Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2403

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: 21358
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:1204 original size:39 final size:39

Alignment explanation

Indices: 1089--1335 Score: 231 Period size: 40 Copynumber: 6.3 Consensus size: 39 1079 AAATCACGTA * * * ** 1089 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATG 1 CCTTCGGGACTTAACCGGATTTAG-TAACTCGCACAAATG * * 1128 CCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATG 1 CCTTCGGGACTTA-ACCGGATT-TAGTAACTCGCACAAATG 1168 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG 1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG 1207 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATATG 1 CCTTCGGGACTTAA-CCGGATTTAGTAACTCGCACAA-ATG * * * 1248 CCTTC-GG-C-T-GCCGGAATTAGTATCTCGCACAAATG 1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG * * * * * 1283 CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G 1 CCTTCGGGA-CTTA-ACCGGATTTAGTAAC-TCGCACAAATG 1323 CCTTCGGGACTTA 1 CCTTCGGGACTTA 1336 GCCCGGACAT Statistics Matches: 176, Mismatches: 19, Indels: 25 0.80 0.09 0.11 Matches are distributed among these distances: 35 10 0.06 36 20 0.11 37 1 0.01 38 2 0.01 39 49 0.28 40 75 0.43 41 19 0.11 ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27 Consensus pattern (39 bp): CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATG Found at i:1225 original size:79 final size:79 Alignment explanation

Indices: 1089--1335 Score: 258 Period size: 79 Copynumber: 3.2 Consensus size: 79 1079 AAATCACGTA * * * ** * 1089 CCTTCGGAATTTAACCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAG 1 CCTTCGGGACTTAACCGGATTTAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAG 1153 TAACTCGCACAAATG 65 TAACTCGCACAAATG * 1168 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT-TAG 1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAG 1232 TAACTCGCACAATATG 65 TAACTCGCACAA-ATG * * * * * * 1248 CCTTC-GG-C-T-GCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGG 1 CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGTTATAG * * 1308 TCACTTAGCACAAA-G 65 TAAC-TCGCACAAATG 1323 CCTTCGGGACTTA 1 CCTTCGGGACTTA 1336 GCCCGGACAT Statistics Matches: 142, Mismatches: 16, Indels: 20 0.80 0.09 0.11 Matches are distributed among these distances: 75 10 0.07 76 44 0.31 77 9 0.06 78 3 0.02 79 66 0.46 80 10 0.07 ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27 Consensus pattern (79 bp): CCTTCGGGACTTAACCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGT AACTCGCACAAATG Found at i:9036 original size:40 final size:40 Alignment explanation

Indices: 8999--9223 Score: 278 Period size: 40 Copynumber: 5.7 Consensus size: 40 8989 GCTACTCGTT * * 8999 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA 9039 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 9079 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA * * * * 9119 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA 1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA ** * * * * 9158 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA * 9199 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAACCCGGA 9224 CATCATTCGA Statistics Matches: 165, Mismatches: 15, Indels: 10 0.87 0.08 0.05 Matches are distributed among these distances: 38 2 0.01 39 32 0.19 40 118 0.72 41 13 0.08 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA Found at i:9183 original size:119 final size:120 Alignment explanation

Indices: 9001--9223 Score: 301 Period size: 119 Copynumber: 1.9 Consensus size: 120 8991 TACTCGTTCA * 9001 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT 1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT * * 9066 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC 66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC * * ** 9121 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG 1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG * * * 9183 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA 64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA 9224 CATCATTCGA Statistics Matches: 90, Mismatches: 10, Indels: 7 0.84 0.09 0.07 Matches are distributed among these distances: 118 4 0.04 119 66 0.73 120 20 0.22 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (120 bp): AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC Found at i:10415 original size:56 final size:56 Alignment explanation

Indices: 10348--10467 Score: 222 Period size: 56 Copynumber: 2.1 Consensus size: 56 10338 TATTAGTTTA * 10348 TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGTT 1 TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGCT * 10404 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGCT 1 TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGCT 10460 TTGCCCAT 1 TTGCCCAT 10468 CATCCCTTGT Statistics Matches: 62, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 56 62 1.00 ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44 Consensus pattern (56 bp): TTGCCCATGCTTCTTATTTTATTATTCCATTAACACAACATGTTTCATGACATGCT Found at i:17504 original size:29 final size:29 Alignment explanation

Indices: 17462--17522 Score: 106 Period size: 29 Copynumber: 2.1 Consensus size: 29 17452 AAAACCAACT 17462 TTTCGCAACCAGAACTCAC-ATTTACTAAA 1 TTTCGCAACCAGAACTCACAATTT-CTAAA 17491 TTTCGCAACCAGAACTCACAATTTCTAAA 1 TTTCGCAACCAGAACTCACAATTTCTAAA 17520 TTT 1 TTT 17523 TGTATACAAC Statistics Matches: 31, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 29 27 0.87 30 4 0.13 ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31 Consensus pattern (29 bp): TTTCGCAACCAGAACTCACAATTTCTAAA Done.