Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1554

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: 30074
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32


Found at i:1523 original size:32 final size:35

Alignment explanation

Indices: 1448--1513 Score: 93 Period size: 32 Copynumber: 1.9 Consensus size: 35 1438 ACCAATTCTA * 1448 TATATAACATATACCAAATCATATCATTTCATAAGT 1 TATA-AACATATACCAAAACATATCATTTCATAAGT 1484 TATAAACATA-A-CAAAACATAT-ATTTCATAA 1 TATAAACATATACCAAAACATATCATTTCATAA 1514 TCTCAAAACA Statistics Matches: 29, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 32 9 0.31 33 9 0.31 34 1 0.03 35 6 0.21 36 4 0.14 ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33 Consensus pattern (35 bp): TATAAACATATACCAAAACATATCATTTCATAAGT Found at i:2691 original size:27 final size:27 Alignment explanation

Indices: 2653--2820 Score: 169 Period size: 27 Copynumber: 6.2 Consensus size: 27 2643 TAAGTTGTAG * * * 2653 AATTACTAAAATACCCTTGGTTTATAA 1 AATTACCAAAATACCCTCGATTTATAA * 2680 AATTACCAAAATACCC-CTGGTTTATAA 1 AATTACCAAAATACCCTC-GATTTATAA * * 2707 AATTACCAAAAAACCC-CTGATTTGTAA 1 AATTACCAAAATACCCTC-GATTTATAA * ** 2734 AATTACTAAAATACCCTCGACCTATAA 1 AATTACCAAAATACCCTCGATTTATAA ** * 2761 AATTACTGAAATACCCTCGACTTATAA 1 AATTACCAAAATACCCTCGATTTATAA * * * 2788 GATTACCAAAGTACCCTCGATTTACAA 1 AATTACCAAAATACCCTCGATTTATAA 2815 AATTAC 1 AATTAC 2821 TGTTTTACCC Statistics Matches: 120, Mismatches: 19, Indels: 4 0.84 0.13 0.03 Matches are distributed among these distances: 27 119 0.99 28 1 0.01 ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29 Consensus pattern (27 bp): AATTACCAAAATACCCTCGATTTATAA Found at i:2810 original size:81 final size:81 Alignment explanation

Indices: 2647--2797 Score: 196 Period size: 81 Copynumber: 1.9 Consensus size: 81 2637 AGTGGATAAG * * *** ** 2647 TTGTAGAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTGGTTTATAAAATTA 1 TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTA 2712 CCAAAAAACCCCTGAT 66 CCAAAAAACCCCTGAT ** * 2728 TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACTGAAATA-CCCTCGACTTATAAGATT 1 TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCT-GACTTATAAAATT 2792 ACCAAA 65 ACCAAA 2798 GTACCCTCGA Statistics Matches: 59, Mismatches: 10, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 80 4 0.07 81 55 0.93 ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30 Consensus pattern (81 bp): TTGTAAAATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTA CCAAAAAACCCCTGAT Found at i:2817 original size:81 final size:81 Alignment explanation

Indices: 2653--2821 Score: 189 Period size: 81 Copynumber: 2.1 Consensus size: 81 2643 TAAGTTGTAG * *** ** 2653 AATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTGGTTTATAAAATTACCAAAA 1 AATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTACCAAAA ** 2718 AACCCCTGATTTGTAA 66 AACCCCTGATTTACAA ** * 2734 AATTACTAAAATACCCTCGACCTATAAAATTACTGAAATA-CCCTCGACTTATAAGATTACCAAA 1 AATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCT-GACTTATAAAATTACCAAA ** 2798 GTA-CCCTCGATTTACAA 65 AAACCCCT-GATTTACAA 2815 AATTACT 1 AATTACT 2822 GTTTTACCCT Statistics Matches: 73, Mismatches: 13, Indels: 4 0.81 0.14 0.04 Matches are distributed among these distances: 80 8 0.11 81 65 0.89 ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30 Consensus pattern (81 bp): AATTACTAAAATACCCTCGACCTATAAAATTACCAAAATACCCCTGACTTATAAAATTACCAAAA AACCCCTGATTTACAA Found at i:2856 original size:27 final size:28 Alignment explanation

Indices: 2732--2858 Score: 120 Period size: 27 Copynumber: 4.7 Consensus size: 28 2722 CCTGATTTGT * * 2732 AAAATTACTA-AAATACCCTCGACCTAT 1 AAAATTACTAGAAATACCCTCGACTTAC * 2759 AAAATTACT-GAAATACCCTCGACTTAT 1 AAAATTACTAGAAATACCCTCGACTTAC * * * * 2786 AAGATTACCA-AAGTACCCTCGATTTAC 1 AAAATTACTAGAAATACCCTCGACTTAC *** * 2813 AAAATTACT-GTTTTACCCTCGATTTAC 1 AAAATTACTAGAAATACCCTCGACTTAC 2840 AAAATTA-TAGAAATACCCT 1 AAAATTACTAGAAATACCCT 2859 TGTAAGGTAG Statistics Matches: 82, Mismatches: 14, Indels: 8 0.79 0.13 0.08 Matches are distributed among these distances: 26 1 0.01 27 81 0.99 ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30 Consensus pattern (28 bp): AAAATTACTAGAAATACCCTCGACTTAC Found at i:2857 original size:54 final size:54 Alignment explanation

Indices: 2732--2858 Score: 139 Period size: 54 Copynumber: 2.4 Consensus size: 54 2722 CCTGATTTGT * * 2732 AAAATTACTAAAATACCCTCGACCTATAAAATTACTGAAATACCCTCGACTTAT 1 AAAATTACTAAAATACCCTCGACCTACAAAATTACTGAAATACCCTCGACTTAC * * * ** *** * 2786 AAGATTACCAAAGTACCCTCGATTTACAAAATTACTGTTTTACCCTCGATTTAC 1 AAAATTACTAAAATACCCTCGACCTACAAAATTACTGAAATACCCTCGACTTAC 2840 AAAATTA-TAGAAATACCCT 1 AAAATTACTA-AAATACCCT 2859 TGTAAGGTAG Statistics Matches: 58, Mismatches: 14, Indels: 2 0.78 0.19 0.03 Matches are distributed among these distances: 53 1 0.02 54 57 0.98 ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30 Consensus pattern (54 bp): AAAATTACTAAAATACCCTCGACCTACAAAATTACTGAAATACCCTCGACTTAC Found at i:2926 original size:27 final size:27 Alignment explanation

Indices: 2849--2929 Score: 99 Period size: 27 Copynumber: 3.0 Consensus size: 27 2839 CAAAATTATA * * 2849 GAAATACCCTTGTAAGGTAGAATTACT 1 GAAATACCCTTGTAGGGTAGAATTACC * * 2876 GAAATACCCCTGTAGGATAGAATTACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 2903 GAGATACCCTTGTGGGGTAAAATTACC 1 GAAATACCCTTGTAGGGTAGAATTACC 2930 ATTTTTCCCC Statistics Matches: 45, Mismatches: 9, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 27 45 1.00 ACGTcount: A:0.35, C:0.19, G:0.21, T:0.26 Consensus pattern (27 bp): GAAATACCCTTGTAGGGTAGAATTACC Found at i:4917 original size:43 final size:42 Alignment explanation

Indices: 4847--5007 Score: 184 Period size: 43 Copynumber: 3.8 Consensus size: 42 4837 GAAAAGCTCG * * * 4847 TACGATGCCAACGTCCCAGATGTGGTCTTACATGTAATCAAA 1 TACGATGCCAACATCCCAGACGTGGTCTTACATGAAATCAAA *** 4889 TATCGATGCCATTGTCCCAGACAG-GGTCTTACATGAAATCAAA 1 TA-CGATGCCAACATCCCAGAC-GTGGTCTTACATGAAATCAAA 4932 TACGATGCCAACATCCCAGACGTGGTCTTACACAT-AAATCATAA 1 TACGATGCCAACATCCCAGACGTGGTCTT--ACATGAAATCA-AA * 4976 GT-TGATGCCAACATCCCAGACGTGGTCTTACA 1 -TACGATGCCAACATCCCAGACGTGGTCTTACA 5008 CGATAACACA Statistics Matches: 104, Mismatches: 8, Indels: 14 0.83 0.06 0.11 Matches are distributed among these distances: 41 1 0.01 42 27 0.26 43 42 0.40 44 33 0.32 45 1 0.01 ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25 Consensus pattern (42 bp): TACGATGCCAACATCCCAGACGTGGTCTTACATGAAATCAAA Found at i:18099 original size:16 final size:16 Alignment explanation

Indices: 18078--18109 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 18068 CATGCATTGA * 18078 ACATAATGAACATAAT 1 ACATAATCAACATAAT 18094 ACATAATCAACATAAT 1 ACATAATCAACATAAT 18110 CTTGCATTTT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25 Consensus pattern (16 bp): ACATAATCAACATAAT Found at i:20355 original size:39 final size:39 Alignment explanation

Indices: 20298--20388 Score: 137 Period size: 39 Copynumber: 2.3 Consensus size: 39 20288 GCATGATACT * * 20298 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC 1 TGGAAACATATCCAGACTTGAGGTCCGCAGGCTACATGC * 20337 TGGAAACATATCCAGACTTGAGGTCCGCAGGCTATATGC 1 TGGAAACATATCCAGACTTGAGGTCCGCAGGCTACATGC * * 20376 CGGAAATATATCC 1 TGGAAACATATCC 20389 GGGCTTAAAG Statistics Matches: 47, Mismatches: 5, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 39 47 1.00 ACGTcount: A:0.27, C:0.24, G:0.26, T:0.22 Consensus pattern (39 bp): TGGAAACATATCCAGACTTGAGGTCCGCAGGCTACATGC Found at i:28228 original size:39 final size:39 Alignment explanation

Indices: 28169--28279 Score: 134 Period size: 39 Copynumber: 2.8 Consensus size: 39 28159 GCATGATACT * * 28169 TGGAAACGTATCCGGACTTGAGGTCCGCAGCCTACGTGC 1 TGGAAACATATCCGGGCTTGAGGTCCGCAGCCTACGTGC * * * 28208 TGGAAACATATCTGGGCTTGAGGTCCGCAGGCTATGTGC 1 TGGAAACATATCCGGGCTTGAGGTCCGCAGCCTACGTGC * * * 28247 T-GAAATATATCCGGGCTTAAAGTCCCGCAGCCT 1 TGGAAACATATCCGGGCTTGAGGT-CCGCAGCCT 28280 TTATGCTAAG Statistics Matches: 61, Mismatches: 10, Indels: 2 0.84 0.14 0.03 Matches are distributed among these distances: 38 18 0.30 39 43 0.70 ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23 Consensus pattern (39 bp): TGGAAACATATCCGGGCTTGAGGTCCGCAGCCTACGTGC Done.