Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: scaffold_4032 Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 16291 ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32 Found at i:3920 original size:27 final size:27 Alignment explanation
Indices: 3887--4063 Score: 189 Period size: 27 Copynumber: 6.6 Consensus size: 27 3877 ATTAAATTAC 3887 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 3914 TGCACTAAGTGTGCGAAATGA-AATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 3939 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 3967 GGCACT-AGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * 3994 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 4021 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 4048 AGCACTGAGTGTGCGA 1 AGCACTAAGTGTGCGA 4064 CTCAATATAC Statistics Matches: 127, Mismatches: 18, Indels: 10 0.82 0.12 0.06 Matches are distributed among these distances: 26 31 0.24 27 87 0.69 28 9 0.07 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:7447 original size:51 final size:51 Alignment explanation
Indices: 7392--7491 Score: 139 Period size: 51 Copynumber: 2.0 Consensus size: 51 7382 CTACCACATA * 7392 ACATGTAA-CACATCCATAATGAACTCGGACCTCTCAACAAGCTTGGATGTT 1 ACATG-AATCACATCCATAATGAACTCAGACCTCTCAACAAGCTTGGATGTT * * * * 7443 ACATGAATCGCATCCATTATGAACTCAGACCTTTCAACGAGCTTGGATG 1 ACATGAATCACATCCATAATGAACTCAGACCTCTCAACAAGCTTGGATG 7492 CTCGCATCCA Statistics Matches: 43, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 50 2 0.05 51 41 0.95 ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26 Consensus pattern (51 bp): ACATGAATCACATCCATAATGAACTCAGACCTCTCAACAAGCTTGGATGTT Found at i:12446 original size:50 final size:50 Alignment explanation
Indices: 12326--12569 Score: 289 Period size: 50 Copynumber: 4.9 Consensus size: 50 12316 GCTATTGTGA * * 12326 GGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAAC-T 1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT * * * 12375 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATG-GTACCTGATAACTT 1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT * ** * ** 12424 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGAT-GGTT 1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT * ** 12474 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAA-TT 1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT * * * 12524 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA 12570 GCTTCGGCTA Statistics Matches: 164, Mismatches: 27, Indels: 8 0.82 0.14 0.04 Matches are distributed among these distances: 48 11 0.07 49 72 0.44 50 74 0.45 51 7 0.04 ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29 Consensus pattern (50 bp): GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAACTT Found at i:12568 original size:99 final size:99 Alignment explanation
Indices: 12328--12569 Score: 301 Period size: 99 Copynumber: 2.4 Consensus size: 99 12318 TATTGTGAGG * * * 12328 TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAACTGGTCGCATGTGTAGTACT 1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTGGTCACATGTGTAGTACT * 12393 AAGTGCAGGCTACTATGGTACCTGATAACTTCGA 66 AAGTGCAGGCTACTACGGTACCTGATAACTTCGA * * * *** * 12427 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAGGTCACGTGTGTAGTAC 1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACT-GGTCACATGTGTAGTAC * 12492 TAAGTGCAGGCTACTACGTGTA-CTGGATAA-TT-GG 65 TAAGTGCAGGCTACTACG-GTACCT-GATAACTTCGA * * * 12526 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA 12570 GCTTCGGCTA Statistics Matches: 123, Mismatches: 17, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 99 79 0.64 100 36 0.29 101 8 0.07 ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29 Consensus pattern (99 bp): TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAACTGGTCACATGTGTAGTACT AAGTGCAGGCTACTACGGTACCTGATAACTTCGA Done.