGGGTGGCTGTGA\nGTTCTGAGTCGGTAGTATATTCTGATATGGCTAAACTCAGAACTCTGAGAAGATTGCTCA\nAAGATGGAGAACCACACGTTAGTTCAGCAAAGGTGGTTTTGGTGGATGGCGTTCCAGGGT\nGCGGGAAAACAAAGGAAATTCTTTCGAGAGTTAATTTCGAAGAAGATCTAATTCTTGTCC\nCTGGTCGTCAAGCTGCCGAGATGATCAGAAGAAGAGCTAATGCGTCGGGCATAATAGTGG\nCTACAAAGGACAATGTGCGTACCGTCGATTCATTTTTGATGAATTACGGGAAAGGGGCAC\nGCTGTCAGTTCAAAAGATTGTTCATAGACGAAGGTTTGATGCTGCATACTGGTTGTGTGA\nATTTCTTGGTTGAAATGTCTCTGTGCGATATTGCATATGTTTATGGAGACACCCAACAAA\nTTCCGTACATCAACAGAGTAACTGGTTTCCCGTACCCTGCACACTTTGCAAAATTGGAGG\nTCGACGAAGTCGAAACAAGAAGAATTACTCTTCGTTGTCCGGCTGATGTCACACACTTCC\nTAAATCAAAGGTATGAAGGACACGTAATGTGCACGTCTTCTGAAAAGAAATCAGTTTCCC\nAGGAAATGGTTAGTGGGGCTGCGTCTATCAATCCTGTGTCCAAGCCGCTTAAAGGGAAAA\nTTTTGACTTTTACACAGTCTGACAAGGAGGCCCTTCTCTCAAGGGGCTATGCAGATGTCC\nATACTGTACATGAGGTACAAGGTGAGACTTATGCAGACGTATCGTTAGTTCGACTAACAC\nCTACGCCTGTATCTATCATCGCAAGAGACAGTCCGCATGTTCTGGTCTCGTTGTCAAGAC\nACACAAAATCCCTAAAGTACTACACCGTTGTGATGGATCCTTTAGTTAGTATCATTAGAG\nATTTAGAACAGGTTAGTAGTTACTTATTAGACATGTACAAAGTAGATGCAGGTACTCAAT\nAGCAATTACAGGTCGACTCTGTGTTTAAGAATTTCAATCTTTTTGTAGCAGCTCCAAAGA\nCTGGAGATATATCTGATATGCAATTTTACTATGATAAGTGTCTTCCTGGGAACAGCACGT\nTGTTGAACAACTACGACGCTGTTACCATGAAATTGACTGACATTTCTCTGAATGTCAAAG\nATTGCATATTAGATATGTCTAAGTCTGTAGCTGCTCCGAAAGATGTCAAACCAACTTTAA\nTACCGATGGTACGAACGGCGGCAGAAATGCCTCGCCAGACTGGACTGTTGGAAAATTTAG\nTTGCGATGATTAAAAGAAATTTTAATTCACCAGAGTTGTCCGGAGTAGTTGATATTGAAA\nATACTGCATCTTTAGTGGTAGATAAGTTTTTTGATAGTTATTTACTTAAGGAAAAAAGAA\nAACCAAACAAAAATTTTTCACTGTTTAGTAGAGAGTCTCTCAATAGGTGGATAGCAAAGC\nAAGAACAAGTCACAATTGGTCAGTTGGCCGATTTTGATTTTGTGGATCTTCCAGCCGTTG\nATCAGTACAGGCATATGATAAAAGCGCAACCGAAGCAGAAACTGGATCTGTCAATTCAGA\nCGGAATATCCAGCGTTGCAAACGATTGTGTATCATTCAAAGAAAATCAACGCAATATTTG\nGTCCTCTTTTCAGTGAGCTTACAAGGCAATTACTTGACAGTATTGACTCAAGCAGATTCT\nTGTTCTTTACGAGAAAGACACCGGCTCAGATCGAAGATTTCTTCGGAGATCTAGACAGTC\nATGTCCCAATGGACGTACTTGAGTTGGATATTTCAAAGTATGATAAGTCTCAAAACGAGT\nTTCATTGTGCTGTTGAGTACGAAATCTGGAGGAGACTGGGTCTGGAGGATTTCTTGGCAG\nAAGTGTGGAAACAAGGGCATAGAAAAACCACTCTGAAAGATTACACTGCTGGTATAAAAA\nCGTGTTTATGGTACCAGAGAAAGAGTGGTGATGTTACAACTTTTATCGGTAATACCGTCA\nTCATTGCTTCGTGTCTTGCATCAATGCTCCCGATGGAAAAATTGATAAAAGGAGCCTTCT\nGCGGAGATGACAGTTTGTTGTACTTTCCTAGAGGTTGTGAGTATCCCGATATACAACAAG\nCTGCTAATCTGATGTGGAATTTTGAGGCCAAACTGTTCAAGAAGCAATATGGGTACTTCT\nGCGGGAGGTACGTGATTCATCACGATAGAGGTTGCATAGTATACTACGACCCTCTGAAGC\nTGATTTCGAAACTTGGTGCTAAACACATCAAGGATTGGGATCATTTGGAGGAGTTCAGAA\nGATCCCTCTGTGATGTTGCTGAGTCGTTGAACAATTGTGCGTATTACACACAATTGGACG\nACGCTGTTGGGGAGGTTCATAAAACCGCCCCACCTGGTTCGTTTGTTTATAGGAGTTTAG\nTTAAGTATTTGTCAGATAAAGTTTTGTTTAGAAGTTTATTTCTTGATGGCTCTAGTTGTT\nAAAGGTAAGGTAAATATTAATGAGTTTATCGATCTGTCAAAGTCTGAGAAACTTCTCCCG\nTCGATGTTCACGCCTGTAAAGAGTGTTATGGTTTCAAAGGTTGATAAGATTATGGTCCAT\nGAAAATGAATCATTGTCTGAAGTAAATCTCTTAAAAGGTGTAAAACTTATAGAAGGTGGG\nTATGTTTGCTTAGTTGGTCTTGTTGTGTCCGGTGAGTGGAATTTACCAGATAATTGCCGT\nGGTGGTGTGAGTGTCTGCATGGTTGACAAGAGAATGGAAAGAGCGGACGAAGCCACACTG\nGGGTCATATTACACTGCTGCTGCTAAAAAGCGGTTTCAGTTTAAAGTGGTCCCAAATTAC\nGGTATTACTACAAAGGATGCAGAAAAGAACATATGGCAGGTCTTAGTAAATATTAAAAAT\nGTAAAAATGAGTGCGGGCTACTGCCCTTTGTCATTAGAATTTGTGTCTGTGTGTATTGTT\nTATAAAAATAATATAAAATTGGGTTTGAGGGAGAAAGTAACGAGTGTGAACGATGGAGGA\nCCCATGGAACTTTCAGAAGAAGTTGTTGATGAGTTCATGGAGAATGTTCCAATGTCGGTT\nAGACTCGCAAAGTTTCGAACCAAAACCTCAAAAAGAGGTCCGAAAAATAATAATAATTTA\nGGTAAGGGGCGTTCAGGCGGAAGGCCTAAACCAAAAAGTTTTGATGAAGTTGAAAAAGAG\nTTTGATAATTTGATTGAAGATGAAGCCGAGACGTCGGTCGCGGATTCTGATTCGTATTAA\nATATGTCTTACTCAATCACTTCTCCATCGCAATTTGTGTTTTTGTCATCTGTATGGGCTG\nACCCTATAGAATTGTTAAACGTTTGTACAAATTCGTTAGGTAACCAGTTTCAAACACAGC\nAAGCAAGAACTACTGTTCAACAGCAGTTCAGCGAGGTGTGGAAACCTTTCCCTCAGAGCA\nCCGTCAGATTTCCTGGCGATGTTTATAAGGTGTACAGGTACAATGCAGTTTTAGATCCTC\nTAATTACTGCGTTGCTGGGGGCCTTCGATACTAAGAATAGAATAATCGAAGTAGAAAACC\nAGCAGAGTCCGACAACAGCTGAAACGTTAGATGCTACCCGCAGGGTAGACGACGCTACGG\nTTGCAATCCGGTCTGCTATAAATAATTTAGTTAATGAACTAGTAAAAGGTACTGGACTGT\nACAATCAGAATACTTTTGAAAGTATGTCTGGGTTGGTCTGGACCTCTGCACCTGCATCTT\nAAATGCATAGGTGCTGAAATATAAAGTTTGTGTTTCTAAAACACACGTGGTACGTACGAT\nAACGTACAGTGTTTTTCCCTCCACTTAAATCGAAGGGTAGTGTCTTGGAGCGCGCGGAGT\nAAACATATATGGTGCATATATGTCCGTAGGCACGTAAAAAAGCGAGGGATTCGAATTCCC\nCCGGAGCACCACTGGTGGTGGCCCA\n>AY184220.1 Human poliovirus 2 strain Sabin 2, complete genome\nTTAAAACAGCTCTGGGGTTGTACCCACCCCAGAGGCCCACGTGGCGGCTAGCACTCCGGT\nATTACGGTACCCTTGTGCGCCTGTTTTATACTCCCCTCCCGCAACTTAGAAGCACGAAAC\nCAAGTTCAATAGAAGGGGGTACAAACCAGTACCACTACGAACAAGCACTTCTGTTTCCCC\nGGTGACATTGCATAGACTGCTCACGCGGTTGAAAGTGATCGATCCGTTACCCGCTTGTGT\nACTTCGAAAAGCCTAGTATCGCCTTGGAATCTTCGACGCGTTGCGCTCAGCACCCGACCC\nCGGGGTGTAGCTTAGGCTGATGAGTCTGGACATTCCTCACCGGTGACGGTGGTCCAGGCT\nGCGTTGGCGGCCTACCTATGGCTAACGCCATAGGACGTTAGATGTGAACAAGGTGTGAAG\nAGCCTATTGAGCTACATAAGAGTCCTCCGGCCCCTGAATGCGGCTAATCCTAACCACGGA\nACAGGCGGTCGCGAACCAGTGACTGGCTTGTCGTAACGCGCAAGTCTGTGGCGGAACCGA\nCTACTTTGGGTGTCCGTGTTTCCTGTTATTTTTATCATGGCTGCTTATGGTGACAATCAG\nAGATTGTTATCATAAAGCGAATTGGATTGGCCATCCGGTGAGTGTTGTGTCAGGTATACA\nACTGTTTGTTGGAACCACTGTGTTAGCTTTACTTCTCATTTAACCAATTAATCAAAAACA\nATACGAGGATAAAACAACAATACTACAATGGGCGCCCAAGTTTCATCACAGAAAGTTGGA\nGCCCACGAAAATTCAAACAGAGCCTATGGCGGGTCCACCATCAATTACACTACAATCAAT\nTACTATAGGGACTCTGCAAGCAATGCAGCAAGCAAGCAAGATTTTGCACAAGATCCGTCC\nAAGTTCACCGAACCCATTAAGGACGTCCTTATTAAGACCGCTCCCATGCTAAACTCCCCA\nAACATTGAGGCGTGTGGTTATAGTGACAGGGTAATGCAGCTAACTCTGGGCAATTCAACG\nATCACCACCCAAGAAGCGGCCAATTCTGTTGTTGCCTACGGTAGATGGCCTGAATACATC\nAGAGATACCGAGGCAAATCCTGTAGACCAACCAACCGAGCCCGATGTAGCCGCGTGCAGG\nTTCTACACATTAGATACCGTCACTTGGCGCAAGGAGTCCAGAGGGTGGTGGTGGAAACTA\nCCAGACGCTTTAAAAGACATGGGGTTATTTGGTCAAAACATGTTTTATCACTATCTTGGG\nAGGGCTGGCTACACAGTGCACGTACAGTGCAATGCTTCAAAGTTTCATCAAGGAGCTCTA\nGGGGTGTTTGCAGTTCCAGAAATGTGTTTAGCTGGTGATAGCACAACTCACATGTTCACA\nAAGTACGAGAATGCGAATCCAGGCGAAAAAGGAGGTGAATTCAAAGGGAGTTTCACCCTT\nGATACCAACGCCACTAACCCTGCACGGAACTTCTGCCCAGTTGATTACCTCTTCGGGAGT\nGGAGTGCTGGTAGGGAATGCATTTGTTTATCCACATCAAATAATAAACCTGCGCACTAAC\nAACTGTGCTACGCTAGTATTGCCCTATGTAAACTCACTCTCAATAGATAGCATGACAAAG\nCACAACAACTGGGGGATCGCTATCCTCCCCCTGGCGCCACTAGACTTTGCCACTGAATCT\nTCCACTGAGATACCCATTACACTGACCATTGCTCCCATGTGCTGCGAATTCAATGGTTTA\nCGCAACATCACTGTGCCAAGAACCCAAGGATTACCAGTCCTGAACACTCCAGGGAGTAAC\nCAGTACCTGACCGCAGACAATTACCAGTCTCCGTGTGCGATACCTGAGTTTGATGTCACT\nCCACCCATAGACATACCAGGGGAGGTGCGCAACATGATGGAATTGGCGGAAATAGACACC\nATGATACCCCTCAACTTGACAAGTCAACGCAAGAACACAATGGACATGTATAGAGTCGAG\nTTGAGCGACACGGCTCACTCTGACACGCCGATCTTGTGTCTCTCGTTGTCCCCCGCTTCA\nGACCCCAGATTGGCACACACTATGTTGGGTGAGATATTAAATTACTACACACACTGGGCA\nGGGTCCTTGAAATTTACCTTTCTCTTTTGCGGCTCAATGATGGCCACCGGAAAGTTATTG\nGTTTCTTACGCACCACCCGGAGCAGAGGCCCCCAAGAGTCGCAAAGAAGCAATGCTTGGG\nACACATGTGATATGGGACATTGGGTTGCAGTCTTCATGCACTATGGTGGTACCTTGGATC\nAGTAATACCACATACAGACAAACCATCAACGATAGTTTCACAGAAGGTGGCTACATTAGC\nATGTTCTATCAAACTAGGGTTGTTGTCCCGTTGTCCACACCCAGAAAGATGGACATCCTG\nGGTTTTGTGTCAGCTTGCAATGACTTCAGTGTGCGCTTACTGCGAGATACAACACACATT\nAGTCAAGAGGCTATGCCACAAGGAATTGGTGACATGATTGAGGGGGCCGTTGAAGGGATT\nACTAAAAATGCATTGGTTCCCCCGACTTCCACCAATAGCCTGCCTGACACAAAGCCGAGC\nGGTCCAGCCCACTCCAAGGAGATACCTGCATTGACAGCCGTGGAGACAGGGGCTACCAAT\nCCGTTGGTGCCTTCGGACACCGTGCAAACGCGCCATGTCATCCAGAGACGAACGCGATCA\nGAGTCCACGGTTGAGTCATTCTTTGCAAGAGGGGCTTGCGTGGCTATCATTGAGGTGGAC\nAATGATGCACCGACAAAGCGCGCCAGCAGATTGTTTTCGGTTTGGAAAATAACTTACAAA\nGATACTGTTCAACTGAGACGCAAACTGGAATTTTTCACATATTCGAGATTTGACATGGAG\nTTCACTTTTGTGGTCACCTCAAACTACATTGATGCAAATAACGGACATGCATTGAACCAA\nGTTTATCAGATAATGTATATACCACCCGGAGCACCTATCCCTGGTAAATGGAATGACTAT\nACGTGGCAGACGTCCTCTAACCCGTCGGTGTTTTACACCTATGGGGCGCCCCCAGCAAGA\nATATCAGTGCCCTACGTGGGAATTGCTAATGCGTATTCCCACTTTTATGATGGGTTTGCA\nAAAGTACCACTAGCGGGTCAAGCCTCAACTGAAGGCGATTCGTTGTACGGTGCTGCCTCA\nCTGAATGATTTTGGATCACTGGCTGTTCGCGTGGTAAATGATCACAACCCCACGCGGCTC\nACCTCCAAGATCAGAGTGTACATGAAGCCAAAGCATGTCAGAGTCTGGTGCCCACGACCT\nCCACGAGCAGTCCCATACTTCGGACCAGGTGTTGATTATAAAGATGGGCTCACCCCACTA\nCCAGAAAAGGGATTAACGACTTATGGATTTGGACACCAAAACAAAGCTGTGTACACAGCT\nGGCTACAAAATTTGCAATTACCACCTAGCTACACAAGAAGACTTGCAAAATGCCGTGAGT\nGTCATGTGGAACAGAGACCTCTTAGTGGCTGAATCAAGGGCCCTTGGCACCGACTCGATC\nGCAAGGTGCAGCTGTAACACGGGTGTGTACTACTGTGAATCCAGGAGAAAATATTATCCA\nGTTTCTTTCATTGGGCCCACCTTCCAATACATGGAAGCCAATGAATATTACCCGGCTAGA\nTATCAATCACACATGCTTATTGGTCATGGGTTTGCATCACCGGGTGATTGTGGTGGCATA\nCTTAGATGTCAACACGGGGTGATAGGAATAATCACTGCTGGTGGGGAAGGCTTGGTTGCA\nTTTTCAGACATTAGAGACCTGTATGCTTATGAGGAGGAAGCTATGGAGCAGGGCATTTCC\nAACTATATTGAGTCACTTGGTGCTGCATTTGGTAGTGGATTCACTCAACAAATTGGTGAT\nAAAGTTTCCGAGCTAACCAGCATGGTAACTAGCACCATTACAGAGAAGTTGCTTAAAAAC\nTTAATCAAAATTATCTCATCACTTGTGATCATTACCAGGAATTATGAGGACACTACCACA\nGTGCTTGCCACCCTCGCCCTCCTTGGGTGCGACATCTCACCGTGGCAGTGGCTAAAGAAG\nAAGGCATGTGACATCCTGGAAATTCCATACGCCATCAAACAAGGAGATAGTTGGTTGAAG\nAAATTCACTGAGGCATGTAATGCTGCAAAGGGACTGGAGTGGGTGTCCAATAAGATATCC\nAAATTCATTAGTTGGTTGCAGGATAAAATCATCCCACAAGCGAGAGACAAATTAGAGTTT\nGTCACTAAACTAAAGCAATTAGAAATGCTTGAAAATCAGATTTCCACCATACACCAATCT\nTGTCCAAGTCAAGAACATCAGGAGATCTTATTCAACAATGTGCGGTGGCTATCTATCCAG\nTCCAAGAGGTTTGCACCACTATATGCACATGAAGCTAAAAGGATTCAAAAGCTGGAGCAT\nACCATAAATAATTACGTACAGTTCAAGAGCAAGCACCGTATTGAGCCAGTATGTTTGTTA\nGTACATGGCAGTCCAGGGACAGGAAAATCAGTTGCAACCAATCTAATTGCTAGAGCAATA\nGCCGAGAAAGAGAACACCTCCACATACTCACTGCCACCTGATCCGTCTCACTTTGATGGC\nTACAAGCAACAGGGTGTGGTTATTATGGATGACCTAAACCAAAATCCAGACGGAGCAGAC\nATGAAACTTTTTTGTCAAATGGTGTCCACTGTGGAGTTTATTCCACCGATGGCCTCGCTA\nGAAGAGAAAGGCATTTTGTTCACATCTAATTACGTTTTAGCCTCCACCAACTCCAGTCGG\nATCACACCACCCACGGTGGCTCACAGTGATGCGCTGGCCAGGAGATTCGCATTTGACGTG\nGACATACAAGTCATGAGCGAGTACTCCAGAGACGGAAAGCTCAACATGGCAATGGCTACT\nGAAATGTGCAAAAACTGTCATCAACCAGCAAACTTCAAAAGATGTTGTCCTTTAGTGTGT\nGGCAAGGCAATTCAGTTAATGGATAAATCTTCCAGGGTTAGATACAGCATTGATCAGATC\nACTACAATGATTGTTAATGAGAGAAACAGAAGATCAAACATTGGTAATTGCATGGAAGCT\nCTATTCCAGGGACCACTGCAGTATAAAGATCTAAAAATAGATGTTAAGACCAGTCCCCCT\nCCGGAGTGTATCAACGATTTGCTCCAGGCAGTTGATTCCCAGGAAGTGAGAGATTACTGT\nGAAAAGAAAGGCTGGATTGTTAACATTACCAGTCAGGTTCAAACAGAGAGGAACATCAAC\nCGGGCGATGACTATCCTACAAGCAGTAACTACTTTCGCTGCAGTAGCCGGTGTCGTGTAC\nGTTATGTACAAGCTGTTCGCTGGGCACCAGGGTGCATACACTGGTTTGCCAAATAAACGA\nCCCAATGTACCCACTATCAGGACAGCAAAAGTGCAAGGCCCTGGGTTTGATTACGCAGTG\nGCCATGGCTAAAAGAAACATTGTTACAGCAACCACCAGCAAAGGGGAGTTTACGATGTTG\nGGAGTCTATGATAATGTGGCCATCTTGCCAACCCACGCCTCACCTGGTGAAAGCATTGCG\nATCGACGGTAAAGAGGTGGAAATTCTTGACGCCAAAGCCCTTGAAGATCAGGCAGGAACT\nAATCTTGAAATTACCATAATTACACTAAAGAGGAACGAGAAGTTCAGAGATATCAGGCCA\nCACATTCCCACCCAAATCACCGAAACAAATGATGGAGTTTTGATCGTGAACACTAGTAAG\nTACCCCAACATGTATGTTCCCGTTGGTGCTGTGACCGAACAGGGGTATCTTAATCTCGGT\nGGACGACAAACCGCTCGTACGCTAATGTACAACTTTCCAACTAGAGCAGGTCAGTGTGGT\nGGTGTCATCACGTGCACTGGTAAAGTCATTGGGATGCATGTTGGTGGGAACGGTTCACAT\nGGGTTCGCGGCGGCCCTAAAGCGGTCATACTTCACTCAGATTCAAGGTGAGATTCAATGG\nATGAAACCATCAAAAGAAGTGGGATACCCGATCATAAATGCTCCGTCCAAAACCAAACTT\nGAACCCAGCGCTTTTCACTATGTGTTTGAAGGGGTGAAGGAACCAGCAGTCCTTACCAAA\nAATGATCCCAGGCTCAGGACAGACTTTGAAGAAGCAATATTCTCTAAGTATGTAGGCAAC\nAAGATCACTGATGTGGATGAGTACATGAAAGAGGCAGTGGATCATTACGCTGGCCAACTC\nATGTCTCTAGACATCAACACAGAACAAATGTGCTTGGAGGACGCCATGTACGGCACCGAT\nGGCCTGGAAGCACTTGACTTGACCACTAGTGCTGGATACCCTTATGTAGCAATGGGAAAG\nAAAAAGAGAGACATCTTGAATAAGCAGACTAGAGACACCAAGGAAATGCGGAGACTCTTA\nGATACTTATGGAATTAACTTACCGCTTGTAACATATGTTAAAGATGAACTAAGGTCAAAA\nACTAAGGTGGAGCAGGGAAAATCCAGATTGATTGAAGCCTCCAGTTTGAATGATTCAGTG\nGCCATGAGAATGGCATTTGGAAATCTCTATGCAGCATTTCACAAAAACCCAGGAGTTGTC\nACTGGCAGTGCAGTTGGTTGTGATCCAGATCTATTTTGGAGCAAGATCCCAGTGCTAATG\nGAAGAGAAGCTCTTTGCTTTTGACTACACAGGTTATGATGCATCACTCAGCCCGGCCTGG\nTTTGAGGCACTCAAAATGGTGCTAGAGAAAATCGGATTTGGGGACAGGGTGGATTATATT\nGATTACCTCAACCATTCCCACCACCTGTACAAAAACAAAACTTATTGCGTAAAAGGCGGC\nATGCCATCTGGCTGCTCAGGCACATCAATTTTTAACTCAATGATTAACAACTTAATCATT\nAGGACACTCCTACTGAAAACCTACAAGGGCATAGATTTAGATCACCTAAAGATGATTGCC\nTATGGTGATGATGTAATTGCTTCCTACCCCCATGAGGTTGATGCTAGTCTCCTAGCCCAA\nTCAGGAAAAGACTATGGACTAACCATGACTCCAGCAGACAAGTCAGCTACCTTTGAAACA\nGTCACATGGGAGAATGTAACATTCTTGAAAAGATTCTTTAGAGCGGATGAGAAGTATCCC\nTTCCTCATACATCCAGTAATGCCAATGAAGGAGATTCATGAATCAATTAGATGGACAAAG\nGATCCCAGAAACACACAGGATCACGTGCGCTCATTGTGCCTATTGGCCTGGCACAACGGC\nGAAGAAGAATACAACAAGTTCTTAGCTAAAATCAGGAGTGTGCCAATTGGGAGAGCTTTA\nTTGCTCCCAGAGTACTCTACATTGTACCGCCGTTGGCTCGACTCTTTTTAGTAACCCTAC\nCTCAGTCGAATTGGATTGGGTCATGCTGTTGTAGGGGTAAATTTTTCTTTAATTCGGGG\n>KM609478.1 Coxsackievirus A8 isolate CVA8/SZ141/CHN/2012, complete genome\nTTAAAACAGCCTGTGGGTTGCACCCACTCACAGGGCCCACTGGGCGCTAGCACTCTGATT\nCTACGGAATCTTTGTGCGCCTGTTTTATAACCCCCTCCCCCAATGTAATTTAGAAGCAAT\nGCACCAATGATCAACAGCAGGCGTGGCGCACCAGCCATGTCTCGATCAAGCACTTCTGTT\nTCCCCGGACAGAGTATCAATAGACTGCTCGCGTGGTCGAAGGAGAAAACGTCCGTTACCC\nGGCTAACTACTTCGAGAAACCTAGTAGCACCAATGAAGCTGCAGAGCGTTTCGCTCAGCA\nCTTACCCCGTGTAGATCAGGCCGATGAGTCACTGCGTTCCCCACGGGCGACCGTGGCAGT\nGGCTGCGTTGGCGGCCTGCCTATGGGGTCACCCATAGGACGCTCTAATGTGGACATGGTG\nCGAAGAGTCTATTGAGCTAGTTAGTAGTCCTCCGGCCCCTGAATGCGGCTAATCCTAACT\nGCGGAGCGCATACCCTCAAACCAGGGGGTGGTGCGTCGTAACGGGTAACTCTGCAGCGGA\nACCGACTACTTTGGGTGTCCGTGTTTCCTTTTATTCTCTTAATGGCTGCTTATGGTGACA\nATTGAGGAATTGTTACCATATAGCTATTGGATTGGCCATCCGGTGTGTAACAGAGCAATT\nATCTACTTGTTTGCAGGATTTACCCCATTAACGTTCAAATCTCTTAACACACTACAGTAC\nATACTAACCTTGAATACAAGAAAATGGGAGCACAAGTTTCGACTCAAAAGTCTGGTAGCC\nACGAGACTGGCAACATAGCCACTGAAGGGTCCACCATTAACTTTACTAACATCAATTATT\nACAAGGACTCGTACGCCGCCTCGGCTAGCAAACAGGACTTCACCCAGGATCCTACTAGGT\nTTACTAGCCCTGTGCTTGATGCGCTGAGGGAAGTGGCACCTCCATTAAAGTCACCCTCAG\nTGGAAGCGTGCGGATACAGTGATAGAGTAGCGCAGTTGACTGTCGGCAATTCAACAATCA\nCCACACAAGAGGCTGCTAACATAGTCCTTGCTTACGGGGAATGGCCTGAGTACTGTCCCG\nACAAAGACGCCACCGCTGTAGATAAGCCTACACGCCCCGATGTGTCGGTTAATAGATTCT\nACACCATGTCTACGCAAATGTGGCAGGACACCTCGAAAGGGTGGTACTGGAAGTTCCCAG\nATGTTCTTACCAAGACTGGTGTCTTTGGACAAAATGCCCAGTATCACTATTTGTACAGAT\nCTGGATTTTGCATACATGTCCAATGCAACGCTAGTAAATTCCATCAAGGAGCACTGTTAG\nTGGCTGCCATCCCAGAGATGGTGTTAGGATCCAATAGCTCAGATCCCAAGCCCAACACTG\nCAAAGCACCCTGAATTCACTACAACAATGCCAGGTGCTAATGGTGGAATTTTTGAAAATC\nCCTATATCTTGGACATGGGGGTTCCCTTGAGCCAAGCTTTGGTGTTTCCACACCAATGGA\nTCAACCTGCGCACTAACAACTGTGCGACCATTATAGTGCCTTATATTAATGCTGTTCCAT\nTTGATTCAGCCATTAACCACAACAACTTCACGCTAGTCGTAATTCCGATTAGCCCGTTAA\nAATACTGCACAGGAGCGACAACAGCCATCCCTATAACAGTAACGATAGCCCCATTAAATT\nCTGAATTTTGTGGGTTGAGGCAAGCTACATCGCAGGGAATACCAGTGGAGCTAAAACCCG\nGCACCAATCAATTTTTGACAACTGATAACGAAGTCTCCGTACCAATCTTACCTGGTTTCC\nAGCCTACACCGGTTATACATATACCAGGGGAGGTGAACAACCTCCTGGAGCTCTGCCAGG\nTTGAATCTATCTTGGAGGTCAATAATGTGACTGGACAAGAAGGGATAAACCGACTCCTTA\nTCCCAGTTTCTACACAAAGTGACAAGGATACTTTGTGTGCATCACTCAGAGTCGATCCAG\nGTAGGGACGGACCGTGGCAATCTACTTTAGTTGGGCAAATATGTAGGTATTACACCCAGT\nGGTCTGGTTCATTAGAGATCACATTCATGTTTACTGGTTCATTCATGGCAACCGGTAAAA\nTGCTGATAGCTTACTCCCCGCCTGGGAGTGCGCAACCAACAACAAGAGACCTGGCAATGC\nTCGGCACGCACGTAGTGTGGGATTTTGGGTTGCAATCATCTATTACTCTTGTGATCCCAT\nGGATCAGCAACACACACTTCAGAACAGGCAAGGTGGGTGGTTACTTTGATTACTATGCGT\nCTGGTATAGTAACTATTTGGTATCAGACAAACTTCGTCGTGCCCCCCGACACGCCGAGTC\nAGGCTCATATAATAGCGTTGGGAGCTGCCCAGAAGAATTTCACGCTTAAACTGTGCAAGG\nATACAGATGAGGTAACACAACAAGCAGTGTTGCAGGGGGACCCCATTGAAGACATAATAA\nCTAGCACAGTCTCCCGCACATTGCAGCAAATTAGCACTCCAACACATAGCACTACTGCAG\nCAAACACCTCTGTGAGTAACCATAAGATAGGCACTGGAGATGTTCCAGCTCTCCAAGCTG\nCGGAGACAGGTGCTACCTCTAACGCCTCGGATGAGAACATGATCGAGACACGCTGCGTGC\nTAAATCGCAATGGAGTCGTGGAAACCAGTCTGGACCACTTCTTCTCAAGAGCAGGTCTGG\nTGGGGGTGATCAATGTGCAAGATGGTAGTACACAGAAGGGATTTGAGGTGTGGGATGTGG\nATGTGATGGGGTTTGTACAGCTCAGAAGGAAGTTGGAAATGTTTACATACATGAGATTCA\nATGCTGAGTTTACATTTGTGTCCACACTTGCAGACGGCACGACTCCCAGGGTGATGTTAC\nAGTACATGTATGTTCCACCTGGTGCCCCCAAACCTCAAGAGAGGGATTCATTCCAATGGC\nAAACAGCGACCAACCCGTCAGTGTTCTGCAAAATGAGCGATCCTCCCCCACAAGTCTCTG\nTCCCTTTCATGTCGCCAGCCAGCGCGTACCAGTGGTTCTATGATGGATATCCTACATTTG\nATGATCGACCTGCCACCTCAAATCACCCGTATGGACAGTGCCCTAATAACATGATGGGCA\nCATTTGCAGTGCGATTTGTCAGCAAGACCCCTGCTATACGGGACTTGCGTGTTAGGGTAT\nATATGCGCCTCAAACACGTGCGCGCTTGGGTACCGAGGCCCATACGATCCCAAGCATACA\nTCTTAAAGAACTATCCAAACTATGACGGGACAAATATAACACCAACATCCAAGGACAGGC\nAAAGCATCAAAACGACTGGGAAATTTGGTCAGCAGTCCGGTGCTATTTATGTGGGCAATT\nACAGAGTAGTTAACAGACACCTTGCCACACACAATGACTGGGCCAACTTAGTATGGGAAG\nACAGCTCCAGGGATCTCCTTGTGTCATCCACGACTGCTCAAGGATGTGACATCATTGCTC\nGTTGCAATTGCCAGACTGGAGTGTATTACTGTAACTCCCAAAGAAAACACTACCCAGTTA\nGCTTTTCAAAGCCTAGCCTGATCTATGTGGAAGCTAGTGAGTATTACCCAGCTAGGTATC\nAATCTCACCTTATGCTCGCACAAGGACACTCAGAACCTGGCGATTGTGGTGGTATCCTCA\nGGTGCCAACACGGCGTTGTCGGCATAGTGTCCACTGGTGGTGACGGACTCGTCGGCTTCG\nCAGATGTCAGGGATCTCCTTTGGTTAGATGAGGAGGCGATGGAGCAAGGTGTGTCTGATT\nACATCAAGGGACTCGGTGATGCATTTGGAACTGGCTTCACTGATGCTGTCTCTAGAGAAG\nTGGAGGCCCTTAAAAACCACCTAATTGGTTCTGAAGGAGCTGTTGAGAAAATCCTCAAGA\nATTTGATCAAGTTAATCTCTGCTCTTGTCATTGTGATTAGGAGTGATTATGACATGGTCA\nCCCTTACAGCAACTCTAGCTTTAATCGGGTGTCACGGTAGTCCTTGGGCATGGATTAAAA\nCAAAGACAGCATCTATTTTAGGCATCCCTATCGCTCAAAAGCAGAGCGCCTCYTGGCTTA\nAAAAGTTCAACGATATGGCCAACGCTGCCAAGGGATTGGAATGGGTTTCTAACAAGATCA\nGCAAATTCATCGATTGGCTCAAGGAAAAAATCATACCAGCAGCCAAGGAGAAGGTCGAGT\nTTTTAAATAACTTGAAACAGTTACCACTGCTAGAGAACCAAATCTCTAATCTGGAACAAT\nCTGCTGCCTCACAAGAGGACCTTGAAGTTATGTTTGGGAATGTGTCATATCTAGCTCACT\nTCTGTCGTAAGTACCAGCCACTATACGCTACAGAAGCCAAAAGAGTCTACACTCTAGAGA\nAGAGGATGAACAACTACATGCAGTTCAAGAGCAAACACCGTATTGAACCTGTATGTCTTA\nTTATCAGGGGTTCACCGGGCACTGGGAAGTCTTTAGCAACTGGCATCATTGCTCGAGCGA\nTAGCTGATAAGTATCACTCCAGTGTCTATTCACTCCCACCAGACCCAGACCACTTTGATG\nGGTACAAGCAGCAAGTGGTTACAGTCATGGATGATCTATGTCAAAATCCTGACGGCAAAG\nATATGTCACTGTTTTGCCAAATGGTGTCTACCGTGGACTTCATTCCTCCAATGGCTTCCT\nTAGAAGAGAAGGGGGTCTCTTTCACATCTAAGTTCGTCATTGCATCCACTAATGCTAGTA\nATATCATAGTGCCAACAGTATCTGATGCAGACGCCATTCGCCGCAGGTTCTATATGGATT\nGTGACATTGAAGTAACAGACTCATATAAAACAGACCTGGGTAGGTTGGATGCCGGGCGAG\nCAGCCAAATTGTGTTCTGAGAACAACACAGCAAATTTCAAGCGTTGCAGCCCATTAGTGT\nGTGGAAAGGCTATTCAATTAAGAGATAGGAAATCTAAGGTCAGATACAGCGTGGACACAG\nTGGTCTCTGAACTCATAAGAGAGCATAATAACAGATCCGCCATTGGTAACACAATTGAGG\nCTTTGTTCCAGGGCCCACCCAAATTTAGACCCATAAGGATTAGTCTTGAAGAAACGCCAG\nCTCCAGATGCTATTAGTGATCTTCTCACTAGTGTGGATAGCGAAGAGGTACGTCAATACT\nGTAGGGATCAAGGTTGGATTATTCCGGAAACCCCTACAAATGTTGAACGACACCTCAACA\nGAGCTGTGTTGATTATGCAATCCATCGCCACGGTAGTGGCGGTTGTCTCATTGGTGTACG\nTCATCTATAAACTCTTTGCTGGGTTCCAGGGCGCATATTCTGGTGCCCCCAAGCAAACGC\nTTAAGAAACCTGTTCTCCGCACAGCAACAGTGCAGGGTCCAAGCCTTGATTTTGCCCTAT\nCACTATTGAGAAGAAACATCAGGCAAGTGCAGACAGATCAAGGGCACTTCACCATGCTGG\nGTATCAGAGATCGCTTGGCTATCCTCCCGCGACATTCTCAACCTGGAAGGACTATCTGGG\nTGGAACACAAACTCGTGAACGTCCTGGATGCTATCGAGCTGGTGGATGAACAAGGGGTCA\nACTTAGAGCTGACCTTAATCACCCTCGACACCAATGAGAAATTCAGGGATATCACCAAGT\nTCATTCCAGAAACCATTAGTGGTGCCAGCGATGCCACCTTAGTGATCAATACAGAGCACA\nTGCCCTCAATGTTTGTGCCAGTAGGTGATGTTGTACAGTATGGCTTCCTAAATCTCAGCG\nGGAAACCGACTCATCGCACTATGATGTATAACTTCCCTACTAAGGCAGGACAATGTGGAG\nGGGTAGTCACATCAGTTGGAAAGATCATTGGCATTCATATAGGAGGTAATGGTAGGCAGG\nGATTCTGTGCGGGACTCAAGAGAAGCTACTTTGCTAGTGAACAGGGAGAGATCCAATGGG\nTTAAACCTAACAAAGAAACAGGAAGACTCAACATCAATGGACCAACTCGCACCAAGCTCG\nAGCCTAGTGTGTTTCATGATGTCTTTGAGGGTGACAAGGAGCCAGCAGTCTTGCATAGTA\nAGGACCCCCGCCTTGAGGTGGACTTCGAGCAAGCATTGTTCTCCAAGTACGTGGGGAACA\nCACTACACGAACCTGATGAGTATATCAGGGAGGCAGCCCTCCACTATGCGAACCAATTAA\nAGCAGCTAGACATAAATACCTCCCAGATGAGCATGGAGGAGGCCTGTTATGGCACAGAAA\nACCTTGAGGCTATTGACCTTCACACTAGTGCGGGATACCCCTATAGCGCGCTGGGAATAA\nAAAAGAGGGATATCTTAGACCCCATTACCAGAGATGTGAGCAAGATGAAGTTCTATATGG\nATAAGTACGGTCTTGACCTCCCTTACTCCACCTATGTCAAAGATGAACTTCGCTCAATAG\nATAAGATTAAGAAGGGGAAGTCTCGCTTGATTGAAGCTAGCAGCTTGAATGACTCGGTCT\nACCTTAGAATGGCCTTTGGGCACCTCTATGAAGCTTTCCATGCGAACCCTGGCACTGTGA\nCTGGCTCAGCTGTGGGGTGTAACCCAGATGTATTTTGGAGCAAGCTACCAATCCTGCTTC\nCTGGTTCCCTCTTCGCTTTTGACTACTCAGGTTACGATGCTAGCCTCAGCCCAGTTTGGT\nTCAGAGCGTTGGAATTAGTCCTTAGAGAGATAGGTTATGGTGATGAGGCAGTCTCACTCA\nTTGAAGGAATCAACCATACACACCATGTGTACCGTAACAAAACCTACTGCGTACTTGGTG\nGAATGCCCTCAGGTTGCTCAGGGACATCCATCTTCAACTCAATGATTAATAACATCATCA\nTCAGAGCACTACTTATTAAAACATTCAAGGGCATTGATCTGGATGAACTCAACATGGTTG\nCCTACGGGGACGATGTGCTCGCTAGTTACCCCTTTCCAATTGACTGCCTGGAGCTAGCAA\nAGACAGGTAAGGAGTATGGCCTAACCATGACCCCTGCAGACAAGTCCCCTTGCTTCAATG\nAAGTTAATTGGGAAAATGCAACCTTCCTCAAGAGAGGCTTCTTGCCTGATGAGCAATTCC\nCGTTTTTGATCCACCCCACCATGCCAATGAAGGAGATTCATGAATCCATTCGGTGGACCA\nAGGATGCACGCAATACTCAAGATCACGTGCGGTCTCTATGTCTGTTGGCATGGCATAACG\nGTAAGCAAGAATATGAAAAATTTGTGAGCTCAATTAGATCCGTCCCAGTAGGAAAAGCAT\nTGGCAATCCCCAACTATGAAAATCTGAGACGTAATTGGCTCGAATTGTTTTAGAGGTTGG\nACAAACGACTCAACCCCACCAGAAATCTGGTCGTGAATGTGACTGGTGGGGGTAAATTTG\nTTATAACCAGAATAGC\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/library/prelim_map.txt", "content": "ACCNUM\tNC_004102.1\tNC_004102\nACCNUM\tEU255973.1\tEU255973\nACCNUM\tKJ207374.1\tKJ207374\nACCNUM\tAY184220.1\tAY184220\nACCNUM\tKM609478.1\tKM609478\nACCNUM\tNC_002058.3\tNC_002058\nACCNUM\tNC_002692.1\tNC_002692\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/accession2taxid/nucl_est.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/accession2taxid/nucl_gb.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\nNC_002058\tNC_002058.3\t138950\t12408699\nNC_002692\tNC_002692.1\t12253\t13357204\nNC_004102\tNC_004102.1\t11103\t22129792\nAY184220\tAY184220.1\t12083\t27085398\nEU255973\tEU255973.1\t31646\t190684443\nKJ207374\tKJ207374.1\t12253\t612340474\nKM609478\tKM609478.1\t42788\t743485545\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/accession2taxid/nucl_gss.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/accession2taxid/nucl_wgs.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/accession2taxid/pdb.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\n5HQL_A\t5HQL_A\t1\t1134776119\n5HQL_B\t5HQL_B\t1\t1134776120\n5HQL_C\t5HQL_C\t1\t1134776121\n5HQL_D\t5HQL_D\t1\t1134776122\n5HQL_E\t5HQL_E\t1\t1134776123\n5HQL_F\t5HQL_F\t1\t1134776124\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/accession2taxid/prot.accession2taxid", "content": "accession\taccession.version\ttaxid\tgi\nNP_041277\tNP_041277.1\t138950\t9627037\nNP_078447\tNP_078447.1\t12253\t13357205\nNP_078446\tNP_078446.1\t12253\t13357206\nNP_078448\tNP_078448.1\t12253\t13357207\nNP_078449\tNP_078449.1\t12253\t13357208\nNP_671491\tNP_671491.1\t11103\t22129793\nNP_803170\tNP_803170.1\t11103\t28921567\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/delnodes.dmp", "content": "" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/gi_taxid_nucl.dmp", "content": "" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/gi_taxid_prot.dmp", "content": "1134776119\t1\n1134776120\t1\n1134776121\t1\n1134776122\t1\n1134776123\t1\n1134776124\t1\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/merged.dmp", "content": "" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/names.dmp", "content": "1\t|\tall\t|\t\t|\tsynonym\t|\n1\t|\troot\t|\t\t|\tscientific name\t|\n10239\t|\tVira\t|\t\t|\tsynonym\t|\n10239\t|\tViridae\t|\t\t|\tsynonym\t|\n10239\t|\tViruses\t|\t\t|\tscientific name\t|\n10239\t|\tviruses\t|\tviruses\t|\tblast name\t|\n11050\t|\tFlaviviridae\t|\t\t|\tscientific name\t|\n11050\t|\tFlavivirus (arbovirus group B)\t|\t\t|\tsynonym\t|\n11102\t|\tHepacivirus\t|\t\t|\tscientific name\t|\n11102\t|\tHepatitis C virus group\t|\t\t|\tsynonym\t|\n11102\t|\tHepatitis C viruses\t|\t\t|\tsynonym\t|\n11102\t|\tHepatitis C-like viruses\t|\t\t|\tsynonym\t|\n11103\t|\tHCV\t|\t\t|\tacronym\t|\n11103\t|\tHepatitis C\t|\t\t|\tmisnomer\t|\n11103\t|\tHepatitis C virus\t|\t\t|\tscientific name\t|\n11103\t|\thepatitis C virus HCV\t|\t\t|\tsynonym\t|\n11103\t|\thuman hepatitis C virus\t|\t\t|\tsynonym\t|\n11103\t|\thuman hepatitis C virus HCV\t|\t\t|\tsynonym\t|\n11103\t|\thuman hepatitis virus C HCV\t|\t\t|\tsynonym\t|\n11103\t|\thuman hepatitis virus HCV\t|\t\t|\tmisnomer\t|\n11103\t|\tpost-transfusion hepatitis non A non B virus\t|\t\t|\tsynonym\t|\n12058\t|\tPicormavirus\t|\t\t|\tmisspelling\t|\n12058\t|\tPicornaviridae\t|\t\t|\tscientific name\t|\n12058\t|\tPicornavirus\t|\t\t|\tsynonym\t|\n12059\t|\tEnterovirus\t|\t\t|\tscientific name\t|\n12059\t|\tEnteroviruses\t|\t\t|\tsynonym\t|\n12059\t|\tRhinovirus\t|\t\t|\tincludes\t|\n12059\t|\tRhinoviruses\t|\t\t|\tincludes\t|\n12059\t|\tcommon cold viruses\t|\t\t|\tincludes\t|\n12083\t|\tHPV-2\t|\t\t|\tacronym\t|\n12083\t|\tHuman Poliovirus type 2\t|\t\t|\tsynonym\t|\n12083\t|\tHuman poliovirus 2\t|\t\t|\tscientific name\t|\n12083\t|\tPoliovirus 2\t|\t\t|\tsynonym\t|\n12083\t|\tPoliovirus type 2\t|\t\t|\tsynonym\t|\n12234\t|\tTobamoviridae\t|\t\t|\tsynonym\t|\n12234\t|\tTobamovirus\t|\t\t|\tscientific name\t|\n12253\t|\tTomato mosaic virus\t|\t\t|\tscientific name\t|\n31646\t|\tHepatitis C virus subtype 1a\t|\t\t|\tscientific name\t|\n31646\t|\tHepatitis C virus type 1a\t|\t\t|\tsynonym\t|\n35278\t|\tssRNA positive-strand viruses, no DNA stage\t|\t\t|\tscientific name\t|\n41856\t|\tHepatitis C virus 1\t|\t\t|\tsynonym\t|\n41856\t|\tHepatitis C virus genotype 1\t|\t\t|\tscientific name\t|\n41856\t|\tHepatitis C virus type 1\t|\t\t|\tsynonym\t|\n41856\t|\thepatitis C virus 1 HCV 1\t|\t\t|\tsynonym\t|\n42788\t|\tCV-A8\t|\t\t|\tgenbank acronym\t|\n42788\t|\tCoxsackievirus A8\t|\t\t|\tscientific name\t|\n42788\t|\tHuman coxsackievirus A8\t|\t\t|\tsynonym\t|\n138948\t|\tCoxsackievirus A\t|\t\t|\tsynonym\t|\n138948\t|\tEnterovirus A\t|\t\t|\tscientific name\t|\n138948\t|\tEnterovirus EV-A\t|\t\t|\tsynonym\t|\n138948\t|\tHuman coxsackievirus A\t|\t\t|\tsynonym\t|\n138948\t|\tHuman enterovirus A\t|\t\t|\tsynonym\t|\n138950\t|\tEnterovirus C\t|\t\t|\tscientific name\t|\n138950\t|\tEnterovirus EV-C\t|\t\t|\tsynonym\t|\n138950\t|\tHuman enterovirus C\t|\t\t|\tsynonym\t|\n138950\t|\tPoliovirus\t|\t\t|\tsynonym\t|\n439488\t|\tssRNA viruses\t|\t\t|\tscientific name\t|\n464095\t|\tPicornavirales\t|\t\t|\tscientific name\t|\n675071\t|\tVirgaviridae\t|\t\t|\tscientific name\t|\n" }, { "path": "tests/input/TestMetagenomicsViralMix/db/taxonomy/nodes.dmp", "content": "1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|\n10239\t|\t1\t|\tsuperkingdom\t|\t\t|\t9\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|\n11050\t|\t35278\t|\tfamily\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n11102\t|\t11050\t|\tgenus\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n11103\t|\t11102\t|\tspecies\t|\tHC\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n12058\t|\t464095\t|\tfamily\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n12059\t|\t12058\t|\tgenus\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n12083\t|\t138950\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n12234\t|\t675071\t|\tgenus\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n12253\t|\t12234\t|\tspecies\t|\tTM\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n31646\t|\t41856\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n35278\t|\t439488\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n41856\t|\t11103\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n42788\t|\t138948\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t1\t|\t0\t|\t\t|\n138948\t|\t12059\t|\tspecies\t|\tEA\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n138950\t|\t12059\t|\tspecies\t|\tEC\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n439488\t|\t10239\t|\tno rank\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n464095\t|\t35278\t|\torder\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n675071\t|\t35278\t|\tfamily\t|\t\t|\t9\t|\t1\t|\t1\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n" }, { "path": "tests/input/TestMinimap2Idxstats/multi-viral-refs.fasta", "content": ">EU255973.1 Hepatitis C virus subtype 1a isolate HCV-1a/US/BID-V180/1990, complete genome\nGAGCCATGGCGTTAGTATGAGTGTCGTGCAGCCTCCAGGACCCCCCCTCCCGGGAGAGCC\nATAGTGGTCTGCGGAACCGGTGAGTACACCGGAATTGCCAGGACGACCGGGTCCTTTCTT\nGGATAAACCCGCTCAATGCCTGGAGATTTGGGCGTGCCCCCGCAAGACTGCTAGCCGAGT\nAGTGTTGGGTCGCGAAAGGCCTTGTGGTACTGCCTGATAGGGTGCTTGCGAGTGCCCCGG\nGAGGTCTCGTAGACCGTGCACCATGAGCACGAATCCTAAACCTCAAAGAAAAACCAAACG\nTAACACCAACCGTCGCCCACAGGACGTCAAGTTCCCGGGTGGCGGTCAGATCGTTGGTGG\nAGTTTACTTGTTGCCGCGCAGGGGCCCTAGATTGGGTGTGCGCGCGACGAGGAAGACTTC\nCGAGCGGTCGCAACCTCGAGGTAGACGTCAGCCTATCCCCAAGGCACGTCGGCCCGAGGG\nCAGGACCTGGGCTCAGCCCGGGTATCCTTGGCCCCTCTATGGCAATGAGGGTTGCGGGTG\nGGCGGGATGGCTCCTGTCTCCCCGAGGCTCTCGGCCTAGTTGGGGCCCCACAGACCCCCG\nGCGTAGGTCGCGCAATCTGGGTAAGGTCATCGATACCCTTACGTGCGGCTTCGCCGACCT\nCATGGGGTACATACCGCTCGTCGGCGCTCCTCTTGGAGGCGCTGCCAGGGCTCTGGCGCA\nTGGCGTCAGGGTTCTGGAAGACGGCGTGAACTATGCAACAGGGAACCTTCCTGGTTGCTC\nTTTCTCTATCTTCCTTCTGGCCCTACTCTCTTGCCTGACCGTGCCCGCCTCAGCCTACCA\nAGTGCGCAACTCCTCGGGGCTTTACCATGTCACCAATGATTGCCCTAACTCGAGTATTGT\nGTACGAGGCGGCCGATGCCATCCTGCACACTCCGGGGTGTGTCCCTTGCGTTCGCGAGGG\nTAACGCCTCGAGGTGTTGGGTGCCGGTGACCCCCACGGTGGCCACCAGGGACGGCAAGCT\nCCCCACAACGCAGCTTCGACGTCATATCGATCTGCTCGTCGGGGGCGCCACCCTCTGCTC\nGGCTCTCTACGTGGGGGACCTGTGCGGGTCTGTCTTTCTTGTCGGCCAGCTGTTTACCCT\nCTCTCCCAGGCGCCACTGGACGACGCAGGGCTGTAATTGTTCTATCTATCCCGGCCATAT\nAACGGGTCACCGCATGGCATGGGATATGATGATGAACTGGTCCCCTACAACGGCGTTGGT\nGGTAGCTCAGCTGCTCCGGATCCCACAAGCCATCATGGACATGATCGCTGGTGCTCACTG\nGGGAGTCCTGGCGGGCATAGCGTACTTCTCCATGGTGGGGAACTGGGCGAAGGTCCTGGT\nAGTGCTACTGCTATTTGCCGGCGTCGACGCGGAAACCCACGTCACCGGGGGAAGTGCCGG\nCCGCACCGTGGCTGGGCTTACTGGTCTCTTCGCACCAGGCGCCAGACAGAACATCCAACT\nGATCAACACCAACGGCAGTTGGCACATCAATAGCACGGCCTTGAACTGCAATGATAGCCT\nTCAAACCGGCTGGATAGCAGGCCTCTTCTATCACCACAAATTCAACTCTTCAGGCTGTTC\nCGAGAGGTTGGCCAGCTGCCGACGCCTTACTGATTTTGCCCAGGGCTGGGGCCCCATCAG\nTTATGCCAACGGAAGCGGCCCCGACGAGCGTCCCTACTGCTGGCACTACCCCCCAAGACC\nTTGTGGTATTGTGCCCGCAAGGAGCGTGTGTGGCCCGGTATATTGCTTCACTCCCAGCCC\nCGTGGTGGTGGGAACGACCGACAGGTCGGGTGCGCCTACCTACAACTGGGGTGAAAATGA\nTACGGACGTTTTCGTCCTCAACAACACCAGGCCACCGCTGGGCAATTGGTTCGGTTGCAC\nCTGGATGAACTCGACTGGATTCACCAAAGTGTGCGGAGCGCCCCCTTGTGTCATCGGAGG\nGGTGGGCAATAACACCTTGCGCTGCCCCACTGATTGCTTCCGCAAGCATCCGGAAGCCAC\nATACTCTCGGTGCGGCTCCGGTCCCTGGATTACACCCAGGTGCATGGTCGACTACCCGTA\nTAGGCTTTGGCATTACCCTTGTACCATCAACTACACCATATTCAAAGTCAGGATGTACGT\nGGGAGGGGTCGAGCACAGGCTGGAAGCTGCCTGCAACTGGACGCGGGGCGAACGCTGCGA\nTCTGGAAGACAGGGACAGGTCCGAGCTCAGCCCATTGCTGCTGTCCACCACACAGTGGCA\nGGTTCTTCCGTGTTCTTTCACGACCCTGCCAGCCTTGTCCACCGGCCTCATCCACCTCCA\nCCAGAACATCGTGGACGTGCAGTACTTGTACGGGGTAGGGTCAAGCATTGCGTCCTGGGC\nCATTAAGTGGGAGTATGTCGTTCTCCTGTTCCTTCTGCTTGCAGACGCGCGCGTCTGCTC\nCTGCTTGTGGATGATGTTACTCATATCCCAAGCGGAGGCGGCTTTGGAGAACCTCGTAAT\nACTCAATGCAGCATCCCTGGCCGGGACGCACGGTCTTGTGTCCTTCCTAGTGTTCTTCTG\nCTTTGCGTGGTATCTGAAGGGTAGGTGGGTGCCCGGAGCGGCATACGCCTTCTACGGGAT\nGTGGCCTCTCCTCCTGCTCCTGCTGGCGTTGCCTCAACGGGCATACGCACTGGACACGGA\nGGTGGCCGCGTCGTGTGGCGGCGTTGTTCTTGTCGGGTTAATGGCGCTGACTCTGTCACC\nATATTACAAGCGCCACATCGGCTGGTGCTTGTGGTGGCTTCAGTATCTTCTGACCAGAGT\nAGAAGCGCATCTGCACGTGTGGGTTCCCCCCCTCAACGTTCGAGGGAGGCGCGATGCCAT\nCATCTTGCTCATGTGTGCTGTACACCCGACTTTGGTATTTGACATCACCAAACTACTGCT\nGGCCGTCTTCGGACCCCTTTGGATTCTCCAAGCCAGTTTGCTCAAAGTCCCCTACTTCGT\nGCGCGTTCAAGGCCTCCTCCGGATCTGCGCGCTAGCGCGGAAGATGGTCGGGGGTCATTA\nCGTGCAGATGGCCATCATCAAGTTAGGGGCGCTTACTGGTACCTATGTTTACAACCACCT\nCACTCCTCTTCGGGACTGGGCGCACAACGGCCTGCAAGATCTGGCCGTGGCTGTGGAACC\nTGTCGTCTTCTCCCCAATGGAGACCAAGCTCATCACGTGGGGGGCGGACACCGCCGCGTG\nCGGCGACATCATCGACGGCTTGCCCGTCTCCGCCCGTAGGGGCCAGGAGATACTGCTTGG\nACCAGCCGACGGAATGGTCTCCAAGGGGTGGAGGTTGCTGGCGCCCATCACGGCGTACGC\nCCAGCAGACGAGAGGCCTCCTAGGGTGTATAATCACCAGCCTGACTGGCCGGGACAAGAA\nCCAAGTGGAGGGTGAGGTCCAGATCGTGTCAACCGCTGCCCAAACTTTCCTGGCAACGTG\nCATCAATGGGGTATGCTGGACTGTCTACCACGGGGCCGGAACGAGGACCATCGCATCACC\nCAAGGGTCCTGTTATCCAGATGTATACCAATGTGGACCAAGACCTCGTGGGCTGGCCCGC\nTCCTCCAGGTTCCCGCTCATTAACACCCTGCACCTGCGGCTCCTCGGACCTCTACCTGGT\nCACGAGGCACGCCGATGTCATTCCCGTGCGCCGGCGGGGTGATAGCAGGGGCAGCCTGCT\nTTCGCCCCGGCCCATCTCCTACTTGAAAGGCTCCTCGGGGGGTCCGCTGTTGTGCCCCGC\nGGGACACGCCGTGGGCATATTCAGGGCCGCGGTGTGCACCCGTGGAGTGGCTAAAGCGGT\nGGACTTTATCCCTGTGGAGAACCTAGAGACAACCATGAGATCCCCGGTGTTCACGGACAA\nCTCCTCTCCACCAGCAGTGCCCCAGAGCTTCCAGGTAGCCCACCTGCATGCTCCCACCGG\nCAGCGGTAAGAGCACCAAGGTTCCGGCTGCGTACGCAGCTCAAGGCTACAAGGTGCTGGT\nGCTCAACCCCTCTGTTGCTGCAACACTGGGCTTTGGTGCTTACATGTCCAAGGCCCATGG\nGGTCGATCCTAACATCAGGACTGGGGTGAGAACAATTACCACTGGCAGCCCCATCACGTA\nCTCCACCTACGGCAAGTTCCTTGCCGACGGCGGGTGCTCAGGGGGTGCTTATGACATAAT\nAATTTGTGACGAGTGCCACTCCACGGATGCTACATCCATCTTGGGCATCGGCACTGTCCT\nTGACCAAGCAGAGACTGCGGGGGCGAGACTGGTTGTGCTCGCCACTGCTACTCCTCCGGG\nCTCCGTCACTGTGCCCCATCCTAACATCGAGGAGGTTGCTCTGTCCACCACCGGAGAGAT\nCCCTTTTTACGGCAAGGCTATTCCCCTCGAGGTGATCAAGGGGGGAAGACATCTCATCTT\nCTGTCACTCAAAGAAGAAGTGCGATGAGCTCGCCGCAAAGCTGGTCGCGTTGGGCGTCAA\nTGCCGTGGCCTACTACCGCGGTCTCGACGTGTCTGTCATCCCGACCAGCGGCGATGTTGT\nCGTCGTGGCGACCGATGCTCTCATGACTGGCTATACCGGCGACTTCGACTCTGTGATAGA\nCTGCAACACGTGTGTCACCCAGACAGTCGATTTCAGCCTTGACCCTACCTTCACCATTGA\nGACAACCACGCTCCCCCAGGATGCTGTCTCCCGGACTCAACGTCGGGGCAGGACTGGCAG\nGGGGAAGCCAGGCATCTACAGATTTGTGGCACCGGGGGAGCGCCCCTCGGGCATGTTCGA\nCTCGTCCGTCCTCTGTGAGTGCTATGACGCGGGCTGTGCTTGGTATGAGCTCACGCCCGC\nCGAGACTACAGTTAGGCTACGAGCGTACATGAACACCCCGGGGCTTCCCGTGTGCCAGGA\nCCATCTTGAATTTTGGGAGGGCGTTTTTACGGGCCTCACTCATATAGATGCCCACTTTCT\nATCCCAGACAAAGCAGAGTGGGGAGAACTTTCCTTACCTGGTAGCGTACCAAGCCACCGT\nGTGCGCTAGGGCTCAAGCCCCGCCCCCATCGTGGGACCAGATGTGGAAGTGTTTGATCCG\nTCTCAAGCCCACCCTCCATGGGCCAACACCCCTGCTATACAGACTGGGCGCTGTTCAGAA\nTGAAGTTACCCTGACGCACCCAATCACCAAATACATCATGACATGCATGTCGGCTGACCT\nGGAGGTCGTCACGAGCACCTGGGTGCTCGTTGGCGGCGTCCTGGCTGCTTTGGCCGCGTA\nTTGCCTGTCAACAGGCTGCGTGGTCATAGTGGGCAGGATTGTCTTGTCCGGGAAGCCGGC\nAGTTATACCTGACAGGGAGGTTCTCTACCGGGAGTTCGATGAGATGGAAGAGTGCTCTCA\nGCACTTACCGTACATCGAGCAAGGGATGATGCTCGCCGAGCAGTTCAAGCAGAAGGCCCT\nCGGCCTCCTGCAGACCGCGTCCCGCCAGGCAGAGGTTATCGCCCCTGCTGTCCAGACCAA\nCTGGCAGAAACTCGAGGCCTTCTGGGCGAAGCATATGTGGAATTTCATCAGTGGGATACA\nATACTTGGCGGGCCTGTCAACGCTGCCTGGTAACCCCGCCATTGCTTCATTGATGGCTTT\nTACAGCTGCTGTCACCAGCCCACTAACCACTAGCCAAACCCTCCTCTTCAACATATTGGG\nGGGGTGGGTGGCTGCCCAGCTCGCTGCCCCCGGTGCCGCTACCGCCTTTGTGGGCGCTGG\nCTTAGCCGGCGCCGCCATCGGCAGTGTTGGGCTGGGGAAGGTCCTCGTGGACATTCTTGC\nAGGATATGGCGCGGGCGTGGCGGGAGCTCTTGTAGCATTCAAGATCATGAGCGGTGAGGT\nCCCCTCCACGGAGGACCTGGTCAATCTGCTGCCCGCCATCCTCTCGCCTGGAGCCCTTGT\nAGTCGGTGTGGTCTGCGCAGCAATACTGCGCCGGCACGTTGGCCCGGGCGAGGGGGCAGT\nGCAATGGATGAACCGGCTAATAGCCTTCGCCTCCCGGGGGAACCATGTTTCCCCCACGCA\nCTACGTGCCGGAGAGCGATGCAGCCGCCCGCGTCACGGCCATACTCAGCAGCCTCACTGT\nAACCCAGCTCCTGAGGCGACTGCACCAGTGGATAAGCTCGGAGTGTACCACTCCATGCTC\nCGGTTCCTGGCTAAGAGACATCTGGGACTGGATATGCGAGGTGCTGAGCGACTTTAAGAC\nCTGGCTGAAAGCCAAGCTCATGCCACAACTGCCTGGGATTCCCTTTGTGTCCTGCCAGCG\nCGGGTATAGGGGGGTCTGGCGGGGAGACGGCATCATGCACACTCGCTGCCACTGTGGAGC\nTGAGATCACTGGACATGTCAAAAACGGGACGATGAGGATCGTCGGTCCTAGGACCTGCAG\nGAACATGTGGAGTGGGACCTTCCCCATTAACGCCTACACCACGGGCCCCTGTACCCCCCT\nTCCTGCGCCGAACTATAAGTTCGCGCTGTGGAGGGTGTCTGCAGAGGAATACGTGGAGAT\nAAGGCAGGTGGGGGACTTCCACTACGTAACGGGCATGACTACTGACAATCTTAAATGCCC\nGTGCCAGGTCCCATCGCCCGAATTCTTCACAGAATTGGACGGGGTGCGCCTACATAGGTA\nTGCGCCCCCTTGCAAGCCCTTGCTGCGGGAGGAGGTATCATTCAGAGTAGGACTCCACGA\nGTACCCGGTGGGGTCGCAACTACCTTGCGAGCCCGAACCGGACGTGGCCGTGTTGACGTC\nCATGCTCACTGATCCCTCCCACATAACAGCGGAGGCGGCCGGGAGAAGGTTGGCGAGGGG\nATCACCCCCTTCTGTGGCCAGCTCCTCGGCTAGCCAGTTGTCCGCTCCATCTCTCAAGGC\nAACTTGCACCGCCAACCATGACTCCCCTGACGCCGAGCTCATAGAGGCTAATCTCCTGTG\nGAGGCAGGAGATGGGCGGCAACATCACCAGGGTTGAGTCAGAGAACAAAGTGGTGATTCT\nGGACTCCTTCGATCCGCTTGTATCAGAGGAGGATGAGCGGGAGATCTCCGTACCCGCAGA\nAATCCTGCGGAAGTCTCGGAGATTCGCCCCGGCCCTGCCCATTTGGGCGCGGCCGGACTA\nCAACCCCCCGCTGGTAGAGACGTGGAAAAAACCTGACTACGAACCACCCGTGGTCCATGG\nCTGCCCGCTACCACCTCCACAGTCCCCTCCTGTGCCTCCGCCTCGGAAGAAGCGAACGGT\nGGTCCTCACCGAATCAACCCTATCTACTGCCTTGGCTGAGCTTGCCACCAAAAGTTTTGG\nCAGCTCCTCAACTTCCGGCATTACGGGCGACAATACGACAACATCCTCTGAGCCCGCCCC\nTTCTGGCTGCTCCCCCGACTCCGACGTTGAGTCCTATTCTTCCATGCCCCCCCTGGAGGG\nGGAGCCTGGAGATCCGGATCTCAGCGACGGGTCATGGTCGACGGTCAGTAGCGGGGCCGA\nCGCGGAGGATGTCGTGTGCTGCTCAATGTCCTATACCTGGACAGGCGCACTCGTCACCCC\nGTGCGCTGCGGAAGAACAAAAACTGCCCATCAACGCACTGAGCAACTCGTTGCTACGTCA\nTCACAATCTGGTGTATTCCACCACTTCACGCAGTGCTTGCCAAAGGCAGAAGAAAGTCAC\nATTTGACAGACTGCAAGTTCTGGACAGCCATTACCAGGACGTGCTCAAGGAGGTTAAGGC\nAGCGGCGTCAAAAGTGAAGGCTAACTTGCTATCCGTAGAGGAAGCTTGCAGCCTGACGCC\nCCCACACTCAGCCAAATCCAAGTTTGGTTATGGGGCGAAAGACGTCCGTTGCCATGCCAG\nAAAGGCCGTAGCCCACATCAACTCCGTGTGGAAAGACCTTCTGGAAGACAGTGTAACACC\nAATAGACACTACCATCATGGCTAAGAACGAGGTTTTCTGTGTTCAGCCTGAGAAGGGGGG\nTCGTAAGCCAGCTCGTCTCATCGTGTTCCCCGACCTGGGCGTGCGCGTGTGCGAGAAGAT\nGGCCCTGTACGATGTGGTTAGCAAGCTCCCCCTGGCCGTGATGGGAAGCTCCTACGGATT\nCCAATACTCACCAGGACAGCGGGTTGAATTCCTCGTGAAAGCGTGGAAGTCCAAGAAGAC\nCCCAATGGGGTTCTCATATGATACCCGCTGTTTTGACTCCACAGTCACTGAGAGCGACAT\nCCGTACGGAGGAGGCAATTTACCAATGTTGTGACCTGGACCCCCAAGCCCGCGTGGCCAT\nCAAGTCCCTCACTGAGAGGCTTTACGTTGGGGGCCCTCTTACCAATTCAAGGGGGGAGAA\nCTGCGGCTACCGCAGGTGCCGCGCGAGCGGCGTACTGACAACTAGCTGTGGTAACACCCT\nCACTTGCTACATCAAGGCCCAAGCAGCCTGTCGAGCCGCAGGGCTCCAGGACTGCACCAT\nGCTCGTGTGTGGCGACGACTTAGTCGTTATCTGTGAAAGTGCGGGGGTCCAGGAGGACGC\nGGCGAGCCTGAGAGCCTTCACGGAGGCTATGACCAGGTACTCCGCCCCCCCCGGGGACCC\nCCCACAACCAGAATACGACTTGGAGCTCATAACATCATGCTCCTCCAACGTGTCAGTCGC\nCCACGACGGCGCTGGAAAGAGGGTCTACTACCTCACCCGTGACCCTACAACCCCCCTCGC\nGAGAGCCGCGTGGGAGACAGCAAGACACACTCCAGTCAATTCCTGGCTAGGCAACATAAT\nCATGTTTGCCCCCACACTGTGGGCGAGGATGATATTGATGACCCACTTCTTTAGCGTCCT\nCATAGCCAGGGACCAGCTTGAACAGGCCCTTGATTGCGAGATCTACGGAGCCTGCTACTC\nCATAGAACCACTGGACCTACCTCCAATCATTCAAAGACTCCATGGCCTCAGCGCATTTTC\nACTCCACAGTTACTCTCCAGGTGAGATCAATAGGGTGGCCGCATGCCTCAGAAAACTTGG\nGGTCCCGCCCTTGCGAGCTTGGAGACACCGGGCCCGGAGCGTCCGCGCTAGGCTTCTGTC\nCAGAGGAGGCAGGGCTGCCATATGTGGCAAGTACCTCTTCAACTGGGCAGTAAGAACAAA\nGCTCAAACTCACTCCAATAGCGGCCGCTGGCCGGCTGGACTTGTCCGGCTGGTTCACGGC\nTGGCTACAGCGGGGGAGACATTTATCACAGCGTGTCTCATGCCCGGCCCCGCTGGTTCTG\nGTTTTGCCTACTCCTGCTCGCTGCAGGGGTAGGCATCTACCTCCTCCCCAACCGATGA\n>KJ207374.1 Tomato mosaic virus isolate Penghu, complete genome\nGTATTTTTACAACAATTACCAACAACAACAACAAACAACAACAACATTACATTTTACATT\nCTACAACTACAATGGCATACACACAAACAGCCACATCGTCCGCTTTGCTTGAGACCGTCC\nGAGGTAACAATACCTTGGTCAACGATCTTGCAAAGCGGCGTCTATATGACACAGCGGTCG\nATGAATTTAATGCTAGGGACCGCAGGCCTAAAGTCAATTTTTCCAAAGTAGTAAGCGAAG\nAACAGACGCTTATTGCAACCAAAGCCTACCCAGAATTCCAAATTACATTCTACAACACGC\nAGAACGCTGTGCATTCCCTTGCAGGCGGTCTCCGATCATTAGAATTGGAATATCTGATGA\nTGCAAATTCCCTACGGATCATTGACATATGATATCGGAGGTAATTTTGCATCTCATCTGT\nTCAAAGGGCGAGCATACGTTCACTGCTGTATGCCGAATCTGGATGTCCGCGACATAATGC\nGGCACGAGGGCCAAAAGGACAGTATTGAACTATACCTTTCTAGGCTCGAAAGGGGCAACA\nAACATGTCCCAAACTTCCAAAAGGAAGCTTTCGACAGATACGCTGAAATGCCAAACGAAG\nTAGTCTGTCACGATACTTTCCAAACGTGTAGGCATTCTCAAGAATGTTACACGGGAAGAG\nTGTATGCTATTGCTTTGCATAGTATATACGATATACCTGCCGACGAGTTCGGCGCGGCAC\nTGCTGAGAAAGAATGTACATGTATGTTATGCCGCTTTCCACTTTTCCGAGAATTTACTTC\nTCGAAGATTCACACGTCAACCTCGATGAGATCAATGCATGTTTCCAAAGAGATGGAGACA\nGGTTGACCTTTTCCTTTGCATCTGAGAGTACTCTTAATTATAGTCATAGTTATTCTAATA\nTTCTTAAGTATGTTTGCAAAACTTACTTCCCAGCCTCTAATAGAGAGGTTTACATGAAGG\nAGTTTTTAGTAACTAGAGTTAATACCTGGTTTTGTAAATTTTCTAGAATAGATACTTTCT\nTATTGTACAAAGGTGTAGCGCATAAGGGTGTAGATAGTGAGCAGTTTTACAAGGCTATGG\nAAGACGCATGGCACTACAAAAAGACTCTTGCGATGTGCAACAGTGAAAGAATCTTGTTAG\nAGGATTCTTCATCAGTTAATTACTGGTTTCCAAAAATGAGGGATATGGTGATAGTTCCAC\nTATTTGACATATCTCTCGAGACTAGTAAAAGAACACGCAAAGAGGTCTTAGTTTCAAAGG\nACTTTGTTTATACAGTGTTAAATCACATTCGTACGTACCAGGCAAAAGCGCTTACTTACT\nCCAACGTGTTATCTTTCGTCGAATCAATTCGTTCGAGAGTGATCATTAACGGGGTTACTG\nCTAGGTCTGAGTGGGATGTCGATAAATCATTATTACAGTCCTTGTCGATGACGTTCTTCC\nTACATACCAAGCTTGCCGTTCTGAAAGACGATCTTTTGATTAGCAAGTTTGCACTTGGTC\nCAAAAACTGTCTCACAACATGTGTGGGATGAGATTTCCCTAGCTTTCGGCAATGCTTTCC\nCATCGATCAAGGAAAGATTGATAAACCGGAAACTGATCAAAATTACGGAGAATGCGTTAG\nAGATCAGGGTGCCCGATCTTTATGTCACTTTCCATGATAGGTTAGTTTCTGAGTACAAAA\nTGTCAGTGGACATGCCGGTGCTAGACATTAGGAAAAAGATGGAAGAAACTGAGGAAATGT\nACAATGCACTGTCCGAACTGTCTGTACTTAAAAATTCAGACAAATTCGATGTTGATGTTT\nTTTCCCAGATGTGCCAATCTTTAGAAGTTGATCCAATGACTGCAGCAAAGGTAATAGTAG\nCAGTTATGAGCAACGAGAGTGGTCTTACTCTCACGTTTGAACAGCCCACCGAAGCTAATG\nTTGCGCTAGCATTGAAAGATTCTGAAAAGGCTTCTGATGGGGCGTTGGTAGTTACCTCAA\nGAGATGTTGAAGAACCGTCCATAAAGGGTTCGATGGCCCGTGGTGAGTTACAATTGGCCG\nGATTATCTGGCGACGTTCCTGAATCTTCATACACTAGGAGCGAGGAAATTGAGTCTCTCG\nAGCAGTTTCATATGGCAACAGCTAGTTCGTTAATTCACAAGCAGATGTGTTCGATCGTGT\nACACGGGCCCTCTTAAAGTTCAACAAATGAAAAACTTTATAGACAGCCTGGTAGCCTCGC\nTCTCTGCTGCGGTGTCGAATCTAGTGAAGATCCTAAAAGATACAGCTGCGATTGACCTTG\nAAACTCGTCAAAAGTTCGGAGTTCTGGATGTTGCTTCGAAAAGGTGGCTAGTTAAACCAT\nCCGCAAAGAACCATGCATGGGGGGTTGTTGAGACTCATGCGAGGAAATATCACGTCGCAT\nTACTGGAGCACGATGAATTTGGCATTATTACGTGCGATAACTGGCGACGGGTGGCTGTGA\nGTTCTGAGTCGGTAGTATATTCTGATATGGCTAAACTCAGAACTCTGAGAAGATTGCTCA\nAAGATGGAGAACCACACGTTAGTTCAGCAAAGGTGGTTTTGGTGGATGGCGTTCCAGGGT\nGCGGGAAAACAAAGGAAATTCTTTCGAGAGTTAATTTCGAAGAAGATCTAATTCTTGTCC\nCTGGTCGTCAAGCTGCCGAGATGATCAGAAGAAGAGCTAATGCGTCGGGCATAATAGTGG\nCTACAAAGGACAATGTGCGTACCGTCGATTCATTTTTGATGAATTACGGGAAAGGGGCAC\nGCTGTCAGTTCAAAAGATTGTTCATAGACGAAGGTTTGATGCTGCATACTGGTTGTGTGA\nATTTCTTGGTTGAAATGTCTCTGTGCGATATTGCATATGTTTATGGAGACACCCAACAAA\nTTCCGTACATCAACAGAGTAACTGGTTTCCCGTACCCTGCACACTTTGCAAAATTGGAGG\nTCGACGAAGTCGAAACAAGAAGAATTACTCTTCGTTGTCCGGCTGATGTCACACACTTCC\nTAAATCAAAGGTATGAAGGACACGTAATGTGCACGTCTTCTGAAAAGAAATCAGTTTCCC\nAGGAAATGGTTAGTGGGGCTGCGTCTATCAATCCTGTGTCCAAGCCGCTTAAAGGGAAAA\nTTTTGACTTTTACACAGTCTGACAAGGAGGCCCTTCTCTCAAGGGGCTATGCAGATGTCC\nATACTGTACATGAGGTACAAGGTGAGACTTATGCAGACGTATCGTTAGTTCGACTAACAC\nCTACGCCTGTATCTATCATCGCAAGAGACAGTCCGCATGTTCTGGTCTCGTTGTCAAGAC\nACACAAAATCCCTAAAGTACTACACCGTTGTGATGGATCCTTTAGTTAGTATCATTAGAG\nATTTAGAACAGGTTAGTAGTTACTTATTAGACATGTACAAAGTAGATGCAGGTACTCAAT\nAGCAATTACAGGTCGACTCTGTGTTTAAGAATTTCAATCTTTTTGTAGCAGCTCCAAAGA\nCTGGAGATATATCTGATATGCAATTTTACTATGATAAGTGTCTTCCTGGGAACAGCACGT\nTGTTGAACAACTACGACGCTGTTACCATGAAATTGACTGACATTTCTCTGAATGTCAAAG\nATTGCATATTAGATATGTCTAAGTCTGTAGCTGCTCCGAAAGATGTCAAACCAACTTTAA\nTACCGATGGTACGAACGGCGGCAGAAATGCCTCGCCAGACTGGACTGTTGGAAAATTTAG\nTTGCGATGATTAAAAGAAATTTTAATTCACCAGAGTTGTCCGGAGTAGTTGATATTGAAA\nATACTGCATCTTTAGTGGTAGATAAGTTTTTTGATAGTTATTTACTTAAGGAAAAAAGAA\nAACCAAACAAAAATTTTTCACTGTTTAGTAGAGAGTCTCTCAATAGGTGGATAGCAAAGC\nAAGAACAAGTCACAATTGGTCAGTTGGCCGATTTTGATTTTGTGGATCTTCCAGCCGTTG\nATCAGTACAGGCATATGATAAAAGCGCAACCGAAGCAGAAACTGGATCTGTCAATTCAGA\nCGGAATATCCAGCGTTGCAAACGATTGTGTATCATTCAAAGAAAATCAACGCAATATTTG\nGTCCTCTTTTCAGTGAGCTTACAAGGCAATTACTTGACAGTATTGACTCAAGCAGATTCT\nTGTTCTTTACGAGAAAGACACCGGCTCAGATCGAAGATTTCTTCGGAGATCTAGACAGTC\nATGTCCCAATGGACGTACTTGAGTTGGATATTTCAAAGTATGATAAGTCTCAAAACGAGT\nTTCATTGTGCTGTTGAGTACGAAATCTGGAGGAGACTGGGTCTGGAGGATTTCTTGGCAG\nAAGTGTGGAAACAAGGGCATAGAAAAACCACTCTGAAAGATTACACTGCTGGTATAAAAA\nCGTGTTTATGGTACCAGAGAAAGAGTGGTGATGTTACAACTTTTATCGGTAATACCGTCA\nTCATTGCTTCGTGTCTTGCATCAATGCTCCCGATGGAAAAATTGATAAAAGGAGCCTTCT\nGCGGAGATGACAGTTTGTTGTACTTTCCTAGAGGTTGTGAGTATCCCGATATACAACAAG\nCTGCTAATCTGATGTGGAATTTTGAGGCCAAACTGTTCAAGAAGCAATATGGGTACTTCT\nGCGGGAGGTACGTGATTCATCACGATAGAGGTTGCATAGTATACTACGACCCTCTGAAGC\nTGATTTCGAAACTTGGTGCTAAACACATCAAGGATTGGGATCATTTGGAGGAGTTCAGAA\nGATCCCTCTGTGATGTTGCTGAGTCGTTGAACAATTGTGCGTATTACACACAATTGGACG\nACGCTGTTGGGGAGGTTCATAAAACCGCCCCACCTGGTTCGTTTGTTTATAGGAGTTTAG\nTTAAGTATTTGTCAGATAAAGTTTTGTTTAGAAGTTTATTTCTTGATGGCTCTAGTTGTT\nAAAGGTAAGGTAAATATTAATGAGTTTATCGATCTGTCAAAGTCTGAGAAACTTCTCCCG\nTCGATGTTCACGCCTGTAAAGAGTGTTATGGTTTCAAAGGTTGATAAGATTATGGTCCAT\nGAAAATGAATCATTGTCTGAAGTAAATCTCTTAAAAGGTGTAAAACTTATAGAAGGTGGG\nTATGTTTGCTTAGTTGGTCTTGTTGTGTCCGGTGAGTGGAATTTACCAGATAATTGCCGT\nGGTGGTGTGAGTGTCTGCATGGTTGACAAGAGAATGGAAAGAGCGGACGAAGCCACACTG\nGGGTCATATTACACTGCTGCTGCTAAAAAGCGGTTTCAGTTTAAAGTGGTCCCAAATTAC\nGGTATTACTACAAAGGATGCAGAAAAGAACATATGGCAGGTCTTAGTAAATATTAAAAAT\nGTAAAAATGAGTGCGGGCTACTGCCCTTTGTCATTAGAATTTGTGTCTGTGTGTATTGTT\nTATAAAAATAATATAAAATTGGGTTTGAGGGAGAAAGTAACGAGTGTGAACGATGGAGGA\nCCCATGGAACTTTCAGAAGAAGTTGTTGATGAGTTCATGGAGAATGTTCCAATGTCGGTT\nAGACTCGCAAAGTTTCGAACCAAAACCTCAAAAAGAGGTCCGAAAAATAATAATAATTTA\nGGTAAGGGGCGTTCAGGCGGAAGGCCTAAACCAAAAAGTTTTGATGAAGTTGAAAAAGAG\nTTTGATAATTTGATTGAAGATGAAGCCGAGACGTCGGTCGCGGATTCTGATTCGTATTAA\nATATGTCTTACTCAATCACTTCTCCATCGCAATTTGTGTTTTTGTCATCTGTATGGGCTG\nACCCTATAGAATTGTTAAACGTTTGTACAAATTCGTTAGGTAACCAGTTTCAAACACAGC\nAAGCAAGAACTACTGTTCAACAGCAGTTCAGCGAGGTGTGGAAACCTTTCCCTCAGAGCA\nCCGTCAGATTTCCTGGCGATGTTTATAAGGTGTACAGGTACAATGCAGTTTTAGATCCTC\nTAATTACTGCGTTGCTGGGGGCCTTCGATACTAAGAATAGAATAATCGAAGTAGAAAACC\nAGCAGAGTCCGACAACAGCTGAAACGTTAGATGCTACCCGCAGGGTAGACGACGCTACGG\nTTGCAATCCGGTCTGCTATAAATAATTTAGTTAATGAACTAGTAAAAGGTACTGGACTGT\nACAATCAGAATACTTTTGAAAGTATGTCTGGGTTGGTCTGGACCTCTGCACCTGCATCTT\nAAATGCATAGGTGCTGAAATATAAAGTTTGTGTTTCTAAAACACACGTGGTACGTACGAT\nAACGTACAGTGTTTTTCCCTCCACTTAAATCGAAGGGTAGTGTCTTGGAGCGCGCGGAGT\nAAACATATATGGTGCATATATGTCCGTAGGCACGTAAAAAAGCGAGGGATTCGAATTCCC\nCCGGAGCACCACTGGTGGTGGCCCA\n>AY184220.1 Human poliovirus 2 strain Sabin 2, complete genome\nTTAAAACAGCTCTGGGGTTGTACCCACCCCAGAGGCCCACGTGGCGGCTAGCACTCCGGT\nATTACGGTACCCTTGTGCGCCTGTTTTATACTCCCCTCCCGCAACTTAGAAGCACGAAAC\nCAAGTTCAATAGAAGGGGGTACAAACCAGTACCACTACGAACAAGCACTTCTGTTTCCCC\nGGTGACATTGCATAGACTGCTCACGCGGTTGAAAGTGATCGATCCGTTACCCGCTTGTGT\nACTTCGAAAAGCCTAGTATCGCCTTGGAATCTTCGACGCGTTGCGCTCAGCACCCGACCC\nCGGGGTGTAGCTTAGGCTGATGAGTCTGGACATTCCTCACCGGTGACGGTGGTCCAGGCT\nGCGTTGGCGGCCTACCTATGGCTAACGCCATAGGACGTTAGATGTGAACAAGGTGTGAAG\nAGCCTATTGAGCTACATAAGAGTCCTCCGGCCCCTGAATGCGGCTAATCCTAACCACGGA\nACAGGCGGTCGCGAACCAGTGACTGGCTTGTCGTAACGCGCAAGTCTGTGGCGGAACCGA\nCTACTTTGGGTGTCCGTGTTTCCTGTTATTTTTATCATGGCTGCTTATGGTGACAATCAG\nAGATTGTTATCATAAAGCGAATTGGATTGGCCATCCGGTGAGTGTTGTGTCAGGTATACA\nACTGTTTGTTGGAACCACTGTGTTAGCTTTACTTCTCATTTAACCAATTAATCAAAAACA\nATACGAGGATAAAACAACAATACTACAATGGGCGCCCAAGTTTCATCACAGAAAGTTGGA\nGCCCACGAAAATTCAAACAGAGCCTATGGCGGGTCCACCATCAATTACACTACAATCAAT\nTACTATAGGGACTCTGCAAGCAATGCAGCAAGCAAGCAAGATTTTGCACAAGATCCGTCC\nAAGTTCACCGAACCCATTAAGGACGTCCTTATTAAGACCGCTCCCATGCTAAACTCCCCA\nAACATTGAGGCGTGTGGTTATAGTGACAGGGTAATGCAGCTAACTCTGGGCAATTCAACG\nATCACCACCCAAGAAGCGGCCAATTCTGTTGTTGCCTACGGTAGATGGCCTGAATACATC\nAGAGATACCGAGGCAAATCCTGTAGACCAACCAACCGAGCCCGATGTAGCCGCGTGCAGG\nTTCTACACATTAGATACCGTCACTTGGCGCAAGGAGTCCAGAGGGTGGTGGTGGAAACTA\nCCAGACGCTTTAAAAGACATGGGGTTATTTGGTCAAAACATGTTTTATCACTATCTTGGG\nAGGGCTGGCTACACAGTGCACGTACAGTGCAATGCTTCAAAGTTTCATCAAGGAGCTCTA\nGGGGTGTTTGCAGTTCCAGAAATGTGTTTAGCTGGTGATAGCACAACTCACATGTTCACA\nAAGTACGAGAATGCGAATCCAGGCGAAAAAGGAGGTGAATTCAAAGGGAGTTTCACCCTT\nGATACCAACGCCACTAACCCTGCACGGAACTTCTGCCCAGTTGATTACCTCTTCGGGAGT\nGGAGTGCTGGTAGGGAATGCATTTGTTTATCCACATCAAATAATAAACCTGCGCACTAAC\nAACTGTGCTACGCTAGTATTGCCCTATGTAAACTCACTCTCAATAGATAGCATGACAAAG\nCACAACAACTGGGGGATCGCTATCCTCCCCCTGGCGCCACTAGACTTTGCCACTGAATCT\nTCCACTGAGATACCCATTACACTGACCATTGCTCCCATGTGCTGCGAATTCAATGGTTTA\nCGCAACATCACTGTGCCAAGAACCCAAGGATTACCAGTCCTGAACACTCCAGGGAGTAAC\nCAGTACCTGACCGCAGACAATTACCAGTCTCCGTGTGCGATACCTGAGTTTGATGTCACT\nCCACCCATAGACATACCAGGGGAGGTGCGCAACATGATGGAATTGGCGGAAATAGACACC\nATGATACCCCTCAACTTGACAAGTCAACGCAAGAACACAATGGACATGTATAGAGTCGAG\nTTGAGCGACACGGCTCACTCTGACACGCCGATCTTGTGTCTCTCGTTGTCCCCCGCTTCA\nGACCCCAGATTGGCACACACTATGTTGGGTGAGATATTAAATTACTACACACACTGGGCA\nGGGTCCTTGAAATTTACCTTTCTCTTTTGCGGCTCAATGATGGCCACCGGAAAGTTATTG\nGTTTCTTACGCACCACCCGGAGCAGAGGCCCCCAAGAGTCGCAAAGAAGCAATGCTTGGG\nACACATGTGATATGGGACATTGGGTTGCAGTCTTCATGCACTATGGTGGTACCTTGGATC\nAGTAATACCACATACAGACAAACCATCAACGATAGTTTCACAGAAGGTGGCTACATTAGC\nATGTTCTATCAAACTAGGGTTGTTGTCCCGTTGTCCACACCCAGAAAGATGGACATCCTG\nGGTTTTGTGTCAGCTTGCAATGACTTCAGTGTGCGCTTACTGCGAGATACAACACACATT\nAGTCAAGAGGCTATGCCACAAGGAATTGGTGACATGATTGAGGGGGCCGTTGAAGGGATT\nACTAAAAATGCATTGGTTCCCCCGACTTCCACCAATAGCCTGCCTGACACAAAGCCGAGC\nGGTCCAGCCCACTCCAAGGAGATACCTGCATTGACAGCCGTGGAGACAGGGGCTACCAAT\nCCGTTGGTGCCTTCGGACACCGTGCAAACGCGCCATGTCATCCAGAGACGAACGCGATCA\nGAGTCCACGGTTGAGTCATTCTTTGCAAGAGGGGCTTGCGTGGCTATCATTGAGGTGGAC\nAATGATGCACCGACAAAGCGCGCCAGCAGATTGTTTTCGGTTTGGAAAATAACTTACAAA\nGATACTGTTCAACTGAGACGCAAACTGGAATTTTTCACATATTCGAGATTTGACATGGAG\nTTCACTTTTGTGGTCACCTCAAACTACATTGATGCAAATAACGGACATGCATTGAACCAA\nGTTTATCAGATAATGTATATACCACCCGGAGCACCTATCCCTGGTAAATGGAATGACTAT\nACGTGGCAGACGTCCTCTAACCCGTCGGTGTTTTACACCTATGGGGCGCCCCCAGCAAGA\nATATCAGTGCCCTACGTGGGAATTGCTAATGCGTATTCCCACTTTTATGATGGGTTTGCA\nAAAGTACCACTAGCGGGTCAAGCCTCAACTGAAGGCGATTCGTTGTACGGTGCTGCCTCA\nCTGAATGATTTTGGATCACTGGCTGTTCGCGTGGTAAATGATCACAACCCCACGCGGCTC\nACCTCCAAGATCAGAGTGTACATGAAGCCAAAGCATGTCAGAGTCTGGTGCCCACGACCT\nCCACGAGCAGTCCCATACTTCGGACCAGGTGTTGATTATAAAGATGGGCTCACCCCACTA\nCCAGAAAAGGGATTAACGACTTATGGATTTGGACACCAAAACAAAGCTGTGTACACAGCT\nGGCTACAAAATTTGCAATTACCACCTAGCTACACAAGAAGACTTGCAAAATGCCGTGAGT\nGTCATGTGGAACAGAGACCTCTTAGTGGCTGAATCAAGGGCCCTTGGCACCGACTCGATC\nGCAAGGTGCAGCTGTAACACGGGTGTGTACTACTGTGAATCCAGGAGAAAATATTATCCA\nGTTTCTTTCATTGGGCCCACCTTCCAATACATGGAAGCCAATGAATATTACCCGGCTAGA\nTATCAATCACACATGCTTATTGGTCATGGGTTTGCATCACCGGGTGATTGTGGTGGCATA\nCTTAGATGTCAACACGGGGTGATAGGAATAATCACTGCTGGTGGGGAAGGCTTGGTTGCA\nTTTTCAGACATTAGAGACCTGTATGCTTATGAGGAGGAAGCTATGGAGCAGGGCATTTCC\nAACTATATTGAGTCACTTGGTGCTGCATTTGGTAGTGGATTCACTCAACAAATTGGTGAT\nAAAGTTTCCGAGCTAACCAGCATGGTAACTAGCACCATTACAGAGAAGTTGCTTAAAAAC\nTTAATCAAAATTATCTCATCACTTGTGATCATTACCAGGAATTATGAGGACACTACCACA\nGTGCTTGCCACCCTCGCCCTCCTTGGGTGCGACATCTCACCGTGGCAGTGGCTAAAGAAG\nAAGGCATGTGACATCCTGGAAATTCCATACGCCATCAAACAAGGAGATAGTTGGTTGAAG\nAAATTCACTGAGGCATGTAATGCTGCAAAGGGACTGGAGTGGGTGTCCAATAAGATATCC\nAAATTCATTAGTTGGTTGCAGGATAAAATCATCCCACAAGCGAGAGACAAATTAGAGTTT\nGTCACTAAACTAAAGCAATTAGAAATGCTTGAAAATCAGATTTCCACCATACACCAATCT\nTGTCCAAGTCAAGAACATCAGGAGATCTTATTCAACAATGTGCGGTGGCTATCTATCCAG\nTCCAAGAGGTTTGCACCACTATATGCACATGAAGCTAAAAGGATTCAAAAGCTGGAGCAT\nACCATAAATAATTACGTACAGTTCAAGAGCAAGCACCGTATTGAGCCAGTATGTTTGTTA\nGTACATGGCAGTCCAGGGACAGGAAAATCAGTTGCAACCAATCTAATTGCTAGAGCAATA\nGCCGAGAAAGAGAACACCTCCACATACTCACTGCCACCTGATCCGTCTCACTTTGATGGC\nTACAAGCAACAGGGTGTGGTTATTATGGATGACCTAAACCAAAATCCAGACGGAGCAGAC\nATGAAACTTTTTTGTCAAATGGTGTCCACTGTGGAGTTTATTCCACCGATGGCCTCGCTA\nGAAGAGAAAGGCATTTTGTTCACATCTAATTACGTTTTAGCCTCCACCAACTCCAGTCGG\nATCACACCACCCACGGTGGCTCACAGTGATGCGCTGGCCAGGAGATTCGCATTTGACGTG\nGACATACAAGTCATGAGCGAGTACTCCAGAGACGGAAAGCTCAACATGGCAATGGCTACT\nGAAATGTGCAAAAACTGTCATCAACCAGCAAACTTCAAAAGATGTTGTCCTTTAGTGTGT\nGGCAAGGCAATTCAGTTAATGGATAAATCTTCCAGGGTTAGATACAGCATTGATCAGATC\nACTACAATGATTGTTAATGAGAGAAACAGAAGATCAAACATTGGTAATTGCATGGAAGCT\nCTATTCCAGGGACCACTGCAGTATAAAGATCTAAAAATAGATGTTAAGACCAGTCCCCCT\nCCGGAGTGTATCAACGATTTGCTCCAGGCAGTTGATTCCCAGGAAGTGAGAGATTACTGT\nGAAAAGAAAGGCTGGATTGTTAACATTACCAGTCAGGTTCAAACAGAGAGGAACATCAAC\nCGGGCGATGACTATCCTACAAGCAGTAACTACTTTCGCTGCAGTAGCCGGTGTCGTGTAC\nGTTATGTACAAGCTGTTCGCTGGGCACCAGGGTGCATACACTGGTTTGCCAAATAAACGA\nCCCAATGTACCCACTATCAGGACAGCAAAAGTGCAAGGCCCTGGGTTTGATTACGCAGTG\nGCCATGGCTAAAAGAAACATTGTTACAGCAACCACCAGCAAAGGGGAGTTTACGATGTTG\nGGAGTCTATGATAATGTGGCCATCTTGCCAACCCACGCCTCACCTGGTGAAAGCATTGCG\nATCGACGGTAAAGAGGTGGAAATTCTTGACGCCAAAGCCCTTGAAGATCAGGCAGGAACT\nAATCTTGAAATTACCATAATTACACTAAAGAGGAACGAGAAGTTCAGAGATATCAGGCCA\nCACATTCCCACCCAAATCACCGAAACAAATGATGGAGTTTTGATCGTGAACACTAGTAAG\nTACCCCAACATGTATGTTCCCGTTGGTGCTGTGACCGAACAGGGGTATCTTAATCTCGGT\nGGACGACAAACCGCTCGTACGCTAATGTACAACTTTCCAACTAGAGCAGGTCAGTGTGGT\nGGTGTCATCACGTGCACTGGTAAAGTCATTGGGATGCATGTTGGTGGGAACGGTTCACAT\nGGGTTCGCGGCGGCCCTAAAGCGGTCATACTTCACTCAGATTCAAGGTGAGATTCAATGG\nATGAAACCATCAAAAGAAGTGGGATACCCGATCATAAATGCTCCGTCCAAAACCAAACTT\nGAACCCAGCGCTTTTCACTATGTGTTTGAAGGGGTGAAGGAACCAGCAGTCCTTACCAAA\nAATGATCCCAGGCTCAGGACAGACTTTGAAGAAGCAATATTCTCTAAGTATGTAGGCAAC\nAAGATCACTGATGTGGATGAGTACATGAAAGAGGCAGTGGATCATTACGCTGGCCAACTC\nATGTCTCTAGACATCAACACAGAACAAATGTGCTTGGAGGACGCCATGTACGGCACCGAT\nGGCCTGGAAGCACTTGACTTGACCACTAGTGCTGGATACCCTTATGTAGCAATGGGAAAG\nAAAAAGAGAGACATCTTGAATAAGCAGACTAGAGACACCAAGGAAATGCGGAGACTCTTA\nGATACTTATGGAATTAACTTACCGCTTGTAACATATGTTAAAGATGAACTAAGGTCAAAA\nACTAAGGTGGAGCAGGGAAAATCCAGATTGATTGAAGCCTCCAGTTTGAATGATTCAGTG\nGCCATGAGAATGGCATTTGGAAATCTCTATGCAGCATTTCACAAAAACCCAGGAGTTGTC\nACTGGCAGTGCAGTTGGTTGTGATCCAGATCTATTTTGGAGCAAGATCCCAGTGCTAATG\nGAAGAGAAGCTCTTTGCTTTTGACTACACAGGTTATGATGCATCACTCAGCCCGGCCTGG\nTTTGAGGCACTCAAAATGGTGCTAGAGAAAATCGGATTTGGGGACAGGGTGGATTATATT\nGATTACCTCAACCATTCCCACCACCTGTACAAAAACAAAACTTATTGCGTAAAAGGCGGC\nATGCCATCTGGCTGCTCAGGCACATCAATTTTTAACTCAATGATTAACAACTTAATCATT\nAGGACACTCCTACTGAAAACCTACAAGGGCATAGATTTAGATCACCTAAAGATGATTGCC\nTATGGTGATGATGTAATTGCTTCCTACCCCCATGAGGTTGATGCTAGTCTCCTAGCCCAA\nTCAGGAAAAGACTATGGACTAACCATGACTCCAGCAGACAAGTCAGCTACCTTTGAAACA\nGTCACATGGGAGAATGTAACATTCTTGAAAAGATTCTTTAGAGCGGATGAGAAGTATCCC\nTTCCTCATACATCCAGTAATGCCAATGAAGGAGATTCATGAATCAATTAGATGGACAAAG\nGATCCCAGAAACACACAGGATCACGTGCGCTCATTGTGCCTATTGGCCTGGCACAACGGC\nGAAGAAGAATACAACAAGTTCTTAGCTAAAATCAGGAGTGTGCCAATTGGGAGAGCTTTA\nTTGCTCCCAGAGTACTCTACATTGTACCGCCGTTGGCTCGACTCTTTTTAGTAACCCTAC\nCTCAGTCGAATTGGATTGGGTCATGCTGTTGTAGGGGTAAATTTTTCTTTAATTCGGGG\n>KM609478.1 Coxsackievirus A8 isolate CVA8/SZ141/CHN/2012, complete genome\nTTAAAACAGCCTGTGGGTTGCACCCACTCACAGGGCCCACTGGGCGCTAGCACTCTGATT\nCTACGGAATCTTTGTGCGCCTGTTTTATAACCCCCTCCCCCAATGTAATTTAGAAGCAAT\nGCACCAATGATCAACAGCAGGCGTGGCGCACCAGCCATGTCTCGATCAAGCACTTCTGTT\nTCCCCGGACAGAGTATCAATAGACTGCTCGCGTGGTCGAAGGAGAAAACGTCCGTTACCC\nGGCTAACTACTTCGAGAAACCTAGTAGCACCAATGAAGCTGCAGAGCGTTTCGCTCAGCA\nCTTACCCCGTGTAGATCAGGCCGATGAGTCACTGCGTTCCCCACGGGCGACCGTGGCAGT\nGGCTGCGTTGGCGGCCTGCCTATGGGGTCACCCATAGGACGCTCTAATGTGGACATGGTG\nCGAAGAGTCTATTGAGCTAGTTAGTAGTCCTCCGGCCCCTGAATGCGGCTAATCCTAACT\nGCGGAGCGCATACCCTCAAACCAGGGGGTGGTGCGTCGTAACGGGTAACTCTGCAGCGGA\nACCGACTACTTTGGGTGTCCGTGTTTCCTTTTATTCTCTTAATGGCTGCTTATGGTGACA\nATTGAGGAATTGTTACCATATAGCTATTGGATTGGCCATCCGGTGTGTAACAGAGCAATT\nATCTACTTGTTTGCAGGATTTACCCCATTAACGTTCAAATCTCTTAACACACTACAGTAC\nATACTAACCTTGAATACAAGAAAATGGGAGCACAAGTTTCGACTCAAAAGTCTGGTAGCC\nACGAGACTGGCAACATAGCCACTGAAGGGTCCACCATTAACTTTACTAACATCAATTATT\nACAAGGACTCGTACGCCGCCTCGGCTAGCAAACAGGACTTCACCCAGGATCCTACTAGGT\nTTACTAGCCCTGTGCTTGATGCGCTGAGGGAAGTGGCACCTCCATTAAAGTCACCCTCAG\nTGGAAGCGTGCGGATACAGTGATAGAGTAGCGCAGTTGACTGTCGGCAATTCAACAATCA\nCCACACAAGAGGCTGCTAACATAGTCCTTGCTTACGGGGAATGGCCTGAGTACTGTCCCG\nACAAAGACGCCACCGCTGTAGATAAGCCTACACGCCCCGATGTGTCGGTTAATAGATTCT\nACACCATGTCTACGCAAATGTGGCAGGACACCTCGAAAGGGTGGTACTGGAAGTTCCCAG\nATGTTCTTACCAAGACTGGTGTCTTTGGACAAAATGCCCAGTATCACTATTTGTACAGAT\nCTGGATTTTGCATACATGTCCAATGCAACGCTAGTAAATTCCATCAAGGAGCACTGTTAG\nTGGCTGCCATCCCAGAGATGGTGTTAGGATCCAATAGCTCAGATCCCAAGCCCAACACTG\nCAAAGCACCCTGAATTCACTACAACAATGCCAGGTGCTAATGGTGGAATTTTTGAAAATC\nCCTATATCTTGGACATGGGGGTTCCCTTGAGCCAAGCTTTGGTGTTTCCACACCAATGGA\nTCAACCTGCGCACTAACAACTGTGCGACCATTATAGTGCCTTATATTAATGCTGTTCCAT\nTTGATTCAGCCATTAACCACAACAACTTCACGCTAGTCGTAATTCCGATTAGCCCGTTAA\nAATACTGCACAGGAGCGACAACAGCCATCCCTATAACAGTAACGATAGCCCCATTAAATT\nCTGAATTTTGTGGGTTGAGGCAAGCTACATCGCAGGGAATACCAGTGGAGCTAAAACCCG\nGCACCAATCAATTTTTGACAACTGATAACGAAGTCTCCGTACCAATCTTACCTGGTTTCC\nAGCCTACACCGGTTATACATATACCAGGGGAGGTGAACAACCTCCTGGAGCTCTGCCAGG\nTTGAATCTATCTTGGAGGTCAATAATGTGACTGGACAAGAAGGGATAAACCGACTCCTTA\nTCCCAGTTTCTACACAAAGTGACAAGGATACTTTGTGTGCATCACTCAGAGTCGATCCAG\nGTAGGGACGGACCGTGGCAATCTACTTTAGTTGGGCAAATATGTAGGTATTACACCCAGT\nGGTCTGGTTCATTAGAGATCACATTCATGTTTACTGGTTCATTCATGGCAACCGGTAAAA\nTGCTGATAGCTTACTCCCCGCCTGGGAGTGCGCAACCAACAACAAGAGACCTGGCAATGC\nTCGGCACGCACGTAGTGTGGGATTTTGGGTTGCAATCATCTATTACTCTTGTGATCCCAT\nGGATCAGCAACACACACTTCAGAACAGGCAAGGTGGGTGGTTACTTTGATTACTATGCGT\nCTGGTATAGTAACTATTTGGTATCAGACAAACTTCGTCGTGCCCCCCGACACGCCGAGTC\nAGGCTCATATAATAGCGTTGGGAGCTGCCCAGAAGAATTTCACGCTTAAACTGTGCAAGG\nATACAGATGAGGTAACACAACAAGCAGTGTTGCAGGGGGACCCCATTGAAGACATAATAA\nCTAGCACAGTCTCCCGCACATTGCAGCAAATTAGCACTCCAACACATAGCACTACTGCAG\nCAAACACCTCTGTGAGTAACCATAAGATAGGCACTGGAGATGTTCCAGCTCTCCAAGCTG\nCGGAGACAGGTGCTACCTCTAACGCCTCGGATGAGAACATGATCGAGACACGCTGCGTGC\nTAAATCGCAATGGAGTCGTGGAAACCAGTCTGGACCACTTCTTCTCAAGAGCAGGTCTGG\nTGGGGGTGATCAATGTGCAAGATGGTAGTACACAGAAGGGATTTGAGGTGTGGGATGTGG\nATGTGATGGGGTTTGTACAGCTCAGAAGGAAGTTGGAAATGTTTACATACATGAGATTCA\nATGCTGAGTTTACATTTGTGTCCACACTTGCAGACGGCACGACTCCCAGGGTGATGTTAC\nAGTACATGTATGTTCCACCTGGTGCCCCCAAACCTCAAGAGAGGGATTCATTCCAATGGC\nAAACAGCGACCAACCCGTCAGTGTTCTGCAAAATGAGCGATCCTCCCCCACAAGTCTCTG\nTCCCTTTCATGTCGCCAGCCAGCGCGTACCAGTGGTTCTATGATGGATATCCTACATTTG\nATGATCGACCTGCCACCTCAAATCACCCGTATGGACAGTGCCCTAATAACATGATGGGCA\nCATTTGCAGTGCGATTTGTCAGCAAGACCCCTGCTATACGGGACTTGCGTGTTAGGGTAT\nATATGCGCCTCAAACACGTGCGCGCTTGGGTACCGAGGCCCATACGATCCCAAGCATACA\nTCTTAAAGAACTATCCAAACTATGACGGGACAAATATAACACCAACATCCAAGGACAGGC\nAAAGCATCAAAACGACTGGGAAATTTGGTCAGCAGTCCGGTGCTATTTATGTGGGCAATT\nACAGAGTAGTTAACAGACACCTTGCCACACACAATGACTGGGCCAACTTAGTATGGGAAG\nACAGCTCCAGGGATCTCCTTGTGTCATCCACGACTGCTCAAGGATGTGACATCATTGCTC\nGTTGCAATTGCCAGACTGGAGTGTATTACTGTAACTCCCAAAGAAAACACTACCCAGTTA\nGCTTTTCAAAGCCTAGCCTGATCTATGTGGAAGCTAGTGAGTATTACCCAGCTAGGTATC\nAATCTCACCTTATGCTCGCACAAGGACACTCAGAACCTGGCGATTGTGGTGGTATCCTCA\nGGTGCCAACACGGCGTTGTCGGCATAGTGTCCACTGGTGGTGACGGACTCGTCGGCTTCG\nCAGATGTCAGGGATCTCCTTTGGTTAGATGAGGAGGCGATGGAGCAAGGTGTGTCTGATT\nACATCAAGGGACTCGGTGATGCATTTGGAACTGGCTTCACTGATGCTGTCTCTAGAGAAG\nTGGAGGCCCTTAAAAACCACCTAATTGGTTCTGAAGGAGCTGTTGAGAAAATCCTCAAGA\nATTTGATCAAGTTAATCTCTGCTCTTGTCATTGTGATTAGGAGTGATTATGACATGGTCA\nCCCTTACAGCAACTCTAGCTTTAATCGGGTGTCACGGTAGTCCTTGGGCATGGATTAAAA\nCAAAGACAGCATCTATTTTAGGCATCCCTATCGCTCAAAAGCAGAGCGCCTCYTGGCTTA\nAAAAGTTCAACGATATGGCCAACGCTGCCAAGGGATTGGAATGGGTTTCTAACAAGATCA\nGCAAATTCATCGATTGGCTCAAGGAAAAAATCATACCAGCAGCCAAGGAGAAGGTCGAGT\nTTTTAAATAACTTGAAACAGTTACCACTGCTAGAGAACCAAATCTCTAATCTGGAACAAT\nCTGCTGCCTCACAAGAGGACCTTGAAGTTATGTTTGGGAATGTGTCATATCTAGCTCACT\nTCTGTCGTAAGTACCAGCCACTATACGCTACAGAAGCCAAAAGAGTCTACACTCTAGAGA\nAGAGGATGAACAACTACATGCAGTTCAAGAGCAAACACCGTATTGAACCTGTATGTCTTA\nTTATCAGGGGTTCACCGGGCACTGGGAAGTCTTTAGCAACTGGCATCATTGCTCGAGCGA\nTAGCTGATAAGTATCACTCCAGTGTCTATTCACTCCCACCAGACCCAGACCACTTTGATG\nGGTACAAGCAGCAAGTGGTTACAGTCATGGATGATCTATGTCAAAATCCTGACGGCAAAG\nATATGTCACTGTTTTGCCAAATGGTGTCTACCGTGGACTTCATTCCTCCAATGGCTTCCT\nTAGAAGAGAAGGGGGTCTCTTTCACATCTAAGTTCGTCATTGCATCCACTAATGCTAGTA\nATATCATAGTGCCAACAGTATCTGATGCAGACGCCATTCGCCGCAGGTTCTATATGGATT\nGTGACATTGAAGTAACAGACTCATATAAAACAGACCTGGGTAGGTTGGATGCCGGGCGAG\nCAGCCAAATTGTGTTCTGAGAACAACACAGCAAATTTCAAGCGTTGCAGCCCATTAGTGT\nGTGGAAAGGCTATTCAATTAAGAGATAGGAAATCTAAGGTCAGATACAGCGTGGACACAG\nTGGTCTCTGAACTCATAAGAGAGCATAATAACAGATCCGCCATTGGTAACACAATTGAGG\nCTTTGTTCCAGGGCCCACCCAAATTTAGACCCATAAGGATTAGTCTTGAAGAAACGCCAG\nCTCCAGATGCTATTAGTGATCTTCTCACTAGTGTGGATAGCGAAGAGGTACGTCAATACT\nGTAGGGATCAAGGTTGGATTATTCCGGAAACCCCTACAAATGTTGAACGACACCTCAACA\nGAGCTGTGTTGATTATGCAATCCATCGCCACGGTAGTGGCGGTTGTCTCATTGGTGTACG\nTCATCTATAAACTCTTTGCTGGGTTCCAGGGCGCATATTCTGGTGCCCCCAAGCAAACGC\nTTAAGAAACCTGTTCTCCGCACAGCAACAGTGCAGGGTCCAAGCCTTGATTTTGCCCTAT\nCACTATTGAGAAGAAACATCAGGCAAGTGCAGACAGATCAAGGGCACTTCACCATGCTGG\nGTATCAGAGATCGCTTGGCTATCCTCCCGCGACATTCTCAACCTGGAAGGACTATCTGGG\nTGGAACACAAACTCGTGAACGTCCTGGATGCTATCGAGCTGGTGGATGAACAAGGGGTCA\nACTTAGAGCTGACCTTAATCACCCTCGACACCAATGAGAAATTCAGGGATATCACCAAGT\nTCATTCCAGAAACCATTAGTGGTGCCAGCGATGCCACCTTAGTGATCAATACAGAGCACA\nTGCCCTCAATGTTTGTGCCAGTAGGTGATGTTGTACAGTATGGCTTCCTAAATCTCAGCG\nGGAAACCGACTCATCGCACTATGATGTATAACTTCCCTACTAAGGCAGGACAATGTGGAG\nGGGTAGTCACATCAGTTGGAAAGATCATTGGCATTCATATAGGAGGTAATGGTAGGCAGG\nGATTCTGTGCGGGACTCAAGAGAAGCTACTTTGCTAGTGAACAGGGAGAGATCCAATGGG\nTTAAACCTAACAAAGAAACAGGAAGACTCAACATCAATGGACCAACTCGCACCAAGCTCG\nAGCCTAGTGTGTTTCATGATGTCTTTGAGGGTGACAAGGAGCCAGCAGTCTTGCATAGTA\nAGGACCCCCGCCTTGAGGTGGACTTCGAGCAAGCATTGTTCTCCAAGTACGTGGGGAACA\nCACTACACGAACCTGATGAGTATATCAGGGAGGCAGCCCTCCACTATGCGAACCAATTAA\nAGCAGCTAGACATAAATACCTCCCAGATGAGCATGGAGGAGGCCTGTTATGGCACAGAAA\nACCTTGAGGCTATTGACCTTCACACTAGTGCGGGATACCCCTATAGCGCGCTGGGAATAA\nAAAAGAGGGATATCTTAGACCCCATTACCAGAGATGTGAGCAAGATGAAGTTCTATATGG\nATAAGTACGGTCTTGACCTCCCTTACTCCACCTATGTCAAAGATGAACTTCGCTCAATAG\nATAAGATTAAGAAGGGGAAGTCTCGCTTGATTGAAGCTAGCAGCTTGAATGACTCGGTCT\nACCTTAGAATGGCCTTTGGGCACCTCTATGAAGCTTTCCATGCGAACCCTGGCACTGTGA\nCTGGCTCAGCTGTGGGGTGTAACCCAGATGTATTTTGGAGCAAGCTACCAATCCTGCTTC\nCTGGTTCCCTCTTCGCTTTTGACTACTCAGGTTACGATGCTAGCCTCAGCCCAGTTTGGT\nTCAGAGCGTTGGAATTAGTCCTTAGAGAGATAGGTTATGGTGATGAGGCAGTCTCACTCA\nTTGAAGGAATCAACCATACACACCATGTGTACCGTAACAAAACCTACTGCGTACTTGGTG\nGAATGCCCTCAGGTTGCTCAGGGACATCCATCTTCAACTCAATGATTAATAACATCATCA\nTCAGAGCACTACTTATTAAAACATTCAAGGGCATTGATCTGGATGAACTCAACATGGTTG\nCCTACGGGGACGATGTGCTCGCTAGTTACCCCTTTCCAATTGACTGCCTGGAGCTAGCAA\nAGACAGGTAAGGAGTATGGCCTAACCATGACCCCTGCAGACAAGTCCCCTTGCTTCAATG\nAAGTTAATTGGGAAAATGCAACCTTCCTCAAGAGAGGCTTCTTGCCTGATGAGCAATTCC\nCGTTTTTGATCCACCCCACCATGCCAATGAAGGAGATTCATGAATCCATTCGGTGGACCA\nAGGATGCACGCAATACTCAAGATCACGTGCGGTCTCTATGTCTGTTGGCATGGCATAACG\nGTAAGCAAGAATATGAAAAATTTGTGAGCTCAATTAGATCCGTCCCAGTAGGAAAAGCAT\nTGGCAATCCCCAACTATGAAAATCTGAGACGTAATTGGCTCGAATTGTTTTAGAGGTTGG\nACAAACGACTCAACCCCACCAGAAATCTGGTCGTGAATGTGACTGGTGGGGGTAAATTTG\nTTATAACCAGAATAGC\n" }, { "path": "tests/input/TestMiseqToBam/RunInfo.xml", "content": "\r\n\r\n \r\n 000000000-AEF96\r\n M04004\r\n 150821\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n" }, { "path": "tests/input/TestMiseqToBam/SampleSheet.csv", "content": "[Header],,,,,,,,,\r\nIEMFileVersion,4,,,,,,,,\r\nInvestigator Name,James,,,,,,,,\r\nExperiment Name,EBoV HS ,,,,,,,,\r\nDate,8/18/2015,,,,,,,,\r\nWorkflow,GenerateFASTQ,,,,,,,,\r\nApplication,FASTQ Only,,,,,,,,\r\nAssay,Nextera XT,,,,,,,,\r\nDescription,,,,,,,,,\r\nChemistry,Amplicon,,,,,,,,\r\n,,,,,,,,,\r\n[Reads],,,,,,,,,\r\n101,,,,,,,,,\r\n101,,,,,,,,,\r\n,,,,,,,,,\r\n[Settings],,,,,,,,,\r\nReverseComplement,0,,,,,,,,\r\n,,,,,,,,,\r\n[Data],,,,,,,,,\r\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\r\nmebv.0.6,,,,N702,CGTACTAG,S502,CTCTCTAT,,\r\nmebv.0.5,,,,N702,CGTACTAG,S503,TATCCTCT,,\r\nmebv.0.4,,,,N702,CGTACTAG,S504,AGAGTAGA,,\r\nmebv.0.3,,,,N702,CGTACTAG,S505,GTAAGGAG,,\r\nmebv.0.1,,,,N702,CGTACTAG,S508,CTAAGCCT,,\r\nmebv.4.6,,,,N703,AGGCAGAA,S502,CTCTCTAT,,\r\nmebv.4.5,,,,N703,AGGCAGAA,S503,TATCCTCT,,\r\nmebv.4.4,,,,N703,AGGCAGAA,S504,AGAGTAGA,,\r\nmebv.4.3,,,,N703,AGGCAGAA,S505,GTAAGGAG,,\r\nmebv.4.1,,,,N703,AGGCAGAA,S508,CTAAGCCT,,\r\nmebv.20.6,,,,N704,TCCTGAGC,S502,CTCTCTAT,,\r\nmebv.20.5,,,,N704,TCCTGAGC,S503,TATCCTCT,,\r\nmebv.20.4,,,,N704,TCCTGAGC,S504,AGAGTAGA,,\r\nmebv.20.3,,,,N704,TCCTGAGC,S505,GTAAGGAG,,\r\nmebv.20.1,,,,N704,TCCTGAGC,S508,CTAAGCCT,,\r\nmebv.48.6,,,,N705,GGACTCCT,S502,CTCTCTAT,,\r\nmebv.48.5,,,,N705,GGACTCCT,S503,TATCCTCT,,\r\nmebv.48.4,,,,N705,GGACTCCT,S504,AGAGTAGA,,\r\nmebv.48.3,,,,N705,GGACTCCT,S505,GTAAGGAG,,\r\nmebv.48.1,,,,N705,GGACTCCT,S508,CTAAGCCT,,\r\n" }, { "path": "tests/input/TestMvicuna/expected_pairedOut.1.fastq", "content": "@from_ebov\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_ebov_dup_first_only\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n" }, { "path": "tests/input/TestMvicuna/expected_pairedOut.2.fastq", "content": "@from_ebov\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n@ from_ebov_dup_first_only\nGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\n+\nEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEF\n" }, { "path": "tests/input/TestMvicuna/expected_unpairedOut.fastq", "content": "" }, { "path": "tests/input/TestMvicuna/in.1.fastq", "content": "@from_ebov\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_ebov_dup1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_ebov_dup_first_only\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n" }, { "path": "tests/input/TestMvicuna/in.2.fastq", "content": "@from_ebov\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n@from_ebov_dup1\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n@ from_ebov_dup_first_only\nGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\n+\nEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEF\n" }, { "path": "tests/input/TestOrderAndOrient/contig.mummer3_fail_lasv.fasta", "content": ">comp1_c0_seq3 len=5847 path=[0:0-1960 17043:1961-1961 1962:1962-1979 1980:1980-1985 1986:1986-2022 17067:2023-2023 2024:2024-2051 17080:2052-2062 17091:2063-2105 17113:2106-2118 17126:2119-2131 14002:2132-2183 13863:2184-2238 2239:2239-2326 17203:2327-2331 13819:2332-2342 2343:2343-2404 13745:2405-2426 2427:2427-2530 13459:2531-2559 2560:2560-2573 2574:2574-2617 17294:2618-2628 17305:2629-2629 13336:2630-2645 13358:2646-2651 13140:2652-2652 13158:2653-2756 2757:2757-2798 2799:2799-2890 12980:2891-2914 2915:2915-2915 2916:2916-2930 2931:2931-2954 2955:2955-2978 2979:2979-3002 3003:3003-3020 3043:3021-3056 3079:3057-3074 3097:3075-3077 3100:3078-3122 3145:3123-3165 9172:3166-3169 9176:3170-3189 3212:3190-3191 9148:3192-3215 3238:3216-3281 3304:3282-3305 3328:3306-3326 3349:3327-3329 3352:3330-3488 8961:3489-3545 3568:3546-3962 8778:3963-4049 4072:4050-4103 4126:4104-4163 4186:4164-4177 8502:4178-4241 8566:4242-4242 4265:4243-4258 8408:4259-4352 4375:4353-4364 4387:4365-4388 8318:4389-4424 8378:4425-4430 8315:4431-4433 4456:4434-4445 8161:4446-4450 8203:4451-4475 4498:4476-4511 4534:4512-4514 4537:4515-4538 4561:4539-4541 4564:4542-4571 7868:4572-4601 4624:4602-4619 7735:4620-4680 4703:4681-4709 7687:4710-4712 7690:4713-4736 4759:4737-4760 7663:4761-4784 4807:4785-4901 4924:4902-5627 5650:5628-5735 7326:5736-5780 7371:5781-5781 7372:5782-5846]\nTCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATCAGCATAGTCCGCAGGT\nCTCTGTTTTGTGAAGATTGAGACAATGTCCACACCCGTCCATTGAACCCTTTGTTTCAAT\nCTATCAGACATCATTGATTTCAATGCACCAACCAAAAGATGCGGGGAACTATCACTAATC\nTCTCTTACAAACATTTCCAAATCTTGATCTTGGATAGATGGTGTAAATGTAGCCACCCTT\nCTATCAGACTCCCACAGTGCTCCCCTACATACAACCAATGGCACTGGTTCGTTGTCAGGT\nCCGACCTTGGAGAAGTCAAACTCACTGAACTGCAGTTTGTCTGGGTTAATGATGAGCTTC\nATGGGTATAACATCCCCCAACTGCTGTGTATCTTTTAAGAATTCATTTACCACATCCGAC\nTCAACAAACCAGGCTGACCTACCTTTGAAAGTTGGACCAGACAAAGCAAGTCTCCAACAG\nTCAGGCAGAACACATGGGCTCACAGACCCAGAATATAGTGCCTGTACATCATTCACCACA\nAACTCACCACACTGATTAACAAGTCCTGTCATGTTGAGATGGATAGAAAAAGTCTCTTTA\nAAACTGGCATCCTGACTCTTGATTTTATATCTAATTGTTTGGTGAAACTGAACAGAGTCC\nATTGGCATTGTACTTAATAAATCAAAGAAATCCTCAAGGGAATCTAGCCTCAGTTCCTCT\nGTCAGGCCTGAGGCAATAAGCTGGTTCAAGTTTATCTGAGCTGGTTCTATGTCAAAGTCT\nATCCATGCATAACCCATCATTAGATCAAATTTAAACATAGGTCTCTCTACCCCTTTGTAA\nATAGCTTTCTCAACAAATGAAGAGAAGGGACCCAGTCGTTGCAGACCTTCACCCTCTGGT\nATTGAGGTTTTGTGAGGGAACCAAGTAAATGACCCAAGCGTCCTTGTTGTTGCTACAAAA\nGAGCGGACATATGACTCAAAGTAGATTTGTCTCATAAAGTTGTCCACTGCATCAGCAGTA\nCTGACCACCCTCTCTTCCATCATGGGCTCATGTGTACGAGAATGTGAGTTTCTCAGTTCA\nGAAGCCAATACAACATAATGCTCCTCCCTCTTCCACTTAACAATATGTGAGACAAGTGAA\nAGTGCCTCGCAATTCACATCTAAAGCAACACAAAGATCAAGGAACTTAATTCTAGGTGAC\nCATTTCATCTTTGTGGAGGCTAAATCACTCATAAATGGCAATATGTGCTTCTCAAATAGA\nGACGGATATAAACGTCTCAAAGAGTGAATGATGTGGCTCATGCCAACCCTATCCTCTAGC\nAGTTTCGAAATAGTGGGTCTCAAGGGGAAGTAATCACAGGGATTATGTTTAAAAAAGTCC\nGAGATCTGAGCTTGTTTTGGTTCCCCGAGCACCCATGCTCCAAGTTCTATAGCTGTAGAT\nAGTGCTATGCACATATAATCCCATAGAAGAGGTCTTAAATAAGTGACAACAGTATCACCT\nCCATCTTTGACTTCTGGTGAAACTTTCCATATCTGGATTCCACTGTCCTCCATCACTGCT\nTCAATACCTTGAGTCTCTAGTAGCTGAGTCTGTATGGATCTAATGTAAAGATTCTCTTTG\nTTGGGGCCTCTGACACACTTGCTACCCAGTGTTCTGCACAACCCTACAAACCCAGATGCT\nATAGAACTTTGGAAAGCTGACTTATTTATTGCTTCAGACAGTAGCTTCTGAGCCCCTCTA\nGTGAATGTCGATGACAACCTATTTTGCAAAGTTTTTACTATTGTAGGGACCTTTTCATCT\nTCCAGATTTACAGCACCAGAATAGATTATCTTTTGCCGCAACACCATTCTAAGTGGGTGA\nTGGGCGGCTAAGTTCAACCAATGAATCCCCAAGTCAGAATCAGACAAAGGTTCAATGCCT\nAGAAGTTTAAACAAATTCTGTAATGATGTTGTGTGTTCACCCAATAGGTAATTGGTAGTA\nAATTCCTCATGAAGCTCACCAGTTTTTAATTTATTGAACAATATCCTAAGCATTGACCTC\nATTCTTTTGCAGGCATCAGGAATTAGCCTCTCAATCTGCCTCATTATTCTATAACTACGA\nTTCCCGTCCACCCAATCTCTTACATCAGTCTCACAGTTCAAAAGGAATGGGTCAATAGGA\nTACTTGGCATAACATAACAAACTTAAGGTCCTCTTCTGAATTTGATTACACAGATCAACT\nGGGACACCATTAGCCACAGATTGATCAATTATGGTATCAATTGTCTCTGCTAATTGATGG\nGGTTCTTTACACTTTATGTTATGTAAAGCCGCAGCAACAAATTTTGTTAGCAGAGGCACC\nTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCAATTGCACTC\nTTTGGGCTCACAAATTTATTCAGCTGGTCACTCATGTAGTAATGGAATTCTAACAATGTT\nTTAAATTCTTCTGTGTCCCTTGAGAGTAACTCTGTTAAGTTCTGATCAAATAATGATATC\nTGATCATCACTGGACGTGTAAGCATCGATTTGTCCTCCAGACACACACCTCACCGCAAAA\nTTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGCAGGATACCCTGT\nCCCATATCAAGGATTGAACTAATGTGTGAGGGGACTGTGCCAACTTGAAAGTTGGAATTG\nAAAAAGTCTTCGGTCAATGATTGAGTTGTCTTCTTTTTCAATCCAAGTTGGGATTTGATG\nTATGATTTCATCATTGCTGACACAACATTAAATGGGATCTCAACCATTTTGTGCATATGC\nCATGTTAATAATGTTGATAGGTAATCTTTGCCTTTTAGATCAGCTTGTAAATCATCAGAA\nAGTAAGATCAGGTTTTGAATTATTGTTAGAAACAGGAAAGGACACATCATAGGGCCCCAC\nTTACTGTGATCCATACTATATGATACATGTGCCGATGAGACATTCAGCTTCATTGACAAA\nATAGCATTGTCAAACTCCTTCTCATTGTTTAGACAGCTGCCTGCCAATTGTGATGTGAGC\nGCCTCAAAGTAATCCTCAATAAGCCTTGTGAACATCTTTGTCCTTAAATCTCCGATGTAC\nAATTCTCTATTGCCTCCCACTTGTTCCTTGTAAGACAAAGAAAATTTTAGTCTACCAGTG\nTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCTTGGCTGTAAAAACACAGATTTTTT\nAACATTGCTGTAGTACAGTTAGTTAAAGACAAGGCCTTACTAAGTGCTTCAGAATTACTC\nTCACGCTCACTTATCCTGACATCATCAGCCAATCTTCCTGTATCAAATTTAAAGTTCAAA\nCATTTACTCTTATAATGAGAATACCTTCCCATCAACCTATTCCCATTCATCACTAGTAAA\nATTGACTTAAAGCACTGGAAATATTCTTGGTCCAAAAAAGTCCTAGTCACCACTGCCTTT\nGTCAGCTCACTAATAGGACATGAATTCATTGGTCCTACATAAAAATATTTACTTCTCAAA\nGAAGCGTCATTGTAGATATTCTCACAAATTTTGATGTATTGATCCTCAGATAGGATTTCT\nCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATCAACCTTATTAAGAGT\nTTTTCTTCTATCACCTTGTCAAGATCAGATATTGAGGGTGTATTGCAGTCTGCCTGCTGC\nTGTCTTTCCGGTTGCTCCCTATACTGACTGATAATATTGTCAACAGTGCACCTTAGTTGG\nTCGAAGTATTCTGATGCTCCTCCATCCAATAGTATCTCATCTAGGTCAGCATTATTGGTA\nTCATCATTCCTTCCTTTGGACCCTAGGACAAGATTACTCATTGCTTGCTGTATCTTGTAA\nTCATAATCCTGTTTGTTAAGCAAGAATTTGCCTTTACGTGCAAACACTTCAGTTAACTGT\nGTGACAGCCAAAGCTGTAAGCTTGTTGAAGTCATAATCCAGAATACGGGACCCATCTGTA\nTACTTATTTACAACAACACTCTTATTACTAGCCAAGTCCAAAGCTGTTGCACAGCCGCTT\nGTAATAAGAGGGTCTCGCAGTGTCTTCTTTACCTCCTTTTCTTTGAACAATGAACCATTA\nTTGAAACTGGACACAAGGAGTGAAATAAATTTCTTGGAAACACCAGGCTTTTTATACCTA\nATTTTTTCCGCATCTGCACAACATTCTTTACTTAGAAACTTTCTTGCATTATAAACCATT\nTCAGCAAGCTCTTCCTCCGATGCATCATCCTTCGGGTTCACACTTACATGTCCAAACTCC\nAATTTGGGTTCAAGGAATTTCTCAAAGCATTTAATCTGGTCAGTCAGTCTGTCAGGTGTT\nTCTTTTGTAATGAAATGACACATATAAGAGATGTTCAAAACAAACTTGAATCTATTGGTC\nATCATACTGACAACTTCTTCAGACAGAATTATCTTCAATAAGTGACGAACAAGTCTGTAG\nAGCAGATATTCGACTTCTGTGATCAAATCCTCCCTGATCTTCTCAATCAAATCCTTGTGA\nTAAAAATCGGACACAAAGGCCATCACAAAGTACCTGATGTTCTGTAAAAATTTTTGACAC\nCTTTTACTAGGATGTGTCAGTATTAAAACTAAAATCATTTTGGTTAACAATTTAATAGTG\nTTCAATTGTTCAGATAACTCTGTGCACTCTTCTATCCAGCTGACCATAACATCGACCACT\nTTCTGCAACACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTGGGATCAGCATAAAAG\nGAACAAACCTCTCCAACTACATTGTTGTTAATAGCATAACATTTTGAGCATTCACCTGTT\nTTTTGATATAATAGTTTGAATCCCATCCTATTGATGAAGAATTCTTGGCAATAGGCCTCT\nTTGCACCTCACAACCTGGTATCTAGAAGGACCAAATTCATTTTGCCTTAGTTTCACTGTA\nGAAGACGTTTTCATTGAGTTGATCAAGGCCAAGCTCAATGATGATAGTCTTTCTAAGTCT\nGTTGCATCTAGAATGTCAATAACGCCAAGAGTGTAAGGGAACATGTCCTCTTGAGTTTTC\nTGGTAACTTATAGTAGGTGTGATGCCGGAGATCTCAATGTCCATGATGGCATCATAAACA\nTCACAATCAAGGATCTTGGAGTCAATTCCATAAGAGTTGGTTTCTATACCAACCTCTCTC\nAAAGCATTAGTAGCTCGAGTTAAAACCCTGTTGATGATGGCAAGGAGCTCACAATTTCGT\nTCCTCTTTAAGTGACAGGACACCTACATTCTTGTCTTTAGTTCTCTTCCTGCTGTCCATC\nCACCGTTTTAGATCTCTTTTTGTTGATTCCAATGAAACTAATCTATCGTTAACACTCACA\nAAACAAGAGCCCAGCCAACCAGCAAGGAGCTTGTCACCATGCCTTATGCGGTCCAGCCGG\nCTAGCAAGAAGAATCAGAACATCAAAAATAAGGAGAAGTTTCCTCCTAGTGTTGAGGATC\nCTCAGGGATTTTATTTTATTTAGAAAAGATCTCCAACACTGCATCTGTTCACTTTGAGGG\nTCAGCAACCTTTTCCTTACCAGAATCCAAATCTGCATACAAGAATTTAAGGACTGGAGAG\nGCTCTTCGGAACTGGAATGTTAACTGTTCAATATTGTCATCACAGGTGCCTATCTTATCA\nCAATACAGCTTTCTGAAATCCTCTAATAATTTCATCTTATCAGTCTTAACAAATTGACTT\nTCTATATTCCCTTGCCTTAGTTTGTTCCTGAAGATTTGATACTCCTCCTCAATTAAACTC\nTTGACTTCATAAGAGGTGAGCTTATTG\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.ebov.doublehit.fasta", "content": ">comp0_c0_seq1 len=6894 path=[0:0-898 923:899-1207 1232:1208-2491 2516:2492-2532 2557:2533-3421 6937:3422-3506 3462:3507-4040 3996:4041-4066 4062:4067-4717 4737:4718-6782 6802:6783-6893]\nCTCTATCTTGGTGATATGGCTCTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCA\nAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAA\nTCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTG\nATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACA\nAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAA\nCAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCA\nCAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGA\nATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGT\nTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTAT\nCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCAT\nGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGT\nCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCG\nCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGC\nCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCT\nATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAAT\nTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACA\nCATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACA\nCCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGT\nGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACA\nAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGA\nGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTT\nCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACT\nGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGT\nTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACA\nATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCT\nTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAAC\nTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAA\nAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGA\nCGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGA\nTGTGGTAGTTGACCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGG\nCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAA\nGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCA\nTACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAAC\nAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTC\nAACCAGCCCTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGA\nCGACGAGACGTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGG\nAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGA\nAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAA\nCCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCT\nAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGT\nAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATA\nTCCACCATGGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGA\nTGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCA\nACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCTAACATT\nAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCA\nCAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTC\nAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGT\nAACTCAATATCTTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTA\nCCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGA\nAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGT\nCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCC\nATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCT\nCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACA\nATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCA\nACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACAT\nTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAAC\nGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCT\nCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCG\nGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCAC\nCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATG\nAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAA\nCTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATG\nATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGG\nGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAG\nGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATG\nCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGA\nGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGC\nTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGA\nGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACA\nCTTGTGAGTATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCA\nTATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATA\nATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCG\nACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAA\nATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTG\nCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGG\nAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCG\nACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGA\nATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTG\nTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCAT\nATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTC\nCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGG\nAGTTCGTTCTTCCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCA\nAACTGATCACTCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAA\nATGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCA\nACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAA\nTAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGG\nGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAA\nATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTC\nCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTC\nTTCCAGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCT\nTCTCAGGGATAGTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAAT\nTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCT\nTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTA\nATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCA\nTTGCACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCC\nAGTGTGACTTGGATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACA\nATCTAAGTACAGACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGA\nCAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGG\nTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACA\nCAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCT\nTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACA\nATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCA\nCAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGC\nCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATG\nAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTG\nAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACA\nAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCT\nTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTG\nTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGA\nGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGAT\nATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGA\nCCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAA\nTATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCG\nAAATTGATACAGCTGTGAAAGACAACTCTTCACTGCGAATTTTTCTAGTGAGGTTTTTTT\nAGTTTCCCAGAAGGCCCACTCCCCGATTGTTGTATCAATTTCGGGGTTGACCTT\n>comp0_c0_seq2 len=4742 path=[0:0-898 923:899-1207 1232:1208-2491 2516:2492-2532 2557:2533-3421 6937:3422-3506 3462:3507-4040 3996:4041-4066 4062:4067-4717 4713:4718-4741]\nCTCTATCTTGGTGATATGGCTCTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCA\nAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAA\nTCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTG\nATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACA\nAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAA\nCAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCA\nCAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGA\nATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGT\nTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTAT\nCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCAT\nGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGT\nCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCG\nCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGC\nCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCT\nATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAAT\nTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACA\nCATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACA\nCCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGT\nGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACA\nAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGA\nGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTT\nCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACT\nGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGT\nTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACA\nATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCT\nTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAAC\nTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAA\nAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGA\nCGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGA\nTGTGGTAGTTGACCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGG\nCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAA\nGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCA\nTACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAAC\nAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTC\nAACCAGCCCTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGA\nCGACGAGACGTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGG\nAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGA\nAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAA\nCCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCT\nAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGT\nAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATA\nTCCACCATGGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGA\nTGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCA\nACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCTAACATT\nAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCA\nCAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTC\nAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGT\nAACTCAATATCTTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTA\nCCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGA\nAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGT\nCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCC\nATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCT\nCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACA\nATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCA\nACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACAT\nTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAAC\nGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCT\nCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCG\nGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCAC\nCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATG\nAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAA\nCTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATG\nATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGG\nGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAG\nGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATG\nCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGA\nGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGC\nTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGA\nGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACA\nCTTGTGAGTATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCA\nTATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATA\nATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCG\nACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAA\nATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTG\nCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGG\nAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCG\nACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGA\nATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTG\nTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGCCTAGAGGAAGCCAAATTGGAA\nTT\n>comp0_c0_seq3 len=4084 path=[0:0-898 923:899-1207 1232:1208-2491 2516:2492-2532 2557:2533-3421 6937:3422-3506 3462:3507-4040 3996:4041-4066 4022:4067-4083]\nCTCTATCTTGGTGATATGGCTCTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCA\nAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAA\nTCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTG\nATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACA\nAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAA\nCAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCA\nCAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGA\nATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGT\nTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTAT\nCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCAT\nGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGT\nCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCG\nCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGC\nCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCT\nATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAAT\nTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACA\nCATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACA\nCCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGT\nGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACA\nAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGA\nGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTT\nCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACT\nGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGT\nTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACA\nATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCT\nTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAAC\nTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAA\nAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGA\nCGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGA\nTGTGGTAGTTGACCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGG\nCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAA\nGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCA\nTACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAAC\nAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTC\nAACCAGCCCTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGA\nCGACGAGACGTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGG\nAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGA\nAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAA\nCCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCT\nAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGT\nAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATA\nTCCACCATGGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGA\nTGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCA\nACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCTAACATT\nAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCA\nCAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTC\nAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGT\nAACTCAATATCTTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTA\nCCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGA\nAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGT\nCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCC\nATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCT\nCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACA\nATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCA\nACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACAT\nTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAAC\nGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCT\nCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCG\nGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCAC\nCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATG\nAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAA\nCTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATG\nATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGG\nGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAG\nGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATG\nCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGA\nGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGC\nTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTCGGAGGGAAAAGA\nGATT\n>comp0_c0_seq4 len=1980 path=[7113:0-132 7246:133-614 7728:615-1078 8216:1079-1650 8788:1651-1868 6802:1869-1979]\nACTGATCCACAAGTCTTACGGGCGATTAGTAGGAGTAATTCCCTATCAGTTAAACTTTCT\nAACTGGTGGTCTTTTTTGCAAAAACTACTGTCACACAAAAATCCTTTTTTCAAGGTCGGA\nCATATGTCTTTAGGTGCTGGAGGAACTGTTAATGGTTCAACTCTCTTCTTATGAAATACA\nGTAGGAACGCGCACTTGTGAGGCGCTCCTTGATTGACGGTACTCACCTCGATAATTCTCT\nCTGGATGATGATCGTGCTCGAACATGGTGGTCGTGTCCATCCCTTGAATGCTGTCTGGCA\nGCTCGGGGGCGTCCTCTCTCATATGAAGCTTCCATTTAAGAGTTGTCTGCACTCACTGTT\nTAAATTTCTATTGACTTTTTTACCAATGCTTTGTGTGTGTTAGGTTACAACTAAATTCTA\nCCGGTTTGCAGATCTGATTATTACAACTTAATAAAAAGGCTTTTTTCCTTTTTCATTAAA\nGACAACTGTCATGATTGTAGAATCAAGGATGAAGACTAAAGATAATCGAAAGATTACCTT\nTTTCTTAATCTTCATCAAGTTTATCATTCTTAAAGATATAGCTAGATTGATGTCAAACCT\nTGTTTATGATTAACTGTGAGTTTAAAGGAGTTAGAATCACATTGGCTATGTTTGAAGCTC\nCAGTGTATTATGTTATCATTTGTCAAGTAATCTTAGATTCAAGTGATTCATATAATTAAA\nTCCTAGTTTCATTGATTTGAGGTTGAGTTTTGCCGTGAAACAATCTGAAGAAAGACTAAA\nAGACAAATTTGCATATACAGAATAAAGCGATAACTGCAATTATAACACCTGTAACTCCAA\nTACCTGCCGGTATCCATTGTCTCCATCCTGTCCACCAATTGTCATTGTCCCCCTGGTCCG\nGAAGGGTTTTATCAACAAAATCATGAATAATCTGATCAATTTTGTCTGTTATGTTCTTGG\nTCCAATCATGTGGTTCGATACAGCAGTCCGGTCCCAAAATGTGGCATGTGCCACCCCATC\nGCTGCAGCAGGAAGTCAATTGCCTTACGGTTGAGGATTGAAAAGGTTCGCAGCTCAGTTG\nTGGCTCTCAGGAACAGTTGGAGAGCTTGAGTCGTTTCGTTGGCCAGCTGCCTCAACCCAC\nAGATTAAACCATCTTGGTTGTGCATTAGCCCCTCTGTGTAAATTCCTTCGGCTGCTGGCC\nCGAAATATGGTATCCAGGCCAATCCGATTGCAGCACCTTCATCCTGAGTAGTCCAGTAAT\nGTAAATTGGGGTTGCATTTGGGTTGAGCATTGACAATTACTTCTCTTCGAGTCCTTCTCC\nCGCCTGTGATCAGTCCTGCTACTCCAGCAATAGTATTGGTAATTAAGCCTAGCTTCCCGC\nTGCTGGCACTCTCTTCTCCGGTATCTTGGTGATGAGTGTTGTTGTTGCCAGCAGTCTCGC\nTGTAGTTTTGGGGGCTTGTCGTGGTGGCGAGGTCCAGGGAGTCAGCGCTCTTACTCGTGT\nTGGTGTTCTCTGCTTTTAAGGGTCCGGCTGCGGTCGTGGCGGGGGGAGTGTCGGAGGCTG\nTGCTGTCGTTGTCTGCTCTACGGTGATGTTGTCCAACTTGAGTTGCCTCAGAGATGTCAA\nGTTTATACACGGGTGTATTATGGGTGCTGTTGTCCGGACCTGTTTTGGTTGTGGGAGGTT\nGAGGACTCGTGGAGATTGTGGCAAGGGTTGTCAGATGCGACACTGCAGCTTTCCTTCCTT\nGACTGTGCACTTGAACCATTGCAGAGGAATTTTCTGAAGCCATGATTTTGTGGTCTTCAT\nTTGTTGTGTTGGTCTCTGGGTCGGAAGAAGTTCGCGCCGGACTCTGACCACTGATGTTTT\nTGGGTCCGTTTGATACAGCTGTGAAAGACAACTCTTCACTGCGAATTTTTCTAGTGAGGT\nTTTTTTAGTTTCCCAGAAGGCCCACTCCCCGATTGTTGTATCAATTTCGGGGTTGACCTT\n>comp0_c0_seq5 len=1880 path=[9164:0-32 7246:33-514 7728:515-978 8216:979-1550 8788:1551-1768 6802:1769-1879]\nGACATATGTCCGACCTTGAAAAAAAGGATTTTTGTGCTGGAGGAACTGTTAATGGTTCAA\nCTCTCTTCTTATGAAATACAGTAGGAACGCGCACTTGTGAGGCGCTCCTTGATTGACGGT\nACTCACCTCGATAATTCTCTCTGGATGATGATCGTGCTCGAACATGGTGGTCGTGTCCAT\nCCCTTGAATGCTGTCTGGCAGCTCGGGGGCGTCCTCTCTCATATGAAGCTTCCATTTAAG\nAGTTGTCTGCACTCACTGTTTAAATTTCTATTGACTTTTTTACCAATGCTTTGTGTGTGT\nTAGGTTACAACTAAATTCTACCGGTTTGCAGATCTGATTATTACAACTTAATAAAAAGGC\nTTTTTTCCTTTTTCATTAAAGACAACTGTCATGATTGTAGAATCAAGGATGAAGACTAAA\nGATAATCGAAAGATTACCTTTTTCTTAATCTTCATCAAGTTTATCATTCTTAAAGATATA\nGCTAGATTGATGTCAAACCTTGTTTATGATTAACTGTGAGTTTAAAGGAGTTAGAATCAC\nATTGGCTATGTTTGAAGCTCCAGTGTATTATGTTATCATTTGTCAAGTAATCTTAGATTC\nAAGTGATTCATATAATTAAATCCTAGTTTCATTGATTTGAGGTTGAGTTTTGCCGTGAAA\nCAATCTGAAGAAAGACTAAAAGACAAATTTGCATATACAGAATAAAGCGATAACTGCAAT\nTATAACACCTGTAACTCCAATACCTGCCGGTATCCATTGTCTCCATCCTGTCCACCAATT\nGTCATTGTCCCCCTGGTCCGGAAGGGTTTTATCAACAAAATCATGAATAATCTGATCAAT\nTTTGTCTGTTATGTTCTTGGTCCAATCATGTGGTTCGATACAGCAGTCCGGTCCCAAAAT\nGTGGCATGTGCCACCCCATCGCTGCAGCAGGAAGTCAATTGCCTTACGGTTGAGGATTGA\nAAAGGTTCGCAGCTCAGTTGTGGCTCTCAGGAACAGTTGGAGAGCTTGAGTCGTTTCGTT\nGGCCAGCTGCCTCAACCCACAGATTAAACCATCTTGGTTGTGCATTAGCCCCTCTGTGTA\nAATTCCTTCGGCTGCTGGCCCGAAATATGGTATCCAGGCCAATCCGATTGCAGCACCTTC\nATCCTGAGTAGTCCAGTAATGTAAATTGGGGTTGCATTTGGGTTGAGCATTGACAATTAC\nTTCTCTTCGAGTCCTTCTCCCGCCTGTGATCAGTCCTGCTACTCCAGCAATAGTATTGGT\nAATTAAGCCTAGCTTCCCGCTGCTGGCACTCTCTTCTCCGGTATCTTGGTGATGAGTGTT\nGTTGTTGCCAGCAGTCTCGCTGTAGTTTTGGGGGCTTGTCGTGGTGGCGAGGTCCAGGGA\nGTCAGCGCTCTTACTCGTGTTGGTGTTCTCTGCTTTTAAGGGTCCGGCTGCGGTCGTGGC\nGGGGGGAGTGTCGGAGGCTGTGCTGTCGTTGTCTGCTCTACGGTGATGTTGTCCAACTTG\nAGTTGCCTCAGAGATGTCAAGTTTATACACGGGTGTATTATGGGTGCTGTTGTCCGGACC\nTGTTTTGGTTGTGGGAGGTTGAGGACTCGTGGAGATTGTGGCAAGGGTTGTCAGATGCGA\nCACTGCAGCTTTCCTTCCTTGACTGTGCACTTGAACCATTGCAGAGGAATTTTCTGAAGC\nCATGATTTTGTGGTCTTCATTTGTTGTGTTGGTCTCTGGGTCGGAAGAAGTTCGCGCCGG\nACTCTGACCACTGATGTTTTTGGGTCCGTTTGATACAGCTGTGAAAGACAACTCTTCACT\nGCGAATTTTTCTAGTGAGGTTTTTTTAGTTTCCCAGAAGGCCCACTCCCCGATTGTTGTA\nTCAATTTCGGGGTTGACCTT\n>comp0_c0_seq6 len=1231 path=[0:0-898 923:899-1207 9265:1208-1230]\nCTCTATCTTGGTGATATGGCTCTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCA\nAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAA\nTCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTG\nATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACA\nAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAA\nCAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCA\nCAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGA\nATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGT\nTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTAT\nCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCAT\nGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGT\nCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCG\nCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGC\nCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCT\nATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAAT\nTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACA\nCATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACA\nCCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGT\nGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACA\nAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGA\nGGTGAACTCCTTGTTCTGTCTTTTGTAGGAT\n>comp0_c0_seq7 len=925 path=[9197:0-23 8216:24-595 8788:596-813 6802:814-924]\nCCCCATCGCTGCAGCAGCGATGGGGTGGCTCTCAGGAACAGTTGGAGAGCTTGAGTCGTT\nTCGTTGGCCAGCTGCCTCAACCCACAGATTAAACCATCTTGGTTGTGCATTAGCCCCTCT\nGTGTAAATTCCTTCGGCTGCTGGCCCGAAATATGGTATCCAGGCCAATCCGATTGCAGCA\nCCTTCATCCTGAGTAGTCCAGTAATGTAAATTGGGGTTGCATTTGGGTTGAGCATTGACA\nATTACTTCTCTTCGAGTCCTTCTCCCGCCTGTGATCAGTCCTGCTACTCCAGCAATAGTA\nTTGGTAATTAAGCCTAGCTTCCCGCTGCTGGCACTCTCTTCTCCGGTATCTTGGTGATGA\nGTGTTGTTGTTGCCAGCAGTCTCGCTGTAGTTTTGGGGGCTTGTCGTGGTGGCGAGGTCC\nAGGGAGTCAGCGCTCTTACTCGTGTTGGTGTTCTCTGCTTTTAAGGGTCCGGCTGCGGTC\nGTGGCGGGGGGAGTGTCGGAGGCTGTGCTGTCGTTGTCTGCTCTACGGTGATGTTGTCCA\nACTTGAGTTGCCTCAGAGATGTCAAGTTTATACACGGGTGTATTATGGGTGCTGTTGTCC\nGGACCTGTTTTGGTTGTGGGAGGTTGAGGACTCGTGGAGATTGTGGCAAGGGTTGTCAGA\nTGCGACACTGCAGCTTTCCTTCCTTGACTGTGCACTTGAACCATTGCAGAGGAATTTTCT\nGAAGCCATGATTTTGTGGTCTTCATTTGTTGTGTTGGTCTCTGGGTCGGAAGAAGTTCGC\nGCCGGACTCTGACCACTGATGTTTTTGGGTCCGTTTGATACAGCTGTGAAAGACAACTCT\nTCACTGCGAATTTTTCTAGTGAGGTTTTTTTAGTTTCCCAGAAGGCCCACTCCCCGATTG\nTTGTATCAATTTCGGGGTTGACCTT\n>comp0_c0_seq8 len=923 path=[0:0-898 899:899-922]\nCTCTATCTTGGTGATATGGCTCTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCA\nAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAA\nTCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTG\nATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACA\nAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAA\nCAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCA\nCAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGA\nATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGT\nTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTAT\nCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCAT\nGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGT\nCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCG\nCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGC\nCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCT\nATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAAC\nCTTTTCTCCTACTACCAATTTCG\n>comp0_c0_seq9 len=905 path=[2557:0-888 3446:889-904]\nTATTGGCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGA\nATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGA\nACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGAT\nTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTG\nAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTT\nAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGC\nCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTT\nCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAA\nGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCAC\nGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAAT\nGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATG\nCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCA\nAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGC\nTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCT\nTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCAGTTGCCGCAGC\nGGTTG\n>comp0_c0_seq10 len=367 path=[9054:0-37 8788:38-255 6802:256-366]\nGACACTGCAGCTTTCCTTCCTTGCCACAATCTCCACGAGTCCGGACCTGTTTTGGTTGTG\nGGAGGTTGAGGACTCGTGGAGATTGTGGCAAGGGTTGTCAGATGCGACACTGCAGCTTTC\nCTTCCTTGACTGTGCACTTGAACCATTGCAGAGGAATTTTCTGAAGCCATGATTTTGTGG\nTCTTCATTTGTTGTGTTGGTCTCTGGGTCGGAAGAAGTTCGCGCCGGACTCTGACCACTG\nATGTTTTTGGGTCCGTTTGATACAGCTGTGAAAGACAACTCTTCACTGCGAATTTTTCTA\nGTGAGGTTTTTTTAGTTTCCCAGAAGGCCCACTCCCCGATTGTTGTATCAATTTCGGGGT\nTGACCTT\n>comp1_c0_seq1 len=1997 path=[0:0-1996]\nGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTT\nTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCC\nTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGCTACTGAG\nTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTT\nATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATA\nACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTC\nGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAA\nGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTT\nAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTT\nTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTAT\nCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGT\nTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTA\nAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTT\nCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCA\nCTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAAT\nGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAA\nGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACAAGCATTA\nAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGC\nAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTA\nTATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTG\nAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATA\nCTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACA\nTCATCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTAT\nACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAGCATGTGT\nGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATAATT\nAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATAT\nCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTT\nTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAG\nCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTA\nAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAATCAGAA\nATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGC\nATTGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCCTGGAAA\nAATGGTCACACACAAAAAAGAAGAAATAGATTTATTTTTAAATTTTTGTGTGCGACCATT\nTTTCCAGGGATCCTTTT\n>comp6_c0_seq1 len=1913 path=[0:0-648 674:649-734 760:735-745 771:746-1333 1359:1334-1443 1469:1444-1838 1864:1839-1844 1870:1845-1912]\nGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTC\nTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTG\nCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAG\nACTGATGCAGGCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGC\nCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACAT\nTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCC\nCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGG\nACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTT\nCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCAT\nCACCTCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGAT\nTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTG\nAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAG\nTTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAG\nAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCT\nGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGT\nGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATG\nGTTTGTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTT\nTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACA\nTTATTAGCCTCTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGG\nAAGATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATC\nCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAA\nTATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATG\nATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAAT\nGCCAAGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGT\nGCATGGCCAAATGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGA\nTCAAGGACAGAAGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCC\nTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAAC\nAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATA\nCTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATCAATAC\nAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCT\nACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGAACAGTGCAACTGCATAATTT\nATAACATTCTGGAAAATAATATTGCTGTCGCGTGCCGATTGGCCACCTCCTGA\n>comp6_c0_seq2 len=674 path=[0:0-648 649:649-673]\nGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTC\nTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTG\nCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAG\nACTGATGCAGGCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGC\nCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACAT\nTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCC\nCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGG\nACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTT\nCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCAT\nCACCTCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGAT\nTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTCATCCATCTCA\nATCATTCGGAGACT\n>comp5_c0_seq1 len=1538 path=[0:0-446 447:447-578 621:579-1537]\nAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATTGGGTATGTTGTGTAGCCA\nTTTAATATCAAGAGGAAGAATGTCAACTGCTTCATCTAAAACACGGAAAGACCCAATAAG\nCAGTTTTTCTTAATCTTCCTCAAGCTTTTTTCTTAACCTACTTATCTAATGTTAGTTACG\nAGTATGGAGTTAGTAATATATATAATTTGTGAAACCTAACACACATGACCTGCGGGTTTA\nGTTACAATTAACCATTTCGTATATTGGATTTCTAGTGATAAAATGCTTATTAATATAATA\nAAGCAATTCTATGATGTTGTCTTGGAATCTCTTATTTGAGGGATTCTGAGTCCTGGTTTT\nTGTAAGGGTGTCAACTTGGAAGCTGGCTTACAGTGAGGATTTATCTGTGGTTAAACAAAT\nTATCAAGAAATATGAGTATTTATTTATTATGCTTATATATCTGATTATGAAGGCAGAGAT\nGTCAAGTTAACTATTGAGTCAGCATATATGAGTTAGCCCAATATGAAGTATTCCATCTTA\nGTTAGATAGCAAGAGAGCTATTGAATTCAAGAATTAAACTTTGCATTCGTGTCGAGGACC\nCTTGTGTAAATGCTTTCAGTGTGGACTCATGAAGGAGGGAAAATTTCGCCGGCCCAGGCT\nTCTTGCGGTTCATTGCCGATTTGTCGGGTTCTTGGAGCTCCACCAGAAAACCCATGTTAG\nTTCGAGTTATGATGATTGTATGATTTTGAGTTCCAATTTCAATACTGCTCAATAATCCAT\nTGTAGTTCACGACATGTAGAGCATCCAATTTGTTAATAAACTTGAGAATATTGGATCGAA\nTCAACGACAGCATTTTTAGGCTCAATTGTTCCTTGACACGTTGTGTTCGCATGTTGAAAT\nGGTTAGTGTTGGTTGTTAGCAGCCAATCAGAGATCAGACCAAGGGCTCCTGCTAAGGGTT\nCAATCAAAGACTGGTCAATTAACTGGTCCTGTATCCCTGCTGCAAGGATGACTCTCAGTG\nCCCACAGCGGTGATTCAATAGTGGAATTCGGATTTTGAAATAAATGGGGAAATAGGTTCC\nTTGTCATTGACCATGCAGGGGCAAAGTCATTAGTTTTCAGTCTATGCAATAGGGCCATTC\nCTTTGTGAGTCACATCAAACTCAATACCAGCCCAATAAACTTTCCACCCTTGAATAGTTT\nGACTAACTAAGAAGTTACAGAGGTCGCTTAAGACAACCCCTTTCTCCAGGTCCTTTTTGG\nGCGATATTAGATTGTATCGTCCCGTAGCTTTGGCCATGGTTTTTTCTCAGGTCTTGCTTG\nGTGTCTGGAGTATCGATATTTTGTTGTCTAGACACTCTCAGTTCAACCTTGTAACCTTGC\nGCTCGATTGTTGGAACGACGCTCTTATTTTTTAATTGTGAGGGTGCTCAAAGTAATGTTC\nGTTGTAGGTGGGCTTCTTTTCAGCCAATGGAGTTGACCTGGTGGAGTTAGCCCAGATTTA\nTGCACTAAATTTTAAATGGCTAAGTTCAATTAGATATT\n>comp5_c0_seq2 len=1133 path=[447:0-131 579:132-173 621:174-1132]\nTATGCTTATATATCTGATTATGAAGGCAGAGATGTCAAGTTAACTATTGAGTCAGCATAT\nATGAGTTAGCCCAATATGAAGTATTCCATCTTAGTTAGATAGCAAGAGAGCTATTGAATT\nCAAGAATTAAACTTTGCATTCGTGTCGAGGACCCATGAGTCCACACTGAAAGCATTTGCA\nTTCGTGTCGAGGACCCTTGTGTAAATGCTTTCAGTGTGGACTCATGAAGGAGGGAAAATT\nTCGCCGGCCCAGGCTTCTTGCGGTTCATTGCCGATTTGTCGGGTTCTTGGAGCTCCACCA\nGAAAACCCATGTTAGTTCGAGTTATGATGATTGTATGATTTTGAGTTCCAATTTCAATAC\nTGCTCAATAATCCATTGTAGTTCACGACATGTAGAGCATCCAATTTGTTAATAAACTTGA\nGAATATTGGATCGAATCAACGACAGCATTTTTAGGCTCAATTGTTCCTTGACACGTTGTG\nTTCGCATGTTGAAATGGTTAGTGTTGGTTGTTAGCAGCCAATCAGAGATCAGACCAAGGG\nCTCCTGCTAAGGGTTCAATCAAAGACTGGTCAATTAACTGGTCCTGTATCCCTGCTGCAA\nGGATGACTCTCAGTGCCCACAGCGGTGATTCAATAGTGGAATTCGGATTTTGAAATAAAT\nGGGGAAATAGGTTCCTTGTCATTGACCATGCAGGGGCAAAGTCATTAGTTTTCAGTCTAT\nGCAATAGGGCCATTCCTTTGTGAGTCACATCAAACTCAATACCAGCCCAATAAACTTTCC\nACCCTTGAATAGTTTGACTAACTAAGAAGTTACAGAGGTCGCTTAAGACAACCCCTTTCT\nCCAGGTCCTTTTTGGGCGATATTAGATTGTATCGTCCCGTAGCTTTGGCCATGGTTTTTT\nCTCAGGTCTTGCTTGGTGTCTGGAGTATCGATATTTTGTTGTCTAGACACTCTCAGTTCA\nACCTTGTAACCTTGCGCTCGATTGTTGGAACGACGCTCTTATTTTTTAATTGTGAGGGTG\nCTCAAAGTAATGTTCGTTGTAGGTGGGCTTCTTTTCAGCCAATGGAGTTGACCTGGTGGA\nGTTAGCCCAGATTTATGCACTAAATTTTAAATGGCTAAGTTCAATTAGATATT\n>comp5_c0_seq3 len=1121 path=[1582:0-29 447:30-161 621:162-1120]\nGAATTAAACTTTGCATTGGGCTAACTCATATATGCTTATATATCTGATTATGAAGGCAGA\nGATGTCAAGTTAACTATTGAGTCAGCATATATGAGTTAGCCCAATATGAAGTATTCCATC\nTTAGTTAGATAGCAAGAGAGCTATTGAATTCAAGAATTAAACTTTGCATTCGTGTCGAGG\nACCCTTGTGTAAATGCTTTCAGTGTGGACTCATGAAGGAGGGAAAATTTCGCCGGCCCAG\nGCTTCTTGCGGTTCATTGCCGATTTGTCGGGTTCTTGGAGCTCCACCAGAAAACCCATGT\nTAGTTCGAGTTATGATGATTGTATGATTTTGAGTTCCAATTTCAATACTGCTCAATAATC\nCATTGTAGTTCACGACATGTAGAGCATCCAATTTGTTAATAAACTTGAGAATATTGGATC\nGAATCAACGACAGCATTTTTAGGCTCAATTGTTCCTTGACACGTTGTGTTCGCATGTTGA\nAATGGTTAGTGTTGGTTGTTAGCAGCCAATCAGAGATCAGACCAAGGGCTCCTGCTAAGG\nGTTCAATCAAAGACTGGTCAATTAACTGGTCCTGTATCCCTGCTGCAAGGATGACTCTCA\nGTGCCCACAGCGGTGATTCAATAGTGGAATTCGGATTTTGAAATAAATGGGGAAATAGGT\nTCCTTGTCATTGACCATGCAGGGGCAAAGTCATTAGTTTTCAGTCTATGCAATAGGGCCA\nTTCCTTTGTGAGTCACATCAAACTCAATACCAGCCCAATAAACTTTCCACCCTTGAATAG\nTTTGACTAACTAAGAAGTTACAGAGGTCGCTTAAGACAACCCCTTTCTCCAGGTCCTTTT\nTGGGCGATATTAGATTGTATCGTCCCGTAGCTTTGGCCATGGTTTTTTCTCAGGTCTTGC\nTTGGTGTCTGGAGTATCGATATTTTGTTGTCTAGACACTCTCAGTTCAACCTTGTAACCT\nTGCGCTCGATTGTTGGAACGACGCTCTTATTTTTTAATTGTGAGGGTGCTCAAAGTAATG\nTTCGTTGTAGGTGGGCTTCTTTTCAGCCAATGGAGTTGACCTGGTGGAGTTAGCCCAGAT\nTTATGCACTAAATTTTAAATGGCTAAGTTCAATTAGATATT\n>comp2_c0_seq1 len=1338 path=[0:0-1337]\nGGATTTGCTAAGCGCGAGTCCTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACC\nCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCCAA\nAATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAAC\nCATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATT\nCTCAAAATCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCA\nAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAG\nTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGC\nATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTT\nAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTC\nATGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTT\nGATCACAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAAC\nTTATTCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAAT\nATATAAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGC\nTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATG\nTTTGACTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTT\nACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAA\nGTTGTGGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTA\nAAAATATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAA\nGATTAATGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCA\nTTCTTCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTT\nTAGCTGTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTC\nTGTACACATCTCATACATTGTATTAGGGGCAATAATGGCTAAGTTCAATTAGATATTATT\nGCCCCTAATACAATGTAT\n>comp7_c0_seq1 len=727 path=[0:0-650 676:651-726]\nAGGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAAT\nCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACT\nGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCA\nATTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAG\nTTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTC\nAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCT\nTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTA\nACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGAT\nTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTA\nCCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTC\nAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATA\nATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAG\nGTTGAGG\n>comp7_c0_seq2 len=676 path=[0:0-650 651:651-675]\nAGGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAAT\nCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACT\nGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCA\nATTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAG\nTTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTC\nAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCT\nTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTA\nACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGAT\nTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTA\nCCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTC\nAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATCCATAGCAG\nCATGGAAGATCCTGTC\n>comp3_c0_seq1 len=1407 path=[0:0-901 902:902-905 909:906-1406]\nGTCTAGTCCTACCTTTCTTTACATGATCTCAATTGCCGTAAGTACTTTGATATCTCATCT\nTGGGTTTGTGACTCATTGGATGACGTTAATTGGCGTGTCCCTTGAGATAATGTAAAGAAA\nGGTAGGACTAGACGATGTGAGATTATTTGATGACCTTCCCTCTTGGATGCTGAGTTATGA\nTCCTGAGATTTCACATTGTGTCTCGATCTATCGAAATTTAGTTTTGGGTTTGCTGTACCG\nCAAGCAGAGTCACTTAGAAATGACTGGAACGACGGACCCTGGTGCGTGTTCTCTTGTGGA\nATTGTCGTTCTTTTTATTTCATGGCTCATTTGCAGGACTAGACTCCGTTCAGTGCCATCA\nTGTGGATCTCTGGTGGTTTGTTCTTGACTTCTCTTAATATGACCATCACTGTTGTTTGTG\nCTTGATCCAGTTGAAGAGTTTCTTGTCAAGTCTTTTCGGTTGCTGTTTCTGTGCCTGCTC\nCTCCAGTACGCCAATGACGCATGGAAGAAATTGCTGGCTGTACTCTTACATGTGTAAACA\nAGATTGTCGTGAGGATGTACATGATCATTTATGGTAGTTTTAAAAGCCTGGTGTCTTGAT\nGAATCATGCACCAGCAGTTCTACGATCTGATGGAGGAAATTATTAACAGGTGTTGGATTT\nTGACCCTCTAATGGATATACTATCCATAAAGGGACAATTGTTCCGCGATTAATTATCCAT\nTCCTTTACAAATGTAAGAAAAGATGAAATGGACGTTCTCAAAAATAACCTGGCCGCATCT\nGAGAGTCCTCTGTCACCTGCAGCACCGCCTATGTAAATAGAAAAATGGGGATCAATACTC\nATTAATCGTGACATAACGCTTGCATGTTTGAATGTTGGCTTAAGTATTCGCAATGAGCGA\nTGTGGTAGATTATGAATTTGGGTAGTTAAGTAATATAAAAAATTGTCAAGTGTTAATTTC\nTTAGTCCGAAGAATTGTATTGCCAAGATAATAACTTACAAAGGCCCCAAAACTGTACAGA\nAGTCCTATTTTGGGATAAGTTAAGAAATGGGTAGTGAATGATCTTGTTTCTCCACTGCTA\nATTGGGTCTGTAGACGAATTATTGCTATCTGAAATAATTGATTGCATGATGGTCTTAGCT\nAGCTCCCATCCAGATAAGTGAGGCAGTCGAATAAGGTCATCTTCTATAATGTTCAGCTGT\nTTGCCTTGGAAAAATGGGTTATCAAATGAGATATTGCAATTGAGTCCTCCTTTTAGAGGA\nTTATTGTCATAAATCAATTCATTTTCTCGGTATCTTGTTAAATCTAAATCCAATGTAGAT\nGTGTATGTTAAGTACTGAGCTGGTACCTCCCGGGTGCAACACTTAGTTAGATGAAGGTGA\nGCACGATTATACTGGATATCTGTAGCC\n>comp3_c0_seq2 len=527 path=[1437:0-21 902:22-25 909:26-526]\nACATTCAAACATGCAAGCGTTATGGTAGATTATGAATTTGGGTAGTTAAGTAATATAAAA\nAATTGTCAAGTGTTAATTTCTTAGTCCGAAGAATTGTATTGCCAAGATAATAACTTACAA\nAGGCCCCAAAACTGTACAGAAGTCCTATTTTGGGATAAGTTAAGAAATGGGTAGTGAATG\nATCTTGTTTCTCCACTGCTAATTGGGTCTGTAGACGAATTATTGCTATCTGAAATAATTG\nATTGCATGATGGTCTTAGCTAGCTCCCATCCAGATAAGTGAGGCAGTCGAATAAGGTCAT\nCTTCTATAATGTTCAGCTGTTTGCCTTGGAAAAATGGGTTATCAAATGAGATATTGCAAT\nTGAGTCCTCCTTTTAGAGGATTATTGTCATAAATCAATTCATTTTCTCGGTATCTTGTTA\nAATCTAAATCCAATGTAGATGTGTATGTTAAGTACTGAGCTGGTACCTCCCGGGTGCAAC\nACTTAGTTAGATGAAGGTGAGCACGATTATACTGGATATCTGTAGCC\n>comp4_c0_seq1 len=1214 path=[0:0-1213]\nGAGGCCCTTCAGGGGGGTTGTTTCGATTTTCCAGTGTGAGGTTATGCGGTGGATTATAAT\nAATCACTGACATGCATATAACACTGTGGGATTGTATAATGCATCCAATTAAAAACATTCT\nTAACACCATAGCAACGGTTGCAATATTCTATAAAAGGTGCTGTAAACTCATACCTAAATG\nCAAGATTGTATTTCTCTAAATCAGTTACAAAGCTACTCCCTCTAACTGTGGCATGCTCAC\nCGAAATCATCACTTGTGTGGTGCCATGATGCTTGATGCAATAAGCTTTCTTTTTGTTCAC\nGTTCCGTAACTACCATCATATTGCTAGGAAATGCTTTAGCAAGACCATCAGCTAACAGAG\nCTTCACAAAGTGTTTGAACATTGCGAGTCGGATAAGGCAATTTTCCGAAAGTTCTACCTA\nCATTCAACTCTTTCTCTTTCAATGAGAAAGAAAAATTCCGATATTGTGGTAGTAGATACT\nCGAGTTTTTGCGCGTAGGAAAGAACATTCTCAATAGAAAAGTTTTCTTGCTCTAAAAATT\nGTTCCGGTACACGTTTGGTACTGAATTTGTGAGGTGGATTATATCCCAGAACATTAGGCT\nCGAATACTGCATCCCAGCATGTCCTTTCTACTGCAGTAGCTCTGTCTTTTATAAAAATAC\nTTAAGTCACTAATAATTTTGGTTGAGAAAAGTGGAGGATGGTCAAGGTGGTAAAATTCCC\nATAGCAGTTCTTTAATCATTGGCAACGGAGGGAATTGATTTCTTTTGATATAAGAATTAA\nGACCTGGTGTTAGATTTCTATCTGAGGTAACACTGTACCAAGATCCTTGACTATCAAAAT\nAATGTTTTGCAATGCTATATTTAAAAACACAATATGTCTCGAAAATCACGATAGGGCGTA\nATGCTTTTAGCACCGTAGCATGTTTTTTAACTTTTTGGATTGCTGTTTCACTATGTAGCA\nCAGGATGCCCCCAGTGTTTTTGTATGGAAAATAGCTCACAAAGTTGTTGTGGCGTCATCT\nCCAGCCTTATCAATGTTCTATGGAATTCACGGATCTTGTGAGCCTGTGAAGGCTTTAGTG\nCACGTATTTCTGTAATTTCTTCCAGGGTGTGATTTACAGCTAAATGCATTTGTGTTAAGA\nATCGGCCCTTCCTCTCGGTGTACTTTGAGCACCATTGTGCTTGGCTAAAATTCAATTGTG\nCTCAAAGTACACCG\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.ebov.fasta", "content": ">comp5_c0_seq1 len=910 path=[0:0-909]\nGTGTCGGAGGCTGTGCTGTCGTTGTCTGCTCTACGGTGATGTTGTCCAACTTGAGTTGCC\nTCAGAGATGTCAAGTTTATACACGGGTGTATTATGGGTGCTGTTGTCCGGACCTGTTTTG\nGTTGTGGGAGGTTGAGGACTCGTGGAGATTGTGGCAAGGGTTGTCAGATGCGACACTGCA\nGCTTTCCTTCCTTGACTGTGCACTTGAACCATTGCAGAGGAATTTTCTGAAGCCATGATT\nTTGTGGTCTTCATTTGTTGTGTTGGTCTCTGGGTCGGAAGAAGTTCGCGCCGGACTCTGA\nCCACTGATGTTTTTGGGTCCGTTTGATACAGCTGTGAAAGACAACTCTTCACTGCGAATT\nTTTCTAGTGAGGTTTTTTTAGTTTCCCAGAAGGCCCACTCCCCGATTGTTGTATCAATTT\nCGGGGTTGACCTTCCAAATTAGTTTTCCCGTGGTGTTGCTCCTCTTCCCACTTGCATATA\nTTGTCTCATTCAGCTGGAGCAGAAACTGTGGTGTGAATCTTGATTCAAGTTGGACGTAGG\nTCAAATTGTCAACCTCGAACAAGTACTCTGTCTCATTAGTTCCAAAACCGGTAGCCTGAT\nATCTAATTGTGGTAGAATAATAGCCACTCGACGGGTCCTCCGTTGCATTGACCGGCTCTC\nTCAAGGGGTGTGAGCTGAAGAAGTCCTTCTTAGCTTGGGGCAGTATCAGAAATGCAACGA\nCACCTTCAGCGAAAGTCGTTCCTCGGTAGATAACTGTGGAAGCAAGTCGATCATACAGGA\nAGAAAGCACCCTCTTTGTGGAAGGCAAAGTCTCCGGCACATGGTCCCGTTCCTGATACTT\nTGTGCACATACCGGCACCGGGGGAAGCCCCGAATCCCGTCTGGCGCTGCTGGTAGACACT\nCACTCCCGTC\n>comp4_c0_seq1 len=2720 path=[0:0-311 312:312-745 746:746-764 765:765-876 2752:877-1615 1616:1616-2719]\nCTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAG\nATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCC\nAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTG\nATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATG\nGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAA\nAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGC\nCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCA\nTGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAA\nCAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGT\nTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTA\nATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGC\nGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACAT\nTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATC\nCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGC\nTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAG\nAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGA\nAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCA\nTCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGAC\nCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTT\nGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAAT\nGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCT\nGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCT\nGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTAT\nGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTT\nAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAA\nCCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGA\nACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTG\nGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCC\nCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCAC\nATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCA\nTCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTT\nGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCT\nTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAG\nATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAA\nAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAAC\nCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCA\nTTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTG\nCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATT\nGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACT\nCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCA\nGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAA\nGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTAC\nAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGC\nAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCC\nCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTC\nCAACTACCCCAGTATTTCAC\n>comp3_c0_seq1 len=1410 path=[0:0-905 906:906-1409]\nCTCCCGTCAGGTTTTTTGATTTCAAGATTGTAGCAGTTTTCAGCCCATTCACCAGCTTCA\nTAATTGACCACCTTTGGTGGGACACCGGACCTGAAGCCCCATCTTTTAGTCACAGATGGC\nACGTCAGTTGCCACTCCATTCCCCTCGAGATTCAGTCCAACTGATCTCAATTGATTTGTG\nGATGACAGTTTGTCACGACAAACTAGTTTGTCGACATCACTAACCTGTAATGTACTATTG\nTGGATAACTCCAAGCGGGATGGAAAATGTTCTTTGGAAAAGGATAATTACCCAAAGAAAG\nAATGATGTCCTCTTGAATCGATCACGAGGTAACTGCAATATTCCTGTAACACCCATTGTG\nTTGTCGCCTCACAATATCCTTCTAGTGAAGCTTATTTTGGTTATCCAATTGAAAAGGACC\nTGATGACCCCTACTCTGGAAGACAAATAATCTAAGAGAGATGAAGATTACGCTCACTGTC\nGGCTTAATCTTCATCGCCGATTTTTTCTTAATTAGAAGAGCAATGTCTGTACTTAGATTG\nTGAACAACTTAGAAATGGGCCCCGATTTTTCCTCCACATCTCCAATCCAAGTCACACTGG\nCTGTCCTCAGATGTAAGCATGTAGGCAATTTGAGGATAAGGACAAAGAGTATGTGCAATG\nAGAAAGATTGACATTTGAATCACCGTATTGATTATAGTAGGATTGTTTGTAATGTTATTA\nGTCATGATCTTTCATCAATCAATCTTTTAAAAACAGGTATATTATGAGTCTTTTGTTAAG\nCTCTACATTTAGGAGAGAAAAGAGACAATGGTGTAAAGCACCTTTAGTATATTGATCAAT\nTAGAAGTATCTCTTCTAGTAGACGGATTATTAAAAAGATGTTATCACTATCCCTGAGAAG\nATTCTGTAAAACTGGATCTGAGTCAATTATTGCAATTACTTCTCAACCACAGCTGGAAGA\nCTTGCAGGAGAATGACACGTGTCACAATCCTGTGTGATTACCATGGTGAGGTCTCCTGGA\nGCCACCGGGTCCAACCCAATGTACTTTGGCAAAAGAACAGGGATGATTGGTTGTCCATTT\nTTGGAAGTCACCTTCTTACCGGTCAGCTTGTGGACCAGAGTTTCTGGCACTTCGATACCC\nATGATATTTTTGGTTGGATCAATTGGAACGATCTTAAAGTCCTGGAGTGAAGTCATTATT\nGCTTGGATTTTCTCCGGAGATGTTAGATCGGCACTGTTCCCCTTCTTCCCACTTTTGTTG\nGGTAAAAGAATGGGGCGAAGTTTTGGATGAAATGAAATTCCTGGACGCAACGCTCCATTT\nGATCCAGTTGGAGTGTCATCGGTCCATGTTGCAGCAGGCAGTGGTTGAGTGATCAGTTTG\nAGTGCTGTCAAATCAAAGGTGAAATACTGG\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.hhv3.fasta", "content": ">comp5_c0_seq1 len=5290 path=[0:0-3277 3278:3278-3376 3390:3377-4571 4585:4572-5289]\nGAAAATGTTTATGATATATACGTACTCGTTACGTATATATCATAAACATTTTCAGGGCCG\nCATTCATTCACTTTGGTCATGTCAGGCCACACTCCAACCTACGCTTCTCATAGGCGTAAC\nCGTGTCAAACTAGTTGAGGCGCATAACCGCGCGGGGTTATTTAAAGAACGGACCCTCGAT\nCTAATCCGTGGGGGTGCGAGTGTACAAGATCCAGCATTTGTGTATGCCTTTACTGCTGCC\nAAAGAGGCCTGCGCCGATTTAAATAACCAGCTCCGCTCTGCAGCTCGCATAGCTTCAGTT\nGAACAGAAGATTCGTGATATACAATCCAAGGTTGAGGAACAAACAAGTATTCAACAGATT\nTTAAATACAAACAGACGCTATATAGCACCCGATTTTATTCGCGGTTTGGATAAAACAGAA\nGACGATAATACCGATAATATAGACAGACTGGAAGACGCGGTAGGACCGAACATCGAACAC\nGAAAATCATACTTGGTTTGGAGAAGACGACGAAGCGTTACTTACACAATGGATGCTGACG\nACACACCCCCCAACCTCCAAATATCTCCAACTGCAGGACCTTTGCGTTCCCACCACAATA\nCCGACGGACATGAACCAAATGCAACCACAGCCGATCAGCAAGAACGAGAATCCACCAACC\nCCACACACGGATGTGTAAATCATCCATGGGCCAATCCGTCAACTGCAACATGCATGGAAT\nCACCAGAACGATCACAACAGACAAGCTTATTTTTATTAAAGCACGGCTTAACGAGAGATC\nCAATACATCAACGCGAAAGGGTGGACGTTTTTCCACAATTTAACAAACCCCCATGGGTTT\nTTAGAATTTCCAAATTATCCCGTTTAATTGTACCCATCTTCACGCTCAATGAACAGTTAT\nGTTTTTCTAAATTACAGATTCGAGATAGACCCAGGTTTGCGGGACGGGGAACGTATGGGC\nGTGTTCATATATACCCATCGTCAAAAATAGCTGTAAAAACCATGGACAGTCGTGTTTTTA\nATAGAGAGTTAATTAACGCGATTTTAGCGAGTGAGGGTTCTATACGAGCAGGGGAAAGGC\nTAGGTATTTCTAGCATAGTTTGCCTTTTAGGTTTTTCGTTACAAACCAAACAGCTACTGT\nTTCCGGCATACGACATGGATATGGATGAATACATTGTTCGCCTGTCCAGACGGTTGACAA\nTACCTGATCACATAGACAGAAAAATTGCCCATGTATTTTTAGATTTGGCTCAAGCGTTGA\nCGTTTTTAAATCGAACGTGCGGCCTGACCCACCTAGATGTGAAATGTGGCAATATTTTTC\nTTAACGTCGACAACTTTGCCTCGTTGGAAATAACCACAGCAGTAATCGGAGACTATAGCC\nTAGTAACATTAAATACGTATTCCCTTTGTACTCGAGCGATATTTGAAGTTGGAAATCCAT\nCCCACCCGGAGCACGTACTACGCGTACCCCGGGATGCATCGCAGATGTCATTTCGTTTGG\nTGTTGAGTCATGGAACAAACCAACCCCCTGAAATCTTGCTTGATTATATTAATGGAACGG\nGCCTTACTAAATATACTGGAACCTTGCCCCAAAGAGTTGGACTTGCGATTGATCTTTATG\nCATTGGGCCAAGCACTCTTAGAAGTTATCCTGCTAGGACGTCTTCCCGGACAACTGCCCA\nTTTCAGTACATCGGACCCCGCATTATCACTACTACGGTCATAAGTTATCACCAGATTTGG\nCGCTTGATACGCTGGCATATCGATGTGTCCTGGCGCCATATATACTCCCATCTGACATCC\nCCGGGGACTTAAATTATAATCCCTTTATACACGCCGGAGAGCTGAACACCCGTATTTCCC\nGGAATTCTTTACGCCGGATATTCCAGTGTCACGCAGTGCGTTACGGCGTAACGCACTCAA\nAGCTTTTCGAAGGCATACGCATTCCGGCCTCATTATACCCAGCCACTGTTGTTACGTCGT\nTGTTGTGTCACGATAATTCAGAAATACGCTCGGATCACCCTTTATTATGGCACGATCGGG\nATTGGATAGGATCGACATAAGCCCCCAGCCAGCCAAAAAAATTGCCCGTGTGGGAGGTCT\nACAGCACCCTTTTGTAAAAACGGATATTAACACGATTAACGTTGAACACCATTTTATAGA\nCACGCTACAGAAGACATCACCGAACATGGACTGTCGCGGGATGACAGCGGGTATTTTTAT\nTCGTTTATCCCACATGTATAAAATTCTAACAACTCTGGAGTCTCCAAATGATGTAACCTA\nCACAACACCCGGTTCTACCAACGCACTGTTCTTTAAGACGTCCACACAGCCTCAGGAGCC\nGCATCCGGAAGAGTTAGCATCCAAATTAACCCAAGACGACATTAAACGTATTCTATTAAC\nGATAGAATCGGAGACTCGTGGTCAGGGCGACAATGCCATTTGGACACTACTCAGACGAAA\nTTTAATCACCGCATCAACTCTTAAATGGAGTGTATCTGGACCCGTCATTCCACCTCAGTG\nGTTTTACCACCATAACACTACAGACACATACGGTGATGCGGCGGCAATGGCGTTTGGAAA\nAACCAACGAACCGGCGGCACGAGCGATAGTTGAAGCATTGTTTATAGATCCGGCTGATAT\nCCGTACTCCTGATCATTTAACGCCAGAAGCTACAACTAAGTTTTTTAATTTTGACATGCT\nCAATACCAAATCTCCAAGTCTCCTTGTGGGTACACCAAGAATCGGAACGTATGAATGTGG\nACTTTTAATCGACGTTCGAACGGGACTTATAGGCGCGTCGTTGGACGTTCTTGTATGTGA\nCAGGGACCCTTTAACTGGCACCCTAAATCCCCACCCTGCAGAAACCGACATTTCATTTTT\nTGAAATTAAATGTCGTGCTAAATACCTCTTTGATCCAGATGACAAAAATAACCCGCTCGG\nTCGGACGTACACCACGTTAATAAATAGACCTACAATGGCAAATCTACGGGACTTTTTATA\nTACTATAAAAAACCCATGTGTAAGCTTCTTTGGACCCTCAGCAAACCCAAGTACACGCGA\nGGCCTTAATAACGGATCACGTTGAATGGAAACGTTTAGGATTTAAAGGTGGGAGGGCCCT\nTACAGAACTCGACGCCCATCATTTGGGCCTCAATCGGACAATCTCATCCCGAGTGTGGGT\nATTTAATGATCCGGACATACAAAAGGGGACAATTACAACCATTGCATGGGCCACTGGAGA\nTACGGCTCTTCAAATTCCTGTATTTGCCAATCCGCGGCACGCTAACTTTAAACAAATTGC\nCGTACAAACCTATGTATTATCCGGTTACTTTCCAGCGCTAAAACTACGGCCCTTCCTTGT\nCACCTTTATAGGACGTGTGCGCCGACCACACGAGGTGGGAGTCCCATTGCGCGTCGATAC\nACAAGCGGCTGCCATTTACGAATATAACTGGCCGACTATCCCACCCCACTGTGCGGTTCC\nGGTTATAGCCGTTCTAACGCCTATCGAAGTTGATGTGCCTAGAGTGACACAAATACTTAA\nAGACACAGGAAACAACGCGATTACATCAGCATTGCGGTCATTGCGATGGGACAATCTTCA\nTCCAGCGGTCGAGGAGGAATCTGTGGATTGTGCAAACGGTACAACGAGCTTGTTACGTGC\nAACGGAGAAACCGTTGCTTTGAACTCAGAGTTCTTTGAAGACTTTGACTTTGATGAGAAT\nGTAACAGAGGACGCCGATAAATCCACACAACGCCGCCCACGAGTGATCGATGTAACACCA\nAAACGAAAACCTTCGGGAAAGAGCTCCCATTCCAAATGCGCAAAATGTTAAACCCTGATA\nAACCCTGATAAACGTTCTAATAAAAACATCAAATCATGGTTGGTTACTGTGAATGTTTGT\nTTTATTGCTTGGGGGTTTACAAGTACAACCCACGCTACTCCCACCCACTGTTTGATCGCT\nCGTATAACAGCTCATCCTCACGGTCCGTTTCATATGTTGAGTCATTTTCATAGACGTAGC\nCGTAGCCTTGTGATGGGTAATTTGTGCGGCGAGAATTTCTATGTGCAGGTTTTACTTTTC\nGTATGTATCCCCGTACCCGCTCGGGTACTCTTCTTACGGCACCGTAGAACCGACTGCGTT\nTCTGTCGATGATACACATATGCACGCATCAATCTGAGAAGCAACATGACAACGGAAAACA\nCGGCCAGGCAAGCCAAGGTTCCCCGAGTTGTGGGAATTAACCGTGGAGATTGAACCGATA\nTAGGGTCATATAATCGGTCCATATACGAGTGCGCGGCGGTTCCCAACGTAGCACAGGCCA\nCGAGCGTTCCCAGGGACGGTCCTATTAACACGTGTATATAATGCGCCAAAATTAATTCTG\nATACTATAAGATATACAACTGACAATGTACTAAATGTAGACATGGCCACGGACACCGATG\nACCACAGTCCCGTATGTAGATGATTCGCCACCACAAGTTCCAGCATTAATGATACAAATA\nGGATACATATCGCCATCAACGCAGCCATCAAATTCACGAACACTGCGCGCGTAGGCCCCG\nCAAGGCGATATAAAAAGACGCTCTGCTGTCGTAAATTTGCGACCGCTTTTATGTTCGTTT\nCGTCCAATTTTCCGCGTCCACAAAAATACGTTGTAAATATTACACTTGTCGCAAAATGTC\nCAAGATATAATGTAGCAGCCACGCCGATTTGCTTGTAAGCTAATAATAACACAACGGCGT\nTTAATAACCACAATGACAAAAGACCCCAAAAAAGTGTTGTGGGATCTACAACTAACCATG\nCAACACCGGAGCTTTGCCGGACACGTTGATTTTTCGTTTCTCGGTGTATAATCGCGGCCG\nTGATCAGTGTATATACCGCCATGGCCATTGCCGTTAAAGCCGTGTAGTAAGTAAATGCCA\nCAACGCTATGTGGTTCCAAAAACAAAACCGGGGCGCTGTATCCACCTCTATTTCCGGACC\nATACCCCCCCATCTAGGGTGGCGTTAAATAACTCATAATCAACTACGGCAGCATAAAAAC\nAAGGGATCCCGGTATATTCAGAAGAGGCGGCAATTAACGTAGCCAGGAGCATTACCGCAC\nCCAAAGTGAACATCATCACCTGAATTATCCAAATTCGCCAATTAAGCGTATCCATTTGAT\nGATCTAACGCTTCCACCTCGGGTGTCGTGGTGTCGTACGGTGAGACTTTTTCAGAACGCG\nGCCCCTTCTTTTGAGTTCCCATGTCTCCCAACACCGGGGAGAGCAACGCCGCCGTCTATG\nCGTCCAGTAC\n>comp5_c0_seq2 len=4596 path=[0:0-3277 3278:3278-3376 3390:3377-4571 5303:4572-4595]\nGAAAATGTTTATGATATATACGTACTCGTTACGTATATATCATAAACATTTTCAGGGCCG\nCATTCATTCACTTTGGTCATGTCAGGCCACACTCCAACCTACGCTTCTCATAGGCGTAAC\nCGTGTCAAACTAGTTGAGGCGCATAACCGCGCGGGGTTATTTAAAGAACGGACCCTCGAT\nCTAATCCGTGGGGGTGCGAGTGTACAAGATCCAGCATTTGTGTATGCCTTTACTGCTGCC\nAAAGAGGCCTGCGCCGATTTAAATAACCAGCTCCGCTCTGCAGCTCGCATAGCTTCAGTT\nGAACAGAAGATTCGTGATATACAATCCAAGGTTGAGGAACAAACAAGTATTCAACAGATT\nTTAAATACAAACAGACGCTATATAGCACCCGATTTTATTCGCGGTTTGGATAAAACAGAA\nGACGATAATACCGATAATATAGACAGACTGGAAGACGCGGTAGGACCGAACATCGAACAC\nGAAAATCATACTTGGTTTGGAGAAGACGACGAAGCGTTACTTACACAATGGATGCTGACG\nACACACCCCCCAACCTCCAAATATCTCCAACTGCAGGACCTTTGCGTTCCCACCACAATA\nCCGACGGACATGAACCAAATGCAACCACAGCCGATCAGCAAGAACGAGAATCCACCAACC\nCCACACACGGATGTGTAAATCATCCATGGGCCAATCCGTCAACTGCAACATGCATGGAAT\nCACCAGAACGATCACAACAGACAAGCTTATTTTTATTAAAGCACGGCTTAACGAGAGATC\nCAATACATCAACGCGAAAGGGTGGACGTTTTTCCACAATTTAACAAACCCCCATGGGTTT\nTTAGAATTTCCAAATTATCCCGTTTAATTGTACCCATCTTCACGCTCAATGAACAGTTAT\nGTTTTTCTAAATTACAGATTCGAGATAGACCCAGGTTTGCGGGACGGGGAACGTATGGGC\nGTGTTCATATATACCCATCGTCAAAAATAGCTGTAAAAACCATGGACAGTCGTGTTTTTA\nATAGAGAGTTAATTAACGCGATTTTAGCGAGTGAGGGTTCTATACGAGCAGGGGAAAGGC\nTAGGTATTTCTAGCATAGTTTGCCTTTTAGGTTTTTCGTTACAAACCAAACAGCTACTGT\nTTCCGGCATACGACATGGATATGGATGAATACATTGTTCGCCTGTCCAGACGGTTGACAA\nTACCTGATCACATAGACAGAAAAATTGCCCATGTATTTTTAGATTTGGCTCAAGCGTTGA\nCGTTTTTAAATCGAACGTGCGGCCTGACCCACCTAGATGTGAAATGTGGCAATATTTTTC\nTTAACGTCGACAACTTTGCCTCGTTGGAAATAACCACAGCAGTAATCGGAGACTATAGCC\nTAGTAACATTAAATACGTATTCCCTTTGTACTCGAGCGATATTTGAAGTTGGAAATCCAT\nCCCACCCGGAGCACGTACTACGCGTACCCCGGGATGCATCGCAGATGTCATTTCGTTTGG\nTGTTGAGTCATGGAACAAACCAACCCCCTGAAATCTTGCTTGATTATATTAATGGAACGG\nGCCTTACTAAATATACTGGAACCTTGCCCCAAAGAGTTGGACTTGCGATTGATCTTTATG\nCATTGGGCCAAGCACTCTTAGAAGTTATCCTGCTAGGACGTCTTCCCGGACAACTGCCCA\nTTTCAGTACATCGGACCCCGCATTATCACTACTACGGTCATAAGTTATCACCAGATTTGG\nCGCTTGATACGCTGGCATATCGATGTGTCCTGGCGCCATATATACTCCCATCTGACATCC\nCCGGGGACTTAAATTATAATCCCTTTATACACGCCGGAGAGCTGAACACCCGTATTTCCC\nGGAATTCTTTACGCCGGATATTCCAGTGTCACGCAGTGCGTTACGGCGTAACGCACTCAA\nAGCTTTTCGAAGGCATACGCATTCCGGCCTCATTATACCCAGCCACTGTTGTTACGTCGT\nTGTTGTGTCACGATAATTCAGAAATACGCTCGGATCACCCTTTATTATGGCACGATCGGG\nATTGGATAGGATCGACATAAGCCCCCAGCCAGCCAAAAAAATTGCCCGTGTGGGAGGTCT\nACAGCACCCTTTTGTAAAAACGGATATTAACACGATTAACGTTGAACACCATTTTATAGA\nCACGCTACAGAAGACATCACCGAACATGGACTGTCGCGGGATGACAGCGGGTATTTTTAT\nTCGTTTATCCCACATGTATAAAATTCTAACAACTCTGGAGTCTCCAAATGATGTAACCTA\nCACAACACCCGGTTCTACCAACGCACTGTTCTTTAAGACGTCCACACAGCCTCAGGAGCC\nGCATCCGGAAGAGTTAGCATCCAAATTAACCCAAGACGACATTAAACGTATTCTATTAAC\nGATAGAATCGGAGACTCGTGGTCAGGGCGACAATGCCATTTGGACACTACTCAGACGAAA\nTTTAATCACCGCATCAACTCTTAAATGGAGTGTATCTGGACCCGTCATTCCACCTCAGTG\nGTTTTACCACCATAACACTACAGACACATACGGTGATGCGGCGGCAATGGCGTTTGGAAA\nAACCAACGAACCGGCGGCACGAGCGATAGTTGAAGCATTGTTTATAGATCCGGCTGATAT\nCCGTACTCCTGATCATTTAACGCCAGAAGCTACAACTAAGTTTTTTAATTTTGACATGCT\nCAATACCAAATCTCCAAGTCTCCTTGTGGGTACACCAAGAATCGGAACGTATGAATGTGG\nACTTTTAATCGACGTTCGAACGGGACTTATAGGCGCGTCGTTGGACGTTCTTGTATGTGA\nCAGGGACCCTTTAACTGGCACCCTAAATCCCCACCCTGCAGAAACCGACATTTCATTTTT\nTGAAATTAAATGTCGTGCTAAATACCTCTTTGATCCAGATGACAAAAATAACCCGCTCGG\nTCGGACGTACACCACGTTAATAAATAGACCTACAATGGCAAATCTACGGGACTTTTTATA\nTACTATAAAAAACCCATGTGTAAGCTTCTTTGGACCCTCAGCAAACCCAAGTACACGCGA\nGGCCTTAATAACGGATCACGTTGAATGGAAACGTTTAGGATTTAAAGGTGGGAGGGCCCT\nTACAGAACTCGACGCCCATCATTTGGGCCTCAATCGGACAATCTCATCCCGAGTGTGGGT\nATTTAATGATCCGGACATACAAAAGGGGACAATTACAACCATTGCATGGGCCACTGGAGA\nTACGGCTCTTCAAATTCCTGTATTTGCCAATCCGCGGCACGCTAACTTTAAACAAATTGC\nCGTACAAACCTATGTATTATCCGGTTACTTTCCAGCGCTAAAACTACGGCCCTTCCTTGT\nCACCTTTATAGGACGTGTGCGCCGACCACACGAGGTGGGAGTCCCATTGCGCGTCGATAC\nACAAGCGGCTGCCATTTACGAATATAACTGGCCGACTATCCCACCCCACTGTGCGGTTCC\nGGTTATAGCCGTTCTAACGCCTATCGAAGTTGATGTGCCTAGAGTGACACAAATACTTAA\nAGACACAGGAAACAACGCGATTACATCAGCATTGCGGTCATTGCGATGGGACAATCTTCA\nTCCAGCGGTCGAGGAGGAATCTGTGGATTGTGCAAACGGTACAACGAGCTTGTTACGTGC\nAACGGAGAAACCGTTGCTTTGAACTCAGAGTTCTTTGAAGACTTTGACTTTGATGAGAAT\nGTAACAGAGGACGCCGATAAATCCACACAACGCCGCCCACGAGTGATCGATGTAACACCA\nAAACGAAAACCTTCGGGAAAGAGCTCCCATTCCAAATGCGCAAAATGTTAAACCCTGATA\nAACCCTGATAAACGTTCTAATAAAAACATCAAATCATGGTTGGTTACTGTGAATGTTTGT\nTTTATTGCTTGGGGGTTTACAAGTACAACCCACGCTACTCCCACCCACTGTTTGATCGCT\nCGTATAACAGCTCATCCTCACGGTCCGTTTCATATGTTGAGTCATTTTCATAGACGTAGC\nCGTAGCCTTGTGATGGGTAATTTGTGCGGCGAGAATTTCTATGTGCAGGTTTTACTTTTC\nGTATGTATCCCCGTACCCGCTCGGGTACTCTTCTTACGGCACCGTAGAACCGACTGCGTT\nTCTGTCGATGATACACATATGCACGCATCAATCTGAGAAGCAACATGACAACGGAAAACA\nCGGCCAGGCAAGCCAAGGTTCCCCGAGTTGTGGGAATTAACCGTGGAGATTGAACCGATA\nTAGGGTCATATAATCGGTCCATATACGAGTGCGCGGCGGTTCCCAACGTAGCACAGGCCA\nCGAGCGTTCCCAGGGACGGTCCTATTAACACGTGTATATAATGCGCCAAAATTAATTCTG\nATACTATAAGATATACAACTGACAATGTACTAAATGTAGACATGGCCACGGACACCGATG\nACCACAGTCCCGTATGTAGATGATTCGCCACCACAAGTTCCAGCATTAATGATACAAATA\nGGATACATATCGCCATCAACGCAGCCATCAAATTCACGAACACTGCGCGCGTAGGCCCCG\nCAAGGCGATATATATCCTATTTGTATCATTAATGCT\n>comp5_c0_seq3 len=2033 path=[5328:0-20 3278:21-119 3390:120-1314 4585:1315-2032]\nCCGGATAATACATAGGTTTGTACGCTAACTTTAAACAAATTGCCGTACAAACCTATGTAT\nTATCCGGTTACTTTCCAGCGCTAAAACTACGGCCCTTCCTTGTCACCTTTATAGGACGTG\nTGCGCCGACCACACGAGGTGGGAGTCCCATTGCGCGTCGATACACAAGCGGCTGCCATTT\nACGAATATAACTGGCCGACTATCCCACCCCACTGTGCGGTTCCGGTTATAGCCGTTCTAA\nCGCCTATCGAAGTTGATGTGCCTAGAGTGACACAAATACTTAAAGACACAGGAAACAACG\nCGATTACATCAGCATTGCGGTCATTGCGATGGGACAATCTTCATCCAGCGGTCGAGGAGG\nAATCTGTGGATTGTGCAAACGGTACAACGAGCTTGTTACGTGCAACGGAGAAACCGTTGC\nTTTGAACTCAGAGTTCTTTGAAGACTTTGACTTTGATGAGAATGTAACAGAGGACGCCGA\nTAAATCCACACAACGCCGCCCACGAGTGATCGATGTAACACCAAAACGAAAACCTTCGGG\nAAAGAGCTCCCATTCCAAATGCGCAAAATGTTAAACCCTGATAAACCCTGATAAACGTTC\nTAATAAAAACATCAAATCATGGTTGGTTACTGTGAATGTTTGTTTTATTGCTTGGGGGTT\nTACAAGTACAACCCACGCTACTCCCACCCACTGTTTGATCGCTCGTATAACAGCTCATCC\nTCACGGTCCGTTTCATATGTTGAGTCATTTTCATAGACGTAGCCGTAGCCTTGTGATGGG\nTAATTTGTGCGGCGAGAATTTCTATGTGCAGGTTTTACTTTTCGTATGTATCCCCGTACC\nCGCTCGGGTACTCTTCTTACGGCACCGTAGAACCGACTGCGTTTCTGTCGATGATACACA\nTATGCACGCATCAATCTGAGAAGCAACATGACAACGGAAAACACGGCCAGGCAAGCCAAG\nGTTCCCCGAGTTGTGGGAATTAACCGTGGAGATTGAACCGATATAGGGTCATATAATCGG\nTCCATATACGAGTGCGCGGCGGTTCCCAACGTAGCACAGGCCACGAGCGTTCCCAGGGAC\nGGTCCTATTAACACGTGTATATAATGCGCCAAAATTAATTCTGATACTATAAGATATACA\nACTGACAATGTACTAAATGTAGACATGGCCACGGACACCGATGACCACAGTCCCGTATGT\nAGATGATTCGCCACCACAAGTTCCAGCATTAATGATACAAATAGGATACATATCGCCATC\nAACGCAGCCATCAAATTCACGAACACTGCGCGCGTAGGCCCCGCAAGGCGATATAAAAAG\nACGCTCTGCTGTCGTAAATTTGCGACCGCTTTTATGTTCGTTTCGTCCAATTTTCCGCGT\nCCACAAAAATACGTTGTAAATATTACACTTGTCGCAAAATGTCCAAGATATAATGTAGCA\nGCCACGCCGATTTGCTTGTAAGCTAATAATAACACAACGGCGTTTAATAACCACAATGAC\nAAAAGACCCCAAAAAAGTGTTGTGGGATCTACAACTAACCATGCAACACCGGAGCTTTGC\nCGGACACGTTGATTTTTCGTTTCTCGGTGTATAATCGCGGCCGTGATCAGTGTATATACC\nGCCATGGCCATTGCCGTTAAAGCCGTGTAGTAAGTAAATGCCACAACGCTATGTGGTTCC\nAAAAACAAAACCGGGGCGCTGTATCCACCTCTATTTCCGGACCATACCCCCCCATCTAGG\nGTGGCGTTAAATAACTCATAATCAACTACGGCAGCATAAAAACAAGGGATCCCGGTATAT\nTCAGAAGAGGCGGCAATTAACGTAGCCAGGAGCATTACCGCACCCAAAGTGAACATCATC\nACCTGAATTATCCAAATTCGCCAATTAAGCGTATCCATTTGATGATCTAACGCTTCCACC\nTCGGGTGTCGTGGTGTCGTACGGTGAGACTTTTTCAGAACGCGGCCCCTTCTTTTGAGTT\nCCCATGTCTCCCAACACCGGGGAGAGCAACGCCGCCGTCTATGCGTCCAGTAC\n>comp5_c0_seq4 len=1339 path=[5328:0-20 3278:21-119 3390:120-1314 5303:1315-1338]\nCCGGATAATACATAGGTTTGTACGCTAACTTTAAACAAATTGCCGTACAAACCTATGTAT\nTATCCGGTTACTTTCCAGCGCTAAAACTACGGCCCTTCCTTGTCACCTTTATAGGACGTG\nTGCGCCGACCACACGAGGTGGGAGTCCCATTGCGCGTCGATACACAAGCGGCTGCCATTT\nACGAATATAACTGGCCGACTATCCCACCCCACTGTGCGGTTCCGGTTATAGCCGTTCTAA\nCGCCTATCGAAGTTGATGTGCCTAGAGTGACACAAATACTTAAAGACACAGGAAACAACG\nCGATTACATCAGCATTGCGGTCATTGCGATGGGACAATCTTCATCCAGCGGTCGAGGAGG\nAATCTGTGGATTGTGCAAACGGTACAACGAGCTTGTTACGTGCAACGGAGAAACCGTTGC\nTTTGAACTCAGAGTTCTTTGAAGACTTTGACTTTGATGAGAATGTAACAGAGGACGCCGA\nTAAATCCACACAACGCCGCCCACGAGTGATCGATGTAACACCAAAACGAAAACCTTCGGG\nAAAGAGCTCCCATTCCAAATGCGCAAAATGTTAAACCCTGATAAACCCTGATAAACGTTC\nTAATAAAAACATCAAATCATGGTTGGTTACTGTGAATGTTTGTTTTATTGCTTGGGGGTT\nTACAAGTACAACCCACGCTACTCCCACCCACTGTTTGATCGCTCGTATAACAGCTCATCC\nTCACGGTCCGTTTCATATGTTGAGTCATTTTCATAGACGTAGCCGTAGCCTTGTGATGGG\nTAATTTGTGCGGCGAGAATTTCTATGTGCAGGTTTTACTTTTCGTATGTATCCCCGTACC\nCGCTCGGGTACTCTTCTTACGGCACCGTAGAACCGACTGCGTTTCTGTCGATGATACACA\nTATGCACGCATCAATCTGAGAAGCAACATGACAACGGAAAACACGGCCAGGCAAGCCAAG\nGTTCCCCGAGTTGTGGGAATTAACCGTGGAGATTGAACCGATATAGGGTCATATAATCGG\nTCCATATACGAGTGCGCGGCGGTTCCCAACGTAGCACAGGCCACGAGCGTTCCCAGGGAC\nGGTCCTATTAACACGTGTATATAATGCGCCAAAATTAATTCTGATACTATAAGATATACA\nACTGACAATGTACTAAATGTAGACATGGCCACGGACACCGATGACCACAGTCCCGTATGT\nAGATGATTCGCCACCACAAGTTCCAGCATTAATGATACAAATAGGATACATATCGCCATC\nAACGCAGCCATCAAATTCACGAACACTGCGCGCGTAGGCCCCGCAAGGCGATATATATCC\nTATTTGTATCATTAATGCT\n>comp67_c0_seq1 len=409 path=[0:0-408]\nCATCTCCATAAGGGGGGATATAACGAGATTGAAAACTATTGGCAATATATGCATCATCCC\nCTATTATGCCGGTAAGATCTATAACCTCGTGATTTAAATCGGCAATACGTGTTTCTTCTG\nCCATTGTAATATGTGACCCTTTAGATGGCTTTATTTTTACCCTCTCTTCCCGTAACCGTT\nTCAGCTCTCCTTCTTTGAACTGGAGCCTTTCGGTCAGATCGCTGTTCACATCCTTGAGAC\nCCTCAATGGTTTTGAATAAATTATTCACATAACCCTCGAGCATGCCGTTGATACTGTTAA\nCCACCGATGTTTTAAACGCACTTTGAACGTTTGTTGTTCCGGACATTGCCCCCCCGTTAA\nAGGATTGGTTGGCCTTGCCAAACCCCGGTTGTGATGTGTCCACCGATCC\n>comp48_c0_seq1 len=366 path=[0:0-365]\nCCGCCGTTGCATCTTCCCTTTCAATATTAGCGGCATGTGGACTGTGGTACGCGGCGGCGT\nTTGGAAAACCCGGGGTTGTCCGTCCAATCTTTGCGTATTTAGGCCCGGAACTCAATCCGA\nAGGGTGAAGACAGAGACTACTTTTGTACTGTCGGATTTCCCGGATGGACCACTCTTCGGA\nCACAAACTCCAGCCGTCGAATCTATTCGCACGGCTACGGAGATGTACATGGAAACGGATG\nGGTTGTGGCCAGTAACCGGTATTCAGGCCTTTCATTATCTAGCCCCCTGGGGACAGCATC\nCCCCCTTACCTCCGCGGGTGCAGGATCTTATTGGGCAAATCCCTCAAGATACTGGACATG\nCAGATG\n>comp27_c0_seq1 len=1171 path=[0:0-1170]\nATGTACTTAAGTCACCGGATCGGGTTAAACAAACATATTAACGAAACTCGTGTGTTTACA\nTATGATTACTTTTTCTATAGTAAACATTTTAAGTAGTAAATTATGGATTTGAGGTCGCGT\nACAGACGATGCTTTGGACATGGAATTGCATGCGGGTTTTGACGCCCCAGAAATCGCCAGA\nGCTGTTTTAACGGAAAAAACGCTTACTGGTTTAATTTCGTCTATATCACCTCTGGTTAAT\nAGACTAAGGGATTCTATTTTAATATTCAGCGACGAAGGATTAATTATTCACTGTAGTTTG\nGAAACAGAACAACTGTATATTCCTATACCGGCAAATATGTTTGACCAGTATAATTGGACT\nGGGCCGAGAATGGTTGTACTCGCGGCAACGGAGGGACGGTCCTCGCTTATTGACGCGTTT\nCGCCATACAAAAGATCCGTCGACCCCAACACGGTTATATTTTAAATTCACCGGACAACCC\nCCCGAGCGGAGTATTATCCAAACGATGGTATGGCAACGCCCGGGTGATTGTGGTCCAGAT\nGATCAAGTACAATGTTACAAACAAGTTGTAAAACGTGAACTCGCTTGTTATACAATGATG\nTTCCCAAATCTAACTCCAGATATAAGCATTTGCTTAAAACGCGATCAATTCACCCGTTTA\nCAGCGACTACTTAAAACTTTTGGGTTTACAACATGCTTCATTCTAACAGCCACGGATATG\nTACATCCAGACCGCCGGGGGTGGTTTTATCTCATTTAATGTTTCCTTGGATATAAACGGA\nAGCAAGCCTACACCATATAATTTAATACGCTCAATCACAAATTCAAAAAGGATCCTTAAT\nAATGTTGTTTATGGCAGCGGGAGTATGCGTGAATTTGGAGTATTATTGGAAACACACAGT\nGGATTCCGTTCTGCCGTACAAAATCTTAAGTTAACACGGGATGAGACGTGTTATATTAAT\nTTTTATCTCGCCTTAACTAACTCCCCCATGGTTGGATTGTATATCCAACGTTCCGCACCC\nGTGCATTCTTTTTTTTATGCAACGTTCTTAAGTCCCAAAGACCTTAAAGAAAAATTAACC\nTCGATGCAATTATTTGCGAACATGGAATCTGTGAAGGATGAACCACCATTAAAAAAAAGA\nCGCAATTTATTAACAAAAAGAAACGAAAAAA\n>comp49_c0_seq1 len=1047 path=[0:0-1046]\nAAGTCTGGCATCCCCGCCCTGTGCAGTTGTCACTTTTAGCGCTGCCTTTGAATTTGTGTA\nTCTTATGGATCGTTACTACCTGTGCCGTTATAACGTTACTTTGGTTGGGTCCTTTGCCAG\nGCGCACGCTTTCCCTGTTAGATATACAAAGACATTTTTTTTTGCATGTATGTTTTCGTAC\nCGATGGAGGGTTACCAGGTATACGACCGCCCCCCGGTAAGGAAATGGCCAACAAAGTAAG\nATATTCCAATTACTCCTTTTTTGTACAGGCGGTAGTTAGGGCTGCATTACTATCGATCAG\nCACGTCTCGTTTAGACGAAACCGAAACGCGTAAGTCATTTTACTTTAATCAGGACGGACT\nGACTGGAGGCCCTCAACCTTTAGCGGCCGCCTTGGCTAATTGGAAAGATTGCGCGCGGAT\nGGTTGACTGTTCATCATCGGAACATCGCACAAGTGGGATGATTACCTGCGCGGAACGTGC\nATTAAAAGAGGATATAGAGTTTGAAGATATATTAATAGACAAACTTAAAAAATCGTCTTA\nCGTAGAAGCAGCTTGGGGTTACGCAGACTTGGCTTTATTATTACTGAGTGGGGTTGCTAC\nTTGGAATGTAGACGAGCGTACAAATTGTGCTATAGAAACTCGCGTTGGATGTGTTAAATC\nATACTGGCAGGCGAACCGGATTGAAAACTCCAGGGACGTTCCAAAACAATTTTCCAAATT\nTACGAGCGAGGATGCCTGTCCCGAAGTAGCATTTGGGCCTATTTTGTTAACTACCTTAAA\nAAACGCAAAGTGCCGTGGTCGCACGAATACCGAATGCATGTTATGTTGTTTATTAACCAT\nAGGGCACTATTGGATCGCTTTGCGGCAGTTTAAAAGGGATATATTAGCATACTCAGCAAA\nTAACACAAGTTTATTTGACTGTATCGAACCTGTAATCAATGCATGGAGCCTAGATAACCC\nCATTAAACTTAAATTTCCATTTAATGATGAGGGTCGATTCATAACCATTGTAAAAGCAGC\nAGGTTCCGAGGCCGTATATAAACATTT\n>comp29_c0_seq1 len=2664 path=[0:0-2663]\nCCTTTGCCATAATTAATCTTCGGTTATAATTATAATAAAGACGCGTCCTATCATAATCCA\nTAATAGCAACATTTTGCATACACTCAACTAGGCTTGTGACAACCGCCGCCCCTCTGGCCA\nACGTTGCATCGGCAACTTTTAACATCTGGGACAGTTCTGCCGCTTGACTCATATACGTAT\nTTAATGGTGCAGGGGTTCCATCCTGTTCTGATCGTACCTTTCTTACAACGGGCACAATAC\nCTACACAGGCTATCCAGTCCACGTATTTGGCAAAACCGACCCTTCCATTTAAACCACTGG\nTATAGAGACAACCGGTTATTCCACGCAGAAACTCAAGTAACGATGACTGTAATGTTTGAC\nGCCAGGTTTCAAAAACCTGATGTGCAAGCCGTACGGCTTCTGATTCTCCACATAACCCAT\nAACGTTCCGCTAGAGCCCCGGCATGCAGGTTACATTGTTGGATGTGGTGTTCCCAATCTG\nCTGCTAGGTCCTCATACCGAGTTGCATCCAACGCGTTCATCAAAACGGTTGCCTGAACTT\nGGCGAATTACAGTTTCCGTAGACCGTACAGCGCTATATATGCCTTGTCCATCGGTATATC\nCAAAGTCACCGGCTAGGATTTTTCGAAACAACATACTTTGCGTGGTTGGGTGTATTAACA\nTCCAGCCATCTTCCTCCGGAAATGTACAAAACCCTATATCCGGGGCGTACTCATTCCAGT\nATATATCGAACATGTTCTTGTATTGGTCATTTGGGTTACTTCCATTCAAGCCCTGGTCAA\nTAGAAACAGAACTTGCTATCCTTTTTTCTTCACTACCGGAACTGTTATTAAAAAGAGACG\nTTATTTCGGCCATTGAAAACCACGATGAAAAGATCAATTTCTGTAGACAGTTCTTCACCC\nAAAAACGTTTTTAATCCAGAGACGCCCAATGGATTTGATGACAGTGTATATTTAAACTTC\nACCTCTATGCATAGCATTCAACCTATCCTCTCACGGATTCGAGAACTTGCCGCAATTACG\nATTCCAAAAGAACGTGTTCCGCGGTTGTGTTGGTTTAAACAGTTACTCGAACTGCAAGCG\nCCTCCTGAAATGCAGAGGAATGAGCTCCCCTTCTCCGTTTATTTAATTAGCGGAAATGCC\nGGCTCCGGAAAAAGCACGTGTATCCAAACGCTTAACGAAGCTATCGATTGCATTATTACC\nGGATCCACCAGGGTTGCTGCCCAAAATGTTCATGCTAAGTTATCAACGGCTTATGCGAGT\nCGTCCGATAAACACAATCTTTCATGAATTTGGTTTTCGCGGAAATCACATTCAGGCTCAG\nCTGGGCCGTTACGCATATAACTGGACTACGACCCCCCCTTCTATTGAGGACCTGCAAAAA\nAGAGATATTGTATACTACTGGGAAGTTTTAATTGATATAACAAAACGAGTGTTTCAAATG\nGGGGACGACGGTCGCGGAGGAACATCGACATTTAAAACCCTGTGGGCAATTGAACGTTTG\nCTTAATAAACCTACAGGCTCAATGTCCGGAACCGCGTTTATCGCATGCGGTTCCCTTCCG\nGCTTTTACCCGGAGCAACGTTATTGTTATTGATGAAGCAGGATTGCTAGGGCGTCATATT\nCTCACGGCCGTTGTTTACTGTTGGTGGCTTTTGAATGCTATATATCAAAGCCCTCAGTAC\nATAAACGGTCGAAAACCGGTCATAGTATGCGTCGGTTCGCCCACCCAAACTGACTCGTTA\nGAATCTCATTTTCAACATGACATGCAGCGTTCACACGTAACTCCTAGTGAAAATATACTC\nACGTATATAATCTGCAATCAAACTCTGCGTCAATATACTAACATCTCACATAACTGGGCA\nATCTTTATTAATAACAAACGATGTCAAGAGGACGATTTTGGAAATCTTTTAAAAACGCTT\nGAGTACGGGCTACCTATTACCGAAGCACATGCGCGTCTGGTCGATACATTTGTTGTACCT\nGCATCCTATATTAACAATCCTGCTAATCTTCCCGGATGGACGCGTCTGTATTCGTCGCAT\nAAGGAGGTGAGCGCGTATATGAGTAAGTTACACGCGCATTTAAAACTATCGAAAAATGAC\nCATTTTTCTGTGTTTGCCTTACCGACTTATACATTCATCCGGCTAACGGCATTTGATGAA\nTACCGCAAATTAACGGGACAACCCGGACTTTCTGTTGAACATTGGATACGGGCAAACTCC\nGGTCGTTTGCACAATTATTCCCAAAGCCGAGATCATGACATGGGAACAGTTAAATACGAA\nACACATTCAAATCGCGACTTAATTGTAGCCCGTACAGACATCACTTACGTGCTAAATAGT\nCTCGTAGTTGTAACCACAAGACTACGTAAGTTAGTTATTGGATTCAGTGGTACATTTCAA\nTCGTTTGCAAAGGTTTTACGTGACGACTCCTTTGTGAAGGCTCGAGGAGAGACATCCATC\nGAATATGCTTACCGGTTTCTGTCAAACCTAATCTTTGGAGGCTTGATTAACTTTTACAAT\nTTTTTGTTAAATAAAAACCTACATCCCGATAAGGTATCGTTAGCATACAAACGGTTAGCT\nGCCTTAACCCTGGAGTTATTGTCTGGAACAAACAAAGCCCCCTTACACGAAGCAGCGGTT\nAATGGGGCGGGTGCCGGGATTGAC\n>comp17_c0_seq1 len=1093 path=[0:0-1092]\nCACGGGGTAGGGGACTCCAACGTCCCAAAGCGTTCATCCCTACGACGCTTTAGACGTTGG\nAGTCCCCTACCCCGTGTTCCACGCGGCAAGGGTCTCTGGGAAACGCAACCCAAATCCCGT\nTTCTGAATTTTGCTATAGATGTAACCCGACGTCATCAGGCCGTTATTCCCGGAATTGGAA\nCGCTTCACAACTGTTGTGAATATATTCCACTGTTCTCGGCTACTGCTCGACGGGCAATGT\nTTGGCGCGTTTCTATCGTCAACAGGGTACAACTGTACCCCCAATGTAGTTTTGAAACCAT\nGGCGATATTCGGTAAATGCAAACGTAAGCCCTGAATTAAAAAAGGCTGTCAGTAGTGTAC\nAGTTTTATGAATATTCACCGGAAGAAGCAGCACCTCATCGAAATGCGTATAGCGGGGTTA\nTGAACACATTTCGCGCGTTTTCTCTGTCGGATAGTTTCTGTCAGTTGTCTACCTTTACAC\nAACGGTTTTCGTACCTTGTGGAAACATCTTTTGAGAGTATTGAAGAGTGTGGAAGTCATG\nGCAAACGCGCAAAGGTTGACGTTCCAATCTATGGCAGATATAAGGGGACGTTGGAACTGT\nTTCAAAAAATGATCCTCATGCACACCACGCATTTTATTTCATCGGTGCTATTGGGCGATC\nATGCCGACAGAGTTGACTGCTTTCTGCGTACAGTGTTTAACACGCCAAGTGTTTCTGACA\nGTGTTTTAGAACACTTCAAACAAAAATCAACTGTGTTTTTGGTACCACGTAGACATGGGA\nAAACATGGTTTCTTGTACCATTAATAGCTTTAGTAATGGCCACGTTTAGAGGAATTAAAG\nTGGGTTATACGGCTCATATACGCAAAGCAACGGAACCCGTGTTTGAGGGTATCAAGTCTC\nGCCTGGAACAGTGGTTTGGGGCAAATTACGTGGATCATGTAAAAGGCGAATCTATTACGT\nTTTCATTTACCGACGGGTCTTACAGCACAGCGGTGTTCGCGTCAAGTCACAACACAAACG\nTGAGTGTTTTATAAATTTAACCTTTAATATATTACTGTAAATGTTGACATATACCTTTCC\nACAACGGCGGTTG\n>comp37_c0_seq1 len=1184 path=[0:0-1183]\nATTTTTATCTGTCGCACCAAATCGTCTGTAGCACGTACAATTGTTGCTAATAAATCATCC\nCGTGTTATTTCAGGATACTTGACCTCACCATTGTTATATGTTTCATAGTCCTTTACGGCT\nTGGTCTACGGCCGCGCTTAGCGTATTAAAGCAAGACAACTCTGCTTCCGCGGAAGCCCGT\nTGCGTTGCGCGTGTATTAATGGTTTTAATTGTACGTGATAATTCATCGAACTCTCGTCTG\nGATAAGTAACCTGCGGTTTGAGCTTCCCCGACTACAGATAACCACGATACGAGAGCCGTG\nTCTGTGTTTAAATCTTCCCCTTCTTTAATAAGCTCTTTTAACAGAGATACGACGGGGAGA\nTTTTGTATAGTCTCAGGAGGAGGGTGTATAGACAGGGACGATATGATTGCCGTTAATTTA\nGCGTCGAATTCCGGAAGAGAATCTAAAAGCCGTTGAATGGGTGCCGTACTTGCGGTCGCG\nACCCGAAAACGCCTAGGGGATTGTTCAGCGATCAAGGCCCGTGTGCTATATAACACTCCG\nCGGGTGAAGTATTCTGTAACAGCCGAGGTCAATAGCATTGTAACTTCGGATCGTATCTCA\nTATACACGCCGAATTAACTCTTCGGGTGGAATGTCGGTTTCTTCCGGGGGTTCCTGGGGA\nACTTCTGGTATTTGAATGGCATCAATTTTATTGCGGGTAGACCGTAATGCATTCTCTAAA\nGCCTTTACACTAGAAACAAGCGCGGTGTGTTCACGCATATAGCGTGTCTCCCGGGCCGAG\nACTAATTCACAAAGAAGACGTATTCGTTCAGACAGGGACCCTGTACGGGTTGGAATAAGC\nTCGGCAAAAAGTCCGGGATGAGAAATAATAGGCGAATTTAGTATACTTATAAGACCTGTC\nGACAGTCTAGAATAGAGGTCTATGGGCGACGAACCTCCTAGATCCGCTTCTAACACATCT\nAGTTCGGCATGTAAAGCGCCGGTTGTATCCTGAACCCGCATGGCAACTAGACCAAACTTA\nGCGATAATGAGCATGCCAATTGTACATTTTTTCCGGAGAACAGTTTTAATAGCATATTCC\nGCCCCCGGCATGTTTGTTAATATCAAACTTGTAACGCGTATAAGTTCCGCGGCGGAGGGA\nAATCCTGTTAAAATTTCCCCAAGGGGACCTATAAAGTCTGATAC\n>comp54_c0_seq1 len=515 path=[0:0-514]\nTTATATATATGTTCCATCTAATAACAATTTAACATACCCCAGGCCTTGAAATATATCTTC\nCGTGTGGTCCATTAAAAGTTTACGTGTATATCTAACGTTGTCGATCATACGCCGACATGC\nCTGGCTTAACAGGGCCAGTGCTCCCAAGGCGGTCCCTCGGACATAACGTCGACCGGTGAC\nTACATCGGCATTAACAACGCGTACGTGCCTAGGAACGCGACATGACCGATGTTCGTCGAG\nACTTAGTACGATAGAATTTTCACTCTCACTGCTATAGCCGTCAGAAGGTTCACTAAAATC\nACTTTCATATAGGTCTCTGTTCGGTGAGTTAAACGGGTTAGAAGATACGCCCCATGTGTG\nTACGTCCCGCGGAAAGTTTGGCGACGGCTGTCTTGTTTTATAGTTTGTCAATAGGTCCGT\nTTGGGGGGCATCGGCTGCCGTGTCAACCCAAGAAGGTAATTGGTTATTTACAGGGTGGAA\nTACTGTTTTGGAGTTATACATTCGAGGGTCATTTT\n>comp14_c0_seq1 len=1226 path=[0:0-1225]\nGTTTGGTACGTACATAAAGCCATTAATACCACAAATGGCTTTATGTACGTACCAAACGAA\nGCCAGTTTTTCATTGGTGTATATGCGTATGTTGGAGTTACCAGAAGGTTTGCAGGAGCTA\nGTGAGTGGATTATTCGACGGGACGCCCGAGATACGAGACGCGCTTAACGGAAGTAACGAC\nGATGAAAAAACAAGTATAATTGTTAGTCGGCGCGCTGCTGATGTGGTTACGGAAGACGTA\nAAAGCAGATGATGTGCCGATTTCGGGTGAACCGTATTCTGAGAAACAGCCTAGACGGCGT\nAAGAAGTCCGATCATATTACACTAAGTAACTTTGTACAGATTAGGACCATCCCCCGGGTA\nATGGACATTTGGGATCCTCGCCATAAAGCCACTACTCATTGTATCCGCGCGTTATCATGT\nGCGGTTTTTTTTGCGGACGAGGTTATATTTAAAGCCAGAAAATGGCCTGGACTTGAAGAT\nGAACTTAATGAAGCCCGTGAGACGATATATACTGCAGTTGTTGCGGTATATGGCGAACGG\nGGGGAACTTCCATTTTTCGGGCATGCTTACGGACGTGATCTGACGTCCTGTCAACGGTTC\nGTGATTGTTCAATATATACTGTCTCGGTGGGAAGCGTTTAATTGTTATGCCGTTATTGAA\nGATTTAACGCGTAGTTATGTTAACGCGTTACCCAGTGATGATGACACGGATCAAGTTGCT\nCAAGATTTAATACGGACCATTGTGGATACAGCAAACAGCCTCTTGAGGGAAGTGGGCTTT\nATTGGCACGTTGGCTGAAACTTTGTTGTTCTTACCACTCCCCCAGCTTCCCTGTTACAAG\nGAAACGTCACATCTTGCAAAAAAGGAAGGTGTGCGAATTTTACGCCTTGCAAAAACAGGA\nGTTGGTTTATCGGATACTGTTCCGGTTGATGTTTCTGTCACGGAAAGGCATGAGTATGAG\nATATCCCGGTACTTAGATACCCTGTACTCTGGAGACCCCTGCTATAACGGCGCTGTGCGT\nCTATGCCGTTTATTGGGATCATCAATTCCCATTGCCCTGTACTACAATACAATATCGGGT\nAATGCCTTTGAACCGTATTTTGCTGGGAGGCGTTATATAGCATATTTAGGCGCTCTATTT\nTTTGGTAGAGTGCACCAAACACCATTTGGGGACGGGAAAAAAACCCAAAGGTAGTGTGTA\nTTATTCGCGAATAAAGTATTGTAGAG\n>comp30_c0_seq1 len=2754 path=[0:0-2753]\nCCCCTTGGTTGTGAGTGGATATAATGCCTTCATCGGGCTTGTTTTAAGTTTAAGCACGTA\nCCGGTACGCAAAAAAGGCCGCTACCAGTCCCGCCAAAACCAATAATCCCACGGCCAATGC\nCCCAAATGGGTTAGATAAAAACGTGGTAAATCCGTGTACGGTGGAAAGCAGCGCTCCCGT\nGGCCCCAAGAACCACATGTCCAACGGCCTGGCCCGCGGTCCCAAGTCCCTGGAAAAACTG\nAGCCATGCCCTGCATAATGGCCGTTCCGCTATCATATTGCACAACCTTGTCTATGTCATA\nAAAACGCAGCGAATGCATTTGATTTCGGCGTTGAATTTCACTGTAGTCTAGTAACCCTGT\nATCCCGCAGCTCGTCTCTTGTATATACTTGCAGCGGCATAAACTCTCTATCTTTAAGAAG\nTGTTAAGTTTAAATCTACGTAAGTGCTAATCATTCCCACATCATGGACTGCGATTTCACG\nGACGTAACGATAATCCTCATAATATACGTAGTGATGCCCAAATAGAAAATATCGCTTGTG\nATTAGCCACGCATGGTTCTAACAGATCTCTGGACATAATTAACTCGTTATCTGTTCCAAG\nCTGGCCCTCCACCGTCCCGGACCCATTTAAACTAACTATTGAAATTAAAGGACGGCTATA\nACAACGCGTAGTACTACCAGATACCCTCATAGAGTTTTGAAGTATAATGCGTGTATCTGA\nTCCCAGTTCTGGACAATTAGAAACGGAGATAACGTCGCCGAGAATACGAGCTTTAACACG\nTTGATCCAAAATGGTGCTCGCTAAAGCACTTGGGTTAATTGGAAATAGTCCGCTCCAAAG\nGGCGCGTTCGCGATTTTGTAGCTGGCACCACGACGAGGAGATACGTGCCAACATTTCATT\nAACATGCTCTTGAATGTGGTCATATGTAAACTGGAGCATAGCAAATTCCACCGATGAGGT\nGGTTGTTATTGTTCTATTGGCACGCAACTCAACTGGCACGCTTCGTCGGGATCTGGTATT\nTCGAGTCGGGTGTTTTTGTGGTGAATGATTAGTGTTTTCACGGACCAATTCTTGGAGATA\nGAGACGGGCGAGGGAATTGCTCAGCAGGGGTTGAAACACCACAACAAACCCCCCTCTGGC\nAAGGTAGGTCTGGATATCCCCGGTTCTAACATGAGATGAGTTGTATCTGGTTGTATAGAT\nCCGGTTAATAATAGCCCGGGCTTCCTCCTTTACACATTGACTGAGATGGATTTGGTTAAG\nATTAAACTCGTTTGTTTCACTTATAAACGTGGTAGAAAGTGTTTTCATTGTAAAGCGAAA\nATTGTGTGCATACTCATCGCGAACTACATCTTCAACCTCACGCCACTTGACAAGCGAACA\nAACTTCCGTTCGTTTTGGCTTCCAGTTCCAACCAACCGTTAAATGAGGCGTGACTAAAAA\nGTTCCGCGCTGCAGGTTCCAGTAATGCTCTAGTGTCAAGATCCCTTTGTCTATAACCCTC\nAAACTGGTGAAAACGATCCATTGCATAATTGGAATGTTCTCTGTATGCACCATCCCGTAG\nGCCAAAAAACGGGGACATGTATATTATATCTCCCGTGGAAAGTCCAAAACTATCATAAGG\nGAATATTGATCTGGCTTCAACTTCCTCAATGATGCAATTCACCGACGTGCCCGTCCTATA\nTGTTCCGGGGGTTCCGGCAACCATGTACGTGTCATTGGTAGTATGCCATGCTTTGGATCC\nCACAGAATTATATTTTGATGCGATTAGAGGCATATCCTGTGGATTTTTATCCTCATTAAA\nGGCTTCAACTTTGTGGTTATTTCGTACGTACGTTGCTTTAGAAGAACACTTGCCAAACTT\nATCAATGGTGTCCGTGATCTCTGAAACGGGAATTGGTACCCTATCCGCATATCTATTAGT\nAATTTGCGTATAAGAACTTCCGGCCCACGCCGTGCTAACGATAACATCTTTGTAATATAC\nCGTCGCCTTAAACTTGTACGCGGCAATGTTTTCTTTATAAACAACAGCAATACCCTCTGT\nAAAGTTTTTACCAAGGTGATAATCCGGACATGTCCGAGTTGGTTCTAATCGTACGATTGT\nGGAGCCTGTTGGCGGTGGGCAGACGTAAAACGTGGGTTTTGTTTCGGCGTCCTGGGACTT\nGTGTATAGCTTCTCTGATTTCATCACCATCGCCCAGATGAGCAGACCGGGTTATATCTTC\nTGATTGTGTGGGCTCTACTTGTAAACTCTCATAAAACGAGCTTGGAGAGACCGACACAAC\nCGCCGTAACAAACATAGAAAATATGCATAAAAAGCATAACCACACCCCCGTAACGGAGGT\nTATGAAAACGCCGGGTCCGTTGAATCCGGAGCCAGCCGCTGCATTAGGGTGTATAGAAGA\nGAAAAAACGTCTGAATCGTAGATTACGACGGTATTCTGGTCGATCCCTGTTTCTCCACTT\nTGAATAATAGCCACAAGGGGACATGTTTCTTCGTACGTTAAATAAATGCCGTCTAAGGGT\nCCGTGGGAACTGCCTATACCTTTAGGTTGAGACGTGCACCCGCGTGGATCCTTACCTAGA\nCGGTCAACGCGACATAACCGCACCTCCCCACAATGGAAAACAGAGGTGAATAGTGTGGTT\nGCAAACACAAGCTCCCTAATATATTTCCAGGCAAGTCTCTGTGCAAAAGTAACGCCTTCT\nACCCCAGAAAAGCAATAAAAGCCCCTAAATGGACTGAGAAGCCAGTTGGAACCA\n>comp26_c0_seq1 len=2623 path=[0:0-2239 2240:2240-2622]\nAACCCCACACCCCCAGAATTCTGTTTACGCCCACCTACAATTTCCTGCACGAAGGAGTCG\nGCCATAAATAAATCTGCAGTGCGCCGCATGGCTCCATCCATTGTGATGAAAACCGGCTTA\nTTTAATACATAACACGAACAAGCTGTGACATCGCTATGTGCTAAAACACGCGGCATGTGA\nTCGTCGCATACATATGTAACAACGTTTAACAACTGATCCGACGATCCACGTAAGTTATAC\nAAAAAACTTGTACTTGCTTTTCCGGTATTTGTTGATGAAACAAAAATAATTTTACAATTG\nGTTTGATTTAAAAATCCGACTATAGTTTGTACAGCATCAGGTCGAATAAAATTAGCTTCA\nTCCACAAACAGAAGATTAAAATCTTGACCTCGGATACCCTGGAACGATAGAAAGATATAT\nAGTTACCCCACCAAAGTTTAAATGTATCCTTAAATACCACGTACGTAAAAAATGTTTGAA\nTACGTACATATTTCTTTTTTTTTTTTCCAGTACAACCATATCCGGTGTATAATGGAAGCC\nCATTTGGCAAATGAAACCAAACATGCACTTTGGCATAATGATCACACAAAAGGATTACTA\nCACGTTGTGATACCTAACGCGGGGCTTATTGCGGCCGGAATAGATCCCGCATTACTGATT\nTTAAAGAAACCCGGACAACGCTTCAAGGTTGAAGTACAAACAAGATATCATGCTACAGGT\nCAATGCGAACCGTGGTGTCAAGTTTTCGCCGCGTACATTCCCGATAACGCCTTAACAAAT\nCTCTTAATACCAAAAACGGAACCATTTGTTTCACACGTTTTTTCGGCCACGCATAATTCA\nGGGGGATTGATTTTATCATTGCCTGTTTATCTTAGCCCCGGTTTATTCTTTGATGCATTT\nAACGTTGTAGCGATACGAATAAATACTGGAAACCGCAAGCACCGTGATATTTGTATTATG\nTATGCAGAACTAATCCCAAACGGAACGCGTTATTTTGCTGATGGACAACGGGTACTTTTA\nTTATGCAAACAGCTGATTGCGTATATCCGATGCACCCCTCGTCTTGCATCGTCTATAAAA\nATATACGCAGAGCATATGGTGGCAGCCATGGGTGAATCACACACGTCAAATGGGGACAAT\nATTGGACCCGTTTCATCCATAATCGATCTTGATCGACAGTTAACTTCTGGAGGTATTGAT\nGACTCCCCTGCTGAAACACGCATACAGGAAAATAATCGGGACGTCCTTGAGCTAATAAAA\nCGGGCCGTAAACATTGTTAACTCCAGGCACCCCGTCCGACCTTCTAGTTCCCGCGTTGCA\nTCTGGGTTGCTTCAAAGTGCAAAGGGCCACGGAGCGCAAACTTCCAACACAGATCCGATC\nAATAACGGTTCCTTTGATGGCGTCCTTGAGCCGCCTGGACAAGGGCGATTTACGGGAAAG\nAAAAACAATTCGTCCGCCAGCATCCCACCTTTACAAGACGTTCTATTGTTTACCCCAGCT\nTCGACAGAACCCCAAAGTCTTATGGAATGGTTCGACATCTGTTATGCCCAATTAGTTAGC\nGGGGACACTCCAGCAGATTTCTGGAAACGGCGTCCCCTATCAATTGTACCGCGACATTAC\nGCAGAATCCCCCAGTCCGTTGATTGTAGTATCTTACAACGGATCCTCTGCCTGGGGAGGA\nCGTATTACCGGAAGTCCAATTTTATATCACTCTGCACAGGCTATTATTGATGCTGCGTGT\nATAAATGCCCGGGTTGACAATCCCCAAAGCCTACATGTGACAGCTCGCCAAGAGCTAGTC\nGCGCGTTTACCGTTTTTGGCTAACGTCCTAAATAATCAAACCCCCTTACCCGCCTTTAAA\nCCAGGCGCCGAAATGTTTTTAAACCAGGTATTTAAACAAGCGTGTGTGACATCGCTAACC\nCAAGGTCTTATAACGGAGTTACAAACGAACCCGACTCTACAACAACTCATGGAATATGAT\nATTGCAGATTCTTCCCAAACGGTTATTGATGAAATTGTAGCCCGCACACCAGACCTGATT\nCAGACTATAGTTTCGGTGTTAACGGAAATGTCAATGGATGCGTTTTATAACAGCTCCTTG\nATGTATGCGGTTTTGGCGTATCTGTCATCTGTATATACACGACCACAAGGTGGGGGGTAT\nATACCCTACCTTCACGCTTCCTTCCCATGCTGGTTAGGTAATCGTTCTATATATTTATTT\nGACTATTATAATTCAGGAGGGGAAATACTTAAGCTTTCCAAGGTCCCCGTTCCCGTAGCC\nTTAGAAAAGGTTGGTATTGGTAATTCCACACAACTGAGGGGTAAATTTATACGCAGCGCG\nGATATTGTTGATATTGAAATTTGTTCTAAGTATTTACCCGGTCAATGTTACGCGTACATT\nTGTCTAGGATTTAACCAGCAATTACAATCCATTTTAGTTTTACCGGGGGGATTTGCGGCA\nTGTTTTTGTATTACCGATACCCTACAGGCAGCACTACCTGCATCGTTAATCGGACCTATT\nCTAGACAGATTCTGCTTCTCTATTCCCAACCCCCATAAATAAATTAGTGTCACTATAAAA\nACATAACACCAGAATCTCTTCATATTTAATTTTACGTCATTTC\n>comp25_c0_seq1 len=1403 path=[0:0-1402]\nTAAACTTCCACGACTAAGCTGGGTTTGATTGTGTCAGAAGCAACAGGAACCCCTACCAAC\nAATGTAATCTTGCGCGGAGCGACGGGGTTTGATGGGAAGTTTAAAAGCGGTAATAATAAC\nTTTCAATTTTTATGTGAACGATATATAGCACCACTGTATACGTTAAATCGGACCACAGAG\nCTGACTGAAATGTTTCCTGGATTAGTTGCTCTTTGTTTAGACGCGCATACCCAGCTTAGT\nCGTGGAAGTTTAGGAAGAACCGTAATAGATATTTCTTCTGGACAGTACCAAGATCGGCTC\nATAAGCTTAATTGCATTGGAATTAGAACACCGCCGACAAAATGTTACATCCCTACCCATA\nGCCGCCGTGGTATCAATACATGACAGTGTTATGTTGCAATATGAACGGGGACTTGGAATG\nTTAATGCACCAACCGCGTGTAAGGGCGGCATTGGAAGAAAGTCGCCGCCTTGCGCAGTTC\nAACGTTAACAGTGACTATGATCTTCTATATTTTGTCTGTTTGGGTGTCATTCCTCAGTTT\nGCCTCCACACCGTGAGTATTCACTATCCGGTCCGTGGGGTGTTTATAATGGCTGCTGAAG\nCTGACGAAGAGAACTGTGAAGCGTTATACGTGGCTGGGTATTTAGCCTTATATTCAAAGG\nACGAAGGGGAATTAAATATTACCCCAGAGATTGTGCGGTCCGCTTTGCCGCCTACTAGTA\nAAATACCAATAAACATCGATCATCGAAAAGACTGTGTCGTGGGTGAAGTAATCGCAATCA\nTTGAGGACATACGCGGACCTTTTTTTTTGGGTATCGTTAGATGCCCTCAACTACATGCGG\nTGCTGTTTGAAGCGGCCCATTCGAATTTTTTTGGAAATAGAGATTCTGTATTATCTCCGC\nTAGAACGTGCGTTATACTTGGTCACAAATTACTTACCCTCCGTATCCCTGTCTTCAAAAC\nGATTGTCCCCGAATGAGATACCAGACGGTAATTTTTTTACCCATGTTGCGTTATGTGTTG\nTTGGAAGACGCGTTGGAACAGTGGTCAATTATGACTGTACCCCGGAATCTTCAATTGAAC\nCATTCCGGGTTTTATCGATGGAAAGTAAAGCGCGGTTATTGTCGCTGGTTAAAGACTACG\nCGGGTTTAAATAAAGTATGGAAGGTTAGCGAAGATAAACTCGCCAAGGTGTTATTATCCA\nCAGCCGTGAACAATATGCTTTTAAGAGATAGATGGGACGTGGTTGCAAAACGTAGACGCG\nAAGCCGGAATTATGGGTCACGTTTATCTTCAGGCTAGCACCGGATATGGACTTGCTCGGA\nTAACCAACGTTAATGGGGTGGAGTCTAAATTACCCAACGCGGGTGTTATAAACGCCACAT\nTCCACCCCGGCGGGCCCATATAC\n>comp40_c0_seq1 len=701 path=[0:0-700]\nAAGTATAATTCAGGCCCATAACTTATGTTTTACCACGCTAACGTTAAATTTTGAGACGGT\nTAAACGTTTGAATCCATCCGATTATGCCACCTTTACAGTTGGAGGAAAACGTCTTTTTTT\nTGTGCGCTCTAACGTTCGAGAAAGTCTGCTGGGTGTTCTTTTAAAAGACTGGTTGGCTAT\nGCGCAAGGCTATTAGAGCGCGCATACCCGGAAGTTCTTCAGATGAAGCAGTGTTATTAGA\nCAAACAACAAGCCGCGATAAAAGTAGTTTGTAATTCCGTGTACGGTTTTACTGGAGTTGC\nGCAGGGATTTCTGCCATGTTTATACGTAGCGGCCACTGTCACTACAATTGGCCGTCAAAT\nGTTATTAAGTACCAGAGATTATATTCATAATAACTGGGCCGCATTTGAACGTTTTATTAC\nAGCGTTTCCAGACATTGAAAGTAGCGTTCTCTCCCAAAAAGCGTACGAGGTAAAGGTTAT\nATATGGAGATACGGATTCTGTGTTTATCCGATTCAAGGGTGTTGGTGTTGAGGGGATAGC\nTAAAATCGGCGAGAAAATGGCACATATAATTTCAACGGCTCTGTTTTGTCCTCCTATAAA\nGTTGGAGTGTGAAAAAACTTTTATAAAACTTTTGCTTATAACAAAGAAAAAGTACATTGG\nGGTAATTTACGGCGGAAAGGTTTTAATGAAGGGAGTCGACT\n>comp24_c0_seq1 len=1228 path=[0:0-1227]\nCTCTTAAAATATAAAATAACCGGGTGGGTGGCATTAAACCCACAAGTACCCGGGCGGCAA\nTCCGCTAGACTGTTTTTCTGCTCATGGAATTACAACGCATATTTCCGCTGTACACCGCTA\nCGGGTGCAGCGCGCAAATTAACCCCCGAGGCAGTTCAGAGACTCTGCGATGCATTAACGC\nTGGATATGGGATTATGGAAGTCCATCCTGACCGATCCCCGGGTGAAAATAATGCGATCAA\nCTGCTTTTATAACTTTAAGGATCGCTCCGTTTATCCCCCTTCAAACGGATACTACTAATA\nTTGCCGTTGTTGTAGCCACAATTTACATCACGCGCCCACGTCAGATGAACTTACCTCCGA\nAGACTTTTCATGTAATTGTAAATTTTAATTACGAGGTCTCGTACGCAATGACGGCGACTT\nTAAGAATTTATCCGGTTGAAAACATAGACCATGTTTTTGGAGCAACGTTTAAGAACCCGA\nTCGCGTACCCCCTTCCAACATCTATTCCGGATCCTCGAGCAGATCCCACCCCCGCAGATC\nTTACACCAACGCCAAACTTAAGCGACTACTTACAACCCCCGCGGCTTCCGAAAAATCCAT\nACGCATGTAAAGTTATTTCTCCGGGAGTGTGGTGGTCAGACGAACGAAGGCGTTTATATG\nTACTGGCTATGGAACCTAATTTAATAGGGCTATGTCCCGCCGGATGGCATGCTCGGATAC\nTTGGCTCTGTATTAAATCGACTCCTCAGCCATGCGGACGGATGTGATGAATGTAATCATA\nGAGTTCACGTGGGGGCACTGTATGCGTTACCCCATGTCACAAATCATGCGGAAGGTTGTG\nTGTGTTGGGCTCCGTGTATGTGGAGAAAGGCCGGTCAGCGGGAATTAAAAGTGGAGGTAG\nACATTGGCGCCACGCAGGTTCTTTTTGTAGATGTCACCACCTGCATTCGAATTACGAGTA\nCTAAAAATCCTCGCATTACCGCAAATCTTGGCGACGTTATAGCGGGAACCAACGCCAGTG\nGTCTCTCTGTACCAGTAAATTCATCTGGGTGGCAGCTTTATATGTTTGGAGAAACATTAA\nGCCGGGCTATTATTAACGGCTGTGGTCTGCTTCAGCGAATTTGCTTCCCCGAGACACAAA\nGATTATCGGGTGAACCGGAACCTACAACCACCTAGTATACCTTAACTCAACCGCCGTTGT\nGGAAAGGACGTGTGCGCCGACCACACGA\n>comp66_c0_seq1 len=720 path=[0:0-719]\nGGTGGAAAAGGCAGAAAACCCGGATTTTATAGCGGATTCGTATTCAATGCGTAGCTCATT\nGACCTCATTGGCCACGCGTAATGCCGATAGTGTAGTTTCTTCCACAATACCTTCATCGGG\nAAGTGCCGGTCGTAAAGATAATCCACCCTGCCTGCATAGCATGGTTCCAAGTTTAACCCC\nAACTGATTTATAACACACTCTATATCGAAGTGGAACCCCATCAGTATCCAAGTAAAAGGT\nTAAATTTTTTCCAAACAAAGCGTCTATAGAAGATCTGGCTTCCCTAAACGTTTGCACCAC\nAGACGCCTCCCCCATAAACGCGGCCACCCGCGCGCGAATGCATCGGGATTGGTCTTCTAG\nACATACACCCGACATGGCGGGAATAGGAGCAAACACTCCGTTTGGAGACGCGGGTGGAAA\nAATCTCAGCATAACTTGCATACAAGCCTAACCGTACCATGAGTAAATTTCGAAATGTCAT\nATACTGTGTTTTTATCCATATAGGCAAATGTGTAAATTGATCGAAATCATGTAATAACAT\nACGAAGAACGTCATGGTCACTCTCCGTTGGAATACGTTCAATTAAAGCTCGTAAGCGAGA\nCGCGGTCTCTTCAAACTGTCTTTGTTTTTGCAACACAACATCCAACGCCGTTTTACGTTC\nCTGTTGCTTTTTGTGGAAACGAAAAACCGTCTCCAAAAAAAGCAACAGGAACGTAAAACG\n>comp20_c0_seq1 len=1333 path=[0:0-959 960:960-1077 1078:1078-1332]\nATGTTGTGCATATACCACGTATTCCCCCCGTATTGATATGATTTAAATGATTATCCTTGG\nTTGGTTTTGGTCTAACATAAGATATAAGCTCTACTATAGCGAGCGTGCATACAACAACCC\nAGGCCAGAATCCGAATGTATGTGGGGTATAATAACGCGCATGGTGTATATGCAACGCCAA\nGCGTTAAAAGCACAATACATCCAGATGATATATGAGCGATAACCTCCAAAAGCATCAATA\nACGTAACACCTTTATGCATATATAAAAAACTTATAGGGTCAGCATTAAATACTTTACTCA\nTACCATCCCGTCGCATGGAAACATCACATAACAACCTTGCCAACTTTGTATATGGGTAAC\nCAAGAAGAATGTTCGAAATAACCCGTGTTACGTAATTCAGTGAATATGATGTGGGGGATA\nTTAACTCACAGGATGATCGGAATGGCCCAAACATACGACGTATTCGTCGAAATTGTAAAT\nACATACCATATACAAACCATGCAAAAAAAATCATTTTTAGCTGCACGCACCAAAAATAAG\nCGTGACAATTACGTGTTCCCAGAACAATTCGAATTTTGTCATGCAAAGGTGTAGAAATAG\nCGGTTTTTACCATAGTATCTCCTGATAATAGATTTTCCCGGCAGCTGTAATCGTATCCAG\nATAGGCCATCCAAAAACGTTGAGTGGTTTACAAACGTTACATATATAAGAGAGTTGTTAT\nAAGACCCCCATACAACCGGTCCACCATTAATCACCGTGGTTGCATACACACACTCATGTT\nCAAACTTTACACGAGCGGTATACCATAGGGTAAAAACAGCATGTCCGCTAAGTAGACACA\nTAATTATAAAATGTTCTGTCTTGATTCCTAAAGCCTGCATGACCCGTGGAAGATGGCAAT\nTCAAGCACGATGTAGTATCACACGGTTGGTGTTAACTCGAAGTTAAATTTGGATAATTAG\nGTACTTCTAGAGTAAAGATTGTATGCATGCGATTGCTATCGCACTTTGTAGCAAAACATT\nGTTGTGCAAGCGAAATACACAAACGGTTGTGATGATCCACTCGCAGAGACACAAATGTCC\nGGGGAGCCGTTCTTCCTCCGCGATGGGGATATCGAAGACAAGTGAACCCTTTTGTTCCGC\nATATGAGCTGAAATAACACCCAGTCCCTTTTGATGGCGATACACTTTGATGATGTTAAGG\nTATATTCGCGATCACGCCCGGGGAAATGAACAGCAATATGCTCCACAATAGATTCTAATA\nTTGTGCTGTCGACAAAGGCCTCCAGTGTAAATGCGTCCAGACAAGTTACCCCGCGCTCTT\nTTAGAGCCTTTGT\n>comp1_c0_seq1 len=1819 path=[0:0-1818]\nTTACTGTAGCGCAACATGTTGTGCTACAGTAATGTCCGGCCTTGCTATAAAATGTTTTTA\nTATCGTCATATTTGCTATAGCAGTGGTTATTTTTATGCATTACGAACAAAGGGTGCAGGT\nAAGCTTGTTTGGGGAAAGTGAAAACTCCCAGAAACATTAATCATGTGACTAAACACGCCC\nATTGCGGGGTTGGGTGAGCCTATAAATTCTACAACATTGGCGGAAGATACAGGCAACTGC\nAAACACGCAATTGTCAGATATTTTGCAGCCATGGCCTCTGCTTCAATTCCAACCGACCCA\nGACGTGTCTACTATTTGTGAAGACTTTATGAATTTGCTACCAGACGAACCTTCGGATGAC\nTTTGCATTGGAAGTCACCGATTGGGCAAATGATGAAGCTATTGGCTCCACTCCAGGCGAG\nGACTCCACAACGTCTAGAACTGTGTATGTGGAGCGTACTGCAGATACAGCATATAATCCA\nCGGTATTCCAAACGAAGGCACGGAAGGCGTGAAAGCTACCACCACAATCGCCCGAAAACT\nTTGGTTGTTGTATTACCCGATTCAAACCATCATGGAGGAAGAGACGTGGAGACTGGATAT\nGCACGCATCGAACGGGGACATCGACGATCATCCAGATCTTATAACACCCAAAGTTCAAGA\nAAACACCGTGATCGATCCCTGTCAAATCGAAGACGGCGTCCTACAACGCCTCCTGCAATG\nACCACGGGAGAAAGAAATGATCAGACACATGACGAATCGTACAGGTTGCGATTTTCCAAG\nAGAGACGCCCGCCGAGAGCGTATTCGAAAAGAGTATGATATCCCGGTCGATCGAATTACG\nGGCCGTGCTATTGAAGTCGTCTCCACCGCGGGAGCCAGCGTGACCATTGACTCGGTACGC\nCATTTAGATGAAACAATTGAAAAACTGGTAGTCCGATATGCCACAATACAAGAGGGTGAT\nTCATGGGCTTCCGGTGGATGTTTTCCGGGGATAAAACAAAACACATCTTGGCCGGAGTTG\nATGTTGTACGGACATGAACTTTATCGTACCTTTGAGTCATATAAAATGGACTCACGTATT\nGCCCGCGCGTTGCGTGAGAGAGTCATACGTGGAGAATCTTTGATTGAAGCGTTGGAGTCT\nGCGGATGAACTGTTAACGTGGATTAAAATGTTAGCGGCAAAAAACTTGCCCATCTACACA\nAATAATCCCATTGTTGCAACCTCGAAGTCACTTTTGGAGAATTTAAAGTTAAAGCTGGGG\nCCTTTTGTAAGATGTCTTCTTCTAAACAGGGACAACGATTTGGGGTCTCGTACTCTCCCC\nGAACTGTTGCGCCAGCAACGTTTTAGTGATATCACGTGTATTACTACTTATATGTTTGTT\nATGATTGCCCGCATTGCTAATATAGTTGTCCGTGGCTCTAAATTTGTGGAATATGATGAT\nATCAGTTGTAACGTTCAAGTGTTACAAGAATATACACCCGGGTCATGTCTGGCCGGTGTT\nTTAGAGGCCCTAATCACCCACCAACGCGAGTGTGGTCGTGTTGAATGTACCCTCTCAACT\nTGGGCCGGGCATCTTTCTGACGCCCGTCCATACGGTAAATATTTTAAGTGTAGTACCTTT\nAACTGCTAAAATAAAAAATACCTTTTTCATGCTTGTCAAAACATACTAATTTGTATTTTT\nAATCATTAAGCATATTTACCTGTTAGAATAGTAAATACCTATTTCATGCTTGTAAAACAT\nATCAATTTATATTTTTAATCATTATACACCACCCCTTGATTTTATCAATTGTTTATGTGA\nTTCTATATTAATAAAAGAC\n>comp11_c0_seq1 len=3180 path=[0:0-3179]\nTTTAAAAATCCATTAAAGAGCCATTTCCATTTTTAGGGGGGGGTGTGGATTATATCCATC\nAAGCTGAAAATCGTCCCATTTAAAGTCGTTTATATCTGTTACATTTCGAATAATTTTAAG\nGCAAGGAAAAGGTTTTGGGGATCGAGCTAGCTGCACTTTTAAAGCATCTATATGATTCAA\nGTAAATATGTGCATCCCCCATTGTATGAATTAAATCTCCGGTTTTAAGTCCTGTAACATG\nCGCTACTATGTAGGTAAGAAGTGCATATCCAGCAATGTTGAACGGTACCCCAAGGCCCAT\nATCCCCCGATCTCTGGTATACTTGGCAGGATAATTCACCGTTTGCAACGTAAAACTGACA\nTAACGTGTGACATGGAGGTAGTACCATTAAGGGGATATCCTTTGGATTCCAAGACGATAT\nAATCATTCGTCGGCTTTCTGGGTTTGTTTTAATTGTATCTATAACAGTTTGCAGCTGATC\nGATTCCTTGCTGTAAATAGTTTGATTGACAGTCTTTATATTCCGCTCCAAAATGTCTCCA\nCTGGAAGCCGTAAATGGGGCCAAGGTCCCCCGTGTGTCTTTTATGGAAGCCATTCCTATT\nTAGAAATTTGCTCGATCCGTATATATCCCATATGTGTATATCTTTAGCGGCGAGTTCTTT\nGGAATCGGTTGACCCGCGGATAAACCATAACAACTCTTCCACGACGGCCCTCCAAAAAAC\nACGCTTTGTAGTTAAAAGAGGAAATTCATTTCGCAAATTGTATCGAGCTTGCATTCCAAA\nTAAAGATAACGTTCCGATTCCTGTTCGATCGCGTTTCCGAACTCCATACCTTAAAATATC\nATCCACTTGTTTTAAGTACTGAAGTTCGCCGGTTAACGTAAAACCCGGCACTTTTGTCCA\nACATGACAAGTCTCCCATGGTACCGGTAATAATCGTTAAATACAAACGACCACTTGATAT\nTGTGGGTACATTAAGTAAAATTTAAAGGAGTAATTCCTTTTATAACCCAATCAACCAATC\nAGACCTTTAAATAACGCAGTCCAATTATTGAACAGAAAATACGCAATAGACTATTTTCTC\nCCAAATCCCCCAATTTTAACCTGGTTGTGGAAATGACCGCCAAAGTGCCTAGTCCATAAC\nTATCTATTAACCGCTGTACTTAATGATGACTCTTAGGCGTATTTTTCCTAAACGTAACCG\nTGGTTTTACATCTAACGGGAACGTCGTTGGGTATAAAATCTGGTGATAAGTCATCGTCTG\nTATGCATGTCTCCGGAGGTGTACCCGTTAAGGCTATCCACATCCGGGTCTGAAGATGAGT\nTAAAACCCACTTCCTTGGGTGGTATATTTTCATATACGTGATCATTTAAAGATGCTTGGG\nTTTCTATGTGACGTAAATCCGATCTTTGGTCAAACATTGTGTTTGATTCATCCCGAACCG\nGACCTTCATATTCCGCCTTTATCCGGGTGTAATGATCAGGATACGTTGGGTCAACTGGAC\nTACCGTCCGTATGGCCTATGTCCAGACAGTGGTTTTTTCGGACAGTTACATCCAAACCCG\nTGTCTGGACGAACTAAAACGCGAGAAGTCCGCTGTCTATTTGTATCGGGTGCTATACTGT\nTTAACGGTGCTTCCGTATTAATTACATGCGAACTTGCATTTACGTCGTCAGATAAATAAT\nTTCCCGTTAAACAGACACATTCCAAATTCCCTATACCTGTCCCTATTGGAGATCCCAGTC\nGATTAAAACGAATATACGGCTGATCAGACACACTCGATGGTTCGGATATACGTCTTAAAT\nGTAACGGAGTATACCGTTTACTGGCGGCAAGAACCTGAGCATAATACTTTGTGGGTTTAC\nCCCCATGTGCTAAAATACTCTGCGCCACGGCCCGGGAAAACCACATATGGGTGCTGGTCT\nCTAACACAACCCAACTGTGTGTTGACATTGTTCTAACCAACTGACCCGCAAAATATAAAA\nACCGTCCCTGGGCGCGTAGCGCCTTTAATATATAAGGATCGTTTAATCCCCCATCCCCCC\nAACATGCATATCCAATAAGCATCATATTAATTAAGTATTGAAAATGGTGGTGCAAAAGCG\nTAATAAGTTCAACCGCCGCAACAATTGCAGCTGCGGTTCCATTTAAACCATCCCGCCACT\nCTTCCTTTCGCCATAATACACTAATACGCAAAAGCGCAGTAAGAGCGCTGGCAGTTGTTG\nCTGCTAAAATAAACGCAACTCCTGTGCCCGCTGAGACCGCAGGACCCGTTTTTAAATGTC\nGTCTAAGCAAATCATCTGGAATAACAGACGCGCGCGGCCCTCGAATCCGTCGAAATTGAA\nGTTTGAGATGGCGACATACCCTGGCGTCCACAACGTCCAAGAACCATAACATCCACCCGT\nAGCCAGTAGCCGTGTAAGCCGCAATTTCTTGTACACGTATTCTTGTATCCGGGCTGGGGT\nTTGTAGGATCATCTGGACGCATAAAATACATATACTTTTGCACAGCTCCTAACGCCTCAC\nGTAGCTCCTGACATATTCCCCGGTAATCCGAATTTATAACTTTAGATTTAAAAGGATGTC\nTGGATATTGGTTTATTGGCAACTACGGATGAAAACAACAAAACCGTGGATTTAGACTTTT\nTATTTACCTTCTCTGAAGTCACCGGTACCTCGGCTCCTGTGGTGTATTTGAGATACTGCC\nAATATGTATTTTCATAAACCCACCAAAGTCCATCCCCAGAAAGTTTCAGGTCATCCAAAC\nATCTTTGAATTGTTTCCATATAACGCTGCATAAACCCGTCATGAACATCGTTAGACATAC\nACGAGACCACCAACGATTCAGGAACATTATTATGGTGTAATCCAAGCAGAACACTGTGTC\nTTTCGGTACTTTGTAAAACCGGCGATGTTAGGCTGTCGGTCTTTTCAGATAAAGCCTTTA\nCCGCCGTCTCCAAAGCCTCGCCGGGCGTTGGAATAAGACATCCATCCCTCACGCGCTCGC\nTGGTTATGCGTTGGGAAATAGAACACCAGTCCCGGGTAGGTGTGGGCAAATCACGTTCGC\nCGGCATTAAAACTTTGGTAACTACCATCATAAGATTTACGCGTTCTATCATCGCTGGAAA\nAGGAACGCGCAAACCGAGAAAACATTGCGATATGGACAAATTATATCTTGTAAAGGTCGA\n>comp38_c0_seq1 len=794 path=[0:0-793]\nCCTGCAACCGTATAAGCGCATCCATAACAGAATGTGACGTTAAGGCGCCTTGATCATACC\nGCCCCCCACGAGCATGAAACTGGTCGCGTGGTAGACGATCATAGCAAAATTGATAACTGT\nTTTTATTTTCGTGTGTTGTCATATAATTCACAAATGTCTCAGTATATTCCGGTAGGTGCT\nCTATAAGGTTCCCGAAGGACGAAACTTGAGGTTCGTGGACACTATTAGATGTCCTATACA\nTTAAATATAAACATAATACCGCACACTCGAACGCGGAGTACGCTCTATCTCCAACATACA\nTTCTCCCGGCGGACTGTAGACATGTTACCGTTGTGTTCATAAACGTACGGGAAATGCGCC\nCGTCTTTACAATCAACTCCGCGTGCAGCTACGGGCCTATCTAACACAAGCCGTTCCTGCA\nGAGTACGATACCATGGCCCGAAAACAATCCCTGGAGAGTTATTGCCCCTTGCCCTTCCCA\nAGTACACCAGGGTGATAAAATCCACTTGAAAGTTTGTATCGTACTGCAACGGTGCATCAT\nTTTTGGCAATCTGTACCTCGGGGTGTATAGACTCATTGCGTATTATTTCTGTACGTGTAC\nATTCCTCAGATTGTGCATCTGCTTCTTCCGCCTCGGCAGCAGCCGTCTCCAGGGAATCCA\nAAACCTTGGCCATGCGCGTTAGTTGGTCTTCGAGGGGCTTTAAACGACGATCTATTTCCG\nTTGGTAACGTAATCGTTTCCCCGCGAAGGTTGTCTAATGCGGCAACGGCCGCCGCATTAG\nACAACCTTCGCGGG\n>comp61_c0_seq1 len=346 path=[7:0-345]\nGTATACGTATCTGTTTGTAATGCCAAAGATAACAGCCCCCCCCGCACATTGCCGATCAAA\nAGCTCGCTTCCGTTGAAATTAACATTATCGACATACGCGCTAAAGGGGGCGGTTGTAAAG\nCTGCTTTCGAAAAGCTCTGCTAATATGGCATATCGACCATCGTAAATAGCTTTCATTAAC\nAGAAACTGAGCATGGACCTCATTGGATGATTTGGGATAGGAAAATTCGTACTGGCAGTAT\nACCAAGTCAATAACCTCGTCGTTAAGTGCCGTAAAAATTACATCATCCGGGTCTTCGGGT\nATGGAGGCCGTTACTTTGGACTCGGGGGCTCTGGTAAAGCAGAAGG\n>comp0_c0_seq1 len=1738 path=[0:0-1298 1299:1299-1737]\nATTCTAATGTCCGGGCATCCAAACGCATGGCAGTTCTGCTACGTGTTTGGATGCCCGGAC\nATTAGAATACAGCCAGTTGTTACCATGGATACCATATTAGCGGGCGGTAGCGGCACCTCC\nGACGCTTCGGATAATACCTGCACCATATGCATGAGCACCGTTTCCGATCTCGGAAAAACC\nATGCCGTGTTTGCACGACTTCTGCTTTGTTTGTATTCGGGCATGGACCTCCACCAGCGTC\nCAGTGTCCTCTCTGCCGGTGTCCAGTGCAATCCATCCTGCATAAGATCGTAAGTGATACA\nAGTTACAAGGAATATGAAGTGCACCCATCCGACGACGATGGTTTTTCTGAGCCGTCATTT\nGAAGATTCCATCGACATCCTACCGGGAGATGTCATAGATCTTCTGCCACCAAGCCCAGGA\nCCGAGTCGGGAGTCCATCCAACAGCCAACATCAAGATCGAGTCGGGAGCCCATTCAATCA\nCCAAACCCTGGGCCCCTTCAATCGTCGGCTAGAGAGCCCACAGCAGAGTCACCAAGTGAC\nTCTCAACAGGATTCTATACAACCACCGACCCGAGACTCGAGCCCTGGTGTAACCAAAACA\nTGCTCTACCGCATCATTTTTACGGAAGGTATTTTTTAAAGACCAACCTGCTGTTCGATCG\nGCGACCCCGGTGGTGTATGGCTCGATTGAATCTGCACAGCAACCCCGGACCGGGGGGCAG\nGACTACCGTGATCGTCCAGTATCTGTGGGAATTAATCAAGACCCACGAACCATGGACAGA\nCTGCCTTTTCGAGCCACGGATAGAGGAACAGAGGGAAACGCGAGATTCCCGTGTTACATG\nCAACCTTTACTCGGATGGCTTGATGATCAACTTGCGGAACTGTATCAACCCGAAATTGTA\nGAGCCTACAAAAATGTTGATATTAAACTATATAGGTATTTACGGGCGTGATGAGGCGGGA\nTTAAAAACATCCCTGCGTTGTCTTTTGCATGATTCAACAGGACCGTTTGTAACAAACATG\nTTATTCTTGTTGGATCGATGTACCGATCCAACCCGCCTAACCATGCAAACCTGGACCTGG\nAAAGATACAGCCATCCAACTAATTACAGGTCCAATTGTAAGACCAGAAACCACCTCAACC\nGGGGAGACCTCTCGTGGCGATGAAAGGGATACCCGATTGGTAAATACACCCCAAAAAGTC\nAGGCTTTTTTCTGTGTTACCGGGGATTAAACCGGGAAGCGCAAGGGGTGCTAAGCGCCGT\nTTATTTCATACCGGCAGAGACGTTAAACGATGCTTAACAATAGACCTGACATCTGAGTCT\nGATTCGGCATGTAAGGGAAGTAAAACCCGCAAAGTTGCCTCTCCACAGGGGGAGTCCAAT\nACCCCCTCCACCTCCGGATCAACATCAGGTTCACTGAAACACCTTACCAAAAAAAGCTCT\nGCCGGTAAAGCGGGTAAAGGTATTCCAAACAAGATGAAGAAGTCCTAGTTTGTTGGGAGG\nGGGAAGGAAATGCCTTAAACATCCACAGTCTGCTTTATTACCAACTGTATGTAAATTATG\nATCATTAAACGTGCATTTTAAAAATACCTGAGTGTTGCTATTGGTCGTAAGGGTTGGTAT\nATCTGGAACCCAAGGTGTAAATACTGCCCCCTGGTAAGTCCGTACACGATTCGGAATGCC\nCGCAATCCGGTCTCGGAGTAACCGGGGCATCCTGCTCTGCAAATACAATAAACATAAC\n>comp0_c0_seq2 len=463 path=[1756:0-23 1299:24-462]\nTCTATTGTTAAGCATCGTTTAACGATAGACCTGACATCTGAGTCTGATTCGGCATGTAAG\nGGAAGTAAAACCCGCAAAGTTGCCTCTCCACAGGGGGAGTCCAATACCCCCTCCACCTCC\nGGATCAACATCAGGTTCACTGAAACACCTTACCAAAAAAAGCTCTGCCGGTAAAGCGGGT\nAAAGGTATTCCAAACAAGATGAAGAAGTCCTAGTTTGTTGGGAGGGGGAAGGAAATGCCT\nTAAACATCCACAGTCTGCTTTATTACCAACTGTATGTAAATTATGATCATTAAACGTGCA\nTTTTAAAAATACCTGAGTGTTGCTATTGGTCGTAAGGGTTGGTATATCTGGAACCCAAGG\nTGTAAATACTGCCCCCTGGTAAGTCCGTACACGATTCGGAATGCCCGCAATCCGGTCTCG\nGAGTAACCGGGGCATCCTGCTCTGCAAATACAATAAACATAAC\n>comp35_c0_seq1 len=1453 path=[0:0-1452]\nCGATACATATGTACCACATAGATAGCATAGATTTATTATAATATAAACACACACGTGATA\nTACTTTAGTGATATGAGATGCCATAAAACAGTCAATAGGTTTAACGCTTAGTCTCATCAT\nCTGAATACACGTCAAACCCGCCGCAACTGTTGATGTTAGAATTATAATAGCTCCCCATGA\nAATGCCGGCAAATGTTACAGCTATACCCGTCACCGAGGTCGTTGTATATAATACAATTAC\nCCATAGGTTTTTTTTTTCTTGATATAAAACGGCAAAACCCTGTAACCCAAATGCTATAAT\nATGACCTCCTATTGAAACTGCTAACGTTACTTGTGTAAGTTTGATAAAATGATTTAATTT\nAATTATATGTGAGATTGCCCACATTAATGGGGTAACTATATATAACACCGGGGGTATAAC\nAGACATTATACGAATTCCTTTAAACACGCGTTTAAGGGTCCGGGAACTTTCTCGATGGTC\nACATACTCTCCCGCGGTCATTTTGTGTATATACAACGGCAAAACCTAAATCTGTATAAGT\nGTTTAATTGCTTATGGCGATTTTTACGATATATACACGTATCTTGCAAATCGGTGGCGGC\nATCGACAATTGAAACTAGTGTGACAATAGATATACACAATCCAATAAGAACCTCATATTT\nACTGACATACATATATAAAATAACGGTTAGTAAACCTCCCAACCCAGTTCCCAACATCAT\nAACATAAAAATAAATATGCGGTCCATTGAATGTCGTAACAAAGTTGTAGTAATGGATATG\nCACAGCAGCCACTGTTCCGGTAATCGCGGATATGGAAATTCCCAGTAATTCTACAAATGG\nAAGATCCCGGGATATTGGGCAACCAACCGCCCATAACACAGCAAAACCCAACACGACCAC\nCGTCTGCAAACATCGTCCCAATTTTGCTAATGTGCGTAGAAATTTCACGGATGTTGGCCA\nTAACCCCGAAACGACGATCAACCCCATAATAGTTGCATTGACGGCAGCTTCGCAGACGTG\nATATTGTAAAATTAACCCGGACGTGATAACACTTGCTTGTAGTCCCACGAGAAACAACCG\nCGATGCTGAGGTTATTGCACACGAATTACATTCTTGAGGGTTTCCGACACATCCTTGGAT\nTGATTGAGCGCGGATTAATTCTCTGTCTAACACACCCAGGTTTTCATCATGGACAGCTCT\nTTCACCATTCACGGCCATGTCTTAAGTTTAATAATTCAAAACAAATAAAAATGTGTTCAT\nCTATGGTACACACAAGTTTGTATGTAAAATATAAGCAAAAGTTGCACTTATTTAACTGTA\nCATATTACGTCAGATTCACGTGATAATTCAGAATAATCCAGGGTTCCTGCAGGGTCCACT\nGGAGGAGCCACACAATATTCGCGAATTCCGATTCCCTCCTGCCATGTGGTTTCGGAATTC\nGCGAATATTGTGT\n>comp34_c0_seq1 len=2955 path=[0:0-2954]\nGAGTAATACCCCATCTTGAATCCATACGTAGGTCAAACCAGGTTAGTACGGCTTCGCGTA\nCGGCACTTTGTCCTGCTTGTGGATTCAAGATGGGGTATTACTCCCCCGGTGGATGTGGGT\nATGACACCTCCTATTTGTGTTGATCCACCGGCTACAGGGTTGGAAGCTGTCATGATAACA\nGAAGCACTAAAGATTGCATATCCTACCGAATATAATCGCTCTAGCGTGTTTGTGGAACCG\nTCGTTTGTGCCTTATATTATTGCAACAAGCACGCTTGATGCCCTTTCGGCAACAATAGCT\nTTGTCTTTTGATACACGGGGAATACAGCAAGCCTTGTCTATTCTTCAGTGGGCTCGCGAT\nTATGGATCCGGAACCGTGCCCAATGCAGATGGATATCGCACAAAACTATCTGCTCTTATA\nACAATATTAGAACCTTTTACCCGTACACACCCCCCAGTACTTTTACCATCTCACGTTTCT\nACTATAGATTCCCTTATATGCGAACTTCATCGGACTGTTGGCATTGCCGTTGACCTGCTT\nCCCCAGCACGTCCGTCCTTTGGTTCCTGACCGTCCTTCTATTACAAATAGCGTTTTTTTA\nGCAACTCTCTATTATGATGAACTTTACGGTCGTTGGACCCGACTGGATAAAACATCGCAG\nGCGTTGGTTGAAAATTTTACATCCAACGCGTTAGTGGTTTCTCGGTACATGTTAATGTTA\nCAAAAATTTTTTGCGTGTCGTTTTTATCCAACGCCAGATCTTCAGGCCGTTGGTATCTGT\nAACCCAAAGGTTGAACGCGATGAACAATTTGGGGTATGGCGTTTAAACGATCTTGCTGAT\nGCGGTTGGTCATATTGTTGGGACAATACAAGGAATCCGAACGCAAATGAGAGTGGGAATA\nTCCAGCCTGCGCACAATTATGGCCGATGCTTCCTCAGCCCTTAGGGAATGTGAAAATTTA\nATGACTAAAACCTCCACTTCTGCTATTGGGCCTCTTTTTTCAACGATGGCTTCCCGGTAT\nGCACGGTTTACACAGGATCAAATGGACATTTTAATGCGTGTTGACAAACTAACAACAGGA\nGAAAATATACCCGGTCTTGCAAATGTAGAGATTTTTTTAAATAGGTGGGAACGAATAGCA\nACAGCTTGTAGGCATGCCACGGCAGTCCCGTCTGCCGAATCTATTGCAACCGTGTGTAAT\nGAATTGAGGCGCGGTTTAAAAAATATACAAGAGGATCGTGTAAATGCCCCAACCTCATAT\nATGAGTCACGCCCGAAATCTGGAAGATCACAAGGCAGCAGTTTCATTCGTTATGGACTCC\nAGGCAACAGTTTATTGTGGATTCTGGACCTCAGATGGGCGCGGTTTTAACTTCACAATGT\nAATATAGGAACATGGGAGAATGTAAATGCAACGTTTTTACACGACAACGTTAAAATAACG\nACAACGGTCAGAGACGTAATTTCAGAGGCTCCGACGCTGATAATAGGACAAAGATGGCTT\nCGTCCAGATGAGATTTTATCTAATGTAGATTTGCGTCTTGGCGTACCCGGGAATACAAGT\nGGGAGTGACCCTTAATATAAAACAGGCGTGTTTATGTACATTAAAGTATTTGTGGTTTTT\nATTGACTGGGCGTTTCGTTTGTATAACGCTGTTGTTGCTAGTATTTTCATAACCTCCTAG\nGTTTTTGGAGCTACACGTGCTTATTCAACGCTCTTTGGGATTTGAATCATCGTAAACGTA\nGCGTCCCTACCAGTTGAGCGCGTAATTTTCGTAAGCAATAAAATGGATATAATTCCGCCT\nATAGCTGTCACTGTTGCGGGAGTGGGAAGCCGTAATCAATTTGACGGTGCCCTGGGACCG\nGCGTCAGGTCTGTCATGTTTAAGAACATCTTTATCGTTTTTGCATATGACATATGCGCAT\nGGAATTAATGCAACCCTGTCATCAGACATGATTGATGGATGTTTACAAGAGGGTGCAGCA\nTGGACTACGGATCTGTCTAATATGGGGAGGGGTGTCCCAGATATGTGTGCTCTTGTTGAT\nCTCCCCAATCGAATTTCATATATTAAACTGGGGGACACTACCAGTACGTGCTGCGTTTTG\nTCTAGAATATACGGCGATAGCCATTTTTTTACCGTTCCAGACGAGGGTTTTATGTGCACA\nCAAATTCCCGCTAGAGCGTTTTTCGATGATGTGTGGATGGGACGTGAAGAGTCGTATACA\nATTATAACTGTAGACTCAACGGGAATGGCCATCTATCGTCAGGGAAACATATCTTTTATT\nTTTGATCCACATGGCCATGGGACTATAGGACAGGCTGTAGTTGTTCGGGTGAATACCACG\nGATGTGTACTCTTATATCGCATCGGAGTATACCCACCGCCCCGATAACGTAGAATCCCAA\nTGGGCCGCTGCATTAGTTTTTTTTGTCACCGCAAACGACGGTCCCGTAAGCGAAGAAGCG\nCTATCTTCGGCAGTAACGCTTATATACGGAAGCTGTGATACATATTTTACAGATGAACAA\nTATTGCGAAAAACTGGTTACAGCTCAACATCCGTTGCTTCTTTCACCTCCTAATTCCACG\nACAATTGTGCTTAATAAATCGTCTATAGTACCTCTTCACCAAAACGTTGGTGAAAGTGTA\nTCCTTGGAAGCAACCCTACATTCAACGTTAACCAACACGGTTGCACTGGACCCTAGATGT\nAGTTACAGCGAGGTTGATCCTTGGCATGCGGTTCTAGAAACAACCTCGACTGGGTCTGGC\nGTTTTGGATTGTCGTCGTAGACGCCGTCCTTCATGGACTCCTCCTTCAAGCGAGGAAAAT\nTTAGCTTGTATCGACGATGGCTTGGTAAATAATACACATTCCACGGATAATTTACATAAA\nCCCGCTAAAAAGGTTCTCAAATTTAAACCAACTGTAGACGTGCCGGATAAAACACAAGTG\nGCACATGTATTACCC\n>comp39_c0_seq1 len=1502 path=[0:0-1501]\nGAGACACACTATATTACAGGTCATATGGGTAAGGACTACACGCAAAAAAGAAAACACAAC\nAGAATATGTAATATTGACTTGTTTATTACGTACACTCACCCGCGTGTGGGCTTTAATTGG\nATAAAGAGGGAGGTTAAATCATTTCCATTGTAATGTTCCCATGTTTTATGGGAATACCAC\nTAAGATCAAAGAGTTCGTCATCTTCGGGGGGTCGTTTAAGACCAGGGACAGTTGACCCTG\nAAATGTTTAATACGTTAGATGTGGTGTCATGGCTTGGTTCACAAGAATCAAAATTAAATG\nCTAGGTTTGTGGGGGTTTCCCCATCTCCCGCTGTCGTTTTTTCATCTAGAATCTTTACGG\nCTTCTAGAGCGCCTTCTACGGTCCAGGGCGTTTCCAGGGTTTGGATAATCTGGTCGTGTA\nACTCCTCCAAGTCTCTGGCTAAAAACTCATCGTCTGTAAGACTTAACCAGTCGTCAAATG\nCCATATGTTGTGCTCGAGCGCCCACTGCACGCACAACCGTGGCGTATATGGCTAATTGAA\nCCATGGCCCCGCCACTGACAATTATACCGCGAACTTGGTCGGATAGGGTGGTTTCTCGAT\nTTCCCGACGAGGGACCTGTTACGGGGCAGATAAAACCTCCTCTAGGACATGCTATTATAA\nAACGGCGAGTGCGATCAAATGTAAATAGCGGGCATACATTTTTACCCCCGTTTAAACCGC\nTCCAATTCCCTGCCTGAAAGACGCGGTTGTTTCCTGCCGCTCCGTGATATTTACTAATGC\nTTATTCCTAAAACGACCATGGGACGTTGATTCATGGCCGCGCGGACTAAATGAGTTGAAG\nTAAAAGCCGTAGTCCATAATTCCGGTAAGTTTTCCGTTTTTTCAAGAAGCGCCTTTGCTT\nGGGTTTCTATGTCCGCGGCGGACGTGACATCTTTACGAATCCAATGCAAAACGGATGATG\nGGTCACGCGGGCGCCTGGCACCCGTAATTATAGAAGTTAAGGTATTTATAAGGTACTGTG\nAATGATCGCAGTATTTAAGAATAAGATTTGCCATATAAAACTGGGCTAATTCTCCTATGC\nAGGTTGGGGGTAGATTAATAAAGTTTATTGCTGCATATTCCTCGGTAAACCGTTTAACAG\nCTGCAATAGTGGTAATCTCTTCGTGTGTAAGTTTATCTGCCGGCATCTGGTTGCGTTGTA\nACAGGGTCCAAAACCACTGCGGGTTGGGGGATTTACTGTTTGGTGGCATACCCCGAGGAA\nATAACAGGCCGTGAAACTGTTTAAGCAAAAACCCTAGGGCCCCGTGTAACATATCCACTC\nTTTTTTCTTGGCGTTGGTACGCACTTGCAAGGCCTACAAGCCTTGCCCGGGCTGCCTCAG\nAGAGATTTGTACAGTTACCTGAAAAAACGACCCTATTTTTAACTCGTATATCCCGAATAA\nCTTCCACGCTTACGCGCGCTAAATCCCCATCAAAGGTACGCCCCGCGGGCGCGTCTTGTC\nCC\n>comp41_c0_seq1 len=938 path=[0:0-937]\nTAGCGTTGGGTTTCTCGGCAAAGGAATGGATCCCTTTGCCGAGAAACCCAACGCTACTGA\nTACCCCAATAGAAGAAATTGGCGACTCACAAAACACTGAACCGTCGGTAAATAGCGGGTT\nTGATCCCGATAAATTTCGAGAAGCCCAGGAAATGATTAAATATATGACGTTAGTATCTGC\nGGCTGAGCGCCAAGAATCTAAAGCCCGCAAAAAAAATAAGACTAGCGCCCTTTTAACTTC\nACGTCTTACCGGCCTTGCTTTACGAAATCGCCGAGGATACTCCCGTGTTCGCACCGAGAA\nTGTAACGGGGGTGTAAATAGCCAGGGGGTTTGTTTTAATTTATTAATAAAAATGTGTATT\nACGTTACTCATGTGTCTCCATTACGCATCACAGGGGGTATTTATACCCGATAATATACAA\nAACGCGTTTTGTACCTCTACCGCACCCGATATCTTAACGGGGTTATTATGGAATCGTCTA\nACATTAACGCGCTACAACAACCGTCGTCTATCGCACATCATCCGTCCAAACAGTGCGCTT\nCAAGTCTCAATGAAACAGTAAAAGATTCTCCCCCCGCGATTTATGAAGATAGGTTAGAAC\nACACGCCGGTACAATTACCCCGCGACGGTACACCCCGAGACGTATGTTCTGTGGGACAGC\nTAACCTGTCGAGCATGTGCAACGAAACCTTTTCGCCTTAACCGCGACAGCCAATACGACT\nACTTAAACACATGTCCAGGGGGCCGTCATATTTCACTGGCACTGGAGATTATAACGGGTC\nGATGGGTTTGCATCCCGCGTGTGTTTCCGGATACCCCAGAGGAAAAATGGATGGCGCCAT\nATATTATTCCAGACCGAGAACAACCATCATCAGGGGATGAAGATTCTGACACCGATTAAA\nTTTAACTTAAATAAAACCTTACCACCCATAAAAACGCC\n>comp50_c0_seq1 len=606 path=[0:0-605]\nGCAACTTTCCCCCCCCCCCGGGGTAAAGGCCAATGTCGATGCAGTTACCCGTATAATGGC\nAACAGATCGTCTTGCGACCATTACTGTACTTGGGCGCATGTGTCTCCCGCCAATTTCCTT\nAGTGTCAATGTGGAATACGCTGCAACCGGAGGAATTCGCATACAGAACACAAGATGATGT\nGGACATTATAGTTGATGCGAGACTGGATTTGTCATCCACGCTTAATGCAAGATTTGATAC\nCGCTCCCAGCAATACCACGTTAGAGTGGAATACAGACCGTAAAGTAATTACAGATGCTTA\nTATTCAAACCGGGGCAACGACAGTTTTTACAGTAACGGGGGCGGCACCAACTCACGTTTC\nTAATGTAACAGCGTTTGACATAGCAACTACGGCTATTTTATTTGGGGCTCCTTTGGTTAT\nTGCCATGGAACTTACATCCGTTTTTTCACAAAATTCCGGACTTACTTTGGGGTTAAAATT\nATTCGATTCCCGGCATATGGCTACAGATTCGGGTATATCCTCAGCCGTATCTCCCGATAT\nTGTTTCTTGGGGGTTACGTTTACTGCATATGGATCCTCACCCAACTGAAAATGCATGTTT\nAACTGT\n>comp47_c0_seq1 len=833 path=[0:0-832]\nGGAGTCCAAGTATAACTCACCACATACAGAGGTTCTGTGCTTATCTGCCCGGTAAGCAAC\nAACAGCGAGTGGGAGATTGCACATCCCTTTGTGGCAAATAATAACCGAATCGTCGGTTTG\nGAGGATTTATCCATAGTTCAATACGTTGGAAAGCCAGTCAATCATGCAGACGGTGTGTGC\nCAGCTTATGTGGATATGCTCGAATACCAACTGAAGAGCCATCTTATGAAGAGGTGCGTGT\nAAACACGCACCCCCAAGGAGCCGCCCTGCTCCGCCTCCAAGAGGCTTTAACCGCTGTGAA\nTGGATTATTGCCTGCACCTCTAACGTTAGAAGACGTAGTCGCTTCTGCAGATAATACCCG\nTCGTTTGGTCCGCGCCCAGGCTTTGGCGCGAACTTACGCTGCATGTTCTCGTAACATTGA\nATGTTTAAAACAGCACCATTTTACTGAAGATAACCCCGGTCTTAACGCCGTGGTCCGTTC\nACACATGGAAAACTCAAAACGGCTTGCTGATATGTGTTTAGCTGCAATTACCCATTTGTA\nTTTATCGGTTGGCGCGGTGGATGTTACTACGGATGATATTGTCGATCAAACCCTGAGAAT\nGACCGCTGAAAGTGAAGTGGTCATGTCTGATGTTGTTCTTTTGGAAAAAACTCTTGGGGT\nCGTTGCTAAACCTCAGGCATCGTTTGATGTTTCCCACAACCATGAATTATCTATAGCTAA\nAGGGGAAAATGTGGGTTTAAAAACATCACCTATTAAATCGGAGGCGACACAATTATCTGA\nAATTAAACCCCCACTTATAGAAGTATCGGATAATAACACATCTAACCTAACAA\n>comp36_c0_seq1 len=1385 path=[0:0-1384]\nGCTTGTGGTAATAACGCACCTGAGGATTGATTATGTGTTTGCTTAAAATATGTTGTCTCT\nCTAGCTTCTGCATGAGAAATTTCATTAAGTAGTATTACGCGTGTCGCTTGTATACTTTCA\nATAAGGGGTCGTGGAGCAAAACAGCGCCGCATAATTTGTCCCAGGCCTCCCGGTGGTAAT\nCCTAAGGCGGGTAATAGCGTTTCATACCGTTTTTCGGTCTCGTTTACTGTCCGTGTATAT\nGTTAACACATACTCGGTAGTAGGAGCGTACGTTTCCACTAATTGGTATGCCAGTCCACCC\nACTAAAGCGAGACATCCTAGTGTTTGTTGGAAATCTGTAATATGCTCGTCTGCTACAACG\nCTTCCGTGAATAAAACCGGCGAGTGTGTGGTGAGCAATAAACCGACGTAGCAATTTGCAT\nGAAAATCTTGTAAACCCGGATTCGGCAAGGGTGCTTATTAACATACTAGGCGATGTACTA\nGCCTGAACCTTTTCCCAAATGCCACGGGTGTGTTCTGCTACATTACTTCCAGATGTGGTT\nTCCGCTTCCGGGTCGGAGTTTAGTAAATGTAACAGCGCCTCAATATGAATTCCGGGGGTG\nGACAACGATAAGAGGTTGCTTTCCCATATACCATTGTCTAATCTAAGTCTCCTAGCAAGC\nATTCCCGGGGATGTCTCAAAAACATAAGGGTCTCGATAAGCCAGAGCTGAAGAAATTCGT\nGACTCGTGCACCGTTCGTGGATTCGTTACCGCTTCTTCGATGGATACGAACGCCTCATCT\nTTAATTAAATTTACAGTATCTGCAAATAATTCTGATATGCTATGTACTGGCGTTTCCGTG\nAGATATTCATCAATCATACAGATTATAAAAAGGGCTCGTGTTAGAGGAGTGAGTGAGCTA\nTTTTGAATCTGATTCCACATAACATTAAACGGAAGAAGCCATCCTGCATATTGTGTTAAA\nACACGAATCCCCTCTTGAACAAATGGCATATCGTAAATGATCGCAAATTTATGTTGTGTT\nAAAGCTGCAATGGCGCTTTCCAACATTCCAATACGAGCGTGAGTGAATGGTGATTCAATG\nGCTGTTGTTGCATCCTTTAAGGCGACCTCGTACATATTTATCCAGTCCGTTATAATGAAG\nTGTATCGAAACGGGTCCAAATTTAGACGAGGTTCGTAATTTATTGGCCGATAAACGATGT\nAACGTCTCGGAATCTTGTACTACACTTGATAGCTGGGTTAAAATTTTTAAGCTATTACCT\nGGCTCCTCTATCGTCCAGTCTAGATCTAGTCTCCAAAACAACAGTCCGGGTAAATTTTCG\nGCCGTGAAAGCAGCCTCCGCCAAAAATGTATTGGAATATACAAAACAGATATTAGAATGC\nAGGGG\n>comp28_c0_seq1 len=2065 path=[0:0-2064]\nGGATATAAACTTGCAAAATCCAATACGACCACCGGATCGATATAAAATCCCGTATCAGGG\nTCAAAAACCCTGGCTCCTTTATATCCTACATTTCGCCCACTTGACGTACCAGTGGGAGAA\nACGCTCTCGTCTTCATCCATCTCTTCCTCAACATCCCCGACATCGGGAATAACATCCTTA\nTATTCAAAAGTAGCTGGGTATCCCCCATCGGGTAAAATAAATCCTCGAGACGAAGCCAGT\nCCTAATAAACAGGTGTAAATCCTAACCTGCTGTCCGTCGTAAATAGCCTTGGTTAAAGTA\nATTCTAGCTAGCCTTGCAACCGCGGATAACTCAAGGTGTGGTAAATATTTAAAAAACAGT\nTTCCCCACAAGAGCCGAGTCTTGTATACAATATTCACCAATAATTCCTCGTGTATTCGGT\nCCACTAGCGTAGTATCCCGGAATGTCTTTGTAGGGCAAATCTCTCTTGGACTCATTTAGA\nGCTTCACGTGCAACCGAATCTAATTTATAACTCGAGAGTTTTAATTTTTCAGTTGCAATT\nGCATACATATCCAGAGATATGAGACCGTTGATCTTTACCTTGCTTCGTCGCTGAAATCCG\nGATTTGCCAACATCCCATATCTTAAACAGACCCCCACGGTTTATACTGCCATAACCATCA\nAGCTTGAGACTGTATATAGAATTAAGTTTCTCCATAATAAACGCCCAATCAAAATTAACA\nATGTTATAACCTGTGGCAAACTCGGGAGCGTACTGTTTTACGAGGGTCATAAATGCAATT\nAATAGCTCGAATTCACTATCAAACTCCAGCACAGTCGGCTCCGGTAACCCCGCGTCCTTC\nATTTCTTGTACATACCTTTGTGGTAAGTCACAAGAGCCAAGGGAAAACAGTAAAATGTGT\nTCTAAAGACTGTCGAGGGATTGAATATAATAGACAAGAAATTTGGATTACAAGATCCTCC\nAGATGTGTTGCATCGGGAAACGCCAGCTCATTAGATCCTCCTGATTTACATTCAATATCG\nAAACATAACAACTTGTAGTCAGGCCATGAGTCATCGTTTGGTATAGCCTGCAGATTATCC\nGACATGCAGTCAATTTCAACGTCGCTTAACGTTAATTGGCGACTTGCCGGTCGAACTCGA\nACACGTTCCCCATCAACTCCAGGTTTTAGTTGATACCAACCAAAACTAACAAAGCCGGGA\nTTATCCATTAGAAAACGAGTGGTAGCGTCTACCCGACCTTCATACTTTTTCAACTCCGGG\nTGAAAGTTATCACAAAGATAATTTGTAAATTTAGATGAGGGAGAATACACCCTGTAAAAC\nGCACATGGCTGTGTATCGTAGTAATAAACATCTGTGCGCTCAATAACCTCAACGCGAAAG\nCTTTCTGGAGATGCGCTTTTAAACGAGGTACCATGAAAAGCGTTCTTGTCTCCATTTAAC\nGTTGCATCATTTTGTGTTATCATAGAACTGCGTAAACACTCGGCAAGTAATACAGATAAC\nTCGCTACCGGAACGTATGCCACAAGCGGTATCCACCTCGGCTTTGTTTATATAAAAATAT\nTGACAGATGCCGTATACATGAACTGCCACCCTTTTTCCACATCGGGACATGCCAAGTAAA\nGTAATAACGGTACCAAGCGGTCGTGTTGCAGTTGCAAACCGGGATACATCTCCATTAGAC\nGCGGCTTCTGTTGTTTCGACAATATCATATACATGGAATGTGTTAAAGCGGGGGTCAAAC\nTTATCCCCACGAAAGTCGATTTCCCCCCAAATATTCACGCGTCTAGGCCAGGGGCTGGAA\nCAACGAAAATCCAGAATCGGAACTTCTTTTCCATTACAGTAAACTTTAGGCGGTCGACTA\nAGTGTACCGACGTGAACCCCCTTTCGTTCTTCCATGGGCACATCTTCATCTAAACATTTA\nGGGGCCAAAAATTGAAACGATGACATGGTAGTTTTGTAACTATGAAGAAATTCTCTGTTA\nCTACCGCGCCCGGTTCTTGGGTTATATGTAATCCCTTTTTAACCCAAGCATCAGGGATTA\nAATATAACCCAAGAACCGGGCGCGG\n>comp59_c0_seq1 len=357 path=[0:0-356]\nGTATAACCGGGATGTTTTGTAAAATTCCACCACAAGCACCTAAAGAAGGCCTTCTAAGGG\nGTAAATCCACCCCACAAGCTGCATTTTCTTCAAACTTTGTTAAAGCGGAACGATGGCATG\nATTTCGCACGCTTTTTCGCAAGAGAACATACGTGAATTTTCTTTTTGCATAGACGTCTTC\nGCTCTCTAACGGACCTTATCGGGGGGGTATATTCCGCTACATTCTCCAAATGCGACGCTA\nGCATAACAAGGTTTCCATGAATCACCTTTGGGGGTAACCGAGTTACCTGTAACAGGTTCA\nGACCCCGTTGAGATACAAACACAAGGAGGGGGGTCACCATTATTTCATCAGATCCCG\n>comp43_c0_seq1 len=1548 path=[0:0-1486 1487:1487-1547]\nCTTTTAAATCGCTGTTCTCAAATTATCGCGATGGATGCTACAGTAAACTCTCAGTTTATT\nGATTTAATCTCCGGATTGCGTGGAGATGAAAACATACACACAATTGTGTGTACATACGCG\nGGAGTTGGGTTCTCCGGAAGAACTTGCACGATCCTGCGTGATATGGGCATCGACACGCTT\nGTGCGAGTCATTAAACGATCTCCTGAACACGAGGATGTACGTACCATACACCAACTACGT\nGGAACATTTTTTGACGAACTAGCACTACGATTACAATGTGGGCATAACATCTGTATATTT\nTCATCAACTTTATCGTTTTCGGAGCTAGTTGCTCAGTTTTGTGCAATATTTACAGACTCT\nATTCTTATTTTAAACTCAACTCGGCCCCTATGTAATGTAAACGAATGGAAACATTTTCGC\nGTGTTGGTGTACACTACCGTCGTGACCGTTGGATTGAGTTTTGACATGGCTCATTTTCAT\nAGCATGTTTGCTTACATAAAGCCAATGTCATATGGGCCGGATATGGTATCGGTCTACCAA\nTCATTAGGGCGTGTACGGTTATTGCTACTTAATGAAGTTTTGATGTACGTCGATGGCTCA\nAGGACCAGATGCGGACCCCTGTTCTCGCCAATGTTACTAAACTTTACCATCGCAAATAAA\nTTTCAATGGTTTCCTACACACACCCAAATAACTAACAAACTGTGCTGTGCATTTAGGCAA\nCGATGTGCAAATGCATTTACACGCTCGAACACCCATCTCTTCTCAAGATTTAAATACAAA\nCACCTTTTCGAGAGATGCTCTCTTTGGAGTTTAGCCGATAGCATTAATATCTTACAAACT\nCTTTTGGCCTCTAACCAAATTTTGGTTGTATTGGATGGCATGGGTCCAATAACGGACGTT\nTCCCCAGTTCAATTTTGTGCATTTATACACGATCTCAGACATAGCGCTAACGCCGTAGCT\nTCCTGTATGCGTTCTCTTAGACAGGACAATGACAGCTGCTTGACCGATTTTGGCCCTTCC\nGGATTTATGGCCGATAACATTACCGCGTTTATGGAAAAGTATCTTATGGAGTCAATTAAT\nACCGAAGAACAAATTAAAGTATTTAAAGCCCTTGCATGTCCAATAGAACAGCCTAGACTA\nGTCAATACGGCAATATTGGGGGCGTGTATACGAATACCTGAAGCGTTGGAAGCATTTGAC\nGTATTTCAAAAAATATACACGCACTACGCTTCCGGTTGGTTTCCCGTCCTGGACAAAACC\nGGGGAATTTAGCATCGCGACTATAACTACCGCCCCAAATTTAACCACACATTGGGAGCTG\nTTTCGCCGTTGTGCCTATATTGCAAAAACACTCAAGTGGAATCCGTCCACCGAAGGCTGT\nGTAACACAAGTTTTGGATACGGACATTAATACACTTTTCAATCAACACGGGGATTCGCTG\nGCTCAACTAATATTTGAGGTTATGCGCTGTAACGTTACCGACGCTAAGATTATGGCATCC\nATCTAAGAATCCGGTTGTTCGCCAAACCGGGCGGTTTAATATAATCTT\n>comp63_c0_seq1 len=449 path=[0:0-448]\nAACGTATCAAAGTATTATCCACCGAACACGTACCGAGTGCGGTGGATAATACTTTGATAC\nGTTACAGTAGGCTGTGTATGTCTGTCCGGTTAAGACTGGATCGCCGACAACGGTAATATT\nTGGACGATAATACGTTGTAACTGTAATACTGTGTTCCGATATGACGTTCTTAGTTTTTGT\nATTAACGACTCGCCAAATATACGTTCCCTCCGTGGTAGCATCCATAGATAAAATTGTTAC\nAGAAAAATCAGACGTTGTTTTAACATCTGGTATTACATAATTTTCCTTAGCGTGTGTAAA\nTATCTCAGGGTTGTTTATTAAGTTTAAATCGGCACTGTTGCTATATAACATAACCGGTAA\nATCTGGCATGCGTATTAACGCATTGCCCAGTTGACGGTGCGGATCTATAAGGTGACGCGT\nAAACCAAACTTCAATATGAAGATCGGGGC\n>comp33_c0_seq1 len=651 path=[0:0-650]\nTATTTTTATTTAAATGTGTAGTTCATAGTCCGCCGACAGCCGCTCGGGCTTTTCCCCCAC\nATACAACATGATCGTATGCCTCGGATGCACCGGTCCAACACTCCGCCGAGAAGGGGGATT\nTACAATGACAGTGATACCCAATAGCCGCCAGATGTACACCCAGCTGTCCGGACTCCAGCA\nTCATCTGCTGAGTTGCGGCGCTGAAGGGTGCATCGCATAGGGTGTTATAATTAGCCATTT\nCCGGTAACAGTCGTTGGGAATTTAGGAGGCTGCAAAACGGCTGTAGGTCAACATACATTG\nGGGATTCAGATGGTTTATCTCGACGTCCAAGTCCAATCAAAAAAGCGTGTAAATCATCAG\nCCCGGCCGCATGTTGCTCGAAGAGCACATAACCTCTTAACACCGTACAGAGGGGATGGCG\nTCGGTGCATGTGAGTTGGCAGGGCATGTCCACGTTGTTTCCAACGCCAGTGGCGGTATAA\nCTTGTGTAAACGACGCCAACGGGTCAGGTTTAAGATTCACTCGGATGGGTTGACTGCTTT\nCGGAAGCTCCCGTTGTATCCATTAATTAAACGTTCGGTACACGTCTGGTGTGTGTTTTAC\nCCGAATCAGAGACGGAATTGCAAAGATATTGGTTTGAAAGCAATGTAATCC\n>comp64_c0_seq1 len=732 path=[0:0-731]\nATCAAAACCAGTACGACCACTTTGGTTAGGTGTATCGTTTGCAAAGTTGGCTGCTCGTAA\nCGCCTCCGCGGAAACAACCGAATCCTCAAAATTAGACAATTCGTCAAAACCGGGTGGATT\nTGAGGGAATAGTGGAGGACCATCCATATGGACTAAATTGTTTTTCAATGTTTTCCACACG\nACGAGTTAGCGTTGTAGCTAGGTCACATACGCCTATAAACTTGCTAGGTTTTGCGGCATA\nCGTAAGACTTAAAGTATATGTTTTAGTAATTGTATATTTATGTCCAATCTCAGGTCCAAG\nTTCAGTGACATCACAAATTACGTTCTTTTTTATATAGTCACGCATGTTGAGACGAGAACG\nTACATGATTAAAAAAATTAGCAGTAGCTCTTTTTCCCAGGTTGGATGATTTTAAGAGGAC\nCGGTTTATTCACAAAATCTGAGTATGTAACCGCTTGTAGGTGGTCTGCGATCTGTTTCCG\nATTGAAACATTCAAAATGTGCCAGATAAATATAATCAACAAATTCACGGTCTGGAACTTT\nAAGGCCTTTTCTATCGTTGGTAATATACTCCGATACTGCGTGTATTTCCGTTGTGTCTGT\nATGTATTCGCTGTAAAATGTACGATAGAGCATTTTTGGCTGTCAAACCTCGTGTATATGT\nTGAGGAACAACAAAACATGGAAAGTTTATCAAAAGACAACAAGTCCGAAATATTGTACCC\nACTACAATTAGG\n>comp15_c0_seq1 len=1965 path=[0:0-1964]\nGTTTTAATGAAGGGAGTCGACTTGGTTAGAAAAAACAACTGTCAATTTATTAACGATTAT\nGCCCGCAAACTTGTAGAACTGTTGTTATATGACGACACCGTCTCGCGTGCTGCGGCGGAG\nGCGTCGTGTGTTTCCATTGCTGAATGGAATAGACGGGCCATGCCGTCTGGGATGGCCGGG\nTTTGGACGCATAATTGCAGATGCACATCGCCAGATTACATCACCCAAATTGGATATTAAT\nAAGTTTGTTATGACGGCCGAGCTTAGTCGTCCACCATCCGCCTACATAAACCGTCGCTTG\nGCTCACTTAACAGTATATTATAAATTAGTAATGAGACAGGGTCAAATCCCAAACGTTCGA\nGAACGCATCCCTTATGTTATTGTGGCCCCCACAGACGAAGTGGAGGCTGATGCAAAAAGT\nGTAGCTTTGCTACGTGGAGATCCTTTACAGAATACCGCAGGTAAACGGTGTGGGGAAGCA\nAAGCGTAAGTTAATAATATCTGACTTAGCGGAAGATCCCATTCACGTAACATCACACGGG\nCTGTCTTTAAACATTGACTATTATTTTTCTCATCTCATTGGGACGGCGAGTGTAACTTTT\nAAGGCGTTATTTGGAAACGACACTAAACTCACAGAACGGCTTTTAAAACGTTTTATTCCA\nGAGACACGAGTTGTTAACGTTAAAATGCTAAACCGCTTGCAGGCGGCAGGCTTTGTTTGT\nATACACGCCCCGTGCTGGGATAATAAAATGAACACTGAAGCTGAAATCACCGAGGAGGAA\nCAAAGTCATCAAATAATGCGTAGAGTCTTTTGTATTCCAAAAGCAATTCTCCATCAAAGT\nTAAGGTCACACATTTTACAGTAAACGTCCGATGTTCCAATGGATGGCACCACAGTCTCTG\nTTTGTTGTTCTGGGTTGCGACATACCGACAGTAAAAATGTTGTCTGCCAAACGTGTGCGA\nCTATTTTATACCCCCGACACGCGGCCTGTATATGATCGATTAGTCTGTAATGGAGGTGAA\nCAGATTTCCCCGGAAATATAACATACATCATAAACCCTCCGGCATCTCCATCACGATAAA\nAAAGTACGCGTATATCTCGCATGCCCCCCTCCCTCATAATATGATACATAAAAAATAATT\nCCGGTTGTGCCAATACGCTCGACAATAGGGGTTCAGCGGACGCTGCTTGCATGTTGGCTC\nGGTCTGATAGCGCCAAAATGGATGCAAGAAACACACGATATTCGTATATGTTGTTAAGCT\nGCTGAACATATGCTAGTATCAGAGCCGCCCGATCGGTTCGACATAGACGCGGTTCTCCAG\nATGCAGTGCATGTCGGACAATAACCTCCGAGACCTAAATGATAACCCATTCCGGATAACG\nACAGGCAGTTATCCGCCACTGTCTGACCCAAGTTAAACGGAAGGGTGACAGGGGTCGTCT\nTAATAATTGGCACGATTAAGCCTCTAACGGTAGCTAGTTCTTCTGGGGGGGACCTTGCGA\nTGTAATTAAAATAATGGCGGTACACAGACCGCTCCTTTGACATAAGTTTTCCTCGAATGG\nTTTGACGGCGGCATGGCGTTCTGGAGCGTACACGCATCGAAGGCCCGCTCCGAGATACGG\nATTTATATCGCCTAGACATACTTCGATAGGGTGTGTTCGAGGGAGACCAGCGATATTGCA\nTGTCGTCGAAGCATAAGTCCTCCATCTCGTATGAATGCGGCATTGGCGGTTGGTTTGCGT\nGGAAAAATCTGGTAGGCTTTAAATGCATACGCCAATGTCCACAGGCCAGCACATACACGA\nCCTTCAAATCTGTTTTGTGCAGCCAGTTGGGCTTTATATAACTCCAACACTTCCTTATCC\nGCGGTTGTAGGATGGGCAAATAAAATTTTAGGGTTTGTCTGTAATTCCGAGGCCGTATAT\nAAACATTTATTTTGCGATCTCCTATGCGCTCTCTCGGAATTACAG\n>comp8_c0_seq1 len=1378 path=[0:0-806 807:807-1377]\nTAATCAAACTCACATCCGATAGCGTCATGGCATCACATAAATGGTTACTGCAGATAGTTT\nTTTTAAAAACTATCACAATCGCGTATTGTCTTCATCTCCAAGACGACACTCCGTTGTTTT\nTTGGAGCCAAACCGCTATCGGATGTGAGTTTGATTATAACGGAACCGTGCGTGTCATCGG\nTATATGAGGCGTGGGACTATGCGGCACCCCCTGTATCAAACCTCAGCGAGGCGCTATCGG\nGAATCGTGGTTAAGACAAAATGTCCAGTACCGGAAGTTATACTTTGGTTTAAAGACAAAC\nAAATGGCGTACTGGACAAATCCATACGTCACCTTAAAGGGGCTGGCACAATCTGTTGGTG\nAAGAACATAAAAGCGGGGACATACGCGATGCTTTGTTGGATGCCCTTTCCGGTGTATGGG\nTAGACTCTACTCCATCTTCCACAAATATCCCGGAAAATGGATGTGTCTGGGGAGCCGACC\nGTTTGTTCCAACGCGTATGCCAATGAAATGAAACTATCGGATTCAAAGGACATTTATGTT\nTTGGCCCATCCGGTTACCAAAAAAACCCGCAAGCGACCCCGCGGGCTGCCTTTGGGGGTT\nAAGCTAGACCCCCCAACCTTCAAGTTAAATAACATGTCACATCATTACGACACGGAAACG\nTTCACCCCCGTCTCTTCGCAACTGGATTCGGTTGAAGTTTTCAGCAAGTTTAACATTTCC\nCCTGAGTGGTATGACCTGTTGTCGGACGAACTTAAAGAGCCGTACGCGAAAGGTATTTTT\nTTAGAATACAATCGTCTTTTAAATTCAGGGGAAGAAATACTTCCATCTACAGGCGATATT\nTTTGCATGGACGCGATTTTGCGGACCCCAGAGCATTCGCGTTGTAATTATTGGTCAAGAT\nCCATACCCTACCGCGGGACATGCACATGGGCTAGCGTTTAGTGTAAAACGTGGCATAACA\nCCACCGTCTAGTCTTAAAAATATTTTTGCGGCCCTCATGGAATCATACCCAAATATGACT\nCCGCCCACTCACGGATGCCTGGAGAGTTGGGCAAGGCAGGGGGTGTTATTGCTGAATACC\nACGCTTACGGTTCGTCGCGGGACTCCGGGGTCGCATGTATACTTAGGCTGGGGGCGGCTG\nGTGCAACGCGTGCTACAGAGGTTATGCGAGAACCGTACAGGGTTAGTTTTTATGCTGTGG\nGGTGCGCATGCACAGAAGACAACCCAACCGAATTCAAGATGTCATCTGGTGCTAACACAC\nGCGCATCCGTCGCCATTGTCCCGTGTTCCATTTCGGAATTGTCGACATTTCGTTCAAGCC\nAATGAGTATTTTACGCGTAAAGGCGAACCCGAGATCGATTGGAGTGTTATATAACACT\n>comp58_c0_seq1 len=409 path=[0:0-408]\nACTCTGGTGCGTCCCAGTTTAAACGCCACCGCCGAGGAAAATCCCGCGTCAGAAACGCGA\nTGTTTATTACGAGTGCTTGCGGGGAGAACTGTAGACCTGCCAGGCGGAGGAACGTTACAC\nATTACCTGTACCAAAACCTATGTAATTATTGGCAAATATAGCAAACCCGGCGAACGTCTT\nAGCCTTGCCCGTCTAATAGGGCGTGCAATGACGCCTGGAGGTGCAAGGACATTTATTATT\nTTGGCGATGAAGGAAAAGCGATCCACAACGCTTGGGTATGAATGTGGTACGGGCTTGCAT\nTTACTGGCTCCATCTATGGGTACATTTCTCCGCACACACGGTTTAAGTAACAGAGATCTC\nTGTTTATGGCGGGGTAATATTTATGATATGCATATGCAACGTCTTATGT\n>comp19_c0_seq1 len=1855 path=[0:0-1039 1040:1040-1854]\nGAAGATCGGTACTGTAACTTATTTTACGTTAGACCCGGAAATAAGTTACAGTACCGATCT\nTCGCATTGCAAAGGTTATGGAGCCTGCGGTATCAAAGGAACTTAATGTATCAAAACGTTG\nCGTTGAACCTGTTACCCTAACAGGCTCTATGTTAGCGCATAATGGGTTTGATGAGTCCTG\nGTTTGCTATGCGCGAATGTACCCGTCGCGAATATATTACGGTCCAAGGATTATACGACCC\nAATTCATTTACGGTATCAGTTTGATACTTCCCGGATGACACCCCCACAGATTTTGAGAAC\nTATACCAGCCCTTCCTAACATGACACTTGGTGAACTTTTATTGATTTTTCCTATTGAATT\nTATGGCCCAGCCAATTTCTATAGAACGTATTTTAGTTGAAGATGTATTTTTAGATAGGCG\nGGCTTCCAGTAAAACACATAAATACGGCCCGCGTTGGAATTCCGTCTACGCACTTCCATA\nTAATGCGGGTAAAATGTATGTACAACACATTCCTGGGTTTTATGACGTGTCCTTACGTGC\nTGTGGGCCAAGGAACGGCCATTTGGCATCACATGATATTATCCACAGCAGCATGCGCTAT\nTTCTAATCGCATTTCACATGGAGATGGATTAGGATTTTTGTTAGACGCGGCAATTCGTAT\nTAGCGCAAACTGTATTTTTTTGGGACGTAACGATAATTTTGGCGTGGGGGATCCATGTTG\nGTTAGAAGACCATCTTGCCGGATTACCACGAGAAGCCGTACCCGACGTACTCCAAGTGAC\nACAGTTGGTTTTGCCAAATCGGGGTCCAACGGTTGCCATTATGCGTGGTTTTTTTGGGGC\nGTTGGCATATTGGCCCGAACTAAGAATTGCTATAAGTGAACCATCTACATCTTTGGTGCG\nATATGCTACCGGTCACATGGAACTTGCCGAATGGTTTTTATTTTCACGTACACATAGTTT\nAAAGCCACAATTTACCCCAACGGAACGGGAAATGTTAGCGTCATTTTTTACGTTGTATGT\nTACTCTTGGTGGAGGAATGTTGAACTGGATCTGTAGAGCAACTGCAATGTATTTAGCTGC\nTCCTTACCATTCCCGTTCGGCTTACATCGCGGTCTGTGAATCTCTGCCCTATTACTATAT\nCCCGGTTAATAGTGACCTGTTATGTGATTTAGAGGTATTACTGTTAGGCGAGGTCGACCT\nCCCAACTGTTTGTGAATCCTACGCAACTATTGCACACGAATTAACCGGATATGAGGCTGT\nTCGCACAGCAGCCACAAATTTTATGATAGAGTTTGCCGATTGTTATAAGGAAAGTGAGAC\nCGATTTAATGGTAAGCGCGTACCTGGGGGCCGTTTTATTGTTACAACGGGTGTTGGGTCA\nTGCAAATCTTCTTTTGTTGCTTCTCTCCGGTGCTGCGTTGTACGGAGGATGTTCAATTTA\nCATCCCCCGAGGTATTTTAGATGCATATAATACTTTAATGTTGGCAGCAAGTCCTCTTTA\nCGCTCACCAAACTTTAACATCCTTTTGGAAAGACCGCGATGATGCAATGCAAACTTTGGG\nGATTCGACCGACAACGGACGTTTTACCCAAAGAGCAAGACAGGATAGTTCAGGCATCACC\nTATAGAGATGAACTTCCGTTTTGTGGGATTGGAGACCATCTATCCCCGAGAACAGCCCAT\nTCCCTCCGTGGACCTAGCCGAAAATCTTATGCAATACAGGAATGAAATTCTGGGTTTGGA\nTTGGAAAAGCGTAGCCATGCATTTACTACGAAAATATTAAGGGTTGTGATTTTTTTCATT\nAGGATGAAAAGAACGTTTCCTAGCCACACCCACAAAGGAGTTTGTAAAATAAAAT\n>comp4_c0_seq1 len=4784 path=[0:0-4783]\nAACATACACCGGATAAAAGCGTACTGTTTTTTATTTAAATTTACACGCTCGACGTTGCCC\nCGGTTCGGTGATCACCGGGTCTTATCTATATACACCGTGTAACTCGAACCCCCGTGACTC\nCCTCCAATCGCGTTACCAAACTCTTCTTCCGTATCCGTAGATTCCGAGTCCTCGAAATCG\nTCCACTGGAAGGCCAGCGTAATACATGCTTTGGTTATACGGGGACTTGTCTACCCTATAG\nGCTTTAACCCTCATTCGTTTAGCCGTACAGATTAAAAATATTACGAGACATAAAAGTACT\nACTGCTGCAAGCCCTCCGGTCCATGCGGCATATCGTAGAAGTGGTGACGTTCCGGGGTTT\nACGGGGGTAATTTCCTTGGGTTTAGTAGTCGCCGGTGGCTGACCGGCCGTTGGCGGAAAT\nCCACGCTCTTCAATTGCGTTTACAAAATGATCTACTGTGGATACAACAGTGTATGCTACG\nGCTTCAACATGCCCGTTAAAATACACCACAAAAACGTATAATCCCGACAAACTCTCGGGT\nGTATCTACAAACTTTAACGTGGTGCCCCCGTCGTGTAAGATTAGACCAAAGCTAGGCTCC\nATATGAGATATTCCCAGACAATATGCGGTGTAGTTATCTGCATGTTCACAATTTTGATAC\nACTGTGCTTGCAACACGCTGGGCTAAATGTGGCGAGGTAAATGTACAACCGGAATTCATA\nTGAGAGAGGCATTGGGGTGCGTTGGGATGATACAAACACGTAGAATATAACCGCATTGGT\nTGACATGTAGGATCGATGGGGACATACAACCACTCTAACAGCAAATCAAATGGCGCTTCA\nTGTATCTTATACTGAAGATGCATTGCCAAGCTAAACGTATCCCCAACTGAAAATACATGC\nGAGTGGTAATTCCACATATGAAACTCAGCCCCTCTTGGTTGAGGAGTTACTGCGGGCGTA\nGGGTTTCTTGTTTTTTCATCCCCTTTCCAGGTGACCAAAAACGTGGCGTAGGTAGACGTA\nCCATCGGAGCCGCGCATGTTCCAAATGTACACACCCAAGTATTGTTTTTCTGTCCGAAGT\nACTTTCAAGACACCCGGTTCAATCTCGGGGGGGTCTAATTCGAGTTCATCAAACAGTGTG\nCTCGTGTTTACAACAATCCACGGTTGGTCCGCTTCCTTCTTACCTTGAAAACGGTAACTG\nATTTCGGCCAACTGATCCTCTTTAGTATTTTCCGCGCAATCCACATCCACCACCACGTCT\nTGAAAGCATGTTGTATGTTTTAAGCATATATGCTGGATGGCGGGCGCTGCGTCTCCCGTA\nCAGGTTAATGACGGCAAAAAGCTCCAAGTCTCGGTGTACCGGACTCCATAAATCCGCTGA\nATCGGTGCGCGTAAAGTAAACGGGTGATTTTCTTCCACTGACACCTCAATGAGTCTTTGG\nCCTTGGGGTTTTGGATTAAGATCTCCTTTAAACACGTCACCGTATTGACGTTGGTCCACA\nTTTACAATTTTATGTCTGTCATCGCCGTTTAACGTAGGGATAACGTGGATGCCCGTATCG\nTCCCCAAGATCCTCCTGTGCAGACATTTGTGTGGGTTGCATTAACCGTTCCCCGCTATCG\nATACCACGGCCCTGATTATACACCCCATGGTGTTCGTGTGCGTTCTCTAAAAATCCATCA\nTAATCATTACGTGGCCATATATAAGGTGAGTTATGATCGTACGCTTTTCGCGAAGACTCT\nCCCCGATTTACCCATGAAGACTCCGCATGATCTGAATGGTAGTAAGGCTCATATACGGAG\nTTTGTATCCAGTTTGTCTTCATCGATGTGAAAATCATCGTATCGCAAGACGGATGCTCTG\nACCGGATTCGTTATACGCAACGTTCCCGTGATAATTCCGAACCCCATCAATACCCCCACC\nACAGGTTTATTAACTGTCCCCATATTACAGGCGACCCTCGGAATATAGTCACTTAAAACC\nACGCAATTCGCCCGAGGTCTAAAACCATGGACTGCTCTCGTGTATACCAGCTCGGCCTTT\nAAGGCTTCATAAAACATCCCCGCCCAAATGTGGGCGTGTTAACTTATAGTTAGGAGATTC\nTTAATCCTTCCCCTCATATCACAACGCGTAATCAAAACGCTAAATAAAACGCATATAGTT\nTATTTAATATAAAATCCGGGATAATTAGTTCTATTTAACAAACGGGTTTACAACGGAATG\nTGGGGGGGATTCTTCGCGAATCGTTGCTAGTTGTGCAATGGCGGCCTCCAACATCACATC\nGGATTCTGGTGTCGCATTTTGTATGCCCCTTCTTGTTTTTGTATTTGGGCGATAAATTGG\nATGTTTTTTAATTCTACGTCGCTTAACGCTTATTACAATAACAATAACCATGGCGGTGAG\nGATCATGACAGACGCTACTATAGGAATAATTATAAGTAGATTTTCTGGAGGATCATTAAG\nGGACTTTTCGGGTAACGTGGACATATCCGTTGGATATACGTGATTTTCTATCCCCTCCTT\nAACAACGGACTTAGTTTCTGTCGTAACAACGTCCTCATGTAACCAAGGGTTATCCTCTAA\nCGATTTACCGGCACGAAGATCAAGCATATGTTGAAACAGGGAGGTACCGGACCCTTTGGG\nTGTCGCGGGTAAATCACACAAACGAGCTTGTTGAAAAAGGGCTCTTGTAGAATATCCATT\nCTGTAGAGACGGAGAAGTGTAGATAACCCCGTGAATGTTGTGATGCGAGCCCGCTGTATA\nTACATTTACACCAAGAATAAAACCATCGGTGGATCTGCTATGGTCTAACCGAACAAGAAG\nTACATACACACCAGCATCATTTATTCCCGGTTTGGTAATTTTCAACATTACACCAGCATC\nCGGCTCTGTTGATATCCGATCCGTTGAGTTACCATAATGCCACGAATGTTTGTACCTACA\nCGAAATAAAAGCGCTCGTTCTAATCCGGGGACATCCGTCGTATCTTATTACTTGTACTGA\nCCGGAAACAAAACGCCACCGTATCCGCGTATAACAGTTCCAGTGTTCCGCTATAGTTTGT\nCCCGGTAGGTAGTTGCTCTCCAATAAAGACAAGCTGTCCTTTTATCTCTGTATAATTATC\nATTTTGCATGGGAATAAGGATAGACGTGAGACTGCTGTTAACTTGCAAGCTCACGTGGTC\nGCCCTTGAAGATCAAAGCGTTGGTCACTTGTATGTAAAATATAACGGCCGATATCAAACA\nTTGGATTAAAAACATCGCGATTAAATGAGGCGCACCAGTATACCCAACTACACCGAAGAG\nCAGCTCTGTGAGCCGGGGGAGGGGACGCTTTTCAGCGCTACTACAATGTTAAGAAAATGA\nTCCCGTGTTTTATCCTTGTTGTAATGGGGCGTGACTCTGTATTAAGTTTCTATTGGTTAT\nGTTATTTATATTAGTATTTCAAAACATTGCGCGTTTGTACCCTATTTGCCTTAACGGGTT\nATACGTTATAAACACAATTTATACAATATTTTATTAACAGGCTTAATGAATTTTAATCTC\nCAACTTCCATTGGATTTGGATATGGATCGGGAAGAGTTTGGAAAACAGAGTGGTTAAGCA\nACACCTCTGCCGATGGTCGATGACGTGCGTCAAACGATAACATCTTACATATCAAATACT\nCCAAATCAATTGGCAACTCATATAGATTTGTCCACAATGGCCTGGATCCGGGTTTTCGAG\nAAGACCGTTTTGCCAAACCAATGTATTGTCGACGAAGATTTGATGTAGGGTTAATGGGAA\nATTCATTGGGATGAGTTCCAGATCGTCGTATAATAAGTTTAATTTGACGCTCACTGTCAC\nAATTGCCATCTAAACCGTCTCGTTCAAATAACGAGTTCTGTCCTGTAGCCATTTCAAATA\nATACAATCCCGGCACTCCATATGTCCACGGCAGGTCCATATGGATCTCTAGCCAATAACT\nCAGGAGAGTTTGTGGCGATTGTTCCAGCCCAGCCATAATACCTGTTGGCATTAATATCCA\nCGGGGAAACACGCTGCTCCAAAGTCTCCCACACAAACATCACCTGGGTGGTTAATAAATA\nTATTTTCAGATTTTATATCACGGTGAATAATACTGTTATTATGAAGATACTGTAACGCGC\nGTAATACAGATCGCTGAATTGCTAAAATGTCACATATGGGGAGGTTGCGCTTTGCAGCTA\nGATAGCAGTATAAATCTGTTCGGTAACGTGGTAATATAAGACATGTCATTTTGTTATACG\nTAAACGTTCCTTTAAGCTGTATAACGGATGGGTGGGTTAACGCTCTTAACACGGTTGCCT\nCGGTGGCCGTTCCTTGACGTTGACCCGCTTTAATGACCACATGTTCACATGTTTTACTGT\nCCATACACGCAAACGCAAAACCTTCCGCCCCTGGTGTAAACGTTTTTAATATTACAAATC\nCCGCTTTATTAATTCCAACGCGTGCTTCTGCACACAATGCCACAGAGGCTTCGGCTTCAG\nTTTCGTGGACACCATCAAATATATTAAAAGACTGTATATCCATGTTAACGTCATAATTGG\nGATCATCCTCAGATTCTATGCCGGGCGACATTTCAACTGGAAACATCTGTTGTATAAACC\nCACATGTTTGCATAATATGTGACGGTGATGTTGAGATGGCGCCACGGAACTTTCCTTGTC\nCAACAAAGGTGTCTGTTGCATCAACGTCGTTCATTATACTTGTATACCCCGACTTATGTT\nGATAGTGTTAATGAACCAAAAACACTATCAACATAAGTCGGGGT\n>comp69_c0_seq1 len=415 path=[0:0-414]\nATCCATATGGATTAAATTGTTTTTCTCTGCTGCCACTGGGATAGCCACACATGATGTATC\nCATCCTGAGTTATAAAACTCCATTAGAAGCCCTCATCGGCCATTCTGAGGTAACTGGACC\nAATGCCTGTATATCGGGTAGCCTTGCCTCAAGGTGCCCAAGCATTTGCTGTTATTGCTAA\nTGATACGTGGTCATCAATAACAAACCGTTACACTTTACCGCACGAGGCTCGATTAATTGC\nGGAGGACCTTAAACAAATTAATCCATGTAATTTTGTTGCCGCTTCACTACGAGATATGCA\nGTTGACTTTACTATTATCTACGTCTGTTAAAAACGTTTCTAAAATTTCATCTAACATACC\nCAAAGATCAGCTTTATATAAACAGGAATGAGCTATTTAATACAAATCTTATAATC\n>comp44_c0_seq1 len=1624 path=[0:0-1623]\nATACGCACACTTAGTGGATGGGAGTCAATAATATTGCGAGCTTGGTACATCCAGTCAACC\nGCCTGAATGTCCAACGTACCAGTTTCTTCTTCCAGACGCCCTAACAGCAATGCAAACTGC\nGTGACAATGTCCTGAACGGAAGTAGATCTATCAATGGCCAATGCAATTGTTTTGGGAGGG\nGGGGTTAGTTTTAATAACGTCTTCAGGTTAGTGAAATCCACGTCTTCTTGTTGCTCAGTG\nGCATTGGCAGTATCAACAATGTTTTGTAAAATTTGTATTGCACGGTTCTTTGTTGCCTGA\nCACACCATACGAAACTGTGCAAGCTCTGCGTTGGCCTCCTTTAGATCGCGGTCTACCATT\nGTTTGTAAAACTCTTTCATATGCCGTTCCTATAAATCGTTTATGATCGAAAGTTGTAAAA\nTACTCTATAGCCCGAATCAATAAACCTTCGCTTGGTAATGTAATGAAGACACCTTCTTTA\nAGTGCAAGTTTAGCCGTTTCGTGTGCCCGAACATGAGTTACTTCCTCCAAAGCCTTATTT\nGCTTCTGTAAGTTTAGCCCCGGCAGCCTGTCTGATGTCTGCTCTAAGTTCACTTAACGTT\nACACTTTCGGTTATAAACTGATCATAAGACCGTGTGTAAAAATCAACATACCCAGCCAAT\nGCGGGTATTTGTAATAGATCCCCCGAGGTTCGTAATATCATATCTCTGTAGTTAGGTATT\nCCATTAATAGACGTATCGGCGGATAATAACACAACCGCGCGAATACGCATAAGCAGAAGG\nAGTCCCTCAATACTAACACCTGGAAACATAACGGTGAATACGGGAGCCGTAATCGAAAAA\nTCATCAAACCATGTTAACCCTCTTAACAAAGCCAAAGGTGGGGGAATATTTGTATTTTCG\nGGGGTATATGGATTGTGGCGAAACACAGTATCTAATGCCGTAACGGCTGTAGTTTCACAT\nGCCGCTACAACCTGACGTGCTTGTGGGTAAACTGCGTGTATATCAAACCCTCCCGCAGCG\nGCCATATCTCGCAACCGTGCCAGTTCTGTCCCGTTAAATATATGGCGCGTTTCCATTGCC\nTCCAGACATGCTATAATATCACGTGTCCAACGCTCATACAAAACCCGAGTCGTTTGTTGT\nTTATGTGCACGTTCACAATCGGTAATTAACACTTTTGCCTGTTCCTTCTTCTCATGTGCC\nATTGTGACGAGTTTATGAAGATCCTTTACTACTCGAGATAAGGTAGATGTCCCAGCAATA\nCAATGGGGGGGTAGCTTTTGCAGTTCAACTTCAACAAGTTTAACCGTATCCATTAGGGCG\nTGCACATTTGTTTGTATTGATAATATCGCATCGTTTATTTCATAATCATCTACATTTGAA\nGATGATATAAACTTCAAGTGTCCAGATGAGACAGCTAGGGTGGAGAAGTCATCTCCAAGT\nCGTTTTTGTAATTCAGTCAACTTATGGGTATTCGTAATTTCTTGTTGTAAAGCCTGATAT\nTTTTTATATAACGACAACACAAAGGATAAGGCTGGCACTGTAGATGAAACTAACGTCGCT\nTTACTAAGAGTTGCAACAACAGCGTTTATGGCGGACTCACTTTCCGGGTTAGTAGATACG\nGTCG\n>comp62_c0_seq1 len=515 path=[0:0-514]\nTTCCGGGTTAGTAGATACGGTCGCGATGTCGGATGCAAGCACATCTGCCACGTCACCAAA\nAAACGCAAGCAATGATGGTCTATACTCCGTAGGTATCGGCACAATTTCGATAATAGCTGT\nAAAACAAGCTCCCAGTCCTCCTAAGACAGATGTGCGTGCGTTTCCGGGATGTTCTAAAAT\nGTCTCGATATTGGTTAAATAACGCCCAGAAATCACCCGTAAGTTGAGAACGGATCTCTAC\nCGGCGCCTCTAAGACTTTGGTCCTGAGATTTACCAGGGCTCCTTGGACATCTAACTCAGA\nAGCAAGTTCCGGTAATAAATCTACTGCAGCCCTAAGTCCCACAAAACCGGTTACCGGGCG\nAAGTAACCCCCCGAGTTTATTATATGCCGCCTGTTTTCGACTCTTTATTGTGTCCTGTGT\nGGTTCGGGCCTCGTTTGCATACGTCTGAACCTCTTTAAGCCTTGTTTCCAATCGTCTTTT\nAATCGAAGGTTGTAAACCGGATTGGATCATTGGAT\n>comp23_c0_seq1 len=770 path=[0:0-769]\nGAACGGCACCACCCAACAGTCTTACGATTGCCTAGACTGCGCTTATGATGGAATCCACAG\nACTTCAGCTGGCTTTTCTAAGAATTCGCAAATGCTGTGTACCGGCTTTTTTAATTCTTTT\nTGGTATTCTCACCCTTACTGCTGTCGTGGTCGCCATTGTTGCCGTTTTTCCCGAGGAACC\nTCCCAACTCAACTACATGAAACTACTGTCCGGAAGGGGAAGGTATTTATTCTCGCTTGCA\nGCTTGTCGCGCGTGTATGCACAACAAAAGCTATATATGTCACCAAAGCCAACGTCGCCAT\nCTGGAGTACTACACCCAGTACGTTGCATAACCTGTCCATTTGCATTTTCAGTTGCGCGGA\nCGCCTTTCTCCGGGATCGTGGCCTTGGGACATCAACCAGTGGAATAAGAACCGCCGGTGG\nTCTTGCCCGAACGACGAGTGGCGACGCGTTGTTCTGCATAAGCTCTGTATGCTGATACAT\nAAACACAGAGTCTGTATCGCTATCAGATTCCCGAACACCTTCCGGTACCCCATACTCCGA\nTACCCTGGACATTGCGGATCCCAAAAATATAATATTAACAGGATTTGCTTATACTTTGCT\nACAGCTTATATAAATTTATGTGCGATACATCTTAAGTGCATCCGTACGTTATTTATACAT\nTGCCGGTCACGTGAAAAGACTGTGTTACCCAATAAAGGTTCTACAAAAAATGCTTTATTG\nGGTGTTTGTTTAATAGCTATTATCGTAACCCACCCCCGTAAAATCATAAA\n>comp7_c0_seq1 len=2194 path=[0:0-289 290:290-2193]\nGGGCGGGGATGCCAGACTTTTCATACATAACATGGCGTAGTCCGCAACCCATTCCGGTGT\nCAGTCCAAATTTACGTTTATACAAATCAAGCGTTCTACAGACCAAACAGGCTCTGTCTAA\nCGCCAAAACGTCTCCAATTTCTTCTATAAATTCAGTGGTACTTGAGGTCATTTCATTATC\nCACACCTACCGCCGAAGAGGCCTCATAAGTGACGTTGTTTTCTATTGCACGGGGAACATT\nTATTAAGTGGGAGGCAAATAACAATTCTGAAAATAACAAATCGTTTTTTAGCAGAAGGGC\nTGGATTATAAGCGATGTACGAATCGGAAAATGCGTCGGAACACCATCCGGAATTAGAAGA\nTGTATTTTCGGAGAATACGGGCGATTCGAATCCATCCATGGGTTCTTCTGATTCTACCCG\nATCCATCTCTGGGATGAGGGCCCGCGATTTAATTACAGACACCGATGTTAATCTATTAAA\nTATCGATGCACTGGAGTCAAAGTATTTTCCTGCTGATAGCACCTTTACTCTTTCCGTTTG\nGTTTGAAAATTTAATTCCCCCGGAAATAGAAGCAATTCTACCTACAACTGACGCTCAATT\nAAATTATATATCATTTACCAGTCGCCTGGCGTCCGTTTTAAAACATAAAGAAAGTAACGA\nTTCAGAAAAATCTGCTTATGTTGTTCCATGTGAACATAGTGCCAGCGTGACCCGTCGCCG\nTGAACGCTTTGCGGGAGTCATGGCCAAATTTCTAGATTTGCATGAAATATTGAAGGATGC\nTTAATACATGGGGAAAATAAACGCATTAATAAGTCGTCAGGGGGTGGATCACTCCAAACT\nCCTCCTATATCCCACGATAAATGGTCTAAATACTTCACGCGTGTGCCTTGGTTTGCAACC\nTTAGATCAATATGTCACGGAGAACGTATGTACGGAGTGAACGCAGGAGGGGTTGCGGAGA\nTAATCTTTTACAACGTATTCGGTTGGTGGTACCAAGCGCTCTTCAATGTTGCGATGGGGA\nTCTTCCAATATTTGATCCACAACGCCCCCCCGCCCGTTGTGTTTTTCAGTTTAACGGCGA\nAGACAACGTATCCGAAGCCTTTCCGGTAGAGTATATTATGCGTTTAATGGCGAATTGGGC\nGCAAGTAGATTGTGACCCTTACATAAAAATTCAAAATACGGGGGTGTCTGTGCTATTTCA\nAGGTTTTTTTTTTCGTCCGACTAACGCACCAGTGGCTGAAGTGTCCATTGACAGTAATAA\nCGTGATTCTTAGTTCAACGTTAAGTACCGGTATCAACCTATCTGCTTTGGAATCAATTAA\nACGAGGTGGGGGTATTGACCGCCGACCTCTCCAGGCTTTAATGTGGGTGAACTGCTTTGT\nGCGAATGCCATATGTTCAGTTATCCTTTCGTTTTATGGGACCGGAAGATCCATCTCGCAC\nCATTAAACTTATGGCCCGCGCCACGGATGCATACATGTATAAGGAAACTGGCAATAATTT\nGGATGAATATATACGCTGGCGGCCTTCATTCAGATCCCCACCCGAGAACGGAAGTCCAAA\nCACGTCTGTTCAAATGCAAAGTGACATTAAACCTGCGTTACCCGATACCCAAACTACGCG\nTGTCTGGAAACTTGCTCTACCCGTAGCTAACGTGACATATGCCCTGTTCGTTGTAATTGT\nACTGGTAGTTGTATTAGGGGCGGTGCTTTTCTGGAAATAAATTGCCTTTCCGTACATATC\nCTGCGCAGATGTACGTGTATGCTGTTATCGATTGTCCCGTAAACTAATAAACGATGACAC\nAACCCGCATCGTCTCGTGTAGTCTTTGATCCCAGCAACCCCACCACATTTTCGGTGGAAG\nCAATTGCGGCTTACACCCCCGTTGCTTTAATACGACTTTTAAACGCCAGTGGACCTTTGC\nAACCTGGTCACCGTGTGGACATCGCTGATGCCAGAAGCATTTACACCGTGGGAGCCGCGG\nCCAGTGCCGCGCGTGCACGCGCTAACCATAATGCAAATACGATACGCCGAACGGCCATGT\nTTGCCGAGACTGACCCTATGACATGGTTAAGACCAACGGTTGGCTTAAAACGTACGTTTA\nACCCGCGTATTATACGACCACAACCCCCAAATCCATCCATGAGTTTGGGAATCTCGGGGC\nCTACTATATTGCCGCAAAAAACACAGAGCGCCGA\n>comp65_c0_seq1 len=396 path=[0:0-395]\nGTAATATAGTGTGTCTCCAACCATTCAGCTTACAGTCCAGTGGACAGTAACAGCCCGATA\nACATGGAATTGGATATTAATCGAACATTGTTGGTTCTACTGGGTCAAGTTTATACGTACA\nTCTTTCAGGTTGAACTGCTACGTCGCTGTGATCCAAGGGTGGCGTGTCGCTTTTTATATC\nGGTTAGCGGCTAACTGTTTGACAGTTCGTTATTTATTAAAGCTGTTTCTCCGGGGATTTA\nATACCCAGCTAAAATTTGGAAACACTCCCACGGTTTGTGCACTGCATTGGGCATTATGTT\nATGTAAAGGGAGAAGGTGAGCGTTTGTTTGAGTTGCTACAACATTTTAAAACGCGTTTTG\nTTTATGGTGAGACCAAAGACTCAAACTGTATCAAAG\n>comp57_c0_seq1 len=437 path=[0:0-436]\nTCTGTCATGTGCTCTAAAGTCCCATATATAAAAGAAGCCCCAACGAGTGTATGCGTATTG\nCGTACCGCGACCCTGGGATGTTTTACAGGCGCGTTTGTTTGTCTCGGTTATAAGTATGCA\nGTCGGGTCATTATAACCGGAGGCAATCCCGCCGACAGCGGATATCGTCTAATACCACAGA\nCTCCCCCCGTCACACACACGGAACACGTTATCGGTCAACCAATTGGTATACACACCCACC\nCCAGATATTGTCCAATTCAGAAACATTAGTTGCGGTTCAAGAACTACTGAACTCCGAGAT\nGGATCAGGACAGCAGTTCTGACGCATCGGATGATTTTCCGGGATACGCCTTACATCATTC\nTACATATAATGGATCCGAACAAAATACATCAACTTCCAGACATGAAAATCGCATATTTAA\nATTAACGGAGAGGGAAG\n>comp16_c0_seq1 len=1479 path=[0:0-1478]\nCATTCGTTCCATGTATTTGTACCCCCCCACACAACCCCCTCTAACCAAATAGTTGGCACG\nTTATAACCTCCGAACCGTTCCATGCGTCTTGTATAACGCACAGACTCTGATGGAATTGTT\nCCAATTAACGTATATGCCGCATACATGCAGGATAATTGTGTGGGAAGTCCCCGAAAATCG\nCCGGTCCATTGATACAATCGCTGTCTAGCCAAGTTCCAATTTACTCCTGTAATTTCGCCA\nATACTACATCGAGGGCTTGTCGGGTCATTGGATAACTGCACAAGCGGCAACGCCCTTGTG\nTTATATGGCTGGTGGGTATTTGCAACCCCTTCAGTCCCCCAGGCGGCATTTTCAGCTCGT\nATGCGTCCTAACAGGAAGCCAATACCACGACCAAAACATTGTTCGTTTAGTTGGCTTAAT\nGCAAGATGCAGTCTTACACCTTCTCGTTGGCGTCGCTGTGTATATACAAAAACCAAGAAC\nACATGCTTCAGTCCGTCCGCGGAAAGATGTAAGTCTTTGTCAACGTCCCAAAATACGCAG\nGCCGGGATGTTGGCTGTGACCCTGCGAGTTGAAGTTTTGTCTGTACGTGCAGCTTCTTGG\nGGACCTTTGGCCACGGCGGTTATATTGCATAAATTATCCTGAATGGTATATTCCAGCAGG\nGACCCAAAAAAACTTATAAATCGATGTGGAAATACATGACATTGTACCATCGCACGTAAA\nCACTCCGAAAACCTTATGAGCCGCGTTTCCATACGACTGCATCCATAGGCAGAAACAATT\nGCTGTTCTGTTGGCATCTGCTGCCTGTTTATCCGTATATTCTTCTGCCCGGCATGCGGCG\nATGAAACTTAATGACGTTACATATGCTCTAAGCCCCCCACCTTCTCCAACGGTCCAAGGA\nGCCGTGCAGGCATTGAATAGGTTTCGTAAACCCTCTAGTATTACATCGGGGTCACGTCCA\nGCCTGTGTAAGTGTATTAGCTTCTCCAATCATGTCAGATGGATGACGAAGGATTAAGACG\nATTGACCCAGCATGCTCAATGTCCGGACGAAAAAAATCGGTTAATGACACTTGTTGGATT\nAGCTGTGTCGTTGATTTAAAATTATTTAACGGGAGTCTAATGGTAACTTGCGGGTTACCA\nATTGAAGTTGGATTTATTTGAATGTTGTTCATGCGATTAATAACAATTGAACGGGGGGTT\nACTTGAATAGACGCGGTTTCTGTACGTTTTGGTGGTCCATGTATCGGTTGTTTGTTCAGA\nCCTCCAAAGCGAGGGCCAATTGTTAAATCGCGACTCCAATTTCCGAAGAAGCCCGGAGCA\nTAAGTCATATGAAGCCCGTTCCCTATTTGAATAAAACGGTTATTTCCTAAAAGACTGATA\nTTAGTTCCACATAGCGTTTGTTCGTTTAAAGTAAAATGCGAGTTGGTTGGTTGACTCCCC\nATAGCTGAGGGGGTAAATTCACACAATGCAATCGTGACG\n>comp55_c0_seq1 len=512 path=[0:0-511]\nTCACACGATCACGGGACGGCAAGTTCGAGGTTAATGTTCCGATAAACGCTTTAATATGGA\nATTTCCATATCATTCAACCGTATCTTATAACGGCGTAACGTTTTATTTTAACGAGCGTGC\nTACCAGGGCGTATTTTATATGCGGGGGATGCTTAATTTCCATACCCCGCAAACATGGAGG\nCGAGATCGCAAAATTTGGACATGTTGTTCGCGGGGTCGGACCCGGTGACAGATCTGTTGC\nCAGTTACGTTCGAAGTGAGCTCAATCGCACCGGGAAGACATGGGCGGTATCATCCAATAA\nTAACTGCGTGTTTTTGGATCGAGTGGCCTTACTTGCAGCGGGATCGGGGGCGGTGGATCG\nCGACCTTTGCGGAACATTTGATGTTGAAGTGGAGGACCCTACGCTCGCAGATTATCTCGT\nGTCCCTCCCCGTGACGCATTTAACATTGGTGGCGGGGGTAGATGTTACGCGCGAGAATAA\nGCTAAAATTGTCTCCAACATACGCATATACAC\n>comp12_c0_seq1 len=7199 path=[0:0-5986 5987:5987-7152 7153:7153-7198]\nCCTTAGGTCCACACCGAATATGAGAAATATATAACTACACGCAAACATTCAAAACACCGT\nGGTATCATTAACGTCATATGAAAAGATCCAATCAATCCAATCAACCACACCTCCTACCGT\nTTAGCACGTCAGCTATGTGACATGCTCCAAACATACGTAAACATTTAGAGAGGGTGTTAT\nAACAGTCTGTCAGGCGGGGTATATTCTACATAATACAAGGATCGGCTTTAACTTTGTCAA\nCATTTTTACTTTGGACTATAAACTGCGACTGAACGTTATGAACCCACCCCAAGCCCGCGT\nCTCGGAACAGACAAAGGACTTGCTTAGCGTTATGGTTAACCAGCACCCCGAAGAGGACGC\nAAAAGTGTGTAAATCCAGTGATAATTCACCGCTTTATAACACCATGGTTATGTTATCGTA\nTGGGGGTGATACGGACTTACTATTAAGCTCTGCATGTACCCGCACATCTACCGTAAACAG\nGTCGGCGTTTACGCAACACTCCGTGTTTTATATTATATCCACGGTGTTGATTCAACCAAT\nATGTTGTATCTTCTTTTTTTTTTACTATAAAGCGACACGCTGTATGCTCTTATTCACAGC\nCGGGTTACTTCTGACGATTCTACATCACTTTCGACTTATTATTATGTTATTGTGTGTCTA\nCAGAAATATACGATCAGACCTGCTACCCTTATCTACATCCCAGCAACTGCTGCTTGGAAT\nTATTGTTGTGACTCGAACAATGCTATTTTGTATTACGGCGTATTATACTCTTTTTATAGA\nCACCCGGGTGTTCTTTTTGATTACCGGACACTTGCAAAGTGAGGTTATTTTTCCAGATAG\nCGTTTCAAAAATACTTCCTGTGTCGTGGGGTCCAAGTCCAGCCGTGTTACTGGTAATGGC\nGGCAGTTATTTACGCTATGGACTGTTTGGTGGACACGGTATCCTTTATTGGGCCAAGGGT\nGTGGGTCCGTGTTATGTTAAAAACATCTATTTCGTTTTAGTCCATTTCAATAAATGTACT\nATAATTGTTCAGTCTAAAAATAATGTTGGGTATTTATAATTACCGCCCCCGTGTTACTTG\nGAAACACCCATACATATGTTCCACTCTACATCAAACTTCTCGCAGTTTTCTTGTTCCCGC\nACACGTTTACACGTCCGGATTCAAGTCGCAACGCTGCTGACAAAATGACAACGGTTTCAT\nGTCCCGCTAACGTGATTACTACAACGGAATCTGATCGTATTGCTGGGTTATTTAACATCC\nCAGCGGGGATCATTCCAACTGGAAATGTGCTGTCAACCATAGAGGTGTGTGCACACCGTT\nGCATTTTTGATTTTTTTAAACAAATACGATCAGATGATAACAGCCTTTACTCGGCTCAAT\nTCGATATTCTTTTGGGGACATACTGCAATACATTAAACTTTGTGCGTTTTCTAGAACTTG\nGACTGTCTGTCGCTTGCATCTGTACTAAATTTCCGGAGCTGGCTTACGTGCGAGATGGCG\nTTATTCAATTTGAGGTACAACAACCCATGATAGCACGTGATGGCCCACATCCCGTCGATC\nAGCCTGTTCATAATTATATGGTTAAGCGGATACACAAGCGTTCGTTAAGCGCTGCGTTTG\nCAATTGCATCGGAAGCGTTGAGTTTGTTAAGTAACACATATGTCGATGGGACAGAGATTG\nACTCATCGTTACGTATAAGAGCTATCCAACAGATGGCTCGTAATTTACGCACCGTTTTGG\nACTCATTTGAACGAGGCACTGCCGATCAACTTCTTGGTGTTCTATTGGAGAAAGCCCCAC\nCGCTATCGCTGCTTTCACCAATTAATAAATTCCAACCCGAGGGACATCTAAATCGTGTTG\nCACGCGCGGCCCTACTTTCGGACCTCAAACGTAGAGTCTGTGCGGATATGTTTTTTATGA\nCCCGACACGCCAGGGAACCTAGGCTGATCTCTGCGTATCTGTCGGATATGGTTTCGTGCA\nCCCAACCATCGGTGATGGTATCACGAATAACTCATACAAACACTCGCGGACGGCAGGTTG\nACGGTGTGTTGGTAACAACAGCAACCTTAAAACGGCAACTATTACAGGGAATTTTACAAA\nTTGACGACACCGCCGCTGACGTACCAGTAACATATGGCGAAATGGTTCTACAGGGGACAA\nACTTGGTAACCGCCCTTGTGATGGGAAAGGCCGTCCGCGGAATGGATGATGTAGCCCGCC\nATCTCCTTGATATAACCGACCCTAACACGTTAAACATACCGTCTATACCCCCACAATCCA\nACTCCGATTCAACGACAGCTGGGCTTCCGGTTAACGCCCGTGTTCCTGCGGATTTAGTGA\nTTGTTGGGGATAAACTTGTATTCTTAGAAGCATTAGAACGGCGGGTCTACCAAGCTACGC\nGCGTTGCCTACCCTCTTATTGGAAATATAGATATTACGTTTATCATGCCAATGGGAGTGT\nTTCAGGCAAACTCCATGGACAGATATACACGACACGCCGGCGATTTTTCAACTGTATCCG\nAACAGGATCCACGTCAATTTCCACCCCAAGAGATTTTTTTTTATAATAAAGATGGGATAT\nTAACACAGTTGACTCTTCGTGATGCAATGGGTACCATCTGCCACAGTTCATTGCTTGATG\nTTGAGGCCACACTTGTTGCCCTCCGCCAACAACATTTAGATCGTCAGTGTTATTTTGGTG\nTATACGTGGCCGAGGGTACAGAGGACACATTGGATGTTCAAATGGGGAGGTTTATGGAAA\nCGTGGGCAGATATGATGCCTCATCACCCTCATTGGGTAAACGAACATTTAACAATTCTAC\nAGTTTATAGCTCCGAGCAACCCGCGTCTAAGGTTTGAATTAAACCCCGCCTTTGATTTTT\nTTGTTGCACCGGGGGACGTAGACCTTCCCGGACCGCAGCGTCCCCCGGAAGCCATGCCAA\nCCGTTAACGCAACATTACGGATTATCAACGGAAACATTCCCGTGCCTCTATGTCCCATTT\nCATTTCGAGACTGTCGCGGAACCCAACTCGGTTTGGGAAGACATACAATGACCCCGGCAA\nCCATTAAAGCCGTAAAGGATACATTTGAAGACCGCGCATACCCAACTATTTTCTACATGC\nTAGAGGCTGTTATTCATGGAAACGAAAGAAACTTCTGTGCGTTACTGCGACTGTTAACAC\nAGTGTATTCGCGGGTATTGGGAGCAATCCCACAGGGTGGCATTTGTAAATAACTTTCACA\nTGTTAATGTACATAACTACATATCTCGGAAACGGTGAGCTTCCCGAAGTCTGTATTAATA\nTATATCGGGATTTACTGCAGCATGTAAGAGCATTACGCCAAACTATAACCGATTTTACAA\nTACAAGGAGAGGGCCATAACGGCGAGACCTCGGAAGCGCTAAATAACATCCTTACGGATG\nACACGTTTATTGCACCTATTCTATGGGATTGTGATGCGTTAATATACCGTGATGAAGCCG\nCCCGAGACCGACTCCCCGCAATTCGTGTAAGCGGGCGAAACGGATACCAAGCCCTTCACT\nTTGTGGATATGGCCGGGCATAACTTCCAACGACGCGATAATGTGTTAATCCACGGGAGAC\nCCGTTCGGGGAGACACGGGTCAGGGTATTCCCATTACCCCACACCATGACCGTGAATGGG\nGTATTCTCTCCAAGATTTACTACTATATTGTCATTCCTGCATTTTCCCGCGGTTCCTGTT\nGTACAATGGGCGTGCGTTATGATCGCCTATACCCTGCGTTACAGGCAGTTATCGTTCCGG\nAAATTCCCGCTGATGAAGAAGCCCCAACTACCCCAGAAGATCCAAGACACCCTCTTCACG\nCACACCAACTCGTTCCGAACTCTCTTAACGTTTACTTCCATAATGCACACCTAACCGTTG\nATGGTGATGCATTGCTCACACTACAAGAGTTAATGGGAGATATGGCTGAACGAACGACGG\nCCATTTTAGTATCAAGCGCCCCCGATGCGGGAGCCGCCACGGCAACAACCAGAAATATGA\nGAATATATGACGGAGCGCTTTACCATGGCCTTATTATGATGGCATATCAGGCGTACGATG\nAAACCATTGCAACGGGTACTTTTTTTTATCCCGTTCCGGTCAACCCTCTGTTTGCATGTC\nCGGAACATTTGGCATCATTGCGTGGAATGACAAATGCTAGGCGGGTTTTGGCAAAAATGG\nTACCACCAATCCCTCCTTTTCTGGGAGCCAACCACCACGCAACTATACGCCAACCCGTTG\nCCTACCATGTAACGCATAGTAAGTCGGATTTTAATACTCTTACATATTCTCTTCTTGGAG\nGGTATTTTAAGTTTACACCAATAGCTCTTACACATCAACTACGAACGGGATTTCACCCCG\nGGATTGCCTTTACCGTAGTGCGCCAGGATCGCTTTGCCACAGAGCAACTTTTATATGCCG\nAGCGTGCTTCTGAATCGTACTTTGTCGGACAAATCCAAGTACACCATCATGATGCTATTG\nGGGGGGTAAACTTTACCCTAACCCAACCCAGAGCTCACGTGGACCTGGGAGTTGGGTATA\nCAGCTGTATGTGCCACAGCAGCCCTGCGATGCCCTCTCACGGATATGGGCAATACTGCCC\nAAAATCTTTTTTTTTCACGAGGAGGAGTGCCAATGTTACATGATAACGTTACCGAATCGT\nTGCGTCGTATAACAGCATCGGGGGGTCGCTTAAATCCCACCGAACCCCTACCCATCTTCG\nGCGGACTGCGTCCTGCTACATCGGCAGGAATTGCACGAGGGCAAGCCTCTGTGTGTGAGT\nTTGTGGCCATGCCGGTGTCCACTGACCTACAATATTTTAGAACTGCATGCAATCCTAGAG\nGTCGAGCATCTGGAATGTTATATATGGGTGACCGTGACGCCGACATAGAGGCTATAATGT\nTTGATCACACACAATCGGATGTTGCTTATACAGATCGAGCAACTCTTAACCCATGGGCAT\nCACAAAAACATTCATACGGTGACAGGCTATACAACGGAACATACAACCTTACAGGCGCTT\nCTCCTATCTACAGCCCATGCTTTAAGTTTTTTACACCAGCGGAGGTTAACACTAATTGTA\nATACACTGGATCGGCTTCTAATGGAGGCAAAGGCTGTGGCGTCGCAAAGCTCCACCGACA\nCTGAATATCAATTTAAACGCCCTCCCGGTTCTACCGAAATGACACAGGATCCGTGTGGCC\nTTTTTCAAGAAGCATATCCACCACTATGCTCAAGCGATGCGGCCATGTTACGAACGGCTC\nACGCGGGAGAAACCGGGGCAGATGAAGTTCACTTAGCCCAATATCTGATTCGAGACGCGT\nCGCCCCTTAGGGGATGTCTTCCTCTTCCGCGATAATTTCACCACGCCCACATACCCACTC\nCCAATAAAAGCCCTGTAGAGCGCATTGGCATCTTACTTGAGATTTGGATACGCTCGGCCG\nACTTGGTCTGTTTCACGCTTCCTTAAACAACATGGCTATGCCATTTGAGATAGAGGTATT\nGTTACCAGGAGACCTATCCCCGGCGGAAACATCTGCATTACAGAAATGTGAGGGAAAAAT\nTATTACCTTCTCAACCCTGCGTCATCGAGCTTCACTGGTGGATATAGCGCTGTCGTCATA\nTTACATTAACGGTGCTCCACCAGACACGCTCTCGCTGTTAGAGGCATACCGAATGCGATT\nCGCGGCAGTTATAACACGGGTCATCCCGGGAAAGTTGTTGGCGCATGCCATTGGCGTGGG\nTACTCCTACACCCGGGTTGTTTATTCAAAATACATCCCCCGTTGATCTTTGTAATGGCGA\nTTACATCTGCTTACTTCCTCCGGTTTTCGGGTCCGCAGACTCAATTCGCTTGGACTCTGT\nAGGACTGGAAATTGTTTTCCCTTTAACCATCCCCCAGACCTTAATGCGAGAAATCATCGC\nCAAAGTGGTTGCACGGGCCGTTGAGCGCACGGCCGCGGGTGCTCAAATTTTACCCCACGA\nAGTTCTACGAGGCGCGGATGTCATTTGTTACAATGGAAGGCGTTATGAACTCGAAACAAA\nTTTACAACATCGGGACGGATCGGATGCGGCTATTCGCACATTGGTTTTAAATCTAATGTT\nTTCCATAAACGAGGGATGTCTGCTTTTATTGGCGCTGATTCCAACTTTGTTAGTCCAAGG\nAGCACACGACGGTTATGTAAATTTATTGATACAAACGGCCAATTGCGTTAGAGAAACCGG\nCCAGTTAATTAATATACCGCCAATGCCGCGGATTCAAGACGGCCATCGCCGATTTCCCAT\nATATGAAACTATTTCATCTTGGATATCAACATCATCTAGACTGGGGGATACCTTGGGAAC\nTCGCGCAATTTTACGCGTCTGTGTGTTTGATGGACCCTCTACTGTTCATCCGGGAGACCG\nCACAGCCGTGATTCAAGTGTAAACAGGTGTTAATAAAAACACAACCAGTCTAGTTACATT\nTCACGCGTCTTGTTTTTATTTAATAGGCATAAACACGGAATCCGGTATACATGAACTGCC\nAATATACACGGACATAATTAATGCAACCATCAGATCATCTGACATTGTTCCCGTGGTACC\nTTTACCCGTGTAAGTTTTTGTGTCTAGATGACCCATACCGCCTTTAATTACCTCTGTCAG\nGTTATCCAACTGTTTACATAGATACTCCACGGGGTCTACACCTAACTTTACTGTTAGGGA\nTACAAGCTCCTGTGAGGCTATTATATTTCCGGAGTTAAATCGTTTAACAAAATAGTCTAC\nGGCCGGCGTTTTTTGTTTTTGTAATAAAAAAAAAGGGTACGCCACGCTACATCCGGGAGG\nTATGGAATGATAAAACAGTAACACTGGAGCGGAAGATAGCACGTTTCCCTTTTCGAGGAC\nAGCAAACTGTTGTGCTATAGCCAACGATATGGCAACTGCAGAATCCTGGCTGCTGTTTCC\nCTCTATAGAAACGTGTACGTTTGTAAATGTATTGGGGTGTAAAGCGAGTATGTGGCCTAA\nGCATTGAGTAACGCAACGCCCTATCTCACTGGAAGACGTGCCAGTTAAAGCTCTAAGAAA\nAAAGTGCTCCAATCCAAATATAATCCAATCCGACTTATAACGACCAACAATCGCTACACC\nAGTACCAGACGCTCCTGCATTTACCTCAAATACACGAGCGTCTGGTACTGGTGTAGCGA\n>comp68_c0_seq1 len=407 path=[0:0-406]\nAATTATGGCAAAGGATGATGTAACGGGCATGAAGGGAGAGTGTTTGGTCGTGTGGCCGCC\nCGTTGTATGTGGGGAGGGTGTAGTATTTGACTCACCCTTACAGCGGCTTTCTGGGGAGGT\nGTTGGCCTGTTATGCATTACGTGAACATGCTCGCGTCTGCCAAGTTTTAAATACAGCCCC\nTTTGCGCGTGTTAATAGGTCGCCGGAATGAAGATGATAGATCTCACAGCACACGTGCGGT\nTGATCGTATAATGGGCGAGAACGATACAACACGGGCTGGATCGGCCGCGTCTAGACTTGT\nAAAGCTAATAGTTAACTTAAAAAACATGAGACATGTTGGAGATATTACCGAAACCGTACG\nTTCCTATCTAGAAGAAACGGGCAATCACATTCTGGAAGGAAGTGGAT\n>comp46_c0_seq1 len=708 path=[0:0-707]\nAAATAAACCTTTTATTTTAAGGATGGGTTGTTGCGGCGTGTTTTTTTGTCATAAAAACAA\nGAAGTTATATGAAGCAAGGGGATCGTCAGTAAATTTCAATGATGGACTTGAAAAATCATT\nATGAGCATCTAGAAGATGGTTAATAATAGTGACAAACGTGTGTATAAGGGGCTTGAGATG\nAGCAGCGCAGTCTATGGGGGGAATACAGGCACACGATGGTAGCAATTCCCAGTAAACAAC\nAGTAGGAGGTCCATGTGGGTTGGGATTACGAACCATAATTATCTGTCTTGGTTTATAATC\nCTTATCTTGCATGTGTCCGTATGTCAGATAAGATGCCGGTATTGCTTTTGTTTCCGAATT\nTTGCTCCTGAAGACTCCAGTATACCGGAGTATAACGGCGATCAAAAACATGTTCAAAAAA\nATCGACGTATGTTTTTCTGGCAGCCTCCACAACTTGTCCGGCCCATATGTCGTATAGGAC\nATGGTCCCATATGCAATTTTCCTGTATCTGTTCTCGAATTTTTGTTGCGGTACATAGGAG\nTCCTGAAAGACGCTCCTTTAAATCTCGCGCCGCCTGACTTCGCCATGGCACGCCAACTAA\nATCCGGAGGCGTGTTTGTTTGTAAATTCCACAGCCAGCTTCCCGTGGTACACCAGGTAAA\nTGCGTGAGTGTACACACCCTCGACCCGGAGTACCGGTTCCATGGCGGG\n>comp21_c0_seq1 len=1029 path=[0:0-1028]\nGTTGGTTAACACCGCCCCACCATCATCTGATTTGCAAACATATCGGCGTCGTCTGCCGTG\nGACCCCTGTATTAAAGGGGCCTTGGAACTAGCCTCCACTGCATTTACATCTTGTCCAACT\nGTATCTGTATGTGGGGTGCTTGTTGTATTTTGGGATGAGCATAGACCCGAAACGCTTTGA\nAGCTGTTTTAATAAAATCGATATTCGAGGATCCCGTGTCCCCTCTGGTATATTTGTATGG\nTGCGACAAAGGCATTTGTGTCCCATTTTGTGATTTTAGCTCTGTAACCTCCTGTTGCAGT\nTTTGCCACAACCCCAGCAAGCTCTTCGTGCTGACCATTAGAAACTCTGTGTCTCCTCTGC\nCAATATGATGGAGAAACTCGACGTCTCCGATGCGTTATATACGTTGGTTCACCGGGAAAA\nTATATATTTGAGGGAAACTCTCCGTCCATTTGAGACTCCCCACTAGAAAAAGAATCCAAT\nTCCCTTTGATCCATGCTCTTGAAATCCCGTTTTCCTGGACGACGGACATCGGTTTTGTCT\nGGAAAATTTACACACGGGGTCTGCAAGTCAATACCCCGTTCGGCGGCCAATGCGTTCATA\nAATGCGGACATTTGCATTTCCAAACGATTGGGTGGTGGATATCCCGGAAACCCGTACGGT\nCCCCCGAAGTGTCCCGGAGGGCAACCATAACCCCCTGTATTAGGTGGGAAGGCAGGCGGG\nTGTGGAGATCCATATGGCCCGACGATATACTGTCCGTTATTTGGAGCTCCAATTGATACC\nTGCGGATTTTTAGTCTGCCCGGTTAACAGCTGTGAATAATACGCGGTAGGTATCAGTACA\nAATTCCCCTCCGGTTGGAACGCCCGACGGGGGCTGTGGTGAGATACCACTAGCGTTACCT\nGCTACAGAAGCCATATCGCTGTCGTTCCTACACAACTGCGTAACCTTTAAATGCGGAACA\nGTCTTTTCACAATCTTCATTTGATTCCCCAACACCCAACGCGAGATCGTATATGGGCCCG\nCCGGGGTGG\n>comp56_c0_seq1 len=388 path=[0:0-387]\nGTCACAAACTCGCCCGGTAACCGTCGTACGTGCCCCTATGGGCTCTGGTAAAACAACAGC\nCTTGCTTGAGTGGCTTCAACACGCGTTAAAGGCAGATATTAGCGTACTGGTTGTCTCATG\nTCGCCGTAGCTTTACCCAGACGTTGATTCAACGGTTTAACGATGCAGGCCTCTCCGGATT\nCGTAACATATTTGACATCCGAGACATATATTATGGGTTTTAAACGTTTGATTGTGCAACT\nTGAAAGCCTACACCGCGTATCCAGCGAAGCTATCGACAGCTACGACGTATTAATACTGGA\nTGAGGTAATGTCAGTGATTGGACAATTATACTCCCCCACAATGAGACGTCTTTCCGCGGT\nTGATAGCCTATTATATCGTCTTTTAAAT\n>comp52_c0_seq1 len=421 path=[0:0-420]\nAAGTCTGATACAACGCTTGTAGCACCATGATGTGTACGTGTTCCATTTTCCACCACAAAT\nCCCGTTAAACGCAAAATGGTGAGGTTAATAAAAAGCTCCAATGGATCCTTTTCGTCTGGC\nATGACCAAGGGCCTTGTTACCCAAATGGGAACATTTGTATGACCGGTAATAACAGTATCC\nAACGTACCCACCGCATTTTGTACGTATCCATTGCTAATTTCATGCCCATGTTGTAGTAGT\nTTTTCGACAACCATGTTGACATCACCACTCTGTTCAAATAGAAATGGCTTCCGATCTTTC\nAAACTGCTTCCTACATTCATGTTCCGTGAAAAAGTGGGACTGGATTCAGGCGTATCTACA\nTTGGATACATTTAACACAACGTCTGGGGTGTTAGCAACTTCTCGTAGGCGGGGTAATACA\nT\n>comp51_c0_seq1 len=509 path=[0:0-508]\nGCTTTAATACACAACGTGTACGTTGGGATCACGTAGAGCGGCAAGAATGTGATCGCTAAT\nTTCTGCGGATTTTTCATATCGTTCCCGTAGAGGGTTTAGATTCATTTTTAAGAACCTAGA\nGGAGACCGTACGCGACATGGCAACATACACACTATTTAGGCGCAGTTTATCCGCCGTAAA\nACAGATAGCTACCTTCTCTAAACTCAGACCCTGTGAGCGTGCAATTGTCATGGCTAGTTT\nAGAACTAAGGCCATAGTCCACCGTGGTGGCCATTGCCAATTCTGCATCCTCTATAGACTC\nGGTAAATTCACATACGTTAGCGTTTACGATGGACACAAACCCATGTTGATCCTGTAAGAC\nCATAAGAGGTACGTGTAGAGCATATAACATTTCGGTAGTTTCGCGGTACAGCTTTTTTCG\nGGTCAGTTCCTCTACAAAGACTGGCACGGGTGCAAAAGTATACCCCAAAAGGGTATACGT\nATCTGTTTGGGGTATACTTTTGCACCCGT\n>comp6_c0_seq1 len=4015 path=[0:0-1206 1207:1207-4014]\nCCGTCCCCCGGCAGGATCTCGGATGGGGACGGAGGTGCTAAAATCATAGCTTCGATGCTA\nCTACCGTAGTTTCTATTTTCAACAACTTTTGCGTAAGGATGATCCGCTCGTACATGTCTC\nGGTTCTTGAGGATGTTTGACCGCATATGCGTCTAACTTACGCTTAATGTGGTGGGTAAGA\nAAACCCACCGACCGTGGTAAATGAACCGAAAATGAGGGTTGTTGAACCAACGGAGATTTG\nTTTTCTTCAACAAGACCACATCTAACTAGAGGCAGTCCCAGTTCTCGGCGGCGGTAATTT\nATTTCCCTCAAGGCAGACGCTGTTAGTGGTTTCCCTTCTAATAACACAATGCCGTGGTTG\nCATAATACAGGATGAAACGCACACGTGAACTGTCGACGTTCGGTCCAGGTGAATTTTAAA\nGCCGCAAACACGTCCGGGTGTGCAGATTGACTGGCGTACAAACGCCAGGAAAATTCACGC\nGTTACGGTTAAATATAAATGTAGGTACAAAAGACGCGCCAAACTTGCCACCTCACGATAA\nTATCTAAGTAGAATACTTTGCCTGAGTTGCGTGTAAGCTTTCTGGTCAGGGTTTTGTATA\nTTAAGACCTATTGTCGTCCTTTTCGCCGTTCCTTGGAGATAACGTATAATCGATTTACAA\nTAAGTAACTAGTAGTTTTGTGTATGCTTCTTCCCGGGCGCGTAGTTCTACGGTAAACGAA\nTCCTGGACCTCCTGAACGTAAGCTGGAAGCCCCGTCGGTTGCTTTGGTGGACTAGGCAAT\nCGAACGGAACCCCGGGTTGTTAAATTAAACATTTCAACATGGTCTTTGGTTGAAACGGTT\nGAGATAACGTCATCTGGATCCGGGGATAAAACCATCATATCGGAATATAGGTCCTCATTA\nATAGGAAAACATGAGAATAAATCCTCGTTCCAGGTTTCAAGACATGATAGTAAACGCGGC\nCCTTCTGAAAAATCAAGATCCCGTATTAACTGTTGATATAAAATTTTAGGGCTAGCTACC\nCAAGGCGGAGACGGAGCAGTTTTAACTGCATGTGAATATAACGACGTTTCGGATCCAATA\nTCCGATGCTACATCACCAAACAACGATTCATCAAATGCGTCCACAACCGCTTGTTCCGTT\nTTACTACGATTCCACGTATCTGTACTATGATGTTCGGTTCCTAAATTACACTCCATACTT\nATAGAGTAAAATCTTTAGTTTAAATAAGCGATTCCCTTTATCAAAACCCGCCGTCTAATG\nGGGTTTGTTTGGTAGCAACTGATTATAAACTGTTCATAATACCACGTGGTACTATTTAAA\nCAGTTTATAATATGTGACATATAATACACATTTATAATAAACACAAACCACGACTGTCTT\nTTATACGTTTATTTATTATACATAATACCGGGTAAACCGTTACTGCGTAATTATATCCCT\nATTTTCGCGCATCAGTTCTTGATGCCGAACGGGCCCTACTTCGATTAGTTATACGCCCAG\nTCGTTTGTGTATCCGTTCGACTTTTTGGCTTACGAACTTGTGCGTACATAGGTTCATTAC\nCCATGCCCCCCTGTAAATCTCCAGTTTTTCGATTATGTCCACGTTTGGATACCGATGCTC\nCTTCACCTAGTTCTGCTTCATTAGCGGCTTGTATTAAATTTAAACCCTCATGCACCGTAA\nTACGAATAACGGCTCCGGTTAACAAACGGTCTAATTCGGCGTTATTCCTTGGGGGATTAC\nTATTCCAAGCCGCTTCGGCAGCCTTTTGTGCCTGCATGGCGGCTACGCGCCGGACCGCTT\nCACAAAAGACGCGTTTGTTATATGATGGCGTAGGACCGCACCACGAGCTTGTTGCGGTTT\nTTGGTGCAGTGCTGAAGGAAATTGGTCTCCCGCTGGCAATTGCGCCCGCTCCCGGGGGAG\nCTCGCTTCGGTGAATCCTCTAATTTAGGTTTAACCGCCGCATTTTTAGTAAAAGATCTAG\nATGGTTTTTCTACACTTAGCGGGTTTTCATATACAGCATCTTCAACCAGTTCATGTCTCA\nAACGGGCCTCCCGAAAGGCGGCCACTACTTCATCGATGTCTTCAAAGTCATCTTCCGATC\nCGCTGGAGTCGTTTGGTTGATGTACGCGAGGGGTCGTATTTTTATGTTCAAAATAAAGAT\nCCGCGTACACTGGAGAAGGAGAATCGGCCCCAACTGTGGTAATGTAACCCAACGAGTCGT\nCTGAATCATCGGGGGGTCCTACGACCACACTTCGCCGCGCGGTTCGATATTGTCCGGAAT\nAACTAGGCGTTGTTTTACGACGCACTGCATTAGAGCGACAAAGTCTGTCACCGTCGGAAG\nATGCCATTACGTAAATAAACGATAGGGTCGTGAAATATCCAAACACGGCAGACCGCGTAT\nTAAACAGGGACCCTCTTATACACGCCTGCCCCTTTTATAGGCAAACGGGTTTACCACGTG\nCTGCGTAATACAGAACGAGTAAATAACCGGAAACACGCATGATAAGCTAACGAAATAAGG\nGCTACACACACCCCCAACAGGGATGCGTAGAAGAAAAGGGTGGTGATCATTGATCCGTCG\nATATAAACTCCACGAGCCGAACAGCTGGCATGCCAAAAATTCCGTTCTGCAAAGTTTGGC\nTCCCCACTGCTGTCTTCACAAAAAAATAAAATTTGCATCGTTATTAATATGAACGAAGCG\nGTAATTGATCCCATCTTGGAAACGGCAGTAAATACAGGTGATATGTTTTGTAGCCAAACT\nATTCCGAATCGGTGTTTAAAAGATACAATTTTAATAGAAGTTCAACCTGAATGTGCAGAT\nACGCTGCAATGCGTGTTAGACGATAAAGTAAGTCGACATCAACCGTTGTTACTCCGGAAC\nCACAAGAAACTCGAACTGCCATCTGAAAAATCTGTAACACGGGGCGGTTTTTATATGCAG\nCAGTTGGAGCTGTTGGTTAAGTCGGCGCCTCCCAATGAATACGCACTGTTGTTAATTCAA\nTGCAAAGATACTGCCCTTGCTGATGAAGACAATTTTTTTGTCGCCAACGGAGTTATTGAT\nGCGGGTTACAGAGGAGTAATTTCAGCCCTTTTGTATTACCGGCCAGGAGTAACCGTTATT\nTTACCCGGACATTTAACAATCTACTTGTTCCCGGTAAAATTAAGACAAAGTCGCCTTCTC\nCCAAAAAACGTTCTTAAACATCTGGATCCAATTTTTAAATCGATACAAGTTCAACCCTTA\nTCAAACTCGCCGTCAAATTATGAAAAACCCGTTATACCTGAATTTGCTGATATTTCCACG\nGTACAGCAGGGGCAACCTTTACATAGGGATTCTGCAGAATACCATATCGATGTTCCCTTA\nACCTACAAACATATCATCAATCCAAAACGCCAAGAAGACGCGGGATATGATATTTGTGTA\nCCATATAACCTATATTTAAAAAGGAATGAATTTATAAAAATTGTCTTACCGATTATAAGA\nGACTGGGACTTACAACATCCGAGTATAAACGCTTATATTTTTGGAAGATCATCGAAAAGC\nCGATCAGGCATTATCGTGTGTCCAACGGCATGGCCTGCAGGAGAACACTGTAAATTCTAC\nGTATATAATCTCACGGGTGATGACATACGTATAAAAACGGGAGATCGTCTTGCACAGGTC\nCTGTTAATAGATCACAACACCCAAATACACTTAAAACACAACGTTTTAAGTAATATTGCA\nTTTCCTTATGCTATCCGCGGTAAATGTGGCATACCGGGTGTACAATGGTATTTTACTAAA\nACGTTAGATCTAATAGCCACACCCAGCGAACGGGGAACGCGTGGATTTGGTTCAACTGAT\nAAAGAAACAAACGATGTCGATTTTCTACTAAAACATTAAATGTAATAACCACGCCAGCCA\nGCAATGTTTTAATTTTATATACAAAATAAAAACATACACCAGAAACGTTTTTAGTTTTTA\nTTTCAATATTTATACAAGCATAACATGGGATTTCTTGATCGCGGGGGTTGTGCGT\n>comp6_c0_seq2 len=1241 path=[0:0-1206 4015:1207-1240]\nCCGTCCCCCGGCAGGATCTCGGATGGGGACGGAGGTGCTAAAATCATAGCTTCGATGCTA\nCTACCGTAGTTTCTATTTTCAACAACTTTTGCGTAAGGATGATCCGCTCGTACATGTCTC\nGGTTCTTGAGGATGTTTGACCGCATATGCGTCTAACTTACGCTTAATGTGGTGGGTAAGA\nAAACCCACCGACCGTGGTAAATGAACCGAAAATGAGGGTTGTTGAACCAACGGAGATTTG\nTTTTCTTCAACAAGACCACATCTAACTAGAGGCAGTCCCAGTTCTCGGCGGCGGTAATTT\nATTTCCCTCAAGGCAGACGCTGTTAGTGGTTTCCCTTCTAATAACACAATGCCGTGGTTG\nCATAATACAGGATGAAACGCACACGTGAACTGTCGACGTTCGGTCCAGGTGAATTTTAAA\nGCCGCAAACACGTCCGGGTGTGCAGATTGACTGGCGTACAAACGCCAGGAAAATTCACGC\nGTTACGGTTAAATATAAATGTAGGTACAAAAGACGCGCCAAACTTGCCACCTCACGATAA\nTATCTAAGTAGAATACTTTGCCTGAGTTGCGTGTAAGCTTTCTGGTCAGGGTTTTGTATA\nTTAAGACCTATTGTCGTCCTTTTCGCCGTTCCTTGGAGATAACGTATAATCGATTTACAA\nTAAGTAACTAGTAGTTTTGTGTATGCTTCTTCCCGGGCGCGTAGTTCTACGGTAAACGAA\nTCCTGGACCTCCTGAACGTAAGCTGGAAGCCCCGTCGGTTGCTTTGGTGGACTAGGCAAT\nCGAACGGAACCCCGGGTTGTTAAATTAAACATTTCAACATGGTCTTTGGTTGAAACGGTT\nGAGATAACGTCATCTGGATCCGGGGATAAAACCATCATATCGGAATATAGGTCCTCATTA\nATAGGAAAACATGAGAATAAATCCTCGTTCCAGGTTTCAAGACATGATAGTAAACGCGGC\nCCTTCTGAAAAATCAAGATCCCGTATTAACTGTTGATATAAAATTTTAGGGCTAGCTACC\nCAAGGCGGAGACGGAGCAGTTTTAACTGCATGTGAATATAACGACGTTTCGGATCCAATA\nTCCGATGCTACATCACCAAACAACGATTCATCAAATGCGTCCACAACCGCTTGTTCCGTT\nTTACTACGATTCCACGTATCTGTACTATGATGTTCGGTTCCTAAATTACACTCCATACTT\nATAGAGTGTAATTTAGGAACCGAACATAGTACAGATACGTG\n>comp45_c0_seq1 len=1423 path=[0:0-1422]\nGGCTATGTTACCTGCACTTACTGTATGTCGAACTAAGGTATTCCTTATAAATCTATGTGC\nATCAAAGGCCGCTTCCTGAATGCGATTGTCGATAATACACCCTGCCTGGGAAACCTTAGC\nTAAAAACACGTTTCGTGCCCCAAACCCATTTTGCATCGAAACAAATGTCTGCAATAAGGC\nCTCTCCATAAACGTTTACCCTGAGTGTTTTTTCTAGCTCTTGGCGCTGTTCGCGGATACA\nTCTACCGAGGCTGGTTAGAGAGCGCTTAGACAGATGTTCAAGATATACTCGTTTTCTTTC\nCGCAGCGTCAATTTTTGCTTTGGATAACAGGTTTTCCCATCCATGAACAGCAAAAGTTAT\nGCTACTATCATCGTTCAGATCACATTCGGATGCTGTAGCGCTGTCACTCGCCTCTTTGGT\nTAAATCATCCTCACACCCAACTCTTTCTAAAAGTTGGCGTAAGGCGGCTTCGTTATCATG\nACTCGGGTTAGAAATGTGACGCATGAGAGGCGACGATAGATGATGGGCATAACAGGCTTT\nAATTAATGCTTCTATCTGACTGTCTGGTGAGGATGAGCGATTGCCAACCAAAATACTATC\nAATTGCATCCAGAGATCCGAGTTCTTCAGAAAACGCCCTATCAAAGTGTATGGGAGTTTT\nTCCAAATAACGCCAACTCAACCGTTACGGCTGTAAGTTCTGCGTGTTTTTCATGTTCGTT\nTAATACATCCAAATTATCAACAAACACGTCTAAAGTACGTTGGGGTCCTTCAGTGGAATT\nAGACGTTAACCAGAATTTAAGCTCGCTGATGGCGTACATACACCGAGGGGCAGGTTTAAA\nAACATTATAAGAATCAAGCATGGTGCTCGCAATTTCGTATGTTTGGTCAAACGTATCGTT\nCTTTGCTCCCATGGGATTGACTACCGTCTTGGTTTGAAGTGTTCGTAACGCTTCAACGGC\nGGATTGACGTTTGATATCCGGTACATCAGGGATATATGGTAAACACCGAATAATATCGTC\nAACATCCACGTTAACCCGAACTTGCTTAGTAACGTGATCGCAGATACATCCTAATAATCT\nACGATGTAAGGTCTCACCTTGGTTAGCTGTTATACATAATTCTTCAAAACATATAGCACA\nTGGATGCGCCGGATCAAACAACTCCACGGGTGGTATTAGACCGCTTCCTATAGTATCTGT\nCATAAACCGCGTCACGGTTTCCAATGTGTTTAGCGCCTCACGAGAAGACGTGATAATATA\nGCAGTAATTAAGCTGTTTTAAAAAATTCTCAATGTCGTGTAAAAACTGAATTTCACTCGA\nTACGTAACCTCCGTATGTTGTTAACGACAGCTCATGGTGATATTGGCAGGTTTTTAAGTT\nAAACGCTGAGACAAAGTAATCTTTGATACAGTTTGAGTCTTTG\n>comp18_c0_seq1 len=4325 path=[0:0-4324]\nCCATTATTTCATCAGATCCCGTGGGTGTGGTTTCCTTTATTAAAGCCACGGTATCCCTCA\nGCTGGCGCATACCCTCGCAAAACTGGTGATACTTAGTAGGGGTATGTATATTAGCGCTAA\nAACGGCAAGATTTTAATTCCACTATAAAACAAACGGTCTTTCCGGCACCACTGGATTCCG\nTTTGTATAATACAAATACAATCGGGGCGTCGGCGTCCCAAATTTACTTCAAACGACATTG\nATATGCGTACAGCCCTTTGAACATCCACGTGGGATAACGGCGACAGGAGTTTTGCCAGCC\nTCGGGTTGAACGCGTCCGCGAAACCTCGACGTACGTTATCAATATCCTTTTTGAGTACAT\nCGTAAAAACGAGTGTGACAACGTTGTCCCAAACGAAAACACTTGGCCCGAATTTGACTAG\nCGGACATATTTGAAGTTCCGTCCCAGAAGATAACCTAAGACGCGTTTGTCTACAATAAAC\nATGTCAACGGATAAAACCGATGTAAAAATGGGCGTTTTGCGTATTTATTTGGACGGGGCG\nTATGGAATTGGAAAAACAACCGCCGCCGAAGAATTTTTACACCACTTTGCAATAACACCA\nAACCGGATCTTACTCATTGGGGAGCCCCTGTCGTATTGGCGTAACCTTGCAGGGGAGGAC\nGCCATTTGCGGAATTTACGGAACACAAACTCGCCGTCTTAATGGAGACGTTTCGCCTGAA\nGACGCACAACGCCTCACGGCTCATTTTCAGAGCCTGTTCTGTTCTCCGCATGCAATTATG\nCATGCGAAAATCTCGGCATTGATGGACACAAGTACATCGGATCTCGTACAAGTAAATAAG\nGAGCCGTATAAAATTATGTTATCCGACCGACACCCAATCGCCTCAACTATATGTTTTCCC\nTTGTCCAGATACTTAGTGGGAGATATGTCCCCAGCGGCGCTTCCTGGGTTATTGTTTACG\nCTTCCCGCTGAACCCCCCGGGACCAACTTGGTAGTTTGTACCGTTTCACTCCCCAGTCAT\nTTATCCAGAGTAAGCAAACGGGCCAGACCGGGAGAAACGGTTAATCTGCCGTTTGTTATG\nGTTCTGAGAAATGTATATATAATGCTTATTAATACAATTATATTTCTTAAAACTAACAAC\nTGGCACGCGGGCTGGAACACACTGTCATTTTGTAATGATGTATTTAAACAGAAATTACAA\nAAATCCGAGTGTATAAAACTACGCGAAGTACCTGGGATTGAAGACACGTTATTCGCCGTG\nCTTAAACTTCCGGAGCTTTGCGGAGAGTTTGGAAATATTCTGCCGTTATGGGCATGGGGA\nATGGAGACCCTTTCAAACTGCTTACGAAGCATGTCTCCGTTCGTATTATCGTTAGAACAG\nACACCCCAGCATGCGGCACAAGAACTAAAAACTCTGCTACCCCAGATGACCCCGGCAAAC\nATGTCCTCCGGTGCATGGAATATATTGAAAGAGCTTGTTAATGCCGTTCAGGACAACACT\nTCCTAAATATACCTAGTATTTACGTATGTACCAGTAAAAAGATGATACACATTGTCATAC\nTCGCGTGTACGTGTTTTTCTTTTTTATATATGCGTCATTTATTACCACATCCTTTAATCC\nCGCCTTTATCTCCCTAAAACGGAGTGGTAATATTAAAAGCCGCCAAGCCTGTTGGTGGGT\nGAGGAGGGGTAAAGGCACGCTGTGTGCATAACGTTGCGGTGATATTGTAGCGCAAGTAAC\nAGCGACTATGTTTGCGCTAGTTTTAGCGGTGGTAATTCTTCCTCTTTGGACCACGGCTAA\nTAAATCTTACGTAACACCAACCCCTGCGACTCGCTCTATCGGACATATGTCTGCTCTTCT\nACGAGAATATTCCGACCGTAATATGTCTCTGAAATTAGAAGCCTTTTATCCTACTGGTTT\nCGATGAAGAACTCATTAAATCACTTCACTGGGGAAATGATAGAAAACACGTTTTCTTGGT\nTATTGTTAAGGTTAACCCTACAACACACGAAGGAGACGTCGGGCTGGTTATATTTCCAAA\nATACTTGTTATCGCCATACCATTTCAAAGCAGAACATCGAGCACCGTTTCCTGCTGGACG\nTTTTGGATTTCTTAGTCACCCTGTGACACCCGACGTGAGCTTCTTTGACAGTTCGTTTGC\nGCCGTATTTAACTACGCAACATCTTGTTGCGTTTACTACGTTCCCACCAAACCCCCTTGT\nATGGCATTTGGAAAGAGCTGAGACCGCAGCAACTGCAGAAAGGCCGTTTGGGGTAAGTCT\nTTTACCCGCTCGCCCAACAGTCCCCAAGAATACTATTCTGGAACATAAAGCGCATTTTGC\nTACATGGGATGCCCTTGCCCGACATACTTTTTTTTCTGCCGAAGCAATTATCACCAACTC\nAACGTTGAGAATACACGTTCCCCTTTTTGGGTCGGTATGGCCAATTCGATACTGGGCCAC\nCGGTTCGGTGCTTCTCACAAGCGACTCGGGTCGTGTGGAAGTAAATATTGGTGTAGGATT\nTATGAGCTCGCTCATTTCTTTATCCTCTGGACTACCGATAGAATTAATTGTTGTACCACA\nTACAGTAAAACTGAACGCGGTTACAAGCGACACCACATGGTTCCAGCTAAATCCACCGGG\nTCCGGATCCGGGGCCATCTTATCGAGTTTATTTACTTGGACGTGGGTTGGATATGAATTT\nTTCAAAGCATGCTACGGTCGATATATGCGCATATCCCGAAGAGAGTTTGGATTACCGCTA\nTCATTTATCCATGGCCCACACGGAGGCTCTGCGGATGACAACGAAGGCGGATCAACATGA\nCATAAACGAGGAAAGCTATTACCATATCGCCGCAAGAATAGCCACATCAATTTTTGCGTT\nGTCGGAAATGGGCCGTACCACAGAATATTTTCTGTTAGATGAGATCGTAGATGTTCAGTA\nTCAATTAAAATTCCTTAATTACATTTTAATGCGGATAGGAGCAGGAGCTCATCCCAACAC\nTATATCCGGAACCTCGGATCTGATCTTTGCCGATCCATCGCAGCTTCATGACGAACTTTC\nACTTCTTTTTGGTCAGGTAAAACCCGCAAATGTCGATTATTTTATTTCATATGATGAAGC\nCCGTGATCAACTAAAGACCGCATACGCGCTTTCCCGTGGTCAAGACCATGTGAATGCACT\nTTCTCTCGCCAGGCGTGTTATAATGAGCATATACAAGGGGCTGCTTGTGAAGCAAAATTT\nAAATGCTACAGAGAGGCAGGCTTTATTTTTTGCCTCAATGATTTTATTAAATTTCCGCGA\nAGGACTAGAAAATTCATCTCGGGTATTAGACGGTCGCACAACTTTGCTTTTAATGACATC\nCATGTGTACGGCAGCTCACGCCACGCAAGCAGCACTTAACATACAAGAAGGCCTGGCATA\nCTTAAATCCTTCAAAACACATGTTTACAATACCAAACGTATACAGTCCTTGTATGGGTTC\nCCTTCGTACAGACCTCACGGAAGAGATTCATGTTATGAATCTCCTGTCGGCAATACCAAC\nACGCCCAGGACTTAACGAGGTATTGCATACCCAACTAGACGAATCTGAAATATTCGACGC\nGGCATTTAAAACCATGATGATTTTTACCACATGGACTGCCAAAGATTTGCATATACTCCA\nCACCCATGTACCAGAAGTATTTACGTGTCAAGATGCAGCCGCGCGTAACGGAGAATATGT\nGCTCATTCTTCCAGCTGTCCAGGGACACAGTTATGTGATTACACGAAACAAACCTCAAAG\nGGGTTTGGTATATTCCCTGGCAGATGTGGATGTATATAACCCCATATCCGTTGTTTATTT\nAAGCAAGGATACTTGCGTGTCTGAACATGGTGTCATAGAGACGGTCGCACTGCCCCATCC\nGGACAATTTAAAAGAATGTTTGTATTGCGGAAGTGTTTTTCTTAGGTATCTAACCACGGG\nGGCGATTATGGATATAATTATTATTGACAGCAAAGATACAGAACGACAACTAGCCGCTAT\nGGGAAACTCCACAATTCCACCCTTTAATCCAGACATGCACGGGGATGACTCTAAGGCTGT\nGTTGTTGTTTCCAAACGGAACTGTGGTAACGCTTCTAGGATTCGAACGACGACAAGCCAT\nACGAATGTCGGGACAATACCTTGGGGCCTCTTTAGGAGGGGCGTTTCTGGCGGTAGTGGG\nGTTTGGTATTATCGGATGGATGTTATGTGGAAATTCCCGCCTTCGAGAATATAATAAAAT\nACCTCTGACATAAAAAACATGTATAATAAAAAGTCACTATAAACGTATTCTCTACAATAC\nTTTAT\n>comp22_c0_seq1 len=2291 path=[0:0-753 754:754-773 774:774-2290]\nTGGGCACTGTCACAGTCTTCCGAGTACTTCACCAAAATGGAAAATACTCAGAAGACTGTG\nACAGTGCCCACGGGGCCCCTGGGTTACGTTTATGCGTGCCGGGTTGAAGATTTGGATCTG\nGAGGAAATTTCATTTTTGGCCGCTCGTAGCACGGACTCTGATTTGGCTTTATTACCTTTG\nATGCGTAATTTGACCGTGGAAAAAACTTTTACATCCAGCCTGGCGGTGGTTTCTGGAGCA\nCGCACTACGGGTCTTGCCGGAGCTGGTATTACCTTAAAACTCACTACCAGTCATTTCTAT\nCCATCTGTCTTTGTCTTTCACGGAGGCAAACACGTTTTACCCAGCTCCGCGGCCCCAAAT\nCTCACACGCGCGTGTAACGCGGCTCGAGAACGGTTTGGGTTTTCACGCTGCCAAGGGCCT\nCCTGTTGACGGTGCTGTTGAGACGACCGGCGCTGAGATATGCACCCGCCTTGGATTAGAG\nCCAGAAAATACAATATTATACTTGGTGGTCACGGCATTGTTTAAGGAAGCCGTATTTATG\nTGCAACGTGTTTCTGCATTATGGAGGACTCGATATTGTTCATATTAACCATGGGGATGTT\nATACGTATACCGTTATTTCCGGTACAACTTTTCATGCCCGATGTTAACCGTCTGGTACCC\nGACCCATTCAACACTCATCACAGGTCTATCGGAGAGGGTTTTGTATACCCAACACCCTTT\nTATAACACCGGGTTGTGCCATTTAATACATGACTGTGTTAAATGGCACAACCCGGTGTTA\nTTGCTCCCATGGCCGTTGCCTTGCGCGTCAGAAATGTAACTGCCGTCGCCCGAGGAGCGG\nCCCACCTTGCTTTTGATGAAAATCACGAGGGGGCAGTACTCCCCCCTGACATTACGTACA\nCGTATTTTCAGTCCTCTTCAAGTGGAACCACTACCGCCCGTGGAGCGCGTCGAAACGATG\nTCAACTCCACGTCTAAGCCTAGCCCATCGGGGGGGTTTGAAAGACGGTTGGCGTCTATTA\nTGGCCGCTGACACAGCCTTGCACGCAGAAGTTATATTCAACACTGGAATTTACGAAGAAA\nCTCCAACAGATATCAAAGAATGGCCAATGTTTATAGGCATGGAGGGCACTTTGCCAAGGC\nTAAACGCTCTGGGGTCATATACCGCTCGTGTGGCCGGGGTCATTGGTGCGATGGTTTTCA\nGCCCAAATTCTGCGTTGTATCTAACTGAGGTGGAGGATAGCGGGATGACCGAAGCCAAGG\nATGGGGGACCGGGTCCATCATTTAATCGATTTTACCAGTTTGCCGGACCTCATTTAGCTG\nCGAATCCCCAAACAGATCGAGATGGCCACGTTCTATCCAGTCAGTCTACGGGTTCATCAA\nACACAGAGTTTAGCGTGGATTATTTGGCACTCATTTGTGGATTTGGAGCACCCCTGTTGG\nCGCGACTGCTTTTTTATCTAGAACGCTGTGACGCTGGTGCGTTTACAGGGGGTCACGGGG\nATGCGTTAAAATATGTTACGGGGACCTTTGACTCTGAAATTCCATGTAGTTTATGTGAAA\nAACATACGCGGCCGGTATGCGCTCACACAACAGTACACCGACTTAGACAACGCATGCCGC\nGATTTGGACAAGCCACCCGTCAACCTATTGGGGTGTTTGGAACAATGAACAGCCAATATA\nGCGACTGCGATCCTCTAGGAAACTATGCTCCATATTTAATCCTTCGAAAACCCGGGGATC\nAAACGGAAGCAGCAAAGGCAACCATGCAGGACACTTATAGGGCTACACTAGAACGCTTGT\nTTATCGATCTAGAACAAGAGCGACTACTGGATCGCGGTGCCCCATGTTCTTCCGAGGGAC\nTATCGTCTGTCATTGTGGATCATCCAACGTTTCGTCGCATATTAGACACACTGCGTGCGC\nGTATAGAACAGACAACAACACAATTTATGAAAGTGTTGGTTGAGACCCGCGATTATAAGA\nTCCGTGAAGGATTATCCGAAGCCACCCATTCAATGGCGTTAACGTTTGATCCATACTCAG\nGAGCATTTTGTCCCATTACCAATTTTTTAGTTAAACGAACACACCTAGCCGTGGTACAAG\nACTTAGCATTAAGCCAGTGTCATTGTGTATTTTACGGACAGCAAGTTGAGGGGCGGAACT\nTTCGTAACCAATTCCAGCCTGTTTTGCGGCGGCGTTTTGTTGACCTGTTTAATGGGGGGT\nTTATATCAACACGCTCTATAACCGTAACATTATCTGAAGGTCCTGTATCCGCCCCAAATC\nCGACATTGGGG\n>comp22_c0_seq2 len=2271 path=[0:0-753 774:754-2270]\nTGGGCACTGTCACAGTCTTCCGAGTACTTCACCAAAATGGAAAATACTCAGAAGACTGTG\nACAGTGCCCACGGGGCCCCTGGGTTACGTTTATGCGTGCCGGGTTGAAGATTTGGATCTG\nGAGGAAATTTCATTTTTGGCCGCTCGTAGCACGGACTCTGATTTGGCTTTATTACCTTTG\nATGCGTAATTTGACCGTGGAAAAAACTTTTACATCCAGCCTGGCGGTGGTTTCTGGAGCA\nCGCACTACGGGTCTTGCCGGAGCTGGTATTACCTTAAAACTCACTACCAGTCATTTCTAT\nCCATCTGTCTTTGTCTTTCACGGAGGCAAACACGTTTTACCCAGCTCCGCGGCCCCAAAT\nCTCACACGCGCGTGTAACGCGGCTCGAGAACGGTTTGGGTTTTCACGCTGCCAAGGGCCT\nCCTGTTGACGGTGCTGTTGAGACGACCGGCGCTGAGATATGCACCCGCCTTGGATTAGAG\nCCAGAAAATACAATATTATACTTGGTGGTCACGGCATTGTTTAAGGAAGCCGTATTTATG\nTGCAACGTGTTTCTGCATTATGGAGGACTCGATATTGTTCATATTAACCATGGGGATGTT\nATACGTATACCGTTATTTCCGGTACAACTTTTCATGCCCGATGTTAACCGTCTGGTACCC\nGACCCATTCAACACTCATCACAGGTCTATCGGAGAGGGTTTTGTATACCCAACACCCTTT\nTATAACACCGGGTTGTGCCATTTAATACATGACTGTGTTATTGCTCCCATGGCCGTTGCC\nTTGCGCGTCAGAAATGTAACTGCCGTCGCCCGAGGAGCGGCCCACCTTGCTTTTGATGAA\nAATCACGAGGGGGCAGTACTCCCCCCTGACATTACGTACACGTATTTTCAGTCCTCTTCA\nAGTGGAACCACTACCGCCCGTGGAGCGCGTCGAAACGATGTCAACTCCACGTCTAAGCCT\nAGCCCATCGGGGGGGTTTGAAAGACGGTTGGCGTCTATTATGGCCGCTGACACAGCCTTG\nCACGCAGAAGTTATATTCAACACTGGAATTTACGAAGAAACTCCAACAGATATCAAAGAA\nTGGCCAATGTTTATAGGCATGGAGGGCACTTTGCCAAGGCTAAACGCTCTGGGGTCATAT\nACCGCTCGTGTGGCCGGGGTCATTGGTGCGATGGTTTTCAGCCCAAATTCTGCGTTGTAT\nCTAACTGAGGTGGAGGATAGCGGGATGACCGAAGCCAAGGATGGGGGACCGGGTCCATCA\nTTTAATCGATTTTACCAGTTTGCCGGACCTCATTTAGCTGCGAATCCCCAAACAGATCGA\nGATGGCCACGTTCTATCCAGTCAGTCTACGGGTTCATCAAACACAGAGTTTAGCGTGGAT\nTATTTGGCACTCATTTGTGGATTTGGAGCACCCCTGTTGGCGCGACTGCTTTTTTATCTA\nGAACGCTGTGACGCTGGTGCGTTTACAGGGGGTCACGGGGATGCGTTAAAATATGTTACG\nGGGACCTTTGACTCTGAAATTCCATGTAGTTTATGTGAAAAACATACGCGGCCGGTATGC\nGCTCACACAACAGTACACCGACTTAGACAACGCATGCCGCGATTTGGACAAGCCACCCGT\nCAACCTATTGGGGTGTTTGGAACAATGAACAGCCAATATAGCGACTGCGATCCTCTAGGA\nAACTATGCTCCATATTTAATCCTTCGAAAACCCGGGGATCAAACGGAAGCAGCAAAGGCA\nACCATGCAGGACACTTATAGGGCTACACTAGAACGCTTGTTTATCGATCTAGAACAAGAG\nCGACTACTGGATCGCGGTGCCCCATGTTCTTCCGAGGGACTATCGTCTGTCATTGTGGAT\nCATCCAACGTTTCGTCGCATATTAGACACACTGCGTGCGCGTATAGAACAGACAACAACA\nCAATTTATGAAAGTGTTGGTTGAGACCCGCGATTATAAGATCCGTGAAGGATTATCCGAA\nGCCACCCATTCAATGGCGTTAACGTTTGATCCATACTCAGGAGCATTTTGTCCCATTACC\nAATTTTTTAGTTAAACGAACACACCTAGCCGTGGTACAAGACTTAGCATTAAGCCAGTGT\nCATTGTGTATTTTACGGACAGCAAGTTGAGGGGCGGAACTTTCGTAACCAATTCCAGCCT\nGTTTTGCGGCGGCGTTTTGTTGACCTGTTTAATGGGGGGTTTATATCAACACGCTCTATA\nACCGTAACATTATCTGAAGGTCCTGTATCCGCCCCAAATCCGACATTGGGG\n>comp60_c0_seq1 len=553 path=[0:0-552]\nGCAGCGTTTCCTCCTTGCCAACTGGATAGTCTGCAAGGAGGAAACGCTGCTGCAATGAGT\nCAGGTTTTTAGGTGAATTAGGTATGATGCATCATTTTTGTTAATGGACTTTTAATGGATT\nGAAACGGATAGAAGGAAACGTGTAGCATAATGGATATTGGTTGATATTTTAAGCACGCTG\nCCAAGTACGCACTAAGAATGCTTAGAAATATTTAAACTGAAATGCGTGGGTTTGGCAAAC\nGTTACCGCAAATCAATCTCAGATCCAAGGGATAATGGCCGTTGGGCAGGCCTCCAAAAGG\nCAATTTGAGCGTTTTCAGTCCGCTTGAAAACGGTCTAAGTATTTGCCATAAATGACCGCG\nAGAGGTATAATATAAACATCTGTTTTCCCGATGACGTGTTAAGAAAAGTGATTATATCAG\nATAACGGGGGACTGTAAAGCTTAATACGTGACATGTGATTGGGTGTATAAATACTACATC\nCAAATCTTGCATGGAAATTCGCTTTGTCGGCACGCCGTGACGTTTGACATATTAAGATCG\nCCCTTTTTAGGAA\n>comp31_c0_seq1 len=1239 path=[0:0-1178 1179:1179-1238]\nCCGTGGTGAATTTTTATACGTTTCAAATAACTGAACATTTTTCGGTGTTACCATGGTGCG\nATTTAACCACCAAAAATATACGCTCTTCTGATATTCCGAATCTCGTAAAGGTCCATTTAA\nCAATCCCGGGGGCACTTGCACCACACCATCTGGACAGGGGGGGGTTCCGTGGGGCAGGTC\nAAAACGCTGACCCACCCCACATGAATATATAGCCTTTATAATATTGGGGGCCGTTCCAGG\nCTGAGGGTTCAGTAACTTAACAAACATATAATGCGGCAATACGCGGGTTTTTGTAAAGGG\nGTTGTTATCAACGACATACATTAGAGTGTTTAACAACCATAAAACTCCCTCATATAAAAA\nCCGACGCATTTTTTCCAAAGGTCCTATTTGACACTCAACGCGTCTAAGATATACAGACAA\nTTGTACAAACAGCGATGGAGATGCCCCGGAGGGCCCAATGCCTTCCAGATACATTAAAAT\nAACACATAAGGTAAAATCTAAAACATTATCCGGGCGGAATAGAGTCATCCGATAGATTAA\nCAGGCGCGGAGGCACCCCCACCGTATACACCCTATCTTCAACCGCAGTTAATACGGAAAA\nAATAAATCCGCGGAACGCTGGTTGAGTAACACACTCCATGTAGTAACGATCACAGGACAC\nCTCACTTGAATCACCATTCAACACTACTAAAACGGTCTCTTGGTGTTCCGGTTTTACGCG\nCAGTGATACAACAGAGTTTGCCAAAAAGCGTGGCTTCAAACCGGTTACCTCCCGCGCCTC\nGCATACGAATCTTGGTATTGCTTGTATTCTAAGATCTTCGATCACGTCGCTCACATCCAA\nCCCCTCTTCGGCTCGTGTTAGTAAGTTGTCGATCGTTACGCTGCAACCTAAAATGCTGGG\nTATATTTATTCCGGACATCCCATCGGCCATCCCCGCGCCTCCGGTTTGCTCGAATTTTAT\nCCAGTAAGGTCGAATCCGCTGCATTTACCTTGTGTACCCGTAACCTCTCAGGGGGGTGTC\nCTTTCATAAAATGGGATAGGTTTTTATATCCAACATGCATGTATTGGTTATTTATTTTAT\nTGGGTTCCGGGATTCTTTCGTCATCTTCTGTAGGGTCAGGCAAACCCCAGGAAGGACTTG\nGCGTTCTCCGTGGGCCCCGTTTTATTACCTCTGCGCGAACCTATTTATCCCAAATCCGAA\nTATTATATGAAATGCAGGTTCGCGCAGAGGTAATAAAAC\n>comp31_c0_seq2 len=357 path=[1216:0-296 1179:297-356]\nTGTTTCCATAGCTCAGACAAACGTTTTATATCATCTCCATAAGGGGGGATATAACACGTT\nTGTCTGAGCTATGGAAACAGGAACTTGTTCGCTGTTTTAAGCTTCACCGGGTAAACAATA\nATCAAGGCCAGGAAATTTCTGTATCATATTCAAATGCGTCAATCTCATTACTAGTTGCGC\nCGTATTTTTCATTCATATTACGGGCCACCCGATTAGGATTCTTGGTAACTCAAAGCGAGG\nTACATAGGTCAGAGGAAGAGTTATGCCAGGCTATTTTTAAAAAGGCGAGAACAGAGTCCT\nATTTATCCCAAATCCGAATATTATATGAAATGCAGGTTCGCGCAGAGGTAATAAAAC\n>comp70_c0_seq1 len=537 path=[0:0-536]\nCGATGAAGAAAACCAAATAATGCATTTATTTTGTAGTAGGGACGTCAACGTTATTTTTTA\nTTTAATTGGTGGATTTTCAACTGGAGATGTACGATCCCGGGTCTGGCCTATATTTTTTTG\nTTGTTTTAAAACCCAAACTGATTTTAAAGCTTTATATAAGGCGTTATGGTATGGAGCACC\nCCTAAATCCGCATATAATATCTGATACCCTATGTATATCGGAGACGTTTGACATTCACTC\nGGAAGTTATACAAACTCTGATGGTAACAACACACCATTTAAACCGAAAGGGATTATCGGA\nCAACGGCCTATGCATCACAGAGGCAACACTCTGCAAGTTAGTTAAAAAATCCGTTGGTCG\nTCAGGAGCTAACATCATTATATGCCCATTACGAACGTCAAGTATTGGCTGCATATCGACG\nACTCTACTGGGGGTATGGATGCTCGCCGTTTTGGTATATTGTTCGATTTGGACCCTCTGA\nAAAAACGCTAGTGTTGGCTACACGCTATTACTTGTTACAAACGGACACAAGTTACAA\n>comp10_c0_seq1 len=1755 path=[0:0-1754]\nGGTTCAGGGCCGAGTTGACACCGGGACGGGCGGGTACCGCCGTTACGGGGAGCGTAGCGT\nCTCCCGTTCCGCATGTAGGCGAAGCCATGGCCACGGGGGAGGCCCTCTGGGCTCTCCCCC\nACGCGGCCGCGGCCGTGGCTATGAGCCGTCGGTACGACCGGGCCCAAAAACACTTTATCC\nTACAGAGTCTCCGCAGAGCCTTTGCCAGCATGGCATACCCCGAGGCAACGGGCTCCAGTC\nCGGCGGCGCGGATCTCCCGCGGTCACCCTTCTCCAACAACCCCGGCCACACAGACTCCCG\nACCCTCAGCCGTCGGCCGCCGCACGCTCTCTTTCTGTGTGTCCACCGGATGATCGTTTAC\nGAACTCCGCGCAAGCGCAAGTCCCAGCCAGTCGAGAGCAGAAGCCTCCTCGACAAGATTA\nGGGAGACACCCGTCGCGGACGCCCGGGTTGCAGACGATCATGTGGTTTCCAAGGCCAAGA\nGGCGGGTATCCGAGCCCGTGACCATCACCTCGGGCCCTGTGGTGGATCCCCCCGCCGTAA\nTAACGATGCCACTTGACGGACCGGCCCCAAACGGGGGATTTCGGCGTATTCCCCGGGGGG\nCCCTGCATACCCCGGTCCCGTCGGACCAGGCTCGCAAGGCGTACTGTACCCCCGAAACCA\nTCGCCCGTCTGGTCGACGACCCATTGTTTCCCACGGCCTGGCGCCCTGCGCTAAGCTTTG\nATCCCGGCGCCTTGGCGGAAATCGCCGCTCGGCGTCCGGGCGGAGGAGACCGACGGTTTG\nGTCCACCCAGCGGAGTGGAGGCGCTGCGACGGAGGTGCGCCTGGATGCGGCAGATCCCAG\nACCCGGAGGATGTGAGGCTTCTGATCATCTACGATCCGTTGCCCGGAGAAGACATCAACG\nGCCCCCTCGAGAGCACCCTCGCGACAGATCCGGGACCGTCATGGAGTCCATCCCGAGGGG\nGACTGTCTGTGGTCCTGGCAGCCCTGAGTAACCGGTTGTGCCTGCCGAGCACTCATGCCT\nGGGCCGGGAACTGGACCGGCCCGCCGGACGTGTCCGCTTTGAACGCCCGGGGCGTTTTAT\nTACTGTCGACCCGAGACCTGGCCTTTGCCGGGGCCGTCGAGTATCTAGGCTCGCGGTTGG\nCCTCTGCCCGGCGCCGGTTGCTGGTGTTGGACGCGGTGGCCCTCGAGAGGTGGCCCAGGG\nATGGACCCGCTTTGTCTCAGTATCACGTGTACGTCCGGGCCCCGGCGCGACCGGACGCCC\nAGGCCGTCGTCCGATGGCCAGACTCGGCGGTCACAGAAGGACTCGCCCGGGCCGTGTTTG\nCATCGTCGCGCACCTTTGGGCCAGCGAGTTTTGCTCGTATCGAGACTGCGTTTGCCAACC\nTGTACCCGGGCGAACAACCCCTGTGTTTGTGCCGCGGTGGGAACGTCGCATACACCGTGT\nGTACCCGCGCGGGCCCCAAGACCCGCGTCCCCCTGTCGCCCCGTGAATACCGGCAGTACG\nTGCTGCCGGGTTTTGACGGTTGCAAGGACCTCGCGCGACAGTCTCGGGGTCTGGGGCTCG\nGGGCAGCCGACTTTGTGGACGAGGCGGCACATAGCCACCGCGCAGCAAACCGATGGGGCC\nTGGGTGCCGCGCTTCGACCCGTCTTCCTTCCCGAGGGACGGAGACCGGGGGCCGCCGGGC\nCGGAGGCCGGCGACGTACCCACCTGGGCGAGGGTGTTTTGCCGCCACGCCCTGCTGGAAC\nCCGACCCTGCCGCAG\n>comp3_c0_seq1 len=1689 path=[0:0-1688]\nTTGGAGTGTTATATAACACTCCAATCGACCCTCTTGCGTACCATAATGTTTTCGGAGTTG\nCCTCCTTCCGTACCGACGGCATTGCTTCAATGGGGTTGGGGATTGCATCGTGGACCGTGT\nTCGATCCCAAATTTTAAACAGGTAGCCAGCCAACACAGTGTTCAGAACGATTTTACAGAA\nAATAGCGTTGATGCAAATGAAAATTTTCCGATTGGGCACGCGGGCTGTATTGAGAAAACC\nAAAGACGACTATGTACCATTTGATACGTTGTTCATGGTATCATCTATTGACGAACTTGGG\nCGGAGACAATTAACCGACACCATCCGCCGCAGCTTGGTTATGAACGCCTGTGAAATAACG\nGTCGCGTGTACGAAAACCGCAGCCTTTTCTGGTCGAGGCGTGTCACGACAAAAACACGTG\nACCCTATCTAAAAATAAATTCAATCCATCCAGTCATAAGAGCCTGCAAATGTTTGTGTTG\nTGTCAAAAAACCCATGCACCCCGTGTCAGAAACCTACTGTACGAGAGTATTCGTGCAAGA\nAGACCTCGCCGATATTACACCCGCTCAACGGACGGAAAATCGCGTCCGTTGGTACCAGTG\nTTTGTGTACGAGTTTACGGCTTTAGATCGTGTCCTTTTACATAAGGAAAATACTTTGACC\nGACCAACCAATTAATACTGAAAATAGCGGTCATGGACGTACGAGAACGTAATGTGTTTGG\nAAATGCCAGCGTTGCCACGCCGGGGGAACATCAGAAATTTGTACGCGAGTTAATTTTGTC\nGGGACACAACAACGTCGTATTACAGACATACACTGGTAAATGGTCAGACTGCCGTAAACA\nCGGTAAATCGGTTATGTATAATACCGGTGAAGCGCGGCACCCAACCTGCAAGGCTCATCA\nACGTTAAGAGGATAGGTGTCTTCAAATTAAAAGCCGTTAAATATAAATTTTTTGTGTCGT\nTTATTCGCGTATGAAATGTAATCAGTTGGGATAAATGTTAGTCTTGAATCTGTCTTTACG\nCGTTTGCGGCGTCCCGTAATATTAACGAAAGAACGTCGTCGTCTGATGTGAAAAAGGCCG\nGTTGTGGTGAAGAAGGACAGTTGGTTTCAGGCTGCCGCCTTTGCGATGTATACTGGTGCG\nGGGTTGGTGTTGGTGTGGTCTGATCGTCAGGTCTGTTTACCCGTAAACCGTATATAACAA\nTTGAGATACACATGGATAGGTCATCTTCCGTTATTACGGATAGTACCCCCCCCACATTAC\nTGTACAGCTGAGATGTTGGGTCAGAACCGACCCAGGACATAAACGGCATCGCAAATGTTG\nCGTGGGGTTTGTCCTGTAAGTGGAAATCCCGGTGCGTAAATGCGTATGATGAAAAGTCAG\nTAGAACAGTCTATGGTTAGCAGGGTCACTGTATGGGTGTGTTGAAGGACGATCATACCAC\nCGCTCATTGTATCACATCGAGCGTCCGTCTTCACCGCCATTGATCTTGACCCGCCCGTAA\nATGCGTAGAGTGTTTGTTCATGATCCGGTAAAGTCCAGTGAAGAACCCGCCTAACCCCAT\nGTAACCTATATAAAATAAACGTCGTTGGGGGTCCAGAGATGCTCATGGCGGGTGTATTTA\nAGACAAAACCTAGAAATGAGAACAGCAAGCCCGCATGCGTGTTTTTATACAATGCTTTAA\nTACACAACG\n>comp32_c0_seq1 len=1119 path=[0:0-1118]\nCTGAAGCCGCTGTGAAACCTTTCACAAGACGATATAAACTTGGTTAAGTGTATTGATGGG\nGCTCTTTGGACTGACACGCTTTATCCATGAACATAAACTGGTTAAACCCAGCATCATTTC\nAACGCCACCCGGAGTTTTAACCCCCGTGGCGGTAGACGTATGGAACGTCATGTACACATT\nGTTGGAACGTTTATACCCTGTGGGTAAACGCGAGAATTTACACGGACCATCTGTAACGAT\nACATTGTCTTGGAGTCTTATTGCGGCTATTAACACAACGGTCATACTATCCGATATTTGT\nATTGGAACGTTGTACAGACGGCCCATTATCACGTGGAGCCAAGGCAATTATGTCACGGGC\nCATGAACCACGATGAAAGGGGAACCTCGGACTTAACCCGTGTTCTACTATCATCCAACAC\nATCATGTTCTATCAAGTATAACAAAACATCGGAAACATATGACAGTGTGTTTCGAAACTC\nTTCCGCGAGTTGTATTCCTAGCGAAGAAAACAAATCCCAGGATATGTTTTTGGACGGTTG\nTCCACGACAAACTGACAAGATGATCTGCCTGCGCGACCAAAACGTATGCAGTCTTACCTC\nTACAATGCCATCCCGAGGACATCCTAACCATCGATTATATCACAAATTGTGTGCAAGTCT\nTATTAGATGGATGGGGTATGCATACGTCGAGGCGGTTGACATTGAGGCGGACGAGGCATG\nTGCAAACTTATTTCATACGCGTACAGTGGCTTTGGTTTATACGACAGATACTGATTTACT\nCTTCATGGGCTGTGATATTTTGTTAGATGCAATTCCTATGTTTGCTCCAGTAGTACGATG\nTCGCGATTTGCTTCAATATTTAGGAATTACATACCCTGAATTTTTGGTTGCCTTTGTTCG\nCTGTCAGACCGATTTGCATACAAGTGACAACCTAAAATCTGTTCAGCAAGTTATTCAGGA\nTACCGGCCTGAAAATTCCACATCAAATGGACACTTCAACGCGCTCCCCCACTTACGACTC\nGTGGAGACATGGCGAGGTTTTCAAAAGTCTTACCGTAGCCACGTCGGGTAAAACAGAAAA\nCGGAGTGTCCGTTTCCAAATATGCATCTAACCGATCGGA\n>comp53_c0_seq1 len=645 path=[0:0-644]\nGCTTATGAGCCATCGCCATTCGTTCTCCCAACAGCGTTACAAAATTACTGCCCCCGCTTG\nGGCACGCCACGTGTATTTTCAAGCACATCAAATGCACTTGGCCCCGCATGCCGAAGCCAT\nGCTACAATTAGCGCTATCGGAACTGTCCCCGGGATCGTGGCCGCGGATAAACGGGGCGGT\nAAATTTTGAAAGTTTATAACCCATTAATACCATATATGGACATCCATAGGGGGGGTTACA\nTAAATACTAAGCCTCTGTACAACACAAAGGGCCTCTAACAATGCACTGAACCACAACCAA\nGCTATGGACGCAACGCAGATTACCTTGGTTAGAGAAAGCGGACACATTTGTGCCGCAAGC\nATATACACATCCTGGACACAGTCCGGACAATTAACACAGAACGGTCTTTCCGTGTTATAC\nTACTTATTATGCAAAAACTCATGTGGGAAATACGTCCCTAAGTTTGCCGAAATTACCGTA\nCAACAAGAGGATTTATGTCGCTACTCCAGGCATGGGGGGAGTGTTTCTGCGGCAACGTTT\nGCGTCTATCTGCAGGGCGGCGTCCTCGGCTGCGTTAGACGCCTGGCCCCTTGAACCACTG\nGGTAACGCAGACACCTGGCGGTGTCTCCATGGCACTGCCCTGGCC\n>comp13_c0_seq1 len=3307 path=[0:0-3306]\nGTAGCCATGTTGACATAATCGGTTCATGACATTATAAACCGATTATGTCAACATGGCTAC\nAAGGAATACATCATTCCGCCCGAATCAACCACACCGGTGGAATTAATGGAGTATATTAGC\nACTATCGTCTCAAAACTTAAGGCGGTGACGCGACAAGATGAGCGAGTGTACCGATGTTGT\nGGAGAACTTATCCATTGCCGTATTAACCTACGATCCGTTTCCATGGAAACGTGGTTGACT\nTCCCCAATTCTCTGTTTAACTCCCCGAGTCCGCCAAGCAATTGAAGGGCGGAGGGACGAA\nATTCGTCGGGCTATATTAGAACCGTTTTTGAAAGATCAATACCCCGCTTTAGCTACCCTT\nGGACTACAGTCTGCTTTAAAGTACGAAGACTTTTATTTAACTAAGTTAGAGGAAGGTAAA\nTTAGAGTCGCTTTGCCAATTCTTTTTAAGACTGGCGGCCACCGTGACAACAGAAATCGTA\nAACCTGCCTAAAATCGCAACTCTTATTCCCGGAATAAATGATGGTTATACATGGACTGAT\nGTCTGTCGGGTATTTTTCACAGCGTTGGCATGTCAGAAAATTGTCCCGGCTACACCGGTT\nATGATGTTTTTAGGTCGAGAGACCGGGGCAACGGCCAGTTGTTATTTAATGGACCCGGAA\nTCCATCACTGTTGGGAGAGCTGTTCGAGCTATCACAGGCGATGTGGGAACGGTATTACAA\nAGTCGAGGCGGAGTGGGAATTTCTCTACAGAGTCTGAATTTAATACCTACGGAAAATCAA\nACGAAAGGTCTTCTTGCAGTTTTAAAACTTTTAGATTGCATGGTTATGGCAATTAACAGT\nGATTGTGAACGACCAACTGGAGTTTGTGTTTACATAGAACCATGGCACGTCGATCTACAA\nACTGTTTTGGCCACACGTGGAATGTTGGTTCGTGATGAAATATTTCGATGTGATAACATA\nTTTTGTTGTTTATGGACCCCAGATTTATTTTTTGAAAGATACCTAAGCTATCTAAAAGGG\nGCTAGTAATGTTCAGTGGACTCTTTTTGATAACAGAGCCGATATCCTTCGAACATTACAC\nGGGGAGGCATTCACTTCAACCTATTTACGTTTAGAGAGAGAAGGATTAGGCGTTTCTTCT\nGTTCCCATTCAAGATATCGCATTCACAATCATACGCAGTGCTGCTGTAACAGGAAGCCCC\nTTTTTAATGTTCAAAGATGCCTGTAATCGTAATTATCATATGAATACCCAAGGAAATGCT\nATCACGGGGTCAAATTTGTGTACGGAAATTGTTCAAAAGGCAGACGCTCATCAACATGGC\nGTATGTAATCTTGCCAGCATAAATCTTACAACGTGCTTATCCAAAGGCCCAGTGTCATTT\nAATTTAAACGACCTTCAATTGACAGCAAGAACGACTGTTATTTTTTTAAACGGGGTCCTG\nGCGGCTGGGAACTTTCCATGTAAAAAATCATGTAAAGGTGTAAAAAACAACCGATCACTT\nGGCATTGGCATACAAGGGTTACATACAACTTGTCTCCGCTTAGGATTTGATTTAACTTCC\nCAACCAGCTAGACGGTTAAATGTACAAATAGCGGAGTTAATGTTGTATGAGACAATGAAA\nACAAGCATGGAAATGTGTAAGATTGGCGGCTTAGCCCCGTTTAAGGGTTTTACCGAAAGT\nAAATATGCTAAGGGATGGTTACACCAAGATGGGTTTTCTACGATAAGTTATTTAGATTTA\nCCATGGTGTACCCTGCGAGATGATATTTGCGCTTATGGGTTATACAACTCGCAGTTCTTA\nGCGTTAATGCCCACAGTTTCATCTGCACAGGTAACGGAGTGCAGTGAGGGTTTCTCTCCA\nATTTATAATAATATGTTTAGTAAGGTCACCACCTCGGGTGAGTTACTTAGACCCAACTTA\nGACCTTATGGACGAACTAAGAGATATGTATTCATGTGAAGAAAAACGACTGGAAGTTATA\nAACATACTTGAGAAAAACCAATGGTCAGTAATACGTTCGTTTGGCTGTTTATCTAATAGT\nCACCCACTCTTAAAATATAAAACAGCGTTTGAATATGAGCAAGAGGATCTCGTTGATATG\nTGTGCAGAAAGGGCGCCATTTATTGACCAAAGTCAATCAATGACTTTATTTATTGAGGAA\nCGCCCAGACGGGACAATTCCCGCCTCCAAAATAATGAATTTGCTTATACGTGCCTATAAA\nGCCGGCCTTAAAACGGGTATGTACTACTGTAAAATTCGTAAAGCTACAAACAGCGGACTG\nTTTGCGGGAGGCGAATTAACCTGTACCAGTTGTGCTTTATAAATTTACACGGGAAACTAT\nTCCAAAATGGATCAGAAAGATTGCAGTCATTTTTTTTACAGGCCGGAGTGTCCAGATATA\nAACAATTTACGTGCCCTGAGCATTTCGAATCGTTGGTTAGAAAGCGATTTTATCATTGAA\nGATGATTATCAATACTTGGACTGTTTAACGGAAGATGAACTAATATTCTACAGATTTATT\nTTTACATTTTTATCGGCGGCAGATGATCTGGTAAATGTTAATTTGGGCTCTCTAACCCAA\nCTCTTTTCCCAAAAGGATATTCACCATTACTACATTGAACAAGAGTGCATCGAGGTTGTC\nCACGCGCGTGTCTATAGTCAAATTCAACTAATGTTGTTCAGAGGGGATGAATCGTTGCGG\nGTACAATACGTAAATGTCACTATTAATAATCCGTCGATCCAACAAAAAGTACAATGGTTG\nGAAGAAAAGGTACGGGACAACCCATCCGTTGCAGAAAAATATATACTAATGATTCTTATA\nGAGGGCATTTTTTTTGTATCATCGTTCGCGGCTATTGCATATTTACGCAATAACGGACTA\nTTTGTTGTAACTTGTCAATTTAACGACCTTATAAGCCGAGATGAAGCCATACATACCAGC\nGCATCGTGTTGTATATACAATAACTATGTACCCGAAAAACCCGCTATCACCAGAATACAT\nCAACTGTTTTCGGAAGCCGTTGAAATCGAGTGTGCGTTTTTAAAATCCCATGCACCCAAA\nACCCGTTTGGTGAACGTCGATGCAATTACACAATACGTGAAATTCAGCGCGGACAGGCTT\nTTATCAGCGATTAATGTACCAAAACTATTTAACACCCCACCTCCAGATTCGGACTTTCCA\nCTTGCATTTATGATTGCAGATAAAAACACAAATTTTTTTGAGAGACACAGTACATCTTAT\nGCGGGCACAGTGATAAACGATTTATAACATGTATATACGAGCAAAATAAAACAATGAACC\nATTAAGT\n>comp71_c0_seq1 len=568 path=[0:0-567]\nATTTAATACAAATCTTATAATCACAAACCTCATACTTGATGTAGACTTTCATATAAGAAA\nACCCATCCCATTGGGTATTTTACATGCCGGCATGCGAGCATTTCGTCATGGTATTTTAAC\nGGCCATGCAATTACTTTTTCCAAAGGCCGTGGTAAACCCTAACAAAGACCCATGTTATTT\nTTATAAAACTGCATGTCCTGAACCTACCGTTGAGGTGTTGGATGATGATAATTTATTGGA\nTATAACCAGCCATTCTGACATCGATTTTTACATAGAAAATGGCGAATTATACACGTGTGT\nAGAAGAGAATTATACAGAGGATGTATGGTTTTTTGATACACAGACAACGTCTGAAGTCCA\nTACACACGCCGATGTATCAAACAATGAAAACTTGCATGAAACTCTACCCTGTAACTGTAA\nAGAGAAAATAGGTTTCAGGGTATGCGTACCAATCCCAAATCCCTATGCGTTAGTGGGGTC\nTTCCACTTTAAAGGGGTTTGCACAAATATTACAACAAGCGGTGTTGCTGGAACGGGAATT\nTGTTGAATATATTGGTCCGTATTTACGG\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.hiv.big_indel.fasta", "content": ">contig_extra_36bp\nGGCCCTAAAAGAATTGTTAAATGTTTCAATTGTGGCAAGGAAGGGCACATAGCCAGAAATTGCAGAGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGGCAGGCAAATTTTTTAGGGAAAATTTGGCCTTCCCACAAGGGGAGGCCAGGAAACTTCCTTCAGAACAGACCAGAACCAACAGCCCCGAATTTCCTTCAGAGCAGACCAGAGCCAACAGCACCACCAGCAGAGAGCTTCAGGTTCGAGGAGACAACCTCCGCTCCGAAGCAGGAGCTGAAGGAGAGGGAACCCTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCCTTGTCTCAATAAAGGTAGGGGGTCAGATAAAGGAGGCTCTCTTAGACACAGGAGCAGATGATACAGTATTAGAAGAA\n>contig_less_36bp\nAGGAAGGGCACATAGCCAGAAATTGCAGAGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGGCAGGCAAATTTTTTAGGGAAAATTTGGCCTTCCCACAAGGGGAGGCCAGGAAACTTCCTTCAGAACAGACCAGAACCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAGGAGACAACCTCCGCTCCGAAGCAGGAGCTGAAGGAGAGGGAACCCTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCCTTGTCTCAATAAAGGTAGGGGGTCAGATAAAGGAGGCTCTCTTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATT\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.hiv.wrapped.fasta", "content": ">comp0_c0_seq1 len=9130 path=[0:0-811 812:812-2598 2648:2599-5168 5218:5169-9129]\nCTTTTAAAATTGTGAATGAATACTGCCATTTGTACTGCTGTCTTAAGGTGCTCAGCTTGC\nTCTCTTACCTGCCCTATGATTTTCTTTAATTCTTTATTCATGGATTCTACTACTCCCTGA\nCTTTGGGGATTGTAGGGAATCCCAAATTCCTGTTGGACCCCTGCCCACCAACAGGCTGCC\nTTAACTGCAGCACTGGTGAAATTAGGGCCATTGTCTGTATGTATTACTTTGACTGGCCAT\nCTTCCTGCTAATTTTAATAGAAAGTATGCTGTTTCTTGTCCTGTTTCTGCTGGGATGACC\nTCTGCCTCTATGTATCCACTGGCTACATGGACTGCTACTAGGATGACTTTTCCTTCTAAA\nTGTGTACAATCTAATTGCCATATCCCTGGACTACAGTCTACTTGCCCATGTATGGCTTCC\nCCTTTTAGCTGACATTTATCACAGCTAGCTACTATTTCTTTTGCTACTATGGGCGGTAGA\nTTAAATTCATTAGCCATTGCTCTCCAATTACTGTGGTACCTTTCATGATCTTCTTGAGCC\nTTATCTATTCCATCCAGAAACAGCACTTTCCTGATTCCACTGCTTACTAATTTATCTACT\nTGTTCATTTCCTCCAATTCCTTTGTGTGCTGGTACCCATGCCAAGTAGACCCTTTCCTTT\nTTTATTAATTCTTCTATTATTTGGTTTACTAACTCTGATTCACTCTTATCTGGTTGTGCT\nTGAATGATTCCTAATGCATACTGTGAGTCTGTTACTATGTTTACTTCTGGTCCTGAATCT\nTGCAAAGCTAGCTGAATTGCTTGTAATTCAGTCTTCTGATTTGTTGTCTCATTTAGAGAA\nATAACCTTCTGTCTTCCTCTGTCAGTAACATACCCTGCTTTTCCCTTTTTAGTTTCCCTA\nTTAGCTGCTCCATCTACATAGAAAGTTTCTGCTTCTGCTATGGGTTCTTTTTCTAGCTGG\nTACCATAATTTCACTAGGGGAGGGGTATTAACAAACTCCCACTCAGGAATCCAGGTGGCT\nTGCCAATAGTCTGTCCACCATATGTCCCATGTTTCTTTCTGGATGGGTAGTCTAAATTTA\nGGAGTCTTTCCCCATATTACTATGCTCTCCAAGGCTATTTTTTGCACTACCTCTGCTAAC\nTGTTTTACATCATTAGTGTGGGCAGTCCTCATTCTTGCATACTTTCCTGTTTTCAGATTT\nTTATGTGGTTCTTGGTAAATTTGATATGTCCACTGGCTCATTCCCTGTTTCTGTATTTCA\nGCTGTTAATTCCTTTGATGGGTCATAATATACTCCATGTACTGGTTCTTTTAGAATTTCC\nCTGTTCTCTGCCAATTCTAATTCTGCTTCTTCAGTTAGTGGTACTATGTCTGTTAGTGCT\nTTGACCCCCCTAAGGAGTTTACAAAGTTGTTTTACTTTAATCCCTGGGTATATCTGGCTT\nGCCCAGTTTAATTTTCCCACTAGCTTCTGTATATCATTGACAGTCCAGCTCTCCTTTTCT\nGGCAGCTGTATAGGCTGTACTGTCCATTTGTCAGGATGGAGTTCATACCCCATCCAAAGA\nAATGGGGGTTCTTTCTGATGTTTCTTGTCTGGTGTGGTAAATCCCCACTTCAATAGATGT\nTCTCTTAGCTCCTCTATTTTTGCTCTATGTTGCCCTATTTCTAAGTCAGATCCTACATAC\nAAGTCATCCATATATTGATAGATGACTATGTCTGGATTCTTTGCCCTAAAGGGCGCTAGG\nATTTTTGTCATGCTACACTGGAATATTGCTGGTGATCCTTTCCATCCCTGTGGGAGCACA\nTTATATTGATATCTAATCCCTGGTGTTTCATTGTTTATACTAGGTATGGTGAATGCAGTA\nTATTTCCTGAAGCTTTCATCTAAAGGAACTGAAAAATATGCATCCCCCACATCCAATACT\nGTCACTGATTTTTTCTTTTTTAACCCTGCTGGGTGAGGTATTCCTAATTGAACTTCCCAA\nAAGTCTTGAGTTCTTTTATTGAGTTCCCTGAAATCTACTAATTTTCTCCACTTAGTACTG\nTCCTTCTTTTTTATGGCAAATATTGGAGTGTTATATGGATTTTCAGGCCCAATTTTTGTA\nATTTTTCCTTCCTCCTCCATTTCTTTACAAATTGCTGTTAATGCTTTTATTTTTTCTTCT\nGTTAATGGCCATTGTTTAACCCTTGGCCCATCCATTCCTGGCTTCAGTTTTACTGGTATA\nGTTTCAATAGGACTAATTGGAAAATTTAATGTGCATCCAAGCTGAGTCAACATATTTCTT\nCCAATTATGTTGACAGGTGTGGGCCCTACTAATACTGAGCCTATAGCTTTTTTCCCACAA\nATTTCTATATGTATTTGATCATATTGTCTTACTTTGATAAAACCTCCAATTCCTCCTATC\nATTTTTGGTTTCCATTTTCCTGGCAAATTTATTTCTTCTAATACTGTGTCATCTGCTCCT\nGTGTCTAAGAGAGCCTCCTTTACCTGGCCCCCTACTTTTATTGAGACAAGGGGTCGTTGC\nCAAAGAGTGATTTGAGGGAAGTTAAGGGTTCCCTGTCCTTCGGTTCCTGCCTCGGAGTGG\nGGGTTGTCTCCTGGAACCTGAAGCTCTCGGCTGGTGGGGCTGTTGGCTCTGGTCTGCTCT\nGAAGGAAATTCCCTGGCCTCCCCTTGTGGGAAGGCCAGATTTTCCCTAAAAAATTAGCCT\nGCCTCTCAGTACAGTCTTTCATTTGGTGTCCTTCGCTTCCACACTTCCAACAGCCCTTTT\nTCCTAGGGGCTCTGCAGTTTCTGGCTATGTGCCCTTCCTTGCCACAATTGAAGCATTTAA\nCAATTCTTTTAGGGCCCTTAAAATTGCTTCTCTGCATCATGATGCTTCCATTTGCTTGGC\nTCATTGCCTCAGCTAACACTCTTGCTTTGTGGCCAGGTCCTCCCACTCCTTGACATGCTG\nTCATCATCTCTTCTAATGTAGCCCCTGGTCCTAATGCTCTTAAAATGGTCTTACAATCTG\nGGTTTGCATTTTGGACTAACAAGGTGTCTGTCATCCAACCTTTTACCTCTTGTGTAGCTT\nGTTCAGCTCTTAAAGTTTTAAAGAACCGGTCTACATAGTCTCTAAAGGGTTCCTTTGGCC\nCTTGTCTTATGTCCAAAATGCTAACAGGGCTATACATTCTCACTATTTTATTTAACCCCA\nTAATTATCCACCTTTTATAGATGTCTCCCACTGGAACAGGTGGGTTAGCTGTCATCCATG\nCTATTTGTTCCTGAAGGGTACTAGTAGTTCCTGCTATGTCACTTCCCCTTGGTTCTCTCA\nATTGACCTGGTGCAACAGGTCCCGCCTGTGCTGGATGTAGTCTATCCCATTCCGCAGCCT\nCCTCATTGATTGTATCTTTTAACATTTGCATGGCTGCTTGATGTCCCCCCACTGTATTTA\nACATGGTGTTTAAATCTTGTGGGGTGGCTCCTTCTGATAATGCTGTAAACATGGGTATTA\nCCTCTGGGCTAAAAGCCTTCTCCTCTATTACTTTTACCCACGCATTCAAAGTTCTAGGTG\nATATGGCTTGGTGTACCATTTGCCCTTGAAGATTCTGCACTATAGGATAATTTTGACTGA\nCCTTTTCGCCAGCCGCTTTTGCTTGCTGTGTTTTCTGCTGACTTTTGTTTTGTTCCTCCT\nCTATCTTGTCTAAGGCTTCCTTGGTGTCTCTTACATCTATCCTTCTATGTACACAATAGA\nGAGTTGCTACTGTGTTAAATAATGATTTAAGTTCCTCTGTTCCTGTCTGAAGAGCTGGTT\nGTAGCTGTGCTAGTATCTGTTTACAGCCTTCTGCTGTTTCTAAAAGGCCAGGGTTAAGTG\nCAAATCTTTCCAGCTCCCTGCTTGCCCATACTATGTGTTTTAGCATATAATGTTTCTTTC\nCTCCTGGCCTTAACCTAATTTTTTCCCATGCATCTAATTTTTCGCCTCTTAATACTGACG\nCTCTCGCACCCATCTCTCTCCTTCTAGCCTCTGCTAGTCAAATAAAATTGGCGTACTCAC\nCAGTCGCCCCCCTCGCCTCTTGCCGAGTGCACTTCAGCAAGCCGAGTCCTGCGTCGAGAG\nATCTTCTCTGGTCTTACTTTCGCTTTCAGGTCCCTGTTCGGGCGCCACTGCTAGAGATTT\nTCCACACTAACACAAAGTGTCTGAGGGATCTCTAGTTACCAGAGTCACACAACAGACGGG\nCACACACTACTTAAAGCGCTCAAGGCAAGCTTTATTGAGGCTTAAGCAGTGGGTTCCCCA\nGGCATCCAGAGAGCTCTCAGGCTCAGATCTGGTCTACCTAGAGAGACCCAGTACAGGCGA\nAAAGCAGCTGCTTATATGCAGCATCTGAGGGTTGACCACTCCCTTGTCCCGCCCAGACCA\nCTCCCCCTGGAACGCCCCAGTGGAAAGTCCCAGGCGGAAAGTCCCTTCTGTGTCAGCAGT\nCTTTGTAAAACTCCGGATGTTTCTCACGGGCCAGGTGTCTGCGTGCTAGGCTGCTGTCAA\nACTTCCATTTTAGTACTTCTCTTTCTGTATCCTCTATTCCATGCTGGCTCATAGGGTGTA\nGCAGGCAGTTGTTTTCTCCTTGGTTGGCCTCTTCTACTTCACTTGGGTCAACTGGTACTA\nGCTTGAAGCACCATCCAAAGGTCAGTGGAAGTCTGACCCCTGGTCCTGGTGTGTAGTTTT\nGCCAATCAGGGAAGAAGCCTTGTGTGTTATAGACCCACAGATCAAGGATCTCTTGCCTTT\nTCTTGGACCAAATTAACCCATCCAGTCCCCCCTTTTCTTTTAAAAAGAAGCTGAGATCGA\nATGCTGCCTTATAAGTCATTGGTCTCAAAGGTACCTGAGGTTTGACTGGAAAGCCTACTT\nCTTCATCTTCCTCCTGTGCTTGCAGCCAGGCACAAGCTTCATTGTTGTGGGCTGTGTTGC\nTGCTTGTAAGTGCTCCATGCTTTTCTAAGTCTCGAGACGCTGCTCCCACTCCCTCTGCTG\nCTCCTACTCTTTCTGCTGCTGGCTCAGTTCTTCTTATTCTTTCTCTTACAGCAGGCCAGC\nTTTTTGACCACTTGTTTCCCATCTTATAGCAAAGCTGCTTCAAAGCCCTGTCTTATTCTT\nCTAGGTGTGTTGCAGATAGCCCTCCAAATTCTTTGTAGCACTTCTATAATCCTATCTGTT\nCCTTCAGCTACTACTATTGCTATAGTATCAAGCAGACTAATAGCACTCTTTTTAAGCTCC\nCCACCCCAATATTGCACAAGGTTCTTCAGGTACTTAAGAGCTTCCCACCCCCTCTGTAGT\nCCCCTGAGACTGCTGCGTCCCAGAAGTTCCGCTGCTCTCGCTGCAATCAATATGAAGTCT\nCTCAATTGGTGGTAGCTGAAAAGGCACAGGCTCCTCAGATCGTCCCAGGCAATCGCTAAG\nAATCCGTTCACTAATCGAATGGATCTGTCTCTGCCTTGCTCTCCACCTTCTTCTTCGATT\nCCTCTGAGCCTGTCGAGTTCCCTCGAGTTTGGGGTAAGGGTCTGCAATGACAAAGGTGAG\nTATCCCTGCCTAACTCTATTTACTATAGAAAGCACAAACAAAATTATTCTCAAACCTATC\nAAGCCTCCTACTATCATGATGAATATTTTTATATACCACAGCCATTGTGTTATGTTAAAC\nCAATTCCATAGATCATTCCACTTGTCCAATGCCAATAAATCTTGTTCATTTTTCTCCTGC\nTGGTTTTGTGATACTTCAAGCAACCTAAATATTGTGTCTGAGTAATTACTAATTTCTCTA\nTCCCACTGCATCCAGGTCATGTTATGCCAAATATCGTTGTAAGTTTTATTACTCCAACTG\nGAGTTCCAAGGCACAGTAGTGGTGCAGATGAGTTTTCCAGAGCAGCCCCAAAGTCCTAGG\nAGCCGTTGATCCTGTAGGTATCTTTCTATAGCCAGGACTCTTGTCTGGAGCTGTTTAATG\nCCCCAGACCGTGAGTTGCAACATATGCTGTTGCGCCTCTATAGCTCTCAGCAGATTGCTC\nTGCTGTTGCACTATACCAGACAACAGTTGTCTGGCTTGTACCGTCAGCGTTATTGACGCT\nGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAACCCAAGGATCAAGGCTCCCATTCCCACT\nGCTCTTTTTTCTCTCTCCACCACTCTCCTTTTTGCATTAGTGGGTGCTATTCCCAATGGC\nTTAATTTCTATTACTTTATATTTATATAATTCACTTCTCCAATTATCCTTCATATTTCCT\nCCTCCAGGTCTGAATATCTCTGTGTTGTTGTCGGGCTCTGTTTTGTTAATCCCTCCATCA\nCGTGTTAATAGTAGCCCTGTGATACTTGAGTTACATGTTATGTTTCCTGCTATGGGAGGG\nGCATACATTGCTCGTCCTACCCTCTGCCACATATTTATAATTTGTTTTATTCTGCATGGG\nAGTATGGTTATGTTTTCTTTTGTCTTTGTTCTATTAAGTTCTGTTTCATTAAACAGGTTT\nGTTGTATTGCAATAGAAAAATTCCCCTCTACAATTAAAACTATGTGTTGTCACCTCTAGG\nTCCCCTCCTGAGGATGGTTCAAATGTTATATTTTTATCAGAGAAGTGTTCTCTTAATTTC\nTCCTTTACCCTTTGTAAAGTGTTGTTCCACTTTGTTGTATTAATGTTACAATGTGCCTTT\nCTTATGTCTCCTATTATGTCATGTGTATAGAATGATTGTCCTGGTCCTATCCTTATACTT\nCTTCTTGTATTATTGGCAATTCTTGTACACGTAATGTTTACAGATTCATTAAAGTGTACT\nATTATTGTTTTGGTATTGTCTGTCAGATTCTCAGACCTAATTATTATGTCTTCTTCTGCT\nAGGCTACCATTTAACAGTAGTTGGGTTGATACTACTGGCTTAATTCCATGTGTACATTGT\nACTGTACTAACATTCTGGCATGGTCCTGTCCCATTGAATGTCTTATTATTACACTTTAGA\nATCGCATAACCAGCTGGAGCACAATAATGTATAGGAATTGGGTCAAAAGTGACCTTTGGA\nCAAGCTTGTGTTATGGTTGAGGTATTGCAATTTATTAATATAGATTCACTATAATTAGAA\nTTCCCATTACTCCGTGATACTAGATCCTGTTTATAAAAAGTTGCATACACACTCTGTTTC\nTTATCTCTTATTCCTGTGGTTGTTTCGAAAGAGCAATTAAATATGTTCTCCTTGTCGGTA\nATATTACCTGTCTGGTAGACCTGAGTAGTTGTACCTGTCTGGGTGACATTTGTACAATTT\nAAAGTGACACAGAGTGGGGTCAACTTTACACAGGGCTTTAGACTTTCATCCCATAAACTG\nATTATATCCTCATGCATCTGATCCACCATGTCATTTTTCCACATGTTAAAATTCTCTGTT\nATATTTCCCAAAACTAGTTCTTGTGGGTTGGGGTCTGTGGGTACACAGGCATGTGTAGCC\nCAGACATTATGCACTTCCTTGTCATATGCTTTAGCATCTGATGCACAGAATAGAGTAGTT\nTTTGCTTCTCTCCACACAGGTACCCCATAATAGACTGTGACCCACATGTTTCCTACCCCT\nCCACTAATTATTATCCAAAAGCCTAAGATGCCCCATATCCACCATTGTGGATAGTTCCTC\nTGTATCCCCCTCACTCTCATTGCCACTGTCTTCTGCTCTTTCCCTAATTCTTTTAATTAA\nGCAGTCTATTTTTCTTTGTCTTACCAATTTCCTATATTCTATATATGCTAAAATCCACAC\nTACTATTGCTATGATTAGTGCTATTATCAGTGCTCCTACTCCTAGTCTATAATCTACTTC\nTTCTAGAAAATTTGACATTACATATACTTACTGCTTTGATATAAGATTTTGATGATCCTC\nACTGCTTGGAGGAGTGCGTCGTCGCTGACTCCGCTTCTTCCTGCCATAGGAAATGCCTAA\nGCCTTTTTTCTGAAAGCAAACTAGACAATGGTAGCTACAGTATTTACAATAGCAATTATT\nACAAGGAGTATTAGGCTGACTTCCTGGATGGTTCCAGGGCTCTAGGTTAGGATCTACTGG\nCTCCATTTCTTGCTCTTCTTTGTGGCATAATTCCTATTCTGCTATGTTGGCACCCAATTC\nTGAAATGAATAAACAGTAGTTGTTGCAGTATTCTTATTAACACTTCAACTCCTGTCCAAG\nTATCCCCATAGGTCTCATAGATATATTGTCCTAAACTATGGAGCCATGGTCCCGGAAAAT\nGTCTGACAGCTTCCTGCTTGAGTTCCTCTAAAATTTCTAATGCCCATTCATTGTATGGTT\nCCCTCTGTGGCCCTTGGTCTTCTGGGGGTTGTTCCATCGATCCTCTACTAATTTTTTAAC\nACTAGGCAGAGGTGGCTTTCTCTTTTTTGGCTTTACTAATGCTGCCAGTGCCAAATATTG\nTAGAGATCCTACCTTCTTGTGTCCTGCTTGATATTCACACCTAGGAATAACTATGTGTCC\nTAATATGGCTTTCCTTATGGCAGAATCTGCAAAACAATCAAAATAATGCTTATGAATTAG\nCTGGTCTGCCAGGTCAGGGTCTACTTGTGTGCTATATTCTTTCAATCTCCATTCTATGGA\nGACTCCATGACCTAAATGCCAAGCTCTTTCTCCTGTTTGCAACCCCCAATATGTTGTTAT\nCACTAATCTAGCCTCCCCTAATGGTATGTGTACTTCTGAACTTACTCTTGGATTTCTGCT\nTTCATAATGATGTCTGTAACACCATCTGCCAGTTTTCTTTGTAATATACATATGATGCTT\nTACTAGGCTATTCCATGTTCTGATCTTCATCCTGTCTACCTGCCACACAATCAGCACCTG\nCCATCTGTTTTCCATAGTCCCTAATGATTTTTGCTTTCCTCCTTGGTACTACCTTTATGT\nCACTGTTATCTTGTATTACTACTGCCCCTTCGCCTTTCCAGAGTAGTTTGGCTGGTCCTT\nTCCAAATGGGGTCTCTGCTGTCTCTGTAATAAACCCGAAAATTTTGAATTTTTATAATTT\nGTTTTTGTAATTCTTTAGTTTGTATGTCTGATGATATTATGTCTAGTATTCATTCACAAT\nTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGAGAAAGAATAATAGACATAATA\nTCATCAGACA\n>comp0_c0_seq2 len=2648 path=[0:0-811 812:812-2598 2599:2599-2647]\nCTTTTAAAATTGTGAATGAATACTGCCATTTGTACTGCTGTCTTAAGGTGCTCAGCTTGC\nTCTCTTACCTGCCCTATGATTTTCTTTAATTCTTTATTCATGGATTCTACTACTCCCTGA\nCTTTGGGGATTGTAGGGAATCCCAAATTCCTGTTGGACCCCTGCCCACCAACAGGCTGCC\nTTAACTGCAGCACTGGTGAAATTAGGGCCATTGTCTGTATGTATTACTTTGACTGGCCAT\nCTTCCTGCTAATTTTAATAGAAAGTATGCTGTTTCTTGTCCTGTTTCTGCTGGGATGACC\nTCTGCCTCTATGTATCCACTGGCTACATGGACTGCTACTAGGATGACTTTTCCTTCTAAA\nTGTGTACAATCTAATTGCCATATCCCTGGACTACAGTCTACTTGCCCATGTATGGCTTCC\nCCTTTTAGCTGACATTTATCACAGCTAGCTACTATTTCTTTTGCTACTATGGGCGGTAGA\nTTAAATTCATTAGCCATTGCTCTCCAATTACTGTGGTACCTTTCATGATCTTCTTGAGCC\nTTATCTATTCCATCCAGAAACAGCACTTTCCTGATTCCACTGCTTACTAATTTATCTACT\nTGTTCATTTCCTCCAATTCCTTTGTGTGCTGGTACCCATGCCAAGTAGACCCTTTCCTTT\nTTTATTAATTCTTCTATTATTTGGTTTACTAACTCTGATTCACTCTTATCTGGTTGTGCT\nTGAATGATTCCTAATGCATACTGTGAGTCTGTTACTATGTTTACTTCTGGTCCTGAATCT\nTGCAAAGCTAGCTGAATTGCTTGTAATTCAGTCTTCTGATTTGTTGTCTCATTTAGAGAA\nATAACCTTCTGTCTTCCTCTGTCAGTAACATACCCTGCTTTTCCCTTTTTAGTTTCCCTA\nTTAGCTGCTCCATCTACATAGAAAGTTTCTGCTTCTGCTATGGGTTCTTTTTCTAGCTGG\nTACCATAATTTCACTAGGGGAGGGGTATTAACAAACTCCCACTCAGGAATCCAGGTGGCT\nTGCCAATAGTCTGTCCACCATATGTCCCATGTTTCTTTCTGGATGGGTAGTCTAAATTTA\nGGAGTCTTTCCCCATATTACTATGCTCTCCAAGGCTATTTTTTGCACTACCTCTGCTAAC\nTGTTTTACATCATTAGTGTGGGCAGTCCTCATTCTTGCATACTTTCCTGTTTTCAGATTT\nTTATGTGGTTCTTGGTAAATTTGATATGTCCACTGGCTCATTCCCTGTTTCTGTATTTCA\nGCTGTTAATTCCTTTGATGGGTCATAATATACTCCATGTACTGGTTCTTTTAGAATTTCC\nCTGTTCTCTGCCAATTCTAATTCTGCTTCTTCAGTTAGTGGTACTATGTCTGTTAGTGCT\nTTGACCCCCCTAAGGAGTTTACAAAGTTGTTTTACTTTAATCCCTGGGTATATCTGGCTT\nGCCCAGTTTAATTTTCCCACTAGCTTCTGTATATCATTGACAGTCCAGCTCTCCTTTTCT\nGGCAGCTGTATAGGCTGTACTGTCCATTTGTCAGGATGGAGTTCATACCCCATCCAAAGA\nAATGGGGGTTCTTTCTGATGTTTCTTGTCTGGTGTGGTAAATCCCCACTTCAATAGATGT\nTCTCTTAGCTCCTCTATTTTTGCTCTATGTTGCCCTATTTCTAAGTCAGATCCTACATAC\nAAGTCATCCATATATTGATAGATGACTATGTCTGGATTCTTTGCCCTAAAGGGCGCTAGG\nATTTTTGTCATGCTACACTGGAATATTGCTGGTGATCCTTTCCATCCCTGTGGGAGCACA\nTTATATTGATATCTAATCCCTGGTGTTTCATTGTTTATACTAGGTATGGTGAATGCAGTA\nTATTTCCTGAAGCTTTCATCTAAAGGAACTGAAAAATATGCATCCCCCACATCCAATACT\nGTCACTGATTTTTTCTTTTTTAACCCTGCTGGGTGAGGTATTCCTAATTGAACTTCCCAA\nAAGTCTTGAGTTCTTTTATTGAGTTCCCTGAAATCTACTAATTTTCTCCACTTAGTACTG\nTCCTTCTTTTTTATGGCAAATATTGGAGTGTTATATGGATTTTCAGGCCCAATTTTTGTA\nATTTTTCCTTCCTCCTCCATTTCTTTACAAATTGCTGTTAATGCTTTTATTTTTTCTTCT\nGTTAATGGCCATTGTTTAACCCTTGGCCCATCCATTCCTGGCTTCAGTTTTACTGGTATA\nGTTTCAATAGGACTAATTGGAAAATTTAATGTGCATCCAAGCTGAGTCAACATATTTCTT\nCCAATTATGTTGACAGGTGTGGGCCCTACTAATACTGAGCCTATAGCTTTTTTCCCACAA\nATTTCTATATGTATTTGATCATATTGTCTTACTTTGATAAAACCTCCAATTCCTCCTATC\nATTTTTGGTTTCCATTTTCCTGGCAAATTTATTTCTTCTAATACTGTGTCATCTGCTCCT\nGTGTCTAAGAGAGCCTCCTTTACCTGGCCCCCTACTTTTATTGAGACAAGGGGTCGTTGC\nCAAAGAGTGATTTGAGGGAAGTTAAGGGTTCCCTGTCCTTCGGTTCCTGCCTCGGAGTGG\nGGGTTGTCTCCTGGAACCTAAGGACAGGGAACCCTTAACTTCCATCAAATCACTCTTTGG\nCAACGACC\n>comp0_c0_seq3 len=836 path=[0:0-811 9203:812-835]\nCTTTTAAAATTGTGAATGAATACTGCCATTTGTACTGCTGTCTTAAGGTGCTCAGCTTGC\nTCTCTTACCTGCCCTATGATTTTCTTTAATTCTTTATTCATGGATTCTACTACTCCCTGA\nCTTTGGGGATTGTAGGGAATCCCAAATTCCTGTTGGACCCCTGCCCACCAACAGGCTGCC\nTTAACTGCAGCACTGGTGAAATTAGGGCCATTGTCTGTATGTATTACTTTGACTGGCCAT\nCTTCCTGCTAATTTTAATAGAAAGTATGCTGTTTCTTGTCCTGTTTCTGCTGGGATGACC\nTCTGCCTCTATGTATCCACTGGCTACATGGACTGCTACTAGGATGACTTTTCCTTCTAAA\nTGTGTACAATCTAATTGCCATATCCCTGGACTACAGTCTACTTGCCCATGTATGGCTTCC\nCCTTTTAGCTGACATTTATCACAGCTAGCTACTATTTCTTTTGCTACTATGGGCGGTAGA\nTTAAATTCATTAGCCATTGCTCTCCAATTACTGTGGTACCTTTCATGATCTTCTTGAGCC\nTTATCTATTCCATCCAGAAACAGCACTTTCCTGATTCCACTGCTTACTAATTTATCTACT\nTGTTCATTTCCTCCAATTCCTTTGTGTGCTGGTACCCATGCCAAGTAGACCCTTTCCTTT\nTTTATTAATTCTTCTATTATTTGGTTTACTAACTCTGATTCACTCTTATCTGGTTGTGCT\nTGAATGATTCCTAATGCATACTGTGAGTCTGTTACTATGTTTACTTCTGGTCCTGAATCT\nTGCAAAGCTAGCTGAATTGCTTGTAATTCAGTTAGCTTTGCAAGATTCAGGACCAG\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.influenza.fasta", "content": ">I1-4\nGCAAAAGCAGGGGAAATTCAAATCAACCAAGATGGAAGCAAAACTGTTTGTGCTATTCTG\nTACATTCACTGTACTGAAAGCTGACACCATCTGTGTGGGCTACCATGCAAACAACTCTAC\nGGACACTGTTGACACAGTATTGGAAAAGAATGTAACTGTGACTCACTCAGTGAATTTGCT\nCGAAGACAGCCATAATGGGAAGCTCTGCAGTCTGAATGGGATAGCTCCTTTACAATTGGG\nGAAGTGTAATGTAGCGGGGTGGCTCCTGGGCAATCCAGAATGTGATCTCCTACTCACTGC\nAAACTCATGGTCCTATATAATAGAGACGTCCAATTCAGAGAACGGGACATGCTATCCCGG\nTGAATTCATAGATTATGAGGAATTAAGGGAGCAGCTGAGTTCAGTTTCTTCTTTTGAAAA\nGTTTGAAATTTTCCCCAGGGCAAACTCATGGCCAAACCATGAGACAACCATAGGTGTTAC\nAGCTGCTTGCTCTTACTCTGGAGCTAGCAGTTTTTATCGAAATTTGCTGTGGATAACAAA\nGAAGGGGACTTCATATCCAAAACTCAGCAAATCATACACGAACAATAAGGGGAAAGAGGT\nGCTCGTGCTCTGGGGAGTGCACCATCCTCCGACCACCAGTGAACAACAAAGTCTATACCA\nGAATACTGATGCATATGTCTCAGTTGGGTCATCAAAGTACAACCGGAGATTCACCCCAGA\nGATAGCAGCTAGACCCAAAGTTAGAGGGCAGGCAGGCAGAATGAACTATTATTGGACACT\nATTAGATCAAGGGGACACCATAACATTTGAGGCCACTGGGAATCTGATAGCACCATGGTA\nTGCCTTCGCATTAAATAAAGGATCTGATTCAGGAATTATAACATCAGATGCTCCAGTTCA\nCAATTGCGACACAAGATGCCAAACCCCCCATGGAGCGTTGAACAGTAGCCTTCCTTTCCA\nGAATGTGCATCCTATCACCATTGGAGAATGTCCCAAATATGTCAAGAGCACCAAGCTAAG\nGATGGCAACAGGACTAAGAAATGTCCCATCCATTCAATCCAGAGGGCTGTTTGGAGCAAT\nTGCCGGATTCATTGAAGGAGGATGGACAGGCATGATAGATGGCTGGTATGGGTACCATCA\nTCAAAATGAACAAGGATCAGGATATGCCGCTGATCAGAAAAGCACACAGAATGCAATTGA\nTGGAATAACAAATAAGGTGAATTCGGTAATTGAAAAAATGAACACTCAATTCACTGCAGT\nGGGTAAAGAATTCAACAACCTAGAGAGGAGGATTGAGAATCTGAATAAAAAAGTCGATGA\nTGGGTTCCTGGATGTTTGGACATACAATGCTGAATTGCTCGTTCTATTGGAAAATGAAAG\nAACTCTTGATTTTCATGATTCCAATGTGAGGAATTTGTATGAGAGAGTCAAATCACAACT\nGAGGAATAACGCCAAAGAAATTGGAAATGGTTGCTTTGAGTTCTATCACAAATGTGATGA\nTGAATGTATGGAAAGTGTGAAGAACGGCACATATGATTATCCCAAATATTCAGAAGAGTC\nTAAATTGAATCGAGAAGAAATAGACGGAGTAAAACTAGAGTCGATGGGAGTTTACCAAAT\nTCTGGCGATCTATTCCACAGTCGCCAGTTCCCTGGTCTTGTTAGTCTCCCTGGGGGCAAT\nCAGCTTCTGGATGTGCTCTAATGGGTCGTTGCAATGCAGAATATGCAT\n>I1-6\nAATGAATCCAAATCAAAAGATAATAACTATTGGGTCAATCTGCATGGTAATTGGAATAAT\nAAGTCTGGTGCTACAAATTGGAAACATAATCTCAATATGGGTTAGCCATTCAATCCAAAC\nTGGAAGCCAGAGCCACCCAGAAACATGCAATCAAAGTGTCATTACCTACGAAAACAATAC\nTTGGGTGAATCAGACATACATCAACATAAGTAATACCAATTTAATTGCAGAGCAGGCTGT\nAGATCCGGTAGCACTAGCAGGTAACTCCTCTCTCTGTCCAATCAGTGGATGGGCTATATA\nCAGCAAGGACAATGGTATAAGAATAGGTTCCAAAGGAGATGTATTTGTCATCAGAGAGCC\nTTTTATTTCATGCTCTCACTTGGAATGCAGGACTTTCTTTCTAACTCAAGGGGCCTTGTT\nGAATGACAAGCATTCTAATGGAACCGTTAAAGACAGAAGCCCTTATAGAACCCTAATGAG\nCTGCCCTGTTGGTGAAGCTCCTTCCCCATACAATTCAAGGTTTGAGTCTGTTGCTTGGTC\nAGCAAGTGCTTGTCATGATGGCATTAGTTGGTTGACAATTGGTATTTCCGGCCCAGACAA\nTGGGGCGGTGGCTGTATTAAAATACAATGGCATAATAACAGATACTATCAAGAGTTGGAG\nAGGCAATATATTAAGAACACAAGAGTCTGAATGTGCCTGCATTAATGGTTCTTGCTTTAC\nCATAATGACTGATGGGCCGAGTAATGGCCAGGCCTCATACAAAATTTTCAAGGTAGAAAA\nGGGAAAGGTAGTCAAATCAGTTGAGTTGAATGCTCCTAATTACCACTATGAGGAGTGCTC\nCTGTTATCCTGATGCTAGCGAGGTAATGTGTGTGTGCAGAGACAATTGGCATGGTTCAAA\nTCGACCATGGGTGTCCTTCAATCAAAATCTAGAATATCAAATAGGATACATATGCAGCGG\nAGTTTTTGGAGACAACCCGCGCCCTAGTGATGGGACAGGCAGTTGTGGTCCAGTTTCTTC\nTAATGGGGCATATGGAGTGAAGGGGTTTTCATTTAAATACGGTAATGGTGTTTGGATAGG\nAAGAACTAAAAGTACTAGCTCAAGGAGTGGGTTTGAGATGATCTGGGATCCTAATGGGTG\nGACTGAGACAGATAGCAGTTTTTCTGTGAAGCAAGATATTGTAGCAATAACTGATTGGTC\nAGGATATAGCGGAAGTTTTGTCCAGCATCCAGAACTGACTGGGTTGGATTGCATGAGGCC\nTTGCTTCTGGGTTGAGCTGATCAGAGGAAGACCCAAGGAGAACACAATCTGGACCAGTGG\nAAGCAGCATTTCTTTTTGTGGAGTGAATAGCGACACTGTGGGTTGGTCTTGGCCAGACGG\nTGCTGAGTTGCCATTCACCATTGACAAGTAGTTTGTTCAAAAAACTCCTTG\n>I1-5\nGTAGATAATCACTCACCGAGTGACATCCACATCATGGCGTCTCAAGGCACCAAACGATCT\nTATGAGCAAATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAAATCAGAGCATCTGTT\nGGGAGAATGGTTGGTGGAATCGGAAGATTCTACATACAGATGTGTACTGAACTCAAGCTC\nAGTGACTATGAAGGGAGGCTGATCCAAAATAGCATAACCATAGAGAGAATGGTTCTCTCG\nGCATTTGATGAGAGGAGAAATAAATATCTGGAAGAGCATCCCAGTGCTGGGAAAGACCCC\nAAGAAGACTGGAGGCCCAATCTACAGAAGAAGAGATGGAAAATGGATGAGAGAGTTGATC\nCTATATGACAAAGAAGAGATCAGGAGGATTTGGCGTCAAGCAAATAACGGAGAAGACGCA\nACTGCTGGTCTCACCCATTTGATGATTTGGCATTCCAATCTGAATGATGCCACATACCAG\nAGAACAAGGGCACTTGTGCGTACTGGGATGGATCCCAGGATGTGCTCCCTGATGCAAGGC\nTCAACTCTTCCAAGAAGATCTGGGGCTGCTGGAGCAGCAGTGAAAGGGGTTGGAACAATG\nGCGATGGAACTGATCCGGATGATCAAGCGAGGTATCAATGATAGGAATTTCTGGAGAGGC\nGAAAATGGACGGAGGACGAGAATTGCTTATGAAAGAATGTGCAACATCCTCAAGGGGAAA\nTTCCAAACAGCAGCACAACGAGCAATGATGGATCAGGTGAGAGAAAGCCGGAATCCTGGG\nAATGCTGAAATTGAAGATCTCATCTTCCTTGCAAGGTCTGCTCTCATTCTGAGAGGATCA\nGTAGCTCATAAGTCCTGCCTGCCTGCTTGTGTGTATGGGCTTGCAGTGGCCAGTGGATAC\nGACTTTGAGAGAGAGGGATATTCCCTAGTCGGAATTGATCCTTTCCGTCTGCTCCAAAAC\nAGTCAAGTCTTCAGCCTCATCAGACCAAACGAAAATCCAGCGCATAAGAGTCAGCTGGTA\nTGGATGGCATGTCACTCTGCTGCATTTGAAGATTTGAGAGTGTCAAGCTTCATCAGAGGA\nACAAGAGTAGTCCCAAGAGGACAACTATCCACCAGAGGAGTTCAGATTGCTTCAAATGAG\nAACATGGAGACAATGGACTCCAGCACTCTTGAACTGAGGAGCAGATACTGGGCTATAAGG\nACAAGAAGCGGAGGGAACACTAACCAGCAGAGAGCATCTGCAGGGCAAATCAGCGTGCAG\nCCCACCTTCTCTGTACAGAGAAACCTCCCATTCGAGAGAGCAACCATTATGGCGGCATTT\nACGGGAAATACCGAGGGTAGAACTTCAGACATGAGGACTGAGATCATAAGGATGATGGAA\nAATGCCAGACCTGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAA\nAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTC\nGGAGACAATGCAGAGGAGTATGACAATTAAAGAAA\n>I1-7\nGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGT\nCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTGTTCGCAGGGAAAAACA\nCCGACCTTGAGGCGCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTA\nAGGGGATCTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTA\nGACGCTTTGTCCAAAATGCCCTTAATGGGAATGGGGATCCAAACAACATGGACAGAGCAG\nTCAAACTGTACAGGAAGCTCAAAAGGGAGATAACATTCCATGGGGCAAAGGAGGTAGCAC\nTCAGTTACTCAACTGGTGCACTTGCCAGCTGCATGGGTCTCATATACAACAGGATGGGGA\nCTGTGACCACTGAAGTGGCATTTGGCCTGGTGTGTGCCACGTGTGAGCAGATTGCTGACT\nCCCAGCATCGGTCTCACAGACAAATGGTAACAACAACCAACCCACTAATAAGACACGAGA\nACAGGATGGTACTGGCTAGTACTACAGCTAAGGCCATGGAGCAAATGGCAGGGTCAAGTG\nAGCAAGCAGCAGAGGCTATGGAGGTTGCTAGTCAGGCTAGACAGATGGTGCAGGCAATGA\nGGACTATTGGGACTCACCCTAGCTCCAGTGCTGGTCTAAAAGATGATCTTCTTGAAAATT\nTGCAGGCCTACCAGAAACGGATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGTT\nATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTC\nTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGA\nGTGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAGTGCTGTGGATGTTGAC\nAATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCT\n>I1-8\nCAGGTAGATTGCTATCTATGGCACATAAGAAAGCTGCTCAGCATGAGAGACATGTGTGAT\nGCTCCCTTTGATGATAGACTCAGAAGAGATCAGAAGGCATTAAAGGGGAGAGGCAGCACA\nCTTGGACTCGACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNACCGACATGAGCATAGAGGAAATAAGCAGGGAGTGGTACATGCTCATGCCAAGGCAG\nAAAATAACAGGGGGTCTGATGGTGAAAATGGACCAGGCCATCATGGACAAGAGGATAATA\nCTCAAGGCAAACTTCTCTGTCCTATTTGATCAACTGGAAACATTAGTCTCACTGAGGGCT\nTTCACAGACGATGGCGCCATTGTAGCTGAAATATCTCCTATTCCTTCCATGCCAGGACAT\nTCTACAGAGGATGTCAAAAATGCAATTGGAATCCTCATCGGTGGACTTGAATGGAATGAT\nAACTCAATTCGAGCGTCTGAAAATATACAGAGATTCGCTTGGGGAGTCCGTGATGAGAAT\nGGGGGACCTCCACTCCCTCCAAAACAGAAACGCTACATGGCGAGAAGAGTTGAGTCAGAA\nGTTTGAAGAGATCAGATGGCTAATTGCAGAGTGCAGAAACATATTAACCAAAACTGAAAA\nCAGCTTCGAGCAGATAACGTTCTTGCAGGCATTGCAACTCTTACTTGAGGTTGAGAGTGA\nGATAAGGACATTTTCTTTTCAGCTTATTTAGTACTAAAAAAC\n>I1-2\nAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGC\nCATAAGCACCACATTCCCGTACACTGGAGACCCTCCATACAGCCATGGAACAGGAACAGG\nATACACCATGGACACGGTCAACAGAACACATCAATATTCAGAAAAGGGGAAATGGACAAC\nAAACTCAGAGACTGGAGCACCCCAACTTAACCCAATTGATGGACCACTGCCCGAGGACAA\nTGAGCCAAGTGGATATGCACAAACGGACTGTGTCCTTGAAGCAATGGCTTTCCTTGAAGA\nATCCCACCCAGGAATCTTTGAAAACTCGTGTCTTGAGACGATGGAAGTTGTTCAACAAAC\nAAGAGTAGACAAATTGACCCAAGGCCGTCAGACCTATGATTGGACATTAAACAGGAATCA\nACCGGCTGCAACTGCATTAGCTAATACTATAGAGGTATTCAGATCGAACGGTCTGACAGC\nTAATGAATCAGGAAGGCTAATAGATTTTCTCAAGGATGTGATGGAATCAATGGATAAAGA\nGGAAATGGAAATAACAACGCATTTCCAAAGGAAAAGAAGAGTAAGGGACAACATGACCAA\nGAAAATGGTCACACAAAGGACAATAGGAAAGAAGAAGCAGAGGCTAAATAAAAAGAGCTA\nTCTAATAAGAGCCTTGACACTGAACACAATGACAAAAGACGCCGAAAGAGGCAAATTAAA\nGAGAAGAGCAATTGCAACACCCGGAATGCAAATCAGAGGATTTGTATACTTTGTTGAAAC\nATTAGCAAGGAGCATTTGTGAGAAGCTTGAACAATCTGGACTCCCAGTTGGAGGCAATGA\nAAAGAAGGCTAAACTGGCAAATGTTGTGAGGAAAATGATGACTAATTCACAAGATACAGA\nACTCTCCTTCACAATCACTGGAGACAACACCAAATGGAATGAAAACCAGAACCCTAGGAT\nGTTTCTGGCAATGATAACATATATAACAAGAAACCAACCTGAATGGTTTAGGAATGTCTT\nGAGCATTGCACCCATAATGTTCTCAAACAAAATGGCAAGGCTAGGGAAAGGATATATGTT\nCGAAAGTAAGAGCATGAAGCTTCGAACACAAATACCGGCAGAAATGCTAGCAAGTATTGA\nTCTGAAATATTTTAATGAGTCGACAAAAAAGAAAATTGAAAAGATAAGACCTCTTCTAAT\nAGATGGTACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTAC\nAGTTTTGGGAGTTTCGATTTTAAATCTAGGACAAAAGAGGTACACCAAAACAACATACTG\nGTGGGACGGGCTCCAATCCTCTGATGACTTTGCTCTCATAGTGAATGCCCCGAATCATGA\nGGGGATACAAGCAGGAGTAGACAGATTCTATAGAACCTGCAAGCTGGTTGGAATCAACAT\nGAGCAAAAAGAAGTCCTACATAAACAGGACAGGAACATTTGAATTCACAAGTTTTTTCTA\nTCGCTATGGATTTGTAGCCAATTTCAGTATGGAGTTGCCCAGCTTTGGAGTGTCTGGGAT\nTAATGAATCTGCAGACATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAA\nTGATCTTGGACCAGCAACAGCTCAAATGGCTCTTCAGCTGTTCATCAAGGATTACAGATA\nCACGTATCGGTGTCACAGAGGAGACACACAAATTCAGACAAGGAGGTCATTCGAGCTGAA\nGAAATTGTGGGAACAAACCCGCTCAAAAGCGGGACTGCTGGTCTCAGACGGAGGACCAAA\nCCTATACAATATCCGGAATCTACACATTCCGGAAGTCTGCTTAAAATGGGAGCTGATGGA\nCGAAGACTATCAGGGAAGGCTTTGCAACCCCCTGAATCCGTTTGTCAGCCACAAGGAGAT\nAGAGTCTGTAAACAATGCTGTGGTGATGCCAGCTCATGGCCCAGCCAAGAGCATGGAGTA\nTGATGCTGTGGCTACTACACACTCCTGGATACCTAAGAGGAATCGCTCTATCCTCAATAC\nAAGCCAAAGGGGAATCCTTGAGGATGAACAGATGTATCAAAAGTGCTGCAATCTATTCGA\nGAAATTCTTCCCTAGCAGCTCATACAGGAGACCGGTTGGAATTTCCAGCATGGTAGAGGC\nCATGGTTTCTAGGGCCCGAATCGATGCGCGAATTGACTTCGAATCTGGACGGATCAAGAA\nAGAGGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAACTCAGACGGCAGAA\nATAGTGAATTTTGCTTGTCCTTCATGAAAAAATGCCTTG\n>I1-1\nTATATTCAATATGGAGAGAATAAAAGAACTAAGAGATTTAATGTCACAATCCCGCACTCG\nCGAGATACTAACCAAAACCACTGTTGACCACATGGCCATAATCAAAAAGTACACATCGGG\nAAGGCAAGAGAAGAACCCCGCACTCAGGATGAAATGGATGATGGCAATGAAATATCCAAT\nCACAGCTGACAAGCGAATAATGGAAATGATCCCTGAAAGGAATGAACAAGGGCAAACCCT\nCTGGAGCAAAACAAACGATGCCGGATCAGACCGAGTGATGGTATCACCCCTGGCTGTAAC\nATGGTGGAATAGGAATGGACCAACAACAAGTACAGTTCACTATCCCAAGGTATATAAAAC\nTTATTTCGAAAAGGTTGAAAGGTTGAAACACGGGACCTTTGGCCCTGTACACTTCAGAAA\nCCAAGTTAAGATAAGACGGAGGGTCGACATAAACCCGGGCCATGCTGACCTCAGTGCCAA\nAGAGGCGCAGGATGTAATCATGGAAGTTGTCTTTCCAAATGAAGTGGGAGCGAGAATACT\nGACGTCGGAATCACAATTGACGATAACAAAGGAGAAGAAAGAAGAACTCCAGGACTGCAA\nAATCGCCCCTCTGATGGTTGCATACATGCTAGAAAGAGAGTTGGTTCGCAAGACAAGGTT\nTCTCCCAGTGGCTGGTGGAACAAGCAGTGTCTACATTGAGGTGCTGCATTTGACCCAGGG\nGACATGCTGGGAGCAGATGTATACTCCGGGAGGAGAAGTGAGAAACGATGATGTAGACCA\nGAGCTTGATTATCGCTGCCAGGAACATAGTGAGAAGAGCAACAGTGTCAGCAGACCCACT\nAGCATCTCTATTGGAGATGTGCCACAGCACACAAATTGGGGGAATAAGGATGGTAGACAT\nTCTCCGGCAAAATCCAACAGAGGAACAAGCCGTGGACATATGCAAGGCAGCAATGGGCTT\nGAGGATTAGCTCATCTTTCAGTTTTGGTGGATTCACTTTTAAAAGAACGAGTGGATCGTC\nAGTCAAAAAGGAAGAAGAAGTGCTTACGGGCAACCTTCAAACATTGAAAATAAGAGTGCA\nTGAGGGGTATGAAGAGTTCACAATGGTTGGAAGAAGAGCAACGGCCATTCTCAGAAAGGC\nAACCAGAAGGCTGATCCAGTTAATAGTAAGTGGAAGAGACGAGCAGTCAATTGCTGAAGC\nAATAATTGTGGCCATGGTATTCTCACAAGAGGACTGCATGATTAAGGCAGTTCGAGGTGA\nTCTGAATTTTGTCAATAGGGCGAACCAGCGGCTGAATCCAATGCATCAGCTCTTGAGACA\nCTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAATTGGGGAATTGAACCCATTGACAATGT\nGATGGGAATGATCGGGATATTGCCTGACATGACCCCAAGTACTGAGATGTCACTGAGGGG\nAATAAGAATCAGTAAGATGGGGGTAGATGAATACTCCAGCACAGAGCGGGTAGTAGTAAG\nCATCGACCGATTTTTAAGAGTTCGAGACCAACGAGGGAACGTGCTATTGTCACCCGAAGA\nAGTCAGCGAGGCACAAGGAACAGAGAAACTGACAATCACTTATTCGTCATCAATGATGTG\nGGAGATTAATGGTCCTGAGTCGGTGTTGGTCAATACTTATCAGTGGATAATCAGAAACTG\nGGAAACTGTAAAAATTCAATGGTCACAGGATCCCACAATGTTGTATAATAAGATGGAATT\nCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCCAGAGGTCAATACAGTGGGTTCGTGAG\nGACACTGTTCCAGCAGATGCGAGATGTGCTTGGAACATTCGACACTGTTCAGATAATAAA\nACTCCTCCCCTTTGCTGCTGCCCCACCGGAACAAAGTAGGATGCAGTTCTCCTCCCTGAC\nTGTGAATGTGAGAGGATCAGGAATGAGAATACTGGTAAGAGGCAATTCCCCAGTGTTCAA\nTTACAACAAGGCCACCAAGAGGCTCACAGTTCTCGGGAAAGATGCAGGTGCATTGACCGA\nAGATCCAGATGAAGGCACAGCTGGAGTGGAGTCTGCTGTTTTAAGAGGATTCCTCATTTT\nGGGCAAAGAAGACAAGAGATATGGCCCAGCATTGAGCATCAATGAGCTGAGCAATCTTGC\nAAAGGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTGATGAAACG\nGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGC\nCATCAATTAGTGTCGAATTGTTTA\n>I1-3\nCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAA\nGGCAATGAAAGAATATGGGGAAGATCCGAAAATTGAAACTAACAAGTTTGCTGCAATATG\nCACCCACTTAGAAGTCTGTTTCATGTATTCGGATTTTCATTTCATCGACGAACGGGGTGA\nATCAATAATTGTAGAATCTGGTGACCCAAATGCATTACTGAAGCACCGATTCGAGATAAT\nTGAAGGAAGAGATCGAACCATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGG\nGGTAGAGAAGCCTAAATTTCTTCCGGATCTGTATGACTACAAGGAGAACAGATTCATTGA\nAATTGGGGTGACACGGAGGGAGGTTCACATATACTACCTAGAAAAAGCCAATAAAATAAA\nATCCGAGAAGACACACATCCACATTTTCTCATTCACTGGAGAGGAAATGGCCACCAAAGC\nGGACTACACCCTTGATGAAGAAAGCAGAGCAAGAATCAAAACCAGATTGTTCACCATAAG\nACAAGAAATGGCCAGTAGAGGTTTGTGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGA\nGACAATTGAAGAAAGATTTGAAATTACAGGAACCATGCGCAGGCTTGCCGACCAAAGTCT\nCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCGAACCGAA\nCGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAAGTGAACGCAAGAATTGAACC\nATTCTTGAAAACAACACCACGCCCACTCAGATTACCTGATGGGCCTCCTTGTTCCCAGCG\nGTCAAAATTTCTGTTGATGGATGCTCTGAAACTAAGTATTGAGGACCCGAGTCATGAGGG\nGGAGGGAATACCGCTATATGATGCAATCAAATGCATGAAGACATTTTTTGGCTGGAAAGA\nACCTAACATAATCAAACCACATGAGAAAGGCATAAACCCCAACTACCTCCTGACTTGGAA\nGCAAGTACTAGCGGAACTCCAAGACATTGAGAATGAAGAGAAGATCCCAAAGACAAAGAA\nCATGAAGAAAACAAGCCAACTGAAGTGGGCACTTGGTGAAAATATGGCACCAGAGAAAGT\nAGACTTTGATGATTGCAAAGATATTAGTGATCTTAAACAGTATGACAGCGATGAGCCAGA\nACCTAGGTCGCTAGCAAGCTGGATCCAAAGTGAATTCAACAAGGCATGTGAATTGACCGA\nTTCAAGCTGGATGGAGCTTGATGAGATAGGGGAAGATGTTGCCCCGATCGAACACATTGC\nAAGCATGAGGAGAAACTATTTTACAGCAGAAGTGTCCCATTGCAGGGCTACTGAGTACAT\nAATGAAGGGAGTGTACATAAACACAGCCTTGCTCAATGCATCTTGTGCAGCCATGGATGA\nCTTCCAGCTGATCCCAATGATAAGCAAATGTAGAACCAAAGAAGGGAGACGGAAAACAAA\nTCTGTATGGATTCATTATAAAAGGAAGGTCTCATTTGAGAAATGACACTGACGTGGTAAA\nTTTTGTGAGTATGGAGTTCTCTCTCACAGACCCGAGACTGGAGCCACACAAATGGGAAAA\nGTACTGTGTTCTCGAAATAGGGGATATGCTCTTGAGGACTGCGATAGGCCAAGTGTCACG\nACCCATGTTCCTATATGTGAGAACCAATGGAACTTCAAAGATCAAGATGAAATGGGGGAT\nGGAAATGAGGCGCTGCCTTCTCCAATCCCTTCAGCAGATTGAGAGCATGATTGAGGCCGA\nGTCTTCCGTCAAAGAGAAAGATATGACAAAGGAATTCTTTGAGAACAAATCAGAAACATG\nGCCAATTGGAGAGTCACCCAAGGGAGTGGAAGAAGGCTCTATTGGGAAAGTATGCAGAAC\nCCTACTGGCAAAGTCTGTATTCAACAGTCTATATGCATCTCCACAACTCGAGGGGTTTTC\nAGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGAACCTGG\nGACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTG\nGGTTTTGCTCAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTGAAATAGTTGTG\nGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTT\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.lasv.fasta", "content": ">comp1_c0_seq1 len=3441 path=[0:0-1842 3476:1843-1879 1843:1880-3145 3161:3146-3440]\nATGTCTGCTGAAATGACAAAAGCACAGTGGATCCTAGGCTATTGGATTGCGCTTTGCTTT\nTGTCATTTCAGCAGACATTCTCAGCCTCTTGTTGCGTGCATTTAACACAACAATCTGGCG\nATGAGTGCCTCAAAGGAAATCAAATCCTTTTTGTGGACACAATCTTTGAGGAGAGAACTA\nTCTGGTTACTGCTCCAACATCAAACTACAGGTGGTGAAAGATGCCCAGGCTCTTTTACAT\nGGACTTGACTTCTCTGAGGTCAGCAATGTTCAACGGTTGATGCGCAAGGAGAGAAGGGAT\nGACAGTGATTTGAAACGATTGAGAGACCTAAATCAAACAGTCAACAATCTTGTTGAATTA\nAAATCAACTCAACAGAAGAGTATACTGAGAGTTGGGACTCTAACCTCAGATGACTTATTA\nATCTTAGCCGCTGATTTAGAGAAGTTGAAGTCAAAGGTGATCAGAACAGAAAGGCCATTG\nAGTGCAGGTGTCTATATGGGCAATCTGAGCTCACAGCAACTTGACCAAAGAAGAGCTCTT\nCTGAATATGATAGGAATGAGTAGTGGTAATCAAGGGGCTCAGGCTGGGAGAGATGGAGTG\nGTAAGAGTTTGGGATGTGAAAAATGCAGAGTTGCTCAATAATCAGTTCGGGACCATGCCA\nAGTCTGACACTGGCATGTCTGACAAAACAGGGGCAGGTTGACTTGAATGATGCAGTACAA\nGCATTAACAGATTTGGGTTTGATCTACACAGCAAAGTATCCCAACACTTCAGACTTAGAC\nAGGCTGACTCAAAGCCACCCCATCCTAAATATGATTGACACCAAGAAAAGCTCCTTAAAT\nATCTCAGGTTACAATTTTAGCTTGGGTGCAGCTGTAAAGGCAGGAGCTTGCATGCTGGAT\nGGTGGCAATATGTTGGAAACAATCAAGGTGTCACCTCAGACAATGGATGGTATCCTCAAA\nTCCATCTTAAAGGTCAAGAAGGCTCTTGGAATGTTCATTTCAGACACCCCTGGCGAGAGG\nAATCCTTATGAAAACATACTCTACAAGATTTGTTTGTCAGGGGATGGATGGCCATATATT\nGCATCAAGAACTTCAATAACAGGAAGGGCCTGGGAAAACACTGTCGTTGATTTGGAATCA\nGATGGGATGCCACAGAAGGCTGGTAGCAGCAGTTCCAATAAATCCCTGCAGTCGGCAGGG\nTTTGTCGCTGGGCTTACCTATTCTCAGCTGATGACCCTCAAAGATGCAATGCTGCAACTT\nGACCCAAATGCTAAGACCTGGATGGATATTGAGGGAAGACCTGAAGATCCAGTGGAAATT\nGCCCTCTATCAACCAAGTTCAGGCTGCTACATACACTTCTTCCGTGAACCTACTGATTTA\nAAGCAGTTCAAACAAGATGCTAAGTACTCACATGGTATTGATGTTACAGACCTCTTCGCT\nGCACAACCGGGCTTGACCAGTGCTGTTATTGATGCACTCCCCCGGAATATGGTCATTACC\nTGTCAGGGGTCCGATGACATAAGGAAACTTCTTGAATCACAAGGAAGAAAGGATATCAAA\nCTAATTGATATTGCCCTCAGCAAAGCTGATTCCAGGAAGTATGAAAATGCAGTCTGGGAT\nCAGTATAAAGACCTATGCCACATGCACACAGGTGTTGTTGTTGAAAAGAAGAAAAGAGGC\nGGCAAGGAGGAAATAACCCCTCACTGTGCACTAATGGACTGCATCATGTATGATGCAGCA\nGTGTCAGGAGGACTGAACACATCAGTTTTGAGAGCAGTGCTGCCCAGAGATATGGTGTTC\nAGAACATCGACACCCAGAGTCGTCCTGTAAATGGACGCCCCCGTGACCCACCGCCAATAG\nGCGGTGGGTCACGGGGGCCCTGACAAGGGTCTCATCTCTTCCATTTTACAGGCACACCAG\nGCTGTTTGTAGAGTCCACAAGAACATATGCCCATGTGATTCAGTCTGTGAGGTTTGGGAC\nACGACTTGCCTACAACATGCCTATGAGTTGGTATTTTGACCAGGTGGAGGAAGATGCTAA\nTGAGATAGAAACTTGTGCTGAACACAAAGAGGTCAACCAGGCCCAATGGTGTCTTCCCCT\nGCCTCTCCATGTACTCCTTCTGTAACATCTCAGTGATCATGTTGTCAGCTTGTTGTTCAA\nTATCATCAGAAAAGTGAGTCTCGTTCAAGTACGAACCATTTGATACAAGCCAACATTTGG\nGCAGTGATGTTTTCCCAGTAGTTGTGTGGTTGAGGTACCAATACTTGCTGTAATTACAGT\nATGGAATTCCCATGATGTCCCGCAGGTGGTTCTTCATTATGAGTTGGTCATTTATTAAAG\nCATTTACTGCTTTGTTGATCAACTGAATGCTCATTTGTGCTTCAGCTTTCAACCTTTGAA\nTGGCTTGTTTATTGAAGTCAAACAGCCTCAGCATGTCACAAAACTCCTCATCATGTTTCT\nCATTACATTTTGCTACAGCTGTGTTCCCGAAGCATTTTAGTTCAGCCTCAATTAGCATCC\nATCTGGTCAGACAATATCCCCCTGGTGCGTCATTGCCTTCAGAATCTGATAGTGTCCATG\nTGAATGTGCCTAGTAGTCTTCTGCTAATGTAAATATCTCTGGTCCTTTGTGAGAGGAGCC\nCAAGGTAACCGATAGGAGATGGTCTCGAGAATTGGCAGTGATCTTCCCAGGTTGTATTTT\nGGATTATTAAATATTGATAACTAGTCATGATACAGTCCCAATTACCATGACCTGAGTCAA\nGAGCAATGTAGCTCCCACCCCAAGCCATCCTCATGAAAGTCTGCAATACACCATTTGCAA\nCAGTGCCACAATGGTTGGCTGCATCTACAGCATAGCTATGACTCAAGTTGTACTGCACAC\nTAATTTTTCCCCCATTAAAATCGCAGCTCATCGCCTCATACTGATTGAAGTTGGGGATGG\nACAAGTGGAAAGTTGAGATTATGCTCATAAGAGCGTGGTCATAGAGGTTCTTTTTGTGGG\nCATCAGACAGATTACAAAATTTATGATTAATAATGCTCGTGTTAGTCAAGGTCAGTTCTA\nGTCCTGTCTCATTGCCCACCCTTATATAATGATGACTGTTGTTCTTTGTGCAGGAGAGAG\nGCATGGTCATATTGAGTGTCTCCATGTTTAGTTCCAGAGTCTGGAGCTCATAAACCCCTT\nTATAGAGGCTGGTTGTGCAAGACTTACCACACAACAGGAGGAAAGTGACCAAACCAACAA\nGGCCACATGTTGCAATGTTGTACAGACCTTTCAACACTGCCAGTATAGACAGTGTAATGA\nGAACAATGTTCATCACCTCTTCTATTACATGAGGCACTTCTTGGAAGAATGTCACTATTT\nGTCCCATTTTAAATAGGACACTTGAATTGCGCAACCAAAAATGCCTAGGATCCCCGGTGC\nGCAATTCAAGTGTCCTATTTA\n>comp1_c0_seq2 len=3404 path=[0:0-1842 1843:1843-3108 3161:3109-3403]\nATGTCTGCTGAAATGACAAAAGCACAGTGGATCCTAGGCTATTGGATTGCGCTTTGCTTT\nTGTCATTTCAGCAGACATTCTCAGCCTCTTGTTGCGTGCATTTAACACAACAATCTGGCG\nATGAGTGCCTCAAAGGAAATCAAATCCTTTTTGTGGACACAATCTTTGAGGAGAGAACTA\nTCTGGTTACTGCTCCAACATCAAACTACAGGTGGTGAAAGATGCCCAGGCTCTTTTACAT\nGGACTTGACTTCTCTGAGGTCAGCAATGTTCAACGGTTGATGCGCAAGGAGAGAAGGGAT\nGACAGTGATTTGAAACGATTGAGAGACCTAAATCAAACAGTCAACAATCTTGTTGAATTA\nAAATCAACTCAACAGAAGAGTATACTGAGAGTTGGGACTCTAACCTCAGATGACTTATTA\nATCTTAGCCGCTGATTTAGAGAAGTTGAAGTCAAAGGTGATCAGAACAGAAAGGCCATTG\nAGTGCAGGTGTCTATATGGGCAATCTGAGCTCACAGCAACTTGACCAAAGAAGAGCTCTT\nCTGAATATGATAGGAATGAGTAGTGGTAATCAAGGGGCTCAGGCTGGGAGAGATGGAGTG\nGTAAGAGTTTGGGATGTGAAAAATGCAGAGTTGCTCAATAATCAGTTCGGGACCATGCCA\nAGTCTGACACTGGCATGTCTGACAAAACAGGGGCAGGTTGACTTGAATGATGCAGTACAA\nGCATTAACAGATTTGGGTTTGATCTACACAGCAAAGTATCCCAACACTTCAGACTTAGAC\nAGGCTGACTCAAAGCCACCCCATCCTAAATATGATTGACACCAAGAAAAGCTCCTTAAAT\nATCTCAGGTTACAATTTTAGCTTGGGTGCAGCTGTAAAGGCAGGAGCTTGCATGCTGGAT\nGGTGGCAATATGTTGGAAACAATCAAGGTGTCACCTCAGACAATGGATGGTATCCTCAAA\nTCCATCTTAAAGGTCAAGAAGGCTCTTGGAATGTTCATTTCAGACACCCCTGGCGAGAGG\nAATCCTTATGAAAACATACTCTACAAGATTTGTTTGTCAGGGGATGGATGGCCATATATT\nGCATCAAGAACTTCAATAACAGGAAGGGCCTGGGAAAACACTGTCGTTGATTTGGAATCA\nGATGGGATGCCACAGAAGGCTGGTAGCAGCAGTTCCAATAAATCCCTGCAGTCGGCAGGG\nTTTGTCGCTGGGCTTACCTATTCTCAGCTGATGACCCTCAAAGATGCAATGCTGCAACTT\nGACCCAAATGCTAAGACCTGGATGGATATTGAGGGAAGACCTGAAGATCCAGTGGAAATT\nGCCCTCTATCAACCAAGTTCAGGCTGCTACATACACTTCTTCCGTGAACCTACTGATTTA\nAAGCAGTTCAAACAAGATGCTAAGTACTCACATGGTATTGATGTTACAGACCTCTTCGCT\nGCACAACCGGGCTTGACCAGTGCTGTTATTGATGCACTCCCCCGGAATATGGTCATTACC\nTGTCAGGGGTCCGATGACATAAGGAAACTTCTTGAATCACAAGGAAGAAAGGATATCAAA\nCTAATTGATATTGCCCTCAGCAAAGCTGATTCCAGGAAGTATGAAAATGCAGTCTGGGAT\nCAGTATAAAGACCTATGCCACATGCACACAGGTGTTGTTGTTGAAAAGAAGAAAAGAGGC\nGGCAAGGAGGAAATAACCCCTCACTGTGCACTAATGGACTGCATCATGTATGATGCAGCA\nGTGTCAGGAGGACTGAACACATCAGTTTTGAGAGCAGTGCTGCCCAGAGATATGGTGTTC\nAGAACATCGACACCCAGAGTCGTCCTGTAAATGGACGCCCCCGTGACAAGGGTCTCATCT\nCTTCCATTTTACAGGCACACCAGGCTGTTTGTAGAGTCCACAAGAACATATGCCCATGTG\nATTCAGTCTGTGAGGTTTGGGACACGACTTGCCTACAACATGCCTATGAGTTGGTATTTT\nGACCAGGTGGAGGAAGATGCTAATGAGATAGAAACTTGTGCTGAACACAAAGAGGTCAAC\nCAGGCCCAATGGTGTCTTCCCCTGCCTCTCCATGTACTCCTTCTGTAACATCTCAGTGAT\nCATGTTGTCAGCTTGTTGTTCAATATCATCAGAAAAGTGAGTCTCGTTCAAGTACGAACC\nATTTGATACAAGCCAACATTTGGGCAGTGATGTTTTCCCAGTAGTTGTGTGGTTGAGGTA\nCCAATACTTGCTGTAATTACAGTATGGAATTCCCATGATGTCCCGCAGGTGGTTCTTCAT\nTATGAGTTGGTCATTTATTAAAGCATTTACTGCTTTGTTGATCAACTGAATGCTCATTTG\nTGCTTCAGCTTTCAACCTTTGAATGGCTTGTTTATTGAAGTCAAACAGCCTCAGCATGTC\nACAAAACTCCTCATCATGTTTCTCATTACATTTTGCTACAGCTGTGTTCCCGAAGCATTT\nTAGTTCAGCCTCAATTAGCATCCATCTGGTCAGACAATATCCCCCTGGTGCGTCATTGCC\nTTCAGAATCTGATAGTGTCCATGTGAATGTGCCTAGTAGTCTTCTGCTAATGTAAATATC\nTCTGGTCCTTTGTGAGAGGAGCCCAAGGTAACCGATAGGAGATGGTCTCGAGAATTGGCA\nGTGATCTTCCCAGGTTGTATTTTGGATTATTAAATATTGATAACTAGTCATGATACAGTC\nCCAATTACCATGACCTGAGTCAAGAGCAATGTAGCTCCCACCCCAAGCCATCCTCATGAA\nAGTCTGCAATACACCATTTGCAACAGTGCCACAATGGTTGGCTGCATCTACAGCATAGCT\nATGACTCAAGTTGTACTGCACACTAATTTTTCCCCCATTAAAATCGCAGCTCATCGCCTC\nATACTGATTGAAGTTGGGGATGGACAAGTGGAAAGTTGAGATTATGCTCATAAGAGCGTG\nGTCATAGAGGTTCTTTTTGTGGGCATCAGACAGATTACAAAATTTATGATTAATAATGCT\nCGTGTTAGTCAAGGTCAGTTCTAGTCCTGTCTCATTGCCCACCCTTATATAATGATGACT\nGTTGTTCTTTGTGCAGGAGAGAGGCATGGTCATATTGAGTGTCTCCATGTTTAGTTCCAG\nAGTCTGGAGCTCATAAACCCCTTTATAGAGGCTGGTTGTGCAAGACTTACCACACAACAG\nGAGGAAAGTGACCAAACCAACAAGGCCACATGTTGCAATGTTGTACAGACCTTTCAACAC\nTGCCAGTATAGACAGTGTAATGAGAACAATGTTCATCACCTCTTCTATTACATGAGGCAC\nTTCTTGGAAGAATGTCACTATTTGTCCCATTTTAAATAGGACACTTGAATTGCGCAACCA\nAAAATGCCTAGGATCCCCGGTGCGCAATTCAAGTGTCCTATTTA\n>comp0_c0_seq1 len=6906 path=[0:0-1456 1457:1457-6905]\nGTGATGGTTGGCTCCCCCGGGGGGACCCCCCGCCGGGGGCCCCCCCGGGGGAGCCAACCA\nTCACCAAAAGACTACTCAATGTCCTCGATACATTCATCTTTCCTAGTCAACTCTTCACAT\nGTTCTGCCCTTCAGTCTCAATTTACCACTACTTGACTGTACCATCACCTTCCCCCTTGAC\nTTACTGTAACAGAGAGCGTAACCCTTGAACTCCACCCAATTGTCCACTGCCTCAAGAACC\nGCACTCAAGATCCCCTCACAACTCGGCGCTGCAGCCCTAAGTGTGGAGATGATGTCCACC\nCCTGACCACTGCATCCTTAATCCCAGCCTATCTATCATCATATCACTCAGTGCCCCAATC\nAGCAGGTCAGACGAAGTGTCCCCAACCTCTCTCACAAACACCTCAAGATCCTGGTCTTGT\nATAACAGGTGTAAAGGATGCTAACCTCCTTCCACATTCCCACAAGCCACCTCTATGCACA\nACCAGAGGGGCTGGTTCAGTGCAAGGACCCACCAATACAAAGTCATACTCCGTAAACTGC\nAACTTTTCCATATCAACAACAATCTCAACAGGGGTCACATGCCCCAGTTGATTTGTATCA\nACCAAAAACTCATTAATGATTTCGGTGTCAACATACCATGCTGATTTGCCCTTGAAAGTG\nGGTCCTGACAAAACCAGTCTCCAGCAGTCTGACAAAACACACGGATTCACTGCACCTGAG\nTACATAACGGTTACATCATGTACTAAATACTTGGCTTGTTGACTCATTGAGCCAGTATAC\nTCCAGGTGGATGGCAAAGCTTTCCTTGAAACTAGCATCTTGACTTTTGACACGGAACCTC\nACTGTCTGACTCAATTTTGCAGACCCTGAAGGTAGTGAAGCTACGGCATCAAAGAAATCC\nTCCAATGAGTCAAACTTGAGATCAACTAAACCAGATGCGATCAATTGATTTTGGTTGAAT\nCTAGCTGGCTCAATATCAAAGTCTATCCAAGCATAACCCATCATCAGATCATGTTTGTAC\nATTGGCCTTTCAACACCTTTGTGAATAACTTTCTCTACAAATGAGGAAAATGGACCCATT\nCTATGCAACCCTTCACCCTCTGGAACTGATGTCTTGTGTGGAAACCACGTGAAGGACCCC\nAATGTTCTTGTAGTCGCAACAAATGGCCTCACATAAGACTCAAAATAAATTTGCCTCATG\nAAATTGTCAACAGCATCGCTAGTGCTCACTACTCTTTCTTCCACCATAGGCTCATGTGTC\nCTACTATGAGATAGCCTCAGCTCAGATGACAACACAATGTAATGTTCCTCCCTTTTCCAT\nTTTACTATATGTGAGACAAGAGACAAGGCTTCACAGTTAACATCCAACGCTACACAGAGA\nTCTAGAAATTTTATTCTGGGTGACCACTTCATTTTAGTTGACGCTAGATCGCTCATGAAT\nGGTAATATGTGTTTTTCAAACACTGATGGGTACAGCCTCCTTAAAGAATGAATGATGTGA\nTTCAAACCAACCCTATCCTCTAATAGTTTTGACGCAGTTGGCTTTAAGGGGAAATAGTCA\nCAGGGGTTATGCTTGAAAAAATCCAACACCTTAACTGTCTTAGGTTCCCCTAAGACCCAT\nGCACCCAGTTCTATTGCAGTTGATAATGATATGCACATATAATCCCATAACAAGGGTCTG\nAAATAACTAATGACATCATCATTTCCACTTCCATTTCTTAGTTCTAACGGAACCTGCCAA\nTATTGAATACCATTAGAATTTGTCAACAATTTGATTCCCTTAACATCAGAAATCAGAGAC\nTGAATGGACTTAATATACAGATTCTCTTTATTTGGTCCCCGAACACATTTGCTACCCAAT\nGTTCTGCATAATCCCACAAAGCCAGATGCAATGGAACTTTGGAATGCAGATTTGTTAATA\nGCTTCAGACAGCAATTTTTGCGCACCTCGAGTAAAAGTGGAAGACAACTTATTTTGGATT\nGTTTTGACAATGGTAGGAATCTTCTCATCATCTAGGTTCACAGCACCTGAATATATTATC\nTTTTGTCTCAACACCATTCTTAAAGGATGATGTGCGGCTAAGTTTAACCAAGAGTACTCA\nAGGTCAGACTCAGATGGAGATTCAACACCTAACAGCTCACAAAGATTTCTTAGTGAAGAG\nAGGTGCTCACTAGACAAATAGTTTGTTGTAAACTCTTCATGGAGTTGCCCAGTCTTCAAC\nCTATTGTACAGTTTTCTTAACATAGATCTAATCTTGCTGCAAGCGTTGGGAATCAATCCC\nTCTATTTGTCTCATGATTCTATAACTACGGTTGCCATCCACCCAATCTCTAACATCTGTC\nTCGCAATTCAATAAAAATGGGTCAATAGGGTATCTTGCATATTGCAAAAGACTTAAGGTT\nCTTTTCTGTATTAGATTGCATAAGTGAACAGGGACACCATTTGCAACCGACTGATCAATG\nATTGTGTCAATTGTTTCTGCCAGTTGGTGTGGCTCTTTACACTTTATATTGTGAAGAGCT\nGCTGCAACGAACTTTGTCAACAATGGCACCTCATCTCCCCAAACAAAAAATCTAGATTTA\nAACTCAGCAACAAACCTGCCAATAACACTTTTAGGGCTCACAAACTTATTGAGTTGATCA\nCTCATATAATAATGGAACTCTATTAGAGTCCTAAATTCTTCTGGGTCCCTCTGCAAAAGC\nTCTGTGAGAGATTGATCAAAGAGAGAAATTTGATCATCACTAGAGGTATAAGCATCTATA\nGTACCACCACATATACAACTGATAGCATAATTAATGAACCTCTCTGAAATAAGGGCATAA\nAAATCTGATGTGTTGTGTAATATTCCCTGACCCATGTCAAGTATTGAACTAATGTGAGAA\nGGCACTACACCGACTTGGAAATTAGAGTAAAAGAAATCTTCTGTTATTGACTGTTTAGTT\nTTCTTCCTTAACCCTAGTTGAGCTTTAATGAAAGACTTCATCATGGCTGTCACCACATTA\nAAAGGTATTTCCACCATTTTGTGCATATGCCACATGAGTAGGGTTGAAAGATAGTCCCTC\nCCTTTTATGTCAGCTTGCAAGTCCCTTGAGAGGAAAATCAAATTCTGTAAGACAGTCAAG\nAACAAAAATGGACACATCATTGGGCCCCACTTACTATGATCCATGCTATAGGACACATGC\nGCTAATGAAACATTCAATTTCATGGAGAGGATAGCATTCTCAAACTCCTTCTCGTTGTTC\nAAGCAACTCCCTGACAACTGTAGGCTTATAGCTTCAAAGTAATCTTCTATAAGTCTAGTA\nAACATCTTTGTTCTAAGATCACCAATATATAGTTCTCTGTTGCCACCCACTTGTTCTTTA\nTATGACAAAGAGAACTTAAGCCTTCCTGTATCAGGTCCCACTGAGTCATAAGATTGTGGC\nGACTCTTGGCTATAAAAACACAAATTCTTTAACATTGCTGTGGTACAGTTTGTCAGTGAC\nAGAGCCTTACTAAGTGCCTCTGAGTTGCTCTCCCTTTCACTAATTCTCACATCATCAGAG\nAGTTTACCCATGTCAAACTTGAAATTAAGGTTCCTTGACTTATAATGAGTGTACCTCCCC\nATAAGTGCATTTGCATTCATGATCAAGAGTATGGACTTAAAACACTGAAAGTATTCATGG\nTTAAAGTATGTCCTTGTTGATACTGCCTTTGTCAACTCTCCAATAGGACACTGTGACATA\nTGTCCACAGTAAAAATACTTCTCCTTCAATCTACTATTCTCATAGACAGCATTACAGAAT\nTCTTCATAAAATTTACCTGGTAAGATATCATAATCAAAATCCTCAACCATGTGATTAGAT\nAATTCACCCTTAATCAACCTAATGTAAAACTTATTTGAGACAATCTCATCTAGATCATTT\nATTGACGGTTGGCCATCACCATTAGGGCCTGAGCCTGGCTTGGTGGGTTCCCTATACTGA\nTCGACAATTTTTTCAACAGTCTCTTTTAGCTGATCAAAATAATCGCTTGCACCTCCATCG\nAGCAAAATTTCATCTAGGTCAGCTCCATCAACATCACTTTTGAGCTGCCCAGATCCTAGA\nACCAAATTGCTCATTGCCTGCTGAACTTTGTATTCATAGTCCTGCTTGTTGAGAAGGTAC\nTTTCCTTTTCTTGAGAAGACTTCAGTGAGCTGCGACACGGCCAGTGCTGTGAGCTTATTG\nAAGTCATAGTTTAATATTCTAGAACCATCTGTGTACTTATTAACAACAACACTTTTGTTG\nCTGGCTAAATCCAAGGCAGTGGCACAGCCACTGGTGATGAGAGGATCTTTGATTTCCCTT\nTTTACTTCCCTCTCCTTAAATAGTGAACCATTGTTGAAAGAAGACGTAAGAAGGGACAAA\nTACTTCTTTGAAACACCAGGCCTTTTATAGTCTGGTCCCTCGACACTTGTGCATCCATCT\nTTACTTAAAAACTTTTTTGCATTATAGACCATGTCGTCCAATTCTTCCTCGGTAGCTGTA\nTCTGCAGGGTTAGTGCTCACATGACCAAATTTCACCTTTGGTTCCAAAAACTTCTCAAAA\nCATTTTATCTGATCTGTTAATCTATCTGGTGTTTCTTTCGTAATGAAGTGGCACATGTAA\nGAAATATTCAAAATGAACTTGAACCTATTGGTCATCATGCTCTTCACATCTTCAGATAAA\nACTAAACTCATTAATGTCCTTATTAACCTATAGAGCAGGAACTCAACATCAGTGATTAAT\nTCTTCCCTTATTTTGTCAACGAGGTCCTTATGATGATAATCTGACACATAAGCCATTACA\nAAATACCTAAGATTTTGGAGGAGCTTTTGAGAACGTTTACTGGGGTGAGCTAAAATTAAA\nACCAGGATCATCTTTGTCAAAAACTTTATGTTGTTCAACTGCCCTTCCAGCTCACTGCAA\nTCTTCTATCCAAGAAATCATAGTGCTTATTGTTGTCTGTAAAACCTCAGCTGAAAATATT\nGCTGGAAAATATCTTTTAGGATCAGCGTAAAATGAGCACACCTCACCAACTTTGTTATCA\nTTAATAGCATAGCACTTCGAGCATTCCCCTGTTTTTTGATAAATCAGTTGGAATTCAGAG\nTTTCCTAATGAAAACTCTTGACAATATGCTTCTTTGCATCTGACCACCTGATACCTTGCG\nGGTCCAAACTCATTCTGCCTCAATTTTACGGTAGAAGAAGTTTTCATAGAGTTCACCAAG\nGCGAGGCTCAATGAAGAAAGTCTCTCTAAGTCAGTGGTTCCCAGTAGTTCCACATCCCCC\nATCACATAAGGGAATGTTTCTTCCTCTGTTCTCTGATAACTGATTGTGGGAACAATTCCG\nGAGACATCAAAATCCATAATCAAATCATAACTATTAAGGCAAACCACCTCCATGTCAATT\nTTATAGTGGTCTACACTGATTCCAACATCCTCTAAAGCAGTGGTGGCCTTCAAAATGGTT\nTTCTGGAATATTGAATTGAGAATTTGGTTCTTACTCAAACACTGGGAGGACTGTGTGTTT\nCTAGATCTCTCAGCCTGTTGCCTCCGCTCAACCCATTTCTCAAGATCCCTTTTTGTTGAC\nTCTAAAGAAACTAGTCTATCATTTACACTTAAGAAGCAAGACCCCAACCACCCTTTTAAA\nCACTTTTGTTTCATTAGGTCATACTTGCTTGCAAGGAGAATTAATGCATCAAAAATTAAT\nAGAAGTTTCCTCCTTGTGTTCAATATCCTCAAAGATTTTACTTTATTCAGGAATGATCTC\nCAGCATTGAACCTGACATTCTCCAATGGTTTGGTTTTCCCTCTTTTCATTCCCCTCCTCA\nATGTTTGCATACAGAAATCTCAATATTGGTGATGCTCTCTTGAACTGATAAATCAAGTGT\nTCGATATTGTCTTCTGCAGCTACCTTATCAGCGTACAAATTATTAAGTTCATTAAGTAAT\nTGGTTCTTATCAACCTTCAGAAACTGACCTTCTATCTCTCCTTTCCTCAATCTGTTCCTA\nAACACTTGATACTCCTCTTCGATCTGCAGCTTTACCTCATGGGCTGTTAACTTATTATTG\nATGCCTTGATGGCATGAGGCAATCACTTCCTCATAATGATTGGAGCGATTGTCCATCAGA\nACATTTAAACTCTCCACCCCTGATAATCTACCCGAAGTCATGGATAAAGATTCACAGAGT\nCTACTATACTCTGATTCTTCAAAAAGTGAATTACTCTCCTGTGCATACTTTAAAAGTGAA\nAAGAGCGTATCCCTCAACTTGTCATTGACCCAGTCAGGTATTTGTTCATTGTAGAATGAT\nGTCCTCCCGTCTATGAGTGGTATTAAATTGATATCGACACTCTTCAAGTCTTCTTTCAAT\nTGCTCTAATTTTTTGAAGTCCTCAATGTACTTCTGCTCAAAGTTAGCAGGAGATGACCTA\nACAAAACACTCCAGCAGTATTAGAACATTGCCCGTCAGTTTGTAACCGTCCGGCACCACA\nAAACATAGTGAAGGTGTCAAGATTCCATGGTCATGGAGAATTCTTTCCACAGATTTGTCC\nTCACTATTATGCTCGCAACCATTTGCGTTGCAAGAATCAACCTCAATACAGAGGGACAAG\nAGTTTCAACCCTTCCATTAGTAGCATCCTAGGCTCTGTCTGTACAAGAAATGCTAACTTC\nTGTCTAGATAATCTCTCATTGTCCACTAGATACTTTGATACTAAGTCTTTGACACAGGCT\nATGTCTTCCTCCATGTCTGGCCACGAGTATGTTGGTCAGAACCCTCAAAACATGTGATCT\nGCTAGAGCAACAGTTCACCACAGGCCAGGGTCCCGTGGGGGGCACAAGGGATACAAGAGG\nCAATTAAAGACAATTAAATTAGATAGCCTTAATGCCTAGGATCCTCGGTGCGAGCATCCT\nAGGCTC\n>comp0_c0_seq2 len=5491 path=[6883:0-41 1457:42-5490]\nATCATTCATTCTTTAAGGAGGCTATACCCATCAGTGTTTGAAAAACACTGATGGGTACAG\nCCTCCTTAAAGAATGAATGATGTGATTCAAACCAACCCTATCCTCTAATAGTTTTGACGC\nAGTTGGCTTTAAGGGGAAATAGTCACAGGGGTTATGCTTGAAAAAATCCAACACCTTAAC\nTGTCTTAGGTTCCCCTAAGACCCATGCACCCAGTTCTATTGCAGTTGATAATGATATGCA\nCATATAATCCCATAACAAGGGTCTGAAATAACTAATGACATCATCATTTCCACTTCCATT\nTCTTAGTTCTAACGGAACCTGCCAATATTGAATACCATTAGAATTTGTCAACAATTTGAT\nTCCCTTAACATCAGAAATCAGAGACTGAATGGACTTAATATACAGATTCTCTTTATTTGG\nTCCCCGAACACATTTGCTACCCAATGTTCTGCATAATCCCACAAAGCCAGATGCAATGGA\nACTTTGGAATGCAGATTTGTTAATAGCTTCAGACAGCAATTTTTGCGCACCTCGAGTAAA\nAGTGGAAGACAACTTATTTTGGATTGTTTTGACAATGGTAGGAATCTTCTCATCATCTAG\nGTTCACAGCACCTGAATATATTATCTTTTGTCTCAACACCATTCTTAAAGGATGATGTGC\nGGCTAAGTTTAACCAAGAGTACTCAAGGTCAGACTCAGATGGAGATTCAACACCTAACAG\nCTCACAAAGATTTCTTAGTGAAGAGAGGTGCTCACTAGACAAATAGTTTGTTGTAAACTC\nTTCATGGAGTTGCCCAGTCTTCAACCTATTGTACAGTTTTCTTAACATAGATCTAATCTT\nGCTGCAAGCGTTGGGAATCAATCCCTCTATTTGTCTCATGATTCTATAACTACGGTTGCC\nATCCACCCAATCTCTAACATCTGTCTCGCAATTCAATAAAAATGGGTCAATAGGGTATCT\nTGCATATTGCAAAAGACTTAAGGTTCTTTTCTGTATTAGATTGCATAAGTGAACAGGGAC\nACCATTTGCAACCGACTGATCAATGATTGTGTCAATTGTTTCTGCCAGTTGGTGTGGCTC\nTTTACACTTTATATTGTGAAGAGCTGCTGCAACGAACTTTGTCAACAATGGCACCTCATC\nTCCCCAAACAAAAAATCTAGATTTAAACTCAGCAACAAACCTGCCAATAACACTTTTAGG\nGCTCACAAACTTATTGAGTTGATCACTCATATAATAATGGAACTCTATTAGAGTCCTAAA\nTTCTTCTGGGTCCCTCTGCAAAAGCTCTGTGAGAGATTGATCAAAGAGAGAAATTTGATC\nATCACTAGAGGTATAAGCATCTATAGTACCACCACATATACAACTGATAGCATAATTAAT\nGAACCTCTCTGAAATAAGGGCATAAAAATCTGATGTGTTGTGTAATATTCCCTGACCCAT\nGTCAAGTATTGAACTAATGTGAGAAGGCACTACACCGACTTGGAAATTAGAGTAAAAGAA\nATCTTCTGTTATTGACTGTTTAGTTTTCTTCCTTAACCCTAGTTGAGCTTTAATGAAAGA\nCTTCATCATGGCTGTCACCACATTAAAAGGTATTTCCACCATTTTGTGCATATGCCACAT\nGAGTAGGGTTGAAAGATAGTCCCTCCCTTTTATGTCAGCTTGCAAGTCCCTTGAGAGGAA\nAATCAAATTCTGTAAGACAGTCAAGAACAAAAATGGACACATCATTGGGCCCCACTTACT\nATGATCCATGCTATAGGACACATGCGCTAATGAAACATTCAATTTCATGGAGAGGATAGC\nATTCTCAAACTCCTTCTCGTTGTTCAAGCAACTCCCTGACAACTGTAGGCTTATAGCTTC\nAAAGTAATCTTCTATAAGTCTAGTAAACATCTTTGTTCTAAGATCACCAATATATAGTTC\nTCTGTTGCCACCCACTTGTTCTTTATATGACAAAGAGAACTTAAGCCTTCCTGTATCAGG\nTCCCACTGAGTCATAAGATTGTGGCGACTCTTGGCTATAAAAACACAAATTCTTTAACAT\nTGCTGTGGTACAGTTTGTCAGTGACAGAGCCTTACTAAGTGCCTCTGAGTTGCTCTCCCT\nTTCACTAATTCTCACATCATCAGAGAGTTTACCCATGTCAAACTTGAAATTAAGGTTCCT\nTGACTTATAATGAGTGTACCTCCCCATAAGTGCATTTGCATTCATGATCAAGAGTATGGA\nCTTAAAACACTGAAAGTATTCATGGTTAAAGTATGTCCTTGTTGATACTGCCTTTGTCAA\nCTCTCCAATAGGACACTGTGACATATGTCCACAGTAAAAATACTTCTCCTTCAATCTACT\nATTCTCATAGACAGCATTACAGAATTCTTCATAAAATTTACCTGGTAAGATATCATAATC\nAAAATCCTCAACCATGTGATTAGATAATTCACCCTTAATCAACCTAATGTAAAACTTATT\nTGAGACAATCTCATCTAGATCATTTATTGACGGTTGGCCATCACCATTAGGGCCTGAGCC\nTGGCTTGGTGGGTTCCCTATACTGATCGACAATTTTTTCAACAGTCTCTTTTAGCTGATC\nAAAATAATCGCTTGCACCTCCATCGAGCAAAATTTCATCTAGGTCAGCTCCATCAACATC\nACTTTTGAGCTGCCCAGATCCTAGAACCAAATTGCTCATTGCCTGCTGAACTTTGTATTC\nATAGTCCTGCTTGTTGAGAAGGTACTTTCCTTTTCTTGAGAAGACTTCAGTGAGCTGCGA\nCACGGCCAGTGCTGTGAGCTTATTGAAGTCATAGTTTAATATTCTAGAACCATCTGTGTA\nCTTATTAACAACAACACTTTTGTTGCTGGCTAAATCCAAGGCAGTGGCACAGCCACTGGT\nGATGAGAGGATCTTTGATTTCCCTTTTTACTTCCCTCTCCTTAAATAGTGAACCATTGTT\nGAAAGAAGACGTAAGAAGGGACAAATACTTCTTTGAAACACCAGGCCTTTTATAGTCTGG\nTCCCTCGACACTTGTGCATCCATCTTTACTTAAAAACTTTTTTGCATTATAGACCATGTC\nGTCCAATTCTTCCTCGGTAGCTGTATCTGCAGGGTTAGTGCTCACATGACCAAATTTCAC\nCTTTGGTTCCAAAAACTTCTCAAAACATTTTATCTGATCTGTTAATCTATCTGGTGTTTC\nTTTCGTAATGAAGTGGCACATGTAAGAAATATTCAAAATGAACTTGAACCTATTGGTCAT\nCATGCTCTTCACATCTTCAGATAAAACTAAACTCATTAATGTCCTTATTAACCTATAGAG\nCAGGAACTCAACATCAGTGATTAATTCTTCCCTTATTTTGTCAACGAGGTCCTTATGATG\nATAATCTGACACATAAGCCATTACAAAATACCTAAGATTTTGGAGGAGCTTTTGAGAACG\nTTTACTGGGGTGAGCTAAAATTAAAACCAGGATCATCTTTGTCAAAAACTTTATGTTGTT\nCAACTGCCCTTCCAGCTCACTGCAATCTTCTATCCAAGAAATCATAGTGCTTATTGTTGT\nCTGTAAAACCTCAGCTGAAAATATTGCTGGAAAATATCTTTTAGGATCAGCGTAAAATGA\nGCACACCTCACCAACTTTGTTATCATTAATAGCATAGCACTTCGAGCATTCCCCTGTTTT\nTTGATAAATCAGTTGGAATTCAGAGTTTCCTAATGAAAACTCTTGACAATATGCTTCTTT\nGCATCTGACCACCTGATACCTTGCGGGTCCAAACTCATTCTGCCTCAATTTTACGGTAGA\nAGAAGTTTTCATAGAGTTCACCAAGGCGAGGCTCAATGAAGAAAGTCTCTCTAAGTCAGT\nGGTTCCCAGTAGTTCCACATCCCCCATCACATAAGGGAATGTTTCTTCCTCTGTTCTCTG\nATAACTGATTGTGGGAACAATTCCGGAGACATCAAAATCCATAATCAAATCATAACTATT\nAAGGCAAACCACCTCCATGTCAATTTTATAGTGGTCTACACTGATTCCAACATCCTCTAA\nAGCAGTGGTGGCCTTCAAAATGGTTTTCTGGAATATTGAATTGAGAATTTGGTTCTTACT\nCAAACACTGGGAGGACTGTGTGTTTCTAGATCTCTCAGCCTGTTGCCTCCGCTCAACCCA\nTTTCTCAAGATCCCTTTTTGTTGACTCTAAAGAAACTAGTCTATCATTTACACTTAAGAA\nGCAAGACCCCAACCACCCTTTTAAACACTTTTGTTTCATTAGGTCATACTTGCTTGCAAG\nGAGAATTAATGCATCAAAAATTAATAGAAGTTTCCTCCTTGTGTTCAATATCCTCAAAGA\nTTTTACTTTATTCAGGAATGATCTCCAGCATTGAACCTGACATTCTCCAATGGTTTGGTT\nTTCCCTCTTTTCATTCCCCTCCTCAATGTTTGCATACAGAAATCTCAATATTGGTGATGC\nTCTCTTGAACTGATAAATCAAGTGTTCGATATTGTCTTCTGCAGCTACCTTATCAGCGTA\nCAAATTATTAAGTTCATTAAGTAATTGGTTCTTATCAACCTTCAGAAACTGACCTTCTAT\nCTCTCCTTTCCTCAATCTGTTCCTAAACACTTGATACTCCTCTTCGATCTGCAGCTTTAC\nCTCATGGGCTGTTAACTTATTATTGATGCCTTGATGGCATGAGGCAATCACTTCCTCATA\nATGATTGGAGCGATTGTCCATCAGAACATTTAAACTCTCCACCCCTGATAATCTACCCGA\nAGTCATGGATAAAGATTCACAGAGTCTACTATACTCTGATTCTTCAAAAAGTGAATTACT\nCTCCTGTGCATACTTTAAAAGTGAAAAGAGCGTATCCCTCAACTTGTCATTGACCCAGTC\nAGGTATTTGTTCATTGTAGAATGATGTCCTCCCGTCTATGAGTGGTATTAAATTGATATC\nGACACTCTTCAAGTCTTCTTTCAATTGCTCTAATTTTTTGAAGTCCTCAATGTACTTCTG\nCTCAAAGTTAGCAGGAGATGACCTAACAAAACACTCCAGCAGTATTAGAACATTGCCCGT\nCAGTTTGTAACCGTCCGGCACCACAAAACATAGTGAAGGTGTCAAGATTCCATGGTCATG\nGAGAATTCTTTCCACAGATTTGTCCTCACTATTATGCTCGCAACCATTTGCGTTGCAAGA\nATCAACCTCAATACAGAGGGACAAGAGTTTCAACCCTTCCATTAGTAGCATCCTAGGCTC\nTGTCTGTACAAGAAATGCTAACTTCTGTCTAGATAATCTCTCATTGTCCACTAGATACTT\nTGATACTAAGTCTTTGACACAGGCTATGTCTTCCTCCATGTCTGGCCACGAGTATGTTGG\nTCAGAACCCTCAAAACATGTGATCTGCTAGAGCAACAGTTCACCACAGGCCAGGGTCCCG\nTGGGGGGCACAAGGGATACAAGAGGCAATTAAAGACAATTAAATTAGATAGCCTTAATGC\nCTAGGATCCTCGGTGCGAGCATCCTAGGCTC\n>comp2_c0_seq1 len=421 path=[0:0-420]\nGGGTGAGAGTGGTGGGGGTCGGTGGGAGACTCAGGGACTGTAGGGTGGGGGTCTGATGCT\nGTCTGCTGCTCTAGTTGGAGGTGCTGTTGGAGTGGCTGATGGTCTCAGCTTTGTGGGGAG\nAGGCATCTTGCAAATGGGGCACCTGTTGCTGACACTCAGAAGTAAGGTGAGGCAGTTGAG\nACACAGATAGTGGTTGTTGCACTCAACCAGGCCCTTGTTTTCGAACCAGCAGCTCTTGCA\nGAACTGTGGCCCTAGATGTGTGGCATCCGGGATCAGGCTGGCTCTTGGACTGTCTCTTGA\nTTCTGGGGCTTTGGATTGCTTGTTTCCCATTTGGAAGAGTTCAGCGTACAAAGCCTCAAA\nAAGAAGAACAACCAAATTGCCTAGGATCCCCGGTGCGCGGGTCCATTTTCCTCATTTGTA\nG\n" }, { "path": "tests/input/TestOrderAndOrient/contigs.lasv.one_small.fasta", "content": ">comp2_c0_seq1 len=421 path=[0:0-420]\nGGGTGAGAGTGGTGGGGGTCGGTGGGAGACTCAGGGACTGTAGGGTGGGGGTCTGATGCT\nGTCTGCTGCTCTAGTTGGAGGTGCTGTTGGAGTGGCTGATGGTCTCAGCTTTGTGGGGAG\nAGGCATCTTGCAAATGGGGCACCTGTTGCTGACACTCAGAAGTAAGGTGAGGCAGTTGAG\nACACAGATAGTGGTTGTTGCACTCAACCAGGCCCTTGTTTTCGAACCAGCAGCTCTTGCA\nGAACTGTGGCCCTAGATGTGTGGCATCCGGGATCAGGCTGGCTCTTGGACTGTCTCTTGA\nTTCTGGGGCTTTGGATTGCTTGTTTCCCATTTGGAAGAGTTCAGCGTACAAAGCCTCAAA\nAAGAAGAACAACCAAATTGCCTAGGATCCCCGGTGCGCGGGTCCATTTTCCTCATTTGTA\nG\n" }, { "path": "tests/input/TestOrderAndOrient/expected.ebov.ambig.fasta", "content": ">KJ660346.2_contigs_ordered_and_oriented\nGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGT\nTACTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGG\nTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGG\nCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGC\nAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAAC\nTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGT\nAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGAT\nTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCAC\nAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCA\nGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCT\nGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCG\nTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCAC\nGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCA\nGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACG\nACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTA\nGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAA\nGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGT\nTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTT\nGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCA\nGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTT\nCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCT\nGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTT\nTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGA\nGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAG\nCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAA\nCTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAA\nAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTG\nGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGAT\nGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAA\nGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGAT\nGATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGAC\nTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCG\nACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACA\nCAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCT\nCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTG\nACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTT\nCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCC\nACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAA\nGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACC\nCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTT\nGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGAT\nGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAA\nAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGG\nCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGC\nATGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAA\nACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAG\nTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTT\nAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAG\nCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACA\nTTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCAT\nCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAG\nCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCA\nAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGG\nAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGC\nATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGA\nCCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGT\nTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAA\nTGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGC\nTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGC\nTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTA\nTGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGT\nTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAA\nACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGG\nAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATT\nGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGC\nCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCA\nCATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACC\nATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACT\nTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGC\nTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTA\nGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTA\nAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAA\nCCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTC\nATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATT\nGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAAT\nTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACAC\nTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACC\nAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAA\nAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTA\nCAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGG\nCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCC\nCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGT\nCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACT\nGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGG\nAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGG\nGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGA\nCTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAAC\nTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCC\nTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGT\nAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAA\nGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAAC\nATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGT\nGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATA\nTACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCC\nTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCC\nTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAG\nATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGC\nTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCAT\nCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAAC\nCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAAT\nATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCT\nTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAG\nTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGT\nTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGANNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGT\nCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCA\nCAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATT\nCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATA\nAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCA\nATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGA\nCTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAA\nTGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGT\nGGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAAT\nATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTA\nATGCGGAGGTTTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTT\nCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCT\nGTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTAC\nACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTT\nAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACC\nTACAACGAACATTACTTTGAGCACCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAA\nTCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCC\nAGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAA\nTATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAG\nTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTC\nACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAA\nTGACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGC\nTGTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTT\nTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACA\nCTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGT\nCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGA\nACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAA\nCTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACC\nGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTA\nCACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTA\nTCTAACTAAGATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAA\nCTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTC\nTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACC\nCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAA\nTTGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAAT\nTGTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTC\nCATACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAA\nAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGAT\nATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTAT\nTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATC\nCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTG\nTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAA\nTTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGT\nTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCA\nAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTT\nCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAA\nCTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATT\nTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTAC\nCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCA\nAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAA\nTGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGG\nTTGAGGACCCATTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGA\nGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCG\nAACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGAT\nTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTG\nCACTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGG\nAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTG\nTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCAT\nTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATT\nATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTC\nTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTAT\nGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAA\nGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCG\nAGCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAAC\nAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCG\nAGTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATG\nTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAG\nCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAAC\nGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCG\nGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTG\nCATTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTA\nAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATT\nATTATAATCCACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTA\nGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTA\nTTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTG\nTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAG\nGCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAG\nTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTA\nTCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGG\nCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTA\nGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAA\nTAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGAT\nTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAA\nTATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGA\nAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTT\nATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGA\nACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAG\nACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACA\nAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGT\nGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGC\nCGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCT\nCTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATACATT\nGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGC\nTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGC\nACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATT\nCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACC\nTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAA\nTGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGA\nAGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGC\nCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCT\nAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGAC\nCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTC\nTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTT\nAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGT\nTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATAT\nCCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCA\nGTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATT\nGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCC\nATTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTT\nATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTC\nGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTA\nTCCCAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATAC\nAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAAT\nTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGT\nTATGTCACGATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGG\nTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCT\nTACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATA\nTCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACT\nGCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACA\nTCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTC\nATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTC\nTTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAAC\nCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAAT\nAAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCT\nAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAA\nTGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACA\nTCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAA\nTGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGA\nTACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGA\nGGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGC\nTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGC\nTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCT\nACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAG\nCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAG\nGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATT\nGTACGAAGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTGTTGAAAGCAGT\nGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGC\nCCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGA\nGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCA\nTCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATA\nCTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCT\nTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAG\nAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATT\nGACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTAC\nTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACA\nAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAG\nTGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCA\nAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATTGAAAGGCTGACAGG\nGCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTAT\nTTTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTC\nTCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTT\nACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAG\nCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTT\nTATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTA\nTCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAAC\nTTAATCTTAAAGATCAGTTTT\n" }, { "path": "tests/input/TestOrderAndOrient/expected.ebov.doublehit.fasta", "content": ">KJ660346.2_contigs_ordered_and_oriented\nCTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTC\nTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCC\nTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAA\nCATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACTT\nTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAA\nAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTC\nTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAA\nGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGT\nGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGG\nTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTA\nCCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGG\nGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGC\nAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGAC\nTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGT\nAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGG\nACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTT\nGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGC\nCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGG\nTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCG\nTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGC\nACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTC\nTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGT\nCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCT\nCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACT\nTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAA\nGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGC\nCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGA\nTGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGA\nTGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGATGA\nTGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTT\nGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGAC\nCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACA\nATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCC\nACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGAC\nCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCC\nGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCAC\nTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGA\nTGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCA\nGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGA\nTGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGG\nTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAA\nAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCC\nAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCAT\nGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAAC\nAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTT\nTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAA\nTGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCG\nATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATT\nTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCC\nTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCT\nGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAA\nACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAA\nGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCAT\nCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACC\nCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTG\nTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATG\nGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTG\nAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTG\nCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATG\nAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTA\nGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAAC\nCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAA\nCTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGG\nACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCC\nTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACA\nTCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCAT\nCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTG\nGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTT\nCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGA\nTAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAA\nGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACC\nCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCAT\nTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGC\nCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTG\nCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTC\nCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAG\nGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAG\nTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACA\nGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCA\nAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCC\nTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCC\nAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGC\nCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAA\nTTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGA\nACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACT\nTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTC\nTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTG\nTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAA\nTCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGT\nAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACAT\nCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGC\nTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATA\nCCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTA\nCTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTT\nATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGAT\nGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTC\nTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCT\nCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCA\nAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATAT\nTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTT\nTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTG\nATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTG\nGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGG\nGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAA\nACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAG\nACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCAT\nGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTT\nCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGC\nCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGG\nAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAA\nCTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAA\nGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGA\nGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGG\nAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTC\nTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTC\nTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTC\nCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAAC\nCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAG\nCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACA\nTCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGC\nCGGACCCTTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGC\nCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCA\nAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGC\nTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGC\nTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAAT\nCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCT\nAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCA\nAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCG\nTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGA\nCTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTAT\nTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGG\nATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGC\nTTTATTCTGTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAAC\nTCAACCTCAAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTAC\nTTGACAAATGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCC\nTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAA\nTGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCC\nTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAG\nTTGTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCA\nTTGGTAAAAAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCT\nTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCAC\nCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGG\nAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACA\nGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGT\nAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTA\nATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGAC\nTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCCAAAATTACC\nTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGAG\nGATTCCAAATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAA\nTCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAG\nGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAA\nGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTG\nAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACA\nTTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCT\nGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACA\nATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCA\nGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAA\nGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCAAT\nATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACT\nCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATG\nATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGG\nAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATAT\nTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAAT\nGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCA\nTCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCTGT\nATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACAC\nATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAG\nTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTA\nCAACGAACATTACTTTGAGCACCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATC\nGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAG\nACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATA\nTCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTT\nAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCAC\nAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATG\nACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTG\nTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTG\nATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACT\nAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCG\nTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAAC\nTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACT\nCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGC\nAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACA\nCAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATC\nTAACTAAGATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACT\nTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTT\nGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCT\nTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATT\nGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTG\nTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCA\nTACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAA\nACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATAT\nTAAATGGCTACACAACATACCCAATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG\nGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATCCG\nCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTT\nACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATT\nCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTC\nTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAA\nAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCA\nATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACT\nCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATTTA\nATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCA\nCTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAA\nGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATG\nTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTT\nGAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNCAATGGTGCTCAAAGTACACCGAGAGGAAGGGCCGATTC\nTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCA\nCTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAG\nATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTG\nCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTA\nCGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTAT\nTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTT\nAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTATGG\nGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGT\nATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAG\nCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAA\nTTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAG\nTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTA\nGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCT\nCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGT\nGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGT\nGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCA\nTTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAG\nAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTAT\nTATAATCCACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGT\nTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATT\nTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTG\nATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGC\nGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTT\nACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATC\nTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCT\nACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGT\nATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATA\nACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTT\nAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATA\nTCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAA\nTGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTAT\nCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAAC\nTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGAC\nTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAA\nCTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGTGG\nCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCG\nAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCT\nAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTG\nCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCT\nTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCA\nCATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTC\nAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACCT\nGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAAT\nGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAA\nGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCC\nATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTA\nATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACC\nCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCT\nTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTTA\nGGTGAGTTTTCAGGAGGTGGCCAATCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGCTACAGATATC\nCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAG\nTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATTG\nATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCA\nTTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTA\nTCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCG\nTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTAT\nCCCAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACA\nATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATT\nCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTT\nATGTCACGATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGT\nGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTT\nACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATAT\nCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTG\nCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACAT\nCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCA\nTTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCT\nTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACC\nACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATA\nAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCTA\nAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAAT\nGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACAT\nCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAAT\nGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCNNNNNNNNNN\nNNNNNNGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAG\nGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCT\nGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGCT\nACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTA\nCCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGC\nCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGG\nCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTG\nTACGAAGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTG\nGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCC\nCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAG\nTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCAT\nCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATAC\nTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTT\nGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGA\nGGTCCACTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTG\nACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACT\nGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACAA\nGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGT\nGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAA\nACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGG\nCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATT\nTTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCT\nCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTA\nCATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAGC\nATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTT\nATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTAT\nCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACT\nGATCTTTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGG\nTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGT\nCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAA\nTCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAAT\nTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCC\nTGGAAAAATGGTCACACACAAAAAAGAAGAAATAGATTTATTTTTAAATTTTTGTGTG\n" }, { "path": "tests/input/TestOrderAndOrient/expected.ebov.small.fasta", "content": ">ref_4kb_contigs_ordered_and_oriented\nTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTG\nCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCT\nTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAA\nAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCA\nCGACTCAGAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAA\nTGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTAT\nGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCC\nAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGG\nCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTC\nTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGG\nTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAG\nCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCAT\nCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTC\nAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATT\nTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTG\nGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCA\nATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTC\nAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTG\nTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAG\nTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTA\nAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAG\nCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATC\nAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGC\nAGCTTTAAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTAT\nTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTG\nTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGG\nTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATT\nCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATG\nGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCC\nACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGG\nGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAA\nAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCC\nATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGG\nATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTC\nCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTC\nAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGC\nGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGA\nAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCAC\nTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGC\nCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAA\nTCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCA\nCCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGG\nTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAG\nTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATAC\nTAAAGGTGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACT\nCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAA\nACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTC\nTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGG\nATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAG\nACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAA\nTCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATT\nGGATAACCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTA\nCAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAA\nTTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTAC\nAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGA\nGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTA\nAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAAT\nGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAG\nCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAA\nCGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATC\nGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTC\nTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCA\nATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCG\nGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAAC\nTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTG\nGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAA\nCAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGA\nAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGC\nGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTC\nAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCA\nTCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCC\nGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAA\n" }, { "path": "tests/input/TestOrderAndOrient/expected.hhv3.fasta", "content": ">gi|59989|emb|X04370.1|_contigs_ordered_and_oriented\nGAACGGCACCACCCAACAGTCTTACGATTGCCTAGACTGCGCTTATGATGGAATCCACAG\nACTTCAGCTGGCTTTTCTAAGAATTCGCAAATGCTGTGTACCGGCTTTTTTAATTCTTTT\nTGGTATTCTCACCCTTACTGCTGTCGTGGTCGCCATTGTTGCCGTTTTTCCCGAGGAACC\nTCCCAACTCAACTACATGAAACTACTGTCCGGAAGGGGAAGGTATTTATTCTCGCTTGCA\nGCTTGTCGCGCGTGTATGCACAACAAAAGCTATATATGTCACCAAAGCCAACGTCGCCAT\nCTGGAGTACTACACCCAGTACGTTGCATAACCTGTCCATTTGCATTTTCAGTTGCGCGGA\nCGCCTTTCTCCGGGATCGTGGCCTTGGGACATCAACCAGTGGAATAAGAACCGCCGGTGG\nTCTTGCCCGAACGACGAGTGGCGACGCGTTGTTCTGCATAAGCTCTGTATGCTGATACAT\nAAACACAGAGTCTGTATCGCTATCAGATTCCCGAACACCTTCCGGTACCCCATACTCCGA\nTACCCTGGACATTGCGGATCCCAAAAATATAATATTAACAGGATTTGCTTATACTTTGCT\nACAGCTTATATAAATTTATGTGCGATACATCTTAAGTGCATCCGTACGTTATTTATACAT\nTGCCGGTCACGTGAAAAGACTGTGTTACCCAATAAAGGTTCTACAAAAAATGCTTTATTG\nGGTGTTTGTTTAATAGCTATTATCGTAACCCACCCCCGTAAAATCATAAANNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTCTGGTGC\nGTCCCAGTTTAAACGCCACCGCCGAGGAAAATCCCGCGTCAGAAACGCGATGTTTATTAC\nGAGTGCTTGCGGGGAGAACTGTAGACCTGCCAGGCGGAGGAACGTTACACATTACCTGTA\nCCAAAACCTATGTAATTATTGGCAAATATAGCAAACCCGGCGAACGTCTTAGCCTTGCCC\nGTCTAATAGGGCGTGCAATGACGCCTGGAGGTGCAAGGACATTTATTATTTTGGCGATGA\nAGGAAAAGCGATCCACAACGCTTGGGTATGAATGTGGTACGGGCTTGCATTTACTGGCTC\nCATCTATGGGTACATTTCTCCGCACACACGGTTTAAGTAACAGAGATCTCTGTTTATGGC\nGGGGTAATATTTATGATATGCATATGCAACGTCTTATGTNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNTATTTTTATTTAAATGTGTAGTTCATAGTCCGCCGACA\nGCCGCTCGGGCTTTTCCCCCACATACAACATGATCGTATGCCTCGGATGCACCGGTCCAA\nCACTCCGCCGAGAAGGGGGATTTACAATGACAGTGATACCCAATAGCCGCCAGATGTACA\nCCCAGCTGTCCGGACTCCAGCATCATCTGCTGAGTTGCGGCGCTGAAGGGTGCATCGCAT\nAGGGTGTTATAATTAGCCATTTCCGGTAACAGTCGTTGGGAATTTAGGAGGCTGCAAAAC\nGGCTGTAGGTCAACATACATTGGGGATTCAGATGGTTTATCTCGACGTCCAAGTCCAATC\nAAAAAAGCGTGTAAATCATCAGCCCGGCCGCATGTTGCTCGAAGAGCACATAACCTCTTA\nACACCGTACAGAGGGGATGGCGTCGGTGCATGTGAGTTGGCAGGGCATGTCCACGTTGTT\nTCCAACGCCAGTGGCGGTATAACTTGTGTAAACGACGCCAACGGGTCAGGTTTAAGATTC\nACTCGGATGGGTTGACTGCTTTCGGAAGCTCCCGTTGTATCCATTAATTAAACGTTCGGT\nACACGTCTGGTGTGTGTTTTACCCGAATCAGAGACGGAATTGCAAAGATATTGGTTTGAA\nAGCAATGTAATCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNGTCTTTTATTAATATAGAATCACATAAACAATTGATAAAATCAAGGGGTGG\nTGTATAATGATTAAAAATATAAATTGATATGTTTTACAAGCATGAAATAGGTATTTACTA\nTTCTAACAGGTAAATATGCTTAATGATTAAAAATACAAATTAGTATGTTTTGACAAGCAT\nGAAAAAGGTATTTTTTATTTTAGCAGTTAAAGGTACTACACTTAAAATATTTACCGTATG\nGACGGGCGTCAGAAAGATGCCCGGCCCAAGTTGAGAGGGTACATTCAACACGACCACACT\nCGCGTTGGTGGGTGATTAGGGCCTCTAAAACACCGGCCAGACATGACCCGGGTGTATATT\nCTTGTAACACTTGAACGTTACAACTGATATCATCATATTCCACAAATTTAGAGCCACGGA\nCAACTATATTAGCAATGCGGGCAATCATAACAAACATATAAGTAGTAATACACGTGATAT\nCACTAAAACGTTGCTGGCGCAACAGTTCGGGGAGAGTACGAGACCCCAAATCGTTGTCCC\nTGTTTAGAAGAAGACATCTTACAAAAGGCCCCAGCTTTAACTTTAAATTCTCCAAAAGTG\nACTTCGAGGTTGCAACAATGGGATTATTTGTGTAGATGGGCAAGTTTTTTGCCGCTAACA\nTTTTAATCCACGTTAACAGTTCATCCGCAGACTCCAACGCTTCAATCAAAGATTCTCCAC\nGTATGACTCTCTCACGCAACGCGCGGGCAATACGTGAGTCCATTTTATATGACTCAAAGG\nTACGATAAAGTTCATGTCCGTACAACATCAACTCCGGCCAAGATGTGTTTTGTTTTATCC\nCCGGAAAACATCCACCGGAAGCCCATGAATCACCCTCTTGTATTGTGGCATATCGGACTA\nCCAGTTTTTCAATTGTTTCATCTAAATGGCGTACCGAGTCAATGGTCACGCTGGCTCCCG\nCGGTGGAGACGACTTCAATAGCACGGCCCGTAATTCGATCGACCGGGATATCATACTCTT\nTTCGAATACGCTCTCGGCGGGCGTCTCTCTTGGAAAATCGCAACCTGTACGATTCGTCAT\nGTGTCTGATCATTTCTTTCTCCCGTGGTCATTGCAGGAGGCGTTGTAGGACGCCGTCTTC\nGATTTGACAGGGATCGATCACGGTGTTTTCTTGAACTTTGGGTGTTATAAGATCTGGATG\nATCGTCGATGTCCCCGTTCGATGCGTGCATATCCAGTCTCCACGTCTCTTCCTCCATGAT\nGGTTTGAATCGGGTAATACAACAACCAAAGTTTTCGGGCGATTGTGGTGGTAGCTTTCAC\nGCCTTCCGTGCCTTCGTTTGGAATACCGTGGATTATATGCTGTATCTGCAGTACGCTCCA\nCATACACAGTTCTAGACGTTGTGGAGTCCTCGCCTGGAGTGGAGCCAATAGCTTCATCAT\nTTGCCCAATCGGTGACTTCCAATGCAAAGTCATCCGAAGGTTCGTCTGGTAGCAAATTCA\nTAAAGTCTTCACAAATAGTAGACACGTCTGGGTCGGTTGGAATTGAAGCAGAGGCCATGG\nCTGCAAAATATCTGACAATTGCGTGTTTGCAGTTGCCTGTATCTTCCGCCAATGTTGTAG\nAATTTATAGGCTCACCCAACCCCGCAATGGGCGTGTTTAGTCACATGATTAATGTTTCTG\nGGAGTTTTCACTTTCCCCAAACAAGCTTACCTGCACCCTTTGTTCGTAATGCATAAAAAT\nAACCACTGCTATAGCAAATATGACGATATAAAAACATTTTATAGCAAGGCCGGACATTAC\nTGTAGCACAACATGTTGTGCATATACCACGTATTCCCCCCGTATTGATATGATTTAAATG\nATTATCCTTGGTTGGTTTTGGTCTAACATAAGATATAAGCTCTACTATAGCGAGCGTGCA\nTACAACAACCCAGGCCAGAATCCGAATGTATGTGGGGTATAATAACGCGCATGGTGTATA\nTGCAACGCCAAGCGTTAAAAGCACAATACATCCAGATGATATATGAGCGATAACCTCCAA\nAAGCATCAATAACGTAACACCTTTATGCATATATAAAAAACTTATAGGGTCAGCATTAAA\nTACTTTACTCATACCATCCCGTCGCATGGAAACATCACATAACAACCTTGCCAACTTTGT\nATATGGGTAACCAAGAAGAATGTTCGAAATAACCCGTGTTACGTAATTCAGTGAATATGA\nTGTGGGGGATATTAACTCACAGGATGATCGGAATGGCCCAAACATACGACGTATTCGTCG\nAAATTGTAAATACATACCATATACAAACCATGCAAAAAAAATCATTTTTAGCTGCACGCA\nCCAAAAATAAGCGTGACAATTACGTGTTCCCAGAACAATTCGAATTTTGTCATGCAAAGG\nTGTAGAAATAGCGGTTTTTACCATAGTATCTCCTGATAATAGATTTTCCCGGCAGCTGTA\nATCGTATCCAGATAGGCCATCCAAAAACGTTGAGTGGTTTACAAACGTTACATATATAAG\nAGAGTTGTTATAAGACCCCCATACAACCGGTCCACCATTAATCACCGTGGTTGCATACAC\nACACTCATGTTCAAACTTTACACGAGCGGTATACCATAGGGTAAAAACAGCATGTCCGCT\nAAGTAGACACATAATTATAAAATGTTCTGTCTTGATTCCTAAAGCCTGCATGACCCGTGG\nAAGATGGCAATTCAAGCACGATGTAGTATCACACGGTTGGTGTTAACTCGAAGTTAAATT\nTGGATAATTAGGTACTTCTAGAGTAAAGATTGTATGCATGCGATTGCTATCGCACTTTGT\nAGCAAAACATTGTTGTGCAAGCGAAATACACAAACGGTTGTGATGATCCACTCGCAGAGA\nCACAAATGTCCGGGGAGCCGTTCTTCCTCCGCGATGGGGATATCGAAGACAAGTGAACCC\nTTTTGTTCCGCATATGAGCTGAAATAACACCCAGTCCCTTTTGATGGCGATACACTTTGA\nTGATGTTAAGGTATATTCGCGATCACGCCCGGGGAAATGAACAGCAATATGCTCCACAAT\nAGATTCTAATATTGTGCTGTCGACAAAGGCCTCCAGTGTAAATGCGTCCAGACAAGTTAC\nCCCGCGCTCTTTTAGAGCCTTTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCGTAAATACGGACCAATATA\nTTCAACAAATTCCCGTTCCAGCAACACCGCTTGTTGTAATATTTGTGCAAACCCCTTTAA\nAGTGGAAGACCCCACTAACGCATAGGGATTTGGGATTGGTACGCATACCCTGAAACCTAT\nTTTCTCTTTACAGTTACAGGGTAGAGTTTCATGCAAGTTTTCATTGTTTGATACATCGGC\nGTGTGTATGGACTTCAGACGTTGTCTGTGTATCAAAAAACCATACATCCTCTGTATAATT\nCTCTTCTACACACGTGTATAATTCGCCATTTTCTATGTAAAAATCGATGTCAGAATGGCT\nGGTTATATCCAATAAATTATCATCATCCAACACCTCAACGGTAGGTTCAGGACATGCAGT\nTTTATAAAAATAACATGGGTCTTTGTTAGGGTTTACCACGGCCTTTGGAAAAAGTAATTG\nCATGGCCGTTAAAATACCATGACGAAATGCTCGCATGCCGGCATGTAAAATACCCAATGG\nGATGGGTTTTCTTATATGAAAGTCTACATCAAGTATGAGGTTTGTGATTATAAGATTTGT\nATTAAATAGCTCATTCCTGTTTATATAAAGCTGATCTTTGGGTATGTTAGATGAAATTTT\nAGAAACGTTTTTAACAGACGTAGATAATAGTAAAGTCAACTGCATATCTCGTAGTGAAGC\nGGCAACAAAATTACATGGATTAATTTGTTTAAGGTCCTCCGCAATTAATCGAGCCTCGTG\nCGGTAAAGTGTAACGGTTTGTTATTGATGACCACGTATCATTAGCAATAACAGCAAATGC\nTTGGGCACCTTGAGGCAAGGCTACCCGATATACAGGCATTGGTCCAGTTACCTCAGAATG\nGCCGATGAGGGCTTCTAATGGAGTTTTATAACTCAGGATGGATACATCATGTGTGGCTAT\nCCCAGTGGCAGCAGAGAAAAACANNNNNNNNNNNNNNNNNNNNNNNNNNNNATCAAAACC\nAGTACGACCACTTTGGTTAGGTGTATCGTTTGCAAAGTTGGCTGCTCGTAACGCCTCCGC\nGGAAACAACCGAATCCTCAAAATTAGACAATTCGTCAAAACCGGGTGGATTTGAGGGAAT\nAGTGGAGGACCATCCATATGGACTAAATTGTTTTTCAATGTTTTCCACACGACGAGTTAG\nCGTTGTAGCTAGGTCACATACGCCTATAAACTTGCTAGGTTTTGCGGCATACGTAAGACT\nTAAAGTATATGTTTTAGTAATTGTATATTTATGTCCAATCTCAGGTCCAAGTTCAGTGAC\nATCACAAATTACGTTCTTTTTTATATAGTCACGCATGTTGAGACGAGAACGTACATGATT\nAAAAAAATTAGCAGTAGCTCTTTTTCCCAGGTTGGATGATTTTAAGAGGACCGGTTTATT\nCACAAAATCTGAGTATGTAACCGCTTGTAGGTGGTCTGCGATCTGTTTCCGATTGAAACA\nTTCAAAATGTGCCAGATAAATATAATCAACAAATTCACGGTCTGGAACTTTAAGGCCTTT\nTCTATCGTTGGTAATATACTCCGATACTGCGTGTATTTCCGTTGTGTCTGTATGTATTCG\nCTGTAAAATGTACGATAGAGCATTTTTGGCTGTCAAACCTCGTGTATATGTTGAGGAACA\nACAAAACATGGAAAGTTTATCAAAAGACAACAAGTCCGAAATATTGTACCCACTACAATT\nAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNTTGTAACTTGTGTCCGTTTGTAACAAGTAATAGCGTGTAGCCAA\nCACTAGCGTTTTTTCAGAGGGTCCAAATCGAACAATATACCAAAACGGCGAGCATCCATA\nCCCCCAGTAGAGTCGTCGATATGCAGCCAATACTTGACGTTCGTAATGGGCATATAATGA\nTGTTAGCTCCTGACGACCAACGGATTTTTTAACTAACTTGCAGAGTGTTGCCTCTGTGAT\nGCATAGGCCGTTGTCCGATAATCCCTTTCGGTTTAAATGGTGTGTTGTTACCATCAGAGT\nTTGTATAACTTCCGAGTGAATGTCAAACGTCTCCGATATACATAGGGTATCAGATATTAT\nATGCGGATTTAGGGGTGCTCCATACCATAACGCCTTATATAAAGCTTTAAAATCAGTTTG\nGGTTTTAAAACAACAAAAAAATATAGGCCAGACCCGGGATCGTACATCTCCAGTTGAAAA\nTCCACCAATTAAATAAAAAATAACGTTGACGTCCCTACTACAAAATAAATGCATTATTTG\nGTTTTCTTCATCGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGAGTCCAAGTATAACTCAC\nCACATACAGAGGTTCTGTGCTTATCTGCCCGGTAAGCAACAACAGCGAGTGGGAGATTGC\nACATCCCTTTGTGGCAAATAATAACCGAATCGTCGGTTTGGAGGATTTATCCATAGTTCA\nATACGTTGGAAAGCCAGTCAATCATGCAGACGGTGTGTGCCAGCTTATGTGGATATGCTC\nGAATACCAACTGAAGAGCCATCTTATGAAGAGGTGCGTGTAAACACGCACCCCCAAGGAG\nCCGCCCTGCTCCGCCTCCAAGAGGCTTTAACCGCTGTGAATGGATTATTGCCTGCACCTC\nTAACGTTAGAAGACGTAGTCGCTTCTGCAGATAATACCCGTCGTTTGGTCCGCGCCCAGG\nCTTTGGCGCGAACTTACGCTGCATGTTCTCGTAACATTGAATGTTTAAAACAGCACCATT\nTTACTGAAGATAACCCCGGTCTTAACGCCGTGGTCCGTTCACACATGGAAAACTCAAAAC\nGGCTTGCTGATATGTGTTTAGCTGCAATTACCCATTTGTATTTATCGGTTGGCGCGGTGG\nATGTTACTACGGATGATATTGTCGATCAAACCCTGAGAATGACCGCTGAAAGTGAAGTGG\nTCATGTCTGATGTTGTTCTTTTGGAAAAAACTCTTGGGGTCGTTGCTAAACCTCAGGCAT\nCGTTTGATGTTTCCCACAACCATGAATTATCTATAGCTAAAGGGGAAAATGTGGGTTTAA\nAAACATCACCTATTAAATCGGAGGCGACACAATTATCTGAAATTAAACCCCCACTTATAG\nAAGTATCGGATAATAACACATCTAACCTAACAANNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGCACAACCCCCGCGATCAAGA\nAATCCCATGTTATGCTTGTATAAATATTGAAATAAAAACTAAAAACGTTTCTGGTGTATG\nTTTTTATTTTGTATATAAAATTAAAACATTGCTGGCTGGCGTGGTTATTACATTTAATGT\nTTTAGTAGAAAATCGACATCGTTTGTTTCTTTATCAGTTGAACCAAATCCACGCGTTCCC\nCGTTCGCTGGGTGTGGCTATTAGATCTAACGTTTTAGTAAAATACCATTGTACACCCGGT\nATGCCACATTTACCGCGGATAGCATAAGGAAATGCAATATTACTTAAAACGTTGTGTTTT\nAAGTGTATTTGGGTGTTGTGATCTATTAACAGGACCTGTGCAAGACGATCTCCCGTTTTT\nATACGTATGTCATCACCCGTGAGATTATATACGTAGAATTTACAGTGTTCTCCTGCAGGC\nCATGCCGTTGGACACACGATAATGCCTGATCGGCTTTTCGATGATCTTCCAAAAATATAA\nGCGTTTATACTCGGATGTTGTAAGTCCCAGTCTCTTATAATCGGTAAGACAATTTTTATA\nAATTCATTCCTTTTTAAATATAGGTTATATGGTACACAAATATCATATCCCGCGTCTTCT\nTGGCGTTTTGGATTGATGATATGTTTGTAGGTTAAGGGAACATCGATATGGTATTCTGCA\nGAATCCCTATGTAAAGGTTGCCCCTGCTGTACCGTGGAAATATCAGCAAATTCAGGTATA\nACGGGTTTTTCATAATTTGACGGCGAGTTTGATAAGGGTTGAACTTGTATCGATTTAAAA\nATTGGATCCAGATGTTTAAGAACGTTTTTTGGGAGAAGGCGACTTTGTCTTAATTTTACC\nGGGAACAAGTAGATTGTTAAATGTCCGGGTAAAATAACGGTTACTCCTGGCCGGTAATAC\nAAAAGGGCTGAAATTACTCCTCTGTAACCCGCATCAATAACTCCGTTGGCGACAAAAAAA\nTTGTCTTCATCAGCAAGGGCAGTATCTTTGCATTGAATTAACAACAGTGCGTATTCATTG\nGGAGGCGCCGACTTAACCAACAGCTCCAACTGCTGCATATAAAAACCGCCCCGTGTTACA\nGATTTTTCAGATGGCAGTTCGAGTTTCTTGTGGTTCCGGAGTAACAACGGTTGATGTCGA\nCTTACTTTATCGTCTAACACGCATTGCAGCGTATCTGCACATTCAGGTTGAACTTCTATT\nAAAATTGTATCTTTTAAACACCGATTCGGAATAGTTTGGCTACAAAACATATCACCTGTA\nTTTACTGCCGTTTCCAAGATGGGATCAATTACCGCTTCGTTCATATTAATAACGATGCAA\nATTTTATTTTTTTGTGAAGACAGCAGTGGGGAGCCAAACTTTGCAGAACGGAATTTTTGG\nCATGCCAGCTGTTCGGCTCGTGGAGTTTATATCGACGGATCAATGATCACCACCCTTTTC\nTTCTACGCATCCCTGTTGGGGGTGTGTGTAGCCCTTATTTCGTTAGCTTATCATGCGTGT\nTTCCGGTTATTTACTCGTTCTGTATTACGCAGCACGTGGTAAACCCGTTTGCCTATAAAA\nGGGGCAGGCGTGTATAAGAGGGTCCCTGTTTAATACGCGGTCTGCCGTGTTTGGATATTT\nCACGACCCTATCGTTTATTTACGTAATGGCATCTTCCGACGGTGACAGACTTTGTCGCTC\nTAATGCAGTGCGTCGTAAAACAACGCCTAGTTATTCCGGACAATATCGAACCGCGCGGCG\nAAGTGTGGTCGTAGGACCCCCCGATGATTCAGACGACTCGTTGGGTTACATTACCACAGT\nTGGGGCCGATTCTCCTTCTCCAGTGTACGCGGATCTTTATTTTGAACATAAAAATACGAC\nCCCTCGCGTACATCAACCAAACGACTCCAGCGGATCGGAAGATGACTTTGAAGACATCGA\nTGAAGTAGTGGCCGCCTTTCGGGAGGCCCGTTTGAGACATGAACTGGTTGAAGATGCTGT\nATATGAAAACCCGCTAAGTGTAGAAAAACCATCTAGATCTTTTACTAAAAATGCGGCGGT\nTAAACCTAAATTAGAGGATTCACCGAAGCGAGCTCCCCCGGGAGCGGGCGCAATTGCCAG\nCGGGAGACCAATTTCCTTCAGCACTGCACCAAAAACCGCAACAAGCTCGTGGTGCGGTCC\nTACGCCATCATATAACAAACGCGTCTTTTGTGAAGCGGTCCGGCGCGTAGCCGCCATGCA\nGGCACAAAAGGCTGCCGAAGCGGCTTGGAATAGTAATCCCCCAAGGAATAACGCCGAATT\nAGACCGTTTGTTAACCGGAGCCGTTATTCGTATTACGGTGCATGAGGGTTTAAATTTAAT\nACAAGCCGCTAATGAAGCAGAACTAGGTGAAGGAGCATCGGTATCCAAACGTGGACATAA\nTCGAAAAACTGGAGATTTACAGGGGGGCATGGGTAATGAACCTATGTACGCACAAGTTCG\nTAAGCCAAAAAGTCGAACGGATACACAAACGACTGGGCGTATAACTAATCGAAGTAGGGC\nCCGTTCGGCATCAAGAACTGATGCGCGAAAATAGGGATATAATTACGCAGTAACGGTTTA\nCCCGGTATTATGTATAATAAATAAACGTATAAAAGACAGTCGTGGTTTGTGTTTATTATA\nAATGTGTATTATATGTCACATATTATAAACTGTTTAAATAGTACCACGTGGTATTATGAA\nCAGTTTATAATCAGTTGCTACCAAACAAACCCCATTAGACGGCGGGTTTTGATAAAGGGA\nATCGCTTATTTAAACTAAAGATTTTACTCTATAAGTATGGAGTGTAATTTAGGAACCGAA\nCATCATAGTACAGATACGTGGAATCGTAGTAAAACGGAACAAGCGGTTGTGGACGCATTT\nGATGAATCGTTGTTTGGTGATGTAGCATCGGATATTGGATCCGAAACGTCGTTATATTCA\nCATGCAGTTAAAACTGCTCCGTCTCCGCCTTGGGTAGCTAGCCCTAAAATTTTATATCAA\nCAGTTAATACGGGATCTTGATTTTTCAGAAGGGCCGCGTTTACTATCATGTCTTGAAACC\nTGGAACGAGGATTTATTCTCATGTTTTCCTATTAATGAGGACCTATATTCCGATATGATG\nGTTTTATCCCCGGATCCAGATGACGTTATCTCAACCGTTTCAACCAAAGACCATGTTGAA\nATGTTTAATTTAACAACCCGGGGTTCCGTTCGATTGCCTAGTCCACCAAAGCAACCGACG\nGGGCTTCCAGCTTACGTTCAGGAGGTCCAGGATTCGTTTACCGTAGAACTACGCGCCCGG\nGAAGAAGCATACACAAAACTACTAGTTACTTATTGTAAATCGATTATACGTTATCTCCAA\nGGAACGGCGAAAAGGACGACAATAGGTCTTAATATACAAAACCCTGACCAGAAAGCTTAC\nACGCAACTCAGGCAAAGTATTCTACTTAGATATTATCGTGAGGTGGCAAGTTTGGCGCGT\nCTTTTGTACCTACATTTATATTTAACCGTAACGCGTGAATTTTCCTGGCGTTTGTACGCC\nAGTCAATCTGCACACCCGGACGTGTTTGCGGCTTTAAAATTCACCTGGACCGAACGTCGA\nCAGTTCACGTGTGCGTTTCATCCTGTATTATGCAACCACGGCATTGTGTTATTAGAAGGG\nAAACCACTAACAGCGTCTGCCTTGAGGGAAATAAATTACCGCCGCCGAGAACTGGGACTG\nCCTCTAGTTAGATGTGGTCTTGTTGAAGAAAACAAATCTCCGTTGGTTCAACAACCCTCA\nTTTTCGGTTCATTTACCACGGTCGGTGGGTTTTCTTACCCACCACATTAAGCGTAAGTTA\nGACGCATATGCGGTCAAACATCCTCAAGAACCGAGACATGTACGAGCGGATCATCCTTAC\nGCAAAAGTTGTTGAAAATAGAAACTACGGTAGTAGCATCGAAGCTATGATTTTAGCACCT\nCCGTCCCCATCCGAGATCCTGCCGGGGGACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTGTCATGTGCTCTAAAGTCCCATATAT\nAAAAGAAGCCCCAACGAGTGTATGCGTATTGCGTACCGCGACCCTGGGATGTTTTACAGG\nCGCGTTTGTTTGTCTCGGTTATAAGTATGCAGTCGGGTCATTATAACCGGAGGCAATCCC\nGCCGACAGCGGATATCGTCTAATACCACAGACTCCCCCCGTCACACACACGGAACACGTT\nATCGGTCAACCAATTGGTATACACACCCACCCCAGATATTGTCCAATTCAGAAACATTAG\nTTGCGGTTCAAGAACTACTGAACTCCGAGATGGATCAGGACAGCAGTTCTGACGCATCGG\nATGATTTTCCGGGATACGCCTTACATCATTCTACATATAATGGATCCGAACAAAATACAT\nCAACTTCCAGACATGAAAATCGCATATTTAAATTAACGGAGAGGGAAGNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNTTATTTTACGTTAGACCCGGAAATAAGTTACAGTACCGATCTTCGCATTGCAAAGG\nTTATGGAGCCTGCGGTATCAAAGGAACTTAATGTATCAAAACGTTGCGTTGAACCTGTTA\nCCCTAACAGGCTCTATGTTAGCGCATAATGGGTTTGATGAGTCCTGGTTTGCTATGCGCG\nAATGTACCCGTCGCGAATATATTACGGTCCAAGGATTATACGACCCAATTCATTTACGGT\nATCAGTTTGATACTTCCCGGATGACACCCCCACAGATTTTGAGAACTATACCAGCCCTTC\nCTAACATGACACTTGGTGAACTTTTATTGATTTTTCCTATTGAATTTATGGCCCAGCCAA\nTTTCTATAGAACGTATTTTAGTTGAAGATGTATTTTTAGATAGGCGGGCTTCCAGTAAAA\nCACATAAATACGGCCCGCGTTGGAATTCCGTCTACGCACTTCCATATAATGCGGGTAAAA\nTGTATGTACAACACATTCCTGGGTTTTATGACGTGTCCTTACGTGCTGTGGGCCAAGGAA\nCGGCCATTTGGCATCACATGATATTATCCACAGCAGCATGCGCTATTTCTAATCGCATTT\nCACATGGAGATGGATTAGGATTTTTGTTAGACGCGGCAATTCGTATTAGCGCAAACTGTA\nTTTTTTTGGGACGTAACGATAATTTTGGCGTGGGGGATCCATGTTGGTTAGAAGACCATC\nTTGCCGGATTACCACGAGAAGCCGTACCCGACGTACTCCAAGTGACACAGTTGGTTTTGC\nCAAATCGGGGTCCAACGGTTGCCATTATGCGTGGTTTTTTTGGGGCGTTGGCATATTGGC\nCCGAACTAAGAATTGCTATAAGTGAACCATCTACATCTTTGGTGCGATATGCTACCGGTC\nACATGGAACTTGCCGAATGGTTTTTATTTTCACGTACACATAGTTTAAAGCCACAATTTA\nCCCCAACGGAACGGGAAATGTTAGCGTCATTTTTTACGTTGTATGTTACTCTTGGTGGAG\nGAATGTTGAACTGGATCTGTAGAGCAACTGCAATGTATTTAGCTGCTCCTTACCATTCCC\nGTTCGGCTTACATCGCGGTCTGTGAATCTCTGCCCTATTACTATATCCCGGTTAATAGTG\nACCTGTTATGTGATTTAGAGGTATTACTGTTAGGCGAGGTCGACCTCCCAACTGTTTGTG\nAATCCTACGCAACTATTGCACACGAATTAACCGGATATGAGGCTGTTCGCACAGCAGCCA\nCAAATTTTATGATAGAGTTTGCCGATTGTTATAAGGAAAGTGAGACCGATTTAATGGTAA\nGCGCGTACCTGGGGGCCGTTTTATTGTTACAACGGGTGTTGGGTCATGCAAATCTTCTTT\nTGTTGCTTCTCTCCGGTGCTGCGTTGTACGGAGGATGTTCAATTTACATCCCCCGAGGTA\nTTTTAGATGCATATAATACTTTAATGTTGGCAGCAAGTCCTCTTTACGCTCACCAAACTT\nTAACATCCTTTTGGAAAGACCGCGATGATGCAATGCAAACTTTGGGGATTCGACCGACAA\nCGGACGTTTTACCCAAAGAGCAAGACAGGATAGTTCAGGCATCACCTATAGAGATGAACT\nTCCGTTTTGTGGGATTGGAGACCATCTATCCCCGAGAACAGCCCATTCCCTCCGTGGACC\nTAGCCGAAAATCTTATGCAATACAGGAATGAAATTCTGGGTTTGGATTGGAAAAGCGTAG\nCCATGCATTTACTACGAAAATATTAAGGGTTGTGATTTTTTTCATTAGGATGAAAAGAAC\nGTTTCCTAGCCACACCCACAAAGGAGTTTGTAAAATAAAATNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCGACCTTTACAAGATATAATTTGT\nCCATATCGCAATGTTTTCTCGGTTTGCGCGTTCCTTTTCCAGCGATGATAGAACGCGTAA\nATCTTATGATGGTAGTTACCAAAGTTTTAATGCCGGCGAACGTGATTTGCCCACACCTAC\nCCGGGACTGGTGTTCTATTTCCCAACGCATAACCAGCGAGCGCGTGAGGGATGGATGTCT\nTATTCCAACGCCCGGCGAGGCTTTGGAGACGGCGGTAAAGGCTTTATCTGAAAAGACCGA\nCAGCCTAACATCGCCGGTTTTACAAAGTACCGAAAGACACAGTGTTCTGCTTGGATTACA\nCCATAATAATGTTCCTGAATCGTTGGTGGTCTCGTGTATGTCTAACGATGTTCATGACGG\nGTTTATGCAGCGTTATATGGAAACAATTCAAAGATGTTTGGATGACCTGAAACTTTCTGG\nGGATGGACTTTGGTGGGTTTATGAAAATACATATTGGCAGTATCTCAAATACACCACAGG\nAGCCGAGGTACCGGTGACTTCAGAGAAGGTAAATAAAAAGTCTAAATCCACGGTTTTGTT\nGTTTTCATCCGTAGTTGCCAATAAACCAATATCCAGACATCCTTTTAAATCTAAAGTTAT\nAAATTCGGATTACCGGGGAATATGTCAGGAGCTACGTGAGGCGTTAGGAGCTGTGCAAAA\nGTATATGTATTTTATGCGTCCAGATGATCCTACAAACCCCAGCCCGGATACAAGAATACG\nTGTACAAGAAATTGCGGCTTACACGGCTACTGGCTACGGGTGGATGTTATGGTTCTTGGA\nCGTTGTGGACGCCAGGGTATGTCGCCATCTCAAACTTCAATTTCGACGGATTCGAGGGCC\nGCGCGCGTCTGTTATTCCAGATGATTTGCTTAGACGACATTTAAAAACGGGTCCTGCGGT\nCTCAGCGGGCACAGGAGTTGCGTTTATTTTAGCAGCAACAACTGCCAGCGCTCTTACTGC\nGCTTTTGCGTATTAGTGTATTATGGCGAAAGGAAGAGTGGCGGGATGGTTTAAATGGAAC\nCGCAGCTGCAATTGTTGCGGCGGTTGAACTTATTACGCTTTTGCACCACCATTTTCAATA\nCTTAATTAATATGATGCTTATTGGATATGCATGTTGGGGGGATGGGGGATTAAACGATCC\nTTATATATTAAAGGCGCTACGCGCCCAGGGACGGTTTTTATATTTTGCGGGTCAGTTGGT\nTAGAACAATGTCAACACACAGTTGGGTTGTGTTAGAGACCAGCACCCATATGTGGTTTTC\nCCGGGCCGTGGCGCAGAGTATTTTAGCACATGGGGGTAAACCCACAAAGTATTATGCTCA\nGGTTCTTGCCGCCAGTAAACGGTATACTCCGTTACATTTAAGACGTATATCCGAACCATC\nGAGTGTGTCTGATCAGCCGTATATTCGTTTTAATCGACTGGGATCTCCAATAGGGACAGG\nTATAGGGAATTTGGAATGTGTCTGTTTAACGGGAAATTATTTATCTGACGACGTAAATGC\nAAGTTCGCATGTAATTAATACGGAAGCACCGTTAAACAGTATAGCACCCGATACAAATAG\nACAGCGGACTTCTCGCGTTTTAGTTCGTCCAGACACGGGTTTGGATGTAACTGTCCGAAA\nAAACCACTGTCTGGACATAGGCCATACGGACGGTAGTCCAGTTGACCCAACGTATCCTGA\nTCATTACACCCGGATAAAGGCGGAATATGAAGGTCCGGTTCGGGATGAATCAAACACAAT\nGTTTGACCAAAGATCGGATTTACGTCACATAGAAACCCAAGCATCTTTAAATGATCACGT\nATATGAAAATATACCACCCAAGGAAGTGGGTTTTAACTCATCTTCAGACCCGGATGTGGA\nTAGCCTTAACGGGTACACCTCCGGAGACATGCATACAGACGATGACTTATCACCAGATTT\nTATACCCAACGACGTTCCCGTTAGATGTAAAACCACGGTTACGTTTAGGAAAAATACGCC\nTAAGAGTCATCATTAAGTACAGCGGTTAATAGATAGTTATGGACTAGGCACTTTGGCGGT\nCATTTCCACAACCAGGTTAAAATTGGGGGATTTGGGAGAAAATAGTCTATTGCGTATTTT\nCTGTTCAATAATTGGACTGCGTTATTTAAAGGTCTGATTGGTTGATTGGGTTATAAAAGG\nAATTACTCCTTTAAATTTTACTTAATGTACCCACAATATCAAGTGGTCGTTTGTATTTAA\nCGATTATTACCGGTACCATGGGAGACTTGTCATGTTGGACAAAAGTGCCGGGTTTTACGT\nTAACCGGCGAACTTCAGTACTTAAAACAAGTGGATGATATTTTAAGGTATGGAGTTCGGA\nAACGCGATCGAACAGGAATCGGAACGTTATCTTTATTTGGAATGCAAGCTCGATACAATT\nTGCGAAATGAATTTCCTCTTTTAACTACAAAGCGTGTTTTTTGGAGGGCCGTCGTGGAAG\nAGTTGTTATGGTTTATCCGCGGGTCAACCGATTCCAAAGAACTCGCCGCTAAAGATATAC\nACATATGGGATATATACGGATCGAGCAAATTTCTAAATAGGAATGGCTTCCATAAAAGAC\nACACGGGGGACCTTGGCCCCATTTACGGCTTCCAGTGGAGACATTTTGGAGCGGAATATA\nAAGACTGTCAATCAAACTATTTACAGCAAGGAATCGATCAGCTGCAAACTGTTATAGATA\nCAATTAAAACAAACCCAGAAAGCCGACGAATGATTATATCGTCTTGGAATCCAAAGGATA\nTCCCCTTAATGGTACTACCTCCATGTCACACGTTATGTCAGTTTTACGTTGCAAACGGTG\nAATTATCCTGCCAAGTATACCAGAGATCGGGGGATATGGGCCTTGGGGTACCGTTCAACA\nTTGCTGGATATGCACTTCTTACCTACATAGTAGCGCATGTTACAGGACTTAAAACCGGAG\nATTTAATTCATACAATGGGGGATGCACATATTTACTTGAATCATATAGATGCTTTAAAAG\nTGCAGCTAGCTCGATCCCCAAAACCTTTTCCTTGCCTTAAAATTATTCGAAATGTAACAG\nATATAAACGACTTTAAATGGGACGATTTTCAGCTTGATGGATATAATCCACACCCCCCCC\nTAAAAATGGAAATGGCTCTTTAATGGATTTTTAAANNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCCAC\nCGAACACGTACCGAGTGCGGTGGATAATACTTTGATACGTTACAGTAGGCTGTGTATGTC\nTGTCCGGTTAAGACTGGATCGCCGACAACGGTAATATTTGGACGATAATACGTTGTAACT\nGTAATACTGTGTTCCGATATGACGTTCTTAGTTTTTGTATTAACGACTCGCCAAATATAC\nGTTCCCTCCGTGGTAGCATCCATAGATAAAATTGTTACAGAAAAATCAGACGTTGTTTTA\nACATCTGGTATTACATAATTTTCCTTAGCGTGTGTAAATATCTCAGGGTTGTTTATTAAG\nTTTAAATCGGCACTGTTGCTATATAACATAACCGGTAAATCTGGCATGCGTATTAACGCA\nTTGCCCAGTTGACGGTGCGGATCTATAAGGTGACGCGTAAACCAAACTTCAATATGAAGA\nTCGGGGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNCGATACATATGTACCACATAGATAGCATAGATTTATTATAATA\nTAAACACACACGTGATATACTTTAGTGATATGAGATGCCATAAAACAGTCAATAGGTTTA\nACGCTTAGTCTCATCATCTGAATACACGTCAAACCCGCCGCAACTGTTGATGTTAGAATT\nATAATAGCTCCCCATGAAATGCCGGCAAATGTTACAGCTATACCCGTCACCGAGGTCGTT\nGTATATAATACAATTACCCATAGGTTTTTTTTTTCTTGATATAAAACGGCAAAACCCTGT\nAACCCAAATGCTATAATATGACCTCCTATTGAAACTGCTAACGTTACTTGTGTAAGTTTG\nATAAAATGATTTAATTTAATTATATGTGAGATTGCCCACATTAATGGGGTAACTATATAT\nAACACCGGGGGTATAACAGACATTATACGAATTCCTTTAAACACGCGTTTAAGGGTCCGG\nGAACTTTCTCGATGGTCACATACTCTCCCGCGGTCATTTTGTGTATATACAACGGCAAAA\nCCTAAATCTGTATAAGTGTTTAATTGCTTATGGCGATTTTTACGATATATACACGTATCT\nTGCAAATCGGTGGCGGCATCGACAATTGAAACTAGTGTGACAATAGATATACACAATCCA\nATAAGAACCTCATATTTACTGACATACATATATAAAATAACGGTTAGTAAACCTCCCAAC\nCCAGTTCCCAACATCATAACATAAAAATAAATATGCGGTCCATTGAATGTCGTAACAAAG\nTTGTAGTAATGGATATGCACAGCAGCCACTGTTCCGGTAATCGCGGATATGGAAATTCCC\nAGTAATTCTACAAATGGAAGATCCCGGGATATTGGGCAACCAACCGCCCATAACACAGCA\nAAACCCAACACGACCACCGTCTGCAAACATCGTCCCAATTTTGCTAATGTGCGTAGAAAT\nTTCACGGATGTTGGCCATAACCCCGAAACGACGATCAACCCCATAATAGTTGCATTGACG\nGCAGCTTCGCAGACGTGATATTGTAAAATTAACCCGGACGTGATAACACTTGCTTGTAGT\nCCCACGAGAAACAACCGCGATGCTGAGGTTATTGCACACGAATTACATTCTTGAGGGTTT\nCCGACACATCCTTGGATTGATTGAGCGCGGATTAATTCTCTGTCTAACACACCCAGGTTT\nTCATCATGGACAGCTCTTTCACCATTCACGGCCATGTCTTAAGTTTAATAATTCAAAACA\nAATAAAAATGTGTTCATCTATGGTACACACAAGTTTGTATGTAAAATATAAGCAAAAGTT\nGCACTTATTTAACTGTACATATTACGTCAGATTCACGTGATAATTCAGAATAATCCAGGG\nTTCCTGCAGGGTCCACTGGAGGAGCCACACAATATTCGCGAATTCCGATTCCCTCCTGCC\nATGTGGTTTCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCGTTTCTTTTTG\nTTAATAAATTGCGTCTTTTTTTTAATGGTGGTTCATCCTTCACAGATTCCATGTTCGCAA\nATAATTGCATCGAGGTTAATTTTTCTTTAAGGTCTTTGGGACTTAAGAACGTTGCATAAA\nAAAAAGAATGCACGGGTGCGGAACGTTGGATATACAATCCAACCATGGGGGAGTTAGTTA\nAGGCGAGATAAAAATTAATATAACACGTCTCATCCCGTGTTAACTTAAGATTTTGTACGG\nCAGAACGGAATCCACTGTGTGTTTCCAATAATACTCCAAATTCACGCATACTCCCGCTGC\nCATAAACAACATTATTAAGGATCCTTTTTGAATTTGTGATTGAGCGTATTAAATTATATG\nGTGTAGGCTTGCTTCCGTTTATATCCAAGGAAACATTAAATGAGATAAAACCACCCCCGG\nCGGTCTGGATGTACATATCCGTGGCTGTTAGAATGAAGCATGTTGTAAACCCAAAAGTTT\nTAAGTAGTCGCTGTAAACGGGTGAATTGATCGCGTTTTAAGCAAATGCTTATATCTGGAG\nTTAGATTTGGGAACATCATTGTATAACAAGCGAGTTCACGTTTTACAACTTGTTTGTAAC\nATTGTACTTGATCATCTGGACCACAATCACCCGGGCGTTGCCATACCATCGTTTGGATAA\nTACTCCGCTCGGGGGGTTGTCCGGTGAATTTAAAATATAACCGTGTTGGGGTCGACGGAT\nCTTTTGTATGGCGAAACGCGTCAATAAGCGAGGACCGTCCCTCCGTTGCCGCGAGTACAA\nCCATTCTCGGCCCAGTCCAATTATACTGGTCAAACATATTTGCCGGTATAGGAATATACA\nGTTGTTCTGTTTCCAAACTACAGTGAATAATTAATCCTTCGTCGCTGAATATTAAAATAG\nAATCCCTTAGTCTATTAACCAGAGGTGATATAGACGAAATTAAACCAGTAAGCGTTTTTT\nCCGTTAAAACAGCTCTGGCGATTTCTGGGGCGTCAAAACCCGCATGCAATTCCATGTCCA\nAAGCATCGTCTGTACGCGACCTCAAATCCATAATTTACTACTTAAAATGTTTACTATAGA\nAAAAGTAATCATATGTAAACACACGAGTTTCGTTAATATGTTTGTTTAACCCGATCCGGT\nGACTTAAGTACATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTGAAGCCGCTGTGAAACCTTTCACAAGAC\nGATATAAACTTGGTTAAGTGTATTGATGGGGCTCTTTGGACTGACACGCTTTATCCATGA\nACATAAACTGGTTAAACCCAGCATCATTTCAACGCCACCCGGAGTTTTAACCCCCGTGGC\nGGTAGACGTATGGAACGTCATGTACACATTGTTGGAACGTTTATACCCTGTGGGTAAACG\nCGAGAATTTACACGGACCATCTGTAACGATACATTGTCTTGGAGTCTTATTGCGGCTATT\nAACACAACGGTCATACTATCCGATATTTGTATTGGAACGTTGTACAGACGGCCCATTATC\nACGTGGAGCCAAGGCAATTATGTCACGGGCCATGAACCACGATGAAAGGGGAACCTCGGA\nCTTAACCCGTGTTCTACTATCATCCAACACATCATGTTCTATCAAGTATAACAAAACATC\nGGAAACATATGACAGTGTGTTTCGAAACTCTTCCGCGAGTTGTATTCCTAGCGAAGAAAA\nCAAATCCCAGGATATGTTTTTGGACGGTTGTCCACGACAAACTGACAAGATGATCTGCCT\nGCGCGACCAAAACGTATGCAGTCTTACCTCTACAATGCCATCCCGAGGACATCCTAACCA\nTCGATTATATCACAAATTGTGTGCAAGTCTTATTAGATGGATGGGGTATGCATACGTCGA\nGGCGGTTGACATTGAGGCGGACGAGGCATGTGCAAACTTATTTCATACGCGTACAGTGGC\nTTTGGTTTATACGACAGATACTGATTTACTCTTCATGGGCTGTGATATTTTGTTAGATGC\nAATTCCTATGTTTGCTCCAGTAGTACGATGTCGCGATTTGCTTCAATATTTAGGAATTAC\nATACCCTGAATTTTTGGTTGCCTTTGTTCGCTGTCAGACCGATTTGCATACAAGTGACAA\nCCTAAAATCTGTTCAGCAAGTTATTCAGGATACCGGCCTGAAAATTCCACATCAAATGGA\nCACTTCAACGCGCTCCCCCACTTACGACTCGTGGAGACATGGCGAGGTTTTCAAAAGTCT\nTACCGTAGCCACGTCGGGTAAAACAGAAAACGGAGTGTCCGTTTCCAAATATGCATCTAA\nCCGATCGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTTAATGGTTCATTGTTTTATTTTGCTCGT\nATATACATGTTATAAATCGTTTATCACTGTGCCCGCATAAGATGTACTGTGTCTCTCAAA\nAAAATTTGTGTTTTTATCTGCAATCATAAATGCAAGTGGAAAGTCCGAATCTGGAGGTGG\nGGTGTTAAATAGTTTTGGTACATTAATCGCTGATAAAAGCCTGTCCGCGCTGAATTTCAC\nGTATTGTGTAATTGCATCGACGTTCACCAAACGGGTTTTGGGTGCATGGGATTTTAAAAA\nCGCACACTCGATTTCAACGGCTTCCGAAAACAGTTGATGTATTCTGGTGATAGCGGGTTT\nTTCGGGTACATAGTTATTGTATATACAACACGATGCGCTGGTATGTATGGCTTCATCTCG\nGCTTATAAGGTCGTTAAATTGACAAGTTACAACAAATAGTCCGTTATTGCGTAAATATGC\nAATAGCCGCGAACGATGATACAAAAAAAATGCCCTCTATAAGAATCATTAGTATATATTT\nTTCTGCAACGGATGGGTTGTCCCGTACCTTTTCTTCCAACCATTGTACTTTTTGTTGGAT\nCGACGGATTATTAATAGTGACATTTACGTATTGTACCCGCAACGATTCATCCCCTCTGAA\nCAACATTAGTTGAATTTGACTATAGACACGCGCGTGGACAACCTCGATGCACTCTTGTTC\nAATGTAGTAATGGTGAATATCCTTTTGGGAAAAGAGTTGGGTTAGAGAGCCCAAATTAAC\nATTTACCAGATCATCTGCCGCCGATAAAAATGTAAAAATAAATCTGTAGAATATTAGTTC\nATCTTCCGTTAAACAGTCCAAGTATTGATAATCATCTTCAATGATAAAATCGCTTTCTAA\nCCAACGATTCGAAATGCTCAGGGCACGTAAATTGTTTATATCTGGACACTCCGGCCTGTA\nAAAAAAATGACTGCAATCTTTCTGATCCATTTTGGAATAGTTTCCCGTGTAAATTTATAA\nAGCACAACTGGTACAGGTTAATTCGCCTCCCGCAAACAGTCCGCTGTTTGTAGCTTTACG\nAATTTTACAGTAGTACATACCCGTTTTAAGGCCGGCTTTATAGGCACGTATAAGCAAATT\nCATTATTTTGGAGGCGGGAATTGTCCCGTCTGGGCGTTCCTCAATAAATAAAGTCATTGA\nTTGACTTTGGTCAATAAATGGCGCCCTTTCTGCACACATATCAACGAGATCCTCTTGCTC\nATATTCAAACGCTGTTTTATATTTTAAGAGTGGGTGACTATTAGATAAACAGCCAAACGA\nACGTATTACTGACCATTGGTTTTTCTCAAGTATGTTTATAACTTCCAGTCGTTTTTCTTC\nACATGAATACATATCTCTTAGTTCGTCCATAAGGTCTAAGTTGGGTCTAAGTAACTCACC\nCGAGGTGGTGACCTTACTAAACATATTATTATAAATTGGAGAGAAACCCTCACTGCACTC\nCGTTACCTGTGCAGATGAAACTGTGGGCATTAACGCTAAGAACTGCGAGTTGTATAACCC\nATAAGCGCAAATATCATCTCGCAGGGTACACCATGGTAAATCTAAATAACTTATCGTAGA\nAAACCCATCTTGGTGTAACCATCCCTTAGCATATTTACTTTCGGTAAAACCCTTAAACGG\nGGCTAAGCCGCCAATCTTACACATTTCCATGCTTGTTTTCATTGTCTCATACAACATTAA\nCTCCGCTATTTGTACATTTAACCGTCTAGCTGGTTGGGAAGTTAAATCAAATCCTAAGCG\nGAGACAAGTTGTATGTAACCCTTGTATGCCAATGCCAAGTGATCGGTTGTTTTTTACACC\nTTTACATGATTTTTTACATGGAAAGTTCCCAGCCGCCAGGACCCCGTTTAAAAAAATAAC\nAGTCGTTCTTGCTGTCAATTGAAGGTCGTTTAAATTAAATGACACTGGGCCTTTGGATAA\nGCACGTTGTAAGATTTATGCTGGCAAGATTACATACGCCATGTTGATGAGCGTCTGCCTT\nTTGAACAATTTCCGTACACAAATTTGACCCCGTGATAGCATTTCCTTGGGTATTCATATG\nATAATTACGATTACAGGCATCTTTGAACATTAAAAAGGGGCTTCCTGTTACAGCAGCACT\nGCGTATGATTGTGAATGCGATATCTTGAATGGGAACAGAAGAAACGCCTAATCCTTCTCT\nCTCTAAACGTAAATAGGTTGAAGTGAATGCCTCCCCGTGTAATGTTCGAAGGATATCGGC\nTCTGTTATCAAAAAGAGTCCACTGAACATTACTAGCCCCTTTTAGATAGCTTAGGTATCT\nTTCAAAAAATAAATCTGGGGTCCATAAACAACAAAATATGTTATCACATCGAAATATTTC\nATCACGAACCAACATTCCACGTGTGGCCAAAACAGTTTGTAGATCGACGTGCCATGGTTC\nTATGTAAACACAAACTCCAGTTGGTCGTTCACAATCACTGTTAATTGCCATAACCATGCA\nATCTAAAAGTTTTAAAACTGCAAGAAGACCTTTCGTTTGATTTTCCGTAGGTATTAAATT\nCAGACTCTGTAGAGAAATTCCCACTCCGCCTCGACTTTGTAATACCGTTCCCACATCGCC\nTGTGATAGCTCGAACAGCTCTCCCAACAGTGATGGATTCCGGGTCCATTAAATAACAACT\nGGCCGTTGCCCCGGTCTCTCGACCTAAAAACATCATAACCGGTGTAGCCGGGACAATTTT\nCTGACATGCCAACGCTGTGAAAAATACCCGACAGACATCAGTCCATGTATAACCATCATT\nTATTCCGGGAATAAGAGTTGCGATTTTAGGCAGGTTTACGATTTCTGTTGTCACGGTGGC\nCGCCAGTCTTAAAAAGAATTGGCAAAGCGACTCTAATTTACCTTCCTCTAACTTAGTTAA\nATAAAAGTCTTCGTACTTTAAAGCAGACTGTAGTCCAAGGGTAGCTAAAGCGGGGTATTG\nATCTTTCAAAAACGGTTCTAATATAGCCCGACGAATTTCGTCCCTCCGCCCTTCAATTGC\nTTGGCGGACTCGGGGAGTTAAACAGAGAATTGGGGAAGTCAACCACGTTTCCATGGAAAC\nGGATCGTAGGTTAATACGGCAATGGATAAGTTCTCCACAACATCGGTACACTCGCTCATC\nTTGTCGCGTCACCGCCTTAAGTTTTGAGACGATAGTGCTAATATACTCCATTAATTCCAC\nCGGTGTGGTTGATTCGGGCGGAATGATGTATTCCTTGTAGCCATGTTGACATAATCGGTT\nTATAATGTCATGAACCGATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATTCGTTCCA\nTGTATTTGTACCCCCCCACACAACCCCCTCTAACCAAATAGTTGGCACGTTATAACCTCC\nGAACCGTTCCATGCGTCTTGTATAACGCACAGACTCTGATGGAATTGTTCCAATTAACGT\nATATGCCGCATACATGCAGGATAATTGTGTGGGAAGTCCCCGAAAATCGCCGGTCCATTG\nATACAATCGCTGTCTAGCCAAGTTCCAATTTACTCCTGTAATTTCGCCAATACTACATCG\nAGGGCTTGTCGGGTCATTGGATAACTGCACAAGCGGCAACGCCCTTGTGTTATATGGCTG\nGTGGGTATTTGCAACCCCTTCAGTCCCCCAGGCGGCATTTTCAGCTCGTATGCGTCCTAA\nCAGGAAGCCAATACCACGACCAAAACATTGTTCGTTTAGTTGGCTTAATGCAAGATGCAG\nTCTTACACCTTCTCGTTGGCGTCGCTGTGTATATACAAAAACCAAGAACACATGCTTCAG\nTCCGTCCGCGGAAAGATGTAAGTCTTTGTCAACGTCCCAAAATACGCAGGCCGGGATGTT\nGGCTGTGACCCTGCGAGTTGAAGTTTTGTCTGTACGTGCAGCTTCTTGGGGACCTTTGGC\nCACGGCGGTTATATTGCATAAATTATCCTGAATGGTATATTCCAGCAGGGACCCAAAAAA\nACTTATAAATCGATGTGGAAATACATGACATTGTACCATCGCACGTAAACACTCCGAAAA\nCCTTATGAGCCGCGTTTCCATACGACTGCATCCATAGGCAGAAACAATTGCTGTTCTGTT\nGGCATCTGCTGCCTGTTTATCCGTATATTCTTCTGCCCGGCATGCGGCGATGAAACTTAA\nTGACGTTACATATGCTCTAAGCCCCCCACCTTCTCCAACGGTCCAAGGAGCCGTGCAGGC\nATTGAATAGGTTTCGTAAACCCTCTAGTATTACATCGGGGTCACGTCCAGCCTGTGTAAG\nTGTATTAGCTTCTCCAATCATGTCAGATGGATGACGAAGGATTAAGACGATTGACCCAGC\nATGCTCAATGTCCGGACGAAAAAAATCGGTTAATGACACTTGTTGGATTAGCTGTGTCGT\nTGATTTAAAATTATTTAACGGGAGTCTAATGGTAACTTGCGGGTTACCAATTGAAGTTGG\nATTTATTTGAATGTTGTTCATGCGATTAATAACAATTGAACGGGGGGTTACTTGAATAGA\nCGCGGTTTCTGTACGTTTTGGTGGTCCATGTATCGGTTGTTTGTTCAGACCTCCAAAGCG\nAGGGCCAATTGTTAAATCGCGACTCCAATTTCCGAAGAAGCCCGGAGCATAAGTCATATG\nAAGCCCGTTCCCTATTTGAATAAAACGGTTATTTCCTAAAAGACTGATATTAGTTCCACA\nTAGCGTTTGTTCGTTTAAAGTAAAATGCGAGTTGGTTGGTTGACTCCCCATAGCTGAGGG\nGGTAAATTCACACAATGCAATCGTGACGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCCTGCATTCTAATATCTG\nTTTTGTATATTCCAATACATTTTTGGCGGAGGCTGCTTTCACGGCCGAAAATTTACCCGG\nACTGTTGTTTTGGAGACTAGATCTAGACTGGACGATAGAGGAGCCAGGTAATAGCTTAAA\nAATTTTAACCCAGCTATCAAGTGTAGTACAAGATTCCGAGACGTTACATCGTTTATCGGC\nCAATAAATTACGAACCTCGTCTAAATTTGGACCCGTTTCGATACACTTCATTATAACGGA\nCTGGATAAATATGTACGAGGTCGCCTTAAAGGATGCAACAACAGCCATTGAATCACCATT\nCACTCACGCTCGTATTGGAATGTTGGAAAGCGCCATTGCAGCTTTAACACAACATAAATT\nTGCGATCATTTACGATATGCCATTTGTTCAAGAGGGGATTCGTGTTTTAACACAATATGC\nAGGATGGCTTCTTCCGTTTAATGTTATGTGGAATCAGATTCAAAATAGCTCACTCACTCC\nTCTAACACGAGCCCTTTTTATAATCTGTATGATTGATGAATATCTCACGGAAACGCCAGT\nACATAGCATATCAGAATTATTTGCAGATACTGTAAATTTAATTAAAGATGAGGCGTTCGT\nATCCATCGAAGAAGCGGTAACGAATCCACGAACGGTGCACGAGTCACGAATTTCTTCAGC\nTCTGGCTTATCGAGACCCTTATGTTTTTGAGACATCCCCGGGAATGCTTGCTAGGAGACT\nTAGATTAGACAATGGTATATGGGAAAGCAACCTCTTATCGTTGTCCACCCCCGGAATTCA\nTATTGAGGCGCTGTTACATTTACTAAACTCCGACCCGGAAGCGGAAACCACATCTGGAAG\nTAATGTAGCAGAACACACCCGTGGCATTTGGGAAAAGGTTCAGGCTAGTACATCGCCTAG\nTATGTTAATAAGCACCCTTGCCGAATCCGGGTTTACAAGATTTTCATGCAAATTGCTACG\nTCGGTTTATTGCTCACCACACACTCGCCGGTTTTATTCACGGAAGCGTTGTAGCAGACGA\nGCATATTACAGATTTCCAACAAACACTAGGATGTCTCGCTTTAGTGGGTGGACTGGCATA\nCCAATTAGTGGAAACGTACGCTCCTACTACCGAGTATGTGTTAACATATACACGGACAGT\nAAACGAGACCGAAAAACGGTATGAAACGCTATTACCCGCCTTAGGATTACCACCGGGAGG\nCCTGGGACAAATTATGCGGCGCTGTTTTGCTCCACGACCCCTTATTGAAAGTATACAAGC\nGACACGCGTAATACTACTTAATGAAATTTCTCATGCAGAAGCTAGAGAGACAACATATTT\nTAAGCAAACACATAATCAATCCTCAGGTGCGTTATTACCACAAGCNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGATTCAAGATGGGGTATTACTCC\nCCCGGTGGATGTGGGTATGACACCTCCTATTTGTGTTGATCCACCGGCTACAGGGTTGGA\nAGCTGTCATGATAACAGAAGCACTAAAGATTGCATATCCTACCGAATATAATCGCTCTAG\nCGTGTTTGTGGAACCGTCGTTTGTGCCTTATATTATTGCAACAAGCACGCTTGATGCCCT\nTTCGGCAACAATAGCTTTGTCTTTTGATACACGGGGAATACAGCAAGCCTTGTCTATTCT\nTCAGTGGGCTCGCGATTATGGATCCGGAACCGTGCCCAATGCAGATGGATATCGCACAAA\nACTATCTGCTCTTATAACAATATTAGAACCTTTTACCCGTACACACCCCCCAGTACTTTT\nACCATCTCACGTTTCTACTATAGATTCCCTTATATGCGAACTTCATCGGACTGTTGGCAT\nTGCCGTTGACCTGCTTCCCCAGCACGTCCGTCCTTTGGTTCCTGACCGTCCTTCTATTAC\nAAATAGCGTTTTTTTAGCAACTCTCTATTATGATGAACTTTACGGTCGTTGGACCCGACT\nGGATAAAACATCGCAGGCGTTGGTTGAAAATTTTACATCCAACGCGTTAGTGGTTTCTCG\nGTACATGTTAATGTTACAAAAATTTTTTGCGTGTCGTTTTTATCCAACGCCAGATCTTCA\nGGCCGTTGGTATCTGTAACCCAAAGGTTGAACGCGATGAACAATTTGGGGTATGGCGTTT\nAAACGATCTTGCTGATGCGGTTGGTCATATTGTTGGGACAATACAAGGAATCCGAACGCA\nAATGAGAGTGGGAATATCCAGCCTGCGCACAATTATGGCCGATGCTTCCTCAGCCCTTAG\nGGAATGTGAAAATTTAATGACTAAAACCTCCACTTCTGCTATTGGGCCTCTTTTTTCAAC\nGATGGCTTCCCGGTATGCACGGTTTACACAGGATCAAATGGACATTTTAATGCGTGTTGA\nCAAACTAACAACAGGAGAAAATATACCCGGTCTTGCAAATGTAGAGATTTTTTTAAATAG\nGTGGGAACGAATAGCAACAGCTTGTAGGCATGCCACGGCAGTCCCGTCTGCCGAATCTAT\nTGCAACCGTGTGTAATGAATTGAGGCGCGGTTTAAAAAATATACAAGAGGATCGTGTAAA\nTGCCCCAACCTCATATATGAGTCACGCCCGAAATCTGGAAGATCACAAGGCAGCAGTTTC\nATTCGTTATGGACTCCAGGCAACAGTTTATTGTGGATTCTGGACCTCAGATGGGCGCGGT\nTTTAACTTCACAATGTAATATAGGAACATGGGAGAATGTAAATGCAACGTTTTTACACGA\nCAACGTTAAAATAACGACAACGGTCAGAGACGTAATTTCAGAGGCTCCGACGCTGATAAT\nAGGACAAAGATGGCTTCGTCCAGATGAGATTTTATCTAATGTAGATTTGCGTCTTGGCGT\nACCCGGGAATACAAGTGGGAGTGACCCTTAATATAAAACAGGCGTGTTTATGTACATTAA\nAGTATTTGTGGTTTTTATTGACTGGGCGTTTCGTTTGTATAACGCTGTTGTTGCTAGTAT\nTTTCATAACCTCCTAGGTTTTTGGAGCTACACGTGCTTATTCAACGCTCTTTGGGATTTG\nAATCATCGTAAACGTAGCGTCCCTACCAGTTGAGCGCGTAATTTTCGTAAGCAATAAAAT\nGGATATAATTCCGCCTATAGCTGTCACTGTTGCGGGAGTGGGAAGCCGTAATCAATTTGA\nCGGTGCCCTGGGACCGGCGTCAGGTCTGTCATGTTTAAGAACATCTTTATCGTTTTTGCA\nTATGACATATGCGCATGGAATTAATGCAACCCTGTCATCAGACATGATTGATGGATGTTT\nACAAGAGGGTGCAGCATGGACTACGGATCTGTCTAATATGGGGAGGGGTGTCCCAGATAT\nGTGTGCTCTTGTTGATCTCCCCAATCGAATTTCATATATTAAACTGGGGGACACTACCAG\nTACGTGCTGCGTTTTGTCTAGAATATACGGCGATAGCCATTTTTTTACCGTTCCAGACGA\nGGGTTTTATGTGCACACAAATTCCCGCTAGAGCGTTTTTCGATGATGTGTGGATGGGACG\nTGAAGAGTCGTATACAATTATAACTGTAGACTCAACGGGAATGGCCATCTATCGTCAGGG\nAAACATATCTTTTATTTTTGATCCACATGGCCATGGGACTATAGGACAGGCTGTAGTTGT\nTCGGGTGAATACCACGGATGTGTACTCTTATATCGCATCGGAGTATACCCACCGCCCCGA\nTAACGTAGAATCCCAATGGGCCGCTGCATTAGTTTTTTTTGTCACCGCAAACGACGGTCC\nCGTAAGCGAAGAAGCGCTATCTTCGGCAGTAACGCTTATATACGGAAGCTGTGATACATA\nTTTTACAGATGAACAATATTGCGAAAAACTGGTTACAGCTCAACATCCGTTGCTTCTTTC\nACCTCCTAATTCCACGACAATTGTGCTTAATAAATCGTCTATAGTACCTCTTCACCAAAA\nCGTTGGTGAAAGTGTATCCTTGGAAGCAACCCTACATTCAACGTTAACCAACACGGTTGC\nACTGGACCCTAGATGTAGTTACAGCGAGGTTGATCCTTGGCATGCGGTTCTAGAAACAAC\nCTCGACTGGGTCTGGCGTTTTGGATTGTCGTCGTAGACGCCGTCCTTCATGGACTCCTCC\nTTCAAGCGAGGAAAATTTAGCTTGTATCGACGATGGCTTGGTAAATAATACACATTCCAC\nGGATAATTTACATAAACCCGCTAAAAAGGTTCTCAAATTTAAACCAACTGTAGACGTGCC\nGGATAAAACACAAGTGGCACATGTATTACCCCGCCTACGAGAAGTTGCTAACACCCCAGA\nCGTTGTGTTAAATGTATCCAATGTAGATACGCCTGAATCCAGTCCCACTTTTTCACGGAA\nCATGAATGTAGGAAGCAGTTTGAAAGATCGGAAGCCATTTCTATTTGAACAGAGTGGTGA\nTGTCAACATGGTTGTCGAAAAACTACTACAACATGGGCATGAAATTAGCAATGGATACGT\nACAAAATGCGGTGGGTACGTTGGATACTGTTATTACCGGTCATACAAATGTTCCCATTTG\nGGTAACAAGGCCCTTGGTCATGCCAGACGAAAAGGATCCATTGGAGCTTTTTATTAACCT\nCACCATTTTGCGTTTAACGGGATTTGTGGTGGAAAATGGAACACGTACACATCATGGTGC\nTACAAGCGTTGTATCAGACTTTATAGGTCCCCTTGGGGAAATTTTAACAGGATTTCCCTC\nCGCCGCGGAACTTATACGCGTTACAAGTTTGATATTAACAAACATGCCGGGGGCGGAATA\nTGCTATTAAAACTGTTCTCCGGAAAAAATGTACAATTGGCATGCTCATTATCGCTAAGTT\nTGGTCTAGTTGCCATGCGGGTTCAGGATACAACCGGCGCTTTACATGCCGAACTAGATGT\nGTTAGAAGCGGATCTAGGAGGTTCGTCGCCCATAGACCTCTATTCTAGACTGTCGACAGG\nTCTTATAAGTATACTAAATTCGCCTATTATTTCTCATCCCGGACTTTTTGCCGAGCTTAT\nTCCAACCCGTACAGGGTCCCTGTCTGAACGAATACGTCTTCTTTGTGAATTAGTCTCGGC\nCCGGGAGACACGCTATATGCGTGAACACACCGCGCTTGTTTCTAGTGTAAAGGCTTTAGA\nGAATGCATTACGGTCTACCCGCAATAAAATTGATGCCATTCAAATACCAGAAGTTCCCCA\nGGAACCCCCGGAAGAAACCGACATTCCACCCGAAGAGTTAATTCGGCGTGTATATGAGAT\nACGATCCGAAGTTACAATGCTATTGACCTCGGCTGTTACAGAATACTTCACCCGCGGAGT\nGTTATATAGCACACGGGCCTTGATCGCTGAACAATCCCCTAGGCGTTTTCGGGTCGCGAC\nCGCAAGTACGGCACCCATTCAACGGCTTTTAGATTCTCTTCCGGAATTCGACGCTAAATT\nAACGGCAATCATATCGTCCCTGTCTATACACCCTCCTCCTGAGACTATACAAAATCTCCC\nCGTCGTATCTCTGTTAAAAGAGCTTATTAAAGAAGGGGAAGATTTAAACACAGACACGGC\nTCTCGTATCGTGGTTATCTGTAGTCGGGGAAGCTCAAACCGCAGGTTACTTATCCAGACG\nAGAGTTCGATGAATTATCACGTACAATTAAAACCATTAATACACGCGCAACGCAACGGGC\nTTCCGCGGAAGCAGAGTTGTCTTGCTTTAATACGCTAAGCGCGGCCGTAGACCAAGCCGT\nAAAGGACTATGAAACATATAACAATGGTGAGGTCAAGTATCCTGAAATAACACGGGATGA\nTTTATTAGCAACAATTGTACGTGCTACAGACGATTTGGTGCGACAGATAAAAATNNNNNN\nNNATCCAATGATCCAATCCGGTTTACAACCTTCGATTAAAAGACGATTGGAAACAAGGCT\nTAAAGAGGTTCAGACGTATGCAAACGAGGCCCGAACCACACAGGACACAATAAAGAGTCG\nAAAACAGGCGGCATATAATAAACTCGGGGGGTTACTTCGCCCGGTAACCGGTTTTGTGGG\nACTTAGGGCTGCAGTAGATTTATTACCGGAACTTGCTTCTGAGTTAGATGTCCAAGGAGC\nCCTGGTAAATCTCAGGACCAAAGTCTTAGAGGCGCCGGTAGAGATCCGTTCTCAACTTAC\nGGGTGATTTCTGGGCGTTATTTAACCAATATCGAGACATTTTAGAACATCCCGGAAACGC\nACGCACATCTGTCTTAGGAGGACTGGGAGCTTGTTTTACAGCTATTATCGAAATTGTGCC\nGATACCTACGGAGTATAGACCATCATTGCTTGCGTTTTTTGGTGACGTGGCAGATGTGCT\nTGCATCCGACATCGCGACCGTATCTACTAACCCGGAAAGTGAGTCCGCCATAAACGCTGT\nTGTTGCAACTCTTAGTAAAGCGACGTTAGTTTCATCTACAGTGCCAGCCTTATCCTTTGT\nGTTGTCGTTATATAAAAAATATCAGGCTTTACAACAAGAAATTACGAATACCCATAAGTT\nGACTGAATTACAAAAACGACTTGGAGATGACTTCTCCACCCTAGCTGTCTCATCTGGACA\nCTTGAAGTTTATATCATCTTCAAATGTAGATGATTATGAAATAAACGATGCGATATTATC\nAATACAAACAAATGTGCACGCCCTAATGGATACGGTTAAACTTGTTGAAGTTGAACTGCA\nAAAGCTACCCCCCCATTGTATTGCTGGGACATCTACCTTATCTCGAGTAGTAAAGGATCT\nTCATAAACTCGTCACAATGGCACATGAGAAGAAGGAACAGGCAAAAGTGTTAATTACCGA\nTTGTGAACGTGCACATAAACAACAAACGACTCGGGTTTTGTATGAGCGTTGGACACGTGA\nTATTATAGCATGTCTGGAGGCAATGGAAACGCGCCATATATTTAACGGGACAGAACTGGC\nACGGTTGCGAGATATGGCCGCTGCGGGAGGGTTTGATATACACGCAGTTTACCCACAAGC\nACGTCAGGTTGTAGCGGCATGTGAAACTACAGCCGTTACGGCATTAGATACTGTGTTTCG\nCCACAATCCATATACCCCCGAAAATACAAATATTCCCCCACCTTTGGCTTTGTTAAGAGG\nGTTAACATGGTTTGATGATTTTTCGATTACGGCTCCCGTATTCACCGTTATGTTTCCAGG\nTGTTAGTATTGAGGGACTCCTTCTGCTTATGCGTATTCGCGCGGTTGTGTTATTATCCGC\nCGATACGTCTATTAATGGAATACCTAACTACAGAGATATGATATTACGAACCTCGGGGGA\nTCTATTACAAATACCCGCATTGGCTGGGTATGTTGATTTTTACACACGGTCTTATGATCA\nGTTTATAACCGAAAGTGTAACGTTAAGTGAACTTAGAGCAGACATCAGACAGGCTGCCGG\nGGCTAAACTTACAGAAGCAAATAAGGCTTTGGAGGAAGTAACTCATGTTCGGGCACACGA\nAACGGCTAAACTTGCACTTAAAGAAGGTGTCTTCATTACATTACCAAGCGAAGGTTTATT\nGATTCGGGCTATAGAGTATTTTACAACTTTCGATCATAAACGATTTATAGGAACGGCATA\nTGAAAGAGTTTTACAAACAATGGTAGACCGCGATCTAAAGGAGGCCAACGCAGAGCTTGC\nACAGTTTCGTATGGTGTGTCAGGCAACAAAGAACCGTGCAATACAAATTTTACAAAACAT\nTGTTGATACTGCCAATGCCACTGAGCAACAAGAAGACGTGGATTTCACTAACCTGAAGAC\nGTTATTAAAACTAACCCCCCCTCCCAAAACAATTGCATTGGCCATTGATAGATCTACTTC\nCGTTCAGGACATTGTCACGCAGTTTGCATTGCTGTTAGGGCGTCTGGAAGAAGAAACTGG\nTACGTTGGACATTCAGGCGGTTGACTGGATGTACCAAGCTCGCAATATTATTGACTCCCA\nTCCACTAAGTGTGCGTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCG\nTTTCCACAAAAAGCAACAGGAACGTAAAACGGCGTTGGATGTTGTGTTGCAAAAACAAAG\nACAGTTTGAAGAGACCGCGTCTCGCTTACGAGCTTTAATTGAACGTATTCCAACGGAGAG\nTGACCATGACGTTCTTCGTATGTTATTACATGATTTCGATCAATTTACACATTTGCCTAT\nATGGATAAAAACACAGTATATGACATTTCGAAATTTACTCATGGTACGGTTAGGCTTGTA\nTGCAAGTTATGCTGAGATTTTTCCACCCGCGTCTCCAAACGGAGTGTTTGCTCCTATTCC\nCGCCATGTCGGGTGTATGTCTAGAAGACCAATCCCGATGCATTCGCGCGCGGGTGGCCGC\nGTTTATGGGGGAGGCGTCTGTGGTGCAAACGTTTAGGGAAGCCAGATCTTCTATAGACGC\nTTTGTTTGGAAAAAATTTAACCTTTTACTTGGATACTGATGGGGTTCCACTTCGATATAG\nAGTGTGTTATAAATCAGTTGGGGTTAAACTTGGAACCATGCTATGCAGGCAGGGTGGATT\nATCTTTACGACCGGCACTTCCCGATGAAGGTATTGTGGAAGAAACTACACTATCGGCATT\nACGCGTGGCCAATGAGGTCAATGAGCTACGCATTGAATACGAATCCGCTATAAAATCCGG\nGTTTTCTGCCTTTTCCACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAACTTTCCCCCCCCCCCGGGGT\nAAAGGCCAATGTCGATGCAGTTACCCGTATAATGGCAACAGATCGTCTTGCGACCATTAC\nTGTACTTGGGCGCATGTGTCTCCCGCCAATTTCCTTAGTGTCAATGTGGAATACGCTGCA\nACCGGAGGAATTCGCATACAGAACACAAGATGATGTGGACATTATAGTTGATGCGAGACT\nGGATTTGTCATCCACGCTTAATGCAAGATTTGATACCGCTCCCAGCAATACCACGTTAGA\nGTGGAATACAGACCGTAAAGTAATTACAGATGCTTATATTCAAACCGGGGCAACGACAGT\nTTTTACAGTAACGGGGGCGGCACCAACTCACGTTTCTAATGTAACAGCGTTTGACATAGC\nAACTACGGCTATTTTATTTGGGGCTCCTTTGGTTATTGCCATGGAACTTACATCCGTTTT\nTTCACAAAATTCCGGACTTACTTTGGGGTTAAAATTATTCGATTCCCGGCATATGGCTAC\nAGATTCGGGTATATCCTCAGCCGTATCTCCCGATATTGTTTCTTGGGGGTTACGTTTACT\nGCATATGGATCCTCACCCAACTGAAAATGCATGTTTAACTGTNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAATGACCCTCGAATGTATAACTC\nCAAAACAGTATTCCACCCTGTAAATAACCAATTACCTTCTTGGGTTGACACGGCAGCCGA\nTGCCCCCCAAACGGACCTATTGACAAACTATAAAACAAGACAGCCGTCGCCAAACTTTCC\nGCGGGACGTACACACATGGGGCGTATCTTCTAACCCGTTTAACTCACCGAACAGAGACCT\nATATGAAAGTGATTTTAGTGAACCTTCTGACGGCTATAGCAGTGAGAGTGAAAATTCTAT\nCGTACTAAGTCTCGACGAACATCGGTCATGTCGCGTTCCTAGGCACGTACGCGTTGTTAA\nTGCCGATGTAGTCACCGGTCGACGTTATGTCCGAGGGACCGCCTTGGGAGCACTGGCCCT\nGTTAAGCCAGGCATGTCGGCGTATGATCGACAACGTTAGATATACACGTAAACTTTTAAT\nGGACCACACGGAAGATATATTTCAAGGCCTGGGGTATGTTAAATTGTTATTAGATGGAAC\nATATATATAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNTCGGCGCTCTGTGTTTTTTGCGGCAATATAGTAGGCCCCGAGATTCC\nCAAACTCATGGATGGATTTGGGGGTTGTGGTCGTATAATACGCGGGTTAAACGTACGTTT\nTAAGCCAACCGTTGGTCTTAACCATGTCATAGGGTCAGTCTCGGCAAACATGGCCGTTCG\nGCGTATCGTATTTGCATTATGGTTAGCGCGTGCACGCGCGGCACTGGCCGCGGCTCCCAC\nGGTGTAAATGCTTCTGGCATCAGCGATGTCCACACGGTGACCAGGTTGCAAAGGTCCACT\nGGCGTTTAAAAGTCGTATTAAAGCAACGGGGGTGTAAGCCGCAATTGCTTCCACCGAAAA\nTGTGGTGGGGTTGCTGGGATCAAAGACTACACGAGACGATGCGGGTTGTGTCATCGTTTA\nTTAGTTTACGGGACAATCGATAACAGCATACACGTACATCTGCGCAGGATATGTACGGAA\nAGGCAATTTATTTCCAGAAAAGCACCGCCCCTAATACAACTACCAGTACAATTACAACGA\nACAGGGCATATGTCACGTTAGCTACGGGTAGAGCAAGTTTCCAGACACGCGTAGTTTGGG\nTATCGGGTAACGCAGGTTTAATGTCACTTTGCATTTGAACAGACGTGTTTGGACTTCCGT\nTCTCGGGTGGGGATCTGAATGAAGGCCGCCAGCGTATATATTCATCCAAATTATTGCCAG\nTTTCCTTATACATGTATGCATCCGTGGCGCGGGCCATAAGTTTAATGGTGCGAGATGGAT\nCTTCCGGTCCCATAAAACGAAAGGATAACTGAACATATGGCATTCGCACAAAGCAGTTCA\nCCCACATTAAAGCCTGGAGAGGTCGGCGGTCAATACCCCCACCTCGTTTAATTGATTCCA\nAAGCAGATAGGTTGATACCGGTACTTAACGTTGAACTAAGAATCACGTTATTACTGTCAA\nTGGACACTTCAGCCACTGGTGCGTTAGTCGGACGAAAAAAAAAACCTTGAAATAGCACAG\nACACCCCCGTATTTTGAATTTTTATGTAAGGGTCACAATCTACTTGCGCCCAATTCGCCA\nTTAAACGCATAATATACTCTACCGGAAAGGCTTCGGATACGTTGTCTTCGCCGTTAAACT\nGAAAAACACAACGGGCGGGGGGGCGTTGTGGATCAAATATTGGAAGATCCCCATCGCAAC\nATTGAAGAGCGCTTGGTACCACCAACCGAATACGTTGTAAAAGATTATCTCCGCAACCCC\nTCCTGCGTTCACTCCGTACATACGTTCTCCGTGACATATTGATCTAAGGTTGCAAACCAA\nGGCACACGCGTGAAGTATTTAGACCATTTATCGTGGGATATAGGAGGAGTTTGGAGTGAT\nCCACCCCCTGACGACTTATTAATGCGTTTATTTTCCCCATGTATTAAGCATCCTTCAATA\nTTTCATGCAAATCTAGAAATTTGGCCATGACTCCCGCAAAGCGTTCACGGCGACGGGTCA\nCGCTGGCACTATGTTCACATGGAACAACATAAGCAGATTTTTCTGAATCGTTACTTTCTT\nTATGTTTTAAAACGGACGCCAGGCGACTGGTAAATGATATATAATTTAATTGAGCGTCAG\nTTGTAGGTAGAATTGCTTCTATTTCCGGGGGAATTAAATTTTCAAACCAAACGGAAAGAG\nTAAAGGTGCTATCAGCAGGAAAATACTTTGACTCCAGTGCATCGATATTTAATAGATTAA\nCATCGGTGTCTGTAATTAAATCGCGGGCCCTCATCCCAGAGATGGATCGGGTAGAATCAG\nAAGAACCCATGGATGGATTCGAATCGCCCGTATTCTCCGAAAATACATCTTCTAATTCCG\nGATGGTGTTCCGACGCATTTTCCGATTCGTACATCGCTTATAATCCAGCCCTTCTGCTAA\nAAAACGATTTGTTATTTTCAGAATTGTTATTTGCCTCCCACTTAATAAATGTTCCCCGTG\nCAATAGAAAACAACGTCACTTATGAGGCCTCTTCGGCGGTAGGTGTGGATAATGAAATGA\nCCTCAAGTACCACTGAATTTATAGAAGAAATTGGAGACGTTTTGGCGTTAGACAGAGCCT\nGTTTGGTCTGTAGAACGCTTGATTTGTATAAACGTAAATTTGGACTGACACCGGAATGGG\nTTGCGGACTACGCCATGTTATGTATGAAAAGTCTGGCATCCCCGCCCTGTGCAGTTGTCA\nCTTTTAGCGCTGCCTTTGAATTTGTGTATCTTATGGATCGTTACTACCTGTGCCGTTATA\nACGTTACTTTGGTTGGGTCCTTTGCCAGGCGCACGCTTTCCCTGTTAGATATACAAAGAC\nATTTTTTTTTGCATGTATGTTTTCGTACCGATGGAGGGTTACCAGGTATACGACCGCCCC\nCCGGTAAGGAAATGGCCAACAAAGTAAGATATTCCAATTACTCCTTTTTTGTACAGGCGG\nTAGTTAGGGCTGCATTACTATCGATCAGCACGTCTCGTTTAGACGAAACCGAAACGCGTA\nAGTCATTTTACTTTAATCAGGACGGACTGACTGGAGGCCCTCAACCTTTAGCGGCCGCCT\nTGGCTAATTGGAAAGATTGCGCGCGGATGGTTGACTGTTCATCATCGGAACATCGCACAA\nGTGGGATGATTACCTGCGCGGAACGTGCATTAAAAGAGGATATAGAGTTTGAAGATATAT\nTAATAGACAAACTTAAAAAATCGTCTTACGTAGAAGCAGCTTGGGGTTACGCAGACTTGG\nCTTTATTATTACTGAGTGGGGTTGCTACTTGGAATGTAGACGAGCGTACAAATTGTGCTA\nTAGAAACTCGCGTTGGATGTGTTAAATCATACTGGCAGGCGAACCGGATTGAAAACTCCA\nGGGACGTTCCAAAACAATTTTCCAAATTTACGAGCGAGGATGCCTGTCCCGAAGTAGCAT\nTTGGGCCTATTTTGTTAACTACCTTAAAAAACGCAAAGTGCCGTGGTCGCACGAATACCG\nAATGCATGTTATGTTGTTTATTAACCATAGGGCACTATTGGATCGCTTTGCGGCAGTTTA\nAAAGGGATATATTAGCATACTCAGCAAATAACACAAGTTTATTTGACTGTATCGAACCTG\nTAATCAATGCATGGAGCCTAGATAACCCCATTAAACTTAAATTTCCATTTAATGATGAGG\nGTCGATTCATAACCATTGTAAAAGCAGCAGGTTCCGAGGCCGTATATAAACATTTNNNNN\nNNNNNNNNNNNNNNNNNNNCTCGGAATTACAGACAAACCCTAAAATTTTATTTGCCCATC\nCTACAACCGCGGATAAGGAAGTGTTGGAGTTATATAAAGCCCAACTGGCTGCACAAAACA\nGATTTGAAGGTCGTGTATGTGCTGGCCTGTGGACATTGGCGTATGCATTTAAAGCCTACC\nAGATTTTTCCACGCAAACCAACCGCCAATGCCGCATTCATACGAGATGGAGGACTTATGC\nTTCGACGACATGCAATATCGCTGGTCTCCCTCGAACACACCCTATCGAAGTATGTCTAGG\nCGATATAAATCCGTATCTCGGAGCGGGCCTTCGATGCGTGTACGCTCCAGAACGCCATGC\nCGCCGTCAAACCATTCGAGGAAAACTTATGTCAAAGGAGCGGTCTGTGTACCGCCATTAT\nTTTAATTACATCGCAAGGTCCCCCCCAGAAGAACTAGCTACCGTTAGAGGCTTAATCGTG\nCCAATTATTAAGACGACCCCTGTCACCCTTCCGTTTAACTTGGGTCAGACAGTGGCGGAT\nAACTGCCTGTCGTTATCCGGAATGGGTTATCATTTAGGTCTCGGAGGTTATTGTCCGACA\nTGCACTGCATCTGGAGAACCGCGTCTATGTCGAACCGATCGGGCGGCTCTGATACTAGCA\nTATGTTCAGCAGCTTAACAACATATACGAATATCGTGTGTTTCTTGCATCCATTTTGGCG\nCTATCAGACCGAGCCAACATGCAAGCAGCGTCCGCTGAACCCCTATTGTCGAGCGTATTG\nGCACAACCGGAATTATTTTTTATGTATCATATTATGAGGGAGGGGGGCATGCGAGATATA\nCGCGTACTTTTTTATCGTGATGGAGATGCCGGAGGGTTTATGATGTATGTTATATTTCCG\nGGGAAATCTGTTCACCTCCATTACAGACTAATCGATCATATACAGGCCGCGTGTCGGGGG\nTATAAAATAGTCGCACACGTTTGGCAGACAACATTTTTACTGTCGGTATGTCGCAACCCA\nGAACAACAAACAGAGACTGTGGTGCCATCCATTGGAACATCGGACGTTTACTGTAAAATG\nTGTGACCTTAACTTTGATGGAGAATTGCTTTTGGAATACAAAAGACTCTACGCATTATTT\nGATGACTTTGTTCCTCCTCGGTGATTTCAGCTTCAGTGTTCATTTTATTATCCCAGCACG\nGGGCGTGTATACAAACAAAGCCTGCCGCCTGCAAGCGGTTTAGCATTTTAACGTTAACAA\nCTCGTGTCTCTGGAATAAAACGTTTTAAAAGCCGTTCTGTGAGTTTAGTGTCGTTTCCAA\nATAACGCCTTAAAAGTTACACTCGCCGTCCCAATGAGATGAGAAAAATAATAGTCAATGT\nTTAAAGACAGCCCGTGTGATGTTACGTGAATGGGATCTTCCGCTAAGTCAGATATTATTA\nACTTACGCTTTGCTTCCCCACACCGTTTACCTGCGGTATTCTGTAAAGGATCTCCACGTA\nGCAAAGCTACACTTTTTGCATCAGCCTCCACTTCGTCTGTGGGGGCCACAATAACATAAG\nGGATGCGTTCTCGAACGTTTGGGATTTGACCCTGTCTCATTACTAATTTATAATATACTG\nTTAAGTGAGCCAAGCGACGGTTTATGTAGGCGGATGGTGGACGACTAAGCTCGGCCGTCA\nTAACAAACTTATTAATATCCAATTTGGGTGATGTAATCTGGCGATGTGCATCTGCAATTA\nTGCGTCCAAACCCGGCCATCCCAGACGGCATGGCCCGTCTATTCCATTCAGCAATGGAAA\nCACACGACGCCTCCGCCGCAGCACGCGAGACGGTGTCGTCATATAACAACAGTTCTACAA\nGTTTGCGGGCATAATCGTTAATAAATTGACAGTTGTTTTTTCTAACCAAGTCGACTCCCT\nTCATTAAAACCTTTCCGCCGTAAATTACCCCAATGTACTTTTTCTTTGTTATAAGCAAAA\nGTTTTATAAAAGTTTTTTCACACTCCAACTTTATAGGAGGACAAAACAGAGCCGTTGAAA\nTTATATGTGCCATTTTCTCGCCGATTTTAGCTATCCCCTCAACACCAACACCCTTGAATC\nGGATAAACACAGAATCCGTATCTCCATATATAACCTTTACCTCGTACGCTTTTTGGGAGA\nGAACGCTACTTTCAATGTCTGGAAACGCTGTAATAAAACGTTCAAATGCGGCCCAGTTAT\nTATGAATATAATCTCTGGTACTTAATAACATTTGACGGCCAATTGTAGTGACAGTGGCCG\nCTACGTATAAACATGGCAGAAATCCCTGCGCAACTCCAGTAAAACCGTACACGGAATTAC\nAAACTACTTTTATCGCGGCTTGTTGTTTGTCTAATAACACTGCTTCATCTGAAGAACTTC\nCGGGTATGCGCGCTCTAATAGCCTTGCGCATAGCCAACCAGTCTTTTAAAAGAACACCCA\nGCAGACTTTCTCGAACGTTAGAGCGCACAAAAAAAAGACGTTTTCCTCCAACTGTAAAGG\nTGGCATAATCGGATGGATTCAAACGTTTAACCGTCTCAAAATTTAACGTTAGCGTGGTAA\nAACATAAGTTATGGGCCTGAATTATACTTGGATATAAACTTGCAAAATCCAATACGACCA\nCCGGATCGATATAAAATCCCGTATCAGGGTCAAAAACCCTGGCTCCTTTATATCCTACAT\nTTCGCCCACTTGACGTACCAGTGGGAGAAACGCTCTCGTCTTCATCCATCTCTTCCTCAA\nCATCCCCGACATCGGGAATAACATCCTTATATTCAAAAGTAGCTGGGTATCCCCCATCGG\nGTAAAATAAATCCTCGAGACGAAGCCAGTCCTAATAAACAGGTGTAAATCCTAACCTGCT\nGTCCGTCGTAAATAGCCTTGGTTAAAGTAATTCTAGCTAGCCTTGCAACCGCGGATAACT\nCAAGGTGTGGTAAATATTTAAAAAACAGTTTCCCCACAAGAGCCGAGTCTTGTATACAAT\nATTCACCAATAATTCCTCGTGTATTCGGTCCACTAGCGTAGTATCCCGGAATGTCTTTGT\nAGGGCAAATCTCTCTTGGACTCATTTAGAGCTTCACGTGCAACCGAATCTAATTTATAAC\nTCGAGAGTTTTAATTTTTCAGTTGCAATTGCATACATATCCAGAGATATGAGACCGTTGA\nTCTTTACCTTGCTTCGTCGCTGAAATCCGGATTTGCCAACATCCCATATCTTAAACAGAC\nCCCCACGGTTTATACTGCCATAACCATCAAGCTTGAGACTGTATATAGAATTAAGTTTCT\nCCATAATAAACGCCCAATCAAAATTAACAATGTTATAACCTGTGGCAAACTCGGGAGCGT\nACTGTTTTACGAGGGTCATAAATGCAATTAATAGCTCGAATTCACTATCAAACTCCAGCA\nCAGTCGGCTCCGGTAACCCCGCGTCCTTCATTTCTTGTACATACCTTTGTGGTAAGTCAC\nAAGAGCCAAGGGAAAACAGTAAAATGTGTTCTAAAGACTGTCGAGGGATTGAATATAATA\nGACAAGAAATTTGGATTACAAGATCCTCCAGATGTGTTGCATCGGGAAACGCCAGCTCAT\nTAGATCCTCCTGATTTACATTCAATATCGAAACATAACAACTTGTAGTCAGGCCATGAGT\nCATCGTTTGGTATAGCCTGCAGATTATCCGACATGCAGTCAATTTCAACGTCGCTTAACG\nTTAATTGGCGACTTGCCGGTCGAACTCGAACACGTTCCCCATCAACTCCAGGTTTTAGTT\nGATACCAACCAAAACTAACAAAGCCGGGATTATCCATTAGAAAACGAGTGGTAGCGTCTA\nCCCGACCTTCATACTTTTTCAACTCCGGGTGAAAGTTATCACAAAGATAATTTGTAAATT\nTAGATGAGGGAGAATACACCCTGTAAAACGCACATGGCTGTGTATCGTAGTAATAAACAT\nCTGTGCGCTCAATAACCTCAACGCGAAAGCTTTCTGGAGATGCGCTTTTAAACGAGGTAC\nCATGAAAAGCGTTCTTGTCTCCATTTAACGTTGCATCATTTTGTGTTATCATAGAACTGC\nGTAAACACTCGGCAAGTAATACAGATAACTCGCTACCGGAACGTATGCCACAAGCGGTAT\nCCACCTCGGCTTTGTTTATATAAAAATATTGACAGATGCCGTATACATGAACTGCCACCC\nTTTTTCCACATCGGGACATGCCAAGTAAAGTAATAACGGTACCAAGCGGTCGTGTTGCAG\nTTGCAAACCGGGATACATCTCCATTAGACGCGGCTTCTGTTGTTTCGACAATATCATATA\nCATGGAATGTGTTAAAGCGGGGGTCAAACTTATCCCCACGAAAGTCGATTTCCCCCCAAA\nTATTCACGCGTCTAGGCCAGGGGCTGGAACAACGAAAATCCAGAATCGGAACTTCTTTTC\nCATTACAGTAAACTTTAGGCGGTCGACTAAGTGTACCGACGTGAACCCCCTTTCGTTCTT\nCCATGGGCACATCTTCATCTAAACATTTAGGGGCCAAAAATTGAAACGATGACATGGTAG\nTTTTGTAACTATGAAGAAATTCTCTGTTACTACCGCGCCCGGTTCTTGGGTTATATGTAA\nTCCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNCGAGTACTTCACCAAAATGGAAAATACTCAGAAGACTGTGACAG\nTGCCCACGGGGCCCCTGGGTTACGTTTATGCGTGCCGGGTTGAAGATTTGGATCTGGAGG\nAAATTTCATTTTTGGCCGCTCGTAGCACGGACTCTGATTTGGCTTTATTACCTTTGATGC\nGTAATTTGACCGTGGAAAAAACTTTTACATCCAGCCTGGCGGTGGTTTCTGGAGCACGCA\nCTACGGGTCTTGCCGGAGCTGGTATTACCTTAAAACTCACTACCAGTCATTTCTATCCAT\nCTGTCTTTGTCTTTCACGGAGGCAAACACGTTTTACCCAGCTCCGCGGCCCCAAATCTCA\nCACGCGCGTGTAACGCGGCTCGAGAACGGTTTGGGTTTTCACGCTGCCAAGGGCCTCCTG\nTTGACGGTGCTGTTGAGACGACCGGCGCTGAGATATGCACCCGCCTTGGATTAGAGCCAG\nAAAATACAATATTATACTTGGTGGTCACGGCATTGTTTAAGGAAGCCGTATTTATGTGCA\nACGTGTTTCTGCATTATGGAGGACTCGATATTGTTCATATTAACCATGGGGATGTTATAC\nGTATACCGTTATTTCCGGTACAACTTTTCATGCCCGATGTTAACCGTCTGGTACCCGACC\nCATTCAACACTCATCACAGGTCTATCGGAGAGGGTTTTGTATACCCAACACCCTTTTATA\nACACCGGGTTGTGCCATTTAATACATGACTGTGTTAAATGGCACAACCCGGTGTTATTGC\nTCCCATGGCCGTTGCCTTGCGCGTCAGAAATGTAACTGCCGTCGCCCGAGGAGCGGCCCA\nCCTTGCTTTTGATGAAAATCACGAGGGGGCAGTACTCCCCCCTGACATTACGTACACGTA\nTTTTCAGTCCTCTTCAAGTGGAACCACTACCGCCCGTGGAGCGCGTCGAAACGATGTCAA\nCTCCACGTCTAAGCCTAGCCCATCGGGGGGGTTTGAAAGACGGTTGGCGTCTATTATGGC\nCGCTGACACAGCCTTGCACGCAGAAGTTATATTCAACACTGGAATTTACGAAGAAACTCC\nAACAGATATCAAAGAATGGCCAATGTTTATAGGCATGGAGGGCACTTTGCCAAGGCTAAA\nCGCTCTGGGGTCATATACCGCTCGTGTGGCCGGGGTCATTGGTGCGATGGTTTTCAGCCC\nAAATTCTGCGTTGTATCTAACTGAGGTGGAGGATAGCGGGATGACCGAAGCCAAGGATGG\nGGGACCGGGTCCATCATTTAATCGATTTTACCAGTTTGCCGGACCTCATTTAGCTGCGAA\nTCCCCAAACAGATCGAGATGGCCACGTTCTATCCAGTCAGTCTACGGGTTCATCAAACAC\nAGAGTTTAGCGTGGATTATTTGGCACTCATTTGTGGATTTGGAGCACCCCTGTTGGCGCG\nACTGCTTTTTTATCTAGAACGCTGTGACGCTGGTGCGTTTACAGGGGGTCACGGGGATGC\nGTTAAAATATGTTACGGGGACCTTTGACTCTGAAATTCCATGTAGTTTATGTGAAAAACA\nTACGCGGCCGGTATGCGCTCACACAACAGTACACCGACTTAGACAACGCATGCCGCGATT\nTGGACAAGCCACCCGTCAACCTATTGGGGTGTTTGGAACAATGAACAGCCAATATAGCGA\nCTGCGATCCTCTAGGAAACTATGCTCCATATTTAATCCTTCGAAAACCCGGGGATCAAAC\nGGAAGCAGCAAAGGCAACCATGCAGGACACTTATAGGGCTACACTAGAACGCTTGTTTAT\nCGATCTAGAACAAGAGCGACTACTGGATCGCGGTGCCCCATGTTCTTCCGAGGGACTATC\nGTCTGTCATTGTGGATCATCCAACGTTTCGTCGCATATTAGACACACTGCGTGCGCGTAT\nAGAACAGACAACAACACAATTTATGAAAGTGTTGGTTGAGACCCGCGATTATAAGATCCG\nTGAAGGATTATCCGAAGCCACCCATTCAATGGCGTTAACGTTTGATCCATACTCAGGAGC\nATTTTGTCCCATTACCAATTTTTTAGTTAAACGAACACACCTAGCCGTGGTACAAGACTT\nAGCATTAAGCCAGTGTCATTGTGTATTTTACGGACAGCAAGTTGAGGGGCGGAACTTTCG\nTAACCAATTCCAGCCTGTTTTGCGGCGGCGTTTTGTTGACCTGTTTAATGGGGGGTTTAT\nATCAACACGCTCTATAACCGTAACATTATCTGAAGGTCCTGTATCCGCCCCAAATCCGAC\nATTGGGACAAGACGCGCCCGCGGGGCGTACCTTTGATGGGGATTTAGCGCGCGTAAGCGT\nGGAAGTTATTCGGGATATACGAGTTAAAAATAGGGTCGTTTTTTCAGGTAACTGTACAAA\nTCTCTCTGAGGCAGCCCGGGCAAGGCTTGTAGGCCTTGCAAGTGCGTACCAACGCCAAGA\nAAAAAGAGTGGATATGTTACACGGGGCCCTAGGGTTTTTGCTTAAACAGTTTCACGGCCT\nGTTATTTCCTCGGGGTATGCCACCAAACAGTAAATCCCCCAACCCGCAGTGGTTTTGGAC\nCCTGTTACAACGCAACCAGATGCCGGCAGATAAACTTACACACGAAGAGATTACCACTAT\nTGCAGCTGTTAAACGGTTTACCGAGGAATATGCAGCAATAAACTTTATTAATCTACCCCC\nAACCTGCATAGGAGAATTAGCCCAGTTTTATATGGCAAATCTTATTCTTAAATACTGCGA\nTCATTCACAGTACCTTATAAATACCTTAACTTCTATAATTACGGGTGCCAGGCGCCCGCG\nTGACCCATCATCCGTTTTGCATTGGATTCGTAAAGATGTCACGTCCGCCGCGGACATAGA\nAACCCAAGCAAAGGCGCTTCTTGAAAAAACGGAAAACTTACCGGAATTATGGACTACGGC\nTTTTACTTCAACTCATTTAGTCCGCGCGGCCATGAATCAACGTCCCATGGTCGTTTTAGG\nAATAAGCATTAGTAAATATCACGGAGCGGCAGGAAACAACCGCGTCTTTCAGGCAGGGAA\nTTGGAGCGGTTTAAACGGGGGTAAAAATGTATGCCCGCTATTTACATTTGATCGCACTCG\nCCGTTTTATAATAGCATGTCCTAGAGGAGGTTTTATCTGCCCCGTAACAGGTCCCTCGTC\nGGGAAATCGAGAAACCACCCTATCCGACCAAGTTCGCGGTATAATTGTCAGTGGCGGGGC\nCATGGTTCAATTAGCCATATACGCCACGGTTGTGCGTGCAGTGGGCGCTCGAGCACAACA\nTATGGCATTTGACGACTGGTTAAGTCTTACAGACGATGAGTTTTTAGCCAGAGACTTGGA\nGGAGTTACACGACCAGATTATCCAAACCCTGGAAACGCCCTGGACCGTAGAAGGCGCTCT\nAGAAGCCGTAAAGATTCTAGATGAAAAAACGACAGCGGGAGATGGGGAAACCCCCACAAA\nCCTAGCATTTAATTTTGATTCTTGTGAACCAAGCCATGACACCACATCTAACGTATTAAA\nCATTTCAGGGTCAACTGTCCCTGGTCTTAAACGACCCCCCGAAGATGACGAACTCTTTGA\nTCTTAGTGGTATTCCCATAAAACATGGGAACATTACAATGGAAATGATTTAACCTCCCTC\nTTTATCCAATTAAAGCCCACACGCGGGTGAGTGTACGTAATAAACAAGTCAATATTACAT\nATTCTGTTGTGTTTTCTTTTTTGCGTGTAGTCCTTACCCATATGACCTGTAATATAGTGT\nGTCTCCAACCATTCAGCTTACAGTCCAGTGGACAGTAACAGCCCGATAACATGGAATTGG\nATATTAATCGAACATTGTTGGTTCTACTGGGTCAAGTTTATACGTACATCTTTCAGGTTG\nAACTGCTACGTCGCTGTGATCCAAGGGTGGCGTGTCGCTTTTTATATCGGTTAGCGGCTA\nACTGTTTGACAGTTCGTTATTTATTAAAGCTGTTTCTCCGGGGATTTAATACCCAGCTAA\nAATTTGGAAACACTCCCACGGTTTGTGCACTGCATTGGGCATTATGTTATGTAAAGGGAG\nAAGGTGAGCGTTTGTTTGAGTTGCTACAACATTTTAAAACGCGTTTTGTTTATGGTGAGA\nCCAAAGACTCAAACTGTATCAAAGATTACTTTGTCTCAGCGTTTAACTTAAAAACCTGCC\nAATATCACCATGAGCTGTCGTTAACAACATACGGAGGTTACGTATCGAGTGAAATTCAGT\nTTTTACACGACATTGAGAATTTTTTAAAACAGCTTAATTACTGCTATATTATCACGTCTT\nCTCGTGAGGCGCTAAACACATTGGAAACCGTGACGCGGTTTATGACAGATACTATAGGAA\nGCGGTCTAATACCACCCGTGGAGTTGTTTGATCCGGCGCATCCATGTGCTATATGTTTTG\nAAGAATTATGTATAACAGCTAACCAAGGTGAGACCTTACATCGTAGATTATTAGGATGTA\nTCTGCGATCACGTTACTAAGCAAGTTCGGGTTAACGTGGATGTTGACGATATTATTCGGT\nGTTTACCATATATCCCTGATGTACCGGATATCAAACGTCAATCCGCCGTTGAAGCGTTAC\nGAACACTTCAAACCAAGACGGTAGTCAATCCCATGGGAGCAAAGAACGATACGTTTGACC\nAAACATACGAAATTGCGAGCACCATGCTTGATTCTTATAATGTTTTTAAACCTGCCCCTC\nGGTGTATGTACGCCATCAGCGAGCTTAAATTCTGGTTAACGTCTAATTCCACTGAAGGAC\nCCCAACGTACTTTAGACGTGTTTGTTGATAATTTGGATGTATTAAACGAACATGAAAAAC\nACGCAGAACTTACAGCCGTAACGGTTGAGTTGGCGTTATTTGGAAAAACTCCCATACACT\nTTGATAGGGCGTTTTCTGAAGAACTCGGATCTCTGGATGCAATTGATAGTATTTTGGTTG\nGCAATCGCTCATCCTCACCAGACAGTCAGATAGAAGCATTAATTAAAGCCTGTTATGCCC\nATCATCTATCGTCGCCTCTCATGCGTCACATTTCTAACCCGAGTCATGATAACGAAGCCG\nCCTTACGCCAACTTTTAGAAAGAGTTGGGTGTGAGGATGATTTAACCAAAGAGGCGAGTG\nACAGCGCTACAGCATCCGAATGTGATCTGAACGATGATAGTAGCATAACTTTTGCTGTTC\nATGGATGGGAAAACCTGTTATCCAAAGCAAAAATTGACGCTGCGGAAAGAAAACGAGTAT\nATCTTGAACATCTGTCTAAGCGCTCTCTAACCAGCCTCGGTAGATGTATCCGCGAACAGC\nGCCAAGAGCTAGAAAAAACACTCAGGGTAAACGTTTATGGAGAGGCCTTATTGCAGACAT\nTTGTTTCGATGCAAAATGGGTTTGGGGCACGAAACGTGTTTTTAGCTAAGGTTTCCCAGG\nCAGGGTGTATTATCGACAATCGCATTCAGGAAGCGGCCTTTGATGCACATAGATTTATAA\nGGAATACCTTAGTTCGACATACAGTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGTTCCAACTGGCTTCTCAGTCCATTTAGGG\nGCTTTTATTGCTTTTCTGGGGTAGAAGGCGTTACTTTTGCACAGAGACTTGCCTGGAAAT\nATATTAGGGAGCTTGTGTTTGCAACCACACTATTCACCTCTGTTTTCCATTGTGGGGAGG\nTGCGGTTATGTCGCGTTGACCGTCTAGGTAAGGATCCACGCGGGTGCACGTCTCAACCTA\nAAGGTATAGGCAGTTCCCACGGACCCTTAGACGGCATTTATTTAACGTACGAAGAAACAT\nGTCCCCTTGTGGCTATTATTCAAAGTGGAGAAACAGGGATCGACCAGAATACCGTCGTAA\nTCTACGATTCAGACGTTTTTTCTCTTCTATACACCCTAATGCAGCGGCTGGCTCCGGATT\nCAACGGACCCGGCGTTTTCATAACCTCCGTTACGGGGGTGTGGTTATGCTTTTTATGCAT\nATTTTCTATGTTTGTTACGGCGGTTGTGTCGGTCTCTCCAAGCTCGTTTTATGAGAGTTT\nACAAGTAGAGCCCACACAATCAGAAGATATAACCCGGTCTGCTCATCTGGGCGATGGTGA\nTGAAATCAGAGAAGCTATACACAAGTCCCAGGACGCCGAAACAAAACCCACGTTTTACGT\nCTGCCCACCGCCAACAGGCTCCACAATCGTACGATTAGAACCAACTCGGACATGTCCGGA\nTTATCACCTTGGTAAAAACTTTACAGAGGGTATTGCTGTTGTTTATAAAGAAAACATTGC\nCGCGTACAAGTTTAAGGCGACGGTATATTACAAAGATGTTATCGTTAGCACGGCGTGGGC\nCGGAAGTTCTTATACGCAAATTACTAATAGATATGCGGATAGGGTACCAATTCCCGTTTC\nAGAGATCACGGACACCATTGATAAGTTTGGCAAGTGTTCTTCTAAAGCAACGTACGTACG\nAAATAACCACAAAGTTGAAGCCTTTAATGAGGATAAAAATCCACAGGATATGCCTCTAAT\nCGCATCAAAATATAATTCTGTGGGATCCAAAGCATGGCATACTACCAATGACACGTACAT\nGGTTGCCGGAACCCCCGGAACATATAGGACGGGCACGTCGGTGAATTGCATCATTGAGGA\nAGTTGAAGCCAGATCAATATTCCCTTATGATAGTTTTGGACTTTCCACGGGAGATATAAT\nATACATGTCCCCGTTTTTTGGCCTACGGGATGGTGCATACAGAGAACATTCCAATTATGC\nAATGGATCGTTTTCACCAGTTTGAGGGTTATAGACAAAGGGATCTTGACACTAGAGCATT\nACTGGAACCTGCAGCGCGGAACTTTTTAGTCACGCCTCATTTAACGGTTGGTTGGAACTG\nGAAGCCAAAACGAACGGAAGTTTGTTCGCTTGTCAAGTGGCGTGAGGTTGAAGATGTAGT\nTCGCGATGAGTATGCACACAATTTTCGCTTTACAATGAAAACACTTTCTACCACGTTTAT\nAAGTGAAACAAACGAGTTTAATCTTAACCAAATCCATCTCAGTCAATGTGTAAAGGAGGA\nAGCCCGGGCTATTATTAACCGGATCTATACAACCAGATACAACTCATCTCATGTTAGAAC\nCGGGGATATCCAGACCTACCTTGCCAGAGGGGGGTTTGTTGTGGTGTTTCAACCCCTGCT\nGAGCAATTCCCTCGCCCGTCTCTATCTCCAAGAATTGGTCCGTGAAAACACTAATCATTC\nACCACAAAAACACCCGACTCGAAATACCAGATCCCGACGAAGCGTGCCAGTTGAGTTGCG\nTGCCAATAGAACAATAACAACCACCTCATCGGTGGAATTTGCTATGCTCCAGTTTACATA\nTGACCACATTCAAGAGCATGTTAATGAAATGTTGGCACGTATCTCCTCGTCGTGGTGCCA\nGCTACAAAATCGCGAACGCGCCCTTTGGAGCGGACTATTTCCAATTAACCCAAGTGCTTT\nAGCGAGCACCATTTTGGATCAACGTGTTAAAGCTCGTATTCTCGGCGACGTTATCTCCGT\nTTCTAATTGTCCAGAACTGGGATCAGATACACGCATTATACTTCAAAACTCTATGAGGGT\nATCTGGTAGTACTACGCGTTGTTATAGCCGTCCTTTAATTTCAATAGTTAGTTTAAATGG\nGTCCGGGACGGTGGAGGGCCAGCTTGGAACAGATAACGAGTTAATTATGTCCAGAGATCT\nGTTAGAACCATGCGTGGCTAATCACAAGCGATATTTTCTATTTGGGCATCACTACGTATA\nTTATGAGGATTATCGTTACGTCCGTGAAATCGCAGTCCATGATGTGGGAATGATTAGCAC\nTTACGTAGATTTAAACTTAACACTTCTTAAAGATAGAGAGTTTATGCCGCTGCAAGTATA\nTACAAGAGACGAGCTGCGGGATACAGGGTTACTAGACTACAGTGAAATTCAACGCCGAAA\nTCAAATGCATTCGCTGCGTTTTTATGACATAGACAAGGTTGTGCAATATGATAGCGGAAC\nGGCCATTATGCAGGGCATGGCTCAGTTTTTCCAGGGACTTGGGACCGCGGGCCAGGCCGT\nTGGACATGTGGTTCTTGGGGCCACGGGAGCGCTGCTTTCCACCGTACACGGATTTACCAC\nGTTTTTATCTAACCCATTTGGGGCATTGGCCGTGGGATTATTGGTTTTGGCGGGACTGGT\nAGCGGCCTTTTTTGCGTACCGGTACGTGCTTAAACTTAAAACAAGCCCGATGAAGGCATT\nATATCCACTCACAACCAAGGGGNNNNNNNNNNNNNNNNAAGGAATGGATCCCTTTGCCGA\nGAAACCCAACGCTACTGATACCCCAATAGAAGAAATTGGCGACTCACAAAACACTGAACC\nGTCGGTAAATAGCGGGTTTGATCCCGATAAATTTCGAGAAGCCCAGGAAATGATTAAATA\nTATGACGTTAGTATCTGCGGCTGAGCGCCAAGAATCTAAAGCCCGCAAAAAAAATAAGAC\nTAGCGCCCTTTTAACTTCACGTCTTACCGGCCTTGCTTTACGAAATCGCCGAGGATACTC\nCCGTGTTCGCACCGAGAATGTAACGGGGGTGTAAATAGCCAGGGGGTTTGTTTTAATTTA\nTTAATAAAAATGTGTATTACGTTACTCATGTGTCTCCATTACGCATCACAGGGGGTATTT\nATACCCGATAATATACAAAACGCGTTTTGTACCTCTACCGCACCCGATATCTTAACGGGG\nTTATTATGGAATCGTCTAACATTAACGCGCTACAACAACCGTCGTCTATCGCACATCATC\nCGTCCAAACAGTGCGCTTCAAGTCTCAATGAAACAGTAAAAGATTCTCCCCCCGCGATTT\nATGAAGATAGGTTAGAACACACGCCGGTACAATTACCCCGCGACGGTACACCCCGAGACG\nTATGTTCTGTGGGACAGCTAACCTGTCGAGCATGTGCAACGAAACCTTTTCGCCTTAACC\nGCGACAGCCAATACGACTACTTAAACACATGTCCAGGGGGCCGTCATATTTCACTGGCAC\nTGGAGATTATAACGGGTCGATGGGTTTGCATCCCGCGTGTGTTTCCGGATACCCCAGAGG\nAAAAATGGATGGCGCCATATATTATTCCAGACCGAGAACAACCATCATCAGGGGATGAAG\nATTCTGACACCGATTAAATTTAACTTAAATAAAACCTTACCACCCATAAAAACGCCNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNGTTGGTTAACACCGCCCCACCATCATCTGATTTGCAAACATATCG\nGCGTCGTCTGCCGTGGACCCCTGTATTAAAGGGGCCTTGGAACTAGCCTCCACTGCATTT\nACATCTTGTCCAACTGTATCTGTATGTGGGGTGCTTGTTGTATTTTGGGATGAGCATAGA\nCCCGAAACGCTTTGAAGCTGTTTTAATAAAATCGATATTCGAGGATCCCGTGTCCCCTCT\nGGTATATTTGTATGGTGCGACAAAGGCATTTGTGTCCCATTTTGTGATTTTAGCTCTGTA\nACCTCCTGTTGCAGTTTTGCCACAACCCCAGCAAGCTCTTCGTGCTGACCATTAGAAACT\nCTGTGTCTCCTCTGCCAATATGATGGAGAAACTCGACGTCTCCGATGCGTTATATACGTT\nGGTTCACCGGGAAAATATATATTTGAGGGAAACTCTCCGTCCATTTGAGACTCCCCACTA\nGAAAAAGAATCCAATTCCCTTTGATCCATGCTCTTGAAATCCCGTTTTCCTGGACGACGG\nACATCGGTTTTGTCTGGAAAATTTACACACGGGGTCTGCAAGTCAATACCCCGTTCGGCG\nGCCAATGCGTTCATAAATGCGGACATTTGCATTTCCAAACGATTGGGTGGTGGATATCCC\nGGAAACCCGTACGGTCCCCCGAAGTGTCCCGGAGGGCAACCATAACCCCCTGTATTAGGT\nGGGAAGGCAGGCGGGTGTGGAGATCCATATGGCCCGACGATATACTGTCCGTTATTTGGA\nGCTCCAATTGATACCTGCGGATTTTTAGTCTGCCCGGTTAACAGCTGTGAATAATACGCG\nGTAGGTATCAGTACAAATTCCCCTCCGGTTGGAACGCCCGACGGGGGCTGTGGTGAGATA\nCCACTAGCGTTACCTGCTACAGAAGCCATATCGCTGTCGTTCCTACACAACTGCGTAACC\nTTTAAATGCGGAACAGTCTTTTCACAATCTTCATTTGATTCCCCAACACCCAACGCGAGA\nTCGTATATGGGCCCGCCGGGGTGGAATGTGGCGTTTATAACACCCGCGTTGGGTAATTTA\nGACTCCACCCCATTAACGTTGGTTATCCGAGCAAGTCCATATCCGGTGCTAGCCTGAAGA\nTAAACGTGACCCATAATTCCGGCTTCGCGTCTACGTTTTGCAACCACGTCCCATCTATCT\nCTTAAAAGCATATTGTTCACGGCTGTGGATAATAACACCTTGGCGAGTTTATCTTCGCTA\nACCTTCCATACTTTATTTAAACCCGCGTAGTCTTTAACCAGCGACAATAACCGCGCTTTA\nCTTTCCATCGATAAAACCCGGAATGGTTCAATTGAAGATTCCGGGGTACAGTCATAATTG\nACCACTGTTCCAACGCGTCTTCCAACAACACATAACGCAACATGGGTAAAAAAATTACCG\nTCTGGTATCTCATTCGGGGACAATCGTTTTGAAGACAGGGATACGGAGGGTAAGTAATTT\nGTGACCAAGTATAACGCACGTTCTAGCGGAGATAATACAGAATCTCTATTTCCAAAAAAA\nTTCGAATGGGCCGCTTCAAACAGCACCGCATGTAGTTGAGGGCATCTAACGATACCCAAA\nAAAAAAGGTCCGCGTATGTCCTCAATGATTGCGATTACTTCACCCACGACACAGTCTTTT\nCGATGATCGATGTTTATTGGTATTTTACTAGTAGGCGGCAAAGCGGACCGCACAATCTCT\nGGGGTAATATTTAATTCCCCTTCGTCCTTTGAATATAAGGCTAAATACCCAGCCACGTAT\nAACGCTTCACAGTTCTCTTCGTCAGCTTCAGCAGCCATTATAAACACCCCACGGACCGGA\nTAGTGAATACTCACGGTGTGGAGGCAAACTGAGGAATGACACCCAAACAGACAAAATATA\nGAAGATCATAGTCACTGTTAACGTTGAACTGCGCAAGGCGGCGACTTTCTTCCAATGCCG\nCCCTTACACGCGGTTGGTGCATTAACATTCCAAGTCCCCGTTCATATTGCAACATAACAC\nTGTCATGTATTGATACCACGGCGGCTATGGGTAGGGATGTAACATTTTGTCGGCGGTGTT\nCTAATTCCAATGCAATTAAGCTTATGAGCCGATCTTGGTACTGTCCAGAAGAAATATCTA\nTTACGGTTCTTCCTAAACTTCCACGACTAAGCTGGGTATGCGCGTCTAAACAAAGAGCAA\nCTAATCCAGGAAACATTTCAGTCAGCTCTGTGGTCCGATTTAACGTATACAGTGGTGCTA\nTATATCGTTCACATAAAAATTGAAAGTTATTATTACCGCTTTTAAACTTCCCATCAAACC\nCCGTCGCTCCGCGCAAGATTACATTGTTGGTAGGGGTTCCTGTTGCTTCTGACACAATCA\nAACCCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNCCTGCAACCGTATAAGCGCATCCATAACAGAATGTGACGTTAAGG\nCGCCTTGATCATACCGCCCCCCACGAGCATGAAACTGGTCGCGTGGTAGACGATCATAGC\nAAAATTGATAACTGTTTTTATTTTCGTGTGTTGTCATATAATTCACAAATGTCTCAGTAT\nATTCCGGTAGGTGCTCTATAAGGTTCCCGAAGGACGAAACTTGAGGTTCGTGGACACTAT\nTAGATGTCCTATACATTAAATATAAACATAATACCGCACACTCGAACGCGGAGTACGCTC\nTATCTCCAACATACATTCTCCCGGCGGACTGTAGACATGTTACCGTTGTGTTCATAAACG\nTACGGGAAATGCGCCCGTCTTTACAATCAACTCCGCGTGCAGCTACGGGCCTATCTAACA\nCAAGCCGTTCCTGCAGAGTACGATACCATGGCCCGAAAACAATCCCTGGAGAGTTATTGC\nCCCTTGCCCTTCCCAAGTACACCAGGGTGATAAAATCCACTTGAAAGTTTGTATCGTACT\nGCAACGGTGCATCATTTTTGGCAATCTGTACCTCGGGGTGTATAGACTCATTGCGTATTA\nTTTCTGTACGTGTACATTCCTCAGATTGTGCATCTGCTTCTTCCGCCTCGGCAGCAGCCG\nTCTCCAGGGAATCCAAAACCTTGGCCATGCGCGTTAGTTGGTCTTCGAGGGGCTTTAAAC\nGACGATCTATTTCCGTTGGTAACGTAATCGTTTCCCCGCGAAGGTTGTCTAATGCGGCAA\nCGGCCGCCGCATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGTAAAATTCCAC\nCACAAGCACCTAAAGAAGGCCTTCTAAGGGGTAAATCCACCCCACAAGCTGCATTTTCTT\nCAAACTTTGTTAAAGCGGAACGATGGCATGATTTCGCACGCTTTTTCGCAAGAGAACATA\nCGTGAATTTTCTTTTTGCATAGACGTCTTCGCTCTCTAACGGACCTTATCGGGGGGGTAT\nATTCCGCTACATTCTCCAAATGCGACGCTAGCATAACAAGGTTTCCATGAATCACCTTTG\nGGGGTAACCGAGTTACCTGTAACAGGTTCAGACCCCGTTGAGATACAAACACAAGGAGGG\nGGGTCACCATTATTTCATCAGATCCCGTGGGTGTGGTTTCCTTTATTAAAGCCACGGTAT\nCCCTCAGCTGGCGCATACCCTCGCAAAACTGGTGATACTTAGTAGGGGTATGTATATTAG\nCGCTAAAACGGCAAGATTTTAATTCCACTATAAAACAAACGGTCTTTCCGGCACCACTGG\nATTCCGTTTGTATAATACAAATACAATCGGGGCGTCGGCGTCCCAAATTTACTTCAAACG\nACATTGATATGCGTACAGCCCTTTGAACATCCACGTGGGATAACGGCGACAGGAGTTTTG\nCCAGCCTCGGGTTGAACGCGTCCGCGAAACCTCGACGTACGTTATCAATATCCTTTTTGA\nGTACATCGTAAAAACGAGTGTGACAACGTTGTCCCAAACGAAAACACTTGGCCCGAATTT\nGACTAGCGGACATATTTGAAGTTCCGTCCCAGAAGATAACCTAAGACGCGTTTGTCTACA\nATAAACATGTCAACGGATAAAACCGATGTAAAAATGGGCGTTTTGCGTATTTATTTGGAC\nGGGGCGTATGGAATTGGAAAAACAACCGCCGCCGAAGAATTTTTACACCACTTTGCAATA\nACACCAAACCGGATCTTACTCATTGGGGAGCCCCTGTCGTATTGGCGTAACCTTGCAGGG\nGAGGACGCCATTTGCGGAATTTACGGAACACAAACTCGCCGTCTTAATGGAGACGTTTCG\nCCTGAAGACGCACAACGCCTCACGGCTCATTTTCAGAGCCTGTTCTGTTCTCCGCATGCA\nATTATGCATGCGAAAATCTCGGCATTGATGGACACAAGTACATCGGATCTCGTACAAGTA\nAATAAGGAGCCGTATAAAATTATGTTATCCGACCGACACCCAATCGCCTCAACTATATGT\nTTTCCCTTGTCCAGATACTTAGTGGGAGATATGTCCCCAGCGGCGCTTCCTGGGTTATTG\nTTTACGCTTCCCGCTGAACCCCCCGGGACCAACTTGGTAGTTTGTACCGTTTCACTCCCC\nAGTCATTTATCCAGAGTAAGCAAACGGGCCAGACCGGGAGAAACGGTTAATCTGCCGTTT\nGTTATGGTTCTGAGAAATGTATATATAATGCTTATTAATACAATTATATTTCTTAAAACT\nAACAACTGGCACGCGGGCTGGAACACACTGTCATTTTGTAATGATGTATTTAAACAGAAA\nTTACAAAAATCCGAGTGTATAAAACTACGCGAAGTACCTGGGATTGAAGACACGTTATTC\nGCCGTGCTTAAACTTCCGGAGCTTTGCGGAGAGTTTGGAAATATTCTGCCGTTATGGGCA\nTGGGGAATGGAGACCCTTTCAAACTGCTTACGAAGCATGTCTCCGTTCGTATTATCGTTA\nGAACAGACACCCCAGCATGCGGCACAAGAACTAAAAACTCTGCTACCCCAGATGACCCCG\nGCAAACATGTCCTCCGGTGCATGGAATATATTGAAAGAGCTTGTTAATGCCGTTCAGGAC\nAACACTTCCTAAATATACCTAGTATTTACGTATGTACCAGTAAAAAGATGATACACATTG\nTCATACTCGCGTGTACGTGTTTTTCTTTTTTATATATGCGTCATTTATTACCACATCCTT\nTAATCCCGCCTTTATCTCCCTAAAACGGAGTGGTAATATTAAAAGCCGCCAAGCCTGTTG\nGTGGGTGAGGAGGGGTAAAGGCACGCTGTGTGCATAACGTTGCGGTGATATTGTAGCGCA\nAGTAACAGCGACTATGTTTGCGCTAGTTTTAGCGGTGGTAATTCTTCCTCTTTGGACCAC\nGGCTAATAAATCTTACGTAACACCAACCCCTGCGACTCGCTCTATCGGACATATGTCTGC\nTCTTCTACGAGAATATTCCGACCGTAATATGTCTCTGAAATTAGAAGCCTTTTATCCTAC\nTGGTTTCGATGAAGAACTCATTAAATCACTTCACTGGGGAAATGATAGAAAACACGTTTT\nCTTGGTTATTGTTAAGGTTAACCCTACAACACACGAAGGAGACGTCGGGCTGGTTATATT\nTCCAAAATACTTGTTATCGCCATACCATTTCAAAGCAGAACATCGAGCACCGTTTCCTGC\nTGGACGTTTTGGATTTCTTAGTCACCCTGTGACACCCGACGTGAGCTTCTTTGACAGTTC\nGTTTGCGCCGTATTTAACTACGCAACATCTTGTTGCGTTTACTACGTTCCCACCAAACCC\nCCTTGTATGGCATTTGGAAAGAGCTGAGACCGCAGCAACTGCAGAAAGGCCGTTTGGGGT\nAAGTCTTTTACCCGCTCGCCCAACAGTCCCCAAGAATACTATTCTGGAACATAAAGCGCA\nTTTTGCTACATGGGATGCCCTTGCCCGACATACTTTTTTTTCTGCCGAAGCAATTATCAC\nCAACTCAACGTTGAGAATACACGTTCCCCTTTTTGGGTCGGTATGGCCAATTCGATACTG\nGGCCACCGGTTCGGTGCTTCTCACAAGCGACTCGGGTCGTGTGGAAGTAAATATTGGTGT\nAGGATTTATGAGCTCGCTCATTTCTTTATCCTCTGGACTACCGATAGAATTAATTGTTGT\nACCACATACAGTAAAACTGAACGCGGTTACAAGCGACACCACATGGTTCCAGCTAAATCC\nACCGGGTCCGGATCCGGGGCCATCTTATCGAGTTTATTTACTTGGACGTGGGTTGGATAT\nGAATTTTTCAAAGCATGCTACGGTCGATATATGCGCATATCCCGAAGAGAGTTTGGATTA\nCCGCTATCATTTATCCATGGCCCACACGGAGGCTCTGCGGATGACAACGAAGGCGGATCA\nACATGACATAAACGAGGAAAGCTATTACCATATCGCCGCAAGAATAGCCACATCAATTTT\nTGCGTTGTCGGAAATGGGCCGTACCACAGAATATTTTCTGTTAGATGAGATCGTAGATGT\nTCAGTATCAATTAAAATTCCTTAATTACATTTTAATGCGGATAGGAGCAGGAGCTCATCC\nCAACACTATATCCGGAACCTCGGATCTGATCTTTGCCGATCCATCGCAGCTTCATGACGA\nACTTTCACTTCTTTTTGGTCAGGTAAAACCCGCAAATGTCGATTATTTTATTTCATATGA\nTGAAGCCCGTGATCAACTAAAGACCGCATACGCGCTTTCCCGTGGTCAAGACCATGTGAA\nTGCACTTTCTCTCGCCAGGCGTGTTATAATGAGCATATACAAGGGGCTGCTTGTGAAGCA\nAAATTTAAATGCTACAGAGAGGCAGGCTTTATTTTTTGCCTCAATGATTTTATTAAATTT\nCCGCGAAGGACTAGAAAATTCATCTCGGGTATTAGACGGTCGCACAACTTTGCTTTTAAT\nGACATCCATGTGTACGGCAGCTCACGCCACGCAAGCAGCACTTAACATACAAGAAGGCCT\nGGCATACTTAAATCCTTCAAAACACATGTTTACAATACCAAACGTATACAGTCCTTGTAT\nGGGTTCCCTTCGTACAGACCTCACGGAAGAGATTCATGTTATGAATCTCCTGTCGGCAAT\nACCAACACGCCCAGGACTTAACGAGGTATTGCATACCCAACTAGACGAATCTGAAATATT\nCGACGCGGCATTTAAAACCATGATGATTTTTACCACATGGACTGCCAAAGATTTGCATAT\nACTCCACACCCATGTACCAGAAGTATTTACGTGTCAAGATGCAGCCGCGCGTAACGGAGA\nATATGTGCTCATTCTTCCAGCTGTCCAGGGACACAGTTATGTGATTACACGAAACAAACC\nTCAAAGGGGTTTGGTATATTCCCTGGCAGATGTGGATGTATATAACCCCATATCCGTTGT\nTTATTTAAGCAAGGATACTTGCGTGTCTGAACATGGTGTCATAGAGACGGTCGCACTGCC\nCCATCCGGACAATTTAAAAGAATGTTTGTATTGCGGAAGTGTTTTTCTTAGGTATCTAAC\nCACGGGGGCGATTATGGATATAATTATTATTGACAGCAAAGATACAGAACGACAACTAGC\nCGCTATGGGAAACTCCACAATTCCACCCTTTAATCCAGACATGCACGGGGATGACTCTAA\nGGCTGTGTTGTTGTTTCCAAACGGAACTGTGGTAACGCTTCTAGGATTCGAACGACGACA\nAGCCATACGAATGTCGGGACAATACCTTGGGGCCTCTTTAGGAGGGGCGTTTCTGGCGGT\nAGTGGGGTTTGGTATTATCGGATGGATGTTATGTGGAAATTCCCGCCTTCGAGAATATAA\nTAAAATACCTCTGACATAAAAAACATGTATAATAAAAAGTCACTATAAACGTATTCTCTA\nCAATACTTTATTCGCGAATAATACACACTACCTTTGGGTTTTTTTCCCGTCCCCAAATGG\nTGTTTGGTGCACTCTACCAAAAAATAGAGCGCCTAAATATGCTATATAACGCCTCCCAGC\nAAAATACGGTTCAAAGGCATTACCCGATATTGTATTGTAGTACAGGGCAATGGGAATTGA\nTGATCCCAATAAACGGCATAGACGCACAGCGCCGTTATAGCAGGGGTCTCCAGAGTACAG\nGGTATCTAAGTACCGGGATATCTCATACTCATGCCTTTCCGTGACAGAAACATCAACCGG\nAACAGTATCCGATAAACCAACTCCTGTTTTTGCAAGGCGTAAAATTCGCACACCTTCCTT\nTTTTGCAAGATGTGACGTTTCCTTGTAACAGGGAAGCTGGGGGAGTGGTAAGAACAACAA\nAGTTTCAGCCAACGTGCCAATAAAGCCCACTTCCCTCAAGAGGCTGTTTGCTGTATCCAC\nAATGGTCCGTATTAAATCTTGAGCAACTTGATCCGTGTCATCATCACTGGGTAACGCGTT\nAACATAACTACGCGTTAAATCTTCAATAACGGCATAACAATTAAACGCTTCCCACCGAGA\nCAGTATATATTGAACAATCACGAACCGTTGACAGGACGTCAGATCACGTCCGTAAGCATG\nCCCGAAAAATGGAAGTTCCCCCCGTTCGCCATATACCGCAACAACTGCAGTATATATCGT\nCTCACGGGCTTCATTAAGTTCATCTTCAAGTCCAGGCCATTTTCTGGCTTTAAATATAAC\nCTCGTCCGCAAAAAAAACCGCACATGATAACGCGCGGATACAATGAGTAGTGGCTTTATG\nGCGAGGATCCCAAATGTCCATTACCCGGGGGATGGTCCTAATCTGTACAAAGTTACTTAG\nTGTAATATGATCGGACTTCTTACGCCGTCTAGGCTGTTTCTCAGAATACGGTTCACCCGA\nAATCGGCACATCATCTGCTTTTACGTCTTCCGTAACCACATCAGCAGCGCGCCGACTAAC\nAATTATACTTGTTTTTTCATCGTCGTTACTTCCGTTAAGCGCGTCTCGTATCTCGGGCGT\nCCCGTCGAATAATCCACTCACTAGCTCCTGCAAACCTTCTGGTAACTCCAACATACGCAT\nATACACCAATGAAAAACTGGCTTCGTTTGGTACGTACATAAAGCCATTTGTGGTATTAAT\nGGCNNNNNNTGTTGGAGACAATTTTAGCTTATTCTCGCGCGTAACATCTACCCCCGCCAC\nCAATGTTAAATGCGTCACGGGGAGGGACACGAGATAATCTGCGAGCGTAGGGTCCTCCAC\nTTCAACATCAAATGTTCCGCAAAGGTCGCGATCCACCGCCCCCGATCCCGCTGCAAGTAA\nGGCCACTCGATCCAAAAACACGCAGTTATTATTGGATGATACCGCCCATGTCTTCCCGGT\nGCGATTGAGCTCACTTCGAACGTAACTGGCAACAGATCTGTCACCGGGTCCGACCCCGCG\nAACAACATGTCCAAATTTTGCGATCTCGCCTCCATGTTTGCGGGGTATGGAAATTAAGCA\nTCCCCCGCATATAAAATACGCCCTGGTAGCACGCTCGTTAAAATAAAACGTTACGCCGTT\nATAAGATACGGTTGAATGATATGGAAATTCCATATTAAAGCGTTTATCGGAACATTAACC\nTCGAACTTGCCGTCCCGTGATCGTGTGANNNNNNNCCTTAGGTCCACACCGAATATGAGA\nAATATATAACTACACGCAAACATTCAAAACACCGTGGTATCATTAACGTCATATGAAAAG\nATCCAATCAATCCAATCAACCACACCTCCTACCGTTTAGCACGTCAGCTATGTGACATGC\nTCCAAACATACGTAAACATTTAGAGAGGGTGTTATAACAGTCTGTCAGGCGGGGTATATT\nCTACATAATACAAGGATCGGCTTTAACTTTGTCAACATTTTTACTTTGGACTATAAACTG\nCGACTGAACGTTATGAACCCACCCCAAGCCCGCGTCTCGGAACAGACAAAGGACTTGCTT\nAGCGTTATGGTTAACCAGCACCCCGAAGAGGACGCAAAAGTGTGTAAATCCAGTGATAAT\nTCACCGCTTTATAACACCATGGTTATGTTATCGTATGGGGGTGATACGGACTTACTATTA\nAGCTCTGCATGTACCCGCACATCTACCGTAAACAGGTCGGCGTTTACGCAACACTCCGTG\nTTTTATATTATATCCACGGTGTTGATTCAACCAATATGTTGTATCTTCTTTTTTTTTTAC\nTATAAAGCGACACGCTGTATGCTCTTATTCACAGCCGGGTTACTTCTGACGATTCTACAT\nCACTTTCGACTTATTATTATGTTATTGTGTGTCTACAGAAATATACGATCAGACCTGCTA\nCCCTTATCTACATCCCAGCAACTGCTGCTTGGAATTATTGTTGTGACTCGAACAATGCTA\nTTTTGTATTACGGCGTATTATACTCTTTTTATAGACACCCGGGTGTTCTTTTTGATTACC\nGGACACTTGCAAAGTGAGGTTATTTTTCCAGATAGCGTTTCAAAAATACTTCCTGTGTCG\nTGGGGTCCAAGTCCAGCCGTGTTACTGGTAATGGCGGCAGTTATTTACGCTATGGACTGT\nTTGGTGGACACGGTATCCTTTATTGGGCCAAGGGTGTGGGTCCGTGTTATGTTAAAAACA\nTCTATTTCGTTTTAGTCCATTTCAATAAATGTACTATAATTGTTCAGTCTAAAAATAATG\nTTGGGTATTTATAATTACCGCCCCCGTGTTACTTGGAAACACCCATACATATGTTCCACT\nCTACATCAAACTTCTCGCAGTTTTCTTGTTCCCGCACACGTTTACACGTCCGGATTCAAG\nTCGCAACGCTGCTGACAAAATGACAACGGTTTCATGTCCCGCTAACGTGATTACTACAAC\nGGAATCTGATCGTATTGCTGGGTTATTTAACATCCCAGCGGGGATCATTCCAACTGGAAA\nTGTGCTGTCAACCATAGAGGTGTGTGCACACCGTTGCATTTTTGATTTTTTTAAACAAAT\nACGATCAGATGATAACAGCCTTTACTCGGCTCAATTCGATATTCTTTTGGGGACATACTG\nCAATACATTAAACTTTGTGCGTTTTCTAGAACTTGGACTGTCTGTCGCTTGCATCTGTAC\nTAAATTTCCGGAGCTGGCTTACGTGCGAGATGGCGTTATTCAATTTGAGGTACAACAACC\nCATGATAGCACGTGATGGCCCACATCCCGTCGATCAGCCTGTTCATAATTATATGGTTAA\nGCGGATACACAAGCGTTCGTTAAGCGCTGCGTTTGCAATTGCATCGGAAGCGTTGAGTTT\nGTTAAGTAACACATATGTCGATGGGACAGAGATTGACTCATCGTTACGTATAAGAGCTAT\nCCAACAGATGGCTCGTAATTTACGCACCGTTTTGGACTCATTTGAACGAGGCACTGCCGA\nTCAACTTCTTGGTGTTCTATTGGAGAAAGCCCCACCGCTATCGCTGCTTTCACCAATTAA\nTAAATTCCAACCCGAGGGACATCTAAATCGTGTTGCACGCGCGGCCCTACTTTCGGACCT\nCAAACGTAGAGTCTGTGCGGATATGTTTTTTATGACCCGACACGCCAGGGAACCTAGGCT\nGATCTCTGCGTATCTGTCGGATATGGTTTCGTGCACCCAACCATCGGTGATGGTATCACG\nAATAACTCATACAAACACTCGCGGACGGCAGGTTGACGGTGTGTTGGTAACAACAGCAAC\nCTTAAAACGGCAACTATTACAGGGAATTTTACAAATTGACGACACCGCCGCTGACGTACC\nAGTAACATATGGCGAAATGGTTCTACAGGGGACAAACTTGGTAACCGCCCTTGTGATGGG\nAAAGGCCGTCCGCGGAATGGATGATGTAGCCCGCCATCTCCTTGATATAACCGACCCTAA\nCACGTTAAACATACCGTCTATACCCCCACAATCCAACTCCGATTCAACGACAGCTGGGCT\nTCCGGTTAACGCCCGTGTTCCTGCGGATTTAGTGATTGTTGGGGATAAACTTGTATTCTT\nAGAAGCATTAGAACGGCGGGTCTACCAAGCTACGCGCGTTGCCTACCCTCTTATTGGAAA\nTATAGATATTACGTTTATCATGCCAATGGGAGTGTTTCAGGCAAACTCCATGGACAGATA\nTACACGACACGCCGGCGATTTTTCAACTGTATCCGAACAGGATCCACGTCAATTTCCACC\nCCAAGAGATTTTTTTTTATAATAAAGATGGGATATTAACACAGTTGACTCTTCGTGATGC\nAATGGGTACCATCTGCCACAGTTCATTGCTTGATGTTGAGGCCACACTTGTTGCCCTCCG\nCCAACAACATTTAGATCGTCAGTGTTATTTTGGTGTATACGTGGCCGAGGGTACAGAGGA\nCACATTGGATGTTCAAATGGGGAGGTTTATGGAAACGTGGGCAGATATGATGCCTCATCA\nCCCTCATTGGGTAAACGAACATTTAACAATTCTACAGTTTATAGCTCCGAGCAACCCGCG\nTCTAAGGTTTGAATTAAACCCCGCCTTTGATTTTTTTGTTGCACCGGGGGACGTAGACCT\nTCCCGGACCGCAGCGTCCCCCGGAAGCCATGCCAACCGTTAACGCAACATTACGGATTAT\nCAACGGAAACATTCCCGTGCCTCTATGTCCCATTTCATTTCGAGACTGTCGCGGAACCCA\nACTCGGTTTGGGAAGACATACAATGACCCCGGCAACCATTAAAGCCGTAAAGGATACATT\nTGAAGACCGCGCATACCCAACTATTTTCTACATGCTAGAGGCTGTTATTCATGGAAACGA\nAAGAAACTTCTGTGCGTTACTGCGACTGTTAACACAGTGTATTCGCGGGTATTGGGAGCA\nATCCCACAGGGTGGCATTTGTAAATAACTTTCACATGTTAATGTACATAACTACATATCT\nCGGAAACGGTGAGCTTCCCGAAGTCTGTATTAATATATATCGGGATTTACTGCAGCATGT\nAAGAGCATTACGCCAAACTATAACCGATTTTACAATACAAGGAGAGGGCCATAACGGCGA\nGACCTCGGAAGCGCTAAATAACATCCTTACGGATGACACGTTTATTGCACCTATTCTATG\nGGATTGTGATGCGTTAATATACCGTGATGAAGCCGCCCGAGACCGACTCCCCGCAATTCG\nTGTAAGCGGGCGAAACGGATACCAAGCCCTTCACTTTGTGGATATGGCCGGGCATAACTT\nCCAACGACGCGATAATGTGTTAATCCACGGGAGACCCGTTCGGGGAGACACGGGTCAGGG\nTATTCCCATTACCCCACACCATGACCGTGAATGGGGTATTCTCTCCAAGATTTACTACTA\nTATTGTCATTCCTGCATTTTCCCGCGGTTCCTGTTGTACAATGGGCGTGCGTTATGATCG\nCCTATACCCTGCGTTACAGGCAGTTATCGTTCCGGAAATTCCCGCTGATGAAGAAGCCCC\nAACTACCCCAGAAGATCCAAGACACCCTCTTCACGCACACCAACTCGTTCCGAACTCTCT\nTAACGTTTACTTCCATAATGCACACCTAACCGTTGATGGTGATGCATTGCTCACACTACA\nAGAGTTAATGGGAGATATGGCTGAACGAACGACGGCCATTTTAGTATCAAGCGCCCCCGA\nTGCGGGAGCCGCCACGGCAACAACCAGAAATATGAGAATATATGACGGAGCGCTTTACCA\nTGGCCTTATTATGATGGCATATCAGGCGTACGATGAAACCATTGCAACGGGTACTTTTTT\nTTATCCCGTTCCGGTCAACCCTCTGTTTGCATGTCCGGAACATTTGGCATCATTGCGTGG\nAATGACAAATGCTAGGCGGGTTTTGGCAAAAATGGTACCACCAATCCCTCCTTTTCTGGG\nAGCCAACCACCACGCAACTATACGCCAACCCGTTGCCTACCATGTAACGCATAGTAAGTC\nGGATTTTAATACTCTTACATATTCTCTTCTTGGAGGGTATTTTAAGTTTACACCAATAGC\nTCTTACACATCAACTACGAACGGGATTTCACCCCGGGATTGCCTTTACCGTAGTGCGCCA\nGGATCGCTTTGCCACAGAGCAACTTTTATATGCCGAGCGTGCTTCTGAATCGTACTTTGT\nCGGACAAATCCAAGTACACCATCATGATGCTATTGGGGGGGTAAACTTTACCCTAACCCA\nACCCAGAGCTCACGTGGACCTGGGAGTTGGGTATACAGCTGTATGTGCCACAGCAGCCCT\nGCGATGCCCTCTCACGGATATGGGCAATACTGCCCAAAATCTTTTTTTTTCACGAGGAGG\nAGTGCCAATGTTACATGATAACGTTACCGAATCGTTGCGTCGTATAACAGCATCGGGGGG\nTCGCTTAAATCCCACCGAACCCCTACCCATCTTCGGCGGACTGCGTCCTGCTACATCGGC\nAGGAATTGCACGAGGGCAAGCCTCTGTGTGTGAGTTTGTGGCCATGCCGGTGTCCACTGA\nCCTACAATATTTTAGAACTGCATGCAATCCTAGAGGTCGAGCATCTGGAATGTTATATAT\nGGGTGACCGTGACGCCGACATAGAGGCTATAATGTTTGATCACACACAATCGGATGTTGC\nTTATACAGATCGAGCAACTCTTAACCCATGGGCATCACAAAAACATTCATACGGTGACAG\nGCTATACAACGGAACATACAACCTTACAGGCGCTTCTCCTATCTACAGCCCATGCTTTAA\nGTTTTTTACACCAGCGGAGGTTAACACTAATTGTAATACACTGGATCGGCTTCTAATGGA\nGGCAAAGGCTGTGGCGTCGCAAAGCTCCACCGACACTGAATATCAATTTAAACGCCCTCC\nCGGTTCTACCGAAATGACACAGGATCCGTGTGGCCTTTTTCAAGAAGCATATCCACCACT\nATGCTCAAGCGATGCGGCCATGTTACGAACGGCTCACGCGGGAGAAACCGGGGCAGATGA\nAGTTCACTTAGCCCAATATCTGATTCGAGACGCGTCGCCCCTTAGGGGATGTCTTCCTCT\nTCCGCGATAATTTCACCACGCCCACATACCCACTCCCAATAAAAGCCCTGTAGAGCGCAT\nTGGCATCTTACTTGAGATTTGGATACGCTCGGCCGACTTGGTCTGTTTCACGCTTCCTTA\nAACAACATGGCTATGCCATTTGAGATAGAGGTATTGTTACCAGGAGACCTATCCCCGGCG\nGAAACATCTGCATTACAGAAATGTGAGGGAAAAATTATTACCTTCTCAACCCTGCGTCAT\nCGAGCTTCACTGGTGGATATAGCGCTGTCGTCATATTACATTAACGGTGCTCCACCAGAC\nACGCTCTCGCTGTTAGAGGCATACCGAATGCGATTCGCGGCAGTTATAACACGGGTCATC\nCCGGGAAAGTTGTTGGCGCATGCCATTGGCGTGGGTACTCCTACACCCGGGTTGTTTATT\nCAAAATACATCCCCCGTTGATCTTTGTAATGGCGATTACATCTGCTTACTTCCTCCGGTT\nTTCGGGTCCGCAGACTCAATTCGCTTGGACTCTGTAGGACTGGAAATTGTTTTCCCTTTA\nACCATCCCCCAGACCTTAATGCGAGAAATCATCGCCAAAGTGGTTGCACGGGCCGTTGAG\nCGCACGGCCGCGGGTGCTCAAATTTTACCCCACGAAGTTCTACGAGGCGCGGATGTCATT\nTGTTACAATGGAAGGCGTTATGAACTCGAAACAAATTTACAACATCGGGACGGATCGGAT\nGCGGCTATTCGCACATTGGTTTTAAATCTAATGTTTTCCATAAACGAGGGATGTCTGCTT\nTTATTGGCGCTGATTCCAACTTTGTTAGTCCAAGGAGCACACGACGGTTATGTAAATTTA\nTTGATACAAACGGCCAATTGCGTTAGAGAAACCGGCCAGTTAATTAATATACCGCCAATG\nCCGCGGATTCAAGACGGCCATCGCCGATTTCCCATATATGAAACTATTTCATCTTGGATA\nTCAACATCATCTAGACTGGGGGATACCTTGGGAACTCGCGCAATTTTACGCGTCTGTGTG\nTTTGATGGACCCTCTACTGTTCATCCGGGAGACCGCACAGCCGTGATTCAAGTGTAAACA\nGGTGTTAATAAAAACACAACCAGTCTAGTTACATTTCACGCGTCTTGTTTTTATTTAATA\nGGCATAAACACGGAATCCGGTATACATGAACTGCCAATATACACGGACATAATTAATGCA\nACCATCAGATCATCTGACATTGTTCCCGTGGTACCTTTACCCGTGTAAGTTTTTGTGTCT\nAGATGACCCATACCGCCTTTAATTACCTCTGTCAGGTTATCCAACTGTTTACATAGATAC\nTCCACGGGGTCTACACCTAACTTTACTGTTAGGGATACAAGCTCCTGTGAGGCTATTATA\nTTTCCGGAGTTAAATCGTTTAACAAAATAGTCTACGGCCGGCGTTTTTTGTTTTTGTAAT\nAAAAAAAAAGGGTACGCCACGCTACATCCGGGAGGTATGGAATGATAAAACAGTAACACT\nGGAGCGGAAGATAGCACGTTTCCCTTTTCGAGGACAGCAAACTGTTGTGCTATAGCCAAC\nGATATGGCAACTGCAGAATCCTGGCTGCTGTTTCCCTCTATAGAAACGTGTACGTTTGTA\nAATGTATTGGGGTGTAAAGCGAGTATGTGGCCTAAGCATTGAGTAACGCAACGCCCTATC\nTCACTGGAAGACGTGCCAGTTAAAGCTCTAAGAAAAAAGTGCTCCAATCCAAATATAATC\nCAATCCGACTTATAACGACCAACAATCGCTACACCAGTACCAGACGCTCCTGCATTTNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nAACCCCACACCCCCAGAATTCTGTTTACGCCCACCTACAATTTCCTGCACGAAGGAGTCG\nGCCATAAATAAATCTGCAGTGCGCCGCATGGCTCCATCCATTGTGATGAAAACCGGCTTA\nTTTAATACATAACACGAACAAGCTGTGACATCGCTATGTGCTAAAACACGCGGCATGTGA\nTCGTCGCATACATATGTAACAACGTTTAACAACTGATCCGACGATCCACGTAAGTTATAC\nAAAAAACTTGTACTTGCTTTTCCGGTATTTGTTGATGAAACAAAAATAATTTTACAATTG\nGTTTGATTTAAAAATCCGACTATAGTTTGTACAGCATCAGGTCGAATAAAATTAGCTTCA\nTCCACAAACAGAAGATTAAAATCTTGACCTCGGATACCCTGGAACGATAGAAAGATATAT\nAGTTACCCCACCAAAGTTTAAATGTATCCTTAAATACCACGTACGTAAAAAATGTTTGAA\nTACGTACATATTTCTTTTTTTTTTTTCCAGTACAACCATATCCGGTGTATAATGGAAGCC\nCATTTGGCAAATGAAACCAAACATGCACTTTGGCATAATGATCACACAAAAGGATTACTA\nCACGTTGTGATACCTAACGCGGGGCTTATTGCGGCCGGAATAGATCCCGCATTACTGATT\nTTAAAGAAACCCGGACAACGCTTCAAGGTTGAAGTACAAACAAGATATCATGCTACAGGT\nCAATGCGAACCGTGGTGTCAAGTTTTCGCCGCGTACATTCCCGATAACGCCTTAACAAAT\nCTCTTAATACCAAAAACGGAACCATTTGTTTCACACGTTTTTTCGGCCACGCATAATTCA\nGGGGGATTGATTTTATCATTGCCTGTTTATCTTAGCCCCGGTTTATTCTTTGATGCATTT\nAACGTTGTAGCGATACGAATAAATACTGGAAACCGCAAGCACCGTGATATTTGTATTATG\nTATGCAGAACTAATCCCAAACGGAACGCGTTATTTTGCTGATGGACAACGGGTACTTTTA\nTTATGCAAACAGCTGATTGCGTATATCCGATGCACCCCTCGTCTTGCATCGTCTATAAAA\nATATACGCAGAGCATATGGTGGCAGCCATGGGTGAATCACACACGTCAAATGGGGACAAT\nATTGGACCCGTTTCATCCATAATCGATCTTGATCGACAGTTAACTTCTGGAGGTATTGAT\nGACTCCCCTGCTGAAACACGCATACAGGAAAATAATCGGGACGTCCTTGAGCTAATAAAA\nCGGGCCGTAAACATTGTTAACTCCAGGCACCCCGTCCGACCTTCTAGTTCCCGCGTTGCA\nTCTGGGTTGCTTCAAAGTGCAAAGGGCCACGGAGCGCAAACTTCCAACACAGATCCGATC\nAATAACGGTTCCTTTGATGGCGTCCTTGAGCCGCCTGGACAAGGGCGATTTACGGGAAAG\nAAAAACAATTCGTCCGCCAGCATCCCACCTTTACAAGACGTTCTATTGTTTACCCCAGCT\nTCGACAGAACCCCAAAGTCTTATGGAATGGTTCGACATCTGTTATGCCCAATTAGTTAGC\nGGGGACACTCCAGCAGATTTCTGGAAACGGCGTCCCCTATCAATTGTACCGCGACATTAC\nGCAGAATCCCCCAGTCCGTTGATTGTAGTATCTTACAACGGATCCTCTGCCTGGGGAGGA\nCGTATTACCGGAAGTCCAATTTTATATCACTCTGCACAGGCTATTATTGATGCTGCGTGT\nATAAATGCCCGGGTTGACAATCCCCAAAGCCTACATGTGACAGCTCGCCAAGAGCTAGTC\nGCGCGTTTACCGTTTTTGGCTAACGTCCTAAATAATCAAACCCCCTTACCCGCCTTTAAA\nCCAGGCGCCGAAATGTTTTTAAACCAGGTATTTAAACAAGCGTGTGTGACATCGCTAACC\nCAAGGTCTTATAACGGAGTTACAAACGAACCCGACTCTACAACAACTCATGGAATATGAT\nATTGCAGATTCTTCCCAAACGGTTATTGATGAAATTGTAGCCCGCACACCAGACCTGATT\nCAGACTATAGTTTCGGTGTTAACGGAAATGTCAATGGATGCGTTTTATAACAGCTCCTTG\nATGTATGCGGTTTTGGCGTATCTGTCATCTGTATATACACGACCACAAGGTGGGGGGTAT\nATACCCTACCTTCACGCTTCCTTCCCATGCTGGTTAGGTAATCGTTCTATATATTTATTT\nGACTATTATAATTCAGGAGGGGAAATACTTAAGCTTTCCAAGGTCCCCGTTCCCGTAGCC\nTTAGAAAAGGTTGGTATTGGTAATTCCACACAACTGAGGGGTAAATTTATACGCAGCGCG\nGATATTGTTGATATTGAAATTTGTTCTAAGTATTTACCCGGTCAATGTTACGCGTACATT\nTGTCTAGGATTTAACCAGCAATTACAATCCATTTTAGTTTTACCGGGGGGATTTGCGGCA\nTGTTTTTGTATTACCGATACCCTACAGGCAGCACTACCTGCATCGTTAATCGGACCTATT\nCTAGACAGATTCTGCTTCTCTATTCCCAACCCCCATAAATAAATTAGTGTCACTATAAAA\nACATAACACCAGAATCTCTTCATATTTAATTTTACGTCATTTCNNNNNNNNNNNNNNNCT\nCTTAAAATATAAAATAACCGGGTGGGTGGCATTAAACCCACAAGTACCCGGGCGGCAATC\nCGCTAGACTGTTTTTCTGCTCATGGAATTACAACGCATATTTCCGCTGTACACCGCTACG\nGGTGCAGCGCGCAAATTAACCCCCGAGGCAGTTCAGAGACTCTGCGATGCATTAACGCTG\nGATATGGGATTATGGAAGTCCATCCTGACCGATCCCCGGGTGAAAATAATGCGATCAACT\nGCTTTTATAACTTTAAGGATCGCTCCGTTTATCCCCCTTCAAACGGATACTACTAATATT\nGCCGTTGTTGTAGCCACAATTTACATCACGCGCCCACGTCAGATGAACTTACCTCCGAAG\nACTTTTCATGTAATTGTAAATTTTAATTACGAGGTCTCGTACGCAATGACGGCGACTTTA\nAGAATTTATCCGGTTGAAAACATAGACCATGTTTTTGGAGCAACGTTTAAGAACCCGATC\nGCGTACCCCCTTCCAACATCTATTCCGGATCCTCGAGCAGATCCCACCCCCGCAGATCTT\nACACCAACGCCAAACTTAAGCGACTACTTACAACCCCCGCGGCTTCCGAAAAATCCATAC\nGCATGTAAAGTTATTTCTCCGGGAGTGTGGTGGTCAGACGAACGAAGGCGTTTATATGTA\nCTGGCTATGGAACCTAATTTAATAGGGCTATGTCCCGCCGGATGGCATGCTCGGATACTT\nGGCTCTGTATTAAATCGACTCCTCAGCCATGCGGACGGATGTGATGAATGTAATCATAGA\nGTTCACGTGGGGGCACTGTATGCGTTACCCCATGTCACAAATCATGCGGAAGGTTGTGTG\nTGTTGGGCTCCGTGTATGTGGAGAAAGGCCGGTCAGCGGGAATTAAAAGTGGAGGTAGAC\nATTGGCGCCACGCAGGTTCTTTTTGTAGATGTCACCACCTGCATTCGAATTACGAGTACT\nAAAAATCCTCGCATTACCGCAAATCTTGGCGACGTTATAGCGGGAACCAACGCCAGTGGT\nCTCTCTGTACCAGTAAATTCATCTGGGTGGCAGCTTTATATGTTTGGAGAAACATTAAGC\nCGGGCTATTATTAACGGCTGTGGTCTGCTTCAGCGAATTTGCTTCCCCGAGACACAAAGA\nTTATCGGGTGAACCGGAACCTACAACCACCTAGTATACCTTAACTCAACCGCCGTTGTGG\nAAAGGTATATGTCAACATTTACAGTAATATATTAAAGGTTAAATTTATAAAACACTCACG\nTTTGTGTTGTGACTTGACGCGAACACCGCTGTGCTGTAAGACCCGTCGGTAAATGAAAAC\nGTAATAGATTCGCCTTTTACATGATCCACGTAATTTGCCCCAAACCACTGTTCCAGGCGA\nGACTTGATACCCTCAAACACGGGTTCCGTTGCTTTGCGTATATGAGCCGTATAACCCACT\nTTAATTCCTCTAAACGTGGCCATTACTAAAGCTATTAATGGTACAAGAAACCATGTTTTC\nCCATGTCTACGTGGTACCAAAAACACAGTTGATTTTTGTTTGAAGTGTTCTAAAACACTG\nTCAGAAACACTTGGCGTGTTAAACACTGTACGCAGAAAGCAGTCAACTCTGTCGGCATGA\nTCGCCCAATAGCACCGATGAAATAAAATGCGTGGTGTGCATGAGGATCATTTTTTGAAAC\nAGTTCCAACGTCCCCTTATATCTGCCATAGATTGGAACGTCAACCTTTGCGCGTTTGCCA\nTGACTTCCACACTCTTCAATACTCTCAAAAGATGTTTCCACAAGGTACGAAAACCGTTGT\nGTAAAGGTAGACAACTGACAGAAACTATCCGACAGAGAAAACGCGCGAAATGTGTTCATA\nACCCCGCTATACGCATTTCGATGAGGTGCTGCTTCTTCCGGTGAATATTCATAAAACTGT\nACACTACTGACAGCCTTTTTTAATTCAGGGCTTACGTTTGCATTTACCGAATATCGCCAT\nGGTTTCAAAACTACATTGGGGGTACAGTTGTACCCTGTTGACGATAGAAACGCGCCAAAC\nATTGCCCGTCGAGCAGTAGCCGAGAACAGTGGAATATATTCACAACAGTTGTGAAGCGTT\nCCAATTCCGGGAATAACGGCCTGATGACGTCGGGTTACATCTATAGCAAAATTCAGAAAC\nGGGATTTGGGTTGCGTTTCCCAGAGACCCTTGCCGCGTGGAACACGGGGTAGGGGACTCC\nAACGTCTAAAGCGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACGTACTCGTTACGTATATA\nTCATAAACATTTTCAGGGCCGCATTCATTCACTTTGGTCATGTCAGGCCACACTCCAACC\nTACGCTTCTCATAGGCGTAACCGTGTCAAACTAGTTGAGGCGCATAACCGCGCGGGGTTA\nTTTAAAGAACGGACCCTCGATCTAATCCGTGGGGGTGCGAGTGTACAAGATCCAGCATTT\nGTGTATGCCTTTACTGCTGCCAAAGAGGCCTGCGCCGATTTAAATAACCAGCTCCGCTCT\nGCAGCTCGCATAGCTTCAGTTGAACAGAAGATTCGTGATATACAATCCAAGGTTGAGGAA\nCAAACAAGTATTCAACAGATTTTAAATACAAACAGACGCTATATAGCACCCGATTTTATT\nCGCGGTTTGGATAAAACAGAAGACGATAATACCGATAATATAGACAGACTGGAAGACGCG\nGTAGGACCGAACATCGAACACGAAAATCATACTTGGTTTGGAGAAGACGACGAAGCGTTA\nCTTACACAATGGATGCTGACGACACACCCCCCAACCTCCAAATATCTCCAACTGCAGGAC\nCTTTGCGTTCCCACCACAATACCGACGGACATGAACCAAATGCAACCACAGCCGATCAGC\nAAGAACGAGAATCCACCAACCCCACACACGGATGTGTAAATCATCCATGGGCCAATCCGT\nCAACTGCAACATGCATGGAATCACCAGAACGATCACAACAGACAAGCTTATTTTTATTAA\nAGCACGGCTTAACGAGAGATCCAATACATCAACGCGAAAGGGTGGACGTTTTTCCACAAT\nTTAACAAACCCCCATGGGTTTTTAGAATTTCCAAATTATCCCGTTTAATTGTACCCATCT\nTCACGCTCAATGAACAGTTATGTTTTTCTAAATTACAGATTCGAGATAGACCCAGGTTTG\nCGGGACGGGGAACGTATGGGCGTGTTCATATATACCCATCGTCAAAAATAGCTGTAAAAA\nCCATGGACAGTCGTGTTTTTAATAGAGAGTTAATTAACGCGATTTTAGCGAGTGAGGGTT\nCTATACGAGCAGGGGAAAGGCTAGGTATTTCTAGCATAGTTTGCCTTTTAGGTTTTTCGT\nTACAAACCAAACAGCTACTGTTTCCGGCATACGACATGGATATGGATGAATACATTGTTC\nGCCTGTCCAGACGGTTGACAATACCTGATCACATAGACAGAAAAATTGCCCATGTATTTT\nTAGATTTGGCTCAAGCGTTGACGTTTTTAAATCGAACGTGCGGCCTGACCCACCTAGATG\nTGAAATGTGGCAATATTTTTCTTAACGTCGACAACTTTGCCTCGTTGGAAATAACCACAG\nCAGTAATCGGAGACTATAGCCTAGTAACATTAAATACGTATTCCCTTTGTACTCGAGCGA\nTATTTGAAGTTGGAAATCCATCCCACCCGGAGCACGTACTACGCGTACCCCGGGATGCAT\nCGCAGATGTCATTTCGTTTGGTGTTGAGTCATGGAACAAACCAACCCCCTGAAATCTTGC\nTTGATTATATTAATGGAACGGGCCTTACTAAATATACTGGAACCTTGCCCCAAAGAGTTG\nGACTTGCGATTGATCTTTATGCATTGGGCCAAGCACTCTTAGAAGTTATCCTGCTAGGAC\nGTCTTCCCGGACAACTGCCCATTTCAGTACATCGGACCCCGCATTATCACTACTACGGTC\nATAAGTTATCACCAGATTTGGCGCTTGATACGCTGGCATATCGATGTGTCCTGGCGCCAT\nATATACTCCCATCTGACATCCCCGGGGACTTAAATTATAATCCCTTTATACACGCCGGAG\nAGCTGAACACCCGTATTTCCCGGAATTCTTTACGCCGGATATTCCAGTGTCACGCAGTGC\nGTTACGGCGTAACGCACTCAAAGCTTTTCGAAGGCATACGCATTCCGGCCTCATTATACC\nCAGCCACTGTTGTTACGTCGTTGTTGTGTCACGATAATTCAGAAATACGCTCGGATCACC\nCTTTATTATGGCACGATCGGGATTGGATAGGATCGACATAAGCCCCCAGCCAGCCAAAAA\nAATTGCCCGTGTGGGAGGTCTACAGCACCCTTTTGTAAAAACGGATATTAACACGATTAA\nCGTTGAACACCATTTTATAGACACGCTACAGAAGACATCACCGAACATGGACTGTCGCGG\nGATGACAGCGGGTATTTTTATTCGTTTATCCCACATGTATAAAATTCTAACAACTCTGGA\nGTCTCCAAATGATGTAACCTACACAACACCCGGTTCTACCAACGCACTGTTCTTTAAGAC\nGTCCACACAGCCTCAGGAGCCGCATCCGGAAGAGTTAGCATCCAAATTAACCCAAGACGA\nCATTAAACGTATTCTATTAACGATAGAATCGGAGACTCGTGGTCAGGGCGACAATGCCAT\nTTGGACACTACTCAGACGAAATTTAATCACCGCATCAACTCTTAAATGGAGTGTATCTGG\nACCCGTCATTCCACCTCAGTGGTTTTACCACCATAACACTACAGACACATACGGTGATGC\nGGCGGCAATGGCGTTTGGAAAAACCAACGAACCGGCGGCACGAGCGATAGTTGAAGCATT\nGTTTATAGATCCGGCTGATATCCGTACTCCTGATCATTTAACGCCAGAAGCTACAACTAA\nGTTTTTTAATTTTGACATGCTCAATACCAAATCTCCAAGTCTCCTTGTGGGTACACCAAG\nAATCGGAACGTATGAATGTGGACTTTTAATCGACGTTCGAACGGGACTTATAGGCGCGTC\nGTTGGACGTTCTTGTATGTGACAGGGACCCTTTAACTGGCACCCTAAATCCCCACCCTGC\nAGAAACCGACATTTCATTTTTTGAAATTAAATGTCGTGCTAAATACCTCTTTGATCCAGA\nTGACAAAAATAACCCGCTCGGTCGGACGTACACCACGTTAATAAATAGACCTACAATGGC\nAAATCTACGGGACTTTTTATATACTATAAAAAACCCATGTGTAAGCTTCTTTGGACCCTC\nAGCAAACCCAAGTACACGCGAGGCCTTAATAACGGATCACGTTGAATGGAAACGTTTAGG\nATTTAAAGGTGGGAGGGCCCTTACAGAACTCGACGCCCATCATTTGGGCCTCAATCGGAC\nAATCTCATCCCGAGTGTGGGTATTTAATGATCCGGACATACAAAAGGGGACAATTACAAC\nCATTGCATGGGCCACTGGAGATACGGCTCTTCAAATTCCTGTATTTGCCAATCCGCGGCA\nCGCTAACTTTAAACAAATTGCCGTACAAACCTATGTATTATCCGGTTACTTTCCAGCGCT\nAAAACTACGGCCCTTCCTTGTCACCTTTATAGGACGTGTGCGCCGACCACACGAGGTGGG\nAGTCCCATTGCGCGTCGATACACAAGCGGCTGCCATTTACGAATATAACTGGCCGACTAT\nCCCACCCCACTGTGCGGTTCCGGTTATAGCCGTTCTAACGCCTATCGAAGTTGATGTGCC\nTAGAGTGACACAAATACTTAAAGACACAGGAAACAACGCGATTACATCAGCATTGCGGTC\nATTGCGATGGGACAATCTTCATCCAGCGGTCGAGGAGGAATCTGTGGATTGTGCAAACGG\nTACAACGAGCTTGTTACGTGCAACGGAGAAACCGTTGCTTTGAACTCAGAGTTCTTTGAA\nGACTTTGACTTTGATGAGAATGTAACAGAGGACGCCGATAAATCCACACAACGCCGCCCA\nCGAGTGATCGATGTAACACCAAAACGAAAACCTTCGGGAAAGAGCTCCCATTCCAAATGC\nGCAAAATGTTAAACCCTGATAAACCCTGATAAACGTTCTAATAAAAACATCAAATCATGG\nTTGGTTACTGTGAATGTTTGTTTTATTGCTTGGGGGTTTACAAGTACAACCCACGCTACT\nCCCACCCACTGTTTGATCGCTCGTATAACAGCTCATCCTCACGGTCCGTTTCATATGTTG\nAGTCATTTTCATAGACGTAGCCGTAGCCTTGTGATGGGTAATTTGTGCGGCGAGAATTTC\nTATGTGCAGGTTTTACTTTTCGTATGTATCCCCGTACCCGCTCGGGTACTCTTCTTACGG\nCACCGTAGAACCGACTGCGTTTCTGTCGATGATACACATATGCACGCATCAATCTGAGAA\nGCAACATGACAACGGAAAACACGGCCAGGCAAGCCAAGGTTCCCCGAGTTGTGGGAATTA\nACCGTGGAGATTGAACCGATATAGGGTCATATAATCGGTCCATATACGAGTGCGCGGCGG\nTTCCCAACGTAGCACAGGCCACGAGCGTTCCCAGGGACGGTCCTATTAACACGTGTATAT\nAATGCGCCAAAATTAATTCTGATACTATAAGATATACAACTGACAATGTACTAAATGTAG\nACATGGCCACGGACACCGATGACCACAGTCCCGTATGTAGATGATTCGCCACCACAAGTT\nCCAGCATTAATGATACAAATAGGATACATATCGCCATCAACGCAGCCATCAAATTCACGA\nACACTGCGCGCGTAGGCCCCGCAAGGCGATATAAAAAGACGCTCTGCTGTCGTAAATTTG\nCGACCGCTTTTATGTTCGTTTCGTCCAATTTTCCGCGTCCACAAAAATACGTTGTAAATA\nTTACACTTGTCGCAAAATGTCCAAGATATAATGTAGCAGCCACGCCGATTTGCTTGTAAG\nCTAATAATAACACAACGGCGTTTAATAACCACAATGACAAAAGACCCCAAAAAAGTGTTG\nTGGGATCTACAACTAACCATGCAACACCGGAGCTTTGCCGGACACGTTGATTTTTCGTTT\nCTCGGTGTATAATCGCGGCCGTGATCAGTGTATATACCGCCATGGCCATTGCCGTTAAAG\nCCGTGTAGTAAGTAAATGCCACAACGCTATGTGGTTCCAAAAACAAAACCGGGGCGCTGT\nATCCACCTCTATTTCCGGACCATACCCCCCCATCTAGGGTGGCGTTAAATAACTCATAAT\nCAACTACGGCAGCATAAAAACAAGGGATCCCGGTATATTCAGAAGAGGCGGCAATTAACG\nTAGCCAGGAGCATTACCGCACCCAAAGTGAACATCATCACCTGAATTATCCAAATTCGCC\nAATTAAGCGTATCCATTTGATGATCTAACGCTTCCACCTCGGGTGTCGTGGTGTCGTACG\nGTGAGACTTTTTCAGAACGCGGCCCCTTCTTTTGAGTTCCCATGTCTCCCAACACCGGGG\nAGAGCAACGCCGCCGTCTATGCGTCCAGTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTCACAAACTCGCCCGGTAACCGTCGTACGTG\nCCCCTATGGGCTCTGGTAAAACAACAGCCTTGCTTGAGTGGCTTCAACACGCGTTAAAGG\nCAGATATTAGCGTACTGGTTGTCTCATGTCGCCGTAGCTTTACCCAGACGTTGATTCAAC\nGGTTTAACGATGCAGGCCTCTCCGGATTCGTAACATATTTGACATCCGAGACATATATTA\nTGGGTTTTAAACGTTTGATTGTGCAACTTGAAAGCCTACACCGCGTATCCAGCGAAGCTA\nTCGACAGCTACGACGTATTAATACTGGATGAGGTAATGTCAGTGATTGGACAATTATACT\nCCCCCACAATGAGACGTCTTTCCGCGGTTGATAGCCTATTATATCGTCTTTTAAATCGCT\nGTTCTCAAATTATCGCGATGGATGCTACAGTAAACTCTCAGTTTATTGATTTAATCTCCG\nGATTGCGTGGAGATGAAAACATACACACAATTGTGTGTACATACGCGGGAGTTGGGTTCT\nCCGGAAGAACTTGCACGATCCTGCGTGATATGGGCATCGACACGCTTGTGCGAGTCATTA\nAACGATCTCCTGAACACGAGGATGTACGTACCATACACCAACTACGTGGAACATTTTTTG\nACGAACTAGCACTACGATTACAATGTGGGCATAACATCTGTATATTTTCATCAACTTTAT\nCGTTTTCGGAGCTAGTTGCTCAGTTTTGTGCAATATTTACAGACTCTATTCTTATTTTAA\nACTCAACTCGGCCCCTATGTAATGTAAACGAATGGAAACATTTTCGCGTGTTGGTGTACA\nCTACCGTCGTGACCGTTGGATTGAGTTTTGACATGGCTCATTTTCATAGCATGTTTGCTT\nACATAAAGCCAATGTCATATGGGCCGGATATGGTATCGGTCTACCAATCATTAGGGCGTG\nTACGGTTATTGCTACTTAATGAAGTTTTGATGTACGTCGATGGCTCAAGGACCAGATGCG\nGACCCCTGTTCTCGCCAATGTTACTAAACTTTACCATCGCAAATAAATTTCAATGGTTTC\nCTACACACACCCAAATAACTAACAAACTGTGCTGTGCATTTAGGCAACGATGTGCAAATG\nCATTTACACGCTCGAACACCCATCTCTTCTCAAGATTTAAATACAAACACCTTTTCGAGA\nGATGCTCTCTTTGGAGTTTAGCCGATAGCATTAATATCTTACAAACTCTTTTGGCCTCTA\nACCAAATTTTGGTTGTATTGGATGGCATGGGTCCAATAACGGACGTTTCCCCAGTTCAAT\nTTTGTGCATTTATACACGATCTCAGACATAGCGCTAACGCCGTAGCTTCCTGTATGCGTT\nCTCTTAGACAGGACAATGACAGCTGCTTGACCGATTTTGGCCCTTCCGGATTTATGGCCG\nATAACATTACCGCGTTTATGGAAAAGTATCTTATGGAGTCAATTAATACCGAAGAACAAA\nTTAAAGTATTTAAAGCCCTTGCATGTCCAATAGAACAGCCTAGACTAGTCAATACGGCAA\nTATTGGGGGCGTGTATACGAATACCTGAAGCGTTGGAAGCATTTGACGTATTTCAAAAAA\nTATACACGCACTACGCTTCCGGTTGGTTTCCCGTCCTGGACAAAACCGGGGAATTTAGCA\nTCGCGACTATAACTACCGCCCCAAATTTAACCACACATTGGGAGCTGTTTCGCCGTTGTG\nCCTATATTGCAAAAACACTCAAGTGGAATCCGTCCACCGAAGGCTGTGTAACACAAGTTT\nTGGATACGGACATTAATACACTTTTCAATCAACACGGGGATTCGCTGGCTCAACTAATAT\nTTGAGGTTATGCGCTGTAACGTTACCGACGCTAAGATTATNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNGCTTATGAGCCATCGCCATTCGTTCTCCCAACAGCGTTACAAAATTACTG\nCCCCCGCTTGGGCACGCCACGTGTATTTTCAAGCACATCAAATGCACTTGGCCCCGCATG\nCCGAAGCCATGCTACAATTAGCGCTATCGGAACTGTCCCCGGGATCGTGGCCGCGGATAA\nACGGGGCGGTAAATTTTGAAAGTTTATAACCCATTAATACCATATATGGACATCCATAGG\nGGGGGTTACATAAATACTAAGCCTCTGTACAACACAAAGGGCCTCTAACAATGCACTGAA\nCCACAACCAAGCTATGGACGCAACGCAGATTACCTTGGTTAGAGAAAGCGGACACATTTG\nTGCCGCAAGCATATACACATCCTGGACACAGTCCGGACAATTAACACAGAACGGTCTTTC\nCGTGTTATACTACTTATTATGCAAAAACTCATGTGGGAAATACGTCCCTAAGTTTGCCGA\nAATTACCGTACAACAAGAGGATTTATGTCGCTACTCCAGGCATGGGGGGAGTGTTTCTGC\nGGCAACGTTTGCGTCTATCTGCAGGGCGGCGTCCTCGGCTGCGTTAGACGCCTGGCCCCT\nTGAACCACTGGGTAACGCAGACACCTGGCGGTGTCTCCATGGCACTGCCCTGGCCNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCGTTGCATCTTC\nCCTTTCAATATTAGCGGCATGTGGACTGTGGTACGCGGCGGCGTTTGGAAAACCCGGGGT\nTGTCCGTCCAATCTTTGCGTATTTAGGCCCGGAACTCAATCCGAAGGGTGAAGACAGAGA\nCTACTTTTGTACTGTCGGATTTCCCGGATGGACCACTCTTCGGACACAAACTCCAGCCGT\nCGAATCTATTCGCACGGCTACGGAGATGTACATGGAAACGGATGGGTTGTGGCCAGTAAC\nCGGTATTCAGGCCTTTCATTATCTAGCCCCCTGGGGACAGCATCCCCCCTTACCTCCGCG\nGGTGCAGGATCTTATTGGGCAAATCCCTCAAGATACTGGACATGCAGATGNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCGCCATGGA\nACCGGTACTCCGGGTCGAGGGTGTGTACACTCACGCATTTACCTGGTGTACCACGGGAAG\nCTGGCTGTGGAATTTACAAACAAACACGCCTCCGGATTTAGTTGGCGTGCCATGGCGAAG\nTCAGGCGGCGCGAGATTTAAAGGAGCGTCTTTCAGGACTCCTATGTACCGCAACAAAAAT\nTCGAGAACAGATACAGGAAAATTGCATATGGGACCATGTCCTATACGACATATGGGCCGG\nACAAGTTGTGGAGGCTGCCAGAAAAACATACGTCGATTTTTTTGAACATGTTTTTGATCG\nCCGTTATACTCCGGTATACTGGAGTCTTCAGGAGCAAAATTCGGAAACAAAAGCAATACC\nGGCATCTTATCTGACATACGGACACATGCAAGATAAGGATTATAAACCAAGACAGATAAT\nTATGGTTCGTAATCCCAACCCACATGGACCTCCTACTGTTGTTTACTGGGAATTGCTACC\nATCGTGTGCCTGTATTCCCCCCATAGACTGCGCTGCTCATCTCAAGCCCCTTATACACAC\nGTTTGTCACTATTATTAACCATCTTCTAGATGCTCATAATGATTTTTCAAGTCCATCATT\nGAAATTTACTGACGATCCCCTTGCTTCATATAACTTCTTGTTTTTATGACAAAAAAACAC\nGCCGCAACAACCCATCCTTAAAATAAAAGGTTTATTTNNNNNNNNNNCCGTGGTGAATTT\nTTATACGTTTCAAATAACTGAACATTTTTCGGTGTTACCATGGTGCGATTTAACCACCAA\nAAATATACGCTCTTCTGATATTCCGAATCTCGTAAAGGTCCATTTAACAATCCCGGGGGC\nACTTGCACCACACCATCTGGACAGGGGGGGGTTCCGTGGGGCAGGTCAAAACGCTGACCC\nACCCCACATGAATATATAGCCTTTATAATATTGGGGGCCGTTCCAGGCTGAGGGTTCAGT\nAACTTAACAAACATATAATGCGGCAATACGCGGGTTTTTGTAAAGGGGTTGTTATCAACG\nACATACATTAGAGTGTTTAACAACCATAAAACTCCCTCATATAAAAACCGACGCATTTTT\nTCCAAAGGTCCTATTTGACACTCAACGCGTCTAAGATATACAGACAATTGTACAAACAGC\nGATGGAGATGCCCCGGAGGGCCCAATGCCTTCCAGATACATTAAAATAACACATAAGGTA\nAAATCTAAAACATTATCCGGGCGGAATAGAGTCATCCGATAGATTAACAGGCGCGGAGGC\nACCCCCACCGTATACACCCTATCTTCAACCGCAGTTAATACGGAAAAAATAAATCCGCGG\nAACGCTGGTTGAGTAACACACTCCATGTAGTAACGATCACAGGACACCTCACTTGAATCA\nCCATTCAACACTACTAAAACGGTCTCTTGGTGTTCCGGTTTTACGCGCAGTGATACAACA\nGAGTTTGCCAAAAAGCGTGGCTTCAAACCGGTTACCTCCCGCGCCTCGCATACGAATCTT\nGGTATTGCTTGTATTCTAAGATCTTCGATCACGTCGCTCACATCCAACCCCTCTTCGGCT\nCGTGTTAGTAAGTTGTCGATCGTTACGCTGCAACCTAAAATGCTGGGTATATTTATTCCG\nGACATCCCATCGGCCATCCCCGCGCCTCCGGTTTGCTCGAATTTTATCCAGTAAGGTCGA\nATCCGCTGCATTTACCTTGTGTACCCGTAACCTCTCAGGGGGGTGTCCTTTCATAAAATG\nGGATAGGTTTTTATATCCAACATGCATGTATTGGTTATTTATTTTATTGGGTTCCGGGAT\nTCTTTCGTCATCTTCTGTAGGGTCAGGCAAACCCCAGGAAGGACTTGGCGTTCTCCGTGG\nGCCCCGTTTTATTACCTCTGCGCGAACCTGCATTTCATATAATATTCGGATTTGGGATAA\nATAGGACTCTGTTCTCGCCTTTTTAAAAATAGCCTGGCATAACTCTTCCTCTGACCTATG\nTACCTCGCTTTGAGTTACCAAGAATCCTAATCGGGTGGCCCGTAATATGAATGAAAAATA\nCGGCGCAACTAGTAATGAGATTGACGCATTTGAATATGATACAGAAATTTCCTGGCCTTG\nATTATTGTTTACCCGGTGAAGCTTAAAACAGCGAACAAGTTCCTGTTTCCATAGCTCAGA\nCAAACGTGTTATATCATCTCCATAAGGGGGGATATAACGAGATTGAAAACTATTGGCAAT\nATATGCATCATCCCCTATTATGCCGGTAAGATCTATAACCTCGTGATTTAAATCGGCAAT\nACGTGTTTCTTCTGCCATTGTAATATGTGACCCTTTAGATGGCTTTATTTTTACCCTCTC\nTTCCCGTAACCGTTTCAGCTCTCCTTCTTTGAACTGGAGCCTTTCGGTCAGATCGCTGTT\nCACATCCTTGAGACCCTCAATGGTTTTGAATAAATTATTCACATAACCCTCGAGCATGCC\nGTTGATACTGTTAACCACCGATGTTTTAAACGCACTTTGAACGTTTGTTGTTCCGGACAT\nTGCCCCCCCGTTAAAGGATTGGTTGGCCTTGCCAAACCCCGGTTGTGATGTGTCCACCGA\nTCCACTTCCTTCCAGAATGTGATTGCCCGTTTCTTCTAGATAGGAACGTACGGTTTCGGT\nAATATCTCCAACATGTCTCATGTTTTTTAAGTTAACTATTAGCTTTACAAGTCTAGACGC\nGGCCGATCCAGCCCGTGTTGTATCGTTCTCGCCCATTATACGATCAACCGCACGTGTGCT\nGTGAGATCTATCATCTTCATTCCGGCGACCTATTAACACGCGCAAAGGGGCTGTATTTAA\nAACTTGGCAGACGCGAGCATGTTCACGTAATGCATAACAGGCCAACACCTCCCCAGAAAG\nCCGCTGTAAGGGTGAGTCAAATACTACACCCTCCCCACATACAACGGGCGGCCACACGAC\nCAAACACTCTCCCTTCATGCCCGTTACATCATCCTTTGCCATAATTAATCTTCGGTTATA\nATTATAATAAAGACGCGTCCTATCATAATCCATAATAGCAACATTTTGCATACACTCAAC\nTAGGCTTGTGACAACCGCCGCCCCTCTGGCCAACGTTGCATCGGCAACTTTTAACATCTG\nGGACAGTTCTGCCGCTTGACTCATATACGTATTTAATGGTGCAGGGGTTCCATCCTGTTC\nTGATCGTACCTTTCTTACAACGGGCACAATACCTACACAGGCTATCCAGTCCACGTATTT\nGGCAAAACCGACCCTTCCATTTAAACCACTGGTATAGAGACAACCGGTTATTCCACGCAG\nAAACTCAAGTAACGATGACTGTAATGTTTGACGCCAGGTTTCAAAAACCTGATGTGCAAG\nCCGTACGGCTTCTGATTCTCCACATAACCCATAACGTTCCGCTAGAGCCCCGGCATGCAG\nGTTACATTGTTGGATGTGGTGTTCCCAATCTGCTGCTAGGTCCTCATACCGAGTTGCATC\nCAACGCGTTCATCAAAACGGTTGCCTGAACTTGGCGAATTACAGTTTCCGTAGACCGTAC\nAGCGCTATATATGCCTTGTCCATCGGTATATCCAAAGTCACCGGCTAGGATTTTTCGAAA\nCAACATACTTTGCGTGGTTGGGTGTATTAACATCCAGCCATCTTCCTCCGGAAATGTACA\nAAACCCTATATCCGGGGCGTACTCATTCCAGTATATATCGAACATGTTCTTGTATTGGTC\nATTTGGGTTACTTCCATTCAAGCCCTGGTCAATAGAAACAGAACTTGCTATCCTTTTTTC\nTTCACTACCGGAACTGTTATTAAAAAGAGACGTTATTTCGGCCATTGAAAACCACGATGA\nAAAGATCAATTTCTGTAGACAGTTCTTCACCCAAAAACGTTTTTAATCCAGAGACGCCCA\nATGGATTTGATGACAGTGTATATTTAAACTTCACCTCTATGCATAGCATTCAACCTATCC\nTCTCACGGATTCGAGAACTTGCCGCAATTACGATTCCAAAAGAACGTGTTCCGCGGTTGT\nGTTGGTTTAAACAGTTACTCGAACTGCAAGCGCCTCCTGAAATGCAGAGGAATGAGCTCC\nCCTTCTCCGTTTATTTAATTAGCGGAAATGCCGGCTCCGGAAAAAGCACGTGTATCCAAA\nCGCTTAACGAAGCTATCGATTGCATTATTACCGGATCCACCAGGGTTGCTGCCCAAAATG\nTTCATGCTAAGTTATCAACGGCTTATGCGAGTCGTCCGATAAACACAATCTTTCATGAAT\nTTGGTTTTCGCGGAAATCACATTCAGGCTCAGCTGGGCCGTTACGCATATAACTGGACTA\nCGACCCCCCCTTCTATTGAGGACCTGCAAAAAAGAGATATTGTATACTACTGGGAAGTTT\nTAATTGATATAACAAAACGAGTGTTTCAAATGGGGGACGACGGTCGCGGAGGAACATCGA\nCATTTAAAACCCTGTGGGCAATTGAACGTTTGCTTAATAAACCTACAGGCTCAATGTCCG\nGAACCGCGTTTATCGCATGCGGTTCCCTTCCGGCTTTTACCCGGAGCAACGTTATTGTTA\nTTGATGAAGCAGGATTGCTAGGGCGTCATATTCTCACGGCCGTTGTTTACTGTTGGTGGC\nTTTTGAATGCTATATATCAAAGCCCTCAGTACATAAACGGTCGAAAACCGGTCATAGTAT\nGCGTCGGTTCGCCCACCCAAACTGACTCGTTAGAATCTCATTTTCAACATGACATGCAGC\nGTTCACACGTAACTCCTAGTGAAAATATACTCACGTATATAATCTGCAATCAAACTCTGC\nGTCAATATACTAACATCTCACATAACTGGGCAATCTTTATTAATAACAAACGATGTCAAG\nAGGACGATTTTGGAAATCTTTTAAAAACGCTTGAGTACGGGCTACCTATTACCGAAGCAC\nATGCGCGTCTGGTCGATACATTTGTTGTACCTGCATCCTATATTAACAATCCTGCTAATC\nTTCCCGGATGGACGCGTCTGTATTCGTCGCATAAGGAGGTGAGCGCGTATATGAGTAAGT\nTACACGCGCATTTAAAACTATCGAAAAATGACCATTTTTCTGTGTTTGCCTTACCGACTT\nATACATTCATCCGGCTAACGGCATTTGATGAATACCGCAAATTAACGGGACAACCCGGAC\nTTTCTGTTGAACATTGGATACGGGCAAACTCCGGTCGTTTGCACAATTATTCCCAAAGCC\nGAGATCATGACATGGGAACAGTTAAATACGAAACACATTCAAATCGCGACTTAATTGTAG\nCCCGTACAGACATCACTTACGTGCTAAATAGTCTCGTAGTTGTAACCACAAGACTACGTA\nAGTTAGTTATTGGATTCAGTGGTACATTTCAATCGTTTGCAAAGGTTTTACGTGACGACT\nCCTTTGTGAAGGCTCGAGGAGAGACATCCATCGAATATGCTTACCGGTTTCTGTCAAACC\nTAATCTTTGGAGGCTTGATTAACTTTTACAATTTTTTGTTAAATAAAAACCTACATCCCG\nATAAGGTATCGTTAGCATACAAACGGTTAGCTGCCTTAACCCTGGAGTTATTGTCTGGAA\nCAAACAAAGCCCCCTTACACGAAGCAGCGGTTAATGGGGCGGGTGCCGGGATTGACNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNCCTTCTGCTTTACCAGAGCCCCCGAGTCCAAAG\nTAACGGCCTCCATACCCGAAGACCCGGATGATGTAATTTTTACGGCACTTAACGACGAGG\nTTATTGACTTGGTATACTGCCAGTACGAATTTTCCTATCCCAAATCATCCAATGAGGTCC\nATGCTCAGTTTCTGTTAATGAAAGCTATTTACGATGGTCGATATGCCATATTAGCAGAGC\nTTTTCGAAAGCAGCTTTACAACCGCCCCCTTTAGCGCGTATGTCGATAATGTTAATTTCA\nACGGAAGCGAGCTTTTGATCGGCAATGTGCGGGGGGGGCTGTTATCTTTGGCATTACAAA\nCAGATACGTATACCCTTTTGGGGTATACTTTTGCACCCGTGCCAGTCTTTGTAGAGGAAC\nTGACCCGAAAAAAGCTGTACCGCGAAACTACCGAAATGTTATATGCTCTACACGTACCTC\nTTATGGTCTTACAGGATCAACATGGGTTTGTGTCCATCGTAAACGCTAACGTATGTGAAT\nTTACCGAGTCTATAGAGGATGCAGAATTGGCAATGGCCACCACGGTGGACTATGGCCTTA\nGTTCTAAACTAGCCATGACAATTGCACGCTCACAGGGTCTGAGTTTAGAGAAGGTAGCTA\nTCTGTTTTACGGCGGATAAACTGCGCCTAAATAGTGTGTATGTTGCCATGTCGCGTACGG\nTCTCCTCTAGGTTCTTAAAAATGAATCTAAACCCTCTACGGGAACGATATGAAAAATCCG\nCAGAAATTAGCGATCACATTCTTGCCGCTCTACGTGATCCCAACGTACACGTTGTGTATT\nAAAGCATTGTATAAAAACACGCATGCGGGCTTGCTGTTCTCATTTCTAGGTTTTGTCTTA\nAATACACCCGCCATGAGCATCTCTGGACCCCCAACGACGTTTATTTTATATAGGTTACAT\nGGGGTTAGGCGGGTTCTTCACTGGACTTTACCGGATCATGAACAAACACTCTACGCATTT\nACGGGCGGGTCAAGATCAATGGCGGTGAAGACGGACGCTCGATGTGATACAATGAGCGGT\nGGTATGATCGTCCTTCAACACACCCATACAGTGACCCTGCTAACCATAGACTGTTCTACT\nGACTTTTCATCATACGCATTTACGCACCGGGATTTCCACTTACAGGACAAACCCCACGCA\nACATTTGCGATGCCGTTTATGTCCTGGGTCGGTTCTGACCCAACATCTCAGCTGTACAGT\nAATGTGGGGGGGGTACTATCCGTAATAACGGAAGATGACCTATCCATGTGTATCTCAATT\nGTTATATACGGTTTACGGGTAAACAGACCTGACGATCAGACCACACCAACACCAACCCCG\nCACCAGTATACATCGCAAAGGCGGCAGCCTGAAACCAACTGTCCTTCTTCACCACAACCG\nGCCTTTTTCACATCAGACGACGACGTTCTTTCGTTAATATTACGGGACGCCGCAAACGCG\nTAAAGACAGATTCAAGACTAACATTTATCCCAACTGATTACATTTCATACGCGAATAAAC\nGACACAAAAAATTTATATTTAACGGCTTTTAATTTGAAGACACCTATCCTCTTAACGTTG\nATGAGCCTTGCAGGTTGGGTGCCGCGCTTCACCGGTATTATACATAACCGATTTACCGTG\nTTTACGGCAGTCTGACCATTTACCAGTGTATGTCTGTAATACGACGTTGTTGTGTCCCGA\nCAAAATTAACTCGCGTACAAATTTCTGATGTTCCCCCGGCGTGGCAACGCTGGCATTTCC\nAAACACATTACGTTCTCGTACGTCCATGACCGCTATTTTCAGTATTAATTGGTTGGTCGG\nTCAAAGTATTTTCCTTATGTAAAAGGACACGATCTAAAGCCGTAAACTCGTACACAAACA\nCTGGTACCAACGGACGCGATTTTCCGTCCGTTGAGCGGGTGTAATATCGGCGAGGTCTTC\nTTGCACGAATACTCTCGTACAGTAGGTTTCTGACACGGGGTGCATGGGTTTTTTGACACA\nACACAAACATTTGCAGGCTCTTATGACTGGATGGATTGAATTTATTTTTAGATAGGGTCA\nCGTGTTTTTGTCGTGACACGCCTCGACCAGAAAAGGCTGCGGTTTTCGTACACGCGACCG\nTTATTTCACAGGCGTTCATAACCAAGCTGCGGCGGATGGTGTCGGTTAATTGTCTCCGCC\nCAAGTTCGTCAATAGATGATACCATGAACAACGTATCAAATGGTACATAGTCGTCTTTGG\nTTTTCTCAATACAGCCCGCGTGCCCAATCGGAAAATTTTCATTTGCATCAACGCTATTTT\nCTGTAAAATCGTTCTGAACACTGTGTTGGCTGGCTACCTGTTTAAAATTTGGGATCGAAC\nACGGTCCACGATGCAATCCCCAACCCCATTGAAGCAATGCCGTCGGTACGGAAGGAGGCA\nACTCCGAAAACATTATGGTACGCAAGAGGGTCGATTGGAGTGTTATATAACACTCCAATC\nGATCTCGGGTTCGCCTTTACGCGTAAAATACTCATTGGCTTGAACGAAATGTCGACAATT\nCCGAAATGGAACACGGGACAATGGCGACGGATGCGCGTGTGTTAGCACCAGATGACATCT\nTGAATTCGGTTGGGTTGTCTTCTGTGCATGCGCACCCCACAGCATAAAAACTAACCCTGT\nACGGTTCTCGCATAACCTCTGTAGCACGCGTTGCACCAGCCGCCCCCAGCCTAAGTATAC\nATGCGACCCCGGAGTCCCGCGACGAACCGTAAGCGTGGTATTCAGCAATAACACCCCCTG\nCCTTGCCCAACTCTCCAGGCATCCGTGAGTGGGCGGAGTCATATTTGGGTATGATTCCAT\nGAGGGCCGCAAAAATATTTTTAAGACTAGACGGTGGTGTTATGCCACGTTTTACACTAAA\nCGCTAGCCCATGTGCATGTCCCGCGGTAGGGTATGGATCTTGACCAATAATTACAACGCG\nAATGCTCTGGGGTCCGCAAAATCGCGTCCATGCAAAAATATCGCCTGTAGATGGAAGTAT\nTTCTTCCCCTGAATTTAAAAGACGATTGTATTCTAAAAAAATACCTTTCGCGTACGGCTC\nTTTAAGTTCGTCCGACAACAGGTCATACCACTCAGGGGAAATGTTAAACTTGCTGAAAAC\nTTCAACCGAATCCAGTTGCGAAGAGACGGGGGTGAACGTTTCCGTGTCGTAATGATGTGA\nCATGTTATTTAACTTGAAGGTTGGGGGGTCTAGCTTAACCCCCAAAGGCAGCCCGCGGGG\nTCGCTTGCGGGTTTTTTTGGTAACCGGATGGGCCAAAACATAAATGTCCTTTGAATCCGA\nTAGTTTCATTTCATTGGCATACGCGTTGGAACAAACGGTCGGCTCCCCAGACACATCCAT\nTTTCCGGGATATTTGTGGAAGATGGAGTAGAGTCTACCCATACACCGGAAAGGGCATCCA\nACAAAGCATCGCGTATGTCCCCGCTTTTATGTTCTTCACCAACAGATTGTGCCAGCCCCT\nTTAAGGTGACGTATGGATTTGTCCAGTACGCCATTTGTTTGTCTTTAAACCAAAGTATAA\nCTTCCGGTACTGGACATTTTGTCTTAACCACGATTCCCGATAGCGCCTCGCTGAGGTTTG\nATACAGGGGGTGCCGCATAGTCCCACGCCTCATATACCGATGACACGCACGGTTCCGTTA\nTAATCAAACTCACATCCGATAGCGGTTTGGCTCCAAAAAACAACGGAGTGTCGTCTTGGA\nGATGAAGACAATACGCGATTGTGATAGTTTTTAAAAAAACTATCTGCAGTAACCATTTAT\nGTGATGCCATGACGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNTTCCTAAAAAGGGCGATCTTAATATGTCAAACGT\nCACGGCGTGCCGACAAAGCGAATTTCCATGCAAGATTTGGATGTAGTATTTATACACCCA\nATCACATGTCACGTATTAAGCTTTACAGTCCCCCGTTATCTGATATAATCACTTTTCTTA\nACACGTCATCGGGAAAACAGATGTTTATATTATACCTCTCGCGGTCATTTATGGCAAATA\nCTTAGACCGTTTTCAAGCGGACTGAAAACGCTCAAATTGCCTTTTGGAGGCCTGCCCAAC\nGGCCATTATCCCTTGGATCTGAGATTGATTTGCGGTAACGTTTGCCAANNNNNNNNNNNN\nNNNNNNNNNNNNACTGAAAACGCTCAAATTGCCTTTTGGAGGCCTGCCCAACGGCCATTA\nTCCCTTGGATCTGAGATTGATTTGCGGTAACGTTTGCCAAACCCACGCATTTCAGTTTAA\nATATTTCTAAGCATTCTTAGTGCGTACTTGGCAGCGTGCTTAAAATATCAACCAATATCC\nATTATGCTACACGTTTCCTTCTATCCGTTTCAATCCATTAAAAGTCCATTAACAAAAATG\nATGCATCATACCTAATTCACCTAAAAACCTGACTCATTGCAGCAGCGTTTCCTCCTTGCA\nGACTATCCAGTTGGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTATGTT\nTATTGTATTTGCAGAGCAGGATGCCCCGGTTACTCCGAGACCGGATTGCGGGCATTCCGA\nATCGTGTACGGACTTACCAGGGGGCAGTATTTACACCTTGGGTTCCAGATATACCAACCC\nTTACGACCAATAGCAACACTCAGGTATTTTTAAAATGCACGTTTAATGATCATAATTTAC\nATACAGTTGGTAATAAAGCAGACTGTGGATGTTTAAGGCATTTCCTTCCCCCTCCCAACA\nAACTAGGACTTCTTCATCTTGTTTGGAATACCTTTACCCGCTTTACCGGCAGAGCTTTTT\nTTGGTAAGGTGTTTCAGTGAACCTGATGTTGATCCGGAGGTGGAGGGGGTATTGGACTCC\nCCCTGTGGAGAGGCAACTTTGCGGGTTTTACTTCCCTTACATGCCGAATCAGACTCAGAT\nGTCAGGTCTATTGTTAAGCATCGTTTAACGTCTCTGCCGGTATGAAATAAACGGCGCTTA\nGCACCCCTTGCGCTTCCCGGTTTAATCCCCGGTAACACAGAAAAAAGCCTGACTTTTTGG\nGGTGTATTTACCAATCGGGTATCCCTTTCATCGCCACGAGAGGTCTCCCCGGTTGAGGTG\nGTTTCTGGTCTTACAATTGGACCTGTAATTAGTTGGATGGCTGTATCTTTCCAGGTCCAG\nGTTTGCATGGTTAGGCGGGTTGGATCGGTACATCGATCCAACAAGAATAACATGTTTGTT\nACAAACGGTCCTGTTGAATCATGCAAAAGACAACGCAGGGATGTTTTTAATCCCGCCTCA\nTCACGCCCGTAAATACCTATATAGTTTAATATCAACATTTTTGTAGGCTCTACAATTTCG\nGGTTGATACAGTTCCGCAAGTTGATCATCAAGCCATCCGAGTAAAGGTTGCATGTAACAC\nGGGAATCTCGCGTTTCCCTCTGTTCCTCTATCCGTGGCTCGAAAAGGCAGTCTGTCCATG\nGTTCGTGGGTCTTGATTAATTCCCACAGATACTGGACGATCACGGTAGTCCTGCCCCCCG\nGTCCGGGGTTGCTGTGCAGATTCAATCGAGCCATACACCACCGGGGTCGCCGATCGAACA\nGCAGGTTGGTCTTTAAAAAATACCTTCCGTAAAAATGATGCGGTAGAGCATGTTTTGGTT\nACACCAGGGCTCGAGTCTCGGGTCGGTGGTTGTATAGAATCCTGTTGAGAGTCACTTGGT\nGACTCTGCTGTGGGCTCTCTAGCCGACGATTGAAGGGGCCCAGGGTTTGGTGATTGAATG\nGGCTCCCGACTCGATCTTGATGTTGGCTGTTGGATGGACTCCCGACTCGGTCCTGGGCTT\nGGTGGCAGAAGATCTATGACATCTCCCGGTAGGATGTCGATGGAATCTTCAAATGACGGC\nTCAGAAAAACCATCGTCGTCGGATGGGTGCACTTCATATTCCTTGTAACTTGTATCACTT\nACGATCTTATGCAGGATGGATTGCACTGGACACCGGCAGAGAGGACACTGGACGCTGGTG\nGAGGTCCATGCCCGAATACAAACAAAGCAGAAGTCGTGCAAACACGGCATGGTTTTTCCG\nAGATCGGAAACGGTGCTCATGCATATGGTGCAGGTATTATCCGAAGCGTCGGAGGTGCCG\nCTACCGCCCGCTAATATGGTATCCATGGTAACAACTGGCTGTATTCTAATGTCCGGGCAT\nCCAAACACGTAGCAGAACTGCCATGCGTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNN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N\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNGTTTTTGGTTCATTAACACTATCAACATAAGTCGGGGTATACAAGTATAATG\nAACGACGTTGATGCAACAGACACCTTTGTTGGACAAGGAAAGTTCCGTGGCGCCATCTCA\nACATCACCGTCACATATTATGCAAACATGTGGGTTTATACAACAGATGTTTCCAGTTGAA\nATGTCGCCCGGCATAGAATCTGAGGATGATCCCAATTATGACGTTAACATGGATATACAG\nTCTTTTAATATATTTGATGGTGTCCACGAAACTGAAGCCGAAGCCTCTGTGGCATTGTGT\nGCAGAAGCACGCGTTGGAATTAATAAAGCGGGATTTGTAATATTAAAAACGTTTACACCA\nGGGGCGGAAGGTTTTGCGTTTGCGTGTATGGACAGTAAAACATGTGAACATGTGGTCATT\nAAAGCGGGTCAACGTCAAGGAACGGCCACCGAGGCAACCGTGTTAAGAGCGTTAACCCAC\nCCATCCGTTATACAGCTTAAAGGAACGTTTACGTATAACAAAATGACATGTCTTATATTA\nCCACGTTACCGAACAGATTTATACTGCTATCTAGCTGCAAAGCGCAACCTCCCCATATGT\nGACATTTTAGCAATTCAGCGATCTGTATTACGCGCGTTACAGTATCTTCATAATAACAGT\nATTATTCACCGTGATATAAAATCTGAAAATATATTTATTAACCACCCAGGTGATGTTTGT\nGTGGGAGACTTTGGAGCAGCGTGTTTCCCCGTGGATATTAATGCCAACAGGTATTATGGC\nTGGGCTGGAACAATCGCCACAAACTCTCCTGAGTTATTGGCTAGAGATCCATATGGACCT\nGCCGTGGACATATGGAGTGCCGGGATTGTATTATTTGAAATGGCTACAGGACAGAACTCG\nTTATTTGAACGAGACGGTTTAGATGGCAATTGTGACAGTGAGCGTCAAATTAAACTTATT\nATACGACGATCTGGAACTCATCCCAATGAATTTCCCATTAACCCTACATCAAATCTTCGT\nCGACAATACATTGGTTTGGCAAAACGGTCTTCTCGAAAACCCGGATCCAGGCCATTGTGG\nACAAATCTATATGAGTTGCCAATTGATTTGGAGTATTTGATATGTAAGATGTTATCGTTT\nGACGCACGTCATCGACCATCGGCAGAGGTGTTGCTTAACCACTCTGTTTTCCAAACTCTT\nCCCGATCCATATCCAAATCCAATGGAAGTTGGAGATTAAAATTCATTAAGCCTGTTAATA\nAAATATTGTATAAATTGTGTTTATAACGTATAACCCGTTAAGGCAAATAGGGTACAAACG\nCGCAATGTTTTGAAATACTAATATAAATAACATAACCAATAGAAACTTAATACAGAGTCA\nCGCCCCATTACAACAAGGATAAAACACGGGATCATTTTCTTAACATTGTAGTAGCGCTGA\nAAAGCGTCCCCTCCCCCGGCTCACAGAGCTGCTCTTCGGTGTAGTTGGGTATACTGGTGC\nGCCTCATTTAATCGCGATGTTTTTAATCCAATGTTTGATATCGGCCGTTATATTTTACAT\nACAAGTGACCAACGCTTTGATCTTCAAGGGCGACCACGTGAGCTTGCAAGTTAACAGCAG\nTCTCACGTCTATCCTTATTCCCATGCAAAATGATAATTATACAGAGATAAAAGGACAGCT\nTGTCTTTATTGGAGAGCAACTACCTACCGGGACAAACTATAGCGGAACACTGGAACTGTT\nATACGCGGATACGGTGGCGTTTTGTTTCCGGTCAGTACAAGTAATAAGATACGACGGATG\nTCCCCGGATTAGAACGAGCGCTTTTATTTCGTGTAGGTACAAACATTCGTGGCATTATGG\nTAACTCAACGGATCGGATATCAACAGAGCCGGATGCTGGTGTAATGTTGAAAATTACCAA\nACCGGGAATAAATGATGCTGGTGTGTATGTACTTCTTGTTCGGTTAGACCATAGCAGATC\nCACCGATGGTTTTATTCTTGGTGTAAATGTATATACAGCGGGCTCGCATCACAACATTCA\nCGGGGTTATCTACACTTCTCCGTCTCTACAGAATGGATATTCTACAAGAGCCCTTTTTCA\nACAAGCTCGTTTGTGTGATTTACCCGCGACACCCAAAGGGTCCGGTACCTCCCTGTTTCA\nACATATGCTTGATCTTCGTGCCGGTAAATCGTTAGAGGATAACCCTTGGTTACATGAGGA\nCGTTGTTACGACAGAAACTAAGTCCGTTGTTAAGGAGGGGATAGAAAATCACGTATATCC\nAACGGATATGTCCACGTTACCCGAAAAGTCCCTTAATGATCCTCCAGAAAATCTACTTAT\nAATTATTCCTATAGTAGCGTCTGTCATGATCCTCACCGCCATGGTTATTGTTATTGTAAT\nAAGCGTTAAGCGACGTAGAATTAAAAAACATCCAATTTATCGCCCAAATACAAAAACAAG\nAAGGGGCATACAAAATGCGACACCAGAATCCGATGTGATGTTGGAGGCCGCCATTGCACA\nACTAGCAACGATTCGCGAAGAATCCCCCCCACATTCCGTTGTAAACCCGTTTGTTAAATA\nGAACTAATTATCCCGGATTTTATATTAAATAAACTATATGCGTTTTATTTAGCGTTTTGA\nTTACGCGTTGTGATATGAGGGGAAGGATTAAGAATCTCCTAACTATAAGTTAACACGCCC\nACATTTGGGCGGGGATGTTTTATGAAGCCTTAAAGGCCGAGCTGGTATACACGAGAGCAG\nTCCATGGTTTTAGACCTCGGGCGAATTGCGTGGTTTTAAGTGACTATATTCCGAGGGTCG\nCCTGTAATATGGGGACAGTTAATAAACCTGTGGTGGGGGTATTGATGGGGTTCGGAATTA\nTCACGGGAACGTTGCGTATAACGAATCCGGTCAGAGCATCCGTCTTGCGATACGATGATT\nTTCACATCGATGAAGACAAACTGGATACAAACTCCGTATATGAGCCTTACTACCATTCAG\nATCATGCGGAGTCTTCATGGGTAAATCGGGGAGAGTCTTCGCGAAAAGCGTACGATCATA\nACTCACCTTATATATGGCCACGTAATGATTATGATGGATTTTTAGAGAACGCACACGAAC\nACCATGGGGTGTATAATCAGGGCCGTGGTATCGATAGCGGGGAACGGTTAATGCAACCCA\nCACAAATGTCTGCACAGGAGGATCTTGGGGACGATACGGGCATCCACGTTATCCCTACGT\nTAAACGGCGATGACAGACATAAAATTGTAAATGTGGACCAACGTCAATACGGTGACGTGT\nTTAAAGGAGATCTTAATCCAAAACCCCAAGGCCAAAGACTCATTGAGGTGTCAGTGGAAG\nAAAATCACCCGTTTACTTTACGCGCACCGATTCAGCGGATTTATGGAGTCCGGTACACCG\nAGACTTGGAGCTTTTTGCCGTCATTAACCTGTACGGGAGACGCAGCGCCCGCCATCCAGC\nATATATGCTTAAAACATACAACATGCTTTCAAGACGTGGTGGTGGATGTGGATTGCGCGG\nAAAATACTAAAGAGGATCAGTTGGCCGAAATCAGTTACCGTTTTCAAGGTAAGAAGGAAG\nCGGACCAACCGTGGATTGTTGTAAACACGAGCACACTGTTTGATGAACTCGAATTAGACC\nCCCCCGAGATTGAACCGGGTGTCTTGAAAGTACTTCGGACAGAAAAACAATACTTGGGTG\nTGTACATTTGGAACATGCGCGGCTCCGATGGTACGTCTACCTACGCCACGTTTTTGGTCA\nCCTGGAAAGGGGATGAAAAAACAAGAAACCCTACGCCCGCAGTAACTCCTCAACCAAGAG\nGGGCTGAGTTTCATATGTGGAATTACCACTCGCATGTATTTTCAGTTGGGGATACGTTTA\nGCTTGGCAATGCATCTTCAGTATAAGATACATGAAGCGCCATTTGATTTGCTGTTAGAGT\nGGTTGTATGTCCCCATCGATCCTACATGTCAACCAATGCGGTTATATTCTACGTGTTTGT\nATCATCCCAACGCACCCCAATGCCTCTCTCATATGAATTCCGGTTGTACATTTACCTCGC\nCACATTTAGCCCAGCGTGTTGCAAGCACAGTGTATCAAAATTGTGAACATGCAGATAACT\nACACCGCATATTGTCTGGGAATATCTCATATGGAGCCTAGCTTTGGTCTAATCTTACACG\nACGGGGGCACCACGTTAAAGTTTGTAGATACACCCGAGAGTTTGTCGGGATTATACGTTT\nTTGTGGTGTATTTTAACGGGCATGTTGAAGCCGTAGCATACACTGTTGTATCCACAGTAG\nATCATTTTGTAAACGCAATTGAAGAGCGTGGATTTCCGCCAACGGCCGGTCAGCCACCGG\nCGACTACTAAACCCAAGGAAATTACCCCCGTAAACCCCGGAACGTCACCACTTCTACGAT\nATGCCGCATGGACCGGAGGGCTTGCAGCAGTAGTACTTTTATGTCTCGTAATATTTTTAA\nTCTGTACGGCTAAACGAATGAGGGTTAAAGCCTATAGGGTAGACAAGTCCCCGTATAACC\nAAAGCATGTATTACGCTGGCCTTCCAGTGGACGATTTCGAGGACTCGGAATCTACGGATA\nCGGAAGAAGAGTTTGGTAACGCGATTGGAGGGAGTCACGGGGGTTCGAGTTACACGGTGT\nATATAGATAAGACCCGGTGATCACCGAACCGGGGCAACGTCGAGCGTGTAAATTTAAATA\nAAAAACAGTACGCTTTTATCCGGTGTATGTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTGACAC\nCGGGACGGGCGGGTACCGCCGTTACGGGGAGCGTAGCGTCTCCCGTTCCGCATGTAGGCG\nAAGCCATGGCCACGGGGGAGGCCCTCTGGGCTCTCCCCCACGCGGCCGCGGCCGTGGCTA\nTGAGCCGTCGGTACGACCGGGCCCAAAAACACTTTATCCTACAGAGTCTCCGCAGAGCCT\nTTGCCAGCATGGCATACCCCGAGGCAACGGGCTCCAGTCCGGCGGCGCGGATCTCCCGCG\nGTCACCCTTCTCCAACAACCCCGGCCACACAGACTCCCGACCCTCAGCCGTCGGCCGCCG\nCACGCTCTCTTTCTGTGTGTCCACCGGATGATCGTTTACGAACTCCGCGCAAGCGCAAGT\nCCCAGCCAGTCGAGAGCAGAAGCCTCCTCGACAAGATTAGGGAGACACCCGTCGCGGACG\nCCCGGGTTGCAGACGATCATGTGGTTTCCAAGGCCAAGAGGCGGGTATCCGAGCCCGTGA\nCCATCACCTCGGGCCCTGTGGTGGATCCCCCCGCCGTAATAACGATGCCACTTGACGGAC\nCGGCCCCAAACGGGGGATTTCGGCGTATTCCCCGGGGGGCCCTGCATACCCCGGTCCCGT\nCGGACCAGGCTCGCAAGGCGTACTGTACCCCCGAAACCATCGCCCGTCTGGTCGACGACC\nCATTGTTTCCCACGGCCTGGCGCCCTGCGCTAAGCTTTGATCCCGGCGCCTTGGCGGAAA\nTCGCCGCTCGGCGTCCGGGCGGAGGAGACCGACGGTTTGGTCCACCCAGCGGAGTGGAGG\nCGCTGCGACGGAGGTGCGCCTGGATGCGGCAGATCCCAGACCCGGAGGATGTGAGGCTTC\nTGATCATCTACGATCCGTTGCCCGGAGAAGACATCAACGGCCCCCTCGAGAGCACCCTCG\nCGACAGATCCGGGACCGTCATGGAGTCCATCCCGAGGGGGACTGTCTGTGGTCCTGGCAG\nCCCTGAGTAACCGGTTGTGCCTGCCGAGCACTCATGCCTGGGCCGGGAACTGGACCGGCC\nCGCCGGACGTGTCCGCTTTGAACGCCCGGGGCGTTTTATTACTGTCGACCCGAGACCTGG\nCCTTTGCCGGGGCCGTCGAGTATCTAGGCTCGCGGTTGGCCTCTGCCCGGCGCCGGTTGC\nTGGTGTTGGACGCGGTGGCCCTCGAGAGGTGGCCCAGGGATGGACCCGCTTTGTCTCAGT\nATCACGTGTACGTCCGGGCCCCGGCGCGACCGGACGCCCAGGCCGTCGTCCGATGGCCAG\nACTCGGCGGTCACAGAAGGACTCGCCCGGGCCGTGTTTGCATCGTCGCGCACCTTTGGGC\nCAGCGAGTTTTGCTCGTATCGAGACTGCGTTTGCCAACCTGTACCCGGGCGAACAACCCC\nTGTGTTTGTGCCGCGGTGGGAACGTCGCATACACCGTGTGTACCCGCGCGGGCCCCAAGA\nCCCGCGTCCCCCTGTCGCCCCGTGAATACCGGCAGTACGTGCTGCCGGGTTTTGACGGTT\nGCAAGGACCTCGCGCGACAGTCTCGGGGTCTGGGGCTCGGGGCAGCCGACTTTGTGGACG\nAGGCGGCACATAGCCACCGCGCAGCAAACCGATGGGGCCTGGGTGCCGCGCTTCGACCCG\nTCTTCCTTCCCGAGGGACGGAGACCGGGGGCCGCCGGGCCGGAGGCCGGCGACGTACCCA\nCCTGGGCGAGGGTGTTTTGCCGCCACGCCCTGCTGGAACCCGACCCTGCCGCAG\n" }, { "path": "tests/input/TestOrderAndOrient/expected.hiv.big_indel.alternates.fasta", "content": ">gi|55139330|gb|AY772699.1|:1408-1768_option_0\nGGCACATAGCCAGAAATTGCAGAGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGG\nAAGGACACCAAATGAAAGATTGTACTGAGAGGCAGGCAAATTTTTTAGGGAAAATTTGGC\nCTTCCCACAAGGGGAGGCCAGGAAACTTCCTTCAGAACAGACCAGAACCAACAGCCCCAC\nCAGCAGAGAGCTTCAGGTTCGAGGAGACAACCTCCGCTCCGAAGCAGGAGCTGAAGGAGA\nGGGAACCCTTAACTTCCCTCAAATCACTCTTTGGCAGCGACCCCTTGTCTCAATAAAGGT\nAGGGGGTCAGATAAAGGAGGCTCTCTTAGACACAGGAGCAGATGATACAGTATTAGAAGA\nA\n>gi|55139330|gb|AY772699.1|:1408-1768_option_1\nGGCACATAGCCAGAAATTGCAGAGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGG\nAAGGACACCAAATGAAAGATTGTACTGAGAGGCAGGCAAATTTTTTAGGGAAAATTTGGC\nCTTCCCACAAGGGGAGGCCAGGAAACTTCCTTCAGAACAGACCAGAACCAACAGCCCCGA\nATTTCCTTCAGAGCAGACCAGAGCCAACAGCACCACCAGCAGAGAGCTTCAGGTTCGAGG\nAGACAACCTCCGCTCCGAAGCAGGAGCTGAAGGAGAGGGAACCCTTAACTTCCCTCAAAT\nCACTCTTTGGCAGCGACCCCTTGTCTCAATAAAGGTAGGGGGTCAGATAAAGGAGGCTCT\nCTTAGACACAGGAGCAGATGATACAGTATTAGAAGAA\n" }, { "path": "tests/input/TestOrderAndOrient/expected.hiv.big_indel.fasta", "content": ">gi|55139330|gb|AY772699.1|_contigs_ordered_and_oriented\nGGCCCTAAAAGAATTGTTAAATGTTTCAATTGTGGCAAGGAAGGGCACATAGCCAGAAAT\nTGCAGAGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAA\nGATTGTACTGAGAGGCAGGCAAATTTTTTAGGGAAAATTTGGCCTTCCCACAAGGGGAGG\nCCAGGAAACTTCCTTCAGAACAGACCAGAACCAACAGCCCCACCAGCAGAGAGCTTCAGG\nTTCGAGGAGACAACCTCCGCTCCGAAGCAGGAGCTGAAGGAGAGGGAACCCTTAACTTCC\nCTCAAATCACTCTTTGGCAGCGACCCCTTGTCTCAATAAAGGTAGGGGGTCAGATAAAGG\nAGGCTCTCTTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGAA\nAATGGAAACCAAAAATGATAGGAGGAATT\n" }, { "path": "tests/input/TestOrderAndOrient/expected.hiv.wrapped.fasta", "content": ">gi|55139330|gb|AY772699.1|_contigs_ordered_and_oriented\nAGGTTCCAGGAGACAACCCCCACTCCGAGGCAGGAACCGAAGGACAGGGAACCCTTAACT\nTCCCTCAAATCACTCTTTGGCAACGACCCCTTGTCTCAATAAAAGTAGGGGGCCAGGTAA\nAGGAGGCTCTCTTAGACACAGGAGCAGATGACACAGTATTAGAAGAAATAAATTTGCCAG\nGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTTTTATCAAAGTAAGACAATATG\nATCAAATACATATAGAAATTTGTGGGAAAAAAGCTATAGGCTCAGTATTAGTAGGGCCCA\nCACCTGTCAACATAATTGGAAGAAATATGTTGACTCAGCTTGGATGCACATTAAATTTTC\nCAATTAGTCCTATTGAAACTATACCAGTAAAACTGAAGCCAGGAATGGATGGGCCAAGGG\nTTAAACAATGGCCATTAACAGAAGAAAAAATAAAAGCATTAACAGCAATTTGTAAAGAAA\nTGGAGGAGGAAGGAAAAATTACAAAAATTGGGCCTGAAAATCCATATAACACTCCAATAT\nTTGCCATAAAAAAGAAGGACAGTACTAAGTGGAGAAAATTAGTAGATTTCAGGGAACTCA\nATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAATACCTCACCCAGCAGGGTTAA\nAAAAGAAAAAATCAGTGACAGTATTGGATGTGGGGGATGCATATTTTTCAGTTCCTTTAG\nATGAAAGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCAG\nGGATTAGATATCAATATAATGTGCTCCCACAGGGATGGAAAGGATCACCAGCAATATTCC\nAGTGTAGCATGACAAAAATCCTAGCGCCCTTTAGGGCAAAGAATCCAGACATAGTCATCT\nATCAATATATGGATGACTTGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAA\nAAATAGAGGAGCTAAGAGAACATCTATTGAAGTGGGGATTTACCACACCAGACAAGAAAC\nATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACTCCATCCTGACAAATGGACAG\nTACAGCCTATACAGCTGCCAGAAAAGGAGAGCTGGACTGTCAATGATATACAGAAGCTAG\nTGGGAAAATTAAACTGGGCAAGCCAGATATACCCAGGGATTAAAGTAAAACAACTTTGTA\nAACTCCTTAGGGGGGTCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAAT\nTAGAATTGGCAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACC\nCATCAAAGGAATTAACAGCTGAAATACAGAAACAGGGAATGAGCCAGTGGACATATCAAA\nTTTACCAAGAACCACATAAAAATCTGAAAACAGGAAAGTATGCAAGAATGAGGACTGCCC\nACACTAATGATGTAAAACAGTTAGCAGAGGTAGTGCAAAAAATAGCCTTGGAGAGCATAG\nTAATATGGGGAAAGACTCCTAAATTTAGACTACCCATCCAGAAAGAAACATGGGACATAT\nGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTGAAATTATGGTACCAGCTAGAAAAAGAACCCATAGCAGAAGCAGAAACTTTCT\nATGTAGATGGAGCAGCTAATAGGGAAACTAAAAAGGGAAAAGCAGGGTATGTTACTGACA\nGAGGAAGACAGAAGGTTATTTCTCTAAATGAGACAACAAATCAGAAGACTGAATTACAAG\nCAATTCAGCTAGCTTTGCAAGATTCAGGACCAGAAGTAAACATAGTAACAGACTCACAGT\nATGCATTAGGAATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTAAACCAAA\nTAATAGAAGAATTAATAAAAAAGGAAAGGGTCTACTTGGCATGGGTACCAGCACACAAAG\nGAATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGCAGTGGAATCAGGAAAGTGCTGT\nTTCTGGATGGAATAGATAAGGCTCAAGAAGATCATGAAAGGTACCACAGTAATTGGAGAG\nCAATGGCTAATGAATTTAATCTACCGCCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTG\nATAAATGTCAGCTAAAAGGGGAAGCCATACATGGGCAAGTAGACTGTAGTCCAGGGATAT\nGGCAATTAGATTGTACACATTTAGAAGGAAAAGTCATCCTAGTAGCAGTCCATGTAGCCA\nGTGGATACATAGAGGCAGAGGTCATCCCAGCAGAAACAGGACAAGAAACAGCATACTTTC\nTATTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAATGGCCCTAATT\nTCACCAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGGGTCCAACAGGAATTTGGGA\nTTCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAA\nTCATAGGGCAGGTAAGAGAGCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTAT\nTCATTCACAATTTTAAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAATGAATAC\nTAGACATAATATCATCAGACATACAAACTAAAGAATTACAAAAACAAATTATAAAAATTC\nAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCCATTTGGAAAGGACCAGCCAAAC\nTACTCTGGAAAGGCGAAGGGGCAGTAGTAATACAAGATAACAGTGACATAAAGGTAGTAC\nCAAGGAGGAAAGCAAAAATCATTAGGGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAAGATCAGAACATGGAATAGCCTAGTAAAGCATCATATGTAT\nATTACAAAGAAAACTGGCAGATGGTGTTACAGACATCATTATGAAAGCAGAAATCCAAGA\nGTAAGTTCAGAAGTACACATACCATTAGGGGAGGCTAGATTAGTGATAACAACATATTGG\nGGGTTGCAAACAGGAGAAAGAGCTTGGCATTTAGGTCATGGAGTCTCCATAGAATGGAGA\nTTGAAAGAATATAGCACACAAGTAGACCCTGACCTGGCAGACCAGCTAATTCATAAGCAT\nTATTTTGATTGTTTTGCAGATTCTGCCATAAGGAAAGCCATATTAGGACACATAGTTATT\nCCTAGGTGTGAATATCAAGCAGGACACAAGAAGGTAGGATCTCTACAATATTTGGCACTG\nGCAGCATTAGTAAAGCCAAAAAAGAGAAAGCCACCTCTGCCTAGTGTTAAAAAATTAGTA\nGAGGATCGATGGAACAACCCCCAGAAGACCAAGGGCCACAGAGGGAACCATACAATGAAT\nGGGCATTAGAAATTTTAGAGGAACTCAAGCAGGAAGCTGTCAGACATTTTCCGGGACCAT\nGGCTCCATAGTTTAGGACAATATATCTATGAGACCTATGGGGATACTTGGACAGGAGTTG\nAAGTGTTAATAAGAATACTGCAACAACTACTGTTTATTCATTTCAGAATTGGGTGCCAAC\nATAGCAGAATAGGAATTATGCCACAAAGAAGAGCAAGAAATGGAGCCAGTAGATCCTAAC\nCTAGAGCCCTGGAACCATCCAGGAAGTCAGCCTAATACTCCTTGTAATAATTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGAAAAAAGGCTTAGGCATTTCCTAT\nGGCAGGAAGAAGCGGAGTCAGCGACGACGCACTCCTCCAAGCAGTGAGGATCATCAAAAT\nCTTATATCAAAGCAGTAAGTATATGTAATGTCAAATTTTCTAGAAGAAGTAGATTATAGA\nCTAGGAGTAGGAGCACTGATAATAGCACTAATCATAGCAATAGTAGTGTGGATTTTAGCA\nTATATAGAATATAGGAAATTGGTAAGACAAAGAAAAATAGACTGCTTAATTAAAAGAATT\nAGGGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAGGGGGATACAGAGGAACTATCCACA\nATGGTGGATATGGGGCATCTTAGGCTTTTGGATAATAATTAGTGGAGGGGTAGGAAACAT\nGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAGAGAAGCAAAAACTACTCTATTCTG\nTGCATCAGATGCTAAAGCATATGACAAGGAAGTGCATAATGTCTGGGCTACACATGCCTG\nTGTACCCACAGACCCCAACCCACAAGAACTAGTTTTGGGAAATATAACAGAGAATTTTAA\nCATGTGGAAAAATGACATGGTGGATCAGATGCATGAGGATATAATCAGTTTATGGGATGA\nAAGTCTAAAGCCCTGTGTAAAGTTGACCCCACTCTGTGTCACTTTAAATTGTACAAATGT\nCACCCAGACAGGTACAACTACTCAGGTCTACCAGACAGGTAATATTACCGACAAGGAGAA\nCATATTTAATTGCTCTTTCGAAACAACCACAGGAATAAGAGATAAGAAACAGAGTGTGTA\nTGCAACTTTTTATAAACAGGATCTAGTATCACGGAGTAATGGGAATTCTAATTATAGTGA\nATCTATATTAATAAATTGCAATACCTCAACCATAACACAAGCTTGTCCAAAGGTCACTTT\nTGACCCAATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTCTAAAGTGTAATAA\nTAAGACATTCAATGGGACAGGACCATGCCAGAATGTTAGTACAGTACAATGTACACATGG\nAATTAAGCCAGTAGTATCAACCCAACTACTGTTAAATGGTAGCCTAGCAGAAGAAGACAT\nAATAATTAGGTCTGAGAATCTGACAGACAATACCAAAACAATAATAGTACACTTTAATGA\nATCTGTAAACATTACGTGTACAAGAATTGCCAATAATACAAGAAGAAGTATAAGGATAGG\nACCAGGACAATCATTCTATACACATGACATAATAGGAGACATAAGAAAGGCACATTGTAA\nCATTAATACAACAAAGTGGAACAACACTTTACAAAGGGTAAAGGAGAAATTAAGAGAACA\nCTTCTCTGATAAAAATATAACATTTGAACCATCCTCAGGAGGGGACCTAGAGGTGACAAC\nACATAGTTTTAATTGTAGAGGGGAATTTTTCTATTGCAATACAACAAACCTGTTTAATGA\nAACAGAACTTAATAGAACAAAGACAAAAGAAAACATAACCATACTCCCATGCAGAATAAA\nACAAATTATAAATATGTGGCAGAGGGTAGGACGAGCAATGTATGCCCCTCCCATAGCAGG\nAAACATAACATGTAACTCAAGTATCACAGGGCTACTATTAACACGTGATGGAGGGATTAA\nCAAAACAGAGCCCGACAACAACACAGAGATATTCAGACCTGGAGGAGGAAATATGAAGGA\nTAATTGGAGAAGTGAATTATATAAATATAAAGTAATAGAAATTAAGCCATTGGGAATAGC\nACCCACTAATGCAAAAAGGAGAGTGGTGGAGAGAGAAAAAAGAGCAGTGGGAATGGGAGC\nCTTGATCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATAACGCT\nGACGGTACAAGCCAGACAACTGTTGTCTGGTATAGTGCAACAGCAGAGCAATCTGCTGAG\nAGCTATAGAGGCGCAACAGCATATGTTGCAACTCACGGTCTGGGGCATTAAACAGCTCCA\nGACAAGAGTCCTGGCTATAGAAAGATACCTACAGGATCAACGGCTCCTAGGACTTTGGGG\nCTGCTCTGGAAAACTCATCTGCACCACTACTGTGCCTTGGAACTCCAGTTGGAGTAATAA\nAACTTACAACGATATTTGGCATAACATGACCTGGATGCAGTGGGATAGAGAAATTAGTAA\nTTACTCAGACACAATATTTAGGTTGCTTGAAGTATCACAAAACCAGCAGGAGAAAAATGA\nACAAGATTTATTGGCATTGGACAAGTGGAATGATCTATGGAATTGGTTTAACATAACACA\nATGGCTGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCTTGATAGGTTTGAGAAT\nAATTTTGTTTGTGCTTTCTATAGTAAATAGAGTTAGGCAGGGATACTCACCTTTGTCATT\nGCAGACCCTTACCCCAAACTCGAGGGAACTCGACAGGCTCAGAGGAATCGAAGAAGAAGG\nTGGAGAGCAAGGCAGAGACAGATCCATTCGATTAGTGAACGGATTCTTAGCGATTGCCTG\nGGACGATCTGAGGAGCCTGTGCCTTTTCAGCTACCACCAATTGAGAGACTTCATATTGAT\nTGCAGCGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGAGGGGGTG\nGGAAGCTCTTAAGTACCTGAAGAACCTTGTGCAATATTGGGGTGGGGAGCTTAAAAAGAG\nTGCTATTAGTCTGCTTGATACTATAGCAATAGTAGTAGCTGAAGGAACAGATAGGATTAT\nAGAAGTGCTACAAAGAATTTGGAGGGCTATCTGCAACACACCTAGAAGAATAAGACAGGG\nCTTTGAAGCAGCTTTGCTATAAGATGGGAAACAAGTGGTCAAAAAGCTGGCCTGCTGTAA\nGAGAAAGAATAAGAAGAACTGAGCCAGCAGCAGAAAGAGTAGGAGCAGCAGAGGGAGTGG\nGAGCAGCGTCTCGAGACTTAGAAAAGCATGGAGCACTTACAAGCAGCAACACAGCCCACA\nACAATGAAGCTTGTGCCTGGCTGCAAGCACAGGAGGAAGATGAAGAAGTAGGCTTTCCAG\nTCAAACCTCAGGTACCTTTGAGACCAATGACTTATAAGGCAGCATTCGATCTCAGCTTCT\nTTTTAAAAGAAAAGGGGGGACTGGATGGGTTAATTTGGTCCAAGAAAAGGCAAGAGATCC\nTTGATCTGTGGGTCTATAACACACAAGGCTTCTTCCCTGATTGGCAAAACTACACACCAG\nGACCAGGGGTCAGACTTCCACTGACCTTTGGATGGTGCTTCAAGCTAGTACCAGTTGACC\nCAAGTGAAGTAGAAGAGGCCAACCAAGGAGAAAACAACTGCCTGCTACACCCTATGAGCC\nAGCATGGAATAGAGGATACAGAAAGAGAAGTACTAAAATGGAAGTTTGACAGCAGCCTAG\nCACGCAGACACCTGGCCCGTGAGAAACATCCGGAGTTTTACAAAGACTGCTGACACAGAA\nGGGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGGGGAGTGGTCTGGGCGGGAC\nAAGGGAGTGGTCAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTCGCCTGTACTGGGT\nCTCTCTAGGTAGACCAGATCTGAGCCTGAGAGCTCTCTGGATGCCTGGGGAACCCACTGC\nTTAAGCCTCAATA\n" }, { "path": "tests/input/TestOrderAndOrient/expected.influenza.fasta", "content": ">gi|8486138|ref|NC_002023.1|_contigs_ordered_and_oriented\nTATATTCAATATGGAGAGAATAAAAGAACTAAGAGATTTAATGTCACAATCCCGCACTCG\nCGAGATACTAACCAAAACCACTGTTGACCACATGGCCATAATCAAAAAGTACACATCGGG\nAAGGCAAGAGAAGAACCCCGCACTCAGGATGAAATGGATGATGGCAATGAAATATCCAAT\nCACAGCTGACAAGCGAATAATGGAAATGATCCCTGAAAGGAATGAACAAGGGCAAACCCT\nCTGGAGCAAAACAAACGATGCCGGATCAGACCGAGTGATGGTATCACCCCTGGCTGTAAC\nATGGTGGAATAGGAATGGACCAACAACAAGTACAGTTCACTATCCCAAGGTATATAAAAC\nTTATTTCGAAAAGGTTGAAAGGTTGAAACACGGGACCTTTGGCCCTGTACACTTCAGAAA\nCCAAGTTAAGATAAGACGGAGGGTCGACATAAACCCGGGCCATGCTGACCTCAGTGCCAA\nAGAGGCGCAGGATGTAATCATGGAAGTTGTCTTTCCAAATGAAGTGGGAGCGAGAATACT\nGACGTCGGAATCACAATTGACGATAACAAAGGAGAAGAAAGAAGAACTCCAGGACTGCAA\nAATCGCCCCTCTGATGGTTGCATACATGCTAGAAAGAGAGTTGGTTCGCAAGACAAGGTT\nTCTCCCAGTGGCTGGTGGAACAAGCAGTGTCTACATTGAGGTGCTGCATTTGACCCAGGG\nGACATGCTGGGAGCAGATGTATACTCCGGGAGGAGAAGTGAGAAACGATGATGTAGACCA\nGAGCTTGATTATCGCTGCCAGGAACATAGTGAGAAGAGCAACAGTGTCAGCAGACCCACT\nAGCATCTCTATTGGAGATGTGCCACAGCACACAAATTGGGGGAATAAGGATGGTAGACAT\nTCTCCGGCAAAATCCAACAGAGGAACAAGCCGTGGACATATGCAAGGCAGCAATGGGCTT\nGAGGATTAGCTCATCTTTCAGTTTTGGTGGATTCACTTTTAAAAGAACGAGTGGATCGTC\nAGTCAAAAAGGAAGAAGAAGTGCTTACGGGCAACCTTCAAACATTGAAAATAAGAGTGCA\nTGAGGGGTATGAAGAGTTCACAATGGTTGGAAGAAGAGCAACGGCCATTCTCAGAAAGGC\nAACCAGAAGGCTGATCCAGTTAATAGTAAGTGGAAGAGACGAGCAGTCAATTGCTGAAGC\nAATAATTGTGGCCATGGTATTCTCACAAGAGGACTGCATGATTAAGGCAGTTCGAGGTGA\nTCTGAATTTTGTCAATAGGGCGAACCAGCGGCTGAATCCAATGCATCAGCTCTTGAGACA\nCTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAATTGGGGAATTGAACCCATTGACAATGT\nGATGGGAATGATCGGGATATTGCCTGACATGACCCCAAGTACTGAGATGTCACTGAGGGG\nAATAAGAATCAGTAAGATGGGGGTAGATGAATACTCCAGCACAGAGCGGGTAGTAGTAAG\nCATCGACCGATTTTTAAGAGTTCGAGACCAACGAGGGAACGTGCTATTGTCACCCGAAGA\nAGTCAGCGAGGCACAAGGAACAGAGAAACTGACAATCACTTATTCGTCATCAATGATGTG\nGGAGATTAATGGTCCTGAGTCGGTGTTGGTCAATACTTATCAGTGGATAATCAGAAACTG\nGGAAACTGTAAAAATTCAATGGTCACAGGATCCCACAATGTTGTATAATAAGATGGAATT\nCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCCAGAGGTCAATACAGTGGGTTCGTGAG\nGACACTGTTCCAGCAGATGCGAGATGTGCTTGGAACATTCGACACTGTTCAGATAATAAA\nACTCCTCCCCTTTGCTGCTGCCCCACCGGAACAAAGTAGGATGCAGTTCTCCTCCCTGAC\nTGTGAATGTGAGAGGATCAGGAATGAGAATACTGGTAAGAGGCAATTCCCCAGTGTTCAA\nTTACAACAAGGCCACCAAGAGGCTCACAGTTCTCGGGAAAGATGCAGGTGCATTGACCGA\nAGATCCAGATGAAGGCACAGCTGGAGTGGAGTCTGCTGTTTTAAGAGGATTCCTCATTTT\nGGGCAAAGAAGACAAGAGATATGGCCCAGCATTGAGCATCAATGAGCTGAGCAATCTTGC\nAAAGGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTGATGAAACG\nGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGC\nCATCAATTAGTGTCGAATTGTTTA\n>gi|8486134|ref|NC_002021.1|_contigs_ordered_and_oriented\nAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGC\nCATAAGCACCACATTCCCGTACACTGGAGACCCTCCATACAGCCATGGAACAGGAACAGG\nATACACCATGGACACGGTCAACAGAACACATCAATATTCAGAAAAGGGGAAATGGACAAC\nAAACTCAGAGACTGGAGCACCCCAACTTAACCCAATTGATGGACCACTGCCCGAGGACAA\nTGAGCCAAGTGGATATGCACAAACGGACTGTGTCCTTGAAGCAATGGCTTTCCTTGAAGA\nATCCCACCCAGGAATCTTTGAAAACTCGTGTCTTGAGACGATGGAAGTTGTTCAACAAAC\nAAGAGTAGACAAATTGACCCAAGGCCGTCAGACCTATGATTGGACATTAAACAGGAATCA\nACCGGCTGCAACTGCATTAGCTAATACTATAGAGGTATTCAGATCGAACGGTCTGACAGC\nTAATGAATCAGGAAGGCTAATAGATTTTCTCAAGGATGTGATGGAATCAATGGATAAAGA\nGGAAATGGAAATAACAACGCATTTCCAAAGGAAAAGAAGAGTAAGGGACAACATGACCAA\nGAAAATGGTCACACAAAGGACAATAGGAAAGAAGAAGCAGAGGCTAAATAAAAAGAGCTA\nTCTAATAAGAGCCTTGACACTGAACACAATGACAAAAGACGCCGAAAGAGGCAAATTAAA\nGAGAAGAGCAATTGCAACACCCGGAATGCAAATCAGAGGATTTGTATACTTTGTTGAAAC\nATTAGCAAGGAGCATTTGTGAGAAGCTTGAACAATCTGGACTCCCAGTTGGAGGCAATGA\nAAAGAAGGCTAAACTGGCAAATGTTGTGAGGAAAATGATGACTAATTCACAAGATACAGA\nACTCTCCTTCACAATCACTGGAGACAACACCAAATGGAATGAAAACCAGAACCCTAGGAT\nGTTTCTGGCAATGATAACATATATAACAAGAAACCAACCTGAATGGTTTAGGAATGTCTT\nGAGCATTGCACCCATAATGTTCTCAAACAAAATGGCAAGGCTAGGGAAAGGATATATGTT\nCGAAAGTAAGAGCATGAAGCTTCGAACACAAATACCGGCAGAAATGCTAGCAAGTATTGA\nTCTGAAATATTTTAATGAGTCGACAAAAAAGAAAATTGAAAAGATAAGACCTCTTCTAAT\nAGATGGTACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTAC\nAGTTTTGGGAGTTTCGATTTTAAATCTAGGACAAAAGAGGTACACCAAAACAACATACTG\nGTGGGACGGGCTCCAATCCTCTGATGACTTTGCTCTCATAGTGAATGCCCCGAATCATGA\nGGGGATACAAGCAGGAGTAGACAGATTCTATAGAACCTGCAAGCTGGTTGGAATCAACAT\nGAGCAAAAAGAAGTCCTACATAAACAGGACAGGAACATTTGAATTCACAAGTTTTTTCTA\nTCGCTATGGATTTGTAGCCAATTTCAGTATGGAGTTGCCCAGCTTTGGAGTGTCTGGGAT\nTAATGAATCTGCAGACATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAA\nTGATCTTGGACCAGCAACAGCTCAAATGGCTCTTCAGCTGTTCATCAAGGATTACAGATA\nCACGTATCGGTGTCACAGAGGAGACACACAAATTCAGACAAGGAGGTCATTCGAGCTGAA\nGAAATTGTGGGAACAAACCCGCTCAAAAGCGGGACTGCTGGTCTCAGACGGAGGACCAAA\nCCTATACAATATCCGGAATCTACACATTCCGGAAGTCTGCTTAAAATGGGAGCTGATGGA\nCGAAGACTATCAGGGAAGGCTTTGCAACCCCCTGAATCCGTTTGTCAGCCACAAGGAGAT\nAGAGTCTGTAAACAATGCTGTGGTGATGCCAGCTCATGGCCCAGCCAAGAGCATGGAGTA\nTGATGCTGTGGCTACTACACACTCCTGGATACCTAAGAGGAATCGCTCTATCCTCAATAC\nAAGCCAAAGGGGAATCCTTGAGGATGAACAGATGTATCAAAAGTGCTGCAATCTATTCGA\nGAAATTCTTCCCTAGCAGCTCATACAGGAGACCGGTTGGAATTTCCAGCATGGTAGAGGC\nCATGGTTTCTAGGGCCCGAATCGATGCGCGAATTGACTTCGAATCTGGACGGATCAAGAA\nAGAGGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAACTCAGACGGCAGAA\nATAGTGAATTTTGCTTGTCCTTCATGAAAAAATGCCTTG\n>gi|8486136|ref|NC_002022.1|_contigs_ordered_and_oriented\nCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAA\nGGCAATGAAAGAATATGGGGAAGATCCGAAAATTGAAACTAACAAGTTTGCTGCAATATG\nCACCCACTTAGAAGTCTGTTTCATGTATTCGGATTTTCATTTCATCGACGAACGGGGTGA\nATCAATAATTGTAGAATCTGGTGACCCAAATGCATTACTGAAGCACCGATTCGAGATAAT\nTGAAGGAAGAGATCGAACCATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGG\nGGTAGAGAAGCCTAAATTTCTTCCGGATCTGTATGACTACAAGGAGAACAGATTCATTGA\nAATTGGGGTGACACGGAGGGAGGTTCACATATACTACCTAGAAAAAGCCAATAAAATAAA\nATCCGAGAAGACACACATCCACATTTTCTCATTCACTGGAGAGGAAATGGCCACCAAAGC\nGGACTACACCCTTGATGAAGAAAGCAGAGCAAGAATCAAAACCAGATTGTTCACCATAAG\nACAAGAAATGGCCAGTAGAGGTTTGTGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGA\nGACAATTGAAGAAAGATTTGAAATTACAGGAACCATGCGCAGGCTTGCCGACCAAAGTCT\nCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCGAACCGAA\nCGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAAGTGAACGCAAGAATTGAACC\nATTCTTGAAAACAACACCACGCCCACTCAGATTACCTGATGGGCCTCCTTGTTCCCAGCG\nGTCAAAATTTCTGTTGATGGATGCTCTGAAACTAAGTATTGAGGACCCGAGTCATGAGGG\nGGAGGGAATACCGCTATATGATGCAATCAAATGCATGAAGACATTTTTTGGCTGGAAAGA\nACCTAACATAATCAAACCACATGAGAAAGGCATAAACCCCAACTACCTCCTGACTTGGAA\nGCAAGTACTAGCGGAACTCCAAGACATTGAGAATGAAGAGAAGATCCCAAAGACAAAGAA\nCATGAAGAAAACAAGCCAACTGAAGTGGGCACTTGGTGAAAATATGGCACCAGAGAAAGT\nAGACTTTGATGATTGCAAAGATATTAGTGATCTTAAACAGTATGACAGCGATGAGCCAGA\nACCTAGGTCGCTAGCAAGCTGGATCCAAAGTGAATTCAACAAGGCATGTGAATTGACCGA\nTTCAAGCTGGATGGAGCTTGATGAGATAGGGGAAGATGTTGCCCCGATCGAACACATTGC\nAAGCATGAGGAGAAACTATTTTACAGCAGAAGTGTCCCATTGCAGGGCTACTGAGTACAT\nAATGAAGGGAGTGTACATAAACACAGCCTTGCTCAATGCATCTTGTGCAGCCATGGATGA\nCTTCCAGCTGATCCCAATGATAAGCAAATGTAGAACCAAAGAAGGGAGACGGAAAACAAA\nTCTGTATGGATTCATTATAAAAGGAAGGTCTCATTTGAGAAATGACACTGACGTGGTAAA\nTTTTGTGAGTATGGAGTTCTCTCTCACAGACCCGAGACTGGAGCCACACAAATGGGAAAA\nGTACTGTGTTCTCGAAATAGGGGATATGCTCTTGAGGACTGCGATAGGCCAAGTGTCACG\nACCCATGTTCCTATATGTGAGAACCAATGGAACTTCAAAGATCAAGATGAAATGGGGGAT\nGGAAATGAGGCGCTGCCTTCTCCAATCCCTTCAGCAGATTGAGAGCATGATTGAGGCCGA\nGTCTTCCGTCAAAGAGAAAGATATGACAAAGGAATTCTTTGAGAACAAATCAGAAACATG\nGCCAATTGGAGAGTCACCCAAGGGAGTGGAAGAAGGCTCTATTGGGAAAGTATGCAGAAC\nCCTACTGGCAAAGTCTGTATTCAACAGTCTATATGCATCTCCACAACTCGAGGGGTTTTC\nAGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGAACCTGG\nGACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTG\nGGTTTTGCTCAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTGAAATAGTTGTG\nGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTT\n>gi|8486125|ref|NC_002017.1|_contigs_ordered_and_oriented\nGCAAAAGCAGGGGAAATTCAAATCAACCAAGATGGAAGCAAAACTGTTTGTGCTATTCTG\nTACATTCACTGTACTGAAAGCTGACACCATCTGTGTGGGCTACCATGCAAACAACTCTAC\nGGACACTGTTGACACAGTATTGGAAAAGAATGTAACTGTGACTCACTCAGTGAATTTGCT\nCGAAGACAGCCATAATGGGAAGCTCTGCAGTCTGAATGGGATAGCTCCTTTACAATTGGG\nGAAGTGTAATGTAGCGGGGTGGCTCCTGGGCAATCCAGAATGTGATCTCCTACTCACTGC\nAAACTCATGGTCCTATATAATAGAGACGTCCAATTCAGAGAACGGGACATGCTATCCCGG\nTGAATTCATAGATTATGAGGAATTAAGGGAGCAGCTGAGTTCAGTTTCTTCTTTTGAAAA\nGTTTGAAATTTTCCCCAGGGCAAACTCATGGCCAAACCATGAGACAACCATAGGTGTTAC\nAGCTGCTTGCTCTTACTCTGGAGCTAGCAGTTTTTATCGAAATTTGCTGTGGATAACAAA\nGAAGGGGACTTCATATCCAAAACTCAGCAAATCATACACGAACAATAAGGGGAAAGAGGT\nGCTCGTGCTCTGGGGAGTGCACCATCCTCCGACCACCAGTGAACAACAAAGTCTATACCA\nGAATACTGATGCATATGTCTCAGTTGGGTCATCAAAGTACAACCGGAGATTCACCCCAGA\nGATAGCAGCTAGACCCAAAGTTAGAGGGCAGGCAGGCAGAATGAACTATTATTGGACACT\nATTAGATCAAGGGGACACCATAACATTTGAGGCCACTGGGAATCTGATAGCACCATGGTA\nTGCCTTCGCATTAAATAAAGGATCTGATTCAGGAATTATAACATCAGATGCTCCAGTTCA\nCAATTGCGACACAAGATGCCAAACCCCCCATGGAGCGTTGAACAGTAGCCTTCCTTTCCA\nGAATGTGCATCCTATCACCATTGGAGAATGTCCCAAATATGTCAAGAGCACCAAGCTAAG\nGATGGCAACAGGACTAAGAAATGTCCCATCCATTCAATCCAGAGGGCTGTTTGGAGCAAT\nTGCCGGATTCATTGAAGGAGGATGGACAGGCATGATAGATGGCTGGTATGGGTACCATCA\nTCAAAATGAACAAGGATCAGGATATGCCGCTGATCAGAAAAGCACACAGAATGCAATTGA\nTGGAATAACAAATAAGGTGAATTCGGTAATTGAAAAAATGAACACTCAATTCACTGCAGT\nGGGTAAAGAATTCAACAACCTAGAGAGGAGGATTGAGAATCTGAATAAAAAAGTCGATGA\nTGGGTTCCTGGATGTTTGGACATACAATGCTGAATTGCTCGTTCTATTGGAAAATGAAAG\nAACTCTTGATTTTCATGATTCCAATGTGAGGAATTTGTATGAGAGAGTCAAATCACAACT\nGAGGAATAACGCCAAAGAAATTGGAAATGGTTGCTTTGAGTTCTATCACAAATGTGATGA\nTGAATGTATGGAAAGTGTGAAGAACGGCACATATGATTATCCCAAATATTCAGAAGAGTC\nTAAATTGAATCGAGAAGAAATAGACGGAGTAAAACTAGAGTCGATGGGAGTTTACCAAAT\nTCTGGCGATCTATTCCACAGTCGCCAGTTCCCTGGTCTTGTTAGTCTCCCTGGGGGCAAT\nCAGCTTCTGGATGTGCTCTAATGGGTCGTTGCAATGCAGAATATGCAT\n>gi|8486129|ref|NC_002019.1|_contigs_ordered_and_oriented\nGTAGATAATCACTCACCGAGTGACATCCACATCATGGCGTCTCAAGGCACCAAACGATCT\nTATGAGCAAATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAAATCAGAGCATCTGTT\nGGGAGAATGGTTGGTGGAATCGGAAGATTCTACATACAGATGTGTACTGAACTCAAGCTC\nAGTGACTATGAAGGGAGGCTGATCCAAAATAGCATAACCATAGAGAGAATGGTTCTCTCG\nGCATTTGATGAGAGGAGAAATAAATATCTGGAAGAGCATCCCAGTGCTGGGAAAGACCCC\nAAGAAGACTGGAGGCCCAATCTACAGAAGAAGAGATGGAAAATGGATGAGAGAGTTGATC\nCTATATGACAAAGAAGAGATCAGGAGGATTTGGCGTCAAGCAAATAACGGAGAAGACGCA\nACTGCTGGTCTCACCCATTTGATGATTTGGCATTCCAATCTGAATGATGCCACATACCAG\nAGAACAAGGGCACTTGTGCGTACTGGGATGGATCCCAGGATGTGCTCCCTGATGCAAGGC\nTCAACTCTTCCAAGAAGATCTGGGGCTGCTGGAGCAGCAGTGAAAGGGGTTGGAACAATG\nGCGATGGAACTGATCCGGATGATCAAGCGAGGTATCAATGATAGGAATTTCTGGAGAGGC\nGAAAATGGACGGAGGACGAGAATTGCTTATGAAAGAATGTGCAACATCCTCAAGGGGAAA\nTTCCAAACAGCAGCACAACGAGCAATGATGGATCAGGTGAGAGAAAGCCGGAATCCTGGG\nAATGCTGAAATTGAAGATCTCATCTTCCTTGCAAGGTCTGCTCTCATTCTGAGAGGATCA\nGTAGCTCATAAGTCCTGCCTGCCTGCTTGTGTGTATGGGCTTGCAGTGGCCAGTGGATAC\nGACTTTGAGAGAGAGGGATATTCCCTAGTCGGAATTGATCCTTTCCGTCTGCTCCAAAAC\nAGTCAAGTCTTCAGCCTCATCAGACCAAACGAAAATCCAGCGCATAAGAGTCAGCTGGTA\nTGGATGGCATGTCACTCTGCTGCATTTGAAGATTTGAGAGTGTCAAGCTTCATCAGAGGA\nACAAGAGTAGTCCCAAGAGGACAACTATCCACCAGAGGAGTTCAGATTGCTTCAAATGAG\nAACATGGAGACAATGGACTCCAGCACTCTTGAACTGAGGAGCAGATACTGGGCTATAAGG\nACAAGAAGCGGAGGGAACACTAACCAGCAGAGAGCATCTGCAGGGCAAATCAGCGTGCAG\nCCCACCTTCTCTGTACAGAGAAACCTCCCATTCGAGAGAGCAACCATTATGGCGGCATTT\nACGGGAAATACCGAGGGTAGAACTTCAGACATGAGGACTGAGATCATAAGGATGATGGAA\nAATGCCAGACCTGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAA\nAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTC\nGGAGACAATGCAGAGGAGTATGACAATTAAAGAAA\n>gi|8486127|ref|NC_002018.1|_contigs_ordered_and_oriented\nTCTCTCTGTCCAATCAGTGGATGGGCTATATACAGCAAGGACAATGGTATAAGAATAGGT\nTCCAAAGGAGATGTATTTGTCATCAGAGAGCCTTTTATTTCATGCTCTCACTTGGAATGC\nAGGACTTTCTTTCTAACTCAAGGGGCCTTGTTGAATGACAAGCATTCTAATGGAACCGTT\nAAAGACAGAAGCCCTTATAGAACCCTAATGAGCTGCCCTGTTGGTGAAGCTCCTTCCCCA\nTACAATTCAAGGTTTGAGTCTGTTGCTTGGTCAGCAAGTGCTTGTCATGATGGCATTAGT\nTGGTTGACAATTGGTATTTCCGGCCCAGACAATGGGGCGGTGGCTGTATTAAAATACAAT\nGGCATAATAACAGATACTATCAAGAGTTGGAGAGGCAATATATTAAGAACACAAGAGTCT\nGAATGTGCCTGCATTAATGGTTCTTGCTTTACCATAATGACTGATGGGCCGAGTAATGGC\nCAGGCCTCATACAAAATTTTCAAGGTAGAAAAGGGAAAGGTAGTCAAATCAGTTGAGTTG\nAATGCTCCTAATTACCACTATGAGGAGTGCTCCTGTTATCCTGATGCTAGCGAGGTAATG\nTGTGTGTGCAGAGACAATTGGCATGGTTCAAATCGACCATGGGTGTCCTTCAATCAAAAT\nCTAGAATATCAAATAGGATACATATGCAGCGGAGTTTTTGGAGACAACCCGCGCCCTAGT\nGATGGGACAGGCAGTTGTGGTCCAGTTTCTTCTAATGGGGCATATGGAGTGAAGGGGTTT\nTCATTTAAATACGGTAATGGTGTTTGGATAGGAAGAACTAAAAGTACTAGCTCAAGGAGT\nGGGTTTGAGATGATCTGGGATCCTAATGGGTGGACTGAGACAGATAGCAGTTTTTCTGTG\nAAGCAAGATATTGTAGCAATAACTGATTGGTCAGGATATAGCGGAAGTTTTGTCCAGCAT\nCCAGAACTGACTGGGTTGGATTGCATGAGGCCTTGCTTCTGGGTTGAGCTGATCAGAGGA\nAGACCCAAGGAGAACACAATCTGGACCAGTGGAAGCAGCATTTCTTTTTGTGGAGTGAAT\nAGCGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCACCATTGACAAG\nTAGTTTGTTCAAAAAACTCCTTG\n>gi|8486122|ref|NC_002016.1|_contigs_ordered_and_oriented\nGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGT\nCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTGTTCGCAGGGAAAAACA\nCCGACCTTGAGGCGCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTA\nAGGGGATCTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTA\nGACGCTTTGTCCAAAATGCCCTTAATGGGAATGGGGATCCAAACAACATGGACAGAGCAG\nTCAAACTGTACAGGAAGCTCAAAAGGGAGATAACATTCCATGGGGCAAAGGAGGTAGCAC\nTCAGTTACTCAACTGGTGCACTTGCCAGCTGCATGGGTCTCATATACAACAGGATGGGGA\nCTGTGACCACTGAAGTGGCATTTGGCCTGGTGTGTGCCACGTGTGAGCAGATTGCTGACT\nCCCAGCATCGGTCTCACAGACAAATGGTAACAACAACCAACCCACTAATAAGACACGAGA\nACAGGATGGTACTGGCTAGTACTACAGCTAAGGCCATGGAGCAAATGGCAGGGTCAAGTG\nAGCAAGCAGCAGAGGCTATGGAGGTTGCTAGTCAGGCTAGACAGATGGTGCAGGCAATGA\nGGACTATTGGGACTCACCCTAGCTCCAGTGCTGGTCTAAAAGATGATCTTCTTGAAAATT\nTGCAGGCCTACCAGAAACGGATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGTT\nATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTC\nTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGA\nGTGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAGTGCTGTGGATGTTGAC\nAATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCT\n>gi|8486131|ref|NC_002020.1|_contigs_ordered_and_oriented\nCAGGTAGATTGCTATCTATGGCACATAAGAAAGCTGCTCAGCATGAGAGACATGTGTGAT\nGCTCCCTTTGATGATAGACTCAGAAGAGATCAGAAGGCATTAAAGGGGAGAGGCAGCACA\nCTTGGACTCGACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNACCGACATGAGCATAGAGGAAATAAGCAGGGAGTGGTACATGCTCATGCCAAGGCAG\nAAAATAACAGGGGGTCTGATGGTGAAAATGGACCAGGCCATCATGGACAAGAGGATAATA\nCTCAAGGCAAACTTCTCTGTCCTATTTGATCAACTGGAAACATTAGTCTCACTGAGGGCT\nTTCACAGACGATGGCGCCATTGTAGCTGAAATATCTCCTATTCCTTCCATGCCAGGACAT\nTCTACAGAGGATGTCAAAAATGCAATTGGAATCCTCATCGGTGGACTTGAATGGAATGAT\nAACTCAATTCGAGCGTCTGAAAATATACAGAGATTCGCTTGGGGAGTCCGTGATGAGAAT\nGGGGGACCTCCACTCCCTCCAAAACAGAAACGCTACATGGCGAGAAGAGTTGAGTCAGAA\nGTTTGAAGAGATCAGATGGCTAATTGCAGAGTGCAGAAACATATTAACCAAAACTGAAAA\nCAGCTTCGAGCAGATAACGTTCTTGCAGGCATTGCAACTCTTACTTGAGGTTGAGAGTGA\nGATAAGGACATTTTCTTTTCAGCTTATTTAGTACTAAAAAAC\n" }, { "path": "tests/input/TestOrderAndOrient/expected.lasv.ambig.fasta", "content": ">KM821998.1|LASV-ISTH2376-S-NG-2012H_contigs_ordered_and_oriented\nACTCGGACTCTCTCTGATTCTGAAGGTAATGAAACACCAGGTGGGTATTGTCTAACAAGA\nTGGATGCTGATTGAGGCCGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCAAAATGCAAT\nGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGCC\nATAAGCAGGCTGAAGACAGAAGCACAAATGAGTATCCAACTGATAAACAAAGCAGTGAAC\nGCACTGATCAATGACCAGCTGATTATGAAGAATCATTTGAGAGATATCATGGGAATTCCT\nTACTGCAATTACAGCAAGTACTGGTATCTGAATCACACTGTAACAGGGAAGACATCATTG\nCCAAGGTGCTGGCTTGTATCAAATGGTTCCTACCTAAATGAAACACACTTTTCTGATGAT\nATTGAACAACAAGCAGACAACATGATAACAGAAATGTTGCAAAAGGAGTACATAGACAGG\nCAAGGGAAGACACCCTTGGGGTTAGTGGATCTTTTTGTCTTCAGCACCAGCTTTTACCTC\nATTAGCATCTTCCTCCACCTGGTTAAAATCCCAACCCACAGACATGTCATAGGAAAACCC\nTGCCCCAAACCACACAGACTCAACCATATGGGCATATGCTCATGTGGTTTATACAAACAT\nCCTGGTGTACCAGTCAAGTGGAAAAGATAAGAGATAGACCCACCCATGGGCCCCCGTGAC\nCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTTG\nAGGTTCTAAACACCATGTCCCTGGGGAGAACTGCCCTCAAAACTGGTATATTGAGTCCTC\nCTGACACAGCTGCATCATACATTATGCAATCCATTAGAGCACAGTGCGGGGTGATTTCCT\nCTTTGCCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTATGCATATGGCATAGATCTT\nTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAACCTTGCTCAGTGCAATGT\nCAATAAGCTTTATGTCCTTTCTTCCTTGGGAGTCCAAGAGTTTCTTGATATCATCTGAAC\nCTTGACAGGTCAGTACCATATTGCGAGGGAGGGCTTCAATGACTGCGCTGGTCAAACCAG\nGCTGAGCAGGGAAGAGATCTGCCACATCAATCCCATGAGAGTATTTGGCATCCTGCTTGA\nACTGTTTTAGGTCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCTGACATAGGTTGGT\nAAAGAGCTATTTCCACAGGGTCTTCTGGACGACCTTCGATGTCTATCCAGGTTTTGGCGC\nTTGGGTCAAGCTGCATCATTGAGTCTTTGAGTGTCATTAATTGAGAATAGGTCAGCCCTG\nTTGGAAACCCTGCTGACTGTAAAGACTTGTTAGACCCAGCAATGCCCACTTTTTGCGGTT\nTTCCATCTGACTCGAGATCCACAGTAGTGTTCTCCCAAGCTCTACCCACAATAGAAGTCC\nTTGAAGCTATGTAGGGCCAGCCGTCACCGGAGAGACAGATCTTGTAAAGTATATTCTCAT\nAAGGGTTCCTCTCACCAGGTGTATCTGAAACAAACATTCCCAAAGATCTTTTTACTTTTA\nAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATGT\nTCCCCCCATCAAGCATACAAGCTCCGGCTTTCACTGCAGCTCCTAAGCTGAAGTTGTAAC\nCAGAAATGTTCAAGGAGCTCTTCTTAGTGTCCACCATATTCAGTATAGGGTGGCTTTGGG\nAAAGTCTGTCCAGGTCGGAGCTATTCGGGTACTTAGCTGTGTATATCAGGCCCAGGTCTG\nTTAGTGCTAAGACGGCATCATTCAAATCAACTTGACCTTGTTTGGTGAGACATGCTAATG\nTCAGACTAGGCATGGTGCCGAACTGGTTGTTCAAAAGGTCCGGATTCTTGACATCCCACA\nCTCTAACGACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATACCTATCA\nTGTTCAGCAATGCCCTTCTCTGCTCAAGCTGCTGTGTACTCAAATTCCCCATATAAACAC\nCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTTTCTAAGTCAGCTG\nCCAGTGTCAGCAGATCATCTGAGGTCAAGGTCCCAACTCTCAAGATACTCTTTTGTTGTG\nTCGATTTGAGTTCTACAAGATTGTTGACAGCCTGATTCAAATCTCTGAGACGTTTTAAGT\nCACTATCATCCCTTTTTTGTTTACGCATTAAGCGCTGCACATTGCTGACTTCAGAAAAAT\nCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGTAGTTTTATATTGGAGCAAT\nAACCTGAAAGCTCCCTCCTCAATGACTGTGTCCAGAGAAATGACTTCACTTCCTTAGAAG\nCACTCATCTTGGTCTGGACACTCGGGGACTTACTGGTTGAAAGTATCACTCAGTGAGTC\n>KM821997.1|LASV-ISTH2376-L-NG-2012H_contigs_ordered_and_oriented\nTTATTGAACAATATCCTAAGCATTGACCTCATCTTTTTACATGCATCAGGAATCAGCCTC\nTCAATTTGCCTCATTATTCTATAACTACGATTCCCATCCACCCAATCTCTTACATCAGTC\nTCACAGTTCAAAAGGAATGGATCAATAGGATACTTAGCATAACATAACAAACTCAAAGTC\nCTCTTCTGAATTTGATTACACAGATCGACTGGGACACCATTAGCCACAGATTGATCAATT\nATGGTGTCAATTGTTTCTGCCAATTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCC\nGCAGCAACAAATTTTGTTAGCAGAGGTACTTCGTCACCCCAGACATAGAACCTTGATTTG\nAACTCTGCGACAAACCTGCCAATTGCACTCTTTGGACTCACAAACTTATTTAGCTGATCA\nCTCATGTAGTAATGAAATTCTAACAATGTTTTGAATTCCTCTGTATCTCTTGAGAGTAAC\nTCTGTTAGGTTCTGATCAAATAAAGATATCTGATCGTCACTGGACGTGTAAGCATCAATT\nTGTCCTCCAGATACACACTTCACTGCAAAATTTATAAATCTTTCAGAAATCAATGCATAA\nAAGTCTGAGGTGTTGTGCAGGATACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAA\nGGGACTATCCCAATTTGAAAGTTGGAATTAAAGAAGTCCTCAGTCATTGATTGTGTTGTC\nTTCTTCTTTAATCCAAGTTGGGATTTGATGTATGACTTCATCATTGCTGATACAACATTA\nAATGGGATCTCAACCATTTTGTGCATATGCCATGTTAATAATGTTGATAGGTAATCTTTA\nCCTTTTAAATCAGCTTGTAAATCATCAGAAAGTAAGATTAGGTTTTGAATTATTGTTAGA\nAATAAGAAAGGACACATCATAGGGCCCCACTTACTGTGGTCCATACTGTATGATACATGT\nGCCGATGAGACATTTAGCTTCATTGACAAAATGGCATTGTCAAACTCCTTCTCATTATTT\nAGACAGCTGCCTGCTAATTGTGATGTGAGCGCTTCAAAGTAATCCTCAATAAGCCTTGTG\nAACATCTTTGTCCTTAAATCTCCGATGTACAACTCTCTATTGCCTCCCACTTGTTCCTTG\nTAAGATAAAGAGAATTTTAGTCTACCAGTGTCAGGGCCAGTTGAATTATAAGACTGAGGT\nGATTCTTGACTGTAAAAACACAGGTTTTTCAACATTGCTGTAGTACAGTTAGTTAGGGAC\nAAGGCCTTGCTAAGTGCCTCAGAATTACTCTCACGCTCACTTATCCTGACATCATCAGCC\nAGTCTTCCTGTATCAAATTTAAAGTTCAGACACTTACTCTTATAATGGGAGTACCTTCCC\nATCAGCTTGTTCCCATTCATCACTAACAAAATTGATTTGAAGCACTGGAAATATTCTTGG\nTCCAAAAAAGTCCTAGTCACTACTGCTTTTGTCAGCTCACTAATAGGACATGAATTCATC\nGGCCCTACATAAAAATACTTACTTCTCAAAGTAGCATCATTGTAGATATTCTCACAAATT\nTTGATGTATTGATCCTCAGACAGGATTTCTCGATCAAAATCTTCTATCATATGGTTCGAA\nAGTTCACATTTTATCAACCTTATTAAGAGTTTTTCTTCCACCACTTTGTCAAGATCAGAT\nATTGAGGGAGCATTGCAGTCTGCCTGCTGCTGTCTCTCTGGTTGCTCTCTATATTGACTG\nACAATATTGTCAACAGTACACCTCAGTTGATCAAAGTATTCTGATGCTCCTCCATCCAAT\nAGTATCTCATCTAGATCAGCATTGTTGGTGTCACCACCCCTTCCTTTGGACCCCAGAACA\nAGATTACTCATTGCTTGCTGTATCTTGTAATCATAATCCTGCTTATTGAGTAAGAATTTA\nCCTTTACGTGCAAATACTTCAGTTAACTGTGTGACAGCCAAAGCTGTAAGCTTGTTGAAG\nTCATAATCTAGAACACGGGACCCATCTGTATACTTATTCACAACGACACTCTTATTACTG\nGCCAAGTCCAAAGCTGTCGCACAGCCGCTTGTAATAAGAGGGTCTCGCAGTGTCTTCTTT\nACTTCCTTTTCTTTAAACAATGAACCATTATTAAAACTAGACACTAGGAGTGAAATAAAT\nTTCTTGGAAACACCAGGCTTTTTATACCTAACCTTTTCCGCATCTGCACAACATTCTTTG\nCCTAGAAACTTTCTTGCATTATAAACCATTTCAGCAAGCTCTTCCTCCAATGCATCATCT\nTTCGGGTTCACACTTACATGCCCAAATTCCAATTTAGGCTCAAGGAATTTTTCAAAGCAT\nTTTATCTGGTCAGTCAGTCTGTCAGGTGTTTCTTTTGTAATGAAATGACACATATAAGAG\nATATTTAAAACAAACTTAAATCTATTGGTCATCATACTGACTACTTCTTCAGACAGAATT\nATTTTTAGTAGGTGACGAACAAGTTTGTAGAGCAGATATTCAACTTCTGTGATTAAATCC\nTCCCTGATCTTCTCAATCAAATCCTTGTGATAAAAATCGGATACAAAGGCCATTACAAAA\nTACCTAATGTTTTGTAAAAACTTCTGACACCTTTTACTAGGATGTGTTAGTATCAAAACC\nAAAATCATCTTGGTTAACAATTTTATAGTAATCAATTGTTCAGATAGCTCTGTGCACTCT\nTCTATCCAGCTGACCATAACATCGACTACTTTCTGTAACACATCACTGGAGAATACTGAA\nGGGAAAAACCGTTTGGGATCAGCATAAAAGGAGCAAACCTCTCCAACTACATTGTTGTTA\nATAGCATAACACTTTGAGCATTCACCTGTCTTTTGATATAGTAGTTTGAATCCCATCCTA\nCTGATGAAGAACTCTTGGCAATAGGCCTCTTTGCACCTTACAACCTGGTATCTAGAGGGT\nCCAAATTCATTTTGTCTTAGTTTCACTGTGGAAGACGTTTTCATTGAGTTGATCAGAGCC\nAGGCTCAATGATGATAGTCTTTCTAAGTCTGTCACATCTAGAATGTCAATAACACCAAGA\nGTATAAGGGAACATGTCTTCCTTAGTTTTCTGGTAACTTATAGTGGGCGTGATACCGGAG\nATCTCAATGTCCATGATGGCATCATAAACATCACAATCAAGGATCTTGAGATCAATTCCA\nTAAGAGTTGGTTTCTATGCCAACCTCCCTCAAAGCATTAGTGGCCCGAGTTAAAACTCTG\nTTAATGATGGCAAGGAGCTCACAATTTCGTTCTTCTTTGAGTGATAGAACACCTGCATTC\nCTGTCTTTAGCTCTCTTCCTACTGTCTATCCACCGTTTNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNCAACACTGCATCTGCTCACTTTGAGAGTCAGCAGCCCTTTCTTCACCAGAATCTAAA\nTCTGCATATAAGAACTTAAGGACTGGAGAGGCTCTTCGGAACTGGTATGTTAACTGCTCA\nATATTGTCATCACAAGTGTCTATTTTATCACTATATAGCTTTCTGAAATCCCCTAACAGC\nTTCATCTTATCAGTTTTAACAAATTGACTTTCTATGTTCCCTTGCCTTAGTTTGTTCCTA\nAAGATTTGATACTCCTCTTCAATTAAACTCTTGACTTCATGAGAGGTGAGCTTGTTATTA\nATGCCCTGATGACAACAAGAAATTATTTCCTCAAAGTGTTTTGCACGCTTGTCAGTTAGA\nACATTAATGCTTTCAATCCCGGAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAAAGT\nCTTGAATACTCAGATTCTTCGAACAATGCATTACTTTCTTGTGAGTATTTTAATAAAGTG\nAACAAGGTGTCCCTGAGTTTGTCATTCACCCAATCAGGTATCTGCTCATTGTAAAAAGTT\nGTCCTACCGTCTATGAGAGGGATAAGATTGATGCCAACGGATTCCAAGTCATTCTTTAAT\nTGTTCTAGCTTCTTGTGATCTTCTAAATACTTCTGTTCAAAATTGGCAGGGGATGATCTG\nACAAAGCACTCAAGTAAGATAAGTACATTACCAGTAAGTTTGTAGCCGTCAGGCACCACA\nAAGCATAAAGCTGGAGTGAGAATCCCATGATCGCTCAGAATGGATTCAACCGTTTTGTCT\nTCAGTGTTATGTTCACATCCATTGGCTTTGCAAGAGTCAATCTCAATGCAAAGAGATAGT\nAGTTTCAATCCCTCCATGAGAAGCATTCTGGGTTCGGTTTGGACCAAAAAGGCTAGCTTT\nTGTCTCGATAGCTTCTCAT\n" }, { "path": "tests/input/TestOrderAndOrient/expected.lasv.fasta", "content": ">gi|23343509|ref|NC_004296.1|_contigs_ordered_and_oriented\nGCACAGTGGATCCTAGGCTATTGGATTGCGCTTTGCTTTTGTCATTTCAGCAGACATTCT\nCAGCCTCTTGTTGCGTGCATTTAACACAACAATCTGGCGATGAGTGCCTCAAAGGAAATC\nAAATCCTTTTTGTGGACACAATCTTTGAGGAGAGAACTATCTGGTTACTGCTCCAACATC\nAAACTACAGGTGGTGAAAGATGCCCAGGCTCTTTTACATGGACTTGACTTCTCTGAGGTC\nAGCAATGTTCAACGGTTGATGCGCAAGGAGAGAAGGGATGACAGTGATTTGAAACGATTG\nAGAGACCTAAATCAAACAGTCAACAATCTTGTTGAATTAAAATCAACTCAACAGAAGAGT\nATACTGAGAGTTGGGACTCTAACCTCAGATGACTTATTAATCTTAGCCGCTGATTTAGAG\nAAGTTGAAGTCAAAGGTGATCAGAACAGAAAGGCCATTGAGTGCAGGTGTCTATATGGGC\nAATCTGAGCTCACAGCAACTTGACCAAAGAAGAGCTCTTCTGAATATGATAGGAATGAGT\nAGTGGTAATCAAGGGGCTCAGGCTGGGAGAGATGGAGTGGTAAGAGTTTGGGATGTGAAA\nAATGCAGAGTTGCTCAATAATCAGTTCGGGACCATGCCAAGTCTGACACTGGCATGTCTG\nACAAAACAGGGGCAGGTTGACTTGAATGATGCAGTACAAGCATTAACAGATTTGGGTTTG\nATCTACACAGCAAAGTATCCCAACACTTCAGACTTAGACAGGCTGACTCAAAGCCACCCC\nATCCTAAATATGATTGACACCAAGAAAAGCTCCTTAAATATCTCAGGTTACAATTTTAGC\nTTGGGTGCAGCTGTAAAGGCAGGAGCTTGCATGCTGGATGGTGGCAATATGTTGGAAACA\nATCAAGGTGTCACCTCAGACAATGGATGGTATCCTCAAATCCATCTTAAAGGTCAAGAAG\nGCTCTTGGAATGTTCATTTCAGACACCCCTGGCGAGAGGAATCCTTATGAAAACATACTC\nTACAAGATTTGTTTGTCAGGGGATGGATGGCCATATATTGCATCAAGAACTTCAATAACA\nGGAAGGGCCTGGGAAAACACTGTCGTTGATTTGGAATCAGATGGGATGCCACAGAAGGCT\nGGTAGCAGCAGTTCCAATAAATCCCTGCAGTCGGCAGGGTTTGTCGCTGGGCTTACCTAT\nTCTCAGCTGATGACCCTCAAAGATGCAATGCTGCAACTTGACCCAAATGCTAAGACCTGG\nATGGATATTGAGGGAAGACCTGAAGATCCAGTGGAAATTGCCCTCTATCAACCAAGTTCA\nGGCTGCTACATACACTTCTTCCGTGAACCTACTGATTTAAAGCAGTTCAAACAAGATGCT\nAAGTACTCACATGGTATTGATGTTACAGACCTCTTCGCTGCACAACCGGGCTTGACCAGT\nGCTGTTATTGATGCACTCCCCCGGAATATGGTCATTACCTGTCAGGGGTCCGATGACATA\nAGGAAACTTCTTGAATCACAAGGAAGAAAGGATATCAAACTAATTGATATTGCCCTCAGC\nAAAGCTGATTCCAGGAAGTATGAAAATGCAGTCTGGGATCAGTATAAAGACCTATGCCAC\nATGCACACAGGTGTTGTTGTTGAAAAGAAGAAAAGAGGCGGCAAGGAGGAAATAACCCCT\nCACTGTGCACTAATGGACTGCATCATGTATGATGCAGCAGTGTCAGGAGGACTGAACACA\nTCAGTTTTGAGAGCAGTGCTGCCCAGAGATATGGTGTTCAGAACATCGACACCCAGAGTC\nGTCCTGTAAATGGACGCCCCCGTGACCCACCGCCAATAGGCGGTGGGTCACGGGGGCCCT\nGACAAGGGTCTCATCTCTTCCATTTTACAGGCACACCAGGCTGTTTGTAGAGTCCACAAG\nAACATATGCCCATGTGATTCAGTCTGTGAGGTTTGGGACACGACTTGCCTACAACATGCC\nTATGAGTTGGTATTTTGACCAGGTGGAGGAAGATGCTAATGAGATAGAAACTTGTGCTGA\nACACAAAGAGGTCAACCAGGCCCAATGGTGTCTTCCCCTGCCTCTCCATGTACTCCTTCT\nGTAACATCTCAGTGATCATGTTGTCAGCTTGTTGTTCAATATCATCAGAAAAGTGAGTCT\nCGTTCAAGTACGAACCATTTGATACAAGCCAACATTTGGGCAGTGATGTTTTCCCAGTAG\nTTGTGTGGTTGAGGTACCAATACTTGCTGTAATTACAGTATGGAATTCCCATGATGTCCC\nGCAGGTGGTTCTTCATTATGAGTTGGTCATTTATTAAAGCATTTACTGCTTTGTTGATCA\nACTGAATGCTCATTTGTGCTTCAGCTTTCAACCTTTGAATGGCTTGTTTATTGAAGTCAA\nACAGCCTCAGCATGTCACAAAACTCCTCATCATGTTTCTCATTACATTTTGCTACAGCTG\nTGTTCCCGAAGCATTTTAGTTCAGCCTCAATTAGCATCCATCTGGTCAGACAATATCCCC\nCTGGTGCGTCATTGCCTTCAGAATCTGATAGTGTCCATGTGAATGTGCCTAGTAGTCTTC\nTGCTAATGTAAATATCTCTGGTCCTTTGTGAGAGGAGCCCAAGGTAACCGATAGGAGATG\nGTCTCGAGAATTGGCAGTGATCTTCCCAGGTTGTATTTTGGATTATTAAATATTGATAAC\nTAGTCATGATACAGTCCCAATTACCATGACCTGAGTCAAGAGCAATGTAGCTCCCACCCC\nAAGCCATCCTCATGAAAGTCTGCAATACACCATTTGCAACAGTGCCACAATGGTTGGCTG\nCATCTACAGCATAGCTATGACTCAAGTTGTACTGCACACTAATTTTTCCCCCATTAAAAT\nCGCAGCTCATCGCCTCATACTGATTGAAGTTGGGGATGGACAAGTGGAAAGTTGAGATTA\nTGCTCATAAGAGCGTGGTCATAGAGGTTCTTTTTGTGGGCATCAGACAGATTACAAAATT\nTATGATTAATAATGCTCGTGTTAGTCAAGGTCAGTTCTAGTCCTGTCTCATTGCCCACCC\nTTATATAATGATGACTGTTGTTCTTTGTGCAGGAGAGAGGCATGGTCATATTGAGTGTCT\nCCATGTTTAGTTCCAGAGTCTGGAGCTCATAAACCCCTTTATAGAGGCTGGTTGTGCAAG\nACTTACCACACAACAGGAGGAAAGTGACCAAACCAACAAGGCCACATGTTGCAATGTTGT\nACAGACCTTTCAACACTGCCAGTATAGACAGTGTAATGAGAACAATGTTCATCACCTCTT\nCTATTACATGAGGCACTTCTTGGAAGAATGTCACTATTTGTCCCATTTTAAATAGGACAC\nTTGAATTGCGCAACCAAAAATGCCTAGGATCCCCGGTGCGC\n>gi|23343512|ref|NC_004297.1|_contigs_ordered_and_oriented\nCGCACCGGGGATCCTAGGCAATTTGGTTGTTCTTCTTTTTGAGGCTTTGTACGCTGAACT\nCTTCCAAATGGGAAACAAGCAATCCAAAGCCCCAGAATCAAGAGACAGTCCAAGAGCCAG\nCCTGATCCCGGATGCCACACATCTAGGGCCACAGTTCTGCAAGAGCTGCTGGTTCGAAAA\nCAAGGGCCTGGTTGAGTGCAACAACCACTATCTGTGTCTCAACTGCCTCACCTTACTTCT\nGAGTGTCAGCAACAGGTGCCCCATTTGCAAGATGCCTCTCCCCACAAAGCTGAGACCATC\nAGCCACTCCAACAGCACCTCCAACTAGAGCAGCAGACAGCATCAGACCCCCACCCTACAG\nTCCCTGAGTCTCCCACCGACCCCCACCACTCNNNNNNNNNNNNNNNNNNCCCCCGGGGGG\nACCCCCCGCCGGGGGCCCCCCCGGGGGAGCCAACCATCACCAAAAGACTACTCAATGTCC\nTCGATACATTCATCTTTCCTAGTCAACTCTTCACATGTTCTGCCCTTCAGTCTCAATTTA\nCCACTACTTGACTGTACCATCACCTTCCCCCTTGACTTACTGTAACAGAGAGCGTAACCC\nTTGAACTCCACCCAATTGTCCACTGCCTCAAGAACCGCACTCAAGATCCCCTCACAACTC\nGGCGCTGCAGCCCTAAGTGTGGAGATGATGTCCACCCCTGACCACTGCATCCTTAATCCC\nAGCCTATCTATCATCATATCACTCAGTGCCCCAATCAGCAGGTCAGACGAAGTGTCCCCA\nACCTCTCTCACAAACACCTCAAGATCCTGGTCTTGTATAACAGGTGTAAAGGATGCTAAC\nCTCCTTCCACATTCCCACAAGCCACCTCTATGCACAACCAGAGGGGCTGGTTCAGTGCAA\nGGACCCACCAATACAAAGTCATACTCCGTAAACTGCAACTTTTCCATATCAACAACAATC\nTCAACAGGGGTCACATGCCCCAGTTGATTTGTATCAACCAAAAACTCATTAATGATTTCG\nGTGTCAACATACCATGCTGATTTGCCCTTGAAAGTGGGTCCTGACAAAACCAGTCTCCAG\nCAGTCTGACAAAACACACGGATTCACTGCACCTGAGTACATAACGGTTACATCATGTACT\nAAATACTTGGCTTGTTGACTCATTGAGCCAGTATACTCCAGGTGGATGGCAAAGCTTTCC\nTTGAAACTAGCATCTTGACTTTTGACACGGAACCTCACTGTCTGACTCAATTTTGCAGAC\nCCTGAAGGTAGTGAAGCTACGGCATCAAAGAAATCCTCCAATGAGTCAAACTTGAGATCA\nACTAAACCAGATGCGATCAATTGATTTTGGTTGAATCTAGCTGGCTCAATATCAAAGTCT\nATCCAAGCATAACCCATCATCAGATCATGTTTGTACATTGGCCTTTCAACACCTTTGTGA\nATAACTTTCTCTACAAATGAGGAAAATGGACCCATTCTATGCAACCCTTCACCCTCTGGA\nACTGATGTCTTGTGTGGAAACCACGTGAAGGACCCCAATGTTCTTGTAGTCGCAACAAAT\nGGCCTCACATAAGACTCAAAATAAATTTGCCTCATGAAATTGTCAACAGCATCGCTAGTG\nCTCACTACTCTTTCTTCCACCATAGGCTCATGTGTCCTACTATGAGATAGCCTCAGCTCA\nGATGACAACACAATGTAATGTTCCTCCCTTTTCCATTTTACTATATGTGAGACAAGAGAC\nAAGGCTTCACAGTTAACATCCAACGCTACACAGAGATCTAGAAATTTTATTCTGGGTGAC\nCACTTCATTTTAGTTGACGCTAGATCGCTCATGAATGGTAATATGTGTTTTTCAAACACT\nGATGGGTACAGCCTCCTTAAAGAATGAATGATGTGATTCAAACCAACCCTATCCTCTAAT\nAGTTTTGACGCAGTTGGCTTTAAGGGGAAATAGTCACAGGGGTTATGCTTGAAAAAATCC\nAACACCTTAACTGTCTTAGGTTCCCCTAAGACCCATGCACCCAGTTCTATTGCAGTTGAT\nAATGATATGCACATATAATCCCATAACAAGGGTCTGAAATAACTAATGACATCATCATTT\nCCACTTCCATTTCTTAGTTCTAACGGAACCTGCCAATATTGAATACCATTAGAATTTGTC\nAACAATTTGATTCCCTTAACATCAGAAATCAGAGACTGAATGGACTTAATATACAGATTC\nTCTTTATTTGGTCCCCGAACACATTTGCTACCCAATGTTCTGCATAATCCCACAAAGCCA\nGATGCAATGGAACTTTGGAATGCAGATTTGTTAATAGCTTCAGACAGCAATTTTTGCGCA\nCCTCGAGTAAAAGTGGAAGACAACTTATTTTGGATTGTTTTGACAATGGTAGGAATCTTC\nTCATCATCTAGGTTCACAGCACCTGAATATATTATCTTTTGTCTCAACACCATTCTTAAA\nGGATGATGTGCGGCTAAGTTTAACCAAGAGTACTCAAGGTCAGACTCAGATGGAGATTCA\nACACCTAACAGCTCACAAAGATTTCTTAGTGAAGAGAGGTGCTCACTAGACAAATAGTTT\nGTTGTAAACTCTTCATGGAGTTGCCCAGTCTTCAACCTATTGTACAGTTTTCTTAACATA\nGATCTAATCTTGCTGCAAGCGTTGGGAATCAATCCCTCTATTTGTCTCATGATTCTATAA\nCTACGGTTGCCATCCACCCAATCTCTAACATCTGTCTCGCAATTCAATAAAAATGGGTCA\nATAGGGTATCTTGCATATTGCAAAAGACTTAAGGTTCTTTTCTGTATTAGATTGCATAAG\nTGAACAGGGACACCATTTGCAACCGACTGATCAATGATTGTGTCAATTGTTTCTGCCAGT\nTGGTGTGGCTCTTTACACTTTATATTGTGAAGAGCTGCTGCAACGAACTTTGTCAACAAT\nGGCACCTCATCTCCCCAAACAAAAAATCTAGATTTAAACTCAGCAACAAACCTGCCAATA\nACACTTTTAGGGCTCACAAACTTATTGAGTTGATCACTCATATAATAATGGAACTCTATT\nAGAGTCCTAAATTCTTCTGGGTCCCTCTGCAAAAGCTCTGTGAGAGATTGATCAAAGAGA\nGAAATTTGATCATCACTAGAGGTATAAGCATCTATAGTACCACCACATATACAACTGATA\nGCATAATTAATGAACCTCTCTGAAATAAGGGCATAAAAATCTGATGTGTTGTGTAATATT\nCCCTGACCCATGTCAAGTATTGAACTAATGTGAGAAGGCACTACACCGACTTGGAAATTA\nGAGTAAAAGAAATCTTCTGTTATTGACTGTTTAGTTTTCTTCCTTAACCCTAGTTGAGCT\nTTAATGAAAGACTTCATCATGGCTGTCACCACATTAAAAGGTATTTCCACCATTTTGTGC\nATATGCCACATGAGTAGGGTTGAAAGATAGTCCCTCCCTTTTATGTCAGCTTGCAAGTCC\nCTTGAGAGGAAAATCAAATTCTGTAAGACAGTCAAGAACAAAAATGGACACATCATTGGG\nCCCCACTTACTATGATCCATGCTATAGGACACATGCGCTAATGAAACATTCAATTTCATG\nGAGAGGATAGCATTCTCAAACTCCTTCTCGTTGTTCAAGCAACTCCCTGACAACTGTAGG\nCTTATAGCTTCAAAGTAATCTTCTATAAGTCTAGTAAACATCTTTGTTCTAAGATCACCA\nATATATAGTTCTCTGTTGCCACCCACTTGTTCTTTATATGACAAAGAGAACTTAAGCCTT\nCCTGTATCAGGTCCCACTGAGTCATAAGATTGTGGCGACTCTTGGCTATAAAAACACAAA\nTTCTTTAACATTGCTGTGGTACAGTTTGTCAGTGACAGAGCCTTACTAAGTGCCTCTGAG\nTTGCTCTCCCTTTCACTAATTCTCACATCATCAGAGAGTTTACCCATGTCAAACTTGAAA\nTTAAGGTTCCTTGACTTATAATGAGTGTACCTCCCCATAAGTGCATTTGCATTCATGATC\nAAGAGTATGGACTTAAAACACTGAAAGTATTCATGGTTAAAGTATGTCCTTGTTGATACT\nGCCTTTGTCAACTCTCCAATAGGACACTGTGACATATGTCCACAGTAAAAATACTTCTCC\nTTCAATCTACTATTCTCATAGACAGCATTACAGAATTCTTCATAAAATTTACCTGGTAAG\nATATCATAATCAAAATCCTCAACCATGTGATTAGATAATTCACCCTTAATCAACCTAATG\nTAAAACTTATTTGAGACAATCTCATCTAGATCATTTATTGACGGTTGGCCATCACCATTA\nGGGCCTGAGCCTGGCTTGGTGGGTTCCCTATACTGATCGACAATTTTTTCAACAGTCTCT\nTTTAGCTGATCAAAATAATCGCTTGCACCTCCATCGAGCAAAATTTCATCTAGGTCAGCT\nCCATCAACATCACTTTTGAGCTGCCCAGATCCTAGAACCAAATTGCTCATTGCCTGCTGA\nACTTTGTATTCATAGTCCTGCTTGTTGAGAAGGTACTTTCCTTTTCTTGAGAAGACTTCA\nGTGAGCTGCGACACGGCCAGTGCTGTGAGCTTATTGAAGTCATAGTTTAATATTCTAGAA\nCCATCTGTGTACTTATTAACAACAACACTTTTGTTGCTGGCTAAATCCAAGGCAGTGGCA\nCAGCCACTGGTGATGAGAGGATCTTTGATTTCCCTTTTTACTTCCCTCTCCTTAAATAGT\nGAACCATTGTTGAAAGAAGACGTAAGAAGGGACAAATACTTCTTTGAAACACCAGGCCTT\nTTATAGTCTGGTCCCTCGACACTTGTGCATCCATCTTTACTTAAAAACTTTTTTGCATTA\nTAGACCATGTCGTCCAATTCTTCCTCGGTAGCTGTATCTGCAGGGTTAGTGCTCACATGA\nCCAAATTTCACCTTTGGTTCCAAAAACTTCTCAAAACATTTTATCTGATCTGTTAATCTA\nTCTGGTGTTTCTTTCGTAATGAAGTGGCACATGTAAGAAATATTCAAAATGAACTTGAAC\nCTATTGGTCATCATGCTCTTCACATCTTCAGATAAAACTAAACTCATTAATGTCCTTATT\nAACCTATAGAGCAGGAACTCAACATCAGTGATTAATTCTTCCCTTATTTTGTCAACGAGG\nTCCTTATGATGATAATCTGACACATAAGCCATTACAAAATACCTAAGATTTTGGAGGAGC\nTTTTGAGAACGTTTACTGGGGTGAGCTAAAATTAAAACCAGGATCATCTTTGTCAAAAAC\nTTTATGTTGTTCAACTGCCCTTCCAGCTCACTGCAATCTTCTATCCAAGAAATCATAGTG\nCTTATTGTTGTCTGTAAAACCTCAGCTGAAAATATTGCTGGAAAATATCTTTTAGGATCA\nGCGTAAAATGAGCACACCTCACCAACTTTGTTATCATTAATAGCATAGCACTTCGAGCAT\nTCCCCTGTTTTTTGATAAATCAGTTGGAATTCAGAGTTTCCTAATGAAAACTCTTGACAA\nTATGCTTCTTTGCATCTGACCACCTGATACCTTGCGGGTCCAAACTCATTCTGCCTCAAT\nTTTACGGTAGAAGAAGTTTTCATAGAGTTCACCAAGGCGAGGCTCAATGAAGAAAGTCTC\nTCTAAGTCAGTGGTTCCCAGTAGTTCCACATCCCCCATCACATAAGGGAATGTTTCTTCC\nTCTGTTCTCTGATAACTGATTGTGGGAACAATTCCGGAGACATCAAAATCCATAATCAAA\nTCATAACTATTAAGGCAAACCACCTCCATGTCAATTTTATAGTGGTCTACACTGATTCCA\nACATCCTCTAAAGCAGTGGTGGCCTTCAAAATGGTTTTCTGGAATATTGAATTGAGAATT\nTGGTTCTTACTCAAACACTGGGAGGACTGTGTGTTTCTAGATCTCTCAGCCTGTTGCCTC\nCGCTCAACCCATTTCTCAAGATCCCTTTTTGTTGACTCTAAAGAAACTAGTCTATCATTT\nACACTTAAGAAGCAAGACCCCAACCACCCTTTTAAACACTTTTGTTTCATTAGGTCATAC\nTTGCTTGCAAGGAGAATTAATGCATCAAAAATTAATAGAAGTTTCCTCCTTGTGTTCAAT\nATCCTCAAAGATTTTACTTTATTCAGGAATGATCTCCAGCATTGAACCTGACATTCTCCA\nATGGTTTGGTTTTCCCTCTTTTCATTCCCCTCCTCAATGTTTGCATACAGAAATCTCAAT\nATTGGTGATGCTCTCTTGAACTGATAAATCAAGTGTTCGATATTGTCTTCTGCAGCTACC\nTTATCAGCGTACAAATTATTAAGTTCATTAAGTAATTGGTTCTTATCAACCTTCAGAAAC\nTGACCTTCTATCTCTCCTTTCCTCAATCTGTTCCTAAACACTTGATACTCCTCTTCGATC\nTGCAGCTTTACCTCATGGGCTGTTAACTTATTATTGATGCCTTGATGGCATGAGGCAATC\nACTTCCTCATAATGATTGGAGCGATTGTCCATCAGAACATTTAAACTCTCCACCCCTGAT\nAATCTACCCGAAGTCATGGATAAAGATTCACAGAGTCTACTATACTCTGATTCTTCAAAA\nAGTGAATTACTCTCCTGTGCATACTTTAAAAGTGAAAAGAGCGTATCCCTCAACTTGTCA\nTTGACCCAGTCAGGTATTTGTTCATTGTAGAATGATGTCCTCCCGTCTATGAGTGGTATT\nAAATTGATATCGACACTCTTCAAGTCTTCTTTCAATTGCTCTAATTTTTTGAAGTCCTCA\nATGTACTTCTGCTCAAAGTTAGCAGGAGATGACCTAACAAAACACTCCAGCAGTATTAGA\nACATTGCCCGTCAGTTTGTAACCGTCCGGCACCACAAAACATAGTGAAGGTGTCAAGATT\nCCATGGTCATGGAGAATTCTTTCCACAGATTTGTCCTCACTATTATGCTCGCAACCATTT\nGCGTTGCAAGAATCAACCTCAATACAGAGGGACAAGAGTTTCAACCCTTCCATTAGTAGC\nATCCTAGGCTCTGTCTGTACAAGAAATGCTAACTTCTGTCTAGATAATCTCTCATTGTCC\nACTAGATACTTTGATACTAAGTCTTTGACACAGGCTATGTCTTCCTCCATGTCTGGCCAC\nGAGTATGTTGGTCAGAACCCTCAAAACATGTGATCTGCTAGAGCAACAGTTCACCACAGG\nCCAGGGTCCCGTGGGGGGCACAAGGGATACAAGAGGCAATTAAAGACAATTAAATTAGAT\nAGCCTTAATGCCTAGGATCCTCGGTGCG\n" }, { "path": "tests/input/TestOrderAndOrient/expected.lasv.promer.fasta", "content": ">pseudo_used_gi|23343509|ref|NC_004296.1|\nCACAGTGGATCCTAGGCTATTGGATTGCGCTTTGCTTTTGTCATTTCAGCAGACATTCTC\nAGCCTCTTGTTGCGTGCATTTAACACAACAATCTGGCGATGAGTGCCTCAAAGGAAATCA\nAATCCTTTTTGTGGACACAATCTTTGAGGAGAGAACTATCTGGTTACTGCTCCAACATCA\nAACTACAGGTGGTGAAAGATGCCCAGGCTCTTTTACATGGACTTGACTTCTCTGAGGTCA\nGCAATGTTCAACGGTTGATGCGCAAGGAGAGAAGGGATGACAGTGATTTGAAACGATTGA\nGAGACCTAAATCAAACAGTCAACAATCTTGTTGAATTAAAATCAACTCAACAGAAGAGTA\nTACTGAGAGTTGGGACTCTAACCTCAGATGACTTATTAATCTTAGCCGCTGATTTAGAGA\nAGTTGAAGTCAAAGGTGATCAGAACAGAAAGGCCATTGAGTGCAGGTGTCTATATGGGCA\nATCTGAGCTCACAGCAACTTGACCAAAGAAGAGCTCTTCTGAATATGATAGGAATGAGTA\nGTGGTAATCAAGGGGCTCAGGCTGGGAGAGATGGAGTGGTAAGAGTTTGGGATGTGAAAA\nATGCAGAGTTGCTCAATAATCAGTTCGGGACCATGCCAAGTCTGACACTGGCATGTCTGA\nCAAAACAGGGGCAGGTTGACTTGAATGATGCAGTACAAGCATTAACAGATTTGGGTTTGA\nTCTACACAGCAAAGTATCCCAACACTTCAGACTTAGACAGGCTGACTCAAAGCCACCCCA\nTCCTAAATATGATTGACACCAAGAAAAGCTCCTTAAATATCTCAGGTTACAATTTTAGCT\nTGGGTGCAGCTGTAAAGGCAGGAGCTTGCATGCTGGATGGTGGCAATATGTTGGAAACAA\nTCAAGGTGTCACCTCAGACAATGGATGGTATCCTCAAATCCATCTTAAAGGTCAAGAAGG\nCTCTTGGAATGTTCATTTCAGACACCCCTGGCGAGAGGAATCCTTATGAAAACATACTCT\nACAAGATTTGTTTGTCAGGGGATGGATGGCCATATATTGCATCAAGAACTTCAATAACAG\nGAAGGGCCTGGGAAAACACTGTCGTTGATTTGGAATCAGATGGGATGCCACAGAAGGCTG\nGTAGCAGCAGTTCCAATAAATCCCTGCAGTCGGCAGGGTTTGTCGCTGGGCTTACCTATT\nCTCAGCTGATGACCCTCAAAGATGCAATGCTGCAACTTGACCCAAATGCTAAGACCTGGA\nTGGATATTGAGGGAAGACCTGAAGATCCAGTGGAAATTGCCCTCTATCAACCAAGTTCAG\nGCTGCTACATACACTTCTTCCGTGAACCTACTGATTTAAAGCAGTTCAAACAAGATGCTA\nAGTACTCACATGGTATTGATGTTACAGACCTCTTCGCTGCACAACCGGGCTTGACCAGTG\nCTGTTATTGATGCACTCCCCCGGAATATGGTCATTACCTGTCAGGGGTCCGATGACATAA\nGGAAACTTCTTGAATCACAAGGAAGAAAGGATATCAAACTAATTGATATTGCCCTCAGCA\nAAGCTGATTCCAGGAAGTATGAAAATGCAGTCTGGGATCAGTATAAAGACCTATGCCACA\nTGCACACAGGTGTTGTTGTTGAAAAGAAGAAAAGAGGCGGCAAGGAGGAAATAACCCCTC\nACTGTGCACTAATGGACTGCATCATGTATGATGCAGCAGTGTCAGGAGGACTGAACACAT\nCAGTTTTGAGAGCAGTGCTGCCCAGAGATATGGTGTTCAGAACATCGACACCCAGAGTCG\nTCCTGTAAATGGACGCCCCCGTGACCCACCGCCAATAGGCGGTGGGTCACGGGGGCCCTG\nACAAGGGTCTCATCTCTTCCATTTTACAGGCACACCAGGCTGTTTGTAGAGTCCACAAGA\nACATATGCCCATGTGATTCAGTCTGTGAGGTTTGGGACACGACTTGCCTACAACATGCCT\nATGAGTTGGTATTTTGACCAGGTGGAGGAAGATGCTAATGAGATAGAAACTTGTGCTGAA\nCACAAAGAGGTCAACCAGGCCCAATGGTGTCTTCCCCTGCCTCTCCATGTACTCCTTCTG\nTAACATCTCAGTGATCATGTTGTCAGCTTGTTGTTCAATATCATCAGAAAAGTGAGTCTC\nGTTCAAGTACGAACCATTTGATACAAGCCAACATTTGGGCAGTGATGTTTTCCCAGTAGT\nTGTGTGGTTGAGGTACCAATACTTGCTGTAATTACAGTATGGAATTCCCATGATGTCCCG\nCAGGTGGTTCTTCATTATGAGTTGGTCATTTATTAAAGCATTTACTGCTTTGTTGATCAA\nCTGAATGCTCATTTGTGCTTCAGCTTTCAACCTTTGAATGGCTTGTTTATTGAAGTCAAA\nCAGCCTCAGCATGTCACAAAACTCCTCATCATGTTTCTCATTACATTTTGCTACAGCTGT\nGTTCCCGAAGCATTTTAGTTCAGCCTCAATTAGCATCCATCTGGTCAGACAATATCCCCC\nTGGTGCGTCATTGCCTTCAGAATCTGATAGTGTCCATGTGAATGTGCCTAGTAGTCTTCT\nGCTAATGTAAATATCTCTGGTCCTTTGTGAGAGGAGCCCAAGGTAACCGATAGGAGATGG\nTCTCGAGAATTGGCAGTGATCTTCCCAGGTTGTATTTTGGATTATTAAATATTGATAACT\nAGTCATGATACAGTCCCAATTACCATGACCTGAGTCAAGAGCAATGTAGCTCCCACCCCA\nAGCCATCCTCATGAAAGTCTGCAATACACCATTTGCAACAGTGCCACAATGGTTGGCTGC\nATCTACAGCATAGCTATGACTCAAGTTGTACTGCACACTAATTTTTCCCCCATTAAAATC\nGCAGCTCATCGCCTCATACTGATTGAAGTTGGGGATGGACAAGTGGAAAGTTGAGATTAT\nGCTCATAAGAGCGTGGTCATAGAGGTTCTTTTTGTGGGCATCAGACAGATTACAAAATTT\nATGATTAATAATGCTCGTGTTAGTCAAGGTCAGTTCTAGTCCTGTCTCATTGCCCACCCT\nTATATAATGATGACTGTTGTTCTTTGTGCAGGAGAGAGGCATGGTCATATTGAGTGTCTC\nCATGTTTAGTTCCAGAGTCTGGAGCTCATAAACCCCTTTATAGAGGCTGGTTGTGCAAGA\nCTTACCACACAACAGGAGGAAAGTGACCAAACCAACAAGGCCACATGTTGCAATGTTGTA\nCAGACCTTTCAACACTGCCAGTATAGACAGTGTAATGAGAACAATGTTCATCACCTCTTC\nTATTACATGAGGCACTTCTTGGAAGAATGTCACTATTTGTCCCATTTTAAATAGGACACT\nTGAATTGCGCAACCAAAAATGCCTAGGATCCCCGGTGCG\n>pseudo_used_gi|23343512|ref|NC_004297.1|\nTTCCAAATGGGAAACAAGCAATCCAAAGCCCCAGAATCAAGAGACAGTCCAAGAGCCAGC\nCTGATCCCGGATGCCACACATCTAGGGCCACAGTTCTGCAAGAGCTGCTGGTTCGAAAAC\nAAGGGCCTGGTTGAGTGCAACAACCACTATCTGTGTCTCAACTGCCTCACCTTACTTCTG\nAGTGTCAGCAACAGGTGCCCCATTTGCAAGATGCCTCTCCCCACAAAGCTGAGACCATCA\nGCCACTCCAACAGCACCTCCAACTAGAGCAGCAGACAGCATCAGACCCCCACCCTACAGT\nCCCTGAGTCTCCCACCGACCCCCACCACTCNNNNNNNNNNNNNNNNNNNCCCCGGGGGGA\nCCCCCCGCCGGGGGCCCCCCCGGGGGAGCCAACCATCACCAAAAGACTACTCAATGTCCT\nCGATACATTCATCTTTCCTAGTCAACTCTTCACATGTTCTGCCCTTCAGTCTCAATTTAC\nCACTACTTGACTGTACCATCACCTTCCCCCTTGACTTACTGTAACAGAGAGCGTAACCCT\nTGAACTCCACCCAATTGTCCACTGCCTCAAGAACCGCACTCAAGATCCCCTCACAACTCG\nGCGCTGCAGCCCTAAGTGTGGAGATGATGTCCACCCCTGACCACTGCATCCTTAATCCCA\nGCCTATCTATCATCATATCACTCAGTGCCCCAATCAGCAGGTCAGACGAAGTGTCCCCAA\nCCTCTCTCACAAACACCTCAAGATCCTGGTCTTGTATAACAGGTGTAAAGGATGCTAACC\nTCCTTCCACATTCCCACAAGCCACCTCTATGCACAACCAGAGGGGCTGGTTCAGTGCAAG\nGACCCACCAATACAAAGTCATACTCCGTAAACTGCAACTTTTCCATATCAACAACAATCT\nCAACAGGGGTCACATGCCCCAGTTGATTTGTATCAACCAAAAACTCATTAATGATTTCGG\nTGTCAACATACCATGCTGATTTGCCCTTGAAAGTGGGTCCTGACAAAACCAGTCTCCAGC\nAGTCTGACAAAACACACGGATTCACTGCACCTGAGTACATAACGGTTACATCATGTACTA\nAATACTTGGCTTGTTGACTCATTGAGCCAGTATACTCCAGGTGGATGGCAAAGCTTTCCT\nTGAAACTAGCATCTTGACTTTTGACACGGAACCTCACTGTCTGACTCAATTTTGCAGACC\nCTGAAGGTAGTGAAGCTACGGCATCAAAGAAATCCTCCAATGAGTCAAACTTGAGATCAA\nCTAAACCAGATGCGATCAATTGATTTTGGTTGAATCTAGCTGGCTCAATATCAAAGTCTA\nTCCAAGCATAACCCATCATCAGATCATGTTTGTACATTGGCCTTTCAACACCTTTGTGAA\nTAACTTTCTCTACAAATGAGGAAAATGGACCCATTCTATGCAACCCTTCACCCTCTGGAA\nCTGATGTCTTGTGTGGAAACCACGTGAAGGACCCCAATGTTCTTGTAGTCGCAACAAATG\nGCCTCACATAAGACTCAAAATAAATTTGCCTCATGAAATTGTCAACAGCATCGCTAGTGC\nTCACTACTCTTTCTTCCACCATAGGCTCATGTGTCCTACTATGAGATAGCCTCAGCTCAG\nATGACAACACAATGTAATGTTCCTCCCTTTTCCATTTTACTATATGTGAGACAAGAGACA\nAGGCTTCACAGTTAACATCCAACGCTACACAGAGATCTAGAAATTTTATTCTGGGTGACC\nACTTCATTTTAGTTGACGCTAGATCGCTCATGAATGGTAATATGTGTTTTTCAAACACTG\nATGGGTACAGCCTCCTTAAAGAATGAATGATGTGATTCAAACCAACCCTATCCTCTAATA\nGTTTTGACGCAGTTGGCTTTAAGGGGAAATAGTCACAGGGGTTATGCTTGAAAAAATCCA\nACACCTTAACTGTCTTAGGTTCCCCTAAGACCCATGCACCCAGTTCTATTGCAGTTGATA\nATGATATGCACATATAATCCCATAACAAGGGTCTGAAATAACTAATGACATCATCATTTC\nCACTTCCATTTCTTAGTTCTAACGGAACCTGCCAATATTGAATACCATTAGAATTTGTCA\nACAATTTGATTCCCTTAACATCAGAAATCAGAGACTGAATGGACTTAATATACAGATTCT\nCTTTATTTGGTCCCCGAACACATTTGCTACCCAATGTTCTGCATAATCCCACAAAGCCAG\nATGCAATGGAACTTTGGAATGCAGATTTGTTAATAGCTTCAGACAGCAATTTTTGCGCAC\nCTCGAGTAAAAGTGGAAGACAACTTATTTTGGATTGTTTTGACAATGGTAGGAATCTTCT\nCATCATCTAGGTTCACAGCACCTGAATATATTATCTTTTGTCTCAACACCATTCTTAAAG\nGATGATGTGCGGCTAAGTTTAACCAAGAGTACTCAAGGTCAGACTCAGATGGAGATTCAA\nCACCTAACAGCTCACAAAGATTTCTTAGTGAAGAGAGGTGCTCACTAGACAAATAGTTTG\nTTGTAAACTCTTCATGGAGTTGCCCAGTCTTCAACCTATTGTACAGTTTTCTTAACATAG\nATCTAATCTTGCTGCAAGCGTTGGGAATCAATCCCTCTATTTGTCTCATGATTCTATAAC\nTACGGTTGCCATCCACCCAATCTCTAACATCTGTCTCGCAATTCAATAAAAATGGGTCAA\nTAGGGTATCTTGCATATTGCAAAAGACTTAAGGTTCTTTTCTGTATTAGATTGCATAAGT\nGAACAGGGACACCATTTGCAACCGACTGATCAATGATTGTGTCAATTGTTTCTGCCAGTT\nGGTGTGGCTCTTTACACTTTATATTGTGAAGAGCTGCTGCAACGAACTTTGTCAACAATG\nGCACCTCATCTCCCCAAACAAAAAATCTAGATTTAAACTCAGCAACAAACCTGCCAATAA\nCACTTTTAGGGCTCACAAACTTATTGAGTTGATCACTCATATAATAATGGAACTCTATTA\nGAGTCCTAAATTCTTCTGGGTCCCTCTGCAAAAGCTCTGTGAGAGATTGATCAAAGAGAG\nAAATTTGATCATCACTAGAGGTATAAGCATCTATAGTACCACCACATATACAACTGATAG\nCATAATTAATGAACCTCTCTGAAATAAGGGCATAAAAATCTGATGTGTTGTGTAATATTC\nCCTGACCCATGTCAAGTATTGAACTAATGTGAGAAGGCACTACACCGACTTGGAAATTAG\nAGTAAAAGAAATCTTCTGTTATTGACTGTTTAGTTTTCTTCCTTAACCCTAGTTGAGCTT\nTAATGAAAGACTTCATCATGGCTGTCACCACATTAAAAGGTATTTCCACCATTTTGTGCA\nTATGCCACATGAGTAGGGTTGAAAGATAGTCCCTCCCTTTTATGTCAGCTTGCAAGTCCC\nTTGAGAGGAAAATCAAATTCTGTAAGACAGTCAAGAACAAAAATGGACACATCATTGGGC\nCCCACTTACTATGATCCATGCTATAGGACACATGCGCTAATGAAACATTCAATTTCATGG\nAGAGGATAGCATTCTCAAACTCCTTCTCGTTGTTCAAGCAACTCCCTGACAACTGTAGGC\nTTATAGCTTCAAAGTAATCTTCTATAAGTCTAGTAAACATCTTTGTTCTAAGATCACCAA\nTATATAGTTCTCTGTTGCCACCCACTTGTTCTTTATATGACAAAGAGAACTTAAGCCTTC\nCTGTATCAGGTCCCACTGAGTCATAAGATTGTGGCGACTCTTGGCTATAAAAACACAAAT\nTCTTTAACATTGCTGTGGTACAGTTTGTCAGTGACAGAGCCTTACTAAGTGCCTCTGAGT\nTGCTCTCCCTTTCACTAATTCTCACATCATCAGAGAGTTTACCCATGTCAAACTTGAAAT\nTAAGGTTCCTTGACTTATAATGAGTGTACCTCCCCATAAGTGCATTTGCATTCATGATCA\nAGAGTATGGACTTAAAACACTGAAAGTATTCATGGTTAAAGTATGTCCTTGTTGATACTG\nCCTTTGTCAACTCTCCAATAGGACACTGTGACATATGTCCACAGTAAAAATACTTCTCCT\nTCAATCTACTATTCTCATAGACAGCATTACAGAATTCTTCATAAAATTTACCTGGTAAGA\nTATCATAATCAAAATCCTCAACCATGTGATTAGATAATTCACCCTTAATCAACCTAATGT\nAAAACTTATTTGAGACAATCTCATCTAGATCATTTATTGACGGTTGGCCATCACCATTAG\nGGCCTGAGCCTGGCTTGGTGGGTTCCCTATACTGATCGACAATTTTTTCAACAGTCTCTT\nTTAGCTGATCAAAATAATCGCTTGCACCTCCATCGAGCAAAATTTCATCTAGGTCAGCTC\nCATCAACATCACTTTTGAGCTGCCCAGATCCTAGAACCAAATTGCTCATTGCCTGCTGAA\nCTTTGTATTCATAGTCCTGCTTGTTGAGAAGGTACTTTCCTTTTCTTGAGAAGACTTCAG\nTGAGCTGCGACACGGCCAGTGCTGTGAGCTTATTGAAGTCATAGTTTAATATTCTAGAAC\nCATCTGTGTACTTATTAACAACAACACTTTTGTTGCTGGCTAAATCCAAGGCAGTGGCAC\nAGCCACTGGTGATGAGAGGATCTTTGATTTCCCTTTTTACTTCCCTCTCCTTAAATAGTG\nAACCATTGTTGAAAGAAGACGTAAGAAGGGACAAATACTTCTTTGAAACACCAGGCCTTT\nTATAGTCTGGTCCCTCGACACTTGTGCATCCATCTTTACTTAAAAACTTTTTTGCATTAT\nAGACCATGTCGTCCAATTCTTCCTCGGTAGCTGTATCTGCAGGGTTAGTGCTCACATGAC\nCAAATTTCACCTTTGGTTCCAAAAACTTCTCAAAACATTTTATCTGATCTGTTAATCTAT\nCTGGTGTTTCTTTCGTAATGAAGTGGCACATGTAAGAAATATTCAAAATGAACTTGAACC\nTATTGGTCATCATGCTCTTCACATCTTCAGATAAAACTAAACTCATTAATGTCCTTATTA\nACCTATAGAGCAGGAACTCAACATCAGTGATTAATTCTTCCCTTATTTTGTCAACGAGGT\nCCTTATGATGATAATCTGACACATAAGCCATTACAAAATACCTAAGATTTTGGAGGAGCT\nTTTGAGAACGTTTACTGGGGTGAGCTAAAATTAAAACCAGGATCATCTTTGTCAAAAACT\nTTATGTTGTTCAACTGCCCTTCCAGCTCACTGCAATCTTCTATCCAAGAAATCATAGTGC\nTTATTGTTGTCTGTAAAACCTCAGCTGAAAATATTGCTGGAAAATATCTTTTAGGATCAG\nCGTAAAATGAGCACACCTCACCAACTTTGTTATCATTAATAGCATAGCACTTCGAGCATT\nCCCCTGTTTTTTGATAAATCAGTTGGAATTCAGAGTTTCCTAATGAAAACTCTTGACAAT\nATGCTTCTTTGCATCTGACCACCTGATACCTTGCGGGTCCAAACTCATTCTGCCTCAATT\nTTACGGTAGAAGAAGTTTTCATAGAGTTCACCAAGGCGAGGCTCAATGAAGAAAGTCTCT\nCTAAGTCAGTGGTTCCCAGTAGTTCCACATCCCCCATCACATAAGGGAATGTTTCTTCCT\nCTGTTCTCTGATAACTGATTGTGGGAACAATTCCGGAGACATCAAAATCCATAATCAAAT\nCATAACTATTAAGGCAAACCACCTCCATGTCAATTTTATAGTGGTCTACACTGATTCCAA\nCATCCTCTAAAGCAGTGGTGGCCTTCAAAATGGTTTTCTGGAATATTGAATTGAGAATTT\nGGTTCTTACTCAAACACTGGGAGGACTGTGTGTTTCTAGATCTCTCAGCCTGTTGCCTCC\nGCTCAACCCATTTCTCAAGATCCCTTTTTGTTGACTCTAAAGAAACTAGTCTATCATTTA\nCACTTAAGAAGCAAGACCCCAACCACCCTTTTAAACACTTTTGTTTCATTAGGTCATACT\nTGCTTGCAAGGAGAATTAATGCATCAAAAATTAATAGAAGTTTCCTCCTTGTGTTCAATA\nTCCTCAAAGATTTTACTTTATTCAGGAATGATCTCCAGCATTGAACCTGACATTCTCCAA\nTGGTTTGGTTTTCCCTCTTTTCATTCCCCTCCTCAATGTTTGCATACAGAAATCTCAATA\nTTGGTGATGCTCTCTTGAACTGATAAATCAAGTGTTCGATATTGTCTTCTGCAGCTACCT\nTATCAGCGTACAAATTATTAAGTTCATTAAGTAATTGGTTCTTATCAACCTTCAGAAACT\nGACCTTCTATCTCTCCTTTCCTCAATCTGTTCCTAAACACTTGATACTCCTCTTCGATCT\nGCAGCTTTACCTCATGGGCTGTTAACTTATTATTGATGCCTTGATGGCATGAGGCAATCA\nCTTCCTCATAATGATTGGAGCGATTGTCCATCAGAACATTTAAACTCTCCACCCCTGATA\nATCTACCCGAAGTCATGGATAAAGATTCACAGAGTCTACTATACTCTGATTCTTCAAAAA\nGTGAATTACTCTCCTGTGCATACTTTAAAAGTGAAAAGAGCGTATCCCTCAACTTGTCAT\nTGACCCAGTCAGGTATTTGTTCATTGTAGAATGATGTCCTCCCGTCTATGAGTGGTATTA\nAATTGATATCGACACTCTTCAAGTCTTCTTTCAATTGCTCTAATTTTTTGAAGTCCTCAA\nTGTACTTCTGCTCAAAGTTAGCAGGAGATGACCTAACAAAACACTCCAGCAGTATTAGAA\nCATTGCCCGTCAGTTTGTAACCGTCCGGCACCACAAAACATAGTGAAGGTGTCAAGATTC\nCATGGTCATGGAGAATTCTTTCCACAGATTTGTCCTCACTATTATGCTCGCAACCATTTG\nCGTTGCAAGAATCAACCTCAATACAGAGGGACAAGAGTTTCAACCCTTCCATTAGTAGCA\nTCCTAGGCTCTGTCTGTACAAGAAATGCTAACTTCTGTCTAGATAATCTCTCATTGTCCA\nCTAGATACTTTGATACTAAGTCTTTGACACAGGCTATGTCTTCCTCCATGTCTGGCCACG\nAGTATGTTGGTCAGAACCCTCAAAACATGTGATCTGCTAGAGCAACAGTTCA\n" }, { "path": "tests/input/TestOrderAndOrient/expected.refsel.ebov.stats.tsv", "content": "ref_num\tref_name\tbase_count\trank\r\n0\tKX009902.1\t18502\t1\r\n1\tKM034550.1\t18572\t0\r\n2\tKT765130.1\t18485\t2\r\n" }, { "path": "tests/input/TestOrderAndOrient/expected.refsel.lasv.stats.tsv", "content": "ref_num\tref_name\tbase_count\trank\r\n0\tgi|23343509|ref|NC_004296.1|\t10671\t0\r\n1\tgi|695316025|gb|KM822128.1|\t6192\t3\r\n2\tLASV-G502-S-Sierra_Leone-2009H\t10655\t1\r\n3\tGU481072\t9213\t2\r\n4\tnomatch.1|LASV-sized-blank-S\t0\t4\r\n" }, { "path": "tests/input/TestOrderAndOrient/ref.ebov.gin.fasta", "content": ">KT765130.1 Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Makona-Conakry-CREMS-1022, complete genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAA\nTTTTCCTCTCATTGAAATTTATATCAGAATTTAAATTGAAATTGTTACTGTAATCATACCTGGTTTGTTT\nCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGT\nTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCC\nAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGGGAA\nTTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAAC\nATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAA\nGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG\nTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCA\nACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTT\nTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAG\nGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGT\nATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCC\nGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGA\nAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGT\nAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAA\nGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTT\nTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCT\nCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTG\nGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATG\nGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGT\nAAATGTTGGAGAACAGTATCAACGGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATAT\nGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAGCTTCCATC\nAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAA\nGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATT\nCCCTTTCCAGGACCCATCAATGATGACAACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGG\nATACGACCATTCCCGATGTGGTAGTTGACCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGA\nAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCA\nGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGAC\nAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACT\nCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAACGAA\nGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTTGCCTTCCGCCCTTAGAGTCAGATGATGAAG\nAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCA\nCTCCGAAAAGAAAGAACTCCTGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAAGAACCAA\nGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCTCCACATTCTAAGATCACAGGGGC\nCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAA\nAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAAT\nGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAAT\nTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCT\nAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAAT\nAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGA\nGTCTTAATGCAAATAAGCGTTAAACCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCGATT\nTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTT\nTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGC\nACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCA\nGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGA\nGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGC\nTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAA\nTTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAAC\nCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATG\nGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGA\nCAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACC\nTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAA\nAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTG\nACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCA\nATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAG\nGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCC\nAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTT\nGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAA\nACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAA\nCTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAA\nTTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATAC\nCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCT\nACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATAT\nGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCA\nACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCAT\nCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATC\nAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATT\nTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTG\nCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGG\nAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCA\nCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTG\nCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCC\nAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCG\nGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATA\nTCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGG\nACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACC\nATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAAT\nTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAATC\nCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTT\nTCGTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCA\nTGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGC\nACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGAT\nTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTC\nTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATT\nTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATA\nTTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACAT\nCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAG\nTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGA\nTCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCT\nTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCT\nTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGG\nTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTG\nCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGT\nTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAAT\nGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTA\nATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACA\nGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATT\nTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCAC\nTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAG\nAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAG\nAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCT\nTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACA\nCCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAACGACA\nGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAGAACACCAACACGAG\nTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCCAAACTACAGCGAGACTGCTGGCAAC\nAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATA\nCTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCA\nACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGG\nATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAA\nTCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGA\nGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGC\nCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATC\nAGATTATTCATGATTTTGTTGATAAAACTCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATG\nGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTGTATA\nTGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCAAATCAATGAAACTA\nGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAATGATAACATAATACACTGGAGCTTC\nAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCT\nAGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTC\nTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTG\nTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAAAAGT\nCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAGAGAGGACGCCCCCG\nAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAAT\nTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGA\nGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTG\nTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATC\nGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAA\nATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCCAAAATTACCTTGTTGACACTGATCAAGACGGC\nAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGT\nGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAG\nGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAG\nTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAAT\nATCGCTCTCCAGTTACCGTGTGAGAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAAT\nCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGG\nCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATC\nAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAA\nTTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGC\nTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTA\nCAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAAAATA\nTTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTAT\nTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGA\nAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCC\nCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTT\nTAGCTGTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATC\nTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAATCTGG\nGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATTACTTTGAGCACC\nCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGT\nCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGG\nGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTT\nCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAA\nGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAACCTAT\nTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTGAGAGTCATCCTTGC\nAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATC\nTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGA\nGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGT\nCGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGA\nACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGC\nCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCA\nAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGGGCTAAC\nTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAAT\nAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTG\nACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCT\nTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACCCGC\nAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAA\nGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGA\nAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTAT\nCATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCT\nTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACC\nAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCAC\nTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATTATTAAGTACAC\nAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAC\nCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATG\nACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGA\nTGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTG\nAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAG\nGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGATTTAATTACATGTCG\nATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCAGTTTGCTCTGATTATCCCAATTTT\nAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAA\nTCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGG\nCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTA\nAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAAC\nAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCA\nAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTT\nTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAA\nATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACT\nGCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATT\nTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTGG\nGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTC\nTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAATTTTTCTTTC\nTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTC\nAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTAC\nGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAG\nCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTATGAAT\nTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTA\nTACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACACTGGAAAAT\nCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAA\nAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGCTTTAAGTTGCGCTC\nAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAG\nCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTG\nGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTT\nGAATGGGGTCCAATTGCCCCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTT\nGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATA\nTCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCT\nCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCA\nTTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGA\nATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGA\nTTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGC\nGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCC\nTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTG\nTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGC\nGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACA\nATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGGAGTCTATGGTTTAG\nTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCA\nCAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCAT\nGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAA\nGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCA\nTCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGGC\nAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAAC\nATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTA\nAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATC\nAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAA\nCACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATA\nAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAATCGTG\nCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTACTTAACATACACATCTACATT\nGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTC\nAATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTA\nTTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAA\nTAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCC\nAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTA\nAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATT\nGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGATTAATGAGTATTGATCCCCATTTT\nTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGT\nCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGAT\nAGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTG\nGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGACAATC\nTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCA\nCAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGT\nCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGC\nAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTC\nATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTG\nAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTCCTAC\nCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGATGAGAT\nATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTC\nTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGG\nCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACAC\nGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCT\nGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACA\nTAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGA\nTGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTACATAAATTGATCTTACACCAT\nGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGC\nTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTC\nTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTC\nAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATT\nTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGT\nATTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCA\nCATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACAT\nATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTAT\nTGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTG\nTGCTATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTAC\nATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGG\nTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTTGTAAAGGTTGGTTATCAACATACA\nGATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGAT\nAACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAATTCACAA\nTACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATAA\nTTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTTGCCAG\nATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAAGATTAAGTTTTTTAT\nAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATT\nAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAAA\nAGACAGGACTGTAAAATCAGAAATACCTTCTTTACAATATACCAGACTAGACAATAATCTTCGTGTTAAT\nGATAATTAAGACATTGACCACGCTCATCAGAAGGCTC\n" }, { "path": "tests/input/TestOrderAndOrient/ref.ebov.lbr.fasta", "content": ">KX009902.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/LBR/2014/Makona-CDC/NIH-1122, partial genome\nTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAAT\nTGAAATTGTTACTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGT\nCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCCTTATCACAT\nCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAG\nCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACT\nGGAGACTCAACAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCA\nCAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATG\nGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAG\nTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTT\nTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTT\nTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATG\nGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGC\nCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCG\nAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAG\nGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAAC\nAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGAT\nGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATC\nATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGA\nGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTT\nTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAG\nTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGC\nAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGAT\nGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACG\nCGATGGTAACTCTCAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAA\nAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCT\nGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGATG\nATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTTGGTCCTATT\nCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAA\nAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCC\nCTCGCAGAACAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTC\nAACCAGCCCTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACG\nTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCA\nCTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACA\nAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAG\nGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGG\nATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATA\nTCCACCATGGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAA\nTTTTATTGGCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCA\nTGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAAT\nTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTT\nATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAG\nCCATAATGGTAACTCAATATCTTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTA\nCCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAAC\nCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGC\nTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAA\nTGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACAT\nCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCG\nAAGATGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACAT\nTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAG\nTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCT\nGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTG\nAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGG\nTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACC\nACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATG\nATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAG\nCAATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCC\nCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTC\nGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGG\nTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCC\nCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACA\nCTTGTGAGTATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTA\nGCAGCTTTAAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAAC\nCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCA\nTCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATA\nTATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTC\nCTGACACCGGAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCG\nACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATC\nGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTAC\nAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCA\nATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGG\nAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTG\nACAGCACTCAAACTGATCACTCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAA\nATGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGG\nGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGAC\nTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACA\nAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACAT\nTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCT\nCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCT\nTCTCAGGGATAGTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATAT\nACTAAAGGTGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATAT\nACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCA\nATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCAAATTGCCTACAT\nGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAA\nGTTGTTCACAATCTAAGTACAGACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGA\nCAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAA\nTTGGATAACCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATA\nTTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAA\nCATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTG\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCA\nACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATG\nAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACC\nAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCA\nTGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTA\nTCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT\nCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACC\nACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGA\nCCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAG\nTGGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGG\nGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGC\nTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC\nACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAG\nGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAAC\nCAAAACAGGTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAA\nGTTGGACAACATCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAG\nCCGGACCCTTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGAC\nAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT\nGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGA\nGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTAC\nTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTAC\nACAGAGGGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTC\nAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAAT\nTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT\nGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGG\nACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGG\nTGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTT\nCACGGCAAAACTCAACCTCAAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTA\nCTTGACAAATGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTC\nACAGTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACTTGATGAAGAT\nTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTT\nAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTG\nTAACCTAACACACACAAAGCATTGGTAAAAAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTT\nAAATGGAAGCTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCA\nCCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCA\nCAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAG\nACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGA\nAAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTA\nAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTC\nCCAAAATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGA\nGGATTCCAAATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTG\nAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAG\nTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACA\nATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTC\nGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACAT\nGCTCATGATCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCAC\nAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAA\nTCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAAGAGGTATGATATAACCCAA\nACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCAATATAACCTGCCAAGCATACCTCTTGCACAA\nAGTGATTCTTGTACACAAATAATGTTTGACTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAA\nGTATTTTATGATTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCT\nTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATA\nTTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTC\nTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATAC\nTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCTGTATACCAGTTGCCCCTGAGATACGCCACAA\nAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGA\nACTTAGCCATTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAG\nAAGCCCACCTACAACGAACATTACTTTGAGCGCCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAAT\nCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGC\nAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGG\nAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTA\nTTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGAC\nTTTGCCCCTGCATGGTCAATGACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTG\nAATCACCGCTGTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTT\nGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTC\nAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTC\nTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAATGGATTATTGAGCAGTATTGAAAT\nTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCC\nGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGA\nAAGCATTTACACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTAT\nCTAACTAAGATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTC\nTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACA\nGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAA\nATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCC\nAATATACGAAATGGTTAATTGTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATAT\nTACTAACTCCATACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAA\nAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCT\nACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTTGTCA\nCTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACA\nTATATACCGTTTAAAATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCC\nATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGT\nGCCAACAGTTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAA\nAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGC\nAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATC\nGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGT\nTTTTTGGAAGATCCCAATTTCACTGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGG\nTATCAGACATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATG\nTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGT\nTGAGGACCCAGTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTAC\nTTACTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAA\nTTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCA\nCACCCTGGAAGAAATTACAGAAATACGTGCACTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCAT\nAGAACATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGG\nGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATT\nACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTATTTTGATAGT\nCAAGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAA\nATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTATGGGAATTTTACCACCTTGACCATCCTCCACT\nTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACA\nTGCTGGGATGCAGTATTCGAGCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTG\nTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGA\nGTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACT\nTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTG\nCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGC\nATCATGGCACCACACAAGTGATGATTTCGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGAT\nTTAGAGAAATACAATCTTGCATTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCT\nATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTA\nTTATAATCCACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGG\nGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTT\nTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTT\nATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTG\nGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATT\nCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGC\nTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACT\nGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGT\nTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAAC\nACTCGGCAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTA\nTCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGT\nTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAA\nCTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCA\nTTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTC\nATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCG\nTTTCGCAGCCGATATATTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGA\nACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGA\nAGATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGC\nTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTA\nGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAAC\nCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGT\nCAAGAAACATATTGTTAGTGCATGGCCAAATGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCA\nTACATTGGATCAAGGACAGAAGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCT\nTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCT\nAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACAT\nTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGA\nGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGC\nACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGA\nAACACTGAGGCTACAGATATCCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGG\nTACCAGCTCAGTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATT\nGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCATTTTTCCAA\nGGCAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTA\nAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCGTCTACAGACCCAATTAGCAGTGGAGAAAC\nAAGATCATTCACTACCCATTTCTTAACTTATCCCAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTA\nAGTTATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAA\nCTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGT\nTATGTCACGATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGA\nCTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGA\nTAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCATTAGAGGGTCAAAATCCAACACCTGT\nTAATAATTTCCTCCATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACT\nACCATAAATGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCT\nTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTC\nTTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACCACCAGAGAT\nCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACGACAATTCCAC\nAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCC\nAAAACTAAATTTCGATAGATCGAGACACAATGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAA\nGGTCATCAAATAATCTCACATCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAA\nCGTCATCCAATGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGA\nTACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGG\nGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTC\nAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGT\nATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATT\nATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAA\nGGCTACCTAGGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATT\nGTACGAAGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAA\nGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGT\nATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATC\nAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTG\nCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCT\nATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAG\nAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAATGAT\nTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAA\nAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACAAGCATTAAAACATAATGGGACATGGCAAGC\nTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGT\nGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAA\nGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTAT\nTTTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCA\nTCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTATACACTATATTTGG\nCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAGCATGTGTGACATATTACTGCTGCAATGAGT\nCTAACGCAACATAATAAACTCCGCACTCTTTATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTT\nATTGATATAGTAATGTTGTATCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTT\nAAAACAAAACTGATCTTTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATG\nGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACANNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNATGATAAAANTNAAAGANAAGACATNACTGTAAANNNNGAAATACCTTCTTTAC\nAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGCATTGACCACGCTCATCAGAAGGC\nTCACTAGAATAAACGTTGC\n" }, { "path": "tests/input/TestOrderAndOrient/ref.ebov.makona_C15.fasta", "content": ">KJ660346.2 Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Makona-Kissidougou-C15, complete genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAA\nTTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCATACCTGGTTTGTTT\nCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGT\nTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCC\nAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAA\nTTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAAC\nATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAA\nGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG\nTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCA\nACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTT\nTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAG\nGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGT\nATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCC\nGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGA\nAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGT\nAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAA\nGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTT\nTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCT\nCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTG\nGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATG\nGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGT\nAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATAT\nGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATC\nAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAA\nGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATT\nCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGG\nATACGACCATTCCCGATGTGGTAGTTGATCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGA\nAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCA\nGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGAC\nAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACT\nCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAACGAA\nGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAG\nAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCA\nCTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAA\nGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGC\nCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAA\nAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAAT\nGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAAT\nTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCT\nAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAAT\nAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGA\nGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCGATT\nTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTT\nTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGC\nACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCA\nGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGA\nGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGC\nTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAA\nTTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAAC\nCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATG\nGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGA\nCAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACC\nTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAA\nAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTG\nACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCA\nATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAG\nGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCC\nAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTT\nGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAA\nACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAA\nCTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAA\nTTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATAC\nCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCT\nACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATAT\nGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCA\nACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCAT\nCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATC\nAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATT\nTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTG\nCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGG\nAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCA\nCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTG\nCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCC\nAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCG\nGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATA\nTCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGG\nACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACC\nATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAAT\nTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAATC\nCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTC\nTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCA\nTGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGC\nACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGAT\nTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTC\nTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATT\nTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATA\nTTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACAT\nCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAG\nTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGA\nTCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGCGACTAAAAGATGGGGCT\nTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCT\nTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGG\nTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTG\nCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGT\nTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAAT\nGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTA\nATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACA\nGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATT\nTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCAC\nTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAG\nAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAG\nAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCT\nTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACA\nCCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAACGACA\nGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAGAACACCAACACGAG\nTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAAC\nAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATA\nCTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCA\nACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGG\nATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAA\nTCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGA\nGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGC\nCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATC\nAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATG\nGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTGTATA\nTGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCAAATCAATGAAACTA\nGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAATGATAACATAATACACTGGAGCTTC\nAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCT\nAGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTC\nTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTG\nTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAAAAGT\nCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAGAGAGGACGCCCCCG\nAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAAT\nTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGA\nGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTG\nTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATC\nGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAA\nATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGC\nAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGT\nGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAG\nGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAG\nTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAAT\nATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAAT\nCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGG\nCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATC\nAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAA\nTTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGC\nTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTA\nCAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAAAATA\nTTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTAT\nTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGA\nAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCC\nCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTT\nTAGCTGTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATC\nTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAATCTGG\nGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATTACTTTGAGCGCC\nCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGT\nCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGG\nGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTT\nCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAA\nGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAACCTAT\nTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTGAGAGTCATCCTTGC\nAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATC\nTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGA\nGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGT\nCGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGA\nACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGC\nCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCA\nAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGGGCTAAC\nTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAAT\nAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTG\nACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCT\nTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACCCGC\nAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAA\nGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGA\nAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTAT\nCATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCT\nTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACC\nAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCAC\nTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATTATTAAGTACAC\nAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAC\nCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATG\nACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGA\nTGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTG\nAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAG\nGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGATTTAATTACATGTCG\nATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCAGTTTGCTCTGATTATCCCAATTTT\nAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAA\nTCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGG\nCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTA\nAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAAC\nAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCA\nAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTT\nTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAA\nATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACT\nGCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATT\nTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTGG\nGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTC\nTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAATTTTTCTTTC\nTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTC\nAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTAC\nGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAG\nCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTATGAGT\nTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTA\nTACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACACTGGAAAAT\nCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAA\nAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTC\nAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAG\nCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTG\nGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTT\nGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTT\nGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATA\nTCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCT\nCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCA\nTTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGA\nATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGA\nTTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGC\nGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCC\nTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTG\nTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGC\nGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACA\nATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGGAGTCTATGGTTTAG\nTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCA\nCAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCAT\nGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAA\nGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCA\nTCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGGC\nAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAAC\nATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTA\nAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATC\nAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAA\nCACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATA\nAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAATCGTG\nCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTACTTAACATACACATCTACATT\nGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTC\nAATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTA\nTTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAA\nTAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCC\nAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTA\nAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATT\nGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGATTAATGAGTATTGATCCCCATTTT\nTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGT\nCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGAT\nAGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTG\nGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGACAATC\nTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCA\nCAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGT\nCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGC\nAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTC\nATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTG\nAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTCCTAC\nCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGATGAGAT\nATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTC\nTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGG\nCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACAC\nGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCT\nGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACA\nTAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGA\nTGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTACATAAATTGATCTTACACCAT\nGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGC\nTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTC\nTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTC\nAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATT\nTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGT\nACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCA\nCATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACAT\nATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTAT\nTGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTG\nTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTAC\nATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGG\nTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTTGTAAAGGTTGGTTATCAACATACA\nGATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGAT\nAACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACA\nATACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATA\nATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTTGCCA\nGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAAGATTAAGTTTTTTA\nTAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGAT\nTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAA\nAAGACATGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAA\nTGATAATTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCCTGG\nAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n\n" }, { "path": "tests/input/TestOrderAndOrient/ref.ebov.sle.fasta", "content": ">KM034550.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-EM095, complete genome\nGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGT\nTACTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGG\nGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTC\nCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTC\nACAGTCAAACAAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCA\nACAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCC\nGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCAC\nAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAG\nTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAG\nTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAA\nAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGC\nGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGA\nAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTA\nGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATAC\nAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTT\nGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATT\nTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTAC\nAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTC\nCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTT\nTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAG\nCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGA\nGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAA\nAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAA\nCTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGG\nACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAA\nGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGATGATGGAGGCT\nACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGA\nCGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAA\nAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAA\nCAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCC\nTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTT\nCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCC\nCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGA\nCCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTAT\nCGCCACATTCTAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTG\nTAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATG\nGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGG\nCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAAT\nGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGT\nCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACT\nAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGG\nTAACTCAATATCTTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGC\nCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCAT\nCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAAC\nAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCC\nCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGA\nTATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGC\nAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCAT\nTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAA\nTGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTT\nGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATT\nGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGA\nATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTA\nACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGC\nCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATT\nGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAA\nATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACA\nTTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATG\nTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAG\nAGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGT\nATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTA\nAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAA\nAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAA\nCGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGC\nCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCG\nGAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCA\nGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAA\nAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGAC\nTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTG\nTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGC\nTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTC\nAAACTGATCACTCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGT\nTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGG\nGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATC\nGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCG\nGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGA\nCCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGT\nCTTCCAGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGA\nTAGTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGT\nGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTT\nTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGA\nTTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATC\nTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCAC\nAATCTAAGTACAGACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCG\nTAATCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAAC\nCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTA\nCCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCA\nTCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAA\nACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTG\nCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTG\nAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCC\nAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGA\nGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAG\nGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTC\nACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGA\nTATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCC\nAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAG\nGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCC\nTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAA\nCGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAAT\nGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAG\nCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGG\nTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAA\nCATCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCT\nTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCA\nAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGC\nGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTC\nGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGA\nAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGG\nCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCC\nAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCT\nGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACC\nAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGG\nACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAAT\nTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAA\nACTCAACCTCAAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAA\nTGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAAT\nCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAA\nGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAA\nGGAAAAAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAAC\nACACACAAAGCATTGGTAAAAAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAG\nCTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCG\nAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGC\nGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTC\nCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAAC\nTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACT\nGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTA\nCCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAA\nATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTG\nTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAAC\nGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAAT\nTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCA\nGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGT\nCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCG\nTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCA\nTTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACC\nAAAGAAAATCATAATCTCGTATCGCTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCT\nTGTACACAAATAATGTTTGACTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTAT\nGATTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGT\nGGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTG\nTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAA\nTAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGG\nATAGTCCAGCTAGTGACACGTCTTTTAGCTGTATACCAGNNNNNNNNNNNNNNNNNNNNNNAAGTGTCTC\nTGAGCTAAAGTGGTCTGTACACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCA\nTTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACC\nTACAACGAACATTACTTTGAGCGCCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAA\nGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGA\nGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGG\nTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGG\nTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCT\nGCATGGTCAATGACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGC\nTGTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACC\nCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGA\nACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTA\nTTAACAAATTGGATGCTCTACATGTCGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCA\nAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCG\nGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTA\nCACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAG\nATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCAT\nAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCC\nTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGAT\nTCCAAGACAACATCATAGAATTGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGA\nAATGGTTAATTGTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTC\nCATACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTA\nTTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACAT\nACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTT\nGCGGGTTGTATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCG\nTTTAAAATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTC\nATAGTCCCAATTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGT\nTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGG\nTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTT\nTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACT\nCTAGATCAACGTGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAA\nGATCCCAATTTCACTGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACA\nTCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAA\nTGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCC\nAGTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCC\nATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGT\nGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGA\nAGAAATTACAGAAATACGTGCACTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTG\nATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTG\nTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTAT\nCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCT\nTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCC\nCTCCGTTGCCAATGATTAAAGAACTGCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAAC\nCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGAT\nGCAGTATTCGAGCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAAC\nAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACT\nACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAA\nTTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCAT\nTTCCTAGCAATATGATGGTAGTTACGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCA\nCCACACAAGTGATGATTTCGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAA\nTACAATCTTGCATTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTA\nAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCC\nACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATG\nGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAA\nTTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTT\nCCCCTTAGAGACTGATGCAGGCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGC\nCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTA\nTCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAAT\nGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAG\nCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGG\nTGAGAATCTTGCAATATCATCACCTCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAA\nACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTG\nAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTT\nATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGC\nCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGC\nCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAG\nCTGACTTCGAAGACGAAATGGTTTGTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGC\nCGATATATTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACA\nTTATTAGCCTCTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACAT\nTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCA\nAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGA\nCCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAAC\nAATGTCCGCAGTGTTCAAATGCCAAGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACA\nTATTGTTAGTGCATGGCCAAATGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGA\nTCAAGGACAGAAGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGG\nCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACC\nATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGA\nAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAG\nCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAG\nCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAG\nGCTACAGATATCCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTC\nAGTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGA\nCAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGCAAACAG\nCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCA\nTGCAATCAATTATTTCAGATAGCAATAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATT\nCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTAT\nCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAA\nTTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACG\nATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGAT\nGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATC\nGCGGAACAATTGTCCCTTTATGGATAGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTT\nCCTCCATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAAT\nGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGT\nCATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGG\nATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGAT\nGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACA\nCGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAA\nTTTCGATAGATCGAGACACAATGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAA\nATAATCTCACATCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCA\nATGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGT\nTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAG\nAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACC\nAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAAT\nGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAAC\nAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTA\nGGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGC\nTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTA\nAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTA\nAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACG\nTAAGATGCCACACCAAAACCATCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAA\nCGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCC\nTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACT\nAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAA\nCAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCA\nATGATTATTTAAAATTCTTTCTTATTGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAA\nGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGT\nTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAG\nGGCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACT\nTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCT\nGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCC\nCTGCGTGATAATCAAAAAATTCACAATACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAA\nCATAATAAACTCCGCACTCTTTATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATA\nGTAATGTTGTATCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAA\nCTGATCTTTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCC\nTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCC\nATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCA\nGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAA\nTAAACGTTGCAAAAAGGATCCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCT\nTTTTTGTGTGT\n" }, { "path": "tests/input/TestOrderAndOrient/ref.ebov.small.fasta", "content": ">ref_4kb\nTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGCGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAA\n" }, { "path": "tests/input/TestOrderAndOrient/ref.hhv3.fasta", "content": ">gi|59989|emb|X04370.1| Human herpesvirus 3 (strain Dumas) complete genome\nAGGCCAGCCCTCTCGCGGCCCCCTCGAGAGAGAAAAAAAAAAGCGACCCCACCTCCCCGCGCGTTTGCGG\nGGCGACCATCGGGGGGGATGGGATTTTTTGCCGGGAAACCCCCCCCCGCCAGCCTTTAACAAAACCCGCG\nCCTTTTGCGTCCACCCCTCGTTTACTGCTCGGATGGCGACCGTGCACTACTCCCGCCGACCTGGGACCCC\nGCCGGTCACCCTCACGTCGTCCCCCAGCATGGATGACGTTGCGACCCCCATCCCCTACCTACCCACATAC\nGCCGAGGCCGTGGCAGACGCGCCCCCCCCTTACAGAAGCCGCGAGAGTCTGGTGTTCTCCCCGCCTCTTT\nTTCCTCACGTGGAGAATGGCACCACCCAACAGTCTTACGATTGCCTAGACTGCGCTTATGATGGAATCCA\nCAGACTTCAGCTGGCTTTTCTAAGAATTCGCAAATGCTGTGTACCGGCTTTTTTAATTCTTTTTGGTATT\nCTCACCCTTACTGCTGTCGTGGTCGCCATTGTTGCCGTTTTTCCCGAGGAACCTCCCAACTCAACTACAT\nGAAACTACTGTCCGGAAGGGGAAGGTATTTATTCTCGCTTGCAGCTTGTCGCGCGTGTATGCACAACAAA\nAGCTATATATGTCACCAAAGCCAACGTCGCCATCTGGAGTACTACACCCAGTACGTTGCATAACCTGTCC\nATTTGCATTTTCAGTTGCGCGGACGCCTTTCTCCGGGATCGTGGCCTTGGGACATCAACCAGTGGAATAA\nGAACCGCCGGTGGTCTTGTTTGAACGACGAGTGGCGACGCGTTGTTCTGCATAAGCTCTGTATGCTGATA\nCATAAACACAGAGTCTGTATCGCTATCAGATTCCCGAACACCTTCCGGTACCCCATACTCCGATACCCTG\nGACATTGCGGATCCCAAAAATATAATATTAACAGGATTTGCTTATACTTTGCTACAGCTTATATAAATTT\nATGTGCGATACATCTTAAGTGCATCCGTACGTTATTTATACATTGCCTGTCACGTGAAAAGACTGTGTTA\nCCCAATAAAGGTTCTACAAAAAATGCTTTATTGGGTGTTTGTTTAATAGCTATTATCGTAACCCACCCCC\nGTAAAATCATAAAATGCATGTAATTTCTGAGACACTTGCATATGGGCATGTTCCCGCATTTATTATGGGC\nTCCACTCTGGTGCGTCCCAGTTTAAACGCCACCGCCGAGGAAAATCCCGCGTCAGAAACGCGATGTTTAT\nTACGAGTGCTTGCGGGGAGAACTGTAGACCTGCCAGGCGGAGGAACGTTACACATTACCTGTACCAAAAC\nCTATGTAATTATTGGCAAATATAGCAAACCCGGCGAACGTCTTAGCCTTGCCCGTCTAATAGGGCGTGCA\nATGACGCCTGGAGGTGCAAGGACATTTATTATTTTGGCGATGAAGGAAAAGCGATCCACAACGCTTGGGT\nATGAATGTGGTACGGGCTTGCATTTACTGGCTCCATCTATGGGTACATTTCTCCGCACACACGGTTTAAG\nTAACAGAGATCTCTGTTTATGGCGGGGTAATATTTATGATATGCATATGCAACGTCTTATGTTTTGGGAG\nAATATCGCGCAAAATACCACTGAAACACCTTGTATAACGTCGACGTTAACATGCAACTTGACAGAAGACT\nCTGGTGAAGCCGCACTTACCACGTCAGACCGACCCACTCTCCCAACCCTAACAGCCCAAGGAAGACCAAC\nAGTTTCCAACATTCGTGGAATATTGAAAGGATCCCCCCGTCAACAGCCGGTCTGTCACCGGGTTAGATTT\nGCCGAACCTACGGAGGGCGTATTGATGTAATCACTAAATAAAATACACCTTTTTTCGATTGTACGTATTT\nTTATTTAAATGTGTAGTTCATAGTCCGCCGACAGCCGCTCGGGCTTTTCCCCCACATACAACATGATCGT\nATGCCTCGGATGCACCGGTCCAACACTCCGCCGAGAAGGGGGATTTACAATGACAGTGATACCCAATAGC\nCGCCAGATGTACACCCAGCTGTCCGGACTCCAGCATCATCTGCTGAGTTGCGGCGCTGAAGGGTGCATCG\nCATAGGGTGTTATAATTAGCCATTTCCGGTAACAGTCGTTGGGAATTTAGGAGGCTGCAAAACGGCTGTA\nGGTCAACATACATTGGGGATTCAGATGGTTTATCTCGACGTCCAAGTCCAATCAAAAAAGCGTGTAAATC\nATCAGCCCGGCCGCATGTTGCTCGAAGAGCACATAACCTCTTAACACCGTACAGAGGGGATGGCGTCGGT\nGCATGTGAGTTGGCAGGGCATGTCCACGTTGTTTCCAACGCCAGTGGCGGTATAACTTGTGTAAACGACG\nCCAACGGGTCAGGTTTAAGATTCACTCGGATGGGTTGACTGCTTTCGGAAGCTCCCGTTGTATCCATTAA\nTTAAACGTTCGGTACACGTCTGGTGTGTGTTTTACCCGAATCAGAGACGGAATTGCAAAGATATTGGTTT\nGAAAGCAATGTAATCCCGCCCATATATCCCCAACGTCGCCTTAAAAACTCCCACAATATTACATTTTTAT\nTAGTCTTTTATTAATATAGAATCACATAAACAATTGATAAAATCAAGGGGTGGTGTATAATGATTAAAAA\nTATAAATTGATATGTTTTACAAGCATGAAATAGGTATTTACTATTCTAACAGGTAAATATGCTTAATGAT\nTAAAAATACAAATTAGTATGTTTTGACAAGCATGAAAAAGGTATTTTTTATTTTAGCAGTTAAAGGTACT\nACACTTAAAATATTTACCGTATGGACGGGCGTCAGAAAGATGCCCGGCCCAAGTTGAGAGGGTACATTCA\nACACGACCACACTCGCGTTGGTGGGTGATTAGGGCCTCTAAAACACCGGCCAGACATGACCCGGGTGTAT\nATTCTTGTAACACTTGAACGTTACAACTGATATCATCATATTCCACAAATTTAGAGCCACGGACAACTAT\nATTAGCAATGCGGGCAATCATAACAAACATATAAGTAGTAATACACGTGATATCACTAAAACGTTGCTGG\nCGCAACAGTTCGGGGAGAGTACGAGACCCCAAATCGTTGTCCCTGTTTAGAAGAAGACATCTTACAAAAG\nGCCCCAGCTTTAACTTTAAATTCTCCAAAAGTGACTTCGAGGTTGCAACAATGGGATTATTTGTGTAGAT\nGGGCAAGTTTTTTGCCGCTAACATTTTAATCCACGTTAACAGTTCATCCGCAGACTCCAACGCTTCAATC\nAAAGATTCTCCACGTATGACTCTCTCACGCAACGCGCGGGCAATACGTGAGTCCATTTTATATGACTCAA\nAGGTACGATAAAGTTCATGTCCGTACAACATCAACTCCGGCCAAGATGTGTTTTGTTTTATCCCCGGAAA\nACATCCACCGGAAGCCCATGAATCACCCTCTTGTATTGTGGCATATCGGACTACCAGTTTTTCAATTGTT\nTCATCTAAATGGCGTACCGAGTCAATGGTCACGCTGGCTCCCGCGGTGGAGACGACTTCAATAGCACGGC\nCCGTAATTCGATCGACCGGGATATCATACTCTTTTCGAATACGCTCTCGGCGGGCGTCTCTCTTGGAAAA\nTCGCAACCTGTACGATTCGTCATGTGTCTGATCATTTCTTTCTCCCGTGGTCATTGCAGGAGGCGTTGTA\nGGACGCCGTCTTCGATTTGACAGGGATCGATCACGGTGTTTTCTTGAACTTTGAGTGTTATAAGATCTGG\nATGATCGTCGATGTCCCCGTTCGATGCGTGCATATCCAGTCTCCACGTCTCTTCCTCCATGATGGTTTGA\nATCGGGTAATACAACAACCAAAGTTTTCGGGCGATTGTGGTGGTAGCTTTCACGCCTTCCGTGCCTTCGT\nTTGGAATACCGTGGATTATATGCTGTATCTGCAGTACGCTCCACATACACAGTTCTAGACGTTGTGGAGT\nCCTCGCCTGGAGTGGAGCCAATAGCTTCATCATTTGCCCAATCGGTGACTTCCAATGCAAAGTCATCCGA\nAGGTTCGTCTGGTAGCAAATTCATAAAGTCTTCACAAATAGTAGACACGTCTGGGTCGGTTGGAATTGAA\nGCAGAGGCCATGGCTGCAAAATATCTGACAATTGCGTGTTTGCAGTTGCCTGTATCTTCCGCCAATGTTG\nTAGAATTTATAGGCTCACCCAACCCCGCAATGGGCGTGTTTAGTCACATGATTAATGCTTCTGGGAGTTT\nTCACTTTCCCCAAACAAGCTTACCTGCACCCTTTGTTCGTAATGCATAAAAATAACCACTGCTATAGCAA\nATATGACGATATAAAAACATTTTATAGCAAGGCCGGACATTACTGTAGCGCAACATGTTGTGCATATACC\nACGTATTCCCCCCGTATTGATATGATTTAAATGATTATCCTTGGTTGGTTTTGGTCTAACATAAGATATA\nAGCTCTACTATAGCGAGCGTGCATACAACAACCCAGGCCAGAATCCGAATGTATGTGGGGTATAATAACG\nCGCATGGTGTATATGCAACGCCAAGCGTTAAAAGCACAATACATCCAGATGATATATGAGCGATAACCTC\nCAAAAGCATCAATAACGTAACACCTTTATGCATATATAAAAAACTTATAGGGTCAGCATTAAATACTTTA\nCTCATACCATCCCGTCGCATGGAAACATCACATAACAACCTTGCCAACTTTGTATATGGGTAACCAAGAA\nGAATGTTCGAAATAACCCGTGTTACGTAATTCAGTGAATATGATGTGGGGGATATTAACTCACAGGATGA\nTCGGAATGGCCCAAACATACGACGTATTCGTCGAAATTGTAAATACATACCATATACAAACCATGCAAAA\nAAAATCATTTTTAGCTGCACGCACCAAAAATAAGCGTGACAATTACGTGTTCCCAGAACAATTCGAATTT\nTGTCATGCAAAGGTGTAGAAATAGCGGTTTTTACCATAGTATCTCCTGATAATAGATTTTCCCGGCAGCT\nGTAATCGTATCCAGATAGGCCATCCAAAAACGTTGAGTGGTTTACAAACGTTACATATATAAGAGAGTTG\nTTATAAGACCCCCATACAACCGGTCCACCATTAATCACCGTGGTTGCATACACACACTCATGTTCAAACT\nTTACACGAGCGGTATACCATAGGGTAAAAACAGCATGTCCGCTAAGTAGACACATAATTATAAAATGTTC\nTGTCTTGATTCCTAAAGCCTGCATGACCCGTGGAAGATGGCAATTCAAGCACGATGTAGTATCACACGGT\nTGGTGTTAACTCGAAGTTAAATTTGGATAATTAGGTACTTCTAGAGTAAAGATTGTATGCATGCGATTGC\nTATCGCACTTTGTAGCAAAACATTGTTGTGCAAGCGAAATACACAAACGGTTGTGATGATCCACTCGCAG\nAGACACAAATGTCCGGGGAGCCGTTCTTCCTCCGCGATGGGGATATCGAAGACAAGTGAACCCTTTTGTT\nCCGCATATGAGCTGAAATAACACCCAGTCCCTTTTGATGGCGATACACTTTGATGATGTTAAGGTATATT\nCGCGATCACGCCCGGGGAAATGAACAGCAATATGCTCCACAATAGATTCTAATATTGTGCTGTCGACAAA\nGGCCTCCAGTGTAAATGCGTCCAGACAAGTTACCCCGCGCTCTTTTAGAGCCTTTGTTAAAGATATTTGC\nGGGGAGCTAAATATTTGTTTATTACGCGCAACCTTACGTTCAAAAAACTCTGCGTATTCCCCCCCAAGGT\nTATGTAAAATAAATTGCACTGGAACATTCGACTGCGGTCTTGAATGAAAATGAAAGTTTGCCGGGTTTCT\nATGTGATGTCACAAACGCTAATATATCAATACACTGCTCAGGTACAACATAAAATGGGAGTAGTTGTCCA\nACCGCCGTCCCTGTGGTTGTTACTTTGGAGAAAAAAGGCAGTCTTAAACTATGTCCGTGGCTATAAACAC\nCAGTATCTATAAACGAAAAGTCCCGTAAATACGGACCAATATATTCAACAAATTCCCGTTCCAGCAACAC\nCGCTTGCTGTAATATTTGTGCAAACCCCTTTAAAGTGGAAGACCCCACTAACGCATAGGGATTTGGGATT\nGGTACGCATACCCTGAAACCTATTTTCTCTTTACAGTTACAGGGTAGAGTTTCATGCAAGTTTTCATTGT\nTTGATACATCGGCGTGTGTATGGACTTCAGACGTTGTCTGTGTATCAAAAAACCATACATCCTCTGTATA\nATTCTCTTCTACACACGTGTATAATTCGCCATTTTCTATGTAAAAATCGATGTCAGAATGGCTGGTTATA\nTCCAATAAATTATCATCATCCAACACCTCAACGGTAGGTTCAGGACATGCAGTTTTATAAAAATAACATG\nGGTCTTTGTTAGGGTTTACCACGGCCTTTGGAAAAAGTAATTGCATGGCCGTTAAAATACCATGACGAAA\nTGCTCGCATGCCGGCATGTAAAATACCCAATGGGATGGGTTTTCTTATATGAAAGTCTACATCAAGTATG\nAGGTTTGTGATTATAAGATTTGTATTAAATAGCTCATTCCTGTTTATATAAAGCTGATCTTTGGGTATGT\nTTGATGAAATTTTAGAAACGTTTTTAACAGACGTAGATAATAGTAAAGTCAACTGCATATCTCGTAGTGA\nAGCGGCAACAAAATTACATGGATTAATTTGTTTAAGGTCCTCCGCAATTAATCGAGCCTCGTGCGGTAAA\nGTGTAACGGTTTGTTATTGATGACCACGTATCATTAGCAATAACAGCAAATGCTTGGGCGCCGTGAGGCA\nAGGCTACCCGATATACAGGCATTGGTCCAGTTACCTCAGAATGGCCGATGAGGGCTTCTAATGGAGTTTT\nATAACTCAGGATGGATACATCATGTGTGGCTATCCCAGTGGCAGCAGAGAAAAACAGTAATAGTTTTGTA\nATCCCCGGGCTCGTATCAAAACCAGTACGACCACTTTGGTTAGGTGTATCGTTTGCAAAGTTGGCTGCTC\nGTAACGCCTCCGCGGAAACACCCGAATCCTCAAAATTAGACAATTCGTCAAAACCGGGTGGATTTGAGGG\nAATAGTGGAGGACCATCCATATGGACTAAATTGTTTTTCAATGTTTTCCACACGACGAGTTAGCGTTGTA\nGCTAGGTCACATACGCCTATAAACTTGCTAGGTTTTGCGGCATACGTAAGACTTAAAGTATATGTTTTAG\nTAATTGTATATTTATGTCCAATCTCAGGTCCAAGTTCAGTGACATCACAAATTACGTTCTTTTTTATATA\nGTCACGCATGTTGAGACGAGAACGTACATGATTAAAAAAATTAGCAGTAGCTCTTTTTCCCAGGTTGGAT\nGATTTTAAGAGGACCGGTTTATTCACAAAATCTGAGTATGTAACCGCTTGTAGGTGGTCTGCGATCTGTT\nTCCGATTGAAACATTCAAAATGTGCCAGATAAATATAATCAACAAATTCACGGTCTGGAACTTTAAGGCC\nTTTTCTATCGTTGGTAATATACTCCGATACTGCGTGTATTTCCGTTGTGTCTGTATGTATTCGCTGTAAA\nATGTACGATAGAGCATTTTTGGCTGTCAAACCTCGTGTATATGTTGAGGAACAACAAAACATGGAAAGTT\nTATCAAAAGACAACAAGTCCGAAATATTGTACCCACTACAATTAGGTAATGCCGGGACTTGGTAAGTTAA\nAAACAAATCTTTAATTGCCTGTAAGTCATATAAGGGGGTTTCCAACGTATTGTAACTTGTGTCCGTTTGT\nAACAAGTAATAGCGTGTAGCCAACACTAGCGTTTTTTCAGAGGGTCCAAATCGAACAATATACCAAAACG\nGCGAGCATCCATACCCCCAGTAGAGTCGTCGATATGCAGCCAATACTTGACGTTCGTAATGGGCATATAA\nTGATGTTAGCTCCTGACGACCAACGGATTTTTTAACTAACTTGCAGAGTGTTGCCTCTGTGATGCATAGG\nCCGTTGTCCGATAATCCCTTTCGGTTTAAATGGTGTGTTGTTACCATCAGAGTTTGTATAACTTCCGAGT\nGAATGTCAAACGTCTCCGATATACATAGGGTATCAGATATTATATGCGGATTTAGGGGTGCTCCATACCA\nTAACGCCTTATATAAAGCTTTAAAATCAGTTTGGGTTTTAAAACAACAAAAAAATATAGGCCAGACCCGG\nGATCGTACATCTCCAGTTGAAAATCCACCAATTAAATAAAAAATAACGTTGACGTCCCTACTACAAAATA\nAATGCATTATTTGGTTTTCTTCATCGTTTTCAGTTACTTCACGTGGGCGTTTAGTTGGGATTACTTGCGT\nGATCTCTTCCCTCCCATTTTTGACAAAGACGTCATCTAAGTCGGGAGTCCAAGTATAACTCACCACATAC\nAGAGGTTCTGTGCTTATCTGCCCGGTAAGCAACAACAGCGAGTGGGAGATTGCACATCCCTTTGTGGCAA\nATAATAACCGAATCGTCGGTTTGGAGGATTTATCCATAGTTCAATACGTTGGAAAGCCAGTCAATCATGC\nAGACGGTGTGTGCCAGCTTATGTGGATATGCTCGAATACCAACTGAAGAGCCATCTTATGAAGAGGTGCG\nTGTAAACACGCACCCCCAAGGAGCCGCCCTGCTCCGCCTCCAAGAGGCTTTAACCGCTGTGAATGGATTA\nTTGCCTGCACCTCTAACGTTAGAAGACGTAGTCGCTTCTGCAGATAATACCCGTCGTTTGGTCCGCGCCC\nAGGCTTTGGCGCGAACTTACGCTGCATGTTCTCGTAACATTGAATGTTTAAAACAGCACCATTTTACTGA\nAGATAACCCCGGTCTTAACGCCGTGGTCCGTTCACACATGGAAAACTCAAAACGGCTTGCTGATATGTGT\nTTAGCTGCAATTACCCATTTGTATTTATCGGTTGGCGCGGTGGATGTTACTACGGATGATATTGTCGATC\nAAACCCTGAGAATGACCGCTGAAAGTGAAGTGGTCATGTCTGATGTTGTTCTTTTGGAGAAAACTCTTGG\nGGTCGTTGCTAAACCTCAGGCATCGTTTGATGTTTCCCACAACCATGAATTATCTATAGCTAAAGGGGAA\nAATGTGGGTTTAAAAACATCACCTATTAAATCGGAGGCGACACAATTATCTGAAATTAAACCCCCACTTA\nTAGAAGTATCGGATAATAACACATCTAACCTAACAAAAAAAACGTATCCGACAGAAACTCTTCAGCCCGT\nGTTGACCCCAAAACAGACGCAAGATGTACAACGCACAACCCCCGCGATCAAGAAATCCCATGTTATGCTT\nGTATAAATATTGAAATAAAAACTAAAAACGTTTCTGGTGTATGTTTTTATTTTGTATATAAAATTAAAAC\nATTGCTGGCTGGCGTGGTTATTACATTTAATGTTTTAGTAGAAAATCGACATCGTTTGTTTCTTTATCAG\nTTGAACCAAATCCACGCGTTCCCCGTTCGCTGGGTGTGGCTATTAGATCTAACGTTTTAGTAAAATACCA\nTTGTACACCCGGTATGCCACATTTACCGCGGATAGCATAAGGAAATGCAATATTACTTAAAACGTTGTGT\nTTTAAGTGTATTTGGGTGTTGTGATCTATTAACAGGACCTGTGCAAGACGATCTCCCGTTTTTATACGTA\nTGTCATCACCCGTGAGATTATATACGTAGAATTTACAGTGTTCTCCTGCAGGCCATGCCGTTGGACACAC\nGATAATGCCTGATCGGCTTTTCGATGATCTTCCAAAAATATAAGCGTTTATACTCGGATGTTGTAAGTCC\nCAGTCTCTTATAATCGGTAAGACAATTTTTATAAATTCATTCCTTTTTAAATATAGGTTATATGGTACAC\nAAATATCATATCCCGCGTCTTCTTGGCGTTTTGGATTGATGATATGTTTGTAGGTTAAGGGAACATCGAT\nATGGTATTCTGCAGAATCCCTATGTAAAGGTTGCCCCTGCTGTACCGTGGAAATATCAGCAAATTCAGGT\nATAACGGGTTTTTCATAATTTGACGGCGAGTTTGATAAGGGTTGAACTTGTATCGATTTAAAAATTGGAT\nCCAGATGTTTAAGAACGTTTTTTGGGAGAAGGCGACTTTGTCTTAATTTTACCGGGAACAAGTAGATTGT\nTAAATGTCCGGGTAAAATAACGGTTACTCCTGGCCGGTAATACAAAAGGGCTGAAATTACTCCTCTGTAA\nCCCGCATCAATAACTCCGTTGGCGACAAAAAAATTGTCTTCATCAGCAAGGGCAGTATCTTTGCATTGAA\nTTAACAACAGTGCGTATTCATTGGGAGGCGCCGACTTAACCAACAGCTCCAACTGCTGCATATAAAAACC\nGCCCCGTGTTACAGATTTTTCAGATGGCAGTTCGAGTTTCTTGTGGTTCCGGAGTAACAACGGTTGATGT\nCGACTTACTTTATCGTCTAACACGCATTGCAGCGTATCTGCACATTCAGGTTGAACTTCTATTAAAATTG\nTATCTTTTAAACACCGATTCGGAATAGTTTGGCTACAAAACATATCACCTGTATTTACTGCCGTTTCCAA\nGATGGGATCAATTACCGCTTCGTTCATATTAATAACGATGCAAATTTTATTTTTTTGTGAAGACAGCAGT\nGGGGAGCCAAACTTTGCAGAACGGAATTTTTGGCATGCCAGCTGTTCGGCTCGTGGAGTTTATATCGACG\nGATCAATGATCACCACCCTTTTCTTCTACGCATCCCTTTTGGGGGTGTGTGTAGCCCTTATTTCGTTAGC\nTTATCATGCGTGTTTCCGGTTATTTACTCGTTCTGTATTACGCAGCACGTGGTAAACCCGTTTGCCTATA\nAAAGGGGCAGGCGTGTATAAGAGGGCCCCTGTTTAATACGCGGTCTGCCGTGTTTGGATATTTCACGACC\nCTATCGTTTATTTACGTAATGGCATCTTCCGACGGTGACAGACTTTGTCGCTCTAATGCAGTGCGTCGTA\nAAACAACGCCTAGTTATTCCGGACAATATCGAACCGCGCGGCGAAGTGTGGTCGTAGGACCCCCCGATGA\nTTCAGACGACTCGTTGGGTTACATTACCACAGTTGGGGCCGATTCTCCTTCTCCAGTGTACGCGGATCTT\nTATTTTGAACATAAAAATACGACCCCTCGCGTACATCAACCAAACGACTCCAGCGGATCGGAAGATGACT\nTTGAAGACATCGATGAAGTAGTGGCCGCCTTTCGGGAGGCCCGTTTGAGACATGAACTGGTTGAAGATGC\nTGTATATGAAAACCCGCTAAGTGTAGAAAAACCATCTAGATCTTTTACTAAAAATGCGGCGGTTAAACCT\nAAATTAGAGGATTCACCGAAGCGAGCTCCCCCGGGAGCAGGCGCAATTGCCAGCGGGAGACCAATTTCCT\nTCAGCACTGCACCAAAAACCGCAACAAGCTCGTGGTGCGGTCCTACGCCATCATATAACAAACGCGTCTT\nTTGTGAAGCGGTCCGGCGCGTAGCCGCCATGCAGGCACAAAAGGCTGCCGAAGCGGCTTGGAATAGTAAT\nCCCCCAAGGAATAACGCCGAATTAGACCGTTTGTTAACCGGAGCCGTTATTCGTATTACGGTGCATGAGG\nGTTTAAATTTAATACAAGCCGCTAATGAAGCAGACCTAGGTGAAGGAGCATCGGTATCCAAACGTGGACA\nTAATCGAAAAACTGGAGATTTACAGGGGGGCATGGGTAATGAACCTATGTACGCACAAGTTCGTAAGCCA\nAAAAGTCGAACGGATACACAAACGACTGGGCGTATAACTAATCGAAGTAGGGCCCGTTCTGCATCAAGAA\nCTGATACGCGAAAATAGGGATATAATTACGCAGTAACGGTTTACCCGGTATTATGTATAATAAATAAACG\nTATAAAAGACAGTCGTGGTTTGTGTTTATTATAAATGTGTATTATATGTCACATATTATAAACTGTTTAA\nATAGTACCACGTGGTATTATGAACAGTTTATAATCAGTTGCTACCAAACAAACCCCATTAGACGGCGGGT\nTTTGATAAAGGGAATCGCTTATTTAAACTAAAGATTTTACTCTATAAGTATGGAGTGTAATTTAGGAACC\nGAACATCCTAGTACAGATACGTGGAATCGTAGTAAAACGGAACAAGCGGTTGTGGACGCATTTGATGAAT\nCGTTGTTTGGTGATGTAGCATCGGATATTGGATTTGAAACGTCGTTATATTCACATGCAGTTAAAACTGC\nTCCGTCTCCGCCTTGGGTAGCTAGCCCTAAAATTTTATATCAACAGTTAATACGGGATCTTGATTTTTCA\nGAAGGGCCGCGTTTACTATCATGTCTTGAAACCTGGAACGAGGATTTATTCTCATGTTTTCCTATTAATG\nAGGACCTATATTCCGATATGATGGTTTTATCCCCGGATCCAGATGACGTTATCTCAACCGTTTCAACCAA\nAGACCATGTTGAAATGTTTAATTTAACAACCCGGGGTTCCGTTCGATTGCCTAGTCCACCAAAGCAACCG\nACGGGGCTTCCAGCTTACGTTCAGGAGGTCCAGGATTCGTTTACCGTAGAACTACGCGCCCGGGAAGAAG\nCATACACAAAACTACTAGTTACTTATTGTAAATCGATTATACGTTATCTCCAAGGAACGGCGAAAAGGAC\nGACAATAGGTCTTAATATACAAAACCCTGACCAGAAAGCTTACACGCAACTCAGGCAAAGTATTCTACTT\nAGATATTATCGTGAGGTGGCAAGTTTGGCGCGTCTTCTGTACCTACATTTATATTTAACCGTAACGCGTG\nAATTTTCCTGGCGTTTGTACGCCAGTCAATCTGCACACCCGGACGTGTTTGCGGCTTTAAAATTCACCTG\nGACCGAACGTCGACAGTTCACGTGTGCGTTTCATCCTGTATTATGCAACCACGGCATTGTGTTATTAGAA\nGGGAAACCACTAACAGCGTCTGCCTTGAGGGAAATAAATTACCGCCGCCGAGAACTGGGACTGCCTCTAG\nTTAGATGTGGTCTTGTTGAAGAAAACAAATCTCCGTTGGTTCAACAACCCTCATTTTCGGTTCATTTACC\nACGGTCGGTGGGTTTTCTTACCCACCACATTAAGCGTAAGTTAGACGCATATGCGGTCAAACATCCTCAA\nGAACCGAGACATGTACGAGCGGATCATCCTTACGCAAAAGTTGTTGAAAATAGAAACTACGGTAGTAGCA\nTCGAAGCTATGATTTTAGCACCTCCGTCCCCATCCGAGATCCTGCCGGGGGACCCACCACGCCCACCCAC\nGTGTGGGTTTTTAACGCGTTAAACGTCATTGGGGTAGAGGGTGTAAATAAATTACGAAAACGTGCATGCG\nTTTTTTATTTTTACAATGCGCCGTATATGGTATGTCTGTCATGTGCTCTAAAGTCCCATATATAAAAGAA\nGCCCCAACGAGTGTATGCGTATTGCGTACCGCGACCCTGGGATGTTTTACAGGCGCGTTTGTTTGTCTCG\nGTTATAAGTATGCAGTCGGGTCATTATAACCGGAGGCAATCCCGCCGACAGCGGATATCGTCTAATACCA\nCAGACTCCCCCCGTCACACACACGGAACACGTTATCGGTCAACCAATTGGTATACACACCCACCCCAGAT\nATTGTCCAATTCAGAAACATTAGTTGCGGTTCAAGAACTACTGAACTCCGAGATGGATCAGGACAGCAGT\nTCTGACGCATCGGATGATTTTCCGGGATACGCCTTACATCATTCTACATATAATGGATCCGAACAAAATA\nCATCAACTTCCAGACATGAAAATCGCATATTTAAATTAACGGAGAGGGAAGCTAATGAGGAAATCAACAT\nCAATACGGACGCGATCGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGACGCGATCGACGAC\nGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGACGCGATTGACGACGAGGGAGAGGCGGAGGAGGGAG\nAGGCGGAGGAGGACGCGATTGACGACGAGGGAGAGGCGGAGGAGGGAGAGGCGGAGGAGGGAGAGGCGGA\nGGAGGGAGAGGCGGAGGAGGACGCGATCGACGACGAGGGAGAGGCGGAGGAGGACGCGGCGGAGGAGGAC\nGCGATCGACGACGAGGGAGAGGCGGAGGAGGATTATTTTTCTGTAAGTCAAGTTTGCAGTCGAGACGCGG\nATGAGGTTTATTTTACGTTAGACCCGGAAATAAGTTACAGTACCGATCTTCGCATTGCAAAGGTTATGGA\nGCCTGCGGTATCAAAGGAACTTAATGTATCAAAACGTTGTGTTGAACCTGTTACCCTAACAGGCTCTATG\nTTAGCGCATAATGGGTTTGATGAGTCCTGGTTTGCTATGCGCGAATGTACCCGTCGCGAATATATTACGG\nTCCAAGGATTATACGACCCAATTCATTTACGGTATCAGTTTGATACTTCCCGGATGACACCCCCACAGAT\nTTTGAGAACTATACCAGCCCTTCCTAACATGACACTTGGTGAACTTTTATTGATTTTTCCTATTGAATTT\nATGGCCCAGCCAATTTCTATAGAACGTATTTTAGTTGAAGATGTATTTTTAGATAGGCGGGCTTCCAGTA\nAAACACATAAATACGGCCCGCGTTGGAATTCCGTCTACGCACTTCCATATAATGCGGGTAAAATGTATGT\nACAACACATTCCTGGGTTTTATGACGTGTCCTTACGTGCTGTGGGCCAAGGAACGGCCATTTGGCATCAC\nATGATATTATCCACAGCAGCATGCGCTATTTCTAATCGCATTTCACATGGAGATGGATTAGGATTTTTGT\nTAGACGCGGCAATTCGTATTAGCGCAAACTGTATTTTTTTGGGACGTAACGATAATTTTGGCGTGGGGGA\nTCCATGTTGGTTAGAAGACCATCTTGCCGGATTACCACGAGAAGCCGTACCCGACGTACTCCAAGTGACA\nCAGTTGGTTTTGCCAAATCGGGGTCCAACGGTTGCCATTATGCGTGGTTTTTTTGGGGCGTTGGCATATT\nGGCCCGAACTAAGAATTGCTATAAGTGAACCATCTACATCTTTGGTGCGATATGCTACCGGTCACATGGA\nACTTGCCGAATGGTTTTTATTTTCACGTACACATAGTTTAAAGCCACAATTTACCCCAACGGAACGGGAA\nATGTTAGCGTCATTTTTTACGTTGTATGTTACTCTTGGTGGAGGAATGTTGAACTGGATCTGTAGAGCAA\nCTGCAATGTATTTAGCTGCTCCTTACCATTCCCGTTCGGCTTACATCGCGGTCTGTGAATCTCTGCCCTA\nTTACTATATCCCGGTTAATAGTGACCTGTTATGTGATTTAGAGGTATTACTGTTAGGCGAGGTCGACCTC\nCCAACTGTTTGTGAATCCTACGCAACTATTGCACACGAATTAACCGGATATGAGGCTGTTCGCACAGCAG\nCCACAAATTTTATGATAGAGTTTGCCGATTGTTATAAGGAAAGTGAGACCGATTTAATGGTAAGCGCGTA\nCCTGGGGGCCGTTTTATTGTTACAACGGGTGTTGGGTCATGCAAATCTTCTTTTGTTGCTTCTCTCCGGT\nGCTGCGTTGTACGGAGGATGTTCAATTTACATCCCCCGAGGTATTTTAGATGCATATAATACTTTAATGT\nTGGCAGCAAGTCCTCTTTACGCTCACCAAACTTTAACATCCTTTTGGAAAGACCGCGATGATGCAATGCA\nAACTTTGGGGATTCGACCGACAACGGACGTTTTACCCAAAGAGCAAGACAGGATAGTTCAGGCATCACCT\nATAGAGATGAACTTCCGTTTTGTGGGATTGGAGACCATCTATCCCCGAGAACAGCCCATTCCCTCCGTGG\nACCTAGCCGAAAATCTTATGCAATACAGGAATGAAATTCTGGGTTTGGATTGGAAAAGCGTAGCCATGCA\nTTTACTACGAAAATATTAAGGGTTGTGATTTTTTTCATTAGGATGAAAAGAACGTTTCCTAGCCACACCC\nACAAAGGAGTTTGTAAAATAAAATCTCTGTTTAGACCTTAAAATTTGTTGTGTGTGTTGTGTGGGGGGTC\nCGTGAGGATCGACCTTTACAAGATATAATTTGTCCATATCGCAATGTTTTCTCGGTTTGCGCGTTCCTTT\nTCCAGCGATGATAGAACGCGTAAATCTTATGATGGTAGTTACCAAAGTTTTAATGCCGGCGAACGTGATT\nTGCCCACACCTACCCGGGACTGGTGTTCTATTTCCCAACGCATAACCAGCGAGCGCGTGAGGGATGGATG\nTCTTATTCCAACGCCCGGCGAGGCTTTGGAGACGGCGGTAAAGGCTTTATCTGAAAAGACCGACAGCCTA\nACATCGCCGGTTTTACAAAGTACCGAAAGACACAGTGTTCTGCTTGGATTACACCATAATAATGTTCCTG\nAATCGTTGGTGGTCTCGTGTATGTCTAACGATGTTCATGACGGGTTTATGCAGCGTTATATGGAAACAAT\nTCAAAGATGTTTGGATGACCTGAAACTTTCTGGGGATGGACTTTGGTGGGTTTATGAAAATACATATTGG\nCAGTATCTCAAATACACCACAGGAGCCGAGGTACCGGTGACTTCAGAGAAGGTAAATAAAAAGTCTAAAT\nCCACGGTTTTGTTGTTTTCATCCGTAGTTGCCAATAAACCAATATCCAGACATCCTTTTAAATCTAAAGT\nTATAAATTCGGATTACCGGGGAATATGTCAGGAGCTACGTGAGGCGTTAGGAGCTGTGCAAAAGTATATG\nTATTTTATGCGTCCAGATGATCCTACAAACCCCAGCCCGGATACAAGAATACGTGTACAAGAAATTGCGG\nCTTACACGGCTACTGGCTACGGGTGGATGTTATGGTTCTTGGACGTTGTGGACGCCAGGGTATGTCGCCA\nTCTCAAACTTCAATTTCGACGGATTCGAGGGCCGCGCGCGTCTGTTATTCCAGATGATTTGCTTAGACGA\nCATTTAAAAACGGGTCCTGCGGTCTCAGCGGGCACAGGAGTTGCGTTTATTTTAGCAGCAACAACTGCCA\nGCGCTCTTACTGCGCTTTTGCGTATTAGTGTATTATGGCGAAAGGAAGAGTGGCGGGATGGTTTAAATGG\nAACCGCAGCTGCAATTGTTGCGGCGGTTGAACTTATTACGCTTTTGCACCACCATTTTCAATACTTAATT\nAATATGATGCTTATTGGATATGCATGTTGGGGGGATGGGGGATTAAACGATCCTTATATATTAAAGGCGC\nTACGTGCCCAGGGACGGTTTTTATATTTTGCGGGTCAGTTGGTCAGAACAATGTCAACACACAGTTGGGT\nTGTGTTAGAGACCAGCACCCATATGTGGTTTTCCCGGGCCGTGGCGCAGAGTATTTTAGCACATGGGGGT\nAAACCCACAAAGTATTATGCTCAGGTTCTTGCCGCCAGTAAACGGTATACTCCGTTACATTTAAGACGTA\nTATCCGAACCATCGAGTGTGTCTGATCAGCCGTATATTCGTTTTAATCGACTGGGATCTCCAATAGGGAC\nAGGTATAGGGAATTTGGAATGTGTCTGTTTAACGGGAAATTATTTATCTGACGACGTAAATGCAAGTTCG\nCATGTAATTAATACAGAAGCACCGTTAAACAGTATAGCACCCGATACAAATAGACAGCGGACTTCTCGCG\nTTTTAGTTCGTCCAGACACGGGTTTGGATGTAACTGTCCGAAAAAACCACTGTCTGGACATAGGCCATAC\nGGACGGTAGTCCAGTTGACCCAACGTATCCTGATCATTACACCCGGATAAAGGCGGAATATGAAGGTCCG\nGTTCGGGATGAATCAAACACAATGTTTGACCAAAGATCGGATTTACGTCACATAGAAACCCAAGCATCTT\nTAAATGATCACGTATATGAAAATATACCACCCAAGGAAGTGGGTTTTAACTCATCTTCAGACCTGGATGT\nGGATAGCCTTAACGGGTACACCTCCGGAGACATGCATACAGACGATGACTTATCACCAGATTTTATACCC\nAACGACGTTCCCGTTAGATGTAAAACCACGGTTACGTTTAGGAAAAATACGCCTAAGAGTCATCATTAAG\nTACAGCGGTTAATAGATAGTTATGGACTAGGCACTTTGGCGGTCATTTCCACAACCAGGTTAAAATTGGG\nGGATTTGGGAGAAAATAGTCTATTGCGTATTTTCTGTTCAATAATTGGACTGCGTTATTTAAAGGTCTGA\nTTGGTTGATTGGGTTATAAAAGGAATTACTCCTTTAAATTTTACTTAATGTACCCACAATATCAAGTGGT\nCGTTTGTATTTAACGATTATTACCGGTACCATGGGAGACTTGTCATGTTGGACAAAGGTGCCGGGTTTTA\nCGTTAACCGGCGAACTTCAGTACTTAAAACAAGTGGATGATATTTTAAGGTATGGAGTTCGGAAACGCGA\nTCGAACAGGAATCGGAACGTTATCTTTATTTGGAATGCAAGCTCGATACAATTTGCGAAATGAATTTCCT\nCTTTTAACTACAAAGCGTGTTTTTTGGAGGGCCGTCGTGGAAGAGTTGTTATGGTTTATCCGCGGGTCAA\nCCGATTCCAAAGAACTCGCCGCTAAAGATATACACATATGGGATATATACGGATCGAGCAAATTTCTAAA\nTAGGAATGGCTTCCATAAAAGACACACGGGGGACCTTGGCCCCATTTACGGCTTCCAGTGGAGACATTTT\nGGAGCGGAATATAAAGACTGTCAATCAAACTATTTACAGCAAGGAATCGATCAGCTGCAAACTGTTATAG\nATACAATTAAAACAAACCCAGAAAGCCGACGAATGATTATATCGTCTTGGAATCCAAAGGATATCCCCTT\nAATGGTACTACCTCCATGTCACACGTTATGTCAGTTTTACGTTGCAAACGGTGAATTATCCTGCCAAGTA\nTACCAGAGATCGGGGGATATGGGCCTTGGGGTACCGTTCAACATTGCTGGATATGCACTTCTTACCTACA\nTAGTAGCGCATGTTACAGGACTTAAAACCGGAGATTTAATTCATACAATGGGGGATGCACATATTTACTT\nGAATCATATAGATGCTTTAAAAGTGCAGCTAGCTCGATCCCCAAAACCTTTTCCTTGCCTTAAAATTATT\nCGAAATGTAACAGATATAAACGACTTTAAATGGGACGATTTTCAGCTTGATGGATATAATCCACACCCCC\nCCCTAAAAATGGAAATGGCTCTTTAATGGATTTTTAAATGTTGTCAAGACAGTAGATGTGTTGCGAATGT\nAATAAAATGATATACACAGACGCGTTTGGTTGGTTTCTGTTTATGAACAGCAACGGATGCATAGGGTTGC\nGATAACTGCGATAAGACCCAATGTCCCAAGGATAGATATCACACCAATTATAACTGCTACAACGGAAAAT\nGTAGTGGCGTAGGTAGATGCATCGTAGGTATAAACGGCCGAAAACGGAGGGAATTTTTTAGGGTAACCAT\nCTAGATGACACGAATAGGTGATAGGTCCGTCGAGTTCCGATGTTGGACAAGAACTTTGCATGTTTACAAA\nCCGTTTGTTTTGATCACACACCCCAGTAATCTCACTGTTTTCGTGGTTAATGGGAGAATCGTTAACCCAC\nCATACGAAATGTACAACGCCACGTGGCACACATTTTGCCGTACATACTATGTGTCCATCAATAATACCTA\nTAGACACGTTGGGAAATGGATAGACGTCAGGGGTAACGACAGCAGAATATTTCATATTAGAGACGCCATC\nCCGAATCCATAAAACATTACATTGGATGGCTGGGGGTGGGTAATCCATTTGTTTTTGCTGTGGAATTCGT\nACCGCCGAAACATAACTAAATAATCCATTGGCATATTCTTGTATTGCATCGGTTATAAAATTTTTTCCGA\nTGTTACCAAACCTTGAAGTCCACCGAACACGTACCGAGTGCGGTGGATAATACTTTGATACGTTACAGTA\nGGCTGCGTATGTCTGTCCGGTTAAGACTGGATCGCCGACAACGGTAATATTTGGACGATAATACGTTGTA\nACTGTAATACTGTGTTCCGATATGACGTTCTTAGTTTTTGTATTAACGACTCGCCAAATATACGTTCCCT\nCCGTGGTAGCATCCATAGATAAAATTGTTACAGAAAAATCAGACGTTGTTTTAACATCTGGTATTACATA\nATTTTCCTTAGCGTGTGTAAATATCTCAGGGTTGTTTATTAAGTTTAAATCGGCACTGTTGCTATATAAC\nATAACCGGTAAATCTGGCATGCGTATTAACGCATTGCCCAGTTGACGGTGCGGATCTATAAGGTGACGCG\nTAAACCAAACTTCAATATGAAGATCGGGGCGTATAAGCGACTTCCACCTTGTTATATTTGAACCTTCCGG\nATCTAAAGAATATTGTTCATATGTTTTTTGTTGCTGCTTAAAGGCCGCCTGTTGTCCGGTCGTTAGACGC\nATGTAACAAGGCATGATAAATGTGTGAAAATAGGGTATGGATTGTATTCCGCCGTGAACGCATTGTATAT\nTTTCATATAGAAAAGGTGGTTGTGAATGTTGGGTGTTGGCTGCGGGATCGGGCTTTCGGGAAGCGGCCGA\nGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGTAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTT\nCGGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGTAGCGGCCGAGGTGGGCGCGACGG\nCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGAAGCGGCCGA\nGGTGGGCGCGACGGCGGGATCGGGCTTTCGGGAAGCGGCCGAGGTGGGCGCGACGGCGGGATCGGGCTTT\nCGGGTAGCGGCCGAGGTATATAATTCAGTTATACTTACGGGTGTGGGTTGAGATTCAGTCGATAATTGTA\nTACACGCGATCGTTAAAATTAAATTTATTTGTATCCGCTTCATCCTGGTTTTTATTGACACATCCACGCT\nCCCCTTAAATAAAAGATTAAAACACCCACCGCGGAATTTAAATGATGGAAACGTTTTTTTCGACATTGGG\nAATAATAAAAACGGCTTTTGCAACTTTAAAAACTTTATTTATCTCGATTACGATACATATGTACCACATA\nGATAGCATAGATTTATTATAATATAAACACACACGTGATATACTTTAGTGATATGAGATGCCATAAAACA\nGTCAATAGGTTTAACGCTTAGTCTCATCATCTGAATACACGTCAAACCCGCCGCAACTGTTGATGTTAGA\nATTATAATAGCTCCCCATGAAATGCCGGCAAATGTTACAGCTATACCCGTCACCGAGGTCGTTGTATATA\nATACAATTACCCATAGGTTTTTTTTTTCTTGATATAAAACGGCAAAACCCTGTAACCCAAATGCTATAAT\nATGACCTCCTATTGAAACTGCTAACGTTACTTGTGTAAGTTTGATAAAATGATTTAATTTAATTATATGT\nGAGATTGCCCACATTAATGGGGTAACTATATATAACACCGGGGGTATAACAGACATTATACGAATTCCTT\nTAAACACGCGTTTAAGGGTCCGGGAACTTTCTCGATGGTCACATACTCTCCCGCGGTCATTTTGTGTATA\nTACAACGGCAAAACCTAAATCTGTATAAGTGTTTAATTGCTTATGGCGATTTTTACGATATATACACGTA\nTCTTGCAAATCGGTGGCGGCATCGACAATTGAAACTAGTGTGACAATAGATATACACAATCCAATAAGAA\nCCTCATATTTACTGACATACATATATAAAATAACGGTTAGTAAACCTCCCAACCCAGTTCCCAACATCAT\nAACATAAAAATAAATATGCGGTCCATTGAATGTCGTAACAAAGTTGTAGTAATGGATATGCACAGCAGCC\nACTGTTCCGGTAATCGCGGATATGGAAATTCCCAGTAATTCTACAAATGGAAGATCCCGGGATATTGGGC\nAACCAACCGCCCATAACACAGCAAAACCCAACACGACCACCGTCTGCAAACATCGTCCCAATTTTGCTAA\nTGTGCGTAGAAATTTCACGGATGTTGGCCATAACCCCGAAACGACGATCAACCCCATAATAGTTGCATTG\nACGGCAGCTTCGCAGACGTGATATTGTAAAATTAACCCGGACGTGATAACGCTTGCTTGTAGTCCCACGA\nGAAACAACCGCGATGCTGAGGTTATTGCACACGAATTACATTCTTGAGGGTTTCCGACACATCCTTGGAT\nTGATTGAGCGCGGATTAATTCTCTGTCTAACACACCCAGGTTTTCATCATGGACAGCTCTTTCACCATTC\nACGGCCATGTCTTAAGTTTAATAATTCAAAACAAATAAAAATGTGTTCATCTATGGTACACACAAGTTTG\nTATGTAAAATATAAGCAAAAGTTGCACTTATTTAACTGTACATATTACGTCAGATTCACGTGATAATTCA\nGAATAATCCAGGGTTCCTGCAGGGTCCACTGGAGGAGCCACACAATATTCGCGAATTCCGATTCCCTCCT\nGCCATGTGGTTTCGGGGAGTTTCCCCCCCATTTTATTTCCGGTATTTTTTTCGTTTCTTTTTGTTAATAA\nATTGCGTCTTTTTTTTAATGGTGGTTCATCCTTCACAGATTCCATGTTCGCAAATAATTGCATCGAGGTT\nAATTTTTCTTTAAGGTCTTTGGGACTTAAGAACGTTGCATAAAAAAAAGAATGCACGGGTGCGGAACGTT\nGGATATACAATCCAACCATGGGGGAGTTAGTTAAGGCGAGATAAAAATTAATATAACACGTCTCATCCCG\nTGTTAACTTAAGATTTTGTACGGCAGAACGGAATCCACTGTGTGTTTCCAATAATACTCCAAATTCACGC\nATACTCCCGCTGCCATAAACAACATTATTAAGGATCCTTTTTGAATTTGTGATTGAGCGTATTAAATTAT\nATGGTGTAGGCTTGCTTCCGTTTATATCCAAGGAAACATTAAATGAGATAAAACCACCCCCGGCGGTCTG\nGATGTACATATCCGTGGCTGTTAGAATGAAGCATGTTGTAAACCCAAAAGTTTTAAGTAGTCGCTGTAAA\nCGGGTGAATTGATCGCGTTTTAAGCAAATGCTTATATCTGGAGTTAGATTTGGAAACATCATTGTATAAC\nAAGCGAGTTCACGTTTTACAACTTGTTTGTAACATTGTACTTGATCATCTGGACCACAATCACCCGGGCG\nTTGCCATACCATCGTTTGGATAATACTCCGCTCGGGGGGTTGTCCGGTAAATTTAAAATATAACCGTGTT\nGGGGTCGACGGATCTTTTGTATGGCGAAACGCGTCAATAAGCGAGGACCGTCCCTCCGTTGCCGCGAGTA\nCAACCATTCTCGGCCCAGTCCAATTATACTGGTCAAACATATTTGCCGGTATAGGAATATACAGTTGTTC\nTGTTTCCAAACTACAGTGAATAATTAATCCTTCGTCGCTGAATATTAAAATAGAATCCCTTAGTCTATTA\nACCAGAGGTGATATAGACGAAATTAAACCAGTAAGCGTTTTTTCCGTTAAAACAGCTCTGGCGATTTCTG\nGGGCGTCAAAACCCGCATGCAATTCCATGTCCAAAGCATCGTCTGTACGCGACCTCAAATCCATAATTTA\nCTACTTAAAATGTTTACTATAGAAAAAGTAATCATATGTAAACACACGAGTTTCGTTAATATGTTTGTTT\nAACCCGATCCGGTGACTTAAGTACATAAACAGGCATGATATTTGAATAGTACGGCCCATGGGAGGGAACA\nTTTCCACGTGTTCCAATACAGGGGGTGTTCCTTAATAGGGACTGTGCAATAAAATACGTAAGAAGTTACC\nAGATTTGATGTAATGTTTGTCATAAAAAATATGTACATCATTATATACGTCTGTAATTAACACAAGATCA\nCATCGAAGAATTACTGAAGCCGCTGTGAAACCTTTCACAAGACGATATAAACTTGGTTAAGTGTATTGAT\nGGGGCTCTTTGGACTGACACGCTTTATCCATGAACATAAACTGGTTAAACCCAGCATCATTTCAACGCCA\nCCCGGAGTTTTAACCCCCGTGGCGGTAGACGTATGGAACGTCATGTACACATTGTTGGAACGTTTATACC\nCTGTGGGTAAACGCGAGAATTTACACGGACCATCTGTAACGATACATTGTCTTGGAGTCTTATTGCGGCT\nATTAACACAACGGTCATACTATCCGATATTTGTATTGGAACGTTGTACAGACGGCCCATTATCACGTGGA\nGCCAAGGCAATTATGTCACGGGCCATGAACCACGATGAAAGGGGAACCTCGGACTTAACCCGTGTTCTAC\nTATCATCCAACACATCATGTTCTATCAAGTATAACAAAACATCGGAAACATATGACAGTGTGTTTCGAAA\nCTCTTCCACGAGTTGTATTCCTAGCGAAGAAAACAAATCCCAGGATATGTTTTTGGACGGTTGTCCACGA\nCAAACTGACAAGACGATCTGCCTGCGCGACCAAAACGTATGCAGTCTTACCTCTACAATGCCATCCCGAG\nGACATCCTAACCATCGATTATATCACAAATTGTGTGCAAGTCTTATTAGATGGATGGGGTATGCATACGT\nCGAGGCGGTTGACATTGAGGCGGACGAGGCATGTGCAAACTTATTTCATACGCGTACAGTGGCTTTGGTT\nTATACGACAGATACTGATTTACTCTTCATGGGCTGTGATATTTTGTTAGATGCAATTCCTATGTTTGCTC\nCAGTAGTACGATGTCGCGATTTGCTTCAATATTTAGGAATTACATACCCTGAATTTTTGGTTGCCTTTGT\nTCGCTGTCAGACCGATTTGCATACAAGTGACAACCTAAAATCTGTTCAGCAAGTTATTCAGGATACCGGC\nCTGAAAGTTCCACATCAAATGGACACTTCAACGCGCTCCCCCACTTACGACTCGTGGAGACATGGCGAGG\nTTTTCAAAAGTCTTACCGTAGCCACGTCGGGTAAAACAGAAAACGGAGTGTCCGTTTCCAAATATGCATC\nTAACCGATCGGAGGTGACAGTAGACGCCAGTTGGGCTTTAAACCTTCTGCCACCCTCATCCTCCCCATTG\nGATAATTTGGAACGCGCATTTGTTGAACATATAATCGCCGTGGTAACTCCATTGACCCGCGGTCGCCTAA\nAGTTAATGAAACGTGTAAATATTATGCAAAATACGGCAGACCCATATATGGTTATTAACACCTTATATCA\nTAACTTAAAGGGGGAAAAAATGGCTCGCCAATACGCACGTATTTTTAAACAGTTTATTCCTACTCCACTC\nCCACTAAACACTGTATTAACAAAATATTGGAATTAAAACACACATAAGAGCGACTTAATGGTTCATTGTT\nTTATTTTGCTCGTATATACATGTTATAAATCGTTTATCACTGTGCCCGCATAAGATGTACTGTGTCTCTC\nAAAAAAATTTGTGTTTTTATCTGCAATCATAAATGCAAGTGGAAAGTCCGAATCGGGAGGTGGGGTGTTA\nAATAGTTTTGGTACATTAATCGCTGATAAAAGCCTGTCCGCGCTGAATTTCACGTATTGTGTAATTGCAT\nCGACGTTCACCAAACGGGTTTTGGGTGCATGGGATTTTAAAAACGCACACTCGATTTCAACGGCTTCCGA\nAAACAGTTGATGTATTCTGGTGATAGCGGGTTTTTCGGGTACATAGTTATTGTATATACAACACGATGCG\nCTGGTATGTATGGCTTCATCTCGGCTTATAAGGTCGTTAAATTGACAAGTTACAACAAATAGTCCGTTAT\nTGCGTAAATATGCAATAGCCGCGAACGATGATACAAAAAAAATGCCCTCTATAAGAATCATTAGTATATA\nTTTTTCTGCAACGGATGGGTTGTCCCGTACCTTTTCTTCCAACCATTGTACTTTTTGTTGGATCGACGGA\nTTATTAATAGTGACATTTACGTATTGTACCCGCAACGATTCATCCCCTCTGAACAACATTAGTTGAATTT\nGACTATAGACACGCGCGTGGACAACCTCGATGCACTCTTGTTCAATGTAGTAATGGTGAATATCCTTTTG\nGGAAAAGAGTTGGGTTAGAGAGCCCAAATTAACATTTACCAGATCATCTGCCGCCGATAAAAATGTAAAA\nATAAATCTGTAGAATATTAGTTCATCTTCCGTTAAACAGTCCAAGTATTGATAATCATCTTCAATGATAA\nAATCGCTTTCTAACCAACGATTCGAAATGCTCAGGGCACGTAAATTGTTTATATCTGGACACTCCGGCCT\nGTAAAAAAAATGACTGCAATCTTTCTGATCCATTTTGGAATAGTTTCCCGTGTAAATTTATAAAGCACAA\nCTGGTACAGGTTAATTCGCCTCCCGCAAACAGTCCGCTGTTCGTAGCTTTACGAATTTTACAGTAGTACA\nTACCCGTTTTAAGGCCGGCTTTATAGGCACGTATAAGCAAATTCATTATTTTGGAGGCGGGAATTGTCCC\nGTCTGGGCGTTCCTCAATAAATAAAGTCATTGATTGACTTTGGTCAATAAATGGCGCCCTTTCTGCACAC\nATATCAACGAGATCCTCTTGCTCATATTCAAACGCTGTTTTATATTTTAAGAGTGGGTGACTATTAGATA\nAACAGCCAAACGAACGTATTACTGACCATTGGTTTTTCTCAAGTATGTTTATAACTTCCAGTCGTTTTTC\nTTCACATGAATACATATCTCTTAGTTCGTCCATAAGGTCTAAGTTGGGTCTAAGTAACTCACCCGAGGTG\nGTGACCTTACTAAACATATTATTATAAATTGGAGAGAAACCCTCACTGCACTCCGTTACCTGTGCAGATG\nAAACTGTGGGCATTAACGCTAAGAACTGCGAGTTGTATAACCCATAAGCGCAAATATCATCTCGCAGGGT\nACACCATGGTAAATCTAAATAACTTATCGTAGAAAACCCATCTTGGTGTAACCATCCCTTAGCATATTTA\nCTTTCGGTAAAACCCTTAAACGGGGCTAAGCCGCCAATCTTACACATTTCCATGCTTGTTTTCATTGTCT\nCATACAACATTAACTCCGCTATTTGTACATTTAACCGTCTAGCTGGTTGGGAAGTTAAATCAAATCCTAA\nGCGGAGACAAGTTGTATGTAACCCTTGTATGCCAATGCCAAGTGATCGGTTGTTTTTTACACCTTTACAT\nGATTTTTTACATGGAAAGTTCCCAGCCGCCAGGACCCCGTTTAAAAAAATAACAGTCGTTCTTGCTGTCA\nATTGAAGGTCGTTTAAATTAAATGACACTGGGCCTTTGGATAAGCACGTTGTAAGATTTATGCTGGCAAG\nATTACATACGCCATGTTGATGAGCGTCTGCCTTTTGAACAATTTCCGTACACAAATTTGACCCCGTGATA\nGCATTTCCTTGGGTATTCATATGATAATTACGATTACAGGCATCTTTGAACATTAAAAAGGGGCTTCCTG\nTTACAGCAGCACTGCGTATGATTGTGAATGCGATATCTTGAATGGGAACAGAAGAAACGCCTAATCCTTC\nTCTCTCTAAACGTAAATAGGTTGAAGTGAATGCCTCCCCGTGTAATGTTCGAAGGATATCGGCTCTGTTA\nTCAAAAAGAGTCCACTGAACATTACTAGCCCCTTTTAGATAGCTTAGGTATCTTTCAAAAAATAAATCTG\nGGGTCCATAAACAACAAAATATGTTATCACATCGAAATATTTCATCACGAACCAACATTCCACGTGTGGC\nCAAAACAGTTTGTAGATCGACGTGCCATGGTTCTATGTAAACACAAACTCCAGTTGGTCGTTCACAATCA\nCTGTTAATTGCCATAACCATGCAATCTAAAAGTTTTAAAACTGCAAGAAGACCTTTCGTTTGATTTTCCG\nTAGGTATTAAATTCAGACTCTGTAGAGAAATTCCCACTCCACCTCGACTTTGTAATACCGTTCCCACATC\nGCCTGTGATAGCTCGAACAGCTCTCCCAACAGTGATGGATTCCGGGTCCATTAAATAACAACTGGCCGTT\nGCCCCGGTCTCTCGACCTAAAAACATCATAACCGGTGTAGCCGGGACAATTTTCTGACATGCCAACGCTG\nTGAAAAATACCCGACAGACATCAGTCCATGTATAACCATCATTTATTCCGGGAATAAGAGTTGCGATTTT\nAGGCAGGTTTACGATTTCTGTTGTCACGGTGGCCGCCAGTCTTAAAAAGAATTGGCAAAGCGACTCTAAT\nTTACCTTCCTCTAACTTAGTTAAATAAAAGTCTTCGTACTTTAAAGCAGACTGTAGTCCAAGGGTAGCTA\nAAGCGGGGTATTGATCTTTCAAAAACGGTTCTAATATAGCCCGACGAATTTCGTCCCTCCGCCCTTCAAT\nTGCTTGGCGGACTCGGGGAGTTAAACAGAGAATTGGGGAAGTCAACCACGTTTCCATGGAAACGGATCGT\nAGGTTAATACGGCAATGGATAAGTTCTCCACAACATCGGTACACTCGCTCATCTTGTCGCGTCACCGCCT\nTAAGTTTTGAGACGATAGTGCTAATATACTCCATTAATTCCACCGGTGTGGTTGATTCGGGCGGAATGAT\nGTATTCCTTGTAGCCATGTTGACATAATCGGTTTATAATGTCATGAACCGTATTAAAAATTCTTTTGAAC\nTCCATAACGGATAACGTATTTAGGCTCCGGAATAAACCTTTAAACCCTAAACTCACAGCTGAGTTAGTTC\nTACAATATTGTAGACTCCCTTATATATGGTTACGTACAGCCTGCCCCTCCCCAGTATATAATATCACGCA\nAAACCCACGCTATGTTAAATTCAGTTTATTTTACATACATGCTTTAATAATAACATTCGTTCCATGTATT\nTGTACCCCCCCACACAACCCCCTCTAACCAAATAGTTGGCACGTTATAACCTCCGAACCGTTCCATGCGT\nCTTGTATAACGCACAGACTCTGATGGAATTGTTCCAATTAACGTATATGCCGCATACATGCAGGATAATT\nGTGTGGGAAGTCCCCGAAAATCGCCGGTCCATTGATACAATCGCTGTCTAGCCAAGTTCCAATTTACTCC\nTGTAATTTCGCCAATACTACATCGAGGGCTTGTCGGGTCATTGGATAACTGCACAAGCGGCAACGCCCTT\nGTGTTATATGGCTGGTGGGTATTTGCAACCCCTTCAGTCCCCCAGGCGGCATTTTCAGCTCGTATGCGTC\nCTAACAGGAAGCCAATACCACGACCAAAACATTGTTCGTTTAGTTGGCTTAATGCAAGATGCAGTCTTAC\nACCTTCTCGTTGGCGTCGCTGTGTATATACAAAAACCAAGAACACATGCTTCAGTCCGTCCGCGGAAAGA\nTGTAAATCTTTGTCAACGTCCCAAAATACGCAGGCCGGGATGTTGGCTGTGACCCTGCGAGTTGAAGTTT\nTGTCTGTACGTGCAGCTTCTTGGGGACCTTTGGCCACGGCGGTTATATTGCATAAATTATCCTGAATGGT\nATATTCCAGCAGGGACCCAAAAAAACTTATAAATCGATGTGGAAATACATGACATTGTACCATCGCACGT\nAAACACTCCGAAAACCTTATGAGCCGCGTTTCCATACGACTGCATCCATAGGCAGAAACAATTGCTGTTC\nTGTTGGCATCCGCTGCCTGTTTATCCGTATATTCTTCTGCCCGGCATGCGGCGATGAAACTTAATGACGT\nTACATATGCTCTAAGCCCCCCACCTTCTCCAACGGTCCAAGGAGCCGTGCAGGCATTGAATAGGTTTCGT\nAAACCCTCTAGTAGTACATCGGGGTCACGTCCAGCCTGTGTAAGTGTATTAGCTTCTCCAATCATGTCAG\nATGGATGACGAAGGATTAAGACGATTGACCCAGCATGCTCAATGTCCGGACGAAAAAAATCGGTTAATGA\nCACTTGTTGGATTAGCTGTGTCGTTGATTTAAAATTATTTAACGGGAGTCTAATGGTAACTTGCGGGTTA\nCCAATTGAAGTTGGATTTATTTGAATGTTGTTCATACGATTAATAACAATTGAACGGGGGGTTACTTGAA\nTAGACGCGGTTTCTGTACGTTTTGGTGGTACATGTATCGGTTGTTTGTTCAGACCTCCAAAGCGAGGGCC\nAATTGTTAAATCGCGACTCCAATTTCCGAAGAAGCCCGGAGCATAAGTCATATGAAGCCCGTTCCCTATT\nTGAATAAAACGGTTATTTCCTAAAAGACTGATATTAGTTCCACATAGCGTTTGTTCGTTTAAAGTAAAAT\nGCGAGTTGGTTGGTTGACTCCCCATAGCTGAGGGGTTAAATTCACACAATGCAATCGTGACGTGGTACTA\nTCTGAAATGTTGCCTGGGGTATGTGTACACATTATACAGTCGTAGTACCGTTTATATAATGTTAGGTAGG\nAGGAGCCTATAAAAATATTTTGATTGGCGTTAAAAGGTTCTTCAACTTACCGTGACGTCCTTTTTATTAA\nCATGCGTTTTTATTGATGTTACATTTATGTCTTTTCATTCCGGACGGATGTAGCTTTTTCATATCACGTT\nATAAAGTTAAGTCAGCGTAGAATATACCATGGAAGAACCAATTTGTTATGATACACAAAAACTTTTGGAT\nGATTTAAGTAACTTGAAAGTACAAGAAGCGGACAACGAAAGACCATGGTCACCAGAGAAAACAGAAATCG\nCCAGAGTTAAGGTAGTTAAGTTTTTACGATCTACCCAGAAAATTCCAGCTAAACATTTTATTCAGATATG\nGGAACCCCTGCATTCTAATATCTGTTTTGTATATTCCAATACATTTTTGGCGGAGGCTGCTTTCACGGCC\nGAAAATTTACCCGGACTGTTGTTTTGGAGACTAGATCTAGACTGGACGATAGAGGAGCCAGGTAATAGCT\nTAAAAATTTTAACCCAGCTATCAAGTGTAGTACAAGATTCCGAGACGTTACATCGTTTATCGGCCAATAA\nATTACGAACCTCGTCTAAATTTGGACCCGTTTCGATACACTTCATTATAACGGACTGGATAAATATGTAC\nGAGGTCGCCTTAAAGGATGCAACAACAGCCATTGAATCACCATTCACTCACGCTCGTATTGGAATGTTGG\nAAAGCGCCATTGCAGCTTTAACACAACATAAATTTGCGATCATTTACGATATGCCATTTGTTCAAGAGGG\nGATTCGTGTTTTAACACAATATGCAGGATGGCTTCTTCCGTTTAATGTTATGTGGAATCAGATTCAAAAT\nAGCTCACTCACTCCTCTAACACGAGCCCTTTTTATAATCTGTATGATTGATGAATATCTCACGGAAACGC\nCAGTACATAGCATATCAGAATTATTTGCAGATACTGTAAATTTAATTAAAGATGAGGCGTTCGTATCCAT\nCGAAGAAGCGGTAACGAATCCACGAACGGTGCACGAGTCACGAATTTCCTCAGCTCTGGCTTATCGAGAC\nCCTTATGTTTTTGAGACATCCCCGGGAATGCTTGCTAGGAGACTTAGATTAGACAATGGTATATGGGAAA\nGCAACCTCTTATCGTTGTCCACCCCCGGAATTCATATTGAGGCGCTGTTACATTTACTAAACTCCGACCC\nGGAAGCGGAAACCACATCTGGAAGTAATGTAGCAGAACACACCCGTGGCATTTGGGAAAAGGTTCAGGCT\nAGTACATCGCCTAGTATGTTAATAAGCACCCTTGCCGAATCCGGGTTTACAAGATTTTCATGCAAATTGC\nTACGTCGGTTTATTGCTCACCACACACTCGCCGGTTTTATTCACGGAAGCGTTGTAGCAGACGAGCATAT\nTACAGATTTCCAACAAACACTAGGATGTCTCGCTTTAGTGGGTGGACTGGCATACCAATTAGTGGAAACG\nTACGCTCCTACTACCGAGTATGTGTTAACATATACACGGACAGTAAACGAGACCGAAAAACGGTATGAAA\nCGCTATTACCCGCCTTAGGATTACCACCGGGAGGCCTGGGACAAATTATGCGGCGCTGTTTTGCTCCACG\nACCCCTTATTGAAAGTATACAAGCGACACGCGTAATACTACTTAATGAAATTTCACATGCAGAAGCTAGA\nGAGACAACATATTTTAAGCAAACACATAATCAATCCTCAGGTGCGTTATTACCACAAGCAGGACAAAGTG\nCCGTACGCGAAGCCGTACTAACCTGGTTTGACCTACGTATGGATTCAAGATGGGGTATTACTCCCCCGGT\nGGATGTGGGTATGACACCTCCTATTTGTGTTGATCCACCGGCTACAGGGTTGGAAGCTGTCATGATAACA\nGAAGCACTAAAGATTGCATATCCTACCGAATATAATCGCTCTAGCGTGTTTGTGGAACCGTCGTTTGTGC\nCTTATATTATTGCAACAAGCACGCTTGATGCCCTTTCGGCAACAATAGCTTTGTCTTTTGATACACGGGG\nAATACAGCAAGCCTTGTCTATTCTTCAGTGGGCTCGCGATTATGGATCCGGAACCGTGCCCAATGCAGAT\nGGATATCGCACAAAACTATCTGCTCTTATAACAATATTAGAACCTTTTACCCGTACACACCCCCCAGTAC\nTTTTACCATCTCACGTTTCTACTATAGATTCCCTTATATGCGAACTTCATCGGACTGTTGGCATTGCCGT\nTGACCTGCTTCCCCAGCACGTCCGTCCTTTGGTTCCTGACCGTCCTTCTATTACAAATAGCGTTTTTTTA\nGCAACTCTCTATTATGATGAACTTTACGGTCGTTGGACCCGACTGGATAAAACATCGCAGGCGTTGGTTG\nAAAATTTTACATCCAACGCGTTAGTGGTTTCTCGGTACATGTTAATGTTACAAAAATTTTTTGCGTGTCG\nTTTTTATCCAACGCCAGATCTTCAGGCTGTTGGTATCTGTAACCCAAAGGTTGAACGCGATGAACAATTT\nGGGGTATGGCGTTTAAACGATCTTGCTGATGCGGTTGGTCATATTGTTGGGACAATACAAGGAATCCGAA\nCGCAAATGAGAGTGGGAATATCCAGCCTGCGCACAATTATGGCCGATGCTTCCTCAGCCCTTAGGGAATG\nTGAAAATTTAATGACTAAAACCTCCACTTCTGCTATTGGGCCTCTTTTTTCAACGATGGCTTCCCGGTAT\nGCACGGTTTACACAGGATCAAATGGACATTTTAATGCGTGTTGACAAACTAACAACAGGAGAAAATATAC\nCCGGTCTTGCAAATGTAGAGATTTTTTTAAATAGGTGGGAACGAATAGCAACAGCTTGTAGGCATGCCAC\nGGCAGTCCCGTCGGCCGAATCTATTGCAACCGTGTGTAATGAATTGAGGCGCGGTTTAAAAAATATACAA\nGAGGATCGTGTAAATGCCCCAACCTCATATATGAGTCACGCCCGAAATCTGGAAGATCACAAGGCAGCAG\nTTTCATTCGTTATGGACTCCAGGCAACAGTTTATTGTGGATTCTGGACCTCAGATGGGCGCGGTTTTAAC\nTTCACAATGTAATATAGGAACATGGGAGAATGTAAATGCAACGTTTTTACATGATAATGTTAAAATAACG\nACAACGGTCAGAGACGTAATTTCAGAGGCTCCGACGCTGATAATAGGACAAAGATGGCTTCGTCCAGATG\nAGATTTTATCTAATGTAGATTTGCGTCTTGGCGTACCCGGGAATACAAGTGGGAGTGACCCTTAATATAA\nAACAGGCGTGTTTATGTACATTAAAGTATTTGTGGTTTTTATTGACTGGGCGTTTCGTTTGTATAACGCT\nGTTGTTGCTAGTATTTTCATAACCTCCTAGGTTTTTGGAGCTACACGTGCTTATTCAACGCTCTTTGGGA\nTTTGAATCATCGTAAACGTAGCGTCCCTACCAGTTGAGCGCGTAATTTTCGTAAGCAATAAAATGGATAT\nAATTCCGCCTATAGCTGTCACTGTTGCGGGAGTGGGAAGCCGTAATCAATTTGACGGTGCCCTGGGACCG\nGCGTCAGGTCTGTCATGTTTAAGAACATCTTTATCGTTTTTGCATATGACATATGCGCATGGAATTAATG\nCAACCCTGTCATCAGACATGATTGATGGATGTTTACAAGAGGGTGCAGCATGGACTACGGATCTGTCTAA\nTATGGGGAGGGGTGTCCCAGATATGTGTGCTCTTGTTGATCTCCCCAATCGAATTTCATATATTAAACTG\nGGGGACACTACCAGTACGTGCTGCGTTTTGTCTAGAATATACGGCGATAGCCATTTTTTTACCGTTCCAG\nACGAGGGTTTTATGTGCACACAAATTCCCGCTAGAGCGTTTTTCGATGATGTGTGGATGGGACGTGAAGA\nGTCGTATACAATTATAACTGTAGACTCAACGGGAATGGCCATCTATCGTCAGGGAAACATATCTTTTATT\nTTTGATCCACATGGCCATGGGACTATAGGACAGGCTGTAGTTGTTCGGGTGAATACCACGGATGTGTACT\nCTTATATCGCATCGGAGTATACCCACCGCCCCGATAACGTAGAATCCCAATGGGCCGCTGCATTAGTTTT\nTTTTGTCACCGCAAACGACGGTCCCGTAAGCGAAGAAGCGCTATCTTCGGCAGTAACGCTTATATACGGA\nAGCTGTGATACATATTTTACAGATGAACAATATTGCGAAAAACTGGTTACAGCTCAACATCCGTTGCTTC\nTTTCACCTCCTAATTCCACGACAATTGTGCTTAATAAATCGTCTATAGTACCTCTTCACCAAAACGTTGG\nTGAAAGTGTATCCTTGGAAGCAACCCTACATTCAACGTTAACCAACACGGTTGCACTGGACCCTAGATGT\nAGTTACAGCGAGGTTGATCCTTGGCATGCGGTTCTAGAAACAACCTCGACTGGGTCTGGCGTTTTGGATT\nGTCGTCGTAGACGCCGTCCTTCATGGACTCCTCCTTCAAGCGAGGAAAATTTAGCTTGTATCGACGATGG\nCTTGGTAAATAATACACATTCCACGGATAATTTACATAAACCCGCTAAAAAGGTTCTCAAATTTAAACCA\nACTGTAGACGTGCCGGATAAAACACAAGTGGCACATGTATTACCCCGCCTACGAGAAGTTGCTAACACCC\nCAGACGTTGTGTTAAATGTATCCAATGTAGATACGCCTGAATCCAGTCCCACTTTTTCACGGAACATGAA\nTGTAGGAAGCAGTTTGAAAGATCGGAAGCCATTTCTATTTGAACAGAGTGGTGATGTCAACATGGTTGTC\nGAAAAACTACTACAACATGGGCATGAAATTAGCAATGGATACGTACAAAATGCGGTGGGTACGTTGGATA\nCTGTTATTACCGGTCATACAAATGTTCCCATTTGGGTAACAAGGCCCTTGGTTATGCCAGACGAAAAGGA\nTCCATTGGAGCTTTTTATTAACCTCACCATTTTGCGTTTAACGGGATTTGTGGTGGAAAATGGAACACGT\nACACATCATGGTGCTACAAGCGTTGTATCAGACTTTATAGGTCCCCTTGGGGAAATTTTAACAGGATTTC\nCCTCCGCCGCGGAACTTATACGCGTTACAAGTTTGATATTAACAAACATGCCGGGGGCGGAATATGCTAT\nTAAAACTGTTCTCCGGAAAAAATGTACAATTGGCATGCTCATTATCGCTAAGTTTGGTCTAGTTGCCATG\nCGGGTTCAGGATACAACCGGCGCTTTACATGCCGAACTAGATGTGTTAGAAGCGGATCTAGGAGGTTCGT\nCGCCCATAGACCTCTATTCTAGACTGTCGACAGGTCTTATAAGTATACTAAATTCGCCTATTATTTCTCA\nTCCCGGACTTTTTGCCGAGCTTATTCCAACCCGTACAGGGTCCCTGTCTGAACGAATACGTCTTCTTTGT\nGAATTAGTCTCGGCCCGGGAGACACGCTATATGCGTGAACACACCGCGCTTGTTTCTAGTGTAAAGGCTT\nTAGAGAATGCATTACGGTCTACCCGCAATAAAATTGATGCCATTCAAATACCAGAAGTTCCCCAGGAACC\nCCCGGAAGAAACCGACATTCCACCCGAAGAGTTAATTCGGCGTGTATATGAGATACGATCCGAAGTTACA\nATGCTATTGACCTCGGCTGTTACAGAATACTTCACCCGCGGAGTGTTATATAGCACACGGGCCTTGATCG\nCTGAACAATCCCCTAGGCGTTTTCGGGTCGCGACCGCAAGTACGGCACCCATTCAACGGCTTTTAGATTC\nTCTTCCGGAATTCGACGCTAAATTAACGGCAATCATATCGTCCCTGTCTATACACCCTCCTCCTGAGACT\nATACAAAATCTCCCCGTCGTATCTCTGTTAAAAGAGCTTATTAAAGAAGGGGAAGATTTAAACACAGACA\nCGGCTCTCGTATCGTGGTTATCTGTAGTCGGGGAAGCTCAAACCGCAGGTTACTTATCCAGACGAGAGTT\nCGATGAATTATCACGTACAATTAAAACCATTAATACACGCGCAACGCAACGGGCTTCCGCGGAAGCAGAG\nTTGTCTTGCTTTAATACGCTAAGCGCGGCCGTAGACCAAGCCGTAAAGGACTATGAAACATATAACAATG\nGTGAGGTCAAGTATCCTGAAATAACACGGGATGATTTATTAGCAACAATTGTACGTGCTACAGACGATTT\nGGTGCGACAGATAAAAATTTTAAGTGATCCAATGATCCAATCCGGTTTACAACCTTCGATTAAAAGACGA\nTTGGAAACAAGGCTTAAAGAGGTTCAGACGTATGCAAACGAGGCCCGAACCACACAGGACACAATAAAGA\nGTCGAAAACAGGCGGCATATAATAAACTCGGGGGGTTACTTCGCCCGGTAACCGGTTTTGTGGGACTTAG\nGGCTGCAGTAGATTTATTACCGGAACTTGCTTCTGAGTTAGATGTCCAAGGAGCCCTGGTAAATCTCAGG\nACCAAAGTCTTAGAGGCGCCGGTAGAGATCCGTTCTCAACTTACGGGTGATTTCTGGGCGTTATTTAACC\nAATATCGAGACATTTTAGAACATCCCGGAAACGCACGCACATCTGTCTTAGGAGGACTGGGAGCTTGTTT\nTACAGCTATTATCGAAATTGTGCCGATACCTACGGAGTATAGACCATCATTGCTTGCGTTTTTTGGTGAC\nGTGGCAGATGTGCTTGCATCCGACATCGCGACCGTATCTACTAACCCGGAAAGTGAGTCCGCCATAAACG\nCTGTTGTTGCAACTCTTAGTAAAGCGACGTTAGTTTCATCTACAGTGCCAGCCTTATCCTTTGTGTTGTC\nGTTATATAAAAAATATCAGGCTTTACAACAAGAAATTACGAATACCCATAAGTTGACTGAATTACAAAAA\nCAACTTGGAGATGACTTCTCCACCCTAGCTGTCTCATCTGGACACTTGAAGTTTATATCATCTTCAAATG\nTAGATGATTATGAAATAAACGATGCGATATTATCAATACAAACAAATGTGCACGCCCTAATGGATACGGT\nTAAACTTGTTGAAGTTGAACTGCAAAAGCTACCCCCCCATTGTATTGCTGGGACATCTACCTTATCTCGA\nGTAGTAAAGGATCTTCATAAACTCGTCACAATGGCACATGAGAAGAAGGAACAGGCAAAAGTGTTAATTA\nCCGATTGTGAACGTGCACATAAACAACAAACGACTCGGGTTTTGTATGAGCGTTGGACACGTGATATTAT\nAGCATGTCTGGAGGCAATGGAAACGCGCCATATATTTAACGGGACAGAACTGGCACGGTTGCGAGATATG\nGCCGCTGCGGGAGGGTTTGATATACACGCAGTTTACCCACAAGCACGTCAGGTTGTAGCGGCATGTGAAA\nCTACAGCCGTTACGGCATTAGATACTGTGTTTCGCCACAATCCATATACCCCCGAAAATACAAATATTCC\nACCACCTTTGGCTTTGTTAAGAGGGTTAACATGGTTTGATGATTTTTCGATTACGGCTCCCGTATTCACC\nGTTATGTTTCCAGGTGTTAGTATTGAGGGACTCCTTCTGCTTATGCGTATTCGCGCGGTTGTGTTATTAT\nCCGCCGATACGTCTATTAATGGAATACCTAACTACCGAGATATGATATTACGAACCTCGGGGGATCTATT\nACAAATACCCGCATTGGCTGGGTATGTTGATTTTTACACACGGTCTTATGATCAGTTTATAACCGAAAGT\nGTAACGTTAAGTGAACTTAGAGCAGACATCAGACAGGCTGCCGGGGCTAAACTTACAGAAGCAAATAAGG\nCTTTGGAGGAAGTAACTCATGTTCGGGCACACGAAACGGCTAAACTTGCACTTAAAGAAGGTGTCTTCAT\nTACATTACCAAGCGAAGGTTTATTGATTCGGGCTATAGAGTATTTTACAACTTTCGATCATAAACGATTT\nATAGGAACGGCATATGAAAGAGTTTTACAAACAATGGTAGACCGCGATCTAAAGGAGGCCAACGCAGAGC\nTTGCACAGTTTCGTATGGTGTGTCAGGCAACAAAGAACCGTGCAATACAAATTTTACAAAACATTGTTGA\nTACGGCCAATGCCACTGAGCAACAAGAAGACGTGGATTTCACTAACCTGAAGACGTTATTAAAACTAACC\nCCCCCTCCCAAAACAATTGCATTGGCCATTGATAGATCTACTTCCGTTCAGGACATTGTCACGCAGTTTG\nCATTGCTGTTAGGGCGTCTGGAAGAAGAAACTGGTACGTTGGACATTCAGGCGGTTGACTGGATGTACCA\nAGCTCGCAATATTATTGACTCCCATCCACTAAGTGTGCGTATAGACGGTACCGGCCCCCTGCATACTTAT\nAAAGATAGGGTGGATAAACTTTATGCGTTACGAACTAAATTAGATCTCCTACGACGACGAATAGAAACCG\nGTGAGGTTACGTGGGACGATGCATGGACAACATTTAAAAGAGAAACGGGGGATATGTTGGCATCGGGGGA\nCACGTACGCTACTTCCGTAGATAGTATAAAGGCACTCCAGGCATCGGCGTCTGTGGTTGACATGCTTTGT\nTCCGAACCCGAATTTTTTTTATTGCCTGTGGAAACGAAAAACCGTCTCCAAAAAAAGCAACAGGAACGTA\nAAACGGCGTTGGATGTTGTGTTGCAAAAACAAAGACAGTTTGAAGAGACCGCGTCTCGCTTACGAGCTTT\nAATTGAACGTATTCCAACGGAGAGTGACCATGACGTTCTTCGTATGTTATTACGTGATTTCGATCAATTT\nACACATTTGCCTATATGGATAAAAACACAGTATATGACATTTCGAAATTTACTCATGGTACGGTTAGGCT\nTGTATGCAAGTTATGCTGAGATTTTTCCACCCGCGTCTCCAAACGGAGTATTTGCTCCTATTCCCGCCAT\nGTCGGGTGTATGTCTAGAAGACCAATCCCGATGCATTCGCGCGCGGGTGGCCGCGTTTATGGGGGAGGCG\nTCTGTGGTGCAAACGTTTAGGGAAGCCAGATCTTCTATAGACGCTTTGTTTGGAAAAAATTTAACCTTTT\nACTTGGATACTGATGGGGTTCCACTTCGATATAGAGTGTGTTATAAATCAGTTGGGGTTAAACTTGGAAC\nCATGCTATGCAGTCAGGGTGGATTATCTTTACGACCGGCACTTCCCGATGAAGGTATTGTGGAAGAAACT\nACACTATCGGCATTACGCGTGGCCAATGAGGTCAATGAGCTACGCATTGAATACGAATCCGCTATAAAAT\nCCGGGTTTTCTGCCTTTTCCACCTTTGTTAGGCATCGCCACGCCGAATGGGGTAAAACCAACGCACGCAG\nAGCCATTGCAGAGATATACGCCGGCCTTATAACAACAACATTGACACGACAATACGGGGTTCATTGGGAC\nAAGCTTATTTATTCTTTTGAAAAACACCACCTAACTTCTGTAATGGGCAATGGACTAACTAAACCAATCC\nAGAGAAGGGGTGATGTACGCGTATTAGAGTTAACCCTATCTGATATTGTAACTATTTTGGTTGCCACAAC\nCCCGGTACATCTTCTCAATTTTGCTAGATTGGATTTAATTAAACAGCATGAGTATATGGCCCGTACCCTC\nAGACCCGTAATCGAGGCCGCATTTAGAGGTCGTTTACTCGTTCGCTCATTGGATGGAGACCCGAAAGGCA\nATGCCCGGGCCTTTTTTAATGCCGCCCCATCCAAACATAAACTCCCGTTAGCTCTTGGATCAAACCAAGA\nTCCTACCGGCGGGAGAATATTTGCATTTCGGATGGCAGATTGGAAACTTGTTAAAATGCCACAGAAAATA\nACGGATCCTTTTGCGCCATGGCAACTTTCCCCCCCCCCCGGGGTAAAGGCCAATGTCGATGCAGTTACCC\nGTATAATGGCAACAGATCGTCTTGCGACCATTACTGTACTTGGGCGCATGTGTCTCCCGCCAATTTCCTT\nAGTGTCAATGTGGAATACGCTGCAACCGGAGGAATTCGCATACAGAACACAAGATGATGTGGACATTATA\nGTTGATGCGAGACTGGATTTGTCATCCACGCTTAATGCAAGATTTGATACCGCTCCCAGCAATACCACGT\nTAGAGTGGAATACAGACCGTAAAGTAATTACAGATGCTTATATTCAAACCGGGGCAACGACAGTTTTTAC\nAGTAACGGGGGCGGCACCAACTCACGTTTCTAATGTAACAGCGTTTGACATAGCAACTACGGCTATTTTA\nTTTGGGGCTCCTTTGGTTATTGCCATGGAACTTACATCCGTTTTTTCACAAAATTCCGGACTTACTTTGG\nGGTTAAAATTATTCGATTCCCGGCATATGGCTACAGATTCGGGTATATCCTCAGCCGTATCTCCCGATAT\nTGTTTCTTGGGGGTTACGTTTACTGCATATGGATCCTCACCCAATTGAAAATGCATGTTTAATTGTCCAA\nCTAGAAAAACTGTCCGCGCTCATTGCAAACAAACCTCTTACAAACAATCCCCCGTGTTTACTGCTATTGG\nACGAACATATGAATCCCTCTTATGTTTTATGGGAACGAAAAGACTCGATTCCAGCTCCGGATTATGTGGT\nCTTTTGGGGGCCAGAATCTCTTATTGATTTGCCGTACATCGACTCCGATGAGGACTCTTTCCCCTCGTGT\nCCCGATGATCCATTTTACTCGCAAATTATTGCCGGTTATGCGCCCCAAGGCCCCCCAAACCTCGACACAA\nCTGATTTTTACCCAACGGAGCCACTATTTAAGTCTCCCGTTCAAGTTGTTAGAAGTTCCAAATGTAAAAA\nAATGCCCGTCCGGCCCGCGCAGCCCGCGCAGCCCGCGCAGCCCGCGCAGCCCGCGCAGACCGTCCAGCCC\nGCGCAGCCCATAGAACCGGGCACACAAATAGTGGTACAAAATTTTAAGAAACCCCAAAGCGTAAAAACAA\nCCCTTAGCCAAAAAGATATTCCCTTGTATGTGGAAACCGAATCAGAAACGGCTGTGCTTATACCTAAGCA\nATTAACCACCTCCATTAAAACAACCGTTTGTAAAAGTATTACCCCACCAAATAACCAATTGTCGGATTGG\nAAAAATAATCCACAGCAAAACCAAACGTTAAACCAAGCGTTCAGTAAACCAATACTTGAGATTACCTCCA\nTTCCGACAGATGACTCGATATCTTACCGGACTTGGATTGAAAAATCAAATCAAACACAAAAACGGCATCA\nAAATGACCCTCGAATGTATAACTCCAAAACAGTATTCCACCCTGTAAATAACCAATTACCTTCTTGGGTT\nGACACGGCAGCCGATGCCCCCCAAACGGACCTATTGACAAACTATAAAACAAGACAGCCGTCGCCAAACT\nTTCCGCGGGACGTACACACATGGGGCGTATCTTCTAACCCGTTTAACTCACCGAACAGAGACCTATATCA\nAAGTGATTTTAGTGAACCTTCTGACGGCTATAGCAGTGAGAGTGAAAATTCTATCGTACTAAGTCTCGAC\nGAACATCGGTCATGTCGCGTTCCTAGGCACGTACGCGTTGTTAATGCCGATGTAGTCACCGGTCGACGTT\nATGTCCGAGGGACCGCCTTGGGAGCACTGGCACTGTTAAGCCAGGCATGTCGGCGTATGATCGACAACGT\nTAGATATACACGTAAACTTTTAATGGACCACACGGAAGATATATTTCAAGGCCTGGGGTATGTTAAATTG\nTTATTAGATGGAACATATATATAAAGTAGCGCCTATTAAAGAAAAAAAAAAAACAACGATTATTTTCTGT\nGTATTTTTATTTACACCCTACGACTTCTTGAAGCGTTTCCAGATTGTCCCGTGTGTGACAAGGTCTGTCC\nCTTACCCCCCTGGGGGGTATTTTGGGTTGGGGGCGGGGTAGACTGTGGCACGCCTTGGGCCGCGGGCGGT\nGATCCGGTTGTTGGCTGGACAGTGCTTGACTGTGCTCCCTGTTGCGGTTGTTGTCCAGAAGACCCCGACA\nCCACGTGTTGCTGTTGTCCAACGGATGCCGACGTCGTTTGAGGTGGGGGGTGTTGCGGGGATGATCCCGA\nAAACGCCAACGCGGCGGGCTGTTGTAAAGCAGACTGATCGGCGCTCTGTGTTTTTTGCGGCAATATAGTA\nGGCCCCGAGATTCCCAAACTCATGGATGGATTTGGGGGTTGTGGTCGTATAATACGCGGGTTAAACGTAC\nGTTTTAAGCCAACCGTTGGTCTTAACCATGTCATAGGGTCAGTCTCGGCAAACATGGCCGTTCGGCGTAT\nCGTATTTGCATTATGGTTAGCGCGTGCACGCGCGGCACTGGCCGCGGCTCCCACGGTGTAAATGCTTCTG\nGCATCAGCGATGTCCACACGGTGACCAGGTTGCAAAGGTCCACTGGCGTTTAAAAGTCGTATTAAAGCAA\nCGGGGGTGTAAGCCGCAATTGCTTCCACCGAAAATGTGGTGGGGTTGCTGGGATCAAAGACTACACGAGA\nCGATGCGGGTTGTGTCATCGTTTATTAGTTTACGGGACAATCGATAACAGCATACACGTACATCTGCGCA\nGGATATGTACGGAAAGGCAATTTATTTCCAGAAAAGCACCGCCCCTAATACAACTACCAGTACAATTACA\nATGAACAGGGCATATGTCACGTTAGCTACGGGTAGAGCAAGTTTCCAGACACGCGTAGTTTGGGTATCGG\nGTAACGCAGGTTTAATGTCACTTTGCATTTGAACAGACGTGTTTGGACTTCCGTTCTCGGGTGGGGATCT\nGAATGAAGGCCGCCAGCGTATATATTCATCCAAATTATTGCCAGTTTCCTTATACATGTATGCATCCGTG\nGCGCGGGCCATAAGTTTAATGGTGCGAGATGGATCTTCCGGTCCCATAAAACGAAAGGATAACTGAACAT\nATGGCATTCGCACAAAGCAGTTCACCCACATTAAAGCCTGGAGAGGTCGGCGGTCAATACCCCCACCTCG\nTTTAATTGATTCCAAAGCAGATAGGTTGATACCGGTACTTAACGTTGAACTAAGAATCACGTTATTACTG\nTCAATGGACACTTCAGCCACTGGTGCGTTAGTCGGACGAAAAAAAAAACCTTGAAATAGCACAGACACCC\nCCGTATTTTGAATTTTTATGTAAGGGTCACAATCTACTTGCGCCCAATTCGCCATTAAACGCATAATATA\nCTCTACCGGAAAGGCTTCGGATACGTTGTCTTCGCCGTTAAACTGAAAAACACAACGGGCGGGGGGGCGT\nTGTGGATCAAATATTGGAAGATCCCCATCGCAACATTGAAGAGCGCTTGGTACCACCAACCGAATACGTT\nGTAAAAGATTATCTCCGCAACCCCTCCTGCGTTCACTCCGTACATACGTTCTCCGTGACATATTGATCTA\nAGGTTGCAAACCAAGGCACACGCGTGAAGTATTTAGACCATTTATCGTGGGATATAGGAGGAGTTTGGAG\nTGATCCACCCCCTGACGACTTATTAATGCGTTTATTTTCCCCATGTATTAAGCATCCTTCAATATTTCAT\nGCAAATCTAGAAATTTGGCCATGACTCCCGCAAAGCGTTCACGGCGACGGGTCACGCTGGCACTATGTTC\nACATGGAACAACATAAGCAGATTTTTCTGAATCGTTACTTTCTTTATGTTTTAAAACGGACGCCAGGCGA\nCTGGTAAATGATATATAATTTAATTGAGCGTCAGTTGTAGGTAGAATTGCTTCTATTTCCGGGGGAATTA\nAATTTTCAAACCAAACGGAAAGAGTAAAGGTGCTATCAGCAGGAAAATACTTTGACTCCAGTGCATCGAT\nATTTAATAGATTAACATCGGTGTCTGTAATTAAATCGCGGGCCCTCATCCCAGAGATGGATCGGGTAGAA\nTCAGAAGAACCCATGGATGGATTCGAATCGCCCGTATTCTCCGAAAATACATCTTCTAATTCCGGATGGT\nGTTCCGACGCATTTTCCGATTCGTACATCGCTTATAATCCAGCCCTTCTGCTAAAAAACGATTTGTTATT\nTTCAGAATTGTTATTTGCCTCCCACTTAATAAATGTTCCCCGTGCAATAGAAAACAACGTCACTTATGAG\nGCCTCTTCGGCGGTAGGTGTGGATAATGAAATGACCTCAAGTACCACTGAATTTATAGAAGAAATTGGAG\nACGTTTTGGCGTTAGACAGAGCCTGTTTGGTCTGCAGAACGCTTGATTTGTATAAACGTAAATTTGGACT\nGACACCGGAATGGGTTGCGGACTACGCCATGTTATGTATGAAAAGTCTGGCATCCCCGCCCTGTGCAGTT\nGTCACTTTTAGCGCTGCCTTTGAATTTGTGTATCTTATGGATCGTTACTACCTGTGCCGTTATAACGTTA\nCTTTGGTTGGGTCCTTTGCCAGGCGCACGCTTTCCCTGTTAGATATACAAAGACATTTTTTTTTGCATGT\nATGTTTTCGTACCGATGGAGGGTTACCAGGTATACGACCGCCCCCCGGTAAGGAAATGGCCAACAAAGTA\nAGATATTCCAATTACTCCTTTTTTGTACAGGCGGTAGTTAGGGCTGCATTACTATCGATCAGCACGTCTC\nGTTTAGACGAAACCGAAACGCGTAAGTCATTTTACTTTAATCAGGACGGACTGACTGGAGGCCCTCAACC\nTTTAGCGGCCGCCTTGGCTAATTGGAAAGATTGCGCGCGGATGGTTGACTGTTCATCATCGGAACATCGC\nACAAGTGGGATGATTACCTGCGCGGAACGTGCATTAAAAGAGGATATAGAGTTTGAAGATATATTAATAG\nACAAACTTAAAAAATCGTCTTACGTAGAAGCAGCTTGGGGTTACGCAGACTTGGCTTTATTATTACTGAG\nTGGGGTTGCTACTTGGAATGTAGACGAGCGTACAAATTGTGCTATAGAAACTCGCGTTGGATGTGTTAAA\nTCATACTGGCAGGCGAACCGGATTGAAAACTCCAGGGACGTTCCAAAACAATTTTCCAAATTTACGAGCG\nAGGATGCCTGTCCCGAAGTAGCATTTGGGCCTATTTTGTTAACTACCTTAAAAAACGCAAAGTGCCGTGG\nTCGCACGAATACCGAATGCATGTTATGTTGTTTATTAACCATAGGGCACTATTGGATCGCTTTGCGGCAG\nTTTAAAAGGGATATATTAGCATACTCAGCAAATAACACAAGTTTATTTGACTGTATCGAACCTGTAATCA\nATGCATGGAGCCTAGATAACCCCATTAAACTTAAATTTCCATTTAATGATGAGGGTCGATTCATAACCAT\nTGTAAAAGCAGCAGGTTCCGAGGCCGTATATAAACATTTATTTTGCGATCTCCTATGCGCTCTCTCGGAA\nTTACAGACAAACCCTAAAATTTTATTTGCCCATCCTACAACCGCGGATAAGGAAGTGTTGGAGTTATATA\nAAGCCCAACTGGCTGCACAAAACAGATTTGAAGGTCGTGTATGTGCTGGCCTGTGGACATTGGCGTATGC\nATTTAAAGCCTACCAGATTTTTCCACGCAAACCAACCGCCAATGCCGCATTCATACGAGATGGAGGACTT\nATGCTTCGACGACATGCAATATCGCTGGTCTCCCTCGAACACACCCTATCGAAGTATGTCTAGGCGATAT\nAAATCCGTATCTCGGAGCGGGCCTTCGATGCGTGTACGCTCCAGAACGCCATGCCGCCGTCAAACCATTC\nGAGGAAAACTTATGTCAAAGGAGCGGTCTGTGTACCGCCATTATTTTAATTACATCGCAAGGTCCCCCCC\nAGAAGAACTAGCTACCGTTAGAGGCTTAATCGTGCCAATTATTAAGACGACCCCTGTCACCCTTCCGTTT\nAACTTGGGTCAGACAGTGGCGGATAACTGCCTGTCGTTATCCGGAATGGGTTATCATTTAGGTCTCGGAG\nGTTATTGTCCGACATGCACTGCATCTGGAGAACCGCGTCTATGTCGAACCGATCGGGCGGCTCTGATACT\nAGCATATGTTCAGCAGCTTAACAACATATACGAATATCGTGTGTTTCTTGCATCCATTTTGGCGCTATCA\nGACCGAGCCAACATGCAAGCAGCGTCCGCTGAACCCCTATTGTCGAGCGTATTGGCACAACCGGAATTAT\nTTTTTATGTATCATATTATGAGGGAGGGGGGCATGCGAGATATACGCGTACTTTTTTATCGTGATGGAGA\nTGCCGGAGGGTTTATGATGTATGTTATATTTCCGGGGAAATCTGTTCACCTCCATTACAGACTAATCGAT\nCATATACAGGCCGCGTGTCGGGGGTATAAAATAGTCGCACACGTTTGGCAGACAACATTTTTACTGTCGG\nTATGTCGCAACCCAGAACAACAAACAGAGACTGTGGTGCCATCCATTGGAACATCGGACGTTTACTGTAA\nAATGTGTGACCTTAACTTTGATGGAGAATTGCTTTTGGAATACAAAAGACTCTACGCATTATTTGATGAC\nTTTGTTCCTCCTCGGTGATTTCAGCTTCAGTGTTCATTTTATTATCCCAGCACGGGGCGTGTATACAAAC\nAAAGCCTGCCGCCTGCAAGCGGTTTAGCATTTTAACGTTAACAACTCGTGTCTCTGGAATAAAACGTTTT\nAAAAGCCGTTCTGTGAGTTTAGTGTCGTTTCCAAATAACGCCTTAAAAGTTACACTCGCCGTCCCAATGA\nGATGAGAAAAATAATAGTCAATGTTTAAAGACAGCCCGTGTGATGTTACGTGAATGGGATCTTCCGCTAA\nGTCAGATATTATTAACTTACGCTTTGCTTCCCCACACCGTTTACCTGCGGTATTCTGTAAAGGATCTCCA\nCGTAGCAAAGCTACACTTTTTGCATCAGCCTCCACTTCGTCTGTGGGGGCCACAATAACATAAGGGATGC\nGTTCTCGAACGTTTGGGATTTGACCCTGTCTCATTACTAATTTATAATATACTGTTAAGTGAGCCAAGCG\nACGGTTTATGTAGGCGGATGGTGGACGACTAAGCTCGGCCGTCATAACAAACTTATTAATATCCAATTTG\nGGTGATGTAATCTGGCGATGTGCATCTGCAATTATGCGTCCAAACCCGGCCATCCCAGACGGCATGGCCC\nGTCTATTCCATTCAGCAATGGAAACACACGACGCCTCCGCCGCAGCACGCGAGACGGTGTCGTCATATAA\nCAACAGTTCTACAAGTTTGCGGGCATAATCGTTAATAAATTGACAGTTGTTTTTTCTAACCAAGTCGACT\nCCCTTCATTAAAACCTTTCCGCCGTAAATTACCCCAATGTACTTTTTCTTTGTTATAAGCAAAAGTTTTA\nTAAAAGTTTTTTCACACTCCAACTTTATAGGAGGACAAAACAGAGCCGTTGAAATTATATGTGCCATTTT\nCTCGCCGATTTTAGCTATCCCCTCAACACTAACACCCTTGAATCGGATAAACACAGAATCCGTATCTCCA\nTATATAACCTTTACCTCGTACGCTTTTTGGGAGAGAACGCTACTTTCAATGTCTGGAAACGCTGTAATAA\nAACGTTCAAATGCGGCCCAGTTATTATGAATATAATCTCTGGTACTTAATAACATTTGACGGCCAATTGT\nAGTGACAGTGGCCGCTACGTATAAACATGGCAGAAATCCCTGCGCAACTCCAGTAAAACCGTACACGGAA\nTTACAAACTACTTTTATCGCGGCTTGTTGTTTGTCTAATAACACTGCTTCATCTGAAGAACTTCCGGGTA\nTGCGCGCTCTAATAGCCTTGCGCATAGCCAACCAGTCTTTTAAAAGAACACCCAGCAGACTTTCTCGAAC\nGTTAGAGCGCACAAAAAAAAGACGTTTTCCTCCAACTGTAAAGGTGGCATAATCGGATGGATTCAAACGT\nTTAACCGTCTCAAAATTTAACGTTAGCGTGGTAAAACATAAGTTATGGGCCTGAATTATACTTGGATATA\nAACTTGCAAAATCCAATACGACCACCGGATCGATATAAAATCCCGTATCAGGGTCAAAAACCCTGGCTCC\nTTTATATCCTACATTTCGCCCACTTGACGTACCAGTGGGAGAAACGCTCTCGTCTTCATCCATCTCTTCC\nTCAACATCCCCGACATCGGGAATAACATCCTTATATTCAAAAGTAGCTGGGTATCCCCCATCGGGTAAAA\nTAAATCCTCGAGACGAAGCCAGTCCTAATAAACAGGTGTAAATCCTAACCTGCTGTCCGTCGTAAATAGC\nCTTGGTTAAAGTAATTCTAGCTAGCCTTGCAACCGCGGATAACTCAAGGTGTGGTAAATATTTAAAAAAC\nAGTTTCCCCACAAGAGCCGAGTCTTGTATACAATATTCACCAATAATTCCTCGTGTATTCGGTCCACTAG\nCGTAATATCCCGGAATGTCTTTGTAGGGCAAATCTCTCTTGGACTCATTTAGAGCTTCACGTGCAACCGA\nATCTAATTTATAACTCGAGAGTTTTAATTTTTCAGTTGCAATTGCATACATATCCAGAGATATGAGACCG\nTTGATCTTTACCTTGCTTCGTCGCTGAAATCCGGATTTGCCAACATCCCATATCTTAAACAGACCCCCAC\nGGTTTATACTGCCATAACCATCAAGCTTGAGACTGTATATAGAATTAAGTTTCTCCATAATAAACGCCCA\nATCAAAATTAACAATGTTATAACCTGTGGCAAACTCGGGAGCGTACTGTTTTACGAGGGTCATAAATGCA\nATTAATAGCTCGAATTCACTATCAAACTCCAGCACAGTCGGCTCCGGTAACCCCGCGTCCTTCATTTCTT\nGTACATACCTTTGTGGTAAGTCACAAGAGCCAAGGGAAAACAGTAAAATGTGTTCTAAAGACTGTCGAGG\nGATTGAATATAATAGACAAGAAATTTGGATTACAAGATCCTCCAGATGTGTTGCATCGGGAAACGCCAGC\nTCATTAGATCCTCCTGATTTACATTCAATATCGAAACATAACAACTTGTAGTCAGGCCATGAGTCATCGT\nTTGGTATAGCCTGCAGATTATCCGACATGCAGTCAATTTCAACGTCGCTTAACGTTAATTGGCGACTTGC\nCGGTCGAACTCGAACACGTTCCCCATCAACTCCAGGTTTTAGTTGATACCAACCAAAACTAACAAAGCCG\nGGATTATCCATTAGAAAACGAGTGGTAGCGTCTACCCGACCTTCATACTTTTTCAACTCCGGGTGAAAGT\nTATCACAAAGATAATTTGTAAATTTAGATGAGGGAGAATACACCCTGTAAAACGCACATGGCTGTGTATC\nGTAGTAATAAACATCTGTGCGCTCAATAACCTCAACGCGAAAGCTTTCTGGAGATGCGCTTTTAAACGAG\nGTACCATGAAAAGCGTTCTTGTCTCCATTTAACGTTGCATCATTTTGTGTTATCATAGAACTGCGTAAAC\nACTCGGCAAGTAATACAGATAACTCGCTACCGGAACGTATGCCACAAGCGGTATCCACCTCGGCTTTGTT\nTATATAAAAATATTGACAGATGCCGTATACATGAACTGCCACCCTTTTTCCACATCGGGACATGCCAAGT\nAAAGTAATAACGGTACCAAGCGGTCGTGTTGCAGTTGCAAACCGGGATACATCTCCATTAGACGCGGCTT\nCTGTTGTTTCGACAATATCATATACATGGAATGTGTTAAAGCGGGGGTCAAACTTATCCCCACGAAAGTC\nGATTTCCCCCCAAATATTCACGCGTCTAGGCCAGGGGCTGGAACAACGAAAATCCAGAATCGGAACTTCT\nTTTCCATTACAGTAAACTTTAGGCGGTCGACTAAGTGTACCGACGTGAACCCCCTTTCGTTCTTCCATGG\nGCACATCTTCATCTAAACATTTAGGGGCCAAAAATTGAAACGATGACATGGTAGTTTTGTAACTATGAAG\nAAATTCTCTGTTACTACCGCGCCCGGTTCTTGGGTTATATTTAATCCCTGATGCTTGGGTTAAAAAGGGA\nTTACAAAACCCCGTTCTGATCGCCATTTTATGTTAACGATTGATAATCTTGTAAAAAGCCAGTGTTACTG\nAGTAACACAACCCCACGCCCTTCTAATACATAAAGTGTAATCACGTGATTTGTTGTGGTTTCCGCATATG\nTAATACCCGTTTAAAAGCCTCTCTTCTTAATGTATCGACAGACTGGGTTTTGGGTGGTCATTTGACCCTG\nCCAACAACCCCCCATTATTACGAGTACTTCACCAAAATGGAAAATACTCAGAAGACTGTGACAGTGCCCA\nCGGGGCCCCTGGGTTACGTTTATGCGTGCCGGGTTGAAGATTTGGATCTGGAGGAAATTTCATTTTTGGC\nCGCTCGTAGCACGGACTCTGATTTGGCTTTATTACCTTTGATGCGTAATTTGACCGTGGAAAAAACTTTT\nACATCCAGCCTGGCGGTGGTTTCTGGAGCACGCACTACGGGTCTTGCCGGAGCTGGTATTACCTTAAAAC\nTCACTACCAGTCATTTCTATCCATCTGTCTTTGTCTTTCACGGAGGCAAACACGTTTTACCCAGCTCCGC\nGGCCCCAAATCTCACACGCGCGTGTAACGCGGCTCGAGAACGGTTTGGGTTTTCACGCTGCCAAGGGCCT\nCCTGTTGACGGTGCTGTTGAGACGACCGGCGCTGAGATATGCACCCGCCTTGGATTAGAGCCAGAAAATA\nCAATATTATACTTGGTGGTCACGGCATTGTTTAAGGAAGCCGTATTTATGTGCAACGTGTTTCTGCATTA\nTGGAGGACTCGATATTGTTCATATTAACCATGGGGATGTTATACGTATACCGTTATTTCCGGTACAACTT\nTTCATGCCCGATGTTAACCGTCTGGTACCCGACCCATTCAACACTCATCACAGGTCTATCGGAGAGGGTT\nTTGTATACCCAACACCCTTTTATAACACCGGGTTGTGCCATTTAATACATGACTGTGTTATTGCTCCCAT\nGGCCGTTGCCTTGCGCGTCAGAAATGTAACTGCCGTCGCCCGAGGAGCGGCCCACCTTGCTTTTGATGAA\nAATCACGAGGGGGCAGTACTCCCCCCTGACATTACGTACACGTATTTTCAGTCCTCTTCAAGTGGAACCA\nCTACCGCCCGTGGAGCGCGTCGAAACGATGTCAACTCCACGTCTAAGCCTAGCCCATCGGGGGGGTTTGA\nAAGACGGTTGGCGTCTATTATGGCCGCTGACACAGCCTTGCACGCAGAAGTTATATTCAACACTGGAATT\nTACGAAGAAACTCCAACAGATATCAAAGAATGGCCAATGTTTATAGGCATGGAGGGCACTTTGCCAAGGC\nTAAACGCTCTGGGGTCATATACCGCTCGTGTGGCCGGGGTCATTGGTGCGATGGTTTTCAGCCCAAATTC\nTGCGTTGTATCTAACTGAGGTGGAGGATAGCGGGATGACCGAAGCCAAGGATGGGGGACCGGGTCCATCA\nTTTAATCGATTTTACCAGTTTGCCGGACCTCATTTAGCTGCGAATCCCCAAACAGATCGAGATGGCCACG\nTTCTATCCAGTCAGTCTACGGGTTCATCAAACACAGAGTTTAGCGTGGATTATTTGGCACTCATTTGTGG\nATTTGGAGCACCCCTGTTGGCGCGACTGCTTTTTTATCTAGAACGCTGTGACGCTGGTGCGTTTACAGGG\nGGTCACGGGGATGCGTTAAAATATGTTACGGGGACCTTTGACTCTGAAATTCCATGTAGTTTATGTGAAA\nAACACACGCGGCCGGTATGCGCTCACACAACAGTACACCGACTTAGACAACGCATGCCGCGATTTGGACA\nAGCCACCCGTCAACCTATTGGGGTGTTTGGAACAATGAACAGCCAATATAGCGACTGCGATCCTCTAGGA\nAACTATGCTCCATATTTAATCCTTCGAAAACCCGGGGATCAAACGGAAGCAGCAAAGGCAACCATGCAGG\nACACTTATAGGGCTACACTAGAACGCTTGTTTATCGATCTAGAACAAGAGCGACTACTGGATCGCGGTGC\nCCCATGTTCTTCCGAGGGACTATCGTCTGTCATTGTGGATCATCCAACGTTTCGTCGCATATTAGACACA\nCTGCGTGCGCGTATAGAACAGACAACAACACAATTTATGAAAGTGTTGGTTGAGACCCGCGATTATAAGA\nTCCGTGAAGGATTATCCGAAGCCACCCATTCAATGGCGTTAACGTTTGATCCATACTCAGGAGCATTTTG\nTCCCATTACCAATTTTTTAGTTAAACGAACACACCTAGCCGTGGTACAAGACTTAGCATTAAGCCAATGT\nCATTGTGTATTTTACGGACAGCAAGTTGAGGGGCGGAACTTTCGTAACCAATTCCAACCTGTTTTGCGGC\nGGCGTTTTGTTGACCTGTTTAATGGGGGGTTTATATCAACACGCTCTATAACCGTAACATTATCTGAAGG\nTCCTGTATCCGCCCCAAATCCGACATTGGGACAAGACGCGCCCGCGGGGCGTACCTTTGATGGGGATTTA\nGCGCGCGTAAGCGTGGAAGTTATTCGGGATATACGAGTTAAAAATAGGGTCGTTTTTTCAGGTAACTGTA\nCAAATCTCTCTGAGGCAGCCCGGGCAAGGCTTGTAGGCCTTGCAAGTGCGTACCAACGCCAAGAAAAAAG\nAGTGGATATGTTACACGGGGCCCTAGGGTTTTTGCTTAAACAGTTTCACGGCCTGTTATTTCCTCGGGGT\nATGCCACCAAACAGTAAATCCCCCAACCCGCAGTGGTTTTGGACCCTGTTACAACGCAACCAGATGCCGG\nCAGATAAACTTACACACGAAGAGATTACCACTATTGCAGCTGTTAAACGGTTTACCGAGGAATATGCAGC\nAATAAACTTTATTAATCTACCCCCAACCTGCATAGGAGAATTAGCCCAGTTTTATATGGCAAATCTTATT\nCTTAAATACTGCGATCATTCACAGTACCTTATAAATACCTTAACTTCTATAATTACGGGTGCCAGGCGCC\nCGCGTGACCCATCATCCGTTTTGCATTGGATTCGTAAAGATGTCACGTCCGCCGCGGACATAGAAACCCA\nAGCAAAGGCGCTTCTTGAAAAAACGGAAAACTTACCGGAATTATGGACTACGGCTTTTACTTCAACTCAT\nTTAGTCCGCGCGGCCATGAATCAACGTCCCATGGTCGTTTTAGGAATAAGCATTAGTAAATATCACGGAG\nCGGCAGGAAACAACCGCGTCTTTCAGGCAGGGAATTGGAGCGGTTTAAACGGGGGTAAAAATGTATGCCC\nGCTATTTACATTTGATCGCACTCGCCGTTTTATAATAGCATGTCCTAGAGGAGGTTTTATCTGCCCCGTA\nACAGGTCCCTCGTCGGGAAATCGAGAAACCACCCTATCCGACCAAGTTCGCGGTATAATTGTCAGTGGCG\nGGGCCATGGTTCAATTAGCCATATACGCCACGGTTGTGCGTGCAGTGGGCGCTCGAGCACAACATATGGC\nATTTGACGACTGGTTAAGTCTTACAGACGATGAGTTTTTAGCCAGAGACTTGGAGGAGTTACACGACCAG\nATTATCCAAACCCTGGAAACGCCCTGGACCGTAGAAGGCGCTCTAGAAGCAGTAAAGATTCTAGATGAAA\nAAACGACAGCGGGAGATGGGGAAACCCCCACAAACCTAGCATTTAATTTTGATTCTTGTGAACCAAGCCA\nTGACACCACATCTAACGTATTAAACATTTCAGGGTCAAACATTTCAGGGTCAACTGTCCCTGGTCTTAAA\nCGACCCCCCGAAGATGACGAACTCTTTGATCTTAGTGGTATTCCCATAAAACATGGGAACATTACAATGG\nAAATGATTTAACCTCCCTCTTTATCCAATTAAAGCCCACACGCGGGTGAGTGTACGTAATAAACAAGTCA\nATATTACATATTCTGTTGTGTTTTCTTTTTTTGTGTGTAGTCCTTACCCATATGACCTGTAATATAGTGT\nGTCTCCAACCATTCAGCTTACAGTCCAGTGGACAGTAACAGCCCGATAACATGGAATTGGATATTAATCG\nAACATTGTTGGTTCTACTGGGTCAAGTTTATACGTACATCTTTCAGGTTGAACTGCTACGTCGATGTGAT\nCCAAGGGTGGCGTGTCGCTTTTTATATCGGTTAGCGGCTAACTGTTTGACAGTTCGTTATTTATTAAAGC\nTGTTTCTCCGGGGATTTAATACCCAGCTAAAATTTGGAAACACTCCCACGGTTTGTGCACTGCATTGGGC\nATTATGTTATGTAAAGGGAGAAGGTGAGCGTTTGTTTGAGTTGCTACAACATTTTAAAACGCGTTTTGTT\nTATGGTGAGACTAAAGACTCAAACTGTATCAAAGATTACTTTGTCTCAGCGTTTAACTTAAAAACCTGCC\nAATATCACCATGAGCTGTCGTTAACAACATACGGAGGTTACGTATCGAGTGAAATTCAGTTTTTACACGA\nCATTGAGAATTTTTTAAAACAGCTTAATTACTGCTATATTATCACGTCTTCTCGTGAGGCGCTAAACACA\nTTGGAAACCGTGACGCGGTTTATGACAGATACTATAGGAAGCGGTCTAATACCACCCGTGGAGTTGTTTG\nATCCGGCGCATCCATGTGCTATATGTTTTGAAGAATTATGTATAACAGCTAACCAAGGTGAGACCTTACA\nTCGTAGATTATTAGGATGTATCTGCGATCACGTTACTAAGCAAGTTCGGGTTAACGTGGATGTTGACGAT\nATTATTCGGTGTTTACCATATATCCCTGATGTACCGGATATCAAACGTCAATCCGCCGTTGAAGCGTTAC\nGAACACTTCAAACCAAGACGGTAGTCAATCCCATGGGAGCAAAGAACGATACGTTTGACCAAACATACGA\nAATTGCGAGCACCATGCTTGATTCTTATAATGTTTTTAAACCTGCCCCTCGGTGTATGTACGCCATCAGC\nGAGCTTAAATTCTGGTTAACGTCTAATTCCACTGAAGGACCCCAACGTACTTTAGACGTGTTTGTTGATA\nATTTGGATGTATTAAACGAACATGAAAAACACGCAGAACTTACAGCCGTAACGGTTGAGTTGGCGTTATT\nTGGAAAAACTCCCATACACTTTGATAGGGCGTTTTCTGAAGAACTCGGATCTCTGGATGCAATTGATAGT\nATTTTGGTTGGCAATCGCTCATCCTCACCAGACAGTCAGATAGAAGCATTAATTAAAGCCTGTTATGCCC\nATCATCTATCGTCGCCTCTCATGCGTCACATTTCTAACCCGAGTCATGATAACGAAGCCGCCTTACGCCA\nACTTTTAGAAAGAGTTGGGTGTGAGGATGATTTAACCAAAGAGGCGAGTGACAGCGCTACAGCATCCGAA\nTGTGATCTGAACGATGATAGTAGCATAACTTTTGCTGTTCATGGATGGGAAAACCTGTTATCCAAAGCAA\nAAATTGACGCTGCGGAAAGAAAACGAGTATATCTTGAACATCTGTCTAAGCGCTCTCTAACCAGCCTCGG\nTAGATGTATCCGCGAACAGCGCCAAGAGCTAGAAAAAACACTCAGGGTAAACGTTTATGGAGAGGCCTTA\nTTGCAGACATTTGTTTCGATGCAAAATGGGTTTGGGGCACGAAACGTGTTTTTAGCTAAGGTTTCCCAGG\nCAGGGTGTATTATCGACAATCGCATTCAGGAAGCGGCCTTTGATGCACATAGATTTATAAGGAATACCTT\nAGTTCGACATACAGTAGATGCGGCTATGTTACCTGCACTTACACATAAATTTTTTGAGTTGGTCAACGGC\nCCATTGTTTAATCACGATGAACACCGTTTTGCACAACCCCCTAACACCGCCTTATTTTTTACCGTGGAAA\nACGTTGGCCTATTTCCGCACTTAAAAGAGGAATTGGCAAAGTTTATGGGCGGTGTCGTTGGTTCCAACTG\nGCTTCTCAGTCCATTTAGGGGCTTTTATTGCTTTTCTGGGGTAGAAGGCGTTACTTTTGCACAGAGACTT\nGCCTGGAAATATATTAGGGAGCTTGTGTTTGCAACCACACTATTCACCTCTGTTTTCCATTGTGGGGAGG\nTGCGGTTATGTCGCGTTGACCGTCTAGGTAAGGATCCACGCGGGTGCACGTCTCAACCTAAAGGTATAGG\nCAGTTCCCACGGACCCTTAGACGGCATTTATTTAACGTACGAAGAAACATGTCCCCTTGTGGCTATTATT\nCAAAGTGGAGAAACAGGGATCGACCAGAATACCGTCGTAATCTACGATTCAGACGTTTTTTCTCTTCTAT\nACACCCTAATGCAGCGGCTGGCTCCGGATTCAACGGACCCGGCGTTTTCATAACCTCCGTTACGGGGGTG\nTGGTTATGCTTTTTATGCATATTTTCTATGTTTGTTACGGCGGTTGTGTCGGTCTCTCCAAGCTCGTTTT\nATGAGAGTTTACAAGTAGAGCCCACACAATCAGAAGATATAACCCGGTCTGCTCATCTGGGCGATGGTGA\nTGAAATCAGAGAAGCTATACACAAGTCCCAGGACGCCGAAACAAAACCCACGTTTTACGTCTGCCCACCG\nCCAACAGGCTCCACAATCGTACGATTAGAACCAACTCGGACATGTCCGGATTATCACCTTGGTAAAAACT\nTTACAGAGGGTATTGCTGTTGTTTATAAAGAAAACATTGCAGCGTACAAGTTTAAGGCGACGGTATATTA\nCAAAGATGTTATCGTTAGCACGGCGTGGGCCGGAAGTTCTTATACGCAAATTACTAATAGATATGCGGAT\nAGGGTACCAATTCCCGTTTCAGAGATCACGGACACCATTGATAAGTTTGGCAAGTGTTCTTCTAAAGCAA\nCGTACGTACGAAATAACCACAAAGTTGAAGCCTTTAATGAGGATAAAAATCCACAGGATATGCCTCTAAT\nCGCATCAAAATATAATTCTGTGGGATCCAAAGCATGGCATACTACCAATGACACGTACATGGTTGCCGGA\nACCCCCGGAACATATAGGACGGGCACGTCGGTGAATTGCATCATTGAGGAAGTTGAAGCCAGATCAATAT\nTCCCTTATGATAGTTTTGGACTTTCCACGGGAGATATAATATACATGTCCCCGTTTTTTGGCCTACGGGA\nTGGTGCATACAGAGAACATTCCAATTATGCAATGGATCGTTTTCACCAGTTTGAGGGTTATAGACAAAGG\nGATCTTGACACTAGAGCATTACTGGAACCTGCAGCGCGGAACTTTTTAGTCACGCCTCATTTAACGGTTG\nGTTGGAACTGGAAGCCAAAACGAACGGAAGTTTGTTCGCTTGTCAAGTGGCGTGAGGTTGAAGACGTAGT\nTCGCGATGAGTATGCACACAATTTTCGCTTTACAATGAAAACACTTTCTACCACGTTTATAAGTGAAACA\nAACGAGTTTAATCTTAACCAAATCCATCTCAGTCAATGTGTAAAGGAGGAAGCCCGGGCTATTATTAACC\nGGATCTATACAACCAGATACAACTCATCTCATGTTAGAACCGGGGATATCCAGACCTACCTTGCCAGAGG\nGGGGTTTGTTGTGGTGTTTCAACCCCTGCTGAGCAATTCCCTCGCCCGTCTCTATCTCCAAGAATTGGTC\nCGTGAAAACACTAATCATTCACCACAAAAACACCCGACTCGAAATACCAGATCCCGACGAAGCGTGCCAG\nTTGAGTTGCGTGCCAATAGAACAATAACAACCACCTCATCGGTGGAATTTGCTATGCTCCAGTTTACATA\nTGACCACATTCAAGAGCATGTTAATGAAATGTTGGCACGTATCTCCTCGTCGTGGTGCCAGCTACAAAAT\nCGCGAACGCGCCCTTTGGAGCGGACTATTTCCAATTAACCCAAGTGCTTTAGCGAGCACCATTTTGGATC\nAACGTGTTAAAGCTCGTATTCTCGGCGACGTTATCTCCGTTTCTAATTGTCCAGAACTGGGATCAGATAC\nACGCATTATACTTCAAAACTCTATGAGGGTATCTGGTAGTACTACGCGTTGTTATAGCCGTCCTTTAATT\nTCAATAGTTAGTTTAAATGGGTCCGGGACGGTGGAGGGCCAGCTTGGAACAGATAACGAGTTAATTATGT\nCCAGAGATCTGTTAGAACCATGCGTGGCTAATCACAAGCGATATTTTCTATTTGGGCATCACTACGTATA\nTTATGAGGATTATCGTTACGTCCGTGAAATCGCAGTCCATGATGTGGGAATGATTAGCACTTACGTAGAT\nTTAAACTTAACACTTCTTAAAGATAGAGAGTTTATGCCGCTGCAAGTATATACAAGAGACGAGCTGCGGG\nATACAGGATTACTAGACTACAGTGAAATTCAACGCCGAAATCAAATGCATTCGCTGCGTTTTTATGACAT\nAGACAAGGTTGTGCAATATGATAGCGGAACGGCCATTATGCAGGGCATGGCTCAGTTTTTCCAGGGACTT\nGGGACCGCGGGCCAGGCCGTTGGACATGTGGTTCTTGGGGCCACGGGAGCGCTGCTTTCCACCGTACACG\nGATTTACCACGTTTTTATCTAACCCATTTGGGGCATTGGCCGTGGGATTATTGGTTTTGGCGGGACTGGT\nAGCGGCCTTTTTTGCGTACCGGTACGTGCTTAAACTTAAAACAAGCCCGATGAAGGCATTATATCCACTC\nACAACCAAGGGGTTAAAACAGTTACCGGAAGGAATGGATCCCTTTGCCGAGAAACCCAACGCTACTGATA\nCCCCAATAGAAGAAATTGGCGACTCACAAAACACTGAACCGTCGGTAAATAGCGGGTTTGATCCCGATAA\nATTTCGAGAAGCCCAGGAAATGATTAAATATATGACGTTAGTATCTGCGGCTGAGCGCCAAGAATCTAAA\nGCCCGCAAAAAAAATAAGACTAGCGCCCTTTTAACTTCACGTCTTACCGGCCTTGCTTTACGAAATCGCC\nGAGGATACTCCCGTGTTCGCACCGAGAATGTAACGGGGGTGTAAATAGCCAGGGGGTTTGTTTTAATTTA\nTTAATAAAAATGTGTATTACGTTACTCATGTGTCTCCATTACGCATCACAGGGGGTATTTATACCCGATA\nATATACAAAACGCGTTTTGTACCTCTACCGCACCCGATATCTTAACGGGGTTATTATGGAATCGTCTAAC\nATTAACGCGCTACAACAACCGTCGTCTATCGCACATCATCCGTCCAAACAGTGCGCTTCAAGTCTCAATG\nAAACAGTAAAAGATTCTCCCCCCGCGATTTATGAAGATAGGTTAGAACACACGCCGGTACAATTACCCCG\nCGACGGTACACCCCGAGACGTATGTTCTGTGGGACAGCTAACCTGTCGAGCATGTGCAACGAAACCTTTT\nCGCCTTAACCGCGACAGCCAATACGACTACTTAAACACATGTCCAGGGGGCCGTCATATTTCACTGGCAC\nTGGAGATTATAACGGGTCGATGGGTTTGCATCCCGCGTGTGTTTCCGGATACCCCAGAGGAAAAATGGAT\nGGCGCCATATATTATTCCAGACCGAGAACAACCATCATCAGGGGATGAAGATTCTGACACCGATTAAATT\nTAACTTAAATAAAACCTTACCACCCATAAAAACGCCTTCTGTTTGTTTAACACGACACCGCTTAACAAAA\nAAAAAAAAACCAAACACGCCTTTTATGAATGTAATACTTTTATTTGTTGGTTAACACCGCCCCACCATCA\nTCTGATTTGCAAACATATCGGCGTCGTCTGCCGTGGACCCCTGTATTAAAGGGGCCTTGGAACTCGCCTC\nCACTGCATTTACATCTTGTCCAACTGTATCTGTATGTGGGGTGCTTGTTGTATTTTGGGATGAGCATAGA\nCCCGAAACGCTTTGAAGCTGTTTTAATAAAATCGATATTCGAGGATCCCGTGTCCCCTCTGGTATATTTG\nTATGGTGCGACAAAGGCATTTGTGTCCCATTTTGTGATTTTAGCTCTGTAACCTCCTGTTGCAGTTTTGC\nCACAACCCCAGCAAGCTCTTCGTGCTGACCATTAGAAACTCTGTGTCTCCTCTGCCAATATGATGGAGAA\nACTCGACGTCTCCGATGCGTTATATACGTTGGTTCACCGGGAAAATATATATTTGAGGGAAACTCTCCGT\nCCATTTGAGACTCCCCACTATAAAAAGAATCCAATTCCCTTTGATCCATGCTCTTGAAATCCCGTTTTCC\nTGGACGACGGACATCGGTTTTGTCTGGAAAATTTACACACGGGGTCTGCAAGTCAATACCCCGTTCGGCG\nGCCAATGCGTTCATAAATGCGGACATTTGCATTTCCAAACGATTGGGTGGTGGATATCCCGGAAACCCGT\nACGGTCCCCCGAAGTGTCCCGGAGGGCAACCATAACCCCCTGTATTAGGTGGGAAGGCAGGCGGGTGTGG\nAGATCCATATGGCCCGACGATATACTGTCCGTTATTTGGAGCTCCAATTGATACCTGCGGATTTTTAGTC\nTGCCCGGTTAACAGCTGTGAATAATACGCGGTAGGTATCAGTACAAATTCCCCTCCGGTTGGAACGCCCG\nACGGGGGCTGTGGTGAGATATTACTAGCGTTACCTGCTACAGAAGCCATATCGCTGTCGTTCCTACACAA\nCTGCGTAACCTTTAAATGCGGAACAGTCTTTTCACAATCTTCATTTGATTCCCCAACACCCAACGCGAGA\nTCGTATATGGGCCCGCCGGGGTGGAATGTGGCGTTTATAACACCCGCGTTGGGTAATTTAGACTCCACCC\nCATTAACGTTGGTTATCCGAGCAAGTCCATATCCGGTGCTAGCCTGAAGATAAACGTGACCCATAATTCC\nGGCTTCGCGTCTACGTTTTGCAACCACGTCCCATCTATCTCTTAAAAGCATATTGTTCACGGCTGTGGAT\nAATAACACCTTGGCGAGTTTATCTTCGCTAACCTTCCATACTTTATTTAAACCCGCGTAGTCTTTAACCA\nGCGACAATAACCGCGCTTTACTTTCCATCGATAAAACCCGGAATGGTTCAATTGAAGATTCCGGGGTACA\nGTCATAATTGACCACTGTTCCAACGCGTCTTCCAACAACACATAACGCAACATGGGTAAAAAAATTACCG\nTCTGGTATCTCATTCGGGGACAATCGTTTTGAAGACAGGGATACGGAGGGTAAGTAATTTGTGACCAAGT\nATAACGCACGTTCTAGCGGAGATAATACAGAATCTCTATTTCCAAAAAAATTCGAATGGGCCGCTTCAAA\nCAGCACCGCATGTAGTTGAGGGCATCTAACGATACCCAAAAAAAAAGGTCCGCGTATGTCCTCAATGATT\nGCGATTACTTCACCCACGACACAGTCTTTTCGATGATCGATGTTTATTGGTATTTTACTAGTAGGCGGCA\nAAGCGGACCGCACAATCTCTGGGGTAATATTTAATTCCCCTTCGTCCTTTGAATATAAGGCTAAATACCC\nAGCCACGTATAACGCTTCACAGTTCTCTTCGTCAGCTTCAGCAGCCATTATAAACACCCCACGGACCGGA\nTAGTGAATACTCACGGTGTGGAGGCAAACTGAGGAATGACACCCAAACAGACAAAATATAGAAGATCATA\nGTCACTGTTAACGTTGAACTGCGCAAGGCGGCGACTTTCTTCCAATGCCGCCCTTACACGCGGTTGGTGC\nATTAACATTCCAAGTCCCCGTTCATATTGCAACATAACACTGTCATGTATTGATACCACGGCGGCTATGG\nGTAGGGATGTAACATTTTGTCGGCGGTGTTCTAATTCCAATGCAATTAAGCTTATGAGCCGATCTTGGTA\nCTGTCCAGAAGAAATATCTATTACGGTTCTTCCTAAACTTCCACGACTAAGCTGGGTATGCGCGTCTAAA\nCAAAGAGCAACTAATCCAGGAAACATTTCAGTCAGCTCTGTGGTCCGATTTAACGTATACAGTGGTGCTA\nTATATCGTTCACATAAAAATTGAAAGTTATTATTACCGCTTTTAAACTTCCCATCAAACCCCGTCGCTCC\nGCGCAAGATTACATTGTTGGTAGGGGTTCCTGTTGCTTCTGACACAATCAAACCCAGTTGAAAATTATTT\nTTTAGTTTATCTCCGTATACGTTCCCGTTCCATAATAAGCGCCTTAATAATAATAACGCCGTAATCGTGT\nCAATTGTTAACCTTAATAGAGTTTGGTCTTCCATAAGAAACACGTTTTGGGCCCGTTCTAAATACGCCGC\nGGCCGCCTGTTGAATCTTGTCCACATATGCGGTATGATTGCGATCAATAATGTCATTAACCCCAGGATTA\nAACTGTCCAGGTGCAGGCGGTAGGACCTGCAACCGTATAAGCGCATCCATAACAGAATGTGACGTTAAGG\nCGCCTTGATCATACCGCCCCCCACGAGCATGAAACTGGTCGCGTGGTAGACGATCATAGCAAAATTGATA\nACTGTTTTTATTTTCGTGTGTTGTCATATAATTCACAAATGTCTCAGTATATTCCGGTAGGTGCTCTATA\nAGGTTCCCGAAGGACGAAACTTGAGGTTCGTGGACACTATTAGATGTCCTATACATTAAATATAAACATA\nATACCGCACACTCGAACGCGGAGTACGCTCTATCTCCAACATACATTCTCCCGGCGGACTGTAGACATGT\nTACCGTTGTGTTCATAAACGTACGGGAAATGCGCCCGTCTTTACAATCAACTCCGCGTGCAGCTACGGGC\nCTATCTAACACAAGCCGTTCCTGCAGAGTACGATACCATGGCCCGAAAACAATCCCTGGAGAGTTATTGC\nCCCTTGCCCTTCCCAAGTACACCAGGGTGATAAAATCCACTTGAAAGTTTGTATCGTACTGCAACGGTGC\nATCATTTTTGGCAATCTGTACCTCGGGGTGTATAGACTCATTGCGTATTATTTCTGTACGTGTACATTCC\nTCAGATTGTGCATCTGCTTCTTCCGCCTCGGCAGCAGCCGTCTCCAGGGAATCCAAAACCTTGGCCATGC\nGCGTTAGTTGTTCTTCGAGGGGCTTTAAACGACGATCTATTTCCGTTGGTAACGTAATCGTTTCCCCGCG\nAAGGTTGTCTAATGCGGCAACGGCCGCCGCATTTTTTAACGTTAACGTATTTTTTTCCAAATCGGGATTC\nATACGCCCTCTTAACTCAAACGCGGGAGCCGTCCAGTAGTGTATGGGGAAGTTGGGGGCTATAAAGTTCT\nTAGTGGTAGACAAAAATATCCCACATTTATTCGGAAACGAGATAGATCCGAACCCATATCTCGCCGTCAT\nGGTGTCTGCAGCAAACAAAGTCAACTGGCGTGAATATAAACCGGTACTGCTTTAAAAGCTGTTTTCTTAC\nCCATGGGAAAACATCCCGGTTATACTTTGTAAAATTCCACCACAAGCACCTAAAGAAGGCCTTCTAAGGG\nGTAAATCCACCCCACAAGCTGCATTTTCTTCAAACTTTGTTAAAGCGGAACGATGGCATGATTTCGCACG\nCTTTTTCGCAAGAGAACATACGTGAATTTTCTTTTTGCATAGACGTCTTCGCTCTCTAACGGACCTTATC\nGGGGGGGTATATTCCGCTACATTCTCCAAATGCGACGCTAGCATAACAAGGTTTCCATGAATCACCTTTG\nGGGGTAACCGAGTTACCTGTAACAGGTTCAGACCCCGTTGAGATACAAACACAAGGAGGGGGGTCACCAT\nTATTTCATCAGATCCCGTGGGTGTGGTTTCCTTTATTAAAGCCATGGTATCCCTCAGCTGGCGCATACCC\nTCGCAAAACTGGTGATACTTAGTAGGGGTATGTATATTAGCGCTAAAACGGCAAGATTTTAATTCCACTA\nTAAAACAAACGGTCTTTCCGGCACCACTGGATTCCGTTTGTATAATACAAACACAATCGGGGCGTCGGCG\nTCCCAAATTTACTTCAAACGACATTGATATGCGTACAGCCCTTTGAACATCCACGTGGGATAACGGCGAC\nAGGAGTTTTGCCAGCCTCGGGTTGAACGCGTCCGCGAAACCTCGACGTACGTTATCAATATCCTTTTTGA\nGTACATCGTAAAAACGAGTGTGGCAACGTTGTCCCAAACGAAAACACTTGGCCCGAATTCGACTAGCGGA\nCATATTTGAAGTTCCGTCCCAGAAGATAACCTAAGACGCGTTTGTCTACAATAAACATGTCAACGGATAA\nAACCGATGTAAAAATGGGCGTTTTGCGTATTTATTTGGACGGGGCGTATGGAATTGGAAAAACAACCGCC\nGCCGAAGAATTTTTACACCACTTTGCAATAACACCAAACCGGATCTTACTCATTGGGGAGCCCCTGTCGT\nATTGGCGTAACCTTGCAGGGGAGGACGCCATTTGCGGAATTTACGGAACACAAACTCGCCGTCTTAATGG\nAGACGTTTCGCCTGAAGACGCACAACGCCTCACGGCTCATTTTCAGAGCCTGTTCTGTTCTCCGCATGCA\nATTATGCATGCGAAAATCTCGGCATTGATGGACACAAGTACATCGGATCTCGTACAAGTAAATAAGGAGC\nCGTATAAAATTATGTTATCCGACCGACACCCAATCGCCTCAACTATATGTTTTCCCTTGTCCAGATACTT\nAGTGGGAGATATGTCCCCAGCGGCGCTTCCTGGGTTATTGTTTACGCTTCCCGCTGAACCCCCCGGGACC\nAACTTGGTAGTTTGTACCGTTTCACTCCCCAGTCATTTATCCAGAGTAAGCAAACGGGCCAGACCGGGAG\nAAACGGTTAATCTGCCGTTTGTTATGGTTCTGAGAAATGTATATATAATGCTTATTAATACAATTATATT\nTCTTAAAACTAACAACTGGCACGCGGGCTGGAACACACTGTCATTTTGTAATGATGTATTTAAACAGAAA\nTTACAAAAATCCGAGTGTATAAAACTACGCGAAGTACCTGGGATTGAAGACACGTTATTCGCCGTGCTTA\nAACTTCCGGAGCTTTGCGGAGAGTTTGGAAATATTCTGCCGTTATGGGCATGGGGAATGGAGACCCTTTC\nAAACTGCTCACGAAGCATGTCTCCGTTCGTATTATCGTTAGAACAGACACCCCAGCATGCGGCACAAGAA\nCTAAAAACTCTGCTACCCCAGATGACCCCGGCAAACATGTCCTCCGGTGCATGGAATATATTGAAAGAGC\nTTGTTAATGCCGTTCAGGACAACACTTCCTAAATATACCTAGTATTTACGTATGTACCAGTAAAAAGATG\nATACACATTGTCATACTCGCGTGTACGTGTTTTTCTTTTTTATATATGCGTCATTTATTACCACATCCTT\nTAATCCCGCCTTTATCTCCCTAAAACGGAGTGGTAATATTAAAAGCCGCCAAGCCTGTTGGTGGGTGAGG\nAGGGGTAAAGGCACGCTGTGTGCATAACGTTGCGGTGATATTGTAGCGCAAGTAACAGCGACTATGTTTG\nCGCTAGTTTTAGCGGTGGTAATTCTTCCTCTTTGGACCACGGCTAATAAATCTTACGTAACACCAACCCC\nTGCGACTCGCTCTATCGGACATATGTCTGCTCTTCTACGAGAATATTCCGACCGTAATATGTCTCTGAAA\nTTAGAAGCCTTTTATCCTACTGGTTTCGATGAAGAACTCATTAAATCACTTCACTGGGGAAATGATAGAA\nAACACGTTTTCTTGGTTATTGTTAAGGTTAACCCTACAACACACGAAGGAGACGTCGGGCTGGTTATATT\nTCCAAAATACTTGTTATCGCCATACCATTTCAAAGCAGAACATCGAGCACCGTTTCCTGCTGGACGTTTT\nGGATTTCTTAGTCACCCTGTGACACCCGACGTGAGCTTCTTTGACAGTTCGTTTGCGCCGTATTTAACTA\nCGCAACATCTTGTTGCGTTTACTACGTTCCCACCAAACCCCCTTGTATGGCATTTGGAAAGAGCTGAGAC\nCGCAGCAACTGCAGAAAGGCCGTTTGGGGTAAGTCTTTTACCCGCTCGCCCAACAGTCCCCAAGAATACT\nATTCTGGAACATAAAGCGCATTTTGCTACATGGGATGCCCTTGCCCGACATACTTTTTTTTCTGCCGAAG\nCAATTATCACCAACTCAACGTTGAGAATACACGTTCCCCTTTTTGGGTCGGTATGGCCAATTCGATACTG\nGGCCACCGGTTCGGTGCTTCTCACAAGCGACTCGGGTCGTGTGGAAGTAAATATTGGTGTAGGATTTATG\nAGCTCGCTCATTTCTTTATCCTCTGGACCACCGATAGAATTAATTGTTGTACCACATACAGTAAAACTGA\nACGCGGTTACAAGCGACACCACATGGTTCCAGCTAAATCCACCGGGTCCGGATCCGGGGCCATCTTATCG\nAGTTTATTTACTTGGACGTGGGTTGGATATGAATTTTTCAAAGCATGCTACGGTCGATATATGCGCATAT\nCCCGAAGAGAGTTTGGATTACCGCTATCATTTATCCATGGCCCACACGGAGGCTCTGCGGATGACAACGA\nAGGCGGATCAACATGACATAAACGAGGAAAGCTATTACCATATCGCCGCAAGAATAGCCACATCAATTTT\nTGCGTTGTCGGAAATGGGCCGTACCACAGAATATTTTCTGTTAGATGAGATCGTAGATGTTCAGTATCAA\nTTAAAATTCCTTAATTACATTTTAATGCGGATAGGAGCAGGAGCTCATCCCAACACTATATCCGGAACCT\nCGGATCTGATCTTTGCCGATCCATCGCAGCTTCATGACGAACTTTCACTTCTTTTTGGTCAGGTAAAACC\nCGCAAATGTCGATTATTTTATTTCATATGATGAAGCCCGTGATCAACTAAAGACCGCATACGCGCTTTCC\nCGTGGTCAAGACCATGTGAATGCACTTTCTCTCGCCAGGCGTGTTATAATGAGCATATACAAGGGGCTGC\nTTGTGAAGCAAAATTTAAATGCTACAGAGAGGCAGGCTTTATTTTTTGCCTCAATGATTTTATTAAATTT\nCCGCGAAGGACTAGAAAATTCATCTCGGGTATTAGACGGTCGCACAACTTTGCTTTTAATGACATCCATG\nTGTACGGCAGCTCACGCCACGCAAGCAGCACTTAACATACAAGAAGGCCTGGCATACTTAAATCCTTCAA\nAACACATGTTTACAATACCAAACGTATACAGTCCTTGTATGGGTTCCCTTCGTACAGACCTCACGGAAGA\nGATTCATGTTATGAATCTCCTGTCGGCAATACCAACACGCCCAGGACTTAACGAGGTATTGCATACCCAA\nCTAGACGAATCTGAAATATTCGACGCGGCATTTAAAACCATGATGATTTTTACCACATGGACTGCCAAAG\nATTTGCATATACTCCACACCCATGTACCAGAAGTATTTACGTGTCAAGATGCAGCCGCGCGTAACGGAGA\nATATGTGCTCATTCTTCCAGCTGTCCAGGGACACAGTTATGTGATTACACGAAACAAACCTCAAAGGGGT\nTTGGTATATTCCCTGGCAGATGTGGATGTATATAACCCCATATCCGTTGTTTATTTAAGCAGGGATACTT\nGCGTGTCTGAACATGGTGTCATAGAGACGGTCGCACTGCCCCATCCGGACAATTTAAAAGAATGTTTGTA\nTTGCGGAAGTGTTTTTCTTAGGTATCTAACCACGGGGGCGATTATGGATATAATTATTATTGACAGCAAA\nGATACAGAACGACAACTAGCCGCTATGGGAAACTCCACAATTCCACCCTTCAATCCAGACATGCACGGGG\nATGACTCTAAGGCTGTGTTGTTGTTTCCAAACGGAACTGTGGTAACGCTTCTAGGATTCGAACGACGACA\nAGCCATACGAATGTCGGGACAATACCTTGGGGCCTCTTTAGGAGGGGCGTTTCTGGCGGTAGTGGGGTTT\nGGTATTATCGGATGGATGTTATGTGGAAATTCCCGCCTTCGAGAATATAATAAAATACCTCTGACATAAA\nAAACATGTATAATAAAAAGTCACTATAAACGTATTCTCTACAATACTTTATTCGCGAATAATACACACTA\nCCTTTGGGTTTTTTTCCCGTCCCCAAATGGTGTTTGGTGCACTCTACCAAAAAATAGAGCGCCTAAATAT\nGCTATATAACGCCTCCCAGCAAAATACGGTTCAAAGGCATTACCCGATATTGTATTGTAGTACAGGGCAA\nTGGGAATTGATGATCCCAATAAACGGCATAGACGCACAGCGCCGTTATAGCAGGGGTCTCCAGAGTACAG\nGGTATCTAAGTACCGGGATATCTCATACTCATGCCTTTCCGTGACAGAAACATCAACCGGAACAGTATCC\nGATAAACCAACTCCTGTTTTTGCAAGGCGTAAAATTCGCACACCTTCCTTTTTTGCAAGATGTGACGTTT\nCCTTGTAACAGGGAAGCTGGGGGAGTGGTAAGAACAACAAAGTTTCAGCCAACGTGCCAATAAAGCCCAC\nTTCCCTCAAGAGGCTGTTTGCTGTATCCACAATGGTCCGTATTAAATCTTGAGCAACTTGATCCGTGTCA\nTCATCACTGGGTAACGCGTTAACATAACTACGCGTTAAATCTTCAATAACGGCATAACAATTAAACGCTT\nCCCACCGAGACAGTATATATTGAACAATCACGAACCGTTGACAGGACGTCAGATCACGTCCGTAAGCATG\nCCCGAAAAATGGAAGTTCCCCCCGTTCGCCATATACCGCAACAACTGCAGTATATATCGTCTCACGGGCT\nTCATTAAGTTCATCTTCAAGTCCAGGCCATTTTCTGGCTTTAAATATAACCTCGTCCGCAAAAAAAACCG\nCACATGATAACGCGCGGATACAATGAGTAGTGGCTTTATGGCGAGGATCCCAAATGTCCATTACCCGGGG\nGATGGTCCTAATCTGTACAAAGTTACTTAGTGTAATATGATCGGACTTCTTACGCCGTCTAGGCTGTTTC\nTCAGAATACGGTTCACCCGAAATCGGCACATCATCTGCTTTTACGTCTTCCGTAACCACATCAGCAGCGC\nGCCGACTAACAATTATACTTGTTTTTTCATCGTCGTTACTTCCGTTAAGCGCGTCTCGTATCTCGGGCGT\nCCCGTCGAATAATCCACTCACTAGCTCCTGCAAACTTTCTGGTAACTCCAACATACGCATATACACCAAT\nGAAAAACTGGCTTCGTTTGGTACGTACATAAAGCCATTTGTGGTATTAATGGCGGTGGGTGTTGGAAACA\nATTTTAGCTTATTCTCGCGCGTAACATCTACCCCCGCCACCAATGTTAAATGCGTCACGGGGAGGGACAC\nGAGATAATCTGCGAGCGTAGGGTCCTCCACTTCAACATCAAATGTTCCGCAAAGGTCGCGATCCACCGCC\nCCCGATCCCGCTGCAAGTAAGGCCACTCGATCCAAAAACACGCAGTTATTATTGGATGATACCGCCCATG\nTCTTCCCGGTGCGATTGAGCTCACTTCGAACGTAACTGGCAACAGATCTGTCACCGGGTCCGACCCCGCG\nAACAACATGTCCAAATTTTGCGATCTCGCCTCCATGTTTGCGGGGTATGGAAATTAAGCATCCCCCGCAT\nATAAAATACGCCCTGGTAGCACGCTCGTTAAAATAAAACGTTACGCCGTTATAAGATACGGTTGAATGAT\nATGGAAATTCCATATTAAAGCGTTTATCGGAACATTAACCTCGAACTTGCCGTCCCGTGATCGTGTGATC\nGCCAACCTTAGGTCCACACCGAATATGAGAAATATATAACTACACGCAAACATTCAAAACACCGTGGTAT\nCATTAACGTCATATGAAAAGATCCAATCAATCCAATCAACCACACCTCCTACCGTTTAGCACGTCAGCTA\nTGTGACATGCTCCAAACATACGTAAACATTTAGAGAGGGTGTTATAACAGTCTGTCAGGCGGGGTATATT\nCTACATAATACAAGGATCGGCTTTAACTTTGTCAACATTTTTACTTTGGACTATAAACTGCGACTGAACG\nTTATGAACCCACCCCAAGCCCGCGTCTCGGAACAGACAAAGGACTTGCTTAGCGTTATGGTTAACCAGCA\nCCCCGAAGAGGACGCAAAAGTGTGTAAATCCAGTGATAATTCACCGCTTTATAACACCATGGTTATGTTA\nTCGTATGGGGGTGATACGGACTTACTATTAAGCTCTGCATGTACCCGCACATCTACCGTAAACAGGTCGG\nCGTTTACGCAACACTCCGTGTTTTATATTATATCCACGGTGTTGATTCAACCAATATGTTGTATCTTCTT\nTTTTTTTTACTATAAAGCGACACGCTGTATGCTCTTATTCACAGCCGGGTTACTTCTGACGATTCTACAT\nCACTTTCGACTTATTATTATGTTATTGTGTGTCTACAGAAATATACGATCAGACCTGCTACCCTTATCTA\nCATCCCAGCAACTGCTGCTTGGAATTATTGTTGTGACTCGAACAATGCTATTTTGTATTACGGCGTATTA\nTACTCTTTTTATAGACACCCGGGTGTTCTTTTTGATTACCGGACACTTGCAAAGTGAGGTTATTTTTCCA\nGATAGCGTTTCAAAAATACTTCCTGTGTCGTGGGGTCCAAGTCCAGCCGTGTTACTGGTAATGGCGGCAG\nTTATTTACGCTATGGACTGTTTGGTGGACACGGTATCCTTTATTGGGCCAAGGGTGTGGGTCCGTGTTAT\nGTTAAAAACATCTATTTCGTTTTAGTCCATTTCAATAAATGTACTATAATTGTTCAGTCTAAAAATAATG\nTTGGGTATTTATAATTACCGCCCCCGTGTTACTTGGAAACACCCATACATATGTTCCACTCTACATCAAA\nCTTCTCGCAGTTTTCTTGTTCCCGCACACGTTTACACGTCCGGATTCAAGTCGCAACGCTGCTGACAAAA\nTGACAACGGTTTCATGTCCCGCTAACGTGATTACTACAACGGAATCTGATCGTATTGCTGGGTTATTTAA\nCATCCCAGCGGGGATCATTCCAACTGGAAATGTGCTGTCAACCATAGAGGTGTGTGCACACCGTTGCATT\nTTTGATTTTTTTAAACAAATACGATCAGATGATAACAGCCTTTACTCGGCTCAATTCGATATTCTTTTGG\nGGACATACTGCAATACATTAAACTTTGTGCGTTTTCTAGAACTTGGACTGTCTGTCGCTTGCATCTGTAC\nTAAATTTCCGGAGCTGGCTTACGTGCGAGATGGCGTTATTCAATTTGAGGTACAACAACCCATGATAGCA\nCGTGATGGCCCACATCCCGTCGATCAGCCTGTTCATAATTATATGGTTAAGCGGATACACAAGCGTTCGT\nTAAGCGCTGCGTTTGCAATTGCATCGGAAGCGTTGAGTTTGTTAAGTAACACATATGTCGATGGGACAGA\nGATTGACTCATCGTTACGTATAAGAGCTATCCAACAGATGGCTCGTAATTTACGCACCGTTTTGGACTCA\nTTTGAACGAGGCACTGCCGATCAACTTCTTGGTGTTCTATTGGAGAAAGCCCCACCGCTATCGCTGCTTT\nCACCAATTAATAAATTCCAACCCGAGGGACATCTAAATCGTGTTGCACGCGCGGCCCTACTTTCGGACCT\nCAAACGTAGAGTCTGTGCGGATATGTTTTTTATGACCCGACACGCCAGGGAACCTAGGCTGATCTCTGCG\nTATCTGTCGGATATGGTTTCGTGCACCCAACCATCGGTGATGGTATCACGAATAACTCATACAAACACTC\nGCGGACGGCAGGTTGACGGTGTGTTGGTAACAACAGCAACCTTAAAACGGCAACTATTACAGGGAATTTT\nACAAATTGACGACACCGCCGCTGACGTACCAGTAACATATGGCGAAATGGTTCTACAGGGGACAAACTTG\nGTAACCGCCCTTGTGATGGGAAAGGCCGTCCGCGGAATGGATGATGTAGCCCGCCATCTCCTTGATATAA\nCCGACCCTAACACGTTAAACATACCGTCTATACCCCCACAATCCAACTCCGATTCAACGACAGCTGGGCT\nTCCGGTTAACGCCCGTGTTCCTGCGGATTTAGTGATTGTTGGGGATAAACTTGTATTCTTAGAAGCATTA\nGAACGGCGGGTCTACCAAGCTACGCGCGTTGCCTACCCTCTTATTGGAAATATAGATATTACGTTTATCA\nTGCCAATGGGAGTGTTTCAGGCAAACTCCATGGACAGATATACACGACACGCCGGCGATTTTTCAACTGT\nATCCGAACAGGATCCACGTCAATTTCCACCCCAAGGGATTTTTTTTTATAATAAAGATGGGATATTAACA\nCAGTTGACTCTTCGTGATGCAATGGGTACCATCTGCCACAGTTCATTGCTTGATGTCGAGGCCACACTTG\nTTGCCCTCCGCCAACAACATTTAGATCGTCAGTGTTATTTTGGTGTATACGTGGCCGAGGGTACAGAGGA\nCACATTGGATGTTCAAATGGGGAGGTTTATGGAAACGTGGGCAGATATGATGCCTCATCACCCTCATTGG\nGTAAACGAACATTTAACAATTCTACAGTTTATAGCTCCGAGCAACCCGCGTCTAAGGTTTGAATTAAACC\nCCGCCTTTGATTTTTTTGTTGCACCGGGGGACGTAGACCTTCCCGGACCGCAGCGTCCCCCGGAAGCCAT\nGCCAACCGTTAACGCAACATTACGGATTATCAACGGAAACATTCCCGTGCCTCTATGTCCCATTTCATTT\nCGAGACTGTCGCGGAACCCAACTCGGTTTGGGAAGACATACAATGACCCCGGCAACCATTAAAGCCGTAA\nAGGATACATTTGAAGACCGCGCATACCCAACTATTTTCTACATGCTAGAGGCTGTTATTCATGGAAACGA\nAAGAAACTTCTGTGCGTTACTGCGACTGTTAACACAGTGTATTCGCGGGTATTGGGAGCAATCCCACAGG\nGTGGCATTTGTAAATAACTTTCACATGTTAATGTACATAACTACATATCTCGGAAACGGTGAGCTTCCCG\nAAGTCTGTATTAATATATATCGGGATTTACTGCAGCATGTAAGAGCATTACGCCAAACTATAACCGATTT\nTACAATACAAGGAGAGGGCCATAACGGCGAGACCTCGGAAGCGCTAAATAACATCCTTACGGATGACACG\nTTTATTGCACCTATTCTATGGGATTGTGATGCGTTAATATACCGTGATGAAGCCGCCCGAGACCGACTCC\nCCGCAATTCGTGTAAGCGGGCGAAACGGATACCAAGCCCTTCACTTTGTGGATATGGCCGGGCATAACTT\nCCAACGACGCGATAATGTGTTAATCCACGGGAGACCCGTTCGGGGAGACACGGGTCAGGGTATTCCCATT\nACTCCACACCATGACCGTGAATGGGGTATTCTCTCCAAGATTTACTACTATATTGTCATTCCTGCATTTT\nCCCGCGGTTCCTGTTGTACAATGGGCGTGCGTTATGATCGCCTATACCCTGCGTTACAGGCAGTTATCGT\nTCCGGAAATTCCCGCTGATGAAGAAGCCCCAACTACCCCAGAAGATCCAAGACACCCTCTTCACGCACAC\nCAACTCGTTCCGAACTCTCTTAACGTTTACTTCCATAATGCACACCTAACCGTTGATGGTGATGCATTGC\nTCACACTACAAGAGTTAATGGGAGATATGGCTGAACGAACGACGGCCATTTTAGTATCAAGCGCCCCCGA\nTGCGGGAGCCGCCACGGCAACAACCAGAAATATGAGAATATATGACGGAGCGCTTTACCATGGCCTTATT\nATGATGGCATATCAGGCGTACGATGAAACCATTGCAACGGGTACTTTTTTTTATCCCGTTCCGGTCAACC\nCTCTGTTTGCATGTCCGGAACATTTGGCATCATTGCGTGGAATGACAAATGCTAGGCGGGTTTTGGCAAA\nAATGGTACCACCAATCCCTCCTTTTCTGGGAGCCAACCACCACGCAACTATACGCCAACCCGTTGCCTAC\nCATGTAACGCATAGTAAGTCGGATTTTAATACTCTTACATATTCTCTTCTTGGAGGGTATTTTAAGTTTA\nCACCAATATCTCTTACACATCAACTACGAACGGGATTTCACCCCGGGATTGCCTTTACCGTAGTGCGCCA\nGGATCGCTTTGCCACAGAGCAACTTTTATATGCCGAGCGTGCTTCTGAATCGTACTTTGTCGGACAAATC\nCAAGTACACCATCATGATGCTATTGGGGGGGTAAACTTTACCCTAACCCAACCCAGAGCTCACGTGGACC\nTGGGAGTCGGGTATACAGCTGTATGTGCCACAGCAGCCCTGCGATGCCCTCTCACGGATATGGGCAATAC\nTGCCCAAAATCTTTTTTTTTCACGAGGAGGAGTGCCAATGTTACATGATAACGTTACCGAATCGTTGCGT\nCGTATAACAGCATCGGGGGGTCGCTTAAATCCCACCGAACCCCTACCCATCTTCGGCGGACTACGTCCTG\nCTACATCGGCAGGAATTGCACGAGGGCAAGCCTCTGTGTGTGAGTTTGTGGCCATGCCGGTGTCCACTGA\nCCTACAATATTTTAGAACTGCATGCAATCCTAGAGGTCGAGCATCTGGAATGTTATATATGGGTGACCGT\nGACGCCGACATAGAGGCTATAATGTTTGATCACACACAATCGGATGTTGCTTATACAGATCGAGCAACTC\nTTAACCCATGGGCATCACAAAAACATTCATACGGTGACAGGCTATACAACGGAACATACAACCTTACAGG\nCGCTTCTCCTATCTACAGCCCATGCTTTAAGTTTTTTACACCAGCGGAGGTTAACACTAATTGTAATACA\nCTGGATCGGCTTCTAATGGAGGCAAAGGCTGTGGCGTCGCAAAGCTCCACCGACACTGAATATCAATTTA\nAACGCCCTCCCGGTTCTACCGAAATGACACAGGATCCGTGTGGCCTTTTTCAAGAAGCATATCCACCACT\nATGCTCAAGCGATGCGGCCATGTTACGAACGGCTCACGCGGGAGAAACCGGGGCAGATGAAGTTCACTTA\nGCCCAATATCTGATTCGAGACGCGTCGCCCCTTAGGGGATGTCTTCCTCTTCCGCGATAATTTCACCACG\nCCCACATACCCACTCCCAATAAAAGCCCTGTAGAGCGCATTGGCATCTTACTTGAGATTTGGATACGCTC\nGGCCGACTTGGTCTGTTTCACGCTTCCTTAAACAACATGGCTATGCCATTTGAGATAGAGGTATTGTTAC\nCAGGAGAACTATCCCCGGCGGAAACATCTGCATTACAGAAATGTGAGGGAAAAATTATTACCTTCTCAAC\nCCTGCGTCATCGAGCTTCACTGGTGGATATAGCGCTGTCGTCATATTACATTAACGGTGCTCCACCAGAC\nACGCTCTCGCTGTTAGAGGCATACCGAATGCGATTCGCGGCAGTTATAACACGGGTCATCCCGGGAAAGT\nTGTTGGCGCATGCCATTGGCGTGGGTACTCCTACACCCGGGTTGTTTATTCAAAATACATCCCCCGTTGA\nTCTTTGTAATGGCGATTACATCTGCTTACTTCCTCCGGTTTTCGGGTCCGCAGACTCAATTCGCTTGGAC\nTCTGTAGGACTGGAAATTGTTTTCCCTTTAACCATCCCCCAGACCTTAATGCGAGAAATCATCGCCAAAG\nTGGTTGCACGGGCCGTTGAGCGCACGGCCGCGGGTGCTCAAATTTTACCCCACGAAGTTCTACGAGGCGC\nGGATGTCATTTGTTACAATGGAAGGCGTTATGAACTCGAAACAAATTTACAACATCGGGACGGATCGGAT\nGCGGCTATTCGCACATTGGTTTTAAATCTAATGTTTTCCATAAACGAGGGATGTCTGCTTTTATTGGCGC\nTGATTCCAACTTTGTTAGTCCAAGGAGCACACGACGGTTATGTAAATTTATTGATACAAACGGCCAATTG\nCGTTAGAGAAACCGGCCAGTTAATTAATATACCGCCAATGCCGCGGATTCAAGACGGCCATCGCCGATTT\nCCCATATATGAAACTATTTCATCTTGGATATCAACATCATCTAGACTGGGGGATACCTTGGGAACTCGCG\nCAATTTTACGCGTCTGTGTGTTTGATGGACCCTCTACTGTTCATCCGGGAGACCGCACGGCCGTGATTCA\nAGTGTAAACAGGTGTTAATAAAAACACAACCAGTCTAGTTACATTTCACGCGTCTTGTTTTTATTTAATA\nGGCATAAACACGGAATCCGGTATACATGAACTGCCAATATACACGGACATAATTAATGCAACCATCAGAT\nCATCTGACATTGTTCCCGTGGTACCTTTACCCGTGTAAGTTTTTGTGTCTAGATTACCCATACCGCCTTT\nAATTACCTCTGTCAGGTTATCCAACTGTTTACATAGATACTCCACGGGGTCTACACCTAACTTTACTGTT\nAGGGATACAAGCTCCTGTGAGGCTATTATATTTCCGGAGTTAAATCGTTTAACAAAATAGTCTACGGCCG\nGCGTTTTTTGTTTTTGTAATAAAAAAAAAGGGTACGCCACGCTACATCCGGGAGGTATGGAATGATAAAA\nCAGTAACACTGGAGCGGAAGATAGCACGTTTCCCTTTTCGAGGACAGCAAACTGTTGTGCTATAGCCAAC\nGATATGGCAACTGCAGAATCCTGGCTGCTGTTTCCCTCTATAGAAACGTGTACGTTTGTAAATGTATTGG\nGGTGTAAAGCGAGTATGTGGCCTAAGCATTGAGTAACGCAACGCCCTATCTCACTGGAAGACGTGCCAGT\nTAAAGCTCTAAGAAAAAAGTGCTCCAATCCAAATATAATCCAATCCGACTTATAACGACCAACAATCGCT\nACACCAGTACCAGACGCTCGTGTATTTGAGGTAAATGCAGGGTCTACGTAAACGTACAACACTGACGATA\nATATAGCACAATTCGCAACGGTTGACGGCCGATATAAAATAAACCTCTCACGGGCAGTTTTTGTAAATAA\nTGGCCGGTCAAACCCCACACCCCCAGAATTCTGTTTACGCCCACCTACAATTTCCTGCACGAAGGAGTCG\nGCCATAAATAAATCTGCAGTGCGCCGCATGGCTCCATCCATTGTGATGAAAACCGGCTTATTTAATACAT\nAACACGAACAAGCTGTGACATCGCTATGTGCTAAAACACGCGGCATGTGATCGTCGCATACATATGTAAC\nAACGTTTAACAACTGATCCGACGATCCACGTAAGTTATACAAAAAACTTGTACTTGCTTTTCCGGTATTT\nGTTGATGAAACAAAAATAATTTTACAATTGGTTTGATTTAAAAATCCGACTATAGTTTGTACAGCATCAG\nGTCGAATAAAATTAGCTTCATCCACAAACAGAAGATTAAAATCTTGACCTCGGATACCCTGGAACGATAG\nAAAGATATATAGTTACCCCACCAAAGTTTAAATGTATCCTTAAATACCACGTACGTAAAAAATGTTTGAA\nTACGTACATATTTCTTTTTTTTTTCCAGTACAACCATATCCGGTGTATAATGGAAGCCCATTTGGCAAAT\nGAAACCAAACATGCACTTTGGCATAATGATCACACAAAAGGATTACTACACGTTGTGATACCTAACGCGG\nGGCTTATTGCGGCCGGAATAGATCCCGCATTACTGATTTTAAAGAAACCCGGACAACGCTTCAAGGTTGA\nAGTACAAACAAGATATCATGCTACAGGTCAATGCGAACCGTGGTGTCAAGTTTTCGCCGCGTACATTCCC\nGATAACGCCTTAACAAATCTCTTAATACCAAAAACGGAACCATTTGTTTCACACGTTTTTTCGGCCACGC\nATAATTCAGGGGGATTGATTTTATCATTGCCTGTTTATCTTAGCCCCGGTTTATTCTTTGATGCATTTAA\nCGTTGTAGCGATACGAATAAATACTGGAAACCGCAAGCACCGTGATATTTGTATTATGTATGCAGAACTA\nATCCCAAACGGAACGCGTTATTTTGCTGATGGACAACGGGTACTTTTATTATGCAAACAGCTGATTGCGT\nATATCCGATGCACCCCTCGTCTTGCATCGTCTATAAAAATATACGCAGAGCATATGGTGGCAGCCATGGG\nTGAATCACACACGTCAAATGGGGACAATATTGGACCCGTTTCATCCATAATCGATCTTGATCGACAGTTA\nACTTCTGGAGGTATTGATGACTCCCCTGCTGAAACACGCATACAGGAAAATAATCGGGACGTCCTTGAGC\nTAATAAAACGGGCCGTAAACATTGTTAACTCCAGGCACCCCGTCCGACCTTCTAGTTCCCGCGTTGCATC\nTGGGTTGCTTCAAAGTGCAAAGGGCCACGGAGCGCAAACTTCCAACACAGATCCGATCAATAACGGTTCC\nTTTGATGGCGTCCTTGAGCCGCCTGGACAAGGGCGATTTACGGGAAAGAAAAACAATTCGTCCGCCAGCA\nTCCCACCTTTACAAGACGTTCTATTGTTTACCCCAGCTTCGACAGAACCCCAAAGTCTTATGGAATGGTT\nCGACATCTGTTATGCCCAATTAGTTAGCGGGGACACTCCAGCAGATTTCTGGAAACGGCGTCCCCTATCA\nATTGTACCGCGACATTACGCAGAATCCCCCAGTCCGTTGATTGTAGTATCTTACAACGGATCCTCTGCCT\nGGGGAGGACGTATTACCGGAAGTCCAATTTTATATCACTCTGCACAGGCTATTATTGATGCTGCGTGTAT\nAAATGCCCGGGTTGACAATCCCCAAAGCCTACATGTGACAGCTCGCCAAGAGCTAGTCGCGCGTTTACCG\nTTTTTGGCTAACGTCCTAAATAATCAAACCCCCTTACCCGCCTTTAAACCAGGCGCCGAAATGTTTTTAA\nACCAGGTATTTAAACAAGCGTGTGTGACATCGCTAACCCAAGGTCTTATAACGGAGTTACAAACGAACCC\nGACTCTACAACAACTCATGGAATATGATATTGCAGATTCTTCCCAAACGGTTATTGATGAAATTGTAGCC\nCGCACACCAGACCTGATTCAGACTATAGTTTCGGTGTTAACGGAAATGTCAATGGATGCGTTTTATAACA\nGCTCCTTGATGTATGCGGTTTTGGCGTATCTGTCATCTGTATATACACGACCACAAGGTGGGGGGTATAT\nACCCTACCTTCACGCTTCCTTCCCATGCTGGTTAGGTAATCGTTCTATATATTTATTTGACTATTATAAT\nTCAGGAGGGGAAATACTTAAGCTTTCCAAGGTCCCCGTTCCCGTAGCCTTAGAAAAGGTTGGTATTGGTA\nATTCCACACAACTGAGGGGTAAATTTATACGCAGCGCGGATATTGTTGATATTGGAATTTGTTCTAAGTA\nTTTACCCGGTCAATGTTACGCGTACATTTGTCTAGGATTTAACCAGCAATTACAATCCATTTTAGTTTTA\nCCGGGGGGATTTGCGGCATGTTTTTGTATTACCGATACCCTACAGGCAGCACTACCTGCATCGTTAATCG\nGACCTATTCTAGACAGATTCTGCTTCTCTATTCCCAACCCCCATAAATAAATTAGTGTCACTATAAAAAC\nATAACACCAGAATCTCTTCATATGTAATTTTACGTCATTTCTCCCGTTTCCACCCCCTCTTAAAATATAA\nAATAACCGGGTGGGTGGCATTAAACCCACAAGTACCCGGGCGGCAATCCGCTAGACTGTTTTTCTGCTCA\nTGGAATTACAACGCATATTTCCGCTGTACACCGCTACGGGTGCAGCGCGCAAATTAACCCCCGAGGCAGT\nTCAGAGACTCTGCGATGCATTAACGCTGGATATGGGATTATGGAAGTCCATCCTGACCGATCCCCGGGTG\nAAAATAATGCGATCAACTGCTTTTATAACTTTAAGGATCGCTCCGTTTATCCCCCTTCAAACGGATACTA\nCTAATATTGCCGTTGTTGTAGCCACAATTTACATCACGCGCCCACGTCAGATGAACTTACCTCCGAAGAC\nTTTTCATGTAATTGTAAATTTTAATTACGAGGTCTCGTACGCAATGACGGCGACTTTAAGAATTTATCCG\nGTTGAAAACATAGACCATGTTTTTGGAGCAACGTTTAAGAACCCGATCGCGTACCCCCTTCCAACATCTA\nTTCCGGATCCTCGAGCAGATCCCACCCCCGCAGATCTTACACCAACGCCAAACTTAAGCAACTACTTACA\nACCCCCGCGGCTTCCGAAAAATCCATACGCATGTAAAGTTATTTCTCCGGGAGTGTGGTGGTCAGACGAA\nCGAAGGCGTTTATATGTACTGGCTATGGAACCTAATTTAATAGGGCTATGTCCCGCCGGATGGCATGCTC\nGGATACTTGGCTCTGTATTAAATCGACTCCTCAGCCATGCGGACGGATGTGATGAATGTAATCATAGAGT\nTCACGTGGGGGCACTGTATGCGTTACCCCATGTCACAAATCATGCGGAAGGTTGTGTGTGTTGGGCTCCG\nTGTATGTGGAGAAAGGCCGGTCAGCGGGAATTAAAAGTGGAGGTAGACATTGGCGCCACGCAGGTTCTTT\nTTGTAGATGTCACCACCTGCATTCGAATTACGAGTACTAAAAATCCTCGCATTACCGCAAATCTTGGCGA\nCGTTATAGCGGGAACCAACGCCAGTGGTCTCTCTGTACCAGTAAATTCATCTGGGTGGCAGCTTTATATG\nTTTGGAGAAACATTAAGCCGGGCTATTATTAACGGCTGTGGTCTGCTTCAGCGAATTTGCTTCCCCGAGA\nCACAAAGATTATCGGGTGAACCGGAACCTACAACCACCTAGTATACCTTAACTCAACCGCCGTTGTGGAA\nAGGTATATGTCAACATTTACAGTAATATATTAAAGGTTAAATTTATAAAACACTCACGTTTGTGTTGTGA\nCTTGACGCGAACACCGCTGTGCTGTAAGACCCGTCGGTAAATGAAAACGTAATAGATTCGCCTTTTACAT\nGATCCACGTAATTTGCCCCAAACCACTGTTCCAGGCGAGACTTGATACCCTCAAACACGGGTTCCGTTGC\nTTTGCGTATATGAGCCGTATAACCCACTTTAATTCCTCTAAACGTGGCCATTACTAAAGCTATTAATGGT\nACAAGAAACCATGTTTTCCCATGTCTACGTGGTACCAAAAACACAGTTGATTTTTGTTTGAAGTGTTCTA\nAAACACTGTCAGAAACACTTGGCGTGTTAAACACTGTACGCAGAAAGCAGTCAACTCTGTCGGCATGATC\nGCCCAATAGCACCGATGAAATAAAATGCGTGGTGTGCATGAGGATCATTTTTTGAAACAGTTCCAACGTC\nCCCTTATATCTGCCATAGATTGGAACGTCAACCTTTGCGCGTTTGCCATGACTTCCACACTCTTCAATAC\nTCTCAAAAGATGTTTCCACAAGGTACGAAAACCGTTGTGTAAAGGTAGACAACTGACAGAAACTATCCGA\nCAGAGAAAACGCGCGAAATGTGTTCATAACACCGCTATACGCATTTCGATGAGGTGCTGCTTCTTCCGGT\nGAATATTCATAAAACTGTACACTACTGACAGCCTTTTTTAATTCAGGGCTTACGTTTGCATTTACCGAAT\nATCGCCATGGTTTCAAAACTACATTGGGGGTACAGTTGTACCCTGTTGACGATAGAAACGCGCCAAACAT\nTGCCCGTCGAGCAGTAGCCGAGAACAGTGGAATATATTCACAACAGTTGTGAAGCGTTCCAATTCCGGGA\nATAACGGCCTGATGACGTCGGGTTACATCTATAGCAAAATTCAGAAACGGGATTTGGGTTGCGTTTCCCA\nGAGACCCTTGCCGCGTGGAACACGGGGTAGGGGACTCCAACGTCCCAAAGCGTTCATCCCTACGACGCTT\nTAGACGTTCAAAATATCTTACAGATTCTTCACCAAGCGTACGACCAAACATTATCAATGACATTTAACAT\nCAATTCACGGAATCCGCCTCATCTCTTGTAAGCAGTAAAACAGGAAGCCGCGTCATCTTACGTACTCGTT\nACGTATATATCATAAACATTTTCAGGGCCGCATTCATTCACTTTGGTCATGTCAGGCCACACTCCAACCT\nACGCTTCTCATAGGCGTAACCGTGTCAAACTAGTTGAGGCGCATAACCGCGCGGGGTTATTTAAAGAACG\nGACCCTCGATCTAATCCGTGGGGGTGCGAGTGTACAAGATCCAGCATTTGTGTATGCCTTTACTGCTGCA\nAAAGAGGCCTGCGCCGATTTAAATAACCAGCTCCGCTCTGCAGCTCGCATAGCTTCAGTTGAACAGAAGA\nTTCGTGATATACAATCCAAGGTTGAGGAACAAACAAGTATTCAACAGATTTTAAATACAAACAGACGCTA\nTATAGCACCCGATTTTATTCGCGGTTTGGATAAAACAGAAGACGATAATACCGATAATATAGACAGACTG\nGAAGACGCGGTAGGACCGAACATCGAACACGAAAATCATACTTGGTTTGGAGAAGACGACGAAGCGTTAC\nTTACACAATGGATGCTGACGACACACCCCCCAACCTCCAAATATCTCCAACTGCAGGACCTTTGCGTTCC\nCACCACAATACCGACGGACATGAACCAAATGCAACCGCAGCCGATCAGCAAGAACGAGAATCCACCAACC\nCCACACACGGATGTGTAAATCATCCATGGGCCAATCCGTCAACTGCAACATGCATGGAATCACCAGAACG\nATCACAACAGACAAGCTTATTTTTATTAAAGCACGGCTTAACGAGAGATCCAATACATCAACGCGAAAGG\nGTGGACGTTTTTCCACAATTTAACAAACCCCCATGGGTTTTTAGAATTTCCAAATTATCCCGTTTAATTG\nTACCCATCTTCACGCTCAATGAACAGTTATGTTTTTCTAAATTACAGATTCGAGATAGACCCAGGTTTGC\nGGGACGGGGAACGTATGGGCGTGTTCATATATACCCATCGTCAAAAATAGCTGTAAAAACCATGGACAGT\nCGTGTTTTTAATAGAGAGTTAATTAACGCGATTTTAGCGAGTGAGGGTTCTATACGAGCAGGGGAAAGGC\nTAGGTATTTCTAGCATAGTTTGCCTTTTAGGTTTTTCGTTACAAACCAAACAGCTACTGTTTCCGGCATA\nCGACATGGATATGGATGAATACATTGTTCGCCTGTCCAGACGGTTGACAATACCTGATCACATAGACAGA\nAAAATTGCCCATGTATTTTTAGATTTGGCTCAAGCGTTGACGTTTTTAAATCGAACGTGCGGCCTGACCC\nACCTAGATGTGAAATGTGGCAATATTTTTCTTAACGTCGACAACTTTGCCTCGTTGGAAATAACCACAGC\nAGTAATCGGAGACTATAGCCTAGTAACATTAAATACGTATTCCCTTTGTACTCGAGCGATATTTGAAGTT\nGGAAATCCATCCCACCCGGAGCACGTACTACGCGTACCCCGGGATGCATCGCAGATGTCATTTCGTTTGG\nTGTTGAGTCATGGAACAAACCAACCCCCTGAAATCTTGCTTGATTATATTAATGGAACGGGCCTTACTAA\nATATACTGGAACCTTGCCCCAAAGAGTTGGACTTGCGATTGATCTTTATGCATTGGGCCAAGCACTCTTA\nGAAGTTATCCTGCTAGGACGTCTTCCCGGACAACTGCCCATTTCAGTACATCGGACCCCGCATTATCACT\nACTACGGTCATAAGTTATCACCAGATTTGGCGCTTGATACGCTGGCATATCGATGTGTCCTGGCGCCATA\nTATACTCCCATCTGACATCCCCGGGGACTTAAATTATAATCCCTTTATACACGCCGGAGAGCTGAACACC\nCGTATTTCCCGGAATTCTTTACGCCGGATATTCCAGTGTCACGCAGTGCGTTACGGCGTAACGCACTCAA\nAGCTTTTCGAAGGCATACGCATTCCGGCCTCATTATACCCAGCCACTGTTGTTACATCGTTGTTGTGTCA\nCGATAATTCAGAAATACGCTCGGATCACCCTTTATTATGGCACGATCGGGATTGGATAGGATCGACATAA\nGCCCCCAGCCAGCCAAAAAAATTGCCCGTGTGGGAGGTCTACAGCACCCTTTTGTAAAAACGGATATTAA\nCACGATTAACGTTGAACACCATTTTATAGACACGCTACAGAAGACATCACCGAACATGGACTGTCGCGGG\nATGACAGCGGGTATTTTTATTCGTTTATCCCACATGTATAAAATTCTAACAACTCTGGAGTCTCCAAATG\nATGTAACCTACACAACACCCGGTTCTACCAACGCACTGTTCTTTAAGACGTCCACACAGCCTCAGGAGCC\nGCGTCCGGAAGAGTTAGCATCCAAATTAACCCAAGACGACATTAAACGTATTCTATTAACAATAGAATCG\nGAGACTCGTGGTCAGGGCGACAATGCCATTTGGACACTACTCAGACGAAATTTAATCACCGCATCAACTC\nTTAAATGGAGTGTATCTGGACCCGTCATTCCACCTCAGTGGTTTTACCACCATAACACTACAGACACATA\nCGGTGATGCGGCGGCAATGGCGTTTGGAAAAACCAACGAACCGGCGGCACGAGCGATAGTTGAAGCATTG\nTTTATAGATCCGGCTGATATCCGTACTCCTGATCATTTAACGCCAGAAGCTACAACTAAGTTTTTTAATT\nTTGACATGCTCAATACCAAATCTCCAAGTCTCCTTGTGGGTACACCAAGAATCGGAACGTATGAATGTGG\nACTTTTAATCGACGTTCGAACGGGACTTATAGGCGCGTCGTTGGACGTTCTTGTATGTGACAGGGACCCT\nTTAACTGGCACCCTAAATCCCCACCCTGCAGAAACCGACATTTCATTTTTTGAAATTAAATGTCGTGCTA\nAATACCTCTTTGATCCAGATGACAAAAATAACCCGCTCGGTCGGACGTACACCACGTTAATAAATAGACC\nTACAATGGCAAATCTACGGGACTTTTTATATACTATAAAAAACCCATGTGTAAGCTTCTTTGGACCCTCA\nGCAAACCCAAGTACACGCGAGGCCTTAATAACGGATCACGTTGAATGGAAACGTTTAGGATTTAAAGGTG\nGGAGGGCCCTTACAGAACTCGACGCCCATCATTTGGGCCTCAATCGGACAATCTCATCCCGAGTGTGGGT\nATTTAATGATCCGGACATACAAAAGGGGACAATTACAACCATTGCATGGGCCACTGGAGATACGGCTCTT\nCAAATTCCTGTATTTGCCAATCCGCGGCACGCTAACTTTAAACAAATTGCCGTACAAACCTATGTATTAT\nCCGGTTACTTTCCAGCGCTAAAACTACGGCCCTTCCTTGTCACCTTTATAGGACGTGTGCGCCGACCACA\nCGAGGTGGGAGTCCCATTGCGCGTCGATACACAAGCGGCTGCCATTTACGAATATAACTGGCCGACTATC\nCCACCCCACTGTGCGGTTCCGGTTATAGCCGTTCTAACGCCTATCGAAGTTGATGTGCCTAGAGTGACAC\nAAATACTTAAAGACACAGGAAACAACGCGATTACATCAGCATTGCGGTCATTGCGATGGGACAATCTTCA\nTCCAGCGGTCGAGGAGGAATCTGTGGATTGTGCAAACGGTACAACGAGCTTGTTACGTGCAACGGAGAAA\nCCGTTGCTTTGAACTCAGAGTTCTTTGAAGACTTTGACTTTGATGAGAATGTAACAGAGGACGCCGATAA\nATCCACACAACGCCGCCCACGAGTGATCGATGTAACACCAAAACGAAAACCTTCGGGAAAGAGCTCCCAT\nTCCAAATGCGCAAAATGTTAAACCCTGATAAACCCTGATAAACGTTCTAATAAAAACATCAAATCATGGT\nTGGTTACTGTGAATGTTTGTTTTATTGCTTGGGGGTTTACAAGTACAACCCACGCTACTCCCACCCACTG\nTTTGATCGCTCGTATAACAGCTCATCCTCGCGGTCCGTTTCATATGTTGAGTCATTTTCATAGACGTAGC\nCGTAGCCTTGTGATGGGTAATTTGTGCGGCGAGAATTTCTATGTGCAGGTTTTACTTTTCGTATGTATCC\nCCGTACCCGCTCGGGTACTCTTCTTACGGCACCGTAGAACCGACTGCGTTTCTGTCGATGATACACATAT\nGCACGCATCAATCTGAGAAGCAACATGACAACGGAAAACACGGCCAGGCAAGCCAAGGTTCCCCGAGTTG\nTGGGAATTAACCGTGGAGATTGAACCGATATAGGGTCATATAATCGGTCCATATACGAGTGCGCGGCGGT\nTCCCAACGTAGCACAGGCCACGAGCGTTCCCAGGGACGGTCCTATTAACACGTGTATATAATGCGCCAAA\nATTAATTCTGATACTATAAGATATACAACTGACAATGTACTAAATGTAGACATGGCCACGGACACCGATG\nACCACAGTCCCGTATGTAGATGATTCGCCACCACAAGTTCCAGCATTAATGATACAAATAGGATACATAT\nCGCCATCAACGCAGCCATCAAATTCACGAACACTGCGCGCGTAGGCCCCGCAAGGCGATATAAAAAGACG\nCTCTGCTGTCGTAAATTTGCGACCGCTTTTATGTTCGTTTCGTCCAATTTTCCGCGTCCACAAAAATACG\nTTGTAAATATTACACTTGTCGCAAAATGTCCAAGATATAATGTAGCAGCCACGCCGATTTGCTTGTAAGC\nTAATAATAACACAACGGCGTTTAATAACCACAATGACAAAAGACCCCAAAAAAGTGTTGTGGGATCTACA\nACTAACCATGCAACACCGGAGCTTTGCCGGACACGTTGATTTTTCGTTTCTCGGTGTATAATCGCGGCCG\nTGATCAGTGTATATACCGCCATGGCCATTGCCGTTAAAGCCGTGTAGTAAGTAAATGCCACAACGCTATG\nTGGTTCCAAAAACAAAACCGGGGCGCTGTATCCACCTCTATTTCCGGACCATACCCCCCCATCTAGGGTG\nGCGTTAAATAACTCATAATCAACTACGGCAGCATAAAAACAAGGGATCCCGGTATATTCAGAAGAGGCGG\nCAATTAACGTAGCCAGGAGCATTACCGCACCCAAAGTGAACATCATCACCTGAATTATCCAAATTCGCCA\nATTAAGCGTATCCATTTGATGATCTAACGCTTCCACCTCGGGTGTCGTGGTGTCGTACGGCGAGACTTTT\nTCAGAACGCGGCCCCTTCTTTTGAGTTCCCATGTCTCCCAACACCGGGGAGAGCAACGCCGCCGTCTATG\nCGTCCAGTACACAGCTCGCGCGGGCGTTATATGGAGGGGATCTGGTTTCGTGGATTAAACACACCCACCC\nGGGAATTAGCCTGGAACTGCAATTGGATGTTCCAGTAAAACTAATAAAACCTGGTATGTCACAAACTCGC\nCCGGTAACCGTCGTACGTGCCCCTATGGGCTCTGGTAAAACAACAGCCTTGCTTGAGTGGCTTCAACACG\nCGTTAAAGGCAGATATTAGCGTACTGGTTGTCTCATGTCGCCGTAGCTTTACCCAGACGTTGATTCAACG\nGTTTAACGATGCAGGCCTCTCCGGATTCGTAACATATTTGACATCCGAGACATATATTATGGGTTTTAAA\nCGTTTGATTGTGCAACTTGAAAGCCTACACCGCGTATCCAGCGAAGCTATCGACAGCTACGACGTATTAA\nTACTGGATGAGGTAATGTCAGTGATTGGACAATTATACTCCCCCACAATGAGACGTCTTTCCGCGGTTGA\nTAGCCTATTATATCGTCTTTTAAATCGCTGTTCTCAAATTATCGCGATGGATGCTACAGTAAACTCGCAG\nTTTATTGATTTAATCTCCGGATTGCGTGGAGATGAAAACATACACACAATTGTGTGTACATACGCGGGAG\nTTGGGTTCTCCGGAAGAACTTGCACGATCCTGCGTGATATGGGCATCGACACGCTTGTGCGAGTCATTAA\nACGATCTCCTGAACACGAGGATGTACGTACCATACACCAACTACGTGGAACATTTTTTGACGAACTAGCA\nCTACGATTACAATGTGGGCATAACATCTGTATATTTTCATCAACTTTATCGTTTTCGGAGCTAGTTGCTC\nAGTTTTGTGCAATATTTACAGACTCTATTCTTATTTTAAACTCAACTCGGCCCCTATGTAATGTAAACGA\nATGGAAACATTTTCGCGTGTTGGTGTACACTACCGTCGTGACCGTTGGATTGAGTTTTGACATGGCTCAT\nTTTCATAGCATGTTTGCTTACATAAAGCCAATGTCATATGGGCCGGATATGGTATCGGTCTACCAGTCAT\nTAGGGCGTGTACGTTTATTGCTACTTAATGAAGTTTTGATGTACGTCGATGGCTCAAGGACCAGATGCGG\nACCCCTGTTCTCGCCAATGTTACTAAACTTTACCATCGCAAATAAATTTCAATGGTTTCCTACACACACC\nCAAATAACTAACAAACTGTGCTGTGCATTTAGGCAACGATGTGCAAATGCATTTACACGCTCGAACACCC\nATCTCTTCTCAAGATTTAAATACAAACACCTTTTCGAGAGATGCTCTCTTTGGAGTTTAGCCGATAGCAT\nTAATATCTTACAAACTCTTTTGGCCTCTAACCAAATTTTGGTTGTATTGGATGGCATGGGTCCAATAACG\nGACGTTTCCCCAGTTCAATTTTGTGCATTTATACACGATCTCAGACATAGCGCTAACGCCGTAGCTTCCT\nGTATGCGTTCTCTTAGACAGGACAATGACAGCTGCTTGACCGATTTTGGCCCTTCCGGATTTATGGCCGA\nTAACATTACCGCGTTTATGGAAAAGTATCTTATGGAGTCAATTAATACCGAAGAACAAATTAAAGTATTT\nAAAGCCCTTGCATGTCCAATAGAACAGCCTAGACTAGTCAATACGGCAATATTGGGGGCGTGTATACGAA\nTACCTGAAGCGTTGGAAGCATTTGACGTATTTCAAAAAATATACACGCACTACGCTTCCGGTTGGTTTCC\nCGTCCTGGACAAAACCGGGGAATTTAGCATCGCGACTATAACTACCGCCCCAAATTTAACCACACATTGG\nGAGCTGTTTCGCCGTTGTGCCTATATTGCAAAAACACTCAAGTGGAATCCGTCCACCGAAGGCTGTGTAA\nCACAAGTTTTGGATACGGACATTAATACACTTTTCAATCAACACGGGGATTCGCTGGCTCAACTAATATT\nTGAGGTTATGCGCTGTAACGTTACTGACGCTAAGATTATATTAAACCGCCCGGTTTGGCGAACAACCGGA\nTTCTTAGATGGATGCCATAATCAATGCTTCCGTCCAATCCCTACAAAACACGAATATAACATTGCTCTAT\nTTCGTTTAATTTGGGAACAATTATTTGGCGCCCGCGTAACTAAAAGTACCCAGACCTTTCCGGGAAGTAC\nTCGTGTGAAAAACCTAAAAAAAAAAGATCTAGAAACTTTACTTGATTCAATTAACGTGGATCGTTCTGCA\nTGTCGTACCTACCGCCAGTTGTATAACCTGCTTATGAGCCAGCGCCATTCGTTCTCTCAACAGCGTTACA\nAAATTACTGCCCCCGCTTGGGCACGCCACGTGTATTTTCAAGCACATCAAATGCACTTGGCCCCGCATGC\nCGAAGCCATGCTACAATTAGCGCTATCGGAACTGTCCCCGGGATCGTGGCCGCGGATAAACGGGGCGGTA\nAATTTTGAAAGTTTATAACCCGTTAATACCATATATGGACATCCATAGGGGGGGTTACATAAATACTAAG\nCCTCTGTACAACACAAAGGGCCTCTAACAATGCACTGAACCACAACCAAGCTATGGACGCAACGCAGATT\nACCTTGGTTAGAGAAAGCGGACACATTTGTGCCGCAAGCATATACACATCCTGGACACAGTCCGGACAAT\nTAACACAGAACGGTCTTTCCGTGTTATACTACTTATTATGCAAAAACTCATGTGGGAAATACGTCCCTAA\nGTTTGCCGAAATTACCGTACAACAAGAGGATTTATGTCGCTACTCCAGGCATGGGGGGAGTGTTTCTGCG\nGCAACGTTTGCGTCTATCTGCAGGGCGGCGTCCTCGGCTGCGTTAGACGCCTGGCCCCTTGAACCACTGG\nGTAACGCAGACACCTGGCGTTGTCTCCATGGCACTGCCCTGGCCACTTTACGGCGCGTATTAGGGTTTAA\nATCGTTTTATTCGCCAGTAACATTCGAGACTGATACGAATACAGGTCTTCTGTTAAAAACAATCCCCGAT\nGAACACGCGTTGAATAATGACAACACGCCATCTACCGGAGTATTGAGGGCTAATTTTCCCGTGGCCATTG\nATGTTTCAGCAGTCAGCGCATGTAACGCCCACACGCAAGGTACGTCGCTAGCCTACGCCCGCCTGACCGC\nACTTAAATCTAACGGTGACACCCAGCAACAAACACCTTTAGACGTGGAGGTAATTACACCAAAGGCCTAC\nATACGTCGGAAATATAAGTCTACGTTTTCCCCCCCTATAGAGCGGGAAGGCCAAACCTCCGATTTGTTTA\nACCTTGAAGAACGCCGCTTGGTTCTTAGTGGCAATCGCGCAATTGTGGTAAGGGTACTCTTACCGTGTTA\nTTTTGACTGTTTAACAACGGATTCCACCGTTACATCTTCCCTTTCAATATTAGCAACATATAGACTGTGG\nTACGCGGCGGCGTTTGGAAAACCCGGGGTTGTCCGTCCAATCTTTGCGTATTTAGGCCCGGAACTCAATC\nCGAAGGGTGAAGACAGAGACTACTTTTGTACTGTCGGATTTCCCGGATGGACCACTCTTCGGACACAAAC\nTCCAGCCGTCGAATCTATTCGCACGGCTACGGAGATGTACATGGAAACGGATGGGTTGTGGCCAGTAACC\nGGTATTCAGGCCTTTCATTATCTAGCCCCCTGGGGACAGCATCCCCCCTTACCTCCGCGGGTGCAGGATC\nTTATTGGGCAAATCCCTCAAGATACTGGACATGCAGATGCAACTGTCAATTGGGACGCGGGCCGGATATC\nTACCGTCTTCAAACAGCCTGTACAACTACAAGATCGTTGGATGGCAAAGTTTGATTTCAGCGCCTTTTTT\nCCCACGATATACTGCGCTATGTTCCCCATGCATTTTAGATTAGGCAAAATCGTCCTGGCTAGAATGCGTC\nGAGGAATGGGGTGCCTAAAACCCGCGTTGGTGTCTTTTTTTGGGGGGTTACGGCACATACTCCCGAGTAT\nATACAAAGCTATTATTTTTATAGCCAATGAAATTAGCCTTTGCGTCGAACAAACGGCCTTGGAACAGGGC\nTTTGCTATATGTACTTATATAAAAGATGGATTTTGGGGAATCTTCACCGATTTACATACGCGCAATGTAT\nGTTCAGATCAGGCACGTTGTTCGGCCTTAAATTTAGCGGCCACCTGCGAAAGAGCAGTCACGGGCTTATT\nACGAATTCAACTAGGTCTTAACTTTACACCCGCCATGGAACCGGTACTCCGGGTCGAGGGTGTGTACACT\nCACGCATTTACCTGGTGTACCACGGGAAGCTGGCTGTGGAATTTACAAACAAACACGCCTCCGGATTTAG\nTTGGCGTGCCATGGCGAAGTCAGGCGGCGCGAGATTTAAAGGAGCGTCTTTCAGGACTCCTATGTACCGC\nAACAAAAATTCGAGAACGGATACAGGAAAATTGCATATGGGACCATGTCCTATACGACATATGGGCCGGA\nCAAGTTGTGGAGGCTGCCAGAAAAACATACGTCGATTTTTTTGAACATGTTTTTGATCGCCGTTATACTC\nCGGTATACTGGAGTCTTCAGGAGCAAAATTCGGAAACAAAAGCAATACCGGCATCTTATCTGACATACGG\nACACATGCAAGATAAGGATTATAAACCAAGACAGATAATTATGGTTCGTAATCCCAACCCACATGGACCT\nCCTACTGTTGTTTACTGGGAATTGCTACCATCGTGTGCCTGTATTCCCCCCATAGACTGCGCTGCTCATC\nTCAAGCCCCTTATACACACGTTTGTCACTATTATTAACCATCTTCTAGATGCTCATAATGATTTTTCAAG\nTCCATCATTGAAATTTACTGACGATCCCCTTGCTTCATATAACTTCTTGTTTTTATGACAAAAAAACACG\nCCGCAACAACCCATCCTTAAAATAAAAGGTTTATTTACTTTACAACCCGTGGTGAATTTTTATACGTTTC\nAAATAACTGAACATTTTTCGGTGTTACCATGGTGCGATTTAACCACCAAAAATATACGCTCTTCTGATAT\nTCCGAATCTCGTAAAGGTCCATTTAACAATCCCGGGGGTACTTGCACCACACCATCTGGACAGGGGGGGG\nTTCCGTGGGGCAGGTCAAAACGCTGACCCACCCCACATGAATATATAGCCTTTATAATATTGGGGGCCGT\nTCCAGGCTGAGGGTTCAGTAACTTAACAAACATATAATGCGGCAATACGCGGGTTTTTGTAAAGGGGTTG\nTTATCAACGACATACATTAGAGTGTTTAACAACCATAAAACTCCCTCATATAAAAACCGACGCATTTTTT\nCCAAAGGTCCTATTTGACACTCAACGCGTCTAAGATATACAGACAATTGTACAAACAGCGATGGAGATGC\nCCCGGAGGGCCCAATGCCTTCCAGATACATTAAAATAACACATAAGGTAAAATCTAGGACATTATCCGGG\nCGGAATAGAGTCATCCGATAGATTAACAGGCGCGGAGGCACCCCCACCGTATACACCCTATCTTCAACCG\nCAGTTAATACGGAAAAAATAAATCCGCGGAACGCTGGTTGAGTAACACACTCCATGTAGTAACGATCACA\nGGACACCTCACTTGAATCACCATTCAACACTACTAAAACGGTCTCTTGGTGTTCCGGTTTTACGCGCAGT\nGATACAACAGAGTTTGCCAAAAAGCGTGGCTTCAAACCGGTTACCTCCCGCGCCTCGCATACGAATCTTG\nGTATTGCTTGTATTCTAAGATCTTCGATCACGTCGCTCACATCCAACCCCTCTTCGGCTCGTGTTAGTAA\nGTTGTCGATCGTTACGCTGCAACCTAAAATGCTGGGTATATTTATTCCGGACATCCCATCGGCCATCCCC\nGCGCCTCCGGTTTGCTCGAATTTTATCCAGTAAGGTCGAATCCGCTGCATTTACCTTGTGTACCCGTAAC\nCTCTCAGGGGGGTGTCCTTTCATAAAATGGGATAGGTTTTTATATCCAACATGCATGTATTGGTTATTTA\nTTTTATTGGGTTCCGGGATTCTTTCGTCATCTTCTGTAGGGTCAGGCAAACCCCAGGAAGGACTTGGTGT\nTCTCCGTGGGCCCCGTTTTATTACCTCTGCGCGAACCTGCATTTCATATAATATTCGGATTTGGGATAAA\nTAGGACTCTGTTCTCGCCTTTTTAAAAATAGCCTGGCATAACTCTTCCTCTGACCTATGTACCTCGCTTT\nGAGTTACCAAGAATCCTAATCGGGTGGCCCGTAATATGAATGAAAAATACGGCGCAACTAGTAATGAGAT\nTGACGCATTTGAATATGATACAGAAATTTCCTGGCCTTGATTATTGTTTACCCGGTGAAGCTTAAAACAG\nCGAACAAGTTCCTGTTTCCATAGCTCAGACAAACGTTTTATATCATCTCCATAAGGGGGGATATAACGAG\nATTGAAAACTATTGGCAATATATGCATCATCCCCTATTATGCCGGTAAGATCTATAACCTCGTGATTTAA\nATCGGCAATACGTGTTTCTTCTGCCATTGTAATATGTGACCCTTTAGATGGCTTTATTTTTACCCTCTCT\nTCCCGTAACCGTTTCAGCTCTCCTTCTTTGAACTGGAGCCTTTCGGTCAGATCGCTGTTCACATCCTTGA\nGACCCTCAATGGTTTTGAATAAATTATTCACATAACCCTCGAGCATGCCGTTGATACTGTTAACCACCGA\nAGTTTTAAACGCACTTTGAACGTTTGTTGTTCCGGACATTGCCCCCCCGTTAAAGGATTGGTTGGCCTTG\nCCAAACCCCGGTTGTGATGTGTCCACCGATCCACTTCCTTCCAGAATGTGATTGCCCGTTTCTTCTAGAT\nAGGAACGTACGGTTTCGGTAATATCTCCAACATGTCTCATGTTTTTTAAGTTAACTATTAGCTTTACAAG\nTCTAGACGCGGCCGATCCAGCCCGTGTTGTATCGTTCTCGCCCATTATACGATCAACCGCACGTGTGCTG\nTGAGATCTATCATCTTCATTCCGGCGACCTATTAACACGCGCAAAGGGGCTGTATTTAAAACTTGGCAGA\nCGCGAGCATGTTCACGTAATGCATAACAGGCCAACACCTCCCCAGAAAGCCGCTGTAAGGGTGAGTCAAA\nTACTACACCCTCCCCACATACAACGGGCGGCCACACGACCAAACACTCTCCCTTCATGCCCGTTACATCA\nTCCTTTGCCATAATTAATCTTCGGTTATAATTATAATAAAGACGCGTCCTATCATAATCCATAATAGCAA\nCATTTTGCATACACTCAACTAGGCTTGTGACAACCGCCGCTCCTCTGGCCAACGTTGCATCGGCAACTTT\nTAACATCTGGGACAGTTCTGCCGCTTGACCCATATACGTATTTAATGGTGCAGGGGTTCCATTCTGTTCT\nGATCGTACCTTTCTTACAACGGGCACAATACCTACACAGGCTATCCAGTCCACGTATTTGGCAAAACCGA\nCCCTTCCATTTAAACCACTGGTATAGAGACAACCGGTTATTCCACGCAGAAACTCAAGTAACGATGACTG\nTAATGTTTGACGCCAGGTTTCAAAAACCTGATGTGCAAGCCGTACGGCTTCTGATTCTCCACATAGCCCA\nTAACGTTCCGCTAGAGCCCCGGCATGCAGGTTACATTGTTGGATGTGGTGTTCCCAATCTGCTGCTAGGT\nCCTCATACCGAGTTGCATCCAACGCGTTCATCAAAACGGTTGCCTGAACTTGGCGAATTACAGTTTCCGT\nAGACCGTACAGCGCTATATATGCCTTGTCCATCGGTATATCCAAAGTCACCGGCTAGGATTTTTCGAAAC\nAACATACTTTGCGTGGTTGGGTGTATTAACATCCAGCCATCTTCCTCCGGAAATGTACAAAACCCTATAT\nCCGGGGCGTACTCATTCCAGTATATATCGAACATGTTCTTGTATTGGTCATTTGGGTTACTTCCATTCAA\nGCCCTGGTCAATAGAAACAGAACTTGCTATCCTTTTTTCTTCACTACCGGAACTGTTATTAAAAAGAGAC\nGTTATTTCGGCCATTGAAAACCACGATGAAAAGATCAATTTCTGTAGACAGTTCTTCACCCAAAAACGTT\nTTTAATCCAGAGACGCCCAATGGATTTGATGACAGTGTATATTTAAACTTCACCTCTATGCATAGCATTC\nAACCTATCCTCTCACGGATTCGAGAACTTGCCGCAATTACGATTCCAAAAGAACGTGTTCCGCGGTTGTG\nTTGGTTTAAACAGTTACTCGAACTGCAAGCGCCTCCTGAAATGCAGAGGAATGAGCTCCCCTTCTCCGTT\nTATTTAATTAGCGGAAATGCCGGCTCCGGAAAAAGCACGTGTATCCAAACGCTTAACGAAGCTATCGATT\nGCATTATTACCGGATCCACCAGGGTTGCTGCCCAAAATGTTCATGCTAAGTTATCAACGGCTTATGCGAG\nTCGTCCGATAAACACAATCTTTCATGAATTTGGTTTTCGCGGAAATCACATTCAGGCTCAGCTGGGCCGT\nTACGCATATAACTGGACTACGACCCCCCCTTCTATTGAGGACCTGCAAAAAAGAGATATTGTATACTACT\nGGGAAGTTTTAATTGATATAACAAAACGAGTGTTTCAAATGGGGGACGACGGTCGCGGAGGAACATCGAC\nATTTAAAACCCTGTGGGCAATTGAACGTTTGCTTAATAAACCTACAGGCTCAATGTCCGGAACCGCGTTT\nATCGCATGCGGTTCCCTTCCGGCTTTTACCCGGAGCAACGTTATTGTTATTGATGAAGCAGGATTGCTAG\nGGCGTCATATTCTCACGGCCGTTGTTTACTGTTGGTGGCTTTTGAATGCTATATATCAAAGCCCTCAGTA\nCATAAACGGTCGAAAACCGGTCATAGTATGCGTCGGTTCGCCCACCCAAACTGACTCGTTAGAATCTCAT\nTTTCAACATGACATGCAGCGTTCACACGTAACTCCTAGTGAAAATATACTCACGTATATAATCTGCAATC\nAAACTCTGCGTCAATATACTAACATCTCACATAACTGGGCAATCTTTATTAATAACAAACGATGTCAAGA\nGGACGATTTTGGAAATCTTTTAAAAACGCTTGAGTACGGGCTACCTATTACCGAAGCACATGCGCGTCTG\nGTCGATACATTTGTTGTACCTGCATCCTATATTAACAATCCTGCTAATCTTCCCGGATGGACGCGTCTGT\nATTCGTCGCATAAGGAGGTGAGCGCGTATATGAGTAAGTTACACGCGCATTTAAAACTATCGAAAAATGA\nCCATTTTTCTGTGTTTGCCTTACCGACTTATACATTCATCCGGCTAACGGCATTTGATGAATACCGCAAA\nTTAACGGGACAACCCGGACTTTCTGTTGAACATTGGATACGGGCAAACTCCGGTCGTTTGCACAATTATT\nCCCAAAGCCGAGATCATGACATGGGAACAGTTAAATACGAAACACATTCAAATCGCGACTTAATTGTAGC\nCCGTACAGACATCACTTACGTGCTAAATAGTCTCGTAGTTGTAACCACAAGACTACGTAAGTTAGTTATT\nGGATTCAGTGGTACATTTCAATCGTTTGCAAAGGTTTTACGTGACGACTCCTTTGTGAAGGCTCGAGGAG\nAGACATCCATCGAATATGCTTACCGGTTTCTGTCAAACCTAATCTTTGGAGGCTTGATTAACTTTTACAA\nTTTTTTGTTAAATAAAAACCTACATCCCGATAAGGTATCGTTAGCATACAAACGGTTAGCTGCCTTAACC\nCTGGAGTTATTGTCTGGAACAAACAAAGCCCCCTTACACGAAGCAGCGGTTAATGGGGCGGGTGCCGGGA\nTTGACTGTGATGGTGCAGCTACTTCTGCCGATAAAGCCTTCTGCTTTACCAAAGCCCCCGAGTCCAAAGT\nAACGGCCTCCATACCCGAAGACCCGGATGATGTAATTTTTACGGCACTTAACGACGAGGTTATTGACTTG\nGTATACTGCCAGTACGAATTTTCCTATCCCAAATCATCCAATGAGGTCCATGCTCAGTTTCTGTTAATGA\nAAGCTATTTACGATGGTCGATATGCCATATTAGCAGAGCTTTTCGAAAGCAGCTTTACAACCGCCCCCTT\nTAGCGCGTATGTCGATAATGTTAATTTCAACGGAAGCGAGCTTTTGATCGGCAATGTGCGGGGGGGGCTG\nTTATCTTTGGCATTACAAACAGATACGTATACCCTTTTGGGGTATACTTTTGCACCCGTGCCAGTCTTTG\nTAGAGGAACTGACCCGAAAAAAGCTGTACCGCGAAACTACCGAAATGTTATATGCTCTACACGTACCTCT\nTATGGTCTTACAGGATCAACATGGGTTTGTGTCCATCGTAAACGCTAACGTATGTGAATTTACCGAGTCT\nATAGAGGATGCAGAATTGGCAATGGCCACCACGGTGGACTATGGCCTTAGTTCTAAACTAGCCATGACAA\nTTGCACGCTCACAGGGTCTGAGTTTAGAGAAGGTAGCTATCTGTTTTACGGCGGATAAACTGCGCCTAAA\nTAGTGTGTATGTTGCCATGTCGCGTACGGTCTCCTCTAGGTTCTTAAAAATGAATCTAAACCCTCTACGG\nGAACGATATGAAAAATCCGCAGAAATTAGCGATCACATTCTTGCCGCTCTACGTGATCCCAACGTACACG\nTTGTGTATTAAAGCATTGTATAAAAACACGCATGCGGGCTTGCTGTTCTCATTTCTAGGTTTTGTCTTAA\nATACACCCGCCATGAGCATCTCTGGACCCCCAACGACGTTTATTTTATATAGGTTACATGGGGTTAGGCG\nGGTTCTTCACTGGACTTTACCGGATCATGAACAAACACTCTACGCATTTACGGGTGGGTCAAGATCAATG\nGCGGTGAAGACGGACGCTCGATGTGATACAATGAGCGGTGGTATGATCGTCCTTCAACACACCCATACAG\nTGACCCTGCTAACCATAGACTGTTCTACTGACTTTTCATCATACGCATTTACGCACCGGGATTTCCACTT\nACAGGACAAACCCCACGCAACATTTGCGATGCCGTTTATGTCCTGGGTCGGTTCTGACCCAACATCTCAG\nCTGTACAGTAATGTGGGGGGGGTACTATCCGTAATAACGGAAGATGACCTATCCATGTGTATCTCAATTG\nTTATATACGGTTTACGGGTAAACAGACCTGACGATCAGACCACACCAACACCAACCCCGCACCAGTATAC\nATCGCAAAGGCGGCAGCCTGAAACCAACTGTCCTTCTTCACCACAACCGGCCTTTTTCACATCAGACGAC\nGACGTTCTTTCGTTAATATTACGGGACGCCGCAAACGCGTAAAGACAGATTCAAGACTAACATTTATCCC\nAACTGATTACATTTCATACGCGAATAAACGACACAAAAAATTTATATTTAACGGCTTTTAATTTGAAGAC\nACCTATCCTCTTAACGTTGATGAGCCTTGCAGGTTGGGTGCCGCGCTTCACCGGTATTATACATAACCGA\nTTTACCGTGTTTACGGCAGTCTGACCATTTACCAGTGTATGTCTGTAATACGACGTTGTTGTGTCCCGAC\nAAAATTAACTCGCGTACAAATTTCTGATGTTCCCCCGGCGTGGCAACGCTGGCATTTCCAAACACATTAC\nGTTCTCGTACGTCCATGACCGCTATTTTCAGTATTAATTGGTTGGTCGGTCAAAGTATTTTCCTTATGTA\nAAAGGACACGATCTAAAGCCGTAAACTCATACACAAACACTGGTACCAACGGACGCGATTTTCCGTCCGT\nTGAGCGGGTGTAATATCGGCGAGGTCTTCTTGCACGAATACTCTCGTACAGTAGGTTTCTGACACGGGGT\nGCATGGGTTTTTTGACACAACACAAACATTTGCAGGCTCTTATGACTGGATGGATTGAATTTATTTTTAG\nATAGGGTCACGTGTTTTTGTCGTGACACGCCTCGACCAGAAAAGGCTGCGGTTTTCGTACACGCGACCGT\nTATTTCACAGGCGTTCATAACCAAGCTGCGGCGGATGGTGTCGGTTAATTGTCTCCGCCCAAGTTCGTCA\nATAGATGATACCATGAACAACGTATCAAATGGTACATAGTCGTCTTTGGTTTTCTCAATACAGCCCGCGT\nGCCCAATCGGAAATTTTTCATTTGCATCAACGCTATTTTCTGTAAAATCGTTCTGAACACTGTGTTGGCT\nGGCTACCTGTTTAAAATTTGGGATCGAACACGGTCCACGATGCAATCCCCAACCCCATTGAAGCAATGCC\nGTCGGTACGGAAGGAGGCAACTCCGAAAACATTATGGTACGCAAGAGGGTCGATTGGAGTGTTATATAAC\nACTCCAATCGATCTCGGGTTCGCCTTTACGCGTAAAATACTCATTGGCTTGAACGAAATGTCGACAATTC\nCGAAATGGAACACGGGACAATGGCGACGGATGCGCGTGTGTTAGCACCAGATGACATCTTGAATTCGGTT\nGGGTTGTCTTCTGTGCATGCGCACCCCACAGCATAAAAACTAACCCTGTACGGTTCTCGCATAACCTCTG\nTAGCACGCGTTGCACCAGCCGCCCCCAGCCTAAGTATACATGCGACCCCGGAGTCCCGCGACGAACCGTA\nAGCGTGGTATTCAGCAATAACACCCCCTGCCTTGCCCAACTCTCCAGGCATCCGTGAGTGGGCGGAGTCA\nTATTTGGGTATGATTCCATGAGGGCCGCAAAAATATTTTTAAGACTAGACGGTGGTGTTATGCCACGTTT\nTACACTAAACGCTAGCCCATGTGCATGTCCCGCGGTAGGGTATGGATCTTGACCAATAATTACAACGCGA\nATGCTCTGGGGTCCGCAAAATCGCGTCCATGCAAAAATATCGCCTGTAGATGGAAGTATTTCTTCCCCTG\nAATTTAAAAGACGATTGTATTCTAAAAAAATACCTTTCGCGTACGGCTCTTTAAGTTCGTCCGACAACAG\nGTCATACCACTCAGGGGAAATGTTAAACTTGCTGAAAACTTCAACCGAATCCAGTTGCGAAGAGACGGGG\nGTGAACGTTTCCGTGTCGTAATGATGTGACATGTTATTTAACTTGAAGGTTGGGGGGTCTAGCTTAACCC\nCCAAAGGCAGCCCGCGGGGTCGCTTGCGGGTTTTTTTGGTAACCGGATGGGCCAAAACATAAATGTCCTT\nTGAATCCGATAGTTTCATTTCATTGGCATACGCGTTGGAACAAACGGTCGGCTCCCCAGACACATCCATT\nTTCCGGGATATTTGTGGAAGATGGAGTAGAGTCTACCCATACACCGGAAAGGGCATCCAACAAAGCATCG\nCGTATGTCCCCGCTTTTATGTTCTTCACCAACAGATTGTGCCAGCCCCTTTAAGGTGACGTATGGATTTG\nTCCAGTACGCCATTTGTTTGTCTTTAAACCAAAGTATAACTTCCGGTACTGGACATTTTGTCTTAACCAC\nGATTCCCGATAGCGCCTCGCTGAGGTTTGATACCGGGGGTGCCGCATAGTCCCACGCCTCATATACCGAT\nGACACGCACGGTTCCGTTATAATCAAACTCACATCCGATAGCGGTTTGGCTCCAAAAAACAACGGAGTGT\nCGTCTTGGAGATGAAGACAATACGCGATTGTGATAGTTTTTAAAAAAACTATCTGCAGTAACCATTTATG\nTGATGCCATGACGCTTGTGTTTTCCCTTCACTACGACGTTGTCGTATCCTTTGAAAAACTTGACCACTCT\nAATGGAAGCATGGACAAGTATGAGTTTTATATATACAGTTGGCCTTTAGTTAAACTCTTGGTGTCATATC\nTCATTTTCCTAAAAAGGGCGATCTTAATATGTCAAACGTCACGGCGTGCCGACAAAGCGAATTTCCATGC\nAAGATTTGGATGTAGTATTTATACACCCAATCACATGTCACGTATTAAGCTTTACAGTCCCCCGTTATCT\nGATATAATCACTTTTCTTAACACGTCATCGGGAAAACAGATGTTTATATTATACCTCTCGCGGTCATTTA\nCGGCAAATACTTAGACCGTTTTCAAGCGGACTGAAAACGCTCAAATTGCCTTTTGGAGGCCTGCCCAACG\nGCCATTATCCCTTGGATCTAAGATTGATTTGCGGTAACGTTTGCCAATCAAGCTTTAAAAACGTACCCCA\nAACTTAAAACGCTCAAATTGCCTTTTGGAGGCCTGCCCAACGGCCATTATCCCTTGGATCTGAGATTGAT\nTTACGGTAACGTTTGCCAAACCCACGCATTTCAGTTTAAATATTTCTAAGCATTCTTAGTGCGTACTTGG\nCAGCGTGCTTAAAATATCAACCAATATCCATTATGCTACACGTTTCCTTCTATCCGTTTCAATCCATTAA\nAAGTCCATTAACAAAAATGATGCATCATACCTAATTCACCTAAAAACCTGACTCATTGCAGCAGCGTTTC\nCTCCTTGCAGACTATCCAGTTGGCATTTTAAACGGGTCCGGCTGCCTAAACCGAAAACACCGTTGCCTTT\nACTGTAAGTACAAAACTAAAATTTATATTTGCGTGCGTATTTTGTAACATATATGCCTTTTATCCCCCCG\nCAAGTTTGCTTTACCCTCGCCTTCACCACCCCCGCCACCTTCCGGCCATTTTAATAACTTTAATTGCTAT\nAAGACATACCCAAACCGGATGATTTTTGCCGCTGGAAAAACAGCTTCTAATTTTCCCGTCTCAACTCGGC\nCTTGGTTGCATCTCCAAGTATACCTTTAGTTTGCTCCCGTAGAGGTGTATAAATACAAACGGTGACAAGT\nATTGAGCGTAATCTCAAATTTTTGTAATTTAGGGCGGAGCGCTTACGACAGCACATGCGTACTGTTAGAC\nTGTTATGTTTATTGTATTTGCAGAGCAGGATGCCCCGGTTACTCCGAGACCGGATTGCGGGCATTCCGAA\nTCGTGTACGGACTTACCAGGGGGCAGTATTTACACCTTGGGTTCCAGATATACCAACCCTTACGACCAAT\nAGCAACACTCAGGTATTTTTAAAATGCACGTTTAATGATCATAATTTACATACAGTTGGTAATAAAGCAG\nACTGTGGATGTTTAAGGCATTTCCTTCCCCCTCCCAACAAACTAGGACTTCTTCATCTTGTTTGGAATAC\nCTTTACCCGCTTTACCGGCAGAGCTTTTTTTGGTAAGGTGTTTCAGTGAACCTGATGTTGATCCGGAGGT\nGGAGGGGGTATTGGACTCCCCCTGTGGAGAGGCAACTTTGCGGGTTTTACTTCCCTTACATGCCGAATCA\nGACTCAGATGTCAGGTCTATTGTTAAGCATCGTTTAACGTCTCTGCCGGTATGAAATAAACGGCGCTTAG\nCACCCCTTGCGCTTCCCGGTTTAATCCCCGGTAACACAGAAAAAAGCCTGACTTTTTGGGGTGTATTTAC\nCAATCGGGTATCCCTTTCATCGCCACGAGAGGTCTCCCCGGTTGAGGTGGTTTCTGGTCTTACAATTGGA\nCCTGTAATTAGTTGGATGGCTGTATCTTTCCAGGTCCAGGTTTGCATGGTTAGGCGGGTTGGATCGGTAC\nATCGATCCAACAAGAATAACATGTTTGTTACAAACGGTCCTGTTGAATCATGCAAAAGACAACGCAGGGA\nTGTTTTTAATCCCGCCTCATCACGCCCGTAAATACCTATATAGTTTAATATCAACATTTTTGTAGGCTCT\nACAATTTCGGGTTGATACAGTTCCGCAAGTTGATCATCAAGCCATCCGAGTAAAGGTTGCATGTAACACG\nGGAATCTCGCGTTTCCCTCTGTTCCTCTATCCGTGGCTCGAAAAGGCAGTCTGTCCATGGTTCGTGGGTC\nTTGATTAATTCCCACAGATACTGGACGATCACGGTAGTCCTGCCCCCCGGTCCGGGGTTGCTGTGCAGAT\nTCAATCGAGCCATACACCACCGGGGTCGCCGATCGAACAGCAGGTTGGTCTTTAAAAAATACCTTCCGTA\nAAAATGATGCGGTAGAGCATGTTTTGGTTACACCAGGGCTCGAGTCTCGGGTCGGTGGTTGTATAGAATC\nCTGTTGAGAGTCACTTGGTGACTCTGCTGTGGGCTCTCTAGCCGACGATTGAAGGGGCCCAGGGTTTGGT\nGATTGAATGGGCTCCCGACTCGATCTTGATGTTGGCTGTTGGATGGACTCCCGACTCGGTCCTGGGCTTG\nGTGGCAGAAGATCTATGACATCTCCCGGTAGGATGTCGATGGAATCTTCAAATGACGGCTCAGAAAAACC\nATCGTCGTCGGATGGGTGCACTTCATATTCCTTGTAACTTGTATCACTTACGATCTTATGCAGGATGGAT\nTGCACTGGACACCGGCAGAGAGGACACTGGACGCTGGTGGAGGTCCATGCCCGAATACAAACAAAGCAGA\nAGTCGTGCAAACACGGCATGGTTTTTCCGAGATCGGAAACGGTGCTCATGCATATGGTGCAGGTATTATC\nCGAAGCGTCGGAGGTGCCGCTACCGCCCGCTAATATGGTATCCATGGTAACAACTGGCTGTATTCTAATG\nTCCGGGCATCCAAACACGTAGCAGAACTGCCATGCGTTCTAAATTGTGAGTTGTGGCGAGTACATTTTTA\nTAATTGGTACCAACGAAGACACACCCCTATATCCCTCCACCCATTTCTTTTAAGTCCCACCCACTAAAAC\nGTGGGTATAAAATGTGTATTGGGGTAGGCGGACAGTCCCAACAAACAGGGAAGTTGATTGGTATAACCTT\nGGGCCGGGTATACAGCTAAGTGACATTTTAGATTCTGTCTTTATTTAGATAAAGAGCGATACGAAGACAT\nTTCTCCACCCCCCTGTAATACCCGTAAATAAAGGTAAGTCCACAAACAAAAGCACTGTATATAGGAAGTC\nGGGTGTATTGGGACAGTTACTCCATTAGAGGCGTACAAACAATACTGGGATAGGGTAATGCAAGTCCCCC\nCCGATGGTCGCCCCGCAAACGCGCGGGGAGGTGGGGTCGCTTTTTTTTTTCTCTCTCGAGGGGGCCGCGA\nGAGGGCTGGCCTCCTCTCCCGGGGTCCGCCGGGCGCCCAGAAACCGGGGGGGGGTTATTTTCGGGGGGGG\nGTCCGACCAGCCCGCCCGTCGCCCGCCCGCACAGACAGACAGACACTTTTTTCATAAAAACCGTTCCGCT\nTTTATTAACAACAAACAGTCCGCGCGCCAGTGGCGCTCACGAGAAAAGGAGGGGACTCCGTCACCCCCGA\nCTCTGCGGGGGGCTCCTCCCCCCGCGCCCTCCCCACACATCGTCCTCGTCCTCGGAGGACGAGGACGAGG\nACAACAGCTCCACCTTGACCGCCGGGCGCAAACCCACCCGGCGGTCTCGCAGCACACCCGGGGCCACCGA\nCACGATGCTCACCCCAAAGGATGACCCCGGTGCGTCCCCGTCGTCCCCGCCCCCCTCCTCGCTGTCCCAC\nGCGTCTTCACACCCCACCTCCCAATCGTCCAGCTCCAAAGCGTGTTCTCTGTCGTCTGCGGTGCGCCGCT\nGTCGCCCCGCCTGGGTTTCTGACGGCCGTTCCGAGCCCCCGTGGTGTCCGAACACGAACCGTGTTCCGTC\nGCTCCCCTCCAACACCGTCTCCGCGGCCCCAAAACCGGGCGGCCACATTACTCTGGGAATCGGGGGGAGG\nGCATTCCGAGCCTCGTCCGCCGACGCATACAGCGCCACCGACCGACCGGCCACGGGTGGAAGCACGAGTG\nGTTCTGCGGCAGGGTCGGGTTCCAGCAGGGCGTGGCGGCAAAACACCCTCGCCCAGGTGGGTACGTCGCC\nGGCCTCCGGCCCGGCGGCCCCCGGTCTCCGTCCCTCGGGAAGGAAGACGGGTCGAAGCGCGGCACCCAGG\nCCCCATCGGTTTGCTGCGCGGTGGCTATGTGCCGCCTCGTCCACAAAGTCGGCTGCCCCGAGCCCCAGAC\nCCCGAGACTGTCGCGCGAGGTCCTTGCAACCGTCAAAACCCGGCAGCACGTACTGCCGGTATTCACGGGG\nCGACAGGGGGACGCGGGTCTTGGGGCCCGCGCGGGTACACACGGTGTATGCGACGTTCCCACCGCGGCAC\nAAACACAGGGGTTGTTCGCCCGGGTACAGGTTGGCAAACGCAGTCTCGATACGAGCAAAACTCGCTGGCC\nCAAAGGTGCGCGACGATGCAAACACGGCCCGGGCGAGTCCTTCTGTGACCGCCGAGTCTGGCCATCGGAC\nGACGGCCTGGGCGTCCGGTCGCGCCGGGGCCCGGACGTACACGTGATACTGAGACAAAGCGGGTCCATCC\nCTGGGCCACCTCTCGAGGGCCACCGCGTCCAACACCAGCAACCGGCGCCGGGCAGAGGCCAACCGCGAGC\nCTAGATACTCGACGGCCCCGGCAAAGGCCAGGTCTCGGGTCGACAGTAATAAAACGCCCCGGGCGTTCAA\nAGCGGACACGTCCGGCGGGCCGGTCCAGTTCCCGGCCCAGGCATGAGTGCTCGGCAGGCACAACCGGTTA\nCTCAGGGCTGCCAGGACCACAGACAGTCCCCCTCGGGATGGACTCCATGACGGTCCCGGATCTGTCGCGA\nGGGTGCTCTCGAGGGGGCCGTTGATGTCCTCTCCGGGCAACGGATCGTAGATGATCAGAAGCCTCACATC\nCTCCGGGTCTGGGATCTGCCGCATCCAGGCGCACCTCCGTCGCAGCGCCTCCACTCCGCTGGGTGGACCA\nAACCGTCGGTCTCCTCCGCCCGGACGCCGAGCGGCGATTTCCGCCAAGGCGCCGGGATCAAAGCTTAGCG\nCAGGGCGCCAGGCCGTGGGAAACAATGGGTCGTCGACCAGACGGGCGATGGTTTCGGGGGTACAGTACGC\nCTTGCGAGCCTGGTCCGACGGGACCGGGGTATGCAGGGCCCCCCGGGGAATACGCCGAAATCCCCCGTTT\nGGGGCCGGTCCGTCAAGTGGCATCGTTATTACGGCGGGGGGATCCACCACAGGGCCCGAGGTGATGGTCA\nCGGGCTCGGATACCCGCCTCTTGGCCTTGGAAACCACATGATCGTCTGCAACCCGGGCGTCCGCGACGGG\nTGTCTCCCTAATCTTGTCGAGGAGGCTTCTGCTCTCGACTGGCTGGGACTTGCGCTTGCGCGGAGTTCGT\nAAACGATCATCCGGTGGACACACAGAAAGAGAGCGTGCGGCGGCCGACGGCTGAGGGTCGGGAGCCTGTG\nTGGCCGGGGTTGTTGGAGAAGGGTGACCGCGGGAGATCCGCGCCGCCGGACTGGAGCCCGTTGCCTCGGG\nGTATGCCATGCTGGCAAAGGCTCTGCGGAGACTCTGTAGGATAAAGTGTTTTTGGGCCCGGTCGTATCGA\nCGGCTCATAGCCACGGCCGCGGCCGCGTGGGGGAGAGCCCAGAGGGCCTCCCCCGTGGCCATGGCTTCGC\nCTACATGCGGAACGGGAGACGCTACGCTCCCCGTAACGGCGGTACCCGCCCGTCCCGGTGGCAACAGCTT\nTTGGTAGAACTGGTTCAGGGCCGAGTTGACACCGGTCAGCTTGGGGTTCTGGAGCCATGCTATAGGGTCT\nCTGTCTGGACAGTAGATCAGGTTAATCAGCGCGCGGTACTGTCTAGCCGGATCTCCCAACTCCGGCACGT\nAAAGCGGCACGGGTTCCGTTGAGGCCTCGTAACGAGCCCGCGCCGCTCTCACAGCCTCATCCTCCCAGTG\nACCCTCTCTGGTCTCCCCGGACGGTCCAAACCGCACCCTGTTGGATGGGAGGGGTGCCGATCCGGGCCAA\nGGGCTTCCGTCGGGCATCATGAGCGGCCCCGACACCGGGGGAATTATCGGGGTTCTGGATCGCGGCAGGG\nAAAATGATTTCTGTCTCTGGCGCCCCGGTTCCCCCGCAAGACGTTTGGTCTTACGAATCCTCGGATCGGG\nACCGCTGATGGATCGATATCCCGGTTGGATATTTTGTTTCGTCGACCCACCATCATTTGAGTCCGAATCA\nTCCGAATTTGACGGGGAAGGGGCGTGTTCGCGTCCGGACCTGCTGCCTGTAGTTTCACTTCCCACCGAAA\nCGCGCCGGGGTTCATCGTCTTCATCCTCCGATGACGATCCCCACGACGAGGAAGAGGATGAAGACGAAAC\nAAACTCACGACTCTTTGGCTTTTTCTCCACTGGGCTGTCATCCTCAATCGGGTCTGGTGCGTGGGATCTT\nCCCGGCAGGGCCAAAAACGCTCTAGGTTTGCCCCCCGACGAACGTCCAGGGACGCGAGGTGTTATACCCC\nGGGCATCATGTTTCCTTGGGCGGGTATCATCGGTCTCAAACGGCAGGTCCGCCTTTGCCCCCTTAGCGGG\nAACGCTGTCCGAAAGGACGTGGTACAATTGCTCAACCGGGCCGGGTACAGGTCCACCGGGTTTCCGCGCC\nGGGAGTGGGACCTTAACCTTCAAAGTCTTTTTCTTCGGGCTCTTTCCCTGAGCGGGCCGTTGAGTTTTCT\nGGAGAACTACTCCGTCCCCCGATGCATGCGCATGACCCGCTTGCTCATCGCCCGGCTTTTTACCCGAGAT\nGGACTGAGTTTGTCTGTCTCGATGGACCACCGACGGCAAACCTGGTGAATTTCCTCTCGTCGTTTGTCGG\nGGTATAGACCGCTGGTCTTCCCGTTGATCGTTCCCGGCGGCGTCTCCAACAGGAGACGCGGGGGATACAG\nGGGAGAAGGCCTGCGGGAACGGAGGGGTCGTACCTCTGCCCGTTTCCCCATCGTTCATCGGTGGTTTTGG\nAGACCTAGCAAGCTTCGTTCCGAGAGAGACTGTCTCAAGGGAGCGATCGGCTCCTGTTGGTTCTCGCGCG\nCCGGCCTCCGAGAATCGGGTGTGGAAGACCTCGGCCAGCGGGATTACAGGCGAGCCCATTAGATCCTGAC\nCGTCCTCGCATACGTAGTCGTCTTGTGTTAGCTCTTCGCCAACATCTTCCGTTCTGGGTTCTGGTTGAAG\nTCCCGATACGGAGGGAATTGAAACGATCTCGTGTTCCCGTCCCACCATGACCCCGTTCTCTCCAAATAGT\nAGATCGTCAGGCTGACTCGAGGTGACCACCCGGGCCCTGTGTTCGGCGGCCGCCGCGGCCGCGTCCAACA\nGGTCCATTAACTCCAAAGTATCAGGCGACCCCGCGCGTTGGGGTGTAGAGCGCTGCATCGGCGGCGTATC\nCATCGCACTGGGGTGAATTTAGACGTACCCGAGTTTTCCAAACGCTCTCGCAGCCTTCAAAGGATTGCGA\nTTGCGGTTGGTGAGGGAGTTCCAACAGTACTTAAAACGTGTTGTGCCCCCCCCTCGACCGCATATTTCCT\nCCCCGTGTCGTCACCGTGTAAATATTCTTAATGATAAGACGATGTAGTGATTGGACGAGACTCGAGGCGG\nGAAGTTCATGGACCATAGTATGCGTTTAAGGAGAGACCGCTGGTTGGCGATGTACGCCCGGTGTCTATTT\nCCGCATACCTTACAACATCATAACAAGGGATACCAGACATGTGAATTTCATTTACATATGTTTAAATAAC\nAACCAATCATCGTGTGTCTACAGACGATATATAATATACATAAACACAATTGGGGTTGTCTCACATGCAA\nAACATCTTATATAACACGGGTTGTTTCCACCCATCCGGCATCTAGTTAATCAAATGCACGTCGACGGTGT\nGTTTGGGTCCCTCTCCGTCGTCATTACGTTCGCGCAATCAACAAGCGTATACACCACCACCCCTCCCAAC\nGATTATGTCAGGCGGCACGAAGCCCGCGATAACCCATAAAATACACACGGGGTTGTGGTGTTCACGTAAC\nCCCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCGATGGGGA\nGGGGGCGCGGTACCCCGCCGATGGGGAGGGGGCGCGGTACCCCGCCGATGGGGAGGGGGCGCGGTACCCC\nGCCGATGTTTATAACCATAATTCTCTAAACCGTTGTAGAAAATCACAAAAAAATTTATTCAAAAACAAGT\nCGAAGAACTTCATATCTGAGGCATGTAAACCCGTTCGCACTTCCTGGGGTGGAATGGGGTGGGGTGGGGG\nGGTGAAAAAGGGGGGGGGTTAAATTGGGCGTCCGCATGTCTGTGGTGTACGCCAATCGGATACACTCTTT\nTGATCTGCATTCGCACTTCCCGTTTTTTCACTGTATGGGTTTTCATGTTTTGGCATGTGTCCAACCACCG\nTTCGCACTTTCTTTCTATATATATATATATATATATATATATATATAGAGAAAGAGAGAGAGTTTCTTGT\nTCGCGCGTGTTCCCGCGATGTCGCGGTTTTATGGGGTGTGGGCGGGCTTTTCACAGAATATATATATTCC\nAAATGGAGCGGCAGGCTTTTTAAAATCGATTTGACGTGATAAAAAAAAACACACGGGGCCCCCCCCTTTT\nTTTGGTGTTATAAAGGCAACCCAATCGAAGGTCTCCCGCCCCGGAATCCCCCATTGCCATTTTACCCAAG\nTAGCCTTATTCATAGATGTAAACGTTTGGGTGTGTGTTTTGTTGTGCAGGGTTCGTCCGATTCATAACGC\nGACAGCGTCGAGTCGGTTTTAAGGGAAAAGGTTACTACGGCCCCAAGGACATGTTTTGCACCTCACCGGC\nTACGCGGGGCGACTCGTCCGAGTCAAAACCCGGGGCATCGGTTGATGTTAACGGAAAGATGGAATATGGA\nTCTGCACCAGGACCCCTGAACGGCCGGGATACGTCGCGGGGCCCCGGCGCGTTTTGTACTCCGGGTTGGG\nAGATCCACCCGGCCAGGCTCGTTGAGGACATCAACCGTGTTTTTTTATGTATTGCACAGTCGTCGGGACG\nCGTCACGCGAGATTCACGAAGATTGCGGCGCATATGCCTCGACTTTTATCTAATGGGTCGCACCAGACAG\nCGTCCCACGTTAGCGTGCTGGGAGGAATTGTTACAGCTTCAACCCACCCAGACGCAGTGCTTACGCGCTA\nCTTTAATGGAAGTGTCCCATCGACCCCCTCGGGGGGAAGACGGGTTCATTGAGGCGCCGAATGTTCCTTT\nGCATAGGAGCGCACTGGAATGTGACGTATCTGATGATGGTGGTGAAGACGATAGCGACGATGATGGGTCT\nACGCCATCGGATGTAATTGAATTTCGGGATTCCGACGCGGAATCATCGGACGGGGAAGACTTTATAGTGG\nAAGAAGAATCAGAGGAGAGCACCGATTCTTGTGAACCAGACGGGGTACCCGGCGATTGTTATCGAGACGG\nGGATGGGTGCAACACCCCGTCCCCAAAGAGACCCCAGCGTGCCATCGAGCGATACGCGGGTGCAGAAACC\nGCGGAATATACAGCCGCGAAAGCGCTCACCGCGTTGGGCGAGGGGGGTGTAGATTGGAAGCGACGTCGAC\nACGAAGCCCCGCGCCGGCATGATATACCGCCCCCCCATGGCGTGTAGTCTTTATAAATAAATACAATGGT\nTTGGCTCGTGTCTTTTTTTGATGTCTGTCTGTGGGGGAGTGGGGTGTTGTGGATATTAGAGGGTAGAGGG\nTGCTGGTTTGAACGTCTCCATTAACCCACGGGGTCCCCACACGGGCCGTGTGGTATGAATCTCTGCGGAT\nCCCGCGGTGAGCACCCGGGCGGTGAATATGCCGGACTTTACTGCACACGACACGATACCCCCGCGCACCA\nGGCTCTCATGAACGACGCCGAACGGTACTTCGCCGCCGCGCTATGCGCCATATCTACCGAGGCCTACGAG\nGCTTTTATACACAGCCCCTCCGAGAGACCGTGCGCGAGTTTGTGGGGGAGGGCAAAGGACGCCTTCGGAC\nGGATGTGCGGGGAGCTCGCAGCGGATAGACAACGTCCACCCTCGGTTCCGCCGATCCGCAGAGCGGTGTT\nATCGTTATTACGCGAGCAATGCATGCCGGATCCACAATCGCATCTGGAGCTCAGCGAGCGGCTGATATTG\nATGGCATATTGGTGCTGTTTGGGACACGCCGGACTTCCGACTATTGGATTGTCGCCCGATAATAAATGCA\nTCCGCGCCGAATTATATGACCGCCCCGGGGGAATTTGTCACAGGCTTTTTGACGCGTACCTGGGCTGCGG\nGTCCCTTGGAGTCCCAAGAACCTACGAGAGATCCTGACACCCCATCCCTTTATATAGAAAAAAAAAATAA\nATTTAAAACATACACCGGATAAAAGCGTACTGTTTTTTATTTAAATTTACACGCTCGGCGTTGCCCCGGT\nTCGGTGATCACCGGGTCTTATCTATATACACCGTGTAACTCGAACCCCCGTGACTCCCTCCAATCGCGTT\nACCAAACTCTTCTTCCGTATCCGTAGATTCCGAGTCCTCGAAATCGTCCACTTATCCAACAAATTGTGAC\nGTTATATATCCCAAGGCAAAGGCCGCTCCCGTCATAGCAAATACAAAGACAATTATTAGCGTAATATAAC\nAGAATTTTTTACGATGATATATTTTATGTTGATATTTTCCAATTCGACGCAAAAATTCATCTGCCGTTTC\nATTTTCGCTATCACTATAATAACACTTTTCAGCCGAACGGCTCGGTTGTATGGCTGTTATCGTTGTATTA\nTTTGGTTGCGCTCGCGGGGTTACCACCGCTTCCATCAGTAAGGCCACGGCCTCACCCTCCATGGTGTTTT\nGTCCGGCCATAGAAATCCAGATTGTAAGGCCAGCAGGCTAGTTTAAAAGTGTTTAATACCACACCTTTTG\nATATTTATATACATGCAAGATTCTAGATTATTCATCAATAGGTCGTTTAAAGCGCGTTTTCATAAACGTT\nGTCAGCTATACCGACATTCTCACAAAGAGGTAAAGTTACCTTACGTTATTATTAAATAAAACATGTAGAC\nATTATTAATAATCCTAGGAACAATCAAATCCATATTTGTAAGTTATGTTTAACCCCTCCCCTTTTTGTCA\nTTATCTCCGCCCTCTTATAATCGGATCACTTTATAAGTGTGTCGGTGAGTATATTTTGTACAGTTGTTGG\nACAACAGGTTTTTGGTTCATTAACACTATCAACATAAGTCGGGGTATACAAGTATAATGAACGACGTTGA\nTGCAACAGACACCTTTGTTGGACAAGGAAAGTTCCGTGGCGCCATCTCAACATCACCGTCACATATTATG\nCAAACATGTGGGTTTATACAACAGATGTTTCCAGTTGAAATGTCGCCCGGCATAGAATCTGAGGATGATC\nCCAATTATGACGTTAACATGGATATACAGTCTTTTAATATATTTGATGGTGTACACGAAACTGAAGCCGA\nAGCCTCTGTGGCATTGTGCGCAGAAGCACGCGTTGGAATTAATAAAGCGGGATTTGTAATATTAAAAACG\nTTTACACCAGGGGCGGAAGGTTTTGCGTTTGCGTGTATGGACAGTAAAACATGTGAACATGTGGTCATTA\nAAGCGGGTCAACGTCAAGGAACGGCCACCGAGGCAACCGTGTTAAGAGCGTTAACCCACCCATCCGTTGT\nACAGCTTAAAGGAACGTTTACGTATAACAAAATGACATGTCTTATATTACCACGTTACCGAACAGATTTA\nTACTGCTATCTAGCTGCAAAGCGCAACCTCCCCATATGTGACATTTTAGCAATTCAGCGATCTGTATTAC\nGCGCGTTACAGTATCTTCATAATAACAGTATTATTCACCGTGATATAAAATCTGAAAATATATTTATTAA\nCCACCCAGGTGATGTTTGTGTGGGAGACTTTGGAGCAGCGTGTTTCCCCGTGGATATTAATGCCAACAGG\nTATTATGGCTGGGCTGGAACAATCGCCACAAACTCTCCTGAGTTATTGGCTAGAGATCCATATGGACCTG\nCCGTGGACATATGGAGTGCCGGGATTGTATTATTTGAAATGGCTACAGGACAGAACTCGTTATTTGAACG\nAGACGGTTTAGATGGCAATTGTGACAGTGAGCGTCAAATTAAACTTATTATACGACGATCTGGAACTCAT\nCCCAATGAATTTCCCATTAACCCTACATCAAATCTTCGTCGACAATACATTGGTTTGGCAAAACGGTCTT\nCTCGAAAACCCGGATCCAGGCCATTGTGGACAAATCTATATGAGTTGCCAATTGATTTGGAGTATTTGAT\nATGTAAGATGTTATCGTTTGACGCACGTCATCGACCATCAGCAGAGGTGTTGCTTAACCACTCTGTTTTC\nCAAACTCTTCCCGATCCATATCCAAATCCAATGGAAGTTGGAGATTAAAATTCATTAAGCCTGTTAATAA\nAATATTGTATAAATTGTGTTTATAACGTATAACCCGTTAAGGCAAATAGGGTACAAACGCGCAATGTTTT\nGAAATACTAATATAAATAACATAACCAATAGAAACTTAATACAGAGTCACGCCCCATTACAACAAGGATA\nAAACACGGGATCATTTTCTTAACATTGTAGTAGCGCTGAAAAGCGTCCCCTCCCCCGGCTCACAGAGCTG\nCTCTTCGGTGTAGTTGGGTATACTGGTGCGCCTCATTTAATCGCGATGTTTTTAATCCAATGTTTGATAT\nCGGCCGTTATATTTTACATACAAGTGACCAACGCTTTGATCTTCAAGGGCGACCACGTGAGCTTGCAAGT\nTAACAGCAGTCTCACGTCTATCCTTATTCCCATGCAAAATGATAATTATACAGAGATAAAAGGACAGCTT\nGTCTTTATTGGAGAGCAACTACCTACCGGGACAAACTATAGCGGAACACTGGAACTGTTATACGCGGATA\nCGGTGGCGTTTTGTTTCCGGTCAGTACAAGTAATAAGATACGACGGATGTCCCCGGATTAGAACGAGCGC\nTTTTATTTCGTGTAGGTACAAACATTCGTGGCATTATGGTAACTCAACGGATCGGATATCAACAGAGCCG\nGATGCTGGTGTAATGTTGAAAATTACCAAACCGGGAATAAATGATGCTGGTGTGTATGTACTTCTTGTTC\nGGTTAGACCATAGCAGATCCACCGATGGTTTCATTCTTGGTGTAAATGTATATACAGCGGGCTCGCATCA\nCAACATTCACGGGGTTATCTACACTTCTCCGTCTCTACAGAATGGATATTCTACAAGAGCCCTTTTTCAA\nCAAGCTCGTTTGTGTGATTTACCCGCGACACCCAAAGGGTCCGGTACCTCCCTGTTTCAACATATGCTTG\nATCTTCGTGCCGGTAAATCGTTAGAGGATAACCCTTGGTTACATGAGGACGTTGTTACGACAGAAACTAA\nGTCCGTTGTTAAGGAGGGGATAGAAAATCACGTATATCCAACGGATATGTCCACGTTACCCGAAAAGTCC\nCTTAATGATCCTCCAGAAAATCTACTTATAATTATTCCTATAGTAGCGTCTGTCATGATCCTCACCGCCA\nTGGTTATTGTTATTGTAATAAGCGTTAAGCGACGTAGAATTAAAAAACATCCAATTTATCGCCCAAATAC\nAAAAACAAGAAGGGGCATACAAAATGCGACACCAGAATCCGATGTGATGTTGGAGGCCGCCATTGCACAA\nCTAGCAACGATTCGCGAAGAATCCCCCCCACATTCCGTTGTAAACCCGTTTGTTAAATAGAACTAATTAT\nCCCGGATTTTATATTAAATAAACTATATGCGTTTTATTTAGCGTTTTGATTACGCGTTGTGATATGAGGG\nGAAGGATTAAGAATCTCCTAACTATAAGTTAACACGCCCACATTTGGGCGGGGATGTTTTATGAAGCCTT\nAAAGGCCGAGCTGGTATACACGAGAGCAGTCCATGGTTTTAGACCTCGGGCGAATTGCGTGGTTTTAAGT\nGACTATATTCCGAGGGTCGCCTGTAATATGGGGACAGTTAATAAACCTGTGGTGGGGGTATTGATGGGGT\nTCGGAATTATCACGGGAACGTTGCGTATAACGAATCCGGTCAGAGCATCCGTCTTGCGATACGATGATTT\nTCACACCGATGAAGACAAACTGGATACAAACTCCGTATATGAGCCTTACTACCATTCAGATCATGCGGAG\nTCTTCATGGGTAAATCGGGGAGAGTCTTCGCGAAAAGCGTACGATCATAACTCACCTTATATATGGCCAC\nGTAATGATTATGATGGATTTTTAGAGAACGCACACGAACACCATGGGGTGTATAATCAGGGCCGTGGTAT\nCGATAGCGGGGAACGGTTAATGCAACCCACACAAATGTCTGCACAGGAGGATCTTGGGGACGATACGGGC\nATCCACGTTATCCCTACGTTAAACGGCGATGACAGACATAAAATTGTAAATGTGGACCAACGTCAATACG\nGTGACGTGTTTAAAGGAGATCTTAATCCAAAACCCCAAGGCCAAAGACTCATTGAGGTGTCAGTGGAAGA\nAAATCACCCGTTTACTTTACGCGCACCGATTCAGCGGATTTATGGAGTCCGGTACACCGAGACTTGGAGC\nTTTTTGCCGTCATTAACCTGTACGGGAGACGCAGCGCCCGCCATCCAGCATATATGTTTAAAACATACAA\nCATGCTTTCAAGACGTGGTGGTGGATGTGGATTGCGCGGAAAATACTAAAGAGGATCAGTTGGCCGAAAT\nCAGTTACCGTTTTCAAGGTAAGAAGGAAGCGGACCAACCGTGGATTGTTGTAAACACGAGCACACTGTTT\nGATGAACTCGAATTAGACCCCCCCGAGATTGAACCGGGTGTCTTGAAAGTACTTCGGACAGAAAAACAAT\nACTTGGGTGTGTACATTTGGAACATGCGCGGCTCCGATGGTACGTCTACCTACGCCACGTTTTTGGTCAC\nCTGGAAAGGGGATGAAAAAACAAGAAACCCTACGCCCGCAGTAACTCCTCAACCAAGAGGGGCTGAGTTT\nCATATGTGGAATTACCACTCGCATGTATTTTCAGTTGGTGATACGTTTAGCTTGGCAATGCATCTTCAGT\nATAAGATACATGAAGCGCCATTTGATTTGCTGTTAGAGTGGTTGTATGTCCCCATCGATCCTACATGTCA\nACCAATGCGGTTATATTCTACGTGTTTGTATCATCCCAACGCACCCCAATGCCTCTCTCATATGAATTCC\nGGTTGTACATTTACCTCGCCACATTTAGCCCAGCGTGTTGCAAGCACAGTGTATCAAAATTGTGAACATG\nCAGATAACTACACCGCATATTGTCTGGGAATATCTCATATGGAGCCTAGCTTTGGTCTAATCTTACACGA\nCGGGGGCACCACGTTAAAGTTTGTAGATACACCCGAGAGTTTGTCGGGATTATACGTTTTTGTGGTGTAT\nTTTAACGGGCATGTTGAAGCCGTAGCATACACTGTTGTATCCACAGTAGATCATTTTGTAAACGCAATTG\nAAGAGCGTGGATTTCCGCCAACGGCCGGTCAGCCACCGGCGACTACTAAACCCAAGGAAATTACCCCCGT\nAAACCCCGGAACGTCACCACTTCTACGATATGCCGCATGGACCGGAGGGCTTGCAGCAGTAGTACTTTTA\nTGTCTCGTAATATTTTTAATCTGTACGGCTAAACGAATGAGGGTTAAAGCCTATAGGGTAGACAAGTCCC\nCGTATAACCAAAGCATGTATTACGCTGGCCTTCCAGTGGACGATTTCGAGGACTCGGAATCTACGGATAC\nGGAAGAAGAGTTTGGTAACGCGATTGGAGGGAGTCACGGGGGTTCGAGTTACACGGTGTATATAGATAAG\nACCCGGTGATCACCGAACCGGGGCAACGCCGAGCGTGTAAATTTAAATAAAAAACAGTACGCTTTTATCC\nGGTGTATGTTTTAAATTTATTTTTTTTTTCTATATAAAGGGATGGGGTGTCAGGATCTCTCGTAGGTTCT\nTGGGACTCCAAGGGACCCGCAGCCCAGGTACGCGTCAAAAAGCCTGTGACAAATTCCCCCGGGGCGGTCA\nTATAATTCGGCGCGGATGCATTTATTATCGGGCGACAATCCAATAGTCGGAAGTCCGGCGTGTCCCAAAC\nAGCACCAATATGCCATCAATATCAGCCGCTCGCTGAGCTCCAGATGCGATTGTGGATCCGGCATGCATTG\nCTCGCGTAATAACGATAACACCGCTCTGCGGATCGGCGGAACCGAGGGTGGACGTTGTCTATCCGCTGCG\nAGCTCCCCGCACATCCGTCCGAAGGCGTCCTTTGCCCTCCCCCACAAACTCGCGCACGGTCTCTCGGAGG\nGGCTGTGTATAAAAGCCTCGTAGGCCTCGGTAGATATGGCGCATAGCGCGGCGGCGAAGTACCGTTCGGC\nGTCGTTCATGAGAGCCTGGTGCGCGGGGGTATCGTGTCGTGTGCAGTAAAGTCCGGCATATTCACCGCCC\nGGGTGCTCACCGCGGGATCCGCAGAGATTCATACCACACGGCCCGTGTGGGGACCCCGTGGGTTAATGGA\nGACGTTCAAACCAGCACCCTCTACCCTCTAATATCCACAACACCCCACTCCCCCACAGACAGACATCAAA\nAAAAGACACGAGCCAAACCATTGTATTTATTTATAAAGACTACACGCCATGGGGGGGCGGTATATCATGC\nCGGCGCGGGGCTTCGTGTCGACGTCGCTTCCAATCTACACCCCCCTCGCCCAACGCGGTGAGCGCTTTCG\nCGGCTGTATATTCCGCGGTTTCTGCACCCGCGTATCGCTCGATGGCACGCTGGGGTCTCTTTGGGGACGG\nGGTGTTGCACCCATCCCCGTCTCGATAACAATCGCCGGGTACCCCGTCTGGTTCACAAGAATCGGTGCTC\nTCCTCTGATTCTTCTTCCACTATAAAGTCTTCCCCGTCCGATGATTCCGCGTCGGAATCCCGAAATTCAA\nTTACATCCGATGGCGTAGACCCATCATCGTCGCTATCGTCTTCACCACCATCATCAGATACGTCACATTC\nCAGTGCGCTCCTATGCAAAGGAACATTCGGCGCCTCAATGAACCCGTCTTCCCCCCGAGGGGGTCGATGG\nGACACTTCCATTAAAGTAGCGCGTAAGCACTGCGTCTGGGTGGGTTGAAGCTGTAACAATTCCTCCCAGC\nACGCTAACGTGGGACGCTGTCTGGTGCGACCCATTAGATAAAAGTCGAGGCATATGCGCCGCAATCTTCG\nTGAATCTCGCGTGACGCGTCCCGACGACTGTGCAATACATAAAAAAACACGGTTGATGTCCTCAACGAGC\nCTGGCCGGGTGGATCTCCCAACCCGGAGTACAAAACGCGCCGGGGCCCCGCGACGTATCCCGGCCGTTCA\nGGGGTCCTGGTGCAGATCCATATTCCATCTTTCCGTTAACATCAACCGATGCCCCGGGTTTTGACTCGGA\nCGAGTCGCCCCGCGTAGCCGGTGAGGTGCAAAACATGTCCTTGGGGCCGTAGTAACCTTTTCCCTTAAAA\nCCGACTCGACGCTGTCGCGTTATGAATCGGACGAACCCTGCACAACAAAACACACACCCAAACGTTTACA\nTCTATGAATAAGGCTACTTGGGTAAAATGGCAATGGGGGATTCCGGGGCGGGAGACCTTCGATTGGGTTG\nCCTTTATAACACCAAAAAAAGGGGGGGGCCCCGTGTGTTTTTTTTTATCACGTCAAATCGATTTTAAAAA\nGCCTGCCGCTCCATTTGGAATATATATATTCTGTGAAAAGCCCGCCCACACCCCATAAAACCGCGACATC\nGCGGGAACACGCGCGAACAAGAAACTCTCTCTCTTTCTCTATATATATATATATATATATATATATATAT\nAGAAAGAAAGTGCGAACGGTGGTTGGACACATGCCAAAACATGAAAACCCATACAGTGAAAAAACGGGAA\nGTGCGAATGCAGATCAAAAGAGTGTATCCGATTGGCGTACACCACAGACATGCGGACGCCCAATTTAACC\nCCCCCCCTTTTTCACCCCCCCACCCCACCCCATTCCACCCCAGGAAGTGCGAACGGGTTTACATGCCTCA\nGATATGAAGTTCTTCGACTTGTTTTTGAATAAATTTTTTTGTGATTTTCTACAACGGTTTAGAGAATTAT\nGGTTATAAACATCGGCGGGGTACCGCGCCCCCTCCCCATCGGCGGGGTACCGCGCCCCCTCCCCATCGGC\nGGGGTACCGCGCCCCCTCCCCATCGGCGGGGTACCGCGCCCCCTCCCCATCGGCGGGGTACCGCGCCCCC\nTCCCCATCGGCGGGGGGTTACGTGAACACCACAACCCCGTGTGTATTTTATGGGTTATCGCGGGCTTCGT\nGCCGCCTGACATAATCGTTGGGAGGGGTGGTGGTGTATACGCTTGTTGATTGCGCGAACGTAATGACGAC\nGGAGAGGGACCCAAACACACCGTCGACGTGCATTTGATTAACTAGATGCCGGATGGGTGGAAACAACCCG\nTGTTATATAAGATGTTTTGCATGTGAGACAACCCCAATTGTGTTTATGTATATTATATATCGTCTGTAGA\nCACACGATGATTGGTTGTTATTTAAACATATGTAAATGAAATTCACATGTCTGGTATCCCTTGTTATGAT\nGTTGTAAGGTATGCGGAAATAGACACCGGGCGTACATCGCCAACCAGCGGTCTCTCCTTAAACGCATACT\nATGGTCCATGAACTTCCCGCCTCGAGTCTCGTCCAATCACTACATCGTCTTATCATTAAGAATATTTACA\nCGGTGACGACACGGGGAGGAAATATGCGGTCGAGGGGGGGGCACAACACGTTTTAAGTACTGTTGGAACT\nCCCTCACCAACCGCAATCGCAATCCTTTGAAGGCTGCGAGAGCGTTTGGAAAACTCGGGTACGTCTAAAT\nTCACCCCAGTGCGATGGATACGCCGCCGATGCAGCGCTCTACACCCCAACGCGCGGGGTCGCCTGATACT\nTTGGAGTTAATGGACCTGTTGGACGCGGCCGCGGCGGCCGCCGAACACAGGGCCCGGGTGGTCACCTCGA\nGTCAGCCTGACGATCTACTATTTGGAGAGAACGGGGTCATGGTGGGACGGGAACACGAGATCGTTTCAAT\nTCCCTCCGTATCGGGACTTCAACCAGAACCCAGAACGGAAGATGTTGGCGAAGAGCTAACACAAGACGAC\nTACGTATGCGAGGACGGTCAGGATCTAATGGGCTCGCCTGTAATCCCGCTGGCCGAGGTCTTCCACACCC\nGATTCTCGGAGGCCGGCGCGCGAGAACCAACAGGAGCCGATCGCTCCCTTGAGACAGTCTCTCTCGGAAC\nGAAGCTTGCTAGGTCTCCAAAACCACCGATGAACGATGGGGAAACGGGCAGAGGTACGACCCCTCCGTTC\nCCGCAGGCCTTCTCCCCTGTATCCCCCGCGTCTCCTGTTGGAGACGCCGCCGGGAACGATCAACGGGAAG\nACCAGCGGTCTATACCCCGACAAACGACGAGAGGAAATTCACCAGGTTTGCCGTCGGTGGTCCATCGAGA\nCAGACAAACTCAGTCCATCTCGGGTAAAAAGCCGGGCGATGAGCAAGCGGGTCATGCGCATGCATCGGGG\nGACGGAGTAGTTCTCCAGAAAACTCAACGGCCCGCTCAGGGAAAGAGCCCGAAGAAAAAGACTTTGAAGG\nTTAAGGTCCCACTCCCGGCGCGGAAACCCGGTGGACCTGTACCCGGCCCGGTTGAGCAATTGTACCACGT\nCCTTTCGGACAGCGTTCCCGCTAAGGGGGCAAAGGCGGACCTGCCGTTTGAGACCGATGATACCCGCCCA\nAGGAAACATGATGCCCGGGGTATAACACCTCGCGTCCCTGGACGTTCGTCGGGGGGCAAACCTAGAGCGT\nTTTTGGCCCTGCCGGGAAGATCCCACGCACCAGACCCGATTGAGGATGACAGCCCAGTGGAGAAAAAGCC\nAAAGAGTCGTGAGTTTGTTTCGTCTTCATCCTCTTCCTCGTCGTGGGGATCGTCATCGGAGGATGAAGAC\nGATGAACCCCGGCGCGTTTCGGTGGGAAGTGAAACTACAGGCAGCAGGTCCGGACGCGAACACGCCCCTT\nCCCCGTCAAATTCGGATGATTCGGACTCAAATGATGGTGGGTCGACGAAACAAAATATCCAACCGGGATA\nTCGATCCATCAGCGGTCCCGATCCGAGGATTCGTAAGACCAAACGTCTTGCGGGGGAACCGGGGCGCCAG\nAGACAGAAATCATTTTCCCTGCCGCGATCCAGAACCCCGATAATTCCCCCGGTGTCGGGGCCGCTCATGA\nTGCCCGACGGAAGCCCTTGGCCCGGATCGGCACCCCTCCCATCCAACAGGGTGCGGTTTGGACCGTCCGG\nGGAGACCAGAGAGGGTCACTGGGAGGATGAGGCTGTGAGAGCGGCGCGGGCTCGTTACGAGGCCTCAACG\nGAACCCGTGCCGCTTTACGTGCCGGAGTTGGGAGATCCGGCTAGACAGTACCGCGCGCTGATTAACCTGA\nTCTACTGTCCAGACAGAGACCCTATAGCATGGCTCCAGAACCCCAAGCTGACCGGTGTCAACTCGGCCCT\nGAACCAGTTCTACCAAAAGCTGTTGCCACCGGGACGGGCGGGTACCGCCGTTACGGGGAGCGTAGCGTCT\nCCCGTTCCGCATGTAGGCGAAGCCATGGCCACGGGGGAGGCCCTCTGGGCTCTCCCCCACGCGGCCGCGG\nCCGTGGCTATGAGCCGTCGATACGACCGGGCCCAAAAACACTTTATCCTACAGAGTCTCCGCAGAGCCTT\nTGCCAGCATGGCATACCCCGAGGCAACGGGCTCCAGTCCGGCGGCGCGGATCTCCCGCGGTCACCCTTCT\nCCAACAACCCCGGCCACACAGGCTCCCGACCCTCAGCCGTCGGCCGCCGCACGCTCTCTTTCTGTGTGTC\nCACCGGATGATCGTTTACGAACTCCGCGCAAGCGCAAGTCCCAGCCAGTCGAGAGCAGAAGCCTCCTCGA\nCAAGATTAGGGAGACACCCGTCGCGGACGCCCGGGTTGCAGACGATCATGTGGTTTCCAAGGCCAAGAGG\nCGGGTATCCGAGCCCGTGACCATCACCTCGGGCCCTGTGGTGGATCCCCCCGCCGTAATAACGATGCCAC\nTTGACGGACCGGCCCCAAACGGGGGATTTCGGCGTATTCCCCGGGGGGCCCTGCATACCCCGGTCCCGTC\nGGACCAGGCTCGCAAGGCGTACTGTACCCCCGAAACCATCGCCCGTCTGGTCGACGACCCATTGTTTCCC\nACGGCCTGGCGCCCTGCGCTAAGCTTTGATCCCGGCGCCTTGGCGGAAATCGCCGCTCGGCGTCCGGGCG\nGAGGAGACCGACGGTTTGGTCCACCCAGCGGAGTGGAGGCGCTGCGACGGAGGTGCGCCTGGATGCGGCA\nGATCCCAGACCCGGAGGATGTGAGGCTTCTGATCATCTACGATCCGTTGCCCGGAGAGGACATCAACGGC\nCCCCTCGAGAGCACCCTCGCGACAGATCCGGGACCGTCATGGAGTCCATCCCGAGGGGGACTGTCTGTGG\nTCCTGGCAGCCCTGAGTAACCGGTTGTGCCTGCCGAGCACTCATGCCTGGGCCGGGAACTGGACCGGCCC\nGCCGGACGTGTCCGCTTTGAACGCCCGGGGCGTTTTATTACTGTCGACCCGAGACCTGGCCTTTGCCGGG\nGCCGTCGAGTATCTAGGCTCGCGGTTGGCCTCTGCCCGGCGCCGGTTGCTGGTGTTGGACGCGGTGGCCC\nTCGAGAGGTGGCCCAGGGATGGACCCGCTTTGTCTCAGTATCACGTGTACGTCCGGGCCCCGGCGCGACC\nGGACGCCCAGGCCGTCGTCCGATGGCCAGACTCGGCGGTCACAGAAGGACTCGCCCGGGCCGTGTTTGCA\nTCGTCGCGCACCTTTGGGCCAGCGAGTTTTGCTCGTATCGAGACTGCGTTTGCCAACCTGTACCCGGGCG\nAACAACCCCTGTGTTTGTGCCGCGGTGGGAACGTCGCATACACCGTGTGTACCCGCGCGGGCCCCAAGAC\nCCGCGTCCCCCTGTCGCCCCGTGAATACCGGCAGTACGTGCTGCCGGGTTTTGACGGTTGCAAGGACCTC\nGCGCGACAGTCTCGGGGTCTGGGGCTCGGGGCAGCCGACTTTGTGGACGAGGCGGCACATAGCCACCGCG\nCAGCAAACCGATGGGGCCTGGGTGCCGCGCTTCGACCCGTCTTCCTTCCCGAGGGACGGAGACCGGGGGC\nCGCCGGGCCGGAGGCCGGCGACGTACCCACCTGGGCGAGGGTGTTTTGCCGCCACGCCCTGCTGGAACCC\nGACCCTGCCGCAGAACCACTCGTGCTTCCACCCGTGGCCGGTCGGTCGGTGGCGCTGTATGCGTCGGCGG\nACGAGGCTCGGAATGCCCTCCCCCCGATTCCCAGAGTAATGTGGCCGCCCGGTTTTGGGGCCGCGGAGAC\nGGTGTTGGAGGGGAGCGACGGAACACGGTTCGTGTTCGGACACCACGGGGGCTCGGAACGGCCGTCAGAA\nACCCAGGCGGGGCGACAGCGGCGCACCGCAGACGACAGAGAACACGCTTTGGAGCTGGACGATTGGGAGG\nTGGGGTGTGAAGACGCGTGGGACAGCGAGGAGGGGGGCGGGGACGACGGGGACGCACCGGGGTCATCCTT\nTGGGGTGAGCATCGTGTCGGTGGCCCCGGGTGTGCTGCGAGACCGCCGGGTGGGTTTGCGCCCGGCGGTC\nAAGGTGGAGCTGTTGTCCTCGTCCTCGTCCTCCGAGGACGAGGACGATGTGTGGGGAGGGCGCGGGGGGA\nGGAGCCCCCCGCAGAGTCGGGGGTGACGGAGTCCCCTCCTTTTCTCGTGAGCGCCACTGGCGCGCGGACT\nGTTTGTTGTTAATAAAAGCGGAACGGTTTTTATGAAAAAAGTGTCTGTCTGTCTGTGCGGGCGGGCGACG\nGGCGGGCTGGTCGGACCCCCCCCCGAAAATAACCCCCCCCCGGTTTCTGGGCGCCCGGCGGACCCCGGGA\nGAGG\n\n" }, { "path": "tests/input/TestOrderAndOrient/ref.hiv.fasta", "content": ">gi|55139330|gb|AY772699.1| HIV-1 isolate 04ZASK146B1 from South Africa, complete genome\nTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCTTCAGTGTTAGTGTGGAAAATCTCTAGCAGT\nGGCGCCCGAACAGGGACCGGAAAGCGAAAGTAAAACCAGAGAAGATCTCTCGACGCAGGACTCGGCTTGC\nTGAAGTGCACTCGGCAAGAGGCGAGAGCGGCGACTGGTGAGTACGCCAATTTTTATTTGACTAGCGGAGG\nCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGAGGCGAAAAATTAGATACATGGGAAAAAAT\nTAGGTTAAGGCCAGGGGGAAAGAAACACTATATGCTAAAACACATAGTATGGGCAAGCAGGGAGCTGGAA\nAGATTTGCACTCAACCCTGGCCTTTTAGAAACATCAGAAGGCTGTAAACAAATATTGGCACAAATACAAC\nCAGCTATTCAGACAGGAACAGAGGAACTTAAATCATTATTCAACACAATAGCAGTTCTCTATTGTGTACA\nTAAAAAGATAGATGTAAGAGACACCAAGGAAGCCTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTCAG\nCAAAAAACACAGCAGGCAAAAGCGGCTGACGAAAAGGTCAGTCAAAATTTTCCTATAGTACAGAATCTTC\nAAGGGCAAATGGTACATCAACCCCTATCACCTAGAACCTTGAATGCATGGGTAAAAGTAATAGAGGAGAA\nGGGTTTTAACCCAGAGGTAATACCCATGTTTACAGCATTATCAGAGGGAGCCACCCCACAAGATTTGAAC\nACCATGCTAAATACGGTGGGGGGACATCAAGCAGCCATGCAGATGTTAAAAGATACCATCAATGAAGAGG\nCTGCAGAATGGGATAGATTACATCCAGTACATGCAGGGCCTGTCGCACCAGGCCAAATGAGAGAACCAAG\nGGGAAGTGACATAGCAGGAACTACTAGTAACCTTCAGGAACAAGTAGCATGGATGACAAGTAACCCACCT\nATTCCAGTGGGAGACATCTATAAAAGATGGATAATTCTGGGATTAAATAAAATAGTGAGGATGTATAGCC\nCGGTCAGCATTTTGGACATAAAACAAGGGCCAAAGGAACCCTTTAGAGACTATGTAGATCGGTTCTTTAA\nAACTTTAAGAGCTGAACAAGCTACACAAGAGGTAAAAAATTGGATGACAGACACCTTGTTGGTCCAAAAT\nGCGAACCCAGATTGTAAGACCATTTTAAGAGCATTAGGACCAGGGGCTACATTAGAAGAAATGATGGCAG\nCATGTCAAGGGGTGGGAGGACCTGGCCACAAGGCAAGAGTGTTGGCTGAGGCAATGAGCCAAATAAACAA\nTGGAAACATAATGATGCAGAGAAGTAATTTTAAAGGCCCTAAAAGAATTGTTAAATGTTTTAACTGTGGC\nAAGGGGAGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAAGGCTGTTGGAAATGTGGAAAGGAAG\nGACACCAAATGAAAGACTGTACTGAAAGGCAGGCTAATTTTTTAGGGAAAATTTGGCCTTCCCAGAAGGG\nGAGGCCAGGGAATTTTCTCCAGAACAGACTAGAGCCAACAGCCCCACCAGCAGAGAGCTTCAGGTTCGAG\nGAGACGACCCCTGCTCCGAAACAGGAGCTGAAAGACAGGGAACCTTTAACTTCCCTCAGATCACTCTTTG\nGCAGCGACCCCTTGTCTCAATAAAAATAGGGGGCCAGACAAGGGAGGCTCTCTTAGACACAGGAGCAGAT\nGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGAGGAATTGGAGGTT\nTTATCAAAGTAAGACAGTATGATCAGATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACAGTATT\nGGTAGGGCCTACACCTGTCAACATAATTGGAAGAAACATGTTGACTCAGCTTGGATGCACACTAAATTTT\nCCAATTAGTCCCATTGAAACTGTACCAGTAAAACTGAAGCCAGGAATGGATGGCCCAAAGGTTAAACAAT\nGGCCATTGTCAGAAGAGAAAATAAAAGCATTAACAGCAATTTGTGAGGAGATGGAGAAGGAAGGAAAAAT\nTACAAAAATCGGGCCTGAAAATCCATATAACACCCCAATATTCGCCATAAAAAAGAAGGACAGTACTAAG\nTGGAGAAAATTAGTAGATTTCAGGGAACTCAATAAAAGAACTCAAGACTTTTGGGAAGTTCAATTAGGAA\nTACCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTGACAGTACTAGATGTGGGGGATGCATATTTTTC\nAGTTCCTCTAGATGAAGGCTTCAGGAAATATACTGCATTCACCATACCTAGTATAAACAATGAAACACCA\nGGGATTAGATATCAATATAATGTGCTCCCACAGGGGTGGAAAGGATCACCAGCAATATTCCAAAGTAGCA\nTGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAAATAGCCATCTATCAATATATGGATGACTT\nGTATGTAGGATCTGACTTAGAAATAGGGCAACATAGAGCAAAAATAGAAGAATTAAGAGAGCATCTATTA\nAGGTGGGATTTACCACACCAGACAAGAAGCATCAGAAAGAACCCCCATTTCTTTGGATGGGGTATGAACT\nTCATCCTGACAAATGGACAGTACAGCCTATACAGCTGCCAGAAAAGGATAGCTGGACTGTCAATGATATA\nCAGAAGTTAGTGGGAAAATTAAACTGGGCAAGTCAGATTTATCCAGGGATTCAAGTAAAACAACTTTGTA\nGACTCCTTAGGGGGGCCAAAGCACTAACAGACATAGTACCACTAACTGAAGAAGCAGAATTAGAATTGGC\nAGAGAACAGGGAAATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAGGACTTGATAGCT\nGAAATACAGAAACAGGGGAATGACCAATGGACATATCAAATTTACCAAGAACCATTCAAAAATCTGAAGA\nCAGGAAAGTATGCAAAAATGAGGACTGCACACACTAATGATGTAAGACAGTTAACAGAGGCAGTGCAAAA\nAATAGCCCTGGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGACTGCCCATCCAAAAAGAAACA\nTGGGAGACATGGTGGACAGACTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTC\nCCCTAGTAAAATTATGGTATCAGCTAGAGAAAGAACCCATAGCAGAAGCAGAAACTTTCTATGTAGATGG\nAGCATCTAATAGAGAAACTAAAAAAGGAAAAGCGGGGTATGTTACTGACAGAGGAAGGCAGAAAATTATC\nACTCTAAGTGAAACAACAAATCAGAAGGCTGAATTACAGGCAATTCAGCTGGCTTTGCAAGATTCAGGAT\nCTGAAGCAAACATAGTAACAGACTCACAGTATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGA\nATCAGAGTTAGTCAACCAAATAATAGAACAATTAATAAGAAAGGATAGGGTCTACCTGTCATGGGTACCA\nGCACACAAAGGTATTGGAGGAAATGAACAAGTAGATAAATTAGTAAGTAGTGGAATCAGGAAAGTACTGT\nTTCTAGATGGAATAGACAAGGCTCAAGAAGAGCATGAAAAGTATCACAACAATTGGAGAGCAATGGCTAG\nTGAATTTAATCTGCCACCCATAGTAGCAAAAGAAATAGTAGCTAGCTGTGACAAATGTCAGCTAAAAGGG\nGAAGCCATGCATGGACAAGTAGACTGTAGTCCGGGGATATGGCAATTAGACTGTACACATTTAGAAGGAA\nAAATCATCCTGGTAGCAGTCCATGTAGCCAGTGGCTACATAGAGGCAGAGGTTATTCCAGCAGAAACAGG\nACAGGAAACAGCATACTACATACTAAAATTAGCAGGAAGATGGCCAGTCAAAGTAATACATACAGACAAT\nGGCAGTAATTTCACTAGTGCTGCAGTTAAGGCAGCCTGTTGGTGGGCAGGCATCCAACAGGAATTTGGGA\nTCCCCTACAATCCCCAAAGTCAGGGAGTAGTAGAATCCATGAATAAAGAATTAAAGAAAATCATAGGACA\nGGTAAGAGATCAAGCTGAGCACCTTAAGACAGCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGA\nAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAATAGACATAATAGCAACAGACTTACAAACTA\nAAGAACTACAAAAACAAATTATAAAAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGACCCTAT\nTTGGAAAGGACCAGCCAAACTACTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAACAGTGACATA\nAAGGTAGTACCAAGGAGGAAAGCAAAAATCATTAGAGACTATGGAAAACAGATGGCAGGTGCTGATTGTG\nTGGCAGGTAGACAGGATGAGGATTAGAACATGGAATAGTTTAGTAAAACATCATATGTATATTTCAAAGA\nGAGCTAGTAGATGGGTCTACAGACATCATTATGAAAGTAGAAATCCAAGAATAAGTTCAGAAGTACACAT\nACCATTAGGGGAGGCTAGATTGGTAATAAAAACATATTGGGGTTTGCATACAGGAGAAAGGGATTGGCAA\nTTGGGTCATGGAGTCTCCATAGAATGGAGATTGAGAAGATATAGCACACAAGTAGACCCTGGCCTGGCAG\nACCAGCTAATTCATATGCATTATTTTGATTGTTTTGCAGACTCTGCCATAAGAAAAGCCATATTAGGACA\nAGTAGTTAGTCCTAGGTGTGATTATCAAGCAGGACATAATAAGGTAGGATCTCTACAATACTTGGCACTG\nACAGCTTTGATAAAGCCAAAAAGGAGAAAGCCACCCCTGCCTAGTGTTAGAAAATTAGTAGAGGATCGAT\nGGAACAACCCCCAGAAGATCAGGGACCGCAGAGGGAACCATACAATGAATGGGCATTAGAGATTTTAGAG\nGAACTCAAGCAGGAAGCTGTCAGACACTTTCCTAGACCATGGCTCCATAATTTAGGACAGTATATCTATG\nCAACCTATGGGGATACCTGGACAGGAGTCGAAGCCCTACTAAGAATACTGCAACAACTACTGTTTATTCA\nTTTCAGAATTGGGTGCCAGCATAGCAGAATAGGAATCTTGCGACAGAGAAGAGCAAGAAATGGAGCCAGT\nAGATCCTAACTTAGAGCCCTGGAACCATCCAGGAAGCCAGCCTAGAACTCCTTGTAATAACTGCTATTGT\nAAATACTGTAGCTACCATTGTCTAGTTTGCTTTCAGGCAAAAGGCTTAGGCATTTCATATGGCAGGAAGA\nAGCGGAGACAGCGACGAAGCACTCCTCCAAGCAGTGAGGATCATCAAGATCCTATATCAAAGCAGTAAGT\nATATGTAATGTCTTTTTTATATGCAAGTGTAGATTATAGATTAGGAGTAGGGGCACTGATAATAGCATTA\nATCCTAGCAATAGTTGTGTGGATCATAGTATATATAGAATATAGGAAATTGCTAAGACAAAGAAAAATAA\nACAAGTTAATTGACAGGATTAGAGACAGAGAAGAAGACAGTGGCAATGAGAGTGAGGGGGATATTGAGGA\nATTGGCCACAATGGTGGATATGGGGCATCTTAGGCTTTTGGATGATAATAATTTGTAGGGGGGAGGAGAA\nCTCGTGGGTCACAGTTTATTATGGGGTACCTGTGTGGACAGAAGCAAAAACTACTCTATTCTGTGCATCA\nGATGCTAAAGCATATGAGAAAGAGGTACATAATGTTTGGGCTACACATGCCTGTGTACCCACAGACCCCA\nGCCCACAAGAACTAGTTTTGGAAAATGTAACAGAAAGTTTTAACATGTGGGAAAATGACATGGTGGATCA\nGATGCATGAGGATATAATCGGTTTATGGGATGAAAGCCTAAAGCCATGTGTAAAATTGACCCCACTCTGT\nGTCACTTTAAATTGCAATACTACTAGCCACAATAATAGCAGCCCCAGCCCCATGACAAATTGCTCTTTCA\nATGCAACCACAGAATTAAGAGATAAGACACAGAAAGTGAATGCACTTTTTTATAGATCGGATATAGTACC\nACTTGAGAAGAATAGCTCTGAGTATATATTAATAAATTGCAATACCTCAACCATAACACAAGCCTGTCCA\nAAGGTTTCTTTTGATCCGATTCCTATACATTATTGTGCTCCAGCTGGTTATGCGATTTTAAAGTGTAATA\nATAAGACATTCAATGGAACAGGACCATGCAGTAATGTCAGCACAGTACAATGTACCCATGGAATTAAGCC\nAGTGGTATCAACTCAACTACTGTTAAATGGTAGCCTAGCAGAAGGGGAGATAATAATTAGATCTGAAAAT\nCTGACAGACAATGCCAAAACAATAATAGTACATCTTAATAAATCTGTAGCAATTGTGTGTACAAGACCCA\nACAATAATACAAGGAAAAGTATAAGGATAGGACCAGGACAAGTATTCTATACAAATGAAATAATAGGAAA\nCATAAGACAAGCACATTGTAACATTAGTAGAGAGCTATGGAACAATACTTTAGAACAGGTAAAGAAGAAA\nTTGAAAGAACACTTTCAGAATAAAACAATAGAATTTCAACCACCCGCAGGAGGGGATCTAGAAGTTACAA\nCACATAGTTTTAATTGTAGAGGAGAATTTTTCTATTGCAATACATCAAATCTGTTTAATATAACTGCAAG\nTAATGCAAGTGATGCAAACAACAACACCATCACACTCCCATGCAAAATAAAACAAATTATAAACATGTGG\nCAGGAGGTAGGACGAGCAATGTATGCCCCTCCCATTGCAGGAAACATAACATGTAACTCAAGTATCACAG\nGACTACTATTGACACGTGATGGAGGCAATAACAATGACACAGGCAATAACAATGACACAGAGATATTCAG\nACCTGGAGGAGGAAATATGAAGGACAATTGGAGAAGTGAGTTATATAAATATAAAGTGGTAGAAATTAAG\nCCATTAGGAATAGCACCCACTAAGGCAAAAAGGAGAGTGGTGGAGAGAGAGAAAAGAGCAGTGGGACTAG\nGAGCTGTACTCCTTGGGTTCTTAGGAACAGCAGGAAGCACTATGGGCGCGGCGTCAATAACGCTGACGGT\nACAGGCCAGGCAACTGTTGTCTGGTATAGTGCAACAGCAAAGCAATTTGCTGAGGGCTATAGAGGCGCAA\nCAGCACATGTTGCAACTCACGGTCTGGGGCATTAAGCAGCTCCAGGCAAGAGTCCTGGCTATAGAAAGAT\nACCTAAAGGATCAACAGCTCCTAGGGCTTTGGGGCTGCTCTGGAAAACTCATCTGCACCACTGCTGTGCA\nTTGGAACTCCAGTTGGAGTAATAAATCTCAAGACTATATTTGGGGTAACATGACATGGATGCAGTGGGAT\nAGAGAAATTAATAATTACACAGACATAATATACACATTGCTTGAAGAATCGCAAAGCCAGCAGGAGAAAA\nATGAAAAAGATTTATTAGCATTGGACAGTTGGAACAATTTGTGGAATTGGTTTAGCATAACAAAGTGGCT\nGTGGTATATAAAAATATTCATCATGATAGTAGGAGGCCTGATAGGTTTAAGAATAATTTTGGGTGTGCTC\nTCTATAGTGAAAAGAGTTAGGCAGGGATACTCACCTTTGTCGTTTCAGACCCTCCCCCCAAACCCGAGGG\nGACCCGACAGGCTCAGAGGAATCGAAGAAGAAGGTGGAGAGCAAGACAAAGACAGATCCATTCGGTTAGT\nGAGCGGATTCTTAGCACTTGTCTGGGAAGACCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGATTGAGA\nGACTTCATATTGATTGCAGGGAGAGCAGCGGAACTTCTGGGACGCAGCAGTCTCAGGGGACTACAGACAG\nGGTGGCAAGCCCTTAAGTATCTGGGAAGCCTTGTGCAGTATTGGGGTCTGGAACTAAAAAAGAGTGCTAT\nAAATCTATTTGATACCACAGCAATAGTAGTAGCTGAAGGAACAGATAGGCTTATTGAAGGCTTACAAGGA\nATTGGTAGAGCTATCTACAACATACCCAGAAGAATAAGGCAGGGCTTTGAAGCAGCTTTGCTATAAAATG\nGGGGGCAAGTGGTCAAAAAGCAGCATAGTTGGATGGCCTGCTATAAGAGAAAGAATCAGACGAACTGAGC\nCAGCAGCAGAGGGAGTAGGAGCAGCATCTCAAGACTTAGATAAACATGGAGCACTAACAAGCAGCAACAC\nACCCCAGAATAATGCTGCTTGTGCCTGGCTGCAAGCACAAGAGGAGGAAGACGAAGTAGGCTTTCCAGTC\nAGGCCTCAGGTGCTTTTGAGACCAATGACATATAAGGGAGCATTCGATCTTAGCTTCTTTTTAAAAGAAA\nAGGGGGGACTGGAAGGGTTAATTTGGTCTAAGAAAAGGCAAGAAATCCTTGATTTGTGGGTCTATAACAC\nACAAGGCTACTTCCCTGATTGGCAAAACTACACACCGGGACCAGGGGTCAGGCTTCCACTGACCTTTGGA\nTGGTGCTTTAAGCTAGTGCCAGTTGACCCAAGGGAAGTAGAAGAGGAGAACAAAGGAGAAAACAACTGTT\nTGCTACACCCTATGAGCCAACATGGAATGGAGGATGAACACAGAGAAGTATTAAAGTGGGTGTTTGACAG\nCAGCCTAGCACGCAGACATCTGGCCCGTGAGAAACATCCGGAGTATTACAAAGACTGCTGACACAGAAGG\nGACTTTCCGCCTGGGACTTTCCACTGGGGCGTTCCAGGAGGAGGGGTCTGGGCGGGACTAGGGAGTGGCC\nAACCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTAGGTAGACCAGATCTG\nAGCCTGGGAGCTCTCTGGCTACTTGGGGAACCCACTGCTTAAGCCTCAATA\n\n" }, { "path": "tests/input/TestOrderAndOrient/ref.influenza.fasta", "content": ">gi|8486138|ref|NC_002023.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 1, complete sequence\nAGCGAAAGCAGGTCAATTATATTCAATATGGAAAGAATAAAAGAACTAAGAAATCTAATGTCGCAGTCTC\nGCACCCGCGAGATACTCACAAAAACCACCGTGGACCATATGGCCATAATCAAGAAGTACACATCAGGAAG\nACAGGAGAAGAACCCAGCACTTAGGATGAAATGGATGATGGCAATGAAATATCCAATTACAGCAGACAAG\nAGGATAACGGAAATGATTCCTGAGAGAAATGAGCAAGGACAAACTTTATGGAGTAAAATGAATGATGCCG\nGATCAGACCGAGTGATGGTATCACCTCTGGCTGTGACATGGTGGAATAGGAATGGACCAATGACAAATAC\nAGTTCATTATCCAAAAATCTACAAAACTTATTTTGAAAGAGTCGAAAGGCTAAAGCATGGAACCTTTGGC\nCCTGTCCATTTTAGAAACCAAGTCAAAATACGTCGGAGAGTTGACATAAATCCTGGTCATGCAGATCTCA\nGTGCCAAGGAGGCACAGGATGTAATCATGGAAGTTGTTTTCCCTAACGAAGTGGGAGCCAGGATACTAAC\nATCGGAATCGCAACTAACGATAACCAAAGAGAAGAAAGAAGAACTCCAGGATTGCAAAATTTCTCCTTTG\nATGGTTGCATACATGTTGGAGAGAGAACTGGTCCGCAAAACGAGATTCCTCCCAGTGGCTGGTGGAACAA\nGCAGTGTGTACATTGAAGTGTTGCATTTGACTCAAGGAACATGCTGGGAACAGATGTATACTCCAGGAGG\nGGAAGTGAAGAATGATGATGTTGATCAAAGCTTGATTATTGCTGCTAGGAACATAGTGAGAAGAGCTGCA\nGTATCAGCAGACCCACTAGCATCTTTATTGGAGATGTGCCACAGCACACAGATTGGTGGAATTAGGATGG\nTAGACATCCTTAAGCAGAACCCAACAGAAGAGCAAGCCGTGGGTATATGCAAGGCTGCAATGGGACTGAG\nAATTAGCTCATCCTTCAGTTTTGGTGGATTCACATTTAAGAGAACAAGCGGATCATCAGTCAAGAGAGAG\nGAAGAGGTGCTTACGGGCAATCTTCAAACATTGAAGATAAGAGTGCATGAGGGATATGAAGAGTTCACAA\nTGGTTGGGAGAAGAGCAACAGCCATACTCAGAAAAGCAACCAGGAGATTGATTCAGCTGATAGTGAGTGG\nGAGAGACGAACAGTCGATTGCCGAAGCAATAATTGTGGCCATGGTATTTTCACAAGAGGATTGTATGATA\nAAAGCAGTTAGAGGTGATCTGAATTTCGTCAATAGGGCGAATCAGCGACTGAATCCTATGCATCAACTTT\nTAAGACATTTTCAGAAGGATGCGAAAGTGCTTTTTCAAAATTGGGGAGTTGAACCTATCGACAATGTGAT\nGGGAATGATTGGGATATTGCCCGACATGACTCCAAGCATCGAGATGTCAATGAGAGGAGTGAGAATCAGC\nAAAATGGGTGTAGATGAGTACTCCAGCACGGAGAGGGTAGTGGTGAGCATTGACCGGTTCTTGAGAGTCC\nGGGACCAACGAGGAAATGTACTACTGTCTCCCGAGGAGGTCAGTGAAACACAGGGAACAGAGAAACTGAC\nAATAACTTACTCATCGTCAATGATGTGGGAGATTAATGGTCCTGAATCAGTGTTGGTCAATACCTATCAA\nTGGATCATCAGAAACTGGGAAACTGTTAAAATTCAGTGGTCCCAGAACCCTACAATGCTATACAATAAAA\nTGGAATTTGAACCATTTCAGTCTTTAGTACCTAAGGCCATTAGAGGCCAATACAGTGGGTTTGTGAGAAC\nTCTGTTCCAACAAATGAGGGATGTGCTTGGGACATTTGATACCGCACAGATAATAAAACTTCTTCCCTTC\nGCAGCCGCTCCACCAAAGCAAAGTAGAATGCAGTTCTCCTCATTTACTGTGAATGTGAGGGGATCAGGAA\nTGAGAATACTTGTAAGGGGCAATTCTCCTGTATTCAACTACAACAAGGCCACGAAGAGACTCACAGTTCT\nCGGAAAGGATGCTGGCACTTTAACCGAAGACCCAGATGAAGGCACAGCTGGAGTGGAGTCCGCTGTTCTG\nAGGGGATTCCTCATTCTGGGCAAAGAAGACAGGAGATATGGGCCAGCATTAAGCATCAATGAACTGAGCA\nACCTTGCGAAAGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTAATGAAACGAAA\nACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAGTGT\nCGAATAGTTTAAAAACGACCTTGTTTCTACT\n\n>gi|8486134|ref|NC_002021.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 2, complete sequence\nAGCGAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACCTTACTTTTCTTAAAAGTGCCAGCACAAA\nATGCTATAAGCACAACTTTCCCTTATACCGGAGACCCTCCTTACAGCCATGGGACAGGAACAGGATACAC\nCATGGATACTGTCAACAGGACACATCAGTACTCAGAAAAGGCAAGATGGACAACAAACACCGAAACTGGA\nGCACCGCAACTCAACCCGATTGATGGGCCACTGCCAGAAGACAATGAACCAAGTGGTTATGCCCAAACAG\nATTGTGTATTGGAAGCAATGGCTTTCCTTGAGGAATCCCATCCTGGTATTTTTGAAAACTCGTGTATTGA\nAACGATGGAGGTTGTTCAGCAAACACGAGTAGACAAGCTGACACAAGGCCGACAGACCTATGACTGGACT\nTTAAATAGAAACCAGCCTGCTGCAACAGCATTGGCCAACACAATAGAAGTGTTCAGATCAAATGGCCTCA\nCGGCCAATGAGTCTGGAAGGCTCATAGACTTCCTTAAGGATGTAATGGAGTCAATGAAAAAAGAAGAAAT\nGGGGATCACAACTCATTTTCAGAGAAAGAGACGGGTGAGAGACAATATGACTAAGAAAATGATAACACAG\nAGAACAATAGGTAAAAGGAAACAGAGATTGAACAAAAGGAGTTATCTAATTAGAGCATTGACCCTGAACA\nCAATGACCAAAGATGCTGAGAGAGGGAAGCTAAAACGGAGAGCAATTGCAACCCCAGGGATGCAAATAAG\nGGGGTTTGTATACTTTGTTGAGACACTGGCAAGGAGTATATGTGAGAAACTTGAACAATCAGGGTTGCCA\nGTTGGAGGCAATGAGAAGAAAGCAAAGTTGGCAAATGTTGTAAGGAAGATGATGACCAATTCTCAGGACA\nCCGAACTTTCTTTGACCATCACTGGAGATAACACCAAATGGAACGAAAATCAGAATCCTCGGATGTTTTT\nGGCCATGATCACATATATGACCAGAAATCAGCCCGAATGGTTCAGAAATGTTCTAAGTATTGCTCCAATA\nATGTTCTCAAACAAAATGGCGAGACTGGGAAAAGGGTATATGTTTGAGAGCAAGAGTATGAAACTTAGAA\nCTCAAATACCTGCAGAAATGCTAGCAAGCATTGATTTGAAATATTTCAATGATTCAACAAGAAAGAAGAT\nTGAAAAAATCCGACCGCTCTTAATAGAGGGGACTGCATCATTGAGCCCTGGAATGATGATGGGCATGTTC\nAATATGTTAAGCACTGTATTAGGCGTCTCCATCCTGAATCTTGGACAAAAGAGATACACCAAGACTACTT\nACTGGTGGGATGGTCTTCAATCCTCTGACGATTTTGCTCTGATTGTGAATGCACCCAATCATGAAGGGAT\nTCAAGCCGGAGTCGACAGGTTTTATCGAACCTGTAAGCTACATGGAATCAATATGAGCAAGAAAAAGTCT\nTACATAAACAGAACAGGTACATTTGAATTCACAAGTTTTTTCTATCGTTATGGGTTTGTTGCCAATTTCA\nGCATGGAGCTTCCCAGTTTTGGTGTGTCTGGGAGCAACGAGTCAGCGGACATGAGTATTGGAGTTACTGT\nCATCAAAAACAATATGATAAACAATGATCTTGGTCCAGCAACAGCTCAAATGGCCCTTCAGTTGTTCATC\nAAAGATTACAGGTACACGTACCGATGCCATAGAGGTGACACACAAATACAAACCCGAAGATCATTTGAAA\nTAAAGAAACTGTGGGAGCAAACCCGTTCCAAAGCTGGACTGCTGGTCTCCGACGGAGGCCCAAATTTATA\nCAACATTAGAAATCTCCACATTCCTGAAGTCTGCCTAAAATGGGAATTGATGGATGAGGATTACCAGGGG\nCGTTTATGCAACCCACTGAACCCATTTGTCAGCCATAAAGAAATTGAATCAATGAACAATGCAGTGATGA\nTGCCAGCACATGGTCCAGCCAAAAACATGGAGTATGATGCTGTTGCAACAACACACTCCTGGATCCCCAA\nAAGAAATCGATCCATCTTGAATACAAGTCAAAGAGGAGTACTTGAAGATGAACAAATGTACCAAAGGTGC\nTGCAATTTATTTGAAAAATTCTTCCCCAGCAGTTCATACAGAAGACCAGTCGGGATATCCAGTATGGTGG\nAGGCTATGGTTTCCAGAGCCCGAATTGATGCACGGATTGATTTCGAATCTGGAAGGATAAAGAAAGAAGA\nGTTCACTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCTCAGACGGCAAAAATAGTGAATTTAGCTT\nGTCCTTCATGAAAAAATGCCTTGTTCCTACT\n\n>gi|8486136|ref|NC_002022.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 3, complete sequence\nAGCGAAAGCAGGTACTGATCCAAAATGGAAGATTTTGTGCGACAATGCTTCAATCCGATGATTGTCGAGC\nTTGCGGAAAAAACAATGAAAGAGTATGGGGAGGACCTGAAAATCGAAACAAACAAATTTGCAGCAATATG\nCACTCACTTGGAAGTATGCTTCATGTATTCAGATTTCCACTTCATCAATGAGCAAGGCGAGTCAATAATC\nGTAGAACTTGGTGATCCTAATGCACTTTTGAAGCACAGATTTGAAATAATCGAGGGAAGAGATCGCACAA\nTGGCCTGGACAGTAGTAAACAGTATTTGCAACACTACAGGGGCTGAGAAACCAAAGTTTCTACCAGATTT\nGTATGATTACAAGGAAAATAGATTCATCGAAATTGGAGTAACAAGGAGAGAAGTTCACATATACTATCTG\nGAAAAGGCCAATAAAATTAAATCTGAGAAAACACACATCCACATTTTCTCGTTCACTGGGGAAGAAATGG\nCCACAAAGGCCGACTACACTCTCGATGAAGAAAGCAGGGCTAGGATCAAAACCAGGCTATTCACCATAAG\nACAAGAAATGGCCAGCAGAGGCCTCTGGGATTCCTTTCGTCAGTCCGAGAGAGGAGAAGAGACAATTGAA\nGAAAGGTTTGAAATCACAGGAACAATGCGCAAGCTTGCCGACCAAAGTCTCCCGCCGAACTTCTCCAGCC\nTTGAAAATTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTACATTGAGGGCAAGCTGTCTCAAAT\nGTCCAAAGAAGTAAATGCTAGAATTGAACCTTTTTTGAAAACAACACCACGACCACTTAGACTTCCGAAT\nGGGCCTCCCTGTTCTCAGCGGTCCAAATTCCTGCTGATGGATGCCTTAAAATTAAGCATTGAGGACCCAA\nGTCATGAAGGAGAGGGAATACCGCTATATGATGCAATCAAATGCATGAGAACATTCTTTGGATGGAAGGA\nACCCAATGTTGTTAAACCACACGAAAAGGGAATAAATCCAAATTATCTTCTGTCATGGAAGCAAGTACTG\nGCAGAACTGCAGGACATTGAGAATGAGGAGAAAATTCCAAAGACTAAAAATATGAAAAAAACAAGTCAGC\nTAAAGTGGGCACTTGGTGAGAACATGGCACCAGAAAAGGTAGACTTTGACGACTGTAAAGATGTAGGTGA\nTTTGAAGCAATATGATAGTGATGAACCAGAATTGAGGTCGCTTGCAAGTTGGATTCAGAATGAGTTCAAC\nAAGGCATGCGAACTGACAGATTCAAGCTGGATAGAGCTTGATGAGATTGGAGAAGATGTGGCTCCAATTG\nAACACATTGCAAGCATGAGAAGGAATTATTTCACATCAGAGGTGTCTCACTGCAGAGCCACAGAATACAT\nAATGAAGGGGGTGTACATCAATACTGCCTTACTTAATGCATCTTGTGCAGCAATGGATGATTTCCAATTA\nATTCCAATGATAAGCAAGTGTAGAACTAAGGAGGGAAGGCGAAAGACCAACTTGTATGGTTTCATCATAA\nAAGGAAGATCCCACTTAAGGAATGACACCGACGTGGTAAACTTTGTGAGCATGGAGTTTTCTCTCACTGA\nCCCAAGACTTGAACCACACAAATGGGAGAAGTACTGTGTTCTTGAGATAGGAGATATGCTTCTAAGAAGT\nGCCATAGGCCAGGTTTCAAGGCCCATGTTCTTGTATGTGAGGACAAATGGAACCTCAAAAATTAAAATGA\nAATGGGGAATGGAGATGAGGCGTTGTCTCCTCCAGTCACTTCAACAAATTGAGAGTATGATTGAAGCTGA\nGTCCTCTGTCAAAGAGAAAGACATGACCAAAGAGTTCTTTGAGAACAAATCAGAAACATGGCCCATTGGA\nGAGTCTCCCAAAGGAGTGGAGGAAAGTTCCATTGGGAAGGTCTGCAGGACTTTATTAGCAAAGTCGGTAT\nTTAACAGCTTGTATGCATCTCCACAACTAGAAGGATTTTCAGCTGAATCAAGAAAACTGCTTCTTATCGT\nTCAGGCTCTTAGGGACAATCTGGAACCTGGGACCTTTGATCTTGGGGGGCTATATGAAGCAATTGAGGAG\nTGCCTAATTAATGATCCCTGGGTTTTGCTTAATGCTTCTTGGTTCAACTCCTTCCTTACACATGCATTGA\nGTTAGTTGTGGCAGTGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTTTCTACT\n\n>gi|8486125|ref|NC_002017.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 4, complete sequence\nAGCAAAAGCAGGGGAAAATAAAAACAACCAAAATGAAGGCAAACCTACTGGTCCTGTTATGTGCACTTGC\nAGCTGCAGATGCAGACACAATATGTATAGGCTACCATGCGAACAATTCAACCGACACTGTTGACACAGTG\nCTCGAGAAGAATGTGACAGTGACACACTCTGTTAACCTGCTCGAAGACAGCCACAACGGAAAACTATGTA\nGATTAAAAGGAATAGCCCCACTACAATTGGGGAAATGTAACATCGCCGGATGGCTCTTGGGAAACCCAGA\nATGCGACCCACTGCTTCCAGTGAGATCATGGTCCTACATTGTAGAAACACCAAACTCTGAGAATGGAATA\nTGTTATCCAGGAGATTTCATCGACTATGAGGAGCTGAGGGAGCAATTGAGCTCAGTGTCATCATTCGAAA\nGATTCGAAATATTTCCCAAAGAAAGCTCATGGCCCAACCACAACACAACCAAAGGAGTAACGGCAGCATG\nCTCCCATGCGGGGAAAAGCAGTTTTTACAGAAATTTGCTATGGCTGACGGAGAAGGAGGGCTCATACCCA\nAAGCTGAAAAATTCTTATGTGAACAAGAAAGGGAAAGAAGTCCTTGTACTGTGGGGTATTCATCACCCGT\nCTAACAGTAAGGATCAACAGAATATCTATCAGAATGAAAATGCTTATGTCTCTGTAGTGACTTCAAATTA\nTAACAGGAGATTTACCCCGGAAATAGCAGAAAGACCCAAAGTAAGAGATCAAGCTGGGAGGATGAACTAT\nTACTGGACCTTGCTAAAACCCGGAGACACAATAATATTTGAGGCAAATGGAAATCTAATAGCACCAAGGT\nATGCTTTCGCACTGAGTAGAGGCTTTGGGTCCGGCATCATCACCTCAAACGCATCAATGCATGAGTGTAA\nCACGAAGTGTCAAACACCCCTGGGAGCTATAAACAGCAGTCTCCCTTTCCAGAATATACACCCAGTCACA\nATAGGAGAGTGCCCAAAATACGTCAGGAGTGCCAAATTGAGGATGGTTACAGGACTAAGGAACATTCCGT\nCCATTCAATCCAGAGGTCTATTTGGAGCCATTGCCGGTTTTATTGAAGGGGGATGGACTGGAATGATAGA\nTGGATGGTACGGTTATCATCATCAGAATGAACAGGGATCAGGCTATGCAGCGGATCAAAAAAGCACACAA\nAATGCCATTAACGGGATTACAAACAAGGTGAACTCTGTTATCGAGAAAATGAACATTCAATTCACAGCTG\nTGGGTAAAGAATTCAACAAATTAGAAAAAAGGATGGAAAATTTAAATAAAAAAGTTGATGATGGATTTCT\nGGACATTTGGACATATAATGCAGAATTGTTAGTTCTACTGGAAAATGAAAGGACTCTGGATTTCCATGAC\nTCAAATGTGAAGAATCTGTATGAGAAAGTAAAAAGCCAATTAAAGAATAATGCCAAAGAAATCGGAAATG\nGATGTTTTGAGTTCTACCACAAGTGTGACAATGAATGCATGGAAAGTGTAAGAAATGGGACTTATGATTA\nTCCCAAATATTCAGAAGAGTCAAAGTTGAACAGGGAAAAGGTAGATGGAGTGAAATTGGAATCAATGGGG\nATCTATCAGATTCTGGCGATCTACTCAACTGTCGCCAGTTCACTGGTGCTTTTGGTCTCCCTGGGGGCAA\nTCAGTTTCTGGATGTGTTCTAATGGATCTTTGCAGTGCAGAATATGCATCTGAGATTAGAATTTCAGAAA\nTATGAGGAAAAACACCCTTGTTTCTACT\n\n>gi|8486129|ref|NC_002019.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 5, complete sequence\nAGCAAAAGCAGGGTAGATAATCACTCACTGAGTGACATCAAAATCATGGCGTCCCAAGGCACCAAACGGT\nCTTACGAACAGATGGAGACTGATGGAGAACGCCAGAATGCCACTGAAATCAGAGCATCCGTCGGAAAAAT\nGATTGGTGGAATTGGACGATTCTACATCCAAATGTGCACAGAACTTAAACTCAGTGATTATGAGGGACGG\nTTGATCCAAAACAGCTTAACAATAGAGAGAATGGTGCTCTCTGCTTTTGACGAAAGGAGAAATAAATACC\nTGGAAGAACATCCCAGTGCGGGGAAGGATCCTAAGAAAACTGGAGGACCTATATACAGAAGAGTAAACGG\nAAAGTGGATGAGAGAACTCATCCTTTATGACAAAGAAGAAATAAGGCGAATCTGGCGCCAAGCTAATAAT\nGGTGACGATGCAACGGCTGGTCTGACTCACATGATGATCTGGCATTCCAATTTGAATGATGCAACTTATC\nAGAGGACAAGGGCTCTTGTTCGCACCGGAATGGATCCCAGGATGTGCTCTCTGATGCAAGGTTCAACTCT\nCCCTAGGAGGTCTGGAGCCGCAGGTGCTGCAGTCAAAGGAGTTGGAACAATGGTGATGGAATTGGTCAGG\nATGATCAAACGTGGGATCAATGATCGGAACTTCTGGAGGGGTGAGAATGGACGAAAAACAAGAATTGCTT\nATGAAAGAATGTGCAACATTCTCAAAGGGAAATTTCAAACTGCTGCACAAAAAGCAATGATGGATCAAGT\nGAGAGAGAGCCGGGACCCAGGGAATGCTGAGTTCGAAGATCTCACTTTTCTAGCACGGTCTGCACTCATA\nTTGAGAGGGTCGGTTGCTCACAAGTCCTGCCTGCCTGCCTGTGTGTATGGACCTGCCGTAGCCAGTGGGT\nACGACTTTGAAAGAGAGGGATACTCTCTAGTCGGAATAGACCCTTTCAGACTGCTTCAAAACAGCCAAGT\nGTACAGCCTAATCAGACCAAATGAGAATCCAGCACACAAGAGTCAACTGGTGTGGATGGCATGCCATTCT\nGCCGCATTTGAAGATCTAAGAGTATTGAGCTTCATCAAAGGGACGAAGGTGGTCCCAAGAGGGAAGCTTT\nCCACTAGAGGAGTTCAAATTGCTTCCAATGAAAATATGGAGACTATGGAATCAAGTACACTTGAACTGAG\nAAGCAGGTACTGGGCCATAAGGACCAGAAGTGGAGGAAACACCAATCAACAGAGGGCATCTGCGGGCCAA\nATCAGCATACAACCTACGTTCTCAGTACAGAGAAATCTCCCTTTTGACAGAACAACCGTTATGGCAGCAT\nTCACTGGGAATACAGAGGGGAGAACATCTGACATGAGGACCGAAATCATAAGGATGATGGAAAGTGCAAG\nACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAGCGAGCCCGATC\nGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAGTACGACAATT\nAAAGAAAAATACCCTTGTTTCTACT\n\n>gi|8486127|ref|NC_002018.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 6, complete sequence\nAGCGAAAGCAGGGGTTTAAAATGAATCCAAATCAGAAAATAATAACCATTGGATCAATCTGTCTGGTAGT\nCGGACTAATTAGCCTAATATTGCAAATAGGGAATATAATCTCAATATGGATTAGCCATTCAATTCAAACT\nGGAAGTCAAAACCATACTGGAATATGCAACCAAAACATCATTACCTATAAAAATAGCACCTGGGTAAAGG\nACACAACTTCAGTGATATTAACCGGCAATTCATCTCTTTGTCCCATCCGTGGGTGGGCTATATACAGCAA\nAGACAATAGCATAAGAATTGGTTCCAAAGGAGACGTTTTTGTCATAAGAGAGCCCTTTATTTCATGTTCT\nCACTTGGAATGCAGGACCTTTTTTCTGACCCAAGGTGCCTTACTGAATGACAGGCATTCAAATGGGACTG\nTTAAGGACAGAAGCCCTTATAGGGCCTTAATGAGCTGCCCTGTCGGTGAAGCTCCGTCCCCGTACAATTC\nAAGATTTGAATCGGTTGCTTGGTCAGCAAGTGCATGTCATGATGGCATGGGCTGGCTAACAATCGGAATT\nTCAGGTCCAGATAATGGAGCAGTGGCTGTATTAAAATACAACGGCATAATAACTGAAACCATAAAAAGTT\nGGAGGAAGAAAATATTGAGGACACAAGAGTCTGAATGTGCCTGTGTAAATGGTTCATGTTTTACTATAAT\nGACTGATGGCCCGAGTGATGGGCTGGCCTCGTACAAAATTTTCAAGATCGAAAAGGGGAAGGTTACTAAA\nTCAATAGAGTTGAATGCACCTAATTCTCACTATGAGGAATGTTCCTGTTACCCTGATACCGGCAAAGTGA\nTGTGTGTGTGCAGAGACAATTGGCATGGTTCGAACCGGCCATGGGTGTCTTTCGATCAAAACCTGGATTA\nTCAAATAGGATACATCTGCAGTGGGGTTTTCGGTGACAACCCGCGTCCCAAAGATGGAACAGGCAGCTGT\nGGTCCAGTGTATGTTGATGGAGCAAACGGAGTAAAGGGATTTTCATATAGGTATGGTAATGGTGTTTGGA\nTAGGAAGGACCAAAAGTCACAGTTCCAGACATGGGTTTGAGATGATTTGGGATCCTAATGGATGGACAGA\nGACTGATAGTAAGTTCTCTGTGAGGCAAGATGTTGTGGCAATGACTGATTGGTCAGGGTATAGCGGGAGT\nTTCGTTCAACATCCTGAGCTAACAGGGCTAGACTGTATAAGGCCGTGCTTCTGGGTTGAATTAATCAGGG\nGACGACCTAAAGAAAAAACAATCTGGACTAGTGCGAGCAGCATTTCTTTTTGTGGCGTGAATAGTGATAC\nTGTAGATTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCACCATTGACAAGTAGTCTGTTCAAAAAACT\nCCTTGTTTCTACT\n\n>gi|8486122|ref|NC_002016.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 7, complete sequence\nAGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATC\nCCGTCAGGCCCCCTCAAAGCCGAGATCGCACAGAGACTTGAAGATGTCTTTGCAGGGAAGAACACCGATC\nTTGAGGTTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATT\nTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTTAAT\nGGGAACGGGGATCCAAATAACATGGACAAAGCAGTTAAACTGTATAGGAAGCTCAAGAGGGAGATAACAT\nTCCATGGGGCCAAAGAAATCTCACTCAGTTATTCTGCTGGTGCACTTGCCAGTTGTATGGGCCTCATATA\nCAACAGGATGGGGGCTGTGACCACTGAAGTGGCATTTGGCCTGGTATGTGCAACCTGTGAACAGATTGCT\nGACTCCCAGCATCGGTCTCATAGGCAAATGGTGACAACAACCAACCCACTAATCAGACATGAGAACAGAA\nTGGTTTTAGCCAGCACTACAGCTAAGGCTATGGAGCAAATGGCTGGATCGAGTGAGCAAGCAGCAGAGGC\nCATGGAGGTTGCTAGTCAGGCTAGGCAAATGGTGCAAGCGATGAGAACCATTGGGACTCATCCTAGCTCC\nAGTGCTGGTCTGAAAAATGATCTTCTTGAAAATTTGCAGGCCTATCAGAAACGAATGGGGGTGCAGATGC\nAACGGTTCAAGTGATCCTCTCGCTATTGCCGCAAATATCATTGGGATCTTGCACTTGATATTGTGGATTC\nTTGATCGTCTTTTTTTCAAATGCATTTACCGTCGCTTTAAATACGGACTGAAAGGAGGGCCTTCTACGGA\nAGGAGTGCCAAAGTCTATGAGGGAAGAATATCGAAAGGAACAGCAGAGTGCTGTGGATGCTGACGATGGT\nCATTTTGTCAGCATAGAGCTGGAGTAAAAAACTACCTTGTTTCTACT\n\n>gi|8486131|ref|NC_002020.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 8, complete sequence\nAGCAAAAGCAGGGTGACAAAGACATAATGGATCCAAACACTGTGTCAAGCTTTCAGGTAGATTGCTTTCT\nTTGGCATGTCCGCAAACGAGTTGCAGACCAAGAACTAGGTGATGCCCCATTCCTTGATCGGCTTCGCCGA\nGATCAGAAATCCCTAAGAGGAAGGGGCAGCACTCTTGGTCTGGACATCGAGACAGCCACACGTGCTGGAA\nAGCAGATAGTGGAGCGGATTCTGAAAGAAGAATCCGATGAGGCACTTAAAATGACCATGGCCTCTGTACC\nTGCGTCGCGTTACCTAACCGACATGACTCTTGAGGAAATGTCAAGGGAATGGTCCATGCTCATACCCAAG\nCAGAAAGTGGCAGGCCCTCTTTGTATCAGAATGGACCAGGCGATCATGGATAAAAACATCATACTGAAAG\nCGAACTTCAGTGTGATTTTTGACCGGCTGGAGACTCTAATATTGCTAAGGGCTTTCACCGAAGAGGGAGC\nAATTGTTGGCGAAATTTCACCATTGCCTTCTCTTCCAGGACATACTGCTGAGGATGTCAAAAATGCAGTT\nGGAGTCCTCATCGGAGGACTTGAATGGAATGATAACACAGTTCGAGTCTCTGAAACTCTACAGAGATTCG\nCTTGGAGAAGCAGTAATGAGAATGGGAGACCTCCACTCACTCCAAAACAGAAACGAGAAATGGCGGGAAC\nAATTAGGTCAGAAGTTTGAAGAAATAAGATGGTTGATTGAAGAAGTGAGACACAAACTGAAGGTAACAGA\nGAATAGTTTTGAGCAAATAACATTTATGCAAGCCTTACATCTATTGCTTGAAGTGGAGCAAGAGATAAGA\nACTTTCTCATTTCAGCTTATTTAATAATAAAAAACACCCTTGTTTCTACT\n\n" }, { "path": "tests/input/TestOrderAndOrient/ref.lasv.BNI_Nig08_A19.fasta", "content": ">GU481072 Lassa virus strain Nig08-A19 glycoprotein precursor (GPC) and nucleoprotein (NP) genes, complete cds\nATTTAGGATTGCGCATTTTTGGAAACCTTATTGGAAATTCATATAATCAGGATGGGACAAATTGTGACATTCTTCCAGGA\nAGTCCCTCATGTTATCGAGGAAGTGATGAATATCGTCCTCATAGCATTGTCAATTTTGGCAATCCTAAAAGGACTCTACA\nACATTGCTACATGTGGCTTGATAGGCCTTGTCACATTCCTCTTACTTTCTGGAAGGTCATGTTCAATGACCTACAAAGGA\nGTTTATGAACTACAGACCCTTGAACTGAACATGAACACTCTGAATATGACTATGCCGCTATCTTGTACAAAGAACAATAG\nTCACCACTACATCATGGTGGGAAACGAGACAGGGCTTGAGCTCACCTTAACCAACACAAGCTTGCTCCATCACAAATTCT\nGCAACCTATCAGATGCTCATAAGAAAAATCTTTATGATCACACTCTCATGAGCATTATCTCCACATTCCATTTGTCCATT\nCCTAACTTTAATCAGTATGAGGCAATGAGTTGTGATTTTAATGGTGGCAAGATCACTGTGCAATACAATCTGAGTCATAG\nCTATGCAATTGATGCAGCAAACCATTGTGGCACAGTGGCAAACGGTGTGTTGCAAACATTTATGAGGATGGCTTGGGGAG\nGTAGTTACATTGCCCTTGATTCCGGACGTGGGAAATGGGATTGTATAATGACCAGTTATCAATACTTAATCATCCAGAAC\nACAACCTGGGAAGATCATTGTCAATTTTCCAGACCATCCCCAATTGGATATCTTGGGCTCCTCTCACAGAGAACTAGAGA\nCATATACATTAGTAGAAGACTACTAGGAACATTTACTTGGACACTTTCTGACTCAGAAGGAAATGAGACACCAGGAGGTT\nACTGTCTCACTAGATGGATGTTGATTGAGGCTGAACTAAAGTGTTTCGGGAATACAGCTGTAGCTAAGTGCAATGAAAAA\nCACGATGAAGAGTTTTGTGACATGCTAAGGCTATTTGACTTCAATAAGCAAGCTATAAGGAGGTTAAAGGCAGAGGCCCA\nAATGAGCATACAGCTGATCAACAAAGCAGTTAATGCTCTAATAAACGATCAGCTGATCATGAAGAATCATCTAAGGGACA\nTCATGGGAATACCATACTGCAATTACAGCAAGTACTGGTATCTCAATCACACCTCAACAGGGAGGACCTCATTACCGAGA\nTGTTGGCTTGTTTCAAATGGGTCATATCTCAATGAAACTCACTTTTCAGATGACATTGAGCAGCAAGCTGATAACATGAT\nAACTGAAATGTTGCAAAAAGAATACCTGGACAGACAAGGAAAGACCCCATTGGGATTGGTAGATCTTTTTGTCTTCAGTA\nCAAGTTTTTACTTAATCAGTATTTTCCTCCATCTGGTCAAAATACCAACCCATAGACACATTGTAGGGAAGCCTTGCCCC\nAAACCTCATAGGTTGAACCACATGGGCATCTGCTCTTGTGGTCTATATAAACAGCCAGGAGTACCCGTTAGATGGAAGAG\nATAAAGATCCCACAGGGCCCCCGTGACCCACCGCCAATTGGCGGTGGGTCACGGGGGCATCCGTTTACAGGACGACTTTG\nGGTGTCGAAGTTCTGAACACCATATCTCTGGGGAGCACAGCCCTCAGGACCTTTGCATCAACTCCTCCTGAGACTGCAGC\nATCAAACATGATGCAGTCCATTAATGCACAATGAGGTGTTATTTCCTCCTTGCCTCCCCTCTTTTTCTTCTCCACAACAA\nTCCCGGTGTGCATGTGACATAAATCCTTGAATTGATCCCACACAGCATTCTCAAATTTTCTTGAGTCCACCTTACTAAGG\nGAAATGTCAATCAGTTTTATATCCCTCCTCCCCTGTGACTCCAGAAGTTTTCTGATGTCTTCTGACCCTTGACAGGTGAT\nGACCATGTTTCTAGGAAGAGCCTCTATCACTGCACTTGTTAACCCTGGCTGTGCAGCAAACAAATCTGTCACATCAATAC\nCATGTGAATATTTTGCATCCTGTTTAAACTGCTTTAAGTCTGTCGGTTCCCTGAAGAAGTGTATATAGCAGCCTGAACTT\nGGTTGATACAGAGCTATTTCAACTGGATCTTCTGGTCTTCCCTCAATATCCATCCAAGTCTTTGCATTTGGGTCAAGCTG\nAAGCATTGAATCCTTTAAGGTCATCAGTTGAGAATAAGTCAGTCCTGCAGCAAACCCTGCAGATTGCAATGACTTATTTG\nAACCCCCATTGCCGGTCTTTTGCGGTTTGTTGTCTGACTCTAAGTCAACCACGGTGTTCTCCCAAGCTCTTCCCACAATT\nGAAGTCCTTGATGCAATGTAAGGCCACCCATCTCCTGAGAGGCAGATTTTGTACAGTATGTTTTCATAAGGGTTCCTTTC\nACCTGGCGTATCTGAGATGAACATTCCCAGGCTTCTCTTGACTTTCAAGATTGACTTCAAGATGCCATCCATGGTTTGAG\nGTGAGACCTTTATAGTCTCTAGCATATTGCCTCCATCAAGCATGCAGGCCCCAGCCTTGACGGCGGCTCCTAAACTAAAA\nTTGTAACCAGAGATGTTAAGGGAGCTCTTCTTAGTATCAATCATGTTCAATATCGGATGGCTCTGGGCCAGCCTGTCCAA\nATCAGATGAATTAGGGTATTTTGCGGTGTAAATCAATCCCAAATCTGTCAAAGCCTGAACAGCATCATTCAAATCCACTT\nGCCCTTGTTTGGTCAAACATGCTAGAGTTAGACTTGGCATTGTCCCAAACTGATTGTTAAGCAGCTCTGCATTCTTGACG\nTCCCAAACTCTCACAATACCATCACTAGTGGTATTCCTTCCCCCATTCCCACCAGTCATGCCAATCATGTTGAGGAGGGC\nCTTCCTCTGATCAAGCTGCTGTGAACTTAGATTCCCCATATAAATTCCTGAGCTCAGGGGTCTTTCTGTCCTAACAACCT\nTTGACTTCAGTTTTTCCAGGTCAGCAGCCAAAACCAATAGATCGTCTGAACTTAGGGTTCCAACCCTCAGCACACTCTTT\nTGTTGAGTTGACTTTAGTTCAACAAGGTTGTTGACTGCTTGATTGAGGTCTCTTAGCCGTTTAAGATCACCATCGTCCCT\nTTTTTGTTTGCGCATCAAGCGTTGAACATTACTGACCTCAGAGAAGTCCAAACCATGAAGGAGAGCTTGAGCATCCTTTA\nCCACCTGGAGTTTTATATTGGAGCAATAGCCAGATAACTCTCTTCTCAGAGACTGAGTCCACAGGAATGATTTCACTTCT\nTTGGAAGCACTCATTATTGTGGTTACTGTATGACTGTCAGAGAATGGCAGATCCTCAACACAGTTGTTCCACAAGTATGA\nGCAGTGCAAAGCGCAATCCAATA\n\n>GU481073 Lassa virus strain Nig08-A19 Z protein (Z) and polymerase (L) genes, complete cds\nAATTTTGTATGCCAATGTTGTGTGCTTCCTATTGAGTCGAGCAATATGGGTGGCAAACACACCAAACCACAGAGAGAATC\nCAACAGTCCCAGAGCCTCTCTAATTCCCGATGCAACACACCTGGGCCCTCAATTTTGCAAGAGTTGTTGGTTTGAGAACA\nAAGGTCTGGTGGAGTGCAACAACCATTACTTATGCCTCAACTGCCTTACTTTACTCCTGTCTGTCAGCAACAGATGCCCC\nATCTGTAAGATGCCCCTCCCCACGAGGCTGAGAGCATCAACCAACCCAACAGCACCCCAGGTCGAACAAGTCGGCCCTAC\nAAATCCTCCACCATACAGTCCCTAACTCATCCCAAACAACAACACACCAGATCTCCCTTCCACCCCCCGACACCCCCCGG\nGGGGACCCCCCGCCGGGGGCCCCCCCGGGGGAGCCACTCCGAAGCTGCTACTCAATATCCTCAACACCTCCCACCTCTTC\nTAGCAACTCCTCACACGTCCTACCCTTAAGCCTCAGCCTCCCACCACTCGACTGTATCATAATTTTCCCTTTGGATTTAC\nTGTAACACAGGGCATACCCCTTAAATTCTACCCATTCATCTATTGATCTTAATACGTTATGTAAAACCCTCATGGCACTA\nTCAGGCATTGCCTTTTTCAATAATTGAACAATATCCACCCCTGACCATTGAACTTTGAGTTTCAATCTATCCGCTATCAT\nGGCAGTCAGCGCTCCAACCATCAGATCATGAGAACTATCATCAATCTCTTTTACAAAAATCTCAAGATCTTGATCTTGAA\nTAACAGGTGTAAATGCTGCCAGTTTTCTGTCACACTCCCAAAGAGCTCCCCTATTGACGACCAATGGGACTGGCTCAGTA\nTGAGGACCTACCTGCACAAAATCATACTCTGTGAACTGCAACTTGTCAACATCCACAACAATTTTAATGGGGGTAACAGG\nGCCGAGCTCCTTTGAGTCTATCAAAAACTCCTTGATGACTTCAGTGTCAACAAACCAAGAAGAGTCATTCTTATAAGTAG\nGTCCTGACAAAACCAGCCTCCAACAATCTGGCAAAACACATGAGTTAACAGAGCCAGAATACATAGCACTCACATCATCG\nACAATGTATCTCCCTTGTTGTGTCATTGATCCAACAAACTCAAGGTGAATGGAGAAGCTCTCCTTAAAACATGCATCCTG\nACTCTTAATCTGAAACCTAATTGTCTGGTTCAATTTTACTGAGCCAGGTGGGAGAGATCCCATAGATTCAAGAAAATCCT\nCCAAGGACTCTAATCTAACATCAACTAACCCTGAAGCTATCAATTGATTCTGATTAAACCTTGCTGGATCAATGTCATAA\nTCTATCCATGCATAACCCATCATTAAATCGTGTTTGAACATCGGCCTCTCAATGCCTTTGTGGATTACTTTCTCCACAAA\nTGAAGAAAAAGGCCCAAGTCTCTGTAAACCTTCCCCCTCTGGAATGGATGTCCTATGTGGGAACCATGTGAAGGACCCCA\nAGGTTCTTGTTGTCGCAACAAATGATCTTACGTATGACTCAAAGTAAATTTGTCTCATAAAGTTGTCGACTGCATCACTA\nGTGCTAACAACCCTCTCTTCTATCATCGGTTCATGTATTCTGCTGTGAGATTGCCTTAATTCAGATGATAGGACGATATA\nGTGTTCTTCTCTTTTCCACTTAACAATGTGTGACACAAGGGACAATGCTTCACAATTCACATCCAGTGCCACACAGAGAT\nCCAGAAACTTAATTCTTGGAGACCACTTCATTTTTGTAGAAGCTAGATCGCTCATAAAAGGCAATATGTGTTTCTCAAAC\nATTGTGGGATACAATCTTCTTAAGGAATGAATAATGTGGTTAACACCCACTCTATCCTCTAGGAGCTTTGATGCTGTGGG\nTTTTAGTGGGAAATAATCACAGGGGTTATGCTTAAAGAATGCCAGTGGCTTTGATTCCTTAGGCTCTCCTAGGACCCATG\nCTCCGAGCTCTATTGCAGTTGATAACGAAATGCACATGTAGTCCCACAATAAAGGTCTGAAATAAGCCAAAACACTCTCA\nCACTCACCCCTGACCTTCAGGGGGACCCTCCAAAACTGCACCCCATGATTGTTTGTGAGCATCTCAATGTCTTTAATACC\nAGCTATTGATGAAATTATTGATCTTATGTAGAGATTCTCCTTATTCGGTCCTCTAACACACTTACTACCCAACGTTCTAC\nACAGTCCTACGAACCCAGAGGCTATGGAGCTTTGGAATGCAGATTTATTTATGGCTTCTGAGAGCAACTTCTGTGCACCC\nCTTGTGAAAGTTGATGACAACTTGTTTTGGATTGTCTTAACAACAGTGGGAATCTTTTCATCATCTAGATTGACAGCACC\nTGAGTAAATAATTTTCTGTCGAAGCACCATTCTTAGTGGGTGATGAGCAGCCAAATTCAGCCAGCATAGCTCCAGATCAG\nCTTTTGATGGGGGCTCCACACCCAACATCTCACTGAGGTTTTCCAAAGATGTCAGGTGCTCACCTGATAAGTAATTGGTT\nGTGAATTCTTCATGTAATTCACCTGTTTTTAGCCTATTGAACAGTCTTCTCAGCATGGACCTTACTCTACGGCATGGCTC\nTGGAGCTAACTTCTCGATCTGCCTCATAATTCTGTATGAACGGTTCCCATCAACCCAATCTCTCACGTCAGTCTCACAGT\nTCAAAAGGAATGGGTCAATGGGATATCTAGCATATTGTAAGAGGGATAATGTCCTCAATTGAATTAAGTTGCACAAGTGA\nACAGGCACTCCATTGGCAACCGATTGATCTATTATTGTATCTATTGTCTCTGCAAGTTGATGGGGCTCTTTACATTTTAT\nGTTATGGAGGGCAGCTGCAACAAACTTTGTTAATAGCGGTACTTCATCACCCCATACATAAAACCTTGATTTGAATTCTG\nCAACAAATCTTCCAATAACACTTTTCGGACTCACAAATTTGTTGAGTTGATCACTCATATATAAGTGAAACTCTAATAAA\nGTCTTAAATTCTTCAGGGTCCCTGGCCATGAGCATGGTGAGGTTTTGATCAAACATTGATATTTGATCATCACTAGAGGT\nGTATGCATCAATTGAACCGTCACAAACACAACTAATGGCGTAGTTTATGAACCTTTCAGAAATTAATGCATAAAAATCTG\nATGTGTTATGCAAAATTCCTTGTCCCATATCAAGAATTGAGCTGATGTGGGAAGGCACCCTACCAACCTGAAAGTTTGAA\nTAGAAAAAATCTTCAGTTGCAGTTTGAGACGTACTCTTTCTTAAACCTAACTGAGCCTTTATATAAGATTTCATCATTGC\nTGACACAACATTAAAGGGTATCTCAACCATTTTATGCATATGCCATGTTAATAAGGTAGAGAGGTAATCACGTCCTTTAA\nTGTCAGCTTGTAAATCCTTTGACATAAACACTAGGTTTTGTAAGACTGCAAGGAACAAGAATGGACACATCATCGGACCC\nCATTTACTATGGTCCATGCTATAAGAAACATGTGCCAAAGACACATTCAATTTCATTGAGAGAATCGCATTCTCAAATTC\nTTTCTCATTGTTCAAACAGCTTCCAGACAACTGCAAACTTAATGCCTCAAAATAATCTTCAATCAACCTGGTGAACATCT\nTCGTCCTAAGGTCTCCGATGTACAACTCCCTGTTGCCACCAACTTGCTCCTTGTAGGACAAAGAGAATTTCAGTCTACCT\nGTGTCTGGCCCAATTGAGTTATAAGACTGTGGTGATTCCTGGCTGTAGAAACACAGATTCTTCAGCATTGCAGTGGTGCA\nGTTTGTCAGAGATAAAGCCTTACTCAGTGCCTCTGAGTTGCTTTCTCTTTCACTAATTCTAGTATCCTCAGTGAGTCTAC\nTCGTGTCAAATTTAAAATTCAAACATCTTGACTTATAATGAGAATACCTTCCCATCAGTTTGTTACCATTCATCAGCAGC\nATTATTGATTTAAAGCATTGAAAGTACTCAAGGTCAAGATATGTTCTTGTGGCTACTGCTTTGGTGAGCTCTCCGATGGG\nACAACCTGTCATAGGTCCGCAATAAAAATACTTATCCTTCATTTCAGAATCATTATAAATAGTGTCACAGAATTCTTTGT\nAGAAGCCTTCTGGTAGGATTTCATAATCAAAATCTTCAACCATATGGTTAGACAACTCACTCTTAATTAGTCTAATGTAA\nAATTTATTAGACACGATCTTCTCTAAATCACTCATTAGAGGGGCACCATCACCCTTCATATGTGAAGGTGACTTGACTGG\nCTCCTTGTATTGATCTATTATCTTTTCAATTGTCCCCCTCAATTCATCGAAATATTCAGATGCCCCTCCATCAAGAAGGG\nCTTCATCTAGATCAGTGCTGTCAATATCAACAGTGCGAGCTTTAGGACCTAATACTAAATTGCTCATTGCCTGTTGTATC\nTTATATTCATAATCTTGCTTGTTAAGTAGATGTTTACCTTTTCGTGAGAATGTCTCAGTCAACTGTGTGACGGCTAATGC\nTGTGAGTTTGTTAAAGTCATAGTTCAGCACCCTAGAGCCATCTGTATACTTGTTGACGACCACACTTTTATTGCTTGCTA\nAGTCTAAAGCTGTTGCACATCCACTTGTGATAAGAGGATCTTTCATTTCTTTCTTTATTTCCTTTCCTTTGAAAAGGGAG\nCCATTATTGAAAGAAGACGCAAGTAAAGATAAATACTTTTTAGAAACACCTGGTTTCTTGTAGCTTAATCTGCTCACTTC\nAGTGCATCCTTTCTTGCTCAAAAACATCTTTGCATTGTAGATCATTTCATCCATTTCATCCTTGGTAGCTAGATCTGTAG\nGATTAACAGTAACATGGCCAAAATCCAACTTCGGTTCAAGAAATTTTTCAAAGCATTTGATTTGGTCTGTCAATCGATCA\nGGGGTTTCCTTCGTAATGAAGTGACACATATAAGAAACATTTAAGACAAATTTAAACCTGTTAGTCAGCATGCTTTTTAC\nATCTTTGTGCAACACAATGTTTAACAGTGCTCTAATGAGTCTATAGAGTAAAAACTCAACTTTTGTGATCAGCCTTTCCT\nTAAGTTTCTGGATCAGCTCTTTGTGATAAAAATCGGAGACATAAGCCATCACAAAGTACCTTAAATTTTGGAGAAGCTTT\nTGACTGCGTTTACTCGGATGTGCTAAGATTAGAATCAAAATCATCTTGGTCAAAGACTTAATGCTGATCATCTGATCTAC\nCAGCTCAGTACATTCTCCAATCCAGCTGACCATAACATCCACAGTTGACTGTAAAACTTCAGCTGAAAATATTGCAGGAA\nAAAACCTCTTTGGGTCTGCATAAAAGGAGCAAACTTCACCAACTGAATTGTTGTTTATAGCATAACACTTAGAGCATTCA\nCCTGTCTTTTGGTAAAGCAGCTGGAAATTTTCTCCGTCTAGAGTAAAATCCTGACTGTATGCCTCTTTGCACTTCACCAC\nTTGATATCTAGCTGCTCCAAATTCATTCTGCCTTATTTTCACGGTTGATGAGGTTTTCATAGAATTGACCAAAGCTAGAC\nTGAGTGATGACAACCTCTCCAAGTCAACTGAGTCCATAATACCAACTGTACCCATTGGATAAGGAAACTTCTCTTCCTCA\nGATTTCTGATAACTGATGGTAGGGGTGATCCCGGAGACATCAAAGCTTAAGACATCATCATAGGTTTGAGGAGTAATTAT\nGTCCATATCAATGCCGTAGTGGCTCACATCTATCCCAACGTCAGCTAAAGCAGAAGTGGCTTTCTCAATGGTCTTTTGAA\nTAATGGTTCTTAAGATTTGATTTTTGTCCAAACAAGGAAGAGGAGCAGTTATATGGGGCTTGGAAACCTCTACTCTACAC\nCTCCTCTCTAACCACTTCTTTAGGTCTCTTTTTGTTGACTCCAAGGAGACCAAACGATCATTTACACTTACAAAGCTGGA\nTCCCAACCATCCTTTTGGGTTGTTGCATTTATTCCTCATAAAATCTCTCCTACTTGCAAGGAGTATCAAGATGTCAAAAA\nCCAACATCAGCTTTCGTCTAGTATTTAAGATCCTTAATGATTTAACCTTATTCAGGAATGATCTCCAGCATTGCATCTGA\nTCCTCAGTAGTCATAATATCTTTGTTGGCTCTGCCCTCAATATCTGCATATAAGAACCTCATAATTGGCGACACTCTCTT\nATATTGATGAATCAAGCAATCAATTGTATCCTCCTGAACCACAACCTCATCACTATATAAGTTATTAAATTTGTGCATCA\nGGTCCTCTTGGTCAACCCTCACAAATTGACTCTCTATATCTCCCTGCCTAATTCTGTTCCTAAAAATTTGATACTCTTCT\nTCAATTTGTGTCCTCACTTCATGAGCTGACATCTTATTATTGATGCCCTGATGGCAAAGAGTGATTATCTCTTCATAGTG\nAGTAGTACGTTTATCTGTTAGGACATTGATGCTCTCTACACCAGAAAGCCTACCAGATGTCATTGACAAGGATTCACAAA\nGCCTAGAATATTCAGACTCCTCAAAAAGTGAATTGCTCTCTTGAGCAAATTTCAACAGTGAAAACAATGTCTCTCTCAAC\nTTGTCATTCACCCAATCTGGTATCTGTTCGTTATAAAAAGATGTTCGCCCATCAATGAGGGGAATGAGGGTGATGTCTAC\nAGATTTCAAGTCATCTTTTAACTGTTCCAACTTTTTAAGGTCTTCAACATACTTCTGCTCAAAATTAGCAGGAGATGATC\nTCACAAAACACTCGAGCAGTATGAGGATGTTGCCTGTCAATTTATATCCATCAGGAACCACGAAACAAAGAGACGGTGTC\nAAGATTCCATGATCATGGAGAATACTTTCAACAGATTTATTCTCAGTGTTGTGCTCACACCCGTTGGCACTGCAAGAGTC\nCACCTCAATACAAAGGGACAAGAGTTTTAAACCTTCCATCAAAAGCATCCTTGGCTCTGTCTGAACAAGGAATGCTAGTT\nTCTGTCTTGAGAGCTTGTCATTATCTATTAGGTATTTTGAGACTAAGTCCTTGACAGAGGCTATGTCCTCCTCCATGACC\nCCTAGGAGCTCCCAGGGGATTTTGGCAAACGGAAATCAAAAGTAGTTCATAGAATAGAACACCAAAAT\n" }, { "path": "tests/input/TestOrderAndOrient/ref.lasv.ISTH2376.fasta", "content": ">KM821998.1|LASV-ISTH2376-S-NG-2012H\nCCTAGGCATTTAGGATTGCGCTTTTAGAGATCTTTGTGTGAGTGAGCTTCATCAAGCCAT\nGGGGCAAATTATAACATTTTTCCAAGAAGTACCTCATGTCATAGAGGAAGTGATGAACAT\nTGTCCTGATTGCTCTCAGCCTTCTGGCAATTCTGAAAGGGATCTACAATGTTGCTACATG\nTGGCCTTTTTGGACTGGTGTCTTTTCTCCTCTTATGTGGAAGATCATGCTCAACAACTTA\nCAAGGGTGTTTATGAGCTACAGACTCTAGAGCTAGACATGGCTAGCCTTAACATGACAAT\nGCCCTTATCTTGCACGAAGAACAACTCCCACCATTACATCATGGTCGGAAATGAGACTGG\nCTTGGAGCTGACTTTAACAAATACAAGTATTATCAACCACAAGTTTTGCAACCTCTCTGA\nTGCACATAAGAAGAATCTTTATGACCATGCTTTAATGAGTATCATCTCAACCTTCCACTT\nATCCATTCCCAACTTTAATCAATATGAAGCGATGAGCTGTGACTTCAATGGGGGGAAGAT\nAAGTGTGCAGTACAACCTCAGCCACACTTACGCTGTGGATGCGGCTAACCACTGTGGGAC\nCATTGCCAATGGCGTTCTTCAGACTTTTATGAGGATGGCTTGGGGTGGCAGTTACATAGC\nACTTGATTCCGGAAAGGGGAATTGGGATTGCATAATGACTTCCTACCAATATTTGATAAT\nCCAAAACACCACTTGGGAAGATCACTGCCAGTTTTCTCGTCCATCCCCCATCGGTTATCT\nGGGGCTACTGTCACAAAGGACCAGGGACATTTATATCAGTCGAAGACTTCTTGGGACTTT\nCACTTGGACTCTCTCTGATTCCGAAGGTAATGAAACACCGGGTGGGTATTGTCTAACAAG\nATGGATGCTGATTGAGGCCGAGTTGAAGTGCTTTGGGAACACAGCAGTTGCAAAATGTAA\nTGAGAAACATGATGAAGAGTTTTGTGACATGTTAAGATTGTTTGACTTTAACAAACAAGC\nTATAAGTAGGCTGAAGACAGAAGCACAGATGAGTATCCAACTGATAAACAAAGCAGTAAA\nTGCACTGATCAATGACCAGCTGATTATGAAGAATCATTTGAGAGATATCATGGGAATTCC\nTTATTGCAATTACAGCAAATATTGGTATCTAAATCACACTGTAACAGGGAAGACATCGTT\nGCCAAGATGCTGGCTTGTGTCAAATGGTTCCTACCTGAATGAAACACATTTTTCTGATGA\nCATTGAACAACAAGCAGACAACATGATAACAGAAATGTTGCAAAAGGAGTACATAGATAG\nGCAAGGGAAAACACCCTTAGGGTTAGTAGATCTTTTTGTCTTCAGCACCAGTTTTTACCT\nTATTAGCATCTTCCTCCACCTGGTTAAAATCCCAACCCACAGACACATCACAGGGAAACC\nCTGCCCCAAACCACACAGACTCAACCACATGGGCATATGCTCATGTGGTCTATACAAACA\nTCCTGGTGTGCCAGTCAAGTGGAAAAGATAGAAGATAGACCCACCCATGGGCCCCCGTGA\nCCCACCGCCGAAAGGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACCTTGGGGCTT\nGAGGTTCTAAACACCATGTCTCTGGGGAGAACTGCTCTTAAAACTGGTATATTGAGTCCC\nCCTGACACAGCTGCATCATACATTATGCAGTCCATCAAAGCACAGTGCGGGGTAATTTCT\nTCTTTACCTCCTCTTTTCTTCTTTTCGACAACCACTCCAGTATGCATATGGCACAGATCC\nCTGCACTGATCCCAAACAGCATTTTCAAATCTCCTAGAGTCAGCCTTACTCAGTGCAATG\nTCAATAAGCTTTATGTCCCTCCTTCCCTGAGAGTCCAAGAGTCTCTTAATATCATCTGAA\nCCTTGACAGGTCAGTACCATGTTGCGAGGAAGGGCTTCAATAACTGCACTGGTCAGGCCA\nGGTTGAGCAGGGAAAAGATCTGCCACATCAATCCCGTGAGAATACTTGGCATCTTGCTTG\nAACTGTTTTAAATCTGTTGGTTCTCTGAAGAAGTGTATGTAACAGCCCGACATGGGTTGG\nTAAAGAGCTATTTCCACAGGATCTTCTGGACGACCTTCAATGTCTATCCATGTTTTGGCA\nCTTGGGTCAAGTTGCATCATTGAGTCCTTAAGTGTCATCAACTGAGAATAGGTCAGCCCC\nGTTGGAAACCCCGCTGACTGTAAAGACTTGTTGGACCCAGCAGCACCCACTTTTTGTGGT\nTTTCCATCTGACTCGAGATCCACAGTAGTATTCTCCCAAGCTCTACCCGCAATAGAAGTC\nCTTGAAGCTATGTAAGGCCAGCCGTCACCGGAAAGACAGATCTTATAAAGTATGTTCTCG\nTAAGGGTTCCTCTCACCAGGTGTGTCTGAAACAAACATTCCCAAGGATCTTTTTACCTTT\nAAAATAGACTTCAAGATGCCATCCATTGTCTGAGGTGTAACCTTGATGGTCTCCAACATG\nTTCCCCCCATCAAGCATACAAGCTCCAGCTTTCACTGCAGCTCCTAAACTGAAGTTATAA\nCCAGAAATGTTCAAGGAGCTCTTCTTGGTGTCCACCATATTCAGTATAGGATGGCTTTGG\nGAGAGTCTGTCCAGGTCGGAGCTATTTGGATACTTAGCTGTGTATATTAGACCCAGGTCT\nGTCAGTGCTAAGACGGCATCATTCAAATCAACTTGACCTTGTTTGGTGAGACATGCTAAT\nGTCAGACTAGGCATGGTGCCGAACTGGTTGTTCAGAAGATCCGGGTTCTTAACATCCCAC\nACCCTAACAACTCCGTCTCTTCCAGGTTGGGTGCCCTGAGCCCCACCAACCATGCCTATC\nATGTTCAGCAATGCTCTTCTTTGCTCAAGCTGCTGTGTACTTAAATTCCCCATATAAACA\nCCTGAGCTTAGTGGCCTTTCTGTTCTAATGACCTTCGACTTTAGTTTCTCTAAGTCAGCT\nGCCAACGTCAACAGGTCATCTGAGGTCAGGGTCCCAACTCTCAAGATGCTCTTTTGTTGC\nGTCGATTTGAGTTCTACAAGATTGTTGACAGCCTGATTCAAATCTCTAAGACGTTTCAGA\nTCACTATCATCCCTTTTTTGTTTGCGCATTAAGCGTTGCACATTGCTGACTTCAGAAAAG\nTCAAGACCATGAAGGAGAGCCTGAGCATCCTTAACAACTTGAAGTTTTATGCTGGAGCAA\nTAACCTGAAAGCTCCCTCCTCAATGACTGTGTCCAGAGAAATGACTTCACTTCCTTGGAA\nGCACTCATCTTAGTCTGGACACCTAGGGATTGACTGGTCAAAAGTTTCACTCAGTAAGTC\nAATGAAAGGCGCAATCCAGTAGCCTAGGATCCACTG\n\n>KM821997.1|LASV-ISTH2376-L-NG-2012H\nATCCTAGGCAATTCAGCTGGACTTCAGTGGTGAGGCTCACTTTGGTGAATTCCTGAATTA\nAAGTACCTAGTCAAAATGGGCAACAGACAGGCCAAATCGACAAAAGTCGATGAACATCAA\nAGAGCTCATCTAGTGCCAGATGCATCCCATCTAGGCCCCCAGTTCTGCAAGAGTTGCTGG\nTTTGAGAACAGAGGGTTGGTAGAGTGCAACAATCACTACCTGTGTCTCAACTGCCTCAGC\nCTGCTCCTCAGTGTCAGCAGCAGATGCCCGATCTGCAAGATGCCCCTTCCCACCAGGCTA\nAAGGCAGCGACACAGCCGAGCGCACCATCAACTGAGGCGACCCAGACCACAACACCTCCA\nCCATACACCCCATGATCCCGGGATCAACACTCCCACCTCCACCGCCCACCCCNNACCCCC\nGGGGGGACCCCCCGCCGGGGGCCCCCCCGGGGGGGCAGGCGGTCCAGCTCTACTCGATGT\nCCTCAACACACTTCTCTGGCCCAAACAACTCCGAACATGTCCTTCCCTTCAGTCTTAGGC\nTACCCCCACTTGACTGTATCATCACTCTTTGCCTTGATTTACTATAGCAAAGAGCATAGC\nCTTTGAAATCAATCCATTCTCCAAGAGATTCAAGAAGTTCACTCAGTATATTAGCATAAT\nCCATAGGTCTCTGTTTAGTAAGGATTGAGACAATGTCCACATCCGTCCATTGAACCCTTT\nGTTTCAATCTATCAGACATCATTGATTTCAATGCACCAACCAAAAGATGCGGGGAACTAT\nCACCAATCTCCCTTACAAACATTTCCAGATCTTGATCTTGGATAGATGGTGTAAATGCAG\nCTACCCTTTTATCAGATTCCCACAGTGCTCCTCTACACACAACCAATGGCACTGGTTCGT\nTGTCAGGTCCGACCTTGGTGAAATCAAACTCACTGAACTGCAGTTTATCTGGATTAATAA\nTCAGCTTCATGGGTATAACATCCCCCAACTGCTGTGTATCCTTTAAGAATTCATTTACCA\nCATCTGATTCAACAAACCAGGATGATCTACCTTTGAAAGTTGGGCCCGACAAAGCAAGTC\nTCCAACAGTCAGGCAGGACACATGGGCTCACAGACCCAGAATATAGTGCCTGTATATCAT\nTCACTACAAACTCACCACATTGATTAACAAGTCCTGTCATGTTGAGATGGATAGAAAAAG\nTCTCTTTAAAACTAGCATCCTGACTCTTGATTTTATACCTAATTGTCTGGTAAAACTGAA\nCAGAGTCTACTGGCATTGTGCTTAACAAATCAAAGAAATCTTCAAGGGAGTCTAACCTCA\nATTCCTCTGTCAGGCCTGAAGCAATGAGCTGGTTCAAGTTTATCTGAGCTGGTTCCATGT\nCAAAATCTATCCATGCATAGCCCATCATTAGATCAAACTTAAACATGGGTCTCTCTATCC\nCTTTGTAAATGGCTTTCTCAATGAATGAAGAGAAGGGACCCAGTCGCTGTAAACCTTCAC\nCCTCTGGTATTGAAGTTTTATGAGGAAACCAAGTGAATGACCCAAGTGTCCTTGTTGTTG\nCTACAAAAGAGCGGACATATGATTCAAAGTAGACTTGTCTCATAAAGTTGTCCACTGCAT\nCAGCAGTACTAACCACCCTTTCCTCCATCATGGGCTCATGTGTGCGAGAGTGTGAGTTTC\nTCAGTTCAGAAGCCAATACAACATAATGTTCCTCCCTTTTCCACTTGACAATGTGTGAAA\nCAAGTGAAAGTGCCTCGCAATTCACATCTAGGGCAACACAAAGGTCAAGGAACTTTATTC\nTAGGTGACCATTTCATCTTTGTGGAAGCTAAATCACTCATAAATGGCAAGATGTGCTTCT\nCAAATAGAGACGGATATAAACGTCTCAAAGAGTGGATGATGTGGCTCATGCCAACCCTGT\nCCTCTAGCAGTTTCGAAACAGTGGGTCTCAAGGGGAAATAATCACAAGGGTTATGCTTAA\nAAAAGTCCAAGATCTGAGCTTGTTTTGGTTCCCCGAGCACCCACGCTCCAAGTTCTATAG\nCTGTAGATAGTGTTATGCACATATAATCCCATAGAAGAGGTCTTAAATAAGTGACAACAG\nTACTACCTCCATCTTTGGCTTCTGGTGAGACTTTCCATATCTGAATTCCATTGTCCCCCA\nTCACTGCTTCAACACCCTGAGTCCCCAATAGTTGAGTCTGTATGGATCTAATGTAAAGAT\nTCTCCTTGTTGGGGCCTCTGACGCACTTGCTACCCAGTGTTCTGCACAACCCCACAAACC\nCAGATGCTATAGAACTTTGGAAAGCTGATTTATTTATTGCTTCAGACAGTAGCTTCTGAG\nCTCCTCTAGTGAATGTGGATGACAACCTATTTTGCAAAGTCTTTACTATTGTAGGGACCC\nTTTCATCTTCCAGATTCACAGCGCCAGAATAGATAATCTTTTGCCGCAACACCATTCTAA\nGTGGGTGATGGGTGGCTAAGTTCAACCAATGAAACCCCAAGTCAGAATCAGACAAAGGTT\nCAATGCCTAGAAGTTTAAACAAATTCTGTAATGATGTTGTGTGTTCACCTGATAGGTAGT\nTGGTGGTGAATTCCTCATGAAGCTCACCAGTTTTTAATTTATTGAACAATATCCTAAGCA\nTTGACCTCATCTTTTTGCATGCATCAGGAATTAGCCTCTCGATCTGCCTCATTATCCTAT\nAGCTACGATTCCCGTCCACCCAATCTCTTACATCAGTCTCGCAGTTCAAAAGGAATGGAT\nCAATAGGATACTTGGCATAACATAACAAACTCAAAGTCCTCTTCTGAATTTGATTGCACA\nGATCAACTGGGACACCATTGGCCACAGACTGATCAATTATGGTATCAATTGTTTCTGCCA\nATTGATGGGGTTCTTTGCACTTTATGTTATGTAAAGCTGCAGCAACAAATTTTGTTAGCA\nGGGGCACCTCGTCACCCCAAACATAGAACCTTGATTTGAACTCTGCAACAAACCTGCCAA\nTTGCACTCTTTGGACTTACAAATTTATTTAACTGATCACTCATGTAGTAATGGAACTCTA\nACAATGTTTTGAATTCTTCTGCATCTCTTGAAAGTAATTCTGTTAAGTTCTGATCAAATA\nATGATATCTGATCGTCACTGGACGTGTAAGCATCAATTTGTCCTCCAGACACACACCTCA\nCCGCAAAATTTATAAATCTTTCAGAAATCAACGCATAAAAGTCTGAGGTGTTGTGTAAGA\nTACCCTGTCCCATATCAAGGATTGAACTAATGTGTGAGGGGACTGTGCCAGTTTGAAAGT\nTGGAATTAAAGAAGTCTTCGGTCATTGATTGAGTTGTCTTCTTCTTCAATCCAAGTTGGG\nACTTGATGTATGATTTCATCATTGCTGATACAACATTAAATGGGATCTCAACCATTTTGT\nGCATATGCCATGTTAATAATGTTGACAAGTAATCTTTACCTTTTAAATCAGCTTGTAAAT\nCATCAGAAAGTAAGATTAAGTTTTGAATTATTGTTAGAAACAAGAAAGGACACATCATAG\nGACCCCACTTACTGTGATCCATACTATATGATACATGTGCCGATGAGACATTCAGTTTCA\nTTGACAAAATGGCATTATCAAACTCCTTCTCATTGTTTAGACAGCTGCCTGCTAATTGTG\nATGTGAGTGCTTCAAAGTAATCCTCAATGAGCCTTGTGAACATTTTTGTCCTTAAATCTC\nCGATGTACAACTCTCTATTGCCACCCACTTGTTCCTTGTAAGACAAAGAAAACTTTAGTC\nTACCAGTGTCAGGGCCAGTTGAATTATAAGATTGAGGTGATTCTTGACTGTAAAAACACA\nGGTTTTTTAGCATTGCTGTAGTACAGTTAGTTAGGGACAAGGCCTTGCTAAGTGCTTCAG\nAGTTACTCTCACGTTCACTTATCCTGACATCATCAGCCAATCTCCCTGTATCAAATTTAA\nAGTTCAGACACTTGCTCTTATAATGAGAGTATCTTCCCATCAGCTTATTCCCATTCATCA\nCTAGTAAAATTGACTTAAAGCACTGAAAATATTCTTGGTCCAAAAAAGTCCTAGTCACTA\nCTGCTTTTGTCAGCTCACTAATAGGACATGAATTCATTGGCCCTACATAAAAATATTTAC\nTTCTCAAAGTAGCATCATTGTAGATATTCTCACAAATTTTGATGTATTGATCTTCAGACA\nGGATCTCTCGATCAAAATCTTCTATCATATGGTTTGAAAGTTCACTTTTTATCAACCTTA\nTTAAGAGTTTTTCTTCCACCACTTTGTCAAGATCAGATATTGAGGGTGCATTGCAGTCTG\nCCTGCTGCTGTCCTTTTGGTTGCTCCCTATACTGACTGACAATATTGTCAACAGTGCACC\nTCAGTTGGTCGAAGTATTCTGATGCTCCTCCATCCAATAGTATCTCATCTAGATCAGCAT\nTGTTGGTGTCACCACTCCCTCCTTTGGACCCCAGAACAAGATTACTCATTGCTTGCTGTA\nTTTTGTAATCATAATCCTGTTTATTAAGCAAGAATTTGCCTTTACGTGCAAACACCTCAG\nTTAACTGTGTGACAGCCAAAGCTGTAAGTTTATTGAAGTCATAATCCAGAATACGGGACC\nCATCTGTATACTTATTCACAACGACGCTCTTATTGCTGGCCAGGTCCAAGGCTGTTGCAC\nAGCCGCTTGTAATAAGAGGGTCTCGCAGTGTCTTTTTTACCTCCTTTTCTTTGAACAATG\nAACCATTGTTAAAACTGGACACAAGGAGTGAAATAAATTTCTTGGAAACACCAGGCTTTT\nTATACCTAACTTTTTCCGCATCTACACAACATTCTTTACTTAGGAATTTTCTTGCATTAT\nAAACCATTTCAACAAGCTCTTCCTCCAATGCATCATCCTTCGGGTTCACACTCACATGTC\nCAAATTCCAACTTGGGCTCAAGGAATTTTTCAAAGCATTTGATCTGGTCAGTCAGTCTGT\nCAGGTGTTTCTTTTGTAATGAAGTGACACATATAGGAGATATTTAAAACAAACTTGAATC\nTATTGGTCATCATACTGACAACTTCTTCAGACAGAATTATCTTTAATAAGTAACGAACAA\nGTCTGTAGAGCAGATATTCTACTTCTGTGATCAAATCCTCCCTGATTTTCTCAATCAAGT\nCCTTATGATAAAAATCGGATACAAAGGCCATCACAAAATACCTGATGTTTTGTAAAAATT\nTTTGACACCTTTTACTAGGGTGTGTCAGTATTAAAACTAAAATCATTTTAGTTAACAATT\nTAATAGTGATCAATTGTTCAGACAACTCTGTGCACTCTTCTATCCAGCTGACCATAACAT\nCGACTACTTTCTGCAGCACATCACTGGAGAAAACTGAAGGAAAAAACCGTTTGGGATCAG\nCATAAAAGGAACAAACCTCTCCAACTACATTATTGTTAATAGCATAACACTTTGAGCATT\nCACCTGTTTTTTGATACAATAGTTTGAATCCCATCTTATTGATGAAGAACTCTTGGCAGT\nAGGCCTCTTTGCACCTCACAACCTGGTATCTAGAGGGTCCAAATTCATTTTGCCTTAGTT\nTCACTGTAGAAGACGTTTTCATTGAGTTAATCAAAGCCAAGCTCAATGATGATAGTCTTT\nCTAAGTCTGTTGCACCTAGAATGTCAATAACGCCAAGAGTATAAGGGAACATGTCTTCCT\nGAGTTTTCTGGTAACTCATAGTGGGTGTGATGCCAGAGATCTCAATGTCCATGATGGCAT\nCATAAACATCACAATCAAGGATTTTGAAATCAATTCCATAAGAGTTGGTTTCTATGCCAA\nCCTCCCTCAAAGCATTAGCGGCTCGAGTTAAAACTCTGTTGATGATGGCAAGGAGCTCAC\nAATTTCGTTCTTCTTTGGGTGATAGGACACCCACGTTCTTGTCTCTAGTTCTCTTCCTGC\nTATCTATCCACCGTTTTAGATCTCTTTTTGTTGATTCCAATGAAACTAATCTGTCGTTAA\nCACTCACAAAACAGGAGCCCAACCAACCAGCAAGGAGCTTGTCACCATGCCTTATACAGT\nCCAGTCGGCTGGCAAGAAGGATCAGAACGTCAAAAACAAGGAGAAGTTTCCTTCTGGTGT\nTGAGGATCCTCAGAGACTTTATCTTATTTAAAAAAGATCTCCAACATTGCATCTGTTCAC\nTTTGAGAGTCAACAGCCTTTTCCTTGCTAGAATCCAAATCTGCATATAAGAATTTAAGGA\nCTGGAGAGGCTCTTCGGAACTGAAATGTTAACTGTTCAATGTTGTCATCACAGGTGTCTA\nTTTTATCACAATATAGCTTTCTGAAATCCTCTAACAACTTCATCTTATCAGTCTTAACAA\nATTGACTTTCTATGTTCCCTTGCCTTAGTTTGTTCCTGAAGATTTGATACTCCTCCTCAA\nTCAAACTCTTGACTTCATGAGAGGTAAGCTTGTTATTAATGCCTTGATGACAACTAGAAA\nTTATTTCTTCAAAGTGTTTTGCACGCTTGTCAATTAGAACATTGATGCTTTCAATTCCTG\nAGAGCCTCCCAGACGTTAAGGCTAAAGATTCACAAAGCCTCGAATATTCAGACTCTTCGA\nACAATGCATTACTTTCTTGTGAATATTTTAACAAGGTGAATAAGGTGTCCCTGAGTTTGT\nCATTCACCCAATCAGGTATCTGTTCATTGTAAAATGTTGTCCTGCCGTCTATGAGAGGGA\nTGAGCTTGATGCCAACAGACTCCAAATCGTTCTTTAATTGTTCTAGTTTCCTGTGATCTT\nCTAAATACTTCTGTTCGAAATTGGCGGGGGATGATCTGACAAAGCACTCAAGTAAGATTA\nGAACATTGCCAGTGAGTTTGTAGCCGTCAGGCACCACAAAGCATAAAGCTGGAGTGAGAA\nTCCCATGATCACTCAGAATGGATTCAACCGTTTTGTCTTCAGTGTTATGTTCACATCCAT\nTGGCCTTACAGGAGTCAATCTCAATGCAAAGAGATAGTAGTTTCAATCCCTCCATAAGCA\nACATTCTGGGTTCGGTTTGGACCAAAAAAGCTAATTTCTGTCTTGACAACTTCTCATTAT\nCTGCAAGGTACTTTGAGATGAGATCTTTAGCATTAGCAATGTCTTCCTCCATCGCCAACT\nGTGGCACCTGTGTTGGGTTTGGGTTTATGCCAATATGGCTTGTGGGTCGGCTGGTGATGT\nCCTAAAGAAGCTCCTACAGAAATGAGAGACAATATGCCTAGGATC\n" }, { "path": "tests/input/TestOrderAndOrient/ref.lasv.KGH_G502.fasta", "content": ">LASV-G502-S-Sierra_Leone-2009H\nGGATCCTAGGCATTTTTGGTTGCGCAATTCAAGTGTCCTATTTCAAAATGGGACAGATAG\nTGACATTCTTCCAGGAAGTACCTCATGTAATAGAAGAGGTGATGAACATTGTTCTCATTG\nCACTGTCTATACTAGCAGTGCTGAAAGGTCTGTATAATTTTGCAACATGTGGCCTCGTTG\nGTCTACTCACCTTCCTCCTATTGTGTGGCAGGTCTTGCACAACCGGACTTTACAAAGGGG\nTTTATGAGCTTCAAACTCTGGAACTAAACATGGAGACACTCAATATGACCATGCCTCTCT\nCCTGCACAAAGAACAACAGTCATCATTATATAATGGTGGGTAATGAGACAGGACTAGAAC\nTGACTTTGACTAACACGAGCATCATTAATCATAAATTTTGCAATCTGTCTGATGCCCACA\nAAAAGAACCTTTATGACCACGCTCTTATGAGCATAATTTCAACTTTCCACTTGTCCATCC\nCCAACTTCAATCAGTATGAGGCAATGAGCTGCGATTTTAATGGGGGAAAGATTAGTGTAC\nAGTACAACCTGAGCCACAGTTATGCTGGGGATGCGGCTGATCATTGTGGCACTGTTGCAA\nATGGTGTCTTGCAGACTTTCATGAGGATGGCCTGGGGTGGGAGCTACATTGCTCTTGACT\nCAGGTCGTGGCAGGTGGGACTGTATTATGACTAGTTATCAATATTTGATAATCCAAAATA\nCAACCTGGGAAGATCACTGCCAGTTCTCAAGACCATCTCCCATCGGTTATCTCGGGCTCC\nTCTCACAAAGAACTAGAGACATTTACATTAGTAGAAGGCTACTAGGCACATTCACATGGA\nCACTGTCAGATTCTGAAGGCAAGGACACACCAGGAGGATATTGTCTGACTAGATGGATGC\nTGATTGAGGCTGAATTAAAATGCTTCGGGAACACAGCTGTAGCAAAATGTAATGAGAAGC\nATGATGAGGAATTTTGTGACATGCTGAGGCTGTTTGACTTCAACAAACAAGCCATTCAAA\nGGTTAAAAGCTGAAGCACAGATGAGCATTCAATTGATCAACAAGGCAGTAAATGCTTTGA\nTAAATGACCAACTTGTAATGAAGAACCACTTACGGGACATCATGGGAATTCCATACTGTA\nATTACAGCAGGTATTGGTATCTCAACCACACAACCACTGGAAGAACATCACTGCCTAAAT\nGTTGGCTTGTGTCAAATGGCTCATACTTAAACGAGACCCACTTTTCTGATGATATTGAGC\nAACAAGCTGACAACATGATCACTGAGATGTTACAGAAGGAATATATGGAAAGGCAGGGAA\nAGACACCATTAGGTCTGGTTGACCTCTTTGTGTTCAGCACAAGTTTCTATCTTATTAGCA\nTCTTCCTTCACCTGGTCAAGATACCAACTCATAGGCATATTGTGGGCAAGTCGTGTCCCA\nAACCTCATAGATTGAATCACATGGGCATATGTTCCTGTGGACTCTACAAACAGCCCGGTG\nTACCTGTGAAATGGAAGAGATGAGACCCCTGTCAGGGCCCCCGTGACCCACCGCCTATTG\nGCGGTGGGTCACGGGGGCGTCCATTTACAGGACGACTCTGGGTGTTGATGTTCTGAATAC\nCATATCTCTAGGCAGCACTGCTCTCAAAACAGATGTGTTCAGTCCTCCTGACACTGCTGC\nATCAAACATGATGCAGTCCATTAGTGCACAGTGAGGGGTTATTTCCTCTTTACCGCCTCT\nTTTCTTCTTTTCAACAACGACACCTGTGTGCATGTGGCACAAGTCCTTATACTGATCCCA\nGACTGCATTTTCATACTTCCTGGAATCAGTTTTGTTGAGGGCAATATCAATTAGTTTGAT\nGTCTTTTCTACCTTGTGATTCAAGGAGTTTCCTTATGTCATCGGACCCCTGACAGGTAAT\nGACCATATTCCGGGGGAGTGCATCTATGACAGCACTGGTCAAGCCCGGTTGTGCAGCGAA\nGAGGTCTGTAACATCAATCCCATGTGAGTACTTAGCATCCTGCTTGAACTGCTTTAAATC\nAGTAGGTTCACGGAAAAAGTGTATGTAGCAGCCTGAACTTGGCTGATAGAGGGCAATTTC\nCACTGGGTCTTCAGGTCTTCCTTCGATGTCCATCCAAGTCTTAGTGTTTGGGTCAAGCTG\nCAGCATCGCATCCTTGAGGGTCATCAGCTGAGAATAGGTAAGCCCAGCGGTAAACCCTGC\nCGACTGCAGGGATTTATTGGAATTGTTGCTGCCAGCTTTCTGTGGCTTCCCATCTGATTC\nTAGGTCAACGACAGTGTTTTCCCAGGCTCTTCCTGTTATTGAAGTTCTTGATGCAATATA\nTGGCCATCCATCTCCTGACAAACAAATCTTGTAGAGTATGTTTTCATAAGGATTCCTTTC\nACCAGGGGTGTCTGAGATGAACATCCCAAGAGCCTTCTTGACCTTTAAGATGGATTTGAG\nGATACCATCCATTGTCTGAGGTGACACTTTGATTGTCTCCAACATATTGCCACCATCCAG\nCATGCAAGCTCCTGCTTTCACAGCTGCACCCAAGCTAAAATTATAACCAGAGATATTCAA\nGGAACTCTTCTTGGTGTCAATCATGTTTAAGATGGGGTGACTTTGAGTCAGCCTATCTAA\nGTCTGAAGTATTGGGATACTTTGCTGTGTAGATCAGACCCAAATCTGTCAGTGCTTGCAC\nTGCATCATTCAAGTCAACCTGCCCCTGTTTTGTCAGACATGCCAGTGTTAGACTTGGCAT\nAGTCCCAAACTGATTATTAAGCAACTCTGCATTTTTCACATCCCAAACTCTCACCACTCC\nATCCTTCCCAGCCCGAACCCCTTGATTACCACCACTCATTCCTATCATACTCAGAAGAGC\nCCGTCTTTGGTCAAGTTGCTGTGAGCTCAAGTTGCCCATATAGACACCTGCACTCAATGG\nCCTTTCTGTCCTGATCACCTTTGATTTCAACTTCTCTAGATCAGCAGCTAAGATTAATAA\nGTCATCTGAGGTTAGAGTCCCAACTCTCAGTATACTCTTTTGTTGAGTTGATTTTAACTC\nAACAAGGTTGTTGACCGCTTGATTTAGGTCCCTCAACCGTTTCAAGTCATTGTCATCCCT\nTCTCTCCTTGCGCATTAACCGTTGAACATTACTGACTTCGGAGAAGTCAAGACCATGCAG\nAAGAGCCTGGGCATCTTTTACCACCTGTAGTTTGATGTTGGAGCAGTAACCAGACAATTC\nCCTCCTCAATGATTGTGTCCACAGAAAGGACTTTATTTCCTTTGAGGCACTCATCACCAG\nATTGTTGTGCTGGATGCACGCAGCAGAAAGCAAAAACTATCTGCCAAAATGATAAAAGCA\nAAGCGCAATCCAATAGCCTAGGATCCACTGTGCG\n\n>LASV-G502-L-Sierra_Leone-2009H\nGGATCCTAGGCAATTTGGTTGTTCTCTTTTGGGTTTTGTGTGCTGAACTCCTCCAGATGG\nGAAACAAGCAAGTCAAAACCCCGGAAGCAAAAGACAGTCCGAGAGCCAGCCTGATCCCAG\nATGCCACACACCTAGGGCCACAGTTCTGCAAGAGCTGCTGGTTCGAAAACAAGGGCCTGG\nTTGAGTGCAACAACCACTATCTGTGTCTCAACTGCCTCACTTTACTTCTAAGTGTTGGCA\nACAGGTGCCCCATTTGCAAGATGCCCCTTCCCACAAAACTGAGACCATCAGTCACTCCAA\nCAGCACCCCCAACCAGAGCAGCGGACAGCATCGGACCCCCACCCTACAGTCCCTGAACCC\nCCATCGACCCCCACCACTCTCACCCTCCCCCCGACACCCCCCGGGGGGACCCCCCGCCGG\nGGGCCCCCCCGGGGGAGCCAGCCATCTCCAAGGGACTACTCAATGTCCTCGATGCACTCA\nTCTCTCCCACCCAGTTCCTCACATGTTCTGCCCTTCAGTCTCAATTTGCCACTACTTGAC\nTGTACCATCACCTTCCCCTTTGACTTGCTGTAACAGAGAGCATAACCCTTGAATTCCACC\nCAGTTGTCCACTGCCTCAAGAACCGCACCTAAGATCCCCTCACAACTGGGCGCTGCAGCC\nCTCAACGTGGAGACAATGTCCACCCCTGACCACTGCATCCTTAATCCCAGTCTGTCTATC\nATCATATCACTCAATGCCCCAATCAGCAGGTCAGATGAAGTGTCCCCAACCTCTCTCACA\nAATACCTCTAGATCCTGGTCTTGTATAACAGGTGTAAAAGATGCCAATTTCTTTCCACAC\nTCCCACAAGCCTCCCCTATGCACAACCAGAGGAGCTGGTTCAGTGCAAGGACCCACCAAT\nACAAAGTCATACTCCGTAAACTGCAGCCTTTCCATGTCAACAACAATTTCAACAGGGGTC\nACATGCCCTAGTTGATTTGTGTCAATTAAAAACTCATTGATAATCTCGGTGTCAACATAC\nCATGCTGATTTGCCCTTGAAAGTAGGTCCTGACAAAACCAGTCTCCAGCAGTCTGTCAAA\nACACACGGGCTTACTGCACCTGAGTACATAACGGATACATCATGTACTAAATATTTGGCT\nTGTTGATTCATTGAGCCAATATACTCAAGGTGGATAGCAAAGCTTTCCTTAAAACTAGCA\nTCTTGACTTTTAATACGGAACCTCACTGTCTGACTCAGTTTCGCAGACCCTGGGGGTAGT\nGAAGCCACAGCATCAAAGAAATCCTCCAATGAGTTAAACTTGGGATCAACTAAACCTGAT\nGCAATCAATTGATTTTGATTGAATCTAGCTGGCTCAATGTCAAAGTCTATCCAAGCATAA\nCCCATCATCAGATCATGCTTAAACATAGGCCTTTCAACACCTTTGTGAATAACTTTCTCT\nACAAATGATGAAAATGGCCCCATTCTATGCAGCCCTTCACCCTCTGGAACTGATGTCTTG\nTGTGGAAACCACGTGAAGGATCCCAATGTCCTTGTAGTCGCAACAAATGGTCTCACATAA\nGACTCAAAATAAATTTGCCTCATGAAATTGTCTATAGCATCATTAGTGCTCACCACCCTT\nTCTTCCACCATGGGTTCATGTGTCCTGCTGTGAGACAACCTCAATTCGGACGATAATACA\nATGTAATGTTCCTCTCTTTTCCATTTTACTATGTGTGAGACAAGAGACAAGGCTTCACAA\nTTAACATCCAATGCTACACAGAGATCTAGAAATTTTATTCTGGGTGACCACTTCATTTTG\nGTTGACGCTAAATCACTCATGAATGGTAATATGTGTTTCTCAAACACTGATGGGTACAGC\nCTTCTTAAGGAATGAATGATGTGATTCAAACCAACCCTATCCTCCAATAATTTTGATGCA\nGTTGGCTTCAAGGGAAAATAGTCACAAGGGTTGTGCTTGAAAAAATCCAACACCTTAACT\nGTCTTAGGTTCTCCCAAGACCCATGCACCCAGTTCTATTGCAGTTGACAAGGAAATGCAC\nATGTAATCCCATAACAAGGGCCTGAAATAACTGACCACACTTTCACTCCCACTTCCCTTT\nCTAAGTTCTAGCGGAACTTGCCAATATTGAATGCCATTAGAGTTTGTCAACAATTTGATT\nTCCTTGACATCAGAAATCAGAGACTGAATGGACTTAATATACAGATTCTCCTTATTTGGT\nCCTCGAACACATTTGCTGCCAAGTGTTCTGCACAACCCCACAAAGCCAGATGCAATGGAA\nCTTTGAAATGCAGATTTGTTGATGGCCTCAGATAGCAGTTTCTGCGCACCTCGAGTGAAG\nGTGGAAGACAATTTGTTTTGGATTGTTTTGACAATGGTGGGGATCTTTTCATCATCTAGG\nTTCACAGCACCTGAGTATATTATCTTTTGTCTCAACACCATTCTTAAAGGGTGATGCGCA\nGCCAAGTTTAACCAAGAATACTCAAGGTCAGACTCGGATGGGGGCTCAACATCCAACAGC\nTCACAAAGATTTCTTAGTGAAGAGAGGTGCTCACTAGACAAATAGTTTGTTGTGAACTCT\nTCATGGAGCTGCCCAGTCTTCAACCTATTGTATAGTTTTCTTAGCATAGATCTAATCTTG\nCTGCAAGCATCAGGAATCAACCCTTCTATTTGTCTCATAATTCTATAACTACGGTTGCCG\nTCTACCCAGTCCCTGACATCTGTCTCGCAATTCAATAAGAATGGGTCAATGGGGTATCTT\nGCATATTGCAAAAGACTTAAGGTTCTTTTCTGTATTAAATTGCACAGGTGAACAGGGACA\nCCATTCGCGACCGACTGATCAATGATTGTGTCAATTGTTTCTGCCAGCTGGTGTGGCTCT\nTTGCACTTTATATTATGAAGAGCTGCTGCAACGAACTTTGTCAATAATGGCACCTCATCT\nCCCCAAACAAAAAATCTAGACTTAAACTCTGCAACAAACCTACCAATGACACTCTTAGGG\nCTCACAAACTTATTAAGTTGGTCACTCATATAATAGTGGAACTCTATTAGAGTCTTAAAT\nTCTTCTGGGTCTCTTTGCAAAAGCTCTGTGAGAGATTGATCAAAGAGAGAAATTTGATCA\nTCACTAGAGGTATAAGCATCTATCGTGCCACCACATATACAACTGATAGCATAATTAATG\nAACCTCTCTGAAATGAGGGCATAAAAATCTGATGTGTTGTGTAATATTCCTTGACCCATG\nTCAAGTATTGAACTGATATGAGAAGGCACTACGCCGATTTGGAAATTGGAGTAAAAGAAA\nTCTTCTGTTATTGACTGTTTGGTTTTCTTCCTTAACCCTAGTTGGGCCTTAATGAAAGAC\nTTCATCATAGCTGTCACCACATTAAAAGGTATTTCTACCATTTTGTGCATATGCCACATA\nAGTAGGGTTGAAAGATAGTCCCTCCCTTTTATGTCAGCTTGCAAGTCTTTTGAGAGGAAA\nATTAAATTCTGTAAGACAGTCAAGAATAAAAATGGACACATCATTGGGCCCCACTTACTA\nTGATCCATGCTATAGGAGACATGTGCCAATGAAACATTCAATTTCATGGAAAGGATAGCA\nTTTTCAAATTCCTTCTCGTTGTTCAGACAACTCCCTGATAACTGTAGGCTTATAGCTTCA\nAAGTAATCTTCTATAAGTCTAGTAAACATCTTTGTTCTAAGATCACCAATATACAATTCT\nCTGTTACCACCCACCTGTTCTTTGTATGACAAAGAAAACTTAAGCCTTCCTGTATCAGGT\nCCCACTGAGTCATAAGATTGTGGCGACTCTTGGCTATAAAAACACAAATTTTTCAACATT\nGCTGTGGTGCAGTTTGTCAGTGACAGAGCCTTACTAAGTGCCTCTGAGTTGCTCTCCCTT\nTCACTAATTCTTACATCATCAGAGAGCTTGCCCATGTCAAACTTGAAGTTAAGGTTCCTT\nGACTTATAATGAGTGTACCTCCCCATAAGTGTATTTGCATTCATGATCAAGAGTATGGAC\nTTAAAACACTGAAAGTATTCATGACTAAAGTATGTCCTTGTTGACACTGCCTTTGTTAAC\nTCACCAATGGGGCATTGTGACATATGTCCACAGTAAAAATACTTTTCCTTCAACCTACTA\nTTCTCATAAACAGCATTACAGAATTCTTCATAAAATTTACCTGGTAAGACATCATGGTCA\nAAGTCTTCAACCATGTGATTGGATAATTCAGCTTTGATCAACCTAATGTAAAACTTATTT\nGATACAATCTCATCTAGATCATTTATAGATGGCTGGCCATCATCATTAGGGCCTGAGCCC\nAGTTTGACAGGTTCCCTATACTGATCAACAATTTTTTCAACAGTTTCCTTTAGCTGATCA\nAAATAATCGCTTGCACCTCCATCGAGTAAGATTTCGTCTAGGTCAGCCCCATTGGCATCA\nCTTTTGCTCTGTCCAGATCCCAAGACCAGGTTGCTCATTGCCTGCTGTACTTTGTATTCA\nTAGTCCTGCTTGTTGAGAAGGTACTTTCCCTTTCTTGAGAAGACTTCAGTGAGCTGCGAT\nACAGCTAGTGCTGTGAGCTTATTGAAGTCATAGTTTAATATTCTGGAACCATCTGTGTAC\nTTATTGACAACAACACTCTTGTTACTGGCTAGATCCAAGGCTGTGGCGCAGCCACTGGTG\nATGAGAGGATCTTTAATTTCCCTTTTTACTTCCTTCTCCTTAAATAGTGAACCATTGTTA\nAAAGAGGACGTCAGGAGGGATAAATATTTCTTTGAAACACCAGGCCTTTTATAGTCTGGT\nCCCTTAACACTAGTGCATCCATCTTTACTTAAAAACTTCTTTGCATTGTAGACCATGTCA\nTCCAATTCCTCCTCAGTGGCTGTGTCTGCAGGATTAGTGCTCACATGACCAAATCTCACC\nTTTGGTTCCAGAAACTTTTCAAAACACTTTATCTGATCTGTCAGTCTATCTGGTGTTTCT\nTTCGTAATGAAGTGGCACATGTAGGAAATATTCAAGATGAACTTGAACCTGTTAGTCATC\nATGCTCTTCACATCCTCAGATAAAACCAGGTTCATTAATGTCCTTATTAATCTATAAAGC\nAGGAACTCAACATCAGTAATTAATTCTTCCCTTATTTTGTCAATAAGGTCCTTATGGTGA\nTAATCTGACACATAAGCCATTACAAAGTACCTGAGATTTTGGAGGAGCTTTTGAGAACGT\nTTACTTGGGTGAGCTAAAATTAAAACCAGGATCATCTTTGTCAAAGATCTGATGTTGTTC\nAACTGCCCTTCCAGCTCACTGCAATCTTCTATCCAAGAAATCATAGTATTCACCGTTGTT\nTGTAAAACCTCAGCTGAAAATATTGCTGGAAAGTATCTTTTAGGATCAGCATAAAATGAG\nCACACTTCACCAACTTTGTTATCATTGATGGCATAACACTTCGAGCACTCCCCTGTCTTT\nTGATAGATCAACTGAAATATAGTATTGCCCAATGAAAACTCTTGACAATATGCTTCTTTG\nCATCTGACCACTTGATACCTTGCAGGTCCAAATTCATTCTGTCTCAACTTTACGGTCGAT\nGAGGTTTTCATGGAGTTCACCAAAGCGAGGCTCAATGAAGAAAGTCTCTCTAAATCAGTG\nGTCTCCAGTAATCCCACATCCCCCATCACATAAGGGAATGTTTCTTCCTCTGCTCTCTGA\nTAACTGATTGTAGGGACAACTCCAGAGACATCAAAATCCATAATCAAATCATAACTATTA\nAGGCAAATCACCTCCATATCAATCTTATAGTGGTCAACACTGATCCCAACATCCTTTAAA\nGCAGTGGTGGCCTTCAAAATGGTTTTCTGGAATATTGAATTGAGAATTTGGTTCTCACTC\nAAGCACTGGGAGGACTGTGTGGTTCTAGATCTCTCAGCCTGTTGCCTCCGCTCAACCCAT\nTTTTTGAGATCCCTTTTTGTTGACTCCAAAGAAACTAATCTATCATTAACACTTATGAAG\nCAAGACCCCAACCACCCTTTTAAACACTTTTGTTTCACTAGATCATGTTTACTTGCAAGG\nAGAATTAGTGCATCAAAAATCAATAGAAGCTTCCTCCTTGTGTTCAATATCCTCAAAGAT\nTTTACTTTATTTAAGAATGATCTCCAACATTGCACCTGACATTCTCCAGCAGCTTGGGTT\nTCCTCTTTCTCATTCCTCTCACCAACATTAGCATACAAAAATCTCAATATTGGCGATGCT\nCTCTTGAACTGATAAATTAAGTGTTCAATATTGTCTTCCGCAGCTACCTTTTCAGCGTAC\nAAGTTATTGAGTTCATTAAGTAACTGGTTCTTGTTAACCTTTAAAAACTGACCTTCTATC\nTCACCTTTTCTCAGTCTGTTCCTAAACACTTGATACTCCTCTTCGATCTGCAGCTTTACT\nTCATAGGCTGTTAACTTATTATTGATGCCTTGGTGGCATGAGGCAATCACCTCCTCATAA\nTGATTAGAGCGATTGTCCATCAGAACATTTAAACTCTCCACTCCTGATAGTCTACCTGAA\nGTCATAGATAAAGATTCACAGAGTCTGCTATACTCTGACTCTTCAAAAAGTGAATTGCTC\nTCCTGCGCATACTTTAAAAGTGAGAAGAGCGTATCCCTCAGCTTATCATTGACCCAGTCA\nGGTATTTGTTCATTGTAGAATGATGTTCTCCCGTCTATAAGTGGTATTAAATTGATATCG\nACACTCTTCAAGTCTTCTTTCAGCTGCTCCAATTTTTTGAAGTCCTCAATGTACTTCTGC\nTCAAAGTTAGCAGGAGATGACCTAACAAAACACTCCAGCAATATTAGAACATTGCCCGTC\nAATTTGTAACCGTCCGGTACCACAAAACATAGTGAAGGAGTCAAGATTCCATGGTCATGG\nAGAATTCTTTCCACAGATTTGTCCTCACTGTTATGTTCACAACCATTTGCGTTACAAGAA\nTCAACCTCAATGCAGAGGGACAGGAGTTTCAACCCTTCTATTAATAGCATCCTGGGCTCT\nGTCTGCACAAGAAATGCCAACTTCTGTCTTGACAATCTCTCGTTGTCCACTAGGTACTTT\nGATACTAAGTCTTTGACATAGGCTATGTCTTCCTCCATGTTTGGTTGTAAGTATGATGGT\nCAGAACCTTCAGAACATGTGCTCTGCTAGAGTAACAGTTCACTTTGAGACAGGTTCTCGT\nAGGAGGCACATAAAAACAAGAGGTAAGAGGTAATTAAAGACAATTTAATAAGATAGCCTT\nAATGCCTAGGATCCTCG\n" }, { "path": "tests/input/TestOrderAndOrient/ref.lasv.nomatch.fasta", "content": ">nomatch.1|LASV-sized-blank-S\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n\n>nomatch.2|LASV-sized-blank-L\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\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GGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\nGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n" }, { "path": "tests/input/TestOrderAndOrient/ref.lasv.pinneo.fasta", "content": ">gi|695316025|gb|KM822128.1| Lassa virus strain Pinneo-NIG-1969 segment S glycoprotein precursor (GPC) and nucleoprotein (NP) genes, complete cds\nCGCACCGGGGATCCTAGGCATTTAGGATTGCGCTTTTAGAGATTCACTACTAGTTAGGAATTCCTAAATC\nATGGGGCAGATTATTACATTCTTTCAAGAAGTGCCACATGTAATAGAGGAAGTCATGAACATTGTGCTAA\nTTGCGCTTTCTCTATTGGCAATCTTGAAGGGCTTGTATAACATCGCTACATGTGGGATTATTGGATTGGT\nTGCCTTTTTATTCTTGTGTGGCAAGTCTTGTTCCCTAACCCTTAAAGGGGGATATGAGCTGCAAACCTTA\nGAATTAAATATGGAGACCCTAAACATGACCATGCCCTTATCATGCACCAAGAACAGCAGTCATCATTACA\nTAAGAGTGGGCAATGAGACTGGATTAGAATTGACTTTAACTAACACCAGCATTATAAATCACAAATTTTG\nCAACTTATCCGATGCTCACAAAAAGAATCTTTATGATCATGCTCTCATGAGCATCATCTCAACATTCCAT\nCTATCCATTCCAAACTTCAATCAGTATGAAGCCATGAGTTGTGATTTCAATGGAGGGAAAATCAGTGTGC\nAATACAACCTCTCTCATTCCTATGCTGGGGATGCGGCCGAACACTGTGGGACAGTTGCCAACGGAGTGTT\nGCAAACATTTATGAGAATGGCCTGGGGTGGAAGATACATTGCATTAGACTCAGGAAAGGGAAACTGGGAC\nTGTATAATGACCAGCTACCAGTACCTGATAATTCAAAATACAACATGGGAGGACCACTGCCAATTCTCAA\nGACCGTCTCCTATCGGGTACCTTGGCCTTTTGTCACAAAGGACAAGAGATATATATATAAGTAGGAGGCT\nCTTGGGGACCTTCACCTGGACATTGTCAGATTCTGAGGGCAATGAAACACCAGGTGGTTATTGTTTAACC\nAGGTGGATGCTAATTGAAGCAGAACTCAAGTGTTTTGGGAATACAGCTGTGGCAAAATGCAATGAGAAGC\nATGATGAGGAGTTTTGTGACATGCTGAGATTGTTTGATTTCAACAAGCAAGCAATCCGTAGGTTGAAGGC\nTGAGGCCCAGATGAGTATTCAATTAATAAATAAAGCCGTGAATGCCTTAATCAATGATCAATTAATCATG\nAAGAACCATTTAAGAGACATCATGGGCATTCCCTACTGCAATTACAGCAAGTATTGGTACCTTAATCATA\nCTAGTAGCGGGAGAACATCACTACCAAAGTGTTGGCTTATATCCAATGGGTCATATCTAAATGAAACCCA\nGTTCTCTGATGACATAGAACAGCAAGCCGACAATATGATCACAGAGATGCTTCAGAAAGAATACATTGAA\nAGACAAGGGAAAACGCCCTTGGGACTAGTGGACATTTTCATCTTTAGCACAAGCTTTTATCTGATCAGCA\nTTTTCTTGCATTTAATTAAAATCCCTACACATCGACACATCGTTGGGAAACCCTGTCCCAAACCCCATAG\nACTAAATCACATGGGAGTATGTTCCTGTGGACTGTACAAACACCCTGGTGTTCCAACAAAGTGGAAGAGA\nTAGACTCCAAACAGGGAGCCCCCGTGACCCACCGCCAATGGCGGTGGGTCACGGGGGCGTTCATTTACAG\nAACGACTTTAGGGGTGCTGGTCCTGAAGACCATGTCTCTGGGAAGTACTGCCCTCAGTGTTGTGATGTTC\nAAACTACCAGTAGTAGCTGCATCAAACATGATGCAGTCCAGTAAAGCGCAATGTGGGGTGATTTCCTCTT\nTTCCACCCCTCTTTTTCTTCTCAACGACTACTCCCGTGTGCATGTGACACAAGTCTTTGTATTGGTCCCA\nCACAGCATTTTCAAACTTCCTTGAATCTGCTTTGCTCAAAGAAATATCAATCAATTTGATGTCTCTTCTC\nCCTTGAGACTCCAACAGCTTTTTGATGTCATCTGACCCCTGGCAGGTCAACACCATATTGCGGGGAAGTG\nCCTCTATGACAGCACTTGTCAGCCCGGGTTGTGTGGAAAAAAGATCTGTAACATCTATCCCATGTGAGTA\nCTTAGCATCCTGTTTGAATTGCTTAAGGTCAGTAGGTTCTCTAAAAAAGTGTATGTAACAACCAGAGCTT\nGGTTGAAACAAAGCAATCTCCACTGGGTCTTCAGGCCTGCCCTCAATATCTATCCATGTTTTGCTACTTG\nGGTCCAACTGTAACATACAATCTTTTAGTGTCATCAGTTGAGAATAGGTCAACCCAGCATTTAGACCTGC\nAGCCTGCAAGCTTTTATTGGAACCAGCGCTATTTAGTTTCGGTGGTTTGTTGTCAGATTCCAAATCAACA\nAGAGTGTTTTCCCAAGCTCTCCCAGTAATTGATGTTCTTGATGCAATATACGGCCAACCTTCACCTGAAA\nGGCAGATCTTATAGAGGATGTTCTCATATGGGTTTCTTTCACCAGGAGTGTCAGAAATGAACATTCCCAG\nTGATCTTTTGACCTTCAGAATAGATTTCAAAATACCGTCCATTGTTTGTGGTGACACTTTTATTGTTTCC\nAACATGTTGCCCCCATCAAGCATGCAAGCACCAGCTTTAACTGCAGCCCCCAGACTGAAGTTGTAACCTG\nAGATGTTCAGGGAACTCTTTTTTGTGTCAACCATTCCTAGTATAGGGTGACTCTGAGTGAGCATGTCTAG\nATCTGAAGAGTTCGGGTACTTTGCTGTGTAAATCAAACCTAAATCTGTTAAAGCTTGCACAGCATCATTG\nAGGTCCACTTGCCCTTGTTTGGTGAGGCACGCCAAGGTGAGGCTTGGCATGGTTCCAAATTGGTTATTGA\nGTAATTCTGCATTTTTTACGTCCCAAACCCTGACGACACCATCCCCACCTGTCCTATTTCCTTGAGGTCC\nACCTGACATCCCAATCATGCTCAAGAGAGCCCTCCTTTGATCAAGCTGTTGTGAGCTTAAATTCCCCATG\nTAAACACCTGAGCTCAAAGGCCTTTCTGTCCTTATGACTTTGGACTTGAGTTTTTCCAGGTCCGCTGCCA\nAAGTTATTAGATCATCTGAACTCAAGGTGCCGACCCTTAAGACATTCTTCTGTTGAGTTGACTTCAGTTC\nAACAAGATTGTTGACAGCTTGATTCAGATCCCTCAGTCGCTTTAGGTCTGCATCATCTCTCTTCTGCTTG\nCGCATCAGCCTCTGCACATTGCTGACCTCAGAAAAGTCAAGGCCATGCAGGAGAGCCTGAGCATCTTTGA\nCAACTTGCAACTTTATGTTAGAACAGTAACCAGATAGTTCCCTTCGTAAGGACTGAGTCCAAAGGAATGA\nTTTGATTTCCTTGGAGTTGCTCATTGCTGATGTGCTTGGAGCAACCTAAAGGTGGAGTGACAAGTGGTTC\nTGTAAGAGTCACTTTACTCTGCACAATTATCACAAAGCGCAATCCAATCGCCTAGGATCCACTGTGCG\n\n>gi|695316022|gb|KM822127.1| Lassa virus strain Pinneo-NIG-1969 segment L Z protein (Z) and polymerase (L) genes, complete cds\nCACCAACCCCAGCAGAGAGCCCCCACAACACAGCCAAGCCCACCCAGCCCCCAGAACCGCCCACATCAGC\nAGGCATGGGCAACAAGCAGACCAGGTCCCCACCCAAACCAGAGCACCCCAGACCAACCCTGCTACCCGAC\nGCATCCCACCTGGGCCCCCAATTCTGCAAGAGCTGCTGGTTTGAGAACAAGGGACTGGTGGAGTGTAATA\nACCATTACCTCTGTCTAAACTGTCTCACACTGCTTCTCAGCGTGAGCGACAGATGTCCTATTTGTAAGAT\nGCCCCTCCCCACCAAGCTGGCAGTCCGAACCCAACCAAGTGCACCCCCACTCAACCAGGGCAACACTCAA\nTCCTCCCCGCCCCCCTACAGCCCCTAACTCTCCCAAGACGGGCCCGCACCCCACACCCAGGAACCCAACC\nAAACACACACACACAGACAAACACATAGAAAGACACACACACACGCACACACACCCACAGTCCCCACCCG\nCACCCCCGGGGGGACCCCCCGCCGGGGGCCCCCCCGGGGGGCTCAGAGGCTGGCATCACTCAATGTCCTC\nTACCTGCACCAGTGTGTCGAACAATTTAATGCACGTCCTTCCCTTCAATCTCAGCTTTCCACTGCTTGAC\nTGGATCATCACTTCTTTTAGTGACTTACTATAACACAGTGAGTAGCCCTTGAAATCCACCCAGTCACCAA\nCTGCTTCAAGAAGCCGAACAAGAATTGGTCTTTGCAATTCTAACACAGTCTTCTTCAACACAGAAACAAT\nGTCGACATCCACCCAGTGCTTCTTGAGCTTCAATCTGTCAGAAAACATTGAGATCAGTGCCTCTATCAAA\nAGATCTTGGGAACCATCCCTAACCTCCCTTATGAACAACTCCAAGTCTTGATCGTGAATTGCTGGGGTAA\nAAGTAGCAAGTCTGCTGTCACATTCCCAAAGGGCTCCTCTACTGATCACTAATGGTACAGGTTCAATTTC\nAGGCCCCACCAGTGTGAAATCATACTGTGAAAACTGCAGCTTCCTCAGATCAACAACTATCTCAATGGGG\nGTTACAGGCCCTAATTCTTTAGTGTCCTCTAGGAACTCATTAATGACCTCAGTATCGACAAACCATGCAG\nATTTCCCCTTGAAAACAGATCCAGACAGCACAAGCCTCCAGCAGTCAGGCAGCACACATTGGTTGACTGA\nTCCGGAAAACATGGCTTCAACATTATCAACTAAATACTTACCCTGATGATTTATTGAGCCAATGAAATTA\nAGATGAATAGAAAAATTTTCTTTAAAACTTGCGTCTTGGCTTCTGATTTGGAATCTTATTGTCTGGCTGA\nATCTCACTGAACCAACTGGTAGTTCACTGATTCCATCTAAGAAGTCTTCAAGACATTTAAATTTGACATC\nAGTTAACCCACACATGATCAACTGACTGTAATTGAGTTTTGCTGGTTCTAAATCATAATCAATCCATGCA\nTAACCCATCATCAAATCATATTTGAACATAGGTCTTTCTATACCTTTGTATACCACCTTCTCAACAAAAG\nAGGAAAAGGGGCCAAGTCTCTGCAAACCTTCACCCTCTGGGATAGAGGTTTTATGAGGGAACCATGTAAA\nTGATCCAAGCGTTCTAGTTGTTGCAACAAACGATCTGATGTACGACTCAAAATAAATCTGTCTCATAAAA\nTTATCAACAACGTCACTCGAGCTGACAACCCTTTCTTCTATCATGGGTTCATGTGTCCTGGTGTGTGACA\nATCTCAGCTCAGATGAAAGCACTATGTAGTGTTCCTCTCTCTTCCACTTCACTATGTGCGAGACAAGAGA\nTAGTGCCTCGCAATTCACATCTAGTGCAACACAAAGATCTAGAAATTTAATTCTAGGTGACCACTTCATT\nTTAGTCGAGGCCAAATCACTCATGAAGGGCAACAAATGTTTCTCAAACAGACTGGGGTACAGTCTCCTTA\nATGAGTGTATTATATGGTTCATGCCAACTCTATCTTCTAGCAATTTAGAAGCAGTAGGTTTTAAGGGAAA\nGTAGTCACATGGGTTATGTTTGAAAAACTCCAGCTGTCCTGCTGGCTTAGGGTTCCCTAGAACCCATGCC\nCCCAACTCTATCGCTGTTGATAATGAAATGCACATATAATCCCATAACAAAGATCTGAAATAAGATAGGA\nCACTCTTCCCTTCAGACTCTTCTCTTACCCTCATTGGGACCCTCCAAATCTGGACTCCAAGGTCGTTAGT\nTAAACACTCAACGCCCTGAATTGCCAGGACCTCAGATTGCAGTGATTTGATGTATAGGTTTTCCTTGTTA\nGACCCCCTCACACACTTGCTGCCAAGTGTTCTGCATAATCCTACAAAGCCTGAAGCGATTGAACTTTGGA\nAAGCAGATTTATTTATGGCCTCAGATAGCAGTTTCTGAGCTCCTCTAGTGAATGTAGAAGACAATTTATT\nCTGAATGGTTTTCACTATTGTTGGTATTCTCTCATCATCTAAACTCACTGCCCCAGCATAAATCACCTTC\nTGTCTCAGCACCATTCTTAATGGGTGATGTGTAGCCAGATTCAACCAACAAATTTCTAGATCAGAGTCAT\nCCAACATCTCAGTACCCATTAACTCGCATAAATTCCTTAATGAAGAAACATGTTCACCTGACAGATAATT\nGGTGGTAAATTCCTCATGCAACTCACCTGTCTTTAATTTGTTAAACAACTTTCTTAGCATTGATCTTACC\nTTACTACAAGCCTCTGGGGCCAACTCTTCAATCAGTCTCATGATCCTGTAACTACGGTTGCCGTCAACCC\nAATCCCTAACATCTGTGTTGCAATTGAGTAAGAATGGGTCAATGGGGTACCTCGCATACTTCAGCAAGTT\nCAAAGTTCTCTTCTGAATAAGATTACATAGGCTAACTGGAACACCGTTAGCAATGGACTGATCAATTATG\nGTGTCAATTGTCTCTGCTAACTGGTGTGGTTCTTTACACTTAACATTATGTAGCGCAGCAGCCACAAACT\nTCGTCAAGAGGGGAACCTCATCACCCCAGACATAAAATCTTGATTTAAATTCTGCTACAAATCTTCCAAT\nCACACTTTTCGGGCTGACAAACTTATTTAACTGATCACTCATATAGTAATGAAATTCTAACAGGGTTTTA\nAACTCATCTTGGTCTCTAGACATTAACTCTGTCAGGTTCTGGTCAAAAAGAGAAATTTGGTCATCACTAG\nAAGTGTAAGCATCAACTTGCCCTCCACAAACACAACTCACAGCATAGTTTATAAATCTCTCCGAAATGAG\nTCCATAAAAGTCTGAAGTGTTGTGCAGAATACCTTGCCCCATGTCAAGGATGGAACTTATATGAGATGGC\nACAACACCCAAATGAAAGTTTGAGTAAAAGAAATCTTCTGTTAGTGTCTGAGATGTACTCTTTCTCAACC\nCAAGTTGTGCCTTTATATAAGATTTCATCATTGCTGACACTACATTAAAGGGAATTTCTACCATCTTGTG\nCATGTGCCATGCCAATAGTGTTGAGAGATAATCCTTTCCTTTGGCATCAGCCTGAGTGTCCCCAGTGAGT\nAGAATTAAGTTCTGTAGGGTTGCAAGGAATAGGAATGGGCACATCATAGGACCCCATTTGCTGTGGTCCA\nTGCTGTAGGATACATGTGCTTGTGAGACATTTAATTTCATTGACAAAATTGCATTCTCAAACTCTCTTTC\nATCATTTAAACAACTTCCCGAGAATTGCGTCGTCAATGCTTCAAAATAATCCTCTATCAATCTTGTGAAC\nATTTTGGTCCTAAGGTCTCCAATATAAAGTTCTCTATTACCTCCAACCTGCTCTTTGTATGACAGCGAGA\nATTTTAGTCTCCCTGTATCAGGACCAACTGAGTTGAATGATTGTGGAGATTCCTGGCTATAAAAACACAG\nATTTTTCAACATGGCAGTTGTGCAATTTGTTAGTGAGAGTGCTTTACTAAGTGCTTCGGAGTTGCTCTCT\nCTTTCACTTATTCTAGTGTCGGTTGACAGTTTGTCTGTGTCAAATTTGAAATTGAGACACTTCGACTTAT\nAGTGGGTATACCTCCCCATCAACCTGTTGCCATTCATCAACAAGAGAATTGATTTGAAACACAGGAAATA\nTTCCTGATCTGAATAAGTCCTGGTTACAACTGCTTTTGTTAGTTCACCAATAGGGCAAGACACCATGGGT\nCCACAATAAAAGTACTTCTGCTTAAACTCTTGGTGGTGATACACTATGTCACAGAACTCTTTATAAAAAG\nTGTCAGGGAGTGTGTTATAATCAAAGTCCTCCACCATGTGGTTTGAGAGTTCCCCTTTAATCAATCTGAT\nGTACAGTTTTTCCTTAACAATCTCATTTAAATCGTCAATTGAACAAATCTCCCCGGTTGTTGAGCGCTGG\nTCCGGTCCTTTCAGATCTCTATACTGATCCACAATTTTTTCTATAGTTTCTTTTAACTCATCAAAATATG\nACATCGCATTCCCTTCAAGCAATATCTCATCCAGGTCGGCCCTGTCTGTTTCTACATCTTTCCCTTGAGA\nCCCCAAAACCAAATTGCTCATAGCCTGCTGGACTTTGTACTCATAGTCTTGCTTATCTAATAAATACTTA\nCCTTTCCTTGAAAAAACCTCGGTCAATTGTGTAACTGCTAAGGCTGTTAGCTTGTTGAAATCATAATTTA\nAGACCCTACATCCATCTGTGTACTTATTAATCACAACACTCTTATTGCTTGCCAGATCTAAAGCAGTCGC\nACAGCCACTGGTTGACAGAGGGTCTTTTAATTCTTTCCTCACTTCTTTTCCTTTAAAGAGTGAACCATTG\nTTAAAAGAAGATGTAAGCAAGGACAAGTACTTCTTGGAGACACCAGGTTTCTTGTACCTTATTTCAGCTG\nATTCCACACAGCATTCCTTACCTAAGAACTTTTTAGCGTTGTACACCATTTCACTCAACTCATCCGACTC\nTGCATGATCCAGAGGATTGACGCTAACATGCCCAAACTCTAGTTTTGGTTCTAAGAATTTCTCAAAGCAC\nTTGATCTGATCTGTTAGTCTATCAGGGGTTTCCTTAGTGATAAAATGACACATGTAAGAAATGTTCAAAA\nCAAATTTGAACCTGTTTGTTAGCATACTAGTCACATTAGGAGATAAAACAGTGCTTAACAGGGCTCTTAC\nCACTCTGAAAAGCAAGTACTCAACATCTGTAATCAGCTTCTCTTTGATCTTGTTGATTAAGTCTTTGTGA\nTAATAATCAGAGACAAAGGCCATTATGAAGTATCTAAGATTTTGCAAAAACTTCTGACATCGCTTACTAG\nGGTGGGTCAAGATTAAAACCAAAATCATTTTGGTTAGCACTTTAATTGAGGATATATCATCCTTAAGCTC\nAGAACAATCTTCAATCCAGCTGACCATGACTTCTACCACCTTTGTCAGAACTTCACTGGAAAAGATTGCG\nGGGAAAAACCTCTTGGGATCCGCATAAAAGGAACAGACTTCACCAACTAAGTTGTTGTTTACCGCATAAC\nATTTTGAACACTCGCCCGTTTTTTGATAAAGTAAGCTATATTCCACTCCATCTATGAAGAACTGTTGACA\nGTATGCTTCTTTGCATCTTACCTTCTGGTATCTTGCTGCTCCAAGCTCATTTTGCCTCAACTTAACAGTG\nGAGGAAGTCTTCATTGAATTCACCAATGCAAGACTCAATGTTGAGAGCCTTTCAAGATCAGCTGACTCTG\nAAACGCTCACTGTGCCCATTGAGTAGGGAAACAGTCCTTCGTCAGACTTTTGATAAGACATTGTTGGCAC\nAACACCTGATGCCTCACAGTTCATAACTTTACTAAATACATGCCCATCCAGAATTGTTAGATCAACCCCA\nTAGGTGTCCACATTTACATTTAGGTCTTTGAGGGCACTTATTGCTTTGGTAACAGTTTTCTGCAACATGC\nAACTCAAGATTTGATTTCTATCTAATCTAACGGAGTGAGTGCTTGATGCTGATTTTGAACATTCAGATTG\nCAATCTTCTATCAACCCACCTTTTCAGGTCCCTCTTAGTGTATTCTAAAGACACCAAGCGGTCATTCACA\nCTGATAAAACTGGATCCTAACCAGCCTTCCTGAGCTTGATCTTCACATTTAATCTTGTCCCTCTCATAAG\nCAAGGAGAATCATTACATCAAAAATCAATAGAAGTTTCCTTCTTGTGTTCAAAATTCTCAAAGATTTGAC\nTTTGTTGAGGAATGACCTCCAACAATGCATCTGACTGCTGTTTGTGGGTGATGATCTATCAACCCCATTG\nGTTAAATCTGCATACAAGAATTTCAACACAGGAGAGGCTCTTTTAAAGGAATACATCAATTCTTCCACTC\nCATCTTCATTAGAAACCATTTCAGAATCATACAAGCAGTGAAATTCTTTTAACAGTCTTTCTTTGTCAAC\nTTTAACAAATTGATCTTCTATTTGGCCCTGCCTTAACTTGTTTCTGAATATCTGATACTCCTCCTCAATC\nTGATTCTTAACCTCATGGGCAGTCATTTTGTTGTTGATGCCTTGATGGCAGCTGGCAATTATATCATCAA\nAATGGTTGGTTCGTTTATCTAATAACACATTGATGCTTTCTATACCTGAAAACCGGCTAGTGCTGACTGA\nAAGAGATTCGCATAATCTAGAGTACTCAGACTCTTCAAAGAGTGAATTGCTCTCCTGAGCATATTTCATC\nAAGGAGAATAGTGTATCTCTGAGTTTGTCATTCACCCAGTCCGGAATTTGTTCATTATAAAATGTAGTTC\nTTCCGTCAATAAGTGGTATTAGGTTTATATCAATTGACTTCAAGTCATTCTTTAGTTGCTCTAACTTCTT\nTAAGTCCTCTAGGTACTTCTGCTCAAAGTTCACTGGGGATGATCTCACAAAGCACTCAAGGAGTATGAGG\nACATTCCCATTCAATTTGAAGCCATCAGGCACAACAAAGCATAATGATGGTGTTAAAATCCCTAATTCAT\nGGAGAATTACCTCAACAGAGCGTGCATTGCTGTTGTGCTCACAACCATTGGCCTTGCAGGAATCAACCTC\nTATACATAAGGATAAAAGTTTTAGTCCTTCCATCAACAACATCCTCGGCTCAGTCTGCACCAAGAATGCC\nAATTTTTGTCTAGATAATCTCTCATCATCAGAAAGATATTTTGAAACAAGATCTTTTACATAAGCTATCT\nCCTCCTCCATTAAAGAAGTTGTCAACAATAGAGCGTCTAAATGCCTAGGATCCTCGGTGCGC\n" }, { "path": "tests/input/TestOrderAndOrient/refs.ebov.fasta", "content": ">KX009902.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/LBR/2014/Makona-CDC/NIH-1122, partial genome\nTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAAT\nTGAAATTGTTACTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGT\nCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCCTTATCACAT\nCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAG\nCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACT\nGGAGACTCAACAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCA\nCAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATG\nGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAG\nTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTT\nTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTT\nTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATG\nGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGC\nCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCG\nAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAG\nGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAAC\nAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGAT\nGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATC\nATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGA\nGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTT\nTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAG\nTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGC\nAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGAT\nGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACG\nCGATGGTAACTCTCAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAA\nAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCT\nGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGATG\nATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTTGGTCCTATT\nCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAA\nAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCC\nCTCGCAGAACAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTC\nAACCAGCCCTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACG\nTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCA\nCTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACA\nAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAG\nGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGG\nATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATA\nTCCACCATGGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAA\nTTTTATTGGCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCA\nTGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAAT\nTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTT\nATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAG\nCCATAATGGTAACTCAATATCTTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTA\nCCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAAC\nCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGC\nTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAA\nTGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACAT\nCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCG\nAAGATGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACAT\nTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAG\nTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCT\nGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTG\nAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGG\nTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACC\nACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATG\nATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAG\nCAATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCC\nCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTC\nGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGG\nTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCC\nCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACA\nCTTGTGAGTATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTA\nGCAGCTTTAAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAAC\nCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCA\nTCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATA\nTATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTC\nCTGACACCGGAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCG\nACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATC\nGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTAC\nAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCA\nATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGG\nAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTG\nACAGCACTCAAACTGATCACTCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAA\nATGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGG\nGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGAC\nTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACA\nAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACAT\nTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCT\nCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCT\nTCTCAGGGATAGTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATAT\nACTAAAGGTGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATAT\nACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCA\nATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCAAATTGCCTACAT\nGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAA\nGTTGTTCACAATCTAAGTACAGACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGA\nCAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAA\nTTGGATAACCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATA\nTTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAA\nCATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTG\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCA\nACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATG\nAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACC\nAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCA\nTGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTA\nTCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT\nCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACC\nACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGA\nCCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAG\nTGGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGG\nGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGC\nTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC\nACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAG\nGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAAC\nCAAAACAGGTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAA\nGTTGGACAACATCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAG\nCCGGACCCTTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGAC\nAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT\nGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGA\nGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTAC\nTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTAC\nACAGAGGGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTC\nAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAAT\nTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT\nGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGG\nACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGG\nTGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTT\nCACGGCAAAACTCAACCTCAAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTA\nCTTGACAAATGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTC\nACAGTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACTTGATGAAGAT\nTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTT\nAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTG\nTAACCTAACACACACAAAGCATTGGTAAAAAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTT\nAAATGGAAGCTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCA\nCCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCA\nCAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAG\nACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGA\nAAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTA\nAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTC\nCCAAAATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGA\nGGATTCCAAATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTG\nAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAG\nTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACA\nATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTC\nGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACAT\nGCTCATGATCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCAC\nAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAA\nTCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAAGAGGTATGATATAACCCAA\nACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCAATATAACCTGCCAAGCATACCTCTTGCACAA\nAGTGATTCTTGTACACAAATAATGTTTGACTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAA\nGTATTTTATGATTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCT\nTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATA\nTTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTC\nTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATAC\nTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCTGTATACCAGTTGCCCCTGAGATACGCCACAA\nAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGA\nACTTAGCCATTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAG\nAAGCCCACCTACAACGAACATTACTTTGAGCGCCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAAT\nCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGC\nAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGG\nAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTA\nTTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGAC\nTTTGCCCCTGCATGGTCAATGACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTG\nAATCACCGCTGTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTT\nGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTC\nAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTC\nTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAATGGATTATTGAGCAGTATTGAAAT\nTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCC\nGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGA\nAAGCATTTACACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTAT\nCTAACTAAGATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTC\nTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACA\nGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAA\nATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCC\nAATATACGAAATGGTTAATTGTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATAT\nTACTAACTCCATACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAA\nAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCT\nACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTTGTCA\nCTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACA\nTATATACCGTTTAAAATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCC\nATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGT\nGCCAACAGTTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAA\nAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGC\nAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATC\nGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGT\nTTTTTGGAAGATCCCAATTTCACTGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGG\nTATCAGACATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATG\nTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGT\nTGAGGACCCAGTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTAC\nTTACTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAA\nTTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCA\nCACCCTGGAAGAAATTACAGAAATACGTGCACTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCAT\nAGAACATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGG\nGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATT\nACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTATTTTGATAGT\nCAAGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAA\nATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTATGGGAATTTTACCACCTTGACCATCCTCCACT\nTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACA\nTGCTGGGATGCAGTATTCGAGCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTG\nTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGA\nGTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACT\nTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTG\nCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGC\nATCATGGCACCACACAAGTGATGATTTCGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGAT\nTTAGAGAAATACAATCTTGCATTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCT\nATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTA\nTTATAATCCACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGG\nGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTT\nTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTT\nATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTG\nGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATT\nCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGC\nTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACT\nGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGT\nTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAAC\nACTCGGCAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTA\nTCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGT\nTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAA\nCTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCA\nTTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTC\nATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCG\nTTTCGCAGCCGATATATTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGA\nACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGA\nAGATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGC\nTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTA\nGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAAC\nCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGT\nCAAGAAACATATTGTTAGTGCATGGCCAAATGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCA\nTACATTGGATCAAGGACAGAAGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCT\nTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCT\nAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACAT\nTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGA\nGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGC\nACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGA\nAACACTGAGGCTACAGATATCCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGG\nTACCAGCTCAGTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATT\nGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCATTTTTCCAA\nGGCAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTA\nAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCGTCTACAGACCCAATTAGCAGTGGAGAAAC\nAAGATCATTCACTACCCATTTCTTAACTTATCCCAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTA\nAGTTATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAA\nCTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGT\nTATGTCACGATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGA\nCTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGA\nTAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCATTAGAGGGTCAAAATCCAACACCTGT\nTAATAATTTCCTCCATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACT\nACCATAAATGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCT\nTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTC\nTTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACCACCAGAGAT\nCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACGACAATTCCAC\nAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCC\nAAAACTAAATTTCGATAGATCGAGACACAATGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAA\nGGTCATCAAATAATCTCACATCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAA\nCGTCATCCAATGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGA\nTACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGG\nGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTC\nAGAAATACCAAGTTAAGACCTTATTCTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGT\nATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATT\nATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAA\nGGCTACCTAGGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATT\nGTACGAAGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAA\nGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGT\nATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATC\nAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTG\nCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCT\nATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAG\nAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAATGAT\nTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAA\nAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACAAGCATTAAAACATAATGGGACATGGCAAGC\nTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGT\nGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAA\nGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTAT\nTTTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCA\nTCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTATACACTATATTTGG\nCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAGCATGTGTGACATATTACTGCTGCAATGAGT\nCTAACGCAACATAATAAACTCCGCACTCTTTATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTT\nATTGATATAGTAATGTTGTATCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTT\nAAAACAAAACTGATCTTTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATG\nGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACANNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNATGATAAAANTNAAAGANAAGACATNACTGTAAANNNNGAAATACCTTCTTTAC\nAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGCATTGACCACGCTCATCAGAAGGC\nTCACTAGAATAAACGTTGC\n>KM034550.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-EM095, complete genome\nGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGT\nTACTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGG\nGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTC\nCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTC\nACAGTCAAACAAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCA\nACAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCC\nGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCAC\nAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAG\nTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAG\nTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAA\nAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGC\nGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGA\nAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTA\nGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATAC\nAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTT\nGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATT\nTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTAC\nAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTC\nCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTT\nTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAG\nCCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGA\nGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAA\nAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAA\nCTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGG\nACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAA\nGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGACCCCGATGATGGAGGCT\nACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGA\nCGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAA\nAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAA\nCAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCC\nTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTT\nCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCC\nCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGA\nCCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTAT\nCGCCACATTCTAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTG\nTAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATG\nGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGG\nCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAAT\nGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGT\nCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACT\nAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGG\nTAACTCAATATCTTAGCCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGC\nCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCAT\nCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAAC\nAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCC\nCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGA\nTATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGC\nAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCAT\nTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAA\nTGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTT\nGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATT\nGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGA\nATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTA\nACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGC\nCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATT\nGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAA\nATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACA\nTTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATG\nTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAG\nAGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGT\nATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTA\nAAGATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAA\nAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAA\nCGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGC\nCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCG\nGAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCA\nGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAA\nAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGAC\nTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTG\nTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGC\nTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTC\nAAACTGATCACTCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGT\nTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGG\nGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATC\nGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCG\nGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGA\nCCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGT\nCTTCCAGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGA\nTAGTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGT\nGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTT\nTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGA\nTTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATC\nTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCAC\nAATCTAAGTACAGACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCG\nTAATCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAAC\nCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTA\nCCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCA\nTCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAA\nACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTG\nCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTG\nAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCC\nAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGA\nGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAG\nGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTC\nACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGA\nTATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCC\nAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAG\nGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCC\nTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAA\nCGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAAT\nGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAG\nCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGG\nTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAA\nCATCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCT\nTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCA\nAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGC\nGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTC\nGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGA\nAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGG\nCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCC\nAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCT\nGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACC\nAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGG\nACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAAT\nTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAA\nACTCAACCTCAAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAA\nTGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAAT\nCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAA\nGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAA\nGGAAAAAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAAC\nACACACAAAGCATTGGTAAAAAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAG\nCTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCG\nAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGC\nGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTC\nCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAAC\nTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACT\nGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTA\nCCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAA\nATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTG\nTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAAC\nGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAAT\nTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCA\nGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGT\nCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCG\nTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCA\nTTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACC\nAAAGAAAATCATAATCTCGTATCGCTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCT\nTGTACACAAATAATGTTTGACTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTAT\nGATTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGT\nGGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTG\nTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAA\nTAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGG\nATAGTCCAGCTAGTGACACGTCTTTTAGCTGTATACCAGNNNNNNNNNNNNNNNNNNNNNNAAGTGTCTC\nTGAGCTAAAGTGGTCTGTACACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCA\nTTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACC\nTACAACGAACATTACTTTGAGCGCCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAA\nGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGA\nGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGG\nTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGG\nTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCT\nGCATGGTCAATGACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGC\nTGTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACC\nCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGA\nACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTA\nTTAACAAATTGGATGCTCTACATGTCGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCA\nAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCG\nGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTA\nCACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAG\nATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCAT\nAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCC\nTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGAT\nTCCAAGACAACATCATAGAATTGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGA\nAATGGTTAATTGTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTC\nCATACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTA\nTTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACAT\nACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTT\nGCGGGTTGTATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCG\nTTTAAAATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTC\nATAGTCCCAATTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGT\nTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGG\nTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTT\nTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACT\nCTAGATCAACGTGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAA\nGATCCCAATTTCACTGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACA\nTCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAA\nTGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCC\nAGTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCC\nATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGT\nGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGA\nAGAAATTACAGAAATACGTGCACTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTG\nATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTG\nTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTAT\nCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCT\nTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCC\nCTCCGTTGCCAATGATTAAAGAACTGCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAAC\nCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGAT\nGCAGTATTCGAGCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAAC\nAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACT\nACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAA\nTTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCAT\nTTCCTAGCAATATGATGGTAGTTACGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCA\nCCACACAAGTGATGATTTCGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAA\nTACAATCTTGCATTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTA\nAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCC\nACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATG\nGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAA\nTTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTT\nCCCCTTAGAGACTGATGCAGGCGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGC\nCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTA\nTCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAAT\nGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAG\nCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGG\nTGAGAATCTTGCAATATCATCACCTCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAA\nACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTG\nAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTT\nATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGC\nCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGC\nCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAG\nCTGACTTCGAAGACGAAATGGTTTGTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGC\nCGATATATTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACA\nTTATTAGCCTCTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACAT\nTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCA\nAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGA\nCCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAAC\nAATGTCCGCAGTGTTCAAATGCCAAGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACA\nTATTGTTAGTGCATGGCCAAATGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGA\nTCAAGGACAGAAGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGG\nCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACC\nATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGA\nAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAG\nCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAG\nCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAG\nGCTACAGATATCCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTC\nAGTACTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGA\nCAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGCAAACAG\nCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCA\nTGCAATCAATTATTTCAGATAGCAATAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATT\nCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTAT\nCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAA\nTTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACG\nATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGAT\nGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATC\nGCGGAACAATTGTCCCTTTATGGATAGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTT\nCCTCCATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAAT\nGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGT\nCATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGG\nATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGAT\nGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACA\nCGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAA\nTTTCGATAGATCGAGACACAATGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAA\nATAATCTCACATCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCA\nATGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGT\nTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAG\nAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACC\nAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAAT\nGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAAC\nAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTA\nGGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGC\nTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTA\nAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTA\nAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACG\nTAAGATGCCACACCAAAACCATCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAA\nCGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCC\nTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACT\nAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAA\nCAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCA\nATGATTATTTAAAATTCTTTCTTATTGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAA\nGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGT\nTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAG\nGGCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACT\nTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCT\nGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCC\nCTGCGTGATAATCAAAAAATTCACAATACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAA\nCATAATAAACTCCGCACTCTTTATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATA\nGTAATGTTGTATCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAA\nCTGATCTTTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCC\nTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCC\nATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCA\nGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAA\nTAAACGTTGCAAAAAGGATCCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCT\nTTTTTGTGTGT\n>KT765130.1 Zaire ebolavirus isolate H.sapiens-wt/GIN/2014/Makona-Conakry-CREMS-1022, complete genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAA\nTTTTCCTCTCATTGAAATTTATATCAGAATTTAAATTGAAATTGTTACTGTAATCATACCTGGTTTGTTT\nCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGT\nTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCC\nAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGGGAA\nTTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAAC\nATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAA\nGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG\nTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCA\nACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTT\nTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAG\nGGCACGGGTTCCGTTTTGAAGTCAAGAAGTGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGT\nATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCC\nGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGA\nAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGT\nAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAA\nGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTT\nTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCT\nCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTG\nGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATG\nGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGT\nAAATGTTGGAGAACAGTATCAACGGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATAT\nGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAGCTTCCATC\nAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAA\nGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATT\nCCCTTTCCAGGACCCATCAATGATGACAACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGG\nATACGACCATTCCCGATGTGGTAGTTGACCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGA\nAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCA\nGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGAC\nAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACT\nCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAACGAA\nGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTTGCCTTCCGCCCTTAGAGTCAGATGATGAAG\nAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCA\nCTCCGAAAAGAAAGAACTCCTGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAAGAACCAA\nGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCTCCACATTCTAAGATCACAGGGGC\nCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAA\nAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAAT\nGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAAT\nTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCT\nAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAAT\nAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGA\nGTCTTAATGCAAATAAGCGTTAAACCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCGATT\nTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTT\nTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGC\nACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCA\nGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGA\nGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGC\nTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAA\nTTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAAC\nCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATG\nGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGA\nCAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACC\nTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAA\nAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTG\nACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCA\nATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAG\nGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCC\nAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTT\nGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAA\nACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAA\nCTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAA\nTTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATAC\nCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCT\nACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATAT\nGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCA\nACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCAT\nCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATC\nAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATT\nTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTG\nCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGG\nAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCA\nCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTG\nCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCC\nAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCG\nGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATA\nTCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGG\nACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACC\nATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAAT\nTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAATC\nCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTT\nTCGTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCA\nTGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGC\nACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGAT\nTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTC\nTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATT\nTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATA\nTTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACAT\nCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAG\nTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGA\nTCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCT\nTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCT\nTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGG\nTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTG\nCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGT\nTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAAT\nGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTA\nATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACA\nGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATT\nTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCAC\nTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAG\nAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAG\nAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCT\nTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACA\nCCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAACGACA\nGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAGAACACCAACACGAG\nTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCCAAACTACAGCGAGACTGCTGGCAAC\nAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATA\nCTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCA\nACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGG\nATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAA\nTCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGA\nGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGC\nCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATC\nAGATTATTCATGATTTTGTTGATAAAACTCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATG\nGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTGTATA\nTGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCAAATCAATGAAACTA\nGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAATGATAACATAATACACTGGAGCTTC\nAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCT\nAGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTC\nTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTG\nTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAAAAGT\nCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAGAGAGGACGCCCCCG\nAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAAT\nTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGA\nGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTG\nTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATC\nGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAA\nATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCCAAAATTACCTTGTTGACACTGATCAAGACGGC\nAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGT\nGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAG\nGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAG\nTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAAT\nATCGCTCTCCAGTTACCGTGTGAGAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAAT\nCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGG\nCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATC\nAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAA\nTTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGC\nTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTA\nCAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAAAATA\nTTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTAT\nTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGA\nAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCC\nCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTT\nTAGCTGTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATC\nTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAATCTGG\nGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATTACTTTGAGCACC\nCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGT\nCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGG\nGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTT\nCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAA\nGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAACCTAT\nTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTGAGAGTCATCCTTGC\nAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATC\nTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGA\nGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGT\nCGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGA\nACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGC\nCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCA\nAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGGGCTAAC\nTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAAT\nAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTG\nACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCT\nTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACCCGC\nAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAA\nGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGA\nAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTAT\nCATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCT\nTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACC\nAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCAC\nTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATTATTAAGTACAC\nAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAC\nCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATG\nACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGA\nTGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTG\nAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAG\nGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGATTTAATTACATGTCG\nATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCAGTTTGCTCTGATTATCCCAATTTT\nAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAA\nTCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGG\nCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTA\nAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAAC\nAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCA\nAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTT\nTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAA\nATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACT\nGCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATT\nTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTGG\nGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTC\nTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAATTTTTCTTTC\nTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTC\nAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTAC\nGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAG\nCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTATGAAT\nTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTA\nTACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACACTGGAAAAT\nCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAA\nAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGCTTTAAGTTGCGCTC\nAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAG\nCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTG\nGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTT\nGAATGGGGTCCAATTGCCCCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTT\nGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATA\nTCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCT\nCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCA\nTTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGA\nATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGA\nTTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGC\nGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCC\nTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTG\nTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGC\nGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACA\nATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGGAGTCTATGGTTTAG\nTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCA\nCAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCAT\nGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAA\nGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCA\nTCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGGC\nAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAAC\nATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTA\nAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATC\nAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAA\nCACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATA\nAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAATCGTG\nCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTACTTAACATACACATCTACATT\nGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTC\nAATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTA\nTTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAA\nTAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCC\nAAAATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTA\nAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATT\nGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGATTAATGAGTATTGATCCCCATTTT\nTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGT\nCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGAT\nAGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTG\nGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGACAATC\nTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCA\nCAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGT\nCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGC\nAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTC\nATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTG\nAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTCCTAC\nCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGATGAGAT\nATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTC\nTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGG\nCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTCTTCAACAC\nGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCT\nGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACA\nTAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGA\nTGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTACATAAATTGATCTTACACCAT\nGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGC\nTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTC\nTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTC\nAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATT\nTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGT\nATTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCA\nCATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACAT\nATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTAT\nTGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTG\nTGCTATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTAC\nATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGG\nTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTTGTAAAGGTTGGTTATCAACATACA\nGATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGAT\nAACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAATTCACAA\nTACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATAA\nTTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTTGCCAG\nATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAAGATTAAGTTTTTTAT\nAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATT\nAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAAA\nAGACAGGACTGTAAAATCAGAAATACCTTCTTTACAATATACCAGACTAGACAATAATCTTCGTGTTAAT\nGATAATTAAGACATTGACCACGCTCATCAGAAGGCTC\n" }, { "path": "tests/input/TestOrderOrientAndImputeFromReference/contigs.influenza.fasta", "content": ">I1-4\nGCAAAAGCAGGGGAAATTCAAATCAACCAAGATGGAAGCAAAACTGTTTGTGCTATTCTG\nTACATTCACTGTACTGAAAGCTGACACCATCTGTGTGGGCTACCATGCAAACAACTCTAC\nGGACACTGTTGACACAGTATTGGAAAAGAATGTAACTGTGACTCACTCAGTGAATTTGCT\nCGAAGACAGCCATAATGGGAAGCTCTGCAGTCTGAATGGGATAGCTCCTTTACAATTGGG\nGAAGTGTAATGTAGCGGGGTGGCTCCTGGGCAATCCAGAATGTGATCTCCTACTCACTGC\nAAACTCATGGTCCTATATAATAGAGACGTCCAATTCAGAGAACGGGACATGCTATCCCGG\nTGAATTCATAGATTATGAGGAATTAAGGGAGCAGCTGAGTTCAGTTTCTTCTTTTGAAAA\nGTTTGAAATTTTCCCCAGGGCAAACTCATGGCCAAACCATGAGACAACCATAGGTGTTAC\nAGCTGCTTGCTCTTACTCTGGAGCTAGCAGTTTTTATCGAAATTTGCTGTGGATAACAAA\nGAAGGGGACTTCATATCCAAAACTCAGCAAATCATACACGAACAATAAGGGGAAAGAGGT\nGCTCGTGCTCTGGGGAGTGCACCATCCTCCGACCACCAGTGAACAACAAAGTCTATACCA\nGAATACTGATGCATATGTCTCAGTTGGGTCATCAAAGTACAACCGGAGATTCACCCCAGA\nGATAGCAGCTAGACCCAAAGTTAGAGGGCAGGCAGGCAGAATGAACTATTATTGGACACT\nATTAGATCAAGGGGACACCATAACATTTGAGGCCACTGGGAATCTGATAGCACCATGGTA\nTGCCTTCGCATTAAATAAAGGATCTGATTCAGGAATTATAACATCAGATGCTCCAGTTCA\nCAATTGCGACACAAGATGCCAAACCCCCCATGGAGCGTTGAACAGTAGCCTTCCTTTCCA\nGAATGTGCATCCTATCACCATTGGAGAATGTCCCAAATATGTCAAGAGCACCAAGCTAAG\nGATGGCAACAGGACTAAGAAATGTCCCATCCATTCAATCCAGAGGGCTGTTTGGAGCAAT\nTGCCGGATTCATTGAAGGAGGATGGACAGGCATGATAGATGGCTGGTATGGGTACCATCA\nTCAAAATGAACAAGGATCAGGATATGCCGCTGATCAGAAAAGCACACAGAATGCAATTGA\nTGGAATAACAAATAAGGTGAATTCGGTAATTGAAAAAATGAACACTCAATTCACTGCAGT\nGGGTAAAGAATTCAACAACCTAGAGAGGAGGATTGAGAATCTGAATAAAAAAGTCGATGA\nTGGGTTCCTGGATGTTTGGACATACAATGCTGAATTGCTCGTTCTATTGGAAAATGAAAG\nAACTCTTGATTTTCATGATTCCAATGTGAGGAATTTGTATGAGAGAGTCAAATCACAACT\nGAGGAATAACGCCAAAGAAATTGGAAATGGTTGCTTTGAGTTCTATCACAAATGTGATGA\nTGAATGTATGGAAAGTGTGAAGAACGGCACATATGATTATCCCAAATATTCAGAAGAGTC\nTAAATTGAATCGAGAAGAAATAGACGGAGTAAAACTAGAGTCGATGGGAGTTTACCAAAT\nTCTGGCGATCTATTCCACAGTCGCCAGTTCCCTGGTCTTGTTAGTCTCCCTGGGGGCAAT\nCAGCTTCTGGATGTGCTCTAATGGGTCGTTGCAATGCAGAATATGCAT\n>I1-6\nAATGAATCCAAATCAAAAGATAATAACTATTGGGTCAATCTGCATGGTAATTGGAATAAT\nAAGTCTGGTGCTACAAATTGGAAACATAATCTCAATATGGGTTAGCCATTCAATCCAAAC\nTGGAAGCCAGAGCCACCCAGAAACATGCAATCAAAGTGTCATTACCTACGAAAACAATAC\nTTGGGTGAATCAGACATACATCAACATAAGTAATACCAATTTAATTGCAGAGCAGGCTGT\nAGATCCGGTAGCACTAGCAGGTAACTCCTCTCTCTGTCCAATCAGTGGATGGGCTATATA\nCAGCAAGGACAATGGTATAAGAATAGGTTCCAAAGGAGATGTATTTGTCATCAGAGAGCC\nTTTTATTTCATGCTCTCACTTGGAATGCAGGACTTTCTTTCTAACTCAAGGGGCCTTGTT\nGAATGACAAGCATTCTAATGGAACCGTTAAAGACAGAAGCCCTTATAGAACCCTAATGAG\nCTGCCCTGTTGGTGAAGCTCCTTCCCCATACAATTCAAGGTTTGAGTCTGTTGCTTGGTC\nAGCAAGTGCTTGTCATGATGGCATTAGTTGGTTGACAATTGGTATTTCCGGCCCAGACAA\nTGGGGCGGTGGCTGTATTAAAATACAATGGCATAATAACAGATACTATCAAGAGTTGGAG\nAGGCAATATATTAAGAACACAAGAGTCTGAATGTGCCTGCATTAATGGTTCTTGCTTTAC\nCATAATGACTGATGGGCCGAGTAATGGCCAGGCCTCATACAAAATTTTCAAGGTAGAAAA\nGGGAAAGGTAGTCAAATCAGTTGAGTTGAATGCTCCTAATTACCACTATGAGGAGTGCTC\nCTGTTATCCTGATGCTAGCGAGGTAATGTGTGTGTGCAGAGACAATTGGCATGGTTCAAA\nTCGACCATGGGTGTCCTTCAATCAAAATCTAGAATATCAAATAGGATACATATGCAGCGG\nAGTTTTTGGAGACAACCCGCGCCCTAGTGATGGGACAGGCAGTTGTGGTCCAGTTTCTTC\nTAATGGGGCATATGGAGTGAAGGGGTTTTCATTTAAATACGGTAATGGTGTTTGGATAGG\nAAGAACTAAAAGTACTAGCTCAAGGAGTGGGTTTGAGATGATCTGGGATCCTAATGGGTG\nGACTGAGACAGATAGCAGTTTTTCTGTGAAGCAAGATATTGTAGCAATAACTGATTGGTC\nAGGATATAGCGGAAGTTTTGTCCAGCATCCAGAACTGACTGGGTTGGATTGCATGAGGCC\nTTGCTTCTGGGTTGAGCTGATCAGAGGAAGACCCAAGGAGAACACAATCTGGACCAGTGG\nAAGCAGCATTTCTTTTTGTGGAGTGAATAGCGACACTGTGGGTTGGTCTTGGCCAGACGG\nTGCTGAGTTGCCATTCACCATTGACAAGTAGTTTGTTCAAAAAACTCCTTG\n>I1-5\nGTAGATAATCACTCACCGAGTGACATCCACATCATGGCGTCTCAAGGCACCAAACGATCT\nTATGAGCAAATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAAATCAGAGCATCTGTT\nGGGAGAATGGTTGGTGGAATCGGAAGATTCTACATACAGATGTGTACTGAACTCAAGCTC\nAGTGACTATGAAGGGAGGCTGATCCAAAATAGCATAACCATAGAGAGAATGGTTCTCTCG\nGCATTTGATGAGAGGAGAAATAAATATCTGGAAGAGCATCCCAGTGCTGGGAAAGACCCC\nAAGAAGACTGGAGGCCCAATCTACAGAAGAAGAGATGGAAAATGGATGAGAGAGTTGATC\nCTATATGACAAAGAAGAGATCAGGAGGATTTGGCGTCAAGCAAATAACGGAGAAGACGCA\nACTGCTGGTCTCACCCATTTGATGATTTGGCATTCCAATCTGAATGATGCCACATACCAG\nAGAACAAGGGCACTTGTGCGTACTGGGATGGATCCCAGGATGTGCTCCCTGATGCAAGGC\nTCAACTCTTCCAAGAAGATCTGGGGCTGCTGGAGCAGCAGTGAAAGGGGTTGGAACAATG\nGCGATGGAACTGATCCGGATGATCAAGCGAGGTATCAATGATAGGAATTTCTGGAGAGGC\nGAAAATGGACGGAGGACGAGAATTGCTTATGAAAGAATGTGCAACATCCTCAAGGGGAAA\nTTCCAAACAGCAGCACAACGAGCAATGATGGATCAGGTGAGAGAAAGCCGGAATCCTGGG\nAATGCTGAAATTGAAGATCTCATCTTCCTTGCAAGGTCTGCTCTCATTCTGAGAGGATCA\nGTAGCTCATAAGTCCTGCCTGCCTGCTTGTGTGTATGGGCTTGCAGTGGCCAGTGGATAC\nGACTTTGAGAGAGAGGGATATTCCCTAGTCGGAATTGATCCTTTCCGTCTGCTCCAAAAC\nAGTCAAGTCTTCAGCCTCATCAGACCAAACGAAAATCCAGCGCATAAGAGTCAGCTGGTA\nTGGATGGCATGTCACTCTGCTGCATTTGAAGATTTGAGAGTGTCAAGCTTCATCAGAGGA\nACAAGAGTAGTCCCAAGAGGACAACTATCCACCAGAGGAGTTCAGATTGCTTCAAATGAG\nAACATGGAGACAATGGACTCCAGCACTCTTGAACTGAGGAGCAGATACTGGGCTATAAGG\nACAAGAAGCGGAGGGAACACTAACCAGCAGAGAGCATCTGCAGGGCAAATCAGCGTGCAG\nCCCACCTTCTCTGTACAGAGAAACCTCCCATTCGAGAGAGCAACCATTATGGCGGCATTT\nACGGGAAATACCGAGGGTAGAACTTCAGACATGAGGACTGAGATCATAAGGATGATGGAA\nAATGCCAGACCTGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAA\nAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTC\nGGAGACAATGCAGAGGAGTATGACAATTAAAGAAA\n>I1-7\nGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGT\nCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTGTTCGCAGGGAAAAACA\nCCGACCTTGAGGCGCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTA\nAGGGGATCTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTA\nGACGCTTTGTCCAAAATGCCCTTAATGGGAATGGGGATCCAAACAACATGGACAGAGCAG\nTCAAACTGTACAGGAAGCTCAAAAGGGAGATAACATTCCATGGGGCAAAGGAGGTAGCAC\nTCAGTTACTCAACTGGTGCACTTGCCAGCTGCATGGGTCTCATATACAACAGGATGGGGA\nCTGTGACCACTGAAGTGGCATTTGGCCTGGTGTGTGCCACGTGTGAGCAGATTGCTGACT\nCCCAGCATCGGTCTCACAGACAAATGGTAACAACAACCAACCCACTAATAAGACACGAGA\nACAGGATGGTACTGGCTAGTACTACAGCTAAGGCCATGGAGCAAATGGCAGGGTCAAGTG\nAGCAAGCAGCAGAGGCTATGGAGGTTGCTAGTCAGGCTAGACAGATGGTGCAGGCAATGA\nGGACTATTGGGACTCACCCTAGCTCCAGTGCTGGTCTAAAAGATGATCTTCTTGAAAATT\nTGCAGGCCTACCAGAAACGGATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGTT\nATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTC\nTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGA\nGTGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAGTGCTGTGGATGTTGAC\nAATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCT\n>I1-8\nCAGGTAGATTGCTATCTATGGCACATAAGAAAGCTGCTCAGCATGAGAGACATGTGTGAT\nGCTCCCTTTGATGATAGACTCAGAAGAGATCAGAAGGCATTAAAGGGGAGAGGCAGCACA\nCTTGGACTCGACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\nNNNACCGACATGAGCATAGAGGAAATAAGCAGGGAGTGGTACATGCTCATGCCAAGGCAG\nAAAATAACAGGGGGTCTGATGGTGAAAATGGACCAGGCCATCATGGACAAGAGGATAATA\nCTCAAGGCAAACTTCTCTGTCCTATTTGATCAACTGGAAACATTAGTCTCACTGAGGGCT\nTTCACAGACGATGGCGCCATTGTAGCTGAAATATCTCCTATTCCTTCCATGCCAGGACAT\nTCTACAGAGGATGTCAAAAATGCAATTGGAATCCTCATCGGTGGACTTGAATGGAATGAT\nAACTCAATTCGAGCGTCTGAAAATATACAGAGATTCGCTTGGGGAGTCCGTGATGAGAAT\nGGGGGACCTCCACTCCCTCCAAAACAGAAACGCTACATGGCGAGAAGAGTTGAGTCAGAA\nGTTTGAAGAGATCAGATGGCTAATTGCAGAGTGCAGAAACATATTAACCAAAACTGAAAA\nCAGCTTCGAGCAGATAACGTTCTTGCAGGCATTGCAACTCTTACTTGAGGTTGAGAGTGA\nGATAAGGACATTTTCTTTTCAGCTTATTTAGTACTAAAAAAC\n>I1-2\nAACCATTTGAATGGATGTCAATCCGACTTTACTTTTCTTGAAAGTTCCAGCGCAAAATGC\nCATAAGCACCACATTCCCGTACACTGGAGACCCTCCATACAGCCATGGAACAGGAACAGG\nATACACCATGGACACGGTCAACAGAACACATCAATATTCAGAAAAGGGGAAATGGACAAC\nAAACTCAGAGACTGGAGCACCCCAACTTAACCCAATTGATGGACCACTGCCCGAGGACAA\nTGAGCCAAGTGGATATGCACAAACGGACTGTGTCCTTGAAGCAATGGCTTTCCTTGAAGA\nATCCCACCCAGGAATCTTTGAAAACTCGTGTCTTGAGACGATGGAAGTTGTTCAACAAAC\nAAGAGTAGACAAATTGACCCAAGGCCGTCAGACCTATGATTGGACATTAAACAGGAATCA\nACCGGCTGCAACTGCATTAGCTAATACTATAGAGGTATTCAGATCGAACGGTCTGACAGC\nTAATGAATCAGGAAGGCTAATAGATTTTCTCAAGGATGTGATGGAATCAATGGATAAAGA\nGGAAATGGAAATAACAACGCATTTCCAAAGGAAAAGAAGAGTAAGGGACAACATGACCAA\nGAAAATGGTCACACAAAGGACAATAGGAAAGAAGAAGCAGAGGCTAAATAAAAAGAGCTA\nTCTAATAAGAGCCTTGACACTGAACACAATGACAAAAGACGCCGAAAGAGGCAAATTAAA\nGAGAAGAGCAATTGCAACACCCGGAATGCAAATCAGAGGATTTGTATACTTTGTTGAAAC\nATTAGCAAGGAGCATTTGTGAGAAGCTTGAACAATCTGGACTCCCAGTTGGAGGCAATGA\nAAAGAAGGCTAAACTGGCAAATGTTGTGAGGAAAATGATGACTAATTCACAAGATACAGA\nACTCTCCTTCACAATCACTGGAGACAACACCAAATGGAATGAAAACCAGAACCCTAGGAT\nGTTTCTGGCAATGATAACATATATAACAAGAAACCAACCTGAATGGTTTAGGAATGTCTT\nGAGCATTGCACCCATAATGTTCTCAAACAAAATGGCAAGGCTAGGGAAAGGATATATGTT\nCGAAAGTAAGAGCATGAAGCTTCGAACACAAATACCGGCAGAAATGCTAGCAAGTATTGA\nTCTGAAATATTTTAATGAGTCGACAAAAAAGAAAATTGAAAAGATAAGACCTCTTCTAAT\nAGATGGTACAGCCTCATTGAGTCCTGGAATGATGATGGGCATGTTCAACATGCTAAGTAC\nAGTTTTGGGAGTTTCGATTTTAAATCTAGGACAAAAGAGGTACACCAAAACAACATACTG\nGTGGGACGGGCTCCAATCCTCTGATGACTTTGCTCTCATAGTGAATGCCCCGAATCATGA\nGGGGATACAAGCAGGAGTAGACAGATTCTATAGAACCTGCAAGCTGGTTGGAATCAACAT\nGAGCAAAAAGAAGTCCTACATAAACAGGACAGGAACATTTGAATTCACAAGTTTTTTCTA\nTCGCTATGGATTTGTAGCCAATTTCAGTATGGAGTTGCCCAGCTTTGGAGTGTCTGGGAT\nTAATGAATCTGCAGACATGAGCATTGGAGTAACAGTGATAAAGAACAACATGATAAACAA\nTGATCTTGGACCAGCAACAGCTCAAATGGCTCTTCAGCTGTTCATCAAGGATTACAGATA\nCACGTATCGGTGTCACAGAGGAGACACACAAATTCAGACAAGGAGGTCATTCGAGCTGAA\nGAAATTGTGGGAACAAACCCGCTCAAAAGCGGGACTGCTGGTCTCAGACGGAGGACCAAA\nCCTATACAATATCCGGAATCTACACATTCCGGAAGTCTGCTTAAAATGGGAGCTGATGGA\nCGAAGACTATCAGGGAAGGCTTTGCAACCCCCTGAATCCGTTTGTCAGCCACAAGGAGAT\nAGAGTCTGTAAACAATGCTGTGGTGATGCCAGCTCATGGCCCAGCCAAGAGCATGGAGTA\nTGATGCTGTGGCTACTACACACTCCTGGATACCTAAGAGGAATCGCTCTATCCTCAATAC\nAAGCCAAAGGGGAATCCTTGAGGATGAACAGATGTATCAAAAGTGCTGCAATCTATTCGA\nGAAATTCTTCCCTAGCAGCTCATACAGGAGACCGGTTGGAATTTCCAGCATGGTAGAGGC\nCATGGTTTCTAGGGCCCGAATCGATGCGCGAATTGACTTCGAATCTGGACGGATCAAGAA\nAGAGGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAACTCAGACGGCAGAA\nATAGTGAATTTTGCTTGTCCTTCATGAAAAAATGCCTTG\n>I1-1\nTATATTCAATATGGAGAGAATAAAAGAACTAAGAGATTTAATGTCACAATCCCGCACTCG\nCGAGATACTAACCAAAACCACTGTTGACCACATGGCCATAATCAAAAAGTACACATCGGG\nAAGGCAAGAGAAGAACCCCGCACTCAGGATGAAATGGATGATGGCAATGAAATATCCAAT\nCACAGCTGACAAGCGAATAATGGAAATGATCCCTGAAAGGAATGAACAAGGGCAAACCCT\nCTGGAGCAAAACAAACGATGCCGGATCAGACCGAGTGATGGTATCACCCCTGGCTGTAAC\nATGGTGGAATAGGAATGGACCAACAACAAGTACAGTTCACTATCCCAAGGTATATAAAAC\nTTATTTCGAAAAGGTTGAAAGGTTGAAACACGGGACCTTTGGCCCTGTACACTTCAGAAA\nCCAAGTTAAGATAAGACGGAGGGTCGACATAAACCCGGGCCATGCTGACCTCAGTGCCAA\nAGAGGCGCAGGATGTAATCATGGAAGTTGTCTTTCCAAATGAAGTGGGAGCGAGAATACT\nGACGTCGGAATCACAATTGACGATAACAAAGGAGAAGAAAGAAGAACTCCAGGACTGCAA\nAATCGCCCCTCTGATGGTTGCATACATGCTAGAAAGAGAGTTGGTTCGCAAGACAAGGTT\nTCTCCCAGTGGCTGGTGGAACAAGCAGTGTCTACATTGAGGTGCTGCATTTGACCCAGGG\nGACATGCTGGGAGCAGATGTATACTCCGGGAGGAGAAGTGAGAAACGATGATGTAGACCA\nGAGCTTGATTATCGCTGCCAGGAACATAGTGAGAAGAGCAACAGTGTCAGCAGACCCACT\nAGCATCTCTATTGGAGATGTGCCACAGCACACAAATTGGGGGAATAAGGATGGTAGACAT\nTCTCCGGCAAAATCCAACAGAGGAACAAGCCGTGGACATATGCAAGGCAGCAATGGGCTT\nGAGGATTAGCTCATCTTTCAGTTTTGGTGGATTCACTTTTAAAAGAACGAGTGGATCGTC\nAGTCAAAAAGGAAGAAGAAGTGCTTACGGGCAACCTTCAAACATTGAAAATAAGAGTGCA\nTGAGGGGTATGAAGAGTTCACAATGGTTGGAAGAAGAGCAACGGCCATTCTCAGAAAGGC\nAACCAGAAGGCTGATCCAGTTAATAGTAAGTGGAAGAGACGAGCAGTCAATTGCTGAAGC\nAATAATTGTGGCCATGGTATTCTCACAAGAGGACTGCATGATTAAGGCAGTTCGAGGTGA\nTCTGAATTTTGTCAATAGGGCGAACCAGCGGCTGAATCCAATGCATCAGCTCTTGAGACA\nCTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAATTGGGGAATTGAACCCATTGACAATGT\nGATGGGAATGATCGGGATATTGCCTGACATGACCCCAAGTACTGAGATGTCACTGAGGGG\nAATAAGAATCAGTAAGATGGGGGTAGATGAATACTCCAGCACAGAGCGGGTAGTAGTAAG\nCATCGACCGATTTTTAAGAGTTCGAGACCAACGAGGGAACGTGCTATTGTCACCCGAAGA\nAGTCAGCGAGGCACAAGGAACAGAGAAACTGACAATCACTTATTCGTCATCAATGATGTG\nGGAGATTAATGGTCCTGAGTCGGTGTTGGTCAATACTTATCAGTGGATAATCAGAAACTG\nGGAAACTGTAAAAATTCAATGGTCACAGGATCCCACAATGTTGTATAATAAGATGGAATT\nCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCCAGAGGTCAATACAGTGGGTTCGTGAG\nGACACTGTTCCAGCAGATGCGAGATGTGCTTGGAACATTCGACACTGTTCAGATAATAAA\nACTCCTCCCCTTTGCTGCTGCCCCACCGGAACAAAGTAGGATGCAGTTCTCCTCCCTGAC\nTGTGAATGTGAGAGGATCAGGAATGAGAATACTGGTAAGAGGCAATTCCCCAGTGTTCAA\nTTACAACAAGGCCACCAAGAGGCTCACAGTTCTCGGGAAAGATGCAGGTGCATTGACCGA\nAGATCCAGATGAAGGCACAGCTGGAGTGGAGTCTGCTGTTTTAAGAGGATTCCTCATTTT\nGGGCAAAGAAGACAAGAGATATGGCCCAGCATTGAGCATCAATGAGCTGAGCAATCTTGC\nAAAGGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTGATGAAACG\nGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGC\nCATCAATTAGTGTCGAATTGTTTA\n>I1-3\nCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAA\nGGCAATGAAAGAATATGGGGAAGATCCGAAAATTGAAACTAACAAGTTTGCTGCAATATG\nCACCCACTTAGAAGTCTGTTTCATGTATTCGGATTTTCATTTCATCGACGAACGGGGTGA\nATCAATAATTGTAGAATCTGGTGACCCAAATGCATTACTGAAGCACCGATTCGAGATAAT\nTGAAGGAAGAGATCGAACCATGGCCTGGACAGTGGTGAATAGTATCTGCAACACCACAGG\nGGTAGAGAAGCCTAAATTTCTTCCGGATCTGTATGACTACAAGGAGAACAGATTCATTGA\nAATTGGGGTGACACGGAGGGAGGTTCACATATACTACCTAGAAAAAGCCAATAAAATAAA\nATCCGAGAAGACACACATCCACATTTTCTCATTCACTGGAGAGGAAATGGCCACCAAAGC\nGGACTACACCCTTGATGAAGAAAGCAGAGCAAGAATCAAAACCAGATTGTTCACCATAAG\nACAAGAAATGGCCAGTAGAGGTTTGTGGGATTCCTTTCGTCAGTCCGAGAGAGGCGAAGA\nGACAATTGAAGAAAGATTTGAAATTACAGGAACCATGCGCAGGCTTGCCGACCAAAGTCT\nCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTGGATGGATTCGAACCGAA\nCGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAAGTGAACGCAAGAATTGAACC\nATTCTTGAAAACAACACCACGCCCACTCAGATTACCTGATGGGCCTCCTTGTTCCCAGCG\nGTCAAAATTTCTGTTGATGGATGCTCTGAAACTAAGTATTGAGGACCCGAGTCATGAGGG\nGGAGGGAATACCGCTATATGATGCAATCAAATGCATGAAGACATTTTTTGGCTGGAAAGA\nACCTAACATAATCAAACCACATGAGAAAGGCATAAACCCCAACTACCTCCTGACTTGGAA\nGCAAGTACTAGCGGAACTCCAAGACATTGAGAATGAAGAGAAGATCCCAAAGACAAAGAA\nCATGAAGAAAACAAGCCAACTGAAGTGGGCACTTGGTGAAAATATGGCACCAGAGAAAGT\nAGACTTTGATGATTGCAAAGATATTAGTGATCTTAAACAGTATGACAGCGATGAGCCAGA\nACCTAGGTCGCTAGCAAGCTGGATCCAAAGTGAATTCAACAAGGCATGTGAATTGACCGA\nTTCAAGCTGGATGGAGCTTGATGAGATAGGGGAAGATGTTGCCCCGATCGAACACATTGC\nAAGCATGAGGAGAAACTATTTTACAGCAGAAGTGTCCCATTGCAGGGCTACTGAGTACAT\nAATGAAGGGAGTGTACATAAACACAGCCTTGCTCAATGCATCTTGTGCAGCCATGGATGA\nCTTCCAGCTGATCCCAATGATAAGCAAATGTAGAACCAAAGAAGGGAGACGGAAAACAAA\nTCTGTATGGATTCATTATAAAAGGAAGGTCTCATTTGAGAAATGACACTGACGTGGTAAA\nTTTTGTGAGTATGGAGTTCTCTCTCACAGACCCGAGACTGGAGCCACACAAATGGGAAAA\nGTACTGTGTTCTCGAAATAGGGGATATGCTCTTGAGGACTGCGATAGGCCAAGTGTCACG\nACCCATGTTCCTATATGTGAGAACCAATGGAACTTCAAAGATCAAGATGAAATGGGGGAT\nGGAAATGAGGCGCTGCCTTCTCCAATCCCTTCAGCAGATTGAGAGCATGATTGAGGCCGA\nGTCTTCCGTCAAAGAGAAAGATATGACAAAGGAATTCTTTGAGAACAAATCAGAAACATG\nGCCAATTGGAGAGTCACCCAAGGGAGTGGAAGAAGGCTCTATTGGGAAAGTATGCAGAAC\nCCTACTGGCAAAGTCTGTATTCAACAGTCTATATGCATCTCCACAACTCGAGGGGTTTTC\nAGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGAACCTGG\nGACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTG\nGGTTTTGCTCAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTGAAATAGTTGTG\nGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTT\n" }, { "path": "tests/input/TestOrderOrientAndImputeFromReference/expected.influenza.impute.mafft.fasta", "content": ">test_influenza.genome-1\nAGCGAAAGCAGGTCAATTATATTCAATATGGAGAGAATAAAAGAACTAAGAGATTTAATG\nTCACAATCCCGCACTCGCGAGATACTAACCAAAACCACTGTTGACCACATGGCCATAATC\nAAAAAGTACACATCGGGAAGGCAAGAGAAGAACCCCGCACTCAGGATGAAATGGATGATG\nGCAATGAAATATCCAATCACAGCTGACAAGCGAATAATGGAAATGATCCCTGAAAGGAAT\nGAACAAGGGCAAACCCTCTGGAGCAAAACAAACGATGCCGGATCAGACCGAGTGATGGTA\nTCACCCCTGGCTGTAACATGGTGGAATAGGAATGGACCAACAACAAGTACAGTTCACTAT\nCCCAAGGTATATAAAACTTATTTCGAAAAGGTTGAAAGGTTGAAACACGGGACCTTTGGC\nCCTGTACACTTCAGAAACCAAGTTAAGATAAGACGGAGGGTCGACATAAACCCGGGCCAT\nGCTGACCTCAGTGCCAAAGAGGCGCAGGATGTAATCATGGAAGTTGTCTTTCCAAATGAA\nGTGGGAGCGAGAATACTGACGTCGGAATCACAATTGACGATAACAAAGGAGAAGAAAGAA\nGAACTCCAGGACTGCAAAATCGCCCCTCTGATGGTTGCATACATGCTAGAAAGAGAGTTG\nGTTCGCAAGACAAGGTTTCTCCCAGTGGCTGGTGGAACAAGCAGTGTCTACATTGAGGTG\nCTGCATTTGACCCAGGGGACATGCTGGGAGCAGATGTATACTCCGGGAGGAGAAGTGAGA\nAACGATGATGTAGACCAGAGCTTGATTATCGCTGCCAGGAACATAGTGAGAAGAGCAACA\nGTGTCAGCAGACCCACTAGCATCTCTATTGGAGATGTGCCACAGCACACAAATTGGGGGA\nATAAGGATGGTAGACATTCTCCGGCAAAATCCAACAGAGGAACAAGCCGTGGACATATGC\nAAGGCAGCAATGGGCTTGAGGATTAGCTCATCTTTCAGTTTTGGTGGATTCACTTTTAAA\nAGAACGAGTGGATCGTCAGTCAAAAAGGAAGAAGAAGTGCTTACGGGCAACCTTCAAACA\nTTGAAAATAAGAGTGCATGAGGGGTATGAAGAGTTCACAATGGTTGGAAGAAGAGCAACG\nGCCATTCTCAGAAAGGCAACCAGAAGGCTGATCCAGTTAATAGTAAGTGGAAGAGACGAG\nCAGTCAATTGCTGAAGCAATAATTGTGGCCATGGTATTCTCACAAGAGGACTGCATGATT\nAAGGCAGTTCGAGGTGATCTGAATTTTGTCAATAGGGCGAACCAGCGGCTGAATCCAATG\nCATCAGCTCTTGAGACACTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAATTGGGGAATT\nGAACCCATTGACAATGTGATGGGAATGATCGGGATATTGCCTGACATGACCCCAAGTACT\nGAGATGTCACTGAGGGGAATAAGAATCAGTAAGATGGGGGTAGATGAATACTCCAGCACA\nGAGCGGGTAGTAGTAAGCATCGACCGATTTTTAAGAGTTCGAGACCAACGAGGGAACGTG\nCTATTGTCACCCGAAGAAGTCAGCGAGGCACAAGGAACAGAGAAACTGACAATCACTTAT\nTCGTCATCAATGATGTGGGAGATTAATGGTCCTGAGTCGGTGTTGGTCAATACTTATCAG\nTGGATAATCAGAAACTGGGAAACTGTAAAAATTCAATGGTCACAGGATCCCACAATGTTG\nTATAATAAGATGGAATTCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCCAGAGGTCAA\nTACAGTGGGTTCGTGAGGACACTGTTCCAGCAGATGCGAGATGTGCTTGGAACATTCGAC\nACTGTTCAGATAATAAAACTCCTCCCCTTTGCTGCTGCCCCACCGGAACAAAGTAGGATG\nCAGTTCTCCTCCCTGACTGTGAATGTGAGAGGATCAGGAATGAGAATACTGGTAAGAGGC\nAATTCCCCAGTGTTCAATTACAACAAGGCCACCAAGAGGCTCACAGTTCTCGGGAAAGAT\nGCAGGTGCATTGACCGAAGATCCAGATGAAGGCACAGCTGGAGTGGAGTCTGCTGTTTTA\nAGAGGATTCCTCATTTTGGGCAAAGAAGACAAGAGATATGGCCCAGCATTGAGCATCAAT\nGAGCTGAGCAATCTTGCAAAGGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTG\nGTGTTGGTGATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACC\nAAAAGAATTCGGATGGCCATCAATTAGTGTCGAATTGTTTAAAAACGACCTTGTTTCTAC\nT\n>test_influenza.genome-2\nAGCGAAAGCAGGTACTGATCCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATG\nATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGATCCGAAAATTGAAACT\nAACAAGTTTGCTGCAATATGCACCCACTTAGAAGTCTGTTTCATGTATTCGGATTTTCAT\nTTCATCGACGAACGGGGTGAATCAATAATTGTAGAATCTGGTGACCCAAATGCATTACTG\nAAGCACCGATTCGAGATAATTGAAGGAAGAGATCGAACCATGGCCTGGACAGTGGTGAAT\nAGTATCTGCAACACCACAGGGGTAGAGAAGCCTAAATTTCTTCCGGATCTGTATGACTAC\nAAGGAGAACAGATTCATTGAAATTGGGGTGACACGGAGGGAGGTTCACATATACTACCTA\nGAAAAAGCCAATAAAATAAAATCCGAGAAGACACACATCCACATTTTCTCATTCACTGGA\nGAGGAAATGGCCACCAAAGCGGACTACACCCTTGATGAAGAAAGCAGAGCAAGAATCAAA\nACCAGATTGTTCACCATAAGACAAGAAATGGCCAGTAGAGGTTTGTGGGATTCCTTTCGT\nCAGTCCGAGAGAGGCGAAGAGACAATTGAAGAAAGATTTGAAATTACAGGAACCATGCGC\nAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTAT\nGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAA\nGTGAACGCAAGAATTGAACCATTCTTGAAAACAACACCACGCCCACTCAGATTACCTGAT\nGGGCCTCCTTGTTCCCAGCGGTCAAAATTTCTGTTGATGGATGCTCTGAAACTAAGTATT\nGAGGACCCGAGTCATGAGGGGGAGGGAATACCGCTATATGATGCAATCAAATGCATGAAG\nACATTTTTTGGCTGGAAAGAACCTAACATAATCAAACCACATGAGAAAGGCATAAACCCC\nAACTACCTCCTGACTTGGAAGCAAGTACTAGCGGAACTCCAAGACATTGAGAATGAAGAG\nAAGATCCCAAAGACAAAGAACATGAAGAAAACAAGCCAACTGAAGTGGGCACTTGGTGAA\nAATATGGCACCAGAGAAAGTAGACTTTGATGATTGCAAAGATATTAGTGATCTTAAACAG\nTATGACAGCGATGAGCCAGAACCTAGGTCGCTAGCAAGCTGGATCCAAAGTGAATTCAAC\nAAGGCATGTGAATTGACCGATTCAAGCTGGATGGAGCTTGATGAGATAGGGGAAGATGTT\nGCCCCGATCGAACACATTGCAAGCATGAGGAGAAACTATTTTACAGCAGAAGTGTCCCAT\nTGCAGGGCTACTGAGTACATAATGAAGGGAGTGTACATAAACACAGCCTTGCTCAATGCA\nTCTTGTGCAGCCATGGATGACTTCCAGCTGATCCCAATGATAAGCAAATGTAGAACCAAA\nGAAGGGAGACGGAAAACAAATCTGTATGGATTCATTATAAAAGGAAGGTCTCATTTGAGA\nAATGACACTGACGTGGTAAATTTTGTGAGTATGGAGTTCTCTCTCACAGACCCGAGACTG\nGAGCCACACAAATGGGAAAAGTACTGTGTTCTCGAAATAGGGGATATGCTCTTGAGGACT\nGCGATAGGCCAAGTGTCACGACCCATGTTCCTATATGTGAGAACCAATGGAACTTCAAAG\nATCAAGATGAAATGGGGGATGGAAATGAGGCGCTGCCTTCTCCAATCCCTTCAGCAGATT\nGAGAGCATGATTGAGGCCGAGTCTTCCGTCAAAGAGAAAGATATGACAAAGGAATTCTTT\nGAGAACAAATCAGAAACATGGCCAATTGGAGAGTCACCCAAGGGAGTGGAAGAAGGCTCT\nATTGGGAAAGTATGCAGAACCCTACTGGCAAAGTCTGTATTCAACAGTCTATATGCATCT\nCCACAACTCGAGGGGTTTTCAGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTT\nAGGGACAACCTGGAACCTGGGACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAG\nTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCATCTTGGTTCAACTCCTTCCTCACA\nCATGCACTGAAATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTA\nCCTTGTCTACT\n>test_influenza.genome-3\nAGCAAAAGCAGGGTAGATAATCACTCACCGAGTGACATCCACATCATGGCGTCTCAAGGC\nACCAAACGATCTTATGAGCAAATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAAATC\nAGAGCATCTGTTGGGAGAATGGTTGGTGGAATCGGAAGATTCTACATACAGATGTGTACT\nGAACTCAAGCTCAGTGACTATGAAGGGAGGCTGATCCAAAATAGCATAACCATAGAGAGA\nATGGTTCTCTCGGCATTTGATGAGAGGAGAAATAAATATCTGGAAGAGCATCCCAGTGCT\nGGGAAAGACCCCAAGAAGACTGGAGGCCCAATCTACAGAAGAAGAGATGGAAAATGGATG\nAGAGAGTTGATCCTATATGACAAAGAAGAGATCAGGAGGATTTGGCGTCAAGCAAATAAC\nGGAGAAGACGCAACTGCTGGTCTCACCCATTTGATGATTTGGCATTCCAATCTGAATGAT\nGCCACATACCAGAGAACAAGGGCACTTGTGCGTACTGGGATGGATCCCAGGATGTGCTCC\nCTGATGCAAGGCTCAACTCTTCCAAGAAGATCTGGGGCTGCTGGAGCAGCAGTGAAAGGG\nGTTGGAACAATGGCGATGGAACTGATCCGGATGATCAAGCGAGGTATCAATGATAGGAAT\nTTCTGGAGAGGCGAAAATGGACGGAGGACGAGAATTGCTTATGAAAGAATGTGCAACATC\nCTCAAGGGGAAATTCCAAACAGCAGCACAACGAGCAATGATGGATCAGGTGAGAGAAAGC\nCGGAATCCTGGGAATGCTGAAATTGAAGATCTCATCTTCCTTGCAAGGTCTGCTCTCATT\nCTGAGAGGATCAGTAGCTCATAAGTCCTGCCTGCCTGCTTGTGTGTATGGGCTTGCAGTG\nGCCAGTGGATACGACTTTGAGAGAGAGGGATATTCCCTAGTCGGAATTGATCCTTTCCGT\nCTGCTCCAAAACAGTCAAGTCTTCAGCCTCATCAGACCAAACGAAAATCCAGCGCATAAG\nAGTCAGCTGGTATGGATGGCATGTCACTCTGCTGCATTTGAAGATTTGAGAGTGTCAAGC\nTTCATCAGAGGAACAAGAGTAGTCCCAAGAGGACAACTATCCACCAGAGGAGTTCAGATT\nGCTTCAAATGAGAACATGGAGACAATGGACTCCAGCACTCTTGAACTGAGGAGCAGATAC\nTGGGCTATAAGGACAAGAAGCGGAGGGAACACTAACCAGCAGAGAGCATCTGCAGGGCAA\nATCAGCGTGCAGCCCACCTTCTCTGTACAGAGAAACCTCCCATTCGAGAGAGCAACCATT\nATGGCGGCATTTACGGGAAATACCGAGGGTAGAACTTCAGACATGAGGACTGAGATCATA\nAGGATGATGGAAAATGCCAGACCTGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAG\nCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGA\nTCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAATTAAAGAAAAATACCCTTGTTT\nCTACT\n>test_influenza.genome-4\nAGCGAAAGCAGGGGTTTAAAATGAATCCAAATCAGAAAATAATAACCATTGGATCAATCT\nGTCTGGTAGTCGGACTAATTAGCCTAATATTGCAAATAGGGAATATAATCTCAATATGGA\nTTAGCCATTCAATTCAAACTGGAAGTCAAAACCATACTGGAATATGCAACCAAAACATCA\nTTACCTATAAAAATAGCACCTGGGTAAAGGACACAACTTCAGTGATATTAACCGGCAATT\nCATCTCTCTGTCCAATCAGTGGATGGGCTATATACAGCAAGGACAATGGTATAAGAATAG\nGTTCCAAAGGAGATGTATTTGTCATCAGAGAGCCTTTTATTTCATGCTCTCACTTGGAAT\nGCAGGACTTTCTTTCTAACTCAAGGGGCCTTGTTGAATGACAAGCATTCTAATGGAACCG\nTTAAAGACAGAAGCCCTTATAGAACCCTAATGAGCTGCCCTGTTGGTGAAGCTCCTTCCC\nCATACAATTCAAGGTTTGAGTCTGTTGCTTGGTCAGCAAGTGCTTGTCATGATGGCATTA\nGTTGGTTGACAATTGGTATTTCCGGCCCAGACAATGGGGCGGTGGCTGTATTAAAATACA\nATGGCATAATAACAGATACTATCAAGAGTTGGAGAGGCAATATATTAAGAACACAAGAGT\nCTGAATGTGCCTGCATTAATGGTTCTTGCTTTACCATAATGACTGATGGGCCGAGTAATG\nGCCAGGCCTCATACAAAATTTTCAAGGTAGAAAAGGGAAAGGTAGTCAAATCAGTTGAGT\nTGAATGCTCCTAATTACCACTATGAGGAGTGCTCCTGTTATCCTGATGCTAGCGAGGTAA\nTGTGTGTGTGCAGAGACAATTGGCATGGTTCAAATCGACCATGGGTGTCCTTCAATCAAA\nATCTAGAATATCAAATAGGATACATATGCAGCGGAGTTTTTGGAGACAACCCGCGCCCTA\nGTGATGGGACAGGCAGTTGTGGTCCAGTTTCTTCTAATGGGGCATATGGAGTGAAGGGGT\nTTTCATTTAAATACGGTAATGGTGTTTGGATAGGAAGAACTAAAAGTACTAGCTCAAGGA\nGTGGGTTTGAGATGATCTGGGATCCTAATGGGTGGACTGAGACAGATAGCAGTTTTTCTG\nTGAAGCAAGATATTGTAGCAATAACTGATTGGTCAGGATATAGCGGAAGTTTTGTCCAGC\nATCCAGAACTGACTGGGTTGGATTGCATGAGGCCTTGCTTCTGGGTTGAGCTGATCAGAG\nGAAGACCCAAGGAGAACACAATCTGGACCAGTGGAAGCAGCATTTCTTTTTGTGGAGTGA\nATAGCGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCACCATTGACA\nAGTAGTTTGTTCAAAAAACTCCTTGTTTCTACT\n>test_influenza.genome-5\nAGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCT\nCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTGTT\nCGCAGGGAAAAACACCGACCTTGAGGCGCTCATGGAATGGCTAAAGACAAGACCAATCCT\nGTCACCTCTGACTAAGGGGATCTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCG\nAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTTAATGGGAATGGGGATCCAAACAA\nCATGGACAGAGCAGTCAAACTGTACAGGAAGCTCAAAAGGGAGATAACATTCCATGGGGC\nAAAGGAGGTAGCACTCAGTTACTCAACTGGTGCACTTGCCAGCTGCATGGGTCTCATATA\nCAACAGGATGGGGACTGTGACCACTGAAGTGGCATTTGGCCTGGTGTGTGCCACGTGTGA\nGCAGATTGCTGACTCCCAGCATCGGTCTCACAGACAAATGGTAACAACAACCAACCCACT\nAATAAGACACGAGAACAGGATGGTACTGGCTAGTACTACAGCTAAGGCCATGGAGCAAAT\nGGCAGGGTCAAGTGAGCAAGCAGCAGAGGCTATGGAGGTTGCTAGTCAGGCTAGACAGAT\nGGTGCAGGCAATGAGGACTATTGGGACTCACCCTAGCTCCAGTGCTGGTCTAAAAGATGA\nTCTTCTTGAAAATTTGCAGGCCTACCAGAAACGGATGGGAGTGCAGATGCAGCGATTCAA\nGTGATCCTCTCGTTATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTC\nTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGC\nCTTCTACGGAAGGAGTGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAGTG\nCTGTGGATGTTGACAATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTACT\n" }, { "path": "tests/input/TestOrderOrientAndImputeFromReference/expected.influenza.impute.mummer.fasta", "content": ">test_influenza.genome-1\nAGCGAAAGCAGGTCAATTATATTCAATATGGAGAGAATAAAAGAACTAAGAGATTTAATG\nTCACAATCCCGCACTCGCGAGATACTAACCAAAACCACTGTTGACCACATGGCCATAATC\nAAAAAGTACACATCGGGAAGGCAAGAGAAGAACCCCGCACTCAGGATGAAATGGATGATG\nGCAATGAAATATCCAATCACAGCTGACAAGCGAATAATGGAAATGATCCCTGAAAGGAAT\nGAACAAGGGCAAACCCTCTGGAGCAAAACAAACGATGCCGGATCAGACCGAGTGATGGTA\nTCACCCCTGGCTGTAACATGGTGGAATAGGAATGGACCAACAACAAGTACAGTTCACTAT\nCCCAAGGTATATAAAACTTATTTCGAAAAGGTTGAAAGGTTGAAACACGGGACCTTTGGC\nCCTGTACACTTCAGAAACCAAGTTAAGATAAGACGGAGGGTCGACATAAACCCGGGCCAT\nGCTGACCTCAGTGCCAAAGAGGCGCAGGATGTAATCATGGAAGTTGTCTTTCCAAATGAA\nGTGGGAGCGAGAATACTGACGTCGGAATCACAATTGACGATAACAAAGGAGAAGAAAGAA\nGAACTCCAGGACTGCAAAATCGCCCCTCTGATGGTTGCATACATGCTAGAAAGAGAGTTG\nGTTCGCAAGACAAGGTTTCTCCCAGTGGCTGGTGGAACAAGCAGTGTCTACATTGAGGTG\nCTGCATTTGACCCAGGGGACATGCTGGGAGCAGATGTATACTCCGGGAGGAGAAGTGAGA\nAACGATGATGTAGACCAGAGCTTGATTATCGCTGCCAGGAACATAGTGAGAAGAGCAACA\nGTGTCAGCAGACCCACTAGCATCTCTATTGGAGATGTGCCACAGCACACAAATTGGGGGA\nATAAGGATGGTAGACATTCTCCGGCAAAATCCAACAGAGGAACAAGCCGTGGACATATGC\nAAGGCAGCAATGGGCTTGAGGATTAGCTCATCTTTCAGTTTTGGTGGATTCACTTTTAAA\nAGAACGAGTGGATCGTCAGTCAAAAAGGAAGAAGAAGTGCTTACGGGCAACCTTCAAACA\nTTGAAAATAAGAGTGCATGAGGGGTATGAAGAGTTCACAATGGTTGGAAGAAGAGCAACG\nGCCATTCTCAGAAAGGCAACCAGAAGGCTGATCCAGTTAATAGTAAGTGGAAGAGACGAG\nCAGTCAATTGCTGAAGCAATAATTGTGGCCATGGTATTCTCACAAGAGGACTGCATGATT\nAAGGCAGTTCGAGGTGATCTGAATTTTGTCAATAGGGCGAACCAGCGGCTGAATCCAATG\nCATCAGCTCTTGAGACACTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAATTGGGGAATT\nGAACCCATTGACAATGTGATGGGAATGATCGGGATATTGCCTGACATGACCCCAAGTACT\nGAGATGTCACTGAGGGGAATAAGAATCAGTAAGATGGGGGTAGATGAATACTCCAGCACA\nGAGCGGGTAGTAGTAAGCATCGACCGATTTTTAAGAGTTCGAGACCAACGAGGGAACGTG\nCTATTGTCACCCGAAGAAGTCAGCGAGGCACAAGGAACAGAGAAACTGACAATCACTTAT\nTCGTCATCAATGATGTGGGAGATTAATGGTCCTGAGTCGGTGTTGGTCAATACTTATCAG\nTGGATAATCAGAAACTGGGAAACTGTAAAAATTCAATGGTCACAGGATCCCACAATGTTG\nTATAATAAGATGGAATTCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCCAGAGGTCAA\nTACAGTGGGTTCGTGAGGACACTGTTCCAGCAGATGCGAGATGTGCTTGGAACATTCGAC\nACTGTTCAGATAATAAAACTCCTCCCCTTTGCTGCTGCCCCACCGGAACAAAGTAGGATG\nCAGTTCTCCTCCCTGACTGTGAATGTGAGAGGATCAGGAATGAGAATACTGGTAAGAGGC\nAATTCCCCAGTGTTCAATTACAACAAGGCCACCAAGAGGCTCACAGTTCTCGGGAAAGAT\nGCAGGTGCATTGACCGAAGATCCAGATGAAGGCACAGCTGGAGTGGAGTCTGCTGTTTTA\nAGAGGATTCCTCATTTTGGGCAAAGAAGACAAGAGATATGGCCCAGCATTGAGCATCAAT\nGAGCTGAGCAATCTTGCAAAGGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTG\nGTGTTGGTGATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACC\nAAAAGAATTCGGATGGCCATCAATTAGTGTCGAATTGTTTAAAAACGACCTTGTTTCTAC\nT\n>test_influenza.genome-2\nAGCGAAAGCAGGTACTGATCCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATG\nATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGATCCGAAAATTGAAACT\nAACAAGTTTGCTGCAATATGCACCCACTTAGAAGTCTGTTTCATGTATTCGGATTTTCAT\nTTCATCGACGAACGGGGTGAATCAATAATTGTAGAATCTGGTGACCCAAATGCATTACTG\nAAGCACCGATTCGAGATAATTGAAGGAAGAGATCGAACCATGGCCTGGACAGTGGTGAAT\nAGTATCTGCAACACCACAGGGGTAGAGAAGCCTAAATTTCTTCCGGATCTGTATGACTAC\nAAGGAGAACAGATTCATTGAAATTGGGGTGACACGGAGGGAGGTTCACATATACTACCTA\nGAAAAAGCCAATAAAATAAAATCCGAGAAGACACACATCCACATTTTCTCATTCACTGGA\nGAGGAAATGGCCACCAAAGCGGACTACACCCTTGATGAAGAAAGCAGAGCAAGAATCAAA\nACCAGATTGTTCACCATAAGACAAGAAATGGCCAGTAGAGGTTTGTGGGATTCCTTTCGT\nCAGTCCGAGAGAGGCGAAGAGACAATTGAAGAAAGATTTGAAATTACAGGAACCATGCGC\nAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTAT\nGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAA\nGTGAACGCAAGAATTGAACCATTCTTGAAAACAACACCACGCCCACTCAGATTACCTGAT\nGGGCCTCCTTGTTCCCAGCGGTCAAAATTTCTGTTGATGGATGCTCTGAAACTAAGTATT\nGAGGACCCGAGTCATGAGGGGGAGGGAATACCGCTATATGATGCAATCAAATGCATGAAG\nACATTTTTTGGCTGGAAAGAACCTAACATAATCAAACCACATGAGAAAGGCATAAACCCC\nAACTACCTCCTGACTTGGAAGCAAGTACTAGCGGAACTCCAAGACATTGAGAATGAAGAG\nAAGATCCCAAAGACAAAGAACATGAAGAAAACAAGCCAACTGAAGTGGGCACTTGGTGAA\nAATATGGCACCAGAGAAAGTAGACTTTGATGATTGCAAAGATATTAGTGATCTTAAACAG\nTATGACAGCGATGAGCCAGAACCTAGGTCGCTAGCAAGCTGGATCCAAAGTGAATTCAAC\nAAGGCATGTGAATTGACCGATTCAAGCTGGATGGAGCTTGATGAGATAGGGGAAGATGTT\nGCCCCGATCGAACACATTGCAAGCATGAGGAGAAACTATTTTACAGCAGAAGTGTCCCAT\nTGCAGGGCTACTGAGTACATAATGAAGGGAGTGTACATAAACACAGCCTTGCTCAATGCA\nTCTTGTGCAGCCATGGATGACTTCCAGCTGATCCCAATGATAAGCAAATGTAGAACCAAA\nGAAGGGAGACGGAAAACAAATCTGTATGGATTCATTATAAAAGGAAGGTCTCATTTGAGA\nAATGACACTGACGTGGTAAATTTTGTGAGTATGGAGTTCTCTCTCACAGACCCGAGACTG\nGAGCCACACAAATGGGAAAAGTACTGTGTTCTCGAAATAGGGGATATGCTCTTGAGGACT\nGCGATAGGCCAAGTGTCACGACCCATGTTCCTATATGTGAGAACCAATGGAACTTCAAAG\nATCAAGATGAAATGGGGGATGGAAATGAGGCGCTGCCTTCTCCAATCCCTTCAGCAGATT\nGAGAGCATGATTGAGGCCGAGTCTTCCGTCAAAGAGAAAGATATGACAAAGGAATTCTTT\nGAGAACAAATCAGAAACATGGCCAATTGGAGAGTCACCCAAGGGAGTGGAAGAAGGCTCT\nATTGGGAAAGTATGCAGAACCCTACTGGCAAAGTCTGTATTCAACAGTCTATATGCATCT\nCCACAACTCGAGGGGTTTTCAGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTT\nAGGGACAACCTGGAACCTGGGACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAG\nTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCATCTTGGTTCAACTCCTTCCTCACA\nCATGCACTGAAATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTA\nCCTTGTTTCTACT\n>test_influenza.genome-3\nAGCAAAAGCAGGGTAGATAATCACTCACCGAGTGACATCCACATCATGGCGTCTCAAGGC\nACCAAACGATCTTATGAGCAAATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAAATC\nAGAGCATCTGTTGGGAGAATGGTTGGTGGAATCGGAAGATTCTACATACAGATGTGTACT\nGAACTCAAGCTCAGTGACTATGAAGGGAGGCTGATCCAAAATAGCATAACCATAGAGAGA\nATGGTTCTCTCGGCATTTGATGAGAGGAGAAATAAATATCTGGAAGAGCATCCCAGTGCT\nGGGAAAGACCCCAAGAAGACTGGAGGCCCAATCTACAGAAGAAGAGATGGAAAATGGATG\nAGAGAGTTGATCCTATATGACAAAGAAGAGATCAGGAGGATTTGGCGTCAAGCAAATAAC\nGGAGAAGACGCAACTGCTGGTCTCACCCATTTGATGATTTGGCATTCCAATCTGAATGAT\nGCCACATACCAGAGAACAAGGGCACTTGTGCGTACTGGGATGGATCCCAGGATGTGCTCC\nCTGATGCAAGGCTCAACTCTTCCAAGAAGATCTGGGGCTGCTGGAGCAGCAGTGAAAGGG\nGTTGGAACAATGGCGATGGAACTGATCCGGATGATCAAGCGAGGTATCAATGATAGGAAT\nTTCTGGAGAGGCGAAAATGGACGGAGGACGAGAATTGCTTATGAAAGAATGTGCAACATC\nCTCAAGGGGAAATTCCAAACAGCAGCACAACGAGCAATGATGGATCAGGTGAGAGAAAGC\nCGGAATCCTGGGAATGCTGAAATTGAAGATCTCATCTTCCTTGCAAGGTCTGCTCTCATT\nCTGAGAGGATCAGTAGCTCATAAGTCCTGCCTGCCTGCTTGTGTGTATGGGCTTGCAGTG\nGCCAGTGGATACGACTTTGAGAGAGAGGGATATTCCCTAGTCGGAATTGATCCTTTCCGT\nCTGCTCCAAAACAGTCAAGTCTTCAGCCTCATCAGACCAAACGAAAATCCAGCGCATAAG\nAGTCAGCTGGTATGGATGGCATGTCACTCTGCTGCATTTGAAGATTTGAGAGTGTCAAGC\nTTCATCAGAGGAACAAGAGTAGTCCCAAGAGGACAACTATCCACCAGAGGAGTTCAGATT\nGCTTCAAATGAGAACATGGAGACAATGGACTCCAGCACTCTTGAACTGAGGAGCAGATAC\nTGGGCTATAAGGACAAGAAGCGGAGGGAACACTAACCAGCAGAGAGCATCTGCAGGGCAA\nATCAGCGTGCAGCCCACCTTCTCTGTACAGAGAAACCTCCCATTCGAGAGAGCAACCATT\nATGGCGGCATTTACGGGAAATACCGAGGGTAGAACTTCAGACATGAGGACTGAGATCATA\nAGGATGATGGAAAATGCCAGACCTGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAG\nCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGA\nTCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAATTAAAGAAAAATACCCTTGTTT\nCTACT\n>test_influenza.genome-4\nAGCGAAAGCAGGGGTTTAAAATGAATCCAAATCAGAAAATAATAACCATTGGATCAATCT\nGTCTGGTAGTCGGACTAATTAGCCTAATATTGCAAATAGGGAATATAATCTCAATATGGA\nTTAGCCATTCAATTCAAACTGGAAGTCAAAACCATACTGGAATATGCAACCAAAACATCA\nTTACCTATAAAAATAGCACCTGGGTAAAGGACACAACTTCAGTGATATTAACCGGCAATT\nCATCTCTCTGTCCAATCAGTGGATGGGCTATATACAGCAAGGACAATGGTATAAGAATAG\nGTTCCAAAGGAGATGTATTTGTCATCAGAGAGCCTTTTATTTCATGCTCTCACTTGGAAT\nGCAGGACTTTCTTTCTAACTCAAGGGGCCTTGTTGAATGACAAGCATTCTAATGGAACCG\nTTAAAGACAGAAGCCCTTATAGAACCCTAATGAGCTGCCCTGTTGGTGAAGCTCCTTCCC\nCATACAATTCAAGGTTTGAGTCTGTTGCTTGGTCAGCAAGTGCTTGTCATGATGGCATTA\nGTTGGTTGACAATTGGTATTTCCGGCCCAGACAATGGGGCGGTGGCTGTATTAAAATACA\nATGGCATAATAACAGATACTATCAAGAGTTGGAGAGGCAATATATTAAGAACACAAGAGT\nCTGAATGTGCCTGCATTAATGGTTCTTGCTTTACCATAATGACTGATGGGCCGAGTAATG\nGCCAGGCCTCATACAAAATTTTCAAGGTAGAAAAGGGAAAGGTAGTCAAATCAGTTGAGT\nTGAATGCTCCTAATTACCACTATGAGGAGTGCTCCTGTTATCCTGATGCTAGCGAGGTAA\nTGTGTGTGTGCAGAGACAATTGGCATGGTTCAAATCGACCATGGGTGTCCTTCAATCAAA\nATCTAGAATATCAAATAGGATACATATGCAGCGGAGTTTTTGGAGACAACCCGCGCCCTA\nGTGATGGGACAGGCAGTTGTGGTCCAGTTTCTTCTAATGGGGCATATGGAGTGAAGGGGT\nTTTCATTTAAATACGGTAATGGTGTTTGGATAGGAAGAACTAAAAGTACTAGCTCAAGGA\nGTGGGTTTGAGATGATCTGGGATCCTAATGGGTGGACTGAGACAGATAGCAGTTTTTCTG\nTGAAGCAAGATATTGTAGCAATAACTGATTGGTCAGGATATAGCGGAAGTTTTGTCCAGC\nATCCAGAACTGACTGGGTTGGATTGCATGAGGCCTTGCTTCTGGGTTGAGCTGATCAGAG\nGAAGACCCAAGGAGAACACAATCTGGACCAGTGGAAGCAGCATTTCTTTTTGTGGAGTGA\nATAGCGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCACCATTGACA\nAGTAGTTTGTTCAAAAAACTCCTTGTTTCTACT\n>test_influenza.genome-5\nAGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCT\nCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTGTT\nCGCAGGGAAAAACACCGACCTTGAGGCGCTCATGGAATGGCTAAAGACAAGACCAATCCT\nGTCACCTCTGACTAAGGGGATCTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCG\nAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTTAATGGGAATGGGGATCCAAACAA\nCATGGACAGAGCAGTCAAACTGTACAGGAAGCTCAAAAGGGAGATAACATTCCATGGGGC\nAAAGGAGGTAGCACTCAGTTACTCAACTGGTGCACTTGCCAGCTGCATGGGTCTCATATA\nCAACAGGATGGGGACTGTGACCACTGAAGTGGCATTTGGCCTGGTGTGTGCCACGTGTGA\nGCAGATTGCTGACTCCCAGCATCGGTCTCACAGACAAATGGTAACAACAACCAACCCACT\nAATAAGACACGAGAACAGGATGGTACTGGCTAGTACTACAGCTAAGGCCATGGAGCAAAT\nGGCAGGGTCAAGTGAGCAAGCAGCAGAGGCTATGGAGGTTGCTAGTCAGGCTAGACAGAT\nGGTGCAGGCAATGAGGACTATTGGGACTCACCCTAGCTCCAGTGCTGGTCTAAAAGATGA\nTCTTCTTGAAAATTTGCAGGCCTACCAGAAACGGATGGGAGTGCAGATGCAGCGATTCAA\nGTGATCCTCTCGTTATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTC\nTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGC\nCTTCTACGGAAGGAGTGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAGTG\nCTGTGGATGTTGACAATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTTGT\nTTCTACT\n" }, { "path": "tests/input/TestOrderOrientAndImputeFromReference/expected.influenza.impute.muscle.fasta", "content": ">test_influenza.genome-1\nAGCGAAAGCAGGTCAATTATATTCAATATGGAGAGAATAAAAGAACTAAGAGATTTAATG\nTCACAATCCCGCACTCGCGAGATACTAACCAAAACCACTGTTGACCACATGGCCATAATC\nAAAAAGTACACATCGGGAAGGCAAGAGAAGAACCCCGCACTCAGGATGAAATGGATGATG\nGCAATGAAATATCCAATCACAGCTGACAAGCGAATAATGGAAATGATCCCTGAAAGGAAT\nGAACAAGGGCAAACCCTCTGGAGCAAAACAAACGATGCCGGATCAGACCGAGTGATGGTA\nTCACCCCTGGCTGTAACATGGTGGAATAGGAATGGACCAACAACAAGTACAGTTCACTAT\nCCCAAGGTATATAAAACTTATTTCGAAAAGGTTGAAAGGTTGAAACACGGGACCTTTGGC\nCCTGTACACTTCAGAAACCAAGTTAAGATAAGACGGAGGGTCGACATAAACCCGGGCCAT\nGCTGACCTCAGTGCCAAAGAGGCGCAGGATGTAATCATGGAAGTTGTCTTTCCAAATGAA\nGTGGGAGCGAGAATACTGACGTCGGAATCACAATTGACGATAACAAAGGAGAAGAAAGAA\nGAACTCCAGGACTGCAAAATCGCCCCTCTGATGGTTGCATACATGCTAGAAAGAGAGTTG\nGTTCGCAAGACAAGGTTTCTCCCAGTGGCTGGTGGAACAAGCAGTGTCTACATTGAGGTG\nCTGCATTTGACCCAGGGGACATGCTGGGAGCAGATGTATACTCCGGGAGGAGAAGTGAGA\nAACGATGATGTAGACCAGAGCTTGATTATCGCTGCCAGGAACATAGTGAGAAGAGCAACA\nGTGTCAGCAGACCCACTAGCATCTCTATTGGAGATGTGCCACAGCACACAAATTGGGGGA\nATAAGGATGGTAGACATTCTCCGGCAAAATCCAACAGAGGAACAAGCCGTGGACATATGC\nAAGGCAGCAATGGGCTTGAGGATTAGCTCATCTTTCAGTTTTGGTGGATTCACTTTTAAA\nAGAACGAGTGGATCGTCAGTCAAAAAGGAAGAAGAAGTGCTTACGGGCAACCTTCAAACA\nTTGAAAATAAGAGTGCATGAGGGGTATGAAGAGTTCACAATGGTTGGAAGAAGAGCAACG\nGCCATTCTCAGAAAGGCAACCAGAAGGCTGATCCAGTTAATAGTAAGTGGAAGAGACGAG\nCAGTCAATTGCTGAAGCAATAATTGTGGCCATGGTATTCTCACAAGAGGACTGCATGATT\nAAGGCAGTTCGAGGTGATCTGAATTTTGTCAATAGGGCGAACCAGCGGCTGAATCCAATG\nCATCAGCTCTTGAGACACTTCCAAAAGGATGCAAAAGTGCTTTTCCAAAATTGGGGAATT\nGAACCCATTGACAATGTGATGGGAATGATCGGGATATTGCCTGACATGACCCCAAGTACT\nGAGATGTCACTGAGGGGAATAAGAATCAGTAAGATGGGGGTAGATGAATACTCCAGCACA\nGAGCGGGTAGTAGTAAGCATCGACCGATTTTTAAGAGTTCGAGACCAACGAGGGAACGTG\nCTATTGTCACCCGAAGAAGTCAGCGAGGCACAAGGAACAGAGAAACTGACAATCACTTAT\nTCGTCATCAATGATGTGGGAGATTAATGGTCCTGAGTCGGTGTTGGTCAATACTTATCAG\nTGGATAATCAGAAACTGGGAAACTGTAAAAATTCAATGGTCACAGGATCCCACAATGTTG\nTATAATAAGATGGAATTCGAGCCATTTCAGTCTCTGGTCCCTAAGGCAGCCAGAGGTCAA\nTACAGTGGGTTCGTGAGGACACTGTTCCAGCAGATGCGAGATGTGCTTGGAACATTCGAC\nACTGTTCAGATAATAAAACTCCTCCCCTTTGCTGCTGCCCCACCGGAACAAAGTAGGATG\nCAGTTCTCCTCCCTGACTGTGAATGTGAGAGGATCAGGAATGAGAATACTGGTAAGAGGC\nAATTCCCCAGTGTTCAATTACAACAAGGCCACCAAGAGGCTCACAGTTCTCGGGAAAGAT\nGCAGGTGCATTGACCGAAGATCCAGATGAAGGCACAGCTGGAGTGGAGTCTGCTGTTTTA\nAGAGGATTCCTCATTTTGGGCAAAGAAGACAAGAGATATGGCCCAGCATTGAGCATCAAT\nGAGCTGAGCAATCTTGCAAAGGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTG\nGTGTTGGTGATGAAACGGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACC\nAAAAGAATTCGGATGGCCATCAATTAGTGTCGAATTGTTTAAAAACGACCTTGTTTCTAC\nT\n>test_influenza.genome-2\nAGCGAAAGCAGGTACTGATCCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATG\nATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAATATGGGGAAGATCCGAAAATTGAAACT\nAACAAGTTTGCTGCAATATGCACCCACTTAGAAGTCTGTTTCATGTATTCGGATTTTCAT\nTTCATCGACGAACGGGGTGAATCAATAATTGTAGAATCTGGTGACCCAAATGCATTACTG\nAAGCACCGATTCGAGATAATTGAAGGAAGAGATCGAACCATGGCCTGGACAGTGGTGAAT\nAGTATCTGCAACACCACAGGGGTAGAGAAGCCTAAATTTCTTCCGGATCTGTATGACTAC\nAAGGAGAACAGATTCATTGAAATTGGGGTGACACGGAGGGAGGTTCACATATACTACCTA\nGAAAAAGCCAATAAAATAAAATCCGAGAAGACACACATCCACATTTTCTCATTCACTGGA\nGAGGAAATGGCCACCAAAGCGGACTACACCCTTGATGAAGAAAGCAGAGCAAGAATCAAA\nACCAGATTGTTCACCATAAGACAAGAAATGGCCAGTAGAGGTTTGTGGGATTCCTTTCGT\nCAGTCCGAGAGAGGCGAAGAGACAATTGAAGAAAGATTTGAAATTACAGGAACCATGCGC\nAGGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTAT\nGTGGATGGATTCGAACCGAACGGCTGCATTGAGGGCAAGCTTTCTCAAATGTCAAAAGAA\nGTGAACGCAAGAATTGAACCATTCTTGAAAACAACACCACGCCCACTCAGATTACCTGAT\nGGGCCTCCTTGTTCCCAGCGGTCAAAATTTCTGTTGATGGATGCTCTGAAACTAAGTATT\nGAGGACCCGAGTCATGAGGGGGAGGGAATACCGCTATATGATGCAATCAAATGCATGAAG\nACATTTTTTGGCTGGAAAGAACCTAACATAATCAAACCACATGAGAAAGGCATAAACCCC\nAACTACCTCCTGACTTGGAAGCAAGTACTAGCGGAACTCCAAGACATTGAGAATGAAGAG\nAAGATCCCAAAGACAAAGAACATGAAGAAAACAAGCCAACTGAAGTGGGCACTTGGTGAA\nAATATGGCACCAGAGAAAGTAGACTTTGATGATTGCAAAGATATTAGTGATCTTAAACAG\nTATGACAGCGATGAGCCAGAACCTAGGTCGCTAGCAAGCTGGATCCAAAGTGAATTCAAC\nAAGGCATGTGAATTGACCGATTCAAGCTGGATGGAGCTTGATGAGATAGGGGAAGATGTT\nGCCCCGATCGAACACATTGCAAGCATGAGGAGAAACTATTTTACAGCAGAAGTGTCCCAT\nTGCAGGGCTACTGAGTACATAATGAAGGGAGTGTACATAAACACAGCCTTGCTCAATGCA\nTCTTGTGCAGCCATGGATGACTTCCAGCTGATCCCAATGATAAGCAAATGTAGAACCAAA\nGAAGGGAGACGGAAAACAAATCTGTATGGATTCATTATAAAAGGAAGGTCTCATTTGAGA\nAATGACACTGACGTGGTAAATTTTGTGAGTATGGAGTTCTCTCTCACAGACCCGAGACTG\nGAGCCACACAAATGGGAAAAGTACTGTGTTCTCGAAATAGGGGATATGCTCTTGAGGACT\nGCGATAGGCCAAGTGTCACGACCCATGTTCCTATATGTGAGAACCAATGGAACTTCAAAG\nATCAAGATGAAATGGGGGATGGAAATGAGGCGCTGCCTTCTCCAATCCCTTCAGCAGATT\nGAGAGCATGATTGAGGCCGAGTCTTCCGTCAAAGAGAAAGATATGACAAAGGAATTCTTT\nGAGAACAAATCAGAAACATGGCCAATTGGAGAGTCACCCAAGGGAGTGGAAGAAGGCTCT\nATTGGGAAAGTATGCAGAACCCTACTGGCAAAGTCTGTATTCAACAGTCTATATGCATCT\nCCACAACTCGAGGGGTTTTCAGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTT\nAGGGACAACCTGGAACCTGGGACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAG\nTGCCTGATTAATGATCCCTGGGTTTTGCTCAATGCATCTTGGTTCAACTCCTTCCTCACA\nCATGCACTGAAATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTA\nCCTTGTTTCTACT\n>test_influenza.genome-3\nAGCAAAAGCAGGGTAGATAATCACTCACCGAGTGACATCCACATCATGGCGTCTCAAGGC\nACCAAACGATCTTATGAGCAAATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAAATC\nAGAGCATCTGTTGGGAGAATGGTTGGTGGAATCGGAAGATTCTACATACAGATGTGTACT\nGAACTCAAGCTCAGTGACTATGAAGGGAGGCTGATCCAAAATAGCATAACCATAGAGAGA\nATGGTTCTCTCGGCATTTGATGAGAGGAGAAATAAATATCTGGAAGAGCATCCCAGTGCT\nGGGAAAGACCCCAAGAAGACTGGAGGCCCAATCTACAGAAGAAGAGATGGAAAATGGATG\nAGAGAGTTGATCCTATATGACAAAGAAGAGATCAGGAGGATTTGGCGTCAAGCAAATAAC\nGGAGAAGACGCAACTGCTGGTCTCACCCATTTGATGATTTGGCATTCCAATCTGAATGAT\nGCCACATACCAGAGAACAAGGGCACTTGTGCGTACTGGGATGGATCCCAGGATGTGCTCC\nCTGATGCAAGGCTCAACTCTTCCAAGAAGATCTGGGGCTGCTGGAGCAGCAGTGAAAGGG\nGTTGGAACAATGGCGATGGAACTGATCCGGATGATCAAGCGAGGTATCAATGATAGGAAT\nTTCTGGAGAGGCGAAAATGGACGGAGGACGAGAATTGCTTATGAAAGAATGTGCAACATC\nCTCAAGGGGAAATTCCAAACAGCAGCACAACGAGCAATGATGGATCAGGTGAGAGAAAGC\nCGGAATCCTGGGAATGCTGAAATTGAAGATCTCATCTTCCTTGCAAGGTCTGCTCTCATT\nCTGAGAGGATCAGTAGCTCATAAGTCCTGCCTGCCTGCTTGTGTGTATGGGCTTGCAGTG\nGCCAGTGGATACGACTTTGAGAGAGAGGGATATTCCCTAGTCGGAATTGATCCTTTCCGT\nCTGCTCCAAAACAGTCAAGTCTTCAGCCTCATCAGACCAAACGAAAATCCAGCGCATAAG\nAGTCAGCTGGTATGGATGGCATGTCACTCTGCTGCATTTGAAGATTTGAGAGTGTCAAGC\nTTCATCAGAGGAACAAGAGTAGTCCCAAGAGGACAACTATCCACCAGAGGAGTTCAGATT\nGCTTCAAATGAGAACATGGAGACAATGGACTCCAGCACTCTTGAACTGAGGAGCAGATAC\nTGGGCTATAAGGACAAGAAGCGGAGGGAACACTAACCAGCAGAGAGCATCTGCAGGGCAA\nATCAGCGTGCAGCCCACCTTCTCTGTACAGAGAAACCTCCCATTCGAGAGAGCAACCATT\nATGGCGGCATTTACGGGAAATACCGAGGGTAGAACTTCAGACATGAGGACTGAGATCATA\nAGGATGATGGAAAATGCCAGACCTGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAG\nCTCTCGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGA\nTCTTATTTCTTCGGAGACAATGCAGAGGAGTATGACAATTAAAGAAAAATACCCTTGTTT\nCTACT\n>test_influenza.genome-4\nAGCGAAAGCAGGGGTTTAAAATGAATCCAAATCAGAAAATAATAACCATTGGATCAATCT\nGTCTGGTAGTCGGACTAATTAGCCTAATATTGCAAATAGGGAATATAATCTCAATATGGA\nTTAGCCATTCAATTCAAACTGGAAGTCAAAACCATACTGGAATATGCAACCAAAACATCA\nTTACCTATAAAAATAGCACCTGGGTAAAGGACACAACTTCAGTGATATTAACCGGCAATT\nCATCTCTCTGTCCAATCAGTGGATGGGCTATATACAGCAAGGACAATGGTATAAGAATAG\nGTTCCAAAGGAGATGTATTTGTCATCAGAGAGCCTTTTATTTCATGCTCTCACTTGGAAT\nGCAGGACTTTCTTTCTAACTCAAGGGGCCTTGTTGAATGACAAGCATTCTAATGGAACCG\nTTAAAGACAGAAGCCCTTATAGAACCCTAATGAGCTGCCCTGTTGGTGAAGCTCCTTCCC\nCATACAATTCAAGGTTTGAGTCTGTTGCTTGGTCAGCAAGTGCTTGTCATGATGGCATTA\nGTTGGTTGACAATTGGTATTTCCGGCCCAGACAATGGGGCGGTGGCTGTATTAAAATACA\nATGGCATAATAACAGATACTATCAAGAGTTGGAGAGGCAATATATTAAGAACACAAGAGT\nCTGAATGTGCCTGCATTAATGGTTCTTGCTTTACCATAATGACTGATGGGCCGAGTAATG\nGCCAGGCCTCATACAAAATTTTCAAGGTAGAAAAGGGAAAGGTAGTCAAATCAGTTGAGT\nTGAATGCTCCTAATTACCACTATGAGGAGTGCTCCTGTTATCCTGATGCTAGCGAGGTAA\nTGTGTGTGTGCAGAGACAATTGGCATGGTTCAAATCGACCATGGGTGTCCTTCAATCAAA\nATCTAGAATATCAAATAGGATACATATGCAGCGGAGTTTTTGGAGACAACCCGCGCCCTA\nGTGATGGGACAGGCAGTTGTGGTCCAGTTTCTTCTAATGGGGCATATGGAGTGAAGGGGT\nTTTCATTTAAATACGGTAATGGTGTTTGGATAGGAAGAACTAAAAGTACTAGCTCAAGGA\nGTGGGTTTGAGATGATCTGGGATCCTAATGGGTGGACTGAGACAGATAGCAGTTTTTCTG\nTGAAGCAAGATATTGTAGCAATAACTGATTGGTCAGGATATAGCGGAAGTTTTGTCCAGC\nATCCAGAACTGACTGGGTTGGATTGCATGAGGCCTTGCTTCTGGGTTGAGCTGATCAGAG\nGAAGACCCAAGGAGAACACAATCTGGACCAGTGGAAGCAGCATTTCTTTTTGTGGAGTGA\nATAGCGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCACCATTGACA\nAGTAGTTTGTTCAAAAAACTCCTTGTTTCTACT\n>test_influenza.genome-5\nAGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCT\nCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTGTT\nCGCAGGGAAAAACACCGACCTTGAGGCGCTCATGGAATGGCTAAAGACAAGACCAATCCT\nGTCACCTCTGACTAAGGGGATCTTAGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCG\nAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTTAATGGGAATGGGGATCCAAACAA\nCATGGACAGAGCAGTCAAACTGTACAGGAAGCTCAAAAGGGAGATAACATTCCATGGGGC\nAAAGGAGGTAGCACTCAGTTACTCAACTGGTGCACTTGCCAGCTGCATGGGTCTCATATA\nCAACAGGATGGGGACTGTGACCACTGAAGTGGCATTTGGCCTGGTGTGTGCCACGTGTGA\nGCAGATTGCTGACTCCCAGCATCGGTCTCACAGACAAATGGTAACAACAACCAACCCACT\nAATAAGACACGAGAACAGGATGGTACTGGCTAGTACTACAGCTAAGGCCATGGAGCAAAT\nGGCAGGGTCAAGTGAGCAAGCAGCAGAGGCTATGGAGGTTGCTAGTCAGGCTAGACAGAT\nGGTGCAGGCAATGAGGACTATTGGGACTCACCCTAGCTCCAGTGCTGGTCTAAAAGATGA\nTCTTCTTGAAAATTTGCAGGCCTACCAGAAACGGATGGGAGTGCAGATGCAGCGATTCAA\nGTGATCCTCTCGTTATTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTC\nTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGC\nCTTCTACGGAAGGAGTGCCTGAGTCTATGAGGGAAGAATATCGGCAGGAACAGCAGAGTG\nCTGTGGATGTTGACAATGGTCATTTTGTCAACATAGAGCTGGAGTAAAAAACTACCTTGT\nTTCTACT\n" }, { "path": "tests/input/TestOrderOrientAndImputeFromReference/ref.influenza_partial.fasta", "content": ">gi|8486138|ref|NC_002023.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 1, complete sequence\nAGCGAAAGCAGGTCAATTATATTCAATATGGAAAGAATAAAAGAACTAAGAAATCTAATGTCGCAGTCTC\nGCACCCGCGAGATACTCACAAAAACCACCGTGGACCATATGGCCATAATCAAGAAGTACACATCAGGAAG\nACAGGAGAAGAACCCAGCACTTAGGATGAAATGGATGATGGCAATGAAATATCCAATTACAGCAGACAAG\nAGGATAACGGAAATGATTCCTGAGAGAAATGAGCAAGGACAAACTTTATGGAGTAAAATGAATGATGCCG\nGATCAGACCGAGTGATGGTATCACCTCTGGCTGTGACATGGTGGAATAGGAATGGACCAATGACAAATAC\nAGTTCATTATCCAAAAATCTACAAAACTTATTTTGAAAGAGTCGAAAGGCTAAAGCATGGAACCTTTGGC\nCCTGTCCATTTTAGAAACCAAGTCAAAATACGTCGGAGAGTTGACATAAATCCTGGTCATGCAGATCTCA\nGTGCCAAGGAGGCACAGGATGTAATCATGGAAGTTGTTTTCCCTAACGAAGTGGGAGCCAGGATACTAAC\nATCGGAATCGCAACTAACGATAACCAAAGAGAAGAAAGAAGAACTCCAGGATTGCAAAATTTCTCCTTTG\nATGGTTGCATACATGTTGGAGAGAGAACTGGTCCGCAAAACGAGATTCCTCCCAGTGGCTGGTGGAACAA\nGCAGTGTGTACATTGAAGTGTTGCATTTGACTCAAGGAACATGCTGGGAACAGATGTATACTCCAGGAGG\nGGAAGTGAAGAATGATGATGTTGATCAAAGCTTGATTATTGCTGCTAGGAACATAGTGAGAAGAGCTGCA\nGTATCAGCAGACCCACTAGCATCTTTATTGGAGATGTGCCACAGCACACAGATTGGTGGAATTAGGATGG\nTAGACATCCTTAAGCAGAACCCAACAGAAGAGCAAGCCGTGGGTATATGCAAGGCTGCAATGGGACTGAG\nAATTAGCTCATCCTTCAGTTTTGGTGGATTCACATTTAAGAGAACAAGCGGATCATCAGTCAAGAGAGAG\nGAAGAGGTGCTTACGGGCAATCTTCAAACATTGAAGATAAGAGTGCATGAGGGATATGAAGAGTTCACAA\nTGGTTGGGAGAAGAGCAACAGCCATACTCAGAAAAGCAACCAGGAGATTGATTCAGCTGATAGTGAGTGG\nGAGAGACGAACAGTCGATTGCCGAAGCAATAATTGTGGCCATGGTATTTTCACAAGAGGATTGTATGATA\nAAAGCAGTTAGAGGTGATCTGAATTTCGTCAATAGGGCGAATCAGCGACTGAATCCTATGCATCAACTTT\nTAAGACATTTTCAGAAGGATGCGAAAGTGCTTTTTCAAAATTGGGGAGTTGAACCTATCGACAATGTGAT\nGGGAATGATTGGGATATTGCCCGACATGACTCCAAGCATCGAGATGTCAATGAGAGGAGTGAGAATCAGC\nAAAATGGGTGTAGATGAGTACTCCAGCACGGAGAGGGTAGTGGTGAGCATTGACCGGTTCTTGAGAGTCC\nGGGACCAACGAGGAAATGTACTACTGTCTCCCGAGGAGGTCAGTGAAACACAGGGAACAGAGAAACTGAC\nAATAACTTACTCATCGTCAATGATGTGGGAGATTAATGGTCCTGAATCAGTGTTGGTCAATACCTATCAA\nTGGATCATCAGAAACTGGGAAACTGTTAAAATTCAGTGGTCCCAGAACCCTACAATGCTATACAATAAAA\nTGGAATTTGAACCATTTCAGTCTTTAGTACCTAAGGCCATTAGAGGCCAATACAGTGGGTTTGTGAGAAC\nTCTGTTCCAACAAATGAGGGATGTGCTTGGGACATTTGATACCGCACAGATAATAAAACTTCTTCCCTTC\nGCAGCCGCTCCACCAAAGCAAAGTAGAATGCAGTTCTCCTCATTTACTGTGAATGTGAGGGGATCAGGAA\nTGAGAATACTTGTAAGGGGCAATTCTCCTGTATTCAACTACAACAAGGCCACGAAGAGACTCACAGTTCT\nCGGAAAGGATGCTGGCACTTTAACCGAAGACCCAGATGAAGGCACAGCTGGAGTGGAGTCCGCTGTTCTG\nAGGGGATTCCTCATTCTGGGCAAAGAAGACAGGAGATATGGGCCAGCATTAAGCATCAATGAACTGAGCA\nACCTTGCGAAAGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTAATGAAACGAAA\nACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAGTGT\nCGAATAGTTTAAAAACGACCTTGTTTCTACT\n\n>gi|8486136|ref|NC_002022.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 3, complete sequence\nAGCGAAAGCAGGTACTGATCCAAAATGGAAGATTTTGTGCGACAATGCTTCAATCCGATGATTGTCGAGC\nTTGCGGAAAAAACAATGAAAGAGTATGGGGAGGACCTGAAAATCGAAACAAACAAATTTGCAGCAATATG\nCACTCACTTGGAAGTATGCTTCATGTATTCAGATTTCCACTTCATCAATGAGCAAGGCGAGTCAATAATC\nGTAGAACTTGGTGATCCTAATGCACTTTTGAAGCACAGATTTGAAATAATCGAGGGAAGAGATCGCACAA\nTGGCCTGGACAGTAGTAAACAGTATTTGCAACACTACAGGGGCTGAGAAACCAAAGTTTCTACCAGATTT\nGTATGATTACAAGGAAAATAGATTCATCGAAATTGGAGTAACAAGGAGAGAAGTTCACATATACTATCTG\nGAAAAGGCCAATAAAATTAAATCTGAGAAAACACACATCCACATTTTCTCGTTCACTGGGGAAGAAATGG\nCCACAAAGGCCGACTACACTCTCGATGAAGAAAGCAGGGCTAGGATCAAAACCAGGCTATTCACCATAAG\nACAAGAAATGGCCAGCAGAGGCCTCTGGGATTCCTTTCGTCAGTCCGAGAGAGGAGAAGAGACAATTGAA\nGAAAGGTTTGAAATCACAGGAACAATGCGCAAGCTTGCCGACCAAAGTCTCCCGCCGAACTTCTCCAGCC\nTTGAAAATTTTAGAGCCTATGTGGATGGATTCGAACCGAACGGCTACATTGAGGGCAAGCTGTCTCAAAT\nGTCCAAAGAAGTAAATGCTAGAATTGAACCTTTTTTGAAAACAACACCACGACCACTTAGACTTCCGAAT\nGGGCCTCCCTGTTCTCAGCGGTCCAAATTCCTGCTGATGGATGCCTTAAAATTAAGCATTGAGGACCCAA\nGTCATGAAGGAGAGGGAATACCGCTATATGATGCAATCAAATGCATGAGAACATTCTTTGGATGGAAGGA\nACCCAATGTTGTTAAACCACACGAAAAGGGAATAAATCCAAATTATCTTCTGTCATGGAAGCAAGTACTG\nGCAGAACTGCAGGACATTGAGAATGAGGAGAAAATTCCAAAGACTAAAAATATGAAAAAAACAAGTCAGC\nTAAAGTGGGCACTTGGTGAGAACATGGCACCAGAAAAGGTAGACTTTGACGACTGTAAAGATGTAGGTGA\nTTTGAAGCAATATGATAGTGATGAACCAGAATTGAGGTCGCTTGCAAGTTGGATTCAGAATGAGTTCAAC\nAAGGCATGCGAACTGACAGATTCAAGCTGGATAGAGCTTGATGAGATTGGAGAAGATGTGGCTCCAATTG\nAACACATTGCAAGCATGAGAAGGAATTATTTCACATCAGAGGTGTCTCACTGCAGAGCCACAGAATACAT\nAATGAAGGGGGTGTACATCAATACTGCCTTACTTAATGCATCTTGTGCAGCAATGGATGATTTCCAATTA\nATTCCAATGATAAGCAAGTGTAGAACTAAGGAGGGAAGGCGAAAGACCAACTTGTATGGTTTCATCATAA\nAAGGAAGATCCCACTTAAGGAATGACACCGACGTGGTAAACTTTGTGAGCATGGAGTTTTCTCTCACTGA\nCCCAAGACTTGAACCACACAAATGGGAGAAGTACTGTGTTCTTGAGATAGGAGATATGCTTCTAAGAAGT\nGCCATAGGCCAGGTTTCAAGGCCCATGTTCTTGTATGTGAGGACAAATGGAACCTCAAAAATTAAAATGA\nAATGGGGAATGGAGATGAGGCGTTGTCTCCTCCAGTCACTTCAACAAATTGAGAGTATGATTGAAGCTGA\nGTCCTCTGTCAAAGAGAAAGACATGACCAAAGAGTTCTTTGAGAACAAATCAGAAACATGGCCCATTGGA\nGAGTCTCCCAAAGGAGTGGAGGAAAGTTCCATTGGGAAGGTCTGCAGGACTTTATTAGCAAAGTCGGTAT\nTTAACAGCTTGTATGCATCTCCACAACTAGAAGGATTTTCAGCTGAATCAAGAAAACTGCTTCTTATCGT\nTCAGGCTCTTAGGGACAATCTGGAACCTGGGACCTTTGATCTTGGGGGGCTATATGAAGCAATTGAGGAG\nTGCCTAATTAATGATCCCTGGGTTTTGCTTAATGCTTCTTGGTTCAACTCCTTCCTTACACATGCATTGA\nGTTAGTTGTGGCAGTGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTGTTTCTACT\n\n>gi|8486129|ref|NC_002019.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 5, complete sequence\nAGCAAAAGCAGGGTAGATAATCACTCACTGAGTGACATCAAAATCATGGCGTCCCAAGGCACCAAACGGT\nCTTACGAACAGATGGAGACTGATGGAGAACGCCAGAATGCCACTGAAATCAGAGCATCCGTCGGAAAAAT\nGATTGGTGGAATTGGACGATTCTACATCCAAATGTGCACAGAACTTAAACTCAGTGATTATGAGGGACGG\nTTGATCCAAAACAGCTTAACAATAGAGAGAATGGTGCTCTCTGCTTTTGACGAAAGGAGAAATAAATACC\nTGGAAGAACATCCCAGTGCGGGGAAGGATCCTAAGAAAACTGGAGGACCTATATACAGAAGAGTAAACGG\nAAAGTGGATGAGAGAACTCATCCTTTATGACAAAGAAGAAATAAGGCGAATCTGGCGCCAAGCTAATAAT\nGGTGACGATGCAACGGCTGGTCTGACTCACATGATGATCTGGCATTCCAATTTGAATGATGCAACTTATC\nAGAGGACAAGGGCTCTTGTTCGCACCGGAATGGATCCCAGGATGTGCTCTCTGATGCAAGGTTCAACTCT\nCCCTAGGAGGTCTGGAGCCGCAGGTGCTGCAGTCAAAGGAGTTGGAACAATGGTGATGGAATTGGTCAGG\nATGATCAAACGTGGGATCAATGATCGGAACTTCTGGAGGGGTGAGAATGGACGAAAAACAAGAATTGCTT\nATGAAAGAATGTGCAACATTCTCAAAGGGAAATTTCAAACTGCTGCACAAAAAGCAATGATGGATCAAGT\nGAGAGAGAGCCGGGACCCAGGGAATGCTGAGTTCGAAGATCTCACTTTTCTAGCACGGTCTGCACTCATA\nTTGAGAGGGTCGGTTGCTCACAAGTCCTGCCTGCCTGCCTGTGTGTATGGACCTGCCGTAGCCAGTGGGT\nACGACTTTGAAAGAGAGGGATACTCTCTAGTCGGAATAGACCCTTTCAGACTGCTTCAAAACAGCCAAGT\nGTACAGCCTAATCAGACCAAATGAGAATCCAGCACACAAGAGTCAACTGGTGTGGATGGCATGCCATTCT\nGCCGCATTTGAAGATCTAAGAGTATTGAGCTTCATCAAAGGGACGAAGGTGGTCCCAAGAGGGAAGCTTT\nCCACTAGAGGAGTTCAAATTGCTTCCAATGAAAATATGGAGACTATGGAATCAAGTACACTTGAACTGAG\nAAGCAGGTACTGGGCCATAAGGACCAGAAGTGGAGGAAACACCAATCAACAGAGGGCATCTGCGGGCCAA\nATCAGCATACAACCTACGTTCTCAGTACAGAGAAATCTCCCTTTTGACAGAACAACCGTTATGGCAGCAT\nTCACTGGGAATACAGAGGGGAGAACATCTGACATGAGGACCGAAATCATAAGGATGATGGAAAGTGCAAG\nACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCGGACGAAAAGGCAGCGAGCCCGATC\nGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTATTTCTTCGGAGACAATGCAGAGGAGTACGACAATT\nAAAGAAAAATACCCTTGTTTCTACT\n\n>gi|8486127|ref|NC_002018.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 6, complete sequence\nAGCGAAAGCAGGGGTTTAAAATGAATCCAAATCAGAAAATAATAACCATTGGATCAATCTGTCTGGTAGT\nCGGACTAATTAGCCTAATATTGCAAATAGGGAATATAATCTCAATATGGATTAGCCATTCAATTCAAACT\nGGAAGTCAAAACCATACTGGAATATGCAACCAAAACATCATTACCTATAAAAATAGCACCTGGGTAAAGG\nACACAACTTCAGTGATATTAACCGGCAATTCATCTCTTTGTCCCATCCGTGGGTGGGCTATATACAGCAA\nAGACAATAGCATAAGAATTGGTTCCAAAGGAGACGTTTTTGTCATAAGAGAGCCCTTTATTTCATGTTCT\nCACTTGGAATGCAGGACCTTTTTTCTGACCCAAGGTGCCTTACTGAATGACAGGCATTCAAATGGGACTG\nTTAAGGACAGAAGCCCTTATAGGGCCTTAATGAGCTGCCCTGTCGGTGAAGCTCCGTCCCCGTACAATTC\nAAGATTTGAATCGGTTGCTTGGTCAGCAAGTGCATGTCATGATGGCATGGGCTGGCTAACAATCGGAATT\nTCAGGTCCAGATAATGGAGCAGTGGCTGTATTAAAATACAACGGCATAATAACTGAAACCATAAAAAGTT\nGGAGGAAGAAAATATTGAGGACACAAGAGTCTGAATGTGCCTGTGTAAATGGTTCATGTTTTACTATAAT\nGACTGATGGCCCGAGTGATGGGCTGGCCTCGTACAAAATTTTCAAGATCGAAAAGGGGAAGGTTACTAAA\nTCAATAGAGTTGAATGCACCTAATTCTCACTATGAGGAATGTTCCTGTTACCCTGATACCGGCAAAGTGA\nTGTGTGTGTGCAGAGACAATTGGCATGGTTCGAACCGGCCATGGGTGTCTTTCGATCAAAACCTGGATTA\nTCAAATAGGATACATCTGCAGTGGGGTTTTCGGTGACAACCCGCGTCCCAAAGATGGAACAGGCAGCTGT\nGGTCCAGTGTATGTTGATGGAGCAAACGGAGTAAAGGGATTTTCATATAGGTATGGTAATGGTGTTTGGA\nTAGGAAGGACCAAAAGTCACAGTTCCAGACATGGGTTTGAGATGATTTGGGATCCTAATGGATGGACAGA\nGACTGATAGTAAGTTCTCTGTGAGGCAAGATGTTGTGGCAATGACTGATTGGTCAGGGTATAGCGGGAGT\nTTCGTTCAACATCCTGAGCTAACAGGGCTAGACTGTATAAGGCCGTGCTTCTGGGTTGAATTAATCAGGG\nGACGACCTAAAGAAAAAACAATCTGGACTAGTGCGAGCAGCATTTCTTTTTGTGGCGTGAATAGTGATAC\nTGTAGATTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCACCATTGACAAGTAGTCTGTTCAAAAAACT\nCCTTGTTTCTACT\n\n>gi|8486122|ref|NC_002016.1| Influenza A virus (A/Puerto Rico/8/1934(H1N1)) segment 7, complete sequence\nAGCGAAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATC\nCCGTCAGGCCCCCTCAAAGCCGAGATCGCACAGAGACTTGAAGATGTCTTTGCAGGGAAGAACACCGATC\nTTGAGGTTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAGGGGATTTTAGGATT\nTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTTAAT\nGGGAACGGGGATCCAAATAACATGGACAAAGCAGTTAAACTGTATAGGAAGCTCAAGAGGGAGATAACAT\nTCCATGGGGCCAAAGAAATCTCACTCAGTTATTCTGCTGGTGCACTTGCCAGTTGTATGGGCCTCATATA\nCAACAGGATGGGGGCTGTGACCACTGAAGTGGCATTTGGCCTGGTATGTGCAACCTGTGAACAGATTGCT\nGACTCCCAGCATCGGTCTCATAGGCAAATGGTGACAACAACCAACCCACTAATCAGACATGAGAACAGAA\nTGGTTTTAGCCAGCACTACAGCTAAGGCTATGGAGCAAATGGCTGGATCGAGTGAGCAAGCAGCAGAGGC\nCATGGAGGTTGCTAGTCAGGCTAGGCAAATGGTGCAAGCGATGAGAACCATTGGGACTCATCCTAGCTCC\nAGTGCTGGTCTGAAAAATGATCTTCTTGAAAATTTGCAGGCCTATCAGAAACGAATGGGGGTGCAGATGC\nAACGGTTCAAGTGATCCTCTCGCTATTGCCGCAAATATCATTGGGATCTTGCACTTGATATTGTGGATTC\nTTGATCGTCTTTTTTTCAAATGCATTTACCGTCGCTTTAAATACGGACTGAAAGGAGGGCCTTCTACGGA\nAGGAGTGCCAAAGTCTATGAGGGAAGAATATCGAAAGGAACAGCAGAGTGCTGTGGATGCTGACGATGGT\nCATTTTGTCAGCATAGAGCTGGAGTAAAAAACTACCTTGTTTCTACT\n\n\n" }, { "path": "tests/input/TestPerSample/ref.fasta", "content": ">chr1\nAGTAGTTCGCCTGTGTGAGCTGACAAACTTAGTAGTGTTTGTGAGGATTAATAACAATTAACACAGTGCG\nAGCTGTTTCTTAGCACGAAGATCTCGATGTCTAAGAAACCAGGAGGGCCCGGCAAGAGCCGGGCTGTCAA\nTATGCTAAAACGCGGAATGCCCCGCGTGTTGTCCTTGATTGGACTGAAGAGGGCTATGTTGAGCCTGATC\nGACGGCAAGGGGCCAATACGATTCGTGTTGGCTCTCTTGGCGTTCTTCAGGTTCACAGCAATTGCTCCGA\nCCCGAGCAGTGCTGGATCGATGGAGAGGTGTGAACAAACAAACAGCGATGAAACACCTTTTGAGTTTTAA\nGAAGGAACTAGGGACCTTGACCAGTGCTATCAATCGGCGGAGCTCAAAACAAAAGAGAAGAGGAGGAAAG\nACCGGAATTGCAGTTATGATTGGCCTGATCGCCAGCGTAGGAGCAGTTACCCTCTCTAACTTCCAAGGGA\nAGGTGATGATGACGGTAAATGCTACTGACGTCACAGATGTCATCACGATTCCAACAGCTGCTGGAAAGAA\nCCTATGCATTGTCAGAGCAATGGATGTGGGATACATGTGCGATGATACTATCACTTATGAATGCCCAGTG\nCTGTCGGCTGGTAATGATCCAGAAGACATCGACTGTTGGTGCACAAAGTCAGCAGTCTACGTCAGGTATG\nGAAGATGCACCAAGACACGCCACTCAAGACGCAGTCGGAGGTCACTGACAGTGCAGACACACGGAGAAAG\nCACTCTAGCGAACAAGAAGGGGGCTTGGATGGACAGCACCAAGGCCACAAGGTATTTGGTAAAAACAGAA\nTCATGGATCTTGAGGAACCCTGGATATGCCCTGGTGGCAGCCGTCATTGGTTGGATGCTTGGGAGCAACA\nCCATGCAGAGAGTTGTGTTTGTCGTGTTATTGCTTTTGGTGGCCCCAGCTTACAGCTTCAACTGCCTTGG\nAATGAGCAACAGAGACTTCTTGGAAGGAGTGTCTGGAGCAACATGGGTGGATTTGGTTCTCGAAGGCGAC\nAGCTGCGTGACTATCATGTCTAAGGACAAGCCTACCATCGATGTGAAGATGATGAATATGGAGGCGGCCA\nACCTGGCAGAGGTCCGCAGTTATTGCTATTTGGCTACCGTCAGCGATCTTTCCACCAAAGCTGCGTGCCC\nAACCATGGGAGAAGCTCACAATGACAAACGTGCTGATCCAGCTTTTGTGTGCAGACAAGGAGTGGTGGAC\nAGGGGCTGGGGCAACGGCTGCGGACTATTTGGCAAAGGAAGCATTGACACATGCGCTAAATTTGCCTGCT\nCTACCAAGGCAATAGGAAGAACCATCTTGAAAGAGAATATCAAGTACGAAGTGGCCATTTTTGTCCATGG\nACCAACTACTGTGGAGTCGCACGGAAACTACTCCACACAGGCTGGAGCCACTCAGGCAGGGAGATTCAGC\nATCACTCCTGCGGCGCCTTCATACACACTAAAGCTTGGAGAATATGGAGAGGTGACAGTGGACTGTGAAC\nCACGGTCAGGGATTGACACCAATGCATACTACGTGATGACTGTTGGAACAAAGACGTTCTTGGTCCATCG\nTGAGTGGTTCATGGACCTCAACCTCCCTTGGAGCAGTGCTGGAAGTACTGTATGGAGGAACAGAGAGACG\nTTAATGGAGTTTGAGGAACCACACGCTACGAAGCAGTCTGTGATAGCATTGGGCTCACAAGAGGGAGCTT\nTGCATCAAGCTTTGGCTGGAGCCATTCCTGTGGAATTTTCAAGCAACACTGTCAAGTTGACGTCGGGTCA\nTTTGAAGTGTAGAGTGAAGATGGAAAAATTGCAGTTGAAGGGAACAACCTATGGCGTCTGTTCAAAGGCT\nTTCAAGTTTCTTGGGACTCCCGCAGACACAGGTCACGGCACTGTGGTGTTGGAATTGCAGTACACTGGCA\nCGGATGGACCTTGCAAAGTTCCTATCTCGTCAGTGGCTTCATTGAACGACCTAACGCCAGTGGGCAGATT\nGGTCACTGTCAACCCTTTTGTTTCAGTGGCCACGGCCAACGCTAAGGTCCTGATTGAATTGGAACCACCC\nTTTGGAGACTCATACATAGTGGTGGGCAGAGGAGAACAACAGATCAATCACCATTGGCACAAGTCTGGAA\nGCAGCATTGGCAAAGCCTTTACAACCACCCTCAAAGGAGCGCAGAGACTAGCCGCTCTAGGAGACACAGC\nTTGGGACTTTGGATCAGTTGGAGGGGTGTTCACCTCAGTTGGGAAGGCTGTCCATCAAGTGTTTGGAGGA\nGCATTCCGCTCACTGTTCGGAGGCATGTCCTGGATAACGCAAGGATTGCTGGGGGCTCTCCTGTTGTGGA\nTGGGCATCAATGCTCGTGATAGGTCCATAGCTCTCACGTTTCTCGCAGTTGGAGGAGTTCTGCTCTTCCT\nCTCCGTGAACGTGCATGCTGACACTGGGTGTGCCATAGACATCAGCCGGCAAGAGCTGAGATGTGGAAGT\nGGAGTGTTCATACACAATGATGTGGAGGCTTGGATGGACCGGTACAAGTATTACCCTGAAACGCCACAAG\nGCCTAGCCAAGATCATTCAGAAAGCTCATAAGGAAGGAGTGTGCGGTCTACGATCAGTTTCCAGACTGGA\nGCATCAAATGTGGGAAGCAGTGAAGGACGAGCTGAACACTCTTTTGAAGGAGAATGGTGTGGACCTTAGT\nGTCGTGGTTGAGAAACAGGAGGGAATGTACAAGTCAGCACCTAAACGCCTCACCGCCACCACGGAAAAAT\nTGGAAATTGGCTGGAAGGCCTGGGGAAAGAGTATTTTATTTGCACCAGAACTCGCCAACAACACCTTTGT\nGGTTGATGGTCCGGAGACCAAGGAATGTCCGACTCAGAATCGCGCTTGGAATAGCTTAGAAGTGGAGGAT\nTTTGGATTTGGTCTCACCAGCACTCGGATGTTCCTGAAGGTCAGAGAGAGCAACACAACTGAATGTGACT\nCGAAGATCATTGGAACGGCTGTCAAGAACAACTTGGCGATCCACAGTGACCTGTCCTATTGGATTGAAAG\nCAGGCTCAATGATACGTGGAAGCTTGAAAGGGCAGTTCTGGGTGAAGTCAAATCATGTACGTGGCCTGAG\nACGCATACCTTGTGGGGCGATGGAATCCTTGAGAGTGACTTGATAATACCAGTCACACTGGCGGGACCAC\nGAAGCAATCACAATCGGAGACCTGGGTACAAGACACAAAACCAGGGCCCATGGGACGAAGGCCGGGTAGA\nGATTGACTTCGATTACTGCCCAGGAACTACGGTCACCCTGAGTGAGAGCTGCGGACACCGTGGACCTGCC\nACTCGCACCACCACGGAGAGCGGAAAGTTGATAACAGATTGGTGCTGCAGGAGCTGCACCTTACCACCAC\nTGCGCTACCAAACTGATAGCGGCTGTTGGTATGGTATGGAGATCAGACCACAGAGACATGATGAAAAGAC\nCCTCGTGCAGTCACAAGTGAATGCTTACAATGCTGATATGATTGACCCTTTTCAGTTGGGCCTTCTGGTC\nGTGTTCTTGGCCACCCAGGAGGTCCTTCGCAAGAGGTGGACAGCCAAGATCAGCATGCCAGCTATACTGA\nTTGCTCTGCTAGTCCTGGTGTTTGGGGGCATTACTTACACTGATGTGTTACGCTATGTCATCTTGGTGGG\nGGCAGCTTTCGCAGAATCTAATTCGGGAGGAGACGTGGTACACTTGGCGCTCATGGCGACCTTCAAGATA\nCAACCAGTGTTTATGGTGGCATCGTTTCTCAAAGCGAGATGGACCAACCAGGAGAACATTTTGTTGATGT\nTGGCGGCTGTTTTCTTTCAAATGGCTTATCACGATGCCCGCCAAATTCTGCTCTGGGAGATCCCTGATGT\nGTTGAATTCACTGGCGGTAGCTTGGATGATACTGAGAGCCATAACATTTACAACGACATCAAACGTGGTT\nGTTCCGCTGCTAGCCCTGCTAACACCCGGGCTGAGATGCTTGAATCTGGATGTGTACAGGATACTGCTGT\nTGATGGTCGGAATAGGCAGCTTGATCAAGGAGAAGAGGAGTGCAGCTGCAAAAAAGAAAGGAGCAAGTCT\nGCTATGCTTGGCTCTGGCCTCAACAGGACTTTTCAACCCCATGATCCTTGCTGCTGGACTGATTGCATGT\nGATCCCAACCGTAAACGCGGATGGCCCGCAACTGAAGTGATGACAGCTGTCGGCCTAATGTTTGCCATCG\nTCGGAGGGCTGGCAGAGCTTGACATTGACTCCATGGCCATTCCAATGACTATCGCGGGGCTCATGTTTGC\nTGCTTTCGTGATTTCTGGGAAATCAACAGATATGTGGATTGAGAGAACGGCGGACATTTCCTGGGAAAGT\nGATGCAGAAATTACAGGCTCGAGCGAAAGAGTTGATGTGCGGCTTGATGATGATGGAAACTTCCAGCTCA\nTGAATGATCCAGGAGCACCTTGGAAGATATGGATGCTCAGAATGGTCTGCCTCGCGATTAGTGCGTACAC\nCCCCTGGGCAATCTTGCCCTCAGTAATTGGATTTTGGATAACTCTCCAATACACAAAGAGAGGAGGCGTG\nTTGTGGGACACTCCCTCACCAAAGGAGTACAAAAAGGGGGACACGACCACCGGCGTCTACAGGATCATGA\nCTCGTGGGCTGCTCGGCAGTTATCAAGCAGGAGCGGGCGTGATGGTTGAAGGTGTTTTTCACACCCTTTG\nGCATACAACAAAAGGAGCCGCTTTGATGAGCGGAGAGGGCCGTCTGGACCCATACTGGGGCAGTGTCAAG\nGAGGATCGACTTTGTTACGGAGGACCCTGGAAATTGCAGCACAAGTGGAACGGGCAGGATGAGGTGCAGA\nTGATTGTGGTGGAACCTGGCAAGAACGTTAAGAACGTCCAGACGAAACCAGGGGTGTTCAAAACACCTGA\nAGGAGAAATCGGGGCCGTGACTTTGGACTTCCCCACTGGAACATCAGGCTCACCAATAGTGGACAAAAAC\nGGTGATGTGATTGGGCTTTATGGCAATGGAGTCATAATGCCCAACGGCTCATACATAAGCGCGATAGTGC\nAGGGTGAAAGGATGGATGAGCCAATCCCAGCCGGATTCGAACCTGAGATGCTGAGGAAAAAACAGATCAC\nTGTACTGGATCTCCATCCCGGCGCCGGTAAAACAAGGAGGATTCTGCCACAGATCATCAAAGAGGCCATA\nAACAGAAGACTGAGAACAGCCGTGCTAGCACCAACCAGGGTTGTGGCTGCTGAGATGGCTGAAGCACTGA\nGAGGACTGCCCATCCGGTACCAGACATCCGCAGTGCCCAGAGAACATAATGGAAATGAGATTGTTGATGT\nCATGTGTCATGCTACCCTCACCCACAGGCTGATGTCTCCTCACAGGGTGCCGAACTACAACCTGTTTGTG\nATGGATGAGGCTCATTTCACCGACCCAGCTAGCATTGCAGCAAGAGGTTACATTTCCACAAAGGTCGAGC\nTAGGGGAGGCGGCGGCAATATTCATGACAGCCACCCCACCAGGCACTTCAGATCCATTCCCAGAGTCCAA\nTTCACCAATTTCCGACTTACAGACTGAGATCCCGGATCGAGCTTGGAACTCTGGATACGAATGGATCACA\nGAATACACCGGGAAGACGGTTTGGTTTGTGCCTAGTGTCAAGATGGGGAATGAGATTGCCCTTTGCCTAC\nAACGTGCTGGAAAGAAAGTAGTCCAATTGAACAGAAAGTCCTACGAGACGGAGTACCCAAAATGTAAGAA\nCGATGATTGGGACTTTGTTATCACAACAGATATATCTGAAATGGGGGCTAACTTCAAGGCGAGCAGGGTG\nATTGACAGTCGGAAGAGTGTGAAACCAACCATCATAACAGAAGGAGAAGGGAGAGTGATCCTGGGAGAAC\nCATCTGCAGTGACAGCAGCTAGTGCCGCCCAGAGACGTGGACGTATCGGTAGAAATCCGTCGCAAGTTGG\nTGATGAGTACTGTTATGGGGGGCACACGAATGAAGACGACTCTAACTTCGCCCATTGGACTGAGGCACGA\nATCATGCTGGACAACATCAACATGCCAAACGGACTGATCGCTCAATTTTACCAACCAGAGCGTGAGAAGG\nTATACACCATGGATGGGGAATACCGGCTCAGAGGAGAAGAGAGAAAAAACTTTCTGGAACTGTTGAGGAC\nTGCAGATCTGCCAGTTTGGCTGGCTTACAAGGTTGCAGCGGCTGGAGTGTCATACCACGACCGGAGGTGG\nTGCTTTGATGGCCCTAGGACAAACACAGTTTTAGAAGACAACAACGAAGTGGAAGTCATCACGAAGCTTG\nGTGAAAGGAAGATTCTGAGGCCGCGCTGGATTGACGCCAGGGTGTACTCGGATCATCAGGCACTAAAGGC\nGTTCAAGGACTTCGCCTCGGGAAAACGTTCTCAGATAGGGCTCATTGAGGTTCTGGGAAAGATGCCTGAG\nCACTTCATGGGGAAGACATGGGAAGCACTCGACACCATGTACGTTGTGGCCACTGCAGAGAAAGGAGGAA\nGAGCTCACAGAATGGCCCTGGAGGAACTGCCAGATGCTCTTCAGACAATTGCCTTGATTGCCTTATTGAG\nTGTGATGACCATGGGAGTATTCTTCCTCCTCATGCAGCGGAAGGGCATTGGAAAGATAGGTCTGGGAGGC\nGCTGTCTTGGGAGTCGCGACCTTTTTCTGTTGGATGGCTGAAGTTCCAGGAACGAAGATCGCCGGAATGT\nTGCTGCTCTCCCTTCTCTTGATGATTGTGCTAATTCCTGAGCCAGAGAAGCAACGTTCGCAGACAGACAA\nCCAGCTAGCCGTGTTCCTGATTTGTGTCATGACCCTTGTGAGCGCAGTGGCAGCCAACGAGATGGGCTGG\nCTAGATAAGACCAAGAGTGACATAAGCAGTTTGTTTGGGCAAAGAATTGAGGTCAAGGAGAATTTTAGCA\nTGGGAGAGTTTCTTCTGGACTTGAGGCCGGCAACAGCCTGGTCACTGTACGCTGTGACAACAGCGGTCCT\nCACTCCACTGCTAAAGCATTTGATTACGTCAGATTACATCAACACCTCATTGACCTCAATAAACGTTCAG\nGCAAGTGCACTATTCACACTCGCGCGAGGCTTCCCCTTCGTCGATGTTGGAGTGTCGGCTCTCCTGCTAG\nCAGCCGGATGCTGGGGACAAGTCACCCTCACCGTTACGGTAACAGCGGCAACACTCCTTTTTTGCCACTA\nTGCCTACATGGTTCCCGGTTGGCAAGCTGAGGCAATGCGCTCAGCCCAGCGGCGGACAGCGGCCGGAATC\nATGAAGAACGCTGTAGTGGATGGCATCGTGGCCACGGACGTCCCCGAATTAGAGCGCACCACACCCATCA\nTGCAGAAGAAAGTTGGACAGATCATGCTGATCTTGGTGTCTCTAGCTGCAGTAGTAGTGAACCCGTCTGT\nGAAGACAGTACGAGAAGCCGGAATTTTGATCACGGCCGCAGCGGTGACGCTTTGGGAGAATGGAGCAAGC\nTCTGTTTGGAACGCAACAACTGCCATCGGACTCTGCCACATTATGCGTGGGGGTTGGTTGTCATGTCTAT\nCCATAACATGGACACTCATAAAGAACATGGAAAAACCAGGACTAAAAAGAGGTGGGGCAAAAGGACGCAC\nCTTGGGAGAGGTTTGGAAAGAAAGACTCAACCAGATGACAAAAGAAGAGTTCACTAGGTACCGCAAAGAG\nGCCATCATCGAAGTCGATCGCTCAGCGGCAAAACACGCCAGGAAAGAAGGCAATGTCACTGGAGGGCATC\nCAGTCTCTAGGGGCACAGCAAAACTGAGATGGCTGGTCGAACGGAGGTTTCTCGAACCGGTCGGAAAAGT\nGATTGACCTTGGATGTGGAAGGGGCGGCTGGTGTTACTATATGGCAACCCAAAAAAGAGTCCAAGAAGTC\nAGAGGGTACACAAAGGGCGGTCCCGGACATGAAGAGCCCCAACTAGTGCAAAGTTATGGATGGAACATTG\nTCACCATGAAGAGTGGAGTGGATGTGTTCTACAGACCTTCTGAGTGTTGTGACACCCTCCTTTGTGACAT\nCGGAGAGTCCTCGTCAAGTGCTGAGGTTGAAGAGCATAGGACGATTCGGGTCCTTGAAATGGTTGAGGAC\nTGGCTGCACCGAGGGCCAAGGGAATTTTGCGTGAAGGTGCTCTGCCCCTACATGCCGAAGGTCATAGAGA\nAGATGGAGCTGCTCCAACGCCGGTATGGGGGGGGACTGATCAGAAACCCACTCTCACGGAATTCCACGCA\nCGAGATGTATTGGGTGAGTCGAGCTTCAGGCAATGTGGTACATTCAGTGAATATGACCAGCCAGGTGCTC\nCTAGGAAGAATGGAAAAAAGGACCTGGAAGGGACCCCAATACGAGGAAGATGTAAACTTGGGAAGTGGAA\nCCAGGGCGGTGGGAAAACCCTTGCTCAACTCAGACACCAGTAAAATCAAGAACAGGATTGAACGACTCAG\nGCGTGAGTACAGTTCGACGTGGCACCACGATGAGAACCACCCATATAGAACCTGGAACTATCACGGTAGT\nTATGATGTGAAGCCCACAGGCTCCGCCAGTTCGCTGGTCAATGGAGTGGTCAGGCTCCTCTCAAAACCAT\nGGGACACCATCACGAATGTTACCACCATGGCCATGACTGACACTACTCCCTTCGGGCAGCAGCGAGTGTT\nCAAAGAGAAGGTGGACACGAAAGCTCCAGAACCGCCAGAAGGAGTGAAGTACGTGCTCAACGAGACCACT\nAACTGGTTGTGGGCGTTTTTGGCCAGAGAAAAACGTCCCAGAATGTGCTCTCGAGAGGAATTCATAAGAA\nAGGTCAACAGCAATGCAGCTTTGGGTGCCATGTTTGAAGAGCAGAATCAATGGAGGAGCGCCAGAGAAGC\nAGTTGAAGATCCAAAATTTTGGGAGATGGTGGATGAGGAGCGCGAGGCACATCTGCGGGGGGAATGTCAC\nACTTGCATTTACAACATGATGGGAAAGAGAGAGAAAAAACCCGGAGAGTTCGGAAAGGCCAAGGGAAGCA\nGAGCCATTTGGTTCATGTGGCTCGGAGCTCGCTTTCTGGAGTTCGAGGCTCTGGGTTTTCTCAATGAAGA\nCCACTGGCTTGGAAGAAAGAACTCAGGAGGAGGTGTCGAGGGCTTGGGCCTCCAAAAACTGGGTTACATC\nCTGCGTGAAGTTGGCACCCGGCCTGGGGGCAAGATCTATGCTGATGACACAGCTGGCTGGGACACCCGCA\nTCACGAGAGCTGACTTGGAAAATGAAGCTAAGGTGCTTGAGTTGCTTGATGGGGAACATCGGCGTCTTGC\nTAGGGCCATCATTGAGCTCACCTATCGTCACAAAGTTGTGAAAGTGATGCGCCCGGCTGCTGATGGAAGA\nACCGTCATGGATGTTATCTCCAGAGAAGATCAGAGGGGGAGTGGACAAGTTGTCACCTACGCCCTAAACA\nCTTTCACCAACCTGGCCGTCCAGCTGGTGAGGATGATGGAAGGGGAAGGAGTGATTGGCCCAGATGATGT\nGGAGAAACTCACAAAAGGGAAAGGACCCAAAGTCAGGACCTGGCTGTTTGAGAATGGGGAAGAAAGACTC\nAGCCGCATGGCTGTCAGTGGAGATGACTGTGTGGTAAAGCCCCTGGACGATCGCTTTGCCACCTCGCTCC\nACTTCCTCAATGCTATGTCAAAGGTTCGCAAAGACATCCAAGAGTGGAAACCGTCAACTGGATGGTATGA\nTTGGCAGCAGGTTCCATTTTGCTCAAACCATTTCACTGAACTGATCATGAAAGATGGAAGAACACTGGTG\nGTTCCATGCCGAGGACAGGATGAATTGGTAGGCAGAGCTCGCATATCTCCAGGGGCCGGATGGAACGTCC\nGTGACACTGCTTGTCTGGCTAAGTCTTATGCCCAGATGTGGCTGCTTCTGTACTTCCACAGAAGAGACCT\nGCGGCTCATGGCCAACGCCATTTGCTCCGCTGTCCCTGTGAATTGGGTCCCTACCGGAAGAACCACGTGG\nTCCATCCATGCAGGAGGAGAGTGGATGACAACAGAGGACATGTTGGAGGTCTGGAACCGTGTTTGGATAG\nAGGAGAATGAATGGATGGAAGACAAAACCCCAGTGGAGAAATGGAGTGACGTCCCATATTCAGGAAAACG\nAGAGGACATCTGGTGTGGCAGCCTGATCGGCACAAGAGCCCGAGCCACGTGGGCAGAAAACATCCAGGTG\nGCTATCAACCAAGTTAGAGCAATCATCGGAGATGAGAAGTATGTGGATTACATGAGTTCACTAAAGAGAT\nATGAAGACACAACTTTGGTTGAGGACACAGTACTGTAGATATTTAATCAATTGTAAATAGACAATATAAG\nTATGTATGAAAGTGTAGTTTATAGTAGTATTTAGTGGTGTTAGTGTAAATAGGTAAGAAAATTTTGAGGA\nGAAAGTCAGGCCGGGAAGTTCCTGCCACCGGAAGTTGAGTAGACGGTGCTGCCTGCGACTCAACCCCAGG\nAGGACTGGGTGAGCAAAGCCGCGAAGTGATCCATGTAAGCCCTCAGAACCG\n>chr2\nAGTAGTTCGCCTGTGTGAGCTGACAAACTTAGTAGTGTTTGTGAGGATTAATAACAATTAACACAGTGCG\nAGCTGTTTCTTAGCACGAAGATCTCGATGTCTAAGAAACCAGGAGGGCCCGGCAAGAGCCGGGCTGTCAA\nTATGCTAAAACGCGGAATGCCCCGCGTGTTGTCCTTGATTGGACTGAAGAGGGCTATGTTGAGCCTGATC\nGACGGCAAGGGGCCAATACGATTCGTGTTGGCTCTCTTGGCGTTCTTCAGGTTCACAGCAATTGCTCCGA\nCCCGAGCAGTGCTGGATCGATGGAGAGGTGTGAACAAACAAACAGCGATGAAACACCTTTTGAGTTTTAA\nGAAGGAACTAGGGACCTTGACCAGTGCTATCAATCGGCGGAGCTCAAAACAAAAGAGAAGAGGAGGAAAG\nACCGGAATTGCAGTTATGATTGGCCTGATCGCCAGCGTAGGAGCAGTTACCCTCTCTAACTTCCAAGGGA\nAGGTGATGATGACGGTAAATGCTACTGACGTCACAGATGTCATCACGATTCCAACAGCTGCTGGAAAGAA\nCCTATGCATTGTCAGAGCAATGGATGTGGGATACATGTGCGATGATACTATCACTTATGAATGCCCAGTG\nCTGTCGGCTGGTAATGATCCAGAAGACATCGACTGTTGGTGCACAAAGTCAGCAGTCTACGTCAGGTATG\nGAAGATGCACCAAGACACGCCACTCAAGACGCAGTCGGAGGTCACTGACAGTGCAGACACACGGAGAAAG\nCACTCTAGCGAACAAGAAGGGGGCTTGGATGGACAGCACCAAGGCCACAAGGTATTTGGTAAAAACAGAA\nTCATGGATCTTGAGGAACCCTGGATATGCCCTGGTGGCAGCCGTCATTGGTTGGATGCTTGGGAGCAACA\nCCATGCAGAGAGTTGTGTTTGTCGTGTTATTGCTTTTGGTGGCCCCAGCTTACAGCTTCAACTGCCTTGG\nAATGAGCAACAGAGACTTCTTGGAAGGAGTGTCTGGAGCAACATGGGTGGATTTGGTTCTCGAAGGCGAC\nAGCTGCGTGACTATCATGTCTAAGGACAAGCCTACCATCGATGTGAAGATGATGAATATGGAGGCGGCCA\nACCTGGCAGAGGTCCGCAGTTATTGCTATTTGGCTACCGTCAGCGATCTTTCCACCAAAGCTGCGTGCCC\nAACCATGGGAGAAGCTCACAATGACAAACGTGCTGATCCAGCTTTTGTGTGCAGACAAGGAGTGGTGGAC\nAGGGGCTGGGGCAACGGCTGCGGACTATTTGGCAAAGGAAGCATTGACACATGCGCTAAATTTGCCTGCT\nCTACCAAGGCAATAGGAAGAACCATCTTGAAAGAGAATATCAAGTACGAAGTGGCCATTTTTGTCCATGG\nACCAACTACTGTGGAGTCGCACGGAAACTACTCCACACAGGCTGGAGCCACTCAGGCAGGGAGATTCAGC\nATCACTCCTGCGGCGCCTTCATACACACTAAAGCTTGGAGAATATGGAGAGGTGACAGTGGACTGTGAAC\nCACGGTCAGGGATTGACACCAATGCATACTACGTGATGACTGTTGGAACAAAGACGTTCTTGGTCCATCG\nTGAGTGGTTCATGGACCTCAACCTCCCTTGGAGCAGTGCTGGAAGTACTGTATGGAGGAACAGAGAGACG\nTTAATGGAGTTTGAGGAACCACACGCTACGAAGCAGTCTGTGATAGCATTGGGCTCACAAGAGGGAGCTT\nTGCATCAAGCTTTGGCTGGAGCCATTCCTGTGGAATTTTCAAGCAACACTGTCAAGTTGACGTCGGGTCA\nTTTGAAGTGTAGAGTGAAGATGGAAAAATTGCAGTTGAAGGGAACAACCTATGGCGTCTGTTCAAAGGCT\nTTCAAGTTTCTTGGGACTCCCGCAGACACAGGTCACGGCACTGTGGTGTTGGAATTGCAGTACACTGGCA\nCGGATGGACCTTGCAAAGTTCCTATCTCGTCAGTGGCTTCATTGAACGACCTAACGCCAGTGGGCAGATT\nGGTCACTGTCAACCCTTTTGTTTCAGTGGCCACGGCCAACGCTAAGGTCCTGATTGAATTGGAACCACCC\nTTTGGAGACTCATACATAGTGGTGGGCAGAGGAGAACAACAGATCAATCACCATTGGCACAAGTCTGGAA\nGCAGCATTGGCAAAGCCTTTACAACCACCCTCAAAGGAGCGCAGAGACTAGCCGCTCTAGGAGACACAGC\nTTGGGACTTTGGATCAGTTGGAGGGGTGTTCACCTCAGTTGGGAAGGCTGTCCATCAAGTGTTTGGAGGA\nGCATTCCGCTCACTGTTCGGAGGCATGTCCTGGATAACGCAAGGATTGCTGGGGGCTCTCCTGTTGTGGA\nTGGGCATCAATGCTCGTGATAGGTCCATAGCTCTCACGTTTCTCGCAGTTGGAGGAGTTCTGCTCTTCCT\nCTCCGTGAACGTGCATGCTGACACTGGGTGTGCCATAGACATCAGCCGGCAAGAGCTGAGATGTGGAAGT\nGGAGTGTTCATACACAATGATGTGGAGGCTTGGATGGACCGGTACAAGTATTACCCTGAAACGCCACAAG\nGCCTAGCCAAGATCATTCAGAAAGCTCATAAGGAAGGAGTGTGCGGTCTACGATCAGTTTCCAGACTGGA\nGCATCAAATGTGGGAAGCAGTGAAGGACGAGCTGAACACTCTTTTGAAGGAGAATGGTGTGGACCTTAGT\nGTCGTGGTTGAGAAACAGGAGGGAATGTACAAGTCAGCACCTAAACGCCTCACCGCCACCACGGAAAAAT\nTGGAAATTGGCTGGAAGGCCTGGGGAAAGAGTATTTTATTTGCACCAGAACTCGCCAACAACACCTTTGT\nGGTTGATGGTCCGGAGACCAAGGAATGTCCGACTCAGAATCGCGCTTGGAATAGCTTAGAAGTGGAGGAT\nTTTGGATTTGGTCTCACCAGCACTCGGATGTTCCTGAAGGTCAGAGAGAGCAACACAACTGAATGTGACT\nCGAAGATCATTGGAACGGCTGTCAAGAACAACTTGGCGATCCACAGTGACCTGTCCTATTGGATTGAAAG\nCAGGCTCAATGATACGTGGAAGCTTGAAAGGGCAGTTCTGGGTGAAGTCAAATCATGTACGTGGCCTGAG\nACGCATACCTTGTGGGGCGATGGAATCCTTGAGAGTGACTTGATAATACCAGTCACACTGGCGGGACCAC\nGAAGCAATCACAATCGGAGACCTGGGTACAAGACACAAAACCAGGGCCCATGGGACGAAGGCCGGGTAGA\nGATTGACTTCGATTACTGCCCAGGAACTACGGTCACCCTGAGTGAGAGCTGCGGACACCGTGGACCTGCC\nACTCGCACCACCACGGAGAGCGGAAAGTTGATAACAGATTGGTGCTGCAGGAGCTGCACCTTACCACCAC\nTGCGCTACCAAACTGATAGCGGCTGTTGGTATGGTATGGAGATCAGACCACAGAGACATGATGAAAAGAC\nCCTCGTGCAGTCACAAGTGAATGCTTACAATGCTGATATGATTGACCCTTTTCAGTTGGGCCTTCTGGTC\nGTGTTCTTGGCCACCCAGGAGGTCCTTCGCAAGAGGTGGACAGCCAAGATCAGCATGCCAGCTATACTGA\nTTGCTCTGCTAGTCCTGGTGTTTGGGGGCATTACTTACACTGATGTGTTACGCTATGTCATCTTGGTGGG\nGGCAGCTTTCGCAGAATCTAATTCGGGAGGAGACGTGGTACACTTGGCGCTCATGGCGACCTTCAAGATA\nCAACCAGTGTTTATGGTGGCATCGTTTCTCAAAGCGAGATGGACCAACCAGGAGAACATTTTGTTGATGT\nTGGCGGCTGTTTTCTTTCAAATGGCTTATCACGATGCCCGCCAAATTCTGCTCTGGGAGATCCCTGATGT\nGTTGAATTCACTGGCGGTAGCTTGGATGATACTGAGAGCCATAACATTTACAACGACATCAAACGTGGTT\nGTTCCGCTGCTAGCCCTGCTAACACCCGGGCTGAGATGCTTGAATCTGGATGTGTACAGGATACTGCTGT\nTGATGGTCGGAATAGGCAGCTTGATCAAGGAGAAGAGGAGTGCAGCTGCAAAAAAGAAAGGAGCAAGTCT\nGCTATGCTTGGCTCTGGCCTCAACAGGACTTTTCAACCCCATGATCCTTGCTGCTGGACTGATTGCATGT\nGATCCCAACCGTAAACGCGGATGGCCCGCAACTGAAGTGATGACAGCTGTCGGCCTAATGTTTGCCATCG\nTCGGAGGGCTGGCAGAGCTTGACATTGACTCCATGGCCATTCCAATGACTATCGCGGGGCTCATGTTTGC\nTGCTTTCGTGATTTCTGGGAAATCAACAGATATGTGGATTGAGAGAACGGCGGACATTTCCTGGGAAAGT\nGATGCAGAAATTACAGGCTCGAGCGAAAGAGTTGATGTGCGGCTTGATGATGATGGAAACTTCCAGCTCA\nTGAATGATCCAGGAGCACCTTGGAAGATATGGATGCTCAGAATGGTCTGCCTCGCGATTAGTGCGTACAC\nCCCCTGGGCAATCTTGCCCTCAGTAATTGGATTTTGGATAACTCTCCAATACACAAAGAGAGGAGGCGTG\nTTGTGGGACACTCCCTCACCAAAGGAGTACAAAAAGGGGGACACGACCACCGGCGTCTACAGGATCATGA\nCTCGTGGGCTGCTCGGCAGTTATCAAGCAGGAGCGGGCGTGATGGTTGAAGGTGTTTTTCACACCCTTTG\nGCATACAACAAAAGGAGCCGCTTTGATGAGCGGAGAGGGCCGTCTGGACCCATACTGGGGCAGTGTCAAG\nGAGGATCGACTTTGTTACGGAGGACCCTGGAAATTGCAGCACAAGTGGAACGGGCAGGATGAGGTGCAGA\nTGATTGTGGTGGAACCTGGCAAGAACGTTAAGAACGTCCAGACGAAACCAGGGGTGTTCAAAACACCTGA\nAGGAGAAATCGGGGCCGTGACTTTGGACTTCCCCACTGGAACATCAGGCTCACCAATAGTGGACAAAAAC\nGGTGATGTGATTGGGCTTTATGGCAATGGAGTCATAATGCCCAACGGCTCATACATAAGCGCGATAGTGC\nAGGGTGAAAGGATGGATGAGCCAATCCCAGCCGGATTCGAACCTGAGATGCTGAGGAAAAAACAGATCAC\nTGTACTGGATCTCCATCCCGGCGCCGGTAAAACAAGGAGGATTCTGCCACAGATCATCAAAGAGGCCATA\nAACAGAAGACTGAGAACAGCCGTGCTAGCACCAACCAGGGTTGTGGCTGCTGAGATGGCTGAAGCACTGA\nGAGGACTGCCCATCCGGTACCAGACATCCGCAGTGCCCAGAGAACATAATGGAAATGAGATTGTTGATGT\nCATGTGTCATGCTACCCTCACCCACAGGCTGATGTCTCCTCACAGGGTGCCGAACTACAACCTGTTTGTG\nATGGATGAGGCTCATTTCACCGACCCAGCTAGCATTGCAGCAAGAGGTTACATTTCCACAAAGGTCGAGC\nTAGGGGAGGCGGCGGCAATATTCATGACAGCCACCCCACCAGGCACTTCAGATCCATTCCCAGAGTCCAA\nTTCACCAATTTCCGACTTACAGACTGAGATCCCGGATCGAGCTTGGAACTCTGGATACGAATGGATCACA\nGAATACACCGGGAAGACGGTTTGGTTTGTGCCTAGTGTCAAGATGGGGAATGAGATTGCCCTTTGCCTAC\nAACGTGCTGGAAAGAAAGTAGTCCAATTGAACAGAAAGTCCTACGAGACGGAGTACCCAAAATGTAAGAA\nCGATGATTGGGACTTTGTTATCACAACAGATATATCTGAAATGGGGGCTAACTTCAAGGCGAGCAGGGTG\nATTGACAGTCGGAAGAGTGTGAAACCAACCATCATAACAGAAGGAGAAGGGAGAGTGATCCTGGGAGAAC\nCATCTGCAGTGACAGCAGCTAGTGCCGCCCAGAGACGTGGACGTATCGGTAGAAATCCGTCGCAAGTTGG\nTGATGAGTACTGTTATGGGGGGCACACGAATGAAGACGACTCTAACTTCGCCCATTGGACTGAGGCACGA\nATCATGCTGGACAACATCAACATGCCAAACGGACTGATCGCTCAATTTTACCAACCAGAGCGTGAGAAGG\nTATACACCATGGATGGGGAATACCGGCTCAGAGGAGAAGAGAGAAAAAACTTTCTGGAACTGTTGAGGAC\nTGCAGATCTGCCAGTTTGGCTGGCTTACAAGGTTGCAGCGGCTGGAGTGTCATACCACGACCGGAGGTGG\nTGCTTTGATGGCCCTAGGACAAACACAGTTTTAGAAGACAACAACGAAGTGGAAGTCATCACGAAGCTTG\nGTGAAAGGAAGATTCTGAGGCCGCGCTGGATTGACGCCAGGGTGTACTCGGATCATCAGGCACTAAAGGC\nGTTCAAGGACTTCGCCTCGGGAAAACGTTCTCAGATAGGGCTCATTGAGGTTCTGGGAAAGATGCCTGAG\nCACTTCATGGGGAAGACATGGGAAGCACTCGACACCATGTACGTTGTGGCCACTGCAGAGAAAGGAGGAA\nGAGCTCACAGAATGGCCCTGGAGGAACTGCCAGATGCTCTTCAGACAATTGCCTTGATTGCCTTATTGAG\nTGTGATGACCATGGGAGTATTCTTCCTCCTCATGCAGCGGAAGGGCATTGGAAAGATAGGTCTGGGAGGC\nGCTGTCTTGGGAGTCGCGACCTTTTTCTGTTGGATGGCTGAAGTTCCAGGAACGAAGATCGCCGGAATGT\nTGCTGCTCTCCCTTCTCTTGATGATTGTGCTAATTCCTGAGCCAGAGAAGCAACGTTCGCAGACAGACAA\nCCAGCTAGCCGTGTTCCTGATTTGTGTCATGACCCTTGTGAGCGCAGTGGCAGCCAACGAGATGGGCTGG\nCTAGATAAGACCAAGAGTGACATAAGCAGTTTGTTTGGGCAAAGAATTGAGGTCAAGGAGAATTTTAGCA\nTGGGAGAGTTTCTTCTGGACTTGAGGCCGGCAACAGCCTGGTCACTGTACGCTGTGACAACAGCGGTCCT\nCACTCCACTGCTAAAGCATTTGATTACGTCAGATTACATCAACACCTCATTGACCTCAATAAACGTTCAG\nGCAAGTGCACTATTCACACTCGCGCGAGGCTTCCCCTTCGTCGATGTTGGAGTGTCGGCTCTCCTGCTAG\nCAGCCGGATGCTGGGGACAAGTCACCCTCACCGTTACGGTAACAGCGGCAACACTCCTTTTTTGCCACTA\nTGCCTACATGGTTCCCGGTTGGCAAGCTGAGGCAATGCGCTCAGCCCAGCGGCGGACAGCGGCCGGAATC\nATGAAGAACGCTGTAGTGGATGGCATCGTGGCCACGGACGTCCCCGAATTAGAGCGCACCACACCCATCA\nTGCAGAAGAAAGTTGGACAGATCATGCTGATCTTGGTGTCTCTAGCTGCAGTAGTAGTGAACCCGTCTGT\nGAAGACAGTACGAGAAGCCGGAATTTTGATCACGGCCGCAGCGGTGACGCTTTGGGAGAATGGAGCAAGC\nTCTGTTTGGAACGCAACAACTGCCATCGGACTCTGCCACATTATGCGTGGGGGTTGGTTGTCATGTCTAT\nCCATAACATGGACACTCATAAAGAACATGGAAAAACCAGGACTAAAAAGAGGTGGGGCAAAAGGACGCAC\nCTTGGGAGAGGTTTGGAAAGAAAGACTCAACCAGATGACAAAAGAAGAGTTCACTAGGTACCGCAAAGAG\nGCCATCATCGAAGTCGATCGCTCAGCGGCAAAACACGCCAGGAAAGAAGGCAATGTCACTGGAGGGCATC\nCAGTCTCTAGGGGCACAGCAAAACTGAGATGGCTGGTCGAACGGAGGTTTCTCGAACCGGTCGGAAAAGT\nGATTGACCTTGGATGTGGAAGGGGCGGCTGGTGTTACTATATGGCAACCCAAAAAAGAGTCCAAGAAGTC\nAGAGGGTACACAAAGGGCGGTCCCGGACATGAAGAGCCCCAACTAGTGCAAAGTTATGGATGGAACATTG\nTCACCATGAAGAGTGGAGTGGATGTGTTCTACAGACCTTCTGAGTGTTGTGACACCCTCCTTTGTGACAT\nCGGAGAGTCCTCGTCAAGTGCTGAGGTTGAAGAGCATAGGACGATTCGGGTCCTTGAAATGGTTGAGGAC\nTGGCTGCACCGAGGGCCAAGGGAATTTTGCGTGAAGGTGCTCTGCCCCTACATGCCGAAGGTCATAGAGA\nAGATGGAGCTGCTCCAACGCCGGTATGGGGGGGGACTGATCAGAAACCCACTCTCACGGAATTCCACGCA\nCGAGATGTATTGGGTGAGTCGAGCTTCAGGCAATGTGGTACATTCAGTGAATATGACCAGCCAGGTGCTC\nCTAGGAAGAATGGAAAAAAGGACCTGGAAGGGACCCCAATACGAGGAAGATGTAAACTTGGGAAGTGGAA\nCCAGGGCGGTGGGAAAACCCTTGCTCAACTCAGACACCAGTAAAATCAAGAACAGGATTGAACGACTCAG\nGCGTGAGTACAGTTCGACGTGGCACCACGATGAGAACCACCCATATAGAACCTGGAACTATCACGGTAGT\nTATGATGTGAAGCCCACAGGCTCCGCCAGTTCGCTGGTCAATGGAGTGGTCAGGCTCCTCTCAAAACCAT\nGGGACACCATCACGAATGTTACCACCATGGCCATGACTGACACTACTCCCTTCGGGCAGCAGCGAGTGTT\nCAAAGAGAAGGTGGACACGAAAGCTCCAGAACCGCCAGAAGGAGTGAAGTACGTGCTCAACGAGACCACT\nAACTGGTTGTGGGCGTTTTTGGCCAGAGAAAAACGTCCCAGAATGTGCTCTCGAGAGGAATTCATAAGAA\nAGGTCAACAGCAATGCAGCTTTGGGTGCCATGTTTGAAGAGCAGAATCAATGGAGGAGCGCCAGAGAAGC\nAGTTGAAGATCCAAAATTTTGGGAGATGGTGGATGAGGAGCGCGAGGCACATCTGCGGGGGGAATGTCAC\nACTTGCATTTACAACATGATGGGAAAGAGAGAGAAAAAACCCGGAGAGTTCGGAAAGGCCAAGGGAAGCA\nGAGCCATTTGGTTCATGTGGCTCGGAGCTCGCTTTCTGGAGTTCGAGGCTCTGGGTTTTCTCAATGAAGA\nCCACTGGCTTGGAAGAAAGAACTCAGGAGGAGGTGTCGAGGGCTTGGGCCTCCAAAAACTGGGTTACATC\nCTGCGTGAAGTTGGCACCCGGCCTGGGGGCAAGATCTATGCTGATGACACAGCTGGCTGGGACACCCGCA\nTCACGAGAGCTGACTTGGAAAATGAAGCTAAGGTGCTTGAGTTGCTTGATGGGGAACATCGGCGTCTTGC\nTAGGGCCATCATTGAGCTCACCTATCGTCACAAAGTTGTGAAAGTGATGCGCCCGGCTGCTGATGGAAGA\nACCGTCATGGATGTTATCTCCAGAGAAGATCAGAGGGGGAGTGGACAAGTTGTCACCTACGCCCTAAACA\nCTTTCACCAACCTGGCCGTCCAGCTGGTGAGGATGATGGAAGGGGAAGGAGTGATTGGCCCAGATGATGT\nGGAGAAACTCACAAAAGGGAAAGGACCCAAAGTCAGGACCTGGCTGTTTGAGAATGGGGAAGAAAGACTC\nAGCCGCATGGCTGTCAGTGGAGATGACTGTGTGGTAAAGCCCCTGGACGATCGCTTTGCCACCTCGCTCC\nACTTCCTCAATGCTATGTCAAAGGTTCGCAAAGACATCCAAGAGTGGAAACCGTCAACTGGATGGTATGA\nTTGGCAGCAGGTTCCATTTTGCTCAAACCATTTCACTGAACTGATCATGAAAGATGGAAGAACACTGGTG\nGTTCCATGCCGAGGACAGGATGAATTGGTAGGCAGAGCTCGCATATCTCCAGGGGCCGGATGGAACGTCC\nGTGACACTGCTTGTCTGGCTAAGTCTTATGCCCAGATGTGGCTGCTTCTGTACTTCCACAGAAGAGACCT\nGCGGCTCATGGCCAACGCCATTTGCTCCGCTGTCCCTGTGAATTGGGTCCCTACCGGAAGAACCACGTGG\nTCCATCCATGCAGGAGGAGAGTGGATGACAACAGAGGACATGTTGGAGGTCTGGAACCGTGTTTGGATAG\nAGGAGAATGAATGGATGGAAGACAAAACCCCAGTGGAGAAATGGAGTGACGTCCCATATTCAGGAAAACG\nAGAGGACATCTGGTGTGGCAGCCTGATCGGCACAAGAGCCCGAGCCACGTGGGCAGAAAACATCCAGGTG\nGCTATCAACCAAGTTAGAGCAATCATCGGAGATGAGAAGTATGTGGATTACATGAGTTCACTAAAGAGAT\nATGAAGACACAACTTTGGTTGAGGACACAGTACTGTAGATATTTAATCAATTGTAAATAGACAATATAAG\nTATGTATGAAAGTGTAGTTTATAGTAGTATTTAGTGGTGTTAGTGTAAATAGGTAAGAAAATTTTGAGGA\nGAAAGTCAGGCCGGGAAGTTCCTGCCACCGGAAGTTGAGTAGACGGTGCTGCCTGCGACTCAACCCCAGG\nAGGACTGGGTGAGCAAAGCCGCGAAGTGATCCATGTAAGCCCTCAGAACCG\n" }, { "path": "tests/input/TestPerSample/ref.fasta.fai", "content": "chr1\t10621\t6\t70\t71\nchr2\t10621\t10785\t70\t71\n" }, { "path": "tests/input/TestPerSample/ref.indels.fasta", "content": ">Seed-stock-137_S2_L001_001\nCACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTA\nATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCA\nTACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGG\nGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCCTTATCACAT\nCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAACATTATTGT\nTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACTTTGATTTTGA\nACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAACATTAGA\nAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCA\nGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGAC\nAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGT\nAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTT\nTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGA\nTTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTT\nTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAG\nTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAA\nTGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAA\nGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACA\nATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAAC\nAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGCCGGACATGA\nTGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTCTATTGAT\nTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCC\nTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTC\nCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAA\nTAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGC\nCCACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGC\nAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACTTGACCATCT\nTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAAT\nCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGAC\nAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGA\nCATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCC\nGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGATCCCGATGATGGAGGCTA\nCGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTTGGTCCTATT\nCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGACCAAGGGTGG\nACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCACGCC\nAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACTCACGGA\nCAATGACAGAAGAAACGGACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAA\nCGAAGAGGCAGACCCACTAGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTAGA\nGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCC\nACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACA\nAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCAGCCAGAACA\nTTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCCGTTTT\nGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAAAGAGTA\nCACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCAT\nGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAA\nTCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAATG\nGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAAT\nTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTTTTGAATTTA\nAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAA\nGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCGATTTATCTA\nAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATC\nGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAA\nTTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACA\nAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAA\nTGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTG\nTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGC\nAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAATTTGCA\nATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAAC\nAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGC\nCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTG\nCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTG\nAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTG\nCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCAT\nTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTT\nCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCC\nACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTC\nATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAA\nTTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTC\nGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGA\nTTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAA\nTTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAACTGCTG\nAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAG\nTCAATTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGT\nAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAA\nAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCA\nTCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTC\nCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTG\nGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCATCGAATC\nCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGT\nCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGA\nAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACT\nCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCA\nATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCC\nTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCC\nAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTGCTGCAA\nCATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTC\nATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCG\nATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCG\nTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACA\nAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGC\nCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGG\nATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAATTGCAAT\nAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAAT\nAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCA\nTTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTT\nAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCA\nATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTCTTTGTCCTTATCCTCAAA\nTTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAA\nAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTCTAATTA\nAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGAT\nTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCT\nTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTAC\nCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAA\nCATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACA\nAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATC\nTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGCGACTAAAAGATGGGGCTTCAGGT\nCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACA\nATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTC\nGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAG\nACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTA\nTCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTA\nAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGT\nCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGA\nCAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACAC\nCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCA\nCGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCT\nTCAGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGC\nTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCC\nAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAAT\nGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCAC\nAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAA\nTACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAG\nAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTT\nAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGAC\nAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGG\nAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGC\nAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAA\nATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGC\nCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACATAGAGGGGCTAATGCACAA\nCCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCA\nACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAAT\nTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTAT\nCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTT\nTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACA\nATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTG\nTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCA\nAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAAT\nGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTC\nACAGTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACT\nTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTA\nCAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTGTAATAA\nTCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAA\nAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAG\nAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGA\nGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCA\nCAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCA\nGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGC\nAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGT\nAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTA\nGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACA\nCTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAA\nTTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTG\nAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAGGCAGAACCC\nGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTA\nTGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCT\nCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCT\nCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGT\nACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGT\nATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAA\nTCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAAGAGGTATGA\nTATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCAATATAACCTGC\nCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTACAGGAG\nGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAA\nAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCT\nATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGT\nTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTC\nTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTT\nAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCTGTATACCAGTT\nGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATCTCATAC\nATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAAT\nCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACA\nTTACTTTGAGCGCCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAG\nGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGC\nAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCCCAAA\nAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACT\nATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATG\nGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAAC\nCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTG\nAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCC\nTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTC\nAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGA\nTCCAATATTCTCAAGTTTATTAACGAATTGGATGCTCTACATGTCGTGAACTACAATGGA\nTTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAAC\nATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCT\nGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCC\nTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGA\nTGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTC\nTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTG\nTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAAC\nCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTA\nTATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAAC\nCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAA\nCTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTAT\nTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCT\nACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGT\nGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATCCGCAACTACGC\nAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACCAAGTTC\nTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAG\nGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAA\nATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGT\nGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGC\nAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGT\nAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATTTAATAGACATC\nTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTGAACACA\nCAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTT\nCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGAT\nTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCA\nGTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTAC\nTTACTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAACCATTGTGC\nTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAA\nATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTAAAGCCT\nTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCA\nCAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGT\nGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATC\nGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTATTTTGATAGT\nCAAGGATCTTGGTACAGTGTTACCTCAGATAGAAATCTAACACCAGGTCTTAATTCTTAT\nATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTATGGGAATTTTAC\nCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATA\nAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTT\nCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAG\nCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTA\nCCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACT\nTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCT\nGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAACAAAAA\nGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAGCATGCC\nACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTAT\nGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTT\nAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCA\nCCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGG\nGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCT\nCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGAC\nAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGACGAGCAGGAA\nCAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCC\nTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGA\nAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATG\nGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACT\nGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATAACCGCAGCT\nTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTTAATAAAGGT\nTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCATTGGCA\nCTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTAC\nCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATG\nATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCC\nATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCA\nTTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAAT\nACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGTGGCTCTTATCA\nTCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGCGGGAAG\nCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATC\nAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGG\nAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAA\nATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTA\nGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTT\nTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACCTGGTGGGAAA\nCCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCATCCCGA\nATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATA\nGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTG\nGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCA\nTTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACAT\nTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCC\nAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTT\nTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTAT\nGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAAT\nCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTATTTAACA\nTACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGAC\nAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTTGATAACCCATTTTTCCAA\nGGCAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTATCTGGATGG\nGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCGTCTACAGAC\nCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATA\nGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGG\nACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTA\nCCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGA\nTTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGA\nCTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTA\nAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCATTAGAG\nGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTGGTGCAT\nGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGAC\nAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTAC\nTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGA\nTCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACCACCAGAGAT\nCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACG\nACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCT\nGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTGAAATCT\nCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTC\nCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAA\nACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTT\nTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGG\nGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCCTTA\nCTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCC\nAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATG\nTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACA\nGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAG\nGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCT\nGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTAGTCCTTAAA\nGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTTTTT\nGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTATCTT\nTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGT\nAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGT\nCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCA\nTCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTA\nGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAATGAT\nTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGA\nCGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACAAGCATTAAAA\nCATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAAT\nAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATAT\nTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGT\nTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTT\nGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCA\nTCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTATACA\nCTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAGCATGTGTGAC\nATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATAATTAAG\nCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTT\nGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAA\nGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCCT\nTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGC\nTACTATTCCATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAATCAGAAATA\nCCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGCATT\nGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCCTGGAAAAAT\nGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGT\n" }, { "path": "tests/input/TestPerSample/ref.indels.fasta.fai", "content": "Seed-stock-137_S2_L001_001\t18950\t28\t60\t61\n" }, { "path": "tests/input/TestPerSample/vphaser_one_sample_2libs_expected.txt", "content": "chr1\t55\tT\tC\t0.8156\tsnp\t16.1017\tC:65:34:45:21:20:13:0.176\tT:13:6:10:6:3:0:0.176\nchr1\t483\tT\tC\t0.5142\tsnp\t23.6111\tC:34:21:24:11:10:10:0.7725\tT:8:9:5:7:3:2:0.7725\nchr1\t573\tT\tC\t0.5073\tsnp\t13.7405\tC:66:47:50:29:16:18:0.1098\tT:12:6:6:3:6:3:0.1098\nchr1\t660\tC\tT\t0.2772\tsnp\t44.2724\tT:109:71:79:43:30:28:0.4651\tC:78:65:55:48:23:17:0.4651\nchr1\t999\tT\tC\t0.9182\tsnp\t12.8478\tC:527:538:349:356:178:182:0.2376\tT:80:77:60:52:20:25:0.2376\nchr1\t1117\tA\tG\t0.838\tsnp\t15.0547\tG:449:482:304:327:145:155:0.4719\tA:84:81:57:50:27:31:0.4719\nchr1\t1293\tT\tC\t0.09971\tsnp\t17.2697\tC:258:245:183:172:75:73:0.5592\tT:63:42:42:29:21:13:0.5592\nchr2\t8766\tT\tC\t0.6568\tsnp\t8.33333\tC:132:99:96:67:36:33:0.4608\tT:13:8:8:5:5:3:0.4608\nchr2\t8808\tT\tC\t0.1318\tsnp\t16.8421\tC:130:107:93:74:37:33:0.6079\tT:32:16:22:10:10:6:0.6079\nchr2\t9123\tT\tC\t0.6938\tsnp\t14.5161\tC:150:168:100:113:50:55:0.5297\tT:24:30:18:21:6:9:0.5297\nchr2\t9151\tT\tC\t0.4294\tsnp\t15\tC:142:147:98:100:44:49:1\tT:22:29:15:20:7:9:1\nchr2\t9272\tG\tA\t0.2018\tsnp\t17.5214\tA:82:111:53:75:29:36:0.8579\tG:28:13:22:5:7:8:0.8579\nchr2\t9687\tT\tC\t0.7036\tsnp\t11.8182\tC:67:127:43:85:24:42:1\tT:8:18:6:11:2:7:1\nchr2\t9912\tT\tC\t0.1715\tsnp\t24.8744\tC:104:195:74:123:30:72:1\tT:42:57:27:39:15:18:1\nchr2\t9960\tC\tT\t0.3394\tsnp\t11.9481\tT:120:219:80:144:40:75:1\tC:13:33:8:22:5:11:1\n" }, { "path": "tests/input/TestPerSample/vphaser_one_sample_3libs_expected.txt", "content": "chr1\t55\tT\tC\t0.8156\tsnp\t16.1017\tC:65:34:45:21:11:8:9:5:0.425\tT:13:6:10:6:2:0:1:0:0.425\nchr1\t483\tT\tC\t0.5142\tsnp\t23.6111\tC:34:21:24:11:5:5:5:5:0.9192\tT:8:9:5:7:1:1:2:1:0.9192\nchr1\t573\tT\tC\t0.5073\tsnp\t13.7405\tC:66:47:50:29:12:10:4:8:0.1632\tT:12:6:6:3:3:2:3:1:0.1632\nchr1\t660\tC\tT\t0.2772\tsnp\t44.2724\tT:109:71:79:43:18:14:12:14:0.6371\tC:78:65:55:48:13:11:10:6:0.6371\nchr1\t999\tT\tC\t0.9182\tsnp\t12.8478\tC:527:538:349:356:81:97:97:85:0.3398\tT:80:77:60:52:10:15:10:10:0.3398\nchr1\t1117\tA\tG\t0.838\tsnp\t15.0547\tG:449:482:304:327:64:81:81:74:0.7364\tA:84:81:57:50:13:14:14:17:0.7364\nchr1\t1293\tT\tC\t0.09971\tsnp\t17.2697\tC:258:245:183:172:32:37:43:36:0.3501\tT:63:42:42:29:10:10:11:3:0.3501\nchr2\t8766\tT\tC\t0.6568\tsnp\t8.33333\tC:132:99:96:67:15:15:21:18:0.5642\tT:13:8:8:5:3:1:2:2:0.5642\nchr2\t8808\tT\tC\t0.1318\tsnp\t16.8421\tC:130:107:93:74:15:17:22:16:0.7091\tT:32:16:22:10:6:0:4:6:0.7091\nchr2\t9123\tT\tC\t0.6938\tsnp\t14.5161\tC:150:168:100:113:25:21:25:34:0.7732\tT:24:30:18:21:3:4:3:5:0.7732\nchr2\t9151\tT\tC\t0.4294\tsnp\t15\tC:142:147:98:100:20:18:24:31:0.801\tT:22:29:15:20:4:4:3:5:0.801\nchr2\t9272\tG\tA\t0.2018\tsnp\t17.5214\tA:82:111:53:75:14:12:15:24:0.8461\tG:28:13:22:5:3:4:4:4:0.8461\nchr2\t9687\tT\tC\t0.7036\tsnp\t11.8182\tC:67:127:43:85:14:19:10:23:0.9523\tT:8:18:6:11:1:4:1:3:0.9523\nchr2\t9912\tT\tC\t0.1715\tsnp\t24.8744\tC:104:195:74:123:18:34:12:38:0.9697\tT:42:57:27:39:7:9:8:9:0.9697\nchr2\t9960\tC\tT\t0.3394\tsnp\t11.9481\tT:120:219:80:144:22:32:18:43:0.5227\tC:13:33:8:22:2:8:3:3:0.5227\n" }, { "path": "tests/input/TestPerSample/vphaser_one_sample_expected.txt", "content": "chr1\t55\tT\tC\t0.8156\tsnp\t16.1017\tC:65:34:65:34:1\tT:13:6:13:6:1\nchr1\t483\tT\tC\t0.5142\tsnp\t23.6111\tC:34:21:34:21:1\tT:8:9:8:9:1\nchr1\t573\tT\tC\t0.5073\tsnp\t13.7405\tC:66:47:66:47:1\tT:12:6:12:6:1\nchr1\t660\tC\tT\t0.2772\tsnp\t44.2724\tT:109:71:109:71:1\tC:78:65:78:65:1\nchr1\t999\tT\tC\t0.9182\tsnp\t12.8478\tC:527:538:527:538:1\tT:80:77:80:77:1\nchr1\t1117\tA\tG\t0.838\tsnp\t15.0547\tG:449:482:449:482:1\tA:84:81:84:81:1\nchr1\t1293\tT\tC\t0.09971\tsnp\t17.2697\tC:258:245:258:245:1\tT:63:42:63:42:1\nchr2\t8766\tT\tC\t0.6568\tsnp\t8.33333\tC:132:99:132:100:1\tT:13:8:13:8:1\nchr2\t8808\tT\tC\t0.1318\tsnp\t16.8421\tC:130:107:130:107:1\tT:32:16:32:16:1\nchr2\t9123\tT\tC\t0.6938\tsnp\t14.5161\tC:150:168:150:168:1\tT:24:30:24:30:1\nchr2\t9151\tT\tC\t0.4294\tsnp\t15\tC:142:147:142:149:1\tT:22:29:22:29:1\nchr2\t9272\tG\tA\t0.2018\tsnp\t17.5214\tA:82:111:82:111:1\tG:28:13:29:13:1\nchr2\t9687\tT\tC\t0.7036\tsnp\t11.8182\tC:67:127:67:127:1\tT:8:18:8:18:1\nchr2\t9912\tT\tC\t0.1715\tsnp\t24.8744\tC:104:195:104:195:1\tT:42:57:42:57:1\nchr2\t9960\tC\tT\t0.3394\tsnp\t11.9481\tT:120:219:120:219:1\tC:13:33:13:33:1\n" }, { "path": "tests/input/TestPerSample/vphaser_one_sample_indels_expected.txt", "content": "Seed-stock-137_S2_L001_001\t6911\tIA\td\t0.1453\tlp\t5.04492\td:1059:315:1132:328:1\tIA:56:10:56:10:1\tIAA:6:0:6:0:1\tIAAA:1:0:1:0:1\nSeed-stock-137_S2_L001_001\t13181\tD1\ti\t0.3567\tlp\t5.71688\ti:879:160:939:166:1\tD1:56:7:56:7:1\n" }, { "path": "tests/input/TestPurgeUnmated/expected1.fastq", "content": "@from_chr9_1/1\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+from_chr9_1/1\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2/1\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+from_chr1_2/1\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n@from_ebov_1/1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+from_ebov_1/1\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n" }, { "path": "tests/input/TestPurgeUnmated/expected2.fastq", "content": "@from_chr9_1/2\nGGGGTGGATCGAGGTGGGTGGTGGCATCTGGGATCTCTGCTTGGCTTCCC\n+from_chr9_1/2\nCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCD\n@from_chr1_2/2\nAATTCTAAGAAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTT\n+from_chr1_2/2\nDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDE\n@from_ebov_1/2\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+from_ebov_1/2\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n" }, { "path": "tests/input/TestPurgeUnmated/in1.fastq", "content": "@from_chr1_1/1\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n@from_ebov_1/1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_chr9_1/1\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2/1\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n" }, { "path": "tests/input/TestPurgeUnmated/in2.fastq", "content": "@from_chr9_1/2\nGGGGTGGATCGAGGTGGGTGGTGGCATCTGGGATCTCTGCTTGGCTTCCC\n+\nCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCD\n@from_chr1_2/2\nAATTCTAAGAAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTT\n+\nDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDE\n@from_ebov_2/2\nGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\n+\nEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEF\n@from_ebov_1/2\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n" }, { "path": "tests/input/TestPurgeUnmated/in_sra1.fastq", "content": "@from_chr1_1.1 XXX XXX\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n@from_ebov_1.1 XXX XXX\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_chr9_1.1 XXX XXX\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2.1 XXX XXX\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n" }, { "path": "tests/input/TestPurgeUnmated/in_sra2.fastq", "content": "@from_chr9_1.2 XXX XXX\nGGGGTGGATCGAGGTGGGTGGTGGCATCTGGGATCTCTGCTTGGCTTCCC\n+\nCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCDCD\n@from_chr1_2.2 XXX XXX\nAATTCTAAGAAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTT\n+\nDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDEDE\n@from_ebov_2.2 XXX XXX\nGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGC\n+\nEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEFEF\n@from_ebov_1.2 XXX XXX\nTTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGA\n+\nBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBCBC\n" }, { "path": "tests/input/TestRefineAssembly/expected.ebov.refine1.fasta", "content": ">test_sub-EBOV.genome-1\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTG\nCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTG\nAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTT\nCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCT\nTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGA\nTACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAG\nTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGAC\nAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTG\nGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTT\nCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAA\nACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGC\nTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCC\nACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCGTAATACACCCGTGTATAAAC\nTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCC\nCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACC\nACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCA\nGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAG\nAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATC\nGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTT\nTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCG\nAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCG\nGACTGCTGTATCGAACCACATGATTGGACCAAGAACAT\n" }, { "path": "tests/input/TestRefineAssembly/expected.ebov.refine1.freebayes.fasta", "content": ">test_sub-EBOV.genome-1\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAA\nTGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCC\nACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAAT\nCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCC\nCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTT\nCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGG\nAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT\nCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTA\nTTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTT\nGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCT\nGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACT\nAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAAC\nTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAAC\nGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC\nACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTG\nCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACG\nAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCGTAATACACCCGTG\nTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAAC\nGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAG\nAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAA\nAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT\nGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATC\nACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCC\nAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCA\nTATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGT\nTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTG\nAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTG\nCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT\nGATTGGACCAAGAACAT\n" }, { "path": "tests/input/TestRefineAssembly/expected.ebov.refine1.new.fasta", "content": ">test_sub-EBOV.genome-1\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAA\nTGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCC\nACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAAT\nCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCC\nCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTT\nCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGG\nAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT\nCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTA\nTTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTT\nGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCT\nGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACT\nAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAAC\nTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAAC\nGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC\nACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTG\nCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACG\nAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCGTAATACACCCGTG\nTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAAC\nGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAG\nAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAA\nAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT\nGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATC\nACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCC\nAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCA\nTATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGT\nTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAACAAGCTCTCCAACTGTTCCTGAGAGCC\nACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAG\nCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGG\nACCAAGAACAT\n" }, { "path": "tests/input/TestRefineAssembly/expected.ebov.refine2.fasta", "content": ">test_sub-EBOV.genome-1\nATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTC\nAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAA\nAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGT\nATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCC\nACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCT\nTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATA\nTCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCA\nAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAAC\nTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGA\nAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAA\nCTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCA\nAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCTCCC\nACAACCAAAACAGGTCCGGACAACAGCACCCGTAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTG\nGACAACATCACCGTAGAGCNGACAACGACNNNNNNGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAA\nAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAAAACTACAGCGAG\nACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCA\nATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAA\nATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGG\nCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCA\nACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGC\nAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAAC\n" }, { "path": "tests/input/TestRefineAssembly/expected.ebov.refine2.freebayes.fasta", "content": ">test_sub-EBOV.genome-1\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAA\nTGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCC\nACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAAT\nCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCC\nCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTT\nCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGG\nAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT\nCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTA\nTTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTT\nGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCT\nGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACT\nAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAAC\nTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAAC\nGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC\nACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTG\nCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACG\nAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCGTAATACACCCGTG\nTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCNGACAAC\nGNCNNNNNNGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAG\nAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAA\nAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT\nGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATC\nACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCC\nAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCA\nTATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGT\nTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTG\nAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTG\nCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT\nGATTGGACCAAGAACAT\n" }, { "path": "tests/input/TestRefineAssembly/impute.ebov.fasta", "content": ">test_sub-EBOV.genome-1\nTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAA\nTGGAGTGGCAACTGACGTGCCATCTGTGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCC\nACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAAT\nCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCC\nCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTT\nCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGG\nAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTT\nCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTA\nTTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTT\nGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCT\nGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACT\nAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAAC\nTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAAC\nGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAAC\nACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTG\nCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACG\nAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACACCCGTG\nTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAAC\nGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAG\nAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAA\nAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGT\nGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATC\nACAGGCGGGAGAAGGACTTAGTAGCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGC\nAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGG\nATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAA\nGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAACAATCTCTCCAGCTGTTCCTG\nAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTG\nCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACAT\nGATTGGACCAAGAACAT\n" }, { "path": "tests/input/TestRunInfo/RunInfo-hiseq.xml", "content": "\r\n\r\n \r\n HVFF2ADXX\r\n SL-HDF\r\n 150821\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n 1\r\n 2\r\n \r\n \r\n" }, { "path": "tests/input/TestRunInfo/RunInfo-miseq.xml", "content": "\r\n\r\n \r\n 000000000-AEF96\r\n M04004\r\n 150821\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n" }, { "path": "tests/input/TestRunInfo/RunInfo-nextseq-1000-2000-p1.xml", "content": "\n\n\t\n\t\tAAG27M7M5\n\t\tVH01619\n\t\t2024-09-27T14:48:52Z\n\t\t\n\t\t\t\n\t\t\t\n\t\t\t\n\t\t\t\n\t\t\n\t\t\n\t\t\t\n\t\t\t\t\n\t\t\t\t\t1_1101\n\t\t\t\t\t1_1102\n\t\t\t\t\t1_1103\n\t\t\t\t\t1_1104\n\t\t\t\t\t1_1201\n\t\t\t\t\t1_1202\n\t\t\t\t\t1_1203\n\t\t\t\t\t1_1204\n\t\t\t\t\t1_1301\n\t\t\t\t\t1_1302\n\t\t\t\t\t1_1303\n\t\t\t\t\t1_1304\n\t\t\t\t\t1_1401\n\t\t\t\t\t1_1402\n\t\t\t\t\t1_1403\n\t\t\t\t\t1_1404\n\t\t\t\t\t1_2101\n\t\t\t\t\t1_2102\n\t\t\t\t\t1_2103\n\t\t\t\t\t1_2104\n\t\t\t\t\t1_2201\n\t\t\t\t\t1_2202\n\t\t\t\t\t1_2203\n\t\t\t\t\t1_2204\n\t\t\t\t\t1_2301\n\t\t\t\t\t1_2302\n\t\t\t\t\t1_2303\n\t\t\t\t\t1_2304\n\t\t\t\t\t1_2401\n\t\t\t\t\t1_2402\n\t\t\t\t\t1_2403\n\t\t\t\t\t1_2404\n\t\t\t\t\n\t\t\t\n\t\t\n\t\t\n\t\t\n\t\t\tgreen\n\t\t\tblue\n\t\t\n\t\n\n" }, { "path": "tests/input/TestRunInfo/RunInfo-nextseq550.xml", "content": "\r\n\r\n \r\n HMTLKAFX2\r\n NB552060\r\n 210221\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n 1_11101\r\n 1_21101\r\n 1_11102\r\n 1_21102\r\n 1_11103\r\n 1_21103\r\n 1_11104\r\n 1_21104\r\n 1_11105\r\n 1_21105\r\n 1_11106\r\n 1_21106\r\n 1_11107\r\n 1_21107\r\n 1_11108\r\n 1_21108\r\n 1_11109\r\n 1_21109\r\n 1_11110\r\n 1_21110\r\n 1_11111\r\n 1_21111\r\n 1_11112\r\n 1_21112\r\n 2_11101\r\n 2_21101\r\n 2_11102\r\n 2_21102\r\n 2_11103\r\n 2_21103\r\n 2_11104\r\n 2_21104\r\n 2_11105\r\n 2_21105\r\n 2_11106\r\n 2_21106\r\n 2_11107\r\n 2_21107\r\n 2_11108\r\n 2_21108\r\n 2_11109\r\n 2_21109\r\n 2_11110\r\n 2_21110\r\n 2_11111\r\n 2_21111\r\n 2_11112\r\n 2_21112\r\n 1_11201\r\n 1_21201\r\n 1_11202\r\n 1_21202\r\n 1_11203\r\n 1_21203\r\n 1_11204\r\n 1_21204\r\n 1_11205\r\n 1_21205\r\n 1_11206\r\n 1_21206\r\n 1_11207\r\n 1_21207\r\n 1_11208\r\n 1_21208\r\n 1_11209\r\n 1_21209\r\n 1_11210\r\n 1_21210\r\n 1_11211\r\n 1_21211\r\n 1_11212\r\n 1_21212\r\n 2_11201\r\n 2_21201\r\n 2_11202\r\n 2_21202\r\n 2_11203\r\n 2_21203\r\n 2_11204\r\n 2_21204\r\n 2_11205\r\n 2_21205\r\n 2_11206\r\n 2_21206\r\n 2_11207\r\n 2_21207\r\n 2_11208\r\n 2_21208\r\n 2_11209\r\n 2_21209\r\n 2_11210\r\n 2_21210\r\n 2_11211\r\n 2_21211\r\n 2_11212\r\n 2_21212\r\n 1_11301\r\n 1_21301\r\n 1_11302\r\n 1_21302\r\n 1_11303\r\n 1_21303\r\n 1_11304\r\n 1_21304\r\n 1_11305\r\n 1_21305\r\n 1_11306\r\n 1_21306\r\n 1_11307\r\n 1_21307\r\n 1_11308\r\n 1_21308\r\n 1_11309\r\n 1_21309\r\n 1_11310\r\n 1_21310\r\n 1_11311\r\n 1_21311\r\n 1_11312\r\n 1_21312\r\n 2_11301\r\n 2_21301\r\n 2_11302\r\n 2_21302\r\n 2_11303\r\n 2_21303\r\n 2_11304\r\n 2_21304\r\n 2_11305\r\n 2_21305\r\n 2_11306\r\n 2_21306\r\n 2_11307\r\n 2_21307\r\n 2_11308\r\n 2_21308\r\n 2_11309\r\n 2_21309\r\n 2_11310\r\n 2_21310\r\n 2_11311\r\n 2_21311\r\n 2_11312\r\n 2_21312\r\n 3_11401\r\n 3_21401\r\n 3_11402\r\n 3_21402\r\n 3_11403\r\n 3_21403\r\n 3_11404\r\n 3_21404\r\n 3_11405\r\n 3_21405\r\n 3_11406\r\n 3_21406\r\n 3_11407\r\n 3_21407\r\n 3_11408\r\n 3_21408\r\n 3_11409\r\n 3_21409\r\n 3_11410\r\n 3_21410\r\n 3_11411\r\n 3_21411\r\n 3_11412\r\n 3_21412\r\n 4_11401\r\n 4_21401\r\n 4_11402\r\n 4_21402\r\n 4_11403\r\n 4_21403\r\n 4_11404\r\n 4_21404\r\n 4_11405\r\n 4_21405\r\n 4_11406\r\n 4_21406\r\n 4_11407\r\n 4_21407\r\n 4_11408\r\n 4_21408\r\n 4_11409\r\n 4_21409\r\n 4_11410\r\n 4_21410\r\n 4_11411\r\n 4_21411\r\n 4_11412\r\n 4_21412\r\n 3_11501\r\n 3_21501\r\n 3_11502\r\n 3_21502\r\n 3_11503\r\n 3_21503\r\n 3_11504\r\n 3_21504\r\n 3_11505\r\n 3_21505\r\n 3_11506\r\n 3_21506\r\n 3_11507\r\n 3_21507\r\n 3_11508\r\n 3_21508\r\n 3_11509\r\n 3_21509\r\n 3_11510\r\n 3_21510\r\n 3_11511\r\n 3_21511\r\n 3_11512\r\n 3_21512\r\n 4_11501\r\n 4_21501\r\n 4_11502\r\n 4_21502\r\n 4_11503\r\n 4_21503\r\n 4_11504\r\n 4_21504\r\n 4_11505\r\n 4_21505\r\n 4_11506\r\n 4_21506\r\n 4_11507\r\n 4_21507\r\n 4_11508\r\n 4_21508\r\n 4_11509\r\n 4_21509\r\n 4_11510\r\n 4_21510\r\n 4_11511\r\n 4_21511\r\n 4_11512\r\n 4_21512\r\n 3_11601\r\n 3_21601\r\n 3_11602\r\n 3_21602\r\n 3_11603\r\n 3_21603\r\n 3_11604\r\n 3_21604\r\n 3_11605\r\n 3_21605\r\n 3_11606\r\n 3_21606\r\n 3_11607\r\n 3_21607\r\n 3_11608\r\n 3_21608\r\n 3_11609\r\n 3_21609\r\n 3_11610\r\n 3_21610\r\n 3_11611\r\n 3_21611\r\n 3_11612\r\n 3_21612\r\n 4_11601\r\n 4_21601\r\n 4_11602\r\n 4_21602\r\n 4_11603\r\n 4_21603\r\n 4_11604\r\n 4_21604\r\n 4_11605\r\n 4_21605\r\n 4_11606\r\n 4_21606\r\n 4_11607\r\n 4_21607\r\n 4_11608\r\n 4_21608\r\n 4_11609\r\n 4_21609\r\n 4_11610\r\n 4_21610\r\n 4_11611\r\n 4_21611\r\n 4_11612\r\n 4_21612\r\n \r\n \r\n \r\n \r\n \r\n Red\r\n Green\r\n \r\n \r\n" }, { "path": "tests/input/TestRunInfo/RunInfo-novaseq-x-plus.xml", "content": 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2_2280\n 2_2281\n 2_2282\n 2_2283\n 2_2284\n 2_2285\n 2_2286\n 2_2287\n 2_2288\n 2_2301\n 2_2302\n 2_2303\n 2_2304\n 2_2305\n 2_2306\n 2_2307\n 2_2308\n 2_2309\n 2_2310\n 2_2311\n 2_2312\n 2_2313\n 2_2314\n 2_2315\n 2_2316\n 2_2317\n 2_2318\n 2_2319\n 2_2320\n 2_2321\n 2_2322\n 2_2323\n 2_2324\n 2_2325\n 2_2326\n 2_2327\n 2_2328\n 2_2329\n 2_2330\n 2_2331\n 2_2332\n 2_2333\n 2_2334\n 2_2335\n 2_2336\n 2_2337\n 2_2338\n 2_2339\n 2_2340\n 2_2341\n 2_2342\n 2_2343\n 2_2344\n 2_2345\n 2_2346\n 2_2347\n 2_2348\n 2_2349\n 2_2350\n 2_2351\n 2_2352\n 2_2353\n 2_2354\n 2_2355\n 2_2356\n 2_2357\n 2_2358\n 2_2359\n 2_2360\n 2_2361\n 2_2362\n 2_2363\n 2_2364\n 2_2365\n 2_2366\n 2_2367\n 2_2368\n 2_2369\n 2_2370\n 2_2371\n 2_2372\n 2_2373\n 2_2374\n 2_2375\n 2_2376\n 2_2377\n 2_2378\n 2_2379\n 2_2380\n 2_2381\n 2_2382\n 2_2383\n 2_2384\n 2_2385\n 2_2386\n 2_2387\n 2_2388\n 2_2401\n 2_2402\n 2_2403\n 2_2404\n 2_2405\n 2_2406\n 2_2407\n 2_2408\n 2_2409\n 2_2410\n 2_2411\n 2_2412\n 2_2413\n 2_2414\n 2_2415\n 2_2416\n 2_2417\n 2_2418\n 2_2419\n 2_2420\n 2_2421\n 2_2422\n 2_2423\n 2_2424\n 2_2425\n 2_2426\n 2_2427\n 2_2428\n 2_2429\n 2_2430\n 2_2431\n 2_2432\n 2_2433\n 2_2434\n 2_2435\n 2_2436\n 2_2437\n 2_2438\n 2_2439\n 2_2440\n 2_2441\n 2_2442\n 2_2443\n 2_2444\n 2_2445\n 2_2446\n 2_2447\n 2_2448\n 2_2449\n 2_2450\n 2_2451\n 2_2452\n 2_2453\n 2_2454\n 2_2455\n 2_2456\n 2_2457\n 2_2458\n 2_2459\n 2_2460\n 2_2461\n 2_2462\n 2_2463\n 2_2464\n 2_2465\n 2_2466\n 2_2467\n 2_2468\n 2_2469\n 2_2470\n 2_2471\n 2_2472\n 2_2473\n 2_2474\n 2_2475\n 2_2476\n 2_2477\n 2_2478\n 2_2479\n 2_2480\n 2_2481\n 2_2482\n 2_2483\n 2_2484\n 2_2485\n 2_2486\n 2_2487\n 2_2488\n 2_1101\n 2_1102\n 2_1103\n 2_1104\n 2_1105\n 2_1106\n 2_1107\n 2_1108\n 2_1109\n 2_1110\n 2_1111\n 2_1112\n 2_1113\n 2_1114\n 2_1115\n 2_1116\n 2_1117\n 2_1118\n 2_1119\n 2_1120\n 2_1121\n 2_1122\n 2_1123\n 2_1124\n 2_1125\n 2_1126\n 2_1127\n 2_1128\n 2_1129\n 2_1130\n 2_1131\n 2_1132\n 2_1133\n 2_1134\n 2_1135\n 2_1136\n 2_1137\n 2_1138\n 2_1139\n 2_1140\n 2_1141\n 2_1142\n 2_1143\n 2_1144\n 2_1145\n 2_1146\n 2_1147\n 2_1148\n 2_1149\n 2_1150\n 2_1151\n 2_1152\n 2_1153\n 2_1154\n 2_1155\n 2_1156\n 2_1157\n 2_1158\n 2_1159\n 2_1160\n 2_1161\n 2_1162\n 2_1163\n 2_1164\n 2_1165\n 2_1166\n 2_1167\n 2_1168\n 2_1169\n 2_1170\n 2_1171\n 2_1172\n 2_1173\n 2_1174\n 2_1175\n 2_1176\n 2_1177\n 2_1178\n 2_1179\n 2_1180\n 2_1181\n 2_1182\n 2_1183\n 2_1184\n 2_1185\n 2_1186\n 2_1187\n 2_1188\n 2_1201\n 2_1202\n 2_1203\n 2_1204\n 2_1205\n 2_1206\n 2_1207\n 2_1208\n 2_1209\n 2_1210\n 2_1211\n 2_1212\n 2_1213\n 2_1214\n 2_1215\n 2_1216\n 2_1217\n 2_1218\n 2_1219\n 2_1220\n 2_1221\n 2_1222\n 2_1223\n 2_1224\n 2_1225\n 2_1226\n 2_1227\n 2_1228\n 2_1229\n 2_1230\n 2_1231\n 2_1232\n 2_1233\n 2_1234\n 2_1235\n 2_1236\n 2_1237\n 2_1238\n 2_1239\n 2_1240\n 2_1241\n 2_1242\n 2_1243\n 2_1244\n 2_1245\n 2_1246\n 2_1247\n 2_1248\n 2_1249\n 2_1250\n 2_1251\n 2_1252\n 2_1253\n 2_1254\n 2_1255\n 2_1256\n 2_1257\n 2_1258\n 2_1259\n 2_1260\n 2_1261\n 2_1262\n 2_1263\n 2_1264\n 2_1265\n 2_1266\n 2_1267\n 2_1268\n 2_1269\n 2_1270\n 2_1271\n 2_1272\n 2_1273\n 2_1274\n 2_1275\n 2_1276\n 2_1277\n 2_1278\n 2_1279\n 2_1280\n 2_1281\n 2_1282\n 2_1283\n 2_1284\n 2_1285\n 2_1286\n 2_1287\n 2_1288\n 2_1301\n 2_1302\n 2_1303\n 2_1304\n 2_1305\n 2_1306\n 2_1307\n 2_1308\n 2_1309\n 2_1310\n 2_1311\n 2_1312\n 2_1313\n 2_1314\n 2_1315\n 2_1316\n 2_1317\n 2_1318\n 2_1319\n 2_1320\n 2_1321\n 2_1322\n 2_1323\n 2_1324\n 2_1325\n 2_1326\n 2_1327\n 2_1328\n 2_1329\n 2_1330\n 2_1331\n 2_1332\n 2_1333\n 2_1334\n 2_1335\n 2_1336\n 2_1337\n 2_1338\n 2_1339\n 2_1340\n 2_1341\n 2_1342\n 2_1343\n 2_1344\n 2_1345\n 2_1346\n 2_1347\n 2_1348\n 2_1349\n 2_1350\n 2_1351\n 2_1352\n 2_1353\n 2_1354\n 2_1355\n 2_1356\n 2_1357\n 2_1358\n 2_1359\n 2_1360\n 2_1361\n 2_1362\n 2_1363\n 2_1364\n 2_1365\n 2_1366\n 2_1367\n 2_1368\n 2_1369\n 2_1370\n 2_1371\n 2_1372\n 2_1373\n 2_1374\n 2_1375\n 2_1376\n 2_1377\n 2_1378\n 2_1379\n 2_1380\n 2_1381\n 2_1382\n 2_1383\n 2_1384\n 2_1385\n 2_1386\n 2_1387\n 2_1388\n 2_1401\n 2_1402\n 2_1403\n 2_1404\n 2_1405\n 2_1406\n 2_1407\n 2_1408\n 2_1409\n 2_1410\n 2_1411\n 2_1412\n 2_1413\n 2_1414\n 2_1415\n 2_1416\n 2_1417\n 2_1418\n 2_1419\n 2_1420\n 2_1421\n 2_1422\n 2_1423\n 2_1424\n 2_1425\n 2_1426\n 2_1427\n 2_1428\n 2_1429\n 2_1430\n 2_1431\n 2_1432\n 2_1433\n 2_1434\n 2_1435\n 2_1436\n 2_1437\n 2_1438\n 2_1439\n 2_1440\n 2_1441\n 2_1442\n 2_1443\n 2_1444\n 2_1445\n 2_1446\n 2_1447\n 2_1448\n 2_1449\n 2_1450\n 2_1451\n 2_1452\n 2_1453\n 2_1454\n 2_1455\n 2_1456\n 2_1457\n 2_1458\n 2_1459\n 2_1460\n 2_1461\n 2_1462\n 2_1463\n 2_1464\n 2_1465\n 2_1466\n 2_1467\n 2_1468\n 2_1469\n 2_1470\n 2_1471\n 2_1472\n 2_1473\n 2_1474\n 2_1475\n 2_1476\n 2_1477\n 2_1478\n 2_1479\n 2_1480\n 2_1481\n 2_1482\n 2_1483\n 2_1484\n 2_1485\n 2_1486\n 2_1487\n 2_1488\n \n \n \n \n \n \n RED\n GREEN\n \n \n\n" }, { "path": "tests/input/TestRunInfo/RunInfo-novel-fcid-and-tilecount.xml", "content": "\n\n \n HMTLKZ0Z0Z\n M312\n 150821\n \n \n \n \n \n \n \n \n" }, { "path": "tests/input/TestRunInfo/RunInfo-novel-fcid.xml", "content": "\n\n \n HMTLKZ0Z0Z\n M04004\n 150821\n \n \n \n \n \n \n \n \n" }, { "path": "tests/input/TestRunInfo/RunInfo-novel-tile-count.xml", "content": "\n\n \n 000000000-AEF96\n M04004\n 150821\n \n \n \n \n \n \n \n \n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-AEHWY-subset.csv", "content": "[Header]\r\nIEMFileVersion,4\r\nDate,8/14/2015\r\nWorkflow,GenerateFASTQ\r\nApplication,FASTQ Only\r\nAssay,Nextera XT\r\nDescription,\r\nChemistry,Amplicon\r\n\r\n[Reads]\r\n101\r\n101\r\n\r\n[Settings]\r\nReverseComplement,0\r\nAdapter,CTGTCTCTTATACACATCT\r\n\r\n[Data]\r\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\r\n16,E023,,,N711,AAGAGGCA,S517,GCGTAAGA,,\r\n17,E024,,,N712,GTAGAGGA,S517,GCGTAAGA,,\r\nMAK_AD,MAK_AD,,,N701,TAAGGCGA,S502,CTCTCTAT,,\r\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-custom-1.txt", "content": "sample\tbarcode_1\tbarcode_2\tlibrary_id_per_sample\nNIHCC_05\tCGTACTAG\tTAGATCGC\tAEL2\nNIHCC_06\tAGGCAGAA\tTAGATCGC\tAEL2\nNIHCC_07\tTCCTGAGC\tTAGATCGC\tAEL2\nNIHCC_08\tTAGGCATG\tTAGATCGC\tAEL2\nNIHCC_09\tGCTACGCT\tTAGATCGC\tAEL2\nNIHCC_10\tCGAGGCTG\tTAGATCGC\tAEL2\nNIHCC_11\tAAGAGGCA\tTAGATCGC\tAEL2\nNIHCC_12\tGTAGAGGA\tTAGATCGC\tAEL2\nNIHCC_13\tCGTACTAG\tCTCTCTAT\tAEL2\nNIHCC_14\tAGGCAGAA\tCTCTCTAT\tAEL2\nNIHCC_15\tTCCTGAGC\tCTCTCTAT\tAEL2\nNIHCC_16\tTAGGCATG\tCTCTCTAT\tAEL2\nNIHCC_17\tGCTACGCT\tCTCTCTAT\tAEL2\nNIHCC_18\tCGAGGCTG\tCTCTCTAT\tAEL2\nNIHCC_19\tAAGAGGCA\tCTCTCTAT\tAEL2\nNIHCC_20\tGTAGAGGA\tCTCTCTAT\tAEL2\nNIHCC_21\tCGTACTAG\tTATCCTCT\tAEL2\nNIHCC_22\tAGGCAGAA\tTATCCTCT\tAEL2\nNIHCC_23\tTCCTGAGC\tTATCCTCT\tAEL2\nNIHCC_24\tTAGGCATG\tTATCCTCT\tAEL2\nNIHCC_25\tGCTACGCT\tTATCCTCT\tAEL2\nNIHCC_26\tCGAGGCTG\tTATCCTCT\tAEL2\nNIHCC_27\tAAGAGGCA\tTATCCTCT\tAEL2\nNIHCC_28\tGTAGAGGA\tTATCCTCT\tAEL2\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-custom-1_macos9-endings.txt", "content": "sample\tbarcode_1\tbarcode_2\tlibrary_id_per_sample\rNIHCC_05\tCGTACTAG\tTAGATCGC\tAEL2\rNIHCC_06\tAGGCAGAA\tTAGATCGC\tAEL2\rNIHCC_07\tTCCTGAGC\tTAGATCGC\tAEL2\rNIHCC_08\tTAGGCATG\tTAGATCGC\tAEL2\rNIHCC_09\tGCTACGCT\tTAGATCGC\tAEL2\rNIHCC_10\tCGAGGCTG\tTAGATCGC\tAEL2\rNIHCC_11\tAAGAGGCA\tTAGATCGC\tAEL2\rNIHCC_12\tGTAGAGGA\tTAGATCGC\tAEL2\rNIHCC_13\tCGTACTAG\tCTCTCTAT\tAEL2\rNIHCC_14\tAGGCAGAA\tCTCTCTAT\tAEL2\rNIHCC_15\tTCCTGAGC\tCTCTCTAT\tAEL2\rNIHCC_16\tTAGGCATG\tCTCTCTAT\tAEL2\rNIHCC_17\tGCTACGCT\tCTCTCTAT\tAEL2\rNIHCC_18\tCGAGGCTG\tCTCTCTAT\tAEL2\rNIHCC_19\tAAGAGGCA\tCTCTCTAT\tAEL2\rNIHCC_20\tGTAGAGGA\tCTCTCTAT\tAEL2\rNIHCC_21\tCGTACTAG\tTATCCTCT\tAEL2\rNIHCC_22\tAGGCAGAA\tTATCCTCT\tAEL2\rNIHCC_23\tTCCTGAGC\tTATCCTCT\tAEL2\rNIHCC_24\tTAGGCATG\tTATCCTCT\tAEL2\rNIHCC_25\tGCTACGCT\tTATCCTCT\tAEL2\rNIHCC_26\tCGAGGCTG\tTATCCTCT\tAEL2\rNIHCC_27\tAAGAGGCA\tTATCCTCT\tAEL2\rNIHCC_28\tGTAGAGGA\tTATCCTCT\tAEL2\r" }, { "path": "tests/input/TestSampleSheet/SampleSheet-custom-1_win-endings.txt", "content": "sample\tbarcode_1\tbarcode_2\tlibrary_id_per_sample\r\nNIHCC_05\tCGTACTAG\tTAGATCGC\tAEL2\r\nNIHCC_06\tAGGCAGAA\tTAGATCGC\tAEL2\r\nNIHCC_07\tTCCTGAGC\tTAGATCGC\tAEL2\r\nNIHCC_08\tTAGGCATG\tTAGATCGC\tAEL2\r\nNIHCC_09\tGCTACGCT\tTAGATCGC\tAEL2\r\nNIHCC_10\tCGAGGCTG\tTAGATCGC\tAEL2\r\nNIHCC_11\tAAGAGGCA\tTAGATCGC\tAEL2\r\nNIHCC_12\tGTAGAGGA\tTAGATCGC\tAEL2\r\nNIHCC_13\tCGTACTAG\tCTCTCTAT\tAEL2\r\nNIHCC_14\tAGGCAGAA\tCTCTCTAT\tAEL2\r\nNIHCC_15\tTCCTGAGC\tCTCTCTAT\tAEL2\r\nNIHCC_16\tTAGGCATG\tCTCTCTAT\tAEL2\r\nNIHCC_17\tGCTACGCT\tCTCTCTAT\tAEL2\r\nNIHCC_18\tCGAGGCTG\tCTCTCTAT\tAEL2\r\nNIHCC_19\tAAGAGGCA\tCTCTCTAT\tAEL2\r\nNIHCC_20\tGTAGAGGA\tCTCTCTAT\tAEL2\r\nNIHCC_21\tCGTACTAG\tTATCCTCT\tAEL2\r\nNIHCC_22\tAGGCAGAA\tTATCCTCT\tAEL2\r\nNIHCC_23\tTCCTGAGC\tTATCCTCT\tAEL2\r\nNIHCC_24\tTAGGCATG\tTATCCTCT\tAEL2\r\nNIHCC_25\tGCTACGCT\tTATCCTCT\tAEL2\r\nNIHCC_26\tCGAGGCTG\tTATCCTCT\tAEL2\r\nNIHCC_27\tAAGAGGCA\tTATCCTCT\tAEL2\r\nNIHCC_28\tGTAGAGGA\tTATCCTCT\tAEL2\r\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-custom-2.txt", "content": "sample\tbarcode_1\tbarcode_2\tlibrary_id_per_sample\tlibrary_strategy\tlibrary_source\tlibrary_selection\tdesign_description\tamplicon_set\tspike_in\nH2OCTL110\tTGCCGGTCAG\tCCTGATACAA\tERCC-00002_RandomPrimer-SSIV_NexteraXT_RNA:0352324801_cDNA:0369438821_LIB:13214803_A1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00002\nMA_MGH_02656\tCACTCAATTC\tTTAAGTTGTG\tERCC-00022_RandomPrimer-SSIV_NexteraXT_RNA:0352324802_cDNA:0369438823_LIB:13214803_B1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00022\nMA_MGH_02657\tTCTCACACGC\tCGGACAGTGA\tERCC-00042_RandomPrimer-SSIV_NexteraXT_RNA:0352324803_cDNA:0369438824_LIB:13214803_C1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00042\nMA_MGH_02658\tTCAATGGAGA\tGCACTACAAC\tERCC-00061_RandomPrimer-SSIV_NexteraXT_RNA:0352324804_cDNA:0369438815_LIB:13214803_D1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00061\nMA_MGH_02659\tATATGCATGT\tTGGTGCCTGG\tERCC-00081_RandomPrimer-SSIV_NexteraXT_RNA:0352309351_cDNA:0369438796_LIB:13214803_E1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00081\nMA_MGH_02660\tATGGCGCCTG\tTCCACGGCCT\tERCC-00108_RandomPrimer-SSIV_NexteraXT_RNA:0352324806_cDNA:0369438814_LIB:13214803_F1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00108\nMA_MGH_02661\tTCCGTTATGT\tTTGTAGTGTA\tERCC-00131_RandomPrimer-SSIV_NexteraXT_RNA:0352324807_cDNA:0369438813_LIB:13214803_G1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00131\nH2OCTL111\tGGTCTATTAA\tCCACGACACG\tERCC-00154_RandomPrimer-SSIV_NexteraXT_RNA:0352324808_cDNA:0369438812_LIB:13214803_H1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00154\nMA_MGH_02662\tCAGCAATCGT\tTGTGATGTAT\tERCC-00003_RandomPrimer-SSIV_NexteraXT_RNA:0352324809_cDNA:0369438826_LIB:13214803_A2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00003\nMA_MGH_02663\tTTCTGTAGAA\tGAGCGCAATA\tERCC-00023_RandomPrimer-SSIV_NexteraXT_RNA:0352324810_cDNA:0369438825_LIB:13214803_B2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00023\nMA_MGH_02664\tGAACGCAATA\tATCTTACTGT\tERCC-00043_RandomPrimer-SSIV_NexteraXT_RNA:0352324811_cDNA:0369438808_LIB:13214803_C2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00043\nMA_MGH_02665\tAGTACTCATG\tATGTCGTGGT\tERCC-00062_RandomPrimer-SSIV_NexteraXT_RNA:0352324812_cDNA:0369438804_LIB:13214803_D2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00062\nMA_MGH_02666\tGGTAGAATTA\tGTAGCCATCA\tERCC-00083_RandomPrimer-SSIV_NexteraXT_RNA:0352324813_cDNA:0369438820_LIB:13214803_E2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00083\nMA_MGH_02667\tTAATTAGCGT\tTGGTTAAGAA\tERCC-00109_RandomPrimer-SSIV_NexteraXT_RNA:0352324814_cDNA:0369438807_LIB:13214803_F2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00109\nMA_MGH_02668\tATTAACAAGG\tTGTTGTTCGT\tERCC-00134_RandomPrimer-SSIV_NexteraXT_RNA:0352324815_cDNA:0369438806_LIB:13214803_G2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00134\nMA_MGH_02669\tTGATGGCTAC\tCCAACAACAT\tERCC-00156_RandomPrimer-SSIV_NexteraXT_RNA:0352324816_cDNA:0369438827_LIB:13214803_H2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00156\nMA_MGH_02670\tGAATTACAAG\tACCGGCTCAG\tERCC-00004_RandomPrimer-SSIV_NexteraXT_RNA:0352324817_cDNA:0369438816_LIB:13214803_A3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00004\nMA_MGH_02671\tTAGAATTGGA\tGTTAATCTGA\tERCC-00024_RandomPrimer-SSIV_NexteraXT_RNA:0352324818_cDNA:0369438800_LIB:13214803_B3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00024\nMA_MGH_02672\tAGGCAGCTCT\tCGGCTAACGT\tERCC-00044_RandomPrimer-SSIV_NexteraXT_RNA:0352324819_cDNA:0369438819_LIB:13214803_C3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00044\nMA_MGH_02673\tATCGGCGAAG\tTCCAAGAATT\tERCC-00067_RandomPrimer-SSIV_NexteraXT_RNA:0352324820_cDNA:0369438811_LIB:13214803_D3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00067\nMA_MGH_02674\tCCGTGACCGA\tCCGAACGTTG\tERCC-00084_RandomPrimer-SSIV_NexteraXT_RNA:0352324821_cDNA:0369438802_LIB:13214803_E3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00084\nMA_MGH_02675\tATACTTGTTC\tTAACCGCCGA\tERCC-00111_RandomPrimer-SSIV_NexteraXT_RNA:0352324822_cDNA:0369438799_LIB:13214803_F3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00111\nMA_MGH_02676\tTCCGCCAATT\tCTCCGTGCTG\tERCC-00136_RandomPrimer-SSIV_NexteraXT_RNA:0352324823_cDNA:0369438798_LIB:13214803_G3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00136\nMA_MGH_02677\tAGGACAGGCC\tCATTCCAGCT\tERCC-00157_RandomPrimer-SSIV_NexteraXT_RNA:0352324824_cDNA:0369438801_LIB:13214803_H3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00157\nMA_MGH_02678\tAGAGAACCTA\tGGTTATGCTA\tERCC-00007_RandomPrimer-SSIV_NexteraXT_RNA:0352324825_cDNA:0369438809_LIB:13214803_A4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00007\nMA_MGH_02679\tGATATTGTGT\tACCACACGGT\tERCC-00025_RandomPrimer-SSIV_NexteraXT_RNA:0352324826_cDNA:0369438791_LIB:13214803_B4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00025\nMA_MGH_02680\tCGTACAGGAA\tTAGGTTCTCT\tERCC-00046_RandomPrimer-SSIV_NexteraXT_RNA:0352324827_cDNA:0369438817_LIB:13214803_C4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00046\nMA_MGH_02681\tCTGCGTTACC\tTATGGCTCGA\tERCC-00069_RandomPrimer-SSIV_NexteraXT_RNA:0352324828_cDNA:0369438803_LIB:13214803_D4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00069\nMA_MGH_02682\tAGGCCGTGGA\tCTCGTGCGTT\tERCC-00085_RandomPrimer-SSIV_NexteraXT_RNA:0352324829_cDNA:0369438822_LIB:13214803_E4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00085\nMA_MGH_02683\tAGGAGGTATC\tCCAGTTGGCA\tERCC-00112_RandomPrimer-SSIV_NexteraXT_RNA:0352324830_cDNA:0369438818_LIB:13214803_F4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00112\nMA_MGH_02684\tGCTGACGTTG\tTGTTCGCATT\tERCC-00137_RandomPrimer-SSIV_NexteraXT_RNA:0352309367_cDNA:0369438805_LIB:13214803_G4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00137\nMA_MGH_02685\tCTAATAACCG\tAACCGCATCG\tERCC-00158_RandomPrimer-SSIV_NexteraXT_RNA:0352324832_cDNA:0369438797_LIB:13214803_H4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00158\nMA_MGH_02686\tTCTAGGCGCG\tCGAAGGTTAA\tERCC-00009_RandomPrimer-SSIV_NexteraXT_RNA:0352324833_cDNA:0369438788_LIB:13214803_A5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00009\nMA_MGH_02687\tATAGCCAAGA\tAGTGCCACTG\tERCC-00028_RandomPrimer-SSIV_NexteraXT_RNA:0352324834_cDNA:0369438792_LIB:13214803_B5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00028\nMA_MGH_02688\tTTCGGTGTGA\tGAACAAGTAT\tERCC-00048_RandomPrimer-SSIV_NexteraXT_RNA:0352324835_cDNA:0369438790_LIB:13214803_C5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00048\nMA_MGH_02689\tATGTAACGTT\tACGATTGCTG\tERCC-00071_RandomPrimer-SSIV_NexteraXT_RNA:0352324836_cDNA:0369438810_LIB:13214803_D5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00071\nMA_MGH_02690\tAACGAGGCCG\tATACCTGGAT\tERCC-00086_RandomPrimer-SSIV_NexteraXT_RNA:0352324837_cDNA:0369438795_LIB:13214803_E5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00086\nMA_MGH_02691\tTGGTGTTATG\tTCCAATTCTA\tERCC-00113_RandomPrimer-SSIV_NexteraXT_RNA:0352324838_cDNA:0369438783_LIB:13214803_F5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00113\nMA_MGH_02692\tTGGCCTCTGT\tTGAGACAGCG\tERCC-00138_RandomPrimer-SSIV_NexteraXT_RNA:0352324839_cDNA:0369438793_LIB:13214803_G5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00138\nMA_MGH_02693\tCCAGGCACCA\tACGCTAATTA\tERCC-00160_RandomPrimer-SSIV_NexteraXT_RNA:0352324840_cDNA:0369438785_LIB:13214803_H5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00160\nMA_MGH_02694\tCCGGTTCCTA\tTATATTCGAG\tERCC-00012_RandomPrimer-SSIV_NexteraXT_RNA:0352324841_cDNA:0369438778_LIB:13214803_A6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00012\nMA_MGH_02695\tGGCCAATATT\tCGGTCCGATA\tERCC-00031_RandomPrimer-SSIV_NexteraXT_RNA:0352324842_cDNA:0369438786_LIB:13214803_B6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00031\nMA_MGH_02696\tGAATACCTAT\tACAATAGAGT\tERCC-00051_RandomPrimer-SSIV_NexteraXT_RNA:0352324843_cDNA:0369438794_LIB:13214803_C6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00051\nMA_MGH_02697\tTACGTGAAGG\tCGGTTATTAG\tERCC-00073_RandomPrimer-SSIV_NexteraXT_RNA:0352324844_cDNA:0369438781_LIB:13214803_D6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00073\nMA_MGH_02698\tCTTATTGGCC\tGATAACAAGT\tERCC-00092_RandomPrimer-SSIV_NexteraXT_RNA:0352324845_cDNA:0369438789_LIB:13214803_E6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00092\nMA_MGH_02699\tACAACTACTG\tAGTTATCACA\tERCC-00116_RandomPrimer-SSIV_NexteraXT_RNA:0352324846_cDNA:0369438782_LIB:13214803_F6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00116\nMA_MGH_02700\tGTTGGATGAA\tTTCCAGGTAA\tERCC-00142_RandomPrimer-SSIV_NexteraXT_RNA:0352324847_cDNA:0369438787_LIB:13214803_G6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00142\nMA_MGH_02701\tAATCCAATTG\tCATGTAGAGG\tERCC-00162_RandomPrimer-SSIV_NexteraXT_RNA:0352324848_cDNA:0369438738_LIB:13214803_H6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00162\nMA_MGH_02702\tTATGATGGCC\tGATTGTCATA\tERCC-00013_RandomPrimer-SSIV_NexteraXT_RNA:0352324849_cDNA:0369438736_LIB:13214803_A7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00013\nMA_MGH_02703\tCGCAGCAATT\tATTCCGCTAT\tERCC-00033_RandomPrimer-SSIV_NexteraXT_RNA:0352324850_cDNA:0369438733_LIB:13214803_B7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00033\nMA_MGH_02704\tACGTTCCTTA\tGACCGCTGTG\tERCC-00053_RandomPrimer-SSIV_NexteraXT_RNA:0352324851_cDNA:0369438772_LIB:13214803_C7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00053\nMA_MGH_02705\tCCGCGTATAG\tTAGGAACCGG\tERCC-00074_RandomPrimer-SSIV_NexteraXT_RNA:0352324852_cDNA:0369438780_LIB:13214803_D7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00074\nMA_MGH_02706\tGATTCTGAAT\tAGCGGTGGAC\tERCC-00095_RandomPrimer-SSIV_NexteraXT_RNA:0352309359_cDNA:0369438771_LIB:13214803_E7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00095\nMA_MGH_02707\tTAGAGAATAC\tTATAGATTCG\tERCC-00117_RandomPrimer-SSIV_NexteraXT_RNA:0352324854_cDNA:0369438768_LIB:13214803_F7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00117\nMA_MGH_02708\tTTGTATCAGG\tACAGAGGCCA\tERCC-00143_RandomPrimer-SSIV_NexteraXT_RNA:0352324855_cDNA:0369438752_LIB:13214803_G7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00143\nMA_MGH_02709\tCACAGCGGTC\tATTCCTATTG\tERCC-00163_RandomPrimer-SSIV_NexteraXT_RNA:0352324856_cDNA:0369438767_LIB:13214803_H7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00163\nMA_MGH_02710\tCCACGCTGAA\tTATTCCTCAG\tERCC-00014_RandomPrimer-SSIV_NexteraXT_RNA:0352324857_cDNA:0369438774_LIB:13214803_A8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00014\nMA_MGH_02711\tGTTCGGAGTT\tCGCCTTCTGA\tERCC-00034_RandomPrimer-SSIV_NexteraXT_RNA:0352324858_cDNA:0369438770_LIB:13214803_B8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00034\nMA_MGH_02712\tATAGCGGAAT\tGCGCAGAGTA\tERCC-00054_RandomPrimer-SSIV_NexteraXT_RNA:0352324859_cDNA:0369438763_LIB:13214803_C8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00054\nMA_MGH_02713\tGCAATATTCA\tGGCGCCAATT\tERCC-00075_RandomPrimer-SSIV_NexteraXT_RNA:0352324860_cDNA:0369438773_LIB:13214803_D8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00075\nMA_MGH_02714\tCTAGATTGCG\tAGATATGGCG\tERCC-00096_RandomPrimer-SSIV_NexteraXT_RNA:0352324861_cDNA:0369438769_LIB:13214803_E8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00096\nMA_MGH_02715\tCGATGCGGTT\tCCTGCTTGGT\tERCC-00120_RandomPrimer-SSIV_NexteraXT_RNA:0352324862_cDNA:0369438762_LIB:13214803_F8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00120\nMA_MGH_02716\tTCCGGACTAG\tGACGAACAAT\tERCC-00144_RandomPrimer-SSIV_NexteraXT_RNA:0352324863_cDNA:0369438777_LIB:13214803_G8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00144\nMA_MGH_02717\tGTGACGGAGC\tTGGCGGTCCA\tERCC-00164_RandomPrimer-SSIV_NexteraXT_RNA:0352324864_cDNA:0369438779_LIB:13214803_H8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00164\nMA_MGH_02718\tAATTCCATCT\tCTTCAGTTAC\tERCC-00016_RandomPrimer-SSIV_NexteraXT_RNA:0352324865_cDNA:0369438760_LIB:13214803_A9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00016\nMA_MGH_02719\tTTAACGGTGT\tTCCTGACCGT\tERCC-00035_RandomPrimer-SSIV_NexteraXT_RNA:0352324866_cDNA:0369438784_LIB:13214803_B9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00035\nMA_MGH_02720\tACTTGTTATC\tCGCGCCTAGA\tERCC-00057_RandomPrimer-SSIV_NexteraXT_RNA:0352324867_cDNA:0369438776_LIB:13214803_C9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00057\nMA_MGH_02721\tCGTGTACCAG\tAGGATAAGTT\tERCC-00076_RandomPrimer-SSIV_NexteraXT_RNA:0352324868_cDNA:0369438755_LIB:13214803_D9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00076\nMA_MGH_02722\tTTAACCTTCG\tAGGCCAGACA\tERCC-00097_RandomPrimer-SSIV_NexteraXT_RNA:0352324869_cDNA:0369438746_LIB:13214803_E9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00097\nMA_MGH_02723\tCATATGCGAT\tCCTTGAACGG\tERCC-00123_RandomPrimer-SSIV_NexteraXT_RNA:0352324870_cDNA:0369438745_LIB:13214803_F9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00123\nMA_MGH_02724\tAGCCTATGAT\tCACCACCTAC\tERCC-00145_RandomPrimer-SSIV_NexteraXT_RNA:0352324871_cDNA:0369438754_LIB:13214803_G9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00145\nMA_MGH_02725\tTATGACAATC\tTTGCTTGTAT\tERCC-00165_RandomPrimer-SSIV_NexteraXT_RNA:0352324872_cDNA:0369438761_LIB:13214803_H9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00165\nMA_MGH_02726\tATGTTGTTGG\tCAATCTATGA\tERCC-00017_RandomPrimer-SSIV_NexteraXT_RNA:0352324873_cDNA:0369438735_LIB:13214803_A10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00017\nMA_MGH_02727\tGCACCACCAA\tTGGTACTGAT\tERCC-00039_RandomPrimer-SSIV_NexteraXT_RNA:0352324874_cDNA:0369438758_LIB:13214803_B10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00039\nMA_MGH_02728\tAGGCGTTCGC\tTTCATCCAAC\tERCC-00058_RandomPrimer-SSIV_NexteraXT_RNA:0352324875_cDNA:0369438775_LIB:13214803_C10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00058\nMA_MGH_02729\tCCTCCGGTTG\tCATAACACCA\tERCC-00077_RandomPrimer-SSIV_NexteraXT_RNA:0352324876_cDNA:0369438759_LIB:13214803_D10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00077\nMA_MGH_02730\tGTCCACCGCT\tTCCTATTAGC\tERCC-00098_RandomPrimer-SSIV_NexteraXT_RNA:0352324877_cDNA:0369438766_LIB:13214803_E10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00098\nMA_MGH_02731\tATTGTTCGTC\tTCTCTAGATT\tERCC-00126_RandomPrimer-SSIV_NexteraXT_RNA:0352324878_cDNA:0369438753_LIB:13214803_F10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00126\nMA_MGH_02732\tGGACCAGTGG\tCGCGAGCCTA\tERCC-00147_RandomPrimer-SSIV_NexteraXT_RNA:0352324879_cDNA:0369438750_LIB:13214803_G10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00147\nMA_MGH_02733\tCCTTCTAACA\tGATAAGCTCT\tERCC-00168_RandomPrimer-SSIV_NexteraXT_RNA:0352324880_cDNA:0369438756_LIB:13214803_H10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00168\nMA_MGH_02734\tCTCGAATATA\tGAGATGTCGA\tERCC-00018_RandomPrimer-SSIV_NexteraXT_RNA:0352324881_cDNA:0369438764_LIB:13214803_A11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00018\nMA_MGH_02735\tGATCGTCGCG\tCTGGATATGT\tERCC-00040_RandomPrimer-SSIV_NexteraXT_RNA:0352324882_cDNA:0369438765_LIB:13214803_B11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00040\nMA_MGH_02736\tTATCCGAGGC\tGGCCAATAAG\tERCC-00059_RandomPrimer-SSIV_NexteraXT_RNA:0352324883_cDNA:0369438747_LIB:13214803_C11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00059\nMA_MGH_02737\tCGCTGTCTCA\tATTACTCACC\tERCC-00078_RandomPrimer-SSIV_NexteraXT_RNA:0352324884_cDNA:0369438751_LIB:13214803_D11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00078\nMA_MGH_02738\tAATGCGAACA\tAATTGGCGGA\tERCC-00099_RandomPrimer-SSIV_NexteraXT_RNA:0352324885_cDNA:0369438749_LIB:13214803_E11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00099\nMA_MGH_02739\tAATTCTTGGA\tTTGTCAACTT\tERCC-00128_RandomPrimer-SSIV_NexteraXT_RNA:0352324886_cDNA:0369438744_LIB:13214803_F11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00128\nMA_MGH_02740\tTTCCTACAGC\tGGCGAATTCT\tERCC-00148_RandomPrimer-SSIV_NexteraXT_RNA:0352324887_cDNA:0369438757_LIB:13214803_G11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00148\nMA_MGH_02741\tATCCAGGTAT\tCAACGTCAGC\tERCC-00170_RandomPrimer-SSIV_NexteraXT_RNA:0352324888_cDNA:0369438748_LIB:13214803_H11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00170\nH2OCTL112\tACGGTCCAAC\tTCTTACATCA\tERCC-00019_RandomPrimer-SSIV_NexteraXT_RNA:0352324889_cDNA:0369438743_LIB:13214803_A12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00019\nMA_MGH_02742\tGTAACTTGGT\tCGCCATACCT\tERCC-00041_RandomPrimer-SSIV_NexteraXT_RNA:0352324890_cDNA:0369438740_LIB:13214803_B12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00041\nMA_MGH_02743\tAGCGCCACAC\tCTAATGTCTT\tERCC-00060_RandomPrimer-SSIV_NexteraXT_RNA:0352324891_cDNA:0369438742_LIB:13214803_C12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00060\nMA_MGH_02744\tTGCTACTGCC\tCAACCGGAGG\tERCC-00079_RandomPrimer-SSIV_NexteraXT_RNA:0352324892_cDNA:0369438741_LIB:13214803_D12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00079\nMA_MGH_02745\tCAACACCGCA\tGGCAGTAGCA\tERCC-00104_RandomPrimer-SSIV_NexteraXT_RNA:0352324893_cDNA:0369438734_LIB:13214803_E12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00104\nMA_MGH_02746\tCACCTTAATC\tTTAGGATAGA\tERCC-00130_RandomPrimer-SSIV_NexteraXT_RNA:0352324894_cDNA:0369438732_LIB:13214803_F12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00130\nMA_MGH_02747\tTTGAATGTTG\tCGCAATCTAG\tERCC-00150_RandomPrimer-SSIV_NexteraXT_RNA:0352324895_cDNA:0369438737_LIB:13214803_G12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00150\nH2OCTL113\tCCGGTAACAC\tGAGTTGTACT\tERCC-00171_RandomPrimer-SSIV_NexteraXT_RNA:0352324896_cDNA:0369438739_LIB:13214803_H12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00171\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-custom-2_win-endings.tsv", "content": "sample\tbarcode_1\tbarcode_2\tlibrary_id_per_sample\tlibrary_strategy\tlibrary_source\tlibrary_selection\tdesign_description\tamplicon_set\tspike_in\r\nH2OCTL110\tTGCCGGTCAG\tCCTGATACAA\tERCC-00002_RandomPrimer-SSIV_NexteraXT_RNA:0352324801_cDNA:0369438821_LIB:13214803_A1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00002\r\nMA_MGH_02656\tCACTCAATTC\tTTAAGTTGTG\tERCC-00022_RandomPrimer-SSIV_NexteraXT_RNA:0352324802_cDNA:0369438823_LIB:13214803_B1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00022\r\nMA_MGH_02657\tTCTCACACGC\tCGGACAGTGA\tERCC-00042_RandomPrimer-SSIV_NexteraXT_RNA:0352324803_cDNA:0369438824_LIB:13214803_C1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00042\r\nMA_MGH_02658\tTCAATGGAGA\tGCACTACAAC\tERCC-00061_RandomPrimer-SSIV_NexteraXT_RNA:0352324804_cDNA:0369438815_LIB:13214803_D1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00061\r\nMA_MGH_02659\tATATGCATGT\tTGGTGCCTGG\tERCC-00081_RandomPrimer-SSIV_NexteraXT_RNA:0352309351_cDNA:0369438796_LIB:13214803_E1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00081\r\nMA_MGH_02660\tATGGCGCCTG\tTCCACGGCCT\tERCC-00108_RandomPrimer-SSIV_NexteraXT_RNA:0352324806_cDNA:0369438814_LIB:13214803_F1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00108\r\nMA_MGH_02661\tTCCGTTATGT\tTTGTAGTGTA\tERCC-00131_RandomPrimer-SSIV_NexteraXT_RNA:0352324807_cDNA:0369438813_LIB:13214803_G1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00131\r\nH2OCTL111\tGGTCTATTAA\tCCACGACACG\tERCC-00154_RandomPrimer-SSIV_NexteraXT_RNA:0352324808_cDNA:0369438812_LIB:13214803_H1\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00154\r\nMA_MGH_02662\tCAGCAATCGT\tTGTGATGTAT\tERCC-00003_RandomPrimer-SSIV_NexteraXT_RNA:0352324809_cDNA:0369438826_LIB:13214803_A2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00003\r\nMA_MGH_02663\tTTCTGTAGAA\tGAGCGCAATA\tERCC-00023_RandomPrimer-SSIV_NexteraXT_RNA:0352324810_cDNA:0369438825_LIB:13214803_B2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00023\r\nMA_MGH_02664\tGAACGCAATA\tATCTTACTGT\tERCC-00043_RandomPrimer-SSIV_NexteraXT_RNA:0352324811_cDNA:0369438808_LIB:13214803_C2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00043\r\nMA_MGH_02665\tAGTACTCATG\tATGTCGTGGT\tERCC-00062_RandomPrimer-SSIV_NexteraXT_RNA:0352324812_cDNA:0369438804_LIB:13214803_D2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00062\r\nMA_MGH_02666\tGGTAGAATTA\tGTAGCCATCA\tERCC-00083_RandomPrimer-SSIV_NexteraXT_RNA:0352324813_cDNA:0369438820_LIB:13214803_E2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00083\r\nMA_MGH_02667\tTAATTAGCGT\tTGGTTAAGAA\tERCC-00109_RandomPrimer-SSIV_NexteraXT_RNA:0352324814_cDNA:0369438807_LIB:13214803_F2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00109\r\nMA_MGH_02668\tATTAACAAGG\tTGTTGTTCGT\tERCC-00134_RandomPrimer-SSIV_NexteraXT_RNA:0352324815_cDNA:0369438806_LIB:13214803_G2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00134\r\nMA_MGH_02669\tTGATGGCTAC\tCCAACAACAT\tERCC-00156_RandomPrimer-SSIV_NexteraXT_RNA:0352324816_cDNA:0369438827_LIB:13214803_H2\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00156\r\nMA_MGH_02670\tGAATTACAAG\tACCGGCTCAG\tERCC-00004_RandomPrimer-SSIV_NexteraXT_RNA:0352324817_cDNA:0369438816_LIB:13214803_A3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00004\r\nMA_MGH_02671\tTAGAATTGGA\tGTTAATCTGA\tERCC-00024_RandomPrimer-SSIV_NexteraXT_RNA:0352324818_cDNA:0369438800_LIB:13214803_B3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00024\r\nMA_MGH_02672\tAGGCAGCTCT\tCGGCTAACGT\tERCC-00044_RandomPrimer-SSIV_NexteraXT_RNA:0352324819_cDNA:0369438819_LIB:13214803_C3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00044\r\nMA_MGH_02673\tATCGGCGAAG\tTCCAAGAATT\tERCC-00067_RandomPrimer-SSIV_NexteraXT_RNA:0352324820_cDNA:0369438811_LIB:13214803_D3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00067\r\nMA_MGH_02674\tCCGTGACCGA\tCCGAACGTTG\tERCC-00084_RandomPrimer-SSIV_NexteraXT_RNA:0352324821_cDNA:0369438802_LIB:13214803_E3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00084\r\nMA_MGH_02675\tATACTTGTTC\tTAACCGCCGA\tERCC-00111_RandomPrimer-SSIV_NexteraXT_RNA:0352324822_cDNA:0369438799_LIB:13214803_F3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00111\r\nMA_MGH_02676\tTCCGCCAATT\tCTCCGTGCTG\tERCC-00136_RandomPrimer-SSIV_NexteraXT_RNA:0352324823_cDNA:0369438798_LIB:13214803_G3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00136\r\nMA_MGH_02677\tAGGACAGGCC\tCATTCCAGCT\tERCC-00157_RandomPrimer-SSIV_NexteraXT_RNA:0352324824_cDNA:0369438801_LIB:13214803_H3\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00157\r\nMA_MGH_02678\tAGAGAACCTA\tGGTTATGCTA\tERCC-00007_RandomPrimer-SSIV_NexteraXT_RNA:0352324825_cDNA:0369438809_LIB:13214803_A4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00007\r\nMA_MGH_02679\tGATATTGTGT\tACCACACGGT\tERCC-00025_RandomPrimer-SSIV_NexteraXT_RNA:0352324826_cDNA:0369438791_LIB:13214803_B4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00025\r\nMA_MGH_02680\tCGTACAGGAA\tTAGGTTCTCT\tERCC-00046_RandomPrimer-SSIV_NexteraXT_RNA:0352324827_cDNA:0369438817_LIB:13214803_C4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00046\r\nMA_MGH_02681\tCTGCGTTACC\tTATGGCTCGA\tERCC-00069_RandomPrimer-SSIV_NexteraXT_RNA:0352324828_cDNA:0369438803_LIB:13214803_D4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00069\r\nMA_MGH_02682\tAGGCCGTGGA\tCTCGTGCGTT\tERCC-00085_RandomPrimer-SSIV_NexteraXT_RNA:0352324829_cDNA:0369438822_LIB:13214803_E4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00085\r\nMA_MGH_02683\tAGGAGGTATC\tCCAGTTGGCA\tERCC-00112_RandomPrimer-SSIV_NexteraXT_RNA:0352324830_cDNA:0369438818_LIB:13214803_F4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00112\r\nMA_MGH_02684\tGCTGACGTTG\tTGTTCGCATT\tERCC-00137_RandomPrimer-SSIV_NexteraXT_RNA:0352309367_cDNA:0369438805_LIB:13214803_G4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00137\r\nMA_MGH_02685\tCTAATAACCG\tAACCGCATCG\tERCC-00158_RandomPrimer-SSIV_NexteraXT_RNA:0352324832_cDNA:0369438797_LIB:13214803_H4\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00158\r\nMA_MGH_02686\tTCTAGGCGCG\tCGAAGGTTAA\tERCC-00009_RandomPrimer-SSIV_NexteraXT_RNA:0352324833_cDNA:0369438788_LIB:13214803_A5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00009\r\nMA_MGH_02687\tATAGCCAAGA\tAGTGCCACTG\tERCC-00028_RandomPrimer-SSIV_NexteraXT_RNA:0352324834_cDNA:0369438792_LIB:13214803_B5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00028\r\nMA_MGH_02688\tTTCGGTGTGA\tGAACAAGTAT\tERCC-00048_RandomPrimer-SSIV_NexteraXT_RNA:0352324835_cDNA:0369438790_LIB:13214803_C5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00048\r\nMA_MGH_02689\tATGTAACGTT\tACGATTGCTG\tERCC-00071_RandomPrimer-SSIV_NexteraXT_RNA:0352324836_cDNA:0369438810_LIB:13214803_D5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00071\r\nMA_MGH_02690\tAACGAGGCCG\tATACCTGGAT\tERCC-00086_RandomPrimer-SSIV_NexteraXT_RNA:0352324837_cDNA:0369438795_LIB:13214803_E5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00086\r\nMA_MGH_02691\tTGGTGTTATG\tTCCAATTCTA\tERCC-00113_RandomPrimer-SSIV_NexteraXT_RNA:0352324838_cDNA:0369438783_LIB:13214803_F5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00113\r\nMA_MGH_02692\tTGGCCTCTGT\tTGAGACAGCG\tERCC-00138_RandomPrimer-SSIV_NexteraXT_RNA:0352324839_cDNA:0369438793_LIB:13214803_G5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00138\r\nMA_MGH_02693\tCCAGGCACCA\tACGCTAATTA\tERCC-00160_RandomPrimer-SSIV_NexteraXT_RNA:0352324840_cDNA:0369438785_LIB:13214803_H5\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00160\r\nMA_MGH_02694\tCCGGTTCCTA\tTATATTCGAG\tERCC-00012_RandomPrimer-SSIV_NexteraXT_RNA:0352324841_cDNA:0369438778_LIB:13214803_A6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00012\r\nMA_MGH_02695\tGGCCAATATT\tCGGTCCGATA\tERCC-00031_RandomPrimer-SSIV_NexteraXT_RNA:0352324842_cDNA:0369438786_LIB:13214803_B6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00031\r\nMA_MGH_02696\tGAATACCTAT\tACAATAGAGT\tERCC-00051_RandomPrimer-SSIV_NexteraXT_RNA:0352324843_cDNA:0369438794_LIB:13214803_C6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00051\r\nMA_MGH_02697\tTACGTGAAGG\tCGGTTATTAG\tERCC-00073_RandomPrimer-SSIV_NexteraXT_RNA:0352324844_cDNA:0369438781_LIB:13214803_D6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00073\r\nMA_MGH_02698\tCTTATTGGCC\tGATAACAAGT\tERCC-00092_RandomPrimer-SSIV_NexteraXT_RNA:0352324845_cDNA:0369438789_LIB:13214803_E6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00092\r\nMA_MGH_02699\tACAACTACTG\tAGTTATCACA\tERCC-00116_RandomPrimer-SSIV_NexteraXT_RNA:0352324846_cDNA:0369438782_LIB:13214803_F6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00116\r\nMA_MGH_02700\tGTTGGATGAA\tTTCCAGGTAA\tERCC-00142_RandomPrimer-SSIV_NexteraXT_RNA:0352324847_cDNA:0369438787_LIB:13214803_G6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00142\r\nMA_MGH_02701\tAATCCAATTG\tCATGTAGAGG\tERCC-00162_RandomPrimer-SSIV_NexteraXT_RNA:0352324848_cDNA:0369438738_LIB:13214803_H6\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00162\r\nMA_MGH_02702\tTATGATGGCC\tGATTGTCATA\tERCC-00013_RandomPrimer-SSIV_NexteraXT_RNA:0352324849_cDNA:0369438736_LIB:13214803_A7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00013\r\nMA_MGH_02703\tCGCAGCAATT\tATTCCGCTAT\tERCC-00033_RandomPrimer-SSIV_NexteraXT_RNA:0352324850_cDNA:0369438733_LIB:13214803_B7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00033\r\nMA_MGH_02704\tACGTTCCTTA\tGACCGCTGTG\tERCC-00053_RandomPrimer-SSIV_NexteraXT_RNA:0352324851_cDNA:0369438772_LIB:13214803_C7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00053\r\nMA_MGH_02705\tCCGCGTATAG\tTAGGAACCGG\tERCC-00074_RandomPrimer-SSIV_NexteraXT_RNA:0352324852_cDNA:0369438780_LIB:13214803_D7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00074\r\nMA_MGH_02706\tGATTCTGAAT\tAGCGGTGGAC\tERCC-00095_RandomPrimer-SSIV_NexteraXT_RNA:0352309359_cDNA:0369438771_LIB:13214803_E7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00095\r\nMA_MGH_02707\tTAGAGAATAC\tTATAGATTCG\tERCC-00117_RandomPrimer-SSIV_NexteraXT_RNA:0352324854_cDNA:0369438768_LIB:13214803_F7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00117\r\nMA_MGH_02708\tTTGTATCAGG\tACAGAGGCCA\tERCC-00143_RandomPrimer-SSIV_NexteraXT_RNA:0352324855_cDNA:0369438752_LIB:13214803_G7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00143\r\nMA_MGH_02709\tCACAGCGGTC\tATTCCTATTG\tERCC-00163_RandomPrimer-SSIV_NexteraXT_RNA:0352324856_cDNA:0369438767_LIB:13214803_H7\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00163\r\nMA_MGH_02710\tCCACGCTGAA\tTATTCCTCAG\tERCC-00014_RandomPrimer-SSIV_NexteraXT_RNA:0352324857_cDNA:0369438774_LIB:13214803_A8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00014\r\nMA_MGH_02711\tGTTCGGAGTT\tCGCCTTCTGA\tERCC-00034_RandomPrimer-SSIV_NexteraXT_RNA:0352324858_cDNA:0369438770_LIB:13214803_B8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00034\r\nMA_MGH_02712\tATAGCGGAAT\tGCGCAGAGTA\tERCC-00054_RandomPrimer-SSIV_NexteraXT_RNA:0352324859_cDNA:0369438763_LIB:13214803_C8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00054\r\nMA_MGH_02713\tGCAATATTCA\tGGCGCCAATT\tERCC-00075_RandomPrimer-SSIV_NexteraXT_RNA:0352324860_cDNA:0369438773_LIB:13214803_D8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00075\r\nMA_MGH_02714\tCTAGATTGCG\tAGATATGGCG\tERCC-00096_RandomPrimer-SSIV_NexteraXT_RNA:0352324861_cDNA:0369438769_LIB:13214803_E8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00096\r\nMA_MGH_02715\tCGATGCGGTT\tCCTGCTTGGT\tERCC-00120_RandomPrimer-SSIV_NexteraXT_RNA:0352324862_cDNA:0369438762_LIB:13214803_F8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00120\r\nMA_MGH_02716\tTCCGGACTAG\tGACGAACAAT\tERCC-00144_RandomPrimer-SSIV_NexteraXT_RNA:0352324863_cDNA:0369438777_LIB:13214803_G8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00144\r\nMA_MGH_02717\tGTGACGGAGC\tTGGCGGTCCA\tERCC-00164_RandomPrimer-SSIV_NexteraXT_RNA:0352324864_cDNA:0369438779_LIB:13214803_H8\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00164\r\nMA_MGH_02718\tAATTCCATCT\tCTTCAGTTAC\tERCC-00016_RandomPrimer-SSIV_NexteraXT_RNA:0352324865_cDNA:0369438760_LIB:13214803_A9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00016\r\nMA_MGH_02719\tTTAACGGTGT\tTCCTGACCGT\tERCC-00035_RandomPrimer-SSIV_NexteraXT_RNA:0352324866_cDNA:0369438784_LIB:13214803_B9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00035\r\nMA_MGH_02720\tACTTGTTATC\tCGCGCCTAGA\tERCC-00057_RandomPrimer-SSIV_NexteraXT_RNA:0352324867_cDNA:0369438776_LIB:13214803_C9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00057\r\nMA_MGH_02721\tCGTGTACCAG\tAGGATAAGTT\tERCC-00076_RandomPrimer-SSIV_NexteraXT_RNA:0352324868_cDNA:0369438755_LIB:13214803_D9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00076\r\nMA_MGH_02722\tTTAACCTTCG\tAGGCCAGACA\tERCC-00097_RandomPrimer-SSIV_NexteraXT_RNA:0352324869_cDNA:0369438746_LIB:13214803_E9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00097\r\nMA_MGH_02723\tCATATGCGAT\tCCTTGAACGG\tERCC-00123_RandomPrimer-SSIV_NexteraXT_RNA:0352324870_cDNA:0369438745_LIB:13214803_F9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00123\r\nMA_MGH_02724\tAGCCTATGAT\tCACCACCTAC\tERCC-00145_RandomPrimer-SSIV_NexteraXT_RNA:0352324871_cDNA:0369438754_LIB:13214803_G9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00145\r\nMA_MGH_02725\tTATGACAATC\tTTGCTTGTAT\tERCC-00165_RandomPrimer-SSIV_NexteraXT_RNA:0352324872_cDNA:0369438761_LIB:13214803_H9\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00165\r\nMA_MGH_02726\tATGTTGTTGG\tCAATCTATGA\tERCC-00017_RandomPrimer-SSIV_NexteraXT_RNA:0352324873_cDNA:0369438735_LIB:13214803_A10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00017\r\nMA_MGH_02727\tGCACCACCAA\tTGGTACTGAT\tERCC-00039_RandomPrimer-SSIV_NexteraXT_RNA:0352324874_cDNA:0369438758_LIB:13214803_B10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00039\r\nMA_MGH_02728\tAGGCGTTCGC\tTTCATCCAAC\tERCC-00058_RandomPrimer-SSIV_NexteraXT_RNA:0352324875_cDNA:0369438775_LIB:13214803_C10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00058\r\nMA_MGH_02729\tCCTCCGGTTG\tCATAACACCA\tERCC-00077_RandomPrimer-SSIV_NexteraXT_RNA:0352324876_cDNA:0369438759_LIB:13214803_D10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00077\r\nMA_MGH_02730\tGTCCACCGCT\tTCCTATTAGC\tERCC-00098_RandomPrimer-SSIV_NexteraXT_RNA:0352324877_cDNA:0369438766_LIB:13214803_E10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00098\r\nMA_MGH_02731\tATTGTTCGTC\tTCTCTAGATT\tERCC-00126_RandomPrimer-SSIV_NexteraXT_RNA:0352324878_cDNA:0369438753_LIB:13214803_F10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00126\r\nMA_MGH_02732\tGGACCAGTGG\tCGCGAGCCTA\tERCC-00147_RandomPrimer-SSIV_NexteraXT_RNA:0352324879_cDNA:0369438750_LIB:13214803_G10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00147\r\nMA_MGH_02733\tCCTTCTAACA\tGATAAGCTCT\tERCC-00168_RandomPrimer-SSIV_NexteraXT_RNA:0352324880_cDNA:0369438756_LIB:13214803_H10\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00168\r\nMA_MGH_02734\tCTCGAATATA\tGAGATGTCGA\tERCC-00018_RandomPrimer-SSIV_NexteraXT_RNA:0352324881_cDNA:0369438764_LIB:13214803_A11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00018\r\nMA_MGH_02735\tGATCGTCGCG\tCTGGATATGT\tERCC-00040_RandomPrimer-SSIV_NexteraXT_RNA:0352324882_cDNA:0369438765_LIB:13214803_B11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00040\r\nMA_MGH_02736\tTATCCGAGGC\tGGCCAATAAG\tERCC-00059_RandomPrimer-SSIV_NexteraXT_RNA:0352324883_cDNA:0369438747_LIB:13214803_C11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00059\r\nMA_MGH_02737\tCGCTGTCTCA\tATTACTCACC\tERCC-00078_RandomPrimer-SSIV_NexteraXT_RNA:0352324884_cDNA:0369438751_LIB:13214803_D11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00078\r\nMA_MGH_02738\tAATGCGAACA\tAATTGGCGGA\tERCC-00099_RandomPrimer-SSIV_NexteraXT_RNA:0352324885_cDNA:0369438749_LIB:13214803_E11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00099\r\nMA_MGH_02739\tAATTCTTGGA\tTTGTCAACTT\tERCC-00128_RandomPrimer-SSIV_NexteraXT_RNA:0352324886_cDNA:0369438744_LIB:13214803_F11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00128\r\nMA_MGH_02740\tTTCCTACAGC\tGGCGAATTCT\tERCC-00148_RandomPrimer-SSIV_NexteraXT_RNA:0352324887_cDNA:0369438757_LIB:13214803_G11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00148\r\nMA_MGH_02741\tATCCAGGTAT\tCAACGTCAGC\tERCC-00170_RandomPrimer-SSIV_NexteraXT_RNA:0352324888_cDNA:0369438748_LIB:13214803_H11\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00170\r\nH2OCTL112\tACGGTCCAAC\tTCTTACATCA\tERCC-00019_RandomPrimer-SSIV_NexteraXT_RNA:0352324889_cDNA:0369438743_LIB:13214803_A12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00019\r\nMA_MGH_02742\tGTAACTTGGT\tCGCCATACCT\tERCC-00041_RandomPrimer-SSIV_NexteraXT_RNA:0352324890_cDNA:0369438740_LIB:13214803_B12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00041\r\nMA_MGH_02743\tAGCGCCACAC\tCTAATGTCTT\tERCC-00060_RandomPrimer-SSIV_NexteraXT_RNA:0352324891_cDNA:0369438742_LIB:13214803_C12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00060\r\nMA_MGH_02744\tTGCTACTGCC\tCAACCGGAGG\tERCC-00079_RandomPrimer-SSIV_NexteraXT_RNA:0352324892_cDNA:0369438741_LIB:13214803_D12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00079\r\nMA_MGH_02745\tCAACACCGCA\tGGCAGTAGCA\tERCC-00104_RandomPrimer-SSIV_NexteraXT_RNA:0352324893_cDNA:0369438734_LIB:13214803_E12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00104\r\nMA_MGH_02746\tCACCTTAATC\tTTAGGATAGA\tERCC-00130_RandomPrimer-SSIV_NexteraXT_RNA:0352324894_cDNA:0369438732_LIB:13214803_F12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00130\r\nMA_MGH_02747\tTTGAATGTTG\tCGCAATCTAG\tERCC-00150_RandomPrimer-SSIV_NexteraXT_RNA:0352324895_cDNA:0369438737_LIB:13214803_G12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00150\r\nH2OCTL113\tCCGGTAACAC\tGAGTTGTACT\tERCC-00171_RandomPrimer-SSIV_NexteraXT_RNA:0352324896_cDNA:0369438739_LIB:13214803_H12\tRNA-Seq\tVIRAL RNA\tcDNA\tRandomPrimer-SSIV_NexteraXT\t\tERCC-00171\r\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-custom-inner-barcodes-outer-collapse.tsv", "content": "sample\tlibrary_id_per_sample\tI7_Index_ID\tbarcode_1\tI5_Index_ID\tbarcode_2\tInline_Index_ID\tbarcode_3\nSAMPLE_19923\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t1\tCGACTTGGT\nSAMPLE_19903\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t2\tGTGGCTGCT\nSAMPLE_19877\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t3\tGCAGTTACT\nSAMPLE_19891\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t4\tCACGATGAT\nSAMPLE_19886\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t5\tCGTGGTAAT\nSAMPLE_19924\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t6\tATAATTCTT\nSAMPLE_19897\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t7\tCTTGGGCCT\nH2O_1\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t8\tATGTTGTAT\nSAMPLE_19888\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t9\tCTGGTTCAT\nSAMPLE_19970\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t10\tGTCCATATT\nSAMPLE_19962\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t11\tGCGAGTTGT\nSAMPLE_19937\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t12\tGCCCTCCGT\nSAMPLE_19925\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t13\tAATAATGTT\nSAMPLE_19929\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t14\tCAAGTGATT\nSAMPLE_19943\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t15\tAAGACGGGT\nSAMPLE_19889\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t16\tGTACCGAGT\nSAMPLE_19910\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t17\tCGCCAGACT\nSAMPLE_19909\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t18\tCCGCGGGAT\nSAMPLE_19918\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t19\tAAGTGCCGT\nSAMPLE_19895\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t20\tACAATCTCT\nSAMPLE_19932\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t21\tCATCTGTAT\nSAMPLE_19930\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t22\tGTCTCCCAT\nSAMPLE_19911\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t23\tCTGTAGGGT\nSAMPLE_19948\tPool_1\t\tCTGATCGT\t\tGCGCATAT\t24\tAGTTAGAGT\nSAMPLE_19894\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t1\tCGACTTGGT\nSAMPLE_19922\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t2\tGTGGCTGCT\nSAMPLE_19969\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t3\tGCAGTTACT\nSAMPLE_19939\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t4\tCACGATGAT\nSAMPLE_19902\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t5\tCGTGGTAAT\nSAMPLE_19952\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t6\tATAATTCTT\nSAMPLE_19941\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t7\tCTTGGGCCT\nH2O_2\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t8\tATGTTGTAT\nSAMPLE_19917\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t9\tCTGGTTCAT\nSAMPLE_19907\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t10\tGTCCATATT\nSAMPLE_19926\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t11\tGCGAGTTGT\nSAMPLE_19899\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t12\tGCCCTCCGT\nSAMPLE_19951\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t13\tAATAATGTT\nSAMPLE_19949\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t14\tCAAGTGATT\nSAMPLE_19893\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t15\tAAGACGGGT\nSAMPLE_19947\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t16\tGTACCGAGT\nSAMPLE_19908\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t17\tCGCCAGACT\nSAMPLE_19957\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t18\tCCGCGGGAT\nSAMPLE_19971\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t19\tAAGTGCCGT\nSAMPLE_19964\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t20\tACAATCTCT\nSAMPLE_19955\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t21\tCATCTGTAT\nSAMPLE_19963\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t22\tGTCTCCCAT\nSAMPLE_19944\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t23\tCTGTAGGGT\nSAMPLE_19931\tPool_2\t\tACTCTCGA\t\tCTGTACCA\t24\tAGTTAGAGT\nSAMPLE_19914\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t1\tCGACTTGGT\nSAMPLE_19883\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t2\tGTGGCTGCT\nSAMPLE_19915\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t3\tGCAGTTACT\nSAMPLE_19904\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t4\tCACGATGAT\nSAMPLE_19945\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t5\tCGTGGTAAT\nSAMPLE_19940\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t6\tATAATTCTT\nSAMPLE_19933\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t7\tCTTGGGCCT\nH2O_3\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t8\tATGTTGTAT\nSAMPLE_19892\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t9\tCTGGTTCAT\nSAMPLE_19956\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t10\tGTCCATATT\nSAMPLE_19900\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t11\tGCGAGTTGT\nSAMPLE_19966\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t12\tGCCCTCCGT\nSAMPLE_19950\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t13\tAATAATGTT\nSAMPLE_19958\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t14\tCAAGTGATT\nSAMPLE_19896\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t15\tAAGACGGGT\nSAMPLE_19906\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t16\tGTACCGAGT\nSAMPLE_19936\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t17\tCGCCAGACT\nSAMPLE_19890\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t18\tCCGCGGGAT\nSAMPLE_19912\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t19\tAAGTGCCGT\nSAMPLE_19887\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t20\tACAATCTCT\nSAMPLE_19878\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t21\tCATCTGTAT\nSAMPLE_19942\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t22\tGTCTCCCAT\nSAMPLE_19927\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t23\tCTGTAGGGT\nSAMPLE_19960\tPool_3\t\tTGAGCTAG\t\tGAACGGTT\t24\tAGTTAGAGT\nSAMPLE_19938\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t1\tCGACTTGGT\nSAMPLE_19921\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t2\tGTGGCTGCT\nSAMPLE_19919\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t3\tGCAGTTACT\nSAMPLE_19946\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t4\tCACGATGAT\nSAMPLE_19913\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t5\tCGTGGTAAT\nSAMPLE_19935\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t6\tATAATTCTT\nSAMPLE_19885\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t7\tCTTGGGCCT\nH2O_4\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t8\tATGTTGTAT\nSAMPLE_19879\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t9\tCTGGTTCAT\nSAMPLE_19928\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t10\tGTCCATATT\nSAMPLE_19954\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t11\tGCGAGTTGT\nSAMPLE_19961\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t12\tGCCCTCCGT\nSAMPLE_19953\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t13\tAATAATGTT\nSAMPLE_19959\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t14\tCAAGTGATT\nSAMPLE_19965\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t15\tAAGACGGGT\nSAMPLE_19967\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t16\tGTACCGAGT\nSAMPLE_19920\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t17\tCGCCAGACT\nSAMPLE_19898\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t18\tCCGCGGGAT\nSAMPLE_19916\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t19\tAAGTGCCGT\nSAMPLE_19901\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t20\tACAATCTCT\nSAMPLE_19934\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t21\tCATCTGTAT\nSAMPLE_19905\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t22\tGTCTCCCAT\nSAMPLE_19884\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t23\tCTGTAGGGT\nSAMPLE_19968\tPool_4\t\tGAGACGAT\t\tACCGGTTA\t24\tAGTTAGAGT\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-hiseq-1.csv", "content": "FCID,Lane,SampleID,SampleRef,Index,Index2,Description,Control,Recipe,Operator,SampleProject,Analysis,Bait,RRBS Restriction Enzyme,RRBS Desired,Investigator Name,referenceSequence,referenceVersion,projectManagerEmail,libraryName\r\nHVFF2ADXX,1,NIH28,Ebola_virus_Sierra_Leone,GTAGAGGA,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH28,Ebola_virus_Sierra_Leone,GTAGAGGA,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH27,Ebola_virus_Sierra_Leone,AAGAGGCA,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH27,Ebola_virus_Sierra_Leone,AAGAGGCA,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH26,Ebola_virus_Sierra_Leone,CGAGGCTG,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH26,Ebola_virus_Sierra_Leone,CGAGGCTG,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH25,Ebola_virus_Sierra_Leone,GCTACGCT,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH25,Ebola_virus_Sierra_Leone,GCTACGCT,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH24,Ebola_virus_Sierra_Leone,TAGGCATG,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH24,Ebola_virus_Sierra_Leone,TAGGCATG,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH23,Ebola_virus_Sierra_Leone,TCCTGAGC,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH23,Ebola_virus_Sierra_Leone,TCCTGAGC,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH22,Ebola_virus_Sierra_Leone,AGGCAGAA,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH22,Ebola_virus_Sierra_Leone,AGGCAGAA,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH21,Ebola_virus_Sierra_Leone,CGTACTAG,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH21,Ebola_virus_Sierra_Leone,CGTACTAG,TATCCTCT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH20,Ebola_virus_Sierra_Leone,GTAGAGGA,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH20,Ebola_virus_Sierra_Leone,GTAGAGGA,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH19,Ebola_virus_Sierra_Leone,AAGAGGCA,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH19,Ebola_virus_Sierra_Leone,AAGAGGCA,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH18,Ebola_virus_Sierra_Leone,CGAGGCTG,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH18,Ebola_virus_Sierra_Leone,CGAGGCTG,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH17,Ebola_virus_Sierra_Leone,GCTACGCT,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH17,Ebola_virus_Sierra_Leone,GCTACGCT,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH16,Ebola_virus_Sierra_Leone,TAGGCATG,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH16,Ebola_virus_Sierra_Leone,TAGGCATG,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH15,Ebola_virus_Sierra_Leone,TCCTGAGC,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH15,Ebola_virus_Sierra_Leone,TCCTGAGC,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH14,Ebola_virus_Sierra_Leone,AGGCAGAA,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH14,Ebola_virus_Sierra_Leone,AGGCAGAA,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH13,Ebola_virus_Sierra_Leone,CGTACTAG,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH13,Ebola_virus_Sierra_Leone,CGTACTAG,CTCTCTAT,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH12,Ebola_virus_Sierra_Leone,GTAGAGGA,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH12,Ebola_virus_Sierra_Leone,GTAGAGGA,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH11,Ebola_virus_Sierra_Leone,AAGAGGCA,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH11,Ebola_virus_Sierra_Leone,AAGAGGCA,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH10,Ebola_virus_Sierra_Leone,CGAGGCTG,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH10,Ebola_virus_Sierra_Leone,CGAGGCTG,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH9,Ebola_virus_Sierra_Leone,GCTACGCT,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH9,Ebola_virus_Sierra_Leone,GCTACGCT,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH8,Ebola_virus_Sierra_Leone,TAGGCATG,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH8,Ebola_virus_Sierra_Leone,TAGGCATG,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH7,Ebola_virus_Sierra_Leone,TCCTGAGC,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH7,Ebola_virus_Sierra_Leone,TCCTGAGC,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH6,Ebola_virus_Sierra_Leone,AGGCAGAA,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH6,Ebola_virus_Sierra_Leone,AGGCAGAA,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,1,NIH5,Ebola_virus_Sierra_Leone,CGTACTAG,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\nHVFF2ADXX,2,NIH5,Ebola_virus_Sierra_Leone,CGTACTAG,TAGATCGC,,,,tamason,IDI,,,Mspl,,alin@broadinstitute.org,Ebola_virus_Sierra_Leone,0,alin@broadinstitute.org,NIH-AEL\r\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-in-Broad-MiSeq-Format_with_Picard_Block.csv", "content": "[Header],,,,\nInvestigator Name,Lisa,,,\nProject Name,WUS lmf 2,,,\nExperiment Name,General,,,\nDate,1/10/2017,,,\nWorkflow,Resequencing,,,\nChemistry,Amplicon,,,\n,,,,\n[Reads],,,,\n150,,,,\nIndex,,,,\nIndex,,,,\n150,,,,\n,,,,\n[Manifests],,,,\nA,ManifestNameHere,,,\n,,,,\n[Settings],,,,\nFilterPCRDuplicates,1,,,\nOnlyGenerateFastq,0,,,\n,,,,\n[Data],,,,\nSample_ID,Sample_Name,GenomeFolder,Index,Index2\n123618_MGH015B_repeat(Lisa),MGH015B_repeat(Lisa),,AGGCAGAA,TATCCTCT\n123617_WB-MF-1e4,WB-MF-1e4,,GGACTCCT,TATCCTCT\n123616_WB-1e4,WB-1e4,,TCCTGAGC,CTCTCTAT\n123615_WB-MF-1e6,WB-MF-1e6,,AGGCAGAA,CTCTCTAT\n123614_WB-1e6,WB-1e6,,CGTACTAG,CTCTCTAT\n123613_Plasma-MF-1e6,Plasma-MF-1e6,,TAAGGCGA,CTCTCTAT\n123612_Plasma-1e6,Plasma-1e6,,GGACTCCT,TAGATCGC\n123611_Plasma-MF-1e4,Plasma-MF-1e4,,TCCTGAGC,TAGATCGC\n123610_Plasma-1e4,Plasma-1e4,,AGGCAGAA,TAGATCGC\n123609_Plasma-MF-1e2,Plasma-MF-1e2,,CGTACTAG,TAGATCGC\n123608_Plasma-1e2,Plasma-1e2,,TAAGGCGA,TAGATCGC\n,,,,\n[Picard],,,,\nanalysisType,WholeGenomeShotgun.AssemblyWithoutReference,,,\nreferenceSequence,,,,\nreferenceVersion,0,,,\nbaitSetName,,,,\nenzyme,Mspl,,,\nfragSizeRange,,,,\nprojectManagerEmail,someone@example.com,,,\nwalkupNotes,Walk Up Sequencing,,,\nlibraryName,EVSpikeins,,,\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-miseq-1.csv", "content": "[Header],,,,,,,,,\r\nIEMFileVersion,4,,,,,,,,\r\nInvestigator Name,James,,,,,,,,\r\nExperiment Name,EBoV HS ,,,,,,,,\r\nDate,8/18/2015,,,,,,,,\r\nWorkflow,GenerateFASTQ,,,,,,,,\r\nApplication,FASTQ Only,,,,,,,,\r\nAssay,Nextera XT,,,,,,,,\r\nDescription,,,,,,,,,\r\nChemistry,Amplicon,,,,,,,,\r\n,,,,,,,,,\r\n[Reads],,,,,,,,,\r\n101,,,,,,,,,\r\n101,,,,,,,,,\r\n,,,,,,,,,\r\n[Settings],,,,,,,,,\r\nReverseComplement,0,,,,,,,,\r\n,,,,,,,,,\r\n[Data],,,,,,,,,\r\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\r\nmebv.0.6,,,,N702,CGTACTAG,S502,CTCTCTAT,,\r\nmebv.0.5,,,,N702,CGTACTAG,S503,TATCCTCT,,\r\nmebv.0.4,,,,N702,CGTACTAG,S504,AGAGTAGA,,\r\nmebv.0.3,,,,N702,CGTACTAG,S505,GTAAGGAG,,\r\nmebv.0.1,,,,N702,CGTACTAG,S508,CTAAGCCT,,\r\nmebv.4.6,,,,N703,AGGCAGAA,S502,CTCTCTAT,,\r\nmebv.4.5,,,,N703,AGGCAGAA,S503,TATCCTCT,,\r\nmebv.4.4,,,,N703,AGGCAGAA,S504,AGAGTAGA,,\r\nmebv.4.3,,,,N703,AGGCAGAA,S505,GTAAGGAG,,\r\nmebv.4.1,,,,N703,AGGCAGAA,S508,CTAAGCCT,,\r\nmebv.20.6,,,,N704,TCCTGAGC,S502,CTCTCTAT,,\r\nmebv.20.5,,,,N704,TCCTGAGC,S503,TATCCTCT,,\r\nmebv.20.4,,,,N704,TCCTGAGC,S504,AGAGTAGA,,\r\nmebv.20.3,,,,N704,TCCTGAGC,S505,GTAAGGAG,,\r\nmebv.20.1,,,,N704,TCCTGAGC,S508,CTAAGCCT,,\r\nmebv.48.6,,,,N705,GGACTCCT,S502,CTCTCTAT,,\r\nmebv.48.5,,,,N705,GGACTCCT,S503,TATCCTCT,,\r\nmebv.48.4,,,,N705,GGACTCCT,S504,AGAGTAGA,,\r\nmebv.48.3,,,,N705,GGACTCCT,S505,GTAAGGAG,,\r\nmebv.48.1,,,,N705,GGACTCCT,S508,CTAAGCCT,,\r\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-submit-1.csv", "content": "NIH5,CGTACTAG,TAGATCGC\rNIH6,AGGCAGAA,TAGATCGC\rNIH7,TCCTGAGC,TAGATCGC\rNIH8,TAGGCATG,TAGATCGC\rNIH9,GCTACGCT,TAGATCGC\rNIH10,CGAGGCTG,TAGATCGC\rNIH11,AAGAGGCA,TAGATCGC\rNIH12,GTAGAGGA,TAGATCGC\rNIH13,CGTACTAG,CTCTCTAT\rNIH14,AGGCAGAA,CTCTCTAT\rNIH15,TCCTGAGC,CTCTCTAT\rNIH16,TAGGCATG,CTCTCTAT\rNIH17,GCTACGCT,CTCTCTAT\rNIH18,CGAGGCTG,CTCTCTAT\rNIH19,AAGAGGCA,CTCTCTAT\rNIH20,GTAGAGGA,CTCTCTAT\rNIH21,CGTACTAG,TATCCTCT\rNIH22,AGGCAGAA,TATCCTCT\rNIH23,TCCTGAGC,TATCCTCT\rNIH24,TAGGCATG,TATCCTCT\rNIH25,GCTACGCT,TATCCTCT\rNIH26,CGAGGCTG,TATCCTCT\rNIH27,AAGAGGCA,TATCCTCT\rNIH28,GTAGAGGA,TATCCTCT" }, { "path": "tests/input/TestSampleSheet/SampleSheet-submit-2.csv", "content": "SampleName,Nextera i7,Nextera i5\r\nG5735-2,TAGATCGC,TAAGGCGA\r\nG4380-1,CTCTCTAT,TAAGGCGA\r\nG4946-1,TATCCTCT,TAAGGCGA\r\nG4441-1,AGAGTAGA,TAAGGCGA\r\nG5361-1,GTAAGGAG,TAAGGCGA\r\nG5237-1,ACTGCATA,TAAGGCGA\r\nG4151-1,AAGGAGTA,TAAGGCGA\r\nG4264-1,CTAAGCCT,TAAGGCGA\r\nG5571-1,TAGATCGC,CGTACTAG\r\nG4382-1,CTCTCTAT,CGTACTAG\r\nG4956-1,TATCCTCT,CGTACTAG\r\nG4445-1,AGAGTAGA,CGTACTAG\r\nG5371-1,GTAAGGAG,CGTACTAG\r\nG4202-1,ACTGCATA,CGTACTAG\r\nG4217-1,AAGGAGTA,CGTACTAG\r\nG4220-2,CTAAGCCT,CGTACTAG\r\nG5520-1,TAGATCGC,AGGCAGAA\r\nG4406-1,CTCTCTAT,AGGCAGAA\r\nG4972-1,TATCCTCT,AGGCAGAA\r\nG4450-1,AGAGTAGA,AGGCAGAA\r\nG5370-1,GTAAGGAG,AGGCAGAA\r\nG4204-1,ACTGCATA,AGGCAGAA\r\nG4221-1,AAGGAGTA,AGGCAGAA\r\nG4255-1,CTAAGCCT,AGGCAGAA\r\nG4388-1,TAGATCGC,TCCTGAGC\r\nG4415-1,CTCTCTAT,TCCTGAGC\r\nG4973-1,TATCCTCT,TCCTGAGC\r\nG4453-1,AGAGTAGA,TCCTGAGC\r\nG5375-1,GTAAGGAG,TCCTGAGC\r\nG4028-1,ACTGCATA,TCCTGAGC\r\nG4235-1,AAGGAGTA,TCCTGAGC\r\nG4286-1,CTAAGCCT,TCCTGAGC\r\nG4389-1,TAGATCGC,GGACTCCT\r\nG4416-1,CTCTCTAT,GGACTCCT\r\nG5059-1,TATCCTCT,GGACTCCT\r\nG4454-1,AGAGTAGA,GGACTCCT\r\nG5304-1,GTAAGGAG,GGACTCCT\r\nG3911-5,ACTGCATA,GGACTCCT\r\nG4236-1,AAGGAGTA,GGACTCCT\r\nG4287-1,CTAAGCCT,GGACTCCT\r\nG4342-1,TAGATCGC,TAGGCATG\r\nG4419-1,CTCTCTAT,TAGGCATG\r\nG5064-1,TATCCTCT,TAGGCATG\r\nG5305-1,GTAAGGAG,TAGGCATG\r\nG3821-5,ACTGCATA,TAGGCATG\r\nG4238-1,AAGGAGTA,TAGGCATG\r\nG4288-1,CTAAGCCT,TAGGCATG\r\nG4345-1,TAGATCGC,CTCTCTAC\r\nG4422-1,CTCTCTAT,CTCTCTAC\r\nG4431-1,TATCCTCT,CTCTCTAC\r\nG4457-1,AGAGTAGA,CTCTCTAC\r\nG5244-1,GTAAGGAG,CTCTCTAC\r\nG3881-6,ACTGCATA,CTCTCTAC\r\nG4250-1,AAGGAGTA,CTCTCTAC\r\nG3997-2,CTAAGCCT,CTCTCTAC\r\nG4312-2,TAGATCGC,CAGAGAGG\r\nG4423-1,CTCTCTAT,CAGAGAGG\r\nG4433-1,TATCCTCT,CAGAGAGG\r\nG4458-1,AGAGTAGA,CAGAGAGG\r\nG5296-1,GTAAGGAG,CAGAGAGG\r\nG3811-2,ACTGCATA,CAGAGAGG\r\nG4251-1,AAGGAGTA,CAGAGAGG\r\nG4034-2,CTAAGCCT,CAGAGAGG\r\nG4346-1,TAGATCGC,GCTACGCT\r\nG4424-1,CTCTCTAT,GCTACGCT\r\nG4437-1,TATCCTCT,GCTACGCT\r\nG4368-2,AGAGTAGA,GCTACGCT\r\nG5295-1,GTAAGGAG,GCTACGCT\r\nG4121-2,ACTGCATA,GCTACGCT\r\nG4252-1,AAGGAGTA,GCTACGCT\r\nG3869-2,CTAAGCCT,GCTACGCT\r\nG4348-1,TAGATCGC,CGAGGCTG\r\nG4323-2,CTCTCTAT,CGAGGCTG\r\nG4438-1,TATCCTCT,CGAGGCTG\r\nG4465-1,AGAGTAGA,CGAGGCTG\r\nG5289-1,GTAAGGAG,CGAGGCTG\r\nG4209-1,ACTGCATA,CGAGGCTG\r\nG4253-1,AAGGAGTA,CGAGGCTG\r\nG4024-2,CTAAGCCT,CGAGGCTG\r\nG4350-1,TAGATCGC,AAGAGGCA\r\nG4527-2,CTCTCTAT,AAGAGGCA\r\nG4439-1,TATCCTCT,AAGAGGCA\r\nG4466-1,AGAGTAGA,AAGAGGCA\r\nG5242-1,GTAAGGAG,AAGAGGCA\r\nG4213-1,ACTGCATA,AAGAGGCA\r\nG4254-1,AAGGAGTA,AAGAGGCA\r\nG3991-3,CTAAGCCT,AAGAGGCA\r\nG4347-1,TAGATCGC,GTAGAGGA\r\nG4837-1,CTCTCTAT,GTAGAGGA\r\nG4440-1,TATCCTCT,GTAGAGGA\r\nG5364-1,AGAGTAGA,GTAGAGGA\r\nG5238-1,GTAAGGAG,GTAGAGGA\r\nG4216-1,ACTGCATA,GTAGAGGA\r\nG4263-1,AAGGAGTA,GTAGAGGA\r\nG3910-3,CTAAGCCT,GTAGAGGA\r\nG3682-1-c1,AGAGTAGA,TAGGCATG\r\n" }, { "path": "tests/input/TestSampleSheet/SampleSheet-submit-3.csv", "content": "SampleName,P7 Barcodes,P5 Barcodes\rNIH5,CGTACTAG,TAGATCGC\rNIH6,AGGCAGAA,TAGATCGC\rNIH7,TCCTGAGC,TAGATCGC\rNIH8,TAGGCATG,TAGATCGC\rNIH9,GCTACGCT,TAGATCGC\rNIH10,CGAGGCTG,TAGATCGC\rNIH11,AAGAGGCA,TAGATCGC\rNIH12,GTAGAGGA,TAGATCGC\rNIH13,CGTACTAG,CTCTCTAT\rNIH14,AGGCAGAA,CTCTCTAT\rNIH15,TCCTGAGC,CTCTCTAT\rNIH16,TAGGCATG,CTCTCTAT\rNIH17,GCTACGCT,CTCTCTAT\rNIH18,CGAGGCTG,CTCTCTAT\rNIH19,AAGAGGCA,CTCTCTAT\rNIH20,GTAGAGGA,CTCTCTAT\rNIH21,CGTACTAG,TATCCTCT\rNIH22,AGGCAGAA,TATCCTCT\rNIH23,TCCTGAGC,TATCCTCT\rNIH24,TAGGCATG,TATCCTCT\rNIH25,GCTACGCT,TATCCTCT\rNIH26,CGAGGCTG,TATCCTCT\rNIH27,AAGAGGCA,TATCCTCT\rNIH28,GTAGAGGA,TATCCTCT" }, { "path": "tests/input/TestSampleSheet/SampleSheet-with-blanklines.csv", "content": "[Header],,,,,,,,,\nIEMFileVersion,4,,,,,,,,\nInvestigator Name,Anne,,,,,,,,\nExperiment Name,AP081616,,,,,,,,\nDate,8/16/16,,,,,,,,\nWorkflow,GenerateFASTQ,,,,,,,,\nApplication,FASTQ Only,,,,,,,,\nAssay,Nextera XT,,,,,,,,\nDescription,CSF,,,,,,,,\nChemistry,Amplicon,,,,,,,,\n,,,,,,,,,\n[Reads],,,,,,,,,\n101,,,,,,,,,\n101,,,,,,,,,\n,,,,,,,,,\n[Settings],,,,,,,,,\nReverseComplement,0,,,,,,,,\nAdapter,CTGTCTCTTATACACATCT,,,,,,,,\n,,,,,,,,,\n[Data],,,,,,,,,\nSample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description\nBWH001lib1,,,,N703,AGGCAGAA,S517,GCGTAAGA,,\nBWH001lib2,,,,N705,GGACTCCT,S517,GCGTAAGA,,\nNEGCSF3lib2,,,,N706,TAGGCATG,S502,CTCTCTAT,,\nNS_guide2_2,,,,172,CCTACCAT,417,CGGTTCTT,,\nC044_rs9283753,,,,44,CTGCGGAT,34,TCTTTCCC,,\nC045_rs9283753,,,,45,TCGGAATG,34,TCTTTCCC,,\nC066_rs9283753,,,,46,TCTGCAAG,34,TCTTTCCC,,\nC067_rs9283753,,,,47,AACTTGAC,34,TCTTTCCC,,\n\nC081_rs9283753,,,,66,TTGAGCCT,34,TCTTTCCC,,\nC082_rs9283753,,,,67,GGTCCAGA,34,TCTTTCCC,,\nNA12872_rs9283753,,,,68,CCAGTTAG,34,TCTTTCCC,,\nNA12812_rs9283753,,,,69,CAATAGTC,34,TCTTTCCC,,\n\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_DQ473496.1_Rhinovirus_A49.fa", "content": ">RVA_DQ473496.1_Rhinovirus_A49 (7106 bp)\nTTAAAACTGGATCCAGGTTGTTCCCACCTGGATCTCCCAAAGGGAGTGGAACTCTGTTATTACGGTAACTTTGTACGCCA\nGTTTTATCCTCCCCCACCCCATGTAACTTAGAAGCTTTTCACAAAGACCAATAGTTGGTAATCATCCAGATTACTTAAGG\nTCAAGCACTTCTGTTTCCCCGGTCAACGTTGATATGCTCTAACAGGGCAAAAACAACTGCGATCGTTATCCGCAAAGCGC\nCTACGCAAAGCCTAGTAACACCTTTGAAATTGTTTGGTTGGTCGTTCCGCCATTTTCCCTGGTAGACCTGGCAGATGAGG\nCTAGAAACACCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGCACACCCTGTGGGTGTGAAGCCAAATAATGGA\nCAAGGTGTGAAGAGCCCCGTGTGCTCGCTTTGAGTCCTCCGGCCCCTGAATGCGGCTAACCTTAACCCTGCAGCTAGAGC\nACACAAGCCAGTGTGTATCTAGTCGTAATGAGTAATTGCGGGACGGGACCGACTACTTTGGGTGTCCGTGTTTCACTTTT\nTACTTATAATTGCTTATGGTGACAATATATATATAGTATATATATTGACACCATGGGCGCACAGGTATCTAGGCAAAATG\nTTGGAACTCATTCTACACAAAACTCCGTATCAAATGGATCTAGTTTGAACTATTTCAACATCAACTACTTTAAAGATGCT\nGCTTCTAATGGCGCATCCAAATTGGAGTTTACTCAAGACCCTAGCAAATTTACAGACCCTGTTAAAGATGTATTAGAGAA\nAGGAATACCAACACTACAATCACCCACAGTCGAGGCTTGTGGATATTCGGATAGAATCATACAAATCACTAGAGGAGATT\nCAACAATAACTTCACAAGATGTGGCAAATGCTGTTGTTGCATATGGTGTTTGGCCACATTATCTATCCTCCAAAGATGCT\nTCTGCAATTGACAAACCTTCTCGTCCGGATACATCTTCTAATAGATTTTATACTTTGAAGAGTGTGACTTGGACCAACTC\nTTCAAAAGGTTGGTGGTGGAAATTGCCAGATGCACTGAGAGAAATGGGCATCTTTGGTGAAAACATGTTTTATCACTATT\nTGGGCAGGAGTGGTTACACAATACATGTACAGTGCAATGCTAGCAAATTCCATCAAGGCACGTTAATCGTTGCACTAATA\nCCTGAACACCAAATTGCAAGCGCCCTTCATGGTGATGTGAATGTTGGTTATAACTTTACCCATCCAGGAGAAACGGGAAG\nGGAGGTCAAAAGTGACAGGAGCATGAACCTTAATTTGCAACCCACTGAAGAGTATTGGCTTAATTTTGATGGAACACTAC\nTCGGAAATATTACTATATTTCCCCATCAATTTATTAACTTGAGAAGCAACAACTCTGCTACAATAATTGCTCCATATGTC\nAATGCAGTCCCTATGGACTCAATGCGCAGCCACAACAACTGGAGTCTGGTGATAATCCCAATATGCCCTCTTGAAACATC\nAAGTACCGTTAACACAATACCTATCACAATATCAATAAGTCCCATGTGTGCAGAGTTCTCTGGTGCGCGTGCTAAGAGTC\nAGGGTTTACCGGTTTTCATCACGCCAGGGTCAGGCCAGTTTCTGACAACAGATGACTTTCAATCCCCATGTGCACTCCCT\nTGGTATCACCCAACCAAAGAAATCTCTATTCCAGGTGAGGTAAAAAATTTAGTTGAAATATGTCAAGTAGATAGTTTAGT\nGCCAATAAATAATACTGAAAATAACATCACTAATGAAAACATGTATTCGGTTGTGCTGCAATCAACAGTTGGAGAACCAG\nATAAAATCTTTTCTATCAAAACAGATGTAGCCTCTCAGCCATTAGCTACTACTCTAATTGGTGAAATATCCAGTTATTAT\nACTCACTGGACAGGAAGTCTCCGCTTCAGCTTCATGTTCTGTGGCACAGCCAATACCACTGTTAAACTCTTGTTAGCCTA\nTACGCCACCTGGCATCGCAGAACCTACTACAAGAAAGGAAGCAATGTTAGGTACTCATGTAATATGGGATGTAGGTCTTC\nAATCTACAATATCAATGGTGGTACCATGGATCAGTGCTAGTCACTACAGGAACACATCACCAGGTACATCTACATCTGGA\nTACATAACATGCTGGTATCAAACTAGGCTAGTAATTCCACCTCAAACTCCAGCCACAGCTAGGTTATTATGTTTTGTATC\nAGGCTGTAAAGATTTTTGTTTACGCATGGCTCGGGACACTAATTTGCATTTGCAGAGTGGGGTAATAGAACAAAATCCTG\nTTGAACACTACATAGATGAGGTCCTTAATGAGGTTTTAGTTGTTCCAAATATTAATAGTAGTCACCCCACGACATCAAAC\nTCTGCTCCAGCATTAGATGCTGCAGAAACAGGGCACACTAGCAATGTGCAACCTGAAGATGTCATTGAAACCAGATATGT\nACAGACATCACAAACAAGAGATGAAATGAGTTTAGAGAGTTTTCTTGGTAGGTCAGGGTGTATACATGAATCCAAACTAG\nAGGTCACACTTACAAATTACAATGAAAATAATTTCAAAGTATGGAACATCAATTTGCAAGAAATGGCCCAGATCAGAAGA\nAAATTTGAACTGTTTACTTACACTAGATTCGATTCTGAAATAACCTTGGTTCCATGCATTTCTGCACTTAGCAAGGATAT\nTGGACACATTACAATGCAATACATGTATGTGCCGCCAGGTGCACCTGTACCAAAGAGCAGAGATGATTATGCATGGCAGT\nCTGGCACTAATGCATCTGTTTTCTGGCAACATGGGCAAGCATACCCAAGATTTTCTCTACCCTTTTTGAGTGTAGCTTCA\nGCTTACTACATGTTTTATGATGGATATAATGAACAGGGCCAAAATTATGGTACGGTAAGTACAAACAACATGGGATCATT\nATGCTCTAGGATAGTAACAGAGAAACACATTCACAGTATGCATATCATGACAAGAATCTATCATAAAGCTAAACACGTCA\nAAGCATGGTGTCCGCGCCCACCCAGAGCACTTGAATATACTCGCGCTCACCGTACTAATTTCAAAGTTGAAGACAGAGAC\nATTAAAACAGGAATCACATCCAGAGCAATTATTACAACAGCTGGTCCTAGTGATATGTATGTTCATGTTGGTAATCTTAT\nCTATAGAAATTTACATCTCTTCAATTCTGAAATGCATGAATCTATACTGGTATCTTATTCATCAGATTTAATCATTTACC\nGAACAAACACCATAGGTGATGATTATATCCCCTCTTGTGATTGCACCCAGGCTACATATTACTGTAAACATAAAAATAGA\nTATTTCCCAATCACAGTGACAAGCCATGACTGGTATGAAATACAGGAAAGTGAATACTACCCCAAGCATATACAATACAA\nTTTACTAATTGGTGAGGGCCCTTGTGAACCAGGTGATTGTGGTGGGAAATTGTTATGTAAACATGGTGTTATTGGTATAG\nTAACAGCTGGTGGTGATAATCATGTGGCTTTTATTGATCTTAGACACTTTCACTGTGCTGAGGAGCAAGGAATTACAGAT\nTACATACACATGTTAGGTGAAGCATTTGGAAATGGATTTGTAGATAGTGTAAAAGAACATATACATGCCATTAATCCAGT\nAGGAAATGTTAGTAAAAAGATCATCAAATGGATGCTGAGGATAATATCAGCAATGGTTATAATAATAAGGAATTCCTCTG\nATCCACAAACTATATTGGCAACACTCACGCTAATTGGATGTTCTGGTTCACCATGGAGATTTTTAAAGGAGAAATTTTGC\nAAATGGACACAACTCAATTATATACATAAAGAATCAGACTCATGGTTGAAAAAATTTACTGAAGCATGCAATGCAGCCAG\nAGGACTTGAGTGGATAGGGAATAAAATATCTAAATTCATTGAATGGATGAAATCAATGCTCCCACAAGCACAACTTAAGG\nTCAAGTACTTAAATGAACTCAAAAAATTGAGCTTGTATGAAAAACAAGTTGAAAGTCTTAGAGTAGCAGATGTAAGAACA\nCAAGAAAAGATTAAAATGGAAATTGATACCCTACATGACTTATCATGCAAATTTTTACCATTGTATGCAGGTGAAGCAAA\nAAGGATAAAGACGTTACATATTAAGTGTGATAACATTATCAAACAAAAGAAAAGGTGTGAACCAGTGGCTATAGTTATCC\nACGGGCCACCTGGTGCTGGAAAATCAATAACAACAAATTTTTTAGCTAGGATGATAACTAATGATAGTGATATATACTCT\nTTACCCCCAGATCCAAAATATTTTGATGGCTACGATCAACAAAGTGTGGTGATAATGGATGATATCATGCAAAATCCAGC\nTGGGGATGACATGACTCTATTCTGTCAAATGGTTTCCAGTGTCACGTTCATACCACCAATGGCTGATTTACCAGATAAGG\nGCAAGGCCTTTGACTCTAGGTTTGTATTATGCAGCACAAATCACTCTCTTTTAGCACCGCCTACAATAACCTCACTGCCT\nGCTATGAACAGAAGATTCTTTTTAGACTTAGACATAATAGTACATGATAATTTCAAGGATTCACAGGGTAAACTTAATGT\nAGCAGCAGCCTTCCAACCATGTAATGTGGACAATAAAATTGGGAATGCTCGTTGTTGCCCATTTGTGTGTGGAAAGGCTT\nTTTCTTTCAAAGATCGCAATTCTTGCAATAAATACACCCTAGCACAAGTGTACAACATAATGCTTGAAGAAGACAAACGG\nAGGAGACAAGTGGTTGACGTCATGTCGGCCATATTCCAAGGACCAATTGACATGAAAAACCCACCACCACCTGCAATTAC\nTGATTTACTCCAGTCAGTTAGGACTCCTGAGGTTATCAAGTATTGTGAAGTTAATAGATGGATAATTCCAGCAGAATGTA\nAAATAGAGAAGGAATTAAATTTAGCCAATACAATCATAACAATCATTGCCAATGTTATTAGTATAGCAGGTATTATATAC\nGTCATCTACAAACTCTTCTGTACACTACAAGGACCATATTCAGGGGAACCTAAACCTAAAACTAAAGTCCCAGAAAGACG\nTGTTGTGGCACAGGGGCCAGAGGAAGAATTTGGAATGTCTTTGATTAAGCACAACTCATGTGTGATTACAACAGAGAATG\nGAAAGTTTACAGGCCTTGGGATATATGACAAGTTTGTGGTTGTACCAACACATGCAGATCCTGGGAAAGAAATTCAGGTT\nGACGGCATAACTACAAAAGTTGCTGACTCATATGATTTATATAATAAAGATGGAATAAAGTTAGAAATAACAGTCTTAAA\nATTAGATAGGAATGAAAAGTTCAGAGACATTAGAAAATACATACCAAATAATGAGGATGACTACCCTGACTGCAACTTAG\nCCTTGTTAGCAAATCAACCTGAACCCACTATAATCAATGTTGGAGATGTTATATCCTATGGCAACATACTGCTTAGTGGT\nAACCAGACAGCTAGAATGCTCAAATACAGCTATCCAACTAAATCTGGGTACTGTGGGGGTGTTTTGTATAAAATTGGGCA\nAGTGCTTGGAATACACGTAGGAGGAAATGGTAGAGATGGATTTTCAGCTATGTTGCTTAGATCTTACTTTACTGATGTGC\nAAGGCCAAATAATCTCATCAAAGAAAACTAGTGAATGTAATCTTCCCAGTATACATAATCCATCCAAAACAAAATTGCAG\nCCCAGTGTCTTCTATGATGTTTTCCCTGGTTCAAAAGAACCAGCTGTGTTGTCTGAGAAAGATACACGGCTTCAGGTTGA\nCTTTAATGAAGCATTATTTTCTAAATACAAAGGAAACACAAACTGCTTTATGAATGATCACATAAGGATTGCATCTTCAC\nACTATGCAGCTCAATTAATCACTTTAGATATTGACCCAAGTCCTATCACCCTTGAAGATAGTGTTTTTGGTACTGATGGA\nTTAGAGGCTCTTGACCTAAATACTAGTGCAGGATTTCCTTACATTACAATGGGGATAAAGAAGAGAGATTTAATAAATAA\nCAAAACCAAAGACATAAGTAAACTTAGGGAAGCAATTGACAAGTATGGAGTTGACTTGCCTATGGTTACTTTCTTAAAAG\nATGAACTTAGAAAACATGAGAAGATAATCAAAGGCAAAACTAGAGTTATTGAAGCTAGTAGTGTGAATGATACTTTGCTG\nTTCAGAACAACTTTTGGGAATCTTTTTTCAAAATTTCATCTAAATCCTGGAATTATCACTGGATCAGCAGTCGGGTGTGA\nCCCAGAAACTTTCTGGTCAAAGATACCAGCAATGTTAGATGATAAGTGTATTATGGCTTTTGATTATACAAATTATGATG\nGTAGTATACACCCTATTTGGTTTGAAGCCCTTAAACAAGTATTGATGGATTTATCCTTTGATCCAATGTTAATAGATAGA\nTTATGCAAATCCAAACACATCTTTAGAAACACATACTATGAGGTTGAAGGAGGTGTTCCATCTGGATGTTCAGGTACTAG\nTATTTTCAACACTATGATTAATAATATTATTATAAGGACCTTAGTGTTAGATGCATATAAAAATATAGATTTAGACAAAC\nTTAAGATAATTGCCTATGGTGATGATGTTATATTTTCATACACACATGAATTGGACATGGAAGCTATAGCAATAGAGGGT\nATTAAATATGGTCTAACCATAACCCCTGCTGACAAATCTACCACTTTTGTAAAGTTAAATTACAATAATGTCACCTTTTT\nGAAAAGAGGATTCAAACAAGATGAGAAATACAACTTCTTGATACACCCCACCTTTCCTGAGAGTGAAATATTTGAATCTA\nTCAGGTGGACAAAGAAACCTTCACAGATGCACGAGCACGTACTATCTCTGTGTCGCTTAATGTGGCACAATGGGCGTGAT\nGCGTATGAAAAGTTTGTGGAGAAGATACGCAGTGTGAGCGCTGGTCGCGCACTGTACATCCCTCCATATAACTTGCTTTT\nGCATGAGTGGTATGAAAAATTTTAAACTGATATAGAAATATTAAACTGTTAGTTTATTAGTTTTAC\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_DQ473498.1_Rhinovirus_A10.fa", "content": ">RVA_DQ473498.1_Rhinovirus_A10 (7137 bp)\nTTAAAACTGGATCCAGATTGTTCCCATCTGGATTTCCCACGTGGAGTTGTACACTATTATTCCGGTAATTTTGTACGCCA\nGTTTTATGTACCCCCCCCTGTAACTTAGAAGTTTTGAACAAGGACCAATAGGCAGTAACCACCCAGGTTGCTAAAGGTCA\nAGCACTTCTGTTTCCCCGGTCAAAGTTGATATGCTCCAACAGGGCAAAAACAACTGAGATCGTTACCCGCAAGGTGCCTA\nCGCAAAGCCTAGTAACCCCTTGAACGATGTGTGGTTGGTCGTTCGGCTGTACCCCACAGTAGACCTGGCAGATGAGGCTA\nGATGTTCCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGCGCACTCTCTGAGTGCGAAGCCATACATTTGACAA\nGGTGTGAAGAGCCCCGTGTGCTCACCTTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAACCCTGCAGCTAGTACATG\nCAATCCAGCATGCAGCTAGTCGTAACGAGCAATTGCGGGACGGGACCAACTACTTTGGGTGTCCGTGTTTCACTTTTTCC\nTTTTATATTTGCTTATGGTGACAATATATAGATTTATATATTGTCACCATGGGCGCTCAAGTATCCAGACAGAATGTTGG\nTACTCACTCAACACAAAATGCAGTTTCAAATGGATCTAGTTTAAATTATTTTAACATCAACTATTTCAAAGATGCAGCAT\nCTAGCGGTGCTTCCAAATTGGAATTTTCACAAGACCCTAGTAAATTTACAGACCCTGTTAAAGATGTCCTTGAGAAAGGA\nATTCCAACATTACAATCTCCAACTGTAGAAGCATGTGGTTACTCAGACAGAATCATTCAGATCACCAGAGGTGATTCAAC\nAATAACTTCACAAGATGTTGCCAATGCAGTGGTGGGTTATGGCGTGTGGCCTCACTATTTAAGTGCAACGGATGCCACTG\nCTATTGACAAACCTACTCAGCCTGACACTTCTTCAAATAGATTTTACACTCTTGAAAGCAAAGTTTGGACGAGCACATCT\nCAGGGTTGGTGGTGGAAGTTACCAGATGCACTTAAGGACATGGGTATTTTTGGAGAAAATATGTTTTATCACTATCTTGG\nCAGGAGTGGATACACAGTACATGTCCAATGCAATGCTAGCAAATTTCATCAGGGGACCTTACTAGTAGTCATGATACCAG\nAACATCAATTGGCAAGTGCACATACTGGTAATGTAACAGCTGGTTATAATTTCACTCATCCAGGAGAAAAGGGTAGGACT\nGTTGGAGATCGTCGTGACCACCATGACAAACAACCTAGTGATGACAATTGGTTGAATTTTGATGGTACTTCACTGGGTAA\nTGCACTAATATTTCCCCATCAATTTATTAATTTGAGGAGTAATAATTCAGCAACTATAATAGTACCTTATGTCAATGCAG\nTCCCAATGGATTCAATGCTTAGGCACAATAATTGGAGTTTAGTAATAATTCCTATTAGTCCTTTAAAGTCAGACCCTAGT\nGCTAGTGCTTTAGTTCCTATAACTATTTCTATCAGTCCAATGTTTGCTGAATTTTCTGGGGCACGTGCTAAAACTGCCGC\nAGCCAATCAAGGACTACCAGTGTATGTTACACCTGGTTCTGGTCAATTTATGACAACTGATGATCTGCAATCACCATCCG\nCATTACCGTGGTATCATCCAACCAAAGAAATCCTAATACCAGGAGAGGTCAAAAATCTAATAGAAATGTGCCAGGTAGAT\nTCACTGATTCCAATCAACAATACCACTGCAAATTTAAGGAAAGTAAATATGTATACAATACAATTGGCAAACCAAACTAA\nTATGGCTGAAGAAATCTTTGCAATTAAGGTGGACATTGCATCACAACCTCTTTCAAATACTATAATTGGAGAAATTGCTA\nGTTACTTCACACATTGGACTGGAAGCCTGCGGTTCAGTTTTATGTTCTGTGGCACTGCAAATACTACCCTTAAATTGTTA\nTTAGCATATACACCACCAGGCATAAAGAAACCAACAAACAGGAAGCAGGCAATGCTTGGTACACACATTGTTTGGGATAT\nTGGGTTACAATCAACCGTATCTCTGGTTGTTCCATGGGTCAGTGCTAGCCATTTCAGGTACACCACTCCAGATACATATT\nCAGCAGCTGGATACATAACATGCTGGTATCAAACCAACTTTGTGTTCCCACCAAACACACCGAGCACTGCAGATATGTTG\nTGTTTTGTGTCAGCATGTAAAGACTTTTGCCTGCGTATGGCTAGAGATACAAATATGCACATACAAAGTGATGCCATTAC\nACAAAATCCAGTTGAAAATTACATTGATAATGTACTTAATGAAGTCCTAGTGGTACCCAACATCAGAGAAAGTCATCCAA\nGCACCTCTAACTCTGCCCCAATTCTCGATGCAGCTGAGACTGGTCATACCAGTAGTGTACAACCAGAAGATACGGTTGAA\nACACGATATGTGCAAACATCCCAGACGAGAGATGAAATGAGTATTGAAAGTTTTCTTGGCAGGTCAGGTTGTATACACAC\nCTCAACAATAACTGTTAATAATACAAGACCCTACAATGAACACACTTTTGACACATGGCAAATAACTCTACAAGAAATGG\nCCCAAATTAGAAGGAAATTTGAAATGTTTACATATGTTAGATTTGACTCAGAAGTCACTTTAGTACCTTGCATCGCAGGC\nAAGGGCGATGACATAGGTCACATAGTTATGCAATATATGTATGTGCCACCTGGGGCTCCAGTACCAACTAAGAGAGATGA\nTTTTGCTTGGCAGTCGGGAACAAATGCATCAGTCTTCTGGCAACATGGACAACCTTTCCCTAGATTTTCTTTACCCTTCT\nTAAGCATTGCATCTGCTTACTACATGTTCTATGATGGTTATGATGGTGATACACATGACTCACGTTATGGCACAACAGTG\nATAAATCACATGGGCACTTTGTGCATGCGAATAGTCACAAACCAGCAAGCACATGAGGTGGAAATTACCACCAGTGTTTA\nTCACAAAGCCAAGCATGTCAAAGCATGGTGTCCAAGACCACCCAGAGCTGTACCATATACACATGCCCATTCCACAAATT\nACAAACCACATGGCAAAGAATTACAAATATTTATTAGGTCTAGAGATGATCCCAAAGTAGTAACTGCTGGACCAAGTGAT\nATGTATGTCCATGTTGGTAATTTAATTTATAGAAACTTACACCTTTTCAATTCAGAAATGCATGATTCAATTCTAGTATC\nATACTCTTCAGATTTAGTCATTTACCGAACAAACACTATAGGTAATGACTACATCCCCACTTGTGATTGCACTGATGCCA\nCTTATTATTGTAAACATAAAGACAGGTACTACCCCATCAAAGTTACTAGTCACGACTGGTATGAGATTCAGGAAAGTGAA\nTATTACCCCAAGCATATTCAATACAATCTCTTAATTGGAGAGGGACCATGTGAGCCTGGTGACTGTGGAGGAAAGTTACT\nCTGTAAACATGGAGTAATTGGAATAATTACTGCTGGTGGAGAGGGGCATGTGGCATTTATAGATCTCAGGCAATTTCATT\nGTGCGGATGAACAAGGAATAACTGACTACATCCACATGTTGGGTGAAGCTTTTGGAACAGGTTTTGTGGACAGTGTCAAA\nGAGCAAATAAATGCCATAAACCCAATAAATAACATAAGTAAGAAAATAATAAAATGGCTTCTTAGAATTATATCTGCAAT\nGGTAATAATTATTAGAAATTCATCTGATCCACAGACAATTATAGCAACTTTAACTCTAATTGGATGTTCAGGCTCACCAT\nGGAGATTTCTTAAGGAAAAGTTTTGTAAATGGACCCAACTTACTTATATTCATAAAGAATCTGACTCATGGCTCAAAAAA\nTTCACGGAAATGTGTAATGCAGCTAGAGGTTTGGAGTGGATCGGGAATAAAATATCTAAATTTATTGAGTGGATGAAGTC\nCATGTTACCCCAAGCTCAGCTTAAAGTTAAGTATCTGAGTGAACTTAAAAAACTAAGCTTCCTGGAGAAACAAATGGAAC\nACCTCAGAGTTGCTGATTCAAAAACCCAAGAGAAGATTAAACATGAGGTGGATACTCTTCATGACCTTTCATGTAAATTT\nCTACCACTCTATGCTAGTGAGGCTAAAAGAATTAAGATTTTACACAATAAGTGTAATACAATCATCAAGCAAAGGAAAAG\nATGTGAGCCAGTAGCAGTTGTGATACATGGTGAACCCGGGACTGGTAAATCAATGACCACAAACTTTCTAGCTAGGATGA\nTAACAAGTGAGAGTGATATCTATTCTCTACCACCTGATCCCAAATACTTTGATGGATATGATCAACAGAGTGTAGTTATT\nATGGATGATGTGATGCAGAACCCAAGTGGAGAAGACATGACCTTGTTTTGCCAAATGGTATCAAGTGTTACATTCATACC\nACCCATGGCAGATCTGCCAGATAAGGGTAAGCCATTTGATTCTAGATTTGTGTTATGTAGTACCAATCATAATCTATTAG\nCACCTCCAACAATAACATCTTTACCAGCCATGAATAGGAGATTTTTCTTTGATCTAGATATCATAGTGTGTGAAAAGTAC\nAAAGACCCACAAGGCAAATTAAATGTGACTGCTGCTTTCCGACCATGTGATGTGGATGCAAAAATTGGCAATGCACGCTG\nTTGTCCATTCATTTGTGGCAAAGCAGTGATGTTCAGAGACCGCAATACATGCCAAACTTACACACTAGCACAAGTGTACA\nATCGAATACTTGATGAAGATAAGCGGCGTAGACAGGTGATCGATGTCATGGCCGCAATTTTTCAGGGACCCATCACTCTT\nGAGGGACCACCACCAGCTGCAATCAGCGACTTATTGCAGTCAGTCAGAACTCCTGAAGTAATTAAATACTGTGAAGGTAA\nCAAATGGATCATACCAGCGGAATGTAAGGTTGAGAGGGATCTTAATATAGCAAACACCATCATCACAATTATTGCCAATA\nTCATTAGTATTTCTGGAATTATTTATGTTATCTACAAGCTATTCTGTACATTGCAGGGACCATATTCAGGGGAACCTAAA\nCCAAAAACCAAGATACCAGAAAGAAGAGTGGTGGCTCAGGGTCCAGAAGAGGAGTTTGGAAGATCACTCATTAAGCACAA\nCTCATGTATTGTGACAACACAAAATGGTAAATTTACAGGCTTAGGAATTTATGACAGAATGTTAATTTTACCAACACATG\nCAGACCCTGGCCGTGAAGTGCAAATAGATGGTATTACAACCAAGGTGGAAGATTCTTTTGACCTGTACAACAAGGATGGG\nGTTAAACTAGAGATTACTGTGCTTAAACTAAAGAGAAATGAAAAATTCAAAGATATTAGGAAATACATACCTGAAAATGA\nAGATGACTATCCAGATTGTAATCTAGCTCTTTCTGCTAATCAACCAGAAACTACTATAATCAATGTAGGGGATGTGGTAT\nCCTATGGAAATATTCTCCTTAGTGGCACTCAAACAGCTAGAATGCTCAAATATAATTACCCAACAAAATCAGGTTATTGT\nGGTGGTATCTTGTATAAAATTGGACAAGTCTTAGGAATCCATGTTGGAGGTAATGGGAGGGATGGATTCGCTGCCATGCT\nATTGAGATCTTACTTTTCTGAAACACAGGGTGAAATAATAATTTCAAAATCCACAAGCGAATGTGGGTTACCCAGTATCC\nACACACCAAGCAAAACCAAACTTCAGCCTAGTGTATTCTTTGATGTATTTCCAGGTACTAAAGAACCAGCTGTCCTCTCA\nAGTAACGATCCTAGATTAGAGGTTGATTTTAATAAAGCTTTGTTTTCTAAGTATAAAGGAAATAATGAGTGTGTTATAAA\nTGATCATGTTAAAGTAGCTGTCTCTCACTACTCAGCCCAACTCATGACCTTAGATATTAATCCAGAGCCTATCTCACTTG\nAGGACAGTGTCTTTGGAACAGAAGGCTTGGAAGCTCTTGATCTTAACACTAGTGCAGGATTTCCATACGTGTCGATGGGC\nATTAAAAAGAAAGATCTAATTAACAAGCAAACAAAGGATGTGACTAAACTTAAAATGGCCCTAGACAAGTATGGTGTTGA\nCTTACCAATGGTTACCTTTCTTAAAGATGAGCTTAGGAAAAGAGAGAAAATCACCGCCGGAAAGACCCGCGTGATTGAAG\nCTAGTAGTGTGAATGACACTGTACTGTTCAGAACAACTTTTGGTAATCTCTTCTCAAAATTTCACTTAAATCCAGGCATT\nGTCACAGGTTCTGCTGTAGGCTGTGATCCTGAAACATTCTGGTCAAAAATACCTGTTATGCTAGATGGAGAATGTATAAT\nGGCATTTGATTACACAAATTATGATGGAAGTATACATCCTATGTGGTTTCAAGCTCTTAAAGAAGTTTTGTCTAATTTAT\nCTTTTGAGGCTAGTTTAATAGATAGACTGTGCAAATCCAAGCACATCTTCAAGAATATGTATTATGAAGTGGAAGGTGGA\nGTTCCATCAGGTTGTTCTGGAACCAGTATATTTAATACAATGATAAATAATATCATTATCAGAACATTAGTGCTAGATGC\nTTATAAGAATATTGACTTGGATAAACTTAAAATTATAGCTTATGGAGATGATGTAATTTTTTCTTACAAATATCAACTTG\nACATGGAAGCAATTGCCAAGGAGGGTACCAAGTATGGATTAACAATAACACCAGCTGACAAATCTGATACTTTCAAACAA\nCTTAATTATGGCAATGTTACATTCCTGAAAAGAGGATTTAAACAAGATGAGAAATATCAGTTTTTGATACACCCAACATT\nTCCAGTTGAAGAAATTCAAGAGTCTATTCGATGGACAAAGAAACCATCCCAAATGCAGGAACATGTCCTGTCGTTGTGTC\nATTTAATGTGGCATAATGGCAGGAGTGTTTACAAGCAGTTTGAGGAGCGGATACGCAGTGTTAGCGCTGGTCGTGCACTG\nTACATTCCTCCTTACGATTTGCTGCTGCATGAGTGGTATGAAAAGTTTTAAATTGTTTAGATATAAAAATATTAAACAAT\nTAGTTTTTTAGTTTTAT\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_DQ473499.1_Human_rhinovirus_A44.fa", "content": ">RVA_DQ473499.1_Human_rhinovirus_A44 (7123 bp)\nTTAAAACTGGGTCCAGGTTGTTCCCACCTGGATCTCCTACATGGAGTTGTACTCTATTATCCCGGTAATCTTGTACGCCA\nGTTTTATATCCCTTCCCTTTTTGTAACTTAGAAGTTAAACACACAGACCAATAGGTGGTGGCTATCCAAGTCATTAATGG\nTCAAGCACTTCTGTTTCCCCGGTTTAGATTGATACGCTCCACCAGGGCGAAAACAATTTAAATCGTTATCCGCAAAATGA\nCTACGCAAAGCCTAGTAATATCTTGAAGGACTTATGGTTGGTCGCTCCACTAAACCCCATAGTAGACCTGGCAGATGAGG\nCTAGAAATACCCCACTGGAGACAGTGTTCTAGCCTGCGTGGCTGCCTGCACACCCTATGGGTGTGAAGCCATACTTTCGA\nCAAGGTGTGAAGAGCCCCGTGTGCTCATTTTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAACCCTGCAGCTAGTGC\nATGCAATCCAGCATGTTGCTAGTCGTAACGAGCAATTGCGGGATGGGACCAACTACTTTGGGTGTCCGTGTTTCACTTTT\nTCCTTTTATTTGCTTATGGTGACAATATATATAGTACATATATATTGGCATCATGGGCGCTCAAGTATCCAGACAGAACG\nTTGGAACTCATTCCACCCAAAATTCAGTTTCAAATGGATCGAGTTTGAATTATTTTAATATAAATTACTTTAAGGATGCT\nGCATCAAGTGGAGCTTCAAAACTTGAATTTTCTCAAGATCCTAGCAAATTCACTGATCCAGTGAAAGATGTTTTAGAAAA\nAGGTATTCCAACACTACAATCTCCTACAGTAGAGGCATGTGGCTATTCAGATAGGATAATGCAAATTACAAGAGGTGACT\nCCACAATAACATCACAAGATGTGGCCAATGCAGTTATAGGTTATGGGGTCTGGCCACACTATCTGAGTGCTGAGGATGCT\nACTGCTATTGACAAACCTACCCAGCCAGACACCTCGTCAAATAGATTTTATACCTTAGAGAGTAAGACATGGGATAGGCA\nATCTAAAGGATGGTGGTGGAAATTGCCAGATGCACTTAAAGACATGGGCATATTTGGAGAAAACATGTATTACCATTACC\nTTGGCAGAAGTGGTTATACAGTACATGTCCAATGCAATGCTAGTAAGTTTCATCAAGGGACATTATTGGTAGTGATGATA\nCTTGAACACCAACTAGCAAGTGTAGGTACTGAGAAGGTCGGGCCTGGATATAATTTCACACATCCTGGTGAGGCAGGTAG\nACAGATTGGCAATGTGAGTGATCGGACTTCAAAGCATCCAAGTGATGACAATTGGCTTAACTTTGATGGCACCTTACTGG\nGTAATGTTCTTATATTCCCACACCAATTTATCAATTTAAGGAGCAATAACTCTGCAACAATAATAGTTCCTTATGTAAAT\nGCTGTTCCAATGGACTCAATGTTAAGACATAACAATTGGAGTTTAGTGATAATCCCAATCAGTGAATTACAAACAGAGAA\nTGCCACTAATCTCACGGTCCCTATCACTGTATCAATTAGCCCAATGTTTGCTGAATTTTCTGGAGCACGTGCAAGGCCAG\nCAAGAGCTGCTGCACAGGGATTACCTATATATATGACACCGGGTTCAGGCCAGTTCATGACAACTGACGATTTCCAATCA\nCCTTCAGCTTTACCGTGGTATCACCCAACAAAAGAAATTTTAATTCCAGGAGAAGTAAAAAATTTAATGGAAATATGCCA\nAGTTGACACATTAATCCCTATCAACAATGTGAATAATAATTTAAGAAAGGTAAATCTTTACACTGTACAATTAACTAGCC\nAAACAACACCAGCTCAGCAGGTTTTTGCCATTAAAGTAGATATTGCTTCACAACCTTTAGCAAATACTATGCTTGGACAA\nATTGCCAGTTACTTCACACACTGGACTGGAAGCTTGCGATTTAGCTTTATGTTCTGTGGGACAGCAAACACCACTCTCAA\nGCTACTTATAGCATATACACCACCTGGTATTGGGAAGCCAGAGAACAGAAAACAGGCGATGCTTGGTACACATATAGTTT\nGGGATGTTGGGTTGCAATCAACAGTATCTTTAGTTGTCCCGTGGGTTAGTGCTAGTCACTTTAGATACACCTCTAGCGAT\nGAACGTTCAGCAGCTGGATACATAACATGTTGGTATCAGACACAACTTGTCTTCCCTCCAAACACTCCAAATACAGCTGA\nTATGTTATGTTTTGTATCAGCTTGTAAGGATTTTTGCTTACGTATGGCTAGAGACACAGACATGCACACTCACAATGAAA\nTTATCACACAGAACCCAGTTGAAAATTATGTGGATGAAGTACTTAATGAAGTCTTAGTTGTGCCTAATATCAGAGAGAGC\nCACCCAAGCACATCTAACTCTGCTCCAATTTTGGATGCTGCTGAAACTGGACATACTAGTAATGTACAACCAGAAGATAC\nCATTGAGACTCGATATGTACAAACCTCACAAACTAGAGATGAAATGAGCATTGAAAGTTTTCTTGGCAGATCAGGGTGTA\nTACATGTTTCAACAATAAAGACAAATCAGGCACACAATACCAAGTTTGATAAATGGAATATCAACTTACAAGAAATGGCT\nCAAATTAGACGCAAATTTGAAATGTTCACATATGTGAGATTTGATTCGGAAATAACTCTAGTTCCATGCATTGCAGGACA\nTGGTGATGATATAGGCCACATAGTTATGCAGTACATGTATGTACTACCTGGAGCTCCAGTACCAGATGACAGAAACCACT\nTTGCATGGCAATCGGGGACTAATGCATCAATATTCTGGCAACATGGTCAACCTTTCCCAAGATTTTCATTGCCATTTCTA\nAGTGTTGCATCTGCCTATTACATGTTTTATGACGGTTATAATGGAGGTGATCATACAGCAACTTATGGCACCACAGTGGT\nTAACCGGATGGGGACGCTTTGCGTCAGGATCGTTACGGGCAAACAGGCTCATGATGTCCAAGTTACAACAAGCATTTATC\nACAAAGCTAAACATGTAAAAGCATGGTGCCCTAGACCACCAAGGGTTGTCCCATACAAGTATGTTGGCCTAACTAATTAC\nACACTTAAAGAAACAGATACAGTTGTGGAACCTAGACACAGCATAATGACAGCTGGACCAAGCGACATGTATGTCCATGC\nTGGTAACTTGATATATAGAAACCTTCATCTTTGCAACTCAGAAATGCATGACTCAATCCTAATATCATATTCATCAGATT\nTAGTCATTTATCGAACAAACACCACAGGTAATGACTATATCCCCACTTGTGACTGCACTGATGCTACTTATTACTGTAAA\nCATAAGGATAGGTACTATCCTATCAAAGTCACTAGTCATGATTGGTATGAGATACAAGAAAGTGAATACTATCCAAAACA\nCATTCAGTATAATCTTTTAATTGGTGAAGGACCATGTGAACCAGGAGATTGTGGAGGAAAATTATTATGTAAACATGGAG\nTAATTGGGATAATCACTGCAGGTGGGGAGGGTCATGTAGCATTCATCGATCTCAGGCAATTCCATTGTGCAGATGAACAA\nGGAATAACTGATTACATCCACATGTTGGGTGAGGCTTTTGGAACAGGTTTTGTTGATAGTGTCAAGGAACAAATAAATGC\nCATTAACCCAATTAACAATATTAGCAAGAAAATAATTAAATGGCTTCTTAGAATAATTTCTGCAATGGTTATAATAATCA\nGGAACTCTTCTGATCCACAGACAATCATAGCCACATTAACTTTAATTGGATGCTCAGGCTCCCCTTGGAGATTTCTTAAA\nGAGAAATTTTGTAAATGGACCCAATTAAACTATATACACAAGGAGTCTGACTCATGGCTTAAAAAATTTACTGAGATGTG\nCAATGCAGCTAGAGGTTTAGAATGGATTGGGAATAAAATATCAAAATTTATTGAATGGATGAAATCTATGCTTCCTCAAG\nCTCAGCTTAAGGTGAAATACTTAAGTGAGCTTAAAAAATTAAGTTTCCTTGAGAAGCAGATAGAACACCTAAGAGTAGCT\nGATACTCAAACTCAGGAAAAGATCAAGCATGAAATTGACACTCTTCATGATCTTTCTTGCAAATTCCTCCCACTTTATGC\nTAGTGAAGCAAAAAGAATCAAGATATTGCACAATAAGTGTAGTACAATAATTAAACAAAGGAAAAGATGTGAGCCAGTTG\nCTGTTGTTATACATGGTGATCCTGGCACTGGTAAATCTATGACTACAAGTTTCCTTGCTAGAATGATAACAAATGAAAGT\nGATATATACTCCTTGCCACCTGACCCCAAATATTTTGATGGATATGACCAGCAAAGTGTGGTTATAATGGATGATGTTAT\nGCAAAATCCAAGTGGAGATGATATGACTTTGTTTTGTCAGATGGTATCCAGTGTTACCTTTATACCTCCCATGGCTGATT\nTACCCGATAAAGGCAAACCCTTTGACTCACGATTTGTACTATGTAGCACTAATCATAATATGCTAGCACCACCTACAATC\nACTTCATTGCCAGCTATGAATAGAAGATTCTTTTTTGATCTAGATATTGTAGTGTGTGATAAGTACAAAGATTCACAAGG\nAAAGCTTAATGTATCAGCTGCCTTCCAACCCTGTGATGTGGATGTAAAGATTGGAAATGCCCGCTGTTGTCCATTTATCT\nGTGGCAAAGCTGTCAATTTTAGGGATCGCAATACTTGTCAGACTTATACTTTAGCACAAGTATACAATCAAATACTTGCT\nGAAGATAAAAGGCGTAGACAGGTTGTTGATGTTATGGCAGCAATTTTCCAGGGTCCTATTACTCTTGAAGGGCCTCCACC\nTGCAGCAATAAATGATCTATTGAAATCAGTTAGAACTCCAGAGGTGATAAAGTATTGTGAGGGAAATAAATGGATAATAC\nCAGCTGAGTGTAAAATTGAAAGAGATCTTAATTTAGCAAACACCATCATCACAATTATTGCTAATATTATTAGTATTTCT\nGGAATCATTTATGTAATATATAAACTTTTCTGTACACTACAAGGACCATACTCAGGTGAACCAAAACCAAAAACAAAGAT\nACCAGAAAGGAGAGTTGTAGCCCAAGGACCGGAAGAAGAATTTGGTAGATCACTTATTAAACATAATTCATGCGTTGTGT\nCGACTCAGAATGGTAAATTTACAGGCTTAGGAATTTATGATAGAACACTAATCTTACCAACACATGCAGATCCTGGTAGT\nGAGGTACAAATTGATGGAATTGCAACTAAAGTAGAGGATTCTTTTGATTTATATAATAAAGATGGGGTTAAGTTGGAGAT\nCACAGTCTTGAAACTCAAGAGGAATGAGAAATTCAAAGACATTAGAAAATACATACCAGAAAATGAAGATGACTATCCAG\nATTGCAACTTGGCCCTGTCTGCCAACCAACCAGAGACTACCATAATTAATGTAGGGGATGTAGTGTCTTATGGTAACATC\nTTACTGAGTGGTAATCAGACTGCTAGAATGCTTAAATATAATTACCCAACAAAATCAGGTTACTGTGGTGGTATTTTGTA\nTAAGATTGGCCAAGTTCTTGGTATTCACGTGGGTGGAAATGGGAAAGATGGGTTTGCTGCCATGTTATTAAGATCATACT\nTTTCTGAAACACAGGGACAGATAATTACTTCCAAATCTACAAGCGAATGTGGTGTACCTAGCATTCACACGCCAAGCAAA\nACTAAGTTGCAACCCAGTGTCTTTTATGATGTCTTTCCAGGTAATAAAGAACCGGCTGTCCTTTCCAGTAATGATCCTAG\nGTTGAAAGTAGATTTTAAGGAAGCTTTATTTTCAAAGTATAAAGGTAATAACCAGTGTATTATGAATGATCATATCAAGG\nTGGCCATCTCACATTATTCAGCACAACTGATGACATTAGATATTGACCCCAAACCTATATCTTTGGAAGAAAGTGTCTTT\nGGTATAGAGGGCTTAGAAGCTTTAGACCTTAATACTAGTGCAGGGTTCCCTTATATATCTATGGGTATCAAGAAAAGAGA\nTTTAATCAACAAGCAAACTAAGGATGTGACAAAACTCAAAATGGCATTAGATAAGTATGGTGTTGATCTACCTATGGTTA\nCTTTTCTCAAAGATGAACTCAGGAAGAGGGAAAAGATTTGTGATGGAAAGACTCGTGTGATTGAAGCCAGTAGCGTGAAT\nGACACTATACTGTTCAGGACAACTTTTGGCAATCTCTTCTCAAAATTTCATTTAAATCCAGGTGTTGTTACTGGTTCTGC\nAGTGGGATGTGATCCAGAAACATTTTGGTCAAAAATACCAGTGATGTTAGATGGGGAATGTATAATGGCTTTTGATTACA\nCGAATTATGATGGAAGTATACACCCTATCTGGTTCCAAGCTTTAAAGGAAGTGTTGGCAAACCTATCATTTGAACCAGCT\nTTAATAGATAGACTGTGTAGATCTAAGCATATTTTCAAAAATACATATTATGAGGTTGAAGGAGGAATCCCATCAGGTTG\nCTCTGGAACTAGCATTTTTAACACTATGATTAATAATGTGATCATTAGAACCCTAGTTTTAGATGCTTATAAAAACATTG\nATTTGGATAAATTAAAGATTCTAGCCTATGGGGATGATGTGATCTTTTCTTATAAATATCAGCTTGACATGGAGGCAATT\nGCCAAAGAGGGTACAAAATATGGGTTAACAATAACGCCCGCTGATAAATCTGATTGTTTTAAACAACTTGATTACAACAA\nTGTGACATTTTTGAAAAGAGGGTTTAGACAGGATGAAAAACATAATTTTCTAATACACCCTACATTTCCAGTAGAAGAGA\nTCCAAGAGTCTATCCGATGGACCAAAAAACCATCTCAGATGCAGGAGCATGTGTTATCACTGTGTCATTTAATGTGGCAT\nGATGGTAGAGATGTGTACAAGCAGTTTGTGGAACGGATACGTAGTGTCAGCGCTGGTCGTGCACTATATATTCCTCCTTA\nTGACTTGCTTTTGCATGAGTGGTATGAAAAATTTTAAATTGTTTAGATATAAAAATATTAAACAGTTAGTTTTTTAGTTT\nTAC\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_DQ473501.1_Rhinovirus_A34.fa", "content": ">RVA_DQ473501.1_Rhinovirus_A34 (7119 bp)\nTTAAAACTGGGTCCAGGTTGTTCCCACCTGGACTTCCCACGTGGAGTTGTGCACTGTTATTCCGGTAACTTTACACGCCA\nGTTTTATCTCCCTTCCCAAATGTAACTTAGAAGATGTACACAGCGACCAATAGGTGGCAACTAGCCAAGTTGCTTAAGGT\nCAAGCACTTCTGTCCCCCCGGTCAATGTTGATACGCTCTCCCAGGGCGAAAACAACTGAGATCGTTATCCGCAAGGCGCC\nTACACAAAACCTAGTAACATCTTGAATGGTATGTGGCTGGTCGTTCCGCTAAACCCCATAGTAGACCTGGCAGATGAGGC\nTAGAAATTCCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGCGTGTCCTTACGGACACGAAGCCATATACTTGA\nCAAGGTGTGAAGAGTCCCGTGTGCTCGTCTTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAACCCTGCAGCCAGTGC\nGCACAAACCAGTGTGTAGCTGGTCGTAATGAGTAATTGCGGGATGGGACCAACTACTTTGGGTGTCCGTGTTTCACTTTT\nTACCTTTTATTATGCTTATGGTGACAATATATAGATGCATATATTGACACCATGGGCGCACAGGTTTCTAGACAGAATGT\nTGGTACACACTCAACTCAGAACACAGTTTCAAATGGTTCAAGTTTAAATTATTTTAACATCAATTATTTTAAAGATGCTG\nCATCACACGGTGCTTCCAAATTAGATTTTTCACAAGATCCAAGCAAATTTACCGACCCTGTTAAAGATGTGCTTGAGAAA\nGGCATTCCTACACTCCAATCCCCAACCGTAGAAGCATGTGGTTATTCAGATAGGATTATACAGATAACAAGAGGGGATTC\nCACAATCACTTCCCAAGATGTAGCAAATGCAGTAGTTGGGTACGGAGTGTGGCCCCACTATTTAACACCACAAGATGCTA\nCAGCTATTGACAAACCCTCGCGGCCAGACACCTCTTCTAATAGATTTTACACTCTGGAGAGCAAAATGTGGGACAGTTCA\nTCAAAGGGATGGTGGTGGAAGTTACCAGATGCCCTCAAGGACATGGGAATTTTTGGTGAAAATATGTATTATCATTTCTT\nGGGGCGAAGTGGTTACACTGTACATGTTCAATGTAATGCCAGCAAATTTCATCAGGGTACACTTATTGTAGCAATGATAC\nCAGAACACCAACTGGCAAGTGCAACCTATGGGAATGTTGCCGCCGGGTATAATTACACACACCCAGGTGAACGTGGCAGA\nGTCATCAATGTTACTACGCGTGAACAAAATGATAAACAACCTAGTGATGACAATTGGCTTAATTTTGATGGTACATTATT\nAGGTAATATCACAATTTACCCACATCAACTCATTAATTTAAGAAGTAATAATTCAGCTACAATTATTGTCCCATATGTTA\nATGCAGTACCTATGGATTCCATGCTTAGACACAATAACTGGAGTTTAGTGATAATACCCATATGCCAACTAGAGGGAACT\nCCAGGCACTGTGCCTATTACCATTTCCATCAGCCCGATGTGTGCTGAGTTCTCAGGGGCTAGAGCAAAAAACCAGGGCTT\nACCAGTTATGTTAACACCTGGCTCTGGACAATTTATGACCACTGATGATTTCCAATCCCCTTGTGCTTTACCTTGGTACC\nACCCTACCAAAGAGATATCTATCCCAGGTCAAGTTAGGAATTTAATTGAATTATGTCAAGTGGATACACTAATACCCATA\nAATAATTTACAACAAAATATCAGCAATACTGATATGTATTCAGTTGTATTAAACAATGAAACAGAACTAGCAAAAGAGAT\nCTTTGCTATCAGGGTTGATATTGCCTCTCAGCCTCTGGCTACCACCCTGCTTGGCGAAATTGCAAGTTACTACACTCATT\nGGACTGGTAGTCTTAGATTTAGTTTTATGTTTTGTGGGTCTGCTAACACCACTCTTAAACTTTTAATAGCATACACACCA\nCCAGGTATTAGCAAACCAACCAAGAGAAAAGAAGCCATGTTAGGAACACATGTTGTCTGGGATGTTGGATTACAGTCCAC\nTATGTCAATGGTAGTCCCTTGGGTGAGTGCTAGTCATTTTAGAAACACAACTCCTGACAAATATTCCTTAGCTGGATACA\nTAACTTGTTGGTATCAAACAAATCTTATAGCACCACAGAACACACCCCAAACAGCCAAGATACTATGCTTTGTTTCGGCA\nTGTAAAGATTTTTGCTTAAGAATGGCAAGAGACACAAACTTACATAAACAATCTGGACCTATAGAACAAAATCCAGTTGA\nAAATTACATAGATGAGGTACTAAATGAGGTATTGGTTGTACCAAACATTAAAGAAAGCCAAGCCACCACATCAAACTCTG\nCCCCCGCACTGGATGCAGCTGAGACTGGTCACACTAGCAGTGTACAACCTGAAGATATGATTGAGACCAGGTACGTACAA\nACATCACAAACAAGAGATGAAATGAGCATTGAGAGTTTCCTGGGTAGGTCTGGCTGTATACACATGTCCAAACTTGTTGT\nAGATTATGAAAATTACAATGCAAAAACAAAGAACTTTATGACATGGCAAATTAATTTACAGGAAATGGCACAGATTAGAA\nGGAAATTTGAAATGTTCACCTACGTCAGATTTGATTCTGAAGTCACCCTAGTACCATCAATAGCGGCCAAAGGTGATGAT\nATTGGACATGTTGTGATGCAATACATGTATGTACCACCAGGTGCACCAATACCTAAAACTAGAGATGATTTTGCATGGCA\nATCTGGAACAAATGCCTCAATATTTTGGCAACATGGTCAAACATACCCTAGATTTTCCCTCCCTTTCTTAAGCATAGCCT\nCAGCATACTACATGTTTTATGATGGATATGATGGTGATCAACATGATTCAAGATATGGTACAGTAGTGACTAATGACATG\nGGTACTTTATGCTCCAGAATTGTAACTGATGAACACCAAAACAGAGTAGAAATAACAACTAGAGTTTATCACAAAGCTAA\nACATGTAAAAACCTGGTGTCCAAGACCACCAAGAGCTGTTGAGTACACACACACACATGTTACTAACTACAAAGTTAGGG\nGTAAAACTGAGAAGACTGCAATCAAACACAGAGCAAAGATCACAATGGCCGGTCCAAGTGATATGTATGTGCATGTAGGG\nAATCTTATATATAGAAACCTACACCTATTCAACTCAGAAATGCATGATTCTATCTTGATTTCTTACTCTTCTGATTTAGT\nCATATACCGCACAAACACAATAGGTGATGACTATATTCCAACATGTGATTGTACTGAAGCCACATACTTTTGCAAACATA\nAAAACAGGTATTTCCCAATTAGAGTTACAAGTCATGACTGGTATGAAATTCAAGAAAGTGAGTACTATCCAAAGCATATA\nCAATATAACCTCTTAATTGGAGAAGGGCCATGTGAACCAGGTGATTGTGGAGGGAAACTATTATGTAAACATGGTGTTAT\nTGGAATTGTAACTGCTGGTGGTGAGGGGCATGTGGCTTTCATTGATCTCAGGCATTTCCATTGTGCTGAAGAACAGGGCA\nTAACCGATTATGTTCATATGCTTGGTGAGGCTTTTGGCTTGGGTTTTGTGGACAGTGTCAAGGACCAAATAAATGCGATT\nAACCCGATTAATGGTATTAGTAAGAAAATCATCAAATGGTTACTGAGAATAATATCAGCAATGGTAATCATAATTAGAAA\nTTCATCTGATCCACAAACAATAATAGCCACATTGACCCTAATTGGTTGTTCAGGATCACCATGGAGATTTTTAAAAGAGA\nAATTCTGTAAATGGACCCAACTTAATTATATTCACAAAGAATCAGATTCATGGCTTAAGAAGTTCACTGAAATGTGCAAT\nGCAGCTAGAGGTTTGGAGTGGATTGGCAATAAGATATCAAAATTTATTGATTGGATGAAATCTATGTTGCCCCAGGCACA\nACTTAAAGTCAAATACCTTAATGAACTAAAGAAATTAAGCTTCCTTGAAAAACAAATGGAACATCTCAGAGTTGCTGATT\nCTCAAACTCAAGAAAAAATAAAATGTGAAATTGACACTTTGCATGATCTATCCTGTAAATTCCTTCCACTTTACGCTAGT\nGAGGCAAAAAGAATAAAGATTTTGCATAATAGATGTAGTACAATCATCAAACAAAGAAAGAGATGTGAACCAGTGGCTGT\nTGTTATACATGGTGAACCTGGTACTGGAAAATCCATGACTACAAACTTCCTGGCAAGAATGATAACAAATGATAGCGACA\nTCTATTCCTTACCACCCGACCCAAAATATTTTGATGGGTATGATCAACAAAGTGTGGTCATTATGGATGATATCATGCAG\nAATCCTAGTGGAGATGACATGACCTTGTTTTGTCAAATGGTATCAAGTGTGACTTTCATACCACCTATGGCAGATTTACC\nAGATAAAGGGAAACCATTTGATTCTAGATTTGTATTGTGCAGTACTAATCATAATTTGTTAGCACCCCCCACCATAACGT\nCTTTACCAGCAATGAATAGAAGGTTTTTCCTTGATTTAGATATTGTAGTGTGTGAGAAATACAAGGATTCACAAGGAAAA\nCTAAATGTTTCTGCTGCCTTCCGACCATGTGATGTCAATACAAAAATTGGCAATGCCCGATGCTGTCCATTCATCTGTGG\nTAAAGCAGTCAATTTCAGAGACCGAAATACATGTCAGACATACACGCTTTCACAAGTGTACAACCAGATGCTTGAAGAGG\nATAAAAGGCGTAGACAAGTCATTGATGTCATGGCAGCAATATTTCAAGGACCTATCTCCATGGAGGGCCCTCCACCAGCA\nGCAATAAGTGACCTGTTGCAATCAGTTAGAACTCCTGAAGTAATTAAATATTGTGAGGTAAATAAATGGATGATTCCAGC\nAGAATGTAAAGTGGAAAGAGATTTAAATATAGCTAACACTATCATCACAATCATAGCAAATATTATTAGTATCTCTGGAA\nTTATTTATGTTATATATAAACTTTTTTGTACATTACAAGGGCCTTATTCTGGAGAACCTAAACCCAAAACAAAAGTGCCA\nGAGAGAAGAGTGGTTGCACAAGGACCTGAGGAGGAATTTGGTAGATCACTCATCAAACATAATTCATGTGTGGTAACTAC\nTGAAAATGGAAAATTCACAGGACTGGGCATCTATGACAGAACATTGATTGTGCCAACACATGCAGACCCTGGTAAGGAGG\nTACAAATAGATGGTATTACTACTAAAGTGGAAGATTCCTTTGATTTGTTTAATAAAGATGGTGTGAAACTGGAAATCACT\nGTGCTAAAATTAAAGAGAAATGAAAAGTTCAAGGACATTAGGAAATATATACCAGAACATGAAGATGATTACCCAGACTG\nCAATCTGGCTTTATCTGCTAATCAGCCAGAAACTACTATAATCAAAGTGGGTGATGTTGTGTCGTATGGGAACATCTTAT\nTAAGTGGTAACCAAACAGCTAGGATGCTTAAGTATAACTACCCAACAAAATCAGGATACTGTGGTGGCATATTATATAAA\nATTGGACAAGTCCTTGGAATCCATGTTGGTGGTAATGGAAGAGATGGATTTGCTGCAATGTTGTTAAGATCTTACTTTAC\nTGAAGCACAAGGTCAAATAATCACCTCCAAAAGCACTGCTGAGTGTAATTTACCTAGCATCCACACACCAAGTAAAACAA\nAATTACAGCCTAGTGTCTTCTATGATGTGTTTCCAGGTAATAAGGAACCAGCTGTTCTTTCAGACCATGACCCAAGATTA\nAAGGTTAATTTCAGTGAGGCACTTTTCTCTAAATATAAAGGTAACAATCAGTGCACCATAAATGATCACATTAAAGTGGC\nCATCTCCCATTACTCGGCACAATTGACCACACTAGATATAGATCCAAATCCTATAACTTTAGAAGAAAGTGTCTTTGGCA\nTAGAGGGTTTAGAGGCACTTGACCTTAATACTAGTGCTGGATTTCCTTATGTGTCAATGGGCATAAAGAAAAGAGATTTA\nATTAACAAACAGACCAAGGACATTTCTAAATTGAAATTGGCATTAGATAAATATGGTGTTGATTTACCCATGGTCACATT\nTCTTAAAGATGAACTTAGAAAGAAAGAGAAGATTTCTGCGGGTAAGACCCGTGTGATAGAAGCTAGTAGTGTGAATGACA\nCTGTATTATTTAGAACAACCTTTGGCAACCTCTTCTCTAAATTTCACCTTAATCCTGGGATTGTTACTGGTTCTGCTGTG\nGACTGCGATCCAGAAACATTTTGGTCGAAAATACCAGTGATGTTAGATGGGGACTGCATTATGGCATTTGATTACACAAA\nTTATGATGGCAGTATACATCCAATTTGGTTTCAAGCATTAAAAGAGGTATTAGGCAATTTGTCATTTGAAGCTAATTTAA\nTAGATAGGTTATGTAATTCCAAACACATCTTTAAGAATGTATATTATGAAGTTGAGGGTGGGGTTCCATCAGGGTGTTCT\nGGTACAAGTATATTCAATACAATGATAAACAACATTATTATTAGGACACTAGTTCTTGATGCATACAAAAATATTGATTT\nGGATAAACTGAAAATAATAGCTTATGGAGATGATGTTATTTTTTCATACAAGTACCAACTTGACATGGAAGCAATTGCTA\nTGGAGGGCACCAAATATGGATTAACAATAACCCCTGCTGACAAGTCGGACAAATTTAAACAGCTTGATTATAGCAATGTG\nACCTTTCTTAAAAGAGGATTTAAGCAAGATGAAAAACACAATTTCCTAATACATCCAACTTTCCCAATTGAAGAAATTCA\nAGAATCTATTCGTTGGACAAAGAAACCATCTCAAATGCAAGAACATGTTCTGTCATTGTGTCATTTAATGTGGCATAATG\nGTAGGGATGTGTACAAGCAGTTTGAGGAGCGAATACGTAGTGTAAGCGCTGGTCGTGCACTATATATCCCTCCTTATGAT\nCTGCTTTTGCATGAGTGGTATGAAAAATTTTAGATTATTTAGATATAAAAGTATTAAATAATTAGTTTTTTAGTTTTGC\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_DQ473507.1_Rhinovirus_A53.fa", "content": ">RVA_DQ473507.1_Rhinovirus_A53 (7143 bp)\nTTAAAACTGGATCTGGGTTGCTCCCACCCAGATTACCCAAGTGGTGTAGTACTCTGTTATTACGGTAGCTTTGTACGCCA\nGTTTTATCACCCCTCCCCACAATGTAACTTAGAAGTTTTACACTTACAGACCAATAGGATGTGATTATCCAAATCACTAA\nAGGTCAAGCACTTCTGTTTCCCCGGTTAGATTTGATACGCTCCAACAGGGCGAAAACAGATCTGATCGTTATCCGCAAGA\nTGCCTACGCAAAGCTTAGTAGCGCTCTGAATGCTTTTTGGCTGGTTGTTCCACTACAAACCCAGTAGTAAACCTGGCAGA\nTGAGGCTAGAAGTTCCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGCACACCCTATGGGTGTGAAGCCAATCA\nGTTGACAGGGTGTGAAGAGCCCCGTGTGCTCATCTTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAAACCCGCAGCC\nAAGGTGTGCAAACCAGCACATTCTTGGTCGTAACGAGTAATTGTGGGATGGGACCAACTACTTTGGGTGTCCGTGTTTCT\nTTTTATTCTTTTACAATGCCTATGGTGACAATATATAGTATATATTGTCATTATGGGCGCTCAGGTATCCAGACAGAATG\nTTGGTACACACAGTACACAAAATGCAGTGACTAATGGTTCAAGTTTAAATTACTTCAACATTAATTACTTTAAAGATGCT\nGCATCCAGTGGAGCCTCCAGATTAGATTTTTCACAAGACCCAAGTAAATTTACTGACCCTGTTAAAGATGTTCTTACAAA\nAGGTATCCCGACTTTGCAATCCCCTTCTGTTGAGGCGTGTGGTTACTCAGATAGAATTATCCAGATAACCCGAGGGAACT\nCAACAATAACTTCACAGGATGTTGCAAATGCTGTAGTGGCTTATGGTGTATGGCCAGAGTATTTATCTGCTCAAGATGCT\nAGTGCCATAGATAAACCTTCACACCCTGATACATCATCAAATAGGTTTTATACATTAGAGAGTAAAAACTGGACAAACAC\nATCTAAGGGGTGGTGGTGGAAACTTCCAGACGCGCTTAAAAACATGGGCATCTTTGGAGAAAACCTCTTCTACCACTTCC\nTTGGAAGGGCTGGATACACGGTTCATGTTCAATGTAATGCTAGTAAATTTCATCAAGGAACCTTAATAGTTGCAGCAATC\nCCAGAACATCAATTAGCCTTTATAAAGAGTGGAAATGTTACAGTTGGTTACAAATATACACATCCTGGAGAACAAGGCAG\nAGAAATAGGGACTTTTGGGGAGAATAGCGTATTAGACAGACAACCCAGTGATGAAAATTGGTTGAATTGTGATGGCACCC\nTCCTTGGGAATATCACAGTGTATCCACATCAGTATATCAACCTTAGAAGCAATAATTCAGCTACATTAATACTTCCCTAT\nGTGAATGCAGTACCAATGGACTCTATGGTTAGACATAACAATTGGAGTATAGTCATAATTCCAATATCTAAATTGGTGTC\nAGTAGGTGGGACAGCATATGTACCCATAACAATATCCATCAGTCCTATGGCATCAGAATTCTCAGGAGCTAGAAATAATA\nGTCCTCAGGGTCTACCAGTCATGTTAACCCCTGGTTCAGAACAATTTCTAACAACTGATGATGCCCAGTCACCTTCTGCT\nTTGCCCTATTTCCATCCAACTAAAGAAATCTTTATTCCAGGTAGGGTCACTAATCTGTCAGAAATTTGTCAGATTGATTC\nAATGATTCCCATAAATAACACCCATGGGGTCAAAAATACAGTAAACATGTATACGGTACAAGTTCAAGAACAAACCACTC\nCGGCAAAAGAGGTATTTGCCATACCAGTGGATGTAGCTTCACAACCTTTGGCCACAACACTGATAGGAGAAATAGCTAGT\nTACTACACTCATTGGACTGGAAGTGTCAGATTTAGTTTTATGTTCTGTGGTACAGCTAATACTAGCCTTAAATTACTCAT\nTGCATACACACCCCCTGGGGTCCCCAAGCCAACCAGTAGAAAAGATGCAATGCTCTCTACTCATGTAGTATGGGATGTTG\nGACTGCAATCTACAATGTCCATGGTAGTACCATGGGTTTCAGCAAGTCACTACAGGTACACAACTCCTGATACATATTCA\nAAGGCTGGATATATCACATGCTGGTATCAGACAAATTTTATAGTCCCTCCTAGCACACCCAACTCAGCAGATATTATATG\nTTTTGTATCAGGATGTAAAGATTTTTGCTTAAGGATGGCAAGAGATACAAATCTACATACACAAGTAGGAGCAATAACAC\nAAAACCCGGTAGAGAAATACACAGAGGCTATCTTAAATGAAGTATTAGTAGTCCCAAACATTAATGCAAGCAATCCACAA\nACTTCAAATTCAGCACCAGCACTAGATGCTGCAGAAACGGGTCATACAAGTCAGACACAACCTGAGGACATGCTGGAAAC\nTAGATATGTCATCACAGACCAAACCCGGGATGAAATGAGCATTGAAAGTTTCTTAGGCAGATCAAGTTGCATTGCTGAGA\nTCCATACCAATTTAGACCATACTGGATACAATGAGCCTGGGAAAAACCACTCAGAATGGAAGATTACACTCAAAGAAATG\nGCCCAGATTAGAAGAAAATGTGAGATGTTCACATATCTTAGATTTGATTCAGAAATAACTATAGTGGTATCAGTGGCTAG\nTAAACAAGGGAATAACGGGCACGTGGTGATACAATACATGTATGTACCACCGGGTGCTCCAATACCCAAAACCAGAGATG\nATTATACCTGGCAATCTGGAACTAATGCTTCAGTCTTTTGGCAACAAGGACAACCATACCCTAGATTCACAATCCCTTTC\nATGAGTATTGCGTCAGCATATTATATGTTCTATGATGGGTATGAAGATGACAATGGCACCACTTATGGGGCTGTTGTTAC\nTAATGATATGGGAACACTTTGTGTGCGCATAGTGACTGAGCAACAGAAAAATGAGGTCAAGATAACCAGTAGGATTTATC\nACAAGGCTAAACATATCAGTGCATGGTGTCCAAGACCACCAAGAGCAGTTGCATATCAACACACATATAGCCCAAATTTT\nGTACCGCAAACAGGAACAGTTGAAACTCACATTAAGTTCAGACCTGATGTTAAAGATGTAACATCAGTAATGACAGCAGG\nTCCATCAGATTTGTATGTGCACTCTAGTAATTTTATTTATAAAAACTTGCACTTGTGTGAACCAGAAAACCTAAATGATT\nCAGTCCTAATCAGTTACTCCAGTGATCTTGTCATTTACCGCACAAATACTACAGGTGATGACATAATCCCAACATGCGAC\nTGTACACTAGGTACTTACTACTGTAAACATAAGGATAGATATTACCCCATTAGTGTGACAAAACATCAGTGGTATGAAAT\nACAAGAATCAGAATATTACCCTAAGCATATCCAATATAACATATTATTAGGTGTAGGACCCTGCAAACCAGGTGATTGTG\nGGGGCAAGCTCCTCTGCAAACACGGTGTGATTGGTATAATAACCGCTGGAGGTGACAATCATGTAGCTTTCATAGATCTT\nAGAGACTTTCAAGTTGCTGAGGAGCAAGGAATACCAGAATACATTCATTCCCTTGGCGAAGCTTTTGGCTCTGGATTTGT\nGGATAACATCAAGGATCAGATCCAAACTATTAATCCAATTAACAAGATATCTAGTAAAATAGTTAAATGGGTAATAAGAA\nTCATTTCAGCTATCACTATAATAATCAGAAACAATGCTGACCCACATACAATAGTAGCCACATTAGCTCTGTTAGGTTGC\nTCAGGTTCACCATGGAGATTTATCAAGGAGAAAGTTTGTGGATGGTTGCAACTTAACTATATACATAAGGAATCTGATGG\nGTGGATAAAGAAATTCACAGAGATGTGTAATGCTGCTAGAGGTCTTGAGTGGTTAGGTAACAAAATATCCAAATTCATTG\nATTGGCTCAAGTCTATGTTACCTCAAGCCAGATTAAAGGTGGATTTTATTAAAAACCTTAAACAATTACCATTATTAGAA\nAAACAGGTAGATGGGTTGAGACTTGCAACACAAAAACAGCAACAGGAGTATATTGATACCCTTACCCTAATGTTGGATTC\nATCAAATAAATTCTTACCCCTTTATGCACTTGAAAACAAGCGAATCAAGGAACTACTCAAGAGGGGCCAGATGATTCTTC\nGCACATCTAAGAGAACTGAACCAGTTGGTGTTATCTTTCATGGTGAGCCAGGGACGGGAAAATCAATCACAACATCTATC\nCTTGCCCGAATGCTTACCTCAGAATCAGATATTTACTCACTACCTCCATCACCCAAATATTTTGATGGGTATGATCAACA\nGAGTGTAGTCATCATGGATGATATAATGCAAAATCCCAGTGGAGAAGACATGTCCTTATTCTGTCAAATGGTATCATCAG\nTACCATTTATACCACCTATGGCAGATCTACCAGACAAAGGAAAACCATTCTCTTCAGACTATGTACTTGCTAGCACTAAT\nCATACTCTACTCCACCCTCCAACAATTACATGCACAACAGCAATGAATAGGAGGTTTTTCTTGGATTTAGATATCATTGT\nTAAAGATGATTATAAATTAGGTCAAGGCAAACTAAATTTACAGTGTGCACTCAAACCATGCAAGGAAGGGAAAATTGGCA\nATGCAAAATGTTGCCCCCTTATTTGTGGGAGAGCCTTACAATTTAGAGATAGAAGTAATGGAGAACACTTGTCCCTTGCC\nACAATATATAATAGGATCACACAGGAAAGCAAAAACAGAAAGGAGTTAACAAACTCACTGCAGGCGATTTTCCAGGGACC\nAATTGATATTGTGAACAAACCACCACCACCAGCTATAGTAGATTTACTTAAATCAGTTAGAAATCCAGATGTAATTAGAT\nATTGTGAAGAAAATAAATGGATAATTCCAGCAGATTGTAAACTTGAAAGGGATCTCAACTATGCTAATGTAATAATATCT\nATGATTGCCAATGTAATTAGTATAATGGGTGTGATTTATATTATATACAAACTATTCTGCTCTTTGCAAGGACCATATTC\nAGGAGAACCAAAACCAGTAACGAAAAAACCAGAGAGAAGGGTGGTCACACAAGGGCCTCAGGAGGAATTTGGACGAAGCC\nTAATGAAACATAATACATGTGTGGTCACAACTAACAATGGAAAGTTCACCGGTTTAGGTATCTATGACAACGTAATGATA\nATACCAACACACGCTGATGCAGGTCAGGAGGTGGAAGTGGATGGGATTAAGACCAAAGTCAGTGATGCATATGATTTATA\nCAACACACAAGGTGTTAAATTAGAAATCACAGTGTTAAAACTAAACAGGAATGAGAAATTCAGAGATATTAGGAAATACA\nTTCCAGAGAGTGAAGATGATTACCCAGAATGCTGCTTGGCACTAGTTGCAAATCAGGTAGAACCCACAATTTTAGAAGTT\nGGTGATTGCTGTTCATATGGAAACATCTTATTAAGTGGTAATCAAACTGCTAGGATGATCAAATACAATTACCCCACTAA\nATCAGGTTTTTGTGGCGGGGTCTTATATAAAATAGGCTTGATCTTGGGTATACATGTGGGAGGCAATGGAAGAGATGGTT\nTTTCTGCAATGTTATTAAGATCTTACTTTAATGAACAACAAGGGAAAATTGTGTCAAAAGCTGAAGTGAAAGAACATAAT\nCTATATAGCATACACACTCCCACTAAGACTAAATTACAACCTAGTGTTTTCCATGATGTGTTCCCAGGTAGCAAAGAGCC\nTGCTGTATTATCCACAAGAGATCCAAGGTTAGAGGTAGATTTGGACAGCTCTATTTTCTCAAAATATAAGGGTAATGAGG\nCAGTAAAAATTTCTGAAAACATGCTTGTTGCTGCTGCGCACTACACGGCCCAGTTGACAACACTAGATATTGACCCACAG\nCCAATTAGTCTAGAGGATAGTGTATATGGAATTGAGGGTTTAGAAGCATTGGATCTCCACACCAGTGCTGGATACCCATA\nCACGGCTCATGGAATTAAGAAGAAAGATCTTATACCAAAAGATAAAAATTTGACAAAACTTAAAATTGCTATGGAGAAGT\nATGGATTGGACTTACCAATGATAACATTTCTCAAGGATGAACTTAGAAAACCAGAGAAAATTAGTGCAGGAAAAACTAGA\nATAATAGAAGCTAGTAGTTTAAATGATACTGTTCAGTTTAGAATGGCATTTGGTAATCTCTTTTCTAAATTCCACAAAAA\nCCCAGGTATTGTCACTGGATCAGCAGTGGGGTGTGATCCAGAGGTGTTTTGGTCAAAAATTCCAGTTATGCTGGACGGGG\nATTGCCTTATGGCATTTGATTATTCCAATTATGATGGCAGTCTGAATCCAGTGTGGTTTGAGCTTCTTGAGAGAGTTTTA\nAATGATCTCGGTTTCCCTGGAAAATTAGTTAATAAATTGTGCCACTCTAAGCATATCTATAAAACAACATACTATGAAGT\nAGAGGGTGGAATGCCATCAGGTTGTGCTGGAACCAGTATATTCAATTCAATGATTAATAATATTATAATTAGGACATTAG\nTTTTAGACACTTATAAATATATTAATCTGGACAAGTTAAAAATACTTGCATATGGTGATGATGTGTTATTCTCTTACCCT\nTATGATTTGGATATGGCAGAACTAGCTAAAGAAGGTAACAAATATGGTCTGACAATCACACCTGCAGATAAATCAGACAA\nATTTGAAAAATTAAACTATGAAAATGCAACCTTTCTGAAACGGGGCTTTAAACAAGATGACAGATATAAATTCTTAATAC\nATCCAATTTACCCAGAAAGTGAGGTTTGGGAATCCATTAGATGGACAAAGAATCCCAGAAATATGCAGGAACATGTTCTT\nTCCCTGTGTCACCTTATGTGGCATAATGGTAAAGACAAATATGATTCATTCGTGAACAAGATCAGGAGTGTTAGTGCTGG\nTCGCGCACTCTATATCCCACCGTATGAACTCTTGTTGCATGAATGGTATGAAAAATTTTAAACAGATATAGAAAGTATAA\nATGAGGTAGTTTATAGTTTTTAT\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_FJ445116.1_Human_rhinovirus_13_strain_ATCC_VR-1123.fa", "content": ">RVA_FJ445116.1_Human_rhinovirus_13_strain_ATCC_VR-1123 (7140 bp)\nTTAAAACTGGGTTCGGGTTGTTCCCACCCAAACCACCCACGTGGTGTAGTACACTGTTATCCCGGTAACTTTGTACGCCA\nGTTTTATCTCCCCACCCCCTTTTGTAACTTAGAAGTTATGCACAATGACCAATAGTGGGCAATCATCCAGATTGTCATCG\nGTCGAGCACTCCTGTTTCCCCGGTTCAAGTTGATATGCTCTAACAGGGCAAAAACAATTTGAATCGTTACCCGCAAGGTG\nCCTACACAGAACTTAGTACCATTCTGGAAAATTCTTGGCTGGTCGCTCAGTTACTACCCCAGTAATAGACCTGGCAGATG\nGGGCTAGAAGTTCCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGCACACCCTTCTTGGGTGTGAAGCCTAGAA\nTTGGACAGGGTGTGAAGAGTCGCGTGTGCTCATCTTGAGTCCTCCGGCCCCTGAATGCGGCTAACCCTAACCCTGCAGCC\nATTGCCCACAACCCAGTGGGTCTATGGTCGTAATGAGCAATTGCGGGATGGGACCGACTACTTTGGGTGTCCGTGTTTCA\nCTTTTTACTTATTATTTGCTTATGGTGACAATATATAGATACATATATTGACACCATGGGCGCCCAAGTTTCTAGGCAGA\nATGTTGGAACTCACTCAACTCAGAATTCAGTTTCAAATGGTTCAAGCCTGAATTACTTCAACATCAACTACTTTAAGGAT\nGCAGCATCAAGCGGTGCTTCTAAATTAGAGTTTTCACAAGATCCAAGCAAATTCACAGATCCAGTTAAGGATGTACTAGA\nAAAGGGAATCCCTACTTTGCAATCTCCAACAGTTGAAGCATGTGGTTATTCAGATAGGATCATTCAAATCACCAGAGGTG\nACTCTACCATAACCTCACAAGATGTTGCCAATGCAGTCGTTGGTTACGGTGTATGGCCACATTATCTTACACCACAAGAT\nGCCACTGCCATAGATAAGCCAACTAGACCTGACACCTCTTCCAATAGGTTCTATACACTAAAAAGTCAGTTGTGGACTGC\nTGAATCCAAAGGCTGGTGGTGGAAACTGCCTGATGCCCTAAAAGATATGGGAATTTTTGGAGAGAATATGTTTTATCACT\nTTTTAGGTAGATGTGGTTACACTGTGCATGTTCAGTGTAACGCTAGCAAATTTCATCAGGGAACTCTTTTAATAGCAATG\nATACCAGAACATCAATTGGCCACTGCTGCTGGTGGAAGTGTTTCTGCAGGGTATAAATACACACATCCTGGTGAGAAAGG\nTAGGGATGTTGGGAAGATAAACCGAGAGAGAAATGACCGGCAGCCCAGTGACGACAATTGGTTAAATTTTGATGGAACTC\nTCTTGGGAAACCTGACCATTTTCCCACATCAGTTTATTAATCTTAGGAGTAACAATTCAGCTACTATCATAGTACCATAT\nGTTAATGCAGTACCAATGGATTCCATGCTTAGGCATAATAACTGGAGCCTGGTAATCATACCTATCTGTGAACTCAAGTG\nCAATAACACTGCCGTCACTGTACCCATCACAATATCTATCAGCCCTATGTGTGCTGAATTCTCTGGTGCTAGAGCTAGGA\nATGTTACTCAAGGTCTGCCCACACTGTTAACACCTGGGTCAGGTCAATTCTTGACAACAGATGATTTCCAGTCCCCTAGT\nGCTTTGCCGTGGTATCACCCAACTAAAGAAATTTCAATTCCAGGGCAAGTCAGAAATTTAATTGAATTGTGTCAAGTTGA\nTACTATGATACCAATTAACAACACCAATGATAATATTAGAGATAAAAGCATGTACACAATTAGACTTGGTGGTGTAACAA\nATGCTAAGGAAGCCATTTTCGCAATGAGAGTTGATATTGCATCTCAACCTTTGGCAACCACAATGATTGGTGAAATTTCC\nAGCTATTACACACATTGGACAGGGAGTCTCCGATTCAGTTTCATGTTTTGTGGTTCTGCTTTTACAACACTTAAATTGTT\nGATTGCATACACACCACCAGGAATCACTGTTCCAGAAAACAGGAAAAAAGCTATGCTTGGCACGCATGTTATATGGGATG\nTCGGGCTTCAATCAACTGTGTCGATGGTGGTTCCATGGGTCAGTGCTAGTCATTACAGAAACACTACACCAGATACTTAT\nTCTGCAGCCGGATACATCACTTGCTGGTATCAAACTGATTTAATAACACCTCCAAACACAGCCCCAGTAGCTGACATGAT\nATGTTTTGTGTCAGGATGTAAAGATTTCTGCCTTCGCATGGCAAGGGATACGAACTTGCATAAGCAAAGTGGGGTTATAG\nCACAAAATCCTGTTGAAAGGTATGTAGATGAAGTCTTGAATGAAGTTCTTGTAGTACCAAATATCAGTGAAAGTAGCTCA\nACTACATCTAATTCAGCTCCAGCCTTAGATGCTGCAGAAACTGGCCACACAAGCAGTGTACAACCAGAAGACATGGTTGA\nAACACGTTATGTCCAAACTTCACAAACTAGGGATGAAATGAGTGTTGAGAGCTTTTTAGGCAGATCTGGTTGTATACACA\nTGTCTACCATGAACATAGATTATACTAATTATGATGATTCTGTTAATAATTTTGTGAAATGGAAAATAAGTTTGCAAGAA\nATGGCCCAAGTGCGCAGAAAATTTGAGTTGTTCACCTATGTAAGATTTGATTCAGAAATAACAATTGTGCCATGTATAGC\nCGGGCAAGGTGGTGATGTCGGACATGTTGTTATGCAATACATGTATGTACCGCCCGGTGCACCCCTTCCAACGAAGAGAA\nATGATTACACATGGCAATCTGGCACCAATGCATCTGTTTTCTGGCAACATGGTCAAATTTACCCCCGATTCTCTTTACCA\nTTTCTTAGTATTGCATCTGCATATTATATGTTTTATGATGGATATAATGGAGATTCCTCAGATGCACGCTATGGGACAAC\nAATCACTAATGATATGGGCACACTTTGCTTCAGAATAGTAACTGAAGAACATACTAACAAGGTCAAGGTTACAACTAGAA\nTCTATCATAAAGCTAAACATGTCAAAGCATGGTGTCCTAGACCTCCCAGAGCTGTTGAATATACTAATGTGCATGTTACA\nAACTACAAACCAGGGACAGGAGATGTTGCAGTCTCCATTGTACCTAGAGCAAATGTTAGGGAAATTAGAAACTTTGGACC\nCAGTGACATGTATGTGCATGTTGGAAATTTAATATATAGAAATTTGCATCTGTTCAATTCAGAAATGCATGACTCAATCT\nTAGTATCCTATTCATCAGATCTAGTCATCTACCGAACAAACACTATAGGTGATGACTACATCCCATCCTGTGATTGCACT\nCAAGCCACATACTACTGCAAACATAAAAACAGATATTATCCAATTGAAGTTACTAGTCATGATTGGTATGAAATACAAGA\nAAGCGAATATTACCCTAAACATATTCAGTACAATCTGTTGATTGGTGAAGGCCCTTGTGAACCTGGAGACTGTGGGGGCA\nAATTACTATGTAAGCATGGAGTGATTGGAATTATCACGGCTGGTGGCGAGGGTCATGTGGCTTTCATTGACTTGAGACAC\nTTCTTGTGTGCTGAGGAGCAAGGTGTTACTGACTATATACATATGCTAGGTGAAGCTTTTGGTAATGGCTTTGTAGATAG\nTGTTAAAGAACATGTCAATGCAATAAATCCCATAAACAATATCAGTAAAAAAGTCATCAAATGGTTATTAAGAATTGTGT\nCTGCTATGGTCATAATCATTAGGAATTCCTCAGATCCACACACCGTCGTTGCTACTCTAACACTAATTGGTTGTTCTGGC\nTCACCATGGAGATTTTTGAAAGAGAAATTTTGTAAGTGGACTCAGTTAAACTATATCCACAAAGAATCTGACTCATGGCT\nTAAAAAATTTACTGAAATGTGCAATGCAGCAAGAGGCCTTGAGTGGATAGGTAATAAGATATCTAAATTTATAGAATGGA\nTGAAATCAATGTTACCACAAGCACAACTCAAAGTTAAGTATTTAAATGAATTAAAGAAATTAAACTTGCTTGAAAAACAG\nGTTGAAAACTTGAGATGTGCTGATACCAAAACTCAAGAGAAAATAAAAGTTGAAATAGACACCTTGCATGATCTATCCTG\nCAAATTTCTCCCACTATATGCTAGTGAAGCCAAAAGAATTAAAGTCATTTACAATAAATGCAATAACATCATCAAACAAA\nGGAAAAGAAGTGAACCTGTGGCAGTAATGATACATGGTTTGCCTGGGACTGGTAAGTCTATTACAACAAGTTTTCTAGCA\nAGAATGATTACTAATGAAAGTGACATATACTCCTTGCCCCCTGACCCAAAGTACTTTGATGGTTACGATCAGCAAAGTGT\nTGTTATAATGGATGATATTATGCAGAACCCTGATGGTGAGGATATGTCACTATTTTGTCAAATGGTTTCTAGTGTTACCT\nTCATTCCGCCAATGGCCGACTTACCAGACAAGGGAAAACCCTTTGACTCAAGATTTGTTCTGTGCAGTACTAATCATTCT\nCTTTTGGCCCCTCCCACTATCACTTCTCTTCAGGCAATGAACAGGCGGTTCTTCTTGGACTTGGACATTGTGGTTCATGA\nTAATTATAAAGATGCACAAGGGAAATTGGATGTGTCCAAAGCATTTAGGCCATGTGATGTTAAGACAAAAATTGGAAATG\nCTCGCTGTTGTCCATTCATATGTGGTAAAGCAGTAACCTTCAAAGATCGTAACACTTGCCAAAGTTACCCATTGAGTCAG\nATTTACAATTTGATTCTTGAAGAAGACAAAAGACGCACTCATGTTGTAGATGTCATGACTGCAATATTCCAAGGGCCAAT\nTTCAATGGAAGTCCCCCCTCCTCCTGCTATAACTGACCTCTTACGCTCTGTCAAGACACCGGAAGTTATCAAATATTGCG\nAAGACAATAAATGGATTATTCCGGCTGATTGTAAAATTGAGCGTGACTTGAATCTTGCAAATAATATTATAGCAATTATT\nGCTAATATAATCAGCATAGCAGGTATTATATACATCATATACAAATTGTTCTGTTCTTTCCAAGGCCCCTACTCAGGTGA\nGCCCAAGCCCAAGACAAAAATCCCAGAAAGAAGGGTGGTTGCACAAGGTCCAGAAGAAGAGTTTGGTCGCTCAATAATCA\nAACACAACACATGTGTGGTTACTACTGATAATGGCAAATTCACTGGATTGGGAATCTATGATAAACTCATGATATTACCC\nACACATGCCGATCCTGGCAAAGAGGTGTGTATCAATGGAATTGCAACCAAAGTTAGTGACTCATATGATTTATATAACAA\nACAAGGTGTTAAATTAGAGATCTCAGCTATAGTATTAGATAGAAATGAGAAATTCAGGGATATACGAAAATACATACCAG\nAGAGAGAGGATGATTACCCTGATTGCAACTTAGCCCTTGTAGCTAACCAACCAGAACCCACCATTATAAATGTAGGAGAC\nGTTATCTCCTATGGGAACATCTTACTTAGTGGCAATCAAACAGCACGGATGCTTAAATATAATTACCCCACAAAATCAGG\nATACTGTGGTGGTGTTCTATATAAAATAGGTCAGATTATAGGGATTCATGTGGGAGGCAATGGTAGAGATGGGTTTTCTG\nCAATGCTACTCAGATCTTATTTTAACCAAACTCAAGGAGAAATAACAGTGACAAAGAAAGTTACTGAATGTGGGCTTCCA\nACAATACACACCCCATCCAAAACCAAGTTGCAACCTAGTGTTTTCTTTGATGTCTTTGAAGGGTCCAAGGAACCAGCTGT\nCCTAACTGATAGAGATCCTCGATTAACCACTGACTTTAATAAGGCTTTATTCTCTAAATATAAGGGTAATATAGAATGTA\nGCATGACTGATCATATGAGAGTTGCTGTATCACATTATTCAGCTCAACTAATGACCTTAGATATTGATTCAGTAAATATA\nTCTTTAGAGGAAAGTGTGTTTGGCACTGAAGGTCTGGAAGCCCTTGATTTAAATACAAGTGCAGGTTTCCCATATATAAG\nTATGGGAATAAAGAAAAGAGATCTAATAAACAACAGCACAAAAGACATAACCAAATTAAAGCTAGCACTTGATAAATATG\nGGGTTGATCTACCAATGGTAACATTTCTTAAAGATGAACTTAGAAAGAAAGAAAAAATATCTACTGGAAAAACAAGAGTC\nATTGAAGCTAGTAGTGTAAATGATACAATAGCCTTTAGAGTAGTGTATGGAAATTTGTTTTCTACTTTTCATAAAAATCC\nTGGTGTAGTTACAGGATCTGCAGTAGGGTGTGACCCTGAGACTTTTTGGTCAAAAATACCAGTAATGTTAGATGGGGACT\nGCATAATGGCGTTTGATTACACTAATTATGATGGTAGCATACACCCAATTTGGTTTGAGGCTCTTAAACAAGTTTTGATA\nAATTTATCATTTGAAGACAAGCTTATAGACAGATTGTGTAGGTCAAAACATATATTCAGAGACACATATTATGAAGTTGA\nAGGTGGGGTACCCTCAGGTTGTTCAGGAACTAGCATATTTAACACTATGATAAATAACATTATCATTAGAACTTTAGTTC\nTTGATGCTTATAAACATATTGATTTGGACAAACTCAAAATAATAGCATATGGTGATGATGTTATTTTTTCCTACAAATAC\nCCTTTAGACATGGAGGCAATTGCTATAGAAGGAAATAAGTACGGTTTGACCATCACACCGGCTGACAAATCAGATACTTT\nCAAGAAGCTTGATTATGACAATGTAACCTTCTTAAAAAGGGGTTTTAAGCAGGATGCTAAATACCCATTCCTGATTCACC\nCAACATTTCCAGTTTCTGAAATCCATGAGTCCATCAGATGGACTAAGAAACCTTCACAAATGCAGGAACATGTCTTGTCC\nTTGTGTCACTTAATGTGGCATAATGGACAGGATGTGTATAAAGAATTTGAGAGGAAGATACGTAGCGTGAGCGCTGGACG\nTGCGCTATATATCCCTCCATATGAATTACTCCTGCATGAGTGGTACGAAAAATTCTGAATTATATATAGAAATATTAAAT\nATTTAGTTTTTTAGTTCTAT\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_FJ445140.1_Human_rhinovirus_56_strain_ATCC_VR-1166.fa", "content": ">RVA_FJ445140.1_Human_rhinovirus_56_strain_ATCC_VR-1166 (7136 bp)\nTTAAAACTGRGTTCAGGTTGTTCCCACCTGGACTTCCTATGTGGAGTTGTACACTGTTATCCCGGTAACCTTGTACGCCA\nGTTTTATACACCCTTCCCTGTAACTTAGAAGTTATAAGCACGAGGACCAATAGGTAGTGACTTTCCAGGTCACTAAAGGT\nCAAGCACTTCTGTCTCCCCGGTCAAAGTTGATATGCTCTCCCCAGGGCAAAAACAATTGAGATCGTTATCCGCAATGTGC\nCTACGCAAAGCCTAGTAATATCTTAGATGATATATGGTTGGTCGCTCCGCCATTTCCCATGGTAGACCTGGCAGATGAGG\nCTAGAAACTCCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGCGCACTCTCTGAGTGCGAAGCCATATATTTGA\nCAAGGTGTGAARAGCCCCGTGTGCTCACATTGAATCCTCCGGCCCCTGAATGTGGCTAACCTTAAACCTGCAGCTAGTGC\nACACAAACCAGTGTGTAGCTAGTCGTAACGAGCAATTGCGGGATGGGACCAACTACTTTGGGTGTCCGTGTTTCACTTTT\nTTCCTTTTATATTTGCTTATGGTGACAATATATATAATACATATATTGACACCATGGGCGCTCAAGTATCTAGACAAAAT\nGTTGGTACACACTCCACTCAAAACACAGTTTCAAATGGATCTAGTCTAAATTATTTCAACATCAATTATTTTAAGGATGC\nTGCTTCTAGCGGTGCATCCAAATTGGAATTTTCACAAGATCCAAGCAAGTTCACTGACCCAGTTAAAGATGTCTTGGAGA\nAAGGAATACCCACTCTGCAATCTCCAACTGTAGAAGCTTGTGGTTATTCAGACAGAATTATACAAATCACTAGAGGAGAT\nTCAACCATCACATCACAAGATGTTGCAAATGCGGTAGTTGGGTATGGTGTGTGGCCTCATTACCTAACACCACAAGATGC\nTACTGCAATAGACAAACCTACTCAACCAGACACTTCCTCCAACAGATTTTATACATTGGAAAGTAAAGTTTGGACACAAA\nCTTCAAAAGGATGGTGGTGGAAATTACCGGATGCTCTAAAAGATATGGGAATCTTTGGGGAAAACATGTTCTACCATTTC\nTTAGGCAGGTCAGGGTACACAGTACATGTACAATGTAATGCAAGTAAATTTCACCAAGGTACCTTATTGGTTGCTATGGT\nTCCAGAACACCAACTAGCAAGTGCAAATAAAGGTAATGTCACAGCAGGATACAACTACACCCATCCTGGTGAGGCTGGCA\nGGGATGTGGGACAAACAAGAGTGAATAATGACAGACAACCCAGTGATGATAATTGGTTAAATTTTGATGGTACTTTTATG\nGGGAATCTGTTGATTTTCCCACATCAATTTATAAACTTAAGGAGTAATAATTCAGCAACTATAATAGTACCATATGTTAA\nTGCAGTGCCAATGGATTCCATGCTTAGACATAACAATTGGAGTTTGTTAATAATACCTGTTAGCCCATTAAAGAGTGACA\nCACTAGCAACATCCCAGGTACCTATCACTATATCTATCAGTCCTATGTGTGCTGAGTTCTCAGGTGCCAGAGCAAAGCCA\nAATGCAGCCCCTCAGGGATTACCAGTTTATGTAACGCCAGGATCTGGTCAATTCATGACAACAGATGATTTGCAATCACC\nCTCTGCACTGCCATGGTATCACCCAACCAAAGAAATATTCATCCCAGGAGAGGTAAAAAATTTGATTGAAATGTGTCAAG\nTAGGCACACTTATACCTGTAAATAATACTGATGCAAACTTGCGAAACATCAATAAATACACTGTTCAATTAAGTAGTCAA\nACTGATTTAGCTAAAGAAATATTTGCAATTAAGGTGGATGTGGCCTCACAACCGCTCTCTAGTACACTTCTTGGAGAAAT\nATGTAGTTACTACACACATTGGACTGGTAGCCTTAGATTTAGCTTTATGTTTTGTGGGACCGCTAACACAACCTTAAAGG\nTTTTGCTTGCCTATACCCCACCTGGCATCAAGAAACCAGAGAGCAGGAAACAGGCTATGTTAGGCACACATATTGTATGG\nGATGTGGGCCTACAATCAACTGTATCTCTAGTAGTACCCTGGGTTAGTGCCAGTCATTTTAGATACACAACTCCTGACAC\nATACTCAGCAGCAGGTTATATCACATGCTGGTATCAAACAAATTTTGTATTTCCACCTAATACACCAAACACTGCTGATA\nTGTTATGCTTTGTCTCTGCGTGTAAAGACTTTTGTTTGCGCATGGCAAGAGATACGGATATGCATGTTCAGAATGTACCA\nATAACACAAAACCCAGTTGAGAGATATGTAGATGATGTTTTAAATGAAGTTTTAGTTGTTCCAAATATTAGGGAGAGCCA\nTCCATCCACATCAAATTCTGCCCCTGCATTAGATGCTGCTGAAACTGGCCATACTAGTGCAATCCAACCAGAAGACACTA\nTAGAAACCAGATATGTACAGACATCACAAACTAGGGATGAAATGAGTATAGAGAGTTTTCTAGGTAGATCAGGTTGTATA\nCATATATCAACTATAACTGTGGATAATGATGTAGATTATAATTCAAAGCATTATAATAAATGGCAAATAACCTTACAAGA\nAATGGCTCAAGTTAGGCGTAAATTTGAATTCTTTACTTATGTCAGATTTGATTCAGAGGTTACTTTGGTACCTTGTGTAG\nCCGGCAAGGGAGATGATATTGGACACATTGTAATGCAATACATGTATGTGCCTCCTGGTGCACCACTTCCAAACTCAAGA\nGATGATTTTACATGGCAATCTGGCACCAATGCTTCTGTCTTTTGGCAACATGGCCAAGCTTTCCCCAGATTCTCTCTACC\nTTTCTTAAGTATTGCTTCTGCTTATTACATGTTTTATGATGGTTATGATGGAGACACTTCAAGCTCCAGATATGGTACAT\nCAGTTACAAACCACATGGGGACACTCTGTTCAAGAATTGTGACAAATAAACAACTTCATCCTGTTGAAGTCACAACTCGT\nGTATATCATAAGGCAAAGCATATTCGAGCATGGTGTCCTAGAGCACCAAGGGCTGTGCCTTATACACATGCTCACGTCAC\nCAATTATAAACCACAAGATGGTGATGTACAGATCTTCTTAAAACCCAGACCCAGCCTAACAACATTTGGACCTAGTGACA\nTGTATGTACATGTTGGAAATCTCATTTACAGAAATCTTCATCTTTTCAATTCAGATATGCATGACTCTATATTAGTTTCT\nTATTCATCTGATTTAGTCATTTACCGCACAAACACTACAGGTGATGACTATATCCCAACATGTGACTGCACCCAAGCTAC\nTTACTACTGTAAACACAAGAATAGATATTTCCCAATTAATGTTAATAGTCATGATTGGTATGAAATCCAGGAAAGTGAGT\nATTACCCAAAACACATACAATACAACCTGCTAATTGGTGAAGGGCCTTGTGAGCCAGGTGATTGTGGTGGCAAATTATTA\nTGTAAACATGGTGTTATAGGCATCATTACTGCTGGTGGAGAGGGACATGTAGCATTTATCGATCTTAGACACTTTCACTG\nTGCTGAGGAACAAGGCATAACTGACTACATACACATGTTGGGTGAAGCTTTTGGAACAGGTTTTGTTGACAGTGTTAAGG\nATCAAATAAGTGCTATAAACCCAATAAACAATATAAGTAAAAAAATAATCAAATGGCTTCTTAGAATTATATCTGCAATG\nGTTATAATTATTAGAAATTCATCTGACCCACAAACAATAATAGCTACTCTAACTTTAATCGGGTGTTCAGGTTCTCCATG\nGCGATTCCTCAAAGAAAAATTCTGTAAATGGACCCAACTTAATTACGTTCACAAAGAGTCTGATTCATGGCTTAAAAAAT\nTCACAGAGATGTGCAATGCAGCCAGAGGCTTAGAATGGATTGGTAACAAAATATCAAAGTTTATTGAGTGGATGAAATCT\nATGTTACCTCAAGCTCAACTTAAAATCAAATATTTAAGTGAACTTAAAAAATTAAATTTTCTAGAAAAACAAATGGAACA\nTCTTAGAATTGCTGATTCACAAACTCAAGAGAAAATAAAACATGAGGTAGACACTCTTCATGATCTTTCATGTAAATTTC\nTTCCACTTTATGCTAGTGAAGCAAAGAGAATTAAAATTTTATACAATAAGTGTAACACAATTATCAAGCAGAGGAAAAGA\nTGTGAACCAGTAGCAGTTGTAATACATGGTGAACCTGGAACTGGCAAATCAATGACCACTAATTTCCTGGCTAGAATGAT\nTACAACTGAGAGTGACATTTACTCTCTACCACCTGATCCCAAATATTTTGATGGATATGATCAACAAAGTGTAGTTATCA\nTGGATGATGTGATGCAAAATCCAAGTGGAGAAGATATGACTCTATTTTGTCAAATGGTATCAAGTGTCACATTTATACCA\nCCAATGGCAGATTTACCAGATAAAGGCAAACCATTTGATTCTAGATTTGTGTTGTGTAGTACTAATCATAATCTATTAGC\nTCCACCAACAATAACCTCTTTGCCAGCTATGAACAGAAGATTTTTCTTTGATTTAGATATCATAGTATGTGATAAATATA\nAGGACCCACAGGGCAAACTGAATGTGTCTGCTGCTTTCCAACCGTGTGATGTTGACACAAAGATTGGCAATGCACGTTGT\nTGTCCATTCATTTGCGGTAAGGCAGTGATGTTTAGGGATCGCAATACATGTCAAACTTACACATTAGCACAAGTGTACAA\nTCAAATACTTGAAGAGGACAGAAGGCGTAGACAGGTGATTGATGTGATGGCTGCAATTTTCCAAGGGCCTATTACCCTTG\nAGGGACCACCACCAGCAGCAATTAGTGACCTGCTACAGTCAGTGAGAACCCCAGAAGTGATTAAGTATTGTGAGAATAAC\nAAATGGATTATACCAGCAGAGTGTAAAATTGAAAGGGACCTTAATATAGCAAATACTATTATTACAATCATTGCTAATAT\nTATTAGTATTTCTGGGATAATTTATGTAATATACAAGTTATTTTGCACACTGCAAGGACCATATTCAGGAGAACCTAAGC\nCAAAAACTAAGATTCCAGAAAGAAGAGTGGTTGCCCAGGGTCCAGAAGAAGAATTTGGAAGATCACTTATTAAGCATAAT\nTCATGTATTGTAACAACACAGAATGGTAAATTTACAGGTCTTGGAATTTATGATAGAGTGTTAATCCTACCAACACATGC\nAGATCCTGGTCATGAAGTACAAATAGATGGCATTACAACTAAAGTAGAGGAGTCATTTGATCTATTTAACAAGGATGGAG\nTCAAGTTAGAAATTACTGTACTCAAATTAAAAAGGAATGAAAAGTTTAAAGACATTAGAAAATACATACCAGAAAATGAG\nGACGATTACCCAGATTGCAATCTAGCCCTTTCTGCCAATCAACCAGAGACCACTATTATTAATGTGGGAGATGTGGTATC\nCTATGGTAACATTCTTCTTAGCGGCACCCAAACAGCTAGAATGCTTAAATATAATTATCCAACAAAGTCTGGTTATTGTG\nGTGGTATCTTATATAAAATAGGACAAGTTCTTGGAATTCATGTAGGAGGAAATGGAAGAGATGGCTTTGCTGCTATGTTG\nTTGAGATCTTACTTTTCAGAGACACAAGGGAAAATAGTCACTTCAAAGTCCACTAGTGAATGTGGTTTGCCTAGTATCCA\nTACACCAAGCAAGACTAAACTCCAACCTAGTGTATTCTTTGATGTATTTCCAGGCACTAAAGAACCAGCTGTTCTCACAA\nATAGTGACCATAGACTAGAGGTGGATTTTAATCAAGCTCTATTTTCTAAATACAAAGGAAATAACCAGTGTGTTATGAAT\nGATCATGTCAAAGTAGCCATTTCTCACTACTCAGCACAACTCATGACTCTGGACATCAACCCAGAACCTATTTCTTTAGA\nAGATAGTGTCTTTGGTACAGAAGGTCTGGAAGCTCTTGACCTTAACACTAGTGCAGGATTCCCATATGTGTCAATGGGCA\nTTAAGAAGAAAGATTTAATCAATAAGCAAACAAAAGATTTGACTAAACTTAAAATAGCATTAGATAAGTATGGTGTTGAT\nTTACCTATGGTTACCTTTCTCAAAGATGAGCTTAGGAAGAAGGAAAAGATTGCTGCTGGGAAAACTCGTGTGATTGAAGC\nTAGTAGTGTGAATGATACTATACTGTTTAGGACAACTTTTGGTAACCTTTTCTCCAAATTTCATTTGAATCCAGGTATTG\nTTACAGGCTCTGCTGTAGGTTGTGATCCAGAGACATTTTGGTCAAAAATTCCAGTTATGTTGGATGGTGAATGCATAATG\nGCTTTTGATTATACTAATTATGATGGAAGCATACACCCCATGTGGTTTCAAGCTCTTAAAGAGGTTTTGTCCAACTTATC\nCTTTGAAGCTAGTTTAATTGACAGATTGTGTAAATCCAAACATATTTTCAAAAATATGTATTATGAAGTGGAGGGTGGAG\nTCCCATCAGGTTGTTCTGGAACTAGCATATTTAATACAATGATTAATAATATTATTATTAGGACACTAGTGTTAGATGCC\nTATAAAAACATTGATTTGGATAAACTCAAGATAATTGCCTATGGAGATGATGTACTCTTTTCATATAAATACCAGCTTGA\nTATGGAAGCTATTGCTAATGAAGGTACCAAATATGGATTAACAATAACACCTGCTGACAAATCTAGTACTTTTAAACAAC\nTTGATTATAGTAATGTTACTTTTCTTAAAAGGGGATTTAAACAAGATGAGAAGTACCAATTCTTAATACACCCAACATTC\nCCAGTTGAAGAGATTCAGGAGTCCATTCGCTGGACAAAGAAACCATCTCAAATGCAGGAGCATGTCTTGTCATTGTGCCA\nCTTAATGTGGCATAATGGTAGAAGTGCCTATAAGCAATTTGAGGAGCGAATTCGCAGTGTTAGTGCTGGTCGCGCACTGT\nATATTCCTCCTTATGACTTGCTCTTGCATGAGTGGTATGAAAAATTTTAAATTGTTTAGATATAGAAGTATTAAACAATT\nAGTTTTTTAGTTTTAT\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_FJ445177.1_Human_rhinovirus_9_strain_ATCC_VR-489.fa", "content": ">RVA_FJ445177.1_Human_rhinovirus_9_strain_ATCC_VR-489 (7132 bp)\nTTAAAACTGGATCTGGGTTGTTCCCACTCAGATCTCCCACGTGGAGTAGTACACTATTATTACGGTAATCTTGTACGCCA\nGTTTTATAATCCCCTTACCCAAGTAACTTAGAAGATAAACACAAAGACCAATAGGAGATGATCATCCAGATCATCATAGG\nTCAAGCACTTCTGTTTCCCCGGTCAAGGTTGATATGCTCTAACAGGGCAAAAACAGCTGAGATCGTTATCCGCAAAGCGC\nCTACGCAAAGCCTAGTAACTATCTGGAAGTTGCTTGGTTGGTCGCTCCGCCATATCCCATGGTAGACCTGGCAGATGAGG\nCTAGAAATTCCCCACTGGTGACAGTGTTCTAGCCTGCGTGGCTGCCTGCACACCCTCTGGGTGTGAAACCAAGTAATGGA\nCAGGGTGTGAAGAGCCCCGTGTGCTCGCTTTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAACCCTGCAGCTAGGGC\nACACAATCCAGTGTGTATCTAGTCGTAATGAGCAATTGCGGGATGGGACCAACTACTTTGGGTGTCCGTGTTTCTTGTTT\nTTCTTTTATGTTTGCTTATGGTGACAATATATAGTAATATATRTTGGCATCATGGGCGCTCAGGTATCTAGACAAAATGT\nTGGGACTCACTCCACACAAAACTCAGTTTCAAATGGATCTAGCCTAAATTATTTCAATATAAATTACTTTAAGGATGCTG\nCATCAAGCGGTGCATCAAAGCTTGAATTTTCACAAGACCCTAGTAAGTTTACTGATCCAGTCAAAGATGTTCTTGAAAAA\nGGGATACCCACTTTGCAATCACCCACTGTTGAGGCGTGTGGATACTCAGACAGAATAATCCAAATCACAAGAGGAGATTC\nAACAATTACTTCACAAGATGTTGCCAATGCAATCGTTGGTTATGGAGTTTGGCCTCATTACCTTACTCCACAAGATGCAA\nCTGCTATAGRCAAGCCTTCTCACCCTGATACTTCGTCAAATAGGTTTTACACCTTGGAGAGCAAAACGTGGAGCAGTGAT\nTCCAAAGGCTGGTGGTGGAAGTTACCTGATGCATTGAAGGACATGGGAATTTTTGGGCAAAATATGTACTACCACTTCCT\nCGGTAGAAGTGGATATACAGTCCATGTGCAATGCAACTCAAGTAAGTTCCACCAAGGGACCTTGATTGTTGCCATGATAC\nCAGAACATCAATTGGCTGCAGCAGAGAGAGGCAATGTCACCGCCGGGTATAACTTCACACACCCTGGTGAACCTGGTAGA\nGAGGTTGGAAAGCCTAACCGTCAGTATACTAGTAAACAACCCAGTGATGATAATTGGCTCAATTTTGATGGCACACTTTT\nGGGCAACATAACTATTTATCCACACCAGTTTATAAACTTAAGAAGCAACAATTCAGCCACAATAATAGTACCATATGTGA\nATGCAGTGCCTATGGACTCTATGCTCAGACACAATAACTGGAGTCTAGTAATTATACCTATCTGCCCACTGCAATCCAGT\nGGAACTGAGTCAAGTACAMTCCCTATTACTATTTCCATTAGCCCCATGTTTGCTGAATTTTCTGGTGCACGTGCGAAGAG\nTCAGGGATTACCCGTGCTAACAACACCAGGATCTGGCCAATTTATGACTACAGATGACTTTCAATCTCCTAGTGCATTAC\nCATGGTTTCATCCAACTAAAGAAATATCTATACCTGGGCAAGTTAGAAACTTAATAGAAATGTGTCAAGTAGATACTATC\nATACCTATAAACAATACTGGAACTAACACTACAAGCATTAACATGTATACAGTACAAGTAGAGAGACAAGCTGATTTGAT\nGAGTGAAGTTTTTGCTATAAATGTAGATATAGCTTCCCACCCCTTAGCAACCACTATGTTAGGAGAGATTGCAAGTTATT\nACACACACTGGACAGGTAGTTTGCGTTTTAGCTTTATGTTCTGTGGGTCAGCTAGTTCCACTTTGAAACTTTTATTAGCA\nTACACCCCACCAGGAATTGCAAAACCTACAAGTAGAAGAGATGCAATGTTAGGTACTCATGTAGTATGGGATGTTGGTTT\nACAATCAACTATATCTATGGTGGTACCTTGGGTTAGTGCTAGTCACTTTAGAAACACAACTCCAGATAAGTACTCATTAG\nCAGGATTTATAACTTGCTGGTACCAAACCAACCTTGTAGTTCCAGCTGACACACCAACTACAGCAAACTTACTTTGCTTT\nGTATCTGCTTGCAAGGACTTCTGCTTGCGAATGGCTCGGGATACCAATCTACACAAGCAAAGTGGCCCAATAACCCAAAA\nTCCAGTGGAGAATTACATAGATCAGGTGCTTAATGAGGTTTTGGTAGTCCCAAACATTAAAGAGAGCAACCCTACAACCT\nCTAACTCAGCTCCAGCTCTAGATGCTGCTGAGACAGGCCATACTAGCAATGTTCAACCTGAAGACATGATTGAAACACGT\nTATGTGCAGACATCACAAACCAGAGATGAAATGAGTCTTGAAAGCTTCTTAGGGAGATCAGGTTGTATACACATATCTAA\nATTGAATATTGATTACAGTGACTATGATAAGAGTGTTGAAAATTTCACAATCTGGAAAATAAATATAAAGGAAATGGCCC\nAGATCAGGAGGAAATTTGAATTGTTTACATATGCAAGATTTGACTCTGAAATAACATTGGTCCCGTGTATAGCAGCAGAA\nAGTGATAGCGTTGGCCATGTTGTTATGCAGTACATGTATGTACCACCAGGGGCACCTTTACCAAGGACTAGAGATGATTA\nTGCATGGCAATCAGGCACAAATGCTTCCATCTTTTGGCAACATGGACAATCATATCCCAGATTTTCACTTCCGTTYTTGA\nGCATTGCCTCTGCATATTACATGTTCTATGATGGTTATGATGGTGGACCAGATTCTCTGTATGGAACAATTGTAACAAAT\nGATATGGGATCTTTATGTTCCCGTGTAGTTACTGAAGAGCATGGACCCCGTGTCAAAATTTCAACCAGAATATATCACAA\nAGCCAAACATGTTAAAGCCTGGTGCCCAAGACCTCCTAGGGCAGTTGAGTATATACATACACATGTCACAAATTACAAGC\nCAAGCACAGGCGATTATGCCACAGTTATACCAGTTAGAGACAATGTTAGGGCAGTAAAGAATGTAGGACCCAGTGATATG\nTATGTTCATGTAGGAAATTTGATATACAGAAATCTCCACTTATTCAACTCAGAAGCAAATGACTCTGTTTTAATATCATA\nCTCATCAGATTTAGTCATATACCGCACAAACACTATAGGTGATGACTATATACCAACTTGTGATTGTACTGATGCCACTT\nACTACTGTAAACATAAAAATAGATATTACCCCATTAAGGTCACCAGTCATGATTGGTATGAAATACAAGAGAGTGAATAC\nTACCCAAAACACATACAATACAATTTGTTAATAGGTGAAGGACCTTGTGAACCTGGTGATTGTGGTGGAAAATTATTATG\nCAAACATGGTGTGATAGGAATAATTACAGCTGGTGGTGAGGGTCATGTTGCATTTATAGATTTAAGACACTTCCATTGTG\nCTGAAGAACAGGGCATTACTGATTACATACACATGCTGGGAGAGGCTTTTGGAAATGGCTTTGTAGATAGTGTTAGGGAT\nCAAGTCAATGCAATAAACCCTATAAATAATATAAGTAAGAAAATAGTCAAATGGATGCTTAGAATAATATCAGCCATGGT\nCATCATTATTAGAAATAGTTCTGATCCACAAACAATAATAGCCACATTGACTTTGATTGGGTGTTCTGGGTCGCCATGGC\nGATTCTTAAAAGAAAAGTTTTGTAAATGGACACAACTGAATTATGTACACAAGGAGTCAGATTCTTGGCTTAAGAAATTC\nACAGAGATGTGTAATGCAGCTAGAGGACTTGAATGGATAGGAAATAAAATATCTAAGTTCATTGATTGGATGAAATCAAT\nGCTACCACAGGCACAGCTTAAGGTCAAATACTTGAGTGAATTAAAGAAGTTAAATTTACTAGAGAAACAAATTGATAACC\nTACGTTGTGCTGACACAAAAGTACAGGAAAAGATAAAATTTGAAATAGACACACTCCATGACTTATCCTGTAAATTTCTT\nCCATTATATGCAAGTGAGGCAAAGAGAATAAAGATTTTGCATAACAAATGTTGTAATATAATTAAACAAAGGAAAAGAAG\nTGAGCCTGTCGCYATCATGATACATGGACCACCTGGTACTGGCAAGTCTATAACAACTAGCTTTCTCGCCAGAATGATAA\nCAAATGAGAGTGACATTTATTCACTACCTCCAGACCCTAAGTACTTTGATGGCTACGACCAACAAAGTGTAGTCATTATG\nGATGATATCATGCAGAATCCTGGTGGTGAAGATATGTCTTTATTTTGTCAGATGGTTTCCAGTGTGACCTTTATACCCCC\nAATGGCTGATTTACCTGATAAAGGAAAACCTTTTGACTCCAGATTTGTTTTTTGTAGTACCAATCATTCACTTCTAGCCC\nCACCCACCATCACTTCACTTTCTGCAATGAATAGAAGATTTTACCTAGATTTGGATATTGTAGTGAATGAGAATTTTAGA\nGACTCTCAAGGGAAATTGGATGTGTCAAAATCATTCAGACCATGTGATATAGATAATAAGATTGGAAATGCAAAGTGCTG\nCCCTTTCATATGTGGAAAAGCAGTTGTGTTCAAGGACAGAAACACATGCCAAACATATACACTGTGCCAGATTTATAACA\nTGATTATTGAGGAGGATAAGCGGCGTAGAAATGTCATTGATGTCATGACTGCAATTTTCCAGGGTCCTATAACTATGAAC\nTCACCACCCCCCCCTGCCATAGCCGACTTGTTACAATCAGTGAGAACTCCAGAAGTTGTTAAATACTGTGAATATAATAA\nATGGATAATCCCAGCTGAATGCAAGATAGAAAGAGATCTGAACCTTGCAAACAATATAATAACAATTATTGCAAATATTA\nTTAGTATAGCAGGTATCATATTTGTTATTTATAAATTATTCTGTTCATTACAGGGACCATATTCGGGCGAACCCAAGCCA\nAAAACAAGAATTCCTGAGAGGAGAGTGGTGGCACAGGGTCCCGAAGAAGAATTTGGCCGCTCACTAATAAAACACAACAC\nATGTGTAGTCACAACTGATAATGGGAAATTCACTGGTTTAGGCATTTATGATAGATACATGATTGTTCCAACACATGCTG\nATCCAGGAAAAACTGTGCAAATTAATGGCATTGTCACAAATGTTGTTGATTCATATGATTTGCATAACAAAGATGGGATT\nAAGCTTGAGATCACAGTCATCAAACTAGACAGAAATGAAAAGTTTAGAGATATACGTAAGTATATACCCGAAAGGGAGGA\nTGACTACCCTGAATGTAATTTGGCACTTGTAGCAAACCAGGTTGAACCAACAATCATTAGTGTAGGTGATGTTATATCAT\nATGGTAATATATTACTTAGTGGTAACCAGACTGCTAGAATGCTTAAATATCATTACCCAACTAAATCTGGGTATTGTGGG\nGGTGTCCTGTATAAAATAGGTAGTATAATAGGAATTCATGTGGGTGGTAATGGTAGAGATGGATTTTCAGCAATGCTACT\nAAGATCATACTTTAATGAAACACAAGGACAAATAATCAGCTCAAGAAATGTTAAAGATCTTGGATACCCAACAATTCACA\nCTCCTAGTAAAACCAAACTACATCCAAGTGTTTTTCATGATGTATTCAAAGGCACAAAAGAACCTGCTGTTTTAACAGAA\nAAAGATCCACGTTTGGAGGTGGATTTTAAAACTTCCTTATTCTCCAAATACAAGGGTAATGTAGACTGCACATTGAATGA\nACACATGAGGGTGGCTATAGCGCATTATTCAGCCCAATTAATGACTCTTGACATAAATCCAGATAACATAACTATGGAAG\nAGAGTGTTTTTGGAACAGATGGTCTGGAGGCCTTGGATTTAAACACAAGTGCAGGATTTCCATATGTGAGTATGGGAATT\nAGAAAGAGGGATCTYATCAATAACAGCACTAAAGATATATCTAAACTAAGAGCAGCACTTGATAAATATGGGGTGGATTT\nGCCTATGGTCACTTTCCTCAAAGATGAACTTAGAAAGAAAGAGAAGATCTCATCTGGGAAAACCAGAGTTATAGAAGCTA\nGTAGTATTAATGATACTGTAGCATTTAGAATGACTTATGGCAATTTGTTTGCATGTTTTCACAAGAACCCTGGAATTATC\nACTGGTTCAGCAGTGGGATGTGATCCTGAAACTTTTTGGTCAAAAATACCTGTGATGTTGGATGGTGAGTGTATAATGGC\nATTTGATTACACAAATTATGATGGCAGTATCCACCCTGTATGGTTTGAAGCATTGAAGGAAATTTTGAAAGAATTGAAAT\nTTGAACATAGATTGATAGACAGGTTATGTAACTCTAGACATATATTTAGGGATTCCTATTATGAGGTTGAAGGGGGGGTA\nCCCTCAGGATGTTCTGGAACTAGTATATTTAACACAATGATTAATAATGTGATTATAAGGACTTTAGTGCTAGATGCTTA\nTAAACATATAGATTTAGATAAACTTAAAATAATAGCTTATGGGGATGATGTTATTTTTTCCTATAAATATCCTCTAGACA\nTGGAAGCTATTGCAATGGAAGGAAAGAAATATGGATTAACCATCACTCCTGCAGACAAGTCTGACACCTTTAAGAAGTTA\nGATTATGACAGTGTCACATTTCTAAAAAGAGGATTTAAACAAGACTCCAAATATCCCTTCCTTATACATCCTACTTTCCC\nAGTGAGTGAAATTCATGAATCAATCAGATGGACAAAGAAACCATCTCAAATGCAGGAACACGTGCTCTCGTTGTGCCATT\nTGATGTGGCATAATGGGCGTGACGTGTATAAGGAGTTCGAGAACGGGATACGCAGCGTCAGCGCTGGACGTGCGTTGTAT\nATTCCGCCTTATGAGCTCCTGTTGCATGAGTGGTATGAAAAATTTTAAACTTTATATATAGAAATAATAAACACTTAGTT\nTATTAGTTTTAT\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_GQ223229.1_Human_rhinovirus_A_isolate_N13.fa", "content": ">RVA_GQ223229.1_Human_rhinovirus_A_isolate_N13 (7136 bp)\nTTGAAACTGAGTGTGGGTTGTTCCCACCCACACTTCCCATGTGGAGTAGTACACTGTTATTACGGTAACCTTGTACGCCA\nGTTTTATCATCCCTTTCCCTTTGTAACTTAGAAGTTTTAAACTTGAGACCAATAGGTGGTGATCAGCCAGATCACTAAAG\nGTCAAGCACTTCTGTCTCCCCGGTCAACGCTGATATGCTCCGCCAGGGCAAAAACAGCTGCGATCGTTATCCGCAAAGTG\nCCTACGCAAAGCCTAGTAATATCTTGAATGATATATGGTTGGTCGTTCAGCTAAACCCCATAGTAGACCTGGCAGATGAG\nGCTGGAAATACCCCACTGGTGACAGTGTTCCAGCCTGCGTGGCTGCCTGCGCACTCTTGCGAGTGCGAAGCCATATATTT\nGACAAGGTGTGAAGAGCCCCGTGTGCTCACTTTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAACCCTGCAGCTAGT\nGCATACAATCCAGTGTGTGGCTAGTCGTAATGAGCAATTGCGGGATGGGACCAACTACTTTGGGTGTCCGTGTTTCACTT\nTTTCCTTTATAATTTGCTTATGGTGACAGTATATAGCTTATATATTGTTACCATGGGCGCACAAGTCTCCAGACAGAATG\nTTGGCACACACTCCACGCAAAACATGGTCTCAAATGGGTCTAGTTTAAATTATTTTAATATAAATTACTTTAAGGATGCA\nGCCTCCAGCGGCGCTTCAAAATTAGAATTTTCACATGACCCAAGCAAATTTACTGACCCAGTCAAAGATGTCCTTGAAAA\nAGGAATTCCAACACTGCAATCTCCTACAGTAGAGGCATGTGGTTATTCAGATAGAATAATGCAAATCACAAGAGGTGACT\nCTACAATAACATCACAGGATGTTGCAAATGCAGTGGTGGGTTATGGGGTGTGGCCACACTATTTAAGTGCAAAGGACGCC\nACTGCTATTGATAAGCCCACACAACCAGACACTTCATCAAACAGATTCTACACACTAGATAGCAAAATATGGAAACCAGG\nTTCTAAGGGCTGGTGGTGGAAGCTACCCGATGCATTGAAGGAAATGGGTATATTTGGAGAAAATATGCACTATCATTATC\nTTGGCAGAAGTGGTTATACTGTACATGTTCAATGCAATGCCAGTAAATTTCATCAAGGGACTTTACTAATTTTGATGATA\nCCTGAGCACCAGTTGGCAAATGCAAATGCTACCAATGCAGACGCTGGATACAATTATACCCATCCTGGTGAACGAGGCAG\nAGAGGTTGGTAGCGATCGTGTTGCTCATGCTAACCTTCCAAGTGATGATAATTGGCTTAATTTTGATGGTACTTTATTGG\nGTAATGCTCTTATATTTCCCCACCAATTCATTAATTTGAGAAGCAACAACTCTGCAACACTGATAGTCCCTTATGTAAAT\nGCTGTTCCAATGGATTCAATGCTTAGACATAATAATTGGAGTTTAGTGATAATTCCAATTTGTGAATTACTAGTAGATGC\nTAATGCCAGTGCTGTAGTTCCAATCACTATATCAATAAGCCCAATGTTTGCCGAATTCTCTGGGGCACGTGCAAAACCAG\nTGGCTGCTCCACAGGGTCTACCAATTTATATGACACCTGGCTCAGGCCAATTTATGACAACTGATGATTTCCAATCACCT\nTCAGCCTTACCATGGTATCACCCAACCAAAGAAATCTTAATTCCAGGGGAGGTCAAAAATTTAATAGAGATGTGTCAGGT\nGGATACTTCGATCCCTATCAATAACACAACACAAAACTTGAGAAAGATAAATATGTATACTATACAGTTAGAAAATCAAA\nCAGAAATGGCCAAAGAGATTTTTGCTATTAAAGTAGATATTGCATCACAACCTTTAGCAAATACCATGATTGGAGAAATT\nGCAAGTTATTTTACACATTGGGCTGGTAGTTTGCGTTTTAGTTTTATGTTCTGTGGTACAGCAAATACCACTCTCAAACT\nACTTCTAGCTTACACACCACCAGGCATAGGCAAACCAAGAGACAGAAAGCAAGCTATGCTTGGGACACACATAGTTTGGG\nACGTTGGGTTGCAATCAACAGTGTCTTTAGTTGTTCCATGGGTTAGTGCCAGTCATTTCAGGTACACATCTAGGGATGAA\nCATTCAGCAGCTGGATTCATAACATGTTGGTATCAGACAAATTTTGTTTTTCCCCCGAACACTCCCAATAGGGCTGACAT\nGCTGTGTTTTGTATCAGCGTGCAAGGATTTCTGCTTGCGTATGGCCAGAGACACGGATATGCACAAACAAGATGATGCCA\nTTGAACAAAACCCAGTTGAAAATTATGTGGGAGAGGCGCTTAATGAGGTCTTGGTTGTACCAAATATCAAAGAGAGTCAT\nCCAAGCACGTCCAACTCTGCCCCAATTTTAGATGCTGCTGAAACTGGGCATACTAGTAATGTACAACCAGAGGATACAAT\nTGAAACCCGATATGTACAAACAACACAAACAAGAGATGAAATGAGCATTGAGAGCTTCCTTGGTAGGTCAGGATGCGTGC\nATTCCTCAACAATAACACATGATGAACAACACACTAAGAAATTTAGAGTGTGGCGCATCAATTTACAAGAAATGGCCCAG\nATTAGGCGTAAATATGAAATGTTTACATATGTAAGATTTGATTCAGAGATGACTATGGTTCCAAGCATTGCAGGGTATGG\nTAATGATGTAGGTCATATAGTTATGCAATACATGTATGTACCGCCTGGAGCTCCAGAACCAACAAGTAGAGAACATTTTG\nCATGGCAATCAGGCACTAATGCATCTATCTTCTGGCAACAAGGACAACCCTTCCCAAGGTTTTCACTACCATTTTTGAGT\nGTTGCATCTGCTTATTACATGTTTTATGATGGTTATAATGGTGACACACCTGGATCCAAATATGGCACCACAGTAGTCAA\nTCGCATGGGTGCACTGTGTATGAGGGTTGTGACAAACAAACAAATCAATAAAGTTGAAATCACAACTAATATATACCATA\nAAGTTAAGCATGTGAAAGCATGGTGTCCCAGACCACCCAGAGCTGTTCCATACAGGTATGTTGGATCAACAAATTATAAA\nAAACCTGATCAGGAAGATGTTACAATTTTCATTGAACGTAGACAAGACCCAAAATTCATTACAACAGGACCAAGTGATTT\nGTTCGTACATGTGGGTAATTTGATATACAGAAATTTACATCTATTTAATTCAGAAGTACATGACTCAGTATTAATATCGT\nATTCCTCAGATTTAGTCATCTACCGCACAAACTCTACAGGTAATGACTACATTCCCACATGTGACTGCACTCAAGCAACC\nTATTATTGTAGACATAAAGATAGGTATTACCCAATTAATGTTACCAGTCATGACTGGTATGAGATTCAAGAAAGTGAATA\nCTACCCAAAACACATTCAATATAACCTTTTGATAGGTGAAGGTCCATGTGAACCAGGAGACTGTGGAGGAAAGCTATTGT\nGTAAACATGGAGTGATTGGAATAATAACAGCAGGTGGAGAGGGTCATGTGGCATTTATTGATCTCAGGCAATTTCATTGT\nGCAGATGAGCAAGGAATAACTGATTACATCCACATGCTGGGTGAAGCCTTTGGATCAGGATTTGTTGACAGTGTTAAAGG\nCCAAATAAACGCTATCAATCCAATTAACAACATTAGTAAAAAGATAGTCAAGTGGTTGCTTAGAATAATCTCTGCAATGG\nTTGTAATTATTAGAAATTCCTCTGATCCACAAACAATCATAGCCACATTAACACTAATTGGATGCTCAGGTTCCCCCTGG\nCGATTTCTTAAAGAAAAATTTTGCAAATGGACCCAATTAAATTACATACACAAGGAATCTGATTCATGGTTAAAGAAATT\nCACCGAAATGTGTAATGCAGCCAGAGGCTTAGAACGGATTGGCAATAAAATATCAAAATTCATTGAATGGATGAAATCTA\nTGCTTCCTCAGGCTCAGCTTAAAATCAAATATTTGAGTGAGCTCAAGAAACTTAGTTTTTTAGAGAAGCAGATGGAGTAC\nTTAAGAGTTGCTGACTCACAAACACAGGAAAAAATTAAATGTGAGATTGACACTTTACATGATCTTTCTTGTAAATTTTT\nACCACTCTATGCTAGTGACGCTAAAAGAATAAAGATATTATATAACAAATGTAACACAATTATTAAACAGAAGAAAAGGT\nGTGAACCAGTTGCAGTTGCCATACATGGTGAACCTGGTACTGGTAAGTCTATGACTACAAACTTTCTTGCTAGAATGATA\nACTAATGATAGTGACATATACTCCTTACCACCTGATCCCAAATACTTTGATGGATACGACCAGCAAAGTGTGGTTATTAT\nGGATGACATTATGCAAAATCCAAGTGGGGAAGATATGACCTTATTCTGTCAAATGGTGTCTAGTGTCACATTCATACCAC\nCGATGGCCGATTTGCCTGATAAGGGTAAACCTTTTGATTCCAGGTTTGTGTTGTGCGGTACTAATCATAATTTATTAGCA\nCCTCCTACAATTACTTCATTGCCAGCTATGAACAGAAGATTCTTTCTAGATTTAGATATTGTGGCGTGTGATAAATACAA\nGGATCCACAGGGAAAGCTAAATGTGGCTGCTGCCTTTCAACCTTGTGATGTAAATACAAAAATTGGAAATGCTCGCTGCT\nGTCCCTTTATCTGTGGTAAAGCTGTCATTTTTAGAGATCGTAATAATTGTCAGACTTACACTCTGGCACAAGTGTATAAT\nCAAATACTTACTGAGGACAAAAGACGTAGGCAAGTAGTAGATGTTATGGCAGCAATTTTTCAGGGACCCATTACTCTTGA\nAGGACCTCCACCTGCAGCAATAAATGATTTATTGAAATCAGTTAGAACTCCAGAAGTCATTAAGTACTGTGAGGACAATA\nAATGGATAGTTCCAGCTGAGTGTAAGGTTGAAAGAGATCTCAATATAGCCAACACTGTTATTACAATTATTGCTAATATT\nATCAGTATTTCTGGAATAATTTATGTTATATATAAACTTTTCTGTACATTACAAGGACCATATTCAGGTGAACCCAAGCC\nCAAAACCAAGATGCCAGAAAGGAGGGTGGTGGCTCAAGGACCAGAAGAGGAGTTTGGTAGGTCCCTTATTAAACACAATT\nCATGCATTGTAACAACACAGAATGGTAAATTCACAGGTCTAGGGATATATGATAGAACACTAATCCTACCAACACATGCA\nGATCCAGGTAGTGAAATACAGATAGATGGCATTACAACTAAAGTGGAAGACTCTTATGACCTATTCAATAAAGATGGAAT\nCAAGCTAGAAATTACAGTGCTTAAACTTAAGAGAAATGAAAAGTTCAAAGATATCAGGAAATACATTCCAGAAAATGAAG\nATGATTACCCAGATTGTAATTTGGCCCTATCTGCTAATCAACCAGAAACCACAATAATCAATGTAGGGGATGTAGTATCA\nTATGGAAACATTTTACTTAGTGGAAATCAAACAGCAAGGATGCTCAAATACAATTACCCAACGAAATCAGGTTATTGTGG\nTGGGATTCTATATAAAATTGGACAAGTTTTGGGAATTCATGTTGGTGGTAATGGAAGAGATGGGTTTGCAGCTATGTTAT\nTAAGATCATATTTTTCAGAAACACAAGGTCAAATAACTACTACTAAACCTACTATTGAATGCAATCTACCTAGTATACAT\nACACCTAGCAAAATCAAGTTACAACCTAGTGTATTTTATGATGTCTTTCCTGGTAGTAAGGAACCAGCTGTGCTCTCAGA\nATTTGATCCCAGATTAGAGGTTGATTTCAAACAAGCCTTATTTTCTAAATACAAAGGTAATAACCAATGTGAAATAAATG\nATCATGTTAGGGTAGCAATTTCCCACTATTCAGCACAGTTGATGACATTGGATATTGATTCAAGTCCAATTTCATTAGAA\nGATAGTGTTTTTGGTACAGAGGGTCTGGAGGCACTCGATCTTACCACTAGTGCTGGATTTCCTTATGTGTCTATGGGCAT\nTAAGAAAAGAGACTTAATTAATAAACAAACAAGAGATATCACAAAACTTAAAATGGCATTGGATAAGTATGGTGTTGACT\nTGCCTATGGTTACACTTCTTAAGGATGAACTTAGAAAGAAGGAGAAAATCTCTGCTGGGAAAACACGTGTCATTGAAGCT\nAGTAGTGTAAATGACACTGTGCTGTTTAGGACAACTTTTGGCAACCTCTTCTCCAAATTTCACTTAAACCCTGGTATCGT\nTACTGGCTCCGCAGTGGGATGCGATCCAGAGACCTTTTGGTCAAAAGTACCAGTAATGTTAGATGGTGAGTGCATAATGG\nCATTTGATTATACAAATTATGATGGTGGTATACATCCAATTTGGTTTAAAGCTCTTAAAGAAGTGCTCTTTAATCTAGGG\nTTTAGGCCCAATCTAATAGATAGGTTGTGTAAATCAAAACACATTTTTAAGAATGTATATTATGAAGTAGAAGGGGGGGT\nCCCATCAGGTTGCTCTGGAACAAGCATATTTAATACAATGATTAATAATATTATTATTAGGACATTAGTTTTGGATGCTT\nACAAAAATATTGATTTAGACAAGCTTAGGATAATAGCTTATGGGGATGACGTCATCTTTTCTTACAAGTATCAGTTGGAC\nATGGAAGCAATTGCTAAAGAAGGTATTAAGTATGGTCTTACAATCACTCCAGCTGACAAATCAAGTGAATTCAAGAAATT\nGGACTATAGTAGTGTGACCTTTCTAAAAAGAGGGTTTAAACAAGATGACAAATACTCATTTTTAATACATCCAACCTTTC\nCAGTTGATGAGATACATGAATCCATTCGATGGACTAAAAAACCATCACAGATGCAAGAGCACGTTCTGTCACTGTGTCAT\nTTAATGTGGCACAATGGTAGGGACGTGTATAAGCAGTTTGAGCAAAGGATACGCAGTGTGAGCGCTGGTCGCGCACTGTA\nTATCCCTCCATATGACCTGCTTTTGCATGAATGGTATGAAAAATTTTAAGTTGTTTAGATATAGAAATAATAAACAATTA\nGTTTTTTAGTTTTATA\n" }, { "path": "tests/input/TestSkaniReferenceSelection/RVA_L24917.1_Human_rhinovirus_type_16_polyprotein_gene.fa", "content": ">RVA_L24917.1_Human_rhinovirus_type_16_polyprotein_gene (7124 bp)\nTTAAAACTGGATCTGGGTTGTTCCCACCCAGATCACCTACATGGTGTTGTACACTATTATTACGGTAATCTTGTACGCCA\nGTTTTATACTCCCTTTCCCAAATGTAACTTAGAAGCAAAGCAAACTGATCAATAGGGGACAATCATCCAGATTGTCAAAG\nATCAAGCACTTCTGTTTCCCCGGTCAAAGTTGATATGCTCCACAAGGGCAAAAACAACTGAGATCGTTATCCGCAAGATG\nCCTACGCAAAGCCTAGTAATACATTGAAAGATACTTGGTTGGTCGCTCAGCTGTTAACCCAACAGTAGACCTGGTAGATG\nAGGCTAGAGATTCCCCTCCGGCGACGGAGTTCTAGCCTGCGTGGCTGCCTGCACACCCACTGGGTGTGAAGCCAAGTATT\nGGACAAGGTGTGAAGAGCCGCGTGTGCTCATCTTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAAACCTGCAGCCAG\nTGCACACAATCCAGTGTGTAGCTGGTCGTAATGAGCAATTGCGGGATGGGACCAACTACTTTGGGTGTCCGTGTCCGTGT\nTTCACTTTTTTTCCTTTTATTATTGCTTATGGTGACAATATATATAGCATATATATATTGTTATCATGGGCGCTCAAGTA\nTCTAGACAGAATGTTGGTACGCACTCAACACAAAATATGGTGTCAAATGGATCCAGCCTCAATTATTTTAACATTAATTA\nTTTCAAAGATGCAGCTTCCAGTGGTGCTTCTCGATTGGACTTCTCTCAAGACCCCAGTAAATTCACAGACCCAGTTAAGG\nATGTGTTGGAGAAAGGCATACCCACTCTGCAATCTCCAAGTGTAGAAGCTTGTGGATACTCTGATAGAATAATCCAAATT\nACAAGAGGCGACTCAACCATAACATCTCAAGATGTTGCTAATGCAGTGGTTGGGTATGGGGTATGGCCACACTACCTAAC\nTCCGCAGGATGCAACGGCTATAGACAAGCCAACACAACCAGATACATCATCAAATAGGTTTTACACACTGGATAGTAAAA\nTGTGGAACAGTACCTCCAAAGGTTGGTGGTGGAAACTACCAGATGCTCTTAAAGACATGGGTATTTTTGGTGAAAATATG\nTTTTATCATTTCTTGGGTAGAAGTGGTTATACAGTGCACGTACAGTGCAATGCAAGTAAATTCCACCAGGGTACACTACT\nAGTGGTTATGATACCAGAACACCAGTTAGCTACAGTAAATAAAGGTAATGTTAATGCAGGTTACAAATACACACATCCTG\nGTGAAGCTGGTAGAGAAGTGGGTACACAAGTTGAAAATGAGAAACAACCTAGTGATGATAATTGGCTAAATTTTGATGGT\nACATTATTGGGCAATTTACTGATATTCCCACACCAGTTTATTAACTTAAGGAGCAATAACTCAGCAACTCTTATAGTACC\nATATGTTAATGCTGTTCCAATGGATTCTATGGTTAGACATAACAATTGGAGTTTGGTAATAATACCAGTTTGTCAACTAC\nAAAGCAACAATATATCCAACATTGTTCCCATCACTGTTTCCATTAGCCCAATGTGTGCTGAATTCTCTGGAGCACGTGCC\nAAAACAGTTGTGCAAGGTCTACCAGTATATGTTACACCAGGATCAGGACAATTCATGACAACAGATGATATGCAATCTCC\nATGTGCACTGCCTTGGTACCATCCAACAAAAGAGATCTTTATACCAGGAGAGGTTAAGAACTTGATTGAAATGTGTCAGG\nTGGATACACTCATACCAATAAATAGCACACAGTCTAACATTGGCAATGTCAGCATGTACACAGTAACTCTATCACCACAA\nACAAAATTAGCTGAAGAAATTTTTGCAATTAAAGTAGATATTGCCTCACATCCCTTAGCCACAACCCTCATTGGTGAGAT\nAGCAAGTTACTTTACACACTGGACAGGGAGCCTGCGATTCAGTTTCATGTTTTGCGGGACTGCAAACACTACCTTAAAAG\nTTTTGCTAGCATATACACCCCCAGGGATTGGTAAGCCTAGAAGTAGAAAGGAAGCAATGTTAGGGACACACGTGGTGTGG\nGATGTAGGTTTACAATCTACAGTGTCATTGGTTGTACCATGGATCAGTGCCAGTCAGTATAGATTCACTACACCAGACAC\nATACTCCTCAGCAGGCTACATTACATGCTGGTATCAAACTAATTTTGTTGTTCCACCAAACACACCTAACACTGCTGAGA\nTGTTGTGTTTTGTATCTGGATGCAACCACTTTTGCCTTCGGATGGCAAGAGACACAGACCTGCACAAGCAAACAGGACCA\nATAACACAAAATCCAGTGGAAAGATATGTAGATGAAGTCTTAAATGAAGTGTTAGTAGTGCCCAATATTAATCAGAGCCA\nCCCTACCACATCAAATGCAGCCCCAGTTTTGGATGCTGCTGAAACAGGACATACCAATAAGATACAGCCAGAAGACACTA\nTAGAAACCAGATATGTGCAATCTTCACAGACATTGGATGAAATGAGTGTGGAAAGCTTCCTAGGCAGATCGGGGTGCATC\nCATGAATCAGTGTTGGATATTGTGGACAATTACAATGATCAAAGTTTCACTAAATGGAACATAAACCTGCAAGAAATGGC\nACAAATTAGAAGAAAATTTGAAATGTTTACTTATGCAAGATTTGACTCTGAAATTACTATGGTACCAAGTGTAGCAGCCA\nAAGATGGTCACATTGGTCATATAGTCATGCAATATATGTATGTACCACCAGGAGCACCTATACCAACAACTAGAGATGAC\nTATGCTTGGCAATCTGGAACAAATGCATCTGTATTTTGGCAGCATGGGCAACCTTTCCCTCGCTTTTCACTTCCCTTTTT\nGAGTATTGCATCAGCATATTACATGTTTTATGATGGTTATGATGGAGACACATATAAATCCAGATATGGAACTGTAGTCA\nCCAATGACATGGGAACTTTGTGTTCGCGTATTGTGACCAGTGAGCAATTACACAAAGTCAAAGTGGTAACAAGGATATAT\nCACAAAGCCAAACACACCAAAGCTTGGTGCCCAAGACCACCCAGAGCTGTTCAATACTCACATACACATACCACCAACTA\nCAAATTGAGTTCAGAAGTACACAATGATGTGGCTATAAGACCTAGAACAAATCTAACAACTGTTGGGCCTAGTGACATGT\nATGTGCATGTTGGTAATCTAATATACAGAAATCTACATTTATTTAACTCTGACATACATGATTCCATTTTAGTGTCTTAT\nTCATCAGATTTAATCATATACCGAACAAGCACACAAGGTGATGGTTATATTCCAACATGTAATTGCACTGAAGCTACATA\nTTACTGCAAACACAAAAACAGGTACTACCCAATTAATGTCACACCTCATGACTGGTATGAGATACAAGAGAGTGAATATT\nATCCAAAACATATCCAGTACAATTTACTAATAGGTGAAGGACCATGTGAACCAGGTGATTGTGGTGGGAAATTATTATGC\nAAACATGGAGTGATAGGTATTATTACAGCAGGTGGTGAGGGCCATGTTGCATTCATAGATCTTAGACACTTTCACTGTGC\nTGAAGAACAAGGAATCACTGATTACATACACATGCTCGGTGAAGCTTTTGGTAGTGGATTTGTAGATAGTGTTAAAGACC\nAGATTAATTCAATAAATCCCATCAATAACATTAGCAGTAAGATGGTTAAATGGATGTTAAGAATTATATCAGCTATGGTT\nATAATTATTAGAAACTCTTCAGATCCGCAAACAATAATTGCCACTTTAACACTGATTGGATGCAATGGTTCTCCTTGGAG\nATTTCTCAAAGAAAAGTTCTGTAAATGGACTCAATTAACTTATATACACAAAGAATCAGATTCATGGCTCAAAAAATTCA\nCTGAGATGTGTAATGCAGCTAGGGGGCTAGAATGGATTGGAAACAAAATATCCAAATTTATCGATTGGATGAAATCAATG\nCTACCCCAGGCACAATTAAAAGTTAAGTATTTGAGTGAACTTAAGAAACTCAACTTTCTGGAGAAACAGGTTGAAAATCT\nCAGAGCAGCTGATACTAACACTCAAGAAAAAATCAAGTGTGAGATAGATACATTGCATGACTTATCCTGTAAGTTTTTAC\nCTCTGTATGCCAGTGAAGCAAAGAGAATTAAAGTGTTGTATCACAAGTGCACTAACATAATTAAACAGAAGAAGAGAAGT\nGAACCTGTAGCAGTTATGATACACGGGCCTCCTGGGACCGGAAAATCAATCACTACAAGCTTCCTGGCTAGAATGATTAC\nTAATGAGAGTGACATATACTCACTTCCACCAGACCCTAAATATTTTGATGGTTATGATAACCAGAGTGTAGTAATAATGG\nATGACATCATGCAAAACCCTGGTGGTGAGGACATGACATTATTCTGTCAGATGGTATCTAGTGTGACTTTTATACCCCCA\nATGGCTGATCTACCAGATAAGGGAAAACCCTTTGATTCTAGATTTGTATTGTGTAGTACTAATCACTCACTCTTGGCACC\nCCCAACTATATCGTCGCTCCCAGCAATGAATAGAAGATTCTATTTAGATTTAGATATTCTTGTGCATGATAACTACAAAG\nATAATCAGGGTAAGTTAGATGTTTCTAGAGCATTTCGGCTATGTGATGTTGATTCAAAGATTGGAAATGCAAAATGTTGT\nCCATTTGTATGTGGCAAGGCAGTGACATTCAAGGACCGCAACACATGTAGAACTTATTCACTTTCCCAAATATACAACCA\nAATTCTTGAGGAAGACAAGAGAAGGAGACAGGTGGTTGATGTCATGTCTGCAATTTTCCAAGGGCCTATATCCATGGATA\nAACCCCCACCACCAGCTATAACAGACCTTTTACGCTCAGTAAGGACACCAGAAGTAATTAAGTACTGCCAAGACAATAAA\nTGGATAGTTCCTGCGGACTGCCAAATTGAAAGGGATCTGAATATAGCTAATAGCATAATCACAATCATAGCTAATATCAT\nCAGTATAGCAGGGATTATATATATAATTTATAAGCTCTTTTGCTCTCTACAGGGCCCTTACTCGGGGGAGCCCAAACCTA\nAGACAAAAGTTCCCGAGAGAAGAGTGGTAGCTCAAGGTCCAGAAGAAGAATTTGGAATGTCTATTATTAAAAATAATACC\nTGTGTTGTGACCACAACAAATGGAAAATTTACAGGATTAGGCATTTATGACAGAATCTTAATATTACCAACACATGCTGA\nCCCGGGCAGTGAAATTCAAGTAAATGGAATACACACCAAAGTGCTTGATTCTTATGACTTATTTAATAAGGAAGGTGTCA\nAGTTGGAAATTACTGTGCTAAAGTTAGATAGAAATGAGAAGTTCAGGGATATACGTAAGTACATACCTGAATCAGAAGAT\nGACTATCCTGAATGCAACCTAGCACTAGTGGCCAATCAAACAGAACCAACTATAATCAAAGTAGGGGATGTTGTGTCTTA\nTGGTAATATATTACTTAGTGGCACACAGACAGCCAGAATGCTTAAATATAACTATCCTACAAAATCTGGGTATTGTGGTG\nGTGTGTTATACAAGATTGGCCAGATCTTAGGTATACATGTGGGTGGCAATGGTAGAGATGGGTTTTCATCTATGCTATTG\nAGATCATACTTCACTGAACAACAAGGCCAAATTCAAATCTCTAAACATGTTAAAGATGTTGGCTTACCCTCAATACATAC\nGCCAACTAAAACTAAATTGCAGCCAAGTGTCTTCTATGACATTTTTCCAGGCAGTAAGGAACCAGCAGTCCTCACAGAAA\nAAGATCCTAGATTGAAAGTGGACTTTGACTCAGCTCTTTTTTCAAAATACAAAGGTAACACAGAGTGCAGTTTGAATGAA\nCATATACAAGTTGCAGTAGCACACTACTCAGCTCAGCTAGCAACACTAGATATAGATCCACAACCAATTGCAATGGAAGA\nTAGTGTTTTTGGAATGGATGGCTTGGAAGCTTTGGATCTGAATACTAGTGCAGGTTATCCCTATGTAACACTAGGAATTA\nAAAAGAAAGATCTTATTAATAACAAGACTAAAGATATTTCCAAACTTAAGCTAGCATTAGACAAATATGATGTTGATTTG\nCCCATGATTACTTTCTTAAAAGATGAACTTAGAAAGAAGGATAAGATAGCAGCAGGCAAAACCAGAGTTATAGAAGCTAG\nTAGTATAAATGATACCATTTTGTTTAGAACAGTTTATGGAAACCTATTTTCTAAATTTCACTTGAACCCAGGAGTGGTAA\nCAGGCTGTGCAGTTGGATGTGATCCAGAAACCTTTTGGTCTAAAATTCCCTTGATGTTAGATGGAGATTGCATCATGGCT\nTTTGATTATACAAATTATGATGGTAGCATTCATCCAATTTGGTTTAAAGCTCTCGGGATGGTACTTGATAATTTATCCTT\nTAACCCTACTCTAATCAATAGACTTTGTAACTCAAAACATATTTTCAAGTCCACATATTATGAAGTTGAAGGTGGTGTGC\nCCTCTGGTTGTTCTGGAACTAGTATATTTAACTCAATGATTAATAATATAATCATTAGAACCTTAGTTTTGGATGCATAT\nAAACATATTGATTTAGATAAACTTAAAATAATTGCCTATGGTGATGATGTGATCTTTTCTTACAAGTATAAACTAGACAT\nGGAAGCCATAGCCAAGGAAGGGCAGAAATATGGACTTACTATAACACCTGCAGATAAATCTAGTGAATTCAAAGAACTTG\nATTATGGAAATGTAACTTTTCTTAAAAGAGGATTTAGACAAGATGATAAATACAAATTTTTGATACATCCTACTTTTCCA\nGTTGAAGAGATTTATGAGTCCATTAGATGGACAAAGAAACCATCTCAAATGCAGGAGCATGTCTTATCCTTGTGTCACTT\nAATGTGGCACAATGGTCCTGAGATTTATAAGGACTTTGAAACAAAGATACGCAGTGTCAGCGCTGGACGTGCACTGTATA\nTCCCTCCTTATGAACTCCTAAGACATGAATGGTATGAAAAATTCTAGATATAGAATTAATAAATGAATAGTTTGTTAGTT\nTTAT\n" }, { "path": "tests/input/TestSkaniReferenceSelection/USA-MA-Broad_BWH-19947-2023.l000013249603_C5.HTKJ7DRX3.1.acellular.dedup.assembly1-spades.fasta", "content": ">NODE_1_length_6988_cov_737.516992\nCCAGTTTTATCTCCCCTCCCCCCCTTATGTAACTTAGAAGTTCTGCACACCGACCAATAG\nCGGACAATCAGCCAGATTGTTTCGGGTCAAGCACTACTGTTTCCCCGGTCGATGTTGATA\nTGCTCCAACAGGGCAAAAACAACAGCGATCGTTATCCGCAAGGTGCCTACACAAAGCCTA\nGTACCATCTTGGAAGAATTGTGGTTGGTCGCTCAGTTGCAAACCCAGCAATAGACCTGGC\nAGATGAGGCTGGACATCCCCCACTGGCGACAGTGGTCCAGCCTGCGTGGCTGCCTGCACA\nCCTCTATGAGGTGTGAAGCCATAATTTCGACAAGGTGCGAAGAGCCGCGTGTGCTCACCT\nTGAGTCCTCCGGCCCCTGAATGCGGCTAACCTTAAACCTGCAGCCATGGTCCACGAACCA\nGTGGATACGTGGTCGTAATGAGCAATTGCGGGATGGGACCGACTACTTTGGGTGTCCGTG\nTTTCCTGTTTTTCTTTTATACTGCTTATGGTGACAATATATACGATATATATTGACACCA\nTGGGCGCACAAGTATCCAGACAGAATGTTGGTACACACTCAACACAAAACACTGTTTCAA\nATGGGTCAAGTCTAAATTATTTCAACATCAATTATTTTAAAGATGCTGCTTCTAGTGGAG\nCCTCCAAGTTAGAATTTTCACAGGATCCAAGCAAGTTTACTGACCCCGTTAAAGATGTTC\nTTGAAAAGGGAATTCCAACTCTACAATCACCAACAGTTGAGGCATGTGGTTATTCTGATA\nGAATTATTCAGATAACCAGAGGAGATTCAACCATCACATCTCAAGATGTTGCAAATGCAG\nTAGTTGCATATGGTGTGTGGCCACATTACCTAACACCGCAAGATGCAACTGCTATTGACA\nAACCATCACAACCTGAAACATCATCCAACAGATTCTACACATTGGAGAGTAAAACCTGGG\nATACATCATCAAAGGGCTGGTGGTGGAAACTACCAGATGCATTGAAGGATATGGGTATAT\nTTGGACAAAACATGTATTACCACTTCCTTGGCAGGAGTGGTTACACAGTACATGTTCAAT\nGCAATGCTAGTAAATTTCATCAAGGCACTTTAATTGTGGCAATGATCCCAGAACATCAAT\nTGGCTAGTGCAAGACATGGAAATCTTACTGCTGGTTACAATTTCACACACCCAGGCGAAA\nATGGGAGAAATGTTGGGCAATTAAGAACAGAATATTTAGACAAGCAACCCAGTGATGACA\nATTGGTTGAACTTTGATGGGACATTGCTTGGCAACATCACAATATTTCCCCATCAATTTA\nTTAATTTAAGAAGTAATAATTCAGCCACAATAATAGTTCCTTATGTGAATGCTGTCCCAA\nTGGATTCTATGCTTAGACATAATAACTGGAGCTTGGTTATTATACCAATATGTGAATTGC\nAGGTAGATACAGGCGTTCCAGCCACTGTACCAATAACCATATCCATAAGCCCAATGTTTG\nCAGAATTCTCAGGAGCAAGAGCAAGGAGCCAAGGTATCCCAACTATGCTTACACCTGGAT\nCAGGGCAATTCATGACTACTGATGACTTTCAATCCCCTAGTGCATTACCGTGGTACCATC\nCCACTAAGGAGATATCCATCCCTGGGCAAGTCAGAAATCTAATCGAATTATGTGAGGTTG\nATACCCTTATACCAGTAAATAACACCTCAGAGAATCTAAAAACCACAAACATGTACACTG\nTTCATTTGGAGAGACGCTCTGATTTGGCACAGGAAATATTTGCAATAAGAGTAGATATTG\nCTTCACAACCCTTGGCAACTACATTAATAGGGGAAATTGCTAGTTATTACACACATTGGA\nCCGGCAGCCTTCGGTTCAGTTTTATGTTTTGTGGATCTGCAAGCACAACTTTAAAACTCT\nTACTAGCATACACACCTCCAGGAATTGCCAAGCCCACTACTAGGAAACAAGCTATGCTAG\nGAACACATGTAGTGTGGGATGTGGGCCTGCAATCGACCATTTCAATGATTGTGCCATGGG\nTTAGTGCTAGTCACTTTAGAAATACAACCCCAGATACTTACTCACTTGCAGGATATGTAA\nCTTGCTGGTACCAAACCAACTTGGTTGTCCCACCCAATACCCCACCTAATGCTAAAATGC\nTCTGTTTTGTTTCTGGTTGTAAAGATTTTTGCTTAAGGATGGCAAGAGATACTAACCTAC\nACAAGCAAAGTGGTGTCATAGAACAAAATCCAGTTGAGAATTATGTAGATGAAATCTTGA\nATCAAGTTTTGGTAGTTCCAAATACAGTAGAGAGTCATCCAACAACATCTAATGCTGCTC\nCAGCTTTAGATGCAGCTGAGACTGGTCACACTAGCCATGTCCAACCAGAAGACATGTTAG\nAAACAAGACAAGTGCAAAATTTCCAAACTAGAGATGAGATGAGTATTGAGAGCTTTCTAG\nGTAGATCTGGATGCATACACATTTCAACACTTGAGATAGATTACACAAATTATAATGGAG\nAAGGCAAAAACTTCACTCAGTGGCCGATCAACTTACAGGAAATGGCTCAGATCAGGAGGA\nAATATGAATTATTCACATATCTTAGATTTGATTCAGAGATTACTTTAGTGCCTTGCATAG\nCAGCCAAAGGAAATGATATAGGTCATGTGGTAATGCAATATATGTATGTACCACCAGGAG\nCTCCAATACCAACAACCAGGAAGGATTACGCATGGCAATCCGGAACAAATGCATCTGTAT\nTTTGGCAACATGGACAAACATTTCCCAGATTCTCGCTGCCATTTCTGAGCATTGCATCAG\nCATATTACATGTTTTATGATGGTTATGAAGGAGATCAAAACACATCCCGTTATGGTACCA\nTTGCCAGTAATCACATGGGGACACTATGCTCCAGAATAGTTACAGAAGAACACCAAAATA\nAAGTTGAAGTGACCACTAGAATATATCATAAAGCCAAACATGTTAAAGCTTGGTGTCCGA\nGACCACCTAGGGCTGTTGAATACACGTTCAGGCGTGTAACAAACTACAAAAGAGATGGGC\nAACAAGTTGAGATTGCTATCGAGCCCAGAAGAGACATTAAGTTTGTAAATGCAGGTCCAA\nCTGACTTGTATGTGCATGTAGGGAATTTAATTTATAGAAATTTGCATCTTTTTAACTCTG\nAACTGCATGATTCCATATTAGTCTCCTATTCATCAGATTTAATCATTTATCGAACAAACA\nCAGTAGGTGATGATTATATTCCAACATGTGATTGCACAGAAGCCACATATTATTGTAGAC\nACAAAAATAGATACTACCCAATTAAAGTAACTAGTCATGATTGGTATGAAATTCAAGAGA\nGTGAATATTATCCTAAACACATACAATATAATTTATTAATAGGAGAGGGCCCATGTGAAC\nCTGGTGACTGTGGTGGAAAATTGCTATGCAGGCATGGAGTGATAGGTATTGTAACAGCTG\nGGGGTGAAGGTCATGTGGCTTTTATTGATTTAAGACAGTTCCACTGTGCTGAAGAACAAG\nGTATAACAGACTACATTCACATGCTTGGTGAAGCCTTTGGTAATGGATTTGTGGAGAGTG\nTCAAAGAACAAGTCAGCGCAATAAATCCAATCAACAATATTAGCAAAAAGATAGTTAAGT\nGGATACTTAGAATAATATCAGCAATGGTTATAATAATTAGAAACAATTCTGACCCTCAAA\nCAATCATCGCTACTCTAACCTTGATTGGGTGTTCGGGATCGCCATGGCGTTTTCTGAAAG\nAGAAATTTTGCAAATGGACACAACTCACTTATATCCACAAGGAATCAGATTCCTGGCTCA\nAGAAATTCACTGAAATGTGTAATGCTGCACGAGGATTGGAATGGATTGGCAATAAGATTT\nCAAAATTCATAGAGTGGATGAAATCCATGTTACCTCAAGCCCAACTTAAAGTGAAATACC\nTTTCTGAACTTCGGAAACTCAATTTACTGGAAAAGCAGATGGAGAACCTAAGAGCAGCAG\nATGCAAACACACAGGAGAAAATTAAGTTAGAGATTGACACCCTCCATGATTTATCATGCA\nAATTTCTGCCATTGTATGCTAGTGAAGCAAAGAGAATTAAAGCTCTACACAACAAATGCA\nACAACATAATTAAACAAAGAAAGAGGAGTGAACCAGTTGCTATAATGATACATGGTCCTC\nCAGGCACTGGAAAATCAATAACCACAAGTTTTCTTGCCAGGATGATAACTAATGAGAGTG\nATGTATATTCTTTGCCACCTGATCCTAAGTATTTTGATGGGTATGATCAACAAAGTGTAG\nTCATAATGGATGATATTATGCAAAATCCAGATGGGGAAGATATGTCATTGTTTTGTCAAA\nTGGTGTCTAGTGTAACTTTTATACCCCCAATGGCTGATCTACCTGATAAAGGAAAACCTT\nTTGACTCTAGGTTTGTATTCTGTAGCACAAATCAAACTCTCTTAGCTCCTCCCACAATTA\nCATCTCTACCAGCTATGAATAGACGTTTCTTTTTAGATTTAGACATAGTGGTTCATGATA\nACTTTAAAGACATTCAGGATAAATTGGATGTTCCAAAAGCATTTAAACCATGTGATATAG\nATACAAAAGTGGGTAATGCCCGCTGTTGTCCATTTATATGTGGTAAAGCTGTAACTTTCA\nAAGACCGCAACACATGCCAGAGTTACACCCTTAGTCAGATTTACAACAAAATACTGGAGG\nAAGATAAACGTCGCAGAAATGTAGTTGATGTCATGTCTGCTATCTTCCAGGGACCCATAA\nCATTGGATGCACCACCACCTCCCGCTATAACAGATTTGTTAAGATCTGTTAGAACTCCAG\nAAGTGATTAAGTATTGTGAGGATAATAAATGGATAATTCCAGCTGACTGTAGAATAGAGA\nGAGATTTAAACTTAGCTAATAATATTATTACAATTATTGCTAATGTAGTTAGTATTGCAG\nGCATCATCTATGTGATATATAAGTTATTTTGTTCACTGCAGGGACCATACTCTGGGGAAC\nCTAAGCCTAAGACTAAGATACCTGAAAGAAGAATAGTAGCTCAGGGCCCAGAAGAAGAAT\nTTGGTCGCTCTCTCATCAAACACAACACATGTGTGGTCACCACTGAAAATGGTAAATTTA\nCAGGGTTAGGTATATATGATAAAGTAATGATTTTACCCACACATGCTGATCCAGGGAAAC\nAAGTTCAGATAAATGGAATTAATGTTAATGTTAGTGACTCATATGATTTATACAATAAAG\nATGGTGTTAAATTAGAAATTACAGTTATTAAGCTGGATAGGAATGAGAAATTTAGGGATA\nTTAGAAAATATATACCAGAGAAAGAAGATGATTATCCAGAATGTAACTTGGCACTTGTAG\nCTAACCAACCAGAACCCACTATAATAGGTGTTGGAGATGTAGTATCATATGGAAACATTT\nTATTGAGTGGAAATCAAACAGCAAGAATGCTTAAATATAACTACCCCACTAAATCAGGCT\nATTGTGGTGGTGTTCTGTATAAAATTGGAAACATCCTAGGAATCCATGTGGGTGGTAATG\nGCAGGGATGGGTTTTCTGCAATGTTGTTGAGATCGTATTTCAATGAAACACAAGGGAAAA\nTAGTTGCAGCCAAGGATGTAAAGAATATTGGGTATCCAACCATCCACACACCTAGCAAAA\nCAAAATTACAGCCAAGTGTTTTCTTTGACGTTTTTGAAGGTACAAAGGAACCAGCAGTGT\nTATCTGAGAGTGATCCACGTCTAAAAACTGATTTCAAAACAGCATTATTTTCAAAATACA\nAGGGAAATCCTGAATGTGAGATGAATGATCATATAAAGGTGGCAATTGCCCACTACTCAG\nCTCAACTGATGACTCTAGATATTCAAACAAATAGTGTTTCATTGGAGGAGAGTGTGTTTG\nGCATCGACGGCCTGGAGGCCTTAGATCTAAATACAAGTGCAGGATTTCCATACATTAGCA\nTGGGTATTAAGAAGAGAGACTTAATCAACAACACAACAAAAGATTTAAGTAAATTAAAAG\nCTGCAATGGACAAATACGGAGTTGACCTACCCATGGTAACTTTTCTAAAAGATGAGCTTA\nGAAAGAAGGAAAAAATTTCTGCTGGCAAAACACGTGTAATAGAGGCCAGCAGTATTAATG\nACACAATAATCTTTAGACAAACCTATGGTAACTTATTTGCAGCATTTCATAAGAATCCTG\nGCATTATCACTGGTTCTGCAGTTGGGTGTGACCCTGAAACCTTTTGGTCGAAGATACCTG\nTAATGTTAGATGGAGATTGCATAATGGCCTTTGATTACACAAATTATGATGGTAGCATAC\nACCCAATTTGGTTTGAAGCCCTAAAGCAGGTATTAAATAACCTATCCTTTGATTCTACAT\nTAATAGATAGATTGTGCAATTCTAAGCACATTTTCAAAAACTCTTACTATGAGGTTGAAG\nGTGGCATCCCCTCTGGATGCTCTGGAACAAGTATTTTCAATACAATGATCAACAATATAA\nTAATAAGAACATTGATACTTGATGCCTATAAATACATTGATCTGGACAAACTTAAAATAA\nTAGCATATGGAGATGACATAATCTTTACATACAAATACCCATTAGAAATGGAAGCTATTG\nCTAAGGAAGGAGTCAAGTATGGCTTAACAATCACACCTGCTGACAAATCAGAGACATTTG\nAGAAGTTAGATTACAATAATGTTACCTTCCTTAAGAGAGGATTCAAACAGGATGCAAAGT\nATCCTTTTTTAGTACACCCCACATTTCCAGTTCAGGAGATACATGAATCAATCAGATGGA\nCAAAGAAACCCTCACAAATGCAGGAGCATGTTCTGTCATTGTGTCACTTAATGTGGCATA\nATGGACCAGAGGTTTATAAGGAGTTTGAGAGTAAAATTCGCAGTGTCAGCGCTGGACGTG\nCACTGTATATACCTCCTTATGACCTCCT\n>NODE_2_length_838_cov_1.593464\nAGCTGGTTCCTGCCGAAGTTTCCCTCAGGATAGCAGTAACGTTTTCAGTTTTATGAGGTA\nAAGCGAATGATTAGAGGCCTTGGGGTTGAAACAACCTTAACCTATTCTCAAACTTTAAAT\nATGTAAGAAGTCCTTGTTACTTAGTTGAACGTGGACATTTGAATGTATCGTTACTAGTGG\nGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGAACGCGAGGTTAAGGTGCC\nGGAATACACGCTCATCAGACACCACAAAAGGTGTTAGTTCATCTAGACAGCAGGACGGTG\nGCCATGGAAGTCGGAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATGAACTAGC\nCCTGAAAATGGATGGCGCTCAAGCGTGTTACCCATACCTCGCCGTCAGCGTTGAAGTGAC\nGCGTTGACGAGTAGGCAGGCGTGGAGGTCAGTGAAGAAGCCTTGGCAGCGATGCTGGGTG\nAAACGGCCTCTAGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAGTGAGATCCTTGAAG\nACTGAAGTGGAGAAAGGTTCCATGGTAACAGCAGTTGGACATGGGTTAGTCGATCCTAAG\nAGATAGGGAAACTCCGTTTTAAAGCGGGCGATTCTTCGCCCCGCCTATCGAAAGGGAATC\nCGGTTAAAATTCCGGAACCAGGATGTGGATCTTTAACGGCAACGTAACTGAACTTGGAGA\nCGTCGGCGAGGGCCCCGGGAAGAGTTATCTTTTCTCCTTAACAGTCTACCACCCTGAAAT\nCGGTTTGTCCGGAGCTAGGGTTCAATGGCTGGTAGAGCGCAACACCTCCGTTGCGTCC\n>NODE_3_length_717_cov_0.905280\nGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCTTAGTAACGG\nCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGCACCTTCGGTGTCCGAGTTGTAAT\nTTGAAGAAGGTAACTTTGGAGTTGGCTCTTGTCTATGTTCCTTGGAACAGGACGTCATAG\nAGGGTGAGAATCCCGTATGTGACCGGCTCTGGCACCTTATGTAAAGCTCCTTCGACGAGT\nCGAGTTGTTTGGGAATGCAGCTCTAAATGGGAGGTAAATTTCTTCTAAAGCTAAATATTG\nGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAG\nAGTTAAAAAGCACGTGAAATTGTTGAAAGGGAAGCGCTTGCAATCAGACTTGGACTTGGC\nTGTTCAACCGGTCTTCTGACCGGCCTACTCAGTCTTGTCCAGGCCAGCATCAGTTTCGGC\nGGCCGGATAAAGGCCTTGGGAATGTGGCTGCCTCTTCGGGGGCAGTGTTATAGCCCAGGG\nTGTAATACGGCCAGCTGGGACTGAGGTCCGCGCTTCGGCTAGGATGCTGGCGTAATGGTC\nGTAATCCGCCCGTCTTGAAACACGGACCAAGGAGTCTAACATCTATGCGAGTGTTCGGGT\nGTCAAACCCCTACGCGTAATGAAAGTGAACGGAGGTGAGAACCGCAAGGTGCATCAT\n>NODE_4_length_651_cov_1.155709\nGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGC\nGTGGAGCCTGCGGCTTAATTTGACCCAACACGGGGAAACTCACCAGGTCCAGACACAATA\nAGGATTGACAGATTGAGAGCTCTTTCTTGATTTTGTGGGTGGTGGTGCATGGCCGTTCTT\nAGTTGGTGGAGTGATTTGTCTGTTTAATTGCGATAACGAACGAGACCTTAACCTGCTAAA\nTAGCCAGGCCCGCTTTGGCGAGTCGCCGGCTTCTTAGAGGGACTATCGGCTCAAGCCGAT\nGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGC\nTACACTGACAGAGCCAGCGAGTCTTCACCTTGGCCGGAAGGTCTGGGTAATCTTGTGAAA\nCTCTGTCGTGCTGGGGATAGAGCATTGCAATTATTGCTCTTCAACGAGGAATACCTAGTA\nAGCGTGAGTCATCAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGC\nTACTACCGATTGAATGGCTTAGTGAGGTCTCCGGATCGGCTTTGGGGAGTCGGCAACGAC\nACCCTTTTGCTGAGAAGCTGATCAAACTTGGTCATTTAGAGGAAGTAAAAG\n>NODE_5_length_624_cov_0.923775\nGCCATTGGCCGCACGCGTCCAATAGGGCAGATAGCGTCCGCTATCGTCCGACCCCTTGGC\nGCGATTATTGACGAACGCTGCGTCCGCGCCGTCGATCGCATTCGGCTCCCATGCCGAATA\nGGTGCCGTTGAAGCCGGGGTTTTGTTCCAGAACCCTCCGCATGATCGCGTTGAACTGGTC\nGCGCCGCGCGCCGCTCGGCGTGCTGCCAACCAGTACCGCGAAGGACTGAGCAGTCGTTCG\nGGCCGCATCGAATGCAACGTTCAATGCGCCCTTCACGGTGTCCGCCTCGACCGCCGCTCG\nATTTTGCAGCGTATCCTTGGCCTGGCTGCTGACAATCCCGCCCACTTCGCTGCTGACATA\nCAGATGCGAGGTGAGCGATGAAATCGCGCTGATCGCAACAAGAATTATGACAGTTATTCC\nCAAACACAGCCCGGAGATTGTCGCGATCTTTCGCTGTAAGGAACGAATCGAGTCGAGGCG\nTTTCATCAAATTCATTGCGTCTTCCAATTTGCGACGAATTAACGCCAAGCGACAGGAGAC\nGCGGCACGACAAAGCGAAACGTCAGTTCTATCATAGGAAATTCGACGACGGATCTTCGGT\nACGGCCGAACAATATTTGCCCCTC\n>NODE_6_length_603_cov_1.162264\nCTTTTATTTCACTGCATCCGACCCGAATGTTCCGCGTCATCGGTTGATGTATCTGGTGAC\nCGAAGCGGCATTTTCACCGCGCTTCTTCACCGAATTGAAGGCCAAATGGGAGGTGGCACG\nGCGCGCAGGTCGTGCGGGTGGCGCATTCGTCACGATCGATAGTTGGCGTGATAGCGCCGG\nCACGCTCTGGAAGCCCAACACCCTCATTGATGTCGACGTCCCGGGCCTGCGCGGCGAGGG\nCCAGATGTGCATCTCCGAGGTGACTTTTCACCGATCGAGCGAACGCGGGACCGTTGCGGA\nCTTGTTCGTCATGCCACCATCGGCATTCGCTCCGGAACCGATCAGTCTGACCAATCTCAA\nCACGGCAGATATTGCGCCAGATTCGACGTCGCAATTGGTGCTGCCATGATGTCGCGAATT\nCTCAATCTGATCGGTCGCGGTCGCCTCACGCTTGTGAAGGACGACAAGGACGTTCAGCGC\nCTTCAAATATCGGAAGGGAACACCGGGAGCGACGAAGGCGAAAGCCTTACGGACGATATC\nGTTATGATTGGCCTGTTCGGCTTATCGAGCAATGCACCGGAAAAAACCGAGGTGGTGCTG\nCTT\n>NODE_7_length_554_cov_0.796258\nGCGACCTTCGACAGCCGTGTGGTGTTCCAGCCGACCAGCGCAACCCCGTTTCGCGGCACG\nCTCAACAGTTACAATCTGAGCTCTGACGTCACCGCGCACAGCCAGATATTGGGCATGGAT\nGCGCTGAGCTTTATCGGGATCTTCTACAACTATCTCGACGGGCAGAATTACTCGTTCAAC\nAAGACGCCTGCAGGCCGCAACGGCATTGGCGCGCCGACCCAGACGGTGTTCGGCGGTGTG\nCGCAATATGGGGGTTCGCGCCCGCGAGGAATTGGCGCTGACGCAGGACCTGCAGCTGATT\nCTTGGCATTGGTTATGAGCATTCGAAGATCGACATGCGCCAGACGAACTACGCCTACCCT\nGTCGGTGCCAATCCGACGCTGACCAATATCCCGGCGATCCGCGATTTCGACAATGTCGCG\nCCCGAGGCGTCGCTGGTATGGCAGGCCGCGCCCGCAGTGCGGCTGCACGCCCGTGTCGGT\nACGGCCGACGGTATTCCGCAGTCAGGCCAGCTTTTCGTCACGACGGCAGGCGTCGCCGGC\nAACAATATCGACCT\n>NODE_8_length_548_cov_1.627368\nGTCCGGGTAATAAGACGACGTCGCTATGGCCTCTCCGGAAGGCGGTGTATGTGCCAAGCG\nATGTTTCATTAATGTCACGGACAGGTCGCTGAGGTGGTTTTCGTTGGGGGCGCCGTCTTT\nGGGGGAGATTGCGTCAATTTTGACTGTCAGATCAGCGACTAGATTTTAGGCAGATTAGTG\nTGCCACCTGAATCAATAGAACAATATCAGTTATGGCGGTGCAGTATACTATACAATGGGT\nTGGGCGCATCTGCATGTCTCATGCTGTCATGGCAATCGACCTCTAGTCTGGGGTGATCCG\nAGGCGCTTCTCTTATTAGGAATAGTGCAGGACCCGAAACCGCCAAAGGGAAAGGGTGAGC\nGAGGTAGCAGCGTAATAATTAGCGGTGGGCAGGAAATGCTTAGTGTTCTGTCTCAAGACC\nTAAGCGACAGCGTGACCTTGTTTCACTTACCTCTGAAGCTCTTCGACGTTATAGATATTG\nGCATCCCTAAACAACGAGTACCTTGTGCTACGACAGAAAAGTGACCTGAAAAAAAAAAAA\nAAAAAAAA\n>NODE_9_length_536_cov_2.790497\nGTGTACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTTGGTCAAGTCCTA\nTAACGAGCGAAACCCTCGTTTTGTGTTGCTGAGACATGCGCCTAAGGAGAAAGTCTTTGC\nAACCGAAGTGAGCCGAGGAGCCGAGTGACGTGCCAGCGCTACTAATTGAGTGCCAGCACG\nTAGCTGTGCTGTCAGTAAGAAGGGAGCCGGCGCCTTTCAAAGCACTTTCTAGTGTGCGCT\nTTAGAAAGATTGCAGCTAGCGCGCTTTACTAATAACACAGAAAGGGCTTTTCTCGCTTGT\nTTAGTAAAGTCAAGTTTTTGGCCTTATCTTGCAGGTGACGACGACGTCGAGTTGGCGGCG\nGAGAAAGACTCGGCATTCAGGCGAGCCGCCCGGTGGTGTGGTACGTAGTGGGTTTAGTAC\nGCCCCGCCAAAACGGCTCCGAAACAAACAAAAAGGTGCGTGCCGCACTCACGAGGGACTG\nCCAGTGATATACTGGAGGAAGGTGGGGATGACGTCAAGTCCGCATGGCCCTTATGG\n>NODE_10_length_535_cov_1.333333\nATCAACTAGAGGCTGTTCACCTTGGAGACCTGCTGCGGTTATGAGTACGACCTCGCGTGA\nAAATCATTCCTTCCGGCGGATTTTCAAGGGTCGTCGAGAGCGCACCGGACAGCACAAAGG\nTGTGCTGCTCTACCTGCCATTAAACCCTAGCTCCGGACAAACCGATTTCAGGGTGATAGA\nCAGTTAAGAAGAAAAGAGAACTCTTCCCGGGGCCCCCGCCGACGTCTCCACCTTCAGTTG\nCGTTGCCGCGGATAATCCACATCGAGGTACCGGAATATTAACCGGTTTCCCTTTCGCCAG\nGCGGCGCCCGAGAGCGCACTTTAAAACGGAGTTTCCCTATGGCTTAGGATCGACTAACCC\nGTGTCCAACTGCTGTTCACACGGAACCTTTCCCCACTTCAGTCCTCAAAGTTCTCATTTG\nAGTATTTGCTACTACCACCAAGATCTGCACTAGAGGCCGTTCTACCCGGGGTCACCCCCA\nAGGCTTCGTCACGGGCCTCCACGCCTGCCTACTCGCTAGGGCATCGTTTCTACCC\n>NODE_11_length_533_cov_1.019565\nGGTCGGCTCCGTGGTTTCGACCGTGGCCCCCCGTCCGTCGGGATAGAGGAGCGCAATTTG\nATAGACCTCGCGCTCTTCTGCCAGCGGCGCATCGACGCCGTCGACCCAGCGCAGGCCCGC\nCCTGCTGCGCCGCACCCACTGCACCGTGACATCCCCATTCCCCACTTCGGACCACGTCAG\nATGCGTTGGCGAAAGCGGCAAGATCGAGGTTCCTGCAAGCGTGAGCGCGACTTCTACCGG\nCCCCTCCACGTCCCCGGGTCCAGACGCCATGATGCGCAGGTCTCCTCCCTGCGCGGTCCC\nAGGCAGGTCGAGCGTTGCGCTTGCGTCCGGCTCGACCAGCACGAAGCGATCGCCCGCGCG\nCTGCGTGCCGATCGCACTCTCGGTCGCGCGCCGCCCGCGGAGCAGCACCGCCAGTCGCCA\nCCGTGTCGCGGTAAGCTGCGTGGCTTCGCCGACTTGCAACAGCTCGTTCCCCACCAGGGC\nTGTATTCAGCCCAGCATCGAGCGCCCCAGCATCGGCTCCAACCAGTGTCATGC\n>NODE_12_length_530_cov_1.921225\nTGCTTATACTTAGACATGCATGGCTTAATCTTTGAGACAAGCATATGACTACTGGCAGAA\nTCAACCAGGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTATAAGCA\nACTATACGGTGAAACTGCGAATGGCTCATTAAATCAGTTATCGTTTATTTGATAGTACCT\nTACTACATGGATAACCGTGGTAATTCTAGAGCTAATACATGCTAAAAACCTCGACTTCGG\nAAGGGGTGTATTTATTAGATAAAAAACCAATGCCCTTCGGGGCTCCTTGGTGAATCATAA\nTAACTTAACGAATCGCATGGCCTTGCGCCGGCGATGGTTCATTCAAATTTCTGCCCTATC\nAACTTTCGATGGTAGGATAGTGGCCTACCATGGTATCAACGGGTAACGGGGAATTAGGGT\nTCGACTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCG\nCAAATTACCCAATCCCGACACGGGGAGGTAGTGACAATAAATACTGATAC\n>NODE_13_length_501_cov_1.207944\nGACCTGGGGATCGCGGACATAGCGTCCGCGCAGACCATTGCCGATCTTCTGCGCCAACTC\nGGTTGAGGACAGGCCCATGGCCGAAATCGTTCCCAGCAGTGGCAGCGAAAGCGTGCCGTC\nCGCCGCGACCTGAACCGTACGGCTCAACTCCGCTACACCATAGACATCGATCGTAACTTT\nATCGAGCGGGCCGATCAGATAGGAACGTTGCTGGAGCAGAAGGTCCTTACGCGTAGGCGG\nCGGGAGTTCGCTCGACGAAACGAGTTTAAGGTCAGGGCGGCCGACAAACTTGGGAGTGGC\nGCAGCCCCCCAAAAGCATTAGCGCGAGCGAAAGGATCAACGCAGAAGATCGCATGAATTT\nTCCTGAAAATGGCCCTGGTTGCGCTATCGTTTTGATGAAATTATTATCTGCGCCTCGTTG\nCCTTATGCCCCGACATCCTATTCCAAAGCAAGACGTGAAACGATGGCGCTTGTCGGTTAT\nGGCGGGTAGGCGGGCATAAGC\n>NODE_14_length_500_cov_0.721311\nGGCCTCAGGTGCGTCCATGCCGCGCCTGAGGCCCGCAGTGGCATTGATCTCACGCGAGTT\nTAGGTACGTCCATGCTGTTAAGCCGGTTTTAAAGGGCTACGGGCCAATTCTGTCCATGCG\nTCTCTCGCTCAGGGCTAGCGCCTGATAGACGTCACGTTAGATTGGGGTAGCTGAGCTCTT\nAGGCGCTGATTTCCATAGTCAGGTCGAATATCTTGTTGTCTGCTTCTGCCAACAACGATA\nGCGCTACGTCTCGCTCAGCCTTCATCAATGCGAGATCAGCCTTTGTAGAACGGTTCTGTT\nTACGCCTTCTGGAGTCAATCTTCCGCTGAGAATCGGGAAGGGTTGAATGGGTTTCGCGCG\nAGTGCTTTTGAATTTCATCAATGAGGAGCGGGTACCTGCTTTTCTTTAAGGCTGATGGGT\nCGCATCCCGCTTCGCGGGCAACGTTATTCTGCGAAATAGATGATCCTTTCGGAAGGACTA\nCGGGCACACCTGATTTCAAA\n>NODE_15_length_484_cov_1.871046\nTCCTATTTCATTATTCCATGCTAATGTATTCGAGCATAGGCCTGCCTGGAGCACTCTAAT\nTTTTTCAAAGTAAAAGTCCTGTTTCCCCGCCACGCCCAGTGAAGGGCATGAGGTTCCCCA\nGAAGGAAAGGCCCGGCCGGACCAGTACACGCGGTGAGGCGGACCGGCCAGCCAGGCCCAA\nGGTTCAACTACGAGCTTTTTAACTGCAACAACTTTAATATACGCTATTGGAGCTGGAATT\nACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGATTTAGATTG\nTACTCATTCCAATTACCAGACTCGTGAGAGCCCGGTATTGTTATTTATTGTCACTACCTC\nCCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTT\nCTCAGGCTCCCTCTCCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATAGCTG\nTCTC\n>NODE_16_length_477_cov_1.576733\nGCCCGGTCGGACAGCCGCAAAAACCAATTATCTGAAACCGCGGTTCCTCTCGTACTAAGC\nGGTATTACCATTGGGACGACGGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTC\nTAAACCCAGCTCACGTTCCCTATTAGTGGGTGAACAATCCAACGCTTACCGAATTCTGCT\nTCGGTATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTT\nGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGGCACCTCTAGCCTCAAATTCC\nGAGGGACTAAAGGATCGATAGGCCACACTTTCATGGTTTGTATTCACACTGAAAATCAAA\nATCAAGGGGACTTTTACCCTTTTGTTCTACTCGAGATTTTGATTTTCAGTGTGAATACAA\nACCATGAAATTGTGGCCTATCGATCCTTTAGTCCCGCGGAATTTGAGGCTAGAGGTG\n>NODE_17_length_471_cov_0.964824\nGCGCGGCCAAGCTCACCCTCTGCTGCCACCCCGTCGCCAATCGCCAGGAAGCTGCGCGCG\nAGCATCGCATGGGCCAGGCCCCAGCTTGGATCGGCCTTGATCGCGGCTTGGGCGTGGCTG\nCGCGCGGCGCTGTAATTGCCGGCCTTCAGCAAGCGCACGCTGAGCGCGAGTTCGGTGCGC\nGCGGTCGCGGCATCGGCATGGGCCGGGCCAGTCGCCGCGATAACCAGCGCCGCACTGATC\nGCGGTCGCGGCGAGGGTGCCGATGGCGATCGAAAGGGATTTACGCATGGAGATCGTAGCT\nCTTTAGCAAATCGTACAGGGTCGGTCGGCTGACCCCTAGCAGCTTGGCGGTATTCGAAAT\nGTTACCCTCGGCGCGGGCGAGTGCTTGCGCGATCGCCGAGCGATCGGCGCTTTCGCGCGC\nGGCGCGCAGGTTGAGCGGCAATTCGGCCCCCCCTTCCGCCAGATCGAGATC\n>NODE_18_length_458_cov_0.800000\nTCTATACCTATGCCGGGCTGAAGAGCGACGCGGATCTCCGCATTTCCGCCAATCAGGAAA\nAGCTCGCTTTGGTCGGCGACATGTTCACCGCGTTTGGCGAAGCGACGTCGTGGATGGCAC\nCCGAGATTCTCACGCTCGGCAAAGCCAAAATCGACGGCTTCATCGCGGCGAACCGGACTC\nTCGCGACGCGGTTCGATTTCTTTCTAGCCGACACGCTGCGGCAAGCCCCGCACACGCTGT\nCCCCCGAGGGCGAAATTCTGCTTGCAGGCGCGGGGGCACCGCTTTCGGGGCCGGGCACGA\nTCCGCGAGCAGCTCGTCGGGTCGGATATTCCCTGGCCGACGATCACCCTGTCGACCGGCA\nAACAGGTCCGCCTCGACGACCAGGCCTATACCTTGAACCGCGACGCGCCCGCGCGCGCCG\nATCGCAAGGCGGTGTTCGACACCTTCTGGGGCGAATAT\n>NODE_19_length_457_cov_1.002604\nTTTGCACCGGCTACTGGCCACCGACGCGGCGCTGTTCGATACGAGCCTTGACGCTTTTGC\nGGTACAATGTCCGGGCAACAAGCAATATCCAGGCTGGCGTGATAGCAATGGGTATTGTTC\nGAAGCCAGAAACGGGGCAAGCGCCAATAATAGGCGATCGACATTGGGATCGCCTCTTTCC\nAGTATTTCATGCTGGCCCCCTTCAGCTTTGCTCCAAGAAAGTGTGTGCGCACGTAGAAGC\nTCGCAACGTCACTCATTGCACGTCTATAGGCCCGGTGGCCCCTGCCAAGGGTGTCACCGA\nAAGCCAGGTCGTAGCCAACGATATCCACCCGGGTGCGTGCAAATTCGTCACGGGCAAGGA\nAGGATTCATTGCCCAATCGACATCCCACCAGCGTATCCGGCACGCACAGCCAAATGGACT\nCTTCGCTCAACATTTTGGCTATGAGATACGTGTGCAC\n>NODE_20_length_450_cov_1.042440\nGCACAAGAATGCACCGCCTGGGACACGCACGACTGTCAAGGCGGGGAGCGGGCCCGCGCC\nTGCAGTGAGCCATGCTTTTGAGCCGGTGCACGGCGGATGAGATCGTGACGATCTCTTTCG\nTCCTCGAACCGAGAATGGAGGCCGAAAATGGCATTGCCTAACAGCGGTCTTCTGCCGGCG\nACATTCCGCGGCGTTCCATTTATCGTCACCAATGACGAAATTGGCGGCGGGCGACGCCAG\nGTTGTCCACCAATATCCAGGGCGCGACGACCCATGGACGGAGGATATGGGTCGCGAAGCC\nCGTCGCTTTCGCTTTCGCGGCTTCATTTTGGACGGATCTATCCGATTTGCGGGCGGCCCT\nGTGCAGTTGCAGCGTGCTTTGCTTATTGCAGCGCTCGAGCGGTCGGGCGCGGGGATGCTC\nACGCATCCAACGCTCGGGATCCTTCAGGTG\n>NODE_21_length_450_cov_0.816976\nGGCGTGGGCAGCGTGCGATAGCCGAAATGGGCGGCTGCGCGGTCGGCGGCGGTTGGGGGA\nTTCGCGGCGACGTTCAGGCACCAGCGCGGCACCGCGCCGACCACGGCCGGGACACGCGCG\nCGTAGCTCCACCAGCCACCGGTTCATATCGGCCAAAGCGGCGTCGGGGCTGGCATAAGCC\nTGACGCGGGTCGCGCCACAAAGCGGAGAAGCGCGCGCCGGTAGTGGCCCCCGCTATCCCC\nAGCCGCGCGAACAGGGCATCGGCGCGGGCGGCGCAGCAGCGGCGTTCGGCCTCCAGCCGG\nGTCGCCGCCGCGCGCGGATCGACGTCATTGCCGAGCTTGCGGCGGAGCAAGAGCGTGGCG\nTGCGCCGGGGTGCGCGGCGGCCCCTTGGCGCGGGGATCGACTGCGAAGCGGCGCACGATC\nTCGAGGTCGATTGCCAGCCCGGCGCGGGCG\n>NODE_22_length_447_cov_0.815508\nCCGATACGGACGGTGCCGACAGCAAGCTGGCCATCGTGCCGCCATCGACAGATACCGCGA\nTGCTCGCCGAATGGAAGGGATCTGAGGCGATCCGCTCCTGGGCCCGCATCCCTCCTCCCT\nTGGCGGCCATCGACCTCCGTCCCTACCTGTTCGTCACCAAGGACCGGAAGGACTATTTCG\nGCCCAGCCTCAGTGCTCGGTCGTCTCGCAGCGGTCGTCGAGAAGCTCCTCGGGTCGAAAC\nTATCGGTGCAAGCCTACGAGGGTGAACTGAAGCAGCTGGTGCCGGCCGAAGCCGCTCAGG\nTCTTCGAGGAGCTGAGAGGTCGCATCATGGGCGGCGACGCCTTCGACACCGCGCCCCCGG\nGCGTTGACGGTATCGGCGTCCTCGTCCGCGCCCACCCGACGTTGCAGGCGAACTTGCTCG\nACTTGCTGGAGGCTCTCCCCGCGGATC\n>NODE_23_length_434_cov_1.041551\nAGGCGTGGGGCGGCTAACCGCGCTGGCCTTCCGGGCGTCGGTCGATCGGCCGGAGCGCTT\nTCGCCGATCCCGCGACGTCGGCGCCCATCTCGGTCTCACGCCCCGGCGGTACCAGTCCGG\nTGATACCGACATCCAGGGACGCATTAGCCGATGCGGTGCGGTAACGTGCTTGCGCGCGCC\nGCGCTCTACGAGGCAGCACACACGCTGCTGAGGCGCTGCCAGAAATGGTCGACGCTCGAA\nGCCTGGGGGATGCGCGTCGCCCAACGCCGCGGCATGGCGAAGGCGCGTGTCGCCGTGGCG\nTGCAAGCTGGCCGTCATCCTACATCGCATGTGGCGATCACGCAGAGTTCCGCTTGGGCAA\nAGCGCCAGCGCTTGCGGTAGCATGAGGAGACACGAACCAGATCTCGCCTGAAGAGGCGGG\nTAGCGGTCGTTCCC\n>NODE_24_length_434_cov_0.659280\nCTTTCGGGATGCCGGTTTCGCGCTCGACCAGGAGGACGTCCTCGGCGTGCACTGGCTTGA\nGATCGCGCAGACGCTCGTAGATCGACGACTGGGAACGGTTCACCAACCGGGCGTATGCCG\nTCTGCGTTCCGACGGCGCGGACCGCAGCTGCGAGCGGTGTGTCTATCGTCGATTCGATAC\nCCATGGCGTTTGACTATCGGTATTCCGATAGGTGGTCAATCGGAAAGTGCTTATGCTTGC\nGCTATTGGTTTTCCGTTAGGTTCGAGCCGTGATTGTCGGGGCCAGAATCGAAGAGCGTTT\nGGTAGCTGTGCAGATGTCGCAGTCGGCGCTCGCGCGTCGTGTGAAGCTCGCGCAAAGCAC\nCATCAACGGACTCGTAAAAGGCGAGCAGCGATCCACGACTAAGCTGCACGAGATTGCTCG\nAGCACTCAAAACGA\n>NODE_25_length_424_cov_0.877493\nGCCTTGCCTTGCAGCGTCGGGAAATCGACCCCGATCGAGCCGCCAATGTCGAGTCGCACG\nATCGCGGCGGCGACTGCGCGCGCGGCGGCGAGCGCGAGCGGATCGAGCGGGGGATAGCCA\nTCGACGTCGAACAGCGTCATCGCGGGCGTCGGGCTCATGCGGAGCGCGCCGCCGACCGGG\nCCGCTGAAGACGATGTCGCCGGTCAGCGCTTCCTCGAGCACCTCCGACCAGCCCGCCGCT\nTCGAGATGATCGGGCTCATGCGCGTGGCAGATCCGCACCGGCACGCCGGTCGCGGTAATG\nCGCTCGAGCAGCGTCGGCCCGGCGCGTTCGGGCCCCTCGGCGGGGGCGCAGCGCGGGAGC\nTTGGTGCGGCCGGGCTCGGGGATCGCCTCGCGCACCAGCTCGACCGTTAGCGCGGCGCCT\nTGGG\n>NODE_26_length_420_cov_1.429395\nCCTGGGAAGAGTTCTCTTTTCTTCTTAACGGCCCGTCACCCTGAAATCGGTTTGTCCGGA\nGCTAGGGTTTAATGGCCGGTAGAGTCCCACACCTTTGTGGGATCCGGTGCGCCCCCGACG\nTCCCTTGAAAATTCGCTGGAAGGAATAGTTTTCACGCCAGGTCGTACTCATAACCGCAGC\nAGGTCTCCAAGGTGAAAAGCCTCTAGTTGATAGAACAAATCTAGGTAACACGGGCTTACG\nCTCAGCAGCTCGTAACAACAAGGCTACTCGACTGCTTACACGACCCGGTTACACGTCTAA\nGTCGTCTGCAAAGGATTCATCCCAGCGCGCTGTCAAATTGCTATCCGCCAATTACCTCTC\nCCGACTTCTACGAGAGAGGAGTTATGGCCTGCTAAGGTCCGGGGCCGAAGCCTATTCGTA\n>NODE_27_length_410_cov_1.154303\nGGATGGGCCCGGGGTCCGTCGTCCTGTTTTTCATGATGGATGATGTGCAAGCGGCTCATG\nGAGGCTTCCCCCAGGGTTCCAACGGCTGCGCGCGCCTTGAGACACGCGATACGCCTGCAA\nCCGGGGATCAGCTCGCGCTCGCGAATGCCCTGTATTTCCAGCAACCAGTGACCGCCTTGG\nTCTACGCCGTCGCACCAACGCAGAATGTCATCGGCCTGACGATCGCCGGGCTTTCGACGG\nCCAGCACCGCGACCAAAGCCGATATTGCGGCAGCCGTTGCGAATGCGCTACTGGTCGCAG\nGGCGGCCAGGCGGTGTCACGAATATATCAGCGATCGAGGCGGCGATCGCGGCCGTGGCAC\nTGACGGGCGGCTTCGTGCTGACCAATGTCTCAGCATCGGCCGGCACAGTC\n>NODE_28_length_406_cov_1.126126\nGTTTACTGTTAAGACTACAACGGTATCTGATCGTTTTCGATCCCCTAACCTTCGTTCTTG\nATTAATGAAAACATCCTTGGCAAATGCTTTCGCAATAGTCGGTCTTGAGTCAATCTAAGA\nATTTCACCTCTAGCGACTCAATACCAATGCCCCCAACTATCCCTATTAATCATTACGGCG\nATCCTAGAAACCAACAAAATAGGACCGCACGTCCTATTCTATTATTCCATGCTAATGTAT\nTCGGGCAAATGCCTGCTTTGAACACTCTAATTTTCTCAAGGTAAAAGTCCTGGTTCCCCG\nACGCGCCCAGTGAAGGGTACGCCGGGGAACCAGGAATTTTAACGTGAGAAAATTAGAGTG\nTTCAAAGCAGGCATTTTCCCGAATACAATAGCATGGAATAAAATAA\n>NODE_29_length_403_cov_0.930303\nTTGGAGGAAGCGTCCAAGTTGCGCGCGGAAGCCGAGGCACAGCTTGCCGAGGCCAAGGCG\nCGTAACGCCGCCAGCGCTGGCGATGCCGCCGCTATCGTCGCCCATGCCGAAGCCGAGGCG\nGCAGCTATGCTGGCCAAGGCTGAAGCCGATCTCACCGATTTGATCGCACGCCGTCAGACG\nATGGCCGAAGACAAGATTGCCGGTGCCGAACGCACCGCCATTGCCGAGGTCCGCGCGCGC\nGCAGCCGATGCTGCAACCCGCGCTGCCGCGACGATCATCGCCCAGCGTCACGGTGCCGAA\nGCGGACAAGACCCTGGTCGACCGGACCATCGCTGGGTTGGGCAAGCTCAACTGACCGTAA\nTGCACCCGTTGTCGCGGGTGCATTTCGTTTCGCCACTTATCGG\n>NODE_30_length_400_cov_0.941896\nGTGGGGGACGATGATCCAACTGAAGCGTCAACTGTACAAAAGGCCGAGTCCTGATCATGC\nGACAGCGTGCCATTGTGTTCGACCTGGGAGTCCTTGAGCATCAGATGGCGAACAGGCACT\nGAACTCAGCCCTGAAGCACATGTGGCGCTCTGGCAAGCGTAGTCAGCGACCTGGCCGACC\nGTGATCAAGCCGGACAGGCCAGCGGTAATCTGATTGCCCGATATGCCATGAACGTGTGGG\nTGAAACCAATACAGTCCCGAAGGGTGCCCTGATGGGACGTCGTACTCGTAGTCAACAGCA\nTCATATTGAACGGTGCCATGCAAATGCTGGGACGCCGCAGGAGTGCCGTTGTTTGAATTG\nAATGCGTAGACGAAGACGTTGTCGCCCCACACGCTAGAGC\n>NODE_31_length_391_cov_0.871069\nGTGAAAAGGTCGCGTCGAGCTGCACCGCCCAGCGGCCATTGTGGAATTTCGAAAGGTCCA\nGCTCGACCCGGGCGATTGGGGTGGAGGACGGCGAATCACCGCGTACCGATACCAGGATCG\nGCAGCGGAGTGTCGGTCAGCACGTCGGTAACAAAGACCATGACTGCTCTCCCATCAACTT\nTGGTGGTCGCTTGCGACTCTCCCGGAGGTCGAGTCGGATTTCGCTTCCACGTATCAAAAG\nCTATTCCTACTACGGTACTAGGCAATAGAGCTGCGCCAGAGCGTATGCCGGTTGCGCCAG\nATCGATAGTCTGTCCCGAAGTGCGGGCAATTGGACGCAGGGAAATCTATCTGGGCGCTAA\nGCTCGGCTATATCGCCGCAGCCGGTGCGTCC\n>NODE_32_length_390_cov_0.728707\nCGATCAGGTCGATTTCGAAGCCGACCTCCAGAAAGCGCGCGAACGTGGCCGCCGTCATCC\nAACCGGCGGTGCCGCCGCCGGCAATGACGATCCGGATCGGTCTGGAGCCATTCGGCTCCG\nCAGGATTGGCCATGGTCCGCGTCCCCGCTTACTCAATTTCAGGTACCGGAAGGGCGAGCG\nGTGAGGAGCCCCCACCGCTCGCCGATGGCATCGTCGTTCAGAACTTGTACGTGACGCCCA\nGATAATAGTCCCGTCCGTAGCGCTGATAATCGATCACCAGGCGCGGGTCGACATTCTGAT\nAGGTCACGAACGGCCGGTCGGTGAGGTTCTTCGCCTGAGCGAGGATCGCGACGCCCTTGA\nGGAAGCCCTCCTGGAATTCATAACCGATCT\n>NODE_33_length_389_cov_0.727848\nGCCTCGCGATCGAACGGTCGCTCAATTACGGCGATTATAGCGTGCCGCTCCACGACGCGC\nTGGCCGACATGGTCGGCCTCGGCACCGATAAGGGCCTGCGCGATTTCTGGCAGCCGACCG\nTGGAGCTGCTCAATCTGCTCGACAAGGGACCGTGCCTCGCCATCGCCGAGCCGATGGTCG\nAGCGCGTGACCTTCGGCACCTGGGCGCGGATGAAGGGTAGCGAGATCTCGCGCCAGGTGC\nTGCAGGTCGTCACCGGACAACATCCCGCGACCCGCGCATCGATGGCGCAGGCTGCGGCGA\nACTGGGTGCATCCGTTGTTGCGCTTCCGCGGCAACGTGCCGGCCGAGGCGGCCGATGCCG\nACGACATGCTTCAGGCGGCTGAGTGATGC\n>NODE_34_length_385_cov_0.983974\nCCTACATGCTTAGTAGCTTTCGCTGTTTCTCCGCTTACATCGAGACCGATTCACACAAGC\nATCGCACTGGTATCAACACCCAGGCGAACCAACTCGAGCGCCGTGACAAATCTAAGCAAC\nCAGTTTCTATGCTGCCTTCGTCGTCGATGGTCGAAGAACGCGCACGTTATGATTCTGACG\nTGCTGCTCGTCTGTGCTCTTCGTAGTAGCTCGTGGGAGCCAGAAGACCGGTAACCTTCTT\nCCACAGCAAGTTCGCCATGTAAGCCTTCCAACATGCTGGGCAATCGGCGTGCTTGACGTC\nGACGTGTTCTGCTTCAGCCTCATTCCAGAGGTCTAGAGTGAGTCTTAGTAAGTCTGTGTT\nAGGAGCGAGCGATGACATTTTTGGG\n>NODE_35_length_384_cov_6.430868\nTCCCGAACCCGTCGGCTGTCGGCGGACTGCTCGAGCTGCTCCCGCGGCGAGAGCGGGTCG\nCCGCGTGCCGGCCGGGGGACGGACTGGGAACGACCGCTTCGGCGGTCTTCCCCGGGCGTC\nGAACAGTCGACTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAG\nCATTGCGATGGTCCCTGCGGATGCTTACGCAATGTGATTTCTGCCCAGTGCTCTGAATGT\nCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAA\nGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCC\nACTGTCCCTGTCTACTATCCAGCG\n>NODE_36_length_381_cov_1.493506\nGAGGAACTTTGCGGCCTTATGGTCGAGGCGGATTTGCGACGGAACCGCCAAGGTTATTCT\nTTCTGATGCGCGTACTCGTCACTGGTGCCACCGGATTTACCGGGAGGCACCTGATAAACG\nTGCTGCACGCGCGGGGCGACGAGCCGTTTGCGTTGCTCGCCGATCTACGGGATGCCGGGG\nGGGTCGCAGCCGAAATCGCTTCCTTGCGCCCTAATGCGGTAATCCACCTTGCTGCCATGG\nCTTTCGTGGCCACTAGCGATTTCGATCCATTTTACGCCATTAACCAGGTTGGATCGTTCC\nATCTGCTTGATGCACTTGCCCGACATGTCCCGGGTATTCCTGTATTGCTCGCCAGCAGTG\nCGCAGGTTTACTTTTCTGGTT\n>NODE_37_length_378_cov_1.593443\nCTTCAAAGGATGGCTGCTTCCAAGCCCACCTCCTGGTTGTCATCGCTCGATCACTTCCTT\nTTCCACTAAGTGATTGCTTAGGGACCTTAGCGTACGATCTGGGCTGTTTCCCTCTCGACT\nTTGGATCTTAGCACCCTAAAAGTCTGTCTGTACAAACGATCTAGGCCTGTATTCGGAGTT\nTCCCTGGGGTTGGTAAGGCGAAATGGGGCCACCCTAGCCCATTGAGTGCTCTACCTCGGG\nCCATCGACATCATACGCTCTACTGAAATAGATTTCGCGGAAAACCAGCTATATCCGATCT\nTGGTAGGCCTTTCACCCCTCGCCACAAGTCATCCCCGTATTTTGCCACATACGAGGGAAA\nGGTGAAAAGAACCCTATT\n>NODE_38_length_378_cov_1.514754\nGGGGGAAGACCCCGGGTAGGGCAAAAGACTGAGAACAGCTGGCTCAAGGCCGGCTGGCCC\nGCGGCAAAGGCCGGCTGAGGAGCAGCCGGCTGGAGTCGTGGCCGGCTGCCTTGGGAGCCG\nGCTGGTTCAAGGTCCACGCTGGTCTGGCCATAGCCATCTGCGCTATGGCTAGGCCGGCTT\nCAACTTGTCATGTCCGGCTTTGTTTGTCTCTCCCCTGACCGGCTCGAAGCTGGTGAGCCT\nTGCAGGAGAAGGAACTGGAAAGGTGATCCGGCTTCCAAAGTCCACGATGATCTCATCTCC\nGTAAAGTACGGGGCACTGTAGAGCAACAGTGCCTCCGCCGGACACGCCATCATGGCTCAC\nGCCGCGCCGTACGGCTAC\n>NODE_39_length_378_cov_1.009836\nGCCGCTGACCACGTTGCAGCTGTCGGTCGTGCAATCGTTGTTGTCGCTGCACGCTGCCGG\nACAAATGGGTCCGATGAAATTTCCGAACGCGTATGGCCTGAGATCCGTAAAGGTGGCGAG\nCACCGCCTTGGTCGCCGTATCGATGATGTTCACGGCAGACGGAGCGTCGGACTTGGCAGC\nAAAAAGTTTCGTACCGTCGGGACTGAATGCAAGACCCGTGTCGGCTTTGACGGGGATCGA\nATCGACGACGGTGTTGGTCGCGATGTCGATGATGGCGATGTAACTGTCCGAACCATGACC\nGACATAGACCCGGCGCCTCTTGCGATCAATCATGCCGGCAACCGGGTCTATGTCGGTCAT\nGGTTCGGACAGTTACATC\n>NODE_40_length_378_cov_1.009836\nTCATAGATCAGCGTGGCGTTGGCGGTGTTGCTGAGGCCAGTCAGCGCGAACTGATCGACA\nTTGGGGTCGCCGCCATTGTTGAAGCCAACGTCACCCTTCACATACGTGAAGCTGCCCGAA\nACACCGATGCCGGTCTGGCCGAAGAAATATTGGCCGGCGATTTCGAAGCCGTAAATCTCC\nGCATCCTTGTTGTTGATCGGGCGCGAGATGGTGAAGTTGTACAGGGGATCGGACGACGAA\nCCGTTGATGTCGACCGCTGACAGGATCTGGTTGACGAAGGCCTGGTCGACCGTCTTGGTG\nACCGAGCTGTAATGCGCGTTGAACTGCGTCGCCGCCGCCGCTGCGCCATCCCGCTGGATC\nAGCGCGGAATAGGTGAAC\n>NODE_41_length_377_cov_0.786184\nTCCCTACGCATTGTGAAATTGCAATTCGTCAGCTCGACCCCAGGACTTCTACCTGGAGCC\nGGTCGCCAACCTGCTAAGGTTCAGGGCCAAAGGCCTATTCGTATCCGACTACGATGTGTA\nGGGGGAAATCGTCCCTTTCTGGCATGGATTCTGACTTAGAGGCGTTCAGCCATAATCCAG\nCAGATGGTAGCTTCGCGGCACTGCCCGGTCGGACAGCCGCAAAAACCAATTATCTGAAAC\nCGCGGTTCCTCTCGTACTAAGCGGTTTTACCCTACTGATGAATGTCGTCCCAATGGTAAT\nACCGCTTAGTACGAGAGGACCCGCGGTTTCAGATAATTGGTTTTTGCGGCTGTCCGACCG\nGGCAGTGCCGCGAAGCT\n>NODE_42_length_377_cov_0.756579\nGTATTATTATAGACACAGATTGTTTCGTAATGTTACAAGCCTTGTAGAATTTACCGATAC\nGTTGCTTGTAGTTGTTGAAGAAGATTTTGCCCCGCGGATTTTGCGGTCCGGGAGCGTCAG\nAACAGACGGCGCAGCGACAGGCTGACGGTGCGACCAAGCGGATCGAGTAGGTCCGGCTGG\nTACAGCAGCGGCGTGGCCCCATTTGCGTCGCGAACGGTCTGGCGGGTGTCGAGCATATTG\nCCGATCGCCAGGCTGACCCGCGTTGCCCGCGCCCAGGCTTGACCCGGAAAGCGTTGTTCA\nAGATTGGCGAAGATCCGCAGATCGAAGGTCGCCAGCGCCGAGAAATGCAGCGATCCGGCC\nGCGTCTGCGGTGGTGGT\n>NODE_43_length_373_cov_0.740000\nGCTCATCGTCGTCAGGGCATCGAGGTAGAAGCCGTTCTTGCGGGCGGCGAGGTGCTCTTT\nCGCGGGCAGGTCCAGCGTGCGGCCCCCAAGCCGCAGGATGTGCTCGAGCGACCCCATGCG\nATCGACGCCCTTCAGCGCTTCATTATCGTCCGCGTCGAAGGGAATATCGAGTTCATCGGC\nGATCCGTTTCCACGCGACGAAATGCAGACGCGCGCTGTCGACCAGCACGCCATCCAGATC\nGAAAAGTGCGGCGCGGAAGGTCATGATACGGTCGCTCGCGCGCTCTGAATTTCCGAGGAC\nGTCGCCACATCGACGCCCGCGATGCGGATCTGCACGGCGTGGTCGCCCCGTACCGATACG\nCGCGCGGTGGCAC\n>NODE_44_length_366_cov_1.051195\nTCACAAACCCCCCCCAGAAACGTCCGAAACTAAAAACCTCTTGTGACTTTCGGACAAAAG\nCCCGAGAATGTCCGAAAGTAGACTTAACCACGGAGTTTCGGACGTGCTGATTGGGTACGC\nTAGGGTTTCAACCCATGAGCAGGACGTTCGGCTTCAGGTGGAAGCTCTCGAGGCCGCGGG\nCTGTACCAAGATCTTCACGGACGAAGGCGTGACTGGTGCAGCCGTCATTAAGCCGGAGCT\nGGTAAAGGCCCTCGCCTATGCTCGTGCCGATGAGGACACGCTTGTCGTATGGAAGCTGGA\nTCGCCTCTCTCGATCCATGCGCGATCTCATAGAGACGGTGCAAGCCATGAAGGCGCGAGG\nCATTGG\n>NODE_45_length_365_cov_1.054795\nTGATAGTATCTATAGTTTCATCTCGCTTAAACAAAATCTTAAATGACCTTCCTTTTCTGT\nGCTCCTCAAATTCTTCCCGTGTAATGTTTATAACAACATTCTCGAAGTTGTCGATAAACA\nAAATTTGCCCTTCCATCCAATTATTACCGATGGTAGCGCGAAGCGGATATTTTTCATCAA\nTAGATGTGAGAATACTTCCTACACTGAATAAATCGCCCCCCTTACTAATATGGTTAACCG\nCTTCTGCTATTAATTGTGTAATGGCCAATAAAGTTTGTTTAGAACCTACAGGCAATGCAA\nCAATTTCTTGCGGACGCTCTCCCGCTATCATTGTAAGAATACCGTTGTCGGGACAAATAA\nTGAAT\n>NODE_46_length_363_cov_1.327586\nCTATGGATAAGCAGCGATGATGGTCGTCCTATCAGGAACCCGCCGACTCGTCCTATCGGG\nAACTGCGGAGTCGTCCTATCGGGAACCGGCGCGGGCCGGAAACCCGCAGAAATCCGCGCG\nAAATTGGCGCCCCTCTAACGGTGCTAATAGAGAAGAATCCTTCGGATTCCTGCTAACGCG\nCCGCGCCGCCGTGGATAATGGCGCCGCCCGCCATTGGCTACGGCCACGCCGCCGGGATGC\nCGCCATGCGGCTTGGCGGTGCGGAATGACGATACTTGTCGGCGACTGCCGCACCGTCATG\nCCGGATCACGGCCCGTTCGACATGATTTTCGGCGATCCGCCCTATGGCGACACGTCGCTG\nGGT\n>NODE_47_length_363_cov_1.062069\nCGAAATCCTGCGCGACATCCCATTCGCAGCCCGACACCGGATCGCGCAACCGCGCCATGA\nTCGTGACCAGCCGTTCGATCATCGACACGCTCCATTTCGGGTGAGGAACCGGCTCCCGCT\nGGCGACCTCCATCAATCCGATAATATACATTATGTTAAATTGAGGCCGTTTCATCAGAGC\nAAGCCTCCCAATACCGATCCAGCCCCGAAAGCGCCCTGCCACAGCACCACCAGCACGAAC\nAGCACGCCGAAGATCGCCACCCAGGCCAGCGCCATCCTGATCGTATCGCCGAGCGGCAAA\nCGGCGCGCCGCTAGCGCGCTGACCGGCAGGATCAGGACCAGCGCGTAAAAGACCAGATCC\nATG\n>NODE_48_length_363_cov_0.896552\nGCCGCGCCATTGGGGGTCGCCGGGCGGAACACGACCAGGCGCGGGCGGCTGATGCCCTGC\nACCGCACGGTCGTTCAGCGTGCGATCCTTGCTGCGCTCGTCGACGGTCTCCAGCGGGAGT\nGTTGGCGGCGCGCCCGGCGCGCCCTTGGGCCACAGGTCCAACGTTTCGTCGGGTTCGGGC\nAGCGCCGTCGCCGGTGCGGCACCGCCAACCCGTGGCGGCGGCGTCTGCGCAAGCCCGCGC\nGCCGCCCACCCGCTCGCCAGTGTCCCGAGGATGGCGCTGCGACGGTCGATCACGGGCATT\nCTCTGGAAAAACGAACGGGCGTCGCCATAGCTTTGGCAACGCCCGAACGGGGAGGAAGGG\nTCT\n>NODE_49_length_362_cov_0.498270\nGAGGATAATAGAGCAGCGCGTTCGGCGGTGGATAAGATTAGATTTCCGTCGTCGTTAGGC\nATATTACCAAATGAGATTGCTGGGCGGGGAGAAGACGGGCTGGTGGATTCTGACACCACC\nAAATGCCGGTTCATCACACACCGTGCATCGAACCGGTACGACGTCAGCGCATCATGCCGA\nCTTTCAATCGGATCGCGTCGAATGTCGGGATAGCTGAACAAACGCTTCTCGCTCGGCTGA\nTTATCGCGGTGGGTCAACCCGATCACGACGACATGGACGTGCGCTGCGCCGCGCGCTTCG\nCTGCCCCAACTGAAGGTGCGATGGGCGAAGGCGATTTCGAGATGGAAGCGATCGAACAGG\nAT\n>NODE_50_length_360_cov_0.912892\nGATCAGCAGCGCTGACGCCAGATCGCGCAAGAGTCCTAGCTTCCAGCACCTGAGCATCTG\nTCATCTTGGCCTTGGCTCTGGCGGCCCTCATCTTTTCTTCAGGCCTGCTCATGCGCTCGC\nGGGTCATCTCAGCCATCTTCTGGCGATTCTCAGGCGCCTCAAGCCGACTGCGCGCGCTGG\nCCCGCAGCCTTTCGTGGACTTCATCACTTGCCATAGCGTCTCTGGTAGCCGTCGATATTG\nCGGCCCTTGCTTCTGGCGACTGCATGCGCTGCTTCTGTGCCTCCGACATGGTCGCCCTGG\nATTCTTCTGTGTGACGATATCCCATCTTCGCAGCCGAGATGTTGGCGCGCCGCTCCTGGC\n>NODE_51_length_358_cov_1.347368\nTTCCGATCGCGGCCGCGCCGATGTGAACGCGGTCTATCTGTCGGATTCGTTCAACATCAC\nCGAAGCGCTGCGGATCGACGCAGGGGTGCGCCACCAGTGGACCGATATCGATTTCACCAT\nCACCGGTAACGGCCTCCCCAACGCAGCGAAAATCCACCGCGAAGCCACGCCGTGGACCGT\nCGGCGTCAACTACCGTGCGCTGCGCAATCTCGACGTCTATGCCCGGATATCGCAGGGGTA\nTCACTCGCCGTCGTTCGACGATGTGCGGTCACAGCTCGGCAATACCGGGCCGCGGCTCGA\nCCTGAACTGGAGCGTGCGCTCCTATGAAGGCGGTGTGAAGTATCGCGGCGGCGGTTTC\n>NODE_52_length_358_cov_0.810526\nCATTGGGGCGGCGACCAAGCGTCTGCCAGTCGCTCGCGACCACGGCCGCCATCGGGTGCG\nCGGCGGTTTCGCGAATGCCGAGCGCCTGGCGTGCCAGCAGCCCGTAAAACGTCTCGCGAT\nATTGCGCCGCGTTCTTCAGCCGGTTCTCGACGCGATCGGGCCGCGCGCACTGCATGTCGG\nCGCGCGCCGCCCAATAGAGTGCCGCCGCGCGCAGGTCGACATCGCTGGCGCGCGCGGCAA\nCGCCCTCGAACAGCGTGCCAGCGGCGGCGCAATCATGCTGCCGCCATGCCGCCAGCGCCC\nCGACCCACTGGCCCTCGACCGCGAAATCGCCATATCCGGCGGCGGCCTTCTGCGCCAT\n>NODE_53_length_355_cov_0.815603\nTGCCGATCTTCCAACGCGAAGCCGCGCGCATGCGCAAGGGGGCTTCGAGTCGCTTGGCCT\nGTGGCAACCCCGCAATCACGCTCCCCCTGGCCCGCTTTACGCCGCGCCGTCGTCCCCATT\nTCGGGTCACCGCACACGCCGTTCTTTCTGGCGCAGCGCTATTGCCTATCTTTTAAGTAGG\nAATACATTTTCCTCTTGGAGGCGTGGCCATGCGGCGTCCCCCTAGAGCACGGGTGGCCAC\nGTCTCTCCGCCCGCTGTTCCGGGGCTTATTGGGAGAGGATCGATGGGTACCTTCTCGAAT\nTTCGACCCCGTTCAGCCGACCATTCTGACCGTTCCGGGCCTGGGTGGCTCGGGGC\n>NODE_54_length_352_cov_1.100358\nGGCTTTGGCGGCAGGTGAGCGATGGATCCTTTCGACCGAGGGGGCGTTGGGGACTTCAGC\nAGACGTCGATTAAGGAAATCCACACCGACTTCCGCTATGGGCGACGTGCAGCATTTTTGC\nTGCACTGCCAGAAAAGATGGCGAGTTTAGGTTTTTTTTGTTTGTTTGAGACGGCGGCTGT\nGCTAGCCGAAAACCGAGTACTGCAGTGAATGCCTCTCACGAGGTTCATCATTAAGTAAGA\nCAGGGAGTTACCAATGAATCTCGCTAAGATCGCAGCCTCGCTTGCCGCAGTGTCGCTGGT\nTGCTATGCCAGTTGTGGCATCGGCCCAGAATCCTGCTGCTTCGCTGTCGCTG\n>NODE_55_length_351_cov_1.406475\nATGAATTGCATTTCAATGGTTTGTTACAGTTCGCGGAATGTTGAAAAATATGGCGACAAA\nACAATCGTATAAGGCGCTAGCGTTGCCGCTCGACCTGCCAGGGCCGGGGTTTGGCGGGGC\nAAACCCAAACGGCAGCTCGCCCGCTTCGTGAGAAGCACGTGTTGCATCACCTTCCCGTCC\nATGCGTATTTCATCGCATTCAGGCGGGGTGGGCAGTTTCACCGTCTATCGGGAATCCGTT\nTCAACGACCGCCTGCCTGCCCGGGAAATGAGGAGCCCTGTCTTGCGTCGACGCGCCATGG\nATTTGAACATGGGGGACATTGCCCAGCTTGCGAACGTGTCAAAGCCAACGG\n>NODE_56_length_351_cov_1.377698\nGTGAAGGGGCAGTAACATGGTCGGCAATGTCATTGACCGGGGCGGCGAGGTTGCTGTCGA\nTACCGTTCCCCCGAGCGAGCAGGACACCCCTGTCGCGCGGAGCGGGGGTTGGGGAAACAT\nCGCCTTTATCGGCGCCGGCATAGGTCTTCTGGGTGCGCTGGGTGGCATCGCGATAGGATA\nCGGAGCGTTCCACCGCACAGCCGTCACGACCACAGCCGCGCAGCCGGCGAAGGCGAGCGA\nGCGCTCCGTTGAGGACGTGATGAACTCGCCTAATGCGCAGCGTGCAGCCCTTGCGGGTCA\nGCTCGGCCAAACCGGTGCGCCTGCTACAGACGTTTTCGGCCGCCCGATAGC\n>NODE_57_length_350_cov_0.826715\nTCCCCGTTCGCATCAACATAATCGATGATGACCTTGCGTTGGTTCAGAACCGGAGCCGAT\nGCATCTCCCAGCCTCATCGATCGCTTTGAAGGATCACCACCTGCCCCCTTATTCGCGCTT\nCTAATTCAAGGAATTATTTCCGACAATTTGCGTGGCGCTCGTCAACGCCGACCTAACCTT\nCTACCGGCAACCATGTCGCTCGACCTGAAAGCCGTCGAAGTAGCCTCGACGGCCAGGCCG\nGGAGCAAGACCAATGACTGGAACCGTGTTTCGGGCATCGCCCGCGTGCGAACTGCGCTGT\nCCGCGCTGCGATGTGCAGTGCGCCGTCATCACCGCGGTGCGCGACCGGCG\n>NODE_58_length_349_cov_1.115942\nTGAGAATGTCGAGGCCGTTCTCCTCCTGCTCGGTCTTTGCATTCGGCTTTGCCGTCGACG\nCCGTCGCATCGTTTTCCGTGCGAGTCTTGGTAGACTTTTTAGGTGCCATTGGAGGTTCCG\nGATGGTGGGGGCAGTGCCACGCGATGCGCGGGTGCATGATCAACTCGGCACGTCTGCACG\nATGTTCCACCTCCCGCGCGGCAAGTTGCCGGCCGGAATGTTAGGGTGATCAGCGGCTTCA\nCGGCGGGCGGCGCTGTCTTCCGTTGGCGGACTAAGACCACCCGCAATCTGCCGATGGACG\nTCCATCACCGGGAACATCGCGTGCGGCAGGCCGTTCGAAATCCTTGAGC\n>NODE_59_length_349_cov_0.797101\nGAGGATGGGCCAGCAGGGCGATGGCCATCGCCATCGGTGCGGCCATCAGTGGGACCGTGT\nGGGCCCAAGCGGGCGCCATCGCATCGAGTGCATCAAGTGCAGCGAGCGAACCAAATGCTG\nCGAGCCCACCCGGCACGCCGGCCGTGCCCAACTCAGCCCCCAGCTCCGCCGCATCAGCCG\nTCACCCTGCCCGCAGCCACCCCAGCCCCCTTGCACGGCATGGTGATCGATGCCGACACCA\nGACAAGGCATCTCCCTGGCCTATGTCGTGAGTGGCGATCTGACCGTGCGCACCGACCACG\nACGGCCGCTTCAGCCTGCCTGCCAATCTGGCCGGGCACACCGTGGGCGC\n>NODE_60_length_347_cov_0.759124\nCTGCAGCGCCCAATCGCAACCAGCTTCAACGGCGGCGAGCTTTCGCCGCGCATGGGTGGC\nCGTGTCGACACGGCGATCTGGTCCGTCGGCATGGACACGTGCGAGAACTTCGTGCCCACG\nGTCGAGGGGGCGTTGGTGAAGCGGCCGGGCTTTGAATATATTCGGCCTGCCGCGCCGACC\nGCGCAGTGGGTGACCGAGTTCCGCTTCAACCTCACGCAGGATTATGTGATCGAGTGGAGC\nGACTATCGCCTCCGCTTCTACACCAATGGCGGCCGGATCGAGACCGCGCCGGGCGTGCCC\nTATGAAGTGATCGTGCCCTATACGGCGGCGGAAGCGCCCTATGTGTC\n>NODE_61_length_344_cov_1.092251\nGCCTTTAAGCAGATCGTCCTGACAGGCCCTCAGCGCCGCCGCCGCGCCCTGCATGCCGGG\nGACTGCGAAGCTTTTGTGGGTTCCGTCGGCCAAAGCGATCGATACGCTGGTCGAGCGCAA\nTAACTTCGCCGCGATATCGCCTTCGGCGTTCAAGGTGGTGAGGGTGTTGTTCCTGGCGGC\nTATGCCATAAACGGCAACGTCGCTCTGGAACGTTTCACCCGACGGCTGCAGGGTCAGCGT\nACCCTTCAATTTCTCGTAGCGTTTTGCGGGCATGCCCGGCGATACCGTGATGACTTCAAG\nCGTGTCGCCGATCGGGAATGGTTTGAACCCGATCGACGTGACTG\n>NODE_62_length_344_cov_0.852399\nGGCCAGACATCCATGGGGGTTCTTGACAGGGCCATGCGCCTGTTCGTGCCACCATCGCAA\nCCCGCTGGCTGTGAAGCAGGGCATCGCCCAGGTAAAGCTTGGTGAAGCGAAGCGGTTCAC\nCAGCAAATCCCGTGTCCCCCACCGGGATTATCGATAATCTATAGTCACACATTTTCGCGC\nCGCCCCATCGGAGTCACCCATGTGGATTGTTCGTGTCGCCTTGCGACGCCCGTACACCTT\nCATCGTTCTGGCGATCTTGCTGACACTGATGGGCTTGTTCACCATCCTGCGCACGGCCAC\nTGACATCTTCCCGGCCATCCGCATTCCGGTTGTCGGGAAGATGT\n>NODE_63_length_342_cov_0.710037\nCTTCCCGACCGCATCATCTGCGAGCTGACCGCGACGCGCACCGTCGCGCTTCAGGACGCC\nTTCGCGCAGAGTCCGTCGATCGCCGTAGCCGCGGTGCTGCACGCCATAGTCCTGTCGACC\nTTCTTCCTCGCTAGCCGGGAGTCCTGCCTTGGCATCTCGGTCAACCGCGCGGTGTTCGCC\nGCCCAGGCGCCTGGTCTCAAGGACAGCCCGGCGGCGAAGGCGATTGCCGAGCGGCACGCG\nCGCTGGCGTGACCGTCTGCCCAAATCCGACAAGGAGATCTGGGACGCGCTTCAGTTGCTC\nGACGGCTCGGAGCAGGCCGCTTTGTTCGCGCATTGCGCGGCC\n>NODE_64_length_341_cov_1.126866\nAGACAGGTGCCGATCTATGGCCTGGTCGGCGACATCATCGGAGATATCATCCTACCCAAG\nCTGGAACGGGGGATGCGTAGCAACAAAATGCGCCGTTGCATGGGGACAAGGGGCTATGAA\nCGCTATCCGATATCCGAAACGGTGTGGAAGGCGCTGAACGAGGGCGATGAGCAGCAGGTG\nCGGCTGATGCAGGCCAAGATCGCTTCAGGTCCGAAGCCACAGGATGCGGCGGTGACGGAA\nTGACCCGGCTGCTCTTGAGCGTGCTTGCGATTCTTGTGATACTGGCATTGCCCGGCAATG\nCTTCGGCCCGAGATAATGCCGGGGTGGTACAACTGCGGACC\n>NODE_65_length_339_cov_1.154135\nGTCGCGGAGCCGATCAGCGACACCGTTTCGAAAGTCGCCCGCTGGGTGGAATCAAGCTCG\nCCAATCAGACGTGCGTCGGTGACACAGTCCGACTCGTCGAGCGTACATACCCAGAGCGCA\nTCCGTCCTCGATCGCAGGAAGAAATCGAGCTCTTCGAAAACGGGCTCAGCTAGGTTGGCG\nACTACCGGATAGAGATGAGGTGACGCCAAACGCGCATAATCGCGAAAGCCTACGACCGAC\nTCTCGGAGAAACGAGGCGGTGGCCAGTTCGACACCATTGAAATCCATGAACGCTCTGGTC\nGGAGCGTCCACGGACTGCGTGTTGGCAATAAGTGCATTC\n>NODE_66_length_338_cov_1.162264\nGTTGGATGGCGCGCTGGAACGGGGTGACCGAGCGATCATTGCGGACCCGGACGGCGGTTA\nTCTGGCTCGTTTCCACGATCGTAGCCGGGGGGACGTGATCCTCAATCCATTCGACCCGAG\nATCCGTCAAATGGAATCCGTTTGCTGAGATTCACACCCCTTACGATGTGGAGCAACTGGC\nCAGCGGCCTGATTCCCTCGACCGAGGATGCATCGAGTCGTGAATGGCGTGGCTATGCGCG\nAACATTTCTCTCGGCGGTCGCCGAGCGTTGTAGTCAGAAAGGTCAGGGTGATGCTGCGCA\nGTTATGGCGGCTGCTGGCCATTGCCTCCAGCTCGGAGT\n>NODE_67_length_338_cov_0.871698\nTTCCACGACGGTTCAACCACTCGCTAGCAACAACTATACAGATCTTGGCTATTACAGAAC\nTCCTGCAGTTCAGTCTCACGCGATCTCGCCAAAACTTGCATGGACTTTACCGGCCGGCTG\nGTCGGCGACGCTGCTGGCCACGTATGGTGAAGATAAGACTGATGTGAATTCGCGATTCTA\nCAGCGGGGGGGGCACTCAGCTTCGCCTCGGTGGGATTCTATCGTAACCGATCGACCCTGA\nTTGAGATGAACGTCGAAGGGAGTCTCGCGCATTTGCCAGGCGGCAATGTGAGGTTGGCCA\nGGGGAGGCGGCTATCGCGGGAACGAACTGATCGCAAAC\n>NODE_68_length_338_cov_0.871698\nTTGTAGCGATTGCCGGAAGTAATAGAGCCCGGCCGTCGCATCGATCCTGCCGCCGCCGGG\nATTGGCGATGCGAACCTCCTGGCTGAATTGCCAGTCGTCGGTCGGCACGGACGCGTTCGT\nGTAGGCCTCGGCGCTCGACAGATCACCGTCGAAACCCGCCCGATAGCGCCATGCGCGATA\nGCCCGTCACCGACGTGATCTCCGCCGCCCCCAGGTCATAGACAAGATTGGCGGTGAGCCC\nGCCCTGGCGAACGCGCAGAAATGTTGGAGCGTTTGCCGTGGTGCGATAACCGGGGCCGCC\nCAGCACCGCATTACCGCCTGCAGCCGCAACCCGCGCAC\n>NODE_69_length_336_cov_0.878327\nGTCTGGTGCATTAAGCGGCTCGATTCACCGTGAGGAGAAGAGCTGCCCCGCCTTATCCGC\nGTAGGCCTTTCTCCGATATTTTGTTGAAACGGATAGAGGAAGGATCGCGTTTCCGATGAG\nCGTCGCACTGAACGGAATCAAGGTTCTCGACCTGTCTCGCGTTTTGGCCGGCCCCTGGGC\nAACAATGACGTTGGGTGATCTCGGTGCTGACGTGCTGAAGATTGAGCAACCTGGAACCGG\nGGACGACACCCGGACGTGGATGCCGCCGGCTGTGGAGGGTGTTTCAACCTACTATCTGGG\nCGCAAATCGCAACAAGAAGAGCGTTGCGATCGACAT\n>NODE_70_length_335_cov_0.854962\nGTATTGCGACCGGGGAGTTTCACGCAAACCTGATCGCCGGGGCCGGCAATTTCGGCAGCT\nACAAAGCCGAGGGACATATCGACTTGCCGTCGGTCGCTGGGATTGCGCTCAAGATCGATG\nGAGTCGTCAGCCACCGCGATCCGCTGGTGAAAAACACGTTGACGGGTGCATCGGGCTTCA\nATGCTTACGACAAGCGCGGCGTTCGCGTGGAAGCGCTGTGGAATCCGACATCGGATTTCA\nGCGCCGATTACGCGTTCGACACCTCTTATGATGCCTCGACGTCGCTGTATCTGCAGTTGC\nTTGCTCCCGGTAGCAACAAGCAGGCACCGCTCGGC\n>NODE_71_length_334_cov_1.180077\nTGTTGTTGGTGCCGATAAATCCTTTTACCAGTTTATTGAGCACATAATATTCTTCTGTAA\nGGCACTGCCCCGATGCATAAAAAGCTACCGAGTCGGGACCATATTTTTGAATAAAAGTTT\nTGAATACAGCTGCTGTTCTGTCGAGTGCCGAATCCCACGATACGGTTTGCCGCGGGCTTT\nGTTTGTTGTACCGCATTTGAGGATAGCATAGCCGGTCGCTTTGATCTATCACTGTATAGT\nGCAGGTTCAAGCCTTTGCTGCACAACATGCCCTTGTTTACCGGGTGGTCTTTATCGCCTT\nCTACGTGCAGCAAAGGCTTGAACCTGCACTATAC\n>NODE_72_length_333_cov_2.450000\nCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGA\nTCGCCCCCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTTGACTATGACAACAG\nTCGCGACTATAAACAGACTCGCGACTATGGCAGGGCGGTATGCTCCGCTCTCTCGCGACC\nCCTACTCTAATCAAAAGACTAAAGGCCCCTACCGAAGATTCAAAAGGCGAGCACTTAAAT\nGAGAAAGGCTTGTAGACTCGTGACGCTGAACGACACATTCTAAAACTAAAGCGCACACTA\nGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCG\n>NODE_73_length_332_cov_1.189189\nGTCTTCGACATATCGACCATAGTGCCTTGGCCTATATCGTTTGCAGCAAAAACGAAGGCC\nGGCAGCAGCCAGTTCGCAGAATAGTTCTGCAAATGTTCGATCGCTGCCTTGATGGTTGGA\nATGTCGAAGTACTGCACCGCTATCCTATCTTGGCTCTACCGGGTTTCCGGAAATTATCTT\nTATTCCCCGACCAGCTTTTCCATAGTGGGGAGGGACTAGCTAAGCGCTTCTGGACTTCCT\nCCCAAGTAGTTAGCTTGTGACCGTCCGATTGGAGCGTAGTCTCAATATAATCAATGTAGT\nCCTCGCTCATGTCGACGCCAACAGCATTACGG\n>NODE_74_length_331_cov_2.251938\nCCCAGCTCCCCGAAAACGACGTTCGACTTGCATGTGTTAAGCATATAGCTAGCGTTCGTC\nGTTTTCGGGGAGCTGGGCAGAAGGAAAATAGGCTCCTAGCTAAAGGTAGCTTGTCTCGCC\nCAGGAGGTGAGAACAGTTGAGAACAAAGTGGCGAACGGGTGCGTAACGCGTGGGAATCTG\nCCGAACAGTTCGGGCCAAATCCTGAAGAAAGCTAAAAAGCGCTGTTTGATGAGCCCGCGT\nAGTATTAGGTAGTTGGTCAGGTAAAGGCTGACCAAGCCAATGATGCTTAGCTGGTCTTTT\nCGGATGATCAGCCACACTGGGACTGAGACAC\n>NODE_75_length_330_cov_1.198444\nTGATGGTCTCGCGACAGACATCGTCAGGCTTCCCGTTCCAGTCCCGGACCGCCAGCACCA\nCCATCTTTTCCATGCGTATGTCGTGCCGGAAGATCATGCTGCGCTTCTGGCCACCGCGCT\nCGATCGACGAGAACGCTGCGTCGTGCATCAGTCCATTGCGCATCATGTAGAGCGCATGCA\nTCTCATCGGCCGAAAGGGTTCCCCACGGCAGCGGAAAGTGATGTAGCGCTCGCTTTATTG\nGGGCGTTCGCCGGCGGCTCTCCAGAGATCGTTTCACTGAACCCATAGCTCTGCCGATCTG\nGTCGAGGATGGCGAAGGCCGCGAGCAGAGC\n>NODE_76_length_329_cov_1.203125\nTTCTCCAGGAGCGGTCTCGAGGCTGGTAGCATCAATGAAAGGCTTTGCGACAATTACGCC\nCAGAGCAAGATCGGATCGACTTTAAGAGTTTATTGATGCTGTTGACAAAAATACTCTCGC\nGGAAAAGAATAGATCGCTGTAAAAATCGTAAAACCCTTGGGGGCATTTGTCGCGCACGCC\nAGTGACGCAGGACTGGAAGGATTGGTATCATGCCGCGTTTGTCGGGAATGGTCCACATCA\nCGTCGATCGAGGACCTGCATGGCGACATGGCCGGTGCCAGCCAAGATGCGATGATCTCGG\nTTCTTGGTCGTCGGAGAATACCGCTGACC\n>NODE_77_length_329_cov_1.000000\nCGACCTTCTGTTGACGGGACCGATGAACCCGGCCCCCCGGAGATCGACGAACCCCTACAG\nTGGAGAGATTGATTGGGGGCCACCAGCATCGACGCGATCGGAGCGATTGCCCCCAATCAA\nAAACTCCACTGTAGGGGTTAGTCGATCTCCGGGGGGCCGTGTTCATAGTTCCCGTCAACA\nCAAGGTCGAACCAACGGAAATCTGTCATCGATCAAGTCGAGCGTAAGCGTTTTTACGAAG\nCGCACGTTATCGGGAGCCGTACGAACTCGAAAACATCCTTGCGCTGGTAAAGCACTTCCG\nCGCTCCGGTCTTCCTTCACGGTCTGGCGA\n>NODE_78_length_327_cov_0.858268\nGCCGGGGGCACCATTCGCATCGCGATCCCGTATCCGGCGGGAGCGGCGGTAGCGAAGGAC\nGCCTATTTTTACCCGATTACGCCCGGGATGATTGACTATGCCAAGCCGCAGAGCGTGGTG\nCGGGATGGCGACCGGCTGGTGGTGGAAACCAAGGCGGCCGCTGGCGCGGGCGCAGCGTCG\nCTAAAGGGCGTGTTGCAGATCGGTGCGCAACAGGGGCTCTTGGTCACGGCAGCGGCGGGC\nAACGTTGCATCGGTTGCCTCGATGGCGTCCGCGTCGAGGGACAATGTGTGGCTGGCGACG\nGCGATTGCCTTTGCCGGGGCAATGTTG\n>NODE_79_length_326_cov_2.059289\nCAATTACAGTTCACTGCGCCCTTTACTAATAGAATCTCAAGTAAAGGGGCTTGCTGGTTT\nTTCCATCAAGCCCCTTTACTTGAGATTCTATTAGTAAAGGGCGCAGTGAACTGTAATTGT\nGAAAAGGTTGGAAGATCTGGCCAAAGAAGGTGATAGCCCTGTAGATTCGTTCCCATGGTT\nCGATCCTTCCCAGTAAAACGCGGCGTGTTCGAATTCTGATCGCTTTTACGCGAGAAAGGG\nGGACCACCCTCTAAGCCTAAGTATTCCTCAATGACCGATAGCGTACAAGTACCGTGAGGG\nAAAGGTGAAAAGAACCCTATTTAGGG\n>NODE_80_length_326_cov_1.213439\nCTCTGGGCCAATCGCCTGTTGCCGCCGCTGCTGCCGCAGCGTGCAGACGCGGAAGTGAAT\nGTCATGTTCGCTTTATGGGGCGTGCTGCTGCTCTACGCCTTTCTGCGCAAACCGACGCGC\nGCGTGGGTTGACCTGCTGGGGTTGACGGCGGGCTTGCTGCTGGCGCTGCCCGTCTTCGAC\nATGCTGGCGACCGACAGGGGGTTGCCTCGGACGATCGCCAGCGGTGACTGGACGCTGGCT\nGGGGTCGATCTGACCTTGCTTGCCTTAGGGTGCGCTTTCGGCTGGATGGCGCGCGCCGTC\nGCGCGGCACCGCGCGCGCCCGCGACG\n>NODE_81_length_325_cov_1.222222\nCTACCGAGCATGCCGGACTCAAGCGCCTGGATGCTGGTAGCCGCGATCTTCGGCACCACG\nATCAGCCCCTATTTGTTTTTCTGGCAGGCCTCCCAGGAAGCAGAAGATGCCAGAGCTAAA\nGCGAAAAGCCTTTCGACATCGGAAGTCAGCGCCGGCGAAGAGCGCCGGATTAGCCTCGAT\nAGCTGGTTCGGTATGTTTTTTTCAAACCTCATTGCCATTTTTATCATCATAACCACCGCC\nGCGACCTTGCATATCGCTGGTATTACGCAGATCGATACGGCCCGCCAGCGGCCTGAGTGC\nTTCGGCCGCCTGCGCGGCCGTATCG\n>NODE_82_length_325_cov_0.916667\nGTGGCGCATCGCTCTCATTCCACGCCTCGTGCTCCACGGTGTCATCAAACACCCAGGCCT\nCACCAGCCCGCCACTCCCTGCGGTCGGCACCCACGCGGAACGTGCATTTCCCCGGGAGCA\nCCAACGGCAGATGCACGGTCAGGCGGGTGTTGGTCGAACCATTGTGCGCCGGAATGTGAC\nTCTTGCCGTCCAGAATTGAAAAGAACGCCGTCGGCCCGTGGCCGCTGATCTCGATGCGAG\nGCGTCCTGGCCAACGCCGCGACCGTGGCGGGACAACGCGCCTGGTGCTCAGGAAACTCCT\nTGCCTTCGCGCCAGAGATAAAAAGC\n>NODE_83_length_324_cov_0.920319\nCGCCTAACCCGTCGCTTCGGAAACTGTCCCGACCGGGCGCGCCGCACGCAGAGCACGTTT\nCGCGAATCGCGCAAAATTGGTCTGGTTAAGGCCAATTATTGGTCACAGGTTCTCTTCAGG\nTTCTATCTACCGCCGGACCACAAAATTTGACGATGTCCGCGCGCCATGCGGTAACTAACC\nGAAATATAACGACTTGTTTCTGCGGTTCCGGCTTGGCCTCCTGTCATTGAAATGCAACTT\nCGGCATAGCTTTTGCCAAATGCATTGGTTATAAATTTCCATACCGTAGCGGTGCAAAAAG\nACACCAATGTGATACCACATGATG\n>NODE_84_length_322_cov_0.871486\nGCAGGAAACGCTGGACGCCAGCGCGAAAGGATGCATCCAGCAAAGTCCGTGTACCATAAA\nCGATTTGGTCAATCCAAGCGGCATATCCGATATTTAGATGCGTATCCGCAGCCGCGTGAA\nTGACGTCGGTCGTATCTTCGGCCAAATCAGGCAAATTTGACAGACTGCCATCTATCGTGG\nTCAGCCAAAGATACTGTTTCTGAACCGGATAACGGGCCCGAAAGGCCGGGGCATTGCGGG\nTGAGCACCGAAACACGCAATCCACCATAGGCAGCTTCGCAACAGGCCAAATAATCTAGTA\nAAGTTCTGCCAACGCAACCCGT\n>NODE_85_length_321_cov_1.991935\nGCAGTGGATCGCTCGAGCCAGCCGCCAGCAGGCTCTTGTTGATGATCCAGGCAAAAGGCT\nCGATTTGCGCGCGCCGCAAATCGTCCTGCAATGCGCTTGCCTGCGAGACAGGTGTGGTCT\nCCGCAAGAGTAACCAGCAGAATATGCGTATAGTCGGGATCCTGGAGCCGCATCAGCGGCG\nTAGTTATGCGGCCGGCAAGGTCGTGCAAAGTCGTTTGTCGTGCTGGACACGGCCCCCACC\nGGTCACAGCCTTCTGCTAATGGATGCGACCGGCGCCTATCACCGCCAAATGACACGGCAA\nTCGACTTTGCACGACCTTGCC\n>NODE_86_length_318_cov_0.710204\nCTAAGAACGGCCATGCACCACTACCCTCAAATTCGTGAAAACGCTGTCAAATTGTCATAC\nCCACTTGAGTTCTGACCTGGTAAGCTTTCCCGTGTTGGGTCAAATTAAACCGCAAGCTCC\nATCGCTTGTGGTAGTCTTCCGTCAATTCCTTTAAGTTTCAACTTTGCAACCATACTTCCC\nCCGGAAACTAGCTTTGGTTTCCCGGAAAGCTACTGAATGCACCATGAAAAGTAGTGACAT\nCCAATTGCTAGCTGTCATCGTTTACAGTTAGAACTAGGGCGGTATCTAATCGCCTTCGAT\nCCTCTAACTTTCGTTCTT\n>NODE_87_length_317_cov_0.819672\nGCTCCCAGCCCGATGCCGCGATTTCGCCGCTTGCCTCACCAGCCGTCGCCCGCTTCCCCC\nTTCCCTTCGCAACCGATTGCGGACAAGCTCTTGCGAACCAGTCGCAGGGGGCGGCGGCGA\nTGGCGGAACAGGGTTGGGCATGGGTGTAAAGAATGGGCGCAAGGCGCCGCCGGCGTGGTT\nGCTGGGCCTCGCCACCCTGGTCAACGGATCCTTGAGCGGCGTGCTCACCGTCACCGTTCC\nGCAGCTGCTCGCCGCCCGGGGCGTGCCCGAGCCGCAGATCGCCGCCATCTCGGGCCTCTC\nCTTCCTGCCGGGGACCT\n>NODE_88_length_311_cov_1.252101\nCACCATAGGTGCGAGCGACGCTCGATAAGACGCCCCCCGATACACGCAATCCGTACACAC\nCGATGGCGAAGATAATGCCATCCAACGGGACAGGTAGGGCAGGACGTCAATATCGGCTGG\nAGCAAGTTCCGTTTTATCCGCGTCTAATTGACCCGGAACACAGGGAAACAGCACGCTATA\nCTGCGTCCGCCCCTGTTCGAAACACCGGAGCGTGCGGCAATGTCTCAGCTTGAATGCAGC\nAGATTCGCGATCGCATCCACACCCCACCTCCTCTATGCTGAACGCACAGCATGGAGGCAG\nCAATGCATCAT\n>NODE_89_length_310_cov_0.974684\nGCCCGCAGGCAGTGTGCCTTGCACAGTCGCGGTCGGCGAGACTTCCTGCCGGGTTCGGCT\nCCCGACCAGGAGAGATGCCAGCTGGCGATTCACGCGAAGCCGCGCGCTGTGTTAGGCGTC\nAGCAGCCCATCGATGACGCTGTTCACGCTGACATCGATATTCACTCGCGCTGCGGCGACG\nCTCGCGGTCGTGAGCTCGCGTTCGATCGCCACCAGGCTCGCCTTCGAAATCACCGCTTCC\nTCGCCGGGCATGGTCGCGATGAAATCACGCAGGATCGCGAGCGTGGTCATCGGCGGTCTC\nCACGAAAGGG\n>NODE_90_length_308_cov_0.978723\nGGATTGAGCTCGACCGACAGGGCATTCACCGTAAAACCGACGATCTGCTGCCCTCGCTTC\nGACCAGCGTTGGTGATTGCATGTGCGGACAGCGAAGCCGACCAGTCGTTCGCCGAGGCTG\nCGCAGCAAGCTATCGAAGACGGTTCACCACTACTGCTCTGCTGTCTCGCGGGCCGCGTCG\nTCCGACTCGGCCCATTGATTGATCCATGTTCATGCTTCACTCGCCCCTCACATCCTCCCC\nCTGACGTTGCGATGCAACGTGCGGAGCCGCTCCACGGTCCGGCCGAAGCCGGCCACCCAC\nCCCTGAAT\n>NODE_91_length_306_cov_2.373391\nGTCCGAGATGATCGACGCCGAACCGACATAGGTCTTGTCGGCCAAATTCTGCACCGATGC\nGTAAAAGGACAAACGCGACCACCAGCCTGCTGCAGCGGGCGGATCGTAATGCAGGTTGAG\nATTGACCAGCGTGTAGCCCGGAATGCGCAGCAAATTGGCATTGTCGATGAAATAGCGCGA\nGCGGTAGGTCACCTCGGCAAAGCCGCCCAACCCGGCGAAGGCACCGTGCGGCTGGTCATA\nGCCCAATCGCCCGTTGGCGAAGGTCGGGATCACGCCCGGAATGCGGTTGTCGGCACGATC\nGAAGGT\n>NODE_92_length_306_cov_0.742489\nTTTAGAATTTGAGCGAGCACCGCCGGGGCAAGGCCGACGCCGCCCTTTTGGGCAATTGCA\nGTCCCGAGCTTTTCAGCGAGAACACCGCGAAACATTTCCTCGCCATGCCCCCCGGAAAAC\nTCGCCGGGCTGCACGCTTTCGAACATCAATTGCGTCATCTGTCCGAGGAACACCGCCTCC\nAAGGACTGGGCGGTGGCCGTGTGCGCGGGCGTTGCGGCCTTGGCGGGTGCCGCGCCGACG\nGTCGCAGCAGGAGTCGGGATTTCGATCGTCATTGGACCTCAATGTCGGCCTGGAGCGCGC\nCTGCAC\n>NODE_93_length_304_cov_0.969697\nCTTGTGGCCGTTGCGAACGGCGCGACCCTCGACATCCCGGATAGGGAGCATGAAGAAATC\nGCGTTTCCCGATCTGTGATTCTAGTCGACACAAATGTTTGGAGCGCGCTGAATCGCCCCG\nCTTCGCATCCATAGGTATCGATCTGGTTTGCGGCAAACGCGCCGCAGGATTGGTTGTCGA\nCGATCGTGATTGCCGAGATCCGTTCTGGCATAGAGAACCCGACAACCGCCGAGCGACGGC\nCAGCCCTGGAGCGCTGGCTCGCCGATATCGAATTGGATCACGCAGGTCGCACGCTATCTT\nTCGA\n>NODE_94_length_299_cov_1.362832\nGCTTGCGGGCTTCCAGCCCTTTTGGGTGTGGCACTGCGCGCAGTTGCTGCCCGCCTGGGC\nATGGAGGGCGGTCGGCGGGGCGCGGTGACACGATGCGCACAGGCCGCGAACATCGGGCCG\nCAACAGTTCATGCGCGAAGCTCGTCTGCGACGCCTTCACCAGTTGCGGCCCGCTATGATC\nGCTGTGGCAGGCCAGACAATTGGGCTGAGCGAGCGACTGGTGAAAGGCGATGCGGCGCTT\nGCCCGCCTCCAGCGGCACGCCCTTGGTGGACCGGATGCCGATATCCGCGACCTTGTGGC\n>NODE_95_length_299_cov_1.203540\nGTCAAGGCTACCGTCGCCCCTGCCGCAAAAAGCGTTGCGGAAAAGGAGATTACCGGAAAT\nGGCGGCAAGGTCATCCTGCGCTACTCGAAGGCGAGGGGAGGGGGATTGACGATCAAGGTT\nCCGCCAAAGGCCGATGCAACGCCGGCTGAGCTGCTGAAGGCGATCGAAGGGTTGCTTGGC\nTAGCCGACATCGAATGCCCTTGGGACGATACCAGTTAGGAACCACATGACCGCTCCCGGC\nCCTGACACCATGCATAATCCCACGCTGCTACCGGACGAAAAGGTTGCCTGGCTCCATTT\n>NODE_96_length_299_cov_1.022124\nGCCTTTATGCCACTTTGGAGGCTTGAGGTAAAGAGTGTATAATACAGCTAGTATCGATAC\nCGTCGCTCGCGCGCTCGTTGATCTGCTGGGGTTTTTCAGCAGCCCGCAGCGCGTGGACCT\nGTTGCTGAAAGAGGCGGGTGTGGTGCTCGACCGCGCGCTGGTGCCGCTGTTGGTGGGGAT\nCGCCACGCGGGGCACGCTGAGCGTGGCGGCGCTGGCCGATCAGGTGGGGCGGGACTCGAC\nGACGGTTAGCCGCCAGATTGCGAAGCTCGAACAATTGGGCCTTATCGCCAAGATTCCCG\n>NODE_97_length_299_cov_1.022124\nGTCATGGGTCGTGGCTGTCGTATTCACGCCTTACCTGGGTGTGAAGCTGCTGCCCGCGCA\nCATGCATCAGGGTCAGCACAACCCCTATGACCGGCCTATCTACACGCGGTTGAGGCGATG\nGGTGGACGCGGCCGTGGCGCACCGCTGGGCTGTGATCACCTGCACAGCAGTGGCCTTCCT\nGGTGGCCGGGGCTGGCATGGGCCTGGTGCAGCAGCAATTCTTCCCCACTGCCTCGCGGCC\nAGAGTTGCTGGTCGAATTGAGGCTGCGAGAAGGCGCGTCCTTTCGAGCCACTCAAGCTG\n>NODE_98_length_298_cov_1.368889\nAATCGAGTGTATGTATCAGCAGCAGCTGCATACTGACCACTCGATTAATGCAGCTCGGTT\nCGACCGAAGCATCGGACCGTTACTGGCTTGGAGAGTCGTTATATCACGCCGGAAACTATC\nAACAGGCTGCTGCGGCATTCGAGCAGGCGGTGCAGATCAGTCCCAAACTTGCGCAAGCAT\nATGTGCGTTTGACGGAAACCTATCTTGCATTACACCTGAAAGATAAAGCGTATCAATCAT\nCGCTTGCCGGTTTGAATGTTGTTGGTGATCCGTATATGAAAGAGCAGCTCTCGAATTT\n>NODE_99_length_298_cov_1.346667\nGTGTGCGGCGCACGGCCCGTTCTTGGTGATCGATGCGATGGGTGAGCGCATCAACTTCCT\nCGCGTGTTGGTATCCCCGCGGTACGCGTCCATTGCTGGAGGTATTGTCCGCTGCTTTGCG\nGATGGAAGGCGGACAATACCTCCAGCAAAGGACGCGTACCGCGGGCTTACCAACACGCGA\nGGAAGTTGATGCGCTCACCCATCGCATCGATCAGCTCGAACGGGCCGTGCGCCGCACACC\nGAGCGCAAAGACTTCCCGCAAGACGAAGGCTCCCCGGAAAACACAGTCTTCCGGGAAG\n>NODE_100_length_298_cov_1.026667\nGATTCACTCTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTT\nCAGTCAATCTACGCAGAGTGAATCGGTCCCTAAGGAACCCCCGAAAGGGCTGCCGTCCGA\nTGGGTACACGAAAGTGACGAAGTTGCTTTGACTACAGAACCATGCCTGTCTGTTGGAGCG\nAATTGGATGATCGGGCCGAGGGCTGCCCCCTCTTCCCCTCACTCTCCTTTCCCTAATATG\nAACCTTGAGTCATCAAAGCCTTTCTGACCGGGCCAGACCGAGTCAGAAAGGCTTTGAT\n>NODE_101_length_298_cov_1.022222\nGGCATTTGACCGCGCGGCCTTCGCCGCCGCCATTGCCCCCGATTGGGCACCGGTATCGCA\nATTGCTGCCCGAGCAACTCGATTCGGCGGCCCCCCCGGCAAGCCCCGCATGGGCGCAAGC\nCGAAAGCGGCCCGCCCCAAGAGGCCGTGACTCGCATCGCCCAATGGAAGGCCGCGCATCC\nGGGCGAAATCGCGCTGCGCGTCGCGCTCCCCGACGGCCCGGGCGCAACCTTGCTCTACGG\nCTATATCGGCGCGGCGTTGGTATCGCTGGGAATCGCGCCCGAGCGGGTTGCCGCCGAT\n>NODE_102_length_297_cov_1.366071\nGTGTTGCTGTTGTTGTGCGGCCTCCATTGCAGCTTGCACTGCGGCCATCGCGGCCTGGTG\nCTGTTGCTGGGCGGCGGCCATCCCTCCTTCTACCGCATCTTGCGCCGGTCGCTGCGAGTC\nGCCTTGCCCGGCGTGCGGTTGCGATGGATCCTGCTCAATCATAAGTGGTACTCGCTTTGG\nGCGCGGCGGCGTCTGAACCCGAGGGGTGATCTTCGCGCACATAGTCCTGGGAGATCGCGA\nCAACCATCCGCAGCGTTTCGATCGCCTTCGTAATCAGATGCTGCCCTTCCTTAGCAG\n>NODE_103_length_296_cov_1.035874\nGCATTACGGCACGAGAGATTCTCGACAAGTCTGCGACTGAGATCAATCGCGACCTCGTCA\nATGATCCCGAGCGTCAGGCTCAGATGATGCATGTGATGGGACAGGTTTATGCCAACCTGG\nGCCTGTACTCGCGCGCTGAGCCGATGCTCCAGCAGTCTGTAGCCATCCGAAGCCGCGTGC\nTCGGGCCGGAGCACGTGACGACGCTGGATTCTCGCAATCTCCTGGTCCAGACTTTGATTT\nCCGCCGGCCGCTATACCGAAGCCGAAAAGATTGCGCGTGAATCGTTGGACACCGCG\n>NODE_104_length_296_cov_1.008969\nTTGTAGAGCAGATACCGCCGCCGCACCGCGTCGTATGCAGCCAAATCCTTGCCCCAACTG\nGCGATAATTTCGTTGGGCGCAACTCCCCCTTCGAGTTGCTGAATCGTGGCATCGTTGCCA\nAGCAACAGAAGGATTTTGCTGTAATCAAAATGTTCGGGATATTTCTTGTGCAGCTCGACG\nGCAATCTCCAGCCCCACGCGCATCGAACGCACTCCTGCACGATCCGTCACGCGAATGCCC\nACGCCGCCGCACCGCTGCCCCGCATATAACCCGCTCACCGGGATAAACGGCTGGTT\n>NODE_105_length_296_cov_0.443946\nGTATAGTATACTGCACCGCCATAACTGATATTGTACTATTGATTCAGGTGTCACACTAAA\nCTGCCTAAAATCTAGACGCTGAACTGACAGTCAAAATTGACGCAAACACCCCCAAAGACG\nGCCCCCCCAACGAAAACCAACAAAGCGAACTGTCCGTTACAATAATAAAACAAAGAAAAG\nGCCACACCGGCAGGCGGTGTATGTGCCTATCGATGTTTCATTCATGTAACGGACAGGGCG\nCTGAGACGGCGCCCCCAACGAAAGCCTCCTCAGCTACCTGTCCGTTACATTAATGA\n>NODE_106_length_294_cov_0.963801\nCCCTTATCCTGCCGCGCTTGGGCTGCGGCGTCGATACGAGCGAGGGCACGGTCGATCCGG\nTCGAGCGCGGCAGGATAAGGGACGTCTGCCATCCTCACGAGATAGCATGGCGCGAGGCGG\nGGACAAGGCGCATTTGTGACGAGTTCGTGTCATCCGTTCGGATTGCACGATGAAGAGGGC\nGGAACGGGGCGGGCGGTTGACGTGCCCGCCTGTCGCCCGCAAAGACGCGCGCATTCGAAG\nGACTCGGTGGCGCGCTGCTACAGGGTCAGCCGCTTGAAGGAGCCAGCATTATGA\n>NODE_107_length_292_cov_1.406393\nGTCGAGAACCCGTCCCTTTATATTGACCTGCCGGGACACGAACTCGACGAAGCGACCTTC\nCTGTCGGAGCTGGCACGGCGCACCGGATGCGGTTTGCTGGTCGATGTGAACAACATCTTC\nGTCAGCGCCGCCAACCTACGGTTCTCGCCCGAGGTTCGGCTCGACGCGATCCCGGCGTCG\nATCATCGGCGAAGTCCATCTCGCCGGGCATCGCCCCGATCCCGACCCTGATAGCGGGTTG\nCTGATCGATAGCCACGATGCGCCGGTCTCCGACCCCGTCTGGCTGCTCTACC\n>NODE_108_length_290_cov_1.064516\nTCCGCACCGTTCACGCCGCGCGGGGTATCGACCCGCGCCATCAGCGCGCGGCGCAGCGCA\nATCGACACCCAGCGCGACGCGACCGGGGTGTTCAACCGTTGCATCAGCACTTCAAGGAAG\nCGGCCGTCGGCGCGGCCAAAGGCGTTCGGCCCCATCGCGCCCTCAGGCGGACCCGCGACA\nCCGACGCGCGCCAGCGACCGGCGCGCGAACGATGGCATGTCGGCGCGCACGAAGGCGGCA\nAAGTCGGTCGGCGCGGGAGGCGTGGCGGCGGGGCTCGGCACAGTCGTCGG\n>NODE_109_length_289_cov_1.745370\nGGGCTGCGATTCGGTGGTTGCGCTCGAGGACGGCTCGATGCTCGACAAGCCGCGCGCGCC\nAAAACCATCGGCGATCAGCGCGGCTTTGGCCGATTCCTCGTCGACGCCTGCGGACACCGG\nCTCGAACGGTACGCCCGCCGCAGTCAACATCGCGCGGCGGGACGCGCTTTGCGATGCCAG\nCACGACTCTCATATATCCCCCCGGACATCACCGCGCCGCTCACCCACCAAAGCGATGATC\nGCTGCTGCCGTTTCCTCGATCGAACGTCGCGTTACGTCGATCACCGGCC\n>NODE_110_length_289_cov_1.425926\nCGATATTGCGGCGCGCGGCCATGGGCGTCGAGCGGCACGTCCAGCGTATAGCCAAGTCGC\nGCGGGCATGGCATCGGTGCCGCGAATCAGTGCCGAGACGTCGGCTTCCACATAAAGGCGC\nGCCATACTGGGCGGGAGGCCTGCCGAATCGGTCGGCTTGAGCCGGACGGTGCTGCGAACG\nGTCGCATCGACGATGACCGGAGCCGCGACGACGAGATCTGCATAATCGGCATAAGCGGGC\nGATGGCGCGGTGCTTTCCGTAGCTATCGGAGCATGTTGCGCCGCAACGG\n>NODE_111_length_287_cov_1.079439\nCCGGTAACGGGACGAAGACGGGTGCGCGCCGTATCGGCATAGAAGGTCGGGGGTAGCGGC\nGCGTCGGCGGCATTGATCTGCACGTCGCGATAGCCCCAGCCCCATTGGCCGACAAAGGGC\nAGAGGTGTCGAACCCGCCTGCGGATCGCGATAGACCAGGTCGTCGACGCAGTGCGCGGCG\nGTGGTGACACCGTAGCGGATGCCGTCGGTAACCGTGAAACCCGTCGTACAGAGATACCGC\nCGCCCATCGGCCGGGCTGACGCCCTCGACTCGCGAGCCGCCTTCGGG\n>NODE_112_length_287_cov_1.060748\nACCTACGCACGATGTTTTACTGGAGTCCGAAAAACGTGAAAGCCGTCGCGGGGGCGAGGC\nGGAAAGCGCGACGCGGGGAACAGGGTCATGGAGAACAGGACACCGCATCGCTTGCGGTTG\nCTCGGTGCGTTTGGGCTGTTCGCGCCTGACGGCACCCGCCTGCAGATCACCAGCCGCAAG\nGGCATTGCCTTGCTCGCCCTGATTGCCCTGGCGCGCTCGGGCGAACGCTCGCGCGCCTGG\nCTGCAAGCGCAACTGTGGGGCGGCCGCGATCCCGATCAAGCCCGAGC\n>NODE_113_length_287_cov_0.962617\nGGCGGACCGTCACGTCCTCCGCAGGCATCTCCTGCATGACGCGCAGGACGAAGTCGTTCG\nCCAGCTCCTCGTGGACACCTACGGCAGGCAGGGGATCGACGAGCACGAAATCCGGGACGA\nGTGCACCGTCGCGGAACTGTCGGAACTGGGGACGTTTCGGTCGCATCTGCGTCTCGTCGC\nGGAGAAGGCGGGCATCCACTTCGAGCGCCTGAAGCGCGTGAGCATGCAGAGACTCCCGAG\nCTGGCGTATCGCCGATGCGCTGAAGCGCCACGGGCAGGAGCGCCCCA\n>NODE_114_length_286_cov_1.446009\nCATTACCAAACAAGTACGGATACAAGCCAAATACAGGCGTAGTTTAGAAGTACTTGAAAC\nCCTGAAAAATGGAGGGATGAGAACGAAAACCGGTATTATGCTTGGTCTTGGTGAAACTAA\nAGAAGAAGTGGTGCAAACCATGAAAGATCTAGTTTCCGCAGGAACAGATGTAATTACATT\nAGGTCAATATCTTCAACCCACAAAAAAACATTTACCTGTACAACGATTTGTTCATCCTGA\nTGAATTTGCTGAACTAAGAGAGATAGGTTACGAAATCGGGTTTGAT\n>NODE_115_length_286_cov_1.084507\nGTTTGCCCACGGCCTGCCATTGGTGCGGATGATGAAGATCACCAGCACCTGTGTCGCCAT\nCGATTCCAGAAACCACGCGGTACGGAATTCAGGCGGTGCGGCATGGAACAGCAGCACCAG\nCCCGGCAAAGGTGAGTAAGTCGAACAGCGAGGAGAGCGGCCCCATGATCGCCGCGAATTT\nTACGAGGTCGCGCAAGTTCCACACTTGTGGCTTCGCAATCGCCTCGGCGCGGACGGTGTC\nGAACGGAATGCCGATTTCGGACACGTCGTAGAGCAGGTTGTTGAGC\n>NODE_116_length_286_cov_0.784038\nAGTGAGAACAGCGTCGTCGTAAGAGACCCAGGCGGACAATGTGGTCGAGCGAATAGGCCG\nTGCAGTAAGAGACAACTCCACACCTTCGCTCTTGGCATTGCCTCCATTGGTTCCATATTG\nGATGCCCAAATCGGTATGCAGGCTGATCTGGATATCCTTCCAGTCTATATAGTAAACCGA\nACCATCAATTGACAAGCGGTCATCGAGAAAGCTCGCATTGACTCCGATTTCATAGTTGCG\nAGTCTTGTCGGGTTTGCTGAACGGAGGTACGCCGCTGACAATGCCA\n>NODE_117_length_285_cov_1.235849\nCCATGGTTGAGCGCGGTCGTAAGCAAGGATATTGAGCGACCAATTCCGCTTCGACGTGAC\nGGGAGGCACGATTGCCGAGGGGCTGACCACGGCCCCTTCCGAGGCGTTGGTCGCGCTCGC\nGGTGCATTTGGCGGGCGAGCATGGGGTGGCGCTCGCTGATGAATTGGCGACGCGTCACCC\nCGCTCCCCGCATGCGCGTGACGGCGCTGCGGGCGCTGGCTTCGCGCCACGCCGGGGAGGC\nGGAGCGGCGCGCAGTGCTCGCACGCGGTCTGGGCGATCCCGATGG\n>NODE_118_length_285_cov_0.584906\nATGAGCCTGCGCAAAGGGCATCGACGTGACCTGGCATTCGATTGCCAGTGCGGTCTTCCC\nGTACATCGAGCCGCTCACTCCGGCACAGAAGACCGCTGAGGCGCAACGGCTTCAGCAGGA\nTCGCGCTGCAATCCGGGCGGCCGTCTGGAACTCGAACGAGGAACGGGCGCTCGATGAGGC\nGCAGAAGGTAATCAAAGAGTACTTTCGTACCCGAGCTGCGCAGGAAGCCAGCAGCTTCGT\nGCAAGAGTGGAAGTCAGCGCGGATCTATCCATACGCCGGAGAGCC\n>NODE_119_length_284_cov_1.445498\nGTGCTGGACGGCCCATGACACCGTCCCCGCCCCGAAACAGCCCGATCGATTTCACCATCG\nAAGAAGAGGCTGCTGCCATGACCAAAATGATCGACCGCCTGACCGCCCTCCACCGCGCAA\nTCGACTCCGCCGTGGCGCGCGAGCGCGCGCGTTTGGCCCCCGATCCTGTGCACATCGCCG\nCGCTGAAGAAGCGCCGCCTCGCGATCAAGGACCATCTTCACCGCGCGCTGACCCGGCGCG\nTCACCGCTACCGCATAAAGGACCCACACCCGTGCAACCCAATGT\n>NODE_120_length_283_cov_1.290476\nACCTTGCCCGGCTGGGTGGCGAATGGCTCGCCCTGTCCAAGGCGAGCGTAGCGCGCAAAT\nCGGCGGCGCTGCGGCGTTTTTTCGCGTTTCTGGCGGATGAGGGGTTGCGGGCGGATGATC\nCCGGCGGTGCCTTGCCGCGTCCGGGTGCATCGCGCGGTTTGCCCAAGGTGCTCGACCATG\nCCGATATCGACCGCCTGTTCGCCACGATCGCCGAGCGGATCGCGCGCGTCCCCGCCGACC\nCCAACGACCTGCGCATGGCGGCGTTGGTCGAGCTATTGTACGG\n>NODE_121_length_281_cov_1.100962\nTTGAATGCCGGTGCCGACGATTATTTGGTGAAGCCGTTTTCCTTCGCCGAGCTGACCGCG\nCGCATCGATGCGATCTTCCGCCGCGTCGATCGTGGTGCGGGGGAGGGGCAGGCGACGCGC\nTTGTCAGTCGGTGATCTGGAAATCGACTTGCTCGGGCGCACAGTCGCCCGCGCGGGGCGG\nCCAATTCAGCTTGGCGCGCGCGAATTCAATCTCCTCGAATATCTCGCGCGCCATGCCGGA\nCAAGTGGTCACGCGCACGATGATGTTGGAGAAGATCTGGAA\n>NODE_122_length_279_cov_0.747573\nGGTCTAATTGAGGCATTTTAAATGCCGTATCAATTATTCTCACTTGCGGGCTTGCCGTAT\nAAGGCTTTGGCCTTTGCGGATAATCATCTTTCCAACCTGCTACCGTAAAGTCTTGATTCA\nAATCTGCATTTACATCTAATGTTCTGTCTGCAATGTCTCTTCCGTCTGCCATACATTCTA\nCTTTATCCATACAGCCTCTTGTAAATTTAAAAGCATACATACCTGCCGATACATCCTTTA\nGTACAATTCCTTTTCTACCTCCGCCAAATGGTTTCAATT\n>NODE_123_length_279_cov_0.747573\nGAGATCGGCGTTGTCGGGCGCTCGCGCATGACCAAAGCCGAACTGATCAAGGCGATTCGC\nGCCGAATGACAGCGGAAGGATGACGGGGGCGGCTGCGGGCGCTAGACCTGCGGCATGGCA\nGACCTTCGCGAAACCGGCCTGGTGCTGGACCCCAAATATGATTCCGCGGGCTTGATCACG\nGCGGTCGCGACCGACCGCGTGTCGGGCGATGTGCTGATGCTCGCCCATATGAATGCCGAG\nGCGCTGCGGTTGACGGTCGAAAGCGGCGAGGCGCATTTC\n>NODE_124_length_279_cov_0.747573\nATTTATAAGTCTTGACCAAACTACGTGCCAGCAGTCGCGGTAATACGTAGGAGGCTAGTG\nTTAGTTATCTTTATTGGGTTTAAAGGGTAAGTAGACGGTAAATTAAACTCTAAACGAGTA\nCTTTTTTACTAGAGTTATATGAGAGAAGGAAGAATTTCTGGAGTAGAGATAAAATTTGAT\nGATACCAGGAGGACTGTCAACGGCGAAGGCGTCCTTCTATGTAATAACTGACGTTGAGAG\nACGAAGGCTTGGGTAGCAAACAGGATTAGATACCCTAAT\n>NODE_125_length_279_cov_0.747573\nGTTATATTGCCAAGCGCAGGGCCGCAAAGCTGGTATCGGGCCGCACCGATATCCCGTTTG\nTGCCCATAAAAGCCGCAGCGGGTTACCTTGCCGGCTATGCCGATCCGGATTTTGTGGACG\nAACTAAACACTTTTACCCTGCCCATGCTTAGCGGCGGCGACTACCGCGCTTTTGAAATAG\nTAGGCGATTCGATGATGCCCACACCCAGCGGCTCTGTAATTGTAGGCGAAAAAGTAGCCA\nACCTCGACGAGGTAAAAAGCAACAATACCTACATTGTGG\n>NODE_126_length_279_cov_0.747573\nGGCGAAGATCAAGTGGGTCGAGGCCTTCGTCGGCGGCGGCATCGCGGCGGTCGCGGCCGC\nCGTCACGGCCGGGCTTGGCGTTGCGCCGCTCGCCGCGCGGATGGCACCGGCGGGCGCGGT\nCGATATCGGACCTGCCGCAAGGTTGCCGCGGCTGCCGCGCTCGGATGTCGTGCTGCATTC\nGCGCGTATCCGATGCGCAGCGCGCAGGGGCGGTGCGCACACTTGCGGCGGCGTTCCGCTC\nGGCCGCGAGCTAAGATCGCACCGCCAACCAGAGCGAGGG\n>NODE_127_length_278_cov_0.751220\nCGCCAGCGTGCCCAGCCCGGCGAACAGATCCGCGCTCACCCGCACTGCGCCAATTGCCTC\nGCGCACCGCCGCAACCAGGCTCGCCTCGCCCTCGCGCGTCGCTTGCAGGAAGCTGCCCGA\nGGGAAAGGGCACCGCCACACCACCGAGCGTGATCGTCACCGCCTCAGGCTCCCAGCGCGT\nTTCGGGGCCGATCCCGTCATCGACCGCCAAGCGCGCAATACCGTGCGTGCCGCAAAACGC\nCGTGATCCCTTCGGCAATCGCCAGCCCCTCGGCCAGCT\n>NODE_128_length_278_cov_0.751220\nGGATTGAGCTGGTGCCCTTAACATATCCCGACTTGCGAACAATGTGGTTCATCCGTTAGC\nGCAATCGCACACGCATGATCGAAAATCACACTACCTCAAAGCGCTCCGACGATCCTGAAG\nGAATTGAGATGCAGTCGTCTAAATCAAACTTGTCCTTTAATCCCCAAAAGCTTCGGCGAA\nCCGTGCTCGACATGGCTTATGTGGGGCGGACCGCTCATATCGGCTGTGCTTTTTCGATCA\nTCGAGTTGCTTGCGGTTCTGTATCGAAACCATTTACGC\n>NODE_129_length_278_cov_0.751220\nTCTCATGGCTGACCGTCACACCGTCCATGTGCCCATTCGTCTCCCAGCTCGCACGGTGCT\nCCTCGCGCGGATCACAGACGATGACCTCGAAACCCATGCTGCGCGCCATCTCGCACAGGT\nAGCGAGACAGGTCACCCGCCCCAATGACGATGATGCGTGCGCGCGGCCCCAGGTAGGTCA\nCGAGCTGGGTGTCGCTCATGGTCGGCACGCCATCGCGCTGCCCCTCTCGCAACTCGACCT\nGCCCGCTTTGCAGATCCAGCACACGTTCGGTGCTGCGC\n>NODE_130_length_278_cov_0.751220\nTGGTCGACCTATGTGACCGATATTCTCGTCGGCGACCACCACCTGTCTCGCATGGCGGTC\nGACACCGGAGACGGCAGCGCCATCACCGTTACCCAGCCAGCATGGTCCGCACTGGCCGAG\nAAACACCGTCCGACCAGTTCGACCATCAGCTACGGCGTTGGCGGGGCAGCGATTGTCGAT\nCTTGCGATCGTGCCCGGAGTGCGCAGCGGGACAGCGCCGGCACGCACCGTCGAAATGCGG\nATCGAGCCTTCGGGCGGCTACACCGCCACGATCGGCAT\n>NODE_131_length_278_cov_0.751220\nGAGTGGTGCCAGACAAATCCAGGGTCAATTGAGCGGAGCTCCCGGTTGCCGTGAGGCGAG\nCCTCCCGGAGCTCGGCGCTTGCGGCCATCGCGGCATTGCCGACAGCCAGGAGCGCAAGGA\nGGCTCGTGACTTGAAACGCCTTCTTTATCATGAGGTTCAGGAGCTAAGTTGTCTCATAAT\nCTACGTTCCGGACGGTCTGTTTTCAACTAGCGACACCCATGATTCACCTAACGCAGATAC\nCGCGGACACGAGATCAACGTGGCCGCGGTATCTGCGTT\n>NODE_132_length_277_cov_1.132353\nATTCCCGTCCGATTGCCGAGAGGTAGGTCTCGCTGACCACCTGTCCATCCCGTTCCCAGG\nCCCGATAACGACTTTCCAACCATATAAGCAGTTCGTCGATCGTTCGCGGAAGCTGAATGT\nCCGGCCCCCCGACCGCACGTTCCAGATGCCATTTGATGAACGCGCGGATCAGTTCGTCGC\nGGGTGCGATAGTGCCGGTAGACGGTCTGTTCGGTAACTTCGGCGACGCGGGCGACCTCCG\nCGATGCTGACCGCGGCGAGATCGGCATTGCGGATGAT\n>NODE_133_length_277_cov_1.132353\nTTTCTACGGTTCGACGCTGGTGCGGGTGCGCGCGAGCGATCCGCCGCCCGCAACGCTGGC\nGCTGGTGGCGGCGGTCGCGTTGGACGAGGTCGTGCGGGCCTATCTTGGCCTTTCGGGGGC\nGGATGAGGCGCTGCTGATCAAATGGCCCAATGATTTGCTGATTGCGGGTGCGAAGCTCTC\nGGGCATTTTGCTCGAACGGGCCGATGACGCGGTAGTGGTGGGGATCGGCGTCAATCTTGC\nCCATTACCCGGATGATACCGATCGCGCCGCCACCAGC\n>NODE_134_length_277_cov_1.049020\nGACATGCAGCCGCGCGGACGAGGCGGCCTGTCTGCTGCTGGACGTCCGCCTTAACGGTTT\nGAACGGGCTCGATTTCCAGCAAGAGCTTCTCGACCGTCATATCCATGTCCCGATCATTCT\nGATGACCGGGCACGGCGACATTCAGATGACAGTGCGCGGGATGAAAGCCGGGGCGGTCAA\nTTTCCTGACGAAGCCATGCAATGACGACGACATACTCGCCGCCATCGCCGGGCCTGGTTG\nAGGGCGACGGCCTCGGCGATGGCGGCGAGTATGTCGT\n>NODE_135_length_277_cov_0.754902\nGCGGACAACGGGTTCGACCCGCGATCGACAGGGTCCCGTCGGTGGTGGTGAACTTGACGA\nGCCGCGCGATATCCGCGCCGCCGAACACGAAGAGCATGGTGGCGTCCACGTCGACGATCC\nGGGCGGTGAGGGCGCCGGTCACCAGCAGACCGAGGGATTCCCGCGCGCCCTCGTCCAGGT\nCGAGCACGCCGTCGACCGTCAGATCACCGTCGACGACGAACATGACGAGCTCACCCAGCG\nATTCGTCCTCCCCGACACCGACCGCCGCCCGCAGATC\n>NODE_136_length_277_cov_0.754902\nTGCCAACCTCATGCGGGAGCAGGTCGATCGGCTGCTCGCCTGTGAGTGGCAGATCCGGTG\nGGATGGTACAGATACCGACGACAACGCCTTTGCAGTCCGCGACGTGAAAATCTCGAACGA\nATATGCAGGATCGCTCGACAAGAATGGCTCATTTGCGCGTGAAATCCGTATGTCGGAGGC\nCTTTTACAGCCACCTCGTCGATCACGCCGTGCCTCTGAACGAAGTCGCTATCCGGGAACT\nAAAGGGCACGCCAACCGCGCTCGACCTCTACACATAC\n>NODE_137_length_277_cov_0.754902\nTGGTAGGAGCGTTCAACCGGAAGGACTGAAGCGATGATCGCGGTCGAAGAGTGCGTGCTG\nATCCTGCTCGCGGCCGGGCGATCGCGCCGGTTCGGTGACGCGGACAAATTGCAGGAACCC\nTTTCTCGGCAAGCCGCTGGCCTATCATGTCGTCACTGCGCTGGAGGACGTGCCGTTCAAG\nGCGCGCTTCGTGGTATGTTCGGGCACCGAGCTCGATTTCGCCAGCCGGGGCTATGCCGTG\nCTCCACAATCACAATCCCGATGACGGCATGTCGGGAT\n>NODE_138_length_277_cov_0.754902\nGGTACCCACCGCGATGCCGGCCGGCCAGGCCAGCGCCGTGCGCATGGCGGCGTTGCGCAC\nGACCACGGCCTCGGCCTGCGGCACCACGCCGGGTTCGTCGAGCATGGCGGCGATGCTGGC\nATCGAGCGCCTCGCGCTGCATGTCGCCGGCGACGATCTCGCGCAGCTGGCCGCGCGCGTC\nGACCAGCGCCACCGAGGGCTAGGCCTGGATGCCGTAGTGCTGCCAGGCGACGAAGTCCGG\nGTCGTTGGCGACCGGGAAGGCCAGGCCGAGCCGGCCG\n>NODE_139_length_276_cov_1.137931\nTCCCTGCACACCCTGATGCAGATGGTGGGCTCAGGGCTCGGCGTCTCCCTCACCCCCGCC\nATGGCCGTGCAGGCGGGACTCACCGACACGGCGGCTGAGGCCGTGCGCCATCTCGCGGCT\nGAAGCCCCCCAGCGCCAGATCGTGGTGGCCTGGCGCGGGGGATCGAGCCGGAGTGAGGAG\nGCGCGGCTCCTGGCCGAGACCCTGAAGGCGGCGTGAGCCGCCCTTCCCCAGCGGCGCCCT\nTGCGAGGGGCGGCGCGGCCTGCCTACAGTCCTGACT\n>NODE_140_length_276_cov_1.137931\nGTGCATCACCTGCAGGCCAAAGGCGGGCGGCTGGTCGACGCGATCGAAGCAGCCTTTCCC\nGGATCTACCGGCCCCGATAGCAATCATGACGTCAAAAGCGCCCGTAACCGGTCATCACTG\nGCTTCGTCGCGCGGTGGCGTCACGCCGAAAAACAATTCGAACGCCAACCCCGCTTGGCCG\nATCAGCATGTCCAGCCCATCGACCGTCCCCAAATCGCGCGCCCGCGCTGCCGCCAGTAGC\nGGCGTTTCGAGCGGGGCATATACGACATCATAGACC\n>NODE_141_length_276_cov_0.758621\nGGCCAGATGTCGGGATCGACGGTATTGTCGAGCAGGTCCGGGCCAACGAAGCGACGGGTC\nGATGGATATCGCTGCAGATAAAGAGCGGAGACCGTTTCTTCCGGGAGAGCGGCCCGGAGG\nGCGTTGTTTTTCGAGATGAGAGACGGCATCTCGATTATTATCGCTCCCATCAGCTCCCCG\nTCGTGGTGGTCCTCCACTATCCCGGGACCGACGATGCGATCTGGCAGTGGGTTTCACCAG\nAAAATCCATCGACAGGAACGGCGCTGCCACCAGAAG\n>NODE_142_length_276_cov_0.758621\nGGATGATCACGCTGTCCCGATTCGGAATCACGGTCACACCTGACATTGTCGGCGCCGCAG\nTGAAATTGAGCGTCCCGCCGCCACCGCTGCCGCTCGAGCTCACACTGACGGTTGCGCTTG\nCTTGCGCGGAACCGTTCACACCGGTGCAGCTCAATGCATACGCCGTGGTGCTGGTGGGAG\nAGACCGTAGCGCTTCCGCTAACGGCCTTTGATCCTGTCCAGCCGCCTGAAGCCGTGCAAG\nCGGTCGCATTCGTGGAAGCCCAGGTCAGGGTTAAGC\n>NODE_143_length_276_cov_0.758621\nGTGTGGTGAGCCTTGAGACCGTGACGCAGGGGCCGGCTCTCGCCCGCGCGGTGGAGATTT\nTCCACGACGTCGAGGCCGCCGGATGGAAGGGGACCGCCGGCAGCGCCATGGCCTGCCGCA\nCGGCGCATGCGGCCTTCGCCCGCGCGGTCTTCCGGGCCGAGGGAGGTCCCGTCGGCATCC\nGGGCCGACATCCTGAGCCGCGATGGAACGACCCTCGCCGTCAGCCTCGCCGTGGTGGCGG\nGGGGAACCGCCTATCTCCTGAAGACTGCCTATGACG\n>NODE_144_length_276_cov_0.758621\nGATTGGCCTCGCCTGTGGCCTACATCGAAAAGCACAGATCGGCAAAGGCATGTGGGCAGC\nGCCTGACCGGATGGCGGCGATGCTCGAACAAAAGATCGCACATCCCCTGGCCGGAGCGAA\nCACCGCGTGGGTACCCTCACCTACCGCGGCCACACTGCATGCACTTCACTATCTCGAAGT\nTGACGTGTTTGCCCGACAGAAGGCTCTGCTGAGCGAATCGGCGGACGACGGCCTGTTGGA\nATTGTTGACTCCGCCGCTTGCCGCCAAGGTATATGG\n>NODE_145_length_276_cov_0.758621\nGTCCCCATGCGGGTGAGCGTTCGCGCGTGCGGTCTTCCATCACGCTTTGCCAGGTCGGCC\nAGAAGCTGACGGGGACGGCGGCGACCACCAACATGTGCGCCCAAAAGGCATTGCGCGACA\nCGATCCACACTAGCAGCGCGGCGAGGCACGCGGCGGTGCAGGCCACTTCGCCGCGCGACG\nGCGCGCTCCACACCGAACGCCGCCAGATCCCGATCGTCACCACCAGACACGCGAGCGTGG\nAGAGCGCGAACACCCAGCCTTGCAGCGCCGCTGGGT\n>NODE_146_length_276_cov_0.679803\nTTCTATCCGTGGGGCTAAACAATGTACCGAAGCCACGGATAGAACCTTTGGTTCTATGGT\nAGGAGAGCGTTCTAATCAGCATAGAAGCCTGACTGTGAAGACAGGTGGAGCGATTAGAAG\nTGAGAATGCCGGTATGAGTAGCGAAAGACAGGTGAGAATCCTGTCTTTCGCGACTCATAC\nCGGCCGTCACACTTCTAATCGCTCCACCAGTCGTCACAGTCCGGCTTCCATGCAGATTAG\nAACGCGCTCCGACCATAGAACCAAAGGTTCTATCCG\n>NODE_147_length_275_cov_0.950495\nATGGTGAGGTCGTCGATCTCAATTTGCAGAGCGGCTAACGGGCGTCCACTTTCGAGCACC\nGCGGCTCCGAGCGGTGCGCAGCGCCAACCGAAACACAATATCTGCCGGAACCAGCTCAGC\nTCGGCGACGCCCGTATAGATCGTGATACCTTGGGCCAGAGCATATTCGGCGAGCGCCGTG\nATCAGTTGGTTACGCGCCGAACGCCGTTCCAAGACCGTCTGGTGACGATCGAGACAGAAT\nCGGGTAATTTCGCGGGTTGAGGGGCCGCTCGGCAC\n>NODE_148_length_275_cov_0.762376\nGGTTATCGATGCGTCGTTCCTTCTCGCTCGCGTTTGCGGGCGTTCTCCTCGGTTGTTCGT\nCAACGGCGGCGCTCGCCCAGTCGGCTACCGCTGCGGAGACGCCCGATGCGCAAGGCGGTG\nACATCATCGTCACCGCGCAGAAGCGCGAGCAGAAGCTCCAGGACGTGCCGATTACGGTGA\nCGGCAGTGACCGGTGCCAAGATGCAGGAGCTTGGTGTCAATTCGCTCGCCGAAGTCGCGA\nTGTATATCCCGGGCCTGCGTATCCAGGAGCAGAGC\n>NODE_149_length_275_cov_0.762376\nGGACGACAAGAGCTTCACCGTGAGCCCGTACTACGAGCTCACGGGCGGCCTGCGCGTCGG\nCCCCGCGGAGCTCTTCGCGTTCTACGGCGTCTCGTGGGTGAACATCGGCGTGTCGCACAC\nGAAGTTCGCGCTCGGCCTCCTGTCTCCTCGCGCCGGCATCGCGCTCGGCTCGCGCATCGG\nACGTGGTCTCGCGGTGCATGGCTTCATCGCCAGCGAGTACAACTGGGGTGTGCTGGGGTT\nCGACGACTTCCGCACGCAGATGATCGGGCTACGCG\n>NODE_150_length_275_cov_0.762376\nGGGCTGGACCGTGTATTTTTCAGCGGCAGCCCTTTGGGGCGCCGCGGTGGCTTTCTTCAC\nCGTGGAGGTGGCGGCGCTGGTGTCTTACAGAATGGCCTGCAACTGCCGCGGCTACGTGGC\nGGGAGGCATTCAGTTTCTGGCGATGTACTCCATCATCTGCGGCGTCTGCGCCTTCCTGGA\nCCTGCCCAGCGAGCAGGTGGCCCGCAGCACACACCTTTTTCTCCTGCCGGCGGGCGCCGG\nGGCCCACATGGGGCTGCGAGGCGCCAAGCCGTGGC\n>NODE_151_length_275_cov_0.762376\nGATGCGATCCGCCGATCCGCCGCCAGATTCGTAGCCATGCGATACAGATAGGCGGCCGGC\nTGGGCGACGGGCGGCGCGCCGTGCTGGTCGAGCTTGAGCCAAATATCCTGCAGCGCATCC\nTCTGCATCGGCGGGATTGCCGAGACGTGCCGCGAGCAAGCGCAACAACATCGGCCGTTCC\nGCCAGGAACACCGCCTTGAGACCGGCCTCGGTCATCGATGAAGAAGCAGCCACGGCATTC\nTGCCGTCTAGAGCGCGCCGCGCGTCACTTCGCAAG\n>NODE_152_length_275_cov_0.762376\nTCATCGACTTGATCGCCTCGACCAGCGTCGGCGGCAATTGCGCCAACTGCGTTTCGCTCA\nACCAGTCGAGATCGCCGTCGGTCGCACGCGTGGTGGCGTCGGACAGGCGCGCATAATAGC\nCGAACGTGTCCTCGCCCTTTTCGCGCTTCTGGATCGAACCGATAATCTGTTGCGCCTGGT\nTGAACACTTCCTGCGCGCGATCCGGATCTGCCTTCAGGTAGATTTCACGCACGTGATATT\nCGGTCGTGCCCTGCTGCTTCTTCAGCTTCTCGATG\n>NODE_153_length_275_cov_0.762376\nTCAGCACCGAGGGGGAGACCTCATCCTGCAGGCCGAGCCCCATTTCGAAGTCGAGGAAGA\nTGTCCATCAGCTCGTGCGGGGTGAGCACGCTGCGGCGCTGGCGGTTGAAGCAGAAGCGCC\nAGAAGCTGACGATGTGGCTGATGACGCCGATCTGTTCGCCCAGCTTCAGGAACATGGCCG\nGCGATTCCAGCAGGAAGTCGCGGAAAGCGATGGCCGAGGCCTTGCTGGATGTCTATGACG\nACGCCTTCGGCGCCTTAACCCAGCACGCCAATCCC\n>NODE_154_length_274_cov_1.641791\nCGGGGGCAGCGCGAATAGCGCTGGTTCGCGCTCAACCTCCGGCCAGAAGAAGACCGCGGG\nCAAGACGCCGGCAAAGAAGTCGGTTGGTGGCTCACGCGGAAAGACGGCCGGTGCGAAGCG\nCGGCAGCAGCTCGGGGAATCGCAGCAGGAAGTAGTACGCAACGTGCGATCGCTGACGACG\nGCGGCATTCATGCGAATGCCGCCGTCGTTGCTTGTTGTGCGGCTCAACGGTGTGCGAAGA\nGCGCACGATCATTGCAGCGGCACACGCGTCAAGG\n>NODE_155_length_274_cov_1.502488\nGGTCTATGCCGACACGTTCACTCGCACCTGGCGAGGGATGTTGGCGCAGAAGCTCGGGTT\nGACGACTCTGGATCGCGCGGGGGACGAGGAGTTGGTGCGGGAGCTGTTCGGGTTGTTGCA\nGCAGACAGAAACCGACATGACGCTGTTTTTCAGAGGGCTGGCGCGAGCGTCGACATCGAG\nTATCGAATCGTTACGTGCTGCGTTCTACGTGGACGGCGAGCCGTCCGAAGCCCATCGGGC\nGCGATTGGTGAAGTGGCTCGCGCAGTACGAGGGC\n>NODE_156_length_274_cov_1.427861\nGATTAAGCGTGCGGTTCTGACCGACGAGCATCGCGAACTCGACGCGTTGGCAAAGCGTAT\nCCTGGCCGAGGTCGGGGGCGATGGCCCGAGCGTGGAGTTGTCGTCGCTGCGCTGGCGGCT\nCAATCGCGTGCTGACCAAGCACCTCGCGATGGAGGACCAACTCCTGTATCCGATTTTGCG\nCGCGAACCCGGCGACGGCTTCGCTGGCCGAGCTAGTGCTGGCCGAGGTTGGCGGCACCGC\nAAGCACCTATGCGGCCTATCATGCAGCTTGGCCG\n>NODE_157_length_274_cov_0.766169\nGGGCCATGCCGCGCCGTTCGATTTTACCGATGCCTATCAACCGGCCAGCGGCATGAAACG\nCTGGTTGGCGGGCACCCCTTCGATGCTGGGGATGGCGGGGCTGGAGGCGGGAGTCGACCT\nGTGGCGCGACGTCGATCAACAGGCGGTGGCGAAGAAGAGCGCGGCGCTGTTCGACCAATT\nCGCCGCCATCGGTGCGCGCCTGAACCTCGAATGCGTCAGCCCCGCCGATCCCGAACGGCG\nCGGCAGCCATATTTCGTTCCGCCATCCCCAGGCC\n>NODE_158_length_274_cov_0.766169\nGCCCAGGCCAGGTCCCTTGCAGCAATGCATCCAGCAGCATGGCGCGCCCTTGAAAGCGTT\nCGATGGCCAAGCGGTAGTGGCCATGCATCTGGCGAAAGAAGTCGATGGCCAACAGGGCTG\nCTTCCATCGTGCGCATCAATCTGCGGCCAGCACGTCCAGTGCGAGCAGCTGCTCTCTCAA\nGGCATGCAGCGCCCGCCAGTTACCTTGTTCAGCAAAGAAGGGGTCCTGCCCCTCGATGGC\nCAGCACCGCTTCGGGCTCCGACCAGTAGATGCGG\n>NODE_159_length_274_cov_0.766169\nGATCGCGGGCTTTGGCTCAGAGCCCGCTGAACCAGTTATAGCCGTACGTTTCCCAATAGC\nCGCCAGTATAGTCATTGCCGATCGCGATCTCGCCAATGTGCTTGGGGTTCTTGAACCCGA\nGCTTCGTCGGCACGCGCAACTTCATCGGGAAGCCGTGCTGGCGGGGCAACACCGCGTCGT\nTCATCCAGAAGCACAGCTGGGTTTGTGGATGGAGCGCGGTCGCCATGTCGATCGAGGTGG\nTGTAATTGTCATCGCAGCGGAAAGTGACGTATTT\n>NODE_160_length_274_cov_0.761194\nGTGTTTTGACAGGGTTGGCGATGACGGCGCTGGTCGCAACGGCCGCAGTGGCAGCGGTTG\nAGCCCGCCTCCAAACATTCGCCGAAGGAGACGCAACGGGCCGTCGCCGCCGGGCTCGCCA\nATGCCGAGCGCGCCGATCAGGCCGGCGATGACGCGCGGCGCAAGGCCGCCGAAGTGCTGG\nCCTTTTCGGGCGTCGGACCGGGCGACGAGGTGATCGATTTCTTGCCCGGTGGCGGTTATT\nGGACGCGCATCTTCACAGGCGTCGTTGGCAAGGC\n>NODE_161_length_274_cov_0.746269\nGTCACCGCTGACCTCATCGGTCAGCACAGCCTTGGTGGCCGCCTTGCGTTCCAAGACACG\nCTCGGCCATGGCCCTGCGCACCTTGGCGGATTGGACGCTCAAGCCCCGCCTACTGGCTGT\nGCCCGGCGTGGCCAAGGTGTCAATCTTTGGTGGCGACGCCAAGGAGATCCAAATCCAAGT\nCCATCGGCATCGCCTGACCAAGTACGGCTTGACGATGAACGACGTGCTGGACGCCGCCCG\nCAAGGCGCTGGGTGTCCACGGTGCAGGCTTTATC\n>NODE_162_length_273_cov_0.770000\nGTTGAATGCCACTGCGTCATTTAGCTTCCAATATCCGACCGCGCCACCGTCGTAGCGGCG\nCGTCTGCAGTATTTCGCGGAATGGCGCACCGGTGGTCGGTAGCACGGCGCCCAGCATCGT\nGCCGCCTTCTCGGCGCTCATCCGTGATGCCTCCGGTGAGAAAGACCGATTGGTCCTTCCC\nCGAATTCCACCATATACGCGGTCGCACGGAGTAGCGACGAAAGCCAGGTATGTCAGCCCA\nGCCGTCGTGGTTAACGTCCTCCCTCGACTGATC\n>NODE_163_length_273_cov_0.770000\nCCGCTACCCCACGCCCAACGCCGCGGCCCTGGCCCTGATGCCGGACGACTACCGCAACAA\nCACGGCGATCTTCCCGCCGGCGGCGGCCATGGCCAAGTGCGAATATGCGCGGTTCGAGAG\nCATCGCCCGCGCCCAGCTCAACGACGAAACCCTGACCCGGATCTTCGCGGCATGAGACAG\nGGAGGCGCGCATGGATGAGTCGTGGAAGCGGGCCAAGGCGGCGTTCCTGGCGCTGGGCGG\nTCCGCCCATCGTGTGGCTGGCCGTGTTCTTCAT\n>NODE_164_length_273_cov_0.770000\nGTACAGGGCAACGGTGACGGGCAGGCCGGCTGCGGAGCTTTTCGCTTTGGGATTTGAGCC\nGATCAGATCGTAGGCACCCCGGTTGATCCAGCGGGTGTCGCCATCGGCGAGTCGGTCCTT\nCACCACGGCGCTCGGCAGCGTCAGCGCACCGACGAGATCCCAGCCCGACAGGGCAAACAC\nGCCTGGTTGGAATGCGTTGTAGAACGCGAGCAGCAGGTGTGTGCGCTCTATCTTCTCGAT\nCTCAACAACTGACAACTTTGAGATGTTCTTTAT\n>NODE_165_length_273_cov_0.770000\nGGACAGATGCTTGCGTGTCCTGGAGATCGATCGTGTTTTTAGATGGTGATGCCCCTGATC\nGATAACCGGCGTTCTGCATTAAGGTAGGATTGCGATATACGCCGAGGGCGATGATCGCTC\nCCTGTTCAAGATGCCAAATGAAATCACGCGTGCGGGTTCGCCCAGATCGTCAGGCGAAAT\nCTGTATATTATTTCACATGCGGCGTAATGATTGCGCGCTTTGATACGGCCCACGCCCTCT\nTTCGCGCTTCGGCACAAAAGCGCGGTGAGAGGG\n>NODE_166_length_273_cov_0.770000\nGCGTAAACCTGGAAGCTGTGGACGAAAACGGGCTTACGCCTTCCTGGCTCACGGTAGATG\nGCAAGCTGTTGCACAATACACCGTTCACTTCCGGATCAGAAATTTCATTTGCCTTTGATG\nCCACCAATCTTTCCATCGGCACCTATTCGGCTTTTGTAACGGCTGCAGCTCCGGGTTACA\nAAACCGCGGTAATAAACGTATTTCTGACTGTTAGATCCGAAGCCTCCGGAAACCTAACGA\nCTTTAAAAGTAAACTTCCAGGATTCTGCAACGG\n>NODE_167_length_273_cov_0.770000\nGATGTCCGGAAATCAGGTTTACCGAGAAGTAAATTCTTATAACAAAACATCAACCTTTTA\nTCCTGAATCTAAACATTTTTATGCAACTGATTCTACATTCACAGTTACCGCAAGTATTTT\nGCTTAATCAAAAAGCAGATCAATTTAAAATCGCTTTAGGATTAAACGAAGAAGCAGAATC\nTCACAAAAAGGCTCTCGAAAATATCAACTTACGAATTGCAAATTTCTTAAAAAGGCTGAG\nTTCATTGGGAATAAAAAAAGAAGAGGTGTATGT\n>NODE_168_length_273_cov_0.770000\nGTTCAACCACCATGACCCGGCTGCGAACGCTGCGGATTACGCGTTTCTGCGCGAGGGCGT\nCCGCCGGTTTCGCGCGGCCCGCTACAACCCGGCAGCCCGCAATCAGTTCTGGCTGATGAC\nCGAATGCCCCGTACCGCCCGCAACGATCCACGCCATATGCGACGCTTTAACGCATGGTCG\nCGACGGGAACGTTTTAACATTCCTTCATGTGGTGCCTGGCCGCCCGGAACCCCGTCTGGC\nGGACCGTATGGACACGCCGAATCTGCGCTGGCT\n>NODE_169_length_273_cov_0.770000\nCGGTCGAGGATCGATTCTGCTGTCGTCACCAGTTGCATCACCACCGATTGCCCGCTCTCG\nAGATGGTGCTGAGCGGCAGCAATGACGGTCGGCAGCTTCATCGAGAGCAGAACCTGGCCG\nAAGAACCGCTGTTTAGTCGACTCGAAGCGGGAGCGAGCAGAGGCTTTGGCGCCGCTATTC\nAGCGTCGCGTTCTCCAGGCCGTCGACGACAGCCGTCAGTTCGAGGGCCTTTTCCATATTC\nTGATGGATGATCGACCAGGCATCCGCATAGGTG\n>NODE_170_length_273_cov_0.765000\nGTTCTCGAGCAAGCACGCTTGCCCCGTGTGCGGCTACAGCGTCCCCACGCTCGAGCCCAA\nATTGTTCTCATTCAACAATCCGGCCGGCGCATGCCCCACCTGCGACGGGTTGGGCACCAA\nGGAGTTTTTCGATCCGCATCGAGTTGTTGTCAATCCGGATCTGTCGCTGGCGAGCGGCGC\nCGTTCGCGGCTGGGACCGGCGCAACGCACACTACTTTCAACTCATTCAGTCACTCGCCAA\nACACTACGCCTTCGACATAGAGACCCCCTGGAC\n>NODE_171_length_273_cov_0.740000\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCTT\nTAATGATACGGCTCCCACCGAGATCTACACAACTTGGTGATCGTCGGCAGCGTCAGATTT\nGTATAAGAGACAACGCTTGCACCCTACGTATTACCGCGGCCTTCGGGTTGTAAACTCCTT\nTCGCCAGGGACGAAGCGTTTTGTGACGGTACCTGGAGAAGAAGCACCGGCTAACTACGTG\nCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCG\n>NODE_172_length_272_cov_0.869347\nGCATGAAGATGGGGCCGATGAAAATGAACGGCGTCAAGGCAACGCTGGCTCCCGACGGCA\nAGACACTCGTTGCCACGCTCGCCAAGCCGCTGACAGCTGGAACGTCCAAGCTCGAGTATC\nATGTCGTCTCGACCGACACCCATCGCATCCAGGGCGGATACACGTTCAAGGTCAAGTAAG\nACCATGCCGGACATGGTGGCAATCGCCGTCAGGCTTGGACTCTATCTTGACCTGATGCTT\nCTTTTTGGGCTGCCGATGTTCGGGCTCTACAC\n>NODE_173_length_272_cov_0.773869\nGTGCCCTTCACATCCGTAATTTCTGAAAATGCGCATTGTATTGGACAAGCTGTGGGTTGG\nCTGCAAGAATTACACTGATCTTGTTGGTTTTGGTGAAGGAGGATGGGGTCGTGTCCTCAT\nCGCTGGCGCGGGCGTCACGTCCGCTATCGCCGTTTTGGGGTTCCTCATCGGGTCTATTCT\nTGGCAGCCTCGTTGCCTGGGCAAAAATGTCACCAATCCGTTTGGCTCGTGGCGTCGCCGA\nCGCTTACACGACCACACTGCGAGGCGTGCCTG\n>NODE_174_length_272_cov_0.773869\nCTTTTGCCGCGTTGAAGCCCGGCGTGACCGAGCTCGAGATTGCAGGTGTTGTCCGGGACT\nACTACAAGGCAAACAATGCGAAGCCGGAATTCACCAGCGTCTGTTTCGGTGAAAATGGCG\nCATATCCGCACCATCACACCGGCGAGCGTGTGCTGAAGGCCAATGAAGCGGTGCTGATCG\nACATTGGCGGGCGCAGTGACGGCTATCCCAGCGACATGACCCGCGTTGCCGTCTGCGGTG\nAAACGCCCGCGGATTTCGACAAGGTGCACGCG\n>NODE_175_length_272_cov_0.773869\nCGACCGTAACGTAGTTCCAGGTTGGCACCTGATTGGCGTCGAGGCCATACCAGTCCGGGC\nTGATATAGCCGTCCGGGCCCTGTACGGTGAACAGGCCGGTCGCTCCGTCGAGATGCCGCG\nCGATGCCGTTGCCGCGCGCGACGTGGAAGGCGAGCGTGGTCTCGCCCTGCCAGACGACGG\nGAAGATGGACAACGCGCGGGCCATCGGGCGTGGCCGCGAACAGCGCGCCGAAGCCGAGTT\nCGGACACCAGCGCCCGCATGGCGTCGCGGTCT\n>NODE_176_length_272_cov_0.773869\nTCACTATCCAGCAGTTTGATCTGGATCAGCGGGGCCTGCCCCGACTGGCTACCCCGGAAG\nAAGGTGTTCGGCCCCCCCGCCGGCGCCGAACTCAGGCCCGTAACCGACGGAAAGACAATC\nGACATGTCTTTCAACGCAGCAGAGGCCGCCGTCTGCAACGAAAAAGCTGCGAGCCGCGAT\nTCGCTGGATCCGTTGTATTGGTAGATTTTTGGGTTGATCTTGCGCTTGGTCCCCGAGCTC\nGACGAAGCCAGCTGCAGCGCGACGCCTTCAAC\n>NODE_177_length_272_cov_0.773869\nGGCGCGAAGGATGGCACAACCGATCGCAAACTGGCTCGAATAGGTGAACACCTGATCGTC\nGCCGGCATATGGATCCTTGGTCGCAAGTCGAACCGACTGAGCGCAAGCAAGACATGCCTC\nGAAGCGACGGACCCAGCCTTGCCCAAAGGGCGCAACCGAATTTGCGACGAAGGAGCCGAC\nAGAGGTAGGCAACACCACATGCAGTTCTGCGCCGCAGGCAACCAACGCCTCAGCCCATAA\nAATGTCCGCTCCGGCAGCCAGCCCCCCATAAG\n>NODE_178_length_272_cov_0.773869\nGGTTATAGCTGCAATACGCTCACTCTCATATCTGAAGCTTCTTAAATCTACCCAACGGTA\nTTCTTTCCCCGCAGGGAATAAAAAATCTTGCTCTCCGTTATACTCTAAAATATTTCCGCG\nAATAAATGAAGGCTGCATATTTACAACGGCATTATCCCATCTGTAATTTTGCAACACCAC\nCATTTTCACTTGCTGCGTTGCACTAAAGGGATCCAGCTTACCCAGGTTAATGCTTATTTG\nTATTTTTTGGTGAGTGGTACCCAGGTTATTAT\n>NODE_179_length_271_cov_1.424242\nCCTGCGCGCTGGCCTGGGTGCCGATCGCGCGTTGACCATCCTTGCCAAACTCGGCGCAGG\nCATGGCCGAAGATACGATTATCACCGGCGGCAAGGGGCGCTTCGGCGTAACGGGGGTCGA\nAGCACAGGCCGAGATCGACAAGTTGAAGGCCGATCCCGAATTCCAGAAACGCGTGATGGT\nGCCCGGATCGGCCGAACGGACGCGGTGGGACCGGCTCAACGCGGCAGCGGCGGCTGGCAA\nGGCGCGCGCGGACCAACAATTGTAAAAAAGA\n>NODE_180_length_271_cov_1.166667\nGGCGACGATGCTGGCGTTCGAACAGGCGCTCGCGCAGACCACCCAAGTCGGCGAAGCCCA\nTCTGATGAGCGGCGAATCGGACTATTTGCTCAAGGTGCTGGTGCGTGAAGACGACAGCTA\nCGAGCGAATCCACCGCGAAGTGCTCTCGACCCTGCCCGGCGTGCATCGGCTGGTGACACA\nGTTCACCATTCGTACATTGGCGAGCGAGGAATGATGTACGTTTGGCCGTGGCGCGTGCCG\nTTGCGGGGGGCGGGGACGCGTGCTATTGCGC\n>NODE_181_length_271_cov_0.777778\nCACTACCAGGATCTTTCGCTTGGCAGGCATTCCTTTCCGCTAGCGCATCGCGGCCCCAGC\nGGGAACACCAAACCGGCACTTGGAGACAATACCCGGTCGATCATTCCCGATGGCGCGTGC\nGATGGCCGGGAAGGTCAGCCCTTTACGAAGGCAAGCAGATCCGGATTGATCACATCGGCA\nTGCGTGGTCAACATGCCGTGCGGATAGCCGGGATAAATTTTGAGCGTCCCGTGCTGCACC\nAGCTTGGCCTGCAGCAAAGAGGCATCCTTAT\n>NODE_182_length_271_cov_0.777778\nGCCCAAAAGACCGCCCTGACGTCCGTAGTCGATCAATTGCAGACCGGCCTTGGATCGCTG\nCGCGCGGTGAACGCTGAAAATGGCCGCCGGACCACGCAAGTTGAATCGATGATCAATAGC\nGGCGACCAGCGGACGACGTTGCTCACCGGGGTGATCGGCGCGAATGAGGACGCCGATCTG\nGGCCAGGTTGCGACCGATATCTCGCAGCAAAAGACGATCCTGGAGGCGAGCTATTCAGTG\nTTTTCGCAGCTCGCCGGTCTGAGCCTTGTGC\n>NODE_183_length_271_cov_0.777778\nTGCCTGGCGTGTTGCTACGCTCGGTCTATCCCTCGCAGACCGGCAATCTCACTCCGCGCG\nCGCCGCAATATATCACCGATCAGAAGAGCCCGCTCAAAGAGCGATGGGGCGGCTGGTACG\nTCACCGGCGCGCTGGCTCCGGCAACGATGGCCAATGCCGCAACCGTTGCGGGGCCTGCCG\nATGTCAGCCCGGGCGCTGACAAGCCGCTGCCCAGGCTCGCTCCACTCGAAAAACCGTTCG\nATGCGTCCGCCTATCTCACCCGGACCAGCGA\n>NODE_184_length_271_cov_0.777778\nGCCTTGGGAAGCAGGCGAGCGTCACGCAAAACACGCTTGGCTTCAAATTCAAGCGCGAGA\nTGTTACGCGGATTTTTGGCTGAAGAAACATATCTTGCGGGCCACCCTGTCGCGCCTACGC\nTCGCCCCCGGGTCGGTGGAAGTTATTGATCGGACCTACGTCTCCAATAGCGACAATTTGC\nCCAAGGCGCGGGCGCTCGGAGCATTTGCAGATTGCGTAGTCTTTAACGATGTGAGCGGGT\nCGGATGCGTTGCTCCGTACTATGCCCGCAAG\n>NODE_185_length_271_cov_0.777778\nGTTCCCACGTGGGGATAAAGGGCTTCAGGAAACAGTTTCGCCACGGCCAGCGGGGTAGCC\nATGTTAAAACAGATTTATATCGTCGATGACGACGAACCGGTGCGTAAATCGCTGCAATCC\nTTGCTCAACATGCGCTCTGAATTCATCATCAGCACCTTCAGTTCGGGCGACGAATTTCTG\nGCGGCGGCACAAACCCTCGAACCCGGAGTCGTGCTGCTCGATGTGCATATGACCGGCGCG\nTCCGGGATCGACGTACTGACCGCCATTAGCG\n>NODE_186_length_270_cov_0.781726\nGGTGGGTAGTGACCTCGGGTAGCATTCAAAGCTCAGCGAGCGTGATGGCGCGTGGTTGAC\nTCACATCAAATCGGAATCCGAGCCATCCGCTAAGGCTGGAACGAAGGGGTGCAAAAAATG\nGCCGATCGACCAGTTAGCAATAGCTCGCCGCAATTCGAGAGTCTCGTCGCGCGCTTGCGA\nGCATTTCTCGCCCGCCGCCACGAATTCGATCTGATGACCGCTCGGGAGGTCGATGAGATT\nGCCCACGAGCTCAATCTTCCGGCATCGGAT\n>NODE_187_length_270_cov_0.781726\nGTCACCCACGAGATCAATTTCGCACGGGAGGTTTCGAACCGCATCATTTTTCTGGAAAAG\nGGTACGCTCATCGCGGACGCGCCGCCCGCAAAACTCTTCTCTGAAGCTGCACCGGACCGC\nTTCAAAAAGTTTATCTCCAAAACCTTACACACTTCCTCCTAGGCCGTCCGCGGCTCCGGT\nTGTGCGGTGCGCCACAACGCTATCGTGTAGCCTCCAAGACACTAAATTCTGAGCGGCATG\nGCGATTGACATGCCGCTATCAGTTATATAC\n>NODE_188_length_270_cov_0.781726\nGTCCGCAGGCGGTGACGCGTGCCTTCGATCGCTTCGCGCAACCGGGGATCACCCGCGACG\nGGGAACGCGCTTTGGGATTGGGCCTGCCGCTCGCCAAGCAGTTTGTCGAGGCGCATGGCG\nGCACGATCGAACTGCTGTCCGAAGCCGGGCAGGGGACGTTGATCACTGCCACCCTGCCGC\nGCCGGTGAAGGCGGAGCGGGGTCGATATGATGCTGACAGGATGTTGAGATGATTCTGGCC\nGGTCCTCAAGCGAGCGAATCATCTCAACAT\n>NODE_189_length_270_cov_0.776650\nCGATCGTGAAGCTCCTCACGCGCGGCGTGTCCGCTGGCCTTGCAGAGGCCGCGTGCGACA\nCGCTGGGAGACGTGCAGTCGCAGGACGCGACCCCCGCGATCGTCCCGTACACGCGTCATC\nGCGAGGTGAAGGTCCGCCGCGCAGCTGCGAAGGCGCTCGCGAAGACGCGCGGCCCGGAGG\nCCATCAAGGCACTCCGCGCGTCGCTCTCCGACAGCGATGCGGTCGTGCGTGGCCTGGCCG\nCGACCGGCCTTGGCTCGCTGAAGGCGAAGG\n>NODE_190_length_269_cov_0.785714\nGTGTAGTGAGAGCGTCGCGTCGCTGACTTCGACGTTGCGCGGCACCTGCGCCAGCGTGTT\nGAACCCGTCGAGATCGAACCCGGCGACCTCCGCCATGTGGGTTTGAGCCGCTCCGCTCCA\nATTGGCCAACGCGACCATCACTGCGCCGCCCTGTGGGATCATCTGCCCGCCGGGAGCCAG\nCAACCGCGATGCCGCATCCGCCAGCGTGTTCAGCACACCTTCGGCGAGCAGGTTGTTCGA\nGACGATTTCGGACACGATCACATCGGCGC\n>NODE_191_length_269_cov_0.785714\nGCTCGATGGCGTCCTCGAGGGTCTTGATGCCCTTGGCGTTGTCGGTCGGGTCGAGGATCA\nGCGCCGCGGAGAAGGCGGGGCGCCAAGGCCGAGGCCGTGCTCACCAAGCTGCGCGCCGGC\nGACAAGCTCGCCCTGCACGACGGCGACACCAAGACCGAGTACGACGGCTTCGCCGGTAAC\nCAATACGTCTCCGCCCGCAGCAAGACCCGCCCGACCGTCATCGACCGCGACCGCTCCCCG\nCTCGCCGAGAGCGACGGCAAGCCCTACGC\n>NODE_192_length_269_cov_0.785714\nGATTGGGGTTGCCCATGGTGATCGAGGTGGTTCCGCCCGCTTCGGCACCCCCGCTCGACC\nGGTTGATGCGCTGACCACCGGCAAGTTGGAAGAAGGACGGGGCGACATAGGAGCGCGAGA\nCCGAAAAACGATACACGCTGTTGCCGGTGGGCCGATAATTGACCGCGAAGCTCGGCAGAA\nCCTTGTCGTAGGTTGTTTTGCTCGATGCAAAATTGCCGGCGATCTCCGCACCGGTGCCGT\nCGGTGGGCAGCACCCAGAAGGTATTGGTG\n>NODE_193_length_268_cov_0.851282\nTAGCAATGCCAGGCGGGATAGTGACACGTCCTGTCGTTGACCAACTGGTGAAGCGCAGCG\nACGGGCGAGGGTGGTCGCCACGCGCAGTCATTGATATCCCGACGCCTGATAGCTTTCTGG\nTTCGCTGACTGACGATGCGCTATTCGTAACCGTCGGGCGTCAACGGATGACGCGGCGCAC\nCCTGACCTATGCGAACGTAGTGTGCCAAAACCAAGGCGGCGATTAGCGCTACGGCGGCCA\nAAAACATGGCGCGAAAACGAGCTATCAA\n>NODE_194_length_268_cov_0.789744\nGCTCATAGGCTTGGTAGCGGGCCATGAAATCCTCCGGGTCGAACGCCGGAGCCGGGATTT\nCGTCGGTCATGATGGATCTCCTTGAAACGCGAAAGCCCGGCGCTGGGCCGGGCTCGATGG\nGGTTCGGGAAAAGAAGGCGGGACGGCCGCAACCGCCCCGCCCGGTGCCGTTATTCGGCGG\nCGACGGCGTAATCGGCCGTCTGGTCGACATCGTCGGCGAGGAAGGCCGGAAGGCTGCTGG\nCATCGTCCGCCGGATCGTCGATCACAGG\n>NODE_195_length_268_cov_0.789744\nTGTAAAGGAACTGAGAAAAATCATAATCTCTACCCAGTTTAAGACGTGCCATGCTTTTTG\nTGTATACCGAGAAAATCGTAGCTTCTTTATTGTCATACAGTTGAATGCTGCCAGCAATCT\nTGGTGGGCACATCAATTCCTGGCGCTGCGTAGAAGCCCGGACCCAAAAACTCACGACCAG\nGAGTGCGTTGAAATATTGGATCAAGGTTAGCCTGCAGGCTTTTCAGATTTTCAGACGCAC\nTCGCGTGCAAACCAACCATGTCCCACTC\n>NODE_196_length_268_cov_0.789744\nGTGTCAGGTAAAGCGCGGCCAATCTGCGGCAAATCCACCTGCAGCGTCGGGTTTTCGATA\nATCAAACCCTCTTCCAGCAAATACTGATAGAAGCCGCGTGCACCTGATAAAAAACGCGCC\nGTTGAGCGTGCCTTATAGCCTGCCTGTAAACGCCAACTTAAATACTCTAATAAAGTATCG\nCGCCGAACTTGTTGCAAAGTCTGCCCGCGTTGTAGCAACCACTGGGCAAACTGCTCCAGA\nTCACTGCGATAGGCCATGCGTGTATTAT\n>NODE_197_length_268_cov_0.789744\nGATCATATTCGACGGCATAGCCCGGCGCGACAATGCGCGCATGCTCAAGCCCCGGGATCG\nAGGCGATCATCGCTGCCTGAATATCAACCGGGAGCGACGTCGAAATCCCGTTGGGATATA\nCGGTCGCGTCGTCCAGACCTTCCGGCTCCAGGAAGATTTGATGGCCGTCCCGTCCCCTGC\nCCCAATTGCATTGCGCGATAACCCGAACGACCCAGGAAACGCATGCGATCATCCGCAGCG\nGACTGGACCGTTCGCCGCTATTTGGTGG\n>NODE_198_length_268_cov_0.789744\nGCTCAAGCGTCTCCTGAGGCATCTCTGCTAGCAGGCGATCTGCGCGCGTGAGACTTTCAG\nGTGGCCGTAATTCAGAAAGAAAACCGGTCGCGCCTTTTCCGTCGCGCTGCTGCTTGTTGT\nAGCGGGCGTATGTCTTGGCCATCTCCTTATCGTCACCGGTGAGCGGCTTGTAGGCCTCAT\nCGGGAATGCCGCGTTCCAGCATCGAACGGTCGAAGACTCCGATCAGGCTGTCCCCGCAAC\nGGATTTGAGCATCAAGGAAGGTCAGTGG\n>NODE_199_length_267_cov_1.190722\nTCGTTCTGTCCGGTCGCGTCCGGATCGGTCGGAGTGATCCTGACCGGCATGGGATCGGAC\nGGGGCGCAAGGCCTGCTCGAAATGCGACGCGCCGGTGCGCGCACGCTGGGGCAGAACCGG\nCAAACCTGCGTGGTCTACGGTATGCCGCGCGCGGCGATGGAAATCGGCGCGGTAATGGAA\nGAAATCAGCCTGTCCGCCATGCCCGAGGCGATCCTTGCGGCATGCCGGGCCAAGCCCCTG\nGGAATTGTCTGATGCCTGCCGCTGCAC\n>NODE_200_length_267_cov_0.793814\nGTCTTCGGGTCAAAGGCTAGATTCCTCACATATTTAGCGGCGCCAACCGATGTTGCCCGG\nTTATATCGCGAGGGGTTGCTGATCAGGCTTTTTGCTTTCTCAAGCGTCGGCGCTCGGTCT\nGCCTTTGCTTTCAAAGCATATTTCTCGCTATAAAAAATGACTTGTTTTTCATCTACTCGT\nTTTTTGATTTTCTTCCCATTTCTTGAGGTTACCATGATTTCCCTTGGATAGAGCCGGGAT\nTTAATCTTGAATCCCTCACCTATGGAC\n>NODE_201_length_267_cov_0.793814\nGTTATTATCTCACCTGAAACATCCACATCTCAATTTATTACCGAACACTTCGGGGGGCGC\nGTAATAAATTGAGATGTGGATGTTTCAGGTGAGATAATAACGCATCGGTATCTGTTTCCA\nGATCCACGCGTTTCAGGGCAACTGTTACCATCTCTGTTTCCGATTCCAACACGGCGAGCT\nCCATTTCGTCAGATGAACCGAATTTGCCGGTGCCTAAAAACAATCTCGACTGAAAAACTT\nTATCAGCTATGATGAGAGGCTTCATAC\n>NODE_202_length_267_cov_0.793814\nGGCTGAAGGTTTGCCATGGACCCAGGATTAAAGGTTTCGGCTAGATGCGGTCCGCGCAGA\nAGGATCGAAGTCGTGTAAGCGTACGTATCAAGGACATTTGCAGCAGCGGCCACGCGAGGA\nTGAAGGCTCGGCAGAGCTGATTCGACCACGCCATCCGGAAGTTCCACATTGTTGATCCTG\nGCCCTCATACGCGAAACAACCATATTGCCCGTACCTGCTATTGCACTTGTGCCAAAAGCC\nAAGTGAGTAAGAAACTTGATCCAGAAT\n>NODE_203_length_267_cov_0.793814\nGGACAATGAATGAACGCCGCCGGAGCGCCTCGCATGAGATTGTGGCGCCTCGAATCGCGG\nCTTATGCCGGATTCCCAACGGATCAGGATGTTCCCGGCGGTGTTCACAACGCGGCGGAAG\nCAAAGAAGTGGGTCGATGCTGTTGCCGCTGCCGGCGCCGACGGCATCAAGTTCCTCGGAT\nCCCCGCCCGATGTCATGCAGGCCGCGTTGGCGGAAGCGAAGGTGAAAGGTCTTCGCAGCG\nCCTGTCACCATGCCCAGCTCGCCGTAT\n>NODE_204_length_267_cov_0.793814\nTCGCGGCAAGACGTTTGGTATCGCGATCCTGGTCCTTTCTACACTCACCGCCTGCATTCC\nGAACCCCGACCGGCCACAACGCGGTTACGACACCCCGCCCCCCTATCAGCCGCGCGACGA\nCCAACGGCCCTATGAACCGCAAGGCGGGGATCGCGCCGAGCGCGAGCAGGAGCGCTACGA\nACCGCAACGCATCGATGCGGGCGTTTCCGCCCTTCCCGCTCCGCCACCAGCCTGGCAGGC\nGCGGCCGGTAACCCCCGATGCCGAGAC\n>NODE_205_length_267_cov_0.793814\nTTGAAATCCTCGACCCCGAAACCGGCCTGGAAGTTCCGGACGGGCAGGAAGGGGAACTGG\nTGGTAACCAACCTGGGAAGGTGGGGGATGCCGGTTATCAGGTATCGTACCGGCGACAAGG\nTTAAGGTTAACCGCAGCCGTTGTGACTGCGGGCGCACCTTTATAAGAATGGAGGGCGGCA\nTCCTGGGCCGGGTGGATGACATGCTCATCGTCAGGGGAGTCAACGTTTTCCCCAGCGCCA\nTTGAAAACATCATCCGGGCTTACGACC\n>NODE_206_length_267_cov_0.788660\nTATTCGACGTCGTCGATATGGCCTTCGCCCCACACCACCCGCAGCAAATGCGCATGAGTC\nAGCAGCTTGCCCGCATGGCGTGCCAGTTCGGCGAGCAGCGCGAATTCCTTGCGGGTGAGC\nTTCACCGATACGCCATCGCGCCAGACCTGATGCGCGGCGAGATCGATTTCGACCGGCCCC\nACCTTCAGCCGGTCCTGCCCAGCCGCTGCCGCATTGTGCCGCCGCAGCGCGACCCGGATG\nCGCGCCAGCAATTCCTCGGTGTCGAAC\n>NODE_207_length_267_cov_0.737113\nACCCGGCCGTGCTCCAACAAATCTGGATGCAAATGCCCCCGGCACCGCCGCCGACCATCG\nGCAACGCGCGCCCGCCACGGACGCCGGACGACAGCGACTGCATTACTAAGGATGCAGGCT\nACAGCCCGTTTTCAACCAGTTGCGATGAAAACGCGAGCCCCTGCGCCGTTCAATAGCGAC\nTGCAAAGCCAATCGCCAAGCGGAATATTATGACCGTCGCGTGACCAATTCGGACGAGTGC\nGTTGCGATCAACGCGCGCGGACGCCCA\n>NODE_208_length_266_cov_1.943005\nGCATATGAAGGATCGTTCGGTGTGGACGACGTGGCTGGTCGCCGACCAGCGCTTCGTCTC\nCAGCCGTCCCGACGTGCTGAGCTATCAGACCGAACGATCCTTCATATGCACCGGCTGGGT\nGACGAACGGCACGGGCTTGGCCGGATCGGAGATGTAGCGTTCCTGGCCAGCCGTGGCGGG\nGGCGGTGAAGCTGAGGCTGTTATCCGCCTGGAGATATAGCGGCGTCGCCTTGCCCGCAGG\nCCAGTGCGTGAAGGACTGCCATTGGC\n>NODE_209_length_266_cov_1.145078\nGCATCCGGCAATCACGCTGATGCAGCTGTCATCGACGCCGGAAGATGTCCTGATCGAAAC\nCTCGAAGCAGGAAAAGGTTCACAGCTTTCGGAAGGATGGCACGCCCAACGTAGTTGTCGA\nGCGGATGAGCTATGCCGAGGCGCGAGCGCTGCGCGTGAGGTGTGCCGAAGCGCTGTTGCC\nGTACCTCGAAAGCAAAAAAACGGTCGCGGTCGACATGACCTTTTCGGGTGTTGCTGACCT\nGATCATCCAGGGCGTCACCCATACCG\n>NODE_210_length_266_cov_1.041451\nTTCATGGTTTGTATTCACACTGAAAATCAAAATCAAGGGGACTTTTGCCCTTTTGCTCTA\nCTGGAGATTTCTGTTCTCCATGAGTCCCCCTTAGGACACCTGCGTTATGGTTTTACAGAT\nGTGCCGCCCCAGCCAAACTCCCCACCTGACAATGTCATCAACCCGGATCAGCCCGCGAAG\nGACTTTAATGCAAGAAAATGGTCGATGAAGACCAGTTCCGCTTCATTGATTAAGTAAAAA\nAACGATAAGGGTAGTGGTATTTCACC\n>NODE_211_length_266_cov_0.797927\nCCGTCCACCCCGTTATATTCGGTCCCCAGACATAGGAAGCACCGACGCCGATCCACTGGA\nCCTTCCACAACTGGTTGAGAAAATCCATTACGAGGCGGCCGTGAAGCTCGTTCATGTGTT\nGGACGTCGAGTCCCCGCTCGAGATCACCGAACATCTCGGTGCGGCTCAGGTAGCCGCCCG\nTTCGCAATTCGTGGCCATGCAGCTCAATTCCAAGCGGGATATCTATGTCGATTTTGTTGC\nCCAGAGAACCCGAGTCGCCGCTGATG\n>NODE_212_length_266_cov_0.797927\nTCTTTAGACATAGGCTTTAATGCATAGTTCATCTTCTTTTCTTGACCAATAGTCGATGAT\nTTTTCATCCGAGAGATGTTTTCCGCAAAGCGATCCTGCTCCGTGTGCTGGATAAACCTCC\nACTGCATCATTGAGCTGGCTCAGCTTGTGGAGACTCTCGTACATAAATCCTGCCAGGTCC\nTTTGCCGAGTATACTTTTTCTGACACGAGATCAGGTCGCCCTACGTCTCCAATGAAAAGT\nGTATCGCCGGTAAAGAGTCTTTCAGG\n>NODE_213_length_266_cov_0.797927\nGTGCTGCGACACGAGCGCGGGGCAAATCCAGCGATCGGCATCATCTTTTCCGGAGTCCGG\nGTTGATCCGTGTGCAGCCGTCCACCTTACCATCGACGCTAATCGACAAATAATACTTGGC\nGTGCATCGCGCTACGATCGTGTTTTATTTCCATCTTGGCGAGTTGCTCGGCCGAAAGCCA\nATCGTCCCTCCTTCGAAGTGGGGCTGGCGGCATACCATTTGGCGCAAATTGCGCAGGGTC\nGGCACCCCACTGAACAAGTTGCTCGG\n>NODE_214_length_266_cov_0.792746\nGGAAAATGAAATGCAACCGGCTCAGCCACTATCCGGAAACCGCCCGAAGTCCCCAGTTCC\nCGCAAATCGCAGAAAACTGTTGCCGAGACGACACGGATGATCAGCCCCATCCCACCGCTC\nCCCGACAATGACGACGTGATGCCCGACGTGACGCGCGCGGCGCAGTTCATCGGCGCGCAT\nCTCGACGATGCGATGACGATCGGCGACGTTGCCGCCGCCGCAGGTGTCGCCCATCGCACG\nCTGTACCGGCATTTCCACGACGTGCG\n>NODE_215_length_265_cov_0.802083\nGTATAGAGATACGCCTCCGGGTTCTGAATCGCCGCGATGTCGGCAACACGCATCATGCGT\nGCGTAGACCTCCTGCGCGAGCTCCGCAGCGTCAGGATGCTTGCGCACGCGCCGATAAAAG\nAAGGCTTCGAGGGCACCTGCGTGTTCGGCGAACAGCCTTTCCAAGAGCGACTTTTTGTTC\nTCGGCCATGGCAGCCTGGGCGCTCGAACCCGCGATTTGCGTACCCTAGCTAGTTACGAGT\nCACTTCGCGCGCATTCGGGTACCCC\n>NODE_216_length_265_cov_0.802083\nTCGTCCTTGAGGTGTCCAAAAACAGTTCCCATCTGTTTTCAGACGACAGTAGATCCAATT\nGTGATCGATTAGCTGCCTGGCATCCGTATTTCTTGAATGCCGGCCCTTTCGTCGCCGGTC\nACGACGGATGATCGTGCGATGCGTCCATAGCGTTCCTCCTAGCTAGGGGCGGAGCCGCCC\nGGAACTTCCAGTTGCCGGCGGTCCTGTTCAAATGCCTATATGCTGCTTCCCCCGATATTG\nGCATGATTCGCGCTCAGGGTCCGGG\n>NODE_217_length_265_cov_0.802083\nTGGAAATTCTGCAGCTGCTTGCTGTTGTAAGTGGAATTGAGCTGATCGAAGCCCGGATAG\nGTGGAAACCGAGTTGCCACTGACCGAGTAGAGCAGGTCGGCCAGCCACTGGTTGCGGTCG\nTTGAGGAGCCGGTACCAGAACATGATCGACCCGTTGTCCATGGTGTGTTTCAACGTGGCG\nGTGAACTGACCGCCGAGGTCGGAAGTGTATTGCGGGTCACGGACGCCATCCGATGAGCGG\nTAGAAGCCGCCGACGCTGCCATACC\n>NODE_218_length_265_cov_0.796875\nTCATAGGCCGGGATGGACGCGGTGCTGAGCGCTTTCGGCCTCGGGATGTTGCCCCAGCAG\nAGGCGCCCGTTGACGAAAACATTGAGGACCGGGGAGTGCAGCACCGGCGTCGCGGCGTTC\nGGACGCTCGCTTGCCGCCAGGGCGTAGACGCCGAGGCCCGAGCGCGTGGCGATGAACAGG\nTGCGCCGGATACGGAACCGGCAGGGTCGTTCGACCGGAGAGCGCCCTGAGGCCGGCGGGA\nGGAGCCGACAGGGCGAAATAAGCGT\n>NODE_219_length_264_cov_1.596859\nGTAGAGCGGAATGCCGTCGAAGGTCAGCGACACGCGCGCGCCGTCGAAGCCGCGAATGCG\nGAGCTGCCCGCCCGACGCACCATAGGGATCGCTATTGGTGAAATTGACGCCGGGGATCTG\nGTTGATCGTGTCGAGGATCGACTGGCCCGGAACGCGGTGGGCGATGAAGTCCTGCGTCAG\nCACCGCCTTTGCCTTGGGCGTGTCGGGAATTTCGATGCCGTTAATGCCCGTCGCGCGTTT\nGCCACTGACGACGATGTCGGTTTC\n>NODE_220_length_264_cov_0.806283\nCAGCGGCAGCGAAGAGCGCGAGTGACTTCTACGACACCAATACCAAGAGGAAGTAGGCAC\nAGCCGACTGCCTCCTGACGCTTTCTAAGGTCTAGCAAAGATGCCCGCCGCCCCAGTCAAC\nATCATGACGCTGTTCACGACGATGTACTCGTATGTTGAAACGGCTATCGCGACGTCTGTT\nGCATCGTTCGGGTCCGGACTGGTCGCCTTCGTTGCGGCACCTCTTGCGCTTGCAGCGACG\nATCTACTTCCTGTTGCTGGGCTTT\n>NODE_221_length_264_cov_0.806283\nGGCATATTGAACATAGGGTCCGGTCTCTCCTTCAAATTGAACCACTTCTTCCAAGTTGAA\nGGAGAGACCGGACCCTATGTTCAATATGCCCATGCACGGGCCCATTCGATCATCCGCAAG\nTATCCGGCTGAATTGGACCTCAGCCAACCACTCGTCATTGAAGATGATTATGGTTGGGAG\nATTATCAAGAAATTAGCAGACTTCTCCCGGATCATCCATCTTGCGGCAGACCGTTATGAA\nCCTTCTGTGATTGCTAAGTATGCG\n>NODE_222_length_264_cov_0.806283\nTAGAAAGACTAAGCGTCGATTGCGGGCCTATTCAACGAGATTGGCAAGATTCTTCAATGA\nCGAATCCATGCCGGCGCGATGGTCAGCTTCGCTGATCCCCGTGGGGACGTTCTCGGCGGT\nGAACGTCACTTTCGTGCCGTTTGCGACGGCCGTGAATATCGTGGTCATCGTCATGGTGCC\nGGCAAAGGCCGGATCGGCGGACTCGAACTCGACAGCCTCGACAATTTTTTCATTCGGTAT\nCAGTTCGATGAAGCGTGCCTCGAC\n>NODE_223_length_264_cov_0.806283\nGCTCTAAGCCGGCCTTCGGAGAGTCGATTGCGAATGCCGAGAACGCTTAGAAAGGAATCG\nTCTAGCGTCCCTCGAGCTTGTTTGGGCGCTTGGTGACGTTCATTAACATAAGTGCTACTG\nCACATGACGCAGCGACAAATGCCGCGGTCCACCTGACCGTGGATACGGCAAAAGCCGCGT\nCAAGCCGCCAGCCATGGGGCGCCGGCTCGGTCGTGGCAAGCGGCACCACGTCCGGGAAGT\nACCAGTTGCAGAACAAAGCGAGTG\n>NODE_224_length_264_cov_0.806283\nGTACAGCGTCGGATTCGATTGCGTGAAATTGCGCTCGATGCGGCAGGATGCCGAGGTCGC\nGGGCCAAGCGGTGTGGGCCGAGAAAGACGATCCAAGAATCACCCGCATTGGGCGCATCAT\nCCGCAAGCTGCGCATCGATGAGCTTCCGCAGACCTGGTCGGTGCTCAAGGGCGAGATGAG\nTTTCGTCGGGCCACGCCCTGAACGGCCACAATTCGTCGAGGATCTCGAACAGCAAATTCC\nCTATTATGCCGAGCGCCATATGGT\n>NODE_225_length_264_cov_0.806283\nGGCGCGGACCGCAGCCAGTCCATGGCACTGGACCTGGATGCCTTGATCAGCGAGTCCCTC\nATCGGTAGCCACGAGGAAGTGGCGTCCCACTACAAGGCCATCGGCACGCGCTACGGGGCC\nACGGGCATTGCCATCGTGCCGACTAGCGCCCAATTCGACACCCACAAGCACATCCTCGCC\nTACTTCGTCGACGAGATCCGCCCCATGCTTGACGGGGACTGAACAAGCCGGCGCGCCGGC\nATGGGTTCAGCGGTAACCCTCTTC\n>NODE_226_length_264_cov_0.806283\nGTGATCATCCGCGCCGGATATTCGCGCGCGAGCGTGTTGGGGTTGAACAACCATGCCTGT\nGCACGGTCGTTGAAATCCGACATCGATCCGAGCACGCGCTCGGCGCTCAGGCCGTCGACC\nACGTCGCAGCCGCTCAGCATCGCAAGCGTGCCAAGCCCCAGCGCGTTGCGCAGGAACAGC\nCGCCGCGTCGGCACGTCGAGGCCGCGCGCGGCGTCGCTCAGGATATAGCGGGTTTCGTCG\nTTCATGGCTCACGCTCCCCGGATC\n>NODE_227_length_264_cov_0.806283\nGTGAAGGACATGCTCGATGTCGCTGGTGCGACGATGACCGGTGCGGAGAGCGGAGAAATT\nGGACTGGCGCTGATCGAGGCGCAGGATTTCGAGATCGTCCTGCTCGATTTACGGATGCCC\nGGTATGGACGGGTTTGAAACGCTGCGGCGCATCCGTGCGCGCGGCGATGCCAAGGCGCAT\nCTCCCGATCATCGTGGTGACTGCGGACACAGCGGTGGATTTGCGCGAGCGTTGCCTTGCA\nCAAGGGGCAGACGAAGTGTTGTTC\n>NODE_228_length_264_cov_0.727749\nTATTCGGTGTTTGGTTAGAGTTGGTAGGTCTCGCGTCCCCCGCATCCATCCTGTGCTCTT\nCCCCCTACGGTTTTCGCTCGAGTCACTACCTCTATAGTTTTCGCGGAGAACCTGCTTTTT\nCCCGTCTTGATTGGCCTTTCACCCCTCAACCCACCACATCCGGGAACTTTTCAACGTTAA\nTCGGTTCGGACCCCCACTGCGTGTTACCGCACCTTCCTCCTGGACATGCCGAGCTCGCCG\nGGTCTCGGGTCTAAACCATCAAAC\n>NODE_229_length_263_cov_1.215789\nCTGGGAGGCCGGTGCCAATTACAGCCGCCGCGAGAAAACCAGCGCCTACCAGTCCTACTT\nCCTCTGCCCCAAGGGCGCGGGCACGAATTGCACCGTCGCAAGCGGCACGCCCACTTCGGC\nACCGATCCCGAGCCAGGCGATCCTCGGCAAGATCCCGCTCGACTATCTCGGTGTGCCGGC\nGGTGCTCGCGCTCAATCCGCTGTATCTCTACAATAACAGCTTCAACACCTTCTACGACAA\nCCGTCCGTCGTCGTTGGTGCGCG\n>NODE_230_length_263_cov_1.189474\nGGGCAGCGTAAGCCGCTGGCGCGAGAGTGATAATCCCTAAGGAGTAGCCAGAATGCCCCC\nCTTTCGGGAGGGGCCGGGTTACGCTAGCGCTACAGGTCGATCAGGCCACGTTTGGCGGCG\nATCGTTACGGCGTGGGTGCGATCAGATGCGCCCAGTTTCGCGAAGATCGCCTTCATATGC\nGCTTTGATGGTGTCTTCGGATACGCCGAGTTTGGCCGCGATCTGCTTGTTGGAATTGCCC\nTGGGCGGCAAGCGAAAGAACGCC\n>NODE_231_length_263_cov_0.810526\nGTCGGATGCCTTCTGGATGCGCTCGCGCATCTGCTCGAACGTGGTCTCCGTGTATTCCTT\nCTTGTTGATGTTGAGATGGTAGAGCTTGTCCTGATCCAGGAGCACGATCTCGGCGGAAGG\nACCCACCGCATTGCGGGCGAGGAAACCCACGAGCTTGGATTTCATTTTGATGTCGCTGTC\nCGTGCGCGAGCGGTCGCCGGAAATGGTCGTCTTGCTCGTGCCGGACATATTGCCGAAGGC\nCATGGCTCCCACACCTTCCACGG\n>NODE_232_length_263_cov_0.810526\nTTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGG\nTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATACGTGTGCATGTGTC\nTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTC\nAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTG\nAACTAGTTTACAGTCCCACCAAC\n>NODE_233_length_263_cov_0.810526\nGGGCCACAACCGACCGCGCAAGCCGCGGGGTCACCCCAGGCGGATTCTGCCAACAGCGAC\nGTCAGCGAATCATCGACGTGGGATTCACCGGCGACCAATGGCCAGGCAAGCGCGCCGGGA\nGGGTCGCAGGGCGGCAGCACTGCAAGAGCGAACCCGCAGGCCAGCAGCGGAGCGCAGGCG\nCCAATATCGGGCGTGGCGCAGCCATTGGGCACGGCGCAGACATCGGCGGCAGCGCAGAGA\nTCGGCTGCGGGCCCGTCTTCAGG\n>NODE_234_length_263_cov_0.810526\nGCCCGCAAGCGCGCGTAGCAAGCTGGTCTTGCCCGATCCGTTGGCACCGATGAGGCCGAA\nCCACGATCCGCGCGCGACCCTCAGATCGACGTCCTGCACGACACGCTGTCCGCTCCGTTC\nAACCGCCGCCCCGGCAAGGTGGATCGCGGGGCTCATGCCAGCAGCCACGTCTTCGTGCGG\nGCCCGGTGTTGCAACTGCCACAGGATCGCGACGGCGAGAAACGGCAAAGCGATCGGCAGG\nAAATAGGCTAGAAACAGGAGCAG\n>NODE_235_length_263_cov_0.794737\nGGGTGGCGCGACGCGCCGCCTGTCGGTGCTGGCAGGGCTGGAAGCGCTGGCGAACGAGCC\nCCCTGCCCATGTGCTCATTCATGACGCCGCCCGCCCTTTCCTGAGCGCGGCGGTGATCGG\nTCGGTTCGTCGCCGGTCCAGCCGCGATGCGCGGCGAGGGCTGTGGCAAAGTGAAAGGCTT\nGCGGGGTCTGGATGCGGTGCAAGGCATCGCGGGCAACGGTTTCGCCCAGCTCGCTCTCGC\nCGCGCGCAAGCGTGTCTGGCACC\n>NODE_236_length_263_cov_0.757895\nGAATAATCGCGGGGCGTTCCTGATTCAGCAGCATTATTGCGACGCCAATGCCGCGCCGAT\nTTATGGCCGGATGTGCGCGGCGGTGGCGGCGGGGCTGACGCGCGACACCGCGATGGGCGC\nGCGCATCCTCGATTGGCCGGGCGAGCCGACGCGCGATGCGTTGCCGCTGCGCTTTTTTGG\nCGGGCTGCATGCGCTGGTGCAGGCGGGCAGGGATGACGGGCTGGCGGCGGTCTTTGCGGG\nACGCGTGACCGAACAGGCCGAGA\n>NODE_237_length_262_cov_1.222222\nGCATCAATGGCCCGAGCAAGGTGTTGTCGACCACCACCAACGGGCGCAGCCCGGTGCGCG\nCGCCAACGGCGTCGGCAATGTCGACGACCAAGGCGATGTCGACGATCGCGGCGGTCGGGT\nTGGCCGGGGTTTCGATCACGATCAGCTTGAGCGGCCCGTGGCTGAGTGCTTCCTCGACCG\nCAGCCGCGATGCTGGCGCGGTCGCACCCGTCGGTAAATTCGGCATGGCTGACGCCGAAGG\nCGGGCATCAGCCCGGTATAGAG\n>NODE_238_length_262_cov_0.851852\nATGCTCTTGCGGTGCAACGCGCGCTCGTTCGCCACGCCGCAGGTCAGGTCGCCGTGCGGC\nCAGCGGTGCCGGCCATAAGGTCGCCGCGAGCCACCCGTCCCGGAGGCTTGTGTTGCAGTC\nTGCCGCAAGGCGCCTTGCGCCCGGCCTATACTCGCTACCTCCAGGGGCTACGTCCGACGC\nAGTTTGGGAGACGGATTCGGTGCGGTTCCGTCTAACCAACAGCGGAGGACGGAGCCCCGG\nGCGGTAGCGAGTATAGGGCGGG\n>NODE_239_length_262_cov_0.814815\nGGCCGCAGCCATCAATTGACCCCATTGGTCCGCGGTCTCGCTCATCGACGAGCTCCCCGG\nCACCAGGACCGCAGCGCTGGCCGATCGTTGAACCGCAAGACGAAGGTGGGGTTGCACGTC\nCCGTCATTCGGCGGAACCGGCTGGACGGTTACAGCCTCGCCCAAAATAAAAACGCGTGGG\nGTCTTTTTGCCCGCCACCGATATGCGTCGTGCTCTCACTGCCGAAAACTTTCGCTCATTG\nCGCATCCTGGGCATCCCCGTTC\n>NODE_240_length_262_cov_0.814815\nGTTCACATTGTGCTGAGCCTTGTCTTCACCCAGGTAGCGCTTCAACAGCTGCTCGGCTTC\nCACCAGCTTGGGAGCCAATTCAATATAAGCATTGAGGCCGGTGGGGCGGGCCTTTTCCTG\nAGTGCGCAGGGCGCGTGTGGTGTACAGGAATTCCGTGGTGAGAGTCCGTTCGTGTTTCTG\nCGGCTTGTAGAACCAGGAACCCACCAGGTAGAACAATGTGTTAAGGCTTAGCGACCAGAG\nCGTGGCATGGGGAATGCTGGGC\n>NODE_241_length_262_cov_0.814815\nGGGTGCCGGAGCTGCTACAATTGCTTTAGCGGGAGCTGCTGTCGGTATTGGAAACGTGTT\nCAGTTCTTTGATCCATTCCGTGGCGCGAAATCCATCATTGGCTAAACAATTATTTGGTTA\nTGCCATTTTGGGCTTTGCTCTAACCGAAGCTATTGCATTGTTTGCCTTAATGATGGCCTT\nTTTGATTTTATTCGTATTCTGATCGAAGAAAGAAGGTTGAACTTTCATAAAGCAAGCACC\nTCTTTCACATAAGAAAATGGAG\n>NODE_242_length_262_cov_0.814815\nGTGCACTATGGTCATATTCATGTCCGTCGTGGTGATACGTGCCGTCCGTGGAGCATCCGC\nAACATCGATACGATCGCACGCGAATGCGTCGACGTTGGCGACGCGCATCGGCATTGTCAA\nCGGCGTCTCCTCTCTCGTCGTGGCGTATCTCCGCGTGCCGACCGTGCGAGGAATGACAGC\nATGAGCACATGCATCTTTTCGACACGTCATGGAAGTTAGAAGAAACATGTCGAGCATCCA\nGCGCATTGGAAAGACTTTTCGC\n>NODE_243_length_262_cov_0.814815\nGGCAATGGCAACGCGTCATGCCAGAGAGTGAGGGCGCTCCAGGCACCATAGATCGTCCCC\nGCCACCAACGCGGTAGGCCAGTCGAAGCCGTGGCGCGCCTCCACGGTTCCGGGGGTAAGG\nGGCATTGGCATGGAGATGTAAAATCCCGCTCCAGAACGTATATCCTAAAACTCTATCAAA\nGTAGTAGGATATACAACGCTGCCGATCTTGGCCTTTGCCAAGTTTTGCTTTTGTCATCTG\nCCCCTCCGGTGTCGGGCCGGGG\n>NODE_244_length_261_cov_0.920213\nCTTTATGACGGCACACGCCGACTACTTCGAAGCGCATTACCATGGCTTCGTCACGATGTT\nGGTGGGCTACGGCGGCATGGAGAATGGTGGGCTGCTCGAAGAAGCGCAGGAACTGCGCGA\nCGCCTACGAAGAGCTTCTTCGACGGATCGTGCTCGCAGGCATCGAATCCGGCCGCTATCG\nAAATACGGATTCCCGGTCGATAAGCCGCGCGATCCTCTCGATGCTGAACTGGATGGTTCG\nCTGGTTCAAGCCAGGGCATGG\n>NODE_245_length_261_cov_0.845745\nCTGCCATGGCCGCCCTTGGCCGGATCGGGCGAATGCATCAGCACGACCGGGCCTCCGGCC\nAAGGGCGGCCATGGCAGTGTCGGCTATCGGGACGTGCTGCTCGAGGTTGTTCGACTGGCT\nCGAGGCGCGGATTGCGGCGGTGGTCGCGGGTGGGGTGGACCGCTCCCGGATCCTCGTTGA\nCCCCGGCATTGGCTTTGGCAAATCGCTGTCGGACAATCTCGCGCTGATCAATGGCCTTGC\nGCTGTTGCACGGCCATTGATC\n>NODE_246_length_261_cov_0.819149\nGTGCTGGACTGGTTCCGCAGGAAGAGGTGTTCGTCGCGCTTCGCGCGCTTGGGCTTGATG\nATCTGGCAACCATCGGTGTGATGGCGCGCGAGCGCATTTTCCTGGATCTTGATGGCACCA\nTCACCGGGCGCGTTGCCGCGCCCCAGATGCAAATCTCCTGGGACCATCTTTATACCGGAT\nTGCGCGACGTGCTTTCGACATCGGACTATCATGTCGGTCGCGATGCGGTGCAGGCAGGAA\nCCGACGACAGCACGGCATGGG\n>NODE_247_length_261_cov_0.819149\nGTAAAGATCCTCTTTAAGATGACTTTCGACCACGATCAACGGTCAAAATCGTATTTTGGG\nTAACTTTTGACCAAGATCAACGGTCAAAATCATCTTTTGGATGGCTTCGAACCACGATCA\nACAGTCAAGATCCACTTTTTGATGACTTTTTATCAAGATCAATGGTCAAGATCGACTTTA\nCGGTAACTTTCTACCAAGATCAATGCTCAAGATCCACTTTTGGATGACTTTTGACCACGA\nTCAATGGTCACAATCGACTTT\n>NODE_248_length_261_cov_0.819149\nGCCTTCCGGCAACATCGAAATGACGCCGGCATTGCCGAACAGGCGATTGTCGCTGTCGAG\nCCACACGGGGGAGGGCGCGAAGCCATATCCCGTTAGAAAGGCGAGCTTGATCGTCCGTGG\nCCCTTGCGGCCCCTCGACCTGCGCCGTCTGCCCGATCGCGATGCTGGCATGGCCCGTCGG\nGAGCAAGTCGATGCCCTTGGCACCCGCCGCGACAAGCGCATCGATATCGAACTCCCCGGC\nGAGCGGCGGGCCGCCATAAGT\n>NODE_249_length_261_cov_0.819149\nGGGTGACCGATATCAAGACCTCGTCGCAGGCCGCCGAAGCGCTGCGCCCGATCGCCGGGG\nTGTTTACCTTCGCGCTGTTCGCCGTTGGGATCATCGCGACGGGGATGCTGGCCGTGCCGG\nTGCTGGCTGGGTCGGCTGCGTACGGCGTGTCCGAGATGCTGGGCTGGACCTCGGGCCTGC\nGCCGCAAACCGCGCGAGGCGCGTGCCTTTTACGCGACCATCGCCGCTGCCACGTTGGGCG\nGGGTCGCGCTCAACTTCACCG\n>NODE_250_length_261_cov_0.819149\nGTTTACCATGATCCGGATGTGTGCTATGTGGTCTTCGTGACCGAACCAAGAGACCGGCAG\nAGTGTGCATCGCCGTTCCATGGAGGTGAATGCCGTGATACCGGCAGTACCAAAATACATG\nTTGTGGTCGGAACAAGAGATCACTTGGTCCTTCAAAGATCACCCAAAGGTGATGCCTAAT\nCCGGGCGGATATGCTCTGGTGGTGGATCCGATCATGCACGGAACATCGTCGCGAGTCCGG\nTTCAGCAAAGTGCTGGTGGAT\n>NODE_251_length_261_cov_0.819149\nGACGCGGACGCAAGGCGTGGAGCTGGAAGCTTCGGCGACGCCGTTGAAGGCGCTTAATGT\nCACCGCCAACTACACCTACCTCGACGCGCAGAACCGCTCGCCGGGCTATGTGGGGCTGCA\nGCTGAACCGCCGGCCACGCAACGCCGCCAATATCAGCACGGACTACAAAGGCTTCGACAA\nGTTCGACCTGTCGGCGTCGCTGCGTTATGCGGGCGAGAGCTTCGACAACGTAGCCAACAC\nCATCCGTCTCAAGTCCTATGT\n>NODE_252_length_261_cov_0.819149\nGATCAAGGCGGGGTTCTAACGCGCGTTCTCCCGCGCAAGCGGGAGCCCAGGGTTGCAGGC\nGCTTCGCTTGTAACCCTGGATCCGCGCTTTTGCGGGAAAACGGCACGAGCCTCGCGAAAC\nAATCCCCTCGTCTCGGCCGGATCGCCCAGCTACATCTTGCCGCAAACGATAAGAGGGCAG\nGGTGGATGCGGGGATTGCGGCGGGAGCTGGCCGGGTTGGGCGTGCTGGTGTTGGTGGTGG\nGTGTCGGGCTCGCCGTGTGGG\n>NODE_253_length_261_cov_0.813830\nGATCGTCTCGGGTCTGGGTGCGACACCGATCGAGATCGGCGTGTTGAGCGCGATCGGTGT\nCGCCCCTCACCCGCGAGCCCTGCGGGTGACTGCTCTTGGCGGGAGAAACGGGTTCGTGGC\nGGGAGTCGTTGCCCCCGCCACGAGCGAGTTTCTCCCGCCATCCGTTCCAGGCGTCACCCC\nGAATGCAGGAGAACCTCGCCCCAGGGACGTCCTTCACGCGAAATCCGCCCTGCAGGCGCC\nGTTTCTCCTGCATTCGAAGTG\n>NODE_254_length_260_cov_1.582888\nATCAGCTTCCTTGCGCCTTACGGGTTTACTGGCCCCTTGACATGTGTGCGAGTCAACGGG\nCCAGTAAACCCGTAAGGCGCAAGGAAGCTGATTGGCGGGATCCCCTTGAGGGTTGCACCG\nCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGAGAGCATACCTGTCGGGACCCGAA\nAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGCAG\nCGGTTCTGACGTGCAAATCG\n>NODE_255_length_260_cov_1.235294\nGCCGTAAAGCGGGTACCGGCGGTGAGCGTCAGCCGCGAGGACACCGGCCAACTCGCCTCG\nCCAAAAGCCGAGAGGCTGTCGGTCATGTTGGTCACGCCGATGATATCGAGCGGCTGATCA\nGGCGGCCCGAGCGCCCGCGCCTGGATATCGCGATCATGCAGGAACGCGACGCCGACCAAC\nCAGCCGATATGATCCGGCACCGCGCGCGACAGTCGCGCCTCCTGCACGAACAAGACATTC\nGACTGTTCGTTGGTGTAGAT\n>NODE_256_length_260_cov_0.823529\nTGCCGAGGCGGCGCGATCTGCGCTTCGTTCCACAACCGCCGCAGGCGAGCTTTGGCGGAC\nCAGATCATTTCCTCAATATTCCGGAACTCGCGGTGGTGCTGGGCGAGGAAACCGAAATCA\nCCCTGCCCGAGGGCGATGTCGTCGGTTACATCCAGATCGCCGCGAGTGGTGACCCCAAAA\nTCAGTTTCTGGTGGGAAAGCACGAAGGCGAAGTACAGCACGCGCAAACCCGTCGACACCG\nCCGCGCCAGCCGCCAAGCCG\n>NODE_257_length_260_cov_0.823529\nGAATGGGGTCGATATATCGACCTCGAATTCTTTCGACCCCACCTAAAGGGGTATCGGCGC\nCGTGGGACATCGCATCGACTACGTGACGGCGCACGATGTCTGCTTGAGCCGAAACAGTCA\nTCGGCCCGTACGCGCTACCCGGGTCCGATCCGGATCGCACGGTCTGCAATCGTCGGGTCA\nGTGCCTGGACAAAGTCCGCCGAGACTGCGCGGTCGACGTAGATCCGCTCGACGCCGACGC\nAGGTCTGCCCCCCATTGGAG\n>NODE_258_length_260_cov_0.823529\nGGCGTGGATATGAAGTTAGGAATCGACATTGCGTCGATTGCCTACAAGAAGCTGGCGGAT\nCGCGTAGTCCTCATCACTGGTGACTGCGATTTTGTTCCGGCCGCAAAGCTAGCTCGCCGC\nGAAGGCTTGGATGTTGTGCTCGACCCGCTCTGGAACCGCGTGGCGCCAAGTCTCCATGAG\nCACATCGATGGCTTGAAGTCAGTCTGGCCGAATCCAGCCACGTCACGGAAAAGCTCCGAG\nGTCCCGACAGTCAGCAGTCC\n>NODE_259_length_260_cov_0.737968\nGGGCGGGAGCGAACGCGTCGTCGGCCGCCAGCGCCTCGTCGTACGCCGTCATCGCGGTCT\nCGTCGTCGCCCGCCTGCTGGGCGATCACGCCCAGGTTGAAGTGGGCGTACTTGTTGTCGG\nGGTCGAGGTCGAGGACCTCGTCGAAGGTCGCCTGCGCCCCGGTCGCGTCACCGCTCGCGA\nGCTGGTCGAGGCCCTTCTGCACGAGAGCGTCGGCGGCCGCCGACTCGGACGAGGCCGCGG\nCCTCGGCGTCGTCCTTCGCG\n>NODE_260_length_260_cov_0.727273\nCCGGATTGATGTCGAACGCCAGCAGACGCGTGCCGCTCAAGCGGAACGACAGGCTGCTAT\nTCACCGCGCCGATCTTGAGCGGCACCGAATAGCGCGCCTCAAAATCGATCCCGCGCGTCT\nTCGCCCCGCCGGTATTGGCCAGCAGGTTGACCGCGCCCGTGATCGCATAGCTGTTGGCAT\nCACGCGGCAGCAGCGAACAATAGGAACTGTTATACGCGACATAGCCGTTCCCGGCATTGC\nCGTAGCAAGCCGTGATGATG\n>NODE_261_length_260_cov_0.721925\nGAGTCGGTCGGTGCGTCGATGCAGTCATGACTTACCGTCCTGCCGCGACGCGGTCGCTTC\nAGTCAGGAACTCGCGCATGAATGCTTCGAAGGCGAAGGCATGATCGAGGCCGCGATTTTC\nTTCGAAGATATCGTTGACCGCCTTGACCACGTCCGACGTCGTGACGCCGCGCGCGACCCC\nATCCGCTTTATCGCGGGTGAAGGCTGCGCGCTTCGCCCGGCCGGGGATCGACGCGGCCAT\nCGCACCTGAAACGATATGCT\n>NODE_262_length_259_cov_1.236559\nGCTCGAAAACCGCTTTGGCGTCGCGGTTAAAAACTTTGCCGCGTCCCTGTTCCTGATAAT\nGCGTGCGTTAGCCGAGGGCGTTCGTATTTTTGCAGCCTCGATCGTCCTCACGGCTGTTTT\nGTCGTCTTCACTGCCAAATTTCCCCAATCTGACGATCTGGTCGATCGTTATCGTCGGCGT\nCTTGACGCTGATCTACACGTTTGAGGGCGGCATCGCGGCCGTCATCTGGACCGACCTGAT\nCCAACTGGTGATCTACATC\n>NODE_263_length_259_cov_0.827957\nGGCATAGATTGGGCCTCTACTGGTATCCCCAGAGAGGCGTTTGTCCTCTCTGCCAAGGAC\nCTAGATGGCATCAGCTTCTGTGACTATCAGCATCGTAGTATTTAGGGTAGTAGGGTATAG\nGATATATCAAGCAAAGTAGTCCTGTAATTAAAGTGCAGAATTGCTTTGCTTGTGTAGTTT\nTATTTAATACCTTTGTTGTGCACCGGGGTTTTTATCAATCTTTGATGCTTTTGTAAGTAG\nATAATTAAACTGTATAAGT\n>NODE_264_length_259_cov_0.827957\nTTCGTGAACAGCGCCTTGTTGTAGTACATCATCGTCGTGGCGATGTCGACGGGGACGCCG\nTAGTTCTTGCCGTCGTACTTCGACGCGTCGATCGCGGTCTTCGGCAGCTTCGCGGTGTCG\nTGCGCGCCTCCCGCGTAGTAGTCGTCGATCGGCTGGAAGAGGCCCTGCGACGCGTAGGCG\nGGGACGCGCGAGAAGTCGAGGGCGACGATGTCGGGGCCGCCCTTAGAGGTCGCTCCGGTC\nAGGAGCTTCTGGTACAGGG\n>NODE_265_length_259_cov_0.822581\nGGCTTACGCTGGCTTTGGCCGCGAGCATGACGTTTGCGGCGGCAGCACAGGCAAACTGCT\nCCGCGACCAAGATCGCGATCGGCCACCAGCGCCTTTTCGTCGATCTCGGCGGCAACGGGC\nCGGTGACGCTGGTGTTCGAAGCGGGCAATGGCGACGATTCGCGGGTCTGGGCCAATTTGG\nTGCCGAAAGCGCAGGCGCTTGGGGTACGGACCTTCGTGTATGATCGCGCCGGGCTGGGCC\nAGAGCGACCGGCGACAAGG\n>NODE_266_length_258_cov_1.470270\nGCCTAAGAGATGAAGACGGTGTTGAGGACGACATCAACGCCCGTATCGCCGCCGCGATTG\nAAAGCGGCCACAATTGCCTGGTCGTCGTCACGGATGTGTCCAAGACCGGTTTGATCGCCC\nCCCGTCTCGATACGGTGTTTCGCCTGAGGGCACGTTATGGCGACCGCATCGATTTCCTGA\nTCGATGGCTGCCAGCTGCGCCTCACACCGGAAACCATTCGGGCCTATCTCGCGCAGGGGT\nTCGCCCTTGCGATAACGG\n>NODE_267_length_258_cov_1.248649\nGTGCGTGATCAGCCCCTGCGTGAACGACGGCGCCGCATAGTCGACGACGAAGCCTTCGAG\nCACCACATCGGTAGACCGCCGGATGGTCAAGGCTTCGCGATGCGGGTCGGTGAACAGCAG\nCTCCGCCTTCAGGCCGGTGAGCGTCACACGGGCGGCGTCGCTGATCATGATCGCCGCACC\nGGCTTCGTCGTCATCGGCGGGGGGATCGATTCGATGCACGCCGTCCGCGAGCTCGATCAC\nCGCGGTGCGCGCGTCATC\n>NODE_268_length_258_cov_1.248649\nGTTGTATATGATCATCCCGAGTTCGGGCCGCCCTTCGACCGCGAAGGACGAGAATTCCAT\nGGCAAGCAGCCCCGCCTCTGGGTGATGGATGCGCTTTACCCCCTCGCCGTGCGCCACCAC\nATCATTGTCTTGCCACAGGGCCTCGAACTGCGGGCTCACGCGACACAATTCACTGACCAG\nCCTGGTTACTGCCGCGCTGTTATTGGCACCGGCACGCGCTACGTCCGCGCGAAAGGCACC\nGACAACGAAGCGGGCGAC\n>NODE_269_length_258_cov_0.832432\nCCTATCATTGGGCCGAAGCGCATTTCGGCGCGTCTGCTGTGGTCAGGGAATCGAGTAAGC\nTCGAAACAGCGTGGCACCATAGACCGCTTCACTGGCTGATGGCCGGCGCGGCCGCGGCCG\nCCGTGCTGGTGCTCGCGTTCGGGATGCAGGTCAGCCGCACCGTCTCGATCGACAATACGA\nGCATTGCGTCCGATGACATGGCCAAGCCGTTGGTGACGGCTGCGCGAGAAATCCGCACTT\nGGCAGCTCCCCGATGGAT\n>NODE_270_length_258_cov_0.832432\nGCTGCAATCGGTGCCGGTGCGACCTCGTCGACGGCAGGGGCCACGACGACCGGTTCGGGC\nACTTCCGGGACCGGGGCCGGAAGCACTGCAGGAACCGGTGGGGTTTTCACCGCAGCGGCG\nGCGGTCCGTGTCTTGGGAGCAGCGGGTTTTGCGGGAGCGACGCCAGCCTCGGCCACGGCC\nGATGGTCCGGCCACCTTCGCGGCCGGTTTTGGGGCTTTCGGTGCCGCGTCTGACTTTGGA\nCCCTTGCTTGCCATGATC\n>NODE_271_length_258_cov_0.827027\nTCGTTAGCCTGTTCTCGATGGCCATCTTCATCGGTGTGCTGTTCGTCCTGCCCCAGTACC\nTGCAGAGCCTGCGCGGTCTCACCGCCCAGCAATCGGGGCTGACCACGTTCCCGCAGGCGA\nTCGGCATCGGCCTGTCCTGGTTCGTGGCCGGGCGGCTGTACAAACGGATCGGTCCGCGAC\nGGCTGATCGCGACGGGGCTGTTCTTCGCGTCCGTCGTGATCTTCGCGTTCCACTGGGTCA\nGCCTGGACACCAACCTGT\n>NODE_272_length_257_cov_1.586957\nCCTATTACCTGAAGCTTGAACCCGGTGCCGAGGTGCCACCGCACTCGCACGCCTCCGTAG\nAGGAGTGCCTGGTCCTGTCCGGCGAAATCGAGGTCGATGGCGACATCGCACGCGAGGGCG\nATCTCCATATTGCCTTTACCGGGCATGATCACGGCACGCTAACCAGCCGCGACGGTGCGC\nTGCTCTATATTCGTGGCCCGCTGGCCCCGCTTGACGAAGACACGCCCGGCGACCCGTTCG\nACCTATAATCCCCGGGG\n>NODE_273_length_257_cov_1.255435\nGTTGTCGCTAGTGTCAGCATCGGTGACGCATATCTTGAACATTATGCCACTCCTGATCCG\nGTGATCTTGAGCCAGATGCCCGATGTTGCACCGGTGTCCTTCTGCTGGAAGCCAAGCGCT\nCCGCTAACAAAGACAAGGCGAATGCCCGTCGCGCTGGAATCGTCACCAAAGCTCGCATCG\nCCTTTTAGTTTAAGGCTGAGCCCCGACCCACCATCGACCACGAACGTCGCCGTCTTGTTG\nGTCGTCATGTTCATGAC\n>NODE_274_length_257_cov_1.244565\nGCGTCAACGGCGCGGAACGCGCAATCGTCAGGCGGTTCGAAGGAGAGGGTATTTCATGCT\nTCGCACCTTTGCTGTGGGGACGAGCGCGTTCGCGCTGGCCTTGGGGACCCTCGTCGGTCC\nCGCCTGTGCCGCGCCTACCGTGGGCGGACTGCTGTCCGACCATAGCGTCGTCCAGCGTAA\nCCAGCCGATCGTGGTGACCGGCGAAGCGATCGCGGGAGAGCCCGTTACCGTCGTGCTGGC\nCGGACAATCGGCCCAAG\n>NODE_275_length_257_cov_0.836957\nGTTTCTGGCGGAGACGCGCAATCCAACGTAGCTGCCGATCTGGCATATTGGGCCGCAGCA\nCCGCGGCGGCAGGTCATCCTGACGCTCGATCGGGCACCCCTTCGAGTGGCTCCGCGCGCT\nCAGACTGCGCATCCGCCGACGGTGATGAAGGCGATGCTGTTTGTTGACGTGCGGGGTTTC\nGGCAGCTTGCGAGATGATCAGATTCCGGCGTTCTTCGGCGTTGTAATGGCGCAAATCGCG\nCAGGCGGTGGCGACGCT\n>NODE_276_length_257_cov_0.836957\nGCCATGCGCCTTTCTTCTTCCCGCCTGCTTTGTTTCTGGTGCTGAATCCGGTGACGATCC\nTGACGTTCGCGGCGTTGACGACCGCAGCGATCGTGCGGCGGCGGCAGACGGAATGGCATC\nGACGGCTGCATTTTTCCGGAATGGCGTTGCTGCTGGGCCCGGCATACGGGCGATTGCTGC\nCGATGCCGTTTCTGATCCCTTACGCTTATGAGGTTGATGTTCTGGCAGTCCTGATCCTCC\nCCATCGTTGGCATGGTG\n>NODE_277_length_257_cov_0.836957\nGTGCGGTTCGCCGTATCAGCTTTGGAGACCGCGAAGTCGCAGCCGACCGCGTGGCGCTTG\nTCCTGCCCGTAGTGCTCGTCGCGCATCGGCAGGAAATCTTCCTTGCGGAGGTACGCCTCG\nGAGTTGTCTCGGGGGTCGTTCAGGTACTCTTGCGAGTAGCCAGCCGCGTCACCGTCGGCC\nACAAACTCATCCTGGATCTCACGCAGATCCTCTGGCCCGAGCAATTCTCCGAGGCCCGGC\nTGCGCGAGATCCAGGAT\n>NODE_278_length_257_cov_0.836957\nTACTTGTGTTGAAGTTTGTGATTCCCGTAGCATGCACGTATGGTGAACCGTTATGTGATG\nAAGTCGGAGCATGATTTATTTATTGATTGTCCTCCTTATGAGTGGCGGTCGGGGACGAGC\nGATGGTCTTTTCCTACCAATCTATCCCCCTAGGAGCATGCGCGTAATACTTTGCTTTGAT\nAACTTGTAGATGTTTGCAATAAGTATATGAGTTCTTTATGACTAATGTTGAGTCCATGGA\nTTATACACACTCTCACC\n>NODE_279_length_257_cov_0.836957\nGTATGAGAGGGAATTGCAAAACTCCATGAGGGAATATTTTCAACGTGGGTTGATTCCAGG\nACCCGGTGAGAGTGAAGAGGCGTTCTTAGTGCGCGTCTCTCGGCTCGCCGTGCAGCCCAA\nTCGAGAAGAGGAAGCTCTAGCGATCACGCGTCGTTTGTTTGGTTTTTCTGTAGATTGGGT\nTCCCATTTTTTATTCAAATCAAAAACTCCATTTTTGGGAAGGAGCGGCGACATGGGTCGA\nCGAGGTCCCTTCGATTC\n>NODE_280_length_257_cov_0.836957\nGTAGGGAGAGGAATAGATGGGACAATGCGTAACGTGACTTTAAATCGAGGCCCCAGTAGG\nATGAAGAAAGTTTCGAATAACATCTCAAACATTGTTCGTCCTGCGCGTACCGGCATACGA\nTACCAACGACTGACCAATGCACATGGAAATGGACACGGAAACAGTTCGACGGACGCCTGA\nGGTTCTGGCTCGTTTTGAACTAGCAACCTTATAAAAGTTAGGCAACGGAATGTAAACTTT\nTATAAGAAGGGTTATGG\n>NODE_281_length_257_cov_0.836957\nGTGCTCGACGGGATGCTCGCCCGCTACAAGGACTTCCTGTTTGCGGTAGATCCGATCACC\nCCCGCCGATATCGCCACCCAGCAACGCGTGGCGGATTATCTGTTGGCGGCGAAGGTCATC\nCCGAGGAAGATCGATGCTGCGGCAGCAACGCCAGATGCGGAATGGTCCGCACCATCTGCA\nAGGTCGGGTCGAGCAACCGCCGCGCGGTTGGCGACACACCGCACAACAGCCCGAGCAGGA\nAACTGATCGCGCCGCCC\n>NODE_282_length_257_cov_0.836957\nGGGATTGGCTGCTGAACTGACTTTGCTGACCAAGGTTGGGTCAGCTTGACAGTGAACGAC\nGGTCACCAGAGCATCGCGAAGCGCATCCTCCACCAAAGAGTTTCCGGTGCGCGCTAAAAT\nCACGAGCGGCTGTCCTTCGCCGGAAAGTCGATCGAACAGCATCCAAGTGTCAGCGTCGCC\nACCAACAGATTGATCGATCGGCGACGTCACTCCAACATCCCCACAAACTTCTCGAACAGA\nTACAGGCTGTCCTGCGG\n>NODE_283_length_257_cov_0.733696\nGGGTGATGTGGTGCGCGAAATGGCCAAGGCTGCTCCGCAGGCGCCCAAGCTGCCCGAGGT\nGCCGCCACCTGCTAAGGCCTCGCCGCCCCCGGCGCCGAAGGTTGATCAGTCGTTTTCATT\nCTCGCCAACCATCAAGCTGGATGTGCAAGGCGATGTGAAGGATCCGGCACAGTTGCTGCG\nTGAGATGGAGGGCGGTGTGCGCGGGCTGTTTGACGCTTGGCAGCGCGAGGTCGCTGCGCG\nCACGGCCTCGTCCCAGT\n>NODE_284_length_256_cov_1.661202\nGATACTGGCATGGCTGCGTTGGGCGTGCGCAGCATTGCGCAATGGCGCAACGTGCCGGGT\nCGAGTGCCAAGCGTCGGATCACGCCCAATAGCGGACATTCGATTTAGCTACACGCAACAT\nCGCAGTGCGATGGATCGCGCGCCAAAGGCGGGTTGGAGGGGCGGGCAAAGCAGCATATAG\nCTGCGGGCATGATAGTCGTGCACGAAGATATAACACAGTCGGAGCTACTGTGTAGATATG\nCCTCGGGGCAGAGGCG\n>NODE_285_length_256_cov_0.841530\nGTGTAGAGCCAGCCGGGCAAGCTCCAGTCGGCGTCGGGATCGTGATCGGCCGAGGGGGGC\nATGCGTGGCTCCGGTTGCTTGTTGTACGATCGTATAATAGGAATTCGCCGACTGCAACAG\nGAACGGATCATGAGCAAACCCGCTTTCTCCCGCGCCGAACCCGATGCGCGCCGCCAGTCG\nCTGATCGAGGCGACCGCGCGCGTGCTGGCGCGCGACGGCGCGACTGGCGCATCGGTGCGT\nGCGATCGCGCTGGAGG\n>NODE_286_length_256_cov_0.841530\nGGGGAGAGAGCCTCAATCGTCGCGTTTCTTCGGGGATTTTAGGCGTGCCATATCAGCTTG\nTTCTTGGTGCGTTCGCAGATCGAGGGGTTACAATCGGGGGATTAACCGGCAAAACCGGTC\nCCGGCGGGGCGTTTTCCCCGAAAATCCCCGGTGAAGGGGGCGTCACCGAACGGGTGCAGC\nAGCAGCCTTTGACGAAGCAGCATCGCTCTGATTGCTGGCGGGGGTAACGGCACTGGGCGC\nGACGCCGAGCTCGGCC\n>NODE_287_length_256_cov_0.841530\nGGCTGGTGCCGCGGTCGTGGGGCTGTACAACGCCAGCACGGGCAGCAGCGTCAACTACGT\nGCGCGAAGACCCGCCGTTTCTGACCCGGGGCGTGGATGTGCTCAGGGTGCTGGCGCTGAT\nTGCAGCAGGTGGCGTGGGAGCAGCCCAAGGCTGGGTGAGCCCGCTTCATGGCCTTGGTGC\nTGCGCTGGCCTATCCCATCCTCGCCCCGCTGTGTCGGCTGGTGCAGCGCCGACGGCTGCA\nAAGCGTGGTGGACGAT\n>NODE_288_length_256_cov_0.841530\nGTCACGCCCGATGGGCGGATTAGACCGGACGGTGAGAAGCTGCTTGCTCGACGAAACCGC\nACGTCGTGAGCCAACCGATCTCTGAGACAATTGCGCTTCGCCCAGGGTTTGAACGTCTCC\nTCTTCGGTGTGCTTCTCGCATCCACCATCGGCGATGAGATTACGCAGGTGGCGCTCGTGT\nTCCGGGTAGCTCCGGCCGGCTCTGGTCCGCAAATAGCAGCCCTGCTGATTGCGCTTCTGC\nTGCCCGGTGCTTTGGT\n>NODE_289_length_256_cov_0.797814\nGCTTATTCCTTGCGCACGTTTTCATCTGCCTCGTGAGGCGCTTGGGCGTTTCCGCCATGT\nGGTGTGTCGTCTCTCATGGGGGAGACTCTATAAGCGCGCCTGTTACTTTCAAAACAGTGA\nTACGTCTTTTTTCGTTGCTCATAAAAAGAAGTCACGCTATTATCCGTTACCAGACCTCAT\nCGAGGATTTAGGGATGGAAGACAAGATAGGAGTATCCCTTCGCGAATTCGCGGAGGGACG\nAACGCAGCCTCAACTG\n>NODE_290_length_255_cov_0.846154\nGGCCACCACATCGTCCATGGAGGCGATCTCCAAGAACGAACGCGGTGCCCTGGTCGCGCA\nGGAGATCGCCTCCATGGACGATGTGGTGGCCGTGGTGGGCACTGCCAACAACTGCTTCTA\nTTGGAGACCTGAGCATGTTCAAACTCACATACCTGCCCATCGTGCTGGCGGTCAGTTCCA\nGTCTGAGCTACGCCCAGAACATCAAGATCGCCCTGACCGGCCCCTTCAGCGGCAGCACCA\nCGCCCGTGTTGGCAG\n>NODE_291_length_255_cov_0.846154\nGGATGGCACCGACGAGCTGAAGCTTGTCGATGAACGGTATTCGATTGGATGGCGAGACGA\nTCGGGACAAATAACTCGCCATACCCGAAGCCGATATCTTGGGTTTGGGCAAAGACATTGA\nTGACCGATACGACGCCGCCAGTCACACGGCGGGAGTCGACGACAAGTCTATTGGACCGAA\nAGCCGGCTCCGAGCGCCAGCCGGACGTCGCCGCCTGGCAGCGTGAACAGCGGGCCTTCGC\nCGCTCAGTTCTATAT\n>NODE_292_length_255_cov_0.846154\nTTGCGAAGCAAGGTGGGGGTGAGTCGCCCCGACCAATCGTTTATCTGGGCCATGCGCTGC\nACATGGCTGATTGCCAGTTCATCTTCTTGTGGATTTAAAAGCAATGCGGCCTTCATCTGA\nTTGCCCTAGTCATTAGCCAATTGACGCCATTTGAGTTTCCCAAGGGAGCGGATAACGGCC\nGCAAGGTTGATTTCATGCTCAGGTGTCCCATCCCATACATCTGCAACTGCTGCGAGCAAA\nAGGTCGCTCTCACGC\n>NODE_293_length_255_cov_0.846154\nGTCATGAGAGCCGCATGAAAGCTCTCTTGGATTCGGCTCTTGGAAGATTGTTCCAGTGCG\nAGCGTCAGCGCTTCAGCAAGCCGAACCCCGTGCTTGCGTCCGTCCGTTTCGTTCTGAAGG\nATGTCGAGACGTAGATCTGTTGGCTGCTCAGGATCAGACGCCTGCACCAGTTTGCGGGCG\nGAATTGCGAAAGAATTTCTCGGCATCGCGTGATTCGTCATGGGCACCGCGAGCCAGTGAT\nCCGAGTAGATTGAGC\n>NODE_294_length_255_cov_0.846154\nGCCATAGCGGAAATCGGGTGAGAGCAGGCCGCTATTGTTGCCTTCGCCGACAGGATTGGA\nAAAGGCGGGCAGCGGCAGCGTCGGCAAGCCGAACAGGTTGATGCGCGCGCCCGTATAATA\nGATCCGGCCGCGATCGGGGCGATAGAGTACGCGAACCGCCGTGATCTTCCATGTCGGCTC\nTTTCGGGCAGTTGCTGGAATCGGTCACCGCGCACGGCGTGTACGCCGCATCCTCCAGCAC\nGACGACTTCATCGAG\n>NODE_295_length_255_cov_0.846154\nGTTCACATCCTGCGCGACGAGATCGTCGACGAAATCGGCGACCTTGGCTTGCAGCTTGGT\nGCGCACGCCGTCTTCGACCGGGACGAGACCCACCGCCTTTTCGGGCGCGAGCGCGGGCAC\nCGGGTCAGGTGGGGTCAGCACCAGGGGGGTCGTTTCGCTATCGGCAGCGGTCGCCATGTC\nGTCACTCCAGCCGGGGATGCCCCTAAATGAAGCGGAATGCTGCGGGGTTCAAGTGTATCG\nTTTTTATAATACACC\n>NODE_296_length_255_cov_0.846154\nGAAAGAAGGTGTCGATCAGCTCGAATTCGCTCAGGCTCATGGCGACATTGTCTCGCCTTT\nGGCCGCGGGCCAGCCCAAACGTCAAAGGCCACCCAACGAACCGATCGTGGGTGGCCCCGA\nCTTCGGTCCACTTTCCTGATGGACCCCCCTGAGCAAATGCCTGTAATTGTGTGGGTGCAA\nCGATAGCATCGAGGTGGGCTCAAGCCCCTCATCTCACGTCTAAACCAACGTTTAAACCGG\nCGCCTCGGCCAGGAT\n>NODE_297_length_255_cov_0.846154\nGTATTTTGGCAGCTCTTCACAGTAAGGAGCAGACCGGAGAAGGAGAAAAGGTTACAGTTT\nCATTGTTCCATACAGCAGTATTCGGGCTGGGACTATATGTGAATGCGGCACAGTACGGAT\nACAATATGCCTATCACTCGCAAAGAACCGCCAAACCCTCTAAACACTACTTACAAATGTG\nCTGACGGAAATTGGCTTCAATTGGCATTTTTCCAATATGACAAGTGGTTCCCGGGATTTT\nGCGATATTGTAATAG\n>NODE_298_length_255_cov_0.835165\nGGCTCGGTCCTCAATGGCGGCAATTCCGGGCCTGGCGGTGACGATTTCGCGCTCGCGCCG\nAAATGGCTGGCCTTGGCCGACGCCTTTTATGATGCCTCGGTCGATCGGTCTGCCGGAGGA\nTCGGGTATCCCGATCCTGTGGGGCATCGATGCCGTCCACGGGCATAGCAACATCATCGGT\nGCGACGTTGTTTCCACAGAATATCGGGCTTGGTGCGACGCGCGACCCTGCGTTGATCGAG\nCGGATCGGTGCCGCG\n>NODE_299_length_255_cov_0.785714\nTATCCAATGGCGGATTCAAAGAACATTGTATGGGCAGTACTACCTGAATATGTTGGTATA\nTCACGAACAAAATCATCAGTTACAACTGCCTCATGATCAAGACTTGTTATCACAGTCGAT\nCGATAAAGAAGGTCAAATTTCAGTTCAACTGAATTTGCCAAATGTTTCTATTCATACTCT\nGAAGCTTGAGCGTGATAATTTCCAAGGCATTAATTTAGCAGAGTGGAAAGTTATTTTTAA\nCAATATGCTCTATCC\n>NODE_300_length_255_cov_0.659341\nATAAGACGACCTCGCTTGGCCCACACCCCTCGGAGCGGTTTGTGCCTAGCGATGTCGTCT\nTATTCCCAGTACACATCATTCCAAATGCCGAGTTTTCGCGCCGCTTATCTATAGTCTTAC\nAATGTTTGAGGCTTCTATGTTCATTTTAGCGGTCTCAAGTCACCGACAATGTATTGGGCG\nGAACTCGCGGAAGTTTAATACGCGGATTTGTGTTTATTGTACATAGACGTTGTCCCTAGA\nTGCCCGAACCAAGCT\n>NODE_301_length_254_cov_1.215470\nTCACGGCCCTGATTGCCCAGGATTGCTGCGATCGTCATCGGCTCTCTCCTACTGCGCTCG\nTCATCCGAGTCTCTCAGGCGCTTGAGGATTTCACGTTTCGCGATCTATGGGAAGCAATGA\nCGACTCCTTCCGGCCTCGATGATCCTGCTTATGCGGCCTTCGCCTGGGCGCGCTTTCGCT\nGCATCCTCGGCTGGATGGCGGTGCTGGCAGCGGTGTTCATCGTCGCGGCGATCGTGGTGC\nTGCAGCATTTTTAT\n>NODE_302_length_254_cov_0.972376\nGCCGAACAGCAGCCAGCCATAAAGCGTGCCCCAGAACCGGCTCGAATAATCCATCGGGAT\nCACGGTCGAGACCGGCGCGCGTCGCAACTGGCGTTGCCCGCAGCAGTGCGCCACGCGCCG\nGTCTCGACCGTGATCCCGATGGATTATTCGAGCCTGTTCTGGGGCACGCTTTATGGCTGG\nCTGCTGTTCGGCACGTTACCCGGCTGGGGCACTGTCCTCGGCGCGCCGATCATCGTGGCG\nAGCGGGCTCTACAT\n>NODE_303_length_254_cov_0.850829\nGGCGATGTTGTAGAGCAGTTCTCCTCGCCTATTCCAATCTACTTTGGACATGGCAAGGCG\nAAAGTATCGTTCAGCATGGTGTGGGTGGCCCAACTCACTAAAGCAAGACCCAATAGCCCA\nGAGCGTATCAACTTCACCTTGCGCGAATGACAAAGCTTTGAAGAACATCGCTTTGGCCTG\nCTTCAGTTCACCAGCTCGATACAGTAGATCGGCCTTGCGATAGAGGGCCAGGTGCAATTC\nCCAGTTCTCGACAG\n>NODE_304_length_254_cov_0.850829\nCGGCGGCGGCGATGGCGCAGGAAGGTGCCGACCGGCCGCATCGCGGCGAGGGTCAGGGCC\nAACGCGAAGGTCGCCCGCAACGCCCGGCGATGATCGGAGACGAAGGTCGCCCGCAATGGC\nGGCGTCCGGAGGGCCAGCCGGCCGGGCAAGCGCCGGTTGCCCGTCCGCCTGCACCCCAGC\nCGCAAGCGCAGCCCCAACCGCAAGCACAACCGCAACCGCAACCGTCTCAGCCCCCACGGT\nGGGATGGCCGCGGT\n>NODE_305_length_254_cov_0.850829\nGCTTCTGCACCATGTCGCAGAAAATGCCGGCTTCTTGCGCGAACAGCGGATCGGTGTGCT\nCGCGCGCCGCCATGTCGGCGAGCAGCAGCGCCGCCAGATCGCGCTGTACTTCGGCGTGGC\nAGATGTCTGCTTCGGCGATGCCGGCGTCGCTCAGCATCGGAAACACGATCTCGTCTTCGA\nCGTCGCCATAGCGCAGCCATGTGCGACCGAGTTCACGCAGTTGCGCGTGGGGCTGTTGGT\nGAATATGACCGGCT\n>NODE_306_length_254_cov_0.850829\nTGGGGGGATCAAGGAAAAAGTGCTTGGTGCACATCGTGCGGGATTCGCAAGATGATTCTT\nCCTAGACGCAATGCACGTGAGTATGAAGACGACGTACCTACGTCTGTTAAAAGCGACATC\nCACGTTGAATACGTTCGTACGATCCAAGATGTGCTGTACGCCGTGTTTGGGGCGAGTCTC\nGAAACACAAATCAGCACCTTGCACGGCGGCCTCGAAGGGCGTCGTCGTTTGCAAGAGCTT\nGATTGGCACAGTCG\n>NODE_307_length_254_cov_0.850829\nTGTCACCTTTGCAGCTCCTCGCCGGCAAGCGGCTCGACCATGGTATCGGCCGCGCATTGA\nGCGACCTGAAGGCATTGTCCCTTTCGCCCAGCGAACTGGGCGTCGATCTGCTCGTCGTGG\nCGGCTCATGTCCACGCCGCCGATACGAGGATCGCGCGCGCGACCGAGGCACAAGACGCAT\nGGACACGCGAAATCCGGCTCGTGGTCCCGGTGAGCGACCCCAATCTTTGGACGGGCGCCG\nCGCCGATCCTCGTG\n>NODE_308_length_254_cov_0.850829\nGTGGAAGCGCGCACCAACGGACAGCGATGTCTTGCTCATCACACGTGATGGCGTTTTCTT\nGCAGCAGATCAGCATCAGCCGCTACAGACTGTCTGAAGCCTTTGCAGGTGAAAAGGTCAC\nAGCTGACACGCCGCCCGAGCAACTGGGGCAATGGCAGCTCAAGCGCTTCAAGGAGGATGA\nGCCCGATCTTGTACGCAAGGTTAGCGAGGAGTCAAAGGGGGTGCTGGCCATGTTTCCGGT\nAGCCAATGCAAGAC\n>NODE_309_length_254_cov_0.850829\nTTCGGGAAGTTCGAGAAGGAATTCCAAACAGACCTCCCGCTGCGCCCGAAAGGCCTGAAG\nTCCGACATCTCGGTGAATGACGTTGACTCCGATGAGATGCGACAGCGCGAGCAGCGCGGC\nGGCGGCGGCGCGAGATTTGCTCATCCCCATGTCGCGGTAGATTTCGGCGATGATCGCGAG\nTCGCTCACTATCGACCTCGGAGATGGCGCGGCGCGCCAGTTCGGAAGACCGCGCCCATTC\nGCGCAGCGCATGTT\n>NODE_310_length_254_cov_0.850829\nGCACTGGCAGCTACACGATCCTCGCGCAGATTGCGGGCGAGGCGCTGGGGCTGCCGATGG\nAGCAGATCGACGTGATCCTGGGCGATACCGATTTGCCGCCGGGCGCGGGCTCGGGCGGGT\nCGTTCGGTGCGGCGAGCGCGGGGTCCTCGGTCGCGCTGGCGTGCGAGGACATCGTCGCGA\nCGCTGGCCGAGCGGATGGGGGCCAAGGCGCAGGACATGACGTTGAAGGACGGTCATGCGG\nTCGCCGGCAACCGG\n>NODE_311_length_254_cov_0.850829\nGTGCATGCCCGTCAACTCCCTGCGGAACTGATTGTCTGCCAGGACCCTTTCCAAAGATGA\nCTTTCAAATCCTTAACCATATCAAATACCTCACCACCAGTATGTTTCGCAGGCTTTGGCC\nGGTGATCTGCCTTGCCGTTGAAATGCTTGCCTTTCTTTCTTAATTTATGATGTCGGGGAA\nGAAATCGACGATGCCCCAGGTACACGTTCTTCTTACAATTACCCAAATATATACTTTCAG\nTCTCATGTAAGCAG\n>NODE_312_length_254_cov_0.795580\nAGAAACCAGTGTCCGCCGAGCTGACTAGCTTGATCATGACCGTGGTCGGCTTAGCCATTA\nCCAGAATTCCTGTCATCTGAAAATTCACAAGCGGCGAACCGGTCGCCGCTCAAAAGCGTC\nGCCCGATGAAGGAAGCAGCGCGTGATGTCCAGCACGACGGGAAGATTCGGCAGGGCTTTA\nGCGCGTGTTTACCACCGCGCGCGCATGATGCACGTCAGTGGGGACGAAATATGGCGGCAC\nCTGACAGCGCATTC\n>NODE_313_length_254_cov_0.773481\nGACCATGGAAATAACCAGCCCGACGACCAGCATCAAAATGAGCGGAGGCCCGGCGATGAT\nCATGATGACCCAGAGTGCCTGGCCCATCGAAACCGAAAAAGGACTGTAGGTCTCCAATTC\nGCCTCCCGCGGTGACGGGGTCGCGGCGCCAGGACGTGCGCCTAGCGATCCTTGCGGGGCG\nAGGGGCGTGGAGCGCGATCATTGCTTCCGATCCGTCTTCCCCACGTCCACTTGCCCCCGC\nGCCACGCTGCGACC\n>NODE_314_length_253_cov_1.283333\nAGCCAGTAGTCGATGTCTGGGCCAATTCTAGCTTAGAGTGTATTGCTGAATCTTTGCCCA\nTGCTATGTTTATCTTGGAGCCTTACACGTTCATAGTGGGAACTCACATGTTTGTTCAAGT\nGATGTGGCGCTCTGCCAATGCCACAGATAACAGGTCAATTGCAATACAACTCACATTTTT\nGTTCAAGTGGGAACTGTTCGCAAAATAGGTCACGTATAACCGATAACTGTAATATTTCAT\nAGTTCAACTCCTT\n>NODE_315_length_253_cov_1.283333\nGAATGGAGCGAGTTCGATCTGGAAGCTGGCCTGTGGATTATCCCTGCCGAGAAGATGAAG\nATGCGAAAAGCCCACCATGTCCCACTGTCGCGGCAGGCAGTCGAACTCTTTAAATATCTG\nCAAGGGATCACAGGGCCTTCGGGTTATGCCTTTCCCTCGGTCCGCAGCCGGGCGCGGCCG\nATGAGCGAGAATACTCTGAATGCGGGACTGCGACGGCTGGGCTATACCAGCGACGAAATG\nACCGGTCATGGAT\n>NODE_316_length_253_cov_1.272222\nCGCGTGACCCGCTAGACCATCGTCATGGTGGGGATGACAGACGAGGAACGCGCAGCAATC\nGACCATGTCGCGACAGCGCCAATGCTGGCGCAGGTTGAAGCGTGGTCGGCGATCAATTCG\nGGCACACGCAATCTCGCAGGCCTGGCGCAAATGGCCGAATTGCTTGTGGCGGCTTTCGGC\nACGCTTCCGGGGGAGCCGGCGCTGGTTGTCGGCAACGCCGCACAGAACGTCGCCCCCGAC\nGGCACGGTGACGG\n>NODE_317_length_253_cov_0.855556\nCGGTTGTTCGCGGCGCTCAACATTGGCGGACTGGCCCTCGGTATCGCGACCTTCCTGGTC\nCTTTACCTGTTCGTGCAGTTCGAAAGCGGTTTTGACCGCGTCTTGCCCGAGCAGGACAGA\nCTGTGGGTAATGGAAGAGCGCTATGTCATGCCGGGATATCCGCCTGACCCCGCATCAACT\nCTCCGGCGGATAGTCGGCGCGTAACTGAACGAGTTCGCTGCCCATCGTGTTGGGATTGGG\nGTCAGGCGGATAT\n>NODE_318_length_253_cov_0.855556\nGTGGCATATTTGCGGTGACGGCTGCAATAGATCACTGGAAAGATTTCAGGGATGGGGTGA\nAAGAGTTCTGGTTTGCCGATTATCCGAAAGCGGAACAGGAATAAAGTCAGGCTTTTGACA\nGTAAGGCCTGTACCAGCAAGGTAAGGGCATTCCCAGACCGCAACCGGTTTACATCACGGT\nGGTTGTAGAAAAAGCCGCGGGCACTGACCAGTGCAGCTTCCAGCTCAAAAGATTCCTGAT\nCTTCCTTCCATGC\n>NODE_319_length_253_cov_0.855556\nGCCTTGCGCAGGAGCACCAGGCGGCGCGCTTCGTCGTCGAGCATGGCACGGGCGTTCCTG\nACGACCGCCTCCGCGTGCGCCGGCGGGAACTTCACGGCGCCGTTCTCGTCCATGTGGATG\nAGCTCGCCCGGCGCCACGTCCATCCCGCCGATCGAGACCGGAACGTTCACCGCCTGCACC\nGCCATCTCGCCGTGGCCCGCCGTGACGCCGCCCAGCAGCAGCTGGAAACGAAGCTTGCGG\nATGGCGTCGATGT\n>NODE_320_length_253_cov_0.855556\nGGCATAGGACGAGATTTGCTGAACCAGCAATTCGAGGGGATCAACCCAGTTCGGTACATG\nATCCTATCGAACGGAAAAAACACGCTTGTGTTCGAATGGACAGAAGGCAAGCCGCTCATT\nGACGCAGAGTTTCACGAATTTCAGACGGGTCATCCCAAGCTGAAGCGCATGCAAACCCTG\nCTTGCGCCAAAGGCAACCGCCGATGTTGCTAGTCCTGTCCAAGCAGCGCACCGCTTCGAG\nCGCAAGTCTATTG\n>NODE_321_length_253_cov_0.855556\nGAGATAGTCGTCGAGGTGGAAGCGGTCATAGGAGGTGACGGTGATCAGGTTGGAATCGCC\nGAACACGGCAACCTCGGTCCGCAAATATCCGCCGCCGCCCGAATATTTTGTACGCGCGTC\nGAAATTGTTGCTGACGTCCTGGTTTTTCTCGCTGATCGTCACGCCCGGAAATACCACTGC\nGGGGGTAAGACCAGCCTGTCCGCGGAACAAAGCATTGGACGCGACGCGGATGAACGGACG\nGCCGACATCGGTG\n>NODE_322_length_253_cov_0.855556\nTAGCGAGACCTTGCGCGATGTCATCCGCCAGATTCTTGCCCATGTGATGGATCAGAAGGT\nCGGAGTAGGGATGTACGGTCAGATTTTGCAGAGCCGCCGTTTCGCTCCTAGGTGGCGTAA\nCCATCGTCGGTGTGTGGCAAAGAGCGCAGCCAATTCCGGGACGATCGGCTGCCGTGCCGA\nACAACTCTTGTCCACGCAAGGCGCTTGCCGAAAAGGTGGCCGGCCTCGGCGCGTCCAGAA\nAGCGCATGAACAT\n>NODE_323_length_253_cov_0.855556\nGGTTGTAGGAGCGATTGCCGTCCTGACGCCCATCCTGACGATTGCCGTCCTGGCGATACC\nCGTTTTGCTGGCCGTTGCCGTTCTGGCCGCCACGCTGCTGATCGCCGCGCGGCTGCTCCG\nGAACGCGCTCGCCCTCATCTTCATAATCGGGCTCGTCTTCATCGAGGGTCGCGCCCTGAA\nTGCGGCGAGTCGACGGCGCGCCGCCATTTTCCTCGAGGCGCGCGCGGGTCTCGGCCAGCA\nCACGAAAGTAATG\n>NODE_324_length_252_cov_1.653631\nGATCATGCCTGGAACGTGACACACGTCGATACGGCGAGCGAGACGAGCTGGCTGACGGGT\nCGGTTAACCTTCATTCGCGAGCCGCTGGCGGAAGCGCTGAACGAGGTTAACCGTTACTCC\nGCGCGCAAGATCGTCTTTGTGGACGGGCCCGCACCGGCGACCAATATTGTCGGGGTGTTT\nGCCGCCGGCGATGTCGACAGCTTCGTTACGGCGCTGGAGTTGAACGGAATCGCGCGGGTC\nTCCGATCGCACC\n>NODE_325_length_252_cov_0.860335\nTATGAAGGCCGCGCTGCAACACCGTGACCGCAGCCTTCATATCAGGTGTTAGGCCGTCTT\nTGCCGAGCAATGTCTCGGCAATCTCCGGAATGGCAGCGTCAGGGATCGCCGAAGGGGATT\nTCCACCGCGACTTCAACTCGGTTGGCAAGGCATCGTAAACCCGCTGCGCCGCCGAACTGC\nTCGCCGAACCGATCGCACCCACCAGCGGACGGATAAGATGGAGCCCAACGCCCAGCGCAG\nCACCACCCACCC\n>NODE_326_length_252_cov_0.860335\nCTCTATGTTGATGTCGCTTAACGCCTGAACTACACGTACGCCGGTCTCTTGTCCGAAGCG\nGCCACCAGTGACATACGACGCGATCGTTTTTTTTAGCGAGTTTGCACCTGCCCCGTAGAT\nTTGAAAGTTAACGGATACGTTTTTGAGGGAAATGAAAGCCATGGTTCTTCAAAGCCAGTA\nGACAACGCGGCGGCGATACTTGGCGAACAGCGCACATGAAATAATAATACTCACCGCTGT\nCCACCCCAGGAT\n>NODE_327_length_252_cov_0.860335\nTCATAATAGTCCGCAAGGTCGATCGGTTGATCCAACTCGCATCCGATTCGGCCGCCAAGT\nGCCCAGCGGATTTCCGCTACCACGACACCGACCACCGGCAACGTGACGCGTAACCGGTCC\nCCCTCGCGATACGGAACCTCGGCGCGCGCCATGAGGCCGAGCGCCGACAGGTTCACGATC\nAGCAACGACACCTGTTGTGCGTCCGGGCCATAAGCCCGAGCGCGATAATGTACTTCGTCG\nCGGGCCAGGGCG\n>NODE_328_length_252_cov_0.860335\nCTACAAGGTGGGCAACTCGATCCCCTTCGGTTCAGAGCAGGCTGCTTAAACCCCAGTCAT\nCTTCAACGACATCATCACCCTGGCTGGCGATATCGAACTGGCGCCTAACTGGCGATTGGT\nGAGCGAGCTGGTGCGCAACATCCAGATGCGCACGGAGAACGGTGCCAACACAGCTGGCGG\nCTACTTGGCCGTACTGCACAAGGTCGGTGATTTCACGCCCTACGTGAGCTATGCGCTGCT\nGCGCTCCATGGG\n>NODE_329_length_252_cov_0.793296\nATGGTAAGAATATAGTTTAGCGGCGCGAAAACAGGGAATTTGGAATGATGTGTACTGGGA\nATAAGACGAAATCGATTGGCACATACACCGCCTTCCGGAGAGGCCATATCGACGTCGTCT\nTATTCCCAGTACACATCATTCCAAATTCCGTGTTTTCGCGCCGCGTATCTATAGTCTTAC\nCAAGTTTTAGGCTTATATGTGCATTTTATCGGTCTCAATTAACCGCCAAAGTATTGGGCG\nGAACTCGCGGAA\n>NODE_330_length_251_cov_1.443820\nACAACAATGGTAAGGGCCCAGCCTCACCTAAGCTCCCTCCAGCCCCAGTTGGTTGGGCTT\nGGTCCCTTAACCAGATCCGTGGCTTTTGGTTAGCAGTGACAAGAACTGAGAAACATTGTC\nCTACATGAACGTCAAGGGATTCGTATGTGTTTTGGACTGTGTGGGAGCCTTCCATCTCAA\nCCAGCTTCATAGCGTGACCTTGGATCCTGAAGTTGAGGGATGCCTTAAGCCCAACATTGC\nAAATTCTGTAC\n>NODE_331_length_251_cov_0.865169\nGCCCTGTATCCTTGCCCAATCAGGCAATCGTGTTGTGCAGCGGTGGAAGTGGATATGGGA\nAACGAGACCGTGGTCAAGGGCTTTAGCCAGACGGAAGGTTAATATGGACGCTAATGAGAA\nGCTTCAGTACGCCAGGACGATATTGTCCGTTAGCTCTCCGTTCTTCGCTACCTTGGCTTT\nGCAGACCAAGGTGTTCTTCAAGGGACCGGAAGAGTCCCCAATACCGACTGCCTGGACCGA\nCGGTCTGCATG\n>NODE_332_length_251_cov_0.865169\nGGTCCAGGCGGTGTCGTCGGCAAACCACCCGGCATCGGTGTGGCCATGCGGGCTGACGAT\nCGGCAAGTCCGCGATTTCCGCGTAAAGCGTGCGCGCAATGGCCCGCGTCGTTGGATCGCT\nGGGAAACAGGCGATCGGGGTTCAGGTCGAGCGGCCGTGCCATTGTCATTCTCCCTCCCCG\nCACTGTTTTATGCGGGCTCTGGTAACCGGTGTCAGGTTGGGTCGCAACCCCGTTAGTGGA\nTGATCTATATG\n>NODE_333_length_251_cov_0.865169\nGGTATTGCCGATGTATTGTTCTCGGGATTGCGGCGACGCGGTAGTTGACGGCTCTTGAGC\nAGCTTCTGCTCCGTAGGCAATCGCTGCCAGGATGTCCTCGCGCACCAGGTGCGGACGAGG\nGAAGTGGGGATTCTTGAATCTTGAGGTGGCTTTCGGAGTTGGTGACCGGAGGTTACCCAT\nGACTGTCGACCCCTGTGCGGACTGAGACGCCCCCTAAGACGGGCGTGTCAGCGACGCTGC\nGACCGCTCTAT\n>NODE_334_length_250_cov_1.305085\nTATTCGGGCAGGCCGGGGATATCGACCGGATCGAAACAGAGCGTGTCGCCCTCGACTCGC\nATCCCGGCAAAGCCCATCGCCAGCGTCGTCCAGCTTCCCGCCAGGGCGGCCATATGCAGC\nCCGTGATCGGTATTGCCGAACAGATCGGACAAATCGGTCAGCGCCGCGACGCGCCAATAA\nTGCGCGGCGCGCGCACCATCACCGGCCCGCGCCGCGGCGGTGGCGAAGGCGCTGGCGGAC\nAACGTCGAAT\n>NODE_335_length_250_cov_1.305085\nGCTCGGGCACGGTCAACACGCGCACGACTTTGCCCACCCACGGTTCGAAATCTTCCGGCG\nTCGGCAGTTTCATAGTCATCCCCCAATGTACCGCTTCGGCGGCGTTGCGATTCATTGGTC\nAATGGTAAAGCCTGCCAGCATGGGCGCAACCACTCAGACGCCGGTCGATCGCCCTTTGCC\nGCGCTTTCCCCTTCCGCGTGCCGCGCCGCCCCAACTCTCGGCTACGCTCCAGGCTGCCGG\nGGTGCGGCTC\n>NODE_336_length_250_cov_1.305085\nGCTCGCGGTTGGCGGGTGTCGGCTGGACGACGTTTCCGCCGATGTGGCGATACAGGTGCT\nGGCAGCACGGCCAAGCGTCAGCGGCCCCGTCCGCGCCGCACGCGCTGACTGTGCGGGCGT\nGCAAGCGACGGGAGCAGCCGTCGACCTAGACGTGGTGCTGAACCGGCAGCTCGACCGATG\nGAAGGGAAAGGCACAGCTTGGTATCGCGGCTGTCGCGCGGAGCGGTGTGGGCGCGCGCAC\nGATCATGGGG\n>NODE_337_length_250_cov_1.288136\nGCGCTGCGGTGGCCGCTGTTGGCGTCCAGCGAACTGGTGACGTCGGCATCGACACGGTCG\nCCACGCAGGCCCACGGAGCTGCGCAGCCAGGGCAGCCAGCGTGTATCGTTCTGGGCGTAG\nAAGCCCAGGCTGTTTTCGGTGACGCGGCTTTCCTGGGTGGTGCTGTCGCGTTGGCCGTTC\nTGGGCCGTGTAGAGGCCAACCGGGTCCAGGTGATCATGGCGCCATTGCAGGCCCAGGGTG\nTTGCGGCTAT\n>NODE_338_length_250_cov_1.186441\nTCGTTGAAGGCCGCAAATGGGGGCTTATCGTCAGCCTCGGCATCGTCCTCTTCGTGTTGC\nTGGCCCTCTACGCTTCGATTCTCGGGGTGCTGTTGCCCAACCAGATCGAGAATCTCGATC\nCGGTCGGCAAGCTTGGGACGTTGGGCGTGGTCTATGCCATCACGTCGGTGTTCAGCACGA\nTCACCACGCCGGTGTCGGGCGCGCTCTCCGACCGGACGCGGTCGCGCTTCGGGCGGCGGA\nCGCCCTGGAT\n>NODE_339_length_250_cov_0.870056\nCCCTTGTACTGGTAGGCGTAGAGGTTCTGGCCGTCCTTCGTCTCGCCGACCTTGCGGATG\nTTTTCCTTGGCCTCGCGAGTGGAGAGCTTCAGCGCTGGATTGCCGAGGAATGCCGAACCG\nAGCCCAAGGATACCACCAAGCAAACCTTGGCTCGCCTGCATCTGCTGATTGTAGATGCCG\nAGCTTCTGGTTGTAGTTGTCGTTGACCAGGCCGGCGTAGTCGACATTCGGTATCGTCGGC\nATGTTGGTGT\n>NODE_340_length_250_cov_0.870056\nGCTCGCCACCGTGCAGACCTTTTGACGCAAACGGGAACTTGCCGGGAGGTTTAAACGTCC\nCGCAGACGGTCGCTCCGTTTGGCGGAGACTGCCGCCTCAATCCGGAGCCTCCCCATGACC\nGACCGTATGCTCTCTATCCTCGGCTGGGTGGCCACCTGCACCGCGATCGCGATGTACGCG\nTCTTACGTCGACCAGATCCGCCTCAATTTGGACGGGCACAAAGGCTCGATCGTTCAACCG\nATCGCAACGG\n>NODE_341_length_250_cov_0.870056\nGCACATGCCAGGCATCCTGCACATGGCTCTGCAACTCGCGACGCGCACGACCGAATATCG\nCATCGATCGCGGTGGCATCGTCCAGACGCTGAAACTGTCGCTGGGCAACCATGACATCGA\nATTTGGCGGCTGGTTCGAGCGGCAAAGCTCTTCGGCCTTCCGTCGCTGGTACGCGCTCGA\nCATCAATAACCCGTCGACGCCATACCAGCGCCCGCGCGACACGCTCAACCCGCTGATCAC\nCCAATATTAT\n>NODE_342_length_250_cov_0.870056\nGAAGAGAGCCGTGCATACTAGCTGTCGTATGTCCTCCCTATGTCGAAGCAACGACTTTTT\nCCGAGGGGGAGGGATGACTTTATCATCTTGTTGTAACTGTGAAGCACTTTCTACGACAAG\nGTGCGTAGCCGCCATGCTGCCTACTCGTTTGCCTAATGCTTGTCCAGGGAAGATGGGTGA\nTGTTTTGAGGAGGAGGGTGAGAATGATAGGACGCGTTGAGATCAGACGATTTGATTGGAT\nCTTAAAGAGT\n>NODE_343_length_250_cov_0.870056\nGTATGGCGATTTGTACGGTGCCATCGAGACCGCGCCCAAGCATGACTGGCGCGGCTATGC\nCCCCGGGCTGGTGGTGGTGCTGATGGGTACGCTGGCCGCCGGGTTCCTGTCTGATCATTA\nTGGCGTGCCGCTGACGCTGATGGCGTTGCTGATCGGCCTGTCGCTCAATTTCCTCAGCGC\nCGATGGGCGACTGACGCCGGGGCTGGCCTTTGCCTCGCGCTCGCTGTTGCGCTGGGGGAT\nCGTGCTGGTC\n>NODE_344_length_250_cov_0.870056\nGCAAAGGCTCCACTTCGTGGCAATCGTCCAGGGCCTGTGCCAAGGCATGGGCGTCGCTGC\nCCCCGCACCGGGCAGTGGCCAGCAGGCCCCGGCCCGGCGCAGTGGCCGCCAGTGCTTCTC\nGCAGACTGCCTTGCAGCACGGGATGACTGGAGACTTCCACGACCACCCCGTCACTGGCCC\nGCAAGGCCGTGCACAGTGCATCGAACCAACTCACCGGCCCGGCCACCGCATCCGCCCAGT\nAGCGCGGGCG\n>NODE_345_length_250_cov_0.870056\nGTCTTAGCAGTGGAACAGATGCGTGCCTATGGCGTCAAATCTTATGAGCAACCACTCCCG\nGCCGATCGTTTTGATGAGCTGGCAGCGCTCACCAAAATCTTTCCCGAGCAAATTTTGGCG\nGATGAGTCTTTGTGTACAGTTGACGATGCTCGTTATTTAGCCGATAAGAAGGTTTGCAGC\nGCCTTCAACATTCGCATTTCGAAAGTTGGCGGAATTCTGGCGGCGCGTCAGATTGCCGCC\nATTGCAAGAG\n>NODE_346_length_250_cov_0.870056\nCGCATAGGCTGCAGAATATGCGCTCTCACCGAGGATGGCGGCGATCGGCTTGCTACCCCG\nCGCGCGGTAGATGGTGTCGACGAGATCGAAGCAGCCGGCGACCTCGCCACCCGGGCTATC\nGAGATCGAACGCGATGGCATCGACATTGGGATCGGCGAGCGCGCGCATGAACTGCAGGCG\nCATGCGATCATATCCGGACATGCCGAACAGGTCGCCATAGGACCACAGCCAGCCGAGCCG\nCTGGATCAGG\n>NODE_347_length_250_cov_0.870056\nGGCGGGGAAGTGGCCGCAAGCCGCGGCGGCTCGCAATTACCCTTTGGTGCAATGGCGCTC\nCGGCGCCGCAGGGCGGAAGGTCGGGCCAGACATCCGGGAATCCCGGCCGAGTCCGAGGAG\nAGAATATCATGCTGCAACAGGCGCTCGACGAGCTTAAGGGCCAGATCGCGATCCGCTCCC\nGCTACGACAATTATATCGGCGGCGAATGGGTGCCGCCAGTGAAGGGCGAATATTTCGACA\nACCCGTCGCC\n>NODE_348_length_250_cov_0.870056\nCTGCTTTCCTTTATGAAAGTGATTGGAGTTTATCCGGCGGGATTGCTCATACGGCTGCCG\nTCCGATCGCCTCGCGGTTACCCTGCTGAACGGTCGCCGTGCATCGCGCGCCAAGGTGCGG\nGTGTTTTATTGTGCCCGGACCCGGACGCCCGTGCCGCTCCAGGATGTCTTCATCGAGGAC\nAACCTTTCCCACGATGAAATTCAGAAGGAACAAGACCCACTCGATTGGGGCATAGCCAAC\nTGGGCAGGCG\n>NODE_349_length_250_cov_0.870056\nGGACTGCACCCGCGTGCTGAAGGCTTGCTCGGGCACGTTCAAGGTGCTGGGCAATTCGGT\nGCAGGGTGGCGCGTCGATCGGCTTGATCGTGACCGAGGCTGGCGAATCGCGCGATCCGAC\nCGATCTCATGCGCCGAGCGGACCTGGCGCTCAACGACGCCAAGCGGGACGGGCGCGGCGT\nGGTGCGCGTGTTCGATGAAAGCATGGACGAGAACATCCGTCTGCGCCGCGCGATCGAGGG\nGGGCCTCTCG\n>NODE_350_length_250_cov_0.870056\nGTTCACGCCCGCGCCGAAATTTGCGATCAGCTTCAACGCGGGTCCCGCGCTTGCGATCAG\nCCCGGCATCGATTTCGTCGGTGACTGTGGGCACCAGCACATCGCATTCCGCCATGGCGGC\nGGCGAGTTCATCGCGGGTAAGGGCGGCGGGGCCGCGGTGGATAGTGGTGTGGAACAATTG\nCTCCATGCGGTCCATTACCGCATCGGGCAATTCGCGGGTCACCCAAACCTTCGGGTTGGG\nCACTCTCGGG\n>NODE_351_length_250_cov_0.706215\nCTCGGGGGATGCCCCCAGCCTCACCGGCCAGGTCGAAATATAGCAAAAAGCCGGATTGGG\nCGGCTTCATCATTACCGTTCGTTGCGCGCCGCGCAGGTCTTAGTCGAGGTTCCTGCTCCG\nGTCCGATCTCAAAATGAGCCCGCACCACTGCGACGTTATTTGCAAGGAGTTCGTCGATGG\nCAGCACCTGGAGGCGTTAGTTGCTTTGCCCATTTCAATCGGCCCGCCTCAGTGAGGTAGG\nCTCGGCGCCG\n>NODE_352_length_249_cov_1.176136\nCCCAAACAACCCGACTCGCCGACAGCGCCTCGTGGTGCGACAGGGGACGGGCACTACGGG\nGCTCTCACCCTCTCCGGCGCCCCCTTCCAGGGGACTTGGGCCCGGTCCGCCGCTGAGGAC\nGCTTCTCCAGACTACAATTCGGAGACGCCCGTGAAGGCGCCCGATTCTCAAGCTGGGCTG\nTTCCCGGTTCGCTCGCCGGTACAAGGGTTCCCCGAGTAACGGCGAGCGAACCGGGAACAG\nCCCAGCGTG\n>NODE_353_length_249_cov_0.875000\nGCATAGATGAGCCAAGGGTTGGTCACGTTAAGTTTGAGGTTTACAGTCTTAACGTGACCA\nACCCTTGGCTCATCTATGCAGACTCTAAGTTGAAGGGACAAGACCCTGAGTATTATCGTT\nATGGAGGTGTCTCACTCCCAACTCCTAAACAATATACGGTAACGCTCAACATACAATACT\nAATTATGAGAAAAACACTATACGCACTTTGTACGCTTGTGCTCTTCTCGGCTTGCAATAA\nGTATCTAAG\n>NODE_354_length_249_cov_0.875000\nTCCACGAGCATGGTGGCAAAGCGGAGGCTGCCATCATGCTCGTGGATGTCCATCCCGGCG\nAGATCGGAGATGAACTTCTGATAGCGAAAACGCTCGATATCGAGGATGAGCAGCCGCTTG\nTCGTGCTGAGCGGTGTTGCCATAGCGCTTGGCGCCGAGGAAGAGTCCCAACTCAAGCGGC\nATATTGAAGCGCGGAAGCTTGTGGTCGTCATCCAGCTCGGTTCGTGAGAGATCATGGATC\nCCGTAGCGG\n>NODE_355_length_249_cov_0.875000\nTTCATGACCAATCCGTCGCTGTCCGGTCGCGGTGCCTCGCTCGCCGCAAGCGGGTCGGTG\nCCGAAGCTGTCGCTGCGAAACCGGCGTTAGTCGCCCGATGGCGACGCTTCTGTTCCGCAA\nGGCGAAACCCGAAATCACGGGAGAACCACGCACCGGCATCATCGACATCGGGTCCAACTC\nGATCCGTCTGGTCGTCTATCAAGGCCCGGAGCGCTTGCCCGCGATCCTGTTCAACGAAAA\nGGTGATGGC\n>NODE_356_length_249_cov_0.875000\nTTCTAGATCCCTCTGAAAAAATCTTCCGAGTTTGCTAGGCACTGATACATAACTCTTTTC\nCAATAATTGGGGAAGTCATTCAAATCTATAATAGGTTTCAGATTTGCTTCAATAAATTCT\nGACTGTAGCTGCTGAAACGTTGCGGTTGAACTATATTTCCTTATAACTTTTACGAAAGAG\nTTTCTTTGAGTAATCACTTCACTCAAGTGCTTCCCTGCCTCCAAACGATACCTGTTAGCA\nATATTTAAT\n>NODE_357_length_249_cov_0.875000\nTTGCTCGGTCGAGCGGATCGGCGTCACGCGCGTGCCCGCTGCCGACGCGGTGAGCATTTG\nGTTGGGAAGCAGGGCGTTCTCCCTGCCGCCGGGGCCGCCGCTCACGCTCACTTTGCCCTC\nGAACAGAGCGACGGCAACGGCGTCCCTGTCGAGCCGGACATCGAAAACCGTGCCGTGCGC\nGGTTATCGTCCGGCCCCCGGCGACGACCTCAAACGGGAGCGCCTGGCCTTTGGCAACATG\nGAACACGGC\n>NODE_358_length_249_cov_0.875000\nCTGTCGCACCGGATCCCGCCGTCCAGGCCATCGTGGCCACCTGGCCGACGAGGGTGGACG\nGAGCTCGCGGAGTCTCCCTGGGACTTCGGGAAGCCGACGACCTGGCCACCACCCTGGCGG\nCGTACCGGAAGAGGTACGTCTGAGGGGCCGAACAAATAGTTCCCGAGCCGTCACAATCTT\nGAGCGGGTCTTGAGGTGGACCTGAGCAGATCTGAATTTTGTCCTGTGGTGAATCAATAAA\nGATTCCCGT\n>NODE_359_length_249_cov_0.863636\nGTGTTTCCTTAGATCTTCAGCCCCAATTGAATCCGAAATTTCCAGCAGTTGCATAGCATT\nCCGTGGCTCCAACAAATGCTCTGCAGTCGCCATCTCACAAAGGCTCTTTAAGGTAGGTGC\nATTATGGTTTTTGACATTGTCTTTTTCTGAGATAAAGAGAACTTCCTCTGACTCAACCTC\nATCAAACACAAAACCCTCATTGAGTTCATCTGGATCACTTTTCAGTTTCCGTTGGGGAGA\nCCCATTTGT\n>NODE_360_length_249_cov_0.823864\nGCTATTTTCTGAGCTTCCTGCGCGATCCGCGCCGCGGCGGCGAGCCGGTCGGCGCGACCG\nGCACCGATTTCACCTTGAGCTAAACCGGCTCGGGCACAATGCGGCCCGAACGATCGACCA\nGTTGGTCGGCAGGCGCGATCCTTACCCCGCGGTTCGTGCCCAATCTGCGCCTCTCGGTCG\nATTGGAGCCGGATCAGCAAGCGCGACAATATCGCCTCGCTCGCGACCTTGTCCTCGCGCG\nACTTTACTT\n>NODE_361_length_248_cov_1.760000\nGTTGTTGATAGGGTCCTTTTTCGGTACGGCCGTTCTGGGGCTGTATGCGCTGGCCGTGCG\nTTTCTTCGATGTGATCTTCCAGACACTGTGTGGTCCCGTTGCCGTGGTGCTGTTTTCCTA\nCCTGGCGCAGACGCACCATGATCTGGCTGAGCTGAGGGCGAGGTATCTGGGCATTTTGCG\nCAACCTTGCTTTGCTGGCTCCTGCGGTGTTTCTGCTGGCTGCCATGGTGTTGCCTGACAT\nGTTGTTGC\n>NODE_362_length_248_cov_1.365714\nCGCAAATACGTGCTGGCAAGCTCGCAATACGAGTGCGCGCTATCAAGCTGCGTAAATTGC\nTAACCTCTTGGCGCGTCAGTTGTCTCTCAATTTCTTTGTCAATTTTCCCCGGATCATAGC\nCACCGGCACCCGTAAGCTGCTTTGCTACTAAGCGAGCCGTGTTTTCATCATCCTGTGATC\nGTACGAATAGAAGGATTGAATTCAAACACGGCTCGCTTAGTAGCAAAGCAGCTTACGGGT\nGCCGGTGG\n>NODE_363_length_248_cov_1.320000\nGGGTCAGGTGCTCTCCGCAACGCTCGATCCGGGCGTTGCGCCTGCTTGACCGTTAGCGTC\nCTGTCTTTTCGCCCCGCACCTGCGCGACCATTTGCGTGATTGCGGCGAGAACGACATCGG\nGGCGGTCTTTCATCACGGCGTGCGAACTGCCGTCGGCGAGCATCGCGCTGCGTCGCGGGT\nTCGCTGCGACGAAGGCCGCGTGCGCGGCCCGCATCCGGGCTGCCTCGTCCGGCGTCTCCG\nCCCAGGAC\n>NODE_364_length_248_cov_1.320000\nGTGTTGCTGTTGCCGTTGGCAGACGCGACCACCTTGCAGTTTACCGTGCCGATCTTCGGC\nACGCTGCTGGGGGCGCTCATCCTCGGCGAACAGGTCGGCATCCACCGCTGGGCCGCGGTC\nGTCGTCGGCTTTATCGGCGTATTGATCGTGACCCAACCGGGGACCGGCGCGTTGCCATTG\nGGCGGGGCGGCGGTCGGCCTTGTCGCGGCGATGTTCGTGGCATTGGTCGCGATCCTGCTG\nCGCCCGAT\n>NODE_365_length_248_cov_0.880000\nCGCATTGCACCGCCGATGAATTTGCCAGACTGCAGCAGCTCAATGCGGACTACAACACCC\nGCTTTGGTTGGCCTTTCATCCTCGCGGTGCAATGCGTGAGACCGGCTTTGCTTTGCTCAT\nTGGTGGATTCGGCTGTGAGCTGCCCGGCCACCGCGGCCTTGCCTGCCAACTCGGGGTGAG\nCACGGATCAAGGCCTTCTGACGGTCTGCGCCAGCTTGTCTCACCACTTGCGCGAGCGCGT\nGCTTGAGG\n>NODE_366_length_248_cov_0.880000\nCTTCTGCACTCAATAACTACCGTTACCCCTTCGGTAATTCCACCTGCTACGGCAATAATG\nTGCTGCACGAACAGGGCTACCGCATCGTTGCAAGGCACGTCGACAGCTGTGACTGGGCTT\nTTGACCGGACCGGCACCGTTGATTTGCACGAAGCCGTCTCGTGCGGTGTGGCGGCGCTGT\nTCCGAAGTGATTTCGTGGGCCACGTCGCATGGGCCGTGCGTGAACGGCAAGGTGGCATCG\nTCCTGATG\n>NODE_367_length_248_cov_0.880000\nGGTTTGGCGAGAACCCGTTTCTGGCCATGCAGGCAAGCCAGCTTTGCCTGGTCGATAATA\nTGCTCAACCGGATCGAGCAGGAGATCTTGGAACGCCAGCTCGATGATGAGCCACCACGCG\nGCCGGATCGCGCAGCTCTCCGCCCTAACGCCTATGTGGATCTATGCCGCCTATGAACTGC\nTGCGCACTTGGCGTCAGCGATGCGAGGAGGTCATCAAGCTCGCTGAGAATGGCGGGATCA\nACCTGAAG\n>NODE_368_length_248_cov_0.880000\nATAGTCAGCCGCGCGCGTCGCTCGCTCCTGTCGGAGCAGAGAAATAGCTTGGTTGGTAAG\nACTTTCGCTCGCCTGTTCAGCCGGCGTATTTCTACGGCTCTGGGCCGAAATGCGGTCGGC\nGGTGGCTTTCGCCAGTTCCTCGTTCAGTGTTTCGAGATCGGTATCGGCAAGGGATCGTTC\nGTGGGTGCCCGCTGCATTGCTCCCTCCCGCCACTCCGGGAAGGTTCACGATTCCCTGCTC\nACCCGCGT\n>NODE_369_length_248_cov_0.880000\nGTACAAACACCGCGACGAAGTGCGCCACCCCGGTCGCCATTTGCCCGGATCGATCGGCAT\nTGGCACGAAACTGGCCGGCCAAAAAATCCGCCTGCCGGTCAAAATCGAGGTATTTCTTCT\nGTAGCTCCCCGCGGAAAAGGGCAAGCGCGTCAGCGGCATGCCCATCCCCGTCCATAGCGA\nTCATTCGCTGCTGCGCCTTTTGATATGAGTCCCAATCCTTCTCCATGGCATCGACCATCG\nGCCTGAGT\n>NODE_370_length_248_cov_0.880000\nTGGTTGCGGTGACGACGATGTCATCGCCATCGGGCGTGGTTTGGGGCGCAGGAGCCGGGG\nGAGGAGTGGTTTGCGACAGGGCGGGCGTGGCAGAAAGCATCGCCAAAGCCGACGCTGCAA\nGCAATTCGAACTTCTTCATGATGGCATCCCCTTGATGGTCAGCCCCAATCTCATGTCGGG\nTGCTGGTTTTCGAATGTACGGTTTGTGAAATAGCGTGTCGTTGAATCGCCCGTCAATGAC\nATAATAAT\n>NODE_371_length_248_cov_0.880000\nCCTATGAGCTACGCCCTTCGCGATGGTCTTGCCTATTGTATCCCTGGCGATCGGACCGTC\nTTTCTCGACATTCCTGCGGGGCGATATTTTTGACTATCCGAATCGAAGGATCTGGCGCTG\nCAGCGATGGCTCGATGCGCAAGCATTGGACGAGGAAGATTTCGCGCATCTCGCCGCACTG\nCTGCGCCAAGGGGTCTTAGTTGCCGCGCCCCGCGATCCGATAGGTCCGCGTAGGCGCCAG\nCCATTGAT\n>NODE_372_length_248_cov_0.880000\nGTATTCGGCCACGATCTGGGCGATCTCCACATGGCTCAGCGCATGGGGCACAGGGGCGTC\nGACCTTGCCTTGGTGCGTGTAGGCCTGCACGCGGGCTGCGATGGCCGATGGTGCGACGGG\nCTGGGCGCCGCCCGTGAGGGCCGGGTGCGTGACGCGACCCACATGCCAGATCTGCGCGAC\nGATCTTGGAGCCGGCTTCGTGCACGGCCTGGGTGATGCGCTTCCAGCCTTCGACCTGCTC\nGTCCGAGT\n>NODE_373_length_248_cov_0.742857\nCGCCCGGATCCTCTGCCAAACGACCCAGCAACGAATGTCGCAGCAATACGGCGTAAAGCT\nCGCCGGTCATCGCCGTACGAAAGCCCGTTACGCGCCCGGCGTCCAGCATCGCCCATTTGC\nTGTGCGGTCCGGGCAGCACGACCACCCCGTCACGCACGCCCGCACCCAGAATCTGCGTTT\nCCTCTCCGCGCATCACGTCGCCCAGTCGAACCGGCTGATCGACCGAGAGCCCGGGCACGA\nTGTGGCAC\n>NODE_374_length_247_cov_1.764368\nGCGCTCGTCCACGGCCGTTAGGCGACCGGTGACGCCTTTGTCCTGACGATCCTCCGTACA\nGACCGACGCCTTCGCGTCCTCGATATGGTGACCCCGCCGAGCCGGGAATCGGGAGGCGGC\nGCGATCGGATCGGGTACCGGCCTTGCCTATATCCGCGCCCGCATCAGCGAAGCGTTCGGT\nGGCAGGACGACAGTGACGACCATCACGATCGTGGTGCGCCACCTGCTCCCACCCATCGGT\nCCGGTCG\n>NODE_375_length_247_cov_0.925287\nTCTATGGCGTGCGCTTTGCCGGCAAGGCTGCGCACGCCATAGATCTGGCTCGACAGGCGA\nAAGCCCTTCACGGCGCTGGCATCCTGATCGACGAGATAGGCGAAGCCGCTGACTGTGCCG\nATGCCGGTCGCATAGCCAAGTACCGCGAAGAGGTTGTTGCCGCCGATGTAGCGCGGCCGC\nGCGCCCGTCCCGTTGCTACCGTTCACGGTCTGCACGTTCCAGCTATAGGCGAGGTCCGCG\nGTGAGTC\n>NODE_376_length_247_cov_0.885057\nGTTAAATCAGGCTCCGGAGCGGAACCTGCACGTCACCCGCGGCGGCAAGGTTGACGACCG\nCGCGCCTGCCAACTAGCCGTCGGCCAACCGCCATGTCCGCGCCCCGGTTGACGGTAAGAA\nCACCTTCTACAATTTTATCCGAGAGAAAGAGGGCAGTAAAGCTGTCGCCCTCCAAGTCGC\nCGCGCAATATCAGCCTCAAGCTGTCGTCGATGCGTCCAGCGACCTGGATGTTGAAATCGT\nACTGGTC\n>NODE_377_length_247_cov_0.885057\nGCCGATTTCCGCTCCGTCGAATCCCCCGCTGACCTGGAAATTGCCTTCGAGGAACTCGGG\nAAACCCTTGATGCTAAAGGCGAGACGCGGCGGGTACGATGGGCGTGGAAATACCCTCCTC\nGACAGCGTCGAAGCGGCCAGGGATTCATTCGGGGACCTGTCAGGCCTTATCGCCGAGGAA\nCTGATCGATTTCGACCGAGAACTCAGTCTCATGGGCGTTCGCGGGCAGACAGGGGCCGAT\nACGTATC\n>NODE_378_length_247_cov_0.885057\nGTACATGCCAGATCCTGAATTAGTAACTGCATCCAATCTCCGAAAAAGTCCCAATTGTTT\nCGAACTTTCGATTTTTGGAATGGGATATTTACGGAATCCCCATGAACAGGATCAAACCTT\nATTCCATGGTATTTCCATGAGATTCCTCCTTCTTATTCTTAAGAAAGCCCCCGAGAGGGC\nTTAGTTGATCCATGATTTATGTTTCATCTTTCTTTTCCTTTTCGTTTGTTTCGAGAAAGA\nTATCGAT\n>NODE_379_length_247_cov_0.885057\nCTGTCAGGCCAGACCGGACTGGCTCTGGAGCCCAAGGCGGCCCAATCGCCTGTGCCGATC\nTGGTTGGCTGGCGATGACGAGGCCGGCATTGAAAAGGCGGCCAGACAAGGTTGGGGCCTG\nATGGCCGCAGCCACGCATACAGCGGCACGCATTGACCGGGCCACACGCATCTACACCGAG\nATCGCCGGCCGCGCCCCGCAGCTCATGCTAGCCCGTTTCGCCTGCCCAGCCGCCACGCGC\nGATGAGG\n>NODE_380_length_247_cov_0.885057\nGGGCTCGACCGAGGCAGCAAAAACGAGGGAATCGTGCGCGCCATGATTACGCTCGGGAAA\nAGCCTTGATCTGGCGATCACCGCCGAGGGCATTGAGGAGATGAGCCAGTGGGCGCATCTG\nTCGGAATGGGGATGCGATTTTGGCCAAGGCTATCTGTTTGGGAAGGGCATGCCGGCCGGA\nAAGGCGAAGGCCCTGATCTCCACCGGCGCGCGCGGGCTGAAAGGTGCTCCACGGTCCCCG\nCTTCGCG\n>NODE_381_length_247_cov_0.885057\nGCGCTGGCTGCGAGGCGAAGACGTCTTGCGCGTGGCCCAGGTCAGCGAGGTGAATGAAGC\nCGAGATGGCCGCCACGTTCGACAAGCTCAAGCAAGTTGCTCCCTGATGCCATGGGATTGG\nCACGTTCCTGACAAGTCCTGTCGAGCCACTGTCAGCTTTGTCGCTCGTTCAGCGCCTCGC\nCATGGTCTTCCCCAGGCAAAGCAGCTTGGCACCGTTTGTGCAATGAAGCCTCCATCCCTT\nCAAGGAG\n>NODE_382_length_247_cov_0.885057\nCCACCGATTACCGATCCCAGCTCGGTGGCATAGGGCATAGCTGTATTTTCAAGCAAGCTT\nCCAAGCCCGACTGCAATGAGTGCACCAACAACGATCGATGCGGCGAGGATGACTACAACT\nTGACCCAAGCTGTCTCGCAACAAGAACCCCTTGGTGGCACCTATTGCACGCAGCGTAGCT\nATATCTCCAGCGCGCTGGATAGTCCACACCAGGAAGAATGCCCCGGTTACAAGGGCAGCA\nATAATAT\n>NODE_383_length_247_cov_0.885057\nGCAACGCCTTGAAACGCGCCGGACGATTGTATGCGTGAACATCGTGCTCGCGTATATCCA\nGGACTGCCGGGTCGTTGGCGAGCGAATCCAGGGCGTCCCATTGCTGTTGCAGCCGCTCAA\nGCTGGGCGTGAGCACCCGGGTTGGAGCGGAGCCAATCCGCGAAAGCTTCCCGTTCTTCCG\nCCGCCATGTCGCCGGAGCGCTGCGCGCTGAACCAACGCGTCGCCTCGGCACGCAAGCCAT\nCTTCGAG\n>NODE_384_length_246_cov_0.890173\nCTTATGCGGTCCTGCTTTTTTCGCCGCTTGATTCAAAACCGGAATTTGAAAAGGTTTTAA\nGCGTGCTTTCGGGAATAAACCCAAAGGATGAAAAAATAAAAAGCGAAAGCTTTTTTATTC\nCGCGGCCCGAAAAAGTATTGACGCCAAGGCAGGCGGCGCTTTGCGAAAGCGAGGAAATCC\nCGCTTGAAAAAAGCCTTGACAGGATATGCGCCGCCGCAAAGGTAAAATGCCCTCCCGGAA\nTACCCG\n>NODE_385_length_246_cov_0.890173\nTTGCAGTACAGCGAGCACCACTTGGTAGACGACAAACAGCGCGACTGCAAACATCGCCAG\nTATTGTCAGCAGAACTTCAACTTCCACACCCACCTCCACAATCTCTAATCGGCCTTGTTG\nAAGGCCCTGTCAATCTTCTTCAACCGATGCTTGGCCTCAGGATTCTGCTTGAGCCAAGAC\nAGGGCTTGATTCAGGGCTTCCTGCAGTGGTGCGGGAAGGTGAAGCTTAGTGTTGACGGTA\nCCGGCT\n>NODE_386_length_246_cov_0.890173\nGGTTTTGGTGCCCGCCTGAATGGCGCGGACATACTCGTCCTCCACATCCAGCGTCGGCAG\nAAGATCACCCTTGCTGGGATGGTAGACGCTCAGAAACAGATCGGCCATGTCCTGCGCGGT\nGAACTCCGGCATACAATAATGATAAGCGCCGCGTTTCAGCCCATGGTGTTTCAGCGCCGC\nCCAATTTTCATCAAATTCGCTGTCTTTTTGATGGACGGCATGCCCCGATGCGCCAAGATA\nCAGTTG\n>NODE_387_length_246_cov_0.890173\nGCCCTTGGACTACCATCTCGTGCGTCGATTGAAGGCGGATCGGCCAAGCCTGACCATCGT\nTCTCAACGGCGGCTTGCCGGATGCGGAGACGGCGCTGGAAGAGATGCGCGGGTTGGACGG\nGGTGATGCTCGGCCGGGCCGCCTATCACACGCCGGAGACGCTTGGCCGGGTGGACCGCTT\nCTTCTATGGCGAGGGCGAGGACGTGGACGCGGAGGCCGCCATCGCCTGCTATCGCCCCTA\nTATGGC\n>NODE_388_length_246_cov_0.890173\nGTACTGTGATGCACCAGCTCTTTTCCCGCAACGAATACGAAGTGCCCCAGGGAGCGGGTT\nCGGGATTCGTCTGGAGCGAGAAGGGCTATATCGTTACCAACTTTCACGTAGTCCATAACG\nCCGACTCGCTGAGCGTCGTCCTGGCGGATCAGTCGACGCACGAAGCCAGAGTGGTGGGTG\nTGGATCCGGACCACGACCTGGCTGTCCTCCAGATCCAGCTGCCGAGAGAGAAGTTGCCCG\nCCATCC\n>NODE_389_length_246_cov_0.890173\nGAACGAAGACCACCATCCCGTTTGGACAGGATCAAGCCGCCGACCGCTCAGCCGGCTGGC\nGTGGGCCGGTGTTTGTTGTTACCACCTCCGCCAAGAGTTTTGGCAGCCGCGAGGACGAAT\nACGCCATTGATACCGACGATGGCCGGTTGATCATGACCACGCTGACCAAAGGTGGCCGAA\nTAGGCAAGGTGGAGATAACGCGAGTGTACGATCGCGTCAAACCTTAACGCACGCTCACTG\nCGGCGG\n>NODE_390_length_246_cov_0.890173\nGGCTTGGCGCGCTGCCGCAGGCCGCTTTGTTGGTGATCGTCGTGATCGGGCTGTTATCCA\nTGGGCGCGCGGTGGGCGTTTGTGTCTGTACTGCTTGGCGTGTTGGTCGCGTTCGGCGGAT\nACCGGGCGGTGATGATCTCATTGGAACCGCACGCGCGCACGCGGAGCTATTTCGGCGTTT\nATACCGTTCATAACGCGGCGACCCAGCGGCAATTGGCACACGGCACTACGGTCCACGGTG\nTCCAGT\n>NODE_391_length_246_cov_0.884393\nGGTATGCTCGCCGACCTCGGGTGGAAGTGTCGGCGGAGCAAACGGACTTTCCGACATGCG\nCAACGGGCTGCGCACGGAGCGGAAGGTGCCGATCCTTTCGGAAGGAACCGAAACGACAGT\nGTCCCGAAGGATTGCAACATCGCTAGCGAACGCCTGGCCGACAGTGCGAAGCTCGCCAGC\nCGGGACTCCGACGGCGCGAAGTTCGGCGAGAAGCTCATGCAGTTTACGATCGCGCAACTT\nGTCCTC\n>NODE_392_length_245_cov_1.343023\nGTACTGGGTCGGATCAGCGACTATCCGCTGATCCCCGGCGTTACGGGTTTCGGCCTGTTC\nGACCGGGTGGTGGTCGATACGCTCGCCACCTGGAACGAGCCGGAACCCTTTTTCCGGGGG\nATGGTGGTCGAAAGCGGCTACCGTCTGGCGCTGGTGCCCGTCGATCGCCCGGCACGCGCT\nGCGGGTACGTCGAAGAACGATGTCGCCGCGCTCGCCTCCTTTGCCCTGTCCGGGCTGGCC\nGGATC\n>NODE_393_length_245_cov_0.895349\nATCTTGCGCACCGGCTTTGCGCGCGGCGGCGATGACTTGCGGATAGACGGCGTCCTTCAC\nGTCGAGGTTGAGGACGATCCGATCCTTCGCGAGTTCCAGCATCTCGTCGAGCGTCAGCAC\nGGCCTGATCAGTCATTGCCGCCGCCGGGCCGCCTTCGCCCTGACGCAGGTGCAATAGCTT\nGATCTGGGCCAAAGTGAGATCGGCGACCTTGCCGCTGCCGTCGGTGGTACGGTCGACACT\nGTCGT\n>NODE_394_length_245_cov_0.895349\nCGCCTAACCTCCGAGATCCAGGCCATGCGCGGCGAGCTTGCGCGTATTGAGTCGGCACGA\nAAGCAGGGGGCAGATGGTCCGATGGATATTGGCGTTGGTGCTTTACCTGAAGCCGCTGCC\nAGTTATGTAAGAGCGGTAAGAGAAGTTAAATACCAGGAGGCGCTGCTCCAAAGCATGCTG\nCGCCAGATGGAGATGGCAAGGCTCGATGAAGCAAAGGAGGGCAACGCCATTCAACAGGTT\nGATGT\n>NODE_395_length_245_cov_0.802326\nAGCAGGAACAGCGCCAATTGCCCACCGGCATGAAGCTGGGCCGCGCGAATCGGGCCCCAG\nTCGGTGGTGTCCGCCGGGTCGTAAAGGCCGAGCAATGCCCGGCCGTCGATCCGCGGCGTT\nGCGAATTGAGAGGTGCTGTGGGTGCTCACGCCACCGACACTACCGCAAGCAGCGTTAGCG\nGATCGTTATAGCCGCCCGACTTTTTTGCGGGCCGTTACGCCGCCAGATCGTAGGGCTTGA\nTATCG\n>NODE_396_length_245_cov_0.784884\nTCCGAGCCGTCCTCCTTAAGCAATTGAACATCGTCACAAGCATTGCTCATCGCAATGGAA\nTAACCTCTCGCATGCATAATTGCTGCCCAAGCGGCTGCTGGCTCCGACTGCGAAAACGTC\nCTCACGAAGCTTACGGCCATCGATCAATCTCCTGTTTTAGTTGTTTGCCGCCGCAGCAGC\nGGCGTCTTGCCAGTCCTTTAGATCGAGCCCATCGAGCGAATCGGAGTTTAGCAGTTCTTT\nCGCAC\n>NODE_397_length_245_cov_0.697674\nCCTATATCCCGACATTGGTGGTGTATGAGCCGCAGCAGACTCGCCGGTTCGAACCCGACG\nAGCAACGCGCGCTGACGCCGCCCGAGGCGGCGTTCGAAGCAAGCCATGCGGCGCAATCGT\nCCAAGCCGGTCGCGGCTTATGATGCGAAGCGCTGGGCGATCATGCAGGACAATGTCCGGC\nGGCTGAAAGCGGCAGGGGTGCGTATCGGCGTCGGCACCGATGCCGGGATCGAGGGTGTGT\nATCAC\n>NODE_398_length_244_cov_1.204678\nGACTGCGTAGCCTGAGGACAGGCGGATTGATCGATGGCGACCGACAGTACACATCGGCAG\nCGCCGCGGCGGTTGCCGCTGGCCTCATAGCTGTCCGCGAGCGGCATTACCCGGTTCCGAC\nATCTCTATGCGCATTTGCCATCACAGGACGCGCCGCCCATTTCTGGTCACCGTGGCGGAA\nGTGCAATGCAACCTCCAGCGCGTCTTGTGATGGCCCCAGCCTTTTGAGCCGCTGGGATGG\nGCTG\n>NODE_399_length_244_cov_1.011696\nATCCATGCTGTGCAGTTACCAGCATGCGCGGTATTTGCTGAACATCCCGAAGAACTGTTC\nGAAGCCTTCATCGTCCATCTTGCGAATGTCCATGCGGGATCGATTGCTGACCTGAAGTGC\nAGCGATCAAGGGATGATCGCTTACCGGGATACCACAGACGATTTCGGCCATCTGTTCTGC\nATCAGCCCGATATCCCATCCAATCGTTGCCATGGACGGTTGGCGATGGCATGGCGGTATT\nAAAG\n>NODE_400_length_244_cov_0.935673\nGGCAATGGGCGCAAACGGCGCGTTGTGATGTAACTGGTCGCATTTTCCGGTGGTGAAACG\nATGTGGCGATGCCGCCATGAGCATCCGGAAGCGGCGTACCAACGCCGACTTTCCGACGCC\nGGACACCCCCGAAAGCAAAATCCCTTCTGCTGTGCCGCTGCCGCAAACCCGCGCCAGCGC\nGTCTGCGAGGGCAGCGCTCTCGGCGATACGGCCGAACAAACGGCGTGTGAACGTGGTATC\nCGAC\n>NODE_401_length_244_cov_0.900585\nTGATTATACAAAGCAAAAGGCCCTGCATTGCTGCAAGGCCTTCGAAACTGAACTTTAAAA\nGAAAACCTGTTTTAAAACCAACTGCCTACAAATTTTTCGTTTACCGGCTCGCCTTTTAGT\nTTGCGCCTGCGGCGGGCCACATCAAACCGGTGCATGATCATGGTGGCTATTATCAGCGGA\nATGAACAAGAGCGTAAGCGGCGGAATGCCGAGGAACGAAATCCATTTGCCGCCATACATA\nCGGC\n>NODE_402_length_244_cov_0.900585\nGGCCATGCTCGAATTTCCACCCGAAGCTGTGGGAGACAACTCGCGAGCCAACGTGTGGCT\nGGCGAGGTTAGCGCACTTCGTGAGCGCTGCCTGACTCCAGGAGGGGCCGGCCGTCTTGCG\nTTCTACAGCGCGGGCCCCTCCGACCACGGGGACGCGGGGGGCTACTTTGCGGGAAGGAGA\nAAGTGAGCTACCCCGCCCCCCACCCCTCGAGGAGGAAACATTGAGAATGGCCATCGGCTA\nCCGC\n>NODE_403_length_244_cov_0.900585\nGGATATCCGTGGTAATTCTAGGGCTAATACATGCACGCAAAGCCGACTTCTGGAAGGCTT\nGTATTTATTAGGTAAAAACCAACGGTGCGTCAGCTCAAGGGCAGGCGCACGATGGTGATC\nCATAATAACTGCGCGAATCGTATGGTCTTGCACCGACGATGAATCATTCAAATTTCTGCC\nCTATCAACTTTGGACGGTAAGATAGAGGCTTACCGTGGTCGTCACGGGTAGCGGAGGATT\nAGGG\n>NODE_404_length_244_cov_0.900585\nGTGCTGACGCCAGAGCGCAGAAGCTGAGCCCCCGCATCGGATTGGCGCGTAGATTAGAAT\nAATTGAAAACTGCTTTACTTTCAGCAGGTTAGCTGCTTGCGCCCAAACTGGCAACGGAAA\nCGGCGATCGTCAAGGGCACAATTCCGTCGCGCCCCAACGATCCCGCCGCCCTCAGCGGGC\nGAGCTCGCGCAATCCGAGCCGGATCAGGGTCTTGGCCTCGGCCCCCTCGCCCGCGTTCTT\nGAGG\n>NODE_405_length_244_cov_0.900585\nGTTCAAACGCCAGAAACTCTCCGATTTCTTCGACCAGGCCCCGGTGACGAAAGCCGGGGT\nCTCGATTTCGGTCGGGCGGTGAAATGGGGCGTCTACGCCTTTTTCGATTATGATGGCGAG\nCCGATCTATGTCGGCCAGACGCGCGAAACCGTGGGCGGGCGGATCGGGCGGCATTTGACC\nAACTAGCGGACCGATGCGGTGGCGATGTCGGTGCTCGATCCATTCGAAGTGCGCACGATC\nAAGG\n>NODE_406_length_244_cov_0.900585\nGTTCACCATGTCCTTGGTGCAGCGATAGAGGTGCATCGCGACGCCGGTCTGCGCGCGCGC\nGCCATCGCCTGCCACCATCATGGTAGTGAGCGAATCGAGCCAGTCGGCATCCACGCCGTC\nGAGTGGCCCCCAGCGCAAGCGATTGGGCGCGAGCGGGGCGTCCGATGGGGCTGCGGTGAA\nCAACGGCGCGCCGTCATAGCGCGTGAACGCCGGATGCGCGGCGGACGGCCGCAAGCGATA\nGAGC\n>NODE_407_length_244_cov_0.900585\nGCCTTCCGGGAATGGCACTTCACCGGCCAAACAGTTGATCACGAAATTCCGGAGGAGACC\nTGCCGCCTTTGTGACAAGGAGGGGCTTCGATACCATTTCGAGATTCGGAACGACCAAACG\nGGTCATCGCCTCGACGTCGGTTCCGAGTGCATCCTCAAATTCCAGGTCGCTGTCTTCGAC\nGAGGGCCGCGAGCTCGAACCGGACGAGGCGCGTAAAGCCCTTGCCGAACGGATGCGGCAG\nATGC\n>NODE_408_length_244_cov_0.900585\nGCTTAGGTCTCACCACAAGGGCCGTTGATTGAGGTCTACTGGCGAGGCTCCGGCGCGGAT\nTGCCGCAGCGATGGAGGTGCCGTCCAGCGCGGCTTGTCGGATCGCTTCGGCACGGGCCCG\nAGCGCCCCTGGTGTCATTGAGCGGTGAGCCCGGAAAATCCGTGATGCCTCACGGTGCGAG\nAACGAGTTTTACAGGCGGCAGCCCTGCAAACCCATGGCTGGAAAAACGACGACCAGCCCG\nCCGG\n>NODE_409_length_244_cov_0.900585\nTGCGGCACGGTCGCCTGATCGTCCTGACGCGGCATGTGGTGCGCGCCATGCGCCATCGGC\nGCGGCGATTGGCATTTCATGGCACGACTGCCCATGCGCTATCGCCGGGATGGCAAAGGCT\nGCCAGCAGCAGCGCAAGGATCAGGCGGGCGAACATCGCGGAAACCCTAGGCCGCGCGTCG\nCCCGCCGACAAGATTAGACGTTGAAGCGGAAATTCAGCACGTCGCCGTCATGGACGACAT\nACTC\n>NODE_410_length_244_cov_0.894737\nTTCCTGTACCTTGGATTTGCCTCCCCTGTCATGCGACGAGCGTGAGATCGATCGGAGCAG\nTCTCTTGAGCAGTAGGCAGGATACTTTCCAGACCTGTAAACGGCTTCGAACTCTGTCATG\nCACATTTCGCATGTCTTCTTGATGATCGGGTGTTTTCTGGTTTGCGGTGGGGCGCACGCC\nTTTGAGCAATACTTCCTCCCCATCGACGGGAAGAGATTCCCGTCGAAGGGGAGGAAGTAT\nTGCT\n>NODE_411_length_243_cov_0.905882\nGTCGATACCCGGATCGTCTGCGCCACGCATCAGGACGTCGATGCGATGGTTGCCTCCGGC\nAGCTTTCGCGAAGACCTTTATTACCGTCTCGCCGAAATCGTCGTTCGCATCCCGTCGTTG\nGCGGAACGTAGCGGTGACGCGGTGTTGCTGGCGCAGCATTTCCTGAAGAGCTACGCCAAA\nTCGATGCACGCCGCCGTTACCGGCCTGTCACCCGATGCCCGTGCCGCGATTGCCGCTTGG\nGGC\n>NODE_412_length_243_cov_0.905882\nCTCTCACCTTCCTCCAGGAAGGTTGACAGAGTCAGGTTGTACTGTGGTGAAATAGCTAGC\nGCAACGGCAAACACACCCTCTCGTCTAGGGGGCGCTGAAAAACGAGATAGAAAAATGATA\nTGGGGTTGACCACCAGCTTGCAAGCATAATGTCATTTTTTGAATCGCAGCATGAGTGGTT\nCGAATCCCTCCGGTACAGCCCAGAATCTCTCACCTTCCTCCAGGAAGGTTGACAGAGTCA\nGGT\n>NODE_413_length_243_cov_0.905882\nCTCGCCGATTGGGCGGGGCGGCGGCAGTCAGGGCTCGAGCGCTTCGGCCTGGCCGGACAG\nGCCGGTATCGGCGTCTTGCTCGGGCTGGTGTGGAGCCCCTGCGTCGGGCCAACCCTGGGT\nGCCGCGACGGTGCTCGCCGCGCAAGGCCAGAATCTGACGGAGGTCGCGCTGGTAATGGCC\nGCCTTCGGGTCCGGGATTGCGACAATGCTGCTGCTGATCGCGACCGCAACGCGCGGTTTC\nCTG\n>NODE_414_length_243_cov_0.905882\nCTTGAAATACTTGACCTCACCCACTACTCCGAAGCAGTTGGTGAGGTCAAGTATTTCAAG\nCTTGCTGGGTTTCCCGGGAAAACAACCGAACTTGCTTCAGACAGTCGATCCGAGCGCATG\nGATGACTCGCCGTCACGCTAGCCAGCAGCAGTCCGATTCCCCAAGCCCTTGGCAAGTTGT\nAGAAAAGATCGGCCTTCGTCTGTTGACGACATCAGAGGAGAAACCATACGGCGGTGTCAA\nGGT\n>NODE_415_length_243_cov_0.905882\nGTTCTTGCTCGTGCGCAGCGTGATCGACAACAGGTTGTCGTACCTGCCCTCGCGACCGAA\nGTTCTTCACGACTGTGTTCTTCCACGAGATCGCTGTCTGCCCGAGGAAGCTGCGCATGCT\nCGTTCCCGGTTCCTGCCACCTGGCGCGGACTGCGCGGCGCTGCGACATGATGGCGGGGTC\nCAGCTGCCTGCGTGTGAGTGCCGCCGGATGGCCGAGCTGGTCGTGGCGGACCATCTGCAG\nGGC\n>NODE_416_length_243_cov_0.905882\nGATCCAATCCGGTACTAGCGCAATCGCACTCCCGGTGCGCCGAGACGCGAATGTTATCGG\nTGCGGTCAACATCGTTTTCTTTTCTTCGGTGCTGACGCCGGCGGTCGCGGCAGCTCGATT\nTCTGCAGCCGTTGCGCGACTGCGTCGAGCGGCTCGAAGCGAGAATCGGTTTCCTCAACTG\nACTGTTCACCAGACGAACAGTCGGGAAGTTCGGCTTGGGGCAACCAGTCGCCCGGGATTA\nGAT\n>NODE_417_length_243_cov_0.905882\nTCCCTGACCAATGCGTGAGCTCCTTATCCCAAACCAATCTCCCTCCAAACCCAACTCCTC\nTCCAGCTCGTCTACTCATCACTCTCTGTCTCCTCTCAAAATCTCCTTAAAGCTCAATCAA\nTGGTGAAGTCCATCCGAGACTCCTCCACAGGTAATAAAAACCGCACAAACGCCGCGAACA\nACTGTCTCGAATTTATCCACAGTTCACAGTACCGGATCTCTAACACCGCCAAATACGCTC\nTCC\n>NODE_418_length_243_cov_0.870588\nCCCCACACCGCATCCGGGGCCCGCAGAGCGTCGCGGTCGCTGCCCGCGCCGACCACGAAA\nTTGCCGTCCAGCATGTTCACCCAAAGCCGCACACCCAGCGATCGCGCGCGTGCCGAAACC\nGTCGTGAGCATCGACAGTGGCAGGCGATCCGGCACTTCGATGCCAACAGGCTTCACGCTG\nCCCGCCATCTGCGCGGTGATGATATCGGCGATGGCGGGCAGCGTGAAGCCTGTTGGCATC\nGAA\n>NODE_419_length_242_cov_0.911243\nTCCTAAGCCCCGGTCGGAGCGCGGCTGGACCGATAGGCGCAATCAGTTGTTGAAAACCGC\nCACAATGGGTCTAGCGCCCGACCGGGGCTTAGGATCACGTCGCCGCAGTTGTTGAAAACC\nGCCACAATGGGTCTAGCGCCCGCGAATGGGTTGTGCTGATCTAGCGGGGAACTTGCGGGG\nGCGTCTTCATGATCGTGTCGGTTAAGCGGCTGGCGGTACGGCTGGGTATGGCCGGCCTCG\nTC\n>NODE_420_length_242_cov_0.911243\nTTGATCTCCGCCGCAGGCGGATGCGTGCGGCTGAACCCGAAGGCTCACGCTCGCGGAGAA\nGCCGTACGCAACCTCCTGCCAAGCGTGGACTTGTTCTAAGAGCAACGGTAATCCGCGCCC\nCAACGGATACAGCTGGATACCCGTCTATGCACCGCCAAATGAGACGGCGCGCACTAGCCT\nCCATGTGGCCCCCCCCACTGTCTTGGATAATAGCAATCATCGCCTCGCTCGGGAACCCGG\nGA\n>NODE_421_length_242_cov_0.911243\nCGATGTCGGACACGGTCAGCATCGCGACATCTTGAAGACCTTCCCCGACATGGTGGAATC\nCTCCGCCATGATCGAGGCGATCATCGAGGCGGCGTCACAAGGGGCGATGGCAGGATTGCA\nTCGCTACGTTGATATGAGCGCCCTGATGATCCGCGATATGAACCAGGCGAGGCTGGCGCC\nGCCACGAGATAGGTCGGCAGGAGGTCGTCCCGCCTCGTCTCCGAAACAGGCAGCGCCAGC\nCT\n>NODE_422_length_242_cov_0.911243\nGCAGAAATAAATTGACTGAAAAGTAAGAAGTTGCTTCAGAAATTGCGCTGTGTTTTAGCA\nTTAGAAGGGAAGATAGCATTTGAAGTAGTGATACTTTAATGGATGGTTCAACTATCTGTG\nTTTCCAGCAGCCATCCAGCACATTTAACTGAAAGGACTGGAACTGGAAAAGGAGCTGGTT\nTGTTGCCACTAAAATAAATGAAGGTGCCAGTTGCCTTTTAGCCAGTAGTAGTGATCCTAC\nTT\n>NODE_423_length_242_cov_0.911243\nTCCTCGACGTCTCGAAGTATTTATCTTTATCTTCGGCCTTAACCGCGCCCATGACGGCGA\nTCCCTTCAGCAGGAGGAGTAGGAGAGCGCGCGATCCCGTTGGGATAGGCGTGGCGCCGAC\nCGGGAATTATTCATCGCGCCCGGCCCGATAGGAGCTTGAGTTGCTGCACCCGCGTCCGGG\nGCGGGGGCGGGCACAGGAGCCGGCCCGGTTCCGCCTGAAGGCGGTGCAACCATCGACTGA\nCC\n>NODE_424_length_241_cov_1.779762\nCCGAGCGCCAAGTCCGGTGTTCGTCGTTTGATTGCGAGCGCTGGTGCCGGTCTGGTTTCG\nCAGCGTGGTGTCGCGTTGATGGTAGGGGCCGGCGATCGCCGTCCCCGCTGCCAGCTTATT\nTCTTGCGGAGTTCGACGATGTCGTGGACCGCGGGAGTGCCATCGGCGACGCTCACATGCG\nCGAAATGGTCATCGAAGATATGATCGATCTTGACGTGCCCGACGGCCACGCGACGGAAGC\nC\n>NODE_425_length_241_cov_0.916667\nGGCATAGATCGGTTCAAGCAGGGCCGAGTCCATCAGGAATTGGCCCTGCTTGAACCGATC\nTATGCCTGCGCGGCATTGGCGACGGCCATCCGCCTGCATCGACTGCATCGCCAAGACCAA\nCATCCTGGGCTTGCCCTGCTGTCTTTCTGGTTCGTCGTCACCCCGCTGGCACTGCTGGTA\nCCCATCGATTGGCTAGAAAACAGTGGGGGCATGGATCGCTTGGGTGCACCATGGCCGTGG\nT\n>NODE_426_length_241_cov_0.916667\nGTCAACCGCCGAGGCGCGCCGGATGCGTCGTAAAGTTGTTGCTCAAACGCAATAGTCGGT\nCCGGAACCGTCCTAATTTTGGATGAACTATCCGCTCTGCGTGAACTTTATGTTGCATTGC\nGAAACGGTCTATGGCGTCATCCGATTCGGAGCAGATGAGGCGAACTCGATTCCGGCAATA\nAAATGTCGCGTTAGAGCGTTCAGCATCACAAGGATTCCACATACATAGATACCGAATGCG\nG\n>NODE_427_length_241_cov_0.916667\nGTTCTGAAACGGGCCACCATGTTGCTGTCTCAGCGGCCGAGCAGCACGCGCGCCTGTCCC\nGCAATCTGCGCCAGCATCGCGGCATTGGGGGCGGGAGCCATGCGCGCGCGATCGACCACC\nGCTTTGAACTGGCCGACGCGGCCGGCATTTTCGGCGAGCCACGTTTCAACCAGCGTCTGC\nGGGTCCGCACCGGGTGCCGCAGCGCCGCGCCCCAGAAATTCCAGCCGCAATTGCTGGAAG\nT\n>NODE_428_length_241_cov_0.916667\nGCCATAGGCCCGTCTTCTTCGTCTCCCCATGACCGAACTGCCAAGGCTGGATGTATTGCG\nGGCGCGGAAGCTCTGGGAGCAGGCGATTCAGTACGCCTACCGGGTTCTCGATAGCCAGGC\nGTTCCACTTTCTTCTCCCACATACGCCGCACAAACTCAGCCGCGTCAATTCTCGCCTGCG\nTTCCGGCGTAGTGACGATTATCGCTCACCCGCCATGCACTGCGCTGGCCGTGAGCGGTAA\nT\n>NODE_429_length_241_cov_0.904762\nGGCAAACACATAGACGTGCCACAGTTGGACGGCACCGCTGACGGTGAGTATGCCGAGCGC\nCAGGGCCAGACTGCCCATCGTTGCCTGTGTGACGAGCAGCAACGTGCGCTGGTCGAGGTG\nATCGGCAGCCGAGCCGGTCCAGGGGAGCAAAAGGAACTGCGGCGCGAACAGGAGCGCCAT\nCACGATGCCGACTGCGGCGGCGCTGTGATGCGTGAGGATGGTCAGCACCAGCCAGTCCTG\nT\n>NODE_430_length_240_cov_1.383234\nGGCTGACGCTCAGCGACTCGTAGCAACAAGGCTACTTGACCGCTTACACGACCCGCTTGG\nTCACATCAGTCGTCTGCAGAGGATTCATCCCCGCGCGAGGTGACATTGCAATCCGCCAGC\nCGGCTCCCAAGGGCTTCTCCCTGGGGGCCGTCGCCAGCCTGCTGAGGTACAGGGCCCGGA\nGGCCTATTCGTATCCAACTACGACGTGCGGGGCAACATCGCCGCGTTCCGGCACGGATTC\n>NODE_431_length_240_cov_0.922156\nGTGTCGGCAAGGCCCGCAATCGGGCGGATAACATGGCGGATAGCCGCCATTACGAGCGCC\nGAGGTCCCGGCGATGCCCAGCAGGACAATCAGGATCAACGCGACCATTGCCACGATCCCT\nACGATCTTGCCGGAATCGGACGCTTGCTTGGCATTTGCCGTAATCGCGTCCGACGCCTTC\nCCCATCGAAACCTCAAGAGTGCGGAACTGATCGAAAAATCCCGGAAGATCCGCCCGGGCC\n>NODE_432_length_240_cov_0.922156\nGGATGCGGGTTATGGGATGCGGGTTCCGGGTTACGGGATGCGGGTTGGATTACGGTTACG\nGATGGGTTAGTGATGCTATCATGCATTCCACTAACATCATTTTCATCCACCCTACCCCTC\nACACCTTCTTCCTTACCCCTTTCTCCTTCTACCTCTTTCTCTACAATATCAAATTGATTT\nAGAGGATTTTGGTTCTCCTCTTCTTCTTCGGGAAATACGAGAGAGCCATCTCCCTTTAAT\n>NODE_433_length_240_cov_0.922156\nGAGCCGGGAAGTTTCCTTGAATTCGACCACCATGTGCCCTTCAGTGACGGCACAGGCCCA\nCTCGAACGAGCGTTGCTGAAACCCGACGGCACCCAATCTGGCGGTAAGCAGTCATCGGTA\nCGCCCAATTTCCGATCAAGATTTCAATCGTATTATCGAACGCGGGCTGTCAGACGGGACT\nGGCTTCCTTCCGCGAACTGGCGATGTTTCAATCGACGAAATATCAAACCGAGTTCTGGAT\n>NODE_434_length_240_cov_0.922156\nGTTATTAACTCTGTTATTCTCCCTGATAGAAATGGGAAACTAGATGATGTTGTTCTTGGA\nTTCGATTCAGTTGATGGCTACAAGAACGATACAACCTACTTTGGAGCCGTTGTTGGACGA\nGTTGCTAACAGAATCGGAGGAGCCAAATTTACTTTGAATGGCACCACATATAATTTAGTT\nGCCAATGAAGGAAAGAACATACTCCATGGTGGTCCCAAAGGATATGGTGATGTTATATGG\n>NODE_435_length_240_cov_0.922156\nGTCGTAGCGCTCCTTGAGACGGTCCATCGCGGCGTTCGCCTCTCGAAAGGGAGGCCACGA\nCCCCACGCTGTCCGGGAGGAACTGCGCGCGGGAGGGCTCGAGCGTCCAGCCGATCTCCTC\nGGCCGTCTGGACCGCCGCTCGGCGCAGCACCTCCGCGTAGAGCTCGTAGGAGCCGGACAT\nGATCTGCGCCTGGATCTCGAAGAACCGGTCGAGGAACGGCCGCTCCTCGATCGTCAGGCC\n>NODE_436_length_240_cov_0.922156\nGTTGGGCAAGGTCGCTTTGCAACCTGCGCGGCAAGCGATCGATATGGTCGATCACCAGCG\nTACCGGCGAGAGCGGCGGCGAGCCGTTCCGCGATCGTCGCGCTGTCGGCGGTCTCCGCGT\nGGAGCGTAACCAGCGGCCCGTCAGCGCGTCCCGATCCTCGATGGATCAGCCGCGCGATCA\nCGGTCTTGCCGGTGCCGGAGGCCCCGCTGACCAGGACCGGAGCTTCGGTCGGCGCGACAC\n>NODE_437_length_240_cov_0.922156\nGCGGGGTTTGCCGGGGGCGGGCGCAATTGCCATGCCGTGGCGATAGGCGGTGGCCAGCGT\nAATCCGCGCATCGGCCTGGTCGCGCACGGCCTCGCTCGCATTCTTGAGCAAATTGAGCAC\nCACTTGCAGCGTCGCGTCGCGGTCGATCTGGACCGGCGGCAGCGACGGATCGAAGCGTTC\nCTCGATCACCACATGCCGCCCGAAACCGGCGAGCGCGACGCGCCGGGCATGATCCAGCAG\n>NODE_438_length_240_cov_0.910180\nGGTCACCCGGACCGGGCGCGTCGCTGGCGACAAGCCCCGCCGCCGAGAACGCCGCCGCGA\nTTGCCGCCGCGCTCCCGCCACGCAGCACATAGCCGCTAGGAATTTCGCCCCGGAAACCCG\nCCGCGCGCGCGGCCAACCCAGCCAGCCCGACACCATCGAGCCCGAACGCCGGGTCGCGCC\nCGTGCAAGCGGAAACGCGCGCCGATCGCACCGCGCGCCGCCGCAATGGCGCGTTCGGCCG\n>NODE_439_length_240_cov_0.784431\nGTGATGAACATGACCCCCTTCGCTGAGCCCGGCTTCTGCCTGACCAGCACGATCCCGGCG\nAGATTGATGCAACGGCCGTCCTTTACGGTCTGTAACTCTGCGCAAGTGATCATCTTGCGC\nGCCCGCAGCTCGTCGCGCAGGAAGGCGAGAGGGTGGGCGCGCAGCGACAGGCCTGAGGCA\nCGATAGTCTTCCACCACCTCCGCACCCACGCCCAAACGCGCGCGGGAGTTAGGGGGGGGG\n>NODE_440_length_239_cov_0.927711\nGTTACCTGGTGAATGACGCCTGTGTATTGCTGCAAAAGCCATTGGTGTATGGTGCTGTTT\nCCCGGTATGAGGGACAGGTGGCAGTATTCAACCACAGTGTAAGTGCCGGCGACATAGCAG\nTTAATTACAGGGACTTATTCCCCCACCCGCCACAGGAAGGGGAAGTGGCCAACTGTGCAG\nAGGCCGGGGTGCTGGGCGTATTGCCCGGAATCATTGGCAGCTTGCAGGCAGCACAAGCC\n>NODE_441_length_239_cov_0.927711\nCTCCGGAATCGAACCCTGATTCCCCGTTACCCGTTACAACCATGGTAGGCGCAGAACCTA\nCCATCGACAGTTGATAAGGCAGACATTTGAAAGATGCGTCGCCGGTGCGAGACCGTGCGA\nTCAGCAAAAAGTTATTCAGAGTCACCAACGATTGCGACGACGCGCGCCGAAGCGACGCGA\nCGCCGATTGGTTTTGATCTAATAAAAGCGCTCCTTCCGTCTCCGGTCAGAGCTCTGTTT\n>NODE_442_length_239_cov_0.927711\nCGCGGGCAACGTCTTTGATAACCGCTTTACTGGTCATGCGGTTGAACGTGATGATTTGCG\nCGACGCGATCTGCACCATACTTTTCGCCGACGTATTTGATTACTTCTTCGCGGCGTTCGA\nTGCAAAAGTCAGTATCGATATCGGGCATCGACTTTCTTTCTGGGTTCAAGAATCGCTCGA\nAGAGCAGGTTGTATTTGATCGGGTCGATGTTTGTGATGCCCAGAGCGTATGCAACAAGG\n>NODE_443_length_239_cov_0.927711\nGCCCAGATCAGGCGACCGCTCACGCCATCATAGCCGAGCTTGGGGGTGAAGTTGGACCGT\nGATGCCTGGCTGCTTTTGGCCAGCGTGACTCGCGCCGCCGCATCCCCGGCAAAGGTCACC\nAGGATCGCATCGACGGGCCCGCCCAGCCGGGCTTGTCCATCGCGCACCACCCGCGCCAGA\nTCGACCAGCGGCGTGGCCCGCCCGGTACGCGCCACCACCGGAGCCTGCGGGTACAGGAT\n>NODE_444_length_239_cov_0.921687\nTATCGTGTTCGGGGAGTGCGACCGGTGAGCAGCGCACGTCTCGCCACCGCGCATCGCATG\nATCGCGCTGTACAACGCGCAGGATGCGGACGGCTACGTCGCGGAAATGACCGGCGATGCG\nTGCGAGGCAATGTACCGCGGTGCCGTGGTACGCGACGGGCAGGAGGGTGTTCGCGCAGGG\nCTGAAGGCGATGTTCACGCAATATCCCGAGAACCGTGCCGAAGTGCTGTCGTCCTATGT\n>NODE_445_length_238_cov_1.800000\nTCTCAACCCCGATTTCTTCCCCAATGCCTGCGCCAGCATCGTCGTCGCGCCCGCAAGGGC\nGAGCTTGGCGCAGGTATAAGAGAAGAAATCGGGGTTGAGATTGGCGATCTTCTGGTCGAG\nCAAATTGACCACCGCTCCCTCCGTCAGATCCTGCTGCTCCGCCAGGGCGTTGGCCAGCAG\nCACCGGGGCCTCGAGATTGACGGCATAATGGCCGGGCGTTGCTGCGCGACCATTATGC\n>NODE_446_length_238_cov_1.393939\nGGTGCAGCCTATTCGGGGGTGAAGGTGGCTGTCGCAAAAAAGCGGGAGGTCGAAGGCCTA\nTTGCTCGAGGGCTTTGGCGCCAAGCGGGTAACCGCACAGACGGGCGTCAGCAACACCACC\nGTCGGCCGTATCCGCAATCGCCTGGTCAAGCGCCTGGCGCTCAAGGGCGAGTGCCTTCCC\nGGATGTGACCTCGCTGGTCGGCGTATCGGTGCCGCCAAGGCATCCACCAACTATATCC\n>NODE_447_length_238_cov_0.933333\nGTTTGATTCTGGCCCCACTCCCGTCTGCTCCGGTGTAGACAGTGGGCGCAGGGAATGAAA\nTTTCTACTTCCACGTCTACAAGGTCATACTCCTTGCCCATCTGGGATTCGACATGAACAT\nTAAAGGTGTCAGTCATTGAGGTATCGCTCCGTCGATCATTGTGATTGATGATTATTCAGC\nAACGCTGAAAGCCTTTACAAGCGCCTCATAGAGCGTCTTTGTGGGAACCCTCTGAGAC\n>NODE_448_length_238_cov_0.933333\nGCCCGGCTCAGGCCAGCGTCGGTTCTGGCAGGGGGACCAAAGCTTAGGGAACGTGGCTCC\nTCCGGGAGTGTTATAGCCCTTTGCTCAATACCCTTGCCGGGACCGAGGTTCGCGCTCTGC\nAAGGACGCTGGCATAATGGTCATCAGCCACCCGTCTTGAAACACGGACCAAGGAGTCGAG\nGTTTTGCGCGAGTGTTTGGGTGTAAAACCCGCACGCGTAATGAAAGTGAACGTAGGTG\n>NODE_449_length_238_cov_0.933333\nCCCTGAACGGGGTTGTCGAGGTAGTAGGTGAAGTTGGAGAACAAGTCCAGATGCGAGCGG\nATCAGGTAAGCATTGGCATGCCATTCGCCATCATCCTGCACCTTGAGCCAGTCCCACGAG\nAGGCTGGTGCGATAGGTCTCACCATGGTCGCTCGGGTCGATCGCGCCGAAGCGCCCGATC\nAAGCCTGCGTCGATGGCGCGCTGAGGCACCTGGTCGGTGCTGTTCCACTTGGCCGTGT\n>NODE_450_length_238_cov_0.793939\nCAGCAGGAAGGCGTCGCCTTCACGCAGGGGCTCGGACGGCTGGTGGGACCACCTCGAACC\nCGAAGACATCGAGCACACCATGCACCAGGCCGAAGACCCCCAGCAGTGGCTCGACCACAT\nGGCCGCGCTGGTGGCCAGCCGCCAGAGACCCCCCCAGGCCAACGACACTGCGGTGACCTC\nGCCCGGGTTACCGACCCAGACAGCCACCGCAGTGTAGTTGTCCTGGTTGGGTATCTGG\n>NODE_451_length_238_cov_0.757576\nCGATCACATAGATTTGCGTTATATCTGAGTTGCCGTCCACACGCTCCATTCTAGGATATA\nAAAGGTTTTGACGCGTGTATTCAAGTCCGGCTTCGTACTACTCGTTTACGGGATTTACAG\nAGAATTCCCGTAAACGAGTAGTACGAAACCGGACTTGAATACACGCGGCAATCCCTTTTA\nTATACTAGAATGGACCATGTGGACGGCAACACAGAGATAACGCTGTATCGTAAACACA\n>NODE_452_length_237_cov_2.347561\nTAGTATGGCGTCACGAAGCCGAAAGCTGGATCAAGCGCGACGATGGGCGCGCTGCCGCCG\nACTGGCCCCGCCGCTGTCGCGACCGCGTTTTGCTCGACGGATACCACGAGCGGCGTTGGA\nCCAGTGGCTGACTGCTTCAACCCGTAAACGTGCCAGCCCTCCCGGATCGAGCCCCGAACG\nGTAAGAATTGCGCGGCTGGCAGCGCTGGGCGCTACGACGGGATCAAGGCTCCATGAC\n>NODE_453_length_237_cov_1.548780\nGAATTAGTCGGCGGAAGGTGAGACAAGGGGCAGGCTGAAGTCGTAGATGTCGAGCATGGA\nCTCGTCTCACCTTCCGCCGACTAATTCCCCGCGTACCAACACAGCCAGAGGCCACGGGGT\nTTCTGGCTTCCTGCCTGCCAAACACGTACCAGAGAATTACGTAACCTATTGATTTCGCTG\nCTGTGAGCAGGGTTCTTGTAATCAGTAGGTTACGTAATTCTCTGGTACGTGTTTGGC\n>NODE_454_length_237_cov_0.939024\nTAATTATTCGGAAACTCTTCGTGAATCTGCGCGGTCAGATCTCCATCCGACATCGCCTTC\nAAGTGGCGCGAAAGCGTATCGACCACAGCATGCTGCGCGATATCCTCCGCCGCCTTGGCG\nTGGTCGGCGGCAGCCTTGGCCACCGCCACGTCGCGGAAGGTGCCGAGTGCACGTGCCATG\nTCGCCCAATTCGTCGGACCGGGCGAGGCCGGGAATGTCCGACGCGGTGTCCCCCGCC\n>NODE_455_length_237_cov_0.939024\nTCCGACGCCATCGAGCGCGCCCTTGCGCATGGTGATAGCGACAAGGTGCGCGCGGCTTAT\nCATCGCGGGGCCCACTGGAAAGAACGCGTGGAGATGGCCCAATGGTGGTCGGATTACCTC\nGACGACCTGCGCAAACAGGATAGCAAATCCAGGGCAGCGGCCTTTGGGACGATCGACATC\nGTCGTCCTCGACGTGTCCGAATCCGCCGCTTCAGGGCCCAAAGTCGTTGCCTAAGGT\n>NODE_456_length_237_cov_0.939024\nCCCCTATGGCCAGACCGGCTTGCCGCTTTCCCTGCTGGTGCAAGGCGAGGACGCGAACAC\nCTTGTTCGACGTCAGCCAGCCGGTGAACGGCGCTGGTGCCGACATCAAGGGTATCGAGGT\nAGCAGTCCAGCACGACTTCACCTTTCTGCCCGGCGCGCTCAAAAATCTTGGCGCTGTGGT\nCAACGGAACGTGGTTCGACGGGCATCAGACCGCCTATTACAACAACGTGCCGAAGGT\n>NODE_457_length_237_cov_0.939024\nCTTCTGAACGTGCGTAATGACCGACTGAAGAATCGGCATGCATTCTTTGTTCAGAACAAC\nTCGCGCCTCGTCATTCTTCAAGGCCATCGCGAGCTCCACCACCTTTACCGCCACCGGGTA\nATACTGCTTTTCGAGATCAGCCAATTGGTCAATCAACTGACGTTCGGCTTCAGGAGCTGC\nCGATTCGGCCAACAATCTTTTCAATTCCGCGAGGCCGTCATTGATGTCCTTTTGCGT\n>NODE_458_length_237_cov_0.939024\nTGCCTTGACTGAGCTGTTCGCTGGGTGCCAGATCCACCAAAGCCAGAAGGCGGCGCTCCC\nCCGGGGTATTGCGGCCCAAATCCTCCAGATCTTCCAGCAATTGGTTTCGGTTGAGCAGTC\nCCGAAACCGGATCGACACGACCGATCGCGTGCTGCAGCTCGATTTGCGACATCACCATGT\nCGGCAAGATCGGTCAAAGCCGCCATCTCTGCCTCGGAAACGGTGCGCGGCTCGTGAC\n>NODE_459_length_237_cov_0.939024\nGGCCTGGGCCTGAACCTGGTGAAGGAAATCATGCAGCTTCACAACGGAGCCATCGAGATC\nGGCAATGGCCCCCTCAAGGGCGCCTGCTTCACGATGCGCTTTTCCAGCGCTGCGGCTTGA\nTGCCGGAAGGTCTATGGCCGCTAGAAAAAGGTCTTGAACACGTCCTGGACGTTATAATCC\nGCGTCGACGAGATACATGATGTCCCATTTGTCGAACGTCGTGCACGGATGTGAAATC\n>NODE_460_length_237_cov_0.939024\nCTCATGCAGTGGCAGGAAAGTCAATACGCTACTGAGACTGAGAAATTGCGGGCGGCACGC\nGGAGCGGTTCGCAATCTCGAGCTGAAACTAGAAGCGGCCAAACGGGATAAGGCTGCCACA\nCAGCGCCAAGTGTCCCAGCGCGAGCGAGAGATTGGTGAGCGCATCGCCGAGTTCGCCAAG\nGCCTTCGGCGCGAATGGCCGCTATATGCCGTTGGAGGAGAAGCGTCCCTTCCAGATG\n>NODE_461_length_236_cov_1.417178\nTCGCCGCGAAGATGACCTCCGGCGCGGTCGAGATGCTCAGCTAGGGCAGGAAATGGTGAT\nCGGTGAGCCAGAAGCTGTGGAACCCGAGCCGATCGGCGAGCACGGCGGCTTCCACGGTGC\nCCTTCAGGGCCTGATGAGGACTGTCGCGGGTCCAGGGCTGCGGTTGGGGAACCTCGTAGA\nAGATGGCGAAGTCCACGTCAGATCCCTGCGGGGTCGATCCGTGCGATGGCAGCGAC\n>NODE_462_length_236_cov_0.944785\nGGTCCCGCTCAATATCCGCGTGAAGGACCCGATCTGGCCTGGCCGCGACATGGTCGACCT\nGTCGGTCAGCGTCCCCGCTGGCACGCCGCGCACACTGTGGCTCGATCTGCGCGACCGCGT\nGCTCTCGAATGACAGCCTCTATCTCAGCATCGCCTCGGCGCTGCCCGGCTTCGATGCCGC\nTGCGCTCAACGGTGCGAAGATCCGATTAGTGTTCAAGGATCGCGCCGCCGCTTTGC\n>NODE_463_length_236_cov_0.944785\nGTGGTAATATTTATGTAAATGCTTTCTACAACAAGTTTAATGGCTTGATTAATAATGCAC\nCTGTAACATTAGATGCAACAAGTGTAATGGCCAATATTAGTCAACAATTCAAATTCAAAA\nAGGGTTGGAGTGCAGAGCTAAGTGGTTTTGCCAGAACAAGAGCTTTAGAAAGTATTTTTA\nATATCGGGGCATTTGGTGTGATGAATGTGGGGGTTGGTAAGCAGGTAATGCATAAT\n>NODE_464_length_236_cov_0.944785\nGCCGCCGGGGTCGGCGCGGTGTCGGCGGGGGTGTCCTTCAGATAGCGGTCGAGAAAGGGC\nTTCATCGTGTTGCGGCGGAATTGCAGCCCGGTATCGCCCTCGAACTGCAATGCGCCAAGA\nCTGGTGCCATCATAATTGACGCCGCTATGCCGCCACGGCCCGATCACCAGCGAAATCGGC\nGCATTCGGGTCCTTGTCCTTCAGCGCCTTGAATACTGCAGGCGCGCCATAGCTGTC\n>NODE_465_length_236_cov_0.944785\nGTACTGGAATCGCGGGTTATCGCGCATGAACGGCTGCCGATGCTGGAGGTGGTGTGCGAC\nCGTGTGGTGCGCGCCTTTTCCAGCTCGATGCGCAATCTGACCTCTGACGCGATCGAGGTC\nAGTCTGGAGGAGGTTACTTCGACGCGCTTTGGCGAGTTCGTAGGGCGCGTTGCATTGCCT\nGCCATGATTGGTGTCTTCCACATTCACGAATGGGAGAATTACGGGCTCGTCACGGT\n>NODE_466_length_236_cov_0.932515\nTCCTTAACCAGGGGCTTGAGGTCACCGCGCAAGTGCTGAACGAACGCGCGCTAATCGCGG\nCGAAATCCGAGCGGGATTTCGTTTTGCACCTTGTCGAACAGCAGCGGGTTCAGCGCGATT\nCCGCCGAGGTTATGCACCTGACGGCGGAAGCGGTCGGCCAATATCTGGGCGTTGACCGGG\nCGGGCTTCTTCGATGTGACCCCGGATCACGTCGTCGAATATGGGCCGAGTTGGGTT\n>NODE_467_length_236_cov_0.932515\nTGCTGACGCCGCAGGACCGCGCGCCGTGGCGTCCGCATGTGACCGTGCAGAACAAGGTCG\nACCCGCCCGTCGCCAAGGCCTTGCAGGCCGAATTGTCGCGCGATTTCCGTCCGCGGCCCG\nTTCGAATCGCGGGGTTGGCGGCATGGTGGTATCGTGGTGGCCCGTGGGAAATGCTGTCGC\nGCCATATGTTCGCTTGACCGCTTCGCTGTGCATTCCTATAGCCCGCGCCTCGCGAG\n>NODE_468_length_236_cov_0.889571\nGGGGCGCAACTCAGAGATAAAGCATATCTTTGTGCTCGCGTGCCGATCTAAGAAGAGACG\nGCGACATAACGTACGACATATTGTGACTTGGTCAACCCGTACGCCTGCTTCGTAATCCGA\nCGGTCCTTTGAAGAGGCTGGCGAAGCAGGCGTACGGGTTTACCATGTCACAAAATGTAGT\nCCGTTTTGTCGCCGTCTCTTCGTTTATTGGCAAGCGAGCACATAGATATGCGTTAT\n>NODE_469_length_236_cov_0.858896\nGGACAAGCAGCAGCGTCGCGTCGAGGCGGCCGTCTATGCCGGATCGACACGCCGTGCCTA\nTCTCAAGGGCATCGGGCTGGCGCGCGGGTGCAAGGTTCCTGCGGCACCGACCGCCGCAGC\nCGTGGCGGACCGGCCGGAACTGCCCTGATTTGTCTGCGGACTGACTGAGCCGCGCAAAAA\nAAGGGCCGGGGTGCGAACCCCGGCCCTTTTCTCTTGGTCCAGCCTGGGCCGGGAGG\n>NODE_470_length_235_cov_0.950617\nATGTTATCCAGTGAGGAGAAATAGGTGTTCTGCTTACCGTTATCCGTTGTCTGAATACGG\nGGAGTTCTGGCTATCGGTGCCAGCATCTGCGCCACACCACCGAGCACCATACTGGCACCG\nAGAGAAAACAGGATGCCGGTCATACCACCGGCCCCAATGGCTGCCCCCCATGCTGCAAGG\nGTGGCTCCGGCGGTAAAGAATGATCCGGCAATGGCGGCAGCCCCCAGGACAATCT\n>NODE_471_length_235_cov_0.950617\nTTGTCACGCTTTGCGGCCGATCAATTATTTGCATTTTATTGTGCTCGCTCAATAACGCTG\nAATAAGCGCTACCAGGGGCGCTACCAGAAGCCCCGAGGCCTGAATGAATGTCCGGAACGA\nGCGAGCACCCCGGTCTTCCCCAACCGAGATGAGATCGTTGGCGTACACTTCGGGATCGGG\nGTAAATGCCTTGGCGAATAGCCCGGACGTCATAAAGCGCGACCATCTGCTTATCG\n>NODE_472_length_235_cov_0.950617\nTACCATAATACCTTCCTACTCGTTGAGATTTCAAATTGCATACGCTTTACGCGCAACAAT\nGATTTTATCTCAACGGCATTGTATCGGCAAACGACTTGAGCGCCATCCATTTTAAGGGCT\nAATTGCTTCGGCAGGTGAGTTGTTACACACTCCTTAGCGGATGACAACTTCCATGTCCAC\nCGTCCTGCTGTCTTCAGCAATCAACACCTTTCATGGTATCGATGATGAGTCGTTT\n>NODE_473_length_235_cov_0.950617\nTCTCCGTACCCTCCACCCGTCCAGATCAGCCGATGGCCGAAGGGAGATTTTCGCGGCTGT\nGGCGTCGAACCGACTGTTCTGCGCGGGCATGCTTGTAGCTCTCGAGCACCGCTCGCATGT\nCGGCGACGGCATGCTCGCGAGCCCTTGTGTCGTTGATTTGCGCGAGCTCTCGTTTCAGCT\nTGGTCGCGAAATCGGCATAGCTGTTCTGCCAGTCGGGTCCGATCACGTCCTGAAG\n>NODE_474_length_235_cov_0.950617\nTTTGCAGCATTGGCTTTTGCTTGGATCTGCCTGACTTTCGCATCGGTTAAAGAGAGGTAA\nGAACAGCCCATCACTATTCCTAGTGAGTATTGAGATGGCCCAAAATTACGCCCGGAGACA\nTGAGCGAGCGCGTAGAGATCGATAACGTCATACAAAAAAGTCGGTTCCGGATGACCTTTT\nTTATGGCAGTTAGCGGTCGCCTCCGAGCGTTCGGTGACGTCAGCAAGCACTCGTT\n>NODE_475_length_235_cov_0.950617\nGATCCGAACAGACGATTGAAGAGCTTCCGGAGTAGCCGGTCTTTCGATTCGTTCGGAAAC\nCGACGTTTCTTTGATCGCTCTCCCCCTACCACTCGTATGGATCCCTGGGTGAGTCTCTTC\nTCGGGCGGCAAAGACTCTTCGTGGGCGCTGTATCGAGCCCTAGAGCGGGGGGCTCCGGTC\nGAACGGCTGGTGACCGTTCATCCGACAGGTGACTCGTTCATGTACCATGTGCCAG\n>NODE_476_length_235_cov_0.950617\nGGCATGTGCATCAACTGCGTCACGCCAGCATACTGCGTTCGTGTGGGTTCATTTCCGTAT\nACAGGTCTGGCAGAAAGCGCGCCAGGTGGTTCATTTCCTCGCCGCAGTGCTGCAGCAGGT\nCGAGCGCCATGCGGTCGCTGACCATCAGGCGCCGCACCAGCCTGCTGTTGAGCACACCAT\nGCAGAGCTTGGTCGACCAGGGCATGGTGATGCCGGATCTCGCCCAGCCAGAAGGC\n>NODE_477_length_235_cov_0.950617\nGTCTGGGTCATTGTGGAAAATGGTGTAGGTGGCATGGCTTGCCGCACGCACGCCACTCGC\nCTTGCGCCAATCGATGAAGCGGCGGATCGTCTCTCCCAGCCGTTCAGGTGCCCCCTTATG\nCGTCAGGAACGCCACGGGAATGTCGGCTTCCTCCCGCACCATCACATCATCGATCGAAAA\nATTCTGCGTCATCATCAGGCTCCGTGCTTCGGCCAGTGGCACCATTGCCGCTGCC\n>NODE_478_length_235_cov_0.950617\nTCCCAATACACCAGTCAGGCCATTCATCTACTAGACCACCTCTCTTCCTCAACGACCTCT\nGTAGAATCATGGATGTGCTGAGAGGCCTCGAACTCAGCCTCCTCACGATTCCGAGAAACA\nATACCAAGCTCCTCCAGGAAAGAAATAGAAGACCTCACAGTATTCCTATCCAGGCCCAAC\nTCCCTAGCAATATTCCTGCAGTAATTCTCCTCCTCCTGGGCCAATACTCCTATGT\n>NODE_479_length_235_cov_0.944444\nCTGTTGCTGCGATCGCCATTTCGGCATGCACCCGAAGACCGAAACGACGACGACCGACAA\nCACGATGGTCACCGATCTGAACTCGACCGACACGATGACCACCAACGACACGATGACGTC\nGACCGACGGCGCGATGGCAAACGACGGTGCGATGGTTTCGAACGACACCATGACCACCAA\nCACCACGTCGACCACGACCACGAACAAGATGTAATTCTTCCCTTTCGGGAAAGAT\n>NODE_480_length_235_cov_0.944444\nGGATAAGGGCACCGTCCTCGCCCAGCCCGTCGAACAAGCCGTCCACCGCCGTGCCATCGG\nCGAGACGCGCGGTCAGCGCGGTACCTGGGCGGTGCGCCCGTTCGATCCAGCGCGCCCGGA\nCGGGCGCAAGCCCCTGCCCTCGCCACAGGCCGAGCCAGCGAGCATACGACTCGGCCAGGG\nTTTGGGCGAAGTCGGCCGGGTCAACGCCCGCGCCCCGCGCCGCGAGGCTGGTGGC\n>NODE_481_length_235_cov_0.932099\nTCACGGTCCGAGGCAAACGGCGCGCTGCGGTAGAGCCGGTCCACCGCCAGATCGAGCGCA\nTGGTGCGCGCGGCGCAGATCGCCCGGCATGGTATCGGGATCATAAAGATCGGCGAGGCTG\nGCGGTCGGGTGCGCGAGGCGCGCATCGAGCACCGCTTGCGCAAGCTGCTCGATTTTCGCG\nCGCTGTGCGGGCGTGGCGTCGGGCCAGGGGAAGGTGTTGTAGACGAGGCCGATTG\n>NODE_482_length_234_cov_0.956522\nGTGCCGAGCGGGCCATTGCCCGATCTCGTGATACTGGCGATGAAGCCGCAGCAATTGGAC\nGACGTCGCGGGGCGCTTTGCGGAGCGCTTGCGGGGCGTGCCGGCGTTGATCTCGATTTTG\nGCGGGCGTGGAAGAGCAAGCGTTGGCCGAGCGGTTTCAGGCCCGGGCGATCGTTCGGGCG\nATGCCCAATCTGCCGGTCGGGATCGGCACTACTGCTGTCGAGCGCCACCACGCC\n>NODE_483_length_234_cov_0.956522\nGGGAAAGGCAGCTCCGCTGGCCACGCCCAGACTGAAGCGTCCCTTGGAAAGCAAGTCCAG\nCGTGGCCACGTTCTCGGCCAGCGCAATGGGGTCGTGCAGGGCTGGCATGCAGGTCATCGC\nGCCGATGCGCGACTTGTTGGTCACCGCGGCCATGTAGCCCAGCATGGCCATGACGGCCCC\nTTGTGGCCATAGGCTGTCGTAGTGGTGTTCGCCAAGCCAGATGTCGTCATAGCC\n>NODE_484_length_234_cov_0.956522\nGATTACCTCTATTTGTGTGGTCCGTTCTAGTGACAGCATTCCTACTTTTATTATCACTTC\nCGGTACTGGCAGGGGCAATTACCATGTTATTAACCGATCGAAACTTTAATACAACCTTTT\nTTGATCCCGCAGGAGGGGGAGACCCCATTTTATACCAGCATCTCTTTTGGTTCTTCGGTC\nATCCAGAGGTGTATATTCTCATTCTGCCTGGATTCGGTATCATAAGTCATATCG\n>NODE_485_length_234_cov_0.956522\nCTCCCTGATGTTGGTGCCGAGCAGGGTGTGCTCCCACGGGACGAACCCCACCGGCAGGGT\nGGCGGCGAACGCGGCGGCCTGAGCGCCGAAGACCCGGCGCAGCCGGATGGGGACGGCCTT\nGCCGCGCGATTCCAGGGTGGACACGGCCTGGTCCATGTCGCCGTCGAAGCGGACGGTGGC\nGGTGACCATCAGCGAGAACCGGACCGACGCCGCGCCGGCGGCGACCTCCTGACG\n>NODE_486_length_234_cov_0.956522\nGCACCAGTGAGCTCATTAGGGTTTGGAGAGTCTTTAGTGAACCAATATGTGAAGCTCATG\nGCACAGTTCACAGTTGTACCTGGAGACATCTTGGGGACTGAAGAGCCTCTGTGGTGTGCT\nTGTACTGGTGGATTTGGCCCAAATCCAACCATGTATGACCTTCCTTTAGGGTTTTTCCCC\nAGCAAGTAATCCATCTGTTGCCTAGCGAAAGCCATGAGGCTGGCTGAGTCAAAT\n>NODE_487_length_234_cov_0.956522\nCATATTGCAGCCGCGCCGCCTCGGCCGAGCGCATGCTGCTGTCGCGCGCGGCATGCGCCT\nCGTCACGGCGCTGCGCGGCGATCACGCCCTCGGCATAGAGCGTATCGGCGCGCTTGCTGG\nAAGTGGCGGCAAGGTTCGCGGCAGCCTGAGCCGATTGCCAGATCGCGCGCAGCGACCCGA\nCATCCTCGCTCCTTGCGCCCGCTTGCGCCACCGCTTGCAACGCCCGCGCCGTAT\n>NODE_488_length_234_cov_0.950311\nTCCTGCGCGGTGATGTTCACCGTCACGAAATTCGAGAAGCGATACTTGCCTGCATAGGAT\nGCCAGCGTTCTGGCGGGCACCGCCGGCTGCGGCGACATCACCGGCAAGGCCGGCTGCGGC\nGGCACAGATGCGAGCACCGCGTCCCAGGCCAGTTCGCTGGCGATCGAGCCGATCTCGACG\nCCGTTGAGCGCGCCCGGCGTGCTCGGATCGGGCGCATCGATTTCGCCGGTGGTG\n>NODE_489_length_233_cov_1.443750\nTTGGCGAGAAGTGGTCAGGTGTGGCGCCCTATATGCGAATCATCCTGGGTGCAGGTGCAG\nTTCTGGCCGTGACCTTCAGTCATACCCCGGTATTTGCGGCGATTGGGCAACCTCGGGTCA\nACCTGCTGGTGTCGACGGTCTCATCGGGTCTTTGGCTGGTATCCCTGCTGTTTTTGCCAA\nAGCTGGGTGCTTTGTATGCCGCGATTTTGTGGGTTGCCCGAATGGCGTTGGGC\n>NODE_490_length_233_cov_1.443750\nGCGTTGCGGAGGGATTGCCGCCGTTCTTTGCCACGGGCGATGCCAGGGCGATCGCGGCGG\nTGTGGGATGGACCGGTAGAGCCGATCTCGCACCCGGAAGATACCAACCGCGTGTTCGAGA\nCTGCGTTGCCGGTGCTGACGGTCGAGGATGGCGGCGAGATCATGCCCGGCATTCCCGATG\nTCGAGGGTGCACGCTGTGCGCTGCGCGCGCTGGAGCTCGCGGCGGGCCTGGTG\n>NODE_491_length_233_cov_0.962500\nCCTTCGCCCTCGGACTTCAACCATAGCCGGTTTATATCGCCGCCGACCCAAGCTTCGCCG\nTCCCAGCGATAGCCGTCACGGCCGGCACGCGCCTGAACCTCGGCGAGGTTGAACATCACC\nTGATAGAGCGTCTGGCCGCCCTGCTCGCGCATCATCGCGGCGCGCGATCGGCTCATGTCA\nGACGCCGGAAAAAAGCGATCGGCGTAATGATCCATCGGCGGCGGGGGTGCTGG\n>NODE_492_length_233_cov_0.962500\nGCGGTGACCACGATGTCGGCAATGCCGCTGTTATCGGGCGGGGTCGCGGCGGGAGCCGCT\nGGCGTGTCCTGCGGCGTGGCCGCAGCGGAAGGAACTGGCGCGACCGCTTGCGCCTGCGCG\nATCGCCGGGAAACTCACCGCGCAAAATAATGCGAACGGCCGCTTCAGAACCTGCATTCCC\nATATTCCTCTCCCCTTGCCTCGTTGGGCAACACCAAGATACGCGCAGCTCATC\n>NODE_493_length_233_cov_0.962500\nGTCCACGATGGCCTGGAAGGGATCGGTCAAATCGGTCGGCATAGCTCCGCGATAGCAGCC\nGCATTCGCAGGTGGCGAGATGGTCGCGTGGCGATTACACCCTGCGGACATGATCCGGTTG\nCTCTCGCTTGCCCTTCTCACTTTGCCCGCAGGTGCCATGCCCGATACTCCGCGCACGCCC\nGAACCGCCCTTGCTCAGCTGGCCCGACTTGACCGGACGGGCACAGCCGAAGCC\n>NODE_494_length_233_cov_0.962500\nGTTGACGCCTGGCCCCTCGGGGCCGGGCGCCGCGCATGATGCCCAAGGCCATTGAAGGTC\nACAGGGGCTTTTTGGCACTTCGTGTTTTGCGAAGTGCCTTTTGCTTTTGGCGCTCGGCCT\nCCTGCTCCGCGGCCACAGCAGCCCACTGCGCGAAGGCTTCGGGCGTTTCCAGCGTGATGC\nGGCCAATGATGGCGCTGCGGAAGTCGTTGAGCACAATCTCGGCGGCCTTCTGC\n>NODE_495_length_233_cov_0.962500\nGTGGACGATCCGGTCTGCCACCAGGCCTTCGACAAGATCAATGCCGACGAGGCCCGCCAG\nTTGGGCGTGGGCTTCCACGTGATGGAGATGCAGGGCTACAACAAGACCTTCATCCAGCTG\nGCCAAGATGGTGCTGCCGCTGCTGGACCCGCGCCTGCTGATCGGCATCCTCATCTACCTG\nCCGTTGCTCAACAAGATGCGCGACAACATCGTCAAGCTGGGCCTGCCCGAGAG\n>NODE_496_length_233_cov_0.962500\nTTGCAAACCCTTTCGGATTGGCTTGGCAACGGCGCACATGCCGCGCAGGCGAGCGAGCGT\nGATGCGAACGCGATTGGATCGGACGACACCGTCGCGCTTCTGGTGCATGAACTGAACCAA\nCCGATGACCGCGATGACCAATTTTCTAGCCGCTGCCCAAATCGCGCTGATGGCGGGTTCT\nTCGCCCGAGACGATCACCGGGTTCGTAAAGGATGCCAGCGCTCAATCCTTGCG\n>NODE_497_length_233_cov_0.818750\nATGTAAGGGACGGACTTGCGGCCAATTTCATCAGTTGCATTCTCGAGGGGCCTGGCGGAT\nCGCTTTGGATGAGCACGAACCGGGGGATCAGCAAGTTCGACCCGGCGCACCGAACATTCA\nCCAATTAGTCCGTTGCGGACGGGTGGCCTGGAAACGATCTGACAGGTTGGGGCTCGTGCT\nCGAAGAGTTCCGGCGGCCGGATGTACTTTGCGGGTTACCCGGGAGCTGTGGGT\n>NODE_498_length_232_cov_1.937107\nGCCCGCCCCTTCAGTGCCCGCGCGAGCAGTTTGCGCAAGGGCGCCAGCACCGCGAACAGC\nGCAGGCGTCAGGATCCAGCATTCCTGCACATCGACGATCGCATGGCTGGCGGGTTCGCTG\nAACCCCAACCGGACCGCACCGCCCTTGACCTCGGCATGGAGCGCCGCACGCCGCCGCGTG\nCGGTCGGGGGACAGTGAAGGCGGTCGAAGCGGTGCCGTCAGCCCCTGGGCGG\n>NODE_499_length_232_cov_0.968553\nGTATTACGCGAGCAAGCGCGGGCATCAGGCCGTACTGGTTGAAGAATGCGCGCTGCGTGC\nCAGGCACGGCTTCGATGTGCGCTGGCTGGACAGCGAGGCGGTCGCAGACGAGTACGGTAT\nCCGCGCACCGGGCGCGATCCTCAGTGCGCTCGCCGCACGCATCGACCCCTACCGGCTCAC\nCTACCAGCCGCGCGTGTGCAGCCGCATCAGCAGCCGGTAGGCTCACCTACCG\n>NODE_500_length_232_cov_0.968553\nGCCCGGTGACCGCGATCGTCACCGAGGCGGACATCGATGCCCAACTCGCCGCCCGAAAAG\nAAGCGCGTGCGGCAAAGAACTTCACCCGATCAGATGAGATTCGCGATGCACTGGCGGCGG\nTCGGTGTCGAGGTGATGGATGGTGATGCGCTGGCCTGGGACTGGAAATTGGCGGTCTAGC\nTCCCTCTTTCCTTCTCACACCTCCTCGTTCAAGCTGCACAGCAGACAATGCG\n>NODE_501_length_232_cov_0.962264\nGGTCCGGCCCTCCGGGATCGGCGCCGACTCGCCTGCATGAGCGGGTTCGCCGTCGCAGGG\nGCTGTCGCCGCCTTCGCGGCTCCGGCGGCGGGCCACGCGGGCGTCATGCCTTCGGCATGT\nACGCTGCTGGCGCTGGCGTTTCTGACGGGACTGAGCGGCACCTATGGGCCGGCGGCCGCA\nCAGGTCGGGACGCTTGTAGCTGTCGTCGCGGTCGTGGCCGTCGGCTTCCCGC\n>NODE_502_length_232_cov_0.955975\nTTATACAATGTAGTAGTTGCAATTGGAGACCCGATTTCAAGGAAAAGAGTTGTAGATAAT\nTTGCCACCACAAACAACGTATACTTCTATCATTCACCCAAGTGCAGTAATATCTGAATGG\nGTAGAAATCGGAGAGGGAAGTATAATTACAGCCGGGACTATTCTGACTTGTAATATAAAA\nATAGGTAAGCACCCCATTTAAACTTGCATACAACTATTGGACACGATTGTAT\n>NODE_503_length_232_cov_0.679245\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGCCTCCTCCCCCGCCCCCCGCGCT\nCTCCTCACGTTTGTTAACGTCGCCACCCCCCCATGGGTAATGGACGATCTGAAATAGGCA\nCAGCGCATCATGACCCTGTCGGTGTGGAAGATGTATCACAACCCCATGCACCGCAAGACC\nAGCCACAGCAGCAGAATACGGTGCAGCCGCAGGCCACCGCGCAGCAGGCGGG\n>NODE_504_length_231_cov_0.974684\nTCCGAGCTCTCTGCGCCAGTGGAAGAAATATGCCGGGAATTTTGTCCCGATGTACTTCTT\nGAAGTCGTTCTGGCTTTGCAGAAGGAATTTAGAGCGCAGTTTTATTTGGCTCAATATATT\nTTTATGACACGTGTGTTTGACTTGCTGCCCCCGGGCGTAATCAAGATAGTCGATACGCAT\nGATGTCTTCTCTACTAAAAAGGCCAAGGTGGCTCGTTACGGGGTCGAGGAT\n>NODE_505_length_231_cov_0.974684\nTCTGACGATTGCCCGCCGCGATCATGACGGTCGGCGCTTCCATCCTAACCGCGACGATCT\nGTATCGTTACCGCCAACGGTTCGCCGAAAAGCTGCGTGGTCGGGGCATCGAAGCGAACGC\nAACACCGGCGCGCGCGCGGGGCATCGATCCCAAGCATGAGCCCATCGCCGCGATTAAAAT\nGCGTAGCAAAGGACAGGTGCCCCGGCTCGATAAGTCGCGCGCGTTGCGCGC\n>NODE_506_length_231_cov_0.974684\nGCAAAGGCGCGGTCATAATAGCCCGCACCTTGCGACGTTTCCCGACGCTTGGCGGATCGG\nGGTTGCGTGGAGCGTGCAACAGGTCGAGTCCTTGCGGACCGAAGCGTGGGACATGCCGCT\nCCACGCCGTCATCACCGAATGTGGATGGATTCCCCGACCATGACCCCAAGTTGGCGTAAA\nCCCGTCGGGATGCTGGCGATTCTGGTGTTGATCGGCGTGTGGTGCATCCTG\n>NODE_507_length_231_cov_0.974684\nGCCCAAGCGATGACGCTGACGGCGGCGGATGGAAAGACCGTCTTTGGGCGGTTGTATCGC\nGCAGAGCATCCCAAGGCGACGATCCTGCTGTTTCATCAGGCGGGATCGAGCAAGGACGAA\nTATAGGACGATCGCGCCGCGGCTGGTCGCAGCCGGATATAGCGCTTTGGCAATCGATCAG\nCGCGCCGGTGGCACGCTCTTCGGCCCGAATGAGTCAAGCGCGCAATATCCG\n>NODE_508_length_231_cov_0.974684\nGCGGTGCCGCGGTCAGGCTCGCCGTCGCGCAGGCGATGCTGGTCACGGGCAAGGCCCCCG\nATTGCATGCCGCCATCATAGCGCATCATCTTGGCGATGTTCTTGGGGTTGGTGATGATAT\nAGCCGACGCGCAGGCCCGCCATGCCGAACAGCTTGGAAAAGGTCCGCATCACAATCACAT\nCGTCATGCTTCACCGCCAGATAGGACGCGACCGGCACGCCCGCGAAGTGGG\n>NODE_509_length_231_cov_0.974684\nGTTATTTACAATGGAAGAAGCAATGGTCTTTTTTATGCAAGGGTCAAAAAGCCTATCCTT\nTTCAGATGGGAAGAATATGGGATGAGGCCAAAAACATCAAGCTGCTTGTAAAAGCAGGTT\nCGAAAATAAATTACAACATCCGAATTGCCGGCGATCAGCAGTTTGAAAAAAACAATTTCG\nCGTATCATGCAGATAGCACTCATTTTTTGGGAAGGCTTACTGCCGCAGAAG\n>NODE_510_length_231_cov_0.968354\nCGCCAGAGCGGCCCGGTGACCAAGACCACCGACCCGAATACCGCCGAAGTCGAATCCTAT\nACCGTTACGCTGATCACGGGCGATCGCCACACCGGCACCCGCGCTGCGATCACCAACGCC\nGCGGGTGGCGGGACGACCTTCACCAAGCCGCTCGACAATACCGGCGTGAAGACGTTCCCC\nGATTATAACAGCTATGCCAAGCAGTTCGTTTACAACGTAAACATTCCCGGT\n>NODE_511_length_231_cov_0.962025\nGTCTGGACCACCGCGCTCGGTGTGACCTTGGTGCTTGGCGTGATGGTCGCATTTTGCCTC\nACGCGTGCGTGCCGATCGGGCACGGAAATTCGCTGGCATTGGGTGATGCTCTGTCTCGCG\nCTGGTGCTCTGGGACATGGCCTATTGGGCGATAACGTGGTTGCAGGCGCATTACCCTGAT\nGGCGCTCGGGTTTATTTCGACGAACTGTTCTTTATGCTTCGGCTGATACCG\n>NODE_512_length_231_cov_0.696203\nCCGGTGTACGGGGCAAATTGCTTGAGCATTTTACCCCTACACCGGCTTCGGCATTGTATC\nCAGAAGCAACATTAAGATCCATATTTACCTGTTCATAGGTAGAGGCAGGTACAATATCTT\nTAAAAATTACGGGGCGGTATGATTGTGAGATGCCGCCATAGATTGTGTTTTCCTTATCCA\nACAAATATTGTGCGCTTACACCCAGAAGCAGAAACTGGTGCGAGATACTGT\n>NODE_513_length_230_cov_1.847134\nAGACAGCATCAGTGCCCAGCGTGCCTATGAGATGAACAGTCGCGTGGTGAAGACGGCTGA\nTGAAATGCTCTCCACTACGGCGCAGATGCGATGAGCACGCCCCTCGGTCGCGCGGCACTC\nTTTGCGCTGCTGGCGTCTGCGCCGGCCATCGCCTGGGCGCAGCCGCCCGAGGCGGTCCGG\nGTCGCAGTGCTCGACCATCCGATCGCGCGCGGCGACGTGCTGGCCCTGGC\n>NODE_514_length_230_cov_1.789809\nTGGCTAGATCGACCGGTTTCGGGTCAAATAGGAAGAACTAGAAGATTCCACCTCTGGAAA\nGCGCCTACACCTAATGGCTTAAGCCGCTGTTCCCATTTTCTCGCTGACCCATCATGCAAA\nAGGTACGCCGTTAGAGTGAGTGCGCTTTACTAATAGAATCTCAAGTAAAGGCTCTAAGCT\nCCGCTCCTTCGACTGATTGTTCGCATCGGATCTCAGGTTCTCTATTGCAC\n>NODE_515_length_230_cov_1.554140\nCGGACCTTGCACTTGCGCGATCGCGGTGGGCCACAGCTCTGCAAGCTCACGAGCGAGCTC\nGGGGACGGGAGCCGTCAGATCAACAGCCCGCAGCAACCCCTCGATCATTTGCCCCAGCGC\nGTTCTCGCTGACGGGCGGACCGCGATAGCTGGTGGCGCGCGCGTGCAGGGTCGCTGGGCC\nGTCTCGCCCGGTGGGCACGCGCCGCGTGAGGCTGCGCGCGATCTGCGCGA\n>NODE_516_length_230_cov_0.980892\nGGATGAACTGGATCGCCCTTCTGGCGGCGCTGTCGGGCGCGATTGCGGTCGGCGCGGGCG\nCGTTCGGCGCGCATGGGGCAAGCGGTCAGGCGGCCGAGTGGCTGAAGACCGGCGCGCACT\nATCAACTGATCCACGCAGTTGTGGCGTTGGTGGCGTGGCGGATGGAGGTGCGCGGCCCGG\nCGTGGTTGTTCATCGGTGGCGGCGCGATATTCGCCGGAACGCTGTATCTG\n>NODE_517_length_230_cov_0.980892\nGTATGAAGCTGTCGGCATCGCTGGAATAGGGAAACGCCGCCGCATTGGGGCTGATCTCGC\nCAGCCTTATAAATCGATGCGAACCAGGACACTGGCAGATCGCGGTTGAAGGCGATGTACA\nCGTTGGTGTCGACGGTCTGCAATCCGGCGACGATGCGTTCCCCGCCAAGTTGGGCCAGGT\nCCGACGGAAAAAAGTAGCCACCAGTGCGATCGCGTAATCCTGCGCAGGAT\n>NODE_518_length_230_cov_0.980892\nGCGTATGCGCCGGTTGCAAAGAGGTAATCGAGAGCGGCCGCGCCGTCCCGCGCAACCACG\nACGTCATTGCCGACGTTGCTCTTCTTGAGCGCGCGCAGGGTCAGTTCCTCGTCCGTGGAA\nTTGTCCTCGACCAGCAGGATGACGTGCAGCGAGCTCATTTCGGGAGATCCTGCTCGTTCA\nGTGTGAAATAAAAGGTCGCCCCGCTTCCGACCGCGCCTTCAGCCCAGATG\n>NODE_519_length_230_cov_0.980892\nGCCTGGAATATGACGATCCGCGCGATGAGATCGCAGCGATCAAGGAAATGTATGGGGTGC\nGGGTTCACGATCCGCGCAGCATGGTTGCGCGCAGCGCGGACTATGACGACACGGCGGCTT\nTGGTTAGCGAGCTCGATCTTGTGATTGCGCCAACGACAAGCGTCATCGATCTATGCGGCG\nCGCTTGGGCGGCCGGCTTGGGCGTTCGCGCCGGTCAATCCGCAATGGCGG\n>NODE_520_length_230_cov_0.980892\nCATCGCCAGCAATGCTGGTGGTGCCGTGCGCAGGCGCTGAGCTGACGGTGAGGCTTGAGT\nGCACACCGCTGACCGAGGCGGTCAGGTCGATCGGGGTGGCGGTGTTATAGCCAACGCTGG\nCGCTCTTGGCGGCAACGGTTGGGGCGGCAGGTGTCGCGACGGTCAGCGTAACGGTGGCAG\nCGGCCGAGGTGCCGCCAGGCCCCGTGGCGGTATAGGCGAAGCTATCGCTG\n>NODE_521_length_230_cov_0.980892\nGTGTTTGCTGTGGGCTTGCCCATGCTGGCGATGTAACCATCCCTGGGGCTGGGGCCAGCA\nTCAAAGTGATAGGCGCAAGCCTCGAAGACTCGGGTACTTTCGGGTTCAAGTTCACGGTTC\nAGTCTGCCTCAGGCAAGCCTTACAAGACCTATGTCGAGCAGATTGCAGCCAGTCGTGGTC\nTGCCTGATTTGTGCAATCACTACACGGTCAATGCAGCGACGGGTACGCCC\n>NODE_522_length_230_cov_0.974522\nGTGTAGAGCACGGTGTCGAAATTCACCGCGTCCATGCCGCTCAAGGCCTTACGGTCGAGC\nCCTTTCAAACGGCGGATATTGTCAAGGGTGCGCGCCTTTTCCGCCGCACGCGCCGCCGGC\nGAGCTGTCGGAGAGCTTGAAACGGAGGTCGGCGTTCGCCCCTTTGTCGAGACCGAGATTA\nGTGGCGAATTCCGGGCTGTGGCGCAGGTTCTCCTGGAAGAAGGCCTCCAG\n>NODE_523_length_230_cov_0.751592\nGGATGGATCTTCGCTTGGCAAGGAAAGGTTCCCATCTTAACTGCACTGGACTCCGCAGCA\nAAGCAAACCGATGCCACGAGCCGCCTGTTCGTAATCGCGGCAGCGTTGGCGGGTTTTGGC\nCTGTCGTACCTGATTGTGCTGCGTTTTGTCGCGGATCTTCGCGACGAGTTCGGCCCGCAA\nGTGCGCGGCTGGATTTTACGTTGGTATGGCGGTGGCATCCTGGTGGGCAC\n>NODE_524_length_229_cov_1.967949\nGGACAAGACCACGGGTTGGGGGGCACCGGCCTGCCCGAACGACGCCGAAAGCGCCGCCTG\nTCGGCGCAGCAAATTCCGCTGAAAATGGTCGGCGGTCTGGTGCAGCAGGGCAGACGCGCT\nCCACAGCAACGTGATTGCGGCGACCAAAGCGATGCCGACATGCAGCGCGATAAATTGCCC\nGAGCAGCGAGCGCGGCGCGCGCATTCTCACGCGGCGGCGACCATCATAT\n>NODE_525_length_229_cov_1.923077\nCTAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTG\nATGGAGTGTTATCGTAATAGTAATTGAACTTAGTACGAGAGGAACCGTTCATTCAGATAT\nTTGGTATTTGCGCCTGTCCGATCGGGCAATGGCGCGAAGCTATCATCTGCTGGATTATGG\nCTGAACGCCTCTAAGTCAGAATCCGTGCTAGAAACGATGATGTTTGTCC\n>NODE_526_length_229_cov_0.987179\nTGCCTCATGCGACCGCGACCAGACCGGTTGCCACGAGTTCTTCCAGCCGCGCGTCCAGGG\nAACCCTCCTCGGCATCGCCCAGCACATAATCGACCGACAACCGCGCCATCAGATCAGCGC\nGGGTCATCCCCGCCTCGCCCAATGCCGCGAGGATTTCCGGCACGGGCGACGTCACCAAAT\nGCGTGATGCCCGACGCGCGGTGGAAAACCGCAGTGAAGCTGTCCAGGTG\n>NODE_527_length_229_cov_0.987179\nTTGTCTGCCAGTATCCGTAAAGACGAATCCAATTTGTTTGGGGTTAATGCCAACCAAAAA\nGGAGTGCCTTTGTACTCTATGGGTCTGGCATGGGAGTTAAATAAGGAAAAGTTTTATCAT\nTTTACTGCTTTACCGAATTTAAAATTAAGGCTTACGTATGGCTACAATGGAAATCTGGAC\nAAAAATCTTTCTGCTTATGTTACCTCAAGTCAATATAATTATCTAAATG\n>NODE_528_length_229_cov_0.987179\nCCTGTCATACCGCAAAACATACTTCTTGTGCAAAATGTATGGCGCTGGTGAGAGAATTGC\nAATCCTTACCGAGCATCAGGTTCTCGTTCTCTCCGGGACACGAAAATCCAGCCATTTGTC\nCTCCGTTCGGAGGACAGGTAACGCTGAAACGTTCCAAATGGGCGGAAACCCATGTCGGCG\nACAGCACCGTCTGACCGGCTAACAGGCTCATCGACTCCGCCTTCGCAGG\n>NODE_529_length_229_cov_0.987179\nGGTCAGCAGATGTACGGGGTGCGGTTCCACTACCCACGCGAAGAGCGGGCAATGGCGACG\nTTGCAGGCGCAGGTTGCCCAGGCTCAGGCGGCTAAGGCTATCGAGACGAACATCGCGCAG\nACGGCGCTCGATCACGCCGTGATCGAGGGCGCGCGGAACATGAAGTACACGGTGCAGGGG\nGACTCCTCGCTGCAGCCATCAGAAATCTCCGACAACGGCGAGTTCACGG\n>NODE_530_length_229_cov_0.987179\nGTAAAAGACTTACAGCATTTTAAAGTACTACAAACCTATATTGATGGGATACTTGTTGCA\nGATAATGGTAAAACCCTTATTTCTTCTGTTCCTGCAAGTATCATTAATACATTTGATTGC\nCAGCCAATTAGCAGGGATCAATTAGCTATTCATGAAAATGAATACCCGCAAAGCGAAGAA\nAAAATACCGGTAATTGAGGCTTTAGATGGACAATTAATTACCAATACAT\n>NODE_531_length_228_cov_0.993548\nTTCGTAGACACCCTCGACCAGCGCCGACATCAGCGATGTCTGGTACAATTCGCCGGATTT\nCGCATCCGCCGCGCGTCCGCCGGCGATCGCAGCCGCCCCGATCATCCCCAGCGCTGAGTC\nCGTCATCACTGCATCTCCTTGCGGCGTTCGGTTTCAAGGCTTTGGAAAACCGTGCCGATC\nGAGCGGCTTGCTACAAAGTCGCGCCTTTCCAGGCACTCATACAAAGGT\n>NODE_532_length_228_cov_0.993548\nCTTCGCGAGCAATTTCGATGGCGCACCGGCTGATCGCGTAGGCCTCACTGAGGCGTTCGG\nGCTTCGCCAGGTGCAGGATGGAAGCGACGATCTCAAAAATTGGTGCGCCGGGAAGGCCAG\nCACGCGCGTGAGCTCGCTCGAGCTTCACCATATCGACGACCGTCAATTGTTCGCGCCGGT\nTCGGATTGGACAGCGCGCGAAGGTAGGATGCTTTCCGTCCGGTAGCCT\n>NODE_533_length_228_cov_0.993548\nGACCGCGCCATCGAGGCCACGTATGTCGCAGGCGACTTGTTGGAGCTATCGCAAGTTGCG\nGTGGCGGACGATATGACTCCGGGTACTTTGGTGTTCGCTGCTCCCCCCTCGTTCGTCTCT\nCGTGCGGAAGGTGTATTTCATATCTTTGGTATGGGCACAGAGGACCCTACGCCTCTACCG\nTCGGCGTTGCGGACGCGTCTTCGGCAAGTGGGAGCTAATCGATTGCTT\n>NODE_534_length_228_cov_0.993548\nGGTAAGGAGAGTGCTAGGGAAGTGCCGCGACAAGAGGGTCCACAAGATAATAATTCGAAT\nACTATTTTACCATTGAGTGATGCGCTTGAAAAATATCCTGTTTGGTTTCGTGTGTATGAT\nGAGCCAACCAGACATTCATTAATTAATGAAACGTTTGTTTTTAAAGACGGTAAAGTTCAA\nAGTTATTATACGGAGAAGATAGACCTACATATTGAAGACGTTATTGAT\n>NODE_535_length_228_cov_0.987097\nCTTCAAGGGAGGACGCGAGTGGCGCGTCGACTCGACGTCGTTTCCGATTTCGAAGACGGA\nGACGGGTGTGATTCTCGATCTCGAACCAGGCGCCCTGCGCGAGCTGCACTGGCACCCGAC\nCTCTGACGAGTGGCAGTACGTCATCGACGGAACCATCAGCGTTACCTTGTTCGGTTCTCA\nCGGCCGGTATCGGACGGAAGAGCTGGAACAGGGGGAGGTGGGCTATAT\n>NODE_536_length_227_cov_1.733766\nTCGATGCACGGCGCAGCATCGCCTTTGTCGTTGGAGCGCATGTGACGCAGCAGGCGCTGG\nTATCGACCCGTTACACCACCGTCAGCCTGTTGCGGACGATCGAGGCGCTGCTGGGGCTGA\nAGCCGCCGTCGCACGGTAGCTCCACGGCGTTGCGGCCATGTCGAACACATCCGCCATCGG\nCAGCGCCAGCGCATCGTTCAGGCCAAGCGGCTTCAGCCCCAGCAGCG\n>NODE_537_length_227_cov_1.000000\nGAATGGAACCGCGACCTGCAGCTGCCCGTTGCGCAGATCAAGGTGGGCATCAATAATAAA\nCATATAGGGCTTTTGGGTTTGCGTGTAGCTGGGCGATGTTTTATATGCGGCGCCTTTTCA\nTGTTTGCCCCACGGCAGCTTTGTACGACAGGGCTGTTGCAATAAAAGATAAAAAGATGAA\nCGCCTATTGGAAAACCGCAGCGCGCGACCGCATCATCAATCACTAAG\n>NODE_538_length_227_cov_1.000000\nGAGCAATAGCTGCCGAGATTATGGCAAAGGCCCATCCGATCTTTGATGTCGAGCTTCATC\nTCGTCCTGGCTACATGCGAACAGGACAAGGAACGGCGTGGCGAAAGCGGCGATCGCGGCC\nGGCCCGCCGGCGAGCGCGGCTGCACCAGCACCGAGCGGCACGAGACCGGACACCTTTCCC\nGCGCAACAATTGATTAAGCCGAATACGGGTTTGTGGCAGGTCTCGCG\n>NODE_539_length_227_cov_1.000000\nGTTCTGTTTGCAGCAAGGCTGCACGAAGCCCCATGAGCATCAGCCCGGCTCCTGCGGCCA\nGCGCTGCCGCTTGGGTCCCGATAGCGATAGCGACGAACATCGATGCAGCGCAGAACGCGG\nTCGGCATCAGCATGCCGATCAATCTGGAGTGTCGTATCCGGCATTGCCCCTCCCCAGCGG\nCCGCGTCGGCGAACAGAAACAGGAAAAACGGGATGGCAAACGTAACG\n>NODE_540_length_227_cov_1.000000\nGACTATCGCTGGGGCGCGAACTCGGTGGCGACGACGCTTGGCGTGCTATGGGCTGGCCAG\nATGTGGCGCGACGTCGGCAGCTTCATCCAATCCGAACAAATCAACGTGCCTGCAGCGATC\nGCCACGCAAGTCTCGGCCGAACGCAAGCTCGCCGCTTTGGGCGAGGCGGTAGATCGATTG\nAACCGCGACTTTGGCGACTGGCGGGTCGGTTGGGGGAAGATCAATCG\n>NODE_541_length_227_cov_0.837662\nGGACAAGGTCAGGCCCGCCCTCAATCGCCAGTTTGATGAGTTGAATGCACATCGCAAGCG\nCGCCACCGCCGACGCGGGCGTTTGGAAGCTGCCGGATGGGGCCGCCTACTATGCCTGGGC\nGTTGAGTGCCGGCACGACCACGCACCTGACTCCCGATGAGATCCATCGCATGGGCCAGGA\nGCAGTTGCGGGAGCTGCAGGGGCAGATGGACGGCATACTCAAGGGAA\n>NODE_542_length_227_cov_0.785714\nTTCAAGGTCGGGCTGCCGCCCTATACGGACGGGGAACTCATCGAGCTGCTCTATGAGATG\nCACGGCCTCACACGGCGCAGTCCGACCTTGAACACTTCGAGCAGCTGCAGCCAGGCATCA\nTTCGACGCACTCCCGGCGGCGGCCCGGCGTAGTTCCAGGTACCGCGTCTGCGCATCGGAG\nTGGACAGCGAGAAGCAGGTCTTCGGTGCTCGAATAGTGGTACATCAC\n>NODE_543_length_226_cov_1.006536\nCTCATACGCAGCGTCATGCTCTGCTTGAACTTACGATTGAGGTCGCTTAGCGACAAGTCG\nAGCAGTACACCCTCTTCGATCAAGCGGGCGACCTGGCCGCGGGAAAGGCAAAGCTTACGG\nGTGAGGATATTGATCAGGCGCACGGGAATGGCCTGTTCAAAGTCGAGGGTGATAGTCACC\nTGTTCGGTGTCAGTGAGGGCATATGGTGATGGCCCGTGTATCTCAT\n>NODE_544_length_226_cov_0.973856\nGGTCTGTTCGCCGCTATCCCGGCGGTGATTTTCTACAACTACTTCCAGACCCAGATCGCC\nGGCTACGGCTCTCGGACGGAAGGCTTCATCGCTGAACTGACCAACGCGATCTCTCGTCAG\nCTCGACAAGGGGGCGTAATAGCGATGGCGGCCAAATTATCAGGCCCCGGAAGCGGATCGA\nAGTACGTCGTTGACGCAAACCACGAGATCAACGTCACCCCCTTCGT\n>NODE_545_length_226_cov_0.699346\nAAGAAATCGACGTTGCCCAAGTTACACGTTCTTCTTACAATTTGGCAAATATACACTTTC\nAGTCTCATGTAAGCTGTGCGTGCTTGCATTGTATCCCTTATTTGACAGTCCGGAAAGGTT\nACTAAGAGCAGGCCAATCATTGATGGTTACGAAAAGCAACGCTCGTAGGTCAAATTCCTC\nTTCTTTGTGCTCATCCCACACACGTACACCAGGTCTGCCCCACAAC\n>NODE_546_length_226_cov_0.568627\nCTTTTTAGTGGATGAGATTTCCGACCGTTGGGCGAACCGGGCCTTGATCGACGCAGACGG\nCGGTAACCCGATGCGCCCGAGGTCGTGTTCGCACATGATGGGCTGCGGGTTACCGCCTTC\nTGCGTCGATCATGGCCCGGTTCGCCCAGCGGTCGGCTATCGCTTCGACTATAAAGGCCGT\nTCGGTTGTATTCAGCGGGGATACGGGGCCAAGCGCATCGCTGGTTG\n>NODE_547_length_225_cov_1.513158\nGTGATTTACCATCCGAAAAATCAGAGACCAATTTCAATGACTTTTCGCTGATGATTTTGA\nAATCACGGCTAGCTTGAGTCATGTTTGCCATCATCACGCCCACTTGGTTTTCATGATTGA\nTAGCCTTGGTTAATTTGTAGATTTCGTTGATAATGTCGAAAATCTTTTCTGTTTCTTTTC\nCTCGTTCAGATATTACATTTAAAATATCTGTTGATTTAGCTATAG\n>NODE_548_length_225_cov_1.013158\nTCCTTCGGCTATGGTGGAGGGCGCATCACGCGCCCTCCACGAAACGGATCGTTGCCGAAA\nCAGCGTTTGACGCTGCCACCCGTTGCGCCGCACTTGGGGGCCACGTAACAGGAGAACCGC\nAATGCGTCTTACCCATCTCTACGCCGCTACCGCCGCCGTGCTGCTCCTTGGTGCACCCGT\nCATCGCACAGATGGCACCGCCCGAGATGTTGCACGGTGCAGGCAC\n>NODE_549_length_225_cov_1.013158\nTGGCGACCTTCATCCTTGCCTGCTTCATTGATCACGCGACCGGCCAGCGCTTGCGACCAG\nGCCAGGGTGATATCGCTGTTGAACAGCGTCAAGGCCTGCAGGGGCGTGGTGGTGACGTCG\nCGCTTCTGGTGCGGCTGCACTGAGTTGGCAGGGTCAAAGCTCACCGTCAGCGGGTAGGGA\nACAGAGCGACGCACGAAGGTGTAGATGCTGCGACGGCGGGCGTCT\n>NODE_550_length_225_cov_1.013158\nTTGTTGACCGTGCTGAGCGTGTTGAGCCCGTTGATGAAGATCGGTGCAGCCGCCCCGAAC\nGCCCCGGTCAACGTGGCGATACCGGTCGGGCTGAGACAGCCCGGTGCGCTGGGGTTACGC\nAGAACTGCAGCGGCGTTGATCGTCGCGACCAGACGGCACGCGGCAAACGCCCCATATTGC\nGAGCCGAATTTGAGGTTGTCGCGAACCGTTAGATCTTCATTGGAG\n>NODE_551_length_225_cov_1.013158\nCGCTTCACCTTCTCCAGAATCGATTCATCCGGTTCGTCGACGATATCTTCGTCTCCCGCA\nCGGCCTACATAACAACGCATCAGAACTTTGTCCGGCGGGGCGGTATGCATCCACTTGGAA\nGAAATCCAGGTACAGGCCGTTATGTTCCGGCCTTCTTTCTTGGGAACCACAAACCCGGTA\nCCATCAAGCGGATACGGAACGTCGGCGGCATGAAACGCCAACAGG\n>NODE_552_length_225_cov_1.013158\nGCGCACGACTCCGCCTTCTACACAGGTTGGTTGTCGTTTGACCCCAGCTTCCAATAGGTC\nGCGTACCGCTCGTGCGCGATCCGGTAATAGGGGACCAGTCGTAGCGGTTGCTGGTCGGCA\nGCGGGGATCGTGAACTCAAGAGGCTTGGCGGTGGCACGGATCGTTTGTGGCAGCGTCTCC\nGGATTCCCCGCGAGCGTCGGCGGTGCGAAAGCCGCGTCGTTATAG\n>NODE_553_length_225_cov_1.013158\nGACACCGACGTTGGTCTATTGAGGTTTCTATTACGGGGTTCGATTCAGATGATGATTACA\nCCTTCACCTTTCCAAATGAGCCTGGTTTGAATGAGATTGCTTGCAAGAGTGTTTTAGGCA\nGCCCAGACGAGGTTCGCCTTAGTGCTTCTGGACTGGTACTTCTACGCGATGAGGCTTCTC\nCAGGAAGAATTTACTTCCGGCCGATTAAATCGGTCGAGGTAATTC\n>NODE_554_length_225_cov_1.013158\nTTGGGCAGCGCGATTGCGCGGTAACCTTGCCGAGGCCCAACGTCTGATTGAGCGGGCTTT\nCGTCAACGTCGATGGGAACACTTCGACGCTCGACCTGCGCGAGGGCCATCTGGTCGCATA\nCGACATTTACAAAAAGACCCACAATCAAGCTCAGGCGTTGGTCCATCTGGAAGCTCTGAA\nAGAAGTCGACGATAAAACCTCCAAGCTCGCCGCGTCTGCCAATAC\n>NODE_555_length_225_cov_0.921053\nTGGGTGGCGTGGCCGCGCGCCCTGATGGCGGCATCGCGTTCGAGTCGCGCGGCCGGGAAT\nATGGCGTCGTGCTCGCTGATATGGGCAGCCGCGAACACGACCGCCTCATCGGCTGCTGCC\nGTGCGCGCGTCGGTGCCCAGACCCGGCATGGCGAGGGCGCGGGCCTCGGCGCCTGCGACC\nATCGTGCGGCGCGTCCGCTCGTCGAAGCCGAGCTGGTCCGCCTCG\n>NODE_556_length_225_cov_0.664474\nGGCTTGGGCTAGGCGCGCCGCATGACCTCGACCAAGACCGCCGCCATCATCGTCGCCGCC\nGGTACCGGCGTCCGCTCGGGCAGCGCCGTTCCAAAGCAATATGCCCGCCTGGGCGGCAAG\nGCGGTGCTGGCATACAGCTATGCCGCCTTGCGCAACCATCCCGCGATCGACCGCGTCATC\nGTGGTGATCGGGGCGGACCAGGAGGCACTCCTGCACGATGCGATC\n>NODE_557_length_225_cov_0.361842\nTAGTTAGCCGTCACATTCTGTTAAGATACCGTCAACGCTCTAGTAGTAACATAGCACGTG\nTACTTCTCAAACAACAGAGATTTACGATCCGAAGACCTTCTTCACTCACGCGGCATTGCT\nCCATCCGGTTTGCACCCTTTGTGGATGATTCCCTACTGCTGCATACCGTAGGAGTCTGGG\nCCGTGTCTCAGTCCCGTAGGGTGATCGGCCACACTGGGACTGAGA\n>NODE_558_length_224_cov_1.529801\nGGCGTGAATGGGTGCGCCGTCCATCCAAGCCTTCAACCGGGTCTGCGATATCTCACCAAC\nCTCCAGCATGTGGAACATCAGCAAGGCCTTGGCGGCATGGCGAGCATGGCGGTCAGGATG\nCCGACGGAAGGAGGCCAGCCGACTGCGTGCTTCGGTCAGCGCGGCATCGACATCATGGAA\nCGCGGTACCGTGACCTGGCACCACAACCCGTACCTGCAGTGATG\n>NODE_559_length_224_cov_1.052980\nATATTCAGTGGGCGGACCCGTTCTCGCTGGAAATGTTGGTCAGCCTCGCCAGGACGCCAC\nCGCAAAACACCCTCGTCATTCTAGCCTATCGCGAAGACGAAGCGCATTTGCATCTGAAGC\nCGTCCGGGTTTCTGGACGCCATCAAATCGCATGCGCTCCCGGTTACTGAAATCGCGTTGG\nCACCGCTGCACGCCGCAGCCATCGTGGAAATGCTCGAATCCACC\n>NODE_560_length_224_cov_1.019868\nTGATTGGTGAGAACGATTGTCGAGAGGGGTTCGTCAAGGTCGCGGCGGTACCAGCAAGAG\nAAACCGGCGGTTCCCCCGCCGTGCGAGACGATGGTCCTTCCATCCACCTCGTCGACTTCC\nCACCCAAAGCCCCAACCGGCGGGCTGACCGTTCGACAGGCTGGCGCTACGCCACATCTTC\nCGCCGAACGCCCGAGCTCAAGATTCGCCCCTGATCCAGGGCAAC\n>NODE_561_length_224_cov_1.019868\nGGAGGAGGTCGAGGTCGATGTGGCTTACAGCACAGCCTACTTCCGACGCGATCCGGGGCA\nGTTGGGGCAGCAGGCCGGCGCTCTGGTCAGCGCCACGCCCACCTTGCCCCGCTCGGGCGT\nGGTGCTGGCGCAAGAGCCCGATGCGCAGGGCACCCCGAGGTGGGTCGTGACCCTGGCGGG\nCTACGATCGTGACCATCCCACCCCCACACTGGACGGCATGCGGC\n>NODE_562_length_224_cov_1.019868\nGGGGGTGGCCGCAGCCGCGAGCAGCAACCCCACGTCAGCCGGTACGGCGCGCCCTGCGGC\nGCGTCGCTCGTCGGCGAAGTCGCCTGCCATCCGGGCGAGCTCGGCGTCCGCCCGCTCCAG\nCAGGCCGCTCACGACGGAGACCGGCACCCCCATGAAGACGAGCTTGAGCACCGCTTGACG\nCCAGGCGGAGGGCTCGAGGTGGCGGGCGGCATACGGACCCATGG\n>NODE_563_length_224_cov_1.019868\nGAATAACCCCGACCCATGAGGATTCCATTGCGCCCGCTTCCCCGCCTCGCCCTGCTCGTC\nCTCACCCTGCTGTTCGCCGGCTGGTGTGTGAAGTCGCTCCGTGGCGATCTGGCCCAGCTT\nTCATTCGCGCGGAACACCTTTGAATCGGAGCGTTGACCGTAGTCACAACGCCGCAAGTTT\nTTTTCGTTAATCTGCAGAATAACCCCGACCCATGAGGATTCCAT\n>NODE_564_length_224_cov_1.019868\nGCAGTTATCCGCCCGCGATGGCGGAGCAATTCGAGCACGCTCTGAACGAGGCAGGCGTCA\nGCTATCGCAGCGAGACATACCCTGCCGCGCACGGATGGATGAAGCCCGACTTCCCCGTCT\nATGACGAGACGGCGGCAGAGCACGGTTGGCGTGAAATGCTGGCTTTCTTCCGTCGAACCC\nTTCGGTGACGGTTTGCGCTTTCGTGCGTCGAGTGGCTCTAATAG\n>NODE_565_length_224_cov_1.019868\nGCAGGACCTATTACCACAAGGCCGCGAAGGTCACCGAGTTGCCTTCCGGAAAGAATCTGG\nCGCGCGTGGCGCTGGAGGAGTACATCGGCAAAGTCTATGCTGTGGAACGTCAAATCAAGC\nAGTTGCGCGAGGAGCGGGAGAAATCCGGCCAAACACTGTCGTTGGAAACGGTACTGAAAA\nTACGCAAGGAACGGTCCGAGCCTCTCATGGAAGCGTTCAAAGAG\n>NODE_566_length_224_cov_1.019868\nTTCCTCGCAGAATACGCGCTCCTGCGCCGCGATTGCGGGCGAGGTGCGGCGGCTCAATGC\nCGCCTTGGGGACCGATGTGGATGTGCCGGGCCAACCCAAGGGCGAAGGGTCCGCGCTCGC\nTGCGGTCGCCGCGCGAACTGCGGTTAATACGCTGATTCCGGGCCTGGGCATCGTGCGTGT\nCATCACCGGGGCGGACAAGCAGCAGCGTCGCGACGAGGCGGCCG\n>NODE_567_length_224_cov_1.019868\nTTGAAGAACTTACCAGACAAATTTTATTGAAAGAAATTGCTCTGGAAAAATTCAACCTCA\nATTACAAATTGAATGTAGCCAAACAGGGAAGATGGAAGGGGTGGCGCTACGCATTAGCGA\nACGAAGCATCAGCCGCGCTTGGTATTGCCGGTGGAATCATCGGAACTGAACAGCGCGGTT\nCGCACTTGCATCGCTCAGACAAAGTAAAAAACTATGTGCAGGAA\n>NODE_568_length_224_cov_1.019868\nTCAGCAGACTGATCGCCGAGCTCAAGGAGGCCAAAGAGATTAGAAATGCGCTGTGCCACG\nGTTCGTGGGGCAAACCCGACGATCAGGGGCGCACGGTGCCCAAGTTCGTGAGGCGCGGCC\nTCCAGATTTTCGAAACGCCGGTTGACGTCGCCTTCTTCAAACAAACCCGCGCCGCGCTAA\nGGGAAATCATCTGCGACATTCTCGATAGCGTGACAATGGTTGGC\n>NODE_569_length_224_cov_1.013245\nGCTTATGAGCGCAACTGCGCTCGTCGGTATTCTCGGGGCTATTCCGAGCGTCACTTTTGC\nGCAAACTGCGCCATCTACGTCTACGAATTCTGTGGAGCCGGCCGCTAATACGATCCAGAC\nGGGTGATCCGAGCGATAATCCTTCCAATGATGGCGAAATCGTCGTCACCGGATCGCGCAT\nCGCGCGTCCGACATCGTCGTAACCGGGACCGGTGACGACAATGT\n>NODE_570_length_224_cov_1.006623\nTCCCCGACCCAATCCACATCCGCCGGATCAACCCGTAATACCGAGTCGCTGTAAATCGTC\nTCATGGATGAAGCGGTGTCCGGCGACGATTTGGTCGATCCCGCGCCAATACATCGCATAG\nCGGTTCACGAAGGTGGCATCCGCATGGAAGAGCGCGCCAAACGCGACCATGTCATGCGCG\nTTCCAGGCCGCTTCAAAGTGCTCGGTAATCCGTTCCGGATGATC\n>NODE_571_length_224_cov_0.986755\nGGCCTATGCCGTGAACAGCACCCCCACCTTCCTCATCAACGGCGTGGCGCAAGCCCATAC\nCTTCACCTGGGCGGCGCTGGAGCCGCTGGTGCGCGCCGCCGTTGCCAAGTAAAAATGCGT\nTTTCTCCAAGGAGCTTATTCGATGAACCCTCGCATCCTGTTCGCCGCGCTGGCTGCCGTT\nTCGCTCGCTTCGTGCGGCGACGCTGTTGCCGCCCGATGCCCCGC\n>NODE_572_length_224_cov_0.655629\nGGACGGAGAGACGCTTGTTCACCGCTCTCTAACGGGGTGGGCTCGTGGAGGTCTGAGAGT\nTCGCGCAAAGCTGCCGTAGCGAAGGCAAGCCGGCCAGCTATTGTCCAATCTATATACGTA\nGACGCCGCAGCGATGGACGTCGCAGCGCTATCAGCGGTCGAAAAGAACCACAGCTCACCT\nGCATAGTCGGGCAAGGCATGGAAGCTGACGACCAGGCTTGGAAG\n>NODE_573_length_208_cov_3.081481\nATGGTTTCAACGGGTAACGGGGAATAAGGGTTCGATTCATTCATAATAACTTTTCGAATC\nGCATGGCCTTGTGCTGGCGATGGTTCATTCAAATTTCTGCCCTATCAACTTTCGATGGTA\nGGATAGTGGCCTACCATGGTTTCAACGGGTAACGGGGAATAAGGGTTCGATTCATTCATA\nATAACTTTTCGAATCGCATGGCCTTGTG\n>NODE_574_length_164_cov_1.032967\nCAGCGACCAAAAGAATGCTAGAGTGGCAACCCAGACTGTTGGTGGTGTAGAGCTTCCTGT\nAGCCACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATGCTAGAGTGGCAA\nCCCAGACTGTTGGTGGTGTAGAGCTTCCTGTAGCCACTCTAGCA\n>NODE_575_length_151_cov_1.230769\nGCCCCCGACCGTCCCTATTAATCATTACGATGGTCCTAGAAACCAACAAAATAGAACCAA\nACGTCCTATTCTAGTGATGCCCCCGACCGTCCCTATTAATCATTACGATGGTCCTAGAAA\nCCAACAAAATAGAACCAAACGTCCTATTCTA\n>NODE_576_length_121_cov_4.125000\nGAAACGGTGCTTTCTGGTAGATATGGCCGCAACCAGTTGATCGGACGGGAAACGGTGCTT\nTCTGGTAGATATGGCCGCAACCAGTTGATCGGACGGGAAACGGTGCTTTCTGGTAGATAT\nG\n>NODE_577_length_99_cov_5.668605\nGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTAAAATTAACCCTCACTAAAGGGAAT\nAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCTTT\n>NODE_578_length_97_cov_12.208333\nGAACTGAAACATCTAAGTACAGGGGAACTGAAACATCTAAGTACAGGGGAACTGAAACAT\nCTAAGTACAGGGGAACTGAAACATCTAAGTACAGGGG\n>NODE_579_length_95_cov_11.181818\nACTTTCCAGAGCGTTCCGCTGCACTTTCCAGAGCGTTCCGCTGCACTTTCCAGAGCGTTC\nCGCTGCACTTTCCAGAGCGTTCCGCTGCACTTTCC\n>NODE_580_length_92_cov_14.473684\nGCTTGTACGCATACGGTCTGCTTGTACGCATACGGTCTGCTTGTACGCATACGGTCTGCT\nTGTACGCATACGGTCTGCTTGTACGCATACGG\n>NODE_581_length_92_cov_13.578947\nAGTCGTTTCTTCTGCTTGTAGTCGTTTCTTCTGCTTGTAGTCGTTTCTTCTGCTTGTAGT\nCGTTTCTTCTGCTTGTAGTCGTTTCTTCTGCT\n>NODE_582_length_76_cov_2.000000\nCATAGTAGGGAGGATATGAGGTGTGAGCGATATACTAGTATTCCTAGAAGTGAGATGGTA\nAATGCTAGTATAATAT\n" }, { "path": "tests/input/TestSnpEff/RBV16.fasta", "content": ">RBV16-1\nACAAAATCAGAGAAGAAGTAGACAGTATCATCTACAAAAAGAAAATGTAACACCTCTACA\nATGGATACCGACAAAATTGTATTCAAAGTCAATAACCAGGTTGTCTCTCTAAAACCTGAA\nATTATTGTAGATCAATATGAGTACAAATACCCGGCTATCAAAGACTTAAAAAAGCCCAGT\nATCTCCCTGGGAAAAGCTCCTGATTTGAACAAGGCGTATAAGTCAATTTTGTCCGGTATG\nAATGCAGCTAAGCTCGACCCTGACGATGTGTGCTCTTACTTGGCAGCTGCAATGCAGTTC\nTTTGAAGGAACATGTCCAGAAGACTGGACTAGCTATGGAATCTTGATTGCAAGGAAAGGA\nGACAAGATAACTCCAAACTCTCTCGTAGACATAAAACGTACAGATGTAGAAGGGAACTGG\nGCTCTAACAGGAGGAATGGAGTTGACTAGGGATCCCACCATTCCAGAACATGCATCTTTG\nGTTGGTCTTCTCCTGAGTTTGTATCGATTGAGCAAAATATCCGGACAGAACACAGGCAAT\nTATAAGACAAATATCTCTGATCGTATAGAGCAGATTTTTGAGACGGCCCCCTTTGTGAAG\nATCGTGGAACATCACACTTTGATGACAACTCACAAAATGTGCGCTAACTGGAGCACCATA\nCCGAACTTTAGATTCCTAGCCGGAACTTATGACATGTTTTTCTCTCGGATTGAACATCTA\nTATTCAGCAATCAGAGTGGGTACAGTTGTCACTGCTTACGAGGACTGCTCAGGGCTAGTA\nTCCTTTACAGGTTTTATAAAGCAGATAAACCTTACAGCAAAGGAAGCAATACTTTATTTC\nTTCCACAAAAATTTTGAGGGAGAGATAAGAAGAATGTTTGAGCCGGGACAGGAAACTGCA\nGTCCCTCACTCCTATTTCATCCATTTCCGGTCTTTGGGCCTTAGTGGGAAATCTCCATAT\nTCGTCAAGTGCAGTTGGTCACGTGTTCAACCTCATTCACTTTGTTGGATGCTATATGGGT\nCAAGTGAGGTCTTTGAATGCAACGGTTATTGCCACATGTGCTCCACATGAGATGTCTGTT\nCTCGGGGGTTATTTGGGGGAGGAGTTCTTTGGCAAGGGGACTTTTGAGAGAAGATTCTTC\nAGAAACGAGAAGGAACTTCAGGACTATGAAGCAGCAGAGTTGACAAAGACTGAGGTCGCT\nCTGGCAGACGACGGAACAGTCAATTCTGACGATGAAGACTACTTCTCTGGTGAAACCAGG\nAGTCCAGAGGCGGTCTATACTCGGATCATGATCAATGGGGGCCGACTCAAAAGATCACAT\nATAAGAAGGTATGTATCAGTCAGTTCCAATCATCAAGCTCGCCCCAATTCATTTGCTGAA\nTTTCTAAACAAGACATATTCTAACGACCCGTAGGGAGTCGAACTTCAAGATTGTCAACAA\nTAATAAATTGTTTAATTCCTCCACGAAAAAAACTAACACCCCTCCTTTTGAACCATCCCA\nAGCATGAGCAAGATTTTTGTCAACCCAAGTGCGATCCGGGCCGGCCTTGCTGACCTAGAG\nATGGCAGAGGAGACTGTAGATCTGATTGCCAGGAACATCGAGGACAATCAGGCTCATCTC\nCAAGGAGAGCCTATAGAAGTAGATAGTCTGCCCGATGACATGAGACGGCTCCACTTGGAT\nAGTGAAAAACCGTCTGGTTTTGACAAGGTGACAAAAGAAGGGGAGAGCAAGTGTCATGAA\nGACTTTCAGATGGATGAAGGGGAGGACCCCAGCCTCTTGTTCCAGTCATACCTGGATAAT\nGTCGGAGTTCAAATAGTCAGGCAAATGAGGTCAGGAGAGAGATTCCTTAAAATATGGTCT\nCAGACTGTGGAGGAGATCATATCCTATGTCATGATCAATTTCCCAGGCTCTTTGGGGAGG\nCCTTCTGAAGACAAGGCCACTCAAACTGCCAATCGGGAACCCAAGAAAGGAGTGGCATCA\nGTTTCGTCTCAACTCGAAGGTCAATCATCCAAAGCGAGAGCGGCAGCCCAAACTGCCTCC\nGGTCCACCTGCCCTAGAATGGTCTGCCACCAACGAAGAAGACGATTTGTCTGTGGAGGCA\nGAGATAGCTCATCAAATTGCCGAGAGCTTCTCCAAGAAGTACAAATTCCCCTCTCGATCA\nTCAGGGATATTCTTGTATAATTTTGAGCAGTTAAAGATGAACCTTGATGACATAGTCAAG\nGAATCAAAGAATGTGCCTGGTGTTACCCGCTTGGCCCATGAAGGGTCTAAACTCCCTCTA\nAGATGTGTACTTGGGTGGGTTGCTCAAGCCAACTCCAGAAAGTTCCAGCTGCTGGTCGAG\nCCTGACAAGCTAAATAAAATAATGCAAGACGACCTAAACCGTTATTTGTCTCGTCAACTA\nAATTTGTAGCCTCAGTCCCATTATGCAATCAAAACCAGTCTGATCCAAAGTCAACGTGAA\nAAAAACAGGCAACACCACTAATACAATGAATTTCCTACGCAAGATAGTGAAGAACTGTAG\nAGATGAGGACGATCAGAAGCCTTCTCTCGCATCGGCCCCCCCAGATGATGATGATCTGTG\nGTTGCCCCCTCCAGAATATGTCCCATTGAAGGAGCTCACAGGGAAGAAGAACATGAGAAA\nCTTCTGTGTTAATGGGGAGGTCAAGGTGTGTAGTCCAAACGGATATTCCTTTAGGATCTT\nGCGTCACATTCTGAAATCGTTCGATGAGATCTATTCCGGAAATCAAAGAATGATTGGGTT\nAGTCAAAGTTGTGGTCGGATTGGCCTTGTCTGGAGCCCCAGTCCCCGAGGGCATGAACTG\nGGTTTACAAACTAAGGAGAACTCTTATTTTCCAATGGGCAGACTCTAGGGGTCCTCTGGA\nAGGGGAAGAGTTGGAGTACTCTCAGGAAATTACCTGGGACGATGACACTGAATTTGTAGG\nGTTGCAAATAAGGGTGAGTGCTAGACAATGCCATATCCAAGGTAGAATCTGGTGCATTAA\nCATGAACTCTAGAGCATGTCAATTGTGGTCTGATATGTCCCTTCAAACTCATAGATCTGA\nGGAGGACAAAGACTCCTCAGTCCTTCTAGAGTAGTCGAATTATATCTCACAAGTTCCTCA\nATTGTCCACCTCTGGAGGAGAGAACACATGGGCTCAACTCCAACCTTCAGGAGCAATAGA\nACAAAAACATGTTATGGTGCCGTTGAATCGCTGCATTTTATCAGAGTCAAATCAATTACA\nATTGCACTTTAAGCCTCTTGGATGTGAAAAAAACTATTAACATCCCTCAAAAGACCTGAG\nGAAAGATGGTCCCTTGGGCCCTTCTGTTTGTGCCTTTTCTGATCTCTTCATTGTGTTTTG\nGGAAGTTCCCTATCTACACAATACCAGACAAGCTAGGTCCTTGGAGTCCTATCGACATAC\nATCATCTCAGTTGTCCCAATAATCTTGTTGTGGAAGACGAGGGGTGTAATAGTCTGTCGG\nGGTTTTCTTACATGGAACTAAAAGTGGGATACATCTCTGCCATAAAAGTGAACGGGTTCA\nCTTGTACTGGTGTCGTGACGGAAGCCGAGACCTACACTAACTTCGTCGGTTATGTCACCA\nCCACATTCAAGAGAAAACACTTTCGCCCGATGCCCGATGCATGTAGATCCGCATACAATT\nGGAAAATGGCAGGCGATCCTAGGTATGAAGAGTCCCTTCACAACCCATACCCTGATTATC\nATTGGCTGCGGACAGTTAAAACCACCAAGGAGTCTCTTATCATCATCTCGCCAAGTGTGG\nCTGACCTAGACCCGTATGACAAATCCCTTCATTCAAGGATTTTTCCTGGGGGGAAATGCA\nCGGGTCTAACAGTCTCTTCCACCTACTGCTCGACCAACCATGACTACACCATCTGGATGC\nCTGAAAAAGCAGGGCTCGGGACATCTTGTGACATCTTCACCAATAGTAAAGGGAAGAGAG\nCATCTAAAGGAGGCAAGACTTGTGGATTTGTGGACGAGAGAGGTTTGTATAAGTCCTTGA\nAAGGAGCTTGTAAGCTCAAACTGTGCGGAGTTTCTGGGCTTAGACTTATGGATGGAACTT\nGGGTTGCGATTCAGACATTGGATGAAACCAAATGGTGCTCTCCTGATCAACTGGTGAATC\nTGCATGACTTCCACTCGGATGAGCTTGAGCATCTTGTTGTAGAGGAGTTGGTTAGAAAGA\nGGGAGGAATGTCTGGATGCATTAGAATCCATCATGACCACCAAATCAGTAAGCTTCAGAC\nGTCTAAGCCACCTGAGAAAACTAGTTCCTGGGTTTGGGAAGGCATACACCATATTCAACA\nAAACCCTAATGGAGGCCGATGCCCACTACAAGTCCGTTCGGACTTGGAGCGAGATCATCC\nCCTCAAAAGGGTGTTTGAGAGTAGGGGGGAGATGTCATCCTCATGTAAATGGAGTATTTT\nTCAATGGCATCATTCTAGGTCCGGACGGGCATGTGTTGATCCCAGAAATGCAGTCATCCC\nTTCTCCAACAACATGTGGAACTGTTGGAGTCCTCTGTGATCCCCCTCATGCACCCCCTGG\nCAGATCCTTCAGCAGTTTTCAAAGATGGTGACGAGGCAGAGGATTTTGTTGAGGTTCATC\nTCCCAGATGTTCACAAACAGATCTCAGGGGTGGACCTAGGCCTCCCAAGCTGGGGAAAGT\nATATGCTGATGATTGCAGGTGCTCTAACGACTCTAATGCTGTTCATCTTCTTGATGACAT\nGTTGCAAAAGAGTCAACAGGACAAAGTCAATACGACAAGGCCCCAGAGAGATGGAAAGAA\nAAGTATCATTTACTCCCCAAAACAAAAAAGTCGTATCTTCATGGGAGTCTTACAAGAGCG\nGAGGCGAGACCAAGCTGTAAGGAGGGCTGCCCCCCCCACACACTATGCTCGGAAAACTGT\nTCCCCTCTGATACATGGAAGAATGTCCTGCCTTGACAATCCCCCACGGACTCTGTCCAAC\nAGGGTAAATTTCGAAGTCAAGAAACTTTCATCGATCATCTCACTCGACCAGACACATTCA\nGGTGGACTTTGATGATGTATGAAGCATTTTTACAGTATCAGCGACTAATGGTGCTCTCAC\nCCTCTAAGGACTGGTACTAAAGGTAGCGGACAGGCTGACTGACATCTCAGACAACCCTGT\nTTCTTAGCTTGGGCAGAGGTTGTGATAAGCTCCTCTACCTTAAACTAAAACAGTGATCAG\nCTGAGAAAACTGATTTGCCTCCTATGAAGGACACAAGCAATAGATCACAATCATCTCACA\nTCCCAATAAGTTGTGCATAACTACAAAGGGCTGGGCCATCTAATCTCCTCAATCAAGAAA\nAAAACTGTGAGACAGAGAAATCCTCAACAACACTTCTCATCCTGAACACTGCACCATGAT\nGATTGATCCAGGGGAGGTTTATGATGACCCCATTGATCCAGTCGAGTCTGAGAGTGAGCC\nAAGAGGAAACTCCAATATCCCCAACATCTTGCGAAATTCTGACTACAATCTCAACTCCCC\nTCTGATCGAGGATTCAGCCAAGCTGATGTTAGAATGGCTGAAAACAGGAAATAGACCTCT\nCCGGATGACCCTGACCGACAATTGTTCTCGGTCTTACAAAGTTCTGAAAGATTACCTCAA\nGAAAGTGGATCTAGGATCTCTCAAAGTGGGCGGAGCTGCAGCACAATCTATGATCTCTCT\nTTGGTTATATGGTGCTCACTCTGAATCAAATAGGAGCAGGAGGTGTATGACTGACTTAGC\nTCAATTCTACTCCAAATCTTCCCCTATAGAGAAGCTGTTAAACTTCACACTCGGGAACAG\nAGGGCTGAGAATCCCCCCTGAGGGAGTCTTAAGCTGTCTTGAGAGGGTGGATTACGATAA\nGGCATTTGGGAGGTATTTGGCCAATATATATTCCTCCTATTTGTTCTTTCATGTGATTAC\nCCTTTACATGAATGCCCTAGATTGGGATGAGGAGAAGACTATCTTGGCACTGTGGAGGGA\nATTGACATCAGTGGATATGGGAAAGGACTTGGTCAAGTTTAAAGATCAGATATGGGGACT\nTCTGATTGTGACTAAAGACTTCATATATTCACAAAGCTCTCACTGTCTCTTTGACAGGAA\nCTATACGCTTATGCTAAAAGACCTTTTTTTGTCCCGGTTCAACTCTCTGATGATTTTGCT\nGTCCCCCCCGGAACCCAGATACTCAGATGACTTGATATCTCAGCTGTGTCAGCTGTACAT\nAGCAGGAGATCAAGTGTTGTCCATGTGCGGAAACTCTGGTTATGAAGTCATAAAAATCTT\nGGAGCCGTATGTTGTAAACAGCTTGGTCTATAGAGCGGAAAAATTCAGGCCTCTTATTCA\nCTCTCTGGGGGACTTCCCTGTTTTTATAAAGGACAAGGTGAATCAACTTGAGGGGACGTT\nTGGTCCTAGTGCGAAGAGATTCTTTAAAGTCTTGGATCAATTCGACAACATACATGATTT\nGGTCTTTGTATACGGTTGTTACAGGCATTGGGGGCACCCTTACATAGACTATAGAAAGGG\nTCTGTCAAAATTGTATGACCAGGTCCACATTAAAAAGGTGATAGATAAGTCCTATCAGGA\nGTGTTTAGCGAGTGACCTGGCCAAAAGAATCCTCAGGTGGGGGTTCGACAAATACTCCAA\nATGGTATCTAGATCCACGACTTCTTGCGAGGGATCACCCCCTGACTCCTTATATCAAGAC\nCCAGACATGGCCTCCCAAGCACATAGTGGATTTGGTAGGTGATACCTGGCATAGACTCCC\nGATCACCCAGATCTTCGAGATCCCTGAATCAATGGACCCATCAGAGATATTAGATGACAA\nATCACACTCTTTCACTAGAACAAGGCTAGCGTCATGGCTTTCGGAAAACAGAGGAGGACC\nGGTTCCAAGTGAGAAGGTCATTATTACGGCTCTCTCCAAACCGCCTGTCAACCCTAGAGA\nGTTTTTGAAATCTATAGACCTTGGGGGGCTGCCAGACGAAGACTTAATCATCGGCTTGAA\nACCCAAAGAAAGGGAGCTGAAGATCGAAGGCCGATTTTTTGCTTTAATGTCTTGGAATTT\nAAGGCTATACTTCGTTATTACAGAGAAGCTCCTGGCCAATTATATATTACCACTCTTTGA\nTGCATTAACCATGACCGACAATTTGAACAAGGTGTTCAAAAAGTTGATTGATCGAGTCAC\nCGGACAAGGGCTCTTAGATTATTCGAGGGTTACATATGCTTTTCACTTGGACTATGAGAA\nGTGGAACAATCATCAGAGACTAGAATCGACTGAGGATGTATTCTCCGTCCTTGATCAAGT\nGTTTGGATTAAAAAGGGTGTTCTCCAGAACTCATGAGTTTTTCCAGAAGTCTTGGATATA\nTTACTCAGATAGATCTGATCTTATAGGATTGTGGGAGGACCAGATATACTGTTTGGACAT\nGTCAAATGGCCCGACGTGCTGGAACGGCCAAGATGGCGGGTTAGAGGGGTTACGACAGAA\nGGGCTGGAGTCTGGTCAGCCTACTGATGATAGATCGAGAGTCTCAGACCAGGAACACAAG\nAACTAAGATACTAGCCCAGGGAGACAACCAAGTTCTATGTCCGACATACATGTTATCGCC\nTGGGCTTTCTAGAGAGGGCCTCCTCTACGAGTTGGAGAGTATATCAAGAAACGCACTCTC\nAATATATCGAGCCATCGAGGAAGGGGCATCTAAACTGGGGCTCATTATAAAGAAGGAGGA\nGACAATGTGCAGCTATGACTTTCTCATTTATGGAAAAACTCCCTTATTTCGAGGTAACAT\nTCTGGTGCCTGAATCCAAAAGGTGGGCTAGAGTCTCCTGTATCTCTAACGACCAAATAGT\nCAACCTCGCTAATATAATGTCAACAGTGTCTACCAATGCTTTGACTGTTGCTCAACACTC\nTCAGTCTTTGATTAAACCGATGAGGGACTTTCTGCTTATGTCAGTGCAAGCCGTTTTTCA\nTTACTTGCTATTTAGCCCCATTTTAAAAGGCAGAGTTTACAAAATACTGAGTGCTGATGG\nGGATCATTTTCTTTTAGCTATGTCTAGAATAGTTTACCTTGACCCCTCATTGGGGGGTGT\nGTCTGGAATGTCTCTTGGGAGGTTTCACATACGCCAGTTTTCAGACCCGGTCTCTGAGGG\nGTTATCTTTTTGGAGAGAGATTTGGTTAAGTTCAAATGAGTCTTGGATCCATGCACTTTG\nTCAAGAAGCAGGAAATCCGGATTTGGGAGAGAGAACACTGGAAAGCTTCACACGCCTTCT\nCGAGGATCCCACTACCCTGAATATAAAAGGAGGGGCCAGTCCAACCATTCTTCTCAAGGA\nTGCAATCAGAAAGGCCCTGTATGATGAAGTGGATAAGGTGGAGAACTCCGAGTTTAGAGA\nAGCAATCCTCTTGTCCAAGACCCATAGGGACAACTTTATACTTTTCTTGAGATCTGTTGA\nGCCTCTCTTTCCTAGATTTCTCAGTGAACTCTTCAGCTCTTCCTTCCTGGGGATTCCTGA\nATCGATTATTGGGCTGATCCAAAATTCTAGAACGATAAGAAGACAGTTTAGGAAGAACCT\nCTCTAGAACCTTAGAAGAGTCTTTCTATAACTCAGAGATTCATGGGATCAATCGGATGAC\nACAGACTCCCCAGAGAATAGGAAGAGTTTGGGCCTGCTCTTCTGAGAGGGCAGATCTCCT\nAAGAGAAATCTCGTGGGGGAGAAAGGTGGTTGGTACAACCGTCCCTCACCCCTCTGAGAT\nGTTGGGGTTGCTTCCTAAATCTTCAATCTCCTGTACTTGTGGCGCAACAGGAGGGGGAAA\nTCCTCGAATATCAGTGTCTGTACTCCCGTCCTTTGATCAGTCGTTCTTTTCCAGAGGCCC\nTCTGAAGGGATACCTGGGCTCATCCACATCTATGTCAACCCAGCTGTTCCATGCTTGGGA\nGAAGGTCACCAATGTTCATGTGGTGAAAAGGGCCCTTTCACTCAAAGAGTCCATAAATTG\nGTTCGTCACAAGAAACTCCAATTTGGCTCAAACTTTAATCAGGAATATAATGTCTCTGAC\nGGGACCAGACTTCCCGCTGGAAGAGGCCCCCGTCTTTAAGAGAACAGGATCAGCTCTGCA\nCAGGTTCAAGTCAGCTAGGTACAGTGAAGGGGGTTATTCCTCTGTCTGTCCCAATCTCCT\nCTCTCATATTTCCGTCAGCACAGACACGATGTCTGACCTGACTCAAGATGGGAAGAACTA\nTGACTTTATGTTCCAGCCGCTGATGCTTTACGCACAGACATGGACATCAGAACTGGTGCA\nGAAGGACATACGGCTGAGAGACTCCACCTTTCACTGGCATCTTCGATGCAATAAGTGTAT\nAAGGTCCATCGATGACATCACTCTAGAGACTTCCCAGATCTTTGAATTCCCGGATGTTTC\nGAAAAGGATATCTAGGATGGTCTCTGGAGCAGTGCCTCACTTTCAAAAACTTCCTGATAT\nTCGTCTAAGACCTGGAGACTTTGAGTCTCTAAGTGACAAAGAGAAGTCACGCCACATAGG\nGTCGGCTCAGGGGCTCTTGTATTCGATCCTGGTTGCGATCCACGACTCTGGGTACAACGA\nTGGAACCATTTTTCCTGTCAACATATATAGCAAGGTCTCCCCGAGAGACTATTTAAGAGG\nTCTCGCCAGAGGAATCTTAATAGGGTCTTCTATCTGCTTTCTAACAAGAATGACAAACAT\nCAACATCAACAGACCCCTTGAACTAATCTCAGGAGTGATCTCATACATCCTCCTTAGATT\nAGACAATCACCCATCCTTATACATCATGCTCAGAGAACCGTCTCTGAGAGGAGAAATATT\nTTCTATTCCCCAAAAGATCCCCGCCGCTTACCCAACCACAATGAAAGAGGGCAACAGATC\nTATCCTGTGTTACCTCCAGCATGTGCTCCGCTATGAGCGGGAGGTAATTACAGCATCCCC\nGGAGAATGATTGGTTATGGATCTTCTCTGACTTCAGAAGTTCCAAAATGACCTATTTAAC\nCCTTATCACCTATCAGTCTCATCTTTTACTTCAGAGGGTTGAGAAGAATCTCTCTAAAAA\nTATGAGGGCCAACCTACGACAGATGAGCTCTCTCATGAGACAAGTATTGGGCGGGCATGG\nCGAAGACACCTTAGAATCAGACGAGGACATTCAGAGGTTGTTGAAAGACTCATTACGTAG\nGACAAGATGGGTAGATCAAGAGGTGCGTCATGCAGCCAGAGCCATGACAGGGGGTTATAG\nCCCCAATAAGAAGATGTCTCGCAAAGCGGGGTGTTCAGAATGGGTCTGCTCTGCCCAACA\nGGTTGCTGTTTCAACCTCAGCAAATCCAGCCCCTGTCTCTGAGCTGGACATCAGGGCTCT\nCTCCAAAAGACTTCAAAACCCGTTGATTTCAGGTCTGAGAGTTGTTCAGTGGGCAACAGG\nCGCTCATTACAAACTCAAACCTATTCTTGATGATCTCAATGTGTTCCCATCCTTATGTCT\nTGTGGTCGGAGACGGGTCAGGGGGGATCTCAAGGGCTGTACTCAATATGTTTCCGGACGC\nTAGGCTCGTGTTCAACAGCCTGTTGGAAGTGAATGACCTGATGGCTTCAGGGACACATCC\nGTTGCCTCCTTCAGCAATCATGAGCGGAGGGGATGATATCATATCTAGGGTGATTGACTT\nTGACTCCATCTGGGAAAAGCCTTCTGACTTAAGGAACTTGACGACATGGAGGTACTTCCA\nGTCGGTTCAAGAACAAGTGAATATGTCCTATGATCTTATTATTTGTGACGCAGAGGTCAC\nTGACATCGCATCAATTAATCGAATAACTCTACTAATGTCTGATTTTGCATTATCAATAGA\nCGGCCCACTTTATTTAGTTTTCAAAACTTATGGAACCATGCTCGTGAATCCTGATTACAG\nAGCCGTTCAACATCTGTCCAGAGCATTTCCCACAGTCACAGGATTCATAACCCAGATGAC\nATCATCCTTCTCGTCTGAGCTATACCTCAGATTCTCTAAAAGGGGAAAATTTTTCCGAGA\nTGCAGAATACTTGACTTCTTCTACTATTAGGGAGATGAGCCTTGTATTGTTCAACTGCAG\nCAGCCCAAAAAGTGAGATGCAGAGGGCCCGCTCTCTGAATTACCAGGACCTTGTAAGAGG\nATTTCCTGAGGAGATCATATCCAACCCATATAATGAGATGATCATAACTCTGATTGACAG\nTGATGTGGAATCTTTCCTGGTTCATAAGATGGTTGATGACCTAGAGTTGCAGCGAGGAAC\nTTTGTCTAAAGTCTCCATTATCGTAGCCATCATGATAGTCTTTTCCAACAGGGTGTTTAA\nTGTCTCGAAACCGTTGACTGACCCTTTATTCAATCCGCCATCTGACCCCAAAATCTTGAG\nACACTTCAATATTTGCTGCAGTACCATGATGTACTTGTCTACTGCTCTGGGGGATGTTCC\nAAGCTTTGCTAGACTTCATGACCTGTATAACAGACCAATAACCTACTATTTCGGGAAGAA\nAGTTATCCGAGGGAACATTTATTTATCCTGGAGTTGGTCTGACGACACTTCAGTGTTCAA\nAAGGGTGGCTTGCAATTCTAGTTTGAGCCTCTCGGCTCACTGGATAAGGCTGATTTACAA\nAATAGTGAAGACTACCAGACTTGTGGGAAATACGGAGAATCTATCCAGGGAGGTCGAAAA\nGCACCTTCGAGGGTACAACAGGTGGATTACCCTAGACGACATAAAATCCAGATCATCTCT\nTCTAGATTACAGCTGCCTATAAAACAGGGCATTTGGGGAGAAATACATGGACCAACACCT\nTGAGACAGTATGCCCTGAAAAAAACAAGACCCTGATTCATAACCTCTATTTGCTTGATGG\nTTTTTTTTGTCTTTGTTGTTTTTTTGTTAA\n" }, { "path": "tests/input/TestSnpEff/msa.fasta", "content": ">JQ685920\nACGCTTAACAACAAAATCAGAGAAGAAGTAGACAGTGTCGTCTACAAAGCAAGAATGTAA\nCACCCCTACAATGGATGCCGACAAGATTGTGTTTAAAGTCAATAATCAGGTGGTCTCTCT\nGAAGCCTGAAATTATAATAGATCAATATGAATACAAGTACCCGGCTATCAAAGATTTGAA\nAAAGCCCAGTATAACCTTAGGAAAAGCCCCTGACTTGAACAAAGCATACAAGTCAATTCT\nGTCCGGCATGAATGCAGCCAAGCTTGACCCTGATGATGTATGCTCTTATCTAGCAGCCGC\nAATGCAGTTCTTTGAGGGGACATGTCCTGATGACTGGACCAGCTATGGAATCCTGATTGC\nACGGAAGGGAGACAAGATTACTCCAAATTCTCTTGTGGACATAAAACGTACTAATGTGGA\nAGGGAACTGGGCTTTGACAGGGGGTATGGAGTTGACGAGAGACCCCACAGTTTCGGAGCA\nTGCATCCCTAGTTGGTCTTCTCTTGAGTCTTTACAGGTTAAGCAAAATATCTGGACAAAA\nCACCGGCAATTACAAAACGAACATCGCAGACAGAATAGAGCAGATTTTCGAGACGGCCCC\nCTTTGTAAAGATCGTAGAGCATCATACCTTGATGACAACCCACAAAATGTGTGCTAACTG\nGAGTACTATACCGAACTTCAGATTTCTGGCCGGAACCTACGATATGTTTTTCTCGCGGGT\nTGAACATCTGTATTCAGCAATTAGAGTGGGTACAGTTGTAACAGCCTATGAGGACTGCTC\nAGGGTTGGTGTCGTTTACAGGGTTTATTAAGCAAATAAATCTCACTGCAAAAGAAGCAAT\nACTATATTTCTTCCACAAGAACTTCGAGGAAGAGATAAGAAGAATGTTCGAGCCGGGGCA\nAGAGACGGCAGTTCCTCACTCCTATTTCATACATTTTCGTTCTTTGGGCCTGAGTGGGAA\nATCTCCGTATTCATCAAATGCAGTTGGTCACGTGTTCAACCTCATTCACTTTGTTGGATG\nTTATATGGGTCAAGTGAGATCTTTGAACGCAACGGTTATTGCTACATGTGCCCCGCATGA\nGATGTCTGTTCTTGGGGGTTATTTGGGGGAGGAGTTTTTCGGAAAAGGGACTTTTGAGAG\nAAGATTCTTTAGGGATGAGAAAGAACTTCAGGAATATGAGGCAGCTGAAGCAACGAAGAC\nTGAAATAGCCTTGGCGGATGACGGAACAGTCAATTCTGATGATGAGGACTACTTCTCTGG\nTGAAACTAGGAGCCCGGAGGCAGTTTATACTCGAATCATGATGAATGGGGGTAGATTAAA\nAAGATCACACATAAGGAGATATGTCTCAGTCAGTTCCAATCATCAAGCTCGCCCTAATTC\nGTTCGCTGAGTTTCTAAGTAAGACATACTCTAGTGATTCATAAAGAATTGAACAACAGGA\nTTGTAAACATTAACAAATTGTGTACATCCTTCACGAAAAAAACTAACACCCCTCCTCTTG\nAACCATCTCAGACATGAGCAAGATTTTTGTTAACCCAAGTGCAATCAGGGCAGGCTTGGC\nTGATCTGGAGATGGCAGAGGAAACTGTAGATCTAGTTGCCAAGAACATCGAAGATAATCA\nAGCTCATCTCCAAGGAGAACCCATAGAGGTGGACAGTCTTCCTGAAGACATGAGACGGCT\nTCAGTTAGACGATGAAAAACCATCTGGCCTCGGTGTGATTGCCAAAGCAGGGGAGAGCAA\nATGTCAGGAAGACTTTCAGATGGACGAGGGGGAGGACCCCGCCCTCTTGTTCCAGTCGTA\nCCTAGACAATATTGGAGTTCAAATGGTCAGACAAATGAGATCAGGAGAGAGGTTCCTCAA\nGATATGGTCTCAGACTGTTGAGGAGATCATATCCTATGTCACGGTCAATTTCCCCAGTCT\nGCCAAGGAAAGCCTCAGAAGACAAGGCTACCCAGACTGCCAACCAGGAACTCAAGAAAAA\nGACAATGTCTGTTTCTTCTCAGCGAGAAAGTAAATCATCTAAAGCTAAAATGGCGGCCCA\nAACCGCCTCCGGTCCTCCTGCTCTAGAATGGTCCGCCACAAACGAGGAGGATGACCTATC\nTGTGGAGGCTGAAATTGCTCACCAGATTGCTGAGAGCTTCTCTAAGAAGTACAAATTCCC\nCTCTCGATCATCAGGGATATTCTTGTATAATTTTGAGCAGTTGAAGATGAACCTTGATGA\nCATCGTTAAGGAGTCGAAAAATGTGCCAAGCGTAACCCGCTTAGCCCATGACGGATCCAA\nACTCCCTCTGAGGTGTGTGCTGGGGTGGGTTGCTCTAGCCAACTCCAAAAAGTTCCAGCT\nGTTAGTTGAGCCTGACAAGCTAAACAAAATAATGCAAGACGACCTGAATCGTTATGTGTT\nCTGCTGACCAAACCCTCAAACTCAGTCGTGCTATGCGATCAAATCCAGCCTGCTCCAAAC\nCCAACGTGAAAAAAACAGGCAACACCACTGATAAAATGAACTTTCTACGCAAGATAGTAA\nAGAACTGTAGAGATGAGGACACTCAGAAGCCCTCTTTCGTGTCGGCTCCTCCAGATGATG\nATGACTTGTGGTTACCCCCTCCGGAATATGTTCCATTGAAGGAACTCTCGGGTAAGAAAA\nACATGAGAAACTTTTGTATAAATGGAGAGGTCAAAGTGTGTAGTCCGAATGGCTATTCAT\nTTAGGATCCTGAGGCACATTTTGAAATCATTCGATGAGATCTATTCTGGAAATCAAAGAA\nTGATAGGGTTAGTTAAAGTTGTTGTTGGACTTGCGTTGTCAGGAGCCCCAGTCCCGGAGG\nGCATGAACTGGGTATACAAATTGAGGAGAACTCTTATCTTCCAGTGGGCTGATTCTAGGG\nGCCCTCTAGAGGGGGAGGAGTTAGAATACTCTCAGGAAATTACCTGGGATGACGATGCCG\nAATTTGTCGGATTGGAAATACGAGTGAGTGCAAGACAGTGCCATATCCAGGGCAGGATTT\nGGTGTATCAACATGAACTCTAGGGCATGTCAACTATGGTCTGACATGTCCCTTCAAACAC\nAAAGGTCTGAGGAGGATAAAGACTCTTCAATGCTTCTGGAATAGTCAATTTACATCCTAC\nAAATTCCTCAATTGTTTACCTCTGGAGGAGAGAGCACATGGACTTAACTCCAACCTTCAG\nGAGCAATAGAACAAAAACATGTTATGGTGCCGTTGAATTGCTGCATTTTATCATAGTCAA\nATCAATTATCTTTACATTTTAAGCCTCTCGGATGTGAAAAAAACTATCAACATCCCTCAA\nAAGACTTAAGGAAACATGATCCCTCAGGCTCTTCTGTTTGTGCCTTTTCTATTTCCCTCG\nTTGTGTCTCGGGAAATTCCCCATCTACACCATACCGGAAAAGCTCGGCCCTTGGAGTCCC\nATCGACATACATCATCTCAGCTGTCCTAACAATTTGGTTGTGGAGGACGAGGGTTGCGAC\nAGTCTGTCAGGGTTTTCTTACATGGAACTGAAGGTGGGTTACATCTCTGCCATAAAGGTG\nAATGGGTTCACTTGTACCGGTGTCGTGACAGAAGCTGAGACCTACACCAACTTTGTTGGT\nTATGTCACCACCACGTTCAAGAGAAAACACTTCCGCCCTATGCCAGATGCATGCAGAGCT\nGCGTACAACTGGAAGACAGCCGGTGACCCTAGATATGAGGAGTCTCTTCACAATCCTTAT\nCCTGATTACCATTGGCTACGGACCGTGAAAACCACCAAAGAATCTCTTGTTATCATATCG\nCCGAGTGTGGCTGATTTGGACCCATATGACAAATCCCTTCATTCAAGAGTTTTCCCTGGT\nGGGAAATGTTTGGGGATAACAATCTCTTCCACCTACTGCTCAACTAACCATGACTATACT\nATCTGGATGCCCGAAGAAGCAAGACTCGGGACATCTTGTGACATTTTTACCAACAGCAAA\nGGGAAGAGGGCATCTAAGGGGGGTAGGACTTGCGGATTCGTGGATGAAAGGGGCTTATAT\nAAGTCTCTAAAAGGGGCATGTAAACTTAAGCTGTGCGGAGTTCCTGGACTTAGACTTATG\nGATGGAACGTGGGTCGCTATTCAGACACCAGGTGAGACCAAATGGTGCTCTCCTGATCAG\nCTGGTAAATCTACATGACTTTCGTTCAGATGAGATAGAACATCTCGTCGTGGAGGAGTTG\nATCAAGAAGAGAGAAGAATGTCTAGATGCACTAGAGTCCATCATGACCACCAAATCAGTA\nAGCTTCAGACGTCTCAGCAACTTGAGAAAACTTGTCCCTGGGTTTGGAAAGGCATACACT\nATATTCAACAAAACCTTGATGGAGGCTGATGCTCACTACAAGTCAGTTCGGACTTGGGAT\nGAAATCATTCCCTCAAAGGGGTGCCTAAGAGTCGGAGGGAGGTGTCATCCTCATGTAAAC\nGGAGTGTTTTTCAATGGTATAATTCTGGGTCCGGATGGACATGTCCTGATTCCAGAGATG\nCAATCGTCCCTCCTCCAACAGCATATGGAGCTGTTGGAATCCTCTGTAATCCCCCTAATA\nCATCCCTTGGCCGACCCATCAACAGTCTTCAAAGACGGTGATGAAGCGGAGGACTTTGTT\nGAGGTTCACCTTCCGGACGTTCACAAGCAGGTCTCAGGGGTCGATCTTGGTCTCCCAAAC\nTGGGGGAAATATGTGCTGATGAGTGCAGGTGTTCTAGCGACCGTGATACTGACAATCTTC\nTTGTTAACATGTTGCAGAAGGGTTAACAGAACAAAACCAAAACAACAAAGTCTTGGGGAG\nTCAGGAAGGAAAGTATCGGTTACTCCTCAAAATGGGAAGGTCATGTCTTCATGGGAGTAT\nTACAAGAGTGAGGGCAGGACCAGTCTGTGAGTGCTGGCCATCTCCTCCATATCTTGCGTT\nCAGAAGATCACCTCTCTTCTAGATCTGGGGGAATCTCTTGTTTTGACAGTCCTTTGTGGA\nCTCCGTGCTACAAGGCAAAATTCGAGAGTCAAGAAACTTTCATTAATCATCCCAACTGAT\nCAGACACAGTTACGTAGGTTCTGATAATGTATGACGTCTTCTGACAGTGTCAGTGACCAA\nTGGTGCTCTCATCCCCCATGGACTGATACCAAAGGTTGTGGACAAACCAACCGATATCTC\nAGATAATTCTAGGCTTGAGCCGGGGCAGGGACCGTGGCTAGTCCCCCTACACTAGACT-A\nAATAATGGTTAGCTGAGGGAAGCGATTTGCCTCCTATGAAGGACATAAGCAATAGATCAC\nAATCATCTTACATCCCGATAAGGTGTGCTTAACTACAAAGGGCTGGGCCATCCAAGCTTT\nTCAGCCAAGAAAAAAACTGTGGAATGGAGGAGTAATTAACAACACTTCTCATCCTGAGAA\nCTGCACCATGATGCTTGATCCAGGGGAGGTTTATGATGACCCCGTTGATCCGATTGAGTC\nAGAGGCCGAGCCGAGAGGGAACCCAACCATTCCCAACATCTTAAGAAACTCTGACTACAA\nTCTCAACTCTCCTCTAATAGAGGATCCAGCCAAACTAATGTTAGAATGGTTGAAGACAGG\nAAATAGGCCTCTCCGGATAACTTTAACAGACAATTGCTCTAGGTCTTACAAAATTTTGAA\nGGATTATTTCAAGAAAGTGGATATAGGATCTATCAAAGTGGGCGGGGCTGCAGCACAATC\nTATGATCTCCCTTTGGTTGCACGGTGCCCACTCTGAATCAAATAGGAGCCGGAAGTGTAT\nAACCGACTTGGCTCAGTTCTATTCCAAGTCTTCCCCCATAGAAAAGCTGTTAAATTACAC\nACTCGGAAATCGAGGGCTGAGGATCCCCCCAGAGGGGGTCCTAAGTTGCCTTGAGAGGGT\nCGATTACGATAAAGCATTTGGGAGGTATCTGGTTAACATATACTCCTCTTACTTATTCTT\nTCACGTGATCACCCTTTACATGAACGCCTTGGACTGGGATGAGGAGAAGACCATTCTAGC\nACTGTGGAGGGATTTAACCTCAATAGATATAGGAAAGGACTTGGTCAAGTTTAAAGATCA\nAATATGGGGATTGCTAATTGTGACCAAGGATTTTGTGTACTCACAAAGTTCTAACTGCCT\nTTTTGATAGAAACTACACGCTTATGCTTAAAGACCTTTTTTTGTCTCGGTTCAACTCTCT\nAATGATTCTCCTTTCTCCTCCGGAACCCAGATATTCAGACGACCTGATATCCCAGCTGTG\nTCAGCTATATATCGCTGGAGATCATGTCTTGTCTATGTGCGGGAACTCTGGTTATGAGGT\nCATTAAAATATTGGAGCCGTACGTTGTGAACAGTTTAGTCCAGAGGGCAGAAAAGTTTAG\nGCCTCTCATTCATTCCCTAGGGGACTTCCCTGTATTTATAAGAGATAAGGTAGGTCAGCT\nTGAAGGAACATTTGGTCCCAGTGCAAAAAGGTTCTTCAGGGTTCTGGATCAATTCGACAA\nTATACACGACTTAGTCTTTGTATACGGCTGTTATAGGCATTGGGGGCATCCTTACATAGA\nTTATAGAAAGGGCTTATCGAAGCTATATGATCAAGTCCACATCAAGAAGGTGATAGATAA\nGACTTACCAGGAGTGTTTGGCCAGCGACCTGGCCAAAAGGATCCTCAGGTGGGGATTTGA\nCAAGTATTCCAAATGGTATATTGATTCAAGACTCCTCTCAAAGGACCACCCCCTAACTCC\nTTATATCAAAACCCAGACGTGGCCTCCAAAACATGTGGTAGATTTGGTGGGTGACACTTG\nGCATAAGCTCCCGATCACCCAGATCTTCGAGATCCCCGAATCAATGGACCCATCTGAGAT\nACTAGATGATAAATCACACTCTTTTACTAGAACTAGACTAGCGTCCTGGCTATCAGAGAA\nCAGAGGAGGGCCGGTCCCCAGCGAGAAGGTCATTATCACTGCTCTTTCCAAGCCTCCTGT\nCAACCCCAGGGAATTTCTGAAATCTATAGACCTGGGAGGATTGCCGGACGAGGATTTGAT\nAATCGGCCTCAAGCCTAAGGAAAGAGAGTTGAAGATAGAAGGTCGGTTTTTTGCCTTGAT\nGTCCTGGAATCTAAGGCTGTATTTTGTCATCACAGAAAAGCTCCTAGCCAATTATATCTT\nGCCACTTTTTGACGCACTGACTATGACAGACAACTTGAACAAAGTGTTTAAAAAGCTGAT\nCGACAGAGTCACCGGACAGGGGCTTTTAGACTACTCCAGAGTTACATACGCTTTTCACCT\nGGACTATGAAAAGTGGAACAATCATCAGAGGCTGGAGTCGACAGAGGATGTATTTTCTGT\nACTTGATCAAGTATTCGGATTAAAGAGGGTGTTTTCCAGAACTCATGAGTTTTTTCAGAA\nGTCTTGGATCTATTACTCAGATAGATCCGACCTCATCGGGTTATGGGAAGATCAAATATA\nCTGTTTGGACATGTCAAACGGCCCGACATGCTGGAACGGCCAGGATGGCGGGCTAGAGGG\nTTTGCGACAGAAAGGCTGGAGTCTGGTTAGCCTATTAATGATAGATCGTGAATCTCAAAC\nCAGGAACACAAGAACTAAAATACTAGCTCAGGGAGACAACCAAGTTCTGTGTCCGACATA\nTATGCTGTCGCCGGGGCTCTCTCGAGAGGGGCTTCTCTACGAGTTGGAGAGCATATCAAG\nAAACGCTCTCTCGATATATCGTGCCATCGAGGAAGGGGCATCCAAACTGGGGCTCATCAT\nAAAGAAGGAAGAGACCATGTGTAGCTATGACTTTCTCATCTATGGGAAAACTCCTTTATT\nTCGAGGTAACATCTTGGTGCCTGAGTCCAAAAGATGGGCTAGGGTCTCCTGTATCTCCAA\nCGACCAGATAGTCAACCTTGCCAATATAATGTCAACTGTATCCACTAATGCATTGACTGT\nCGCCCAACACTCTCAGTCTTTGATTAAACCGATGAGGGACTTCCTGCTTATGTCAGTACA\nAGCTGTCTTCCATTACTTGCTGTTTAGCCCCATCTTGAAAGGCAGAGTTTACAAGATCCT\nGGGTGCCGAGGGGGACAATTTTCTTCTAGCTATGTCTAGGATAATTTATTTAGACCCCTC\nATTGGGGGGAGTATCTGGAATGTCTCTTGGAAGGTTCCACATACGTCAGTTCTCAGATCC\nTGTCTCAGAAGGGTTGTCCTTCTGGAGAGAGATATGGCTGAGCTCCAGTGAGTCTTGGGT\nTCATGCACTGTGTCAAGAGGCAGGAAACCCAGATCTGGGAGAGAGAACACTGGAAAGCTT\nCACTCGCCTGCTCGAGGATCCTACTACCCTAAACATTAAAGGAGGGGCCAGTCCTACCAT\nTCTTCTCAAAGATGCGATCAGAAAAGCCTTGTATGATGAGGTAGACAAGGTGGAGAACTC\nAGAGTTTAGGGAAGCGATCCTCTTGTCTAAGACTCATAGGGATAATTTCATACTCTTCTT\nGAAATCTGTTGAGCCTTTGTTCCCCCGATTTCTCAGTGAGCTCTTCAGTTCATCATTCCT\nGGGGATTCCCGAATCAATCATTGGGTTGATACAAAACTCCAGAACAATAAGAAGACAGTT\nTAGGAGGAGTCTCTCAAGAACCTTGGAAGAGTCCTTTTATAACTCAGAGATCCATGGGAT\nCAACCGGATGACCCAGACTCCCCAGAGGGTCGGGAGAGTTTGGCCCTGCTCTTCTGAGAG\nGGCAGACCTCCTAAGAGAAATCTCATGGGGAAGGAAGGTGGTCGGCACAACAGTTCCTCA\nCCCCTCTGAGATGTTGGGGTTGATTCCCAAATCCTCTATTTCCTGTACTTGTGGAGTAAC\nAGGAGGGGGAAACCCTCGAATATCAGTGTCTGTGCTTCCATCTTTTGATCAGTCATTTTT\nTTCGAGAGGCTCTCTGAAAGGATATCTGGGCTCATCCACTTCCATGTCGACCCAGCTATT\nCCATGCCTGGGAGAAAGTCACCAATGTTCATGTGGTGAAAAGAGCTCTGTCACTCAAGGA\nATCTATAAACTGGTTCATTACAAGAGACTCAAATTTGGCCCAAACTTTGATTAGGAACAT\nAATGTCTCTGACAGGCCCAGATTTTCCTCTGGAAGAGGCCCCTGTCTTCAAGAGGACAGG\nGTCTGCCCTGCATAGGTTCAAGTCGGCTAGATACAGTGAAGGGGGGTACTCTTCAGTTTG\nTCCAAATCTCCTCTCTCACATCTCTGTCAGTACAGACACGATGTCTGATTTGACTCATGA\nTGGGATAAATTATGACTTTATGTTTCAGCCGTTGATGCTTTATGCGCAAACATGGACATC\nAGAACTGGTGCAAAAAGATACACGGCTGAAAGATTCTACCTTTCACTGGCATCTTCGATG\nTAACAAGTGCATAAGGCCCATCGATGATATCACCCTTGATACCTCTCAGATCTTCGAGTT\nCCCAGATGTCTCAAGAAGGATATCTAGGATGGTTTCTGGAGCTGTGCCTCATTTCAGAAA\nGCTTCCTGATATTCGTTTGAGACCAGGTGACTTCGAATCTCTAAGTGGTAAAGAGAAGTC\nTCGCCACATAGGATCGGCCCAAGGACTCTTGTATTCAATCTTGGTTGCGATCCATGACTC\nTGGGTATAATGATGGAACCATTTTCCCTGTCAACATATATAGCAAGGTCTCCCCTAGAGA\nCTATTTGAGAGGGCTTGCGAGAGGAGTCTTGATAGGGTCCTCGATTTGCTTCTTGACAAG\nAATGACAAACATTAACATCAATAGACCTCTTGAACTGATCTCAGGAGTGATATCATACAT\nCCTCTTGAGACTGGACAATCACCCATCCTTGTATATAATGCTCAGAGAGCCATCCCTTAG\nAGGAGAGATATTTTCTATTCCCCAAAAGGTCCCCGCTGCTTACCCGACCACGATGAAAGA\nAGGTAACAGATCTGTTCTGTGCTACCTCCAACATGTGTTGCGCTACGAACGAGAGGTGAT\nCACTGCATCTCCGGAGAATGACTGGTTGTGGATCTTCTCGGACTTTAGAAGCTCTAAGAT\nGACATATCTGACTCTCATCACCTACCAGTCTCATCTGTTACTTCAGAAGGTTGAGAAGAA\nTCTCTCCAAGAGTATGAGAGCCAACCTACGGCAAATGAGCTCTCTGATGAGGCAGGTGCT\nGGGTGGCCATGGTGAAGACACCTTAGAGTCAGACGAAGACATCCAGAGGCTGTTAAGAGA\nCTCTCTGCGTAGGACAAGGTGGGTAGACCAGGAAGTGCGCCATGCAGCGAGAACTATGAC\nAGGAGTTTACAGCCCCACCAAGAAGATGTCACGCAAAGCCGGGTGTTCAGAATGGGTCTG\nCTCTGCACAGCAGGTTGCGGTTTCGACCTCATCGAACCCAGCCCCTGTTTCAGAGCTGGA\nCGTCAGAGCCCTCTCCAAAAGGCTTCAAAACCCGTTGATCTCTGGACTGAGAGTGGTTCA\nGTGGGCGACAGGGGCCCATTATAAGCTCAAACCTATTCTGGATGATCTCAATGTCTTTCC\nATCTCTATGTCTTGTGGTCGGGGATGGGTCAGGGGGGATATCAAGAGCAGTACTTAACAT\nGTTTCCTGATGCCAAACTCGTATTCAACAGCCTGTTAGAAGTAAATGACCTGATGGCATC\nAGGAACACATCCGTTGCCCCCCTCAGCAATCATGAGTGGAGGAGATGACATCATATCCAG\nGGTAATTGGCTTCGACTCCATCTGGGAGAAACCTTCTGACTTGAGGAACTTGACCACATG\nGAGGTACTTCCAGTCAGTCCAAGAACAAGTAAATATGTCATACGACCTTATCATTTGTGA\nTGCAGAGGTCACTGACATTGCATCAATCAACCGAATAACCCTGCTAATGTCTGATTTTGC\nATTGTCCATAGACGGCCCACTTTATCTGGTTTTCAAAACTTACGGTACCATGCTTGTAAA\nCCCTGACTACAGAGCAATTCAACATCTATCCAGAGCATTTCCTGCGGTCACTGGATTCAT\nAACTCAGATGACCTCGTCCTTCTCATCCGAGCTATATCTCAGATTCTCAAAGCGGGGGAA\nGTTCTTCCGGGATGCAGAGTATTTGACTTCTTCCACCCTTCGAGAAATGAGCCTTGTATT\nGTTCAACTGTAGCAGCCCCAAGAGTGAGATGCAGAGAGCCCGCTCTCTAAATTACCAAGA\nTCTTGTAAGAGGATTCCCAGATGAGATCATATCCAATCCTTACAGCGAAATGATCATAAC\nTCTGATTGACAGTGATGTAGAATCTTTCCTGGTTCACAAAATGGTAGATGATCTAGAGTT\nGCAGCGAGGAACTTTGTCTAAAGTTTCTATCATTATAGCCATCATGATAGTCTTCTCCAA\nTAGGGTGTTCAATGTCTCAAAACCACTGACTGACCCTTTATTCTATCCGCCATCTGATCC\nCAAGATCTTGAGACACTTCAACATATGCTGCGGCACCATGATGTACTTGTCTACCGCCTT\nAGGGGATGTGCCCAGCTTCTCGAGACTTCATGACCTGTACAACAGACCCATAACTTATTA\nTTTTAGGAAGCAAGTCATCCGGGGGAGTGTTTACCTGTCCTGGAGTTGGTCTGATGACAC\nTTCAGTGTTTAAAAGGGTGGCTTGCAACTCTAGCTTGAGTCTCTCATCTCACTGGATCAG\nGTTGATTTACAAAATAGTGAAGACCACCAGACTTGTAGGAAGGGTCGAGGACCTGTCCAG\nGGAGGTAGAGAGGCACCTTCGGGGGTACAACAGATGGATCACCCTCGATGACATTAGATC\nCCGATCATCTCTGTTAGATTATAGCTGCTTGTAAGACTAAGCACTCTCGAGGGAATGTAC\nAGACTAAGATTATGGGACGGTGTAACCTGAAAAAAACAAGATCCCGATTCATAACTTCTG\nTTTACTTGATTG-TTTTTCCATCTTTATTGTTTTTTTGTTAAGCGT\n>RBV16-1\n----------ACAAAATCAGAGAAGAAGTAGACAGTATCATCTACAAAAAGAAAATGTAA\nCACCTCTACAATGGATACCGACAAAATTGTATTCAAAGTCAATAACCAGGTTGTCTCTCT\nAAAACCTGAAATTATTGTAGATCAATATGAGTACAAATACCCGGCTATCAAAGACTTAAA\nAAAGCCCAGTATCTCCCTGGGAAAAGCTCCTGATTTGAACAAGGCGTATAAGTCAATTTT\nGTCCGGTATGAATGCAGCTAAGCTCGACCCTGACGATGTGTGCTCTTACTTGGCAGCTGC\nAATGCAGTTCTTTGAAGGAACATGTCCAGAAGACTGGACTAGCTATGGAATCTTGATTGC\nAAGGAAAGGAGACAAGATAACTCCAAACTCTCTCGTAGACATAAAACGTACAGATGTAGA\nAGGGAACTGGGCTCTAACAGGAGGAATGGAGTTGACTAGGGATCCCACCATTCCAGAACA\nTGCATCTTTGGTTGGTCTTCTCCTGAGTTTGTATCGATTGAGCAAAATATCCGGACAGAA\nCACAGGCAATTATAAGACAAATATCTCTGATCGTATAGAGCAGATTTTTGAGACGGCCCC\nCTTTGTGAAGATCGTGGAACATCACACTTTGATGACAACTCACAAAATGTGCGCTAACTG\nGAGCACCATACCGAACTTTAGATTCCTAGCCGGAACTTATGACATGTTTTTCTCTCGGAT\nTGAACATCTATATTCAGCAATCAGAGTGGGTACAGTTGTCACTGCTTACGAGGACTGCTC\nAGGGCTAGTATCCTTTACAGGTTTTATAAAGCAGATAAACCTTACAGCAAAGGAAGCAAT\nACTTTATTTCTTCCACAAAAATTTTGAGGGAGAGATAAGAAGAATGTTTGAGCCGGGACA\nGGAAACTGCAGTCCCTCACTCCTATTTCATCCATTTCCGGTCTTTGGGCCTTAGTGGGAA\nATCTCCATATTCGTCAAGTGCAGTTGGTCACGTGTTCAACCTCATTCACTTTGTTGGATG\nCTATATGGGTCAAGTGAGGTCTTTGAATGCAACGGTTATTGCCACATGTGCTCCACATGA\nGATGTCTGTTCTCGGGGGTTATTTGGGGGAGGAGTTCTTTGGCAAGGGGACTTTTGAGAG\nAAGATTCTTCAGAAACGAGAAGGAACTTCAGGACTATGAAGCAGCAGAGTTGACAAAGAC\nTGAGGTCGCTCTGGCAGACGACGGAACAGTCAATTCTGACGATGAAGACTACTTCTCTGG\nTGAAACCAGGAGTCCAGAGGCGGTCTATACTCGGATCATGATCAATGGGGGCCGACTCAA\nAAGATCACATATAAGAAGGTATGTATCAGTCAGTTCCAATCATCAAGCTCGCCCCAATTC\nATTTGCTGAATTTCTAAACAAGACATATTCTAACGACCCGTAGGGAGTCGAACTTCAAGA\nTTGTCAACAATAATAAATTGTTTAATTCCTCCACGAAAAAAACTAACACCCCTCCTTTTG\nAACCATCCCAAGCATGAGCAAGATTTTTGTCAACCCAAGTGCGATCCGGGCCGGCCTTGC\nTGACCTAGAGATGGCAGAGGAGACTGTAGATCTGATTGCCAGGAACATCGAGGACAATCA\nGGCTCATCTCCAAGGAGAGCCTATAGAAGTAGATAGTCTGCCCGATGACATGAGACGGCT\nCCACTTGGATAGTGAAAAACCGTCTGGTTTTGACAAGGTGACAAAAGAAGGGGAGAGCAA\nGTGTCATGAAGACTTTCAGATGGATGAAGGGGAGGACCCCAGCCTCTTGTTCCAGTCATA\nCCTGGATAATGTCGGAGTTCAAATAGTCAGGCAAATGAGGTCAGGAGAGAGATTCCTTAA\nAATATGGTCTCAGACTGTGGAGGAGATCATATCCTATGTCATGATCAATTTCCCAGGCTC\nTTTGGGGAGGCCTTCTGAAGACAAGGCCACTCAAACTGCCAATCGGGAACCCAAGAAAGG\nAGTGGCATCAGTTTCGTCTCAACTCGAAGGTCAATCATCCAAAGCGAGAGCGGCAGCCCA\nAACTGCCTCCGGTCCACCTGCCCTAGAATGGTCTGCCACCAACGAAGAAGACGATTTGTC\nTGTGGAGGCAGAGATAGCTCATCAAATTGCCGAGAGCTTCTCCAAGAAGTACAAATTCCC\nCTCTCGATCATCAGGGATATTCTTGTATAATTTTGAGCAGTTAAAGATGAACCTTGATGA\nCATAGTCAAGGAATCAAAGAATGTGCCTGGTGTTACCCGCTTGGCCCATGAAGGGTCTAA\nACTCCCTCTAAGATGTGTACTTGGGTGGGTTGCTCAAGCCAACTCCAGAAAGTTCCAGCT\nGCTGGTCGAGCCTGACAAGCTAAATAAAATAATGCAAGACGACCTAAACCGTTATTTGTC\nTCGTCAACTAAATTTGTAGCCTCAGTCCCATTATGCAATCAAAACCAGTCTGATCCAAAG\nTCAACGTGAAAAAAACAGGCAACACCACTAATACAATGAATTTCCTACGCAAGATAGTGA\nAGAACTGTAGAGATGAGGACGATCAGAAGCCTTCTCTCGCATCGGCCCCCCCAGATGATG\nATGATCTGTGGTTGCCCCCTCCAGAATATGTCCCATTGAAGGAGCTCACAGGGAAGAAGA\nACATGAGAAACTTCTGTGTTAATGGGGAGGTCAAGGTGTGTAGTCCAAACGGATATTCCT\nTTAGGATCTTGCGTCACATTCTGAAATCGTTCGATGAGATCTATTCCGGAAATCAAAGAA\nTGATTGGGTTAGTCAAAGTTGTGGTCGGATTGGCCTTGTCTGGAGCCCCAGTCCCCGAGG\nGCATGAACTGGGTTTACAAACTAAGGAGAACTCTTATTTTCCAATGGGCAGACTCTAGGG\nGTCCTCTGGAAGGGGAAGAGTTGGAGTACTCTCAGGAAATTACCTGGGACGATGACACTG\nAATTTGTAGGGTTGCAAATAAGGGTGAGTGCTAGACAATGCCATATCCAAGGTAGAATCT\nGGTGCATTAACATGAACTCTAGAGCATGTCAATTGTGGTCTGATATGTCCCTTCAAACTC\nATAGATCTGAGGAGGACAAAGACTCCTCAGTCCTTCTAGAGTAGTCGAATTATATCTCAC\nAAGTTCCTCAATTGTCCACCTCTGGAGGAGAGAACACATGGGCTCAACTCCAACCTTCAG\nGAGCAATAGAACAAAAACATGTTATGGTGCCGTTGAATCGCTGCATTTTATCAGAGTCAA\nATCAATTACAATTGCACTTTAAGCCTCTTGGATGTGAAAAAAACTATTAACATCCCTCAA\nAAGACCTGAGGAAAGATGGTCCCTTGGGCCCTTCTGTTTGTGCCTTTTCTGATCTCTTCA\nTTGTGTTTTGGGAAGTTCCCTATCTACACAATACCAGACAAGCTAGGTCCTTGGAGTCCT\nATCGACATACATCATCTCAGTTGTCCCAATAATCTTGTTGTGGAAGACGAGGGGTGTAAT\nAGTCTGTCGGGGTTTTCTTACATGGAACTAAAAGTGGGATACATCTCTGCCATAAAAGTG\nAACGGGTTCACTTGTACTGGTGTCGTGACGGAAGCCGAGACCTACACTAACTTCGTCGGT\nTATGTCACCACCACATTCAAGAGAAAACACTTTCGCCCGATGCCCGATGCATGTAGATCC\nGCATACAATTGGAAAATGGCAGGCGATCCTAGGTATGAAGAGTCCCTTCACAACCCATAC\nCCTGATTATCATTGGCTGCGGACAGTTAAAACCACCAAGGAGTCTCTTATCATCATCTCG\nCCAAGTGTGGCTGACCTAGACCCGTATGACAAATCCCTTCATTCAAGGATTTTTCCTGGG\nGGGAAATGCACGGGTCTAACAGTCTCTTCCACCTACTGCTCGACCAACCATGACTACACC\nATCTGGATGCCTGAAAAAGCAGGGCTCGGGACATCTTGTGACATCTTCACCAATAGTAAA\nGGGAAGAGAGCATCTAAAGGAGGCAAGACTTGTGGATTTGTGGACGAGAGAGGTTTGTAT\nAAGTCCTTGAAAGGAGCTTGTAAGCTCAAACTGTGCGGAGTTTCTGGGCTTAGACTTATG\nGATGGAACTTGGGTTGCGATTCAGACATTGGATGAAACCAAATGGTGCTCTCCTGATCAA\nCTGGTGAATCTGCATGACTTCCACTCGGATGAGCTTGAGCATCTTGTTGTAGAGGAGTTG\nGTTAGAAAGAGGGAGGAATGTCTGGATGCATTAGAATCCATCATGACCACCAAATCAGTA\nAGCTTCAGACGTCTAAGCCACCTGAGAAAACTAGTTCCTGGGTTTGGGAAGGCATACACC\nATATTCAACAAAACCCTAATGGAGGCCGATGCCCACTACAAGTCCGTTCGGACTTGGAGC\nGAGATCATCCCCTCAAAAGGGTGTTTGAGAGTAGGGGGGAGATGTCATCCTCATGTAAAT\nGGAGTATTTTTCAATGGCATCATTCTAGGTCCGGACGGGCATGTGTTGATCCCAGAAATG\nCAGTCATCCCTTCTCCAACAACATGTGGAACTGTTGGAGTCCTCTGTGATCCCCCTCATG\nCACCCCCTGGCAGATCCTTCAGCAGTTTTCAAAGATGGTGACGAGGCAGAGGATTTTGTT\nGAGGTTCATCTCCCAGATGTTCACAAACAGATCTCAGGGGTGGACCTAGGCCTCCCAAGC\nTGGGGAAAGTATATGCTGATGATTGCAGGTGCTCTAACGACTCTAATGCTGTTCATCTTC\nTTGATGACATGTTGCAAAAGAGTCAACAGGACAAAGTCAATACGACAAGGCCCCAGAGAG\nATGGAAAGAAAAGTATCATTTACTCCCCAAAACAAAAAAGTCGTATCTTCATGGGAGTCT\nTACAAGAGCGGAGGCGAGACCAAGCTGTAAG-GAGGGCTGCCCCCCCCACACACTATGCT\nCGGAAAACTGTTCCCCTCTGATACATGGAAGAATGTCCTGCCTTGACAATCCCCCACGGA\nCTCTGTCCAACAGGGTAAATTTCGA-AGTCAAGAAACTTTCATCGATCATCTCACTCGAC\nCAGACACATTCAGGTGGACTTTGATGATGTATGAAGCATTTTTACAGTATCAGCGACTAA\nTGGTGCTCTCACCCTCTAAGGACTGGTACTAAAGGTAGCGGACAGGCTGACTGACATCTC\nAGACAACCCTGTTTCTTAGCTTGGGCAGAGGTTGTGATAAGCTCCTCTACCTTAAACTAA\nAACAGTGATCAGCTGAGAAAACTGATTTGCCTCCTATGAAGGACACAAGCAATAGATCAC\nAATCATCTCACATCCCAATAAGTTGTGCATAACTACAAAGGGCTGGGCCATCTAATCTCC\nTCAATCAAGAAAAAAACTGTGAGACAGAGAAATCCTCAACAACACTTCTCATCCTGAACA\nCTGCACCATGATGATTGATCCAGGGGAGGTTTATGATGACCCCATTGATCCAGTCGAGTC\nTGAGAGTGAGCCAAGAGGAAACTCCAATATCCCCAACATCTTGCGAAATTCTGACTACAA\nTCTCAACTCCCCTCTGATCGAGGATTCAGCCAAGCTGATGTTAGAATGGCTGAAAACAGG\nAAATAGACCTCTCCGGATGACCCTGACCGACAATTGTTCTCGGTCTTACAAAGTTCTGAA\nAGATTACCTCAAGAAAGTGGATCTAGGATCTCTCAAAGTGGGCGGAGCTGCAGCACAATC\nTATGATCTCTCTTTGGTTATATGGTGCTCACTCTGAATCAAATAGGAGCAGGAGGTGTAT\nGACTGACTTAGCTCAATTCTACTCCAAATCTTCCCCTATAGAGAAGCTGTTAAACTTCAC\nACTCGGGAACAGAGGGCTGAGAATCCCCCCTGAGGGAGTCTTAAGCTGTCTTGAGAGGGT\nGGATTACGATAAGGCATTTGGGAGGTATTTGGCCAATATATATTCCTCCTATTTGTTCTT\nTCATGTGATTACCCTTTACATGAATGCCCTAGATTGGGATGAGGAGAAGACTATCTTGGC\nACTGTGGAGGGAATTGACATCAGTGGATATGGGAAAGGACTTGGTCAAGTTTAAAGATCA\nGATATGGGGACTTCTGATTGTGACTAAAGACTTCATATATTCACAAAGCTCTCACTGTCT\nCTTTGACAGGAACTATACGCTTATGCTAAAAGACCTTTTTTTGTCCCGGTTCAACTCTCT\nGATGATTTTGCTGTCCCCCCCGGAACCCAGATACTCAGATGACTTGATATCTCAGCTGTG\nTCAGCTGTACATAGCAGGAGATCAAGTGTTGTCCATGTGCGGAAACTCTGGTTATGAAGT\nCATAAAAATCTTGGAGCCGTATGTTGTAAACAGCTTGGTCTATAGAGCGGAAAAATTCAG\nGCCTCTTATTCACTCTCTGGGGGACTTCCCTGTTTTTATAAAGGACAAGGTGAATCAACT\nTGAGGGGACGTTTGGTCCTAGTGCGAAGAGATTCTTTAAAGTCTTGGATCAATTCGACAA\nCATACATGATTTGGTCTTTGTATACGGTTGTTACAGGCATTGGGGGCACCCTTACATAGA\nCTATAGAAAGGGTCTGTCAAAATTGTATGACCAGGTCCACATTAAAAAGGTGATAGATAA\nGTCCTATCAGGAGTGTTTAGCGAGTGACCTGGCCAAAAGAATCCTCAGGTGGGGGTTCGA\nCAAATACTCCAAATGGTATCTAGATCCACGACTTCTTGCGAGGGATCACCCCCTGACTCC\nTTATATCAAGACCCAGACATGGCCTCCCAAGCACATAGTGGATTTGGTAGGTGATACCTG\nGCATAGACTCCCGATCACCCAGATCTTCGAGATCCCTGAATCAATGGACCCATCAGAGAT\nATTAGATGACAAATCACACTCTTTCACTAGAACAAGGCTAGCGTCATGGCTTTCGGAAAA\nCAGAGGAGGACCGGTTCCAAGTGAGAAGGTCATTATTACGGCTCTCTCCAAACCGCCTGT\nCAACCCTAGAGAGTTTTTGAAATCTATAGACCTTGGGGGGCTGCCAGACGAAGACTTAAT\nCATCGGCTTGAAACCCAAAGAAAGGGAGCTGAAGATCGAAGGCCGATTTTTTGCTTTAAT\nGTCTTGGAATTTAAGGCTATACTTCGTTATTACAGAGAAGCTCCTGGCCAATTATATATT\nACCACTCTTTGATGCATTAACCATGACCGACAATTTGAACAAGGTGTTCAAAAAGTTGAT\nTGATCGAGTCACCGGACAAGGGCTCTTAGATTATTCGAGGGTTACATATGCTTTTCACTT\nGGACTATGAGAAGTGGAACAATCATCAGAGACTAGAATCGACTGAGGATGTATTCTCCGT\nCCTTGATCAAGTGTTTGGATTAAAAAGGGTGTTCTCCAGAACTCATGAGTTTTTCCAGAA\nGTCTTGGATATATTACTCAGATAGATCTGATCTTATAGGATTGTGGGAGGACCAGATATA\nCTGTTTGGACATGTCAAATGGCCCGACGTGCTGGAACGGCCAAGATGGCGGGTTAGAGGG\nGTTACGACAGAAGGGCTGGAGTCTGGTCAGCCTACTGATGATAGATCGAGAGTCTCAGAC\nCAGGAACACAAGAACTAAGATACTAGCCCAGGGAGACAACCAAGTTCTATGTCCGACATA\nCATGTTATCGCCTGGGCTTTCTAGAGAGGGCCTCCTCTACGAGTTGGAGAGTATATCAAG\nAAACGCACTCTCAATATATCGAGCCATCGAGGAAGGGGCATCTAAACTGGGGCTCATTAT\nAAAGAAGGAGGAGACAATGTGCAGCTATGACTTTCTCATTTATGGAAAAACTCCCTTATT\nTCGAGGTAACATTCTGGTGCCTGAATCCAAAAGGTGGGCTAGAGTCTCCTGTATCTCTAA\nCGACCAAATAGTCAACCTCGCTAATATAATGTCAACAGTGTCTACCAATGCTTTGACTGT\nTGCTCAACACTCTCAGTCTTTGATTAAACCGATGAGGGACTTTCTGCTTATGTCAGTGCA\nAGCCGTTTTTCATTACTTGCTATTTAGCCCCATTTTAAAAGGCAGAGTTTACAAAATACT\nGAGTGCTGATGGGGATCATTTTCTTTTAGCTATGTCTAGAATAGTTTACCTTGACCCCTC\nATTGGGGGGTGTGTCTGGAATGTCTCTTGGGAGGTTTCACATACGCCAGTTTTCAGACCC\nGGTCTCTGAGGGGTTATCTTTTTGGAGAGAGATTTGGTTAAGTTCAAATGAGTCTTGGAT\nCCATGCACTTTGTCAAGAAGCAGGAAATCCGGATTTGGGAGAGAGAACACTGGAAAGCTT\nCACACGCCTTCTCGAGGATCCCACTACCCTGAATATAAAAGGAGGGGCCAGTCCAACCAT\nTCTTCTCAAGGATGCAATCAGAAAGGCCCTGTATGATGAAGTGGATAAGGTGGAGAACTC\nCGAGTTTAGAGAAGCAATCCTCTTGTCCAAGACCCATAGGGACAACTTTATACTTTTCTT\nGAGATCTGTTGAGCCTCTCTTTCCTAGATTTCTCAGTGAACTCTTCAGCTCTTCCTTCCT\nGGGGATTCCTGAATCGATTATTGGGCTGATCCAAAATTCTAGAACGATAAGAAGACAGTT\nTAGGAAGAACCTCTCTAGAACCTTAGAAGAGTCTTTCTATAACTCAGAGATTCATGGGAT\nCAATCGGATGACACAGACTCCCCAGAGAATAGGAAGAGTTTGGGCCTGCTCTTCTGAGAG\nGGCAGATCTCCTAAGAGAAATCTCGTGGGGGAGAAAGGTGGTTGGTACAACCGTCCCTCA\nCCCCTCTGAGATGTTGGGGTTGCTTCCTAAATCTTCAATCTCCTGTACTTGTGGCGCAAC\nAGGAGGGGGAAATCCTCGAATATCAGTGTCTGTACTCCCGTCCTTTGATCAGTCGTTCTT\nTTCCAGAGGCCCTCTGAAGGGATACCTGGGCTCATCCACATCTATGTCAACCCAGCTGTT\nCCATGCTTGGGAGAAGGTCACCAATGTTCATGTGGTGAAAAGGGCCCTTTCACTCAAAGA\nGTCCATAAATTGGTTCGTCACAAGAAACTCCAATTTGGCTCAAACTTTAATCAGGAATAT\nAATGTCTCTGACGGGACCAGACTTCCCGCTGGAAGAGGCCCCCGTCTTTAAGAGAACAGG\nATCAGCTCTGCACAGGTTCAAGTCAGCTAGGTACAGTGAAGGGGGTTATTCCTCTGTCTG\nTCCCAATCTCCTCTCTCATATTTCCGTCAGCACAGACACGATGTCTGACCTGACTCAAGA\nTGGGAAGAACTATGACTTTATGTTCCAGCCGCTGATGCTTTACGCACAGACATGGACATC\nAGAACTGGTGCAGAAGGACATACGGCTGAGAGACTCCACCTTTCACTGGCATCTTCGATG\nCAATAAGTGTATAAGGTCCATCGATGACATCACTCTAGAGACTTCCCAGATCTTTGAATT\nCCCGGATGTTTCGAAAAGGATATCTAGGATGGTCTCTGGAGCAGTGCCTCACTTTCAAAA\nACTTCCTGATATTCGTCTAAGACCTGGAGACTTTGAGTCTCTAAGTGACAAAGAGAAGTC\nACGCCACATAGGGTCGGCTCAGGGGCTCTTGTATTCGATCCTGGTTGCGATCCACGACTC\nTGGGTACAACGATGGAACCATTTTTCCTGTCAACATATATAGCAAGGTCTCCCCGAGAGA\nCTATTTAAGAGGTCTCGCCAGAGGAATCTTAATAGGGTCTTCTATCTGCTTTCTAACAAG\nAATGACAAACATCAACATCAACAGACCCCTTGAACTAATCTCAGGAGTGATCTCATACAT\nCCTCCTTAGATTAGACAATCACCCATCCTTATACATCATGCTCAGAGAACCGTCTCTGAG\nAGGAGAAATATTTTCTATTCCCCAAAAGATCCCCGCCGCTTACCCAACCACAATGAAAGA\nGGGCAACAGATCTATCCTGTGTTACCTCCAGCATGTGCTCCGCTATGAGCGGGAGGTAAT\nTACAGCATCCCCGGAGAATGATTGGTTATGGATCTTCTCTGACTTCAGAAGTTCCAAAAT\nGACCTATTTAACCCTTATCACCTATCAGTCTCATCTTTTACTTCAGAGGGTTGAGAAGAA\nTCTCTCTAAAAATATGAGGGCCAACCTACGACAGATGAGCTCTCTCATGAGACAAGTATT\nGGGCGGGCATGGCGAAGACACCTTAGAATCAGACGAGGACATTCAGAGGTTGTTGAAAGA\nCTCATTACGTAGGACAAGATGGGTAGATCAAGAGGTGCGTCATGCAGCCAGAGCCATGAC\nAGGGGGTTATAGCCCCAATAAGAAGATGTCTCGCAAAGCGGGGTGTTCAGAATGGGTCTG\nCTCTGCCCAACAGGTTGCTGTTTCAACCTCAGCAAATCCAGCCCCTGTCTCTGAGCTGGA\nCATCAGGGCTCTCTCCAAAAGACTTCAAAACCCGTTGATTTCAGGTCTGAGAGTTGTTCA\nGTGGGCAACAGGCGCTCATTACAAACTCAAACCTATTCTTGATGATCTCAATGTGTTCCC\nATCCTTATGTCTTGTGGTCGGAGACGGGTCAGGGGGGATCTCAAGGGCTGTACTCAATAT\nGTTTCCGGACGCTAGGCTCGTGTTCAACAGCCTGTTGGAAGTGAATGACCTGATGGCTTC\nAGGGACACATCCGTTGCCTCCTTCAGCAATCATGAGCGGAGGGGATGATATCATATCTAG\nGGTGATTGACTTTGACTCCATCTGGGAAAAGCCTTCTGACTTAAGGAACTTGACGACATG\nGAGGTACTTCCAGTCGGTTCAAGAACAAGTGAATATGTCCTATGATCTTATTATTTGTGA\nCGCAGAGGTCACTGACATCGCATCAATTAATCGAATAACTCTACTAATGTCTGATTTTGC\nATTATCAATAGACGGCCCACTTTATTTAGTTTTCAAAACTTATGGAACCATGCTCGTGAA\nTCCTGATTACAGAGCCGTTCAACATCTGTCCAGAGCATTTCCCACAGTCACAGGATTCAT\nAACCCAGATGACATCATCCTTCTCGTCTGAGCTATACCTCAGATTCTCTAAAAGGGGAAA\nATTTTTCCGAGATGCAGAATACTTGACTTCTTCTACTATTAGGGAGATGAGCCTTGTATT\nGTTCAACTGCAGCAGCCCAAAAAGTGAGATGCAGAGGGCCCGCTCTCTGAATTACCAGGA\nCCTTGTAAGAGGATTTCCTGAGGAGATCATATCCAACCCATATAATGAGATGATCATAAC\nTCTGATTGACAGTGATGTGGAATCTTTCCTGGTTCATAAGATGGTTGATGACCTAGAGTT\nGCAGCGAGGAACTTTGTCTAAAGTCTCCATTATCGTAGCCATCATGATAGTCTTTTCCAA\nCAGGGTGTTTAATGTCTCGAAACCGTTGACTGACCCTTTATTCAATCCGCCATCTGACCC\nCAAAATCTTGAGACACTTCAATATTTGCTGCAGTACCATGATGTACTTGTCTACTGCTCT\nGGGGGATGTTCCAAGCTTTGCTAGACTTCATGACCTGTATAACAGACCAATAACCTACTA\nTTTCGGGAAGAAAGTTATCCGAGGGAACATTTATTTATCCTGGAGTTGGTCTGACGACAC\nTTCAGTGTTCAAAAGGGTGGCTTGCAATTCTAGTTTGAGCCTCTCGGCTCACTGGATAAG\nGCTGATTTACAAAATAGTGAAGACTACCAGACTTGTGGGAAATACGGAGAATCTATCCAG\nGGAGGTCGAAAAGCACCTTCGAGGGTACAACAGGTGGATTACCCTAGACGACATAAAATC\nCAGATCATCTCTTCTAGATTACAGCTGCCTATAAAACAGGGCATTTGGGGAGAAATACAT\nGGACCAACACCTTGAGACAGTATGCCCTGAAAAAAACAAGACCCTGATTCATAACCTCTA\nTTTGCTTGATGGTTTTTTTTGTCTTTGTTGTTTTTTTGTTAA----\n" }, { "path": "tests/input/TestSnpEff/ref-rabies-JQ685920.fasta", "content": ">JQ685920\nACGCTTAACAACAAAATCAGAGAAGAAGTAGACAGTGTCGTCTACAAAGCAAGAATGTAA\nCACCCCTACAATGGATGCCGACAAGATTGTGTTTAAAGTCAATAATCAGGTGGTCTCTCT\nGAAGCCTGAAATTATAATAGATCAATATGAATACAAGTACCCGGCTATCAAAGATTTGAA\nAAAGCCCAGTATAACCTTAGGAAAAGCCCCTGACTTGAACAAAGCATACAAGTCAATTCT\nGTCCGGCATGAATGCAGCCAAGCTTGACCCTGATGATGTATGCTCTTATCTAGCAGCCGC\nAATGCAGTTCTTTGAGGGGACATGTCCTGATGACTGGACCAGCTATGGAATCCTGATTGC\nACGGAAGGGAGACAAGATTACTCCAAATTCTCTTGTGGACATAAAACGTACTAATGTGGA\nAGGGAACTGGGCTTTGACAGGGGGTATGGAGTTGACGAGAGACCCCACAGTTTCGGAGCA\nTGCATCCCTAGTTGGTCTTCTCTTGAGTCTTTACAGGTTAAGCAAAATATCTGGACAAAA\nCACCGGCAATTACAAAACGAACATCGCAGACAGAATAGAGCAGATTTTCGAGACGGCCCC\nCTTTGTAAAGATCGTAGAGCATCATACCTTGATGACAACCCACAAAATGTGTGCTAACTG\nGAGTACTATACCGAACTTCAGATTTCTGGCCGGAACCTACGATATGTTTTTCTCGCGGGT\nTGAACATCTGTATTCAGCAATTAGAGTGGGTACAGTTGTAACAGCCTATGAGGACTGCTC\nAGGGTTGGTGTCGTTTACAGGGTTTATTAAGCAAATAAATCTCACTGCAAAAGAAGCAAT\nACTATATTTCTTCCACAAGAACTTCGAGGAAGAGATAAGAAGAATGTTCGAGCCGGGGCA\nAGAGACGGCAGTTCCTCACTCCTATTTCATACATTTTCGTTCTTTGGGCCTGAGTGGGAA\nATCTCCGTATTCATCAAATGCAGTTGGTCACGTGTTCAACCTCATTCACTTTGTTGGATG\nTTATATGGGTCAAGTGAGATCTTTGAACGCAACGGTTATTGCTACATGTGCCCCGCATGA\nGATGTCTGTTCTTGGGGGTTATTTGGGGGAGGAGTTTTTCGGAAAAGGGACTTTTGAGAG\nAAGATTCTTTAGGGATGAGAAAGAACTTCAGGAATATGAGGCAGCTGAAGCAACGAAGAC\nTGAAATAGCCTTGGCGGATGACGGAACAGTCAATTCTGATGATGAGGACTACTTCTCTGG\nTGAAACTAGGAGCCCGGAGGCAGTTTATACTCGAATCATGATGAATGGGGGTAGATTAAA\nAAGATCACACATAAGGAGATATGTCTCAGTCAGTTCCAATCATCAAGCTCGCCCTAATTC\nGTTCGCTGAGTTTCTAAGTAAGACATACTCTAGTGATTCATAAAGAATTGAACAACAGGA\nTTGTAAACATTAACAAATTGTGTACATCCTTCACGAAAAAAACTAACACCCCTCCTCTTG\nAACCATCTCAGACATGAGCAAGATTTTTGTTAACCCAAGTGCAATCAGGGCAGGCTTGGC\nTGATCTGGAGATGGCAGAGGAAACTGTAGATCTAGTTGCCAAGAACATCGAAGATAATCA\nAGCTCATCTCCAAGGAGAACCCATAGAGGTGGACAGTCTTCCTGAAGACATGAGACGGCT\nTCAGTTAGACGATGAAAAACCATCTGGCCTCGGTGTGATTGCCAAAGCAGGGGAGAGCAA\nATGTCAGGAAGACTTTCAGATGGACGAGGGGGAGGACCCCGCCCTCTTGTTCCAGTCGTA\nCCTAGACAATATTGGAGTTCAAATGGTCAGACAAATGAGATCAGGAGAGAGGTTCCTCAA\nGATATGGTCTCAGACTGTTGAGGAGATCATATCCTATGTCACGGTCAATTTCCCCAGTCT\nGCCAAGGAAAGCCTCAGAAGACAAGGCTACCCAGACTGCCAACCAGGAACTCAAGAAAAA\nGACAATGTCTGTTTCTTCTCAGCGAGAAAGTAAATCATCTAAAGCTAAAATGGCGGCCCA\nAACCGCCTCCGGTCCTCCTGCTCTAGAATGGTCCGCCACAAACGAGGAGGATGACCTATC\nTGTGGAGGCTGAAATTGCTCACCAGATTGCTGAGAGCTTCTCTAAGAAGTACAAATTCCC\nCTCTCGATCATCAGGGATATTCTTGTATAATTTTGAGCAGTTGAAGATGAACCTTGATGA\nCATCGTTAAGGAGTCGAAAAATGTGCCAAGCGTAACCCGCTTAGCCCATGACGGATCCAA\nACTCCCTCTGAGGTGTGTGCTGGGGTGGGTTGCTCTAGCCAACTCCAAAAAGTTCCAGCT\nGTTAGTTGAGCCTGACAAGCTAAACAAAATAATGCAAGACGACCTGAATCGTTATGTGTT\nCTGCTGACCAAACCCTCAAACTCAGTCGTGCTATGCGATCAAATCCAGCCTGCTCCAAAC\nCCAACGTGAAAAAAACAGGCAACACCACTGATAAAATGAACTTTCTACGCAAGATAGTAA\nAGAACTGTAGAGATGAGGACACTCAGAAGCCCTCTTTCGTGTCGGCTCCTCCAGATGATG\nATGACTTGTGGTTACCCCCTCCGGAATATGTTCCATTGAAGGAACTCTCGGGTAAGAAAA\nACATGAGAAACTTTTGTATAAATGGAGAGGTCAAAGTGTGTAGTCCGAATGGCTATTCAT\nTTAGGATCCTGAGGCACATTTTGAAATCATTCGATGAGATCTATTCTGGAAATCAAAGAA\nTGATAGGGTTAGTTAAAGTTGTTGTTGGACTTGCGTTGTCAGGAGCCCCAGTCCCGGAGG\nGCATGAACTGGGTATACAAATTGAGGAGAACTCTTATCTTCCAGTGGGCTGATTCTAGGG\nGCCCTCTAGAGGGGGAGGAGTTAGAATACTCTCAGGAAATTACCTGGGATGACGATGCCG\nAATTTGTCGGATTGGAAATACGAGTGAGTGCAAGACAGTGCCATATCCAGGGCAGGATTT\nGGTGTATCAACATGAACTCTAGGGCATGTCAACTATGGTCTGACATGTCCCTTCAAACAC\nAAAGGTCTGAGGAGGATAAAGACTCTTCAATGCTTCTGGAATAGTCAATTTACATCCTAC\nAAATTCCTCAATTGTTTACCTCTGGAGGAGAGAGCACATGGACTTAACTCCAACCTTCAG\nGAGCAATAGAACAAAAACATGTTATGGTGCCGTTGAATTGCTGCATTTTATCATAGTCAA\nATCAATTATCTTTACATTTTAAGCCTCTCGGATGTGAAAAAAACTATCAACATCCCTCAA\nAAGACTTAAGGAAACATGATCCCTCAGGCTCTTCTGTTTGTGCCTTTTCTATTTCCCTCG\nTTGTGTCTCGGGAAATTCCCCATCTACACCATACCGGAAAAGCTCGGCCCTTGGAGTCCC\nATCGACATACATCATCTCAGCTGTCCTAACAATTTGGTTGTGGAGGACGAGGGTTGCGAC\nAGTCTGTCAGGGTTTTCTTACATGGAACTGAAGGTGGGTTACATCTCTGCCATAAAGGTG\nAATGGGTTCACTTGTACCGGTGTCGTGACAGAAGCTGAGACCTACACCAACTTTGTTGGT\nTATGTCACCACCACGTTCAAGAGAAAACACTTCCGCCCTATGCCAGATGCATGCAGAGCT\nGCGTACAACTGGAAGACAGCCGGTGACCCTAGATATGAGGAGTCTCTTCACAATCCTTAT\nCCTGATTACCATTGGCTACGGACCGTGAAAACCACCAAAGAATCTCTTGTTATCATATCG\nCCGAGTGTGGCTGATTTGGACCCATATGACAAATCCCTTCATTCAAGAGTTTTCCCTGGT\nGGGAAATGTTTGGGGATAACAATCTCTTCCACCTACTGCTCAACTAACCATGACTATACT\nATCTGGATGCCCGAAGAAGCAAGACTCGGGACATCTTGTGACATTTTTACCAACAGCAAA\nGGGAAGAGGGCATCTAAGGGGGGTAGGACTTGCGGATTCGTGGATGAAAGGGGCTTATAT\nAAGTCTCTAAAAGGGGCATGTAAACTTAAGCTGTGCGGAGTTCCTGGACTTAGACTTATG\nGATGGAACGTGGGTCGCTATTCAGACACCAGGTGAGACCAAATGGTGCTCTCCTGATCAG\nCTGGTAAATCTACATGACTTTCGTTCAGATGAGATAGAACATCTCGTCGTGGAGGAGTTG\nATCAAGAAGAGAGAAGAATGTCTAGATGCACTAGAGTCCATCATGACCACCAAATCAGTA\nAGCTTCAGACGTCTCAGCAACTTGAGAAAACTTGTCCCTGGGTTTGGAAAGGCATACACT\nATATTCAACAAAACCTTGATGGAGGCTGATGCTCACTACAAGTCAGTTCGGACTTGGGAT\nGAAATCATTCCCTCAAAGGGGTGCCTAAGAGTCGGAGGGAGGTGTCATCCTCATGTAAAC\nGGAGTGTTTTTCAATGGTATAATTCTGGGTCCGGATGGACATGTCCTGATTCCAGAGATG\nCAATCGTCCCTCCTCCAACAGCATATGGAGCTGTTGGAATCCTCTGTAATCCCCCTAATA\nCATCCCTTGGCCGACCCATCAACAGTCTTCAAAGACGGTGATGAAGCGGAGGACTTTGTT\nGAGGTTCACCTTCCGGACGTTCACAAGCAGGTCTCAGGGGTCGATCTTGGTCTCCCAAAC\nTGGGGGAAATATGTGCTGATGAGTGCAGGTGTTCTAGCGACCGTGATACTGACAATCTTC\nTTGTTAACATGTTGCAGAAGGGTTAACAGAACAAAACCAAAACAACAAAGTCTTGGGGAG\nTCAGGAAGGAAAGTATCGGTTACTCCTCAAAATGGGAAGGTCATGTCTTCATGGGAGTAT\nTACAAGAGTGAGGGCAGGACCAGTCTGTGAGTGCTGGCCATCTCCTCCATATCTTGCGTT\nCAGAAGATCACCTCTCTTCTAGATCTGGGGGAATCTCTTGTTTTGACAGTCCTTTGTGGA\nCTCCGTGCTACAAGGCAAAATTCGAGAGTCAAGAAACTTTCATTAATCATCCCAACTGAT\nCAGACACAGTTACGTAGGTTCTGATAATGTATGACGTCTTCTGACAGTGTCAGTGACCAA\nTGGTGCTCTCATCCCCCATGGACTGATACCAAAGGTTGTGGACAAACCAACCGATATCTC\nAGATAATTCTAGGCTTGAGCCGGGGCAGGGACCGTGGCTAGTCCCCCTACACTAGACTAA\nATAATGGTTAGCTGAGGGAAGCGATTTGCCTCCTATGAAGGACATAAGCAATAGATCACA\nATCATCTTACATCCCGATAAGGTGTGCTTAACTACAAAGGGCTGGGCCATCCAAGCTTTT\nCAGCCAAGAAAAAAACTGTGGAATGGAGGAGTAATTAACAACACTTCTCATCCTGAGAAC\nTGCACCATGATGCTTGATCCAGGGGAGGTTTATGATGACCCCGTTGATCCGATTGAGTCA\nGAGGCCGAGCCGAGAGGGAACCCAACCATTCCCAACATCTTAAGAAACTCTGACTACAAT\nCTCAACTCTCCTCTAATAGAGGATCCAGCCAAACTAATGTTAGAATGGTTGAAGACAGGA\nAATAGGCCTCTCCGGATAACTTTAACAGACAATTGCTCTAGGTCTTACAAAATTTTGAAG\nGATTATTTCAAGAAAGTGGATATAGGATCTATCAAAGTGGGCGGGGCTGCAGCACAATCT\nATGATCTCCCTTTGGTTGCACGGTGCCCACTCTGAATCAAATAGGAGCCGGAAGTGTATA\nACCGACTTGGCTCAGTTCTATTCCAAGTCTTCCCCCATAGAAAAGCTGTTAAATTACACA\nCTCGGAAATCGAGGGCTGAGGATCCCCCCAGAGGGGGTCCTAAGTTGCCTTGAGAGGGTC\nGATTACGATAAAGCATTTGGGAGGTATCTGGTTAACATATACTCCTCTTACTTATTCTTT\nCACGTGATCACCCTTTACATGAACGCCTTGGACTGGGATGAGGAGAAGACCATTCTAGCA\nCTGTGGAGGGATTTAACCTCAATAGATATAGGAAAGGACTTGGTCAAGTTTAAAGATCAA\nATATGGGGATTGCTAATTGTGACCAAGGATTTTGTGTACTCACAAAGTTCTAACTGCCTT\nTTTGATAGAAACTACACGCTTATGCTTAAAGACCTTTTTTTGTCTCGGTTCAACTCTCTA\nATGATTCTCCTTTCTCCTCCGGAACCCAGATATTCAGACGACCTGATATCCCAGCTGTGT\nCAGCTATATATCGCTGGAGATCATGTCTTGTCTATGTGCGGGAACTCTGGTTATGAGGTC\nATTAAAATATTGGAGCCGTACGTTGTGAACAGTTTAGTCCAGAGGGCAGAAAAGTTTAGG\nCCTCTCATTCATTCCCTAGGGGACTTCCCTGTATTTATAAGAGATAAGGTAGGTCAGCTT\nGAAGGAACATTTGGTCCCAGTGCAAAAAGGTTCTTCAGGGTTCTGGATCAATTCGACAAT\nATACACGACTTAGTCTTTGTATACGGCTGTTATAGGCATTGGGGGCATCCTTACATAGAT\nTATAGAAAGGGCTTATCGAAGCTATATGATCAAGTCCACATCAAGAAGGTGATAGATAAG\nACTTACCAGGAGTGTTTGGCCAGCGACCTGGCCAAAAGGATCCTCAGGTGGGGATTTGAC\nAAGTATTCCAAATGGTATATTGATTCAAGACTCCTCTCAAAGGACCACCCCCTAACTCCT\nTATATCAAAACCCAGACGTGGCCTCCAAAACATGTGGTAGATTTGGTGGGTGACACTTGG\nCATAAGCTCCCGATCACCCAGATCTTCGAGATCCCCGAATCAATGGACCCATCTGAGATA\nCTAGATGATAAATCACACTCTTTTACTAGAACTAGACTAGCGTCCTGGCTATCAGAGAAC\nAGAGGAGGGCCGGTCCCCAGCGAGAAGGTCATTATCACTGCTCTTTCCAAGCCTCCTGTC\nAACCCCAGGGAATTTCTGAAATCTATAGACCTGGGAGGATTGCCGGACGAGGATTTGATA\nATCGGCCTCAAGCCTAAGGAAAGAGAGTTGAAGATAGAAGGTCGGTTTTTTGCCTTGATG\nTCCTGGAATCTAAGGCTGTATTTTGTCATCACAGAAAAGCTCCTAGCCAATTATATCTTG\nCCACTTTTTGACGCACTGACTATGACAGACAACTTGAACAAAGTGTTTAAAAAGCTGATC\nGACAGAGTCACCGGACAGGGGCTTTTAGACTACTCCAGAGTTACATACGCTTTTCACCTG\nGACTATGAAAAGTGGAACAATCATCAGAGGCTGGAGTCGACAGAGGATGTATTTTCTGTA\nCTTGATCAAGTATTCGGATTAAAGAGGGTGTTTTCCAGAACTCATGAGTTTTTTCAGAAG\nTCTTGGATCTATTACTCAGATAGATCCGACCTCATCGGGTTATGGGAAGATCAAATATAC\nTGTTTGGACATGTCAAACGGCCCGACATGCTGGAACGGCCAGGATGGCGGGCTAGAGGGT\nTTGCGACAGAAAGGCTGGAGTCTGGTTAGCCTATTAATGATAGATCGTGAATCTCAAACC\nAGGAACACAAGAACTAAAATACTAGCTCAGGGAGACAACCAAGTTCTGTGTCCGACATAT\nATGCTGTCGCCGGGGCTCTCTCGAGAGGGGCTTCTCTACGAGTTGGAGAGCATATCAAGA\nAACGCTCTCTCGATATATCGTGCCATCGAGGAAGGGGCATCCAAACTGGGGCTCATCATA\nAAGAAGGAAGAGACCATGTGTAGCTATGACTTTCTCATCTATGGGAAAACTCCTTTATTT\nCGAGGTAACATCTTGGTGCCTGAGTCCAAAAGATGGGCTAGGGTCTCCTGTATCTCCAAC\nGACCAGATAGTCAACCTTGCCAATATAATGTCAACTGTATCCACTAATGCATTGACTGTC\nGCCCAACACTCTCAGTCTTTGATTAAACCGATGAGGGACTTCCTGCTTATGTCAGTACAA\nGCTGTCTTCCATTACTTGCTGTTTAGCCCCATCTTGAAAGGCAGAGTTTACAAGATCCTG\nGGTGCCGAGGGGGACAATTTTCTTCTAGCTATGTCTAGGATAATTTATTTAGACCCCTCA\nTTGGGGGGAGTATCTGGAATGTCTCTTGGAAGGTTCCACATACGTCAGTTCTCAGATCCT\nGTCTCAGAAGGGTTGTCCTTCTGGAGAGAGATATGGCTGAGCTCCAGTGAGTCTTGGGTT\nCATGCACTGTGTCAAGAGGCAGGAAACCCAGATCTGGGAGAGAGAACACTGGAAAGCTTC\nACTCGCCTGCTCGAGGATCCTACTACCCTAAACATTAAAGGAGGGGCCAGTCCTACCATT\nCTTCTCAAAGATGCGATCAGAAAAGCCTTGTATGATGAGGTAGACAAGGTGGAGAACTCA\nGAGTTTAGGGAAGCGATCCTCTTGTCTAAGACTCATAGGGATAATTTCATACTCTTCTTG\nAAATCTGTTGAGCCTTTGTTCCCCCGATTTCTCAGTGAGCTCTTCAGTTCATCATTCCTG\nGGGATTCCCGAATCAATCATTGGGTTGATACAAAACTCCAGAACAATAAGAAGACAGTTT\nAGGAGGAGTCTCTCAAGAACCTTGGAAGAGTCCTTTTATAACTCAGAGATCCATGGGATC\nAACCGGATGACCCAGACTCCCCAGAGGGTCGGGAGAGTTTGGCCCTGCTCTTCTGAGAGG\nGCAGACCTCCTAAGAGAAATCTCATGGGGAAGGAAGGTGGTCGGCACAACAGTTCCTCAC\nCCCTCTGAGATGTTGGGGTTGATTCCCAAATCCTCTATTTCCTGTACTTGTGGAGTAACA\nGGAGGGGGAAACCCTCGAATATCAGTGTCTGTGCTTCCATCTTTTGATCAGTCATTTTTT\nTCGAGAGGCTCTCTGAAAGGATATCTGGGCTCATCCACTTCCATGTCGACCCAGCTATTC\nCATGCCTGGGAGAAAGTCACCAATGTTCATGTGGTGAAAAGAGCTCTGTCACTCAAGGAA\nTCTATAAACTGGTTCATTACAAGAGACTCAAATTTGGCCCAAACTTTGATTAGGAACATA\nATGTCTCTGACAGGCCCAGATTTTCCTCTGGAAGAGGCCCCTGTCTTCAAGAGGACAGGG\nTCTGCCCTGCATAGGTTCAAGTCGGCTAGATACAGTGAAGGGGGGTACTCTTCAGTTTGT\nCCAAATCTCCTCTCTCACATCTCTGTCAGTACAGACACGATGTCTGATTTGACTCATGAT\nGGGATAAATTATGACTTTATGTTTCAGCCGTTGATGCTTTATGCGCAAACATGGACATCA\nGAACTGGTGCAAAAAGATACACGGCTGAAAGATTCTACCTTTCACTGGCATCTTCGATGT\nAACAAGTGCATAAGGCCCATCGATGATATCACCCTTGATACCTCTCAGATCTTCGAGTTC\nCCAGATGTCTCAAGAAGGATATCTAGGATGGTTTCTGGAGCTGTGCCTCATTTCAGAAAG\nCTTCCTGATATTCGTTTGAGACCAGGTGACTTCGAATCTCTAAGTGGTAAAGAGAAGTCT\nCGCCACATAGGATCGGCCCAAGGACTCTTGTATTCAATCTTGGTTGCGATCCATGACTCT\nGGGTATAATGATGGAACCATTTTCCCTGTCAACATATATAGCAAGGTCTCCCCTAGAGAC\nTATTTGAGAGGGCTTGCGAGAGGAGTCTTGATAGGGTCCTCGATTTGCTTCTTGACAAGA\nATGACAAACATTAACATCAATAGACCTCTTGAACTGATCTCAGGAGTGATATCATACATC\nCTCTTGAGACTGGACAATCACCCATCCTTGTATATAATGCTCAGAGAGCCATCCCTTAGA\nGGAGAGATATTTTCTATTCCCCAAAAGGTCCCCGCTGCTTACCCGACCACGATGAAAGAA\nGGTAACAGATCTGTTCTGTGCTACCTCCAACATGTGTTGCGCTACGAACGAGAGGTGATC\nACTGCATCTCCGGAGAATGACTGGTTGTGGATCTTCTCGGACTTTAGAAGCTCTAAGATG\nACATATCTGACTCTCATCACCTACCAGTCTCATCTGTTACTTCAGAAGGTTGAGAAGAAT\nCTCTCCAAGAGTATGAGAGCCAACCTACGGCAAATGAGCTCTCTGATGAGGCAGGTGCTG\nGGTGGCCATGGTGAAGACACCTTAGAGTCAGACGAAGACATCCAGAGGCTGTTAAGAGAC\nTCTCTGCGTAGGACAAGGTGGGTAGACCAGGAAGTGCGCCATGCAGCGAGAACTATGACA\nGGAGTTTACAGCCCCACCAAGAAGATGTCACGCAAAGCCGGGTGTTCAGAATGGGTCTGC\nTCTGCACAGCAGGTTGCGGTTTCGACCTCATCGAACCCAGCCCCTGTTTCAGAGCTGGAC\nGTCAGAGCCCTCTCCAAAAGGCTTCAAAACCCGTTGATCTCTGGACTGAGAGTGGTTCAG\nTGGGCGACAGGGGCCCATTATAAGCTCAAACCTATTCTGGATGATCTCAATGTCTTTCCA\nTCTCTATGTCTTGTGGTCGGGGATGGGTCAGGGGGGATATCAAGAGCAGTACTTAACATG\nTTTCCTGATGCCAAACTCGTATTCAACAGCCTGTTAGAAGTAAATGACCTGATGGCATCA\nGGAACACATCCGTTGCCCCCCTCAGCAATCATGAGTGGAGGAGATGACATCATATCCAGG\nGTAATTGGCTTCGACTCCATCTGGGAGAAACCTTCTGACTTGAGGAACTTGACCACATGG\nAGGTACTTCCAGTCAGTCCAAGAACAAGTAAATATGTCATACGACCTTATCATTTGTGAT\nGCAGAGGTCACTGACATTGCATCAATCAACCGAATAACCCTGCTAATGTCTGATTTTGCA\nTTGTCCATAGACGGCCCACTTTATCTGGTTTTCAAAACTTACGGTACCATGCTTGTAAAC\nCCTGACTACAGAGCAATTCAACATCTATCCAGAGCATTTCCTGCGGTCACTGGATTCATA\nACTCAGATGACCTCGTCCTTCTCATCCGAGCTATATCTCAGATTCTCAAAGCGGGGGAAG\nTTCTTCCGGGATGCAGAGTATTTGACTTCTTCCACCCTTCGAGAAATGAGCCTTGTATTG\nTTCAACTGTAGCAGCCCCAAGAGTGAGATGCAGAGAGCCCGCTCTCTAAATTACCAAGAT\nCTTGTAAGAGGATTCCCAGATGAGATCATATCCAATCCTTACAGCGAAATGATCATAACT\nCTGATTGACAGTGATGTAGAATCTTTCCTGGTTCACAAAATGGTAGATGATCTAGAGTTG\nCAGCGAGGAACTTTGTCTAAAGTTTCTATCATTATAGCCATCATGATAGTCTTCTCCAAT\nAGGGTGTTCAATGTCTCAAAACCACTGACTGACCCTTTATTCTATCCGCCATCTGATCCC\nAAGATCTTGAGACACTTCAACATATGCTGCGGCACCATGATGTACTTGTCTACCGCCTTA\nGGGGATGTGCCCAGCTTCTCGAGACTTCATGACCTGTACAACAGACCCATAACTTATTAT\nTTTAGGAAGCAAGTCATCCGGGGGAGTGTTTACCTGTCCTGGAGTTGGTCTGATGACACT\nTCAGTGTTTAAAAGGGTGGCTTGCAACTCTAGCTTGAGTCTCTCATCTCACTGGATCAGG\nTTGATTTACAAAATAGTGAAGACCACCAGACTTGTAGGAAGGGTCGAGGACCTGTCCAGG\nGAGGTAGAGAGGCACCTTCGGGGGTACAACAGATGGATCACCCTCGATGACATTAGATCC\nCGATCATCTCTGTTAGATTATAGCTGCTTGTAAGACTAAGCACTCTCGAGGGAATGTACA\nGACTAAGATTATGGGACGGTGTAACCTGAAAAAAACAAGATCCCGATTCATAACTTCTGT\nTTACTTGATTGTTTTTCCATCTTTATTGTTTTTTTGTTAAGCGT\n" }, { "path": "tests/input/TestSplitReads/expected.fasta.01", "content": ">from_chr9\nAGCTCTGACCCTGGCCAATCATGGCACTGACCTATGCCACCATATGGGGGCCCCCCC\n>from_ebov_1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n" }, { "path": "tests/input/TestSplitReads/expected.fasta.02", "content": ">from_chr1\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n>from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n" }, { "path": "tests/input/TestSplitReads/expected.fastq.01", "content": "@from_chr1_1 with spaces\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n@from_ebov_1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n" }, { "path": "tests/input/TestSplitReads/expected.fastq.02", "content": "@from_chr9_1\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n" }, { "path": "tests/input/TestSplitReads/expected.fastq.03", "content": "@from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n+\nEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n" }, { "path": "tests/input/TestSplitReads/expected.fastq.1", "content": "@from_chr1_1 with spaces\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n@from_ebov_1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_chr9_1\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n" }, { "path": "tests/input/TestSplitReads/expected.fastq.2", "content": "@from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n+\nEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n" }, { "path": "tests/input/TestSplitReads/in.fasta", "content": ">from_chr9\nAGCTCTGACCCTGGCCAATCATGGCACTGACCTATGCCACCATATGGGGG\nCCCCCCC\n>from_ebov_1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n>from_chr1\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n>from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n" }, { "path": "tests/input/TestSplitReads/in.fastq", "content": "@from_chr1_1 with spaces\nTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\n+\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n@from_ebov_1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n+\nBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n@from_chr9_1\nACAAGTGTGCCTTTGAAGGAGGAGGAGGAAGAGAGGAAGAAAGGAGAAGT\n+\nCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n@from_chr1_2\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n+\nDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD\n@from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n+\nEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n" }, { "path": "tests/input/TestSplitcodeDemuxFastqs/RunInfo.xml", "content": "\n\n\t\n\t\tTESTFC01\n\t\tTEST001\n\t\t2025-01-01T10:00:00Z\n\t\t\n\t\t\t\n\t\t\t\n\t\t\t\n\t\t\t\n\t\t\n\t\t\n\t\t\t\n\t\t\t\t\n\t\t\t\t\t1_1101\n\t\t\t\t\t1_1102\n\t\t\t\t\t1_1103\n\t\t\t\t\t1_1201\n\t\t\t\t\t1_1202\n\t\t\t\t\t1_1203\n\t\t\t\t\n\t\t\t\n\t\t\n\t\n\n" }, { "path": "tests/input/TestSplitcodeDemuxFastqs/SampleSheet.csv", "content": "[Header],,,,\nIEMFileVersion,4,,,\nInvestigator Name,TestUser,,,\nExperiment Name,TestExperiment,,,\nDate,01/01/2025,,,\nWorkflow,GenerateFASTQ,,,\nApplication,NovaSeq FASTQ Only,,,\nAssay,Nextera XT,,,\nDescription,,,,\nChemistry,Amplicon,,,\n,,,,\n[Settings],,,,\nOverrideCycles,Y50;I8;I8;Y50,,,\n[Data],,,,\nSample_ID,Sample_Name,Lane,Index,Index2,\nTESTFC01_1_TEST001_TestPool1,TEST001_TestPool1,1,ATCGATCG,GCTAGCTA,\nTESTFC01_1_TEST001_TestPool2,TEST001_TestPool2,1,CTGATCGT,TAGATCGC,\nTESTFC01_1_TEST001_TestPool3,TEST001_TestPool3,1,GGAATTCC,CCGGAATT,\n" }, { "path": "tests/input/TestSplitcodeDemuxFastqs/samples_3bc.tsv", "content": "sample\tlibrary_id_per_sample\tI7_Index_ID\tbarcode_1\tI5_Index_ID\tbarcode_2\tInline_Index_ID\tbarcode_3\nTestSample1\tL1\t\tATCGATCG\t\tGCTAGCTA\t\tAAAAAAAA\nTestSample2\tL1\t\tATCGATCG\t\tGCTAGCTA\t\tCCCCCCCC\nTestSample3\tL1\t\tATCGATCG\t\tGCTAGCTA\t\tGGGGTTTT\nTestSampleEmpty\tL1\t\tATCGATCG\t\tGCTAGCTA\t\tTTTTGGGG\nTestSample5\tL2\t\tCTGATCGT\t\tTAGATCGC\t\tAAAAAAAA\nTestSample6\tL2\t\tCTGATCGT\t\tTAGATCGC\t\tCCCCCCCC\nTestSampleNoSplitcode\tL3\t\tGGAATTCC\t\tCCGGAATT\t\t\n" }, { "path": "tests/input/TestSplitcodeDemuxFastqs/samples_3bc_i5_rc_with_n.tsv", "content": "sample\tlibrary_id_per_sample\tI7_Index_ID\tbarcode_1\tI5_Index_ID\tbarcode_2\tInline_Index_ID\tbarcode_3\nTestSample1_N\tL1\t\tATCGCCATAT\t\tACGTTACGCA\t\tAAAAAAAA\nTestSample2_N\tL1\t\tATCGCCATAT\t\tACGTTACGCA\t\tCCCCCCCC\nTestSample3_N\tL1\t\tATCGCCATAT\t\tACGTTACGCA\t\tGGGGTTTT\n" }, { "path": "tests/input/TestSplitcodeDemuxFastqs/samples_3bc_i5_revcomp.tsv", "content": "sample\tlibrary_id_per_sample\tI7_Index_ID\tbarcode_1\tI5_Index_ID\tbarcode_2\tInline_Index_ID\tbarcode_3\nTestSample1_RC\tL1\t\tATCGATCG\t\tGCTAGCTA\t\tAAAAAAAA\nTestSample2_RC\tL1\t\tATCGATCG\t\tGCTAGCTA\t\tCCCCCCCC\nTestSample3_RC\tL1\t\tATCGATCG\t\tGCTAGCTA\t\tGGGGTTTT\n" }, { "path": "tests/input/TestSplitcodeDemuxIntegration/RunInfo.xml", "content": "\n\n \n TESTFLOW\n TEST001\n 250101\n \n \n \n \n \n \n \n \n\n" }, { "path": "tests/input/TestSplitcodeDemuxIntegration/SampleSheet.tsv", "content": "sample\tbarcode_1\tbarcode_2\tbarcode_3\tlibrary_id_per_sample\nTestSample1\tATCGATCG\tGCTAGCTA\tAAAAAAAA\tL1\nTestSample2\tATCGATCG\tGCTAGCTA\tCCCCCCCC\tL1\n" }, { "path": "tests/input/TestSplitcodeLookupTable/AAAAAAAA-TTTTTTTT.lLibA_summary.json", "content": "{\n \"n_processed\": 50000,\n \"n_assigned\": 48000,\n \"tag_qc\": [\n {\n \"tag\": \"PoolA_S1.lLibA_R1\",\n \"distance\": 0,\n \"count\": 25000\n },\n {\n \"tag\": \"PoolA_S1.lLibA_R1\",\n \"distance\": 1,\n \"count\": 1000\n },\n {\n \"tag\": \"PoolA_S2.lLibA_R1\",\n \"distance\": 0,\n \"count\": 20000\n },\n {\n \"tag\": \"PoolA_S2.lLibA_R1\",\n \"distance\": 1,\n \"count\": 2000\n }\n ]\n}\n" }, { "path": "tests/input/TestSplitcodeLookupTable/ATCGATCG-GCTAGCTA.lB1_summary.json", "content": "{\n \"n_processed\": 100000,\n \"n_assigned\": 95000,\n \"tag_qc\": [\n {\n \"tag\": \"Sample1.lB1_R1\",\n \"distance\": 0,\n \"count\": 30000\n },\n {\n \"tag\": \"Sample1.lB1_R1\",\n \"distance\": 1,\n \"count\": 1500\n },\n {\n \"tag\": \"Sample2.lB1_R1\",\n \"distance\": 0,\n \"count\": 45000\n },\n {\n \"tag\": \"Sample2.lB1_R1\",\n \"distance\": 1,\n \"count\": 2000\n },\n {\n \"tag\": \"Sample3.lB1_R1\",\n \"distance\": 0,\n \"count\": 15000\n },\n {\n \"tag\": \"Sample3.lB1_R1\",\n \"distance\": 1,\n \"count\": 1500\n }\n ]\n}\n" }, { "path": "tests/input/TestSplitcodeLookupTable/ATCGATCG-GCTAGCTA.lL1_summary.json", "content": "{\n \"n_processed\": 100000,\n \"n_assigned\": 95000,\n \"tag_qc\": [\n {\n \"tag\": \"Sample1.lL1_R1\",\n \"distance\": 0,\n \"count\": 30000\n },\n {\n \"tag\": \"Sample1.lL1_R1\",\n \"distance\": 1,\n \"count\": 1500\n },\n {\n \"tag\": \"Sample2.lL2_R1\",\n \"distance\": 0,\n \"count\": 45000\n },\n {\n \"tag\": \"Sample2.lL2_R1\",\n \"distance\": 1,\n \"count\": 2000\n },\n {\n \"tag\": \"Sample3.lL3_R1\",\n \"distance\": 0,\n \"count\": 15000\n },\n {\n \"tag\": \"Sample3.lL3_R1\",\n \"distance\": 1,\n \"count\": 1500\n }\n ]\n}\n" }, { "path": "tests/input/TestSplitcodeLookupTable/GGGGGGGG-CCCCCCCC.lLibB_summary.json", "content": "{\n \"n_processed\": 60000,\n \"n_assigned\": 58500,\n \"tag_qc\": [\n {\n \"tag\": \"PoolB_S1.lLibB_R1\",\n \"distance\": 0,\n \"count\": 30000\n },\n {\n \"tag\": \"PoolB_S1.lLibB_R1\",\n \"distance\": 1,\n \"count\": 500\n },\n {\n \"tag\": \"PoolB_S2.lLibB_R1\",\n \"distance\": 0,\n \"count\": 27000\n },\n {\n \"tag\": \"PoolB_S2.lLibB_R1\",\n \"distance\": 1,\n \"count\": 1000\n }\n ]\n}\n" }, { "path": "tests/input/TestSplitcodeLookupTable/TTTTAAAA-CCCCGGGG.lB2_summary.json", "content": "{\n \"n_processed\": 0,\n \"n_assigned\": 0,\n \"tag_qc\": []\n}\n" }, { "path": "tests/input/TestSplitcodeLookupTable/sample_sheet_basic.tsv", "content": "sample\tbarcode_1\tbarcode_2\tbarcode_3\tlibrary_id_per_sample\nSample1\tATCGATCG\tGCTAGCTA\tAAAACCCC\tB1\nSample2\tATCGATCG\tGCTAGCTA\tGGGGTTTT\tB1\nSample3\tATCGATCG\tGCTAGCTA\tCCCCGGGG\tB1\n" }, { "path": "tests/input/TestSplitcodeLookupTable/sample_sheet_multi_pool.tsv", "content": "sample\tbarcode_1\tbarcode_2\tbarcode_3\tlibrary_id_per_sample\nPoolA_S1\tAAAAAAAA\tTTTTTTTT\tACGTACGT\tLibA\nPoolA_S2\tAAAAAAAA\tTTTTTTTT\tTGCATGCA\tLibA\nPoolB_S1\tGGGGGGGG\tCCCCCCCC\tATATATAT\tLibB\nPoolB_S2\tGGGGGGGG\tCCCCCCCC\tGCGCGCGC\tLibB\n" }, { "path": "tests/input/TestSplitcodeLookupTable/sample_sheet_unique_lib_ids.tsv", "content": "sample\tbarcode_1\tbarcode_2\tbarcode_3\tlibrary_id_per_sample\nSample1\tATCGATCG\tGCTAGCTA\tAAAACCCC\tL1\nSample2\tATCGATCG\tGCTAGCTA\tGGGGTTTT\tL2\nSample3\tATCGATCG\tGCTAGCTA\tCCCCGGGG\tL3\n" }, { "path": "tests/input/TestSplitcodeLookupTable/sample_sheet_zero_reads.tsv", "content": "sample\tbarcode_1\tbarcode_2\tbarcode_3\tlibrary_id_per_sample\nSample4\tTTTTAAAA\tCCCCGGGG\tATATAT\tB2\n" }, { "path": "tests/input/TestTaxonomy/simple.m8", "content": 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\t1.0e-09\t69.3\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t97.0\t33\t1\t0\t99\t1\t96\t128\t1.3e-09\t68.9\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t97.0\t33\t1\t0\t99\t1\t96\t128\t3.0e-09\t67.8\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t97.0\t33\t1\t0\t99\t1\t96\t128\t3.0e-09\t67.8\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\nM04004:13:000000000-AGV3H:1:1111:10629:26101/1\tgi|1|\t93.9\t33\t2\t0\t99\t1\t96\t128\t3.9e-09\t67.4\n" }, { "path": "tests/input/TestToolKrakenExecute/empty-report.txt", "content": "100.00 \t0\t0\tU\t0\tunclassified\n" }, { "path": "tests/input/TestToolKrakenExecute/expected-kraken-mix.reads.txt", "content": "U\tgi|119508057|dbj|AB286861.1|_287_800_2:0:0_1:0:0_4\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_3290_3781_2:0:0_0:0:0_8\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_4601_5090_2:0:0_1:0:0_3\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_5358_5878_1:0:0_4:0:0_9\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_5999_6601_0:0:0_3:0:0_5\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_6324_6759_2:0:0_4:0:0_1\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_665_1133_3:0:0_4:0:0_2\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_6849_7314_0:0:0_4:1:0_6\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_6883_7438_3:0:0_1:0:0_0\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|119508057|dbj|AB286861.1|_9070_9569_1:0:0_0:0:0_7\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_1209_1703_1:0:0_0:0:0_8\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_2053_2542_1:0:0_2:0:0_7\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_2438_2927_2:0:0_2:0:0_6\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_270_736_6:1:0_3:0:0_2\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_3621_4066_2:0:0_0:0:0_5\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_3920_4406_1:0:0_1:0:0_4\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_4892_5368_2:0:0_1:0:0_0\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_4956_5479_4:0:0_1:0:0_1\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_6_495_2:0:0_1:0:0_3\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|18656709|gb|AF453389.1|_782_1446_4:0:0_1:0:0_9\t0\t203\tP=0.000\t0:71 A:31 0:71\nC\tgi|190684443|gb|EU255973.1|_1943_2436_0:0:0_2:0:0_5\t31646\t203\tP=0.775\t31646:71 A:31 31646:1 0:32 31646:38\nC\tgi|190684443|gb|EU255973.1|_2042_2576_2:0:0_3:0:0_2\t31646\t203\tP=0.606\t0:16 31646:48 0:7 A:31 0:31 31646:38 0:2\nC\tgi|190684443|gb|EU255973.1|_3761_4305_2:0:0_1:0:0_8\t31646\t203\tP=0.535\t0:35 31646:36 A:31 31646:20 0:31 31646:20\nC\tgi|190684443|gb|EU255973.1|_3769_4295_2:0:0_1:0:0_7\t31646\t203\tP=0.718\t0:37 31646:34 A:31 31646:68 0:3\nC\tgi|190684443|gb|EU255973.1|_4554_5009_3:0:0_4:0:0_0\t31646\t203\tP=0.408\t31646:32 0:39 A:31 0:11 31646:8 0:34 31646:18\nC\tgi|190684443|gb|EU255973.1|_4878_5402_4:0:0_3:0:0_1\t31646\t203\tP=0.296\t0:33 31646:28 0:10 A:31 0:26 31646:14 0:31\nC\tgi|190684443|gb|EU255973.1|_5031_5460_2:0:0_3:0:0_3\t31646\t203\tP=0.394\t31646:6 0:33 31646:9 0:23 A:31 31646:41 0:30\nC\tgi|190684443|gb|EU255973.1|_520_1046_4:0:0_3:0:0_4\t31646\t203\tP=0.444\t0:2 31646:18 0:38 31646:13 A:31 0:3 31646:32 0:36\nC\tgi|190684443|gb|EU255973.1|_5255_5746_0:0:0_2:0:0_9\t31646\t203\tP=0.761\t31646:71 A:31 0:3 31646:19 0:31 31646:18\nC\tgi|190684443|gb|EU255973.1|_5750_6229_1:0:0_1:1:0_6\t31646\t203\tP=0.810\t31646:56 0:15 A:31 31646:59 0:12\nC\tgi|27085398|gb|AY184220.1|_1827_2229_3:0:0_2:0:0_7\t12083\t203\tP=0.197\t0:71 A:31 12083:28 0:43\nC\tgi|27085398|gb|AY184220.1|_2385_2815_0:0:0_3:0:0_3\t12083\t203\tP=0.845\t12083:71 A:31 0:6 12083:49 0:16\nC\tgi|27085398|gb|AY184220.1|_3263_3818_1:0:0_4:0:0_2\t12083\t203\tP=0.408\t12083:56 0:15 A:31 0:25 12083:2 0:44\nC\tgi|27085398|gb|AY184220.1|_3457_3924_0:0:0_0:1:0_8\t12083\t203\tP=0.782\t12083:3 0:31 12083:37 A:31 12083:71\nC\tgi|27085398|gb|AY184220.1|_3622_4164_2:0:0_3:0:0_5\t12083\t203\tP=0.451\t12083:47 0:24 A:31 0:38 12083:17 0:16\nC\tgi|27085398|gb|AY184220.1|_3938_4518_2:0:0_3:0:0_1\t12083\t203\tP=0.437\t0:11 12083:8 0:31 12083:11 0:10 A:31 12083:43 0:28\nC\tgi|27085398|gb|AY184220.1|_5760_6270_3:0:0_4:0:0_9\t12083\t203\tP=0.408\t0:17 12083:8 0:34 12083:12 A:31 12083:38 0:33\nC\tgi|27085398|gb|AY184220.1|_6007_6457_2:0:0_2:0:0_6\t12083\t203\tP=0.380\t12083:4 0:60 12083:7 A:31 0:9 12083:43 0:19\nC\tgi|27085398|gb|AY184220.1|_6350_6823_4:0:0_1:0:0_4\t12083\t203\tP=0.408\t12083:12 0:31 12083:28 A:31 0:53 12083:18\nC\tgi|27085398|gb|AY184220.1|_889_1388_2:0:0_0:0:0_0\t12083\t203\tP=0.908\t0:2 12083:58 0:11 A:31 12083:71\nU\tgi|342360485|gb|JF799977.1|_1149_1707_1:0:0_2:0:0_1\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_1814_2294_1:0:0_2:0:0_2\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_2596_3175_2:0:0_1:0:0_3\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_3238_3701_1:0:0_2:0:0_0\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_4618_5119_2:0:0_5:0:0_5\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_5061_5547_2:0:0_3:0:0_8\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_548_970_1:0:0_2:0:0_6\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_5967_6490_3:0:0_1:0:0_7\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_6163_6614_2:0:0_0:0:0_9\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|342360485|gb|JF799977.1|_645_1178_4:0:0_1:0:0_4\t0\t203\tP=0.000\t0:71 A:31 0:71\nC\tgi|612340474|gb|KJ207374.1|_1477_2003_0:0:0_2:0:0_3\t12253\t203\tP=0.746\t0:5 12253:12 0:31 12253:23 A:31 12253:71\nC\tgi|612340474|gb|KJ207374.1|_1674_2176_0:0:0_4:0:0_6\t12253\t203\tP=0.599\t12253:71 A:31 0:8 12253:6 0:31 12253:8 0:18\nC\tgi|612340474|gb|KJ207374.1|_2168_2657_6:0:0_1:0:0_9\t12253\t203\tP=0.465\t12253:48 0:23 A:31 0:18 12253:18 0:35\nC\tgi|612340474|gb|KJ207374.1|_3065_3466_4:0:0_2:0:0_0\t12253\t203\tP=0.211\t12253:4 0:53 12253:14 A:31 0:11 12253:12 0:48\nC\tgi|612340474|gb|KJ207374.1|_306_843_1:0:0_3:0:0_7\t12253\t203\tP=0.415\t0:22 12253:8 0:31 12253:2 0:8 A:31 0:22 12253:49\nC\tgi|612340474|gb|KJ207374.1|_3683_4217_2:0:0_1:0:0_4\t12253\t203\tP=0.493\t12253:15 0:41 12253:15 A:31 12253:31 0:31 12253:9\nC\tgi|612340474|gb|KJ207374.1|_4011_4502_2:0:0_1:0:0_1\t12253\t203\tP=0.718\t0:8 12253:63 A:31 0:24 12253:39 0:8\nC\tgi|612340474|gb|KJ207374.1|_4199_4745_2:0:0_1:0:0_5\t12253\t203\tP=0.549\t0:26 12253:45 A:31 0:38 12253:33\nC\tgi|612340474|gb|KJ207374.1|_4819_5287_2:0:0_1:0:0_8\t12253\t203\tP=0.577\t0:29 12253:42 A:31 12253:9 0:31 12253:31\nC\tgi|612340474|gb|KJ207374.1|_5508_5966_1:0:0_2:0:0_2\t12253\t203\tP=0.754\t0:6 12253:65 A:31 12253:42 0:29\nC\tgi|743485545|gb|KM609478.1|_1615_2117_3:0:0_1:0:0_7\t42788\t203\tP=0.585\t0:3 42788:25 0:43 A:31 0:13 42788:58\nC\tgi|743485545|gb|KM609478.1|_2826_3319_1:0:0_3:0:0_2\t42788\t203\tP=0.366\t0:29 42788:42 A:31 0:29 42788:8 0:31 42788:2 0:1\nC\tgi|743485545|gb|KM609478.1|_3526_4103_2:0:0_1:0:0_0\t42788\t203\tP=0.586\tA:31 0:2 42788:38 A:31 0:44 42788:27\nC\tgi|743485545|gb|KM609478.1|_369_845_2:0:0_1:0:0_3\t42788\t203\tP=0.514\t0:38 42788:33 A:31 42788:18 0:31 42788:22\nC\tgi|743485545|gb|KM609478.1|_382_889_0:0:0_4:0:0_5\t42788\t203\tP=0.585\t42788:64 12059:4 42788:3 A:31 0:23 42788:16 0:32\nC\tgi|743485545|gb|KM609478.1|_4745_5304_2:0:1_2:0:0_6\t42788\t203\tP=0.289\t0:25 42788:22 0:24 A:31 0:52 42788:19\nC\tgi|743485545|gb|KM609478.1|_5348_5900_1:0:0_0:0:0_8\t42788\t203\tP=0.958\t42788:71 A:31 0:6 42788:65\nC\tgi|743485545|gb|KM609478.1|_5470_5974_3:0:0_0:0:0_9\t42788\t203\tP=0.746\t42788:27 0:31 42788:8 0:5 A:31 42788:71\nC\tgi|743485545|gb|KM609478.1|_6345_6872_6:0:0_1:0:0_4\t42788\t203\tP=0.514\t42788:55 0:16 A:31 0:25 42788:18 0:28\nC\tgi|743485545|gb|KM609478.1|_6742_7260_0:0:0_4:1:0_1\t42788\t203\tP=0.599\t42788:71 A:31 0:17 42788:6 0:31 42788:8 0:9\nU\tgi|84873482|gb|DQ340570.1|_1463_1926_0:0:0_2:0:0_9\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_1707_2126_2:0:0_1:0:0_8\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_2025_2506_1:0:0_0:0:0_7\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_2139_2695_2:0:0_2:0:0_6\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_2153_2689_1:0:0_0:0:0_3\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_4041_4516_4:0:0_4:0:0_5\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_4075_4604_4:0:0_4:0:0_0\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_4234_4682_4:0:0_3:0:0_4\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_4473_4946_0:0:0_1:0:0_1\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|84873482|gb|DQ340570.1|_4665_5136_2:0:0_3:0:0_2\t0\t203\tP=0.000\t0:71 A:31 0:71\nC\tgi|89519418|gb|DQ418789.1|_126_590_3:0:0_3:0:0_1\t31646\t203\tP=0.197\t0:43 31646:28 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_1964_2513_0:0:0_2:0:0_9\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_3586_4097_3:0:0_3:0:0_3\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_4944_5550_1:0:0_2:0:0_2\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_6966_7530_0:0:0_2:0:0_5\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_7070_7507_1:0:0_0:0:0_6\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_7588_8095_3:0:0_0:0:0_7\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_8011_8531_4:0:0_1:0:0_8\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_8423_8836_3:0:0_3:0:0_0\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\tgi|89519418|gb|DQ418789.1|_8544_9076_4:0:0_2:0:0_4\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_1813_2413_2:0:0_1:0:0_8\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_2622_3050_4:0:0_1:0:0_7\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_2783_3283_3:0:0_5:0:0_6\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_2869_3356_0:0:0_2:0:0_9\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_2997_3500_1:0:0_3:0:0_3\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_3772_4274_2:0:0_1:0:0_4\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_4358_4818_4:0:0_0:0:1_2\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_662_1078_2:0:0_3:1:0_5\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_680_1169_2:0:0_4:0:0_1\t0\t203\tP=0.000\t0:71 A:31 0:71\nU\thuman_5000bp_826_1283_1:0:0_2:0:0_0\t0\t203\tP=0.000\t0:71 A:31 0:71\n" }, { "path": "tests/input/TestToolKrakenExecute/expected-kraken-mix.report.txt", "content": " 59.00\t59\t59\tU\t0\tunclassified\n 41.00\t41\t0\t-\t1\troot\n 41.00\t41\t0\tD\t10239\t Viruses\n 41.00\t41\t0\t-\t439488\t ssRNA viruses\n 41.00\t41\t0\t-\t35278\t ssRNA positive-strand viruses, no DNA stage\n 20.00\t20\t0\tO\t464095\t Picornavirales\n 20.00\t20\t0\tF\t12058\t Picornaviridae\n 20.00\t20\t0\tG\t12059\t Enterovirus\n 10.00\t10\t0\tS\t138948\t Enterovirus A\n 10.00\t10\t10\t-\t42788\t Coxsackievirus A8\n 10.00\t10\t0\tS\t138950\t Enterovirus C\n 10.00\t10\t10\t-\t12083\t Human poliovirus 2\n 11.00\t11\t0\tF\t11050\t Flaviviridae\n 11.00\t11\t0\tG\t11102\t Hepacivirus\n 11.00\t11\t0\tS\t11103\t Hepatitis C virus\n 11.00\t11\t0\t-\t41856\t Hepatitis C virus genotype 1\n 11.00\t11\t11\t-\t31646\t Hepatitis C virus subtype 1a\n 10.00\t10\t0\tF\t675071\t Virgaviridae\n 10.00\t10\t0\tG\t12234\t Tobamovirus\n 10.00\t10\t10\tS\t12253\t Tomato mosaic virus\n" }, { "path": "tests/input/TestToolPicard/in.dict", "content": "@HD\tVN:1.4\n@SQ\tSN:from_chr9\tLN:57\tUR:file:/Users/dpark/dev/viral-ngs/test/input/TestToolPicard/in.fasta\tM5:e619b7ec4224c26f20993903b80e1c8e\n@SQ\tSN:from_ebov_1\tLN:50\tUR:file:/Users/dpark/dev/viral-ngs/test/input/TestToolPicard/in.fasta\tM5:9d0d8dcb3f1cfcb203ceab0c23a24358\n@SQ\tSN:from_chr1\tLN:50\tUR:file:/Users/dpark/dev/viral-ngs/test/input/TestToolPicard/in.fasta\tM5:5046b0acf637bca46fbafb571e4fc991\n@SQ\tSN:from_ebov_2\tLN:50\tUR:file:/Users/dpark/dev/viral-ngs/test/input/TestToolPicard/in.fasta\tM5:42819f6a988627298972d9585e8d890b\n" }, { "path": "tests/input/TestToolPicard/in.fasta", "content": ">from_chr9\nAGCTCTGACCCTGGCCAATCATGGCACTGACCTATGCCACCATATGGGGG\nCCCCCCC\n>from_ebov_1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n>from_chr1\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n>from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n" }, { "path": "tests/input/TestToolPicard/messy-headers.fasta", "content": ">Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-1\nCTGGAGCAAGACAAATGATGCCGGATCAGATCGAGTGATGGTATCACCCCTGGCTGTGAC\nATGGTGGAATAGGAATGGACCAACAACAAGTACAATTCACTATCCAAAGGTATACAAAAC\nAAAGGGAGAGAAGGCTAATGTGCTAATTGGGCAAGGAGACGTGGTGTTGGTGATGAAACG\nGAAACGGGACTCTAGCATACTTACTGACAGCCAGACAGCGACCAAAAGAATTCGGATGGC\nCATCAATTAGTGTGGAATTGTTTAAAAACGACCTTGTTTCTACT\n>Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-2\nCGAAAGCAGGCAAACCATTTGAATGGATGTCAATCCGACCTTACTCTTCTTGAAAGTTCC\nAGCGCAAAATGCCATAAGCACCACATTCCCGTATACTGGAGATCCTCCATACAGCCATGG\nACGGATTAAGAAGGAGGAGTTTGCTGAGATCATGAAGATCTGTTCCACCATTGAAGAGCT\nCAGACGGCAGAAATAGTGAATTTAGCTTGTCCTTCATGAAAAAATGCCTTGTTTCTACT\n>Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-3\nAAGCAGGTACTGATTCAAAATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATTGT\nCGAGCTTGCGGAAAAAGCAATGAAAGAACATGGGGAAGATCCGAAAATCGAGACAAACAA\nGATTAACGATCCCTGGGTTTTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGC\nACTGAAATAGTTGTGGCAATGCTACTATTTGCTATCCATACTGTCCAAAAAAGTACCTTG\nTTTCTACT\n>Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-4\nGCAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGCGACGAATTCATCAGAGTGCCGG\nAATGGTCTTACATAGTGGAGCGGGCTAACCCAGCTAATGACCTCTGTTACCCAGGGAGCC\nTATCTTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGAATTTGCATTTAGATTTATG\nAGCTCAGATTGTAGTTAAAAACACCCTTGTTTCT\n>Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-5\nAAGCAGGGTAGATAATCACTCACTGAGTGACATCCACATCATGGCGTCTCAAGGCACCAA\nATCTGTTGGAAGAATGGTTGGCGGAATCGGGAGATTCTACATACAGATGTGCACTGAGCT\nGGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAACAATGAAGGATCTTA\nTTTCTTCGGAGACAATGCAGAGGAGTATGACAATTAAAGAAAAATACCCTTGTTTCTACT\n>Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-6\nCGGGCAATTCATCTCTTTGCCCTATTAGTGGGTGGGCAATATACAGTAAGGACAACGGTA\nTAAGAATTGGATCTAAGGGGGATGTGTTTGTTATAAGAGAACCATTCATCTCATGCTCCC\nGTGGTGTAAATAGTGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTCA\nCCATTGACAAGTAGTTTGTTCAAAAAACTCCTTGTTTCTACT\n>Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-7\nAAGCAGGTAGATATTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTA\nTCGTCCCGTCGGGCCCCCTCAAAGCCGAGATCGCGCAGAGACTTGAAGATGTCTTTGCAG\nGGAAGAACACCGATCTTGAGGCTCTCATGGAATGGCTAAAGACAAGACCAATCCTGTCAC\nCTCTGACCAAGGGGATTTTGGGATTTGTGTTCACGCTCACCGTGCCCAGTGAGCGAGGAC\nCT\n>Influenza A virus A/bovine_milk/USA/Broad_MC_023/2024(H5N1))-8\nAGCDGGGTGACAAAAACATAATGGATTCCAACACTGTGTTAAGCTTTCAGGTAGACTGCT\nTTCTTTGGCATGTCCGCAAACGATTTGCAGACCAAGAACTGGGTGATGCCCCATTCCTTG\nTCGAGACGGCCACTCGTGCTGGGAAGCAGATAGTGGAGAGGATTCTGGAGGAAGAATCCG\nTCGTTTCAGCTTATTTAATAATAAAAAACACCCTTGTTTCTACT\n" }, { "path": "tests/input/TestToolPicard/simple.sam", "content": "@HD\tVN:1.4\tSO:queryname\n@RG\tID:A\tPL:9.75\tLB:Alexandria\tSM:FreeSample\tCN:KareemAbdul-Jabbar\nmyseq\t77\t*\t0\t0\t*\t*\t0\t0\tTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\t\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\tRG:Z:A\nmyseq\t141\t*\t0\t0\t*\t*\t0\t0\tAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\t\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\tRG:Z:A\n" }, { "path": "tests/input/TestToolSamtools/in.fasta", "content": ">from_chr9\nAGCTCTGACCCTGGCCAATCATGGCACTGACCTATGCCACCATATGGGGG\nCCCCCCC\n>from_ebov_1\nGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCAC\n>from_chr1\nAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGTTTTGAATTTT\n>from_ebov_2\nCCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTC\n" }, { "path": "tests/input/TestToolSamtools/in.fasta.fai", "content": "from_chr9\t57\t11\t50\t51\nfrom_ebov_1\t50\t83\t50\t51\nfrom_chr1\t50\t145\t50\t51\nfrom_ebov_2\t50\t209\t50\t51\n" }, { "path": "tests/input/TestToolSamtools/indel_cigar.sam", "content": 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AACATCTGACATATTGTTAAACCGAGCTTATCAGAAGAGAATTTGGAAAGCCATCGGGTGTGTAATCTATTGCTTTGGTTTGC\tABBA@BEFEFFFGGGGGGGGFGHHHHHGHHHHHHHHHHHGGGGGGGGHHHHGHHGHGHHHHHGGGHHHGGHHGGGGFEGGHHHHHHHHHHEHHHHHHHHFE\tLB:Z:Mock1\tMC:Z:101M\tMD:Z:101\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tNM:i:0\tMQ:i:70\tUQ:i:0\tAS:i:0\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\nAPCJ3:1:1105:10708:23204\t99\tMock1-1\t15033\t70\t101M\t=\t15050\t118\tCATCTGACATATTGTTAAACCGAGCTTATCAGAAGAGAATTTGGAAAGCCATCGGGTGTGTAATCTATTGCTTTGGTTTGCTCACCCCGGATGTTGAAGAT\tACCACEEFFFFFGGGGGGGFFGGGGGHHHGHHHHHHHHHHHHHHHHHHGHHHHFFFHFFFHHHHHHFHHHGHHHHHHHHGFHGHGHHEGGGGGHHHHHHHH\tLB:Z:Mock1\tMC:Z:101M\tMD:Z:101\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tAM:i:70\tNM:i:0\tSM:i:70\tMQ:i:70\tPQ:i:5\tUQ:i:0\tAS:i:0\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\nAPCJ3:1:2112:16035:6267\t163\tMock1-1\t15036\t70\t101M\t=\t15092\t157\tCTGACATATTGTTAAACCGAGCTTATCAGAAGAGAATTTGGAAAGCCATCGGGTGTGTAATCTATTGCTTTGGTTTGCTCACCCCGGATGTTGAAGATTCT\t@AAB@EEFFFFFGBGGGGCAEFGHHHHHGBDFFA23GGHHFGFFEGHGGHG?EHAGAGGHGGHGGHGHHHHHHHHHEGHGHGGHGGGGFFHHHHGFHHHGH\tLB:Z:Mock1\tMC:Z:101M\tMD:Z:101\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tAM:i:70\tNM:i:0\tSM:i:70\tMQ:i:70\tPQ:i:3\tUQ:i:0\tAS:i:0\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\nAPCJ3:1:1105:13024:17729\t163\tMock1-1\t15044\t70\t101M\t=\t15164\t224\tTTGTTAAACCGAGCTTATCAGAAGAGAATTTGGAAAGCCATCGGGTGTGTAATCTATTGCTTTGGTTTGCTCACCCCGGATGTTGAAGATTCTGAGCGCAT\tBBBBBFFFEFCCGFGGGGFGGGHHHHHHHHHHHHHHHHHGHHGGGHGGGHHHHHHHHHGHHGHGGHHHGHHGHGGHGGGGGGHHGHHHHHHHGGHGFFEGG\tLB:Z:Mock1\tMC:Z:64M3D37M\tMD:Z:101\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tAM:i:7\tNM:i:0\tSM:i:70\tMQ:i:70\tPQ:i:100\tUQ:i:0\tAS:i:0\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\nAPCJ3:1:1105:10708:23204\t147\tMock1-1\t15050\t70\t101M\t=\t15033\t-118\tAACCGAGCTTATCAGAAGAGAATTTGGAAAGCCATCGGGTGTGTAATCTATTGCTTTGGTTTGCTCACCCCGGATGTTGAAGATTCTGAGCGCATTGATGT\tGGFFGHGGHHHHGHGHHHHHHHGHHHGHHHHGGGGGFEFHGHGHHHHGHHHHHHHHHGHGGGHHGGGGGGGHGHHHHHGGGFGGGGGFGCCFFEFFABBAB\tLB:Z:Mock1\tMC:Z:101M\tMD:Z:101\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tAM:i:70\tNM:i:0\tSM:i:70\tMQ:i:70\tPQ:i:5\tUQ:i:0\tAS:i:0\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\nAPCJ3:1:1106:11686:10415\t147\tMock1-1\t15053\t70\t101M\t=\t14982\t-172\tCGAGCTTATCAGAAGAGAATTTGGAAAGCCATCGGGTGTGTAATCTATTGCTTTGGTTTGCTCACCCCGGATGTTGAAGATTCTGAGCGCATTGATGTTGA\tFFGFGHHHHGHFHHGHGHHHHHFGHHHGGGGGGGGGHGHGHHHHGHHGHHGHHHGGHHHHHGGGGGFFHHHHHHHHHHGGGGGGGGFGFFFFFEEEABBAB\tLB:Z:Mock1\tMC:Z:101M\tMD:Z:101\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tAM:i:70\tNM:i:0\tSM:i:70\tMQ:i:70\tPQ:i:2\tUQ:i:0\tAS:i:0\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\nAPCJ3:1:2112:16035:6267\t83\tMock1-1\t15092\t70\t101M\t=\t15036\t-157\tGTAATCTATTGCTTTGGTTTGCTCACCCCGGATGTTGAAGATTCTGAGCGCATTGATGTTGATAATGACATACCCGATTATGATATTCACGGGGACATAAT\tFHHHHHFHHHFGHHHGGHHHGHFGEGGFGGGHHHHHHHHGHHHHGGGGGHHHHHHHHGHHGHHHHHHHHHGGGGGGGDFGGFGFGGCGGBBFEEDE@AAAA\tLB:Z:Mock1\tMC:Z:101M\tMD:Z:101\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tAM:i:70\tNM:i:0\tSM:i:70\tMQ:i:70\tPQ:i:3\tUQ:i:0\tAS:i:0\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\nAPCJ3:1:1105:13024:17729\t83\tMock1-1\t15164\t70\t64M3D37M\t=\t15044\t-224\tCCCGATTATGATATTCACGGGGACATAATTTAAATCGACTAAAGACTCCTCTGGCATTACACATCAAAAAGTGCCAAACTAGCATCCAAATTCTTCTAAAC\tGGGGHHHHHHHHHGGFGGGGFFHHHHHHHHHGHGGGHHGIIHIGHFHFHHGHGHHHHHHHHHHGGHHHHHGHGGHHHHGGGFGGGGGGGFFFFFEEBBBBB\tLB:Z:Mock1\tMC:Z:101M\tMD:Z:64^CAC37\tPG:Z:MarkDuplicates.3\tRG:Z:APCJ3.1\tAM:i:7\tNM:i:3\tSM:i:7\tMQ:i:70\tPQ:i:100\tUQ:i:100\tAS:i:100\tPU:Z:APCJ3.1.TAGGCATG-GCGTAAGA\n" }, { "path": "tests/input/TestToolSamtools/simple.sam", "content": "@HD\tVN:1.4\tSO:queryname\n@RG\tID:A\tPL:9.75\tLB:Alexandria\tSM:FreeSample\tCN:KareemAbdul-Jabbar\nmyseq\t77\t*\t0\t0\t*\t*\t0\t0\tTCAATAAAAAAAAAAAAGAAAGAAAAAAAAATTCTCCTCATTTTTGTTGT\t\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\tRG:Z:A\nmyseq\t141\t*\t0\t0\t*\t*\t0\t0\tAATTATATTATTTCTTTGATAATTTCCTCTCCTCTTGTTTCTTTGTTTCT\t\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\"#\tRG:Z:A\n" }, { "path": "tests/input/TestTrimRmdupSubsamp/clipDb.fasta", "content": ">NuGEN\nTCTATAGTTTAGGTAACTTTGTGTTTGA\n>TruSeq3_IndexedAdapter\nAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n>TruSeq3_UniversalAdapter\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA\n>PrefixPE/1\nTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PrefixPE/2\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n>PE1_rc\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA\n>PrefixNX/1\nAGATGTGTATAAGAGACAG\n>PrefixNX/2\nAGATGTGTATAAGAGACAG\n>Trans1\nTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG\n>Trans1_rc\nCTGTCTCTTATACACATCTGACGCTGCCGACGA\n>Trans2\nGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG\n>Trans2_rc\nCTGTCTCTTATACACATCTCCGAGCCCACGAGAC\n>TruSeq2_SE\nAGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG\n>TruSeq2_PE_f\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\n>TruSeq2_PE_r\nAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG\n>PCR_Primer1_rc\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT\n>PCR_Primer2\nCAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n>PCR_Primer2_rc\nAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG\n>FlowCell1\nTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC\n>FlowCell2\nTTTTTTTTTTCAAGCAGAAGACGGCATACGA\n>TruSeq Universal Adapter\t\t\t\t\t\t\nAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>TruSeq Adapter, Index 1\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 2\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 3\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 4\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 5\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 6\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 7\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 8\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 9\t\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 10\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 11\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG\n>TruSeq Adapter, Index 12\t\t\t\t\t\t\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG\n>Illumina Single End Adapter 1\nACACTCTTTCCCTACACGACGCTGTTCCATCT\n>Illumina Single End Adapter 2\nCAAGCAGAAGACGGCATACGAGCTCTTCCGATCT\n>Illumina Paired End Adapter 2\nCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT\n>Illumina Paried End Sequencing Primer 1\nACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>Illumina Paired End Sequencing Primer 2\nCGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT\n>Illumina Multiplexing Adapter 1\nGATCGGAAGAGCACACGTCT\n>Illumina Multiplexing Index Sequencing Primer\nGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\n>Illumina Multiplexing Read2 Sequencing Primer\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n>Illumina PCR Primer Index 1\nCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC\n>Illumina PCR Primer Index 2\nCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC\n>Illumina PCR Primer Index 3\nCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC\n>Illumina PCR Primer Index 4\nCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC\n>Illumina PCR Primer Index 5\nCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC\n>Illumina PCR Primer Index 6\nCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC\n>Illumina PCR Primer Index 7\nCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC\n>Illumina PCR Primer Index 8\nCAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC\n>Illumina PCR Primer Index 9\nCAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC\n>Illumina PCR Primer Index 10\nCAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC\n>Illumina PCR Primer Index 11\nCAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC\n>Illumina PCR Primer Index 12\nCAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC\n>RNA PCR Primer, Index 1\nCAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 2\nCAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 3\nCAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 4\nCAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 5\nCAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 6\nCAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 7\nCAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 8\nCAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 9\nCAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 10\nCAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 11\nCAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 12\nCAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 13\nCAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 14\nCAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 15\nCAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 16\nCAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 17\nCAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 18\nCAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 19\nCAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 20\nCAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 21\nCAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 22\nCAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 23\nCAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 24\nCAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 25\nCAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 26\nCAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 27\nCAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 28\nCAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 29\nCAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 30\nCAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 31\nCAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 32\nCAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 33\nCAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 34\nCAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 35\nCAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 36\nCAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 37\nCAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 38\nCAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 39\nCAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 40\nCAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 41\nCAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 42\nCAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 43\nCAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 44\nCAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 45\nCAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 46\nCAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 47\nCAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>RNA PCR Primer, Index 48\nCAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA\n>Custom add, Illumina Paired End Adapter 2\nGATCGGAAGAGCGGTTCAGCAGGAATGC\n>Nextera S501\nAATGATACGGCGACCACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTC\n>Nextera S502\nAATGATACGGCGACCACCGAGATCTACACCTCTCTATTCGTCGGCAGCGTC\n>Nextera S503\nAATGATACGGCGACCACCGAGATCTACACTATCCTCTTCGTCGGCAGCGTC\n>Nextera S504\nAATGATACGGCGACCACCGAGATCTACACAGAGTAGATCGTCGGCAGCGTC\n>Nextera S505\nAATGATACGGCGACCACCGAGATCTACACGTAAGGAGTCGTCGGCAGCGTC\n>Nextera S506\nAATGATACGGCGACCACCGAGATCTACACACTGCATATCGTCGGCAGCGTC\n>Nextera S507\nAATGATACGGCGACCACCGAGATCTACACAAGGAGTATCGTCGGCAGCGTC\n>Nextera S508\nAATGATACGGCGACCACCGAGATCTACACCTAAGCCTTCGTCGGCAGCGTC\n>Nextera N711fw\nCAAGCAGAAGACGGCATACGAGATAAGAGGCAGTCTCGTGGGCTCGG\n>Nextera N703fw\nCAAGCAGAAGACGGCATACGAGATAGGCAGAAGTCTCGTGGGCTCGG\n>Nextera N708fw\nCAAGCAGAAGACGGCATACGAGATCAGAGAGGGTCTCGTGGGCTCGG\n>Nextera N710fw\nCAAGCAGAAGACGGCATACGAGATCGAGGCTGGTCTCGTGGGCTCGG\n>Nextera N702fw\nCAAGCAGAAGACGGCATACGAGATCGTACTAGGTCTCGTGGGCTCGG\n>Nextera N707fw\nCAAGCAGAAGACGGCATACGAGATCTCTCTACGTCTCGTGGGCTCGG\n>Nextera N709fw\nCAAGCAGAAGACGGCATACGAGATGCTACGCTGTCTCGTGGGCTCGG\n>Nextera N705fw\nCAAGCAGAAGACGGCATACGAGATGGACTCCTGTCTCGTGGGCTCGG\n>Nextera N712fw\nCAAGCAGAAGACGGCATACGAGATGTAGAGGAGTCTCGTGGGCTCGG\n>Nextera N701fw\nCAAGCAGAAGACGGCATACGAGATTAAGGCGAGTCTCGTGGGCTCGG\n>Nextera N706fw\nCAAGCAGAAGACGGCATACGAGATTAGGCATGGTCTCGTGGGCTCGG\n>Nextera N704fw\nCAAGCAGAAGACGGCATACGAGATTCCTGAGCGTCTCGTGGGCTCGG\n>Nextera N701\nCAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGG\n>Nextera N702\nCAAGCAGAAGACGGCATACGAGATCTAGTACGGTCTCGTGGGCTCGG\n>Nextera N703\nCAAGCAGAAGACGGCATACGAGATTTCTGCCTGTCTCGTGGGCTCGG\n>Nextera N704\nCAAGCAGAAGACGGCATACGAGATGCTCAGGAGTCTCGTGGGCTCGG\n>Nextera N705\nCAAGCAGAAGACGGCATACGAGATAGGAGTCCGTCTCGTGGGCTCGG\n>Nextera N706\nCAAGCAGAAGACGGCATACGAGATCATGCCTAGTCTCGTGGGCTCGG\n>Nextera N707\nCAAGCAGAAGACGGCATACGAGATGTAGAGAGGTCTCGTGGGCTCGG\n>Nextera N708\nCAAGCAGAAGACGGCATACGAGATCCTCTCTGGTCTCGTGGGCTCGG\n>Nextera N709\nCAAGCAGAAGACGGCATACGAGATAGCGTAGCGTCTCGTGGGCTCGG\n>Nextera N710\nCAAGCAGAAGACGGCATACGAGATCAGCCTCGGTCTCGTGGGCTCGG\n>Nextera N711\nCAAGCAGAAGACGGCATACGAGATTGCCTCTTGTCTCGTGGGCTCGG\n>Nextera N712\nCAAGCAGAAGACGGCATACGAGATTCCTCTACGTCTCGTGGGCTCGG\n>Broad Barcode tagged_57\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTAGAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_100\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACACGATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_473\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCGCGGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_373\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGATCGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_498\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTTACCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_861\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCTTGGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_23\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACGCATTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_109\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGGTATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_218\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTAAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_3\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACAATGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_163\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGTATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_220\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTCGCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_375\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGCTTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_726\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTCCAGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_880\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTGGCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_214\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGATCTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_754\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTGATGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_223\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTTATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_309\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTCTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_379\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAACATTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_500\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTAACTCGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_291\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_504\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTACCAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_534\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGCGGATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_630\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACATCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_741\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTATAACAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_367\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCATAGCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_579\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACAGTAAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_938\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTACGCACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_745\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCATCTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_542\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGTAATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_655\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCGTCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_732\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAACATCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_567\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAAGGAAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_584\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCTAACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_117\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACCAACTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_908\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCTCGACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_954\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTCGCTGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_357\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGAGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_426\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTATGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_959\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGAATAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_438\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTTCGCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_778\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAAGCACAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_821\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATCTGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_924\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGTAATCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_868\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGCTAGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_899\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCAAGTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_934\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAATCAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_190\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCAATTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_34\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTTGACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_927\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGTCGGATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_866\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGCCTTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_38\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGACACTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_875\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTCGGTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_78\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATGTTCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_151\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTAAGACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_288\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTATCAAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_110\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTTGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_195\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCATGGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_222\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGTGCGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_236\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTGCTTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_332\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACATCCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_289\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTATGTTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_250\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGCGTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_352\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGCAAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_298\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTGTCTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_355\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGCGGTAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_469\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCCTTCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_509\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTATGCGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_320\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAATAGTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_474\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCTATGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_544\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCTGTGGCGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_393\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAGTTAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_869\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGGAATGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_422\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTACCATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_564\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAAGAAGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_851\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCAGCAAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_559\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAACCTAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_581\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCAGGAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_657\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCTAGCCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_747\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCACAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_583\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACCGTTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_616\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGATATCCAATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_652\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCGCAACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_960\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGAGCCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_52\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGATGTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_800\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTACTTAGCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_293\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCTAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_388\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAGAGCTATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_786\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATGAACATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_818\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTATCCAGGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_910\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGCTGCTGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_968\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGTCTATATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_878\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTCTGCAAGATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_923\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGTAACTCATCTCGTATGCCGTCTTCTGCTTG\n>Broad Barcode tagged_944\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTATATCTATCTCGTATGCCGTCTTCTGCTTG" }, { "path": "tests/input/TestTrimmomatic/clip.fasta", "content": ">Broad Barcode tagged_57\nGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTAGAGATCTCGTATGCCGTCTTCTGCTTG\n" }, { "path": "tests/input/TestTrimmomatic/empty.fastq", "content": "" }, { "path": "tests/input/TestTrimmomatic/expected1.fastq", "content": "@lowQuality-trim\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTG\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD\n@barcodeAtEnd-trim\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n" }, { "path": "tests/input/TestTrimmomatic/expected1.maxinfo.fastq", "content": "@lowQuality-trim\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGA\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD9\n@barcodeAtEnd-trim\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n" }, { "path": "tests/input/TestTrimmomatic/expected2.fastq", "content": "@test1\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTG\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD\n@test3\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n" }, { "path": "tests/input/TestTrimmomatic/expected2.maxinfo.fastq", "content": "@test1\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGA\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD9\n@test3\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n" }, { "path": "tests/input/TestTrimmomatic/in1.fastq", "content": "@lowQuality-trim\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGA\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD9\n@barcodeAtStart-eliminate\nTAGAGATCTCGTATGCCGTCTTCTGCTTGCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDDIJJIJJFHGIIJJGHHHBDFDDDDDDDDD\n@barcodeAtEnd-trim\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTCGATCGGAAGAGCACACGTCTGAACTCCAG\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDDDIJJIJJFHGIIJJGHHHBDFDDDDDDDD\n" }, { "path": "tests/input/TestTrimmomatic/in2.fastq", "content": "@test1\nAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGA\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDD9\n@test2\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n@test3\nCGGGCTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACTTCGTGATCTGCCCGCCTCGGCCTC\n+\nCCCFFFFFHHHHHJJJJJJJJJJJJJJJHIIIIJJJJHIJIIJJIJJFHGIIJJGHHHBDFDDDDDDD\n" }, { "path": "tests/input/TestTsvJoin/expected-out.txt", "content": "h1\th2\th3\th5\none\tA\tX\t20\ntwo\tb\tY\t21\nthree\tC\t\t22\nfour\td\t\t23\nfive\te\t\t24\n" }, { "path": "tests/input/TestTsvJoin/tab-1.txt", "content": "h1\th2\th3\none\tA\tX\ntwo\t\tY\nthree\tC\t\n" }, { "path": "tests/input/TestTsvJoin/tab-2.txt", "content": "h1\th2\th5\none\ta\t20\ntwo\tb\t21\nthree\tc\t22\nfour\td\t23\nfive\te\t24\n" }, { "path": "tests/input/TestUtilMisc/cfg1.yaml", "content": "# Example config files for testing util.misc.load_config()\n\nparamA: 3\nparamB: 5\nenv_vars:\n var_A: 1\n var_B: 2\nparamZ: 22\n\nstd_methods:\n - a\n - b\n - c\n\nempty_subtree:\n\nstage1:\n stage2:\n step_num: 3\n step_list:\n - 5\n - 10\n - 15\n stage3:\n step_num: 31\n step_list:\n - 51\n - 101\n - 151\n\nstd_param_A_old: 111\n\n" }, { "path": "tests/input/TestUtilMisc/cfg2.yaml", "content": "# Example config files for testing util.misc.load_config()\n\ninclude: \"cfg1.yaml\"\n\nparamB: 10\nparamC: 15\n\nenv_vars:\n var_B: 3\n var_C: 4\n\nparamZ: \"\"\n\nstage1:\n stage3:\n step_list:\n - 3\n - 33\n\nempty_subtree:\n x: 1\n\n" }, { "path": "tests/input/TestUtilMisc/cfg_std.yaml", "content": "# Example config files for testing util.misc.load_config()\n\nstd_param_A_new: 239\n\n" }, { "path": "tests/input/TestUtilMisc/empty.yaml", "content": "# empty config file\n" }, { "path": "tests/input/TestVPhaser2/expected.cpickle", "content": "(lp1\n(lp2\nS'chr1'\np3\naS'55'\np4\naS'T'\naS'C'\naS'0.8156'\np5\naS'snp'\np6\naS'16.1'\np7\naS'C:65:34'\np8\naS'T:13:6'\np9\naa(lp10\ng3\naS'104'\np11\naS'G'\naS'A'\naS'0.1708'\np12\naS'snp'\np13\naS'14.29'\np14\naS'A:65:49'\np15\naS'G:14:5'\np16\naa(lp17\ng3\naS'210'\np18\naS'T'\naS'C'\naS'0.05316'\np19\naS'snp'\np20\naS'12'\np21\naS'C:59:51'\np22\naS'T:12:3'\np23\naa(lp24\ng3\naS'483'\np25\naS'T'\naS'C'\naS'0.5142'\np26\naS'snp'\np27\naS'23.61'\np28\naS'C:34:21'\np29\naS'T:8:9'\np30\naa(lp31\ng3\naS'562'\np32\naS'T'\naS'C'\naS'0.7799'\np33\naS'snp'\np34\naS'12.17'\np35\naS'C:61:40'\np36\naS'T:9:5'\np37\naa(lp38\ng3\naS'573'\np39\naS'T'\naS'C'\naS'0.5073'\np40\naS'snp'\np41\naS'13.74'\np42\naS'C:66:47'\np43\naS'T:12:6'\np44\naa(lp45\ng3\naS'660'\np46\naS'C'\naS'T'\naS'0.2772'\np47\naS'snp'\np48\naS'44.27'\np49\naS'C:78:65'\np50\naS'T:109:71'\np51\naa(lp52\ng3\naS'666'\np53\naS'C'\naS'T'\naS'0.345'\np54\naS'snp'\np55\naS'4.805'\np56\naS'C:11:5'\np57\naS'T:180:137'\np58\naa(lp59\ng3\naS'825'\np60\naS'G'\naS'T'\naS'0'\naS'snp'\np61\naS'1.381'\np62\naS'G:10:0'\np63\naS'T:364:350'\np64\naa(lp65\ng3\naS'826'\np66\naS'G'\naS'T'\naS'0'\naS'snp'\np67\naS'0.4202'\np68\naS'G:3:0'\np69\naS'T:373:338'\np70\naa(lp71\ng3\naS'828'\np72\naS'T'\naS'G'\naS'0'\naS'snp'\np73\naS'0.4121'\np74\naS'A:1:0'\np75\naS'G:362:362'\np76\naS'T:3:0'\np77\naa(lp78\ng3\naS'858'\np79\naS'T'\naS'C'\naS'1'\naS'snp'\np80\naS'1.037'\np81\naS'C:442:417'\np82\naS'T:4:5'\np83\naa(lp84\ng3\naS'999'\np85\naS'T'\naS'C'\naS'0.9182'\np86\naS'snp'\np87\naS'12.85'\np88\naS'C:527:538'\np89\naS'T:80:77'\np90\naa(lp91\ng3\naS'1075'\np92\naS'A'\naS'G'\naS'1'\naS'snp'\np93\naS'0.815'\np94\naS'A:5:5'\np95\naS'G:610:607'\np96\naa(lp97\ng3\naS'1117'\np98\naS'A'\naS'G'\naS'0.838'\np99\naS'snp'\np100\naS'15.05'\np101\naS'A:84:81'\np102\naS'G:449:482'\np103\naa(lp104\ng3\naS'1293'\np105\naS'T'\naS'C'\naS'0.09971'\np106\naS'snp'\np107\naS'17.18'\np108\naS'A:1:1'\np109\naS'C:258:245'\np110\naS'G:0:1'\np111\naS'T:63:42'\np112\naa(lp113\ng3\naS'1431'\np114\naS'T'\naS'C'\naS'0.03124'\np115\naS'snp'\np116\naS'13.55'\np117\naS'C:101:84'\np118\naS'T:22:7'\np119\naa(lp120\nS'chr2'\np121\naS'8565'\np122\naS'T'\naS'C'\naS'1'\naS'snp'\np123\naS'2.74'\np124\naS'C:40:31'\np125\naS'T:1:1'\np126\naa(lp127\ng121\naS'8766'\np128\naS'T'\naS'C'\naS'0.6568'\np129\naS'snp'\np130\naS'8.3'\np131\naS'A:0:1'\np132\naS'C:132:99'\np133\naS'T:13:8'\np134\naa(lp135\ng121\naS'8808'\np136\naS'T'\naS'C'\naS'0.1318'\np137\naS'snp'\np138\naS'16.84'\np139\naS'C:130:107'\np140\naS'T:32:16'\np141\naa(lp142\ng121\naS'8863'\np143\naS'G'\naS'A'\naS'-2.316e+77'\np144\naS'snp'\np145\naS'0.8499'\np146\naS'A:202:148'\np147\naS'G:1:2'\np148\naa(lp149\ng121\naS'8996'\np150\naS'C'\naS'A'\naS'0'\naS'snp'\np151\naS'1.406'\np152\naS'A:286:205'\np153\naS'C:0:7'\np154\naa(lp155\ng121\naS'9000'\np156\naS'A'\naS'G'\naS'0.1478'\np157\naS'snp'\np158\naS'1.6'\np159\naS'A:1:7'\np160\naS'G:285:207'\np161\naa(lp162\ng121\naS'9002'\np163\naS'A'\naS'G'\naS'0'\naS'snp'\np164\naS'1.389'\np165\naS'A:0:7'\np166\naS'G:288:209'\np167\naa(lp168\ng121\naS'9020'\np169\naS'A'\naS'G'\naS'0'\naS'snp'\np170\naS'1.667'\np171\naS'A:8:0'\np172\naS'G:247:225'\np173\naa(lp174\ng121\naS'9021'\np175\naS'A'\naS'G'\naS'0'\naS'snp'\np176\naS'1.131'\np177\naS'A:5:0'\np178\naS'G:249:188'\np179\naa(lp180\ng121\naS'9123'\np181\naS'T'\naS'C'\naS'0.6938'\np182\naS'snp'\np183\naS'14.48'\np184\naS'C:150:168'\np185\naS'G:1:0'\np186\naS'T:24:30'\np187\naa(lp188\ng121\naS'9151'\np189\naS'T'\naS'C'\naS'0.4294'\np190\naS'snp'\np191\naS'15'\np192\naS'C:142:147'\np193\naS'T:22:29'\np194\naa(lp195\ng121\naS'9272'\np196\naS'G'\naS'A'\naS'0.2018'\np197\naS'snp'\np198\naS'17.52'\np199\naS'A:82:111'\np200\naS'G:28:13'\np201\naa(lp202\ng121\naS'9439'\np203\naS'A'\naS'G'\naS'1'\naS'snp'\np204\naS'10.2'\np205\naS'A:4:6'\np206\naS'G:37:51'\np207\naa(lp208\ng121\naS'9450'\np209\naS'G'\naS'A'\naS'0.6596'\np210\naS'snp'\np211\naS'16.49'\np212\naS'A:30:51'\np213\naS'G:11:5'\np214\naa(lp215\ng121\naS'9603'\np216\naS'G'\naS'A'\naS'0.1377'\np217\naS'snp'\np218\naS'14.29'\np219\naS'A:37:71'\np220\naS'G:3:15'\np221\naa(lp222\ng121\naS'9687'\np223\naS'T'\naS'C'\naS'0.7036'\np224\naS'snp'\np225\naS'11.82'\np226\naS'C:67:127'\np227\naS'T:8:18'\np228\naa(lp229\ng121\naS'9912'\np230\naS'T'\naS'C'\naS'0.1715'\np231\naS'snp'\np232\naS'24.87'\np233\naS'C:104:195'\np234\naS'T:42:57'\np235\naa(lp236\ng121\naS'9960'\np237\naS'C'\naS'T'\naS'0.3394'\np238\naS'snp'\np239\naS'11.95'\np240\naS'C:13:33'\np241\naS'T:120:219'\np242\naa(lp243\ng121\naS'10347'\np244\naS'C'\naS'T'\naS'1.224'\np245\naS'snp'\np246\naS'16'\np247\naS'C:2:2'\np248\naS'T:9:12'\np249\naa." }, { "path": "tests/input/ebola.fasta", "content": ">Bundibugyo_ebolavirus_complete_genome\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGTGTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCTAATCTCGACGGATCGATCCCCAATACCAACACTGAGAATTGGCCTGAAGAAGTCATCTGCTCCTTGGCAAAACCAAGAGCAGGCCCAAAGGGCCATTAGGCCACATCTGCTGAGCCTGCAGAACACGCAGGACTTACTTAGCAGAAGAGAGCGCGTGCCGAAACCAGCCAACAAATTGACACAGCTGCTCACTCTGACCCTGAATTCATAAACAATATTAAGTTGACAACAGAGATACTAATCCAATATTTGGATCAAGAATCAAAATAGTGAAACGACTGACTATCCCTCCTTAGAATTAGCAAAGATCCTTTTGTAGACTATTGTGCTACATTCTCTATCCAAGACCTCAAAATGGATCCTCGTCCAATCAGAACCTGGATGATGCATAACACATCTGAAGTTGAAGCAGACTACCATAAGATTCTAACTGCCGGATTGTCCGTCCAGCAAGGCATTGTGAGACAAAGAATCATTCCTGTTTACCAAATCTCAAACCTGGAGGAAGTATGTCAACTCATCATACAGGCATTCGAGGCTGGCGTCGACTTCCAGGATAGTGCAGATAGCTTTTTGTTAATGCTATGTCTGCATCATGCCTATCAAGGGGATTATAAACAATTTTTGGAAAGTAATGCGGTAAAATACCTTGAAGGTCATGGATTCCGTTTTGAGATGAAGAAAAAGGAAGGTGTCAAGCGCCTGGAGGAACTACTCCCTGCTGCCTCGAGTGGAAAGAACATCAAGAGAACATTGGCTGCAATGCCCGAGGAGGAAACAACAGAAGCAAATGCTGGACAATTTCTTTCATTTGCTAGTCTGTTTCTCCCAAAATTGGTTGTCGGAGAAAAGGCCTGTCTGGAGAAGGTTCAACGACAAATCCAAGTGCACGCAGAACAAGGTCTGATTCAATACCCGACATCTTGGCAATCGGTGGGACATATGATGGTCATCTTCAGACTAATGCGAACCAACTTCCTGATTAAGTTCCTCCTAATACATCAAGGAATGCATATGGTTGCAGGGCATGATGCTAATGATGCCGTCATTGCCAACTCTGTAGCTCAAGCTCGTTTCTCCGGATTGTTGATAGTCAAAACAGTGCTTGATCATATCCTCCAAAAAACAGAGCACGGAGTTCGCCTGCATCCCTTGGCGCGAACAGCCAAAGTCAAAAATGAGGTGAGCTCTTTTAAGGCCGCTTTAGCCTCACTAGCACAACATGGAGAATATGCCCCGTTTGCTCGTCTGCTGAATCTATCTGGGGTTAATAATCTTGAGCATGGGCTTTTCCCTCAACTTTCTGCAATTGCTTTGGGAGTAGCAACTGCACATGGGAGCACTCTGGCTGGAGTCAATGTAGGAGAGCAATACCAACAACTGCGAGAAGCAGCCACTGAGGCCGAAAAGCAGTTGCAGAAATATGCTGAATCTCGTGAACTTGATCACCTAGGTCTTGATGATCAGGAAAAGAAAATCCTAAAAGACTTCCATCAGAAAAAGAATGAGATCAGCTTCCAGCAGACGACAGCCATGGTCACACTGCGGAAAGAGAGATTGGCCAAATTGACCGAAGCTATTACTTCCACCTCTATCCTCAAAACAGGAAGGCGGTATGATGATGACAATGACATACCCTTTCCAGGGCCAATCAATGATAACGAGAACTCTGGTCAGAACGATGACGATCCAACAGACTCCCAGGATACCACAATCCCGGATGTAATAATCGATCCAAACGATGGTGGGTATAATAATTACAGCGATTATGCAAATGATGCTGCAAGTGCTCCTGATGACCTAGTTCTTTTTGACCTTGAGGACGAGGATGATGCTGATAACCCGGCTCAAAACACGCCAGAAAAAAATGATAGACCAGCAACAACAAAGCTGAGAAATGGACAGGACCAGGATGGAAACCAAGGCGAAACTGCATCCCCACGGGTAGCCCCCAACCAATACAGAGACAAGCCAATGCCACAAGTACAGGACAGATCCGAAAATCATGACCAAACCCTTCAAACACAGTCCAGGGTTTTGACTCCTATCAGCGAGGAAGCAGACCCCAGCGACCACAACGATGGTGACAATGAAAGCATTCCTCCCCTGGAATCAGACGACGAGGGTAGCACTGATACTACTGCAGCAGAAACAAAGCCTGCCACTGCACCTCCCGCTCCCGTCTACCGAAGTATCTCCGTAGATGATTCTGTCCCCTCAGAGAACATTCCCGCACAGTCCAATCAAACGAACAATGAGGACAATGTCAGGAACAATGCTCAGTCGGAGCAATCCATTGCAGAAATGTATCAACATATCTTGAAAACACAAGGACCTTTTGATGCCATCCTTTACTACCATATGATGAAAGAAGAGCCCATCATTTTCAGCACTAGTGATGGGAAGGAGTATACATATCCAGACTCTCTTGAAGATGAGTATCCACCCTGGCTCAGCGAGAAGGAAGCCATGAACGAAGACAATAGATTCATAACCATGGATGGTCAGCAGTTTTACTGGCCTGTGATGAATCATAGAAATAAATTCATGGCAATCCTCCAGCATCACAGGTGATCCGACCTCTAAAACTGAGCTCCTAACTACAAGCTACCCCATCACTCTGCCGGAATGCCAGAACCTCCCTCCAAAACAGCTCCACATCGAGAACCTCCGACGCGGTACACAGGCAAGACAGGCAACCTAATGATGTTCCTGTTCACCCACAACCGCAACCAACACTTGATCGACTTCCAAGACAACTACAACCCCCTTAGCCAACTCCACCACAGAAGCACCACCCCATAACAACAACCCCAAACCAACAACACTGCATGTAAGTATTGTCTCACCCCAAGATGATCCCTGGACACCAACAACCCCCTAACCTCCCCAAGTTGTCATTAAGAAAAAATATATGATGAAGATTAAAACCTTCATCAGAGCTATTTCTTCTACGCTTGGTTAGGACCAGTATTCACAAACTATTTTACAATCCCTACCCAATATGACCTCTAACAGAGCAAGGGTGACTTACAACCCACCACCAACAACCACAGGCACACGATCGTGTGGGCCGGAACTTTCCGGGTGGATCTCTGAGCAATTGATGACAGGCAAGATTCCGATTACCGATATCTTCAATGAAATTGAAACCTTACCTAGTATAAGTCCCTCGATCCACTCCAAAATCAAAACCCCAAGTGTTCAAACACGCAGTGTCCAGACCCAAACTGACCCAAATTGTAATCATGATTTTGCAGAGGTTGTGAAAATGCTAACATCTCTAACCCTTGTCGTACAAAAACAAACCCTTGCAACTGAATCACTTGAGCAACGCATTACTGACCTGGAAGGTAGCCTGAAACCAGTGTCTGAGATCACCAAGATTGTTTCTGCACTAAATAGATCCTGTGCAGAGATGGTGGCCAAATATGATCTTCTAGTAATGACGACTGGTCGTGCAACTGCCACTGCTGCAGCTACTGAAGCATACTGGGCAGAACATGGACGTCCTCCACCGGGGCCCTCATTGTACGAGGAGGATGCAATCAGGACTAAAATTGGAAAACAAGGGGATATGGTACCCAAGGAAGTGCAAGAGGCCTTCCGTAATCTGGATAGTACTGCCCTTCTAACGGAAGAGAATTTTGGGAAACCAGACATATCCGCAAAAGACTTGCGCAATATCATGTATGATCACCTCCCAGGTTTTGGCACAGCATTTCATCAACTAGTGCAAGTTATCTGCAAGTTAGGGAAGGACAATTCCTCACTTGATGTAATTCATGCAGAATTTCAGGCCAGCCTTGCTGAAGGAGACTCTCCTCAGTGTGCCCTGATTCAGATAACCAAACGGATTCCTATTTTCCAAGATGCAGCACCACCCGTAATCCATATTCGGTCACGCGGTGATATACCAAAGGCGTGTCAAAAGAGCCTCCGCCCTGTTCCACCATCACCAAAGATTGATAGGGGTTGGGTATGCATATTCCAGCTACAAGACGGAAAAACACTCGGACTCAAAATCTAAGGTGAACAATTGCGCAACCTCCACAGTCGCCTATATTGCTTCCTTCCGGAATCAGGGTATGATCGCGTAAAAAATAAGCTTCCAACATATTGATACACGATCCATATCCATAATGCCATCTCCAGGAATATGAGAACGCAAGGCCATATCAGGACCCGATCTCAATTCCAATGCAACCTACTGTTAAGAATAAAATAACCAATGTCCTCTAGCCTTATATGTTCTCAAAAATACAAGTGATGAAGATTAAGAAAAAGCATCCTTTACTTGAGAGGAGCTAATTCTTTATACTTCATCTAATCTTTAAGTAAGTTGATCACTACCACCATGAGGAGGGCAATTCTACCTACTGCACCGCCAGAATACATAGAGGCTGTCTACCCAATGAGAACGGTTAGTACTAGTATCAACAGTACTGCCAGTGGTCCGAACTTTCCAGCACCGGATGTAATGATGAGTGATACACCCTCCAACTCACTCCGACCAATTGCTGATGATAACATCGATCATCCAAGTCATACACCAACCAGTGTTTCATCAGCCTTTATACTCGAGGCAATGGTGAATGTGATATCGGGGCCGAAGGTACTAATGAAGCAAATTCCTATATGGCTCCCCTTGGGTGTTGCTGATCAAAAAACATATAGTTTTGACTCAACTACAGCTGCAATTATGCTCGCATCGTACACCATCACTCACTTTGGCAAAACCTCCAATCCGCTTGTGAGAATCAATCGACTTGGTCCTGGGATCCCCGATCACCCGTTGCGGCTTCTAAGAATAGGAAATCAAGCCTTCTTGCAAGAGTTTGTGCTGCCTCCAGTTCAATTGCCGCAGTATTTCACTTTTGACCTGACGGCTCTAAAGCTGATCACTCAACCTCTCCCGGCAGCAACCTGGACGGATGATACTCCGACCGGTCCTACAGGAATACTTCGTCCTGGAATTTCCTTTCATCCCAAACTGAGACCTATCCTATTGCCAGGGAAGACCGGGAAAAGAGGATCCAGCTCCGATCTTACTTCTCCTGATAAAATACAAGCAATAATGAACTTTCTCCAAGACCTCAAACTCGTGCCGATTGATCCAGCCAAGAACATTATGGGTATTGAAGTGCCGGAACTCTTGGTCCACAGACTAACTGGAAAGAAAATCACAACAAAAAATGGTCAACCAATAATTCCTATTCTTCTACCAAAGTATATTGGCATGGATCCCATTTCTCAGGGAGACCTCACAATGGTCATCACTCAAGACTGTGACACTTGCCATTCTCCTGCTAGTCTTCCTCCAGTCAGCGAGAAATGAGCATGAAGTCCGAGGCTGCCCGGCCCACACGACCCCCAGGGCCTTCGTCCGGCTACCGAACCAACCATCCGACCTTCATCAAAACCAAAAAATACCGCCACGCGAAAGCTAAAATGCAGGACCACAATCCAACCAGCAACACCATCCATACACAGGTATCAATTGGGCTGCCGCAGCATATAGACCCAATAGCAAGCTGCTGTCCAGAAAATAGTTCCGGAAAGTAACTCAACCATCGCAAGCCCAATGCAGCTTTCAGAAATCCGCCAGCAACCCAACTCCACTGTACCCCCAATATTAACCTGAATCGACTAACCGCACTTTAATTTGAAGTACATTTGTTCAATGGGTTCATTATTAACAGTGTTGCTTTTAGATTGTACCTTTGCTCACAGATAGTAAATTGTTATGGTATCAAATCTTATTAAGAAAAAGAACACGATGAAGATTAACGCGACCTAGAGCGCTGCCTTCATCTCATCAATTTAACTTGTCAATAGAGCAACCTAGTTTGTGATTACTCATCTTCCGTAGTTGACAAACACTTTGCTGGTTAATTGTAAATATACCACAGTCATCATGGTTACATCAGGAATTCTACAATTGCCCCGTGAACGCTTCAGAAAAACATCATTTTTTGTTTGGGTAATAATCCTATTTCACAAAGTTTTCCCTATCCCATTGGGCGTAGTTCACAACAACACTCTCCAGGTAAGTGATATAGATAAATTGGTGTGCCGGGATAAACTTTCCTCCACAAGTCAGCTGAAATCGGTCGGGCTTAATCTAGAAGGTAATGGAGTTGCCACAGATGTACCAACAGCAACGAAGAGATGGGGATTCCGAGCTGGTGTTCCACCCAAAGTGGTGAACTACGAAGCTGGGGAGTGGGCTGAAAACTGCTACAACCTGGACATCAAGAAAGCAGATGGTAGCGAATGCCTACCTGAAGCCCCTGAGGGTGTAAGAGGCTTCCCTCGCTGCCGTTATGTGCACAAGGTTTCTGGAACAGGGCCGTGCCCTGAAGGTTACGCTTTCCACAAAGAAGGCGCTTTCTTCCTGTATGATCGACTGGCATCAACAATCATCTATCGAAGCACCACGTTTTCAGAAGGTGTTGTGGCTTTCTTGATCCTCCCCGAAACTAAAAAGGACTTTTTCCAATCGCCACCACTACATGAACCGGCCAATATGACAACAGACCCATCCAGCTACTACCACACAGTCACACTTAATTATGTGGCTGACAATTTTGGGACCAATATGACTAACTTTCTGTTTCAAGTGGATCATCTAACTTATGTGCAACTTGAACCAAGATTCACACCACAATTTCTTGTCCAACTCAATGAGACCATTTATACTAATGGGCGTCGCAGCAACACCACAGGAACACTAATTTGGAAAGTAAATCCTACTGTTGACACCGGCGTAGGTGAATGGGCCTTCTGGGAAAATAAAAAAACTTCACAAAAACCCTTTCAAGTGAAGAGCTGTCTGTCATATTTGTACCAAGAGCCCAGGATCCAGGCAGCAACCAGAAGACGAAGGTCACTCCCACCAGCTTCGCCAACAACCAAACCTCCAAGAACCACGAAGACTTGGTTCCAGAGGATCCCGCTTCAGTGGTTCAAGTGCGAGACCTCCAGAGGGAAAACACAGTGCCGACCCCACCCCCAGACACAGTCCCCACAACTCTGATCCCCGACACAATGGAGGAACAAACCACCAGCCACTACGAACCACCAAACATTTCCAGAAACCATCAAGAGAGGAACAACACCGCACACCCCGAAACTCTCGCCAACAATCCCCCAGACAACACAACCCCGTCGACACCACCTCAAGACGGTGAGCGGACAAGTTCCCACACAACACCCTCCCCCCGCCCAGTCCCAACCAGCACAATCCATCCCACCACACGAGAGACTCACATTCCCACCACAATGACAACAAGCCATGACACCGACAGCAATCGACCCAACCCAATTGACATCAGCGAGTCTACAGAGCCAGGACCACTCACCAACACCACAAGAGGGGCTGCAAATCTGCTGACAGGCTCAAGAAGAACCCGAAGGGAAATCACCCTGAGAACACAAGCCAAATGCAACCCAAACCTACACTATTGGACAACCCAAGATGAAGGGGCTGCCATTGGTTTAGCCTGGATACCTTACTTCGGGCCCGCAGCAGAGGGAATTTATACGGAAGGGATAATGCACAATCAAAATGGGCTAATTTGCGGGTTGAGGCAGCTAGCAAATGAGACGACTCAAGCCCTACAGTTATTCTTGCGTGCTACCACGGAATTGCGCACTTTCTCTATATTGAATCGAAAAGCCATCGACTTTTTACTCCAAAGATGGGGAGGAACGTGCCACATCTTAGGCCCAGATTGCTGTATTGAGCCCCATGATTGGACTAAGAACATTACTGACAAAATAGATCAAATCATTCATGATTTCATTGATAAACCTCTACCAGATCAAACAGATAATGACAATTGGTGGACAGGGTGGAGGCAATGGGTTCCTGCCGGGATCGGGATCACGGGGGTAATAATCGCAGTTATAGCACTGCTGTGTATTTGCAAATTTCTACTCTAATCTAGTCCGACTCTGTACCAGCATAATGGCCTCTAAAATAAGCTTTTGCTTCTGCTTCCTATAGTTAATACATTTCAGCAAAAATCAACTATTAAGTCAAAAGAAGATCCCTCTAATAATCCTAATTACCTTCAAAAATCTAGAACTTTATTAATTCTCAGGGTATTTAGAACAGCCAGATGACTTGACTAAGTTTGTACTGTAATAAAAAGATACTTGATGAAGATTAAGAAAAAGACAGTCTTGTGATTGTCACTAATCTTCATCTCAAAACATATTATTTTACCAGAAGCTACTATAGCCTACCTCCTTGACACATAGCAAACCTTACTCATGTTGATAATTGTTTGCCTGCTATTTACATATTTACTAACTTACAAAATTATCTTGGGGATTTCTCTGAACATATAATCAGAATTGGCATTTAAAACACAAGTTAGTCCTAATGGACTCATTTCATGAGAGAGGGCGTAGCAGAACTATTCGACAGAGTGCAAGAGATGGGCCGAGTCATCAAGTAAGAACAAGATCATCCTCCAGAGACAGCCACCGCAGCGAATATCATACACCTAGGAGCTCTTCCCAAGTTCGAGTCCCGACTGTGTTTCATCGGAAGCGTACTGATTCTTTGACAGTTCCACCAGCACCAAAGGACATATGTCCTACCTTAAGGAAAGGATTTTTGTGTGACAGCAATTTTTGTAAAAAGGACCATCAACTAGAAAGTTTAACAGATAGGGAGCTGCTTTTGCTGATTGCACGGAAAACCTGCGGCTCCCTTGAACAACAATTGAACATCACTGCTCCTAAAGATACACGATTAGCAAATCCAATTGCAGATGATTTCCAACAAAAAGACGGCCCAAAAATTACACTATTGACACTTTTGGAGACTGCGGAGTATTGGTCAAAACAAGATATCAAGGGCATTGATGACTCAAGACTAAGAGCATTACTAACCCTTTGTGCCGTCATGACGAGGAAATTCTCAAAATCCCAGCTTAGTCTATTGTGTGAGAGTCATCTACGACGAGAAGGGCTAGGACAGGATCAATCAGAATCTGTTCTTGAAGTGTATCAGCGCTTACATAGCGACAAAGGCGGAAATTTTGAGGCAGCCCTATGGCAACAATGGGACCGACAGTCCTTGATCATGTTTATAACAGCATTTCTTAATATTGCTTTACAATTACCCTGTGAAAGTTCATCTGTTGTTATTTCAGGATTAAGGCTGCTAGTGCCTCAATCAGAAGATACCGAGACCTCAACCTACACCGAGACACGTGCATGGTCAGAGGAAGGTGGCCCCCATTAACATCTTCCACAGTCGAATCTACCATAATTTCCCTATTCAACGCAGATAAGAATCAGTACTAAACCACAAGTGCAAAAATTAACAAAACACCAGCATAAGTGAAATCCTGTCTGTGATTAGCAACACGAATGATCTTCAATCCTGTTGCAATTCGCCAGTGATAATTGTATTCACATTGTGGCCACAATATACTGTCTTTTCCCATTGAAAAATAAGGCTGAATCTATTACGCTACACAAACTTACAGGATTAGCACCACGACGGCTCAATACTATACCTATTGGTCACGGCTCGATGTGTTAATCACTTATATTGTATTCATTTGAAATTACTCATTAGGCAAATACTTTGATTAAGAAAAAATAATTGGAAAACCAGAAAATCCCTAGGTATTTAAATTCCTATCTCCGGAGATCCGAGATAATTAATCAAGCAATGAGGGAACAATGGTGAACAACAACATATTGTTGCCCCCTTTAGATTGGTCAGTTCCAAAAACAAGTGATGAAGATTAATGCAGATGTCCAAGGAACACATATTTGTGATTTAAACGTTCCAGTTAGACTCTGTTCAAGGATCTTCATCTTTTGTAGCTCCACTCTGAGTCACAACATAATTGAGTTTTTGCTCAGAACAGTTATCAGGATTAAATTCTCTCAAATAACTGAAACTACTAGCATCACTCTCAATTTCATTACTTACGACAATCATTATCTTAATAATATTTCTCTAAATTACTGACTTAATTAGCTTGTAATCAGATAATATCGAAACCAATTTATCATAAGGCATAATTTGTATAAGTGATTTAGGATTTACCCCAGAAGTGAAATAATTCTTAGAATAAAAGACCGACTAGAATATCCTTAAGGCTGTCTAACGTGCCACACAGCTAGGGTTAGCCTGACATCTGGAACAAGATCGATACTAATATAGGGATTTGTTTCATACTAGCTCTCTGCAAACACAATGGCTAAGGCAACAGGTAGGTACAACTTGGTTTCACCTAAAAAGGACCTCGAGAGGGGGCTTGTTTTGAGTGATTTGTGCACGTTTTTAGTTGATCAGACTATCCAGGGGTGGCGGGTGACTTGGGTTGGGATTGAATTTGACATCGCCCAGAAAGGGATGGCTCTACTGCATCGGTTAAAAACTGCTGACTTCGCTCCTGCATGGTCGATGACAAGGAATTTATTTCCTCATTTATTTCAAAATTCAAATTCTACTATTGAGTCTCCCCTCTGGGCATTACGAGTGATTCTGGCAGCTGGTATTCAAGACCAGTTAATTGACCAATCCTTGGTAGAACCGTTGGCCGGAGCCCTGAGCTTAGTCTCCGATTGGCTTCTTACAACAAACACAAACCATTTTCAAATGCGCACGCAGCACGCTAAAGAGCAACTGAGCTTGAAGATGCTATCATTAGTGCGCTCTAATATCTTGAAATTCATCAGTCAATTGGACGCACTACATGTCGTGAACTACAATGGACTCTTGAGCAGTATCGAAATTGGCACTAGAAATCATACCATTATCATCACAAGAACCAACATGGGTTTCCTGGTAGAATTACAGGAGCCTGATAAATCTGCCATGAATCAAAAGAAACCAGGACCAGTCAAGTTCTCCCTCCTGCATGAATCAACCTTCAAGGCTCTAATCAAAAAACCCGCAACTAAGATGCAGGCCTTGATTCTGGAATTTAACAGCTCCCTGGCAATATAGTCCAACGCTACCAACCATCATTTTTTGTAACTGCATCTCTTTTATTTCCTTTCTAACTTGATACAATTATAATCAAGATCCCTAATCCCTTTTGACGAAGTGGGCTAATTTTTGCTCATTCTAATAATAAATCATAACCTGAATAAAAGACACCACAATATTATAACCCAATAACACCTAGAGAATTTCTGAATTGCTAAAGATTATATACTCGCACTAAGAGACAAGTTAATCAATCTTTACTTAATAATATACTAAATGCTAGATAGCTCTGGCTAACTAACCTGAGTTGTGGATTACTCCTTTTAAAAGTCTATCAATTTAAGCTTATCACTAATATTAAGGAGGACTTTTTAAATAAGAGCAAGTGTTATGTAGTCTTACTAAGAATGATTTGAGGAAGATTAAGAAAAAGTGCTTGTGGGGTCTTTCCGTTGTAGAGGACACACGAGCAAACTTCTTCCTCTAATTTTAATATGGCAACTCAACATACACAATATCCAGATGCAAGATTATCTTCACCCATTGTCTTAGATCAATGTGATCTTGTCACCCGTGCTTGCGGTCTGTATTCTTCATACTCATTAAATCCTCAGTTGAAAAATTGTAGACTACCAAAACATATTTACCGCCTCAAATTTGATGCTACGGTTACAAAATTTTTAAGCGATGTTCCAATAGTTACATTGCCGATAGATTACTTGACCCCTTTACTTTTACGAACTTTATCCGGGGAGGGCTTATGCCCTGTCGAACCAAAGTGCAGCCAATTCTTAGATGAAATAGTAAGTTATGTTTTGCAGGATGCACGTTTTTTAAGATACTATTTTAGGCATGTTGGAGTACACGATGACAATGTTGGAAAAAATTTTGAGCCAAAGATTAAGGCTTTGATTTATGATAATGAATTTCTGCAACAATTGTTTTATTGGTACGATTTAGCAATCCTAACGCGTAGAGGGCGCCTGAATCGAGGGAATAACCGTTCAACATGGTTTGCAAATGACGATTTAATAGACATTCTCGGGTACGGTGATTATATTTTCTGGAAAATACCGTTGTCATTGTTGTCACTCAACACAGAGGGGATTCCTCATGCAGCTAAGGACTGGTATCACGCATCAATCTTCAAAGAAGCGGTTCAAGGTCACACACATATCGTGTCAGTTTCCACTGCAGATGTTTTAATTATGTGTAAGGACATCATAACCTGTCGTTTCAATACCACACTCATTGCAGCATTGGCAAATTTAGAAGATTCTATCTGTTCTGACTATCCACAACCTGAAACAATCTCTAATCTGTATAAGGCAGGGGATTACTTAATCTCGATACTGGGTTCAGAAGGTTATAAGGTCATAAAGTTTTTAGAACCACTATGTTTAGCTAAGATCCAATTGTGCTCAAATTACACTGAGAGGAAAGGGAGATTCCTTACTCAAATGCATTTGGCCGTTAATCACACACTTGAAGAACTTATTGAGGGCCGGGGATTGAAGTCACAACAAGACTGGAAGATGAGGGAATTTCACCGAATCTTAGTAAATTTAAAGTCAACACCACAACAACTCTGTGAATTGTTTTCAGTGCAAAAGCATTGGGGGCATCCTGTGCTACATAGCGAGAAGGCTATTCAGAAAGTAAAGAAACATGCAACCGTAATAAAAGCATTGCGTCCCGTAATCATCTTTGAGACATATTGTGTGTTCAAGTACAGCATTGCCAAACATTATTTTGATAGCCAAGGGTCATGGTATAGTGTAATCTCAGATAAACATCTAACACCAGGTTTACACTCTTACATTAAGAGGAACCAATTTCCGCCACTGCCTATGATTAAAGACTTATTGTGGGAATTCTATCACCTTGATCATCCTCCCTTATTTTCCACCAAGATTATTAGTGACTTGAGTATTTTCATTAAGGATCGCGCTACCGCAGTGGAAAAAACATGTTGGGATGCAGTTTTCGAGCCTAATGTTCTTGGATATAGTCCTCCAAACAAGTTCTCAACTAAGAGGGTTCCTGAACAGTTTCTTGAACAAGAAAATTTCTCGATTGATAGTGTTCTCACTTATGCCCAGCGCCTGGATTATCTACTTCCACAATACCGGAATTTTTCTTTCTCACTTAAGGAAAAAGAATTAAATGTAGGACGAGCTTTTGGTAAGCTACCTTATCCTACACGTAATGTTCAAACTTTATGTGAAGCCTTATTGGCAGATGGATTAGCTAAAGCCTTTCCTAGTAACATGATGGTTGTAACAGAGCGTGAGCAGAAGGAAAGCCTCTTGCACCAGGCGTCGTGGCACCACACAAGTGACGATTTCGGTGAGAATGCCACTGTTAGAGGCAGCAGTTTTGTTACCGACCTAGAAAAATACAACTTGGCATTTAGATATGAGTTTACAGCTCCATTTATTGAATACTGTAATCGATGTTATGGTGTAAAAAATTTATTCAATTGGATGCATTATACGATACCGCAATGTTATATACATGTAAGTGATTATTATAATCCCCCTCATGGAGTTTCGCTAGAAAATCGGGAAGATCCCCCGGAAGGCCCTAGCTCTTACCGTGGTCATCTTGGGGGAATTGAGGGACTCCAACAGAAACTCTGGACCAGCATTTCATGTGCACAAATCTCATTAGTTGAGATCAAGACTGGTTTCAAATTGAGATCTGCGGTAATGGGTGATAATCAATGCATCACAGTTCTTTCCGTATTTCCTCTAGAGACAGATTCCAATGAGCAAGAGCATAGCTCCGAGGACAATGCTGCTCGCGTAGCAGCCAGTTTAGCCAAAGTCACGAGTGCCTGTGGCATCTTCCTAAAACCAGATGAGACTTTTGTGCATTCAGGCTTTATTTATTTCGGTAAGAAGCAATATTTAAATGGCGTTCAATTGCCACAATCACTCAAGACTGCTACCAGGATTGCTCCCTTGTCAGATGCAATCTTTGATGACCTTCAGGGAACTCTGGCTAGTATAGGAACGGCATTTGAGAGATCTATATCCGAGACTAGACATGTATACCCTTGCCGGGTGGTTGCCGCATTCCATACATTCTTCTCCGTTAGGATCCTCCAATACCACCACCTTGGTTTCAACAAAGGAACCGATCTAGGTCAACTATCACTAAGCAAACCGTTGGATTTCGGAACTATCACTCTTGCTTTAGCGGTACCTCAAGTTCTAGGAGGTTTATCGTTTTTAAACCCAGAGAAATGTTTTTATCGCAACCTTGGAGACCCCGTGACCTCCGGCCTATTCCAACTTAGGACTTACCTGCAAATGATCAACATGGACGACTTATTTCTACCTTTAATTGCCAAGAACCCCGGGAACTGTAGTGCAATTGACTTTGTACTCAACCCAAGCGGATTGAATGTCCCTGGGTCACAAGACCTAACATCTTTTTTACGTCAGATAGTGCGTAGAACAATCACATTGAGTGCAAAAAATAAGCTAATAAACACATTGTTTCACTCCTCAGCCGATTTAGAAGATGAGATGGTATGTAAATGGCTACTTTCTTCAACACCTGTAATGAGTCGGTTTGCTGCTGATATATTCTCTCGTACTCCGAGTGGGAAGCGCTTGCAGATCCTAGGTTATTTAGAAGGGACTAGAACCTTGCTAGCCTCCAAAGTCATCAATAACAATGCAGAGACTCCTATTTTAGATAGGTTGAGGAAAATCACACTGCAGAGATGGAGTTTGTGGTTTAGCTACCTAGACCACTGTGATCAGGTTCTAGCAGATGCTTTAATAAAAGTTTCTTGTACAGTTGATTTGGCGCAAATTTTACGTGAATATACCTGGGCACACATACTAGAGGGAAGACAGCTCATTGGTGCAACACTTCCTTGCATGTTAGAACAATTTAATGTGTTTTGGCTCAAATCGTACGAACAATGCCCTAAATGTGCAAAATCTAGAAATCCAAAAGGAGAGCCATTTGTGTCAATTGCAATTAAGAAACAAGTTGTGAGTGCATGGCCGAATCAGTCACGGTTAAATTGGACCATTGGGGACGGTGTACCTTACATCGGGTCTCGAACAGAGGACAAGATTGGGCAGCCAGCAATCAAGCCTAAGTGTCCCTCTGCTGCCTTACGTGAAGCAATAGAGTTGACATCTAGACTAACATGGGTTACCCAAGGTGGTGCCAATAGTGATTTGCTAGTTAAACCTTTTGTAGAGGCACGAGTAAACCTGAGTGTGCAGGAGATCCTTCAAATGACGCCTTCTCATTATTCAGGGAACATCGTACATCGGTATAATGACCAATACAGCCCTCATTCTTTCATGGCAAATAGAATGAGTAATTCCGCGACGAGATTGGTGGTGTCGACAAATACTCTCGGGGAGTTCTCAGGTGGGGGGCAATCAGCAAGGGACAGCAATATCATCTTTCAAAATGTAATCAATTTTTCGGTTGCCCTATTTGATTTACGATTTCGGAACACCGAAACATCCTCCATTCAGCATAATCGTGCCCATCTCCATCTTTCACAGTGTTGCACACGGGAAGTCCCAGCTCAATACCTAACCTACACGTCTACGCTTTCCTTGGATCTCACAAGGTACCGAGAGAATGAGTTAATTTATGATAACAATCCGTTAAAAGGTGGACTTAATTGCAACCTATCCTTTGATAATCCACTTTTCAAGGGCCAAAGGCTCAATATCATAGAGGAGGATTTGATTAGATTTCCTCATCTATCTGGGTGGGAACTTGCGAAAACCATCATTCAGTCCATTATCTCAGACAGCAATAACTCATCCACAGACCCCATTAGCAGTGGAGAAACACGATCATTCACAACTCACTTTCTCACATATCCTAAGGTTGGGCTCCTCTATAGTTTCGGCGCCATCGTGAGTTATTACTTAGGGAATACCATTATTAGGACCAAAAAGCTAGACCTCAGTCATTTTATGTATTACTTAACAACTCAAATCCATAATTTGCCACATCGCTCGTTGAGGATACTTAAGCCCACCTTTAAACATGTTAGTGTGATATCAAGACTAATGAGTATTGATCCTCATTTTTCAATCTACATCGGGGGTACGGCAGGTGATCGAGGGCTTTCGGATGCTACCAGACTATTCCTTCGAGTGGCCATTTCTTCCTTCCTTCAATTTATCAAAAAATGGATCGTGGAATACAAGACAGCTATTCCTCTGTGGGTTATATACCCTTTGGAGGGACAAAATCCAGATCCAATTAATAGCTTTCTACATCTGATTATAGCCTTACTGCAAAATGAATCCCCTCAAAACAACATCCAATTCCAAGAAGACAGAAATAATCAACAGTTGTCCGATAATCTAGTTTACATGTGCAAGAGCACTGCCAGTAATTTCTTCCATGCATCACTTGCCTATTGGAGGAGCCGGCACAAAGGACGGCCCAAAAATCGATCGACCGAAGAACAGACAGTTAAACCCATACCATATGATAATTTTCATTCTGTTAAATGTGCCTCAAACCCACCAAGCATCCCCAAATCTAAGTCAGGAACTCAAGGTTCAAGCGCATTTTTTGAGAAACTTGAATATGATAAAGAAAGAGAATTGCCAACAGCTTCCACACCAGCCGAACAATCCAAGACCTATATCAAGGCCCTATCCAGCCGAATTTATCATGGTAAAACACCATCCAATGCCGCAAAAGATGATTCAACAACCTCCAAGGGCTGCGATTCCAAAGAAGAAAATGCCGTTCAAGCTTCACACCGAATTGTCCTACCATTTTTTACATTGTCACAGAACGACTACAGAACTCCCTCAGCTAAAAAGTCAGAGTATATAACTGAAATCACCAAACTAATTCGACAATTAAAGGCAATTCCAGATACCACTGTATACTGTCGCTTTACAGGGGTTGTATCTTCAATGCATTATAAGCTTGATGAGGTTCTCTGGGAATTCGATAGTTTCAAAACTGCTGTGACTCTAGCTGAAGGAGAAGGGTCAGGTGCCTTATTACTACTACAAAAATATAAGGTCAGAACAATCTTTTTTAACACTTTAGCTACAGAGCATAGCATCGAGGCAGAAATAGTTTCTGGGACAACCACACCTCGAATGCTCCTTCCTGTAATGGCCAAACTTCATGATGATCAAATAAATGTAATATTAAACAATTCTGCTAGCCAGGTTACTGATATCACTAACCCTGCATGGTTCACTGACCAGAAATCTAGAATCCCCACACAAGTTGAGATTATGACTATGGATGCTGAAACGACAGAAAATATTAATCGGTCAAAATTATATGAGGCTATTCAGCAATTAATTGTTTCACACATTGATACAAGGGTGCTAAAGATTGTTATTATAAAGGTTTTTTTAAGTGATATTGAAGGTCTCCTGTGGCTTAATGACCATCTTGCCCCTTTATTCGGATCCGGCTATTTAATTAAACCTATTACTTCGAGTCCAAAGTCAAGCGAATGGTACTTATGTCTTTCAAATTTCCTTTCAGCCTCTCGACGACGGCCTCATCAGGGTCATGCTACCTGTATGCAAGTCATCCAAACAGCGCTACGACTCCAAGTTCAAAGGAGTTCATACTGGCTTAGCCATTTAGTGCAATATGCTGATATTAATTTGCACTTGAGTTATGTTAATTTGGGTTTCCCTTCATTGGAAAAGGTTCTTTACCATCGATATAACCTAGTTGATTCACGGAAGGGTCCACTGGTCTCGATCCTTTACCATTTAACACACTTGCAAGCAGAGATTAGAGAATTAGTGTGTGACTATAATCAGCAACGACAAAGTCGAACCCAAACATACCACTTCATCAAAACGACAAAGGGCCGGATTACAAAATTAGTCAATGACTACCTTAAATTTTATCTCGTAGTGCAAGCACTGAAGCATAATTGTCTTTGGCAGGAAGAACTCAGAACACTTCCTGACTTAATCAATGTTTGCAATCGATTTTACCATATAAGGGACTGCTCATGTGAAGATCGATTTTTAATTCAAACTCTTTACTTAACCCGTATGCAAGACTCAGAAGCAAAATTAATGGAGAGATTAACCGGGTTTCTAGGATTGTATCCTAATGGTATTAACGCTTAAGATCCCCTTAGAGGCATCGCAATATGACTCCAAACATTAAATGATATTGCTGTCAATACATCTACCTGACCGAGAGCAAGGTTTATTATAAAAAACCTATACACATGACTGCAATGCGTAATTTATACCGAAACACAGTGAGGGCTGCACATGCAGGTTCCTGTTGAGCTTTAAAAGATCATGCAATATAAAATGATATTTGTATACTAATCATGTTAGTACTAACTAACAGTACTCACTGCATATACTCTATCAATTAAGAAAAATTACTGTGGTTTATGCATTTAAATGACATCACAGATGGATATAATATAGTTAATTCTTACCTAAATGTTGAGTTATAGTAATTTGAAGTTATAATTATGATTAGTGCTTATACTATAAATAATAGCTATACCAAGTATACACAAGAAGTTATGATTTTGTATTCAAATTATATTCACAGGAACTTGTGATTAATAATAAAAGTCTCAGTTGTTGGTTGTTGAGTTGTAAAACTCCCGTTAAAAATTTATTTTCCACTTATAACTAATAATAATCATAGATCAGTATGAGTTGAGGCTATTCAAACCTTAGAAAAATTGTGCGATGTTTTTTACCATGTCAATCTTGATTTCAATGATATTGGAGGGCTTGTCGATAAATTCAGTAATTAACATTAAGTCAGTGTGGAACCTCATTGGATATTTGATCGTACACAAAATATCTTTACAAAATTGTTTTCTCTTTTTTGTGTGTCCA\n>Bundibugyo_ebolavirus_isolate_EboBund-14_2012_complete_genome\nCGGACACACAAAAAGAATGAAGGATTTTGAATCTTTATTGTGTGCGAGTAACTACGAGGAAGATTAAAGATTTTCCTCTCATTGAAATTGAAATTGAGATTCTAATCTCGACGGATCGATCCCCAATACCAACACTGAGAATTGGCCTGAAGAAGTCATCTGCTCCTTGGCAAAACCAAGAGCAGGCCCAAAGGGCCATTAGGCCACATCTGTTGAGCCTGCAGAACACGCAGGACTTACTTAGCAGAAGAGAGCGCGTGCCGAAGCCAGCCAACAAATTGACACAGCTGCTCACTCTGACCCTGAATTCATAAACAATATTAAGTTGACAACAGAGATACTAATCCAATATTTGGATCAAGAATCAAAATAGTGAAACGACTGACTATCCCTCCTTAGAATTAGCAAAGATCCTTTTGTAGACTATTGTGCTACATTTTCTATCCAAGACCTCAAAATGGATCCTCGTCCAATCAGAACCTGGATGATGCATAACACATCTGAAGTTGAAGCAGACTACCATAAGATTTTAACTGCCGGATTGTCCGTCCAGCAAGGCATTGTGAGACAAAGAATCATTCCTGTTTACCAAATCTCAAACCTGGAGGAAGTATGTCAACTCATCATACAGGCATTCGAGGCCGGTGTCGACTTCCAGGATAGTGCAGATAGCTTTTTGTTAATGCTATGTCTGCATCATGCCTATCAAGGGGATTATAAACAATTTTTGGAAAGTAATGCGGTAAAATACCTTGAAGGTCATGGATTCCGTTTTGAGATGAAGAAAAAGGAAGGTGTCAAGCGCCTGGAGGAACTACTCCCTGCTGCCTCGAGTGGAAAGAACATCAAGAGAACATTGGCTGCAATGCCCGAGGAGGAAACAACAGAAGCAAATGCTGGACAATTTCTTTCATTTGCTAGTCTGTTTCTCCCAAAATTGGTTGTCGGAGAAAAGGCCTGTCTGGAGAAGGTTCAACGACAAATCCAAGTGCACGCAGAACAAGGTCTGATTCAATATCCGACATCTTGGCAATCGGTGGGACATATGATGGTCATCTTCAGACTAATGCGAACCAACTTCCTGATTAAGTTCCTCCTAATACATCAGGGAATGCATATGGTTGCAGGGCATGATGCTAATGATGCCGTCATTGCCAACTCTGTAGCTCAAGCTCGTTTCTCCGGATTGTTGATAGTCAAAACAGTGCTTGATCATATCCTCCAAAAAACAGAGCACGGAGTTCGCCTGCATCCCTTGGCGCGAACAGCCAAAGTCAAAAATGAGGTAAGCTCTTTTAAGGCCGCTTTAGCCTCACTAGCACAACATGGAGAATATGCCCCGTTCGCTCGTCTGCTGAATCTATCTGGGGTTAACAATCTTGAGCATGGGCTTTTCCCTCAACTTTCTGCAATTGCTTTGGGAGTAGCAACTGCACATGGGAGCACTCTGGCAGGAGTCAATGTAGGAGAGCAATACCAACAACTGCGAGAAGCAGCCACTGAGGCCGAAAAGCAGTTGCAGAAATATGCTGAATCTCGTGAACTTGATCACCTAGGTCTTGATGATCAGGAAAAGAAAATCCTAAAAGACTTCCATCAGAAAAAGAATGAGATCAGCTTCCAGCAGACGACAGCCATGGTCACACTGCGGAAAGAGAGATTGGCCAAATTGACTGAAGCTATTACTTCCACCTCCATCCTCAAAACAGGAAGGCGGTATGATGATGACAATGACATACCCTTTCCAGGGCCAATCAATGATAACGAGAACTCTGGTCAGAACGATGACGATCCAACAGACTCCCAGGATACCACAATCCCGGATGTAATAATCGATCCAAACGATGGTGGGTATAATAACTACAGCGATTATGCAAATGATGCTGCAAGTGCTCCTGATGACCTAGTTCTTTTTGACCTTGAGGACGAGGATGATGCTGATAACCCGGCTCAGAACACGCCAGAAAAAAATGATAGACCAGCAACAACAAAGCTGAGAAATGGACGGGACCAGGATGGAAACCAAAGCGAAACTGCATCCCCACGGGCAGCCCCCAACCAATACAGAGACAAGCCAATGCCACAAGTACAGAGCAGATCCGAAAATCATGACCAAACCCTTCAAACACAGCCCAGGGTTTTGACTCCTATCAGCGAGGAAGCAGACCCCAGCGACCACAACGATGGCGACAATGAAAGCATTCCTCCCCTGGAATCAGACGACGAGGGTAGCACTGATACTACTGCAGCAGAAACAAAGCCTGCCACTGCACCTCCCGCTCCCGTCTACCGAAGTATCTCCGTAGATGATTCTGTCCCCTTAGAGAACATTCCCGCACAGTCCAATCAAACGAACAATGAGGACAATGTCAGGAACAATGCCCAGTCGGAGCAATCCATTGCAGAAATGTATCAACATATCTTGAAAACACAAGGACCTTTTGATGCCATCCTTTACTACCATATGATGAAAGAAGAGCCCATCATTTTCAGCACTAGTGATGGGAAGGAGTATACATATCCAGACTCTCTTGAAGATGAATATCCACCCTGGCTCAGCGAGAAGGAAGCCATGAATGAAGACAATAGATTCATAACCATGGATGGTCAGCAGTTTTACTGGCCTGTGATGAATCATAGAAATAAATTCATGGCAATCCTCCAACATCACAGGTGACCCGACCTCTAAAACTGAGCTCTTAACTACAAGCTACCCCATCACTCTGCCGGAATGCCAGAACCTCCCTCCAAAACAGCTCCACATCGAGAACCTCCGACGTGGTACACAGGCAAGACAGGCAACCCAATGATGTTCCTGTTCACCTACAACCGCAACCAACACTTGATCGACTTCCAAGACAACTACAACCCCCTTAGCCAACTCCACCACAGAAGCACTACCCCATAACAACAACCCCAAATCAACGACACTGCATGTAAGTATTGTCTCACCCCAAGATGCTCCCTGGACACCAACAACCCCCTAACCTCCCCAAGTTGTCATTAAGAAAAAATATATGATGAAGATTAAAACCTTCATCGGAGCTATTTCTTCTACGCTTGGTTAGGACCAGTATTCACAAACTATTTTACAATCCCTACCCAATATGACCTCTAACAGAGCAAGGGTGACTTACAACCCACCACCAACAACCACAGGCACACGATCGTGTGGGCCGGAACTTTCCGGGTGGATCTCTGAGCAATTGATGACAGGCAAGATTCCGATTACCGATATCTTCAATGAAATTGAAACCTTACCTAGTATAAGTCCCTCGATCCACTCCAAAATCAAAACCCCAAGTGTTCAAACACGCAGTGTCCAGACCCAAACTGACCCAAATTGTAATCATGATTTTGCAGAGGTTGTGAAAATGCTAACATCTCTAACCCTTGTCGTACAAAAACAAACCCTTGCAACTGAATCACTTGAGCAACGCATTACCGACCTGGAAGGTAGCCTGAAACCAGTGTCTGAGATCACCAAGATTGTTTCTGCACTAAATAGATCCTGTGCAGAGATGGTGGCCAAATATGATCTTCTAGTAATGACAACTGGTCGTGCAACTGCCACTGCTGCAGCTACTGAAGCATACTGGGCAGAACATGGACGTCCTCCACCGGGGCCCTCATTGTACGAAGAGGATGCAATCAGGACTAAAATTGAAAAACAAGGGGATATAGTACCCAAGGAAGTGCAAGAGGCCTTCCGTAATCTGGATAGTACTGCCCTTCTAACGGAAGAGAATTTTGGGAAACCAGACATATCCGCAAAAGACTTGCGCAATATCATGTATGATCACCTCCCAGGTTTTGGCACAGCATTTCATCAACTAGTGCAAGTTATCTGCAAGTTAGGGAAGGACAATTCCTCACTTGATGTAATTCATGCAGAATTTCAGGCCAGCCTTGCTGAAGGAGACTCTCCTCAGTGTGCCCTGATTCAGATAACCAAACGGATTCCTATTTTCCAAGATGCAGCACCACCCGTAATCCATATTCGTTCACGCGGTGATATACCAAAGGCGTGTCAAAAGAGCCTCCGCCCAGTTCCACCATCACCAAAGATTGATAGGGGTTGGGTATGCATATTCCAGCTACAAGACGGAAAAACACTCGGACTCAAAATCTAAGGTGAACAATTGCACAACCTCCACAGTCGCCTATATTGCTTCCTTCCGGAATTAGGGTATGATCGCGTAAAAAATAAGCTTCCAACATATTGATATACGATCCATACCCATAATGCCATCTCCAGGAATATGAGAACGCAAGGCCATATCAGGACCCGATCTCAATTCCAATGCAACCTACTGTTAAGAATAAAATAACCAATGTCCTCTAGCCTCATATGTTCTCAAAAATACAAGTGATGAAGATTAAGAAAAAGCATCCTTTACTTGAGAGGAGCTAATTCTTTATACTTCATCTAATCTTTAAGTAAGTTGATCATTACCACCATGAGGAGGGCAATTCTACCTACTGCACCGCCAGAATACATGGAGGCTGTCTACCCAATGAGAACGGTTAGTACTAATATCAGCAGTACCTCCAGTGGTCCGAACTTTCCAGCACCGGATGTAATGATGAGTGATACACCCTCCAACTCACTCAGACCAATTGCTGATGATAATATCGATCATCCAAGTCATACACCAACCAGTGTTTCATCAGCCTTTATACTCGAGGCAATGGTGAATGTGATATCGGGGCCGAAGGTACTAATGAAGCAAATTCCTATATGGCTCCCCTTGGGTGTTGCTGATCAAAAAACATATAGTTTTGACTCAACTACAGCTGCAATTATGCTCGCATCGTACACCATCACTCACTTTGGCAAAACCTCCAATCCGCTTGTGAGAATCAATCGACTTGGTCCTGGGATCCCTGATCACCCGTTGCGGCTTCTAAGAATAGGAAATCAAGCCTTCTTGCAAGAGTTTGTGCTGCCTCCAGTGCAATTGCCGCAGTATTTCACTTTTGACCTGACGGCTCTAAAGCTGATCACTCAACCTCTCCCGGCAGCAACCTGGACAGATGATACTCCGACCGGTCCTACAGGAATACTTCGTCCTGGAATTTCCTTTCATCCCAAACTGAGACCTATCCTATTGCCAGGGAAGACCGGGAAAAGAGGATCCAGCTCCGATCTTACTTCTCCTGATAAAATACAAGCAATAATGAACTTTCTCCAAGACCTCAAACTCGTGCCGATTGATCCAGCCAAGAACATTATGGGTATTGAAGTGCCGGAACTCTTGGTCCACAGACTAACTGGAAAGAAAATCACAACAAAAAATGGTCAACCAATAATTCCTATTCTTCTACCAAAGTATATTGGCATGGATCCCATTTCTCAGGGAGACCTCACAATGGTCATCACTCAAGACTGTGACACTTGCCATTCTCCTGCTAGTCTTCCTCCAGTCAGCGAGAAATAAGCATGAAGTCCGAGGCTGCCTGGCCCACACGGCCCCCAGGGCCTTCGTCCGACCACCGAACCAACCATCTGACCTTCATCAAAACCAAAAAATACCACCACGCGAAAGCTAAAATGCAGGACCACAATCCAACCAGCAACACCATCCATACACAGGCATCAATTGGGCTACCGCAGCATATAGACCCAATAGCAAGCTGCTGTCCAGAAAACAGTTCCAGAAAGTAACTCAACCATCGCAAGCCCAATGCAGCTTTCAGAAATCCGCCAGCAACCCAACTCCACTGTACCACCAATATTAACCTGAATCGACTAACCGCACTTTAATTTGAAGCACATTTGTTCAATGGGTTCATTATTAACAGTGTTGCTTTTAGATTGTACCTTTGCTCACAGATAGTAAATTGTTATGGTATCTAATCTTATTAAGAAAAAGAACACGATGAAGATTAACGCGACCTAGAGCGCTGCCTTCATCTCATCAATTCAACTTGTCAATAGCGCAACCTAGTTTGTGATTACTCATCTTTCGTAGTTGGCAAACACTTTGCTAATTAATTGTAGATATACCACAGTCATCATGGTTACATCAGGAATTCTACAATTGCCCCGTGAACGCTTCAGAAAAACATCATTTTTTGTTTGGGTAATAATCCTATTTCACAAAGTTTTCCCTATCCCATTGGGCGTAGTTCACAACAACACTCTCCAGGTAAGTGATATAGATAAATTGGTGTGCCGGGATAAACTTTCCTCCACAAGTCAGCTGAAATCGGTCGGGCTTAATCTAGAAGGTAATGGAGTTGCCACAGATGTACCAACAGCAACGAAGAGATGGGGATTCCGAGCCGGTGTTCCACCCAAAGTGGTGAACTACGAAGCTGGGGAGTGGGCTGAAAACTGCTACAACCTGGACATCAAGAAAGCAGATGGTAGCGAATGCCTACCTGAAGCCCCTGAGGGTGTAAGAGGCTTCCCTCGCTGCCGTTATGTGCACAAGGTTTCTGGAACAGGGCCGTGTCCTGAAGGTTTCGCTTTCCACAAAGAAGGCGCTTTCTTCCTGTATGATCGACTGGCATCAACAATCATCTATCGAAGCACCACGTTTTCAGAAGGTGTTGTGGCTTTCTTGATCCTCCCCAAGACTAAAAAGGACTTTTTCCAATCACCACCACTACATGAACCGGCCAATATGACAACAGACCCATCCAGCTACTACCACACAGTCACACTTAATTATGTGGCTGACAATTTTGGGACCAATATGACTAACTTTCTGTTTCAAGTGGATCATCTAACTTATGTGCAACTTGAACCAAGATTCACACCACAATTTCTTGTCCAACTCAATGAGACCATTTATACTAATGGGCGTCGCAGCAACACCACAGGAACACTAATTTGGAAAGTAAATCCTACTGTTGACACCGGCGTAGGTGAATGGGCCTTCTGGGAAAATAAAAAAACTTCACAAAAACCCTTTCAAGTGAAGAGCTGTCTGTCATACTTGTACCAAGAGCCCAGGATCCAGGCAGCAACCAGAAGACGAAGGTCACTCCCACCAGCTTCGCCAACAACCAAACCTCCAAGAACCACGAAGACTTGGTTCCAAAGGATCCCGCTTCAGTGGTTCAAGTGCGAGACCTCCAGAGGGAAAACACAGTGCCGACCTCACCCTTGAACACAGTCCCCACAACTCTGATCCCCGACACAATGGAGGAACAAACCACCAGCCACTACGAACTACCAAACATTTCCGGAAACCATCAAGAGAGGAACAACACCGCACACCCCGAAACTCTCGCCAACAATCCTCCAGACAACACAACCCCGTCGACACCACCTCAAGACGGTGAGCGGACAAGTTCCCACACAACACCCTCCCCCCGCCCAGTCCCAACCAGCACAATCCATCCCACCACACGAGAGACTCAAATTCCCACCACAATGATAACAAGCCATGATACTGACAGTAATCGACCCAACCCAATTGACATCAGCGAGTCTACAGAGCCAGGACTACTCACCAACACCATAAGAGGGGTTGCAAATTTGCTGACAGGTTCAAGAAGAACCCGGAGGGAAATCACCTTGAGAACACAAGCCAAATGTAATCCGAACCTACACTATTGGACAACCCAAGATGAAGGGGCTGCCATTGGTCTAGCCTGGATACCTTACTTCGGGCCCGCAGCAGAGGGAATTTATACGGAAGGAATAATGCACAATCAAAATGGGCTAATTTGCGGGTTGAGGCAGCTAGCAAATGAGACGACTCAAGCCCTACAGTTATTCTTGCGTGCTACCACGGAATTGCGCACTTTCTCCATATTGAATCGAAAAGCCATCGACTTTTTACTTCAAAGATGGGGAGGAACGTGCCACATCTTAGGCCCAGATTGCTGTATTGAGCCCCATGATTGGACTAAGAACATTACTGACAAAATAGATCAAATCATTCATGATTTCATTGATAAACCTCTACCAGATCAAACAGATAATGACAATTGGTGGACAGGGTGGAGGCAATGGGTTCCTGCCGGGATTGGGATCACGGGGGTAATAATCGCAGTTATAGCACTGCTGTGTATTTGCAAATTTCTACTCTAATCTAGTCCGACTCTGTACCAGCATAATGGCCTCTAAAATAAGCTTTTGCTTCTGCTTCCTATAGTTAATACATCTCAGCAAAAATCAACTATTAAGTTAAAAGAAGATCCCTCTAATAATCCTAATTACCTTCAAAAATCTAGAACTTTATTAATTCTCAGGGTATTTAGAACAGCCAGATGACTTGACTAAGTTTGTACTGTAATAAAAAGATACTTGATGAAGATTAAGAAAAAAACAGTCTTGTGATTGTCACTAATCTTCATCTCAAAACATATTATTTTACCAGAAGCTACCATAGCCTACCTCCTTGACACATAGCAAACCTTACTCATGTTGATAATTGTTTGCCTGCTATTTACATATTTACTAACTTACAAAATTATCTTGGGGATTTCTCTGAACATATAATCAGGATTGGCATTTAAAACACAAGTTAGTCCTAATGGACTCATTTCATGAAAGAGGGCGTAGCAGAACTATTCGACAGAGTGCAAGAGATGGGCCGAGTCATCAAGTAAGAACAAGATCATCCTCCAGAGACAGCCACCGCAGCGAATATCATACACCTAGGAGCTCTTCCCAAGTTCGAGTCCCGACTGTGTTTCATCGGAAGCGTACTGATTTTTTGACAGTTCCACCAGCACCAAAGGACATATGTCCTACCTTAAGGAAAGGATTTTTGTGTGACAGCAATTTTTGTAAAAAAGACCATCAACTAGAAAGTTTAACAGATAGGGAGCTGCTTTTGCTGATTGCACGGAAAACCTGCGGCTCCCTTGAACAACAATTGAACATCACTGCTCCTAAAGATACACGATTAGCAAATCCAATTGCAGATGATTTCCAACAAAAAGACGGCCCAAAAATTACACTATTGACACTTTTGGAGACTGCGGAGTATTGGTCAAAACAAGATATCAAGGGCATTGATGATTCAAGACTAAGAGCATTACTAACCCTTTGTGCCGTCATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTATTGTGTGAGAGTCATCTACGACGAGAAGGGCTAGGACAGGATCAATCAGAATCTGTTCTTGAAGTGTACCAGCGCTTGCATAGCGACAAAGGCGGAAATTTTGAGGCAGCCCTATGGCAACAATGGGACCGACAGTCCTTGATCATGTTTATAACAGCATTTCTTAATATTGCTTTACAATTACCCTGTGAAAGTTCATCTGTTGTTATTTCAGGATTAAGGCTGCTAGTGCCTCAATCAGAAGATACCGAGACCTCAACCTACACCGAGACACGTGCATGGTCAGAGGAAGGTGGCCCCCATTAACATCTTCCACAGTTGAATCTACCATAACTTCCCTATTCAACGCAGGTAAGAATCAGTACTAAACCACAAGTGCAAAAATTAACAAAACACCAGCATAAGTGAAATCTTGTCTGTGATTAGCAAGACGAATGATCTTCAATCCTGTTGCAATTCGCCAGTGATAATTGTATTCACATTGTGGCCACAATATACTGTTTTTTCCATTGAAAAACAAGGCTGAATCTATTGCGCTACACAAACTTACAGGATTAGCACCACGACGGCTCAATACTATACCTATTGGTCACGGCTCGATGTGTTAATCACTTATATTGTATTCATTTGAAATTATTCATTAGGCAAATATTTTGATTAAGAAAAAATAATTGGAAAACCAGAAAATCCCTAGGTATTTAAATTCCTATCTCCGGAGATCCGAGATAATTAATCAAGCAATGAAGGAACAATGGTGAACAACAACATATTGTTGCCCCCTTTAGATTGGTCAGTTCCAAAAACAAGTGATGAAGATTAATGCAGATGTCCAAGGAACACATATTTGTGATTTAAACGTTCCAGTTAGACTCTGTTCAAGGATCTTCATCTTTTGTAGCTCCACTCTGAGTCACAACATAATTGAGTTTTTGCTCAGAACAGTTATCAGGATTAAATTCTCTCAAATAACTGAAACTACTAGCATCACTCTCAATTTCATTACTTACGACAATCATTATCTTAATAATATTTCCCTAAATTACTGACTTAATCAGCTTGTAATCAGATAATATCGAAACCAATTTATCATAAGGTATAATTTGTATAAGTGATTTAGGATTTACCCCAGAAGTGAAATAATTCTTAGAATAAAAGACCGACTAGAATATCCTTAAGGCTGTCTGACGTGCCACACAGCTAGGGTTAGCCTGACATCTGGAACAAGATCGATACTAATATAGGGATTTGTTTCATACTAACTCTCTGCAAACACAATGGCTAAGGCAACAGGTAGGTACAACTTGGTTTCACCTAAAAAGGACCTCGAGAGGGGGCTAGTTTTGAATGATTTGTGCACGTTTTTAGTTGATCAGACTATCCAGGGGTGGCGGGTGACTTGGGTTGGGATTGAATTTGATATCGCCCAGAAAGGGATGGCTCTACTGCATCGGTTAAAAACTGCTGACTTCGCTCCTGCATGGTCGATGACAAGGAATTTATTTCCTCATTTATTCCAAAATTCAAATTCTACTATTGAGTCTCCCCTCTGGGCATTACGAGTGATTCTGGCAGCTGGTATTCAAGACCAGTTAATTGACCAATCCTTGGTAGAACCGTTGGCCGGAGCCCTGAGTTTAGTCTCCGATTGGCTTCTCACAACAAACACAAACCATTTTCAAATGCGCACGCAGCACGCTAAAGAGCAACTGAGCTTGAAGATGCTATCATTAGTGCGCTCTAATATCCTGAAATTCATCAGTCAATTGGACGCACTACATGTCGTGAACTACAATGGACTCTTGAGCAGTATCGAAATTGGCACTAGAAATCATACCATTATCATCACAAGAACCAACATGGGTTTCCTGGTAGAATTACAGGAGCCTGATAAATCTGCCATGAATCAAAAGAAACCAGGACCAGTCAAGTTCTCCCTCCTGCATGAATCAACCTTCAAGGCTCTAATCAAAAAACCCGCAACTAAGATGCAGGCCTTGATTCTGGAATTTAACAGCTCCCTGGCAATATAGTCCAACGATACCAACCATCATTTTTTGTAACTGCATCTCTTTTATTTCCTTTCTAACTTGATACAATTATAATCAAGATCCCTAATCCCTTTTGACGAAGTGGGCTAATTTTTGCTCATTCTAATAATAAATCATAACCTGAATAAAAGACACCACAATATTATAACCCAATAACACCTAGAGAATTGCTAAATTGCTAAAGATTATATACTCGCACTAAGGGACAAGTTAATCAATCTTTACTTAATAATATACTAAATGCTAGATAGCTCTGGCTAATTAACCTGAGTTGTGGATTACTCCTTTTAAAAGTCTATCAATTTAAGCTTATCACTAATATTAAGGAGGACTTTTTAAATAAGAGCAAGTGTTATGTAGTCTTACTAAGAATGATTTGAGGAAGATTAAGAAAAAGTGCTTGTGGGGTCTTTCCGTTGTGGAGGACACACGAGCAAACTTCTTCCTCTAATTTTAATATGGCAACTCAACATACACAATATCCAGATGCAAGATTATCTTCACCCATTGTCTTAGATCAATGTGATCTTGTCACTCGTGCTTGCGGTCTGTATTCTTCATATTCATTAAATCCTCAGTTGAAAAATTGTAGACTACCAAAACATATTTACCGCCTCAAATTTGATGCTACGGTTACAAAATTTTTAAGCGATGTTCCAATAGTTACATTGCCAATAGATTACTTGACCCCTTTACTTTTACGAACTTTATCCGGGGAGGGCTTATGCCCTGTCGAACCAAAGTGCAGCCAATTCTTAGATGAAATAGTAAGTTATGTTTTGCAGGATGCACGTTTTTTAAGACACTATTTTAGGCATGTTGGAGTACACGATGACAATGTGGGGAAAAATTTTGAGCCAAAGATTAAGGCTTTGATTTATGATAATGAATTTCTGCAACAATTGTTTTATTGGTACGATTTAGCAATCCTAACGCGTAGAGGGCGCCTGAATCGAGGGAATAACCGTTCAACATGGTTTGCAAATGACGATTTAATAGACATTCTCGGGTACGGTGATTATATTTTCTGGAAAATACCGTTGTCATTGTTGTCACTCAACACAGAGGGGATTCCTCATGCAGCTAAGGACTGGTATCACGCATCAATCTTCAAAGAAGCGGTTCAAGGTCACACACATATCGTGTCAGTTTCCACTGCAGATGTTTTAATTATGTGTAAGGACATCATAACCTGTCGTTTCAATACCACACTCATTGCAGCATTGGCAAATTTAGAAGATTCTATCTGTTCTGACTATCCACAACCTGAAACAATCTCTAATCTGTATAAAGCAGGGGATTACTTAATTTCGATATTGGGTTCAGAAGGTTATAAGGTCATAAAGTTTTTAGAACCACTATGTTTAGCTAAGATCCAATTGTGCTCAAATTACACTGAGAGGAAAGGGAGATTCCTTACTCAAATGCATTTGGCCGTTAATCACACACTTGAAGAACTTATTGAGGGCCGGGGATTGAAGTCACAACAAGACTGGAAGATGAGGGAATTTCACCGAATCTTAGTAAATTTAAAGTCAACACCACAACAACTCTGTGAATTGTTTTCAGTGCAAAAGCATTGGGGGCATCCTGTGCTACATAGTGAGAAGGCTATTCAGAAAGTAAAGAAACATGCAACCATAATAAAAGCATTGCGTCCTATAATCATCTTTGAGACATATTGTGTGTTCAAGTACAGCATTGCCAAACATTATTTTGATAGCCAAGGGTCATGGTATAGTGTAATCTCAGATAAACATCTAACACCAGGTTTACATTCTTACATTAAGAGGAACCAATTTCCGCCACTGCCTATGATTAAAGACTTATTGTGGGAATTCTATCACCTTGATCATCCTCCCTTATTTTCCACCAAGATTATTAGTGACTTGAGTATTTTCATTAAGGATCGCGCTACCGCAGTGGAAAAAACATGTTGGGATGCAGTTTTCGAACCTAATGTTCTTGGATATAGTCCTCCAAACAAGTTCTCAACTAAGAGGGTTCCTGAACAGTTTCTTGAACAAGAAAATTTCTCGATTGATAGTGTTCTCACTTATGCCCAGCGCCTGGATTATCTACTTCCACAATACCGGAATTTTTCTTTCTCACTTAAGGAAAAGGAATTAAATGTAGGACGAGCTTTTGGTAAGCTACCTTATCCTACACGTAATGTTCAAACTTTATGTGAAGCCTTATTGGCAGATGGATTAGCTAAAGCCTTTCCTAGTAACATGATGGTTGTAACAGAGCGTGAACAGAAGGAAAGCCTCTTGCACCAGGCGTCGTGGCACCACACAAGTGACGATTTCGGTGAGAATGCCACTGTTAGAGGCAGCAGTTTTGTTACCGACCTAGAAAAATACAACTTGGCATTTAGATATGAGTTTACAGCTCCATTTATTGAATACTGTAATCGATGTTATGGTGTAAAAAATTTATTCAATTGGATGCATTATACGATACCGCAATGTTATATACATGTAAGTGATTATTATAATCCCCCTCATGGAGTTTCGCTAGAAAATCGGGAAGATCCTCCGGAAGGCCCTAGCTCTTACCGGGGTCATCTTGGGGGAATTGAGGGACTCCAACAGAAACTCTGGACCAGCATTTCATGTGCGCAAATCTCATTAGTTGAGATCAAGACTGGTTTCAAGTTGAGATCTGCGGTAATGGGTGATAATCAATGCATCACAGTTCTTTCCGTATTCCCTCTAGAGACAGATTCCAATGAGCAAGAGCATAGCTCCGAGGACAATGCTGCTCGCGTAGCAGCCAGTTTAGCCAAAGTCACGAGTGCCTGTGGCATCTTCCTAAAACCAGATGAGACTTTTGTGCATTCAGGCTTTATTTATTTCGGTAAGAAGCAATATTTAAATGGCGTTCAATTGCCACAATCACTCAAGACTGCTACCAGGATTGCTCCCTTGTCAGATGCAATCTTTGATGACCTTCAGGGAACTCTGGCTAGTATAGGAACGGCATTTGAGAGATCTATATCCGAGACTAGACATGTATACCCTTGCCGGGTGGTTGCCGCATTCCATACATTCTTCTCCGTTAGGATCCTCCAATACCACCACCTTGGTTTCAACAAAGGAACTGATCTAGGTCAACTATCACTAAGCAAACCGTTGGATTTCGGAACTATCACTCTTGCTTTAGCGGTACCTCAAGTTCTAGGAGGTTTATCGTTTTTGAACCCAGAAAAATGTTTTTATCGCAACCTTGGAGACCCCGTGACCTCTGGCCTATTCCAACTTAGGACTTACCTGCAAATGATCAACATGGACGACTTATTTCTACCTTTAATTGCCAAGAACCCCGGGAACTGTAGTGCAATTGACTTTGTACTCAACCCAAGCGGATTGAATGTCCCTGGGTCACAAGACCTAACATCTTTTTTACGTCAGATAGTGCGTAGAACAATCACATTGAGTGCAAAAAATAAGCTAATAAACACATTGTTTCACTCCTCAGCCGATTTAGAAGATGAGATGGTATGTAAATGGCTACTTTCTTCAACACCTGTAATGAGTCGGTTTGCTGCTGATATATTCTCTCGTACTCCGAGTGGGAAGCGCCTGCAGATCCTAGGTTATTTAGAAGGGACTAGAACCTTGCTAGCCTCCAAAGTCATCAATAACAATGCAGAGACTCCTATTTTAGATAGGTTGAGGAAAATCACACTGCAGAGATGGAGTTTATGGTTTAGCTACCTAGACCACTGTGATCAGGTTCTAGCAGATGCTTTAATAAAAGTTTCTTGTACAGTTGATTTGGCGCAAATTTTACGTGAATATACCTGGGCACACATACTAGAGGGAAGACAGCTCATTGGTGCAACACTTCCTTGCATGTTAGAACAATTTAATGTGTTTTGGCTCAAATCGTACGAACAATGCCCTAAATGTGCAAGATCTAGAAATCCAAAAGGAGAGCCATTTGTGTCAATTGCAATTAAGAAACAAGTTGTGAGTGCATGGCCGAATCAGTCACGGTTAAATTGGACCATTGGGGACGGTGTACCTTACATCGGGTCTCGAACAGAGGACAAGATTGGGCAGCCAGCAATCAAGCCTAAGTGTCCCTCTGCTGCCTTACGTGAAGCAATAGAGTTGACATCTAGACTAACATGGGTTACCCAAGGTGGTGCCAATAGTGATTTGCTAGTCAAACCTTTTGTAGAAGCACGAGTAAACCTGAGTGTGCAGGAGATCCTTCAAATGACGCCTTCTCATTATTCAGGGAACATCGTACATCGGTATAATGACCAATACAGCCCTCATTCTTTCATGGCAAATAGAATGAGTAATTCCGCGACGAGATTGGTGGTGTCGACAAATACTCTCGGGGAGTTCTCAGGTGGGGGGCAATCAGCAAGGGACAGCAATATCATCTTTCAAAATGTAATCAATTTTGCGGTTGCCCTATTTGATTTACGATTTCGGAACACCGAAACATCCTCCATTCAGCATAACCGTGCCCATCTCCATCTTTCACAGTGTTGCACACGGGAAGTCCCAGCTCAATACCTAACCTACACGTCTACGCTTTCCTTGGATCTCACAAGGTACCGAGAGAATGAGTTAATTTATGATAACAATCCATTAAAAGGTGGACTTAATTGCAACCTATCCTTTGATAATCCACTTTTCAAGGGCCAAAGGCTCAATATCATAGAGGAGGATTTGATTAGATTTCCACATTTATCTGGGTGGGAACTTGCGAAAACCATCATTCAGTCCATTATCTCAGACAGCAATAACTCATCCACAGACCCCATTAGCAGTGGAGAAACACGATCATTCACAACTCACTTTCTCACATATCCTAAGGTTGGGCTCCTCTATAGTTTCGGCGCCATCGTGAGTTATTACTTAGGGAATACCATTATTAGGACCAAAAAGCTAGACCTCAGTCATTTCATGTATTACTTAACAACTCAAATCCATAATTTGCCACATCGCTCGTTGAGGATACTTAAGCCCACTTTTAAACATGTTAGTGTGATATCAAGACTAATGAGTATTGATCCTCATTTTTCAATCTACATCGGGGGTACAGCAGGTGATCGAGGGCTTTCGGATGCTACCAGACTATTCCTTCGAGTGGCCATTTCTTCCTTCCTTCAATTTGTCAAAAAGTGGATCGTGGAATACAGGACAGCTATTCCTCTGTGGGTTGTATACCCTTTGGAGGGACAAAATCCAGATCCAATTAATAGCTTTCTACATCAGATTATAGCCTTACTGCAAAATGAATCCCCTCAAAACAACATCCAATTCCAAGAAGGCAGAAATAATCAACAGTTGTCCGATAATCTAGTTTACATGTGCAAGAGCACTGCCAGTAATTTCTTCCATGCATCACTTGCCTATTGGAGGAGCCGGCACAAAGGACGGCCCAAAAATCGATCGACCGAAGAACAGACAGTTAAACCCAGACCATATAATAATTTTCATTCTGTTAAATGTGCCTCAAACCCACCAAGCATCCCCAAATCTAAGTCAGGAACTCAAGGCTCAAGCGCATTTTTTGAGAAACTTGAATATGATAAAGAAATAGAATTGCCAACAGCTTCCACACCAGCCGAAAAACCCAAGACCTATACCAAGGCCCTATCCAGCCGAATTTACCATGGTAAAACACCATCCAATGCCGCAAAAGATGATTCAACAACCTCCAAGGGCTGCGATTCCAAAGAAGAAAATGCCGTTCAAGCTTCACACCGAATTGTCCTACCATTTTTTACATTGTCACAGAACGGCTACAGAACTCCCTCAGTTAAAAAGTCAGAGTATGTAACTGAAATCACCAAACTAATTCGACAATTAAAGGCAATTCCAGATACCACTGTATACTGTCGCTTTACAGGGGTTGTGTCTTCAATGCATTATAAGCTTGATGAGGTTCTCTGGGAATTCGATAGTTTCAAAACTGCTGTGACTCTAGCTGAAGGAGAAGGGTCAGGTGCCTTATTACTACTACAAAAATATAAGGTTAGAACAATCTTTTTTAACACTTTAGCTACAGAGCATAGCATCGAGGCAGAAATAGTTTCTGGGACAACCACACCTCGAATGCTCCTTCCTGTAATGGCCAAACTTCATGATGATCAAATAAATGTAATATTAAACAATTCTGCTAGCCAGGTTACTGATATCACTAACCCTGCATGGTTCACTGACCAGAAATCTAGAATCCCCACACAAGTTGAGATTATGACTATGGATGCTGAAACGACAGAAAATATTAATCGGTCAAAATTATACGAAGCTATCCAGCAATTAATTGTTTCACACATTGATACAAGGGTGCTAAAGATTGTTATTATAAAGGTTTTTTTAAGTGATATTGATGGTCTACTGTGGCTTAATGACCATCTTGCCCCTTTATTCGGATCCGGCTATTTAATTAAGCCGATTACTTCGAGTCCAAAGTCAAGCGAATGGTACTTATGTCTTTCAAATTTCCTTTCAGCTTCTCGACGACGGCCTCATCAGGGTCATGCTACCTGTATGCAAGTCATCCAAACAGCGCTACGACTCCAAGTTCAAAGGAGTTCATACTGGCTTAGCCATTTAGTGCAATATGCTGATATTAATTTGCACTTGAGTTATGTTAATTTGGGTTTCCCTTCATTGGAAAAGGTTCTTTACCATCGATATAACCTAGTTGATTCACGGAAGGGTCCACTGGTCTCGATCCTTTACCATTTAACACACTTGCAAGCAGAAATTAGAGAATTGGTGTGTGACTATAATCAGCAACGACAAAGTCGAACCCAAACATACCACTTCATCAAAACGACAAAGGGCCGGATTACAAAATTAGTCAATGACTACCTTAAATTTTATCTCGTAGTGCAAGCACTGAAGCATAATTGTCTTTGGCAGGAAGAACTCAGAACACTTCCTGACTTAATCAATGTTTGCAATCGATTTTACCATATAAGGGACTGCTCATGTGAAGATCGATTTTTAATTCAAACTCTTTACTTAACCCGTATGCAAGACTCAGAAGTAAAATTAATGGAGAGATTAACCGGGTTTCTAGGATTGTATCCTAATGGTATTAACACTTAAGATCCCCTTAGAGGCATCGCAATATGACTCCAAACATTAAATGATATTGCTGTCAATATATCTACCTGACCGAGAGTAAGGTTTATTATAAAAAATCTATACACATGACTGCAATGCGTGATTTATACCGAAACACAGTGAGGGCTGCACATGCAGGTTCCTGTTGAGCTTAAAAAGATCATGCAATACAAAATGATATTTGTATACTAATCATGTTAATACTAACTAACAGTACTCACTGCATATACCATATCAATTAAGAAAAATTACTGTGGTTTATGCATTTAAATGACATCACGGATGGATATAATATAGTTAATTCTTACCTAAATGTTGAGTTATAGTAATTTGAAGTTGTAATTATGATTAGTGCTTATACTATAAATAATAGCTATACCAAGTATACACAAGAAGTTATGATTTTGTATTTAAGTTATATTCACAGGAACTTGTGATTAATAACAAAAGTCTCAGTTGTTGGTTGTTGAGTTGCAAAACCCCCGTTAAAAATTTATTTTCCACTTATAACTAATAATAATCATAGATCAGTATGAGTTGAGGCTATTTAGACCTTAGAAAAATTGTGCGATGTTTTTTACCATATCAATCTTGATTTCAATGATATTGGAGGGCTTGTCGATAAATTTAGTAATTAACATTAAGTCAGTGTGGAACCTCATTGGATATTTGATCGTACACAAAAATATCTTTACAAAATTGTTTTCTCTTTTTTGTGTGTCC\n>Cote_dIvoire_ebolavirus_complete_genome\nCGGACACACAAAAAGAAAGAAGGTTTTTTGATCTTTATTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGACACTTACATTAAGATTAAGATTCTCATTGATCTGTTACTTACTCTGAGGATAATAATTGGTGTTCAGAAGTACCCCATTCCCCAGTGGGGGCAAAGACAGTCCAAAAGACTCAACTTGTCCTATTCAACTAATCTGTTTTGTCTCAGTAGTTCACATATTGATCATACCCAGGAGTTGGACCTAATTCCAAAGCTTAGAGTGGGACCTAGTGTATCCTCGGGGCTGTAATATAATCAGCCATTTAACACATAACAAGCCCTACTGTTTTCTTGTTTTGCCGTGCATTTAGAATAAGAGACAACTTAAACCTCCGATTCGGCAACACAGGGAATAATCTCACCAGACCCGGCAGTGTCTTCAGGCTTCATAGCCCCAAGATGGAGAGTCGGGCCCACAAAGCATGGATGACGCACACCGCATCAGGTTTCGAAACAGATTACCATAAGATTTTAACAGCAGGATTGTCAGTCCAACAAGGCATTGTGAGACAACGGGTCATTCAAGTCCACCAGGTTACAAACCTAGAAGAAATATGCCAATTGATCATTCAAGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCAGACAGTTTCTTGCTGATGCTATGTTTACATCATGCTTATCAGGGTGACTACAAGCAATTCTTGGAAAGCAATGCAGTCAAGTACCTTGAGGGTCATGGCTTTCGCTTTGAGGTCAGGAAAAAGGAAGGAGTCAAGCGACTCGAAGAATTGCTTCCTGCTGCATCCAGTGGCAAGAGCATCAGGAGAACACTGGCTGCAATGCCTGAAGAGGAGACAACAGAAGCAAATGCCGGACAGTTCCTCTCTTTTGCTAGCTTATTTCTTCCTAAGCTAGTTGTCGGAGAAAAAGCCTGTCTAGAAAAGGTGCAGCGGCAAATTCAAGTTCATTCTGAGCAGGGATTGATCCAATACCCCACAGCCTGGCAGTCAGTTGGACACATGATGGTCATTTTCAGACTGATGAGAACAAATTTTCTAATTAAGTTCCTCCTTATACATCAAGGGATGCATATGGTAGCAGGACACGATGCTAACGATGCTGTCATCGCAAACTCTGTAGCTCAAGCACGTTTTTCAGGATTATTGATCGTTAAAACAGTGCTAGATCACATCCTTCAGAAAACAGAGCACGGAGTGCGTCTTCATCCTTTGGCAAGAACTGCTAAGGTCAAGAACGAAGTAAATTCCTTTAAGGCTGCCCTTAGCTCGCTAGCACAACATGGAGAGTATGCTCCTTTTGCTCGCTTGCTGAATCTTTCTGGAGTCAACAATCTCGAGCACGGACTGTTTCCTCAGCTTTCTGCAATTGCCCTAGGTGTCGCAACGGCACACGGCAGTACCCTGGCAGGAGTAAATGTGGGGGAACAGTATCAGCAACTACGAGAAGCAGCCACTGAGGCAGAAAAACAATTGCAGAAATACGCTGAATCTCGCGAGCTTGACCATCTAGGTCTCGATGATCAAGAGAAGAAGATCTTGAAAGACTTCCATCAGAAGAAAAATGAAATCAGCTTCCAGCAGACAACAGCCATGGTCACACTACGGAAGGAAAGGCTAGCCAAGCTCACTGAGGCAATCACCTCCACATCCCTTCTCAAGACAGGAAAACAGTATGATGATGACAACGATATCCCCTTTCCTGGGCCCATCAATGATAACGAAAACTCAGAACAGCAAGACGATGATCCAACAGATTCTCAGGACACTACCATCCCTGATATCATTGTTGACCCGGATGATGGCAGATACAACAATTATGGAGACTATCCTAGTGAGACGGCGAATGCCCCTGAAGACCTTGTTCTTTTTGACCTTGAAGATGGTGACGAGGATGATCACCGACCGTCAAGTTCATCAGAGAACAACAACAAACACAGTCTTACAGGAACTGACAGTAACAAAACAAGTAACTGGAATCGAAACCCGACTAATATGCCAAAGAAAGACTCCACACAAAACAATGACAATCCTGCACAGCGGGCTCAAGAATACGCCAGGGATAACATCCAGGATACACCAACACCCCATCGAGCTCTAACTCCCATCAGCGAAGAAACCGGCTCCAATGGTCACAATGAAGATGACATTGATAGCATCCCTCCTTTGGAATCAGACGAAGAAAACAACACTGAGACAACCATTACCACCACAAAAAATACCACTGCTCCACCAGCACCTGTTTATCGGAGTAATTCAGAAAAGGAGCCCCTCCCGCAAGAAAAATCCCAGAAGCAACCAAACCAAGTGAGTGGTAGTGAGAATACCGACAATAAACCTCACTCAGAGCAATCAGTGGAAGAAATGTATCGACACATCCTCCAAACACAAGGACCATTTGATGCCATCCTATACTATTACATGATGACGGAGGAGCCGATTGTCTTTAGCACTAGTGATGGGAAAGAATACGTATACCCTGATTCTCTTGAAGGGGAGCATCCACCGTGGCTCAGTGAAAAAGAGGCCTTGAATGAGGACAATAGGTTTATCACAATGGATGATCAACAATTCTACTGGCCTGTAATGAATCACAGGAACAAATTCATGGCTATCCTTCAGCACCACAAGTAATTTCTTCATAATGACAGATCATTGTAAGGTTATTACCACCATCCCTGCAACAAAGCATGAAAACCACACTCAACAACGCCCTACCACAGGATACCTTGGAGACCATACACCAAGATCAGCAGCTGTGCAACCACCCCCATGCGAATCCACCACCACAACCACCAAACAATAATCCCAAGACCAAACCGCACACATCCAGATCAACCCAAACCCTCAAACACCACCCCACTCCGCGATCCCAGACCAAACTCCGCCCCAGACAAGCACCCCACCCATCCCAGAAACCGCACGGCCGAGAATCGATCCCCAGCATTCAAAATGCGTTATTAAGAAAAAACATATGATGAAGATTAAAACCTTCATCAACATTGCACAGACTTTGATCCTTAGGAGTTTATTCTAGCTATCTACAAAACGGGTCCAAAACGGAATGATTTCCACTAGGGCTGCAGCAATCAATGATCCTTCATTACCAATCAGAAACCAGTGTACACGTGGCCCTGAACTATCAGGATGGATCTCCGAACAATTAATGACAGGCAAAATTCCGGTACATGAAATCTTCAACGACACTGAGCCCCACATAAGCTCAGGGTCCGACTGCCTTCCCAGACCCAAAAACACGGCCCCCCGGACTCGCAACACCCAGACACAGACCGATCCGGTTTGCAATCACAATTTTGAAGACGTTACACAAGCACTAACATCATTAACCAATGTCATACAAAAACAGGCTCTTAACTTAGAGTCTCTCGAACAACGCATCATAGATCTAGAGAATGGCTTAAAGCCAATGTATGACATGGCTAAAGTCATTTCTGCATTGAATAGATCTTGTGCTGAGATGGTAGCAAAATATGATCTCCTGGTGATGACAACTGGCCGCGCAACCGCCACCGCCGCTGCAACTGAGGCTTATTGGGAGGAACATGGACAACCACCACCTGGACCATCACTTTATGAAGAGAGTGCGATTAGAGGCAAGATTAACAAGCAAGAGGATAAAGTACCTAAGGAAGTTCAAGAAGCTTTTCGTAATCTGGACAGTACCAGCTCACTAACAGAAGAGAACTTTGGCAAGCCAGATATATCTGCAAAGGACCTACGAGACATCATGTATGACCACCTACCAGGCTTCGGTACGGCTTTTCACCAACTGGTCCAGGTAATTTGCAAGCTAGGAAAAGACAATTCTGCATTGGACATTATTCATGCTGAGTTCCAAGCCAGCCTTGCTGAAGGTGATTCTCCCCAATGTGCCCTGATCCAAATAACAAAACGGATCCCCATCTTCCAGGATGCCACTCCGCCCACAATTCACATCCGCTCTCGTGGTGACATCCCACGTGCCTGCCAAAAAAGTCTCCGTCCAGTTCCTCCATCACCAAAAATAGACAGAGGTTGGGTTTGCATTTTCCAATTGCAGGACGGGAAGACACTTGGGCTCAAGATATAGGGTCCCCCAGTCAAAGACACGTGCGGTCCCATCCTCCCTCACCTTCAGACATCAACGCATGGCAGTCCCAAACACCGGTGAGGGAGGCGCCCGGCGACAACACATGATGATAGGCTGATCTTCGGGATAAGAGACATGAAAAACCAAAAAGCCGTTTACATCCAGATCCAAGATCAAGAGTGGCTTGGAAATAAGGGGCACTTGTTCTTTGTCTCAAAGGACTTACAAAAACAAGGGTGATGAAGATTAAGAAAAAGCCTCCTTCAGTTGCAAGGAGCTAATTCTTAAAACTTCATCTAGACTAAGGATAAATCGATTCCAATCACGATGAGGAGAATCATCCTACCCACGGCACCACCTGAATACATGGAGGCTGTTTACCCAATGAGAACAATGAATTCTGGTGCAGACAACACTGCCAGTGGCCCTAATTACACAACAACTGGTGTGATGACAAATGATACTCCCTCTAATTCACTCCGACCAGTTGCAGATGATAATATTGATCATCCGAGCCACACGCCTAACAGTGTTGCCTCTGCATTTATATTGGAAGCTATGGTGAATGTAATATCTGGCCCGAAAGTGCTGATGAAGCAAATCCCAATCTGGCTTCCTCTGGGTGTCTCTGACCAGAAGACATATAGCTTTGATTCAACCACTGCTGCCATTATGCTAGCATCATATACCATCACTCATTTTGGCAAAACCTCAAATCCCCTTGTGAGAATCAACCGACTTGGTCCTGGCATACCTGATCACCCACTACGACTCCTAAGAATAGGAAATCAAGCCTTCCTACAAGAGTTTGTGCTACCTCCTGTACAACTGCCACAATACTTCACTTTTGATCTGACAGCGCTGAAGCTGATCACCCAGCCACTCCCAGCGGCAACCTGGACAGATGAAACTCCAGCTGTGTCAACTGGCACGCTCCGCCCAGGGATCTCATTCCATCCCAAATTAAGGCCTATCCTGCTACCAGGAAGAGCTGGAAAGAAGGGCTCCAACTCCGATCTAACATCTCCTGACAAAATCCAGGCTATAATGAATTTCCTACAAGACCTCAAAATTGTACCAATCGATCCAACCAAGAATATCATGGGTATTGAAGTGCCAGAACTCCTGGTTCACAGGCTGACTGGGAAGAAGACAACTACCAAGAATGGTCAACCAATCATTCCAATTCTGCTACCAAAGTACATTGGTCTTGATCCTCTATCTCAAGGTGATCTCACAATGGTGATCACTCAGGACTGTGATTCCTGCCACTCCCCGGCCAGTCTTCCCCCAGTCAATGAAAAATGACCATGAGACTCAACATCACACTGCCAGAGCACCTCACCGCAAGTCTATACAACAATCAACCCCGGCATCTACAACCTGCAAAAACCAGCCCATCTGATACTCCTGGCATCGGGGGCAAGACAAGGCAGCCAAGCAGCAGCCCCCGAGCCGAGCCCAAACCCATTACACCCGAGCCCAACACCCATCCAGCAACCCACAACCGTCAAACGCACAGATGGACAAGCAAAGAACATCAAGCCAGGAGCAACACAGACCCCAAGTCTAAGCTGATCAACCCCTCCCGCAATCCCACCAACGCCAGCAAAAATCCCCCAACTCGATACCAACCCCAAGCAAATCAGCTCAAACCGTCTATCTCTCCCCGCTTCACTCCACACCCCAGATTCAGCAAACGATCAACGCACTTCTTATGCCACAGCTTATATTAAGAAAAAGAACTTGATGAAGATTAAGGCAACCAGTGGTGCTATCTTCATCTCTTTGATTTGAGTCTTAAGTGAATACACAGGTTCTAATACTGTTCTTCTGTCCAACGGTATAATTCAGCCAGGCCTAAGACAGTAGCTAATCACAGTCATCATGGGAGCGTCAGGGATTCTGCAATTGCCCCGTGAGCGCTTCAGGAAAACATCTTTCTTTGTTTGGGTAATAATCCTATTCCATAAAGTCTTTTCAATCCCGTTGGGGGTTGTACACAACAATACCCTACAAGTGAGTGATATTGACAAGTTTGTGTGCCGAGACAAACTCTCTTCAACTAGCCAATTGAAGTCAGTCGGGTTGAACTTGGAGGGCAATGGAGTAGCAACTGATGTACCAACGGCAACCAAAAGATGGGGTTTTCGAGCTGGTGTTCCACCAAAGGTGGTAAATTGCGAAGCTGGAGAATGGGCTGAGAACTGTTATAACCTGGCTATAAAGAAAGTTGATGGTAGTGAGTGCCTACCAGAAGCCCCTGAGGGAGTGAGGGATTTTCCCCGTTGCCGCTATGTACACAAAGTCTCAGGAACTGGACCATGCCCAGGAGGACTCGCCTTTCACAAAGAAGGAGCCTTCTTCCTGTATGACCGACTCGCATCAACAATCATTTATCGGGGTACAACCTTTGCCGAAGGAGTTATTGCATTTCTGATCTTGCCTAAGGCGCGAAAGGATTTTTTCCAGTCTCCTCCATTGCATGAGCCTGCCAACATGACCACGGATCCCTCCAGTTACTATCACACGACAACAATAAACTACGTGGTTGATAATTTTGGAACCAACACCACAGAGTTTCTGTTCCAAGTCGATCATTTGACGTATGTGCAGCTCGAGGCAAGATTCACACCACAATTCCTTGTCCTCCTAAATGAAACCATCTACTCTGATAACCGCAGAAGTAACACAACAGGAAAACTAATCTGGAAAATAAATCCCACTGTTGATACCAGCATGGGTGAGTGGGCTTTCTGGGAAAATAAAAAAACTTCACAAAAACCCTTTCAAGTGAAGAGTTGTCTTTCGTACCTGTACCAGAAACCCAGAACCAGGTCCTTGACACGACAGCGACGGTCTCTCCTCCCATCTCCGCCCACAACCACGCAGCCGAAGACCACAAAGAATTGGTTTCAGAGGATTCCACTCCAGTGGTTCAGATGCAAAACATCAAGGGAAAGGACACAATGCCAACCACAGTGACGGGTGTACCAACAACCACACCCTCTCCATTTCCAATCAATGCTCGCAACACTGATCATACCAAATCATTTATCGGCCTGGAGGGGCCCCAAGAAGACCACAGCACCACACAGCCTGCCAAGACCACCAGCCAACCAACCAACAGCACAGAATCGACGACACTAAACCCAACATCAGAGCCCTCCAGTAGAGGCACGGGACCATCCAGCCCCACGGTCCCCAACACCACAGAAAGCCACGCCGAACTTGGCAAGACAACCCCAACCACACTCCCAGAACAGCACACTGCCGCCAGTGCCATTCCAAGAGCCGTGCACCCCGACGAACTCAGTGGACCTGGCTTCCTGACGAACACAATACGGGGGGTTACAAATCTCCTGACAGGATCCAGAAGAAAGCGAAGGGATGTCACTCCCAATACACAACCCAAATGCAACCCAAACCTGCACTATTGGACAGCCTTGGATGAGGGTGCTGCCATAGGTTTAGCCTGGATACCATACTTCGGGCCAGCAGCTGAGGGAATTTACACTGAAGGCATAATGGAGAATCAAAATGGATTGATCTGTGGATTGAGGCAGCTGGCCAACGAAACGACACAAGCTCTTCAATTGTTCTTAAGGGCAACTACTGAGTTGCGTACATTCTCTATACTAAATCGGAAAGCAATAGACTTCTTGCTCCAAAGATGGGGAGGAACATGTCACATTCTAGGGCCTGATTGTTGCATTGAACCCCAAGATTGGACCAAAAATATCACTGATAAAATTGATCAAATAATCCATGACTTTGTCGATAATAATCTTCCAAATCAGAATGATGGCAGCAACTGGTGGACTGGATGGAAACAATGGGTTCCTGCTGGAATAGGAATCACAGGAGTAATCATTGCTATTATTGCTTTGCTGTGCATTTGCAAATTCATGCTTTGAACTAATATAGCATCATACTTTCTAATATTCCCCCAATATGAATTTTTGTTTTCGATTTTATTTAATGATATATCCTCTGTATACCTCACTAATGTACTCGAGCATAATTTCCCTGATAGACTTGATTGTATTTGATGATTAAGGACCTCACAAAATTCCTGGGGATTGAAAAGAACTGGATAACTCAATAAATTTTATGCTAGGACCACAAATACACTTGATGAAGATTAAGAAAAAGATAATCTTATGATTATCATTGATCTTCATCTATACCTTAAATACTCTATTCAAGGAGAGTATGACAAAACCAAGTAGTATTGGATAAACTTGTCCTGCATTCAAATCTGAAGACATACGGCTTATCTATTCACTATTGTATTAGAAAATCTAGGGAATATCATTTGAAACTAATTAGTGACTAAAACACACAACTCAAGTCGGCCAGAATGGAAGTTGTTCATGAAAGAGGTCGCTCCAGGATCTCCCGACAAAACACAAGGGATGGACCTAGTCATTTAGTACGGGCGAGATCATCCTCTCGAGCTAGTTATCGAAGTGAATACCATACACCAAGGAGTGCCTCGCAGATCCGTGTCCCCACTGTCTTTCATCGGAAAAAGACAGATTTATTGACAGTTCCACCAGCACCTAAAGATGTATGCCCGACTTTAAAGAAAGGGTTTCTATGTGACAGCAATTTCTGTAAAAAGGATCACCAACTTGAAAGCTTAACAGATAGAGAGTTACTCTTGCTGATTGCACGCAAGACATGTGGATCCACGGAACAACAACTAAGCATAGTTGCTCCAAAAGATTCACGTCTGGCTAATCCTATTGCTGAGGATTTCCAACAAAAAGATGGGCCTAAGGTAACACTGTCGATGCTTATAGAGACAGCAGAGTATTGGTCCAAACAGGACATTAAGAACATCGATGATTCAAGATTAAGAGCTTTATTGACCCTTTGTGCTGTTATGACGCGCAAATTTTCAAAATCTCAACTTAGCTTGCTATGTGAAAGCCACTTACGGCGAGAAGGACTTGGTCAAGACCAATCAGAGTCAGTTCTGGAGGTATATCAACGCTTACACAGCGATAAAGGTGGGAATTTCGAGGCAGCACTATGGCAGCAGTGGGATCGGCAATCATTGATAATGTTCATAACAGCATTTTTAAATATTGCATTACAATTACCATGTGAGAGTTCATCTGTTGTTATTTCAGGTTTGAGAATGCTGATACCCCAGTCGGAAGCCACTGAGGTTGTAACCCCCTCCGAAACCTGCACATGGTCAGAAGGAGGAAGTTCCCATTGAAGCCCCAAATCACAAGGCGAGCTAAAAAATCCCTTTTGAACATGCATAACATCACATACAATTTCAAAGGCATTGGAATAAATGGTGATTTCAGGAAGATTAGTGTTTGCCCTCAAAATCAGATCCGAGCAATAATCATCTACTCTACAGCCAGTTAATTTCTAATATAAAGGTTAAAAAAATGCTGCAGGCCAGCTATTGTTCCACAGGTCCCAATTCTTCTTGTTAAATTGTAGGAGCTAGCACAAGTGATGCAATTAAATGATACTAGTATATACAATGCCACCAACTTAATTCTAAGATTTTGTATATCTCGGAAATTCAAAATTAAATGCTACGTTATTGATTCAATTAAGAAAAAGACAATGGACCATCAAAATTAGTTCAATACCTGAACTAATGCACTTATAGAAACAGGAGAACCAGCCAGACAGCAGACAAATAACAATGAACCACAATATGTTACTGCTATAATGAAGTTCGTTAATTCAAAAACAAATGATGAAGATTAATGCAGATGTCTAAAGGATAAACACTCCATGCATCAGTGTTATAATTGGGCTCTGTAGAAAATCTTCATCTCCTCCAACCTACCTCAAAGAAGGATTTTACCGCGATTGGGAGTTATAACGACAATAGGGACAACCACCTTTGACACTAGCCAAGCTTGTCGTGGGCACACAGCATTTTATCTTGCAACGTCGACATTCCCATCAATCTGAGGAGTAACAGCTATCAAAACAACGCATATGTAGACATTGTCGGTAATAGTACTGCCTAAGACAACTATTTATAATAACAGTTGGAATTCATTTTTTCACCCAAGCTATTCTCAAGTTAACAGTTGAAACAGGACTCGACCCAGGACAACTCCGGATACGTAACATAAGAAAAGAACAACCCTTGACCCAGAGTGAACAAGCTCATACTATCAAGGCTAATCCTCGGGCCTGCCTGGAGTCCACAATGGCCAAGGCTACTGGGAGGTACAACCTTATCTCCCCAAAGAAAGATCTTGAAAAAGGGCTGGTTCTGAATGACCTTTGCACTCTCTCAGTGGCCCAGACGGTCCAGGGATGGAAGGTTACCTGGGCTGGGATTGAATTTGATGTTACACAGAAAGGGATGGCCTTATTGCACAGGCTCAAGACCAGTGATTTTGCTCCAGCCTGGTCAATGACCAGGAACTTATTTCCACATCTCTTTCAAAACCCGAACTCTACAATTGAGTCGCCACTTTGGGCACTGCGGGTCATACTAGCAGCAGGTATTCAAGATCAGCTAATTGATCAATCGTTGATCGAACCCTTGGCAGGAGCGCTAGGCTTAATTGCTGATTGGCTTCTTACTACTGGAACAAACCACTTTCAAATGCGCACACAACAGGCTAAGGAGCAACTAAGTCTAAAAATGTTGTCCCTGGTGCGATCAAACATCCTAAAGTTCATCAACCAACTAGATGCACTACATGTTGTGAATTACAATGGACTTCTCAGTAGCATTGAAATTGGCACCAAAAGCCATACAATTATAATTACCCGGACAAATATGGGTTTTTTGGTAGAGTTGCAAGAGCCTGACAAATCAGCCATGAACACCAGAAAACCAGGACCAGTCAAATTCTCCCTCCTCCATGAATCAACCTTGAAGACACTTGCTAAAAAACCTGCGACCCAGATGCAAGCACTAATCTTAGAATTCAATAGTTCTCTCGCTATTTAACTCAACTCATCAAAATGCTAACTTGTGATCCTTAAGCTGCACCTTAGACTTTTGATAAGAATACTAACTATTGATGATTGTCTTTGACATGAGGATAAGAACACTGCCCATTAGATAGATGGGGTTCACCATTAATACACAATTACCCAATCATGTTAACAGCAGTTAGATCCCTCAAGTATATCAAGTTCATTCTACCCTTTGCATTGTCACTCTAATTAAATCACCTGATACAATTATGTTAATTAGCTAGATTCTCTCATTTTTAGACTTGTTTGCTAGAATAATTGATCATCCACTTGATTACACATCCAACTAGGGTCTAGTTCATAGATTGCTAATAATCTTTAGTTCAATACTAATGACAAAGAGATTAGATTAGCTATAGCTTGAGGAAGATTAAGAAAAAGTGTCTGTGGGGTCTTTCCGTGTAGAAGGGCACACAGCCATAATTCTTCCTCTTTATACAACATGGCTACACAACATACGCAATATCCAGACGCAAGGTTATCATCACCTATAGTTTTAGATCAGTGTGATCTTGTCACTCGTGCTTGTGGATTGTATTCCGCATACTCCTTAAATCCCCAACTAAAGAACTGTAGACTACCGAAACATATATACCGACTAAAATATGACACCACTGTTACAGAGTTTTTGAGTGATGTGCCGGTAGCAACATTGCCAGCGGATTTTTTAGTACCTACATTTCTTAGGACTCTATCAGGAAATGGTTCTTGTCCAATTGATCCAAAATGCAGTCAATTTTTAGAAGAAATTGTCAATTATACTCTACAAGATATTCGCTTCCTAAACTATTACCTCAATCGAGCCGGAGTGCATAACGATCATGTGGATAGGGATTTTGGACAAAAAATTCGCAATCTAATTTGCGACAATGAGGTTTTACATCAAATGTTTCACTGGTATGATCTTGCAATTCTAGCACGTAGAGGGCGACTAAATAGAGGGAATAATCGCTCAACATGGTTTGCAAGTGATAATTTGGTAGATATCCTAGGTTATGGAGATTATATTTTTTGGAAAATACCATTATCACTACTACCAGTGGATACACAAGGCCTCCCACATGCAGCCAAGGACTGGTATCATGAATCGGTTTTCAAGGAGGCTATTCAAGGCCATACACACATCGTGTCCATCTCTACAGCAGATGTCTTAATCATGTGTAAGGACATAATCACCTGTCGATTTAATACTTTACTGATTGCTGCTGTGGCAAATCTAGAGGATTCAGTTCATTCAGATTACCCTTTACCAGAAACAGTGTCTGACCTATACAAAGCAGGAGATTATTTAATCTCATTGCTAGGATCAGAAGGTTACAAAGTCATAAAATTCCTTGAGCCGTTATGCTTAGCAAAGATCCAACTCTGCTCAAATTACACTGAGAGGAAAGGAAGATTCCTCACTCAAATGCATTTAGCTGTAAATCATACACTTGAGGAACTTACAGGGTCCCGAGAATTAAGGCCACAACAGATTCGGAAGGTAAGGGAATTCCATCAAATGCTGATAAACCTTAAGGCAACTCCTCAACAACTCTGTGAGTTGTTTTCAGTGCAAAAGCATTGGGGGCACCCTGTCTTGCATAGCGAAAAGGCTATCCAAAAAGTAAAGAAGCATGCAACAGTGATAAAAGCATTGCGCCCAATAATAATCTTTGAAACATATTGTGTGTTTAAATACAGCATTGCAAAACATTATTTTGATAGTCAGGGTACGTGGTACAGTGTGACTTCTGACAGATGCTTAACACCAGGCCTTTCCTCTTACATCAAAAGAAACCAATTTCCTCCACTACCTATGATCAAAGAACTTTTGTGGGAATTTTATCACTTAGATCATCCTCCGTTATTCTCCACCAAAGTGATTAGTGATTTGAGTATCTTTATTAAAGATCGTGCTACTGCAGTCGAGAAAACATGCTGGGACGCAGTTTTTGAACCCAATGTTCTTGGTTATAACCCACCGAATAAATTTGCTACAAAAAGGGTACCTGAGCAATTCCTTGAACAGGAGAATTTCTCAATAGAGAGTGTCCTACATTATGCTCAACGTCTGGAATATCTTCTCCCGGAGTACCGGAACTTCTCTTTTTCACTCAAGGAGAAGGAGTTAAACATTGGACGAGCTTTTGGGAAATTGCCATATCCAACACGCAATGTTCAAACTCTGTGCGAAGCTTTGTTAGCAGATGGTTTGGCGAAAGCATTCCCAAGCAATATGATGGTTGTGACAGAGCGCGAGCAAAAAGAAAGCCTTTTGCATCAAGCGTCTTGGCATCACACAAGTGATGATTTTGGTGAGAATGCTACTGTTAGAGGCAGTAGTTTTGTAACAGACTTGGAAAAATACAATTTAGCATTCCGATATGAGTTTACAGCTCCTTTTATTGAATACTGTAATCGTTGTTACGGTGTAAGAAATTTGTTTAATTGGATGCACTACACTATACCACAGTGTTATATACATGTGAGTGATTATTATAACCCCCCACATGGAGTCTCTCTCGAAAACCGAGAAAATCCACCAGAAGGTCCAAGCTCTTACCGTGGTCATCTAGGCGGGATTGAGGGACTTCAACAAAAACTCTGGACAAGCATCTCATGTGCACAGATTTCATTAGTTGAAATCAAAACCGGTTTTAAACTGCGATCTGCGGTAATGGGTGACAATCAATGTATAACTGTACTCTCTGTATTTCCCCTCGAAACTGAGTCTAGTGAGCAAGAATTAAGTTCTGAAGATAATGCCGCTAGAGTAGCTGCTAGCTTAGCAAAAGTCACAAGTGCCTGCGGCATCTTTTTAAAACCTGATGAAACTTTTGTTCACTCAGGTTTCATTTATTTTGGCAAAAAACAATATTTGAATGGAGTACAATTACCTCAATCACTGAAAACTGCTACTAGAATTGCACCCTTGTCAGATGCTATCTTTGATGATCTTCAAGGGACACTAGCTAGCATAGGCACGGCTTTTGAAAGATCTATCTCCGAAACTAGGCACGTAGTCCCTTGTAGAGTAGCAGCTGCATTCCATACCTTTTTTTCCGTAAGAATCTTACAATATCATCATCTTGGCTTCAACAAGGGAACAGACCTGGGTCAATTGTCATTAAGCAAGCCATTAGATTTTGGAACTATAACTTTGGCCTTGGCAGTACCACAAGTCTTGGGTGGCTTATCATTCCTAAATCCAGAAAAATGTTTTTATAGAAATCTGGGTGATCCTGTTACTTCAGGGCTGTTTCAGCTCAAGACATATCTTCAAATGATCCACATGGATGATTTGTTTTTACCTTTGATCGCAAAGAACCCAGGGAACTGTAGCGCAATTGACTTTGTGTTAAACCCTAGTGGGTTAAACGTACCGGGGTCACAGGATTTGACATCCTTCCTACGTCAGATAGTGCGCCGAACAATTACTCTAAGTGCTAAAAATAAATTAATAAACACTTTGTTCCATTCTTCTGCTGATTTAGAAGATGAAATGGTTTGCAAATGGTTGCTTTCTTCTACACCAGTCATGAGTAGGTTTGCCGCCGATATATTTTCTCGCACTCCCAGTGGGAAACGTTTACAGATCTTAGGTTACCTTGAAGGGACTAGAACATTGTTAGCCTCTAAAATTATAAATCATAATACTGAGACACCTATCCTAGATCGATTGAGGAAAATTACGCTGCAAAGGTGGAGCCTGTGGTTTAGTTATCTCGACCACTGTGATCAAGTTCTGGCTGATGCCCTAACTCAGATAACCTGCACTGTGGACTTAGCACAGATTCTTCGCGAGTACACCTGGGCACACATACTAGAGGGAAGGCAGCTCATTGGAGCAACACTTCCTTGTATACTAGAACAACTAAATGTCATCTGGCTCAAACCATATGAGCATTGCCCTAAATGTGCAAAGTCAGCAAACCCTAAAGGGGAACCTTTTGTTTCTATTGCAATTAAAAAACATGTAGTAAGTGCTTGGCCTGATCAATCACGACTTAGTTGGACAATTGGAGATGGCATCCCTTATATCGGATCTCGAACAGAGGATAAGATTGGGCAGCCAGCCATCAAACCAAAATGCCCTTCAGCAGCCTTACGTGAAGCAATTGAGTTGACATCAAGATTGACTTGGGTTACTCAAGGTGGAGCAAACAGCGACTTACTAGTTAAACCCTTCATAGAAGCACGAGTAAATTTAAGCGTACAGGAAATTCTCCAAATGACACCTTCTCATTACTCCGGCAACATTGTGCATCGATATAATGATCAATATAGTCCACACTCATTTATGGCAAATAGGATGAGTAATTCTGCTACTAGGTTAGTTGTTTCGACAAACACTCTTGGAGAATTTTCAGGAGGAGGTCAGTCAGCAAGAGATAGTAATATTATCTTCCAGAATGTCATTAATTTTGCTGTTGCACTTTTTGATCTACGATTTAGGAACGTGGCTACTTCTTCTATACAACATCATCGGGCTCATCTTCATTTGTCAAAGTGTTGCACGCGAGAGGTTCCAGCCCAATATTTAGTTTATACATCAACATTGCCATTGGACCTTACACGGTATCGGGATAATGAGTTGATTTACGATGACAATCCATTAAGAGGTGGTTTAAATTGCAATCTTTCTTTTGATAATCCGCTTTTCAAGGGCCAGAGACTTAACATAATTGAAGAAGACTTGATTAGACTACCTTACTTATCAGGATGGGAGCTAGCTAAAACTGTTATCCAATCTATAATTTCTGACAGCAACAATTCATCAACGGATCCAATCAGTAGTGGGGAAACACGATCATTCACCACTCACTTCTTGACATATCCTAAGATTGGACTACTATATAGTTTTGGTGCACTCATCAGTTATTATCTAGGCAACACCATTATTAGAACCAAAAAATTGACTCTTAACAACTTCATATATTACCTAGCTACTCAAATACATAATTTACCTCATCGCTCGTTGAGAATCCTTAAACCTACTTTGAAACACGCTAGTGTTATCTCGAGATTAATAAGTATTGACTCTCACTTCTCAATTTATATTGGAGGAACTGCTGGTGATCGAGGACTTTCCGATGCGGCAAGATTGTTTCTTAGAACTGCCATTACTGTCTTCCTTCAATTCGTTAGAAAGTGGATAGTTGAACGCAAGACAGCTATTCCACTGTGGGTCATCTACCCTCTAGAAGGTCAAAGTCCTAGTCCGATCAACAGTTTTCTACACCACGTCATCGCATTGTTGCAACATGAGTCCTCCCACGATCATGTTTGTGCTGCAGAAGCCCACAGTCGAGTGGAGACATTTGATAATTTAGTTTATATGTGTAAAAGCACAGCAAGTAACTTCTTTCATGCTTCATTAGCATACTGGAGAAGTCGATCTAAAAATCAAGACAAAAGAGAGATGACAAAGATATTATCTTTGACGCAAACGGAAAAGAAAAATTCATTCGGCTATACAGCACATCCAGAAAGCACTGCTGTTCTTGGTTCCCTCCAGACCAGCCTTGCTCCACCTCCATCTGCTGACGAGGCTACATATGATAGGAAAAACAAAGTTTTGAAAGCTTCCAGACCTGGCAAGTATTCCCAGAATACAACCAAAGCCCCACCCAACCAAACCAGTTGTCGCGATGTATCTCCCAATATCACAGGCACAGATGGGTGCCCTTCTGCCAATGAGGGTTCTAACAGCAATAACAATAATTTAGTCTCGCACAGAATTGTACTGCCGTTTTTTACATTGTCTCATAATTATAACGAAAGACCCTCTATCAGAAAGTCTGAGGGGACAACAGAGATTGTAAGGCTTACTCGGCAGCTGAGGGCAATACCAGACACCACAATATATTGCCGCTTCACGGGAATAGTTTCTTCAATGCACTATAAGCTCGATGAAGTCCTTTGGGAATTTGATAATTTTAAGTCTGCTATAACACTTGCCGAAGGTGAAGGTTCGGGTGCATTACTCTTATTACAAAAATATAAAGTAGAAACCTTGTTTTTTAATACACTAGCCACAGAACACAGCATTGAAGCAGAAATTATTTCTGGAATAACTACACCAAGAATGCTTCTCCCTATTATGTCTAGGTTCCATGGTGGACAAATAAAAGTCACTTTAAACAATTCTGCAAGCCAGATTACCGATATTACTAATCCAAGTTGGTTGGCAGACCAAAAATCTAGGATCCCTAAGCAAGTAGAGATTATAACCATGGATGCTGAAACAACAGAAAACATTAATCGGTCAAAATTGTACGAAGCAGTCCAACAGCTGATTGTCTCACATATTGATCCGAATGCACTCAAAGTTGTGGTTCTTAAAGTTTTCTTAAGTGACATTGATGGAATCCTATGGCTGAATGATAACCTTACCCCTTTGTTTGGGCTGGGTTACTTGATCAAGCCGATCACCTCTAGCCCAAAATCTAGTGAGTGGTACCTATGTCTCTCAAACCTTCTTTCAACTTCAAGACGATTACCTCATCAGAGTCATACTACTTGCATGCATGTTATTCAAACAGCACTCCAGCTACAAATTCAGAGGAGCTCATATTGGCTTAGCCACCTTGTCCAGTATGCCAATCATAATTTGCATTTAGATTATATTAATCTCGGTTTCCCTTCATTGGAGAGGGTTTTATACCATAGATACAATTTAGTCGATTCTCAGAAAGGCCCTTTGACTTCCATTGTCCAACATCTAGCGCACCTGCAGACCGAGATTAGGGAGTTGGTTAATGACTATAATCAACAAAGACAAAGTCGAACCCAAACATATCATTTCATTAAAACAATAAAAGGTCGTATTACAAAATTGGTAAATGATTACCTTAAGTTCTTTCTAATAATACAAGCCTTAAAGCACAATTGCACATGGCAAGAGGAACTAAGAGCTCTTCCAGATCTAATTAGTGTCTGCACTCGATTCTATCATACTCGAAACTGTTCATGTGAAAACCGGTTCCTAGTACAGACTTTATACTTATCACGCATGCAGGATTCGGAAATCAAACTAATAGATAGATTGACCGGCCTTCTTAGTCTATGTCCAAATGGTTTTTTTCGGTAAGGACTCTTGACGTACAAACTCCACATAGTTATACAATGGTACCAGGACACTATATGTAAATTGACCCTAAGAAAGAGTAATTCGACACACAGAGTTCTCAAGTGAAACCCCTCATCTCAGATTATCTGTGGTTGCAATTCTAATATCCGATTGTTACCCCGTGAGTATAACTCCAGATTAATATAAGAAAATACCTTTTGTCCTGCAAATTTATCTTAAATTCAAGTACATACGCTCCAAATCGTATAAAATATTAAGAAAAAGTTAATCTGCTTGCTTTAATTATAACTTTAATATTCGACAAATAGTTAACGGTCTCATCACTCAAAAATTTCATTAACAAAAGAAGTACTCTGAGTATATTCACATATCATATGTGATTAACATATAAGCAACGCATGATGCGCCTTCCTCTTACTTATTGTGTTGTCACGCAGTCGTTGTACTACCTCGAAAATTCCAAACAATAAATCGTGTCTATCCCGCATTTAGTGTCTTTAATTTAAGATCTCAAATCCAAAAAACTGGGTTTATGTTGATGTAAATCAATAATACCGAAATTGCTTGATATTAAAATAAAGCTTAAAGGATTTTTCCTTAAACGGTGATGTTAGGTATATAGGAAAGCTCGATCACGATGTCCCTTACTCAGAAAAAGAAAAACGGAAGCCCTATTGGCCATTTAATCGTACACAAAAATATCTTTACCAAATTGTTTTCTCTTTTTTGTGTGTCCA\n>Reston_ebolavirus_isolate_RESTV/M.fascicularis-tc/PHL-USA/1996/Ferlite_Philippines/Alice_TX_complete_genome\nCGGACACACAAAAAGAAAAAAGGTTTTTTAAGATTTTTTGTGTGCGAGTAACTATGAGGAAGATTAACAGTTTTCCTCAGTTTAAGGTATACACTGAAATTGAGATTGAGATTCTCCTCTTTGCTATTCTGTAACTTTCCCTGGTTGTGACAATTGAATCAGTTTTATCTATTACCAATTACCATCAACATGGTATGTCTAGTGATCTTGGGACTCTTCTTCATCTGGTTTTTCCTAGAGCTCTGAATCTATTTTGTGAGAAGTTCATCCAAACGACCCAGTGTCTGAAAATACAAGAGGTTCCCCTTTCCGTCAAGTTTAAGGGGTTGTTTTGATTGTGTGTAGATTTTATAATCCTAGAGTGCCAAGGAGTTGCGTGTCATCATTAATTGGGAAGATCAAGGAAACAATTTGTTCCAATAATATCGTACATCTTGACTAAGTCGAACAAGGGGAAGTCGATATGGATCGTGGGACCAGAAGAATCTGGGTGTCGCAAAATCAAGGTGATACTGATTTAGATTATCATAAAATTTTGACAGCTGGCCTTACTGTTCAACAGGGAATTGTCAGGCAGAAAATAATTTCTGTATATCTTGTTGATAACTTGGAGGCTATGTGTCAATTGGTAATACAAGCCTTTGAGGCCGGAATTGATTTCCAAGAAAATGCCGACAGCTTCCTTCTGATGCTTTGCCTACATCATGCTTACCAAGGTGACTATAAATTGTTCTTGGAGAGCAATGCTGTACAGTATTTGGAAGGTCATGGATTCAAATTTGAGCTCCGGAAGAAGGACGGTGTCAATCGGCTCGAGGAATTGCTTCCTGCTGCAACGAGTGGAAAAAACATCAGGCGTACGTTGGCCGCACTGCCTGAAGAGGAGACTACAGAAGCAAATGCAGGGCAATTTCTCTCATTTGCGAGTTTGTTTCTTCCCAAACTGGTTGTGGGAGAGAAGGCTTGCTTGGAAAAAGTCCAGCGACAAATTCAGGTTCATGCAGAACAGGGTTTAATTCAATATCCCACTGCATGGCAATCAGTTGGACACATGATGGTAATCTTCAGATTGATGAGGACTAATTTCTTGATTAAATATTTACTGATCCACCAGGGTATGCATATGGTAGCTGGCCACGATGCCAATGATGCTGTCATTGCTAATTCAGTTGCTCAGGCTCGCTTTTCAGGACTCCTAATTGTCAAAACCGTTCTTGATCATATTCTGCAGAAAACCGACCAAGGAGTAAGACTTCACCCTTTGGCCCGAACAGCCAAAGTGCGTAATGAGGTTAATGCATTTAAGGCCGCCCTAAGCTCACTTGCTAAGCATGGGGAATATGCCCCTTTTGCTCGCCTTCTCAATCTCTCGGGAGTTAACAACCTAGAACATGGTCTCTACCCACAGTTATCAGCAATTGCTCTTGGAGTTGCCACAGCACATGGTAGCACCCTTGCAGGAGTTAATGTTGGTGAGCAGTATCAGCAGCTTAGAGAGGCTGCCACTGAAGCTGAGAAGCAACTCCAACAATATGCTGAGTCCAGAGAACTCGACAGCCTAGGCCTAGACGATCAGGAAAGAAGAATACTAATGAACTTCCATCAGAAGAAAAATGAAATTAGTTTCCAGCAGACCAATGCAATGGTAACCCTTAGGAAAGAGCGACTGGCCAAATTAACAGAAGCTATAACGCTGGCCTCAAGACCTAACCTCGGGTCTAGACAAGACGACGACAATGAAATACCGTTCCCTGGGCCTATAAGCAACAACCCAGACCAAGATCATCTGGAGGATGATCCTAGAGACTCCAGAGACACTATCATTCCTAATAGTGCAATTGACCCCGAGGATGGTGATTTTGAAAATTACAATGGCTATCATGATGATGAAGTTGGGACGGCAGGTGACTTGGTCTTGTTCGATCTTGACGATCATGAGGATGACAATAAAGCTTTTGAGCTACAGGACAGCTCACCACAATCCCAAAGGGAAATAGAGAGAGAAAGATTAATTCATCCACCCCCAGGCAACAACAAGGACGACAATCGGGCCTCAGACAACAATCAACAATCAGCAGATTCTGAGGAACAAGAAGGTCAATACAACAGGCACCGAGGCCCAGAACGTACGACCGCCAATCGAAGACTCTCACCAGTGCACGAAGAGGACACCCCTATAGATCAAGGCGATGATGATCCCTCAAGCCCACCTCCGCTGGAATCTGATGATGACGATGCATCAAGTAGCCAACAAGATCCCGATTATACAGCTGTTGCCCCTCCTGCTCCTGTATACCGCAGTGCAGAAGCCCACGAGCCTCCCCACAAATCCTCGAACGAGCCAGCTGAAACATCACAATTGAATGAAGACCCTGATATCGGTCAATCAAAGTCTATGCAAAAATTAGAAGAGACATATCACCATCTGCTGAGAACTCAAGGTCCATTTGAAGCTATCAATTATTATCACATGATGAAGGATGAGCCGGTAATATTTAGCACTGATGATGGGAAGGAATACACCTACCCGGATTCACTTGAGGAAGCCTATCCTCCATGGCTCACCGAGAAAGAACGACTGGACAATGAAAATCGATACATTTACATAAATAATCAACAGTTCTTCTGGCCTGTCATGAGTCCCAGAGACAAATTTCTTGCAATCTTGCAGCACCATCAGTAACCACAGCACAAAGCGCGGTCCACTTCGTAAAGCTAAATACACTTAAAGCTTGACCGATTCATCTACAAAAACTAATCCATTATAACTTATTAGTGCTACTTTTCTATAAGTGATTCTCAATCTAAGGCCATTAAGAGTTTAAGCAATATACATATACACTTACACCGGTCTATCCAAGATGTGGCTCAATGTTCTTAATTTGAACATAGTCATAAGGGGATAAATAATACTTTATATTTCTGATTGTGGATTGACCCATTCTGCTTAAAATGCTTCGCCCATTAAAAATGTGATCTAATAGATAGCCCTGACTAGACCAATTAAGAAAAACATTTGATGAAGATTAAAACCTTCATCGCCAGTAAATGATTATATTGTCTGTAGGCAGGTGTTTACTCCACCTTAAAGTCGGAAATATCCTACCTTAGGACCATTGTTAAGAGGTGCATAGGCATTACCATCCTTGAGAACATGTATAATAATAAATTGAAGATATGTTCAGGCCCAGAAACAACTGGATGGATTTCTGAGCAACTAATGACAGGTAAGATTCCAGTAACTGATATATTCATTGATATTGATAACAAGCCAGATCAAATGGAAGTCCGGCTCAAACCATCATCAAGGAGCTCAACCAGAACTTGTACAAGTAGCAGTCAGACGGAGGTCAACTATGTACCTCTCCTTAAAAAGGTTGAGGATACATTAACTATGCTAGTGAGTGCAACCAGTCGTCAGAATGCTGCAATCGAGGCCCTTGAAAACCGCCTCAGCACACTTGAGAGTAGCTTAAAGCCAATCCAAGACATGGGTAAAGTGATTTCATCATTGAATCGCAGTTGTGCCGAAATGGTGGCAAAATATGATCTTCTAGTTATGACAACTGGACGGGCTACTTCAACCGCAGCTGCAGTAGATGCGTACTGGAAAGAGCACAAACAGCCACCACCAGGGCCAGCGTTGTATGAAGAGAATGCGCTTAAAGGAAAAATCGATGATCCAAACAGCTATGTACCAGATGCTGTGCAGGAGGCTTACAAGAACCTTGACAGTACATCGACCCTGACCGAGGAAAATTTTGGGAAACCTTATATATCTGCTAAAGATCTGAAGGAGATCATGTATGATCATCTACCTGGTTTTGGGACTGCCTTTCACCAACTTGTTCAAGTGATTTGTAAAATAGGAAAGGATAACAACCTCTTGGACACAATCCATGCTGAGTTCCAGGCAAGTCTAGCAGATGGTGACTCTCCCCAATGTGCACTCATACAGATAACCAAAAGAGTCCCAATCTTTCAGGATGTGCCGCCCCCGACAATCCACATTAGATCCCGTGGTGATATCCCACGAGCATGCCAAAAGAGTCTCCGACCAGCACCACCATCACCCAAAATTGATCGTGGTTGGGTTTGTTTGTTTAAGATGCAAGATGGTAAAACGCTTGGACTTAAGATCTAAGGATCAAGATTTATTTAACAAGGCAAGCCACAACCTTAGATAGAACCTCAGCCAGACTATTGAACTATTGACGCTGTTGATGATAATATATAATTAATGGTCATATTTGAATATGACAACATCTTGCTTCTTGTTTTGCCTTGTATCTCTTTGAGTTGGAAGATCATTCCAAACTTACAAACATGCACAAGATGTTATGGTTTAGCAAAGAATTGATAGGAGTACTGGTATATAATGTAAATATAACAAGTGATGAAGATTAAGAAAAACCAGTCGGTATTTTCCAGACTTGGCATTTCTTATCTTCATCTTCTAAAGTGAGATATTTTATCATCAAAAAATGAGACGCGGAGTGTTACCAACGGCTCCTCCAGCATATAATGATATTGCATACTCTATGAGCATACTCCCAACCCGACCAAGTGTCATAGTCAATGAGACCAAATCAGATGTACTGGCAGTGCCAGGAGCAGATGTTCCATCAAACTCCATGAGACCAGTGGCTGATGATAACATTGATCACTCAAGCCATACTCCAAGCGGAGTAGCTTCTGCCTTTATATTGGAAGCTAAAGTGAATGTAATTTCGGGAACAAAAGTCCTGATGAAGCAAATACCTATTTGGCTTCCACTGGGTGTAGCTGATCAGAAGATATACAGCTTTGATTCAACAACAGCCGCAATTATGTTGGCTTCCTACACAGTGACACACTTCGGGAAGATATCTAACCCGCTGGTACGTGTCAACAGGCTAGGCCCAGGAATACCCGATCATCCGCTACGACTCCTAAGGTTGGGCAATCAGGCATTCCTTCAAGAGTTTGTTCTTCCACCAGTCCAGCTTCCCCAGTATTTCACATTTGATCTAACAGCTCTAAAGCTCATCACTCAACCATTGCCAGCTGCAACCTGGACAGACGAAACTCCAGCAGGAGCAGTCAATGCTCTTCGTCCTGGGCTCTCACTCCATCCCAAGCTTCGTCCAATTCTTCTACCGGGGAAGATAGGAAAGAAAGGTCATGCTTCAGACTTAACATCACCTGACAAAATTCAAACAATCATGAATGCAATACCGGACCTCAAAATTGTCCCGATTGATCCAATCAAGAACATAGTTGGAATTGAGGTTCCAGAATTACTAGTTCAAAGGCTGACCGGCAAAAAACCACAACCCAAAAATGGCCAACCAATTATTCCAGTTCTTCTTCCGAAATATGTTGGACTTGATCCTATATCGCCAGGGGACTTAACTATGGTTATCACCCAGGATTGTGATTCATGCCACTCTCCAGCCAGCCATCCGTATCACATGGACAAGCAGGATAGTTACCAATAATTTAAATTCCATTCGAGCTATTATTCTGCTAGTAATTCCGACGGGATCAATAGACTAAAAATCTGATTGTATAGAATTATAAAAGAATCAAGCAGAGGCAACAGACTCACAGCTTACGCCTAGATGACTAATATTAAGGAGTTTTTTAATCTAATTTTCCAGTCTTAAGTAATAATCATTTCTTTTGTAATTAATTATGCATTTGTTAACTTATCGGTGCGAGATTTCCTTGAGAACCCGGCGGGGCTTCTACTATCTGTAGTAACCAGAAGAGAAGTTCAACCCAGTCAAAACTAAACCAAGCAATATTCTGAATGCTCTATAGTCTATTCTAATCAGAGGTATAACAATGGCTAAGATTTCAATGACTCGTTAACAATCGCTAGTAATTTTAATCTCCAGATTAAGAAAAAGATATACGATGAAGATTAAGGCGACAACGAGTCGAAACTTCATCTCTTTTAAAGATCTAACATTATCTGTTCCAAAGTCATACAAGGACACATTCAAATCAGGGATTGTAAGCTGCTATTTCTTACCTCCCCAAATCACCTATACAACATGGGGTCAGGATATCAACTTCTCCAATTGCCTCGGGAACGTTTTCGTAAAACTTCGTTCTTAGTATGGGTAATCATCCTCTTCCAGCGAGCAATCTCCATGCCGCTTGGTATAGTGACAAATAGCACTCTCAAAGCAACAGAAATTGATCAATTGGTTTGTCGGGACAAACTGTCATCAACCAGTCAGCTCAAGTCTGTGGGGCTGAATCTGGAAGGAAATGGAATTGCAACCGATGTCCCATCAGCAACAAAACGCTGGGGATTCCGTTCAGGTGTGCCTCCCAAGGTGGTCAGCTATGAAGCCGGAGAATGGGCAGAAAATTGCTACAATCTGGAGATCAAAAAGTCAGACGGAAGTGAGTGCCTCCCTCTCCCTCCCGACGGTGTACGGGGATTCCCTAGATGTCGCTATGTCCACAAAGTTCAAGGAACAGGTCCTTGTCCCGGTGACTTAGCTTTCCATAAAAATGGGGCTTTTTTCTTGTATGATAGATTGGCCTCAACTGTCATCTACCGTGGGACAACTTTTGCTGAAGGTGTCATAGCTTTTTTAATTCTGTCAGAGCCCAAGAAGCATTTTTGGAAGGCTACACCAGCTCATGAACCGGTGAACACAACAGATGATTCCACAAGCTACTACATGACCCTGACACTCAGCTACGAGATGTCAAATTTTGGAGGCGAGGAAAGTAACACCCTTTTTAAGGTAGACAACCACACATATGTGCAACTAGATCGTCCACACACTCCGCAGTTCCTTGTTCAGCTCAATGAAACACTTCGAAGAAATAATCGCCTTAGCAACAGTACAGGGAGATTGACTTGGACATTGGATCCCAAAATTGAACCAGATGTTGGTGAGTGGGCCTTCTGGGAAACTAAAAAAACTTTTCCCAACAACTTCATGGAGAAAACTTGCATTTCCAAATTCTATCAACCCACACCAACAACTCCTCAGATCAGAGCCCGGCGGGAACTGTCCAAGGAAAAATTAGCTACCACCCACCCACCAACAACTCCGAGCTGGTTCCAACGGATTCCCCTCCAGTGGTTTCAGTGCTCACTGCAGGACGGACAGAGGAAATGTCGACCCAAGGTCTAACTAACGGAGAGACAATCACAGGTTTCACCGCGAACCCAATGACAACCACCATTGCCCCAAGTCCAACCATGACAAGCGAGGTTGATAACAATGTACCAAGTGAACAACCGAACAACACAGCATCCATTGAAGACTCCCCCCCATCGGCAAGCAACGAGACAATTGACCACTCCGAAATGAATTCGATCCAAGGCTCGAACAACTCCGCCCAGAGCCCACAGACCAAGGCCACGCCAGCGCCCACAGCATCCCCGATGACCCTGGACCCGCAAGAGACGGCCAACAGCAGCAAACCAGGAACCAGCCCAGGAAGCGCAGCCGAACCAAGTCAGCCCGGACTCACTATAAATACAATAAGTAAGGTAGCTGATTCACTGAGTCCCACCAGGAAACAAAAGCGATCGGTTCGACAAAACACCGCTAATAAATGTAACCCAGATCTTCACTATTGGACAGCTGTTGATGAGGGGGCAGCAGTAGGATTGGCATGGATTCCATATTTTGGACCTGCAGCAGAAGGCATCTACATTGAGGGTGTAATGCATAATCAGAATGGGCTTATTTGCGGGCTACGTCAGCTAGCCAATGAAACTACCCAGGCTCTTCAATTATTTCTGCGGGCCACAACAGAACTGAGGACTTACTCACTTCTTAACAGAAAAGCTATTGATTTTCTTCTTCAACGATGGGGAGGTACCTGTCGAATCCTAGGACCATCTTGTTGCATTGAGCCACATGATTGGACAAAAAATATTACTGATGAAATTAACCAAATTAAACATGACTTTATTGACAATCCCCTACCAGACCACGGAGATGATCTTAATCTATGGACAGGTTGGAGACAATGGATCCCGGCTGGAATTGGGATTATTGGAGTTATAATTGCTATAATAGCCCTACTTTGTATATGTAAGATTTTGTGTTGATTTATTCTGAGATCTGAGAGAAAAAAATCTCAGGGTTACTCTAAGGAGAAATATTATTTTTAAAATTTACTTAAATGCTGACCACTTATCTTAAATGAGCAATTAATAATATGTTTTTCTGCTTCTTTGCTTGATTTACAATATGATATTTCTCTTAATAATGATTAATATATTAAGAAAAACTTATGACGAAGATTAAAGGGGAGGATCGTTAACGGGAAAATCTCCCATCTCGTTCGTCGAAGCCACGTTGGTGGTGCTTGCAGCTGAGAACAACTCCAGAGATTGTAGGTAGAAAGGACCAGCATTTATAGGTAGGGGTCAGAAAGCAACAATAGCCATAAAAGGAGAGCCTGACATTGCTATTTAATATCCTAGAACCTGATTTCTAGGTTCTAGTTGTACAATCCGGATGATGGAGCATTCAAGAGAACGGGGTAGATCTAGCAACATGCGACATAATAGCCGGGAACCATACGAAAATCCATCAAGGTCTCGCTCATTATCTCGGGACCCTAATCAGGTTGATCGTAGGCAGCCTCGAAGTGCATCCCAAATTCGTGTTCCGAATCTGTTCCATCGGAAAAAGACTGATGCACTCATAGTTCCTCCGGCTCCCAAAGATATATGCCCAACACTCAAAAAAGGATTCCTCTGCGATAGTAAATTTTGCAAAAAAGATCACCAATTGGATAGCTTAAATGATCATGAATTACTACTGCTAATTGCAAGAAGAACATGTGGAATTATCGAGAGCAATTCGCAGATTACATCCCCAAAAGATATGCGGTTAGCGAATCCAACAGCTGAAGACTTCTCACAAGGTAATAGTCCTAAATTAACACTTGCAGTCCTTCTTCAAATTGCTGAACATTGGGCAACCAGAGACCTAAGGCAAATTGAGGACTCTAAACTTAGAGCTCTTTTAACCCTTTGTGCCGTATTAACAAGGAAATTTTCTAAATCCCAACTGGGTCTTCTATGTGAGACCCACCTACGGCATGAGGGCCTCGGACAGGACCAAGCTGATTCTGTATTAGAGGTCTACCAAAGACTCCACAGTGATAAAGGAGGGAATTTTGAGGCTGCCCTGTGGCAACAATGGGACCGACAGTCGTTAATAATGTTCATCTCTGCTTTTCTCAACATTGCTCTCCAGACACCTTGTGAAAGTTCTAGTGTCGTAGTCTCAGGTCTTGCCACATTGTACCCAGCACAAGACAATTCTACACCATCCGAGGCAACTAATGATACCACCTGGTCAAGTACAGTTGAATAGAAAACCACTGGAGCTATTTTTCCACGATTGCTCTCAGTCAATAAATTAATATAGATATAATACGACTTCGGTGTGCAATTGTCAAGGGTTCCATTTGGTAATAATGATTCTTAAAACAATCTACTATCGTAATTATCGATGGATCTACCCTATTTGACGGTACATGACTTGAATGTAATAAGGTAAGTTGGTATCTGAGGTATTTTGTCTAGAGTATACTCAAAATCGTATGTCTAGCAAATTATCAATAGCAAAGTTAAATTCTCCTAACCTCATATTTTGATCAAGTAATCATGATTTTATGGTAATTCTTTGCAGATTATCGGTTTAATCTTTATTAAGAAAAAATCATGATTGTAGACAATTTACTGGTAGTCCCTGGGTATCCAAGTTTATGAACAGAGCTAGAGAGAATTTGCTACTTCCGAGGTATAACTTTATTATTTGCTACTTCGAATGCCTAAAACCAGTAATGCAGGATGAAGATTAATTGCGGAGGAATCAGGAATTCAACTTTAGTTCCTTAAGGCCTCGTCTGAATCTTCATCAGTTAGTAAGTTCTTTTATAGAAGTCATTAGCTTCTAAGGTGATTATATTTTAGTATTAAATTTTGTTAATTGCTTGCTATAAAGTTGAAGTGTCTAATGCTTAAATGAACATTTCTTTGAAGCTGACATACGAATACATCATATCATATGAAAACATCGCAATTAGAGCGTCCTTGAAGTCTGGCATTGACAGTCACCAGGCTGTTCTCAGTAGTCTGTCCTTGGAAGCTCTTGGGGAGACAAGAAGAGGTCCCAGAGAGTCCCAACAGGTTGGCATAAGGTCATTAACACCAGCATAGTCAGCTCGATCAAGACTGTAAGCGAGTCGATTGCAACTAAAAAGATTATTTCTTGTTGTTTAAACAAATTCCTTTTGTGTGAGACACCCTCAAGGCACAAGATGGCTAAAGCCACAGGCCGATACAATCTCGTGCCCCCAAAGAAAGATATGGAAAAGGGAGTGATTTTTAGTGATCTTTGTAATTTCTTGATTACTCAAACCCTGCAAGGTTGGAAGGTTTATTGGGCAGGAATTGAGTTTGATGTAAGTCAAAAAGGCATGGCTCTTCTGACAAGACTCAAAACAAATGACTTTGCTCCTGCCTGGGCGATGACAAGAAATCTCTTCCCACATCTGTTCCAAAACCCAAATTCGGTTATTCAATCTCCCATCTGGGCTTTGAGGGTAATTTTGGCAGCCGGATTGCAGGATCAGTTGTTAGACCATTCATTGGTTGAGCCATTGACAGGGGCTCTCGGTCTAATTTCTGATTGGCTCCTAACTACAACGTCAACACATTTCAATCTTCGTACTAGAAGCGTAAAGGACCAGCTTAGTTTTCGTATGTTATCTTTGATCAGGTCAAACATCTTGCAGTTCATCAACAAGCTTGACGCCCTGCATGTTGTCAATTACAATGGTTTACTCAGTAGTATTGAGATCGGGACTTCTACACACACAATCATTATAACTCGTACAAATATGGGTTTTCTCGTGGAAGTTCAGGAGCCTGACAAATCAGCTATGAATTCTAAGCGCCCAGGACCAGTCAAGTTCTCATTACTTCATGAGTCTGCCTTCAAACCTTTCACTCGTGTTCCACAATCTGGGATGCAATCATTAATAATGGAGTTCAACAGTTTGTTGGCAATTTAACAAGGTGATCTTAAAATAAGTACATGAATGAGAATTAGTTGTGGGTCTTACCTAGCATTGTTGAGTTAGCTATCTAATCTATTTTCACTAATTGCATTGAGCACTGCTAGTAGGTTTGCACCACGTTAAAGATTCAGAGTGTATGAATTGTGCAGATTTAAACTTGGGTTTTGCCTTATGCTTCATAGGTGGTCTTTTTAAAATGGAGATTATCAGCATTTCTTCAATGGGAGGAGTTAGCAATCAGAAATTGGAGATAAATGGACATCGGGATAGAACAATGCCTAACTATTGGGCGGCTTTCATTTTTAAATGTGTATATAACCAATCTTTTCCTATCTTTGCTTATATTGGTGTAACTTTACTTTAATAACATGTCAATGCTATACTGTTAAGAGAAGGTCTGAGGAAGATTAAGAAAAAGGTCTCGTGTTCACTTGGTTGCCGTCAAGTATCCTGTGGTTTTTTTCTACCTAACTTCCTCATGCCATATGGCTACCCAGCATACCCAGTACCCGGATGCACGTTTATCTTCACCTATAGTCCTGGATCAATGTGATTTGGTAACTCGAGCATGTGGGTTATATTCATCTTATTCTCTAAATCCTCAGCTAAGGCAATGTAAATTACCAAAACATATATATCGACTTAAGTTCGACACAATAGTATCCAAATTCCTAAGTGATACACCTGTAGCAACACTGCCGATAGACTATTTAGTACCAATTCTCCTGCGTTCCCTAACGGGGCACGGTGATAGGCCGTTGACCCCGACTTGTAATCAATTCCTTGATGGAATTATTAATTACACTCTTCATGATGCAGCCTTTCTTGATTACTATCTCAAGGCAACAGGTGCACAGGACCATTTGACAAACATTACAACTAGAGAGAAGCTTAAAAACGAAATTCTAAACAATGATTATGTCCATCAATTGTTCTTCTGGCATGACCTGTCTATTTTGGCTCGACGTGGGCGTCTGAATCGCGGGAACAACCGTTCAACCTGGTTTGTTCATGATGAATTCATTGATATTTTAGGATATGGCGATTATATTTTTTGGAAAATACCTTTATCATTATTACCAGTTACTATAGACGGGGTCCCACACGCGGCAACTGACTGGTATCAACCGACTCTTTTTAAAGAATCCATCCTAGGGCACAGCCAAATCCTATCTGTGTCGACAGCTGAAATACTAATTATGTGTAAAGATATTATCACCTGTAGGTTTAATACATCACTGATTGCATCCATTGCAAAATTAGAGGATGTAGATGTGTCTGATTATCCTGACCCGAGTGATATTCTTAAGATATACAATGCTGGAGACTATGTAATATCTATTCTTGGCTCAGAAGGTTATAAGATAATAAAGTACCTTGAACCACTTTGTTTGGCCAAAATCCAACTTTGCTCTAAATTCACAGAAAGAAAAGGTCGTTTCCTCACACAGATGCATTTATCAGTAATAAATGATCTTCGGGAGTTGATTTCTAACCGCAGGTTAAAGGACTATCAGCAAGAGAAGATTAGGGATTTTCACAAAATATTATTACAATTGCAATTATCTCCTCAACAGTTTTGTGAATTATTCTCTGTTCAAAAACATTGGGGGCATCCAATTTTACATAGTGAGAAAGCTATACAAAAAGTAAAACGGCATGCAACCATCCTTAAGGCTCTCAGACCTAATGTCATTTTTGAGACATATTGTGTATTCAAGTACAATATTGCCAAGCACTATTTCGACAGCCAAGGAACTTGGTACAGTGTAATCTCAGACAGGAATTTAACTCCAGGACTCAACTCCTTCATAAAACGTAATCACTTTCCTTCACTACCCATGATTAAGGATCTTCTATGGGAATTCTATCATCTTAATCACCCTCCGTTATTCTCTACAAAGGTGATTAGTGACTTAAGTATTTTCATCAAGGATAGGGCCACAGCTGTTGAACAGACATGTTGGGATGCAGTCTTTGAACCCAATGTGCTAGGTTACAATCCTCCAAACAAATTCTCCACTAAAAGGGTGCCGGAACAATTTCTAGAACAGGAGGATTTTTCAATCGAAAGTGTCCTGAATTATGCACAGGAATTACATTATTTATTACCACAGAATAGGAATTTTTCCTTTTCTCTTAAAGAAAAAGAATTAAATATTGGACGAACATTTGGTAAGCTACCATATCTCACACGGAATGTCCAAACTTTATGTGAGGCTCTGTTAGCAGATGGACTGGCTAAGGCCTTCCCCAGTAACATGATGGTAGTAACTGAACGTGAACAAAAAGAGAGCCTTCTTCATCAGGCATCATGGCACCACACCAGTGATGATTTTGGAGAGAATGCTACCGTTCGAGGGAGTAGTTTTGTAACTGATTTAGAGAAGTACAATCTTGCATTTCGCTATGAGTTCACTGCACCATTTATTGAGTACTGCAACCATTGCTATGGTGTGCGTAATGTCTTTAATTGGATGCATTATTTAATCCCGCAGTGTTACATGCATGTAAGTGATTATTATAATCCGCCTCACAATGTTAATCTTAGCAATCGAGAATATCCTCCTGAAGGCCCGAGTTCGTACCGAGGGCACTTAGGAGGCATAGAGGGATTACAACAAAAACTGTGGACGAGTATATCCTGTGCACAAATCTCCTTAGTGGAAATTAAAACTGGTTTTAAGTTACGATCAGCGGTCATGGGAGACAATCAGTGTATAACCGTATTGTCTGTTTTTCCACTTGAAACAGACCCTGAAGAGCAGGAGCAAAGCGCCGAAGACAATGCTGCAAGAGTAGCAGCAAGTCTTGCAAAAGTAACCAGTGCATGTGGGATCTTTCTTAAACCAGAAGAGACATTCGTACACTCAGGTTTCATTTATTTCGGAAAAAAACAATATCTCAATGGTGTACAATTACCGCAATCACTCAAAACAGCAGCAAGAATGGCGCCACTCTCTGATGCTATATTCGATGATCTACAAGGAACACTTGCCAGTATTGGAACTGCCTTCGAACGTGCTATATCGGAAACGCGACATATCCTCCCATGTCGTATTGTAGCAGCTTTCCATACGTATTTCGCCGTTCGGATTTTACAATATCACCATCTTGGATTTAATAAAGGCATCGATTTAGGGCAGTTGTCACTTAGTAAACCATTAGACTATGGGACTATTACTCTAACATTGGCGGTTCCACAAGTCCTTGGGGGATTGTCTTTTCTAAATCCAGAAAAGTGTTTTTATCGAAACTTCGGAGATCCTGTGACTTCTGGACTTTTCCAGCTACGGGTGTACCTAGAAATGGTTAACATGAAAGACCTATTTTATCCATTAATATCGAAAAATCCAGGAAATTGTAGTGCCATTGATTTTGTCTTAAATCCATCCGGATTAAATGTTCCAGGATCACAAGACTTGACATCCTTTTTGCGACAGATCGTTAGGCGTAGTATTACACTAACTGCAAGAAATAAGTTAATTAACACTCTCTTCCATGCCTCTGCTGATTTGGAAGATGAGATGGTTTGTAAATGGCTCCTTTCATCAAACCCTGTCATGAGTCGCTTTGCAGCGGATATTTTTTCCAGGACACCTAGTGGTAAACGTCTCCAAATATTAGGTTATCTTGAAGGGACCAGGACTCTATTGGCCTCCAAAATCATAAACAACAACAGTGAGACACCTGTACTTGATAAGCTGAGGAAGATCACCCTACAAAGATGGAATCTGTGGTTCAGTTATTTGGACCATTGTGACCAATTACTAGCAGATGCTCTACAGAAAATTAGTTGCACAGTGGATTTGGCCCAGATTTTGCGTGAGTATACATGGTCACACATCTTAGAGGGTAGACCATTGATCGGAGCGACATTACCATGTATGGTGGAGCAATTCAAAGTTAAGTGGCTAAGACAATATGAACCTTGTCCAGAATGCCTCAACAAAAAAGGCTCAAATGCTTATGTCTCAGTTGCAGTCAAAGATCAAGTGGTCAGTGCTTGGCCTAATACTTCTCGAATAAGTTGGACAATAGGGAGTGGTGTCCCCTATATAGGGTCAAGAACCGAGGATAAAATCGGACAGCCTGCAATCAAGCCGCGATGCCCTTCATCTGCCCTCAAGGAGGCTATAGAATTAGCATCAAGGCTCACTTGGGTTACACAAGGAAGTTCTAATAGTGAACAATTAATCCGGCCTTTCTTAGAAGCGAGAGTCAACCTTAGTGTCAGTGAAGTCCTGCAAATGACACCATCACATTATTCAGGAAATATTGTCCATCGATATAACGACCAATATAGCCCGCACTCATTTATGGCGAATCGCATGAGCAATACTGCGACCCGTCTCATAGTGTCAACTAATACACTTGGAGAATTTTCAGGTGGAGGGCAGGCCGCCAGGGATAGCAATATAATTTTCCAGAATGTTATAAATTTAGCAGTTGCCCTTTATGATATTAGATTCCGGAATACGAACACCTCTGATATAAGGCATAATAGGGCTCATCTTCACCTGACAGAGTGCTGTACTAAAGAGGTCCCGGCCCAGTATTTGACATATACAAGTGCACTCAATCTGGATTTAAGCCGTTATCGTGATAATGAACTAATATATGACTCAAATCCACTGAGGGGAGGATTGAACTGCAATTTAACAATGGATAGTCCTTTAGTGAAGGGTCCTAGGCTTAACATGATTGAAGATGATCTTCTCCGCTTTCCACACCTTTCTGGATGGGAGTTAGCGAAAACGGTGGTACAATCCATCATCTCAGACAATAGCAACTCATCAACAGATCCAATCAGTAGCGGAGAAACACGCTCTTTCACAACTCATTTTCTCACTTACCCTCAGATTGGCCTTCTTTACAGTTTCGGGGCAGTATTATGCTTTTATCTAGGCAATACTATCCTATGGACTAAAAAACTTGATTATGAACAGTTTCTATATTATTTGCATAACCAGCTGCACAACTTACCTCATCGAGCACTCCGTGTTTTTAAACCAACATTTAAGCATGCCAGTGTGATGTCCCGATTAATGGAAATTGATTCCAACTTCTCAATTTATATTGGCGGGACATCTGGAGATCGAGGGCTGTCTGATGCTGCTCGACTGTTTCTTCGGACAGCAATCGCGAGTTTTTTACAATTTCTTAAAAGCTGGATCATCGATCGCCAAAAGACAATTCCTTTATGGATAGTATATCCGCTTGAAGGTCAACAGCCGGAATCCATCAATGAATTTCTACATAAAATTTTTGGTCTGCTCAAACAAGGCCCCAAAAATATTCCAAAGGAGGTCAGCATTCAAAATGATGGACATTTGGATTTGGCAGAAAATAATTATGTTTACAATAGTAAGAGCACTGCTAGTAATTTCTTCCATGCATCCTTAGCTTACTGGAGAAGTAGGAAATCTCGGAAAACTCAAGACCATAATGATTTCTCAAGAGGGGATGGAACACTTACAGAACCCGTGTGTAAGTTCTCAAGCAATCATCAGTCAGATGAAAAGTACTACAATGTGACATGTGGAAAGTCACCGAAGCCGCAAGAACGCAAAGACTTCTCGCAATACAGACTCAGCAATAACGGGCAAACAATGAGTAATCATCGTAAGAAAGGGAAGTTCCACAAGTGGAATCCCTGCAAAGTGTTAATGGAGAGTCAAAGGGGAACTGTTCTAAAAGAGGGTGACTACTTTCAAAACAATACTCCACCAACAGATGATGTATCAAGTCCTCACCGACTCATTCTACCATTTTTTAAATTGGGAAATCACAACCATGCACATGATCAAGATGCCCAAGAATTGATAAATCAAAATATTAAACAGTACCTACATCAGCTAAGGTCTATGTTGGACACCACTATATATTGTAGATTCACAGGGATTGTCTCATCCATGCATTACAAATTGGACGAAGTTCTTCTAGAATACAATGGTTTCGATTCAGCTATCACATTAGCTGAAGGTGAGGGGTCAGGGGCTCTATTACTTTTGCAGAAATATAGTACAAGGTTATTATTTTTGAACACATTGGCAACAGAACACAGTATAGAGTCAGAAGTTGTATCAGGTTTTTCTACTCCGAGAATGTTGTTACCAATAATGCAAAAGGTTCATGAAGGACAAGTCACTGTTATCTTAAATAATTCAGCAAGTCAGATAACTGACATAACTAGCTCAATGTGGTTAAGTAATCAAAAATATAATCTACCTTGTCAAGTTGAAATCATTACGATGGATGCTGAAACAACAGAGAACTTAAACAGGTCCCAACTCTACCGAGCAGTATATAACTTAATACTTGATCACATTGATCCGCAGTATCTCAAGGTGGTGGTACTCAAAGTATTTCTGAGTGATATAGAAGGAATATTATGGATTAATGATTACTTGGCTCCATTATTCGGGGCTGGTTACTTGATTAAACCGATTACATCAAGTGCCCGGTCAAGTGAATGGTACCTTTGCTTATCAAATTTGATATCTACTAACAGGAGATCGGCCCATCAGACTCACAAGGCATGTCTTGGTGTTATCAGAGATGCTTTGCAAGCACAAGTCCAGCGAGGCGTGTACTGGTTGAGTCACATCGCACAGTATGCTACAAAGAATCTCCATTGTGAATACATATGCCTTGGTTTCCCACCTCTAGAAAAGGTCCTATATCACAGGTATAATCTAGTTGATACTGGACTCGGTCCATTGTCGTCAGTTATTAGACATTTAACTAACCTCCAGGCAGAGATACGAGACTTAGTATTAGATTATACCCTGATGAGAGAGAGTCGCACTCAAACGTACCATTTTATTAAGACTGCAAAAGGCAGAATCACAAAGTTAGTCAATGACTTTCTGAAGTTTTCTTTAATTGTCCAGGCACTCAAAAATAATTCTTCTTGGTATACTGAGCTTAAAAAATTACCTGAGGTGATTAATGTGTGTAATCGATTTTATCATACTCACAGTTGCGAATGTCAGGAAAAATTCTTTGTCCAGACGCTTTATTTACAACGCCTACGCGATGCAGAAATCAAGCTAATTGAACGCCTTACCGGGTTAATGCGATTTTATCCAGAAGGGTTAATATATTCCAATCACACATAGGTACTAAATCATCATAGTATGAGGAATAAAATAATGATAATTCCTGACGACAGTTTTAGTTCCGATTCTAAGTATATCGGAAGAGAGTATGCCAATCTTAATTATTAAAGGTAACAAGCTATTAGTTATTACTTATTGATAAGAATAAACTTTATCATAGCGTAACACATCATAACTTTATAGCGATTTTGCATTTCTAATCCTAGTATTTATTAGAATGTACTATCAGAGAAATGACCCCAGTTCCTATCTTTAAATAATGATTGTGTGTATTAAATTATTAGTTTATTAGGTTTATGAGTTGGTTACACAGTGAGTATTAGTAATTGAGGATTATGTAGATAGGTAATCTAACACTGAATCACCCATCTGATGTCACCATATCCAAATATTGTGCTAGTCGCATTTAAACATGCTATCTTCAGTTAAGTAACATAGACTGAAAATGCTAAGAAGAGATTGGAGTAAAAGTATAAAATAAATTTAATTAAACTTCAAAGTGATTAAATGATAATGATCTTGGGAACTCGATATGACCTCAAGTCAAAAATAATGTCAATATAATTGTTTAGTAATATGAGTTATAATGTGAATTTTGATAACTAACTAGCTTTAGTAGTTAAGATCAAATGCAAACATTCTAAGAATGTTAAGCGCACACAAAAACATTATAAAAAACCAATTTTTTCCTTTTTGTGTGTCC\n>Reston_ebolavirus_isolate_RESTV/Sus-wt/PHL/2009/09A_Farm_A_complete_genome\nCGGACACACAAAAAGAAAAAAGATTTTTTAAGACTTTTTGTGTGCGAGTAACTATGAGGAAGATTAACAGTTTTCCTCAGTTTAAGATATACACTGAAATTGAGATTGAGATTCTCCTCTTTGCTATTCTGTAACTTTCCCTGGTTGTAACAATTGAATCAGTTTTATCTATTACCAATTACCATCAACAAGGTATATCTAGTGATCTTGGGACTCTTCTTCATCTGGTTTTTCCTAGAGCTCTGAATCCATTTTGCGAGAAGTTCATCCAAACGATTCAGTGTCTGAAAATATAAAAGGTTCCCCTTTCCGTCAAGTTTAAGGGGTTGTTTTGATTGTGTGTAGATCTTATAATCCTAGAGTGCCAAGGAGTTGCGTGTCATCATTGATTGGGAAGATCAGGAAAACAATCTATTCCAATAATATCGTACATCTTGACTAAGTTAAACAAGGGGAAGTCGATATGGATCGTGGGACCAGAAGAATCTGGGTGTCGCAAAATCAAGGTGATACTGATTTAGATTATCATAAAATTTTGACAGCTGGCCTCACTGTTCAACAAGGAATTGTCAGGCAGAAAATAATTTCTGTATATCTTGTTGATAACTTGGAGGCTATGTGTCAATTGGTAATACAAGCCTTTGAGGCCGGAATTGATTTCCAAGAAAATGCCGACAGCTTCCTTCTGATGCTTTGCCTACATCATGCTTACCAAGGTGATTATAAATTGTTCTTGGAGAGCAATGCCGTACAGTATTTGGAAGGTCATGGATTCAAATTTGAGCTCCGGAAGAGGGACGGTGTCAATCGGCTCGAGGAATTGCTTCCTGCTGCAACGAGTGGAAAAAACATCAGGCGTACGTTGGCCGCATTGCCTGAAGAGGAGACTACAGAAGCAAATGCAGGGCAATTTCTCTCATTTGCGAGTTTGTTTCTTCCCAAACTGGTTGTGGGAGAAAAGGCTTGCTTGGAAAAAGTCCAGCGACAAATTCAGGTTCATGCAGAACAGGGTTTAATTCAATATCCCACTGCATGGCAATCAGTTGGACACATGATGGTAATCTTTAGATTGATGAGGACTAATTTCTTGATTAAATATTTACTGATCCACCAGGGCATGCATATGGTAGCTGGCCACGATGCCAATGATGCTGTCATTGCTAATTCAGTTGCTCAGGCTCGCTTTTCAGGACTCCTAATTGTCAAAACCGTTCTTGACCATATTCTGCAAAAAACCGACCAAGGAGTAAGACTTCACCCTTTGGCCCGAACAGCCAAAGTGCGTAATGAGGTTAATGCATTTAAGGCCGCCCTAAGCTCACTTGCTAAGCACGGGGAATATGCCCCTTTTGCTCGCCTTCTCAATCTCTCGGGAGTTAACAACCTTGAACATGGTCTCTACCCACAGTTATCAGCAATTGCTCTTGGAGTTGCCACAGCACATGGTAGCACCCTTGCAGGAGTTAATGTTGGTGAGCAGTATCAGCAGCTCAGAGAGGCTGCCACTGAAGCTGAGAAGCAACTCCAACAATATGCTGAGTCCAGAGAACTCGACAGCCTAGGCCTAGACGATCAGGAAAGAAGAATACTAATGAACTTCCATCAGAAGAAAAATGAAATTAGTTTCCAGCAGACCAATGCAATGGTCACCCTTAGGAAAGAGCGACTGGCTAAATTAACAGAAGCTATAACGCTGGCTTCAAGACCTAACCTCGGGTCTAGACAAGACGACGACAATGAAATACCGTTTCCTGGGCCTATAAGCAACAACCCAGACCAAGATCATCTGGAGGATGATCCCATAGACTCCAGAGACACCATCATTCCTAATAGTGCAATTGACCCCGAGGATGGTGATTTTGAAAATTACAATGGCTATCATGATGATGAAGTTGGGACGGCAGGTGACTTGGTCCTGTTCGATCTTGACGATCATGAGGATGACAATAAAGCTTTTGAGCCACAGGACAGCTCACCACAATCCCAAAGGGGAATAGAGAGAGAAAGATTAATTCATCCACCCCTAGGCAACAACAAGGACGACAATCGGGCTTCAGACAACAATCAACAATCAGCAGATTCTGAGGAACAAGAAGATCGATACAACAGGCACCGAGGCCCAGAACGTACGACCGCCAATCGAAGACTCTCACCAGTGTACGAGGAGGACACCCTTATAGATCAAGGCGATGATGATCCCTCAGGCCCACCTCCGCTGGAATCTGATGATGACGATGCATCAAGTAGCCAACAAGATCCAGATTATACAGCTGTTGCCCCTCCTGCTCCTGTATACCGCAGTGCAGAAGCCCACGAGCCTCCCCACAAATCCTCGAACGAGCCAGCTGAAACATCACAATTGAATGAAGACCCTGATATCGGTCAATCAAAGTCTATGCAAAAATTAGAAGAGACATATCACCATCTGCTGAGAACTCAAGGTCCATTTGAAGCCATCAATTATTATCACATGATGAAGGATGAGCCGGTAATATTTAGCACTGATGATGGGAAGGAATACACCTACCCGGATTCACTTGAGGAAGCCTATCCTCCATGGCTCACCGAGAAAGAACGACTGGACAATGAGAATCGATACATTTACATAAATAATCAACAGTTCTTCTGGCCTGTCATGAGTCCCAGAGATAAGTTTCTTGCAATCTTGCAGCACCATCAGTAACCACAGCACAAAGCGCGGTCCACTTCGTAAAGCTAAATACACTTAAGACTTGACCAATTCATCTACAAAAACTAATCCATTATAACTGATTAGTGCTACTTTTCTATAAGTGATTCTTAATCTAAGGCCATTAAGAGTTTAAGCAATATACATATGTACTTACACTGGTTTATCCAAGATGTGGCTCAATGTTCTTAATTTGAACATAGTTATAAGGGGATAAATAATACTTTATATTTCTGATTGTGGATTGACCCATTCTGCTTAAAATGCTTTGCCCGTTAAAAATGTGATCTAATAGATAGCCCTGACTAGCAAAATTAAGAAAAACATTTGATGAAGATTAAAACCTTCATCGCCAGTAAATGATCATATTGTCTGTAGACAGGTGTTTACTCCACCTCAAAGTCGGAAATATCCTACCTTAGGACCATTGTCAAGAGGTGCATAGGCATTACCATCCTTGAGAATATGTACAATAATAAATTGAAGATATGTTCAGGCCCAGAAACGACTGGATGGATTTCTGAGCAACTAATGACAGGTAAGATTCCAGTAACTGATATATTCATTGATATTGATAACAAGCCAGATCAAATGGAAGTCCGACTCAAACCATCATCAAGGAGCTCAACAAGAACTTGTACAAGTAGCAGTCAGACGGAGGCCAACTATGTACCTCTTCTTAAAAAGGTTGAGGATACATTAACTATGCTAGTGAGTGCCACCAGTCGTCAGAATGCTGCAATCGAGGCCCTTGAAAACCGCCTCAGCACACTTGAGAGTAGCTTAAAGCCAATCCAAGACATGGGTAAAGTGATTTCATCATTGAATCGCAGTTGTGCCGAAATGGTGGCAAAATATGATCTTCTAGTTATGACAACTGGACGGGCTACTTCAACTGCAGCTGCAGTAGATGCGTACTGGAAAGAGCACAAACAGCCACCACCAGGGCCAGCATTGTATGAAGAGAATGCGCTAAAAGGAAAAATCGATGATCCAAACAGCTATGTACCAGATGCTGTGCAGGAGGCTTACAAGAACCTTGACAGTACATCGACCCTGACCGAGGAAAATTTTGGGAAACCTTATATATCTGCTAAAGATCTGAAGGAGATCATGTATGATCATCTACCTGGTTTTGGGACTGCCTTTCACCAACTTGTTCAAGTGATTTGTAAAATAGGAAAGGATAACAACCTTTTGGACACAATTCATGCTGAGTTCCAGGCAAGTCTAGCAGATGGTGACTCTCCCCAATGTGCACTCATACAGATAACCAAAAGAGTCCCAATCTTTCAGGATGTGCCGCCCCCGACAATCCACATTAGATCTCGTGGTGATATCCCACGAGCATGCCAAAAGAGTCTCCGACCAGCACCACCATCACCCAAAATTGATCGTGGTTGGGTTTGTTTGTTTAAGATGCAAGATGGTAAAACGCTTGGACTTAAGATCTAAGGATCAAGATTTATTTAACAAGGCAAGCCACAACCTTAGACGGAACCTCAGCCAGACCATTGAACTATTAACGCTGTTGATGATAATATATAATTAATGGTCATATTTGAATATGATAACATCTTGCTTCTTGTTCTGTCTTGTAGCTCTTTGAATTGGAAGATCATTCCAGACGTACAAACATGCACAAGATGTTATGGTTTAGCAAAGAATTGATAGGAGTACTGGTATATAATGTAAATATAACAAGTGATGAAGATTAAGAAAAACCAGTCAGGATTTTCCAGACTTGGCATTTCTTATCTTCATCTTCTAAAGTGAGATACTTTATCATCAAAAAATGAGGCGCGGAGTGTTACCAACGGCTCCCCCAGCATATAATGATATTACATACCCTATGAGCATACTCCCAACCCGACCAAGTGTCATAGTCAATGAGACCAAGTCAGATGTACTGGCAGTGCCAGGGGCAGATGTTCCATCAAACTCCATGAGACCAGTGGCTGATGATAACATTGATCACTCAAGCCATACTCCAAGCGGAGTAGCTTCTGCCTTTATATTAGAAGCTACAGTGAATGTAATTTCGGGAACAAAAGTCCTGATGAAGCAAATACCTATTTGGCTTCCACTGGGTGTAGCCGATCAGAAGATATACAGCTTTGATTCAACAACAGCCGCAATTATGTTGGCTTCCTACACAGTGACACACTTCGGGAAGATATCTAGCCCGCTGGTACGTGTCAACAGGCTAGGCCCAGGAATACCCGATCATCCGCTACGACTCCTAAGGTTGGGCAATCAGGCATTCCTTCAAGAGTTTGTTCTTCCACCAGTCCAGCTTCCCCAGTATTTCACATTTGATCTAACAGCTCTAAAGTTCATCACTCAACCATTGCCAGCTGCAACCTGGACAGACGAAACTCCAGCAGGAGCAGTCAATGTTCTTCGTCCTGGGCTTTCACTCCATCCCAAGCTTCGTCCAATTCTTCTGCCGGGGAAGACAGGAAAGAAAGGGCATGCTTCAGACTTAACATCCCCTGACAAGATTCAAACAATCATGAATGCAATACCGGACCTCAAAATTGTCCCGATTGATCCAACCAAGAACATAGTTGGAATTGAGGTTCCAGAATTGCTAGTTCAAAGGCTGACCGGCAAAAAACCACAACCCAAAAGTGGCCAACCAATTATTCCAGTTCTTCTTCCGAAATATGTTGGACTTGATCCTATATCGCCAGGGGACTTAACCATGGTTATCGCCCAGGATTGTGATTCATGTCACTCTCCAGCCAGCCATCCGTATCACATGGACAAGCAGAATAGTTACCAATAATTTAAATTCCATTCGAGCTATTATTCTGCTAGTAATTCCGACGGGATCAATAGACTAAAAATCTGATTGTGTAAAATTATAAAAGAATCAAGCAGAGGCAACAGACCCACAGCTTAAGCCTAGATAACTAATATTAAGGAGTCCTTTAATCGAATTTTCCAGTCTTAAGTAATAATCATTTCTTTTGTAATTAATTATGAATTTGTTAGCTTATCGGTGCGAGATTCCCTTGAGAACCCGGCGGAGCTTCTACTATCTGCAGTAACCAGAGGAGAAGTTCAACCTAGTCAAAACTAAACCAAGCAATATTCTGGATGCTCTATAGTCTATTCTAATCAGAGGTATAACAATGGCTAAGATTTCAATGACTCGTTAACAATCGCTAGTGATTTTAATCTTCAGATTAAGAAAAAGATATACGATGAAGATTAAGGCGACAACGAGCCGAAACTTCATCTCTTTTAAATATCTAACATTACCCGTTCCAAAGTCATACAAGGACACATTCAAATCAGGGATTGTAAGCTGCTATTTCTTACCTCCCCAAATTACCTATACAACATGGGGTCAGGGTATCAACTTCTCCAATTGCCTCGGGGACGTTTTCGTCAAACTTCGCTCTTAGTATGGGTAATCATCCTCTTCCAGCGAGCAATCTCCATGCCGCTTGGTATAGTGACAAATAGCACTCTCAAAGCAACAGAAATTGATCAATTGGTTTGTCGGGACAAACTGTCATCAACCAGTCAGCTCAAGTCCGTGGGGCTGAATCTGGAAGGAAATGGAATTGCTACCGATGTCCCATCAGCAACAAAACGCTGGGGATTTCGTTCAGGTGTGCCTCCCAAGGTGGTCAGCTATGAAGCTGGAGAATGGGCAGAAAATTGCTACAATCTGGAGATCAAAAAGTCAGACGGAAGTGAATGCCTCCCTCTCCCCCCCGACGGTGTACGAGGATTCCCTAGATGTCGCTATGTCCACAAAGTTCAAGGAACAGGTCCTTGTCCCGGTGACTTAGCTTTCCATAAAAATGGGGCTTTTTTCTTGTATGATAGATTGGCATCAACTGTCATCTACCGTGGGACAACTTTTGCTGAAGGTGTCGTAGCTTTTTTAATTCTGTCAGAGCCCAAGAAGCATTTTTGGAAGGCTACACCAGCTCATGAACCGGTGAACACAACAGATGATTCCACAAGCTACTACATGACTCTGACACTCAGCTACGAGATGTCAAATTTTGGGGGCGAGGAAAGTAACACCCTTTTTAAGGTAGACAACCACACATATGTGCAACTAGATCGTCCACACACTCCGCAGTTCCTTGTTCAGCTCAATGAAACACTTCGAAGAAATAATCGCCTTGGCAACAGTACAGGGAGATTGACTTGGACATTGGATCCTAAAATTGAACCAGATGTTGGTGAGTGGGCCTTCTGGGAAACTAAAAAAACTTTTCCCAACAACTTCATGGAGAAAAATTGCATTTCCAAATTCTATCAACCCACACCAACAACTCCTCAGATCAGAGCCCAGCGGGAACTGTCCAAGGAAAAATTGGCTTCCACCCACCCACCAACAACTCCGAACTGGTTCCAACGGATTCCTCTCCAGTGGTTTCAGTGCTCACTGCAGGACGGACAGAGGAAATGTCGACCCAAGGTCCAACCAACGGAGAGACAATCACAGGTTTCACCGCGAACCCAATGACAACCACCATTGCCCCAAGTCCAACCATGACAAGCGAGGTTGATAACAATGTACCAAGTGAACAACCGAACAGCACAGCATCCATTGAAAACTCCCCCCCATCGGCGAGCAACGGGACAATCAACCGCCCCGAGATGAATCCGACCCAAGGACCGAACAACTCCGCCCAGAGCCCACAGACCAAGACCACGCCAGCACCCACAGCATCCCCGACGACCCAGGACCCGCAAGAAACGACCAACAGCAGCAAACCAGGAACCAGCCCAGGAAGCACAGCCGAACCAAGTCAGCCCGGATTCACCACAAATACAGTAAGTAAGGTAGCTGATTCAGTGAGTACCACCAGGAAACAAAAGCGATCGATTCGCCAAAACACCGCTAACAAATGTAACCCAGATCTTCACTATTGGACAGCTGTTGATGAGGGCGCAGCAGTAGGATTGGCATGGATTCCATATTTTGGACCTGCAGCAGAAGGCATCTACATTGAGGGTGTAATGCATAATCAGAATGGGCTTATTTGCGGGCTACGTCAGCTAGCCAATGAAACTACTCAGGCTCTTCAATTGTTTCTGCGGGCCACAACAGAACTGAGGACTTACTCACTTCTTAATAGAAAAGCTATTGATTTTCTTCTTCAACGATGGGGAGGTACCTGTCGAATCCTAGGACCATCTTGTTGTATTGAGCCACATGATTGGACAAAAAATATTACTGATGAAATTAACCAAATTAAACATGACTTTATTGACAATCCCCTACCAGACCACGGAGATGATCTTAATCTATGGACAGGTTGGAGACAATGGATCCCGGCTGGAATTGGGATTATTGGAGTTATAATTGCTATAATAGCCCTACTTTGTATATGTAAGATTTTGTGTTGATTTATTCTGAGATCTGAGAGAGAAAAATCTCAGGGTTACTCCAAGGAGAAATATTATCTCTAAGGTTTACTTGAATGCTGACCACTTATCTTAAATGAGCAACTAATAATATGTTTTTCTGCTTCTTAGCTTGATTCACAATATAATATTTCTCTTAATAATGATTAATATATTAAGAAAAACTTATGATGAAGATTAAAGGGGAGGATCGCTAACGTGAAAATCTCCCATCTCGCTTGTCGAAGCCACGTTGGTGGTGCTTGCAGCTGAGAACAACTCCAGAGATTGTAGGTAGAAAGGACCAGCATTTATAGGTAGGGGTCAGAAAGCAACAATAACCATAAAAGGAGAGCCTGACATTGCTATTTAGTATCCTAGAACCTGATTTCTAGGTTCTAGTTGTACAATCCGGATGATGGAGCATTCAAGAGAACGGGGTAGATCTAGCAACATGCGACATAATAGCCGGGAACCATACGAAAATCCATCAAGGTCTCGCTCATTATCTCGGGACCCTAATCAGGTTGATCGTAGGCAGCCTCGAAGTGCATCCCAAATTCGTGTTCCGAATCTGTTCCATCGGAAAAAGACTGATACGCTCATAGTTCCTCCGGCTCCTAAGGATATATGCCCAACACTCAAAAAAGGATTCCTCTGCGATAGTAAATTTTGCAAAAAAGACCACCAATTGGATAGCTTAAATGATCATGAATTACTACTGCTAATTGCAAGAAGAACATGTGGAATTATCGAGAGCAATTCGCAGATCACATCCCCAAAAGATATGCGGTTAGCGAATCCAACAGCTGAAGACTTCTCACAAGGTAATAGTCCTAAATTAACACTTGCAGTCCTTCTTCAAATTGCTGAACATTGGGCAACCAGAGACCTAAGGCAAATTGAGGACTCTAAACTTAGAGCTCTTTTAACCCTTTGTGCCGTATTAACAAGGAAATTTTCTAAATCCCAACTGGGTCTTCTATGTGAGACCCACCTACGGCATGAGGGCCTCGGACAGGACCAAGCTGATTCTGTATTAGAGGTCTACCAAAGACTCCACAGTGATAAAGGAGGGAATTTTGAGGCTGCCTTGTGGCAACAATGGGACCGACAGTCATTAATAATGTTCATCTCTGCTTTTCTCAACATTGCTCTCCAGACACCTTGTGAAAGTTCTAGTGTCGTAGTCTCAGGTCTTGCCACATTGTACCCAGCACAAGACAATTCTACACCATCCGAGGCAACTAATGATACCACTTAGTCAAGTACAGTTGAATAGAAAACCATTAGAGCTATTTTTCCACGATTGCTCTCAGTCAATAAATTAATATAGATATAATACGACTTCGGTGTGCAATTGTCAAGGGTTCCATTTAGTAATAATGATCCTTAAAACAGTCTACTATCGCAATTATCGATGGATTTACCCTATTTGACGGTACATGACTTGAATGCAATAAGGTAAGTTGGTATTTGAGGTATTTTGTCTAGGGTATACTCAAAGTCGTATGTCTAGCAAATTATCAATAGCAAAGTTAAATTCTCATAACCTCATATTTTGATTAAGTAATCATGATTTTATGATAACCCTTTGCAGATTATCAGTTTAATCTTTATTAAGAAAAAATCATGATTGTAGACAATTTACTGGTAGTCCTTGGGTATCCAAGTTTATGAACAGAGCTAGAGAGAATTTGCTACTTCCGAGGTATAACTTTATTATTTGCTACTTCGAATGCCTAAGACCAGTAATGCAGGATGAAGATTAATTGCGGAGGAATCAGGAATTCAACCTTAGTTCCTTAAGGCCTCGTCTGAATCTTCATCAGTTAGTAAGTTCTTTTATAGAAGTCATTAGCTTCTAAGGTGATTATATTTTAGTATTAAATTTTGTTAATTGCTTGCTATAAAGTTGAAATGTCTAATGCTTAAATGAACATTTTTGAAGCTGACATACGACTACATCATATCATATGAAAACATCGTAATTAGAGCGTCCTTGAAGTCTGGCATTGACAGTTACCAGGCTGTTCTCAGTAGTCTGTCCTTGGAAGCTCTTGGGGAGACAAAAGAGGTCCCAGAGAGTCCCAACAGGTTGGCATAAGGTCATTAACACCAGCATAGTCGGCTCGATCAAGACTGTAAGCGAGTCGATTTCAACTAAAAAGATTATTTCTTGTTGTCTAAACAAATTCCTTTGTGTGAGACATCTTCAAGGCACAAGATGGCTAAAGCCACAGGCCGATACAATCTCGTGCCCCCAAAGAAAGATATGGAAAAGGGAGTGATTTTTAGTGATCTTTGTAATTTCTTGATTACTCAAACCCTGCAAGGTTGGAAGGTTTATTGGGCAGGAATTGAGTTTGATGTAAGTCAAAAAGGCATGGCTCTTCTGACAAGACTCAAAACAAATGACTTTGCTCCTGCCTGGGCGATGACAAGAAATCTTTTCCCACATCTGTTCCAAAACCCAAATTCGGTTATTCAATCTCCCATCTGGGCTTTGAGGGTAATTTTGGCAGCCGGATTGCAGGATCAGTTGTTAGACCATTCATTGGTTGAGCCCTTGACAGGGGCTCTCGGTCTAATTTCTGATTGGCTCCTAACTACAACGTCAACACATTTCAATCTTCGTACTAGAAGCGTAAAGGACCAGCTTAGTCTTCGTATGTTATCTTTGATTAGGTCAAACATCTTGCAGTTCATCAACAAGCTTGACGCCCTGCATGTTGTCAATTACAATGGTTTACTCAGTAGTATTGAGATCGGGACCTCTACACACACAATCATTATAACTCGTACAAACATGGGTTTTCTCGTGGAAGTTCAGGAGCCTGACAAATCAGCTATGAATTCTAAGCGCCCAGGACCAGTCAAGTTCTCATTACTTCATGAGTCTGCCTTCAAACCTTTCACTCGTGTTCAACAATCTGGGATGCAATCATTAATAATGGAGTTCAACAGTTTGTTGGCGATTTAACAAGGTGATCTTAAAATAAGTACATGAATGAGAATTAGTTGTGGGTCTTGCCTAGCATTGTTGAGTTAGCTATCTAATCTATTTTCGCTAATTACATTGAACACTGTTAATAGGTTTGTATCACGTTAAAGATTTAGAGTGTATGAATTGTGCAGATTTAAACCTGGGTTTTGCCTTATGCTTCATAGGTGGCCTTTTTGAAATGGGGATTATCAGCATTTCTTCAATAGGAGGAGTTAGCAATCAGGAATTGAAGAGAAATGGACATCGGGATAGAACGATGCTTAACTATTGGGCAGCTTCCATTTTTACATGTGTGTATAACCAATCTTTTCCTATCTTTGCTTATATTGGTGTAACTTTATTTTAATAACATGTCAATGCTATACTGTTAAGAGAAAGTCTGAGGAAGATTAAGAAAAAGGCCTCGTGTTCACTTGGTTGCTGTCAAGTATCCTGTGGTTTTTTTCTACCTAACTTCCTCATGCCATATGGCTACCCAGCATACCCAGTACCCGGATGCACGCTTATCTTCACCTATAGTCCTGGATCAATGTGATTTGGTAACTCGAGCATGTGGGTTATATTCATCTTATTCTCTAAATCCTCAACTAAGGCAATGTAAATTACCAAAACATATATATCGACTTAAGTTCGACACAATAGTATCCAAATTCCTAAGTGATACACCTGTAGCAACACTGCCGATAGACTATTTAGTACCAATTCTCCTGCGTTCCCTAACGGGGCACGGTGATAGGCCGTTGACCCCGACTTGCAATCAATTCCTTGATGAAATTATTAATTACACTCTTCATGATGCAGCCTTTCTTGATTACTATCTCAAGGCAACAGGCGCACAGGACCGTTTGACAAACATTACAACTAGAGAGAAGCTTAAAAACGAGATTTTAAACAATGATTATGTCCATCAATTGTTCTTCTGGCATGACCTTTCTATTTTGGCTCGACGTGGGCGTCTGAATCGCGGGAACAACCGTTCAACCTGGTTTGTTCATGATGAATTCATTGATATTTTAGGATATGGCGATTATATTTTTTGGAAAATACCTTTATCATTATTACCGGTTACTATAGACGGGGTCCCACACGCAGCAACTGACTGGTATCAACCGACTCTTTTTAAAGAATCCATCCTAGGGCACAGCCAAATCCTATCTGTGTCAACAGCTGAAATATTAATTATGTGTAAAGATATTATCACCTGTAGGTTTAATACATCACTGATTGCATCCATTGCAAAATTAGAAGATGTAGATGTGTCTGATTATCCTGACCCGAGTGATATTCTTAAGATATACAATGCTGGAGACTATGTAATATCTATTCTCGGCTCAGAGGGTTATAAGATAATAAAGTACCTTGAACCACTTTGTTTGGCCAAAATCCAACTTTGCTCTAAATTCACAGAAAGAAAAGGTCGTTTCCTCACACAGATGCATTTATCAGTAATAAATGATCTTCGGGAGTTGATTTCTAACCGCAGGTTAAAGGACTATCAGCGAGAGAAGATTAGGGATTTTCACAAAATATTATTACAATTGCAATTATCTCCTCAACAGTTTTGTGAATTATTCTCTGTTCAAAAACATTGGGGGCATCCAATTTTGCATAGTGAGAAAGCTATACAAAAAGTAAAACGGCATGCAACCATCCTTAAGGCTCTCAGACCTAATGTCATCTTTGAAACATACTGTGTATTCAAGTACAATATTGCCAAGCACTATTTCGACAGCCAAGGAACTTGGTACAGTGTGATCTCAGACAGGAATTTAACTCCAGGACTCAATTCCTTTATAAAACGTAATCACTTTCCTTCACTACCCATGATTAAGGATCTTCTATGGGAATTCTATCATCTTAATCACCCTCCGTTATTCTCTACAAAGGTGATTAGTGACTTAAGTATTTTCATCAAGGATAGGGCCACTGCTGTTGAACAGACATGTTGGGATGCAGTCTTTGAACCCAATGTGCTAGGTTACAATCCTCCAAACAAATTCTCCACTAAAAGGGTGCCGGAACAATTTCTAGAACAAGAGGATTTTTCAATCGAAAGTGTCCTGAATTATGCACAGGAATTACATTATTTATTACCACAGAATAGGAATTTTTCTTTTTCTCTTAAAGAAAAAGAATTAAATATTGGGCGAACATTTGGGAAGCTACCATATCTCACACGGAATGTCCAAACTTTATGTGAGGCCCTGTTAGCAGATGGACTGGCCAAGGCCTTCCCCAGTAACATGATGGTAGTAACTGAACGTGAACAAAAGGAGAGCCTTCTTCATCAGGCATCATGGCACCACACCAGTGATGATTTTGGAGAGAATGCTACCGTTCGAGGGAGTAGTTTTGTAACTGATTTAGAGAAGTACAATCTTGCATTTCGCTATGAGTTCACTGCACCATTTATTGAGTACTGCAACCATTGCTATGGTGTGCGTAATGTCTTTAATTGGATGCATTATTTAATCCCGCAGTGTTACATGCATGTAAGTGATTATTATAATCCGCCTCACAATGTTAATCTTAGCAATCGAGAATATCCTCCTGAAGGCCCGAGTTCGTACCGAGGGCACTTAGGAGGCATAGAGGGCTTACAACAAAAACTGTGGACGAGTATATCCTGTGCACAAATCTCCTTGGTGGAAATTAAAACTGGTTTTAAGTTACGATCAGCGGTCATGGGAGACAATCAGTGTATAACTGTATTATCTGTTTTTCCACTTGAAACAGATCCTGAAGAGCAGGAGCAAAGCGCCGAAGACAATGCTGCAAGAGTAGCAGCAAGTCTTGCAAAAGTAACCAGTGCATGTGGGATCTTTCTTAAACCAGAAGAGACATTTGTACACTCAGGTTTCATTTATTTCGGAAAAAAACAATATCTCAATGGTGTACAATTACCGCAATCACTCAAAACAGCAGCAAGAATGGCACCACTCTCTGATGCTATATTCGATGATCTACAAGGAACACTTGCCAGTATTGGAACTGCCTTCGAACGTGCTATATCGGAAACGCGACATATCCTCCCATGTCGTATTGTAGCAGCTTTCCATACGTATTTCGCCGTTCGGATTTTACAATATCACCATCTTGGATTTAATAAAGGCATCGATTTAGGACAGTTGTCACTTAGTAAACCATTAGACTATGGGACTATTACTCTAACATTGGCGGTTCCACAAGTCCTTGGGGGATTGTCTTTTCTAAATCCAGAAAAGTGTTTTTATCGGAACTTCGGAGATCCTGTGACTTCTGGACTTTTCCAGCTACGGGTGTACTTAGAAATGGTTAACATGAAAGACCTATTTTGTCCATTAATATCGAAAAATCCAGGAAATTGTAGTGCCATTGATTTTGTCTTAAATCCATCCGGATTAAATGTTCCAGGATCACAAGACTTGACATCCTTTTTGCGACAGATCGTTAGGCGTAGTATTACACTAACTGCAAGAAATAAGTTAATTAACACTCTCTTCCATGCCTCTGCTGATTTGGAAGATGAGATGGTTTGTAAATGGCTCCTTTCATCAAACCCTGTCATGAGTCGCTTTGCAGCGGATATTTTTTCCAGGACACCTAGTGGTAAACGTCTCCAAATATTAGGTTATCTTGAAGGGACCCGGACTCTATTGGCCTCCAAAATCATAAACAACAACAGTGAGACACCTGTACTCGATAAGCTGAGGAAGATCACCCTACAAAGATGGAATCTGTGGTTCAGTTATTTGGACCATTGTGACCAATTACTAGCAGATGCTCTACAAAAAATTAGTTGCACGGTGGATTTGGCCCAGATTTTGCGTGAGTATACATGGTCACACATCTTAGAGGGTAGACCATTGATCGGAGCGACATTACCATGTATGGTGGAGCAATTCAAAGTTAAGTGGCTAGGACAATATGAACCTTGTCCAGAATGTCTCAACAAAAAAGGCTCAAATGCTTATGTCTCAGTTGCAGTCAAAGATCAAGTGGTCAGTGCTTGGCCTAATACTTCTCGAATAAGTTGGACAATAGGGAGTGGTGTCCCCTATATAGGGTCAAGAACCGAGGATAAAATCGGACAGCCTGCTATCAAGCCGCGATGCCCTTCATCTGCCCTCAAGGAGGCTATAGAATTAGCATCAAGGCTCACTTGGGTTACACAAGGGAGTTCTAATAGTGAACAATTAATCCGACCTTTCTTAGAAGCGAGAGTCAACCTTAGTGTCAACGAAGTCCTGCAAATGACACCATCACATTATTCAGGAAATATTGTCCATCGATATAATGACCAATATAGCCCGCACTCATTTATGGCGAATCGCATGAGCAATACTGCAACCCGTCTCATAGTGTCAACTAATACACTTGGAGAATTTTCAGGTGGAGGGCAGGCTGCCAGGGACAGCAATATAATTTTCCAGAATGTTATAAATTTAGCAGTTGCCCTTTATGATATTAGATTCCGGAATACGAACACCTCTGATATAAAGCATAATAGGGCTCATCTTCACCTGACAGAGTGCTGTACTAAAGAGGTCCCGGCCCAGTATTTAACATATACAAGTGCACTTAATCTGGATTTAAGCCGTTACCGTGATAATGAACTAATATATGACTCAAATCCACTGAGGGGAGGATTGAACTGCAATTTAACAATGGATAGTCCTTTAGTGAAGGGTCCTAGGCTTAACATGATTGAAGATGATCTTCTCCGCTTTCCACACCTTTCTGGATGGGAGTTAGCGAAAACGGTGGTGCAATCCATCATCTCGGACAATAGCAACTCATCAACAGATCCAATCAGTAGTGGAGAAACACGCTCTTTCACAACTCATTTTCTCACTTATCCTCAGATTGGTCTCCTTTACAGTTTCGGGGCAGTATTATGCTTTTATCTAGGCAATACTATCCTATGGACTAAAAAACTTGATTATGAACAGTTTCTATATTATTTGCATAACCAGCTGCACAACTTACCTCACCGAGCACTCCGTGTTTTTAAACCAACATTTAAGCATGCCAGTGTGATGTCCCGACTAATGGAAATTGACTCCAACTTCTCAATTTATATTGGCGGGACATCTGGAGATCGAGGGTTGTCTGATGCTGCTCGATTGTTTCTTCGGACAGCAATCGCGGGTTTTTTACAATTTCTTAAGAGCTGGATCATCGATCGCCAAAAAACAATCCCTTTATGGATAGTATATCCGCTTGAAGGTCAACAGCCGGAACCCATCAATGAATTTCTACATAAAATTTTAGGTCTGCTCAAACAAGGCCCCAAAAGTATTCCAAAGGAGGTCAGCATTCAAAATGATGGACATTTGGATTTGGCAGAAAATAATTATGTTTACAGTAGTAAGAGCACTGCTAGTAATTTCTTCCATGCATCCTTAGCTTACTGGAGAAGTAGGAAATCTCGGAAAACTCAAGACCATAATGATTTCTCAAGAGGGAATGGAACACTTACAGAACCCGTGCGTAAGTTATCAAGCAATCAACAGTCAGATGAAAAGTACTACAGTGTAACATGTGGAAAGTCACCGAAGCCGCAAGAACGCAAAGACTTCTCGCAATACAGACTCAGCAATAACGGGCAAACAATGAGTAATCATCGTAAGAAAGGGAAGTTCCACAAGTGGAATCCCTGCAAAGTGTTAATGGAGAATCAAAGGGGAACTGTTCTAACAGAGGGTGACTACTTTCAAGACAATACTCCACCAACAGATGTTGTATCAAGTCCTCATCGACTCATTCTACCATTTTTCAAATTGGGAAATCACAACCATGCAAATGATCAAGATGCCCAAGAATTGATAAATCAAAATATTAAACAGTACCTACACCAGATAAGGTCTATGTTGGACACCACTATATATTGTAGATTCACAGGGATTGTCTCATCCATGCATTACAAATTGGACGAAGTTCTTCTAGAATACAATAGTTTCGATTCAGCTATCACATTAGCTGAAGGTGAGGGGTCAGGGGCTCTATTACTTTTGCAAAAATATAGTACAAGGTTGTTGTTTTTGAACACATTGGCAACAGAACACAGTATAGAGTCAGAGGTTGTATCAGGTTTTTCTACTCCGAGAATGTTGTTACCAATAATGCAAAAGGTTCATGAAGGACAAATCACTGTTATCTTAAATAATTCGGCAAGTCAGATAACTGACATAACTAGCTCAAAGTGGTTAAGTAATCAAAAATATAATCTACCTTGTCAAGTTGAAATCATTACGATGGATGCTGAAACAACAGAGAACTTAAACAGGTCCCAACTCTACCGAGCAGTATATAACTTAATACTTGATCACATTGATCCGCAGTATCTCAAGGTGGTGGTACTCAAAGTATTCCTGAGTGATATAGAAGGAATATTATGGATTAATGATTACTTGGCTCCATTATTCGGGGCTGGTTACTTGATTAAACCGATTACATCAAGTGCCCGGTCAAGTGAATGGTACCTTTGCTTATCAAATTTGATATCTACTAACAGGAGATCGGCCCATCAGACTCACAAGGCATGTCTTGGTGTTATCAGGGATGCTTTGCAAGCACAAGTCCAGCGAGGCGTGTACTGGTTGAGTCACATCGCACAGTATACTACAAGGAATCTCCATTGTGAATACATATGCCTTGGTTTCCCACCTCTAGAAAAGGTCCTATATCACAGGTATAATCTAGTTGATACTGGACTTGGTCCATTGTCGTCAGTTACTAGACATTTAACTAACCTCCAGGCAGAGATACGAGACTTAGTATTAGATTATACCCTGATGAGAGAGAGTCGCACTCAAACGTACCATTTTATTAAGACTGCAAAAGGCAGAATCACAAAGTTGGTCAATGACTTTCTGAAGTTTTCTTTAATTGTCCAGGCACTCAAAAATAATTCTTCCTGGTATACTGAGCTTAAAAAATTACCCGAGGTGATTAATGTGTGTAATCGATTTTATCATACTCACAGTTGCGAATGTCAGGAAAAATTCTTTGTCCAGACGCTTTATTTACAGCGCCTACGCGATGCAGAAATCAAGCTAATTGAACGCCTTACCGGGTTAATGCGATTTTATCCAGAAGGGTTAATATGTTCCAACCATACATAGGTACTAGATCATCATAGTATGAGGAATAAAATAATGATAATCCCTGACGACAGTTTTAGTTCCGATTCTAAGTATATCGGAAGAGAGTATGCCAATTTAAATTATTAAAGGTAACAAGCTATTAGTTATTACTTATTGATAAGAATAAACTTTATCATAGTGTAACACATCATAACTTTATGACGATTTTGCATTTCTAATCCTAGTATTTATTAGAATGTACTATCAGAGAAATGACCCCAGTTCCTATCTTTAAATAATAATTGTGTGTATTAAGTTGTTAGTTTATTAAGTTTATGAGTTGGTTACACAGTGAGTATTAGTAATTGAGGATTAGGTAGATAGGTAATCTAACACTGAATCACCCATCTGATGTAACCATATCCAAATATTGTGCTAGTCGCATTTAAACATGCTATCTTCAGTTAAGTAACATAGACTGAAAATGCTGAGAAGAGTTTGGAGTAAAAGTATAAAATAAATTTAATTAAACTTCAAAGTGCTTAAATGATAAAGATCTTGGGAACTCGATATAACCTCAAATCAAAAATAATGTCAATATAATTGTTTAGTAATATGAGTGATAATGTGAATTTTGATAACTAACTAGCTTTCGTAGTTAAGATCAAATGCAAACATTATAAGAATGTTAAGCGCACACAAAAACATTATAAAAAACCAATTTTTTCCTTTTTGTGTGTCC\n>Reston_ebolavirus_-_Reston_strain_Reston08-C_complete_genome\nCGGACACACAAAAAGAAAAAAGGTTTTTTAAGATTTTTTGTGTGCGAGTAACTATGAGGAAGATTAACAGTTCTCCTCAGTTTAAGATATACACTGAAATTGAGATTGAGATTCTCCTCTTTGCTATTCTGTCACTTTCCCTGGTTGTGACGATTGAGCCAGTTTTATCTATTACCAATTACCGTCAACATGGTATGTCTAGTGGTCTTGGGACTCTTCTTCATCTGGTGTTTCCTAGAGCTCTGAATCGATTTTGCGAGAAGTTCATCCGAATGACCCAGTGTCTGAAAATACAAAAGGTTCCCCTTTCCGTCAAGTTTAAGGGGTTGTTTTGATTGTGTGTAGATTTTATAATCCTAGAGTGCCAAGGAGTTGCGTGTCATCATTGATTGGGAAGATCAAGGAAACAATTTGTTCCAATAATATCATACATCTTGACTAAGTCGAACAAGGGGAATTCGATATGGATCGTGGGACCAGAAGAATCTGGGTGTCGCAGAATCAAGGTGATACTGATGTAGATTATCATAAAATTCTGACAGCTGGCCTTACTGTTCAACAGGGAATTGTCAGGCAGAAAATAATTTCTGTATATCTTGTTGATAACTTGGAGGCTATGTGCCAATTGGTAATACAAGCCTTTGAGGCCGGAATTGATTTCCAAGAAAATGCCGACAGCTTCCTTCTGATGCTTTGCCTACATCATGCTTACCAAGGTGACTATAAATTGTTCTTGGAGAGCAATGCTGTACAGTATTTGGAAGGTCATGGATTCAAATTTGAGCTCCGGAAGAAGGACGGTGTCAATCGACTCGAGGAATTGCTTCCTGCTGCAACGAGTGGAAAAAACATCAGGCGTACGTTGGCTGCACTGCCTGAAGAGGAGACTACAGAAGCAAATGCAGGGCAATTTCTCTCATTTGCGAGTTTGTTTCTTCCCAAACTGGTTGTGGGAGAGAAGGCTTGCTTGGAAAAAGTCCAGCGACAAATTCAGGTTCATGCAGAACAAGGTTTAATTCAATATCCTACTGCATGGCAATCAGTTGGACACATGATGGTAATCTTCAGATTGATGAGGACTAATTTCTTGATTAAATATTTACTGATCCACCAGGGTATGCATATGGTAGCTGGCCACGATGCCAATGATGCTGTCATTGCTAATTCAGTTGCTCAGGCTCGCTTTTCAGGACTCCTAATTGTCAAGACCGTTCTTGATCATATTCTGCAAAAAACCGACCAAGGAGTAAGACTTCACCCTTTGGCCCGAACAGCCAAAGTACGCAATGAGGTTAATGCATTTAAGGCCGCCCTAAGCTCACTTGCTAAGCATGGAGAATATGCCCCTTTTGCTCGCCTTCTCAATCTCTCGGGAGTTAACAACCTAGAACATGGTCTCTACCCACAGTTATCAGCAATTGCTCTTGGAGTTGCCACAGCACATGGTAGCACCCTTGCAGGAGTTAATGTTGGTGAGCAGTATCAGCAGCTTAGAGAGGCTGCAACTGAAGCTGAGAAGCAACTCCAACAATATGCTGAGTCCAGAGAACTCGACAGCCTAGGCCTGGACGATCAGGAAAGAAGGATACTAATGAACTTCCATCAGAAGAAAAATGAAATTAGTTTCCAGCAGACCAATGCAATGGTAACCCTTAGGAAAGAGCGACTGGCTAAATTAACAGAAGCTATAACGCTGGCCTCAAGACCTAACCTCGGGTCTAGACAAGATGACGACAATGAAATACCGTTCCTTGGGCCTATAAACAACAACCCAGACCGAGATCATCTGGAGGATGATCCTAGAAACTCCAGAGACACCATCATTCCTAGTGGTGCAATTGACCCTGAGGATGGTGATTTTGAGAATTACAATGGCTATCATGATGATGAAGTTGGGACGGCAGGTGACTTGGTCCTGTTCGATCTTGACGATCATGAGGATGACAATAAAGCTTTTGAGCCACAGGACAGCTCACCGCAATCCCGAAGGGAAATAGAAAGAGAAAGATTAATTCATCCACCCCCGAGCAACAACAAGGACGACAATCGGGTCTCAGCCAACAATCAACAATCAGCAAGTTTTGAGGAACAAGAAGATCAATACAACAGGCACCGAGGCCCAGAACGTACGACCGCCCATCGAAGACTCTCACCAGTGTACGAAGAGGACACCCTTATGGATCACGGCGATGATGATCCCTCAAGCTTACCTTCGCTGGAATCTGATGATGACGATGCATCAAGTAGCCAACAAGATCCCGATTATACAGCTGTTGCCCCTCCTGCTCCTGTATACCGCAGTGCAGAAGCCCACGAGCCTCCTCATAACTCCTCGAACGAGCCAGCTGAAACATCACAACTGAATGAAGACCCTGATATCGGTCAATCAAAGCCTATGCAAAAATTAGAAGAGACATATCACCATCTGCTGAGGACTCAAGGTCCATTTGAGGCCATCAGTTATTATCACATGATGAAGGATGAGCCGGTAATATTTAGCACTAATGATGGGAAGGAATACACCTACCCGGATTCACTTGAGGAAGCCTATCCTCCATGGCTCACCGAGAAAGAACGACTGGACAAAGAGAATCAATACATTTACATAAATAATCAACAGTTCTTCTGGCCTGTAATGAGCTTCAGAGACAAATTTCTTGCAATCTTGCAGCACCATCAGTGACCACAGCACAAAGCGCGGTCCACTTCGTAAAGCTAAATACACTCAAGACTTGACCGACTCATCTACAAGAACTAATCCATTATAACTTGTTAGTACTACCTTTCTATAAGTGATTCTTGATTTAAGGCCATTAAGAGTTTAAATAATATACATATACACTTACACCGGTCTATCCAAGATGTGGCTCAATGTTCTTAATTTGAACATAGTCATAAGGAAATAAATGATACTTTCTGTTTCTGATTGTAGATTGACTCATTCTGCTTAAAACGCTTCGCCCATTGAAAATGTGATCTAATAGATAGCCCTAACTAGACAAATTAAGAAAAACATTTGATGAAGATTAAAACCTTCATCACCAGTAAATGATTATATTGTCTGTAGGCAGGTGTTTACTCCACCTTAAATTTGGAAATATCCTGCCTTAGGACCATTGTTAAGAGGTGCACAGGCATTACCATCCTTGAGAACATGTACAATAATAAATTGAAGATATGTTCAGGCCCAGAAACGACTGGATGGATTTCTGAGCAACTTATGACAGGTAAGATTCCAGTAACTGATATATTCACTGATATTGATAACAAGCTAGATCAAATGGAAGTTCGACTCAAACCATCAGCAAGGAGCTCAACAAGAACTTGTACAAGTRGCAGTCAGACGGAGGTCAACTATGTACCTCTCCTTAAAAAGGTTGAGGATACATTAACTATGCTAGTGAATGCCACCAGTCGTCAAAATGCTGCAATTGAGGCCCTTGAAAACCGCCTCAGCACACTTGAGAGTAGCTTAAAGCCAATCCAAGACATGGGTAAAGTGATTTCATCATTGAATCGCAGTTGCGCCGAAATGGTTGCAAAATATGATCTTTTAGTTATGACAACTGGACGGGCTACTTCAACTGCAGCTGCAGTAGATGCGTATTGGAAAGAGCACAAACAGCCACCACCAGGGCCAGCACTGTACGAAGAGAATGCGCTTAAAGGAAAAATTGATGATCCAAACAGCTATGTACCAGATGCTGTGCAGGAGGCTTACAAGAATCTTGACAGTACATCGACCCTGACCGAGGAAAATTTTGGGAAACCTTATATATCTGCCAAAGACCTGAAGGAAATCATGTATGATCATCTACCTGGTTTTGGGACTGCCTTTCACCAACTTGTTCAAGTGATTTGTAAAATAGGAAAGGATAACAATCTTTTGGACACAATCCATGCTGAGTTCCAGGCAAGTCTAGCAGATGGTGACTCTCCCCAATGTGCACTCATACAGATAACCAAAAGAGTCCCAATCTTTCAGGATGTGCCGCCCCCGACAATCCACATTAGATCTCGTGGTGATATCCCACGAGCATGCCAAAAGAGCCTCCGACCAGCACCACCATCACCCAAAATTGATCGTGGTTGGGTTTGTTTGTTTAAGATGCAAGATGGTAAAACGCTAGGACTTAAGATCTAAGAATCGAGATTTATTTAACAAGACAAGCCACAACCTTAGATGAAGCCCCAGCCAGACCATTGAACCATTGACGCTGTTGATGATAATATATAATAAATGGTCATATTTGAATATGACAACATCTTGCTTCTTGTTCTGCCTTGTAGCTCTTTGAATTGGAAGACCATTCCAAACTTACAAACATGCACAAGATGTTATGGTTTAGCAAAGAATTGATAAGAGTACCGGTATATAATGTAAATATAACAAGTGAAGAAGATTAAGAAAAACCAGTCTGTATTTTCCAGACTTGGCATTTCTTATCTTCATCTTCGAAAGTGAGATATTTTATCATCAAAAAATGAAGCGCGGAGTGTTACCGACGGCTCCTCCAGCATATAATGATATTGCATACCCTGTGAGCATACTCCCAACCCGACCAAGTGTCATAATCAATGAGACCAAATCAGATGTACTGGCAGTGCCAGGGGCAGATGTTCCATCAAACTCCATGAGACCAGTGGCTGATGATAACATTGATCACTCAAGCCATACTCCAAGCGGAGTAGCGTCTGCCTTTATATTGGAAGCTACAGTGAATGTAATTTCGGGAACAAAAGTCCTAATGAAGCAAATACCTATTTGGCTTCCACTGGGTGTAGCTGATCAGAAGATATACAGCTTTAATTCAACAACAGCCGCAATTATGTTAGCTTCCTACACAGTGACACACTTCGGGAAGATATCTAACCCGCTGGTACGTGTCAACAGGCTAGGTCCAGGAATACCCGATCATCCGCTGCGACTCCTAAAGTTGGGCAATCAGGCATTCCTTCAAGAGTTTGTGCTTCCACCAGTCCAACTTCCCCAGTATTTTACATTTGATCTAACAGCTCTAAAGCTCATCACTCAACCATTGCCAGCTGCAACCTGGACAGACGAAACTCCTGCAGGAGCAGTCAATGTTCTTCGTCCTGGACTCTCACTCCATCCCAAGCTTCGTCCAATTCTTCTGCCGGGGAAGATAGGAAAGAAAGGACATGCTTCAGACTTAACATCACCTGACAAGATTCAAACAATCATGAATGCCATACCGGACCTCAAAATTGTCCCGATTGATCCTACCAAGAACATAGTTGGAATTGAGGTTCCAGAATTACTGGTTCAAAGGTTGACCGGCAAAAAACCACAACCCCAAAATGGCCAACCAATTATTCCAGTTCTTCTTCCGAAATATGTTGGACTTGATCCTATATCGCCAGGGGACTTGACTATGGTTATCACCCAGGATTGTGATTCATGCCACTCTCCAGCCAGTTATCCGTATCACATGGACAAGCAGAATAGTTACTAATAATTTAAATTCCATTCGAGCTATTATTCTGCTAGTAATCCCAACGGGCTCAATAGACTAAAAATCTGATTGTATAGAATTATAAAAGAATTAAGCAGGGGCAACAGAATCACAGCTTACGCCTAGATAACTAATATTAAGGAGTTTTTTAATCTAATTTTCCAGTCTTAAGTAATAATCATTTCTTTTGTAATTAATTATGCATTTGTTAACTTATCGATGTGAGATTTCCTTGGGAACCCGGCGGGGCCCCTACTATCCGCAGTAACCAGAAGAGAAGTTCAACCCAGTCACAACCAAACCAAGCAATATTCTGAACGCCCTATAATCTATTCTAACCAGAGGCATAACAATGGCTAATATTTCAATGACTCGTTAACAATCGTTAGCAATTTTAATCTCCAGATTAAGAAAAAGATATACGATGAAGATTAAGGCAATAACGAGCCGAAACTTCATCTTTCTTAAAGATCTAACATCATCTGTTCCAAAGTCATACAAGGACACATTCAAATCAGGGGTTGTAAGCTGCTATTTCTTACCTTCCCGAATTACCTATACAACATGGGGTCAGGATATCAACTTCTCCAATTGCCTCAGGGATGTTTTCGTAAAACTTCGTTCTTTGTATGGGTAATCATCCTCTTCCAGCGAGCAATCTCTATGCCGCTTGGTATAGTGACAAATAGCACTCTCAGAGCAACAGAAATTGATCAATTGGTTTGTCGGGACAAACTGTCATCAACTAGTCAGCTCAAGTCTGTGGGGCTGAATTTGGAAGGAAATGGAATTGCAACCGATGTTCTATCAGCAACAAAACGCTGGGGATTTCGTTCAGGTGTGCCCCCCAAGGTGGTCAGCTATGAAGCCGGAGAATGGGCAGAAAATTGCTACAATCTGGAGATCAAAAAGTTGGACGGAAGTGAATGCCTCCCTCTCCCTCCCGACGGTGTACGAGGATTCCCTAGATGTCGCTATGTCCACAAAGTTCAAGGAACAGGTCCCTGTCCCGGTGACTTAGCTTTCCATAAAAATGGGGCTTTTTTCTTGTATGATAGATTGGCCTCAACTGTTATCTACCGAGGGACAACTTTTGCTGAAGGTGTCGTAGCTTTTTTAATTCTGTCGGAACCCAAGAAGCATTTTTGGAAGGCCACACCAGCTCATGAACCGATGAACACAACAGATGATTCCACAGGCCACTATATGACCCTGACACTCAGCTACGAGGTGTCAAATTTTGGGGGCAATGAAAGTAACACCCTTTTAAAGGTAGACAACCACACATATGTGCAACTAGATCGTCCACACACTCCGCAGTTCCTTGTTCAGCTCAATGAAACACTTCGAAGAAATAATAGTCTTAGCAACAGTACAGGGAGATTGATTTGGATATTGGATCCTGAGATTGAACCCGATGTTGATGAGTGGGCCTTCTGGGAAACTAAAAAAACTTTTCCCAACAACTTCATGGAGAAAACTTGCATTTACAAATTCTATCAACCCACAACAACAACTCCTCAGATCAGAGCCCGGCGGGAATTGTCCAAAGAAAAATTAGCTACCACCCACCCACCAACAACTCCGAGCTGGTTCCAACGGATCCCCCTCCAGTGGTTTCAGTGCTCACTGCAGGACGGACAGAGGAAATGTCGACCCAAGGTCTAACCAACGGAGAGACACTCACAGGTTTCACCGCGACCCCAGTGACAACCACCATTGCCCCAAGTCCAACCATGACAAGCAAGGCTGATAACAATGTACCAAGTGAACAGCCGAACAACACAGAATCCATTGAATACTCCCCCCCATCGGTGAGCAACGAGACAACTGACCACCCCGAGATGAACTTGATCCAAGGCCCGAACAACTCCGCCCAGAGCCCACAGACCAAGACCACGTCAGCACCCACAGCATCTCCGATGACCCAGGACCCGCAAGCGACGGTCAACAGCAGCAAATCAGGAACCAGCCCAGGAAGTGCAGCCGAACCAAGTCAGCCCGGACTCATCATAAATACAGTAAGTGAGGTAGCTGGTTCACTGAGCCCCACCAGGAAACAAAAGCAATCAGCTCGACAAAACACTGCCAATAAATGTAATCCAGATCTTCACTATTGGACAGCTGTTGATGAGGGGGCAGCAGTAGGGTTGGCATGGATTCCATATTTTGGACCTGCAGCAGAAGGCATCTACATTGAGGGTGTAATGCACAATCAGAATGGGCTTATTTGCGGGCTACGTCAGCTAGCCAATGAGACTACCCAGGCTCTTCAATTATTTCTGCGGGCCACAACAGAACTGAGGACTTACTCACTTCTTAACAGAAAAGCTATTGATTTTCTTCTTCAACGATGGGGGGGTACCTGTCGAATCTTAGGACCATCTTGTTGCATTGAGCCACATGATTGGACAAAAAATATTACTGATGAAATTAACCAAATTAGACATGACTTTATTGATAATCCCCTACCAAACCACGGAGATGATCTCATTCTATGGACAGGTTGGAGACAATGGATCCCGGCTGGAATTGGGATTATCGGGGTCATAATTGCTATAATAGCCCTACTTTGTATATGTAAGATTTTGTGTTGATTTATTCTGAGATCTGAGAGAGAAAAATCTCAGGGTTACTCTAAGGAGAAATATTATTTTTAAGATTTACTTGAATGTTGACCACTTATCTTGAATGAGCAATTAACAATATGTTTTTCTGCTTCTTTACTTGATTTACAATATGATATTTCTCTTAATAATGATTAATATATTAAGAAAAACGTATGACGAAGATTAAAGGGGAGGATCGTTAACGGAAAAACTTCCCATCTCGTTCGTCGAAGTCACGTTGGTGGTGCTTGCAGCTGAGAACAACCCCAGAGATTGTAGGTAGATAAGACCAACACTTATAGGTAGGGGTCAGAAAGTAACAATAACCATAAAAGGAGGGCCTGATATTGCTATTTAATATCCTAGCACCTGATTTCTAGGTTCTAGTTGTACAATCCGAATGATGGAGCATTCAAGAGAACGGGGTAGATCTCGCAACATACGACATAATAGCCGGGAACCATATGAAAATCCATCAAGGTCTCGCTCATTATCTCGGGACCCCAATCAGATCGATCGTAGACAGCCTCGAAGTGCATCCCAAATTCGTGTTCCGAATCTGTTCCATCGGAAAAAGACTGATGCACTCATTGTTCCTCCGGCTCCTAAGGATATATGCCCAACACTCAAAAAAGGATTCCTCTGCGATAGTAACTTTTGCAAAAAAGATCACCAATTGGATAGCTTAAATGATCATGAATTACTACTGCTAATTGCAAGAAGAACATGTGGAATTATCGAGAGCAATTCGCAGATTACATCCCCAAAAGATATGCGATTAGCGAATCCAACAGCTGAAGACTTCTCACAAGGTAATAGTCCTAAATTAACACTTGCAGTCCTTCTTCAAATTGCTGAACATTGGGCAACCAGAGACCTAAGGCAAATTGAGGACTCTAAACTTAGAGCTCTTTTAACCCTTTGTGCCGTATTAACAAGGAAATTTTCTAAATCCCAACTGAGTCTTCTATGTGAGACCCACCTACGGCATGAGGGCCTCGGGCAGGACCAAGCTGATTCTGTATTAGAGGTCTACCAAAGACTCCACAGTGATAAGGGAGGGAATTTTGAGGCTGCCCTGTGGCAACAATGGGACCGACAATCATTAATAATGTTCATCTCTGCTTTTCTCAACATTGCTCTCCAGATACCTTGTGAAAGTTCTAGTGTCGTAGTCTCAGGTATTGCCACATTGTACCCAGCACAAGACAATTCTACACCATCCGAGGCAACTAATGATACCACCTGGTCAAGTACAGTTGGATAGAAAACCACTGGAGCTATTTTTCCACGATTGCTCTCAGTCAATAAATTAATATAGATATAACCCGACTTCGGTGTGCAATTGTCAAGAGTTCCATTTAGTAATAATGATTCTTAAAACAATCTACTATCGCAATTATCGATAGATCTATCCTATTTGACGGTACATGACTTGAATGTAATAAGGTGAGTTGGTATCTGAGGTATTTTGTCTAGAGTATACTCAAAATTGTGTGTCGAGCAAATTATCAATAACAAAGTTAAATTCTCCTAACCTCACATTTTGATCAAGTAATCATGATTTTACGATAATTCTTTGCAGATTATCGGCTTAATCTTTATTAAGAAAAAATCATGATTGTAGACAATTTACTGGTAGTCCTTGGGTATCCAAGTTTATGAACAGAGCTAGAGAGAATTTGCTACTTCCGATGTATAATTTTATTATTTGCTACTTCAAGTGCCTAAAACCAGTAACGCAGGATGAAGATTAATTGCGGAGGAATCAGGAATTCAACTTTAATTCCTTAAGGCCTCATCCGAATCTTCATCAGTTAGCACGTTCTTTTATAGAAGCCATTAGCTTCTAGAGTGATTATATTTTAGTATTAAATTTTGCTAATTGCTTGCTATAAAGTTGAAATGTCTAATGTTTAAATGAACATTTTTTTGAAGCTGACATACGAATACATCATATCATATGAAAACATCGCAGTTAGAGCATCCTTGAAATCTGGTATTGACAGCCACCAGGCTGTTCTCAGTAGTCTGTCCTTAGAAGCTCTTGGGGAGACAAAAAGGAGTCCCAGAGAGTCCTAACAGGTTGGCATAAGGTCATTAACACCAGCATAGTCGGCTCGATCAAGGCTGCAAGCGAGTCGATCTCAACTAAAAAGATTATTTTTTATTGCTTAAACAAATTCCTTTTGTGTGAGACATCCTCAAGGCACAAAATGGCTAAAGCCACAGGCCGATACAATCTCGTGTCTCCAAAGAAAGATATGGAAAAGGGAGTGATTTTGAGTGATCTTTGTAATTTCTTGATTACTCAAACCCTGCAAGGTTGGAAGGTCTATTGGGCAGGAATTGAGTTTGATGTAAGTCAAAAAGGCATGGCCCTTCTGACAAGACTCAAAACAAATGACTTCGCTCCTGCCTGGGCGATGACAAGAAATCTTTTCCCACATCTGTTCCAAAACCCAAATTCGGTTATTCAATCTCCTATCTGGGCTCTGAGGGTAATTTTGGCAGCCGGATTGCAGGATCAGTTGTTAGACCATTCATTAGTTGAGCCATTGACAGGGGCTCTCGGTCTAATTTCTGATTGGCTCCTAACTACAACGTCAACACATTTCAATCTTCGTACTAGAAGCGTAAAGGATCAACTTAGTCTTCGTATGTTATCTTTGATCAGGTCAAACATCTTGCAATTCATCAACAAGCTTGACGCCCTGCATGTTGTCAATTACAATGGTTTACTCAGTAGTATTGAGATCGGGACTTCTACACACACAATCATTATAACTCGTACAAATATGGGTTTTCTCGTGGAAGTTCAGGAGCCTGACAAATCAGCTATGAATTCTAAGCACCCAGGACCAGTCAAATTCTCATTACTTCATGAGTCTGCCTTCAAACCTTTCACTCGTGTTCCACAATCTGGGATGCAATCATTAATAATGGAGTTCAACAGCTTGTTAGCAATTTAACAAGATGATCTTAAAATAAGTACATGAATGAGAATTAGTTGTGGGTCTTATCTAGCATTGCTGAGTTAGCTATCTAATCTATTTTCACTAATTGCTTTAAGCACTGCTAATAGGTTTGTATCACGTTAAGGATTTAGAGTGTATGAATTGTGCAGATTTAAACTTGGGTTTTGCCTTATGCTTCATGGGTGGTCTTTTTGAAATGGAGATTATCAGCATTTCTTTAATGGGAGGAGTTAGCAATCAGAAATTGAAGATAGATGGGCATCGGGATAGAACAATGCCTAACTATTGGGTGGCTTCCATTTTTACATGTGTATATCACCAATTTTTTCCTATCTTTGCTTATATTGGTGTAACTTTATTTAAATAACATGTCAATGCTATACTGTTAAGGGAAGGTCTGAGGAAGATTAAGAAAAAGGCCTTGTGTTCACTTGGTTGCCGTCAAGTATCCTGTGGTCTTTTTCTACCTAGCTTCCTCATGCCATATGGCCACCCAGCATACCCAGTACCCGGATGCACGTTTATCCTCACCTATAGTCCTGGATCAATGTGATTTGGTAACTCGGGCATGTGGGTTATATTCATCTTATTCTCTAAATCCTCAACTAAGGCGATGTAAATTACCAAAACATATATATCGACTTAAGTTCGACACAATAGTATCCAAATTCCTTAGTGATACACCTGTAGCAACACTGCCGATAGACTATTTAGTGCCAATTCTCCTGCGTTCCCTAACGGGGCACGGTGATAGGCCATTGACCCCGACTTGCAATCAATTCCTTGATGAAATTATTAATTACACTCTTCATGATGCAGCCTTTCTTGAGTATTATCTCAAGGCAACAGGTGCACAGGACCATTTGACAAACATTACAACTAGAGAGAAGCTTAAAAACGAAATTCTAAACAATGAGTATGTCCATCAATTGTTCTTCTGGCATGACCTTTCTATTTTGGCTCGACGTGGACGTCTGAATCGCGGGAACAACCGTTCAACCTGGTTTGTTCATGATGAATTCATTGATATTTTAGGATATGGCGATTATATTTTTTGGAAAATACCTTTATCATTATTACCAGTTACTATAGACGGAGTTCCACACGCAGCAACAGACTGGTATCAACCGACTCTTTTTAAAGAATCCATCCTAGGGCACAGCCAAATCCTATCTGTGTCAACAGCTGAGATACTAATTATGTGTAAAGATATTATCACCTGTAGGTTTAATACATCACTGATTGCATCCATTGCAAAATTAGAGGATGTAGATGTGTCTGATTATCCTGACCCGAGTGATATTCTTAAGATATACAATGCTGGAGACTATGTAATATCTATTCTTGGCTCAGAGGGTTATAAGATAATAAAGTACCTCGAACCACTTTGTTTGGCCAAAATCCAACTTTGCTCTAAATTCACAGAAAGAAAAGGTCGTTTCCTCACACAGATGCATTTGTCAGTAATAAATGATCTTCGGGAGTTGATTTCTAACCGCAGGTTAAAGGACTATCAGCAAGAGAAGATTAGGGATTTTCACAAGATATTATTACAATTACAATTATCTCCTCAACAGTTTTGTGAATTATTCTCTGTTCAAAAACATTGGGGGCATCCAATTTTACATAGTGAGAAAGCTATACAAAAAGTAAAACGGCATGCAACCATCCTTAAGGCTCTCAGACCTAATGTCATCTTTGAGACATATTGTGTATTCAAGTACAGTATTGCCAAACACTATTTCGACAGCCAAGGAACTTGGTACAGTGTAATCTCAGATAGGAATTTAACTCCAGGACTCAACTCCTTCATAAAACGTAATCACTTTCCTTCACTACCCATGATTAAGGATCTTCTATGGGAATTCTATCATCTTAATCACCCTCCGTTATTCTCTACGAAGGTGATTAGTGACTTAAGTATTTTCATCAAGGATAGGGCCACAGCTGTTGAACAGACATGTTGGGATGCAGTCTTTGAACCCAATGTGCTAGGTTACAATCCCCCAAACAAATTCTCCACTAAAAGGGTGCCGGAACAATTTTTAGAACAAGAGGATTTTTCAATCGAAAGTGTCCTGAATTATGCACAGGGATTACATTATTTATTACCACAGAATAGGAATTTTTCATTTTCTCTTAAAGAAAAGGAATTAAATATTGGACGAACATTTGGGAAGCTACCATATCTCACACGGAATGTCCAAACTTTATGTGAGGCTCTGTTAGCAGATGGACTGGCTAAGGCCTTCCCCAGTAACATGATGGTAGTAACGGAACGTGAACAAAAAGAGAGCCTTCTTCATCAGGCATCATGGCACCATACCAGTGATGATTTTGGAGAGAATGCTACCGTTCGAGGGAGTAGTTTTGTAACTGATTTAGAGAAGTATAATCTTGCATTTCGCTATGAGTTCACTGCACCATTTATTGAGTATTGCAACCATTGCTATGGCGTGCGTAATGTCTTTAATTGGATGCATTATTTAATCCCGCAGTGTTACATGCATGTAAGTGATTATTATAATCCGCCTCACAATGTTAATCTTAGCAATCGAGAGTATCCTCCTGAAGGCCCGAGTTCATACCGAGGGCATTTAGGAGGCATAGAGGGATTACAACAAAAACTGTGGACAAGTATATCCTGTGCACAAATCTCCTTAGTGGAAATTAAAACTGGTTTTAAGTTACGATCAGCGGTCATGGGAGACAATCAGTGTATAACCGTATTGTCTGTTTTCCCACTTGAAACAGACCCTGAAGAGCAGGAGCAAAGCGCCGAAGACAATGCTGCAAGAGTAGCAGCAAGTCTTGCAAAAGTAACCAGTGCATGTGGGATCTTTCTTAAACCAGATGAGACATTTGTACACTCAGGTTTCATTTATTTCGGAAAAAAACAATATCTCAATGGTGTACAATTACCGCAATCACTCAAAACAGCAGCAAGAATGGCACCACTCTCTGATGCTATATTTGATGATCTACAGGGAACACTTGCCAGTATTGGAACTGCCTTCGAACGTGCTATATCGGAAACGCGACATATCCTCCCATGTCGTATTGTAGCAGCTTTCCATACATATTTCGCCGTTCGGATTTTACAATATCACCATCTTGGATTTAATAAAGGCATCGATTTAGGACAGTTGTCACTTAGTAAACCATTAGACTATGGGACTATTACTCTAACATTGGCGGTTCCACAAGTCCTTGGGGGATTGTCTTTTCTAAATCCAGAAAAGTGTTTTTATCGAAATTTCGGAGATCCTGTGACGTCTGGACTTTTCCAGCTACGGGTGTACCTAGAAATGGTCAACATGAAAGACTTATTTTGTCCATTAATATCGAAAAATCCAGGAAATTGTAGTGCCATTGATTTTGTATTAAATCCATCCGGATTAAATGTTCCAGGATCACAAGACTTGACATCCTTTTTGCGACAGATCGTTAGGCGTAGTATTACACTAACTGCAAGAAATAAGTTAATTAACACTCTCTTCCATGCCTCTGCTGATTTGGAAGATGAGATGGTTTGTAAGTGGCTCCTTTCATCAAACCCTGTCATGAGTCGCTTTGCAGCGGATATTTTTTCCAGGACACCTAGTGGGAAACGTCTCCAAATATTAGGTTATCTTGAAGGGACCAGGACTCTATTGGCCTCCAAAATCATAAACAATAACAGTGAGACACCTGTACTTGATAAGCTGAGGAAGATCACCCTACAAAGATGGAATCTGTGGTTCAGTTATTTGGACCATTGTGACCAATTACTAGCAGATGCTCTACAGAAAATTAGTTGCACGGTGGATTTGGCCCAGATTTTGCGTGAGTATACATGGTCACACATCTTAGAGGGTAGATCATTGATCGGGGCGACATTACCATGTATGGTGGAGCAATTCAAAGTTAAGTGGCTAGGACAATATGAACCTTGTCCAGAATGTCTGAACAAAAAAGGCTCGAATGCTTATGTCTCAGTTGCAGTCAAAGATCAAGTGGTCAGTGCTTGGCCTAATACTTCTCGAATAAGTTGGACAATAGGGAGTGGTGTCCCCTATATAGGATCAAGAACCGAGGATAAAATCGGACAGCCTGCTATCAAGCCGCGGTGCCCTTCATCTGCCCTCAAGGAGGCTATAGAATTAGCCTCAAGGCTCACTTGGGTTACACAAGGAGGTTCTAATAGTGAACAATTAATCCGGCCTTTCTTGGAAGCAAGAGTCAACCTTAGTGTCAGTGAAGTCCTACAAATGACACCATCACATTATTCAGGAAATATTGTCCATCGATATAACGACCAATATAGCCCGCACTCATTTATGGCGAATCGTATGAGCAATACTGCGACCCGTCTCATAGTGTCAACTAATACACTTGGAGAATTCTCAGGTGGAGGGCAGGCCGCCAGGGATAGCAATATAATTTTCCAGAATGTTATAAATTTAGCAGTTGCCCTTTATGATATTAGATTCCGGAATACAAACACCTCTGATATAAGACATAATAGGGCTCATCTCCACCTGACAGAGTGCTGTACTAAAGAGGTCCCGGCCCAGTATTTGACGTATACAAGTGCACTTAATCTGGATTTAAGCCGTTATCGTGATAATGAACTAATATATGACTCAAATCCACTGAAGGGAGGATTGAACTGCAATTTAACAATAGATAGCCCTTTAGTGAAGGGTCCTAGGCTTAACATGATTGAAGATGATCTTCTCCGCTTTCCACACCTTTCCGGATGGGAGTTAGCGAAAACGGTGGTACAATCCATCATCTCAGACAATAGCAACTCATCAACAGATCCAATCAGTAGCGGAGAAACACGCTCTTTCACAACTCATTTTCTCACTTACCCTCAGATTGGCCTTCTTTACAGTTTCGGGGCAGTATTATGCTTTTATCTAGGCAATACTATCCTATGGACTAAAAAACTTGATTATGAACAGTTTCTATATTATTTGCATAACCAGCTGCACAACTTACCTCATCGAGCACTCCGTGTCTTTAAACCAACATTTAAGCATGCTAGTGTGATGTCCCGATTAATGGAAATTGATTCCAACTTCTCAATTTATATTGGCGGGACATCTGGAGATAGAGGGCTGTCTGATGCTGCTCGACTGTTTCTTCGGACAGCAATCGCGAGCTTTTTACAATTTCTTAAAAGCTGGATCATCGACCGCCAAAAGACAATTCCTTTATGGATAGTATATCCGCTTGAAGGTCAACAACCGGAATCCATCAATGAATTCCTACATAAAATTTTGGGTCTGCTCAAGCAAGGCCCCAAAAGTATTCCAAAGGAGGTCAGCATTCAAAATAATGGGCATTTGGATTTGGCAGAAAATAATTATGTTTACAATAGTAAGAGCACTGCTAGTAATTTCTTTCATGCATCCTTAGCTTACTGGAGAGGTAGGAAATCTCGGAAGACTCAAGACCATAATGATTTCTCAAGTGGGGATGGAACATTCACAGAACCCGTGCGTAAGTTCTCAAGCAATCATCAGTCAGATGAGAAGTACTACAAAGTGACATGTGGAAAGTCACCGAAACCGCAAGAACGCAAAGACTTCTCGCAACACAGACTCAGCAATAACGGGCAAACAATGAGTAATCATCGTAAGAAAGGGAAGTTCCACAAGTGGAATCCCTGCAAAGTGTTAATGGAGAGTCAAAGGGGAGCTGTTCTAACAGAGGGTGACTACCTTCAAAACAATACTCCACCAACAGATGATGTATCAAGTCCTCACCGACTCATTCTACCATTTTTTAAATTGGGAAATCACAATCATGCACATGGTCAAGATGACCAAGAATTGATGAATCAAAATATTAAACAGTACCTACATCAGCTAAAGTCTATGTTGGACACCACTATATATTGTAGATTCACAGGGATTGTCTCATCCATGCATTACAAATTAGACGAAGTTCTTATGGAATACAATAGTTTCGATTCAGCTATCACATTAGCTGAAGGTGAGGGGTCAGGGGCACTATTACTTTTGCAAAAATATAATACAAGGTTATTATTTTTGAACACATTGGCAACAGAACACAGTATAGAATCAGAAGTTGTATCAGGTTTTTCTACTCCGAGAATGTTGTTACCAATAATGCAAAAGGTTCATGAAGGACAAGTCACTGTTATCTTAAATAATTCAGCAAGTCAGATAACTGACATAACTAGCTCAATGTGGTTAAGTAATCAAAAATATAATCTACCTTGTCAAGTTGAAATCATTACGATGGATGCTGAAACAACAGAGAACTTAAACAGGTCCCAACTCTACCGAGCAGTGTATAATTTAATACTTGATCACATTGATCCGCAGTATCTCAAGGTGGTGGTACTCAAAGTATTTCTGAGTGATATAGAAGGAATATTATGGATTAATGATTACTTGGCTCCACTGTTCGGAGCTGGTTACTTGATTAAGCCGATTACATCAAGTGCCCGGTCAAGTGAATGGTACCTTTGCTTATCAAATTTGATATCTACTAACAGGAGATCGGCCCATCAGACTCACAAGGCATGCCTTGGTGTTATCAGAGATGCTCTGCAAGCACAAGTCCAGCGAGGCGTGTACTGGTTGAGTCACATCGCACAGTATGCTACAAAGAATCTCCATTGTGAATACATATGCCTTGGTTTTCCATCTCTAGAAAAGGTCCTATATCACAGGTATAATCTAGTCGATACTGGACTCGGTCCATTGTCGTCAGTTACTAGACATTTAACTAACCTCCAGGCAGAGATACGAGACTTAGTATTAGATTATAACCTGATGAGAGAGAGTCGCACTCAAACGTACCATTTTATTAAGACTGCAAAAGGCAGAATCACAAAATTGGTCAATGACTTTCTGAAGTTTTCTTTAATTGTTCAGGCACTCAAAAATAATTCTTCTTGGTATACTGAGCTTAAAAAATTACCTGAGGTGATTAATGTGTGTAATCGATTTTATCATACTCACGGTTGCGAATGTCAGGAAAAATTCTTTGTCCAGACGCTTTATTTACAACGCCTACGTGATGCAGAAATCAAGCTAATTGAACGCCTTACCGGATTAATGCGATTTTATCCAGAAGGGTTAATATATTCCAATCACACATAAGTACTAAATCATCATAGTATGAGGAATAAGATAATGACAATTCCTGACGACAGTTTTAGTTCCTATTCTAAGTATATCGAAAGAGAGTATGCCAATCTTAATTATTAAAGGTAACAAGCTATTATTTACTACTTATTAATAAGAATAAACTTTATCATAGCGTAACACATCATAACTTTATAACGATTTTGCATTTCTAATCCTAGTATTTATTAGAATGTACTATCAGAGAAATGGCCCCAGTTCCTATCTTTAAATAATGATTGTGTGTTTTAAATTATTATTTTATTAGGTTTATGAGTTGGTCACACAGTGAGTATCAGTGATTGAGGATTATGTAGATAGGTAATCTAACACTGAATCACCTATCTGATGTCACCATACCCTAATGTTGTGCTAGTTGCATTTAAACATGCTATCCTCAGTTAAGTAACATAGACTGAAAATGCTAAGAAGAGATTGGAGTAAAAGTATAAAATAAAGTTAATTGAACTTCAAAATGATTAAATGATAATGATCTTGGGAACTCAATATGACCTCAAGTCAAAAATAATGTCAATATAATTATTTAGTAATATGAGTGATAATGTAAATTTTGATAATTAACTAACTGTAGTAATTAAGGTCAAATGCAAACATTATAAGAAT\n>Reston_ebolavirus_-_Reston_strain_Reston08-E_complete_genome\nGTGTGCGAGTAACTATGAGGAAGATTAACAGTTTTCCTCAGTTTAAGGTATACACTGAAATTGAAATTGAGATTCTCCTCTTTGATATTCTGTAACTTTCCCTAGTTGTGACAATTGAATCAGTTTTATCTATTACCAATTACCATCAACGTGGTATGTCTAGTGATCTTGGGACTCTTCTTCATCTGGTTTTTCCTAGAGCTCTGAATCTATTTTGTGAGAAGTTCATCCAAACGACCCAGTGTCTGAAAATACAAGAGGTTCCCCTTTCCGTCAAGTTTAAGGGGTTGTTTTGATTGTGTGTAGATTTTATAATCCTAGAGTGCCAGGGAGTTGCGTGTCATCATTAATTAGGAAGATCAAGGAAACAGTTTGTTCCAATAATATCGTATATCTTGACTAAGTCGAACAAGGGGAAGTCAATATGGATCGTGGGACCAGAAGAATCTGGGTGTCGCAAAATCAAGGTGATACTGATTTAGATTATCATAAAATTTTGACAGCTGGCCTTACTGTTCAACAGGAAATTGTCAGGCAGAAAATAATTTCTGTATATCTTGTTGATAACTTGGAGGCTATGTGTCAATTGGTAATACAAGCCTTTGAGGCCGGAATTGATTTCCAAGAAAATGCTGACAGCTTCCTTCTGATGCTTTGCCTACATCATGCTTACCAAGGTGACTATAAATTGTTCTTGGAGAGCAATGCTGTACAGTATTTGGAAGGTCATGGATTCAAATTTGAGCTCCGGAAGAAGGACGGTGTCAATCGGCTCGAGGAATTGCTTCCTGCTGCAACGAGTGGAAAAAACATTAGGCGTACGTTGGCCGCACTGCCTGAAGAGGAGACTACAGAAGCAAATGCAGGGCAATTTCTCTCATTTGCGAGTTTGTTTCTTCCCAAACTGGTTGTGGGAGAGAAGGCTTGCTTGGAAAAAGTCCAGCGACAAATTCAGGTTCATGCAGAACAGGGTTTAATTCAATATCCCACTGCATGGCAATCAGTTGGACACATGATGGTAATCTTCAGATTGATGAGGACTAATTTCTTGATTAAATATTTACTGATTCACCAGGGTATGCATATGGTAGCTGGCCACGATGCCAATGATGCTGTCATTGCTAATTCAGTTGCTCAGGCTCGCTTTTCGGGACTCCTAATTGTCAAAACCGTTCTTGATCATATTCTGCAGAAAACCGACCAAGGAGTAAGACTTCACCCTTTGGCCCGAACAGCCAAAGTGCGTAATGAGGTTAATGCATTTAAGGCCGCCCTAAGCTCACTTGCTAAGCATGGGGAATATGCCCCTTTTGCTCGCCTTCTCAATCTCTCAGGAGTTAACAACCTAGAACATGGTCTCTACCCACAGTTATCAGCAATTGCTCTTGGAGTTGCCACAGCACATGGTAGCACCCTTGCAGGAGTTAATGTTGGTGAGCAGTATCAGCAACTTAGAGAGGCTGCAACTGAAGCTGAGAAGCAACTCCAACAATATGCTGAGTCCAGGGAACTCGACAGCCTAGGCCTAGACGATCAGGAAAGAAGAATACTAATGAACTTCCATCAGAAGAAAAATGAAATTAGTTTCCAGCAGACCAATGCAATGGTAACCCTTAGGAAAGAGCGACTGGCTAAATTAACAGAAGCTATAACGCTGGCCTCAAGACCTAACCTCGGGTCTAAACAAGACGACGACAATGAAATACCGTTCCCTGGGCCTATAAGCAACAACCCAGACCAAGATCATCTGGAGGATGATCCTAGAGACTCCAGAGACACTATCATTCCTAATAGTGCAATTGACCCCGAGGATGGTGATTTCGAAAATTATAATGGCTATCATGATGATGAAGTTGGGACGGCAGGTGACTTGGTCTTGTTCGACCTTGACGATCATGAGGATGACAATAAAGCTTTTGAGCCACAGAACAGCTCACCACAATCCCAAAGGGAAATAGAGAGAGAAAGATTAATTCACCCACCCCCAGGCAACAATAAGGACGACAATCGGGCTTCAGACAACAATCAACAATCAGCAGATTCTGAGGAACAAGAAGATCAATACAACAGGCACCGAGGCCCAGAACGTACGACCGCCAATCGAAGACTCTCACCAGTGCACGAGGAGGACACCCTTATAGATCAAGGCGATGATGATCTCTCAAGCCCACCTCCGCTGGAATCTGATGATGACGATGCATCAAGTAGCCAACAAGATCCCGATTATACAGCTGTTGCCCCTCCTGCTCCTGTATACCGCAGTGCAGAAGCCCACGAGCCTCCCCACAAATCCTCGAACGAGCCAGCTGAAACATCACAATTGGATGAAGACCCTGATATCGGTCAATCAAAATCTATGCAAAAATTAGAAGAGACATATCACCATCTGCTGAGAACTCAAGGTCCATTTGAGGCTATCAATTATTATCACATTATGAAGGATGAGCCGGTAATATTTAGCACTGATGATGGGAAGGAATACACCTACCCGGATTCACTTGAGGAAGCCTATCCTCCATGGCTCACCGAGAAAGAACGACTGGACAATGAAAATCGATACATTTACATAAATAATCAACAGTTCTTCTGGCCTGTCATGAGTCCCAGAGACAAATTTCTTGCAATCTTGCAGCACCATCAGTAACCACAGCACAAAGCGCGGTCCACTTCGTAAAGCTAAATACACTTAAAGCTTGACCGATTCATCTACAAAAGCTAATCCATTATAACTTATTAGTGCTACTTTTCTATAAGTGATTCTCAATCTAAGGCCATTAAGAGTTTAAGCAATATACATATACACTTACACCGGTCTATCCAAGATGTGGCTCAATGTTCTTAATTTGAACATAGTCACAAGGGGATAAATAATACTTTATATTTCTGATTGTAGATTGACCCATTCTGCTTAAAATACTTCGCCCATTAAAAATGTGATCTAATAGATAGCCCTGACTAGACAAATTAAGAAAAACATTTGATGAAGATTAAAACCTTCATCGCCAGTAAATGATTATATTGTCTGTAGGCAGGTGTTTACTCCACCTTAAAGTCGGAAATATCCTACCTTAGGACCATTGTTAAGAGGTGCATAGGCATTACCATCCTTGAGAACATGTACAATAATAAATTGAAGATATGTTCAGGCCCAGAGACGACTGGATGGATCTCTGAGCAACTAATGACAGGTAAGATTCCAGTAACTGATATATTCATTGATATTGATAACAAGCCAGATCAAATGGAAGTCCGGCTCAAACCATCATCAAGGAGCTCAACAAGAACTTGTACAAGTAGCAGTCAGACGGAGGTCAACTATGTACCTCTCCTTAAAAAGGTTGAGGATACATTAACTATGCTAGTGAGTGCCACCAGTCGTCAGAATGCTGCAATCGAGGCCCTTGAAAACCGCCTCAGCACACTTGAGAGTAGCTTAAAGCCAATCCAAGACATGGGTAAAGTGATTTCATCATTGAATCGCAGTTGTGCCGAAATGGTGGCAAAATATGATCTTCTAGTTATGACAACTGGACGGGCTACTTCAACTGCAGCTGCAGTAGATGCGTACTGGAAAGAGCACAAACAGCCACCACCAGGGCCAGCGTTGTATGAAGAGAATGCGCTTAAAAGAAAAATCGATGATCCAAACAGCTATGTACCAGATGCTGTGCAGGAGGCTTACAAGAACCTTGACAGTACATCGACCCTGACCGAGGAAAATTTTGGGAAACCTTATATATCTGCTAAAGATCTGAAGGAGATCATGTATGATCATCTACCTGGTTTTGGGACTGCCTTTCACCAACTTGTTCAAGTGATTTGTAAAATAGGAAAGGATAACAACCTCTTGGACACAATCCATGCTGAGTTCCAGGCAAGTCTAGCAGATGGTGACTCTCCCCAATGTGCACTCATACAGATAACCAAAAGAGTCCCAATCTTTCAGGATGTGCCACCCCCGACAATCCACATTAGATCCCGTGGTGATATCCCACGAGCATGCCAAAAGAGTCTCCGACCAGCACCACCATCACCCAAAATTGACCGTGGTTGGGTTTGTTTGTTTAAGATGCAAGATGGTAAAACGCTTGGACTTAAGATCTAAGAATCAAGATTTATTTAACAAGACAAGCCACAACCTTAGATAGAACCTCAGCCAGACTATTGAACTATTGACGCTGTTGATGATAATATATAATTAATGGTCATACTTGAATATGACAACATCTTGCTTCTTGTTTTGCCTTGTGTTTCTTTGAATTGAAAGATCATTCCAAACTTACAAACATGCACAAGATGTTATGGTTTAGCAAAGAATTGATAGGAGTACTGGTATATAATGTAAATATAATAAGTGATGAAGATTAAGAAAAACCAGTCGGTATTTTCCAGGCTTGGCATTTCTTATCTTCATCTTCTAAAGTGAGATATTTTATCATCAAAAAATGAGGCGCGGAGTGTTACCAACGGCTCCTCCAGCATATAATGATATTGCATACTCTATGAGCATACTCCCCACCCGACCAAGTGTCATAGTCAATGAAACCAAATCAGATGTACTGGCAGTGCCAGGAGCAGATGTTCCATCAAACTCCATGAGACCAGTGGCTGATGATAACATTGATCACTCAAGCCATACTCCAAGCGGAGTAGCTTCTGCCTTTATATTGGAAGCTACAGTGAATGTAATTTCGGGGACAAAAGTCCTGATGAAGCAAATACCTATTTGGCTTCCACTGGGTGTAGCTGATCAGAAGATATACAGCTTTGATTCAACAACAGCCGCAATTATGTTGGCTTCCTACACAGTGACACACTTCGGGAAGATATCTAATCCGTTGGTACGTGTCAACAGGCTAGGCCCAGGAATACCCGATCATCCGCTACGACTCCTAAGGTTGGGCAATCAGGCATTCCTTCAAGAGTTTGTTCTTCCACCGGTTCAGCTTCCCCAGTATTTCACATTTGATCTAACAGCTCTAAAGCTCATCACTCAACCATTGCCAGCTGCAACCTGGACAGACGAAACTCCAGCAGGAGCAGTCAATGCTCTTCGTCCTGGGCTCTCACTCCATCCCAAGCTTCGTCCAATTCTTCTACCGGGGAAGATAGGAAAGAAAGGTCATGCTTCAGACTTAACATCACCTGACAAAATTCAAACAATCATGAATGCAATACCGGACCTCAAAATTGTCCCGATTGATCCAACCAAGAACATAGTTGGAATTGAGGTTCCAGAATTACTAGTTCAAAGGCTGACCGGCAAAAAGCCACAACCCAAAAATGGCCAACCAATTATTCCAGTTCTTCTTCCGAAATATGTTGGATTTGATCCTATATCGCCAGGGGACTTAACTATGGTTATCACCCAGGACTGCGATTCATGCCACTCTCCAGCCAGCCATCCGTATCACATGGACAAGCAGGATAGTTACCAATAATTTTAATTCTATTCGAGCTATTATTCTGCTAGTAATTTCGACGGGATCAATAGACTAAAAATCTGATTGTATAGAATTATAAAAGAATCAAGCAGAGGCAACAGACTCACAGCTTACGCCTAGATAACTAATATTAAGGAGTTTTTTAATCTAATTTTCAAGTCTTAAGTAATAAGTATTTCTTTTGTAATTAATTATGCATTTGTTAACTTATCGGTGCGAGATTTCCTTGAGAGCCCGGCGGGGCTTCTACTATCTGTAGTAACCAGAAGAGAAGTTCAACTCAGTCAAAACTAAACCAAGTAATATTCTGAATGCTCTATAGTCTATTCTAATCAGAGGTATAACAATGGCTAGGATTTCAATGACTCTTTAACAATCGCTAGTAATTTTAATCTCCAGATTAAGAAAAAGATATACGATGAAGATTAAGGCGACAACAAGCCGAAACTTCATCTCTTTTAAAGATCTAGCATTATCTGTTCCAAAGTCATACAAGGACACATTCAAATCAGGGATTGTAAGCTGCTATTTCTTACCTCCCCAAATCACCTATACAACATGGGGTCAGGATATCAACTTCTTCAATTGCCTCGGGAACGTTTTCGTAAAACTTCATTCCTAGTATGGGCAATCATCCTCTTCCAGCGAGCAATCTCCATGCCGCTTGGTATAGTGACAAATAGCACTCTCAAAGCAACAGAGATTGATCAATTGGTTTGTCGGGACAAACTGTCATCAACCAGTCAGCTCAAGTCTGTGGGGCTGAATCTGGAAGGAAATGGAATTGCAACTGATGTCCCATCAGCAACAAAACGCTGGGGATTCCGTTCAGGTGTGCCTCCCAAGGTAGTCAGCTATGAAGCCGGAGAATGGGCAGAAAATTGCTACAATCTGGAGATCAAAAAGTCAGACGGAAGTGAGTGCCTCCCTCCCCCTCCCGACGGTGTACGGGGATTCCCTAGATGTCGCTATGTCCACAAAGTTCAAGGAACAGGTCCTTGTCCCGGTGACTTAGCTTTCCATAAAAATGGGGCTTTTTTCTTGTATGATAGATTGGCCTCAACTGTCATCTACCGTGGGACAACTTTTGCTGAAGGTGTCATAGCTTTTTTAATTCTGTCAGAGCCCAGGAAGCATTTTTGGAAGGCTACACCAGCTCATGAACCGGTGAACACAACAGATGATTCCACAAGCTACTACATAACCCTGACACTCAGCTACGAGATGTCAAATTTTGGAGGCGAGGAAAGTAACACCCTTTTTAAGGTGGACAACCACACATATGTGCAACTAGATCGTCCACACACTCCGCAGTTCCTTGTTCAGCTCAATGAAACACTTCGGAGAAATAATCGCCTTAGCAACAGTACAGGGAGATTAACTTGGACATTGGATCCCAAAATTGAACCAAATGTTGGTGAGTGGGCCTTTTGGGAAACTAAAAAAACTTTTCCAAACAACTTCAGGGAGAAAACTTGCATTTCCAAATTCTATCAACCCACACCAACAACTCCTCAGATCAGAGCCCGGCGGGAACTGTCCAAGGAAAAATTAGCTACCACCCACCCACCAACAATTCCGAGCTGGTTCCAACGGATTCCCCTCCAGTGGTTTCAGTGCTCACTGCAGGACGGACAGAGGAAATGTCGACCCAAGGTCTAACTAACGGAGAGACAATCACAGGTTTCACCGCGAACCCAATGACAACCACCATTGCCCTAAGTCCAACCATGACAAGCAAGGTTGACAACAATGTACCAAGTGAACAACCGAACAACACGACATCCATTGAAGACTCCCCCCCATCGGCAAGCAACGAGACAATTGACCACTCCGAAATGAATTCGATCCAGGGCTCGAACAACTCCACCCAGAGCCCACAGACCAAGACCAAGCCAGCGCCCACAGCATCCCTGATGACCCTGGGCCCGCAAGAGACGGCCAACAGCAGCAAACCAGGAACCAGCCCAGGAAGCGCAGCCGAACCAAGTCAGCCTGGACTCACTATAAATACAGTAAGTAAGGTAGCTGATTCACTGAGTCCCACCAGGAAACAAAAGCGATCGGTTCGACAAAACACCGCTAATGAATGTAACCCAGATCTTCACTATTGGACAGCTGTTGATGAGGGGGCAGCAGTAGGATTGGCATGGATTCCATATTTTGGACCTGCAGCAGAAGGCATCTACATTGAGGGTGTAATGCATAATCAGAATGGGCTTATTTGCGGGCTACGTCAGCTAGCCAATGAAACTACCCAGGCTCTTCAATTATTTCTGCGGGCCACAACAGAACTGAGGACTTACTCACTTCTTAACAGAAAAGCTATTGATTTTCTTCTTCAACGATGGGGAGGTACCTGTCGAATCTTAGGACCATCTTGTTGTATTGAGCCACATGATTGGACAAAAAATATTACTGATGAAATTAACCAAATTAAACATGACTTTATTGACAATCCCCTACCAGACCACGGAGATGATCTTAATCTATGGACAGGTTGGAGACAATGGATCCCGGCTGGAATTGGGATTATTGGAGTTATAATTGCTATAACAGCCCTACTTTGTATATGTAAGATTTTGTGTTGATTTATTCTGAGATCTGAGAGAAAGAAATCTCAGGGTTACTCTAAGGAGAAGTATTATTTTTAAAATTTACTTAAATGCTGACCACTTATCTTAAATGATCAATTAATGATATGTTTTTCTGCTTCTTTGCTTGATTTACAATATGATATTTCTCTTAATAATGATTAATATATTAAGAAAAACTTATGACGAAGATTAAAGGGGAGGATCGTTAACGGGAAAATCTCCCATCTCGTTCGTCGAGGCCACGTTGGTGGTGCTTGCAGCTGAGAACCACTCCAGAGATTGTAGGTAGAAAGGACCAGCATTTATAGGTAGGGGTCAGAAAGCAACAATAACCATAAAAAGAGAGCCTGACATTGCTATTTAATATCCTAGAACCTGATTTCTAGGTTCTAGTTGTACAATCCGGATGATGGAGCATTCAAGAGAACGGGGTAGATCTAGCAACATGCGACATAATAGCCGGGAACCATACGAAAATCCATCAAGGTCTCGCTCATTATCTCGGGACCCTAATCAGGTTGATCGTAGACAGCCTCGAAGTGCATCCCAAATTCGTGTTCCGAATCTGTTCCATCGGAAAAAGACTGATGCACTCATAGTTCCTCCGGCTCCCAAAGATATATGCCCAACACTCAAAAAAGGATTCCTCTGCGATAGTCAATTTTGCAAAAAAGATCACCAATTGGATAGCTTAAATGATCATGAATTACTACTGCTAATTGCAAGAAGAACATGTGGAATTATCGAGAGCAATTCGCAGATTACATCCCCAAAAGATATGCGGTTAGCAAATCCAACAGCTGAGGACTTCTCACAAGGTAATAGTCCTAAATTAACACTTGGAGTCCTTCTTCAAATTGCTGAACATTGGGCAACCAGAGACCTAAGGCAAATTGAGGACTCTAAACTTAGAGCTCTTTTAACCCTTTGTGCCGTATTAACAAGGAAATTTTCTAAATCCCAACTGGGTCTTCTATGCGAGACCCACCTACGGCATGAGGGCCTCGGACAGGACCAAGCTGATTCTGTATTAGAGGTCTACCAAAGACTCCACAGTGATAAAGGAGGGAATTTTGAGGCTGCCCTGTGGCAACAATGGGACCGACAGTCGTTAATAATGTTCATCTCTGCTTTTCTCAACATTGCTCTCCAGACGCCTTGTGAAAGTTCTAGTGTCGTAGTCTCAGGTCTTGCCACATTGTACCCAACACAAGACAATTCTAAACCATCCGAGGCAACTAATGATACCACCTGGTCAAGTACAGTTGAATAGAAAACCACTGGAGCTATTTTTCCACGATTGCTCTCAGTCAATAAATTAATATAGATATAATACGACTTCGGTGTGCAATTGTCAAGGGTTCCATTTAGTAATAATGATTCTTAAAACAATCTACTATCGCAATTATCGATGGATCTACCTTATTTGACGGTACATGACTTGAATGTAATAAGGTAAGTTGGTATCTGAGGTATTTTGTCTAGAGTATACTCAAAATCGTATGTCTAGCAAATTATCAATAGCAAAGTTAAACTCTCCTAACCTCATATTTTGATCAAGTAATCATGATTTTATGGTAATTCTTTGCAGATTATCGGTTTAATCTTTATTAAGAAAAAATCATGAGTGTAGACAATTTACTGGTAGTCCCTGGGTATCCAAGTTTATGAACAGAGCTAGAGAGAATTTGCTACTTCCGAGGTATAACTTTATTATTTGCTACTTCGAATGCCTAAAACCAGTAATGCAGGATGAAGATTAATTGCGGAGGAATCAGGAATTCAACTTTAGTTCCTTAAGGCCTCGTCTGAATCTTCATCAGTTAGCAAGTTCCTTTATAGAAGTCATTAGCCTCTAAGGTGATTATATTTTAGTATTAAATTCTGTTAATTGCTTGCTATAAAGTTGAAATGTCTAATGCTTAAATGAACATTTCTTTGAAGCTGACATACGAATACATCATATCATATGAAAACATCGCAATTAGAGCGTCCTTGAAGTCTGGCATTGACAGTCACCAGGCTGTTCTCAGTAGTCTGTCCTTGGAAGCTCTTGGGGAGACAAAAAGAGGTCCCAGAGAGTCCCAACAGGTTGGCGTAAGGTCATTAACACCAGCATAGTCAGTTCGATCAAGACTGTAAGCGAGTCGATTGCAACTAAAAAGATTATTTCTTGTTGTTTAAACAAATTCCTTTTGTGTGAGACATCCTCAAGGCACAAGATGGCTAAAGCCACAGGCCGATACAATCTCGTGCCCCCAAAGAAAGATATGGAAAAGGGAGTGATTTTTAGTGATCTTTGTAATTTCTTGATTACTCAAACCCTGCAAGGTTGGAAGGTTTATTGGGCAGGAATTGAGTTTGATGTAAGTCAAAAAGGCATGGCTCTTCTGACAAGACTCAAAACAAATGACTTTGCTCCTGCCTGGGCGATGACAAGAAATCTCTTCCCACATCTGTTCCAAAACCCAAATTCGGTTATTCAATCTCCCATCTGGGCTTTGAGGGTAATTTTGGCAGCCGGATTGCAGGATCAGTTGTTAGACCATTCATTGGTTGAGCCATTGACAGGGGCTCTCGGTCTAATTTCTGATTGGCTCCTAACTACAACGTCAACACATTTCAATCTTCGTACTAGAAGCGTAAAGGACCAGCTTAGTCTTCGTATGTTATCTTTGATCAGGTCAAACATCTTGCAGTTCATCAACAAGCTTGACGCCCTGCATGTTGTCAATTACAATGGTTTACTCAGTAGTATTGAAATCGGGACTTCTACACACACAATCATTATAACTCGTACAAATATGGGTTTTCTCGTGGAAGTTCAGGAACCTGACAAATCAGCTATGAATTCTAAGCGCCCAGGACCAGTCAAGTTCTCATTACTTCATGAGTCTGCCTTCAAACCTTTCACTCGTGTTCCGCAATCTGGGATGCAATCATTAATAATGGAGTTCAACAGTTTGTTGGCAATTTAACAAGGTGATCTTAAAATAAGTACATGAATGAGAATTAGTTGTGGGTCTTACCTAGCATTGTTGAGTTAGCTACCTAATCTATTTTCACTAACTGCATTGAGCACTGCTAGTAGGTTTGCATTACGTTAAAGATTCAGAGTGTATGAATTGTGAAGATTTAAACTTGGGTTTTGCCTTATGCTTCATAGGTGGTCTTTTTAAGATGGAGATTATCAGCATTTCTTCAATGGGAGGAGTTAGCAATCAGGAATTGGAGATAAATGGACATCGGGATAGAACAATGCCTAACTATTGGGCGGCTTTCATTTTTAAATGTGTATATAACCAATCTTTTCCTATCTTTGCTTATATTGGTATAACTTTACTTTAATAACATGTCAATGCTATACTGTTAAGAGAAGGTCTGAGGAAGATTAAGAAAAAGGCCTCGTGTTCACTTGGTTGCCGTCAAGTATCCTGTGGTTTTTTTCTACCTAACTTCCTCATGCCATATGGCTACCCAGCATACCCAGTACCCGGATGCACGTTTATCTTCACCTATAGTCCTGGATCAATGTGATTTGGTAACTCGAGCATGTGGGTTATATTCATCTTATTCTCTAAATCCTCAACTAAGGCAATGTAAGTTGCCAAAACATATATATCGACTTAAGTTCGACACAATAGTATCCAAATTCTTAAGTGATACACCTGTAGCAACACTGCCGATAGACTATTTAGTACCAATTCTCCTGCGTTCCCTAACGGGGCACGGTGATAGGCCGTTGACCCCGACTTGCAATCAATTCCTAGATGAAATTATTAATTACACTCTTCATGATGCAGCCTTTCTTGATTACTATCTCAAGGCAACAGGTGCACAGGACCATTTGACAAACATTACAACTAGAGAGAAGCTTAAAAACGAAATTCTAAACAATGATTATGTCCATCAATTGTTCTTCTGGCATGACCTGTCTATTTTGGCTCGACGTGGGCGTCTGAATCGCGGGAACAACCGTTCAACCTGGTTTGTTCATGATGAATTCATTGATATTTTAGGATATGGCGATTATATTTTTTGGAAAATACCTTTATCATTATTACCGGTTACTATAGACGGGGTCCCACACGCAGCAACTGACTGGTATCAACCGACTCTTTTTAAAGAATCCATCCTAGGACACAGCCAAATCCTATCTGTGTCGACAGCTGAAATACTAATTATGTGTAAAGATATTATCACCTGTAGGTTCAATACATCACTGATTGCATCCATTGCAAAATTAGAGGATGTAGATGTGTCTGATTATCCTGACCCGAGTGATATTCTTAAGATATACAATGCTGGAGACTATGTAATATCTATTCTTGGCTCAGAAGGTTATAAGATAATAAAGTACCTTGAACCACTTTGTTTGGCCAAAATCCAACTTTGCTCTAAATTCACAGAGAGAAAAGGTCGTTTCCTCACACAGATGCATTTATCAGTAATAAATGATCTTCGGGAGTTGATTTCTAACCGCAGGTTAAAGGACTATCAGCAAGAGAAGATTAGGGATTTTCACAAAATATTATTACAATTACAATTATCTCCTCAACAGTTTTGTGAATTATTCTCTGTTCAAAAACATTGGGGGCATCCAATTTTACATAGTGAGAAAGCTATACAAAAAGTAAAACGGCATGCAACCATCCTTAAAGCTCTCAGACCTAATGTCATTTTTGAGACATATTGTGTATTCAAGTACAATATTGCCAAGCACTATTTCGACAGCCAAGGAACTTGGTACAGTGTAATCTCAGACAGGAATTTAACTCCGGGACTCAACTCCTTCATAAAACGTAATCACTTTCCTTCACTACCCATGATTAAGGATCTTCTATGGGAATTCTATCATCTTAATCACCCTCCGTTATTCTCTACAAAGGTGATTAGTGACTTAAGTATTTTCATCAAAGATAGGGCCACAGCTGTTGAACAGACATGTTGGGATGCAGTCTTTGAACCCAATGTGCTAGGTTACAATCCTCCGAACAAATTCTCCACTAAAAGGGTGCCGGAACAATTTCTAGAACAGGAGGATTTTTCAATCGAAAGTGTCTTGAATTATGCACAGGAATTACGTTATTTATTACCACAGAATAGGAATTTTTCCTTTTCTCTTAAAGAAAAGGAATTAAATATTGGACGAACATTTGGGAAGCTACCATATCTCACACGGAATGTCCAAACTTTATGTGAGGCTCTGTTAGCAGATGGACTGGCTAAGGCCTTCCCCAGTAACATGATGGTAGTAACTGAACGTGAACAAAAAGAGAGCCTTCTTCATCAGGCATCATGGCACCACACCAGTGATGATTTTGGAGAGAATGCTACCGTTCGAGGGAGTAGTTTTGTAACTGATTTAGAGAAGTACAATCTTGCATTTCGCTATGAGTTCACTGCACCATTTATTGAGTACTGCAACCATTGCTATGGTGTGCGTAATGTCTTTAATTGGATGCATTATTTAATCCCGCAGTGTTACATGCATGTAAGTGATTATTATAATCCGCCTCACAATGTTAATCTTAGCAATCGAGAATATCCTCCTGAAGGCCCGAGTTCGTACCGAGGACACTTAGGAGGCATAGAGGGATTACAACAAAAACTGTGGACGAGTATATCCTGTGCACAAATCTCCTTAGTGGAAATTAAAACTGGTTTTAAGTTACGATCAGCGGTCATGGGAGACAATCAGTGTATAACCGTATTGTCTGTTTTTCCACTTGAAACAGACCCTGAAGAGCAGGAGCAAAGCGCCGAAGACAATGCTGCAAGAGTAGCAGCAAGTCTTGCAAAAGTAACCAGTGCATGTGGGATCTTTCTTAAACCAGAAGAGACATTCGTACACTCAGGTTTCATTTATTTCGGAAAAAAACAATATCTCAACGGTGTACAATTACCGCAATCACTCAAAACAGCAGCAAGAATGGCGCCACTCTCTGATGCTATATTCGATGATCTACAAGGAACACTTGCCAGTATTGGAACTGCCTTCGAACGTGCTATATCGGAAACGCGACATATCCTCCCATGTCGTATCGTAGCAGCTTTCCATACGTATTTCGCCGTTCGGATTTTACAATATCACCATCTTGGATTTAATAAAGGCATCGATTTAGGGCAGTTGTCACTTAGTAAACCATTAGACTATGGGACTATTACTCTAACATTGGCGGTTCCACAAGTCCTTGGGGGATTGTCTTTTCTAAATCCAGAAAAGTGTTTTTATCGAAACTTCGGAGATCCTGTGACTTCTGGACTTTTCCAGCTACGGGTGTACCTAGAAATGGTTAACATGAAAGACTTATTTTATCCATTAATATCGAAAAATCCAGGAAATTGTAGTGCCATTGATTTTGTCTTAAATCCATCCGGATTAAATGTTCCAGGATCACAAGACTTGACATCCTTTTTGCGACAGATCGTTAGGCGTAGTATTACGCTAACTGCAAGAAATAAGTTAATTAACACTCTCTTCCATGCCTCTGCTGATTTGGAAGATGAGATGGTTTGTAAATGGCTCCTTTCATCAAACCCTGTTATGAGTCGCTTTGCAGCAGATATTTTTTCCAGGACACCTAGTGGTAAACGTCTCCAAATATTAGGTTATCTTGAAGGGACCAGGACTCTATTGGCCTCCAAAATCATAAACAACAACAGTGAGACACCTGTACTTGATAAGCTGAGGAAGATCACCCTACAAAGATGGAATCTGTGGTTCAGTTATTTGGACCATTGTGACCAATTACTAGCAGATGCTCTACAGAAGATTAGTTGCACGGTGGATTTGGCCCAGATTTTGCGTGAGTATACATGGTCACACATCTTAGAAGGTAGACCATTGATCGGAGCAACATTACCATGTATGGTGGAGCAATTCAAAGTTAAGTGGCTAGGACAGTATGAACCTTGTCCAGAATGCCTCAACAAAAAAGGCTCAAATGCTTATGTCTCAGTTGCAGTCAAAGATCAAGTGGTCAGTGCTTGGCCTAATACTTCTCGAATAAGTTGGACAATAGGGAGTGGTGTCCCCTATATAGGGTCAAGAACCGAGGATAAAATCGGACAGCCTGCAATCAAGCCGCGATGCCCTTCATCTGCCCTCAAGGAGGCTATAGAATTAGCATCAAGGCTCACTTGGGTTACACAAGGAAGTTCTAATAGTGAACAATTAATCCGGCCTTTCTTAGAAGCGAGAGTCAACCTTAGTGTCAGTGAAGTCCTGCAAATGACACCATCACATTATTCAGGAAATATTGTCCATCGATATAACGACCAATATAGCCCGCACTCATTTATGGCGAATCGCATGAGCAATACTGCGACCCGTCTCATAGTGTCAACTAATACACTTGGAGAATTTTCAGGTGGAGGGCAGGCCGCCAGGGATAGCAATATAATTTTCCAGAATGTTATAAATTTAGCAGTTGCCCTTTATGATATTAGATTCCGGAATACGAACACCTCTGATATAAGGCACAATAGGGCTCATCTTCACCTGACAGAGTGCTGTACTAAAGAGGTCCCGGCCCAGTATTTGACATATACAAGTGCACTTAATCTGGATTTAAGCCGTTATCGTGATAATGAACTAATATATGACTCAAATCCACTGAGGGGGGGATTGAACTGCAATTTAACAATGGATAGTCCCTTAGTGAAGGGTCCTAGGCTTAACATGATTGAAGATGATCTTCTCCGCTTTCCACACCTTTCTGGATGGGAGTTAGCGAAAACGGTGGTACAATCCATCATCTCAGACAATAGCAACTCATCAACAGATCCAATCAGCAGCGGAGAAACACGCTCTTTCACAACTCATTTCCTCACTTACCCTCAGATTGGCCTTCTTTACAGTTTCGGGGCAGTATTATGCTTTTATCTAGGCAATACTATCCTATGGACTAAAAAACTTGATTATGAACAGTTTCTATATTATTTGCATAACCAGCTGCACAACTTACCTCATCGAGCACTCCGTGTTTTTAAACCAACATTTAAGCATGCCAGTGTGATGTCCCGATTAATGGAGATTGATTCCAACTTCTCAATTTATATTGGCGGGACATCTGGAGATCGAGGGCTGTCTGATGCTGCTCGACTGTTTCTTCGGACAGCAATTGCGAGTTTTTTACAATTTCTTAAAAGCTGGATCATCGATCGCCAAAAGACAATTCCTTTATGGATAGTATATCCGCTTGAAGGTCAACAGCCGGAATCCATCAATGAATTTCTACATAAAATTTTGGGTCTGCTCAAACAAGGCCCCAAAAGTATTCCGAAGGAGGTCAGCATTCAAAATGATGGACATTTGGATTTAACAGAAAATAATTATGTTTACAATAGTAAGAGCACTGCTAGTAATTTCTTCCATGCATCCTTAGCTTACTGGAGAAGTAGGAAATCTTGGAAAACTCAAGACCATAATGATTTCTCAAGAAGGGATGGAACACTTACAGAACCCGTGTGTAAGTTCTCAAGCAATCATCAGTCAGATGAAAAGTACTACAATGTGACATGTGGAAAGTCACCAAAGCCACAAGAACGCAAAGACTTCTCGCAATACAGACTCAGCAATAACAGACGAACAATGAGTAATCATCGTAAGAAAGGGAAGTTCCACAAGTGGAATCCTTGCAAAGTGTTGATGGAGAGTCAAAGGGGAACTGTTCTAAAAGAAGGTGACTACTTTCAAAACAATACTCCACCAACAGATGATGTATCAAGTCCTCACCGACTCATTCTACCATTTTTTAAATTGGGAAATCACAACCATGCACATGATCAGGATGCCCAAGAATTGATAAGTCAAAATATTAAACAGTACCTACATCAGCTAAGGTCTATGTTGGACACTACTATATATTGTAGATTCACAGGGATTGTCTCATCCATGCATTACAAATTGGACGAAGTTCTTCTAGAATACAATAGTTTCGATTCAGCTATCACATTAGCTGAAGGTGAGGGGTCAGGGGCTCTATTACTTTTGCAGAAATATAGTACAAGGTTATTATTTTTGAACACATTGGCAACAGAACACAGTATAGAGTCAGAAGTTGTATCAGGTTTTTCTACTCCGAGAATGTTGTTACCAATAATGCAAAAGGTTCATGAAGGACAAGTCTCTGTTATCTTAAATAATTCAGCAAGTCAGATAACTGACATAACTAGCTCAATGTGGTTAAGTAATCAAAAATATAATCTACCTTGTCAAGTTGAAATCATTACGATGGATGCTGAAACAACAGAGAACTTAAACAGGTCCCAACTCTACCGAGCAGTATATAACTTAATACTTGATCACATTGATCCGCAGTATCTCAAGGTGGTGGTACTCAAAGTATTTCTGAGTGATATAGAAGGAATATTATGGATTAATGATTACTTGGCTCCATTATTCGGGGCTGGTTACTTGATTAAACCGATTACATCAAGTGCCCGGTCAAGTGAATGGTACCTTTGCTTATCAAATTTGATATCTACTAACAGGAGATCGGCCCATCAGACTCACAAGGCATGTCTTGGTGTTATCAGAGATGCTTTGCAAGCACAAGTCCAGCGAGGCGTGTACTGGTTGAGTCACATCGCACAGTATGCTACAAGGAATCTCCATTGTGAATACATATGCCTTGGTTTCCCACCTCTAGAAAAGGTCCTATATCACAGGTATAATCTAGTTGATACTGGACTCGGTCCATTGTCGTCAGTTATTAGACATTTAACTAACCTCCAGGCAGAGATACGAGACTTAGTATTGGATTATACCCTGATGAGAGAGAGTCGCACTCAAACGTACCATTTTATTAAGACTGCAAAAGGCAGAATCACAAAGTTAGTCAATGACTTTCTGAAGTTTTCTTTAATTGTCCAGGCGCTCAGAAATAATTCTTCTTGGTATACTGAGCTTAAAAAATTACCTGAGGTGATTAATGTGTGTAATCGATTTTATCATACTCACAGTTGCGAATGTCAGGAAAAATTCTTTGTCCAGACGCTTTATTTACAACGCCTACGCGATGCAGAAATCAAGCTAATTGAACGCCTTACCGGGTTAATGCGATTTTATCCAGAAGGGTTAATATATTCCAATCACACATAGGTACTAAATCATCATAGTATGAGGAATAAAATAATGATAATTCCTGACGACAGTTCTAGTTCCGATTCTAAGTATATCGGAAGAGAGTATGCCAATCTTAATCATCAAAGGTAACAAGCTATTAGTTATTACTTATTGATAAGAATAAACTTTATCATAGCGTAACACATCATAACTTTATAACGATTTTGCATTTCTAATCCTAGTATTTATTAGAATGTACTATCAGAGAAATGACCCCAGTCCCTACCTTTAAATAATGATTGTGTGTATTAAATTATTAGTTTATTAGGTTTATGAGTTGGTTACACAGTGAGTATTAGTAATTGAGGATTATGTAGATAGGCAATCTAATACTGAATCACCCATCTGATGTCACCATATCCAAATATTGTGCTAGTCACATTTAAACATGCTATCTTCAGTTAAGTAACATGGACTGAAAATGCTAAGAAGAGATTGGAGTAAAAGTATAAAGTAAATTTAATCAAACTTCAAAGTGATTAAATGATAATGATCTTGGGTACTCGATATGACCTCAAGTCAAAAATAATGTCAATATAATTGTTTAGTAATATGAGTTATAATGTGAATTTTGATAACTAACTAACTTTAGTAGTTAAGATCAAATGCAAACATTCTAAGAA\n>Reston_Ebola_virus_strain_Pennsylvania_complete_genome\nCGGACACACAAAAAGAAAAAAGGTTTTTTAAGACTTTTTGTGTGCGAGTAACTATGAGGAAGATTAACAGTTTTCCTCAGTTTAAGATATACACTGAAATTGAGATTGAGATTCTCCTCTTTGCTATTCTGTAACTTTCCCTGGTTGTGACAATTGAATCAGTTTTATCTATTACCAATTACCATCAACATGGTATGTCTAGTGATCTTGGGACTCTTCTTCATCTGGTTTTTCCTAGAGCTCTGAATCCATTTTGCGAGAAGTTCATCCAAACGACCCAGTGTCTGAAAATACAAAAGGTTCCCCTTTCCGTCAAGTTTAAGGGGTTGTTTTGATTGTGTGTAGATTTTATAATCCTAGAGTGCCAAGGAGTTGCGTGTCATCATTGATTGGGAAGATCAAGGAAACAATTTGTTCCAATAATATCGTACATCTTGACTAAGTCGAACAAGGGGAAGTCGATATGGATCGTGGGACCAGAAGAATCTGGGTGTCGCAAAATCAAGGTGATACTGATTTAGATTATCATAAAATTTTGACAGCTGGCCTTACTGTTCAACAGGGAATTGTCAGGCAGAAAATAATTTCTGTATATCTTGTTGATAACTTGGAGGCTATGTGTCAATTGGTAATACAAGCCTTTGAGGCCGGAATTGATTTCCAAGAAAATGCCGACAGCTTCCTTCTGATGCTTTGCCTACATCATGCTTACCAAGGTGACTATAAATTGTTCTTGGAGAGCAATGCTGTACAGTATTTGGAAGGTCATGGATTCAAATTTGAGCTCCGGAAGAAGGACGGTGTCAATCGGCTCGAGGAATTGCTTCCTGCTGCAACGAGTGGAAAAAACATCAGGCGTACGTTGGCCGCACTGCCTGAAGAGGAGACTACAGAAGCAAATGCAGGGCAATTTCTCTCATTTGCGAGTTTGTTTCTTCCCAAACTGGTTGTGGGAGAGAAGGCTTGCTTGGAAAAAGTCCAGCGACAAATTCAGGTTCATGCAGAACAGGGTTTAATTCAATATCCCACTGCATGGCAATCAGTTGGACACATGATGGTAATCTTCAGATTGATGAGGACTAATTTCTTGATTAAATATTTACTGATCCACCAGGGTATGCATATGGTAGCTGGCCACGATGCCAATGATGCTGTCATTGCTAATTCAGTTGCTCAGGCTCGCTTTTCAGGACTCCTAATTGTCAAAACCGTTCTTGATCATATTCTGCAAAAAACCGACCAAGGAGTAAGACTTCACCCTTTGGCCCGAACAGCCAAAGTGCGTAATGAGGTTAATGCATTTAAGGCCGCCCTAAGCTCACTTGCTAAGCATGGGGAATATGCCCCTTTTGCTCGCCTTCTCAATCTCTCGGGAGTTAACAACCTAGAACATGGTCTCTACCCACAGTTATCAGCAATTGCTCTTGGAGTTGCCACAGCACATGGTAGCACCCTTGCAGGAGTTAATGTTGGTGAGCAGTATCAGCAGCTTAGAGAGGCTGCCACTGAAGCTGAGAAGCAACTCCAACAATATGCTGAGTCCAGAGAACTCGACAGCCTAGGCCTGGACGATCAGGAAAGAAGAATACTAATGAACTTCCATCAGAAGAAAAACGAAATTAGTTTCCAGCAGACCAATGCAATGGTAACCCTTAGGAAAGAGCGACTGGCTAAATTAACAGAAGCTATAACGCTGGCCTCAAGACCTAACCTCGGGTCTAGACAAGACGACGGCAATGAAATACCGTTCCCTGGGCCTATAAGCAACAACCCAGACCAAGATCATCTGGAGGATGATCCTAGAGACTCCAGAGACACCATCATTCCTAATGGTGCAATTGACCCCGAGGATGGTGATTTTGAAAATTACAATGGCTATCATGATGATGAAGTTGGGACGGCAGGTGACTTGGTCCTGTTCGATCTTGACGATCATGAGGATGACAATAAAGCTTTTGAGCCACAGGACAGCTCGCCACAATCCCAAAGGGAAATAGAGAGAGAAAGATTAATTCATCCACCCCCAGGCAACAACAAGGACGACAATCGAGCCTCAGACAACAATCAACAATCAGCAGATTCTGAGGAACAAGGAGGTCAATACAACTGGCACCGAGGCCCAGAACGTACGACCGCCAATCGAAGACTCTCACCAGTGCACGAAGAGGACACCCTTATGGATCAAGGTGATGATGATCCCTCAAGCTTACCTCCGCTGGAATCTGATGATGACGATGCATCAAGTAGCCAACAAGATCCCGATTATACAGCTGTTGCCCCTCCTGCTCCTGTATACCGCAGTGCAGAAGCCCACGAGCCTCCCCACAAATCCTCGAACGAGCCAGCTGAAACATCACAATTGAATGAAGACCCTGATATCGGTCAATCAAAGTCTATGCAAAAATTAGAAGAGACATATCACCATCTGCTGAGAACTCAAGGTCCATTTGAAGCCATCAATTATTATCACATGATGAAGGATGAGCCGGTAATATTTAGCACTGATGATGGGAAGGAATACACCTACCCGGATTCACTTGAGGAAGCCTATCCTCCATGGCTCACCGAGAAAGAACGACTGGACAAAGAGAATCGCTACATTTACATAAATAATCAACAGTTCTTCTGGCCTGTCATGAGTCCCAGAGACAAATTTCTTGCAATCTTGCAGCACCATCAGTAACCACAGCACAAAGCGCGGTCCACTTCGTAAAGCTAAATACACTTAAGACTTGACCGATTCATCTACAAAAACTAATCCATTATAACTTATTAGTGCTACTTTTCTATAAGTGATTCTTAATCTAAGGCCATTAAGAGTTTAAGTAATATACATATACACTTACACCGGTCTATCCAAGATGTGGCTCAATGTTCTTGATTTGAACATAGTCATAAGGGGATAAATAATACTTTATATTTCTGATTGTGGATTGACCCATTCTGCTTAAAATGCTTCGCCCATTGAAAATGTGATCTAATAGATAGCCCTGACTAGACAAATTAAGAAAAACATTTGATGAAGATTAAAACCTTCATCGCCAGTAAATGATTATATTGTCTGTAGGCAGGTGTTTACTCCACCTTAAATTTGGAAATATCCTACCTTAGGACCATTGTCAAGAGGTGCATAGGCATTACCACCCTTGAGAACATGTACAATAATAAATTGAAGGTATGTTCAGGCCCAGAAACGACTGGATGGATTTCTGAGCAACTTATGACAGGTAAGATTCCAGTAACTGATATATTCATTGATATTGATAACAAGCCAGATCAAATGGAAGTCCGACTCAAACCATCATCAAGGAGCTCAACAAGAACTTGTACAAGTAGCAGTCAGACGGAGGTCAACTATGTACCTCTCCTTAAAAAGGTTGAGGATACATTAACTATGCTAGTGAATGCCACCAGTCGTCAGAATGCTGCAATCGAGGCCCTTGAAAACCGCCTCAGCACACTTGAGAGTAGCTTAAAGCCAATCCAAGACATGGGTAAAGTGATTTCATCATTGAATCGCAGTTGTGCCGAAATGGTTGCAAAATATGATCTTCTAGTTATGACAACTGGACGGGCTACTTCAACTGCAGCTGCAGTAGATGCGTATTGGAAAGAGCACAAACAGCCACCACCAGGGCCAGCGTTGTATGAAGAGAATGCGCTTAAAGGAAAAATCGATGATCCAAACAGCTATGTACCAGATGCTGTGCAAGAGGCTTACAAGAACCTTGACAGTACATCGACCCTGACCGAGGAAAATTTTGGGAAACCTTATATATCTGCTAAAGACCTGAAGGAGATCATGTATGATCATCTACCTGGTTTTGGGACTGCCTTTCACCAACTTGTTCAAGTGATTTGTAAAATAGGAAAGGATAACAACCTTTTGGACACAATCCATGCTGAGTTCCAGGCAAGTCTAGCAGATGGTGACTCTCCCCAATGTGCACTCATACAGATAACCAAAAGGGTCCCAATCTTTCAGGATGTGCCGCCCCCGATAATCCATATTAGATCCCGTGGTGACATCCCACGAGCATGCCAAAAGAGTCTCCGACCAGCACCACCATCACCCAAAATTGATCGTGGTTGGGTTTGTTTGTTTAAGATGCAAGATGGTAAAACGCTTGGACTTAAGATCTAAGAATCAAGATTTATTTAACAAGGCAAGCCACAACCTTAGATGGAACCTCAGCCAGACTATTGAACTATTGACGCTGTTGATGATAATATATAATTAATGGTCTTATTTGAATATGACAACATCTTGCTTCTTGTTCTGCCTTGTAGCTCTTTGAATTGGAAGATCATTCCAAACTTACAAACATGCACAAGATGTTATGGTTTAGCAAAGAATTGATAGGAGTACTGGTATATAATGTAAATATAACAAGTGATGAAGATTAAGAAAAACCAGTCGGTATTTTCCAGACTTGGCATTTCTTATCTTCATCTTCTAAAGTGAGATATTTTATCATCAAAAAATGAGGCGCGGAGTGTTACCAACGGCTCCTCCAGCATATAATGATATTGCATACCCTATGAGCATACTCCCAACCCGACCAAGTGTCATAGTCAATGAGACCAAATCAGATGTACTGGCAGTGCCAGGGGCAGATGTTCCATCAAACTCCATGAGACCAGTGGCTGATGATAACATTGATCACTCAAGCCATACTCCAAGCGGAGTAGCTTCTGCCTTTATATTGGAAGCTACAGTGAATGTAATTTCGGGAACAAAAGTCCTGATGAAGCAAATACCTATTTGGCTTCCACTGGGTGTAGCTGATCAGAAGATATACAGCTTTGATTCAACAACAGCCGCAATTATGTTGGCTTCCTACACAGTGACACACTTCGGGAAGATATCTAACCCGCTGGTACGTGTCAACAGGCTAGGCCCAGGAATACCCGATCATCCGCTACGACTCCTAAGGTTGGGCAATCAGGCATTCCTTCAAGAGTTTGTTCTTCCACCAGTCCAGCTTCCCCAGTATTTCACATTTGATCTAACAGCTCTAAAGCTCATCACTCAACCATTGCCAGCTGCAACCTGGACAGACGAAACTCCAGCAGGAGCAGTCAATGCTCTTCGTCCTGGGCTCTCACTCCATCCCAAGCTTCGTCCAATTCTCCTGCCGGGGAAGACAGGAAAGAAAGGACATGCTTCAGACTTAACATCACCTGACAAGATTCAAACAATCATGAATGCAATACCGGACCTCAAAATTGTCCCGATTGATCCAACCAAGAACATAGTTGGAATTGAGGTTCCAGAATTACTAGTTCAAAGGCTGACCGGCAAAAAACCACAACCCAAAAATGGCCAACCAATTATTCCAGTTCTTCTTCCGAAATATGTTGGACTTGATCCTATATCGCCAGGGGACTTAACTATGGTTATCACCCAGGATTGTGATTCATGCCACTCTCCAGCCAGCCATCCGTATCACATGGACAAGCAGAATAGTTACCAATAATTTAAATTCCATTCGAGCTATTATTCTGCTAGTAATTCCGACGGGATCAATAGACTAAAAATCTGATTGTATAGAATTATAAAAGAATCAAGCAGAGGCAACAGACTCACAGCTTACGCCTAGATAACTAATATTAAGGAGTTTTTTAATCTAATTTTCCAGTCTTGAGTAATAATCATTTCTTTTGTAATTAATTATGCATTTGTTAACTTATCGGTGCGAGATTTCCTTGAGAACCCGGCGGAGCTTCTACTATCTGCAGTAACCAGAAGAGAAGTTCAACCCAGTCAAAACTAAACCAAGCAATATTCTGAATGCTCTATAGTCTATTCTAATCAGAGGTATAACAATGGCTAAGATTTCAATGACTCGTTAACAATCGCTAGTAATTTTAATCTCCAGATTAAGAAAAAGATATACGATGAAGATTAAGGCGACAACGAGCCGAAACTTCATCTCTTTTAAAGATCTAACATTATCTGTTCCAAAGTCATACAAGGACACATTCAAATCAGGGATTGTAAGCTGCTATTTCTTACCTCCCCAAATTACCTATACAACATGGGGTCAGGATATCAACTTCTCCAATTGCCTCGGGAACGTTTTCGTAAAACTTCGTTCTTAGTATGGGTAATCATCCTCTTCCAGCGAGCAATCTCCATGCCGCTTGGTATAGTGACAAATAGCACTCTCAAAGCAACAGAAATTGATCAATTGGTTTGTCGGGACAAACTGTCATCAACCAGTCAGCTCAAGTCTGTGGGGCTGAATCTGGAAGGAAATGGAATTGCAACCGATGTCCCATCAGCAACAAAACGCTGGGGATTTCGTTCAGGTGTGCCTCCCAAGGTGGTCAGCTATGAAGCCGGAGAATGGGCAGAAAATTGCTACAATCTGGAGATCAAAAAGTCAGACGGAAGTGAATGCCTCCCTCTCCCTCCCGACGGTGTACGAGGATTCCCTAGATGTCGCTATGTCCACAAAGTTCAAGGAACAGGTCCTTGTCCTGGTGACTTAGCTTTCCATAAAAATGGGGCTTTTTTCTTGTATGATAGATTGGCCTCAACTGTCATCTACCGAGGGACAACTTTTGCTGAAGGTGTCGTAGCTTTTTTAATTCTGTCAGAGCCCAAGAAGCATTTTTGGAAGGCTACACCAGCTCATGAACCGGTGAACACAACAGATGATTCCACAAGCTACTACATGACCCTGACACTCAGCTACGAGATGTCAAATTTTGGGGGCAATGAAAGCAACACCCTTTTTAAGGTAGACAACCACACATATGTGCAACTAGATCGTCCACACACTCCGCAGTTCCTTGTTCAGCTCAATGAAACACTTCGAAGAAATAATCGCCTTAGCAACAGTACAGGGAGATTGACTTGGACATTGGATCCTAAAATTGAACCAGATGTTGGTGAGTGGGCCTTCTGGGAAACTAAAAAAACTTTTCCCAACAACTTCATGGAGAAAACTTGCATTTCCAAATTCCATCAACCCACACCAACAACTCCTCAGATCAGAGCCCGGCGGGAACTGTCCAAGGAAAAATTAGCTACCACCCACCCGCCAACAACTCCGAGCTGGTTCCAACGGATTCCCCTCCAGTGGTTTCAGTGCTCACTGCAGGACGGACAGAGGAAATGTCGACCCAAGGTCTAACCAACGGAGAGACAATCACAGGTTTCACCGCGAACCCAATGACAACCACCATTGCCCCAAGTCCAACCATGACAAGCGAGGTTGATAACAATGTACCAAGTGAACAGCCGAACAACACAGCATCCATTGAAGACTCCCCCCCATCGGCAAGCAACGAGACAATTTACCACTCCGAGATGGATCCGATCCAAGGCTCGAACAACTCCGCCCAGAGCCCACAGACCAAGACCACGCCAGCACCCACAACATCCCCGATGACCCAGGACCCGCAAGAGACGGCCAACAGCAGCAAACCAGGAACCAGCCCAGGAAGCGCAGCCGGACCAAGTCAGCCCGGACTCACTATAAATACAGTAAGTAAGGTAGCTGATTCACTGAGTCCCACCAGGAAACAAAAGCGATCGGTTCGACAAAACACCGCTAATAAATGTAACCCAGATCTTTACTATTGGACAGCTGTTGATGAGGGGGCAGCAGTAGGATTGGCATGGATTCCATATTTCGGACCTGCAGCAGAAGGCATCTACATTGAGGGTGTAATGCATAATCAGAATGGGCTTATTTGCGGGCTACGTCAGCTAGCCAATGAAACTACCCAGGCTCTTCAATTATTTCTGCGGGCCACAACAGAACTGAGGACTTACTCACTTCTTAACAGAAAAGCTATTGATTTTCTTCTTCAACGATGGGGAGGTACCTGTCGAATCCTAGGACCATCTTGTTGCATTGAGCCACATGATTGGACAAAAAATATTACTGATGAAATTAACCAAATTAAACATGACTTTATTGACAATCCCCTACCAGACCACGGAGATGATCTTAATCTATGGACAGGTTGGAGACAATGGATCCCGGCTGGAATTGGGATTATTGGAGTTATAATTGCTATAATAGCCCTACTTTGTATATGTAAGATTTTGTGTTGATTTATTCTGAGATCTGAGAGAGAAAAATCTCAGGGTTACTCTAAGGAGAAATATTATTTTTAAAATTTACTTGAATGCTGACCACTTATCTTAAATGAGCAATTAATAATATGTTTTTCTGCTTCTTTGCTTGATTTACAATATGATATTTCTCTTAATAATGATTAATATATTAAGAAAAACTTATGACGAAGATTAAAGGAGAGGATCGTTAACGGGAAAACCTCCCATCTCGTTCGTCGAAGCCACGTTGGTGGTGCTTGCAGCTGAGAACAACTCCAGAGATTGTAGGTAGAAAGGACCAACATTTATAGGTAGGGGTCAGAAAGCAACAATAACCATAAAAGGAGAGCCTGACATTGCTATTTAATATCCTAGAACCTGATTTCTAGGTTCTAGCTTTAAAATCCGGATGATGGAGCATTCAAGAGAACGGGGTAGATCTAGCAACATGCGACATAATAGCCGGGAACCATACGAAAATCCATCAAGGTCTCGCTCATTATCTCGGGACCCTAATCAGGTTGATCGTAGACAGCCTCGAAGTGCATCCCAAATTCGTGTTCCGAATCTGTTCCATCGGAAAAAGACTGATGCACTCATAGTTCCTCCGGCTCCTAAAGATATATGCCCAACACTCAAAAAAGGATTCCTCTGCGATAGCAAATTTTGCAAAAAAGATCACCAATTGGATAGCTTAAATGATCATGAATTACTACTGCTAATTGCAAGAAGAACATGTGGAATTATCGAGAGCAATTCGCAGATTACATCCCCAAAAGATATGCGGTTAGCGAATCCAACAGCTGAAGACTTCTCACAAGGTAATAGTCCTAAATTAACACTTGCAGTCCTTCTTCAAATTGCTGAACATTGGGCAACCAGAGACCTAAGGCAAATTGAGGACTCTAAACTTAGAGCTCTTTTAACCCTTTGTGCCGTATTAACAAGGAAATTTTCTAAATCCCAACTGGGTCTTCTATGTGAGACCCACCTACGGCATGAGGGCCTCGGACAGGACCAAGCTGATTCTGTATTAGAGGTCTACCAAAGACTCCACAGTGATAAAGGAGGGAATTTTGAGGCTGCCCTGTGGCAACAATGGGACCGACAGTCATTAATAATGTTCATCTCTGCTTTTCTCAACATTGCTCTCCAGATACCTTGTGAAAGTTCTAGTGTCGTAGTCTCAGGTCTTGCCACATTGTACCCAGCACAAGACAATTCTACACCATCCGAGGCAACTAATGATACCACCTGGTCAAGTACAGTTGAATAGAAAACCACTGGAGCTATTTTTCCACGATTGCTCTCAGTCAATAAATTAATATAGATATAATACGACTTCGGTGTGCAATTGTCAAGAGTTCCATTTAGTAATAATGATTCTTAAAACAATCTACTATCGCAATTATCGATGGATCTACCCTATTTGACGGTACATGACTTGAATGTAATAAGGTAAGTTGGTATCTGAGGTATTTTGTCTAGAGTATACTCAAAATCGTATGTCTAGCAAATTATCAATAGCAAAGTTAAATTCTCCTAACCTCATATTTTGATCAAGTAATCATGATTTTATGATAATTCTTTTCAGATTATCGGTTTAATCTTTATTAAGAAAAAATCATGATTGTAGACAATTTACTGGTAGTCCTTGGGTATCCAAGTTTATGAATAGAGCTAGAGAGAATTTGCTACTTCCGAGGTATAACTTTATTATTTGCTACTTCGAATGCCTAAAACCAGTAATGCAGGATGAAGATTAATTGCGGAGGAATCAGGAATTCAACTTTAGTTCCTTAAGGCCTCGTCCGAATCTTCATCAGTTCGTAAGTTCTTTTATAGAAGTCATTAGCTTCTAAGGTGATTATATTTTAGTATTAAATTTTGCTAATTGCTTGCTATAAAGTTGAAATGTCTAATGCTTAAATGAACACTTTTTTGAAGCTGACATACGAATACATCATATCATATGAAAACATCGCAATTAGAGCGTCCTTGAAGTCTGGCATTGACAGTCACCAGGCTGTTCTCAGTAGTCTGTCCTTGGAAGCTCTTGGGGAGACAAAAAGAGGTCCCAGAGAGTCCCAACAGGTTGGCATAAGGTCATTAACACCAGCATAGTCGGCTCGACCAAGACTGTAAGCGAGTCGATTTCAACTAAAAAGATTATTTCTTGTTGTTTAAACAAATTCCTTTTGTGTGAGACATCCTCAAGGCACAAGATGGCTAAAGCCACAGGCCGATACAATCTCGTGCCCCCAAAGAAAGATATGGAAAAGGGAGTGATTTTTAGTGATCTTTGTAATTTCTTGATTACTCAAACCCTGCAAGGTTGGAAGGTTTATTGGGCAGGAATTGAGTTTGATGTAAGTCAAAAAGGCATGGCTCTTCTGACAAGACTCAAAACAAATGACTTTGCTCCTGCCTGGGCGATGACAAGAAATCTTTTCCCACATCTGTTCCAGAACCCAAATTCGGTTATTCAATCTCCCATCTGGGCTTTGAGGGTAATTTTGGCAGCCGGATTGCAGGATCAGTTGTTAGACCATTCATTGGTTGAGCCATTGACAGGGGCTCTCGGTCTAATTTCTGATTGGCTCCTAACTACAACGTCAACACATTTCAATCTTCGTACTAGAAGCGTAAAGGACCAGCTTAGTCTTCGTATGTTATCTTTGATCAGGTCAAACATCTTGCAGTTCATCAACAAGCTTGACGCCCTGCATGTTGTCAATTACAATGGTTTACTCAGTAGTATTGAGATCGGGACTTCTACACACACAATCATTATAACTCGTACAAATATGGGTTTTCTCGTGGAAGTTCAAGAGCCTGACAAATCAGCTATGAATTCTAAGCGCCCAGGACCAGTCAAGTTCTCATTACTTCATGAGTCTGCCTTCAAACCTTTCACTCGTGTTCCACAATCTGGGATGCAATCATTAATAATGGAGTTCAACAGTTTGTTGGCAATTTAACAAGGTAATCTTAAAATAAGTACATGAATGAGAATTAGTTGTGGGTCTTATCTAGCATTGTTGAGTTAACTATCTAATCTATTTTCGCTAATTGCATTGAGCACTGCTAATAGGTTTGTATCACGTTAAAGATTTAGAGTGTATGAATTGTGCAGATTTAAACTTGGGTTTTGCCTTATGCTTCATAGGTGGTCTTTTTGAAATGGAGATTATCAGCATTTCTTAAATGGGAGGAGTTAGCAATCAGAAATTGGAGATAAATGGACATCGGGATAGAACAATGCCTAACTATTGGGCGGCTTCCATTTTTACATGTGTATATAACCAATCTTTTCCTATCTTTGCTTATATTGGTGTAACTTTATTTTAATAACATGTCAATGCTATACTGTTAAGAGAAGGTCTGAGGAAGATTAAGAAAAAGGCCTCGTGTTCACTTGGTTGCCGTCAAGTATCCTGTGGTTTTTTTCTACCTAACTTCCTCATGCCATATGGCTACCCAGCATACCCAGTACCCGGATGCACGTTTATCCTCACCTATAGTCCTGGATCAATGTGATTTGGTAACTCGAGCATGTGGGTTATATTCATCTTATTCTCTAAATCCTCAACTAAGGCAATGTAAATTACCAAAACATATATATCGACTTAAGTTCGACACAATAGTATCCAAATTCCTAAGTGATACACCTGTAGCAACACTGCCGATAGACTATTTAGTACCAATTCTCCTGCGTTCCCTAACGGGGCACGGTGATAGGCCATTGACCCCGACTTGCAATCAATTCCTTGATGAAATTATTAATTACACTCTTCATGATGCAGCCTTTCTTGATTACTATCTCAAGGCAACAGGTGCACAGGACCATTTGACAAACATTGCAACTAGAGAGAAGCTTAAAAACGAAATTCTAAACAATGATTATGTCCATCAATTGTTCTTCTGGCATGACCTTTCTATTTTGGCTCGACGTGGGCGTCTGAATCGCGGGAACAACCGTTCAACCTGGTTTGTTCATGATGAATTCATTGATATTTTAGGATATGGCGATTATATTTTTTGGAAAATACCTTTATCATTATTACCAGTTACTATAGACGGGGTCCCACACGCAGCAACTGACTGGTATCAACCGACTCTTTTTAAAGAATCCATCCTAGGGCATAGCCAAATCCTATCTGTGTCAACAGCTGAAATACTAATTATGTGTAAAGATATTATCACCTGTAGGTTTAATACATCACTGATTGCATCCATTGCAAAATTAGAGGATGTAGATGTGTCTGATTATCCTGACCCGAGTGATATTCTTAAGATATACAATGCTGGAGACTATGTAATATCTATTCTTGGCTCAGAGGGTTATAAGATAATAAAGTACCTTGAACCACTTTGTTTGGCCAAAATCCAACTTTGCTCTAAATTCACAGAAAGAAAAGGTCGTTTCCTCACACAGATGCATTTATCAGTAATAAATGATCTTCGGGAGTTGATTTCTAACCGCAGGTTAAAGGACTATCAGCAAGAGAAGATTAGAGATTTTCACAAAATATTATTACAATTGCAATTATCTCCTCAACAGTTTTGTGAATTATTCTCTGTTCAAAAACATTGGGGGCATCCAATTTTACATAGTGAGAAAGCTATACAAAAAGTAAAACGGCATGCAACCATCCTTAAGGCTCTCAGACCTAATGTCATCTTTGAGACATATTGTGTATTCAAGTACAATATTGCCAAGCACTATTTCGACAGCCAAGGAACTTGGTACAGTGTAATCTCAGACAGGAATTTAACTCCAGGACTCAACTCCTTCATAAAACGTAATCACTTTCCTTCACTACCCATGATTAAGGATCTTCTATGGGAATTCTATCATCTTAATCACCCTCCGTTATTCTCTACAAAGGTGATTAGTGACTTAAGTATTTTCATCAAAGATAGGGCCACAGCTGTTGAACAGACATGTTGGGATGCAGTCTTTGAACCCAATGTGCTAGGTTACAATCCTCCAAACAAATTCTCCACTAAAAGGGTGCCGGAACAATTTCTAGAACAAGAGGATTTTTCAATCGAAAGTGTCCTGAATTATGCACAGGAATTACATTATTTATTACCACAGAATAGGAATTTTTCCTTTTCTCTCAAAGAAAAGGAATTAAATATTGGACGAACATTTGGGAAGCTACCATATCTCACACGGAATGTCCAAACTTTATGTGAGGCTCTGTTAGCAGATGGACTGGCCAAGGCCTTCCCCAGTAACATGATGGTAGTAACTGAACGTGAACAAAAAGAGAGCCTTCTTCATCAGGCATCATGGCACCACACCAGTGATGATTTTGGAGAGAATGCTACCGTTCGAGGGAGTAGTTTTGTAACTGATTTAGAGAAGTACAATCTTGCATTTCGCTATGAGTTCACTGCACCATTTATTGAGTACTGCAACCATTGCTATGGTGTGCGTAATGTCTTTAATTGGATGCATTATTTAATCCCGCAGTGTTACATGCATGTAAGTGATTATTATAATCCGCCTCACAATGTTAATCTTAGCAATCGAGAATATCCTCCTGAAGGCCCGAGTTCGTACCGAGGGCACTTAGGAGGCATAGAGGGATTACAACAAAAACTGTGGACGAGTATATCCTGTGCACAAATCTCCTTAGTGGAAATTAAAACTGGTTTTAAGTTACGATCAGCGGTCATGGGAGACAATCAGTGTATAACCGTATTGTCTGTTTTTCCACTTAAAACAGACCCTGAAGAGCAGGAGCAAAGCGCCGAAGACAATGCTGCAAGAGTAGCAGCAAGTCTTGCAAAAGTAACCAGTGCATGTGGGATCTTTCTTAAACCAGATGAGACATTTGTACACTCAGGTTTCATTTATTTCGGAAAAAAACAATATCTCAATGGTGTACAATTACCGCAATCACTCAAAACAGCAGCAAGAATGGCACCACTCTCTGATGCTATATTCGATGATCTACAAGGAACACTTGCCAGTATTGGAACTGCCTTCGAACGTGCTATATCGGAAACGCGACATATCCTCCCATGTCGTATTGTAGCAGCTTTCCATACGTATTTCGCCGTTCGGATTTTACAATATCACCATCTTGGATTTAATAAAGGCATCGATTTAGGACAGTTGTCACTTAGTAAACCATTAGACTATGGGACTATTACTCTAACATTGGCGGTTCCACAAGTCCTTGGGGGATTGTCTTTTCTAAATCCAGAAAAGTGTTTTTATCGAAACTTCGGAGATCCTGTGACTTCTGGACTTTTCCAGCTACGGGTGTACCTAGAAATGGTTAACATGAAAGACCTATTTTGTCCATTAATATCGAAAAATCCAGGAAATTGTAGTGCCATTGATTTTGTCTTAAATCCATCCGGATTAAATGTTCCAGGATCACAAGACTTGACATCCTTTTTGCGACAAATCGTTAGGCGTAGTATTACCCTAACTGCTAGAAATAAGTTAATTAACACTCTCTTCCATGCCTCTGCTGATTTGGAAGATGAGATGGTTTGTAAGTGGCTCCTTTCATCAAACCCTGTCATGAGTCGCTTTGCAGCGGATATTTTTTCCAGGACACCGAGTGGTAAACGTCTCCAAATATTAGGTTATCTTGAAGGGACCAGGACTCTATTGGCCTCCAAAATCATAAACAACAACAGTGAGACACCTGTACTTGATAAGCTGAGGAAGATCACCCTACAAAGATGGAATCTGTGGTTCAGTTATTTGGACCATTGTGACCAATTACTAGCAGATGCTCTACAGAAAATTAGTTGCACGGTGGATTTGGCCCAGATTTTGCGTGAGTATACATGGTCACACATCTTAGAGGGTAGATCATTGATCGGAGCGACATTACCATGTATGGTGGAGCAATTCAAAGTTAAGTGGCTAGGACAATATGAACCTTGTCCAGAATGTCTCAACAAAAAAGGCTCAAATGCTTATGTCTCAGTTGCAGTCAAAGATCAAGTGGTCAGTGCTTGGCCTAATACTTCTCGAATAAGTTGGACAATAGGGAGTGGTGTCCCCTATATAGGGTCAAGAACCGAGGATAAAATCGGACAGCCTGCTATCAAGCCGCGATGCCCTTCATCTGCCCTCAAGGAGGCTATAGAATTAGCATCAAGGCTCACTTGGGTTACACAAGGAGGTTCTAATAGTGAACAATTAATCCGGCCTTTCTTGGAAGCGAGAGTCAACCTTAGTGTCAGTGAAGTCCTGCAAATGACACCATCACATTATTCAGGAAATATTGTCCATCGATATAACGACCAATACAGCCCGCACTCATTTATGGCGAATCGCATGAGCAATACTGCGACCCGTCTCATAGTGTCAACTAATACACTTGGAGAATTTTCAGGTGGAGGGCAGGCCGCCAGGGATAGCAATATAATTTTCCAGAATGTTATAAATTTAGCAGTTGCCCTTTATGATATTAGATTCCGGAATACAAACACCTCTGATATAAGGCATAATAGGGCTCATCTTCACCTGACAGAGTGCTGTACTAAAGAGGTCCCGGCCCAGTATTTGACATATACAAGTGCACTTAATCTGGATTTAAGCCGTTATCGTGATAATGAACTAATATATGACTCAAATCCACTGAAGGGAGGATTGAACTGCAATTTAACAATAGATAGTCCTTTAGTGAAGGGTCCTAGGCTTAACATGATTGAAGATGATCTTCTCCGCTTTCCACACCTTTCTGGATGGGAGTTAGCGAAAACGGTGGTACAATCCATCATCTCAGACAATAGCAACTCATCAACAGATCCAATCAGTAGCGGAGAAACACGCTCTTTCACAACTCATTTTCTCACTTACCCTCAGATTGGCCTTCTTTACAGTTTCGGAGCAGTATTATGCTTTTATCTAGGCAATACTATCCTATGGACTAAAAAACTTGATTACGAACAGTTTCTATATTATTTGCATAACCAGCTGCACAACTTACCTCATCGAGCACTCCGTGTTTTTAAACCAACATTTAAGCATGCCAGTGTGATGTCCCGATTAATGGAAATTGATTCTAACTTCTCAATTTATATTGGCGGGACATCTGGAGATCGAGGGCTGTCTGATGCTGCTCGACTGTTTCTTCGGACAGCAATCGCGAGTTTTTTACAATTTCTTAAAAGCTGGATCATCGATCGCCAAAAGACAATTCCTTTATGGATAGTATATCCGCTTGAAGGTCAACAGCCGGAATCCATCAATGAATTTCTACATAAAATTTTGGGTCTGCTCAAACAAGGCCCCAAAAGTATTCCAAAGGAGGTCAGCATCCAAAATGATGGACATTTGGATTTGGCAGAAAATAATTATGTTTACAATAGTAAGAGCACTGCTAGTAATTTCTTCCATGCATCCTTAGCTTACTGGAGAAGTAGGAAATCTCGGAAAACTCAAGACCATAATGATTTCTCAAGAGGGGATGGAACACTTACAGAACCCGTGCGTAAGTTTTCAAGCAATCATCAGTCAGATGAAAAGTACTACAATGTGACATGTGGAAAGTCACCGAAGCCGCAAGAACGCAAAGACTTCTCGCAATACAGACTCAGCAATAACGGGCAAACAATGAGTAATCATCGTAAGAAAGGGAAGTTCCACAAGTGGAATCCCTGCAAAATGTTAATGGAGAGTCAAAGGGGAACTGTTCTAACAGAGGGTGACTACTTTCAAAACAATACTCCACCAACAGATGATGTATCAAGTCCTCACCGACTCATTCTACCATTTTTTAAATTGGGAAATCACAACCATGCACATGATCAAGATGCCCAAGAATTGATGAATCAAAATATTAAACAGTACCTACATCAGCTAAGGTCTATGTTGGACACCACTATATATTGTAGATTCACAGGGATTGTCTCATCCATGCATTACAAATTGGACGAAGTTCTTCTAGAATACAATAGTTTCGATTCAGCTATCACATTAGCTGAAGGTGAGGGGTCAGGGGCTCTATTACTTTTGCAAAAATATAGTACAAGGTTATTATTTTTGAACACATTGGCAACAGAACACAGTATAGAATCAGAAGTTGTATCAGGTTTTTCTACTCCGAGAATGTTGTTACCAATAATGCAAAAGGTTCATGAAGGACAAGTCACTGTTATCTTAAATAATTCAGCAAGTCAGATAACTGACATAACTAGCTCAATGTGGTTAAGTAATCAAAAATATAATCTACCTTGTCAAGTTGAAATCATTATGATGGATGCTGAAACAACAGAGAACTTAAACAGGTCCCAACTCTACCGAGCAGTATATAACTTAATACTTGATCACATTGATCCGCAGTATCTCAAGGTGGTGGTACTCAAAGTATTTCTGAGTGATATAGAAGGAATATTATGGATTAATGATTACTTGGCTCCATTATTCGGGGCTGGTTACTTGATTAAACCGATTACATCAAGTGCCCGGTCAAGTGAATGGTACCTTTGCTTATCAAATTTGATATCTACTAACAGGAGATCGGCCCATCAGACTCACAAGGCATGTCTTGGTGTTATCAGAGATGCTTTGCAAGCACAAGTCCAGCGAGGCGTGTACTGGTTGAGTCACATCGCACAGTATGCTACAAAGAATCTCCATTGTGAATACATAGGCCTTGGTTTCCCATCTCTAGAAAAGGTCCTATATCACAGGTATAATCTAGTTGATACTGGACTCGGTCCATTGTCGTCAGTTATTAGACATTTAACTAACCTCCAGGCAGAGATACGAGACTTAGTATTAGATTATAACCTGATGAGGGAGAGTCGCACTCAAACGTACCATTTTATTAAGACTGCAAAAGGCAGAATCACAAAGTTAGTCAATGACTTTCTGAAGTTTTCTTTAATTGTCCAGGCACTCAAAAATAATTCTTCTTGGTATACTGAGCTTAAAAAATTACCTGAGGTTATTAATGTGTGTAATCGATTTTATCATACTCACAATTGCGAATGTCAGGAAAAATTCTTTGTCCAGACGCTTTATTTACAACGCCTACGCGATGCAGAAATCAAGCTAATTGAACGCCTTACCGGGTTAATGCGATTTTATCCAGAAGGGTTAATATATTCCAATCACACATAGGTACTAAATCATCATAGTATGAGGAATAAGATAATGATAATTCCTGACGACAGTTTTAGTTCCGATTCTAAGTATATCGGAAGAGAGTATGCCAATCTTAATTGTTAGAGGTAACAAGCTATTAGTTATTACTTATTGATAAGAATACACTTTATCATAGCGTAACACATCATAACTTTATAACGATTTTGCATTTCTAATCCTAGTATTTATTAGAATGTACTACCAGAGAAATGACCCCAGTTCCTATCTTTAAATAATGATTGTGTGTATTAAATTATTAGTTTATTAGGTTTATGAGTTGGTTACACAGTGAGTATTAGTAATTGAGGATTATGTAGATAGGTAATCTAACACTGAATCACCCATCTGATGTCACCATATCCAAATGTTGTGCTAGTCGCATTTAAACATGCTATCTTCAGTTAAGTAACATAGACTGAAAATGCTAAGAAGAGATTGGAGTAAAAGTATAAAATAAATTTAATTAAACTTCAAAGTGATTAAATGATAATGATCTTGGGAACTCGATATGACCTCAAGTCAAAAATAATGTCAATATAATTGTTTAGTAATATGAGTGATAATGTAAATTTTGATAACTAACTAGCTTTAGTAGTTAAGATCAAATGCAAACATTATAAGAATGTTAAGCGCACACAAAAACATTATAAAAAACCAATTTTTTCCTTTTTGTGTGTCC\n>Sudan_ebolavirus_isolate_EboSud-609_2012_complete_genome\nCGGACACACAAAAAGAAAGAAAAGTTTTTTAGACTTTTTGTGTGCGAATAACTATGAGGAAGATTAATCATTTTCCTCAAACTCAAACTAATATTAACATTGAGATTGATCTCATCATTTACCAATTGGAGACAATTTAACTAGTCAATCCCCCATTTGGGGGCATTCCTAAAGTGTTGCAAAGGTATGTGGGTCGTATTGTTTTGCCTTTTCCTAACCTGGCTCCTCCTACAATTCTAACCTGCTTGATAAGTGTGATTACCTGAGTAATAGACTAATTTCGTCCTGGTAATTAGCATTTTCTAGCAAAACCAATACTATCTCAAGTCCTAAGAGAAGGTGAGAAGAGGGTCCCGAGGTATCCCTCCAGTCCACAAAATCTAGCTAATTTTAGCTGAGTGGACTGATTACTCTCATCACACGCTAACTACTAAGGGTTTACCTGAGAGCCTACAACATGGATAAACGGGTGAGAGGTTCATGGGCCCTGGGAGGACAATCTGAAGTTGATCTTGACTACCACAAAATATTAACAGCCGGGCTTTCGGTCCAACAAGGGATTGTGCGACAAAGAGTCATCCCGGTATATGTTGTGAGTGATCTTGAGGGTATTTGTCAACATATCATTCAGGCCTTTGAAGCAGGCGTAGATTTCCAAGATAATGCTGACAGCTTCCTTTTACTTTTATGTTTACATCATGCTTACCAAGGAGATCATAGGCTCTTCCTCAAAAGTGATGCAGTTCAATACTTAGAGGGCCATGGTTTCAGGTTTGAGGTCCGAGAAAAGGAGAATGTGCACCGTCTGGATGAATTGTTGCCCAATGTCACCGGTGGAAAAAATCTTAGGAGAACATTGGCTGCAATGCCTGAAGAGGAGACAACAGAAGCTAATGCTGGTCAGTTTTTATCCTTTGCCAGTTTGTTTCTACCCAAACTTGTCGTTGGGGAGAAAGCGTGTCTGGAAAAAGTACAAAGGCAGATTCAGGTCCATGCAGAACAAGGGCTCATTCAATATCCAACTTCCTGGCAATCAGTTGGACACATGATGGTGATCTTCCGTTTGATGAGAACAAACTTTTTAATCAAGTTCCTACTAATACATCAGGGGATGCACATGGTCGCAGGCCATGATGCGAACGACACAGTAATATCTAATTCTGTTGCCCAAGCAAGGTTCTCTGGTCTTCTGATTGTAAAGACTGTTCTGGACCACATCCTACAAAAAACCGATCTTGGAGTACGACTTCATCCACTGGCCAGGACAGCAAAAGTCAAGAATGAGGTCAGTTCATTCAAGGCAGCTCTTGGCTCACTTGCCAAGCATGGAGAATATGCTCCATTTGCACGTCTCCTCAATCTTTCTGGAGTCAACAACTTGGAACATGGGCTTTATCCACAACTCTCAGCCATTGCTTTGGGTGTTGCAACTGCCCACGGGAGCACGCTGGCTGGTGTTAATGTAGGGGAGCAATATCAGCAACTGCGTGAGGCTGCTACTGAAGCTGAAAAGCAACTCCAACAATATGCTGAGACACGTGAGTTGGACAACCTTGGGCTTGATGAGCAGGAAAAGAAGATTCTCATGAGCTTCCACCAGAAGAAGAATGAGATCAGCTTCCAGCAAACTAACGCAATGGTAACCTTGAGGAAAGAGCGGCTGGCCAAACTGACCGAAGCCATCACGACTGCATCAAAGATCAAGGTTGGAGATCGTTATCCTGATGACAATGATATTCCATTTCCCGGGCCGATCTATGATGAAACCCACCCCAACCCTTCTGATGATAATCCTGATGATTCACGTGATACAACTATCCCAGGTGGTGTTGTTGACCCGTATGATGATGAGAGTAATAATTATCCTGACTACGAGGATTCGGCTGAAGGCACCACAGGAGATCTTGATCTCTTCAATTTGGACGACGACGATGACGACAGCCAACCAGGACCACCAGACAGGGGGCAGAGCAAGGAGAGAGCGGCTCGGACACATGGCCTCCAAGATCCGACCTTGGACGGAGCGAAAAAGGTGCCGGAGTTAACCCCAGGTTCCCACCAACCAGGCAACCTCCACATCACCAAGCCGGGTTCAAACACCAACCAACCACAAGGCAATATGTCATCTACTCTCCAGAGTATGACCCCTATACAGGAAGAATCAGAGCCCGATGATCAGAAAGATGATGATGACGAGAGTCTCACATCCCTTGACTCTGAAGGTGACGAAGATGTTGAGAGCGTATCAGGGGAGAACAACCCAACTGTAGCTCCACCAGCACCAGTCTACAAAGATACTGGAGTAGACACTAATCAGCAAAATGGACCAAGCAATGCTGTAGATGGTCAAGGTTCTGAAAGTGAAGCTCTCCCAATCAACCCCGAAAAGAGATCTGCACTGGAAGAAACATATTATCATCTCCTAAAAACACAGGGTCCATTTGAGGCAATCAATTATTATCACCTAATGAGTGATGAGCCCATTGCTTTTAGCACTGAAAGTGGCAAGGAATATCTCTTCCCAGATTCTCTTGAAGAAGCCTACCCGCCTTGGTTGAGTGAGAAGGAGGCCTTAGAGAAAGAAAATCGTTATCTGGTCATTGATGGCCAGCAATTCTTCTGGCCAGTAATGAGCCTACAGGACAAGTTCCTTGCTGTTCTTCAACATGACTGAGGACCCATGATTAGTAGATTTTGTTTATTCTGAGCTTGATTATAATTGTTTTGATAATTCAAGTATGAGCACCCAACCCGAAATATAAACCCTATTTTAGTTATGAGGAAATTAAATAAATAATCTGTAAGTTGTAGGACTATGAAGAGCTGCTTGTGTCAATTTATCACGGGTTAATACCCATACCGCAAGAATAATTATTTAGTAATTTTGATCAGCTTATGATATGTACCAATAGGAAAACATTATAGCATTAAAACATAAAGTATCCTTCGATGAGCTTAGGAGGATAATATCCTGATGAATTCTATAGAACTTAGGATTAAGAAAAAATTCATGATGAAGATTAAAACCTTCATCATCCTTTAAAAAGAGAGCTATTCTTTATCTGAATGCCCTTATTAATGTCTAAGAGCTATTATTTTGTACCCTCTTAGCCTAGACACTGCCCAACATATAAATCATGCAGCAGGATAGGACTTATAGACATCATGGACCCGAAGTGTCTGGCTGGTTTTCTGAGCAATTAATGACCGGCAAAATACCGCTAACAGAGGTGTTTGTTGATGTTGAAAACAAACCAAGTCCTGCCCCGATAACCATTATTAGTAAGAATCCCAAGACAACACGTAAAAGTGATAAGCAAGTCCAAACAGATGATGCCAGTAGCTTATTGACAGAAGAAGTCAAGGCTGCCATAAATTCGGTGATATCAGCTGTGCGTCGGCAAACCAATGCTATTGAATCACTAGAAGGTCGAGTAACAACTCTTGAGGCCAGCTTAAAACCAGTTCAAGACATGGCAAAGACCATATCATCCCTGAATCGCAGCTGTGCCGAAATGGTTGCAAAATACGACCTACTGGTGATGACCACTGGGCGAGCAACTGCCACTGCTGCAGCAACAGAAGCATATTGGAATGAACATGGACAAGCACCTCCAGGCCCATCATTGTACGAGGATGATGCTATTAAGGCTAAATTGAAAGATCCGAACGGGAAGGTTCCAGAAAGTGTCAAACAGGCCTACACAAATCTAGATAGCACAAGTGCCCTCAATGAGGAAAATTTCGGGCGACCTTACATTTCAGCAAAAGATCTCAAGGAAATCATCTATGACCATCTCCCAGGATTTGGGACAGCTTTTCATCAGTTGGTGCAGGTTATCTGCAAAATTGGTAAGGATAATAATATCCTAGACATAATTCATGCAGAATTCCAAGCAAGCTTGGCTGAGGGAGACTCCCCCCAGTGTGCATTAATCCAGATAACAAAACGGATCCCTGCTTTCCAAGATGCCTCTCCTCCAATTGTGCATATCAAGTCTCGAGGAGATATACCCAAAGCCTGTCAGAAAAGCCTCCGGCCGGTCCCGCCGTCACCAAAGATCGATAGAGGTTGGGTCTGTATTTTTCAATTCCAAGACGGGAAGGCCCTTGGGCTAAAAATATGATACAGAAGCAAGGTAAGCTCATTTTGCGATGGCCAAATGATACTTATGACTGTTTAAAATCAAGTTAGACTAATAGTCTATCATGTCATAAGCTTATAAGTCAGTTTTAAATTTCCCCTCTATCCTAATCAATTGATAATGCTGTCAATAGGAAAATTCCCCTGTATTGTAATAAGACCTCATTAACACATTTCCTCTGCTTAGTACTATGCAGAAACCCCCGAGCAAATTAAAATTGATGAAGATTAAGAAAAAGAGGGATTTTCTCAGGAAAAATCTTTTTTCTTACCTTCATCTCATTTAAACAAATTTAGGACTCAGGAAAAATGAAAAGGGTCACTGTGCCGACTGCACCACCTGCCTATGCTGACATTGGCTATCCTATGAGCATGCTTCCCATCAAGTCAAGCAGGGCTGTGAGTGGAATTCAACAGAAACAAGAGGTCCTTCCTGGAATGGATACACCATCAAATTCTATGAGACCTGTTGCTGATGATAACATTGATCATACAAGTCATACCCCGAACGGAGTGGCCTCAGCATTCATCTTGGAGGCAACTGTCAATGTGATCTCGGGGCCCAAAGTCCTCATGAAACAAATCCCTATTTGGTTGCCACTCGGAATTGCTGACCAAAAAACGTACAGTTTTGACTCAACAACAGCAGCAATTATGCTCGCATCTTATACGATCACCCATTTTGGAAAGGCCAACAACCCCCTCGTTAGAGTGAATCGACTTGGTCAGGGAATACCGGATCACCCACTCAGATTGCTCAGGATGGGGAACCAGGCTTTCCTTCAAGAGTTTGTGCTACCACCAGTTCAACTGCCGCAATATTTCACTTTTGATCTGACTGCACTCAAATTAGTGACACAGCCTCTCCCTGCTGCGACATGGACAGATGAGACTCCGAGCAACCTTTCAGGAGCACTTCGTCCCGGGCTTTCATTTCACCCAAAGCTGAGACCCGTTCTACTTCCAGGCAAAACGGGAAAGAAAGGGCATGTTTCTGATCTGACTGCTCCAGACAAAATTCAGACAATTGTGAACCTGATGCAAGATTTCAAAATCGTGCCAATTGATCCAGCTAAGAGTATCATTGGGATCGAGGTTCCAGAATTGCTGGTCCACAAGCTCACTGGGAAGAAAATGAGTCAGAAGAATGGACAGCCTATAATTCCTGTCTTACTTCCAAAATACATTGGGCTAGATCCAATCTCACCTGGAGACCTGACTATGGTCATAACACCAGATTATGATGATTGTCATTCACCTGCCAGTTGCTCTTATCTCAGTGAAAAGTGATTCTCACAAAGTGAGAGAAACACCTCCAGTAAAGAAATCAAATCTTGTCTATAGCAACTCAATCGACTTTTAGGAAGCTAGCAGTACATATACTATGGGACAACTCAACCCTCTTGTTAAAATGTACTAATCGGGTCAAAGAACTCTCACTGATCAAGCCTGAATCCAAGATAGAACCAGCCCAAAGGGCCTCCCCAGAGTCTCTTACAAACTTAGCCAATCAATTAACATGCATAAGCGATCCATACTTCACCCAATCAGTGTCCGATGTTCACCCCTTCAAGCCTCCTTCCTAGCAAATTGAACTAGCTGTACCAAGAGGTTCCCTCAGCCTCCTTCTCAAATAACCTGATCCTTGAGGGTTACACCTTCACCACTCTATGCTCATTTCACCCAAACATAAAATGAAATGTCTTAACATGATTGCACCATTAAGAAAAACAAATCTGATGAAGATTAAGCCTGATTAAGGCCCAACCTTCATCTTTTTACCATAATCTTGTTCTCAGTACCATTTGATAAGGGTACACTTGCCAAAACGCCCCCATCCTAAGGGTCTCGCAATGGGGGGTCTTAGCCTACTCCAATTGCCCAGGGACAAGTTTCGGAAAAGCTCTTTCTTTGTTTGGGTCATCATCTTATTCCAAAAGGCCTTTTCCATGCCTTTGGGTGTTGTGACTAACAGCACTTTAGAAGTAACAGAGATTGACCAGCTAGTCTGCAAGGATCATCTTGCATCTACTGACCAGCTGAAATCAGTTGGTCTCAACCTCGAGGGGAGCGGAGTATCTACTGATATCCCATCTGCAACAAAGCGTTGGGGCTTCAGATCTGGTGTTCCTCCCAAGGTGGTCAGCTATGAAGCGGGAGAATGGGCTGAAAATTGCTACAATCTTGAAATAAAGAAGCCGGACGGGAGCGAATGCTTACCCCCACCGCCAGATGGTGTCAGAGGCTTTCCAAGGTGCCGCTATGTGCACAAAGCCCAAGGAACCGGGCCCTGCCCAGGTGACTACGCCTTTCACAAGGATGGAGCTTTCTTTCTCTATGACAGGCTGGCTTCAACTGTAATTTACAGAGGAGTCAATTTTGCTGAGGGGGTGATTGCATTCTTGATATTGGCTAAACCAAAAGAAACGTTCCTTCAGTCACCCCCCATTCGAGAGGCAGTAAACTACACTGAAAATACATCAAGTTATTATGCCACATCCTACTTGGAGTATGAAATCGAAAATTTTGGTGCTCAACACTCCACGACCCTTTTCAAAATTGACAATAATACTTTTGTTCGTCTGGACAGGCCCCACACGCCTCAGTTCCTTTTCCAGCTGAACGACACCATTCACCTTCACCAACAGTTGAGTAATACAACTGGGAGACTAATTTGGACACTAGATGCTAATATCAATGCTGATATTGGTGAATGGGCTTTTTGGGAAAATAAAAAAATCTCTCCGAACAACTACGTGGAGAAGAGCTGTCTTTCGAAGCTTTATCGCTCAACGAGACAGAAGACGATGATGCGGCATCGTCGAGAATTACAAAGGGAAGAATCTCCGACCGGGCCACCAGGCAGTATTCGGACCTGGTTCCAAAGAATCCCCCTGGGATGGTTCCATTGCACATACCAGAAGGGGAAACAACATTGCCGTCTCAGAATTCGACAGAAGGTCGAAGAGTAAGTGTGAACACTCAGGAGACCATCACAGAGACAGCTGCAACAATTATAGGCACTAACGGCAACCATATGCAGATCTCCACCATCGGGATAAGACCGAGCTCCAGCCAAATCCCGAGTTCCTCACCGACCACGGCACCAAGCCCTGAGGCTCAGACCCCCACAACCCACACATCAGGTCCATCAGTGATGGCCACCGAGGAACCAACAACACCACCGGGAAGCTCCCCCGGCCCAACAACAGAAGCACCCACTCTCACCACCCCAGAAAATATAACAACAGCGGTTAAAACTGTCCTGCCACAGGAGTCCACAAGCAACGGTCTAATAACTTCAACAGTAACAGGGATTCTTGGGAGTCTTGGGCTTCGAAAACGCAGCAGAAGACAAACTAACACCAAAGCCACGGGTAAGTGCAATCCCAACTTACACTACTGGACTGCACAAGAACAACATAATGCTGCTGGGATTGCCTGGATCCCGTACTTTGGACCGGGTGCGGAAGGCATATACACTGAAGGCCTGATGCATAACCAAAATGCCTTAGTCTGTGGACTTAGGCAACTTGCAAATGAAACAACTCAAGCTCTGCAGCTTTTCTTAAGAGCCACAACGGAGCTGCGGACATATACCATACTCAACAGGAAGGCCATAGATTTCCTTCTGCGACGATGGGGCGGGACATGCAGGATCCTGGGACCAGATTGTTGCATTGAGCCACATGATTGGACAAAAAACATCACTGATAAAATCAACCAAATCATCCATGATTTCATCGACAACCCCTTACCTAATCAGGATAATGATGATAATTGGTGGACAGGCTGGAGACAGTGGATCCCTGCAGGAATAGGCATTACTGGAATTATTATTGCAATTATTGCTCTTCTTTGCGTTTGCAAGCTGCTTTGCTGAATATCAATTTGAATCATCAATTTAAGCTTGATACATTTCTAGCATTTTAAATTATAAACCGATACTGATACTTGAAAATCAGGCTAATGCCAAGTTCTGTGCAAAACTTGAAAGTAAGCTTACAAAAATCCTTTGAACTGGAATGCTTTGATACTCTTTCTCAATACTATATAAGTTCCTTCCCAAGAATAATATTGATGAAGATTAAGAAAAAGTGACATTGTGCCCACTTTTGTAATCTTCATCCACCTACACATTCATATTCAGGAATCTTTGAATTAACCCTCACACTTGCTTAGGAAAGAGCCTATCCTCTACAAGAATCCCGAGGCGGCAATTCAGTTAATTTCATATCAAGATAACATCCATTTCCAAGACCACAGATAACTATATTATTAATCTTTACCACAAATATGGAGAGGGGTCGTGAGCGCGGGAGATCAAGGAATTCACGTGCCGACCAGCAAAATTCAACAGGTCCTCAATTTAGGACAAGATCCATTTCCCGGGATAAGACAACAACAGACTACCGTAGTAGTCGAAGTACTTCGCAAGTTAGAGTCCCTACGGTTTTCCATAAGAAAGGTACTGGGACCCTTACTGTCCCTCCAGCACCTAAGGATATTTGTCCTACTCTCAGAAAAGGATTTCTATGTGACAGTAATTTCTGTAAAAAGGACCATCAACTTGAAAGCCTAACCGACCGGGAGCTCCTACTTCTTATAGCACGGAAGACCTGTGGATCAACTGATTCATCGCTTAATATAGCTGCTCCTAAAGACCTAAGACTAGCAAATCCTACGGCTGATGACTTCAAGCAAGACGGCAGTCCAAAATTAACCCTAAAATTACTAGTCGAGACTGCTGAGTTTTGGGCCAATCAGAATATTAATGAAGTAGATGATGCAAAACTCCGTGCTCTCTTGACGTTGAGTGCTGTCTTAGTGCGGAAATTCTCTAAGTCACAGCTTAGTCAATTATGTGAGAGTCATCTTAGGAGGGAAAACTTAGGACAAGACCAAGCTGAATCAGTTCTCGAGGTTTATCAACGTTTACATAGTGATAAAGGAGGTGCTTTTGAGGCAGCACTATGGCAACAGTGGGATAGACAATCATTAACTATGTTTATATCTGCTTTCCTCCATGTAGCATTGCAACTTTCCTGTGAGAGCTCCACTGTAGTGATATCAGGCCTACGCTTACTTGCCCCCCCAAGCGTTAATGAAGGGCTCCCTCCTGCACCAGGGGAATATACTTGGTCAGAAGATAGTACAACTTAGCCTATAGGGAGGACAAGTAAAACAAGATGCCCTTATCCTCTATAGATGGTATTTTTAAAGAGGGGGACAGGATAGGAATAAAGATAATGACTAAAGCCAATATAAAGATACGAACACAAGTAGAAATTAAAATAGAAATCAAAACAATCTCCCCTTGTTCAATATGAAATATAATAGTGAGTATTTGTTTCATGATGTCAATCATTTATTGTTAAAAATAAACAAAGTCAGTAAGAGTGTTAGGATCGTTATATTGCAAGGATCCTCCCTAGAAGCGTTGAATCATCTCAAGTAGCCTAGAACAAGAACAGCAGAGCATTAAATTGAAATAGATAATAAGGATATTGCTTGTTTTTAAGATAGTTTTAGGAAGTTTAAAATTAAGAAAAAGAACCCATGGACACACTCTAGCATTGAGGATGGGGTTCCCTTGATGATAGTATAGTCTTAGGTATAGGGTAGTCCTACACGTCCTATATTATACAGTCTAAACTTGTAAAATTAAACTACAAGAACATGATGAAAATTAATGAGAAGGTTCCAAGATTGACTTCAATCCAAACACCTTGCTCTGCCAATTTTCATCTCCTTAAGATATATGATTTTGTTCCTGCGAGATAAGGTTATCAAATAGGGTGTGTATCTCTTTTACATATTTGGGCTCCCACTAGGCTAGGGTTTATAGTTAAGGAAGACTCATCACATTTTTAATTGAACTAGTCTACTCGCAGAATCCTACCGGGAATAGAAATTAGAACATTTGTGATACTTTGACTATAGGAAATAATTTTCAACACTACCTGAGATCAGGTTATTCTTCCAACTTATTCTGCAAGTAATTGTTTAGCATCATAACAACAACGTTATAATTTAAGAATCAAGTCTTGTAACAGAAATAAAGATAACAGAAAGAACCTTTATTATACGGGTCCATTAATTTTATAGGAGAAGCTCCTTTTACAAGCCTAAGATTCCATTAGAGATAACCAGAATGGCTAAAGCCACAGGCCGGTACAACTTGGTAACACCAAAACGGGAGCTAGAGCAAGGAGTTGTGTTTAGCGACCTATGCAACTTCCTAGTGACTCCAACTGTGCAAGGATGGAAGGTTTACTGGGCTGGACTTGAGTTTGATGTCAACCAAAAGGGTATTACCCTGTTAAATCGTCTTAAAGTGAATGATTTTGCTCCTGCATGGGCGATGACCCGGAACCTCTTCCCACACTTGTTCAAAAACCAACAGTCTGAAGTCCAAACTCCCATTTGGGCCTTAAGGGTAATTCTTGCCGCCGGGATTCTTGACCAATTAATGGATCATTCCCTCATTGAGCCGCTATCAGGGGCCCTGAACCTAATTGCTGATTGGTTACTAACAACATCTACTAATCACTTCAACATGAGAACTCAACGAGTAAAGGACCAACTGAGTATGAGGATGTTATCTCTTATAAGGTCAAATATTATTAACTTTATAAATAAGCTCGAGACTCTTCATGTCGTTAATTACAAGGGACTTCTAAGCAGTGTTGAGATAGGAACACCAAGCTATGCAATCATCATTACCAGGACTAATATGGGTTATCTTGTCGAAGTTCAGGAACCAGATAAATCTGCAATGGATATACGACACCCTGGTCCTGTCAAATTCTCCCTACTACATGAATCGACACTTAAACCTGTTGCCACTCCTAAACCGTCAAGCATTACTTCATTGATCATGGAGTTCAACAGTTCTTTGGCAATTTAATTGCCGTAATAACAATTGTACGATAGGGCTAACATTGATTCCATAATCCATCGTAGGACAGAATCATTTTCCTGTATGATCTTAGTTTAATCTCTCTTTATACAATGATTAATAAGGAGCTTGTTTAGAATGTTACAAAAGTATACTGTTTGACCCCCTAGTATCCCTGTAAATATCCTCATTCAATTTTTTGCTTTTACATGTGTAGTCACCTGTATAGCATGACCCTAGTCATGCCTTTAATTAATACTTAATCTAACAGTTAATATAATGTATAACTTTCCATGTTCAAAGAGTAGTCAAAACAATGTGAGATCCAGTTTCACTCACAGCATCTATTCACTATTTACAGTATGATGAGCCCAAATTAACACAGTAGAGGTCTAGATTTATTAATAGAATGAGGAAGATTAAGAAAAAGTCCATAATGCTGGGGAGGCAATCCTTGCCACCATAGGACTTTTTCAATTCCTCTATTTTATGATGGCTACCCAACATACACAATATCCTGATGCAAGATTGTCTTCCCCAATTGTCTTAGACCAATGTGACCTAGTGACAAGAGCTTGTGGACTTTACTCTGAGTATTCGCTGAACCCTAAACTAAGGACATGCCGTTTACCGAAACATATCTACAGATTAAAATATGACACTATTGTTTTACGATTTATCAGTGATGTCCCTGTAGCTACAATCCCAATAGACTACATTGCTCCGATGTTAATAAATGTTCTGGCAGATAGTAAAAATGTACCATTGGAACCTCCCTGCTTGAGTTTCTTGGATGAAATAGTCAATTATACCGTGCAGGATGCAGCATTCCTTAATTATTACATGAATCAGATTAAAACACAGGAAGGAGTAATTACAGATCAATTGAAACAGAACATTCGTAGGGTCATTCACAAAAACAGATATCTATCTGCTCTATTCTTCTGGCATGATCTTGCCATCCTCACCCGTCGAGGGAGAATGAACCGAGGAAATGTGCGCTCTACTTGGTTTGTAACGAATGAGGTTGTTGACATTCTAGGATATGGTGATTATATCTTCTGGAAGATCCCTATTGCTCTATTACCAATGAACACAGCTAATGTTCCACATGCATCAACTGACTGGTACCAACCTAATATCTTCAAGGAGGCTATTCAAGGACACACACATATTATTTCAGTCTCTACAGCCGAGGTCCTTATTATGTGTAAGGATCTTGTCACAAGTCGTTTTAATACCCTTCTGATTGCTGAGTTAGCCAGGTTGGAAGATCCAGTGTCTGCTGATTATCCACTAGTAGATAATATTCAATCTCTGTATGACGCAGGAGACTACCTGTTGTCCATATTGGGATCAGAGGGGTACAAAATAATCAAATATCTCGAACCTCTGTGTTTGGCTAAGATTCAACTATGTTCCCAATATACAGAACGAAAAGGGCGGTTTTTAACCCAGATGCATCTTGCAGTTATTCAGACATTGCGTGAACTCCTCCTTAATAGAGGGTTGAAAAAATCACAATTGTCTAAAATCCGCGAATTTCACCAACTGTTGCTCAGACTCCGATCTACACCACAACAATTATGTGAATTATTTTCAATCCAAAAACACTGGGGCCACCCAGTTCTGCATAGTGAAAAGGCCATCCAAAAGGTTAAAAATCATGCAACAGTTCTAAAGGCATTGCGGCCGATTATCATCTTTGAAACGTATTGTGTGTTCAAGTATAGTGTTGCAAAACATTTCTTTGATAGTCAAGGCACTTGGTACAGTGTGATATCAGACCGATGTTTAACGCCGGGATTGAATTCCTACATTAGGCGAAATCAATTCCCTCCACTTCCAATGATCAAAGATCTTTTATGGGAATTTTACCATTTGGATCATCCTCCATTATTCTCCACGAAGATCATTAGTGACCTCAGCATTTTCATTAAAGACCGCGCAACAGCAGTTGAACAGACCTGTTGGGATGCAGTTTTTGAGCCTAACGTTTTGGGCTACAGTCCACCTTATCGATTCAATACCAAACGTGTACCTGAACAATTCCTGGAGCAAGAGGATTTTTCTATTGAGAGTGTCTTACAATACGCCCAAGAACTTAGGTACTTATTGCCCCAGAATCGAAATTTTTCTTTTTCATTGAAGGAAAAAGAATTAAATGTTGGTAGGACATTTGGAAAATTGCCTTATTTAACCAGGAATGTCCAAACCCTCTGCGAAGCATTACTTGCAGATGGTTTGGCTAAAGCCTTTCCAAGCAATATGATGGTGGTCACAGAGAGGGAACAAAAGGAGAGCCTCCTTCACCAAGCATCCTGGCACCATACAAGTGATGATTTCGGAGAGCATGCCACAGTTCGTGGAAGTAGTTTTGTCACAGACCTGGAAAAATACAATCTGGCCTTCAGGTATGAATTCACAGCTCCCTTCATCAAATATTGCAACCAATGCTATGGGGTTCGCAATGTCTTTGATTGGATGCACTTCCTAATTCCACAGTGTTACATGCATGTTAGTGATTATTATAACCCACCACATAATGTAACCTTAGAGAATAGGGAATATCCCCCCGAAGGACCAAGTGCTTATAGAGGCCACCTTGGCGGTATTGAGGGGCTTCAACAAAAGTTATGGACTAGTATCTCATGTGCTCAAATCTCATTGGTAGAGATCAAGACCGGGTTCAAATTGCGATCAGCAGTCATGGGGGATAATCAATGTATTACAGTATTATCAGTCTTTCCACTAGAATCTAGTCCGAATGAGCAGGAGAGATGCGCAGAAGACAATGCAGCCAGAGTGGCTGCTAGCTTGGCCAAAGTCACAAGTGCCTGTGGGATATTCCTCAAGCCTGATGAGACTTTCGTACACTCAGGCTTTATCTATTTTGGCAAAAAGCAATACTTGAACGGAATTCAATTACCTCAATCACTCAAGACAGCAGCTAGGATGGCCCCTCTCTCAGATGCAATTTTTGATGACTTGCAAGGTACACTTGCTAGTATAGGAACTGCCTTTGAGCGATCAATCTCCGAAACTAGACATATTTTACCATGTCGTGTTGCAGCTGCCTTTCATACATATTTCTCTGTTCGGATCTTACAACATCATCACCTTGGTTTCCATAAGGGTTCAGACCTTGGACAATTGGCAATCAATAAACCTCTTGATTTCGGGACCATTGCACTATCCCTAGCAGTTCCTCAGGTATTGGGTGGATTATCCTTCCTAAATCCAGAAAAGTGCCTTTATCGCAACTTGGGTGATCCTGTAACTTCAGGCCTATTCCAGTTGAAGCATTATCTGTCAATGGTGGGTATGAGTGATATCTTTCATGCACTTGTTGCAAAAAGCCCAGGGAATTGTAGCGCGATTGACTTTGTTCTAAACCCAGGCGGGTTAAATGTCCCTGGATCACAGGATTTAACATCTTTCCTTCGTCAGATTGTCAGAAGGAGTATCACACTTTCGGCAAGGAACAAGTTAATCAACACGTTATTTCACGCTTCTGCAGATCTTGAAGACGAATTAGTATGTAAATGGTTACTTTCTTCAACGCCCGTGATGAGTCGTTTCGCAGCCGATATTTTCTCACGAACACCAAGCGGGAAAAGATTACAAATCTTGGGATACCTCGAGGGAACCAGAACTTTATTAGCATCTAAAATGATAAGCAATAATGCAGAGACACCAATCTTGGAGAGGCTCAGAAAAATAACACTTCAAAGATGGAATCTATGGTTTAGTTACCTAGACCATTGTGACCCAGCTTTAATGGAAGCAATTCAACCAATTAAGTGTACTGTTGATATTGCTCAAATTCTTAGAGAATACTCCTGGGCTCATATTCTTGATGGTAGACAGTTAATAGGGGCAACACTGCCATGTATACCTGAGCAGTTCCAAACCACATGGTTAAAACCTTACGAGCAATGTGTGGAATGTTCATCCACAAACAATACTAGTCCATATGTATCAGTTGCATTAAAAAGGAACGTGGTTAGTGCTTGGCCTGATGCATCTAGATTGGGGTGGACGATTGGTGATGGGATTCCCTACATAGGCTCAAGAACTGAGGACAAGATAGGTCAGCCCGCTATTAAGCCGAGGTGCCCATCAGCTGCATTAAGAGAAGCTATTGAATTGACCTCTAGGTTGACCTGGGTCACTCAAGGTAGTGCAAACAGCGATCAGTTAATTCGCCCTTTTCTTGAGGCAAGAGTAAACTTGAGTGTACAAGAGATTCTTCAAATGACCCCCTCACATTACTCCGGTAATATTGTGCATCGGTATAATGATCAGTATAGCCCTCACTCCTTTATGGCTAACCGCATGAGTAACACAGCAACGCGCTTGATGGTATCTACCAACACACTAGGAGAGTTTTCCGGAGGGGGTCAGGCTGCACGTGATAGCAACATTATATTTCAAAATGTGATTAACTTTGCAGTGGCCTTGTATGACATTAGGTTTCGGAACACTTGTACATCTTCTATTCAATATCACAGGGCCCATATTCACCTGACGAATTGTTGTACGAGGGAAGTACCGGCCCAATACTTAACATACACAACCACGCTAAATCTAGATTTGAGTAAGTACCGTAATAATGAACTGATTTATGATTCAGAGCCACTAAGAGGAGGTCTCAACTGCAACTTATCGATTGACAGTCCTTTGATGAAGGGCCCACGTTTAAATATTATTGAGGATGACTTAATACGGTTGCCACATTTATCCGGCTGGGAATTAGCAAAAACAGTCTTGCAATCAATAATCTCTGATAGTAGCAATTCATCAACAGATCCCATTAGCAGCGGTGAAACAAGATCCTTCACAACCCACTTCTTAACGTATCCCAAAATAGGGCTCCTATACAGTTTTGGAGCCCTCATAAGTTTTTATTTGGGTAATACTATTCTGTGCACGAAAAAGATCGGACTCACAGAATTTCTATACTATCTCCAGAATCAGATCCACAACTTATCACATAGATCCCTTCGAATCTTCAAACCGACATTTAGACACTCAAGTGTCATGTCCAGGTTGATGGATATAGACCCCAACTTCTCAATATATATTGGTGGGACTGCAGGTGACCGTGGATTATCGGACGCTGCAAGATTATTTCTCCGAATTGCAATTTCAACTTTCTTGAGCTTTGTTGAGGAGTGGGTTATCTTTAGGAAGGCAAACATCCCACTATGGGTTATCTATCCTCTCGAAGGCCAACGCCCTGATCCTCCTGGCGAATTTTTGAACCGAGTAAAATCTCTAATTGTTGGGACTGAAGATGATAAAAATAAAGGCTCTATACTTTCAAGATCTGGAGAGAAATGCTCTTCAAATCTAGTTTATAATTGCAAGAGTACAGCAAGCAATTTTTTCCATGCATCATTGGCTTATTGGAGAGGTCGACACAGACCTAAGAAGACTATAGGTGCAACCAACGCGACAACAGCTCCACACATCATCCTGCCACCAGGAAACTCTGATCGACCGCCTGGCCTAGACCTTAATAGGAACGATGATACTTTCATTCCTACCAGAATTAAACAGATAGTCCAAGGAGACTCTAGAAACGACAGAACGACCACCACGAGATTTCCACCCAAAAGTAGGTCCACTCCAACATCAGCAACCGAGCCTCCTACAAAAATGTATGAGGGTTCGACAACCCACCAAGGGAAATTAACAGATACACATTTGGATGAGGATCACAATGCCAAAGAGTTCCCATCCAATCCGCATCGTTTAGTAGTACCATTCTTTAAATTAACAAAAGATGGGGAATACAGTATCGAACCTTCTACTGAAGAAAGCCGCAGTAATATAAAAGGGTTACTTCAACATTTAAGAACCATGGTTGATACTACCATATATTGTCGCTTCACTGGAATTGTTTCATCAATGCATTATAAGTTAGATGAAGTACTATGGGAATATAATAAATTTGAATCAGCTGTAACCCTAGCAGAAGGGGAGGGTTCAGGTGCCTTACTACTGATCCAAAAATACGGCGTTAAGAAGTTATTTTTGAATACACTTGCTACTGAACATAGTATTGAGAGTGAAGTTATATCAGGTTACACCACTCCAAGGATGCTACTCTCAATTATGCCTAAAACACATCGTGGTGAGCTAGAGGTCATATTAAATAACTCAGCTAGTCAAATAACTGACATTACACACCGAGATTGGTTTTCAAATCAAAAAAATAGGATTCCAAATGATGCTGATATTATTACCATGGATGCTGAAACTACAGAAAACTTAGATCGTTCCAGATTATATGAAGCAGTATATACGATTATTTGTAATCATATCAATCCTAAAACTTTGAAAGTGGTCATCTTAAAAGTCTTCCTCAGCGATTTGGATGGGATGTGCTGGATTAACAATTATCTTGCTCCTATGTTTGGATCAGGATATTTAATCAAACCTATAACATCAAGTGCAAAGTCAAGTGAGTGGTATTTATGCTTATCTAATCTACTTTCAACCTTGAGAACTACTCAGCATCAAACCCAGGCAAACTGTCTCCATGTCGTACAATGTGCTCTTCAACAGCAAGTACAAAGAGGGTCATACTGGCTAAGTCATCTTACCAAATACACCACAAGTAGATTGCACAATAGTTATATCGTATTTGGTTTTCCTTCATTAGAGAAGGTCCTATATCATAGGTATAACCTCGTTGATTCGAGAAACGGACCATTAGTTTCTATAACGAGACACCTTGCCCTCCTCCAAACTGAGATCCGGGAGTTGGTAACTGATTATAATCAGCTGCGACAAAGTCGAACCCAGACTTATCATTTCATAAAAACATCCAAGGGACGGATAACTAAACTAGTGAATGATTATCTAAGATTTGAGTTGGTTATACGGGCTCTTAAAAATAATTCTACATGGCACCATGAGTTATACTTGCTACCAGAACTTATAGGTGTTTGCCATCGATTTAATCATACACGTAACTGTACATGCAGTGAAAGGTTCCTGGTTCAAACTTTATATCTACACCGAATGAGTGATGCTGAGATAAAACTTATGGACCGGCTCACCAGCCTAGTCAATATGTTTCCTGAAGGTTTCAGGTCTAGTTCAGTCTAATTCTAACTGCACCAAAGGCTCTAGAAATATTTTAAATAACCAGGTGTATATCAAAGTCAATACAAGTGTAAAAACAATATGCAAGGGACCACATTTAGGATCAGTTTATTGACTCTTCCAATACACAGAGTTGGAAGCACCGATTCAAGGTTTCTAAGACGCTCTATCAATTATGTTGATAATGTAAATAATAGCTTTTCCTGTCTATTATGACTTAAATAAACATATCTATAACGACCATCACAGCTAAGTCGTTGCCCTAGTTCATATATTAAATTAAAATTTAGAAGCTAGGTTAACTCTAATTACATAAGTATTAAGAAAAAATTACTAAGACTAATACTCTCATGCCAAGAACTAGTAATGTGTTTCACATGACAGATTATTTCTAACACTAAATTGCAATTTCAATTTTAAAGCTAAGTTTAACACCTATACAGCCAAAATATTTCATAGGGCCGATGGGAATAACATAAGAGGAACATGATCAATGAACCCTTTATTCCAACTAGGCAGTTGATTGATAATCTACAAATTCCATAAGATGTTCTTACGATATTCTTTTGTTTTTAATCTCAATGTCAATGATTTAATAAGTAATAATAAAAAAATCACATTAAAGATGCAGGAAGATCTTGACCTCGCCAGGAAAATTAAGCGCACACAAATAAATTAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCC\n>Sudan_ebolavirus_isolate_EboSud-639_complete_genome\nCGGACACACAAAAAGAAAGAAAAGTTTTTTAGACTTTTTGTGTGCGAATAACTATGAGGAAGATTAATCATTTTCCTCAAACTCAAACTAATATTAACATTGAGATTGATCTCATCATTTACCAATTGGAGACTGTTTAACTAGTCAATCCCCCATTTGGGGGCATTCCTAAAGTGTTGCAAAGGTATGTGGGTCGTATTGCTTTGCCTTTTCCTAACCTGGCTCCTCCTACAATTCTAACCTGCTTGAGAAGTGTGATTACCTGAGTAATAGACTAATTTCGTCCTGGTAATTAGCATTTTCTAGTAAAATCAATACTATCTCAAGTCCTAAGAGAAGGTGAAAAGAGGGTCCCGAGGTATCCCTCCAGTCCACAAAATCTAGCTAATTTTAGCTGAGTGGACTGATTACTCTCATCACACGCTAACTACTAAGGGTTTACCTGAGAGCCTACAACATGGATAAACGGGTGAGAGGTTCATGGGCCCTGGGAGGACAATCTGAAGTTGATCTTGACTACCACAAAATATTAACAGCCGGGCTTTCGGTCCAACAAGGGATTGTGCGACAAAGAGTCATCCCGGTATATGTTGTGAGTGATCTTGAGGGTATTTGTCAACATATCATTCAGGCCTTTGAAGCAGGCGTAGATTTCCAAGATAATGCTGACAGCTTCCTTTTACTTTTATGTTTACATCATGCTTACCAAGGAGATCATAGGCTCTTCCTCAAAAGTGATGCAGTTCAATACTTAGAGGGCCATGGTTTCAGGTTTGAGGTCCGAGAAAAGGAGAATGTGCACCGTCTGGATGAATTGTTGCCCAATGTCACCGGTGGAAAAAATCTTAGGAGAACATTGGCTGCAATGCCTGAAGAGGAGACAACAGAAGCTAATGCTGGTCAGTTCTTATCCTTTGCCAGTTTGTTTCTACCCAAACTTGTCGTTGGGGAGAAAGCGTGTCTGGAAAAAGTACAAAGGCAGATTCAGGTCCATGCAGAACAAGGGCTCATTCAATATCCAACTTCCTGGCAATCAGTTGGACACATGATGGTGATCTTCCGTTTGATGAGAACAAACTTTTTAATCAAGTTCCTACTAATACATCAGGGGATGCACATGGTCGCAGGCCATGATGCGAATGACACAGTAATATCTAATTCTGTTGCCCAAGCAAGGTTCTCTGGTCTTCTGATTGTAAAGACTGTTCTGGACCACATCCTACAAAAAACAGATCTTGGAGTACGACTTCATCCACTGGCCAGGACAGCAAAAGTCAAGAATGAGGTCAGTTCATTCAAGGCAGCTCTTGGCTCACTTGCCAAGCATGGAGAATATGCTCCATTTGCACGTCTCCTCAATCTTTCTGGAGTCAACAACTTGGAACATGGGCTTTATCCACAACTCTCAGCCATTGCTTTGGGTGTTGCAACTGCCCACGGGAGCACGCTTGCTGGTGTTAATGTAGGGGAGCAATATCAGCAACTGCGTGAGGCTGCTACTGAAGCTGAAAAGCAACTCCAACAATATGCTAAAACACGTGAGTTGGACAACCTTGGGCTTGATGAACAGGAAAAGAAGATTCTCATGAGCTTCCACCAGAAGAAGAATGAGATCAGCTTCCAGCAAACTAACGCAATGGTAACCTTGAGGAAAGAGCGGCTGGCCAAACTGACCGAAGCCATCACGACTGCATCAAAGATCAAGGTTGGAGATCGTTATCCTGATGACAATGATATTCCATTTCCCGGGCCGATCTATGATGAAACCCACCCCAACCCTTCTGATGATAATCCTGATGATTCACGTGATACAACTATCCCAGGTGGTGTTGTTGACCCGTATGATGATGAGAGTAATAATTATCCTGACTACGAGGATTCGGCTGAAGGCACCACAGGAGATCTTGATCTCTTCAATTTGGACGACGACGATGACGACAGCCAACCAGGACCACCAGACAGGGGGCAGAGCAAGGAGAGAGCGGCTCGGACACATGGCCTCCAAGATCCGACCTTGGACGGAGCGAAAAAGGTGCCGGAGTTGACCCCAGGTTCCCACCAACCAGGCAACCTCCACATCACCAAGCCGGGTTCAAACACCAACCAACCACAAGGCAATATGTCATCTACTCTCCAGAGTATGACCCCTATACAGGAAGAATCAGAGCCCGATGATCAGAAAGATGATGATGACGAGAGTCTCACATCCCTTGACTCTGAAGGTGACGAAGATGTTGAGAGCGTATCAGGGGAGAACAACCCAACTGTAGCTCCACCAGCACCAGTCTACAAAGATGCTGGAGTAGACACTAATCAGCAAAATGGACCAAGCAATGCTGTAGATGGTCAAGGTTCTGAAAGTGAAGCTCTCCCAATCAACCCCGAAAAGAGATCTGCACTGGAAGAAACATATTATCATCTCCTAAAAACACAGGGTCCATTTGAGGCAATCAATTATTATCACCTAATGAGTGATGAGCCCATTGCTTTTAGCACTGAAAGTGGCAAGGAATATATCTTCCCAGATTCTCTTGAAGAAGCCTACCCGCCTTGGTTGAGTGAGAAGGAGGCCTTAGAGAAAGAAAATCGTTATCTGGTCATTGATGGCCAGCAATTCCTCTGGCCAGTAATGAGCCTACAGGACAAGTTCCTTGCTGTTCTTCAACATGACTGAGGACCCATGATTAGTAGATTTTGTTTATTCTGAGCTTGATTACAATTGTTTTGATAATTCAAGTATGAGCACCCAACCCGAAATATAAACCCTATCTTGGTTATGAGGAAATTAAATAAATAATCTGTAAGTTGTAGGACTATGAAGAGCTGCTTGTGTCAATTTATCACGGGTTAATACCCATACCGCAAGAATAATTATTTAGTAATTTTGATCAACTTATGATATGTACCGATAGGAAAACATTATAGCATTAAAACATAAAGTATCCTTCGATGAGCTTAGGAGGATAATATCCTGATGAATTCTATAGAACTTAGGATTAAGAAAAAATCCATGATGAAGATTAAAACCTTCATCATCCTTTAAAAAGAGAGCTATTCTTTATCTGAATGTCCTTATTAATGTCTAAGAGCTATTATTTTGTACCCTCTTAGCCTAGACACTGCCCAACATATAAGCCATGCAGCAGGATAGGACTTATAGACATCATGGACCCGAAGTGTCTGGCTGGTTTTCTGAGCAATTAATGACCGGCAAAATACCACTAACAGAGGTGTTTGTTGATGTTGAAAACAAACCAAGTCCTGCTCCGATAACCATTATTAGTAAGAATCCCAAGACAACACGTAAAAGTGATAAGCAGGTCCAAACAGATGATGCCAGTAGCTTATTGACAGAAGAAGTCAAGGCTGCCATAAATTCGGTGATATCAGCTGTGCGTCGGCAAACCAATGCTATTGAATCACTAGAAGGTCGAGTAACAACTCTTGAGGCCAGCTTAAAACCAGTTCAAGACATGGCAAAGACTATATCATCCCTGAATCGCAGCTGTGCCGAAATGGTTGCAAAATACGACCTACTGGTGATGACCACTGGGCGAGCAACTGCCACTGCTGCAGCAACAGAAGCATATTGGAATGAACATGGACAAGCACCTCCAGGCCCATCATTGTACGAAGATGATGCTATTAAGGCTAAATTGAAAGATCCGAACGGGAAGGTTCCAGAAAGTATCAAACAGGCCTACACAAATCTAGATAGCACAAGTGCCCTCAATGAGGAAAATTTCGGGCGACCTTACATTTCAGCAAAAGATCTCAAGGAAATCATCTATGACCATCTCCCAGGATTTGGGACAGCTTTTCATCAGTTGGTGCAGGTTATCTGCAAAATTGGTAAGGATAATAATATCCTAGACATAATTCATGCAGAATTCCAAGCAAGCTTGGCTGAGGGAGACTCCCCCCAGTGTGCATTAATCCAGATAACAAAACGGATCCCTGCTTTCCAAGATGCCTCTCCTCCAATTGTGCATATCAAGTCTCGAGGAGATATACCCAAAGCCTGTCAGAAAAGCCTCCGGCCGGTCCCACCGTCACCAAAGATCGATAGAGGTTGGGTCTGTATTTTTCAATTCCAAGACGGGAAGGCCCTTGGGCTAAAAATATGATACAGAAGCAAGGTAAGCTCATTTTGCGATGGCCAAATGATACTCATGACTGTTTAAAATCAAGTTAGACTAATAGTCTATCATGTCATAAGCTTATAAGTCAGTTTTTAATTTCCCCTCTATCCTAATCAATTGATAATGCTGTCAATAGGGAAATTCCCCTGTATTGTAATAAGACATTTTTAACATATTTCCCCTGCTTAGTACTATGCAGAAACCCCCGAGCAAATTAAAATTGATGAAGATTAAGAAAAAGAGGGATTTTCTCAGGAAAAATCTTTTTTCTTACCTTCATCTCATTTAAACAAATTTAGGACTCAGGAAAAATGAGAAGGGTCACTGTGCCGACTGCACCACCTGCCTATGCTGACATTGGCTATCCTATGAGCATGCTTCCCATCAAGTCAAGCAGGGCTGTGAGTGGAATTCAACAGAAACAAGAAGTCCTTCCTGGAATGGATACACCATCAAATTCTATGAGACCTGTTGCTGATGATAACATTGATCATACAAGTCATACCCCGAATGGAGTGGCCTCAGCATTCATCTTGGAGGCAACTGTCAATGTGATCTCGGGGCCCAAAGTCCTCATGAAACAAATCCCTATTTGGTTGCCACTCGGAATTGCTGACCAAAAAACGTACAGTTTTGACTCAACAACAGCAGCAATTATGCTCGCATCTTATACGATCACCCATTTTGGAAAGGCCAACAACCCCCTCGTCAGAGTGAATCGACTTGGTCAGGGAATACCGGATCACCCACTCAGATTGCTCAGGATGGGGAACCAGGCTTTCCTTCAAGAGTTTGTGCTACCACCAGTTCAACTGCCGCAATATTTCACTTTTGATCTGACTGCACTCAAATTAGTGACACAGCCTCTCCCTGCTGCAACATGGACAGATGAGACTCCGAGCAACCTTTCAGGAGCACTTCGTCCCGGGCTTTCATTTCACCCAAAGCTGAGACCCGTTCTACTTCCAGGCAAGACGGGAAAGAAAGGGCATGTTTCTGATCTGACTGCCCCAGACAAAATTCAGACAATTGTGAACCTGATGCAAGATTTCAAAATCGTGCCAATTGATCCAGCTAAGAGTATCATTGGGATCGAGGTTCCAGAATTGCTGGTCCACAAGCTCACTGGGAAGAAAATGAGTCAGAAGAATGGACAGCCCATAATTCCTGTCTTACTTCCAAAATACATTGGGCTAGATCCAATCTCACCTGGAGACCTGACTATGGTCATAACACCGGATTATGATGATTGTCATTCACCTGCCAGTTGCTCTTATCTCAGTGAAAAGTGATTCTCACAAAGTGAGAGAAACACCTCCAGTAAAGAAATCAAATCTTATCTATAGCAACTCAATCGACTTTTAGGAGGCTAGCAGTATATATACTATGGGACAACTCAACCCTCTTGTTAAAATGTACTAATCGGGTCAAGGAACTCTCACTGATCAAGCCTGAATCCAAGATAGAACCAGCCCAAAGGGCCTCCCCAGAGTCTCTCACAAGCTTAGCCAATCAATTAACATGCATAAGCGATCCATACTTCGCCCAATTAGTATCCGATGTTCACCCCTTCAAGCCTCCTTCCTAGCAAATTGACCTAGCTGTACCAAGAGATTCCCTCAGCCTCCTTCTCAAATAACCTGATCCTTGAGGGTTACACCTTCACCACTCTATGCTCATTTCACCCAAACATAAAATGAAATGTCTTAACATGATTGCACCATTAAGAAAAACAAATCTGATGAAGATTAAGCCTGATTAAGGCCCAACCTTCATCTTTTTACCATAATCTTGTTCTCAGTACCATTTGATAAGGGTACACTTGCCAAAACGCCCCCATCCTAAGGGTCTCGCAATGGGGGGTCTTAGCCTACTCCAATTGCCCAGGGACAAATTTCGGAAAAGCTCTTTCTTTGTTTGGGTCATCATCTTATTCCAAAAGGCCTTTTCCATGCCTTTGGGTGTTGTGACTAACAGCACTTTAGAAGTAACAGAGATTGACCAGCTAGTCTGCAAGGATCATCTTGCATCTACTGACCAGCTGAAATCAGTTGGTCTCAACCTCGAGGGGAGCGGAGTATCTACTGATATCCCATCTGCAACAAAGCGTTGGGGCTTCAGATCTGGTGTTCCTCCTAAGGTGGTCAGCTATGAAGCGGGAGAATGGGCTGAAAATTGCTACAATCTTGAAATAAAGAAGCCGGACGGGAGCGAATGCTTACCCCCACCGCCAGATGGTGTCAGAGGCTTTCCAAGGTGCCGCTATGTTCACAAAGCCCAAGGAACCGGGCCCTGCCCAGGTGACTACGCCTTTCACAAGGATGGAGCTTTCTTCCTCTATGACAGGCTGGCTTCAACTGTAATTTACAGAGGAGTCAATTTTGCTGAGGGGGTAATTGCATTCTTGATATTGGCTAAACCAAAAGAAACGTTCCTTCAGTCACCCCCCATTCGAGAGGCAGTAAACTACACTGAAAATACATCAAGTTATTATGCCACATCCTACTTGGAGTATGAAATCGAAAATTTTGGTGCTCAACACTCCACGACCTTTTTCAAAATTGACAATAATACTTTTGTTCGTCTGGACAGGCCCCACACGCCTCAGTTCCTTTTCCAGCTGAATGATACCATTCACCTTCACCAACAGTTGAGCAATACCACTGGGAGACTGATTTGGACACTAGATGCTAATATCAATGCTGATATTGGTGAATGGGCTTTTTGGGAAAATAAAAAAATCTCTCCGAACAACTACGTGGAGAAGAGCTGTCTTTCGAAGCTTTATCGCTCAACGAGACAGAAGACGATGATGCGGCATCGTCGAGAATTACAAAGGGAAGAATCTCCGACCGGGCCACCAGGAAGTATTCGGACCTGGTTCCAAAGAATTCCCCTGGGATGGTTCCATTGCACATACCAGAAGGGGAAACAACATTGCCGTCTCAGAATTCGACAGAAGGTCGAAGAGTAGGTGTGAATACTCAGGAGACCATTACAGAGACAGCTGCAACAATTATAGGCACTAACGGCAACCATATGCAGATCTCCACCATCGGGATAAGACCGAGCTCCAGCCAAATCCCGAGTTCCTCACCGACCATGGCACTAAGCCCTGAGGCTCAGACCCCCACAACCCACACATCAGGTCCATCAGTGATGGCCACCGAGGAACCAACAACACCACCGGGAAGCTCCCCTGGCTCAACAACAGAAGCGCCCACTCTCACCACCCCAGAAAATATAACAACAGCGGTTAAAACTGTCTTGCCACAGGAGTCCACAAGTAACGGTCTAATAACTTCAACAGTAACAGGGATTCTTGGGAGTCTTGGGCTTCGAAAACGCAGCAGAAGACAAACTAACACCAAAGCCACGGGTAAGTGCAATCCCAACTTACACTACTGGACTGCACAAGAACAACATAATGCTGCTGGGATTGCCTGGATCCCGTACTTTGGACCGGGTGCGGAAGGCATATACACTGAAGGCCTGATGCATAACCAAAATGCCTTAGTCTGTGGACTTAGGCAACTTGCAAATGAAACAACTCAAGCTCTGCAGCTTTTCTTAAGAGCCACAACGGAGCTGCGGACATATACCATACTCAATAGGAAGGCCATAGATTTCCTTCTGCGACGATGGGGCGGGACATGCAGGATCCTGGGACCAGATTGTTGCATTGAGCCACATGATTGGACAAAAAACATCACTGATAAAATCAACCAAATCATCCATGATTTCATCGACAACCCCTTACCTAATCAGGATAATGATGATAATTGGTGGACGGGCTGGAGACAGTGGATCCCTGCAGGAATCGGCATTACTGGAATTATTATTGCAATTATTGCTCTTCTTTGCGTTTGCAAGCTGCTTTGCTGAATATCAATTTGAATCATCAATTTAAGCTTGATACATTTCTAGCATTTTAAATTATAAACCGATACTGATACTTGAAAATCAGGCTAATGCCAAGTTCTGTGCAAAACTTGAAAGTAGGTTTACAAAAATCCTTTGAACTGGAATGCTTTGATACTCTTTCTCAATACTATATAAGTTCCTTCCCAAGAATAATATTGATGAAGATTAAGAAAAAGTGACATTGTGCCCACTTTTGTAATCTTCATCCACCTACACATCCATATTCAGGAATCTTTGAATTAACCCTCACACTTGCTTAGGAAAGAGCCTATCTTCTACAAGAATCCCGAGGCGGCAATTCAGTTAATTTCATATCAAGATAACATCCATTTCCAAGACCACAGATAACTATATTATTAATCTTTACCACAAATATGGAGAGGGGTCGTGAGCGCGGGAGATCAAGGAATTCACGTGCCGACCAGCAAAATTCAACAGGTCCTCAATTTAGGACAAGATCCATTTCTCGGGATAAGACAACAACAGACTACCGTAGTAGTCGAAGTACTTCGCAAGTTAGAGTCCCTACGGTTTTCCATAAGAAAGGTACTGGGGCCCTTACTGTCCCTCCAGCACCTAAGGATATTTGTCCTACTCTCAGAAAAGGATTTCTATGTGATAGTAATTTCTGTAAAAAGGACCATCAACTTGAAAGCCTAACCGACCGGGAGCTCCTACTTCTTATAGCACGGAAGACCTGTGGATCAACTGATTCATCGCTTAATATAGCTGCTCCTAAAGACCTAAGACTAGCAAATCCTACGGCTGATGACTTCAAGCAAGACGGCAGTCCAAAATTAACCCTAAAATTACTAGTCGAGACTGCTGAGTTTTGGGCCAATCAGAATATTAATGAAGTAGATGATGCAAAACTCCGTGCTCTCTTGACGTTGAGTGCTGTCTTAGTGCGGAAATTCTCTAAGTCACAGCTTAGTCAATTATGTGAGAGTCATCTTAGGAGGGAAAACTTAGGACAAGACCAAGCTGAATCAGTTCTCGAGGTTTATCAACGTTTACATAGTGATAAAGGAGGTGCTTTTGAGGCAGCACTATGGCAACAATGGGATAGACAATCATTAACTATGTTTATATCTGCTTTCCTCCATGTAGCATTGCAACTTTCCTGTGAGAGCTCCACTGTAGTGATATCAGGCCTACGCTTACTTGCCCCCCCAAGCGTTAATGAAGGGCTCCCTCCTGCACCAGGGGAATATACTTGGTCAGAAGATAGTACAACTTAGCCTGTAGGGAGGACAAGTAAAACAAGATGCCCTTATCCTCTATAGATGGTATTTTTAAAGAGGGGGACAGGATAAGAATAAAGATAATGACTAAAGCCAATATAAAGATACGAACACAAGTAGAAATTAAAATAGAAATCAAAACAATCTCCCCTTATTCAATATGAAATATAATAGTGAGTATTTGTTTCATGATGTCAATCATTTATTGTTAAAAATAAACAAAGTCAGTAAGAGTGTTAGGATCGTTATATTGCAAGGATCCTCCCTAGAAGCGTTGAATCATCTCAAGTAGCCTAGAACAAGAACAGCAGAGCATTAAATTGAAATAGATAATAAGGATATTGCTTGTTTTTAAGATAGTTTTAGGGAGTTTAAAATTAAGAAAAAGAACCCATGGACACACTCTAACATTGAGGATGGGGTTCCCTTGATGATAGTATAGTCTTAGGTATAGGGTAGTCCTACACGTCCTATATTATACAGTCTAAACTTGTAAAATTAAACTACAAGAACATGATGAAAATTAATGAGAAGGTTCCAAGATTGACTTCAATCCAAACACCTTGCTCTGCCAATTTTCATCTCCTTAAGATATATGATTTTGTTCCTGCGAGATAAGGTTATCAAATAGGGTGTGTATCTCTTTTACATATTGGGGCCCCCACTAGGCTAGGGTTTATAGTTAAGGAAGACTCATCACATTTTTTATTGAACTAGTCTACTCGCAGAATCCTACCGGGAATAGAAATTAGAACATTTGTGATACTTTGACTATAGGAAATAATTTTCAACACTACCTGAGATCAGGTTATTCTTCCAACTTATTCTACAAGTAATTGTTTAGCATCATAACAACAACGTTATAATTTAAGAATCAAGTCTTGTAACAGAAATAAGGATAACAGAAAGAACCTTGATTATACGGGTCCATTAATTTTATAGGAGAAGCTCCTTTTACAAGCCTAAGATTCCATTAGAGATAACCAGAATGGCTAAAGCCACAGGCCGGTACAACTTGGTAACACCAAAACGGGAGCTAGAGCAAGGAGTTGTGTTTAGCGACCTATGCAATTTCCTAGTGACTCCAACTGTACAAGGATGGAAGGTTTACTGGGCTGGACTTGAGTTTGATGTCAACCAAAAGGGTATTACCCTGTTAAATCGTCTTAAAGTGAATGATTTTGCTCCTGCATGGGCGATGACCCGGAACCTTTTCCCACACTTGTTCAAAAACCAACAGTCTGAAGTCCAAACTCCCATTTGGGCCTTGAGGGTAATTCTTGCCGCCGGGATTCTTGACCAATTAATGGATCATTCCCTCATTGAGCCGCTATCAGGGGCCCTGAACTTAATTGCTGATTGGTTACTAACAACATCTACTAATCACTTCAACATGAGAACTCAACGAGTGAAGGACCAACTGAGCATGAGGATGTTATCTCTTATAAGGTCAAATATTATTAACTTTATAAATAAGCTCGAGACTCTTCATGTCGTTAATTACAAGGGACTTCTAAGCAGTGTTGAGATAGGAACACCAAGCTATGCAATCATCATTACCAGGACTAATATGGGTTATCTTGTCGAGGTTCAGGAACCAGATAAATCTGCGATGGATATACGACACCCTGGTCCTGTCAAATTCTCCCTACTACATGAATCGACACTTAAACCTGTTGCCACTCCTAAACCGTCAAGCATTACTTCATTGATCATGGAGTTCAACAGTTCTTTGGCAATTTAATTGCCGTAATAAAAATTGTATGATAGGGCTAACATTAATTCCATAATCCATCGTAGGACAGAATCATTTTCCTGTATGATCTTAGTTTAATCTCTCTTTATACAATGATTAATAAGGAGCTTGTTTAAAATGTTACAAAAGTATACTGTTTGAACCCCTAGTATCCCTGTAAATATCCTCATTCAATTGTTTGCTTTTACATGTGTAGTCACCTGTATAGCATGACCCTAGTCATGCCTTTAATTAATACTTAATCTAACAGTTAATATAATGTATAACTTTCCATGCTCAAAGAGTAGTCAAAACAATGTGAGATCCAGTTTCACTCACAGCATCTATTCACTATTTACAGTATGATGAGCCCAAATTAACACAGTAGAGGTCTAGATTTATTAATAGAACGAGGAAGATTAAGAAAAAGTCCATAATGCTGGGGAGGCAATCCTTGCCACCATAGGACTTTTTCAATTCCTCTACTTTATGATGGCTACCCAACATACACAATATCCTGATGCAAGATTGTCTTCCCCAATTGTCTTAGACCAATGTGACCTAGTGACAAGAGCATGTGGACTCTACTCTGAGTATTCGCTGAACCCTAAACTAAGGACATGCCGTTTACCGAAACATATCTATAGATTAAAATATGACACCATTGTTTTACGATTTATTAGTGATGTCCCTGTAGCTACAATCCCAATAGACTACATTGCTCCGATGTTAACAAATGTTCTGGCAGATAGTAAAAATGTACCATTGGAACCTCCCTGCTTGAGTTTCTTGGATGAAATAGTCAATTATACCGTGCAGGATGCAGCATTCCTTAATTATTACATGAATCAGATTAAAACACAGGAAGGAGTAATTACAGATCAATTAAAACAGAACATTCGTAGGGTCATTCACAAAAACAGATATCTATCTGCTCTATTCTTCTGGCATGATCTTGCCATCCTCACCCGTCGAGGGAGAATGAACCGAGGAAATGTGCGCTCTACTTGGTTTGTAACGAATGAGGTTGTTGACATTCTAGGATATGGTGATTATATCTTCTGGAAGATCCCTATTGCTCTATTACCAATGAACACAGCTAATGTTCCACATGCATCAACTGACTGGTACCAACCTAATATCTTCAAGGAGGCTATTCAAGGACACACACATATTATTTCAGTTTCTACAGCCGAGGTCCTTATTATGTGTAAGGATCTTGTCACAAGTCGTTTTAATACCCTTCTGATTGCTGAGTTAGCCAGGTTGGAAGATCCAGTGTCTGCTGATTATCCACTAGTAGATAATATTCAATCTCTGTATAACGCAGGAGACTACCTGTTGTCCATATTGGGATCAGAGGGGTACAAAATAATCAAATATCTCGAACCTCTGTGTTTGGCTAAGATTCAACTATGTTCCCAATATACAGAACGAAAAGGGCGGTTTTTAACCCAGATGCATCTTGCAGTTATTCAGACATTGCGTGAACTCCTCCTTAATAGAGGGTTGAAAAAATCACAATTGTCTAAAATCCGCGAGTTTCACCAACTGTTGCTCAGACTCCGATCTACACCACAACAATTATGTGAATTATTTTCAATCCAAAAACACTGGGGCCACCCAGTTCTGCATAGTGAAAAGGCCATCCAAAAGGTTAAAAATCATGCAACAGTTCTAAAGGCATTGCGGCCGATTATCATCTTTGAAACGTATTGTGTATTCAAGTATAGTGTTGCAAAACATTTCTTTGATAGTCAAGGCACTTGGTACAGTGTGATATCAGACCGATGTTTAACGCCAGGATTGAATTCCTACATTAGGCGAAATCAATTCCCTCCACTTCCAATGATCAAAGATCTTTTATGGGAATTTTACCATTTGGATCATCCTCCATTATTCTCCACGAAGATCATTAGTGACCTCAGCATTTTCATTAAAGACCGCGCAACAGCAGTTGAACAAACCTGTTGGGATGCAGTTTTTGAGCCTAACGTTTTGGGCTACAGTCCACCTTATCGATTCAATACCAAACGTGTACCTGAACAATTCCTGGAGCAAGAGGATTTTTCTATTGAGAGTGTCTTACAATACGCCCAAGAACTTAGGTACTTATTGCCCCAGAATCGAAATTTTTCTTTTTCATTGAAGGAAAAAGAATTAAATGTTGGTAGGACATTTGGAAAATTGCCTTATTTAACCAGGAATGTCCAAACCCTCTGCGAAGCATTACTTGCAGATGGTTTGGCTAAAGCCTTTCCAAGCAATATGATGGTTGTCACAGAGAGGGAACAAAAGGAGAGCCTCCTTCACCAAGCATCCTGGCATCATACAAGTGATGATTTCGGAGAGCATGCCACAGTTCGTGGAAGTAGTTTTGTCACAGACCTGGAAAAATACAATCTGGCCTTCAGGTATGAATTCACAGCTCCCTTCATCAAATATTGCAACCAATGCTATGGGGTTCGCAATGTCTTTGATTGGATGCACTTCCTAATTCCGCAATGTTACATGCATGTTAGTGATTATTATAACCCACCACATAATGTAACCTTAGAGAATAGGGCATATCCTCCCGAAGGACCAAGTGCTTATAGAGGCCACCTTGGCGGTATTGAGGGGCTTCAACAAAAGTTATGGACTAGTATCTCATGTGCTCAAATCTCATTGGTAGAGATCAAGACCGGGTTCAAATTGCGATCAGCAGTCATGGGGGATAATCAATGTATTACAGTATTATCAGTCTTTCCACTAGAATCTAGTCCGAATGAGCAGGAGAGATGCGCAGAAGACAATGCAGCCAGAGTGGCTGCTAGCTTGGCCAAAGTCACAAGTGCCTGTGGGATATTCCTCAAGCCTGATGAGACTTTTGTACACTCAGGCTTTATCTATTTTGGCAAAAAGCAATACTTGAACGGAATTCAATTACCTCAATCACTCAAGACAGCAGCTAGGATGGCCCCTCTCTCAGATGCAATTTTTGATGACTTGCAAGGTACACTTGCCAGTATAGGAACTGCCTTTGAGCGATCAATCTCCGAAACTAGACATATTTTACCATGTCGTGTTGCAGCTGCCTTTCATACATATTTCTCTGTTCGGATCTTACAACATCATCACCTTGGTTTCCATAAGGGTTCAGACCTTGGACAATTGGCAATCAATAAACCTCTTGATTTCGGGACCATTGCACTATCCTTAGCAGTTCCTCAGGTATTGGGTGGATTATCCTTCCTAAATCCAGAAAAGTGCCTTTATCGCAACTTGGGTGATCCTGTAACTTCAGGCCTATTTCAGTTGAAGCATTATCTGTCAATGGTGGGTATGAGTGATATCTTTCATGCACTTGTTGCAAAAAGCCCAGGGAATTGTAGCGCAATTGACTTTGTTCTAAACCCAGGCGGGTTAAATGTCCCTGGATCACAGGATTTAACATCTTTCCTTCGTCAGATTGTCAGAAGGAGTATCACACTTTCGGCAAGGAACAAGTTAATCAACACGTTATTTCACGCTTCTGCAGATCTTGAAGACGAATTAGTATGTAAATGGTTACTTTCTTCAACGCCCGTTATGAGCCGTTTCGCAGCCGATATTTTCTCACGAACACCAAGCGGGAAAAGATTACAAATCTTGGGATACCTCGAGGGAACCAGAACTTTATTAGCATCCAAAATGATAAGCAATAATGCAGAGACACCAATCTTGGAGAGGCTCAGAAAAATAACACTTCAAAGATGGAATCTATGGTTTAGTTATCTAGACCATTGTGACCCAGCTTTAATGGAAGCAATTCAACCAATTAAGTGTACTGTTGATATTGCTCAAATTCTTAGAGAATACTCCTGGGCTCATATTCTTGATGGTAGACAGTTAATAGGGGCAACACTGCCATGTATACCTGAGCAGTTCCAAACCACATGGTTAAAACCTTACGAGCAATGTGTGGAATGTTCATCCACAAACAATTCTAGTCCATATGTATCAGTTGCATTAAAAAGGAACGTGGTTAGTGCTTGGCCTGATGCATCTAGATTGGGGTGGACGATTGGTGATGGGATTCCCTACATAGGCTCAAGAACTGAGGACAAGATAGGTCAGCCCGCTATTAAGCCGAGGTGCCCATCAGCTGCATTAAGAGAAGCTATTGAATTGACCTCTAGGTTGACCTGGGTCACTCAAGGTAGTGCAAACAGCGATCAGTTAATTCGCCCTTTTCTTGAGGCAAGGGTAAACTTGAGTGTACAAGAGATTCTTCAAATGACACCCTCACATTACTCCGGTAATATTGTGCATCGGTATAATGATCAGTATAGCCCTCACTCCTTTATGGCTAACCGCATGAGTAACACAGCAACGCGCTTGATGGTATCTACCAACACACTAGGAGAGTTTTCCGGAGGGGGTCAGGCTGCACGTGATAGCAACATTATATTTCAAAATGTGATTAACTTTGCAGTGGCCTTGTATGACATTAGGTTTCGGAACACTTGTACATCTTCTATTCAATATCACAGGGCCCATATTCACCTGACGAATTGTTGTACGAGGGAAGTACCGGCCCAATACTTAACATACACAACCACGCTAAATCTAGATTTGAGTAAGTACCGTAATAATGAACTGATTTATGATTCAGAGCCACTAAGAGGAGGTCTCAACTGCAACTTATCGATTGACAGTCCTTTGATGAAGGGCCCACGTTTAAATATTATTGAGGATGACTTAATACGGTTGCCACATTTATCCGGCTGGGAATTAGCAAAAACAGTCTTGCAATCAATAATCTCTGATAGTAGCAATTCATCAACAGATCCCATTAGCAGCGGTGAAACAAGATCCTTTACAACCCACTTCTTAACGTATCCTAAAATAGGGCTCCTATACAGTTTTGGAGCCCTCATAAGTTTTTATTTGGGTAATACTATTCTGTGCACGAAAAAGATCGGACTCACAGAATTTCTATACTATCTCCAGAATCAGATTCACAACTTATCACATAGATCCCTTCGAATCTTCAAACCGACATTTAGACACTCAAGTGTCATGTCCAGGTTGATGGATATAGACCCCAACTTCTCAATATATATTGGTGGGACTGCAGGTGACCGTGGATTATCGGATGCTGCAAGATTATTTCTCCGAATTGCAATTTCAACTTTCTTGAGCTTTGTTGAGGAGTGGGTTATCTTTAGGAAGGCGAACATCCCACTATGGGTTATCTATCCTCTCGAAGGCCAACGCCCTGATCCTCCTGGCGAATTTTTGAACCGAGTAAAATCTCTAATTGTTGGGACTGAAGATGATAAAAATAAAGGCTCTATACTTTCAAGATCTGGAGAGAAATGCTCTTCAAATCTAGTTTATAATTGCAAGAGTACGGCAAGCAATTTTTTCCATGCATCATTGGCTTATTGGAGAGGTCGACATAGACCTAAGAAGACTATAGGTGCAACTAACGCGACAACAGTTCCACATATCATTTTGCCACTAGGAAATTCTGATCGACCGCCTGGCCTAGACCTTAATAGGAACAATGATACTTTCATTCCTACCAGAATTAAACAGATAGTCCAAGGAGACTCTAGAAACGACAGAACGACCACCACGAGATTTCCACCCAAAAGTAGGTCCACTCCAACATCAGCAACCGAGCCTCCTACAAAAATGTATGAGGGTTCGACTACCCACCAAGGGAAATTAACAGATACACATTTGGATGAGGATCACAATGCCAAAGAGTTTCCATCCAATCCGCATCGTTTAGTAGTACCATTCTTTAAATTAACAAAAGATGGGGAATACAGTATCGAACCTTCTCCTGAAGAAAGCCGCAGTAATATAAAAGGATTACTTCAACATTTAAGAACCATGGTTGATACTACCATATATTGTCGCTTCACTGGAATTGTTTCATCAATGCATTATAAGTTAGATGAAGTACTATGGGAATATAATAAATTTGAATCAGCTGTAACCCTAGCAGAAGGGGAGGGTTCAGGTGCCTTACTACTGATCCAAAAATACGGCGTTAAGAAGTTATTTTTGAATACACTTGCTACTGAACATAGTATTGAGAGTGAAGTGATATCAGGTTACACCACTCCAAGGATGCTACTCTCAATTATGCCTAAAACACATCGTGGTGAGCTAGAGGTCATATTAAATAACTCAGCTAGTCAAATAACTGATATTACACACCGAGATTGGTTTTCAAATCAAAAAAATAGGATTCCAAATGATGCTGATATTATTACCATGGATGCTGAAACTACAGAAAACTTAGATCGTTCCAGATTATATGAAGCAGTATATACGATTATTTGTAATCATATCAATCCTAAAACTTTGAAAGTGGTCATCTTAAAAGTCTTCCTCAGCGATTTGGATGGGATATGCTGGATTAACAATTATCTTGCTCCTATGTTTGGATCAGGATATTTAATCAAGCCTATAACATCAAGTGCAAAGTCAAGTGAGTGGTATTTATGCTTATCTAATCTACTTTCAACCTTGAGAACTACTCAGCATCAAACCCAGGCAAACTGTCTCCATGTCGTACAATGTGCTCTTCAACAGCAAGTACAAAGAGGGTCATATTGGCTAAGTCATCTTACCAAATACACCACAAGTAGATTGCACAATAGTTATATTGCATTTGGTTTTCCTTCATTAGAGAAGGTCCTATATCATAGGTATAACCTTGTTGATTCGAGAAATGGACCATTAGTTTCTATAACGAGACACCTTGCCCTCCTCCAAACTGAGATCCGGGAGTTGGTAACTGATTATAATCAGCTGCGACAAAGTCGAACCCAGACTTATCATTTCATAAAAACATCCAAGGGACGGATAACTAAACTAGTGAATGATTATCTAAGATTTGAGTTGGTTATACGGGCTCTTAAAAATAATTCTACATGGCACCATGAGTTATACTTGCTACCAGAACTTATAGGTGTTTGCCATCGATTTAATCATACACGTAACTGTACATGCAGTGAAAGGTTCCTGGTTCAAACTTTATACCTACACCGAATGAGTGATGCTGAGATAAAACTTATGGACCGGCTCACCAGCCTAGTCAATATGTTTCCTGAAGGTTTCAGGTCTAGTTCAGTCTAATTCTAACTGCACCAAAGGCTCTAGAAATATTTTAAATAACCAGGTGTATATCAAAGTCAATACAAGTGTAAAAACAATATGCAAGGGACTACATTTAGGATCAGTTTATTGACTCTTCCAATATACAGAGTTGGAAGCACCGATTCAAGGTTTCTAAGACGCTCTATCGATTATGTTGATAATGTAAATAACAGCTTTTCCTGTCCATTATGACTTAAATAAACATATCTATAACGACCATCACAGCTAAGTCGTTGCCCTAGTTCATATATTAAATTAAAATTTAGAAGCTAAGTTAACTCTAATTACATAAGTATTAAGAAAAAATTACTAAGACTAATACTCTCATGCCAAGAACTAGTAATGTGTTTCACATGACAGATTATTTCTAACACTAAATTGCAATTTCAATTTAAAAGCTAAGGTTAGCACCTATACAGCCAAAATATTTCATAGGGCCGATGGGAATAACATAAGAGGAACATGATCAATGAACCCTTTATTCCAACTAGGCAGTTGATTGATAATCTACAAATTCCATAAGATGTTCTTACGATTTTCTTTTGTTTTTAATCTCAATGTCAATGATTTAATAAGTAATAATAAAAAAATCACATTAAAGATGCAGGAAGATCTTGACCTCGCCAGGAAAATTAAGCGCACACAAATAAATTAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCCA\n>Sudan_ebolavirus_isolate_EBOV-S-2004_from_Sudan_complete_genome\nCGGACACACAAAAAGAAAGAAAAGTTTTTAAGACTTTTTGTGTGCGAATAACTATGAGGAAGATTAATCATTTTCCTCAAACTCAAACTAATATTGACATTGAGATTGATCTCATCATTTACCAATTGGAGACAATTTAACTAGTTAATCCCCCATTTGGGGGCATTCCTAAAGTGTTGCGAAGGTATGTGGGTCGTATTGCTTGGCCTTTTCCTAACCTGGCTCCTCCTACAATTCTAACCTTCTTGATAAGTGTGGTTACCAGAGTAATAGACTAAATTTGTCCTGGTAGTTAGCATTTTCTAGTAAGACCGATACTATCCCAAGTCTCAAGAGAGGGTGAGAGGAGGGCCCCGAGGTATCCCGTTAGTCCACAAAATCTAGCCAATTTTAGCTAAGTGGACTGATTACCTTCATCACACGCTATCTACTAAGGGTTTACCTGAGAGCCTACAACATGGATAAACGGGTGAGAGGTTCATGGGCCCTGGGAGGACAATCTGAGGTTGATCTTGACTACCACAAGATATTAACAGCCGGGCTTTCAGTCCAACAGGGGATTGTGCGACAAAGAGTCATCCCGGTATATGTCGTGAATGATCTTGAGGGTATTTGTCAACATATCATTCAGGCTTTTGAAGCAGGTGTAGATTTCCAGGATAATGCTGATAGCTTCCTCTTACTTTTATGTTTACATCATGCCTACCAAGGAGATCATAGGCTCTTCCTCAAAAGTGATGCAGTTCAATATTTAGAGGGCCATGGCTTCAGGTTTGAGGTCCGAGAAAAGGAGAATGTGCACCGTCTGGATGAATTGTTGCCCAATGTTACCGGTGGAAAAAATCTCAGGAGAACATTGGCTGCTATGCCCGAAGAGGAGACAACGGAAGCTAATGCTGGTCAGTTTCTATCCTTTGCCAGTTTGTTTCTACCCAAACTTGTCGTTGGGGAGAAAGCGTGCCTGGAAAAAGTACAAAGGCAAATTCAGGTCCATGCAGAACAAGGGCTCATTCAATATCCAACTTCCTGGCAATCAGTTGGACACATGATGGTGATCTTCCGTTTGATGAGGACAAACTTTTTAATCAAGTTTCTACTAATACATCAAGGGATGCACATGGTTGCAGGTCATGATGCGAATGACACAGTAATATCTAATTCTGTTGCCCAGGCAAGGTTCTCTGGTCTTCTGATTGTAAAGACTGTTCTGGATCACATCCTACAAAAAACAGATCTCGGAGTACGACTTCATCCGCTGGCCAGGACAGCAAAAGTGAAGAATGAGGTCAGTTCATTCAAGGCGGCTCTTGGTTCACTTGCCAAGCATGGAGAATATGCTCCGTTTGCACGTCTCCTTAATCTTTCTGGAGTCAACAACTTGGAACATGGGCTTTATCCACAACTTTCAGCCATCGCTTTGGGTGTTGCAACTGCCCACGGGAGTACGCTTGCTGGTGTGAATGTAGGGGAGCAATATCAGCAACTACGTGAGGCTGCTACTGAGGCTGAAAAGCAACTCCAACAATATGCTGAAACACGTGAGTTGGATAACCTTGGGCTTGATGAACAGGAGAAGAAGATTCTTATGAGCTTCCACCAGAAGAAGAATGAGATCAGCTTCCAGCAGACTAATGCAATGGTAACCTTGAGGAAAGAACGGCTGGCTAAATTGACCGAAGCCATCACGACTGCATCGAAGATCAAGGTTGGAGACCGTTATCCTGATGACAATGATATTCCATTTCCCGGGCCGATCTATGATGACACTCACCCCAATCCCTCTGATGATAATACTGATGATTCACGTGATACAACTATTCCAGGTGGTGTTGTTGACCCGTATGATGATGAGAGTAATAATTATCCTGACTACGAGGATTCGGCTGAAGGCACCACAGGAGACCTTGATCTCTTCAATTTGGACGACGACGATGATGACAGCCGACCAGGACCACCAGACAGGGAGCAGAACAAGGAGAGGGCGGCCCGGACATATGGCCTCCAAGATCCGACCTTGGACGGAGCGAAAAAGGTGTCGGAGTTGACCCCAGGTTCCCATCAACCAGGCAACCTCCACATCACCAAGTCGGGTTCAAACACCAACCAACCACAAGGCAATATGTCATCTACTCTCCATAGTATGACCCCTATACAGGAAGAATCAGAGCCCGATGATCAAAAAGATAATGATGACGAGAGTCTCACATCCCTTGACTCTGAAGGTGACGAAGATGGTGAGAGCATCTCTGAGGAGAACACCCCAACTGTAGCTCCACCAGCACCAGTCTACAAAGACACTGGAGTAGACACTAATCAGCAGAATGGACCAAGCAGTACTGTAGATAGTCAAGGTTCTGAAAGTGGAGCTCTCCCAATCAACTCTAAAAAGAGTTCCGCACTAGAAGAAACATATTATCATCTCCTAAAAACACAGGGTCCATTTGAGGCAATCAATTATTATCACCTAATGAGTGATGAACCCATTGCTTTTAGCACTGAAAGTGGCAAGGAATATATCTTTCCAGACTCCCTTGAAGAAGCCTACCCGCCGTGGTTGAGTGAGAAGGAGGCCTTAGAGAAGGAAAATCGTTATCTGGTCATTGATGGCCAGCAATTCTTCTGGCCGGTAATGAGCCTACAGGACAAGTTCCTTGCCGTTCTTCAACATGACTGAGGACCTATGATTGGTGGATCTTGTTTATTCCGAGCCTGATTATAATTGTTCTGATAATTCAAGTATAAGCACCTACCCCGAAATATAAACCCTATCTTAGTTATAAGGAAATTAAATAAATAACCTGTAAGTTATAGGACTACGAAGAGCTGCTTGTGTCAATTTATCATGGGTTGATACCCGTACCGCAAGAATCATTATTTAGTAGTTTTGGTCAGCTTCTGATATGTACCAATAAGAAAACATTATAGCATTAAAACATAAGGTATCTTTCAATGAGCTTAGGAGGATAATATCCTGATAAATTCTATAGAACTTAAGATTAAGAAAAAATCCATGATGAAGATTAAAACCTTCATCATCTTTTAAAAAGAGAGCTATTTCTGATCTAAATGTTCTTATTAATGTCAAAGAGCTATTAGTTTGTATCCTCTTAGCCTAGACGCTGCCTAACATATAAGCCATGCAGCAGGATAAGACTTATAGACATCATGGACCCGAAGTGTCTGGCTGGTTTTCTGAGCAATTAATGACCGGCAAAATACCGCTAACAGAGGTGTTTGTTGACGTTGAAACCAAGCCAAGTCCTACCCCGATAACCATTATTAGTAAGAATCCTAAAACAACGCGTAAAAGTGATAAGCAAGTCCAAACAGATGATGCTAGTAGCTTATTGACAGAAGAGGTCAAGACTGCCATAAATTCGGTGATATCAGCTGTGCGTCGGCAAACCAATGCTATTGAATCACTAGAAAGTCGAATAGCAAACCTTGAGGCCAGCTTAAAACCAGTTCAAGATATGGCAAAGACCATTTCATCCCTGAATCGCAGTTGTGCTGAAATGGTTGCAAAATACGACCTACTGGTGATGACCACTGGACGCGCAACTGCCACTGCTGCAGCAACAGAAGCATATTGGAATGAACATGGACAAGCACCTCCAGGCCCATCATTGTACGAAGATGATGCTATCAAGGCTAAATTGAAAGATCCGAACGGGAGGGTTCCAGAGAGTGTCAAACAGGCCTACACAAATCTGGATAGCACAAGTGCCCTCAATGAGGAAAATTTTGGGCGACCTTACATCTCAGCAAAAGATCTCAAGGAAATCATCTATGATCATCTCCCAGGGTTTGGGACAGCCTTTCATCAGCTGGTGCAGGTTATCTGCAAAATTGGTAAGGATAATAATATCCTAGACATAATCCATGCAGAATTCCAAGCAAGCTTGGCTGAGGGAGACTCCCCCCAATGTGCCTTAATCCAGATAACAAAACGGATCCCTACTTTCCAAGATGCCTCTCCTCCAATCGTGCATATAAAGTCTCGAGGAGATATACCCAAAGCCTGTCAGAAAAGCCTCCGGCCGGTCCCACCATCACCAAAGATCGATAGAGGTTGGGTCTGTATTTTTCAATTTCAAGACGGGAAGACCCTTGGGCTAAAAATATGATACAGAAGCAAGGTAAGCTCATTTTGCGATGACAAAGTGATACTTATGACTGTTTGGAATCAAGTTAGACTCATAGTCTATCACGTCATAAGCTTATAAGTCAGTTAAAAATTTATCCTCTATCCTAATCAATTGATGATGCTGTCAATAGGGAGATTCCCCTGTATTGTAATAAAACCTCATTAACATATCTCCCCTGCTTGGTACTATGTAGAAACCCTTGAATAAATCAAAATTGATGAAGATTAAGAAAAAGAGGGATTTTCTCAGGAAAAATCTTCTTTCTTACCTTCATCTTATTTAGATAAATCTAGGATTTAGGGAAAATGAGAAGGGTTACTGTGCCGACTGCACCACCTGCATATGCTGACATTGGCTATCCTATGAGCATGCTTCCAATCAAGTCAAGCAGGGCTGTAAGTGGAATTCAACAGAAACAAGAGGTCCTTCCTGGAATGGATACACCATCGAACTCTATGAGACCTGTTGCTGATGATAACATTGATCACACAAGTCATACCCCAAACGGAGTGGCCTCAGCATTCATCTTGGAGGCAACTGTCAATGTGATCTCGGGGCCCAAAGTCCTCATGAAACAAATCCCTATTTGGTTGCCACTCGGAATTGCTGACCAAAAAACATACAGCTTTGACTCAACAACAGCAGCAATTATGCTCGCATCCTACACGATCACTCATTTTGGAAAGGCCAACAACCCCCTCGTCAGAGTGAATCGACTTGGTCAAGGAATACCGGATCACCCACTCAGATTGCTCAGGATGGGGAACCAGGCTTTCCTTCAAGAGTTTGTGCTACCACCAGTTCAACTGCCGCAATATTTCACTTTTGATCTGACTGCACTCAAATTAGTGACACAGCCTCTCCCTGCTGCAACATGGACAGATGAGACTCCGAGCAACCTTTCAGGAGCACTCCGTCCAGGGCTCTCATTTCACCCGAAACTGAGACCCGTTCTACTTCCAGGCAAGACGGGAAAGAAAGGGCATGTTTCTGATCTGACCGCCCCAGACAAAATCCAGACAATTGTGAACCTGATGCAAGATTTCAAGATTGTGCCAATCGACCCAGCCAAGAGCATCATTGGGATCGAGGTTCCAGAATTGCTGGTCCACAAGCTCACCGGGAAGAAAATGAGTCAGAAGAACGGACAGCCTATAATTCCTGTCTTACTCCCAAAATACATTGGGCTAGATCCAATCTCGCCCGGAGACCTAACTATGGTCATAACACCAGATTATGATGATTGTCATTCACCCGCCAGTTGCTCTTATCTCAGTGAAAAGTGATTCTCACAAAGTGAGAGAGACACCTCCAGTAAAGAAATCAAATCTTATCTATAGCAACTCAATCGACTTTTGGAAGGCTAGCAGTACATATACTATGGGACAACTCAACCCTCCAGTCAAAATGTACTAATCGGGTCAAGGAACTCTCACTGATCAAGTCTAAATCCAGGATAGAACCAGCCCAAAGGGTCTCCTCCAAGTCTCCCACAAGCTTAGCCAATCAATTTACATGCGTAAGCGATCCATACTTAATCCAATTAGTGTTCGATGCTCACCCCTCCAAGCCTCCTTCCTGGCAAATCAACCTAGCTGTACCAGGAGATTCCCTCAGTCTCCTTCTCAAATGACCTGATACTTGAGGGTTACATCCTCACCAATCTATGCTTATTTAACCCAAACATAAAAAGCAATGCCTTTACATGATTGCACTATTAAGAAAAACAAATTTGATGAAGATTAAGCCTGATTAAGGCCCAACCTTCATCTTTTTACCATAATCTTGTTCTCAATACCATTTAATAGGGGTATACTTGCCAAAGCGCCCCCATCCTCAGGATCTCGCAATGGAGGGTCTTAGCCTACTCCAATTGCCCAGAGATAAATTTCGAAAAAGCTCTTTCTTTGTTTGGGTCATCATCTTATTTCAAAAGGCCTTTTCCATGCCTTTGGGTGTTGTGACCAACAGCACTTTAGAAGTAACAGAGATTGACCAGCTAGTCTGCAAGGATCATCTTGCATCCACTGACCAGCTGAAATCAGTTGGTCTCAACCTCGAGGGGAGCGGAGTATCTACTGATATCCCATCTGCGACAAAGCGTTGGGGCTTCAGATCTGGTGTGCCTCCCAAGGTGGTCAGCTATGAAGCAGGAGAATGGGCTGAAAATTGCTACAATCTTGAAATAAAGAAGCCGGACGGGAGCGAATGCTTACCCCCACCGCCGGATGGTGTCAGAGGCTTTCCAAGGTGCCGCTATGTTCACAAAGCCCAAGGAACCGGGCCCTGCCCGGGTGACTATGCCTTTCACAAGGATGGAGCCTTCTTCCTCTATGACAGGCTGGCTTCAACTGTAATTTACAGAGGAGTCAATTTTGCTGAGGGGGTAATTGCATTCTTGATATTGGCTAAACCAAAGGAAACGTTCCTTCAATCACCCCCCATTCGAGAGGCAGTAAACTACACTGAAAACACATCAAGTTACTATGCCACATCCTACTTGGAGTACGAAATCGAAAATTTTGGTGCTCAACACTCCACAACCCTTTTCAAAATTAACAATAATACTTTTGTTCTTCTGGACAGGCCCCACACGCCTCAGTTCCTTTTCCAGCTGAATGATACCATTCACCTTCACCAACAATTGAGCAACACAACTGGGAAACTAATTTGGACACTAGATGCTAATATCAATGCTGATATTGGTGAATGGGCTTTTTGGGAAAATAAAAAAATCTCTCCGAACAACTACGTGGAGAAGAGCTGTCTTTCGAAACTTTATCGCTCAACGAGACAGAAGACGATGATGCGACATCGTCGAGAACTACAAAGGGAAGAATCTCCGACCGGGCCACCAGGAAGTATTCGGACCTGGTTCCAAAGGATTCCCCTGGGATGGTTTCATTGCACGTACCAGAAGGGGAAACAACATTGCCGTCTCAGAATTCGACAGAAGGTCGAAGAGTAGATGTGAATACTCAGGAAACTATCACAGAGACCACTGCAACAATCATAGGCACTAACGGTAACAACATGCAGATCTCCACCATCAGGACAGGACTGAGCTCCAGCCAAATCCTGAGTTCCTCACCGACCATGGCACCAAGCCCTGAGACTCAGACCTCCACAACCTACACACCAAAGCTACCAGTGATGACCACCGAGGAACCAACAACACCACCGAGAAACTCTCCTGGCTCAACAACAGAAGCACCCACTCTCACCACCCCAGAGAATATAACAACAGCGGTTAAAACTGTTTTGCCACAAGAGTCCACAAGCAACGGTCTAATAACTTCAACAGTAACAGGGATTCTTGGGAGCCTTGGACTTCGAAAACGCAGCAGAAGACAAGTTAACACCAGGGCCACGGGTAAATGCAATCCCAACTTACACTACTGGACTGCACAAGAACAACATAATGCTGCTGGGATTGCCTGGATCCCGTACTTTGGACCGGGTGCAGAAGGCATATACACTGAAGGCCTTATGCACAACCAAAATGCCTTAGTCTGTGGACTCAGACAACTTGCAAATGAAACAACTCAAGCTCTGCAGCTTTTCTTAAGGGCCACGACGGAGCTGCGGACATATACCATACTCAATAGGAAGGCCATAGATTTCCTTCTGCGACGATGGGGCGGGACATGTAGGATCCTGGGACCAGATTGTTGCATTGAGCCACATGATTGGACCAAAAACATCACTGATAAAATCAACCAAATCATCCATGATTTCATCGACAACCCTTTACCCAATCAGGATAATGATGATAATTGGTGGACGGGCTGGAGACAGTGGATCCCTGCAGGAATAGGCATTACTGGAATTATTATTGCAATCATTGCTCTTCTTTGCGTCTGCAAGCTGCTTTGTTGAATATCAACTTGAATCATTAATTTAAAGTTGATACATTTCTAACATTATAAATTATAATCTGATATTAATACTTGAAAATAAGGCTAATGCCAAATTCTGTGCAAAACTTGAAAGTAGGTTTACAAAAATCCTTTGAACTGGAATGCTTTAATGCTCTTTCTCAATACTATATAAGTTCCTTCCCAAAAATAATATTGATGAAGATTAAGAAAAAGTGACATTGTGTCCACTTTTGTAATCTTCATCCACCTAAACATCCGTTGTCAGGAATCTTTGAATCAACCCTTACACTTGCTTAGGAAAGAGCCTGTCCTCGACAAGAATTCCGAGGCGGCAATTCAGTTAATTTAATATCAAGATAACATCCATTTCCAAGGCCACCGCTAGTTATATTATTAACTTTTATCACAAATATGGAGAGGGGTCGTGAGCGCGGGAGATCAAGAAGTTCACGTGCTGACCAGCAAAATTCAACAGGTCCGCAATTTAGGACAAGATCCATTTCCCGGGATAAGACAACAACAGACTACCGTAGTAGTCGAAGCACTTCGCAAGTTAGAGTCCCTACAGTCTTCCATAAGAAAGGTACCGGGACCCTTACTGTCCCTCCAGCACCTAAGGATATCTGTCCTACTCTTAGAAAAGGATTTCTGTGTGATAGCAATTTCTGTAAAAAGGACCACCAACTTGAAAGCCTAACCGACCGGGAGCTCCTGCTTCTTATAGCACGGAAGACCTGTGGATCAACTGATTCATCACTTAATATAGCTGCTCCTAAAGACTTAAGACTGGCAAATCCTACGGCTGATGACTTCAAGCAGGACGGCAGTCCAAAATTAACCCTAAAATTACTAGTAGAAACTGCTGAGTTTTGGGCTAATCAGAATATTAATGAGGTAGATGATGCAAAACTCCGTGCTCTTTTGACGTTGAGTGCTGTTCTAGTGCGGAAATTCTCTAAATCACAACTTAGTCAATTATGTGAGAGTCATCTTAGGAGGGAAAACTTGGGGCAAGACCAAGCTGAATCAGTTCTCGAGGTTTATCAACGTTTACATAGTGATAAAGGTGGTGCTTTCGAGGCAGCACTATGGCAACAGTGGGATAGACAATCATTGACTATGTTTATATCTGCTTTTCTCCATGTAGCATTGCAACTTTCCTGTGAGAGCTCCACCGTAGTGATATCAGGCCTACGCTTACTTGCCCCTCCAAGCGTGAATGAAGGGCTCCCTCCTGCACCAGGAGAATATACTTGGTCAGAAGATAGTACAACTTAGTCCGTAGGGAGGACAAGTCAAATAAGATATCCTTATCCTCTATAGGAGGTATTTTTTAAGAGGGGGACAGGATATGAATAAGGATAACGACTAAAGCCAATATAAAGATAAGAACACAAATAGGAATTAAAATAGAAATCAAAACAATCTCCCCTTATTAAATATGAAACACAATGGTGAGTATTTGTTTCCTGATATTAATCATTTATTGTTAAAAATAAACAAAGTCAGTAAGAGTGTTAGGATCATTATATTGTAAGGATCTTCCCTTGAAGCGTTGAATCATCTCAAGTAGCCCAGAACCAAAACAGTAGAGCATTAAATTGTAATAGATAATAGGGACATTACTTGTTTTTAAGATAATTTTGGGAAGTTTAAAATTAAGAAAAAGAACCCATGGACACACTCTAACATTGAGGATAGGGTTTCCTTGATGATAGTCTAGTCTTAGGTACAGGGTAGTCCTACACGCCCTATATTATACAATCTAAACTTGTAAAATTGAACTACAAAAACATGATGAAAATTAATGAGAAGGTTCCAAGATTGACTTCAATCCAAACACCTTGCTCTGCCAATTTTCATCTCCTTAAGATATATGATTTTGTTCCTGCAAGATAAGGGCATCAAACAGGGTGTGTAGCTCTTTCACATATTTGGGCTCCTACTGGGCTAGGGTTTATAGTTAAGGAAGACTCACCTCATTTCTCATTGAACTATTCTACTCGTAGGATCCTACTGGGAATATAAATCAGAACATCTGTGACACTTTGACTATAGGAAATAATTTTCAAAACTACCTGAGATCGGGTCATTTCTCCAACTCATTCTGCAAGTAATTGTTTAGCATCATAACAACAGCGTTATAATTTAAAAATCAAGTCTTGTAACAAAAATAAGGATAACAGAAAGAACCCTTCTTATACGGGTTCACTAATTTTGTAGGAGAAGCTCCTTTTGCAAGCCTAAGATTCCATTAGAGATAACCAGAATGGCTAAAGCCACAGGCCGGTACAACTTGGTAACACCAAAACGGGAGCTAGAGCAAGGAGTTGTATTTAGCGACCTATGCAACTTCCTAGTGACTCCAACTGTGCAAGGATGGAAGGTTTACTGGGCTGGACTTGAGTTTGATGTCAACCAAAAGGGTATTACCCTGTTAAATCGTCTTAAAGTGAATGATTTTGCTCCTGCATGGGCGATGACCCGGAACCTTTTCCCACACTTGTTCAAAAACCAACAGTCTGAAGTCCAAACTCCCATTTGGGCCTTGAGGGTAATTCTTGCCGCCGGGATTCTTGACCAATTAATGGATCATTCCCTCATCGAGCCACTATCAGGGGCCCTGAACTTGATTGCTGATTGGTTACTAACAACATCTACTAATCACTTCAACATGAGAACGCAACGAGTGAAGGACCAACTGAGCATGAGGATGTTATCTCTTATAAGGTCAAATATTATTAACTTTATAAATAAGCTCGAAACTCTTCATGTTGTTAATTACAAGGGACTTCTAAGCAGTGTTGAGATAGGAACACCAAGCTATGCAATCATAATTACTAGAACTAATATGGGCTATCTTGTCGAAGTTCAGGAACCAGATAAATCTGCGATGGATATACGACACCCTGGTCCTGTCAAGTTCTCTCTACTGCATGAATCGACCCTCAAACCTGTTGCCACTTCTAAACCGTCAAGCATTACTTCATTGATCATGGAGTTCAATAGTTCTTTGGCAATTTAATTGCCATAACAAAGATTGTATGATAGGGCTAATATTGATTCAATAATCTATCGTAGGACAGAATCATTTCCCTGTATGATCTCAGTTTAATCTCTCTTTATGCAATAATTAATAAGGAGCTTGTTTAAAACGTTACAAAAGTATAATGTTTGAATCTCTAGTATCCCTGTAAATATTTTCATTCAATTGTCAGCCCTTACATGTGTAGTCACTTGTGTAGCATGACACTAGTTTTGCCTTCAATTAATATCTAACCTAACAGTCAATATAATGTATAACTTTCTATGTTTAAAGAGTAGTCAAAACAATGTGAGATCCAGTTTCACTCACAGCATCTATTCAATATTTACAGTATGATGAGTCCGAATTAACACAGTAGAGGTCTAGGTGTATTAACAGAACGAGGAAGATTAAGAAAAAGTCCATAATGCTGGGTGGGCAATCCTTGCCACCATAGGACTTTTTCAATTCCTCTACTTTATGATGGCTACCCAACATACACAATATCCTGATGCAAGATTGTCTTCCCCAATCGTTTTAGACCAATGTGACCTAGTGACAAGAGCATGCGGACTGTACTCTGAGTATTCGCTGAACCCTAAACTAAGAACATGCCGCTTGCCGAAACATATCTATAGATTAAAATATGACGCCATTGTTTTAAGATTTATCAGTGATGTCCCTGTAGCTACAATCCCAATAGATTACATTGCTCCAATGTTAATAAATGTTCTGGCAGATAGTAAAAATGCACCATTAGAACCTCCCTGTTTGAGCTTCCTAGATGAGATAGTCAATTATACTGTGCAGGATGCGGCATTCCTTAATTATTACATGAATCAGATTAAAACACAGGAAGGAGTAATTACAGATCAATTAAAACAGAACATTCGTAGGGTCATTCACAAAAACAGATATTTATCTGCTCTATTTTTCTGGCATGATCTCTCCATCCTCACCCGTCGAGGGAGAATGAACCGAGGAAATGTGCGCTCCACTTGGTTTGTAACGAATGAGGTTGTTGATATCCTAGGATATGGTGATTATATTTTCTGGAAGATCCCTATTGCTCTATTACCAATGAACACAGCTAATGTTCCTCATGCATCGACTGACTGGTACCAACCTAATATCTTCAAGGAGGCTATTCAAGGACACACACATATTATTTCAGTCTCTACAGCCGAGGTTCTTATTATGTGTAAGGATCTTGTCACAAGTCGTTTTAACACCCTTCTGATTGCTGAGTTAGCCAGGTTGGAAGATCCAGTGTCCGCTGATTATCCACTGGTAGATGATATTCAATCTCTGTATAATGCAGGAGACTACTTGTTGTCCATATTGGGATCGGAGGGGTACAAAATAATCAAGTATCTCGAGCCTCTGTGTTTGGCTAAGATTCAACTATGTTCCCAATATACAGAACGAAAAGGGCGGTTTTTAACCCAGATGCATCTTGCAGTTATTCAAACATTGCGTGAACTTCTCCTTAATAGAGGGTTGAAAAAATCACAGCTTTCTAAAATCCGTGAGTTCCACCAACTGTTGCTCAGACTTCGATCTACACCACAACAATTATGTGAATTATTTTCAATCCAAAAGCACTGGGGCCATCCAGTTCTGCATAGTGAAAAGGCCATACAAAAGGTTAAAAATCATGCAACAGTTCTAAAGGCATTGCGTCCGATTATCATCTTTGAAACGTACTGTGTATTCAAGTACAGTGTTGCAAAACATTTCTTTGATAGCCAAGGCACTTGGTACAGTGTGATATCAGACCGATGTTTAACGCCGGGATTGAATTCCTACATTAGGCGAAATCAATTCCCACCACTTCCAATGATCAAAGATCTTCTATGGGAATTTTACCATTTGGATCATCCTCCATTATTCTCCACGAAGATCATTAGTGATCTCAGCATTTTCATTAAAGACCGTGCAACAGCAGTTGAACAAACCTGTTGGGATGCAGTTTTCGAGCCTAACGTTTTGGGCTACAGTCCACCTTATCGATTCAACACCAAACGTGTACCAGAACAATTCCTGGAGCAAGAGGATTTTTCTATTGAGAGTGTCTTACAATACGCCCAAGAACTTAGGTACCTATTGCCCCAGAATCGAAATTTTTCTTTTTCATTGAAAGAAAAAGAATTAAATGTTGGTAGGACATTTGGAAAATTGCCTTATTTAACTAGGAATGTCCAAACCCTCTGCGAAGCATTACTTGCAGATGGTTTGGCTAAAGCCTTTCCAAGCAACATGATGGTTGTCACAGAGAGGGAACAAAAGGAGAGCCTCCTTCACCAAGCATCTTGGCATCATACGAGTGATGATTTCGGAGAGCATGCCACAGTTCGCGGGAGTAGTTTTGTCACAGACCTAGAGAAATATAATCTGGCTTTCAGGTATGAATTCACAGCTCCCTTCATCAAATATTGCAACCAATGCTATGGGGTTCGCAATGTCTTTGATTGGATGCACTTCCTAATTCCGCAATGTTACATGCATGTTAGTGATTATTATAACCCACCACATAATGTAACTTTAGAGAATAGGGAATATCCTCCCGAAGGACCAAGTGCTTATCGAGGCCACCTTGGTGGTATTGAGGGGCTTCAACAAAAGTTATGGACTAGCATCTCATGTGCTCAAATTTCATTGGTAGAGATCAAGACCGGATTCAAATTGCGATCAGCAGTCATGGGGGATAATCAATGTATCACAGTATTATCAGTCTTTCCACTAGAATCCAGTCCGAATGAGCAAGAGAGATGTGCAGAAGACAATGCAGCCAGAGTAGCTGCTAGCTTGGCCAAAGTCACAAGTGCCTGTGGGATATTCCTCAAGCCTGATGAGACTTTCGTACACTCAGGCTTTATCTATTTTGGCAAAAAGCAATACTTAAACGGAATTCAATTGCCTCAATCACTCAAGACAGCAGCTAGGATGGCCCCTCTCTCAGATGCAATTTTTGATGACTTGCAGGGTACACTTGCCAGTATAGGAACTGCCTTTGAGCGATCAATCTCCGAAACTAGACATATTTTACCATGTCGTGTTGCAGCTGCCTTTCATACATATTTCTCTGTTCGGATCTTACAACATCATCACCTTGGCTTCCATAAAGGTTCAGACCTTGGACAATTGGCAATCAATAAACCTCTTGATTTTGGGACCATTGCACTATCCTTAGCAGTTCCCCAGGTACTGGGTGGATTATCCTTCCTAAATCCAGAAAAATGTCTTTATCGCAACCTGGGTGACCCTGTGACTTCAGGCCTATTCCAGTTGAAGCATTATCTATCAATGGTAGGTATGAGTGATATCTTTCACGCACTTGTTGCAAAAAGTCCAGGGAATTGTAGCGCAATTGACTTTGTTCTAAACCCAGGAGGGTTAAATGTCCCTGGATCACAGGATCTAACATCTTTCCTTCGTCAGATTGTCAGAAGGAGTATCACACTTTCGGCAAGGAATAAGTTAATCAACACGCTGTTTCATGCCTCTGCAGATCTTGAAGATGAATTAGTTTGTAAATGGTTACTTTCTTCAACGCCCGTCATGAGCCGTTTCGCAGCCGATATTTTCTCACGAACACCAAGCGGGAAAAGATTACAAATCTTGGGATATCTCGAGGGAACCAGAACTTTATTAGCATCTAAAATGATAAGCAATAATGCAGAGACACCAATCTTAGAGAGACTCAGAAAGATAACACTTCAAAGATGGAATTTATGGTTTAGTTACCTAGACCATTGTGACTCAGCTTTAATGGAAGCAATTCAACCAATTAGGTGTACTGTTGATATTGCTCAAATTCTTAGAGAATACTCCTGGGCTCATATTCTTGACGGTAGACAGTTAATAGGGGCAACATTGCCATGTATACCTGAGCAGTTCCAAACCACATGGTTAAAACCTTACGAGCAATGTGTGGAATGTTCATCCACAAACAATTCTAGTCCATATGTATCAGTTGCATTAAAAAGGAACGTGGTCAGCGCTTGGCCTGACGCATCTAGATTGGGGTGGACGATTGGTGATGGGATTCCCTATATAGGCTCAAGAACTGAGGACAAGATAGGTCAGCCCGCTATTAAGCCGAGGTGCCCATCAGCTGCATTGAGGGAAGCTATTGAATTGACCTCTAGGTTAACCTGGGTCACTCAAGGTAGTGCAAATAGCGATCAGTTAATTCGTCCTTTTCTTGAGGCAAGAGTGAATTTGAGTGTACAAGAAATTCTTCAAATGACACCCTCACATTATTCCGGTAATATTGTGCATCGGTATAATGATCAGTATAGCCCTCACTCCTTTATGGCCAACCGCATGAGTAACACAGCAACGCGCTTGATGGTATCTACAAACACACTAGGAGAGTTCTCCGGAGGGGGCCAAGCTGCACGTGATAGCAACATTATATTCCAAAATGTGATTAATTTTGCAGTAGCCTTGTATGACATTAGGTTTCGGAACACCTGTACATCCTCTATTCAATATCACAGGGCTCATATTCACCTGACAGATTGTTGTACGAGGGAAGTACCAGCCCAATACTTAACATACACAACCACGCTAAATCTAGATTTGAGTAAGTATCGTAATAATGAACTGATTTATGATTCAGAGCCACTAAGAGGAGGTCTAAACTGCAACTTATCGATTGACAGTCCTTTGATGAAGGGCCCACGTTTAAATATTATTGAGGATGACTTAATACGGTTGCCACATTTATCCGGTTGGGAATTAGCAAAAACAGTTTTGCAATCCATAATTTCTGATAGTAGCAATTCATCAACAGATCCCATTAGCAGCGGTGAAACAAGATCCTTTACAACCCACTTCTTAACGTATCCTAAAATAGGGCTCTTATACAGTTTTGGAGCCCTCATAAGTTTTTATTTGGGTAATACTATCTTGTGCACGAAAAAGATCGGACTTACAGAATTTCTATACTATCTCCAGAACCAGATCCACAACTTATCACATAGATCCCTTCGAATCTTCAAACCGACATTCAGACACTCAAGTGTCATGTCTAGGTTGATGGATATAGACCCCAACTTCTCAATATATATTGGTGGGACTGCAGGTGATCGTGGATTATCGGATGCTGCAAGATTATTTCTCCGAATCGCAATTTCAACTTTCTTGAGCTTTGTTGAGGAGTGGGTTATCTTTAGGAAGGCAAACATTCCACTATGGGTTGTCTATCCTCTCGAAGGCCAACGCCCTGATCCTCCTGGTGAATTTTTAAACCGAGTAAAATCTTTAATTGTTGGGATTGAGGATGATAAAAATAAAGGCTCTATACTTTCAAGATCTGAAGAGAAGTGCTCTTCAAATCTAGTTTATAATTGCAAAAGTACAGCAAGCAATTTTTTCCACGCATCATTGGCTTATTGGAGAGGTCGACATAGACCTAAGAAGACTATAGGTGCAACTAAAGCGACAACAGCTCCACACATCATTTTGCCGCTAGGAAATTCTGATCGACCGCCTGGCCTAGATCTTAATCAGAGCAATGATACTTTTATTCCTACCAGAATTAAACAGATAGTCCAAGGAGACTCTAGAAATGACAGAACAACCACCACGAGACTTCCACCCAAAAGTAGGTCCACCCCAACATCAGCAACCGAGCCTCCTACAAAAATATATGAGGGTTCGACAACCTATCGAGGAAAATCAACAGATACACATTTGGATGAGGGTCATAATGCCAAAGAGTTCCCATTCAATCCACATCGTTTAGTAGTACCATTTTTTAAATTAACAAAAGATGGGGAATACAGTATCGAACCTTCCCCTGAAGAAAGCCGCAGTGATATAAAAGGGTTACTTCAACATTTAAGAACCATGGTTGATACTACCATATATTGTCGCTTCACTGGGATTGTTTCATCAATGCATTATAAATTAGATGAAGTACTATGGGAATATAATAAATTTGAATCAGCTGTAACCCTAGCAGAGGGGGAGGGTTCAGGTGCTTTACTACTGATCCAAAAATACGGCGTTAAGAAGTTATTTTTGAATACACTTGCTACTGAACATAGTATTGAGAGTGAAGTGATATCAGGTTACACCACCCCAAGAATGCTACTCTCAGTTATGCCTAGAACACATCGTGGTGAGCTAGAGGTCATATTAAATAACTCAGCTAGTCAAATAACTGATATTACACACCGAGATTGGTTTTCAAATCAAAAAAATAGGATTCCAAATGATGTTGATATTATTACCATGGATGCTGAAACTACAGAAAATTTAGATCGTTCAAGATTATATGAAGCAGTATATACGATTATTTGTAATCATATCAATCCTAAAACTTTAAAAGTGGTCATCTTAAAAGTCTTCCTCAGCGATTTGGATGGGATGTGCTGGATTAACAATTATCTTGCTCCTATGTTTGGATCAGGATACTTAATCAAACCTATAACATCAAGTGCAAGGTCAAGTGAGTGGTATTTATGCTTATCTAATCTACTTTCAACTTTGAGAACTACTCAGCATCAAACCCAAGCAAACTGTCTTCATGTCGTACAATGTGCTCTTCAACAGCAAGTTCAAAGAGGGTCATATTGGCTAAGTCATCTCACCAAATACACCACAAGTAGATTGCACAATAGTTATATTGCATTTGGTTTTCCTTCGTTAGAGAAGGTCCTATATCATAGATATAATCTTGTTGATTCGAGAAATGGACCATTGGTTTCTATCACAAGACACCTTGCCCTCCTCCAAACTGAGATCCGGGAGTTGGTAACTGATTATAATCAGCTGCGACAAAGTCGAACCCAGACTTATCATTTCATAAAAACATCCAAGGGACGGATAACTAAACTAGTGAATGATTATCTAAGATTTGAGTTGGTTATACGGGCTCTTAAAAATAATTCTACATGGCACCATGAGTTGTACTTACTACCAGAACTTATAGGTGTTTGCCATCGATTTAATCATACACGCAACTGTACATGCAGTGAAAGGTTCCTGGTTCAAACCTTATATCTACACCGGATGAGTGATGCTGAGATAAAACTTATGGACCGGCTCACCAGCCTAGTCAATATGTTTCCCGAAGGTTTCAGGTCTAGTTCAGTCTAATTCTAACTGCATCTCAGGTTCTAGAAGTATTTTAAATAACCAGGTATATATCAAAATCAATATAAGTGTAAGAACAATATGCAAGGGACCACATTTGGCATTAGTTTATTGACTCTTCCAATATACAGCGTTGGAAGCATCGATTCAAGGTTTCGAAGACACTCTATTGATTATGTTGATAATGTAAATAATAATTTTTCCTAGCTATTATGACTAAAATAAACAAATCTATAACGAACATCACAACCAAATTGTTGCCCTAGTTCATATATTAAATTCAAATTTAGAAGCTAGGTTGACTCCAGTTACATAAGTATTAAGAAAAAATTACTAAGACTAATACTCTTATGCTAAGAACTAGTAATATGTTTCACATGACAGGTTATTTCTGATACTAAATTGCAATTTCACTTTTAAAGCTAAGTTTAATACTTATACAGCCAAAATATTTCCTAGGGCCGGTGGGAATAACATAAGAAGAACACGGTCAATGAACCTTTTATTCCAACCAGGTAGTTGATTGATAATCTACAAATTCCATAAGATGTTCTTACGACATTTTTTTGTTTTTAATCTCAATGTCAATGATTTAATTAGTAGTAAGAAAAAAGTTACATTAGAGGTGCAGGAAGATCTTAACCTCACCAGGAAAATTAAGCGCACACAAATAAATTAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCCA\n>Sudan_ebolavirus_-_Nakisamata_complete_genome\nCGGACACACAAAAAGAAAGAAAAGTTTTTTAGACTTTTTGTGTGCGAATAACTATGAGGAAGATTAATCATTTTCCTCAAACTCAAACTAATATTAACATTGAGATTGATCTCATCATTTACCAATTGGAGACAATTTAACTAGTCAATCCCCCATTTGGGGGCATTCCTAAAGTGTTGCAAAGGTATGTGGGTCGTATTGCTTTGCCTTTTCCTAACCTGGCTCCTCCTACAATTCTAACCTGCTTGATAAGTGTGATTACCTGAGTAATAGACTAATTTCGTCCTGGTAATTAGCATTTTCTAGTAAAACCGATACTATCTCAAGTCCTAAGAGAAGGTGAGAAGAGGGTCCCGAGGTATCCCTCCAGTCCACAAAATCTAGCTAATTTTAGCTGAGTGGACTGATTACTCTCATCACACGCTAACTACTAAGGGTTTACCTGAGAGCCTACAACATGGATAAACGGGTGAGAGGTTCATGGGCCCTGGGAGGACAATCTGAAGTTGATCTTGACTACCACAAAATATTAACAGCCGGGCTTTCGGTCCAACAAGGGATTGTGCGACAAAGAATCATCCCGGTATATGTTGTGAGTGATCTTGAGGGTATTTGTCAACATATCATTCAGGCCTTTGAAGCAGGCGTAGATTTCCAAGATAATGCTGACAGCTTCCTTTTACTTTTATGTTTACATCATGCTTACCAAGGAGATCACAGGCTCTTCCTCAAAAGTGATGCAGTTCAATACTTAGAGGGCCATGGTTTCAGGTTTGAGGTCCGAGAAAAGGAGAATGTGCACCGTCTGGATGAATTGTTGCCCAATGTCACCGGTGGAAAAAATCTTAGGAGAACATTGGCTGCAATGCCTGAAGAGGAGACAACAGAAGCTAATGCTGGTCAGTTTTTATCCTTTGCCAGTTTGTTTCTACCCAAACTTGTCGTTGGGGAGAAAGCGTGTCTGGAAAAAGTACAAAGGCAGATTCAGGTCCATGCAGAACAAGGGCTCATTCAATATCCAACTTCCTGGCAATCAGTTGGACACATGATGGTGATCTTCCGCTTGATGAGAACAAACTTTTTAATCAAGTTCCTACTAATACATCAGGGGATGCACATGGTCGCAGGCCATGATGCGAATGACACAGTAATATCTAATTCTGTTGCCCAAGCAAGGTTCTCTGGTCTTCTGATTGTAAAGACTGTTCTGGACCACATCCTACAAAAAACAGATCTTGGAGTACGACTTCATCCACTGGCCAGGACAGCAAAAGTCAAGAATGAGGTCAGTTCATTCAAGGCAGCTCTTGGCTCACTTGCCAAGCATGGAGAATATGCTCCATTTGCACGTCTCCTCAATCTTTCTGGAGTCAACAACTTGGAACATGGGCTTTATCCACAACTCTCAGCCATTGCTTTGGGTGTTGCAACTGCCCACGGGAGCACGCTGGCTGGTGTTAATGTAGGGGAGCAATATCAGCAACTGCGTGAGGCTGCTACTGAAGCTGAAAAGCAACTCCAACAATATGCTGAAACACGTGAGTTGGACAACCTTGGGCTTGATGAACAGGAAAAGAAGATTCTCATAAGCTTCCACCAGAAGAAGAATGAGATCAGCTTCCAGCAAACTAACGCAATGGTAACCTTGAGGAAAGAGCGGCTGGCCAAGCTGACCGAAGCCATCACGACTGCATCAAAGATCAAGGTTGGAGATCGTTATCCTGATGACAATGATATTCCATTTCCCGGGCCGATCTATGATGAAACCCACCCCAACCCTTCTGATGATAATCCTGATGATTCACGTGATACAACTATCCCAGGTGGTGTTGTTGACCCGTATGATGATGAGAGTAATAATTATCCTGACTACGAGGATTCGGCTGAAGGCACCACAGGAGATCTTGATCTCTTCAATTTGGACGACGACGATGACGACAGCCAACCAGGACCACCAGACAGGGGGCAGAGCAAGGAGAGAGCAGCTCGGACACATGGCCTCCAAGATCCGACCTTGGACGGAGCGAAAAAGGTGCCGGAGTTGACCCCAGGTTCTCACCAACCAGGCAACCTCCACATCACCAAGCCGGGTTTAAACACCAACCAACCACAAGGCAATATGTCATCTACTCTCCAGAGTATGACCCCTATACAGGAAGAATCAGAGCCCGATGATCAGAAAGATGATGATGACGAGAGTCTCACATCTCTTGACTCTGAAGGTGACGAAGATGTTGAGAGCGTATCAGGGGAGAACAACCCAACTGTAGCTCCACCAGCACCAGTCTACAAAGATACTGGAGTAGACACTAATCAGCAAAATGGACCAAGCAATGCTGTAGATGGTCAAGGTTCTGAAAGTGAAGCTCTCCCAATCAACCCCGAAAAGAGATCTGCACTGGAAGAAACATATTATCATCTCCTAAAAACACAGGGTCCATTTGAGGCAATCAATTATTATCACCTAATGAGTGATGAGCCCATTGCTTTTAGCACTGAAAGTGGCAAGGAATATATCTTCCCAGATTCTCTTGAAGAAGCCTACCCGCCTTGGTTGAGTGAGAAGGAGGCCTTAGAGAAAGAAAATCGTTATCTGGTCATTGATGGCCAGCAATTCTTCTGGCCAGTAATGAGCCTACAGGACAAGTTCCTTGCTGTTCTTCAACATGACTGAGGACCCATGATTAGTAGATTTTGTTTATTCTGAGCTTGATTATAATTGTTTTGATAATTCAAGTATGAGCACCCAACCCGAAATATAAACCCTATTTTAGTTATGAGGAAATTAAATAAATAATCTGTAAGTTGTAGGACTATGAAGAGCTGCTTGTGTCAATTTATCACGGGTTAATACCCATACCGCAAGAATAATTATTTAGTAATTTTGATCAGCTTATGATATGTACCAATAGGAAAACATTATAGCATTAAAACATAAAGTATCCTTCGATGAGCTTAGGAGGATAATATCCTGATGAATTCTATAGAACTTAGGATTAAGAAAAAATTCATGATGAAGATTAAAACCTTCATCATCCTTTAAAAAGAGAGCTATTCTTTATCTGAATGTCCTTATTAATGTCTAAGAGCTATTATTTTGTACCCTCTTAGCCTAGACACTGCCCAACATATAAGCCATGCAGCAGGATAGGACTTATAGACATCATGGACCCGAAGTGTCTGGCTGGTTTTCTGAGCAGTTAATGACCGGCAAAATACCGCTAACAGAGGTGTTTGTTGATGTTGAAAACAAACCAAGTCCTGCCCCGATAACCATTATTAGTAAGAATCCCAAGACAACACGTAAAAGTGATAAGCAAGTCCAAACAGATGATGCCAGTAGCTTATTGACAGAAGAAGTCAAGGCTGCCATAAATTCGGTGATATCAGCTGTGCGTCGGCAAACCAATGCCATTGAATCACTAGAAGGTCGAGTAACAACTCTTGAGGCCAGCTTAAAACCAGTTCAAGACATGGCAAAGACCATATCATCCCTGAATCGCAGCTGTGCCGAAATGGTTGCAAAATACGACCTACTGGTGATGACCACTGGGCGAGCAACTGCCACTGCTGCAGCAACAGAAGCATATTGGAGTGAACATGGACAAGCACCTCCAGGCCCATCATTGTACGAGGATGATGCTATTAAGGCTAAATTGAAAGATCCGAACGGGAAGGTTCCAGAAAGTGTCAAACAGGCCTACACAAATCTAGATAGCACAAGTGCCCTCAATGAGGAAAATTTCGGGCGACCTTACATTTCAGCAAAAGATCTCAAGGAAATCATCTATGACCATCTCCCAGGATTTGGGACAGCTTTTCATCAGTTGGTGCAGGTTATCTGCAAAATTGGTAAGGATAATAATATCCTAGACATAATTCATGCAGAATTCCAAGCAAGCTTGGCTGAGGGGGACTCCCCCCAGTGTGCATTAATCCAGATAACAAAACGGATCCCTGCTTTCCAAGATGCCTCTCCTCCAATTGTGCATATCAAGTCTCGAGGAGATATACCCAAAGCCTGTCAGAAAAGCCTCCGGCCGGTCCCACCGTCACCAAAGATCGATAGAGGTTGGGTCTGTATTTTTCAATTCCAAGACGGGAAGGCCCTTGGGCTAAAAATATGATACAGAAGCAAGGTAAGCTCATTTTGCGATGGCCAAATGATACTTATGACTGTTCAAAATCAAGTTAGACTAATAGTCTATCATGTCATAAGCTTATAAGTCAGTTTTAAATTTCCTCTCTATCCTAATCAATTGATAATGCTGTCAATAGGGAAATTCCCCTGTATTGTAATAAAACCTCATTAACATATTTCCCCTGCTTAGTACTATGCAGAAACCCCCGAGCAAATTAAAATTGATGAAGATTAAGAAAAAGAGGGATTTTCTCAGGAAAAATCTTTTTTCTTACCTTCATCTCATTTAAACAAATTTAGGACTCAGGAAAAATGAAAAGGGTCACTGTGCCGACTGCACCACCTGCCTATGCTGACATTGGCTATCCTATGAGCATGCTTCCCATCAAGTCAAGCAGGGCTGTGAGTGGAATTCAACAGAAACAAGAGGTCCTTCCTGGAATGGATACACCATCAAATTCTATGAGACCTGTTGCTGATGATAACATTGATCATACAAGTCATACCCCGAACGGAGTGGCCTCAGCATTCATCTTGGAGGCAACTGTCAATGTGATCTCGGGGCCCAAAGTCCTCATGAAACAAATCCCTATTTGGTTGCCACTCGGAATTGCTGACCAAAAAATGTACAGTTTTGACTCAACAACAGCAGCAATTATGCTCGCATCTTATACGATCACCCATTTTGGAAAGGCCAACAACCCCCTCGTTAGAGTGAATCGACTTGGTCAGGGAATACCGGATCACCCACTCAGATTGCTCAGGATGGGGAACCAGGCTTTCCTTCAAGAGTTTGTGCTACCACCAGTTCAACTGCCGCAATATTTCACTTTTGATCTGACTGCACTCAAATTAGTGACACAGCCTCTCCCTGCTGCAACATGGACAGATGAGACTCCGAGCAACCTTTCAGGAGCACTTCGTCCCGGGCTTTCATTTCACCCAAAGCTGAGACCCGTTCTACTTCCAGGCAAAACGGGAAAGAAAGGGCATGTTTCTGATCTGACTGCCCCAGACAAAATTCAGACAATTGTGAACCTGATGCAAGATTTCAAAATCGTGCCAATTGATCCAGCTAAGAGTATCATTGGGATCGAGGTTCCAGAATTGCTGGTCCACAAGCTCACCGGGAAGAAAATGAGTCAGAAGAATGGACAGCCTATAATTCCTGTCTTACTTCCAAAATACATCGGGCTAGATCCAATCTCACCTGGAGACCTGACTATGGTCATAACACCAGATTATGATGATTGTCATTCACCTGCCAGTTGCTCTTATCTCAGTGAAAAGTGATTCTCACAAAGTGAGAGAAACACCTCCAGTAAAGAAATCAAATCTTATCTATAGCAACTCAATCGACTTTTAGGAAGCTAGCAGTACATATACTATGGGACAACTCAACCCTCTTGTTAAAATGTACTAATCGGTTCAAGGAACTCTCACTGATCAAGCCTGAATCCAAGACAGAACCAGACCAAAGGGCCTCCCCAGAGTCTCTTACAAGCTTAGCCAATCAATTAACATGCATAAGCGATCCATACTTCGCCCAATCAGTGTCCGATGTTCACCCCTTCAAGCCTCCTTCCTAGCAAATTGACCTAGCTGTACCAAGAGATTCCCTCAGCCTCCTTCTCAAATAACCTGATCCTTGAGGGTTATACCTTCACCACTCTATGCTCATTTCACCCAAACATAAAATGAAATGTCTTAACATGATTGCACCATTAAGAAAAACAAATCTGATGAAGATTAAGCCTGATTAAGGCCCAACCTTCATCTTTTTACCATAATCTTGTTCTCAGTACCATTTGATAAGGGTACACTTGCCAAAACGCCCCCATCCTAAGGGTCTCGCAATGGGGGGTCTTAGCCTACTCCAATTGCCCAGGGACAAATTTCGGAAAAGCTCTTTCTTTGTTTGGGTCATCATCTTATTCCAAAAGGCCTTTTCCATGCCTTTGGGTGTTGTGACTAACAGCACTTTAGAAGTAACAGAGATTGACCAGCTAGTCTGCAAGGATCATCTTGCATCTACTGACCAGCTGAAATCAGTTGGTCTCAACCTCGAGGGGAGCGGAGTATCTACTGATATCCCATCTGCAACAAAGCGTTGGGGCTTCAGATCTGGTGTTCCTCCCAAGGTGGTCAGCTATGAAGCGGGAGAATGGGCTGAAAATTGCTACAATCTTGAAATAAAGAAGCCGGACGGGAGCGAATGCTTACCCCCACCGCCAGATGGTGTCAGAGGCTTTCCAAGGTGCCGCTATGTTCACAAAGCCCAAGGAACCGGGCCTTGCCCAGGTGACTACGCCTTTCATAAGGATGGAGCTTTCTTCCTCTATGACAGGCTGGCTTCAACTGTAATTTACAGAGGAGTCAATTTTGCTGAGGGGGTAATTGCATTCTTGATATTGGCTAAACCAAAAGAAACGTTCCTTCAGTCACCCCCCATTCGAGAGGCAGTAAACTACACTGAAAATACATCAAGTTATTATGCCACATCCTACTTGGAGTATGAAATCGAAAATTTTGGTGCTCAACACTCCACGACCCTTTTCAAAATTGACAATAATACTTTTGTTCGTCTGGACAGGCCCCACACGCCTCAGTTCCTTTTCCAGCTGAATGATACCATTCACCTTCACCAACAGTTGAGTAATACAACTGGGAGACTAATTTGGACACTAGATGCTAATATCAATGCTGATATTGGTGAATGGGCTTTTTGGGAAAATAAAAAAATCTCTCCGAACAACTACGTGGAGAAGAGCTGTCTTTCGAAGCTTTATCGCTCAACGAGACAGAAGACGATGATGCGGCATCGTCGAGAATTACAAAGGGAAGAATCTCCGACCGGGCCACCAGGAAGTATTCGGACCTGGTTCCAAAGAATTCCCCTGGGATGGTTCCATTGCACATACCAGAAGGGGAAACAACATTGCCGTCTCAGAATTCGACAGAAGGTCGAAGAGTAGGTGTGAATACTCAGGAGACCATCACAGAGACAGCTGCAACAATTATAGGCACTAACGGCAATCATATGCAGATCTCCACCATCGGGATGAGACCGAGCTCCAGCCAAATCCCGAGTTCCTCACCGACCACGGCACCAAGCCCTGAGGCTCAGACCCCCACAACCCACACATCAGGTCCATCAGTGATGGCCACCGAGGAACCAACAACACCACCGGGAAGCTCCCCCGGCCCAACAACAGAAGCACCCACTCTCACCACCCCAGAAAATATAACAACAGCGGTTAAAACTGTCCTGCCACAGGAGTCCACAAGCAACGGTCTAATAACTTCAACAGTAACAGGAATTCTTGGGAGTCTTGGGCTTCGAAAACGCAGCAGAAGACAAACTAACACCAAAGCCACGGGTAAGTGCAATCCCAACTTACACTACTGGACTGCACAAGAACAACATAATGCTGCTGGGATTGCCTGGATCCCGTACTTTGGACCGGGTGCGGAAGGCATATACACTGAAGGCCTGATGCATAACCAAAATGCCTTAGTCTGTGGACTTAGGCAACTTGCAAATGAAACAACTCAAGCTCTGCAGCTTTTCTTAAGAGCCACAACGGAGCTGCGGACATATACCATACTCAATAGGAAGGCCATAGATTTCCTTCTGCGACGATGGGGCGGGACATGCAGGATCCTGGGACCAGATTGTTGCATTGAGCCACATGATTGGACAAAAAACATCACTGATAAAATCAACCAAATCATCCATGATTTCATCGACAACCCCTTACCTAATCAGGATAATGATGATAATTGGTGGACGGGCTGGAGACAGTGGATCCCTGCAGGAATAGGCATTACTGGAATTATTATTGCAATTATTGCTCTTCTTTGCGTTTGCAAGCTGCTTTGCTGAATATCAATTTGAATCATCAATTTAAGCTTGATACATTTCTAGCATTTTAAATTATAAACCGATACTGATACTTGAAAATCAGGCTAATGCCAAGTTCTGTGCAAAACTTGAAAGTAGGTTTACAAAAATCCTTTGAACTGGAATGCTTTGATACTCTTTCTCAATACTATATAAGTTCCTTCCCAAGAATAATATTGATGAAGATTAAGAAAAAGTGACATTGTGCCCACTTTTGTAATCTTCATCCACCTACACATTCATATTCAGGAATCTTTGAATTAACCCTCACACTTGCTTAGGAAAGAGCCTATCCTCTACAAGAATCCCGAGGCGGCAATTCAGTTAATTTCATATAAAGATAACATCCATTTCCAAGACCACAGATAACTATATTATTAATCTTTACCACAAATATGGAGAGGGGTCGTGAGCGCGGGAGATCAAGGAATTCACGTGCCGACCAGCAAAATTCAACAGGTCCTCAATTTAGGACAAGATCCATTTCCCGGGATAAGACAACAACAGACTACCGTAGTAGTCGTAGTACTTCGCAAGTTAGAGTCCCTACGGTTTTCCATAAGAAAGGTACTGGGACCCTTACTGTCCCTCCAGCACCTAAGGATATTTGTCCTACTCTCAGAAAAGGATTTCTATGTGATAGTAATTTCTGTAAAAAGGACCATCAACTTGAAAGCCTAACCGACCGGGAGCTCCTACTTCTTATAGCACGGAAGACCTGTGGATCAACTGATTCATCGCTTAATATAGCTGCTCCTAAAGACCTAAGACTAGCAAATCCTACGGCTGATGACTTCAAGCAAGACGGCAGTCCAAAATTAACCCTAAAATTACTAGTCGAGACTGCTGAGTTTTGGGCCAATCAGAATATTAATGAAGTAGATGATGCAAAACTCCGTGCTCTCTTGACGTTGAGTGCTGTCTTAGTGCGGAAATTCTCTAAGTCACAGCTTAGTCAATTATGTGAGAGTCATCTTAGGAGGGAAAACTTAGGACAAGACCAAGCTGAATCAGTTCTCGAGGTTTATCAACGTTTACATAGTGATAAAGGAGGTGCTTTTGAGGCAGCACTATGGCAACAGTGGGATAGACAATCATTAACTATGTTTATATCTGCTTTCCTCCATGTAGCATTGCAACTTTCCTGTGAGAGCTCCACTGTAGTGATATCAGGCCTACGCTTACTTGCCCCCCCAAGCGTTAATGAAGGGCTCCCTCCTGCACCAGGGGAATATACTTGGTCAGAAGATAGTACAACTTAGCCTGTAGGGAGGACAAGTAAAACAAGATGCCCTTATCCTCTATAGATGGTATTTTTAAAGAGGGGGACAGGATAGGAATAAAGATAATGACTAAAGCCAATATAAAAATACGAACACAAGTAGAAATTAAAATAGAAATCAAAACAATCTCCCCTTATTCAATATGAAATATAATAGTGAGTATTTGTTTCATGATGTCAATCATTTATTGTTAAAAATAAACAAAGTCAGTAAGAGTGTTAGGATCGTTATATTGCAAGGATCCTCCCTAGAAGCGTTGAATCATCTCAAGTAGCCTAGAACAAGAACAGCAGAGCATTAAATTGAAATAGATAATAAGGATATCGCTTGTTTTTAAGATAGTTTTAGGAAGTTTAAAATTAAGAAAAAGAACCCATGGACACACTCTAGCATTGAGGATGGGGTTCCCTTGATGATAGTATAATCTTAGGTATAGGGTAGTCCTACACGTCCTATATTATACAGTCTAAACTTGTAAAATTAAACTACAAGAACATGATGAAAATTAATGAGAAGGTTCCAAGATTGACTTCAATCCAAACACCTTGCTCTGCCAATTTTCATCTCCTTAAGATATATGATTCTGTTCCTGCGAGATAAGGTTATCAAATAGGGTGTGTATCTCTTTTACATATTTGGGCTCCCACTAGGCTAGAGTTTATAGTTAAGGAAGACTCATCACATTTTTTATTGAACTAGTCTACTCGCAGAATCCTACCGGGAATAGAAATTAGAACATTTGTGATACTTTGACTATAGGAAATAATTTTCAACACTACCTGAGATCAGGTTATTCTTCCAATTTATTCTGCAAGTAATTGTTTAGCATCATAACAACAACGTTATAATTTAAGAATCAAGTCTTGTAACAGAAATAAAGATAACAGAAAGAACCTTTATTATACGGGTCCATTAATTTTATAGGAGAAGCTCCTTTTACAAGCCTAAGATTCCATTAGAGATAACCAGAATGGCTAAAGCCACAGGCCGGTACAACTTGGTAACACCAAAACGGGAGCTAGAGCAAGGAGTTGTGTTTAGCGACCTATGCAACTTCCTAGTGACTCCAACTGTGCAAGGATGGAAGGTTTACTGGGCTGGACTTGAGTTTGATGTCAACCAAAAGGGTATTACCCTGTTAAATCGTCTTAAAGTGAATGATTTTGCTCCTGCATGGGCGATGACCCGGAACCTCTTCCCACACTTGTTCAAAAACCAACAGTCTGAAGTCCAAACTCCCATTTGGGCTTTGAGGGTAATTCTTGCCGCCGGGATTCTTGACCAATTAATGGATCATTCCCTCATTGAGCCGCTATCAGGGGCCCTGAACCTAATTGCTGATTGGTTACTAACAACATCTACTAATCACTTCAACATGAGAACTCAACGAGTAAAGGACCAACTGAGCATGAGGATGTTATCTCTTATAAGGTCAAATATTATTAACTTTATAAATAAGCTCGAGACTCTTCATGTCGTTAATTACAAGGGACTTCTAAGCAGTGTTGAGATAGGAACACCAAGCTATGCAATCATTATTACCAGGACTAATATGGGTTATCTTGTCGAGGTTCAGGAACCAGATAAATCTGCGATGGATATACGACACCCTGGTCCTGTCAAATTCTCCCTACTACATGAATCGACACTTAAACCTGTTGCCACTCCTAAACCGTCAAGCATTACTTCATTGATCATGGAGTTCAACAGTTCTTTGGCAATTTAATTGTCGTAATAAAAATTGTACGATAGGGCTAACATTGATTCCATAATCCATCGTAGGACAGAATCATTTTCCTGTATGATCTTAGTTTAATCTCTCTTTATACAATGATGAATAAGGAGCTTGTTTAAAATGTTACAAAAGTATACTGTTTGAACCCCTAGTATCCCTGTAAATATCCTCATTCAATTTTTTGCTTTTACATGTGTAGTCACCTGTATAGCATGACCCTAGTCATGCCTTTAATTAATACTTAATCTAACAGTTAATATAATGTATAACTTTCCATGTTCAAAGAGTAGTCAAAACAATGTGAGATCCAGTTTCACTCACAGCATCTATTCACTATTTACAGTATGATGAGCCCAAATTAACACAGTAGAGGTCTAGATTTATTAATAGAACGAGGAAGATTAAGAAAAAGTCCATAATGCTGGGGAGGCAATCCCTACCACCATAGGACTTTTTCAATTCCTCTATTTTATGATGGCTACCCAACATACACAATATCCTGATGCAAGATTGTCTTCCCCAATTGTCTTAGACCAATGTGACCTAGTGACAAGAGCATGTGGACTTTACTCTGAGTATTCGCTGAACCCTAAACTAAGGACATGCCGTTTACCGAAACATATCTATAGATTGAAATATGACACTATTGTTTTACGATTTATTAGTGATGTCCCTGTAGCTACAATCCCAATAGACTACATTGCTCCGATGTTAATAAATGTTCTGGCAGATAGTAAAAATGTACCATTGGAACCTCCCTGCTTGAGTTTCTTGGATGAAATAGTCAATTATACCGTGCAGGATGCAGCATTCCTTAATTATTACATGAATCAGATTAAAACACAGGAAGGAGTAATTACAGATCAATTAAAACAGAACATTCGTAGGGTCATTCACAAAAACAGATATCTATCTGCTCTATTCTTCTGGCATGATCTTGCCATCCTCACCCGTCGAGGGAGAATGAACCGAGGAAATGTGCGCTCCACTTGGTTTGTAACGAATGAGGTTGTTGACATTCTAGGATATGGTGATTATATCTTCTGGAAGATCCCTATTGCTCTATTACCAATGAACACAGCTAATGTTCCACATGCATCAACTGACTGGTACCAACCTAATATCTTCAAGGAGGCTATTCAAGGACACACACATATTATTTCAGTCTCTACAGCCGAGGTCCTTATTATGTGTAAGGATCTTGTCACAAGTCGTTTTAATACCCTTCTGATTGCTGAGTTAGCCAGGTTGGAAGATCCAGTGTCTGCTGATTATCCACTAGTAGATAATATTCAATCTCTGTATAACGCAGGAGACTACCTGTTGTCCATATTGGGATCAGAGGGGTACAAAATAATCAAATATCTCGAACCTCTGTGTTTGGCTAAGATTCAACTATGTTCCCAATATACAGAACGAAAAGGGCGGTTTTTAACCCAGATGCATCTTGCAGTTATTCAGACATTGCGTGAACTCCTCCTTAATAGAGGGTTGAAAAAATCACAATTGTCTAAAATCCGCGAGTTTCACCAACTGTTGCTCAGACTCCGATCCACACCACAACAATTATGTGAATTATTTTCAATCCAAAAACACTGGGGCCACCCAGTTCTGCATAGTGAAAAGGCCATCCAAAAGGTTAAAAATCATGCAACAGTTCTAAAGGCATTGCGGCCGATTATCATCTTTGAAACGTATTGTGTATTCAAGTATAGTGTTGCAAAACATTTCTTTGATAGTCAAGGCACTTGGTACAGTGTGATATCAGACCGATGTTTAACGCCGGGATTGAATTCCTACATTAGGCGAAATCAATTCCCTCCACTTCCAATGATCAAAGATCTTTTATGGGAATTTTACCATTTGGATCATCCTCCATTATTCTCCACGAAGATCATTAGTGACCTCAGCATTTTCATTAAAGACCGCGCAACAGCAGTTGAACAAACCTGTTGGGATGCAGTTTTTGAGCCTAACGTTTTGGGCTACAGTCCACCTTATCGATTCAATACCAAACGTGTACCTGAACAATTCCTGGAGCAAGAGGATTTTTCTATTGAGAGTGTCTTACAATACGCCCAAGAACTTAGGTACTTATTGCCCCAGAATCGAAATTTTTCTTTTTCATTGAAGGAAAAAGAATTAAATGTTGGTAGGACATTTGGAAAATTGCCTTATTTAACCAGGAATGTCCAAACCCTCTGCGAAGCATTACTTGCAGATGGTTTGGCTAAAGCCTTTCCAAGCAATATGATGGTTGTCACAGAGAGGGAACAAAAGGAGAGCCTCCTTCACCAAGCATCCTGGCACCATACAAGTGATGATTTCGGAGAGCATGCCACAGTTCGTGGAAGTAGTTTTGTCACAGACCTGGAAAAATACAATCTGGCCTTCAGGTATGAATTCACAGCTCCCTTCATCAAATATTGCAACCAATGCTATGGGGTTCGCAATGTCTTTGATTGGATGCACTTCCTAATTCCGCAATGTTACATGCATGTTAGTGATTATTATAACCCACCACATAATGTAACCTTAGAGAATAGGGAATATCCCCCCGAAGGACCAAGTGCTTATAGAGGCCACCTTGGCGGTATTGAGGGGCTTCAACAAAAGTTATGGACTAGTATCTCATGTGCTCAAATCTCATTGGTAGAGATCAAGACCGGGTTCAAATTGCGATCAGCAGTCATGGGGGATAATCAATGTATTACAGTATTATCAGTCTTTCCACTAGAATCTAGTCCGAATGAGCAGGAGAGATGCGCAGAAGACAATGCAGCCAGAGTGGCTGCTAGCTTGGCCAAAGTCACAAGTGCCTGTGGGATATTCCTCAAGCCTGATGAGACTTTTGTACACTCAGGCTTTATCTATTTTGGCAAAAAGCAATATTTGAACGGAATTCAATTACCTCAATCACTCAAGACAGCAGCTAGGATGGCCCCTCTCTCAGATGCAATTTTTGATGACTTGCAAGGTACACTTGCCAGTATAGGAACTGCCTTTGAGCGATCAATCTCCGAAACTAGACATATTTTACCATGTCGTGTTGCAGCTGCCTTTCATACATATTTCTCTGTTCGGATCTTACAACATCATCACCTTGGTTTCCATAAGGGTTCAGACCTTGGACAATTGGCAATCAATAAACCTCTTGATTTCGGAACCATTGCACTATCCTTAGCAGTTCCTCAGGTATTGGGTGGATTATCCTTCCTAAATCCAGAAAAGTGCCTTTATCGCAACTTGGGTGATCCTGTAACTTCAGGCCTATTTCAGTTGAAGCATTATCTGTCAATGGTGGGTATGAGTGATATCTTTCATGCACTTGTTGCAAAAAGCCCAGGGAATTGTAGCGCAATTGACTTTGTTCTAAACCCAGGCGGGTTAAATGTCCCTGGATCACAGGATTTAACATCTTTCCTTCGTCAGATTGTCAGAAGGAGTATCACACTTTCGGCAAGGAACAAGTTAATCAACACGTTATTTCACGCTTCTGCAGATCTTGAAGACGAATTAGTATGTAAATGGTTACTTTCTTCAACGCCCGTGATGAGCCGTTTCGCAGCCGATATTTTCTCACGAACACCAAGCGGGAAAAGATTACAAATCTTGGGATACCTCGAGGGAACCAGAACTTTATTAGCATCCAAAATGATAAGCAATAATGCAGAGACACCAATCTTGGAGAGGCTCAGAAAAATAACGCTTCAAAGATGGAATCTATGGTTTAGTTACCTAGACCATTGTGACCCAGCTTTAATGGAAGCAATTCAACCAATTAAGTGTACTGTTGATATTGCTCAAATTCTTAGAGAATACTCCTGGGCTCATATTCTTGATGGTAGACAGTTAATAGGGGCGACACTGCCATGTATACCTGAGCAGTTCCAAACCACATGGTTAAAACCTTACGAGCAATGTGTGGAATGTTCATCCACAAACAATTCTAGTCCATATGTATCAGTTGCATTAAAAAGGAACGTGGTTAGTGCTTGGCCTGATGCATCTAGATTGGGGTGGACGATTGGTGATGGGATTCCCTACATAGGCTCAAGAACTGAGGACAAGATAGGTCAGCCCGCTATTAAGCCGAGGTGCCCATCAGCTGCATTAAGAGAAGCTATTGAATTGACCTCTAGGTTGACCTGGGTCACTCAAGGTAGTGCAAACAGCGATCAGTTAATTCGCCCTTTTCTTGAGGCAAGAGTAAACTTGAGTGTACAAGAGATTCTTCAAATGACCCCCTCACATTACTCCGGTAATATTGTGCATCGGTATAATGATCAGTATAGCCCTCACTCCTTTATGGCTAACCGCATGAGTAACACAGCAACGCGCTTGATGGTATCTACCAACACACTAGGAGAGTTTTCCGGAGGGGGTCAGGCTGCACGTGATAGCAACATTATATTTCAAAATGTGATTAACTTTGCAGTGGCCTTGTATGACATTAGGTTTCGGAACACTTGTACATCTTCTATTCAATATCACAGGGCCCATATTCACCTGACGAATTGTTGTACGAGGGAAGTACCGGCCCAATACTTAACATACACAACCACGCTAAATCTAGATTTGAGTAAGTACCGTAATAATGAACTGATTTATGATTCAGAGCCACTAAGAGGAGGTCTCAACTGCAACTTATCGATTGACAGTCCTTTGATGAAGGGCCCACGTTTAAATATTATTGAGGATGACTTAATACGGTTGCCACATTTATCCGGCTGGGAATTAGCAAAAACAGTCTTACAATCAATAATCTCTGATAGTAGCAATTCATCAACAGATCCCATTAGCAGCGGTGAAACAAGATCCTTCACAACCCACTTCTTAACGTATCCCAAAATAGGGCTCCTATACAGTTTTGGAGCCCTCATAAGTTTTTATTTGGGTAATACTATTCTGTGCACGAAAAAGATCGGACTCACAGAATTTCTATACTATCTCCAGAATCAGATCCACAACTTATCACACAGATCCCTTCGAATCTTCAAACCGACATTTAGACACTCAAGTGTCATGTCCAGGTTGATGGATATAGACCCCAACTTCTCAATATATATTGGTGGGACTGCAGGTGACCGTGGATTATCGGACGCTGCAAGATTATTTCTCCGAATTGCAATTTCAACTTTCTTGAGCTTTGTTGAGGAGTGGGTTATCTTTAGGAAGGCAAACATCCCACTATGGGTTATCTATCCTCTCGAAGGCCAACGCCCTGATCCTCCTGGCGAATTTTTGAACCGAGTAAAATCTCTAATTGTTGGGACTGAAGATGATAAAAATAAAGGCTCTATACTTTCAAGATCTGGAGAGAAATGCTCTTCAAATCTAGTTTATAATTGCAAGAGTACAGCAAGCAATTTTTTCCATGCATCATTGGCTTATTGGAGAGGTCGACATAGACCTAAGAAGACTATAGGTGCAACTAACGCGACAACAGCTCCACATATCATTTTGCCACTAGGAAATTCTGATCGACCGCCTGGCCTAGACCTTAATAGGAACAATGATACTTTCATTCCTACCAGAATTAAACAGATAGTCCAAGGAGACTCTAGAAACGACAGAACGACCACCACGAGATTTCCACCCAAAAGTAGGTCCACTCCAACATCAGCAACCGAGCCTCCTACAAAAATGTATGAGGGTTCGACAACCCACCAAGGGAAATTAACAGATACACATTTGGATGAGGATCACAATGCCAAAGAGTTCCCATCCAATCCGCATCGTTTAGTAGTACCATTCTTTAAATTAACAAAAGATGGGGAATACAGTATCGAACCTTCTCCTGAAGAAAGCCGCAGTAATATAAAAGGGTTACTTCAACATTTAAGAACCATGGTTGATACTACCATATATTGTCGCTTCACTGGAATTGTTTCATCAATGCATTATAAGTTAGATGAAGTACTATGGGAATATAATAAATTTGAATCAGCTGTAACCCTAGCAGAAGGGGAGGGTTCAGGTGCCTTACTACTGATCCAAAAATACGGCGTTAAGAAGTTATTTTTGAATACACTTGCTACTGAACATAGTATTGAGAGTGAAGTAATATCAGGTTACACCACTCCAAGGATGCTACTCTCAATTATGCCTAAAACACATCGTGGTGAGCTAGAGGTCATATTAAATAACTCAGCTAGTCAAATAACTGATATTACACACCGAGATTGGTTTTCAAATCAAAGAAATAGGATTCCAAATGATGCTGATATTATTACCATGGATGCTGAAACCACAGAAAACTTAGATCGTTCCAGATTATATGAAGCAGTATATACGATTATTTGTAATCATATCAATCCTAAAACTTTGAAAGTGGTCATCTTAAAAGTCTTCCTCAGCGATTTGGATGGGATGTGCTGGATTAACAATTATCTTGCTCCTATGTTTGGATCAGGATATTTAATCAAACCTATAACATCAAGTGCAAAGTCAAGTGAGTGGTATTTATGCTTATCTAATCTACTTTCAACCTTGAGAACTACTCAGCATCAAACCCAGGCAAACTGTCTCCAGGTCGTACAATGTGCTCTTCAACAGCAAGTACAAAGAGGGTCATATTGGCTAAGTCATCTTACTAAATACACCACAAGTAGATTGCACAATAGTTATATTGCATTTGGTTTTCCTTCATTAGAGAAGGTCCTATATCATAGGTATAACCTTGTTGATTCGAGAAACGGACCATTAGTTTCTATAACGAGACACCTTGCCCTCCTCCAAACTGAGATCCGGGAGTTGGTAACTGATTATAATCAGCTGCGACAAAGTCGAACCCAGACTTATCATTTCATAAAAACATCCAAGGGACGGATAACTAAACTAGTGAATGATTATCTAAGATTTGAGTTGGTTATACGGGCTCTTAAAAATAATTCTACATGGCACCATGAGTTATACTTGCTACCAGAACTTATAGGTGTTTGCCATCGATTTAATCATACACGTAACTGTACATGCAGCGAAAGGTTCCTGGTTCAAACTTTATATCTACACCGAATGAGTGATGCTGAGATAAAACTTATGGACCGGCTCACCAGCCTAGTCAATATGTTTCCTGAAGGTTTCAGGTCTAGTTCAGTCTAATTCTAACTGCACCAAAGGCTCTAGAGATATTTTAAATAACCAGGTGTATATCAAAGTCAATACAAGTGTAAAAACAATATGCAAGGGACCACATTGAGGATCAGTTTATTGACTCTTCCAATACACAGAGTTGGAAGCACCGATTCAAGGTTTCTAAGACGCTCTATCAATTATGTTGATAATGTAAATAATAGCTTTTCCTGTCTATTATGACTTAAATAAACATATCTATAACGACCATCACAGCTAAGTCGTTGCCCTAGTTCATATATTAAATTAAAATTTAGAAGCTAGGTTAACTCTAATTACATAAGTATTAAGAAAAAATTACTAAGACTAATACTCTCATGCCAAGAACTAGTAATGTGTTTCACATGACAGATTATTTCTAACACTAAATTGCAATTTCAATTTTAAAGCTAAGTTTAACACCTATACAGCCAAAATATTTCATAGGGCCGATGGGAATAACATAAGAGGAACATGATCAATGAACCCTTTATTCCAACTAGGCAGTTGATTGATAATCTACAAATTCCATAAGATGTTCTTACGATATTCTTTTGTTTTTAATCTCAATGTCAATGATTTAATAAGTAATAATAAAAAAATCACATTAAAGATGCAGGAAGATCTTGACCTCGCCAGGAAAATTAAGCGCACACAAATAAATTAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCCA\n>Sudan_ebolavirus_strain_Gulu_complete_genome\nCGGACACACAAAAAGAAAGAAAAGTTTTTTATACTTTTTGTGTGCGAATAACTATGAGGAAGATTAATCATTTTCCTCAAACTCAAACTAATATTAACATTGAGATTGATCTCATCATTTACCAATTGGAGACAATTTAACTAGTCAATCCCCCATTTGGGGGCATTCCTAAAGTGTTGCAAAGGTATGTGGGTCGTATTGCTTTGCCTTTTCCTAACCTGGCTCCTCCTACAATTCTAACCTGCTTGATAAGTGTGATTACCTGAGTAATAGACTAATTTCGTCCTGGTAATTAGCATTTTCTAGTAAAACCAATACTATCTCAAGTCCTAAGAGAAGGTGAGAAGAGGGTCCCGAGGTATCCCTCCAGTCCACAAAATCTAGCTAATTTTAGCTGAGTGGACTGATTACTCTCATCACACGCTAACTACTAAGGGTTTACCTGAGAGCCTACAACATGGATAAACGGGTGAGAGGTTCATGGGCCCTGGGAGGACAATCTGAAGTTGATCTTGACTACCACAAAATATTAACAGCCGGGCTTTCGGTCCAACAAGGGATTGTGCGACAAAGAGTCATCCCGGTATATGTTGTGAGTGATCTTGAGGGTATTTGTCAACATATCATTCAGGCCTTTGAAGCAGGCGTAGATTTCCAAGATAATGCTGACAGCTTCCTTTTACTTTTATGTTTACATCATGCTTACCAAGGAGATCATAGGCTCTTCCTCAAAAGTGATGCAGTTCAATACTTAGAGGGCCATGGTTTCAGGTTTGAGGTCCGAGAAAAGGAGAATGTGCACCGTCTGGATGAATTGTTGCCCAATGTCACCGGTGGAAAAAATCTTAGGAGAACATTGGCTGCAATGCCTGAAGAGGAGACAACAGAAGCTAATGCTGGTCAGTTTTTATCCTTTGCCAGTTTGTTTCTACCCAAACTTGTCGTTGGGGAGAAAGCGTGTCTGGAAAAAGTACAAAGGCAGATTCAGGTCCATGCAGAACAAGGGCTCATTCAATATCCAACTTCCTGGCAATCAGTTGGACACATGATGGTGATCTTCCGTTTGATGAGAACAAACTTTTTAATCAAGTTCCTACTAATACATCAGGGGATGCACATGGTCGCAGGCCATGATGCGAATGACACAGTAATATCTAATTCTGTTGCCCAAGCAAGGTTCTCTGGTCTTCTGATTGTAAAGACTGTTCTGGACCACATCCTACAAAAAACAGATCTTGGAGTACGACTTCATCCACTGGCCAGGACAGCAAAAGTCAAGAATGAGGTCAGTTCATTCAAGGCAGCTCTTGGCTCACTTGCCAAGCATGGAGAATATGCTCCATTTGCACGTCTCCTCAATCTTTCTGGAGTCAACAACTTGGAACATGGGCTTTATCCACAACTCTCAGCCATTGCTTTGGGTGTTGCAACTGCCCACGGGAGCACGCTGGCTGGTGTTAATGTAGGGGAGCAATATCAGCAACTGCGTGAGGCTGCTACTGAAGCTGAAAAGCAACTCCAACAATATGCTGAAACACGTGAGTTGGACAACCTTGGGCTTGATGAACAGGAAAAGAAGATTCTCATGAGCTTCCACCAGAAGAAGAATGAGATCAGCTTCCAGCAAACTAACGCAATGGTAACCCTGAGGAAAGAGCGGCTGGCCAAACTGACCGAAGCCATCACGACTGCATCAAAGATCAAGGTTGGAGATCGTTATCCTGATGACAATGATATTCCATTTCCCGGGCCGATCTATGATGAAACCCACCCCAACCCTTCTGATGATAATCCTGATGATTCACGTGATACAACTATCCCAGGTGGTGTTGTTGACCCGTATGATGATGAGAGTAATAATTATCCTGACTACGAGGATTCGGCTGAAGGCACCACAGGAGATCTTGATCTCTTCAATTTGGACGACGACGATGACGACAGCCAACCAGGACCACCAGACAGGGGGCAGAGCAAGGAAAGAGCGGCTCGGACACATGGCCTCCAAGATCCGACCTTGGACGGAGCGAAAAAGGTGCCGGAGTTGACCCCAGGTTCCCACCAACCAGGCAACCTCCACATCACCAAGCCGGGTTCAAACACCAACCAACCACAAGGCAATATGTCATCTACTCTCCAGAGTATGACCCCTATACAGGAAGAATCAGAGCCCGATGATCAGAAAGATGATGATGACGAGAGTCTCACATCCCTTGACTCTGAAGGTGACGAAGATGTTGAGAGCGTATCAGGGGAGAACAACCCAACTGTAGCTCCACCAGCACCAGTCTACAAAGATACTGGAGTAGACACTAATCAGCAAAATGGACCAAGCAATGCTGTAGATGGTCAAGGTTCTGAAAGTGAAGCTCTCCCAATCAACCCCGAAAAGGGATCTGCACTGGAAGAAACATATTATCATCTCCTAAAAACACAGGGTCCATTTGAGGCAATCAATTATTATCACCTAATGAGTGATGAGCCCATTGCTTTTAGCACTGAAAGTGGCAAGGAATATATCTTCCCAGATTCTCTTGAAGAAGCCTACCCGCCTTGGTTGAGTGAGAAGGAGGCCTTAGAGAAAGAAAATCGTTATCTGGTCATTGATGGCCAGCAATTCCTCTGGCCAGTAATGAGCCTACAGGACAAGTTCCTTGCTGTTCTTCAACATGACTGAGGACCCATGATTAGTAGATTTTGTTTATTCTGAGCTTGATTATAATTGTTTTGATAATTCAAGTATGAGCAACCAACCCGAAATATAAACCCTATTTTAGTTATGAGGAAATTAAATAAATAATCTGTAAGTTGTAGGACTATGAAGAGCTGCTTGTGTCAATTTATCACGGGCTAATACCCATACCGCAAGAATAATTATTTAGTAATTTTGATCAGCTTATGATATGTACCAATAGGAAAACATTATAGCATTAAAACATAAAGTATCCTTCGATGAGCTTAGGAGGATAATATCCTGATGAATTCTATAGAACTTAGGATTAAGAAAAAATTCATGATGAAGATTAAAACCTTCATCATCCTTTAAAAAGAGAGCTATTCTTTATCTGAATGTCCTTATTAATGTCTAAGAGCTATTATTTTGTACCCTCTTAGCCTAGACACTGCCCAGCATATAAGCCATGCAGCAGGATAGGACTTATAGACATCATGGACCCGAAGTGTCTGGCTGGTTTTCTGAGCAATTAATGACCGGCAAAATACCGCTAACAGAGGTGTTTGTTGATGTTGAAAACAAACCAAGTCCTGCCCCGATAACCATTATTAGTAAGAATCCCAAGACAACACGTAAAAGTGATAAGCAAGTCCAAACAGATGATGCCAGTAGCTTATTGACAGAAGAAGTCAAGGCTGCCATAAATTCGGTGATATCAGCTGTGCGTCGGCAAACCAATGCTATTGAATCACTAGAAGGTCGAGTAACAACTCTTGAGGCCAGCTTAAAACCCGTTCAAGACATGGCAAAGACCATATCATCCCTGAATCGCAGCTGTGCCGAAATGGTTGCAAAATACGACCTACTGGTGATGACCACTGGGCGAGCAACTGCCACTGCTGCAGCAACAGAAGCATATTGGAATGAACATGGACAAGCACCTCCAGGCCCATCATTGTACGAGGATGATGCTATTAAGGCTAAATTGAAAGATCCGAACGGGAAGGTTCCAGAAAGTGTCAAACAGGCCTACATAAATCTAGATAGCACAAGTGCCCTCAATGAGGAAAATTTCGGGCGACCTTACATTTCAGCAAAAGATCTCAAGGAAATCATCTATGACCATCTCCCAGGATTTGGGACAGCTTTTCATCAGTTGGTGCAGGTTATCTGCAAAATTGGTAAGGATAATAATATCCTAGACATAATTCATGCAGAATTCCAAGCAAGCTTGGCTGAGGGAGACTCCCCCCAGTGTGCATTAATCCAGATAACAAAACGGATCCCTGCTTTCCAAGATGCCTCTCCTCCAATTGTGCATATCAAGTCTCGAGGAGATATACCCAAAGCCTGTCAGAAAAGCCTCCGGCCGGTCCCACCGTCACCAAAGATCGATAGAGGTTGGGTCTGTATTTTTCAATTCCAAGACGGGAAGGCCCTTGGGCTAAAAATATGATACAGAAGCAAGGTAAGCTCATTTTGCGATGGCCAAATGATACTTATGACTGTTTAAAATCAAGTTAGACTAATAGTCTATTGTGTCATAAGCTTATAAGTCAGTTTTAAATTTCCCCTCTATCCTAATCAATTGATAATGCTGTCAATAGGGAAATTCCCCTGTATTGTAATAAGACCTCATTAACATATTTCCCCTGCTTAGTACTATGCAGAAACCCCCGAGCAAATTAAAATTGATGAAGATTAAGAAAAAGAGGGATTTTCTCAGGAAAAATCTTTTTTCTTACCTTCATCTCATTTAAACAAATTTAGGACTCAGGAAAAATGAGAAGGGTCACTGTGCCGACTGCACCACCTGCCTATGCTGACATTGGCTATCCTATGAGCATGCTTCCCATCAAGTCAAGCAGGGCTGTGAGTGGAATTCAACAGAAACAAGAGGTCCTTCCTGGAATGGATACACCATCAAATTCTATGAGACCTGTTGCTGATGATAACATTGATCATACAAGTCATACCCCGAACGGAGTGGCCTCAGCATTCATCTTGGAGGCAACTGTCAATGTGATCTCGGGGCCCAAAGTCCTCATGAAACAAATCCCTATTTGGTTGCCACTCGGAATTGCTGACCAAAAAACGTACAGTTTTGACTCAACAACAGCAGCAATTATGCTCGCATCTTATACGATCACCCATTTTGGAAAGGCCAACAACCCCCTCGTTAGAGTGAATCGACTTGGTCAGGGAATACCGGATCACCCACTCAGATTGCTCAGGATGGGGAACCAGGCTTTCCTTCAAGAGTTTGTGCTACCACCAGTTCAACTGCCGCAATATTTCACTTTTGATCTGACTGCACTCAAACTAGTGACACAGCCTCTCCCTGCTGCAACATGGACAGATGAGACTCCGAGCAACCTTTCAGGAGCCCTTCGTCCCGGGCTTTCATTTCACCCAAAGCTGAGACCCGTTCTACTTCCAGGCAAGACGGGAAAGAAAGGGCATGTTTCTGATCTGACTGCCCCAGACAAAATTCAGACAATTGTGAACCTGATGCAAGATTTCAAAATCGTGCCAATTGATCCAGCTAAGAGTATCATTGGGATCGAGGTTCCAGAATTGCTGGTCCACAAGCTCACTGGGAAGAAAATGAGTCAGAAGAATGGACAGCCTATAATTCCTGTCTTACTCCCAAAATACATTGGGCTAGATCCAATCTCACCTGGAGACCTGACTATGGTCATAACACCAGATTATGATGATTGTCATTCACCTGCCAGTTGCTCTTATCTCAGTGAAAAGTGATTCTCACAAAGTGAGAGAAACACCTCCAGTAAAGAAATCAAATCTTATCTATAGCAACTCAATCGACTTTTAGGAAGCTAGCAGTCCATATACTATGGGACAACTCAACCCTCTTGTTAAAATGTACTAATCGGGTCAAGGAACTCTCACTGATCAAGCCTGAATCCAAGATAGAACCAGCCCAAAGGGCCTCCCCAGAGTCTCTTACAAGCTTAGCCAATCAATTAACATGCATAAGCGATCCATACTTCGCCCAATCAGTGTCCGATGTTCACCCCTTCAAGCCTCCTTCCTAGCAAATTGACCTAGCTGTACCAAGAGATTCCCTCAGCCTCCTTCTCAAATAACCTGATCCTCGAGGGTTACACCTTCACCACTCTATGCTCATTTCACCCAAACATAAAATGAAATGTCTTAACATGATTGCACCATTAAGAAAAACAAATCTGATGAAGATTAAGCCTGATGAAGGCCCAACCTTCATCTTTTTACCATAATCTTGTTCTCAGTACCATTTGATAAGGGTACACTTGCCAATACGCCCCCATCCTAAGGGTCTCGCAATGGGGGGTCTTAGCCTACTCCAATTGCCCAGGGACAAATTTCGGAAAAGCTCTTTCTTTGTTTGGGTCATCATCTTATTCCAAAAGGCCTTTTCCATGCCTTTGGGTGTTGTGACTAACAGCACTTTAGAAGTAACAGAGATTGACCAGCTAGTCTGCAAGGATCATCTTGCATCTACTGACCAGCTGAAATCAGTTGGTCTCAACCTCGAGGGGAGCGGAGTATCTACTGATATCCCATCTGCAACAAAGCGTTGGGGCTTCAGATCTGGTGTTCCTCCCAAGGTGGTCAGCTATGAAGCGGGAGAATGGGCTGAAAATTGCTACAATCTTGAAATAAAGAAGCCGGACGGGAGCGAATGCTTACCCCCACCGCCAGATGGTGTCAGAGGCTTTCCAAGGTGCCGCTATGTTCACAAAGCCCAAGGAACCGGGCCCTGCCCAGGTGACTACGCCTTTCACAAGGATGGAGCTTTCTTCCTCTATGACAGGCTGGCTTCAACTGTAATTTACAGAGGAGTCAATTTTGCTGAGGGGGTAATTGCATTCTTGATATTGGCTAAACCAAAAGAAACGTTCCTTCAGTCACCCCCCATTCGAGAGGCAGTAAACTACACTGAAAATACATCAAGTTATTATGCCACATCCTACTTGGAGTATGAAATCGAAAATTTTGGTGCTCAACACTCCACGACCCTTTTCAAAATTGACAATAATACTTTTGTTCGTCTGGACAGGCCCCACACGCCTCAGTTCCTTTTCCAGCTGAATGATACCATTCACCTTCACCAACAGTTGAGTAATACAACTGGGAGACTAATTTGGACACTAGATGCTAATATCAATGCTGATATTGGTGAATGGGCTTTTTGGGAAAATAAAAAAATCTCTCCGAACAACTACGTGGAGAAGAGCTGTCTTTCGAAGCTTTATCGCTCAACGAGACAGAAGACGATGATGCGGCATCGTCGAGAATTACAAAGGGAAGAATCTCCGACCGGGCCACCAGGAAGTATTCGGACCTGGTTCCAAAGAATTCCCCTGGGATGGTTCCATTGCACATACCAGAAGGGGAAACAACATTGCCGTCTCAGAATTCGACAGAAGGTCGAAGAGTAGGTGTGAACACTCAGGAGACCATTACAGAGACAGCTGCAACAATTATAGGCACTAACGGCAACCATATGCAGATCTCCACCATCGGGATAAGACCGAGCTCCAGCCAAATCCCGAGTTCCTCACCGACCACGGCACCAAGCCCTGAGGCTCAGACCCCCACAACCCACACATCAGGTCCATCAGTGATGGCCACCGAGGAACCAACAACACCACCGGGAAGCTCCCCCGGCCCAACAACAGAAGCACCCACTCTCACCACCCCAGAAAATATAACAACAGCGGTTAAAACTGTCCTGCCACAGGAGTCCACAAGCAACGGTCTAATAACTTCAACAGTAACAGGGATTCTTGGGAGTCTTGGGCTTCGAAAACGCAGCAGAAGACAAACTAACACCAAAGCCACGGGTAAGTGCAATCCCAACTTACACTACTGGACTGCACAAGAACAACATAATGCTGCTGGGATTGCCTGGATCCCGTACTTTGGACCGGGTGCGGAAGGCATATACACTGAAGGCCTGATGCATAACCAAAATGCCTTAGTCTGTGGACTTAGGCAACTTGCAAATGAAACAACTCAAGCTCTGCAGCTTTTCTTAAGAGCCACAACGGAGCTGCGGACATATACCATACTCAATAGGAAGGCCATAGATTTCCTTCTGCGACGATGGGGCGGGACATGCAGGATCCTGGGACCAGATTGTTGCATTGAGCCACATGATTGGACAAAAAACATCACTGATAAAATCAACCAAATCATCCATGATTTCATCGACAACCCCTTACCTAATCAGGATAATGATGATAATTGGTGGACGGGCTGGAGACAGTGGATCCCTGCAGGAATAGGCATTACTGGAATTATTATTGCAATTATTGCTCTTCTTTGCGTTTGCAAGCTGCTTTGCTGAATATCAATTTGAATCATCAATTTAAGCTTGATACATTTCTAGCATTTTAAATTATAAACCGATACTGATACTTGAAAATCAGGCTAATGCCAAGTTCTGTGCAAAACTTGAAAGTAGGTTTACAAAAATCCTTTGGACTGGAATGCTTTGATACTCTTTCTCAATACTATATAAGTTCCTTCCCAAGAATAATATTGATGAAGATTAAGAAAAAGTGACATTGTGCCCACTTTTGTAATCTTCATCCACCTACACATTCATATTCAGGAATCTTTGAATTAACCCTCACACTTGCTTAGGAAAGAGCCTATCCTCTACAAGAATCCCGAGGCGGCAATTCAGTTAATTTCATATCAAGATAACATCCATTTCCAAGACCACAGATAACTATATTATTAATCTTTACCACAAATATGGAGAGGGGTCGTGAGCGCGGGAGATCAAGGAATTCACGTGCCGACCAGCAAAATTCAACAGGTCCTCAATTTAGGACAAGATCCATTTCCCGGGATAAGACAACAACAGACTACCGTAGTAGTCGAAGTACTTCGCAAGTTAGAGTCCCTACGGTTTTCCATAAGAAAGGTACTGGGACCCTTACTGTCCCTCCAGCACCTAAGGATGTTTGTCCTACTCTCAGAAAAGGATTTCTATGTGATAGTAATTTCTGTAAAAAGGACCATCAACTTGAAAGCCTAACCGACCGGGAGCTCCTACTTCTTATAGCACGGAAGACCTGTGGATCAACTGATTCATCGCTTAATATAGCTGCTCCTAAAGACCTAAGACTAGCAAATCCTACGGCTGATGACTTCAAGCAAGACGGCAGTCCAAAATTAACCCTAAAATTACTAGTCGAGACTGCTGAGTTTTGGGCCAATCAGAATATTAATGAAGTAGATGATGCAAAACTCCGTGCTCTCTTGACGTTGAGTGCTGTCTTAGTGCGGAAATTCTCTAAGTCACAGCTTAGTCAATTATGTGAGAGTCATCTTAGGAGGGAAAACTTAGGACAAGACCAAGCTGAATCAGTTCTCGAGGTTTATCAACGTTTACATAGTGACAAAGGAGGTGCTTTTGAGGCAGCACTATGGCAACAGTGGGATAGACAATCATTAACTATGTTTATATCTGCTTTCCTCCATGTAGCATTGCAACTTTCCTGTGAGAGCTCCACTGTAGTGATATCAGGCCTACGCTTACTTGCCCCCCCAAGCGTTAATGAAGGGCTCCCTCCTGCACCAGGGGAATATACTTGGTCAGAAGATAGTACAACTTAGCCTGTAGGGAGGACAAGTAAAACAAGATGCCCTTATCCTCTATAGATGGTATTTTTAGAGAGGGGGACAGGATAGGAATAAAGATAATGACTAAAGCCAATATAAAGATACGAACACAAGTAGAAATTAAAATAGAAATCAAAACAATCTCCCCTTATTCAATATGAAATATAATAGTGAGTATTTGTTTCATGATGTCAATCATTTATTGTTAAAAATAAACAAAGTCAGTAAGAGTGTTAGGATCGTTATATTGCAAGGATCCTCCCTAGAAGCGTTGAATCATCTCAAGTAGCCTAGAACAAGAACAGCAGAGCATTAAATTGAAATAGATAATAAGGATATTGCTTGTTTTTAAGATAGTTTTAGGAAGTTTAAAATTAAGAAAAAGAACCCATGGACACACTCTAGCATTGAGGATGGGGTTCCCTTGATGATAGTATAGTCTTAGGTATAGGGTAGTCCTACACGTACTATATTATACAGTCTAAACTTGTAAAATTAAACTACAAGAACATGATGAAAATTAATGAGAAGGTTCCAAGATTGACTTCAATCCAAACACCTTGCTCTGCCAATTTTCATCTCCTTAAGATATATGATTTTGTTCCTGCGAGATAAGGTTATCAAATAGGGTGTGTATCTCTTTTACATATTTGGGCTCCCACTAGGCTAGGGTTTATAGTTAAGGAAGACTCATCACATTTTTTATTGAACTAGTCTACTCGCAGAATCCTACCGGGAATAGAAATTAGAACATTTGTGATACTTTGACTATAGGAAATAATTTTCAACACTACCTGAGATCAGGTTATTCTTCCAACTTATTCTGCAAGTAATTGTTTAGCATCATAACAACAACGTTATAATTTAAGAATCAAGTCTTGTAACAGAAATAAAGATAACAGAAAGAACCTTTATTATACGGGTCCATTAATTTTATAGGAGAAGCTCCTTTTACAAGCCTAAGATTCCATTAGAGATAACCAGAATGGCTAAAGCCACAGGCCGGTACAACTTGGTAACACCAAAACGGGAGCTAGAGCAAGGAGTTGTGTTTAGCGACCTATGCAACTTCCTAGTGACTCCAACTGTGCAAGGATGGAAGGTTTACTGGGCTGGACTTGAGTTTGATGTCAACCAAAAGGGTATTACCCTGTTAAATCGTCTTAAAGTGAATGATTTTGCTCCTGCATGGGCGATGACCCGGAACCTCTTCCCACACTTGTTCAAAAACCAACAGTCTGAAGTCCAAACTCCCATTTGGGCCTTGAGGGTAATTCTTGCCGCCGGGATTCTTGACCAATTAATGGATCATTCCCTCATTGAGCCGCTATCAGGGGCCCTGAACCTAATTGCTGATTGGTTACTAACAACATCTACTAATCACTTCAACATGAGAACTCAACGAGTAAAGGACCAACTGAGCATGAGGATGTTATCTCTTATAAGGTCAAATATTATTAACTTTATAAATAAGCTCGAGACTCTTCATGTCGTTAATTACAAGGGACTTCTAAGCAGTGTTGAGATAGGAACACCAAGCTATGCAATCATCATTACCAGGACTAATATGGGTTATCTTGTCGAGGTTCAGGAACCAGATAAATCTGCGATGGATATACGACACCCTGGTCCTGTCAAATTCTCCTTACTACATGAATCGACACTTAAACCTGTTGCCACTCCTAAACCATCAAGCATTACTTCATTGATCATGGAGTTCAACAGTTCTTTGGCAATTTAATTGCCGTAATAAAAATTGTACGATAGGGCTAACATTGATTCCATAATCCATCGTAGGACAGAATCATTTTCCTGTATGATCTTAGTTTAATCTCTCTTTATACAATGATTAATAAGGAGCCTGTTTAAAATGTTACAAAAGTATACTGTTTGAACCCCTAGTATCCCTGTAAATATCCTCATTCAATTTTTTGCTTTTACATGTGTAGTCACCTGTATAGCATGACCCTAGTCATGCCTTTAATTAATACTTAATCTAACAGTTAATATAATGTATAACTTTCCATGTTCAAAGAGTAGTCAAAACAATGTGAGATCCAGTTTCACTCACAGCATCTATTCACTATTTACAGTATGATGAGCCCAAATTAACACGGTAGAGGTCTAGATTTATTAATAGAACGAGGAAGATTAAGAAAAAGTCCATAATGCTGGGGAGGCAATCCTTGCCACCATAGGACTTTTTCAATTCCTCTATTTTATGATGGCTACCCAACATACACAATATCCTGATGCAAGATTGTCTTCCCCAATTGTCTTAGACCAATGTGACCTAGTGACAAGAGCATGTGGACTTTACTCTGAGTATTCGCTGAACCCTAAACTAAAGACATGCCGTTTACCGAAACATATCTATAGATTAAAATATGACACTATTGTTTTACGATTTATTAGTGATGTCCCTGTAGCTACAATCCCAATAGACTACATTGCTCCGATGTTAATAAATGTTCTGGCAGATAGTAAAAATGTACCATTGGAACCTCCCTGCTTGAGTTTCTTGGATGAAATAGTCAATTATACCGTGCAGGATGCAGCCTTCCTTAATTATTACATGAATCAGATTAAAACACAGGAAGGAGTAATTACAGATCAATTAAAACAGAACATTCGTAGGGTCATTCACAAAAACAGATATCTATCTGCTCTATTCTTCTGGCATGATCTTGCCATCCTCACCCGTCGAGGGAGAATGAACCGAGGAAATGTGCGCTCCACTTGGTTTGTAACGAATGAGGTTGTTGACATTCTAGGATATGGTGATTATATCTTCTGGAAGATCCCTATTGCTCTATTACCAATGAACACAGCTAATGTTCCACATGCATCAACTGACTGGTACCAACCTAATATCTTCAAGGAGGCTATTCAAGGACACACACATATTATTTCAGTCTCTACAGCCGAGGTCCTTATTATGTGTAAGGATCTTGTCACAAGTCGTTTTAATACCCTTCTGATTGCTGAGTTAGCCAGGTTGGAAGATCCAGTGTCTGCTGATTATCCACTAGTAGATAATATTCAATCTCTGTATAACGCAGGAGACTACCTGTTGTCCATATTGGGATCAGAGGGGTACAAAATAATCAAATATCTCGAACCTCTGTGTTTGGCTAAGATTCAACTATGTTCCCAATATACAGAACGAAAAGGGCGGTTTTTAACCCAGATGCATCTTGCAGTTATTCAGACATTGCGTGAACTCCTCCTTAATAGAGGGTTGAAAAAATCACAATTGTCTAAAATCCGCGAGTTTCACCAACTGTTGCTCAGACTCCGATCTACACCACAACAATTATGTGAATTATTTTCAATCCAAAAACACTGGGGCCACCCAGTTCTGCATAGTGAAAAGGCCATCCAAAAGGTTAAAAATCATGCAACAGTTCTAAAGGCATTGCGGCCGATTATCATCTTTGAAACGTATTGTGTATTCAAGTATAGTGTTGCAAAACATTTCTTTGATAGTCAAGGCACTTGGTACAGTGTGATATCAGACCGATGTTTAACGCCGGGATTGAATTCCTACATTAGGCGAAATCAATTCCCTCCACTTCCAATGATCAAAGATCTTTTATGGGAATTTTACCATTTGGATCATCCTCCATTATTCTCCACGAAGATCATTAGTGACCTCAGCATTTTCATTAAAGACCGCGCAACAGCAGTTGAACAAACCTGTTGGGATGCAGTTTTTGAGCCTAACGTTTTGGGCTACAGTCCACCTTATCGATTCAATACCAAACGTGTACCTGAACAATTCCTGGAGCAAGAGGATTTTTCTATTGAGAGTGTCTTACAATACGCCCAAGAACTTAGGTACTTATTGCCCCAGAATCGAAATTTTTCTTTTTCATTGAAGGAAAAAGAATTAAATGTTGGTAGGACATTTGGAAAATTGCCTTATTTAACCAGGAATGTCCAAACCCTCTGCGAAGCATTACTTGCAGATGGTTTGGCTAAAGCCTTTCCAAGCAATATGATGGTTGTCACAGAGAGGGAACAAAAGGAGAGCCTCCTTCACCAAGCATCCTGGCACCATACAAGTGATGATTTCGGAGAGCATGCCACAGTTCGTGGAAGTAGTTTTGTCACAGACCTGGAAAAATACAATCTGGCCTTCAGGTATGAATTCACAGCTCCCTTCATCAAATATTGCAACCAATGCTATGGGGTTCGCAATGTCTTTGATTGGATGCACTTCCTAATTCCGCAATGTTACATGCATGTTAGTGATTATTATAACCCACCACATAATGTAACCTTAGAGAATAGGGAATATCCCCCCGAAGGACCAAGTGCTTATAGAGGCCACCTTGGCGGTATTGAGGGGCTTCAACAAAAGTTATGGACTAGTATCTCATGTGCTCAAATCTCATTGGTAGAGATCAAGACCGGGTTCAAATTGCGATCAGCAGTCATGGGGGATAATCAATGTATTACAGTATTATCAGTCTTTCCACTAGAATCTAGTCCGAATGAGCAGGAGAGATGCGCAGAAGACAATGCAGCCAGAGTGGCTGCTAGCTTGGCCAAAGTCACAAGTGCCTGTGGGATATTCCTCAAGCCTGATGAGACTTTCGTACACTCAGGCTTTATCTATTTTGGCAAAAAGCAATACTTGAACGGAATTCAATTACCTCAATCACTCAAGACAGCAGCTAGGATGGCCCCTCTCTCAGATGCAATTTTTGATGACTTGCAAGGTACACTTGCCAGTATAGGAACTGCCTTTGAGCGATCAATCTCCGAAACTAGACATATTTTACCATGCCGTGTTGCAGCTGCCTTTCATACATATTTCTCTGTTCGGATCTTACAACATCATCACCTTGGTTTCCATAAGGGTTCAGACCTTGGACAATTGGCAATCAATAAACCTCTTGATTTCGGGACCATTGCACTATCCTTAGCAGTTCCTCAGGTATTGGGTGGATTATCCTTCCTAAATCCAGAAAAGTGCCTTTATCGCAACTTGGGTGATCCTGTAACTTCAGGCCTATTTCAGTTGAAGCATTATCTGTCAATGGTGGGTATGAGTGATATCTTTCATGCACTTATTGCAAAAAGCCCAGGGAATTGTAGCGCAATTGACTTTGTTCTAAACCCAGGCGGGTTAAATGTCCCTGGATCACAGGATTTAACATCTTTCCTTCGTCAGATTGTCAGAAGGAGTATCACACTTTCGGCAAGGAACAAGTTAATCAACACGTTATTTCACGCTTCTGCAGATCTTGAAGACGAATTAGTATGTAAATGGTTACTTTCTTCAACGCCCGTGATGAGCCGTTTTGCAGCCGATATTTTCTCACGAACACCAAGCGGGAAAAGATTACAAATCTTGGGATACCTCGAGGGAACCAGAACTTTATTAGCATCCAAAATGATAAGCAATAATGCAGAGACACCAATCTTGGAGAGGCTCAGAAAAATAACACTTCAAAGATGGAATCTATGGTTTAGTTACCTAGACCATTGTGACCCAGCTTTAATGGAAGCAATTCAACCAATTAAGTGTACTGTTGATATTGCTCAAATTCTTAGAGAATACTCCTGGGCTCATATCCTTGATGGTAGACAGTTAATAGGGGCAACACTGCCATGTATACCTGAGCAGTTCCAAACCACATGGTTAAAACCTTACGAGCAATGTGTGGAATGTTCATCCACAAACAATTCTAGTCCATATGTATCAGTTGCATTAAAAAGGAACGTGGTTAGTGCTTGGCCTGATGCATCTAGATTGGGGTGGACGATTGGTGATGGGATTCCCTACATAGGCTCAAGAACTGAGGACAAAATAGGTCAGCCCGCTATTAAGCCGAGGTGCCCATCAGCTGCATTAAGAGAAGCTATTGAATTGACCTCTAGGTTGACCTGGGTCACTCAAGGTAGTGCAAACAGCGATCAGTTAATTCGCCCTTTTCTTGAGGCAAGAGTAAACTTGAGTGTACAAGAGATTCTTCAAATGACCCCCTCACATTACTCCGGTAATATTGTGCATCGGTATAATGATCAGTATAGCCCTCACTCCTTTATGGCTAACCGCATGAGTAACACAGCAACGCGCTTGATGGTATCTACCAACACACTAGGAGAGTTTTCCGGAGGGGGTCAGGCTGCACGTGATAGCAACATTATATTTCAAAATGTGATTAACTTTGCAGTGGCCTTGTATGACATTAGGTTTCGGAACACTTGTACATCTTCTATTCAATATCACAGGGCCCATATTCACCTGACGAATTGTTGTACGAGGGAAGTACCGGCCCAATACTTAACATACACAACCACGCTAAATCTAGATTTGAGTAAGTACCGTAATAATGAACTGATTTATGATTCAGATCCACTAAGAGGAGGTCTCAACTGCAACTTATCGATTGACAGTCCTTTGATGAAGGGCCCACGTTTAAATATTATTGAGGATGACTTAATACGGTTGCCACATTTATCCGGCTGGGAATTAGCAAAAACAGTCTTGCAATCAATAATCTCTGATAGTAGCAATTCATCAACAGATCCCATTAGCAGCGGTGAAACAAGATCCTTCACAACCCACTTCTTAACGTATCCCAAAATAGGGCTTCTATACAGTTTTGGAGCCCTCATAAGTTTTTATTTGGGTAATACTATTCTATGCACGAAAAAGATCGGACTCACAGAATTTCTATACTATCTCCAGAATCAGATCCACAACTTATCACATAGATCCCTTCGAATCTTCAAACCGACATTTAGACACTCAAGTGTCATGTCCAGGTTGATGGATATAGACCCCAACTTCTCAATATATATTGGTGGGACTGCAGGTGACCGTGGATTATCGGACGCTGCAAGATTATTTCTCCGAATTGCAATTTCAACTTTCTTGAGCTTTGTTGAGGAGTGGGTTATCTTTAGGAAGGCAAACATCCCACTATGGGTTATCTATCCTCTCGAAGGCCAACGCTCTGATCCTCCTGGCGAATTTTTGAACCGAGTAAAATCTCTAATTGTTGGGACTGAAGATGATAAAAATAAAGGCTCTATACTTTCAAGATCTGGAGAGAAATGCTCTTCAAATCTAGTTTATAATTGCAAGAGTACAGCAAGCAATTTTTTCCATGCATCATTGGCTTACTGGAGAGGTCGACATAGACCTAAGAAGACTATAGGTGCAACTAACGCGACAACAGCTCCACATATCATTTTGCCACTGGGAAATTCTGATCGACCGCCTGGCCTAGACCTTAATAGGAACAATGATACTTTCATTCCTACCAGAATTAAACAGATAGTCCAAGGAGACTCTAGAAACGACAGAACGACCACCACGAGATTTCCACCCAAAAGTAGGTCCACTCCAACATCAGCAACCGAGCCTCCTACAAAAATGTATGAGGGTTCGACAACCCACCAAGGGAAATTAACAGATACACATTTGGATGAGGATCACAATGCCAAAGAGTTCCCATCCAATCCGCATCGTTTAGTAGTACCATTCTTTAAATTAACAAAAGATGGGGAATACAGCATCGAACCTTCTCCTGAAGAAAGCCGCAGTAATATAAAAGGGTTACTTCAACATTTAAGAACCATGGTTGATACTACCATATATTGTCGCTTCACTGGAATTGTTTCATCAATGCATTATAAGTTAGATGAAGTACTATGGGAATATAATAAATTTGAATCAGCTGTAACCCTAGCAGAAGGGGAGGGTTCAGGTGCCTTACTACTGATCCAAAAATACGGCGTTAAGAAGTTATTTTTGAATACACTTGCTACTGAACATAGTATTGAGAGTGAAGTGATATCAGGTTACACCACTCCAAGGATGCTACTCCCAATTATGCCTAAAACACATCGTGGTGAGCTAGAGGTCATATTAAATAACTCAGCTAGTCAAATAACTGATATTACACATCGAGATTGGTTTTCAAATCAAAAAAATAGGATTCCAAATGATGCTGATATTATTACCATGGATGCTGAAACTACAGAAAACTTAGATCGTTCCAGATTATATGAAGCAGTATATACGATTATTTGTAATCATATCAATCCTAAAACTTTGAAAGTGGTCATCTTAAAAGTCTTCCTCAGCGATTTGGATGGGATGTGCTGGATTAACAATTATCTTGCTCCTATGTTTGGATCAGGATATTTAATCAAACCTATAACATCAAGTGCAAAGTCAAGTGAGTGGTATTTATGCTTATCTAATCTACTTTCAACCTTGAGAACTACTCAGCATCAAACCCAGGCAAACTGTCTCCATGTCGTACAATGTGCTCTTCAACAGCAAGTACAAAGAGGGTCATATTGGCTAAGTCATCTTACCAAATACACCACAAGTAGATTGCACAATAGTTATATTGCATTTGGTTTTCCTTCATTAGAGAAGGTCCTATATCATAGGTATAACCTTGTTGATTCGAGAAATGGACCATTAGTTTCTATAACGAGACACCTTGCCCTCCTCCAAACTGAGATCCGGGAGTTGGTAACTGATTATAATCAGCTGCGACAAAGTCGAACCCAGACTTATCATTTCATAAAAACATCCAAGGGACGGATAACTAAACTAGTGAATGATTATCTAAGATTTGAGTTGGTTATACGGGCTCTTAAAAATAATTCTACATGGCACCATGAGTTATACTTGCTACCAGAACTTATAGGTGTTTGCCATCGATTTAATCATACACGTAACTGTACATGCAGTGAAAGGTTCCTGGTTCAAACTTTATATCTACACCGAATGAGTGATGCTGAGATAAAACTTATGGACCGGCTCACCAGCCTAGTCAATATGTTTCCTGAAGGTTTCAGGTCTAGTTCAGTCTAATTCTAACTGCACCAAAGGCTCTAAAAATATTTTAAATAACCAGGTGTATATCAAAGTCAATACAAGTGTAAAAACAATATGCAAGGGACCACATTTAGGATCAGTTTATTGACTCTTCCAATACACAGAGTTGGAAGCACCGATTCAAGGTTTCTAAGACGCCCTATCGATTATGTTGATAATGTAAATAATAGCTTTTCCTGTCTATTATGACTTAAATAATCATATCTATAACGACCATCACAGCTAAGTCGTTGCCCTAGTTCATATATTAAATTAAAATTTAGAAGCTAGGTTGACTCTAATTACATAAGTATTAAGAAAAAATTACTAAGACTAATACTCTCATGCCAAGAACTAGTAATGTGTTTCACATGACAGATTATTTCTAACACTAAATTGCAATTTCAATTTTAAAGCTAAGTTTAACACCTATACAGCCAAAATATTTCATAGGGCCGATGGGAATAACATAAGAGGAACATGATCAATGAACCCTTTATTCCAACTAGGCAGTTGATTGATAATCTACAAATTCCATAAGATGTTCTTACGATATTCTTTTGTTTTTAATCTCAATGTCAATGATTTAATAAGTAATAATAAAAAAATCACATTAAAGATGCAGGAAGATCTTGACCTCGCCAGGAAAATTAAGCGCACACAAATAAATTAAAAAATCTGTATTTTCTCTTTTTTGTGTGTCCA\n>Zaire_ebolavirus_isolate_EBOV/H.sapiens-tc/COD/1977/Bonduni_complete_genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGATAGAGAACAACCTAGGTCTCCGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCCAACAACCTTAATAGAAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGGTTTTGAACTTGAACACTTAGGGGATTGAAGATTCAACAACCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAATCTGGATGGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAAGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAGGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACAACTGAAGCTAATGCCGGTCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTCTGATCAAATTTCTCCTAATACACCAAGGGATGCACATGGTTGCCGGGCATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGCTTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTATCGGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGTACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAACTCAGAGAGGCTGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCGTCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTGGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGAAAACGGCATGAATGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACTAAGCCAGTGCCTAATAGATCGACCAAGGGTGGACAACAGAAGAACAGTCAAAAGGGCCAGCATATAGAGGGCAGACAGACACAATCCAGGCCAATTCAAAATGTCCCAGGCCCTCACAGAACAATCCACCACGCCAGTGCGCCACTCACGGACAATGACAGAAGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATTAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTGGAGTCAGATGATGAAGAGCAGGACAGGGACGGAACTTCCAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAAAGAAAGAACTCCCGCAAGACGAGCAACAAGATCAGGACCACACTCAAGAGGCCAGGAACCAGGACAGTGACAACACCCAGTCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCTGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAAAGAGTACACGTATCCAGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCTATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTGATGAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAACAATGGGATGATTCAACCGACAAATAGCTAACATTAAGTAGTCAAGGAACGAAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAGGCGTTAAGCCACAGTTATAGCCATAATTGTAACTCAATATTCTAACTAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGTCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGCGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGACGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCCGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAAACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAGCTTGCGTCCAGTCCCACCATCGCCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCCCTTCCCTCCGAAAGAGGCGAATAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTACGTTACATTAATGATACACTTGTGAGTATCAGCCCTGGATAATATAAGTCAATTAAACGACCAAGATAAAATTGTTCATATCTCGCTAGCAGCTTAAAATATAAATGTAATAGGAGCTATATCTCTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAACCAAAAGTGATGAAGATTAAGAAAAACCTACCTCGGCTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGAGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCATCGAATCCACTCAGGCCAATTGCCGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTTGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATACACTATCACCCATTTCGGCAAGGCAACCAATCCACTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCATCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTCAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGAATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGATTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTATAGAATCTTCTCAGGGATAGTGATAACATCTATTTAGTAATCCGTCCATTAGAGGAGACACTTTTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTTTTTTCTCTCCTAAATGTAGAACTTAACAAAAGACTCATAATATACTTGTTTTTAAAGGATTGATTGATGAAAGATCATAACTAATAACATTACAAATAATCCTACTATAATCAATACGGTGATTCAAATGTTAATCTTTCTCATTGCACATACTTTTTGCCCTTATCCTCAAATTGCCTGCATGCTTACATCTGAGGATAGCCAGTGTGACTTGGATTGGAAATGTGGAGAAAAAATCGGGACCCATTTCTAGGTTGTTCACAATCCAAGTACAGACATTGCCCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTTTTCCAGAGTAGGGGTCGTCAGGTCCTTTTCAATCGTGTAACCAAAATAAACTCCACTAGAAGGATATTGTGGGGCAACAACACAATGGGCGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAGCACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCGTGTGCCGGAGACTTTGCCTTCCATAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACCAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATACAAGTGGGAAAAGGAGCAATACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGTTGTATCAAACGGAGCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGGGACCAACACAACAACTGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTAACAACCCTTGCCACAATCTCCACGAGTCCCCAATCCCTCACAACCAAACCAGGTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGACAGCACAGCCTCCGACACTCCCTCTGCCACGACCGCAGCCGGACCCCCAAAAGCAGAGAACACCAACACGAGCAAGAGCACTGACTTCCTGGACCCCGCCACCACAACAAGTCCCCAAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTCGCAGGACTGATCACAGGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAACCCTAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGACTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACACAGAGGGGCTAATGCACAATCAAGATGGTTTAATCTGTGGGTTGAGACAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTGTTCCTGAGAGCCACAACTGAGCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGCCACATTCTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGAAAAGCTCAGCCTCAAATCAATGAAACCAGGATTTAATTATATGGATTACTTGAATCTAAGATTACTTGACAAATGATAATATAATACACTGGAGCTTTAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCTAGTTATCTCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAATCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGGTCAAAAAGTCAATAGAAATTTAAACAGTGAGTGGAGACAACTTTTAAATGGAAGCTTCATATGAGAGAGGACGCCCACGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAGAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCAGAACCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGCGAGGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATTGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATGTGCATGATTGCCCTAATATATGAAGAGGTATGATACAACCCTAACAGTGATCAAAGAAAATCATAATCTCGTATCGCTCGTAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACTCTACAGGAGGTAGCAACGATCCATCCCATCAAAAAATAAGTATTTCATGACTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTATGCTTCAAGCTGTGGAGGAGGTGTTTGGTATTGGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAAGAGGTAGATTGTGACCGGAAATGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTGGCACGTCTTTTAGCTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTCTCTAAGCTAAATTGGTCTGTACACATCCCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCTGGGCTAACACCACCAGGTCAACTCCATTGGCTGAAAAGAAGCTTACCTACAACGAACATCACTTTGAGCGCCCTCACAATTAAAAAATAGGAACGTCGTTCCAACAATCGAGCGCAAGGTTTCAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATTGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGCCAAACTATTCAGGGGTGGAAGGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAATCTCTTTCCTCATTTATTTCAAAATCCGAATTCCACAATTGAATCACCGCTGTGGGCATTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAACGGATTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCATGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGATCCTCGACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGGTAGAATACTTCATATTGAGCTAACTCATATATGCTGACTCAATAGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAACAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATGAATAAGCATTTTATCACCAGAAATCCTATATACTAAATGGTTAATTGTAACTGAACCCGCAGGTCACATGTGTTAGGTTTCACAGATTCTATATATTACTAACTCTATACTCGTAATTAACATTAGATAAGTAGATTAAGAAAAAAGCCTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGAAATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCTAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACCAAGTTCTTGAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAGTTCTTCTCAAGGCACTGTCAGGCAATGGATTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATCATTAAGTACACAATGCAAGATGCTCTCTTCTTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAACACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGATCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCAATGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGACTGGTATCAGGCATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACTGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTAAAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCCAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACTTCAGATAGGAATCTAACACCGGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTACTATGGGAATTTTACCACCTTGACCACCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACCGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTTAGTACTAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCACAAAAACTCGAGTATCTACTACCACAATATCGGAACTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACCTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAACATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCACATAACCTCACACTGGAGAATCGAGACAACCCCCCCGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGGTGACAATCAGTGCATTACTGTTTTATCAGTCTTCCCCTTAGAGACTGACGCAGACGAGCAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGCACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGGATAACCGCAGCTTTCCATACGTTTTTTTCGGTGAGAATCTTGCAATATCATCATCTCGGGTTCAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGCTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTCCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGCAGGACCATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTGTAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGATATCTTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACACCGGTTTTGGACAGACTGAGGAAAATAACATTGCAAAGGTGGAGCCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATTCTGAGGGAATATTCATGGGCTCATATTTTAGAGGGAAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGTTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCAAAGCAACCAGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGACAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAATTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTATTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAGTAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTCGATAATCCATTTTTCCAAGGTAAACGGCTGAACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACCATCATGCAATCAATTATTTCAGATAGCAACAATTCATCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACTCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGATCCTCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCGCTAGAGGGTCAAAACCCAACACCTGTGAATAATTTTCTCTATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACAACAGGCTTTTAAAACTACCATAAGTGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCATCATTGGCGTACTGGAGGAGCAGACACAGAAACAGCAACCGAAAATACTTGGCAAGAGACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAATCTAGTCCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAACACGCACCAGGGTCCGTCGTTCCAGTCCTTTCTAAGTGACTCTGCTTGTGGTACAGCAAATCCAAAACTAAATTTCGATCGATCGAGACACAATGTGAAATTTCAGGATCATAACTCGGCATCCAAGAGGGAAGGTCATCAAATAATCTCACACCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGACGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGATTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAGTTTCAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAAGCAAGTCGAGGTTATAACCATGGATGCAGAGACAACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAATTGATCTTACACCATATTGATCCTAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGTTATGGCTAAATGATAATTTAGCCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGAAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGTGAGTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCCACTAGTCTCTATCACTCAGCACTTAGCACATCTTAGAGCAGAGATTCGAGAATTAACTAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTACCATATTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCGGATGGTCTCTACAGGTTTGATTGAATTACCGTGCATAGTATCCTGATACTTGCAAAGGTTGGTTATTAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCTAATCTCAATAAACAACTATTTAAATAACGAAAGGAGTCCCTATATTATATACTATATTTAGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATGCAGCATGTGTGACATATTACTGCCGCAATGAATTTAACGCAACATAATAAACTCTGCACTCTTTATAATTAAGCTTTAACGAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTGTATCAATATCCTGTCAGATGGAATAGTGTTTTGGTTGATAACACAACTTCTTAAAACAAAATTGATCTTTAAGATTAAGTTTTTTATAATTATCATTACTTTAATTTGTCGTTTTAAAAACGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACCTTAACATTTTTGTCTAGTAAGCTACTATTTCATACAGAATGATAAAATTAAAAGAAAAGGCAGGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGACATTGACCACGCTCATCAGAAGGCTCGCCAGAATAAACGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n>Zaire_ebolavirus_isolate_EBOV/H.sapiens-tc/COD/2007/43_Luebo_complete_genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGTTTTGTTTCAGAGCCATGTCACAAAGATAGAGAACAACCTAGGTCTCCGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGTCTTATCACATCACAGGTTCCACCTCAGGCTCTGCAGGGTGATCCAACAACCTTAATAGAAACATTATTGTTAAAGGACAACATTAGGTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGATTTTGAACTTGAACACCTAGAGGATTGGAGATTCAACAACCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTAACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCAAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGCCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTCTTGATCAAATTTCTCCTAATACACCAAGGGATGCACATGGTTGCCGGGCATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTTTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTCTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTATCGGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGCACCCTCGCAGGAGTAAATGTGGGAGAACAGTATCAACAGCTCAGAGAGGCTGCCACTGAAGCTGAGAAGCAACTCCAACAATATGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATCCTTATGAACTTCCATCAGAAGAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACCGCTGCGTCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCTATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGAAAACGGTATGAATGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACTAAGCCAGTGCCTAACAGATCGACCAAGGGTGAACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCAGGCCAACTCAAAATGTCCCAGGCCCTCGCAGAACAATCCACCATGCCAGCGCTCCACTCACGGACAATGACAGAAGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATTAACGAGGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCCAGCCTTCCGCCCTTGGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCCAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAAAGAAAGAACTCCCGCAAGATGAGCAACAAGACCAGGACCACACTCAAGAGGCCAAGAACCAGGACAGTGACAACACCCAGCCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAAGGGCCATTTGATGCTGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTAATGAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAATAATGGGATGATTTAACCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAGGCGTTAAGCCACAGTTATAACCATAATTGTAACTCAATATCTTAGCTAGTGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACTTATTAGCCCGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTAGTCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCTAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAAACGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGACGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAGCAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAGTTAGTACAAGTGATTTGTAAATTGGGAAAGGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATCACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTACGTCCAGTCCCGCCATCGCCCAAGATTGATCGAGGTTGGATATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCCCTTCCCTCCGAACGAGGCGACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTACGTTACATTAATGATACACTTGTGAGCATCAGCCCTAAATAATATAAGTCAATTAAACGACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTAAAATATAAATGTAATAGGAGCTATATCTGTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTCCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCATCAAATCCACTCAGACCAATTGCTGATGACACCATCGACCATGCTAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTTGAAGCTATGGTGAATGTCATATCGGGCCCTAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCACTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACAGGATCAAACGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAATGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATTATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGCTCGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGGTAACATCTATTTAGTAATCCGTCTATTAGAGGAGATACTTTTAATTGATCAATATACTAAAGGTGCTTTACACCGTTGTCTCTTTTTTCTCCTAAATGTAGAACTTAACAAAAAACTCATAATATACTTGTCTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAATAATCCTACTATAATCAATACGGTGATTCAAATGTTAATCTTTCTCATTGCACATACTCTTTGCCCTTATCCTCAAATTGCCTACATGCTTACATTTGGGGATAACCAGTGTGACTTGGATTGGAGATGTGAAGAAAAAATCGGGACCCATTTCTAGGTTGTTCACAATCCAGGTACAGACATTGCCCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTTTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATCGTATAACCAAAGTAAACTTCACTAGAAGGATATTGTGGGGCAACAACACAATGGGTGTCACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAGCACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGATGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACAGGACCGTGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATTTACCGAGGGACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACCAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAAAGGAGCAACACCACGGGAAAACTAATTTGGAAAGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGAGCCAAAAACCTCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAAAGACCAACACAACAACTGAAGACCACAAAATCGTGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCCCCCACAACCAAACCAGGTCCGGACAACAGCACTTATAATACACCCGTATATAAACTTGACACCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACACCCAAAAGCAGAGAACACCAACACGAGCAAGAGCGCTGACTCCCTGGACCCCGCCACCACGACAAGTCCCCCAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTCGCAGGACTGATCACAGGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAACCCTAACTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACACAGAGGGGCTAATGCACAATCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTGTTCCTGAGAGCTACAACTGAGCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGCCATATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGCAAAGCTCAGCCTCAAATCAATGAAATTAGGATTTAATTATATGGATCACTTGAATCTAAGATTACTTGACAAATGATAATATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCTAGTTATATCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAATCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGGTCAAAAAGTCAATAGAAATTTAAACAGTGAGTGGAGACAACTTTTAAATGGAAGCTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAAAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCAGAACCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCCGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGCGAGGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTGTATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATATGCATAATTGCCTTAATATATGAAGAGGTATGATACAACCCTAACAGTGACAAAAGAAAATCATAATCTCGTATCGCTCGTAATATAACCTGCCAAGCATACCTCTTACACAAAGTGATTCTTGTACACAAATAATGTTTTACTCTACAGGAGGTAGCAACGATCCATCCCATCGAAAAATAAGTATTTTATGACTTACTAATGATCTCTTATAATATTAAGAAAAACTGATGGAACATAAATCCTTTCTACTTCAAGTTGTGGAGGAGGTCTTTGGTATTGGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAAGAAGTAGATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCTCTCCAGCAAAGCACTATTTCAGGGTAGTCCAATTAGTGACACGTCCTTTAGCTGTATACCAGTCGCCCTTGAGATACGCCACAAAAGTGTCTCCAAGCTAAATTGGTCTGTACACATCTCATACATTGTATTAGAGGCAATAGTATCTAACTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCTGGGCTAACTCCCCCAGGTTAACTCCATTAGCTGAAAAGAAGCCCACCCACAACGAACATCACTTTGAGCGCCCTCACAATTTAAAAATAGGAGCGTCGTTCCAACAATCGAGCGCAAGGTTTCAGGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACTATTCAAGGGTGGAAGGTCTATTGGGCTGGTATTGAGTTTGATGTGACTAACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCGATGACAAGGAATCTATTTCCTCATTTATTTCAAAATCCGAATTCTACAATTGAATCACCGCTGTGGGCATTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAACGGATTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCAACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGATAGAATACTTCATATTGAGCTAACTCATATATGCTGACTCAATGGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAAGCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTACTTTATTATATGAATAAGCATTTTATCACCAGAAATCCAATATACTAAATGGTTAATTGTAACTGAACCCGCAGGTCACGTGTGTTAGGTTTCACAGATTATATATATTACTAACTCTATACTCGTAATTAACATTAGATAAGTAGATTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCATACTCCCTTAATCCACAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTAAAATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTGTCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATCATTAAGTACACAATGCAAGATGCTCTCTTCTTGAAATATTACCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCGATTTCAATGTTACCACTGAACTCACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGGCATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATGCGTGCGCTAAAGTCTTCACAGGCACAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCAGAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGCAAAACATTATTTTGATAGTCAAGGGTCTTGGTACAGTGTTACTTCAGATAGGAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTACTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGATTTAAGTATTTTTATAAAAGACAGAGCTACCGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTCAGTACTAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACACTGGAAAATCGAGACAACCCCCCCGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGACGCAGACGAGCAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCTGCCAGCCTAGCAAAAGTTACAAGTGCTTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGCACTGCTTTTGAGCGATCCATCTCTGAGACACGACACATCTTTCCTTGCAGGATAACCGCAGCTTTCCATACGTTTTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTCAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCGTTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGCTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGCTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGTTAAATCCTAGCGGATTAAATGTCCCTGGGTCACAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTGTAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCAGCCGATATTTTTTCACGTACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACACCGGTTTTGGACAGACTGAGGAAAATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTTTGGTTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCAAAGCAACCTGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGACAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAATTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGTGGTGGCCAGTCTGCACGTGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTATTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTTAATTGCAATATCTCATTCGATAACCCATTTTTCCAAGGTAAACGGCTGAACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACCATCATGCAATCAATCATTTCAGATAGCAACAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGATCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGATCCTCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGATTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGGACAATTGTCCCTTTATGGATAGTATATCCGCTAGAGGGTCAAAACCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAATTGCTGGTGCATGATTCATCAAGACAACAGGCTCTAAAAACTACCATAAGTGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAATACTTGGCAAGAGATTCTTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGGTGGCACTGAACGGAATCTAGTCCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAACACGCACCAGGGTCCGTCATTCCAGTCATTTCTAAGTGACTCTGCTTGTGGTACAGCAAATTCAAAACTAAATTTCGATAGATCGAGACACAATGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGATCATCAAATAATCTCACACCGTCTAGTCCTACCCTTCTTTACATTATCTCAAGGGACACGCAAATTAACGTCATCCAATGAGTCACAAACCCAAGACGAGATATCAAAATACTTACGGCAATTAAGATCCGTAATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCTATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAGTTTTAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAGTTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGACGCAGAGACAACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAATTGATCTTACACCATATTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGTTATGGCTAAATGATAATTTAGCCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATCTAGTGAATGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTCGTCGATTCAAAGAGAGGTCCACTAGTCTCTATCACTCAGCACTTAGCACATCTTAGAGCAGAGATTCGAGAATTGACTAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTATCATATTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATTGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCGGATGGTCTCTACAGGTTTGATTGAATTACCGTGTATAGTATCCTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCTAATTTCAATAAATAACTATTTAAATAACAAAAGAGGTCCTTATATTATACACTGTATTTAGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATGCAGCATGTGTGACATATTACTGCCGCAATGAATCTAACACAACATAATAAACTCTGCACTCTTTATAATTAAGCTTTAATGAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTGTATCAATATCCTGTCAGGTGGAATAGTGTTTTGGTTGATAACACGACTTCTTAAAACAAAATTGATCTTTAAGATTAAGTTTTTTATAATTATCATTACTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTGGGTGTAATAACTTTAACTTTTTGTCTAGTAAGCTACTATTTCATACAGAACGATAAAATTAAAAGAAAAGGCATGATTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGACATTGACCACGCTCATCAGAAGGCTCGCCAGAATAAACGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n>Zaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/1Eko_complete_genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGATAGAGAACAACCTAGGTCTCTGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGAAGATCCCTTGTCAACATCTAGGTCTTATCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCCAACAACCTTAATAGAAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGGTTTTGAACTTGAACACTTAGAGGATTGGAGATTCAACAACCCTAAAGCTTGGGGTAAAGCATTGGAAATAGTTGAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAGATTTGCCAACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAGGGAGATTGCAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACAACTGAAGCCAATGCCGGTCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTCCTAATACACCAAGGGATGCACATGGTTGCCGGGCATGATGCCAACGACGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTTTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTATCAGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGTACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAACTCAGAGAGGCTGCCACTGAGGCTGAGAAGCAACTCCAACAATACGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAATTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAAGAAAGAGCGCCTGGCCAAGCTGACGGAAGCTATCACTGCTGCGTCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTGGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGAAAACGGCATGAATGCACCAGATGATTTGATCCTATTCGATCTAGACGAGGACGATGAGGACACTAAGCCAGTGCCTAATAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCAGGCCAACTCAAAATATCCCAGGCCCTCACAGAACAATCCACCACGCAAGTGCTCCACTCACGGACAATGACAGAAGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTGGAGTCAGATGAAGAAGAACAGGACAGGGACGGAACCTCCAATCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAAAGAAAGAACTCCCGCAAGATGAGCGACAAGATCAGGACCACACTCAAGAGGCCAGGAACCAGGACAGTGACAACACCCAGCCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCTGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAAAGAGTACACGTATCCAGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCTATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTAATGAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAACAATGGGATGATTCAACCGACAAATAGCTAACATTAAGTAGTCAAGGAACGAAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAGGCGTTAAGCCACAGTTATAGCCATAATTGTAACTCAATATCCTAACTAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTACCCAACATTTACACGATCATTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGTCTAACAAGATGACAACCAGAACAAAGAGCAGGGGCCACACTGCGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGACGCGCAACAGTCAAACCCAAACGGATCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTAGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCCGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAGCTTGCGTCCAGTCCCACCATCGCCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCCCTTCCCTCCGAAAGAGGCGACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTACGTTACATTAATGATACACTTGTGAGTATCAGCCCTGGATAATATAAGTCAATTAAACGACCAAGATAAAATTGTCCTTATCTCGCTAGCAGCTTAAAATATAAATGTAATAGGAGCTATATCTCTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAACCAAAAGTGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTCCATTGACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGAGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCATCGAATCCACTCAGGCCAATTGCCGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTTGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACTAATCCACTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGACTCCTGCGAATTGGAAACCAGGCCTTCCTCCAGGAGTTCGTTCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGTTGCGCCCAGGAATTTCATTTCATCCAAAACTGCGCCCCATTCTTTTACCCAACAAGAGTGGGAAGAAGGGGAATAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGAATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGTTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCGAGTCTTCCAGCTGTGATTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTATTTAGTAATCCGTCCATTAGAGGAGATACTTTAAATTGATCGATATACTAAAGGTGCTTTACACCATTGTCTTTTTTCTCTCCTAAATGTAGAACTTAACAAAAGACTCATAATATACTTGGTTTTAAAAGATTGATTGATAGAAGATCATAACTAATAACATTACAAATAATCCTACTATAATCAATACGGTGATTCAAATGTTAATCTTTCTCATTGCGCATACTCTTTGCCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGATAGCCAGTGTGACTTGGATTGGAGATGTGGAGAAAAAATCGGGACCCATTTCTAGTTTGTTCACCATCCAAGTACAGACATTGCCCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCCTCCAGAGCAGGGATCGTCAGGTTCTTTTCAATCGTATAACCAAAATAAACTTCACTAGAAGGATATTGTGGGGCAACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAGCACATTACAGGTTAGTGATGTCGACAAACTGGTTTGCCGTGACAAACTGTCATCCACGAATCAATTGAGATCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAAGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCGTGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTGGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGCTTTGGAACCAATGAGACAGAGTATTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATACAAGTGGGAAAAGGAGCAATACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACAGAGCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGGGACCAACACAACAACTGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCTTCAACCCCCCACAACCAAACCAGGTCCGGACAACAGCACCCACAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGCCAGCACAACCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCCTAAAAGCAGAGAACACCAACACGAGCAAGGGCACTGACCTCCTGGACCCCGCCACCACAACAAGTCCCCAAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTCGCAGGACTGATCACAGGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAACCCTAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGACTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACACAGAGGGGCTGATGCACAATCAAGATGGTTTAATCTGTGGGTTGAGACAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTATTCCTGAGAGCCACAACCGAGCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACTAAGAACATAACGGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAGTGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTGATGGCAAAGCTCAGCCTCAAATCAATGAAACCAGGATTTAATTATATGGATTACTTGAATCTAAGATTACTTGACAAATGATAATATAATACACTGGAACTTTAAACATAGCCAATGTGATTCTAACTCTTTTAAACTCACAGTTAATCATAAATAAGGTTTGACATCAATCTAGTTATCTCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAATCTTCATCCTTGATTCTACAATCATAACAGTTATCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGATCAAAAAGTCAATAGAAATTTAAACAGTGAGTGGAGGCAACTTTTAAATGGAAGCTTCATATGAGAGAGGACGCCCACGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAGAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCAAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACTCTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCAGAACCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCTGTGATGACGAGGAAGTTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGCGAGGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCGCTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATCACCTTCTACTTGATCACAATACTCCGTATACCTGTTATCATATATTTAATCAAGACGATATCCTTTAAGACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATGTGCATGATTGCCTTAATATATGAAGAGGTATGATACAACCCTAACAGTGACCAAAGAAAATCATAATCTCGTATCGCTCGTAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACCCTACAGGAGGCAGCAACGATCCATCCCATCAAAAAATAAGTATTTTATGACTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTGTTTGGTATTTGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAAGAGGTAGATTGTGGCCGGAAATGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTGACACGTCCCTTAGTTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTCTCTAAGCTAAATTGGTCTGTACACATCCCATACATTGTATTGGGGGCAATAATATCTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGTTGAAAAAAGGCCTACCTACAACGAACATCACTTTGAGCGCCCTCACATTTAAAAAATAGGAACGTCGTTCCAACAATCGAGCGCAAGGTTTCAAAGTTGAACTGAGAGTGTCTAGACAACAAAGTATCGATACTCCAGACACCAGGCAAGACCTGAGAAAAAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAAAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGCCAAACTATTCAGGGGTGGAAGGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAATCTCTTTCCTCATTTATTTCAAAATCCGAATTCCACAATTGAATCACCGCTGTGGGCATTGAGAGTCATCCTTGCAGCAGGGATACAAGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAACGGATTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGATCCTCGACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGAGCTAACTCATATATGCTGACTCAATAGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATTCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATCATATGAATAAGTATTTTATCACCAGAAACCTTATATACTAAATGGTTAATTGTAACTGAATCCGCAGGTCACATGTGTTAGGTTTCACAGATTCTGTATATTACTAACTCTATACTCGTAATTAACATTAGATAAGTAGATTAAGAAAAAAGCCTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGAAATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCGGACGCTAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACCAAGTTCTTGAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTGTCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAGATCATCAAGTACACAATGCAAGATGCTCTCTTCTTGAAATACTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAGAAAATCTTATCTGCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGATCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGTTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCAATGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGACTGGTATCAGGCATCAGTATTCAAAGAAGCAGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACGACTCTAATCTCAAAAATAGCAGAGATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGATCTGATGGGTATAAAATTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACCGAGAGGAAAGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTAAAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCCAAACATTATTTTGATAGCCAAGGGTCTTGGTACAGTGTTACTTCAGATAGGAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTACTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACCGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTTAGTACTAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAAAATGTTCTTTCCTACGCGCAAAAACTTGAGTATCTACTACCACAATATCGGAACTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACCTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTGGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACGCAAGTGATGATTTTGGTGAACATGCCACAGTTAGAGGGAGTAGTTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACCTTTTATCGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCACATAACCTCATACTGGAAAATCGAGACAACCCCCCCGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGGCGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGACGCAGACGAGCAGGAACAGAGTGCCGAAGACAATGCAGCGAGGGTGGCCGCTAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTAGCTAGTATAGGCACCGCTTTTGAGCGGTCCATTTCTGAGACACGACATATCTTTCCTTGCAGGATAACCGCAGCTTTCCATACATTTTTTTCGGTGAGAATCTTGCAATATCATCATCTCGGGTTCAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGTAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGATTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGCTTATTCCAGTTAAAAACTTATCTCCGAATGATTGGGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTCCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGCAGGACCATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTGTAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGATATCTTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACAATAATCCAGAGACACCGGTTTTGGACAGACTGAGGAAAATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCTCATATTTTAGAGGGAAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGTTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCGAAGCAACCAGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCGTCCCGACTAAGCTGGACTATCGGGGATGGAATCCCTTACATTGGATCAAGGACAGAAGATAAGATAGGACAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAGCCATTTTTGGAAGCACGAGTAAATTTGAGTGTTCAAGAAATACTTCAAATGACTCCTTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGCATGAGTAATTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTATTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTCGATAACCCATTTTTCCAAGGTAAACAGCTGAACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACCATCATGCAATCAATTATTTCAGATAGCAACAATTCATCTACAGACCCAATTAGCAGCGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAACACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGATCCTCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCTATTTCATCTTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCGCTAGAGGGTCAAAACCCAACACCTGTTAATAATTTTCTCTATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACGACAGGCTTTTAAAACTACCATAAGTGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCATCATTGGCATACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAATACTTGGCAAGAGACTCTTCAACTGAATCAAGCACAAACAACAGTGATGGTCATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAATCTAGTTCTACAAATGAGCCATGAAATAGAAAGAACGACAATTCCACAAGAAAACACGCACCAGGGTCCGTCGTTCCAGTCCTTTCTAAGTGACTCTGCTTGTGGTACAGCAAATCCAAAACTAAATTTCGATCGATCGAGACACAATGTGAAATCTCAGGATCATAACTCGGCATCCAAGAGGGAAGGTCATCAAATAATCTCGCACCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTGACGTCATCCAATGAGTCACAAACCCAAGACGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAGTTTTAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATAACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAAGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAACTGATCTTACACCATATTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGTTATGGCTAAATGATAATTTAGCCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGAAAGATGCCACACCAAAACCATCTCAGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGTGATTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCCACTAGTCTCTATCACTCAGCACTTAGCACATCTTAGAGCAGAGATTCGAGAATTAACTAATGATTATAATCAACAGCGACAAAGTCGAACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTACCATATTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTGAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCGGATGGTCTCTACAGGTTTGATTGAATTACCGTGCATAGTATCCTGATACCTGCAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCCGATTTCAATAAACAACTATTTAAATAACGAAAGGAGTCCCTATATTATACACTATATTTAGCCTCTCTCCCTGCTTGATAATCAAAAAATTCACAATGCAGCATGTGTGACATATTACTGCCGCAATGAATTTAACGCAACATAATAAACTCTGCACTCTTTATAATTAAGCTTTAACGAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTATATCAATATCCTGTCAGATGGAATAGTGTTTTGGTTGATAACACGACTTCTTAAAACAAAATTGATCTTTAAGATTAAGTTTTTATAATTATCATTACTTTAATTTGTCGATTTAAAAATGGTGATAGACTTAATCTCTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTTCATACAGAATGATAAAATTAAAAGAAGAGGCAGGACTGTAAAATCATAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGACATTGACCACGCTCATCAGAAGGCTCGCCAAAATAAACGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n>Zaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/2Nza_complete_genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGATAGAGAACAACCTAGGTCTCTGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGTCTTATCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCCAACAACCTTAATAGAAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGGTTTTGAACTTGAACACTTAGAGGATTGGAGATTCAACAACCCTAAAGCTTGGGGTAAAGCATTGGAAATAGTTGAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAGATTTGCCAACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAGGGAGATTGCAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACAACTGAAGCTAATGCCGGTCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTCCTAATACACCAAGGGATGCACATGGTTGCCGGGCATGATGCCAACGACGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTTTATTGATTGTCAAAACAGTACTTGATCATATCCTACAGAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTATCAGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGTACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAACTCAGAGAGGCTGCCACTGAGGCTGAGAAGCAACTCCAACAATACGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAATTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGACGGAAGCCATCACTGCTGCGTCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTGGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGAAAACGGCATGAATGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGATGAGGACACTAAGCCAGTGCCTAATAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCAGGCCAACTCAAAATGTCCCAGGCCCTCACAGAACAATCCACCACGCAAGTGCTCCACTCACGGACAATGACAGAAGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTGGAGTCAGATGATGAAGAACAGGACAGGGGCGGAACCTCCAATCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAAAGAAAGAACTCCCGCAAGATGAGCGACAAGATCAGGACCACACTCAAGAGGCCAGGAACCAGGACAGTGACAACACCCAGCCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCTGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAAAGAGTACACGTATCCCGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCTATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTAATGAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAACAATGGGATGATTCAACCGACAAATAGCTAACATTAAGTAGTCAAGGAACGAAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCATAATAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTCCTTCAAAGTTCAATTTGAGTCTTAATGCAAATAGGCGTTAAGCCACAGTTATAGCCATAATTGTAACTCAATATCCTAACTAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTACCCAACATTTACACGATCATTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTTATCATCCTTACGTCAATTGAATTCTCTAGCACTCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGTCTAACAAGATGACAACCAGAACAAAGAGCAGGGGCCACACTGCGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAGACGAAGCCAAACCCGAAGACGCGCAACAGTCAAACCCAAACGGATCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAGACATTAGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGCGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCCGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAGCTTGCGTCCAGTCCCACCATCGCCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCCCTTCCCTCCGAAGGAGGCGACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTACGTTACATTAATGATACACTTGTGAGTATTAGCCCTGGATAATATAAGTCAATTAAACGACCAAGATAAAATTGTCCTTATCTCGCTAGCAGCTTAAAATATAAATGTAATAGGAGCTATATCTCTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAACCAAAAGTGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTCCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGAGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCATCGAATCCACTCAGGCCAATTGCCGATGACACCATCGACCATGCCAGCCACATACCAGGCAGTGTTTCATCAGCATTCATCCTTGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACTAATCCACTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGACTCCTGCGAATTGGAAACCAGGCCTTCCTCCAGGAGTTCGTTCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGTTGCGCCCAGGAATTTCATTTCATCCAAAACTGCGCCCCATTCTTTTACCCAACAAGAGTGGGAAGAAGGGGAATAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGAATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGTTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCGAGTCTTCCAGCTGTGATTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTATTTAGTAATCCGTCCATTAGAGGAGATACTTTAAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTTTTTTCTCTCCTAAATGTAGAACTTAACAAAAGACTCATAATATACTTGGTTTTAAAAGATTGATTGATAGAAGATCATAACTAATAACATTACAAATAATCCTACTATAATCAATACGGTGATTCAAATGTTAATCTTTCTCATTGCACATACTCTTTGCCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGATAGCCAGTGTGACTTGGATTGGAGATGTGGAGAAAAAATCGGGACCCATTTCTAGTTTGTTCACCATCCAAGTACAGACATTGCCCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCCTCCAGAGCAGGGATCGTCAGGTTCTTTTCAATCGTATAACCAAAATAAACTTCACTAGAAGGATATTGTGGGGCAACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAGCACATTACAGGTTAGTGATGTCGACAAACTGGTTTGCCGTGACAAACTGTCATCCACGAATCAATTGAGATCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAAGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCGTGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTGGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCTTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAAATATCAGGCTACCGGCTTTGGAACCAATGAGACAGAGTATTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATACAAGTGGGAAAAGGAGCAATACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACAGAGCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGGGACCAACACAACAACTGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTGACAACCCCTGCCACAATCTCCACGAGTCTTCAACCCCCCACAACCAAACCAGGTCCGGACAACAGCACCCACAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGCCAGCACAACCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCCTAAAAGCAGAGAACACCAACACGAGCAAGGGCACTGACCTCCTGGACCCCGCCACCACAACAAGTCCCCAAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTACCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTCGCAGGACTGATCACAGGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAACCCTAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGACTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACACAGAGGGGCTGATGCACAATCAAGATGGTTTAATCTGTGGGTTGAGACAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTATTCCTGAGAGCCACAACCGAGCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACTAAGAACATAACGGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAGTGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGCAAAGCTCAGCCTCAAATCAATGAAACCAGGATTTAATTATATGGATTACTTGAATCTAAGATTACTTGACAAATGATAATGTAATACACTGGAGCTTTAAACATAGCCAATGTGATTCTAACTCTTTTAAACTCACAGTTAATCATAAATAAGGTTTGACATCAATCTAGTTATCTCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAATCTTCATCCTTGATTCTACAATCATAACAGTTATCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGATCAAAAAGTCAATAGAAATTTAAACAGTGAGTGGAGGCAACTTTTAAATGGAAGCTTCATATGAGAGAGGACGCCCACGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAATCATCGAGGCGAGCACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAGAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCAAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACTCTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCAGAACCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCTGTGATGACGAGGAAGTTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGCGAGGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATTATCATATATTTAATCAAGACGATATCCTTTAAGACTTACTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATGTGCATGATTGCCCTAATATATGAAGAGGTATGATACAACCCTAACAGTGACCAAAGAAAATCATAATCTCGTATCGCTCGTAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACCCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGACTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCCGCTTCAAGTTGTGGAGGAGGTGTTTGGTATTTGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAAGAGGTAGATTGTGGCCGGAAATGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTGACACGTCCCTTAGTTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTCTCTAAGCTAAATTGGTCTGTACACATCCCATACATTGTATTGGGGGCAATAATATCTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGTTGAAAAAAGGCCTACCTACAACGAACATCACTTTGAGCGCCCTCACATTTAAAAAATAGGAACGTCGTTCCAACAATCGAGCGCAAGGTTTCAAAGTTGAACTGAGAGTGTCTAGACAACAAAGTATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAAAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGCCAAACTATTCAGGGGTGGAAGGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAATCTCTTTCCTCATTTATTTCAAAATCCGAATTCCACAATTGAGTCACCGCTGTGGGCATTGAGAGTCATCCTTGCAGCAGGGATACAAGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAACGGATTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGATCCTCGACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGAGCTAACTCATATATGCTGACTCAATAGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATCATATGAATAAGCATTTTATCACCAGAAACCTTATATACTAAATGGTTAATTGTAACTGAATCCGCAGGTCACATGTGTTAGGTTTCACAGATTCTGTATATTACTAACTCTATACTCGTAATTAACATTAGATAAGTAGATTAAGAAAAAAGCCTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGAAATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCGGACGCTAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACCAAGTTCTTGAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTGTCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAGATCATCAAGTACACAATGCAAGATGCTCTCTTCTTGAAATACTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGATCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGTTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCAATGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGACTGGTATCAGGCATCAGTATTCAAAGAAGCAGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACGACTCTAATCTCAAAAATAGCAGAGATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGATCTGATGGGTATAAAATTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTAAAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAACAGCTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCCAAACATTATTTTGATAGCCAAGGGTCTTGGTACAGTGTTACTTCAGATAGGAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTACTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACCGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTTAGTACTAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTTGAGTATCTACTACCACAATATCGGAACTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACCTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTGGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACGCGAGTGATGATTTTGGTGAACATGCCACAGTTAGAGGGAGTAGTTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACCTTTTATCGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCACATAACCTCACACTGGAAAATCGAGACAACCCCCCCGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGGCGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGACGCAGACGAGCAGGAACAGAGTGCCGAAGACAATGCAGCGAGGGTGGCCGCTAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTAGCTAGTATAGGCACCGCTTTTGAGCGGTCCATTTCTGAGACACGACATATCTTTCCTTGCAGGATAACCGCAGCTTTCCATACATTTTTTTCGGTGAGAATCTTGCAATATCATCATCTCGGGTTCAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGTAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGATTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGCTTATTCCAGTTAAAAACTTATCTCCGAATGATTGGGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTCCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGCAGGACCATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTGTAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGATATCTTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACACCGGTTTTGGACAGACTGAGGAAAATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAACAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCTCATATTTTAGAGGGAAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGTTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCAAAGCAACCAGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCGTCCCGACTAAGCTGGACTATCGGGGATGGAATCCCTTACATTGGATCAAGGACAGAAGATAAGATAGGACAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAGCCATTTTTGGAAGCACGAGTAAATTTGAGTGTTCAAGAAATACTTCAAATGACTCCTTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAATTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCCGCTCAGTATTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTCGATAACCCATTTTTCCAAGGTAAACAGCTGAACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACCATCATGCAATCAATTATTTCAGATAGCAACAATTCATCTACAGACCCAATTAGCAGCGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAACACAATTCTTCGGACCAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGTGTTATGTCACGGTTAATGAGTATTGATCCTCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCTATTTCATCTTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCGCTAGAGGGTCAAAACCCAACACCTGTTAATAATTTTCTCTATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACGACAGGCTTTTAAAACTACCATAAGTGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCATCATTGGCATACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAATACTTGGCAAGAGACTCTTCAACTGAATCAAGCACAAACAACAGTGATGGTCATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAATCTAGTTCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAACACGCACCAGGGTCCGTCGTTCCAGTCCTTTCTAAGTGACTCTGCTTGTGGTACAGCAAATCCAAGACTAAATTTCGATCGATCGAGACACAATGTGAAATCTCAGGATCATAACTCGGCATCCAAGAGGGAAGGTCATCAAATAATCTCACACCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTGACGTCATCCAATGAGTCACAAACCCAAGACGAGATATCAAAGTACTTGCGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAGTTTTAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATAACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAAGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAACTGATCTTACACCATATTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGTTATGGCTAAATGATAATTTAGCCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGAAAGATGCCACACCAAAACCATCTCAGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGTGACTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCCACTAGTCTCTATCACTCAGCACTTAGCACATCTTAGAGCAGAGATTCGAGAATTAACTAATGATTATAATCAACAGCGACAAAGTCGAACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATCAGTGTGTGCAATAGGTTCTACCATATTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTGAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCGGATGGTCTCTACAGGTTTGATTGAATTACCGTGCATAGTATCCTGATACTTGCAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCCGATTTCAATAAACAACTATTTAAACAACGAAAGGAGTCCCTATATTATACACTATATTTAGCCTCTCTCCCTGCTTGATAATCAAAAAATTCACAATGCAGCATGTGTGACATATTACTGCCGCAATGAATTTAACGCAACATAATAAACTCTGCACTCTTTAGAATTAAGCTTTAACGAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTATATCAATATCCTGTCAGATGGAATAGTGTTTTGGTTGATAACACGACTTCTTAAAACAAAATTGATCTTTAAGATTAAGTTTTTTATAATTATCATTACTTTAATTTGTCGATTTAAAAATGGTGATAGACTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTCTTGTCTAGTAAGCTACTATTTCATACAGAATGATAAAATTAAAAGAAGAGGCAGGACTGTAAAATCATAAATACCTTCTTTACAATACAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGACATTGACCACGCTCATCAGAAGGCTCACCAAAATAAACGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n>Zaire_ebolavirus_isolate_EBOV/H.sapiens-tc/GAB/1996/Ilembe_complete_genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGATAGAGAACAGCCTAGGTCTCCGAAGGGAACAAGGGCACCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGTCTTATCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCCAACAACCCTAATAGAAAAATTATTGTTAACGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGATTTTGAACTTCAACACCTAGAGGATTGGAGATTCAACAACCCTAAAACTTGGGGTAAAACATTGGAAATAGTTGAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTTACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATCACAAACTTTTCTTGGAAAGTGGTGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAACGTGATGGGGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTTCTCTCTTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAAGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTCCTAATACACCAAGGGATGCACATGGTTGCCGGGCATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTTTATTGATTGTCAAAACAGTCCTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACTGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTATCGGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGCACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCTGCCACTGAAGCTGAGAAGCAACTCCAACAATATGCAGAATCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACCTTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTGGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGAAAACGGCATGAATGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACTAAGCCAGTGCCTAACAGATTGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCAGGCCAACTCAAAATGTCCCAGGCCCTCGCAGAACAATCCACCACGCCAGTGCTCCACTCACGGACAACGACAGAGGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATTAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGTCTTCCGCCCTTGGAGTCAGACGATGAAGAACAGGACAGGGACGAAACTTCCAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAAAGAAAGAACTCCCGCAAGATGAGCAGCAAGATCAGGACCACACTCAAGAGGCCAGGAACCAGGACAGTGACAACACCCAGCCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGACCATTTGATGCTGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACTAGTGATGGCAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTAATGAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGAATGGAATAATGGGATGATTTAACCGACAAATAGCTAACATTAAATAGTCAAGAAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAGGCGTTAAGCCACAGTTATAGCCATAATTGTAACTCAATATCTTAGCTAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGTCCAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCCGAGCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGTTACGCATCCCAAATGCAACAAACAAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAACTATCGCATCAGAATCATTAGAACAACGTATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCACTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCAATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCAGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAACTCATTGGATATCATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAGCTTGCGTCCAGTCCCGCCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTCCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCCCTTCCCTCCGAAAGAGGCGACCAATAGCAGAGGCTTCAACTGCTGAACTACAGGGTACGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAATTAAACGACCAAGCCAAAATTGTTCATATCCCGCTAGCAGCTTAAAATATAAATGAAATAGGAGCTATATCTCTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTCCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTACGAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAACAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCTAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTTGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCACTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCCTTCCTCCAGGAGTTCGTTCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGCTGCGTCCAGGAATTTCGTTTCATCCAAAACTTCGCCCCATTCTTTTACCTAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCAGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGATTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTATTTAGTAATCCGTCTATTAGAGGAGATACTTTTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTTTTTTCTCTCCTAAATGTAGAACTTAACAAAAGACTCACAATATACTTGTCTTAAAGAGATTGATTGATGAAAGATCATGACTAATAACATTACAAATAATCCTACTATAATCAATACGGTGATTCAAATATTAATCTTTCTAATTGCACATACTCTCTGCCCCTATCCTCAAATTGCCTACATGCCTACATCTGAGGATAGCCAGTGTGACTTGGATTGGAGATGTAGGGAAGAAATCGGAACCCATCTCCAGGTTGTTCACAATCCAAGCACAGACATCGCCCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGCAATCTTCATCTCTCTTAGATTATTTGTTTTCCAGAGTAGGGGTCATCAGGTCCTTTCCAATCATATAACCAAAATAAACTTCACTAGAAGGATATTGTGAGGCAACAACACAATGGGTATTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAGCACATTACAAGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCTCCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCGTGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCCAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACCAATGAGACGGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACGCCACAGTTTTTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAAAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGAGCCAAAGACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCTACACAACAACTGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAATCAAGGAAGGGAAGCTGCAGTGTCGCATCTGATAACCCTTGCCACAATCTCCACGAGTCCTCAATCCCCTACAACCAAACCAGGTCAGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCATCGCAGAACAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCCCAAAAGCAGAGAACATCAACACGAGCAAGAGCGCTGACTCCCTGGACCCCGCCACCACGACAAGTCCCCAAAACTACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCGGCAGCGGGAAGCTGGGCTTGATTGCCAATACTATTGCTGGAGTCGCAGGGCTGATCACAGGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAACCCCAATCTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACACAGAGGGGCTAATGCACAATCAAGATGGTTTAATCTGTGGATTGAGGCAGCTGGCCAATGAGACGACTCAAGCTCTTCAACTGTTCCTGAGAGCCACAACTGAGCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACTGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTGCAGTTATTGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGCAAAGCTCAGCCTCAAATCAATGAGATTAGGATTTAATTATATGGATCACTTGAATCTAAGATTACTTGACAAATGATAATATAATACACTGGAGCTTTAAATATAGCCAATGTGATTCTAACTCCTTTAAACTCACAATTAATCATAAACAAGGTTTGACATCAATCTAGTTATATCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAGTGACAAGGGAAAGAAGCCTTTTTAGTAAGTTGTAATAATCAGATCTGCGAACCGGTAGAGTTTAATTGCAACCTAACACACATAAAGCATTGGTCAAAAAGTCAATAGAAATTTAAACAGTGAGTGGAGACAACTTTCAAATGGAAGCTCCATACGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCATCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAGGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAAAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCAGGACCACAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTGAGGCGCGAGGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTCGAAGCTGCACTATGGCAACAATGGGATCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGATGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTCAATCAAGACGGTATCCTTTAAAACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATATGCATAATTGCTTTAATATATGAAGAGGTATGATACAACCCTAACAGTGATCAAAGAAAATCATAATCTCTTATCGCTCGTAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACTCTACAGGAGGTAGCAACGATCCATCCCATCAAAAAATAAGTATTTTATGACTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACACAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTTTGGTATTGGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAAGAGGTAGATTGTGACCGGAAACGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTGACACGTCTTTTAGCTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTCTCTAAGCTAAATTGGTCTGTACACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAACCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATCACTTTGAGCGCCCTTACAATTAAAAAATAGGAACGTCGTTCCAACAATTGAGCGCAAGGTTTCAAGGTTGAACTGAGAGTGCCTAAACACCAAAATATCGATAATTCAGACACCAAGCAAGACCTGAGAAGGAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCCTAGTTAGTCAAACTATTCAAGGGTGGAAGGTCTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAATCTATTTCCTCATTTATTTCAAAATCCGAATTCCACAATTGAGTCACCACTGTGGGCATTGAGAGTCATCCTTGCAGCAGGGGTACAGGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTTAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACCAATTGGATGCTCTACATGTCGTGAACTACAACGGGTTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATTATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAATTAAGATGGAATACTTCATATTGAGCTAACTCATATATGCTGACTCAATAGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTAACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATGAATAAGCATGTTATCACCAGAAATCCAATATACTAAATAGTTAATTGTAACTGAACCCGCAGGTCACGTGTGTTAGGTTTCACAGATTATATATATTACTAACTCCATACCCGTAATTAACATTAGATAAGTAGATTAAGAAAAACGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTAAAATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCAATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTGTCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGTCAACAGTTCTTAGATGAAATCATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAGGACTGTGTTGATGACCACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTCTTCTGGTATGACCTGGCTATTTTGACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCAATGTTACCCCTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGGCATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAGATAGCAGAGGTTGAGGATCCAGTTTGTTCTGATTATCCCGATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATGCGTGCACTAAAGCCTTCACAGGATCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCCACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATATTGTGTTTTTAAATATAGTATTGCAAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACTTCAGATAGGAATTTAACGCCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCCCCGTTGCCAATGATTAAAGAACTACTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACCGCAGTGGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTCAGTACTAAACGTGTACCAGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATACCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTCACAGAGCGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACCTTTTATAGAATATTGTAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCCCAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACTCTGGAAAATCGAGACAACCCCCCCGAAGGGCCCAGTTCATACAGAGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATAAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGACGCAGACGAGCAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGCACTGCTTTTGAACGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGGATAACCGCAGCTTTCCATACGTTTTTTTCGGTGAGAATCTTGCAACATCATCACCTCGGGTTCAATAAGGGTTTTGACCTTGGACAGTTGACACTTGGCAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATTTAGGAGATCCAGTTACCTCAGGCTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTCCCCGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTGCGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACTTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTGTAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGATATCTTTTCACGCACGCCCAGTGGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAAACACCGGTTTTGGACAGACTGAGGAAAATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCAGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTTCCATGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCAAAGCAACCTGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGACAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAACTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGATTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATCAATATAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAATTCAGCGACGCGATTGATTGTTTCTACTAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTATTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTCGATAACCCATTTTTCCAAGGTAAACGGCTAAACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACCATCATGCAATCAATTATTTCAGATAGCAACAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTATAAGTTATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGATCCTCATTTTTCTATTTACATAGGCGGTGCGGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTGCATTTATAAAAGAGTGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCGCTAGAGGGTCAAAACCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACAACAGGCTTTTAAAACTACCATAAGTGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGAAGCAGGCACAGAAACAGCAATCGAAAATACTTGGCAAGAGACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAATCTAGTCCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAGCACGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCTGCTTGTGGTACAGCAAATCCAAAACTAAATTTCGATAGATCGAGACATAATGTGAAATCTCAGGATCATAACTCGGCATCCAAGAGGGAAGGTCATCAAATAATCTCACACCGTCTAGTCCTACCTTTCTTTACATTGTCTCAAGGGACGCGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGACGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAGTTTTAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAACGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAATTCGGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTCAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAAAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAATTGATCTTACACCATATTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGTTATGGCTAAATGATAATTTAGCCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCCACTAGTCTCTATCACTCAGCACTTGGCACATCTTAGAGCAGAGATTCGAGAATTGACTAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTATCATATTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATCTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTCCCGGATGGTCTCTACAGGTTTGATTGAATTACCGTGCATAGTATCCTGATACTTGTGAAGGTTGATTATCAACGTACAGATTATAAAAAACTCACAAATTGCTCTCATACATCATATTGATCGAATTTCAATAAATAACTATTTAAATAACGAAAGAAGTCCTTATATTATACACTATATTTAGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATGCAGCATGTGTGACATATTACTTCCGCGATGAATCTAACGCAACATAATAAACTCTGCACTCTTTATAATTAAGCTTTAACAAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTGTATCAATATCCTGTCAGATGGAATAGTGTTTTGGTTGATAACACGACTTCTTAAAACAAAATTGATCTTCAAGATTAAGTTTTTTATAATTATCATTACTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTGTCTAGTAAGCTACTATTTCATACAGAATGATAAAATTAAAAGAAAAGGCATGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGACATTGACCACGCTCATCAGGAGGCTCGCCAGGATAAACGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n>Zaire_ebolavirus_isolate_H.sapiens-wt/GIN/2014/Gueckedou-C05_complete_genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCCAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAACATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCAACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCCGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAAGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGTACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATATGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGGATACGACCATTCCCGATGTGGTAGTTGATCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGAAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCAGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACTCACGGACAATGACAGAAGAAACGGACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAACGAAGAGGCAGACCCACTAGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAGAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAAGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAAAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAATGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCTAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGAGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAACCAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCAGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAACCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTTGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAATTAAACAACCAAGATAAAATTGTTCATATCTCGCTAGCAGCTTAAAATATAAATGTAATAGGAGCTATACCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCAACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCATCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCACCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAATCCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTCTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCATGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGCACATACTTTTTGCCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGATTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATATTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAGTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGCGACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTAATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCAGGGAAACTAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCCCAATCCCTCACAACCAAACCAGGTCCGGACAACAGCACCCATAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAGAACACCAACACGAGTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCAACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAATCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGAGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCAAATCAATGAAACTAGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAATGATAACATAATACACTGGAGCTTCAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCTAGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAAAAGTCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAGAGAGGACGCCCCCGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAGGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATCAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAATTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGCTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTACAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGAAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTTTAGCTGTATACCAGTGCCCCGAGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATCTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATTACTTTGAGCGCCCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGTCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAACCTATTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTGAGAGTCATCCTTGCAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGTCGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACCCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACCAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATTATTAAGTACACAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGATGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCAGTTTGCTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTAAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAACAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTTTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGGAATCTAACGCCGGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTGCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTGGGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAATTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAGCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACACTGGAAAATCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGACGAGCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCTCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTGTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACAATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGGAGTCTATGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAAGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCATCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGGCAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTATTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTCGATAATCCATTTTTCCAAGGTAAACAGCTGAACATTATAGAAGATGACCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAATAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGATTAATGAGTATTGATCCCCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGTCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGCAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTCATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTGAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGATGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTACATAAATTGATCTTACACCATGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGCTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTCAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCACATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGGTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTTGTAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGATAACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATAATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTTGCCAGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAAGATTAAGTTTTTTATAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAAAAGACATGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAATGATAATTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n>Zaire_ebolavirus_strain_Zaire_1995_complete_genome\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAATTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTTCAGAGCCACATCACAAAGATAGAGAACAACCTAGGTCTCTGAAGGGAGCAAGGGCATCAGTGTGCTCAGTTGAAAATCCCTTGTCAACATCTAGGTCTTATCACATCACAAGTCCCACCTCAGACTCTGCAGGGTGATCCAACAACCTTAATAGAAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAATTAACCTTGGTTTTGAACTTGAATACTTAGAGGATTGGAGATTCAACAACCCTAAAGCTTGGGGTAAAACATTGGAAATAGTTAAAAGACAAATTGCTCGGAATCACAACATTCCGAGTATGGATTCTCGTCCTCAGAAAGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCGTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAGATTTGCCAACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTTTGTCTTCATCATGCGTACCAGGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAGGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGTATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACAACTGAAGCTAATGCCGGTCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGTCTTGAGAAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGTAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTCCTAATACACCAAGGGATGCACATGGTTGCCGGGCATGATGCCAACGACGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTTTTTCAGGTTTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGCGGAGTTCGTCTCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTGGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATGGTCTTTTCCCTCAACTATCAGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGTACCCTCGCAGGAGTAAATGTTGGAGAACAGTATCAACAACTCAGAGAGGCTGCCACTGAGGCTGAGAAGCAACTCCAACAATACGCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATCAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGAGCGCCTGGCCAAGCTGACGGAAGCTATCACTGCTGCGTCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATTCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCAACTGACTCACAAGATACGACCATTCCTGATGTGGTGGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGAAAACGGCATGAATGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGATGAGGACACTAAGCCAGTGCCTAATAGATCAACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGACAGACACAATCCAGGCCAACTCAAAATGTCCCAGGCCCTCACAGAACAATCCACCACGCCAGTGCTCCACTCACGGATAATGACAGAAGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATCAACGAAGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCCTGGAGTCAGACGATGAAGAACAGGACAGGGACGGAACTTCCAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCACTCTGAAAAGAGAGAACTCCCGCAAGATGAGCAACAAGATCAGGACCACACTCAAGAGGCCAGGAACCAGGACAGTGACAACACCCAGCCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGCCATTTGATGCTGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAAAGAGTACACGTATCCAGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCTATGAATGAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTAATGAATCACAAGAATAAATTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAACAATGGGATGATTCAACCGACAAATAGCTAACATTAGGTAGTCAAGGAACGAAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAATAAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTCCAATTTGAGTCTTAATGCAAATAGGCGTTAAGCCACAGTTATAGCCATAATTGTAACTCAATATCCTAACTAGCGATTTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTACCCAACATTTACACGATCATTTTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGCACTCGAAGCTTATTGTCCTCAATGTAAAAGAAAAGCTGGTCTAACAAGATGACAACCAGAACAAAGGGCAGGGGCCACACTGCGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGAGCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGCTACGCATCCCAAATGCAACAAACCAAGCCAAACCCGAAGACGCGCAACAGTCAAACCCAAACGGACCCAATTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTAGCTTCATTGGCTACTGTTGTGCAACAACAAACCATTGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATGGCTAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGACAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCCGAACATGGTCAACCACCACCTGGACCATCACTTTATGAAGAAAGTGCAATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAAAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTGACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCAATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAGGCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCCAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAGCTTGCGTCCAGTCCCACCATCGCCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAAACACTTGGACTCAAAATTTGAGCCCATCTTCCTTCCCTCCGAAAGAGGCGACTAATAGCAGAGGCTTCAACTGCTGAACTATAGGGTACGTTACATTAATGATACACTTGTGAGTATCAGCCCTGGATAATATAAGTCAATTAAACGACCAAGATAAAATTGTTCTTATCTCGCTAGCAGCTTAAAATATGAATGTAATAGGAGCTATATCTCTGACAGTATTATAATCAATCGTTATTAAGTAACCCAAACCAAAAGTGATGAAGATTAAGAAAAACCTACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATATGAGGCGGGTTATATTACCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCAACAATTGCTAGAGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCATCGAATCCACTCAGGCCAATTGCCGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATCAGCATTCATCCTTGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATTTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACAACGGCCGCCATCATGCTTGCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCACTTGTCAGAGTCAATCGGCTGGGTCCTGGAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCCTTCCTCCAGGAGTTCGTTCTTCCGCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTGCTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGTTGCGCCCAGGGATTTCATTTCATCCAAAACTTCGCCCCATTCTTTTACCCAACAAGAGTGGGAAGAAGGGGAATAGTGCCGATCTAACATCTCCGGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATATCATGGGAATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGGACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGTTTGGACCCGGTGGCTCCAGGAGACCTCACCATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCGAGTCTTCCAGCTGTGATTGAGAAGTAATTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTATTTAGTAATCCGTCCATTAGAGGAGATACTTTTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTTTTTCCTCTCCTAAATGTAGAACTTAACAAAAGACTCATAATATACTTGTTTTTAAAAGATTGATTGATGAAAGATCATAACTAATAACATTACAAATAATCCTACTATAATCAATACGGTGATCCAAATGTTAATCTTTCTCATTGCAAATACTCTTTGCCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGATAGCCAGTGTGACTTGGATTGGAGATGTGGAGAAAAAATCGGGACCCATTTCTAGGTTGTTCACCATCCAAGTACAGACATTGCCCTTCTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATTTGTCCTCCAGAGTAGGGATCGTCAGGTCCTTTTCAATCGTATAACCAAAATAAACTTCACTAGAAGGATATTGTGGGGCAACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACATCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAGCACATTACAGGTTAGTGAGGTCGACAAACTGGTTTGCCGTGACAAACTGTCATCCACAAATCAATTGAGATCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCTTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCTTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGGTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCGTGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTGCTTTCTTCCTGTATGACCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGTTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAATGCAACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAAGCTACCGGTTTTGGAACCAATGAGACAGAGTATTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACAGTTTCTGCTCCAGCTGAATGAGACAATATATACAAGTGGGAAAAGGAGCAATACCACGGGAAAACTAATTTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAAACCTCACTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACAGAGCCAAAAACATCAGTGGTCAGAGTCCGGCGCGAACTTCTTCCGACCCAGGGACCAACACAACAACTGAAGACCACAAAATCATGGCTTCAGAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTGACAACCCTTGCCACAATCTCCACGAGTCCTCAACCCCCCACAACCAAACCAGGTCCGGACAACAGCACCCACAATACACCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGACAGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCCCAAAAGCAGAGAACACCAACACGAGCAAGGGTACCGACCTCCTGGACCCCGCCACCACAACAAGTCCCCAAAACCACAGCGAGACCGCTGGCAACAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATACTATTGCTGGAGTCGCAGGACTGATCACAGGCGGGAGGAGAGCTCGAAGAGAAGCAATTGTCAATGCTCAACCCAAATGCAACCCTAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGACTGGCCTGGATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACACAGAGGGGCTGATGCACAATCAAGATGGTTTAATCTGTGGGTTGAGACAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTGTTCCTGAGAGCCACAACCGAGCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGCCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATCAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATGGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTGCAGTTATCGCTTTATTCTGTATATGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGCAAAGCTCAGCCTCAAATCAATGAAACCAGGATTTAATTATATGGATTACTTGAATCTAAGATTACTTGACAAATGATAATATAATACACTGGAGCTTTAAACATAGCCAATGTGATTCTAACTCTTTTAAACTCACAGTTAATCATAAATAAGGTTTGACATCAATCTAGTTATCTCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAATCTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTGTAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGATCAAAAAGTCAATAGAAATTTAAACAGTGAGTGGAGACAACTTTTAAATGGAAGCTTCATATGAGAGAGGACGCCCACGAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAATTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGAGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTGTGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAGAGTTTAACTGATAGGGAATTACTCCTACTAATCGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAAATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACTCTGATCAAGACGGCAGAACACTGGGCGAGACAAGACATCAGAACCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGTGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGTGAGGGGCTTGGGCAAGATCAGGCAGAACCTGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAGTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAATATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAATCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGGCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATTATCATATATTTAATCAAGACGATATCCTTTAAGACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATGTGCATGATTGCCCTAATATATGAAGAGGTATGATACAACCCTAACAGTGACCAAAGAAAATCATAATCTCGTATCGCTCGTAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACCCTACAGGAGGTAGCAACGATCCATCCCATCAAAAAATAAGTATTTTATGACTTACTAATGACCTCTTAAAATATTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTGTTTGGTATTGGCTATTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAAGAGGTAGATTGTGGCTGGAAATGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCCCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTGACACGTCTCTTAGCTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTCTCTAAGCTAAATTGGTCTGTACACATCTCATACATTGTATTAGGGACAATAATATCTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCTGGGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCTACCTACAACGAACATCACTTTGAGCGCCCTCACATTTAAAAAATAGGAACGTCGTTCCAACAATCGAGCGCAAGGTTTCAAGGTTGAACTGAGAGTGTCTAGACAACAAAGTATCGATCCTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCTAAAGCTACGGGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTTCTTAGTTAGCCAAACTATTCAGGGGTGGAAGGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAAGGAATGGCCCTATTGCAAAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAATCTCTTTCCTCATTTATTTCAAAATCCGAATTCCACAATTGAATCACCGCTGTGGGCATTGAGAGTCATCCTTGCAGCAGGGATACAAGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAGATTGGATGCTCTACATGTCGTGAACTACAACGGATTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGATCCTCAACACGAATGCAAAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGAGCTAACTCATATATGCTGACTCAATAGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAATAAATACGCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATCATATGAATAAGCATTTTATCACCAGAAATCTTATATACTAAATGGTTAATTGTAACTGAACCCGCAGGTCACATGTGTTAGGTTTCACAGATTTTATATATTACTAACTCTATACTCGTAATTAACATTAGATAAGTAGATTAAGAAAAAAGCCTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGAAATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCGGACGCTAGGTTATCATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCATACTCCCTTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACCAAGTTCTTGAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCACTGTCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATCATTAAGTACACAATGCAAGATGCTCTCTTCTTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGACCACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATGATCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACATGGTTTGTTCATGATGATTTAATAGACATCTTAGGTTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCAATGTTACCACTGAACACACAAGGAATCCCCCATGCTGCTATGGACTGGTATCAGGCATCAGTATTCAAAGAAGCGGTTCAAGGGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCGATTCAACACAACTCTAATCTCAAAAATAGCAGAGATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTTAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAATTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACCGAGAGGAAGGGCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTAAAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAACAGCTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCAAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCCAAACATTATTTTGATAGTCAAGGGTCTTGGTACAGTGTTACTTCAGATAGGAATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACTACTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATTTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAGGATATAATCCACCTCACAAATTTAGTACTAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTCTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAACTTTTCTTTCTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACCTTCGGAAAATTGCCTTATCCGACTCGCAATGTTCAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTACGGAACGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAACATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGTTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTATACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCACATAACCTCACACTGGAAAATCGAGACAACCCCCCCGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAAAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTACGCTCAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGACGCAGACGAGCAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCCGCTAGCCTAGCAAAAGTTACAAGTGCCTGTGGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTTGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTTGATGATCTTCAAGGGACCCTAGCTAGTATAGGCACTGCTTTTGAGCGATCCATCTCTGAGACACGACATATCTTTCCTTGCAGGATAACCGCAGCTTTCCATACGTTTTTTTCGGTGAGAATCTTGCAATATCATCATCTCGGGTTCAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGTAAACCTCTGGATTTCGGAACAATATCATTGGCACTAGCGGTACCGCAGGTGCTTGGAGGATTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGAATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGATTTATTCTTACCTTTAATTGCAAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGCGGATTAAATGTCCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGCAGGACCATCACCCTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTGTAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGATATCTTTTCACGCACGCCGAGCGGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAGGATCATCAACAATAATACAGAGACACCGGTTTTGGACAGACTGAGGAAAATAACATTGCAAAGGTGGAGTCTGTGGTTTAGTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCACAGATCCTGAGGGAATATTCATGGGCTCATATTTTAGAGGGAAGACCTCTTATTGGAGCCACACTCCCATGTATGATTGAGCAATTCAAAGTGTTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCAAAGCAACCAGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCTAACGCATCCCGACTAAGCTGGACTATCGGGGATGGAATCCCTTACATTGGATCAAGGACAGAAGATAAGATAGGACAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAACATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAGCCATTTTTGGAAGCACGAGTAAATTTAAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATCAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAATTCAGCAACGCGATTGATTGTTTCTACAAACACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCCAGAATGTTATAAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTGCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTATTTAACATACACATCTACATTGGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTCAATTGCAATATCTCATTCGATAACCCATTTTTCCAAGGTAAACAGCTGAACATTATAGAAGATGATCTTATTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACCATCATGCAATCAATTATTTCAGATAGCAACAATTCATCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCCAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTAAGAAATTGACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATTGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGATCCTCATTTTTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGTCTATTTCATCTTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGATAGTATATCCGCTAGAGGGTCAAAACCCAACACCTGTTAATAATTTTCTCTATCAGATCGTAGAACTGCTGGTGCATGATTCATCAAGACAACAGGCTTTAAAAACTACCATAAGTGATCATGTACATCCTCACGACAATCTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCATCATTGGCGTACTGGAGGAGCAGGCACAGAAACAGCAACCGAAAATACTTGGCAAGAGACTCTTCAACTAGATCAAGCACAAACAACAGTGATGGTCATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAATCTAGTTCTACAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAACACGCACCAGGGTCCGTCGTTCCAGTCCTTTCTAAGTTACTCTGCTTGTGGTACAGCAAATCCAAAACTAAATTTCGATCGATCGAGACACAATGTGAAATCTCAGGATCATAACTCGGCATCCAAGAGGGAAGGTCATCAAATAATCTCACACCGTCTAGTCCTACCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCTAATGAGTCACAGACCCAAGACGAGATATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTCTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAGTTTTAAGTCGGCTGTGACGCTAGCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACACGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCTGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACATAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAAGCAAGTCGAGGTTATAACCATGGATGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAACTGATCTTACACCATATTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTCCTAAGTGATACTGAGGGTATGTTATGGCTAAATGATAATTTAGCCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATCTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGAAAGATGCCACACCAAAACCATCTCAGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATTTAACTCAGTATGCTGACTGTGATTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGTACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCCACTAGTCTCTATCACTCAGCACTTAGCACATCTTAGAGCAGAGATTCGAGAATTAACTAATGATTATAATCAACAGCGACAAAGTCGAACTCAAACATATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTATTGTGCAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTGTGCAATAGGTTCTACCATATTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTACATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCGGATGGTCTCTACAGGTTTGATTGAATTACCGTGCATAGTATCCTGATACTTGCAAAGGTTGGTTATCAACATACAGATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCTGATTTCAATAAACAACTATTTAAATAACGAAAGGAGTCCCTATATTATACACTATATTTAGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACAATGCAGCATGTGTGACATATTAATGCCGCAATGAATTTAACGCAACATAATAAACTCTGCACTCTTTATAATTAAGCTTTAACGAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTATATCAATGTCCTGTCAGATGGAATAGTGTTTTGGTTGATAACACGACTTCTTAAAACAAAATTGATCTTTAAGATTAAGTTTTTTATAATTATCATTACTTTAATTTATCGATTTGAAAATGGTAATAGCCTTAATCTTTGTGTAAAATAAGAGATTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGTTACTATTTCATACAGAATGATAAAATTAAAAGAAAAGGCAGGACTGTAAAATCATAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTTGTGTTAATGATAATTAAGACATTGACCACGCTCATCAGAAGGCTCGCCAAAATAAACGTTGCAAAAAGGATTCCTGGAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCAA\n" }, { "path": "tests/input/ebov-makona.fasta", "content": ">KJ660346.2\nCGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAA\nTTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCATACCTGGTTTGTTT\nCAGAGCCATATCACCAAGATAGAGAACAACCTAGGTCTCCGGAGGGGGCAAGGGCATCAGTGTGCTCAGT\nTGAAAATCCCTTGTCAACATCTAGGCCTTATCACATCACAAGTTCCGCCTTAAACTCTGCAGGGTGATCC\nAACAACCTTAATAGCAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAA\nTTAACTTTGATTTTGAACCTGAACACCCAGAGGACTGGAGACTCAACAACCCTAAAGCCTGGGGTAAAAC\nATTAGAAATAGTTTAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAA\nGTCTGGATGACGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG\nTTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAGGAAATTTGCCA\nACTTATCATACAGGCCTTTGAAGCTGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTT\nTGTCTTCATCATGCGTACCAAGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAG\nGGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGT\nATCTAGTGGGAGAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACGACTGAAGCTAATGCC\nGGTCAGTTCCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGA\nAGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGT\nAGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTTTGATCAAATTTCTTCTAATACACCAA\nGGGATGCACATGGTTGCCGGACATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTT\nTTTCAGGTCTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCT\nCCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTCAAGGCTGCACTCAGCTCCCTG\nGCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATG\nGTCTTTTCCCTCAACTGTCGGCAATTGCACTCGGAGTCGCCACAGCCCACGGGAGCACCCTCGCAGGAGT\nAAATGTTGGAGAACAGTATCAACAGCTCAGAGAGGCAGCCACTGAGGCTGAGAAGCAACTCCAACAATAT\nGCGGAGTCTCGTGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATC\nAGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCGATGGTAACTCTAAGAAAAGAGCGCCTGGCCAA\nGCTGACAGAAGCTATCACTGCTGCATCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATT\nCCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGG\nATACGACCATTCCCGATGTGGTAGTTGATCCCGATGATGGAGGCTACGGCGAATACCAAAGTTACTCGGA\nAAACGGCATGAGTGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACCAAGCCA\nGTGCCTAACAGATCGACCAAGGGTGGACAACAGAAAAACAGTCAAAAGGGCCAGCATACAGAGGGCAGAC\nAGACACAATCCACGCCAACTCAAAACGTCACAGGCCCTCGCAGAACAATCCACCATGCCAGTGCTCCACT\nCACGGACAATGACAGAAGAAACGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACCCCAATCAACGAA\nGAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTAGAGTCAGATGATGAAG\nAACAGGACAGGGACGGAACTTCTAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCA\nCTCCGAAAAGAAAGAACTCCCGCAAGATGAACAACAAGATCAGGACCACATTCAAGAGGCCAGGAACCAA\nGACAGTGACAACACCCAGCCAGAACATTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGC\nCATTTGATGCCGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGTAA\nAGAGTACACGTATCCGGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCCATGAAT\nGATGAGAATAGATTTGTTACACTGGATGGTCAACAATTTTATTGGCCAGTAATGAATCACAGGAATAAAT\nTCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGTAATAATGGGATGATTTAATCGACAAATAGCT\nAACATTAAATAGTCAAGGAACGCAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAAT\nAAAAGTGATTCTTAGTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGA\nGTCTTAATGCAAATAAGCGTTAAGCCACAGTTATAGCCATAATGGTAACTCAATATCTTAGCCAGCGATT\nTATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTT\nTATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGC\nACTAGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGCCTAACAAGATGACAACTAGAACAAAGGGCA\nGGGGCCATACTGTGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGA\nGCAGCTAATGACCGGAAGGATTCCTGTAAACGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGC\nTACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGATGCGCAACAGTCAAACCCAAACGGACCCAA\nTTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAAC\nCATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATG\nGCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGA\nCAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCTGAACATGGTCAACCACCACC\nTGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACTGTCCCTCAA\nAGTGTTAGGGAGGCATTCAACAATCTAGACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTG\nACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCA\nATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAATTCATTGGACATTATTCATGCTGAGTTCCAG\nGCCAGCCTGGCTGAAGGAGACTCCCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCC\nAAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAGAGCTT\nGCGTCCAGTCCCACCATCACCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAA\nACACTTGGACTCAAAATTTGAGCCAATCTCTTTTCCCTCCGAAAGAGGCAACTAATAGCAGAGGCTTCAA\nCTGCTGAACTATAGGGTATGTTACATTAATGATACACTTGTGAGTATCAGCCCTAGATAATATAAGTCAA\nTTAAACAACCAAGATAAAATTGTTCATATCCCGCTAGCAGCTTTAAAGATAAATGTAATAGGAGCTATAC\nCTCTGACAGTATTATAATTAATTGTTATTAAGTAACCCAAACCAAAAATGATGAAGATTAAGAAAAACCT\nACCTCGACTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATAT\nGAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGCCAGGTCAAATTCA\nACAATTGCTAGGGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGAGACACTCCAT\nCGAATCCACTCAGGCCAATTGCTGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATC\nAGCATTCATCCTCGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATT\nTGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTG\nCTTCATATACTATCACCCATTTCGGCAAGGCAACCAATCCGCTTGTCAGAGTCAATCGGCTGGGTCCTGG\nAATCCCGGATCACCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCA\nCCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACTCAACCACTGCCTG\nCTGCAACATGGACCGATGACACTCCAACTGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCC\nAAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCG\nGAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATA\nTCATGGGTATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCCAAAAATGG\nACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACC\nATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGGTTGAGAAGTAAT\nTGCAATAATTGACTCAGATCCAGTTTTACAGAATCTTCTCAGGGATAGTGATAACATCTTTTTAATAATC\nCGTCTACTAGAAGAGATACTTCTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTCTTTTCTC\nTCCTAAATGTAGAGCTTAACAAAAGACTCATAATATACCTGTTTTTAAAAGATTGATTGATGAAAGATCA\nTGACTAATAACATTACAAACAATCCTACTATAATCAATACGGTGATTCAAATGTCAATCTTTCTCATTGC\nACATACTCTTTGTCCTTATCCTCAAATTGCCTACATGCTTACATCTGAGGACAGCCAGTGTGACTTGGAT\nTGGAGATGTGGAGGAAAAATCGGGGCCCATTTCTAAGTTGTTCACAATCTAAGTACAGACATTGCTCTTC\nTAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATT\nTGTCTTCCAGAGTAGGGGTCATCAGGTCCTTTTCAATTGGATAACCAAAATAAGCTTCACTAGAAGGATA\nTTGTGAGGCGACAACACAATGGGTGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACAT\nCATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCGCTTGGAGTTATCCACAATAG\nTACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGA\nTCAGTTGGACTGAATCTCGAGGGGAATGGAGTGGCAACTGACGTGCCATCTGCGACTAAAAGATGGGGCT\nTCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCT\nTGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGG\nTGCCGGTATGTGCACAAAGTATCAGGAACGGGACCATGTGCCGGAGACTTTGCCTTCCACAAAGAGGGTG\nCTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGT\nTGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAAT\nGCAACGGAGGACCCGTCGAGTGGCTATTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACTA\nATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACA\nGTTTCTGCTCCAGCTGAATGAGACAATATATGCAAGTGGGAAGAGGAGCAACACCACGGGAAAACTAATT\nTGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCAC\nTAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGCTGTATCAAACGGACCCAAAAACATCAGTGGTCAG\nAGTCCGGCGCGAACTTCTTCCGACCCAGAGACCAACACAACAAATGAAGACCACAAAATCATGGCTTCAG\nAAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGAAAGCTGCAGTGTCGCATCTGACAACCCT\nTGCCACAATCTCCACGAGTCCTCAACCTCCCACAACCAAAACAGGTCCGGACAACAGCACCCATAATACA\nCCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGGACAACATCACCGTAGAGCAGACAACGACA\nGCACAGCCTCCGACACTCCCCCCGCCACGACCGCAGCCGGACCCTTAAAAGCAGAGAACACCAACACGAG\nTAAGAGCGCTGACTCCCTGGACCTCGCCACCACGACAAGCCCCCAAAACTACAGCGAGACTGCTGGCAAC\nAACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATA\nCTATTGCTGGAGTAGCAGGACTGATCACAGGCGGGAGAAGGACTCGAAGAGAAGTAATTGTCAATGCTCA\nACCCAAATGCAACCCCAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGATTGGCCTGG\nATACCATATTTCGGGCCAGCAGCCGAAGGAATTTACACAGAGGGGCTAATGCACAACCAAGATGGTTTAA\nTCTGTGGGTTGAGGCAGCTGGCCAACGAAACGACTCAAGCTCTCCAACTGTTCCTGAGAGCCACAACTGA\nGCTGCGAACCTTTTCAATCCTCAACCGTAAGGCAATTGACTTCCTGCTGCAGCGATGGGGTGGCACATGC\nCACATTTTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATC\nAGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATG\nGAGACAATGGATACCGGCAGGTATTGGAGTTACAGGTGTTATAATTGCAGTTATCGCTTTATTCTGTATA\nTGCAAATTTGTCTTTTAGTCTTTCTTCAGATTGTTTCACGGCAAAACTCAACCTCAAATCAATGAAACTA\nGGATTTAATTATATGAATCACTTGAATCTAAGATTACTTGACAAATGATAACATAATACACTGGAGCTTC\nAAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCT\nAGCTATATCTTTAAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAGTC\nTTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAATGAAAAAGGAAAAAAGCCTTTTTATTAAGTTG\nTAATAATCAGATCTGCAAACCGGTAGAATTTAGTTGTAACCTAACACACACAAAGCATTGGTAAAAAAGT\nCAATAGAAATTTAAACAGTGAGTGCAGACAACTCTTAAATGGAAGCTTCATATGAGAGAGGACGCCCCCG\nAGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAAT\nTATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGA\nGAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTG\nTGACAGTAGTTTTTGCAAAAAAGACCACCAGTTAGAAAGTTTAACTGATAGGGAATTACTCCTACTAATC\nGCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAA\nATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGC\nAGAACACTGGGCGAGACAAGACATCCGAACCATAGAGGATTCCAAATTAAGGGCATTGTTAACTCTATGT\nGCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTGTGTGAGACACACCTAAGGCGCGAAG\nGGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAG\nTTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAAT\nATCGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAAT\nCAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGG\nCTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATC\nAAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCATTTCAAATTGATAAGATATGCATAA\nTTGCCTTAATATATAAAGAGGTATGATATAACCCAAACATTGACCAAAGAAAATCATAATCTCGTATCGC\nTCGCAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTGACTCTA\nCAGGAGGTAGCAACGATCCATCTCATCAAAAAATAAGTATTTTATGATTTACTAATGATCTCTTAAAATA\nTTAAGAAAAACTGACGGAACATAAATTCTTTCTGCTTCAAGTTGTGGAGGAGGTCTATGGTATTCGCTAT\nTGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAGGAGGTATATTGTGACCGGA\nAAAGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATGAGAATAAACCTTATTATTCAGATTAGGCC\nCCAAGAGGCATTCTTCATCTCCTTTTAGCAAAATACTATTTCAGGATAGTCCAGCTAGTGACACGTCTTT\nTAGCTGTATACCAGTTGCCCCTGAGATACGCCACAAAAGTGTCTCTGAGCTAAAGTGGTCTGTACACATC\nTCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCATTTAAAATTTAGTGCATAAATCTGG\nGCTAACTCCACCAGGTCAACTCCATTGGCTGAAAAGAAGCCCACCTACAACGAACATTACTTTGAGCGCC\nCTCACAATTAAAAAATAAGAGCGTCGTTCCAACAATCGAGCGCAAGGTTACAAGGTTGAACTGAGAGTGT\nCTAGACAACAAAATATCGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCCAAAGCTACGG\nGACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTT\nCTTAGTTAGTCAAACTATTCAAGGGTGGAAAGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAA\nGGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAACCTAT\nTTCCCCATTTATTTCAAAATCCGAATTCCACTATTGAATCACCGCTGTGGGCACTGAGAGTCATCCTTGC\nAGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATC\nTCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGA\nGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGT\nCGTGAACTACAATGGATTATTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGA\nACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGC\nCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCA\nAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGGAATACTTCATATTGGGCTAAC\nTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAAT\nAAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTG\nACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCT\nTTATTATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACCCGC\nAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCGTAACTAACATTAGATAA\nGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGA\nAGCAGTTGACATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTAT\nCATCACCAATTGTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCGGGTTGTATTCATCATACTCCCT\nTAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATATACCGTTTAAAATATGATGTAACTGTTACC\nAAGTTCTTAAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAATTCTTCTCAAGGCAC\nTATCAGGCAATGGGTTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATTATTAAGTACAC\nAATGCAAGATGCTCTCTTCCTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAC\nCACTTTCAAGAAAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATG\nACCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACGTGGTTTGTTCATGA\nTGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCACTGTTACCACTG\nAACACACAAGGAATCCCCCATGCTGCTATGGATTGGTATCAGACATCAGTATTCAAAGAAGCGGTTCAAG\nGGCATACACACATTGTTTCTGTTTCTACTGCCGATGTCTTGATAATGTGCAAAGATTTAATTACATGTCG\nATTCAACACAACTCTAATCTCAAAAATAGCAGAGGTTGAGGACCCAGTTTGCTCTGATTATCCCAATTTT\nAAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAA\nTCATTAAGTTTCTCGAACCATTGTGCTTGGCTAAAATTCAATTGTGCTCAAAGTACACCGAGAGGAAGGG\nCCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTGGAAGAAATTACAGAAATACGTGCACTA\nAAGCCTTCACAGGCTCACAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAAC\nAACTTTGTGAGCTATTTTCCATACAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCA\nAAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATCGTGATTTTCGAGACATATTGTGTT\nTTTAAATATAGCATTGCAAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACCTCAGATAGAA\nATCTAACACCAGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACT\nGCTATGGGAATTTTACCACCTTGACCATCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATT\nTTTATAAAAGACAGAGCTACTGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTGG\nGATATAATCCACCTCACAAATTCAGTACCAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTC\nTATTGAGAATGTTCTTTCCTACGCGCAAAAACTCGAGTATCTACTACCACAATATCGGAATTTTTCTTTC\nTCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACTTTCGGAAAATTGCCTTATCCGACTCGCAATGTTC\nAAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTAC\nGGAACGTGAACAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTCGGTGAG\nCATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGGTATGAGT\nTTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTA\nTACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCGCATAACCTCACACTGGAAAAT\nCGAAACAACCCCCCTGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAA\nAACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTGCGCTC\nAGCTGTGATGGGTGACAATCAGTGCATTACCGTTTTATCAGTCTTCCCCTTAGAGACTGATGCAGGCGAG\nCAGGAACAGAGCGCCGAGGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTG\nGAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTT\nGAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTT\nGATGATCTTCAAGGGACCCTGGCTAGTATAGGTACTGCTTTTGAGCGATCCATCTCTGAGACACGACATA\nTCTTTCCTTGCAGAATAACCGCAGCTTTCCATACGTTCTTTTCGGTGAGAATCTTGCAATATCATCACCT\nCGGATTTAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCA\nTTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGA\nATCTAGGAGATCCAGTTACCTCAGGTTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGA\nTTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGC\nGGATTAAATGTTCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGTAGGACTATCACCC\nTAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCATCAGCTGACTTCGAAGACGAAATGGTTTG\nTAAGTGGCTCTTATCATCAACTCCTGTTATGAGTCGTTTCGCAGCCGATATATTTTCACGCACGCCGAGC\nGGGAAGCGATTGCAAATTCTAGGATACTTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACA\nATAATACAGAGACGCCGGTTTTGGACAGACTGAGGAAGATAACATTGCAAAGGTGGAGTCTATGGTTTAG\nTTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCA\nCAGATCCTGAGGGAATATTCATGGGCACATATTTTAGAGGGGAGACCTCTTATTGGAGCCACACTCCCAT\nGTATGATTGAGCAATTCAAAGTGGTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCCAA\nGCAACCTGGTGGGAAACCATTCGTGTCAGTAGCAGTCAAGAAACATATTGTTAGTGCATGGCCAAATGCA\nTCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGGC\nAACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAAC\nATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTA\nAGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCGGGAAATATTGTTCATAGGTACAACGATC\nAATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAACTCAGCAACGCGATTGATTGTTTCTACAAA\nCACTTTAGGTGAGTTTTCAGGAGGTGGCCAATCGGCACGCGACAGCAATATTATTTTCCAGAATGTTATA\nAATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAGTATAATCGTG\nCTCACCTTCATCTAACTAAGTGTTGCACCCGGGAGGTACCAGCTCAGTACTTAACATACACATCTACATT\nGGATTTAGATTTAACAAGATACCGAGAAAATGAATTGATTTATGACAATAATCCTCTAAAAGGAGGACTC\nAATTGCAATATCTCATTTGATAACCCATTTTTCCAAGGCAAACAGCTGAACATTATAGAAGATGACCTTA\nTTCGACTGCCTCACTTATCTGGATGGGAGCTAGCTAAGACCATCATGCAATCAATTATTTCAGATAGCAA\nTAATTCGTCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCC\nAAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTA\nAGAAATTAACACTTGACAATTTTTTATATTACTTAACTACCCAAATTCATAATCTACCACATCGCTCATT\nGCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGATTAATGAGTATTGATCCCCATTTT\nTCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGT\nCCATTTCATCTTTTCTTACATTTGTAAAGGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGAT\nAGTATATCCATTAGAGGGTCAAAATCCAACACCTGTTAATAATTTCCTCCATCAGATCGTAGAACTGCTG\nGTGCATGATTCATCAAGACACCAGGCTTTTAAAACTACCATAAATGATCATGTACATCCTCACGACAATC\nTTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCGTCATTGGCGTACTGGAGGAGCAGGCA\nCAGAAACAGCAACCGAAAAGACTTGACAAGAAACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGT\nCATATTAAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAGTCTAGTCCTGC\nAAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAGAACACGCACCAGGGTCCGTCGTTCCAGTC\nATTTCTAAGTGACTCTGCTTGCGGTACAGCAAACCCAAAACTAAATTTCGATAGATCGAGACACAATGTG\nAAATCTCAGGATCATAACTCAGCATCCAAGAGGGAAGGTCATCAAATAATCTCACATCGTCTAGTCCTAC\nCTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGATGAGAT\nATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGGTTTACCGGTATAGTC\nTCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAATTTTAAGTCGGCTGTGACGCTGG\nCAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACAC\nGCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCT\nGTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACA\nTAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAGGCAAGTCGAGGTTATAACCATGGA\nTGCAGAGACGACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTACATAAATTGATCTTACACCAT\nGTTGATCCCAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACCGAGGGTATGTTATGGC\nTAAATGATAATCTAGCCCCGTTTTTTGCCACTGGGTATTTAATTAAGCCAATAACGTCAAGTGCCAGGTC\nTAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTC\nAGTTGTAAGCAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGGAGCCCATACTGGCTAAGTCATT\nTAACTCAGTATGCTGACTGCGATTTACATTTAAGCTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGT\nACTATACCACAGGTATAACCTTGTCGATTCAAAAAGAGGTCCACTAGTCTCTGTCACTCAGCACTTAGCA\nCATCTTAGGGCAGAGATTCGAGAATTGACCAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACAT\nATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTAT\nTGTACAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTG\nTGCAATAGGTTCTATCATATTAGAGATTGTAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTAC\nATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCAGATGG\nTCTCTACAGGTTCGATTGAATAACCGTGCATAGTATTTTGATACTTGTAAAGGTTGGTTATCAACATACA\nGATTATAAAAAACTCATAAATTGCTCTCATACATCATCTTGATCTGATTTCAATAAATAACTATTTAGAT\nAACGAAAGGAGTCCTTACATTATACACTATATTTGGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACA\nATACAGCATGTGTGACATATTACTGCTGCAATGAGTCTAACGCAACATAATAAACTCCGCACTCTTTATA\nATTAAGCTTTAACGATAGGTCTGGGCTCATATTGTTATTGATATAGTAATGTTGTATCAATATCTTGCCA\nGATGGAATAGTGCTTTGGTTGATAACACGACTTCTTAAAACAAAACTGATCTTTAAGATTAAGTTTTTTA\nTAATTGTCATTGCTTTAATTTGTCGATTTAAAAATGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGAT\nTAGGTGTAATAACTTTAACATTTTTGTCTAGTAAGCTACTATTCCATTCAGAATGATAAAATTAAAAGAA\nAAGACATGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAA\nTGATAATTAAGGCATTGACCACGCTCATCAGAAGGCTCACTAGAATAAACGTTGCAAAAAGGATCCCTGG\nAAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA\n" }, { "path": "tests/input/empty.fasta", "content": "" }, { "path": "tests/input/ref.lasv.fasta", "content": ">gi|23343509|ref|NC_004296.1| Lassa virus segment S, complete sequence\nCGCACAGTGGATCCTAGGCTATTGGATTGCGCTTTGCTTTTGTCATTTTGGCAGATAGTCTCAGTTCTTT\nGTTGCGTGCATACAACACAACAATCTGGCGATGAGTGCCTCAAAGGAAATAAAATCCTTTTTGTGGACAC\nAATCTTTGAGGAGGGAATTATCTGGTTACTGCTCCAACATCAAACTACAGGTGGTGAAAGATGCCCAGGC\nTCTTTTACATGGACTTGACTTCTCCGAAGTCAGTAATGTTCAACGGTTGATGCGCAAGGAGAGAAGGGAT\nGACAATGATTTGAAACGGTTGAGGGACCTAAATCAAGCGGTCAACAATCTTGTTGAATTAAAATCAACTC\nAACAAAAGAGTATACTGAGAGTTGGGACTCTAACCTCAGATGACTTATTAATCTTAGCCGCTGATCTAGA\nGAAGTTAAAGTCAAAGGTGATCAGAACAGAAAGGCCATTAAGTGCAGGTGTCTATATGGGCAACCTAAGC\nTCACAGCAACTTGACCAAAGAAGAGCTCTCCTGAATATGATAGGAATGAGTGGTGGTAATCAAGGGGCTC\nGGGCTGGGAGAGATGGAGTGGTGAGAGTTTGGGATGTGAAAAATGCAGAGTTGCTCAATAATCAGTTCGG\nGACCATGCCAAGTCTGACACTGGCATGTCTGACAAAACAGGGGCAGGTTGACTTGAATGATGCAGTACAA\nGCATTGACAGATTTGGGTTTGATCTACACAGCAAAGTATCCCAACACTTCAGACTTAGACAGGCTGACTC\nAAAGTCATCCCATCCTAAATATGATTGACACCAAGAAAAGCTCTTTGAATATCTCAGGTTATAATTTTAG\nCTTGGGTGCAGCTGTGAAGGCAGGAGCTTGCATGCTGGATGGTGGCAATATGTTGGAGACAATCAAGGTG\nTCACCTCAGACAATGGATGGTATCCTCAAATCCATTTTAAAGGTCAAGAAGGCTCTTGGAATGTTCATTT\nCAGACACCCCTGGTGAAAGGAATCCTTATGAAAACATACTCTACAAGATTTGTTTGTCAGGAGATGGATG\nGCCATATATTGCATCAAGAACCTCAATAACAGGAAGGGCCTGGGAAAACACTGTCGTTGATCTGGAATCA\nGATGGGAAGCCACAGAAAGCTGACAGCAACAATTCCAGTAAATCCCTGCAGTCGGCAGGGTTTACCGCTG\nGGCTTACCTATTCTCAGCTGATGACCCTCAAGGATGCAATGCTGCAACTTGACCCAAATGCTAAGACCTG\nGATGGACATTGAAGGAAGACCTGAAGATCCAGTGGAAATTGCCCTCTATCAACCAAGTTCAGGCTGCTAC\nATACACTTCTTCCGTGAACCTACTGATTTAAAGCAGTTCAAGCAGGATGCTAAGTACTCACATGGGATTG\nATGTCACAGACCTCTTCGCTACACAACCGGGCTTGACCAGTGCTGTCATTGATGCACTCCCCCGGAATAT\nGGTCATTACCTGTCAGGGGTCCGATGACATAAGGAAACTCCTTGAATCACAAGGAAGAAAAGACATTAAA\nCTAATTGATATTGCCCTCAGCAAAACTGATTCCAGGAAGTATGAAAATGCAGTCTGGGACCAGTATAAAG\nACTTATGCCACATGCACACAGGTGTCGTTGTTGAAAAGAAGAAAAGAGGCGGTAAAGAGGAAATAACCCC\nTCACTGTGCACTAATGGACTGCATCATGTTTGATGCAGCAGTGTCAGGAGGACTGAACACATCGGTTTTG\nAGAGCAGTGCTGCCCAGAGATATGGTGTTCAGAACATCGACACCTAGAGTCGTTCTGTAAATGGACGCCC\nCCGTGACCCACCGCCAATAGGCGGTGGGTCACGGGGGCCCTGACAAGGGTCTCATCTCTTCCATTTCACA\nGGCACACCAGGCTGTTTGTAGAGTCCACAGGAACAAATGCCCATATGATTCAATCTGTGAGGTTTGGGAC\nACGACTTGCCTACAATATGCCTATGAGTTGGTATTTTGACTAGGTGAAGGAAGATGCTAATAAGATAGAA\nACTTGTACTGAACACAAAGAGGTCAACTAGACCCAATGGTGTCTTCCCCTGCCTCTCCATATACTCCTTC\nTGTAACATCTCAGTGATCATATTGTCAGCTTGTTGTTCAATATCATCAGAAAAGTGGGTCTCGTTCAAGT\nATGAACCATTTGATACAAGCCAACATTTGGGCAGTGATGTTCTCCCAGTAGTTGTGTGGTTGAGGTACCA\nATACTTGCTGTAATTACAGTATGGAATTCCCATGATGTCCCGTAGATGGTTCTTCATTATAAGTTGGTCA\nTTTATCAAAGCATTTACTGCTTTGTTGATCAACTGAATGCTCATTTGTGCTTCAGCTTTCAACCTTTGAA\nTGGCTTGTTTGTTGAAGTCAAACAGCCTCAGCATGTCACAAAATTCCTCATCATGCTTCTCATTACATTT\nTGCCACAGCTGTGTTCCCGAAGCATTTTAGTTCAGCCTCAATTAGCATCCACCTGGTCAGACAATATCCC\nCCTGGTGTGTCTTTACCTTCAGAATCTGACAGTGTCCATGTGAATGTGCCTAGCAATCTTCTACTAATAT\nAAATATCTCTAGTCCTTTGTGAGAGGAGCCCGAGATAACCGATGGGAGATGGTCTCGAGAATTGGCAGTG\nATCTTCCCAGGTTGTATTTTGGATTATCAGATATTGATAACTAGTCATAATACAGTCCCAGTTGCCACGG\nCCTGAGTCAAGAGCAATGTAGCTCCCACCCCAAGCCATCCTCATAAAAGTCTGTAACACACCATTTGCAA\nCAGTACCACAATGGTTGGCTGCATCCCCAGCATAGCTGTGACTCAGGTTGTACTGCACACTAATCTTTCC\nCCCATTAAAATCGCAGCTCATTGCCTCATACTGATTGAAGTTGGGGATGGACAAGTGGAAAGTTGAGATT\nATGCTCATAAGAGCGTGGTCATAGAGGTTCTTTTTGTGGGCATCAGACAGATTGCAAAATTTGTGATTAA\nTAATGCTCGTGTTGGTCAAGGTCAGTTCTAGTCCTGTCTCATTGCCCACCATTATATAATGATGACTGTT\nGTTCTTTGTGCAGGAGAGAGGCATGGTCATATTGAGTGTCTCCATGTTTAGTTCCAGAGTCTGAAGCTCA\nTAAACCCCTTTATAAAGACTGGTTGTGCAAGACCTACCACACAACAGGAGGAAAGTGACCAAACCAACAA\nGGCCACACGTTGCAAAATTGTACAGACCTTTCAGCACTGCTAGTACAGACAGTGCAATGAGAACAATGTT\nCATCACCTCTTCTATTACATGAGGCACTTCCTGGAAGAATGTCACTATTTGTCCCATTTTAAATAGGACA\nCTTGAATTGCGCAACCAAAAATGCCTAGGATCCCCGGTGCGC\n\n>gi|23343512|ref|NC_004297.1| Lassa virus segment L, complete sequence\nCGCACCGGGGATCCTAGGCAATTTGGTTGTCTTTTTTTGAGGCCTTGTGCGCTGTACTTCTCCAAATGGG\nAAACAAGCAAGCCAAAGCCCCAGAATCAAAAGACAGTCCGAGAGCCAGCCTGATCCCAGATGCCACACAT\nCTAGGGCCACAGTTCTGTAAGAGCTGCTGGTTCGAAAACAAGGGCCTGGTTGAGTGCAACAACCACTATC\nTGTGTCTCAACTGCCTCACCTTACTTCTAAGTGTCAGCAACAGGTGTCCCATTTGCAAGATGCCTCTCCC\nCACAAAACTGAGACCATCAGCCGCTCCAACAGCACCTCCAACCGGAGCAGCGGACAGCATCAGACCCCCA\nCCCTACAGTCCCTGAATCTCCCACCGACCCCCACCACTCCCATCCTCCCCCCGACACCCCCCGGGGGGAC\nCCCCCGCCGGGGGCCCCCCCGGGGGAGCCAACCATCACCAAAAAACTACTCAATGTCTTCGATGCATTCA\nTCCTTCCTAGTCAGCTCCTCACATGTTCTGCCCTTCAATCTCAATTTACCACCACTTGATTGTACCATCA\nCCTTTCCCCTTGACTTACTATAACAGAGAGCATAACCCTTGAACTCCACCCAGTTGTCCACTGCCTCAAG\nAACCGCACTCAAGATCCCCTCACAACTCGGCGCTGCAGCCCTAAGTGTGGAGACAATGTCCACCCCTGAC\nCACTGCATCCTTAACCCCAGCCTGTCTATCATCATATCACTCAATGCCCCAATCAGCAGGTCAGACGAAG\nTGTCCCCAACCTCTCTCACAAATATCTCAAGATCCTGGTCTTGTATAACAGGTGTAAAGGATGCCAATTT\nCTTTCCACATTCCCACAAGCCTCCCCTATGCACAACCAGGGGGGTTGGTTCAGTGCAAGGACCCACCAAT\nACAAAGTCATACTCCGTAAACTGCAACCTTTCCATATCAACAACAATCTCAACAGGGGTCACATGCCCTA\nGTTGATTTGTGTCAATTAAAAACTCATTAATGATCTCGGTGTCAACATACCATGCTGATTTGCCCTTGAA\nAGTAGGTCCTGACAAAACCAGTCTCCAACAGTCTGACAAGACACACGGACTCACTGCACCTGAGTACATA\nACGGTTACATCATGTACTAGATACTTGGCCTGTTGATTCATTGAGCCAGTATACTCAAGGTGGATGGCAA\nAGCTTTCCTTAAAACTAGCATCTTGACTTTTAACACGGAACCTCACTGTCTGACTCAGTTTTGCAGACCC\nTGGAGGTAGTGAAGCTACGGCATCAAAGAAATCCTCCAATGAGTCAAACTTAGGATCAACTAAACCTGAT\nGCGATCAATTGATTTTGATTGAATCTAGCTGGCTCAATATCAAAGTCTATCCAAGCATAACCCATCATCA\nGATCATGCTTAAACATTGGCCTTTCAACACCTTTGTGAATAACTTTCTCTACAAATGAAGAAAATGGACC\nCATTCTATGCAACCCTTCACCCTCTGGAACTGATGTCTTGTGTGGAAACCACGTGAAGGACCCCAATGTT\nCTTGTAGTCGCAACAAATGGTCTCACGTAAGACTCAAAATAAATTTGCCTCATGAAATTGTCAACAGCAT\nCACTAGTGCTCACTACTCTTTCTTCCACCATGGGTTCATGTGTCCTACTGTGAGACAACCTCAATTCAGA\nTGATAACACAATGTAATGTTCCTCTCTTTTCCATTTTACTATGTGTGAGACAAGAGACAAGGCTTCACAG\nTTAACATCCAACGCTACACAGAGATCTAGAAATTTTATTCTGGGTGACCACTTCATTTTGGTTGACGCTA\nGATCGCTCATGAATGGTAATATGTGTTTCTCAAACACTGATGGGTACAGCCTTCTTAAAGAATGAATGAT\nGTGATTCAAACCAACCCTATCCTCCAATAGTTTTGATGCAGTTGGCTTTAAGGGAAAATAGTCACAAGGG\nTTATGTTTGAAAAAATCAAACACCTTAACTGTCTTAGGTTCCCCTAAGACCCATGCACCCAGTTCTATTG\nCAGTTGATAAGGAGATGCACATATAATCCCATAACAAGGGTCTGAAATAACTGACCACACTTTCACCTCC\nACTTCCATTTCTAAGTTCTAGCGGAACTTGCCAATATTGAATGCCATTAGAATTTGTCAACAATTTGATT\nCCCTTGACATCAGAAATCAGAGACTGAATGGACTTAATATACAGATTCTCTTTATTTGGTCCCCGAACAC\nATTTGCTACCCAATGTTCTGCACAATCCTACAAAGCCAGATGCAATGGAACTTTGGAATGCAGATTTGTT\nGATAGCTTCAGACAGCAATTTTTGCGCACCTCGAGTGAAAGTGGAAGACAACTTATTTTGGATTGTTTTG\nACAATGGTAGGAATCTTCTCATCATCTAGGTTCACAGCACCTGAATATATTATCTTTTGTCTCAACACCA\nTTCTTAAAGGATGATGCGCAGCCAAGTTTAGCCAAGAATACTCAAGGTCAGACTCAGATGGGGGCTCAAC\nATCCAACAGCTCACAAAGATTTCTTAGTGATGAGAGGTGCTCACTAGACAAATAGTTTGTTGTGAACTCT\nTCATGGAGTTGCCCAGTCTTCAACCTATTGTACAGTTTTCTTAACATAGATCTAATCTTGCTGCAAGCAT\nTAGGAATCAATCCCTCTATTTGCCTCATAATCCTATAACTACGGTTGCCATCTACCCAGTCTCTAACATC\nTGTCTCGCAATTCAATAAGAATGGGTCAATAGGGTATCTTGCATATTGCAAAGGATTTAAGGTTCTTTTC\nTGTATTAGATTACATAAGTGAACAGGGACACCATTCGCAACCGACTGATCAATGATTGTGTCAATTGTTT\nCTGCCAGTTGGTGTGGCTCTTTACACTTTATATTGTGAAGAGCTGCTGCAACGAACTTTGTCAATAATGG\nCACTTCATCTCCCCAAACAAAAAATCTAGATTTAAACTCTGCAACAAACCTGCCAATGACACTTTTAGGG\nCTCACAAACTTATTGAGTTGATCACTCATATAATAGTGGAACTCTATTAGAGTCCTAAATTCTTCTGGGT\nCTCTTTGCAAAAGCTCTGTGAGAGATTGATCAAAGAGAGAAATCTGATCATCACTAGAGGTATAAGCATC\nTATCGTACCACCGCATATACAACTGATAGCATAATTAATGAACCTCTCTGAAATGAGGGCATAAAAATCT\nGATGTGTTGTGTAATATTCCTTGACCCATGTCAAGTATTGAACTGATGTGAGAAGGCACTACACCAGCTT\nGGAAATTAGAGTAAAAGAAATCTTCTGTTATTGACTGTTTAGTTTTCTTCCTTAACCCTAGTTGGGCTTT\nAATGAAAGACTTCATCATGGCTGTCACCACATTAAAAGGTATTTCCACCATTTTGTGCATATGCCACATA\nAGTAGGGTTGAGAGATAGTCCCTCCCTTTTATGTCAGCTTGCAAGTCCTTTGAGAGGAAAATTAAATTCT\nGTAAGACAGTCAAGAACAAAAATGGACACATCATTGGGCCCCACTTACTATGATCCATGCTATAAGACAC\nATGTGCCAATGAAACATTCAATTTCATGGAAAGGATAGCATTTTCAAATTCCTTCTCGTTGTTCAGGCAA\nCTCCCTGATAACTGTAGGCTTATAGCTTCAAAGTAATCTTCTATAAGTCTAGTAAACATCTTTGTTCTAA\nGATCACCAATATATAATTCTCTGTTACCACCCACTTGTTCTTTATATGACAAAGAAAACTTAAGCCTTCC\nTGTATCAGGTCCCACTGAGTCATAAGATTGTGGCGACTCTTGGCTATAAAAACACAAATTCTTTAACATT\nGCTGTGGTACAGTTTGTCAGTGACAGAGCCTTACTAAGTGCCTCTGAATTGCTCTCCCTTTCACTAATTC\nTTACATCATCAGAGAGTTTACCCATATCAAACTTGAAATTAAGGTTCCTTGACTTATAATGAGTGTACCT\nCCCCATAAGTGTATTCGCATTCATGATCAAGAGTATGGACTTAAAACACTGAAAGTATTCATGGTTAAAG\nTATGTCCTTGTTGACACTGCCTTTGTCAACTCTCCAATAGGACACTGTGACATATGTCCACAGTAAAAAT\nACTTCTGCTTCAATCTACTATTCTCATAGACAGCATTACAGAATTCTTCATAAAATTTACCTGGTAAGAT\nATCATGATCAAACTCCTCAACCATGTGATTGGATAATTCACCCTTGATCAACCTAATGTAAAACTTATTT\nGAGACAATCTCATCTAGATCATTTATTGATGGTTGGCCATCACCATTAGGGCCTGAGCCTAGCTTGACAG\nGTTCCCTATACTGATCAACAATTTTTTCAACAGTCTCCTTTAGCTGATCAAAATAATCGCTTGCACCTCC\nATCGAGCAAAATTTCGTCTAGGTCAGCCCCATCAGCATCACTTTTGAGCTGCCCAGATCCTAGAACCAAA\nTTGCTCATTGCCTGCTGAACTTTGTACTCATAGTCCTGCTTGTTGAGAAGGTACTTTCCTTTCCTTGAGA\nAGACTTCAGTGAGCTGCGACACGGCCAGTGCTGTGAGCTTATTGAAGTCATAGTTTAATATTCTAGAACC\nATCTGTGTATTTATTAACAACAACACTTTTCTTGCTGGCTAAATCCAAGGCTGCACTGCCACTGGTGATG\nAGAGGATCTTTGATTTCCCTTTTTACTTCCCTCTCCTTAAATAGTGAACCATTGTTAAAAGAGGATGTAA\nGAAGAGATAAATACTTCTTTGAAACACCAGGCCTTTTATAATCTGGTCCCTCGATAGTTGTGCATCCATC\nTTTACTTAAAAACTTTTTTGCATTGTAGACCATGTCATCCAATTCTTCCTCAGTGGCTGTGTCTGCAGGA\nTTAGTGCTCACATGACCAAATCTCACCTTTGGTTCCAGAAACTTCTCAAAACATTTTATCTGATCTGTCA\nATCTATCTGGTGTTTCTTTCGTAATGAAGTGGCACATGTAGGAAACATTCAAAATGAACTTGAACCTATT\nAGTCATCATGCTCTTCACATCCTCAGATAAAACCAGATTCATTAATGTCCTTATTAACCTATAGAGCAGG\nAACTCAACATCAGTGATTAATTCTTCCCTTATTTTGTCAATGAGGTCCTTATGATGATAATCTGATAGAT\nAAGCCATTACAAAGTACCTAAGATTTTGGAGGAGCTTTTGAGAACGTTTACTGGGGTGAGCTAAAATTAA\nAACCAGGATCATCTTTGTCAGAGACCTGATATTGTTCAACTGCCCTTCCAGCTCATTGCAATCTTCTATC\nCAAGAAATCATAGTGCTTATTGTTGTTTGTAAAACCTCAGCTGAAAATATTGCTGGAAAATATCTTTTAG\nGATCAGCATAAAATGAGCACACCTCACCAACTTTGTTATCATTAATAGCATAGCACTTCGAGCACTCCCC\nTGTCTTTTGATAAATCAGTTGTAATTCAGTGTTACCCAATGAAAACTCTTGACAATATGCTTCTTTGCAT\nCTGACCACTTGATACCTTGCGGGTCCAAATTCATTCTGTCTCAGCTTTACGGTAGAAGAAGTTTTCATAG\nAGTTCACCAAAGCGAGGCTCAATGAGGAAAGTCTCTCTAAGTCAGTGGTTCCCAGTAGTTCCACATCCCC\nCATCACATAAGGGAATGTTTCTTCCTCTGTTCTCTGATAACTGATTGTTGGGACAACTCCGGAGACATCA\nAAGTCCATAATCAAATCATAGCTGTTAAGGCAGATCACCTCCATATCAATTTTATAGTGGTCCACACTGA\nTCCCAACATCCTTTAAAGCAGTGGTGGCCTTCAAAATGGTTTTCTGGAATATTGAATTGAGGATTTGATT\nCTTACTCAAACACTGGGAGGACTGTGTGATTCTAGATCTTAGCCTGTTGCCTCGCTCTCCCCATTTCTCG\nAGATCCCTCTTTGTTGCCTCCAAAGAAACTAGTCTATCTTTAACTCTTAAGAAGCAAGACCCCAACCACC\nCTTTTAAACACTTTTGTTTCATCAGGTCATGCTTACTTGCAAGGAGAATTAGTGCATCAAAAATTAATAG\nAAGTTTCCTCCTTGTGTTCAATATCCTCAAAGATTTTACTTTATTTAGGAATGATCTCCAGCATTGAACC\nTGACATTCTCCAATAGTTTGGTTTCCCCTTTTTTCATTCCCCTCATCAACATTTGCATACAAAAATCTCA\nATATTGGTGATGCTCTCTTGAACTGGTAAATTAAGTGTTCGATATTGTCTTCTGCAACTACCTTATCAGC\nGTACAAATTGTTAAGCTCATTAAGTAACTGGCTCTTATCAACCTTTAAAAACTGACCTTCTATCTCTCCT\nTTCCTCAATCTGTTCCTAAACACTTGATACTCCTCTTCGATCTGCAGCTTTACCTCATGAGCTGTTAATT\nTATTATTGATGCCCTGGTGGCATGAGGCAATCACTTCCTCATAATGATTAGAGCGATTGTCCATCAGAAC\nATTTAAACTCTCCACCCCTGATAATCTACCCGAAGTCATGAATAAAGATTCACAGAGTCTGCTATACTCT\nGACTCTTCAAAAAGTGAATTACTCTCCTGTGCATACTTTAAAAGTGAGAAGAGCGTATCCCTCAACTTAT\nCATTGACCCAGTCAGGTATTTGTTCATTGTAGAATGATGTTCTCCCGTCTATAAGTGGTATTAAATTGAT\nGTCGACACTCTTCAGGTCTTCTTTCAGCTGCTCTAATTTTTTGAAGTCCTCAATGTACTTCTGCTCAAAG\nTTAGCAGGAGATGATCTAACAAAACACTCCAGCAGTATTAGAACATTGCCCGTCAGTTTGTAACCGTCCG\nGGTACCACAAACATAGTGAAGGTGTCAAGATTCCATGGTCATGGAGAATTCTTTCCACAGATTTGTCCTC\nACTGTTATGCTCGCAACCATTTGCGTTGCAAGAATCAACCTCAATACAGAGGGACAAGAGTTTCAACCCT\nTCCATTAATAGCATCCTAGGCTCTGTCTGCACAAGAAATGCTAACTTCTGTCTTGACAATCTCTCGTTGT\nCCACTAGGTATTTTGATACTAAGTCTTTGACACAGGCTATGTCTTCCTCCATGTTTAGCTGCAGGTATGA\nTGTTCAGAACCCTCAGAACATGTGGTCTGCTAGAGCAACAGTTCGCTATGGGATAGGGTCCCGTAGGGGC\nACAGAAGACACAAGAGGCAATTAAAGACAATTAAATAAGATAGCCTTAATGCCTAGGATCCTCGGTGCG\n\n" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/hybsel_probe_adapters.fasta", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/hybsel_probe_adapters.nhr", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/hybsel_probe_adapters.nin", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/hybsel_probe_adapters.nsq", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/metag_v3.ncRNA.mRNA.mitRNA.consensus.dict", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/metag_v3.ncRNA.mRNA.mitRNA.consensus.fasta.fai", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/metag_v3.ncRNA.mRNA.mitRNA.consensus.nhr", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/metag_v3.ncRNA.mRNA.mitRNA.consensus.nin", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/blast/metag_v3.ncRNA.mRNA.mitRNA.consensus.nix", "content": "" }, { "path": 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"tests/input/s3/sabeti-public-dbs/bmtagger/metagenomics_contaminants_v3.srprism.ss", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/bmtagger/metagenomics_contaminants_v3.srprism.ssa", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/bmtagger/metagenomics_contaminants_v3.srprism.ssd", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/bwa/hg19.amb", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/bwa/hg19.ann", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/bwa/hg19.bwt", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/bwa/hg19.pac", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/bwa/hg19.sa", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/kaiju/nr/nr.fmi", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/krakenuniq/database.idx", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/krakenuniq/database.jdb", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/krakenuniq/database.kdb", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/krakenuniq/lca.complete", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/krona/taxonomy.tab", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/rna_bwa/human_viral_rrna.amb", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/rna_bwa/human_viral_rrna.ann", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/rna_bwa/human_viral_rrna.bwt", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/rna_bwa/human_viral_rrna.pac", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/rna_bwa/human_viral_rrna.sa", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/spikeins/ercc_spike-ins.fasta", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/taxonomy/merged.dmp", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/taxonomy/names.dmp", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/taxonomy/nodes.dmp", "content": "" }, { "path": "tests/input/s3/sabeti-public-dbs/trim_clip/contaminants.fasta", "content": "" }, { "path": "tests/unit/assemble/test_assembly.py", "content": "# Unit tests for viral_ngs.assembly.py\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport viral_ngs.assembly\nimport viral_ngs.core.cmd\nimport viral_ngs.core.file\nimport Bio.SeqIO\nimport Bio.Data.IUPACData\nimport unittest\nimport argparse\nimport csv\nimport glob\nimport os\nimport os.path\nimport shutil\nimport subprocess\nimport tempfile\nimport argparse\nimport itertools\nimport pytest\nimport viral_ngs.assemble.mummer\nimport viral_ngs.assemble.skani\nimport viral_ngs.assemble.wgsim\nimport viral_ngs.core.minimap2\nimport viral_ngs.core.picard\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp, _CPUS, IS_ARM\n\n\ndef makeFasta(seqs, outFasta):\n with open(outFasta, 'wt') as outf:\n for line in viral_ngs.core.file.fastaMaker(seqs):\n outf.write(line)\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in viral_ngs.assembly.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n\nclass TestRefineAssemble(TestCaseWithTmp):\n ''' Test edge cases of the de novo assembly pipeline '''\n\n def _align_with_minimap2(self, refFasta, inBam):\n \"\"\"Align reads to reference with minimap2, return indexed BAM path.\"\"\"\n mm2 = viral_ngs.core.minimap2.Minimap2()\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n outBam = viral_ngs.core.file.mkstempfname('.aligned.bam')\n mm2.align_bam(inBam, refFasta, outBam, options=['-x', 'sr'])\n samtools.index(outBam)\n return outBam\n\n def test_empty_input_bam_assembly(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebov-makona.fasta')\n inFasta = viral_ngs.core.file.mkstempfname('.ref.fasta')\n shutil.copyfile(orig_ref, inFasta)\n\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n alignedBam = self._align_with_minimap2(inFasta, inBam)\n outFasta = viral_ngs.core.file.mkstempfname('.refined.fasta')\n\n viral_ngs.assembly.refine_assembly(\n inFasta, inBam, outFasta,\n already_realigned_bam=alignedBam,\n chr_names=['G5012.3'], min_coverage=3)\n\n self.assertTrue(os.path.isfile(outFasta))\n self.assertTrue(os.path.getsize(outFasta) == 0)\n\n def test_aligned_empty_input_bam_assembly(self):\n mm2 = viral_ngs.core.minimap2.Minimap2()\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n with viral_ngs.core.file.tempfname('.ref.fasta') as inFasta:\n with viral_ngs.core.file.tempfname('.bam') as inBam:\n with viral_ngs.core.file.tempfname('.refined.fasta') as outFasta:\n with viral_ngs.core.file.tempfname('.vcf.gz') as outVcf:\n shutil.copyfile(os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebov-makona.fasta'), inFasta)\n mm2.align_bam(os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam'), inFasta, inBam,\n options=['-x', 'sr'])\n samtools.index(inBam)\n\n # run refine_assembly\n args = [inFasta, inBam, outFasta, \"--already_realigned_bam\", inBam, '--outVcf', outVcf]\n args = viral_ngs.assembly.parser_refine_assembly(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n # the expected output is an empty fasta file\n self.assertTrue(os.path.isfile(outFasta))\n self.assertTrue(os.path.getsize(outFasta) == 0)\n self.assertTrue(os.path.isfile(outVcf))\n self.assertTrue(os.path.getsize(outVcf) > 0)\n\n def test_empty_input_fasta_assembly(self):\n # empty input fasta should produce empty output regardless of reads\n inFasta = viral_ngs.core.file.mkstempfname('.input.fasta')\n viral_ngs.core.file.touch(inFasta)\n\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n outFasta = viral_ngs.core.file.mkstempfname('.refined.fasta')\n\n viral_ngs.assembly.refine_assembly(inFasta, inBam, outFasta,\n chr_names=['G5012.3'], min_coverage=3)\n\n self.assertTrue(os.path.isfile(outFasta))\n self.assertTrue(os.path.getsize(outFasta) == 0)\n\n def test_empty_input_succeed(self):\n # both empty fasta and empty bam should produce empty output\n inFasta = viral_ngs.core.file.mkstempfname('.input.fasta')\n viral_ngs.core.file.touch(inFasta)\n\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n outFasta = viral_ngs.core.file.mkstempfname('.refined.fasta')\n\n viral_ngs.assembly.refine_assembly(inFasta, inBam, outFasta,\n chr_names=['G5012.3'], min_coverage=3)\n\n self.assertTrue(os.path.isfile(outFasta))\n self.assertTrue(os.path.getsize(outFasta) == 0)\n\n\nclass TestNormalizeCoverage(TestCaseWithTmp):\n '''Test the normalize_coverage command'''\n\n def test_help_parser(self):\n parser = viral_ngs.assembly.parser_normalize_coverage(argparse.ArgumentParser())\n helpstring = parser.format_help()\n self.assertIn('max_coverage', helpstring)\n self.assertIn('seed', helpstring)\n\n def test_normalize_coverage_on_aligned_bam(self):\n '''normalize_coverage should downsample and produce a sorted, indexed BAM'''\n mm2 = viral_ngs.core.minimap2.Minimap2()\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n inDir = viral_ngs.core.file.get_test_input_path()\n inBam = os.path.join(inDir, 'G5012.3.testreads.bam')\n refFasta = os.path.join(inDir, 'ebov-makona.fasta')\n\n with viral_ngs.core.file.tempfname('.aligned.bam') as alignedBam, \\\n viral_ngs.core.file.tempfname('.normalized.bam') as outBam:\n mm2.align_bam(inBam, refFasta, alignedBam, options=['-x', 'sr'])\n samtools.index(alignedBam)\n\n viral_ngs.assembly.normalize_coverage(alignedBam, outBam, max_coverage=10, seed=42)\n\n self.assertTrue(os.path.isfile(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n # index file should also exist\n self.assertTrue(os.path.isfile(outBam + '.bai'))\n # output should have fewer or equal reads compared to input\n self.assertLessEqual(samtools.count(outBam), samtools.count(alignedBam))\n\n\nclass TestAssembleSpades(TestCaseWithTmp):\n ''' Test the assemble_spades command (no validation of output) '''\n\n def test_assembly(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')\n clipDb = os.path.join(inDir, 'clipDb.fasta')\n with viral_ngs.core.file.tempfname('.fasta') as outFasta:\n viral_ngs.assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, min_contig_len=180, out_fasta=outFasta)\n self.assertGreater(os.path.getsize(outFasta), 0)\n contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))\n #import sys\n #print('test_assembly_contigs_lens:', contig_lens, file=sys.stderr)\n self.assertEqual(contig_lens, [200, 201, 210, 222, 243, 244, 268, 294, 300, 328, 348, 376, 381, 430])\n\n def test_assembly_with_previously_assembled_contigs(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n inBam = os.path.join(inDir, '..', 'G5012.3.subset.bam')\n clipDb = os.path.join(inDir, 'clipDb.fasta')\n previously_assembled_contigs = os.path.join(inDir, 'trinity_contigs.fasta')\n with viral_ngs.core.file.tempfname('.fasta') as outFasta:\n viral_ngs.assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, contigs_untrusted=previously_assembled_contigs,\n out_fasta=outFasta, mem_limit_gb=1)\n self.assertGreater(os.path.getsize(outFasta), 0)\n contig_lens = list(sorted(len(seq.seq) for seq in Bio.SeqIO.parse(outFasta, 'fasta')))\n #import sys\n #print('test_assembly_with_previously_assembled_contigs_contigs_lens:', contig_lens, file=sys.stderr)\n self.assertEqual(contig_lens, [200, 201, 210, 222, 243, 244, 268, 294, 300, 328, 348, 376, 381, 430])\n\n def test_empty_input_succeed(self):\n inDir = viral_ngs.core.file.get_test_input_path()\n inBam = os.path.join(inDir, 'empty.bam')\n clipDb = os.path.join(inDir, 'clipDb.fasta')\n with viral_ngs.core.file.tempfname('fasta') as outFasta:\n viral_ngs.assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta)\n self.assertEqual(os.path.getsize(outFasta), 0)\n\n def test_always_succeed(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n inBam = os.path.join(inDir, '..', 'almost-empty.bam')\n clipDb = os.path.join(inDir, 'clipDb.fasta')\n with viral_ngs.core.file.tempfname('.fasta') as outFasta:\n viral_ngs.assembly.assemble_spades(in_bam=inBam, clip_db=clipDb, out_fasta=outFasta, spades_opts='--bad-option',\n always_succeed=True)\n self.assertEqual(os.path.getsize(outFasta), 0)\n\n\nclass TestAmbiguityBases(unittest.TestCase):\n\n def test_non_failure(self):\n ''' Make sure that alleles_to_ambiguity runs without errors for every possible\n combination of inputs. Check that the output is one-character long and uppercase.\n '''\n bases = ('A', 'C', 'T', 'G')\n for i in range(1, 5):\n for alleles in itertools.permutations(bases, i):\n out = viral_ngs.assembly.alleles_to_ambiguity(alleles)\n self.assertEqual(1, len(out))\n self.assertEqual(out, out.upper())\n\n\nclass TestUndirectedGraph(unittest.TestCase):\n def test_simple(self):\n g = viral_ngs.assemble.skani.UndirectedGraph()\n g.add_edge('a', 'b')\n g.add_edge('a', 'c')\n g.add_edge('b', 'd')\n actual = list(sorted(g.get_clusters()))\n self.assertEqual(actual, [{'a', 'b', 'c', 'd'}])\n\n def test_disconnected(self):\n g = viral_ngs.assemble.skani.UndirectedGraph()\n g.add_edge('a', 'b')\n g.add_edge('c', 'd')\n actual = list(sorted(g.get_clusters()))\n self.assertEqual(actual, [{'a', 'b'}, {'c', 'd'}])\n\n def test_both(self):\n g = viral_ngs.assemble.skani.UndirectedGraph()\n g.add_edge(1, 2)\n g.add_edge(11,12)\n g.add_edge(18,15)\n g.add_node(12)\n g.add_node(22)\n g.add_node(55)\n g.add_edge(25,22)\n g.add_edge(7,2)\n g.add_edge(12,18)\n actual = list(sorted(g.get_clusters()))\n self.assertEqual(actual, [{1, 2, 7}, {11, 12, 15, 18}, {22, 25}, {55}])\n\n\nclass TestOrderAndOrient(TestCaseWithTmp):\n ''' Test the MUMmer-based order_and_orient command '''\n\n def test_varicella_big(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.hhv3.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.hhv3.fasta'),\n os.path.join(inDir, 'ref.hhv3.fasta'),\n outFasta)\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_lassa_multisegment(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.lasv.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.lasv.fasta'),\n os.path.join(viral_ngs.core.file.get_test_input_path(), 'ref.lasv.fasta'),\n outFasta)\n self.assertEqualContents(outFasta, expected)\n os.unlink(outFasta)\n\n def test_lassa_multisegment_refsel(self):\n with viral_ngs.core.file.tempfnames(('.out.fasta', '.out_ref.fasta', '.stats.tsv')) \\\n as (outFasta, outReference, outStats):\n contigs, expected, expectedStats = self.inputs('contigs.lasv.fasta', \n 'expected.lasv.fasta', \n 'expected.refsel.lasv.stats.tsv')\n refs = [self.input('ref.lasv.{}.fasta'.format(strain))\n for strain in ('josiah', 'pinneo', 'KGH_G502', 'BNI_Nig08_A19', 'nomatch')]\n viral_ngs.assembly.order_and_orient(contigs, refs, outFasta,\n outReference=outReference, outStats=outStats)\n self.assertEqualContents(outFasta, expected)\n self.assertEqualFasta(outReference, refs[0])\n self.assertEqualContents(outStats, expectedStats)\n\n def test_influenza_multisegment(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.influenza.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.influenza.fasta'),\n os.path.join(inDir, 'ref.influenza.fasta'),\n outFasta)\n self.assertEqualContents(outFasta, expected)\n os.unlink(outFasta)\n\n def test_ebov_palindrome(self):\n # this tests a scenario where show-aligns has more alignments than show-tiling\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.ebov.doublehit.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.ebov.doublehit.fasta'),\n os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebov-makona.fasta'),\n outFasta)\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_ebov_palindrome_refsel(self):\n # this tests a scenario where show-aligns has more alignments than show-tiling\n with viral_ngs.core.file.tempfnames(('.out.fasta', '.stats.tsv')) as (outFasta, outStats):\n contigs, expected, expectedStats = self.inputs('contigs.ebov.doublehit.fasta',\n 'expected.ebov.doublehit.fasta',\n 'expected.refsel.ebov.stats.tsv')\n refs = self.inputs('ref.ebov.lbr.fasta','ref.ebov.sle.fasta','ref.ebov.gin.fasta')\n viral_ngs.assembly.order_and_orient(contigs, refs, outFasta, outStats=outStats)\n self.assertEqualFastaSeqs(outFasta, expected)\n self.assertEqualContents(outStats, expectedStats)\n\n def test_hiv_wraparound(self):\n # this tests a misassembly from Trinity and checks that we still use some of the contig\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.hiv.wrapped.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.hiv.wrapped.fasta'),\n os.path.join(inDir, 'ref.hiv.fasta'),\n outFasta)\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_alternate_contigs(self):\n # this tests that --outAlternateContigs works as expected\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n altFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.hiv.big_indel.fasta')\n expectedAlt = os.path.join(inDir, 'expected.hiv.big_indel.alternates.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.hiv.big_indel.fasta'),\n os.path.join(inDir, 'ref.hiv.fasta'),\n outFasta,\n outAlternateContigs=altFasta)\n self.assertEqualContents(outFasta, expected)\n self.assertEqualContents(altFasta, expectedAlt)\n\n @unittest.skip('promer alignments not implemented for custom scaffolding step')\n def test_lassa_protein(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.lasv.promer.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.lasv.fasta'),\n os.path.join(viral_ngs.core.file.get_test_input_path(), 'ref.lasv.fasta'),\n outFasta,\n aligner='promer')\n self.assertEqualContents(outFasta, expected)\n os.unlink(outFasta)\n\n def test_multi_overlap(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.ebov.small.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.ebov.fasta'),\n os.path.join(inDir, 'ref.ebov.small.fasta'),\n outFasta)\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_ambig_align(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n contigs_gz = os.path.join(inDir, 'contigs.lasv.ambig.fasta.gz')\n contigs = viral_ngs.core.file.mkstempfname('.fasta')\n with viral_ngs.core.file.open_or_gzopen(contigs_gz, 'rb') as f_in:\n with open(contigs, 'wb') as f_out:\n shutil.copyfileobj(f_in, f_out)\n expected = os.path.join(inDir, 'expected.lasv.ambig.fasta')\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n viral_ngs.assembly.order_and_orient(\n contigs,\n os.path.join(inDir, 'ref.lasv.ISTH2376.fasta'),\n outFasta)\n def get_seqs(fasta):\n return [str(s.seq) for s in Bio.SeqIO.parse(fasta, 'fasta')]\n self.assertEqual(get_seqs(outFasta), get_seqs(expected))\n\n def test_ambig_align_ebov(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n contigs_gz = os.path.join(inDir, 'contigs.ebov.ambig.fasta.gz')\n contigs = viral_ngs.core.file.mkstempfname('.fasta')\n with viral_ngs.core.file.open_or_gzopen(contigs_gz, 'rb') as f_in:\n with open(contigs, 'wb') as f_out:\n shutil.copyfileobj(f_in, f_out)\n expected = os.path.join(inDir, 'expected.ebov.ambig.fasta')\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n viral_ngs.assembly.order_and_orient(\n contigs,\n os.path.join(inDir, 'ref.ebov.makona_C15.fasta'),\n outFasta)\n def get_seqs(fasta):\n return [str(s.seq) for s in Bio.SeqIO.parse(fasta, 'fasta')]\n self.assertEqual(get_seqs(outFasta), get_seqs(expected))\n\n def test_obscure_mummer3_bug(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.lasv.bug.fasta')\n # under mummer3, this fails with a weird error in nucmer,\n # causing a CalledProcessError. We want this to succeed\n # nucmer, but fail later on due to IncompleteAssemblyError\n self.assertRaises(viral_ngs.assembly.IncompleteAssemblyError,\n viral_ngs.assembly.order_and_orient,\n os.path.join(inDir, 'contig.mummer3_fail_lasv.fasta'),\n os.path.join(inDir, 'ref.lasv.ISTH2376.fasta'),\n outFasta)\n\n def test_not_all_segments_fail(self):\n # IncompleteAssemblyError is thrown when only some but not all segments are recovered\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n self.assertRaises(viral_ngs.assembly.IncompleteAssemblyError,\n viral_ngs.assembly.order_and_orient,\n os.path.join(inDir, 'contigs.lasv.one_small.fasta'),\n os.path.join(inDir, 'ref.lasv.ISTH2376.fasta'),\n outFasta)\n\n def test_not_all_segments_succeed(self):\n # ... unless we specifically allow for partial outputs\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(inDir, 'contigs.lasv.one_small.fasta'),\n os.path.join(inDir, 'ref.lasv.ISTH2376.fasta'),\n outFasta,\n allow_incomplete_output=True)\n\n def test_empty_output_succeed(self):\n # a completely empty output should be possible if we allow it\n inDir = viral_ngs.core.file.get_test_input_path(self)\n emptyFasta = os.path.join(inDir, '..', 'empty.fasta')\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n viral_ngs.assembly.order_and_orient(\n emptyFasta,\n os.path.join(inDir, 'ref.influenza.fasta'),\n outFasta,\n allow_incomplete_output=True)\n self.assertEqualContents(outFasta, emptyFasta)\n\n@unittest.skipIf(IS_ARM, \"gap2seq requires x86-only bioconda package (not available on ARM)\")\nclass TestGap2Seq(TestCaseWithTmp):\n '''Test gap-filling tool Gap2Seq'''\n\n def test_gapfill(self):\n join = os.path.join\n inDir = viral_ngs.core.file.get_test_input_path()\n in_scaffold = join(inDir, 'TestOrderAndOrient', 'expected.ebov.doublehit.fasta')\n with viral_ngs.core.file.tempfname(suffix='.filled.fasta') as filled:\n viral_ngs.assembly.gapfill_gap2seq(in_scaffold=in_scaffold,\n in_bam=join(inDir, 'G5012.3.testreads.bam'),\n out_scaffold=filled, random_seed=23923937, threads=1)\n shutil.copyfile(filled, '/tmp/filled.fasta')\n self.assertEqualContents(filled, join(inDir, 'TestGap2Seq', 'expected.ebov.doublehit.gapfill.fasta'))\n\n def test_empty_fasta_input(self):\n inDir = viral_ngs.core.file.get_test_input_path()\n empty_fasta = os.path.join(inDir, 'empty.fasta')\n out_fasta = viral_ngs.core.file.mkstempfname('.fasta')\n viral_ngs.assembly.gapfill_gap2seq(in_scaffold=empty_fasta,\n in_bam=os.path.join(inDir, 'G5012.3.testreads.bam'),\n out_scaffold=out_fasta, random_seed=23923937, threads=1)\n self.assertEqualContents(out_fasta, empty_fasta)\n\n\nclass TestImputeFromReference(TestCaseWithTmp):\n ''' Test the impute_from_reference command (align and modify_contig) '''\n\n @unittest.skip('requires 10 mins and 16GB RAM')\n def test_varicella_big_muscle(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.hhv3.muscle.fasta')\n inDirBase = viral_ngs.core.file.get_test_input_path()\n viral_ngs.assembly.impute_from_reference(\n os.path.join(inDirBase, 'TestOrderAndOrient', 'expected.hhv3.fasta'),\n os.path.join(inDirBase, 'TestOrderAndOrient', 'ref.hhv3.fasta'),\n outFasta,\n minLengthFraction=0.8,\n minUnambig=0.6,\n replaceLength=55,\n newName='HHV3-test')\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_varicella_big_mummer(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.hhv3.mummer.fasta')\n inDirBase = viral_ngs.core.file.get_test_input_path()\n viral_ngs.assembly.impute_from_reference(\n os.path.join(inDirBase, 'TestOrderAndOrient', 'expected.hhv3.fasta'),\n os.path.join(inDirBase, 'TestOrderAndOrient', 'ref.hhv3.fasta'),\n outFasta,\n minLengthFraction=0.8,\n minUnambig=0.6,\n replaceLength=55,\n aligner='mummer',\n newName='HHV3-test')\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_small_muscle(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.sub.ebov.impute.fasta')\n viral_ngs.assembly.impute_from_reference(\n os.path.join(inDir, 'test.pseudo.fasta'),\n os.path.join(inDir, 'ref.sub.ebov.fasta'),\n outFasta,\n minLengthFraction=0.8,\n minUnambig=0.2,\n replaceLength=5,\n newName='test_sub-EBOV.genome',\n aligner='muscle')\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_small_mafft(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.sub.ebov.impute.fasta')\n viral_ngs.assembly.impute_from_reference(\n os.path.join(inDir, 'test.pseudo.fasta'),\n os.path.join(inDir, 'ref.sub.ebov.fasta'),\n outFasta,\n minLengthFraction=0.8,\n minUnambig=0.2,\n replaceLength=5,\n newName='test_sub-EBOV.genome',\n aligner='mafft')\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_small_mummer(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(inDir, 'expected.sub.ebov.impute.fasta')\n viral_ngs.assembly.impute_from_reference(\n os.path.join(inDir, 'test.pseudo.fasta'),\n os.path.join(inDir, 'ref.sub.ebov.fasta'),\n outFasta,\n minLengthFraction=0.8,\n minUnambig=0.2,\n replaceLength=5,\n newName='test_sub-EBOV.genome',\n aligner='mummer')\n self.assertEqual(\n str(Bio.SeqIO.read(outFasta, 'fasta').seq),\n str(Bio.SeqIO.read(expected, 'fasta').seq))\n\n def test_empty_fasta_input(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n empty_fasta = os.path.join(inDir, '..', 'empty.fasta')\n outFasta = viral_ngs.core.file.mkstempfname('.fasta')\n viral_ngs.assembly.impute_from_reference(\n empty_fasta,\n os.path.join(inDir, 'ref.sub.ebov.fasta'),\n outFasta,\n minLengthFraction=0.0,\n minUnambig=0.0,\n replaceLength=5,\n newName='test_sub-EBOV.genome',\n aligner='mummer')\n self.assertEqualContents(outFasta, empty_fasta)\n\nclass TestSkaniReferenceSelection(TestCaseWithTmp):\n ''' Test Skani-based reference selection '''\n\n def test_skani_contigs_to_refs(self):\n '''\n Test the skani_contigs_to_refs function.\n Test inputs include LASV MAGs/contigs against various EBOV and LASV references.\n The only references that should hit are the LASV Josiah and KGH_G502 references.\n Additionally, skani should identify them as being from the same cluster.\n No EBOV references should be selected.\n '''\n\n inDir = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestOrderAndOrient')\n with viral_ngs.core.file.tempfnames(('.skani.dist.out', '.skani.dist.filtered', '.clusters.filtered')) \\\n as (out_skani_dist, out_skani_dist_filtered, out_clusters_filtered):\n contigs = os.path.join(inDir, 'contigs.lasv.fasta')\n refs = [os.path.join(inDir, 'ref.lasv.{}.fasta'.format(strain))\n for strain in ('josiah', 'pinneo', 'KGH_G502', 'BNI_Nig08_A19', 'nomatch')] + \\\n [os.path.join(inDir, 'ref.ebov.{}.fasta'.format(strain))\n for strain in ('lbr', 'sle', 'gin')]\n\n viral_ngs.assembly.skani_contigs_to_refs(contigs, refs, out_skani_dist, out_skani_dist_filtered, out_clusters_filtered, threads=1)\n\n with open(out_clusters_filtered, 'r') as inf:\n clusters = inf.readlines()\n self.assertEqual(len(clusters), 1)\n actual_cluster = set([os.path.basename(f) for f in clusters[0].strip().split('\\t')])\n expected_cluster = set(['ref.lasv.{}.fasta'.format(strain) for strain in ('josiah', 'pinneo', 'KGH_G502', 'BNI_Nig08_A19')])\n self.assertEqual(actual_cluster, expected_cluster)\n\n def test_skani_no_big_contigs(self):\n '''\n Test that skani_dist tolerates empty (or practically empty) input query fasta\n '''\n\n inDir = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestOrderAndOrient')\n with viral_ngs.core.file.tempfnames(('.skani.dist.out', '.skani.dist.filtered', '.clusters.filtered')) \\\n as (out_skani_dist, out_skani_dist_filtered, out_clusters_filtered):\n contigs = os.path.join(inDir, 'contigs.lasv.one_small.fasta')\n refs = [os.path.join(inDir, 'ref.ebov.{}.fasta'.format(strain))\n for strain in ('lbr', 'sle', 'gin')]\n\n viral_ngs.assembly.skani_contigs_to_refs(contigs, refs, out_skani_dist, out_skani_dist_filtered, out_clusters_filtered, threads=1)\n\n with open(out_clusters_filtered, 'r') as inf:\n clusters = inf.readlines()\n self.assertEqual(len(clusters), 0)\n with open(out_skani_dist, 'r') as inf:\n lines = inf.readlines()\n self.assertEqual(len(lines), 1)\n\n def test_skani_no_matches(self):\n '''\n Test that skani_dist tolerates empty outputs (no matches)\n '''\n\n inDir = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestOrderAndOrient')\n with viral_ngs.core.file.tempfnames(('.skani.dist.out', '.skani.dist.filtered', '.clusters.filtered')) \\\n as (out_skani_dist, out_skani_dist_filtered, out_clusters_filtered):\n contigs = os.path.join(inDir, 'contigs.lasv.fasta')\n refs = [os.path.join(inDir, 'ref.ebov.{}.fasta'.format(strain))\n for strain in ('lbr', 'sle', 'gin')]\n\n viral_ngs.assembly.skani_contigs_to_refs(contigs, refs, out_skani_dist, out_skani_dist_filtered, out_clusters_filtered, threads=1)\n\n with open(out_clusters_filtered, 'r') as inf:\n clusters = inf.readlines()\n self.assertEqual(len(clusters), 0)\n with open(out_skani_dist, 'r') as inf:\n lines = inf.readlines()\n self.assertEqual(len(lines), 1)\n\n def test_output_sorted_by_product(self):\n '''\n Test that skani.find_closest_reference output tsv is sorted by the product\n of ANI * Total_bases_covered (and not just the default ANI-based sort order)\n '''\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.core.file.tempfnames(('.skani.dist.out', '.skani.dist.filtered', '.clusters.filtered')) \\\n as (out_skani_dist, out_skani_dist_filtered, out_clusters_filtered):\n contigs = os.path.join(inDir, 'USA-MA-Broad_BWH-19947-2023.l000013249603_C5.HTKJ7DRX3.1.acellular.dedup.assembly1-spades.fasta')\n refs = glob.glob(os.path.join(inDir, 'RVA*.fa'))\n\n viral_ngs.assembly.skani_contigs_to_refs(contigs, refs, out_skani_dist, out_skani_dist_filtered, out_clusters_filtered, threads=1)\n\n with open(out_clusters_filtered, 'r') as inf:\n clusters = inf.readlines()\n self.assertEqual(len(clusters), 1)\n with open(out_skani_dist, 'r') as inf:\n hits = list(row['Ref_name'].split()[0].split('_')[1] for row in csv.DictReader(inf, delimiter='\\t'))\n self.assertEqual(len(hits), 10)\n expected = ['FJ445177.1','L24917.1','FJ445116.1','DQ473501.1','DQ473496.1','DQ473507.1','DQ473499.1','FJ445140.1','DQ473498.1','GQ223229.1']\n self.assertEqual(hits, expected)\n\n def test_sort_skani_table_empty_file(self):\n \"\"\"Test _sort_skani_table_by_product handles completely empty input file\"\"\"\n skani = viral_ngs.assemble.skani.SkaniTool()\n with viral_ngs.core.file.tempfnames(('.empty.tsv', '.out.tsv')) as (in_tsv, out_tsv):\n # Create empty file (0 bytes)\n open(in_tsv, 'w').close()\n\n # Should not raise exception\n skani._sort_skani_table_by_product(in_tsv, out_tsv)\n\n # Output should exist and have header only (not be empty)\n self.assertTrue(os.path.exists(out_tsv))\n with open(out_tsv) as f:\n lines = f.readlines()\n self.assertEqual(len(lines), 1)\n self.assertTrue(lines[0].startswith('Ref_file'))\n\n def test_sort_skani_table_header_only(self):\n \"\"\"Test _sort_skani_table_by_product handles header-only input file\"\"\"\n skani = viral_ngs.assemble.skani.SkaniTool()\n header = 'Ref_file\\tQuery_file\\tANI\\tAlign_fraction_ref\\tAlign_fraction_query\\t' \\\n 'Ref_name\\tQuery_name\\tNum_ref_contigs\\tNum_query_contigs\\tANI_5_percentile\\t' \\\n 'ANI_95_percentile\\tStandard_deviation\\tRef_90_ctg_len\\tRef_50_ctg_len\\t' \\\n 'Ref_10_ctg_len\\tQuery_90_ctg_len\\tQuery_50_ctg_len\\tQuery_10_ctg_len\\t' \\\n 'Avg_chain_len\\tTotal_bases_covered\\n'\n\n with viral_ngs.core.file.tempfnames(('.header.tsv', '.out.tsv')) as (in_tsv, out_tsv):\n with open(in_tsv, 'w') as f:\n f.write(header)\n\n skani._sort_skani_table_by_product(in_tsv, out_tsv)\n\n # Output should have header only\n with open(out_tsv) as f:\n lines = f.readlines()\n self.assertEqual(len(lines), 1)\n self.assertTrue(lines[0].startswith('Ref_file'))\n\n\nclass TestMutableSequence(unittest.TestCase):\n ''' Test the MutableSequence class '''\n\n def test_bad_coords(self):\n self.assertRaises(Exception, viral_ngs.assembly.MutableSequence, 'chr', 0, 4)\n self.assertRaises(Exception, viral_ngs.assembly.MutableSequence, 'chr', 5, 4)\n self.assertRaises(Exception, viral_ngs.assembly.MutableSequence, 'chr', -2, 4)\n self.assertRaises(Exception, viral_ngs.assembly.MutableSequence, 'chr', 5, 6, 'G')\n\n def test_good_coords(self):\n x = viral_ngs.assembly.MutableSequence('chr', 1, 5)\n x = viral_ngs.assembly.MutableSequence('chr', 5, 5)\n x = viral_ngs.assembly.MutableSequence('chr', 100, 2000)\n x = viral_ngs.assembly.MutableSequence('chr name with spaces 5 @#$ --', 1, 5)\n x = viral_ngs.assembly.MutableSequence('chr', 5, 5, 'A')\n x = viral_ngs.assembly.MutableSequence('chr', 5, 6, 'AT')\n\n def test_modify_one(self):\n x = viral_ngs.assembly.MutableSequence('chr', 5, 8, 'ATCG')\n self.assertRaises(Exception, x.modify, 4, 'G')\n self.assertRaises(Exception, x.modify, 9, 'G')\n self.assertEqual(x.emit(), ('chr', 'ATCG'))\n x.modify(5, 'G')\n self.assertEqual(x.emit(), ('chr', 'GTCG'))\n x.modify(6, 'G')\n self.assertEqual(x.emit(), ('chr', 'GGCG'))\n x.modify(7, 'G')\n self.assertEqual(x.emit(), ('chr', 'GGGG'))\n x.modify(8, 'G')\n self.assertEqual(x.emit(), ('chr', 'GGGG'))\n x.modify(6, 'j')\n self.assertEqual(x.emit(), ('chr', 'GjGG'))\n x.modify(8, 'Y')\n self.assertEqual(x.emit(), ('chr', 'GjGY'))\n\n def test_modify_blank(self):\n x = viral_ngs.assembly.MutableSequence('chr', 5, 8)\n self.assertEqual(x.emit(), ('chr', 'NNNN'))\n x.modify(6, 'G')\n self.assertEqual(x.emit(), ('chr', 'NGNN'))\n\n def test_modify_insertions(self):\n x = viral_ngs.assembly.MutableSequence('chr', 5, 8, 'ATCG')\n x.modify(6, 'insert')\n self.assertEqual(x.emit(), ('chr', 'AinsertCG'))\n x.modify(8, 'tail')\n self.assertEqual(x.emit(), ('chr', 'AinsertCtail'))\n x.modify(5, 'headA')\n self.assertEqual(x.emit(), ('chr', 'headAinsertCtail'))\n\n def test_modify_deletions(self):\n x = viral_ngs.assembly.MutableSequence('chr', 5, 8, 'ATCG')\n self.assertRaises(Exception, x.replace, 6, 9, 'AT')\n x.replace(6, 7, 'CT')\n self.assertEqual(x.emit(), ('chr', 'ACTG'))\n x.replace(6, 7, '')\n self.assertEqual(x.emit(), ('chr', 'AG'))\n x.modify(7, 'x')\n self.assertEqual(x.emit(), ('chr', 'AxG'))\n x.modify(6, 'y')\n self.assertEqual(x.emit(), ('chr', 'AyxG'))\n x.replace(7, 7, '123')\n self.assertEqual(x.emit(), ('chr', 'Ay123G'))\n x.modify(7, 'z')\n self.assertEqual(x.emit(), ('chr', 'AyzG'))\n\n def test_modify_deletions_simple(self):\n x = viral_ngs.assembly.MutableSequence('chr', 5, 8, 'ATCG')\n x.replace(6, 7, 'T')\n self.assertEqual(x.emit(), ('chr', 'ATG'))\n\n def test_modify_deletions_remember(self):\n x = viral_ngs.assembly.MutableSequence('chr', 5, 8, 'ATCG')\n x.replace(6, 7, 'T')\n self.assertEqual(x.emit(), ('chr', 'ATG'))\n x.modify(7, 'x')\n self.assertEqual(x.emit(), ('chr', 'ATxG'))\n x.replay_deletions()\n self.assertEqual(x.emit(), ('chr', 'ATG'))\n\n\nclass TestManualSnpCaller(unittest.TestCase):\n ''' Test the vcfrow_parse_and_call_snps method.. lots of edge cases. '''\n\n def test_missing_dp(self):\n ''' VCF files might contain rows with no calls or any kind of data and that's okay. '''\n row = ['chr10', '105', '.', 'G', '.', '.', '.', '.', 'GT', './.']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))\n self.assertEqual(out, [])\n\n def test_dp_inaccurate(self):\n ''' The DP might not equal the sum of the ADs and that's okay apparently. '''\n row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:5:2,2']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))\n self.assertEqual(set(out[0][4]), set(['G', 'A']))\n row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:2:3,3']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(set(out[0][4]), set(['G', 'A']))\n row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:10:2,0']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(out, [])\n\n def test_invariant_sites(self):\n ''' Invariant site handling is slightly different in code, so test it specially. '''\n row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT:DP', '0/0:3']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])\n row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', '0/0']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=0))\n self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])\n row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', '0/0']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))\n self.assertEqual(out, [])\n row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', './.']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))\n self.assertEqual(out, [])\n row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT:DP', './.:10']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))\n self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])\n\n def test_het_edgecases(self):\n ''' The interplay between min_coverage and major_cutoff is not obvious, here's\n what I understand from Kristian about the desired behavior.\n for min_dp=3:\n 3G, 4A, 5C -> G/A/C\n 2G, 3A, 3T -> A/T\n 2A, 2T -> no call\n 2G, 3C -> C\n 2A, 3C, 4T -> T\n for min_dp=2:\n 2A, 2T -> A/T\n '''\n row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:3,4,5,0']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(set(out[0][4]), set(['G', 'A', 'C']))\n row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:2,3,0,3']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(set(out[0][4]), set(['A', 'T']))\n row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,0,2']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(out, [])\n row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,0,2']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=2))\n self.assertEqual(set(out[0][4]), set(['A', 'T']))\n row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:2,0,3,0']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(out[0][4], ['C'])\n row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,3,4']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(out[0][4], ['T'])\n\n def test_indels(self):\n ''' Indel handling '''\n row = ['thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD', '0/1:5,10,1']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(set(out[0][4]), set(['GA']))\n row = ['thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD', '0/1:5,5,2']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(set(out[0][4]), set(['G', 'GA']))\n row = ['thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD', '0/1:5,5,3']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))\n self.assertEqual(set(out[0][4]), set(['G', 'GA', 'T']))\n row = ['thecontig', '105000', '.', 'AT', 'A', '.', '.', '.', 'GT:AD', '0/1:2,10']\n out = list(viral_ngs.assembly.vcfrow_parse_and_call_snps(row, ['s1']))\n self.assertEqual(out, [('thecontig', 105000, 105001, 's1', ['A'])])\n\n def test_vcf_to_seqs_indels1(self):\n input = ['thecontig', '5', '.', 'AT', 'A', '.', '.', '.', 'GT:AD', '0/1:2,10']\n actual = viral_ngs.assembly.vcf_to_seqs([input], {'thecontig': 10}, ['s1'], min_dp=2)\n actual = list(actual)[0][1].strip('N')\n self.assertEqual(actual, 'A')\n actual = viral_ngs.assembly.vcf_to_seqs([input], {'thecontig': 10}, ['s1'], min_dp=2)\n actual = list(actual)[0][1]\n self.assertEqual(actual, 'NNNNANNNN')\n\n def test_vcf_to_seqs_indels2(self):\n ''' More end-to-end indel handling '''\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n input = os.path.join(myInputDir, 'indel.vcf.gz')\n expected = os.path.join(myInputDir, 'output.fasta')\n chrlens = {'EBOV_2014_G6060.1': 18962}\n samples = ['G6060.1']\n expected = str(Bio.SeqIO.read(expected, 'fasta').seq)\n actual = viral_ngs.assembly.vcf_to_seqs(viral_ngs.core.file.read_tabfile(input), chrlens, samples, min_dp=2)\n actual = list(actual)[0][1].strip('N')\n self.assertEqual(actual, expected)\n\n\nclass TestDeambigAndTrimFasta(TestCaseWithTmp):\n ''' Test the deambig_fasta and trim_fasta commands. '''\n\n def run_method(self, inseqs, parser_fun):\n fasta_in = viral_ngs.core.file.mkstempfname()\n fasta_out = viral_ngs.core.file.mkstempfname()\n makeFasta([(str(i), inseqs[i]) for i in range(len(inseqs))], fasta_in)\n args = parser_fun(argparse.ArgumentParser()).parse_args([fasta_in, fasta_out])\n args.func_main(args)\n return (fasta_in, fasta_out)\n\n def test_trim_fasta(self):\n ''' Simple test of the trim_fasta command '''\n inseqs = ['NNnnNNnNaslkdfjasdkfNNNN', 'NNNnnN', 'NNN123', 'ATCG']\n expected = ['aslkdfjasdkf', '', '123', 'ATCG']\n expected = dict((str(i), expected[i]) for i in range(len(expected)))\n fasta_in, fasta_out = self.run_method(inseqs, viral_ngs.assembly.parser_trim_fasta)\n with open(fasta_out, 'rt') as fa:\n for record in Bio.SeqIO.parse(fa, 'fasta'):\n self.assertIn(record.id, expected)\n self.assertEqual(str(record.seq), expected[record.id])\n\n def test_deambig_fasta(self):\n ''' Simple test of the deambig_fasta command '''\n table = [(k, v) for k, v in Bio.Data.IUPACData.ambiguous_dna_values.items() if k != 'X']\n keys = [k for k, v in table]\n vals = [set(v) for k, v in table]\n keys = keys + [k.lower() for k in keys]\n vals = vals + vals\n inseq = ''.join(keys)\n fasta_in, fasta_out = self.run_method([inseq], viral_ngs.assembly.parser_deambig_fasta)\n with open(fasta_out, 'rt') as fa:\n for rec in Bio.SeqIO.parse(fa, 'fasta'):\n self.assertEqual(rec.id, '0')\n outseq = str(rec.seq)\n for i in range(len(outseq)):\n self.assertIn(outseq[i], vals[i])\n\n\nclass TestContigChooser(unittest.TestCase):\n ''' Test the contig_chooser heuristic used by our MUMmer-based custom scaffolder. '''\n\n def test_no_seqs(self):\n for test_len in (7,2,228,52):\n actual = viral_ngs.assemble.mummer.contig_chooser([], test_len)\n self.assertEqual(actual, ['N' * test_len])\n\n def test_one_seq(self):\n for test_seq in ('A', '', 'GACTGATG', 'non-biological :characters!'):\n actual = viral_ngs.assemble.mummer.contig_chooser([test_seq], 90)\n self.assertEqual(actual, [test_seq])\n\n def test_most_popular_seq(self):\n alt_seqs = ['AA', 'aa', 'GGA', 'T', 'GGA']\n expected_choice = 'GGA'\n expected_alts = set(('AA', 'aa', 'T'))\n actual = viral_ngs.assemble.mummer.contig_chooser(alt_seqs, 2)\n self.assertEqual(actual[0], expected_choice)\n self.assertEqual(set(actual[1:]), expected_alts)\n\n def test_most_popular_seq_len(self):\n alt_seqs = ['AA', 'GGA', 'aa', 'GGA', 'T', 'GGC', 'aa']\n actual = viral_ngs.assemble.mummer.contig_chooser(alt_seqs, 2)\n self.assertEqual(actual[0], 'aa')\n self.assertEqual(set(actual[1:]), set(('AA', 'GGA', 'T', 'GGC')))\n actual = viral_ngs.assemble.mummer.contig_chooser(alt_seqs, 3)\n self.assertEqual(actual[0], 'GGA')\n self.assertEqual(set(actual[1:]), set(('AA', 'aa', 'T', 'GGC')))\n alt_seqs = ['AA', 'GGA', 'aa', 'GGA', 'T', 'GGC']\n actual = viral_ngs.assemble.mummer.contig_chooser(alt_seqs, 20)\n self.assertEqual(actual[0], 'GGA')\n self.assertEqual(set(actual[1:]), set(('AA', 'aa', 'T', 'GGC')))\n actual = viral_ngs.assemble.mummer.contig_chooser(alt_seqs, 1)\n self.assertEqual(actual[0], 'GGA')\n self.assertEqual(set(actual[1:]), set(('AA', 'aa', 'T', 'GGC')))\n\n def test_same_as_ref_len(self):\n alt_seqs = ['AA', 'GGA', 'aa', 'GGA', 'T', 'GGC', 'aa']\n actual = viral_ngs.assemble.mummer.contig_chooser(alt_seqs, 1)\n self.assertEqual(actual[0], 'T')\n\n\nclass TestWgsimTool(TestCaseWithTmp):\n ''' Test wgsim tool wrapper helper methods '''\n\n def test_slice_fasta_whole_sequence(self):\n ''' Test slicing a fasta to a specific sequence ID without coordinate range '''\n wgsim = viral_ngs.assemble.wgsim.WgsimTool()\n\n # Create test fasta with multiple sequences\n in_fasta = viral_ngs.core.file.mkstempfname('.fasta')\n seqs = [('seq1', 'ACGTACGTACGT'), ('seq2', 'GGGGCCCCAAAA'), ('seq3', 'TTTTTTTTTTTT')]\n makeFasta(seqs, in_fasta)\n\n # Slice to seq2\n out_fasta = viral_ngs.core.file.mkstempfname('.sliced.fasta')\n wgsim.slice_fasta(in_fasta, out_fasta, seq_id='seq2')\n\n # Verify only seq2 is in output\n records = list(Bio.SeqIO.parse(out_fasta, 'fasta'))\n self.assertEqual(len(records), 1)\n self.assertEqual(records[0].id, 'seq2')\n self.assertEqual(str(records[0].seq), 'GGGGCCCCAAAA')\n\n def test_slice_fasta_with_coordinates(self):\n ''' Test slicing a fasta to a specific coordinate range '''\n wgsim = viral_ngs.assemble.wgsim.WgsimTool()\n\n # Create test fasta\n in_fasta = viral_ngs.core.file.mkstempfname('.fasta')\n seqs = [('seq1', 'ACGTACGTACGTACGT')]\n makeFasta(seqs, in_fasta)\n\n # Slice to positions 5-10 (1-based inclusive)\n out_fasta = viral_ngs.core.file.mkstempfname('.sliced.fasta')\n wgsim.slice_fasta(in_fasta, out_fasta, seq_id='seq1', start=5, end=10)\n\n # Verify sliced sequence\n records = list(Bio.SeqIO.parse(out_fasta, 'fasta'))\n self.assertEqual(len(records), 1)\n self.assertEqual(str(records[0].seq), 'ACGTAC')\n\n def test_slice_fasta_no_params(self):\n ''' Test that slice_fasta with no optional params is a no-op '''\n wgsim = viral_ngs.assemble.wgsim.WgsimTool()\n\n # Create test fasta\n in_fasta = viral_ngs.core.file.mkstempfname('.fasta')\n seqs = [('seq1', 'ACGTACGT'), ('seq2', 'GGGGCCCC')]\n makeFasta(seqs, in_fasta)\n\n # Slice with no params\n out_fasta = viral_ngs.core.file.mkstempfname('.sliced.fasta')\n wgsim.slice_fasta(in_fasta, out_fasta)\n\n # Verify all sequences are in output (no-op)\n records = list(Bio.SeqIO.parse(out_fasta, 'fasta'))\n self.assertEqual(len(records), 2)\n self.assertEqual(str(records[0].seq), 'ACGTACGT')\n self.assertEqual(str(records[1].seq), 'GGGGCCCC')\n\n def test_coverage_to_read_pairs(self):\n ''' Test coverage to read pairs calculation '''\n wgsim = viral_ngs.assemble.wgsim.WgsimTool()\n\n # Test case 1: 20X coverage, 1000bp sequence, 150bp reads\n # Expected: (20 * 1000) / (2 * 150) = 66.67 -> 67 pairs\n pairs = wgsim.coverage_to_read_pairs(20, 1000, 150)\n self.assertEqual(pairs, 67)\n\n # Test case 2: 10X coverage, 5000bp sequence, 100bp reads\n # Expected: (10 * 5000) / (2 * 100) = 250 pairs\n pairs = wgsim.coverage_to_read_pairs(10, 5000, 100)\n self.assertEqual(pairs, 250)\n\n # Test case 3: Fractional coverage (0.5X)\n # Expected: (0.5 * 1000) / (2 * 150) = 1.67 -> 2 pairs\n pairs = wgsim.coverage_to_read_pairs(0.5, 1000, 150)\n self.assertEqual(pairs, 2)\n\n # Test case 4: High coverage\n # Expected: (100 * 3000) / (2 * 150) = 1000 pairs\n pairs = wgsim.coverage_to_read_pairs(100, 3000, 150)\n self.assertEqual(pairs, 1000)\n\n\nclass TestSimulateIlluminaReads(TestCaseWithTmp):\n ''' Test simulate_illumina_reads command for generating synthetic reads '''\n\n def setUp(self):\n super(TestSimulateIlluminaReads, self).setUp()\n self.in_fasta = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ref.lasv.fasta')\n # Calculate expected sequence lengths\n self.seq_lengths = {}\n for record in Bio.SeqIO.parse(self.in_fasta, 'fasta'):\n self.seq_lengths[record.id] = len(record.seq)\n\n def count_bam_reads(self, bam_file):\n ''' Count the number of reads in a BAM file '''\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n read_count = int(subprocess.check_output(\n [samtools.install_and_get_path(), 'view', '-c', bam_file]\n ).decode('UTF-8').strip())\n return read_count\n\n def expected_read_count(self, coverage, seq_length, read_length=150):\n ''' Calculate expected number of individual reads (not pairs) '''\n # Each read pair contributes 2 reads\n pairs = viral_ngs.assemble.wgsim.WgsimTool().coverage_to_read_pairs(\n coverage, seq_length, read_length\n )\n return pairs * 2\n\n def test_simulate_uniform_coverage(self):\n ''' Test simulating reads with uniform coverage across all sequences '''\n out_bam = viral_ngs.core.file.mkstempfname('.bam')\n coverage = 20.0\n read_length = 150\n\n # Run simulate_illumina_reads with uniform coverage\n args = [self.in_fasta, out_bam, str(coverage), '--read_length', str(read_length), '--random_seed', '12345']\n args = viral_ngs.assembly.parser_simulate_illumina_reads(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n # Verify BAM was created\n self.assertTrue(os.path.isfile(out_bam))\n self.assertGreater(os.path.getsize(out_bam), 0)\n\n # Count reads in output\n actual_reads = self.count_bam_reads(out_bam)\n\n # Calculate expected reads (sum across all sequences)\n expected_reads = sum(\n self.expected_read_count(coverage, seq_len, read_length)\n for seq_len in self.seq_lengths.values()\n )\n\n # Verify within 10% tolerance\n tolerance = 0.10\n self.assertGreater(actual_reads, expected_reads * (1 - tolerance))\n self.assertLess(actual_reads, expected_reads * (1 + tolerance))\n\n def test_simulate_per_sequence_coverage(self):\n ''' Test simulating reads with per-sequence coverage specification '''\n out_bam = viral_ngs.core.file.mkstempfname('.bam')\n read_length = 150\n\n # Get sequence IDs\n seq_ids = list(self.seq_lengths.keys())\n # Specify different coverage for each sequence\n coverage_spec = f\"{seq_ids[0]}:20x {seq_ids[1]}:5x\"\n\n # Run simulate_illumina_reads with per-sequence coverage\n args = [self.in_fasta, out_bam, coverage_spec, '--read_length', str(read_length), '--random_seed', '12345']\n args = viral_ngs.assembly.parser_simulate_illumina_reads(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n # Verify BAM was created\n self.assertTrue(os.path.isfile(out_bam))\n self.assertGreater(os.path.getsize(out_bam), 0)\n\n # Count reads in output\n actual_reads = self.count_bam_reads(out_bam)\n\n # Calculate expected reads\n expected_reads = (\n self.expected_read_count(20, self.seq_lengths[seq_ids[0]], read_length) +\n self.expected_read_count(5, self.seq_lengths[seq_ids[1]], read_length)\n )\n\n # Verify within 10% tolerance\n tolerance = 0.10\n self.assertGreater(actual_reads, expected_reads * (1 - tolerance))\n self.assertLess(actual_reads, expected_reads * (1 + tolerance))\n\n def test_simulate_bed_coverage(self):\n ''' Test simulating reads with BED file coverage specification '''\n out_bam = viral_ngs.core.file.mkstempfname('.bam')\n bed_file = viral_ngs.core.file.mkstempfname('.bed')\n read_length = 150\n\n # Get sequence IDs\n seq_ids = list(self.seq_lengths.keys())\n\n # Create BED file with different coverage for different regions\n with open(bed_file, 'w') as f:\n # First sequence: 10x coverage for positions 1-2000\n f.write(f\"{seq_ids[0]}\\t0\\t2000\\t.\\t10\\n\")\n # Second sequence: 25x coverage for positions 1-3000\n f.write(f\"{seq_ids[1]}\\t0\\t3000\\t.\\t25\\n\")\n\n # Run simulate_illumina_reads with BED file\n args = [self.in_fasta, out_bam, bed_file, '--read_length', str(read_length), '--random_seed', '12345']\n args = viral_ngs.assembly.parser_simulate_illumina_reads(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n # Verify BAM was created\n self.assertTrue(os.path.isfile(out_bam))\n self.assertGreater(os.path.getsize(out_bam), 0)\n\n # Count reads in output\n actual_reads = self.count_bam_reads(out_bam)\n\n # Calculate expected reads\n expected_reads = (\n self.expected_read_count(10, 2000, read_length) +\n self.expected_read_count(25, 3000, read_length)\n )\n\n # Verify within 10% tolerance\n tolerance = 0.10\n self.assertGreater(actual_reads, expected_reads * (1 - tolerance))\n self.assertLess(actual_reads, expected_reads * (1 + tolerance))\n\n\ndef _find_script(script_name):\n \"\"\"Find script in Docker path or git clone path.\"\"\"\n # Docker-installed location\n docker_path = f'/opt/viral-ngs/scripts/{script_name}'\n if os.path.exists(docker_path):\n return docker_path\n # Git clone location (relative to this test file)\n git_path = os.path.join(os.path.dirname(__file__), '..', '..', '..', 'docker', 'scripts', script_name)\n if os.path.exists(git_path):\n return git_path\n raise FileNotFoundError(f\"Script {script_name} not found in Docker or git paths\")\n\n\nclass TestFastaTrimTerminalAmbigs(TestCaseWithTmp):\n ''' Test fasta-trim-terminal-ambigs.pl script functionality '''\n\n def test_script_runs_successfully(self):\n ''' Test that fasta-trim-terminal-ambigs.pl can run without errors '''\n # Create a test FASTA with terminal ambiguous bases\n in_fasta = viral_ngs.core.file.mkstempfname('.fasta')\n out_fasta = viral_ngs.core.file.mkstempfname('.trimmed.fasta')\n\n # Create sequences with terminal Ns and ambiguous bases\n test_seqs = [\n ('seq1', 'NNNNNATCGATCGATCGNNNN'),\n ('seq2', 'WWWWATCGATCGATCGYYYYY'),\n ('seq3', 'RRRRATCGATCGATCGSSS'),\n ]\n makeFasta(test_seqs, in_fasta)\n\n # Run fasta-trim-terminal-ambigs.pl\n script_path = _find_script('fasta-trim-terminal-ambigs.pl')\n cmd = [script_path, in_fasta]\n\n result = subprocess.run(cmd, capture_output=True, text=True, cwd=os.getcwd())\n\n # Check that script runs successfully\n self.assertEqual(result.returncode, 0,\n f\"Script failed with stderr: {result.stderr}\\nstdout: {result.stdout}\")\n\n # Verify output contains trimmed sequences\n self.assertIn('ATCGATCGATCG', result.stdout)\n\n def test_script_with_3rules_option(self):\n ''' Test fasta-trim-terminal-ambigs.pl with --3rules option '''\n # Use the ebov-makona.fasta from test inputs\n in_fasta = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebov-makona.fasta')\n\n # Run with --3rules and standard parameters\n script_path = _find_script('fasta-trim-terminal-ambigs.pl')\n cmd = [\n script_path,\n '--3rules',\n '--ten', '4',\n '--fifty', '15',\n '--maxfrac', '0.9',\n in_fasta\n ]\n\n result = subprocess.run(cmd, capture_output=True, text=True, cwd=os.getcwd())\n\n # Check that script runs successfully\n self.assertEqual(result.returncode, 0,\n f\"Script failed with stderr: {result.stderr}\\nstdout: {result.stdout}\")\n\n # Verify output was produced\n self.assertGreater(len(result.stdout), 0, \"No output produced\")\n self.assertIn('>', result.stdout, \"No FASTA header in output\")\n" }, { "path": "tests/unit/assemble/test_assembly_integration.py", "content": "# Integration tests for viral_ngs.assembly.py\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport os\nimport shutil\nimport tempfile\nimport itertools\nimport unittest\nimport pytest\n\nimport Bio.SeqIO\n\nimport viral_ngs.assembly\nimport viral_ngs.core.cmd\nimport viral_ngs.core.file\nimport viral_ngs.core.minimap2\nimport viral_ngs.core.picard\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp, _CPUS\n\n\ndef _align_with_minimap2(refFasta, inBam):\n \"\"\"Align reads to reference with minimap2, return indexed BAM path.\"\"\"\n mm2 = viral_ngs.core.minimap2.Minimap2()\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n outBam = viral_ngs.core.file.mkstempfname('.aligned.bam')\n mm2.align_bam(inBam, refFasta, outBam, options=['-x', 'sr'])\n samtools.index(outBam)\n return outBam\n\n\nclass TestRefineAssembly(TestCaseWithTmp):\n def test_ebov_refine1(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n inFasta = os.path.join(inDir, 'impute.ebov.fasta')\n imputeFasta = viral_ngs.core.file.mkstempfname('.imputed.fasta')\n refine1Fasta = viral_ngs.core.file.mkstempfname('.refine1.fasta')\n shutil.copy(inFasta, imputeFasta)\n viral_ngs.core.picard.CreateSequenceDictionaryTool().execute(imputeFasta, overwrite=True)\n viral_ngs.core.samtools.SamtoolsTool().faidx(imputeFasta, overwrite=True)\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.mini.bam')\n alignedBam = _align_with_minimap2(imputeFasta, inBam)\n viral_ngs.assembly.refine_assembly(\n imputeFasta, inBam, refine1Fasta,\n already_realigned_bam=alignedBam,\n min_coverage=2)\n actual = str(Bio.SeqIO.read(refine1Fasta, 'fasta').seq)\n expected = str(Bio.SeqIO.read(os.path.join(inDir, 'expected.ebov.refine1.freebayes.fasta'), 'fasta').seq)\n self.assertEqual(actual, expected)\n\n def test_ebov_refine2(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n inFasta = os.path.join(inDir, 'expected.ebov.refine1.fasta')\n refine1Fasta = viral_ngs.core.file.mkstempfname('.refine1.fasta')\n refine2Fasta = viral_ngs.core.file.mkstempfname('.refine2.fasta')\n shutil.copy(inFasta, refine1Fasta)\n viral_ngs.core.picard.CreateSequenceDictionaryTool().execute(refine1Fasta, overwrite=True)\n viral_ngs.core.samtools.SamtoolsTool().faidx(refine1Fasta, overwrite=True)\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.mini.bam')\n alignedBam = _align_with_minimap2(refine1Fasta, inBam)\n viral_ngs.assembly.refine_assembly(\n refine1Fasta, inBam, refine2Fasta,\n already_realigned_bam=alignedBam,\n min_coverage=3)\n actual = str(Bio.SeqIO.read(refine2Fasta, 'fasta').seq)\n expected = str(Bio.SeqIO.read(os.path.join(inDir, 'expected.ebov.refine2.freebayes.fasta'), 'fasta').seq)\n self.assertEqual(actual, expected)\n\n\nclass TestOrderOrientAndImputeFromReference(TestCaseWithTmp):\n # common setup\n def setUp(self):\n super(TestOrderOrientAndImputeFromReference, self).setUp()\n self.inDir = viral_ngs.core.file.get_test_input_path(self)\n\n self.refFasta = os.path.join(self.inDir, 'ref.influenza_partial.fasta')\n self.outOrientFasta = viral_ngs.core.file.mkstempfname('.fasta')\n viral_ngs.assembly.order_and_orient(\n os.path.join(self.inDir, 'contigs.influenza.fasta'),\n self.refFasta,\n self.outOrientFasta)\n\n # common teardown\n def tearDown(self):\n os.unlink(self.outOrientFasta)\n super(TestOrderOrientAndImputeFromReference, self).tearDown()\n\n def test_impute_from_oriented_muscle(self):\n self.influenza_impute(\"muscle\")\n\n def test_impute_from_oriented_mafft(self):\n self.influenza_impute(\"mafft\")\n\n def test_impute_from_oriented_mummer(self):\n self.influenza_impute(\"mummer\")\n\n # common impute function using the specified aligner\n def influenza_impute(self, aligner):\n outImputeFasta = viral_ngs.core.file.mkstempfname('.fasta')\n expected = os.path.join(self.inDir, 'expected.influenza.impute.'+aligner+'.fasta')\n # ensure we can run impute_from_reference from the output of order_and_orient\n # without errors, but don't actually check the output\n viral_ngs.assembly.impute_from_reference(\n self.outOrientFasta,\n self.refFasta,\n outImputeFasta,\n minLengthFraction=0.8,\n minUnambig=0.2,\n replaceLength=5,\n newName='test_influenza.genome',\n aligner=aligner)\n\n # if we were interested in checking the output...\n # self.assertEqualContents(\n # outImputeFasta,\n # expected\n # )\n" }, { "path": "tests/unit/assemble/test_util_vcf.py", "content": "# Unit tests for util/vcf.py\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport viral_ngs.assemble.vcf\nimport viral_ngs.core.file\nimport unittest\n'''\nTODO\nmake_intervals\nsliding_windows\ncalc_maf\nTabixReader - edge cases in a simple file\nVcfReader - proper one-based genomic coordinates\nVcfReader - haploid cases, diploid cases\nVcfReader.getFullSequences and replaceAlleles - this needs a whole battery of tests,\n since it does so much and is subject to so many edge cases and weird scenarios and\n keeps breaking each time we refactor.\n'''\n\n\nclass StubGenome:\n ''' This is a mock genome that should satisfy very simple functions in assemble.vcf\n like get_chrlens, GenomePosition, make_intervals, sliding_windows, etc.\n It simply contains a list of chromosome names and lengths.\n '''\n\n def __init__(self, chromlist):\n self.chrs = [c for c, clen in chromlist]\n self.chrlen = dict(chromlist)\n self.totlen = sum(clen for c, clen in chromlist)\n\n def chrlens(self):\n return [(c, self.chrlen[c]) for c in self.chrs]\n\n\nclass TestGenomePosition(unittest.TestCase):\n ''' Test the GenomePosition class which maps chr,pos pairs to a single gpos int and vice versa '''\n\n def test_fail_OOB_get_gpos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n invalids = [('SDF', 0), ('SDF', 124), ('ASDF', -1), ('lala', 48), ('lala', 200), ('sdf', 80), ('la', 2),\n (None, 3)]\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n for c, p in invalids:\n self.assertRaises(Exception, gmap.get_gpos, c, p)\n\n def test_fail_OOB_get_chr_pos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n invalids = [0, -1, genome.totlen + 1, genome.totlen * 2]\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n for gpos in invalids:\n self.assertRaises(Exception, gmap.get_chr_pos, gpos)\n\n def test_fail_non_int_pos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n invalids = [('SDF', 5.3), ('lala', '10'), ('ASDF', None)]\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n for c, p in invalids:\n self.assertRaises(Exception, gmap.get_gpos, c, p)\n self.assertRaises(Exception, gmap.get_chr_pos, p)\n\n def test_spotcheck_edges(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n knowns = [('SDF', 1, 1), ('SDF', 123, 123), ('ASDF', 1, 124), ('ASDF', 256, 379), ('lala', 1, 380),\n ('lala', 47, 426)]\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n for c, p, gpos in knowns:\n self.assertEqual(gpos, gmap.get_gpos(c, p))\n self.assertEqual((c, p), gmap.get_chr_pos(gpos))\n\n def test_equality_1chrGenome(self):\n genome = StubGenome([('one chr', 10)])\n c = genome.chrs[0]\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n for i in range(1, genome.totlen + 1):\n self.assertEqual(i, gmap.get_gpos(c, i)) # c,p -> gpos should produce p=gpos\n self.assertEqual((c, i), gmap.get_chr_pos(i)) # gpos -> c,p should produce p=gpos\n\n def test_equality_3chrGenome(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n # test gpos -> c,p -> same gpos\n for gpos in range(1, genome.totlen + 1):\n c, p = gmap.get_chr_pos(gpos)\n gpos2 = gmap.get_gpos(c, p)\n self.assertEqual(gpos, gpos2)\n # test c,p -> gpos -> same c,p\n for c, clen in genome.chrlen.items():\n for p in range(1, clen + 1):\n gpos = gmap.get_gpos(c, p)\n c2, p2 = gmap.get_chr_pos(gpos)\n self.assertEqual(c, c2)\n self.assertEqual(p, p2)\n\n def test_gpos_inbounds(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n for c, clen in genome.chrlen.items():\n for p in range(1, clen + 1):\n gpos = gmap.get_gpos(c, p)\n self.assertIsNotNone(gpos)\n self.assertIsInstance(gpos, int)\n self.assertLessEqual(1, gpos)\n self.assertLessEqual(gpos, genome.totlen)\n\n def test_chr_pos_inbounds(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n for gpos in range(1, genome.totlen + 1):\n c, p = gmap.get_chr_pos(gpos)\n self.assertIsNotNone(c)\n self.assertIn(c, genome.chrlen)\n self.assertIsNotNone(p)\n self.assertIsInstance(p, int)\n self.assertLessEqual(1, p)\n self.assertLessEqual(p, genome.chrlen[c])\n\n def test_unique_gpos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n seen = set()\n for c, clen in genome.chrlen.items():\n for p in range(1, clen + 1):\n gpos = gmap.get_gpos(c, p)\n self.assertNotIn(gpos, seen)\n seen.add(gpos)\n self.assertEqual(len(seen), genome.totlen)\n\n def test_unique_chr_pos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.assemble.vcf.GenomePosition(genome)\n seen = set()\n for gpos in range(1, genome.totlen + 1):\n c, p = gmap.get_chr_pos(gpos)\n self.assertNotIn((c, p), seen)\n seen.add((c, p))\n self.assertEqual(len(seen), genome.totlen)\n\n\nclass TestVcfContigHeaderParsing(unittest.TestCase):\n '''Test that parse_contig_header handles various VCF contig header formats'''\n\n def test_simple_contig_header(self):\n c, clen = viral_ngs.assemble.vcf.parse_contig_header('##contig=')\n self.assertEqual(c, 'seg1')\n self.assertEqual(clen, 2334)\n\n def test_contig_header_with_assembly(self):\n c, clen = viral_ngs.assemble.vcf.parse_contig_header('##contig=')\n self.assertEqual(c, 'seg1')\n self.assertEqual(clen, 2334)\n\n def test_contig_header_with_multiple_extra_attrs(self):\n c, clen = viral_ngs.assemble.vcf.parse_contig_header('##contig=')\n self.assertEqual(c, 'chr1')\n self.assertEqual(clen, 100000)\n\n def test_multiple_contigs_mixed_formats(self):\n headers = [\n '##contig=',\n '##contig=',\n '##contig=',\n ]\n result = dict(viral_ngs.assemble.vcf.parse_contig_header(h) for h in headers)\n self.assertEqual(result, {'seg1': 2334, 'seg2': 5000, 'seg3': 800})\n\n def test_contig_header_without_length_raises(self):\n with self.assertRaises(ValueError):\n viral_ngs.assemble.vcf.parse_contig_header('##contig=')\n\n def test_invalid_header_raises(self):\n with self.assertRaises(ValueError):\n viral_ngs.assemble.vcf.parse_contig_header('##INFO=')\n\n\nclass TestVcfReaderPositions(unittest.TestCase):\n ''' Test the OBO errors in the pysam-based VCFReader class (it's prone to such errors) '''\n\n def setUp(self):\n self.vcf_fname = viral_ngs.core.file.get_test_path() + '/input/one_gene.vcf.gz'\n self.vcf_window = ('Pf3D7_13_v3', 1724817, 1726997)\n try:\n self.basestring = basestring\n except NameError:\n self.basestring = str\n\n def test_sample_names(self):\n expected = ['3D7', 'SenT001.08', 'SenT001.11', 'SenT002.07', 'SenT002.09']\n vcfdb = viral_ngs.assemble.vcf.VcfReader(self.vcf_fname)\n self.assertEqual(expected, vcfdb.samples())\n for s in vcfdb.samples():\n self.assertIsInstance(s, self.basestring)\n\n def test_get_one_base(self):\n vcfdb = viral_ngs.assemble.vcf.VcfReader(self.vcf_fname)\n genos = vcfdb.get_snp_genos(self.vcf_window[0], 1726432)\n alleles = [genos[s] for s in vcfdb.samples()]\n expected = ['T', 'T', 'T', 'G', 'T']\n self.assertEqual(expected, alleles)\n for a in alleles:\n self.assertIsInstance(a, self.basestring)\n\n def test_get_positions_edges(self):\n vcfdb = viral_ngs.assemble.vcf.VcfReader(self.vcf_fname)\n out = list(vcfdb.get_positions(self.vcf_window[0]))\n self.assertEqual(out[0][1], self.vcf_window[1])\n self.assertEqual(out[-1][2], self.vcf_window[2])\n\n def test_get_range_edges(self):\n vcfdb = viral_ngs.assemble.vcf.VcfReader(self.vcf_fname)\n out = [p for c, p, alleles, genos in vcfdb.get_range(self.vcf_window[0])]\n self.assertEqual(out[0], self.vcf_window[1])\n self.assertEqual(out[-1], self.vcf_window[2])\n" }, { "path": "tests/unit/classify/__init__.py", "content": "\n" }, { "path": "tests/unit/classify/fixtures.py", "content": "import gzip\nimport os\nfrom os.path import join\nimport shutil\n\nfrom viral_ngs.classify import krona as krona_module\nfrom viral_ngs.core import file\n\n# @pytest.fixture(scope='module')\ndef krona():\n krona_tool = krona_module.Krona()\n krona_tool.install()\n return krona_tool\n\n\n# @pytest.fixture(scope='module', params=['TestMetagenomicsSimple', 'TestMetagenomicsViralMix'])\ndef db_type(request):\n return request.param\n\n\n# @pytest.fixture(scope='module')\ndef krona_db(request, tmpdir_module, krona, db_type):\n data_dir = join(file.get_test_input_path(), db_type)\n db_dir = join(data_dir, 'db')\n\n db = join(tmpdir_module, 'krona_db_{}'.format(db_type))\n os.mkdir(db)\n for d in ('names.dmp', 'nodes.dmp'):\n src = join(db_dir, 'taxonomy', d)\n dest = join(db, d)\n if os.path.isfile(src):\n os.symlink(src, dest)\n krona.create_db(db)\n return db\n\n\ndef taxonomy_db(request, tmpdir_module, db_type):\n taxonomy = join(tmpdir_module, db_type, 'taxonomy')\n shutil.copytree(join(file.get_test_input_path(), db_type, 'db', 'taxonomy'),\n taxonomy)\n prot = join(taxonomy, 'accession2taxid', 'prot.accession2taxid')\n prot_gz = prot + '.gz'\n\n with open(prot, 'rb') as f_in:\n with gzip.open(prot_gz, 'wb') as f_out:\n shutil.copyfileobj(f_in, f_out)\n\n return taxonomy\n" }, { "path": "tests/unit/classify/test_integration_kb.py", "content": "# Integration tests for kb-python\nimport argparse\nimport os\nimport platform\nfrom pathlib import Path\n\nimport anndata\nimport pytest\n\nfrom viral_ngs import metagenomics\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.core import picard\n\n# Skip all tests on ARM platforms - kallisto/kb-python are x86-only (no ARM64 builds)\nIS_ARM = platform.machine() in ('arm64', 'aarch64')\npytestmark = pytest.mark.skipif(IS_ARM, reason=\"kallisto/kb-python require x86-only bioconda packages (not available on ARM)\")\n\n\n@pytest.fixture(scope='module')\ndef kb_inputs():\n base = os.path.join(util_file.get_test_input_path(), 'TestKbPython')\n fastq = os.path.join(base, 'SRR12340077.2.sample.fastq.gz')\n index = os.path.join(base, 'palmdb.corona.idx')\n t2g = os.path.join(base, 'palmdb_clustered_t2g.txt')\n ref_fasta = os.path.join(base, 'palmdb_rdrp_seqs.corona.fa')\n for path in (fastq, index, t2g, ref_fasta):\n if not os.path.exists(path):\n pytest.skip(f\"Required kb test input missing: {path}\")\n return {'fastq': fastq, 'index': index, 't2g': t2g, 'ref_fasta': ref_fasta}\n\n\n@pytest.fixture(scope='module')\ndef kb_bam(tmp_path_factory, kb_inputs):\n workdir = tmp_path_factory.mktemp('kb_input_bam')\n bam_path = Path(workdir) / 'input.bam'\n try:\n picard = picard.FastqToSamTool()\n picard.execute(kb_inputs['fastq'], None, 'kb_sample', str(bam_path))\n except Exception as exc:\n pytest.skip(f\"Unable to create BAM for kb tests: {exc}\")\n return str(bam_path)\n\n\n@pytest.fixture(scope='module')\ndef kb_count_result(tmp_path_factory, kb_inputs, kb_bam):\n workdir = tmp_path_factory.mktemp('kb_count')\n out_dir = Path(workdir) / 'counts'\n out_dir.mkdir()\n argv = [\n '--index', kb_inputs['index'],\n '--t2g', kb_inputs['t2g'],\n '--kmer_len', '31',\n '--technology', 'bulk',\n '--h5ad',\n '--out_dir', str(out_dir),\n '--threads', '4',\n kb_bam,\n ]\n _run_metagenomics(metagenomics.parser_kb, argv, cwd=str(workdir))\n h5ad_dir = out_dir / 'counts_unfiltered'\n h5ad_files = list(h5ad_dir.glob('*.h5ad'))\n assert h5ad_files, f\"No h5ad produced under {h5ad_dir}\"\n return {\n 'workdir': Path(workdir),\n 'out_dir': out_dir,\n 'h5ad': h5ad_files[0],\n }\n\n\n@pytest.fixture(scope='module')\ndef kb_extract_result(tmp_path_factory, kb_inputs, kb_bam):\n workdir = tmp_path_factory.mktemp('kb_extract')\n out_dir = Path(workdir) / 'extract'\n out_dir.mkdir()\n argv = [\n '--index', kb_inputs['index'],\n '--t2g', kb_inputs['t2g'],\n '--out_dir', str(out_dir),\n '--targets', 'u100031',\n '--protein',\n '--threads', '4',\n kb_bam\n ]\n _run_metagenomics(metagenomics.parser_kb_extract, argv, cwd=str(workdir))\n extracted = out_dir / 'u100031' / '1.fastq.gz'\n assert extracted.exists(), f\"Expected extracted reads at {extracted}\"\n count = util_file.count_fastq_reads(str(extracted))\n return {'workdir': Path(workdir), 'reads': extracted, 'count': count}\n\n\n@pytest.fixture(scope='module')\ndef kb_ref_result(tmp_path_factory, kb_inputs):\n workdir = tmp_path_factory.mktemp('kb_ref')\n out_dir = Path(workdir) / 'ref'\n out_dir.mkdir()\n idx_path = out_dir / 'index.idx'\n fasta_path = Path(kb_inputs['ref_fasta'])\n argv = [\n '--index', str(idx_path),\n '--workflow', 'custom',\n '--kmer_len', '31',\n '--protein',\n '--threads', '2',\n str(fasta_path),\n ]\n _run_metagenomics(metagenomics.parser_kb_build, argv, cwd=str(workdir))\n assert idx_path.exists(), f\"Index not created at {idx_path}\"\n return {'workdir': Path(workdir), 'index': idx_path}\n\n\ndef _run_metagenomics(parser_fn, argv, cwd=None):\n parser = parser_fn(argparse.ArgumentParser())\n args = parser.parse_args(argv)\n prev_cwd = os.getcwd()\n try:\n if cwd:\n os.chdir(cwd)\n args.func_main(args)\n finally:\n if cwd:\n os.chdir(prev_cwd)\n\n\ndef test_kb_help_reports_usage():\n parser = metagenomics.parser_kb(argparse.ArgumentParser())\n help_str = parser.format_help()\n assert '--index' in help_str\n assert '--t2g' in help_str\n assert 'kb_out' in help_str\n\n\ndef test_kb_count_produces_h5ad(kb_count_result):\n adata = anndata.read_h5ad(str(kb_count_result['h5ad']))\n assert adata.shape[0] > 0\n assert float(adata.X.sum()) >= 0\n\n\ndef test_kb_extract_yields_expected_reads(kb_extract_result):\n assert kb_extract_result['count'] == 3\n\n\ndef test_kb_ref_builds_index(kb_ref_result):\n assert kb_ref_result['index'].stat().st_size > 0\n" }, { "path": "tests/unit/classify/test_integration_kraken2.py", "content": "# Integration tests for kraken2\nimport argparse\nimport binascii\nimport os\nimport os.path\nfrom os.path import join\n\n#import lxml.html.clean\nimport pytest\n\nfrom viral_ngs import metagenomics\nimport shutil\nimport unittest\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs import core as tools\nfrom viral_ngs.classify import kraken2\nfrom viral_ngs.classify import krona\nfrom viral_ngs.core import picard\nimport tests.unit.classify.fixtures\n\n\ndef is_gz_file(filepath):\n with open(filepath, 'rb') as test_f:\n return binascii.hexlify(test_f.read(2)) == b'1f8b'\n\n\nkrona = pytest.fixture(scope='module')(tests.unit.classify.fixtures.krona)\nkrona_db = pytest.fixture(scope='module')(tests.unit.classify.fixtures.krona_db)\n\n\n@pytest.fixture()\ndef input_bam(db_type):\n data_dir = join(util_file.get_test_input_path(), db_type)\n return join(data_dir, 'test-reads.bam')\n\n@pytest.fixture(scope='module')\ndef kraken2_tool():\n tool = kraken2.Kraken2()\n tool.install()\n return tool\n\n\n@pytest.fixture(scope='module', params=['TestMetagenomicsSimple', 'TestMetagenomicsViralMix'])\ndef db_type(request):\n return request.param\n\n\n@pytest.fixture(scope='module')\ndef kraken2_db(request, tmpdir_module, kraken2_tool, db_type):\n data_dir = join(util_file.get_test_input_path(), db_type)\n db_dir = join(data_dir, 'db')\n\n db = join(tmpdir_module, 'kraken2_db_{}'.format(db_type))\n parser = metagenomics.parser_kraken2_build(argparse.ArgumentParser())\n cmd = [db, '--tax_db', join(db_dir, 'taxonomy')]\n util_file.mkdir_p(db)\n shutil.copytree(os.path.join(db_dir, 'library'), os.path.join(db, 'library'))\n\n parser.parse_args(cmd)\n args = parser.parse_args(cmd)\n args.func_main(args)\n return db\n\n\ndef test_kraken2(kraken2_db, input_bam):\n out_report = util_file.mkstempfname('.report')\n out_reads = util_file.mkstempfname('.reads')\n cmd = [kraken2_db, input_bam, '--outReports', out_report, '--outReads', out_reads]\n parser = metagenomics.parser_kraken2(argparse.ArgumentParser())\n args = parser.parse_args(cmd)\n args.func_main(args)\n\n with util_file.open_or_gzopen(out_reads, 'r') as inf:\n assert len(inf.read()) > 0\n with util_file.open_or_gzopen(out_report) as inf:\n report_lines = [x.strip().split('\\t') for x in inf.readlines()]\n report_lines = [x for x in report_lines if x]\n\n #assert is_gz_file(out_reads)\n assert os.path.getsize(out_report) > 0\n\n if 'TestMetagenomicsSimple' in kraken2_db:\n zaire_found = False\n tai_found = False\n for line in report_lines:\n if 'Zaire ebolavirus' in line[-1] and float(line[0]) > 90:\n zaire_found = True\n elif 'Tai Forest' in line[-1]:\n tai_found = True\n assert zaire_found\n assert not tai_found\n\n\ndef test_kraken2_krona(kraken2_db, krona_db, input_bam):\n out_report = util_file.mkstempfname('.report')\n out_reads = util_file.mkstempfname('.reads.gz')\n\n cmd = [kraken2_db, input_bam, '--outReport', out_report, '--outReads', out_reads]\n parser = metagenomics.parser_kraken2(argparse.ArgumentParser())\n args = parser.parse_args(cmd)\n args.func_main(args)\n\n out_html = util_file.mkstempfname('.krona.html')\n parser = metagenomics.parser_krona(argparse.ArgumentParser())\n args = parser.parse_args(['--inputType', 'kraken2', out_report, krona_db, out_html])\n args.func_main(args)\n\n ''' well... this doesn't actually find Zaire ebolavirus!\n if 'TestMetagenomicsSimple' in kraken2_db:\n ebola_found = False\n cleaner = lxml.html.clean.Cleaner(remove_unknown_tags=False, page_structure=False)\n tree = cleaner.clean_html(lxml.html.parse(out_html))\n root_node = tree.xpath('//krona/node')[0]\n for n in root_node.iterdescendants():\n if n.get('name') == 'Zaire ebolavirus':\n if int(n.xpath('magnitude/val')[0].text) > 0:\n ebola_found = True\n assert ebola_found\n '''\n\ndef test_kraken2_on_empty(kraken2_db, input_bam):\n if 'TestMetagenomicsViralMix' not in kraken2_db:\n return\n input_bam = join(util_file.get_test_input_path(), 'empty.bam')\n out_report = util_file.mkstempfname('.report')\n out_reads = util_file.mkstempfname('.reads')\n cmd = [kraken2_db, input_bam, '--outReport', out_report, '--outReads', out_reads]\n parser = metagenomics.parser_kraken2(argparse.ArgumentParser())\n args = parser.parse_args(cmd)\n args.func_main(args)\n\n with util_file.open_or_gzopen(out_reads, 'r') as inf:\n assert len(inf.read()) == 0\n\n #assert is_gz_file(out_reads)\n with open(out_report, 'rt') as inf:\n lines = [line.strip() for line in inf.readlines() if not line.startswith('#') and not line.startswith('%')]\n out_report_contents = [line for line in lines if line]\n assert len(out_report_contents) == 0\n #assert out_report_contents[0].split('\\t') == ['100.00', '0', '0', '0', '0', 'NA', '0', 'no rank', 'unclassified']\n" }, { "path": "tests/unit/classify/test_integration_taxon_filter.py", "content": "# Integration tests for taxon_filter.py\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport os\nimport tempfile\nimport subprocess\nimport shutil\n\nimport argparse\n\nfrom viral_ngs import taxon_filter\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.classify import last\nfrom viral_ngs.classify import bmtagger\nfrom viral_ngs.classify import blast\nfrom tests import assert_equal_bam_reads, TestCaseWithTmp, IS_ARM\n\n\n@unittest.skipIf(IS_ARM, \"bmtagger requires x86-only bioconda package (not available on ARM)\")\nclass TestDepleteHuman(TestCaseWithTmp):\n '''\n This class should move to test/integration. \n\n How test data was created:\n exported 5kb region of chr6\n created pan-viral fasta file from all NCBI viral accessions\n used wgsim to create simulated reads\n '''\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.tempDir = tempfile.mkdtemp()\n myInputDir = util_file.get_test_input_path()\n ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')\n self.database_prefix_path = os.path.join(self.tempDir, \"5kb_human_from_chr6\")\n\n # create blast db\n self.blastdb_path = blast.MakeblastdbTool().build_database(ref_fasta, self.database_prefix_path)\n\n # create bmtagger db\n taxon_filter.bmtagger_build_db(ref_fasta, self.tempDir, \"5kb_human_from_chr6\", word_size=8)\n\n def test_deplete_human(self):\n myInputDir = util_file.get_test_input_path(self)\n\n # Run deplete_human\n args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args(\n [\n os.path.join(myInputDir, 'test-reads.bam'),\n # output files\n os.path.join(self.tempDir, 'test-reads.revert.bam'),\n os.path.join(self.tempDir, 'test-reads.minimap.bam'),\n os.path.join(self.tempDir, 'test-reads.bwa.bam'),\n os.path.join(self.tempDir, 'test-reads.bmtagger.bam'),\n os.path.join(self.tempDir, 'test-reads.blastn.bam'),\n # DBs\n \"--blastDbs\", self.blastdb_path,\n \"--bmtaggerDbs\", self.database_prefix_path,\n \"--chunkSize\", \"0\",\n \"--srprismMemory\", '1500',\n ]\n )\n args.func_main(args)\n\n # Compare to expected\n for fname in [\n 'test-reads.revert.bam',\n 'test-reads.bwa.bam',\n 'test-reads.bmtagger.bam',\n 'test-reads.blastn.bam'\n ]:\n assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), os.path.join(myInputDir, 'expected', fname))\n\n def test_deplete_human_aligned_input(self):\n myInputDir = util_file.get_test_input_path(self)\n\n # Run deplete_human\n args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args(\n [\n os.path.join(myInputDir, 'test-reads-aligned.bam'),\n # output files\n os.path.join(self.tempDir, 'test-reads.revert.bam'),\n os.path.join(self.tempDir, 'test-reads.minimap.bam'),\n os.path.join(self.tempDir, 'test-reads.bwa.bam'),\n os.path.join(self.tempDir, 'test-reads.bmtagger.bam'),\n os.path.join(self.tempDir, 'test-reads.blastn.bam'),\n # DBs\n \"--blastDbs\", self.blastdb_path,\n \"--bmtaggerDbs\", self.database_prefix_path,\n \"--srprismMemory\", '1500',\n ]\n )\n args.func_main(args)\n\n # Compare to expected\n for fname in [\n 'test-reads.revert.bam',\n 'test-reads.bwa.bam',\n 'test-reads.bmtagger.bam',\n 'test-reads.blastn.bam'\n ]:\n assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), os.path.join(myInputDir, 'aligned-expected', fname))\n\n def test_deplete_empty(self):\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n\n # Run deplete_human\n args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args(\n [\n empty_bam,\n # output files\n os.path.join(self.tempDir, 'deplete-empty.revert.bam'),\n os.path.join(self.tempDir, 'deplete-empty.minimap.bam'),\n os.path.join(self.tempDir, 'deplete-empty.bwa.bam'),\n os.path.join(self.tempDir, 'deplete-empty.bmtagger.bam'),\n os.path.join(self.tempDir, 'deplete-empty.blastn.bam'),\n # DBs\n \"--blastDbs\", self.blastdb_path,\n \"--bmtaggerDbs\", self.database_prefix_path,\n \"--srprismMemory\", '1500',\n ]\n )\n args.func_main(args)\n\n # Compare to expected\n for fname in [\n 'deplete-empty.bmtagger.bam', 'deplete-empty.blastn.bam',\n ]:\n assert_equal_bam_reads(self, os.path.join(self.tempDir, fname), empty_bam)\n" }, { "path": "tests/unit/classify/test_kmer_utils.py", "content": "\"\"\"Unit tests for kmer_utils.py\"\"\"\n\n__author__ = \"ilya@broadinstitute.org\"\n\nimport os\nimport sys\nimport collections\nimport argparse\nimport logging\nimport itertools\nimport unittest\n\nimport Bio.SeqIO\nfrom Bio.Seq import Seq\nfrom Bio.SeqRecord import SeqRecord\nimport pytest\n\nfrom viral_ngs import kmer_utils\nfrom viral_ngs import read_utils\nfrom viral_ngs.core import cmd as util_cmd\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.core import misc as util_misc\nfrom viral_ngs.classify import kmc\nfrom viral_ngs.core import samtools\n\n\n_log = logging.getLogger(__name__) # pylint: disable=invalid-name\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in kmer_utils.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n#################################\n# Some general utils used below #\n#################################\n\ndef _seq_as_str(s): # pylint: disable=invalid-name\n \"\"\"Return a sequence as a str, regardless of whether it was a str, a Seq or a SeqRecord\"\"\"\n if isinstance(s, Seq):\n return str(s)\n if isinstance(s, SeqRecord):\n return str(s.seq)\n return s\n\ndef _yield_seq_recs(seq_file):\n \"\"\"Yield sequence records from the file, regardless of file format.\"\"\"\n with util_file.tmp_dir(suffix='_seqs_as_strs') as t_dir:\n if seq_file.endswith('.bam'):\n t_fa = os.path.join(t_dir, 'bam2fa.fasta')\n samtools.SamtoolsTool().bam2fa(seq_file, t_fa, append_mate_num=True)\n seq_file = t_fa\n with util_file.open_or_gzopen(seq_file, 'rt') as seq_f:\n for rec in Bio.SeqIO.parse(seq_f, util_file.uncompressed_file_type(seq_file)[1:]):\n yield rec\n\ndef _list_seq_recs(seq_file):\n \"\"\"Return a list of sequence records from the file, regardless of file format.\"\"\"\n return list(_yield_seq_recs(seq_file))\n\n\ndef _yield_seqs_as_strs(seqs):\n \"\"\"Yield sequence(s) from `seqs` as strs. seqs can be a str/SeqRecord/Seq, a filename of a sequence file,\n or an iterable of these. If a filename of a sequence file, all sequences from that file are yielded.\"\"\"\n for seq in util_misc.make_seq(seqs, (str, SeqRecord, Seq)):\n seq = _seq_as_str(seq)\n if not any(seq.endswith(ext) for ext in '.fasta .fasta.gz .fastq .fastq.gz .bam'):\n yield seq\n else:\n for rec in _yield_seq_recs(seq):\n yield str(rec.seq)\n\ndef _list_seqs_as_strs(seqs):\n \"\"\"Return a list of sequence(s) from `seqs` as strs. seqs can be a str/SeqRecord/Seq, a filename of a sequence file,\n or an iterable of these. If a filename of a sequence file, all sequences from that file are yielded.\"\"\"\n return list(_yield_seqs_as_strs(seqs))\n\ndef _getargs(args, valid_args):\n \"\"\"Extract valid args from an argparse.Namespace or a dict. Returns a dict containing keys from `args`\n that are in `valid_args`; `valid_args` is a space-separated list of valid args.\"\"\"\n return util_misc.subdict(vars(args) if isinstance(args, argparse.Namespace) else args, valid_args.split())\n\ndef _strip_mate_num(rec_id):\n \"\"\"Name of a read, with any /1 or /2 at the end removed\"\"\"\n return rec_id[:-2] if rec_id.endswith('/1') or rec_id.endswith('/2') else rec_id\n\n#################################################################################################################\n\n\nclass KmcPy(object):\n \"\"\"Reimplementation of some kmc functions in simple Python code.\n\n To help generate the expected correct output, we reimplement in simple Python code some\n of KMC's functionality. This is also to make up for KMC's lack of a public test suite\n ( https://github.com/refresh-bio/KMC/issues/55 ).\n \"\"\"\n\n def _revcomp(self, kmer):\n \"\"\"Return the reverse complement of a kmer, given as a string\"\"\"\n assert isinstance(kmer, str)\n return str(SeqRecord(Seq(kmer), annotations={\"molecule_type\": \"DNA\"}).seq.reverse_complement())\n\n def _canonicalize(self, kmer):\n \"\"\"Return the canonical version of a kmer\"\"\"\n return min(kmer, self._revcomp(kmer))\n\n def _compute_kmers_iter(self, seq_strs, kmer_size, single_strand, **ignore):\n \"\"\"Yield kmers of seq(s). Unless `single_strand` is True, each kmer\n is canonicalized before being returned. Note that\n deduplication is not done, so each occurrence of each kmer is\n yielded. Kmers containing non-TCGA bases are skipped.\n \"\"\"\n for seq in seq_strs:\n n_kmers = len(seq)-kmer_size+1\n\n # mark kmers containing invalid base(s)\n valid_kmer = [True] * n_kmers\n for i in range(len(seq)): # pylint: disable=consider-using-enumerate\n if seq[i].upper() not in 'TCGA':\n invalid_lo = max(0, i-kmer_size+1)\n invalid_hi = min(n_kmers, i+1)\n valid_kmer[invalid_lo:invalid_hi] = [False]*(invalid_hi-invalid_lo)\n\n for i in range(n_kmers):\n if valid_kmer[i]:\n kmer = seq[i:i+kmer_size]\n yield kmer if single_strand else self._canonicalize(kmer)\n\n def _compute_kmers(self, *args, **kw):\n \"\"\"Return list of kmers of seq(s). Unless `single_strand` is True, each kmer\n is canonicalized before being returned. Note that\n deduplication is not done, so each occurrence of each kmer is\n yielded. Kmers containing non-TCGA bases are skipped.\n \"\"\"\n return list(self._compute_kmers_iter(*args, **kw))\n\n def compute_kmer_counts(self, seq_files, kmer_size, min_occs, max_occs,\n counter_cap, single_strand, **ignore):\n \"\"\"Yield kmer counts of seq(s). Unless `single_strand` is True, each kmer is\n canonicalized before being counted. Kmers containing non-TCGA bases are skipped.\n Kmers with fewer than `min_occs` or more than `max_occs` occurrences\n are dropped, and kmer counts capped at `counter_cap`, if these args are given.\n \"\"\"\n counts = collections.Counter(self._compute_kmers(_list_seqs_as_strs(seq_files), kmer_size, single_strand))\n return self._filter_kmer_counts(counts=counts, min_occs=min_occs, max_occs=max_occs, counter_cap=counter_cap)\n\n def _filter_kmer_counts(self, counts, min_occs=None, max_occs=None, counter_cap=None):\n \"\"\"From a dict of kmer counts, drop kmers with counts below `min_occs` or above `max_occs`, and\n cap counter values at `counter_cap`.\"\"\"\n return collections.Counter({kmer : min(count, counter_cap or count) \\\n for kmer, count in counts.items() \\\n if (count >= (min_occs or count)) and \\\n (count <= (max_occs or count))})\n\n\n def filter_reads(self, db_kmer_counts, in_reads, kmer_size, single_strand,\n db_min_occs, db_max_occs, read_min_occs, read_max_occs,\n read_min_occs_frac, read_max_occs_frac, **ignore):\n \"\"\"Fiter sequences based on their kmer contents; returns the ids of the passing seqs.\n\n Inputs:\n in_reads: sequences to filter, as a fasta/fastq/bam\n\n Params:\n db_kmer_counts: a collections.Counter mapping kmers to their counts in the kmer database\n kmer_size: kmer size\n single_strand: if False, kmers are canonicalized\n db_min_occs: drop from db_kmer_counts kmers with counts below this\n db_max_occs: drop from db_kmer_counts kmers with counts above this\n read_min_occs: drop reads with fewer than this many occurrences of kmers from the database\n read_max_occs: drop reads with more than this many occurrences of kmers from the database\n read_min_occs_frac: only keep reads with at least this many occurrences of kmers from database,\n interpreted as a fraction of read length in kmers\n read_max_occs_frac: only keep reads with no more than this many occurrence of kmers from the database.\n interpreted as a fraction of read length in kmers.\n \"\"\"\n db_kmers = self._filter_kmer_counts(counts=db_kmer_counts, min_occs=db_min_occs, max_occs=db_max_occs).keys()\n\n seqs_ids_out = set()\n rel_thresholds = (read_min_occs_frac, read_max_occs_frac) != (0., 1.)\n in_recs = _list_seq_recs(in_reads)\n\n seq_occs_hist = collections.Counter()\n mate_cnt = collections.Counter()\n\n for rec in in_recs:\n seq = str(rec.seq)\n seq_kmer_counts = self.compute_kmer_counts(seq, kmer_size=kmer_size, single_strand=single_strand,\n min_occs=1, max_occs=util_misc.MAX_INT32,\n counter_cap=util_misc.MAX_INT32)\n assert not single_strand\n seq_occs = sum([seq_count for kmer, seq_count in seq_kmer_counts.items() \\\n if kmer in db_kmers])\n seq_occs_hist[seq_occs] += 1\n\n if rel_thresholds:\n n_seq_kmers = len(seq)-kmer_size+1\n read_min_occs_seq, read_max_occs_seq = (int(read_min_occs_frac * n_seq_kmers),\n int(read_max_occs_frac * n_seq_kmers))\n else:\n read_min_occs_seq, read_max_occs_seq = (read_min_occs, read_max_occs)\n\n if read_min_occs_seq <= seq_occs <= read_max_occs_seq:\n seqs_ids_out.add(rec.id)\n mate_cnt[rec.id[-2:] if rec.id[-2:] in ('/1', '/2') else '/0'] += 1\n\n\n _log.debug('kmer occs histogram: %s', sorted(seq_occs_hist.items()))\n _log.debug('filter_reads: %d of %d passed; mate_cnt=%s', len(seqs_ids_out), len(in_recs),\n mate_cnt)\n\n return seqs_ids_out\n\n def binary_op(self, op, kmer_counts_1, kmer_counts_2, result_counter_cap=255):\n assert isinstance(kmer_counts_1, collections.Counter)\n assert isinstance(kmer_counts_2, collections.Counter)\n if op == 'intersect':\n result = kmer_counts_1 & kmer_counts_2\n elif op == 'union':\n result = collections.Counter({k: (kmer_counts_1[k] + kmer_counts_2[k])\n for k in (set(kmer_counts_1.keys()) | set(kmer_counts_2.keys()))})\n elif op == 'kmers_subtract':\n result = collections.Counter(util_misc.subdict(kmer_counts_1,\n set(kmer_counts_1.keys()) - set(kmer_counts_2.keys())))\n elif op == 'counters_subtract':\n result = kmer_counts_1 - kmer_counts_2\n else:\n raise ValueError('Unknown operation: {}'.format(op))\n return self._filter_kmer_counts(counts=result, counter_cap=result_counter_cap)\n\n# end: class KmcPy \n\nkmcpy = KmcPy()\n\ndef _inp(fname):\n \"\"\"Return full path to a test input file for this module\"\"\"\n return os.path.join(util_file.get_test_input_path(), 'TestKmers', fname)\n\ndef _stringify(arg):\n \"\"\"Return a string based on `arg`, suitable for use as a pytest test id\"\"\"\n return util_file.string_to_file_name(str(arg))\n\ndef _do_build_kmer_db(t_dir, val_cache, seq_files, kmer_db_opts):\n \"\"\"Build a database of kmers from given sequence file(s) using given options.\n\n Args:\n t_dir: dir where to build the kmer dbase\n val_cache: a dict where results can be cached\n seq_files: a string of sequence file name(s), space-separated\n kmer_db_opts: options to build_kmer_db command, as one string\n Returns:\n an argparse.Namespace() with the following attrs:\n kmer_db: path to the kmer db created from seq_files\n kmc_kmer_counts: map from kmer to count, as computed by kmc\n kmc_db_args: the result of parsing kmer_db_opts\n \"\"\"\n key = (seq_files, kmer_db_opts)\n if key in val_cache:\n _log.debug('reusing cached kmer db: %s', key)\n return val_cache[key]\n\n _log.debug('constructing kmer db: %s', key)\n\n k_db = os.path.join(t_dir, 'bld_kmer_db_{}'.format(hash(key)))\n assert not kmc.KmcTool().is_kmer_db(k_db)\n seq_files = list(map(_inp, seq_files.split()))\n kmer_db_args = util_cmd.run_cmd(module=kmer_utils, cmd='build_kmer_db',\n args=seq_files + [k_db] + kmer_db_opts.split() + ['--memLimitGb', 4]).args_parsed\n assert kmc.KmcTool().is_kmer_db(k_db)\n kmc_kmer_counts=kmc.KmcTool().get_kmer_counts(k_db, threads=kmer_db_args.threads)\n _log.debug('KMER_DB_FIXTURE: param=%s counts=%d db=%s', key, len(kmc_kmer_counts), k_db)\n return val_cache.setdefault(key, argparse.Namespace(kmer_db=k_db,\n kmc_kmer_counts=kmc_kmer_counts,\n kmer_db_args=kmer_db_args))\n\nKMER_DBS_EMPTY = [('empty.fasta', '')]\n\nKMER_DBS_SMALL = [\n ('ebola.fasta.gz', '-k 7'),\n ('almost-empty-2.bam', '-k 23 --singleStrand'),\n ('almost-empty-2.bam', '-k 5 --minOccs 1 --maxOccs 5 --counterCap 3'),\n ('tcgaattt.fasta', '-k 7'),\n ('ambig_bases.fasta', '-k 7'),\n ('palindromic_kmers.fasta', '-k 7')\n]\n\nKMER_DBS_MEDIUM = [\n ('test-reads.bam test-reads-human.bam', '-k 17'),\n]\n\n@pytest.fixture(scope='module')\ndef dict_module():\n return dict()\n\n@pytest.fixture(scope='module', params=KMER_DBS_EMPTY+KMER_DBS_SMALL, ids=_stringify)\ndef kmer_db_fixture(request, tmpdir_module, dict_module):\n yield _do_build_kmer_db(tmpdir_module, dict_module, *request.param)\n\n@pytest.fixture(scope='module', params=KMER_DBS_EMPTY+KMER_DBS_SMALL, ids=_stringify)\ndef kmer_db_fixture2(request, tmpdir_module, dict_module):\n yield _do_build_kmer_db(tmpdir_module, dict_module, *request.param)\n\n@pytest.mark.parametrize(\"kmer_db_fixture\", KMER_DBS_EMPTY+KMER_DBS_SMALL+KMER_DBS_MEDIUM,\n ids=_stringify, indirect=[\"kmer_db_fixture\"])\ndef test_build_kmer_db(kmer_db_fixture):\n _test_build_kmer_db(kmer_db_fixture)\n\ndef _test_build_kmer_db(kmer_db_fixture):\n assert kmc.KmcTool().is_kmer_db(kmer_db_fixture.kmer_db)\n\n kmer_db_info = kmc.KmcTool().get_kmer_db_info(kmer_db_fixture.kmer_db)\n assert kmer_db_info.kmer_size == kmer_db_fixture.kmer_db_args.kmer_size\n assert kmer_db_info.min_occs == kmer_db_fixture.kmer_db_args.min_occs\n assert kmer_db_info.max_occs == kmer_db_fixture.kmer_db_args.max_occs\n\n kmcpy_kmer_counts = kmcpy.compute_kmer_counts(**vars(kmer_db_fixture.kmer_db_args))\n assert kmer_db_info.total_kmers == len(kmcpy_kmer_counts)\n assert kmer_db_fixture.kmc_kmer_counts == kmcpy_kmer_counts\n\n###########\nSEQ_FILES = [ \n # 'empty.fasta',\n # 'ebola.fasta.gz',\n # 'almost-empty-2.bam',\n # 'test-reads.bam',\n # 'test-reads-human.bam',\n # 'tcgaattt.fasta',\n 'G5012.3.fasta',\n 'G5012.3.mini.bam',\n]\n\nKMER_SIZES = [1, 2, 7, 17, 27, 31, 55, 63]\n#KMER_SIZES = [1, 17, 31, 55]\nSTRAND_OPTS = ['', '--singleStrand']\nKMER_OCCS_OPTS = [ '', '--minOccs 1', '--minOccs 10', '--maxOccs 10' ]\nNTHREADS = [1, 2, 12]\nCOMBO_OPTS = [(seq_file, '-k{} {} {} --threads {}'.format(kmer_size, strand_opt, kmer_occs_opt, nthreads))\n for seq_file, kmer_size, strand_opt, kmer_occs_opt, nthreads \\\n in itertools.product(SEQ_FILES, KMER_SIZES, STRAND_OPTS,\n KMER_OCCS_OPTS, NTHREADS)]\n\n@pytest.mark.slow\n@pytest.mark.parametrize(\"kmer_db_fixture\", COMBO_OPTS, ids=_stringify, indirect=[\"kmer_db_fixture\"])\ndef test_build_kmer_db_combo(kmer_db_fixture):\n _test_build_kmer_db(kmer_db_fixture)\n\n\n##############################################################################################\n\ndef _test_filter_reads(kmer_db_fixture, reads_file, filter_opts, tmpdir_function):\n \"\"\"Test read filtering.\n\n Args:\n kmer_size: kmer size\n single_strand: whether to canonicalize kmers\n kmers_fasta: kmers for filtering will be extracted from here\n reads_bam: reads to filter with kmers extracted from kmers_fasta\n\n \"\"\"\n assert kmc.KmcTool().is_kmer_db(kmer_db_fixture.kmer_db)\n\n reads_file = _inp(reads_file)\n reads_file_out = os.path.join(tmpdir_function, 'reads_out' + util_file.uncompressed_file_type(reads_file))\n\n filter_args = util_cmd.run_cmd(module=kmer_utils, cmd='filter_reads',\n args=[kmer_db_fixture.kmer_db, \n reads_file, reads_file_out] + filter_opts.split()).args_parsed\n\n _log.debug('Running filte: kmer_db_args=%s filter_arg=%s', kmer_db_fixture.kmer_db_args, filter_args)\n filtered_ids_expected = kmcpy.filter_reads(db_kmer_counts=kmer_db_fixture.kmc_kmer_counts,\n kmer_size=kmer_db_fixture.kmer_db_args.kmer_size,\n single_strand=kmer_db_fixture.kmer_db_args.single_strand,\n **vars(filter_args))\n\n reads_file_out_ids_txt = reads_file_out+'.ids.txt'\n read_utils.read_names(reads_file_out, reads_file_out_ids_txt)\n reads_out_ids = util_file.slurp_file(reads_file_out_ids_txt).strip().split()\n\n _log.debug('FILT %d %d %s %s %s', len(_list_seq_recs(reads_file)), len(_list_seq_recs(reads_file_out)),\n kmer_db_fixture.kmer_db, reads_file, filter_opts)\n def normed_read_ids(ids): return set(map(_strip_mate_num, ids))\n\n assert normed_read_ids(reads_out_ids) == normed_read_ids(filtered_ids_expected)\n\n# end: def _test_filter_reads(kmer_db_fixture, reads_file, filter_opts, tmpdir_function)\n\n@pytest.mark.parametrize(\"kmer_db_fixture\", [('empty.fasta', '')], ids=_stringify, indirect=[\"kmer_db_fixture\"])\n@pytest.mark.parametrize(\"reads_file\", ['empty.fasta', 'tcgaattt.fasta', 'G5012.3.subset.bam'])\n@pytest.mark.parametrize(\"filter_opts\", ['', '--readMinOccs 1', '--readMaxOccs 2'])\ndef test_filter_with_empty_db(kmer_db_fixture, reads_file, filter_opts, tmpdir_function):\n _test_filter_reads(**locals())\n\n@pytest.mark.parametrize(\"kmer_db_fixture\", [('ebola.fasta.gz', '-k 7')], ids=_stringify, indirect=[\"kmer_db_fixture\"])\n@pytest.mark.parametrize(\"reads_file\", [pytest.param('G5012.3.testreads.bam', marks=pytest.mark.slow),\n 'G5012.3.subset.bam'])\n@pytest.mark.parametrize(\"filter_opts\", ['--dbMinOccs 7 --readMinOccs 93',\n '--dbMinOccs 4 --readMinOccsFrac .6',\n '--readMinOccsFrac .4 --readMaxOccsFrac .55'])\ndef test_filter_reads(kmer_db_fixture, reads_file, filter_opts, tmpdir_function):\n _test_filter_reads(**locals())\n\n\n@pytest.mark.parametrize(\"kmer_db_fixture\", KMER_DBS_EMPTY+KMER_DBS_SMALL[:1], ids=_stringify, indirect=[\"kmer_db_fixture\"])\n@pytest.mark.parametrize(\"set_to_val\", [1, util_misc.MAX_INT32])\ndef test_kmer_set_counts(kmer_db_fixture, tmpdir_function, set_to_val):\n db_with_set_counts = os.path.join(tmpdir_function, 'set_counts_db')\n util_cmd.run_cmd(module=kmer_utils, cmd='kmers_set_counts',\n args=[kmer_db_fixture.kmer_db, set_to_val, db_with_set_counts])\n new_counts = kmc.KmcTool().get_kmer_counts(db_with_set_counts)\n assert set(new_counts.keys()) == set(kmer_db_fixture.kmc_kmer_counts.keys())\n assert not new_counts or set(new_counts.values()) == set([set_to_val])\n\n\n@pytest.mark.parametrize(\"op\", ('intersect', 'union', 'kmers_subtract', 'counters_subtract'))\ndef test_kmers_binary_op(kmer_db_fixture, kmer_db_fixture2, op, tmpdir_function):\n if kmer_db_fixture.kmer_db_args.kmer_size != kmer_db_fixture2.kmer_db_args.kmer_size:\n pytest.skip('(always skip) binary ops not defined on kmers of different size')\n db_result = os.path.join(tmpdir_function, 'op_result')\n _log.debug('fixture1args=%s', kmer_db_fixture.kmer_db_args)\n _log.debug('fixture2args=%s', kmer_db_fixture2.kmer_db_args)\n _log.debug('op=%s', op)\n args = util_cmd.run_cmd(module=kmer_utils, cmd='kmers_binary_op',\n args=[op, kmer_db_fixture.kmer_db, kmer_db_fixture2.kmer_db, db_result]).args_parsed\n\n kmc_counts = kmc.KmcTool().get_kmer_counts(db_result)\n kmcpy_counts = kmcpy.binary_op(op, kmer_db_fixture.kmc_kmer_counts, kmer_db_fixture2.kmc_kmer_counts,\n result_counter_cap=args.result_counter_cap)\n\n assert kmc_counts == kmcpy_counts\n" }, { "path": "tests/unit/classify/test_metagenomics.py", "content": "# Unit tests for metagenomics.py\nfrom builtins import super\nimport six\nimport argparse\nfrom collections import Counter\nimport copy\nimport os.path\nfrom os.path import join\nimport tempfile\nimport textwrap\nimport unittest\nimport pytest\n\nfrom unittest import mock\nfrom unittest.mock import patch\n\nfrom viral_ngs.core import picard\nfrom viral_ngs import metagenomics\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.core import misc as util_misc\nfrom tests import TestCaseWithTmp, assert_equal_bam_reads, _CPUS\n\nif six.PY2:\n from StringIO import StringIO\nelse:\n from io import StringIO\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in metagenomics.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n\nclass TestKronaCalls(TestCaseWithTmp):\n\n def setUp(self):\n super().setUp()\n patcher = patch('viral_ngs.metagenomics.krona.Krona', autospec=True)\n self.addCleanup(patcher.stop)\n self.mock_krona = patcher.start()\n\n self.inTsv = util_file.mkstempfname('.tsv')\n self.db = tempfile.mkdtemp('db')\n\n def test_krona_import_taxonomy(self):\n out_html = util_file.mkstempfname('.html')\n metagenomics.main_krona([self.inTsv], self.db, out_html, queryColumn=3, taxidColumn=5, scoreColumn=7,\n noHits=True, noRank=True, inputType='tsv')\n self.mock_krona().import_taxonomy.assert_called_once_with(\n self.db, [self.inTsv + ',' + os.path.basename(self.inTsv)], out_html, query_column=3, taxid_column=5, score_column=7,\n no_hits=True, no_rank=True, magnitude_column=None)\n\n\n@pytest.fixture\ndef taxa_db_simple():\n db = metagenomics.TaxonomyDb()\n db.gis = {1:2, 2:3, 3:4, 4:5}\n db.parents = {1: 1, 2: 1, 3: 2, 4: 3, 5: 4}\n return db\n\n\n@pytest.fixture\ndef taxa_db(parents, names, ranks):\n db = metagenomics.TaxonomyDb()\n db.parents = parents\n db.names = names\n db.ranks = ranks\n return db\n\n\n@pytest.fixture\ndef parents():\n return {\n 1: 1,\n 3: 1,\n 6: 3,\n 7: 6,\n 8: 7,\n 10: 6,\n 11: 7,\n 12: 8,\n 13: 12\n }\n\n\n@pytest.fixture\ndef names():\n names = {\n 1: \"root\",\n 2: \"two\",\n 3: \"three\",\n 4: \"four\",\n 6: \"six\",\n 7: \"seven\",\n 8: \"eight\",\n 10: \"ten\",\n 11: \"eleven\",\n 12: \"twelve\",\n 13: \"thirteen\"\n }\n return names\n\n\n@pytest.fixture\ndef ranks():\n return {\n 1: \"root\",\n 2: \"\",\n 3: \"superkingdom\",\n 4: \"kingdom\",\n 6: \"\",\n 7: \"\",\n 8: \"\",\n 10: \"\",\n 11: \"genus\",\n 12: \"species\",\n 13: \"\"\n }\n\n\n@pytest.fixture\ndef simple_m8():\n test_path = join(util_file.get_test_input_path(),\n 'TestTaxonomy')\n return open(join(test_path, 'simple.m8'))\n\n\ndef test_tree_level_lookup(parents):\n level_cache = {1: 1}\n assert metagenomics.tree_level_lookup(parents, 1, level_cache) == 1\n assert metagenomics.tree_level_lookup(parents, 3, level_cache) == 2\n assert metagenomics.tree_level_lookup(parents, 12, level_cache) == 6\n level_cache = {1: 1}\n assert metagenomics.tree_level_lookup(parents, 12, level_cache) == 6\n assert metagenomics.tree_level_lookup(parents, 8, level_cache) == 5\n\n\ndef test_push_up_tree_hits(parents):\n hits = Counter({1: 3, 3: 5, 6: 3, 7: 3, 13: 5})\n with pytest.raises(AssertionError):\n metagenomics.push_up_tree_hits(parents, hits)\n\n expected = hits.copy()\n assert metagenomics.push_up_tree_hits(parents, hits.copy(), min_support=1) == expected\n\n expected = Counter({3: 5, 6: 6, 13: 5})\n assert metagenomics.push_up_tree_hits(parents, hits.copy(), min_support=5) == expected\n\n assert (metagenomics.push_up_tree_hits(parents, hits.copy(), min_support=10) ==\n Counter({6: 11}))\n assert (metagenomics.push_up_tree_hits(parents, hits.copy(), min_support=18) ==\n Counter({1: 19}))\n assert (metagenomics.push_up_tree_hits(parents, hits.copy(), min_support_percent=100) ==\n Counter({1: 19}))\n\n\ndef test_parents_to_children(parents):\n children = metagenomics.parents_to_children(parents)\n assert children[1] == [3]\n\n\ndef test_rank_code():\n assert metagenomics.rank_code('species') == 'S'\n assert metagenomics.rank_code('genus') == 'G'\n assert metagenomics.rank_code('superkingdom') == 'D'\n assert metagenomics.rank_code('nonexist') == '-'\n\n\ndef test_blast_records(simple_m8):\n test_path = join(util_file.get_test_input_path(),\n 'TestTaxonomy')\n with simple_m8 as f:\n records = list(metagenomics.blast_records(f))\n assert len(records) == 110\n assert records[0].bit_score == 63.5\n assert records[-1].bit_score == 67.4\n\n\ndef test_blast_lca(taxa_db_simple, simple_m8):\n test_path = join(util_file.get_test_input_path(),\n 'TestTaxonomy')\n expected = textwrap.dedent(\"\"\"\\\n C\\tM04004:13:000000000-AGV3H:1:1101:12068:2105\\t2\n C\\tM04004:13:000000000-AGV3H:1:1101:13451:2146\\t2\n C\\tM04004:13:000000000-AGV3H:1:1101:13509:2113\\t2\n C\\tM04004:13:000000000-AGV3H:1:1101:14644:2160\\t2\n C\\tM04004:13:000000000-AGV3H:1:1101:18179:2130\\t2\n C\\tM04004:13:000000000-AGV3H:1:1111:10629:2610\\t2\n C\\tM04004:13:000000000-AGV3H:1:1111:10629:26101\\t2\n \"\"\")\n out = StringIO()\n with simple_m8 as f:\n taxa_db_simple.blast_lca(f, out, paired=True)\n out.seek(0)\n assert out.read() == expected\n\n\ndef test_paired_query_id():\n tup = ['query', 'gi|10|else', 90., 80, 60, 2, 30, 80,\n 1100, 1150, 1e-7, 64.5, []]\n\n blast1 = metagenomics.BlastRecord(*tup)\n assert metagenomics.paired_query_id(blast1) == blast1\n\n new_tup = copy.copy(tup)\n new_tup[0] = 'query/1'\n new_blast1 = metagenomics.BlastRecord(*new_tup)\n assert metagenomics.paired_query_id(new_blast1) == blast1\n\n new_tup = copy.copy(tup)\n new_tup[0] = 'query/2'\n new_blast1 = metagenomics.BlastRecord(*new_tup)\n assert metagenomics.paired_query_id(new_blast1) == blast1\n\n new_tup = copy.copy(tup)\n new_tup[0] = 'query/3'\n new_blast1 = metagenomics.BlastRecord(*new_tup)\n assert metagenomics.paired_query_id(new_blast1) == new_blast1\n\n\ndef test_translate_gi_to_tax_id(taxa_db_simple):\n tup = ['query', 'gi|4|else', 90., 80, 60, 2, 30, 80,\n 1100, 1150, 1e-7, 64.5, []]\n blast1 = metagenomics.BlastRecord(*tup)\n\n tup[1] = 5\n expected = metagenomics.BlastRecord(*tup)\n assert taxa_db_simple.translate_gi_to_tax_id(blast1) == expected\n\n\ndef test_ancestor_lookup(taxa_db_simple):\n assert taxa_db_simple.get_ordered_ancestors(4) == [3, 2, 1]\n\n\ndef test_kraken_dfs_report(taxa_db):\n hits = Counter({1: 101, 3: 103, 10: 105, 12: 107})\n\n expected = textwrap.dedent('''\\\n 100.00\\t416\\t101\\t-\\t1\\troot\n 75.72\\t315\\t103\\tD\\t3\\t three\n 50.96\\t212\\t0\\t-\\t6\\t six\n 25.24\\t105\\t105\\t-\\t10\\t ten\n 25.72\\t107\\t0\\t-\\t7\\t seven\n 25.72\\t107\\t0\\t-\\t8\\t eight\n 25.72\\t107\\t107\\tS\\t12\\t twelve\n ''')\n report = taxa_db.kraken_dfs_report(hits)\n text_report = '\\n'.join(list(report)) + '\\n'\n assert text_report == expected\n\n\ndef test_coverage_lca(taxa_db):\n assert metagenomics.coverage_lca([10, 11, 12], taxa_db.parents) == 6\n assert metagenomics.coverage_lca([1, 3], taxa_db.parents) == 1\n assert metagenomics.coverage_lca([6, 7, 8], taxa_db.parents) == 6\n assert metagenomics.coverage_lca([10, 11, 12], taxa_db.parents, 50) == 7\n assert metagenomics.coverage_lca([9], taxa_db.parents) is None\n\n@pytest.mark.skip(reason=\"KrakenUniq disabled from future versions for now, pending conda rebuild of @yesimon's custom fork\")\ndef test_krakenuniq():\n with patch('viral_ngs.metagenomics.kraken.KrakenUniq.pipeline') as p:\n args = [\n 'db',\n 'input.bam',\n '--outReports', 'output.report',\n '--outReads', 'output.reads',\n ]\n args = metagenomics.parser_krakenuniq(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n p.assert_called_with('db', ['input.bam'], num_threads=mock.ANY, filter_threshold=mock.ANY, out_reports=['output.report'], out_reads=['output.reads'])\n\n\nclass TestBamFilter(TestCaseWithTmp):\n def test_bam_filter_simple(self):\n temp_dir = tempfile.gettempdir()\n input_dir = util_file.get_test_input_path(self)\n taxonomy_dir = os.path.join(util_file.get_test_input_path(),\"TestMetagenomicsSimple\",\"db\",\"taxonomy\")\n\n filtered_bam = util_file.mkstempfname('.bam')\n args = [\n os.path.join(input_dir,\"input.bam\"),\n os.path.join(input_dir,\"input.kraken-reads.tsv.gz\"),\n filtered_bam,\n os.path.join(taxonomy_dir,\"nodes.dmp\"),\n os.path.join(taxonomy_dir,\"names.dmp\"),\n \"--taxNames\",\n \"Ebolavirus\"\n ]\n args = metagenomics.parser_filter_bam_to_taxa(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n expected_bam = os.path.join(input_dir,\"expected.bam\")\n assert_equal_bam_reads(self, filtered_bam, expected_bam)\n\n def test_bam_filter_by_tax_id(self):\n temp_dir = tempfile.gettempdir()\n input_dir = util_file.get_test_input_path(self)\n taxonomy_dir = os.path.join(util_file.get_test_input_path(),\"TestMetagenomicsSimple\",\"db\",\"taxonomy\")\n\n filtered_bam = util_file.mkstempfname('.bam')\n args = [\n os.path.join(input_dir,\"input.bam\"),\n os.path.join(input_dir,\"input.kraken-reads.tsv.gz\"),\n filtered_bam,\n os.path.join(taxonomy_dir,\"nodes.dmp\"),\n os.path.join(taxonomy_dir,\"names.dmp\"),\n \"--taxIDs\",\n \"186538\"\n ]\n args = metagenomics.parser_filter_bam_to_taxa(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n expected_bam = os.path.join(input_dir,\"expected.bam\")\n assert_equal_bam_reads(self, filtered_bam, expected_bam)\n" }, { "path": "tests/unit/classify/test_taxon_filter.py", "content": "# Unit tests for taxon_filter.py\n\n__author__ = \"dpark@broadinstitute.org, irwin@broadinstitute.org,\" \\\n + \"hlevitin@broadinstitute.org\"\n\nimport unittest\nimport glob\nimport os, os.path\nimport platform\nimport tempfile\nimport shutil\nimport filecmp\nimport subprocess\n\nimport argparse\n\nfrom viral_ngs import read_utils\nfrom viral_ngs import taxon_filter\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.core import misc as util_misc\nfrom viral_ngs.core import samtools\n\nfrom viral_ngs.classify import last\nfrom viral_ngs.classify import bmtagger\nfrom viral_ngs.classify import blast\n\nfrom tests import assert_equal_contents, assert_equal_bam_reads, assert_md5_equal_to_line_in_file, TestCaseWithTmp\n\n# Skip bmtagger tests on ARM platforms - bmtagger is x86-only (no ARM64 builds in bioconda)\nIS_ARM = platform.machine() in ('arm64', 'aarch64')\nSKIP_BMTAGGER_REASON = \"bmtagger requires x86-only bioconda package (not available on ARM)\"\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in taxon_filter.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n\n\nclass TestFilterLastal(TestCaseWithTmp):\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.polio_fasta = os.path.join(\n util_file.get_test_input_path(),\n 'TestMetagenomicsViralMix', 'db', 'library', 'Viruses', 'Enterovirus_C', 'GCF_000861165.1_ViralProj15288_genomic.fna'\n )\n dbDir = tempfile.mkdtemp()\n self.lastdb_path = last.Lastdb().build_database(self.polio_fasta, os.path.join(dbDir, 'NC_002058'))\n\n def test_filter_lastal_bam_polio(self):\n inBam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.blastn.bam')\n outBam = util_file.mkstempfname('-out-taxfilt.bam')\n args = taxon_filter.parser_filter_lastal_bam(argparse.ArgumentParser()).parse_args([\n inBam, self.lastdb_path, outBam])\n args.func_main(args)\n expectedOut = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.taxfilt.imperfect-2.bam')\n assert_equal_bam_reads(self, outBam, expectedOut)\n\n def test_lastal_empty_input(self):\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n outBam = util_file.mkstempfname('-out-taxfilt.bam')\n taxon_filter.filter_lastal_bam(\n empty_bam,\n self.lastdb_path,\n outBam\n )\n assert_equal_bam_reads(self, outBam, empty_bam)\n\n def test_lastal_empty_output(self):\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n in_bam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads-human.bam')\n outBam = util_file.mkstempfname('-out-taxfilt.bam')\n taxon_filter.filter_lastal_bam(\n in_bam,\n self.lastdb_path,\n outBam\n )\n assert_equal_bam_reads(self, outBam, empty_bam)\n\n def test_lastal_unbuilt_db(self):\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n in_bam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads-human.bam')\n outBam = util_file.mkstempfname('-out-taxfilt.bam')\n taxon_filter.filter_lastal_bam(\n in_bam,\n self.polio_fasta,\n outBam\n )\n assert_equal_bam_reads(self, outBam, empty_bam)\n\n\n@unittest.skipIf(IS_ARM, SKIP_BMTAGGER_REASON)\nclass TestBmtagger(TestCaseWithTmp):\n '''\n How test data was created:\n exported 5kb region of chr6\n created pan-viral fasta file from all NCBI viral accessions\n used wgsim to create simulated reads\n '''\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.tempDir = tempfile.mkdtemp()\n ref_fasta = os.path.join(util_file.get_test_input_path(), '5kb_human_from_chr6.fasta')\n self.database_prefix_path = os.path.join(self.tempDir, \"5kb_human_from_chr6\")\n taxon_filter.bmtagger_build_db(ref_fasta, self.tempDir, \"5kb_human_from_chr6\", word_size=8)\n\n def test_deplete_bmtagger_bam(self):\n inBam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')\n outBam = util_file.mkstempfname('-out.bam')\n args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([\n inBam, self.database_prefix_path, outBam, '--srprismMemory', '1500'])\n args.func_main(args)\n expectedOut = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam')\n assert_equal_bam_reads(self, outBam, expectedOut)\n\n @unittest.skip(\"too slow for real word size of 18bp\")\n def test_deplete_bmtagger_fasta_db(self):\n inBam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')\n ref_fasta = os.path.join(util_file.get_test_input_path(), '5kb_human_from_chr6.fasta')\n outBam = util_file.mkstempfname('-out.bam')\n args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([\n inBam, ref_fasta, outBam, '--srprismMemory', '1500'])\n args.func_main(args)\n expectedOut = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam')\n assert_equal_bam_reads(self, outBam, expectedOut)\n\n def test_deplete_bmtagger_tar_db(self):\n inBam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')\n outBam = util_file.mkstempfname('-out.bam')\n tar_db_tgz = util_file.mkstempfname('.db.tar.gz')\n cmd = ['tar', '-C', os.path.dirname(self.database_prefix_path), '-cvzf', tar_db_tgz, '.']\n subprocess.check_call(cmd)\n args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([\n inBam, tar_db_tgz, outBam, '--srprismMemory', '1500'])\n args.func_main(args)\n expectedOut = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'expected', 'test-reads.bmtagger.bam')\n assert_equal_bam_reads(self, outBam, expectedOut)\n os.unlink(tar_db_tgz)\n\n def test_bmtagger_empty_input(self):\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n out_bam = util_file.mkstempfname('-out.bam')\n args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([\n empty_bam, self.database_prefix_path, out_bam, '--srprismMemory', '1500'])\n args.func_main(args)\n assert_equal_bam_reads(self, out_bam, empty_bam)\n\n def test_bmtagger_empty_output(self):\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n in_bam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads-human.bam')\n out_bam = util_file.mkstempfname('-out.bam')\n args = taxon_filter.parser_deplete_bam_bmtagger(argparse.ArgumentParser()).parse_args([\n in_bam, self.database_prefix_path, out_bam, '--srprismMemory', '1500'])\n args.func_main(args)\n assert_equal_bam_reads(self, out_bam, empty_bam)\n\n\nclass TestBlastnDbBuild(TestCaseWithTmp):\n\n def test_blastn_db_build(self):\n commonInputDir = util_file.get_test_input_path()\n refFasta = os.path.join(commonInputDir, 'ebola.fasta')\n\n myInputDir = util_file.get_test_input_path(self)\n tempDir = tempfile.mkdtemp()\n\n output_prefix = self.__class__.__name__\n\n args = taxon_filter.parser_blastn_build_db(argparse.ArgumentParser()).parse_args(\n [\n # input fasta\n refFasta,\n # output directory\n tempDir,\n \"--outputFilePrefix\",\n output_prefix\n ]\n )\n args.func_main(args)\n\n # nhr=header. nin=index, nsq=sequence\n for ext in [\".nhr\", \".nsq\"]: # \".nin\" can change\n assert_equal_contents(\n self, os.path.join(tempDir, output_prefix + ext),\n os.path.join(myInputDir, \"expected\", output_prefix + ext)\n )\n\n def test_blastn_db_build_gz(self):\n commonInputDir = util_file.get_test_input_path()\n refFasta = os.path.join(commonInputDir, 'ebola.fasta.gz')\n\n myInputDir = util_file.get_test_input_path(self)\n tempDir = tempfile.mkdtemp()\n\n output_prefix = self.__class__.__name__\n\n args = taxon_filter.parser_blastn_build_db(argparse.ArgumentParser()).parse_args(\n [\n # input fasta\n refFasta,\n # output directory\n tempDir,\n \"--outputFilePrefix\",\n output_prefix\n ]\n )\n args.func_main(args)\n\n # nhr=header. nin=index, nsq=sequence\n for ext in [\".nhr\", \".nsq\"]: # \".nin\" can change\n assert_equal_contents(\n self, os.path.join(tempDir, output_prefix + ext),\n os.path.join(myInputDir, \"expected\", output_prefix + ext)\n )\n\n commonInputDir = util_file.get_test_input_path()\n\n refFasta = os.path.join(commonInputDir, 'ebola.fasta.lz4')\n args = taxon_filter.parser_blastn_build_db(argparse.ArgumentParser()).parse_args(\n [\n # input fasta\n refFasta,\n # output directory\n tempDir,\n \"--outputFilePrefix\",\n output_prefix\n ]\n )\n args.func_main(args)\n\n\n@unittest.skipIf(IS_ARM, SKIP_BMTAGGER_REASON)\nclass TestBmtaggerDbBuild(TestCaseWithTmp):\n\n def test_bmtagger_db_build(self):\n os.environ.pop('TMPDIR', None)\n util_file.set_tmp_dir(None)\n commonInputDir = util_file.get_test_input_path()\n refFasta = os.path.join(commonInputDir, 'ebola.fasta')\n\n myInputDir = util_file.get_test_input_path(self)\n tempDir = tempfile.mkdtemp()\n\n output_prefix = self.__class__.__name__\n\n args = taxon_filter.parser_bmtagger_build_db(argparse.ArgumentParser()).parse_args(\n [\n # input fasta\n refFasta,\n # output directory\n tempDir,\n \"--outputFilePrefix\",\n output_prefix,\n \"--word_size\",\n \"8\",\n ]\n )\n args.func_main(args)\n\n for ext in [\n \".bitmask\", \".srprism.amp\", \".srprism.imp\", \".srprism.pmp\", \".srprism.rmp\",\n \".srprism.ssa\", \".srprism.ssd\"\n ]:\n assert_equal_contents(\n self, os.path.join(tempDir, output_prefix + ext),\n os.path.join(myInputDir, \"expected\", output_prefix + ext)\n )\n\n for ext in [\".srprism.map\", \".srprism.idx\", \".srprism.ss\"]:\n assert_md5_equal_to_line_in_file(self, os.path.join(tempDir, output_prefix + ext), os.path.join(myInputDir, \"expected\", output_prefix + ext+\".md5\"))\n\n def test_bmtagger_db_build_gz(self):\n commonInputDir = util_file.get_test_input_path()\n refFasta = os.path.join(commonInputDir, 'ebola.fasta.gz')\n myInputDir = util_file.get_test_input_path(self)\n tempDir = tempfile.mkdtemp()\n output_prefix = self.__class__.__name__\n args = taxon_filter.parser_bmtagger_build_db(argparse.ArgumentParser()).parse_args(\n [\n # input fasta\n refFasta,\n # output directory\n tempDir,\n \"--outputFilePrefix\",\n output_prefix,\n \"--word_size\",\n \"8\",\n ]\n )\n args.func_main(args)\n refFasta = os.path.join(commonInputDir, 'ebola.fasta.lz4')\n args = taxon_filter.parser_bmtagger_build_db(argparse.ArgumentParser()).parse_args(\n [\n # input fasta\n refFasta,\n # output directory\n tempDir,\n \"--outputFilePrefix\",\n output_prefix,\n \"--word_size\",\n \"8\",\n ]\n )\n args.func_main(args)\n\n\nclass TestLastalDbBuild(TestCaseWithTmp):\n\n def test_lastal_db_build(self):\n commonInputDir = util_file.get_test_input_path()\n refFasta = os.path.join(commonInputDir, 'ebola.fasta')\n\n myInputDir = util_file.get_test_input_path(self)\n tempDir = tempfile.mkdtemp()\n\n output_prefix = self.__class__.__name__\n\n args = taxon_filter.parser_lastal_build_db(argparse.ArgumentParser()).parse_args(\n [\n # input fasta\n refFasta,\n # output directory\n tempDir,\n \"--outputFilePrefix\",\n output_prefix\n ]\n )\n args.func_main(args)\n\n for ext in [\".bck\", \".des\", \".prj\", \".sds\", \".ssp\", \".tis\"]:\n self.assertGreater(os.path.getsize(os.path.join(tempDir, output_prefix + ext)), 0)\n #assert_equal_contents(\n # self, os.path.join(tempDir, output_prefix + ext),\n # os.path.join(myInputDir, \"expected\", output_prefix + ext)\n #)\n\n for ext in [\".suf\"]:\n self.assertGreater(os.path.getsize(os.path.join(tempDir, output_prefix + ext)), 0)\n # assert_md5_equal_to_line_in_file(self, os.path.join(tempDir, output_prefix + ext), os.path.join(myInputDir, \"expected\", output_prefix + ext+\".md5\"))\n\nclass TestDepleteBlastnBam(TestCaseWithTmp):\n '''\n How test data was created:\n humanChr1Subset.fa has 200 bases from human chr1\n humanChr9Subset.fa has 200 bases from human chr9\n in.fastq \"reads\" are from humanChr[19]Subset.fa and ebola genome,\n with arbitrary quality scores.\n '''\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.tempDir = tempfile.mkdtemp()\n commonInputDir = util_file.get_test_input_path()\n ref_fasta = os.path.join(commonInputDir, '5kb_human_from_chr6.fasta')\n self.database_prefix_path = os.path.join(self.tempDir, \"5kb_human_from_chr6\")\n\n # create blast db\n self.blastdb_path = blast.MakeblastdbTool().build_database(ref_fasta, self.database_prefix_path)\n\n # create multiple dbs\n self.blastdbs_multi = []\n for db in ['humanChr1Subset.fa', 'humanChr9Subset.fa']:\n dbPath = blast.MakeblastdbTool().build_database(\n os.path.join(util_file.get_test_input_path(self), db),\n os.path.join(self.tempDir, db[:-3]))\n self.blastdbs_multi.append(dbPath)\n\n # tar one db, but not the other\n tar_db_tgz = util_file.mkstempfname('-humanChr9Subset.blastn.db.tar.gz')\n cmd = ['tar', '-C', self.tempDir, '-cvzf', tar_db_tgz] + list(os.path.basename(f) for f in glob.glob(os.path.join(self.tempDir, \"humanChr9Subset.n*\")))\n subprocess.check_call(cmd)\n self.blastdbs_multi[1] = tar_db_tgz\n for idx in glob.glob(os.path.join(self.tempDir, \"humanChr9Subset.n*\")):\n os.unlink(idx)\n\n def test_deplete_blastn_bam(self):\n tempDir = tempfile.mkdtemp()\n myInputDir = util_file.get_test_input_path(self)\n\n # Run deplete_blastn_bam\n inBam = os.path.join(myInputDir, 'in.bam')\n outBam = os.path.join(tempDir, 'out.bam')\n args = taxon_filter.parser_deplete_blastn_bam(argparse.ArgumentParser()).parse_args(\n [inBam] + self.blastdbs_multi + [outBam, \"--chunkSize\", \"0\"]\n )\n args.func_main(args)\n\n # samtools view for out.sam and compare to expected\n outSam = os.path.join(tempDir, 'out.sam')\n samtools_tool = samtools.SamtoolsTool()\n samtools_tool.view(['-h'], outBam, outSam)\n\n assert_equal_bam_reads(self,\n outSam,\n os.path.join(myInputDir, 'expected.sam'))\n\n def test_deplete_blastn_bam_chunked(self):\n tempDir = tempfile.mkdtemp()\n myInputDir = util_file.get_test_input_path(self)\n\n # Run deplete_blastn_bam\n inBam = os.path.join(myInputDir, 'in.bam')\n outBam = os.path.join(tempDir, 'out.bam')\n args = taxon_filter.parser_deplete_blastn_bam(argparse.ArgumentParser()).parse_args(\n [inBam] + self.blastdbs_multi + [outBam, \"--chunkSize\", \"1\"]\n )\n args.func_main(args)\n\n # samtools view for out.sam and compare to expected\n outSam = os.path.join(tempDir, 'out.sam')\n samtools_tool = samtools.SamtoolsTool()\n samtools_tool.view(['-h'], outBam, outSam)\n\n assert_equal_bam_reads(self,\n outSam,\n os.path.join(myInputDir, 'expected.sam'))\n\n def test_blastn_empty_input(self):\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n out_bam = util_file.mkstempfname('-out.bam')\n taxon_filter.multi_db_deplete_bam(\n empty_bam,\n [self.blastdb_path],\n taxon_filter.deplete_blastn_bam,\n out_bam\n )\n self.assertEqual(0, samtools.SamtoolsTool().count(out_bam))\n\n def test_blastn_empty_output(self):\n in_bam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads-human.bam')\n out_bam = util_file.mkstempfname('-out.bam')\n taxon_filter.multi_db_deplete_bam(\n in_bam,\n [self.blastdb_path],\n taxon_filter.deplete_blastn_bam,\n out_bam\n )\n self.assertEqual(0, samtools.SamtoolsTool().count(out_bam))\n\n\nclass TestDepleteMinimap2Bam(TestCaseWithTmp):\n '''\n Tests for minimap2-based read depletion.\n Reuses test data from TestDepleteBlastnBam/TestBmtagger.\n '''\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.tempDir = tempfile.mkdtemp()\n commonInputDir = util_file.get_test_input_path()\n # Reuse existing test reference fasta\n self.ref_fasta = os.path.join(commonInputDir, '5kb_human_from_chr6.fasta')\n\n def test_deplete_minimap2_bam(self):\n '''Basic depletion test - remove human reads from mixed input'''\n inBam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')\n outBam = util_file.mkstempfname('-out.bam')\n args = taxon_filter.parser_deplete_minimap2_bam(argparse.ArgumentParser()).parse_args([\n inBam, self.ref_fasta, outBam])\n args.func_main(args)\n # Should have fewer reads than input after depletion\n samtools_tool = samtools.SamtoolsTool()\n self.assertLess(samtools_tool.count(outBam), samtools_tool.count(inBam))\n\n def test_minimap2_empty_input(self):\n '''Empty input BAM should produce empty output BAM'''\n empty_bam = os.path.join(util_file.get_test_input_path(), 'empty.bam')\n out_bam = util_file.mkstempfname('-out.bam')\n taxon_filter.multi_db_deplete_bam(\n empty_bam,\n [self.ref_fasta],\n taxon_filter.deplete_minimap2_bam,\n out_bam\n )\n self.assertEqual(0, samtools.SamtoolsTool().count(out_bam))\n\n def test_minimap2_empty_output(self):\n '''All-human input should result in empty output after depletion'''\n in_bam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads-human.bam')\n out_bam = util_file.mkstempfname('-out.bam')\n taxon_filter.multi_db_deplete_bam(\n in_bam,\n [self.ref_fasta],\n taxon_filter.deplete_minimap2_bam,\n out_bam\n )\n self.assertEqual(0, samtools.SamtoolsTool().count(out_bam))\n\n\nclass TestDepletePipeline(TestCaseWithTmp):\n '''\n Tests for the full deplete pipeline (main_deplete) including minimap2 depletion.\n '''\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.tempDir = tempfile.mkdtemp()\n commonInputDir = util_file.get_test_input_path()\n self.ref_fasta = os.path.join(commonInputDir, '5kb_human_from_chr6.fasta')\n\n def test_deplete_pipeline_with_minimap(self):\n '''Test full deplete pipeline with minimap2 depletion enabled'''\n inBam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')\n revertBam = util_file.mkstempfname('-revert.bam')\n minimapBam = util_file.mkstempfname('-minimap.bam')\n bwaBam = util_file.mkstempfname('-bwa.bam')\n bmtaggerBam = util_file.mkstempfname('-bmtagger.bam')\n blastnBam = util_file.mkstempfname('-blastn.bam')\n\n args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args([\n inBam,\n revertBam,\n minimapBam,\n bwaBam,\n bmtaggerBam,\n blastnBam,\n '--minimapDbs', self.ref_fasta\n ])\n args.func_main(args)\n\n samtools_tool = samtools.SamtoolsTool()\n # Verify output files exist and have fewer reads than input\n self.assertTrue(os.path.exists(minimapBam))\n self.assertLess(samtools_tool.count(minimapBam), samtools_tool.count(inBam))\n\n def test_deplete_pipeline_empty_minimap_dbs(self):\n '''Test deplete pipeline with empty minimapDbs (default behavior)'''\n inBam = os.path.join(util_file.get_test_input_path(), 'TestDepleteHuman', 'test-reads.bam')\n revertBam = util_file.mkstempfname('-revert.bam')\n minimapBam = util_file.mkstempfname('-minimap.bam')\n bwaBam = util_file.mkstempfname('-bwa.bam')\n bmtaggerBam = util_file.mkstempfname('-bmtagger.bam')\n blastnBam = util_file.mkstempfname('-blastn.bam')\n\n args = taxon_filter.parser_deplete(argparse.ArgumentParser()).parse_args([\n inBam,\n revertBam,\n minimapBam,\n bwaBam,\n bmtaggerBam,\n blastnBam,\n '--bwaDbs', self.ref_fasta # Use bwa instead of minimap\n ])\n args.func_main(args)\n\n samtools_tool = samtools.SamtoolsTool()\n # Verify minimap output exists (should be copy of input since no minimap dbs)\n self.assertTrue(os.path.exists(minimapBam))\n # With no minimap dbs, minimapBam should have same count as reverted input\n # BWA depletion happens after, so bwaBam should have fewer reads\n self.assertLess(samtools_tool.count(bwaBam), samtools_tool.count(inBam))\n" }, { "path": "tests/unit/classify/test_taxonomy.py", "content": "import os.path\nfrom os.path import join\n\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs import metagenomics\n\n\ndef test_taxonomy_subset_zaire(request, tmpdir_factory):\n data_dir = join(util_file.get_test_input_path(), 'TestMetagenomicsSimple')\n db_dir = join(data_dir, 'db', 'taxonomy')\n sub_dir = str(tmpdir_factory.mktemp('taxonomy_subset'))\n # Zaire species\n metagenomics.subset_taxonomy(db_dir, sub_dir, whitelistTaxids=[], whitelistTreeTaxids=[186538])\n\n tax_db = metagenomics.TaxonomyDb(sub_dir, load_nodes=True, load_names=True)\n assert 186538 in tax_db.parents # Zaire species\n assert 186540 not in tax_db.parents # Sudan species\n assert 2 not in tax_db.parents # Bacteria\n" }, { "path": "tests/unit/classify/test_tools_kb_python.py", "content": "# Unit tests for kb_python\nimport os\nfrom unittest.mock import patch, MagicMock\n\nimport pytest\n\nfrom viral_ngs.classify import kb\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.core import misc as util_misc\n\n\n@pytest.fixture\ndef kb_tool():\n with patch('viral_ngs.classify.kb.shutil.which', return_value='/usr/bin/kb'):\n yield kb.kb()\n\n\n@pytest.fixture\ndef kb_inputs():\n base = os.path.join(util_file.get_test_input_path(), 'TestKbPython')\n paths = {\n 'fastq': os.path.join(base, 'SRR12340077.2.sample.fastq.gz'),\n 'bam': os.path.join(util_file.get_test_input_path(), 'G5012.3.testreads.bam'),\n 'index': os.path.join(base, 'palmdb.corona.idx'),\n 't2g': os.path.join(base, 'palmdb_clustered_t2g.txt'),\n }\n for p in paths.values():\n assert os.path.exists(p), f'Missing expected kb test input: {p}'\n return paths\n\n\ndef test_build_invokes_kb_ref_with_expected_arguments(kb_tool, kb_inputs):\n with patch('viral_ngs.classify.kb.subprocess.Popen', autospec=True) as mock_popen:\n mock_process = mock_popen.return_value\n mock_process.communicate.return_value = ('', '')\n mock_process.returncode = 0\n\n kb_tool.build(kb_inputs['fastq'], kb_inputs['index'], workflow='custom', kmer_len=27, protein=True, num_threads=9)\n\n args = mock_popen.call_args[0][0]\n assert ['kb', 'ref'] == args[:2]\n assert util_misc.list_contains(['-i', kb_inputs['index']], args)\n assert util_misc.list_contains(['-k', '27'], args)\n assert util_misc.list_contains(['--workflow', 'custom'], args)\n assert '--aa' in args\n expected_threads = str(util_misc.sanitize_thread_count(9))\n assert util_misc.list_contains(['-t', expected_threads], args)\n assert args[-1] == kb_inputs['fastq']\n\n\ndef test_classify_runs_kb_count_single_end_from_bam(kb_tool, kb_inputs):\n \"\"\"Test classify with BAM input - should convert to FASTQ via Picard\"\"\"\n mkstemp_vals = ['single.1.fastq', 'single.2.fastq', 'single.s.fastq']\n size_map = {\n 'single.2.fastq': 1,\n 'single.s.fastq': 10,\n }\n\n with patch('viral_ngs.classify.kb.file.mkstempfname', side_effect=mkstemp_vals), \\\n patch('viral_ngs.classify.kb.os.unlink'), \\\n patch('viral_ngs.classify.kb.picard.SamToFastqTool', autospec=True) as picard_cls, \\\n patch('viral_ngs.classify.kb.picard.PicardTools.dict_to_picard_opts', return_value='clip-opts'), \\\n patch('viral_ngs.classify.kb.samtools.SamtoolsTool', autospec=True) as samtools_cls, \\\n patch('viral_ngs.classify.kb.subprocess.Popen', autospec=True) as mock_popen, \\\n patch('viral_ngs.classify.kb.os.path.getsize', side_effect=lambda path: size_map.get(path, 1000)), \\\n patch('viral_ngs.classify.kb.glob.glob', return_value=[]):\n\n picard_cls.illumina_clipping_attribute = 'XT'\n picard = picard_cls.return_value\n picard.jvmMemDefault = '4G'\n picard.execute.return_value = None\n\n samtools = samtools_cls.return_value\n samtools.isEmpty.return_value = False\n\n mock_process = mock_popen.return_value\n mock_process.communicate.return_value = ('', '')\n mock_process.returncode = 0\n\n kb_tool.classify(kb_inputs['bam'], kb_inputs['index'], 'out_dir', kb_inputs['t2g'], num_threads=3, loom=True)\n\n args = mock_popen.call_args[0][0]\n assert ['kb', 'count'] == args[:2]\n assert args[-1] == 'single.s.fastq'\n assert util_misc.list_contains(['--parity', 'single'], args)\n assert '--loom' in args\n assert '--h5ad' not in args\n expected_threads = str(util_misc.sanitize_thread_count(3))\n assert util_misc.list_contains(['-t', expected_threads], args)\n picard.execute.assert_called_once_with(\n kb_inputs['bam'],\n 'single.1.fastq',\n 'single.2.fastq',\n outFastq0='single.s.fastq',\n picardOptions='clip-opts',\n JVMmemory='4G',\n )\n\n\ndef test_classify_runs_kb_count_with_fastq_input(kb_tool, kb_inputs):\n \"\"\"Test classify with FASTQ input - should skip Picard and use file directly\"\"\"\n with patch('viral_ngs.classify.kb.os.path.exists', return_value=True), \\\n patch('viral_ngs.classify.kb.subprocess.Popen', autospec=True) as mock_popen, \\\n patch('viral_ngs.classify.kb.samtools.SamtoolsTool', autospec=True) as samtools_cls, \\\n patch('viral_ngs.classify.kb.glob.glob', return_value=[]):\n\n samtools = samtools_cls.return_value\n samtools.isEmpty.return_value = False\n\n mock_process = mock_popen.return_value\n mock_process.communicate.return_value = ('', '')\n mock_process.returncode = 0\n\n kb_tool.classify(kb_inputs['fastq'], kb_inputs['index'], 'out_dir', kb_inputs['t2g'], num_threads=3, h5ad=True)\n\n args = mock_popen.call_args[0][0]\n assert ['kb', 'count'] == args[:2]\n assert args[-1] == kb_inputs['fastq']\n assert util_misc.list_contains(['--parity', 'single'], args)\n assert '--h5ad' in args\n expected_threads = str(util_misc.sanitize_thread_count(3))\n assert util_misc.list_contains(['-t', expected_threads], args)\n\n\ndef test_classify_returns_early_when_bam_is_empty(kb_tool, kb_inputs):\n mkstemp_vals = ['ignored.1.fastq', 'ignored.2.fastq', 'ignored.s.fastq']\n\n with patch('viral_ngs.classify.kb.file.mkstempfname', side_effect=mkstemp_vals), \\\n patch('viral_ngs.classify.kb.os.unlink'), \\\n patch('viral_ngs.classify.kb.picard.SamToFastqTool', autospec=True) as picard_cls, \\\n patch('viral_ngs.classify.kb.picard.PicardTools.dict_to_picard_opts', return_value='clip-opts'), \\\n patch('viral_ngs.classify.kb.samtools.SamtoolsTool', autospec=True) as samtools_cls, \\\n patch('viral_ngs.classify.kb.subprocess.Popen', autospec=True) as mock_popen:\n\n picard_cls.illumina_clipping_attribute = 'XT'\n picard = picard_cls.return_value\n picard.jvmMemDefault = '4G'\n picard.execute.return_value = None\n\n samtools = samtools_cls.return_value\n samtools.isEmpty.return_value = True\n\n mock_process = mock_popen.return_value\n mock_process.communicate.return_value = ('', '')\n mock_process.returncode = 0\n\n kb_tool.classify(kb_inputs['bam'], kb_inputs['index'], 'out_dir', kb_inputs['t2g'])\n\n mock_popen.assert_not_called()\n picard.execute.assert_not_called()\n" }, { "path": "tests/unit/classify/test_tools_kma.py", "content": "# Unit tests for KMA\nimport os\nfrom unittest.mock import patch, mock_open\n\nimport pytest\n\nfrom viral_ngs.classify import kma\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.core import misc as util_misc\n\n\n@pytest.fixture\ndef kma_tool():\n with patch('viral_ngs.classify.kma.shutil.which', return_value='/usr/bin/kma'):\n yield kma.KMA()\n\n\n@pytest.fixture\ndef kma_inputs():\n base = os.path.join(util_file.get_test_input_path(), 'TestKMA')\n paths = {\n 'bam': os.path.join(util_file.get_test_input_path(), 'G5012.3.testreads.bam'),\n 'db_prefix': os.path.join(base, 'test_db'),\n 'ref_fasta': os.path.join(base, 'ref.fasta'),\n }\n return paths\n\n\ndef test_build_invokes_kma_index_with_expected_arguments(kma_tool, kma_inputs):\n with patch('viral_ngs.classify.kma.subprocess.check_call', autospec=True) as mock_check_call:\n kma_tool.build(kma_inputs['ref_fasta'], kma_inputs['db_prefix'], num_threads=9)\n\n args = mock_check_call.call_args[0][0]\n assert 'kma_index' == args[0]\n assert util_misc.list_contains(['-i', kma_inputs['ref_fasta']], args)\n assert util_misc.list_contains(['-o', kma_inputs['db_prefix']], args)\n expected_threads = str(util_misc.sanitize_thread_count(9))\n assert util_misc.list_contains(['-t', expected_threads], args)\n\n\ndef test_classify_single_end_from_bam(kma_tool, kma_inputs):\n \"\"\"Test classify with BAM input in single-end mode\"\"\"\n mkstemp_vals = ['single.1.fastq', 'single.2.fastq', 'single.s.fastq']\n size_map = {\n 'single.2.fastq': 1,\n 'single.s.fastq': 10,\n }\n\n with patch('viral_ngs.classify.kma.file.mkstempfname', side_effect=mkstemp_vals), \\\n patch('viral_ngs.classify.kma.os.unlink'), \\\n patch('viral_ngs.classify.kma.picard.SamToFastqTool', autospec=True) as picard_cls, \\\n patch('viral_ngs.classify.kma.picard.PicardTools.dict_to_picard_opts', return_value='clip-opts'), \\\n patch('viral_ngs.classify.kma.samtools.SamtoolsTool', autospec=True) as samtools_cls, \\\n patch('viral_ngs.classify.kma.subprocess.check_call', autospec=True) as mock_check_call, \\\n patch('viral_ngs.classify.kma.os.path.getsize', side_effect=lambda path: size_map.get(path, 1000)):\n\n picard_cls.illumina_clipping_attribute = 'XT'\n picard = picard_cls.return_value\n picard.jvmMemDefault = '4G'\n picard.execute.return_value = None\n\n samtools = samtools_cls.return_value\n samtools.isEmpty.return_value = False\n\n kma_tool.classify(kma_inputs['bam'], kma_inputs['db_prefix'], 'out_prefix', num_threads=3)\n\n args = mock_check_call.call_args[0][0]\n assert 'kma' == args[0]\n assert util_misc.list_contains(['-t_db', kma_inputs['db_prefix']], args)\n assert util_misc.list_contains(['-o', 'out_prefix'], args)\n assert util_misc.list_contains(['-i', 'single.s.fastq'], args)\n expected_threads = str(util_misc.sanitize_thread_count(3))\n assert util_misc.list_contains(['-t', expected_threads], args)\n picard.execute.assert_called_once_with(\n kma_inputs['bam'],\n 'single.1.fastq',\n 'single.2.fastq',\n outFastq0='single.s.fastq',\n picardOptions='clip-opts',\n JVMmemory='4G',\n )\n\n\ndef test_classify_paired_end_from_bam(kma_tool, kma_inputs):\n \"\"\"Test classify with BAM input in paired-end mode\"\"\"\n mkstemp_vals = ['paired.1.fastq', 'paired.2.fastq', 'paired.s.fastq']\n size_map = {\n 'paired.2.fastq': 10,\n 'paired.s.fastq': 1,\n }\n\n with patch('viral_ngs.classify.kma.file.mkstempfname', side_effect=mkstemp_vals), \\\n patch('viral_ngs.classify.kma.os.unlink'), \\\n patch('viral_ngs.classify.kma.picard.SamToFastqTool', autospec=True) as picard_cls, \\\n patch('viral_ngs.classify.kma.picard.PicardTools.dict_to_picard_opts', return_value='clip-opts'), \\\n patch('viral_ngs.classify.kma.samtools.SamtoolsTool', autospec=True) as samtools_cls, \\\n patch('viral_ngs.classify.kma.subprocess.check_call', autospec=True) as mock_check_call, \\\n patch('viral_ngs.classify.kma.os.path.getsize', side_effect=lambda path: size_map.get(path, 1000)):\n\n picard_cls.illumina_clipping_attribute = 'XT'\n picard = picard_cls.return_value\n picard.jvmMemDefault = '4G'\n picard.execute.return_value = None\n\n samtools = samtools_cls.return_value\n samtools.isEmpty.return_value = False\n\n kma_tool.classify(kma_inputs['bam'], kma_inputs['db_prefix'], 'out_prefix', num_threads=4)\n\n args = mock_check_call.call_args[0][0]\n assert 'kma' == args[0]\n assert util_misc.list_contains(['-t_db', kma_inputs['db_prefix']], args)\n assert util_misc.list_contains(['-o', 'out_prefix'], args)\n assert util_misc.list_contains(['-ipe', 'paired.1.fastq paired.2.fastq'], args)\n expected_threads = str(util_misc.sanitize_thread_count(4))\n assert util_misc.list_contains(['-t', expected_threads], args)\n picard.execute.assert_called_once_with(\n kma_inputs['bam'],\n 'paired.1.fastq',\n 'paired.2.fastq',\n outFastq0='paired.s.fastq',\n picardOptions='clip-opts',\n JVMmemory='4G',\n )\n\n\ndef test_classify_returns_early_when_bam_is_empty(kma_tool, kma_inputs):\n mkstemp_vals = ['ignored.1.fastq', 'ignored.2.fastq', 'ignored.s.fastq']\n\n with patch('viral_ngs.classify.kma.file.mkstempfname', side_effect=mkstemp_vals), \\\n patch('viral_ngs.classify.kma.os.unlink'), \\\n patch('viral_ngs.classify.kma.picard.SamToFastqTool', autospec=True) as picard_cls, \\\n patch('viral_ngs.classify.kma.picard.PicardTools.dict_to_picard_opts', return_value='clip-opts'), \\\n patch('viral_ngs.classify.kma.samtools.SamtoolsTool', autospec=True) as samtools_cls, \\\n patch('viral_ngs.classify.kma.subprocess.check_call', autospec=True) as mock_check_call, \\\n patch('viral_ngs.classify.kma.open', mock_open()) as mocked_open:\n\n picard_cls.illumina_clipping_attribute = 'XT'\n picard = picard_cls.return_value\n picard.jvmMemDefault = '4G'\n picard.execute.return_value = None\n\n samtools = samtools_cls.return_value\n samtools.isEmpty.return_value = True\n\n kma_tool.classify(kma_inputs['bam'], kma_inputs['db_prefix'], 'out_prefix')\n\n mock_check_call.assert_not_called()\n picard.execute.assert_not_called()\n mocked_open.assert_called_once_with('out_prefix.res', 'wt')\n" }, { "path": "tests/unit/classify/test_tools_krona.py", "content": "# Unit tests for krona\nfrom builtins import super\nimport os.path\nimport tempfile\nimport unittest\nfrom unittest.mock import patch\nfrom viral_ngs.core import file as util_file\nfrom viral_ngs.core import misc as util_misc\nfrom viral_ngs.classify import krona\nfrom tests import TestCaseWithTmp\n\n\nclass TestToolKrona(TestCaseWithTmp):\n\n def setUp(self):\n super().setUp()\n self.krona = krona.Krona()\n self.krona.install()\n\n patcher = patch('subprocess.check_call', autospec=True)\n self.addCleanup(patcher.stop)\n self.mock_run = patcher.start()\n\n self.db = tempfile.mkdtemp('db')\n\n def test_import_taxonomy(self):\n in_tsv = util_file.mkstempfname('.tsv')\n output = util_file.mkstempfname('.output')\n self.krona.import_taxonomy(\n self.db, [in_tsv], output, query_column=3, taxid_column=5, score_column=7, no_hits=True, no_rank=True\n )\n args = self.mock_run.call_args[0][0]\n self.assertEqual('ktImportTaxonomy', os.path.basename(args[0]))\n self.assertTrue(util_misc.list_contains(['-tax', self.db], args))\n self.assertTrue(util_misc.list_contains(['-q', '3'], args))\n self.assertTrue(util_misc.list_contains(['-t', '5'], args))\n self.assertTrue(util_misc.list_contains(['-s', '7'], args))\n self.assertIn('-i', args)\n self.assertIn('-k', args)\n\n self.krona.import_taxonomy(self.db, [in_tsv], output)\n args = self.mock_run.call_args[0][0]\n self.assertEqual('ktImportTaxonomy', os.path.basename(args[0]))\n self.assertTrue(util_misc.list_contains(['-tax', self.db], args))\n self.assertFalse(util_misc.list_contains(['-q', '3'], args))\n self.assertFalse(util_misc.list_contains(['-t', '5'], args))\n self.assertFalse(util_misc.list_contains(['-s', '7'], args))\n self.assertNotIn('-i', args)\n self.assertNotIn('-k', args)\n\n def test_create_db(self):\n self.krona.create_db(self.db)\n args = self.mock_run.call_args[0][0]\n self.assertEqual('updateTaxonomy.sh', os.path.basename(args[0]))\n self.assertTrue(util_misc.list_contains(['--only-build', self.db], args))\n self.assertIn(self.db, args)\n" }, { "path": "tests/unit/core/test_conftest.py", "content": "\"\"\"Unit tests for pytest customizations\"\"\"\n\nimport sys\nimport os\nimport os.path\nimport functools\nimport pytest\n\nimport viral_ngs.core\nfrom viral_ngs.core.file import slurp_file, get_test_input_path\n\n\ndef test_monkeypatch_function_result(monkeypatch_function_result):\n assert list(viral_ngs.core.misc.unique([])) == []\n with monkeypatch_function_result(viral_ngs.core.misc.unique, [], patch_result=[1]):\n assert list(viral_ngs.core.misc.unique([])) == [1]\n assert list(viral_ngs.core.misc.unique([2,1,2])) == [2, 1]\n assert list(viral_ngs.core.misc.unique([])) == []\n\n inp = functools.partial(os.path.join, get_test_input_path())\n\n with pytest.raises(Exception):\n slurp_file('/some/file')\n\n with monkeypatch_function_result(slurp_file, '/some/file', patch_result='some_content',\n patch_module=sys.modules[__name__]):\n assert slurp_file('/some/file') == 'some_content'\n assert slurp_file(inp('ebov-makona.fasta')).startswith('>KJ660346.2')\n with monkeypatch_function_result(slurp_file, inp('ebov-makona.fasta'), patch_result='something_else',\n patch_module=sys.modules[__name__]):\n assert slurp_file('/some/file') == 'some_content'\n assert slurp_file(inp('ebov-makona.fasta')) == 'something_else'\n assert slurp_file(inp('ebov-makona.fasta')).startswith('>KJ660346.2')\n\n with monkeypatch_function_result(slurp_file, inp('ebov-makona.fasta'), patch_exception=RuntimeError(),\n patch_module=sys.modules[__name__]):\n with pytest.raises(Exception):\n slurp_file(inp('ebov-makona.fasta'))\n assert slurp_file('/some/file') == 'some_content'\n\n with pytest.raises(Exception):\n slurp_file('/some/file')\n" }, { "path": "tests/unit/core/test_file_utils.py", "content": "# Unit tests for ncbi.py\n\n__author__ = \"tomkinsc@broadinstitute.org\"\n\n# built-ins\nimport os\nimport tempfile\nimport unittest\nimport argparse\n\n# module-specific\nimport viral_ngs.file_utils\nimport viral_ngs.core\nfrom tests import TestCaseWithTmp\n\nclass TestCommandHelp(unittest.TestCase):\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_func in viral_ngs.file_utils.__commands__:\n parser = parser_func(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\nclass TestTarballMerger(TestCaseWithTmp):\n def setUp(self):\n super(TestTarballMerger, self).setUp()\n self.input_dir = viral_ngs.core.file.get_test_input_path(self)\n self.raw_files = [\"file{}\".format(x) for x in range(1,5)]\n self.input_mixed_files = list(os.path.join(self.input_dir, \"mixed-compressed-input\", fn)\n for fn in sorted(os.listdir(os.path.join(self.input_dir, \"mixed-compressed-input\"))))\n \n def test_simple_merge(self):\n \"\"\"\n Simple execution\n \"\"\"\n temp_dir = tempfile.gettempdir()\n out_tarball_file = os.path.join(temp_dir,\"out.tar.gz\")\n\n viral_ngs.file_utils.merge_tarballs( out_tarball_file,\n self.input_mixed_files\n )\n\nclass TestTsvJoin(TestCaseWithTmp):\n \n def test_join(self):\n infiles = list(os.path.join(viral_ngs.core.file.get_test_input_path(self), x) for x in ('tab-1.txt', 'tab-2.txt'))\n expected = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'expected-out.txt')\n actual = viral_ngs.core.file.mkstempfname('.joined.txt')\n viral_ngs.file_utils.tsv_join(infiles, actual, join_id='h1')\n self.assertEqualContents(expected, actual)\n" }, { "path": "tests/unit/core/test_illumina.py", "content": "# Unit tests for illumina.py\n# -*- coding: utf-8 -*-\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport os\nimport os.path\nimport tempfile\nimport argparse\nimport filecmp\nimport shutil\nimport json\nimport gzip\nimport pytest\nimport viral_ngs.core\nimport viral_ngs.illumina\nimport viral_ngs.core.samtools\nimport viral_ngs.core.picard\nfrom tests import TestCaseWithTmp, assert_equal_bam_reads\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in viral_ngs.illumina.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n\nclass TestSampleSheet(TestCaseWithTmp):\n\n def test_miseq(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-miseq-1.csv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 20)\n\n def test_broad_platform(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-hiseq-1.csv'), only_lane=2)\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 24)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-hiseq-1.csv'), allow_non_unique=True)\n self.assertEqual(len(samples.get_rows()), 48)\n\n def test_walkup_submission_no_header_no_lf(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-submit-1.csv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 24)\n\n def test_walkup_submission(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-submit-2.csv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 96)\n\n def test_walkup_submission_no_lf(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-submit-3.csv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 24)\n\n def test_tabfile(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 24)\n\n def test_dup_index_collapse_at_init(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(\n os.path.join(inDir, 'SampleSheet-custom-inner-barcodes-outer-collapse.tsv'),\n collapse_duplicates=True,\n allow_non_unique = True)\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(samples.duplicate_rows_collapsed, True)\n self.assertEqual(len(samples.get_rows()), 4)\n\n def test_dup_index_collapse(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(\n os.path.join(inDir, 'SampleSheet-custom-inner-barcodes-outer-collapse.tsv'),\n allow_non_unique = True\n )\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(samples.duplicate_rows_collapsed, False)\n self.assertEqual(samples.can_be_collapsed, True)\n self.assertEqual(samples.num_samples, 96)\n\n samples.collapse_sample_index_duplicates()\n\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(samples.duplicate_rows_collapsed, True)\n self.assertEqual(samples.can_be_collapsed, False)\n self.assertEqual(len(samples.get_rows()), 4)\n\n # check that unique values in grouped rows are preserved\n # and others are collapsed to the md5sum of the (joined) unique values\n collapsed_row = next((r for r in samples.get_rows() if r[\"sample\"] == \"CTGATCGT-GCGCATAT\" and r[\"barcode_1\"] == \"CTGATCGT\" and r[\"barcode_2\"] == \"GCGCATAT\"), None)\n self.assertEqual(collapsed_row[\"library_id_per_sample\"], \"Pool_1\")\n self.assertEqual(collapsed_row[\"barcode_3\"],\"2e094627_muxed\")\n\n # check for dups in the collapsed output\n self.assertEqual(len(set((r[\"barcode_1\"] for r in samples.get_rows()))), len(list((r[\"barcode_1\"] for r in samples.get_rows()))))\n self.assertEqual(len(set((r[\"barcode_2\"] for r in samples.get_rows()))), len(list((r[\"barcode_2\"] for r in samples.get_rows()))))\n\n # check that the collapsed output is what we expect\n self.assertEqual(tuple(r[\"barcode_1\"] for r in samples.get_rows()), (\"CTGATCGT\",\"ACTCTCGA\",\"TGAGCTAG\",\"GAGACGAT\"))\n self.assertEqual(tuple(r[\"barcode_2\"] for r in samples.get_rows()), (\"GCGCATAT\",\"CTGTACCA\",\"GAACGGTT\",\"ACCGGTTA\"))\n\n def test_tabfile_win_endings(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1_win-endings.txt'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 24)\n\n def test_gz_tabfile_win_endings(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1_win-endings.txt.gz'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 24)\n\n def test_tabfile_macos9_endings(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1_macos9-endings.txt'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 24)\n\n def test_tabfile_extras(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-2.txt'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 96)\n\n def test_tabfile_extras_win(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-2_win-endings.tsv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 96)\n\n def test_blank_line_in_tabular_section(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-with-blanklines.csv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 12)\n\n def test_picard_block(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-in-Broad-MiSeq-Format_with_Picard_Block.csv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 11)\n\n def test_rev_comp_barcode_values(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'))\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"TAGATCGC\")\n samples.rev_comp_barcode_values()\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"GCGATCTA\")\n\n def test_rev_comp_barcode_value_barcode2_at_load(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'), rev_comp_barcode_2=True)\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"GCGATCTA\")\n self.assertTrue(samples.barcodes_revcomped_relative_to_input)\n self.assertIn(\"barcode_2\", samples.barcodes_revcomped_column_names)\n self.assertNotIn(\"barcode_1\", samples.barcodes_revcomped_column_names)\n\n def test_rev_comp_barcode_values_specified_at_load_two_columns(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'), barcode_columns_to_revcomp=[\"barcode_1\",\"barcode_2\"])\n self.assertEqual(samples.get_rows()[23][\"barcode_1\"], \"TCCTCTAC\")\n self.assertEqual(samples.get_rows()[23][\"barcode_2\"], \"AGAGGATA\")\n self.assertTrue(samples.barcodes_revcomped_relative_to_input)\n self.assertIn(\"barcode_1\", samples.barcodes_revcomped_column_names)\n self.assertIn(\"barcode_2\", samples.barcodes_revcomped_column_names)\n\n def test_rev_comp_barcode_values_specified_one_column(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'))\n self.assertEqual(samples.get_rows()[23][\"barcode_1\"], \"GTAGAGGA\")\n samples.rev_comp_barcode_values(barcode_columns_to_revcomp=[\"barcode_1\"])\n self.assertEqual(samples.get_rows()[23][\"barcode_1\"], \"TCCTCTAC\")\n # barcode_2 should be unchanged\n self.assertEqual(samples.get_rows()[23][\"barcode_2\"], \"TATCCTCT\")\n self.assertIn(\"barcode_1\", samples.barcodes_revcomped_column_names)\n self.assertNotIn(\"barcode_2\", samples.barcodes_revcomped_column_names)\n\n def test_rev_comp_barcode_values_specified_two_columns(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'))\n self.assertEqual(samples.get_rows()[23][\"barcode_1\"], \"GTAGAGGA\")\n self.assertEqual(samples.get_rows()[23][\"barcode_2\"], \"TATCCTCT\")\n samples.rev_comp_barcode_values(barcode_columns_to_revcomp=[\"barcode_1\",\"barcode_2\"])\n self.assertEqual(samples.get_rows()[23][\"barcode_1\"], \"TCCTCTAC\")\n self.assertEqual(samples.get_rows()[23][\"barcode_2\"], \"AGAGGATA\")\n self.assertIn(\"barcode_1\", samples.barcodes_revcomped_column_names)\n self.assertIn(\"barcode_2\", samples.barcodes_revcomped_column_names)\n\n def test_rev_comp_barcode_values_undo(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'))\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"TAGATCGC\")\n samples.rev_comp_barcode_values()\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"GCGATCTA\")\n samples.rev_comp_barcode_values()\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"TAGATCGC\")\n\n def test_rev_comp_barcode_values_not_inplace(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-custom-1.txt'))\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"TAGATCGC\")\n samples_revcomped = samples.rev_comp_barcode_values(inplace=False)\n # the original shet should be unchanged\n self.assertEqual(samples.get_rows()[0][\"barcode_2\"], \"TAGATCGC\")\n # the returned copy should be rev-comped\n self.assertEqual(samples_revcomped.get_rows()[0][\"barcode_2\"], \"GCGATCTA\")\n\nclass TestRunInfo(TestCaseWithTmp):\n\n def test_miseq(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-miseq.xml'))\n self.assertEqual(runinfo.get_flowcell(), 'AEF96')\n self.assertEqual(runinfo.get_rundate_american(), '08/21/2015')\n self.assertEqual(runinfo.get_rundate_iso(), '2015-08-21')\n self.assertEqual(runinfo.get_machine(), 'M04004')\n self.assertEqual(runinfo.get_read_structure(), '101T8B8B101T')\n self.assertEqual(runinfo.num_reads(), 2)\n self.assertEqual(runinfo.get_machine_model(), \"Illumina MiSeq\")\n self.assertEqual(runinfo.get_flowcell_lane_count(), 1)\n\n def test_hiseq(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-hiseq.xml'))\n self.assertEqual(runinfo.get_flowcell(), 'HVFF2ADXX')\n self.assertEqual(runinfo.get_rundate_american(), '08/21/2015')\n self.assertEqual(runinfo.get_rundate_iso(), '2015-08-21')\n self.assertEqual(runinfo.get_machine(), 'SL-HDF')\n self.assertEqual(runinfo.get_read_structure(), '101T8B8B101T')\n self.assertEqual(runinfo.num_reads(), 2)\n self.assertEqual(runinfo.get_machine_model(), \"Illumina HiSeq 2500\")\n self.assertEqual(runinfo.get_flowcell_lane_count(), 2)\n\n def test_novaseq(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-novaseq.xml'))\n self.assertEqual(runinfo.get_flowcell(), 'HCYTJDMXX')\n self.assertEqual(runinfo.get_rundate_american(), '06/27/2018')\n self.assertEqual(runinfo.get_rundate_iso(), '2018-06-27')\n self.assertEqual(runinfo.get_machine(), 'A00198')\n self.assertEqual(runinfo.get_read_structure(), '101T8B8B101T')\n self.assertEqual(runinfo.num_reads(), 2)\n self.assertEqual(runinfo.get_machine_model(), \"Illumina NovaSeq 6000\")\n self.assertEqual(runinfo.get_flowcell_lane_count(), 2)\n\n def test_nextseq550(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-nextseq550.xml'))\n self.assertEqual(runinfo.get_flowcell(), 'HMTLKAFX2')\n self.assertEqual(runinfo.get_rundate_american(), '02/21/2021')\n self.assertEqual(runinfo.get_rundate_iso(), '2021-02-21')\n self.assertEqual(runinfo.get_machine(), 'NB552060')\n self.assertEqual(runinfo.get_read_structure(), '149T10B10B149T')\n self.assertEqual(runinfo.num_reads(), 2)\n self.assertEqual(runinfo.get_machine_model(), \"NextSeq 550\")\n self.assertEqual(runinfo.get_flowcell_lane_count(), 4)\n\n def test_novaseq_x_plus(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-novaseq-x-plus.xml'))\n self.assertEqual(runinfo.get_flowcell(), '22J5GLLT4')\n self.assertEqual(runinfo.get_rundate_american(), '12/17/2024')\n self.assertEqual(runinfo.get_rundate_iso(), '2024-12-17')\n self.assertEqual(runinfo.get_machine(), 'LH00118')\n self.assertEqual(runinfo.get_read_structure(), '151T10B10B151T')\n self.assertEqual(runinfo.num_reads(), 2)\n self.assertEqual(runinfo.get_machine_model(), \"Illumina NovaSeq X Plus\")\n self.assertEqual(runinfo.get_flowcell_lane_count(), 8)\n\n def test_nextseq_1000_2000_p1(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-nextseq-1000-2000-p1.xml'))\n self.assertEqual(runinfo.get_flowcell(), 'AAG27M7M5')\n self.assertEqual(runinfo.get_rundate_american(), '09/27/2024')\n self.assertEqual(runinfo.get_rundate_iso(), '2024-09-27')\n self.assertEqual(runinfo.get_machine(), 'VH01619')\n self.assertEqual(runinfo.get_read_structure(), '151T8B8B151T')\n self.assertEqual(runinfo.num_reads(), 2)\n self.assertEqual(runinfo.get_machine_model(), \"NextSeq 1000/2000\")\n self.assertEqual(runinfo.get_flowcell_lane_count(), 1)\n\n def test_novel_tile_count_but_known_fcid(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-novel-tile-count.xml'))\n self.assertEqual(runinfo.get_machine_model(), \"Illumina MiSeq\")\n\n def test_novel_fcid_but_known_tile_count(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-novel-fcid.xml'))\n self.assertEqual(runinfo.get_machine_model(), \"Illumina MiSeq\")\n\n def test_novel_tile_count_and_fcid(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n runinfo = viral_ngs.illumina.RunInfo(os.path.join(inDir, 'RunInfo-novel-fcid-and-tilecount.xml'))\n self.assertEqual(runinfo.get_machine_model(), \"UNKNOWN\")\n\n\nclass TestIlluminaDir(TestCaseWithTmp):\n\n def test_directory(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n test_in = os.path.join(inDir, 'empty_dir')\n with viral_ngs.illumina.IlluminaDirectory(test_in) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n\n def test_tarball_normal(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-plain.tgz')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-plain.tar.bz2')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-plain.tar.lz4')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n\n def test_tarball_indented(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-indented.tgz')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n\n def test_tarball_sample_sheet(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-samplesheet.tar.gz')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-both.tar.gz')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)\n\n def test_tarball_uncompressed(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-both-uncompressed.tar')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)\n\n def test_tarball_deep_dir_tree(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-both-broad_full_path.tar.gz')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)\n\n def test_zip_archive(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-both-2.zip')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)\n\n def test_tarball_run_info(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-runinfo.tar.gz')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n self.assertEqual(idir.get_RunInfo().get_flowcell(), 'AHVPA')\n self.assertEqual(idir.get_RunInfo().get_machine(), 'M04004')\n self.assertEqual(idir.get_RunInfo().get_rundate_iso(), '2015-08-27')\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-both.tar.gz')) as idir:\n self.assertTrue(os.path.isdir(idir.get_BCLdir()))\n self.assertEqual(idir.get_RunInfo().get_flowcell(), 'AHVPA')\n self.assertEqual(idir.get_RunInfo().get_read_structure(), '101T8B8B101T')\n\n def test_tarball_fail_missing_data(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-runinfo.tar.gz')) as idir:\n self.assertRaises(Exception, idir.get_SampleSheet)\n with viral_ngs.illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-samplesheet.tar.gz')) as idir:\n self.assertRaises(Exception, idir.get_RunInfo)\n\n\nclass TestDifficultSampleNames(TestCaseWithTmp):\n\n def test_paired_1(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n outHeader = viral_ngs.core.file.mkstempfname('.txt')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-0-1_S5_L001_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-0-1_S5_L001_R2_001.fastq.gz'))\n viral_ngs.illumina.miseq_fastq_to_bam(outBam, sampleSheet, fastq[0], inFastq2=fastq[1], runInfo=runInfo)\n rgs = list(viral_ngs.core.samtools.SamtoolsTool().getReadGroups(outBam).values())\n self.assertEqual(len(rgs), 1)\n rgs = rgs[0]\n self.assertEqual(rgs.get('ID'), 'AEF96')\n self.assertEqual(rgs.get('PL'), 'illumina')\n self.assertEqual(rgs.get('PU'), 'AEF96.1.CGTACTAG-CTAAGCCT')\n self.assertEqual(rgs.get('LB'), u'GID-14-E021.ldifficult-value+for_-Sénégalsample_name0.1')\n self.assertEqual(rgs.get('SM'), u'GID-14-E021')\n self.assertEqual(rgs.get('CN'), 'M04004')\n self.assertTrue(rgs.get('DT','').startswith('2015-08-2'))\n\n def test_inline_commas_strings(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n samples = viral_ngs.illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-inline-commas-strings.csv'))\n self.assertEqual(samples.num_indexes(), 2)\n self.assertEqual(len(samples.get_rows()), 18)\n\n sample_names = [r[\"sample\"] for r in samples.get_rows()]\n names_to_validate = [\n 'Zika \"seedstock_1 (in K562, 5ng)',\n \"Zika 'seedstock_3 (in K562, 5ng)\",\n \"Zika seedstock_7 (in K562, 10pg)\"\n ]\n for sample_name in names_to_validate:\n assert viral_ngs.core.file.string_to_file_name(sample_name) in sample_names\n\n\nclass TestIlluminaBarcodeHelper(TestCaseWithTmp):\n def test_one_correction(self):\n dir_prefix = \"one_correction\"\n in_dir = viral_ngs.core.file.get_test_input_path(self)\n in_barcodes = os.path.join(in_dir,dir_prefix,\"barcodes.txt\")\n in_metrics = os.path.join(in_dir,dir_prefix,\"metrics.txt\")\n out_report = viral_ngs.core.file.mkstempfname('.txt')\n expected = os.path.join(in_dir,dir_prefix,\"expected.txt\")\n\n args = [in_barcodes, in_metrics, out_report]\n args = viral_ngs.illumina.parser_guess_barcodes(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n self.assertEqualContents(out_report, expected)\n\n def test_ambiguous(self):\n dir_prefix = \"ambiguous\"\n in_dir = viral_ngs.core.file.get_test_input_path(self)\n in_barcodes = os.path.join(in_dir,dir_prefix,\"barcodes.txt\")\n in_metrics = os.path.join(in_dir,dir_prefix,\"metrics.txt\")\n out_report = viral_ngs.core.file.mkstempfname('.txt')\n expected = os.path.join(in_dir,dir_prefix,\"expected.txt\")\n\n args = [in_barcodes, in_metrics, out_report]\n args = viral_ngs.illumina.parser_guess_barcodes(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n self.assertEqualContents(out_report, expected)\n\n def test_single_index_run(self):\n dir_prefix = \"single_index\"\n in_dir = viral_ngs.core.file.get_test_input_path(self)\n in_barcodes = os.path.join(in_dir,dir_prefix,\"barcodes.txt\")\n in_metrics = os.path.join(in_dir,dir_prefix,\"metrics.txt\")\n out_report = viral_ngs.core.file.mkstempfname('.txt')\n expected = os.path.join(in_dir,dir_prefix,\"expected.txt\")\n\n args = [in_barcodes, in_metrics, out_report]\n args = viral_ngs.illumina.parser_guess_barcodes(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n self.assertEqualContents(out_report, expected)\n\n def test_single_index_i5_only_run(self):\n dir_prefix = \"single_index_i5_only\"\n in_dir = viral_ngs.core.file.get_test_input_path(self)\n in_barcodes = os.path.join(in_dir,dir_prefix,\"barcodes.txt\")\n in_metrics = os.path.join(in_dir,dir_prefix,\"metrics.txt\")\n out_report = viral_ngs.core.file.mkstempfname('.txt')\n expected = os.path.join(in_dir,dir_prefix,\"expected.txt\")\n\n args = [in_barcodes, in_metrics, out_report]\n args = viral_ngs.illumina.parser_guess_barcodes(argparse.ArgumentParser()).parse_args(args)\n args.func_main(args)\n\n self.assertEqualContents(out_report, expected)\n\n def test_few_assigned(self):\n dir_prefix = \"few_assigned\"\n in_dir = viral_ngs.core.file.get_test_input_path(self)\n in_barcodes = os.path.join(in_dir,dir_prefix,\"barcodes.txt\")\n in_metrics = os.path.join(in_dir,dir_prefix,\"metrics.txt\")\n out_report = viral_ngs.core.file.mkstempfname('.txt')\n\n self.assertRaises(Exception, viral_ngs.illumina.main_guess_barcodes, in_barcodes, in_metrics, out_report)\n\nclass TestMiseqToBam(TestCaseWithTmp):\n\n def test_paired_1(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n outHeader = viral_ngs.core.file.mkstempfname('.txt')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-0-1_S5_L001_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-0-1_S5_L001_R2_001.fastq.gz'))\n viral_ngs.illumina.miseq_fastq_to_bam(outBam, sampleSheet, fastq[0], inFastq2=fastq[1], runInfo=runInfo)\n rgs = list(viral_ngs.core.samtools.SamtoolsTool().getReadGroups(outBam).values())\n self.assertEqual(len(rgs), 1)\n rgs = rgs[0]\n self.assertEqual(rgs.get('ID'), 'AEF96')\n self.assertEqual(rgs.get('PL'), 'illumina')\n self.assertEqual(rgs.get('PU'), 'AEF96.1.CGTACTAG-CTAAGCCT')\n self.assertEqual(rgs.get('LB'), 'mebv.0.1')\n self.assertEqual(rgs.get('SM'), 'mebv.0.1')\n self.assertEqual(rgs.get('CN'), 'M04004')\n self.assertTrue(rgs.get('DT','').startswith('2015-08-2'))\n\n def test_paired_2(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n outHeader = viral_ngs.core.file.mkstempfname('.txt')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-48-5_S17_L001_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_S17_L001_R2_001.fastq.gz'))\n viral_ngs.illumina.miseq_fastq_to_bam(outBam, sampleSheet, fastq[0], inFastq2=fastq[1], runInfo=runInfo)\n rgs = list(viral_ngs.core.samtools.SamtoolsTool().getReadGroups(outBam).values())\n self.assertEqual(len(rgs), 1)\n rgs = rgs[0]\n self.assertEqual(rgs.get('ID'), 'AEF96')\n self.assertEqual(rgs.get('PL'), 'illumina')\n self.assertEqual(rgs.get('PU'), 'AEF96.1.GGACTCCT-TATCCTCT')\n self.assertEqual(rgs.get('LB'), 'mebv.48.5')\n self.assertEqual(rgs.get('SM'), 'mebv.48.5')\n self.assertEqual(rgs.get('CN'), 'M04004')\n self.assertTrue(rgs.get('DT','').startswith('2015-08-2'))\n\n def test_paired_custom_seq_center(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n outHeader = viral_ngs.core.file.mkstempfname('.txt')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-48-5_S17_L001_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_S17_L001_R2_001.fastq.gz'))\n viral_ngs.illumina.miseq_fastq_to_bam(outBam, sampleSheet, fastq[0], inFastq2=fastq[1], runInfo=runInfo, sequencing_center='CustomSeqCenter')\n rgs = list(viral_ngs.core.samtools.SamtoolsTool().getReadGroups(outBam).values())\n self.assertEqual(len(rgs), 1)\n rgs = rgs[0]\n self.assertEqual(rgs.get('ID'), 'AEF96')\n self.assertEqual(rgs.get('PL'), 'illumina')\n self.assertEqual(rgs.get('PU'), 'AEF96.1.GGACTCCT-TATCCTCT')\n self.assertEqual(rgs.get('LB'), 'mebv.48.5')\n self.assertEqual(rgs.get('SM'), 'mebv.48.5')\n self.assertEqual(rgs.get('CN'), 'CustomSeqCenter')\n self.assertTrue(rgs.get('DT','').startswith('2015-08-2'))\n\n def test_fail_missing_pair(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-48-5_S17_L001_R1_001.fastq.gz'),)\n self.assertRaises(Exception, viral_ngs.illumina.miseq_fastq_to_bam, outBam, sampleSheet, fastq[0], runInfo=runInfo)\n\n def test_fail_backwards_pair(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-48-5_S17_L001_R2_001.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_S17_L001_R1_001.fastq.gz'))\n self.assertRaises(Exception, viral_ngs.illumina.miseq_fastq_to_bam, outBam, sampleSheet, fastq[0], fastq2=fastq[1], runInfo=runInfo)\n\n def test_fail_mismatched_pair(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-48-5_S16_L001_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_S17_L001_R2_001.fastq.gz'))\n self.assertRaises(Exception, viral_ngs.illumina.miseq_fastq_to_bam, outBam, sampleSheet, fastq[0], fastq2=fastq[1], runInfo=runInfo)\n\n def test_fail_oob_index(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-48-5_S33_L001_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_S33_L001_R2_001.fastq.gz'))\n self.assertRaises(Exception, viral_ngs.illumina.miseq_fastq_to_bam, outBam, sampleSheet, fastq[0], fastq2=fastq[1], runInfo=runInfo)\n\n def test_fail_bad_format(self):\n inDir = viral_ngs.core.file.get_test_input_path(self)\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n sampleSheet = os.path.join(inDir, 'SampleSheet.csv')\n runInfo = os.path.join(inDir, 'RunInfo.xml')\n fastq = (os.path.join(inDir, 'mebv-48-5_S17_L001_R1_002.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_S17_L001_R2_002.fastq.gz'))\n self.assertRaises(Exception, viral_ngs.illumina.miseq_fastq_to_bam, outBam, sampleSheet, fastq[0], fastq2=fastq[1], runInfo=runInfo)\n fastq = (os.path.join(inDir, 'mebv-48-5_S17_L002_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_S17_L002_R2_001.fastq.gz'))\n self.assertRaises(Exception, viral_ngs.illumina.miseq_fastq_to_bam, outBam, sampleSheet, fastq[0], fastq2=fastq[1], runInfo=runInfo)\n fastq = (os.path.join(inDir, 'mebv-48-5_17_L001_R1_001.fastq.gz'),\n os.path.join(inDir, 'mebv-48-5_17_L001_R2_001.fastq.gz'))\n self.assertRaises(Exception, viral_ngs.illumina.miseq_fastq_to_bam, outBam, sampleSheet, fastq[0], fastq2=fastq[1], runInfo=runInfo)\n\n\nclass TestSplitcodeDemuxIntegration(TestCaseWithTmp):\n \"\"\"\n End-to-end integration test for splitcode_demux command.\n\n Tests a typical workflow:\n - Input: BAM files from outer barcode demux (one per pool)\n - Sample sheet with inner barcodes (barcode_3)\n - RunInfo.xml with run metadata\n - Output: Per-sample BAM files after inner barcode demux\n \"\"\"\n\n def setUp(self):\n super().setUp()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.picard = viral_ngs.core.picard.FastqToSamTool()\n\n def create_test_bam_with_inline_barcodes(self, output_bam, barcode_reads):\n \"\"\"\n Create a test BAM file with reads containing inline barcodes.\n\n This simulates what Picard creates from a sequencer with read structure \"50T8B8B50T\":\n - R1: 50bp template (first 8bp are inline barcode, remaining 42bp are actual sequence)\n - R2: 50bp template\n - The index reads (8B8B) are not included in the BAM template sequences\n\n Args:\n output_bam: Path to output BAM file\n barcode_reads: Dict mapping barcode -> num_reads\n e.g., {\"AAAACCCC\": 10, \"GGGGTTTT\": 5}\n \"\"\"\n r1_fastq = viral_ngs.core.file.mkstempfname('.fastq')\n r2_fastq = viral_ngs.core.file.mkstempfname('.fastq')\n\n with open(r1_fastq, 'w') as f1, open(r2_fastq, 'w') as f2:\n read_id = 0\n for barcode, num_reads in barcode_reads.items():\n for _ in range(num_reads):\n # R1: 50bp total (8bp inline barcode + 42bp sequence)\n # Picard treats all 50bp as template, doesn't know about the inline barcode\n seq_r1 = barcode + (\"ACGT\" * 10) + \"AC\" # 8bp + 40bp + 2bp = 50bp\n qual_r1 = \"I\" * len(seq_r1)\n\n # R2: 50bp template\n seq_r2 = \"TGCA\" * 12 + \"TG\" # 50bp\n qual_r2 = \"I\" * len(seq_r2)\n\n f1.write(f\"@read{read_id}\\n{seq_r1}\\n+\\n{qual_r1}\\n\")\n f2.write(f\"@read{read_id}\\n{seq_r2}\\n+\\n{qual_r2}\\n\")\n read_id += 1\n\n # Convert to BAM\n self.picard.execute(\n r1_fastq,\n r2_fastq,\n \"PoolSample\",\n output_bam,\n picardOptions=['LIBRARY_NAME=TestPool', 'PLATFORM=ILLUMINA']\n )\n\n os.unlink(r1_fastq)\n os.unlink(r2_fastq)\n\n return output_bam\n\n def create_expected_output_bam(self, output_bam, sample_name, barcode, num_reads, sample_idx=0, starting_read_id=0):\n \"\"\"\n Create an expected output BAM file with reads after splitcode demux.\n\n After demuxing with splitcode using read structure \"50T8B8B50T\":\n - R1: Original 50bp read (barcode trimmed off)\n - R2: Original 50bp read (unchanged)\n\n Args:\n output_bam: Path to output BAM file\n sample_name: Sample name for read group\n barcode: The inline barcode (for verification, not included in output)\n num_reads: Number of reads to create\n sample_idx: Sample index (0-based) for read group name generation\n starting_read_id: Starting read ID number (for sequential read numbering)\n \"\"\"\n r1_fastq = viral_ngs.core.file.mkstempfname('.fastq')\n r2_fastq = viral_ngs.core.file.mkstempfname('.fastq')\n\n with open(r1_fastq, 'w') as f1, open(r2_fastq, 'w') as f2:\n for i in range(num_reads):\n read_id = starting_read_id + i\n # After splitcode demux:\n # R1: The barcode is trimmed, leaving only the 42bp sequence after barcode\n # (splitcode trims the 8bp inline barcode from the start of the 50bp R1)\n seq_r1 = (\"ACGT\" * 10) + \"AC\" # 42bp (barcode already removed)\n qual_r1 = \"I\" * len(seq_r1)\n\n # R2: Unchanged 50bp\n seq_r2 = \"TGCA\" * 12 + \"TG\" # 50bp\n qual_r2 = \"I\" * len(seq_r2)\n\n f1.write(f\"@read{read_id}\\n{seq_r1}\\n+\\n{qual_r1}\\n\")\n f2.write(f\"@read{read_id}\\n{seq_r2}\\n+\\n{qual_r2}\\n\")\n\n # Convert to BAM with same read group structure as splitcode_demux output\n # Read group name format: {sequencing_center}.{lane}.{sample_idx+1}\n read_group_name = f\"TEST.1.{sample_idx + 1}\"\n self.picard.execute(\n r1_fastq,\n r2_fastq,\n sample_name,\n output_bam,\n picardOptions=[\n f'LIBRARY_NAME=L1',\n 'PLATFORM=ILLUMINA',\n 'SEQUENCING_CENTER=TEST',\n f'RUN_DATE=2025-01-01',\n f'READ_GROUP_NAME={read_group_name}',\n ]\n )\n\n os.unlink(r1_fastq)\n os.unlink(r2_fastq)\n\n return output_bam\n\n def test_splitcode_demux_basic(self):\n \"\"\"\n Test splitcode_demux command with minimal realistic input.\n\n Simulates a pool with 2 samples distinguished by inner barcodes.\n Verifies that:\n - Command runs without error\n - Output BAM files are created for each sample\n - Output BAMs contain expected number of reads\n - Output BAM content matches expected (reads correctly demuxed and trimmed)\n \"\"\"\n # Get test input directory\n inDir = viral_ngs.core.file.get_test_input_path(self)\n\n # Define expected read counts per sample\n sample1_reads = 100\n sample2_reads = 50\n\n # Create temporary directories\n with tempfile.TemporaryDirectory() as input_bams_dir:\n with tempfile.TemporaryDirectory() as outDir:\n with tempfile.TemporaryDirectory() as expectedDir:\n # Create a pool BAM file with reads from 2 barcodes\n # Pool identifier from sample sheet: ATCGATCG-GCTAGCTA.lL1.TESTFLOW.1\n pool_bam = os.path.join(input_bams_dir, 'ATCGATCG-GCTAGCTA.lL1.TESTFLOW.1.bam')\n self.create_test_bam_with_inline_barcodes(\n pool_bam,\n {\n \"AAAAAAAA\": sample1_reads, # TestSample1 barcode\n \"CCCCCCCC\": sample2_reads, # TestSample2 barcode\n }\n )\n\n # Create expected output BAM files\n expected_sample1_bam = os.path.join(expectedDir, 'TestSample1.lL1.TESTFLOW.1.bam')\n expected_sample2_bam = os.path.join(expectedDir, 'TestSample2.lL1.TESTFLOW.1.bam')\n\n self.create_expected_output_bam(\n expected_sample1_bam,\n \"TestSample1\",\n \"AAAAAAAA\",\n sample1_reads,\n sample_idx=0, # First sample in samplesheet\n starting_read_id=0 # Reads 0-99\n )\n self.create_expected_output_bam(\n expected_sample2_bam,\n \"TestSample2\",\n \"CCCCCCCC\",\n sample2_reads,\n sample_idx=1, # Second sample in samplesheet\n starting_read_id=sample1_reads # Reads 100-149\n )\n\n # Run splitcode_demux\n out_meta_by_sample = os.path.join(outDir, 'test_meta_by_sample.txt')\n viral_ngs.illumina.splitcode_demux(\n inDir=input_bams_dir,\n lane=\"1\",\n outDir=outDir,\n sampleSheet=os.path.join(inDir, 'SampleSheet.tsv'),\n runinfo=os.path.join(inDir, 'RunInfo.xml'),\n flowcell=\"TESTFLOW\",\n run_id=\"TESTFLOW.1\",\n run_date=\"2025-01-01\",\n read_structure=\"50T8B8B50T\",\n platform_name=\"ILLUMINA\",\n sequencing_center=\"TEST\",\n unmatched_name=\"Unmatched\",\n max_hamming_dist=1,\n threads=1,\n out_meta_by_sample=out_meta_by_sample\n )\n\n # Verify output files exist and have correct read counts\n actual_sample1_bam = os.path.join(outDir, 'TestSample1.lL1.TESTFLOW.1.bam')\n actual_sample2_bam = os.path.join(outDir, 'TestSample2.lL1.TESTFLOW.1.bam')\n\n # Verify files exist\n self.assertTrue(\n os.path.exists(actual_sample1_bam),\n f\"Expected output BAM not found: {actual_sample1_bam}\"\n )\n self.assertTrue(\n os.path.exists(actual_sample2_bam),\n f\"Expected output BAM not found: {actual_sample2_bam}\"\n )\n\n # Verify read counts match expected\n actual_sample1_count = self.samtools.count(actual_sample1_bam)\n actual_sample2_count = self.samtools.count(actual_sample2_bam)\n expected_sample1_count = self.samtools.count(expected_sample1_bam)\n expected_sample2_count = self.samtools.count(expected_sample2_bam)\n\n self.assertEqual(\n actual_sample1_count,\n expected_sample1_count,\n f\"TestSample1 read count mismatch: got {actual_sample1_count}, expected {expected_sample1_count}\"\n )\n self.assertEqual(\n actual_sample2_count,\n expected_sample2_count,\n f\"TestSample2 read count mismatch: got {actual_sample2_count}, expected {expected_sample2_count}\"\n )\n\n # Verify BAM content matches expected\n assert_equal_bam_reads(self, actual_sample1_bam, expected_sample1_bam)\n assert_equal_bam_reads(self, actual_sample2_bam, expected_sample2_bam)\n\n\nclass TestParseIlluminaFastqFilename(unittest.TestCase):\n \"\"\"Test parsing of Illumina DRAGEN FASTQ filename patterns.\n\n DRAGEN format: {flowcell}_{lane}_{numeric_id}_{sample_name}_{S#}_{L00#}_{R#}_{chunk}.fastq.gz\n Example: 22J5GLLT4_6_0420593812_B13Pool1a_S1_L006_R1_001.fastq.gz\n \"\"\"\n\n def test_standard_dragen_format_r1(self):\n \"\"\"Test standard DRAGEN FASTQ naming with flowcell ID.\"\"\"\n filename = \"22J5GLLT4_6_0420593812_B13Pool1a_S1_L006_R1_001.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n\n self.assertEqual(result['flowcell'], '22J5GLLT4')\n self.assertEqual(result['lane_short'], 6)\n self.assertEqual(result['numeric_id'], '0420593812')\n self.assertEqual(result['sample_name'], 'B13Pool1a')\n self.assertEqual(result['sample_number'], 1)\n self.assertEqual(result['lane'], 6)\n self.assertEqual(result['read'], 1)\n self.assertEqual(result['chunk'], 1)\n\n def test_standard_dragen_format_r2(self):\n \"\"\"Test standard DRAGEN format for R2 file.\"\"\"\n filename = \"22J5GLLT4_6_0420593812_B13Pool1a_S1_L006_R2_001.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n\n self.assertEqual(result['flowcell'], '22J5GLLT4')\n self.assertEqual(result['sample_name'], 'B13Pool1a')\n self.assertEqual(result['read'], 2)\n\n def test_sample_name_with_underscores(self):\n \"\"\"Test sample names containing underscores.\"\"\"\n filename = \"22J5GLLT4_6_0420593812_RS_Batch_20_NTC_01_S5_L006_R1_001.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n\n self.assertEqual(result['flowcell'], '22J5GLLT4')\n self.assertEqual(result['lane_short'], 6)\n self.assertEqual(result['numeric_id'], '0420593812')\n self.assertEqual(result['sample_name'], 'RS_Batch_20_NTC_01')\n self.assertEqual(result['sample_number'], 5)\n self.assertEqual(result['lane'], 6)\n self.assertEqual(result['read'], 1)\n\n def test_different_flowcells(self):\n \"\"\"Test parsing files from different flowcell IDs.\"\"\"\n test_cases = [\n \"ABCDEFGH1_1_1234567890_Sample1_S1_L001_R1_001.fastq.gz\",\n \"22J5GLLT4_1_1234567890_Sample1_S1_L001_R1_001.fastq.gz\",\n \"H7YVLDSXY_1_1234567890_Sample1_S1_L001_R1_001.fastq.gz\",\n ]\n expected_flowcells = ['ABCDEFGH1', '22J5GLLT4', 'H7YVLDSXY']\n\n for filename, expected_fc in zip(test_cases, expected_flowcells):\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n self.assertEqual(result['flowcell'], expected_fc)\n\n def test_different_lane_numbers(self):\n \"\"\"Test parsing files from different lanes.\"\"\"\n for lane in [1, 2, 3, 4, 5, 6, 7, 8]:\n filename = f\"22J5GLLT4_{lane}_0420593812_Sample1_S1_L00{lane}_R1_001.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n self.assertEqual(result['lane'], lane)\n self.assertEqual(result['lane_short'], lane)\n\n def test_different_sample_numbers(self):\n \"\"\"Test parsing files with various sample numbers.\"\"\"\n test_cases = [\n (\"22J5GLLT4_6_0420593812_Sample1_S1_L006_R1_001.fastq.gz\", 1),\n (\"22J5GLLT4_6_0420593812_Sample1_S10_L006_R1_001.fastq.gz\", 10),\n (\"22J5GLLT4_6_0420593812_Sample1_S100_L006_R1_001.fastq.gz\", 100),\n ]\n for filename, expected_num in test_cases:\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n self.assertEqual(result['sample_number'], expected_num)\n\n def test_different_chunk_numbers(self):\n \"\"\"Test parsing files with different chunk numbers.\"\"\"\n filename = \"22J5GLLT4_6_0420593812_Sample1_S1_L006_R1_002.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n self.assertEqual(result['chunk'], 2)\n\n filename = \"22J5GLLT4_6_0420593812_Sample1_S1_L006_R1_003.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n self.assertEqual(result['chunk'], 3)\n\n def test_with_full_path(self):\n \"\"\"Test parsing filename with full directory path.\"\"\"\n filename = \"/path/to/data/22J5GLLT4_6_0420593812_Sample1_S1_L006_R1_001.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n\n self.assertEqual(result['flowcell'], '22J5GLLT4')\n self.assertEqual(result['sample_name'], 'Sample1')\n self.assertEqual(result['lane'], 6)\n\n def test_without_gz_extension(self):\n \"\"\"Test parsing filename without .gz extension.\"\"\"\n filename = \"22J5GLLT4_6_0420593812_Sample1_S1_L006_R1_001.fastq\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n\n self.assertEqual(result['flowcell'], '22J5GLLT4')\n self.assertEqual(result['sample_name'], 'Sample1')\n\n def test_simple_format_without_flowcell(self):\n \"\"\"Test simple Illumina format without flowcell ID (backward compatibility).\n\n Format: {sample_name}_{S#}_{L00#}_{R#}_{chunk}.fastq.gz\n Example: mebv-48-5_S17_L001_R1_001.fastq.gz\n \"\"\"\n filename = \"mebv-48-5_S17_L001_R1_001.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n\n self.assertEqual(result['sample_name'], 'mebv-48-5')\n self.assertEqual(result['sample_number'], 17)\n self.assertEqual(result['lane'], 1)\n self.assertEqual(result['read'], 1)\n self.assertEqual(result['chunk'], 1)\n self.assertIsNone(result.get('flowcell'))\n\n def test_simple_format_r2(self):\n \"\"\"Test simple format for R2 file.\"\"\"\n filename = \"Sample1_S5_L001_R2_001.fastq.gz\"\n result = viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n\n self.assertEqual(result['sample_name'], 'Sample1')\n self.assertEqual(result['sample_number'], 5)\n self.assertEqual(result['lane'], 1)\n self.assertEqual(result['read'], 2)\n\n def test_malformed_invalid_format(self):\n \"\"\"Test error handling for completely invalid filename.\"\"\"\n filename = \"random_file.fastq.gz\"\n with self.assertRaises(ValueError) as context:\n viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n self.assertIn(\"does not match\", str(context.exception).lower())\n\n def test_empty_filename(self):\n \"\"\"Test error handling for empty filename.\"\"\"\n with self.assertRaises(ValueError):\n viral_ngs.illumina.parse_illumina_fastq_filename(\"\")\n\n def test_malformed_missing_read_number(self):\n \"\"\"Test error handling for filename missing read number.\"\"\"\n filename = \"22J5GLLT4_6_0420593812_Sample1_S1_L006_001.fastq.gz\"\n with self.assertRaises(ValueError) as context:\n viral_ngs.illumina.parse_illumina_fastq_filename(filename)\n self.assertIn(\"does not match\", str(context.exception).lower())\n\n def test_index_reads_not_supported(self):\n \"\"\"Test that index reads (I1, I2) are handled appropriately.\n\n Note: DRAGEN may not produce I1/I2 files in the same way as bcl2fastq.\n This test documents expected behavior if encountered.\n \"\"\"\n # If DRAGEN produces index files, they might follow a different pattern\n # For now, test that we handle them gracefully or raise appropriate errors\n pass\n\n\nclass TestNormalizeBarcode(unittest.TestCase):\n \"\"\"Test barcode normalization function.\"\"\"\n\n def test_uppercase_conversion(self):\n \"\"\"Test that lowercase barcodes are converted to uppercase.\"\"\"\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"acgt\"), \"ACGT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"atcgatcg\"), \"ATCGATCG\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"aCgT\"), \"ACGT\")\n\n def test_whitespace_trimming(self):\n \"\"\"Test that leading and trailing whitespace is removed.\"\"\"\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\" ACGT \"), \"ACGT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"\\tACGT\\n\"), \"ACGT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\" ATCGATCG \"), \"ATCGATCG\")\n\n def test_combined_normalization(self):\n \"\"\"Test combined uppercase conversion and whitespace trimming.\"\"\"\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\" acgt \"), \"ACGT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"\\tatcg\\n\"), \"ATCG\")\n\n def test_already_normalized(self):\n \"\"\"Test that already-normalized barcodes pass through unchanged.\"\"\"\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"ACGT\"), \"ACGT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"ATCGATCG\"), \"ATCGATCG\")\n\n def test_empty_string(self):\n \"\"\"Test handling of empty strings.\"\"\"\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"\"), \"\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\" \"), \"\")\n\n def test_valid_characters_only(self):\n \"\"\"Test validation that only ACGTN characters are allowed.\"\"\"\n # Valid barcodes\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"ACGT\"), \"ACGT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"AAACCCGGGTTT\"), \"AAACCCGGGTTT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"ACGTN\"), \"ACGTN\") # N for ambiguous base\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"NNNACGT\"), \"NNNACGT\")\n\n def test_invalid_characters(self):\n \"\"\"Test that invalid characters raise ValueError.\"\"\"\n with self.assertRaises(ValueError) as context:\n viral_ngs.illumina.normalize_barcode(\"ACGTX\")\n self.assertIn(\"invalid\", str(context.exception).lower())\n\n with self.assertRaises(ValueError):\n viral_ngs.illumina.normalize_barcode(\"ACG-TGC\")\n\n with self.assertRaises(ValueError):\n viral_ngs.illumina.normalize_barcode(\"ACG TGC\") # space in middle\n\n with self.assertRaises(ValueError):\n viral_ngs.illumina.normalize_barcode(\"123\")\n\n def test_mixed_case_with_n(self):\n \"\"\"Test mixed case barcodes containing N.\"\"\"\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"acgtn\"), \"ACGTN\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"NNNacgt\"), \"NNNACGT\")\n\n def test_typical_illumina_barcodes(self):\n \"\"\"Test with real Illumina barcode sequences.\"\"\"\n # Typical 8bp dual index barcodes\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"CTGATCGT\"), \"CTGATCGT\")\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"ctgatcgt\"), \"CTGATCGT\")\n\n # Typical 10bp barcode\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\"AACCGGTTAA\"), \"AACCGGTTAA\")\n\n # With whitespace (common in CSV files)\n self.assertEqual(viral_ngs.illumina.normalize_barcode(\" CTGATCGT \"), \"CTGATCGT\")\n\n def test_none_input(self):\n \"\"\"Test handling of None input.\"\"\"\n with self.assertRaises((ValueError, TypeError)):\n viral_ngs.illumina.normalize_barcode(None)\n\n def test_non_string_input(self):\n \"\"\"Test handling of non-string input.\"\"\"\n with self.assertRaises((ValueError, TypeError)):\n viral_ngs.illumina.normalize_barcode(12345)\n\n with self.assertRaises((ValueError, TypeError)):\n viral_ngs.illumina.normalize_barcode(['A', 'C', 'G', 'T'])\n\n\nclass TestBarcodeOrientationAutoDetection(unittest.TestCase):\n \"\"\"\n Test suite for automatic i5 (barcode_2) orientation detection.\n\n Tests the match_barcodes_with_orientation() function which automatically\n tries reverse complement of barcode_2 when direct matching fails.\n\n Note: Only barcode_2 (i5) orientation is auto-detected because this is the\n only barcode that varies in orientation across Illumina sequencer generations.\n barcode_1 (i7) is consistent across all platforms.\n \"\"\"\n\n def test_direct_match(self):\n \"\"\"Test that direct barcode match works without reverse complement.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n {'sample': 'S2', 'barcode_1': 'AAAAAAAA', 'barcode_2': 'TTTTTTTT'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'S1')\n self.assertFalse(info['barcode_2_revcomp'])\n\n def test_barcode2_revcomp_match(self):\n \"\"\"Test that reverse complement of barcode_2/i5 is auto-detected.\"\"\"\n # Samplesheet has ACTGCAGCCG, FASTQ has reverse complement CGGCTGCAGT\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'AGTTAATGCT', 'barcode_2': 'ACTGCAGCCG'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'AGTTAATGCT', 'CGGCTGCAGT', sample_rows # CGGCTGCAGT = revcomp(ACTGCAGCCG)\n )\n self.assertEqual(len(matched), 1)\n self.assertTrue(info['barcode_2_revcomp'])\n self.assertEqual(info['matched_bc2'], 'ACTGCAGCCG')\n\n def test_no_match_returns_empty(self):\n \"\"\"Test that no match returns empty list with skipped_reason='no_match'.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # Use completely different barcodes that won't match\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'GGGGGGGG', 'CCCCCCCC', sample_rows\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'no_match')\n\n def test_single_barcode_matching(self):\n \"\"\"Test matching with only barcode_1 (barcode_2 is None).\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': ''},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', None, sample_rows\n )\n self.assertEqual(len(matched), 1)\n\n def test_case_insensitive_matching(self):\n \"\"\"Test that barcode matching is case-insensitive.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'atcgatcg', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'gctagcta', sample_rows\n )\n self.assertEqual(len(matched), 1)\n\n def test_multiple_samples_same_outer_barcodes(self):\n \"\"\"Test matching returns all samples with same outer barcodes (3-barcode case).\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA', 'barcode_3': 'AAAAAAAA'},\n {'sample': 'S2', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA', 'barcode_3': 'CCCCCCCC'},\n {'sample': 'S3', 'barcode_1': 'GGGGGGGG', 'barcode_2': 'TTTTTTTT', 'barcode_3': 'AAAAAAAA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 2)\n self.assertEqual({r['sample'] for r in matched}, {'S1', 'S2'})\n\n def test_barcode2_revcomp_with_multiple_samples(self):\n \"\"\"Test i5 auto-detection works when multiple samples share outer barcodes.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA', 'barcode_3': 'AAAAAAAA'},\n {'sample': 'S2', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA', 'barcode_3': 'CCCCCCCC'},\n ]\n # TAGCTAGC = revcomp(GCTAGCTA)\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'TAGCTAGC', sample_rows\n )\n self.assertEqual(len(matched), 2)\n self.assertTrue(info['barcode_2_revcomp'])\n\n def test_n_wildcard_in_fastq_barcode(self):\n \"\"\"Test that N bases in FASTQ barcodes match any base in samplesheet.\n\n This handles sequencer no-call bases where a position couldn't be\n confidently determined. The N should act as a wildcard.\n \"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # FASTQ has N at position 3, samplesheet has G\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCNATCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'S1')\n self.assertFalse(info['barcode_2_revcomp'])\n\n def test_n_wildcard_in_barcode2(self):\n \"\"\"Test N wildcard matching in barcode_2.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # FASTQ has N at position 2 of barcode_2\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCNAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'S1')\n\n def test_n_wildcard_with_revcomp(self):\n \"\"\"Test N wildcard matching combined with i5 reverse complement detection.\n\n This is the real-world case: FASTQ barcode_2 has N bases AND needs\n reverse complement to match samplesheet.\n \"\"\"\n # Samplesheet has TTCCGACATT, revcomp is AATGTCGGAA\n sample_rows = [\n {'sample': 'VGG_21775', 'barcode_1': 'TAAGGAGGAA', 'barcode_2': 'TTCCGACATT'},\n ]\n # FASTQ has AANGTCGGAA (N at position 2, should match T in revcomp AATGTCGGAA)\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'TAAGGAGGAA', 'AANGTCGGAA', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'VGG_21775')\n self.assertTrue(info['barcode_2_revcomp'])\n\n def test_multiple_n_wildcards(self):\n \"\"\"Test multiple N bases in a barcode (up to 50% N allowed).\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # FASTQ has N at positions 0 and 4 (2/8 = 25% N, under threshold)\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'NTCGNTCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 1)\n\n def test_high_n_fraction_returns_empty(self):\n \"\"\"Test that barcodes with >50% N bases return empty (too low confidence).\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # FASTQ with >50% N bases should return empty, not raise error\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'NNNNNNNN', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'high_n_fraction')\n\n def test_high_n_fraction_in_bc2_returns_empty(self):\n \"\"\"Test that barcode_2 with >50% N bases also returns empty.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # bc2 has >50% N\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'NNNNNNCTA', sample_rows\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'high_n_fraction')\n\n def test_exactly_50_percent_n_allowed(self):\n \"\"\"Test that exactly 50% N bases is allowed (boundary case).\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # 4/8 = exactly 50% N is allowed (threshold is >50%)\n # NNNNATCG matches ATCGATCG at positions 4-7\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'NNNNATCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertNotIn('skipped_reason', info)\n\n # 5/8 = 62.5% > 50%, should be rejected\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'NNNNNTCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'high_n_fraction')\n\n def test_ambiguous_n_match_returns_empty(self):\n \"\"\"Test that N-wildcard matching multiple distinct barcode pairs returns empty.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n {'sample': 'S2', 'barcode_1': 'GTCGATCG', 'barcode_2': 'GCTAGCTA'}, # differs only in first base\n ]\n # FASTQ with N at position 0 matches both S1 (A) and S2 (G) - ambiguous!\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'NTCGATCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'ambiguous')\n\n def test_n_in_samplesheet_does_not_match_with_strict(self):\n \"\"\"Test that N in samplesheet barcode does NOT act as wildcard with max_mismatches=0.\n\n Only N in the FASTQ (observed) barcode should be a wildcard.\n N in samplesheet is treated as a concrete base; with strict matching (max_mismatches=0),\n G vs N is a mismatch and should not match.\n \"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCNATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # FASTQ has G where samplesheet has N - with strict matching, should not match\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCTAGCTA', sample_rows, max_mismatches=0\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'no_match')\n\n def test_n_in_samplesheet_matches_with_fuzzy(self):\n \"\"\"N in samplesheet vs non-N in FASTQ is treated as a regular mismatch.\n\n With max_mismatches=1, this 1-base difference is tolerated.\n \"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCNATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCTAGCTA', sample_rows, max_mismatches=1\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'S1')\n\n def test_n_wildcard_no_false_positives(self):\n \"\"\"Test that N wildcard doesn't cause incorrect matches.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'AAAAAAAA', 'barcode_2': 'TTTTTTTT'},\n {'sample': 'S2', 'barcode_1': 'CCCCCCCC', 'barcode_2': 'GGGGGGGG'},\n ]\n # FASTQ with 2 N bases (25%) should still only match one sample\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ANAAANNA', 'TTTTTTTT', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'S1')\n\n\nclass TestBarcodeFuzzyMatching(unittest.TestCase):\n \"\"\"Test suite for barcode_matches_fuzzy() function.\"\"\"\n\n def test_exact_match_zero_mismatches(self):\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCGATCG', 'ATCGATCG', 1)\n self.assertTrue(ok)\n self.assertEqual(mm, 0)\n\n def test_one_mismatch_allowed(self):\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCGATCG', 'ATCAATCG', 1)\n self.assertTrue(ok)\n self.assertEqual(mm, 1)\n\n def test_two_mismatches_rejected_at_threshold_1(self):\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCGATCG', 'ATAAATCG', 1)\n self.assertFalse(ok)\n self.assertEqual(mm, 2)\n\n def test_two_mismatches_allowed_at_threshold_2(self):\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCGATCG', 'ATAAATCG', 2)\n self.assertTrue(ok)\n self.assertEqual(mm, 2)\n\n def test_n_not_counted_as_mismatch(self):\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCNATCG', 'ATCGATCG', 0)\n self.assertTrue(ok)\n self.assertEqual(mm, 0)\n\n def test_n_plus_real_mismatch(self):\n # N at pos 3 (wildcard), real mismatch at pos 0 (A->G)\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCNATCG', 'GTCGATCG', 1)\n self.assertTrue(ok)\n self.assertEqual(mm, 1)\n\n def test_length_mismatch(self):\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCGATCG', 'ATCGATC', 1)\n self.assertFalse(ok)\n\n def test_zero_max_mismatches_is_strict(self):\n # With max_mismatches=0, a single non-N mismatch should fail\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCGATCG', 'ATCAATCG', 0)\n self.assertFalse(ok)\n self.assertEqual(mm, 1)\n\n # But N should still be a wildcard\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('ATCNATCG', 'ATCGATCG', 0)\n self.assertTrue(ok)\n self.assertEqual(mm, 0)\n\n def test_all_n_matches_anything(self):\n ok, mm = viral_ngs.illumina.barcode_matches_fuzzy('NNNNNNNN', 'ATCGATCG', 0)\n self.assertTrue(ok)\n self.assertEqual(mm, 0)\n\n\nclass TestFuzzyMatchInOrientation(unittest.TestCase):\n \"\"\"Test fuzzy matching integration in match_barcodes_with_orientation().\"\"\"\n\n def test_fuzzy_match_one_mismatch_bc1(self):\n \"\"\"1 mismatch in bc1 should match with max_mismatches=1.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCAATCG', 'GCTAGCTA', sample_rows, max_mismatches=1\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'S1')\n\n def test_fuzzy_match_one_mismatch_bc2(self):\n \"\"\"1 mismatch in bc2 should match with max_mismatches=1.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCTAGCGA', sample_rows, max_mismatches=1\n )\n self.assertEqual(len(matched), 1)\n\n def test_fuzzy_match_rejected_at_zero_tolerance(self):\n \"\"\"1 mismatch should fail with max_mismatches=0.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCAATCG', 'GCTAGCTA', sample_rows, max_mismatches=0\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'no_match')\n\n def test_fuzzy_prefers_exact_over_fuzzy(self):\n \"\"\"When one row is exact and another is 1-mismatch away, prefer exact.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n {'sample': 'S2', 'barcode_1': 'ATCAATCG', 'barcode_2': 'GCTAGCTA'}, # 1 mismatch from ATCGATCG\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCTAGCTA', sample_rows, max_mismatches=1\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(matched[0]['sample'], 'S1')\n\n def test_fuzzy_ambiguous_same_distance(self):\n \"\"\"Two rows at same mismatch distance should be flagged ambiguous.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n {'sample': 'S2', 'barcode_1': 'GTCGATCG', 'barcode_2': 'GCTAGCTA'}, # also 1 mismatch from CTCGATCG\n ]\n # CTCGATCG is 1 mismatch from both ATCGATCG (A->C) and GTCGATCG (G->C)\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'CTCGATCG', 'GCTAGCTA', sample_rows, max_mismatches=1\n )\n self.assertEqual(len(matched), 0)\n self.assertEqual(info.get('skipped_reason'), 'ambiguous')\n\n def test_fuzzy_match_with_revcomp(self):\n \"\"\"Fuzzy matching should work combined with i5 reverse complement.\"\"\"\n # Samplesheet has GCTAGCTA, revcomp is TAGCTAGC\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # FASTQ bc1 has 1 mismatch, bc2 needs revcomp\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCAATCG', 'TAGCTAGC', sample_rows, max_mismatches=1\n )\n self.assertEqual(len(matched), 1)\n self.assertTrue(info['barcode_2_revcomp'])\n\n\nclass TestSamplesheetAuthoritativeBarcodes(unittest.TestCase):\n \"\"\"Test that orientation_info returns samplesheet barcode values, not FASTQ-observed.\"\"\"\n\n def test_matched_bc_contains_samplesheet_values(self):\n \"\"\"matched_bc1/bc2 should be samplesheet values, not FASTQ-observed.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(info['matched_bc1'], 'ATCGATCG')\n self.assertEqual(info['matched_bc2'], 'GCTAGCTA')\n\n def test_matched_bc_with_n_contains_samplesheet_values(self):\n \"\"\"When FASTQ has N, matched values should be samplesheet truth (no N).\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCNATCG', 'GCTAGCTA', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(info['matched_bc1'], 'ATCGATCG') # samplesheet, not ATCNATCG\n self.assertEqual(info['matched_bc2'], 'GCTAGCTA')\n\n def test_matched_bc_with_mismatch_contains_samplesheet_values(self):\n \"\"\"When FASTQ has a mismatch, matched values should be samplesheet truth.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCAATCG', 'GCTAGCTA', sample_rows, max_mismatches=1\n )\n self.assertEqual(len(matched), 1)\n self.assertEqual(info['matched_bc1'], 'ATCGATCG') # samplesheet, not ATCAATCG\n self.assertEqual(info['matched_bc2'], 'GCTAGCTA')\n\n def test_matched_bc_with_revcomp_contains_samplesheet_values(self):\n \"\"\"When revcomp is used, matched_bc2 should be samplesheet value.\"\"\"\n sample_rows = [\n {'sample': 'S1', 'barcode_1': 'ATCGATCG', 'barcode_2': 'GCTAGCTA'},\n ]\n # TAGCTAGC = revcomp(GCTAGCTA)\n matched, info = viral_ngs.illumina.match_barcodes_with_orientation(\n 'ATCGATCG', 'TAGCTAGC', sample_rows\n )\n self.assertEqual(len(matched), 1)\n self.assertTrue(info['barcode_2_revcomp'])\n self.assertEqual(info['matched_bc1'], 'ATCGATCG')\n self.assertEqual(info['matched_bc2'], 'GCTAGCTA') # samplesheet, not TAGCTAGC\n\n\nclass TestConsensusBarcodeFromFastq(unittest.TestCase):\n \"\"\"Test consensus_barcode_from_fastq() function.\"\"\"\n\n def setUp(self):\n self.tmpdir = tempfile.mkdtemp()\n\n def tearDown(self):\n shutil.rmtree(self.tmpdir, ignore_errors=True)\n\n def _write_fastq(self, path, reads):\n \"\"\"Write a gzipped FASTQ file with given read headers.\n\n Args:\n path: Output file path\n reads: List of (header, seq) tuples. Quality will be auto-generated.\n \"\"\"\n with gzip.open(path, 'wt') as f:\n for header, seq in reads:\n f.write(f\"{header}\\n\")\n f.write(f\"{seq}\\n\")\n f.write(\"+\\n\")\n f.write(\"I\" * len(seq) + \"\\n\")\n\n def test_identical_reads(self):\n \"\"\"10 reads all with same barcode → that barcode.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = [\n (f\"@INST:1:FC:1:1:1:{i} 1:N:0:ATCGATCG+GCTAGCTA\", \"ACGTACGT\")\n for i in range(10)\n ]\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n self.assertEqual(bc1, 'ATCGATCG')\n self.assertEqual(bc2, 'GCTAGCTA')\n\n def test_consensus_resolves_single_n(self):\n \"\"\"9 reads with 'G' at pos 3, 1 read with 'N' → consensus has 'G'.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = []\n for i in range(9):\n reads.append((f\"@INST:1:FC:1:1:1:{i} 1:N:0:ATCGATCG+GCTAGCTA\", \"ACGTACGT\"))\n reads.append((\"@INST:1:FC:1:1:1:9 1:N:0:ATCNATCG+GCTAGCTA\", \"ACGTACGT\"))\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n self.assertEqual(bc1, 'ATCGATCG') # G wins over N\n\n def test_consensus_majority_vote(self):\n \"\"\"7 reads with 'A', 3 reads with 'G' at pos 0 → consensus has 'A'.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = []\n for i in range(7):\n reads.append((f\"@INST:1:FC:1:1:1:{i} 1:N:0:ATCGATCG+GCTAGCTA\", \"ACGTACGT\"))\n for i in range(3):\n reads.append((f\"@INST:1:FC:1:1:1:{7+i} 1:N:0:GTCGATCG+GCTAGCTA\", \"ACGTACGT\"))\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n self.assertEqual(bc1, 'ATCGATCG') # A wins over G (7 vs 3)\n\n def test_consensus_all_n_stays_n(self):\n \"\"\"All reads have N at a position → consensus has N.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = [\n (f\"@INST:1:FC:1:1:1:{i} 1:N:0:ATCNATCG+GCTAGCTA\", \"ACGTACGT\")\n for i in range(10)\n ]\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n self.assertEqual(bc1, 'ATCNATCG') # all N → stays N\n\n def test_empty_fastq_returns_none(self):\n \"\"\"Empty FASTQ → (None, None).\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n with gzip.open(fq, 'wt') as f:\n pass # empty file\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n self.assertIsNone(bc1)\n self.assertIsNone(bc2)\n\n def test_single_barcode_no_plus(self):\n \"\"\"Single-index barcodes (no +) → bc2 is None.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = [\n (f\"@INST:1:FC:1:1:1:{i} 1:N:0:ATCGATCG\", \"ACGTACGT\")\n for i in range(5)\n ]\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=5)\n self.assertEqual(bc1, 'ATCGATCG')\n self.assertIsNone(bc2)\n\n def test_single_read(self):\n \"\"\"With num_reads=1, same as reading just the first read.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = [\n (\"@INST:1:FC:1:1:1:0 1:N:0:ATCGATCG+GCTAGCTA\", \"ACGTACGT\"),\n (\"@INST:1:FC:1:1:1:1 1:N:0:GTCGATCG+GCTAGCTA\", \"ACGTACGT\"),\n ]\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=1)\n self.assertEqual(bc1, 'ATCGATCG') # only first read\n\n def test_consensus_resolves_mismatch(self):\n \"\"\"Real-world scenario: 1 read has mismatched barcode, 9 have correct.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = []\n # First read has T->C mismatch (the bug scenario)\n reads.append((\"@INST:1:FC:1:1:1:0 1:N:0:ACCGATCG+GCTAGCTA\", \"ACGTACGT\"))\n # Remaining 9 reads have correct barcode\n for i in range(1, 10):\n reads.append((f\"@INST:1:FC:1:1:1:{i} 1:N:0:ATCGATCG+GCTAGCTA\", \"ACGTACGT\"))\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n self.assertEqual(bc1, 'ATCGATCG') # consensus corrects the mismatch\n\n def test_consensus_tie_returns_n(self):\n \"\"\"Even split (5 A vs 5 G) at a position → N (no strict majority).\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n reads = []\n for i in range(5):\n reads.append((f\"@INST:1:FC:1:1:1:{i} 1:N:0:ATCGATCG+GCTAGCTA\", \"ACGTACGT\"))\n for i in range(5):\n reads.append((f\"@INST:1:FC:1:1:1:{5+i} 1:N:0:GTCGATCG+GCTAGCTA\", \"ACGTACGT\"))\n self._write_fastq(fq, reads)\n bc1, bc2 = viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n self.assertEqual(bc1[0], 'N') # tie at pos 0 → N\n self.assertEqual(bc1[1:], 'TCGATCG') # rest is unanimous\n\n def test_unparseable_headers_raises(self):\n \"\"\"FASTQ with reads but no parseable barcode headers raises ValueError.\"\"\"\n fq = os.path.join(self.tmpdir, 'test.fastq.gz')\n with gzip.open(fq, 'wt') as f:\n # Write reads with non-standard headers (no barcode field)\n for i in range(3):\n f.write(f\"@read_{i}\\n\")\n f.write(\"ACGTACGT\\n\")\n f.write(\"+\\n\")\n f.write(\"IIIIIIII\\n\")\n with self.assertRaises(ValueError):\n viral_ngs.illumina.consensus_barcode_from_fastq(fq, num_reads=10)\n\n\nclass TestParseBarcode(unittest.TestCase):\n \"\"\"Test _parse_barcode_from_header() helper.\"\"\"\n\n def test_dual_index(self):\n bc1, bc2 = viral_ngs.illumina._parse_barcode_from_header(\n \"@INST:1:FC:1:1:1:1 1:N:0:ATCGATCG+GCTAGCTA\"\n )\n self.assertEqual(bc1, 'ATCGATCG')\n self.assertEqual(bc2, 'GCTAGCTA')\n\n def test_single_index(self):\n bc1, bc2 = viral_ngs.illumina._parse_barcode_from_header(\n \"@INST:1:FC:1:1:1:1 1:N:0:ATCGATCG\"\n )\n self.assertEqual(bc1, 'ATCGATCG')\n self.assertIsNone(bc2)\n\n def test_invalid_header(self):\n bc1, bc2 = viral_ngs.illumina._parse_barcode_from_header(\"@bad\")\n self.assertIsNone(bc1)\n self.assertIsNone(bc2)\n\n\nclass TestBuildRunInfoJson(TestCaseWithTmp):\n \"\"\"Test run_info.json construction.\"\"\"\n\n def test_build_with_all_parameters(self):\n \"\"\"Test building run_info.json with all parameters provided.\"\"\"\n run_info_data = viral_ngs.illumina.build_run_info_json(\n sequencing_center=\"BROAD\",\n run_start_date=\"2024-01-15\",\n read_structure=\"76T8B8B76T\",\n indexes=2,\n run_id=\"FLOWCELL123.1\",\n lane=1,\n flowcell=\"FLOWCELL123\",\n lane_count=8,\n surface_count=2,\n swath_count=3,\n tile_count=4,\n total_tile_count=192,\n sequencer_model=\"NextSeq 2000\"\n )\n\n self.assertEqual(run_info_data['sequencing_center'], 'BROAD')\n self.assertEqual(run_info_data['run_start_date'], '2024-01-15')\n self.assertEqual(run_info_data['read_structure'], '76T8B8B76T')\n self.assertEqual(run_info_data['indexes'], '2')\n self.assertEqual(run_info_data['run_id'], 'FLOWCELL123.1')\n self.assertEqual(run_info_data['lane'], '1')\n self.assertEqual(run_info_data['flowcell'], 'FLOWCELL123')\n self.assertEqual(run_info_data['lane_count'], '8')\n self.assertEqual(run_info_data['surface_count'], '2')\n self.assertEqual(run_info_data['swath_count'], '3')\n self.assertEqual(run_info_data['tile_count'], '4')\n self.assertEqual(run_info_data['total_tile_count'], '192')\n self.assertEqual(run_info_data['sequencer_model'], 'NextSeq 2000')\n\n def test_build_with_minimal_parameters(self):\n \"\"\"Test building with only required parameters.\"\"\"\n run_info_data = viral_ngs.illumina.build_run_info_json(\n sequencing_center=\"BROAD\",\n run_start_date=\"2024-01-15\",\n read_structure=\"76T8B76T\",\n indexes=1,\n run_id=\"FC123.1\",\n lane=1,\n flowcell=\"FC123\"\n )\n\n # Required fields should be present\n self.assertEqual(run_info_data['sequencing_center'], 'BROAD')\n self.assertEqual(run_info_data['run_start_date'], '2024-01-15')\n self.assertEqual(run_info_data['read_structure'], '76T8B76T')\n self.assertEqual(run_info_data['flowcell'], 'FC123')\n self.assertEqual(run_info_data['lane'], '1')\n self.assertEqual(run_info_data['indexes'], '1')\n\n # Optional fields should NOT be present when not provided\n self.assertNotIn('lane_count', run_info_data)\n self.assertNotIn('surface_count', run_info_data)\n self.assertNotIn('sequencer_model', run_info_data)\n\n def test_integer_to_string_conversion(self):\n \"\"\"Test that integer parameters are converted to strings.\"\"\"\n run_info_data = viral_ngs.illumina.build_run_info_json(\n sequencing_center=\"BROAD\",\n run_start_date=\"2024-01-15\",\n read_structure=\"76T\",\n indexes=0,\n run_id=\"FC.1\",\n lane=3, # integer\n flowcell=\"FC\",\n lane_count=8 # integer\n )\n\n # All numeric fields should be strings in the output\n self.assertIsInstance(run_info_data['lane'], str)\n self.assertEqual(run_info_data['lane'], '3')\n self.assertIsInstance(run_info_data['lane_count'], str)\n self.assertEqual(run_info_data['indexes'], '0')\n\n def test_consistency_with_existing_output_schema(self):\n \"\"\"Test that output matches the schema used by illumina_demux and splitcode_demux.\"\"\"\n run_info_data = viral_ngs.illumina.build_run_info_json(\n sequencing_center=\"SEQ_CENTER\",\n run_start_date=\"2024-01-15\",\n read_structure=\"76T8B8B76T\",\n indexes=2,\n run_id=\"RUN.1\",\n lane=1,\n flowcell=\"FLOWCELL\",\n lane_count=8,\n surface_count=2,\n swath_count=3,\n tile_count=4,\n total_tile_count=192,\n sequencer_model=\"NextSeq\"\n )\n\n # Verify all expected keys are present\n expected_keys = [\n 'sequencing_center', 'run_start_date', 'read_structure', 'indexes',\n 'run_id', 'lane', 'flowcell', 'lane_count', 'surface_count',\n 'swath_count', 'tile_count', 'total_tile_count', 'sequencer_model'\n ]\n for key in expected_keys:\n self.assertIn(key, run_info_data, f\"Missing expected key: {key}\")\n\n def test_none_values_handled(self):\n \"\"\"Test that None values for optional parameters are handled gracefully.\"\"\"\n run_info_data = viral_ngs.illumina.build_run_info_json(\n sequencing_center=\"BROAD\",\n run_start_date=\"2024-01-15\",\n read_structure=\"76T\",\n indexes=0,\n run_id=\"FC.1\",\n lane=1,\n flowcell=\"FC\",\n lane_count=None,\n sequencer_model=None\n )\n\n # Function should handle None gracefully\n self.assertIsNotNone(run_info_data)\n self.assertEqual(run_info_data['flowcell'], 'FC')\n\n\nclass TestIlluminaMetadata(TestCaseWithTmp):\n \"\"\"\n Test suite for illumina_metadata entry point.\n\n Tests metadata JSON generation from RunInfo.xml and SampleSheet.csv\n without processing any read data. This function is designed to be run\n once per sequencing run to generate metadata that's shared across all\n parallel demux jobs.\n\n Outputs tested:\n - run_info.json: Run metadata (flowcell, dates, read structure, instrument)\n - meta_by_sample.json: Sample metadata indexed by sample name\n - meta_by_filename.json: Sample metadata indexed by library ID\n \"\"\"\n\n def setUp(self):\n super().setUp()\n # Share test data with TestSplitcodeDemuxFastqs\n # Use the test input directory path construction that works\n test_dir = viral_ngs.core.file.get_test_path()\n self.input_dir = os.path.join(test_dir, 'input', 'TestSplitcodeDemuxFastqs')\n\n # Metadata input files\n self.runinfo_xml = os.path.join(self.input_dir, 'RunInfo.xml')\n self.samplesheet_csv = os.path.join(self.input_dir, 'SampleSheet.csv')\n\n # Verify test input files exist\n for f in [self.runinfo_xml, self.samplesheet_csv]:\n self.assertTrue(os.path.exists(f), f\"Test input file missing: {f}\")\n\n def test_runinfo_xml_parsing(self):\n \"\"\"Test that RunInfo.xml can be parsed correctly.\"\"\"\n runinfo = viral_ngs.illumina.RunInfo(self.runinfo_xml)\n\n # Verify basic metadata extraction\n self.assertEqual(runinfo.get_flowcell(), 'TESTFC01')\n self.assertEqual(runinfo.get_run_id(), '250101_TEST_0001_BTESTFC01')\n self.assertEqual(runinfo.get_machine(), 'TEST001')\n self.assertEqual(runinfo.get_lane_count(), 1)\n\n # Verify read structure\n read_structure = runinfo.get_read_structure()\n self.assertIn('50T', read_structure) # 50bp template reads\n self.assertIn('8B', read_structure) # 8bp barcode reads\n\n def test_samplesheet_parsing(self):\n \"\"\"Test that SampleSheet.csv can be parsed correctly.\"\"\"\n samples = viral_ngs.illumina.SampleSheet(\n self.samplesheet_csv,\n only_lane=1,\n allow_non_unique=False\n )\n\n # Verify we got the expected samples\n rows = list(samples.get_rows())\n self.assertGreater(len(rows), 0, \"SampleSheet should contain samples\")\n\n # Verify sample metadata structure\n for row in rows:\n self.assertIn('sample', row)\n self.assertIn('barcode_1', row)\n self.assertIn('barcode_2', row)\n\n def test_metadata_json_generation(self):\n \"\"\"\n Test complete metadata JSON generation workflow.\n\n This is the main workflow test that verifies illumina_metadata\n can generate all three output JSON files with correct schemas.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Output paths\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n # Call illumina_metadata (will fail until implemented - expected per TDD)\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=self.samplesheet_csv,\n lane=1,\n sequencing_center='Broad',\n out_runinfo=out_runinfo,\n out_meta_by_sample=out_meta_by_sample,\n out_meta_by_filename=out_meta_by_filename\n )\n\n # Verify all output files were created\n self.assertTrue(os.path.exists(out_runinfo), \"run_info.json not created\")\n self.assertTrue(os.path.exists(out_meta_by_sample), \"meta_by_sample.json not created\")\n self.assertTrue(os.path.exists(out_meta_by_filename), \"meta_by_filename.json not created\")\n\n # Verify run_info.json schema\n with open(out_runinfo, 'r') as f:\n run_info = json.load(f)\n\n required_fields = [\n 'sequencing_center', 'run_start_date', 'read_structure',\n 'indexes', 'run_id', 'lane', 'flowcell', 'lane_count',\n 'surface_count', 'swath_count', 'tile_count',\n 'total_tile_count', 'sequencer_model'\n ]\n for field in required_fields:\n self.assertIn(field, run_info, f\"Missing required field: {field}\")\n\n # Verify specific values\n self.assertEqual(run_info['sequencing_center'], 'Broad')\n self.assertEqual(run_info['flowcell'], 'TESTFC01')\n self.assertEqual(run_info['lane'], '1')\n\n # Verify meta_by_sample.json schema\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n self.assertIsInstance(meta_by_sample, dict, \"meta_by_sample should be a dict\")\n self.assertGreater(len(meta_by_sample), 0, \"meta_by_sample should not be empty\")\n\n # Each sample should have metadata with lane added\n for sample_name, metadata in meta_by_sample.items():\n self.assertIn('lane', metadata, \"Sample metadata should include lane\")\n self.assertEqual(metadata['lane'], '1')\n\n # Verify meta_by_filename.json schema\n with open(out_meta_by_filename, 'r') as f:\n meta_by_filename = json.load(f)\n\n self.assertIsInstance(meta_by_filename, dict, \"meta_by_filename should be a dict\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_metadata_generation_with_optional_params(self):\n \"\"\"Test metadata generation with optional parameters omitted.\"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Generate only run_info.json (omit sample metadata outputs)\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=self.samplesheet_csv,\n lane=1,\n out_runinfo=out_runinfo,\n out_meta_by_sample=None, # Optional\n out_meta_by_filename=None # Optional\n )\n\n # Only run_info.json should exist\n self.assertTrue(os.path.exists(out_runinfo))\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'meta_by_sample.json')))\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'meta_by_filename.json')))\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_metadata_consistency_with_existing_demux(self):\n \"\"\"\n Test that illumina_metadata output matches the schema produced\n by existing illumina_demux and splitcode_demux functions.\n\n This ensures compatibility and validates that the refactoring\n maintains the same output format.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=self.samplesheet_csv,\n lane=1,\n sequencing_center='Broad',\n out_runinfo=out_runinfo\n )\n\n with open(out_runinfo, 'r') as f:\n run_info = json.load(f)\n\n # Verify the schema matches what build_run_info_json() produces\n # All values should be strings (as per existing implementation)\n for field in ['lane', 'lane_count', 'surface_count', 'swath_count',\n 'tile_count', 'total_tile_count']:\n self.assertIsInstance(run_info[field], str,\n f\"{field} should be a string for compatibility\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_invalid_runinfo_path(self):\n \"\"\"Test error handling for invalid RunInfo.xml path.\"\"\"\n with self.assertRaises((FileNotFoundError, IOError)):\n viral_ngs.illumina.illumina_metadata(\n runinfo='/nonexistent/RunInfo.xml',\n samplesheet=self.samplesheet_csv,\n lane=1\n )\n\n def test_invalid_samplesheet_path(self):\n \"\"\"Test error handling for invalid SampleSheet path.\"\"\"\n with self.assertRaises((FileNotFoundError, IOError)):\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet='/nonexistent/SampleSheet.csv',\n lane=1\n )\n\n def test_illumina_metadata_via_parser(self):\n \"\"\"\n Test illumina_metadata command via argument parser.\n\n This tests the full CLI code path including:\n - Parser argument processing\n - Argument validation\n - Main function invocation\n\n Regression test for issue #127 where split_args=True caused\n TypeError with main_illumina_metadata(args) signature.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Output paths\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n # Call via parser (like CLI does)\n parser = viral_ngs.illumina.parser_illumina_metadata(argparse.ArgumentParser())\n args = parser.parse_args([\n '--runinfo', self.runinfo_xml,\n '--samplesheet', self.samplesheet_csv,\n '--lane', '1',\n '--sequencing_center', 'Broad',\n '--out_runinfo', out_runinfo,\n '--out_meta_by_sample', out_meta_by_sample,\n '--out_meta_by_filename', out_meta_by_filename\n ])\n args.func_main(args)\n\n # Verify all output files were created\n self.assertTrue(os.path.exists(out_runinfo), \"run_info.json not created\")\n self.assertTrue(os.path.exists(out_meta_by_sample), \"meta_by_sample.json not created\")\n self.assertTrue(os.path.exists(out_meta_by_filename), \"meta_by_filename.json not created\")\n\n # Basic validation that JSON files are valid\n with open(out_runinfo, 'r') as f:\n run_info = json.load(f)\n self.assertEqual(run_info['sequencing_center'], 'Broad')\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_three_barcode_samplesheet(self):\n \"\"\"\n Test illumina_metadata with pure 3-barcode samplesheet.\n\n This tests a samplesheet where all samples share outer barcodes (barcode_1 + barcode_2)\n but differ in inner barcodes (barcode_3). This is the typical use case for\n splitcode demultiplexing.\n\n Expected behavior:\n - Should handle samples with duplicate barcode_1+barcode_2 combinations\n - barcode_3 column should be preserved in output metadata\n - num_indexes should reflect the number of outer barcodes (2)\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Use the 3-barcode samplesheet\n samples_3bc = os.path.join(self.input_dir, 'samples_3bc.tsv')\n self.assertTrue(os.path.exists(samples_3bc), f\"Test file missing: {samples_3bc}\")\n\n try:\n # Output paths\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n\n # Call illumina_metadata with 3-barcode samplesheet\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=samples_3bc,\n lane=1,\n sequencing_center='Broad',\n out_runinfo=out_runinfo,\n out_meta_by_sample=out_meta_by_sample\n )\n\n # Verify output files were created\n self.assertTrue(os.path.exists(out_runinfo), \"run_info.json not created\")\n self.assertTrue(os.path.exists(out_meta_by_sample), \"meta_by_sample.json not created\")\n\n # Verify run_info.json has correct index count (should be 2, not 3)\n with open(out_runinfo, 'r') as f:\n run_info = json.load(f)\n self.assertEqual(run_info['indexes'], '2',\n \"num_indexes should be 2 (outer barcodes only)\")\n\n # Verify meta_by_sample.json includes all samples with barcode_3\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n # Should have samples from all three pools (7 samples total)\n self.assertEqual(len(meta_by_sample), 7,\n \"Should have all 7 samples from 3-barcode samplesheet\")\n\n # Verify 3-barcode samples have barcode_3 field\n three_bc_samples = ['TestSample1', 'TestSample2', 'TestSample3',\n 'TestSampleEmpty', 'TestSample5', 'TestSample6']\n for sample_name in three_bc_samples:\n self.assertIn(sample_name, meta_by_sample,\n f\"Sample {sample_name} missing from metadata\")\n self.assertIn('barcode_3', meta_by_sample[sample_name],\n f\"Sample {sample_name} should have barcode_3 field\")\n self.assertNotEqual(meta_by_sample[sample_name]['barcode_3'], '',\n f\"Sample {sample_name} should have non-empty barcode_3\")\n\n # Verify 2-barcode sample has empty barcode_3\n self.assertIn('TestSampleNoSplitcode', meta_by_sample)\n # barcode_3 should either be empty string or not present (both acceptable)\n bc3 = meta_by_sample['TestSampleNoSplitcode'].get('barcode_3', '')\n self.assertEqual(bc3, '',\n \"2-barcode sample should have empty barcode_3\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_mixed_two_and_three_barcode_samplesheet(self):\n \"\"\"\n Test illumina_metadata with mixed 2-barcode and 3-barcode samples.\n\n This tests a samplesheet containing both:\n - Samples with 3 barcodes (barcode_1 + barcode_2 + barcode_3)\n - Samples with 2 barcodes (barcode_1 + barcode_2, empty barcode_3)\n\n The same samplesheet is used for both scenarios since samples_3bc.tsv\n already contains this mix.\n\n Expected behavior:\n - Should handle both types of samples in the same samplesheet\n - All samples should be included in metadata output\n - barcode_3 field should be present for all samples (empty for 2-barcode samples)\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Use the mixed barcode samplesheet\n samples_3bc = os.path.join(self.input_dir, 'samples_3bc.tsv')\n\n try:\n # Output paths\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n\n # Call illumina_metadata\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=samples_3bc,\n lane=1,\n out_meta_by_sample=out_meta_by_sample\n )\n\n # Verify metadata includes both types of samples\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n # Count samples with and without barcode_3\n samples_with_bc3 = []\n samples_without_bc3 = []\n\n for sample_name, metadata in meta_by_sample.items():\n bc3 = metadata.get('barcode_3', '')\n if bc3 and bc3.strip():\n samples_with_bc3.append(sample_name)\n else:\n samples_without_bc3.append(sample_name)\n\n # Should have 6 samples with barcode_3 (from Pool 1 and Pool 2)\n self.assertEqual(len(samples_with_bc3), 6,\n f\"Should have 6 samples with barcode_3, got: {samples_with_bc3}\")\n\n # Should have 1 sample without barcode_3 (from Pool 3)\n self.assertEqual(len(samples_without_bc3), 1,\n f\"Should have 1 sample without barcode_3, got: {samples_without_bc3}\")\n self.assertIn('TestSampleNoSplitcode', samples_without_bc3,\n \"TestSampleNoSplitcode should have empty barcode_3\")\n\n # Verify specific samples are categorized correctly\n self.assertIn('TestSample1', samples_with_bc3)\n self.assertIn('TestSample2', samples_with_bc3)\n self.assertIn('TestSample5', samples_with_bc3)\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_three_barcode_barcode_uniqueness(self):\n \"\"\"\n Test that illumina_metadata properly handles duplicate outer barcodes in 3-barcode sheets.\n\n In 3-barcode samplesheets, multiple samples share the same barcode_1+barcode_2\n combination (outer barcodes) and differ only in barcode_3 (inner barcode).\n\n Expected behavior:\n - Should NOT raise an error about non-unique barcodes\n - Should successfully generate metadata for all samples\n - The function should internally handle allow_non_unique=True for 3-barcode sheets\n\n This is a regression test to ensure the function doesn't fail when samples\n share outer barcodes.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n samples_3bc = os.path.join(self.input_dir, 'samples_3bc.tsv')\n\n try:\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n\n # This should NOT raise an error even though Pool 1 has 4 samples\n # sharing ATCGATCG+GCTAGCTA outer barcodes\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=samples_3bc,\n lane=1,\n out_meta_by_sample=out_meta_by_sample\n )\n\n # Verify all Pool 1 samples are present (they share outer barcodes)\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n pool1_samples = ['TestSample1', 'TestSample2', 'TestSample3', 'TestSampleEmpty']\n for sample in pool1_samples:\n self.assertIn(sample, meta_by_sample,\n f\"Pool 1 sample {sample} should be in metadata\")\n # All should have same outer barcodes\n self.assertEqual(meta_by_sample[sample]['barcode_1'], 'ATCGATCG')\n self.assertEqual(meta_by_sample[sample]['barcode_2'], 'GCTAGCTA')\n\n # All Pool 1 samples should have different barcode_3\n bc3_values = [meta_by_sample[s]['barcode_3'] for s in pool1_samples]\n self.assertEqual(len(set(bc3_values)), len(bc3_values),\n \"Pool 1 samples should have unique barcode_3 values\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_optional_lane_parameter(self):\n \"\"\"\n Test illumina_metadata with lane=None (optional lane parameter).\n\n Verifies that:\n 1. lane=None is accepted as a valid input\n 2. run_info.json uses default lane value of \"0\"\n 3. Sample metadata preserves lane values from samplesheet when present\n 4. Sample metadata uses \"0\" when lane not in samplesheet\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Output paths\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n\n # Call illumina_metadata with lane=None\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=self.samplesheet_csv,\n lane=None, # Test optional lane parameter\n sequencing_center='Broad',\n out_runinfo=out_runinfo,\n out_meta_by_sample=out_meta_by_sample\n )\n\n # Verify outputs were created\n self.assertTrue(os.path.exists(out_runinfo), \"run_info.json not created\")\n self.assertTrue(os.path.exists(out_meta_by_sample), \"meta_by_sample.json not created\")\n\n # Verify run_info.json uses default lane value of \"0\"\n with open(out_runinfo, 'r') as f:\n run_info = json.load(f)\n self.assertEqual(run_info['lane'], \"0\",\n \"run_info.json should use lane='0' when lane=None\")\n\n # Verify sample metadata has lane field\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n # All samples should have a lane value (either from samplesheet or default \"0\")\n for sample_name, sample_meta in meta_by_sample.items():\n self.assertIn('lane', sample_meta,\n f\"Sample {sample_name} should have lane field\")\n # Lane should be a string\n self.assertIsInstance(sample_meta['lane'], str,\n f\"Lane for {sample_name} should be a string\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_optional_lane_backwards_compatibility(self):\n \"\"\"\n Test that existing code with explicit lane parameter still works.\n\n Ensures backwards compatibility - explicitly providing lane should work\n exactly as before.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Output paths\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n\n # Call illumina_metadata with explicit lane=1\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=self.samplesheet_csv,\n lane=1, # Explicit lane value\n sequencing_center='Broad',\n out_runinfo=out_runinfo,\n out_meta_by_sample=out_meta_by_sample\n )\n\n # Verify outputs were created\n self.assertTrue(os.path.exists(out_runinfo))\n self.assertTrue(os.path.exists(out_meta_by_sample))\n\n # Verify run_info.json uses the specified lane\n with open(out_runinfo, 'r') as f:\n run_info = json.load(f)\n self.assertEqual(run_info['lane'], \"1\",\n \"run_info.json should use specified lane value\")\n\n # Verify all samples have the specified lane\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n for sample_name, sample_meta in meta_by_sample.items():\n self.assertEqual(sample_meta['lane'], \"1\",\n f\"Sample {sample_name} should have lane='1'\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_metadata_with_append_run_id(self):\n \"\"\"\n Test illumina_metadata with --append_run_id flag.\n\n When append_run_id=True, the 'run' field in metadata should include\n the flowcell ID and lane suffix (e.g., 'sample.l1.TESTFC01.1').\n This ensures metadata matches BAM filenames when demux commands\n use --append_run_id.\n\n Fixes GitHub issue #150.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n # Call illumina_metadata with append_run_id=True\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=self.samplesheet_csv,\n lane=1,\n append_run_id=True,\n out_meta_by_filename=out_meta_by_filename\n )\n\n # Verify output was created\n self.assertTrue(os.path.exists(out_meta_by_filename))\n\n # Verify run field includes flowcell.lane suffix\n with open(out_meta_by_filename, 'r') as f:\n meta = json.load(f)\n\n # All keys (run values) should end with .TESTFC01.1 (flowcell.lane)\n self.assertGreater(len(meta), 0, \"Should have at least one sample\")\n for run_key in meta.keys():\n self.assertTrue(\n run_key.endswith('.TESTFC01.1'),\n f\"Expected run key to end with '.TESTFC01.1', got: {run_key}\"\n )\n # Also verify the 'run' field in the metadata matches the key\n self.assertEqual(meta[run_key]['run'], run_key)\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_metadata_without_append_run_id(self):\n \"\"\"\n Test illumina_metadata without --append_run_id flag (default behavior).\n\n When append_run_id=False (default), the 'run' field should NOT include\n the flowcell ID and lane suffix.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n # Call illumina_metadata without append_run_id (default=False)\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=self.samplesheet_csv,\n lane=1,\n out_meta_by_filename=out_meta_by_filename\n )\n\n # Verify output was created\n self.assertTrue(os.path.exists(out_meta_by_filename))\n\n # Verify run field does NOT include flowcell.lane suffix\n with open(out_meta_by_filename, 'r') as f:\n meta = json.load(f)\n\n self.assertGreater(len(meta), 0, \"Should have at least one sample\")\n for run_key in meta.keys():\n self.assertFalse(\n run_key.endswith('.TESTFC01.1'),\n f\"Expected run key to NOT end with '.TESTFC01.1', got: {run_key}\"\n )\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_metadata_append_run_id_via_parser(self):\n \"\"\"\n Test illumina_metadata --append_run_id via argument parser.\n\n Verifies the argument is properly wired up through the parser.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n # Build args via parser\n parser = viral_ngs.illumina.parser_illumina_metadata(argparse.ArgumentParser())\n args = parser.parse_args([\n '--runinfo', self.runinfo_xml,\n '--samplesheet', self.samplesheet_csv,\n '--lane', '1',\n '--append_run_id',\n '--out_meta_by_filename', out_meta_by_filename\n ])\n\n # Call via main function attached to parser\n args.func_main(args)\n\n # Verify run field includes flowcell.lane suffix\n with open(out_meta_by_filename, 'r') as f:\n meta = json.load(f)\n\n self.assertGreater(len(meta), 0, \"Should have at least one sample\")\n for run_key in meta.keys():\n self.assertTrue(\n run_key.endswith('.TESTFC01.1'),\n f\"Expected run key to end with '.TESTFC01.1', got: {run_key}\"\n )\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_illumina_metadata_runinfo_only(self):\n \"\"\"\n Test illumina_metadata with only --runinfo and --out_runinfo (no samplesheet).\n\n This tests the run-info-only mode where samplesheet is optional.\n The function should generate run_info.json without requiring a samplesheet.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n\n # Call illumina_metadata with only runinfo (no samplesheet)\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=None, # No samplesheet\n lane=1,\n out_runinfo=out_runinfo\n )\n\n # Verify run_info.json is created\n self.assertTrue(os.path.exists(out_runinfo),\n \"run_info.json should be created without samplesheet\")\n\n # Verify run_info.json has valid structure\n with open(out_runinfo, 'r') as f:\n run_info = json.load(f)\n\n self.assertIn('sequencing_center', run_info)\n self.assertIn('flowcell', run_info)\n self.assertIn('lane', run_info)\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_illumina_metadata_sample_output_requires_samplesheet(self):\n \"\"\"\n Test that illumina_metadata raises error when sample metadata is requested without samplesheet.\n\n When --out_meta_by_sample or --out_meta_by_filename is provided,\n the samplesheet parameter becomes required.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n\n # Should raise ValueError when sample metadata requested without samplesheet\n with self.assertRaises(ValueError) as context:\n viral_ngs.illumina.illumina_metadata(\n runinfo=self.runinfo_xml,\n samplesheet=None, # No samplesheet\n lane=1,\n out_meta_by_sample=out_meta_by_sample # But requesting sample metadata\n )\n\n self.assertIn('samplesheet', str(context.exception).lower(),\n \"Error should mention samplesheet is required\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_illumina_metadata_optional_samplesheet_via_parser(self):\n \"\"\"\n Test illumina_metadata optional samplesheet via argument parser.\n\n Verifies the CLI correctly handles:\n 1. --runinfo alone with --out_runinfo (should work)\n 2. The samplesheet argument is optional\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_runinfo = os.path.join(out_dir, 'run_info.json')\n\n # Build args via parser - only runinfo, no samplesheet\n parser = viral_ngs.illumina.parser_illumina_metadata(argparse.ArgumentParser())\n args = parser.parse_args([\n '--runinfo', self.runinfo_xml,\n '--lane', '1',\n '--out_runinfo', out_runinfo\n # Note: no --samplesheet argument\n ])\n\n # Call via main function attached to parser\n args.func_main(args)\n\n # Verify run_info.json is created\n self.assertTrue(os.path.exists(out_runinfo),\n \"run_info.json should be created via parser without samplesheet\")\n\n finally:\n shutil.rmtree(out_dir)\n\n\nclass TestSplitcodeDemuxFastqs(TestCaseWithTmp):\n \"\"\"\n Test suite for splitcode_demux_fastqs entry point.\n\n Tests SIMPLIFIED demultiplexing from paired DRAGEN FASTQ files using 3-barcode scheme:\n - Input: Paired R1/R2 FASTQ files + custom 3-barcode samplesheet ONLY\n - Output: Per-sample unaligned BAMs + demux metrics + barcode reports\n - Does NOT generate: run_info.json, meta_by_sample.json, meta_by_filename.json\n (use illumina_metadata entry point for those)\n\n Test data includes both 3-barcode and 2-barcode samples:\n\n - TestPool1 (ATCGATCG+GCTAGCTA) - 3 barcodes:\n * TestSample1 (AAAAAAAA): 100 reads\n * TestSample2 (CCCCCCCC): 75 reads\n * TestSample3 (GGGGTTTT): 50 reads\n * TestSampleEmpty (TTTTGGGG): 0 reads (empty sample)\n * Unmatched (NNNNANNN): 25 reads\n\n - TestPool3 (GGAATTCC+CCGGAATT) - 2 barcodes only (no barcode_3):\n * TestSampleNoSplitcode: 80 reads (should bypass splitcode, direct FASTQ→BAM)\n\n Note: This simplified version does NOT require RunInfo.xml or Illumina SampleSheet.csv.\n \"\"\"\n\n def setUp(self):\n super().setUp()\n self.input_dir = viral_ngs.core.file.get_test_input_path(self)\n\n # Input FASTQ files\n self.r1_fastq = os.path.join(self.input_dir, 'TestPool1_S1_L001_R1_001.fastq.gz')\n self.r2_fastq = os.path.join(self.input_dir, 'TestPool1_S1_L001_R2_001.fastq.gz')\n\n # Custom 3-barcode samplesheet\n self.samples_3bc = os.path.join(self.input_dir, 'samples_3bc.tsv')\n\n # RunInfo.xml for richer BAM metadata\n self.runinfo_xml = os.path.join(self.input_dir, 'RunInfo.xml')\n\n # Verify test input files exist\n for f in [self.r1_fastq, self.r2_fastq, self.samples_3bc, self.runinfo_xml]:\n self.assertTrue(os.path.exists(f), f\"Test input file missing: {f}\")\n\n def test_parse_fastq_filename_from_test_data(self):\n \"\"\"Test that our test FASTQ filenames can be parsed correctly.\"\"\"\n # Test with simple format (no flowcell ID prefix)\n result = viral_ngs.illumina.parse_illumina_fastq_filename(self.r1_fastq)\n\n self.assertEqual(result['sample_name'], 'TestPool1')\n self.assertEqual(result['sample_number'], 1)\n self.assertEqual(result['lane'], 1)\n self.assertEqual(result['read'], 1)\n self.assertEqual(result['chunk'], 1)\n self.assertFalse(result.get('is_index', False))\n\n def test_barcode_normalization_on_samplesheet(self):\n \"\"\"Test that barcodes from samplesheet can be normalized.\"\"\"\n # Read the custom 3-barcode samplesheet\n # Note: allow_non_unique=True because samples share index1+index2, differ only in barcode_3\n samples = viral_ngs.illumina.SampleSheet(self.samples_3bc, allow_non_unique=True)\n\n # Get first sample's barcodes\n first_sample = samples.get_rows()[0]\n\n # Test normalization of each barcode\n bc1 = viral_ngs.illumina.normalize_barcode(first_sample['barcode_1'])\n bc2 = viral_ngs.illumina.normalize_barcode(first_sample['barcode_2'])\n bc3 = viral_ngs.illumina.normalize_barcode(first_sample['barcode_3'])\n\n # Should all be uppercase, valid DNA\n self.assertTrue(all(c in 'ACGTN' for c in bc1))\n self.assertTrue(all(c in 'ACGTN' for c in bc2))\n self.assertTrue(all(c in 'ACGTN' for c in bc3))\n\n def test_basic_demux_workflow(self):\n \"\"\"\n Test basic demultiplexing workflow from paired FASTQs.\n\n Simplified workflow (no RunInfo.xml or Illumina SampleSheet.csv required):\n 1. Parse FASTQ filenames for metadata\n 2. Load custom 3-barcode samplesheet\n 3. Run splitcode demultiplexing\n 4. Verify output BAMs are created\n 5. Verify demux metrics and barcode reports\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Call the main function (will fail until implemented in Phase 3)\n # NOTE: Simplified interface - no runinfo_xml or illumina_samplesheet needed\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Verify expected output BAMs exist (library name format: {sample}.l{library_id}.bam)\n expected_bams = [\n os.path.join(out_dir, 'TestSample1.lL1.bam'),\n os.path.join(out_dir, 'TestSample2.lL1.bam'),\n os.path.join(out_dir, 'TestSample3.lL1.bam'),\n os.path.join(out_dir, 'TestSampleEmpty.lL1.bam'),\n ]\n\n for bam in expected_bams:\n self.assertTrue(os.path.exists(bam), f\"Expected output BAM missing: {bam}\")\n\n # Verify demux metrics (but NOT metadata JSONs or barcode reports)\n self.assertTrue(os.path.exists(os.path.join(out_dir, 'demux_metrics.json')))\n\n # Should NOT generate these (use illumina_metadata or illumina_demux instead)\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'run_info.json')))\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'meta_by_sample.json')))\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'meta_by_filename.json')))\n # Note: barcodes_common.txt and barcodes_outliers.txt are not generated by\n # splitcode_demux_fastqs (use illumina_demux for comprehensive barcode reporting)\n\n def test_barcode_matching_perfect_match(self):\n \"\"\"\n Test that reads with perfect barcode matches are assigned correctly.\n\n Verify:\n - TestSample1 (AAAAAAAA) gets exactly 100 reads\n - TestSample2 (CCCCCCCC) gets exactly 75 reads\n - TestSample3 (GGGGTTTT) gets exactly 50 reads\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Simplified call - no RunInfo.xml needed\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Use samtools to count reads in each output BAM\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n # BAM filenames now use library name format: {sample}.l{library_id_per_sample}.bam\n sample1_bam = os.path.join(out_dir, 'TestSample1.lL1.bam')\n sample2_bam = os.path.join(out_dir, 'TestSample2.lL1.bam')\n sample3_bam = os.path.join(out_dir, 'TestSample3.lL1.bam')\n\n # Count read pairs (samtools.count returns total reads, divide by 2 for pairs)\n sample1_pairs = samtools.count(sample1_bam) // 2\n sample2_pairs = samtools.count(sample2_bam) // 2\n sample3_pairs = samtools.count(sample3_bam) // 2\n\n self.assertEqual(sample1_pairs, 100, \"TestSample1 should have exactly 100 read pairs\")\n self.assertEqual(sample2_pairs, 75, \"TestSample2 should have exactly 75 read pairs\")\n self.assertEqual(sample3_pairs, 50, \"TestSample3 should have exactly 50 read pairs\")\n\n def test_unmatched_barcodes(self):\n \"\"\"\n Test handling of reads with unmatched inline barcodes.\n\n Verify:\n - Reads with outlier barcodes (GGAATTTT, CCCCAAAA, ATATAGAG totaling 25 reads)\n are handled without errors\n - No crashes when some reads don't match any sample\n - Unassigned reads are written to unassigned FASTQs\n\n Note: This test does NOT check barcodes_outliers.txt (not generated by\n splitcode_demux_fastqs). Use illumina_demux for comprehensive barcode reporting.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Should not crash even with unmatched barcodes\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Verify unassigned FASTQs exist\n unassigned_r1 = os.path.join(out_dir, 'unassigned_R1.fastq.gz')\n unassigned_r2 = os.path.join(out_dir, 'unassigned_R2.fastq.gz')\n self.assertTrue(os.path.exists(unassigned_r1), \"Unassigned R1 should exist\")\n self.assertTrue(os.path.exists(unassigned_r2), \"Unassigned R2 should exist\")\n\n # Verify unassigned files are not empty (should have 25 read pairs)\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n # We'd need to convert FASTQ to BAM to count, but that's overkill.\n # Just verify the files have non-zero size.\n self.assertGreater(os.path.getsize(unassigned_r1), 0,\n \"Unassigned R1 should have content\")\n self.assertGreater(os.path.getsize(unassigned_r2), 0,\n \"Unassigned R2 should have content\")\n\n def test_empty_barcode_sample(self):\n \"\"\"\n Test handling of sample with zero matching reads.\n\n Verify:\n - TestSampleEmpty (TTTTGGGG) is in samplesheet but has 0 reads\n - Empty BAM file is still created (or noted in metrics)\n - No errors/crashes when sample has zero reads\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Should not raise an exception even though TestSampleEmpty has 0 reads\n # Simplified call - no RunInfo.xml needed\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Empty sample should either:\n # 1. Have an empty BAM file created, OR\n # 2. Be noted in metrics as having 0 reads\n\n empty_bam = os.path.join(out_dir, 'TestSampleEmpty.lL1.bam')\n\n if os.path.exists(empty_bam):\n # If BAM exists, it should have 0 reads\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n read_count = samtools.count(empty_bam)\n self.assertEqual(read_count, 0, \"Empty sample should have 0 reads\")\n else:\n # If no BAM, check metrics mentions this sample\n metrics_file = os.path.join(out_dir, 'demux_metrics.json')\n with open(metrics_file, 'r') as f:\n metrics = json.load(f)\n\n # TestSampleEmpty should be mentioned somewhere in metrics\n self.assertIn('TestSampleEmpty', str(metrics), \"Empty sample should be mentioned in metrics\")\n\n def test_output_schema_consistency(self):\n \"\"\"\n Test that output files match expected schema.\n\n Verify:\n - demux_metrics.json has expected fields\n - BAM files are valid\n - Barcode reports are NOT generated (use illumina_demux for those)\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Simplified call - no RunInfo.xml needed\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Check demux_metrics.json has expected structure\n metrics_file = os.path.join(out_dir, 'demux_metrics.json')\n with open(metrics_file, 'r') as f:\n metrics = json.load(f)\n\n # Should have sample-level information\n self.assertIsInstance(metrics, (dict, list), \"demux_metrics.json should be JSON dict or list\")\n\n # Barcode reports should NOT be generated (not part of simplified workflow)\n common_file = os.path.join(out_dir, 'barcodes_common.txt')\n outliers_file = os.path.join(out_dir, 'barcodes_outliers.txt')\n\n self.assertFalse(os.path.exists(common_file),\n \"barcodes_common.txt should not be generated by splitcode_demux_fastqs\")\n self.assertFalse(os.path.exists(outliers_file),\n \"barcodes_outliers.txt should not be generated by splitcode_demux_fastqs\")\n\n def test_multi_pool_samplesheet_collapsibility_check(self):\n \"\"\"\n Test that collapsibility is checked only on the filtered pool, not the entire samplesheet.\n\n This is a regression test for GitHub Copilot comment #2510390315.\n The bug: can_be_collapsed was checking the entire samplesheet instead of just\n the filtered samples for the current pool.\n\n Scenario:\n - Samplesheet contains multiple pools:\n * Pool 1 (ATCGATCG+GCTAGCTA): 3-barcode samples (collapsible)\n * Pool 2 (CTGATCGT+TAGATCGC): 3-barcode samples (collapsible)\n * Pool 3 (GGAATTCC+CCGGAATT): 2-barcode sample (unique, not collapsible)\n - FASTQ file contains only Pool 1 data (ATCGATCG+GCTAGCTA)\n - Should succeed even though Pool 3 exists with unique outer barcodes\n\n Before fix: Would fail because can_be_collapsed checked entire samplesheet\n After fix: Succeeds because collapsibility is checked only on Pool 1\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # The test samplesheet already has this structure:\n # - Pool 1: ATCGATCG+GCTAGCTA with 3-barcode samples (TestSample1-4)\n # - Pool 2: CTGATCGT+TAGATCGC with 3-barcode samples (TestSample5-6)\n # - Pool 3: GGAATTCC+CCGGAATT with 2-barcode sample (TestSampleNoSplitcode)\n\n # The test FASTQ contains Pool 1 data only (ATCGATCG+GCTAGCTA)\n # This should succeed even though the samplesheet contains Pool 3 with unique outer barcodes\n\n # This call should NOT raise ValueError about non-collapsible barcodes\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc, # Multi-pool samplesheet\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Verify successful demux - BAMs should be created for Pool 1 samples\n # (library name format: {sample}.l{library_id}.bam)\n expected_bams = [\n os.path.join(out_dir, 'TestSample1.lL1.bam'),\n os.path.join(out_dir, 'TestSample2.lL1.bam'),\n os.path.join(out_dir, 'TestSample3.lL1.bam'),\n os.path.join(out_dir, 'TestSampleEmpty.lL1.bam'),\n ]\n\n for bam in expected_bams:\n self.assertTrue(os.path.exists(bam), f\"Expected output BAM missing: {bam}\")\n\n # Pool 2 and Pool 3 samples should NOT be created (different outer barcodes)\n pool2_bams = [\n os.path.join(out_dir, 'TestSample5.lL2.bam'),\n os.path.join(out_dir, 'TestSample6.lL2.bam'),\n ]\n pool3_bams = [\n os.path.join(out_dir, 'TestSampleNoSplitcode.lL3.bam'),\n ]\n\n for bam in pool2_bams + pool3_bams:\n self.assertFalse(os.path.exists(bam),\n f\"BAM from different pool should not be created: {bam}\")\n\n def test_fastq_filename_parsing(self):\n \"\"\"\n Test extraction of metadata from FASTQ filenames.\n\n Verify:\n - Pool/sample name extracted correctly\n - Lane number extracted correctly\n - Read number (R1/R2) extracted correctly\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Simplified call - no RunInfo.xml needed\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Metadata extracted from FASTQ filename should be used in output\n # Check demux_metrics.json for evidence of correct parsing\n metrics_file = os.path.join(out_dir, 'demux_metrics.json')\n with open(metrics_file, 'r') as f:\n metrics = json.load(f)\n\n # Should have metadata about the pool/samples\n # Exact structure TBD, but should contain sample information\n self.assertIsInstance(metrics, (dict, list), \"Metrics should be valid JSON\")\n\n def test_two_barcode_sample_bypass_splitcode(self):\n \"\"\"\n Test handling of 2-barcode samples (empty barcode_3).\n\n This tests a mixed samplesheet where some rows have 3 barcodes (requiring\n splitcode demux) and other rows have only 2 barcodes (empty barcode_3).\n\n For 2-barcode rows, splitcode_demux_fastqs should:\n - Skip splitcode demultiplexing\n - Perform direct FASTQ → BAM conversion\n - Produce exactly one output BAM (the pool itself)\n - Still generate standard output files (JSONs, metrics)\n\n Test data:\n - TestPool3 (GGAATTCC+CCGGAATT): 80 reads, no inline barcode\n - Expected: Single BAM file with all 80 reads\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n # Use TestPool3 which has empty barcode_3 (2-barcode sample)\n r1_fastq = os.path.join(self.input_dir, 'TestPool3_S3_L001_R1_001.fastq.gz')\n r2_fastq = os.path.join(self.input_dir, 'TestPool3_S3_L001_R2_001.fastq.gz')\n\n # Verify test files exist\n self.assertTrue(os.path.exists(r1_fastq), f\"Test FASTQ missing: {r1_fastq}\")\n self.assertTrue(os.path.exists(r2_fastq), f\"Test FASTQ missing: {r2_fastq}\")\n\n # Run demux on 2-barcode sample\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=r1_fastq,\n fastq_r2=r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # For 2-barcode sample, should produce exactly one BAM file\n # (the entire pool, no splitcode demux)\n # BAM filename uses library name format: {sample}.l{library_id}.bam\n expected_bam = os.path.join(out_dir, 'TestSampleNoSplitcode.lL3.bam')\n self.assertTrue(os.path.exists(expected_bam),\n \"2-barcode sample should produce a single BAM file\")\n\n # Verify all 80 reads are in the output BAM\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n total_reads = samtools.count(expected_bam)\n read_pairs = total_reads // 2\n self.assertEqual(read_pairs, 80,\n \"All 80 read pairs should be in the 2-barcode sample BAM\")\n\n # Verify standard output files still exist (but NOT metadata JSONs)\n self.assertTrue(os.path.exists(os.path.join(out_dir, 'demux_metrics.json')))\n\n # Should NOT generate run_info.json (use illumina_metadata instead)\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'run_info.json')))\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'meta_by_sample.json')))\n self.assertFalse(os.path.exists(os.path.join(out_dir, 'meta_by_filename.json')))\n\n def test_splitcode_demux_fastqs_via_parser(self):\n \"\"\"\n Test splitcode_demux_fastqs command via argument parser.\n\n This tests the full CLI code path including:\n - Parser argument processing\n - Argument validation\n - Main function invocation\n\n Regression test for issue #127 where split_args=True caused\n TypeError with main_splitcode_demux_fastqs(args) signature.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Call via parser (like CLI does)\n parser = viral_ngs.illumina.parser_splitcode_demux_fastqs(argparse.ArgumentParser())\n args = parser.parse_args([\n '--fastq_r1', self.r1_fastq,\n '--fastq_r2', self.r2_fastq,\n '--samplesheet', self.samples_3bc,\n '--runinfo', self.runinfo_xml,\n '--outdir', out_dir\n ])\n args.func_main(args)\n\n # Verify output files were created\n self.assertTrue(os.path.exists(os.path.join(out_dir, 'demux_metrics.json')))\n\n # Verify at least one BAM file was created\n bam_files = [f for f in os.listdir(out_dir) if f.endswith('.bam')]\n self.assertGreater(len(bam_files), 0, \"Should produce at least one BAM file\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_i5_reverse_complement_3bc_demux(self):\n \"\"\"\n Test 3-barcode demultiplexing when i5 barcode requires reverse complement.\n\n This is a regression test for issue #133.\n\n Scenario:\n - Samplesheet has barcode_2 = GCTAGCTA (forward orientation)\n - FASTQ headers have barcode_2 = TAGCTAGC (reverse complement)\n - The function should auto-detect the i5 reverse complement orientation\n - Demux should succeed using the corrected barcode values\n\n Expected behavior:\n - Auto-detection logs i5 reverse complement match\n - 3-barcode demultiplexing succeeds\n - Output BAMs created with correct read counts\n - No \"no_3bc_match\" error\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Use test files with reverse complement i5\n r1_fastq = os.path.join(self.input_dir, 'TestPool1_RC_S4_L001_R1_001.fastq.gz')\n r2_fastq = os.path.join(self.input_dir, 'TestPool1_RC_S4_L001_R2_001.fastq.gz')\n samples_rc = os.path.join(self.input_dir, 'samples_3bc_i5_revcomp.tsv')\n\n # Verify test input files exist\n self.assertTrue(os.path.exists(r1_fastq), f\"Test FASTQ missing: {r1_fastq}\")\n self.assertTrue(os.path.exists(r2_fastq), f\"Test FASTQ missing: {r2_fastq}\")\n self.assertTrue(os.path.exists(samples_rc), f\"Test samplesheet missing: {samples_rc}\")\n\n # Run splitcode demux with i5 reverse complement scenario\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=r1_fastq,\n fastq_r2=r2_fastq,\n samplesheet=samples_rc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Verify expected output BAMs exist (library name format: {sample}.l{library_id}.bam)\n expected_bams = [\n os.path.join(out_dir, 'TestSample1_RC.lL1.bam'),\n os.path.join(out_dir, 'TestSample2_RC.lL1.bam'),\n os.path.join(out_dir, 'TestSample3_RC.lL1.bam')\n ]\n\n for bam in expected_bams:\n self.assertTrue(os.path.exists(bam), f\"Expected output BAM missing: {bam}\")\n\n # Verify read counts using samtools\n # Note: samtools.count() returns total reads (R1 + R2 for paired-end)\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n # TestSample1_RC (AAAAAAAA): should have 2 read pairs = 4 total reads\n count1 = int(samtools.count(expected_bams[0]))\n self.assertEqual(count1, 4, \"TestSample1_RC should have 2 read pairs (4 total reads)\")\n\n # TestSample2_RC (CCCCCCCC): should have 2 read pairs = 4 total reads\n count2 = int(samtools.count(expected_bams[1]))\n self.assertEqual(count2, 4, \"TestSample2_RC should have 2 read pairs (4 total reads)\")\n\n # TestSample3_RC (GGGGTTTT): should have 1 read pair = 2 total reads\n count3 = int(samtools.count(expected_bams[2]))\n self.assertEqual(count3, 2, \"TestSample3_RC should have 1 read pair (2 total reads)\")\n\n # Verify demux metrics exist and indicate success (not \"no_3bc_match\")\n metrics_file = os.path.join(out_dir, 'demux_metrics.json')\n self.assertTrue(os.path.exists(metrics_file))\n\n with open(metrics_file, 'r') as f:\n metrics = json.load(f)\n\n # Should NOT have demux_type of \"no_3bc_match\"\n demux_type = metrics.get('demux_type', '')\n self.assertNotEqual(demux_type, 'no_3bc_match',\n \"Should successfully demux, not fail with no_3bc_match\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_splitcode_demux_3bc_with_n_bases_in_bc2_and_i5_rc(self):\n \"\"\"\n Test 3-barcode demultiplexing with N bases in barcode_2 AND i5 reverse complement.\n\n This is a regression test for a bug where N-wildcard matching failed in the\n second filtering step for 3-barcode demux.\n\n Scenario:\n - Samplesheet has barcode_2 = ACGTTACGCA (forward orientation)\n - FASTQ headers have barcode_2 = TGNGTAACGT (reverse complement with N base)\n - After RC: TGNGTAACGT -> ACGTTACNCA\n - Should match ACGTTACGCA via N wildcard (N at position 8, 10% N fraction < 50% threshold)\n\n Expected behavior:\n - Auto-detection logs i5 reverse complement match\n - N-wildcard matching works in BOTH filtering steps (initial match + 3bc filter)\n - 3-barcode demultiplexing succeeds\n - Output BAMs created with correct read counts\n - No \"no_3bc_match\" or \"no_match\" error\n\n Bug being tested:\n The code had TWO filtering steps for 3-barcode samples:\n 1. Initial match via match_barcodes_with_orientation() - uses N-wildcard matching ✓\n 2. DataFrame filtering at lines 1094-1098 - used exact match, failed with N ✗\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Use test files with N bases in barcode_2 + reverse complement i5\n r1_fastq = os.path.join(self.input_dir, 'TestPool1_N_S5_L001_R1_001.fastq.gz')\n r2_fastq = os.path.join(self.input_dir, 'TestPool1_N_S5_L001_R2_001.fastq.gz')\n samples_n = os.path.join(self.input_dir, 'samples_3bc_i5_rc_with_n.tsv')\n\n # Verify test input files exist\n self.assertTrue(os.path.exists(r1_fastq), f\"Test FASTQ missing: {r1_fastq}\")\n self.assertTrue(os.path.exists(r2_fastq), f\"Test FASTQ missing: {r2_fastq}\")\n self.assertTrue(os.path.exists(samples_n), f\"Test samplesheet missing: {samples_n}\")\n\n # Run splitcode demux with N bases + i5 reverse complement scenario\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=r1_fastq,\n fastq_r2=r2_fastq,\n samplesheet=samples_n,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n threads=1\n )\n\n # Verify expected output BAMs exist (library name format: {sample}.l{library_id}.bam)\n expected_bams = [\n os.path.join(out_dir, 'TestSample1_N.lL1.bam'),\n os.path.join(out_dir, 'TestSample2_N.lL1.bam'),\n os.path.join(out_dir, 'TestSample3_N.lL1.bam')\n ]\n\n for bam in expected_bams:\n self.assertTrue(os.path.exists(bam), f\"Expected output BAM missing: {bam}\")\n\n # Verify read counts using samtools\n # Note: samtools.count() returns total reads (R1 + R2 for paired-end)\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n # TestSample1_N (AAAAAAAA): should have 2 read pairs = 4 total reads\n count1 = int(samtools.count(expected_bams[0]))\n self.assertEqual(count1, 4, \"TestSample1_N should have 2 read pairs (4 total reads)\")\n\n # TestSample2_N (CCCCCCCC): should have 2 read pairs = 4 total reads\n count2 = int(samtools.count(expected_bams[1]))\n self.assertEqual(count2, 4, \"TestSample2_N should have 2 read pairs (4 total reads)\")\n\n # TestSample3_N (GGGGTTTT): should have 1 read pair = 2 total reads\n count3 = int(samtools.count(expected_bams[2]))\n self.assertEqual(count3, 2, \"TestSample3_N should have 1 read pair (2 total reads)\")\n\n # Verify demux metrics exist and indicate success (not \"no_3bc_match\" or \"no_match\")\n metrics_file = os.path.join(out_dir, 'demux_metrics.json')\n self.assertTrue(os.path.exists(metrics_file))\n\n with open(metrics_file, 'r') as f:\n metrics = json.load(f)\n\n # Should NOT have demux_type indicating failure\n demux_type = metrics.get('demux_type', '')\n self.assertNotIn('no_3bc_match', demux_type,\n \"Should successfully demux, not fail with no_3bc_match\")\n self.assertNotIn('no_match', demux_type,\n \"Should successfully demux, not fail with no_match\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_no_barcode_match_produces_zero_bams(self):\n \"\"\"\n Test that when FASTQ barcodes don't match any samplesheet entry,\n zero BAMs are produced but metrics files are still generated.\n\n This tests the behavior change where we emit zero BAMs instead of\n an empty BAM when there's no barcode match.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Create test FASTQ files with barcodes that don't match the samplesheet\n # The samplesheet has entries for ATCGATCG+GCTAGCTA, CTGATCGT+TAGATCGC, GGAATTCC+CCGGAATT\n # We'll use AAAAAAAA+TTTTTTTT which uses valid DNA chars but matches none of them\n nonmatch_r1 = os.path.join(out_dir, 'NonMatch_S99_L001_R1_001.fastq.gz')\n nonmatch_r2 = os.path.join(out_dir, 'NonMatch_S99_L001_R2_001.fastq.gz')\n\n # Create R1 FASTQ with non-matching barcodes\n with gzip.open(nonmatch_r1, 'wt') as f:\n f.write(\"@TEST001:1:TESTFC01:1:1101:1000:2000 1:N:0:AAAAAAAA+TTTTTTTT\\n\")\n f.write(\"ACGTACGTACGTACGT\\n\")\n f.write(\"+\\n\")\n f.write(\"IIIIIIIIIIIIIIII\\n\")\n\n # Create R2 FASTQ\n with gzip.open(nonmatch_r2, 'wt') as f:\n f.write(\"@TEST001:1:TESTFC01:1:1101:1000:2000 2:N:0:AAAAAAAA+TTTTTTTT\\n\")\n f.write(\"TGCATGCATGCATGCA\\n\")\n f.write(\"+\\n\")\n f.write(\"IIIIIIIIIIIIIIII\\n\")\n\n # Run splitcode_demux_fastqs - should not raise an exception\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=nonmatch_r1,\n fastq_r2=nonmatch_r2,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n threads=1\n )\n\n # Verify NO BAM files were created (zero BAMs for no match)\n bam_files = [f for f in os.listdir(out_dir) if f.endswith('.bam')]\n self.assertEqual(len(bam_files), 0,\n f\"Expected zero BAM files for no barcode match, found: {bam_files}\")\n\n # Verify metrics files ARE created\n metrics_file = os.path.join(out_dir, 'demux_metrics.json')\n self.assertTrue(os.path.exists(metrics_file),\n \"demux_metrics.json should be created even with no match\")\n\n picard_metrics_file = os.path.join(out_dir, 'demux_metrics_picard-style.txt')\n self.assertTrue(os.path.exists(picard_metrics_file),\n \"demux_metrics_picard-style.txt should be created even with no match\")\n\n # Verify metrics indicate no_barcode_match\n with open(metrics_file, 'r') as f:\n metrics = json.load(f)\n\n demux_type = metrics.get('demux_type', '')\n self.assertIn('no_barcode_match', demux_type,\n f\"demux_type should indicate no_barcode_match, got: {demux_type}\")\n\n # Verify read_count is 0\n samples = metrics.get('samples', {})\n for sample_name, sample_info in samples.items():\n self.assertEqual(sample_info.get('read_count'), 0,\n f\"Sample {sample_name} should have 0 reads\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_append_run_id_3bc(self):\n \"\"\"\n Test that append_run_id=True produces BAM filenames with flowcell and lane.\n\n Expected output format: {sample}.l{library_id}.{flowcell}.{lane}.bam\n Example: TestSample1.lL1.TESTFC01.1.bam\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n append_run_id=True,\n threads=1\n )\n\n # Verify BAM filenames include flowcell and lane\n # TESTFC01 is the flowcell from RunInfo.xml, lane 1 from FASTQ filename\n expected_bams = [\n os.path.join(out_dir, 'TestSample1.lL1.TESTFC01.1.bam'),\n os.path.join(out_dir, 'TestSample2.lL1.TESTFC01.1.bam'),\n os.path.join(out_dir, 'TestSample3.lL1.TESTFC01.1.bam'),\n ]\n\n for bam in expected_bams:\n self.assertTrue(os.path.exists(bam), f\"Expected output BAM missing: {bam}\")\n\n # Verify read counts\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n sample1_pairs = samtools.count(expected_bams[0]) // 2\n sample2_pairs = samtools.count(expected_bams[1]) // 2\n sample3_pairs = samtools.count(expected_bams[2]) // 2\n\n self.assertEqual(sample1_pairs, 100, \"TestSample1 should have 100 read pairs\")\n self.assertEqual(sample2_pairs, 75, \"TestSample2 should have 75 read pairs\")\n self.assertEqual(sample3_pairs, 50, \"TestSample3 should have 50 read pairs\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_append_run_id_2bc(self):\n \"\"\"\n Test that append_run_id=True works for 2-barcode samples.\n\n Expected output format: {sample}.l{library_id}.{flowcell}.{lane}.bam\n Example: TestSampleNoSplitcode.lL3.TESTFC01.1.bam\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Use Pool 3 files which have 2-barcode sample (no barcode_3)\n r1_fastq = os.path.join(self.input_dir, 'TestPool3_S3_L001_R1_001.fastq.gz')\n r2_fastq = os.path.join(self.input_dir, 'TestPool3_S3_L001_R2_001.fastq.gz')\n\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=r1_fastq,\n fastq_r2=r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n append_run_id=True,\n threads=1\n )\n\n # Verify BAM filename includes flowcell and lane\n expected_bam = os.path.join(out_dir, 'TestSampleNoSplitcode.lL3.TESTFC01.1.bam')\n self.assertTrue(os.path.exists(expected_bam),\n f\"Expected output BAM missing: {expected_bam}\")\n\n # Verify all 80 reads are in the output BAM\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n read_pairs = samtools.count(expected_bam) // 2\n self.assertEqual(read_pairs, 80, \"All 80 read pairs should be present\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_append_run_id_requires_flowcell(self):\n \"\"\"\n Test that append_run_id=True without flowcell raises ValueError.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n with self.assertRaises(ValueError) as context:\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n # No runinfo and no flowcell_id\n append_run_id=True,\n threads=1\n )\n\n self.assertIn('flowcell', str(context.exception).lower(),\n \"Error should mention flowcell requirement\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_splitcode_demux_fastqs_metadata_output(self):\n \"\"\"\n Test that splitcode_demux_fastqs generates metadata JSON files when requested.\n\n Verifies:\n - meta_by_sample.json is created when --out_meta_by_sample is provided\n - meta_by_filename.json is created when --out_meta_by_filename is provided\n - Both JSONs contain the expected sample metadata structure\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n append_run_id=True,\n out_meta_by_sample=out_meta_by_sample,\n out_meta_by_filename=out_meta_by_filename,\n threads=1\n )\n\n # Verify both JSON files are created\n self.assertTrue(os.path.exists(out_meta_by_sample),\n \"meta_by_sample.json should be created\")\n self.assertTrue(os.path.exists(out_meta_by_filename),\n \"meta_by_filename.json should be created\")\n\n # Verify meta_by_sample.json structure\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n # Should have entries for matched samples\n self.assertIsInstance(meta_by_sample, dict)\n self.assertGreater(len(meta_by_sample), 0, \"meta_by_sample should have entries\")\n\n # Each entry should have required fields\n for sample_name, metadata in meta_by_sample.items():\n self.assertIn('sample', metadata)\n self.assertIn('lane', metadata)\n self.assertIn('run', metadata)\n\n # Verify meta_by_filename.json structure\n with open(out_meta_by_filename, 'r') as f:\n meta_by_filename = json.load(f)\n\n self.assertIsInstance(meta_by_filename, dict)\n self.assertGreater(len(meta_by_filename), 0, \"meta_by_filename should have entries\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_splitcode_demux_fastqs_metadata_lane_from_fastq(self):\n \"\"\"\n Test that metadata lane field uses actual lane from FASTQ filename.\n\n This is the critical fix: the lane value should come from the FASTQ filename\n (e.g., L001 -> lane=1) and NOT be a default value like 0.\n\n Test FASTQ: TestPool1_S1_L001_R1_001.fastq.gz (lane=1)\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq, # TestPool1_S1_L001_R1_001.fastq.gz\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n append_run_id=True,\n out_meta_by_sample=out_meta_by_sample,\n threads=1\n )\n\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n # All samples should have lane=1 (from L001 in filename)\n for sample_name, metadata in meta_by_sample.items():\n self.assertEqual(metadata['lane'], '1',\n f\"Sample {sample_name} lane should be '1' from FASTQ filename, not '0'\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_splitcode_demux_fastqs_metadata_run_matches_bam(self):\n \"\"\"\n Test that metadata 'run' field matches BAM filenames when append_run_id=True.\n\n This is the core fix for the metadata mismatch bug:\n - BAM filename: {sample}.l{library_id}.{flowcell}.{lane}.bam\n - Metadata 'run' field should match: {sample}.l{library_id}.{flowcell}.{lane}\n\n The metadata 'run' field is used as the key in meta_by_filename.json.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=self.r1_fastq,\n fastq_r2=self.r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n append_run_id=True,\n out_meta_by_filename=out_meta_by_filename,\n threads=1\n )\n\n with open(out_meta_by_filename, 'r') as f:\n meta_by_filename = json.load(f)\n\n # Get list of output BAMs\n bam_files = [f for f in os.listdir(out_dir) if f.endswith('.bam')]\n self.assertGreater(len(bam_files), 0, \"Should have output BAMs\")\n\n # For each BAM, verify there's a matching metadata entry\n for bam_file in bam_files:\n bam_basename = bam_file.replace('.bam', '')\n self.assertIn(bam_basename, meta_by_filename,\n f\"meta_by_filename should have key matching BAM basename: {bam_basename}\")\n\n finally:\n shutil.rmtree(out_dir)\n\n def test_splitcode_demux_fastqs_2bc_metadata(self):\n \"\"\"\n Test metadata generation for 2-barcode samples (bypass splitcode path).\n\n 2-barcode samples skip splitcode and go directly to FASTQ→BAM conversion.\n Metadata should still be generated correctly with proper lane values.\n \"\"\"\n out_dir = tempfile.mkdtemp()\n\n try:\n # Use 2-barcode sample FASTQs\n r1_fastq = os.path.join(self.input_dir, 'TestPool3_S3_L001_R1_001.fastq.gz')\n r2_fastq = os.path.join(self.input_dir, 'TestPool3_S3_L001_R2_001.fastq.gz')\n\n # Skip if test files don't exist\n if not os.path.exists(r1_fastq) or not os.path.exists(r2_fastq):\n self.skipTest(\"2-barcode test FASTQs not available\")\n\n out_meta_by_sample = os.path.join(out_dir, 'meta_by_sample.json')\n out_meta_by_filename = os.path.join(out_dir, 'meta_by_filename.json')\n\n viral_ngs.illumina.splitcode_demux_fastqs(\n fastq_r1=r1_fastq,\n fastq_r2=r2_fastq,\n samplesheet=self.samples_3bc,\n outdir=out_dir,\n runinfo=self.runinfo_xml,\n append_run_id=True,\n out_meta_by_sample=out_meta_by_sample,\n out_meta_by_filename=out_meta_by_filename,\n threads=1\n )\n\n # Verify metadata files are created for 2-barcode case\n self.assertTrue(os.path.exists(out_meta_by_sample),\n \"meta_by_sample.json should be created for 2-barcode samples\")\n self.assertTrue(os.path.exists(out_meta_by_filename),\n \"meta_by_filename.json should be created for 2-barcode samples\")\n\n # Verify lane is correct\n with open(out_meta_by_sample, 'r') as f:\n meta_by_sample = json.load(f)\n\n for sample_name, metadata in meta_by_sample.items():\n self.assertEqual(metadata['lane'], '1',\n \"Lane should be '1' from FASTQ filename\")\n\n finally:\n shutil.rmtree(out_dir)\n\n\nclass TestMergeDemuxMetrics(TestCaseWithTmp):\n \"\"\"\n Test suite for merge_demux_metrics entry point.\n\n Regression tests for issue #127 CLI argument parsing.\n \"\"\"\n\n def test_merge_demux_metrics_via_parser(self):\n \"\"\"\n Test merge_demux_metrics command via argument parser.\n\n This tests the full CLI code path including:\n - Parser argument processing\n - Argument validation\n - Main function invocation\n\n Regression test for issue #127 where split_args=True caused\n TypeError with main_merge_demux_metrics(args) signature.\n \"\"\"\n # Get test input files\n test_dir = viral_ngs.core.file.get_test_path()\n input1 = os.path.join(test_dir, 'input', 'TestIlluminaBarcodeHelper', 'single_index', 'metrics.txt')\n input2 = os.path.join(test_dir, 'input', 'TestIlluminaBarcodeHelper', 'one_correction', 'metrics.txt')\n\n self.assertTrue(os.path.exists(input1), f\"Test input missing: {input1}\")\n self.assertTrue(os.path.exists(input2), f\"Test input missing: {input2}\")\n\n out_file = viral_ngs.core.file.mkstempfname('.txt')\n\n try:\n # Call via parser (like CLI does)\n parser = viral_ngs.illumina.parser_merge_demux_metrics(argparse.ArgumentParser())\n args = parser.parse_args([input1, input2, out_file])\n args.func_main(args)\n\n # Verify output file was created\n self.assertTrue(os.path.exists(out_file), \"Merged metrics file should be created\")\n\n # Verify it has content\n with open(out_file, 'r') as f:\n content = f.read()\n self.assertGreater(len(content), 0, \"Merged file should have content\")\n\n finally:\n if os.path.exists(out_file):\n os.remove(out_file)\n" }, { "path": "tests/unit/core/test_read_utils.py", "content": "# Unit tests for read_utils.py\n\n__author__ = \"irwin@broadinstitute.org\"\n\nimport unittest\nimport argparse\nimport filecmp\nimport os\nimport glob\nimport platform\n\nimport pysam\nimport viral_ngs.read_utils\nimport shutil\nimport tempfile\nimport viral_ngs.core\nimport viral_ngs.core.bwa\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp, assert_equal_bam_reads\n\n# Skip tests requiring x86-only tools on ARM platforms\nIS_ARM = platform.machine() in ('arm64', 'aarch64')\nSKIP_X86_ONLY_REASON = \"Requires x86-only bioconda package (not available on ARM)\"\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in viral_ngs.read_utils.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n\nclass TestBwamemIdxstats(TestCaseWithTmp):\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.tempDir = tempfile.mkdtemp()\n self.ebolaRef = viral_ngs.core.file.mkstempfname('.fasta', directory=self.tempDir)\n shutil.copyfile(os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.fasta'), self.ebolaRef)\n self.bwa = viral_ngs.core.bwa.Bwa()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.bwa.index(self.ebolaRef)\n\n def test_bwamem_idxstats(self):\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n outBam = viral_ngs.core.file.mkstempfname('.bam', directory=self.tempDir)\n outStats = viral_ngs.core.file.mkstempfname('.stats.txt', directory=self.tempDir)\n viral_ngs.read_utils.bwamem_idxstats(inBam, self.ebolaRef, outBam, outStats)\n with open(outStats, 'rt') as inf:\n actual_count = int(inf.readline().strip().split('\\t')[2])\n self.assertEqual(actual_count, self.samtools.count(outBam, opts=['-F', '4']))\n self.assertGreater(actual_count, 18000)\n\n def test_bwamem_idxstats_with_filtering(self):\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n outBam = viral_ngs.core.file.mkstempfname('.bam', directory=self.tempDir)\n outStats = viral_ngs.core.file.mkstempfname('.stats.txt', directory=self.tempDir)\n viral_ngs.read_utils.bwamem_idxstats(inBam, self.ebolaRef, outBam, outStats, filterReadsAfterAlignment=True)\n with open(outStats, 'rt') as inf:\n actual_count = int(inf.readline().strip().split('\\t')[2])\n self.assertEqual(actual_count, self.samtools.count(outBam, opts=['-F', '4']))\n self.assertLess(actual_count, 18000)\n\n outBamNoFiltering = viral_ngs.core.file.mkstempfname('.bam', directory=self.tempDir)\n outStatsNoFiltering = viral_ngs.core.file.mkstempfname('.stats.txt', directory=self.tempDir)\n viral_ngs.read_utils.bwamem_idxstats(inBam, self.ebolaRef, outBamNoFiltering, outStatsNoFiltering, filterReadsAfterAlignment=False)\n with open(outStatsNoFiltering, 'rt') as inf:\n count_without_filtering = int(inf.readline().strip().split('\\t')[2])\n\n # the filtered count should be less than the count without filtering\n self.assertLess(actual_count, count_without_filtering)\n\n def test_bwamem_idxstats_no_bam_output(self):\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n outStats = viral_ngs.core.file.mkstempfname('.stats.txt', directory=self.tempDir)\n viral_ngs.read_utils.bwamem_idxstats(inBam, self.ebolaRef, None, outStats)\n with open(outStats, 'rt') as inf:\n actual_count = int(inf.readline().strip().split('\\t')[2])\n self.assertGreater(actual_count, 18000)\n\n\nclass TestMinimap2Idxstats(TestCaseWithTmp):\n \"\"\"Tests for the minimap2_idxstats command with new PAF-based implementation.\"\"\"\n\n def setUp(self):\n TestCaseWithTmp.setUp(self)\n self.tempDir = tempfile.mkdtemp()\n self.ebolaRef = viral_ngs.core.file.mkstempfname('.fasta', directory=self.tempDir)\n shutil.copyfile(os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.fasta'), self.ebolaRef)\n\n def test_minimap2_idxstats(self):\n \"\"\"Test basic minimap2_idxstats with new signature (no outBam parameter).\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n outStats = viral_ngs.core.file.mkstempfname('.stats.txt', directory=self.tempDir)\n\n # New signature: minimap2_idxstats(inBam, refFasta, outStats, outReadlist=None, threads=None)\n viral_ngs.read_utils.minimap2_idxstats(inBam, self.ebolaRef, outStats)\n\n with open(outStats, 'rt') as inf:\n actual_count = int(inf.readline().strip().split('\\t')[2])\n self.assertGreater(actual_count, 18000)\n\n def test_minimap2_idxstats_with_readlist(self):\n \"\"\"Test minimap2_idxstats with optional readlist output.\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n outStats = viral_ngs.core.file.mkstempfname('.stats.txt', directory=self.tempDir)\n outReadlist = viral_ngs.core.file.mkstempfname('.readlist.txt', directory=self.tempDir)\n\n viral_ngs.read_utils.minimap2_idxstats(inBam, self.ebolaRef, outStats, outReadlist=outReadlist)\n\n # Verify stats file\n with open(outStats, 'rt') as inf:\n stats_count = int(inf.readline().strip().split('\\t')[2])\n self.assertGreater(stats_count, 18000)\n\n # Verify readlist file\n with open(outReadlist, 'rt') as inf:\n read_ids = [line.strip() for line in inf if line.strip()]\n self.assertGreater(len(read_ids), 0)\n\n # All read IDs should be unique\n self.assertEqual(len(read_ids), len(set(read_ids)))\n\n # Readlist contains unique read pairs (~half of stats count for paired-end data)\n self.assertGreater(len(read_ids), 9000)\n\n\nclass TestFastqBam(TestCaseWithTmp):\n 'Class for testing fastq <-> bam conversions'\n\n def test_fastq_bam(self):\n import pysam\n\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n\n # Define file names\n inFastq1 = os.path.join(myInputDir, 'in1.fastq')\n inFastq2 = os.path.join(myInputDir, 'in2.fastq')\n inHeader = os.path.join(myInputDir, 'inHeader.txt')\n expected1_7Sam = os.path.join(myInputDir, 'expected.java1_7.sam')\n outBamCmd = viral_ngs.core.file.mkstempfname('.bam')\n outBamTxt = viral_ngs.core.file.mkstempfname('.bam')\n\n # in1.fastq, in2.fastq -> out.bam; header params from command-line\n # Note: --JVMmemory is kept for backwards compatibility but ignored with samtools\n parser = viral_ngs.read_utils.parser_fastq_to_bam(argparse.ArgumentParser())\n args = parser.parse_args([inFastq1,\n inFastq2,\n outBamCmd,\n '--sampleName',\n 'FreeSample',\n '--JVMmemory',\n '1g',\n '--picardOptions',\n 'LIBRARY_NAME=Alexandria',\n 'PLATFORM=9.75',\n 'SEQUENCING_CENTER=KareemAbdul-Jabbar',])\n args.func_main(args)\n\n # Verify BAM was created with reads\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.assertEqual(samtools.count(outBamCmd), 2)\n\n # Verify RG tags match expected values\n with pysam.AlignmentFile(outBamCmd, 'rb', check_sq=False) as bam:\n rg_list = bam.header.get('RG', [])\n self.assertEqual(len(rg_list), 1)\n rg = rg_list[0]\n self.assertEqual(rg.get('SM'), 'FreeSample')\n self.assertEqual(rg.get('LB'), 'Alexandria')\n self.assertEqual(rg.get('PL'), '9.75')\n self.assertEqual(rg.get('CN'), 'KareemAbdul-Jabbar')\n\n # Verify reads match expected (flags and sequences)\n assert_equal_bam_reads(self, outBamCmd, expected1_7Sam)\n\n # Test with header file\n parser = viral_ngs.read_utils.parser_fastq_to_bam(argparse.ArgumentParser())\n args = parser.parse_args([inFastq1, inFastq2, outBamTxt, '--header', inHeader])\n args.func_main(args)\n\n # Verify header was replaced correctly\n with pysam.AlignmentFile(outBamTxt, 'rb', check_sq=False) as bam:\n rg_list = bam.header.get('RG', [])\n self.assertEqual(len(rg_list), 1)\n rg = rg_list[0]\n # Values should come from inHeader.txt\n self.assertEqual(rg.get('SM'), 'txtSample')\n self.assertEqual(rg.get('LB'), 'txtLib')\n self.assertEqual(rg.get('PL'), 'txtPlatform')\n self.assertEqual(rg.get('CN'), 'txtCenter')\n self.assertEqual(rg.get('DT'), '2014-11-10')\n\n def test_fastq_to_bam_empty_inputs(self):\n \"\"\"Test that fastq_to_bam handles empty FASTQ files correctly.\n\n Empty FASTQ inputs should produce a valid BAM file with:\n - A proper BAM header (non-zero file size)\n - Zero reads (SamtoolsTool.isEmpty should return True)\n - Readable by samtools (no corruption)\n \"\"\"\n # Create empty FASTQ files\n emptyFastq1 = viral_ngs.core.file.mkstempfname('.fastq')\n emptyFastq2 = viral_ngs.core.file.mkstempfname('.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n # Create zero-byte FASTQ files\n open(emptyFastq1, 'w').close()\n open(emptyFastq2, 'w').close()\n\n # Convert empty FASTQs to BAM (should now succeed with defensive code)\n viral_ngs.read_utils.fastq_to_bam(\n emptyFastq1,\n emptyFastq2,\n outBam,\n sampleName='EmptySample',\n picardOptions=['LIBRARY_NAME=EmptyLibrary']\n )\n\n # Verify the BAM file was created\n self.assertTrue(os.path.exists(outBam), \"Output BAM file should exist\")\n\n # Verify the BAM file is non-zero (contains header)\n bam_size = os.path.getsize(outBam)\n self.assertGreater(bam_size, 0, \"BAM file should be non-zero (contains header)\")\n\n # Verify the BAM file is empty (no reads) using SamtoolsTool\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.assertTrue(samtools.isEmpty(outBam), \"BAM should be empty (no reads)\")\n\n # Verify the BAM file has zero reads via count\n read_count = samtools.count(outBam)\n self.assertEqual(read_count, 0, \"BAM should contain zero reads\")\n\n # Verify the BAM file is readable (has valid header)\n header_file = viral_ngs.core.file.mkstempfname('.txt')\n samtools.dumpHeader(outBam, header_file)\n header_size = os.path.getsize(header_file)\n self.assertGreater(header_size, 0, \"BAM header should be non-empty\")\n\n\nclass TestRmdupUnaligned(TestCaseWithTmp):\n @unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\n def test_mvicuna_canned_input(self):\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'input.bam')\n expected_bam = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'expected.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n viral_ngs.read_utils.rmdup_mvicuna_bam(\n input_bam,\n output_bam\n )\n\n self.assertEqual(samtools.count(output_bam), samtools.count(expected_bam))\n\n @unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\n def test_mvicuna_empty_input(self):\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n empty_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n viral_ngs.read_utils.rmdup_mvicuna_bam(\n empty_bam,\n output_bam\n )\n self.assertEqual(samtools.count(output_bam), 0)\n\n @unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\n def test_cdhit_canned_input(self):\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'input.bam')\n expected_bam = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'expected.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n viral_ngs.read_utils.rmdup_cdhit_bam(\n input_bam,\n output_bam\n )\n\n self.assertEqual(samtools.count(output_bam), 1772)\n\n @unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\n def test_cdhit_empty_input(self):\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n empty_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n viral_ngs.read_utils.rmdup_cdhit_bam(\n empty_bam,\n output_bam\n )\n self.assertEqual(samtools.count(output_bam), 0)\n\n\nclass TestReadIdStore(TestCaseWithTmp):\n \"\"\"Tests for ReadIdStore SQLite-backed read ID storage.\"\"\"\n\n def test_add_from_fastq_paired(self):\n \"\"\"Test adding read IDs from paired-end interleaved FASTQ.\"\"\"\n # Create a test FASTQ with paired reads\n fastq_path = viral_ngs.core.file.mkstempfname('.fastq')\n with open(fastq_path, 'wt') as f:\n # Write 3 read pairs (6 entries, but only 3 unique IDs)\n for i in range(3):\n f.write('@read{}/1\\nACGT\\n+\\nIIII\\n'.format(i))\n f.write('@read{}/2\\nACGT\\n+\\nIIII\\n'.format(i))\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n added = store.add_from_fastq(fastq_path)\n self.assertEqual(added, 3) # 3 unique read IDs\n self.assertEqual(len(store), 3)\n\n def test_add_from_fastq_single_end(self):\n \"\"\"Test adding read IDs from single-end FASTQ.\"\"\"\n fastq_path = viral_ngs.core.file.mkstempfname('.fastq')\n with open(fastq_path, 'wt') as f:\n for i in range(5):\n f.write('@read{}\\nACGT\\n+\\nIIII\\n'.format(i))\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n added = store.add_from_fastq(fastq_path)\n self.assertEqual(added, 5)\n self.assertEqual(len(store), 5)\n\n def test_deduplication(self):\n \"\"\"Test that duplicate read IDs are ignored.\"\"\"\n fastq_path = viral_ngs.core.file.mkstempfname('.fastq')\n with open(fastq_path, 'wt') as f:\n # Write same read ID multiple times\n for _ in range(10):\n f.write('@duplicate_read\\nACGT\\n+\\nIIII\\n')\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.add_from_fastq(fastq_path)\n self.assertEqual(len(store), 1) # Only 1 unique ID\n\n def test_write_to_file(self):\n \"\"\"Test writing read IDs to file.\"\"\"\n fastq_path = viral_ngs.core.file.mkstempfname('.fastq')\n with open(fastq_path, 'wt') as f:\n for i in range(5):\n f.write('@read{}\\nACGT\\n+\\nIIII\\n'.format(i))\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n out_path = viral_ngs.core.file.mkstempfname('.txt')\n\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.add_from_fastq(fastq_path)\n written = store.write_to_file(out_path)\n self.assertEqual(written, 5)\n\n # Verify file contents\n with open(out_path, 'rt') as f:\n lines = [line.strip() for line in f]\n self.assertEqual(len(lines), 5)\n self.assertEqual(set(lines), {'read0', 'read1', 'read2', 'read3', 'read4'})\n\n def test_write_to_file_with_downsampling(self):\n \"\"\"Test random downsampling when writing to file.\"\"\"\n fastq_path = viral_ngs.core.file.mkstempfname('.fastq')\n with open(fastq_path, 'wt') as f:\n for i in range(100):\n f.write('@read{}\\nACGT\\n+\\nIIII\\n'.format(i))\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n out_path = viral_ngs.core.file.mkstempfname('.txt')\n\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.add_from_fastq(fastq_path)\n self.assertEqual(len(store), 100)\n written = store.write_to_file(out_path, max_reads=20)\n self.assertEqual(written, 20)\n\n # Verify file has exactly 20 lines\n with open(out_path, 'rt') as f:\n lines = [line.strip() for line in f]\n self.assertEqual(len(lines), 20)\n\n def test_empty_fastq(self):\n \"\"\"Test handling of empty FASTQ file.\"\"\"\n fastq_path = viral_ngs.core.file.mkstempfname('.fastq')\n with open(fastq_path, 'wt') as f:\n pass # Empty file\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n added = store.add_from_fastq(fastq_path)\n self.assertEqual(added, 0)\n self.assertEqual(len(store), 0)\n\n def test_add_single(self):\n \"\"\"Test adding a single read ID.\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n self.assertTrue(store.add('read1'))\n self.assertEqual(len(store), 1)\n # Adding same ID again should return False\n self.assertFalse(store.add('read1'))\n self.assertEqual(len(store), 1)\n # Adding different ID should work\n self.assertTrue(store.add('read2'))\n self.assertEqual(len(store), 2)\n\n def test_extend(self):\n \"\"\"Test adding multiple read IDs efficiently.\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n # Add from a list\n added = store.extend(['read1', 'read2', 'read3'])\n self.assertEqual(added, 3)\n self.assertEqual(len(store), 3)\n\n # Add with some duplicates\n added = store.extend(['read3', 'read4', 'read5'])\n self.assertEqual(added, 2) # Only read4 and read5 are new\n self.assertEqual(len(store), 5)\n\n def test_extend_generator(self):\n \"\"\"Test extend with a generator (O(1) memory).\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n # Use a generator expression\n added = store.extend('read{}'.format(i) for i in range(100))\n self.assertEqual(added, 100)\n self.assertEqual(len(store), 100)\n\n def test_contains(self):\n \"\"\"Test membership testing with 'in' operator.\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(['read1', 'read2', 'read3'])\n self.assertIn('read1', store)\n self.assertIn('read2', store)\n self.assertNotIn('read4', store)\n\n def test_iter(self):\n \"\"\"Test iteration over read IDs in insertion order.\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(['read3', 'read1', 'read2'])\n # Should iterate in insertion order\n result = list(store)\n self.assertEqual(result, ['read3', 'read1', 'read2'])\n\n def test_delitem(self):\n \"\"\"Test deleting read IDs with del operator.\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(['read1', 'read2', 'read3'])\n self.assertEqual(len(store), 3)\n\n del store['read2']\n self.assertEqual(len(store), 2)\n self.assertNotIn('read2', store)\n self.assertIn('read1', store)\n self.assertIn('read3', store)\n\n # Deleting non-existent ID should raise KeyError\n with self.assertRaises(KeyError):\n del store['nonexistent']\n\n def test_discard(self):\n \"\"\"Test discard method (no error if absent).\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(['read1', 'read2'])\n\n store.discard('read1')\n self.assertEqual(len(store), 1)\n self.assertNotIn('read1', store)\n\n # Discarding non-existent ID should not raise\n store.discard('nonexistent') # Should not raise\n self.assertEqual(len(store), 1)\n\n def test_shrink_to_subsample_basic(self):\n \"\"\"Test shrink_to_subsample reduces store to n elements.\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n # Add 100 read IDs\n original_ids = set('read{}'.format(i) for i in range(100))\n store.extend(original_ids)\n self.assertEqual(len(store), 100)\n\n # Shrink to 25\n store.shrink_to_subsample(25)\n self.assertEqual(len(store), 25)\n\n # All remaining IDs should be from original set\n remaining = set(store)\n self.assertTrue(remaining.issubset(original_ids))\n\n def test_shrink_to_subsample_larger_than_store(self):\n \"\"\"Test shrink_to_subsample with n >= store size does nothing.\"\"\"\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(['read{}'.format(i) for i in range(50)])\n self.assertEqual(len(store), 50)\n\n # Request 100, but only have 50\n store.shrink_to_subsample(100)\n self.assertEqual(len(store), 50) # Unchanged\n\n def test_shrink_to_subsample_randomness(self):\n \"\"\"Test that shrink_to_subsample produces different results on repeated calls.\"\"\"\n original_ids = ['read{}'.format(i) for i in range(100)]\n\n # Create two stores and subsample each\n db_path1 = viral_ngs.core.file.mkstempfname('.db')\n db_path2 = viral_ngs.core.file.mkstempfname('.db')\n\n with viral_ngs.read_utils.ReadIdStore(db_path1) as store1:\n store1.extend(original_ids)\n store1.shrink_to_subsample(10)\n result1 = set(store1)\n\n with viral_ngs.read_utils.ReadIdStore(db_path2) as store2:\n store2.extend(original_ids)\n store2.shrink_to_subsample(10)\n result2 = set(store2)\n\n # Very unlikely to be identical (1 in C(100,10) chance)\n # We allow this test to pass even if they match, just check both are valid\n self.assertEqual(len(result1), 10)\n self.assertEqual(len(result2), 10)\n\n def test_filter_bam_by_ids_include(self):\n \"\"\"Test filter_bam_by_ids with include=True keeps only matching reads.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n # Get some read names from the input BAM\n read_names = set()\n with pysam.AlignmentFile(input_bam, 'rb', check_sq=False) as bam:\n for i, read in enumerate(bam):\n if i < 10: # Get first 10 reads (5 pairs)\n read_names.add(read.query_name)\n else:\n break\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(read_names)\n store.filter_bam_by_ids(input_bam, output_bam, include=True)\n\n # Output should have exactly len(read_names) * 2 reads (paired-end)\n output_count = samtools.count(output_bam)\n self.assertEqual(output_count, len(read_names) * 2)\n\n def test_filter_bam_by_ids_exclude(self):\n \"\"\"Test filter_bam_by_ids with include=False excludes matching reads.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n input_count = samtools.count(input_bam)\n\n # Get some read names from the input BAM\n read_names = set()\n with pysam.AlignmentFile(input_bam, 'rb', check_sq=False) as bam:\n for i, read in enumerate(bam):\n if i < 10: # Get first 10 reads (5 pairs)\n read_names.add(read.query_name)\n else:\n break\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(read_names)\n store.filter_bam_by_ids(input_bam, output_bam, include=False)\n\n # Output should have input_count - (len(read_names) * 2) reads\n output_count = samtools.count(output_bam)\n expected = input_count - (len(read_names) * 2)\n self.assertEqual(output_count, expected)\n\n def test_filter_bam_by_ids_header_preserved(self):\n \"\"\"Test that BAM headers are semantically equivalent after filtering.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n output_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n # Get some read names\n read_names = set()\n with pysam.AlignmentFile(input_bam, 'rb', check_sq=False) as bam:\n for i, read in enumerate(bam):\n if i < 5:\n read_names.add(read.query_name)\n else:\n break\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(read_names)\n store.filter_bam_by_ids(input_bam, output_bam, include=True)\n\n # Compare headers\n with pysam.AlignmentFile(input_bam, 'rb', check_sq=False) as inb:\n input_header = inb.header\n\n with pysam.AlignmentFile(output_bam, 'rb', check_sq=False) as outb:\n output_header = outb.header\n\n # Check header keys match\n self.assertEqual(set(input_header.keys()), set(output_header.keys()))\n\n # Check RG entries preserved\n if 'RG' in input_header:\n self.assertEqual(input_header['RG'], output_header['RG'])\n\n # Check HD header preserved\n if 'HD' in input_header:\n self.assertEqual(dict(input_header['HD']), dict(output_header['HD']))\n\n def test_filter_bam_by_ids_empty_input(self):\n \"\"\"Test filter_bam_by_ids handles empty input BAM.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n output_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n store.extend(['read1', 'read2'])\n store.filter_bam_by_ids(input_bam, output_bam, include=True)\n\n self.assertEqual(samtools.count(output_bam), 0)\n\n def test_filter_bam_by_ids_empty_store_include(self):\n \"\"\"Test include mode with empty store produces empty BAM with header.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n # Empty store\n store.filter_bam_by_ids(input_bam, output_bam, include=True)\n\n # Output should have 0 reads\n self.assertEqual(samtools.count(output_bam), 0)\n\n # But should have valid header\n with pysam.AlignmentFile(output_bam, 'rb', check_sq=False) as bam:\n self.assertIsNotNone(bam.header)\n\n def test_filter_bam_by_ids_empty_store_exclude(self):\n \"\"\"Test exclude mode with empty store keeps all reads.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n input_count = samtools.count(input_bam)\n\n db_path = viral_ngs.core.file.mkstempfname('.db')\n with viral_ngs.read_utils.ReadIdStore(db_path) as store:\n # Empty store\n store.filter_bam_by_ids(input_bam, output_bam, include=False)\n\n # Output should have all input reads\n self.assertEqual(samtools.count(output_bam), input_count)\n\n\nclass TestRmdupBbnorm(TestCaseWithTmp):\n \"\"\"Tests for rmdup_bbnorm_bam using BBNorm for deduplication/normalization.\"\"\"\n\n def setUp(self):\n super(TestRmdupBbnorm, self).setUp()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_bbnorm_canned_input(self):\n \"\"\"Test rmdup_bbnorm_bam with standard paired-end input.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n\n # Use low memory and single thread for CI compatibility\n viral_ngs.read_utils.rmdup_bbnorm_bam(input_bam, output_bam, threads=1, memory='250m')\n\n # Output should have reads and be <= input count\n input_count = self.samtools.count(input_bam)\n output_count = self.samtools.count(output_bam)\n self.assertGreater(output_count, 0)\n self.assertLessEqual(output_count, input_count)\n\n def test_bbnorm_empty_input(self):\n \"\"\"Test rmdup_bbnorm_bam handles empty BAM.\"\"\"\n empty_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n\n # Empty input doesn't call bbnorm, so no need for memory/threads\n viral_ngs.read_utils.rmdup_bbnorm_bam(empty_bam, output_bam)\n\n self.assertEqual(self.samtools.count(output_bam), 0)\n\n def test_bbnorm_multi_library(self):\n \"\"\"Test rmdup_bbnorm_bam with multiple libraries/read groups.\"\"\"\n # G5012.3.testreads.bam has 18710 reads, 12 RGs, 2 libraries\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n\n # Use low memory and single thread for CI compatibility\n viral_ngs.read_utils.rmdup_bbnorm_bam(input_bam, output_bam, threads=1, memory='250m')\n\n # Output should have reads\n input_count = self.samtools.count(input_bam)\n output_count = self.samtools.count(output_bam)\n self.assertGreater(output_count, 0)\n self.assertLessEqual(output_count, input_count)\n\n def test_bbnorm_single_end(self):\n \"\"\"Test rmdup_bbnorm_bam with single-end reads.\"\"\"\n # in.2libs3rgs.bam has 2850 single-end reads\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestPerSample', 'in.2libs3rgs.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n\n # Use low memory and single thread for CI compatibility\n viral_ngs.read_utils.rmdup_bbnorm_bam(input_bam, output_bam, threads=1, memory='250m')\n\n # Output should have reads\n input_count = self.samtools.count(input_bam)\n output_count = self.samtools.count(output_bam)\n self.assertGreater(output_count, 0)\n self.assertLessEqual(output_count, input_count)\n\n def test_bbnorm_min_input_reads_skip(self):\n \"\"\"Test that min_input_reads skips processing when below threshold.\"\"\"\n # input.bam has 1794 reads, set threshold to 2000\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n\n # min_input_reads causes skip, so bbnorm isn't called\n viral_ngs.read_utils.rmdup_bbnorm_bam(input_bam, output_bam, min_input_reads=2000)\n\n # Output should equal input (copied, not processed)\n input_count = self.samtools.count(input_bam)\n output_count = self.samtools.count(output_bam)\n self.assertEqual(output_count, input_count)\n\n def test_bbnorm_min_input_reads_process(self):\n \"\"\"Test that min_input_reads processes when above threshold.\"\"\"\n # input.bam has 1794 reads, set threshold to 1000\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n\n # Use low memory and single thread for CI compatibility\n viral_ngs.read_utils.rmdup_bbnorm_bam(input_bam, output_bam, min_input_reads=1000,\n threads=1, memory='250m')\n\n # Output should have reads (processing occurred)\n input_count = self.samtools.count(input_bam)\n output_count = self.samtools.count(output_bam)\n self.assertGreater(output_count, 0)\n self.assertLessEqual(output_count, input_count)\n\n def test_bbnorm_max_output_reads_downsample(self):\n \"\"\"Test that max_output_reads downsamples the keep-list.\"\"\"\n input_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n output_bam = viral_ngs.core.file.mkstempfname(\"output.bam\")\n\n # Set max_output_reads to 500 (less than expected bbnorm output)\n # Use low memory and single thread for CI compatibility\n max_output_reads = 500\n viral_ngs.read_utils.rmdup_bbnorm_bam(input_bam, output_bam, max_output_reads=max_output_reads,\n threads=1, memory='250m')\n\n # Output should be approximately max_output_reads (tolerance for pairs)\n output_count = self.samtools.count(output_bam)\n # For paired reads, we downsample read IDs, so output is ~2x the ID count\n # Allow some tolerance over exactly 2x\n expected_max_reads = max_output_reads * 2 + 100 # IDs * 2 reads/pair + tolerance\n self.assertLessEqual(output_count, expected_max_reads)\n\n\n@unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\nclass TestMvicuna(TestCaseWithTmp):\n \"\"\"\n Input consists of 3 read pairs.\n Second read pair is identical to first.\n Third read pair has same 5' read as first, but different 3' read.\n What Mvicuna did was create paired output files in which the 2nd read\n was deleted. It created an empty unpaired output file. Although\n it initially created the postDupRm pair, it renamed them to the output\n pair.\n [IJ:]I have no idea if this is the correct behavior, but test checks that it\n doesn't change.\n \"\"\"\n\n def test_mvicuna(self):\n tempDir = tempfile.mkdtemp()\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n\n # Run mvicuna\n inFastq1 = os.path.join(myInputDir, 'in.1.fastq')\n inFastq2 = os.path.join(myInputDir, 'in.2.fastq')\n pairedOutFastq1 = os.path.join(tempDir, 'pairedOut.1.fastq')\n pairedOutFastq2 = os.path.join(tempDir, 'pairedOut.2.fastq')\n unpairedOutFastq = os.path.join(tempDir, 'unpairedOut.fastq')\n viral_ngs.core.mvicuna.MvicunaTool().rmdup(\n (inFastq1, inFastq2), (pairedOutFastq1, pairedOutFastq2),\n outUnpaired=unpairedOutFastq)\n\n # Compare to expected\n for filename in ['pairedOut.1.fastq', 'pairedOut.2.fastq', 'unpairedOut.fastq']:\n self.assertEqualContents(os.path.join(tempDir, filename), os.path.join(myInputDir, 'expected_' + filename))\n\n\n\nclass TestAlignAndFix(TestCaseWithTmp):\n def setUp(self):\n super(TestAlignAndFix, self).setUp()\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebov-makona.fasta')\n self.refFasta = viral_ngs.core.file.mkstempfname('.ref.fasta')\n shutil.copyfile(orig_ref, self.refFasta)\n\n @unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\n def test_novoalign(self):\n self.simple_execution('novoalign')\n\n def test_bwa(self):\n self.simple_execution('bwa')\n\n def test_minimap2(self):\n self.simple_execution('minimap2')\n\n def simple_execution(self, aligner):\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBamAll = viral_ngs.core.file.mkstempfname('.outBamAll.bam')\n outBamFiltered = viral_ngs.core.file.mkstempfname('.outBamFiltered.bam')\n\n args = viral_ngs.read_utils.parser_align_and_fix(argparse.ArgumentParser()).parse_args(\n [inBam, self.refFasta, '--outBamAll', outBamAll, '--outBamFiltered', outBamFiltered, '--aligner', aligner])\n args.func_main(args)\n\n def test_empty_reads(self):\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n args = viral_ngs.read_utils.parser_align_and_fix(argparse.ArgumentParser()).parse_args(\n [inBam, self.refFasta, '--aligner', 'minimap2',\n '--outBamAll', viral_ngs.core.file.mkstempfname('.outBamAll.bam'),\n '--outBamFiltered', viral_ngs.core.file.mkstempfname('.outBamFiltered.bam')])\n args.func_main(args)\n\n def test_dup_marker_sambamba(self):\n \"\"\"Test using sambamba for duplicate marking\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBamAll = viral_ngs.core.file.mkstempfname('.outBamAll.bam')\n\n args = viral_ngs.read_utils.parser_align_and_fix(argparse.ArgumentParser()).parse_args(\n [inBam, self.refFasta, '--outBamAll', outBamAll,\n '--aligner', 'minimap2', '--dupMarker', 'sambamba'])\n args.func_main(args)\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.assertTrue(os.path.exists(outBamAll))\n self.assertFalse(samtools.isEmpty(outBamAll))\n\n def test_dup_marker_picard_explicit(self):\n \"\"\"Test explicitly using Picard for duplicate marking\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBamAll = viral_ngs.core.file.mkstempfname('.outBamAll.bam')\n\n args = viral_ngs.read_utils.parser_align_and_fix(argparse.ArgumentParser()).parse_args(\n [inBam, self.refFasta, '--outBamAll', outBamAll,\n '--aligner', 'minimap2', '--dupMarker', 'picard'])\n args.func_main(args)\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.assertTrue(os.path.exists(outBamAll))\n self.assertFalse(samtools.isEmpty(outBamAll))\n\n def test_dup_marker_default_is_sambamba(self):\n \"\"\"Verify default duplicate marker is sambamba\"\"\"\n parser = viral_ngs.read_utils.parser_align_and_fix(argparse.ArgumentParser())\n args = parser.parse_args(['in.bam', 'ref.fasta'])\n self.assertEqual(args.dup_marker, 'sambamba')\n\n def test_align_and_fix_full_sambamba_pipeline(self):\n \"\"\"End-to-end test with sambamba for markdup and indexing\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBamAll = viral_ngs.core.file.mkstempfname('.outBamAll.bam')\n outBamFiltered = viral_ngs.core.file.mkstempfname('.outBamFiltered.bam')\n\n args = viral_ngs.read_utils.parser_align_and_fix(argparse.ArgumentParser()).parse_args(\n [inBam, self.refFasta, '--outBamAll', outBamAll, '--outBamFiltered', outBamFiltered,\n '--aligner', 'minimap2', '--dupMarker', 'sambamba'])\n args.func_main(args)\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.assertTrue(os.path.exists(outBamAll))\n self.assertTrue(os.path.exists(outBamFiltered))\n self.assertFalse(samtools.isEmpty(outBamAll))\n # Verify index files exist\n self.assertTrue(os.path.exists(outBamAll + '.bai') or os.path.exists(outBamAll.replace('.bam', '.bai')))\n\n\nclass TestDownsampleBams(TestCaseWithTmp):\n def setUp(self):\n super(TestDownsampleBams, self).setUp()\n orig_larger_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n orig_smaller_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.mini.bam')\n orig_with_dup = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned','input.bam')\n self.larger_bam = viral_ngs.core.file.mkstempfname('.larger.bam')\n self.smaller_bam = viral_ngs.core.file.mkstempfname('.smaller.bam')\n self.with_dups = viral_ngs.core.file.mkstempfname('.with_dups.bam')\n shutil.copyfile(orig_larger_bam, self.larger_bam)\n shutil.copyfile(orig_smaller_bam, self.smaller_bam)\n shutil.copyfile(orig_with_dup, self.with_dups)\n\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_normalization_to_lowest_cardinality(self):\n \"\"\" Also tests subdir output \"\"\"\n temp_dir = tempfile.mkdtemp()\n\n target_count = self.samtools.count(self.smaller_bam)\n # target count not passed in since we are checking that the count of the smaller file is used\n viral_ngs.read_utils.main_downsample_bams([self.larger_bam, self.smaller_bam], temp_dir, JVMmemory=\"1g\")\n\n output_bams = list(glob.glob(os.path.join(temp_dir, '*.bam')))\n \n self.assertGreater(len(output_bams), 0, msg=\"No output found\")\n for out_bam in output_bams:\n self.assertAlmostEqual(self.samtools.count(out_bam), target_count, delta=10, msg=\"{} not downsampled to the target size: {}\".format(os.path.basename(out_bam),target_count))\n\n def test_downsample_to_target_count(self):\n \"\"\" Also tests subdir output \"\"\"\n temp_dir = tempfile.mkdtemp()\n\n target_count = 4000\n viral_ngs.read_utils.main_downsample_bams([self.larger_bam, self.smaller_bam], temp_dir, specified_read_count=target_count, JVMmemory=\"1g\")\n\n output_bams = list(glob.glob(os.path.join(temp_dir, '*.bam')))\n \n self.assertGreater(len(output_bams), 0, msg=\"No output found\")\n for out_bam in output_bams:\n self.assertAlmostEqual(self.samtools.count(out_bam), target_count, delta=10, msg=\"{} not downsampled to the target size: {}\".format(os.path.basename(out_bam),target_count))\n\n def test_downsample_to_target_count_without_subdir(self):\n target_count = 4000\n viral_ngs.read_utils.main_downsample_bams([self.larger_bam], out_path=None, specified_read_count=target_count, JVMmemory=\"1g\")\n\n output_bams = list(glob.glob(os.path.join(os.path.dirname(self.larger_bam), '*downsampled-*.bam')))\n \n print(output_bams)\n self.assertGreater(len(output_bams), 0, msg=\"No output files matching *downsampled-*.bam found\")\n for out_bam in output_bams:\n self.assertAlmostEqual(self.samtools.count(out_bam), target_count, delta=10, msg=\"{} not downsampled to the target size: {}\".format(os.path.basename(out_bam),target_count))\n\n @unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\n def test_downsample_with_dedup_after(self):\n \"\"\" Also tests subdir output \"\"\"\n temp_dir = tempfile.mkdtemp()\n\n target_count = 1500\n viral_ngs.read_utils.main_downsample_bams([self.with_dups], temp_dir, deduplicate_after=True, specified_read_count=target_count, JVMmemory=\"1g\")\n\n output_bams = list(glob.glob(os.path.join(temp_dir, '*.bam')))\n \n self.assertGreater(len(output_bams), 0, msg=\"No output found\")\n for out_bam in output_bams:\n self.assertLess(self.samtools.count(out_bam), target_count, msg=\"{} not downsampled to the target size: {}\".format(os.path.basename(out_bam),target_count))\n\n @unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\n def test_downsample_with_dedup_before(self):\n \"\"\" Also tests subdir output \"\"\"\n temp_dir = tempfile.mkdtemp()\n\n target_count = 1500\n viral_ngs.read_utils.main_downsample_bams([self.with_dups], temp_dir, deduplicate_before=True, specified_read_count=target_count, JVMmemory=\"1g\")\n\n output_bams = list(glob.glob(os.path.join(temp_dir, '*.bam')))\n \n self.assertGreater(len(output_bams), 0, msg=\"No output found\")\n for out_bam in output_bams:\n self.assertAlmostEqual(self.samtools.count(out_bam), target_count, delta=10, msg=\"{} not downsampled to the target size: {}\".format(os.path.basename(out_bam),target_count))\n\n def test_downsample_to_too_large_target_count(self):\n \"\"\" Should fail \"\"\"\n temp_dir = tempfile.mkdtemp()\n\n target_count = 20000\n\n with self.assertRaises(ValueError):\n viral_ngs.read_utils.main_downsample_bams([self.larger_bam, self.smaller_bam], temp_dir, specified_read_count=target_count, JVMmemory=\"1g\")\n\n\nclass TestTrimRmdupSubsamp(TestCaseWithTmp):\n '''Test the trim_rmdup_subsamp command.\n\n Tests ported from viral-assemble/test/unit/test_assembly.py.\n Uses threads=1 to avoid overwhelming CI runners during parallel test execution.\n '''\n\n def test_subsamp_empty(self):\n \"\"\"Test with empty BAM input - should return all zeros.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path()\n inBam = os.path.join(inDir, 'empty.bam')\n clipDb = os.path.join(inDir, 'TestTrimRmdupSubsamp', 'clipDb.fasta')\n outBam = viral_ngs.core.file.mkstempfname('.out.bam')\n read_stats = viral_ngs.read_utils.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=10, threads=1)\n os.unlink(outBam)\n self.assertEqual(read_stats, (0, 0, 0, 0, 0, 0))\n\n def test_subsamp_small_50(self):\n \"\"\"Test subsampling to 50 reads from small input.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path()\n inBam = os.path.join(inDir, 'G5012.3.subset.bam')\n clipDb = os.path.join(inDir, 'TestTrimRmdupSubsamp', 'clipDb.fasta')\n outBam = viral_ngs.core.file.mkstempfname('.out.bam')\n read_stats = viral_ngs.read_utils.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=50, threads=1)\n os.unlink(outBam)\n self.assertEqual(read_stats, (200, 172, 172, 50, 50, 0))\n\n def test_subsamp_small_90(self):\n \"\"\"Test subsampling to 90 reads.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path()\n inBam = os.path.join(inDir, 'G5012.3.subset.bam')\n clipDb = os.path.join(inDir, 'TestTrimRmdupSubsamp', 'clipDb.fasta')\n outBam = viral_ngs.core.file.mkstempfname('.out.bam')\n read_stats = viral_ngs.read_utils.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=90, threads=1)\n os.unlink(outBam)\n # counts are individual reads\n self.assertEqual(read_stats, (200, 172, 172, 90, 90, 0))\n\n def test_subsamp_small_200(self):\n \"\"\"Test where unpaired reads are needed to reach threshold.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path()\n inBam = os.path.join(inDir, 'G5012.3.subset.bam')\n clipDb = os.path.join(inDir, 'TestTrimRmdupSubsamp', 'clipDb.fasta')\n outBam = viral_ngs.core.file.mkstempfname('.out.bam')\n read_stats = viral_ngs.read_utils.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=200, threads=1)\n os.unlink(outBam)\n self.assertEqual(read_stats, (200, 172, 172, 185, 172, 13))\n\n def test_subsamp_big_500(self):\n \"\"\"Test with larger input file.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path()\n inBam = os.path.join(inDir, 'G5012.3.testreads.bam')\n clipDb = os.path.join(inDir, 'TestTrimRmdupSubsamp', 'clipDb.fasta')\n outBam = viral_ngs.core.file.mkstempfname('.out.bam')\n read_stats = viral_ngs.read_utils.trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=500, threads=1)\n os.unlink(outBam)\n self.assertEqual(read_stats, (18710, 16310, 16310, 500, 500, 0))\n" }, { "path": "tests/unit/core/test_tools.py", "content": "# Unit tests for tool installation\n\n__author__ = \"yesimon@broadinstitute.org\"\n\nimport platform\nimport pytest\nimport viral_ngs.core\n\n# Platform detection for x86-only tools\nIS_ARM = platform.machine() in ('arm64', 'aarch64')\n\n# Tool class names that require x86-only bioconda packages\nX86_ONLY_TOOLS = {'NovoalignTool', 'MvicunaTool'}\n\n\n# Simply do nothing to override stub_conda in conftest.py\n@pytest.fixture(autouse=True)\ndef stub_conda():\n pass\n\n\n@pytest.fixture(params=viral_ngs.core.all_tool_classes())\ndef tool_class(request):\n return request.param\n\n\ndef test_tool_install(tool_class):\n if IS_ARM and tool_class.__name__ in X86_ONLY_TOOLS:\n pytest.skip(f\"{tool_class.__name__} requires x86-only bioconda package (not available on ARM)\")\n t = tool_class()\n t.install()\n assert t.is_installed()\n" }, { "path": "tests/unit/core/test_tools_bbmap.py", "content": "# Unit tests for bbmap aligner and related tools\n\n__author__ = \"ilya@broadinstitute.org\"\n\nimport unittest\nimport os.path\nimport shutil\nimport viral_ngs.core\nimport viral_ngs.core.bbmap\nimport viral_ngs.core.samtools\nimport pysam\nfrom tests import TestCaseWithTmp, assert_md5_equal_to_line_in_file\n\n\nclass TestToolBBMap(TestCaseWithTmp):\n\n def setUp(self):\n super(TestToolBBMap, self).setUp()\n self.bbmap = viral_ngs.core.bbmap.BBMapTool()\n self.bbmap.install()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_align(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebola.fasta')\n inRef = viral_ngs.core.file.mkstempfname('.fasta')\n shutil.copyfile(orig_ref, inRef)\n reads = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'ebov_reads.bam')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n # Use conservative memory and single thread for CI compatibility\n # BBMap alignment needs more memory than bbnorm for index building\n self.bbmap.align(inBam=reads, refFasta=inRef, outBam=outBam,\n threads=1, Xmx='1g')\n self.assertTrue(os.path.isfile(outBam))\n self.assertTrue(os.path.getsize(outBam))\n\n def test_bbnorm_paired_interleaved(self):\n \"\"\"Test bbnorm on paired-end interleaved FASTQ file.\"\"\"\n # Create interleaved FASTQ from TestRmdupUnaligned BAM\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestRmdupUnaligned', 'input.bam')\n inFastq = viral_ngs.core.file.mkstempfname('.fastq')\n outFastq = viral_ngs.core.file.mkstempfname('.fastq')\n\n # Convert BAM to interleaved FASTQ\n self.samtools.bam2fq(inBam, inFastq)\n self.assertGreater(os.path.getsize(inFastq), 0)\n\n # Count input reads\n with open(inFastq, 'rt') as f:\n input_lines = sum(1 for _ in f)\n input_reads = input_lines // 4\n\n # Run bbnorm (auto-detects interleaved format)\n # Use low memory and single thread for CI compatibility\n with viral_ngs.core.file.tmp_dir('_bbnorm_test') as tmpdir:\n self.bbmap.bbnorm(inFastq, outFastq, tmpdir=tmpdir, target=50,\n threads=1, memory='250m')\n\n # Verify output exists and has reads\n self.assertTrue(os.path.isfile(outFastq))\n self.assertGreater(os.path.getsize(outFastq), 0)\n\n # Count output reads\n with open(outFastq, 'rt') as f:\n output_lines = sum(1 for _ in f)\n output_reads = output_lines // 4\n\n # Output should have reads and be <= input\n self.assertGreater(output_reads, 0)\n self.assertLessEqual(output_reads, input_reads)\n\n def test_bbnorm_single_end(self):\n \"\"\"Test bbnorm on single-end FASTQ file.\"\"\"\n # Create single-end FASTQ from TestPerSample/in.2libs3rgs.bam\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestPerSample', 'in.2libs3rgs.bam')\n inFastq = viral_ngs.core.file.mkstempfname('.fastq')\n outFastq = viral_ngs.core.file.mkstempfname('.fastq')\n\n # Convert BAM to FASTQ (single-end)\n self.samtools.bam2fq(inBam, inFastq)\n self.assertGreater(os.path.getsize(inFastq), 0)\n\n # Count input reads\n with open(inFastq, 'rt') as f:\n input_lines = sum(1 for _ in f)\n input_reads = input_lines // 4\n\n # Run bbnorm (auto-detects single-end format)\n # Use low memory and single thread for CI compatibility\n with viral_ngs.core.file.tmp_dir('_bbnorm_test') as tmpdir:\n self.bbmap.bbnorm(inFastq, outFastq, tmpdir=tmpdir, target=50,\n threads=1, memory='250m')\n\n # Verify output exists and has reads\n self.assertTrue(os.path.isfile(outFastq))\n self.assertGreater(os.path.getsize(outFastq), 0)\n\n # Count output reads\n with open(outFastq, 'rt') as f:\n output_lines = sum(1 for _ in f)\n output_reads = output_lines // 4\n\n # Output should have reads and be <= input\n self.assertGreater(output_reads, 0)\n self.assertLessEqual(output_reads, input_reads)\n" }, { "path": "tests/unit/core/test_tools_bwa.py", "content": "# Unit tests for bwa aligner\n\n__author__ = \"tomkinsc@broadinstitute.org\"\n\nimport os.path\nimport tempfile\nimport subprocess\nimport viral_ngs.core\nimport viral_ngs.core.bwa\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp\n\nclass TestToolBwa(TestCaseWithTmp):\n\n def setUp(self):\n super(TestToolBwa, self).setUp()\n self.bwa = viral_ngs.core.bwa.Bwa()\n self.bwa.install()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n self.tempDir = tempfile.mkdtemp()\n root_input_dir = viral_ngs.core.file.get_test_input_path()\n ref_fasta = os.path.join(root_input_dir, '5kb_human_from_chr6.fasta')\n\n self.database_prefix_path = os.path.join(self.tempDir, \"5kb_human_from_chr6\")\n\n # create bwa db\n self.bwadb_path = self.bwa.index(ref_fasta, output=self.database_prefix_path)\n\n def test_working_bam(self):\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), \"TestDepleteHuman\", 'test-reads-human.bam')\n\n outfile = viral_ngs.core.file.mkstempfname('.bam')\n self.bwa.mem(in_bam, self.bwadb_path, outfile, options=['-a'])\n\n self.assertEqual(self.samtools.count(outfile), 20)\n\n os.unlink(outfile)\n\n def test_corrupt_bam(self):\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'broken.bam')\n\n outfile = viral_ngs.core.file.mkstempfname('.bam')\n\n # pipe.poll() should raise an exception\n self.assertRaises(subprocess.CalledProcessError, self.bwa.mem, in_bam, self.bwadb_path, outfile, options=['-a'])\n\n os.unlink(outfile)\n" }, { "path": "tests/unit/core/test_tools_fastqc.py", "content": "# Unit tests for viral_ngs.core.fastqc\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport os\nimport zipfile\nfrom html.parser import HTMLParser\nimport viral_ngs.core\nimport viral_ngs.core.fastqc\nfrom tests import TestCaseWithTmp\n\n\nclass HTMLValidator(HTMLParser):\n \"\"\"Simple HTML validator to check if HTML can be parsed without errors\"\"\"\n def __init__(self):\n super().__init__()\n self.valid = True\n self.error_msg = None\n\n def error(self, message):\n self.valid = False\n self.error_msg = message\n\n\nclass TestToolFastQC(TestCaseWithTmp):\n\n def _validate_html(self, html_path):\n \"\"\"Validate that a file contains parseable HTML\"\"\"\n with open(html_path, 'rt') as f:\n html_content = f.read()\n\n parser = HTMLValidator()\n try:\n parser.feed(html_content)\n self.assertTrue(parser.valid, f\"HTML parsing failed: {parser.error_msg}\")\n except Exception as e:\n self.fail(f\"HTML parsing raised exception: {e}\")\n\n def _validate_zip(self, zip_path):\n \"\"\"Validate that a file is a valid zip archive\"\"\"\n try:\n with zipfile.ZipFile(zip_path, 'r') as zf:\n # testzip() returns None if the archive is valid\n result = zf.testzip()\n self.assertIsNone(result, f\"ZIP validation failed: {result}\")\n except zipfile.BadZipFile as e:\n self.fail(f\"Invalid ZIP file: {e}\")\n\n def test_fastqc_nonempty_bam(self):\n \"\"\"Test FastQC on a non-empty BAM file\"\"\"\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n out_html = viral_ngs.core.file.mkstempfname('.html')\n out_zip = viral_ngs.core.file.mkstempfname('.zip')\n\n fastqc = viral_ngs.core.fastqc.FastQC()\n fastqc.execute(in_bam, out_html, out_zip=out_zip)\n\n # Verify HTML file is created and non-empty\n self.assertTrue(os.path.exists(out_html), \"HTML output file should exist\")\n self.assertGreater(os.path.getsize(out_html), 0, \"HTML file should not be empty\")\n\n # Validate HTML is parseable\n self._validate_html(out_html)\n\n # Verify ZIP file is created and is valid\n self.assertTrue(os.path.exists(out_zip), \"ZIP output file should exist\")\n self.assertGreater(os.path.getsize(out_zip), 0, \"ZIP file should not be empty\")\n\n # Validate ZIP file\n self._validate_zip(out_zip)\n\n # Verify ZIP contains FastQC output files\n with zipfile.ZipFile(out_zip, 'r') as zf:\n namelist = zf.namelist()\n self.assertGreater(len(namelist), 0, \"ZIP should contain FastQC output files\")\n\n def test_fastqc_empty_bam(self):\n \"\"\"Test FastQC on an empty BAM file (zero reads)\"\"\"\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n out_html = viral_ngs.core.file.mkstempfname('.html')\n out_zip = viral_ngs.core.file.mkstempfname('.zip')\n\n fastqc = viral_ngs.core.fastqc.FastQC()\n fastqc.execute(in_bam, out_html, out_zip=out_zip)\n\n # Verify HTML file is created and non-empty\n self.assertTrue(os.path.exists(out_html), \"HTML output file should exist\")\n self.assertGreater(os.path.getsize(out_html), 0, \"HTML file should not be empty\")\n\n # Validate HTML is parseable\n self._validate_html(out_html)\n\n # Verify HTML contains expected message about empty input\n with open(out_html, 'rt') as f:\n html_content = f.read()\n self.assertIn('zero reads', html_content.lower(), \"HTML should mention zero reads\")\n\n # Verify ZIP file is created and is a valid (empty) zip\n self.assertTrue(os.path.exists(out_zip), \"ZIP output file should exist\")\n\n # A valid empty zip file should be 22 bytes (zip structure overhead)\n self.assertEqual(os.path.getsize(out_zip), 22, \"Empty ZIP should be 22 bytes (valid zip structure)\")\n\n # Validate ZIP file\n self._validate_zip(out_zip)\n\n # Verify ZIP has no files (empty)\n with zipfile.ZipFile(out_zip, 'r') as zf:\n namelist = zf.namelist()\n self.assertEqual(len(namelist), 0, \"Empty BAM should produce empty ZIP (0 files)\")\n\n def test_fastqc_without_zip(self):\n \"\"\"Test FastQC when --out_zip is not specified\"\"\"\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n out_html = viral_ngs.core.file.mkstempfname('.html')\n\n fastqc = viral_ngs.core.fastqc.FastQC()\n fastqc.execute(in_bam, out_html, out_zip=None)\n\n # Verify HTML file is created\n self.assertTrue(os.path.exists(out_html), \"HTML output file should exist\")\n self.assertGreater(os.path.getsize(out_html), 0, \"HTML file should not be empty\")\n\n # Validate HTML is parseable\n self._validate_html(out_html)\n" }, { "path": "tests/unit/core/test_tools_minimap2.py", "content": "# Unit tests for minimap2 aligner\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport os\nimport os.path\nimport shutil\nimport tempfile\nimport subprocess\nimport viral_ngs.core\nimport viral_ngs.core.minimap2\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp\n\nclass TestToolMinimap2(TestCaseWithTmp):\n\n def setUp(self):\n super(TestToolMinimap2, self).setUp()\n self.mm2 = viral_ngs.core.minimap2.Minimap2()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.tempDir = tempfile.mkdtemp()\n root_input_dir = viral_ngs.core.file.get_test_input_path()\n self.ref_fasta = os.path.join(root_input_dir, '5kb_human_from_chr6.fasta')\n\n def test_human_bam(self):\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), \"TestDepleteHuman\", 'test-reads-human.bam')\n with viral_ngs.core.file.tempfname('.bam') as outfile:\n self.mm2.align_bam(in_bam, self.ref_fasta, outfile, options=['-x', 'sr'])\n self.assertEqual(self.samtools.count(outfile), 20)\n\n def test_ebola_bam(self):\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n ref_fasta = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebov-makona.fasta')\n with viral_ngs.core.file.tempfname('.bam') as outfile:\n self.mm2.align_bam(in_bam, ref_fasta, outfile)\n self.assertEqual(self.samtools.count(outfile), 18843)\n\n def test_corrupt_bam(self):\n # pipe.poll() should raise an exception\n in_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'broken.bam')\n with viral_ngs.core.file.tempfname('.bam') as outfile:\n self.assertRaises(subprocess.CalledProcessError, self.mm2.align_bam, in_bam, self.ref_fasta, outfile)\n\n\nclass TestMinimap2Idxstats(TestCaseWithTmp):\n \"\"\"Tests for the Minimap2.idxstats() method - PAF-based read counting.\"\"\"\n\n def setUp(self):\n super(TestMinimap2Idxstats, self).setUp()\n self.mm2 = viral_ngs.core.minimap2.Minimap2()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.tempDir = tempfile.mkdtemp()\n self.root_input_dir = viral_ngs.core.file.get_test_input_path()\n\n def test_idxstats_basic(self):\n \"\"\"Basic functionality: single reference, verify idxstats format and counts.\"\"\"\n in_bam = os.path.join(self.root_input_dir, 'G5012.3.testreads.bam')\n ref_fasta = os.path.join(self.root_input_dir, 'ebov-makona.fasta')\n\n with viral_ngs.core.file.tempfname('.idxstats.txt') as out_stats:\n self.mm2.idxstats(in_bam, ref_fasta, out_stats)\n\n # Verify file exists and has content\n self.assertTrue(os.path.isfile(out_stats))\n self.assertGreater(os.path.getsize(out_stats), 0)\n\n # Parse and validate idxstats format\n with open(out_stats, 'rt') as f:\n lines = [line.strip().split('\\t') for line in f if line.strip()]\n\n # Should have at least one line (the reference sequence)\n self.assertGreater(len(lines), 0)\n\n # Each line should have 4 tab-separated columns\n for line in lines:\n self.assertEqual(len(line), 4, f\"Expected 4 columns, got {len(line)}: {line}\")\n\n # First line should be the reference: name, length, mapped, unmapped\n ref_name, ref_len, mapped_count, unmapped_count = lines[0]\n self.assertEqual(ref_name, 'KJ660346.2') # ebov-makona reference name\n self.assertGreater(int(ref_len), 0)\n self.assertGreater(int(mapped_count), 18000) # Should be close to 18843\n self.assertEqual(int(unmapped_count), 0) # Always 0 in our implementation\n\n def test_idxstats_with_readlist(self):\n \"\"\"Test optional read list output.\"\"\"\n in_bam = os.path.join(self.root_input_dir, 'G5012.3.testreads.bam')\n ref_fasta = os.path.join(self.root_input_dir, 'ebov-makona.fasta')\n\n with viral_ngs.core.file.tempfname('.idxstats.txt') as out_stats:\n with viral_ngs.core.file.tempfname('.readlist.txt') as out_readlist:\n self.mm2.idxstats(in_bam, ref_fasta, out_stats, outReadlist=out_readlist)\n\n # Verify read list file is created\n self.assertTrue(os.path.isfile(out_readlist))\n self.assertGreater(os.path.getsize(out_readlist), 0)\n\n # Parse read list\n with open(out_readlist, 'rt') as f:\n read_ids = [line.strip() for line in f if line.strip()]\n\n # Should have reads\n self.assertGreater(len(read_ids), 0)\n\n # All read IDs should be unique\n self.assertEqual(len(read_ids), len(set(read_ids)),\n \"Read list should contain unique read IDs only\")\n\n # Verify stats count (counts R1 + R2 separately, like samtools idxstats)\n with open(out_stats, 'rt') as f:\n first_line = f.readline().strip().split('\\t')\n mapped_count = int(first_line[2])\n self.assertGreater(mapped_count, 18000)\n\n # Readlist contains unique read pairs (~half of mapped count for paired-end data)\n self.assertGreater(len(read_ids), 9000)\n\n def test_idxstats_no_readlist(self):\n \"\"\"Test that readlist output can be skipped (outReadlist=None).\"\"\"\n in_bam = os.path.join(self.root_input_dir, 'G5012.3.testreads.bam')\n ref_fasta = os.path.join(self.root_input_dir, 'ebov-makona.fasta')\n\n with viral_ngs.core.file.tempfname('.idxstats.txt') as out_stats:\n # Call without readlist\n self.mm2.idxstats(in_bam, ref_fasta, out_stats, outReadlist=None)\n\n # idxstats should still work\n self.assertTrue(os.path.isfile(out_stats))\n with open(out_stats, 'rt') as f:\n lines = [line.strip().split('\\t') for line in f if line.strip()]\n self.assertGreater(len(lines), 0)\n\n def test_idxstats_empty_input(self):\n \"\"\"Edge case: empty BAM input should produce zero counts.\"\"\"\n in_bam = os.path.join(self.root_input_dir, 'empty.bam')\n ref_fasta = os.path.join(self.root_input_dir, 'ebov-makona.fasta')\n\n with viral_ngs.core.file.tempfname('.idxstats.txt') as out_stats:\n self.mm2.idxstats(in_bam, ref_fasta, out_stats)\n\n # Should have output with zero counts\n self.assertTrue(os.path.isfile(out_stats))\n with open(out_stats, 'rt') as f:\n lines = [line.strip().split('\\t') for line in f if line.strip()]\n\n # Reference should be listed but with 0 mapped count\n self.assertEqual(len(lines), 1)\n ref_name, ref_len, mapped_count, unmapped_count = lines[0]\n self.assertEqual(int(mapped_count), 0)\n\n def test_idxstats_empty_reference(self):\n \"\"\"Edge case: empty FASTA reference should handle gracefully.\"\"\"\n in_bam = os.path.join(self.root_input_dir, 'G5012.3.testreads.bam')\n ref_fasta = os.path.join(self.root_input_dir, 'empty.fasta')\n\n with viral_ngs.core.file.tempfname('.idxstats.txt') as out_stats:\n self.mm2.idxstats(in_bam, ref_fasta, out_stats)\n\n # Should produce empty output (no references = no lines)\n self.assertTrue(os.path.isfile(out_stats))\n with open(out_stats, 'rt') as f:\n lines = [line.strip() for line in f if line.strip()]\n self.assertEqual(len(lines), 0)\n\n def test_idxstats_multi_reference(self):\n \"\"\"Multi-reference: counts should be correctly separated per reference sequence.\"\"\"\n in_bam = os.path.join(self.root_input_dir, 'TestMinimap2Idxstats', 'multi-viral-reads.bam')\n ref_fasta = os.path.join(self.root_input_dir, 'TestMinimap2Idxstats', 'multi-viral-refs.fasta')\n\n with viral_ngs.core.file.tempfname('.idxstats.txt') as out_stats:\n self.mm2.idxstats(in_bam, ref_fasta, out_stats)\n\n # Parse output\n with open(out_stats, 'rt') as f:\n lines = [line.strip().split('\\t') for line in f if line.strip()]\n\n # Should have 4 references (HCV, Tomato mosaic, Poliovirus, Coxsackievirus)\n self.assertEqual(len(lines), 4)\n\n # Validate format for each line\n ref_names = []\n total_mapped = 0\n for line in lines:\n self.assertEqual(len(line), 4)\n ref_name, ref_len, mapped_count, unmapped_count = line\n ref_names.append(ref_name)\n self.assertGreater(int(ref_len), 0)\n self.assertGreaterEqual(int(mapped_count), 0)\n self.assertEqual(int(unmapped_count), 0)\n total_mapped += int(mapped_count)\n\n # Reference names should include our expected sequences\n expected_refs = ['EU255973.1', 'KJ207374.1', 'AY184220.1', 'KM609478.1']\n for expected in expected_refs:\n self.assertIn(expected, ref_names)\n" }, { "path": "tests/unit/core/test_tools_novoalign.py", "content": "# Unit tests for Novoalign aligner\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport os.path\nimport platform\nimport shutil\nimport viral_ngs.core\nimport viral_ngs.core.novoalign\nimport viral_ngs.core.samtools\nimport pysam\nfrom tests import TestCaseWithTmp, assert_md5_equal_to_line_in_file\n\n# Skip all tests on ARM platforms - novoalign is x86-only (no ARM64 builds in bioconda)\nIS_ARM = platform.machine() in ('arm64', 'aarch64')\nSKIP_X86_ONLY_REASON = \"novoalign requires x86-only bioconda package (not available on ARM)\"\n\n\n@unittest.skipIf(IS_ARM, SKIP_X86_ONLY_REASON)\nclass TestToolNovoalign(TestCaseWithTmp):\n\n def setUp(self):\n super(TestToolNovoalign, self).setUp()\n self.novoalign = viral_ngs.core.novoalign.NovoalignTool()\n self.novoalign.install()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_index(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebola.fasta')\n inRef = viral_ngs.core.file.mkstempfname('.fasta')\n shutil.copyfile(orig_ref, inRef)\n self.novoalign.index_fasta(inRef)\n outfile = inRef[:-6] + '.nix'\n\n self.assertTrue(os.path.isfile(outfile))\n self.assertTrue(os.path.getsize(outfile))\n\n def test_align(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebola.fasta')\n inRef = viral_ngs.core.file.mkstempfname('.fasta')\n shutil.copyfile(orig_ref, inRef)\n self.novoalign.index_fasta(inRef)\n reads = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'ebov_reads.bam')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n self.novoalign.execute(reads, inRef, outBam)\n self.assertTrue(os.path.isfile(outBam))\n self.assertTrue(os.path.getsize(outBam))\n self.assertTrue(os.path.isfile(outBam[:-1] + 'i'))\n\n def test_align_filter(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebola.fasta')\n inRef = viral_ngs.core.file.mkstempfname('.fasta')\n shutil.copyfile(orig_ref, inRef)\n self.novoalign.index_fasta(inRef)\n reads = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'ebov_reads.bam')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n self.novoalign.execute(reads, inRef, outBam, min_qual=1)\n self.assertTrue(os.path.isfile(outBam))\n self.assertTrue(os.path.getsize(outBam))\n self.assertTrue(os.path.isfile(outBam[:-1] + 'i'))\n\n def test_multi_read_groups(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.fasta')\n inRef = viral_ngs.core.file.mkstempfname('.fasta')\n shutil.copyfile(orig_ref, inRef)\n self.novoalign.index_fasta(inRef)\n\n # align with Novoalign (BAM input, BAM output)\n reads = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n self.novoalign.execute(reads, inRef, outBam)\n self.assertTrue(os.path.isfile(outBam))\n self.assertTrue(os.path.getsize(outBam))\n self.assertTrue(os.path.isfile(outBam[:-1] + 'i'))\n sam_in = viral_ngs.core.file.mkstempfname('.in.sam')\n sam_out = viral_ngs.core.file.mkstempfname('.out.sam')\n self.samtools.view([], reads, sam_in)\n self.samtools.view([], outBam, sam_out)\n\n # assert that all reads are present in output\n self.assertEqual(self.samtools.count(reads), self.samtools.count(outBam))\n\n # assert that all read groups are described exactly the same\n # in the output header (not necessarily same order, but same content)\n orig_rgs = self.samtools.getReadGroups(reads)\n new_rgs = self.samtools.getReadGroups(outBam)\n self.assertTrue(len(orig_rgs) > 1)\n self.assertTrue(len(new_rgs) > 1)\n for rgid in new_rgs.keys():\n self.assertIn(rgid, orig_rgs)\n orig_rg = orig_rgs[rgid]\n new_rg = new_rgs[rgid]\n if 'DT' in orig_rg and 'DT' in new_rg:\n # don't bother comparing the date because Novoalign seems\n # to enjoy doing senseless time zone conversions on the\n # ISO date string\n del orig_rg['DT']\n del new_rg['DT']\n self.assertEqual(orig_rgs[rgid], new_rgs[rgid])\n\n # if any RGs are missing, it should be because they were never really there\n for rgid in orig_rgs.keys():\n if rgid not in new_rgs:\n self.assertEqual(0, self.samtools.count(reads, ['-r', rgid]))\n\n # assert that all reads retained their original RG assignments\n read_to_rg = {}\n read_seen = set()\n with open(sam_in, 'rt') as inf:\n for read in inf:\n read = read.rstrip('\\n').split('\\t')\n tags = [t[5:] for t in read[11:] if t.startswith('RG:Z:')]\n self.assertTrue(len(tags) == 1)\n read_to_rg[read[0]] = tags[0]\n with open(sam_out, 'rt') as inf:\n for read in inf:\n read = read.rstrip('\\n').split('\\t')\n tags = [t[5:] for t in read[11:] if t.startswith('RG:Z:')]\n self.assertTrue(len(tags) == 1)\n self.assertIn(read[0], read_to_rg)\n self.assertEqual(tags[0], read_to_rg[read[0]])\n read_seen.add(read[0])\n self.assertEqual(len(read_seen), len(read_to_rg))\n\n # clean up\n for fn in (sam_in, sam_out, outBam, inRef):\n os.unlink(fn)\n\n def test_multi_read_groups_filter(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.fasta')\n inRef = viral_ngs.core.file.mkstempfname('.fasta')\n shutil.copyfile(orig_ref, inRef)\n self.novoalign.index_fasta(inRef)\n\n # align with Novoalign (BAM input, BAM output)\n reads = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n self.novoalign.execute(reads, inRef, outBam, min_qual=1)\n self.assertTrue(os.path.isfile(outBam))\n self.assertTrue(os.path.getsize(outBam))\n self.assertTrue(os.path.isfile(outBam[:-1] + 'i'))\n" }, { "path": "tests/unit/core/test_tools_picard.py", "content": "# Unit tests for tools.PicardTools\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport re\nimport os\nimport tempfile\nimport shutil\nimport viral_ngs.core\nimport viral_ngs.core\nimport viral_ngs.core\nimport viral_ngs.core.picard\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp\n\n\nclass TestToolPicard(TestCaseWithTmp):\n\n def test_fasta_index(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'in.fasta')\n expected_dict = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'in.dict')\n picard_index = viral_ngs.core.picard.CreateSequenceDictionaryTool()\n with open(expected_dict, 'rt') as inf:\n expected_first3 = [x.strip().split('\\t')[:3] for x in inf.readlines()]\n for ext in ('.fasta', '.fa'):\n inRef = viral_ngs.core.file.mkstempfname(ext)\n shutil.copyfile(orig_ref, inRef)\n outDict = inRef[:-len(ext)] + '.dict'\n\n picard_index.execute(inRef, overwrite=True)\n\n # the dict files will not be exactly the same, just the first 3 cols\n with open(outDict, 'rt') as inf:\n # .replace(\"VN:1.5\",\"VN:1.4\") ==> because the header version may be 1.[4|5|6]\n actual_first3 = [re.sub(r'VN:1\\.[4-6]','VN:1.4',x.strip()).split('\\t')[:3] for x in inf.readlines()]\n self.assertEqual(actual_first3, expected_first3)\n\n def test_messy_fasta_index(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'messy-headers.fasta')\n picard_index = viral_ngs.core.picard.CreateSequenceDictionaryTool()\n with viral_ngs.core.file.tempfname('.fasta') as inRef:\n shutil.copyfile(orig_ref, inRef)\n picard_index.execute(inRef, overwrite=True)\n with open(inRef[:-6] + '.dict', 'rt') as inf:\n seqnames = set()\n for line in inf:\n if line.startswith('@SQ'):\n seq_name = dict(x.split(':', maxsplit=1) for x in line.strip().split('\\t')[1:])['SN']\n # old versions of code cut this off at \"Influenza\"\n self.assertGreater(len(seq_name), 50)\n seqnames.add(seq_name)\n # require that all sequence names are unique\n self.assertEqual(len(seqnames), 8)\n\n def test_sam_downsample(self):\n desired_count = 100\n tolerance = 0.02\n\n in_sam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n out_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n downsamplesam = viral_ngs.core.picard.DownsampleSamTool()\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n downsamplesam.downsample_to_approx_count(in_sam, out_bam, desired_count)\n\n assert samtools.count(out_bam) in range(\n int(desired_count - (desired_count * tolerance)), int(desired_count + (desired_count * tolerance))+1\n ), \"Downsampled bam file does not contain the expected number of reads within tolerance: %s\" % tolerance\n\n def test_revert_bam_empty_input(self):\n empty_bam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n out_bam = viral_ngs.core.file.mkstempfname()\n viral_ngs.core.picard.RevertSamTool().execute(\n empty_bam,\n out_bam,\n picardOptions=['SORT_ORDER=queryname', 'SANITIZE=true']\n )\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n assert samtools.count(out_bam) == 0\n" }, { "path": "tests/unit/core/test_tools_sambamba.py", "content": "# Unit tests for viral_ngs.core.sambamba\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport os\nimport tempfile\nimport shutil\n\nimport pytest\n\nimport viral_ngs.core\nimport viral_ngs.core\nimport viral_ngs.core.sambamba\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp\n\n\nclass TestToolSambamba(TestCaseWithTmp):\n \"\"\"Tests for SambambaTool - high-performance BAM processing\"\"\"\n\n def setUp(self):\n super().setUp()\n self.sambamba = viral_ngs.core.sambamba.SambambaTool()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_sambamba_installed(self):\n \"\"\"Verify sambamba is installed and accessible\"\"\"\n self.sambamba.install()\n self.assertTrue(os.path.isfile(self.sambamba.install_and_get_path()))\n\n def test_version(self):\n \"\"\"Verify version detection works\"\"\"\n self.sambamba.install()\n version = self.sambamba.version()\n self.assertIsNotNone(version)\n self.assertIn('.', version) # Version should contain a dot (e.g., \"1.0.1\")\n\n\nclass TestSambambaSort(TestCaseWithTmp):\n \"\"\"Tests for sambamba sort functionality\"\"\"\n\n def setUp(self):\n super().setUp()\n self.sambamba = viral_ngs.core.sambamba.SambambaTool()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_sort_coordinate(self):\n \"\"\"Test coordinate sort (default)\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n\n self.sambamba.sort(inBam, outBam)\n\n # Verify output exists and is non-empty\n self.assertTrue(os.path.exists(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n\n # Verify read count matches input\n expected_count = self.samtools.count(inBam)\n actual_count = self.samtools.count(outBam)\n self.assertEqual(actual_count, expected_count)\n\n def test_sort_queryname(self):\n \"\"\"Test queryname sort\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBam = viral_ngs.core.file.mkstempfname('.namesorted.bam')\n\n self.sambamba.sort(inBam, outBam, sort_order='queryname')\n\n # Verify output exists\n self.assertTrue(os.path.exists(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n\n # Verify read count is preserved\n expected_count = self.samtools.count(inBam)\n actual_count = self.samtools.count(outBam)\n self.assertEqual(actual_count, expected_count)\n\n def test_sort_with_threads(self):\n \"\"\"Test multi-threaded sorting\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n outBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n\n # Should work with explicit thread count\n self.sambamba.sort(inBam, outBam, threads=2)\n\n self.assertTrue(os.path.exists(outBam))\n expected_count = self.samtools.count(inBam)\n actual_count = self.samtools.count(outBam)\n self.assertEqual(actual_count, expected_count)\n\n\nclass TestSambambaIndex(TestCaseWithTmp):\n \"\"\"Tests for sambamba index functionality\"\"\"\n\n def setUp(self):\n super().setUp()\n self.sambamba = viral_ngs.core.sambamba.SambambaTool()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_index_basic(self):\n \"\"\"Test creating .bai index file (not .bam.bai)\"\"\"\n # First, sort the BAM (indexing requires coordinate-sorted BAM)\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n sortedBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n self.sambamba.sort(inBam, sortedBam)\n\n # Now index it\n self.sambamba.index(sortedBam)\n\n # Verify index file was created with .bai (not .bam.bai)\n indexFile = sortedBam[:-4] + '.bai' # sorted.bai, not sorted.bam.bai\n self.assertTrue(os.path.exists(indexFile))\n self.assertGreater(os.path.getsize(indexFile), 0)\n # Verify the .bam.bai was NOT left behind\n self.assertFalse(os.path.exists(sortedBam + '.bai'))\n\n def test_index_with_threads(self):\n \"\"\"Test multi-threaded indexing\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n sortedBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n self.sambamba.sort(inBam, sortedBam)\n\n self.sambamba.index(sortedBam, threads=2)\n\n indexFile = sortedBam[:-4] + '.bai' # sorted.bai, not sorted.bam.bai\n self.assertTrue(os.path.exists(indexFile))\n\n def test_index_file_exists(self):\n \"\"\"Verify .bai file is created in expected location (not .bam.bai)\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n sortedBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n self.sambamba.sort(inBam, sortedBam)\n\n # Remove any existing index files\n indexFile = sortedBam[:-4] + '.bai' # sorted.bai\n if os.path.exists(indexFile):\n os.unlink(indexFile)\n if os.path.exists(sortedBam + '.bai'): # sorted.bam.bai\n os.unlink(sortedBam + '.bai')\n\n self.sambamba.index(sortedBam)\n\n self.assertTrue(os.path.exists(indexFile))\n\n\n@pytest.mark.skip(reason=\"sambamba merge is disabled due to segfault bug in sambamba 1.0.1\")\nclass TestSambambaMerge(TestCaseWithTmp):\n \"\"\"Tests for sambamba merge functionality\"\"\"\n\n def setUp(self):\n super().setUp()\n self.sambamba = viral_ngs.core.sambamba.SambambaTool()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_merge_two_bams(self):\n \"\"\"Test merging two BAM files\"\"\"\n # Sort both input BAMs first (merge requires sorted input)\n inBam1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n inBam2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.mini.bam')\n\n sortedBam1 = viral_ngs.core.file.mkstempfname('.sorted1.bam')\n sortedBam2 = viral_ngs.core.file.mkstempfname('.sorted2.bam')\n self.sambamba.sort(inBam1, sortedBam1)\n self.sambamba.sort(inBam2, sortedBam2)\n\n outBam = viral_ngs.core.file.mkstempfname('.merged.bam')\n self.sambamba.merge([sortedBam1, sortedBam2], outBam)\n\n # Verify output exists\n self.assertTrue(os.path.exists(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n\n def test_merge_preserves_reads(self):\n \"\"\"Verify read count equals sum of inputs\"\"\"\n inBam1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n inBam2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.mini.bam')\n\n sortedBam1 = viral_ngs.core.file.mkstempfname('.sorted1.bam')\n sortedBam2 = viral_ngs.core.file.mkstempfname('.sorted2.bam')\n self.sambamba.sort(inBam1, sortedBam1)\n self.sambamba.sort(inBam2, sortedBam2)\n\n count1 = self.samtools.count(sortedBam1)\n count2 = self.samtools.count(sortedBam2)\n\n outBam = viral_ngs.core.file.mkstempfname('.merged.bam')\n self.sambamba.merge([sortedBam1, sortedBam2], outBam)\n\n merged_count = self.samtools.count(outBam)\n self.assertEqual(merged_count, count1 + count2)\n\n\nclass TestSambambaFlagstat(TestCaseWithTmp):\n \"\"\"Tests for sambamba flagstat functionality\"\"\"\n\n def setUp(self):\n super().setUp()\n self.sambamba = viral_ngs.core.sambamba.SambambaTool()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_flagstat_basic(self):\n \"\"\"Test getting alignment statistics\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n\n stats = self.sambamba.flagstat(inBam)\n\n # Should return a dictionary with statistics\n self.assertIsInstance(stats, dict)\n\n def test_flagstat_returns_dict(self):\n \"\"\"Verify parsed output structure\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n\n stats = self.sambamba.flagstat(inBam)\n\n # Should contain standard flagstat keys\n self.assertIn('total', stats)\n\n def test_flagstat_empty_bam(self):\n \"\"\"Test flagstat on empty BAM file\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n\n stats = self.sambamba.flagstat(inBam)\n\n self.assertIsInstance(stats, dict)\n self.assertEqual(stats.get('total', 0), 0)\n\n\nclass TestSambambaMarkdup(TestCaseWithTmp):\n \"\"\"Tests for sambamba markdup functionality\"\"\"\n\n def setUp(self):\n super().setUp()\n self.sambamba = viral_ngs.core.sambamba.SambambaTool()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def test_markdup_basic(self):\n \"\"\"Test basic duplicate marking on aligned BAM\"\"\"\n # Use the larger test file which should have duplicates\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n\n # Sort first (markdup requires coordinate-sorted input)\n sortedBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n self.sambamba.sort(inBam, sortedBam)\n\n outBam = viral_ngs.core.file.mkstempfname('.deduped.bam')\n self.sambamba.markdup(sortedBam, outBam)\n\n # Verify output exists\n self.assertTrue(os.path.exists(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n\n # Read count should be preserved (duplicates are marked, not removed)\n in_count = self.samtools.count(sortedBam)\n out_count = self.samtools.count(outBam)\n self.assertEqual(out_count, in_count)\n\n def test_markdup_with_threads(self):\n \"\"\"Test multi-threaded duplicate marking\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n sortedBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n self.sambamba.sort(inBam, sortedBam)\n\n outBam = viral_ngs.core.file.mkstempfname('.deduped.bam')\n self.sambamba.markdup(sortedBam, outBam, threads=2)\n\n self.assertTrue(os.path.exists(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n\n def test_markdup_empty_input(self):\n \"\"\"Test handling of empty BAM file\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')\n\n # Sort the empty BAM (should still work)\n sortedBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n self.sambamba.sort(inBam, sortedBam)\n\n outBam = viral_ngs.core.file.mkstempfname('.deduped.bam')\n self.sambamba.markdup(sortedBam, outBam)\n\n # Output should exist and be empty\n self.assertTrue(os.path.exists(outBam))\n self.assertTrue(self.samtools.isEmpty(outBam))\n\n def test_markdup_removes_duplicates(self):\n \"\"\"Test remove_duplicates=True flag\"\"\"\n inBam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')\n sortedBam = viral_ngs.core.file.mkstempfname('.sorted.bam')\n self.sambamba.sort(inBam, sortedBam)\n\n outBam = viral_ngs.core.file.mkstempfname('.deduped.bam')\n self.sambamba.markdup(sortedBam, outBam, remove_duplicates=True)\n\n # Output should exist\n self.assertTrue(os.path.exists(outBam))\n\n # When removing duplicates, output should have fewer or equal reads\n in_count = self.samtools.count(sortedBam)\n out_count = self.samtools.count(outBam)\n self.assertLessEqual(out_count, in_count)\n" }, { "path": "tests/unit/core/test_tools_samtools.py", "content": "# Unit tests for viral_ngs.core.samtools\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport os, os.path\nimport tempfile\nimport shutil\nimport Bio.SeqIO, Bio.SeqRecord, Bio.Seq\nimport viral_ngs.core\nimport viral_ngs.core\nimport viral_ngs.core\nimport viral_ngs.core.samtools\nfrom tests import TestCaseWithTmp\n\n\nclass TestToolSamtools(TestCaseWithTmp):\n\n def test_count_bam(self):\n sam = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'simple.sam')\n n = viral_ngs.core.samtools.SamtoolsTool().count(sam, ['-S'])\n self.assertEqual(n, 2)\n\n def test_fasta_index(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'in.fasta')\n expected_fai = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'in.fasta.fai')\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n for ext in ('.fasta', '.fa'):\n inRef = viral_ngs.core.file.mkstempfname(ext)\n shutil.copyfile(orig_ref, inRef)\n outFai = inRef + '.fai'\n samtools.faidx(inRef)\n self.assertEqualContents(outFai, expected_fai)\n\n def test_messy_fasta_index(self):\n orig_ref = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestToolPicard', 'messy-headers.fasta')\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n with viral_ngs.core.file.tempfname('.fasta') as inRef:\n shutil.copyfile(orig_ref, inRef)\n samtools.faidx(inRef, overwrite=True)\n with open(inRef + '.fai', 'rt') as inf:\n seqnames = set()\n for line in inf:\n seq_name = line.strip().split('\\t')[0]\n # old versions of code cut this off at \"Influenza\"\n self.assertGreater(len(seq_name), 50)\n seqnames.add(seq_name)\n # require that all sequence names are unique\n self.assertEqual(len(seqnames), 8)\n\n def test_isEmpty(self):\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n self.assertTrue(samtools.isEmpty(os.path.join(viral_ngs.core.file.get_test_input_path(), 'empty.bam')))\n self.assertFalse(samtools.isEmpty(os.path.join(viral_ngs.core.file.get_test_input_path(), 'almost-empty.bam')))\n self.assertFalse(samtools.isEmpty(os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')))\n self.assertFalse(samtools.isEmpty(os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.testreads.bam')))\n\n def test_sam_downsample(self):\n desired_count = 100\n tolerance = 0.1\n\n in_sam = os.path.join(viral_ngs.core.file.get_test_input_path(), 'G5012.3.subset.bam')\n out_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n samtools.downsample_to_approx_count(in_sam, out_bam, desired_count)\n\n assert samtools.count(out_bam) in range(\n int(desired_count - (desired_count * tolerance)), int(desired_count + (desired_count * tolerance))+1\n ), \"Downsampled bam file does not contain the expected number of reads within tolerance: %s\" % tolerance\n\n def test_filterByCigarString(self):\n # The test input contains three reads to remove; one each: \n # leading indel, trailing indel, both leading and trailing\n # It also has a cigar string with an indel between alignment matches\n in_sam = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'indel_cigar.sam')\n out_bam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n # We'll use the default regex, which matches leading or trailing indels.\n # It is reproduced here in case the default changes:\n # '^((?:[0-9]+[ID]){1}(?:[0-9]+[MNIDSHPX=])+)|((?:[0-9]+[MNIDSHPX=])+(?:[0-9]+[ID]){1})$'\n samtools.filterByCigarString(in_sam, out_bam)\n\n assert samtools.count(out_bam)==39, \"Output read count does not match the expected count.\"\n\n def test_bam2fa(self):\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n sam = os.path.join(viral_ngs.core.file.get_test_input_path(self), 'simple.sam')\n\n with samtools.bam2fa_tmp(sam) as (fa1, fa2):\n for fa in (fa1, fa2):\n assert len(list(Bio.SeqIO.parse(fa, 'fasta')))==1\n\n assert not os.path.isfile(fa1) and not os.path.isfile(fa2)\n\n\nclass TestSamtoolsImport(TestCaseWithTmp):\n \"\"\"Tests for samtools import (FASTQ to BAM conversion)\"\"\"\n\n def test_import_paired_fastq_basic(self):\n \"\"\"Test basic paired FASTQ to BAM conversion with sample name only\"\"\"\n # Use existing test FASTQ files from TestFastqBam\n inFastq1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in1.fastq')\n inFastq2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in2.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n samtools.import_fastq(inFastq1, inFastq2, outBam, sample_name='TestSample')\n\n # Verify BAM file was created and is non-empty\n self.assertTrue(os.path.exists(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n\n # Verify read count matches input (1 read pair = 2 reads)\n self.assertEqual(samtools.count(outBam), 2)\n\n # Verify BAM is not flagged as empty\n self.assertFalse(samtools.isEmpty(outBam))\n\n def test_import_with_full_read_group(self):\n \"\"\"Test that all RG tags are correctly set in BAM header\"\"\"\n import pysam\n\n inFastq1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in1.fastq')\n inFastq2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in2.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n samtools.import_fastq(\n inFastq1, inFastq2, outBam,\n sample_name='FreeSample',\n library_name='Alexandria',\n platform='illumina',\n read_group_id='MyRG',\n platform_unit='FC001.1.ATCG',\n sequencing_center='BroadInstitute',\n run_date='2024-12-14'\n )\n\n # Read BAM header and verify RG tags\n with pysam.AlignmentFile(outBam, 'rb', check_sq=False) as bam:\n rg_list = bam.header.get('RG', [])\n self.assertEqual(len(rg_list), 1)\n rg = rg_list[0]\n\n self.assertEqual(rg.get('ID'), 'MyRG')\n self.assertEqual(rg.get('SM'), 'FreeSample')\n self.assertEqual(rg.get('LB'), 'Alexandria')\n self.assertEqual(rg.get('PL'), 'illumina')\n self.assertEqual(rg.get('PU'), 'FC001.1.ATCG')\n self.assertEqual(rg.get('CN'), 'BroadInstitute')\n self.assertEqual(rg.get('DT'), '2024-12-14')\n\n def test_import_rg_defaults(self):\n \"\"\"Test that RG defaults are applied correctly when optional params omitted\"\"\"\n import pysam\n\n inFastq1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in1.fastq')\n inFastq2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in2.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n samtools.import_fastq(inFastq1, inFastq2, outBam, sample_name='TestSample')\n\n with pysam.AlignmentFile(outBam, 'rb', check_sq=False) as bam:\n rg_list = bam.header.get('RG', [])\n self.assertEqual(len(rg_list), 1)\n rg = rg_list[0]\n\n # ID should default to 'A' (matching Picard default)\n self.assertEqual(rg.get('ID'), 'A')\n self.assertEqual(rg.get('SM'), 'TestSample')\n # LB should default to sample_name if not specified\n self.assertEqual(rg.get('LB'), 'TestSample')\n # PL should default to 'illumina'\n self.assertEqual(rg.get('PL'), 'illumina')\n # Optional tags should not be present\n self.assertIsNone(rg.get('PU'))\n self.assertIsNone(rg.get('CN'))\n self.assertIsNone(rg.get('DT'))\n\n def test_import_read_flags(self):\n \"\"\"Test that paired-end read flags are set correctly (77/141 for unmapped pairs)\"\"\"\n import pysam\n\n inFastq1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in1.fastq')\n inFastq2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in2.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n samtools.import_fastq(inFastq1, inFastq2, outBam, sample_name='TestSample')\n\n with pysam.AlignmentFile(outBam, 'rb', check_sq=False) as bam:\n reads = list(bam.fetch(until_eof=True))\n self.assertEqual(len(reads), 2)\n\n # First read should have flag 77 (paired, unmapped, mate unmapped, first in pair)\n # Second read should have flag 141 (paired, unmapped, mate unmapped, second in pair)\n flags = sorted([r.flag for r in reads])\n self.assertEqual(flags, [77, 141])\n\n def test_import_read_rg_tag(self):\n \"\"\"Test that reads have the RG tag set correctly\"\"\"\n import pysam\n\n inFastq1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in1.fastq')\n inFastq2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in2.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n samtools.import_fastq(\n inFastq1, inFastq2, outBam,\n sample_name='TestSample',\n read_group_id='CustomRG'\n )\n\n with pysam.AlignmentFile(outBam, 'rb', check_sq=False) as bam:\n for read in bam.fetch(until_eof=True):\n self.assertTrue(read.has_tag('RG'))\n self.assertEqual(read.get_tag('RG'), 'CustomRG')\n\n def test_import_empty_fastq(self):\n \"\"\"Test handling of empty FASTQ inputs - should create empty BAM with header\"\"\"\n import pysam\n\n # Create empty FASTQ files\n emptyFastq1 = viral_ngs.core.file.mkstempfname('.fastq')\n emptyFastq2 = viral_ngs.core.file.mkstempfname('.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n open(emptyFastq1, 'w').close()\n open(emptyFastq2, 'w').close()\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n samtools.import_fastq(\n emptyFastq1, emptyFastq2, outBam,\n sample_name='EmptySample',\n library_name='EmptyLib'\n )\n\n # Verify BAM was created\n self.assertTrue(os.path.exists(outBam))\n self.assertGreater(os.path.getsize(outBam), 0)\n\n # Verify BAM is empty (no reads)\n self.assertTrue(samtools.isEmpty(outBam))\n self.assertEqual(samtools.count(outBam), 0)\n\n # Verify header has RG\n with pysam.AlignmentFile(outBam, 'rb', check_sq=False) as bam:\n rg_list = bam.header.get('RG', [])\n self.assertEqual(len(rg_list), 1)\n self.assertEqual(rg_list[0].get('SM'), 'EmptySample')\n self.assertEqual(rg_list[0].get('LB'), 'EmptyLib')\n\n def test_import_multithreaded(self):\n \"\"\"Test that threads parameter works without error\"\"\"\n inFastq1 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in1.fastq')\n inFastq2 = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestFastqBam', 'in2.fastq')\n outBam = viral_ngs.core.file.mkstempfname('.bam')\n\n samtools = viral_ngs.core.samtools.SamtoolsTool()\n # Should work with explicit thread count\n samtools.import_fastq(\n inFastq1, inFastq2, outBam,\n sample_name='TestSample',\n threads=2\n )\n\n self.assertTrue(os.path.exists(outBam))\n self.assertEqual(samtools.count(outBam), 2)\n\n" }, { "path": "tests/unit/core/test_tools_splitcode.py", "content": "# Unit tests for viral_ngs.core.splitcode\n# -*- coding: utf-8 -*-\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport unittest\nimport os\nimport os.path\nimport tempfile\nimport filecmp\nimport shutil\nimport json\nimport viral_ngs.core\nimport viral_ngs.core\nimport viral_ngs.core.splitcode\nimport viral_ngs.core.samtools\nimport viral_ngs.core.picard\nfrom tests import TestCaseWithTmp, assert_equal_bam_reads\n\n\nclass TestSplitcodeLookupTable(TestCaseWithTmp):\n \"\"\"Test cases for create_splitcode_lookup_table function.\"\"\"\n\n def test_basic_single_pool(self):\n \"\"\"Test basic functionality with a single pool.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path(self)\n sample_sheet = os.path.join(inDir, 'sample_sheet_basic.tsv')\n\n with tempfile.TemporaryDirectory() as tmpdir:\n csv_out = os.path.join(tmpdir, 'lut.csv')\n\n # Copy summary JSON to tmpdir where function expects it\n import shutil\n shutil.copy(\n os.path.join(inDir, 'ATCGATCG-GCTAGCTA.lB1_summary.json'),\n os.path.join(tmpdir, 'ATCGATCG-GCTAGCTA.lB1_summary.json')\n )\n\n result_path = viral_ngs.core.splitcode.create_splitcode_lookup_table(\n sample_sheet, csv_out, unmatched_name=\"Unmatched\"\n )\n\n # Verify output file was created\n self.assertTrue(os.path.exists(result_path))\n\n # Read and validate output CSV\n import pandas as pd\n df = pd.read_csv(result_path, dtype=str)\n\n # Check for expected columns\n expected_cols = [\n 'sample', 'library_id', 'barcode_1', 'barcode_2',\n 'inline_barcode', 'run', 'muxed_pool',\n 'num_reads_hdistance0', 'num_reads_hdistance1', 'num_reads_total'\n ]\n for col in expected_cols:\n self.assertIn(col, df.columns, f\"Missing column: {col}\")\n\n # Check number of rows (3 samples + 1 unmatched)\n self.assertEqual(len(df), 4)\n\n # Verify sample names\n sample_names = set(df['sample'].tolist())\n self.assertIn('Sample1', sample_names)\n self.assertIn('Sample2', sample_names)\n self.assertIn('Sample3', sample_names)\n\n # Verify unmatched row\n unmatched_rows = df[df['sample'].str.contains('Unmatched')]\n self.assertEqual(len(unmatched_rows), 1)\n unmatched_row = unmatched_rows.iloc[0]\n self.assertTrue(unmatched_row['inline_barcode'].replace('N', '') == '')\n # Unmatched count should be n_processed - n_assigned = 100000 - 95000 = 5000\n self.assertEqual(int(unmatched_row['num_reads_hdistance0']), 5000)\n\n # Verify read counts for Sample2 (should have highest count)\n sample2_row = df[df['sample'] == 'Sample2'].iloc[0]\n self.assertEqual(int(sample2_row['num_reads_hdistance0']), 45000)\n self.assertEqual(int(sample2_row['num_reads_hdistance1']), 2000)\n self.assertEqual(int(sample2_row['num_reads_total']), 47000)\n\n # Verify barcode values\n self.assertEqual(sample2_row['barcode_1'], 'ATCGATCG')\n self.assertEqual(sample2_row['barcode_2'], 'GCTAGCTA')\n self.assertEqual(sample2_row['inline_barcode'], 'GGGGTTTT')\n\n def test_zero_reads_pool(self):\n \"\"\"Test handling of pool with zero reads.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path(self)\n sample_sheet = os.path.join(inDir, 'sample_sheet_zero_reads.tsv')\n\n with tempfile.TemporaryDirectory() as tmpdir:\n csv_out = os.path.join(tmpdir, 'lut.csv')\n\n # Copy summary JSON\n import shutil\n shutil.copy(\n os.path.join(inDir, 'TTTTAAAA-CCCCGGGG.lB2_summary.json'),\n os.path.join(tmpdir, 'TTTTAAAA-CCCCGGGG.lB2_summary.json')\n )\n\n result_path = viral_ngs.core.splitcode.create_splitcode_lookup_table(\n sample_sheet, csv_out, unmatched_name=\"Unmatched\"\n )\n\n # Read output\n import pandas as pd\n df = pd.read_csv(result_path, dtype=str)\n\n # Should have 1 sample + 1 unmatched\n self.assertEqual(len(df), 2)\n\n # Verify sample has 0 reads\n sample_row = df[df['sample'] == 'Sample4'].iloc[0]\n self.assertEqual(int(sample_row['num_reads_hdistance0']), 0)\n self.assertEqual(int(sample_row['num_reads_hdistance1']), 0)\n self.assertEqual(int(sample_row['num_reads_total']), 0)\n\n def test_multi_pool(self):\n \"\"\"Test with multiple pools.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path(self)\n sample_sheet = os.path.join(inDir, 'sample_sheet_multi_pool.tsv')\n\n with tempfile.TemporaryDirectory() as tmpdir:\n csv_out = os.path.join(tmpdir, 'lut.csv')\n\n # Copy both summary JSONs\n import shutil\n shutil.copy(\n os.path.join(inDir, 'AAAAAAAA-TTTTTTTT.lLibA_summary.json'),\n os.path.join(tmpdir, 'AAAAAAAA-TTTTTTTT.lLibA_summary.json')\n )\n shutil.copy(\n os.path.join(inDir, 'GGGGGGGG-CCCCCCCC.lLibB_summary.json'),\n os.path.join(tmpdir, 'GGGGGGGG-CCCCCCCC.lLibB_summary.json')\n )\n\n result_path = viral_ngs.core.splitcode.create_splitcode_lookup_table(\n sample_sheet, csv_out, unmatched_name=\"Unmatched\"\n )\n\n # Read output\n import pandas as pd\n df = pd.read_csv(result_path, dtype=str)\n\n # Should have 4 samples + 2 unmatched (one per pool)\n self.assertEqual(len(df), 6)\n\n # Verify both barcode groups are present in muxed_pool\n pools = set(df['muxed_pool'].tolist())\n self.assertIn('AAAAAAAA-TTTTTTTT.lLibA', pools)\n self.assertIn('GGGGGGGG-CCCCCCCC.lLibB', pools)\n\n # Check unmatched counts\n unmatched_rows = df[df['sample'].str.contains('Unmatched')]\n self.assertEqual(len(unmatched_rows), 2)\n\n # Verify LibA unmatched count: 50000 - 48000 = 2000\n # Unmatched rows use the barcode group (outer barcodes only) as muxed_pool\n liba_unmatched = df[df['muxed_pool'] == 'AAAAAAAA-TTTTTTTT']\n liba_unmatched = liba_unmatched[liba_unmatched['sample'].str.contains('Unmatched')].iloc[0]\n self.assertEqual(int(liba_unmatched['num_reads_hdistance0']), 2000)\n\n def test_append_run_id(self):\n \"\"\"Test append_run_id parameter.\"\"\"\n inDir = viral_ngs.core.file.get_test_input_path(self)\n sample_sheet = os.path.join(inDir, 'sample_sheet_basic.tsv')\n\n with tempfile.TemporaryDirectory() as tmpdir:\n csv_out = os.path.join(tmpdir, 'lut.csv')\n\n import shutil\n # Copy JSON file with run suffix - this matches what splitcode actually creates\n shutil.copy(\n os.path.join(inDir, 'ATCGATCG-GCTAGCTA.lB1_summary.json'),\n os.path.join(tmpdir, 'ATCGATCG-GCTAGCTA.lB1.FLOWCELL123_summary.json')\n )\n\n result_path = viral_ngs.core.splitcode.create_splitcode_lookup_table(\n sample_sheet, csv_out,\n unmatched_name=\"Unmatched\",\n append_run_id=\"FLOWCELL123\"\n )\n\n # Read output\n import pandas as pd\n df = pd.read_csv(result_path, dtype=str)\n\n # Verify run IDs contain flowcell ID\n sample_row = df[df['sample'] == 'Sample1'].iloc[0]\n self.assertIn('FLOWCELL123', sample_row['run'])\n self.assertIn('FLOWCELL123', sample_row['muxed_pool'])\n\n def test_unique_library_ids_per_sample(self):\n \"\"\"Test that lookup works when library_id_per_sample differs per sample\n within the same barcode_1+barcode_2 group (issue #1037).\n\n When each sample has a unique library_id_per_sample, each gets its own\n muxed_pool value, but splitcode produces only ONE summary JSON per outer\n barcode group. The function must find and reuse that single JSON for all\n samples in the group.\n \"\"\"\n inDir = viral_ngs.core.file.get_test_input_path(self)\n sample_sheet = os.path.join(inDir, 'sample_sheet_unique_lib_ids.tsv')\n\n with tempfile.TemporaryDirectory() as tmpdir:\n csv_out = os.path.join(tmpdir, 'lut.csv')\n\n # Copy the ONE JSON that exists for this barcode pair\n # (named with the first muxed_pool value, as splitcode would produce)\n shutil.copy(\n os.path.join(inDir, 'ATCGATCG-GCTAGCTA.lL1_summary.json'),\n os.path.join(tmpdir, 'ATCGATCG-GCTAGCTA.lL1_summary.json')\n )\n\n result_path = viral_ngs.core.splitcode.create_splitcode_lookup_table(\n sample_sheet, csv_out, unmatched_name=\"Unmatched\"\n )\n\n # Verify output file was created\n self.assertTrue(os.path.exists(result_path))\n\n # Read and validate output CSV\n import pandas as pd\n df = pd.read_csv(result_path, dtype=str)\n\n # Check number of rows (3 samples + 1 unmatched)\n self.assertEqual(len(df), 4)\n\n # Verify all sample names present\n sample_names = set(df['sample'].tolist())\n self.assertIn('Sample1', sample_names)\n self.assertIn('Sample2', sample_names)\n self.assertIn('Sample3', sample_names)\n\n # Verify unmatched row\n unmatched_rows = df[df['sample'].str.contains('Unmatched')]\n self.assertEqual(len(unmatched_rows), 1)\n unmatched_row = unmatched_rows.iloc[0]\n # Unmatched count should be n_processed - n_assigned = 100000 - 95000 = 5000\n self.assertEqual(int(unmatched_row['num_reads_hdistance0']), 5000)\n\n # Verify read counts for Sample2 (should have highest count)\n sample2_row = df[df['sample'] == 'Sample2'].iloc[0]\n self.assertEqual(int(sample2_row['num_reads_hdistance0']), 45000)\n self.assertEqual(int(sample2_row['num_reads_hdistance1']), 2000)\n self.assertEqual(int(sample2_row['num_reads_total']), 47000)\n\n # Verify barcode values are correct\n self.assertEqual(sample2_row['barcode_1'], 'ATCGATCG')\n self.assertEqual(sample2_row['barcode_2'], 'GCTAGCTA')\n self.assertEqual(sample2_row['inline_barcode'], 'GGGGTTTT')\n\n\nclass TestSplitcodeIntegration(TestCaseWithTmp):\n \"\"\"\n Test our assumptions about splitcode behavior and file formats.\n\n These tests create minimal test data to validate splitcode integration\n without testing the external splitcode tool itself.\n \"\"\"\n\n def setUp(self):\n super().setUp()\n self.temp_dir = tempfile.mkdtemp()\n self.samtools = viral_ngs.core.samtools.SamtoolsTool()\n\n def tearDown(self):\n shutil.rmtree(self.temp_dir, ignore_errors=True)\n super().tearDown()\n\n def create_test_bam_with_inline_barcodes(self, output_bam, num_reads=10, barcode=\"AAAAAAAA\"):\n \"\"\"\n Create a test BAM file with reads containing inline barcodes in R1.\n\n Args:\n output_bam: Path to output BAM file\n num_reads: Number of read pairs to create\n barcode: 8bp inline barcode to prepend to R1 sequences\n \"\"\"\n # Create temp FASTQs with inline barcodes\n r1_fastq = viral_ngs.core.file.mkstempfname('.fastq')\n r2_fastq = viral_ngs.core.file.mkstempfname('.fastq')\n\n with open(r1_fastq, 'w') as f1, open(r2_fastq, 'w') as f2:\n for i in range(num_reads):\n # R1 has inline barcode prepended\n seq_r1 = barcode + \"ACGTACGTACGT\" # 8bp barcode + 12bp insert\n qual_r1 = \"I\" * len(seq_r1)\n\n # R2 is just normal sequence\n seq_r2 = \"TGCATGCATGCA\"\n qual_r2 = \"I\" * len(seq_r2)\n\n f1.write(f\"@read{i}\\n{seq_r1}\\n+\\n{qual_r1}\\n\")\n f2.write(f\"@read{i}\\n{seq_r2}\\n+\\n{qual_r2}\\n\")\n\n # Convert to BAM\n viral_ngs.core.picard.FastqToSamTool().execute(\n r1_fastq,\n r2_fastq,\n \"TestSample\",\n output_bam,\n picardOptions=['LIBRARY_NAME=TestLib', 'PLATFORM=ILLUMINA']\n )\n\n return output_bam\n\n def test_run_splitcode_on_pool_basic(self):\n \"\"\"\n Test run_splitcode_on_pool with a simple single-barcode pool.\n\n This test focuses on validating our assumptions about splitcode's behavior:\n - Summary JSON is created in expected location\n - JSON has expected structure (tag_qc array with tag, count, distance)\n - We're NOT testing the keep file format here (too complex) - just JSON output\n\n Validates:\n - Splitcode runs successfully on BAM input\n - Summary JSON location and format\n \"\"\"\n # Create test BAM with reads containing AAAAAAAA barcode\n pool_bam = os.path.join(self.temp_dir, 'test_pool.bam')\n self.create_test_bam_with_inline_barcodes(pool_bam, num_reads=5, barcode=\"AAAAAAAA\")\n\n # Create splitcode config file\n # Format: tag, id, locations, distance, left, right\n # The \"id\" column must match what's in the keep file\n splitcode_config = os.path.join(self.temp_dir, 'config.txt')\n sample_id = \"Sample1_R1\" # This matches illumina.py convention: f\"{sample_library_id}_R1\"\n with open(splitcode_config, 'w') as f:\n f.write(\"tag\\tid\\tlocations\\tdistance\\tleft\\tright\\n\")\n # AAAAAAAA barcode, ID=Sample1_R1, in file 0 (R1) from position 0 to 8, distance=0 (exact match), trim from left\n # locations format: FILE_NUMBER:START_BP:END_BP (0:0:8 means R1, positions 0-8)\n f.write(f\"AAAAAAAA\\t{sample_id}\\t0:0:8\\t0\\t1\\t0\\n\")\n\n # Create keep file matching the config file ID\n # Format: barcode_id (from config) output_prefix\n splitcode_keepfile = os.path.join(self.temp_dir, 'keep.txt')\n output_prefix = os.path.join(self.temp_dir, 'Sample1')\n with open(splitcode_keepfile, 'w') as f:\n # Column 1 must match the \"id\" from config file\n f.write(f\"{sample_id}\\t{output_prefix}\\n\")\n\n pool_id = \"TestPool\"\n out_demux_dir = self.temp_dir\n\n # Run splitcode\n result = viral_ngs.core.splitcode.run_splitcode_on_pool(\n pool_id=pool_id,\n pool_bam_file=pool_bam,\n splitcode_config=splitcode_config,\n splitcode_keepfile=splitcode_keepfile,\n out_demux_dir_path=out_demux_dir,\n unmatched_name=\"unmatched\",\n threads_per_worker=1,\n out_dir_path=out_demux_dir,\n out_demux_dir_path_tmp=self.temp_dir\n )\n\n # Verify return value\n self.assertEqual(result[0], 0, \"Splitcode should return 0 on success\")\n self.assertEqual(result[1], pool_id, \"Should return the pool_id\")\n\n # Verify summary JSON exists in expected location\n # This is the KEY assumption we need to validate\n expected_summary = os.path.join(out_demux_dir, f'{pool_id}_summary.json')\n self.assertTrue(os.path.exists(expected_summary),\n f\"Summary JSON should exist at {expected_summary}\")\n\n # Verify JSON structure - this is what create_splitcode_lookup_table depends on\n with open(expected_summary) as f:\n summary = json.load(f)\n\n self.assertIn('tag_qc', summary, \"JSON should have 'tag_qc' field\")\n self.assertIsInstance(summary['tag_qc'], list, \"'tag_qc' should be a list\")\n\n # Find Sample1_R1 in tag_qc (splitcode uses the ID as the tag name in output)\n # Note: tag_qc has multiple entries per tag (one for each distance level)\n # We want to check that at least one distance level has count > 0\n matching_entries = [item for item in summary['tag_qc'] if item['tag'] == sample_id]\n self.assertGreater(len(matching_entries), 0, f\"{sample_id} should appear in tag_qc\")\n\n # Check that we have at least one entry with count > 0\n total_count = sum(item['count'] for item in matching_entries)\n self.assertGreater(total_count, 0, f\"{sample_id} should have matched some reads across all distance levels\")\n\n def test_run_splitcode_on_pool_empty_output(self):\n \"\"\"\n Test run_splitcode_on_pool when a barcode matches zero reads.\n\n Validates:\n - Splitcode runs successfully even with empty barcode outputs\n - Summary JSON shows count=0 for unmatched barcodes\n - Output files for empty barcodes may not exist or are empty\n \"\"\"\n # Create test BAM with AAAAAAAA barcode only\n pool_bam = os.path.join(self.temp_dir, 'test_pool.bam')\n self.create_test_bam_with_inline_barcodes(pool_bam, num_reads=3, barcode=\"AAAAAAAA\")\n\n # Config with BC1 (present) and BC2 (absent)\n # IDs must match illumina.py convention: f\"{sample_library_id}_R1\"\n splitcode_config = os.path.join(self.temp_dir, 'config.txt')\n sample_id_1 = \"Sample1_R1\"\n sample_id_2 = \"Sample2_R1\"\n with open(splitcode_config, 'w') as f:\n f.write(\"tag\\tid\\tlocations\\tdistance\\tleft\\tright\\n\")\n # locations format: FILE_NUMBER:START_BP:END_BP\n f.write(f\"AAAAAAAA\\t{sample_id_1}\\t0:0:8\\t0\\t1\\t0\\n\")\n f.write(f\"CCCCCCCC\\t{sample_id_2}\\t0:0:8\\t0\\t1\\t0\\n\") # Won't match any reads\n\n # Keep file for both barcodes\n splitcode_keepfile = os.path.join(self.temp_dir, 'keep.txt')\n output_prefix1 = os.path.join(self.temp_dir, 'Sample1')\n output_prefix2 = os.path.join(self.temp_dir, 'Sample2')\n with open(splitcode_keepfile, 'w') as f:\n f.write(f\"{sample_id_1}\\t{output_prefix1}\\n\")\n f.write(f\"{sample_id_2}\\t{output_prefix2}\\n\")\n\n pool_id = \"TestPool\"\n out_demux_dir = self.temp_dir\n\n # Run splitcode\n result = viral_ngs.core.splitcode.run_splitcode_on_pool(\n pool_id=pool_id,\n pool_bam_file=pool_bam,\n splitcode_config=splitcode_config,\n splitcode_keepfile=splitcode_keepfile,\n out_demux_dir_path=out_demux_dir,\n unmatched_name=\"unmatched\",\n threads_per_worker=1,\n out_dir_path=out_demux_dir,\n out_demux_dir_path_tmp=self.temp_dir\n )\n\n self.assertEqual(result[0], 0, \"Splitcode should succeed even with empty outputs\")\n\n # Verify summary JSON\n expected_summary = os.path.join(out_demux_dir, f'{pool_id}_summary.json')\n with open(expected_summary) as f:\n summary = json.load(f)\n\n # Sample1_R1 should have reads (check total across all distance levels)\n sample1_entries = [item for item in summary['tag_qc'] if item['tag'] == sample_id_1]\n self.assertGreater(len(sample1_entries), 0, f\"{sample_id_1} should appear in tag_qc\")\n sample1_total = sum(item['count'] for item in sample1_entries)\n self.assertGreater(sample1_total, 0, f\"{sample_id_1} should have matched some reads\")\n\n # Sample2_R1 might appear with count=0 (check total across all distance levels)\n sample2_entries = [item for item in summary['tag_qc'] if item['tag'] == sample_id_2]\n if len(sample2_entries) > 0:\n sample2_total = sum(item['count'] for item in sample2_entries)\n self.assertEqual(sample2_total, 0,\n f\"{sample_id_2} should have 0 reads total if it appears in tag_qc\")\n\n # Sample1 files should exist and be non-empty\n self.assertTrue(os.path.exists(f\"{output_prefix1}_R1.fastq\"))\n self.assertGreater(os.path.getsize(f\"{output_prefix1}_R1.fastq\"), 0)\n\n # Sample2 files might not exist, or if they do, should be empty\n sample2_r1 = f\"{output_prefix2}_R1.fastq\"\n if os.path.exists(sample2_r1):\n # File exists but should be empty (0 reads = 0 lines)\n with open(sample2_r1) as f:\n lines = f.readlines()\n self.assertEqual(len(lines), 0,\n \"Empty barcode output file should have 0 lines\")\n\n def test_splitcode_json_output_format(self):\n \"\"\"\n Test that splitcode JSON output has the expected structure.\n\n Validates our assumptions about JSON format:\n - Has 'tag_qc' array\n - Each entry has 'tag', 'count', 'distance' fields\n - These fields are the correct types\n \"\"\"\n # Create minimal test\n pool_bam = os.path.join(self.temp_dir, 'test_pool.bam')\n self.create_test_bam_with_inline_barcodes(pool_bam, num_reads=10, barcode=\"GGGGGGGG\")\n\n splitcode_config = os.path.join(self.temp_dir, 'config.txt')\n sample_id = \"Sample3_R1\"\n with open(splitcode_config, 'w') as f:\n f.write(\"tag\\tid\\tlocations\\tdistance\\tleft\\tright\\n\")\n # locations format: FILE_NUMBER:START_BP:END_BP\n f.write(f\"GGGGGGGG\\t{sample_id}\\t0:0:8\\t1\\t1\\t0\\n\")\n\n splitcode_keepfile = os.path.join(self.temp_dir, 'keep.txt')\n output_prefix = os.path.join(self.temp_dir, 'Sample3')\n with open(splitcode_keepfile, 'w') as f:\n f.write(f\"{sample_id}\\t{output_prefix}\\n\")\n\n pool_id = \"TestPool\"\n\n viral_ngs.core.splitcode.run_splitcode_on_pool(\n pool_id=pool_id,\n pool_bam_file=pool_bam,\n splitcode_config=splitcode_config,\n splitcode_keepfile=splitcode_keepfile,\n out_demux_dir_path=self.temp_dir,\n unmatched_name=\"unmatched\",\n threads_per_worker=1,\n out_dir_path=self.temp_dir,\n out_demux_dir_path_tmp=self.temp_dir\n )\n\n # Read and validate JSON structure\n summary_file = os.path.join(self.temp_dir, f'{pool_id}_summary.json')\n with open(summary_file) as f:\n summary = json.load(f)\n\n # Validate top-level structure\n self.assertIsInstance(summary, dict, \"Summary should be a dictionary\")\n self.assertIn('tag_qc', summary, \"Summary must have 'tag_qc' key\")\n self.assertIsInstance(summary['tag_qc'], list, \"'tag_qc' must be a list\")\n\n # Validate tag_qc entries\n self.assertGreater(len(summary['tag_qc']), 0, \"tag_qc should have at least one entry\")\n\n for entry in summary['tag_qc']:\n self.assertIsInstance(entry, dict, \"Each tag_qc entry should be a dict\")\n\n # Required fields our code depends on\n self.assertIn('tag', entry, \"Entry must have 'tag' field\")\n self.assertIn('count', entry, \"Entry must have 'count' field\")\n\n # Validate types (important for create_splitcode_lookup_table)\n # Note: with our pandas dtype=str fix, these get converted to strings\n self.assertIsInstance(entry['tag'], str, \"'tag' should be string\")\n # 'count' is numeric in JSON but we convert to string in pandas\n self.assertIsInstance(entry['count'], int, \"'count' should be int in JSON\")\n\n if 'distance' in entry:\n self.assertIsInstance(entry['distance'], int, \"'distance' should be int in JSON\")\n\n def test_splitcode_output_file_locations(self):\n \"\"\"\n Test that splitcode creates output files in expected locations.\n\n Validates:\n - Summary JSON location: {out_demux_dir_path}/{pool_id}_summary.json\n - FASTQ location: {output_prefix}_R1.fastq, {output_prefix}_R2.fastq\n - Unmatched FASTQ location: {unmatched_name}.{pool_id}_R1.fastq\n \"\"\"\n pool_bam = os.path.join(self.temp_dir, 'test_pool.bam')\n self.create_test_bam_with_inline_barcodes(pool_bam, num_reads=8, barcode=\"TTTTTTTT\")\n\n splitcode_config = os.path.join(self.temp_dir, 'config.txt')\n sample_id = \"MySample_R1\"\n with open(splitcode_config, 'w') as f:\n f.write(\"tag\\tid\\tlocations\\tdistance\\tleft\\tright\\n\")\n # locations format: FILE_NUMBER:START_BP:END_BP\n f.write(f\"TTTTTTTT\\t{sample_id}\\t0:0:8\\t0\\t1\\t0\\n\")\n\n splitcode_keepfile = os.path.join(self.temp_dir, 'keep.txt')\n sample_output_prefix = os.path.join(self.temp_dir, 'MySample')\n with open(splitcode_keepfile, 'w') as f:\n f.write(f\"{sample_id}\\t{sample_output_prefix}\\n\")\n\n pool_id = \"MyPool\"\n unmatched_name = \"unassigned\"\n out_demux_dir = self.temp_dir\n\n viral_ngs.core.splitcode.run_splitcode_on_pool(\n pool_id=pool_id,\n pool_bam_file=pool_bam,\n splitcode_config=splitcode_config,\n splitcode_keepfile=splitcode_keepfile,\n out_demux_dir_path=out_demux_dir,\n unmatched_name=unmatched_name,\n threads_per_worker=1,\n out_dir_path=out_demux_dir,\n out_demux_dir_path_tmp=self.temp_dir\n )\n\n # Verify expected file locations\n\n # 1. Summary JSON: {out_demux_dir_path}/{pool_id}_summary.json\n expected_summary = os.path.join(out_demux_dir, f'{pool_id}_summary.json')\n self.assertTrue(os.path.exists(expected_summary),\n f\"Summary should be at {expected_summary}\")\n\n # 2. Matched FASTQs: {output_prefix}_R1.fastq, {output_prefix}_R2.fastq\n expected_r1 = f\"{sample_output_prefix}_R1.fastq\"\n expected_r2 = f\"{sample_output_prefix}_R2.fastq\"\n self.assertTrue(os.path.exists(expected_r1),\n f\"Matched R1 should be at {expected_r1}\")\n self.assertTrue(os.path.exists(expected_r2),\n f\"Matched R2 should be at {expected_r2}\")\n\n # 3. Unmatched FASTQs: {unmatched_name}.{pool_id}_R1.fastq\n expected_unmatched_r1 = os.path.join(self.temp_dir, f'{unmatched_name}.{pool_id}_R1.fastq')\n expected_unmatched_r2 = os.path.join(self.temp_dir, f'{unmatched_name}.{pool_id}_R2.fastq')\n self.assertTrue(os.path.exists(expected_unmatched_r1),\n f\"Unmatched R1 should be at {expected_unmatched_r1}\")\n self.assertTrue(os.path.exists(expected_unmatched_r2),\n f\"Unmatched R2 should be at {expected_unmatched_r2}\")\n\n def test_splitcode_barcode_trimming(self):\n \"\"\"\n Test that splitcode correctly trims inline barcodes from R1.\n\n Validates:\n - With left=1, barcode is removed from R1 sequences\n - R2 sequences are unchanged\n - Read count is preserved\n \"\"\"\n # Create BAM where R1 = AAAAAAAA + ACGTACGTACGT (20bp total)\n pool_bam = os.path.join(self.temp_dir, 'test_pool.bam')\n self.create_test_bam_with_inline_barcodes(pool_bam, num_reads=5, barcode=\"AAAAAAAA\")\n\n splitcode_config = os.path.join(self.temp_dir, 'config.txt')\n sample_id = \"Sample1_R1\"\n with open(splitcode_config, 'w') as f:\n f.write(\"tag\\tid\\tlocations\\tdistance\\tleft\\tright\\n\")\n # left=1 means trim the barcode from the left side\n # locations format: FILE_NUMBER:START_BP:END_BP\n f.write(f\"AAAAAAAA\\t{sample_id}\\t0:0:8\\t0\\t1\\t0\\n\")\n\n splitcode_keepfile = os.path.join(self.temp_dir, 'keep.txt')\n output_prefix = os.path.join(self.temp_dir, 'Sample1')\n with open(splitcode_keepfile, 'w') as f:\n f.write(f\"{sample_id}\\t{output_prefix}\\n\")\n\n viral_ngs.core.splitcode.run_splitcode_on_pool(\n pool_id=\"TestPool\",\n pool_bam_file=pool_bam,\n splitcode_config=splitcode_config,\n splitcode_keepfile=splitcode_keepfile,\n out_demux_dir_path=self.temp_dir,\n unmatched_name=\"unmatched\",\n threads_per_worker=1,\n out_dir_path=self.temp_dir,\n out_demux_dir_path_tmp=self.temp_dir\n )\n\n # Read output FASTQ and verify barcode was trimmed\n output_r1 = f\"{output_prefix}_R1.fastq\"\n with open(output_r1) as f:\n lines = f.readlines()\n\n # Should have 5 reads * 4 lines/read = 20 lines\n self.assertEqual(len(lines), 20, \"Should have 5 reads in output\")\n\n # Check first read's sequence (line 1, 0-indexed)\n first_seq = lines[1].strip()\n\n # After trimming 8bp barcode, should have 12bp remaining\n self.assertEqual(len(first_seq), 12,\n \"Sequence should be 12bp after trimming 8bp barcode\")\n\n # Should NOT start with the barcode\n self.assertFalse(first_seq.startswith(\"AAAAAAAA\"),\n \"Barcode should be trimmed from output\")\n\n # Should be the insert sequence\n self.assertEqual(first_seq, \"ACGTACGTACGT\",\n \"After trimming barcode, should have insert sequence\")\n\n def test_splitcode_with_append_run_id(self):\n \"\"\"\n Test that summary JSON lookup works correctly with append_run_id parameter.\n\n This tests the bug we fixed where append_run_id suffix was breaking JSON file lookup.\n\n Validates:\n - Summary JSON filename doesn't include append_run_id suffix\n - JSON can be found correctly even when pool_id has suffix appended\n \"\"\"\n pool_bam = os.path.join(self.temp_dir, 'test_pool.bam')\n self.create_test_bam_with_inline_barcodes(pool_bam, num_reads=3, barcode=\"GGGGGGGG\")\n\n splitcode_config = os.path.join(self.temp_dir, 'config.txt')\n sample_id = \"Sample1_R1\"\n with open(splitcode_config, 'w') as f:\n f.write(\"tag\\tid\\tlocations\\tdistance\\tleft\\tright\\n\")\n # locations format: FILE_NUMBER:START_BP:END_BP\n f.write(f\"GGGGGGGG\\t{sample_id}\\t0:0:8\\t0\\t1\\t0\\n\")\n\n splitcode_keepfile = os.path.join(self.temp_dir, 'keep.txt')\n output_prefix = os.path.join(self.temp_dir, 'Sample1')\n with open(splitcode_keepfile, 'w') as f:\n f.write(f\"{sample_id}\\t{output_prefix}\\n\")\n\n base_pool_id = \"Pool1\"\n out_demux_dir = self.temp_dir\n\n # Run splitcode (this doesn't use append_run_id directly, but creates the JSON)\n viral_ngs.core.splitcode.run_splitcode_on_pool(\n pool_id=base_pool_id,\n pool_bam_file=pool_bam,\n splitcode_config=splitcode_config,\n splitcode_keepfile=splitcode_keepfile,\n out_demux_dir_path=out_demux_dir,\n unmatched_name=\"unmatched\",\n threads_per_worker=1,\n out_dir_path=out_demux_dir,\n out_demux_dir_path_tmp=self.temp_dir\n )\n\n # Verify summary JSON is created with base pool_id (no suffix)\n expected_summary = os.path.join(out_demux_dir, f'{base_pool_id}_summary.json')\n self.assertTrue(os.path.exists(expected_summary),\n \"Summary JSON should use base pool_id without suffix\")\n\n # Now test that our lookup logic would work if pool_id had a suffix\n # This simulates what happens in create_splitcode_lookup_table\n pool_id_with_suffix = f\"{base_pool_id}.FLOWCELL123\"\n\n # The fix in illumina.py strips the suffix when looking for JSON file\n # Simulate that logic here\n append_run_id = \"FLOWCELL123\"\n if append_run_id and pool_id_with_suffix.endswith(f\".{append_run_id}\"):\n pool_for_lookup = pool_id_with_suffix[:-len(f\".{append_run_id}\")]\n else:\n pool_for_lookup = pool_id_with_suffix\n\n # Should find the file with the base pool_id\n import glob\n found_files = glob.glob(f\"{out_demux_dir}/{pool_for_lookup}_summary.json\")\n self.assertEqual(len(found_files), 1,\n \"Should find exactly one summary JSON file\")\n self.assertEqual(found_files[0], expected_summary,\n \"Should find the summary JSON with base pool_id\")\n\n\nclass TestGenerateSplitcodeConfigAndKeepFiles(TestCaseWithTmp):\n \"\"\"\n Test generate_splitcode_config_and_keep_files function.\n\n This function takes sample metadata and generates splitcode config/keep files.\n It's a pure text-file transformation that's ideal for unit testing.\n \"\"\"\n\n def setUp(self):\n super().setUp()\n self.temp_dir = tempfile.mkdtemp()\n\n def tearDown(self):\n shutil.rmtree(self.temp_dir, ignore_errors=True)\n super().tearDown()\n\n def test_basic_single_pool(self):\n \"\"\"Test basic config/keep generation with a single pool containing 2 samples.\"\"\"\n import pandas as pd\n import csv\n\n # Create test DataFrame matching inner_demux_mapper output\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA', 'CCCCCCCC'],\n 'run': ['Sample1.lLib1', 'Sample2.lLib1'],\n 'muxed_run': ['Pool1', 'Pool1']\n }, index=['Sample1', 'Sample2'])\n\n config_file, keep_file, sample_ids = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir, max_hamming_dist=1\n )\n\n # Verify return values\n self.assertTrue(os.path.exists(config_file), \"Config file should exist\")\n self.assertTrue(os.path.exists(keep_file), \"Keep file should exist\")\n self.assertEqual(sample_ids, ['Sample1.lLib1', 'Sample2.lLib1'])\n\n # Verify config file format\n with open(config_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n rows = list(reader)\n\n # Check header\n self.assertEqual(rows[0], ['tag', 'id', 'locations', 'distance', 'left', 'right'])\n\n # Check Sample1 config line\n self.assertEqual(rows[1][0], 'AAAAAAAA') # barcode\n self.assertEqual(rows[1][1], 'Sample1.lLib1') # ID (no _R1 suffix when using --keep-r1-r2)\n self.assertEqual(rows[1][2], '0:0:8') # locations\n self.assertEqual(rows[1][3], '1') # distance\n self.assertEqual(rows[1][4], '1') # left trim\n self.assertEqual(rows[1][5], '0') # right trim\n\n # Check Sample2 config line\n self.assertEqual(rows[2][0], 'CCCCCCCC')\n self.assertEqual(rows[2][1], 'Sample2.lLib1') # ID (no _R1 suffix when using --keep-r1-r2)\n self.assertEqual(rows[2][2], '0:0:8')\n\n # Verify keep file format (NO header)\n with open(keep_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n keep_rows = list(reader)\n\n # Should have 2 rows, no header\n self.assertEqual(len(keep_rows), 2)\n\n # Check Sample1 keep line (no _R1 suffix when using --keep-r1-r2)\n self.assertEqual(keep_rows[0][0], 'Sample1.lLib1')\n self.assertEqual(keep_rows[0][1], f'{self.temp_dir}/Sample1.lLib1')\n\n # Check Sample2 keep line (no _R1 suffix when using --keep-r1-r2)\n self.assertEqual(keep_rows[1][0], 'Sample2.lLib1')\n self.assertEqual(keep_rows[1][1], f'{self.temp_dir}/Sample2.lLib1')\n\n def test_variable_barcode_lengths(self):\n \"\"\"Test that config correctly handles different barcode lengths.\"\"\"\n import pandas as pd\n import csv\n\n df = pd.DataFrame({\n 'barcode_3': ['AAAA', 'CCCCCCCCCC', 'GGGGGGGG'], # 4bp, 10bp, 8bp\n 'run': ['S1.lL1', 'S2.lL1', 'S3.lL1'],\n 'muxed_run': ['Pool1', 'Pool1', 'Pool1']\n }, index=['S1', 'S2', 'S3'])\n\n config_file, keep_file, sample_ids = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir\n )\n\n with open(config_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n rows = list(reader)\n\n # Check locations are adjusted for barcode length\n self.assertEqual(rows[1][2], '0:0:4') # 4bp barcode\n self.assertEqual(rows[2][2], '0:0:10') # 10bp barcode\n self.assertEqual(rows[3][2], '0:0:8') # 8bp barcode\n\n def test_hamming_distance_parameter(self):\n \"\"\"Test that max_hamming_dist parameter is correctly written to config.\"\"\"\n import pandas as pd\n import csv\n\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA'],\n 'run': ['Sample1.lLib1'],\n 'muxed_run': ['Pool1']\n }, index=['Sample1'])\n\n # Test distance=0 (exact match only)\n config_file, _, _ = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir, max_hamming_dist=0\n )\n\n with open(config_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n rows = list(reader)\n\n self.assertEqual(rows[1][3], '0') # distance column\n\n # Test distance=2\n config_file, _, _ = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir, max_hamming_dist=2\n )\n\n with open(config_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n rows = list(reader)\n\n self.assertEqual(rows[1][3], '2') # distance column\n\n def test_r1_trim_bp_right_of_barcode(self):\n \"\"\"Test that r1_trim_bp_right_of_barcode correctly sets left trim parameter.\"\"\"\n import pandas as pd\n import csv\n\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA'],\n 'run': ['Sample1.lLib1'],\n 'muxed_run': ['Pool1']\n }, index=['Sample1'])\n\n # Test default (None) - should be \"1\"\n config_file, _, _ = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir, r1_trim_bp_right_of_barcode=None\n )\n\n with open(config_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n rows = list(reader)\n\n self.assertEqual(rows[1][4], '1') # left column: \"1\" means trim barcode only\n\n # Test with 5 extra bp\n config_file, _, _ = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir, r1_trim_bp_right_of_barcode=5\n )\n\n with open(config_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n rows = list(reader)\n\n self.assertEqual(rows[1][4], '1:5') # left column: \"1:5\" means trim barcode + 5bp\n\n def test_multi_pool_filtering(self):\n \"\"\"Test that function correctly filters to only the specified pool.\"\"\"\n import pandas as pd\n import csv\n\n # DataFrame with samples from two different pools\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA', 'CCCCCCCC', 'GGGGGGGG'],\n 'run': ['S1.lL1', 'S2.lL1', 'S3.lL1'],\n 'muxed_run': ['Pool1', 'Pool2', 'Pool1'] # Mixed pools\n }, index=['S1', 'S2', 'S3'])\n\n # Generate for Pool1 only\n config_file, keep_file, sample_ids = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir\n )\n\n # Should only have S1 and S3 (Pool1 samples)\n self.assertEqual(sample_ids, ['S1.lL1', 'S3.lL1'])\n\n with open(config_file) as f:\n reader = csv.reader(f, delimiter='\\t')\n rows = list(reader)\n\n # Header + 2 sample rows (S1 and S3)\n self.assertEqual(len(rows), 3)\n self.assertEqual(rows[1][0], 'AAAAAAAA') # S1 barcode\n self.assertEqual(rows[2][0], 'GGGGGGGG') # S3 barcode\n\n # S2 (Pool2) should NOT be present\n barcodes_in_config = [row[0] for row in rows[1:]]\n self.assertNotIn('CCCCCCCC', barcodes_in_config)\n\n def test_empty_pool_raises_error(self):\n \"\"\"Test that requesting a non-existent pool raises ValueError.\"\"\"\n import pandas as pd\n\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA'],\n 'run': ['Sample1.lLib1'],\n 'muxed_run': ['Pool1']\n }, index=['Sample1'])\n\n # Try to generate for Pool2 (which doesn't exist)\n with self.assertRaises(ValueError) as context:\n viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool2', self.temp_dir\n )\n\n self.assertIn('No samples found', str(context.exception))\n self.assertIn('Pool2', str(context.exception))\n\n def test_config_keep_id_matching(self):\n \"\"\"\n Test the critical requirement: config file \"id\" must match keep file column 1.\n\n This is the most common source of splitcode errors.\n \"\"\"\n import pandas as pd\n import csv\n\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA', 'TTTTTTTT'],\n 'run': ['MySample.lMyLib.FC.1', 'Other.lLib2.FC.1'],\n 'muxed_run': ['Pool1', 'Pool1']\n }, index=['MySample', 'Other'])\n\n config_file, keep_file, _ = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', self.temp_dir\n )\n\n # Read both files\n with open(config_file) as f:\n config_rows = list(csv.reader(f, delimiter='\\t'))\n\n with open(keep_file) as f:\n keep_rows = list(csv.reader(f, delimiter='\\t'))\n\n # Extract IDs from config file (column 1, skip header)\n config_ids = [row[1] for row in config_rows[1:]]\n\n # Extract IDs from keep file (column 0, no header)\n keep_ids = [row[0] for row in keep_rows]\n\n # They MUST match exactly\n self.assertEqual(config_ids, keep_ids)\n # No _R1 suffix when using --keep-r1-r2 mode (splitcode adds the suffixes automatically)\n self.assertEqual(config_ids, ['MySample.lMyLib.FC.1', 'Other.lLib2.FC.1'])\n\n def test_output_prefix_path_construction(self):\n \"\"\"Test that keep file constructs correct output paths.\"\"\"\n import pandas as pd\n import csv\n\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA'],\n 'run': ['Sample1.lLib1.FLOWCELL.1'],\n 'muxed_run': ['Pool1']\n }, index=['Sample1'])\n\n output_dir = \"/custom/output/path\"\n _, keep_file, _ = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, 'Pool1', output_dir\n )\n\n with open(keep_file) as f:\n keep_rows = list(csv.reader(f, delimiter='\\t'))\n\n # Output prefix should be: {output_dir}/{sample_library_id}\n expected_prefix = f\"{output_dir}/Sample1.lLib1.FLOWCELL.1\"\n self.assertEqual(keep_rows[0][1], expected_prefix)\n\n # Note: splitcode will append _R1.fastq and _R2.fastq to this prefix\n\n def test_complex_realistic_scenario(self):\n \"\"\"\n Test a realistic scenario with multiple samples, realistic IDs, and mixed parameters.\n \"\"\"\n import pandas as pd\n import csv\n\n # Realistic sample sheet data\n df = pd.DataFrame({\n 'barcode_3': ['AAAAAAAA', 'CCCCCCCC', 'GGGGGGGG', 'TTTTTTTT'],\n 'run': [\n 'Sample1.lPool_1.HHJYWDRX5.6',\n 'Sample2.lPool_1.HHJYWDRX5.6',\n 'Sample3.lPool_2.HHJYWDRX5.6',\n 'Sample4.lPool_2.HHJYWDRX5.6'\n ],\n 'muxed_run': [\n 'ATCGATCG-GCTAGCTA.lPool_1.HHJYWDRX5.6',\n 'ATCGATCG-GCTAGCTA.lPool_1.HHJYWDRX5.6',\n 'TTTTAAAA-CCCCGGGG.lPool_2.HHJYWDRX5.6',\n 'TTTTAAAA-CCCCGGGG.lPool_2.HHJYWDRX5.6'\n ]\n }, index=['Sample1', 'Sample2', 'Sample3', 'Sample4'])\n\n # Generate for Pool_1 only\n pool_id = 'ATCGATCG-GCTAGCTA.lPool_1.HHJYWDRX5.6'\n config_file, keep_file, sample_ids = viral_ngs.core.splitcode.generate_splitcode_config_and_keep_files(\n df, pool_id, '/output', max_hamming_dist=1, r1_trim_bp_right_of_barcode=3\n )\n\n # Should have Sample1 and Sample2\n self.assertEqual(len(sample_ids), 2)\n self.assertIn('Sample1.lPool_1.HHJYWDRX5.6', sample_ids)\n self.assertIn('Sample2.lPool_1.HHJYWDRX5.6', sample_ids)\n\n # Verify config file\n with open(config_file) as f:\n config_rows = list(csv.reader(f, delimiter='\\t'))\n\n # Header + 2 samples\n self.assertEqual(len(config_rows), 3)\n\n # Verify first sample (no _R1 suffix when using --keep-r1-r2)\n self.assertEqual(config_rows[1][0], 'AAAAAAAA')\n self.assertEqual(config_rows[1][1], 'Sample1.lPool_1.HHJYWDRX5.6')\n self.assertEqual(config_rows[1][2], '0:0:8')\n self.assertEqual(config_rows[1][3], '1')\n self.assertEqual(config_rows[1][4], '1:3') # Trim barcode + 3bp\n\n # Verify keep file (no _R1 suffix when using --keep-r1-r2)\n with open(keep_file) as f:\n keep_rows = list(csv.reader(f, delimiter='\\t'))\n\n self.assertEqual(len(keep_rows), 2)\n self.assertEqual(keep_rows[0][0], 'Sample1.lPool_1.HHJYWDRX5.6')\n self.assertEqual(keep_rows[0][1], '/output/Sample1.lPool_1.HHJYWDRX5.6')\n\n\nclass TestSplitcodeSummaryJSONErrorHandling(TestCaseWithTmp):\n \"\"\"\n Test error handling when loading splitcode summary JSON files.\n\n These tests validate that we provide helpful debugging information\n when JSON files are missing or malformed.\n \"\"\"\n\n def setUp(self):\n super().setUp()\n self.temp_dir = tempfile.mkdtemp()\n\n def tearDown(self):\n shutil.rmtree(self.temp_dir, ignore_errors=True)\n super().tearDown()\n\n def test_missing_json_file_provides_debugging_info(self):\n \"\"\"Test that missing JSON file error includes directory listing.\"\"\"\n import pandas as pd\n\n # Create a sample sheet pointing to a pool\n sample_sheet = os.path.join(self.temp_dir, 'samples.tsv')\n with open(sample_sheet, 'w') as f:\n f.write(\"sample\\tlibrary_id_per_sample\\tbarcode_1\\tbarcode_2\\tbarcode_3\\n\")\n f.write(\"Sample1\\tLib1\\tATCGATCG\\tGCTAGCTA\\tAAAAAAAA\\n\")\n\n # Create the output directory with some files but NOT the expected JSON\n out_dir = os.path.join(self.temp_dir, 'output')\n os.makedirs(out_dir, exist_ok=True)\n\n # Create some dummy files to appear in the directory listing\n with open(os.path.join(out_dir, 'other_file.txt'), 'w') as f:\n f.write(\"dummy\")\n with open(os.path.join(out_dir, 'wrong_pool_summary.json'), 'w') as f:\n f.write('{\"tag_qc\": []}')\n\n # csv_out determines outDir - put it in the output directory\n csv_out = os.path.join(out_dir, 'lut.csv')\n\n # Should raise FileNotFoundError with helpful message\n with self.assertRaises(FileNotFoundError) as context:\n viral_ngs.core.splitcode.create_splitcode_lookup_table(\n sample_sheet,\n csv_out,\n unmatched_name=\"Unmatched\"\n )\n\n # Check that error message mentions the pool\n error_msg = str(context.exception)\n self.assertIn('ATCGATCG-GCTAGCTA', error_msg)\n self.assertIn('summary.json', error_msg)\n\n def test_malformed_json_provides_file_preview(self):\n \"\"\"Test that malformed JSON error includes file content preview.\"\"\"\n import pandas as pd\n\n # Create a sample sheet\n sample_sheet = os.path.join(self.temp_dir, 'samples.tsv')\n with open(sample_sheet, 'w') as f:\n f.write(\"sample\\tlibrary_id_per_sample\\tbarcode_1\\tbarcode_2\\tbarcode_3\\n\")\n f.write(\"Sample1\\tLib1\\tATCGATCG\\tGCTAGCTA\\tAAAAAAAA\\n\")\n\n out_dir = os.path.join(self.temp_dir, 'output')\n os.makedirs(out_dir, exist_ok=True)\n\n # Create a malformed JSON file\n pool_name = \"ATCGATCG-GCTAGCTA.lLib1\"\n malformed_json = os.path.join(out_dir, f'{pool_name}_summary.json')\n with open(malformed_json, 'w') as f:\n f.write('{\"tag_qc\": [this is not valid json}')\n\n # csv_out determines outDir - put it in the output directory\n csv_out = os.path.join(out_dir, 'lut.csv')\n\n # Should raise JSONDecodeError\n with self.assertRaises(json.JSONDecodeError):\n viral_ngs.core.splitcode.create_splitcode_lookup_table(\n sample_sheet,\n csv_out,\n unmatched_name=\"Unmatched\"\n )\n\n\nclass TestConvertSplitcodeMetricsToPicardStyle(TestCaseWithTmp):\n \"\"\"\n Test convert_splitcode_demux_metrics_to_picard_style function.\n\n This function converts splitcode CSV metrics into Picard-style TSV format.\n It's a pure data transformation function ideal for unit testing.\n\n Input CSV format (from create_splitcode_lookup_table):\n - sample, barcode_1, barcode_2, inline_barcode, library_id, run\n - num_reads_hdistance0, num_reads_hdistance1, num_reads_total\n\n Output TSV format (Picard-style ExtractIlluminaBarcodes.BarcodeMetric):\n - BARCODE, BARCODE_WITHOUT_DELIMITER, BARCODE_NAME, LIBRARY_NAME\n - READS, PF_READS, PERFECT_MATCHES, PF_PERFECT_MATCHES\n - ONE_MISMATCH_MATCHES, PF_ONE_MISMATCH_MATCHES\n - PCT_MATCHES, RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT\n - PF_PCT_MATCHES, PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT, PF_NORMALIZED_MATCHES\n \"\"\"\n\n def setUp(self):\n super().setUp()\n self.temp_dir = tempfile.mkdtemp()\n\n def tearDown(self):\n shutil.rmtree(self.temp_dir, ignore_errors=True)\n super().tearDown()\n\n def test_basic_conversion(self):\n \"\"\"Test basic conversion with minimal input.\"\"\"\n import pandas as pd\n import csv\n\n # Create minimal input CSV\n # Note: Numeric columns are strings because that's how create_splitcode_lookup_table writes them\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1'],\n 'barcode_1': ['ATCGATCG'],\n 'barcode_2': ['GCTAGCTA'],\n 'inline_barcode': ['AAAAAAAA'],\n 'library_id': ['Lib1'],\n 'run': ['Sample1.lLib1'],\n 'num_reads_hdistance0': [100],\n 'num_reads_hdistance1': [10],\n 'num_reads_total': [110]\n })\n df_input.to_csv(input_csv, index=False)\n\n # Convert\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv\n )\n\n # Verify output exists\n self.assertTrue(os.path.exists(output_tsv))\n\n # Read output\n with open(output_tsv) as f:\n lines = f.readlines()\n\n # Check header comment\n self.assertTrue(lines[0].startswith('## METRICS CLASS'))\n\n # Parse TSV data (skip header comment)\n with open(output_tsv) as f:\n next(f) # Skip comment line\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n self.assertEqual(len(rows), 1)\n\n # Check barcode formatting\n self.assertEqual(rows[0]['BARCODE'], 'ATCGATCG-GCTAGCTA-AAAAAAAA')\n self.assertEqual(rows[0]['BARCODE_WITHOUT_DELIMITER'], 'ATCGATCGGCTAGCTAAAAAAAAA')\n self.assertEqual(rows[0]['BARCODE_NAME'], 'Sample1')\n self.assertEqual(rows[0]['LIBRARY_NAME'], 'Sample1.lLib1')\n\n # Check read counts\n self.assertEqual(rows[0]['READS'], '110')\n self.assertEqual(rows[0]['PF_READS'], '110')\n self.assertEqual(rows[0]['PERFECT_MATCHES'], '100')\n self.assertEqual(rows[0]['PF_PERFECT_MATCHES'], '100')\n self.assertEqual(rows[0]['ONE_MISMATCH_MATCHES'], '10')\n self.assertEqual(rows[0]['PF_ONE_MISMATCH_MATCHES'], '10')\n\n def test_missing_required_column_raises_error(self):\n \"\"\"Test that missing required columns raise ValueError.\"\"\"\n import pandas as pd\n\n # Create CSV missing required column\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1'],\n 'barcode_1': ['ATCGATCG'],\n # Missing 'barcode_2'\n 'num_reads_hdistance0': [100],\n 'num_reads_hdistance1': [10],\n 'num_reads_total': [110]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n\n with self.assertRaises(ValueError) as context:\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv\n )\n\n self.assertIn('barcode_2', str(context.exception))\n self.assertIn('missing', str(context.exception).lower())\n\n def test_empty_required_column_raises_error(self):\n \"\"\"Test that entirely empty required columns raise ValueError.\"\"\"\n import pandas as pd\n\n # Create CSV with empty required column\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1'],\n 'barcode_1': ['ATCGATCG'],\n 'barcode_2': ['GCTAGCTA'],\n 'num_reads_hdistance0': [None], # Empty column\n 'num_reads_hdistance1': [10],\n 'num_reads_total': [110]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n\n with self.assertRaises(ValueError) as context:\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv\n )\n\n self.assertIn('num_reads_hdistance0', str(context.exception))\n self.assertIn('empty', str(context.exception).lower())\n\n def test_barcode_combination_without_inline(self):\n \"\"\"Test barcode combination when inline_barcode is missing.\"\"\"\n import pandas as pd\n import csv\n\n # Create input CSV without inline_barcode column\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1'],\n 'barcode_1': ['ATCGATCG'],\n 'barcode_2': ['GCTAGCTA'],\n 'library_id': ['Lib1'],\n 'num_reads_hdistance0': [100],\n 'num_reads_hdistance1': [10],\n 'num_reads_total': [110]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv\n )\n\n # Read output\n with open(output_tsv) as f:\n next(f) # Skip comment\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Should only have barcode_1 and barcode_2\n self.assertEqual(rows[0]['BARCODE'], 'ATCGATCG-GCTAGCTA')\n self.assertEqual(rows[0]['BARCODE_WITHOUT_DELIMITER'], 'ATCGATCGGCTAGCTA')\n\n def test_library_name_fallback(self):\n \"\"\"Test LIBRARY_NAME falls back to library_id if 'run' is missing.\"\"\"\n import pandas as pd\n import csv\n\n # Create input CSV with library_id but no 'run' column\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1'],\n 'barcode_1': ['ATCGATCG'],\n 'barcode_2': ['GCTAGCTA'],\n 'library_id': ['MyLibraryID'],\n 'num_reads_hdistance0': [100],\n 'num_reads_hdistance1': [10],\n 'num_reads_total': [110]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n self.assertEqual(rows[0]['LIBRARY_NAME'], 'MyLibraryID')\n\n def test_library_name_uses_barcode_name_fallback(self):\n \"\"\"Test LIBRARY_NAME falls back to BARCODE_NAME if both run and library_id missing.\"\"\"\n import pandas as pd\n import csv\n\n # Create input CSV without run or library_id\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1'],\n 'barcode_1': ['ATCGATCG'],\n 'barcode_2': ['GCTAGCTA'],\n 'num_reads_hdistance0': [100],\n 'num_reads_hdistance1': [10],\n 'num_reads_total': [110]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n self.assertEqual(rows[0]['LIBRARY_NAME'], 'Sample1')\n\n def test_combine_innerbarcode_unmatched_false(self):\n \"\"\"Test that unmatched rows are NOT collapsed when combine_innerbarcode_unmatched=False.\"\"\"\n import pandas as pd\n import csv\n\n # Create input with multiple unmatched (all-N inline barcode) rows\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1', 'Sample2', 'Sample3'],\n 'barcode_1': ['ATCGATCG', 'ATCGATCG', 'GCTAGCTA'],\n 'barcode_2': ['GCTAGCTA', 'GCTAGCTA', 'ATCGATCG'],\n 'inline_barcode': ['NNNNNNNN', 'NNNNNNNN', 'AAAAAAAA'],\n 'library_id': ['Lib1', 'Lib1', 'Lib2'],\n 'num_reads_hdistance0': [100, 50, 200],\n 'num_reads_hdistance1': [10, 5, 20],\n 'num_reads_total': [110, 55, 220]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n combine_innerbarcode_unmatched=False\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Should have all 3 rows (no collapsing)\n self.assertEqual(len(rows), 3)\n\n def test_combine_innerbarcode_unmatched_true_with_report_within_pools_true(self):\n \"\"\"Test that unmatched rows ARE collapsed when combine_innerbarcode_unmatched=True.\"\"\"\n import pandas as pd\n import csv\n\n # Create input with multiple unmatched (all-N inline barcode) rows in same pool\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Unmatched.Pool1', 'Unmatched.Pool1_2', 'Sample3'],\n 'barcode_1': ['ATCGATCG', 'ATCGATCG', 'GCTAGCTA'],\n 'barcode_2': ['GCTAGCTA', 'GCTAGCTA', 'ATCGATCG'],\n 'inline_barcode': ['NNNNNNNN', 'NNNNNNNN', 'AAAAAAAA'],\n 'library_id': ['Lib1', 'Lib1', 'Lib2'],\n 'num_reads_hdistance0': [100, 50, 200],\n 'num_reads_hdistance1': [10, 5, 20],\n 'num_reads_total': [110, 55, 220]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n combine_innerbarcode_unmatched=True,\n report_within_pools=True\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Should have 2 rows: collapsed N row + Sample3\n self.assertEqual(len(rows), 2)\n\n # Find the collapsed row\n n_row = [r for r in rows if r['BARCODE'] == 'N'][0]\n\n # Check that reads were summed\n self.assertEqual(n_row['READS'], str(110 + 55))\n self.assertEqual(n_row['PERFECT_MATCHES'], str(100 + 50))\n self.assertEqual(n_row['ONE_MISMATCH_MATCHES'], str(10 + 5))\n\n def test_combine_innerbarcode_unmatched_true_with_report_within_pools_false(self):\n \"\"\"Test all-N detection uses entire barcode when report_within_pools=False.\"\"\"\n import pandas as pd\n import csv\n\n # Create input with all-N full barcodes (not just inline)\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Unmatched1', 'Unmatched2', 'Sample3'],\n 'barcode_1': ['NNNNNNNN', 'NNNNNNNN', 'ATCGATCG'],\n 'barcode_2': ['NNNNNNNN', 'NNNNNNNN', 'GCTAGCTA'],\n 'inline_barcode': ['NNNNNNNN', 'NNNNNNNN', 'AAAAAAAA'],\n 'library_id': ['Lib1', 'Lib1', 'Lib2'],\n 'num_reads_hdistance0': [100, 50, 200],\n 'num_reads_hdistance1': [10, 5, 20],\n 'num_reads_total': [110, 55, 220]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n combine_innerbarcode_unmatched=True,\n report_within_pools=False\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Should have 2 rows: collapsed N row + Sample3\n self.assertEqual(len(rows), 2)\n\n n_row = [r for r in rows if r['BARCODE'] == 'N'][0]\n self.assertEqual(n_row['READS'], str(110 + 55))\n\n def test_stats_computation_global(self):\n \"\"\"Test statistics are computed globally when report_within_pools=False.\"\"\"\n import pandas as pd\n import csv\n\n # Create input with 2 samples\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1', 'Sample2'],\n 'barcode_1': ['ATCGATCG', 'GCTAGCTA'],\n 'barcode_2': ['GCTAGCTA', 'ATCGATCG'],\n 'library_id': ['Lib1', 'Lib2'],\n 'num_reads_hdistance0': [100, 200],\n 'num_reads_hdistance1': [10, 20],\n 'num_reads_total': [110, 220]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n report_within_pools=False\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Sample2 has max reads (220), so it should have ratio=1.0\n sample2 = [r for r in rows if r['BARCODE_NAME'] == 'Sample2'][0]\n self.assertEqual(float(sample2['RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT']), 1.0)\n\n # Sample1 has 110 reads, ratio should be 110/220 = 0.5\n sample1 = [r for r in rows if r['BARCODE_NAME'] == 'Sample1'][0]\n self.assertAlmostEqual(float(sample1['RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT']), 0.5, places=6)\n\n def test_stats_computation_within_pools(self):\n \"\"\"Test statistics are computed per pool when report_within_pools=True.\"\"\"\n import pandas as pd\n import csv\n\n # Create input with 2 pools, 2 samples each\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['S1', 'S2', 'S3', 'S4'],\n 'barcode_1': ['ATCGATCG', 'ATCGATCG', 'GCTAGCTA', 'GCTAGCTA'],\n 'barcode_2': ['GCTAGCTA', 'GCTAGCTA', 'ATCGATCG', 'ATCGATCG'],\n 'inline_barcode': ['AAAAAAAA', 'CCCCCCCC', 'GGGGGGGG', 'TTTTTTTT'],\n 'library_id': ['Lib1', 'Lib1', 'Lib2', 'Lib2'],\n 'num_reads_hdistance0': [100, 200, 50, 150],\n 'num_reads_hdistance1': [10, 20, 5, 15],\n 'num_reads_total': [110, 220, 55, 165]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n report_within_pools=True\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Pool 1 (ATCGATCG-GCTAGCTA): S2 has max (220)\n s2 = [r for r in rows if r['BARCODE_NAME'] == 'S2'][0]\n self.assertEqual(float(s2['RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT']), 1.0)\n\n # Pool 1: S1 has 110, ratio = 110/220 = 0.5\n s1 = [r for r in rows if r['BARCODE_NAME'] == 'S1'][0]\n self.assertAlmostEqual(float(s1['RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT']), 0.5, places=6)\n\n # Pool 2 (GCTAGCTA-ATCGATCG): S4 has max (165)\n s4 = [r for r in rows if r['BARCODE_NAME'] == 'S4'][0]\n self.assertEqual(float(s4['RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT']), 1.0)\n\n # Pool 2: S3 has 55, ratio = 55/165 ≈ 0.333\n s3 = [r for r in rows if r['BARCODE_NAME'] == 'S3'][0]\n self.assertAlmostEqual(float(s3['RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT']), 55/165, places=6)\n\n def test_pct_matches_computation(self):\n \"\"\"Test PCT_MATCHES is computed correctly.\"\"\"\n import pandas as pd\n import csv\n\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1', 'Sample2'],\n 'barcode_1': ['ATCGATCG', 'ATCGATCG'],\n 'barcode_2': ['GCTAGCTA', 'GCTAGCTA'],\n 'library_id': ['Lib1', 'Lib1'],\n 'num_reads_hdistance0': [100, 200],\n 'num_reads_hdistance1': [10, 20],\n 'num_reads_total': [110, 220]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n report_within_pools=True\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Total reads in pool: 110 + 220 = 330\n # Sample1 perfect matches: 100, PCT_MATCHES = 100/330\n s1 = [r for r in rows if r['BARCODE_NAME'] == 'Sample1'][0]\n self.assertAlmostEqual(float(s1['PCT_MATCHES']), 100/330, places=6)\n\n # Sample2 perfect matches: 200, PCT_MATCHES = 200/330\n s2 = [r for r in rows if r['BARCODE_NAME'] == 'Sample2'][0]\n self.assertAlmostEqual(float(s2['PCT_MATCHES']), 200/330, places=6)\n\n def test_normalized_matches_excludes_all_n(self):\n \"\"\"Test PF_NORMALIZED_MATCHES excludes all-N rows from mean calculation.\"\"\"\n import pandas as pd\n import csv\n\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1', 'Sample2', 'Unmatched'],\n 'barcode_1': ['ATCGATCG', 'ATCGATCG', 'ATCGATCG'],\n 'barcode_2': ['GCTAGCTA', 'GCTAGCTA', 'GCTAGCTA'],\n 'inline_barcode': ['AAAAAAAA', 'CCCCCCCC', 'NNNNNNNN'],\n 'library_id': ['Lib1', 'Lib1', 'Lib1'],\n 'num_reads_hdistance0': [100, 200, 50],\n 'num_reads_hdistance1': [10, 20, 5],\n 'num_reads_total': [110, 220, 55]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n report_within_pools=True\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # Mean PF_READS should exclude unmatched (all-N)\n # Mean = (110 + 220) / 2 = 165\n # Sample1: PF_NORMALIZED_MATCHES = 100 / 165\n s1 = [r for r in rows if r['BARCODE_NAME'] == 'Sample1'][0]\n self.assertAlmostEqual(float(s1['PF_NORMALIZED_MATCHES']), 100/165, places=6)\n\n def test_custom_demux_function_name(self):\n \"\"\"Test that custom demux_function parameter appears in header.\"\"\"\n import pandas as pd\n\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1'],\n 'barcode_1': ['ATCGATCG'],\n 'barcode_2': ['GCTAGCTA'],\n 'library_id': ['Lib1'],\n 'num_reads_hdistance0': [100],\n 'num_reads_hdistance1': [10],\n 'num_reads_total': [110]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n custom_name = \"MyCustomDemuxFunction\"\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv,\n demux_function=custom_name\n )\n\n with open(output_tsv) as f:\n header = f.readline()\n\n self.assertIn(custom_name, header)\n\n def test_zero_reads_handling(self):\n \"\"\"Test that zero reads don't cause division by zero errors.\"\"\"\n import pandas as pd\n import csv\n\n input_csv = os.path.join(self.temp_dir, 'input.csv')\n df_input = pd.DataFrame({\n 'sample': ['Sample1', 'Sample2'],\n 'barcode_1': ['ATCGATCG', 'GCTAGCTA'],\n 'barcode_2': ['GCTAGCTA', 'ATCGATCG'],\n 'library_id': ['Lib1', 'Lib2'],\n 'num_reads_hdistance0': [0, 0],\n 'num_reads_hdistance1': [0, 0],\n 'num_reads_total': [0, 0]\n })\n df_input.to_csv(input_csv, index=False)\n\n output_tsv = os.path.join(self.temp_dir, 'output.tsv')\n # Should not raise any errors\n viral_ngs.core.splitcode.convert_splitcode_demux_metrics_to_picard_style(\n input_csv,\n output_tsv\n )\n\n with open(output_tsv) as f:\n next(f)\n reader = csv.DictReader(f, delimiter='\\t')\n rows = list(reader)\n\n # All percentage/ratio columns should be 0\n for row in rows:\n self.assertEqual(float(row['PCT_MATCHES']), 0.0)\n self.assertEqual(float(row['RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT']), 0.0)\n self.assertEqual(float(row['PF_NORMALIZED_MATCHES']), 0.0)\n" }, { "path": "tests/unit/core/test_tools_trimmomatic.py", "content": "# Unit tests for Trimmomatic tool\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport os\nimport unittest\nimport viral_ngs.core\nimport viral_ngs.core\nimport viral_ngs.core.trimmomatic\nfrom tests import TestCaseWithTmp, assert_equal_contents\n\nclass TestTrimmomatic(TestCaseWithTmp):\n\n def test_trimmomatic_paired(self):\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n inFastq1 = os.path.join(myInputDir, 'in1.fastq')\n inFastq2 = os.path.join(myInputDir, 'in2.fastq')\n pairedOutFastq1 = viral_ngs.core.file.mkstempfname('.out1.fastq')\n pairedOutFastq2 = viral_ngs.core.file.mkstempfname('.out2.fastq')\n clipFasta = os.path.join(myInputDir, 'clip.fasta')\n viral_ngs.core.trimmomatic.TrimmomaticTool().execute(inFastq1, inFastq2, pairedOutFastq1, pairedOutFastq2, clipFasta)\n\n # Check that results match expected\n expected1Fastq = os.path.join(myInputDir, 'expected1.fastq')\n expected2Fastq = os.path.join(myInputDir, 'expected2.fastq')\n assert_equal_contents(self, pairedOutFastq1, expected1Fastq)\n assert_equal_contents(self, pairedOutFastq2, expected2Fastq)\n\n\n def test_trimmomatic_paired_maxinfo(self):\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n inFastq1 = os.path.join(myInputDir, 'in1.fastq')\n inFastq2 = os.path.join(myInputDir, 'in2.fastq')\n clipFasta = os.path.join(myInputDir, 'clip.fasta')\n with viral_ngs.core.file.tempfnames(('.out1.fastq', '.out2.fastq')) as (pairedOutFastq1, pairedOutFastq2):\n viral_ngs.core.trimmomatic.TrimmomaticTool().execute(inFastq1, inFastq2, pairedOutFastq1, pairedOutFastq2, clipFasta,\n maxinfo_target_length=30, maxinfo_strictness=.3)\n\n # Check that results match expected\n expected1Fastq = os.path.join(myInputDir, 'expected1.maxinfo.fastq')\n expected2Fastq = os.path.join(myInputDir, 'expected2.maxinfo.fastq')\n assert_equal_contents(self, pairedOutFastq1, expected1Fastq)\n assert_equal_contents(self, pairedOutFastq2, expected2Fastq)\n\n\n def test_trimmomatic_single(self):\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n inFastq1 = os.path.join(myInputDir, 'in1.fastq')\n pairedOutFastq1 = viral_ngs.core.file.mkstempfname('.out1.fastq')\n pairedOutFastq2 = viral_ngs.core.file.mkstempfname('.out2.fastq')\n unpairedOutFastq1 = viral_ngs.core.file.mkstempfname('.out3.fastq')\n unpairedOutFastq2 = viral_ngs.core.file.mkstempfname('.out4.fastq')\n clipFasta = os.path.join(myInputDir, 'clip.fasta')\n viral_ngs.core.trimmomatic.TrimmomaticTool().execute(inFastq1, None, pairedOutFastq1, pairedOutFastq2, clipFasta,\n unpairedOutFastq1=unpairedOutFastq1, unpairedOutFastq2=unpairedOutFastq2)\n\n # Check that results match expected\n emptyFastq = os.path.join(myInputDir, 'empty.fastq')\n expectedFastq = os.path.join(myInputDir, 'expected1.fastq')\n assert_equal_contents(self, pairedOutFastq1, emptyFastq)\n assert_equal_contents(self, pairedOutFastq2, emptyFastq)\n assert_equal_contents(self, unpairedOutFastq1, expectedFastq)\n" }, { "path": "tests/unit/core/test_util_file.py", "content": "# Unit tests for viral_ngs.core.file.py\n\n__author__ = \"ilya@broadinstitute.org\"\n\nimport os, sys, os.path\nimport builtins\nimport shutil\nimport filecmp\nimport subprocess\nimport tarfile\nimport tempfile\nimport viral_ngs.core\nfrom tests import TestCaseWithTmp\nimport pytest\nfrom unittest.mock import patch\n\nif sys.version_info >= (3, 10, 12):\n '''\n Set the default extraction filter at class instance level for the tarfile\n module, to avoid needing to specify it every time we extract a tarball.\n The extraction filter avoids extracting \"unsafe\" items from tarballs, and\n is available in Python 3.10.12+. This sets the default to \"tar_filter\".\n For other filter types and general info on the tarfile module, see:\n https://docs.python.org/3.12/library/tarfile.html#tarfile.tar_filter\n https://docs.python.org/3.12/library/tarfile.html#extraction-filters\n '''\n tarfile.TarFile.extraction_filter = staticmethod(tarfile.tar_filter) if hasattr(tarfile, 'data_filter') else (lambda member, path: member)\n\ndef testTempFiles():\n '''Test creation of tempfiles using context managers, as well as dump_file/slurp_file routines'''\n tmp_fns = []\n sfx='tmp-file-test'\n with viral_ngs.core.file.tempfname(sfx) as my_tmp_fn:\n tmp_dir_listing = os.listdir( os.path.dirname( my_tmp_fn ) )\n assert os.path.basename( my_tmp_fn ) in tmp_dir_listing\n\n with viral_ngs.core.file.tempfnames((sfx+'-A',sfx+'-B')) as my_tmp_fns:\n\n assert len(my_tmp_fns)==2\n for fn in my_tmp_fns:\n assert os.path.dirname(fn) == os.path.dirname(my_tmp_fn)\n assert os.path.basename(fn) not in tmp_dir_listing\n\n for fn in my_tmp_fns:\n\n assert sfx in fn\n assert os.path.isfile(fn)\n assert os.path.getsize(fn)==0\n assert os.access(fn, os.R_OK | os.W_OK)\n\n fileValue='my\\ntest\\ndata\\n' + fn + '\\n'\n viral_ngs.core.file.dump_file( fname=fn, value=fileValue )\n assert os.path.isfile(fn)\n assert os.path.getsize(fn) == len(fileValue)\n assert viral_ngs.core.file.slurp_file(fn) == fileValue\n\n viral_ngs.core.file.make_empty(fn)\n assert os.path.getsize(fn)==0\n\n tmp_fns.append(fn)\n\n assert os.path.isfile(my_tmp_fn) and not os.path.isfile(my_tmp_fns[0]) and not os.path.isfile(my_tmp_fns[1])\n\n largeString = 'A' * (2*1024*1024)\n viral_ngs.core.file.dump_file(fname=my_tmp_fn, value=largeString)\n with pytest.raises(RuntimeError):\n viral_ngs.core.file.slurp_file(my_tmp_fn, maxSizeMb=1)\n\n assert not os.path.isfile(my_tmp_fn)\n\ndef test_check_paths(tmpdir):\n '''Test the viral_ngs.core.file.check_paths()'''\n from os.path import join\n from viral_ngs.core.file import check_paths\n inDir = viral_ngs.core.file.get_test_input_path()\n def test_f(f):\n return join(inDir, f)\n check_paths(read=test_f('empty.bam'))\n check_paths(read=[test_f('empty.bam')])\n with pytest.raises(Exception):\n check_paths(read=test_f('non_existent_file'))\n with pytest.raises(Exception):\n check_paths(write='/non/writable/dir/file.txt')\n writable_dir = str(tmpdir)\n check_paths(write=(join(writable_dir, 'mydata1.txt'),\n join(writable_dir, 'mydata2.txt')))\n with pytest.raises(Exception):\n check_paths(write=writable_dir)\n\n viral_ngs.core.file.make_empty(join(writable_dir, 'myempty.dat'))\n check_paths(read_and_write=join(writable_dir, 'myempty.dat'))\n\ndef test_uncompressed_file_type():\n \"\"\"Test viral_ngs.core.file.uncompressed_file_type()\"\"\"\n uft = viral_ngs.core.file.uncompressed_file_type\n assert uft('test.fasta.gz') == '.fasta'\n assert uft('test.fasta.bz2') == '.fasta'\n assert uft('test.fasta') == '.fasta'\n assert uft('test.fa.zst') == '.fa'\n assert uft('test.txt.lz4') == '.txt'\n assert uft('test.gz') == ''\n\n assert uft('/tmp/test.fasta.gz') == '.fasta'\n assert uft('/test/dir/test.fasta.bz2') == '.fasta'\n assert uft('/a/b/c/test.fasta') == '.fasta'\n assert uft('/a/test.gz') == ''\n\ndef test_string_to_file_name():\n \"\"\"Test viral_ngs.core.file.string_to_file_name()\"\"\"\n\n unichr = getattr(builtins, 'unichr', chr)\n\n test_fnames = (\n 'simple', 'simple.dat', 'a/b', '/a', '/a/b', '/a/b/', 'a\\\\b', \n 'a^b&c|d\" e::f!g;*?`test`', '(somecmd -f --flag < input > output) && ls',\n 'long' * 8000, 'oddchars\\\\xAA\\\\o037',\n ''.join(map(chr, range(128))) * 20,\n ''.join(map(unichr, range(1000))),\n )\n\n with viral_ngs.core.file.tmp_dir() as tmp_d:\n for test_fname in test_fnames:\n t_path = os.path.join(tmp_d, viral_ngs.core.file.string_to_file_name(test_fname, tmp_d))\n viral_ngs.core.file.make_empty(t_path)\n assert os.path.isfile(t_path) and os.path.getsize(t_path) == 0\n\n\n@pytest.fixture(scope='module', params=['', '.bz2', '.gz', '.lz4', '.zst'])\ndef compressed_input_file(request):\n return os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebola.fasta' + request.param)\n\n@pytest.fixture(scope='module')\ndef expected_plaintext():\n return os.path.join(viral_ngs.core.file.get_test_input_path(), 'ebola.fasta')\n\ndef test_decompress_shutil_copyfileobj(request, expected_plaintext, compressed_input_file):\n out = viral_ngs.core.file.mkstempfname(os.path.basename(compressed_input_file)+'.fa')\n with viral_ngs.core.file.open_or_gzopen(compressed_input_file, 'rt') as inf, open(out, 'wt') as outf:\n shutil.copyfileobj(inf, outf)\n assert filecmp.cmp(out, expected_plaintext, shallow=False)\n\ndef test_decompress_line_by_line(request, expected_plaintext, compressed_input_file):\n out = viral_ngs.core.file.mkstempfname(os.path.basename(compressed_input_file)+'.fa')\n with viral_ngs.core.file.open_or_gzopen(compressed_input_file, 'rt', newline=None) as inf, open(out, 'wt') as outf:\n for line in inf:\n outf.write(line)\n assert filecmp.cmp(out, expected_plaintext, shallow=False)\n\n\nclass TestExtractTarball(TestCaseWithTmp):\n def setUp(self):\n super(TestExtractTarball, self).setUp()\n self.input_dir = os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestTarballMerger')\n self.input_mixed_files = list(os.path.join(self.input_dir, \"mixed-compressed-input\", fn)\n for fn in sorted(os.listdir(os.path.join(self.input_dir, \"mixed-compressed-input\"))))\n self.expected_outputs = list(os.path.join(self.input_dir, \"raw-input\", fn)\n for fn in sorted(os.listdir(os.path.join(self.input_dir, \"raw-input\"))))\n\n def test_simple_extract(self):\n for tarfile, expected in zip(self.input_mixed_files, self.expected_outputs):\n temp_dir = tempfile.mkdtemp()\n viral_ngs.core.file.extract_tarball(tarfile, out_dir=temp_dir)\n out_files = os.listdir(temp_dir)\n self.assertEqual(len(out_files), 1)\n self.assertEqualContents(os.path.join(temp_dir, out_files[0]), expected)\n\nclass TestTarballMerger(TestCaseWithTmp):\n def setUp(self):\n super(TestTarballMerger, self).setUp()\n self.input_dir = viral_ngs.core.file.get_test_input_path(self)\n self.raw_files = [\"file{}\".format(x) for x in range(1,5)]\n self.input_tgz_files = list(os.path.join(self.input_dir, \"compressed-input\", fn)\n for fn in sorted(os.listdir(os.path.join(self.input_dir, \"compressed-input\"))))\n self.input_mixed_files = list(os.path.join(self.input_dir, \"mixed-compressed-input\", fn)\n for fn in sorted(os.listdir(os.path.join(self.input_dir, \"mixed-compressed-input\"))))\n\n def test_simple_merge(self):\n \"\"\"\n Simple repack test\n \"\"\"\n temp_dir = tempfile.gettempdir()\n out_tarball_file = os.path.join(temp_dir,\"out.tar.gz\")\n\n viral_ngs.core.file.repack_tarballs(out_tarball_file,\n self.input_mixed_files\n )\n\n tb = tarfile.open(out_tarball_file)\n tb.extractall(path=temp_dir)\n\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(temp_dir,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n\n def test_merge_with_extract(self):\n \"\"\"\n Test streaming repack with intermediate extraction to disk\n \"\"\"\n temp_dir = tempfile.gettempdir()\n out_tarball_file = os.path.join(temp_dir,\"out.tar.gz\")\n out_extracted_path = os.path.join(temp_dir,\"extracted\")\n\n viral_ngs.core.file.repack_tarballs(out_tarball_file,\n self.input_mixed_files,\n extract_to_disk_path=out_extracted_path\n )\n\n tb = tarfile.open(out_tarball_file)\n tb.extractall(path=temp_dir)\n\n # inspect merged\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(temp_dir,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n\n # inspect extracted\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(out_extracted_path,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n\n def test_merge_with_extract_repack_from_disk(self):\n \"\"\"\n Test with repack from disk source after extraction\n \"\"\"\n temp_dir = tempfile.gettempdir()\n out_tarball_file = os.path.join(temp_dir,\"out.tar.gz\")\n out_extracted_path = os.path.join(temp_dir,\"extracted\")\n\n viral_ngs.core.file.repack_tarballs(out_tarball_file,\n self.input_mixed_files,\n extract_to_disk_path=out_extracted_path,\n avoid_disk_roundtrip=False\n )\n\n tb = tarfile.open(out_tarball_file)\n tb.extractall(path=temp_dir)\n\n # inspect merged\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(temp_dir,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n\n # inspect extracted\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(out_extracted_path,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n\n def test_piped_in_merge(self):\n \"\"\"\n Test with streamed input\n \"\"\"\n temp_dir = tempfile.gettempdir()\n out_tarball_file = os.path.join(temp_dir,\"out.tar.gz\")\n\n ps = subprocess.Popen(\"cat {files}\".format(files=' '.join(self.input_tgz_files)).split(), stdout=subprocess.PIPE)\n with patch('sys.stdin', ps.stdout):\n viral_ngs.core.file.repack_tarballs(out_tarball_file,\n [\"-\"],\n pipe_hint_in=\"gz\")\n ps.wait()\n\n tb = tarfile.open(out_tarball_file)\n tb.extractall(path=temp_dir)\n\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(temp_dir,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n\n @pytest.fixture(autouse=True)\n def capsys(self, capsys):\n self.capsys = capsys\n\n def test_piped_out_merge(self):\n \"\"\"\n Test with streamed output\n \"\"\"\n temp_dir = tempfile.gettempdir()\n out_tarball_file = os.path.join(temp_dir,\"out.tar.gz\")\n\n with open(out_tarball_file, \"wb\", 0) as outf:\n # temporarily disable pytest's capture of sys.stdout\n with self.capsys.disabled():\n with patch('sys.stdout', outf):\n viral_ngs.core.file.repack_tarballs(\"-\",\n self.input_mixed_files,\n pipe_hint_out=\"gz\")\n\n tb = tarfile.open(out_tarball_file)\n tb.extractall(path=temp_dir)\n\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(temp_dir,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n\n def test_merge_piped_in_and_out(self):\n \"\"\"\n Test with streamed input and output\n \"\"\"\n temp_dir = tempfile.gettempdir()\n\n out_tarball_file = os.path.join(temp_dir,\"out.tar.gz\")\n\n ps = subprocess.Popen(\"cat {files}\".format(files=' '.join(self.input_tgz_files)).split(), stdout=subprocess.PIPE)\n with patch('sys.stdin', ps.stdout):\n with open(out_tarball_file, \"wb\", 0) as outf:\n # temporarily disable pytest's capture of sys.stdout\n with self.capsys.disabled():\n with patch('sys.stdout', outf):\n viral_ngs.core.file.repack_tarballs( \"-\",\n [\"-\"],\n pipe_hint_out=\"gz\",\n pipe_hint_in=\"gz\")\n ps.wait()\n\n tb = tarfile.open(out_tarball_file)\n tb.extractall(path=temp_dir)\n\n for i in range(len(self.raw_files)):\n inf = os.path.join(self.input_dir,\"raw-input\",self.raw_files[i])\n outf = os.path.join(temp_dir,self.raw_files[i])\n\n self.assertEqualContents(inf, outf)\n" }, { "path": "tests/unit/core/test_util_misc.py", "content": "# Unit tests for viral_ngs.core.misc.py\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport os, random, collections\nimport unittest\nimport subprocess\nimport multiprocessing\nimport viral_ngs.core\nimport pytest\n\n\nclass TestRunAndPrint(unittest.TestCase):\n \n def testBasicRunSuccess(self):\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=False, buffered=False, check=False)\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=False, buffered=False, check=True)\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=True, buffered=False, check=False)\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=True, buffered=False, check=True)\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=False, buffered=True, check=False)\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=False, buffered=True, check=True)\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=True, buffered=True, check=False)\n viral_ngs.core.misc.run_and_print(['cat', '/dev/null'],\n silent=True, buffered=True, check=True)\n \n def testBasicRunFailDontCare(self):\n viral_ngs.core.misc.run_and_print(['cat', '/notdev/notnull'],\n silent=False, buffered=False, check=False)\n viral_ngs.core.misc.run_and_print(['cat', '/notdev/notnull'],\n silent=True, buffered=False, check=False)\n viral_ngs.core.misc.run_and_print(['cat', '/notdev/notnull'],\n silent=False, buffered=True, check=False)\n viral_ngs.core.misc.run_and_print(['cat', '/notdev/notnull'],\n silent=True, buffered=True, check=False)\n\n def testBasicRunFailAndCatch(self):\n self.assertRaises(subprocess.CalledProcessError,\n viral_ngs.core.misc.run_and_print, ['cat', '/notdev/notnull'],\n silent=False, buffered=False, check=True)\n self.assertRaises(subprocess.CalledProcessError,\n viral_ngs.core.misc.run_and_print, ['cat', '/notdev/notnull'],\n silent=False, buffered=True, check=True)\n self.assertRaises(subprocess.CalledProcessError,\n viral_ngs.core.misc.run_and_print, ['cat', '/notdev/notnull'],\n silent=True, buffered=False, check=True)\n self.assertRaises(subprocess.CalledProcessError,\n viral_ngs.core.misc.run_and_print, ['cat', '/notdev/notnull'],\n silent=True, buffered=True, check=True)\n\n\nclass TestFeatureSorter(unittest.TestCase):\n\n def testBasicSortingWithOverlap(self):\n fs = viral_ngs.core.misc.FeatureSorter((\n ('abca', 10, 20),\n ('abca', 25, 35),\n ('abca', 15, 30),\n ))\n self.assertEqual(\n list(fs.get_features()),\n [\n ('abca', 10, 20, '+', None),\n ('abca', 15, 30, '+', None),\n ('abca', 25, 35, '+', None),\n ]\n )\n\n def testBasicIntervalsWithOverlap(self):\n fs = viral_ngs.core.misc.FeatureSorter((\n ('abca', 10, 20),\n ('abca', 25, 35),\n ('abca', 15, 30),\n ))\n self.assertEqual(\n list(fs.get_intervals()),\n [\n ('abca', 10, 14, 1, [('abca', 10, 20, '+', None),]),\n ('abca', 15, 20, 2, [('abca', 10, 20, '+', None),('abca', 15, 30, '+', None),]),\n ('abca', 21, 24, 1, [('abca', 15, 30, '+', None),]),\n ('abca', 25, 30, 2, [('abca', 15, 30, '+', None),('abca', 25, 35, '+', None),]),\n ('abca', 31, 35, 1, [('abca', 25, 35, '+', None),]),\n ]\n )\n\n def testDisjointAndOverlappingIntervals(self):\n fs = viral_ngs.core.misc.FeatureSorter((\n ('abca', 10, 20),\n ('abca', 80, 90, '+', None),\n ('abca', 25, 35, '-'),\n ('abca', 15, 30),\n ))\n self.assertEqual(\n list(fs.get_intervals()),\n [\n ('abca', 10, 14, 1, [('abca', 10, 20, '+', None),]),\n ('abca', 15, 20, 2, [('abca', 10, 20, '+', None),('abca', 15, 30, '+', None),]),\n ('abca', 21, 24, 1, [('abca', 15, 30, '+', None),]),\n ('abca', 25, 30, 2, [('abca', 15, 30, '+', None),('abca', 25, 35, '-', None),]),\n ('abca', 31, 35, 1, [('abca', 25, 35, '-', None),]),\n ('abca', 36, 79, 0, []),\n ('abca', 80, 90, 1, [('abca', 80, 90, '+', None),]),\n ]\n )\n\n def testMultiChrWindowedFeatures(self):\n fs = viral_ngs.core.misc.FeatureSorter((\n ('abca', 10, 20),\n ('aaaa', 17, 33),\n ('abca', 80, 90),\n ('abca', 25, 35),\n ('abca', 15, 30),\n ))\n self.assertEqual(\n list(fs.get_features('abca', 11, 22)),\n [\n ('abca', 10, 20, '+', None),\n ('abca', 15, 30, '+', None),\n ]\n )\n\n def testOpenWindowRight(self):\n fs = viral_ngs.core.misc.FeatureSorter((\n ('abca', 10, 20),\n ('aaaa', 17, 33),\n ('abca', 80, 90),\n ('abca', 25, 35),\n ('abca', 15, 30),\n ))\n self.assertEqual(\n list(fs.get_features('abca', 22)),\n [\n ('abca', 15, 30, '+', None),\n ('abca', 25, 35, '+', None),\n ('abca', 80, 90, '+', None),\n ]\n )\n\n def testOpenWindowLeft(self):\n fs = viral_ngs.core.misc.FeatureSorter((\n ('abca', 10, 20),\n ('aaaa', 17, 33),\n ('abca', 80, 90),\n ('abca', 25, 35),\n ('abca', 15, 30),\n ))\n self.assertEqual(\n list(fs.get_features('abca', right=18)),\n [\n ('abca', 10, 20, '+', None),\n ('abca', 15, 30, '+', None),\n ]\n )\n\n def testMultiChrWithPayloadIntervals(self):\n fs = viral_ngs.core.misc.FeatureSorter((\n ('abca', 10, 20),\n ('aaaa', 17, 33, '-', [100, 'name', []]),\n ('abca', 80, 90, '+', ['other info']),\n ('abca', 25, 35, '-'),\n ('abca', 15, 30),\n ))\n self.assertEqual(\n list(fs.get_intervals()),\n [\n ('abca', 10, 14, 1, [('abca', 10, 20, '+', None),]),\n ('abca', 15, 20, 2, [('abca', 10, 20, '+', None),('abca', 15, 30, '+', None),]),\n ('abca', 21, 24, 1, [('abca', 15, 30, '+', None),]),\n ('abca', 25, 30, 2, [('abca', 15, 30, '+', None),('abca', 25, 35, '-', None),]),\n ('abca', 31, 35, 1, [('abca', 25, 35, '-', None),]),\n ('abca', 36, 79, 0, []),\n ('abca', 80, 90, 1, [('abca', 80, 90, '+', ['other info']),]),\n ('aaaa', 17, 33, 1, [('aaaa', 17, 33, '-', [100, 'name', []]),]),\n ]\n )\n\n\nclass TestConfigIncludes(unittest.TestCase):\n\n def testConfigIncludes(self):\n\n def test_fn(f): return os.path.join(viral_ngs.core.file.get_test_input_path(), 'TestUtilMisc', f)\n cfg1 = viral_ngs.core.misc.load_config(test_fn('cfg1.yaml'))\n cfg2 = viral_ngs.core.misc.load_config(test_fn('cfg2.yaml'), std_includes=[test_fn('cfg_std.yaml')],\n param_renamings={'std_param_A_old': 'std_param_A_new'})\n \n self.assertIn('paramA', cfg2)\n self.assertEqual(cfg2[\"env_vars\"][\"var_A\"],1)\n self.assertEqual(cfg2[\"env_vars\"][\"var_B\"],3)\n self.assertEqual(cfg2[\"env_vars\"][\"var_C\"],4)\n with self.assertRaises(KeyError): cfg2[\"env_vars\"][\"var_E\"]\n with self.assertRaises(KeyError): cfg2[\"var_A\"]\n self.assertFalse(cfg2[\"paramZ\"])\n self.assertTrue(cfg1[\"paramZ\"])\n self.assertEqual(cfg2[\"empty_subtree\"][\"x\"], 1)\n\n self.assertEqual(cfg2[\"std_methods\"], ['a','b','c'])\n self.assertEqual(cfg2[\"stage1\"][\"stage2\"][\"step_num\"],3)\n self.assertEqual(cfg2[\"stage1\"][\"stage2\"][\"step_list\"],[5,10,15])\n self.assertEqual(cfg2[\"stage1\"][\"stage3\"][\"step_list\"],[3,33])\n self.assertEqual(cfg1[\"stage1\"][\"stage3\"][\"step_list\"],[51,101,151])\n\n self.assertEqual(cfg2[\"std_param_A_new\"], 111) # specified as std_param_A_old in cfg1.yaml\n\n self.assertEqual(viral_ngs.core.misc.load_config(test_fn('empty.yaml')), {})\n\ndef test_as_type():\n \"\"\"Test viral_ngs.core.misc.as_type()\"\"\"\n\n as_type = viral_ngs.core.misc.as_type\n\n test_data = (\n ('1', int, 1, int),\n ('1', (int,), 1, int),\n ('1', (int, float), 1, int),\n ('1', (float, int), 1., float),\n ('1.2', (float, int), 1.2, float),\n ('1.2', (int, float), 1.2, float),\n (1, int, 1, int),\n ('1.', (int, float), 1., float),\n (1., int, 1, int),\n (1.2, (int, float), 1, int),\n ('1e3', (int, float), 1000., float),\n ('1e3', (float, int), 1000., float),\n ('1.1e3', (int, float), 1100., float),\n ('-1.1e3', (float, int), -1100., float),\n )\n\n for val, types, out_val, out_type in test_data:\n result = as_type(val, types)\n assert result == out_val\n assert type(result) == out_type\n\n err_data = (\n ('1.', int), ('1.', (int,)), ('1e3', int), ('1e3', (int,)), ([1], int),\n ('', int), ('', (int, float)), ('', (float, int))\n )\n\n for val, types in err_data:\n with pytest.raises(TypeError):\n as_type(val, types)\n\n@pytest.mark.parametrize(\"iter_d\", [False, True])\n@pytest.mark.parametrize(\"iter_subset\", [False, True])\ndef test_subdict(iter_d, iter_subset):\n \"\"\"Test viral_ngs.core.misc.subdict()\"\"\"\n def subdict(d, subset): \n return viral_ngs.core.misc.subdict(iter(d.items()) if iter_d else d, \n iter(subset) if iter_subset else subset)\n\n test_data = (\n ({}, {}, {}),\n ({1:2}, {}, {}),\n ({1:2}, {1}, {1:2}),\n ({1:2}, {2}, {}),\n ({1:2}, {1,2}, {1:2}),\n ({1:2,3:4}, {1,2,3}, {1:2,3:4}),\n ({1:2,3:4}, {2,3,5}, {3:4}),\n )\n\n for d, subset, expected in test_data:\n assert subdict(d, subset) == expected\n\n assert set(subdict(d, subset).keys()) == (set(d.keys()) & set(subset))\n assert subdict(d, {}) == {}\n assert subdict(d, d.keys()) == d\n assert subdict(d, list(d.keys())*2) == d\n\ndef test_chk():\n chk = viral_ngs.core.misc.chk\n chk(True, 'no error')\n with pytest.raises(RuntimeError):\n chk(False)\n with pytest.raises(RuntimeError):\n chk(2 == 3, 'Something wrong')\n with pytest.raises(TypeError):\n chk(isinstance(None, int), 'Expected an int', TypeError)\n\ndef test_available_cpu_count(monkeypatch_function_result):\n reported_cpu_count = viral_ngs.core.misc.available_cpu_count()\n assert reported_cpu_count >= int(os.environ.get('PYTEST_XDIST_WORKER_COUNT', '1'))\n assert viral_ngs.core.misc.available_cpu_count() == reported_cpu_count\n\n # cgroup v2 limited to 1 cpu\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=True, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu.max', patch_result=\"100000 100000\"):\n assert viral_ngs.core.misc.available_cpu_count() == 1\n\n # cgroup v2 limited to 2 cpu\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=True, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu.max', patch_result=\"200000 100000\"):\n assert viral_ngs.core.misc.available_cpu_count() == 2\n\n # cgroup v2 with no CPU limit imposed on cgroup\n # (fall back to /proc/self/status method, with limit imposed there):\n # 'Cpus_allowed: d' = 0b1101 bitmask (meaning execution allowed on 3 CPUs)\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=True, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu.max', patch_result=\"max 100000\"), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/proc/self/status', patch_result='Cpus_allowed: d'):\n assert viral_ngs.core.misc.available_cpu_count() == 3\n\n # cgroup v1 limited to 2 CPUs\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=False, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_quota_us', patch_result='200000'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_period_us', patch_result='100000'):\n \n assert viral_ngs.core.misc.available_cpu_count() == 2\n\n # cgroup v1 limited to 1 CPU\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=False, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_quota_us', patch_result='1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_period_us', patch_result='1'):\n \n assert viral_ngs.core.misc.available_cpu_count() == 1\n\n # cgroup v1 with no limit imposed on the cgroup\n # (fall back to /proc/self/status method, with limit imposed there):\n # 'Cpus_allowed: c' = 0b1100 bitmask (meaning execution allowed on 2 CPUs)\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=False, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_quota_us', patch_result='-1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_period_us', patch_result='1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/proc/self/status', patch_result='Cpus_allowed: c'):\n \n assert viral_ngs.core.misc.available_cpu_count() == 2\n\n # cgroup v1 with no limit imposed on the cgoup or via /proc/self/status\n # (fall back to /proc/self/status method, with no limit imposed there)\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=False, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_quota_us', patch_result='-1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_period_us', patch_result='1'):\n \n assert viral_ngs.core.misc.available_cpu_count() == reported_cpu_count\n\n # cgroup v1 with no limit imposed on the cgoup\n # with 'Cpus_allowed' not present in /proc/self/status\n # (fall back to multiprocessing.cpu_count() method)\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=False, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_quota_us', patch_result='-1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_period_us', patch_result='1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/proc/self/status', patch_result='unexpected_key: 1'):\n \n assert viral_ngs.core.misc.available_cpu_count() == reported_cpu_count\n\n # cgroup v1 with no limit imposed on the cgoup\n # with 'Cpus_allowed' not present in /proc/self/status\n # (fall back to multiprocessing.cpu_count() method with CPU count of 2 reported)\n with monkeypatch_function_result(os.path.exists, \"/sys/fs/cgroup/cgroup.controllers\", patch_result=False, patch_module=os.path), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_quota_us', patch_result='-1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/sys/fs/cgroup/cpu/cpu.cfs_period_us', patch_result='1'), \\\n monkeypatch_function_result(viral_ngs.core.file.slurp_file, '/proc/self/status', patch_result='unexpected_key: 1'), \\\n monkeypatch_function_result(multiprocessing.cpu_count, patch_result=2, patch_module=multiprocessing):\n \n assert viral_ngs.core.misc.available_cpu_count() == 2" }, { "path": "tests/unit/phylo/__init__.py", "content": "\n" }, { "path": "tests/unit/phylo/test_interhost.py", "content": "# Unit tests for interhost.py\n\n__author__ = \"irwin@broadinstitute.org\"\n\nimport viral_ngs.interhost\nimport viral_ngs.core.file\nimport unittest\nimport argparse\nimport itertools\n\nfrom tests import TestCaseWithTmp\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in viral_ngs.interhost.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n\ndef makeTempFasta(seqs):\n fn = viral_ngs.core.file.mkstempfname('.fasta')\n with open(fn, 'wt') as outf:\n for line in viral_ngs.core.file.fastaMaker(seqs):\n outf.write(line)\n return fn\n\n\nclass TestCoordMapper(TestCaseWithTmp):\n\n def setUp(self):\n super(TestCoordMapper, self).setUp()\n self.genomeA = makeTempFasta([('chr1', 'ATGCACGTACGTATGCAAATCGG'), ('chr2', 'AGTCGGTTTTCAG'),])\n self.genomeB = makeTempFasta([('first_chrom', 'GCACGTACGTATTTGCAAATC'), ('second_chr', 'AGTCGGTTTCCAC'),])\n self.cm = viral_ngs.interhost.CoordMapper()\n self.cm.align_and_load_sequences([self.genomeA, self.genomeB])\n\n def test_no_indels(self):\n for pos in range(1, 14):\n self.assertEqual(self.cm.mapAtoB('chr2', pos), ('second_chr', pos))\n self.assertEqual(self.cm.mapBtoA('second_chr', pos), ('chr2', pos))\n\n def test_map_indels(self):\n expLists = [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, [11, 13], 14, 15, 16, 17, 18, 19, 20, 21],\n [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 13, 13, 14, 15, 16, 17, 18, 19, 20, 21],]\n for mapper, fromChrom, goodRange, toChrom, expected in [\n [self.cm.mapAtoB, 'chr1', range(3, 22), 'first_chrom', expLists[0]], [self.cm.mapBtoA, 'first_chrom',\n range(1, 22), 'chr1', expLists[1]]\n ]:\n result = [mapper(fromChrom, pos) for pos in goodRange]\n for chrom, mappedPos in result:\n self.assertEqual(chrom, toChrom)\n self.assertEqual(expected, [mappedPos for chrom, mappedPos in result])\n\n def test_side_param(self):\n self.assertEqual(self.cm.mapAtoB('chr1', 13), ('first_chrom', [11, 13]))\n self.assertEqual(self.cm.mapAtoB('chr1', 13, 0), ('first_chrom', [11, 13]))\n self.assertEqual(self.cm.mapAtoB('chr1', 13, -1), ('first_chrom', 11))\n self.assertEqual(self.cm.mapAtoB('chr1', 13, 1), ('first_chrom', 13))\n self.assertEqual(self.cm.mapAtoB('chr1', 12), ('first_chrom', 10))\n self.assertEqual(self.cm.mapAtoB('chr1', 12, 0), ('first_chrom', 10))\n self.assertEqual(self.cm.mapAtoB('chr1', 12, -1), ('first_chrom', 10))\n self.assertEqual(self.cm.mapAtoB('chr1', 12, 1), ('first_chrom', 10))\n\n def test_oob_errors(self):\n for pos in [-1, 0, 1, 2, 22, 23, 24]:\n self.assertEqual(self.cm.mapAtoB('chr1', pos), ('first_chrom', None))\n for pos in [-1, 0, 14, 15]:\n self.assertEqual(self.cm.mapBtoA('second_chr', pos), ('chr2', None))\n\n def test_invalid_pos_error(self):\n with self.assertRaises(TypeError):\n self.cm.mapAtoB('chr1', 1.5)\n with self.assertRaises(TypeError):\n self.cm.mapBtoA('second_chr', 4.5)\n\n def test_invalid_chr_error(self):\n with self.assertRaises(KeyError):\n self.cm.mapAtoB('nonexistentchr', 2)\n with self.assertRaises(KeyError):\n self.cm.mapBtoA('nonexistentchr', 2)\n\n def test_unequal_genomes_error(self):\n genomeA = makeTempFasta([('chr1', 'ATGCACGTACGTATGCAAATCGG'), ('chr2', 'AGTCGGTTTTCAG'),])\n genomeB = makeTempFasta([('first_chrom', 'GCACGTACGTATTTGCAAATC')])\n with self.assertRaises(viral_ngs.core.file.TranspositionError):\n cm = viral_ngs.interhost.CoordMapper()\n cm.align_and_load_sequences([genomeA, genomeB])\n\n def test_map_chr_only(self):\n self.assertEqual(self.cm.mapAtoB('chr1'), 'first_chrom')\n self.assertEqual(self.cm.mapBtoA('first_chrom'), 'chr1')\n self.assertEqual(self.cm.mapAtoB('chr2'), 'second_chr')\n self.assertEqual(self.cm.mapBtoA('second_chr'), 'chr2')\n with self.assertRaises(KeyError):\n self.cm.mapAtoB('nonexistentchr')\n\n\nclass TestCoordMapperMultipleSeqs(TestCaseWithTmp):\n\n def setUp(self):\n super(TestCoordMapperMultipleSeqs, self).setUp()\n self.genomeA = makeTempFasta([\n ('chr1', 'ATGCACGTACGTATGCAAATCGG'),\n ('chr2', 'AGTCGGTTTTCAG'),\n ('chr3', 'GACTTTTGGCTGA'),\n ])\n self.genomeB = makeTempFasta([\n ('first_chrom', 'GCACGTACGTATTTGCAAATC'),\n ('second_chr', 'AGTCGGTTTCCAC'),\n ('third_chr', 'CACCTTTGGCTGA'),\n ])\n self.cm = viral_ngs.interhost.CoordMapper()\n self.cm.align_and_load_sequences([self.genomeA, self.genomeB])\n\n def test_legacy_call(self):\n '''\n If mapAtoB or mapBtoA is called on a CoordMapper object with >2 sequences,\n an AssertionError should be raised.\n '''\n self.assertRaises(LookupError, self.cm.mapAtoB, 'chr1', 1)\n self.assertRaises(LookupError, self.cm.mapBtoA, 'chr2', 1)\n\n def test_no_indels(self):\n for pos in range(1, 14):\n self.assertEqual(self.cm.mapChr('chr2', 'second_chr', pos), ('second_chr', pos))\n self.assertEqual(self.cm.mapChr('second_chr', 'chr2', pos), ('chr2', pos))\n\n def test_map_indels(self):\n expLists = [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, [11, 13], 14, 15, 16, 17, 18, 19, 20, 21],\n [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 13, 13, 14, 15, 16, 17, 18, 19, 20, 21],]\n for mapper, fromChrom, goodRange, toChrom, expected in [\n [self.cm.mapChr, 'chr1', range(3, 22), 'first_chrom', expLists[0]], [self.cm.mapChr, 'first_chrom',\n range(1, 22), 'chr1', expLists[1]]\n ]:\n result = [mapper(fromChrom, toChrom, pos) for pos in goodRange]\n for chrom, mappedPos in result:\n self.assertEqual(chrom, toChrom)\n self.assertEqual(expected, [mappedPos for chrom, mappedPos in result])\n\n def test_side_param(self):\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 13), ('first_chrom', [11, 13]))\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 13, 0), ('first_chrom', [11, 13]))\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 13, -1), ('first_chrom', 11))\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 13, 1), ('first_chrom', 13))\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 12), ('first_chrom', 10))\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 12, 0), ('first_chrom', 10))\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 12, -1), ('first_chrom', 10))\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', 12, 1), ('first_chrom', 10))\n\n def test_oob_errors(self):\n for pos in [-1, 0, 1, 2, 22, 23, 24]:\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom', pos), ('first_chrom', None))\n for pos in [-1, 0, 14, 15]:\n self.assertEqual(self.cm.mapChr('second_chr', 'chr2', pos), ('chr2', None))\n\n def test_invalid_pos_error(self):\n with self.assertRaises(TypeError):\n self.cm.mapChr('chr1', 'first_chrom', 1.5)\n with self.assertRaises(TypeError):\n self.cm.mapChr('second_chr', 'chr2', 4.5)\n\n def test_invalid_chr_error(self):\n self.assertRaises(KeyError, self.cm.mapChr, 'nonexistentchr', 'chr1', 2)\n self.assertRaises(KeyError, self.cm.mapChr, 'chr1', 'nonexistentchr', 2)\n\n def test_unequal_genomes_error(self):\n genomeA = makeTempFasta([('chr1', 'ATGCACGTACGTATGCAAATCGG'), ('chr2', 'AGTCGGTTTTCAG'),])\n genomeB = makeTempFasta([('first_chrom', 'GCACGTACGTATTTGCAAATC')])\n with self.assertRaises(Exception):\n cm = viral_ngs.interhost.CoordMapper()\n cm.align_and_load_sequences([genomeA, genomeB])\n\n def test_duplicate_chr_names_error(self):\n genomeA = makeTempFasta([('chr1', 'ATGCACGTACGTATGCAAATCGG'),])\n genomeB = makeTempFasta([('chr1', 'GCACGTACGTATTTGCAAATC')])\n with self.assertRaises(Exception):\n cm = viral_ngs.interhost.CoordMapper()\n cm.align_and_load_sequences([genomeA, genomeB])\n\n def test_multiple_input_genomes(self):\n genomeA = makeTempFasta([('chr1', 'ATGCACGTACGTATGCAAATCGG'),])\n genomeB = makeTempFasta([('first_chr', 'ATGCACTACGTATGCAAATCGG')])\n genomeC = makeTempFasta([('chr_one', 'ATGCACGTACGTATGCAATCGG')])\n cm = viral_ngs.interhost.CoordMapper()\n cm.align_and_load_sequences([genomeA, genomeB, genomeC])\n # check that toChrom is in the map\n self.assertEqual(cm.mapChr('chr1', 'chr_one'), 'chr_one')\n\n def test_single_chr_error(self):\n genomeA = makeTempFasta([('chr1', 'ATGCACGTACGTATGCAAATCGG'),])\n genomeB = makeTempFasta([])\n with self.assertRaises(Exception):\n cm = viral_ngs.interhost.CoordMapper()\n cm.align_and_load_sequences([genomeA, genomeB])\n\n def test_map_chr_only(self):\n self.assertEqual(self.cm.mapChr('chr1', 'first_chrom'), 'first_chrom')\n self.assertEqual(self.cm.mapChr('first_chrom', 'chr1'), 'chr1')\n self.assertEqual(self.cm.mapChr('chr2', 'second_chr'), 'second_chr')\n self.assertEqual(self.cm.mapChr('second_chr', 'chr2'), 'chr2')\n self.assertEqual(self.cm.mapChr('chr3', 'third_chr'), 'third_chr')\n self.assertEqual(self.cm.mapChr('third_chr', 'chr3'), 'chr3')\n self.assertRaises(KeyError, self.cm.mapChr, 'nonexistentchr', 'chr1')\n\n\nclass TestSpecificAlignments(TestCaseWithTmp):\n \"\"\" For the most part, CoordMapper2Seqs is tested implicitly when\n CoordMapper is tested. Focus here on special cases that are hard\n or impossible to get out of the aligner.\n \"\"\"\n\n def test_basic_alignment(self):\n alignment = makeTempFasta([('s1', 'ATCG'), ('s2', 'ACCG'), ('s3', 'AG-T'),])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment])\n\n def test_unequal_len(self):\n alignment = makeTempFasta([('s1', 'AA'), ('s2', 'A'),])\n cm = viral_ngs.interhost.CoordMapper()\n with self.assertRaises(Exception):\n cm.load_alignments([alignment])\n\n def test_no_real_bases_in_sample(self):\n alignment1 = makeTempFasta([('s1', 'AA'), ('s2', '--'),])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment1])\n with self.assertRaises(Exception):\n cm.mapChr('s1', 's2', 1)\n\n alignment2 = makeTempFasta([('s1', '--'), ('s2', 'AA'), ('s3', 'TT'),])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment2])\n with self.assertRaises(Exception):\n cm.mapChr('s2', 's1', 1)\n\n def test_no_real_bases_at_position(self):\n alignment = makeTempFasta([('s1', 'AT-G'), ('s2', 'AC-G'), ('s3', 'AG-T'),])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment])\n for i in (1, 2, 3):\n self.assertEqual(cm.mapChr('s1', 's2', i), ('s2', i))\n self.assertEqual(cm.mapChr('s2', 's1', i), ('s1', i))\n self.assertEqual(cm.mapChr('s1', 's3', i), ('s3', i))\n self.assertEqual(cm.mapChr('s3', 's1', i), ('s1', i))\n self.assertEqual(cm.mapChr('s2', 's3', i), ('s3', i))\n self.assertEqual(cm.mapChr('s3', 's2', i), ('s2', i))\n\n def test_aligned_gaps(self):\n alignment = makeTempFasta([('s1', 'ATCG'), ('s2', 'AC-G'), ('s3', 'AG-T'),])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment])\n for i in (1, 2, 3):\n self.assertEqual(cm.mapChr('s2', 's3', i), ('s3', i))\n self.assertEqual(cm.mapChr('s3', 's2', i), ('s2', i))\n for x, y in ((1, 1), (2, 2), (3, 2), (4, 3)):\n self.assertEqual(cm.mapChr('s1', 's2', x), ('s2', y))\n self.assertEqual(cm.mapChr('s1', 's3', x), ('s3', y))\n for x, y in ((1, 1), (2, [2, 3]), (3, 4)):\n self.assertEqual(cm.mapChr('s2', 's1', x), ('s1', y))\n self.assertEqual(cm.mapChr('s3', 's1', x), ('s1', y))\n\n def test_adjacent_gaps(self):\n alignment = makeTempFasta([\n ('s1', 'ATCTG'),\n ('s2', 'AC--G'),\n ('s3', 'A-TTG'),\n ('s4', 'A-C-G'),\n ('s5', 'A--CG'),\n ])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment])\n for x, y in ((1, 1), (2, 2), (3, 2), (4, 2), (5, 3)):\n self.assertEqual(cm.mapChr('s1', 's2', x), ('s2', y))\n for x, y in ((1, 1), (2, [2, 4]), (3, 5)):\n self.assertEqual(cm.mapChr('s2', 's1', x), ('s1', y))\n for x, y in ((1, 1), (2, 1), (3, 2), (4, 3), (5, 4)):\n self.assertEqual(cm.mapChr('s1', 's3', x), ('s3', y))\n for x, y in ((1, [1, 2]), (2, 3), (3, 4), (4, 5)):\n self.assertEqual(cm.mapChr('s3', 's1', x), ('s1', y))\n for x, y in ((1, 1), (2, [2, 3]), (3, 4)):\n self.assertEqual(cm.mapChr('s2', 's3', x), ('s3', y))\n for x, y in ((1, 1), (2, 2), (3, 2), (4, 3)):\n self.assertEqual(cm.mapChr('s3', 's2', x), ('s2', y))\n for a, b in itertools.combinations(('s2', 's4', 's5'), 2):\n for i in (1, 2, 3):\n self.assertEqual(cm.mapChr(a, b, i), (b, i))\n self.assertEqual(cm.mapChr(b, a, i), (a, i))\n\n def test_one_real_base(self):\n alignment = makeTempFasta([('s1', 'AC-'), ('s2', '-CA'),])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment])\n self.assertEqual(cm.mapChr('s1', 's2', 1), ('s2', None))\n self.assertEqual(cm.mapChr('s1', 's2', 2), ('s2', 1))\n self.assertEqual(cm.mapChr('s2', 's1', 1), ('s1', 2))\n self.assertEqual(cm.mapChr('s2', 's1', 2), ('s1', None))\n\n def test_exactly_two_pairs(self):\n alignment = makeTempFasta([('s1', 'A--T'), ('s2', 'AGGT'),])\n cm = viral_ngs.interhost.CoordMapper()\n cm.load_alignments([alignment])\n self.assertEqual(cm.mapChr('s1', 's2', 1), ('s2', [1, 3]))\n self.assertEqual(cm.mapChr('s1', 's2', 2), ('s2', 4))\n self.assertEqual(cm.mapChr('s2', 's1', 1), ('s1', 1))\n self.assertEqual(cm.mapChr('s2', 's1', 2), ('s1', 1))\n self.assertEqual(cm.mapChr('s2', 's1', 3), ('s1', 1))\n self.assertEqual(cm.mapChr('s2', 's1', 4), ('s1', 2))\n" }, { "path": "tests/unit/phylo/test_intrahost.py", "content": "# Unit tests for intrahost.py\n\n__author__ = \"dpark@broadinstitute.org\"\n\n# built-ins\nfrom collections import OrderedDict\nimport os\nimport os.path\nimport shutil\nimport tempfile\nimport itertools\nimport argparse\nimport unittest\n\n# third-party\nimport Bio\nimport Bio.SeqRecord\nimport Bio.Seq\n\n# module-specific\nimport viral_ngs.intrahost\nimport viral_ngs.core.file\nimport viral_ngs.phylo.vcf\nfrom viral_ngs.intrahost import AlleleFieldParser\nimport viral_ngs.phylo.mafft\nfrom tests import TestCaseWithTmp, _CPUS\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in viral_ngs.intrahost.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\n\ndef makeTempFasta(seqs):\n fn = viral_ngs.core.file.mkstempfname('.fasta')\n with open(fn, 'wt') as outf:\n for line in viral_ngs.core.file.fastaMaker(seqs):\n outf.write(line)\n return fn\n\n\nclass MockVphaserOutput:\n ''' This creates test data that pretends to be the output from\n viral_ngs.core.vphaser2.Vphaser2Tool.iterate\n '''\n\n def __init__(self):\n self.isnvs = {}\n self.chroms = []\n\n def add_snp(self, chrom, pos, acounts, libinfo=None):\n # Add an iSNP at this chrom,pos. acounts is a list of triples:\n # (allele, fwd count, rev count).\n assert isinstance(pos, int) and pos > 0 and len(acounts) > 1\n for a, f, r in acounts:\n assert a in ('A', 'C', 'G', 'T')\n assert f >= 0 and r >= 0 and f + r > 0\n\n # Add libinfo to acounts\n if libinfo is None:\n acounts = [[a, f, r, 1, [[f, r]]] for a, f, r in acounts]\n else:\n # ...\n raise Exception\n\n acounts = reversed(sorted((acount[1] + acount[2],) + tuple(acount) for acount in acounts))\n acounts = [tuple(acount[1:]) for acount in acounts]\n if chrom not in self.chroms:\n self.chroms.append(chrom)\n self.isnvs.setdefault(chrom, {})\n self.isnvs[chrom].setdefault(pos, {})\n self.isnvs[chrom][pos]['snp'] = acounts\n\n def add_indel(self, chrom, pos, acounts, libinfo=None):\n ''' Add an iSNP at this chrom,pos. acounts is a list of triples:\n (allele, fwd count, rev count). allele is simply a small\n sequence with no \"I\" or \"D\" prefixing it (we'll add the I/D).\n '''\n assert isinstance(pos, int) and pos > 0 and len(acounts) > 1\n for a, f, r in acounts:\n assert isinstance(a, str)\n assert f >= 0 and r >= 0 and f + r > 0\n assert '' in set(a for a, f, r in acounts)\n\n # Add libinfo to acounts\n if libinfo is None:\n acounts = [[a, f, r, 1, [[f, r]]] for a, f, r in acounts]\n else:\n # ...\n raise Exception\n\n acounts = reversed(sorted((acount[1] + acount[2],) + tuple(acount) for acount in acounts))\n acounts = [list(acount[1:]) for acount in acounts]\n\n # vphaser funniness here\n if acounts[0][0] == '':\n # this is a set of insertions against the consensus\n acounts[0][0] = 'd'\n for i in range(1, len(acounts)):\n acounts[i][0] = 'I' + acounts[i][0]\n else:\n # this is a deletion against the consensus\n for i in range(1, len(acounts)):\n n_deleted = len(acounts[0][0]) - len(acounts[i][0])\n assert n_deleted > 0\n assert acounts[0][0][n_deleted:] == acounts[i][0]\n acounts[i][0] = 'D' + str(n_deleted)\n acounts[0][0] = 'i'\n\n if chrom not in self.chroms:\n self.chroms.append(chrom)\n self.isnvs.setdefault(chrom, {})\n self.isnvs[chrom].setdefault(pos, {})\n self.isnvs[chrom][pos]['lp'] = acounts\n\n def __iter__(self):\n for c in self.chroms:\n for p in sorted(self.isnvs[c].keys()):\n for model in self.isnvs[c][p].keys():\n acounts = self.isnvs[c][p][model]\n mac = sum(acount[1] + acount[2] for acount in acounts[1:])\n tot = sum(acount[1] + acount[2] for acount in acounts)\n yield [c, str(p), acounts[1][0], acounts[0][0],\n '0.5', model, str(float(mac) / tot * 100.0)] \\\n + [str(AlleleFieldParser(None, *acount))\n for acount in acounts]\n\n\nclass TestIntrahostFilters(unittest.TestCase):\n ''' This tests step 1 of the iSNV calling process\n (viral_ngs.intrahost.vphaser_one_sample), which runs V-Phaser2 on\n a single sample, reformats the output slightly, and performs\n strand-bias filtering and adds library-bias statistics.\n These unit tests mock the vphaser tool output and just test\n the filtering/statistics/etc.\n '''\n\n def test_single_strand_bias_hard_filter(self):\n data = MockVphaserOutput()\n data.add_snp('c1', 100, [('A', 10, 20), ('T', 5, 2), ('C', 30, 500), ('G', 60, 40)])\n data.add_snp('c2', 100, [('C', 10, 2), ('T', 2, 8)])\n output = list(viral_ngs.intrahost.filter_strand_bias(data))\n expected = ['c1', '100', 'A', 'G', None, 'snp', 23.076923076923078, 'G:60:40:60:40:1', 'A:10:20:10:20:1']\n self.assertEqual(len(output), 1)\n self.assertEqual(output[0][:4], expected[:4])\n self.assertEqual(output[0][5], expected[5])\n self.assertAlmostEqual(float(output[0][6]), expected[6], places=4)\n self.assertEqual(output[0][7:], expected[7:])\n\n\n#@unittest.skipIf(viral_ngs.core.is_osx(), \"vphaser2 osx binary from bioconda has issues\")\n@unittest.skip(\"vphaser2 behaving unpredictably; not used in WDL pipelines\")\nclass TestPerSample(TestCaseWithTmp):\n ''' This tests step 1 of the iSNV calling process\n (viral_ngs.intrahost.vphaser_one_sample), which runs V-Phaser2 on\n a single sample, reformats the output slightly, and performs\n strand-bias filtering and adds library-bias statistics.\n '''\n\n def test_vphaser_one_sample(self):\n # Files here were created as follows:\n # - in.bam was copied from input directory for TestVPhaser2; see notes\n # there on how it was created.\n # - ref.fasta was created by making two identical chromosomes, chr1\n # and chr2, with the sequence from West Nile virus isolate\n # WNV-1/US/BID-V7821/2011. That genome is a guess for the reference\n # of the V-Phaser 2 test file because BLAST matches the reads to\n # West Nile virus and that isolate has the size reported in the bam file.\n # Note that ref.fasta is not exactly the consensus of the reads in in.bam;\n # for example, pos 660 is C in ref.fasta, but more reads have T there\n # than C in in.bam. So we are actually testing the case that\n # V-Phaser 2 consensus != our consensus.\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n inBam = os.path.join(myInputDir, 'in.bam')\n refFasta = os.path.join(myInputDir, 'ref.fasta')\n outTab = viral_ngs.core.file.mkstempfname('.txt')\n viral_ngs.intrahost.vphaser_one_sample(inBam, refFasta, outTab, vphaserNumThreads=_CPUS, minReadsEach=6, maxBias=3)\n expected = os.path.join(myInputDir, 'vphaser_one_sample_expected.txt')\n self.assertEqualContents(outTab, expected)\n\n\nclass VcfMergeRunner:\n ''' This creates test data and feeds it to viral_ngs.intrahost.merge_to_vcf\n '''\n\n def __init__(self, ref_genome=None):\n self.genomes = {} # {sample : {chrom : bases, ...}, ...}\n self.genomeFastas = OrderedDict() # {sample: fastaFileName, ...\n self.alignedFastas = [] # [chr1, chr2, ...]\n self.isnvs = {}\n self.sample_order = []\n self.sequence_order = OrderedDict() # { sample: [seq1, seq2, ... ], ... }\n if ref_genome:\n self.set_ref(ref_genome)\n\n def set_ref(self, genome):\n self.ref = makeTempFasta(genome)\n\n def add_genome(self, sample_name, genome):\n self.genomes[sample_name] = dict(genome)\n self.genomeFastas[sample_name] = makeTempFasta(genome)\n if sample_name not in self.sample_order:\n self.sample_order.append(sample_name)\n self.isnvs.setdefault(sample_name, MockVphaserOutput())\n\n def add_snp(self, sample, chrom, pos, acounts, libinfo=None):\n assert sample in self.genomeFastas\n assert chrom in self.genomes[sample]\n assert 1 <= pos <= len(self.genomes[sample][chrom])\n assert self.genomes[sample][chrom][pos - 1] in [a for a, f, r in acounts]\n self.isnvs[sample].add_snp(chrom, pos, acounts, libinfo)\n\n def add_indel(self, sample, chrom, pos, acounts, libinfo=None):\n assert sample in self.genomeFastas\n assert sample in self.genomeFastas\n assert chrom in self.genomes[sample]\n assert 1 <= pos <= len(self.genomes[sample][chrom])\n if acounts[0][0] != '': # deletion\n assert self.genomes[sample][chrom][pos - 1:].startswith(acounts[0][0])\n self.isnvs[sample].add_indel(chrom, pos, acounts, libinfo)\n\n def dump_isnv_tmp_file(self, sample):\n fn = viral_ngs.core.file.mkstempfname('.txt')\n with open(fn, 'wt') as outf:\n for row in self.isnvs[sample]:\n outf.write('\\t'.join(map(str, row)) + '\\n')\n return fn\n\n def run_and_get_vcf_rows(self, retree=1, omit_samplenames=False):\n outVcf = viral_ngs.core.file.mkstempfname('.vcf.gz')\n\n self.multi_align_samples(retree=retree)\n\n if not omit_samplenames:\n viral_ngs.intrahost.merge_to_vcf(self.ref, outVcf, self.sample_order, list(self.dump_isnv_tmp_file(s) for s in self.sample_order),\n self.alignedFastas)\n else:\n viral_ngs.intrahost.merge_to_vcf(self.ref, outVcf, [], list(self.dump_isnv_tmp_file(s) for s in self.sample_order),\n self.alignedFastas)\n\n\n with viral_ngs.phylo.vcf.VcfReader(outVcf) as vcf:\n rows = list(vcf.get())\n return rows\n\n def multi_align_samples(self, retree=1):\n\n # store here a dict, {sample_name: [sequence_id1, sequence_id2, ...]}\n\n # because in Python3 OrderedDict does not have iteritems(), it simply has items()\n if hasattr(self.genomeFastas, \"iteritems\"):\n genomeKVIterator = self.genomeFastas.iteritems()\n else:\n genomeKVIterator = self.genomeFastas.items()\n\n for sampleName, fastaFile in genomeKVIterator:\n with viral_ngs.core.file.open_or_gzopen(fastaFile, 'r') as inf:\n for seq in Bio.SeqIO.parse(inf, 'fasta'):\n self.sequence_order.setdefault(sampleName, default=[])\n self.sequence_order[sampleName].append(seq.id)\n\n inputFastas = []\n inputFastas.append(self.ref)\n inputFastas.extend(self.genomeFastas.values())\n transposedFiles = viral_ngs.core.file.transposeChromosomeFiles(inputFastas)\n\n # since the FASTA files are\n for idx, filePath in enumerate(transposedFiles):\n\n outFile = viral_ngs.core.file.mkstempfname('.fasta')\n outFilePath = os.path.dirname(outFile)\n\n alignedOutFile = viral_ngs.phylo.mafft.MafftTool().execute(\n inFastas=[os.path.abspath(filePath)],\n outFile=os.path.join(outFilePath, \"{}{}.fasta\".format(\"aligned\", idx)),\n localpair=False,\n globalpair=True,\n preservecase=True,\n reorder=None,\n gapOpeningPenalty=None,\n offset=None,\n verbose=False,\n outputAsClustal=None,\n maxiters=1000,\n threads=_CPUS,\n retree=retree)\n self.alignedFastas.append(alignedOutFile)\n\n\nclass TestVcfMerge(TestCaseWithTmp):\n ''' This tests step 2 of the iSNV calling process\n (viral_ngs.intrahost.merge_to_vcf), which gets really nasty and tricky\n and has lots of edge cases. These unit tests mock the vphaser\n tool output and just tests the merge and VCF stuff.\n '''\n\n def test_empty_output(self):\n ref = makeTempFasta([('ref1', 'ATCGCA')])\n s1 = makeTempFasta([('s1-1', 'ATCGCA')])\n emptyfile = viral_ngs.core.file.mkstempfname('.txt')\n outVcf = viral_ngs.core.file.mkstempfname('.vcf')\n #viral_ngs.intrahost.merge_to_vcf(ref, outVcf, ['s1'], [emptyfile], [s1])\n self.assertRaises(LookupError, viral_ngs.intrahost.merge_to_vcf, ref, outVcf, ['s1'], [emptyfile], [s1])\n self.assertGreater(os.path.getsize(outVcf), 0)\n with viral_ngs.core.file.open_or_gzopen(outVcf, 'rt') as inf:\n for line in inf:\n self.assertTrue(line.startswith('#'))\n outVcf = viral_ngs.core.file.mkstempfname('.vcf.gz')\n #viral_ngs.intrahost.merge_to_vcf(ref, outVcf, ['s1'], [emptyfile], [s1])\n self.assertRaises(LookupError, viral_ngs.intrahost.merge_to_vcf, ref, outVcf, ['s1'], [emptyfile], [s1])\n self.assertGreater(os.path.getsize(outVcf), 0)\n with viral_ngs.core.file.open_or_gzopen(outVcf, 'rt') as inf:\n for line in inf:\n self.assertTrue(line.startswith('#'))\n\n def test_headers_with_two_samps(self):\n ref = makeTempFasta([('ref1', 'ATCGTTCA'), ('ref2', 'GGCCC')])\n s1 = makeTempFasta([('s1-1', 'ATCGCA'), ('s1-2', 'GGCCC')])\n s2 = makeTempFasta([('s2-1', 'ATCGTTCA'), ('s2-2', 'GGCCC')])\n emptyfile = viral_ngs.core.file.mkstempfname('.txt')\n outVcf = viral_ngs.core.file.mkstempfname('.vcf.gz')\n self.assertRaises(\n LookupError, viral_ngs.intrahost.merge_to_vcf, ref, outVcf, [\n 's1', 's2'\n ], [\n emptyfile, emptyfile\n ], [\n s1, s2\n ])\n with viral_ngs.phylo.vcf.VcfReader(outVcf) as vcf:\n self.assertEqual(vcf.samples(), ['s1', 's2'])\n self.assertEqual(vcf.chrlens(), {'ref1': 8, 'ref2': 5})\n\n def test_simple_snps(self):\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGGAC')])\n # ATCGGAC-\n merger.add_genome('s2', [('s2-1', 'TCGGACT')])\n # -TCGGACT\n merger.add_genome('s3', [('s3-1', 'TCGGACT')])\n # -TCGGACT\n merger.add_snp('s1', 's1-1', 3, [('C', 80, 80), ('A', 20, 20)])\n merger.add_snp('s2', 's2-1', 2, [('C', 90, 90), ('A', 10, 10)])\n merger.add_snp('s3', 's3-1', 5, [('A', 70, 70), ('T', 30, 30)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 2)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 3)\n self.assertEqual(rows[0].ref, 'C')\n self.assertEqual(rows[0].alt, 'A')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '0:0.2')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '0:0.1')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '0:0.0')\n self.assertEqual(rows[1].contig, 'ref1')\n self.assertEqual(rows[1].pos + 1, 6)\n self.assertEqual(rows[1].ref, 'A')\n self.assertEqual(rows[1].alt, 'T')\n self.assertEqual(':'.join(rows[1][0].split(':')[:2]), '0:0.0')\n self.assertEqual(':'.join(rows[1][1].split(':')[:2]), '0:0.0')\n self.assertEqual(':'.join(rows[1][2].split(':')[:2]), '0:0.3')\n\n def test_simple_snps_guess_samplenames(self):\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGGAC')])\n # ATCGGAC-\n merger.add_genome('s2', [('s2-1', 'TCGGACT')])\n # -TCGGACT\n merger.add_genome('s3', [('s3-1', 'TCGGACT')])\n # -TCGGACT\n merger.add_snp('s1', 's1-1', 3, [('C', 80, 80), ('A', 20, 20)])\n merger.add_snp('s2', 's2-1', 2, [('C', 90, 90), ('A', 10, 10)])\n merger.add_snp('s3', 's3-1', 5, [('A', 70, 70), ('T', 30, 30)])\n rows = merger.run_and_get_vcf_rows(omit_samplenames=True)\n self.assertEqual(len(rows), 2)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 3)\n self.assertEqual(rows[0].ref, 'C')\n self.assertEqual(rows[0].alt, 'A')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '0:0.2')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '0:0.1')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '0:0.0')\n self.assertEqual(rows[1].contig, 'ref1')\n self.assertEqual(rows[1].pos + 1, 6)\n self.assertEqual(rows[1].ref, 'A')\n self.assertEqual(rows[1].alt, 'T')\n self.assertEqual(':'.join(rows[1][0].split(':')[:2]), '0:0.0')\n self.assertEqual(':'.join(rows[1][1].split(':')[:2]), '0:0.0')\n self.assertEqual(':'.join(rows[1][2].split(':')[:2]), '0:0.3')\n\n def test_snps_with_varying_read_depth(self):\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGGAC')])\n # ATCGGAC-\n merger.add_genome('s2', [('s2-1', 'TCGGACT')])\n # -TCGGACT\n merger.add_genome('s3', [('s3-1', 'TCGGACT')])\n # -TCGGACT\n merger.add_snp('s1', 's1-1', 3, [('C', 60, 100), ('A', 25, 15)])\n merger.add_snp('s2', 's2-1', 2, [('C', 12, 6), ('A', 2, 0)])\n merger.add_snp('s3', 's3-1', 5, [('A', 7, 4), ('T', 2, 3)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 2)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 3)\n self.assertEqual(rows[0].ref, 'C')\n self.assertEqual(rows[0].alt, 'A')\n self.assertEqual(':'.join(rows[0][0].split(':')[:3]), '0:0.2:200')\n self.assertEqual(':'.join(rows[0][1].split(':')[:3]), '0:0.1:20')\n self.assertEqual(':'.join(rows[0][2].split(':')[:3]), '0:0.0:.')\n self.assertEqual(rows[1].contig, 'ref1')\n self.assertEqual(rows[1].pos + 1, 6)\n self.assertEqual(rows[1].ref, 'A')\n self.assertEqual(rows[1].alt, 'T')\n self.assertEqual(':'.join(rows[1][0].split(':')[:3]), '0:0.0:.')\n self.assertEqual(':'.join(rows[1][1].split(':')[:3]), '0:0.0:.')\n self.assertEqual(':'.join(rows[1][2].split(':')[:3]), '0:0.3125:16')\n\n def test_snps_downstream_of_indels(self):\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGTTGACT')])\n merger.add_genome('s2', [('s2-1', 'TCGTTGACT')])\n merger.add_genome('s3', [('s3-1', 'TCGGCCT')])\n merger.add_snp('s1', 's1-1', 8, [('A', 80, 80), ('C', 20, 20)])\n merger.add_snp('s2', 's2-1', 7, [('A', 90, 90), ('C', 10, 10)])\n merger.add_snp('s3', 's3-1', 5, [('C', 70, 70), ('A', 30, 30)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 6)\n self.assertEqual(rows[0].ref, 'A')\n self.assertEqual(rows[0].alt, 'C')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '0:0.2')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '0:0.1')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '1:0.7')\n\n def test_sample_major_allele_not_ref_allele(self):\n # make sure we can invert the allele frequency of the isnv\n # if necessary to match the reference's definition of ref & alt\n merger = VcfMergeRunner([('ref1', 'ATCGCAC')])\n merger.add_genome('s1', [('s1-1', 'ATAGCCC')])\n merger.add_snp('s1', 's1-1', 3, [('C', 10, 10), ('A', 90, 90)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 3)\n self.assertEqual(rows[0].ref, 'C')\n self.assertEqual(rows[0].alt, 'A')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '1:0.9')\n\n def test_backfill_sample_from_assembly(self):\n # one sample has no isnv, but another does, so we fill it in\n # 100% with its assembly allele, unless it doesn't have one\n # REF C\n # S1 A (isnv)\n # S2 A (consensus, no isnv)\n # S3 N (no consensus, no isnv)\n merger = VcfMergeRunner([('ref1', 'ATCG')])\n merger.add_genome('s1', [('s1-1', 'ATCG')])\n merger.add_genome('s2', [('s2-1', 'ATAG')])\n merger.add_genome('s3', [('s3-1', 'ATNG')])\n merger.add_snp('s1', 's1-1', 3, [('C', 90, 90), ('A', 10, 10)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 3)\n self.assertEqual(rows[0].ref, 'C')\n self.assertEqual(rows[0].alt, 'A')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '0:0.1')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '1:1.0')\n self.assertEqual(rows[0][2], '.:.:.:.:.')\n\n def test_simple_insertions(self):\n # IA, ITCG, etc\n # V-Phaser outputs a position that is just prior to where the new\n # bases come in. For example: ATCG -> ATiiiCG is at position 2.\n # This is consistent with what the VCF conventional position.\n # V-Phaser outputs an allele that does not include the position.\n # For example: ATCG -> ATAAACG is considered \"IAAA\" at position 2.\n # This is not the same as the VCF convention, which includes the\n # initial invariant base as part of the allele (it's a T -> TAAA\n # variant at position 2).\n merger = VcfMergeRunner([('ref1', 'ATCG')])\n merger.add_genome('s1', [('s1-1', 'ATCG')])\n merger.add_genome('s2', [('s2-1', 'ATCG')])\n merger.add_genome('s3', [('s3-1', 'ATCG')])\n merger.add_indel('s1', 's1-1', 2, [('', 80, 80), ('AA', 20, 20)])\n merger.add_indel('s2', 's2-1', 2, [('', 90, 90), ('AT', 10, 10)])\n merger.add_indel('s3', 's3-1', 2, [('', 80, 80), ('GCC', 15, 15), ('AA', 5, 5)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 2)\n self.assertEqual(rows[0].ref, 'T')\n self.assertEqual(rows[0].alt, 'TAA,TGCC,TAT')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '0:0.2,0.0,0.0')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '0:0.0,0.0,0.1')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '0:0.05,0.15,0.0')\n\n def test_simple_deletions(self):\n # D1, D2, etc...\n # V-Phaser outputs a position that describes the deleted base and\n # the number of bases deleted (but does not tell you what bases\n # were deleted). For example: ATCGAT -> ATAT is considered\n # a \"D2\" deletion at position 3.\n # This is not the same as the VCF convention, which anchors on\n # a preceeding invariant base. The above example is considered\n # to be a TCG -> T variant at position 2.\n merger = VcfMergeRunner([('ref1', 'ATCGAT')])\n merger.add_genome('s1', [('s1-1', 'ATCGAT')])\n merger.add_genome('s2', [('s2-1', 'ATCGAT')])\n merger.add_genome('s3', [('s3-1', 'ATCGAT')])\n merger.add_indel('s1', 's1-1', 3, [('CG', 80, 80), ('', 20, 20)])\n merger.add_indel('s2', 's2-1', 3, [('C', 90, 90), ('', 10, 10)])\n merger.add_indel('s3', 's3-1', 3, [('CG', 80, 80), ('G', 15, 15), ('', 5, 5)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 2)\n self.assertEqual(rows[0].ref, 'TCG')\n self.assertEqual(rows[0].alt, 'TG,T')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '0:0.0,0.2')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '0:0.1,0.0')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '0:0.15,0.05')\n\n def test_deletion_spans_deletion(self):\n # sample assembly has deletion against reference and isnv deletes even more\n # POS is anchored right before the deletion\n # REF: ATCGTTCA\n # S1: ATCG--CA\n # isnv: x (position 5, D1)\n merger = VcfMergeRunner([('ref1', 'ATCGTTCA')])\n merger.add_genome('s1', [('s1-1', 'ATCGCA')])\n merger.add_indel('s1', 's1-1', 5, [('C', 90, 90), ('', 10, 10)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 4)\n self.assertEqual(rows[0].ref, 'GTTC')\n self.assertEqual(rows[0].alt, 'GC,G')\n self.assertEqual(rows[0][0], '1:0.9,0.1:200:0,1,1:.,1.0,1.0')\n\n def test_insertion_spans_deletion(self):\n # sample assembly has deletion against reference and isnv inserts back into it\n # POS is anchored right before the deletion\n # REF: ATCGTTGA\n # S1: ATCG--GA\n # isnv: T (position 4, IT)\n # isnv: TT (position 4, ITT)\n # isnv: TTC (position 4, ITTC)\n merger = VcfMergeRunner([('ref1', 'ATCGTTCACC')])\n merger.add_genome('s1', [('s1-1', 'ATCGCACC')])\n merger.add_genome('s2', [('s2-1', 'ATCGCACC')])\n merger.add_genome('s3', [('s3-1', 'ATCGCACC')])\n merger.add_indel('s1', 's1-1', 4, [('', 70, 70), ('T', 30, 30)])\n merger.add_indel('s2', 's2-1', 4, [('', 80, 80), ('TT', 20, 20)])\n merger.add_indel('s3', 's3-1', 4, [('', 90, 90), ('TTC', 10, 10)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 4)\n self.assertEqual(rows[0].ref, 'GTT')\n self.assertEqual(rows[0].alt, 'G,GT,GTTC')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '1:0.7,0.3,0.0')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '1:0.8,0.0,0.0')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '1:0.9,0.0,0.1')\n\n def test_snp_within_insertion(self):\n # sample assembly has insertion against reference and isnp modifies it\n # REF: ATCG--GA\n # S1: ATCGTTGA\n # isnv: C\n # isnv: C\n # isnv: C\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGTTGACT')])\n merger.add_genome('s2', [('s2-1', 'TCGTTGACT')])\n merger.add_genome('s3', [('s3-1', 'TCGTTGACT')])\n merger.add_snp('s1', 's1-1', 4, [('G', 70, 70), ('C', 30, 30)])\n merger.add_snp('s2', 's2-1', 4, [('T', 80, 80), ('C', 20, 20)])\n merger.add_snp('s3', 's3-1', 5, [('T', 90, 90), ('C', 10, 10)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 4)\n self.assertEqual(rows[0].ref, 'G')\n self.assertEqual(rows[0].alt, 'GTT,CTT,GCT,GTC')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '1:0.7,0.3,0.0,0.0')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '1:0.8,0.0,0.2,0.0')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '1:0.9,0.0,0.0,0.1')\n\n def test_2snps_within_insertion_same_sample(self):\n # Sample assembly has insertion against reference containing two SNPs\n # in the same sample.\n # We don't handle this because we can't see phasing; it should be\n # handled by the variant caller.\n # REF: ATCG--GACT\n # S1: ATCGTTGACT\n # isnv: C\n # isnv: C\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGTTGACT')])\n merger.add_snp('s1', 's1-1', 5, [('T', 80, 80), ('C', 20, 20)])\n merger.add_snp('s1', 's1-1', 6, [('T', 90, 90), ('C', 10, 10)])\n self.assertRaises(NotImplementedError, merger.run_and_get_vcf_rows)\n\n def test_deletion_past_end_of_some_consensus(self):\n # Some sample contains a deletion beyond the end of the consensus\n # sequence of another sample with a SNP. It should skip latter rather\n # than crashing.\n # REF: ATCGAAC\n # S1: ATCG--C\n # S1isnv: ATCA--C\n # S2: ATCT\n # S2isnv: ATCC\n merger = VcfMergeRunner([('ref1', 'ATCGAAC')])\n merger.add_genome('s1', [('s1-1', 'ATCGC')])\n merger.add_snp('s1', 's1-1', 4, [('G', 70, 70), ('A', 30, 30)])\n merger.add_genome('s2', [('s2-1', 'ATCT')])\n merger.add_snp('s2', 's2-1', 4, [('T', 80, 80), ('C', 20, 20)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 2)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 4)\n self.assertEqual(rows[0].ref, 'GAA')\n # multiple options because the allele frequencies can be the same\n self.assertIn(rows[0].alt, ['C,G,A', 'G,C,A'])\n self.assertIn(rows[0][0], ['2:0.0,0.7,0.3:200:0,0,1,1:.,.,1.0,1.0', '1:0.7,0.0,0.3:200:0,1,0,1:.,1.0,.,1.0'])\n self.assertIn(rows[0][1], ['1:1.0,0.0,0.0:.:.:.', '2:0.0,1.0,0.0:.:.:.'])\n self.assertEqual(rows[1].contig, 'ref1')\n self.assertEqual(rows[1].pos + 1, 7)\n self.assertEqual(rows[1].ref, 'C')\n self.assertEqual(rows[1].alt, 'T')\n self.assertEqual(rows[1][0], '0:0.0:.:.:.')\n self.assertEqual(rows[1][1], '1:0.8:200:1,1:1.0,1.0')\n\n def test_snp_past_end_of_some_consensus(self):\n # Some sample contains SNP beyond the end of the consensus\n # sequence of another. It should skip latter rather\n # than crashing.\n # REF: AT\n # S1: AT\n # S1isnv: AG\n # S2: A\n merger = VcfMergeRunner([('ref1', 'AT')])\n merger.add_genome('s1', [('s1-1', 'AT')])\n merger.add_snp('s1', 's1-1', 2, [('T', 70, 70), ('G', 30, 30)])\n merger.add_genome('s2', [('s2-1', 'A')])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 2)\n self.assertEqual(rows[0].ref, 'T')\n self.assertEqual(rows[0].alt, 'G')\n self.assertEqual(rows[0][0], '0:0.3:200:1,1:1.0,1.0')\n self.assertEqual(rows[0][1], '.:.:.:.:.')\n\n def test_deletion_within_insertion(self):\n # sample assembly has insertion against reference and isnv deletes from it\n # REF: ATCG--GA\n # S1: ATCGTTGA\n # isnv: x (position 5, D1) s1 => GTG\n # isnv: xx (position 5, D2) s1 => GG\n # isnv: xxx (position 5, D3) s1 => G\n # isnv: x (position 6, D1) s2, s3 => GTG\n # isnv: xx (position 6, D2) s3 => GT\n # isnv: x (position 7, D1) s4 => GTT\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGTTGACT')])\n merger.add_genome('s2', [('s2-1', 'TCGTTGACT')])\n merger.add_genome('s3', [('s3-1', 'TCGTTGACT')])\n merger.add_genome('s4', [('s4-1', 'TCGTTGACT')])\n merger.add_indel('s1', 's1-1', 5, [('TTG', 40, 40), ('TG', 30, 30), ('G', 20, 20), ('', 10, 10)])\n merger.add_indel('s2', 's2-1', 4, [('T', 80, 80), ('', 20, 20)])\n merger.add_indel('s3', 's3-1', 5, [('TG', 85, 85), ('G', 10, 10), ('', 5, 5)])\n merger.add_indel('s4', 's4-1', 6, [('G', 90, 90), ('', 10, 10)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 4)\n self.assertEqual(rows[0].ref, 'GG')\n self.assertEqual(rows[0].alt, 'GTTG,GTG,GTT,G,GT')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '1:0.4,0.3,0.0,0.1,0.0')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '1:0.8,0.2,0.0,0.0,0.0')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '1:0.85,0.1,0.0,0.0,0.05')\n self.assertEqual(':'.join(rows[0][3].split(':')[:2]), '1:0.9,0.0,0.1,0.0,0.0')\n\n def test_insertion_within_insertion(self):\n # sample assembly has insertion against reference and isnv puts even more in\n # REF: ATCG--GA\n # S1: ATCGTTGA\n # isnv: ^ (position 4, IA)\n # isnv: ^ (position 5, IA)\n # isnv: ^ (position 6, IA)\n merger = VcfMergeRunner([('ref1', 'ATCGGACT')])\n merger.add_genome('s1', [('s1-1', 'ATCGTTGACT')])\n merger.add_genome('s2', [('s2-1', 'TCGTTGACT')])\n merger.add_genome('s3', [('s3-1', 'TCGTTGACT')])\n merger.add_indel('s1', 's1-1', 4, [('', 70, 70), ('A', 30, 30)])\n merger.add_indel('s2', 's2-1', 4, [('', 80, 80), ('A', 20, 20)])\n merger.add_indel('s3', 's3-1', 5, [('', 90, 90), ('A', 10, 10)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 4)\n self.assertEqual(rows[0].ref, 'G')\n self.assertEqual(rows[0].alt, 'GTT,GATT,GTAT,GTTA')\n self.assertEqual(':'.join(rows[0][0].split(':')[:2]), '1:0.7,0.3,0.0,0.0')\n self.assertEqual(':'.join(rows[0][1].split(':')[:2]), '1:0.8,0.0,0.2,0.0')\n self.assertEqual(':'.join(rows[0][2].split(':')[:2]), '1:0.9,0.0,0.0,0.1')\n\n def test_indel_collapse(self):\n # vphaser describes insertions and deletions separately\n # test appropriate collapse of coincident insertions and deletions into\n # a single output VCF row\n # isnv: (position 2, IA)\n # isnv: (position 3, D1)\n # Note: This is where V-Phaser gets weird. For sites that have both\n # insertions and deletions, the insertions are described on one row\n # and the deletions get described on a separate row. But both rows\n # will have a read count for the majority/consensus allele\n # (called \"i\" in one and \"d\" in the other), but the counts for\n # that allele often do not agree between the two rows!\n # So in this scenario, we ought to average them.\n merger = VcfMergeRunner([('ref1', 'ATCG')])\n merger.add_genome('s1', [('s1-1', 'ATCG')])\n merger.add_indel('s1', 's1-1', 2, [('', 40, 40), ('A', 20, 20)])\n merger.add_indel('s1', 's1-1', 3, [('C', 60, 60), ('', 30, 30)])\n rows = merger.run_and_get_vcf_rows()\n self.assertEqual(len(rows), 1)\n self.assertEqual(rows[0].contig, 'ref1')\n self.assertEqual(rows[0].pos + 1, 2)\n self.assertEqual(rows[0].ref, 'TC')\n self.assertEqual(rows[0].alt, 'T,TAC')\n self.assertEqual(rows[0][0].split(':')[0], '0') # s1 is 0.5 TC, 0.3 T, 0.2 TAC\n for actual, expected in zip(rows[0][0].split(':')[1].split(','), [0.3, 0.2]):\n self.assertAlmostEqual(float(actual), expected, places=2)\n" }, { "path": "tests/unit/phylo/test_ncbi.py", "content": "# Unit tests for ncbi.py\n\n__author__ = \"tomkinsc@broadinstitute.org\"\n\n# built-ins\nimport os\nimport tempfile\nimport unittest\nimport argparse\n\n# module-specific\nimport viral_ngs.ncbi as ncbi\nimport viral_ngs.core.file\nimport viral_ngs.phylo.genbank\nfrom tests import (assert_equal_bam_reads, TestCaseWithTmp, assert_equal_contents,\n assert_md5_equal_to_line_in_file, assert_valid_feature_table)\n\n\nclass TestCommandHelp(unittest.TestCase):\n\n def test_help_parser_for_each_command(self):\n for cmd_name, parser_fun in viral_ngs.ncbi.__commands__:\n parser = parser_fun(argparse.ArgumentParser())\n helpstring = parser.format_help()\n\nclass TestFeatureReader(TestCaseWithTmp):\n def setUp(self):\n super(TestFeatureReader, self).setUp()\n self.input_dir = viral_ngs.core.file.get_test_input_path(self)\n\n def test_read_seq_id_simple(self):\n accessions = ('GU481072.1', 'GU481073.1',\n 'KM821772.1', 'KM821773.1')\n for acc in accessions:\n self.assertEqual(acc, viral_ngs.phylo.genbank.get_feature_table_id(os.path.join(self.input_dir, acc+'.tbl')))\n\n def test_read_seq_id_different_fnames(self):\n self.assertEqual('KM821998.1', viral_ngs.phylo.genbank.get_feature_table_id(os.path.join(self.input_dir,\n 'test1-S.tbl')))\n self.assertEqual('KM821997.1', viral_ngs.phylo.genbank.get_feature_table_id(os.path.join(self.input_dir,\n 'test2-L.tbl')))\n\n def test_read_seq_id_refseq(self):\n self.assertEqual('NC_026438.1', viral_ngs.phylo.genbank.get_feature_table_id(os.path.join(self.input_dir,\n 'NC_026438.1.tbl')))\n\n def test_read_seq_id_ddbj(self):\n self.assertEqual('LC889323.1', viral_ngs.phylo.genbank.get_feature_table_id(os.path.join(self.input_dir,\n 'LC889323.1.tbl')))\n\n def test_seq_location_str_format(self):\n \"\"\"Test SeqLocation string format - continuation lines should not have trailing tabs.\"\"\"\n from viral_ngs.phylo.feature_table import SeqLocation, SeqPosition\n\n # First line with feature type - should have 3 columns\n first = SeqLocation(SeqPosition(100), SeqPosition(200), feature_type='CDS')\n self.assertEqual(str(first), \"100\\t200\\tCDS\")\n\n # Continuation line without feature type - should have 2 columns, NO trailing tab\n continuation = SeqLocation(SeqPosition(300), SeqPosition(400), feature_type=None)\n self.assertEqual(str(continuation), \"300\\t400\") # NOT \"300\\t400\\t\"\n\nclass TestFeatureTransfer(TestCaseWithTmp):\n def setUp(self):\n super(TestFeatureTransfer, self).setUp()\n self.input_dir = viral_ngs.core.file.get_test_input_path(self)\n\n def test_synthetic_feature_table(self):\n input_dir = os.path.join(self.input_dir, \"synthetic\", \"input\")\n expected_dir = os.path.join(self.input_dir, \"synthetic\", \"expected\")\n temp_dir = tempfile.gettempdir()\n\n in_tbl = os.path.join(input_dir,\"ref.tbl\")\n out_tbl = os.path.join(temp_dir,\"sample.tbl\")\n expected = os.path.join(expected_dir, \"mapped.tbl\")\n\n ncbi.tbl_transfer_prealigned( \n os.path.join(input_dir,\"aligned_1.fasta\"),\n os.path.join(input_dir,\"ref.fasta\"), \n [in_tbl], \n temp_dir)\n\n assert_equal_contents(self, out_tbl, expected)\n\n def test_synthetic_feature_table_oob_clip(self):\n input_dir = os.path.join(self.input_dir, \"synthetic_oob_clip\", \"input\")\n expected_dir = os.path.join(self.input_dir, \"synthetic_oob_clip\", \"expected\")\n temp_dir = tempfile.gettempdir()\n\n in_tbl = os.path.join(input_dir,\"ref.tbl\")\n out_tbl = os.path.join(temp_dir,\"sample.tbl\")\n expected = os.path.join(expected_dir, \"mapped.tbl\")\n\n ncbi.tbl_transfer_prealigned(\n os.path.join(input_dir,\"aligned_1.fasta\"),\n os.path.join(input_dir,\"ref.fasta\"),\n [in_tbl],\n temp_dir,\n oob_clip=True)\n\n assert_equal_contents(self, out_tbl, expected)\n\n # Validate with table2asn\n assert_valid_feature_table(\n self,\n out_tbl,\n os.path.join(input_dir, \"aligned_1.fasta\"),\n temp_dir\n )\n\n def test_synthetic_feature_table_ignore_ambiguous_edges(self):\n input_dir = os.path.join(self.input_dir, \"synthetic_ignore_ambig_edges\", \"input\")\n expected_dir = os.path.join(self.input_dir, \"synthetic_ignore_ambig_edges\", \"expected\")\n temp_dir = tempfile.gettempdir()\n\n in_tbl = os.path.join(input_dir,\"ref.tbl\")\n out_tbl = os.path.join(temp_dir,\"sample.tbl\")\n expected = os.path.join(expected_dir, \"mapped.tbl\")\n\n ncbi.tbl_transfer_prealigned( \n os.path.join(input_dir,\"aligned_1.fasta\"),\n os.path.join(input_dir,\"ref.fasta\"), \n [in_tbl], \n temp_dir,\n ignore_ambig_feature_edge=True)\n\n assert_equal_contents(self, out_tbl, expected)\n\n def test_severely_truncated_assembly_oob_clip(self):\n \"\"\"Test annotation transfer with severely truncated assembly (adenovirus-like scenario).\n\n This reproduces issue #67 where a ~50% truncated assembly creates invalid\n feature table syntax with coordinates but no feature keys.\n \"\"\"\n input_dir = os.path.join(self.input_dir, \"adenovirus_truncated\", \"input\")\n expected_dir = os.path.join(self.input_dir, \"adenovirus_truncated\", \"expected\")\n temp_dir = tempfile.gettempdir()\n\n in_tbl = os.path.join(input_dir, \"ref.tbl\")\n out_tbl = os.path.join(temp_dir, \"sample.tbl\")\n expected = os.path.join(expected_dir, \"mapped.tbl\")\n\n ncbi.tbl_transfer_prealigned(\n os.path.join(input_dir, \"aligned_1.fasta\"),\n os.path.join(input_dir, \"ref.fasta\"),\n [in_tbl],\n temp_dir,\n oob_clip=True\n )\n\n # Verify output is valid feature table syntax\n # First interval line has 3 fields (start, end, feature_type)\n # Continuation lines have exactly 2 fields (start, end) - NO trailing tab\n with open(out_tbl, 'r') as f:\n for line in f:\n line = line.rstrip('\\n')\n if not line or line.startswith('>') or line.startswith('\\t'):\n continue\n # Lines with coordinates must be properly tab-delimited\n parts = line.split('\\t')\n if len(parts) >= 2 and parts[0] and parts[1]:\n # Must have 2 or 3 columns\n self.assertTrue(len(parts) in (2, 3),\n f\"Invalid line (must have 2 or 3 tab-delimited fields): {line}\")\n # If 3 columns, the 3rd must not be empty (that's a trailing tab)\n if len(parts) == 3:\n self.assertNotEqual(parts[2], '',\n f\"Line has trailing tab (continuation lines should have 2 columns): {line}\")\n\n assert_equal_contents(self, out_tbl, expected)\n\n # Validate with table2asn\n assert_valid_feature_table(\n self,\n out_tbl,\n os.path.join(input_dir, \"aligned_1.fasta\"),\n temp_dir\n )\n\n def test_partial_symbols_column_placement(self):\n \"\"\"Test that < only appears in column 1 and > only appears in column 2.\n\n Issue #72: Partial stop coordinates incorrectly used '<' instead of '>'.\n Per NCBI spec, '<' always goes in column 1, '>' always goes in column 2,\n regardless of strand.\n \"\"\"\n input_dir = os.path.join(self.input_dir, \"negative_strand_partial\", \"input\")\n expected_dir = os.path.join(self.input_dir, \"negative_strand_partial\", \"expected\")\n temp_dir = tempfile.gettempdir()\n\n in_tbl = os.path.join(input_dir, \"ref.tbl\")\n out_tbl = os.path.join(temp_dir, \"sample.tbl\")\n expected = os.path.join(expected_dir, \"mapped.tbl\")\n\n ncbi.tbl_transfer_prealigned(\n os.path.join(input_dir, \"aligned_1.fasta\"),\n os.path.join(input_dir, \"ref.fasta\"),\n [in_tbl],\n temp_dir,\n oob_clip=True\n )\n\n # Verify partial symbols are in correct columns per NCBI spec\n with open(out_tbl, 'r') as f:\n for line_num, line in enumerate(f, 1):\n line = line.rstrip('\\n')\n if not line or line.startswith('>Feature') or line.startswith('\\t'):\n continue\n parts = line.split('\\t')\n if len(parts) >= 2:\n col1, col2 = parts[0], parts[1]\n # < must only appear in column 1 (start position)\n self.assertFalse(col2.startswith('<'),\n f\"Line {line_num}: '<' in column 2 is invalid per NCBI spec (must be '>'): {line}\")\n # > must only appear in column 2 (end position)\n self.assertFalse(col1.startswith('>'),\n f\"Line {line_num}: '>' in column 1 is invalid per NCBI spec (must be '<'): {line}\")\n\n assert_equal_contents(self, out_tbl, expected)\n\n # Validate with table2asn\n assert_valid_feature_table(\n self,\n out_tbl,\n os.path.join(input_dir, \"aligned_1.fasta\"),\n temp_dir\n )\n\n def test_internal_partials_dropped(self):\n \"\"\"Test that multi-interval features with internal partials are dropped.\n\n Issue #74: table2asn rejects features where partial symbols appear\n on internal intervals rather than the true 5'/3' ends. When a\n multi-interval feature is truncated such that a partial symbol would\n appear on an internal interval, the entire feature should be dropped.\n \"\"\"\n input_dir = os.path.join(self.input_dir, \"internal_partials\", \"input\")\n expected_dir = os.path.join(self.input_dir, \"internal_partials\", \"expected\")\n temp_dir = tempfile.gettempdir()\n\n in_tbl = os.path.join(input_dir, \"ref.tbl\")\n out_tbl = os.path.join(temp_dir, \"sample.tbl\")\n expected = os.path.join(expected_dir, \"mapped.tbl\")\n\n ncbi.tbl_transfer_prealigned(\n os.path.join(input_dir, \"aligned_1.fasta\"),\n os.path.join(input_dir, \"ref.fasta\"),\n [in_tbl],\n temp_dir,\n oob_clip=True\n )\n\n # Feature with internal partials should be dropped entirely\n assert_equal_contents(self, out_tbl, expected)\n\n # Validate with table2asn - should pass since feature was dropped\n assert_valid_feature_table(\n self,\n out_tbl,\n os.path.join(input_dir, \"aligned_1.fasta\"),\n temp_dir\n )\n\n def test_lasv_oob_clip(self):\n input_dir = os.path.join(self.input_dir, \"lasv\", \"input\")\n expected_dir = os.path.join(self.input_dir, \"lasv\", \"expected\")\n temp_dir = tempfile.gettempdir()\n\n infastas = [os.path.join(input_dir, f) for f in [\n \"align_mafft-ref-lasv-ISTH2376_1.fasta\",\n \"align_mafft-ref-lasv-ISTH2376_2.fasta\"\n ]\n ]\n\n intables =[os.path.join(input_dir, f) for f in [\n \"KM821997.1.tbl\",\n \"KM821998.1.tbl\"\n ]\n ]\n\n out_table_names = [\n \"LASV_NGA_2018_0026-1.tbl\",\n \"LASV_NGA_2018_0026-2.tbl\",\n \"LASV_NGA_2018_0097-1.tbl\",\n \"LASV_NGA_2018_0097-2.tbl\",\n \"LASV_NGA_2018_0541-1.tbl\",\n \"LASV_NGA_2018_0541-2.tbl\",\n \"LASV_NGA_2018_0611-1.tbl\",\n \"LASV_NGA_2018_0611-2.tbl\",\n \"LASV_NGA_2018_0664-1.tbl\",\n \"LASV_NGA_2018_0664-2.tbl\",\n \"LASV_NGA_2018_0959-1.tbl\",\n \"LASV_NGA_2018_0959-2.tbl\",\n \"LASV_NGA_2018_0998-1.tbl\",\n \"LASV_NGA_2018_0998-2.tbl\",\n \"LASV_NGA_2018_1024-1.tbl\",\n \"LASV_NGA_2018_1024-2.tbl\",\n \"LASV_NGA_2018_1079-1.tbl\",\n \"LASV_NGA_2018_1079-2.tbl\",\n \"LASV_NGA_2018_1177-1.tbl\",\n \"LASV_NGA_2018_1177-2.tbl\",\n \"LASV_NGA_2018_1375-1.tbl\",\n \"LASV_NGA_2018_1375-2.tbl\",\n \"LASV_NGA_2018_1381-1.tbl\",\n \"LASV_NGA_2018_1381-2.tbl\",\n \"LASV_NGA_2018_1392-1.tbl\",\n \"LASV_NGA_2018_1392-2.tbl\",\n \"LASV_NGA_2018_1643-1.tbl\",\n \"LASV_NGA_2018_1643-2.tbl\"\n ]\n out_tbls =[os.path.join(temp_dir, f) for f in out_table_names]\n expected_tbls = [os.path.join(expected_dir, f) for f in out_table_names]\n\n\n for i in range(0, len(infastas)):\n ncbi.tbl_transfer_prealigned( \n infastas[i],\n os.path.join(input_dir,\"ref-lasv-ISTH2376.fasta\"), \n intables, \n temp_dir,\n oob_clip=True)\n\n for i in range(0,len(out_table_names)):\n out_tbl = out_tbls[i]\n expected_tbl = expected_tbls[i]\n assert_equal_contents(self, out_tbl, expected_tbl)\n" }, { "path": "tests/unit/phylo/test_tools.py", "content": "# Unit tests for tools/__init__.py\n\n__author__ = \"yesimon@broadinstitute.org\"\n\nimport pytest\nimport viral_ngs.core\nfrom viral_ngs.core import Tool, PrexistingUnixCommand\n\n@pytest.fixture(params=viral_ngs.core.all_tool_classes())\ndef tool_class(request):\n return request.param\n\n@pytest.mark.slow\ndef test_tool_install(tool_class):\n t = tool_class()\n t.install()\n assert t.is_installed()\n" }, { "path": "tests/unit/phylo/test_tools_vphaser2.py", "content": "# Unit tests for vphaser tool\n\n__author__ = \"irwin@broadinstitute.org\"\n\nimport os\nimport pickle\nimport unittest\nimport viral_ngs.core.file\nimport viral_ngs.core\nfrom viral_ngs.intrahost import vphaser_main\nfrom tests import TestCaseWithTmp, _CPUS\n\n\n#@unittest.skipIf(viral_ngs.core.is_osx(), \"vphaser2 osx binary from bioconda has issues\")\n@unittest.skip(\"vphaser2 behaving unpredictably; not used in WDL pipelines\")\nclass TestVPhaser2(TestCaseWithTmp):\n\n def test_vphaser2(self):\n myInputDir = viral_ngs.core.file.get_test_input_path(self)\n inBam = os.path.join(myInputDir, 'in.bam')\n outTab = viral_ngs.core.file.mkstempfname('.txt')\n vphaser_main(inBam, outTab, numThreads=_CPUS)\n with open(outTab, 'rt') as outf:\n recs = map(lambda s: s.strip('\\n').split('\\t'), outf.readlines())\n with open(os.path.join(myInputDir, 'expected.cpickle'), 'rb') as expf:\n expectedRecs = pickle.load(expf)\n # Vphaser2 p-val calculation is unstable and sometimes varies from\n # run to run, so exclude it from comparison.\n self.assertEqual([rec[:4] + rec[5:] for rec in recs], [rec[:4] + rec[5:] for rec in expectedRecs])\n \"\"\"\n Creation of in.bam:\n Start with test file that ships with V-Phaser 2.\n cp 4528.454.indelRealigned.bam orig.bam\n samtools index orig.bam\n samtools view -h orig.bam V4528_assembly:1-100 V4528_assembly:950-1050 >c1.sam\n samtools view -h orig.bam V4528_assembly:8950-9050 V4528_assembly:9900-9950 >c2.sam\n Change all occurences of V4528_assembly in c1.sam to chr1,\n Change all occurences of V4528_assembly in c2.sam to chr2,\n Move the @SQ line from c2.sam to c1.sam and delete header of c2.sam.\n cat c1.sam c2.sam >new.sam\n samtools view -bh new.sam >new.bam\n\n Creation of expected.cpickle:\n cPickle.dump(list(Vphaser2Tool().iterate(inBam, numThreads = 8)),\n open('expected.cpickle', 'w'))\n \"\"\"\n" }, { "path": "tests/unit/phylo/test_util_vcf.py", "content": "# Unit tests for util/vcf.py\n\n__author__ = \"dpark@broadinstitute.org\"\n\nimport viral_ngs.phylo.vcf\nimport viral_ngs.core.file\nimport unittest\n'''\nTODO\nmake_intervals\nsliding_windows\ncalc_maf\nTabixReader - edge cases in a simple file\nVcfReader - proper one-based genomic coordinates\nVcfReader - haploid cases, diploid cases\nVcfReader.getFullSequences and replaceAlleles - this needs a whole battery of tests,\n since it does so much and is subject to so many edge cases and weird scenarios and\n keeps breaking each time we refactor.\n'''\n\n\nclass StubGenome:\n ''' This is a mock genome that should satisfy very simple functions in phylo.vcf\n like get_chrlens, GenomePosition, make_intervals, sliding_windows, etc.\n It simply contains a list of chromosome names and lengths.\n '''\n\n def __init__(self, chromlist):\n self.chrs = [c for c, clen in chromlist]\n self.chrlen = dict(chromlist)\n self.totlen = sum(clen for c, clen in chromlist)\n\n def chrlens(self):\n return [(c, self.chrlen[c]) for c in self.chrs]\n\n\nclass TestGenomePosition(unittest.TestCase):\n ''' Test the GenomePosition class which maps chr,pos pairs to a single gpos int and vice versa '''\n\n def test_fail_OOB_get_gpos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n invalids = [('SDF', 0), ('SDF', 124), ('ASDF', -1), ('lala', 48), ('lala', 200), ('sdf', 80), ('la', 2),\n (None, 3)]\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n for c, p in invalids:\n self.assertRaises(Exception, gmap.get_gpos, c, p)\n\n def test_fail_OOB_get_chr_pos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n invalids = [0, -1, genome.totlen + 1, genome.totlen * 2]\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n for gpos in invalids:\n self.assertRaises(Exception, gmap.get_chr_pos, gpos)\n\n def test_fail_non_int_pos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n invalids = [('SDF', 5.3), ('lala', '10'), ('ASDF', None)]\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n for c, p in invalids:\n self.assertRaises(Exception, gmap.get_gpos, c, p)\n self.assertRaises(Exception, gmap.get_chr_pos, p)\n\n def test_spotcheck_edges(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n knowns = [('SDF', 1, 1), ('SDF', 123, 123), ('ASDF', 1, 124), ('ASDF', 256, 379), ('lala', 1, 380),\n ('lala', 47, 426)]\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n for c, p, gpos in knowns:\n self.assertEqual(gpos, gmap.get_gpos(c, p))\n self.assertEqual((c, p), gmap.get_chr_pos(gpos))\n\n def test_equality_1chrGenome(self):\n genome = StubGenome([('one chr', 10)])\n c = genome.chrs[0]\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n for i in range(1, genome.totlen + 1):\n self.assertEqual(i, gmap.get_gpos(c, i)) # c,p -> gpos should produce p=gpos\n self.assertEqual((c, i), gmap.get_chr_pos(i)) # gpos -> c,p should produce p=gpos\n\n def test_equality_3chrGenome(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n # test gpos -> c,p -> same gpos\n for gpos in range(1, genome.totlen + 1):\n c, p = gmap.get_chr_pos(gpos)\n gpos2 = gmap.get_gpos(c, p)\n self.assertEqual(gpos, gpos2)\n # test c,p -> gpos -> same c,p\n for c, clen in genome.chrlen.items():\n for p in range(1, clen + 1):\n gpos = gmap.get_gpos(c, p)\n c2, p2 = gmap.get_chr_pos(gpos)\n self.assertEqual(c, c2)\n self.assertEqual(p, p2)\n\n def test_gpos_inbounds(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n for c, clen in genome.chrlen.items():\n for p in range(1, clen + 1):\n gpos = gmap.get_gpos(c, p)\n self.assertIsNotNone(gpos)\n self.assertIsInstance(gpos, int)\n self.assertLessEqual(1, gpos)\n self.assertLessEqual(gpos, genome.totlen)\n\n def test_chr_pos_inbounds(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n for gpos in range(1, genome.totlen + 1):\n c, p = gmap.get_chr_pos(gpos)\n self.assertIsNotNone(c)\n self.assertIn(c, genome.chrlen)\n self.assertIsNotNone(p)\n self.assertIsInstance(p, int)\n self.assertLessEqual(1, p)\n self.assertLessEqual(p, genome.chrlen[c])\n\n def test_unique_gpos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n seen = set()\n for c, clen in genome.chrlen.items():\n for p in range(1, clen + 1):\n gpos = gmap.get_gpos(c, p)\n self.assertNotIn(gpos, seen)\n seen.add(gpos)\n self.assertEqual(len(seen), genome.totlen)\n\n def test_unique_chr_pos(self):\n genome = StubGenome([('SDF', 123), ('ASDF', 256), ('lala', 47)])\n gmap = viral_ngs.phylo.vcf.GenomePosition(genome)\n seen = set()\n for gpos in range(1, genome.totlen + 1):\n c, p = gmap.get_chr_pos(gpos)\n self.assertNotIn((c, p), seen)\n seen.add((c, p))\n self.assertEqual(len(seen), genome.totlen)\n\n\nclass TestVcfReaderPositions(unittest.TestCase):\n ''' Test the OBO errors in the pysam-based VCFReader class (it's prone to such errors) '''\n\n def setUp(self):\n self.vcf_fname = viral_ngs.core.file.get_test_path() + '/input/one_gene.vcf.gz'\n self.vcf_window = ('Pf3D7_13_v3', 1724817, 1726997)\n try:\n self.basestring = basestring\n except NameError:\n self.basestring = str\n\n def test_sample_names(self):\n expected = ['3D7', 'SenT001.08', 'SenT001.11', 'SenT002.07', 'SenT002.09']\n vcfdb = viral_ngs.phylo.vcf.VcfReader(self.vcf_fname)\n self.assertEqual(expected, vcfdb.samples())\n for s in vcfdb.samples():\n self.assertIsInstance(s, self.basestring)\n\n def test_get_one_base(self):\n vcfdb = viral_ngs.phylo.vcf.VcfReader(self.vcf_fname)\n genos = vcfdb.get_snp_genos(self.vcf_window[0], 1726432)\n alleles = [genos[s] for s in vcfdb.samples()]\n expected = ['T', 'T', 'T', 'G', 'T']\n self.assertEqual(expected, alleles)\n for a in alleles:\n self.assertIsInstance(a, self.basestring)\n\n def test_get_positions_edges(self):\n vcfdb = viral_ngs.phylo.vcf.VcfReader(self.vcf_fname)\n out = list(vcfdb.get_positions(self.vcf_window[0]))\n self.assertEqual(out[0][1], self.vcf_window[1])\n self.assertEqual(out[-1][2], self.vcf_window[2])\n\n def test_get_range_edges(self):\n vcfdb = viral_ngs.phylo.vcf.VcfReader(self.vcf_fname)\n out = [p for c, p, alleles, genos in vcfdb.get_range(self.vcf_window[0])]\n self.assertEqual(out[0], self.vcf_window[1])\n self.assertEqual(out[-1], self.vcf_window[2])\n" } ]