Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3153

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: 41451
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30


Found at i:4105 original size:79 final size:82

Alignment explanation

Indices: 3994--4178 Score: 229 Period size: 79 Copynumber: 2.3 Consensus size: 82 3984 GCTACTCGTT * * * 3994 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC * * 4057 GGATTTAGTAAC-TCGCA 65 GGATATAGTAACTTAGCA * ** 4074 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG * * 4137 GATATGGTCACTTAGCA 66 GATATAGTAACTTAGCA 4154 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 4179 CATCATTCAA Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.59 80 34 0.37 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25 Consensus pattern (82 bp): CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG GATATAGTAACTTAGCA Found at i:4178 original size:40 final size:40 Alignment explanation

Indices: 3975--4178 Score: 229 Period size: 40 Copynumber: 5.1 Consensus size: 40 3965 CGGAATTTAA ** * 3975 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC 1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC * * * 4015 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * 4055 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * 4094 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT 1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC * * * 4134 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC 1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC 4174 CCGGA 1 CCGGA 4179 CATCATTCAA Statistics Matches: 139, Mismatches: 18, Indels: 14 0.81 0.11 0.08 Matches are distributed among these distances: 38 2 0.01 39 33 0.24 40 92 0.66 41 12 0.09 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC Found at i:21219 original size:49 final size:49 Alignment explanation

Indices: 21159--21341 Score: 231 Period size: 49 Copynumber: 3.7 Consensus size: 49 21149 ATCTGGTACG * 21159 ATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACAC 1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAC * * * 21208 GTAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGGACAC 1 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAC * * * * * * * 21257 ATAGTAGCATGCACTTAGTACTACACACGTGATCAAAGTTTTCGGGTACGC 1 ATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACAC ** 21308 ATAGTAGCCTGTGCTTAGTACTACACATGCGACC 1 ATAGTAGCCTGCACTTAGTACTACACATGCGACC 21342 TCACAATAGA Statistics Matches: 114, Mismatches: 18, Indels: 3 0.84 0.13 0.02 Matches are distributed among these distances: 49 74 0.65 50 4 0.04 51 36 0.32 ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25 Consensus pattern (49 bp): ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACAC Found at i:21330 original size:100 final size:98 Alignment explanation

Indices: 21159--21341 Score: 240 Period size: 100 Copynumber: 1.8 Consensus size: 98 21149 ATCTGGTACG * * * * 21159 ATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTT 1 ATAGTAGCATGCACATAGTACTACACACGCGACAAATTATCCGGTACACATAGTAGCCTGCACTT * 21224 AGTACTACACATGTGACCAATTATCCGGGACAC 66 AGTACTACACATGCGACCAATTATCCGGGACAC * * * * * ** 21257 ATAGTAGCATGCACTTAGTACTACACACGTGATCAAAGTTTTCGGGTACGCATAGTAGCCTGTGC 1 ATAGTAGCATGCACATAGTACTACACACGCGA-CAAA-TTATCCGGTACACATAGTAGCCTGCAC 21322 TTAGTACTACACATGCGACC 64 TTAGTACTACACATGCGACC 21342 TCACAATAGA Statistics Matches: 71, Mismatches: 12, Indels: 2 0.84 0.14 0.02 Matches are distributed among these distances: 98 28 0.39 99 3 0.04 100 40 0.56 ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25 Consensus pattern (98 bp): ATAGTAGCATGCACATAGTACTACACACGCGACAAATTATCCGGTACACATAGTAGCCTGCACTT AGTACTACACATGCGACCAATTATCCGGGACAC Found at i:24534 original size:24 final size:23 Alignment explanation

Indices: 24482--24536 Score: 58 Period size: 24 Copynumber: 2.3 Consensus size: 23 24472 CAACCGAATT * 24482 TGCACACATAGTGCTCATCACAC 1 TGCACACATAGTGCTCATCAAAC * 24505 TCGCACACATAGTGC-CATAGTAAAC 1 T-GCACACATAGTGCTCAT--CAAAC 24530 TGCACAC 1 TGCACAC 24537 TCAGTGTATT Statistics Matches: 27, Mismatches: 2, Indels: 5 0.79 0.06 0.15 Matches are distributed among these distances: 23 4 0.15 24 19 0.70 25 4 0.15 ACGTcount: A:0.33, C:0.33, G:0.15, T:0.20 Consensus pattern (23 bp): TGCACACATAGTGCTCATCAAAC Found at i:26768 original size:27 final size:27 Alignment explanation

Indices: 26714--26768 Score: 83 Period size: 27 Copynumber: 2.0 Consensus size: 27 26704 CATAAGGAAG * * 26714 GAATAGCCTTTGTGGAAAACTATGAAA 1 GAATAGCCTTCGTGGAAAACTATAAAA * 26741 GAATAGCCTTCGTGGAAAACTTTAAAA 1 GAATAGCCTTCGTGGAAAACTATAAAA 26768 G 1 G 26769 GAATCCATTT Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25 Consensus pattern (27 bp): GAATAGCCTTCGTGGAAAACTATAAAA Found at i:26782 original size:27 final size:26 Alignment explanation

Indices: 26714--26784 Score: 72 Period size: 27 Copynumber: 2.6 Consensus size: 26 26704 CATAAGGAAG * 26714 GAATAGCCTTTGTGGAAAACTATGAAA 1 GAATA-CCTTTGTGGAAAACTATAAAA * * 26741 GAATAGCCTTCGTGGAAAACTTTAAAA 1 GAATA-CCTTTGTGGAAAACTATAAAA 26768 GGAAT-CCATTTGTGGAA 1 -GAATACC-TTTGTGGAA 26785 TATTTTGAAT Statistics Matches: 38, Mismatches: 4, Indels: 4 0.83 0.09 0.09 Matches are distributed among these distances: 26 2 0.05 27 32 0.84 28 4 0.11 ACGTcount: A:0.38, C:0.13, G:0.23, T:0.27 Consensus pattern (26 bp): GAATACCTTTGTGGAAAACTATAAAA Found at i:30732 original size:38 final size:40 Alignment explanation

Indices: 30642--30852 Score: 262 Period size: 38 Copynumber: 5.5 Consensus size: 40 30632 CGGATGATAA * * * 30642 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT 30682 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-T-TAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 30720 CCGGGCTAAGTCCCGAAGGCA-TT-TGCGAG-TACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * 30757 CCGGGCTAAGT-CCGAAGGCATTGGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * 30796 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT * * 30835 CC-GGTTAAATCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 30853 TACTTGGCTT Statistics Matches: 153, Mismatches: 10, Indels: 18 0.85 0.06 0.10 Matches are distributed among these distances: 35 2 0.01 36 16 0.10 37 18 0.12 38 43 0.28 39 34 0.22 40 40 0.26 ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Found at i:38706 original size:40 final size:40 Alignment explanation

Indices: 38651--38827 Score: 227 Period size: 40 Copynumber: 4.5 Consensus size: 40 38641 TGGATGATAA * * * 38651 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT 38691 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * 38731 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT * * * 38771 CCGGGCTATGTCCCGAAGGCA-TTGAGTGAG-TAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT * * 38810 CC-GGTTAAATCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 38828 TACTTGGCTT Statistics Matches: 124, Mismatches: 11, Indels: 6 0.88 0.08 0.04 Matches are distributed among these distances: 38 15 0.12 39 15 0.12 40 94 0.76 ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT Done.