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rneherrneher
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Merge pull request #446 from nextstrain/andv
andv: initial addition
2 parents 41c473c + ca1b713 commit 331bdbc

48 files changed

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‎data/nextstrain/collection.json‎

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"nextstrain/flu/h2n2/na",
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"nextstrain/flu/h2n2/mp",
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"nextstrain/flu/h2n2/ns",
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"nextstrain/wnv/all-lineages"
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"nextstrain/wnv/all-lineages",
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"nextstrain/orthohantavirus/andv/l",
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"nextstrain/orthohantavirus/andv/m",
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"nextstrain/orthohantavirus/andv/s"
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]
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}

‎data/nextstrain/orthohantavirus/andv/l/CHANGELOG.md‎

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## Unreleased
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- initial release

‎data/nextstrain/orthohantavirus/andv/l/README.md‎

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# Andesvirus segment L dataset
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| Key | Value |
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| :-- | :-- |
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| name | Andes virus segment L Tree |
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| authors | [Nextstrain](https://nextstrain.org) |
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| reference | NC_003468 |
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| workflow | https://github.com/nextstrain/andv/tree/main/nextclade |
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| path | `nextstrain/orthohantavirus/andv/l` |
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## What are Nextclade datasets
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Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

‎data/nextstrain/orthohantavirus/andv/l/genome_annotation.gff3‎

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##gff-version 3
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#!gff-spec-version 1.21
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#!processor NCBI annotwriter
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##sequence-region NC_003468.2 1 6562
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##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1980456
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NC_003468.2 RefSeq region 1 6562 . + . ID=NC_003468.2:1..6562;Dbxref=taxon:1980456;Name=L;gbkey=Src;genome=genomic;mol_type=genomic RNA;old-name=Andes virus;segment=L;strain=Chile-9717869
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NC_003468.2 RefSeq CDS 36 6497 . + 0 Name=RdRp;gbkey=CDS;locus_tag=ANDVsLgp1;protein_id=NP_604473.1;product=RNA polymerase;ID=cds-NP_604473.1;Dbxref=GenBank:NP_604473.1,GeneID:991234

‎data/nextstrain/orthohantavirus/andv/l/pathogen.json‎

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{
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"$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
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"files": {
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"reference": "reference.fasta",
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"pathogenJson": "pathogen.json",
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"genomeAnnotation": "genome_annotation.gff3",
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"treeJson": "tree.json",
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"examples": "sequences.fasta",
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"readme": "README.md",
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"changelog": "CHANGELOG.md"
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},
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"schemaVersion": "3.0.0",
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"defaultCds": "RdRp",
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"attributes": {
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"name": "Andesvirus (segment L)",
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"reference name": "Chile-9717869",
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"reference accession": "NC_003468"
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},
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"experimental": true,
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"alignmentParams": {
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"penaltyGapExtend": 1,
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"penaltyGapOpen": 8,
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"penaltyGapOpenInFrame": 9,
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"penaltyGapOpenOutOfFrame": 10,
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"penaltyMismatch": 1,
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"scoreMatch": 5,
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"retryReverseComplement": true,
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"allowedMismatches": 10,
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"minSeedCover": 0.12,
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"minLength": 100
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},
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"qc": {
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"missingData": {
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"enabled": true,
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"missingDataThreshold": 200,
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"scoreBias": 100
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},
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"mixedSites": {
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"enabled": true,
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"mixedSitesThreshold": 4
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},
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"frameShifts": {
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"enabled": true
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},
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"stopCodons": {
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"enabled": true
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},
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"privateMutations": {
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"enabled": true,
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"cutoff": 150,
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"typical": 100,
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"weightLabeledSubstitutions": 1,
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"weightReversionSubstitutions": 1,
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"weightUnlabeledSubstitutions": 1
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},
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"snpClusters": {
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"enabled": true,
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"clusterCutOff": 15,
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"scoreWeight": 50,
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"windowSize": 50
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}
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}
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}

‎data/nextstrain/orthohantavirus/andv/l/reference.fasta‎

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>NC_003468.2 Andes virus segment L, complete genome
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TAGTAGTAGACTCCGGGATAGAAAAAGTTAGAAAAATGGAAAAGTATAGAGAGATTCATC
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AGAGAGTTAGGGACCTTGCACCTGGAACGGTATCAGCATTAGAATGCATAGATCTACTGG
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ATAGGCTCTACGCTGTCAGACATGACCTGGTTGACCAGATGATAAAACATGACTGGTCTG
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ATAATAAAGATGTAGAAAGACCTATAGGTCAAGTTTTACTGATGGCTGGCATACCTAATG
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ATATTATACAAGGCATGGAGAAGAAGATTATACCAAATAGCCCTTCTGGACAAGTATTGA
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AAAGCTTTTTCCGAATGACACCAGATAATTATAAAATTACAGGTAACTTGATTGAGTTTA
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TTGAAGTGACTGTAACAGCTGATGTGTCACGAGGTATTAGGGAGAAGAAAATAAAGTATG
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AAGGAGGCCTCCAATTTGTTGAGCACTTACTGGAAACTGAATCAAGGAAGGGTAATATAC
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CGCAACCTTATAAAATAACATTCTCAGTGGTTGCAGTTAAAACAGATGGATCAAACATCT
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CGACTCAGTGGCCCAGTCGGAGGAACGATGGGGTAGTTCAGCACATGCGTCTAGTCCAAG
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CTGATATAAATTATGTCAGAGAGCATTTAATAAAGTTAGATGAGAGAGCATCTTTGGAGG
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CAATGTTTAACTTAAAGTTCCATGTATCAGGCCCTAAACTGAGATACTTTAACATCCCTG
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ATTATAGACCACAGCAGCTATGTGAACCACGGATTGACAACTTAATACAATATTGCAAGA
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ATTGGTTGACAAAAGAACATAAGTTTGTATTCAAAGAAGTCAGTGGAGCTAATGTGATTC
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AAGCATTTGAGAGTCATGAACAGTTACATTTACAGAAATACAACGAATCACGAAAACCAA
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GAAATTTTTTACTCTTGCAGCTTACAGTGCAAGGGGCATATCTACCATCAACAATCAGTT
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CTGACCAGTGCAATACTAGGATTGGGTGTCTAGAAATATCAAAAAACCAACCAGAAACAC
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CAGTACAGATGCTTGCATTGGATATATCTTATAAGTATCTGAGTCTTACAAGGGATGAGT
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TGATCAATTATTATAGCCCTAGAGTGCACTTTCAATCGAGCCCTAATGTGAAGGAACCAG
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GGACACTGAAGTTAGGATTATCACAATTAAATCCACTCTCTAAATCAATTCTTGACAATG
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TTGGAAAGCATAAAAAGGATAAAGGATTATTTGGTGAGATCATAGATAGCATAAATGTGG
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CAAGTCAAATACAGATCAATGCATGTGCAAAAATAATTGAGCAGATCTTATCAAATCTTG
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AAATAAACATTGGAGAAATAAATGCTAGTATGCCTTCTCCTAATAAGACAACAGGTGTAG
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ATGACCTGTTAAATAAATTTTATGATAATGAGCTTGGTAAATATATGTTATCCATTCTGA
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GGAAAACAGCAGCATGGCATATAGGCCATCTAGTCAGAGATATCACAGAAAGTTTAATTG
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CACATGCTGGGCTGCGCCGTTCTAAATATTGGTCAGTACATGCATATGACCATGGGAATG
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TAATTTTGTTTATCTTGCCATCAAAGTCACTAGAGGTAGTAGGTTCTTATATAAGGTATT
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TCACAGTATTTAAAGATGGTATAGGGTTGATAGACGCAGATAATATTGATTCTAAGGCCG
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AAATTGATGGTGTCACCTGGTGTTATTCTAAGGTCATGAGTATTGATTTAAACAGGTTAT
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TGGCTTTGAACATAGCTTTTGAGAAGTCACTTCTTGCCACGGCTACATGGTTCCAATATT
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ATACTGAAGACCAAGGCCATTTTCCCCTTCAACATGCATTAAGGTCAATCTTTTCTTTCC
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ACTTTTTACTCTGTGTGTCACAAAAGATGAAGCTATGTGCAATATTTGATAACCTTCGTT
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ATCTGATACCATCAGTAACATCTTTGTACTCTGGGTACGAGTTGTTAATAGAAAAATTCT
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TTGAGAGACCATTTAAGAGTTCACTGGATGTATACCTTTATTCTATCATAAAATCTCTAT
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TAATTAGTTTGGCACAAAATAATAAAGTTCGATTTTACTCAAGAGTTCGTTTGTTAGGAT
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TGACAGTTGATCACTCCACGGTCGGAGCAAGTGGTGTTTACCCCTCTTTAATGTCCCGTG
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TTGTTTACAAACATTACAGAAGTTTAATCTCTGAAGCTACAACTTGTTTTTTCTTATTTG
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AAAAGGGTTTGCATGGGAATTTACCAGAAGAGGCTAAAATACATCTTGAAACCATTGAAT
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GGGCTCGGAAGTTCCAGGAGAAAGAAAAACAATATGGTGATATTCTTCTAAAGGAAGGCT
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ATACAATTGAATCTGTAATCAATGGAGAAGTTGATGTAGAACAACAGCTTTTTTGTCAGG
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AGGTCTCAGAGCTAAGTGCACAAGAGCTCAACAAATATTTACAGGCAAAATCTCAAGTTT
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TATGTGCTAATATCATGAATAAACACTGGGACAAACCATATTTCAGTCAAACACGCAATA
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TCAGTCTCAAGGGAATGTCTGGGGCATTGCAAGAGGATGGACATTTAGCTGCTAGTGTGA
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CACTGATTGAAGCAATTAGGTTTTTAAATAGATCACAAACCAATCCAAATGTTATTGATA
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TGTATGAGCAGACTAAACAATCAAAGGCACAAGCTAGGATTGTTAGGAAATACCAGAGAA
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CAGAAGCAGATAGAGGATTTTTTATCACAACATTACCAACTAGGGTGCGATTAGAAATAA
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TAGAAGATTATTTCGATGCAATTGCAAAGGTTGTGCCTGAAGAATATATTTCTTATGGTG
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GGGATAAAAAAGTTCTAAATATTCAGAATGCACTAGAGAAAGCACTTAGATGGGCATCTG
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GAGTATCAGAAATTACAACAAGCACTGGTAAAAGCATCAAGTTTAAGCGGAAATTAATGT
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ATGTTAGTGCTGATGCCACAAAATGGTCACCAGGAGATAATTCTGCTAAGTTTAGGAGAT
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TTACACAAGCAATATATGATGGCTTATCAGACAACAAACTGAAATGTTGTGTTGTTGATG
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CATTACGTAACATTTATGAGACTGAATTTTTTATGTCCAGGAAATTACACCGATATATTG
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ATAGTATGGAAAATCATTCAGATGCGGTTGAAGATTTCTTGGCATTTTTCTCAAATGGAG
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TCTCAGCCAATGTAAAGGGAAACTGGCTTCAAGGGAACTTAAATAAATGCTCATCATTAT
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TTGGTGCTGCTGTCTCATTACTTTTTCGGGAGGTCTGGAAACAATTGTTTCCAGAATTAG
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AGTGTTTTTTTGAATTTGCACATCATTCAGATGATGCATTGTTCATTTATGGCTATCTGG
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AGCCTGAAGATGATGGAACAGATTGGTTTTTGTATGTATCACAGCAGATACAGGCAGGAA
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ACTTTCATTGGCATGCTATAAATCAAGAGATGTGGAAGAGCATGTTTAATCTACATGAGC
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ACTTACTATTAATGGGTTCTATTAAAGTGTCACCTAAGAAGACAACAGTATCACCTACTA
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ATGCAGAATTTCTTTCTACTTTTTTTGAAGGTTGTGCTGTGTCAATCCCTTTTGTTAAAA
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TCTTACTGGGTTCATTATCAGATCTTCCTGGGTTAGGTTTCTTTGATGATTTAGCAGCAG
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CACAAAGCAGATGTGTAAAGTCACTAGATTTGGGTGCTTGCCCACAATTAGCTCAACTAG
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CTATAGTATTATGCACAAGCAAAGTTGAGAGGTTGTATGGTACTGCTGATGGAATGGTAA
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ACTCTCCAACAGCATTCCTTAAGGTGAATAAAGCACACGTACCAGTACCACTTGGTGGTG
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ATGGCTCAATGTCTATTATGGAGCTTGCAACAGCTGGTTTTGGGATGGCAGATAAGAATA
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TTTTAAAAAATGCATTCATATCTTATAAGCATACTCGTAGAGATGGTGATAGGTACGTAT
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TGGGTTTATTTAAATTTTTGATGTCATTAAGTGAGGATGTATTCCAGCACGACCGATTGG
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GTGAGTTTAGTTTTGTAGGTAAAGTTCAATGGAAAGTGTTCACTCCTAAAGCTGAATTTG
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AATTTCATGATCAATTTTCACATAATTATTTATTAGAGTGGACACGTCAACATCCTGTGT
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ATGACTATATTATTCCTAGAAATAGAGATAATTTGCTTGTATACCTTGTAAGAAAGTTGA
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ATGATCCTAGCATCATTACAGCTATGACTATGCAGTCACCATTACAACTTCGTTTCCGTA
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TGCAAGCAAAGCAACATATGAAAGTATGCCGGTATGAAGGTGAATGGGTCACATTCAGGG
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AGGTACTTGCTGCAGCTGATAGTTTTGCTACGAGTTACCAACCTACTGAAAGGGACATGG
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ATCTCTTTAATACACTTGTAAGTTGTACATTTTCTAAAGAGTATGCTTGGAAAGACTTTT
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TAAATGAAGTAAGGTGTGAGGTCTTAACAACAAGACATGTACATAGGCCTAAAATTGCTA
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GGACATTCACTGTTAGAGAAAAGGACCAGGCTATACAAAATCCAATAAATTCGGTGATTG
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GCTATAAGTATGCTCTTACAGTGGATGAAGTCAGTGATGTTCTTGATAGTGCATTCTTCC
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CAGAGTCTCTATCTGCAGACTTACAGGTTATGAAAGATGGAGTTTACAGAGAATTAGGAC
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TTGATATAAGTTCTCCTGAAGTCCTAAAACGCATAGCACCACTATTATATAAGGCAGGAA
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GGTCACGTGTTGTTATTGTGGAAGGAAATGTAGAAGGGACAGCTGAGTCAATCTGTAGTT
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ATTGGCTCAAGACAATGTCACTGATTAAAACAATCAGAGTAAGACCTAAGAAGGAGGTAC
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TGAAAGCTATGTCTTTATATAGTGTTAAAGAAAATATTGGATTGCAGGATGATATTGCAG
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CAACTCGACTATGCATAGAAATCTGGAGATGGTGTAAGGCAAATGAACAGGATGTTAAAG
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AATGGCTAACATCTCTGTACTTTGAAAAACAGACATTGATGGATTGGGTAGAAAGGTTTA
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GAAGGAAAGGAGTTGTTCCTATTGATCCTGAAATACAATGTATTGGCCTACTCTTATATG
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ATGTATTAGGTTATAAAAGTGTGTTACAAATGCAAGCAAACCGAAGAGCCTATTCAGGTA
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AGCAATATGATGCATACTGTGTGCAAACATATAACGAGGAAACAAAACTATATGAAGGTG
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ACCTTCGTGTTACTTTTAATTTTGGTTTAGATTGTGCAAGGTTAGAAGTTTTTTGGGATA
90+
AAAAAGAGTATATCTTAGAGACATCTATCACCCAACGACATGTGTTGCGGTTACTGATGG
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AAGAAGTGTCACAAGAATTAATTAGATGTGGAATGAGATTCAAAACAGAGCAAGTCAATC
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AAACTCGGAGCTTAGTGTTATTCAAAACAGAGGCTGGTTTTGAATGGGGTAAGCCTAATG
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TGCCATGTATTGTATATAAACACTGTGTCTTGAGAACTGGGCTTCGTACGAAACAGCCAA
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TTAATAAAGAGTTCATGATAAATGTACAAAGTGATGGTTTCCGTGCAATAGCACAGATGG
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ATATTGAGAGTCCACGGTTCTTGTTAGCACATGCATATCATACACTGCGTGATATTAGAT
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ATCAAGCAGTGCAGGCAGTAGGGAATGTATGGTTTAAAACAGAACAGCACAAACTATTTA
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TTAACCCAATTATATCATCAGGGCTTTTAGAAAACTTTATGAAAGGCTTACCTGCTGCCA
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TACCTCCTGCTGCATATTCCCTCATAATGAACAAGGCTAAGATTTCTGTGGATTTGTTTA
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TGTTCAATGAGCTATTAGCACTTATAAATAGGAATAATATCCTCAACCTTGATGGGATTG
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AAGAAACATCTGAAGGTTATAGTACTGTGACATCAATGTCTAGCAAGCAGTGGTCTGAAG
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AGATGAGTTTAATGTCTGATGATGATATTGATGATATGGAGGACTTTACTATAGCACTGG
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ATGATATTGACTTTGAACAAATAAATTTGGAAGAGGATATACAACACTTTCTGCAGGATG
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AATCAGCATATGTTGGTGATTTATTGATTCAGACAGAAGACATTGAGGTTAAAAAGATAC
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GTGGGGTGACAAGAGTATTAGAGCCAGTCAAGCTATTAAAAAGCTGGGTTTCTAAAGGCC
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TTGCTATAGACAAAGTATACAATCCTATCGGGATAATCTTAATGGCAAGATACATGTCAA
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AAACATACAATTTCAGTTCAACACCTCTTGCACTATTAAATCCATATGACTTGACAGAAC
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TTGAAAGTGTTGTAAAGGGATGGGGAGAAACTGTAAATGATCGATTCAAAGATTTAGATA
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TTGAGGCACAAACAGTTGTTAAAGAAAAGGGTGTACAGCCAGAAGATGTACTCCCTGATT
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CATTATTCTCTTTCAGGCATGTTGATGTTTTGCTGCGAAGGTTGTTCCCGCGTGACCCTG
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TATCAACATTCTATTAGTGGATTTTATACCTTATTCATACAGTATGTATATTGTAGTGTT
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CTTTTCCCGGAGCATACTACTA

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