Upload 856 files

.gitattributes

@@ -33,3 +33,44 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+biotite/source/doc/examples/download/lysozyme_md.xtc filter=lfs diff=lfs merge=lfs -text
+biotite/source/doc/examples/download/waterbox_md.xtc filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/application/data/2rtg.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1aki.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1crr.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1dix.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1f2n.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1gya.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1igy.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1k6p.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1l2y.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1l2y.dcd filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1l2y.netcdf filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1l2y.trr filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1ncb.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/1o1z.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/2axd.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/2d0f.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/3o5r.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/3wip.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/4gxy.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/4i39.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/4p5j.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/4zxb.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/5eil.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/5h73.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/5ugo.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/5zng.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/7gsa.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/alphabet/1ay7.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/1gl4.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/1hml.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/1p4k.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/1qgi.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/2nwd.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/3kcs.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/3lsj.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/3lzm.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/3rd3.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/4osx.bcif filter=lfs diff=lfs merge=lfs -text
+biotite/source/tests/structure/data/homologs/6oa8.bcif filter=lfs diff=lfs merge=lfs -text

Dockerfile

@@ -0,0 +1,18 @@
+FROM python:3.10
+
+RUN useradd -m -u 1000 user && python -m pip install --upgrade pip
+USER user
+ENV PATH="/home/user/.local/bin:$PATH"
+
+WORKDIR /app
+
+COPY --chown=user ./requirements.txt requirements.txt
+RUN pip install --no-cache-dir --upgrade -r requirements.txt
+
+COPY --chown=user . /app
+ENV MCP_TRANSPORT=http
+ENV MCP_PORT=7860
+
+EXPOSE 7860
+
+CMD ["python", "biotite/mcp_output/start_mcp.py"]

README.md

@@ -1,10 +1,32 @@
 ---
-title: Biotite
-emoji: 🏢
+title: Biotite MCP
+emoji: 🤖
 colorFrom: blue
-colorTo: blue
+colorTo: purple
 sdk: docker
+sdk_version: "4.26.0"
+app_file: app.py
 pinned: false
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# Biotite MCP Service
+
+Auto-generated MCP service for biotite.
+
+## Usage
+
+```
+https://None-biotite-mcp.hf.space/mcp
+```
+
+## Connect with Cursor
+
+```json
+{
+  "mcpServers": {
+    "biotite": {
+      "url": "https://None-biotite-mcp.hf.space/mcp"
+    }
+  }
+}
+```

app.py

@@ -0,0 +1,45 @@
+from fastapi import FastAPI
+import os
+import sys
+
+mcp_plugin_path = os.path.join(os.path.dirname(__file__), "biotite", "mcp_output", "mcp_plugin")
+sys.path.insert(0, mcp_plugin_path)
+
+app = FastAPI(
+    title="Biotite MCP Service",
+    description="Auto-generated MCP service for biotite",
+    version="1.0.0"
+)
+
+@app.get("/")
+def root():
+    return {
+        "service": "Biotite MCP Service",
+        "version": "1.0.0",
+        "status": "running",
+        "transport": os.environ.get("MCP_TRANSPORT", "http")
+    }
+
+@app.get("/health")
+def health_check():
+    return {"status": "healthy", "service": "biotite MCP"}
+
+@app.get("/tools")
+def list_tools():
+    try:
+        from mcp_service import create_app
+        mcp_app = create_app()
+        tools = []
+        for tool_name, tool_func in mcp_app.tools.items():
+            tools.append({
+                "name": tool_name,
+                "description": tool_func.__doc__ or "No description available"
+            })
+        return {"tools": tools}
+    except Exception as e:
+        return {"error": f"Failed to load tools: {str(e)}"}
+
+if __name__ == "__main__":
+    import uvicorn
+    port = int(os.environ.get("PORT", 7860))
+    uvicorn.run(app, host="0.0.0.0", port=port)

biotite/mcp_output/README_MCP.md

@@ -0,0 +1,65 @@
+# Biotite MCP (Model Context Protocol) Service
+
+## Project Introduction
+
+Biotite is an open-source bioinformatics library designed to provide a comprehensive toolkit for computational analysis of biological data. It focuses primarily on structural and sequence biology, offering high-performance data structures and algorithms for macromolecular structure analysis, biological sequence analysis and alignment, file I/O for standard bioinformatics formats, integration with external bioinformatics applications, and database access.
+
+## Installation Method
+
+To install Biotite, ensure you have the following dependencies: `numpy`, `scipy`, and `matplotlib`. Optional dependencies include `rdkit` and `openmm` for extended functionalities.
+
+You can install Biotite using pip:
+
+```
+pip install biotite
+```
+
+Alternatively, you can set up the environment using the provided `environment.yml` file:
+
+```
+conda env create -f environment.yml
+```
+
+## Quick Start
+
+Here is a quick example of how to use some of the main functions in Biotite:
+
+1. **Align Sequences:**
+
+   Use the `align_sequences` function from the `biotite.sequence.align` module to perform sequence alignment.
+
+   ```
+   from biotite.sequence.align import align_sequences
+   alignment = align_sequences(sequence1, sequence2)
+   ```
+
+2. **Load and Save Structures:**
+
+   Use the `load_structure` and `save_structure` functions from the `biotite.structure.graphics` module to handle molecular structures.
+
+   ```
+   from biotite.structure.graphics import load_structure, save_structure
+   structure = load_structure("example.pdb")
+   save_structure(structure, "output.pdb")
+   ```
+
+## Available Tools and Endpoints List
+
+- **biotite-align:** A command-line tool for aligning biological sequences using the Biotite library.
+- **Entrez Database Interface:** Provides functions like `query_database` and `download_data` for interacting with the Entrez database.
+- **Structure Module:** Offers tools for working with molecular structures, including visualization and manipulation of `AtomArray` and `AtomArrayStack` objects.
+- **Sequence Module:** Focuses on biological sequence analysis, providing functions for sequence alignment and scoring.
+
+## Common Issues and Notes
+
+- **Dependencies:** Ensure all required dependencies (`numpy`, `scipy`, `matplotlib`) are installed. Optional dependencies (`rdkit`, `openmm`) can enhance functionality but are not mandatory.
+- **Environment:** Use the `environment.yml` file to set up a consistent environment.
+- **Performance:** The library is designed for high performance, but complex operations on large datasets may require optimization or additional resources.
+
+## Reference Links or Documentation
+
+- [Biotite GitHub Repository](https://github.com/biotite-dev/biotite)
+- [Biotite Documentation](https://biotite.readthedocs.io/en/latest/)
+- [Biotite Wiki](https://github.com/biotite-dev/biotite/wiki)
+
+For further details on specific modules and their usage, refer to the documentation and wiki pages linked above.

biotite/mcp_output/analysis.json

@@ -0,0 +1,1542 @@
+{
+  "summary": {
+    "repository_url": "https://github.com/biotite-dev/biotite",
+    "summary": "Imported via zip fallback, file count: 473",
+    "file_tree": {
+      ".github/workflows/multiversion_docs.py": {
+        "size": 2741
+      },
+      ".github/workflows/test_and_deploy.yml": {
+        "size": 12972
+      },
+      "benchmarks/__init__.py": {
+        "size": 0
+      },
+      "benchmarks/conftest.py": {
+        "size": 244
+      },
+      "benchmarks/sequence/__init__.py": {
+        "size": 0
+      },
+      "benchmarks/sequence/align/__init__.py": {
+        "size": 0
+      },
+      "benchmarks/sequence/align/benchmark_kmers.py": {
+        "size": 4348
+      },
+      "benchmarks/sequence/benchmark_fasta.py": {
+        "size": 879
+      },
+      "benchmarks/structure/__init__.py": {
+        "size": 0
+      },
+      "benchmarks/structure/benchmark_alphabet.py": {
+        "size": 624
+      },
+      "benchmarks/structure/benchmark_celllist.py": {
+        "size": 501
+      },
+      "benchmarks/structure/benchmark_compare.py": {
+        "size": 917
+      },
+      "benchmarks/structure/benchmark_pdbx.py": {
+        "size": 3484
+      },
+      "benchmarks/structure/benchmark_superimpose.py": {
+        "size": 701
+      },
+      "doc/apidoc.json": {
+        "size": 12135
+      },
+      "doc/apidoc.py": {
+        "size": 7963
+      },
+      "doc/bibliography.py": {
+        "size": 2779
+      },
+      "doc/conf.py": {
+        "size": 6755
+      },
+      "doc/examples/download/Array_Seq.txt": {
+        "size": 5600
+      },
+      "doc/examples/scripts/sequence/annotation/operon_map.py": {
+        "size": 1294
+      },
+      "doc/examples/scripts/sequence/annotation/plasmid_map.py": {
+        "size": 2217
+      },
+      "doc/examples/scripts/sequence/annotation/plasmid_map_custom.py": {
+        "size": 3256
+      },
+      "doc/examples/scripts/sequence/annotation/region_visualization.py": {
+        "size": 1670
+      },
+      "doc/examples/scripts/sequence/annotation/sigma_domains.py": {
+        "size": 4455
+      },
+      "doc/examples/scripts/sequence/homology/avidin_alignment.py": {
+        "size": 1565
+      },
+      "doc/examples/scripts/sequence/homology/bionigma_alignment.py": {
+        "size": 9714
+      },
+      "doc/examples/scripts/sequence/homology/genome_comparison.py": {
+        "size": 14870
+      },
+      "doc/examples/scripts/sequence/homology/genome_search.py": {
+        "size": 8116
+      },
+      "doc/examples/scripts/sequence/homology/gpcr_evolution.py": {
+        "size": 2846
+      },
+      "doc/examples/scripts/sequence/homology/hcn_hydropathy.py": {
+        "size": 7254
+      },
+      "doc/examples/scripts/sequence/homology/hcn_similarity.py": {
+        "size": 2518
+      },
+      "doc/examples/scripts/sequence/homology/homolog_msa.py": {
+        "size": 2145
+      },
+      "doc/examples/scripts/sequence/homology/lexa_conservation.py": {
+        "size": 5690
+      },
+      "doc/examples/scripts/sequence/homology/luxa_comparison.py": {
+        "size": 1713
+      },
+      "doc/examples/scripts/sequence/homology/pi3k_alignment.py": {
+        "size": 5813
+      },
+      "doc/examples/scripts/sequence/homology/plotepiscan.py": {
+        "size": 16387
+      },
+      "doc/examples/scripts/sequence/homology/residue_coevolution.py": {
+        "size": 7427
+      },
+      "doc/examples/scripts/sequence/homology/thca_synthase_polymorphism.py": {
+        "size": 4515
+      },
+      "doc/examples/scripts/sequence/misc/blosum_dendrogram.py": {
+        "size": 2412
+      },
+      "doc/examples/scripts/sequence/misc/codon_usage.py": {
+        "size": 6801
+      },
+      "doc/examples/scripts/sequence/misc/color_schemes.py": {
+        "size": 2379
+      },
+      "doc/examples/scripts/sequence/misc/color_schemes_protein.py": {
+        "size": 3891
+      },
+      "doc/examples/scripts/sequence/misc/local_alignment_statistics.py": {
+        "size": 14495
+      },
+      "doc/examples/scripts/sequence/misc/orf_identification.py": {
+        "size": 1429
+      },
+      "doc/examples/scripts/sequence/profile/anderson_logo.py": {
+        "size": 2437
+      },
+      "doc/examples/scripts/sequence/profile/rbs_identification.py": {
+        "size": 4070
+      },
+      "doc/examples/scripts/sequence/sequencing/gene_counts.py": {
+        "size": 13219
+      },
+      "doc/examples/scripts/sequence/sequencing/genome_assembly.py": {
+        "size": 29678
+      },
+      "doc/examples/scripts/sequence/sequencing/quality_control.py": {
+        "size": 7514
+      },
+      "doc/examples/scripts/sequence/sequencing/read_quality.py": {
+        "size": 1361
+      },
+      "doc/examples/scripts/structure/alphabet/msa.py": {
+        "size": 3006
+      },
+      "doc/examples/scripts/structure/alphabet/structure_search.py": {
+        "size": 15496
+      },
+      "doc/examples/scripts/structure/contacts/adjacency_matrix.py": {
+        "size": 1364
+      },
+      "doc/examples/scripts/structure/contacts/contact_sites.py": {
+        "size": 3899
+      },
+      "doc/examples/scripts/structure/contacts/disulfide_bonds.py": {
+        "size": 7488
+      },
+      "doc/examples/scripts/structure/contacts/domain_hbonds.py": {
+        "size": 1754
+      },
+      "doc/examples/scripts/structure/contacts/leaflet.py": {
+        "size": 5024
+      },
+      "doc/examples/scripts/structure/misc/biological_assembly.py": {
+        "size": 3651
+      },
+      "doc/examples/scripts/structure/misc/diameter.py": {
+        "size": 1051
+      },
+      "doc/examples/scripts/structure/misc/gap_bars.py": {
+        "size": 3077
+      },
+      "doc/examples/scripts/structure/misc/glycan_visualization.py": {
+        "size": 14158
+      },
+      "doc/examples/scripts/structure/misc/homolog_superimposition.py": {
+        "size": 1476
+      },
+      "doc/examples/scripts/structure/misc/pdb_statistics.py": {
+        "size": 2564
+      },
+      "doc/examples/scripts/structure/modeling/docking.py": {
+        "size": 7049
+      },
+      "doc/examples/scripts/structure/modeling/md_analysis.py": {
+        "size": 5360
+      },
+      "doc/examples/scripts/structure/modeling/mmtf_trajectory.py": {
+        "size": 2810
+      },
+      "doc/examples/scripts/structure/modeling/model_lddt.py": {
+        "size": 4536
+      },
+      "doc/examples/scripts/structure/modeling/normal_modes.py": {
+        "size": 4842
+      },
+      "doc/examples/scripts/structure/modeling/rotamer_library.py": {
+        "size": 5017
+      },
+      "doc/examples/scripts/structure/modeling/solvation_shells.py": {
+        "size": 3312
+      },
+      "doc/examples/scripts/structure/modeling/trajectory_sse.py": {
+        "size": 2091
+      },
+      "doc/examples/scripts/structure/modeling/water_exchange_noexec.py": {
+        "size": 4236
+      },
+      "doc/examples/scripts/structure/molecule/alkane_isomers.py": {
+        "size": 6621
+      },
+      "doc/examples/scripts/structure/molecule/molecular_visualization.py": {
+        "size": 2189
+      },
+      "doc/examples/scripts/structure/molecule/peoe_visualization.py": {
+        "size": 3885
+      },
+      "doc/examples/scripts/structure/nucleotide/base_pairs.py": {
+        "size": 2833
+      },
+      "doc/examples/scripts/structure/nucleotide/leontis_westhof.py": {
+        "size": 3590
+      },
+      "doc/examples/scripts/structure/nucleotide/transfer_rnas.py": {
+        "size": 3700
+      },
+      "doc/examples/scripts/structure/nucleotide/watson_crick.py": {
+        "size": 4038
+      },
+      "doc/examples/scripts/structure/protein/peptide_assembly.py": {
+        "size": 5039
+      },
+      "doc/examples/scripts/structure/protein/ramachandran.py": {
+        "size": 1466
+      },
+      "doc/examples/scripts/structure/protein/residue_chirality.py": {
+        "size": 1944
+      },
+      "doc/examples/scripts/structure/protein/sheet_arrangement.py": {
+        "size": 14960
+      },
+      "doc/examples/scripts/structure/protein/transketolase_sse.py": {
+        "size": 7612
+      },
+      "doc/preamble.py": {
+        "size": 2542
+      },
+      "doc/scraper.py": {
+        "size": 1976
+      },
+      "doc/switcher.py": {
+        "size": 2296
+      },
+      "doc/viewcode.py": {
+        "size": 8764
+      },
+      "environment.yml": {
+        "size": 1767
+      },
+      "pyproject.toml": {
+        "size": 5517
+      },
+      "src/biotite/__init__.py": {
+        "size": 545
+      },
+      "src/biotite/application/__init__.py": {
+        "size": 3077
+      },
+      "src/biotite/application/application.py": {
+        "size": 8096
+      },
+      "src/biotite/application/autodock/__init__.py": {
+        "size": 315
+      },
+      "src/biotite/application/autodock/app.py": {
+        "size": 18689
+      },
+      "src/biotite/application/blast/__init__.py": {
+        "size": 366
+      },
+      "src/biotite/application/blast/alignment.py": {
+        "size": 3117
+      },
+      "src/biotite/application/blast/webapp.py": {
+        "size": 14307
+      },
+      "src/biotite/application/clustalo/__init__.py": {
+        "size": 326
+      },
+      "src/biotite/application/clustalo/app.py": {
+        "size": 7414
+      },
+      "src/biotite/application/dssp/__init__.py": {
+        "size": 323
+      },
+      "src/biotite/application/dssp/app.py": {
+        "size": 7612
+      },
+      "src/biotite/application/localapp.py": {
+        "size": 10257
+      },
+      "src/biotite/application/mafft/__init__.py": {
+        "size": 315
+      },
+      "src/biotite/application/mafft/app.py": {
+        "size": 3281
+      },
+      "src/biotite/application/msaapp.py": {
+        "size": 11974
+      },
+      "src/biotite/application/muscle/__init__.py": {
+        "size": 338
+      },
+      "src/biotite/application/muscle/app3.py": {
+        "size": 7653
+      },
+      "src/biotite/application/muscle/app5.py": {
+        "size": 4474
+      },
+      "src/biotite/application/sra/__init__.py": {
+        "size": 553
+      },
+      "src/biotite/application/sra/app.py": {
+        "size": 15574
+      },
+      "src/biotite/application/tantan/__init__.py": {
+        "size": 328
+      },
+      "src/biotite/application/tantan/app.py": {
+        "size": 7438
+      },
+      "src/biotite/application/util.py": {
+        "size": 2503
+      },
+      "src/biotite/application/viennarna/__init__.py": {
+        "size": 472
+      },
+      "src/biotite/application/viennarna/rnaalifold.py": {
+        "size": 10681
+      },
+      "src/biotite/application/viennarna/rnafold.py": {
+        "size": 7908
+      },
+      "src/biotite/application/viennarna/rnaplot.py": {
+        "size": 6363
+      },
+      "src/biotite/application/viennarna/util.py": {
+        "size": 2635
+      },
+      "src/biotite/application/webapp.py": {
+        "size": 2145
+      },
+      "src/biotite/copyable.py": {
+        "size": 1897
+      },
+      "src/biotite/database/__init__.py": {
+        "size": 725
+      },
+      "src/biotite/database/afdb/__init__.py": {
+        "size": 333
+      },
+      "src/biotite/database/afdb/download.py": {
+        "size": 6868
+      },
+      "src/biotite/database/entrez/__init__.py": {
+        "size": 388
+      },
+      "src/biotite/database/entrez/check.py": {
+        "size": 2114
+      },
+      "src/biotite/database/entrez/dbnames.py": {
+        "size": 2772
+      },
+      "src/biotite/database/entrez/download.py": {
+        "size": 7235
+      },
+      "src/biotite/database/entrez/key.py": {
+        "size": 1108
+      },
+      "src/biotite/database/entrez/query.py": {
+        "size": 7354
+      },
+      "src/biotite/database/error.py": {
+        "size": 410
+      },
+      "src/biotite/database/pubchem/__init__.py": {
+        "size": 669
+      },
+      "src/biotite/database/pubchem/download.py": {
+        "size": 9902
+      },
+      "src/biotite/database/pubchem/error.py": {
+        "size": 878
+      },
+      "src/biotite/database/pubchem/query.py": {
+        "size": 26086
+      },
+      "src/biotite/database/pubchem/throttle.py": {
+        "size": 3286
+      },
+      "src/biotite/database/rcsb/__init__.py": {
+        "size": 332
+      },
+      "src/biotite/database/rcsb/download.py": {
+        "size": 6788
+      },
+      "src/biotite/database/rcsb/query.py": {
+        "size": 32898
+      },
+      "src/biotite/database/uniprot/__init__.py": {
+        "size": 334
+      },
+      "src/biotite/database/uniprot/check.py": {
+        "size": 1378
+      },
+      "src/biotite/database/uniprot/download.py": {
+        "size": 4266
+      },
+      "src/biotite/database/uniprot/query.py": {
+        "size": 7510
+      },
+      "src/biotite/file.py": {
+        "size": 6733
+      },
+      "src/biotite/interface/__init__.py": {
+        "size": 717
+      },
+      "src/biotite/interface/openmm/__init__.py": {
+        "size": 587
+      },
+      "src/biotite/interface/openmm/state.py": {
+        "size": 2723
+      },
+      "src/biotite/interface/openmm/system.py": {
+        "size": 7018
+      },
+      "src/biotite/interface/pymol/__init__.py": {
+        "size": 6648
+      },
+      "src/biotite/interface/pymol/cgo.py": {
+        "size": 9859
+      },
+      "src/biotite/interface/pymol/convert.py": {
+        "size": 6044
+      },
+      "src/biotite/interface/pymol/display.py": {
+        "size": 8458
+      },
+      "src/biotite/interface/pymol/object.py": {
+        "size": 44280
+      },
+      "src/biotite/interface/pymol/shapes.py": {
+        "size": 6066
+      },
+      "src/biotite/interface/pymol/startup.py": {
+        "size": 4619
+      },
+      "src/biotite/interface/rdkit/__init__.py": {
+        "size": 532
+      },
+      "src/biotite/interface/rdkit/mol.py": {
+        "size": 19679
+      },
+      "src/biotite/interface/version.py": {
+        "size": 2952
+      },
+      "src/biotite/interface/warning.py": {
+        "size": 577
+      },
+      "src/biotite/sequence/__init__.py": {
+        "size": 3423
+      },
+      "src/biotite/sequence/align/__init__.py": {
+        "size": 4711
+      },
+      "src/biotite/sequence/align/alignment.py": {
+        "size": 24372
+      },
+      "src/biotite/sequence/align/buckets.py": {
+        "size": 2464
+      },
+      "src/biotite/sequence/align/cigar.py": {
+        "size": 14335
+      },
+      "src/biotite/sequence/align/matrix.py": {
+        "size": 22360
+      },
+      "src/biotite/sequence/align/primes.txt": {
+        "size": 10140
+      },
+      "src/biotite/sequence/align/statistics.py": {
+        "size": 9652
+      },
+      "src/biotite/sequence/alphabet.py": {
+        "size": 17227
+      },
+      "src/biotite/sequence/annotation.py": {
+        "size": 29705
+      },
+      "src/biotite/sequence/codon.py": {
+        "size": 16346
+      },
+      "src/biotite/sequence/codon_tables.txt": {
+        "size": 10209
+      },
+      "src/biotite/sequence/graphics/__init__.py": {
+        "size": 1153
+      },
+      "src/biotite/sequence/graphics/alignment.py": {
+        "size": 39369
+      },
+      "src/biotite/sequence/graphics/color_schemes/3di_flower.json": {
+        "size": 917
+      },
+      "src/biotite/sequence/graphics/color_schemes/autumn.json": {
+        "size": 842
+      },
+      "src/biotite/sequence/graphics/color_schemes/blossom.json": {
+        "size": 843
+      },
+      "src/biotite/sequence/graphics/color_schemes/clustalx_dna.json": {
+        "size": 249
+      },
+      "src/biotite/sequence/graphics/color_schemes/clustalx_protein.json": {
+        "size": 704
+      },
+      "src/biotite/sequence/graphics/color_schemes/flower.json": {
+        "size": 842
+      },
+      "src/biotite/sequence/graphics/color_schemes/jalview_buried.json": {
+        "size": 777
+      },
+      "src/biotite/sequence/graphics/color_schemes/jalview_hydrophobicity.json": {
+        "size": 785
+      },
+      "src/biotite/sequence/graphics/color_schemes/jalview_prop_helix.json": {
+        "size": 780
+      },
+      "src/biotite/sequence/graphics/color_schemes/jalview_prop_strand.json": {
+        "size": 781
+      },
+      "src/biotite/sequence/graphics/color_schemes/jalview_prop_turn.json": {
+        "size": 779
+      },
+      "src/biotite/sequence/graphics/color_schemes/jalview_taylor.json": {
+        "size": 702
+      },
+      "src/biotite/sequence/graphics/color_schemes/jalview_zappo.json": {
+        "size": 701
+      },
+      "src/biotite/sequence/graphics/color_schemes/ocean.json": {
+        "size": 841
+      },
+      "src/biotite/sequence/graphics/color_schemes/pb_flower.json": {
+        "size": 676
+      },
+      "src/biotite/sequence/graphics/color_schemes/rainbow_dna.json": {
+        "size": 248
+      },
+      "src/biotite/sequence/graphics/color_schemes/rainbow_protein.json": {
+        "size": 753
+      },
+      "src/biotite/sequence/graphics/color_schemes/spring.json": {
+        "size": 842
+      },
+      "src/biotite/sequence/graphics/color_schemes/sunset.json": {
+        "size": 842
+      },
+      "src/biotite/sequence/graphics/color_schemes/wither.json": {
+        "size": 842
+      },
+      "src/biotite/sequence/graphics/colorschemes.py": {
+        "size": 5518
+      },
+      "src/biotite/sequence/graphics/dendrogram.py": {
+        "size": 7671
+      },
+      "src/biotite/sequence/graphics/features.py": {
+        "size": 17297
+      },
+      "src/biotite/sequence/graphics/logo.py": {
+        "size": 3692
+      },
+      "src/biotite/sequence/graphics/plasmid.py": {
+        "size": 26002
+      },
+      "src/biotite/sequence/io/__init__.py": {
+        "size": 314
+      },
+      "src/biotite/sequence/io/fasta/__init__.py": {
+        "size": 720
+      },
+      "src/biotite/sequence/io/fasta/convert.py": {
+        "size": 16632
+      },
+      "src/biotite/sequence/io/fasta/file.py": {
+        "size": 9052
+      },
+      "src/biotite/sequence/io/fastq/__init__.py": {
+        "size": 588
+      },
+      "src/biotite/sequence/io/fastq/convert.py": {
+        "size": 3632
+      },
+      "src/biotite/sequence/io/fastq/file.py": {
+        "size": 17817
+      },
+      "src/biotite/sequence/io/genbank/__init__.py": {
+        "size": 473
+      },
+      "src/biotite/sequence/io/genbank/annotation.py": {
+        "size": 9431
+      },
+      "src/biotite/sequence/io/genbank/file.py": {
+        "size": 20354
+      },
+      "src/biotite/sequence/io/genbank/metadata.py": {
+        "size": 9351
+      },
+      "src/biotite/sequence/io/genbank/sequence.py": {
+        "size": 5504
+      },
+      "src/biotite/sequence/io/general.py": {
+        "size": 6694
+      },
+      "src/biotite/sequence/io/gff/__init__.py": {
+        "size": 923
+      },
+      "src/biotite/sequence/io/gff/convert.py": {
+        "size": 4611
+      },
+      "src/biotite/sequence/io/gff/file.py": {
+        "size": 16076
+      },
+      "src/biotite/sequence/phylo/__init__.py": {
+        "size": 1261
+      },
+      "src/biotite/sequence/profile.py": {
+        "size": 19248
+      },
+      "src/biotite/sequence/search.py": {
+        "size": 3090
+      },
+      "src/biotite/sequence/seqtypes.py": {
+        "size": 23246
+      },
+      "src/biotite/sequence/sequence.py": {
+        "size": 11691
+      },
+      "src/biotite/setup_ccd.py": {
+        "size": 6051
+      },
+      "src/biotite/structure/__init__.py": {
+        "size": 5487
+      },
+      "src/biotite/structure/alphabet/__init__.py": {
+        "size": 928
+      },
+      "src/biotite/structure/alphabet/encoder.py": {
+        "size": 11379
+      },
+      "src/biotite/structure/alphabet/i3d.py": {
+        "size": 3009
+      },
+      "src/biotite/structure/alphabet/layers.py": {
+        "size": 2087
+      },
+      "src/biotite/structure/alphabet/pb.py": {
+        "size": 5994
+      },
+      "src/biotite/structure/alphabet/unkerasify.py": {
+        "size": 3301
+      },
+      "src/biotite/structure/atoms.py": {
+        "size": 52346
+      },
+      "src/biotite/structure/basepairs.py": {
+        "size": 49881
+      },
+      "src/biotite/structure/box.py": {
+        "size": 23396
+      },
+      "src/biotite/structure/chains.py": {
+        "size": 9347
+      },
+      "src/biotite/structure/compare.py": {
+        "size": 27437
+      },
+      "src/biotite/structure/density.py": {
+        "size": 4196
+      },
+      "src/biotite/structure/dotbracket.py": {
+        "size": 7197
+      },
+      "src/biotite/structure/error.py": {
+        "size": 783
+      },
+      "src/biotite/structure/filter.py": {
+        "size": 20113
+      },
+      "src/biotite/structure/geometry.py": {
+        "size": 29281
+      },
+      "src/biotite/structure/graphics/__init__.py": {
+        "size": 352
+      },
+      "src/biotite/structure/graphics/atoms.py": {
+        "size": 8116
+      },
+      "src/biotite/structure/graphics/rna.py": {
+        "size": 11841
+      },
+      "src/biotite/structure/hbond.py": {
+        "size": 15238
+      },
+      "src/biotite/structure/info/__init__.py": {
+        "size": 697
+      },
+      "src/biotite/structure/info/atom_masses.json": {
+        "size": 2383
+      },
+      "src/biotite/structure/info/atoms.py": {
+        "size": 3271
+      },
+      "src/biotite/structure/info/bonds.py": {
+        "size": 4644
+      },
+      "src/biotite/structure/info/ccd.py": {
+        "size": 5849
+      },
+      "src/biotite/structure/info/groups.py": {
+        "size": 3183
+      },
+      "src/biotite/structure/info/masses.py": {
+        "size": 4555
+      },
+      "src/biotite/structure/info/misc.py": {
+        "size": 3428
+      },
+      "src/biotite/structure/info/radii.py": {
+        "size": 7287
+      },
+      "src/biotite/structure/info/standardize.py": {
+        "size": 7739
+      },
+      "src/biotite/structure/integrity.py": {
+        "size": 6764
+      },
+      "src/biotite/structure/io/__init__.py": {
+        "size": 998
+      },
+      "src/biotite/structure/io/dcd/__init__.py": {
+        "size": 388
+      },
+      "src/biotite/structure/io/dcd/file.py": {
+        "size": 2224
+      },
+      "src/biotite/structure/io/general.py": {
+        "size": 8452
+      },
+      "src/biotite/structure/io/gro/__init__.py": {
+        "size": 408
+      },
+      "src/biotite/structure/io/gro/file.py": {
+        "size": 12740
+      },
+      "src/biotite/structure/io/mol/__init__.py": {
+        "size": 582
+      },
+      "src/biotite/structure/io/mol/convert.py": {
+        "size": 3789
+      },
+      "src/biotite/structure/io/mol/ctab.py": {
+        "size": 14120
+      },
+      "src/biotite/structure/io/mol/header.py": {
+        "size": 3425
+      },
+      "src/biotite/structure/io/mol/mol.py": {
+        "size": 5461
+      },
+      "src/biotite/structure/io/mol/sdf.py": {
+        "size": 32975
+      },
+      "src/biotite/structure/io/netcdf/__init__.py": {
+        "size": 350
+      },
+      "src/biotite/structure/io/netcdf/file.py": {
+        "size": 2192
+      },
+      "src/biotite/structure/io/pdb/__init__.py": {
+        "size": 733
+      },
+      "src/biotite/structure/io/pdb/convert.py": {
+        "size": 13827
+      },
+      "src/biotite/structure/io/pdb/file.py": {
+        "size": 54558
+      },
+      "src/biotite/structure/io/pdbqt/__init__.py": {
+        "size": 441
+      },
+      "src/biotite/structure/io/pdbqt/convert.py": {
+        "size": 4008
+      },
+      "src/biotite/structure/io/pdbqt/file.py": {
+        "size": 26645
+      },
+      "src/biotite/structure/io/pdbx/__init__.py": {
+        "size": 717
+      },
+      "src/biotite/structure/io/pdbx/bcif.py": {
+        "size": 21248
+      },
+      "src/biotite/structure/io/pdbx/cif.py": {
+        "size": 34979
+      },
+      "src/biotite/structure/io/pdbx/component.py": {
+        "size": 8398
+      },
+      "src/biotite/structure/io/pdbx/compress.py": {
+        "size": 13407
+      },
+      "src/biotite/structure/io/pdbx/convert.py": {
+        "size": 81166
+      },
+      "src/biotite/structure/io/trajfile.py": {
+        "size": 25393
+      },
+      "src/biotite/structure/io/trr/__init__.py": {
+        "size": 359
+      },
+      "src/biotite/structure/io/trr/file.py": {
+        "size": 1235
+      },
+      "src/biotite/structure/io/util.py": {
+        "size": 1016
+      },
+      "src/biotite/structure/io/xtc/__init__.py": {
+        "size": 357
+      },
+      "src/biotite/structure/io/xtc/file.py": {
+        "size": 1235
+      },
+      "src/biotite/structure/mechanics.py": {
+        "size": 2587
+      },
+      "src/biotite/structure/molecules.py": {
+        "size": 15291
+      },
+      "src/biotite/structure/pseudoknots.py": {
+        "size": 22090
+      },
+      "src/biotite/structure/rdf.py": {
+        "size": 8102
+      },
+      "src/biotite/structure/repair.py": {
+        "size": 6996
+      },
+      "src/biotite/structure/residues.py": {
+        "size": 28403
+      },
+      "src/biotite/structure/rings.py": {
+        "size": 15678
+      },
+      "src/biotite/structure/segments.py": {
+        "size": 10785
+      },
+      "src/biotite/structure/sequence.py": {
+        "size": 4245
+      },
+      "src/biotite/structure/spacegroups.json": {
+        "size": 51558
+      },
+      "src/biotite/structure/sse.py": {
+        "size": 11404
+      },
+      "src/biotite/structure/superimpose.py": {
+        "size": 19562
+      },
+      "src/biotite/structure/tm.py": {
+        "size": 20967
+      },
+      "src/biotite/structure/transform.py": {
+        "size": 26975
+      },
+      "src/biotite/structure/util.py": {
+        "size": 4400
+      },
+      "src/biotite/visualize.py": {
+        "size": 13955
+      },
+      "tests/__init__.py": {
+        "size": 0
+      },
+      "tests/application/__init__.py": {
+        "size": 0
+      },
+      "tests/application/test_autodock.py": {
+        "size": 3417
+      },
+      "tests/application/test_blast.py": {
+        "size": 4631
+      },
+      "tests/application/test_dssp.py": {
+        "size": 1648
+      },
+      "tests/application/test_msa.py": {
+        "size": 10410
+      },
+      "tests/application/test_rnaalifold.py": {
+        "size": 2727
+      },
+      "tests/application/test_rnafold.py": {
+        "size": 2370
+      },
+      "tests/application/test_rnaplot.py": {
+        "size": 947
+      },
+      "tests/application/test_sra.py": {
+        "size": 2094
+      },
+      "tests/application/test_tantan.py": {
+        "size": 2623
+      },
+      "tests/conftest.py": {
+        "size": 558
+      },
+      "tests/database/__init__.py": {
+        "size": 0
+      },
+      "tests/database/test_afdb.py": {
+        "size": 3899
+      },
+      "tests/database/test_entrez.py": {
+        "size": 2018
+      },
+      "tests/database/test_pubchem.py": {
+        "size": 7518
+      },
+      "tests/database/test_rcsb.py": {
+        "size": 14887
+      },
+      "tests/database/test_uniprot.py": {
+        "size": 2102
+      },
+      "tests/interface/__init__.py": {
+        "size": 0
+      },
+      "tests/interface/data/smiles.txt": {
+        "size": 9195
+      },
+      "tests/interface/pymol/__init__.py": {
+        "size": 0
+      },
+      "tests/interface/pymol/conftest.py": {
+        "size": 143
+      },
+      "tests/interface/pymol/test_cgo.py": {
+        "size": 2067
+      },
+      "tests/interface/pymol/test_command.py": {
+        "size": 3811
+      },
+      "tests/interface/pymol/test_conversion.py": {
+        "size": 3556
+      },
+      "tests/interface/pymol/test_display.py": {
+        "size": 1056
+      },
+      "tests/interface/pymol/test_selection.py": {
+        "size": 1328
+      },
+      "tests/interface/pymol/test_shapes.py": {
+        "size": 686
+      },
+      "tests/interface/pymol/test_startup.py": {
+        "size": 768
+      },
+      "tests/interface/test_openmm.py": {
+        "size": 5826
+      },
+      "tests/interface/test_rdkit.py": {
+        "size": 8394
+      },
+      "tests/interface/test_version.py": {
+        "size": 718
+      },
+      "tests/sequence/__init__.py": {
+        "size": 0
+      },
+      "tests/sequence/align/__init__.py": {
+        "size": 0
+      },
+      "tests/sequence/align/conftest.py": {
+        "size": 644
+      },
+      "tests/sequence/align/test_alignment.py": {
+        "size": 2915
+      },
+      "tests/sequence/align/test_banded.py": {
+        "size": 8388
+      },
+      "tests/sequence/align/test_cigar.py": {
+        "size": 5023
+      },
+      "tests/sequence/align/test_kmeralphabet.py": {
+        "size": 3931
+      },
+      "tests/sequence/align/test_kmersimilarity.py": {
+        "size": 2302
+      },
+      "tests/sequence/align/test_kmertable.py": {
+        "size": 16228
+      },
+      "tests/sequence/align/test_localgapped.py": {
+        "size": 7333
+      },
+      "tests/sequence/align/test_localungapped.py": {
+        "size": 7643
+      },
+      "tests/sequence/align/test_matrix.py": {
+        "size": 3169
+      },
+      "tests/sequence/align/test_multiple.py": {
+        "size": 1474
+      },
+      "tests/sequence/align/test_pairwise.py": {
+        "size": 7870
+      },
+      "tests/sequence/align/test_permutation.py": {
+        "size": 4515
+      },
+      "tests/sequence/align/test_selector.py": {
+        "size": 6750
+      },
+      "tests/sequence/align/test_statistics.py": {
+        "size": 6033
+      },
+      "tests/sequence/data/distances.txt": {
+        "size": 1599
+      },
+      "tests/sequence/data/newick_upgma.txt": {
+        "size": 339
+      },
+      "tests/sequence/test_alphabet.py": {
+        "size": 5976
+      },
+      "tests/sequence/test_annotation.py": {
+        "size": 4442
+      },
+      "tests/sequence/test_codon.py": {
+        "size": 1621
+      },
+      "tests/sequence/test_fasta.py": {
+        "size": 7102
+      },
+      "tests/sequence/test_fastq.py": {
+        "size": 4595
+      },
+      "tests/sequence/test_genbank.py": {
+        "size": 7444
+      },
+      "tests/sequence/test_generalio.py": {
+        "size": 2211
+      },
+      "tests/sequence/test_gff.py": {
+        "size": 6463
+      },
+      "tests/sequence/test_graphics.py": {
+        "size": 1245
+      },
+      "tests/sequence/test_phylo.py": {
+        "size": 11742
+      },
+      "tests/sequence/test_profile.py": {
+        "size": 5680
+      },
+      "tests/sequence/test_search.py": {
+        "size": 726
+      },
+      "tests/sequence/test_seqtypes.py": {
+        "size": 3910
+      },
+      "tests/sequence/test_sequence.py": {
+        "size": 2361
+      },
+      "tests/structure/__init__.py": {
+        "size": 0
+      },
+      "tests/structure/alphabet/__init__.py": {
+        "size": 0
+      },
+      "tests/structure/alphabet/test_i3d.py": {
+        "size": 4202
+      },
+      "tests/structure/alphabet/test_pb.py": {
+        "size": 2659
+      },
+      "tests/structure/data/base_pairs/1gid_edges.json": {
+        "size": 2132
+      },
+      "tests/structure/data/base_pairs/1gid_sugar.json": {
+        "size": 1777
+      },
+      "tests/structure/data/base_pairs/1nkw_edges.json": {
+        "size": 848
+      },
+      "tests/structure/data/base_pairs/1nkw_sugar.json": {
+        "size": 698
+      },
+      "tests/structure/data/base_pairs/1xnr_edges.json": {
+        "size": 20145
+      },
+      "tests/structure/data/base_pairs/1xnr_sugar.json": {
+        "size": 16850
+      },
+      "tests/structure/data/base_pairs/create_bond_orientation_test_data.py": {
+        "size": 2151
+      },
+      "tests/structure/data/base_pairs/create_interacting_edge_test_data.py": {
+        "size": 2458
+      },
+      "tests/structure/data/create_test_structures.py": {
+        "size": 2855
+      },
+      "tests/structure/data/ids.txt": {
+        "size": 129
+      },
+      "tests/structure/data/misc/dihedrals.json": {
+        "size": 3387
+      },
+      "tests/structure/data/misc/dihedrals.py": {
+        "size": 1655
+      },
+      "tests/structure/data/misc/hbond.json": {
+        "size": 151784
+      },
+      "tests/structure/data/misc/hbond.py": {
+        "size": 1611
+      },
+      "tests/structure/data/misc/rdf.json": {
+        "size": 4907
+      },
+      "tests/structure/data/misc/rdf.py": {
+        "size": 814
+      },
+      "tests/structure/data/misc/sasa.json": {
+        "size": 49198
+      },
+      "tests/structure/data/misc/sasa.py": {
+        "size": 1022
+      },
+      "tests/structure/data/molecules/create_v3000_sdf.py": {
+        "size": 413
+      },
+      "tests/structure/data/pseudoknots/test0_knotted.json": {
+        "size": 361
+      },
+      "tests/structure/data/pseudoknots/test0_unknotted.json": {
+        "size": 1910
+      },
+      "tests/structure/data/pseudoknots/test10_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test10_unknotted.json": {
+        "size": 3825
+      },
+      "tests/structure/data/pseudoknots/test11_knotted.json": {
+        "size": 359
+      },
+      "tests/structure/data/pseudoknots/test11_unknotted.json": {
+        "size": 2734
+      },
+      "tests/structure/data/pseudoknots/test12_knotted.json": {
+        "size": 361
+      },
+      "tests/structure/data/pseudoknots/test12_unknotted.json": {
+        "size": 1271
+      },
+      "tests/structure/data/pseudoknots/test13_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test13_unknotted.json": {
+        "size": 250
+      },
+      "tests/structure/data/pseudoknots/test14_knotted.json": {
+        "size": 359
+      },
+      "tests/structure/data/pseudoknots/test14_unknotted.json": {
+        "size": 808
+      },
+      "tests/structure/data/pseudoknots/test15_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test15_unknotted.json": {
+        "size": 1098
+      },
+      "tests/structure/data/pseudoknots/test16_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test16_unknotted.json": {
+        "size": 204
+      },
+      "tests/structure/data/pseudoknots/test17_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test17_unknotted.json": {
+        "size": 611
+      },
+      "tests/structure/data/pseudoknots/test18_knotted.json": {
+        "size": 361
+      },
+      "tests/structure/data/pseudoknots/test18_unknotted.json": {
+        "size": 5138
+      },
+      "tests/structure/data/pseudoknots/test19_knotted.json": {
+        "size": 357
+      },
+      "tests/structure/data/pseudoknots/test19_unknotted.json": {
+        "size": 1426
+      },
+      "tests/structure/data/pseudoknots/test1_knotted.json": {
+        "size": 360
+      },
+      "tests/structure/data/pseudoknots/test1_unknotted.json": {
+        "size": 810
+      },
+      "tests/structure/data/pseudoknots/test20_knotted.json": {
+        "size": 360
+      },
+      "tests/structure/data/pseudoknots/test20_unknotted.json": {
+        "size": 4658
+      },
+      "tests/structure/data/pseudoknots/test2_knotted.json": {
+        "size": 360
+      },
+      "tests/structure/data/pseudoknots/test2_unknotted.json": {
+        "size": 454
+      },
+      "tests/structure/data/pseudoknots/test3_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test3_unknotted.json": {
+        "size": 1433
+      },
+      "tests/structure/data/pseudoknots/test4_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test4_unknotted.json": {
+        "size": 2529
+      },
+      "tests/structure/data/pseudoknots/test5_knotted.json": {
+        "size": 360
+      },
+      "tests/structure/data/pseudoknots/test5_unknotted.json": {
+        "size": 901
+      },
+      "tests/structure/data/pseudoknots/test6_knotted.json": {
+        "size": 356
+      },
+      "tests/structure/data/pseudoknots/test6_unknotted.json": {
+        "size": 181
+      },
+      "tests/structure/data/pseudoknots/test7_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test7_unknotted.json": {
+        "size": 247
+      },
+      "tests/structure/data/pseudoknots/test8_knotted.json": {
+        "size": 358
+      },
+      "tests/structure/data/pseudoknots/test8_unknotted.json": {
+        "size": 1114
+      },
+      "tests/structure/data/pseudoknots/test9_knotted.json": {
+        "size": 359
+      },
+      "tests/structure/data/pseudoknots/test9_unknotted.json": {
+        "size": 730
+      },
+      "tests/structure/data/tm/tm.py": {
+        "size": 1405
+      },
+      "tests/structure/data/tm/tm_scores.json": {
+        "size": 982
+      },
+      "tests/structure/io/__init__.py": {
+        "size": 0
+      },
+      "tests/structure/io/test_gro.py": {
+        "size": 4869
+      },
+      "tests/structure/io/test_mol.py": {
+        "size": 13464
+      },
+      "tests/structure/io/test_pdb.py": {
+        "size": 19710
+      },
+      "tests/structure/io/test_pdbqt.py": {
+        "size": 1996
+      },
+      "tests/structure/io/test_pdbx.py": {
+        "size": 44386
+      },
+      "tests/structure/io/test_trajectory.py": {
+        "size": 9558
+      },
+      "tests/structure/test_atoms.py": {
+        "size": 7396
+      },
+      "tests/structure/test_basepairs.py": {
+        "size": 12779
+      },
+      "tests/structure/test_bonds.py": {
+        "size": 18391
+      },
+      "tests/structure/test_box.py": {
+        "size": 10981
+      },
+      "tests/structure/test_celllist.py": {
+        "size": 5099
+      },
+      "tests/structure/test_chains.py": {
+        "size": 2765
+      },
+      "tests/structure/test_charges.py": {
+        "size": 16096
+      },
+      "tests/structure/test_compare.py": {
+        "size": 13488
+      },
+      "tests/structure/test_density.py": {
+        "size": 3062
+      },
+      "tests/structure/test_dotbracket.py": {
+        "size": 3008
+      },
+      "tests/structure/test_filter.py": {
+        "size": 8520
+      },
+      "tests/structure/test_generalio.py": {
+        "size": 4954
+      },
+      "tests/structure/test_geometry.py": {
+        "size": 8370
+      },
+      "tests/structure/test_hbond.py": {
+        "size": 6899
+      },
+      "tests/structure/test_info.py": {
+        "size": 7615
+      },
+      "tests/structure/test_integrity.py": {
+        "size": 2345
+      },
+      "tests/structure/test_mechanics.py": {
+        "size": 1340
+      },
+      "tests/structure/test_molecules.py": {
+        "size": 3709
+      },
+      "tests/structure/test_pseudoknots.py": {
+        "size": 5459
+      },
+      "tests/structure/test_rdf.py": {
+        "size": 5100
+      },
+      "tests/structure/test_repair.py": {
+        "size": 2131
+      },
+      "tests/structure/test_residues.py": {
+        "size": 4007
+      },
+      "tests/structure/test_rings.py": {
+        "size": 7580
+      },
+      "tests/structure/test_sasa.py": {
+        "size": 2278
+      },
+      "tests/structure/test_sequence.py": {
+        "size": 2930
+      },
+      "tests/structure/test_sse.py": {
+        "size": 3780
+      },
+      "tests/structure/test_superimpose.py": {
+        "size": 10591
+      },
+      "tests/structure/test_tm.py": {
+        "size": 7342
+      },
+      "tests/structure/test_transform.py": {
+        "size": 12451
+      },
+      "tests/test_doctest.py": {
+        "size": 8979
+      },
+      "tests/test_modname.py": {
+        "size": 1970
+      },
+      "tests/test_repr.py": {
+        "size": 2807
+      },
+      "tests/test_version.py": {
+        "size": 203
+      },
+      "tests/util.py": {
+        "size": 831
+      }
+    },
+    "processed_by": "zip_fallback",
+    "success": true
+  },
+  "structure": {
+    "packages": [
+      "source.benchmarks",
+      "source.benchmarks.sequence",
+      "source.benchmarks.structure",
+      "source.src.biotite",
+      "source.tests",
+      "source.tests.application",
+      "source.tests.database",
+      "source.tests.interface",
+      "source.tests.sequence",
+      "source.tests.structure"
+    ]
+  },
+  "dependencies": {
+    "has_environment_yml": true,
+    "has_requirements_txt": false,
+    "pyproject": true,
+    "setup_cfg": false,
+    "setup_py": false
+  },
+  "entry_points": {
+    "imports": [],
+    "cli": [],
+    "modules": []
+  },
+  "llm_analysis": {
+    "core_modules": [
+      {
+        "package": "source.src.biotite.structure",
+        "module": "graphics",
+        "functions": [
+          "load_structure",
+          "save_structure"
+        ],
+        "classes": [
+          "AtomArray",
+          "AtomArrayStack"
+        ],
+        "description": "Provides tools for working with molecular structures, including visualization and manipulation of AtomArray and AtomArrayStack objects."
+      },
+      {
+        "package": "source.src.biotite.sequence",
+        "module": "align",
+        "functions": [
+          "align_sequences",
+          "calculate_alignment_score"
+        ],
+        "classes": [
+          "Alignment",
+          "Sequence"
+        ],
+        "description": "Focuses on biological sequence analysis, providing functions for sequence alignment and scoring."
+      },
+      {
+        "package": "source.src.biotite.database",
+        "module": "entrez",
+        "functions": [
+          "query_database",
+          "download_data"
+        ],
+        "classes": [
+          "EntrezQuery"
+        ],
+        "description": "Interfaces with the Entrez database for querying and downloading biological data."
+      }
+    ],
+    "cli_commands": [
+      {
+        "name": "biotite-align",
+        "module": "source.src.biotite.sequence.align",
+        "description": "Command-line tool for aligning biological sequences using the Biotite library."
+      }
+    ],
+    "import_strategy": {
+      "primary": "import",
+      "fallback": "cli",
+      "confidence": 0.85
+    },
+    "dependencies": {
+      "required": [
+        "numpy",
+        "scipy",
+        "matplotlib"
+      ],
+      "optional": [
+        "rdkit",
+        "openmm"
+      ]
+    },
+    "risk_assessment": {
+      "import_feasibility": 0.9,
+      "intrusiveness_risk": "low",
+      "complexity": "medium"
+    }
+  },
+  "deepwiki_analysis": {
+    "repo_url": "https://github.com/biotite-dev/biotite",
+    "repo_name": "biotite",
+    "content": "biotite-dev/biotite\nStructure Module\nAtomArray and AtomArrayStack\nChemical Bond Management\nBase Pair Detection and Analysis\nStructure Filtering and Selection\nRNA Secondary Structure Analysis\nGeometric Calculations\nPartial Charge Calculation\nSequence Module\nSequence Types and Alphabets\nSequence Alignment\nSequence Annotation\nSequence Visualization\nStructure File Formats\nSequence File Formats\nTrajectory Files\nApplication Interfaces\nSRA Tools Interface\nRNA Structure Visualization\nDatabase Interfaces\nDevelopment\nCI/CD Pipeline\nDocumentation System\nsrc/biotite/__init__.py\nsrc/biotite/structure/graphics/__init__.py\nsrc/biotite/structure/graphics/atoms.py\nPurpose and Scope\nBiotite is a Python package for bioinformatics that provides extensive tools for working with biological data, focusing primarily on structural and sequence biology. This overview introduces the library's architecture, main components, and their relationships. For detailed information about specific modules, refer to their respective wiki pages.\nIntroduction to Biotite\nBiotite is an open-source bioinformatics library designed to provide a comprehensive toolkit for computational analysis of biological data. The package is authored by Patrick Kunzmann as indicated in the package metadata (src/biotite/__init__.py13), with additional contributors for various modules.\nThe library offers high-performance data structures and algorithms for:\nMacromolecular structure analysis (proteins, DNA, RNA)\nBiological sequence analysis and alignment\nFile I/O for standard bioinformatics formats\nIntegration with external bioinformatics applications\nDatabase access\nSources:src/biotite/__init__.py5-9\nLibrary Architecture\nBiotite is organized into a modular architecture with two main biological domains (structural and sequence biology) supported by common infrastructure and external interfaces:\nFile I/OSequence BiologyStructural BiologyCore ComponentsExternal IntegrationsApplication InterfacesDatabase InterfacesFile (Abstract Base Class)Copyable (Base Class)Visualization UtilitiesAtomArray/AtomArrayStackBondListStructure Analysis ToolsGeometry UtilitiesStructure VisualizationSequence TypesSequence AlignmentSequence AnnotationSequence VisualizationStructure I/O (PDB, CIF, etc.)Sequence I/O (FASTA, GenBank, etc.)Trajectory Files\nSequence Biology\nStructural Biology\nCore Components\nExternal Integrations\nApplication Interfaces\nDatabase Interfaces\nFile (Abstract Base Class)\nCopyable (Base Class)\nVisualization Utilities\nAtomArray/AtomArrayStack\nStructure Analysis Tools\nGeometry Utilities\nStructure Visualization\nSequence Types\nSequence Alignment\nSequence Annotation\nSequence Visualization\nStructure I/O (PDB, CIF, etc.)\nSequence I/O (FASTA, GenBank, etc.)\nTrajectory Files\nDiagram Title: High-level Architecture of Biotite\nSources:src/biotite/__init__.py15-18\nMain Components\nCore Components\nThe core components provide foundational functionality used throughout the library:\nStructural Biology Module\nThe structural biology module (Structure Module) provides tools for working with molecular structures:\nSources:src/biotite/structure/graphics/atoms.py14-66src/biotite/structure/graphics/atoms.py114-178src/biotite/structure/graphics/__init__.py5-7\nSequence Biology Module\nThe sequence biology module (Sequence Module) focuses on biological sequence analysis:\nFile I/O System\nThe file I/O system (File I/O) provides interfaces for reading and writing biological data:\nFile I/O SystemFile (Abstract Base Class)TextFile (Abstract Base Class)load_structure (Function)save_structure (Function)load_sequence (Function)save_sequence (Function)PDBFileCIFFile/BinaryCIFFileMMTFFileTrajectoryFileFastaFileGenBankFileGFFFileAtomArray/AtomArrayStackSequence Types\nFile I/O System\nFile (Abstract Base Class)\nTextFile (Abstract Base Class)\nload_structure (Function)\nsave_structure (Function)\nload_sequence (Function)\nsave_sequence (Function)\nCIFFile/BinaryCIFFile\nTrajectoryFile\nGenBankFile\nAtomArray/AtomArrayStack\nSequence Types\nDiagram Title: File I/O System Architecture\nSources: Based on the provided system architecture diagrams\nExternal Integrations\nBiotite provides interfaces to external applications and databases:\nData Structures and Their Relationships\nThe following diagram illustrates the relationships between the primary data structures in Biotite:\n1110..10..1many«Abstract»Copyable+copy() : Copyable«Abstract»File+read()+write()AtomArray+coord : ndarray+bonds : BondList+array_length() : int+get_atoms() : AtomArray+copy() : AtomArrayAtomArrayStack+coord : ndarray+bonds : BondList+stack_depth() : int+stack_length() : int+copy() : AtomArrayStackBondList+add_bond(int, int)+remove_bond(int, int)+contains_bond(int, int) : bool+copy() : BondList«Abstract»Sequence+alphabet : Alphabet+get_symbol(int) : str+copy() : SequenceNucleotideSequence+copy() : NucleotideSequenceProteinSequence+copy() : ProteinSequenceAlignment+sequences : list+trace : list+score : float+copy() : AlignmentAnnotation+add_feature(Feature)+get_features() : list+copy() : Annotation\n+copy() : Copyable\n+coord : ndarray\n+bonds : BondList\n+array_length() : int\n+get_atoms() : AtomArray\n+copy() : AtomArray\nAtomArrayStack\n+coord : ndarray\n+bonds : BondList\n+stack_depth() : int\n+stack_length() : int\n+copy() : AtomArrayStack\n+add_bond(int, int)\n+remove_bond(int, int)\n+contains_bond(int, int) : bool\n+copy() : BondList\n+alphabet : Alphabet\n+get_symbol(int) : str\n+copy() : Sequence\nNucleotideSequence\n+copy() : NucleotideSequence\nProteinSequence\n+copy() : ProteinSequence\n+sequences : list\n+trace : list\n+score : float\n+copy() : Alignment\n+add_feature(Feature)\n+get_features() : list\n+copy() : Annotation\nDiagram Title: Core Data Structure Relationships\nSources: Based on the provided system architecture diagrams\nUsage Areas\nBiotite is designed to support a wide range of bioinformatics analyses:\nStructural Biology:Molecular structure analysis and manipulationBond and interaction identificationGeometric measurementsStructure visualizationRNA secondary structure analysis\nStructural Biology:\nMolecular structure analysis and manipulation\nBond and interaction identification\nGeometric measurements\nStructure visualization\nRNA secondary structure analysis\nSequence Biology:Sequence manipulation and comparisonSequence alignment (pairwise and multiple)Feature annotationSequence visualization\nSequence Biology:\nSequence manipulation and comparison\nSequence alignment (pairwise and multiple)\nFeature annotation\nSequence visualization\nData Access:Reading/writing various file formatsDatabase accessIntegration with external applications\nData Access:\nReading/writing various file formats\nDatabase access\nIntegration with external applications\nDevelopment and Extension\nBiotite follows object-oriented design principles with a focus on extensibility. The library implements inheritance hierarchies (e.g., File -> TextFile -> PDBFile) that allow for easy addition of new file formats and analysis methods.\nFor development-related information, refer to theDevelopmentsection of the wiki.\nSources: Based on the provided system architecture diagrams and file listings\nRefresh this wiki\nOn this page\nPurpose and Scope\nIntroduction to Biotite\nLibrary Architecture\nMain Components\nCore Components\nStructural Biology Module\nSequence Biology Module\nFile I/O System\nExternal Integrations\nData Structures and Their Relationships\nUsage Areas\nDevelopment and Extension",
+    "model": "gpt-4o-2024-08-06",
+    "source": "selenium",
+    "success": true
+  },
+  "deepwiki_options": {
+    "enabled": true,
+    "model": "gpt-4o-2024-08-06"
+  },
+  "risk": {
+    "import_feasibility": 0.9,
+    "intrusiveness_risk": "low",
+    "complexity": "medium"
+  }
+}

biotite/mcp_output/diff_report.md

@@ -0,0 +1,73 @@
+# Biotite Project Difference Report
+
+**Repository:** Biotite  
+**Project Type:** Python Library  
+**Main Features:** Basic Functionality  
+**Report Date:** January 31, 2026  
+**Intrusiveness:** None  
+**Workflow Status:** Success  
+**Test Status:** Failed  
+
+## Project Overview
+
+The Biotite project is a Python library designed to provide basic functionality for bioinformatics applications. It aims to offer a robust and efficient toolkit for handling biological data, with a focus on ease of use and integration into existing workflows.
+
+## Difference Analysis
+
+### New Files
+
+In this update, 8 new files have been introduced to the repository. These files are likely intended to expand the library's capabilities or improve existing functionalities. However, no existing files were modified, indicating that the new additions are supplementary rather than replacements or updates to current features.
+
+### Modified Files
+
+There were no modifications to existing files in this update. This suggests that the current functionality remains unchanged, and the focus was on adding new capabilities or resources.
+
+## Technical Analysis
+
+### Workflow Status
+
+The workflow status is marked as successful, indicating that the integration and deployment processes were executed without errors. This suggests that the new files were correctly integrated into the project structure.
+
+### Test Status
+
+The test status is marked as failed, which is a critical issue. This failure indicates that the new additions may have introduced bugs or compatibility issues that need to be addressed. It is essential to identify the root cause of these failures to ensure the library's reliability and functionality.
+
+## Recommendations and Improvements
+
+1. **Conduct Thorough Testing:** 
+   - Perform a detailed analysis of the test failures to identify specific issues.
+   - Ensure that all new files are covered by unit tests and integration tests.
+
+2. **Review New Additions:**
+   - Conduct a code review of the new files to ensure they adhere to the project's coding standards and best practices.
+   - Verify that the new functionalities align with the project's goals and user needs.
+
+3. **Enhance Documentation:**
+   - Update the project documentation to include information about the new files and functionalities.
+   - Provide clear usage examples and guidelines to help users integrate the new features into their workflows.
+
+4. **Improve Test Coverage:**
+   - Increase the test coverage for both new and existing functionalities to prevent future test failures.
+   - Implement automated testing tools to streamline the testing process.
+
+## Deployment Information
+
+The deployment of the new files was successful, as indicated by the workflow status. However, due to the test failures, it is advisable to hold off on any public releases until the issues are resolved. Ensure that all tests pass successfully before proceeding with deployment to production environments.
+
+## Future Planning
+
+1. **Bug Fixes and Patches:**
+   - Prioritize resolving the test failures and any identified bugs in the new files.
+   - Release patches or updates as soon as the issues are fixed to maintain user trust and satisfaction.
+
+2. **Feature Expansion:**
+   - Consider user feedback and requests for future feature expansions.
+   - Plan for iterative updates that enhance the library's capabilities while maintaining stability.
+
+3. **Community Engagement:**
+   - Engage with the user community to gather insights and suggestions for future improvements.
+   - Encourage contributions and collaborations to foster a vibrant development ecosystem.
+
+## Conclusion
+
+The recent update to the Biotite project introduces new files that potentially expand its functionality. However, the test failures highlight the need for immediate attention to ensure the library's reliability. By addressing these issues and implementing the recommended improvements, the project can continue to provide valuable tools for the bioinformatics community.

biotite/mcp_output/mcp_plugin/adapter.py

@@ -0,0 +1,147 @@
+import os
+import sys
+
+# Path settings
+source_path = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), "source")
+sys.path.insert(0, source_path)
+
+# Import statements
+try:
+    from src.biotite.sequence.align import Alignment
+    from src.biotite.sequence.annotation import Annotation
+    from src.biotite.sequence import Sequence
+    from src.biotite.structure import AtomArray
+    from src.biotite.structure import AtomArrayStack
+    from src.biotite.structure import BondList
+except ImportError as e:
+    print(f"Import failed: {e}. Ensure the source directory is correctly set.")
+
+class Adapter:
+    """
+    Adapter class for MCP plugin, providing access to Biotite library functionalities.
+    """
+
+    def __init__(self):
+        self.mode = "import"
+
+    # -------------------- Sequence Module --------------------
+
+    def create_sequence(self, alphabet, symbols):
+        """
+        Create a Sequence object.
+
+        Parameters:
+        - alphabet: The alphabet for the sequence.
+        - symbols: The symbols in the sequence.
+
+        Returns:
+        - dict: Status and Sequence object or error message.
+        """
+        try:
+            sequence = Sequence(alphabet, symbols)
+            return {"status": "success", "sequence": sequence}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def create_alignment(self, sequences, trace, score):
+        """
+        Create an Alignment object.
+
+        Parameters:
+        - sequences: List of sequences to align.
+        - trace: Trace of the alignment.
+        - score: Alignment score.
+
+        Returns:
+        - dict: Status and Alignment object or error message.
+        """
+        try:
+            alignment = Alignment(sequences, trace, score)
+            return {"status": "success", "alignment": alignment}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def create_annotation(self, features):
+        """
+        Create an Annotation object.
+
+        Parameters:
+        - features: Features to annotate.
+
+        Returns:
+        - dict: Status and Annotation object or error message.
+        """
+        try:
+            annotation = Annotation(features)
+            return {"status": "success", "annotation": annotation}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    # -------------------- Structure Module --------------------
+
+    def create_atom_array(self, coord, bonds):
+        """
+        Create an AtomArray object.
+
+        Parameters:
+        - coord: Coordinates of the atoms.
+        - bonds: Bond list for the atoms.
+
+        Returns:
+        - dict: Status and AtomArray object or error message.
+        """
+        try:
+            atom_array = AtomArray(coord, bonds)
+            return {"status": "success", "atom_array": atom_array}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def create_atom_array_stack(self, coord, bonds):
+        """
+        Create an AtomArrayStack object.
+
+        Parameters:
+        - coord: Coordinates of the atoms.
+        - bonds: Bond list for the atoms.
+
+        Returns:
+        - dict: Status and AtomArrayStack object or error message.
+        """
+        try:
+            atom_array_stack = AtomArrayStack(coord, bonds)
+            return {"status": "success", "atom_array_stack": atom_array_stack}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    def create_bond_list(self, bonds):
+        """
+        Create a BondList object.
+
+        Parameters:
+        - bonds: List of bonds.
+
+        Returns:
+        - dict: Status and BondList object or error message.
+        """
+        try:
+            bond_list = BondList(bonds)
+            return {"status": "success", "bond_list": bond_list}
+        except Exception as e:
+            return {"status": "error", "message": str(e)}
+
+    # -------------------- Error Handling --------------------
+
+    def handle_import_failure(self):
+        """
+        Handle import failure gracefully.
+
+        Returns:
+        - dict: Status and error message.
+        """
+        return {"status": "error", "message": "Failed to import necessary modules. Please check the source path and module availability."}
+
+# Example usage
+if __name__ == "__main__":
+    adapter = Adapter()
+    result = adapter.create_sequence("DNA", "ATCG")
+    print(result)

biotite/mcp_output/mcp_plugin/main.py

@@ -0,0 +1,13 @@
+"""
+MCP Service Auto-Wrapper - Auto-generated
+"""
+from mcp_service import create_app
+
+def main():
+    """Main entry point"""
+    app = create_app()
+    return app
+
+if __name__ == "__main__":
+    app = main()
+    app.run()

biotite/mcp_output/mcp_plugin/mcp_service.py

@@ -0,0 +1,61 @@
+import os
+import sys
+
+# Add the local source directory to sys.path
+source_path = os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), "source")
+if source_path not in sys.path:
+    sys.path.insert(0, source_path)
+
+from fastmcp import FastMCP
+from biotite.sequence.align import alignment
+from biotite.structure import atoms
+
+# Create the FastMCP service application
+mcp = FastMCP("biotite_service")
+
+@mcp.tool(name="align_sequences", description="Align biological sequences using Biotite.")
+def align_sequences(seq1: str, seq2: str) -> dict:
+    """
+    Align two biological sequences.
+    
+    Parameters:
+    - seq1: The first sequence to align.
+    - seq2: The second sequence to align.
+    
+    Returns:
+    A dictionary containing the alignment result.
+    """
+    try:
+        # Perform sequence alignment
+        result = alignment.align(seq1, seq2)
+        return {"success": True, "result": result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+@mcp.tool(name="analyze_atoms", description="Analyze atoms in a molecular structure.")
+def analyze_atoms(structure_file: str) -> dict:
+    """
+    Analyze atoms in a given molecular structure file.
+    
+    Parameters:
+    - structure_file: Path to the molecular structure file.
+    
+    Returns:
+    A dictionary containing the atom analysis result.
+    """
+    try:
+        # Load and analyze atoms
+        atom_array = atoms.load_structure(structure_file)
+        analysis_result = atoms.analyze(atom_array)
+        return {"success": True, "result": analysis_result, "error": None}
+    except Exception as e:
+        return {"success": False, "result": None, "error": str(e)}
+
+def create_app() -> FastMCP:
+    """
+    Create and return the FastMCP application instance.
+    
+    Returns:
+    The FastMCP instance for the service.
+    """
+    return mcp

biotite/mcp_output/requirements.txt

@@ -0,0 +1,13 @@
+fastmcp
+fastapi
+uvicorn[standard]
+pydantic>=2.0.0
+numpy >= 1.25
+biotraj >= 1.0, < 2.0
+requests >= 2.12
+msgpack >= 0.5.6
+networkx >= 2.0
+packaging >= 24.0
+rdkit >=2024.09.1
+scipy
+matplotlib

biotite/mcp_output/start_mcp.py

@@ -0,0 +1,30 @@
+
+"""
+MCP Service Startup Entry
+"""
+import sys
+import os
+
+project_root = os.path.dirname(os.path.abspath(__file__))
+mcp_plugin_dir = os.path.join(project_root, "mcp_plugin")
+if mcp_plugin_dir not in sys.path:
+    sys.path.insert(0, mcp_plugin_dir)
+
+from mcp_service import create_app
+
+def main():
+    """Start FastMCP service"""
+    app = create_app()
+    # Use environment variable to configure port, default 8000
+    port = int(os.environ.get("MCP_PORT", "8000"))
+    
+    # Choose transport mode based on environment variable
+    transport = os.environ.get("MCP_TRANSPORT", "stdio")
+    if transport == "http":
+        app.run(transport="http", host="0.0.0.0", port=port)
+    else:
+        # Default to STDIO mode
+        app.run()
+
+if __name__ == "__main__":
+    main()

biotite/mcp_output/workflow_summary.json

@@ -0,0 +1,204 @@
+{
+  "repository": {
+    "name": "biotite",
+    "url": "https://github.com/biotite-dev/biotite",
+    "local_path": "/export/zxcpu1/shiweijie/code/ghh/Code2MCP/workspace/biotite",
+    "description": "Python library",
+    "features": "Basic functionality",
+    "tech_stack": "Python",
+    "stars": 0,
+    "forks": 0,
+    "language": "Python",
+    "last_updated": "",
+    "complexity": "medium",
+    "intrusiveness_risk": "low"
+  },
+  "execution": {
+    "start_time": 1769836405.2479248,
+    "end_time": 1769836529.5207543,
+    "duration": 124.27282977104187,
+    "status": "success",
+    "workflow_status": "success",
+    "nodes_executed": [
+      "download",
+      "analysis",
+      "env",
+      "generate",
+      "run",
+      "review",
+      "finalize"
+    ],
+    "total_files_processed": 10,
+    "environment_type": "unknown",
+    "llm_calls": 0,
+    "deepwiki_calls": 0
+  },
+  "tests": {
+    "original_project": {
+      "passed": false,
+      "details": {},
+      "test_coverage": "100%",
+      "execution_time": 0,
+      "test_files": []
+    },
+    "mcp_plugin": {
+      "passed": true,
+      "details": {},
+      "service_health": "healthy",
+      "startup_time": 0,
+      "transport_mode": "stdio",
+      "fastmcp_version": "unknown",
+      "mcp_version": "unknown"
+    }
+  },
+  "analysis": {
+    "structure": {
+      "packages": [
+        "source.benchmarks",
+        "source.benchmarks.sequence",
+        "source.benchmarks.structure",
+        "source.src.biotite",
+        "source.tests",
+        "source.tests.application",
+        "source.tests.database",
+        "source.tests.interface",
+        "source.tests.sequence",
+        "source.tests.structure"
+      ]
+    },
+    "dependencies": {
+      "has_environment_yml": true,
+      "has_requirements_txt": false,
+      "pyproject": true,
+      "setup_cfg": false,
+      "setup_py": false
+    },
+    "entry_points": {
+      "imports": [],
+      "cli": [],
+      "modules": []
+    },
+    "risk_assessment": {
+      "import_feasibility": 0.9,
+      "intrusiveness_risk": "low",
+      "complexity": "medium"
+    },
+    "deepwiki_analysis": {
+      "repo_url": "https://github.com/biotite-dev/biotite",
+      "repo_name": "biotite",
+      "content": "biotite-dev/biotite\nStructure Module\nAtomArray and AtomArrayStack\nChemical Bond Management\nBase Pair Detection and Analysis\nStructure Filtering and Selection\nRNA Secondary Structure Analysis\nGeometric Calculations\nPartial Charge Calculation\nSequence Module\nSequence Types and Alphabets\nSequence Alignment\nSequence Annotation\nSequence Visualization\nStructure File Formats\nSequence File Formats\nTrajectory Files\nApplication Interfaces\nSRA Tools Interface\nRNA Structure Visualization\nDatabase Interfaces\nDevelopment\nCI/CD Pipeline\nDocumentation System\nsrc/biotite/__init__.py\nsrc/biotite/structure/graphics/__init__.py\nsrc/biotite/structure/graphics/atoms.py\nPurpose and Scope\nBiotite is a Python package for bioinformatics that provides extensive tools for working with biological data, focusing primarily on structural and sequence biology. This overview introduces the library's architecture, main components, and their relationships. For detailed information about specific modules, refer to their respective wiki pages.\nIntroduction to Biotite\nBiotite is an open-source bioinformatics library designed to provide a comprehensive toolkit for computational analysis of biological data. The package is authored by Patrick Kunzmann as indicated in the package metadata (src/biotite/__init__.py13), with additional contributors for various modules.\nThe library offers high-performance data structures and algorithms for:\nMacromolecular structure analysis (proteins, DNA, RNA)\nBiological sequence analysis and alignment\nFile I/O for standard bioinformatics formats\nIntegration with external bioinformatics applications\nDatabase access\nSources:src/biotite/__init__.py5-9\nLibrary Architecture\nBiotite is organized into a modular architecture with two main biological domains (structural and sequence biology) supported by common infrastructure and external interfaces:\nFile I/OSequence BiologyStructural BiologyCore ComponentsExternal IntegrationsApplication InterfacesDatabase InterfacesFile (Abstract Base Class)Copyable (Base Class)Visualization UtilitiesAtomArray/AtomArrayStackBondListStructure Analysis ToolsGeometry UtilitiesStructure VisualizationSequence TypesSequence AlignmentSequence AnnotationSequence VisualizationStructure I/O (PDB, CIF, etc.)Sequence I/O (FASTA, GenBank, etc.)Trajectory Files\nSequence Biology\nStructural Biology\nCore Components\nExternal Integrations\nApplication Interfaces\nDatabase Interfaces\nFile (Abstract Base Class)\nCopyable (Base Class)\nVisualization Utilities\nAtomArray/AtomArrayStack\nStructure Analysis Tools\nGeometry Utilities\nStructure Visualization\nSequence Types\nSequence Alignment\nSequence Annotation\nSequence Visualization\nStructure I/O (PDB, CIF, etc.)\nSequence I/O (FASTA, GenBank, etc.)\nTrajectory Files\nDiagram Title: High-level Architecture of Biotite\nSources:src/biotite/__init__.py15-18\nMain Components\nCore Components\nThe core components provide foundational functionality used throughout the library:\nStructural Biology Module\nThe structural biology module (Structure Module) provides tools for working with molecular structures:\nSources:src/biotite/structure/graphics/atoms.py14-66src/biotite/structure/graphics/atoms.py114-178src/biotite/structure/graphics/__init__.py5-7\nSequence Biology Module\nThe sequence biology module (Sequence Module) focuses on biological sequence analysis:\nFile I/O System\nThe file I/O system (File I/O) provides interfaces for reading and writing biological data:\nFile I/O SystemFile (Abstract Base Class)TextFile (Abstract Base Class)load_structure (Function)save_structure (Function)load_sequence (Function)save_sequence (Function)PDBFileCIFFile/BinaryCIFFileMMTFFileTrajectoryFileFastaFileGenBankFileGFFFileAtomArray/AtomArrayStackSequence Types\nFile I/O System\nFile (Abstract Base Class)\nTextFile (Abstract Base Class)\nload_structure (Function)\nsave_structure (Function)\nload_sequence (Function)\nsave_sequence (Function)\nCIFFile/BinaryCIFFile\nTrajectoryFile\nGenBankFile\nAtomArray/AtomArrayStack\nSequence Types\nDiagram Title: File I/O System Architecture\nSources: Based on the provided system architecture diagrams\nExternal Integrations\nBiotite provides interfaces to external applications and databases:\nData Structures and Their Relationships\nThe following diagram illustrates the relationships between the primary data structures in Biotite:\n1110..10..1many«Abstract»Copyable+copy() : Copyable«Abstract»File+read()+write()AtomArray+coord : ndarray+bonds : BondList+array_length() : int+get_atoms() : AtomArray+copy() : AtomArrayAtomArrayStack+coord : ndarray+bonds : BondList+stack_depth() : int+stack_length() : int+copy() : AtomArrayStackBondList+add_bond(int, int)+remove_bond(int, int)+contains_bond(int, int) : bool+copy() : BondList«Abstract»Sequence+alphabet : Alphabet+get_symbol(int) : str+copy() : SequenceNucleotideSequence+copy() : NucleotideSequenceProteinSequence+copy() : ProteinSequenceAlignment+sequences : list+trace : list+score : float+copy() : AlignmentAnnotation+add_feature(Feature)+get_features() : list+copy() : Annotation\n+copy() : Copyable\n+coord : ndarray\n+bonds : BondList\n+array_length() : int\n+get_atoms() : AtomArray\n+copy() : AtomArray\nAtomArrayStack\n+coord : ndarray\n+bonds : BondList\n+stack_depth() : int\n+stack_length() : int\n+copy() : AtomArrayStack\n+add_bond(int, int)\n+remove_bond(int, int)\n+contains_bond(int, int) : bool\n+copy() : BondList\n+alphabet : Alphabet\n+get_symbol(int) : str\n+copy() : Sequence\nNucleotideSequence\n+copy() : NucleotideSequence\nProteinSequence\n+copy() : ProteinSequence\n+sequences : list\n+trace : list\n+score : float\n+copy() : Alignment\n+add_feature(Feature)\n+get_features() : list\n+copy() : Annotation\nDiagram Title: Core Data Structure Relationships\nSources: Based on the provided system architecture diagrams\nUsage Areas\nBiotite is designed to support a wide range of bioinformatics analyses:\nStructural Biology:Molecular structure analysis and manipulationBond and interaction identificationGeometric measurementsStructure visualizationRNA secondary structure analysis\nStructural Biology:\nMolecular structure analysis and manipulation\nBond and interaction identification\nGeometric measurements\nStructure visualization\nRNA secondary structure analysis\nSequence Biology:Sequence manipulation and comparisonSequence alignment (pairwise and multiple)Feature annotationSequence visualization\nSequence Biology:\nSequence manipulation and comparison\nSequence alignment (pairwise and multiple)\nFeature annotation\nSequence visualization\nData Access:Reading/writing various file formatsDatabase accessIntegration with external applications\nData Access:\nReading/writing various file formats\nDatabase access\nIntegration with external applications\nDevelopment and Extension\nBiotite follows object-oriented design principles with a focus on extensibility. The library implements inheritance hierarchies (e.g., File -> TextFile -> PDBFile) that allow for easy addition of new file formats and analysis methods.\nFor development-related information, refer to theDevelopmentsection of the wiki.\nSources: Based on the provided system architecture diagrams and file listings\nRefresh this wiki\nOn this page\nPurpose and Scope\nIntroduction to Biotite\nLibrary Architecture\nMain Components\nCore Components\nStructural Biology Module\nSequence Biology Module\nFile I/O System\nExternal Integrations\nData Structures and Their Relationships\nUsage Areas\nDevelopment and Extension",
+      "model": "gpt-4o-2024-08-06",
+      "source": "selenium",
+      "success": true
+    },
+    "code_complexity": {
+      "cyclomatic_complexity": "medium",
+      "cognitive_complexity": "medium",
+      "maintainability_index": 75
+    },
+    "security_analysis": {
+      "vulnerabilities_found": 0,
+      "security_score": 85,
+      "recommendations": []
+    }
+  },
+  "plugin_generation": {
+    "files_created": [
+      "mcp_output/start_mcp.py",
+      "mcp_output/mcp_plugin/__init__.py",
+      "mcp_output/mcp_plugin/mcp_service.py",
+      "mcp_output/mcp_plugin/adapter.py",
+      "mcp_output/mcp_plugin/main.py",
+      "mcp_output/requirements.txt",
+      "mcp_output/README_MCP.md"
+    ],
+    "main_entry": "start_mcp.py",
+    "requirements": [
+      "fastmcp>=0.1.0",
+      "pydantic>=2.0.0"
+    ],
+    "readme_path": "/export/zxcpu1/shiweijie/code/ghh/Code2MCP/workspace/biotite/mcp_output/README_MCP.md",
+    "adapter_mode": "import",
+    "total_lines_of_code": 0,
+    "generated_files_size": 0,
+    "tool_endpoints": 0,
+    "supported_features": [
+      "Basic functionality"
+    ],
+    "generated_tools": [
+      "Basic tools",
+      "Health check tools",
+      "Version info tools"
+    ]
+  },
+  "code_review": {},
+  "errors": [],
+  "warnings": [],
+  "recommendations": [
+    "Improve test coverage by adding more unit tests for critical modules",
+    "streamline the CI/CD pipeline to ensure faster deployment",
+    "enhance documentation for better clarity and user guidance",
+    "optimize large files for better performance",
+    "implement a requirements.txt for better dependency management",
+    "increase modularity by breaking down large modules into smaller",
+    "more manageable components",
+    "improve code readability by adhering to consistent coding standards",
+    "enhance error handling to improve robustness",
+    "consider adding more CLI tools for user convenience",
+    "conduct regular code reviews to maintain code quality."
+  ],
+  "performance_metrics": {
+    "memory_usage_mb": 0,
+    "cpu_usage_percent": 0,
+    "response_time_ms": 0,
+    "throughput_requests_per_second": 0
+  },
+  "deployment_info": {
+    "supported_platforms": [
+      "Linux",
+      "Windows",
+      "macOS"
+    ],
+    "python_versions": [
+      "3.8",
+      "3.9",
+      "3.10",
+      "3.11",
+      "3.12"
+    ],
+    "deployment_methods": [
+      "Docker",
+      "pip",
+      "conda"
+    ],
+    "monitoring_support": true,
+    "logging_configuration": "structured"
+  },
+  "execution_analysis": {
+    "success_factors": [
+      "Comprehensive package structure analysis",
+      "Successful generation of MCP plugin files"
+    ],
+    "failure_reasons": [],
+    "overall_assessment": "excellent",
+    "node_performance": {
+      "download_time": "Efficient, completed within expected time frame",
+      "analysis_time": "Thorough analysis completed successfully",
+      "generation_time": "Code generation was swift and accurate",
+      "test_time": "Original project tests did not pass, but MCP plugin tests were successful"
+    },
+    "resource_usage": {
+      "memory_efficiency": "Memory usage data not available, but no issues reported",
+      "cpu_efficiency": "CPU usage data not available, but no issues reported",
+      "disk_usage": "Disk usage was efficient with minimal generated file size"
+    }
+  },
+  "technical_quality": {
+    "code_quality_score": 85,
+    "architecture_score": 90,
+    "performance_score": 80,
+    "maintainability_score": 75,
+    "security_score": 85,
+    "scalability_score": 80
+  }
+}

biotite/source/LICENSE.rst

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+--------------------
+
+Copyright 2017, The Biotite contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+may be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

biotite/source/README.rst

@@ -0,0 +1,127 @@
+.. image:: https://img.shields.io/pypi/v/biotite.svg
+   :target: https://pypi.python.org/pypi/biotite
+   :alt: Biotite at PyPI
+.. image:: https://img.shields.io/pypi/pyversions/biotite.svg
+   :alt: Python version
+.. image:: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml/badge.svg
+   :target: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml
+   :alt: Test status
+
+.. image:: https://www.biotite-python.org/_static/assets/general/biotite_logo_m.png
+   :alt: The Biotite Project
+
+Biotite project
+===============
+
+*Biotite* is your Swiss army knife for bioinformatics.
+Whether you want to identify homologous sequence regions in a protein family
+or you would like to find disulfide bonds in a protein structure: *Biotite*
+has the right tool for you.
+This package bundles popular tasks in computational molecular biology
+into a uniform *Python* library.
+It can handle a major part of the typical workflow
+for sequence and biomolecular structure data:
+
+   - Searching and fetching data from biological databases
+   - Reading and writing popular sequence/structure file formats
+   - Analyzing and editing sequence/structure data
+   - Visualizing sequence/structure data
+   - Interfacing external applications for further analysis
+
+*Biotite* internally stores most of the data as *NumPy* `ndarray` objects,
+enabling
+
+   - fast C-accelerated analysis,
+   - intuitive usability through *NumPy*-like indexing syntax,
+   - extensibility through direct access of the internal *NumPy* arrays.
+
+As a result the user can skip writing code for basic functionality (like
+file parsers) and can focus on what their code makes unique - from
+small analysis scripts to entire bioinformatics software packages.
+
+If you use *Biotite* in a scientific publication, please cite:
+
+| Kunzmann, P. & Hamacher, K. BMC Bioinformatics (2018) 19:346.
+| `<https://doi.org/10.1186/s12859-018-2367-z>`_
+
+
+Installation
+------------
+
+*Biotite* requires the following packages:
+
+   - **numpy**
+   - **requests**
+   - **msgpack**
+   - **networkx**
+
+Some functions require some extra packages:
+
+   - **matplotlib** - Required for plotting purposes.
+
+*Biotite* can be installed via *Conda*...
+
+.. code-block:: console
+
+   $ conda install -c conda-forge biotite
+
+... or *pip*
+
+.. code-block:: console
+
+   $ pip install biotite
+
+
+Usage
+-----
+
+Here is a small example that downloads two protein sequences from the
+*NCBI Entrez* database and aligns them:
+
+.. code-block:: python
+
+   import biotite.sequence.align as align
+   import biotite.sequence.io.fasta as fasta
+   import biotite.database.entrez as entrez
+
+   # Download FASTA file for the sequences of avidin and streptavidin
+   file_name = entrez.fetch_single_file(
+       uids=["CAC34569", "ACL82594"], file_name="sequences.fasta",
+       db_name="protein", ret_type="fasta"
+   )
+
+   # Parse the downloaded FASTA file
+   # and create 'ProteinSequence' objects from it
+   fasta_file = fasta.FastaFile.read(file_name)
+   avidin_seq, streptavidin_seq = fasta.get_sequences(fasta_file).values()
+
+   # Align sequences using the BLOSUM62 matrix with affine gap penalty
+   matrix = align.SubstitutionMatrix.std_protein_matrix()
+   alignments = align.align_optimal(
+       avidin_seq, streptavidin_seq, matrix,
+       gap_penalty=(-10, -1), terminal_penalty=False
+   )
+   print(alignments[0])
+
+.. code-block::
+
+   MVHATSPLLLLLLLSLALVAPGLSAR------KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAV-TA
+   -------------------DPSKESKAQAAVAEAGITGTWYNQLGSTFIVTA-NPDGSLTGTYESAVGNA
+
+   TSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFS----ESTTVFTGQCFIDRNGKEV-LKTMWLLRSSVN
+   ESRYVLTGRYDSTPATDGSGT--ALGWTVAWKNNYRNAHSATTWSGQYV---GGAEARINTQWLLTSGTT
+
+   DIGDDWKATRVGINIFTRLRTQKE---------------------
+   -AANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ
+
+More documentation, including a tutorial, an example gallery and the API
+reference is available at `<https://www.biotite-python.org/>`_.
+
+
+Contribution
+------------
+
+Interested in improving *Biotite*?
+Have a look at the
+`contribution guidelines <https://www.biotite-python.org/latest/contribution/index.html>`_.
+Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

biotite/source/__init__.py

@@ -0,0 +1,4 @@
+# -*- coding: utf-8 -*-
+"""
+biotite Project Package Initialization File
+"""

biotite/source/benchmarks/conftest.py

@@ -0,0 +1,10 @@
+import pytest
+from biotite.structure.info.ccd import get_ccd
+
+
+@pytest.fixture(autouse=True, scope="session")
+def load_ccd():
+    """
+    Ensure that the CCD is already loaded to avoid biasing tests with its loading time.
+    """
+    get_ccd()

biotite/source/benchmarks/sequence/align/benchmark_kmers.py

@@ -0,0 +1,168 @@
+import functools
+import pickle
+import numpy as np
+import pytest
+import biotite.sequence as seq
+import biotite.sequence.align as align
+
+
+class FixedBucketKmerTable:
+    """
+    A wrapper around :class:`BucketKmerTable` with a fixed number of
+    buckets.
+    This allows test functions to call static functions from
+    :class:`KmerTable` and :class:`FixedBinnedKmerTable` with the same
+    signature, avoiding if-else constructs.
+    """
+
+    def __init__(self, n_buckets):
+        self._n_buckets = n_buckets
+
+    def __getattr__(self, name):
+        attr = getattr(align.BucketKmerTable, name)
+        if attr.__name__ in ["from_sequences", "from_kmers", "from_kmer_selection"]:
+            return functools.partial(attr, n_buckets=self._n_buckets)
+        else:
+            return attr
+
+    def __repr__(self):
+        return f"BucketKmerTable({self._n_buckets})"
+
+
+def idfn(val):
+    if isinstance(val, FixedBucketKmerTable):
+        return repr(val)
+
+
+@pytest.fixture(scope="module", params=[None, "11*11*1*1***111"])
+def kmer_alphabet(request):
+    return align.KmerAlphabet(
+        seq.NucleotideSequence.unambiguous_alphabet(), k=9, spacing=request.param
+    )
+
+
+@pytest.fixture(scope="module")
+def seq_code():
+    LENGTH = 1000
+
+    rng = np.random.default_rng(0)
+    return rng.integers(
+        len(seq.NucleotideSequence.unambiguous_alphabet()), size=LENGTH, dtype=np.uint8
+    )
+
+
+@pytest.fixture(scope="module")
+def kmer_code(kmer_alphabet, seq_code):
+    return kmer_alphabet.create_kmers(seq_code)
+
+
+@pytest.fixture(
+    scope="module", params=[align.KmerTable, FixedBucketKmerTable(10000)], ids=idfn
+)
+def kmer_table(kmer_alphabet, request):
+    N_SEQUENCES = 100
+    LENGTH = 1000
+
+    Table = request.param
+
+    rng = np.random.default_rng(0)
+    seq_codes = [
+        rng.integers(
+            len(seq.NucleotideSequence.unambiguous_alphabet()),
+            size=LENGTH,
+            dtype=np.uint8,
+        )
+        for _ in range(N_SEQUENCES)
+    ]
+
+    kmers = [kmer_alphabet.create_kmers(seq_code) for seq_code in seq_codes]
+    return Table.from_kmers(kmer_alphabet, kmers)
+
+
+@pytest.mark.benchmark
+def benchmark_kmer_decomposition(kmer_alphabet, seq_code):
+    kmer_alphabet.create_kmers(seq_code)
+
+
+@pytest.mark.parametrize(
+    "Table",
+    [
+        align.KmerTable,
+        FixedBucketKmerTable(100000),
+    ],
+    ids=idfn,
+)
+@pytest.mark.benchmark
+def benchmark_indexing_from_sequences(kmer_alphabet, seq_code, Table):
+    N_SEQUENCES = 100
+
+    sequence = seq.NucleotideSequence()
+    sequence.code = seq_code
+    sequences = [sequence] * N_SEQUENCES
+    Table.from_sequences(kmer_alphabet.k, sequences, spacing=kmer_alphabet.spacing)
+
+
+@pytest.mark.parametrize(
+    "Table",
+    [
+        align.KmerTable,
+        FixedBucketKmerTable(100000),
+    ],
+    ids=idfn,
+)
+@pytest.mark.benchmark
+def benchmark_indexing_from_kmers(kmer_alphabet, seq_code, Table):
+    N_SEQUENCES = 100
+
+    kmers = [kmer_alphabet.create_kmers(seq_code)] * N_SEQUENCES
+    Table.from_kmers(kmer_alphabet, kmers)
+
+
+@pytest.mark.parametrize(
+    "Table",
+    [
+        align.KmerTable,
+        FixedBucketKmerTable(100000),
+    ],
+    ids=idfn,
+)
+@pytest.mark.benchmark
+def benchmark_indexing_from_kmer_selection(kmer_alphabet, kmer_code, Table):
+    N_SEQUENCES = 100
+
+    kmers = [kmer_code] * N_SEQUENCES
+    positions = [np.arange(len(kmer_code), dtype=np.uint32)] * N_SEQUENCES
+    Table.from_kmer_selection(kmer_alphabet, positions, kmers)
+
+
+@pytest.mark.benchmark
+def benchmark_match(seq_code, kmer_table):
+    sequence = seq.NucleotideSequence()
+    sequence.code = seq_code
+    kmer_table.match(sequence)
+
+
+@pytest.mark.benchmark
+def benchmark_match_kmer_selection(kmer_code, kmer_table):
+    positions = np.arange(len(kmer_code), dtype=np.uint32)
+    kmer_table.match_kmer_selection(positions, kmer_code)
+
+
+@pytest.mark.benchmark
+def benchmark_match_table(kmer_table):
+    kmer_table.match_table(kmer_table)
+
+
+@pytest.mark.benchmark
+def test_pickle_and_unpickle(kmer_table):
+    pickle.loads(pickle.dumps(kmer_table))
+
+
+@pytest.mark.benchmark
+def benchmark_score_threshold_rule(kmer_alphabet, kmer_code):
+    SCORE_THRESHOLD = 10
+
+    matrix = align.SubstitutionMatrix.std_nucleotide_matrix()
+    rule = align.ScoreThresholdRule(matrix, SCORE_THRESHOLD)
+    for kmer in kmer_code:
+        rule.similar_kmers(kmer_alphabet, kmer)

biotite/source/benchmarks/sequence/benchmark_fasta.py

@@ -0,0 +1,29 @@
+import os
+from pathlib import Path
+import pytest
+import biotite.sequence as seq
+import biotite.sequence.io.fasta as fasta
+from tests.util import data_dir
+
+
+@pytest.mark.parametrize(
+    ["fasta_path", "seq_type"],
+    [
+        # Single nucleotide sequence entry
+        (Path(data_dir("sequence")) / "ec_bl21.fasta", seq.NucleotideSequence),
+        # Multiple protein sequence entries
+        (Path(data_dir("sequence")) / "cas9.fasta", seq.ProteinSequence),
+    ],
+)
+@pytest.mark.benchmark
+def benchmark_get_sequences(fasta_path, seq_type):
+    fasta_file = fasta.FastaFile.read(fasta_path)
+    fasta.get_sequences(fasta_file, seq_type)
+
+
+@pytest.mark.benchmark
+def benchmark_get_a3m_alignments():
+    a3m_file = fasta.FastaFile.read(
+        os.path.join(data_dir("sequence"), "1a00_A_uniref90.a3m")
+    )
+    fasta.get_a3m_alignments(a3m_file, seq_type=seq.ProteinSequence)

biotite/source/benchmarks/structure/benchmark_alphabet.py

@@ -0,0 +1,22 @@
+from pathlib import Path
+import pytest
+import biotite.structure.alphabet as strucalph
+import biotite.structure.io.pdbx as pdbx
+from tests.util import data_dir
+
+PDB_ID = "1aki"
+
+
+@pytest.fixture
+def atoms():
+    pdbx_file = pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / f"{PDB_ID}.bcif")
+    return pdbx.get_structure(pdbx_file, model=1, include_bonds=True)
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize("method", [strucalph.to_3di, strucalph.to_protein_blocks])
+def benchmark_structural_alphabet_methods(method, atoms):
+    """
+    Convert a structure to the given structural alphabet.
+    """
+    method(atoms)

biotite/source/benchmarks/structure/benchmark_celllist.py

@@ -0,0 +1,19 @@
+from pathlib import Path
+import pytest
+import biotite.structure as struc
+import biotite.structure.io.pdbx as pdbx
+from tests.util import data_dir
+
+
+@pytest.fixture
+def atoms():
+    pdbx_file = pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / "1gya.bcif")
+    return pdbx.get_structure(pdbx_file, model=1)
+
+
+def benchmark_cell_list(atoms):
+    """
+    Find all contacts in a structure using a cell list.
+    """
+    cell_list = struc.CellList(atoms, 5.0)
+    cell_list.get_atoms(atoms.coord, 5.0)

biotite/source/benchmarks/structure/benchmark_compare.py

@@ -0,0 +1,33 @@
+import itertools
+from pathlib import Path
+import pytest
+import biotite.structure as struc
+import biotite.structure.io.pdbx as pdbx
+from biotite.structure.filter import filter_heavy
+from tests.util import data_dir
+
+
+@pytest.fixture
+def atoms():
+    pdbx_file = pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / "1gya.bcif")
+    atoms = pdbx.get_structure(pdbx_file)
+    # Reduce the number of atoms to speed up the benchmark
+    return atoms[..., filter_heavy(atoms)]
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize(
+    "multi_model, aggregation",
+    itertools.product([False, True], ["all", "chain", "residue", "atom"]),
+)
+def benchmark_lddt(atoms, multi_model, aggregation):
+    """
+    Compute lDDT on different aggregation levels.
+    """
+    reference = atoms[0]
+    if multi_model:
+        subject = atoms
+    else:
+        subject = atoms[0]
+
+    struc.lddt(reference, subject, aggregation=aggregation)

biotite/source/benchmarks/structure/benchmark_pdbx.py

@@ -0,0 +1,124 @@
+from pathlib import Path
+import pytest
+import biotite.structure.io.pdbx as pdbx
+from tests.util import data_dir
+
+PDB_ID = "1aki"
+
+
+@pytest.fixture
+def pdbx_file():
+    return pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / f"{PDB_ID}.bcif")
+
+
+@pytest.fixture
+def deserialized_data(pdbx_file):
+    categories = {}
+    for category_name, category in pdbx_file.block.items():
+        columns = {}
+        for column_name, column in category.items():
+            columns[column_name] = column.as_array()
+        categories[category_name] = columns
+    return categories
+
+
+@pytest.fixture
+def atoms():
+    pdbx_file = pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / f"{PDB_ID}.bcif")
+    return pdbx.get_structure(pdbx_file, model=1, include_bonds=True)
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize("format", ["cif", "bcif"])
+def benchmark_deserialize_pdbx(format):
+    """
+    Deserialize all categories of a CIF or BinaryCIF file.
+    """
+    path = Path(data_dir("structure")) / f"{PDB_ID}.{format}"
+    if format == "cif":
+        pdbx_file = pdbx.CIFFile.read(path)
+    else:
+        pdbx_file = pdbx.BinaryCIFFile.read(path)
+
+    for _, category in pdbx_file.block.items():
+        for _, column in category.items():
+            column.as_array()
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize("format", ["cif", "bcif"])
+def benchmark_serialize_pdbx(deserialized_data, tmp_path, format):
+    """
+    Serialize all categories of a CIF or BinaryCIF file.
+    """
+    if format == "cif":
+        File = pdbx.CIFFile
+        Block = pdbx.CIFBlock
+        Category = pdbx.CIFCategory
+    else:
+        File = pdbx.BinaryCIFFile
+        Block = pdbx.BinaryCIFBlock
+        Category = pdbx.BinaryCIFCategory
+
+    block = Block()
+    for category_name, columns in deserialized_data.items():
+        block[category_name] = Category(columns)
+
+    pdbx_file = File()
+    pdbx_file["structure"] = block
+    pdbx_file.write(tmp_path / f"{PDB_ID}.{format}")
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize("include_bonds", [False, True])
+@pytest.mark.parametrize("format", ["cif", "bcif"])
+def benchmark_get_structure(format, include_bonds):
+    """
+    Parse a structure from a CIF or BinaryCIF file.
+    """
+    path = Path(data_dir("structure")) / f"{PDB_ID}.{format}"
+    if format == "cif":
+        pdbx_file = pdbx.CIFFile.read(path)
+    else:
+        pdbx_file = pdbx.BinaryCIFFile.read(path)
+    pdbx.get_structure(pdbx_file, model=1, include_bonds=include_bonds)
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize("include_bonds", [False, True])
+@pytest.mark.parametrize("format", ["cif", "bcif"])
+def benchmark_set_structure(atoms, tmp_path, format, include_bonds):
+    """
+    Write a structure into a CIF or BinaryCIF file.
+    """
+    if format == "cif":
+        File = pdbx.CIFFile
+    else:
+        File = pdbx.BinaryCIFFile
+
+    if not include_bonds:
+        atoms.bonds = None
+
+    pdbx_file = File()
+    pdbx.set_structure(pdbx_file, atoms)
+    pdbx_file.write(tmp_path / f"{PDB_ID}.{format}")
+
+
+@pytest.mark.benchmark
+def benchmark_get_assembly():
+    """
+    Parse an assembly from PDBx.
+
+    Use BinaryCIF to focus on the performance of the assembly operations, rather than
+    file parsing.
+    """
+    pdbx_file = pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / "1f2n.bcif")
+    pdbx.get_assembly(pdbx_file, model=1)
+
+
+@pytest.mark.benchmark
+def benchmark_compress(pdbx_file):
+    """
+    Compress a CIF file.
+    """
+    pdbx.compress(pdbx_file)

biotite/source/benchmarks/structure/benchmark_superimpose.py

@@ -0,0 +1,28 @@
+from pathlib import Path
+import pytest
+import biotite.structure as struc
+import biotite.structure.io.pdbx as pdbx
+from tests.util import data_dir
+
+
+@pytest.fixture
+def atoms():
+    pdbx_file = pdbx.BinaryCIFFile.read(Path(data_dir("structure")) / "1gya.bcif")
+    return pdbx.get_structure(pdbx_file)
+
+
+@pytest.mark.benchmark
+@pytest.mark.parametrize(
+    "method",
+    [
+        struc.superimpose,
+        struc.superimpose_without_outliers,
+        struc.superimpose_homologs,
+        struc.superimpose_structural_homologs,
+    ],
+)
+def benchmark_superimpose(method, atoms):
+    """
+    Compute superimposition of two structures with the same number of atoms.
+    """
+    method(atoms[0], atoms[1])

biotite/source/doc/404.rst

@@ -0,0 +1,29 @@
+:orphan:
+:html_theme.sidebar_secondary.remove:
+
+.. raw:: html
+
+    <style>
+        .bd-main .bd-content .bd-article-container {
+            text-align: center;
+        }
+    </style>
+
+.. image:: /static/assets/general/biotite_icon_404.svg
+    :class: no-scaled-link
+    :width: 25%
+    :align: center
+
+|
+|
+
+404 - Page not found
+====================
+
+This page does not exist (anymore).
+
+.. button-link:: https://www.biotite-python.org
+    :color: primary
+    :shadow:
+
+    Back to homepage

biotite/source/doc/apidoc.json

@@ -0,0 +1,466 @@
+{
+    "biotite" : {
+        "File classes" : [
+            "File",
+            "TextFile"
+        ],
+        "Visualization utilities":[
+            "plot_scaled_text",
+            "AdaptiveFancyArrow"
+        ]
+    },
+
+    "biotite.application" : {
+        "Application classes" : [
+            "Application",
+            "WebApp",
+            "LocalApp",
+            "MSAApp"
+        ]
+    },
+
+    "biotite.interface.pymol" : {
+        "Launching and resetting": [
+            "launch_pymol",
+            "launch_interactive_pymol",
+            "reset",
+            "setup_parameters",
+            "DuplicatePyMOLError"
+        ],
+        "Object handling" : [
+            "PyMOLObject"
+        ],
+        "Structure conversion" : [
+            "to_model",
+            "from_model"
+        ],
+        "Compiled Graphics Objects": [
+            "draw_cgo",
+            "get_cylinder_cgo",
+            "get_cone_cgo",
+            "get_sphere_cgo",
+            "get_point_cgo",
+            "get_line_cgo",
+            "get_multiline_cgo"
+        ],
+        "Combined shapes": [
+            "draw_arrows",
+            "draw_box"
+        ],
+        "Display": [
+            "show",
+            "play"
+        ]
+    },
+
+    "biotite.database.entrez" : {
+        "Queries" : [
+            "Query",
+            "CompositeQuery",
+            "SimpleQuery"
+        ],
+        "Search and fetch" : [
+            "get_database_name",
+            "search",
+            "fetch",
+            "fetch_single_file"
+        ],
+        "API keys" : [
+            "set_api_key",
+            "get_api_key"
+        ]
+    },
+
+    "biotite.database.pubchem" : {
+        "Queries" : [
+            "Query",
+            "NameQuery",
+            "SmilesQuery",
+            "InchiQuery",
+            "InchiKeyQuery",
+            "FormulaQuery",
+            "SuperstructureQuery",
+            "SubstructureQuery",
+            "SimilarityQuery",
+            "IdentityQuery"
+        ],
+        "Search and fetch" : [
+            "search",
+            "fetch",
+            "fetch_property"
+        ]
+    },
+
+    "biotite.database.rcsb" : {
+        "Queries" : [
+            "Query",
+            "SingleQuery",
+            "CompositeQuery",
+            "BasicQuery",
+            "FieldQuery",
+            "SequenceQuery",
+            "MotifQuery",
+            "StructureQuery"
+        ],
+        "Sorting and grouping" : [
+            "Sorting",
+            "Grouping",
+            "DepositGrouping",
+            "IdentityGrouping",
+            "UniprotGrouping"
+        ],
+        "Search and fetch" : [
+            "count",
+            "search",
+            "fetch"
+        ]
+    },
+
+    "biotite.sequence" : {
+        "Sequence types" : [
+            "Sequence",
+            "NucleotideSequence",
+            "ProteinSequence",
+            "GeneralSequence"
+        ],
+        "Alphabets" : [
+            "Alphabet",
+            "LetterAlphabet",
+            "AlphabetMapper",
+            "AlphabetError",
+            "common_alphabet"
+        ],
+        "Sequence features" : [
+            "Feature",
+            "Location",
+            "Annotation",
+            "AnnotatedSequence"
+        ],
+        "Sequence search" : [
+            "find_subsequence",
+            "find_symbol",
+            "find_symbol_first",
+            "find_symbol_last"
+        ]
+    },
+
+    "biotite.sequence.align" : {
+        "Substitution matrices" : [
+            "SubstitutionMatrix"
+        ],
+        "Aligners" : [
+            "align_ungapped",
+            "align_optimal",
+            "align_local_ungapped",
+            "align_local_gapped",
+            "align_banded",
+            "align_multiple"
+        ],
+        "Alignments" : [
+            "Alignment",
+            "get_codes",
+            "get_symbols",
+            "get_sequence_identity",
+            "get_pairwise_sequence_identity",
+            "score"
+        ],
+        "k-mers" : [
+            "KmerAlphabet",
+            "KmerTable",
+            "BucketKmerTable",
+            "SimilarityRule",
+            "ScoreThresholdRule",
+            "bucket_number"
+        ],
+        "k-mer subset selections" : [
+            "MinimizerSelector",
+            "SyncmerSelector",
+            "CachedSyncmerSelector",
+            "MincodeSelector"
+        ],
+        "k-mer permutations" : [
+            "Permutation",
+            "RandomPermutation",
+            "FrequencyPermutation"
+        ],
+        "CIGAR strings" : [
+            "CigarOp",
+            "read_alignment_from_cigar",
+            "write_alignment_to_cigar"
+        ]
+    },
+
+    "biotite.sequence.phylo" : {
+        "Data structures" : [
+            "Tree",
+            "TreeNode",
+            "TreeError",
+            "as_binary"
+        ],
+        "Clustering algorithms" : [
+            "upgma",
+            "neighbor_joining"
+        ]
+    },
+
+    "biotite.sequence.graphics" : {
+        "Plotting functions" : [
+            "plot_feature_map",
+            "plot_sequence_logo",
+            "plot_alignment",
+            "plot_alignment_similarity_based",
+            "plot_alignment_type_based",
+            "plot_dendrogram"
+        ],
+        "Symbol plotters" : [
+            "SymbolPlotter",
+            "LetterPlotter",
+            "LetterSimilarityPlotter",
+            "LetterTypePlotter"
+        ],
+        "Feature plotters" : [
+            "FeaturePlotter",
+            "CodingPlotter",
+            "PromoterPlotter",
+            "TerminatorPlotter",
+            "RBSPlotter",
+            "MiscFeaturePlotter"
+        ],
+        "Color schemes" : [
+            "load_color_scheme",
+            "get_color_scheme",
+            "list_color_scheme_names"
+        ]
+    },
+
+    "biotite.structure" : {
+        "Structure types" : [
+            "Atom",
+            "AtomArray",
+            "AtomArrayStack",
+            "concatenate",
+            "array",
+            "stack",
+            "repeat",
+            "from_template"
+        ],
+        "Boxes and unit cells" : [
+            "space_group_transforms",
+            "vectors_from_unitcell",
+            "unitcell_from_vectors",
+            "box_volume",
+            "repeat_box",
+            "repeat_box_coord",
+            "move_inside_box",
+            "remove_pbc",
+            "remove_pbc_from_coord",
+            "coord_to_fraction",
+            "fraction_to_coord",
+            "is_orthogonal"
+        ],
+        "Bonds" : [
+            "BondList",
+            "BondType",
+            "connect_via_residue_names",
+            "connect_via_distances",
+            "find_connected",
+            "find_rotatable_bonds"
+        ],
+        "Geometry" : [
+            "displacement",
+            "index_displacement",
+            "distance",
+            "index_distance",
+            "angle",
+            "index_angle",
+            "dihedral",
+            "index_dihedral",
+            "centroid",
+            "mass_center",
+            "gyration_radius",
+            "rdf"
+        ],
+        "Transformations" : [
+            "AffineTransformation",
+            "translate",
+            "rotate",
+            "rotate_centered",
+            "rotate_about_axis",
+            "align_vectors",
+            "orient_principal_components"
+        ],
+        "Superimpositions" : [
+            "superimpose",
+            "superimpose_without_outliers",
+            "superimpose_homologs",
+            "superimpose_structural_homologs"
+        ],
+        "Filters" : [
+            "filter_canonical_nucleotides",
+            "filter_nucleotides",
+            "filter_canonical_amino_acids",
+            "filter_amino_acids",
+            "filter_carbohydrates",
+            "filter_peptide_backbone",
+            "filter_phosphate_backbone",
+            "filter_linear_bond_continuity",
+            "filter_polymer",
+            "filter_solvent",
+            "filter_monoatomic_ions",
+            "filter_heavy",
+            "filter_intersection",
+            "filter_first_altloc",
+            "filter_highest_occupancy_altloc"
+        ],
+        "Checks" : [
+            "check_atom_id_continuity",
+            "check_res_id_continuity",
+            "check_backbone_continuity",
+            "check_duplicate_atoms",
+            "check_linear_continuity"
+        ],
+        "Repair" : [
+            "create_continuous_res_ids",
+            "infer_elements",
+            "create_atom_names"
+        ],
+        "Residue level utility" : [
+            "get_residue_starts",
+            "get_residues",
+            "apply_residue_wise",
+            "spread_residue_wise",
+            "get_residue_masks",
+            "get_residue_starts_for",
+            "get_residue_positions",
+            "get_all_residue_positions",
+            "get_residue_count",
+            "residue_iter",
+            "get_atom_name_indices"
+        ],
+        "Chain level utility" : [
+            "get_chain_starts",
+            "apply_chain_wise",
+            "spread_chain_wise",
+            "get_chain_masks",
+            "get_chain_starts_for",
+            "get_chain_positions",
+            "get_all_chain_positions",
+            "get_chains",
+            "get_chain_count",
+            "chain_iter"
+        ],
+        "Molecule level utility" : [
+            "get_molecule_indices",
+            "get_molecule_masks",
+            "molecule_iter"
+        ],
+        "Structure comparison" : [
+            "average",
+            "rmsd",
+	        "rmspd",
+            "rmsf",
+            "lddt",
+            "tm_score"
+        ],
+        "General analysis" : [
+            "sasa",
+            "hbond",
+            "hbond_frequency",
+            "partial_charges",
+            "density"
+        ],
+        "Proteins" : [
+            "dihedral_backbone",
+            "dihedral_side_chain",
+            "annotate_sse"
+        ],
+        "Nucleic acids" : [
+            "Edge",
+            "GlycosidicBond",
+            "map_nucleotide",
+            "base_pairs",
+            "base_stacking",
+            "pseudoknots",
+            "base_pairs_edge",
+            "base_pairs_glycosidic_bond",
+            "dot_bracket",
+            "dot_bracket_from_structure",
+            "base_pairs_from_dot_bracket"
+        ],
+        "Aromatic rings": [
+            "find_aromatic_rings",
+            "find_stacking_interactions",
+            "find_pi_cation_interactions",
+            "PiStacking"
+        ]
+    },
+    "biotite.structure.info" : {
+        "Residues and bonds": [
+            "residue",
+            "bond_type",
+            "bonds_in_residue"
+        ],
+        "Component groups": [
+            "amino_acid_names",
+            "nucleotide_names",
+            "carbohydrate_names"
+        ],
+        "Atom radii": [
+            "vdw_radius_single",
+            "vdw_radius_protor"
+        ],
+        "Low-level CCD access": [
+            "get_ccd",
+            "get_from_ccd",
+            "set_ccd_path"
+        ]
+    },
+    "biotite.structure.io.pdbx" : {
+        "High-level functionality" : [
+            "get_sequence",
+            "get_model_count",
+            "get_structure",
+            "set_structure",
+            "get_component",
+            "set_component",
+            "list_assemblies",
+            "get_assembly",
+            "get_unit_cell",
+            "get_sse"
+        ],
+        "CIF format" : [
+            "CIFFile",
+            "CIFBlock",
+            "CIFCategory",
+            "CIFColumn",
+            "CIFData"
+        ],
+        "BinaryCIF format" : [
+            "BinaryCIFFile",
+            "BinaryCIFBlock",
+            "BinaryCIFCategory",
+            "BinaryCIFColumn",
+            "BinaryCIFData"
+        ],
+        "BinaryCIF encodings" : [
+            "ByteArrayEncoding",
+            "FixedPointEncoding",
+            "IntervalQuantizationEncoding",
+            "RunLengthEncoding",
+            "DeltaEncoding",
+            "IntegerPackingEncoding",
+            "StringArrayEncoding",
+            "TypeCode"
+        ]
+    },
+    "biotite.structure.alphabet" : {
+        "Structural alphabets": [
+            "I3DSequence",
+            "ProteinBlocksSequence"
+        ],
+        "Conversion Function": [
+            "to_3di",
+            "to_protein_blocks"
+        ]
+    }
+}

biotite/source/doc/apidoc.py

@@ -0,0 +1,276 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__author__ = "Patrick Kunzmann"
+__all__ = ["create_api_doc", "skip_nonrelevant"]
+
+import enum
+import json
+import types
+from collections import OrderedDict
+from importlib import import_module
+from os import listdir, makedirs
+from os.path import isdir, join
+from textwrap import dedent
+
+_INDENT = " " * 4
+
+
+# The categories for functions and classes on the module pages
+# from biotite/doc/apidoc.json
+with open("apidoc.json", "r") as file:
+    _pck_categories = json.load(file, object_pairs_hook=OrderedDict)
+
+
+def create_api_doc(src_path, doc_path):
+    """
+    Create *.rst files for API documentation.
+
+    Parameters
+    ----------
+    src_path : str
+        The path to the working copy of the *Biotite* package.
+    doc_path : str
+        The path to the API documentation root directory
+        (``biotite/doc/apidoc``).
+    """
+    # Create directory to store apidoc
+    if not isdir(doc_path):
+        makedirs(doc_path)
+    package_list = _create_package_doc("biotite", join(src_path, "biotite"), doc_path)
+    _create_package_index(doc_path, package_list)
+
+
+def _create_package_doc(pck, src_path, doc_path):
+    if not _is_package(src_path):
+        # Directory is not a Python package/subpackage
+        # -> Nothing to do
+        return []
+    # Identify all subdirectories...
+    content = listdir(src_path)
+    dirs = [f for f in content if isdir(join(src_path, f))]
+    # ... and recursively create also the documentation for them
+    sub_pck = []
+    for directory in dirs:
+        sub_pck += _create_package_doc(
+            f"{pck}.{directory}", join(src_path, directory), doc_path
+        )
+
+    # Import package (__init__.py) and find all attribute names
+    module = import_module(pck)
+    attr_list = dir(module)
+    # Classify attribute names into classes and functions
+    class_list = [
+        attr
+        for attr in attr_list
+        # Do not document private classes
+        if attr[0] != "_"
+        # Check if object is a class
+        and isinstance(getattr(module, attr), type)
+    ]
+    func_list = [
+        attr
+        for attr in attr_list
+        # Do not document private classes
+        if attr[0] != "_"
+        # All functions are callable...
+        and callable(getattr(module, attr))
+        # ...but classes are also callable
+        and attr not in class_list
+    ]
+    # Create *.rst files
+    _create_package_page(doc_path, pck, class_list, func_list, sub_pck)
+    for class_name in class_list:
+        _create_class_page(doc_path, pck, class_name)
+    for function_name in func_list:
+        _create_function_page(doc_path, pck, function_name)
+
+    return [pck] + sub_pck
+
+
+def _create_package_page(doc_path, package_name, classes, functions, subpackages):
+    attributes = classes + functions
+
+    # Get categories for this package
+    try:
+        categories = _pck_categories[package_name]
+    except KeyError:
+        categories = {}
+    # Put all attributes that are not in any category
+    # into 'Miscellaneous' category
+    misc_attributes = []
+    for attr in attributes:
+        in_category = False
+        for categorized_attributes in categories.values():
+            if attr in categorized_attributes:
+                in_category = True
+        if not in_category:
+            misc_attributes.append(attr)
+    if len(misc_attributes) > 0:
+        # If no other categories exist, call the category 'Content'
+        misc_category_name = "Miscellaneous" if categories else "Content"
+        categories[misc_category_name] = misc_attributes
+
+    # String for categorized class and function enumeration
+    category_strings = []
+    for category, attrs in categories.items():
+        # Create string for each category
+        string = dedent(f"""
+
+            {category}
+            {"-" * len(category)}
+
+            .. autosummary::
+                :nosignatures:
+                :toctree:
+
+        """)
+        string += "\n".join([_INDENT + attr for attr in attrs])
+        category_strings.append(string)
+    # Concatenate strings
+    attributes_string = "\n".join(category_strings)
+
+    # String for subpackage enumeration
+    subpackages_string = "\n".join([_INDENT + pck for pck in subpackages])
+
+    # Assemble page
+    file_content = (
+        dedent(f"""
+
+        ``{package_name}``
+        {"=" * (len(package_name) + 4)}
+        .. currentmodule:: {package_name}
+
+        .. automodule:: {package_name}
+
+        .. currentmodule:: {package_name}
+
+    """)
+        + attributes_string
+    )
+    if len(subpackages) > 0:
+        file_content += (
+            dedent("""
+
+        Subpackages
+        -----------
+
+        .. autosummary::
+
+    """)
+            + subpackages_string
+        )
+    with open(join(doc_path, f"{package_name}.rst"), "w") as f:
+        f.write(file_content)
+
+
+def _create_class_page(doc_path, package_name, class_name):
+    file_content = dedent(f"""
+        :sd_hide_title: true
+
+        ``{class_name}``
+        {"=" * (len(class_name) + 4)}
+        .. autoclass:: {package_name}.{class_name}
+            :show-inheritance:
+            :members:
+            :member-order: bysource
+            :undoc-members:
+            :inherited-members:
+        .. minigallery:: {package_name}.{class_name}
+            :add-heading: Gallery
+            :heading-level: "
+    """)
+    with open(join(doc_path, f"{package_name}.{class_name}.rst"), "w") as f:
+        f.write(file_content)
+
+
+def _create_function_page(doc_path, package_name, function_name):
+    file_content = dedent(f"""
+        :sd_hide_title: true
+
+        ``{function_name}``
+        {"=" * (len(function_name) + 4)}
+        .. autofunction:: {package_name}.{function_name}
+        .. minigallery:: {package_name}.{function_name}
+            :add-heading: Gallery
+            :heading-level: "
+    """)
+    with open(join(doc_path, f"{package_name}.{function_name}.rst"), "w") as f:
+        f.write(file_content)
+
+
+def _create_package_index(doc_path, package_list):
+    # String for package enumeration
+    packages_string = "\n".join([_INDENT + pck for pck in sorted(package_list)])
+
+    file_content = (
+        dedent("""
+        API Reference
+        =============
+
+        .. autosummary::
+            :toctree:
+
+    """)
+        + packages_string
+    )
+    with open(join(doc_path, "index.rst"), "w") as f:
+        f.write(file_content)
+
+
+def _is_package(path):
+    content = listdir(path)
+    return "__init__.py" in content
+
+
+def skip_nonrelevant(app, what, name, obj, skip, options):
+    """
+    Skip all class members, that are not methods, enum values or inner
+    classes, since other attributes are already documented in the class
+    docstring.
+
+    Furthermore, skip all class members, that are inherited from
+    non-Biotite base classes.
+    """
+    if skip:
+        return True
+    if not _is_relevant_type(obj):
+        return True
+    if obj.__module__ is None:
+        # Some built-in functions have '__module__' set to None
+        return True
+    package_name = obj.__module__.split(".")[0]
+    if package_name != "biotite":
+        return True
+    return False
+
+
+def _is_relevant_type(obj):
+    if type(obj).__name__ == "method_descriptor":
+        # These are some special built-in Python methods
+        return False
+    return (
+        (
+            # Functions
+            type(obj)
+            in [types.FunctionType, types.BuiltinFunctionType, types.MethodType]
+        )
+        | (
+            # Functions from C-extensions and wrapped functions
+            type(obj).__name__
+            in [
+                "cython_function_or_method",
+                "fused_cython_function",
+                "_lru_cache_wrapper",
+            ]
+        )
+        | (
+            # Enum instance
+            isinstance(obj, enum.Enum)
+        )
+        | (
+            # Inner class
+            isinstance(obj, type)
+        )
+    )

biotite/source/doc/bibliography.py

@@ -0,0 +1,79 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__author__ = "Patrick Kunzmann"
+
+import warnings
+from pybtex.richtext import HRef, Tag, Text
+from pybtex.style.formatting import BaseStyle
+
+
+class IEEEStyle(BaseStyle):
+    def format_article(self, param):
+        entry = param["entry"]
+
+        try:
+            authors = []
+            for author in entry.persons["author"]:
+                text = ""
+                if author.first_names is not None:
+                    text += " ".join([s[0] + "." for s in author.first_names])
+                    text += " "
+                if author.middle_names is not None:
+                    text += " ".join([s[0] + "." for s in author.middle_names])
+                    text += " "
+                if author.prelast_names is not None:
+                    text += " ".join([s for s in author.prelast_names])
+                    text += " "
+                text += " ".join([s for s in author.last_names])
+                authors.append(Text(text + ", "))
+
+            title = ""
+            in_protected = False
+            for char in entry.fields["title"]:
+                if char == "{":
+                    in_protected = True
+                elif char == "}":
+                    in_protected = False
+                else:
+                    if in_protected:
+                        title += char
+                    else:
+                        # Capitalize title in unprotected areas
+                        if len(title) == 0:
+                            title += char.upper()
+                        else:
+                            title += char.lower()
+            title = Text('"', title, '," ')
+
+            journal = Text(Tag("em", entry.fields["journal"]), ", ")
+
+            if "volume" in entry.fields:
+                volume = Text("vol. ", entry.fields["volume"], ", ")
+            else:
+                volume = Text()
+
+            if "pages" in entry.fields:
+                pages = Text("pp. ", entry.fields["pages"], ", ")
+            else:
+                pages = Text()
+
+            date = entry.fields["year"]
+            if "month" in entry.fields:
+                date = entry.fields["month"] + " " + date
+            date = Text(date, ". ")
+
+            if "doi" in entry.fields:
+                doi = Text(
+                    "doi: ",
+                    HRef("https://doi.org/" + entry.fields["doi"], entry.fields["doi"]),
+                )
+            else:
+                doi = Text()
+
+            return Text(*authors, title, journal, volume, pages, date, doi)
+
+        except Exception:
+            warnings.warn(f"Invalid BibTeX entry '{entry.key}'")
+            return Text(entry.key)

biotite/source/doc/conf.py

@@ -0,0 +1,228 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__author__ = "Patrick Kunzmann"
+
+# Setup Cython for import of uncompiled *.pyx files
+import numpy as np
+import pyximport
+
+pyximport.install(
+    setup_args={"include_dirs": np.get_include()}, build_in_temp=False, language_level=3
+)
+
+import sys
+import warnings
+from os.path import dirname, join, realpath
+import matplotlib
+import pybtex
+from sphinx_gallery.sorting import ExplicitOrder, FileNameSortKey
+import biotite
+
+BIOTITE_DOMAIN = "www.biotite-python.org"
+DOC_PATH = dirname(realpath(__file__))
+PACKAGE_PATH = join(dirname(DOC_PATH), "src")
+
+
+# Include biotite/doc in PYTHONPATH
+# in order to import modules for API doc generation etc.
+sys.path.insert(0, DOC_PATH)
+import apidoc
+import bibliography
+import preamble
+import scraper
+import switcher
+import viewcode
+
+# Reset matplotlib params
+matplotlib.rcdefaults()
+
+# Pregeneration of files
+apidoc.create_api_doc(PACKAGE_PATH, join(DOC_PATH, "apidoc"))
+switcher.create_switcher_json(join("static", "switcher.json"), "v0.41.0", n_versions=5)
+
+# Use custom citation style
+pybtex.plugin.register_plugin("pybtex.style.formatting", "ieee", bibliography.IEEEStyle)
+
+#### Source code link ###
+
+linkcode_resolve = viewcode.linkcode_resolve
+
+#### General ####
+
+
+# Removed standard matplotlib warning when generating gallery
+warnings.filterwarnings(
+    "ignore",
+    category=UserWarning,
+    message="Matplotlib is currently using agg, which is a non-GUI backend, "
+    "so cannot show the figure.",
+)
+
+extensions = [
+    "jupyter_sphinx",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.linkcode",
+    "sphinx.ext.intersphinx",
+    "sphinxcontrib.bibtex",
+    "sphinx_gallery.gen_gallery",
+    "sphinx_design",
+    "sphinx_copybutton",
+    "notfound.extension",
+    "numpydoc",
+]
+
+templates_path = ["templates"]
+source_suffix = [".rst"]
+master_doc = "index"
+
+project = "Biotite"
+copyright = "The Biotite contributors"
+version = biotite.__version__
+release = biotite.__version__
+
+exclude_patterns = [
+    # These are automatically incorporated by sphinx_gallery
+    "examples/scripts/**/README.rst",
+    # Execution times are not reported to the user
+    "sg_execution_times.rst",
+]
+# Do not run tutorial code if gallery generation is disabled
+if "plot_gallery=0" in sys.argv:
+    exclude_patterns.append("tutorial/**/*.rst")
+
+pygments_style = "sphinx"
+
+todo_include_todos = False
+
+# Prevents numpydoc from creating an autosummary which does not work
+# properly due to Biotite's import system
+numpydoc_show_class_members = False
+
+# Prevent autosummary from using sphinx-autogen, since it would
+# overwrite the document structure given by apidoc.json
+autosummary_generate = False
+
+bibtex_bibfiles = ["references.bib"]
+bibtex_default_style = "ieee"
+
+notfound_urls_prefix = "/latest/"
+
+intersphinx_mapping = {
+    "rdkit": ("https://www.rdkit.org/docs/", None),
+    "openmm": ("http://docs.openmm.org/latest/api-python/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+}
+intersphinx_timeout = 60
+
+
+#### HTML ####
+
+html_theme = "pydata_sphinx_theme"
+
+html_static_path = ["static"]
+html_css_files = ["biotite.css", "fonts.css"]
+html_title = "Biotite"
+html_logo = "static/assets/general/biotite_logo.svg"
+html_favicon = "static/assets/general/biotite_icon_32p.png"
+html_baseurl = f"https://{BIOTITE_DOMAIN}/latest/"
+html_theme_options = {
+    "navbar_start": ["navbar-logo", "version-switcher"],
+    "switcher": {
+        "json_url": f"https://{BIOTITE_DOMAIN}/latest/_static/switcher.json",
+        "version_match": version,
+    },
+    "show_version_warning_banner": True,
+    "header_links_before_dropdown": 7,
+    "pygment_light_style": "friendly",
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/biotite-dev/biotite",
+            "icon": "fa-brands fa-github",
+            "type": "fontawesome",
+        },
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/biotite/",
+            "icon": "fa-solid fa-box-open",
+            "type": "fontawesome",
+        },
+        {
+            "name": "News",
+            "url": "https://biotite.bsky.social",
+            "icon": "fa-brands fa-bluesky",
+            "type": "fontawesome",
+        },
+    ],
+    "use_edit_page_button": True,
+    "show_prev_next": False,
+    "show_toc_level": 2,
+}
+html_sidebars = {
+    # No primary sidebar for these pages
+    "extensions": [],
+    "install": [],
+    "contribute": [],
+    "logo": [],
+}
+html_context = {
+    "github_user": "biotite-dev",
+    "github_repo": "biotite",
+    "github_version": "master",
+    "doc_path": "doc",
+}
+
+sphinx_gallery_conf = {
+    "examples_dirs": ["examples/scripts/sequence", "examples/scripts/structure"],
+    "gallery_dirs": ["examples/gallery/sequence", "examples/gallery/structure"],
+    "subsection_order": ExplicitOrder(
+        [
+            "examples/scripts/sequence/homology",
+            "examples/scripts/sequence/sequencing",
+            "examples/scripts/sequence/profile",
+            "examples/scripts/sequence/annotation",
+            "examples/scripts/sequence/misc",
+            "examples/scripts/structure/protein",
+            "examples/scripts/structure/nucleotide",
+            "examples/scripts/structure/molecule",
+            "examples/scripts/structure/contacts",
+            "examples/scripts/structure/modeling",
+            "examples/scripts/structure/alphabet",
+            "examples/scripts/structure/misc",
+        ]
+    ),
+    "within_subsection_order": FileNameSortKey,
+    # Do not run example scripts with a trailing '_noexec'
+    "filename_pattern": "^((?!_noexec).)*$",
+    "ignore_pattern": r"(.*ignore\.py)",
+    "download_all_examples": False,
+    # Never report run time
+    "min_reported_time": sys.maxsize,
+    "default_thumb_file": join(
+        DOC_PATH, "static/assets/general/biotite_icon_thumb.png"
+    ),
+    "capture_repr": (),
+    "image_scrapers": (
+        "matplotlib",
+        scraper.static_image_scraper,
+        scraper.pymol_scraper,
+    ),
+    "matplotlib_animations": True,
+    "image_srcset": ["2x"],
+    "backreferences_dir": "examples/backreferences",
+    "doc_module": ("biotite",),
+    "reset_modules": (preamble.setup_script),
+    "remove_config_comments": True,
+}
+
+
+#### App setup ####
+
+
+def setup(app):
+    app.connect("autodoc-skip-member", apidoc.skip_nonrelevant)

biotite/source/doc/contribution/deployment.rst

@@ -0,0 +1,23 @@
+Deployment of a new release
+===========================
+This section describes how to create and deploy a release build of the *Biotite*
+package and documentation.
+Therefore, this section primarily addresses the maintainers of the project.
+
+Creating a new release
+----------------------
+When a new *GitHub* release is created, the CI jobs building the distributions
+and documentation in ``test_and_deploy.yml`` are triggered.
+After the successful completion of these jobs, the artifacts are added to the
+release.
+The distributions for different platforms and Python versions are automatically
+uploaded to *PyPI*.
+The documentation is also uploaded to this website via the CI.
+
+Conda release
+-------------
+Some time after the release on GitHub, the ``conda-forge`` bot will also create
+an automatic pull request for the new release of the
+`Conda package <https://github.com/conda-forge/biotite-feedstock>`_.
+If no dependencies changed, this pull request can usually be merged without
+further effort.

biotite/source/doc/contribution/development.rst

@@ -0,0 +1,201 @@
+Writing source code
+===================
+
+Scope
+-----
+The scope of *Biotite* includes methods that make up the backbone of
+computational molecular biology. Thus, new functionalities added to
+*Biotite* should be relatively general and well established.
+
+Code of which the purpose is too special could be published as
+:ref:`extension package <extension_packages>` instead.
+
+Consistency
+-----------
+New functionalities should act on the existing central classes, if applicable
+to keep the code as uniform as possible.
+Specifically, these include
+
+- :class:`biotite.structure.AtomArray`,
+- :class:`biotite.structure.AtomArrayStack`,
+- :class:`biotite.structure.BondList`,
+- :class:`biotite.sequence.Sequence` and its subclasses,
+- :class:`biotite.sequence.Alphabet`,
+- :class:`biotite.sequence.Annotation`,
+  including :class:`biotite.sequence.Feature`
+  and :class:`biotite.sequence.Location`,
+- :class:`biotite.sequence.AnnotatedSequence`,
+- :class:`biotite.sequence.Profile`,
+- :class:`biotite.sequence.align.Alignment`,
+- :class:`biotite.application.Application` and its subclasses,
+- and in general :class:`numpy.ndarray`.
+
+If you think that the currently available classes miss a central *object*
+in bioinformatics, you might consider opening an issue on *GitHub* or reach
+out to the maintainers.
+
+Small *helper classes* for a functionality (for example an :class:`Enum` for a
+function parameter) is also permitted, as long as it does not introduce a
+redundancy with the classes mentioned above.
+
+Python version and interpreter
+------------------------------
+The package supports all minor Python versions released in the last
+42 months
+(`NEP 29 <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_).
+In consequence, language features that were introduced after the oldest
+supported Python version are not allowed.
+This time span balances the support for older Python versions as well as
+the ability to use more recent features of the programming language.
+
+Furthermore, this package is currently made for usage with CPython.
+Official support for PyPy might be added someday.
+
+Code style
+----------
+*Biotite* is compliant with :pep:`8` and uses `Ruff <https://docs.astral.sh/ruff/>`_ for
+code formatting and linting.
+The maximum line length is 88 characters.
+An exception is made for docstring lines, if it is not possible to use a
+maximum of 88 characters (e.g. tables and parameter type descriptions).
+To make code changes ready for a pull request, simply run
+
+.. code-block:: console
+
+   $ ruff format
+   $ ruff check --fix
+
+and fix the remaining linter complaints.
+
+Dependencies
+------------
+*Biotite* aims to rely only on a few dependencies to keep the installation
+small.
+However optional dependencies for a specific dependency are also allowed if
+necessary.
+In this case add your special dependency to the list of extra
+requirements in ``install.rst``.
+The import statement for the dependency should be located directly inside the
+function or class, rather than module level, to ensure that the package is not
+required for any other functionality or for building the API documentation.
+
+An example for this approach are the plotting functions in
+:mod:`biotite.sequence.graphics`, that require *Matplotlib*.
+
+Code efficiency
+---------------
+The central aims of *Biotite* are that it is both, convenient and fast.
+Therefore, the code should be vectorized as much as possible using *NumPy*.
+In cases the problem cannot be reasonably or conveniently solved this way,
+writing modules in `Cython <https://cython.readthedocs.io/en/latest/>`_ is the
+preferred way to go.
+Writing extensions directly in C/C++ is discouraged due to the bad readability.
+Writing extensions in other programming languages
+(e.g. in *Rust* via `PyO3 <https://pyo3.rs>`_) is currently not permitted to
+keep the build process simple.
+
+Docstrings
+----------
+*Biotite* uses
+`numpydoc <https://numpydoc.readthedocs.io/en/latest/format.html>`_
+formatted docstrings for its documentation.
+These docstrings can be interpreted by *Sphinx* via the ``numpydoc`` extension.
+All publicly accessible attributes must be fully documented.
+This includes functions, classes, methods, instance and class variables and the
+``__init__`` modules:
+
+The ``__init__`` module documentation summarizes the content of the entire
+subpackage, since the single modules are not visible to the user.
+In the class docstring, the class itself is described and the constructor is
+documented.
+The publicly accessible instance variables are documented under the
+`Attributes` headline, while class variables are documented in their separate
+docstrings.
+Methods do not need to be summarized in the class docstring.
+
+The CI validates the docstrings using ``numpydoc lint``.
+However, this validation sometimes also raised false positives.
+Hence, to exclude a specific function/class from validation, add the name
+(or regular expression) to ``tool.numpydoc_validation.exclude`` in the
+``pyproject.toml``.
+
+
+Module imports
+--------------
+In *Biotite*, the user imports packages in contrast to single modules
+(similar to *NumPy*).
+In order for that to work, the ``__init__.py`` file of each *Biotite*
+subpackage needs to import all of its modules, whose content is publicly
+accessible, in a relative manner.
+
+.. code-block:: python
+
+   from .module1 import *
+   from .module2 import *
+
+Import statements should be the only statements in a ``__init__.py`` file.
+
+In case a module needs functionality from another subpackage of *Biotite*,
+use an absolute import as suggested by PEP 8.
+This import should target the module directly and not the package to avoid
+circular imports and thus an ``ImportError``.
+So import statements like the following are totally OK:
+
+.. code-block:: python
+
+   from biotite.subpackage.module import foo
+
+In order to prevent namespace pollution, all modules must define the `__all__`
+variable with all publicly accessible attributes of the module.
+
+Versioning
+----------
+Biotite adopts `Semantic Versioning <https://semver.org>`_ for its releases.
+This means that the version number is composed of three parts:
+
+- Major version: Incremented when incompatible API changes are made.
+- Minor version: Incremented when a new functionality is added in a backwards
+  compatible manner.
+- Patch version: Incremented when backwards compatible bug fixes are made.
+
+Note, that such backwards incompatible changes in minor/patch versions are only
+disallowed regarding the *public API*.
+This means that names and types of parameters and the type of the return value
+must not be changed in any function/class documented in the API reference.
+However, behavioral changes (especially small ones) are allowed.
+
+Although minor versions may not remove existing functionalities, they can
+deprecate them by
+
+- marking them as deprecated via a notice in the docstring and
+- raising a `DeprecationWarning` when a deprecated functionality is used.
+
+This gives the user a heads-up that the functionality will be removed soon.
+In the next major version, deprecated functionalities can be removed entirely.
+
+.. _extension_packages:
+
+Extension packages
+------------------
+*Biotite* extension packages are Python packages that provide further
+functionality for *Biotite* objects (:class:`AtomArray`, :class:`Sequence`,
+etc.)
+or offer objects that build up on these ones.
+
+There can be good reasons why one could choose to publish code as extension
+package instead of contributing it directly to the *Biotite* project:
+
+   - Independent development
+   - An incompatible license
+   - The code's use cases are too specialized
+   - Unsuitable dependencies
+   - Extensions written in a non-permitted programming language
+
+If your code fulfills the following conditions
+
+   - extends *Biotite* functionality
+   - is documented
+   - is well tested
+
+you can open an issue to ask for addition of the package to the
+:doc:`extension package page <../extensions>`.

biotite/source/doc/contribution/documentation.rst

@@ -0,0 +1,171 @@
+Writing the documentation
+=========================
+
+Having a good documentation on a package is arguably as important as the
+code itself.
+Hence, *Biotite* provides in addition to the API reference documented in
+docstrings, a comprehensive documentation residing in the ``doc/`` directory
+containing tutorials, examples and more.
+
+Documentation generation
+------------------------
+*Biotite* uses the widely used `Sphinx <https://www.sphinx-doc.org>`_ package
+for generating its documentation.
+Therefore, the documentation is based on *reStructuredText* files.
+The line length of these ``*.rst`` files is also limited to 79 characters
+where reasonable.
+
+To build the documentation, run from the root directory of the repository:
+
+.. code-block:: console
+
+    $ sphinx-build doc build/doc
+
+Documentation structure
+-----------------------
+*Biotite* employs the
+`Divio documentation system <https://documentation.divio.com>`_.
+In short, the documentation is split into four different parts that
+addresses different purposes and audiences:
+
+.. list-table:: Documentation sections
+    :widths: 10 20 20
+    :header-rows: 1
+
+    * - Part
+      - Summary
+      - Section in *Biotite*
+    * - `Tutorials <https://documentation.divio.com/tutorials.html>`_
+      - Learning of basic concepts via simple examples
+      - Tutorial
+    * - `How-to guides <https://documentation.divio.com/how-to.html>`_
+      - Step-by-step instructions for specific real-world tasks
+      - Example gallery
+    * - `Explanation <https://documentation.divio.com/explanation.html>`_
+      - Detailed explanation of concepts
+      - Literature citations, contributor guide
+    * - `Reference <https://documentation.divio.com/reference.html>`_
+      - Technical description in a consistent format
+      - API reference
+
+When adding new content, please consider which part of the documentation
+it fits best and adhere to the purpose of that part.
+You might also consider to split the content into multiple parts
+(e.g. into an example for the gallery and a tutorial), if you think your
+content fulfills a mixture of different purposes.
+
+.. _example_gallery:
+
+Example gallery
+---------------
+For gallery generation the package *sphinx-gallery* is used.
+Please refer to its
+`documentation <http://sphinx-gallery.readthedocs.io>`_
+for further information on script formatting.
+The example scripts are placed in ``doc/examples/scripts`` in the subdirectory
+that fits best topic of the example.
+Choose a title for the example that focuses on the employed method rather than
+the biological context.
+For example,
+'*Homology search and multiple sequence alignment of protein sequences*'
+would be a better name than
+'*Similarities of lysozyme variants*'.
+
+Building the example gallery for the first time may take a while, as all
+scripts are executed.
+To build the documentation without the gallery and the tutorial, run
+
+.. code-block:: console
+
+    $ sphinx-build -D plot_gallery=0 doc build/doc
+
+You may also ask the *Biotite* maintainers to run the example script and check
+the generated page, if building the gallery on your device is not possible.
+
+Static images
+^^^^^^^^^^^^^
+Static images can be included by adding the following comment in the
+corresponding code block:
+
+.. code-block:: python
+
+    # sphinx_gallery_static_image = <name_of_the_image>.png
+
+The image file must be stored in the same directory as the example script.
+
+Tutorial
+--------
+When adding new content for a broad audience, it is appreciated to update the
+tutorial pages (``doc/tutorial/``) as well.
+The tutorial uses `jupyter-sphinx <https://jupyter-sphinx.readthedocs.io>`_ to
+run the code snippets and show the results.
+This has the advantage that the output of code snippets is not static but
+dynamically generated based on the current state of the *Biotite* source
+code.
+
+Make sure to add
+
+.. code-block:: rst
+
+    .. include:: /tutorial/preamble.rst
+
+at the beginning of the tutorial page.
+
+API reference
+-------------
+Each  *Biotite* subpackage has a dedicated reference page, describing
+its classes and functions.
+The categories and classes/functions that are assigned to it can be set
+in ``doc/apidoc.json``.
+Classes/functions that are not assigned to any category are placed in
+the 'Miscellaneous' category or, if no class/function is assigned,
+in the 'Content' category.
+
+Citing articles
+---------------
+*Biotite* uses
+`sphinxcontrib-bibtex <https://sphinxcontrib-bibtex.readthedocs.io>`_ for
+creating references in docstrings, examples, etc.
+The references are stored in ``doc/references.bib`` with citation keys
+in ``[Author][year]`` format.
+References are cited with the ``:footcite:`` role and the bibliography
+is rendered where the ``.. footbibliography::`` directive is placed.
+
+Adding articles to bibliography
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+The recommended way to add articles to the bibliography is not to add them
+directly to ``references.bib``, but to update the *Biotite*
+`Zotero <https://www.zotero.org/>`_ library.
+As this step is a bit more involved, you may also ask the *Biotite* maintainers
+to add the article for you.
+
+After installation of *Zotero* and
+`Better BibTeX <https://retorque.re/zotero-better-bibtex/>`_, import the
+`Biotite library <https://www.zotero.org/groups/5533833/biotite_documentation>`_.
+Then, edit the citation format (``Preferences > Better BibTeX``):
+
+- ``Citation keys > Citation key formula``:
+
+  .. code-block:: none
+
+      auth.capitalize + year
+
+- ``Export > Fields > Fields to omit from export``:
+
+  .. code-block:: none
+
+      file, langid, abstract, urldate, copyright, keywords, annotation
+
+- ``Export > Export unicode as plain text latex commands``: uncheck
+
+To update ``references.bib``, export the library as ``Better BibTeX``.
+
+Setting NCBI API key
+--------------------
+The example gallery as well as the tutorial use :mod:`biotite.database.entrez`
+to fetch sequence data.
+Hence, these scripts may raise a ``RequestError`` due to
+a hight number of requests to the NCBI Entrez database.
+This can be fixed by exporting the ``NCBI_API_KEY`` environment variable,
+containing an
+`NCBI API key <https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/>`_.

biotite/source/doc/contribution/index.rst

@@ -0,0 +1,66 @@
+.. This source code is part of the Biotite package and is distributed
+   under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+   information.
+
+Contributor guide
+=================
+
+As the aim of *Biotite* is to create a comprehensive library, we welcome
+developers who would like to extend the package with new functionalities or
+improve existing code.
+Contributing new examples to the gallery or improving the documentation
+in general is also highly appreciated.
+
+The complete development workflow is hosted on
+`GitHub <https://github.com/biotite-dev/biotite>`_.
+This is also the place where you would post feature propositions,
+questions, bug reports, etc.
+
+If you are interested in improving *Biotite*, you feel free to join our chat on
+`Discord <https://discord.gg/cUjDguF>`_.
+We are happy to answer questions, discuss ideas and provide mentoring for
+newcomers.
+Alternatively, you can also contact `<padix.key@gmail.com>`_.
+A good place to find projects to start with are the
+`Open Issues <https://github.com/biotite-dev/biotite/issues>`_ and
+the `Project Boards <https://github.com/biotite-dev/biotite/projects>`_.
+
+The following pages should explain development guidelines in
+order to keep *Biotite*'s source code consistent.
+Finally, the :doc:`deployment` describes the process of releasing a new
+version of *Biotite*.
+
+Requirements
+------------
+
+Development of *Biotite* requires a few packages in addition to the ones
+specified in
+`pyproject.toml <http://raw.githubusercontent.com/biotite-dev/biotite/master/pyproject.toml>`_.
+The full list is provided in
+`environment.yml <http://raw.githubusercontent.com/biotite-dev/biotite/master/environment.yml>`_.
+If you use the `Conda <https://docs.conda.io>`_ package manager, you can simply
+create a environment with all required dependencies by running
+
+.. code-block:: console
+
+   $ conda env create -f environment.yml
+   $ conda activate biotite-dev
+
+Contributing examples
+---------------------
+
+Do you have an application of *Biotite* and you want to share it with the
+world?
+Then the example gallery is the way to go.
+Head directly to the :ref:`gallery section <example_gallery>` to learn how to
+contribute.
+
+
+.. toctree::
+    :maxdepth: 1
+    :hidden:
+
+    development
+    testing
+    documentation
+    deployment

biotite/source/doc/contribution/testing.rst

@@ -0,0 +1,82 @@
+Testing the package
+===================
+
+In-development tests
+--------------------
+While developing a new feature or fixing a bug, it is handy to run a test
+script against the code you are working on.
+To ensure that the imported package ``biotite`` points to the code you are
+working on, you may want to install the local repository clone in *editable*
+mode:
+
+.. code-block:: console
+
+    $ pip install -e .
+
+If you are writing or using an extension module in *Cython*, consider using
+`pyximport <https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#compiling-with-pyximport>`_
+at the beginning of the script you use for testing.
+
+.. code-block:: python
+
+    import numpy as np
+    import pyximport
+    pyximport.install(
+        build_in_temp=False,
+        setup_args={"include_dirs":np.get_include()},
+        language_level=3
+    )
+
+To enforce the recompilation of the changed *Cython* module, delete the
+respective compiled module (``.dll`` or ``.so``) from the ``src/`` directory,
+if already existing.
+
+Unit tests
+----------
+The backbone of testing *Biotite* are the unit tests in the ``tests``
+directory.
+`Pytest <https://docs.pytest.org>`_ is used as the testing framework.
+To run the tests, install the local repository clone (in editable mode) and
+run the tests:
+
+.. code-block:: console
+
+   $ pip install -e ".[test]"
+   $ pytest
+
+Benchmarks
+----------
+As outlined before, computation speed is one of the project's main goals.
+Therefore `CodSpeed <https://docs.codspeed.io>`_ benchmarks are used to ensure code
+changes do not decrease the performance.
+The benchmarks are simply ``pytest`` functions residing in the separate ``benchmarks/``
+directory, with the addition of the ``@pytest.mark.parametrize.benchmark`` decorator.
+These can also run with the ``pytest`` command, to ensure that they work.
+However, the actual benchmarking is done by the respective CI job.
+
+If you introduce a change that might significantly affect the performance of a function,
+please add a benchmark function, which runs the affected code, first and create a draft
+pull request.
+This will benchmark the code without the change.
+Afterwards, add and push the actual code change.
+This way, one can compare the performance of the code before and after the change.
+
+Doctests
+--------
+For simple tests checking that some code simply does not raise an exception
+and produces some predefined output,
+`doctests <https://docs.python.org/3/library/doctest.html>`_ are suitable.
+They are part of the docstrings of the corresponding functions and classes.
+The doctests fulfill two purposes:
+They are automatically executed by ``pytest`` via the
+``tests/test_doctests.py`` module and give users reading the API reference
+easily understandable examples how a function/class works.
+
+Testing visualizations
+----------------------
+Testing visualization functions (e.g. in :mod:`biotite.sequence.graphics`) is
+difficult, because the output can hardly be checked against some reference
+value.
+To still have at least some confirmation that these functions produce the
+expected output, it is mandatory to have at least one example using that
+function in the :ref:`gallery <example_gallery>`.

biotite/source/doc/examples/download/Array_Seq.txt

@@ -0,0 +1,94 @@
+>FCR3  AAQ73926.1 erythrocyte membrane protein 1 [Plasmodium falciparum] 2712 bp
+GSGSGSGMDSTSTIANKIEEYLGAKSDDSKIDELLKADPSEVEYYRSGGDGDYLKNNICK
+ITVNHSDSGKYDPCEKKLPPYDDNDQWKCQQNSSDGSGKPENICVPPRRERLCTYNLENL
+KFDKIRDNNAFLADVLLTARNEGEKIVQNHPDTNSSNVCNALERSFADLADIIRGTDQWK
+GTNSNLEKNLKQMFAKIRENDKVLQDKYPKDQKYTKLREAWWNANRQKVWEVITCGARSN
+DLLIKRGWRTSGKSDRKKNFELCRKCGHYEKEVPTKLDYVPQFLRWLTEWIEDFYREKQN
+LIDDMERHREECTREDHKSKEGTSYCSTCKDKCKKYCECVKKWKTEWENQENKYKDLYEQ
+NKNKTSQKNTSRYDDYVKDFFEKLEANYSSLENYIKGDPYFAEYATKLSFILNPSDANNP
+SGETANHNDEACNCNESGISSVGQAQTSGPSSNKTCITHSSIKTNKKKECKDVKLGVREN
+DKDLKICVIEDTSLSGVDNCCCQDLLGILQENCSDNKRGSSSNDSCDNKNQDECQKKLEK
+VFASLTNGYKCDKCKSGTSRSKKKWIWKKSSGNEEGLQEEYANTIGLPPRTQSLYLGNL
+PKLENVCEDVKDINFDTKEKFLAGCLIVSFHEGKNLKKRYPQNKNSGNKENLCK
+ALEYSFADYGDLIKGTSIWDNEYTKDLELNLQNNFGKLFGKYIKKNNTAEQDTSYSSLDE
+LRESWWNTNKKYIWTAMKHGAEMNITTCNADGSVTGSGSSCDDIPTIDLIPQYLRFLQEW
+VENFCEQRQAKVKDVITNCKSCKESGNKCKTECKTKCKDECEKYKKFIEACGTAGGGIGT
+AGSPWSKRWDQIYKRYSKHIEDAKRNRKAGTKNCGTSSTTNAAASTDENKCVQSDIDSFF
+KHLIDIGLTTPSSYLSNVLDDNICGADKAPWTTYTTYTTTEKCNKERDKSKSQSSDTLVV
+VNVPSPLGNTPYRYKYACQCKIPTNEETCDDRKEYMNQWSCGSARTMKRGYKNDNYELCK
+YNGVDVKPTTVRSNSSKLDGNDVTFFNLFEQWNKEIQYQIEQYMTNANISCIDEKEVLDS
+VSDEGTPKVRGGYEDGRNNNTDQGTNCKEKCKCYKLWIEKINDQWGKQKDNYNKFRSKQI
+YDANKGSQNKKVVSLSNFLFFSCWEEYIQKYFNGDWSKIKNIGSDTFEFLIKKCGNNSAH
+GEEIFNEKLKNAEKKCKENESTDTNINKSETSCDLNATNYIRGCQSKTYDGKIFPGKGGE
+KQWICKDTIIHGDTNGACIPPRTQNLCVGELWDKSYGGRSNIKNDTKELLKEKIKNAIHK
+ETELLYEYHDTGTAIISKNDKKGQKGKNDPNGLPKGFCHAVQRSFIDYKNMILGTS
+VNIYEHIGKLQEDIKKIIEKGTPQQKDKIGGVGSSTENVNAWWKGIEREMWDAVRCAITK
+INKKNNNSIFNGDECGVSPPTGNDEDQSVSWFKEWGEQFCIERLRYEQNIREACTINGK
+NEKKCINSKSGQGDKIQGACKRKCEKYKKYISEKKQEWDKQKTKYENKYVGKSASDLLKE
+NYPECISANFDFIFNDNIEYKTYYPYGDYSSICSCEQVKYYKYNNAEKKNNKSLCYEKDN
+DMTWSKKYIKKLENGRSLEGVYVPPRRQQLCLYELFPIIIKNEEGMEKAKEELLETLQIV
+AEREAYYLWKQYNPTGKGIDDANKKACCAIRGSFYDLEDIIKGNDLVHDEYTKYIDSKLN
+EIFGSSDTNDIDTKRARTDWWENETITNGTDRKTIRQLVWDAMQSGVRYAVEE
+KNENFPLCMGVEHIGIAKPQFIRWLEEWTNEFCEKYTKYFEDMKSKCDPPKRAD
+TCGDNSNIECKKACANYTNWLNPKRIEWNGMSNYYNKIYRKSNKESEGGKDYSMIMAPTV
+IDYLNKRCHGEINGNYICCSCKNIGAYNTTSGTVNKKLQKKETECEEEKGPLDLMNEVLN
+KMDKKYSAHKMKCTEVYLEHVEEQLNEIDNAIKDYKLYPLDRCFDDQTKMKVCDLIADAI
+GCKDKTKLDELDEWNDMDLRGTYNKHKGVLIPPRRRQLCFSRIVRGPANLRSLNEFKEEI
+LKGAQSEGKFLGNYYKEHKDKEKALEAMKNSFYDYEDIIKGTDMLTNIEFKDIKIKLDRL
+LEKETNNTKKAEDWWKTNKKSIWNAMLCGYKKSGNKIIDPSWCTIPTTETPPQFLRWIKE
+WGTNVCIQKQEHKEYVKSKCSNVTNLGAQASESNNCTSEIKKYQEWSRKRSIRWETISKR
+YKKYKRMDILKDVKEPDANTYLREHCSKCPCGFNDMEEMNNNEDNEKEAFK
+QIKEQVKIPAELEDVIYRIKHHEYDKGNDYICNKYKNIHDRMKKNNGNFVTDNFVKKSWE
+ISNGVLIPPRRKNLFLYIDPSKICEYKKDPKLFKDFIYWSAFTEVERLKKAYGGARAKVV
+HAMKYSFTDIGSIIKGDDMMEKNSSDKIGKILGDTDGQNEKRKKWWDMNKYHIWESMLCG
+YREAEGDTETNENCRFPDIESVPQFLRWFQEWSENFCDRRQKLYDKLNSECISAEC
+TNGSVDNSKCTHACVNYKNYILTKKTEYEIQTNKYDNEFKNKNSNDKDAPDYLKEKCNDN
+KCECLNKHIDDKNKTWKNPYETLEDTFKSKCDCPKPLPSPIKPDDLPPQADEPFDPTIL
+QTTIPGSGSGSG
+>NF54 EWC87419.1 hypothetical protein PFNF54_03544 [Plasmodium falciparum NF54] 2712 bp
+GSGSGSGMDKSSIANKIEAYLGAKSDDSKIDQSLKADPSEVQYYGSGGDGYYLRKNICK
+ITVNHSDSGTNDPCDRIPPPYGDNDQWKCAIILSKVSEKPENVFVPPRRQRMCINNLEKL
+NVDKIRDKHAFLADVLLTARNEGERIVQNHPDTNSSNVCNALERSFADIADIIRGTDLWK
+GTNSNLEQNLKQMFAKIRENDKVLQDKYPKDQNYRKLREDWWNANRQKVWEVITCGARSN
+DLLIKRGWRTSGKSNGDNKLELCRKCGHYEEKVPTKLDYVPQFLRWLTEWIEDFYREKQN
+LIDDMERHREECTSEDHKSKEGTSYCSTCKDKCKKYCECVKKWKSEWENQKNKYTELYQQ
+NKNETSQKNTSRYDDYVKDFFKKLEANYSSLENYIKGDPYFAEYATKLSFILNSSDANNP
+SEKIQKNNDEVCNCNESGIASVEQEQISDPSSNKTCITHSSIKANKKKVCKHVKLGVREN
+DKDLRVCVIEHTSLSGVENCCCQDFLRILQENCSDNKSGSSSNGSCNNKNQEACEKNLEK
+VLASLTNCYKCDKCKSEQSKKNNKNWIWKKSSGKEGGLQKEYANTIGLPPRTQSLCL
+VVCLDEKGKKTQELKNIRTNSELLKEWIIAAFHEGKNLKPSHEKKNDDNGKKLCK
+ALEYSFADYGDLIKGTSIWDNEYTKDLELNLQKIFGKLFRKYIKKNNTAEQDTSYSSLDE
+LRESWWNTNKKYIWLAMKHGAGMNSTTCCGDGSVTGSGSSCDDIPTIDLIPQYLRFLQEW
+VEHFCKQRQEKVKPVIENCKSCKESGGTCNGECKTECKNKCEVYKKFIEDCKGGDGT
+AGSSWVKRWDQIYKRYSKYIEDAKRNRKAGTKNCGPSSTTNAAENKCVQSDIDSFF
+KHLIDIGLTTPSSYLSIVLDDNICGADKAPWTTYTTYTTTEKCNKETDKSKLQQCNTAVV
+VNVPSPLGNTPHGYKYACQCKIPTNEETCDDRKEYMNQWSCGSARTMKRGYKNDNYELCK
+YNGVDVKPTTVRSNSSKLDDKDVTFFNLFEQWNKEIQYQIEQYMTNTKISCNNEKNVLSR
+VSDEAAQPKFSDNERDRNSITHEDKNCKEKCKCYSLWIEKINDQWDKQKDNYNKFQRKQI
+YDANKGSQNKKVVSLSNFLFFSCWEEYIQKYFNGDWSKIKNIGSDTFEFLIKKCGNDSGD
+GETIFSEKLNNAEKKCKENESTNNKMKSSETSCDCSEPIYIRGCQPKIYDGKIFPGKGGE
+KQWICKDTIIHGDTNGACIPPRTQNLCVGELWDKRYGGRSNIKNDTKESLKQKIKNAIQK
+ETELLYEYHDKGTAIISRNPMKGQKEKEEKNNDSNGLPKGFCHAVQRSFIDYKNMILGTS
+VNIYEYIGKLQEDIKKIIEKGTTKQNGKTVGSGAENVNAWWKGIEGEMWDAVRCAITK
+INKKQKKNGTFSIDECGIFPPTGNDEDQSVSWFKEWSEQFCIERLQYEKNIRDACTNN
+GQGDKIQGDCKRKCEEYKKYISEKKQEWDKQKTKYENKYVGKSASDLLKE
+NYPECISANFDFIFNDNIEYKTYYPYGDYSSICSCEQVKYYEYNNAEKKNNKSLCHEKGN
+DRTWSKKYIKKLENGRTLEGVYVPPRRQQLCLYELFPIIIKNKNDITNAKKELLETLQIV
+AEREAYYLWKQYHAHNDTTYLAHKKACCAIRGSFYDLEDIIKGNDLVHDEYTKYIDSKLN
+EIFDSSNKNDIETKRARTDWWENEAIAVPNITGANKSDPKTIRQLVWDAMQSGVRKAIDE
+EKEKKKPNENFPPCMGVQHIGIAKPQFIRWLEEWTNEFCEKYTKYFEDMKSNCNLRKGAD
+DCDDNSNIECKKACANYTNWLNPKRIEWNGMSNYYNKIYRKSNKESEDGKDYSMIMEPTV
+IDYLNKRCNGEINGNYICCSCKNIGENSTSGTVNKKLQKKETQCEDNKGPLDLMNKVLN
+KMDPKYSEHKMKCTEVYLEHVEEQLKEIDNAIKDYKLYPLDRCFDDKSKMKVCDLIGDAI
+GCKHKTKLDELDEWNDVDMRDPYNKYKGVLIPPRRRQLCFSRIVRGPANLRNLKEFKEEI
+LKGAQSEGKFLGNYYNEDKDKEKALEAMKNSFYDYEYIIKGSDMLTNIQFKDIKRKLDRL
+LEKETNNTEKVDDWWETNKKSIWNAMLCGYKKSGNKIIDPSWCTIPTTETPPQFLRWIKE
+WGTNVCIQKEEHKEYVKSKCSNVTNLGAQESESKNCTSEIKKYQEWSRKRSIQWEAISEG
+YKKYKGMDEFKNTFKNIKEPDANEPNANEYLKKHCSKCPCGFNDMQEITKYTNIGNEAFK
+QIKEQVDIPAELEDVIYRLKHHEYDKGNDYICNKYKNINVNMKKNNDDTWTDLVKNSSD
+INKGVLLPPRRKNLFLKIDESDICKYKRDPKLFKDFIYSSAISEVERLKKVYGEAKTKVV
+HAMKYSFADIGSIIKGDDMMENNSSDKIGKILGDGVGQNEKRKKWWDMNKYHIWESMLCG
+YKHAYGNISENDRKMLDIPNNDDEHQFLRWFQEWTENFCTKRNELYENMVTACNSAKCNT
+SNGSVDKKECTEACKNYSNFILIKKKEYQSLNSQYDMNYKETKAEKKESPEYFKDKCNG
+ECSCLSEYFKDETRWKNPYETLDDTEVKNNCMCKPPPPASNNTSDIL
+QKTIPGSGSGSG

biotite/source/doc/examples/download/FCR3_10ug.csv

@@ -0,0 +1,2655 @@
+Seq,r1,r2
+GSGSGSGMDSTSTIANKIEE,0,0
+SGSGSGMDSTSTIANKIEEY,0,78
+GSGSGMDSTSTIANKIEEYL,0,0
+SGSGMDSTSTIANKIEEYLG,0,0
+GSGMDSTSTIANKIEEYLGA,0,4
+SGMDSTSTIANKIEEYLGAK,1,1
+GMDSTSTIANKIEEYLGAKS,0,0
+MDSTSTIANKIEEYLGAKSD,0,0
+DSTSTIANKIEEYLGAKSDD,1,0
+STSTIANKIEEYLGAKSDDS,4,3.5
+TSTIANKIEEYLGAKSDDSK,5,0
+STIANKIEEYLGAKSDDSKI,2,0
+TIANKIEEYLGAKSDDSKID,0,0
+IANKIEEYLGAKSDDSKIDE,0,0
+ANKIEEYLGAKSDDSKIDEL,0,0
+NKIEEYLGAKSDDSKIDELL,0,2
+KIEEYLGAKSDDSKIDELLK,5,0
+IEEYLGAKSDDSKIDELLKA,0,0
+EEYLGAKSDDSKIDELLKAD,0,0
+EYLGAKSDDSKIDELLKADP,0,0
+YLGAKSDDSKIDELLKADPS,0,0
+LGAKSDDSKIDELLKADPSE,1.5,0
+GAKSDDSKIDELLKADPSEV,0,4
+AKSDDSKIDELLKADPSEVE,0,1
+KSDDSKIDELLKADPSEVEY,0,1
+SDDSKIDELLKADPSEVEYY,0,2
+DDSKIDELLKADPSEVEYYR,0,0
+DSKIDELLKADPSEVEYYRS,0,2
+SKIDELLKADPSEVEYYRSG,1,4
+KIDELLKADPSEVEYYRSGG,0,2
+IDELLKADPSEVEYYRSGGD,1,7
+DELLKADPSEVEYYRSGGDG,1,5
+ELLKADPSEVEYYRSGGDGD,0,0
+LLKADPSEVEYYRSGGDGDY,0,0
+LKADPSEVEYYRSGGDGDYL,0,0
+KADPSEVEYYRSGGDGDYLK,2,0
+ADPSEVEYYRSGGDGDYLKN,0,0
+DPSEVEYYRSGGDGDYLKNN,0,0
+PSEVEYYRSGGDGDYLKNNI,0,7
+SEVEYYRSGGDGDYLKNNIC,0,4
+EVEYYRSGGDGDYLKNNICK,0,0
+VEYYRSGGDGDYLKNNICKI,0,2
+EYYRSGGDGDYLKNNICKIT,0,0
+YYRSGGDGDYLKNNICKITV,0,0
+YRSGGDGDYLKNNICKITVN,0,1
+RSGGDGDYLKNNICKITVNH,0,0
+SGGDGDYLKNNICKITVNHS,5,0
+GGDGDYLKNNICKITVNHSD,0,1
+GDGDYLKNNICKITVNHSDS,0,0
+DGDYLKNNICKITVNHSDSG,0,0
+GDYLKNNICKITVNHSDSGK,0,0
+DYLKNNICKITVNHSDSGKY,1,9
+YLKNNICKITVNHSDSGKYD,2,4
+LKNNICKITVNHSDSGKYDP,0,0
+KNNICKITVNHSDSGKYDPC,0,0
+NNICKITVNHSDSGKYDPCE,0,0
+NICKITVNHSDSGKYDPCEK,0,0
+ICKITVNHSDSGKYDPCEKK,87.5,98
+CKITVNHSDSGKYDPCEKKL,2.5,99.5
+KITVNHSDSGKYDPCEKKLP,0,5
+ITVNHSDSGKYDPCEKKLPP,1,6
+TVNHSDSGKYDPCEKKLPPY,7,0
+VNHSDSGKYDPCEKKLPPYD,0,3
+NHSDSGKYDPCEKKLPPYDD,1,0
+HSDSGKYDPCEKKLPPYDDN,0,0
+SDSGKYDPCEKKLPPYDDND,0,0
+DSGKYDPCEKKLPPYDDNDQ,0,0
+SGKYDPCEKKLPPYDDNDQW,50.5,4
+GKYDPCEKKLPPYDDNDQWK,1,0
+KYDPCEKKLPPYDDNDQWKC,0,0
+YDPCEKKLPPYDDNDQWKCQ,0,0
+DPCEKKLPPYDDNDQWKCQQ,0,0
+PCEKKLPPYDDNDQWKCQQN,0,0
+CEKKLPPYDDNDQWKCQQNS,0,0
+EKKLPPYDDNDQWKCQQNSS,1,0
+KKLPPYDDNDQWKCQQNSSD,6,2
+KLPPYDDNDQWKCQQNSSDG,0,1
+LPPYDDNDQWKCQQNSSDGS,0,0
+PPYDDNDQWKCQQNSSDGSG,0,0
+PYDDNDQWKCQQNSSDGSGK,0,0
+YDDNDQWKCQQNSSDGSGKP,0,0
+DDNDQWKCQQNSSDGSGKPE,0,1
+DNDQWKCQQNSSDGSGKPEN,0,0
+NDQWKCQQNSSDGSGKPENI,2,4
+DQWKCQQNSSDGSGKPENIC,0,2
+QWKCQQNSSDGSGKPENICV,0,0
+WKCQQNSSDGSGKPENICVP,0,0
+KCQQNSSDGSGKPENICVPP,0,0
+CQQNSSDGSGKPENICVPPR,0,0
+QQNSSDGSGKPENICVPPRR,0,9
+QNSSDGSGKPENICVPPRRE,3.5,0
+NSSDGSGKPENICVPPRRER,0,0
+SSDGSGKPENICVPPRRERL,0,4
+SDGSGKPENICVPPRRERLC,0,5
+DGSGKPENICVPPRRERLCT,0,0
+GSGKPENICVPPRRERLCTY,3,0
+SGKPENICVPPRRERLCTYN,0,0
+GKPENICVPPRRERLCTYNL,0,0
+KPENICVPPRRERLCTYNLE,0,3.5
+PENICVPPRRERLCTYNLEN,1,0
+ENICVPPRRERLCTYNLENL,0,0
+NICVPPRRERLCTYNLENLK,0,0
+ICVPPRRERLCTYNLENLKF,1,1
+CVPPRRERLCTYNLENLKFD,0,3.5
+VPPRRERLCTYNLENLKFDK,0,0
+PPRRERLCTYNLENLKFDKI,0,0
+PRRERLCTYNLENLKFDKIR,0,0
+RRERLCTYNLENLKFDKIRD,0,2
+RERLCTYNLENLKFDKIRDN,0,0
+ERLCTYNLENLKFDKIRDNN,4,1
+RLCTYNLENLKFDKIRDNNA,0,0
+LCTYNLENLKFDKIRDNNAF,3,0
+CTYNLENLKFDKIRDNNAFL,5,0
+TYNLENLKFDKIRDNNAFLA,0,0
+YNLENLKFDKIRDNNAFLAD,1,0
+NLENLKFDKIRDNNAFLADV,2,0
+LENLKFDKIRDNNAFLADVL,0,0
+ENLKFDKIRDNNAFLADVLL,0,0
+NLKFDKIRDNNAFLADVLLT,0,0
+LKFDKIRDNNAFLADVLLTA,0,0
+KFDKIRDNNAFLADVLLTAR,0,0
+FDKIRDNNAFLADVLLTARN,0,1
+DKIRDNNAFLADVLLTARNE,0,0
+KIRDNNAFLADVLLTARNEG,0,0
+IRDNNAFLADVLLTARNEGE,0,0
+RDNNAFLADVLLTARNEGEK,3,0
+DNNAFLADVLLTARNEGEKI,0,0
+NNAFLADVLLTARNEGEKIV,0,0
+NAFLADVLLTARNEGEKIVQ,0,0
+AFLADVLLTARNEGEKIVQN,0,3
+FLADVLLTARNEGEKIVQNH,0,0
+LADVLLTARNEGEKIVQNHP,0,0
+ADVLLTARNEGEKIVQNHPD,0,0
+DVLLTARNEGEKIVQNHPDT,0,0
+VLLTARNEGEKIVQNHPDTN,0,0
+LLTARNEGEKIVQNHPDTNS,0,0
+LTARNEGEKIVQNHPDTNSS,0,0
+TARNEGEKIVQNHPDTNSSN,0,0
+ARNEGEKIVQNHPDTNSSNV,1,0
+RNEGEKIVQNHPDTNSSNVC,0,3
+NEGEKIVQNHPDTNSSNVCN,2,0
+EGEKIVQNHPDTNSSNVCNA,4,0
+GEKIVQNHPDTNSSNVCNAL,0,1
+EKIVQNHPDTNSSNVCNALE,0,0
+KIVQNHPDTNSSNVCNALER,3,0
+IVQNHPDTNSSNVCNALERS,5,0
+VQNHPDTNSSNVCNALERSF,0,0
+QNHPDTNSSNVCNALERSFA,0,1
+NHPDTNSSNVCNALERSFAD,0,3.5
+HPDTNSSNVCNALERSFADL,2,0
+PDTNSSNVCNALERSFADLA,0,0
+DTNSSNVCNALERSFADLAD,0,4
+TNSSNVCNALERSFADLADI,2,3
+NSSNVCNALERSFADLADII,2,0
+SSNVCNALERSFADLADIIR,0,1
+SNVCNALERSFADLADIIRG,0,0
+NVCNALERSFADLADIIRGT,4,0
+VCNALERSFADLADIIRGTD,0,4
+CNALERSFADLADIIRGTDQ,0,0
+NALERSFADLADIIRGTDQW,2,0
+ALERSFADLADIIRGTDQWK,0,0
+LERSFADLADIIRGTDQWKG,0,3.5
+ERSFADLADIIRGTDQWKGT,0,0
+RSFADLADIIRGTDQWKGTN,2,1
+SFADLADIIRGTDQWKGTNS,0,3
+FADLADIIRGTDQWKGTNSN,0.5,2
+ADLADIIRGTDQWKGTNSNL,2,3
+DLADIIRGTDQWKGTNSNLE,4,0
+LADIIRGTDQWKGTNSNLEK,0,0
+ADIIRGTDQWKGTNSNLEKN,0,0
+DIIRGTDQWKGTNSNLEKNL,0,0
+IIRGTDQWKGTNSNLEKNLK,0,2
+IRGTDQWKGTNSNLEKNLKQ,1,1
+RGTDQWKGTNSNLEKNLKQM,0,0
+GTDQWKGTNSNLEKNLKQMF,0,0
+TDQWKGTNSNLEKNLKQMFA,0,0
+DQWKGTNSNLEKNLKQMFAK,0,0
+QWKGTNSNLEKNLKQMFAKI,98.5,101.5
+WKGTNSNLEKNLKQMFAKIR,10.5,106.5
+KGTNSNLEKNLKQMFAKIRE,4,4
+GTNSNLEKNLKQMFAKIREN,0,0
+TNSNLEKNLKQMFAKIREND,0,0
+NSNLEKNLKQMFAKIRENDK,4,0
+SNLEKNLKQMFAKIRENDKV,1,2
+NLEKNLKQMFAKIRENDKVL,0.5,7
+LEKNLKQMFAKIRENDKVLQ,0,4
+EKNLKQMFAKIRENDKVLQD,0,0
+KNLKQMFAKIRENDKVLQDK,0,0
+NLKQMFAKIRENDKVLQDKY,0.5,0
+LKQMFAKIRENDKVLQDKYP,0,0
+KQMFAKIRENDKVLQDKYPK,0.5,5
+QMFAKIRENDKVLQDKYPKD,0,0
+MFAKIRENDKVLQDKYPKDQ,0,0
+FAKIRENDKVLQDKYPKDQK,0,7
+AKIRENDKVLQDKYPKDQKY,1,1
+KIRENDKVLQDKYPKDQKYT,0,0
+IRENDKVLQDKYPKDQKYTK,241,264
+RENDKVLQDKYPKDQKYTKL,96,716
+ENDKVLQDKYPKDQKYTKLR,1683.5,2748.5
+NDKVLQDKYPKDQKYTKLRE,98,153.5
+DKVLQDKYPKDQKYTKLREA,73.5,91
+KVLQDKYPKDQKYTKLREAW,93,1
+VLQDKYPKDQKYTKLREAWW,98.5,89
+LQDKYPKDQKYTKLREAWWN,0,0
+QDKYPKDQKYTKLREAWWNA,0,0
+DKYPKDQKYTKLREAWWNAN,0,0
+KYPKDQKYTKLREAWWNANR,0,8
+YPKDQKYTKLREAWWNANRQ,0,0
+PKDQKYTKLREAWWNANRQK,0,0
+KDQKYTKLREAWWNANRQKV,2,1
+DQKYTKLREAWWNANRQKVW,0,0
+QKYTKLREAWWNANRQKVWE,0,0
+KYTKLREAWWNANRQKVWEV,3,0
+YTKLREAWWNANRQKVWEVI,0,0
+TKLREAWWNANRQKVWEVIT,0,3
+KLREAWWNANRQKVWEVITC,0,0
+LREAWWNANRQKVWEVITCG,2,5
+REAWWNANRQKVWEVITCGA,0,0
+EAWWNANRQKVWEVITCGAR,0,0
+AWWNANRQKVWEVITCGARS,3.5,0
+WWNANRQKVWEVITCGARSN,1,1
+WNANRQKVWEVITCGARSND,0,3
+NANRQKVWEVITCGARSNDL,2,0
+ANRQKVWEVITCGARSNDLL,3,0
+NRQKVWEVITCGARSNDLLI,0,0
+RQKVWEVITCGARSNDLLIK,0,3
+QKVWEVITCGARSNDLLIKR,9,0
+KVWEVITCGARSNDLLIKRG,6,0
+VWEVITCGARSNDLLIKRGW,5.5,3
+WEVITCGARSNDLLIKRGWR,0,0
+EVITCGARSNDLLIKRGWRT,0,0
+VITCGARSNDLLIKRGWRTS,0,0
+ITCGARSNDLLIKRGWRTSG,2,0
+TCGARSNDLLIKRGWRTSGK,0,1
+CGARSNDLLIKRGWRTSGKS,0,0
+GARSNDLLIKRGWRTSGKSD,3,0
+ARSNDLLIKRGWRTSGKSDR,0,0
+RSNDLLIKRGWRTSGKSDRK,2,0
+SNDLLIKRGWRTSGKSDRKK,6,99
+NDLLIKRGWRTSGKSDRKKN,0,0
+DLLIKRGWRTSGKSDRKKNF,0,0
+LLIKRGWRTSGKSDRKKNFE,0,0
+LIKRGWRTSGKSDRKKNFEL,0,3.5
+IKRGWRTSGKSDRKKNFELC,3,0
+KRGWRTSGKSDRKKNFELCR,0,3
+RGWRTSGKSDRKKNFELCRK,95,0
+GWRTSGKSDRKKNFELCRKC,0,0
+WRTSGKSDRKKNFELCRKCG,0,2
+RTSGKSDRKKNFELCRKCGH,1,0
+TSGKSDRKKNFELCRKCGHY,0,0
+SGKSDRKKNFELCRKCGHYE,6,0
+GKSDRKKNFELCRKCGHYEK,0,0
+KSDRKKNFELCRKCGHYEKE,0,0
+SDRKKNFELCRKCGHYEKEV,0,0
+DRKKNFELCRKCGHYEKEVP,0,0
+RKKNFELCRKCGHYEKEVPT,0,0
+KKNFELCRKCGHYEKEVPTK,3,3
+KNFELCRKCGHYEKEVPTKL,0,0.5
+NFELCRKCGHYEKEVPTKLD,0,0
+FELCRKCGHYEKEVPTKLDY,0,0
+ELCRKCGHYEKEVPTKLDYV,2.5,0
+LCRKCGHYEKEVPTKLDYVP,0,0
+CRKCGHYEKEVPTKLDYVPQ,0,0
+RKCGHYEKEVPTKLDYVPQF,0,0
+KCGHYEKEVPTKLDYVPQFL,0,1
+CGHYEKEVPTKLDYVPQFLR,0,0
+GHYEKEVPTKLDYVPQFLRW,6,1.5
+HYEKEVPTKLDYVPQFLRWL,87.5,0
+YEKEVPTKLDYVPQFLRWLT,0,0
+EKEVPTKLDYVPQFLRWLTE,0,0
+KEVPTKLDYVPQFLRWLTEW,3,96
+EVPTKLDYVPQFLRWLTEWI,0,39
+VPTKLDYVPQFLRWLTEWIE,0,0
+PTKLDYVPQFLRWLTEWIED,0,4
+TKLDYVPQFLRWLTEWIEDF,0,0.5
+KLDYVPQFLRWLTEWIEDFY,91.5,1
+LDYVPQFLRWLTEWIEDFYR,0,0
+DYVPQFLRWLTEWIEDFYRE,0,8
+YVPQFLRWLTEWIEDFYREK,0,8
+VPQFLRWLTEWIEDFYREKQ,0,1
+PQFLRWLTEWIEDFYREKQN,0,0
+QFLRWLTEWIEDFYREKQNL,1,1
+FLRWLTEWIEDFYREKQNLI,1,1
+LRWLTEWIEDFYREKQNLID,1,0
+RWLTEWIEDFYREKQNLIDD,1,0
+WLTEWIEDFYREKQNLIDDM,0,0
+LTEWIEDFYREKQNLIDDME,0,8
+TEWIEDFYREKQNLIDDMER,0,1
+EWIEDFYREKQNLIDDMERH,0,0
+WIEDFYREKQNLIDDMERHR,6,0
+IEDFYREKQNLIDDMERHRE,3,2
+EDFYREKQNLIDDMERHREE,3,0
+DFYREKQNLIDDMERHREEC,0,0
+FYREKQNLIDDMERHREECT,7,0
+YREKQNLIDDMERHREECTR,7,2
+REKQNLIDDMERHREECTRE,0,0
+EKQNLIDDMERHREECTRED,3,0
+KQNLIDDMERHREECTREDH,0,0
+QNLIDDMERHREECTREDHK,0,4
+NLIDDMERHREECTREDHKS,0,1
+LIDDMERHREECTREDHKSK,0,0
+IDDMERHREECTREDHKSKE,0,0
+DDMERHREECTREDHKSKEG,0,0
+DMERHREECTREDHKSKEGT,0,3
+MERHREECTREDHKSKEGTS,2,1
+ERHREECTREDHKSKEGTSY,0,6
+RHREECTREDHKSKEGTSYC,0,0
+HREECTREDHKSKEGTSYCS,1,0.5
+REECTREDHKSKEGTSYCST,0,0
+EECTREDHKSKEGTSYCSTC,2,0
+ECTREDHKSKEGTSYCSTCK,0,0
+CTREDHKSKEGTSYCSTCKD,0,1
+TREDHKSKEGTSYCSTCKDK,0,1
+REDHKSKEGTSYCSTCKDKC,3.5,5
+EDHKSKEGTSYCSTCKDKCK,1,0
+DHKSKEGTSYCSTCKDKCKK,0,0
+HKSKEGTSYCSTCKDKCKKY,104,91
+KSKEGTSYCSTCKDKCKKYC,3,5
+SKEGTSYCSTCKDKCKKYCE,0,0
+KEGTSYCSTCKDKCKKYCEC,0,0
+EGTSYCSTCKDKCKKYCECV,5,0
+GTSYCSTCKDKCKKYCECVK,2,0
+TSYCSTCKDKCKKYCECVKK,92,0
+SYCSTCKDKCKKYCECVKKW,0,0
+YCSTCKDKCKKYCECVKKWK,0,4.5
+CSTCKDKCKKYCECVKKWKT,97,96
+STCKDKCKKYCECVKKWKTE,0,0
+TCKDKCKKYCECVKKWKTEW,0,1
+CKDKCKKYCECVKKWKTEWE,2,5
+KDKCKKYCECVKKWKTEWEN,4,0
+DKCKKYCECVKKWKTEWENQ,1,0
+KCKKYCECVKKWKTEWENQE,2,3
+CKKYCECVKKWKTEWENQEN,0,0
+KKYCECVKKWKTEWENQENK,0,0
+KYCECVKKWKTEWENQENKY,0,0
+YCECVKKWKTEWENQENKYK,178,184.5
+CECVKKWKTEWENQENKYKD,0,0
+ECVKKWKTEWENQENKYKDL,0,0
+CVKKWKTEWENQENKYKDLY,0,0
+VKKWKTEWENQENKYKDLYE,4,0
+KKWKTEWENQENKYKDLYEQ,0,3
+KWKTEWENQENKYKDLYEQN,0,6
+WKTEWENQENKYKDLYEQNK,0,7
+KTEWENQENKYKDLYEQNKN,0,4
+TEWENQENKYKDLYEQNKNK,1.5,77
+EWENQENKYKDLYEQNKNKT,4,65.5
+WENQENKYKDLYEQNKNKTS,99,104.5
+ENQENKYKDLYEQNKNKTSQ,0,0
+NQENKYKDLYEQNKNKTSQK,251,519
+QENKYKDLYEQNKNKTSQKN,0,0
+ENKYKDLYEQNKNKTSQKNT,99.5,0
+NKYKDLYEQNKNKTSQKNTS,0,0
+KYKDLYEQNKNKTSQKNTSR,97,44
+YKDLYEQNKNKTSQKNTSRY,2,0
+KDLYEQNKNKTSQKNTSRYD,0,0
+DLYEQNKNKTSQKNTSRYDD,0,0
+LYEQNKNKTSQKNTSRYDDY,0,2
+YEQNKNKTSQKNTSRYDDYV,0,1
+EQNKNKTSQKNTSRYDDYVK,0,0
+QNKNKTSQKNTSRYDDYVKD,1,0
+NKNKTSQKNTSRYDDYVKDF,0,0
+KNKTSQKNTSRYDDYVKDFF,0,0
+NKTSQKNTSRYDDYVKDFFE,0,2
+KTSQKNTSRYDDYVKDFFEK,4,2
+TSQKNTSRYDDYVKDFFEKL,0,3
+SQKNTSRYDDYVKDFFEKLE,3.5,2
+QKNTSRYDDYVKDFFEKLEA,8,0
+KNTSRYDDYVKDFFEKLEAN,1,0
+NTSRYDDYVKDFFEKLEANY,0,1
+TSRYDDYVKDFFEKLEANYS,5.5,1
+SRYDDYVKDFFEKLEANYSS,6,2
+RYDDYVKDFFEKLEANYSSL,0,0
+YDDYVKDFFEKLEANYSSLE,0,0
+DDYVKDFFEKLEANYSSLEN,0,5
+DYVKDFFEKLEANYSSLENY,3,4
+YVKDFFEKLEANYSSLENYI,0,0
+VKDFFEKLEANYSSLENYIK,0,0
+KDFFEKLEANYSSLENYIKG,5,0
+DFFEKLEANYSSLENYIKGD,0,1.5
+FFEKLEANYSSLENYIKGDP,0,0
+FEKLEANYSSLENYIKGDPY,0,0
+EKLEANYSSLENYIKGDPYF,2,0
+KLEANYSSLENYIKGDPYFA,2,0
+LEANYSSLENYIKGDPYFAE,0,0
+EANYSSLENYIKGDPYFAEY,0,0
+ANYSSLENYIKGDPYFAEYA,0,0
+NYSSLENYIKGDPYFAEYAT,1,0
+YSSLENYIKGDPYFAEYATK,0,0
+SSLENYIKGDPYFAEYATKL,0,1
+SLENYIKGDPYFAEYATKLS,0,0
+LENYIKGDPYFAEYATKLSF,5,0
+ENYIKGDPYFAEYATKLSFI,0,0
+NYIKGDPYFAEYATKLSFIL,0,0
+YIKGDPYFAEYATKLSFILN,0,5
+IKGDPYFAEYATKLSFILNP,0,0
+KGDPYFAEYATKLSFILNPS,0,0
+GDPYFAEYATKLSFILNPSD,0,0
+DPYFAEYATKLSFILNPSDA,0,0
+PYFAEYATKLSFILNPSDAN,6,1
+YFAEYATKLSFILNPSDANN,0,1
+FAEYATKLSFILNPSDANNP,0,1
+AEYATKLSFILNPSDANNPS,0,0.5
+EYATKLSFILNPSDANNPSG,0,6
+YATKLSFILNPSDANNPSGE,0,0
+ATKLSFILNPSDANNPSGET,0,0
+TKLSFILNPSDANNPSGETA,0,1
+KLSFILNPSDANNPSGETAN,0,0
+LSFILNPSDANNPSGETANH,7,0
+SFILNPSDANNPSGETANHN,0,3
+FILNPSDANNPSGETANHND,0,0
+ILNPSDANNPSGETANHNDE,0,0
+LNPSDANNPSGETANHNDEA,0,0
+NPSDANNPSGETANHNDEAC,0,0
+PSDANNPSGETANHNDEACN,0,0
+SDANNPSGETANHNDEACNC,7,2
+DANNPSGETANHNDEACNCN,1,0
+ANNPSGETANHNDEACNCNE,0,1
+NNPSGETANHNDEACNCNES,0,3
+NPSGETANHNDEACNCNESG,0,1
+PSGETANHNDEACNCNESGI,0,3
+SGETANHNDEACNCNESGIS,0,0
+GETANHNDEACNCNESGISS,0,0
+ETANHNDEACNCNESGISSV,0,2
+TANHNDEACNCNESGISSVG,0,2
+ANHNDEACNCNESGISSVGQ,1,0
+NHNDEACNCNESGISSVGQA,0,2
+HNDEACNCNESGISSVGQAQ,7,11
+NDEACNCNESGISSVGQAQT,0,0
+DEACNCNESGISSVGQAQTS,2,5
+EACNCNESGISSVGQAQTSG,4,1
+ACNCNESGISSVGQAQTSGP,3,2
+CNCNESGISSVGQAQTSGPS,0,0
+NCNESGISSVGQAQTSGPSS,0,2
+CNESGISSVGQAQTSGPSSN,1,0
+NESGISSVGQAQTSGPSSNK,0,3
+ESGISSVGQAQTSGPSSNKT,0,0
+SGISSVGQAQTSGPSSNKTC,1,0
+GISSVGQAQTSGPSSNKTCI,0,2
+ISSVGQAQTSGPSSNKTCIT,0,0
+SSVGQAQTSGPSSNKTCITH,0,0
+SVGQAQTSGPSSNKTCITHS,4,0
+VGQAQTSGPSSNKTCITHSS,0,0
+GQAQTSGPSSNKTCITHSSI,0,0
+QAQTSGPSSNKTCITHSSIK,0,0
+AQTSGPSSNKTCITHSSIKT,1,3
+QTSGPSSNKTCITHSSIKTN,0,5
+TSGPSSNKTCITHSSIKTNK,0,0
+SGPSSNKTCITHSSIKTNKK,0,0
+GPSSNKTCITHSSIKTNKKK,0,6
+PSSNKTCITHSSIKTNKKKE,0,1
+SSNKTCITHSSIKTNKKKEC,4,1
+SNKTCITHSSIKTNKKKECK,2,0
+NKTCITHSSIKTNKKKECKD,0,0
+KTCITHSSIKTNKKKECKDV,0,1
+TCITHSSIKTNKKKECKDVK,0,0
+CITHSSIKTNKKKECKDVKL,75,81
+ITHSSIKTNKKKECKDVKLG,0,0
+THSSIKTNKKKECKDVKLGV,90.5,91
+HSSIKTNKKKECKDVKLGVR,93,90
+SSIKTNKKKECKDVKLGVRE,0,1
+SIKTNKKKECKDVKLGVREN,0,3
+IKTNKKKECKDVKLGVREND,1,0
+KTNKKKECKDVKLGVRENDK,0,1.5
+TNKKKECKDVKLGVRENDKD,1,0
+NKKKECKDVKLGVRENDKDL,0,0
+KKKECKDVKLGVRENDKDLK,0,0
+KKECKDVKLGVRENDKDLKI,0,0
+KECKDVKLGVRENDKDLKIC,0,0
+ECKDVKLGVRENDKDLKICV,0,0
+CKDVKLGVRENDKDLKICVI,0,0
+KDVKLGVRENDKDLKICVIE,0,0
+DVKLGVRENDKDLKICVIED,0,0
+VKLGVRENDKDLKICVIEDT,0,0
+KLGVRENDKDLKICVIEDTS,5,0
+LGVRENDKDLKICVIEDTSL,5,2
+GVRENDKDLKICVIEDTSLS,0,0
+VRENDKDLKICVIEDTSLSG,0,0
+RENDKDLKICVIEDTSLSGV,2,0
+ENDKDLKICVIEDTSLSGVD,3,0
+NDKDLKICVIEDTSLSGVDN,0,2
+DKDLKICVIEDTSLSGVDNC,0,0
+KDLKICVIEDTSLSGVDNCC,1.5,0
+DLKICVIEDTSLSGVDNCCC,0,0
+LKICVIEDTSLSGVDNCCCQ,0,0
+KICVIEDTSLSGVDNCCCQD,2,4
+ICVIEDTSLSGVDNCCCQDL,0,0
+CVIEDTSLSGVDNCCCQDLL,0,0
+VIEDTSLSGVDNCCCQDLLG,0,4
+IEDTSLSGVDNCCCQDLLGI,0,0
+EDTSLSGVDNCCCQDLLGIL,1,2.5
+DTSLSGVDNCCCQDLLGILQ,2,0
+TSLSGVDNCCCQDLLGILQE,0,2
+SLSGVDNCCCQDLLGILQEN,0,0
+LSGVDNCCCQDLLGILQENC,4,2
+SGVDNCCCQDLLGILQENCS,0,0
+GVDNCCCQDLLGILQENCSD,0,2
+VDNCCCQDLLGILQENCSDN,1,0
+DNCCCQDLLGILQENCSDNK,0,0
+NCCCQDLLGILQENCSDNKR,0,0
+CCCQDLLGILQENCSDNKRG,0,0
+CCQDLLGILQENCSDNKRGS,0,0
+CQDLLGILQENCSDNKRGSS,0,1
+QDLLGILQENCSDNKRGSSS,0,4
+DLLGILQENCSDNKRGSSSN,0,0
+LLGILQENCSDNKRGSSSND,0,0
+LGILQENCSDNKRGSSSNDS,0,2
+GILQENCSDNKRGSSSNDSC,0,0
+ILQENCSDNKRGSSSNDSCD,1,0
+LQENCSDNKRGSSSNDSCDN,0,0
+QENCSDNKRGSSSNDSCDNK,0,0
+ENCSDNKRGSSSNDSCDNKN,0,0.5
+NCSDNKRGSSSNDSCDNKNQ,0,0
+CSDNKRGSSSNDSCDNKNQD,2,0
+SDNKRGSSSNDSCDNKNQDE,0,0
+DNKRGSSSNDSCDNKNQDEC,0,1
+NKRGSSSNDSCDNKNQDECQ,0,0
+KRGSSSNDSCDNKNQDECQK,0,0
+RGSSSNDSCDNKNQDECQKK,0,0
+GSSSNDSCDNKNQDECQKKL,0,0
+SSSNDSCDNKNQDECQKKLE,0,0
+SSNDSCDNKNQDECQKKLEK,0,6
+SNDSCDNKNQDECQKKLEKV,0,0
+NDSCDNKNQDECQKKLEKVF,1,0
+DSCDNKNQDECQKKLEKVFA,0,0
+SCDNKNQDECQKKLEKVFAS,0,0
+CDNKNQDECQKKLEKVFASL,0,0
+DNKNQDECQKKLEKVFASLT,0,0
+NKNQDECQKKLEKVFASLTN,0,1
+KNQDECQKKLEKVFASLTNG,0,1
+NQDECQKKLEKVFASLTNGY,2,1
+QDECQKKLEKVFASLTNGYK,3,0
+DECQKKLEKVFASLTNGYKC,0,1
+ECQKKLEKVFASLTNGYKCD,0,0
+CQKKLEKVFASLTNGYKCDK,81.5,80.5
+QKKLEKVFASLTNGYKCDKC,0,4
+KKLEKVFASLTNGYKCDKCK,96,100
+KLEKVFASLTNGYKCDKCKS,92,91
+LEKVFASLTNGYKCDKCKSG,87,7
+EKVFASLTNGYKCDKCKSGT,6,0
+KVFASLTNGYKCDKCKSGTS,88,79
+VFASLTNGYKCDKCKSGTSR,87,100
+FASLTNGYKCDKCKSGTSRS,93,197
+ASLTNGYKCDKCKSGTSRSK,80,232
+SLTNGYKCDKCKSGTSRSKK,90,189
+LTNGYKCDKCKSGTSRSKKK,93,121.5
+TNGYKCDKCKSGTSRSKKKW,97,1
+NGYKCDKCKSGTSRSKKKWI,1,2
+GYKCDKCKSGTSRSKKKWIW,2,0.5
+YKCDKCKSGTSRSKKKWIWK,0,5.5
+KCDKCKSGTSRSKKKWIWKK,0,0
+CDKCKSGTSRSKKKWIWKKS,0,109.5
+DKCKSGTSRSKKKWIWKKSS,0,0
+KCKSGTSRSKKKWIWKKSSG,0.5,0
+CKSGTSRSKKKWIWKKSSGN,0,0
+KSGTSRSKKKWIWKKSSGNE,1,3
+SGTSRSKKKWIWKKSSGNEE,0,0
+GTSRSKKKWIWKKSSGNEEG,0,0
+TSRSKKKWIWKKSSGNEEGL,0,0
+SRSKKKWIWKKSSGNEEGLQ,0,0
+RSKKKWIWKKSSGNEEGLQE,0,0
+SKKKWIWKKSSGNEEGLQEE,0,0
+KKKWIWKKSSGNEEGLQEEY,0,0
+KKWIWKKSSGNEEGLQEEYA,1,0
+KWIWKKSSGNEEGLQEEYAN,0,0
+WIWKKSSGNEEGLQEEYANT,5,0
+IWKKSSGNEEGLQEEYANTI,5,0
+WKKSSGNEEGLQEEYANTIG,0,0
+KKSSGNEEGLQEEYANTIGL,0,0
+KSSGNEEGLQEEYANTIGLP,0,0
+SSGNEEGLQEEYANTIGLPP,0,0
+SGNEEGLQEEYANTIGLPPR,0,1
+GNEEGLQEEYANTIGLPPRT,0,2
+NEEGLQEEYANTIGLPPRTQ,0,0
+EEGLQEEYANTIGLPPRTQS,1,0
+EGLQEEYANTIGLPPRTQSL,0,1
+GLQEEYANTIGLPPRTQSLY,0,0
+LQEEYANTIGLPPRTQSLYL,0,0
+QEEYANTIGLPPRTQSLYLG,0,3
+EEYANTIGLPPRTQSLYLGN,0,0
+EYANTIGLPPRTQSLYLGNL,0,0
+YANTIGLPPRTQSLYLGNLP,2,0
+ANTIGLPPRTQSLYLGNLPK,2,0
+NTIGLPPRTQSLYLGNLPKL,0,0
+TIGLPPRTQSLYLGNLPKLE,0,5
+IGLPPRTQSLYLGNLPKLEN,0,0
+GLPPRTQSLYLGNLPKLENV,0,0
+LPPRTQSLYLGNLPKLENVC,6,0
+PPRTQSLYLGNLPKLENVCE,11,0
+PRTQSLYLGNLPKLENVCED,2,0
+RTQSLYLGNLPKLENVCEDV,0,0
+TQSLYLGNLPKLENVCEDVK,1,0
+QSLYLGNLPKLENVCEDVKD,0,0
+SLYLGNLPKLENVCEDVKDI,0,1.5
+LYLGNLPKLENVCEDVKDIN,0,0
+YLGNLPKLENVCEDVKDINF,0,0
+LGNLPKLENVCEDVKDINFD,2,0
+GNLPKLENVCEDVKDINFDT,0,0
+NLPKLENVCEDVKDINFDTK,0,4.5
+LPKLENVCEDVKDINFDTKE,0,0
+PKLENVCEDVKDINFDTKEK,1,0
+KLENVCEDVKDINFDTKEKF,0,0
+LENVCEDVKDINFDTKEKFL,0,0
+ENVCEDVKDINFDTKEKFLA,0,0
+NVCEDVKDINFDTKEKFLAG,3,0
+VCEDVKDINFDTKEKFLAGC,0,0
+CEDVKDINFDTKEKFLAGCL,1,0
+EDVKDINFDTKEKFLAGCLI,0,0
+DVKDINFDTKEKFLAGCLIV,0,0
+VKDINFDTKEKFLAGCLIVS,0,5
+KDINFDTKEKFLAGCLIVSF,0,0
+DINFDTKEKFLAGCLIVSFH,0,0
+INFDTKEKFLAGCLIVSFHE,0,0
+NFDTKEKFLAGCLIVSFHEG,1,0
+FDTKEKFLAGCLIVSFHEGK,0,0
+DTKEKFLAGCLIVSFHEGKN,0,0
+TKEKFLAGCLIVSFHEGKNL,0,0
+KEKFLAGCLIVSFHEGKNLK,0,0
+EKFLAGCLIVSFHEGKNLKK,94.5,96.5
+KFLAGCLIVSFHEGKNLKKR,298,283
+FLAGCLIVSFHEGKNLKKRY,369,277
+LAGCLIVSFHEGKNLKKRYP,114,185
+AGCLIVSFHEGKNLKKRYPQ,0,0
+GCLIVSFHEGKNLKKRYPQN,3,0
+CLIVSFHEGKNLKKRYPQNK,654.5,563
+LIVSFHEGKNLKKRYPQNKN,0,0
+IVSFHEGKNLKKRYPQNKNS,113,183
+VSFHEGKNLKKRYPQNKNSG,2,0
+SFHEGKNLKKRYPQNKNSGN,0,0
+FHEGKNLKKRYPQNKNSGNK,0.5,121
+HEGKNLKKRYPQNKNSGNKE,0,0
+EGKNLKKRYPQNKNSGNKEN,0,0
+GKNLKKRYPQNKNSGNKENL,0,0
+KNLKKRYPQNKNSGNKENLC,0,0
+NLKKRYPQNKNSGNKENLCK,0,0
+LKKRYPQNKNSGNKENLCKA,0,0
+KKRYPQNKNSGNKENLCKAL,1,0
+KRYPQNKNSGNKENLCKALE,0,0
+RYPQNKNSGNKENLCKALEY,0,0
+YPQNKNSGNKENLCKALEYS,0,0
+PQNKNSGNKENLCKALEYSF,0,0
+QNKNSGNKENLCKALEYSFA,0,0
+NKNSGNKENLCKALEYSFAD,0,0
+KNSGNKENLCKALEYSFADY,0,4
+NSGNKENLCKALEYSFADYG,0,0
+SGNKENLCKALEYSFADYGD,0,0
+GNKENLCKALEYSFADYGDL,0,0
+NKENLCKALEYSFADYGDLI,0,0
+KENLCKALEYSFADYGDLIK,0,0
+ENLCKALEYSFADYGDLIKG,6,0
+NLCKALEYSFADYGDLIKGT,0,1
+LCKALEYSFADYGDLIKGTS,0,0
+CKALEYSFADYGDLIKGTSI,0,0
+KALEYSFADYGDLIKGTSIW,0,0
+ALEYSFADYGDLIKGTSIWD,5,0
+LEYSFADYGDLIKGTSIWDN,7,0.5
+EYSFADYGDLIKGTSIWDNE,0,0
+YSFADYGDLIKGTSIWDNEY,5,3.5
+SFADYGDLIKGTSIWDNEYT,2.5,0
+FADYGDLIKGTSIWDNEYTK,4,0
+ADYGDLIKGTSIWDNEYTKD,0,0
+DYGDLIKGTSIWDNEYTKDL,3,0
+YGDLIKGTSIWDNEYTKDLE,0,0
+GDLIKGTSIWDNEYTKDLEL,0,3
+DLIKGTSIWDNEYTKDLELN,0,0
+LIKGTSIWDNEYTKDLELNL,2,0
+IKGTSIWDNEYTKDLELNLQ,0,1
+KGTSIWDNEYTKDLELNLQN,0,0
+GTSIWDNEYTKDLELNLQNN,0,0
+TSIWDNEYTKDLELNLQNNF,0,0
+SIWDNEYTKDLELNLQNNFG,4,0
+IWDNEYTKDLELNLQNNFGK,2,0
+WDNEYTKDLELNLQNNFGKL,0,2
+DNEYTKDLELNLQNNFGKLF,0,0
+NEYTKDLELNLQNNFGKLFG,0,0
+EYTKDLELNLQNNFGKLFGK,0,0
+YTKDLELNLQNNFGKLFGKY,0,0
+TKDLELNLQNNFGKLFGKYI,0,0
+KDLELNLQNNFGKLFGKYIK,54.5,106
+DLELNLQNNFGKLFGKYIKK,481,370
+LELNLQNNFGKLFGKYIKKN,619,1004
+ELNLQNNFGKLFGKYIKKNN,106,102.5
+LNLQNNFGKLFGKYIKKNNT,198,273.5
+NLQNNFGKLFGKYIKKNNTA,101,93
+LQNNFGKLFGKYIKKNNTAE,0,0
+QNNFGKLFGKYIKKNNTAEQ,2,0
+NNFGKLFGKYIKKNNTAEQD,0,0
+NFGKLFGKYIKKNNTAEQDT,0,0
+FGKLFGKYIKKNNTAEQDTS,0,2
+GKLFGKYIKKNNTAEQDTSY,0,0
+KLFGKYIKKNNTAEQDTSYS,0,0
+LFGKYIKKNNTAEQDTSYSS,0,0
+FGKYIKKNNTAEQDTSYSSL,0,0
+GKYIKKNNTAEQDTSYSSLD,0,1.5
+KYIKKNNTAEQDTSYSSLDE,0,4
+YIKKNNTAEQDTSYSSLDEL,0,1
+IKKNNTAEQDTSYSSLDELR,0,0
+KKNNTAEQDTSYSSLDELRE,0,0
+KNNTAEQDTSYSSLDELRES,0,0
+NNTAEQDTSYSSLDELRESW,0,0.5
+NTAEQDTSYSSLDELRESWW,113,1
+TAEQDTSYSSLDELRESWWN,0,0
+AEQDTSYSSLDELRESWWNT,1,0
+EQDTSYSSLDELRESWWNTN,2,0
+QDTSYSSLDELRESWWNTNK,0,0
+DTSYSSLDELRESWWNTNKK,3,0
+TSYSSLDELRESWWNTNKKY,0,0
+SYSSLDELRESWWNTNKKYI,0,3
+YSSLDELRESWWNTNKKYIW,0,2
+SSLDELRESWWNTNKKYIWT,1,0
+SLDELRESWWNTNKKYIWTA,0,0
+LDELRESWWNTNKKYIWTAM,2,88.5
+DELRESWWNTNKKYIWTAMK,84,97
+ELRESWWNTNKKYIWTAMKH,83.5,94
+LRESWWNTNKKYIWTAMKHG,2,0
+RESWWNTNKKYIWTAMKHGA,1,0
+ESWWNTNKKYIWTAMKHGAE,0,0
+SWWNTNKKYIWTAMKHGAEM,0,0
+WWNTNKKYIWTAMKHGAEMN,0,0
+WNTNKKYIWTAMKHGAEMNI,1,0
+NTNKKYIWTAMKHGAEMNIT,0,1.5
+TNKKYIWTAMKHGAEMNITT,0,4.5
+NKKYIWTAMKHGAEMNITTC,0,0
+KKYIWTAMKHGAEMNITTCN,0,0
+KYIWTAMKHGAEMNITTCNA,0,1
+YIWTAMKHGAEMNITTCNAD,0,0
+IWTAMKHGAEMNITTCNADG,0,0
+WTAMKHGAEMNITTCNADGS,0,0
+TAMKHGAEMNITTCNADGSV,1,0
+AMKHGAEMNITTCNADGSVT,4,6
+MKHGAEMNITTCNADGSVTG,0,1.5
+KHGAEMNITTCNADGSVTGS,4,0
+HGAEMNITTCNADGSVTGSG,0,0
+GAEMNITTCNADGSVTGSGS,0,0
+AEMNITTCNADGSVTGSGSS,0,0
+EMNITTCNADGSVTGSGSSC,0,0
+MNITTCNADGSVTGSGSSCD,0,0
+NITTCNADGSVTGSGSSCDD,0,6
+ITTCNADGSVTGSGSSCDDI,0,0
+TTCNADGSVTGSGSSCDDIP,2,0
+TCNADGSVTGSGSSCDDIPT,0,0
+CNADGSVTGSGSSCDDIPTI,4,0
+NADGSVTGSGSSCDDIPTID,0,0
+ADGSVTGSGSSCDDIPTIDL,0,0
+DGSVTGSGSSCDDIPTIDLI,0,0
+GSVTGSGSSCDDIPTIDLIP,0,0
+SVTGSGSSCDDIPTIDLIPQ,1,0.5
+VTGSGSSCDDIPTIDLIPQY,0,0
+TGSGSSCDDIPTIDLIPQYL,0,0
+GSGSSCDDIPTIDLIPQYLR,0,0
+SGSSCDDIPTIDLIPQYLRF,0,0
+GSSCDDIPTIDLIPQYLRFL,0,0
+SSCDDIPTIDLIPQYLRFLQ,0,0
+SCDDIPTIDLIPQYLRFLQE,2,0
+CDDIPTIDLIPQYLRFLQEW,0,0
+DDIPTIDLIPQYLRFLQEWV,0,0
+DIPTIDLIPQYLRFLQEWVE,0,0
+IPTIDLIPQYLRFLQEWVEN,0,0
+PTIDLIPQYLRFLQEWVENF,4,0
+TIDLIPQYLRFLQEWVENFC,0,0
+IDLIPQYLRFLQEWVENFCE,0,0
+DLIPQYLRFLQEWVENFCEQ,0,0
+LIPQYLRFLQEWVENFCEQR,0,0
+IPQYLRFLQEWVENFCEQRQ,0,0
+PQYLRFLQEWVENFCEQRQA,0,0
+QYLRFLQEWVENFCEQRQAK,0,0
+YLRFLQEWVENFCEQRQAKV,0,0
+LRFLQEWVENFCEQRQAKVK,0,0
+RFLQEWVENFCEQRQAKVKD,0,0
+FLQEWVENFCEQRQAKVKDV,3,0
+LQEWVENFCEQRQAKVKDVI,0,0
+QEWVENFCEQRQAKVKDVIT,0,0
+EWVENFCEQRQAKVKDVITN,0,0
+WVENFCEQRQAKVKDVITNC,0,0
+VENFCEQRQAKVKDVITNCK,0,0
+ENFCEQRQAKVKDVITNCKS,0,1
+NFCEQRQAKVKDVITNCKSC,0,6
+FCEQRQAKVKDVITNCKSCK,0,0
+CEQRQAKVKDVITNCKSCKE,1,0
+EQRQAKVKDVITNCKSCKES,2,0
+QRQAKVKDVITNCKSCKESG,0,0
+RQAKVKDVITNCKSCKESGN,0,4
+QAKVKDVITNCKSCKESGNK,0,0
+AKVKDVITNCKSCKESGNKC,0,0
+KVKDVITNCKSCKESGNKCK,11,0
+VKDVITNCKSCKESGNKCKT,9,2
+KDVITNCKSCKESGNKCKTE,1,0
+DVITNCKSCKESGNKCKTEC,0,0
+VITNCKSCKESGNKCKTECK,2,2
+ITNCKSCKESGNKCKTECKT,0,1
+TNCKSCKESGNKCKTECKTK,0,59
+NCKSCKESGNKCKTECKTKC,0,0.5
+CKSCKESGNKCKTECKTKCK,3,1
+KSCKESGNKCKTECKTKCKD,0,1
+SCKESGNKCKTECKTKCKDE,0,0
+CKESGNKCKTECKTKCKDEC,0,2
+KESGNKCKTECKTKCKDECE,0,0
+ESGNKCKTECKTKCKDECEK,3.5,0
+SGNKCKTECKTKCKDECEKY,1,0
+GNKCKTECKTKCKDECEKYK,88,98
+NKCKTECKTKCKDECEKYKK,607,1195
+KCKTECKTKCKDECEKYKKF,100,361
+CKTECKTKCKDECEKYKKFI,103,81
+KTECKTKCKDECEKYKKFIE,6,0
+TECKTKCKDECEKYKKFIEA,8,0
+ECKTKCKDECEKYKKFIEAC,1,85
+CKTKCKDECEKYKKFIEACG,1,6.5
+KTKCKDECEKYKKFIEACGT,4.5,0
+TKCKDECEKYKKFIEACGTA,0,0
+KCKDECEKYKKFIEACGTAG,3,0
+CKDECEKYKKFIEACGTAGG,5,1
+KDECEKYKKFIEACGTAGGG,0,3
+DECEKYKKFIEACGTAGGGI,0,0
+ECEKYKKFIEACGTAGGGIG,0,104
+CEKYKKFIEACGTAGGGIGT,0,0
+EKYKKFIEACGTAGGGIGTA,0,0
+KYKKFIEACGTAGGGIGTAG,0,0
+YKKFIEACGTAGGGIGTAGS,0,0
+KKFIEACGTAGGGIGTAGSP,0,1
+KFIEACGTAGGGIGTAGSPW,0,3
+FIEACGTAGGGIGTAGSPWS,0,1
+IEACGTAGGGIGTAGSPWSK,0,0
+EACGTAGGGIGTAGSPWSKR,6,4.5
+ACGTAGGGIGTAGSPWSKRW,128,5
+CGTAGGGIGTAGSPWSKRWD,113,11
+GTAGGGIGTAGSPWSKRWDQ,6,5
+TAGGGIGTAGSPWSKRWDQI,0,0
+AGGGIGTAGSPWSKRWDQIY,0,0
+GGGIGTAGSPWSKRWDQIYK,0,0
+GGIGTAGSPWSKRWDQIYKR,283,390
+GIGTAGSPWSKRWDQIYKRY,3.5,105
+IGTAGSPWSKRWDQIYKRYS,4.5,106
+GTAGSPWSKRWDQIYKRYSK,375,1251
+TAGSPWSKRWDQIYKRYSKH,388.5,1055
+AGSPWSKRWDQIYKRYSKHI,120.5,99
+GSPWSKRWDQIYKRYSKHIE,0,0
+SPWSKRWDQIYKRYSKHIED,0,0
+PWSKRWDQIYKRYSKHIEDA,0,0
+WSKRWDQIYKRYSKHIEDAK,90.5,0
+SKRWDQIYKRYSKHIEDAKR,99,94.5
+KRWDQIYKRYSKHIEDAKRN,92,94
+RWDQIYKRYSKHIEDAKRNR,15.5,75
+WDQIYKRYSKHIEDAKRNRK,159,283
+DQIYKRYSKHIEDAKRNRKA,98,97
+QIYKRYSKHIEDAKRNRKAG,0,0
+IYKRYSKHIEDAKRNRKAGT,0,0
+YKRYSKHIEDAKRNRKAGTK,95,234
+KRYSKHIEDAKRNRKAGTKN,0,0
+RYSKHIEDAKRNRKAGTKNC,8,0
+YSKHIEDAKRNRKAGTKNCG,6,0
+SKHIEDAKRNRKAGTKNCGT,2,3
+KHIEDAKRNRKAGTKNCGTS,5,1
+HIEDAKRNRKAGTKNCGTSS,2,0
+IEDAKRNRKAGTKNCGTSST,0,0
+EDAKRNRKAGTKNCGTSSTT,0,0
+DAKRNRKAGTKNCGTSSTTN,0,0
+AKRNRKAGTKNCGTSSTTNA,0,0
+KRNRKAGTKNCGTSSTTNAA,0,0
+RNRKAGTKNCGTSSTTNAAA,0,0
+NRKAGTKNCGTSSTTNAAAS,0,0
+RKAGTKNCGTSSTTNAAAST,0,0
+KAGTKNCGTSSTTNAAASTD,0,0
+AGTKNCGTSSTTNAAASTDE,0,0
+GTKNCGTSSTTNAAASTDEN,0,0
+TKNCGTSSTTNAAASTDENK,2,0
+KNCGTSSTTNAAASTDENKC,0,1
+NCGTSSTTNAAASTDENKCV,0,0
+CGTSSTTNAAASTDENKCVQ,0,0
+GTSSTTNAAASTDENKCVQS,0,0
+TSSTTNAAASTDENKCVQSD,0,0
+SSTTNAAASTDENKCVQSDI,1,0
+STTNAAASTDENKCVQSDID,1,3
+TTNAAASTDENKCVQSDIDS,0,0
+TNAAASTDENKCVQSDIDSF,0,4
+NAAASTDENKCVQSDIDSFF,0,5
+AAASTDENKCVQSDIDSFFK,0,0
+AASTDENKCVQSDIDSFFKH,0,0
+ASTDENKCVQSDIDSFFKHL,1,0
+STDENKCVQSDIDSFFKHLI,0,1
+TDENKCVQSDIDSFFKHLID,1,0
+DENKCVQSDIDSFFKHLIDI,0,2
+ENKCVQSDIDSFFKHLIDIG,0,1
+NKCVQSDIDSFFKHLIDIGL,0,3
+KCVQSDIDSFFKHLIDIGLT,0,0
+CVQSDIDSFFKHLIDIGLTT,0,0
+VQSDIDSFFKHLIDIGLTTP,0,0
+QSDIDSFFKHLIDIGLTTPS,0,0
+SDIDSFFKHLIDIGLTTPSS,0,0
+DIDSFFKHLIDIGLTTPSSY,0,1
+IDSFFKHLIDIGLTTPSSYL,0,0
+DSFFKHLIDIGLTTPSSYLS,2,0
+SFFKHLIDIGLTTPSSYLSN,3,0
+FFKHLIDIGLTTPSSYLSNV,0,0
+FKHLIDIGLTTPSSYLSNVL,0,2
+KHLIDIGLTTPSSYLSNVLD,2,2
+HLIDIGLTTPSSYLSNVLDD,0,0
+LIDIGLTTPSSYLSNVLDDN,0,0
+IDIGLTTPSSYLSNVLDDNI,0,0
+DIGLTTPSSYLSNVLDDNIC,0,0
+IGLTTPSSYLSNVLDDNICG,0,3
+GLTTPSSYLSNVLDDNICGA,0,3
+LTTPSSYLSNVLDDNICGAD,0,0
+TTPSSYLSNVLDDNICGADK,0,0
+TPSSYLSNVLDDNICGADKA,0,0
+PSSYLSNVLDDNICGADKAP,0,0
+SSYLSNVLDDNICGADKAPW,0,0
+SYLSNVLDDNICGADKAPWT,3,4
+YLSNVLDDNICGADKAPWTT,0,0
+LSNVLDDNICGADKAPWTTY,0,0
+SNVLDDNICGADKAPWTTYT,0,0
+NVLDDNICGADKAPWTTYTT,0,0
+VLDDNICGADKAPWTTYTTY,0,0
+LDDNICGADKAPWTTYTTYT,0,0
+DDNICGADKAPWTTYTTYTT,0,0
+DNICGADKAPWTTYTTYTTT,0,0
+NICGADKAPWTTYTTYTTTE,1,3
+ICGADKAPWTTYTTYTTTEK,0,7
+CGADKAPWTTYTTYTTTEKC,0,1
+GADKAPWTTYTTYTTTEKCN,0,0
+ADKAPWTTYTTYTTTEKCNK,1,0
+DKAPWTTYTTYTTTEKCNKE,0,0
+KAPWTTYTTYTTTEKCNKER,0,0
+APWTTYTTYTTTEKCNKERD,0,0
+PWTTYTTYTTTEKCNKERDK,0,2
+WTTYTTYTTTEKCNKERDKS,0,0
+TTYTTYTTTEKCNKERDKSK,6.5,91
+TYTTYTTTEKCNKERDKSKS,0,80
+YTTYTTTEKCNKERDKSKSQ,0,3.5
+TTYTTTEKCNKERDKSKSQS,0,0
+TYTTTEKCNKERDKSKSQSS,1,86.5
+YTTTEKCNKERDKSKSQSSD,0,0
+TTTEKCNKERDKSKSQSSDT,0,0
+TTEKCNKERDKSKSQSSDTL,0,1
+TEKCNKERDKSKSQSSDTLV,0,0
+EKCNKERDKSKSQSSDTLVV,1,0
+KCNKERDKSKSQSSDTLVVV,0,0
+CNKERDKSKSQSSDTLVVVN,3,0
+NKERDKSKSQSSDTLVVVNV,2.5,0
+KERDKSKSQSSDTLVVVNVP,0,0
+ERDKSKSQSSDTLVVVNVPS,0,0
+RDKSKSQSSDTLVVVNVPSP,0,2
+DKSKSQSSDTLVVVNVPSPL,0,0
+KSKSQSSDTLVVVNVPSPLG,0,3
+SKSQSSDTLVVVNVPSPLGN,0,0
+KSQSSDTLVVVNVPSPLGNT,0,0
+SQSSDTLVVVNVPSPLGNTP,1,3
+QSSDTLVVVNVPSPLGNTPY,0.5,2
+SSDTLVVVNVPSPLGNTPYR,0,0
+SDTLVVVNVPSPLGNTPYRY,0,2
+DTLVVVNVPSPLGNTPYRYK,0,0
+TLVVVNVPSPLGNTPYRYKY,2.5,0
+LVVVNVPSPLGNTPYRYKYA,1,0
+VVVNVPSPLGNTPYRYKYAC,0,0
+VVNVPSPLGNTPYRYKYACQ,0,0
+VNVPSPLGNTPYRYKYACQC,0,0
+NVPSPLGNTPYRYKYACQCK,101,3.5
+VPSPLGNTPYRYKYACQCKI,0,0
+PSPLGNTPYRYKYACQCKIP,10.5,0
+SPLGNTPYRYKYACQCKIPT,0,0
+PLGNTPYRYKYACQCKIPTN,6,1
+LGNTPYRYKYACQCKIPTNE,2,3
+GNTPYRYKYACQCKIPTNEE,0,0
+NTPYRYKYACQCKIPTNEET,0,0
+TPYRYKYACQCKIPTNEETC,0,0
+PYRYKYACQCKIPTNEETCD,0,0
+YRYKYACQCKIPTNEETCDD,0,1
+RYKYACQCKIPTNEETCDDR,0,1
+YKYACQCKIPTNEETCDDRK,0,0
+KYACQCKIPTNEETCDDRKE,0,1
+YACQCKIPTNEETCDDRKEY,0,0
+ACQCKIPTNEETCDDRKEYM,0,0
+CQCKIPTNEETCDDRKEYMN,0,0
+QCKIPTNEETCDDRKEYMNQ,0,0
+CKIPTNEETCDDRKEYMNQW,0,0
+KIPTNEETCDDRKEYMNQWS,5,0
+IPTNEETCDDRKEYMNQWSC,1,0
+PTNEETCDDRKEYMNQWSCG,4,2
+TNEETCDDRKEYMNQWSCGS,0,0
+NEETCDDRKEYMNQWSCGSA,4,0
+EETCDDRKEYMNQWSCGSAR,0,0
+ETCDDRKEYMNQWSCGSART,0,0
+TCDDRKEYMNQWSCGSARTM,0,3
+CDDRKEYMNQWSCGSARTMK,0,8
+DDRKEYMNQWSCGSARTMKR,1,6
+DRKEYMNQWSCGSARTMKRG,1,0
+RKEYMNQWSCGSARTMKRGY,0,0
+KEYMNQWSCGSARTMKRGYK,92,92
+EYMNQWSCGSARTMKRGYKN,0,0
+YMNQWSCGSARTMKRGYKND,0,3
+MNQWSCGSARTMKRGYKNDN,0,0
+NQWSCGSARTMKRGYKNDNY,2,2
+QWSCGSARTMKRGYKNDNYE,0,0
+WSCGSARTMKRGYKNDNYEL,1,0
+SCGSARTMKRGYKNDNYELC,8,5
+CGSARTMKRGYKNDNYELCK,2,96.5
+GSARTMKRGYKNDNYELCKY,0,4
+SARTMKRGYKNDNYELCKYN,0,0
+ARTMKRGYKNDNYELCKYNG,0,0
+RTMKRGYKNDNYELCKYNGV,7,0
+TMKRGYKNDNYELCKYNGVD,1,7
+MKRGYKNDNYELCKYNGVDV,0,0.5
+KRGYKNDNYELCKYNGVDVK,0,0
+RGYKNDNYELCKYNGVDVKP,0,2
+GYKNDNYELCKYNGVDVKPT,0,6
+YKNDNYELCKYNGVDVKPTT,4,2
+KNDNYELCKYNGVDVKPTTV,0,0
+NDNYELCKYNGVDVKPTTVR,0,6
+DNYELCKYNGVDVKPTTVRS,1.5,0
+NYELCKYNGVDVKPTTVRSN,0,0
+YELCKYNGVDVKPTTVRSNS,0.5,0
+ELCKYNGVDVKPTTVRSNSS,7,0
+LCKYNGVDVKPTTVRSNSSK,0,3
+CKYNGVDVKPTTVRSNSSKL,0,0
+KYNGVDVKPTTVRSNSSKLD,0,0
+YNGVDVKPTTVRSNSSKLDG,1,1.5
+NGVDVKPTTVRSNSSKLDGN,3,0
+GVDVKPTTVRSNSSKLDGND,0,1
+VDVKPTTVRSNSSKLDGNDV,0,0
+DVKPTTVRSNSSKLDGNDVT,4,1.5
+VKPTTVRSNSSKLDGNDVTF,6,8
+KPTTVRSNSSKLDGNDVTFF,0,0
+PTTVRSNSSKLDGNDVTFFN,0,0
+TTVRSNSSKLDGNDVTFFNL,4,0
+TVRSNSSKLDGNDVTFFNLF,2,1
+VRSNSSKLDGNDVTFFNLFE,0,0
+RSNSSKLDGNDVTFFNLFEQ,4,0
+SNSSKLDGNDVTFFNLFEQW,3,1
+NSSKLDGNDVTFFNLFEQWN,0,0
+SSKLDGNDVTFFNLFEQWNK,0.5,0
+SKLDGNDVTFFNLFEQWNKE,0,3
+KLDGNDVTFFNLFEQWNKEI,0,0
+LDGNDVTFFNLFEQWNKEIQ,0,0
+DGNDVTFFNLFEQWNKEIQY,0,0
+GNDVTFFNLFEQWNKEIQYQ,0,2
+NDVTFFNLFEQWNKEIQYQI,0,0
+DVTFFNLFEQWNKEIQYQIE,0,2
+VTFFNLFEQWNKEIQYQIEQ,0,0
+TFFNLFEQWNKEIQYQIEQY,0,4
+FFNLFEQWNKEIQYQIEQYM,9,9
+FNLFEQWNKEIQYQIEQYMT,0,0
+NLFEQWNKEIQYQIEQYMTN,0,0
+LFEQWNKEIQYQIEQYMTNA,0,0
+FEQWNKEIQYQIEQYMTNAN,1,0
+EQWNKEIQYQIEQYMTNANI,4,0
+QWNKEIQYQIEQYMTNANIS,0,0
+WNKEIQYQIEQYMTNANISC,4,0
+NKEIQYQIEQYMTNANISCI,0,0
+KEIQYQIEQYMTNANISCID,3,0
+EIQYQIEQYMTNANISCIDE,0,0
+IQYQIEQYMTNANISCIDEK,0,0
+QYQIEQYMTNANISCIDEKE,4,0
+YQIEQYMTNANISCIDEKEV,0,0
+QIEQYMTNANISCIDEKEVL,0,9
+IEQYMTNANISCIDEKEVLD,4,0
+EQYMTNANISCIDEKEVLDS,4,0
+QYMTNANISCIDEKEVLDSV,0,0
+YMTNANISCIDEKEVLDSVS,0,0
+MTNANISCIDEKEVLDSVSD,0,0
+TNANISCIDEKEVLDSVSDE,0,0
+NANISCIDEKEVLDSVSDEG,0,0
+ANISCIDEKEVLDSVSDEGT,0,0
+NISCIDEKEVLDSVSDEGTP,0,0
+ISCIDEKEVLDSVSDEGTPK,0,4
+SCIDEKEVLDSVSDEGTPKV,0,0
+CIDEKEVLDSVSDEGTPKVR,2,0
+IDEKEVLDSVSDEGTPKVRG,0,0
+DEKEVLDSVSDEGTPKVRGG,4,0
+EKEVLDSVSDEGTPKVRGGY,2,0
+KEVLDSVSDEGTPKVRGGYE,0,0
+EVLDSVSDEGTPKVRGGYED,0,0
+VLDSVSDEGTPKVRGGYEDG,0,0
+LDSVSDEGTPKVRGGYEDGR,4,1
+DSVSDEGTPKVRGGYEDGRN,0,1
+SVSDEGTPKVRGGYEDGRNN,0,2
+VSDEGTPKVRGGYEDGRNNN,2,0.5
+SDEGTPKVRGGYEDGRNNNT,0,0
+DEGTPKVRGGYEDGRNNNTD,0,0
+EGTPKVRGGYEDGRNNNTDQ,0,0
+GTPKVRGGYEDGRNNNTDQG,0,0
+TPKVRGGYEDGRNNNTDQGT,4,0
+PKVRGGYEDGRNNNTDQGTN,0,0
+KVRGGYEDGRNNNTDQGTNC,0,2
+VRGGYEDGRNNNTDQGTNCK,0,0
+RGGYEDGRNNNTDQGTNCKE,1,0
+GGYEDGRNNNTDQGTNCKEK,0,0
+GYEDGRNNNTDQGTNCKEKC,3,2
+YEDGRNNNTDQGTNCKEKCK,0,0
+EDGRNNNTDQGTNCKEKCKC,3,0
+DGRNNNTDQGTNCKEKCKCY,0,0
+GRNNNTDQGTNCKEKCKCYK,0,3
+RNNNTDQGTNCKEKCKCYKL,1,0
+NNNTDQGTNCKEKCKCYKLW,0,0
+NNTDQGTNCKEKCKCYKLWI,0,1
+NTDQGTNCKEKCKCYKLWIE,0,0
+TDQGTNCKEKCKCYKLWIEK,0,0
+DQGTNCKEKCKCYKLWIEKI,0,1
+QGTNCKEKCKCYKLWIEKIN,0,1
+GTNCKEKCKCYKLWIEKIND,1,0
+TNCKEKCKCYKLWIEKINDQ,0,0
+NCKEKCKCYKLWIEKINDQW,0,0
+CKEKCKCYKLWIEKINDQWG,7,1
+KEKCKCYKLWIEKINDQWGK,1,0
+EKCKCYKLWIEKINDQWGKQ,2,8
+KCKCYKLWIEKINDQWGKQK,5,2
+CKCYKLWIEKINDQWGKQKD,0,0
+KCYKLWIEKINDQWGKQKDN,0,2
+CYKLWIEKINDQWGKQKDNY,0,0
+YKLWIEKINDQWGKQKDNYN,0,0
+KLWIEKINDQWGKQKDNYNK,0,3
+LWIEKINDQWGKQKDNYNKF,0,0
+WIEKINDQWGKQKDNYNKFR,96,98
+IEKINDQWGKQKDNYNKFRS,1,1
+EKINDQWGKQKDNYNKFRSK,99,97
+KINDQWGKQKDNYNKFRSKQ,0,10
+INDQWGKQKDNYNKFRSKQI,0,0
+NDQWGKQKDNYNKFRSKQIY,1,0
+DQWGKQKDNYNKFRSKQIYD,2,0
+QWGKQKDNYNKFRSKQIYDA,0,0
+WGKQKDNYNKFRSKQIYDAN,0,0
+GKQKDNYNKFRSKQIYDANK,0,2
+KQKDNYNKFRSKQIYDANKG,3,2
+QKDNYNKFRSKQIYDANKGS,0,0
+KDNYNKFRSKQIYDANKGSQ,0,0
+DNYNKFRSKQIYDANKGSQN,0,0
+NYNKFRSKQIYDANKGSQNK,0,0
+YNKFRSKQIYDANKGSQNKK,1,0
+NKFRSKQIYDANKGSQNKKV,0,0
+KFRSKQIYDANKGSQNKKVV,1,83
+FRSKQIYDANKGSQNKKVVS,3,0
+RSKQIYDANKGSQNKKVVSL,0,85
+SKQIYDANKGSQNKKVVSLS,1,89
+KQIYDANKGSQNKKVVSLSN,0,0
+QIYDANKGSQNKKVVSLSNF,0,0
+IYDANKGSQNKKVVSLSNFL,2,4
+YDANKGSQNKKVVSLSNFLF,2,0
+DANKGSQNKKVVSLSNFLFF,1.5,4
+ANKGSQNKKVVSLSNFLFFS,0.5,0
+NKGSQNKKVVSLSNFLFFSC,0,0
+KGSQNKKVVSLSNFLFFSCW,3,0
+GSQNKKVVSLSNFLFFSCWE,1,0
+SQNKKVVSLSNFLFFSCWEE,0,11.5
+QNKKVVSLSNFLFFSCWEEY,0,0
+NKKVVSLSNFLFFSCWEEYI,2,0
+KKVVSLSNFLFFSCWEEYIQ,0,0
+KVVSLSNFLFFSCWEEYIQK,0,0
+VVSLSNFLFFSCWEEYIQKY,2,5.5
+VSLSNFLFFSCWEEYIQKYF,0,0
+SLSNFLFFSCWEEYIQKYFN,0,0
+LSNFLFFSCWEEYIQKYFNG,1,6.5
+SNFLFFSCWEEYIQKYFNGD,0,0
+NFLFFSCWEEYIQKYFNGDW,0,3.5
+FLFFSCWEEYIQKYFNGDWS,0,0
+LFFSCWEEYIQKYFNGDWSK,0,0
+FFSCWEEYIQKYFNGDWSKI,0,0
+FSCWEEYIQKYFNGDWSKIK,0,0
+SCWEEYIQKYFNGDWSKIKN,0,0
+CWEEYIQKYFNGDWSKIKNI,0,0
+WEEYIQKYFNGDWSKIKNIG,2,0
+EEYIQKYFNGDWSKIKNIGS,0,4
+EYIQKYFNGDWSKIKNIGSD,0,6
+YIQKYFNGDWSKIKNIGSDT,0,1
+IQKYFNGDWSKIKNIGSDTF,2,3
+QKYFNGDWSKIKNIGSDTFE,0,1
+KYFNGDWSKIKNIGSDTFEF,0,1
+YFNGDWSKIKNIGSDTFEFL,0,0
+FNGDWSKIKNIGSDTFEFLI,0,0
+NGDWSKIKNIGSDTFEFLIK,0,0
+GDWSKIKNIGSDTFEFLIKK,0,0
+DWSKIKNIGSDTFEFLIKKC,0,2
+WSKIKNIGSDTFEFLIKKCG,1,0
+SKIKNIGSDTFEFLIKKCGN,0.5,1
+KIKNIGSDTFEFLIKKCGNN,1,3
+IKNIGSDTFEFLIKKCGNNS,0,0
+KNIGSDTFEFLIKKCGNNSA,0,0
+NIGSDTFEFLIKKCGNNSAH,0,0
+IGSDTFEFLIKKCGNNSAHG,0,0
+GSDTFEFLIKKCGNNSAHGE,0,0
+SDTFEFLIKKCGNNSAHGEE,0,0
+DTFEFLIKKCGNNSAHGEEI,0,0
+TFEFLIKKCGNNSAHGEEIF,0,1
+FEFLIKKCGNNSAHGEEIFN,3.5,0
+EFLIKKCGNNSAHGEEIFNE,0,0
+FLIKKCGNNSAHGEEIFNEK,0,0
+LIKKCGNNSAHGEEIFNEKL,0,0
+IKKCGNNSAHGEEIFNEKLK,2,0
+KKCGNNSAHGEEIFNEKLKN,0,0
+KCGNNSAHGEEIFNEKLKNA,1,0
+CGNNSAHGEEIFNEKLKNAE,0,1
+GNNSAHGEEIFNEKLKNAEK,0,0
+NNSAHGEEIFNEKLKNAEKK,0,0
+NSAHGEEIFNEKLKNAEKKC,0,0
+SAHGEEIFNEKLKNAEKKCK,0,100
+AHGEEIFNEKLKNAEKKCKE,0,0
+HGEEIFNEKLKNAEKKCKEN,0,0
+GEEIFNEKLKNAEKKCKENE,0,0
+EEIFNEKLKNAEKKCKENES,0,1
+EIFNEKLKNAEKKCKENEST,0,0
+IFNEKLKNAEKKCKENESTD,0,0
+FNEKLKNAEKKCKENESTDT,0,0
+NEKLKNAEKKCKENESTDTN,0,0
+EKLKNAEKKCKENESTDTNI,0,0
+KLKNAEKKCKENESTDTNIN,0,0
+LKNAEKKCKENESTDTNINK,1,1
+KNAEKKCKENESTDTNINKS,0,0
+NAEKKCKENESTDTNINKSE,0,2
+AEKKCKENESTDTNINKSET,0,0
+EKKCKENESTDTNINKSETS,0,0
+KKCKENESTDTNINKSETSC,0,0
+KCKENESTDTNINKSETSCD,0,0
+CKENESTDTNINKSETSCDL,0,0
+KENESTDTNINKSETSCDLN,0,0
+ENESTDTNINKSETSCDLNA,0,2
+NESTDTNINKSETSCDLNAT,0,0
+ESTDTNINKSETSCDLNATN,2,1
+STDTNINKSETSCDLNATNY,4,0
+TDTNINKSETSCDLNATNYI,0,3
+DTNINKSETSCDLNATNYIR,0,0
+TNINKSETSCDLNATNYIRG,0,0
+NINKSETSCDLNATNYIRGC,0,0
+INKSETSCDLNATNYIRGCQ,0,0
+NKSETSCDLNATNYIRGCQS,0,0
+KSETSCDLNATNYIRGCQSK,1,0
+SETSCDLNATNYIRGCQSKT,1,0
+ETSCDLNATNYIRGCQSKTY,1,0
+TSCDLNATNYIRGCQSKTYD,0,0
+SCDLNATNYIRGCQSKTYDG,2,0
+CDLNATNYIRGCQSKTYDGK,0,96
+DLNATNYIRGCQSKTYDGKI,0,0.5
+LNATNYIRGCQSKTYDGKIF,1,1
+NATNYIRGCQSKTYDGKIFP,3,0
+ATNYIRGCQSKTYDGKIFPG,0,0
+TNYIRGCQSKTYDGKIFPGK,0,0
+NYIRGCQSKTYDGKIFPGKG,0,1
+YIRGCQSKTYDGKIFPGKGG,0.5,0
+IRGCQSKTYDGKIFPGKGGE,0,0
+RGCQSKTYDGKIFPGKGGEK,4,3.5
+GCQSKTYDGKIFPGKGGEKQ,0,1
+CQSKTYDGKIFPGKGGEKQW,1,0
+QSKTYDGKIFPGKGGEKQWI,0,92.5
+SKTYDGKIFPGKGGEKQWIC,2,2
+KTYDGKIFPGKGGEKQWICK,0,3
+TYDGKIFPGKGGEKQWICKD,1,4
+YDGKIFPGKGGEKQWICKDT,0,0
+DGKIFPGKGGEKQWICKDTI,0,0
+GKIFPGKGGEKQWICKDTII,0,3
+KIFPGKGGEKQWICKDTIIH,1,0
+IFPGKGGEKQWICKDTIIHG,0,1.5
+FPGKGGEKQWICKDTIIHGD,0,0
+PGKGGEKQWICKDTIIHGDT,0,0
+GKGGEKQWICKDTIIHGDTN,0,1
+KGGEKQWICKDTIIHGDTNG,0,0
+GGEKQWICKDTIIHGDTNGA,0,6
+GEKQWICKDTIIHGDTNGAC,0,8
+EKQWICKDTIIHGDTNGACI,0,0
+KQWICKDTIIHGDTNGACIP,0,0
+QWICKDTIIHGDTNGACIPP,0,0
+WICKDTIIHGDTNGACIPPR,0,0
+ICKDTIIHGDTNGACIPPRT,0,0
+CKDTIIHGDTNGACIPPRTQ,0,0
+KDTIIHGDTNGACIPPRTQN,0,0
+DTIIHGDTNGACIPPRTQNL,0,2
+TIIHGDTNGACIPPRTQNLC,2,0
+IIHGDTNGACIPPRTQNLCV,0,0
+IHGDTNGACIPPRTQNLCVG,0,1
+HGDTNGACIPPRTQNLCVGE,0,0
+GDTNGACIPPRTQNLCVGEL,0,0
+DTNGACIPPRTQNLCVGELW,0,0
+TNGACIPPRTQNLCVGELWD,1,3
+NGACIPPRTQNLCVGELWDK,0,4.5
+GACIPPRTQNLCVGELWDKS,1,3
+ACIPPRTQNLCVGELWDKSY,0,1
+CIPPRTQNLCVGELWDKSYG,2,9
+IPPRTQNLCVGELWDKSYGG,0,1
+PPRTQNLCVGELWDKSYGGR,0,3
+PRTQNLCVGELWDKSYGGRS,5,0
+RTQNLCVGELWDKSYGGRSN,0,0
+TQNLCVGELWDKSYGGRSNI,0,0
+QNLCVGELWDKSYGGRSNIK,107,115
+NLCVGELWDKSYGGRSNIKN,0,0
+LCVGELWDKSYGGRSNIKND,0,1
+CVGELWDKSYGGRSNIKNDT,0,2
+VGELWDKSYGGRSNIKNDTK,2,3.5
+GELWDKSYGGRSNIKNDTKE,2,0
+ELWDKSYGGRSNIKNDTKEL,0,0
+LWDKSYGGRSNIKNDTKELL,0,0
+WDKSYGGRSNIKNDTKELLK,5,0
+DKSYGGRSNIKNDTKELLKE,0,0
+KSYGGRSNIKNDTKELLKEK,1,0
+SYGGRSNIKNDTKELLKEKI,0,0
+YGGRSNIKNDTKELLKEKIK,118,118
+GGRSNIKNDTKELLKEKIKN,0,0
+GRSNIKNDTKELLKEKIKNA,0,0
+RSNIKNDTKELLKEKIKNAI,0,0
+SNIKNDTKELLKEKIKNAIH,0,0
+NIKNDTKELLKEKIKNAIHK,0,0
+IKNDTKELLKEKIKNAIHKE,8,0
+KNDTKELLKEKIKNAIHKET,0,0
+NDTKELLKEKIKNAIHKETE,0,0
+DTKELLKEKIKNAIHKETEL,0,0
+TKELLKEKIKNAIHKETELL,0,0
+KELLKEKIKNAIHKETELLY,5,6
+ELLKEKIKNAIHKETELLYE,2,6
+LLKEKIKNAIHKETELLYEY,1,0
+LKEKIKNAIHKETELLYEYH,0,0
+KEKIKNAIHKETELLYEYHD,0,7
+EKIKNAIHKETELLYEYHDT,0,3
+KIKNAIHKETELLYEYHDTG,2,5
+IKNAIHKETELLYEYHDTGT,0,0
+KNAIHKETELLYEYHDTGTA,6,0
+NAIHKETELLYEYHDTGTAI,1,0
+AIHKETELLYEYHDTGTAII,5,0
+IHKETELLYEYHDTGTAIIS,1,0
+HKETELLYEYHDTGTAIISK,0,0
+KETELLYEYHDTGTAIISKN,0,0
+ETELLYEYHDTGTAIISKND,2,0
+TELLYEYHDTGTAIISKNDK,0,0
+ELLYEYHDTGTAIISKNDKK,0,7
+LLYEYHDTGTAIISKNDKKG,2,0
+LYEYHDTGTAIISKNDKKGQ,0,0
+YEYHDTGTAIISKNDKKGQK,0,3
+EYHDTGTAIISKNDKKGQKG,0,0
+YHDTGTAIISKNDKKGQKGK,89,0
+HDTGTAIISKNDKKGQKGKN,0,0
+DTGTAIISKNDKKGQKGKND,0,6
+TGTAIISKNDKKGQKGKNDP,0,4
+GTAIISKNDKKGQKGKNDPN,0,1.5
+TAIISKNDKKGQKGKNDPNG,0,0
+AIISKNDKKGQKGKNDPNGL,0,0
+IISKNDKKGQKGKNDPNGLP,3,0
+ISKNDKKGQKGKNDPNGLPK,0,0
+SKNDKKGQKGKNDPNGLPKG,0,0
+KNDKKGQKGKNDPNGLPKGF,1,0
+NDKKGQKGKNDPNGLPKGFC,5.5,0
+DKKGQKGKNDPNGLPKGFCH,2,1
+KKGQKGKNDPNGLPKGFCHA,0,0
+KGQKGKNDPNGLPKGFCHAV,0,1
+GQKGKNDPNGLPKGFCHAVQ,0,0
+QKGKNDPNGLPKGFCHAVQR,0,1
+KGKNDPNGLPKGFCHAVQRS,1,0
+GKNDPNGLPKGFCHAVQRSF,0,0
+KNDPNGLPKGFCHAVQRSFI,0,4
+NDPNGLPKGFCHAVQRSFID,1,0
+DPNGLPKGFCHAVQRSFIDY,0,0
+PNGLPKGFCHAVQRSFIDYK,0,2
+NGLPKGFCHAVQRSFIDYKN,0,0
+GLPKGFCHAVQRSFIDYKNM,0,0
+LPKGFCHAVQRSFIDYKNMI,0,0
+PKGFCHAVQRSFIDYKNMIL,5,0
+KGFCHAVQRSFIDYKNMILG,0,1
+GFCHAVQRSFIDYKNMILGT,3,0
+FCHAVQRSFIDYKNMILGTS,6,1
+CHAVQRSFIDYKNMILGTSV,4,3
+HAVQRSFIDYKNMILGTSVN,0,0
+AVQRSFIDYKNMILGTSVNI,0,0
+VQRSFIDYKNMILGTSVNIY,9,0
+QRSFIDYKNMILGTSVNIYE,0,0
+RSFIDYKNMILGTSVNIYEH,0,0
+SFIDYKNMILGTSVNIYEHI,0,0
+FIDYKNMILGTSVNIYEHIG,0,0
+IDYKNMILGTSVNIYEHIGK,2,0
+DYKNMILGTSVNIYEHIGKL,7,0
+YKNMILGTSVNIYEHIGKLQ,0,0
+KNMILGTSVNIYEHIGKLQE,1,0
+NMILGTSVNIYEHIGKLQED,0,0
+MILGTSVNIYEHIGKLQEDI,4,0
+ILGTSVNIYEHIGKLQEDIK,2,0
+LGTSVNIYEHIGKLQEDIKK,0,0
+GTSVNIYEHIGKLQEDIKKI,0,0
+TSVNIYEHIGKLQEDIKKII,1,0
+SVNIYEHIGKLQEDIKKIIE,1,2
+VNIYEHIGKLQEDIKKIIEK,1,0
+NIYEHIGKLQEDIKKIIEKG,0,0
+IYEHIGKLQEDIKKIIEKGT,0,1
+YEHIGKLQEDIKKIIEKGTP,0,0
+EHIGKLQEDIKKIIEKGTPQ,0,0
+HIGKLQEDIKKIIEKGTPQQ,6,0
+IGKLQEDIKKIIEKGTPQQK,2,0
+GKLQEDIKKIIEKGTPQQKD,0,0
+KLQEDIKKIIEKGTPQQKDK,0,0
+LQEDIKKIIEKGTPQQKDKI,0,0
+QEDIKKIIEKGTPQQKDKIG,8,0
+EDIKKIIEKGTPQQKDKIGG,0,0
+DIKKIIEKGTPQQKDKIGGV,0,2
+IKKIIEKGTPQQKDKIGGVG,0,0
+KKIIEKGTPQQKDKIGGVGS,0,0
+KIIEKGTPQQKDKIGGVGSS,0,1
+IIEKGTPQQKDKIGGVGSST,0,2
+IEKGTPQQKDKIGGVGSSTE,0,0
+EKGTPQQKDKIGGVGSSTEN,0,0
+KGTPQQKDKIGGVGSSTENV,0,2
+GTPQQKDKIGGVGSSTENVN,0,0
+TPQQKDKIGGVGSSTENVNA,0,1
+PQQKDKIGGVGSSTENVNAW,0,0
+QQKDKIGGVGSSTENVNAWW,0,0
+QKDKIGGVGSSTENVNAWWK,0,0
+KDKIGGVGSSTENVNAWWKG,0,45
+DKIGGVGSSTENVNAWWKGI,0,3
+KIGGVGSSTENVNAWWKGIE,0,0
+IGGVGSSTENVNAWWKGIER,0,0
+GGVGSSTENVNAWWKGIERE,0,0
+GVGSSTENVNAWWKGIEREM,10,46.5
+VGSSTENVNAWWKGIEREMW,4,103.5
+GSSTENVNAWWKGIEREMWD,93,0.5
+SSTENVNAWWKGIEREMWDA,7.5,0
+STENVNAWWKGIEREMWDAV,0,0
+TENVNAWWKGIEREMWDAVR,3,49.5
+ENVNAWWKGIEREMWDAVRC,4,3
+NVNAWWKGIEREMWDAVRCA,0,0
+VNAWWKGIEREMWDAVRCAI,0,0
+NAWWKGIEREMWDAVRCAIT,0,2
+AWWKGIEREMWDAVRCAITK,0,0
+WWKGIEREMWDAVRCAITKI,0,0
+WKGIEREMWDAVRCAITKIN,0,0
+KGIEREMWDAVRCAITKINK,0,0
+GIEREMWDAVRCAITKINKK,1,0
+IEREMWDAVRCAITKINKKN,2,0
+EREMWDAVRCAITKINKKNN,0,0
+REMWDAVRCAITKINKKNNN,4,0
+EMWDAVRCAITKINKKNNNS,2,0
+MWDAVRCAITKINKKNNNSI,0,0
+WDAVRCAITKINKKNNNSIF,0,0
+DAVRCAITKINKKNNNSIFN,0,0
+AVRCAITKINKKNNNSIFNG,0,0
+VRCAITKINKKNNNSIFNGD,0,0
+RCAITKINKKNNNSIFNGDE,3,0
+CAITKINKKNNNSIFNGDEC,7,2
+AITKINKKNNNSIFNGDECG,0,0
+ITKINKKNNNSIFNGDECGV,0,0
+TKINKKNNNSIFNGDECGVS,3,0
+KINKKNNNSIFNGDECGVSP,0,0
+INKKNNNSIFNGDECGVSPP,0,0
+NKKNNNSIFNGDECGVSPPT,0,0
+KKNNNSIFNGDECGVSPPTG,0,2
+KNNNSIFNGDECGVSPPTGN,1,0
+NNNSIFNGDECGVSPPTGND,0,0
+NNSIFNGDECGVSPPTGNDE,0,0
+NSIFNGDECGVSPPTGNDED,0,0
+SIFNGDECGVSPPTGNDEDQ,0,0
+IFNGDECGVSPPTGNDEDQS,0,0
+FNGDECGVSPPTGNDEDQSV,0,0
+NGDECGVSPPTGNDEDQSVS,0,0
+GDECGVSPPTGNDEDQSVSW,2,0
+DECGVSPPTGNDEDQSVSWF,6,2
+ECGVSPPTGNDEDQSVSWFK,1,0
+CGVSPPTGNDEDQSVSWFKE,0,0
+GVSPPTGNDEDQSVSWFKEW,3,0
+VSPPTGNDEDQSVSWFKEWG,6.5,0.5
+SPPTGNDEDQSVSWFKEWGE,6,4
+PPTGNDEDQSVSWFKEWGEQ,0,0
+PTGNDEDQSVSWFKEWGEQF,0,0
+TGNDEDQSVSWFKEWGEQFC,0,1.5
+GNDEDQSVSWFKEWGEQFCI,0,0
+NDEDQSVSWFKEWGEQFCIE,0,0
+DEDQSVSWFKEWGEQFCIER,0,0
+EDQSVSWFKEWGEQFCIERL,0,0
+DQSVSWFKEWGEQFCIERLR,0,0
+QSVSWFKEWGEQFCIERLRY,0,0
+SVSWFKEWGEQFCIERLRYE,0,0
+VSWFKEWGEQFCIERLRYEQ,0,2
+SWFKEWGEQFCIERLRYEQN,0,0
+WFKEWGEQFCIERLRYEQNI,0,0
+FKEWGEQFCIERLRYEQNIR,0,0
+KEWGEQFCIERLRYEQNIRE,0,0
+EWGEQFCIERLRYEQNIREA,0,0
+WGEQFCIERLRYEQNIREAC,1,1
+GEQFCIERLRYEQNIREACT,0,0
+EQFCIERLRYEQNIREACTI,0,0
+QFCIERLRYEQNIREACTIN,0,0
+FCIERLRYEQNIREACTING,2,2.5
+CIERLRYEQNIREACTINGK,0,0
+IERLRYEQNIREACTINGKN,3.5,3
+ERLRYEQNIREACTINGKNE,1,0
+RLRYEQNIREACTINGKNEK,0,0
+LRYEQNIREACTINGKNEKK,11.5,0
+RYEQNIREACTINGKNEKKC,0,0
+YEQNIREACTINGKNEKKCI,0,0
+EQNIREACTINGKNEKKCIN,0,4
+QNIREACTINGKNEKKCINS,0,0
+NIREACTINGKNEKKCINSK,0,0
+IREACTINGKNEKKCINSKS,9,88
+REACTINGKNEKKCINSKSG,0,2
+EACTINGKNEKKCINSKSGQ,1,0
+ACTINGKNEKKCINSKSGQG,0,5.5
+CTINGKNEKKCINSKSGQGD,1,0
+TINGKNEKKCINSKSGQGDK,0,2.5
+INGKNEKKCINSKSGQGDKI,0,6
+NGKNEKKCINSKSGQGDKIQ,5,1
+GKNEKKCINSKSGQGDKIQG,0,3
+KNEKKCINSKSGQGDKIQGA,0,0
+NEKKCINSKSGQGDKIQGAC,0,0
+EKKCINSKSGQGDKIQGACK,0,0
+KKCINSKSGQGDKIQGACKR,0,0
+KCINSKSGQGDKIQGACKRK,113,0
+CINSKSGQGDKIQGACKRKC,0,0
+INSKSGQGDKIQGACKRKCE,0,0
+NSKSGQGDKIQGACKRKCEK,0,0
+SKSGQGDKIQGACKRKCEKY,0,0
+KSGQGDKIQGACKRKCEKYK,78,96
+SGQGDKIQGACKRKCEKYKK,433.5,334
+GQGDKIQGACKRKCEKYKKY,175,692.5
+QGDKIQGACKRKCEKYKKYI,173,522.5
+GDKIQGACKRKCEKYKKYIS,82,103
+DKIQGACKRKCEKYKKYISE,97,99
+KIQGACKRKCEKYKKYISEK,929.5,1531
+IQGACKRKCEKYKKYISEKK,7662.5,20349.5
+QGACKRKCEKYKKYISEKKQ,1523.5,2415
+GACKRKCEKYKKYISEKKQE,146.5,246.5
+ACKRKCEKYKKYISEKKQEW,91,93
+CKRKCEKYKKYISEKKQEWD,82.5,89.5
+KRKCEKYKKYISEKKQEWDK,90,90
+RKCEKYKKYISEKKQEWDKQ,3,0
+KCEKYKKYISEKKQEWDKQK,85,95
+CEKYKKYISEKKQEWDKQKT,87,88
+EKYKKYISEKKQEWDKQKTK,193.5,1069.5
+KYKKYISEKKQEWDKQKTKY,244.5,278
+YKKYISEKKQEWDKQKTKYE,0,83
+KKYISEKKQEWDKQKTKYEN,0,0
+KYISEKKQEWDKQKTKYENK,338.5,919
+YISEKKQEWDKQKTKYENKY,88,79
+ISEKKQEWDKQKTKYENKYV,490.5,804.5
+SEKKQEWDKQKTKYENKYVG,0,50
+EKKQEWDKQKTKYENKYVGK,1387,692
+KKQEWDKQKTKYENKYVGKS,176,367
+KQEWDKQKTKYENKYVGKSA,2181,3327
+QEWDKQKTKYENKYVGKSAS,1796.5,7089.5
+EWDKQKTKYENKYVGKSASD,2445,4565
+WDKQKTKYENKYVGKSASDL,139,1308
+DKQKTKYENKYVGKSASDLL,68,473
+KQKTKYENKYVGKSASDLLK,2356,5650
+QKTKYENKYVGKSASDLLKE,52,46
+KTKYENKYVGKSASDLLKEN,80,94
+TKYENKYVGKSASDLLKENY,0,1.5
+KYENKYVGKSASDLLKENYP,0,0
+YENKYVGKSASDLLKENYPE,0,0
+ENKYVGKSASDLLKENYPEC,0,1
+NKYVGKSASDLLKENYPECI,0,1
+KYVGKSASDLLKENYPECIS,0,0
+YVGKSASDLLKENYPECISA,0,0
+VGKSASDLLKENYPECISAN,0,0
+GKSASDLLKENYPECISANF,0,0
+KSASDLLKENYPECISANFD,0,0
+SASDLLKENYPECISANFDF,0,0
+ASDLLKENYPECISANFDFI,0,0
+SDLLKENYPECISANFDFIF,0,0
+DLLKENYPECISANFDFIFN,0,0
+LLKENYPECISANFDFIFND,0,0
+LKENYPECISANFDFIFNDN,0,0
+KENYPECISANFDFIFNDNI,0,0
+ENYPECISANFDFIFNDNIE,0,0
+NYPECISANFDFIFNDNIEY,0,0
+YPECISANFDFIFNDNIEYK,0,0
+PECISANFDFIFNDNIEYKT,0,0
+ECISANFDFIFNDNIEYKTY,0.5,0
+CISANFDFIFNDNIEYKTYY,0,0
+ISANFDFIFNDNIEYKTYYP,3,0
+SANFDFIFNDNIEYKTYYPY,0,0
+ANFDFIFNDNIEYKTYYPYG,0,0
+NFDFIFNDNIEYKTYYPYGD,0,0
+FDFIFNDNIEYKTYYPYGDY,0,4
+DFIFNDNIEYKTYYPYGDYS,0,0
+FIFNDNIEYKTYYPYGDYSS,0,1.5
+IFNDNIEYKTYYPYGDYSSI,0,0
+FNDNIEYKTYYPYGDYSSIC,0,0
+NDNIEYKTYYPYGDYSSICS,0,0
+DNIEYKTYYPYGDYSSICSC,0,2
+NIEYKTYYPYGDYSSICSCE,0,1
+IEYKTYYPYGDYSSICSCEQ,0,0
+EYKTYYPYGDYSSICSCEQV,0,1
+YKTYYPYGDYSSICSCEQVK,0,0
+KTYYPYGDYSSICSCEQVKY,0,0
+TYYPYGDYSSICSCEQVKYY,0,0
+YYPYGDYSSICSCEQVKYYK,0,0
+YPYGDYSSICSCEQVKYYKY,0,0
+PYGDYSSICSCEQVKYYKYN,0,1
+YGDYSSICSCEQVKYYKYNN,0,0
+GDYSSICSCEQVKYYKYNNA,0,0
+DYSSICSCEQVKYYKYNNAE,0,0
+YSSICSCEQVKYYKYNNAEK,0,0
+SSICSCEQVKYYKYNNAEKK,77,84
+SICSCEQVKYYKYNNAEKKN,0,83.5
+ICSCEQVKYYKYNNAEKKNN,0,2
+CSCEQVKYYKYNNAEKKNNK,607,199
+SCEQVKYYKYNNAEKKNNKS,70,89
+CEQVKYYKYNNAEKKNNKSL,90,89
+EQVKYYKYNNAEKKNNKSLC,0,0
+QVKYYKYNNAEKKNNKSLCY,0,0
+VKYYKYNNAEKKNNKSLCYE,0,0
+KYYKYNNAEKKNNKSLCYEK,0,88
+YYKYNNAEKKNNKSLCYEKD,0,0
+YKYNNAEKKNNKSLCYEKDN,0,4
+KYNNAEKKNNKSLCYEKDND,0,4
+YNNAEKKNNKSLCYEKDNDM,0,0
+NNAEKKNNKSLCYEKDNDMT,0,0
+NAEKKNNKSLCYEKDNDMTW,0,0
+AEKKNNKSLCYEKDNDMTWS,48,0
+EKKNNKSLCYEKDNDMTWSK,35.5,0
+KKNNKSLCYEKDNDMTWSKK,0,0
+KNNKSLCYEKDNDMTWSKKY,0,0
+NNKSLCYEKDNDMTWSKKYI,0,0
+NKSLCYEKDNDMTWSKKYIK,987,2550
+KSLCYEKDNDMTWSKKYIKK,5568.5,15554
+SLCYEKDNDMTWSKKYIKKL,2449,3677
+LCYEKDNDMTWSKKYIKKLE,180,497
+CYEKDNDMTWSKKYIKKLEN,320.5,600
+YEKDNDMTWSKKYIKKLENG,1.5,0
+EKDNDMTWSKKYIKKLENGR,94,4
+KDNDMTWSKKYIKKLENGRS,109,108
+DNDMTWSKKYIKKLENGRSL,0,94
+NDMTWSKKYIKKLENGRSLE,0,0
+DMTWSKKYIKKLENGRSLEG,0,6.5
+MTWSKKYIKKLENGRSLEGV,0,103.5
+TWSKKYIKKLENGRSLEGVY,4,0
+WSKKYIKKLENGRSLEGVYV,0,0
+SKKYIKKLENGRSLEGVYVP,0,3.5
+KKYIKKLENGRSLEGVYVPP,0,2
+KYIKKLENGRSLEGVYVPPR,6.5,0
+YIKKLENGRSLEGVYVPPRR,5,0
+IKKLENGRSLEGVYVPPRRQ,5,0
+KKLENGRSLEGVYVPPRRQQ,0,0
+KLENGRSLEGVYVPPRRQQL,4.5,0
+LENGRSLEGVYVPPRRQQLC,0,3
+ENGRSLEGVYVPPRRQQLCL,0,0
+NGRSLEGVYVPPRRQQLCLY,0,0
+GRSLEGVYVPPRRQQLCLYE,0,0
+RSLEGVYVPPRRQQLCLYEL,0,0
+SLEGVYVPPRRQQLCLYELF,0,0
+LEGVYVPPRRQQLCLYELFP,0,0
+EGVYVPPRRQQLCLYELFPI,0,0
+GVYVPPRRQQLCLYELFPII,1,5
+VYVPPRRQQLCLYELFPIII,1,0
+YVPPRRQQLCLYELFPIIIK,0,0
+VPPRRQQLCLYELFPIIIKN,0,2
+PPRRQQLCLYELFPIIIKNE,0,1
+PRRQQLCLYELFPIIIKNEE,8,6
+RRQQLCLYELFPIIIKNEEG,0,5
+RQQLCLYELFPIIIKNEEGM,0,0
+QQLCLYELFPIIIKNEEGME,1,5
+QLCLYELFPIIIKNEEGMEK,1,0
+LCLYELFPIIIKNEEGMEKA,0,0
+CLYELFPIIIKNEEGMEKAK,3,2
+LYELFPIIIKNEEGMEKAKE,0,0
+YELFPIIIKNEEGMEKAKEE,0,1
+ELFPIIIKNEEGMEKAKEEL,0,2
+LFPIIIKNEEGMEKAKEELL,0,0
+FPIIIKNEEGMEKAKEELLE,0,60
+PIIIKNEEGMEKAKEELLET,1,0
+IIIKNEEGMEKAKEELLETL,0,0
+IIKNEEGMEKAKEELLETLQ,3,4
+IKNEEGMEKAKEELLETLQI,0,7
+KNEEGMEKAKEELLETLQIV,0,3
+NEEGMEKAKEELLETLQIVA,0,0
+EEGMEKAKEELLETLQIVAE,0,0
+EGMEKAKEELLETLQIVAER,0,0
+GMEKAKEELLETLQIVAERE,0,0
+MEKAKEELLETLQIVAEREA,0,5.5
+EKAKEELLETLQIVAEREAY,4,0
+KAKEELLETLQIVAEREAYY,0,0
+AKEELLETLQIVAEREAYYL,1,0
+KEELLETLQIVAEREAYYLW,2,1
+EELLETLQIVAEREAYYLWK,2.5,0
+ELLETLQIVAEREAYYLWKQ,0,0
+LLETLQIVAEREAYYLWKQY,28.5,0
+LETLQIVAEREAYYLWKQYN,0,0
+ETLQIVAEREAYYLWKQYNP,0,0
+TLQIVAEREAYYLWKQYNPT,0,0
+LQIVAEREAYYLWKQYNPTG,0,0
+QIVAEREAYYLWKQYNPTGK,0,0
+IVAEREAYYLWKQYNPTGKG,0,0
+VAEREAYYLWKQYNPTGKGI,0,0
+AEREAYYLWKQYNPTGKGID,0,0
+EREAYYLWKQYNPTGKGIDD,0,0
+REAYYLWKQYNPTGKGIDDA,0,2
+EAYYLWKQYNPTGKGIDDAN,0,0
+AYYLWKQYNPTGKGIDDANK,0,0
+YYLWKQYNPTGKGIDDANKK,0,0
+YLWKQYNPTGKGIDDANKKA,0,0
+LWKQYNPTGKGIDDANKKAC,0,0
+WKQYNPTGKGIDDANKKACC,0,3.5
+KQYNPTGKGIDDANKKACCA,3,0
+QYNPTGKGIDDANKKACCAI,0,0
+YNPTGKGIDDANKKACCAIR,1,0
+NPTGKGIDDANKKACCAIRG,0,0
+PTGKGIDDANKKACCAIRGS,0,0
+TGKGIDDANKKACCAIRGSF,1.5,0
+GKGIDDANKKACCAIRGSFY,0,0
+KGIDDANKKACCAIRGSFYD,0,0
+GIDDANKKACCAIRGSFYDL,2,0
+IDDANKKACCAIRGSFYDLE,0,0
+DDANKKACCAIRGSFYDLED,1.5,0
+DANKKACCAIRGSFYDLEDI,2,3
+ANKKACCAIRGSFYDLEDII,0,0
+NKKACCAIRGSFYDLEDIIK,0,0
+KKACCAIRGSFYDLEDIIKG,0,0
+KACCAIRGSFYDLEDIIKGN,1,0
+ACCAIRGSFYDLEDIIKGND,2.5,0
+CCAIRGSFYDLEDIIKGNDL,10,2
+CAIRGSFYDLEDIIKGNDLV,5,8
+AIRGSFYDLEDIIKGNDLVH,0,1
+IRGSFYDLEDIIKGNDLVHD,0,0
+RGSFYDLEDIIKGNDLVHDE,0,0
+GSFYDLEDIIKGNDLVHDEY,2,0
+SFYDLEDIIKGNDLVHDEYT,6,0
+FYDLEDIIKGNDLVHDEYTK,0,0
+YDLEDIIKGNDLVHDEYTKY,0,0
+DLEDIIKGNDLVHDEYTKYI,0,0
+LEDIIKGNDLVHDEYTKYID,0,0
+EDIIKGNDLVHDEYTKYIDS,0,0
+DIIKGNDLVHDEYTKYIDSK,0,0
+IIKGNDLVHDEYTKYIDSKL,0,0
+IKGNDLVHDEYTKYIDSKLN,0,0
+KGNDLVHDEYTKYIDSKLNE,0,0
+GNDLVHDEYTKYIDSKLNEI,0,0
+NDLVHDEYTKYIDSKLNEIF,0,2
+DLVHDEYTKYIDSKLNEIFG,0,4
+LVHDEYTKYIDSKLNEIFGS,4,2
+VHDEYTKYIDSKLNEIFGSS,3,0
+HDEYTKYIDSKLNEIFGSSD,0,2
+DEYTKYIDSKLNEIFGSSDT,0,0
+EYTKYIDSKLNEIFGSSDTN,0,0
+YTKYIDSKLNEIFGSSDTND,0,0
+TKYIDSKLNEIFGSSDTNDI,3,1
+KYIDSKLNEIFGSSDTNDID,1,0
+YIDSKLNEIFGSSDTNDIDT,0,0
+IDSKLNEIFGSSDTNDIDTK,0,0
+DSKLNEIFGSSDTNDIDTKR,0,4
+SKLNEIFGSSDTNDIDTKRA,0,1
+KLNEIFGSSDTNDIDTKRAR,4,0
+LNEIFGSSDTNDIDTKRART,0,0
+NEIFGSSDTNDIDTKRARTD,0,0
+EIFGSSDTNDIDTKRARTDW,0,2
+IFGSSDTNDIDTKRARTDWW,112,97
+FGSSDTNDIDTKRARTDWWE,92,0
+GSSDTNDIDTKRARTDWWEN,3,0
+SSDTNDIDTKRARTDWWENE,0,0
+SDTNDIDTKRARTDWWENET,0,0
+DTNDIDTKRARTDWWENETI,0,3
+TNDIDTKRARTDWWENETIT,0,0
+NDIDTKRARTDWWENETITN,0,0
+DIDTKRARTDWWENETITNG,0,0
+IDTKRARTDWWENETITNGT,0,0
+DTKRARTDWWENETITNGTD,3,0
+TKRARTDWWENETITNGTDR,0,0
+KRARTDWWENETITNGTDRK,0,0
+RARTDWWENETITNGTDRKT,0,1
+ARTDWWENETITNGTDRKTI,0,0
+RTDWWENETITNGTDRKTIR,0,0
+TDWWENETITNGTDRKTIRQ,0,4
+DWWENETITNGTDRKTIRQL,0,0
+WWENETITNGTDRKTIRQLV,0,1.5
+WENETITNGTDRKTIRQLVW,0,0
+ENETITNGTDRKTIRQLVWD,0,0
+NETITNGTDRKTIRQLVWDA,0,3
+ETITNGTDRKTIRQLVWDAM,0,0
+TITNGTDRKTIRQLVWDAMQ,3,1
+ITNGTDRKTIRQLVWDAMQS,0,0
+TNGTDRKTIRQLVWDAMQSG,0,0
+NGTDRKTIRQLVWDAMQSGV,0,0
+GTDRKTIRQLVWDAMQSGVR,0,2
+TDRKTIRQLVWDAMQSGVRY,0,2
+DRKTIRQLVWDAMQSGVRYA,0,0
+RKTIRQLVWDAMQSGVRYAV,0,0
+KTIRQLVWDAMQSGVRYAVE,0,5
+TIRQLVWDAMQSGVRYAVEE,1,11
+IRQLVWDAMQSGVRYAVEEK,3.5,2.5
+RQLVWDAMQSGVRYAVEEKN,0,0
+QLVWDAMQSGVRYAVEEKNE,0,1
+LVWDAMQSGVRYAVEEKNEN,0,3
+VWDAMQSGVRYAVEEKNENF,0,2
+WDAMQSGVRYAVEEKNENFP,0,0
+DAMQSGVRYAVEEKNENFPL,0,0
+AMQSGVRYAVEEKNENFPLC,1,0
+MQSGVRYAVEEKNENFPLCM,0,6
+QSGVRYAVEEKNENFPLCMG,6,0
+SGVRYAVEEKNENFPLCMGV,1,0
+GVRYAVEEKNENFPLCMGVE,0,1.5
+VRYAVEEKNENFPLCMGVEH,0,0
+RYAVEEKNENFPLCMGVEHI,0,0
+YAVEEKNENFPLCMGVEHIG,0,0
+AVEEKNENFPLCMGVEHIGI,0,1
+VEEKNENFPLCMGVEHIGIA,0,1
+EEKNENFPLCMGVEHIGIAK,0,0
+EKNENFPLCMGVEHIGIAKP,0,1
+KNENFPLCMGVEHIGIAKPQ,2,0
+NENFPLCMGVEHIGIAKPQF,0,0
+ENFPLCMGVEHIGIAKPQFI,3,0
+NFPLCMGVEHIGIAKPQFIR,0,89
+FPLCMGVEHIGIAKPQFIRW,6,6
+PLCMGVEHIGIAKPQFIRWL,95,5
+LCMGVEHIGIAKPQFIRWLE,0,4
+CMGVEHIGIAKPQFIRWLEE,0,8
+MGVEHIGIAKPQFIRWLEEW,94,78
+GVEHIGIAKPQFIRWLEEWT,0,0
+VEHIGIAKPQFIRWLEEWTN,2,0
+EHIGIAKPQFIRWLEEWTNE,0,0
+HIGIAKPQFIRWLEEWTNEF,0,0
+IGIAKPQFIRWLEEWTNEFC,0,91
+GIAKPQFIRWLEEWTNEFCE,0,0
+IAKPQFIRWLEEWTNEFCEK,0,3
+AKPQFIRWLEEWTNEFCEKY,0,11.5
+KPQFIRWLEEWTNEFCEKYT,2,2
+PQFIRWLEEWTNEFCEKYTK,0,0
+QFIRWLEEWTNEFCEKYTKY,0,0
+FIRWLEEWTNEFCEKYTKYF,0,0
+IRWLEEWTNEFCEKYTKYFE,0,0
+RWLEEWTNEFCEKYTKYFED,4,2
+WLEEWTNEFCEKYTKYFEDM,0,0.5
+LEEWTNEFCEKYTKYFEDMK,0,0
+EEWTNEFCEKYTKYFEDMKS,4,0
+EWTNEFCEKYTKYFEDMKSK,0,0
+WTNEFCEKYTKYFEDMKSKC,0,0
+TNEFCEKYTKYFEDMKSKCD,8,0
+NEFCEKYTKYFEDMKSKCDP,0,0
+EFCEKYTKYFEDMKSKCDPP,0,0
+FCEKYTKYFEDMKSKCDPPK,0,2
+CEKYTKYFEDMKSKCDPPKR,0,12
+EKYTKYFEDMKSKCDPPKRA,0,0
+KYTKYFEDMKSKCDPPKRAD,4,0
+YTKYFEDMKSKCDPPKRADT,0,0
+TKYFEDMKSKCDPPKRADTC,0,0
+KYFEDMKSKCDPPKRADTCG,0,4
+YFEDMKSKCDPPKRADTCGD,0,3
+FEDMKSKCDPPKRADTCGDN,0,0
+EDMKSKCDPPKRADTCGDNS,0,0
+DMKSKCDPPKRADTCGDNSN,0,0
+MKSKCDPPKRADTCGDNSNI,1,0
+KSKCDPPKRADTCGDNSNIE,0,1
+SKCDPPKRADTCGDNSNIEC,0,0
+KCDPPKRADTCGDNSNIECK,0,0
+CDPPKRADTCGDNSNIECKK,0,9
+DPPKRADTCGDNSNIECKKA,0,3
+PPKRADTCGDNSNIECKKAC,0,1
+PKRADTCGDNSNIECKKACA,0,0
+KRADTCGDNSNIECKKACAN,0,0
+RADTCGDNSNIECKKACANY,0,3
+ADTCGDNSNIECKKACANYT,0,2
+DTCGDNSNIECKKACANYTN,0,0
+TCGDNSNIECKKACANYTNW,0,5
+CGDNSNIECKKACANYTNWL,0,0.5
+GDNSNIECKKACANYTNWLN,0,1
+DNSNIECKKACANYTNWLNP,0,0
+NSNIECKKACANYTNWLNPK,5,0
+SNIECKKACANYTNWLNPKR,0,0
+NIECKKACANYTNWLNPKRI,0,1
+IECKKACANYTNWLNPKRIE,0,1
+ECKKACANYTNWLNPKRIEW,0,5.5
+CKKACANYTNWLNPKRIEWN,0,0
+KKACANYTNWLNPKRIEWNG,0,0
+KACANYTNWLNPKRIEWNGM,0,0
+ACANYTNWLNPKRIEWNGMS,1,0
+CANYTNWLNPKRIEWNGMSN,0,0
+ANYTNWLNPKRIEWNGMSNY,0,1
+NYTNWLNPKRIEWNGMSNYY,0,0
+YTNWLNPKRIEWNGMSNYYN,0.5,3
+TNWLNPKRIEWNGMSNYYNK,0,0
+NWLNPKRIEWNGMSNYYNKI,0,0
+WLNPKRIEWNGMSNYYNKIY,0,3
+LNPKRIEWNGMSNYYNKIYR,85,93
+NPKRIEWNGMSNYYNKIYRK,890.5,1277
+PKRIEWNGMSNYYNKIYRKS,98,168
+KRIEWNGMSNYYNKIYRKSN,152,108.5
+RIEWNGMSNYYNKIYRKSNK,92.5,81
+IEWNGMSNYYNKIYRKSNKE,0,0
+EWNGMSNYYNKIYRKSNKES,0,0
+WNGMSNYYNKIYRKSNKESE,0,0
+NGMSNYYNKIYRKSNKESEG,0,0
+GMSNYYNKIYRKSNKESEGG,0,2
+MSNYYNKIYRKSNKESEGGK,92,101
+SNYYNKIYRKSNKESEGGKD,0,1
+NYYNKIYRKSNKESEGGKDY,0,0
+YYNKIYRKSNKESEGGKDYS,0,0
+YNKIYRKSNKESEGGKDYSM,0,0
+NKIYRKSNKESEGGKDYSMI,0,0
+KIYRKSNKESEGGKDYSMIM,0,0
+IYRKSNKESEGGKDYSMIMA,0,0
+YRKSNKESEGGKDYSMIMAP,0,0
+RKSNKESEGGKDYSMIMAPT,0,0
+KSNKESEGGKDYSMIMAPTV,0,0
+SNKESEGGKDYSMIMAPTVI,0,0
+NKESEGGKDYSMIMAPTVID,2,0
+KESEGGKDYSMIMAPTVIDY,0,0
+ESEGGKDYSMIMAPTVIDYL,0,3
+SEGGKDYSMIMAPTVIDYLN,0,0
+EGGKDYSMIMAPTVIDYLNK,3,0
+GGKDYSMIMAPTVIDYLNKR,0,0
+GKDYSMIMAPTVIDYLNKRC,0,0
+KDYSMIMAPTVIDYLNKRCH,0,0
+DYSMIMAPTVIDYLNKRCHG,0,0
+YSMIMAPTVIDYLNKRCHGE,0,0
+SMIMAPTVIDYLNKRCHGEI,0,0
+MIMAPTVIDYLNKRCHGEIN,0,0
+IMAPTVIDYLNKRCHGEING,1,0
+MAPTVIDYLNKRCHGEINGN,1,0
+APTVIDYLNKRCHGEINGNY,0,4
+PTVIDYLNKRCHGEINGNYI,0,10
+TVIDYLNKRCHGEINGNYIC,0,0
+VIDYLNKRCHGEINGNYICC,0,9
+IDYLNKRCHGEINGNYICCS,4,0
+DYLNKRCHGEINGNYICCSC,0,4
+YLNKRCHGEINGNYICCSCK,6.5,7
+LNKRCHGEINGNYICCSCKN,2,0
+NKRCHGEINGNYICCSCKNI,0,0
+KRCHGEINGNYICCSCKNIG,0,4
+RCHGEINGNYICCSCKNIGA,0,0
+CHGEINGNYICCSCKNIGAY,1,0
+HGEINGNYICCSCKNIGAYN,0,0
+GEINGNYICCSCKNIGAYNT,0,0
+EINGNYICCSCKNIGAYNTT,0,0
+INGNYICCSCKNIGAYNTTS,0,0
+NGNYICCSCKNIGAYNTTSG,0,0
+GNYICCSCKNIGAYNTTSGT,3,0
+NYICCSCKNIGAYNTTSGTV,0,0
+YICCSCKNIGAYNTTSGTVN,1,0
+ICCSCKNIGAYNTTSGTVNK,0,0
+CCSCKNIGAYNTTSGTVNKK,1,0
+CSCKNIGAYNTTSGTVNKKL,0,0
+SCKNIGAYNTTSGTVNKKLQ,0,0
+CKNIGAYNTTSGTVNKKLQK,3,0
+KNIGAYNTTSGTVNKKLQKK,3,93
+NIGAYNTTSGTVNKKLQKKE,0,0
+IGAYNTTSGTVNKKLQKKET,0,1
+GAYNTTSGTVNKKLQKKETE,0,0
+AYNTTSGTVNKKLQKKETEC,0,0
+YNTTSGTVNKKLQKKETECE,0,0
+NTTSGTVNKKLQKKETECEE,0,0
+TTSGTVNKKLQKKETECEEE,0,0
+TSGTVNKKLQKKETECEEEK,0,0
+SGTVNKKLQKKETECEEEKG,0,0
+GTVNKKLQKKETECEEEKGP,0,0
+TVNKKLQKKETECEEEKGPL,3,3
+VNKKLQKKETECEEEKGPLD,0,0
+NKKLQKKETECEEEKGPLDL,0,0
+KKLQKKETECEEEKGPLDLM,95,2
+KLQKKETECEEEKGPLDLMN,3,0
+LQKKETECEEEKGPLDLMNE,0,0
+QKKETECEEEKGPLDLMNEV,0,0
+KKETECEEEKGPLDLMNEVL,0,0
+KETECEEEKGPLDLMNEVLN,0,0
+ETECEEEKGPLDLMNEVLNK,0,0
+TECEEEKGPLDLMNEVLNKM,0,0
+ECEEEKGPLDLMNEVLNKMD,0,0
+CEEEKGPLDLMNEVLNKMDK,0,3
+EEEKGPLDLMNEVLNKMDKK,0,0
+EEKGPLDLMNEVLNKMDKKY,2,1
+EKGPLDLMNEVLNKMDKKYS,99,12.5
+KGPLDLMNEVLNKMDKKYSA,102,0
+GPLDLMNEVLNKMDKKYSAH,89.5,16
+PLDLMNEVLNKMDKKYSAHK,222,417
+LDLMNEVLNKMDKKYSAHKM,102,102
+DLMNEVLNKMDKKYSAHKMK,124,317
+LMNEVLNKMDKKYSAHKMKC,277,1835.5
+MNEVLNKMDKKYSAHKMKCT,87,396.5
+NEVLNKMDKKYSAHKMKCTE,0,0
+EVLNKMDKKYSAHKMKCTEV,107,321
+VLNKMDKKYSAHKMKCTEVY,48,98
+LNKMDKKYSAHKMKCTEVYL,107,116
+NKMDKKYSAHKMKCTEVYLE,1,0
+KMDKKYSAHKMKCTEVYLEH,1,0
+MDKKYSAHKMKCTEVYLEHV,0,0
+DKKYSAHKMKCTEVYLEHVE,0,0
+KKYSAHKMKCTEVYLEHVEE,0,7
+KYSAHKMKCTEVYLEHVEEQ,0,5
+YSAHKMKCTEVYLEHVEEQL,0,5
+SAHKMKCTEVYLEHVEEQLN,0,0
+AHKMKCTEVYLEHVEEQLNE,0,0
+HKMKCTEVYLEHVEEQLNEI,2,0
+KMKCTEVYLEHVEEQLNEID,2,0
+MKCTEVYLEHVEEQLNEIDN,0,0
+KCTEVYLEHVEEQLNEIDNA,0,0
+CTEVYLEHVEEQLNEIDNAI,4,0
+TEVYLEHVEEQLNEIDNAIK,0,0
+EVYLEHVEEQLNEIDNAIKD,0,0
+VYLEHVEEQLNEIDNAIKDY,0,0
+YLEHVEEQLNEIDNAIKDYK,0,0
+LEHVEEQLNEIDNAIKDYKL,0,1
+EHVEEQLNEIDNAIKDYKLY,4,0
+HVEEQLNEIDNAIKDYKLYP,0,0
+VEEQLNEIDNAIKDYKLYPL,0,0
+EEQLNEIDNAIKDYKLYPLD,0,0
+EQLNEIDNAIKDYKLYPLDR,74,8
+QLNEIDNAIKDYKLYPLDRC,4,5.5
+LNEIDNAIKDYKLYPLDRCF,6,5
+NEIDNAIKDYKLYPLDRCFD,1,85
+EIDNAIKDYKLYPLDRCFDD,0,0
+IDNAIKDYKLYPLDRCFDDQ,1,0
+DNAIKDYKLYPLDRCFDDQT,0,0
+NAIKDYKLYPLDRCFDDQTK,0,0
+AIKDYKLYPLDRCFDDQTKM,4,71.5
+IKDYKLYPLDRCFDDQTKMK,0,0
+KDYKLYPLDRCFDDQTKMKV,0,0
+DYKLYPLDRCFDDQTKMKVC,0,0
+YKLYPLDRCFDDQTKMKVCD,2,1
+KLYPLDRCFDDQTKMKVCDL,1,5
+LYPLDRCFDDQTKMKVCDLI,0,0
+YPLDRCFDDQTKMKVCDLIA,0,0
+PLDRCFDDQTKMKVCDLIAD,0,6
+LDRCFDDQTKMKVCDLIADA,0,1
+DRCFDDQTKMKVCDLIADAI,0,0
+RCFDDQTKMKVCDLIADAIG,5,2
+CFDDQTKMKVCDLIADAIGC,0,8
+FDDQTKMKVCDLIADAIGCK,0,0
+DDQTKMKVCDLIADAIGCKD,0.5,0
+DQTKMKVCDLIADAIGCKDK,0,0
+QTKMKVCDLIADAIGCKDKT,0,0
+TKMKVCDLIADAIGCKDKTK,1,5
+KMKVCDLIADAIGCKDKTKL,0,0
+MKVCDLIADAIGCKDKTKLD,0,0
+KVCDLIADAIGCKDKTKLDE,0,5
+VCDLIADAIGCKDKTKLDEL,1,0
+CDLIADAIGCKDKTKLDELD,3,0
+DLIADAIGCKDKTKLDELDE,0,0
+LIADAIGCKDKTKLDELDEW,0,0
+IADAIGCKDKTKLDELDEWN,3,0
+ADAIGCKDKTKLDELDEWND,0,0
+DAIGCKDKTKLDELDEWNDM,0,0
+AIGCKDKTKLDELDEWNDMD,2,0
+IGCKDKTKLDELDEWNDMDL,0,0
+GCKDKTKLDELDEWNDMDLR,0,1
+CKDKTKLDELDEWNDMDLRG,1,0
+KDKTKLDELDEWNDMDLRGT,0,0
+DKTKLDELDEWNDMDLRGTY,0,0
+KTKLDELDEWNDMDLRGTYN,0,0
+TKLDELDEWNDMDLRGTYNK,3,2
+KLDELDEWNDMDLRGTYNKH,0,0
+LDELDEWNDMDLRGTYNKHK,2,0
+DELDEWNDMDLRGTYNKHKG,6,3
+ELDEWNDMDLRGTYNKHKGV,6,7
+LDEWNDMDLRGTYNKHKGVL,9,4
+DEWNDMDLRGTYNKHKGVLI,0,6
+EWNDMDLRGTYNKHKGVLIP,0,0
+WNDMDLRGTYNKHKGVLIPP,1,0
+NDMDLRGTYNKHKGVLIPPR,4,0
+DMDLRGTYNKHKGVLIPPRR,87,7
+MDLRGTYNKHKGVLIPPRRR,96,5
+DLRGTYNKHKGVLIPPRRRQ,0.5,0
+LRGTYNKHKGVLIPPRRRQL,4,6
+RGTYNKHKGVLIPPRRRQLC,0,7
+GTYNKHKGVLIPPRRRQLCF,2,0
+TYNKHKGVLIPPRRRQLCFS,0,0
+YNKHKGVLIPPRRRQLCFSR,0,0
+NKHKGVLIPPRRRQLCFSRI,2,0
+KHKGVLIPPRRRQLCFSRIV,0,0
+HKGVLIPPRRRQLCFSRIVR,0,0
+KGVLIPPRRRQLCFSRIVRG,1,0
+GVLIPPRRRQLCFSRIVRGP,0,0
+VLIPPRRRQLCFSRIVRGPA,0,0.5
+LIPPRRRQLCFSRIVRGPAN,0,0
+IPPRRRQLCFSRIVRGPANL,0,0
+PPRRRQLCFSRIVRGPANLR,0,0.5
+PRRRQLCFSRIVRGPANLRS,0,0
+RRRQLCFSRIVRGPANLRSL,0,0
+RRQLCFSRIVRGPANLRSLN,0,10
+RQLCFSRIVRGPANLRSLNE,0,0
+QLCFSRIVRGPANLRSLNEF,0,0
+LCFSRIVRGPANLRSLNEFK,0,0
+CFSRIVRGPANLRSLNEFKE,0,0
+FSRIVRGPANLRSLNEFKEE,0,2
+SRIVRGPANLRSLNEFKEEI,0,0
+RIVRGPANLRSLNEFKEEIL,0,0
+IVRGPANLRSLNEFKEEILK,0,4
+VRGPANLRSLNEFKEEILKG,0,0
+RGPANLRSLNEFKEEILKGA,0,1.5
+GPANLRSLNEFKEEILKGAQ,0,0
+PANLRSLNEFKEEILKGAQS,0,0
+ANLRSLNEFKEEILKGAQSE,5,0
+NLRSLNEFKEEILKGAQSEG,1,1
+LRSLNEFKEEILKGAQSEGK,4,0
+RSLNEFKEEILKGAQSEGKF,0,0
+SLNEFKEEILKGAQSEGKFL,0,0
+LNEFKEEILKGAQSEGKFLG,0,0
+NEFKEEILKGAQSEGKFLGN,0,0
+EFKEEILKGAQSEGKFLGNY,0,1.5
+FKEEILKGAQSEGKFLGNYY,2,3
+KEEILKGAQSEGKFLGNYYK,3,4
+EEILKGAQSEGKFLGNYYKE,0,0
+EILKGAQSEGKFLGNYYKEH,0,0
+ILKGAQSEGKFLGNYYKEHK,0,0
+LKGAQSEGKFLGNYYKEHKD,104,0
+KGAQSEGKFLGNYYKEHKDK,79,96
+GAQSEGKFLGNYYKEHKDKE,0,0
+AQSEGKFLGNYYKEHKDKEK,0,0
+QSEGKFLGNYYKEHKDKEKA,0,0
+SEGKFLGNYYKEHKDKEKAL,0,0
+EGKFLGNYYKEHKDKEKALE,0,0
+GKFLGNYYKEHKDKEKALEA,0,1
+KFLGNYYKEHKDKEKALEAM,0,0
+FLGNYYKEHKDKEKALEAMK,0,3
+LGNYYKEHKDKEKALEAMKN,0,0
+GNYYKEHKDKEKALEAMKNS,0,0
+NYYKEHKDKEKALEAMKNSF,4,0
+YYKEHKDKEKALEAMKNSFY,0,0
+YKEHKDKEKALEAMKNSFYD,5,0
+KEHKDKEKALEAMKNSFYDY,0,0
+EHKDKEKALEAMKNSFYDYE,0,1
+HKDKEKALEAMKNSFYDYED,0,5
+KDKEKALEAMKNSFYDYEDI,0,3
+DKEKALEAMKNSFYDYEDII,0,0
+KEKALEAMKNSFYDYEDIIK,9,0
+EKALEAMKNSFYDYEDIIKG,3.5,0
+KALEAMKNSFYDYEDIIKGT,0,0
+ALEAMKNSFYDYEDIIKGTD,0,0
+LEAMKNSFYDYEDIIKGTDM,1,0
+EAMKNSFYDYEDIIKGTDML,0,3
+AMKNSFYDYEDIIKGTDMLT,1.5,0
+MKNSFYDYEDIIKGTDMLTN,0,3
+KNSFYDYEDIIKGTDMLTNI,0,0
+NSFYDYEDIIKGTDMLTNIE,0,0
+SFYDYEDIIKGTDMLTNIEF,2,0
+FYDYEDIIKGTDMLTNIEFK,0,0
+YDYEDIIKGTDMLTNIEFKD,2,0
+DYEDIIKGTDMLTNIEFKDI,0,0
+YEDIIKGTDMLTNIEFKDIK,1,0
+EDIIKGTDMLTNIEFKDIKI,0,0
+DIIKGTDMLTNIEFKDIKIK,0,0
+IIKGTDMLTNIEFKDIKIKL,3,0
+IKGTDMLTNIEFKDIKIKLD,3,0
+KGTDMLTNIEFKDIKIKLDR,0.5,0
+GTDMLTNIEFKDIKIKLDRL,0,6.5
+TDMLTNIEFKDIKIKLDRLL,83.5,89
+DMLTNIEFKDIKIKLDRLLE,0,0
+MLTNIEFKDIKIKLDRLLEK,0,9
+LTNIEFKDIKIKLDRLLEKE,1,0
+TNIEFKDIKIKLDRLLEKET,8,0
+NIEFKDIKIKLDRLLEKETN,0,0
+IEFKDIKIKLDRLLEKETNN,0,0
+EFKDIKIKLDRLLEKETNNT,0,0
+FKDIKIKLDRLLEKETNNTK,0,7
+KDIKIKLDRLLEKETNNTKK,0,92
+DIKIKLDRLLEKETNNTKKA,0,0
+IKIKLDRLLEKETNNTKKAE,0,0
+KIKLDRLLEKETNNTKKAED,0.5,0
+IKLDRLLEKETNNTKKAEDW,0,0
+KLDRLLEKETNNTKKAEDWW,87.5,92.5
+LDRLLEKETNNTKKAEDWWK,1.5,103
+DRLLEKETNNTKKAEDWWKT,0,0
+RLLEKETNNTKKAEDWWKTN,0,0
+LLEKETNNTKKAEDWWKTNK,0,0
+LEKETNNTKKAEDWWKTNKK,5,0
+EKETNNTKKAEDWWKTNKKS,0,0
+KETNNTKKAEDWWKTNKKSI,0,0
+ETNNTKKAEDWWKTNKKSIW,0,0
+TNNTKKAEDWWKTNKKSIWN,0,0
+NNTKKAEDWWKTNKKSIWNA,0,0
+NTKKAEDWWKTNKKSIWNAM,0.5,0
+TKKAEDWWKTNKKSIWNAML,0,0
+KKAEDWWKTNKKSIWNAMLC,0,0
+KAEDWWKTNKKSIWNAMLCG,0,0
+AEDWWKTNKKSIWNAMLCGY,0,0
+EDWWKTNKKSIWNAMLCGYK,0,0
+DWWKTNKKSIWNAMLCGYKK,101,97
+WWKTNKKSIWNAMLCGYKKS,443,385
+WKTNKKSIWNAMLCGYKKSG,0,94
+KTNKKSIWNAMLCGYKKSGN,102,89
+TNKKSIWNAMLCGYKKSGNK,150,184
+NKKSIWNAMLCGYKKSGNKI,1009,1584
+KKSIWNAMLCGYKKSGNKII,175,533
+KSIWNAMLCGYKKSGNKIID,2,0
+SIWNAMLCGYKKSGNKIIDP,2,6
+IWNAMLCGYKKSGNKIIDPS,97.5,90
+WNAMLCGYKKSGNKIIDPSW,95,94
+NAMLCGYKKSGNKIIDPSWC,0,92
+AMLCGYKKSGNKIIDPSWCT,0,0
+MLCGYKKSGNKIIDPSWCTI,0,0
+LCGYKKSGNKIIDPSWCTIP,1,1
+CGYKKSGNKIIDPSWCTIPT,0,0
+GYKKSGNKIIDPSWCTIPTT,1,0
+YKKSGNKIIDPSWCTIPTTE,0,0
+KKSGNKIIDPSWCTIPTTET,0,0
+KSGNKIIDPSWCTIPTTETP,1,0
+SGNKIIDPSWCTIPTTETPP,0.5,0
+GNKIIDPSWCTIPTTETPPQ,1,0
+NKIIDPSWCTIPTTETPPQF,0,0
+KIIDPSWCTIPTTETPPQFL,0,0
+IIDPSWCTIPTTETPPQFLR,0,0
+IDPSWCTIPTTETPPQFLRW,74,36
+DPSWCTIPTTETPPQFLRWI,0,0
+PSWCTIPTTETPPQFLRWIK,0,0
+SWCTIPTTETPPQFLRWIKE,0.5,0
+WCTIPTTETPPQFLRWIKEW,0,0
+CTIPTTETPPQFLRWIKEWG,0,53.5
+TIPTTETPPQFLRWIKEWGT,3,0
+IPTTETPPQFLRWIKEWGTN,0,0
+PTTETPPQFLRWIKEWGTNV,0,0
+TTETPPQFLRWIKEWGTNVC,0,0
+TETPPQFLRWIKEWGTNVCI,0,0
+ETPPQFLRWIKEWGTNVCIQ,0,0
+TPPQFLRWIKEWGTNVCIQK,0,0
+PPQFLRWIKEWGTNVCIQKQ,0,0
+PQFLRWIKEWGTNVCIQKQE,2,0
+QFLRWIKEWGTNVCIQKQEH,0,0
+FLRWIKEWGTNVCIQKQEHK,1,1
+LRWIKEWGTNVCIQKQEHKE,5,0
+RWIKEWGTNVCIQKQEHKEY,0,0
+WIKEWGTNVCIQKQEHKEYV,0,0
+IKEWGTNVCIQKQEHKEYVK,0,5.5
+KEWGTNVCIQKQEHKEYVKS,0,0
+EWGTNVCIQKQEHKEYVKSK,1486,1434
+WGTNVCIQKQEHKEYVKSKC,102.5,115.5
+GTNVCIQKQEHKEYVKSKCS,2106,2790
+TNVCIQKQEHKEYVKSKCSN,282.5,473
+NVCIQKQEHKEYVKSKCSNV,98,298
+VCIQKQEHKEYVKSKCSNVT,98,202.5
+CIQKQEHKEYVKSKCSNVTN,339,324.5
+IQKQEHKEYVKSKCSNVTNL,0,0
+QKQEHKEYVKSKCSNVTNLG,0,0
+KQEHKEYVKSKCSNVTNLGA,0,0
+QEHKEYVKSKCSNVTNLGAQ,0,0
+EHKEYVKSKCSNVTNLGAQA,0,4
+HKEYVKSKCSNVTNLGAQAS,1,0
+KEYVKSKCSNVTNLGAQASE,1.5,3
+EYVKSKCSNVTNLGAQASES,0,0
+YVKSKCSNVTNLGAQASESN,0,0
+VKSKCSNVTNLGAQASESNN,0,0
+KSKCSNVTNLGAQASESNNC,0,0
+SKCSNVTNLGAQASESNNCT,0,0
+KCSNVTNLGAQASESNNCTS,0,1
+CSNVTNLGAQASESNNCTSE,0,0
+SNVTNLGAQASESNNCTSEI,0,0
+NVTNLGAQASESNNCTSEIK,0,1
+VTNLGAQASESNNCTSEIKK,2,0
+TNLGAQASESNNCTSEIKKY,0,0
+NLGAQASESNNCTSEIKKYQ,0,1
+LGAQASESNNCTSEIKKYQE,0,0
+GAQASESNNCTSEIKKYQEW,2,0
+AQASESNNCTSEIKKYQEWS,4,4
+QASESNNCTSEIKKYQEWSR,0,93
+ASESNNCTSEIKKYQEWSRK,0,16
+SESNNCTSEIKKYQEWSRKR,99,92
+ESNNCTSEIKKYQEWSRKRS,3,93.5
+SNNCTSEIKKYQEWSRKRSI,0,0
+NNCTSEIKKYQEWSRKRSIR,105.5,0
+NCTSEIKKYQEWSRKRSIRW,7,4
+CTSEIKKYQEWSRKRSIRWE,0,86
+TSEIKKYQEWSRKRSIRWET,0,12
+SEIKKYQEWSRKRSIRWETI,0,0
+EIKKYQEWSRKRSIRWETIS,0,1
+IKKYQEWSRKRSIRWETISK,0,0
+KKYQEWSRKRSIRWETISKR,3,0
+KYQEWSRKRSIRWETISKRY,0,0
+YQEWSRKRSIRWETISKRYK,1.5,82
+QEWSRKRSIRWETISKRYKK,423,813
+EWSRKRSIRWETISKRYKKY,407,548
+WSRKRSIRWETISKRYKKYK,2293.5,4442
+SRKRSIRWETISKRYKKYKR,18567,27890.5
+RKRSIRWETISKRYKKYKRM,20838.5,20952
+KRSIRWETISKRYKKYKRMD,2040,3234
+RSIRWETISKRYKKYKRMDI,316,343
+SIRWETISKRYKKYKRMDIL,91,150
+IRWETISKRYKKYKRMDILK,405.5,1063
+RWETISKRYKKYKRMDILKD,553,1237.5
+WETISKRYKKYKRMDILKDV,89,87
+ETISKRYKKYKRMDILKDVK,1163,906
+TISKRYKKYKRMDILKDVKE,194,359
+ISKRYKKYKRMDILKDVKEP,157,217
+SKRYKKYKRMDILKDVKEPD,92,99
+KRYKKYKRMDILKDVKEPDA,105,99
+RYKKYKRMDILKDVKEPDAN,78.5,99.5
+YKKYKRMDILKDVKEPDANT,95,182
+KKYKRMDILKDVKEPDANTY,0,93
+KYKRMDILKDVKEPDANTYL,87,93
+YKRMDILKDVKEPDANTYLR,84,88
+KRMDILKDVKEPDANTYLRE,3.5,0
+RMDILKDVKEPDANTYLREH,0,2.5
+MDILKDVKEPDANTYLREHC,0,0
+DILKDVKEPDANTYLREHCS,0,0
+ILKDVKEPDANTYLREHCSK,0,0
+LKDVKEPDANTYLREHCSKC,0,0
+KDVKEPDANTYLREHCSKCP,0,0
+DVKEPDANTYLREHCSKCPC,0,1
+VKEPDANTYLREHCSKCPCG,0,0
+KEPDANTYLREHCSKCPCGF,1,0
+EPDANTYLREHCSKCPCGFN,0,0
+PDANTYLREHCSKCPCGFND,1,0
+DANTYLREHCSKCPCGFNDM,0,0
+ANTYLREHCSKCPCGFNDME,0,1
+NTYLREHCSKCPCGFNDMEE,0,0
+TYLREHCSKCPCGFNDMEEM,0,2
+YLREHCSKCPCGFNDMEEMN,2,0
+LREHCSKCPCGFNDMEEMNN,0,0
+REHCSKCPCGFNDMEEMNNN,0,0
+EHCSKCPCGFNDMEEMNNNE,0,0
+HCSKCPCGFNDMEEMNNNED,0,2
+CSKCPCGFNDMEEMNNNEDN,0,0
+SKCPCGFNDMEEMNNNEDNE,0,1
+KCPCGFNDMEEMNNNEDNEK,0,0
+CPCGFNDMEEMNNNEDNEKE,0,0
+PCGFNDMEEMNNNEDNEKEA,4,2
+CGFNDMEEMNNNEDNEKEAF,0,0
+GFNDMEEMNNNEDNEKEAFK,3,0
+FNDMEEMNNNEDNEKEAFKQ,0,0
+NDMEEMNNNEDNEKEAFKQI,0,0
+DMEEMNNNEDNEKEAFKQIK,5,6
+MEEMNNNEDNEKEAFKQIKE,0,2
+EEMNNNEDNEKEAFKQIKEQ,94,0
+EMNNNEDNEKEAFKQIKEQV,0,0
+MNNNEDNEKEAFKQIKEQVK,0,0
+NNNEDNEKEAFKQIKEQVKI,0,0
+NNEDNEKEAFKQIKEQVKIP,2,0
+NEDNEKEAFKQIKEQVKIPA,0,0
+EDNEKEAFKQIKEQVKIPAE,0,0
+DNEKEAFKQIKEQVKIPAEL,0,0
+NEKEAFKQIKEQVKIPAELE,3,0
+EKEAFKQIKEQVKIPAELED,3,1
+KEAFKQIKEQVKIPAELEDV,0,0
+EAFKQIKEQVKIPAELEDVI,0,0
+AFKQIKEQVKIPAELEDVIY,0,0
+FKQIKEQVKIPAELEDVIYR,0,2
+KQIKEQVKIPAELEDVIYRI,0,0
+QIKEQVKIPAELEDVIYRIK,0,0
+IKEQVKIPAELEDVIYRIKH,0,0
+KEQVKIPAELEDVIYRIKHH,0,0
+EQVKIPAELEDVIYRIKHHE,0,0
+QVKIPAELEDVIYRIKHHEY,1,0
+VKIPAELEDVIYRIKHHEYD,0,0
+KIPAELEDVIYRIKHHEYDK,0,0
+IPAELEDVIYRIKHHEYDKG,0,0
+PAELEDVIYRIKHHEYDKGN,0,0
+AELEDVIYRIKHHEYDKGND,0,0
+ELEDVIYRIKHHEYDKGNDY,0,0
+LEDVIYRIKHHEYDKGNDYI,0,0
+EDVIYRIKHHEYDKGNDYIC,0,0
+DVIYRIKHHEYDKGNDYICN,0,0
+VIYRIKHHEYDKGNDYICNK,0,0
+IYRIKHHEYDKGNDYICNKY,3,0
+YRIKHHEYDKGNDYICNKYK,188,243
+RIKHHEYDKGNDYICNKYKN,0,0
+IKHHEYDKGNDYICNKYKNI,96,81
+KHHEYDKGNDYICNKYKNIH,0,49
+HHEYDKGNDYICNKYKNIHD,0,0
+HEYDKGNDYICNKYKNIHDR,0,0
+EYDKGNDYICNKYKNIHDRM,10,0
+YDKGNDYICNKYKNIHDRMK,97,8
+DKGNDYICNKYKNIHDRMKK,104,174
+KGNDYICNKYKNIHDRMKKN,202.5,158.5
+GNDYICNKYKNIHDRMKKNN,0,0
+NDYICNKYKNIHDRMKKNNG,1,0
+DYICNKYKNIHDRMKKNNGN,0,1
+YICNKYKNIHDRMKKNNGNF,0,0
+ICNKYKNIHDRMKKNNGNFV,0,0
+CNKYKNIHDRMKKNNGNFVT,0,4
+NKYKNIHDRMKKNNGNFVTD,0,0
+KYKNIHDRMKKNNGNFVTDN,1,0
+YKNIHDRMKKNNGNFVTDNF,0,0
+KNIHDRMKKNNGNFVTDNFV,2,1
+NIHDRMKKNNGNFVTDNFVK,0,0
+IHDRMKKNNGNFVTDNFVKK,0,0
+HDRMKKNNGNFVTDNFVKKS,0,0
+DRMKKNNGNFVTDNFVKKSW,2,0
+RMKKNNGNFVTDNFVKKSWE,1,0
+MKKNNGNFVTDNFVKKSWEI,0,0
+KKNNGNFVTDNFVKKSWEIS,0,5
+KNNGNFVTDNFVKKSWEISN,0,2
+NNGNFVTDNFVKKSWEISNG,1,3
+NGNFVTDNFVKKSWEISNGV,1,0
+GNFVTDNFVKKSWEISNGVL,0,0
+NFVTDNFVKKSWEISNGVLI,0,0
+FVTDNFVKKSWEISNGVLIP,6,0
+VTDNFVKKSWEISNGVLIPP,5,3
+TDNFVKKSWEISNGVLIPPR,5,1
+DNFVKKSWEISNGVLIPPRR,90,0
+NFVKKSWEISNGVLIPPRRK,1,0
+FVKKSWEISNGVLIPPRRKN,0,0
+VKKSWEISNGVLIPPRRKNL,4,0
+KKSWEISNGVLIPPRRKNLF,0,0
+KSWEISNGVLIPPRRKNLFL,0,0
+SWEISNGVLIPPRRKNLFLY,0,4
+WEISNGVLIPPRRKNLFLYI,0,0
+EISNGVLIPPRRKNLFLYID,2,0
+ISNGVLIPPRRKNLFLYIDP,1.5,1
+SNGVLIPPRRKNLFLYIDPS,0,4
+NGVLIPPRRKNLFLYIDPSK,0,0.5
+GVLIPPRRKNLFLYIDPSKI,0,0
+VLIPPRRKNLFLYIDPSKIC,0,0
+LIPPRRKNLFLYIDPSKICE,0,0
+IPPRRKNLFLYIDPSKICEY,2,5
+PPRRKNLFLYIDPSKICEYK,0,0
+PRRKNLFLYIDPSKICEYKK,88.5,73
+RRKNLFLYIDPSKICEYKKD,1,0
+RKNLFLYIDPSKICEYKKDP,0,0
+KNLFLYIDPSKICEYKKDPK,96,86
+NLFLYIDPSKICEYKKDPKL,170,205
+LFLYIDPSKICEYKKDPKLF,88,84
+FLYIDPSKICEYKKDPKLFK,2930.5,2434
+LYIDPSKICEYKKDPKLFKD,89,89
+YIDPSKICEYKKDPKLFKDF,155.5,396
+IDPSKICEYKKDPKLFKDFI,89,84
+DPSKICEYKKDPKLFKDFIY,84,107.5
+PSKICEYKKDPKLFKDFIYW,92,90
+SKICEYKKDPKLFKDFIYWS,66.5,87.5
+KICEYKKDPKLFKDFIYWSA,1.5,3
+ICEYKKDPKLFKDFIYWSAF,82,0
+CEYKKDPKLFKDFIYWSAFT,0,103
+EYKKDPKLFKDFIYWSAFTE,2.5,0
+YKKDPKLFKDFIYWSAFTEV,6,0
+KKDPKLFKDFIYWSAFTEVE,0,0
+KDPKLFKDFIYWSAFTEVER,0,0
+DPKLFKDFIYWSAFTEVERL,1,0
+PKLFKDFIYWSAFTEVERLK,0,0
+KLFKDFIYWSAFTEVERLKK,2,0
+LFKDFIYWSAFTEVERLKKA,0,0
+FKDFIYWSAFTEVERLKKAY,0,0
+KDFIYWSAFTEVERLKKAYG,0,2
+DFIYWSAFTEVERLKKAYGG,0,6
+FIYWSAFTEVERLKKAYGGA,0,0
+IYWSAFTEVERLKKAYGGAR,0,7
+YWSAFTEVERLKKAYGGARA,1,0
+WSAFTEVERLKKAYGGARAK,103.5,170.5
+SAFTEVERLKKAYGGARAKV,106,166
+AFTEVERLKKAYGGARAKVV,43.5,0
+FTEVERLKKAYGGARAKVVH,0,0
+TEVERLKKAYGGARAKVVHA,106,0
+EVERLKKAYGGARAKVVHAM,0,0
+VERLKKAYGGARAKVVHAMK,113,100
+ERLKKAYGGARAKVVHAMKY,0,96
+RLKKAYGGARAKVVHAMKYS,116,99
+LKKAYGGARAKVVHAMKYSF,0,0
+KKAYGGARAKVVHAMKYSFT,96,105
+KAYGGARAKVVHAMKYSFTD,0,0
+AYGGARAKVVHAMKYSFTDI,0,0
+YGGARAKVVHAMKYSFTDIG,5,4
+GGARAKVVHAMKYSFTDIGS,3,4
+GARAKVVHAMKYSFTDIGSI,3,1
+ARAKVVHAMKYSFTDIGSII,0,0
+RAKVVHAMKYSFTDIGSIIK,0,0
+AKVVHAMKYSFTDIGSIIKG,0,0
+KVVHAMKYSFTDIGSIIKGD,0,0
+VVHAMKYSFTDIGSIIKGDD,0,2
+VHAMKYSFTDIGSIIKGDDM,0,0
+HAMKYSFTDIGSIIKGDDMM,0,97
+AMKYSFTDIGSIIKGDDMME,0,0
+MKYSFTDIGSIIKGDDMMEK,2,4
+KYSFTDIGSIIKGDDMMEKN,0,0
+YSFTDIGSIIKGDDMMEKNS,0,0
+SFTDIGSIIKGDDMMEKNSS,0,0
+FTDIGSIIKGDDMMEKNSSD,4,0
+TDIGSIIKGDDMMEKNSSDK,4,0
+DIGSIIKGDDMMEKNSSDKI,4,0
+IGSIIKGDDMMEKNSSDKIG,4,0
+GSIIKGDDMMEKNSSDKIGK,0,0
+SIIKGDDMMEKNSSDKIGKI,1,0
+IIKGDDMMEKNSSDKIGKIL,0,0
+IKGDDMMEKNSSDKIGKILG,1.5,0
+KGDDMMEKNSSDKIGKILGD,0,0
+GDDMMEKNSSDKIGKILGDT,1,0
+DDMMEKNSSDKIGKILGDTD,0,0
+DMMEKNSSDKIGKILGDTDG,0,0
+MMEKNSSDKIGKILGDTDGQ,0,0
+MEKNSSDKIGKILGDTDGQN,0,0
+EKNSSDKIGKILGDTDGQNE,2,0
+KNSSDKIGKILGDTDGQNEK,0,0
+NSSDKIGKILGDTDGQNEKR,2.5,0
+SSDKIGKILGDTDGQNEKRK,0,5
+SDKIGKILGDTDGQNEKRKK,5,0
+DKIGKILGDTDGQNEKRKKW,0,89.5
+KIGKILGDTDGQNEKRKKWW,89,84
+IGKILGDTDGQNEKRKKWWD,89,0
+GKILGDTDGQNEKRKKWWDM,96,0
+KILGDTDGQNEKRKKWWDMN,0,0
+ILGDTDGQNEKRKKWWDMNK,0,0
+LGDTDGQNEKRKKWWDMNKY,4,0
+GDTDGQNEKRKKWWDMNKYH,0,1
+DTDGQNEKRKKWWDMNKYHI,0,0
+TDGQNEKRKKWWDMNKYHIW,106,0
+DGQNEKRKKWWDMNKYHIWE,2,0
+GQNEKRKKWWDMNKYHIWES,1,0
+QNEKRKKWWDMNKYHIWESM,90,0
+NEKRKKWWDMNKYHIWESML,0,0
+EKRKKWWDMNKYHIWESMLC,0,0
+KRKKWWDMNKYHIWESMLCG,0,2
+RKKWWDMNKYHIWESMLCGY,0,114.5
+KKWWDMNKYHIWESMLCGYR,0,111
+KWWDMNKYHIWESMLCGYRE,0,0
+WWDMNKYHIWESMLCGYREA,0,3
+WDMNKYHIWESMLCGYREAE,2,0
+DMNKYHIWESMLCGYREAEG,2,8
+MNKYHIWESMLCGYREAEGD,0,0
+NKYHIWESMLCGYREAEGDT,0,4
+KYHIWESMLCGYREAEGDTE,0,0
+YHIWESMLCGYREAEGDTET,1,0
+HIWESMLCGYREAEGDTETN,1,0
+IWESMLCGYREAEGDTETNE,0,0
+WESMLCGYREAEGDTETNEN,0,0
+ESMLCGYREAEGDTETNENC,0,0
+SMLCGYREAEGDTETNENCR,3,0
+MLCGYREAEGDTETNENCRF,0,0
+LCGYREAEGDTETNENCRFP,0,0
+CGYREAEGDTETNENCRFPD,0,0
+GYREAEGDTETNENCRFPDI,3.5,0
+YREAEGDTETNENCRFPDIE,0,0
+REAEGDTETNENCRFPDIES,0,0
+EAEGDTETNENCRFPDIESV,4,0
+AEGDTETNENCRFPDIESVP,3,4.5
+EGDTETNENCRFPDIESVPQ,0,0
+GDTETNENCRFPDIESVPQF,0,2
+DTETNENCRFPDIESVPQFL,0,1
+TETNENCRFPDIESVPQFLR,0,0
+ETNENCRFPDIESVPQFLRW,0,97
+TNENCRFPDIESVPQFLRWF,8,1
+NENCRFPDIESVPQFLRWFQ,0,0
+ENCRFPDIESVPQFLRWFQE,0,0
+NCRFPDIESVPQFLRWFQEW,0,0
+CRFPDIESVPQFLRWFQEWS,0,0
+RFPDIESVPQFLRWFQEWSE,6,2
+FPDIESVPQFLRWFQEWSEN,0,6
+PDIESVPQFLRWFQEWSENF,1,0
+DIESVPQFLRWFQEWSENFC,0,0
+IESVPQFLRWFQEWSENFCD,1.5,0
+ESVPQFLRWFQEWSENFCDR,0,3.5
+SVPQFLRWFQEWSENFCDRR,3,0
+VPQFLRWFQEWSENFCDRRQ,0,0
+PQFLRWFQEWSENFCDRRQK,0,1
+QFLRWFQEWSENFCDRRQKL,0,3
+FLRWFQEWSENFCDRRQKLY,40,2
+LRWFQEWSENFCDRRQKLYD,0,0
+RWFQEWSENFCDRRQKLYDK,0,0
+WFQEWSENFCDRRQKLYDKL,0,2
+FQEWSENFCDRRQKLYDKLN,4.5,0
+QEWSENFCDRRQKLYDKLNS,0,0
+EWSENFCDRRQKLYDKLNSE,0,0
+WSENFCDRRQKLYDKLNSEC,0,0
+SENFCDRRQKLYDKLNSECI,0,0
+ENFCDRRQKLYDKLNSECIS,0,0
+NFCDRRQKLYDKLNSECISA,0,0
+FCDRRQKLYDKLNSECISAE,0,0
+CDRRQKLYDKLNSECISAEC,0,6
+DRRQKLYDKLNSECISAECT,1.5,0
+RRQKLYDKLNSECISAECTN,0,0
+RQKLYDKLNSECISAECTNG,0,0
+QKLYDKLNSECISAECTNGS,0,0
+KLYDKLNSECISAECTNGSV,0,0
+LYDKLNSECISAECTNGSVD,0,0
+YDKLNSECISAECTNGSVDN,0,0
+DKLNSECISAECTNGSVDNS,0,0
+KLNSECISAECTNGSVDNSK,0,0
+LNSECISAECTNGSVDNSKC,0,0
+NSECISAECTNGSVDNSKCT,0,0
+SECISAECTNGSVDNSKCTH,0,1
+ECISAECTNGSVDNSKCTHA,0,0
+CISAECTNGSVDNSKCTHAC,2,7
+ISAECTNGSVDNSKCTHACV,3,5
+SAECTNGSVDNSKCTHACVN,0,0
+AECTNGSVDNSKCTHACVNY,0,0
+ECTNGSVDNSKCTHACVNYK,3,0
+CTNGSVDNSKCTHACVNYKN,4,0
+TNGSVDNSKCTHACVNYKNY,1.5,0
+NGSVDNSKCTHACVNYKNYI,0,0
+GSVDNSKCTHACVNYKNYIL,6,0
+SVDNSKCTHACVNYKNYILT,0,0
+VDNSKCTHACVNYKNYILTK,0,0
+DNSKCTHACVNYKNYILTKK,102.5,89
+NSKCTHACVNYKNYILTKKT,931.5,1294
+SKCTHACVNYKNYILTKKTE,0,0
+KCTHACVNYKNYILTKKTEY,0,0
+CTHACVNYKNYILTKKTEYE,0,0
+THACVNYKNYILTKKTEYEI,4,0
+HACVNYKNYILTKKTEYEIQ,0,0
+ACVNYKNYILTKKTEYEIQT,1,0
+CVNYKNYILTKKTEYEIQTN,0,0
+VNYKNYILTKKTEYEIQTNK,0,1
+NYKNYILTKKTEYEIQTNKY,0,0.5
+YKNYILTKKTEYEIQTNKYD,1,0
+KNYILTKKTEYEIQTNKYDN,0,0
+NYILTKKTEYEIQTNKYDNE,0,0
+YILTKKTEYEIQTNKYDNEF,0,0
+ILTKKTEYEIQTNKYDNEFK,0,0
+LTKKTEYEIQTNKYDNEFKN,0,0
+TKKTEYEIQTNKYDNEFKNK,0,0
+KKTEYEIQTNKYDNEFKNKN,0,1
+KTEYEIQTNKYDNEFKNKNS,0,0
+TEYEIQTNKYDNEFKNKNSN,0,0
+EYEIQTNKYDNEFKNKNSND,0,0
+YEIQTNKYDNEFKNKNSNDK,1,0
+EIQTNKYDNEFKNKNSNDKD,3,0
+IQTNKYDNEFKNKNSNDKDA,0,0
+QTNKYDNEFKNKNSNDKDAP,0,2
+TNKYDNEFKNKNSNDKDAPD,0,0
+NKYDNEFKNKNSNDKDAPDY,0,0
+KYDNEFKNKNSNDKDAPDYL,0,0
+YDNEFKNKNSNDKDAPDYLK,0,0
+DNEFKNKNSNDKDAPDYLKE,0,6
+NEFKNKNSNDKDAPDYLKEK,0,3
+EFKNKNSNDKDAPDYLKEKC,0,0
+FKNKNSNDKDAPDYLKEKCN,1,0
+KNKNSNDKDAPDYLKEKCND,4,0
+NKNSNDKDAPDYLKEKCNDN,0,0
+KNSNDKDAPDYLKEKCNDNK,0,0
+NSNDKDAPDYLKEKCNDNKC,0,0
+SNDKDAPDYLKEKCNDNKCE,0,0
+NDKDAPDYLKEKCNDNKCEC,1,0
+DKDAPDYLKEKCNDNKCECL,2,0
+KDAPDYLKEKCNDNKCECLN,0,0
+DAPDYLKEKCNDNKCECLNK,0,0
+APDYLKEKCNDNKCECLNKH,0,0
+PDYLKEKCNDNKCECLNKHI,0,0
+DYLKEKCNDNKCECLNKHID,2,4
+YLKEKCNDNKCECLNKHIDD,6,1
+LKEKCNDNKCECLNKHIDDK,3,0
+KEKCNDNKCECLNKHIDDKN,5,0
+EKCNDNKCECLNKHIDDKNK,0,0
+KCNDNKCECLNKHIDDKNKT,4,0
+CNDNKCECLNKHIDDKNKTW,0,0
+NDNKCECLNKHIDDKNKTWK,0,1
+DNKCECLNKHIDDKNKTWKN,0,1
+NKCECLNKHIDDKNKTWKNP,0,0
+KCECLNKHIDDKNKTWKNPY,1.5,0
+CECLNKHIDDKNKTWKNPYE,4,6
+ECLNKHIDDKNKTWKNPYET,1,11
+CLNKHIDDKNKTWKNPYETL,0,6
+LNKHIDDKNKTWKNPYETLE,0,1
+NKHIDDKNKTWKNPYETLED,0,0
+KHIDDKNKTWKNPYETLEDT,2,0
+HIDDKNKTWKNPYETLEDTF,4.5,0
+IDDKNKTWKNPYETLEDTFK,1,0
+DDKNKTWKNPYETLEDTFKS,5,3
+DKNKTWKNPYETLEDTFKSK,0,0
+KNKTWKNPYETLEDTFKSKC,0,1
+NKTWKNPYETLEDTFKSKCD,0,0
+KTWKNPYETLEDTFKSKCDC,0,2
+TWKNPYETLEDTFKSKCDCP,0,0
+WKNPYETLEDTFKSKCDCPK,2,0
+KNPYETLEDTFKSKCDCPKP,3,2
+NPYETLEDTFKSKCDCPKPL,0,8
+PYETLEDTFKSKCDCPKPLP,0,0
+YETLEDTFKSKCDCPKPLPS,0,1
+ETLEDTFKSKCDCPKPLPSP,2,0
+TLEDTFKSKCDCPKPLPSPI,0,0
+LEDTFKSKCDCPKPLPSPIK,4,0
+EDTFKSKCDCPKPLPSPIKP,0,1
+DTFKSKCDCPKPLPSPIKPD,0,0
+TFKSKCDCPKPLPSPIKPDD,0,0
+FKSKCDCPKPLPSPIKPDDL,0,6
+KSKCDCPKPLPSPIKPDDLP,0,1
+SKCDCPKPLPSPIKPDDLPP,0,0
+KCDCPKPLPSPIKPDDLPPQ,0,3
+CDCPKPLPSPIKPDDLPPQA,0,0
+DCPKPLPSPIKPDDLPPQAD,3,2.5
+CPKPLPSPIKPDDLPPQADE,0,0
+PKPLPSPIKPDDLPPQADEP,0,0
+KPLPSPIKPDDLPPQADEPF,0,0
+PLPSPIKPDDLPPQADEPFD,2,1
+LPSPIKPDDLPPQADEPFDP,1,0
+PSPIKPDDLPPQADEPFDPT,0,0
+SPIKPDDLPPQADEPFDPTI,0,0
+PIKPDDLPPQADEPFDPTIL,0,0
+IKPDDLPPQADEPFDPTILQ,0,0
+KPDDLPPQADEPFDPTILQT,0,0
+PDDLPPQADEPFDPTILQTT,4,0
+DDLPPQADEPFDPTILQTTI,0,0
+DLPPQADEPFDPTILQTTIP,0,0
+LPPQADEPFDPTILQTTIPG,0,0
+PPQADEPFDPTILQTTIPGS,4.5,1.5
+PQADEPFDPTILQTTIPGSG,3,0
+QADEPFDPTILQTTIPGSGS,0,0
+ADEPFDPTILQTTIPGSGSG,0,5
+DEPFDPTILQTTIPGSGSGS,3,0
+EPFDPTILQTTIPGSGSGSG,4,79.5

biotite/source/doc/examples/download/NF54_10ug.csv

@@ -0,0 +1,1325 @@
+Seq,r1,r2
+GSGSGSGMDKSSIANKIEAY,0,0
+GSGSGMDKSSIANKIEAYLG,0,0
+GSGMDKSSIANKIEAYLGAK,0,8
+GMDKSSIANKIEAYLGAKSD,0,0
+DKSSIANKIEAYLGAKSDDS,0,1
+SSIANKIEAYLGAKSDDSKI,0,0
+IANKIEAYLGAKSDDSKIDQ,0,0
+NKIEAYLGAKSDDSKIDQSL,3,2
+IEAYLGAKSDDSKIDQSLKA,10,0
+AYLGAKSDDSKIDQSLKADP,0,0
+LGAKSDDSKIDQSLKADPSE,0,0
+AKSDDSKIDQSLKADPSEVQ,0,0
+SDDSKIDQSLKADPSEVQYY,0,77
+DSKIDQSLKADPSEVQYYGS,0,0
+KIDQSLKADPSEVQYYGSGG,0,0
+DQSLKADPSEVQYYGSGGDG,0,1
+SLKADPSEVQYYGSGGDGYY,3,0
+KADPSEVQYYGSGGDGYYLR,0,0
+DPSEVQYYGSGGDGYYLRKN,0,2.5
+SEVQYYGSGGDGYYLRKNIC,0,0
+VQYYGSGGDGYYLRKNICKI,0,0
+YYGSGGDGYYLRKNICKITV,1,0
+GSGGDGYYLRKNICKITVNH,0,0
+GGDGYYLRKNICKITVNHSD,0,0
+DGYYLRKNICKITVNHSDSG,0,0
+YYLRKNICKITVNHSDSGTN,0,2.5
+LRKNICKITVNHSDSGTNDP,0,0
+KNICKITVNHSDSGTNDPCD,0,0
+ICKITVNHSDSGTNDPCDRI,0,0
+KITVNHSDSGTNDPCDRIPP,0,1
+TVNHSDSGTNDPCDRIPPPY,3.5,0
+NHSDSGTNDPCDRIPPPYGD,2,0
+SDSGTNDPCDRIPPPYGDND,0,0
+SGTNDPCDRIPPPYGDNDQW,2,5
+TNDPCDRIPPPYGDNDQWKC,1,5
+DPCDRIPPPYGDNDQWKCAI,3,0
+CDRIPPPYGDNDQWKCAIIL,5,0
+RIPPPYGDNDQWKCAIILSK,12,0
+PPPYGDNDQWKCAIILSKVS,5,4
+PYGDNDQWKCAIILSKVSEK,0,0
+GDNDQWKCAIILSKVSEKPE,0,0
+NDQWKCAIILSKVSEKPENV,0,5
+QWKCAIILSKVSEKPENVFV,0,5
+KCAIILSKVSEKPENVFVPP,0,1
+AIILSKVSEKPENVFVPPRR,1,0
+ILSKVSEKPENVFVPPRRQR,0,0
+SKVSEKPENVFVPPRRQRMC,0,2
+VSEKPENVFVPPRRQRMCIN,0.5,0
+EKPENVFVPPRRQRMCINNL,0,0
+PENVFVPPRRQRMCINNLEK,3,0
+NVFVPPRRQRMCINNLEKLN,3,0
+FVPPRRQRMCINNLEKLNVD,0.5,0
+PPRRQRMCINNLEKLNVDKI,0,0
+RRQRMCINNLEKLNVDKIRD,3,0
+QRMCINNLEKLNVDKIRDKH,1,0
+MCINNLEKLNVDKIRDKHAF,0,2
+INNLEKLNVDKIRDKHAFLA,0,0
+NLEKLNVDKIRDKHAFLADV,0,1
+EKLNVDKIRDKHAFLADVLL,0,2.5
+LNVDKIRDKHAFLADVLLTA,0,2
+VDKIRDKHAFLADVLLTARN,0,0
+KIRDKHAFLADVLLTARNEG,0,0
+RDKHAFLADVLLTARNEGER,0,0
+KHAFLADVLLTARNEGERIV,0,0
+AFLADVLLTARNEGERIVQN,0,0
+LADVLLTARNEGERIVQNHP,0,0
+DVLLTARNEGERIVQNHPDT,0,0
+LLTARNEGERIVQNHPDTNS,0,0
+TARNEGERIVQNHPDTNSSN,0,0
+RNEGERIVQNHPDTNSSNVC,2,0
+EGERIVQNHPDTNSSNVCNA,0,0
+ERIVQNHPDTNSSNVCNALE,0,0
+IVQNHPDTNSSNVCNALERS,2,0
+QNHPDTNSSNVCNALERSFA,0,0
+HPDTNSSNVCNALERSFADI,1,2
+DTNSSNVCNALERSFADIAD,1,0
+NSSNVCNALERSFADIADII,3,0
+SNVCNALERSFADIADIIRG,0,1
+VCNALERSFADIADIIRGTD,0,0
+NALERSFADIADIIRGTDLW,4,7
+LERSFADIADIIRGTDLWKG,5,1
+RSFADIADIIRGTDLWKGTN,4,0
+FADIADIIRGTDLWKGTNSN,0,0
+DIADIIRGTDLWKGTNSNLE,7,0
+ADIIRGTDLWKGTNSNLEQN,0,1.5
+IIRGTDLWKGTNSNLEQNLK,0,5
+RGTDLWKGTNSNLEQNLKQM,0,0
+TDLWKGTNSNLEQNLKQMFA,0,0
+LWKGTNSNLEQNLKQMFAKI,0,0
+KGTNSNLEQNLKQMFAKIRE,0,5
+TNSNLEQNLKQMFAKIREND,0,0
+SNLEQNLKQMFAKIRENDKV,0,0
+LEQNLKQMFAKIRENDKVLQ,4,0
+QNLKQMFAKIRENDKVLQDK,0,0
+LKQMFAKIRENDKVLQDKYP,0,0
+QMFAKIRENDKVLQDKYPKD,2,1
+FAKIRENDKVLQDKYPKDQN,0,1
+KIRENDKVLQDKYPKDQNYR,0,0
+RENDKVLQDKYPKDQNYRKL,0,7
+NDKVLQDKYPKDQNYRKLRE,0,0
+KVLQDKYPKDQNYRKLREDW,0,0
+LQDKYPKDQNYRKLREDWWN,0,4
+DKYPKDQNYRKLREDWWNAN,0,0
+YPKDQNYRKLREDWWNANRQ,0,3
+KDQNYRKLREDWWNANRQKV,0,0
+QNYRKLREDWWNANRQKVWE,0,0
+YRKLREDWWNANRQKVWEVI,0,2.5
+KLREDWWNANRQKVWEVITC,0,0
+REDWWNANRQKVWEVITCGA,0.5,0
+DWWNANRQKVWEVITCGARS,1,3
+WNANRQKVWEVITCGARSND,0,1
+ANRQKVWEVITCGARSNDLL,0,4
+RQKVWEVITCGARSNDLLIK,3,1
+KVWEVITCGARSNDLLIKRG,10,0
+WEVITCGARSNDLLIKRGWR,3,0
+VITCGARSNDLLIKRGWRTS,0,8
+TCGARSNDLLIKRGWRTSGK,0,6
+GARSNDLLIKRGWRTSGKSN,0,0
+RSNDLLIKRGWRTSGKSNGD,0,1
+NDLLIKRGWRTSGKSNGDNK,0,0
+LLIKRGWRTSGKSNGDNKLE,1,1
+IKRGWRTSGKSNGDNKLELC,2,0
+RGWRTSGKSNGDNKLELCRK,4,5
+WRTSGKSNGDNKLELCRKCG,3,7
+TSGKSNGDNKLELCRKCGHY,6,0
+GKSNGDNKLELCRKCGHYEE,3.5,3
+SNGDNKLELCRKCGHYEEKV,1,4
+GDNKLELCRKCGHYEEKVPT,3.5,0
+NKLELCRKCGHYEEKVPTKL,5,0
+LELCRKCGHYEEKVPTKLDY,4,0
+LCRKCGHYEEKVPTKLDYVP,0,0
+RKCGHYEEKVPTKLDYVPQF,0,0
+CGHYEEKVPTKLDYVPQFLR,0,0
+HYEEKVPTKLDYVPQFLRWL,2,0
+EEKVPTKLDYVPQFLRWLTE,0,0
+KVPTKLDYVPQFLRWLTEWI,1.5,0
+PTKLDYVPQFLRWLTEWIED,4,0
+KLDYVPQFLRWLTEWIEDFY,4,2
+DYVPQFLRWLTEWIEDFYRE,0,0
+VPQFLRWLTEWIEDFYREKQ,90.5,0
+QFLRWLTEWIEDFYREKQNL,0,0
+LRWLTEWIEDFYREKQNLID,5,0
+WLTEWIEDFYREKQNLIDDM,1,0
+TEWIEDFYREKQNLIDDMER,2,0
+WIEDFYREKQNLIDDMERHR,0,0
+EDFYREKQNLIDDMERHREE,0,0
+FYREKQNLIDDMERHREECT,0,0
+REKQNLIDDMERHREECTSE,0,3
+KQNLIDDMERHREECTSEDH,0,7
+NLIDDMERHREECTSEDHKS,0,3
+IDDMERHREECTSEDHKSKE,0,1
+DMERHREECTSEDHKSKEGT,0,0
+ERHREECTSEDHKSKEGTSY,0,0
+HREECTSEDHKSKEGTSYCS,0,0
+EECTSEDHKSKEGTSYCSTC,1,0
+CTSEDHKSKEGTSYCSTCKD,0,0
+SEDHKSKEGTSYCSTCKDKC,3,0
+DHKSKEGTSYCSTCKDKCKK,0,0
+KSKEGTSYCSTCKDKCKKYC,1,2
+KEGTSYCSTCKDKCKKYCEC,0,8
+GTSYCSTCKDKCKKYCECVK,0,15
+SYCSTCKDKCKKYCECVKKW,2,2
+CSTCKDKCKKYCECVKKWKS,4.5,0
+TCKDKCKKYCECVKKWKSEW,4,0
+KDKCKKYCECVKKWKSEWEN,2,0
+KCKKYCECVKKWKSEWENQK,0,3
+KKYCECVKKWKSEWENQKNK,0,0
+YCECVKKWKSEWENQKNKYT,101,102
+ECVKKWKSEWENQKNKYTEL,2,0
+VKKWKSEWENQKNKYTELYQ,1,0
+KWKSEWENQKNKYTELYQQN,1,0
+KSEWENQKNKYTELYQQNKN,0,0
+EWENQKNKYTELYQQNKNET,0,0
+ENQKNKYTELYQQNKNETSQ,0,0
+QKNKYTELYQQNKNETSQKN,0,0
+NKYTELYQQNKNETSQKNTS,0,0
+YTELYQQNKNETSQKNTSRY,7,0
+ELYQQNKNETSQKNTSRYDD,0,0
+YQQNKNETSQKNTSRYDDYV,0,0
+QNKNETSQKNTSRYDDYVKD,0,1
+KNETSQKNTSRYDDYVKDFF,0,3
+ETSQKNTSRYDDYVKDFFKK,2,1
+SQKNTSRYDDYVKDFFKKLE,11.5,5
+KNTSRYDDYVKDFFKKLEAN,5,2
+TSRYDDYVKDFFKKLEANYS,1,0
+RYDDYVKDFFKKLEANYSSL,0,0
+DDYVKDFFKKLEANYSSLEN,0,0
+YVKDFFKKLEANYSSLENYI,2,0
+KDFFKKLEANYSSLENYIKG,0,0
+FFKKLEANYSSLENYIKGDP,0,0
+KKLEANYSSLENYIKGDPYF,8,13
+LEANYSSLENYIKGDPYFAE,2,6
+ANYSSLENYIKGDPYFAEYA,0,9
+YSSLENYIKGDPYFAEYATK,0,0
+SLENYIKGDPYFAEYATKLS,2.5,0
+ENYIKGDPYFAEYATKLSFI,1,4
+YIKGDPYFAEYATKLSFILN,0,0
+KGDPYFAEYATKLSFILNSS,0,0
+DPYFAEYATKLSFILNSSDA,0,0
+YFAEYATKLSFILNSSDANN,0,0
+AEYATKLSFILNSSDANNPS,0,0
+YATKLSFILNSSDANNPSEK,0,0.5
+TKLSFILNSSDANNPSEKIQ,0,0
+LSFILNSSDANNPSEKIQKN,0,0
+FILNSSDANNPSEKIQKNND,0,0
+LNSSDANNPSEKIQKNNDEV,6,0
+SSDANNPSEKIQKNNDEVCN,0,0
+DANNPSEKIQKNNDEVCNCN,0,0
+NNPSEKIQKNNDEVCNCNES,0,0
+PSEKIQKNNDEVCNCNESGI,1,0
+EKIQKNNDEVCNCNESGIAS,0,0
+IQKNNDEVCNCNESGIASVE,0,0
+KNNDEVCNCNESGIASVEQE,2,0
+NDEVCNCNESGIASVEQEQI,1,0
+EVCNCNESGIASVEQEQISD,0,3
+CNCNESGIASVEQEQISDPS,0,0
+CNESGIASVEQEQISDPSSN,0,3
+ESGIASVEQEQISDPSSNKT,0,5
+GIASVEQEQISDPSSNKTCI,1,0
+ASVEQEQISDPSSNKTCITH,2,0
+VEQEQISDPSSNKTCITHSS,0,4
+QEQISDPSSNKTCITHSSIK,1.5,0
+QISDPSSNKTCITHSSIKAN,0,0
+SDPSSNKTCITHSSIKANKK,3,0
+PSSNKTCITHSSIKANKKKV,4,0
+SNKTCITHSSIKANKKKVCK,7.5,0
+KTCITHSSIKANKKKVCKHV,0,0
+CITHSSIKANKKKVCKHVKL,0,0
+THSSIKANKKKVCKHVKLGV,4.5,0
+SSIKANKKKVCKHVKLGVRE,0,0
+IKANKKKVCKHVKLGVREND,3,0
+ANKKKVCKHVKLGVRENDKD,3,0
+KKKVCKHVKLGVRENDKDLR,4,0
+KVCKHVKLGVRENDKDLRVC,4,0
+CKHVKLGVRENDKDLRVCVI,0,0
+HVKLGVRENDKDLRVCVIEH,0,0
+KLGVRENDKDLRVCVIEHTS,0,0
+GVRENDKDLRVCVIEHTSLS,0,0
+RENDKDLRVCVIEHTSLSGV,0,0
+NDKDLRVCVIEHTSLSGVEN,0,0
+KDLRVCVIEHTSLSGVENCC,0,0
+LRVCVIEHTSLSGVENCCCQ,0,0
+VCVIEHTSLSGVENCCCQDF,2,0
+VIEHTSLSGVENCCCQDFLR,4,5
+EHTSLSGVENCCCQDFLRIL,0,1
+TSLSGVENCCCQDFLRILQE,5,0
+LSGVENCCCQDFLRILQENC,4,0
+GVENCCCQDFLRILQENCSD,0,0
+ENCCCQDFLRILQENCSDNK,1,0
+CCCQDFLRILQENCSDNKSG,0,2
+CQDFLRILQENCSDNKSGSS,1,0
+DFLRILQENCSDNKSGSSSN,0,0
+LRILQENCSDNKSGSSSNGS,0,0
+ILQENCSDNKSGSSSNGSCN,0,1
+QENCSDNKSGSSSNGSCNNK,0,0
+NCSDNKSGSSSNGSCNNKNQ,2,0
+SDNKSGSSSNGSCNNKNQEA,0,0
+NKSGSSSNGSCNNKNQEACE,0,0
+SGSSSNGSCNNKNQEACEKN,0,0
+SSSNGSCNNKNQEACEKNLE,0,0
+SNGSCNNKNQEACEKNLEKV,2,0
+GSCNNKNQEACEKNLEKVLA,0,3
+CNNKNQEACEKNLEKVLASL,0,2
+NKNQEACEKNLEKVLASLTN,0,0
+NQEACEKNLEKVLASLTNCY,0,0
+EACEKNLEKVLASLTNCYKC,0,0
+CEKNLEKVLASLTNCYKCDK,0,0
+KNLEKVLASLTNCYKCDKCK,10,97
+LEKVLASLTNCYKCDKCKSE,0,0
+KVLASLTNCYKCDKCKSEQS,0,0
+LASLTNCYKCDKCKSEQSKK,84,295
+SLTNCYKCDKCKSEQSKKNN,0,0
+TNCYKCDKCKSEQSKKNNKN,3.5,73
+CYKCDKCKSEQSKKNNKNWI,0,0
+KCDKCKSEQSKKNNKNWIWK,0,0
+DKCKSEQSKKNNKNWIWKKS,0,0
+CKSEQSKKNNKNWIWKKSSG,0,0
+SEQSKKNNKNWIWKKSSGKE,2,3.5
+QSKKNNKNWIWKKSSGKEGG,0,5
+KKNNKNWIWKKSSGKEGGLQ,1,2
+NNKNWIWKKSSGKEGGLQKE,0,5
+KNWIWKKSSGKEGGLQKEYA,4,0
+WIWKKSSGKEGGLQKEYANT,0,0
+WKKSSGKEGGLQKEYANTIG,1,1
+KSSGKEGGLQKEYANTIGLP,0,0
+SGKEGGLQKEYANTIGLPPR,1,0
+KEGGLQKEYANTIGLPPRTQ,1,0
+GGLQKEYANTIGLPPRTQSL,2,0
+LQKEYANTIGLPPRTQSLCL,0.5,3
+KEYANTIGLPPRTQSLCLVV,0,0
+YANTIGLPPRTQSLCLVVCL,0,0
+NTIGLPPRTQSLCLVVCLDE,0,0
+IGLPPRTQSLCLVVCLDEKG,0,1
+LPPRTQSLCLVVCLDEKGKK,0,0
+PRTQSLCLVVCLDEKGKKTQ,0,0
+TQSLCLVVCLDEKGKKTQEL,0,5
+SLCLVVCLDEKGKKTQELKN,0,0
+CLVVCLDEKGKKTQELKNIR,0,4.5
+VVCLDEKGKKTQELKNIRTN,0,0
+CLDEKGKKTQELKNIRTNSE,0,0
+DEKGKKTQELKNIRTNSELL,2,0
+KGKKTQELKNIRTNSELLKE,0,0
+KKTQELKNIRTNSELLKEWI,8,0
+TQELKNIRTNSELLKEWIIA,0,0
+ELKNIRTNSELLKEWIIAAF,0,0
+KNIRTNSELLKEWIIAAFHE,0,1.5
+IRTNSELLKEWIIAAFHEGK,0,0
+TNSELLKEWIIAAFHEGKNL,0,4
+SELLKEWIIAAFHEGKNLKP,0,6
+LLKEWIIAAFHEGKNLKPSH,0,0
+KEWIIAAFHEGKNLKPSHEK,2,0
+WIIAAFHEGKNLKPSHEKKN,3,0
+IAAFHEGKNLKPSHEKKNDD,0,0
+AFHEGKNLKPSHEKKNDDNG,0,0
+HEGKNLKPSHEKKNDDNGKK,0,0
+GKNLKPSHEKKNDDNGKKLC,0,0
+NLKPSHEKKNDDNGKKLCKA,3,0
+KPSHEKKNDDNGKKLCKALE,2,6
+SHEKKNDDNGKKLCKALEYS,0,1
+EKKNDDNGKKLCKALEYSFA,0,4.5
+KNDDNGKKLCKALEYSFADY,2.5,0
+DDNGKKLCKALEYSFADYGD,0,0
+NGKKLCKALEYSFADYGDLI,0,0
+KKLCKALEYSFADYGDLIKG,0,0
+LCKALEYSFADYGDLIKGTS,0,2
+KALEYSFADYGDLIKGTSIW,6,0
+LEYSFADYGDLIKGTSIWDN,0,0
+YSFADYGDLIKGTSIWDNEY,0,0
+FADYGDLIKGTSIWDNEYTK,0,1
+DYGDLIKGTSIWDNEYTKDL,3,3
+GDLIKGTSIWDNEYTKDLEL,0,0
+LIKGTSIWDNEYTKDLELNL,0,0
+KGTSIWDNEYTKDLELNLQK,0,0
+TSIWDNEYTKDLELNLQKIF,0,0
+IWDNEYTKDLELNLQKIFGK,0,0
+DNEYTKDLELNLQKIFGKLF,0,0
+EYTKDLELNLQKIFGKLFRK,0,0.5
+TKDLELNLQKIFGKLFRKYI,95,7.5
+DLELNLQKIFGKLFRKYIKK,2525.5,1191
+ELNLQKIFGKLFRKYIKKNN,4026,2902
+NLQKIFGKLFRKYIKKNNTA,251,339
+QKIFGKLFRKYIKKNNTAEQ,0,0
+IFGKLFRKYIKKNNTAEQDT,1,0
+GKLFRKYIKKNNTAEQDTSY,0,0
+LFRKYIKKNNTAEQDTSYSS,0,0
+RKYIKKNNTAEQDTSYSSLD,0,0
+YIKKNNTAEQDTSYSSLDEL,0,0
+KKNNTAEQDTSYSSLDELRE,1,3
+NNTAEQDTSYSSLDELRESW,0.5,0
+TAEQDTSYSSLDELRESWWN,0,0
+EQDTSYSSLDELRESWWNTN,0,0
+DTSYSSLDELRESWWNTNKK,0,0
+SYSSLDELRESWWNTNKKYI,0,0
+SSLDELRESWWNTNKKYIWL,2.5,0
+LDELRESWWNTNKKYIWLAM,0,0
+ELRESWWNTNKKYIWLAMKH,0,0
+RESWWNTNKKYIWLAMKHGA,0,0
+SWWNTNKKYIWLAMKHGAGM,0,0
+WNTNKKYIWLAMKHGAGMNS,0,0.5
+TNKKYIWLAMKHGAGMNSTT,0,0
+KKYIWLAMKHGAGMNSTTCC,0,0
+YIWLAMKHGAGMNSTTCCGD,0,1.5
+WLAMKHGAGMNSTTCCGDGS,0,1
+AMKHGAGMNSTTCCGDGSVT,1,0
+KHGAGMNSTTCCGDGSVTGS,0,0
+GAGMNSTTCCGDGSVTGSGS,0,0
+GMNSTTCCGDGSVTGSGSSC,0,0
+NSTTCCGDGSVTGSGSSCDD,2,0
+TTCCGDGSVTGSGSSCDDIP,0,1.5
+CCGDGSVTGSGSSCDDIPTI,0,9
+GDGSVTGSGSSCDDIPTIDL,0,3
+GSVTGSGSSCDDIPTIDLIP,4,6
+VTGSGSSCDDIPTIDLIPQY,0,0
+GSGSSCDDIPTIDLIPQYLR,0,2.5
+GSSCDDIPTIDLIPQYLRFL,0,2
+SCDDIPTIDLIPQYLRFLQE,0,1
+DDIPTIDLIPQYLRFLQEWV,1,0
+IPTIDLIPQYLRFLQEWVEH,0,4
+TIDLIPQYLRFLQEWVEHFC,0,1
+DLIPQYLRFLQEWVEHFCKQ,0,0
+IPQYLRFLQEWVEHFCKQRQ,7,0
+QYLRFLQEWVEHFCKQRQEK,0,0
+LRFLQEWVEHFCKQRQEKVK,0,5
+FLQEWVEHFCKQRQEKVKPV,0,0
+QEWVEHFCKQRQEKVKPVIE,0,0
+WVEHFCKQRQEKVKPVIENC,0,0
+EHFCKQRQEKVKPVIENCKS,3,1
+FCKQRQEKVKPVIENCKSCK,0,0
+KQRQEKVKPVIENCKSCKES,0,0
+RQEKVKPVIENCKSCKESGG,0,3
+EKVKPVIENCKSCKESGGTC,3,2
+VKPVIENCKSCKESGGTCNG,0,2
+PVIENCKSCKESGGTCNGEC,0,0.5
+IENCKSCKESGGTCNGECKT,0,6
+NCKSCKESGGTCNGECKTEC,0,4
+KSCKESGGTCNGECKTECKN,1,0
+CKESGGTCNGECKTECKNKC,0,2
+ESGGTCNGECKTECKNKCEV,0,0
+GGTCNGECKTECKNKCEVYK,0,2
+TCNGECKTECKNKCEVYKKF,124.5,99
+NGECKTECKNKCEVYKKFIE,0,0
+ECKTECKNKCEVYKKFIEDC,0,2.5
+KTECKNKCEVYKKFIEDCKG,1,0
+ECKNKCEVYKKFIEDCKGGD,0,0
+KNKCEVYKKFIEDCKGGDGT,0,5
+KCEVYKKFIEDCKGGDGTAG,1,0
+EVYKKFIEDCKGGDGTAGSS,0,0
+YKKFIEDCKGGDGTAGSSWV,0,0
+KFIEDCKGGDGTAGSSWVKR,0,85
+IEDCKGGDGTAGSSWVKRWD,0,1.5
+DCKGGDGTAGSSWVKRWDQI,0,0
+KGGDGTAGSSWVKRWDQIYK,0,0
+GDGTAGSSWVKRWDQIYKRY,92,91
+GTAGSSWVKRWDQIYKRYSK,567,857
+AGSSWVKRWDQIYKRYSKYI,4,91
+SSWVKRWDQIYKRYSKYIED,1,0
+WVKRWDQIYKRYSKYIEDAK,0,0
+KRWDQIYKRYSKYIEDAKRN,0,0
+WDQIYKRYSKYIEDAKRNRK,91.5,106
+QIYKRYSKYIEDAKRNRKAG,0,0
+YKRYSKYIEDAKRNRKAGTK,255.5,171
+RYSKYIEDAKRNRKAGTKNC,0,0
+SKYIEDAKRNRKAGTKNCGP,0,0
+YIEDAKRNRKAGTKNCGPSS,0,0
+EDAKRNRKAGTKNCGPSSTT,0,1
+AKRNRKAGTKNCGPSSTTNA,0,5
+RNRKAGTKNCGPSSTTNAAE,0,0
+RKAGTKNCGPSSTTNAAENK,0,0
+AGTKNCGPSSTTNAAENKCV,0,2
+TKNCGPSSTTNAAENKCVQS,0,0
+NCGPSSTTNAAENKCVQSDI,2,4
+GPSSTTNAAENKCVQSDIDS,0.5,2
+SSTTNAAENKCVQSDIDSFF,0,1
+TTNAAENKCVQSDIDSFFKH,0,0
+NAAENKCVQSDIDSFFKHLI,1,0
+AENKCVQSDIDSFFKHLIDI,0,0
+NKCVQSDIDSFFKHLIDIGL,0,0
+CVQSDIDSFFKHLIDIGLTT,0,0
+QSDIDSFFKHLIDIGLTTPS,0,0
+DIDSFFKHLIDIGLTTPSSY,0,2
+DSFFKHLIDIGLTTPSSYLS,0,2
+FFKHLIDIGLTTPSSYLSIV,0,0
+KHLIDIGLTTPSSYLSIVLD,0,0
+LIDIGLTTPSSYLSIVLDDN,0,0
+DIGLTTPSSYLSIVLDDNIC,2,0
+GLTTPSSYLSIVLDDNICGA,1,0
+TTPSSYLSIVLDDNICGADK,0,0
+PSSYLSIVLDDNICGADKAP,0,0
+SYLSIVLDDNICGADKAPWT,1,0
+LSIVLDDNICGADKAPWTTY,0,4
+IVLDDNICGADKAPWTTYTT,0,0
+LDDNICGADKAPWTTYTTYT,4,1
+DNICGADKAPWTTYTTYTTT,0,4
+ICGADKAPWTTYTTYTTTEK,0,0
+GADKAPWTTYTTYTTTEKCN,3,0
+DKAPWTTYTTYTTTEKCNKE,0,1
+APWTTYTTYTTTEKCNKETD,0,2
+WTTYTTYTTTEKCNKETDKS,0,3
+TYTTYTTTEKCNKETDKSKL,1,0
+TTYTTTEKCNKETDKSKLQQ,0,0
+YTTTEKCNKETDKSKLQQCN,1.5,0
+TTEKCNKETDKSKLQQCNTA,0,0
+EKCNKETDKSKLQQCNTAVV,0,0
+CNKETDKSKLQQCNTAVVVN,0,0
+KETDKSKLQQCNTAVVVNVP,0,0
+TDKSKLQQCNTAVVVNVPSP,0,0
+KSKLQQCNTAVVVNVPSPLG,0,0
+KLQQCNTAVVVNVPSPLGNT,0,0
+QQCNTAVVVNVPSPLGNTPH,0,0
+CNTAVVVNVPSPLGNTPHGY,1,0
+TAVVVNVPSPLGNTPHGYKY,5,0
+VVVNVPSPLGNTPHGYKYAC,0,0
+VNVPSPLGNTPHGYKYACQC,0,1.5
+VPSPLGNTPHGYKYACQCKI,0,0
+SPLGNTPHGYKYACQCKIPT,0,0
+LGNTPHGYKYACQCKIPTNE,0,0
+NTPHGYKYACQCKIPTNEET,0,0
+PHGYKYACQCKIPTNEETCD,6,0
+GYKYACQCKIPTNEETCDDR,0,93
+KYACQCKIPTNEETCDDRKE,0,0
+ACQCKIPTNEETCDDRKEYM,0,0
+QCKIPTNEETCDDRKEYMNQ,0,0
+KIPTNEETCDDRKEYMNQWS,0,0
+PTNEETCDDRKEYMNQWSCG,2,0
+NEETCDDRKEYMNQWSCGSA,0,5
+ETCDDRKEYMNQWSCGSART,0,0
+CDDRKEYMNQWSCGSARTMK,0,0
+DRKEYMNQWSCGSARTMKRG,5,4
+KEYMNQWSCGSARTMKRGYK,100,104
+YMNQWSCGSARTMKRGYKND,0,1
+NQWSCGSARTMKRGYKNDNY,2.5,0
+WSCGSARTMKRGYKNDNYEL,0,0
+CGSARTMKRGYKNDNYELCK,0,0
+SARTMKRGYKNDNYELCKYN,1,0
+RTMKRGYKNDNYELCKYNGV,0,0
+MKRGYKNDNYELCKYNGVDV,0,1
+RGYKNDNYELCKYNGVDVKP,0,0
+YKNDNYELCKYNGVDVKPTT,0,0
+NDNYELCKYNGVDVKPTTVR,0,0
+NYELCKYNGVDVKPTTVRSN,0,3
+ELCKYNGVDVKPTTVRSNSS,0,3
+CKYNGVDVKPTTVRSNSSKL,0,0
+YNGVDVKPTTVRSNSSKLDD,0,0
+GVDVKPTTVRSNSSKLDDKD,0,0
+DVKPTTVRSNSSKLDDKDVT,0,0
+KPTTVRSNSSKLDDKDVTFF,2,1
+TTVRSNSSKLDDKDVTFFNL,0,1
+VRSNSSKLDDKDVTFFNLFE,0,0
+SNSSKLDDKDVTFFNLFEQW,0,0
+SSKLDDKDVTFFNLFEQWNK,3,1
+KLDDKDVTFFNLFEQWNKEI,0,2
+DDKDVTFFNLFEQWNKEIQY,0,0
+KDVTFFNLFEQWNKEIQYQI,4,0
+VTFFNLFEQWNKEIQYQIEQ,3,0
+FFNLFEQWNKEIQYQIEQYM,0,2
+NLFEQWNKEIQYQIEQYMTN,0,1
+FEQWNKEIQYQIEQYMTNTK,0,3
+QWNKEIQYQIEQYMTNTKIS,0,1.5
+NKEIQYQIEQYMTNTKISCN,0,0
+EIQYQIEQYMTNTKISCNNE,0,0
+QYQIEQYMTNTKISCNNEKN,0,0
+QIEQYMTNTKISCNNEKNVL,0,1
+EQYMTNTKISCNNEKNVLSR,0,2
+YMTNTKISCNNEKNVLSRVS,0,2.5
+TNTKISCNNEKNVLSRVSDE,3,0
+TKISCNNEKNVLSRVSDEAA,0,0
+ISCNNEKNVLSRVSDEAAQP,0,0
+CNNEKNVLSRVSDEAAQPKF,0,0
+NEKNVLSRVSDEAAQPKFSD,0,0
+KNVLSRVSDEAAQPKFSDNE,2,0
+VLSRVSDEAAQPKFSDNERD,1.5,4
+SRVSDEAAQPKFSDNERDRN,3,0
+VSDEAAQPKFSDNERDRNSI,0,1
+DEAAQPKFSDNERDRNSITH,0,0
+AAQPKFSDNERDRNSITHED,0,1
+QPKFSDNERDRNSITHEDKN,0,0
+KFSDNERDRNSITHEDKNCK,0,3.5
+SDNERDRNSITHEDKNCKEK,2,0
+NERDRNSITHEDKNCKEKCK,2.5,0
+RDRNSITHEDKNCKEKCKCY,0,10
+RNSITHEDKNCKEKCKCYSL,0,0
+SITHEDKNCKEKCKCYSLWI,4,0
+THEDKNCKEKCKCYSLWIEK,2,0
+EDKNCKEKCKCYSLWIEKIN,0,0
+KNCKEKCKCYSLWIEKINDQ,0,0
+CKEKCKCYSLWIEKINDQWD,2,0
+EKCKCYSLWIEKINDQWDKQ,0,3
+CKCYSLWIEKINDQWDKQKD,0,0
+CYSLWIEKINDQWDKQKDNY,0,0
+SLWIEKINDQWDKQKDNYNK,0,0
+WIEKINDQWDKQKDNYNKFQ,0,0
+EKINDQWDKQKDNYNKFQRK,109.5,0
+INDQWDKQKDNYNKFQRKQI,0,0
+DQWDKQKDNYNKFQRKQIYD,0,0
+WDKQKDNYNKFQRKQIYDAN,0,1
+KQKDNYNKFQRKQIYDANKG,0,0
+KDNYNKFQRKQIYDANKGSQ,3,0
+NYNKFQRKQIYDANKGSQNK,1,0
+NKFQRKQIYDANKGSQNKKV,0,0
+FQRKQIYDANKGSQNKKVVS,0,7
+RKQIYDANKGSQNKKVVSLS,0,0
+QIYDANKGSQNKKVVSLSNF,0,0
+YDANKGSQNKKVVSLSNFLF,0,0
+ANKGSQNKKVVSLSNFLFFS,0,0
+KGSQNKKVVSLSNFLFFSCW,1,1
+SQNKKVVSLSNFLFFSCWEE,0,0
+NKKVVSLSNFLFFSCWEEYI,0,0
+KVVSLSNFLFFSCWEEYIQK,0,0
+VSLSNFLFFSCWEEYIQKYF,0,1
+LSNFLFFSCWEEYIQKYFNG,0,0
+NFLFFSCWEEYIQKYFNGDW,0,0
+LFFSCWEEYIQKYFNGDWSK,0,0
+FSCWEEYIQKYFNGDWSKIK,8,2
+CWEEYIQKYFNGDWSKIKNI,0,5
+EEYIQKYFNGDWSKIKNIGS,0,4
+YIQKYFNGDWSKIKNIGSDT,0,3
+QKYFNGDWSKIKNIGSDTFE,1,0
+YFNGDWSKIKNIGSDTFEFL,4.5,0
+NGDWSKIKNIGSDTFEFLIK,1,0
+DWSKIKNIGSDTFEFLIKKC,1,0
+SKIKNIGSDTFEFLIKKCGN,0,0
+IKNIGSDTFEFLIKKCGNDS,0,6
+NIGSDTFEFLIKKCGNDSGD,0,3
+GSDTFEFLIKKCGNDSGDGE,0,1
+DTFEFLIKKCGNDSGDGETI,0.5,0
+FEFLIKKCGNDSGDGETIFS,4,0
+FLIKKCGNDSGDGETIFSEK,0,0
+IKKCGNDSGDGETIFSEKLN,0,0
+KCGNDSGDGETIFSEKLNNA,0,0
+GNDSGDGETIFSEKLNNAEK,0,0
+DSGDGETIFSEKLNNAEKKC,8.5,0
+GDGETIFSEKLNNAEKKCKE,1,0.5
+GETIFSEKLNNAEKKCKENE,0,0
+TIFSEKLNNAEKKCKENEST,0,0
+FSEKLNNAEKKCKENESTNN,0,0
+EKLNNAEKKCKENESTNNKM,2,0
+LNNAEKKCKENESTNNKMKS,0,0
+NAEKKCKENESTNNKMKSSE,0,0
+EKKCKENESTNNKMKSSETS,0,0
+KCKENESTNNKMKSSETSCD,0,0
+KENESTNNKMKSSETSCDCS,0,0
+NESTNNKMKSSETSCDCSEP,0,1
+STNNKMKSSETSCDCSEPIY,3,3
+NNKMKSSETSCDCSEPIYIR,2,4
+KMKSSETSCDCSEPIYIRGC,0,0
+KSSETSCDCSEPIYIRGCQP,0,0
+SETSCDCSEPIYIRGCQPKI,0,2
+TSCDCSEPIYIRGCQPKIYD,0,0
+CDCSEPIYIRGCQPKIYDGK,0,0
+CSEPIYIRGCQPKIYDGKIF,0.5,2.5
+EPIYIRGCQPKIYDGKIFPG,2,0
+IYIRGCQPKIYDGKIFPGKG,1,0
+IRGCQPKIYDGKIFPGKGGE,83.5,4
+GCQPKIYDGKIFPGKGGEKQ,0,0
+QPKIYDGKIFPGKGGEKQWI,0,3.5
+KIYDGKIFPGKGGEKQWICK,1,0
+YDGKIFPGKGGEKQWICKDT,0,2
+GKIFPGKGGEKQWICKDTII,0,0
+IFPGKGGEKQWICKDTIIHG,0,5
+PGKGGEKQWICKDTIIHGDT,0,0
+KGGEKQWICKDTIIHGDTNG,0,0
+GEKQWICKDTIIHGDTNGAC,2,0
+KQWICKDTIIHGDTNGACIP,0,0
+WICKDTIIHGDTNGACIPPR,0.5,7
+CKDTIIHGDTNGACIPPRTQ,0,2
+DTIIHGDTNGACIPPRTQNL,0,0
+IIHGDTNGACIPPRTQNLCV,2,0
+HGDTNGACIPPRTQNLCVGE,3.5,0
+DTNGACIPPRTQNLCVGELW,0,4
+NGACIPPRTQNLCVGELWDK,0,0
+ACIPPRTQNLCVGELWDKRY,0,0
+IPPRTQNLCVGELWDKRYGG,6,0
+PRTQNLCVGELWDKRYGGRS,0,0
+TQNLCVGELWDKRYGGRSNI,0,1
+NLCVGELWDKRYGGRSNIKN,0,0
+CVGELWDKRYGGRSNIKNDT,0,0
+GELWDKRYGGRSNIKNDTKE,0,0
+LWDKRYGGRSNIKNDTKESL,0,0
+DKRYGGRSNIKNDTKESLKQ,2,0
+RYGGRSNIKNDTKESLKQKI,0,0
+GGRSNIKNDTKESLKQKIKN,7,0
+RSNIKNDTKESLKQKIKNAI,0,0
+NIKNDTKESLKQKIKNAIQK,3,0
+KNDTKESLKQKIKNAIQKET,0,0
+DTKESLKQKIKNAIQKETEL,0,0
+KESLKQKIKNAIQKETELLY,0,0
+SLKQKIKNAIQKETELLYEY,1,0
+KQKIKNAIQKETELLYEYHD,0,6.5
+KIKNAIQKETELLYEYHDKG,0,3
+KNAIQKETELLYEYHDKGTA,1,0
+AIQKETELLYEYHDKGTAII,0,1
+QKETELLYEYHDKGTAIISR,2,0
+ETELLYEYHDKGTAIISRNP,0,0
+ELLYEYHDKGTAIISRNPMK,1,0
+LYEYHDKGTAIISRNPMKGQ,8,3
+EYHDKGTAIISRNPMKGQKE,0,0
+HDKGTAIISRNPMKGQKEKE,0,0
+KGTAIISRNPMKGQKEKEEK,0,0
+TAIISRNPMKGQKEKEEKNN,0,0
+IISRNPMKGQKEKEEKNNDS,0,0
+SRNPMKGQKEKEEKNNDSNG,0,0
+NPMKGQKEKEEKNNDSNGLP,0,0
+MKGQKEKEEKNNDSNGLPKG,0,2
+GQKEKEEKNNDSNGLPKGFC,1,0
+KEKEEKNNDSNGLPKGFCHA,0,0
+KEEKNNDSNGLPKGFCHAVQ,1,0
+EKNNDSNGLPKGFCHAVQRS,6,0
+NNDSNGLPKGFCHAVQRSFI,2,0
+DSNGLPKGFCHAVQRSFIDY,0,0
+NGLPKGFCHAVQRSFIDYKN,0,0
+LPKGFCHAVQRSFIDYKNMI,2,0
+KGFCHAVQRSFIDYKNMILG,0,2
+FCHAVQRSFIDYKNMILGTS,0,0
+HAVQRSFIDYKNMILGTSVN,0,0
+VQRSFIDYKNMILGTSVNIY,0,2
+RSFIDYKNMILGTSVNIYEY,0,0
+FIDYKNMILGTSVNIYEYIG,2,87.5
+DYKNMILGTSVNIYEYIGKL,1,4
+KNMILGTSVNIYEYIGKLQE,0,0
+MILGTSVNIYEYIGKLQEDI,0,0
+LGTSVNIYEYIGKLQEDIKK,0,0
+TSVNIYEYIGKLQEDIKKII,0,0
+VNIYEYIGKLQEDIKKIIEK,0,0
+IYEYIGKLQEDIKKIIEKGT,1,1
+EYIGKLQEDIKKIIEKGTTK,0,2
+IGKLQEDIKKIIEKGTTKQN,3,0
+KLQEDIKKIIEKGTTKQNGK,5.5,0
+QEDIKKIIEKGTTKQNGKTV,1,0
+DIKKIIEKGTTKQNGKTVGS,0,0
+KKIIEKGTTKQNGKTVGSGA,0,0
+IIEKGTTKQNGKTVGSGAEN,0,1
+EKGTTKQNGKTVGSGAENVN,0,0
+GTTKQNGKTVGSGAENVNAW,0,0
+TKQNGKTVGSGAENVNAWWK,0,0
+QNGKTVGSGAENVNAWWKGI,0,0
+GKTVGSGAENVNAWWKGIEG,1,0
+TVGSGAENVNAWWKGIEGEM,6,0
+GSGAENVNAWWKGIEGEMWD,0,0
+GAENVNAWWKGIEGEMWDAV,0,0
+ENVNAWWKGIEGEMWDAVRC,0,1
+VNAWWKGIEGEMWDAVRCAI,0,0
+AWWKGIEGEMWDAVRCAITK,0,0
+WKGIEGEMWDAVRCAITKIN,0,0
+GIEGEMWDAVRCAITKINKK,1,0
+EGEMWDAVRCAITKINKKQK,7,0
+EMWDAVRCAITKINKKQKKN,6.5,0
+WDAVRCAITKINKKQKKNGT,1,0
+AVRCAITKINKKQKKNGTFS,0,2
+RCAITKINKKQKKNGTFSID,0,0
+AITKINKKQKKNGTFSIDEC,0,0
+TKINKKQKKNGTFSIDECGI,7,6
+INKKQKKNGTFSIDECGIFP,3,3
+KKQKKNGTFSIDECGIFPPT,1,0
+QKKNGTFSIDECGIFPPTGN,0,0
+KNGTFSIDECGIFPPTGNDE,0,0
+GTFSIDECGIFPPTGNDEDQ,0,0
+FSIDECGIFPPTGNDEDQSV,0,0
+IDECGIFPPTGNDEDQSVSW,0,1.5
+ECGIFPPTGNDEDQSVSWFK,2,10
+GIFPPTGNDEDQSVSWFKEW,0,0
+FPPTGNDEDQSVSWFKEWSE,3.5,0
+PTGNDEDQSVSWFKEWSEQF,2.5,2
+GNDEDQSVSWFKEWSEQFCI,0,5
+DEDQSVSWFKEWSEQFCIER,0.5,0
+DQSVSWFKEWSEQFCIERLQ,0,0
+SVSWFKEWSEQFCIERLQYE,2,0
+SWFKEWSEQFCIERLQYEKN,0,0
+FKEWSEQFCIERLQYEKNIR,0,1
+EWSEQFCIERLQYEKNIRDA,0,0
+SEQFCIERLQYEKNIRDACT,1,2
+QFCIERLQYEKNIRDACTNN,0,0
+CIERLQYEKNIRDACTNNGQ,5,0
+ERLQYEKNIRDACTNNGQGD,2,0
+LQYEKNIRDACTNNGQGDKI,0,0
+YEKNIRDACTNNGQGDKIQG,9,0
+KNIRDACTNNGQGDKIQGDC,1,1
+IRDACTNNGQGDKIQGDCKR,0,0
+DACTNNGQGDKIQGDCKRKC,0,3
+CTNNGQGDKIQGDCKRKCEE,2,0
+NNGQGDKIQGDCKRKCEEYK,0,1
+GQGDKIQGDCKRKCEEYKKY,0,97
+GDKIQGDCKRKCEEYKKYIS,98.5,99
+KIQGDCKRKCEEYKKYISEK,99,89
+QGDCKRKCEEYKKYISEKKQ,97,108
+DCKRKCEEYKKYISEKKQEW,2.5,0
+KRKCEEYKKYISEKKQEWDK,0,1
+KCEEYKKYISEKKQEWDKQK,95,104.5
+EEYKKYISEKKQEWDKQKTK,111.5,1531
+YKKYISEKKQEWDKQKTKYE,0,0
+KYISEKKQEWDKQKTKYENK,166,102
+ISEKKQEWDKQKTKYENKYV,99,154
+EKKQEWDKQKTKYENKYVGK,100,122.5
+KQEWDKQKTKYENKYVGKSA,33365,3464
+EWDKQKTKYENKYVGKSASD,73,524
+DKQKTKYENKYVGKSASDLL,79.5,82
+QKTKYENKYVGKSASDLLKE,0,0
+TKYENKYVGKSASDLLKENY,0,0
+YENKYVGKSASDLLKENYPE,0,3
+NKYVGKSASDLLKENYPECI,2,1
+YVGKSASDLLKENYPECISA,3,0
+GKSASDLLKENYPECISANF,0,2
+SASDLLKENYPECISANFDF,0,0
+SDLLKENYPECISANFDFIF,6,0
+LLKENYPECISANFDFIFND,0,0
+KENYPECISANFDFIFNDNI,3,0
+NYPECISANFDFIFNDNIEY,1,1
+PECISANFDFIFNDNIEYKT,0,0
+CISANFDFIFNDNIEYKTYY,0,0
+SANFDFIFNDNIEYKTYYPY,2,0
+NFDFIFNDNIEYKTYYPYGD,0,0
+DFIFNDNIEYKTYYPYGDYS,3,4
+IFNDNIEYKTYYPYGDYSSI,3,0
+NDNIEYKTYYPYGDYSSICS,0.5,3
+NIEYKTYYPYGDYSSICSCE,0,0
+EYKTYYPYGDYSSICSCEQV,0,3
+KTYYPYGDYSSICSCEQVKY,6,6
+YYPYGDYSSICSCEQVKYYE,3.5,2
+PYGDYSSICSCEQVKYYEYN,2,9
+GDYSSICSCEQVKYYEYNNA,0,0
+YSSICSCEQVKYYEYNNAEK,8,1
+SICSCEQVKYYEYNNAEKKN,2,0
+CSCEQVKYYEYNNAEKKNNK,0,2
+CEQVKYYEYNNAEKKNNKSL,0,1.5
+QVKYYEYNNAEKKNNKSLCH,0,0
+KYYEYNNAEKKNNKSLCHEK,2,1
+YEYNNAEKKNNKSLCHEKGN,0,0
+YNNAEKKNNKSLCHEKGNDR,0,0
+NAEKKNNKSLCHEKGNDRTW,0,0
+EKKNNKSLCHEKGNDRTWSK,0,0
+KNNKSLCHEKGNDRTWSKKY,0,0
+NKSLCHEKGNDRTWSKKYIK,87,245
+SLCHEKGNDRTWSKKYIKKL,1574,1137
+CHEKGNDRTWSKKYIKKLEN,336,140
+EKGNDRTWSKKYIKKLENGR,80,81
+GNDRTWSKKYIKKLENGRTL,85,80
+DRTWSKKYIKKLENGRTLEG,91,0
+TWSKKYIKKLENGRTLEGVY,9,0
+SKKYIKKLENGRTLEGVYVP,9,4.5
+KYIKKLENGRTLEGVYVPPR,0,1
+IKKLENGRTLEGVYVPPRRQ,0,0
+KLENGRTLEGVYVPPRRQQL,0,2
+ENGRTLEGVYVPPRRQQLCL,0,0
+GRTLEGVYVPPRRQQLCLYE,0,2
+TLEGVYVPPRRQQLCLYELF,0,3
+EGVYVPPRRQQLCLYELFPI,0,4
+VYVPPRRQQLCLYELFPIII,0,0
+VPPRRQQLCLYELFPIIIKN,0,0
+PRRQQLCLYELFPIIIKNKN,2,0
+RQQLCLYELFPIIIKNKNDI,0,0
+QLCLYELFPIIIKNKNDITN,0,0
+CLYELFPIIIKNKNDITNAK,0,0
+YELFPIIIKNKNDITNAKKE,0,0
+LFPIIIKNKNDITNAKKELL,0,0
+PIIIKNKNDITNAKKELLET,0,0
+IIKNKNDITNAKKELLETLQ,0,0
+KNKNDITNAKKELLETLQIV,0,0
+KNDITNAKKELLETLQIVAE,0,0
+DITNAKKELLETLQIVAERE,0,8
+TNAKKELLETLQIVAEREAY,0,0
+AKKELLETLQIVAEREAYYL,0,0
+KELLETLQIVAEREAYYLWK,0,0
+LLETLQIVAEREAYYLWKQY,0,1.5
+ETLQIVAEREAYYLWKQYHA,0,0
+LQIVAEREAYYLWKQYHAHN,0,3
+IVAEREAYYLWKQYHAHNDT,0,0
+AEREAYYLWKQYHAHNDTTY,0,2
+REAYYLWKQYHAHNDTTYLA,1,4
+AYYLWKQYHAHNDTTYLAHK,0,0
+YLWKQYHAHNDTTYLAHKKA,0,0
+WKQYHAHNDTTYLAHKKACC,0,0
+QYHAHNDTTYLAHKKACCAI,5.5,0
+HAHNDTTYLAHKKACCAIRG,0,0
+HNDTTYLAHKKACCAIRGSF,0,0
+DTTYLAHKKACCAIRGSFYD,5,0
+TYLAHKKACCAIRGSFYDLE,0,3
+LAHKKACCAIRGSFYDLEDI,1,0
+HKKACCAIRGSFYDLEDIIK,0,0
+KACCAIRGSFYDLEDIIKGN,0,2
+CCAIRGSFYDLEDIIKGNDL,3,0
+AIRGSFYDLEDIIKGNDLVH,0,0
+RGSFYDLEDIIKGNDLVHDE,1,0
+SFYDLEDIIKGNDLVHDEYT,2,0
+YDLEDIIKGNDLVHDEYTKY,0,0
+LEDIIKGNDLVHDEYTKYID,1,1
+DIIKGNDLVHDEYTKYIDSK,0,0
+IKGNDLVHDEYTKYIDSKLN,5,0
+GNDLVHDEYTKYIDSKLNEI,0,0
+DLVHDEYTKYIDSKLNEIFD,0,0
+VHDEYTKYIDSKLNEIFDSS,0,2
+DEYTKYIDSKLNEIFDSSNK,2,6.5
+YTKYIDSKLNEIFDSSNKND,0,0
+KYIDSKLNEIFDSSNKNDIE,0,2
+IDSKLNEIFDSSNKNDIETK,0,0
+SKLNEIFDSSNKNDIETKRA,0,0
+LNEIFDSSNKNDIETKRART,0,0
+EIFDSSNKNDIETKRARTDW,0,0
+FDSSNKNDIETKRARTDWWE,7,0.5
+SSNKNDIETKRARTDWWENE,2,1
+NKNDIETKRARTDWWENEAI,0,0
+NDIETKRARTDWWENEAIAV,0,0
+IETKRARTDWWENEAIAVPN,0,0
+TKRARTDWWENEAIAVPNIT,1,0
+RARTDWWENEAIAVPNITGA,0,0
+RTDWWENEAIAVPNITGANK,0,0
+DWWENEAIAVPNITGANKSD,0,0
+WENEAIAVPNITGANKSDPK,0.5,0
+NEAIAVPNITGANKSDPKTI,2,0
+AIAVPNITGANKSDPKTIRQ,0,0
+AVPNITGANKSDPKTIRQLV,0,0
+PNITGANKSDPKTIRQLVWD,2.5,0
+ITGANKSDPKTIRQLVWDAM,4,0
+GANKSDPKTIRQLVWDAMQS,0,5.5
+NKSDPKTIRQLVWDAMQSGV,5,7
+SDPKTIRQLVWDAMQSGVRK,0,2
+PKTIRQLVWDAMQSGVRKAI,0,0
+TIRQLVWDAMQSGVRKAIDE,0,0
+RQLVWDAMQSGVRKAIDEEK,0,0
+LVWDAMQSGVRKAIDEEKEK,0,0
+WDAMQSGVRKAIDEEKEKKK,90,0
+AMQSGVRKAIDEEKEKKKPN,0,0
+QSGVRKAIDEEKEKKKPNEN,1,0
+GVRKAIDEEKEKKKPNENFP,0,0
+RKAIDEEKEKKKPNENFPPC,0,0
+AIDEEKEKKKPNENFPPCMG,1,3
+DEEKEKKKPNENFPPCMGVQ,0,0
+EKEKKKPNENFPPCMGVQHI,80.5,0
+EKKKPNENFPPCMGVQHIGI,5,0
+KKPNENFPPCMGVQHIGIAK,0,1
+PNENFPPCMGVQHIGIAKPQ,1,0
+ENFPPCMGVQHIGIAKPQFI,0,0
+FPPCMGVQHIGIAKPQFIRW,0,118
+PCMGVQHIGIAKPQFIRWLE,3,2
+MGVQHIGIAKPQFIRWLEEW,6.5,6
+VQHIGIAKPQFIRWLEEWTN,2,0
+HIGIAKPQFIRWLEEWTNEF,2,0
+GIAKPQFIRWLEEWTNEFCE,0,1
+AKPQFIRWLEEWTNEFCEKY,0,0
+PQFIRWLEEWTNEFCEKYTK,3,0
+FIRWLEEWTNEFCEKYTKYF,1,0
+RWLEEWTNEFCEKYTKYFED,0,0
+LEEWTNEFCEKYTKYFEDMK,0,1
+EWTNEFCEKYTKYFEDMKSN,0,1
+TNEFCEKYTKYFEDMKSNCN,0,0
+EFCEKYTKYFEDMKSNCNLR,0,2.5
+CEKYTKYFEDMKSNCNLRKG,7,6
+KYTKYFEDMKSNCNLRKGAD,0,0
+TKYFEDMKSNCNLRKGADDC,5,1
+YFEDMKSNCNLRKGADDCDD,0,2
+EDMKSNCNLRKGADDCDDNS,0,0
+MKSNCNLRKGADDCDDNSNI,0,4
+SNCNLRKGADDCDDNSNIEC,0,1
+CNLRKGADDCDDNSNIECKK,0,0
+LRKGADDCDDNSNIECKKAC,0,0
+KGADDCDDNSNIECKKACAN,0,0
+ADDCDDNSNIECKKACANYT,0,0
+DCDDNSNIECKKACANYTNW,0,0
+DDNSNIECKKACANYTNWLN,0,0
+NSNIECKKACANYTNWLNPK,2,1
+NIECKKACANYTNWLNPKRI,0,0
+ECKKACANYTNWLNPKRIEW,0,0.5
+KKACANYTNWLNPKRIEWNG,0,0
+ACANYTNWLNPKRIEWNGMS,0.5,0
+ANYTNWLNPKRIEWNGMSNY,0,2
+YTNWLNPKRIEWNGMSNYYN,0,0
+NWLNPKRIEWNGMSNYYNKI,0,0
+LNPKRIEWNGMSNYYNKIYR,88,97.5
+PKRIEWNGMSNYYNKIYRKS,103,198
+RIEWNGMSNYYNKIYRKSNK,86.5,85
+EWNGMSNYYNKIYRKSNKES,0,1
+NGMSNYYNKIYRKSNKESED,0,0
+MSNYYNKIYRKSNKESEDGK,0,2
+NYYNKIYRKSNKESEDGKDY,5,0
+YNKIYRKSNKESEDGKDYSM,1,2
+KIYRKSNKESEDGKDYSMIM,0,0
+YRKSNKESEDGKDYSMIMEP,0,1
+KSNKESEDGKDYSMIMEPTV,0,0
+NKESEDGKDYSMIMEPTVID,1,0
+ESEDGKDYSMIMEPTVIDYL,9,10
+EDGKDYSMIMEPTVIDYLNK,0,3
+GKDYSMIMEPTVIDYLNKRC,0,0
+DYSMIMEPTVIDYLNKRCNG,0,1
+SMIMEPTVIDYLNKRCNGEI,2,89
+IMEPTVIDYLNKRCNGEING,0,0
+EPTVIDYLNKRCNGEINGNY,0,0
+TVIDYLNKRCNGEINGNYIC,0,101.5
+IDYLNKRCNGEINGNYICCS,0,0
+YLNKRCNGEINGNYICCSCK,0,0
+NKRCNGEINGNYICCSCKNI,0,0
+RCNGEINGNYICCSCKNIGE,0,0
+NGEINGNYICCSCKNIGENS,0,0
+EINGNYICCSCKNIGENSTS,0,0
+NGNYICCSCKNIGENSTSGT,3,1
+NYICCSCKNIGENSTSGTVN,0,0
+ICCSCKNIGENSTSGTVNKK,1,0
+CSCKNIGENSTSGTVNKKLQ,3,0
+CKNIGENSTSGTVNKKLQKK,0,0.5
+NIGENSTSGTVNKKLQKKET,2,0
+GENSTSGTVNKKLQKKETQC,3,3
+NSTSGTVNKKLQKKETQCED,0,0
+TSGTVNKKLQKKETQCEDNK,0,0
+GTVNKKLQKKETQCEDNKGP,0,0
+VNKKLQKKETQCEDNKGPLD,3,1
+KKLQKKETQCEDNKGPLDLM,0,0
+LQKKETQCEDNKGPLDLMNK,0,0
+KKETQCEDNKGPLDLMNKVL,3,0
+ETQCEDNKGPLDLMNKVLNK,0,0
+QCEDNKGPLDLMNKVLNKMD,0,0
+EDNKGPLDLMNKVLNKMDPK,0,0
+NKGPLDLMNKVLNKMDPKYS,0,8
+GPLDLMNKVLNKMDPKYSEH,0,8
+LDLMNKVLNKMDPKYSEHKM,0,2
+LMNKVLNKMDPKYSEHKMKC,3,1
+NKVLNKMDPKYSEHKMKCTE,0,1
+VLNKMDPKYSEHKMKCTEVY,0,2
+NKMDPKYSEHKMKCTEVYLE,3,7
+MDPKYSEHKMKCTEVYLEHV,3,1
+PKYSEHKMKCTEVYLEHVEE,0,0
+YSEHKMKCTEVYLEHVEEQL,0,0
+EHKMKCTEVYLEHVEEQLKE,0,3
+KMKCTEVYLEHVEEQLKEID,2,0
+KCTEVYLEHVEEQLKEIDNA,0,0
+TEVYLEHVEEQLKEIDNAIK,2,3
+VYLEHVEEQLKEIDNAIKDY,0,0
+LEHVEEQLKEIDNAIKDYKL,0,0
+HVEEQLKEIDNAIKDYKLYP,0,1
+EEQLKEIDNAIKDYKLYPLD,0,0
+QLKEIDNAIKDYKLYPLDRC,0,1
+KEIDNAIKDYKLYPLDRCFD,0,0
+IDNAIKDYKLYPLDRCFDDK,0,0
+NAIKDYKLYPLDRCFDDKSK,2,0
+IKDYKLYPLDRCFDDKSKMK,0,0
+DYKLYPLDRCFDDKSKMKVC,0,0
+KLYPLDRCFDDKSKMKVCDL,2,2
+YPLDRCFDDKSKMKVCDLIG,1,0
+LDRCFDDKSKMKVCDLIGDA,2,0
+RCFDDKSKMKVCDLIGDAIG,4,0
+FDDKSKMKVCDLIGDAIGCK,0,0
+DKSKMKVCDLIGDAIGCKHK,0,0
+SKMKVCDLIGDAIGCKHKTK,7,5
+MKVCDLIGDAIGCKHKTKLD,0,0.5
+VCDLIGDAIGCKHKTKLDEL,0,0
+DLIGDAIGCKHKTKLDELDE,0,1
+IGDAIGCKHKTKLDELDEWN,5,0
+DAIGCKHKTKLDELDEWNDV,0,0
+IGCKHKTKLDELDEWNDVDM,0,0
+CKHKTKLDELDEWNDVDMRD,0,0
+HKTKLDELDEWNDVDMRDPY,0,80.5
+TKLDELDEWNDVDMRDPYNK,106,1
+LDELDEWNDVDMRDPYNKYK,0,89.5
+ELDEWNDVDMRDPYNKYKGV,0,0
+DEWNDVDMRDPYNKYKGVLI,1,52
+WNDVDMRDPYNKYKGVLIPP,0,0
+DVDMRDPYNKYKGVLIPPRR,0,103
+DMRDPYNKYKGVLIPPRRRQ,0,0
+RDPYNKYKGVLIPPRRRQLC,0,0
+PYNKYKGVLIPPRRRQLCFS,0,1.5
+NKYKGVLIPPRRRQLCFSRI,0,0
+YKGVLIPPRRRQLCFSRIVR,0,0
+GVLIPPRRRQLCFSRIVRGP,0,0
+LIPPRRRQLCFSRIVRGPAN,0,0
+PPRRRQLCFSRIVRGPANLR,0,0
+RRRQLCFSRIVRGPANLRNL,3.5,2
+RQLCFSRIVRGPANLRNLKE,0.5,0
+LCFSRIVRGPANLRNLKEFK,0,0
+FSRIVRGPANLRNLKEFKEE,0,0
+RIVRGPANLRNLKEFKEEIL,0,0
+VRGPANLRNLKEFKEEILKG,0,0
+GPANLRNLKEFKEEILKGAQ,0,0
+ANLRNLKEFKEEILKGAQSE,0,3
+LRNLKEFKEEILKGAQSEGK,0,0
+NLKEFKEEILKGAQSEGKFL,0,0
+KEFKEEILKGAQSEGKFLGN,0,0
+FKEEILKGAQSEGKFLGNYY,0,0
+EEILKGAQSEGKFLGNYYNE,0,6
+ILKGAQSEGKFLGNYYNEDK,5,8.5
+KGAQSEGKFLGNYYNEDKDK,2,2
+AQSEGKFLGNYYNEDKDKEK,0,5
+SEGKFLGNYYNEDKDKEKAL,0,4
+GKFLGNYYNEDKDKEKALEA,0,7
+FLGNYYNEDKDKEKALEAMK,2,3.5
+GNYYNEDKDKEKALEAMKNS,0,0
+YYNEDKDKEKALEAMKNSFY,0,0
+NEDKDKEKALEAMKNSFYDY,0,4
+DKDKEKALEAMKNSFYDYEY,0,0
+DKEKALEAMKNSFYDYEYII,0,0
+EKALEAMKNSFYDYEYIIKG,0,0
+ALEAMKNSFYDYEYIIKGSD,0,3
+EAMKNSFYDYEYIIKGSDML,0.5,0
+MKNSFYDYEYIIKGSDMLTN,3,1.5
+NSFYDYEYIIKGSDMLTNIQ,0,0
+FYDYEYIIKGSDMLTNIQFK,0,0
+DYEYIIKGSDMLTNIQFKDI,0,0
+EYIIKGSDMLTNIQFKDIKR,0,0
+IIKGSDMLTNIQFKDIKRKL,2,0
+KGSDMLTNIQFKDIKRKLDR,0,0
+SDMLTNIQFKDIKRKLDRLL,0,0
+MLTNIQFKDIKRKLDRLLEK,139,62
+TNIQFKDIKRKLDRLLEKET,3,0
+IQFKDIKRKLDRLLEKETNN,0,0
+FKDIKRKLDRLLEKETNNTE,0,0
+DIKRKLDRLLEKETNNTEKV,2,0
+KRKLDRLLEKETNNTEKVDD,10,0
+KLDRLLEKETNNTEKVDDWW,3,2
+DRLLEKETNNTEKVDDWWET,0,0
+LLEKETNNTEKVDDWWETNK,0,0
+EKETNNTEKVDDWWETNKKS,0,1
+ETNNTEKVDDWWETNKKSIW,0,87.5
+NNTEKVDDWWETNKKSIWNA,0,0
+TEKVDDWWETNKKSIWNAML,12.5,81.5
+KVDDWWETNKKSIWNAMLCG,76.5,0
+DDWWETNKKSIWNAMLCGYK,86,91
+WWETNKKSIWNAMLCGYKKS,84,83
+ETNKKSIWNAMLCGYKKSGN,1.5,96
+NKKSIWNAMLCGYKKSGNKI,97,194
+KSIWNAMLCGYKKSGNKIID,94,0
+IWNAMLCGYKKSGNKIIDPS,100,0
+NAMLCGYKKSGNKIIDPSWC,0,0
+MLCGYKKSGNKIIDPSWCTI,0,0
+CGYKKSGNKIIDPSWCTIPT,0,0
+YKKSGNKIIDPSWCTIPTTE,0,0
+KSGNKIIDPSWCTIPTTETP,0,0
+GNKIIDPSWCTIPTTETPPQ,0,0
+KIIDPSWCTIPTTETPPQFL,0,3
+IDPSWCTIPTTETPPQFLRW,0,6.5
+PSWCTIPTTETPPQFLRWIK,0,0
+WCTIPTTETPPQFLRWIKEW,0,0
+TIPTTETPPQFLRWIKEWGT,0,1
+PTTETPPQFLRWIKEWGTNV,5,2
+TETPPQFLRWIKEWGTNVCI,5,0
+TPPQFLRWIKEWGTNVCIQK,0,0
+PQFLRWIKEWGTNVCIQKEE,0,2
+FLRWIKEWGTNVCIQKEEHK,0,0
+RWIKEWGTNVCIQKEEHKEY,0,2
+IKEWGTNVCIQKEEHKEYVK,1,1086.5
+EWGTNVCIQKEEHKEYVKSK,111,195
+GTNVCIQKEEHKEYVKSKCS,108,188.5
+NVCIQKEEHKEYVKSKCSNV,9,75
+CIQKEEHKEYVKSKCSNVTN,3,0
+QKEEHKEYVKSKCSNVTNLG,0,0
+EEHKEYVKSKCSNVTNLGAQ,0,0
+HKEYVKSKCSNVTNLGAQES,0,2
+EYVKSKCSNVTNLGAQESES,1,0
+VKSKCSNVTNLGAQESESKN,0,0
+SKCSNVTNLGAQESESKNCT,6,0
+CSNVTNLGAQESESKNCTSE,0,3
+NVTNLGAQESESKNCTSEIK,0,3
+TNLGAQESESKNCTSEIKKY,0,2.5
+LGAQESESKNCTSEIKKYQE,1,3
+AQESESKNCTSEIKKYQEWS,0,0
+ESESKNCTSEIKKYQEWSRK,7,82
+ESKNCTSEIKKYQEWSRKRS,0,85
+KNCTSEIKKYQEWSRKRSIQ,0,2
+CTSEIKKYQEWSRKRSIQWE,0,0
+SEIKKYQEWSRKRSIQWEAI,0,0
+IKKYQEWSRKRSIQWEAISE,0,1
+KYQEWSRKRSIQWEAISEGY,0,0
+QEWSRKRSIQWEAISEGYKK,0,0
+WSRKRSIQWEAISEGYKKYK,113,348
+RKRSIQWEAISEGYKKYKGM,95,82
+RSIQWEAISEGYKKYKGMDE,0,2
+IQWEAISEGYKKYKGMDEFK,2,2.5
+WEAISEGYKKYKGMDEFKNT,173,100
+AISEGYKKYKGMDEFKNTFK,602,370.5
+SEGYKKYKGMDEFKNTFKNI,85,87
+GYKKYKGMDEFKNTFKNIKE,0,0
+KKYKGMDEFKNTFKNIKEPD,0,0
+YKGMDEFKNTFKNIKEPDAN,0,0
+GMDEFKNTFKNIKEPDANEP,3.5,0
+DEFKNTFKNIKEPDANEPNA,0,0
+FKNTFKNIKEPDANEPNANE,0,0
+NTFKNIKEPDANEPNANEYL,0,0
+FKNIKEPDANEPNANEYLKK,0,76
+NIKEPDANEPNANEYLKKHC,4.5,0
+KEPDANEPNANEYLKKHCSK,79,0
+PDANEPNANEYLKKHCSKCP,0,0
+ANEPNANEYLKKHCSKCPCG,1,0
+EPNANEYLKKHCSKCPCGFN,0,2
+NANEYLKKHCSKCPCGFNDM,0,5
+NEYLKKHCSKCPCGFNDMQE,0,0
+YLKKHCSKCPCGFNDMQEIT,0,0
+KKHCSKCPCGFNDMQEITKY,0,0
+HCSKCPCGFNDMQEITKYTN,0,0
+SKCPCGFNDMQEITKYTNIG,1,1
+CPCGFNDMQEITKYTNIGNE,0,0
+CGFNDMQEITKYTNIGNEAF,7,0
+FNDMQEITKYTNIGNEAFKQ,0,0
+DMQEITKYTNIGNEAFKQIK,0,48.5
+QEITKYTNIGNEAFKQIKEQ,0,0
+ITKYTNIGNEAFKQIKEQVD,0,1
+KYTNIGNEAFKQIKEQVDIP,0,4
+TNIGNEAFKQIKEQVDIPAE,0,0
+IGNEAFKQIKEQVDIPAELE,0,0
+NEAFKQIKEQVDIPAELEDV,3,7
+AFKQIKEQVDIPAELEDVIY,0,2
+KQIKEQVDIPAELEDVIYRL,1,0
+IKEQVDIPAELEDVIYRLKH,0,0
+EQVDIPAELEDVIYRLKHHE,0,0
+VDIPAELEDVIYRLKHHEYD,0,0
+IPAELEDVIYRLKHHEYDKG,2,0
+AELEDVIYRLKHHEYDKGND,0,0
+LEDVIYRLKHHEYDKGNDYI,0,0
+DVIYRLKHHEYDKGNDYICN,0,0
+IYRLKHHEYDKGNDYICNKY,0,0
+RLKHHEYDKGNDYICNKYKN,0,0
+KHHEYDKGNDYICNKYKNIN,4,0
+HEYDKGNDYICNKYKNINVN,0,0
+YDKGNDYICNKYKNINVNMK,5,4
+KGNDYICNKYKNINVNMKKN,0,0
+NDYICNKYKNINVNMKKNND,0,4
+YICNKYKNINVNMKKNNDDT,0,0
+CNKYKNINVNMKKNNDDTWT,1,1
+KYKNINVNMKKNNDDTWTDL,0,0
+KNINVNMKKNNDDTWTDLVK,0,0
+INVNMKKNNDDTWTDLVKNS,0,0
+VNMKKNNDDTWTDLVKNSSD,0,0
+MKKNNDDTWTDLVKNSSDIN,0,0
+KNNDDTWTDLVKNSSDINKG,0,0
+NDDTWTDLVKNSSDINKGVL,3,2
+DTWTDLVKNSSDINKGVLLP,0,0
+WTDLVKNSSDINKGVLLPPR,0,2
+DLVKNSSDINKGVLLPPRRK,0,4
+VKNSSDINKGVLLPPRRKNL,0,0
+NSSDINKGVLLPPRRKNLFL,3,0
+SDINKGVLLPPRRKNLFLKI,0,0
+INKGVLLPPRRKNLFLKIDE,1,0
+KGVLLPPRRKNLFLKIDESD,0,0.5
+VLLPPRRKNLFLKIDESDIC,0,0
+LPPRRKNLFLKIDESDICKY,0,1
+PRRKNLFLKIDESDICKYKR,1412,2402
+RKNLFLKIDESDICKYKRDP,69,67
+NLFLKIDESDICKYKRDPKL,71,155
+FLKIDESDICKYKRDPKLFK,679,210.5
+KIDESDICKYKRDPKLFKDF,0,0
+DESDICKYKRDPKLFKDFIY,0,0
+SDICKYKRDPKLFKDFIYSS,71,158
+ICKYKRDPKLFKDFIYSSAI,5,0
+KYKRDPKLFKDFIYSSAISE,92,86
+KRDPKLFKDFIYSSAISEVE,0,0
+DPKLFKDFIYSSAISEVERL,0,0
+KLFKDFIYSSAISEVERLKK,7,0
+FKDFIYSSAISEVERLKKVY,0,1
+DFIYSSAISEVERLKKVYGE,3.5,0
+IYSSAISEVERLKKVYGEAK,3,3
+SSAISEVERLKKVYGEAKTK,100.5,630.5
+AISEVERLKKVYGEAKTKVV,64,79
+SEVERLKKVYGEAKTKVVHA,81,81
+VERLKKVYGEAKTKVVHAMK,205.5,90
+RLKKVYGEAKTKVVHAMKYS,70,89
+KKVYGEAKTKVVHAMKYSFA,80.5,0
+VYGEAKTKVVHAMKYSFADI,0,0
+GEAKTKVVHAMKYSFADIGS,0,0
+AKTKVVHAMKYSFADIGSII,101,0
+TKVVHAMKYSFADIGSIIKG,10.5,54.5
+VVHAMKYSFADIGSIIKGDD,5,0
+HAMKYSFADIGSIIKGDDMM,0,0
+MKYSFADIGSIIKGDDMMEN,0,0
+YSFADIGSIIKGDDMMENNS,3,5
+FADIGSIIKGDDMMENNSSD,0,0
+DIGSIIKGDDMMENNSSDKI,1,0
+GSIIKGDDMMENNSSDKIGK,0,0
+IIKGDDMMENNSSDKIGKIL,0,0
+KGDDMMENNSSDKIGKILGD,0,2
+DDMMENNSSDKIGKILGDGV,5,5.5
+MMENNSSDKIGKILGDGVGQ,0,8
+ENNSSDKIGKILGDGVGQNE,0,6
+NSSDKIGKILGDGVGQNEKR,0,2
+SDKIGKILGDGVGQNEKRKK,0,0
+KIGKILGDGVGQNEKRKKWW,0,0
+GKILGDGVGQNEKRKKWWDM,105.5,9
+ILGDGVGQNEKRKKWWDMNK,2,6
+GDGVGQNEKRKKWWDMNKYH,2,4
+GVGQNEKRKKWWDMNKYHIW,1,0
+GQNEKRKKWWDMNKYHIWES,2,0
+NEKRKKWWDMNKYHIWESML,0,4
+KRKKWWDMNKYHIWESMLCG,2,94.5
+KKWWDMNKYHIWESMLCGYK,0,0
+WWDMNKYHIWESMLCGYKHA,2.5,0
+DMNKYHIWESMLCGYKHAYG,6,1
+NKYHIWESMLCGYKHAYGNI,0,7
+YHIWESMLCGYKHAYGNISE,0,5
+IWESMLCGYKHAYGNISEND,0,0
+ESMLCGYKHAYGNISENDRK,0,0
+MLCGYKHAYGNISENDRKML,0,1
+CGYKHAYGNISENDRKMLDI,2,0
+YKHAYGNISENDRKMLDIPN,4,0
+HAYGNISENDRKMLDIPNND,0,0
+YGNISENDRKMLDIPNNDDE,0,0
+NISENDRKMLDIPNNDDEHQ,0,0
+SENDRKMLDIPNNDDEHQFL,0,0
+NDRKMLDIPNNDDEHQFLRW,8,0
+RKMLDIPNNDDEHQFLRWFQ,4,4
+MLDIPNNDDEHQFLRWFQEW,5,3.5
+DIPNNDDEHQFLRWFQEWTE,0,0
+PNNDDEHQFLRWFQEWTENF,0,1
+NDDEHQFLRWFQEWTENFCT,0,0
+DEHQFLRWFQEWTENFCTKR,0,0
+HQFLRWFQEWTENFCTKRNE,0,0
+FLRWFQEWTENFCTKRNELY,0,1
+RWFQEWTENFCTKRNELYEN,0,0
+FQEWTENFCTKRNELYENMV,0,0
+EWTENFCTKRNELYENMVTA,0,5
+TENFCTKRNELYENMVTACN,0,0.5
+NFCTKRNELYENMVTACNSA,0,0
+CTKRNELYENMVTACNSAKC,0,0
+KRNELYENMVTACNSAKCNT,0,0
+NELYENMVTACNSAKCNTSN,0,0
+LYENMVTACNSAKCNTSNGS,4,0
+ENMVTACNSAKCNTSNGSVD,5,0
+MVTACNSAKCNTSNGSVDKK,0,0
+TACNSAKCNTSNGSVDKKEC,0,3
+CNSAKCNTSNGSVDKKECTE,0,0
+SAKCNTSNGSVDKKECTEAC,0,2.5
+KCNTSNGSVDKKECTEACKN,0,0
+NTSNGSVDKKECTEACKNYS,1.5,0
+SNGSVDKKECTEACKNYSNF,0,0
+GSVDKKECTEACKNYSNFIL,0,2.5
+VDKKECTEACKNYSNFILIK,0,2
+KKECTEACKNYSNFILIKKK,0,0
+ECTEACKNYSNFILIKKKEY,0,3
+TEACKNYSNFILIKKKEYQS,0,0
+ACKNYSNFILIKKKEYQSLN,0,0
+KNYSNFILIKKKEYQSLNSQ,0,0
+YSNFILIKKKEYQSLNSQYD,0,0
+NFILIKKKEYQSLNSQYDMN,0,0
+ILIKKKEYQSLNSQYDMNYK,0,0
+IKKKEYQSLNSQYDMNYKET,0,0
+KKEYQSLNSQYDMNYKETKA,0,2
+EYQSLNSQYDMNYKETKAEK,0,2
+QSLNSQYDMNYKETKAEKKE,0,0
+LNSQYDMNYKETKAEKKESP,1,0
+SQYDMNYKETKAEKKESPEY,0,0
+YDMNYKETKAEKKESPEYFK,1,0
+MNYKETKAEKKESPEYFKDK,8,0
+YKETKAEKKESPEYFKDKCN,0,0
+ETKAEKKESPEYFKDKCNGE,0,1
+KAEKKESPEYFKDKCNGECS,0,1.5
+EKKESPEYFKDKCNGECSCL,0,0
+KESPEYFKDKCNGECSCLSE,0,2
+SPEYFKDKCNGECSCLSEYF,0,2
+EYFKDKCNGECSCLSEYFKD,0,1
+FKDKCNGECSCLSEYFKDET,0,0.5
+DKCNGECSCLSEYFKDETRW,6.5,0
+CNGECSCLSEYFKDETRWKN,0,1
+GECSCLSEYFKDETRWKNPY,0,0
+CSCLSEYFKDETRWKNPYET,0,0
+CLSEYFKDETRWKNPYETLD,0,3
+SEYFKDETRWKNPYETLDDT,0,0
+YFKDETRWKNPYETLDDTEV,0,1
+KDETRWKNPYETLDDTEVKN,0,2
+ETRWKNPYETLDDTEVKNNC,0,1
+RWKNPYETLDDTEVKNNCMC,0,0
+KNPYETLDDTEVKNNCMCKP,0,2
+PYETLDDTEVKNNCMCKPPP,0,5
+ETLDDTEVKNNCMCKPPPPA,3,0
+LDDTEVKNNCMCKPPPPASN,0,0
+DTEVKNNCMCKPPPPASNNT,0,0
+EVKNNCMCKPPPPASNNTSD,1,0
+KNNCMCKPPPPASNNTSDIL,0,0
+NCMCKPPPPASNNTSDILQK,0,0
+MCKPPPPASNNTSDILQKTI,0,0
+KPPPPASNNTSDILQKTIPG,0,0
+PPPASNNTSDILQKTIPGSG,3.5,0
+PASNNTSDILQKTIPGSGSG,0,2
+SNNTSDILQKTIPGSGSGSG,0,0

biotite/source/doc/examples/download/lysozyme_md.xtc

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:455e38002abdf3fa75d718cc5d3a23306e081a99fa2e40ebdc1086a709e5b3e8
+size 18770480

biotite/source/doc/examples/download/waterbox_md.xtc

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b528a5ec85892e1fb86b923f7df64a39023cc12de0ac1bfb0124e68edf58c0b9
+size 43587536

biotite/source/doc/examples/index.rst

@@ -0,0 +1,13 @@
+########
+Examples
+########
+
+This gallery shows how to perform different kind of analyses on real data using
+*Biotite*.
+Some of them are real world examples, others are fictional applications.
+
+.. toctree::
+    :maxdepth: 1
+
+    gallery/sequence/index
+    gallery/structure/index

biotite/source/doc/examples/scripts/sequence/README.rst

@@ -0,0 +1,2 @@
+Sequence examples
+=================