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LCrossmanLCrossman
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Merge pull request #35 from microBioRust/feature/gbk-speedup
Feature/gbk speedup from kh3rld
2 parents e96dfd0 + c1769d8 commit 12da3a4

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‎microBioRust/new_output_embl.gbk‎

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LOCUS source_1 928 bp DNA linear CON 24-NOV-2025
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DEFINITION Escherichia coli K-12 substr. MG1655.
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ACCESSION source_1
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KEYWORDS .
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SOURCE Escherichia coli K-12 substr. MG1655
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ORGANISM Escherichia coli K-12 substr. MG1655
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FEATURES Location/Qualifiers
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source 1..910
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/organism="K-12 substr. MG1655"
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/mol_type="DNA"
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/strain="K-12 substr. MG1655"
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/db_xref="PRJNA57779"
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gene complement(1..354)
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/locus_tag="b3304"
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CDS complement(1..354)
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/locus_tag="b3304"
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/codon_start="1"
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/gene="rplR"
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/translation="MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGS
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LVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQAL
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DAAREAGLQ"
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/product="50S ribosomal subunit protein L18"
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gene complement(364..897)
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/locus_tag="b3305"
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CDS complement(364..897)
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/locus_tag="b3305"
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/codon_start="1"
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/gene="rplF"
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/translation="MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKH
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NTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLS
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GFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYAD
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VVRTKEAKK"
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/product="50S ribosomal subunit protein L6"
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ORIGIN
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1 acctctacct tagaactgaa ggccagcttc acgggcagca tctgccagtg cctggacacg
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61 accatgatat tggaacccgg aacggtcaaa ggatacatct ttgatgcctt tttccagagc
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121 gcgttcagcg acagctttac ccacagctgc agccgcgtct ttgttaccgg tgtacttcag
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181 ttgttcagcg atagcttttt ctacagtaga agcagctacc agaacttcag aaccgttcgg
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241 tgcaattacc tgtgcgtaaa tgtgacgcgg ggtacgatgt accaccaggc gagttgcgcc
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301 cagctcctgg agcttgcggc gtgcgcgggt cgcacgacgg atacgagcag atttcttatc
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361 catagtgtta ccttacttct tcttagcctc tttggtacgc acgacttcgt cggcgtaacg
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421 aacacccttg cctttataag gctcaggacg acggtaggcg cgcagatccg ctgcaacctg
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481 gccgatcacc tgcttatcag cgcctttcag cacgatttca gtctgagtcg gacattcagc
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541 agtgataccc gcaggcagct gatggtcaac aggatgagag aaacccagag acaggttaat
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601 cacattgcct ttaaccgctg cacggtaacc tacaccaacc agctgcagct tcttagtgaa
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661 gccttcggta acaccgataa ccattgagtt cagcagggca cgcgcggtac cagcctgtgc
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721 ccaaccgtct gcgtaaccat cacgcggacc gaaggtcagg gtattatctg catgtttaac
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781 ttcaacagca tcgttgagag tacgagtcag ctcgccgttt ttacctttga tcgtaataac
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841 ctgaccgttg atttttacgt caacgccggc aggaacaacg accggtgctt tagcaacacg
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901 agacattttt tcc
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//

‎microBioRust/new_output_embl.gff‎

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##gff-version 3
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##sequence-region source_1 1 910
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source_1 . CDS 1 354 0 - 0 id=b3304;name=source_1;gene=rplR;locus_tag=b3304;product=50S ribosomal subunit protein L18
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source_1 . CDS 364 897 0 - 0 id=b3305;name=source_1;gene=rplF;locus_tag=b3305;product=50S ribosomal subunit protein L6
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##FASTA
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acctctaccttagaactgaaggccagcttcacgggcagcatctgccagtgcctggacacg
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accatgatattggaacccggaacggtcaaaggatacatctttgatgcctttttccagagc
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gcgttcagcgacagctttacccacagctgcagccgcgtctttgttaccggtgtacttcag
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ttgttcagcgatagctttttctacagtagaagcagctaccagaacttcagaaccgttcgg
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tgcaattacctgtgcgtaaatgtgacgcggggtacgatgtaccaccaggcgagttgcgcc
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cagctcctggagcttgcggcgtgcgcgggtcgcacgacggatacgagcagatttcttatc
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catagtgttaccttacttcttcttagcctctttggtacgcacgacttcgtcggcgtaacg
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aacacccttgcctttataaggctcaggacgacggtaggcgcgcagatccgctgcaacctg
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gccgatcacctgcttatcagcgcctttcagcacgatttcagtctgagtcggacattcagc
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agtgatacccgcaggcagctgatggtcaacaggatgagagaaacccagagacaggttaat
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cacattgcctttaaccgctgcacggtaacctacaccaaccagctgcagcttcttagtgaa
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gccttcggtaacaccgataaccattgagttcagcagggcacgcgcggtaccagcctgtgc
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ccaaccgtctgcgtaaccatcacgcggaccgaaggtcagggtattatctgcatgtttaac
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ttcaacagcatcgttgagagtacgagtcagctcgccgtttttacctttgatcgtaataac
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ctgaccgttgatttttacgtcaacgccggcaggaacaacgaccggtgctttagcaacacg
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agacattttttcc

‎microBioRust/src/gbk.rs‎

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//! # A Genbank to GFF parser
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//!
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//!
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//!
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//! You are able to parse genbank and save as a GFF (gff3) format as well as extracting DNA sequences, gene DNA sequences (ffn) and protein fasta sequences (faa)
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//!
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//! You can also create new records and save as a genbank (gbk) format

‎microBioRust/test_output.gff‎

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##gff-version 3
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##sequence-region source_NC_000913_1 1 913
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source_NC_000913_1 . CDS 10 363 0 - 0 id=b3304;name=source_NC_000913_1;gene=rplR;locus_tag=b3304;product=50S ribosomal subunit protein L18
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source_NC_000913_1 . CDS 373 906 0 - 0 id=b3305;name=source_NC_000913_1;gene=rplF;locus_tag=b3305;product=50S ribosomal subunit protein L6
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##FASTA
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acctctaccttagaactgaaggccagcttcacgggcagcatctgccagtgcctggacacgaccatgatattggaacccggaacggtcaaaggatacatctttgatgcctttttccagagcgcgttcagcgacagctttacccacagctgcagccgcgtctttgttaccggtgtacttcagttgttcagcgatagctttttctacagtagaagcagctaccagaacttcagaaccgttcggtgcaattacctgtgcgtaaatgtgacgcggggtacgatgtaccaccaggcgagttgcgcccagctcctggagcttgcggcgtgcgcgggtcgcacgacggatacgagcagatttcttatccatagtgttaccttacttcttcttagcctctttggtacgcacgacttcgtcggcgtaacgaacacccttgcctttataaggctcaggacgacggtaggcgcgcagatccgctgcaacctggccgatcacctgcttatcagcgcctttcagcacgatttcagtctgagtcggacattcagcagtgatacccgcaggcagctgatggtcaacaggatgagagaaacccagagacaggttaatcacattgcctttaaccgctgcacggtaacctacaccaaccagctgcagcttcttagtgaagccttcggtaacaccgataaccattgagttcagcagggcacgcgcggtaccagcctgtgcccaaccgtctgcgtaaccatcacgcggaccgaaggtcagggtattatctgcatgtttaacttcaacagcatcgttgagagtacgagtcagctcgccgtttttacctttgatcgtaataacctgaccgttgatttttacgtcaacgccggcaggaacaacgaccggtgctttagcaacacgagacattttttcc

‎microBioRust/test_output_embl.gff‎

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##gff-version 3
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##sequence-region source_AM236082_1 1 6666
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source_AM236082_1 . CDS 1 1197 0 + 0 id=pRL80001;name=source_AM236082_1;gene=repAp8;locus_tag=pRL80001;product=replication protein RepA
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source_AM236082_1 . CDS 1321 2280 0 + 0 id=pRL80002;name=source_AM236082_1;gene=repBp8;locus_tag=pRL80002;product=replication protein RepB
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source_AM236082_1 . CDS 2455 3672 0 + 0 id=pRL80003;name=source_AM236082_1;gene=repCp8;locus_tag=pRL80003;product=replication RepC protein
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source_AM236082_1 . CDS 3811 6666 0 + 0 id=pRL80004;name=source_AM236082_1;locus_tag=pRL80004;product=hypothetical protein
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##FASTA
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gtggagaatcccgctcagcttcagaaggctattcataaactgatagcggcccacgcgcgagatctctcgggcgcgcttcacgagcatcgtgtgaagctttatccgcctgaagctcgaaagacgcttcggtcattttcgtcgatagaggctgcgaagctcattggcgtcaacgatggctatctccgccatctttcgctcgagggtaaggggccgcagcctgagatcggaaataacaatcgccgttcgtattcggtcgagactattcaggcgctccgcgagtatctcgacgagaacggcaagggtgaccgtcggtactcaccacgccggagcggtcgtgagcatttgcaggttataaccgcagtgaacttcaagggaggcagcggtaagaccacgacggctgctcatcttgctcagtatcttgcgcttaatggataccgggttcttgcgattgatcttgatccgcaggccagcatgtccgctttgcacggattccagcctgagtttgacgttggcgacaacgaaacgctctacggcgccgttcgttatgatgaagagcggcgcccgctgaaggatataatcaagaaaacctactttgcgaaccttgatctcgttccgggcaacctcgagcttatggaattcgagcacgacaccgctaaagtgctcggctctaacgaccgcaagaacatcttcttcacgcgaatggatgacgcaatcgcgtcagtggcggacgactatgacgttgtcgtcgtcgactgccctccccagctcggctttctgacgatctcggctctatgcgcggcaaccgccgttcttgttactgtacatcctcagatgctcgatgtgatgtcgatgtgccagtttctgctgatgacctcagaacttctgagcgtcgttgcggatgctggcgggagcatgaactacgattggatgcgttatctcgttacgcgctacgagccgggagacggaccgcaaaaccagatggtgtcgttcatgcgcacgatgtttggcgaccatgtcctgaaccacccgatgctcaagagcacagccatttcagacgcggggattactaagcagactctctatgaggtgagccgcgaccagttcacgcgagcaacatacgaccgagccatggaatcgctcgacaacgtgaacagcgaaatcgaacaactcattcaatcatcttggggtcgcaaatgatggctctagagatctcagaaaacgcgacattgatggagaagttgccagccggaaacttttcggaatttgcactctctatgtcgaggaatccggcttgtcacgagtacctcaggggaaagcaagatggctagaaaacacctcctttcagatttgaaagctcctgcttcatcatctacggagttcgatgaagctagggctgcagacgtccctactccgcagtatgcgcctcgaggtgcaatcggtgccgtctcgcgatcgattgaagctttgaagtcgcagggactgagtgaactcgatcccgaactgatagatgcgccgtccgttactgatcgccttgatgaggatggggctcagtttgaggagttcgctcgcaacatccgtgagaatgggcagcaggttccgattcttgtccggcctcacccgaccgtggaaggacggtatcagattgcctacggccggagacggttgagagcggtcaaggcggccggcctcaaggtcaaagccgcaatcagaaatctgacagatgacgagcttgtactggcgcaaggtcaggaaaacagcgcgcgtcaggatctgtcgtttatcgagcgggcgctctatgcagcccagctcgaagcgagtggctaccagcgtcccgtcatcatggcagcgctggctgtcgacaaaagtaacctttcgcggttgattcaggctgcgacccaattgccggacgacgtcatccgactaattggtgctgcgcctaagaccggccgtgatcgctggtacgagctatcatcgcggttggctgcagaaggtgctgcggagaaggcgcgcgctcttctttcgactagcgaggttggctccctgggttctgatgagcgatttgttcgcgttttcgacgcggttgcgccgaagaaatctaagaaggaaaaagttcaggcggatgtctggcaagctgacgatggggtcaaggctgcgagtttccgccaggacaaacgaacactgacattgatgatcgacaagaaggcagcgccggaattcggtgagtacctgatgtcggctctccccgagatctacgcttcgttcaagaagtcgaagcaatagatgagtcgtaacgaagaaaggtgccgatagcgcaaagaaaaagccctccgaaacggtgttccagaaggcctctctcagtttggtcgcttagagaatcgcatttcccggaatcacagtcaagagtcaacgccacaccggcgtagccttttctttgccttgcgaaaggtgaaggacatggaaacgggttatatcacgacgccctttgggcggcggccgatgacgcttgctctggtgaagcgtcaggttaagaccgagcaggcaatagcggatggctcggtcgacaagtggcgcgtgtttcgcgacataagcgacgcccgctcacgccttggccttcaagatcgagccttggcggtcttgaatgcacttttaacattcttcccagttgctgaactcagcaatgagaggaacctggtcgtctttccatcaaatgctcagctatcagcccgcacaaacggtatcgctgggacaactctgcgcaagtgcctcggttcgctggtggaggccggtgtaatcatccgcaaggatagccctaacggtaagcgatatgctcgaaaaggcaaagaaggaaacatagaggacgcctacggcttcagtctggcaccgcttcttgcgcgcgccggcgagtttgctagcctcgcccaagacgtggctgctgaacagcgccgcttccgcatcacgaaagaccgcctcacgatcgttcggcgagatgtccgcaagctgatcaccgtcgggatggaagagaaccttgccggcgattggattgccgcggaaacgtgctttgtcgagattgtgggaaggttcgttcggcacccgacgctccaggacctgatttcgagcctcgacgagatgagccttcttcacgaagaagtctccaggatgctggaaattaaagaagaaaccgcaaaaagtgatggcaatgccatcccggacggatgccacatacagaattcaaataccgaatcctgccatgaacttgaaccccgctccgaaaagaagcagggcgaaaagtccgagccaaacaagaaaacggagcggaaagacgaaccggaagcgtttccgttgtccatggtgttgcgtgcctgcccggagatcaacgcatttggccctggtggatcgattggaagctggcgcgaaatgatgtcagcggcggtaacggttcggtccatgcttggcgtcagcccctctgcctatcaggaggcatgcgaggtgatggggcaggccggagcggcgatagcaatagcttgcatttaccagcgtggcgggcacatcaactcggcggggggatatcttcgggatctaacggggaaggcgcggcgaggggagttttcacttgggccaatgctgtttacgcaattgcgggcgaactcgggcaccgtcaaggcgtcagcgtaggtcaaagtatcatgattgtttagcctaaccggttgaactaattaacctattttgactagtttccggctggcaactttatctcgatctaaagcgtcgagtgaatggcagaagataatcttcctgatgggcgtccgtataatgaccgaaattgtgcttccgaccgaaaacacgatcatcgcggcagccaaaaaacttgacgcggccgcatcgcagctggtggcagagacgttctttgccattcggcatgggatgtcaatcaatccaattggtcgcaacccggatgggcagaccatcaagggataccctgacattactgggcgggtgccgggtgagaagaagtacctgatcgaagtcacgaaggacgactggcgcacacatcttcagagcgatctatcaaaactgtcccgcctgcagaaaggagcctacgcgggtttcctacttctctgcttccgaaagtccgagtccgaactcactcaaagcaacaggaagaaggcacgggaaaccgtccagcaggccgagagccggattgaaaagcttttgggtgtccaggcaggacaggtagaattcgtctttcttggcgagttcgcgcgtgaggtcagatcggcgaaataccaccgcgtattgctggctctgggtctcgagcttgtgccagcgccattctacacggatttgcgcttcgtgcagggcttagccgatttcgtaccgaccgctgaggaatatgaggctgagagtgttgttcctcgcgatgaggtaagccggacctatgagcgggtcttcaaaaacagactaacgttgatcgaaggcgagggcggtagcggcaaaacaagcctggccctagccgttgcgacggagcatcggaagcaaggcgagatctttctgttcttagacgcctctgtcgctgactggaagagcggttcggagcgagctcgcctcgttgacgtagcggcgatgttcgcggaatcgaatgtcctgattatattggacaacgtacatctgggcgatgcgtccggcatttctgaactgattacaaatgtccaggcgtccggttatgatttccgctttttgatgacgacgcgcagcagcgacgaagttgaacaatggaagcgcctgggaaatatcgagcttctccgcagagttccgtctggagccgatgtcaactctgcctatcaccgcctgctcactcaaaagtttcccggaagcagtttcaacgatattcccccagcggtgaccacacgatggtcaaatcaaattcccaatctggttattctcacgcttgctcttgaaggtctcacaaagagaggcggctatgatcgcgattgggcgatcaaggttgaggacgcaggcacataccttcaagctaagttcatctcgaagctgtcgtccgacgacgtcaaacaggtgggcaagatcgctgcgctctcacttctggaaattcccacctcgctcaggtcgctcgaccaccgggttccaaagtctgctgtggatctgggcttcgttcgtctgaactcgagttcaacaactcagcgatatgagctcgttcaccacgaactgggcaagctgatcacgtccttcaaagatccggatatcaaggcgcggctgggagaggtgatgtccgctgatcccttccaggcaacatatatcgggctgaagcttatcggaaacggagaagccagcctggcaaaggaattgttgtcgtcagtcctttctcaatcactcacactctcgccagatttctcgatgggaaactccggcggagtcttcggtatcctggtccagtccaacgtgactacctatcccgaaattgagcgtatccttcttcctgatatcggcgcctttttcgatacaaagccggatattgtaaccggccttagctccttcctcggggctgcctccgaaaacatggagcgcgtatacaatgccattgtggaaaaacttgccgaacaggaaacgattcgacggatcgaagagcttctcccatccgtcggcccgacgactttcgcgacactttaccgatgcgcgaactcacggaacctcccgtttctttcaacgcttcgaaaatatctcaacagagggaagcgtatagattcctttgcctatcgatgcaggtctgaaagtccgagtaaggtcgagatctgctggggcctgattgatgagttctttccacaccacaaggcccggtttgaagttgtgcttcgctctgccctcgccgagggatacatcgagcgccttatcccggaagagcttattgagtctcgctcttcaagggctgttcagacggcgatccgatgcgcaaatagcgaagttttcaaacggtacatcacgttccgtgactgcagcgacgcgacgctgttgcttctggcccacacgatgcacgacatgggcaggaatgatctctcggaggtcgcagctgaccgagttgcaggcaggacgacctcttcaatctggtatcatcgtcgcaccggtggcagggcgttgctgactattttgcggagagcatcgatatctgcagaaggagatgttcagaaaattctgatgcggcttgaggctgaaggaaaaatgagggccattgtgaatggaatgcggccttatcgcctagcgaattttattttcgtgatctgggatcggcacgagcaatttacttcattcatctcgaagacagatcttcaggaaattacaaaccgccggttcaaagcgcgagcggcagagttctctgaagagcgacaagcgtccatctacattgcaggaatctatgcgctggtaggcctcgacataccgcgggacgagtggagcgcggtcgacgtcactgaagacgatttcattggaaaccagaacaacccggtcttctggatcggtctcaaggctctggaagaaaatggcatgatacgccttgcccatcgaagcagatttccgacatctgtcgcggcgctagatactcattcggaaaacaccagccggatcatgaacgatttgaaaaactgggctgcgaccaggtaa

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