Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold949

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: 28394
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:6610 original size:10 final size:10

Alignment explanation

Indices: 6597--6627 Score: 53 Period size: 10 Copynumber: 3.0 Consensus size: 10 6587 TTTTCAAATT 6597 TTTTTTTTGA 1 TTTTTTTTGA 6607 TTTTTTTTCGA 1 TTTTTTTT-GA 6618 TTTTTTTTGA 1 TTTTTTTTGA 6628 ATCTACAATT Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 10 10 0.50 11 10 0.50 ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77 Consensus pattern (10 bp): TTTTTTTTGA Found at i:6610 original size:11 final size:11 Alignment explanation

Indices: 6596--6625 Score: 51 Period size: 11 Copynumber: 2.7 Consensus size: 11 6586 TTTTTCAAAT * 6596 TTTTTTTTTGA 1 TTTTTTTTCGA 6607 TTTTTTTTCGA 1 TTTTTTTTCGA 6618 TTTTTTTT 1 TTTTTTTT 6626 GAATCTACAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83 Consensus pattern (11 bp): TTTTTTTTCGA Found at i:8614 original size:14 final size:14 Alignment explanation

Indices: 8597--8636 Score: 53 Period size: 14 Copynumber: 2.9 Consensus size: 14 8587 CGAATGGAAT * 8597 GGTAGGAACGAAAG 1 GGTAGGAACAAAAG 8611 GGTAGGAACAAAAG 1 GGTAGGAACAAAAG * * 8625 GATATGAACAAA 1 GGTAGGAACAAA 8637 TTGGTCAGTT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 14 23 1.00 ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10 Consensus pattern (14 bp): GGTAGGAACAAAAG Found at i:10987 original size:23 final size:22 Alignment explanation

Indices: 10935--10987 Score: 56 Period size: 23 Copynumber: 2.4 Consensus size: 22 10925 TCCACGTCTT * 10935 TTTCTTTTGTTTCTTTTTCTAA 1 TTTCTTTTCTTTCTTTTTCTAA 10957 -TTCATTTTCTCTTCTTTCTTC-AA 1 TTTC-TTTTCT-TTCTTT-TTCTAA 10980 TTTCTTTT 1 TTTCTTTT 10988 TCACTCTCAA Statistics Matches: 26, Mismatches: 1, Indels: 7 0.76 0.03 0.21 Matches are distributed among these distances: 21 3 0.12 22 5 0.19 23 12 0.46 24 6 0.23 ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70 Consensus pattern (22 bp): TTTCTTTTCTTTCTTTTTCTAA Found at i:14653 original size:18 final size:18 Alignment explanation

Indices: 14632--14675 Score: 54 Period size: 18 Copynumber: 2.4 Consensus size: 18 14622 ATACTCACTC 14632 TCTTTTTCAATTT-TCTTT 1 TCTTTTTCAATTTCT-TTT ** 14650 TCTTGATCAATTTCTTTT 1 TCTTTTTCAATTTCTTTT 14668 TCTTTTTC 1 TCTTTTTC 14676 TCATTCTTTT Statistics Matches: 21, Mismatches: 4, Indels: 2 0.78 0.15 0.07 Matches are distributed among these distances: 18 20 0.95 19 1 0.05 ACGTcount: A:0.11, C:0.18, G:0.02, T:0.68 Consensus pattern (18 bp): TCTTTTTCAATTTCTTTT Found at i:15675 original size:30 final size:31 Alignment explanation

Indices: 15641--15737 Score: 101 Period size: 30 Copynumber: 3.2 Consensus size: 31 15631 AGCTCACTTC * 15641 TAGCTC-ACTTTCAACTCACGAGCTAAACCT 1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT * * * * * 15671 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT 1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT * * 15701 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT 1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT 15731 TAGCTCA 1 TAGCTCA 15738 TTTTAGTTTA Statistics Matches: 51, Mismatches: 14, Indels: 4 0.74 0.20 0.06 Matches are distributed among these distances: 30 47 0.92 31 4 0.08 ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28 Consensus pattern (31 bp): TAGCTCAACTTTCAGCTCACGAGCTAAACCT Found at i:19527 original size:17 final size:18 Alignment explanation

Indices: 19490--19527 Score: 51 Period size: 17 Copynumber: 2.2 Consensus size: 18 19480 GATTGAGAGT * * 19490 GAAAAGGAATGTGAAACA 1 GAAAAGAAATGTGAAAAA 19508 GAAAAGAAAT-TGAAAAA 1 GAAAAGAAATGTGAAAAA 19525 GAA 1 GAA 19528 GTTGAAGAAA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 17 9 0.50 18 9 0.50 ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11 Consensus pattern (18 bp): GAAAAGAAATGTGAAAAA Found at i:19540 original size:13 final size:12 Alignment explanation

Indices: 19509--19563 Score: 51 Period size: 12 Copynumber: 4.6 Consensus size: 12 19499 TGTGAAACAG * 19509 AAAAGAAATTGA 1 AAAAGAAGTTGA 19521 AAAAGAAGTTGA 1 AAAAGAAGTTGA * 19533 AGAAAGAAG-AGA 1 A-AAAGAAGTTGA * 19545 AAATG-AGTTAGA 1 AAAAGAAGTT-GA 19557 AAAAGAA 1 AAAAGAA 19564 ACAAAAGGCT Statistics Matches: 34, Mismatches: 5, Indels: 7 0.74 0.11 0.15 Matches are distributed among these distances: 10 2 0.06 11 3 0.09 12 21 0.62 13 8 0.24 ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13 Consensus pattern (12 bp): AAAAGAAGTTGA Found at i:20784 original size:11 final size:10 Alignment explanation

Indices: 20759--20819 Score: 54 Period size: 10 Copynumber: 6.1 Consensus size: 10 20749 ACCAATAAAA 20759 TAAA-TGAGC 1 TAAATTGAGC * 20768 TGAATTGTAGC 1 TAAATTG-AGC 20779 TAAATTGAGC 1 TAAATTGAGC ** 20789 TCGATTGAGC 1 TAAATTGAGC 20799 TGAAA-TGAGC 1 T-AAATTGAGC * 20809 TCAATTGAGC 1 TAAATTGAGC 20819 T 1 T 20820 GGTCGGAGTT Statistics Matches: 41, Mismatches: 7, Indels: 7 0.75 0.13 0.13 Matches are distributed among these distances: 9 5 0.12 10 26 0.63 11 10 0.24 ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30 Consensus pattern (10 bp): TAAATTGAGC Found at i:20820 original size:20 final size:20 Alignment explanation

Indices: 20760--20820 Score: 79 Period size: 20 Copynumber: 3.0 Consensus size: 20 20750 CCAATAAAAT * 20760 AAATGAGCTGAATTGTAGCT- 1 AAATGAGCTCAATTG-AGCTG * 20780 AAATTGAGCTCGATTGAGCTG 1 AAA-TGAGCTCAATTGAGCTG 20801 AAATGAGCTCAATTGAGCTG 1 AAATGAGCTCAATTGAGCTG 20821 GTCGGAGTTG Statistics Matches: 36, Mismatches: 3, Indels: 4 0.84 0.07 0.09 Matches are distributed among these distances: 20 23 0.64 21 13 0.36 ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28 Consensus pattern (20 bp): AAATGAGCTCAATTGAGCTG Done.