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dezordi
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Add orov dataset
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‎data/community/itps/orov/L/refseq/CHANGELOG.md‎

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## Unreleased
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Initial release of a Oropouch Virus (OROV) dataset for segment L based on NCBI refseq reference genome.
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Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

‎data/community/itps/orov/L/refseq/README.md‎

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# Nextclade Dataset for "oroV" L segment based on RefSeq reference genome
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## Dataset Attributes
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| Attribute | Value |
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| -------------------- | ---------------------------------------- |
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| Name | orov/L/refseq |
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| RefName | Oropouche virus segment L |
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| RefAccession | NC_005776.1 |
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## Scope of This Dataset
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The dataset aims to enable the quality control of segment L of Oropouche virus using ncbi refseq as reference.
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The source code is available at [InstitutoTodosPelaSaude/nextclade-datasets-workflows](https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/tree/main/orov).
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For bugs, please open an [issue](https://github.com/InstitutoTodosPelaSaude/nextclade-datasets-workflows/issues).
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Read more about Nextclade datasets in the Nextclade documentation: [Nextclade Datasets](https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html).

‎data/community/itps/orov/L/refseq/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_005776.1 1 6846
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##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=118655
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NC_005776.1 RefSeq region 1 6846 . + . ID=NC_005776.1:1..6846;Dbxref=taxon:118655;Name=L;gbkey=Src;genome=genomic;mol_type=genomic RNA;segment=L
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NC_005776.1 GenBank gene 44 6796 . + . gene_name=L

‎data/community/itps/orov/L/refseq/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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"alignmentParams": {
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"retryReverseComplement": true
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},
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"attributes": {
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"name": "orov/L/refseq",
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"reference accession": "NC_005776.1",
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"reference name": "Oropouche virus, L segment"
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},
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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},
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"placementMaskRanges": [
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{
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"begin": 0,
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"end": 44
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},
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{
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"begin": 6797,
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"end": 6846
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}
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],
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"deprecated": false,
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"enabled": true,
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"experimental": true,
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"files": {
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"changelog": "CHANGELOG.md",
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"examples": "sequences.fasta",
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"genomeAnnotation": "genome_annotation.gff3",
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"pathogenJson": "pathogen.json",
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"readme": "README.md",
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"reference": "reference.fasta",
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"treeJson": "tree.json"
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},
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"meta": {
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"bugs": "https://github.com/dezordi/nextclade_data_workflows/issues",
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"source code": "https://github.com/dezordi/nextclade_data_workflows/tree/main/oroV"
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},
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"qc": {
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"frameShifts": {
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"enabled": true,
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"ignoredFrameShifts": [
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{
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"codonRange": {
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"begin": 788,
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"end": 792
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},
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"cdsName": "L"
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},
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{
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"codonRange": {
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"begin": 797,
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"end": 800
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},
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"cdsName": "L"
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},
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{
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"codonRange": {
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"begin": 846,
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"end": 855
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},
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"cdsName": "L"
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}
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]
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},
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"missingData": {
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"enabled": true,
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"missingDataThreshold": 1369,
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"scoreBias": 95
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},
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"mixedSites": {
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"enabled": true,
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"mixedSitesThreshold": 7
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},
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"privateMutations": {
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"cutoff": 20,
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"enabled": true,
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"typical": 10,
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"weightLabeledSubstitutions": 2,
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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": false
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},
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"stopCodons": {
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"enabled": true
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}
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},
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"schemaVersion": "3.0.0",
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"version": {
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"tag": "unreleased"
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},
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"defaultCds": "L"
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}

‎data/community/itps/orov/L/refseq/reference.fasta‎

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>NC_005776.1 Oropouche virus segment L, complete genome
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AGTAGTGTGCTCCTATTCCGAAACAAACAAAAACAATCTCAAAATGTCACAACTGTTGCT
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CAACCAATATCGGAATAGGATATTGCACTGCCGTGAACCTGAGATAGCAAAGGATATATG
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GCGAGATCTATTAAATGATCGACACAATTACTTTTCTCGGGAATTTTGCAGAGCTGCAAA
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TCTTGAGTACAGAAATGATGTTCCTGCTGAGGATATTTGTGCTGAAGTTCTTGATGGTTA
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TAAAGCAAGGAAAGTTCGCTTTTGTACACCTGATAATTACTTACTACATGATGGAAAGAT
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GTATATAATAGACTTCAAAGTGTCTGTAGACGACCGATCTTCTAGAATCACAAGGGAGAA
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ATATAATGAGATTTTTGGAGAGGTATTCAATCCAGAAGGTGTAGATTTTGAAATTGTTAT
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TATTAGATTAGATCCTTCAAATATGACGATACATGTGGACTCTCGAGATTTCGTGAATAC
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AATTGGGCCGATTACATTAAACATTAGTATGCAATGGTTTTTTGATATGAAAGACTTCTT
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GTTCGGGAAATTTCGGGATGATGATAAATTCCATGCTATAATAAGTCAAGGAGAATTCAC
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AATGACATTGCCATGGATTGAAGAAGACACCCCAGAATTGCTTACTCATCCTATATACAA
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TGAATTCATGAGTTCAATGCCAGAGGCAGAACAGGCCCTATTCAAGGAAGCATTGGAATT
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CAAATCATTTGGGGCAGAAAAATGGAATATCTTTTTGAAGGGGGTGATGTCAAAGTATGG
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TGAATATTATAAAGAATTTACTAAAGGACATGCTCATTCTATATTTCTGACAACAGGGGA
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CTACCCCAAGCCAGACAAAGACCAAATTTCAGCAGGTTGGAGAGAAATGGTAAACAGAGT
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AAGCTCTGAACGTGACATGTCAAATGACATAAATCAGGAAAAACCAAGCATGCATTTTAT
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ATGGGCAAAGAATGATTCAAATAGCAACAATAATATACAAAAGCTAATCAAACTATCTAA
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ATCACTGCAAGCTATGAGCGGGACAGGGAGCTATGTAAATGCTTTCAAGTCATTAGGGAG
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ATTAATGGATATATCATCAGATGTTAAAAAATATGAATCATTTTGTGGGAAATTGAAATC
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TCTGGCAAGGTCTAGTATAAAAAAACTTGACAGGAAAATAGAGCCAATACAAATTGGGAC
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TGCAACTGTCTTATGGGAACAGCAATTTAAACTAGATACAGATGTTATAAAAAGAGAAGA
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CAGAATACATTTAATGAAAGATTATCTTGGGATCGGTAAGCACAAATCATTTTCAAAGAA
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ATTAAACAACGACATAAATACTGATAAGCCTAAAATATTAAATTTCAACAATGATGATAT
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AGTCAGGAAATGCAAAGATAAATATAATCAAGTCATACATAACCTATCCCAAATCAATGA
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ATTAGATAAGATTGGAAACTACCTAGAGCACTTTTCAGCTAAAATTAGTGCCTGCAGTGT
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AGAAATGTGGGATTTTATATATAATACAACCAAAACTAAATACTGGCAATGCATCAATGA
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CTATTCCACCCTAATGAAAAACATGTTAGCTGTCTCTCAATATAATAGACACAATACGTT
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TAGAATTGTCTCATGTGCAAACAATAATGTATTTGGTCTAGTAATGCCAAGCTCAGATAT
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AAAGACAAAAAAAGCAACTTTAGTCTATGCAATAATGGCTCTCCATAATGAGGAGGCAGA
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AATAGCAGAACTTGGCTCACTCTACTCAACTTTTAAGACAGCAACAGGATATATTTCAAT
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ATCAAAGGCTTTTAGGCTGGATAAAGAAAGATGCCAACGCATAGTATCCTCTCCAGGCTT
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GTTCCTCATGACAAGCTGCCTATTATTCAACGGTAACAAGAGTTTAGAATTTGATAAATT
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ACTAGGATTTTCATTTTTTACGTCAATATCAATTACGAAAGCTATGCTCTCCCTTACTGA
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GCCTTCACGTTATATGATCATGAACTCGTTAGCAGTTTCCAGCCATGTAAGAGAGTATAT
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ATCTGAAAAATTCTCCCCTTATACAAAAACATCATTTTCTGTGGTAATGACAGACTTAAT
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CAAGAAGGGTTGCTATTCAGCATATGAACAGAGAAAAAAAGTACAAATAAGAGACATAAA
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ATTAACAGATTATGATATAACACAAAAGGGAGTGGATTCCAAAAGAGATCTTAAATCTAT
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TTGGTTCCCAGGAAAGGTAAACCTGAAAGAATATTTAAACCAAATTTATCTACCATTTTA
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TTTTAACTCTAAAGGATTACATGAAAAACATCATGTCTTGATAGATTTGGCTAAAACAGT
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ACTAGAAATCGAAAAAGAGCAAAGGGAGTCATTACCTGAGCCATGGTCAGAGATACCTGC
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TAAGCGACTGTCACTTAATGTTTTAATTTACTCATTGCAGGAACTGAATTTAGATACTTC
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AAGACATAATTTTGTAAGAAGCCGGGTGGAAAACGCAAATAATTTCAACAGATCTATAAC
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GACAATATCTACTTTTACCAGCTCAAAATCATGCATTAAGATTGGTGATTTTGAAGAAGA
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AAAAAGAGAAAAACTAAGAATGATACAAAAGAAACTTGCAAAGGATATTTCTAAATTAAC
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CATAGCCAACCCAGCATTCTTAGATGAGATCACAAACGAACATGAGATAAGGCATTCAAC
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TTATGAGGACTTAAAACAATCTATCCCAGATTACACAGATTATATGTCTGTGAAAGTTTT
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TGACAGATTGTACGAGAAGATTACTACCAATGAAATAAATGATAAGGAAACAGTCAAGCT
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GATTCTAGAGACCATGAAAAAACATAAAATATTTCATTTTGGATTCTTCAATAAAGGACA
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AAAAACAGCCAAAGATAGAGAAATATTTTTAGGTGAATTTGAAGCAAAAATGTGTCTGTA
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CCTTGTCGAAAGAATAGCTAAAGAGAGGTGCAAATTAAACCCTGAAGAAATGATAAGTGA
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ACCAGGCGACTCGAAACTAAGGGTATTAGAGAAGCAATCAGAAGACGAAATCAGGTATAT
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TAGCAATACAATAAAGACATTAGGGAATGCCATAGAGAACTTGCAATCTGGATCTTTAAA
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TTGGGCAGATATATGCGAAAACAAAGCAAGAGGACTTAAGATAGAAATAAATGCTGATAT
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GTCCAAATGGAGTGCCCAAGATGTACTTTTTAAATATTTTTGGTTGATAGTGCTTGATCC
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CATCTTATATCCTGCTGAGAGGAAAAGGATAATTTATTTCCTCTGTAATTATATGCAGAA
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AAGGCTTATAATGCCCGATGAATTGCTCACTACTATATTGGATCAAAGAGTTCCTTATTC
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AAATGACATAATTGGATTAATGACAAACAATTATAGGTCTAATACAGTAGAAATAAAGCG
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TAACTGGCTTCAAGGCAACTTAAATTATACAAGCAGTTACTTACACAGCTGTAGTATGTC
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TGTGTACAAAGATATAATAAGAGAAGCAGCAATATTATTAGAAGGAGAAGCCCTTGTGAA
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CTCAATGGTACATTCTGATGATAATCAAACATCTATATGTATGGTGCAGAATAAATTACC
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AGATGACAATATAATTGAATTTTGCATTAAGATATTCGAGAAGATATGCTTAACTTTTGG
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CAATCAGGCAAATATGAAGAAGACATATCTAACTAACTTCATCAAAGAGTTTGTTTCTTT
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ATTTAATATACATGGAGAACCATTTTCTATATATGGGAGATTTCTACTCACAGCAGTAGG
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AGACTGTGCCTATCTAGGGCCTTATGAAGATTTAGCAAGTAGGCTATCTGCAACACAAAC
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TGCTATAAAGCATGGTTGCCCACCATCACTTGCATGGGTATCTATCGCTCTAAATCACTG
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GATAACCCACACTACATATAATATGTTGCCTGGCCAAAATAATGACCCGTTACCATTCTT
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CCCTACTAACAATAGAAGTGAAATACCAGTAGAGATGTGCGGAATACTAGAAAGTGATTT
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ATCAACAATTGCACTAACTGGTTTAGAAGCAGGGAATGTCACGTTTCTAACAAATATAGC
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AAGGAAGTTATCATCCCCAATCTTACAAAGAGAAAGTATTCAAGATCAATACAATTCTAT
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AGAAAAGTGGGATCTGAGCAAATTATCACAGATCGACATTCTAAGGCTTAAAATGCTCAG
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GTATATATCTCTTGATAGTTCAGTCACATCTGATGATGGTATGGGGGAGACTAGTGAAAT
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GAGATCTCGATCACTTTTAACACCTCGTAAATTCACAACAAGTGGGTCACTTAATAGGTT
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GAAATCATATAAAGACTTTCAAGATATAATAGCAGATGAGGACAAGACAAACGAACTATT
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TGAGAATTTCATTAGACACCCAGAGTTACTGGTTACAAAAGGCGAAACATTTGAAGAATT
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TGTTAATACGATATTATTTAGGTACAATTCAAAGAAATTCAAAGAATCTTTGTCAATACA
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AAACCCAGCACAGCTTTTTATTGAGCAAATATTATTTTCCAATAAACCAGTAATTGACTA
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CACTAGCATACATGACAAGATTTTTGGATTACAAGACATGCCAGGAATTGAAGAACTAGA
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TACAATTATAGGTCGCAAAACATTTGTTGAGAGTTATGTTCAAATCGTAGATGACTTAAG
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CAATTTAACATTGGATATAAACGATGTCAAGACTATATTTGCCTTTTGTCTTATGAATGA
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CCCACTACTGATCACATCTGCTAACAATATAATAATGTCTGTTAAGGGACATAGTCAAGA
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AAGAATAGGTCAATCAGCATGCAAAATGCCAGAGGTCCGAAGTCTAAAACTCATACATTA
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TTCACCAGCAGTTGTTTTGAGAGCCTATGTGAGAGGGCCAACAAATGTACCGAATGTAGA
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TATAGATGAACTTGCAAGGGATCTATCTCATTTAGAAGACTTCATACAAAGTACAAAACT
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CAGAGAAAATATGAGAGAGAGAATAGAAATAAATGAGAAGCGGCACTTAGGAAGGGATTT
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CAAATTTGAAATCAAAGAACTAACTAGATTTTACCAAGTGTGTTATGATTACATAAAGTC
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TACAGAACATAAAGTCAAGGTATTCATATTGCCATACAAAGTTTTCACATCAATAGAATT
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CTGCGGGGCACTGACAGGTAACTTGATAAATGACAAATTATGGTACATAACGCATTATCT
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GAAAAATATAGTGTCTACTACACATAAGGCACAAATTTCTTCTTCACCTGAATTGGAATT
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GCAAATTGCTGATGAGGCACTAAGACTAGTAGCACATTTTGCTGATACTTTCTTGGCATC
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AGAATCAAGAATACAATTTCTGAAGAAAATTATTGAAGAATTCACATACAAAGGGATACC
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TGTAAAACATTTATACTCAAAAATAAAGAACTCCAAGTTGAGGGTTAAATTTCTAGGGAT
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TCTTTTATGGTTAGATGATCTAACACAGAATGATCTGGATAAATTTGATGCAGATAAATC
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AGATGAAAAGATTATATGGAATAACTGGCAAGTGTCAAGAGATATGAATACTGGACCAAT
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AGACTTAATGATAAGCGGTTACTCTAGACAGCTGCGGATCACTGGGGAAGATGACAAATT
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GATTGCTGCTGAATTGCAGGTTACTAGATTGTCAGAAGATTTAATTTATAGACACGGTCA
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GGCAATGTTGAATAAGCCACACGGCTTAAAGCTTGAAAAAATGCAACCTGTGACTGAGAT
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GTCTAAACGATTACATTATATCGTTTTCCAGCAAAGATCACGGAAACGATACTTCTATTC
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TATATTACCCACCCAAGTAATTGAGGACCATAATTCTAGAGTTGAATCATCTAGGCTAAG
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CAGAGATTCAAAATGGGTTCCTGTATGCCCTGTTGCAATATCAAAACTCTACCAACAAGG
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ACGGCCTATACTTTCCAAAGTTAGAAATCTGAATATGCAGACTCATTCGCTTTCCAGAAT
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ACAAGTTAATGTAGATGAATATGCCATCACGAGAAGAGCACATTTTCAGAAAATGCCTTT
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CTTCGAAGGACCATCAATCCCTTCTGGTGGTATGGATTTGTCTGAGTTGATGAAATCTAC
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ATCCCTATTAAGCTTGAATTATGATAACATAAAAAATGCATCCTTATTGGACATGTCTAG
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GGTATTTAAGTGCAATGGCAGTGGAGATGACCAAATGGCTTTCGAATTTCTATCGGACGA
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AATTTTGGAGCAAGATGTAGTTGAAGAAATAGAATGCAACCCTATATTTTCTATTAGTTA
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TACAAAAAGAGGAGAATCCAATATGACTTATAAAAATGCTTTCCACAAAGCCTTAATCTC
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AGAATGTGACAAATTTGAAGAAGCATTTGACTTCCTCGACATGGGATTTTGCTCGAATGA
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AAATCTTAGTATTCTGGAGGAAATACATTGGATAATCAGTTATTTAAAAACAAATCAATG
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GTCTACGGAACTAGACAATTGTATTCACATGTGCATGTACAGGAATGGATATGATGCAGA
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ATATCATAAATTTGATATACCCTCTAAATTCCTCAAAGACCCAATAAACCGAACAATAAA
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TTGGACTGAAGTCATTGAATTTATATTATTAATTGAAGATTTCCAAACAAAAATTGAGCC
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ATGGTCTAGTATGAAGTCACACTTCTGTTCAAAAGCACACAGTGTAGCACTAGAGTGTAT
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GAAAAATGAGAAAAGATCATTGGCAGAATTTGTAGACAAAAGTAAGAAAACTGGCAAATC
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CAAATTTGACTTCTAAGGTATACACATGTAAAAGTAGTGTTTGTTTCTAAATAGGAGCAC
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ACTACT

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