mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-11-09 09:24:41 +00:00
Eric Coissac
49225030ca
This update introduces the core clustering algorithm, including parallel execution, dynamic block sizing, and SIMD-accelerated scoring methods. It also adds robust sequence preparation, k-mer analysis, and comprehensive test data fixtures for validation.
102 lines
10 KiB
Plaintext
102 lines
10 KiB
Plaintext
f2v8s26 f2v8s26 0.000000 T 863655 tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f10v3s80 f2v8s26 0.000000 F 863655 tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f2v0s18 f2v8s26 0.000000 F 863655 tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f2v7s25 f2v8s26 0.000000 F 863655 tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f10v9s86 f2v8s26 0.000000 F 863655 tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f2v3s21 f2v8s26 0.014925 F 863655 tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
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f6v1s61 f2v8s26 0.014925 F 863655 tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
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f2v2s20 f2v8s26 0.014925 F 863655 tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
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f3v3s34 f3v3s34 0.000000 T 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
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f4v0s44 f3v3s34 0.000000 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
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f3v0s31 f3v3s34 0.000000 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
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f0v7s7 f0v7s7 0.000000 T 281628 ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
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f1v2s11 f0v7s7 0.000000 F 281628 ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
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f1v1s10 f0v7s7 0.000000 F 281628 ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
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f3v6s37 f3v3s34 0.064103 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
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f5v0s53 f3v3s34 0.064103 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
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f11v7s98 f3v3s34 0.064103 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
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f2v4s22 f2v8s26 0.029412 F 863655 tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
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f10v7s84 f10v7s84 0.000000 T 905994 gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
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f10v0s77 f10v7s84 0.040541 F 905994 ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
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f5v6s59 f2v8s26 0.014925 F 863655 ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f2v10s28 f2v8s26 0.014925 F 863655 ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f1v5s14 f1v5s14 0.000000 T 234004 ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
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f0v4s4 f1v5s14 0.000000 F 234004 ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
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f0v1s1 f1v5s14 0.000000 F 234004 ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
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f0v3s3 f1v5s14 0.000000 F 234004 ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
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f5v3s56 f5v3s56 0.000000 T 192648 ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
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f10v2s79 f10v7s84 0.080000 F 905994 ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
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f10v13s90 f10v7s84 0.092105 F 905994 tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
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f1v4s13 f1v4s13 0.000000 T 304149 gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
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f10v4s81 f10v7s84 0.066667 F 905994 ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
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f10v5s82 f10v7s84 0.054054 F 905994 ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
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f4v8s52 f4v8s52 0.000000 T 359938 ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
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f2v11s29 f2v8s26 0.044118 F 863655 tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
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f0v6s6 f1v5s14 0.075000 F 234004 ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
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f1v3s12 f1v5s14 0.075000 F 234004 ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
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f0v0s0 f0v7s7 0.083333 F 281628 ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
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f0v2s2 f0v7s7 0.083333 F 281628 ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
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f1v7s16 f1v4s13 0.086420 F 304149 gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
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f2v5s23 f1v4s13 0.086420 F 304149 gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
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f3v12s43 f3v3s34 0.051282 F 838714 cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
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f8v0s68 f8v0s68 0.000000 T 507278 aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
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f2v1s19 f1v4s13 0.097561 F 304149 gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
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f1v8s17 f1v4s13 0.097561 F 304149 gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
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f10v11s88 f10v7s84 0.066667 F 905994 ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
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f3v5s36 f3v3s34 0.026316 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
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f8v7s75 f8v0s68 0.031250 F 507278 aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
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f10v12s89 f10v7s84 0.066667 F 905994 ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
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f4v2s46 f4v8s52 0.061538 F 359938 ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
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f8v2s70 f8v0s68 0.074627 F 507278 aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
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f11v8s99 f11v8s99 0.000000 T 421503 agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
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f7v0s64 f7v0s64 0.000000 T 114016 gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
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f11v1s92 f11v8s99 0.055556 F 421503 agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
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f3v2s33 f3v3s34 0.051948 F 838714 cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
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f8v3s71 f8v0s68 0.047619 F 507278 aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
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f4v3s47 f4v8s52 0.076923 F 359938 ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
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f10v10s87 f10v7s84 0.093333 F 905994 tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
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f11v0s91 f11v8s99 0.014085 F 421503 agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
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f8v5s73 f8v0s68 0.046875 F 507278 aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
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f8v4s72 f8v0s68 0.015873 F 507278 aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
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f3v1s32 f3v3s34 0.025641 F 838714 cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
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f3v4s35 f3v3s34 0.051948 F 838714 cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
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f11v6s97 f11v8s99 0.068493 F 421503 agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
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f4v1s45 f4v8s52 0.089552 F 359938 ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
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f0v5s5 f1v5s14 0.075000 F 234004 ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
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f5v5s58 f5v3s56 0.090909 F 192648 cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
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f1v0s9 f1v4s13 0.024691 F 304149 gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
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f8v6s74 f8v0s68 0.030769 F 507278 aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
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f6v0s60 f6v0s60 0.000000 T 100983 catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
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f10v8s85 f10v7s84 0.080000 F 905994 ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
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f10v1s78 f10v7s84 0.066667 F 905994 ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
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f5v4s57 f5v3s56 0.075758 F 192648 cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
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f3v10s41 f3v3s34 0.051282 F 838714 cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
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f3v7s38 f3v3s34 0.025974 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
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f10v6s83 f10v7s84 0.067568 F 905994 ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
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f11v2s93 f11v8s99 0.041667 F 421503 agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
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f3v9s40 f3v3s34 0.013158 F 838714 cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
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f11v4s95 f11v8s99 0.055556 F 421503 agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
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f8v1s69 f8v0s68 0.015625 F 507278 aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
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f11v5s96 f11v8s99 0.055556 F 421503 agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
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f6v2s62 f6v0s60 0.031746 F 100983 catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
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f4v6s50 f4v8s52 0.089552 F 359938 ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
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f9v0s76 f9v0s76 0.000000 T 29993 gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
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f2v12s30 f2v8s26 0.044776 F 863655 tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
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f11v9s100 f11v8s99 0.027778 F 421503 agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
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f4v5s49 f4v8s52 0.075758 F 359938 ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
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f2v9s27 f2v8s26 0.014925 F 863655 tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
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f7v3s67 f7v0s64 0.016393 F 114016 gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
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f0v8s8 f0v7s7 0.094118 F 281628 ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
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f2v6s24 f2v8s26 0.059701 F 863655 tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
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f11v3s94 f11v8s99 0.041667 F 421503 agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
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f6v3s63 f6v0s60 0.046154 F 100983 catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
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f3v11s42 f3v3s34 0.026316 F 838714 cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
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f4v4s48 f4v8s52 0.076923 F 359938 ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
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f3v8s39 f3v3s34 0.051948 F 838714 cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
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f7v1s65 f7v0s64 0.032258 F 114016 gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
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f5v1s54 f5v3s56 0.076923 F 192648 cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
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f4v7s51 f4v7s51 0.000000 T 8599 cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
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f7v2s66 f7v0s64 0.048387 F 114016 gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
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f1v6s15 f1v4s13 0.049383 F 304149 gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
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f5v2s55 f5v3s56 0.092308 F 192648 cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact
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