Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007352.1 Corchorus capsularis cultivar CVL-1 contig07373, whole genome shotgun sequence

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: 33556
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:3556 original size:22 final size:22

Alignment explanation

Indices: 3528--3573 Score: 65 Period size: 22 Copynumber: 2.1 Consensus size: 22 3518 CAATTCAAGC * * * 3528 ATCATGTCAGGCTGATGATCAT 1 ATCATGTCAAGCTCATAATCAT 3550 ATCATGTCAAGCTCATAATCAT 1 ATCATGTCAAGCTCATAATCAT 3572 AT 1 AT 3574 GATATATGAA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 22 21 1.00 ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33 Consensus pattern (22 bp): ATCATGTCAAGCTCATAATCAT Found at i:6798 original size:49 final size:50 Alignment explanation

Indices: 6722--6836 Score: 144 Period size: 49 Copynumber: 2.3 Consensus size: 50 6712 AAATGTGAAG * * ** * 6722 AGAAAACT-GGACCATCCGACCGGGAAGGGGCATTTTGGG-AATAAAGAA 1 AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAAGAA * 6770 AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAATAA 1 AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAAGAA * * 6820 AGAGAACAGGGACCTTC 1 AGAAAACTGGGACCTTC 6837 TGACCTGGAA Statistics Matches: 57, Mismatches: 8, Indels: 2 0.85 0.12 0.03 Matches are distributed among these distances: 48 8 0.14 49 27 0.47 50 22 0.39 ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15 Consensus pattern (50 bp): AGAAAACTGGGACCTTCCAACCAAGAAGGGGCATTTTGGGAAACAAAGAA Found at i:7290 original size:32 final size:32 Alignment explanation

Indices: 7244--7307 Score: 94 Period size: 32 Copynumber: 2.0 Consensus size: 32 7234 ATTTCATCAT * * 7244 TTACTTAAAGGTTCAAT-TTTTATTTACAAAAA 1 TTACTTAAAAGTTCAATGTTTTAATTA-AAAAA 7276 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA 1 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA 7308 CTCAATCATT Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 32 21 0.72 33 8 0.28 ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42 Consensus pattern (32 bp): TTACTTAAAAGTTCAATGTTTTAATTAAAAAA Found at i:7545 original size:51 final size:51 Alignment explanation

Indices: 7456--7631 Score: 246 Period size: 51 Copynumber: 3.5 Consensus size: 51 7446 ACCACACTTC * ** * * 7456 TATTTACAAATTAATCATCAA-TTCCATCATTTGGTTCAAAGATATCATTTT 1 TATTTACAAATTAATCA-CAAGTTCAATCATTTAATTCAAAGCTCTCATTTT * 7507 TATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGCTCTCATTTT 1 TATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT * * 7558 TATTTACAAATTACTTACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT 1 TATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT * * 7609 TATTTACAAATTACTCAAAAGTT 1 TATTTACAAATTAATCACAAGTT 7632 TAATTATTAG Statistics Matches: 113, Mismatches: 11, Indels: 2 0.90 0.09 0.02 Matches are distributed among these distances: 50 3 0.03 51 110 0.97 ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41 Consensus pattern (51 bp): TATTTACAAATTAATCACAAGTTCAATCATTTAATTCAAAGCTCTCATTTT Found at i:9773 original size:20 final size:20 Alignment explanation

Indices: 9748--9786 Score: 69 Period size: 20 Copynumber: 1.9 Consensus size: 20 9738 AAAAAGAGCA 9748 CCAATTTGCAAATCAAATGT 1 CCAATTTGCAAATCAAATGT * 9768 CCAATTTGTAAATCAAATG 1 CCAATTTGCAAATCAAATG 9787 CCTTGTATTT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31 Consensus pattern (20 bp): CCAATTTGCAAATCAAATGT Found at i:9952 original size:14 final size:14 Alignment explanation

Indices: 9933--9960 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 9923 TGATATTAAT 9933 CTAAATGGACTAAA 1 CTAAATGGACTAAA 9947 CTAAATGGACTAAA 1 CTAAATGGACTAAA 9961 GTTAATATGC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21 Consensus pattern (14 bp): CTAAATGGACTAAA Found at i:10331 original size:27 final size:28 Alignment explanation

Indices: 10284--10360 Score: 93 Period size: 27 Copynumber: 2.8 Consensus size: 28 10274 AAGTGAACTT 10284 AAAATGACCAAAATACCCCCTAAATGCA 1 AAAATGACCAAAATACCCCCTAAATGCA * * ** 10312 AAAATGACCAAAATA-TCCCTGAATGTG 1 AAAATGACCAAAATACCCCCTAAATGCA * * 10339 AAAACGACCAAAATGCCCCCTA 1 AAAATGACCAAAATACCCCCTA 10361 GGTGACGATA Statistics Matches: 40, Mismatches: 8, Indels: 2 0.80 0.16 0.04 Matches are distributed among these distances: 27 21 0.52 28 19 0.47 ACGTcount: A:0.47, C:0.27, G:0.10, T:0.16 Consensus pattern (28 bp): AAAATGACCAAAATACCCCCTAAATGCA Found at i:11732 original size:8 final size:7 Alignment explanation

Indices: 11706--11752 Score: 51 Period size: 7 Copynumber: 6.6 Consensus size: 7 11696 ACCCTAGAGC * 11706 TTTCTTC 1 TTTCTTT * 11713 TTTATTT 1 TTTCTTT 11720 TTTCTTGT 1 TTTCTT-T 11728 TTTC-TT 1 TTTCTTT 11734 TTTCTTT 1 TTTCTTT 11741 CTTTCTTT 1 -TTTCTTT 11749 TTTC 1 TTTC 11753 ATTGCACTTG Statistics Matches: 34, Mismatches: 3, Indels: 6 0.79 0.07 0.14 Matches are distributed among these distances: 6 5 0.15 7 17 0.50 8 12 0.35 ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79 Consensus pattern (7 bp): TTTCTTT Found at i:12503 original size:33 final size:33 Alignment explanation

Indices: 12428--12514 Score: 149 Period size: 32 Copynumber: 2.7 Consensus size: 33 12418 TTGTAACATT * 12428 TTTTTGGAAACCATGACTCTCTTTTGAAAAACA 1 TTTTTGAAAACCATGACTCTCTTTTGAAAAACA * 12461 -TTTTGAAAACCTTGACTCTCTTTTGAAAAACA 1 TTTTTGAAAACCATGACTCTCTTTTGAAAAACA 12493 TTTTTGAAAACCATGACTCTCT 1 TTTTTGAAAACCATGACTCTCT 12515 ACCATTCCAA Statistics Matches: 50, Mismatches: 3, Indels: 2 0.91 0.05 0.04 Matches are distributed among these distances: 32 30 0.60 33 20 0.40 ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38 Consensus pattern (33 bp): TTTTTGAAAACCATGACTCTCTTTTGAAAAACA Found at i:17308 original size:49 final size:49 Alignment explanation

Indices: 17233--17566 Score: 283 Period size: 49 Copynumber: 6.9 Consensus size: 49 17223 AAATGTGAAG * * * * 17233 AGAAAACT-GGACCATCTGACCGGGAAGGGGCATTTTGGGAATAAAGAA 1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA * ** * * * 17281 AGAAAACTGGGACCTTCCAACCAGGAA-GAGCA----GGAAACAAATAA 1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA * * * * ** * 17325 AGAGAACAGGGACCTTTCGACTGGGAAAGGGCATTTTAGAAAATGAATAA 1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTT-GGGAATAAATAA * ** * * 17375 AGAAAACAGGGACCTTTTGACTGGGAAGGGGCATTTTGGAAACAAATAA 1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA * * * 17424 AGAAAACAGTGACCTTCCGACTGGGAAGGGGCTTTTTGGGAA-ACAGATAA 1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATA-A-ATAA * * * 17474 AGGAAA-TAGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAATAAGA-AA 1 AGAAAACT-GGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAA-ATAA * * 17523 AGAAAACTGTGACCTTCCGACTGGGAAGGGGC-TTTTTGGAATAA 1 AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAA 17567 GAAAAGCAGA Statistics Matches: 236, Mismatches: 38, Indels: 24 0.79 0.13 0.08 Matches are distributed among these distances: 44 30 0.13 45 4 0.02 48 25 0.11 49 90 0.38 50 86 0.36 51 1 0.00 ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19 Consensus pattern (49 bp): AGAAAACTGGGACCTTCCGACTGGGAAGGGGCATTTTGGGAATAAATAA Found at i:17397 original size:50 final size:50 Alignment explanation

Indices: 17254--17563 Score: 295 Period size: 50 Copynumber: 6.4 Consensus size: 50 17244 CCATCTGACC * * * * * * 17254 GGGAAGGGGCATTTTGGGAATA-AAGAAAGAAAACTGGGACCTTCCAACC 1 GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT * * * * 17303 AGGAA-GAGCA----GGAAACA-AATAAAGAGAACAGGGACCTTTCGACT 1 GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT * * ** 17347 GGGAAAGGGCATTTTAGAAA-ATGAATAAAGAAAACAGGGACCTTTTGACT 1 GGGAAGGGGCATTTTGGAAACA-GAATAAAGAAAACAGGGACCTTCCGACT * 17397 GGGAAGGGGCATTTTGGAAACA-AATAAAGAAAACAGTGACCTTCCGACT 1 GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT * * * * 17446 GGGAAGGGGCTTTTTGGGAAACAG-ATAAAGGAAATAGGGACCTTCCGACC 1 GGGAAGGGGCATTTT-GGAAACAGAATAAAGAAAACAGGGACCTTCCGACT * * 17496 GGGAAGGGGCATTTTTGGAATA-AG-A-AAAGAAAACTGTGACCTTCCGACT 1 GGGAAGGGGCA-TTTTGGAA-ACAGAATAAAGAAAACAGGGACCTTCCGACT * 17545 GGGAAGGGGCTTTTTGGAA 1 GGGAAGGGGCATTTTGGAA 17564 TAAGAAAAGC Statistics Matches: 217, Mismatches: 32, Indels: 25 0.79 0.12 0.09 Matches are distributed among these distances: 44 30 0.14 45 4 0.02 48 13 0.06 49 75 0.35 50 89 0.41 51 6 0.03 ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19 Consensus pattern (50 bp): GGGAAGGGGCATTTTGGAAACAGAATAAAGAAAACAGGGACCTTCCGACT Found at i:17561 original size:99 final size:100 Alignment explanation

Indices: 17254--17561 Score: 325 Period size: 99 Copynumber: 3.2 Consensus size: 100 17244 CCATCTGACC * * * * * * * 17254 GGGAAGGGGCATTTTGGG--AATAAAGAAAGAAAACTGGGACCTTCCAACCAGGAA-GAGCA--- 1 GGGAAGGGGCTTTTTGGGAAAATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTT * * * 17313 -GGAAACAAATAAAGAGAACAGGGACCTTTCGACT 66 TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT * * * ** * 17347 GGGAAAGGGCATTTT-AGAAAATGAATAAAGAAAACAGGGACCTTTTGACTGGGAAGGGGCATTT 1 GGGAAGGGGCTTTTTGGGAAAATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTT 17411 TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT 66 TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT * * 17446 GGGAAGGGGCTTTTTGGGAAACA-G-ATAAAGGAAATAGGGACCTTCCGACCGGGAAGGGGCATT 1 GGGAAGGGGCTTTTTGGGAAA-ATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCA-T * * 17509 TTTGGAATA-AGA-AAAGAAAACTGTGACCTTCCGACT 64 TTTGGAA-ACAAATAAAGAAAACAGTGACCTTCCGACT 17545 GGGAAGGGGCTTTTTGG 1 GGGAAGGGGCTTTTTGG 17562 AATAAGAAAA Statistics Matches: 180, Mismatches: 24, Indels: 16 0.82 0.11 0.07 Matches are distributed among these distances: 92 1 0.01 93 14 0.08 94 28 0.16 95 4 0.02 99 116 0.64 100 15 0.08 101 2 0.01 ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19 Consensus pattern (100 bp): GGGAAGGGGCTTTTTGGGAAAATGAATAAAGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTT TGGAAACAAATAAAGAAAACAGTGACCTTCCGACT Found at i:17669 original size:40 final size:40 Alignment explanation

Indices: 17576--17910 Score: 331 Period size: 40 Copynumber: 8.1 Consensus size: 40 17566 AGAAAAGCAG * * 17576 ACAACACCTTCC-AGTGAGGAAGGGCACGA-TAGGAAATCTAA 1 ACAACACCTTCCGA-TGAGGAAGGGCA-AACTGGGAAA-CTAA * * 17617 ACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTTA 1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA * * 17657 ACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAGACTAA 1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA * * * 17697 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAATTCGGCAACTAA 1 ACAACACCTTCCGATGAGGAAGGGCAAACT-G------GGAAACTAA * 17744 ACAACACC-TCTCGACTG-GGAAGGGC-AAGTCGGGAAAACTAA 1 ACAACACCTTC-CGA-TGAGGAAGGGCAAACT-GGG-AAACTAA ** 17785 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAA 1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA * 17825 ACAACACCTTCCGATGGGGAAGGGCAAAACT-GGAAACTAA 1 ACAACACCTTCCGATGAGGAAGGGC-AAACTGGGAAACTAA * * * * 17865 ACAACACCTTTCGGTGAGGAAGGGCAAACTGAGAATAATAA 1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAA-ACTAA 17906 ACAAC 1 ACAAC 17911 TAAACAACAT Statistics Matches: 250, Mismatches: 26, Indels: 36 0.80 0.08 0.12 Matches are distributed among these distances: 39 5 0.02 40 134 0.54 41 72 0.29 42 6 0.02 46 6 0.02 47 25 0.10 48 2 0.01 ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15 Consensus pattern (40 bp): ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAA Found at i:17793 original size:128 final size:128 Alignment explanation

Indices: 17613--17857 Score: 365 Period size: 128 Copynumber: 1.9 Consensus size: 128 17603 GATAGGAAAT * * 17613 CTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTTAACAACACCTTCCGGTGAGGAA 1 CTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGAGGAA * 17678 GGGCAAACTGGGAGA-CTAAACAACACCTTCCGGTGGGGAAGGGC-AAACTGGTAATTCGGCAA 66 GGGCAAACTGGGA-ATCTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGGTAATTCGGCAA * 17740 CTAAACAACACC-TCTCGACT-GGGAAGGGC-AAGTCGGGAAAACTAAACAACACCTTCCGATGA 1 CTAAACAACACCTTC-CGA-TGGGGAAGGGCAAACT-GGG-AAACTAAACAACACCTTCCGATGA * 17802 GGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGG 62 GGAAGGGCAAACTGGGAATCTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGG 17858 AAACTAAACA Statistics Matches: 107, Mismatches: 5, Indels: 10 0.88 0.04 0.08 Matches are distributed among these distances: 126 5 0.05 127 28 0.26 128 67 0.63 129 7 0.07 ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15 Consensus pattern (128 bp): CTAAACAACACCTTCCGATGGGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGAGGAA GGGCAAACTGGGAATCTAAACAACACCTTCCGATGGGGAAGGGCAAAACTGGTAATTCGGCAA Found at i:17967 original size:49 final size:48 Alignment explanation

Indices: 17860--17989 Score: 140 Period size: 49 Copynumber: 2.7 Consensus size: 48 17850 AAAACTGGAA * * * 17860 ACTAAACAACACCTTTCGGTGAGGAAGGGCAAACTGAGAATAATAAAC 1 ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATAACAAAC * * * 17908 AACTAAACAACATCTTCCGATGAGGAAGGGCAGACTGGGAATCAGACAAAC 1 -ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAAT-A-ACAAAC * 17959 -CTAGACAACACCTTCC-AGTG-GGAAGGGCAAA 1 ACTAAACAACACCTTCCGA-TGAGGAAGGGCAAA 17990 TTAGGAATTT Statistics Matches: 69, Mismatches: 9, Indels: 7 0.81 0.11 0.08 Matches are distributed among these distances: 48 11 0.16 49 52 0.75 50 1 0.01 51 5 0.07 ACGTcount: A:0.41, C:0.22, G:0.23, T:0.15 Consensus pattern (48 bp): ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGAGAATAACAAAC Found at i:17997 original size:48 final size:45 Alignment explanation

Indices: 17692--18082 Score: 169 Period size: 47 Copynumber: 8.7 Consensus size: 45 17682 AAACTGGGAG * * * * 17692 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACT-GGTAATTCGGCA 1 ACTAGACAACACCTTCCGAT-GGGAAGGGCAAAATAGG-AATT-GACA * * * * 17739 ACTAAACAACACC-TCTCGACTGGGAAGGGC-AAGTCGG----GAAA 1 ACTAGACAACACCTTC-CGA-TGGGAAGGGCAAAATAGGAATTGACA * * * 17780 ACTAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATT---- 1 ACTAGACAACACCTTCCGATG-GGAAGGGCAAAATAGGAATTGACA * 17822 --TAAACAACACCTTCCGATGGGGAAGGGCAAAACT--G----GA-A 1 ACTAGACAACACCTTCCGAT-GGGAAGGGCAAAA-TAGGAATTGACA * * * * * 17860 ACTAAACAACACCTTTCGGTGAGGAAGGGCAAACT-GAGAATAATAAACA 1 ACTAGACAACACCTTCCGATG-GGAAGGGCAAAATAG-GAAT--T-GACA * * * * * * 17909 ACTAAACAACATCTTCCGATGAGGAAGGGCAGACTGGGAATCAGACAA 1 ACTAGACAACACCTTCCGATG-GGAAGGGCAAAATAGGAAT-TGAC-A * 17957 ACCTAGACAACACCTTCC-AGTGGGAAGGGCAAATTAGGAATTTGACA 1 A-CTAGACAACACCTTCCGA-TGGGAAGGGCAAAATAGGAA-TTGACA * * * 18004 ACTAAACAACACCTTCCAACTGGGAATGGCAAAATAGGAAATTGACA 1 ACTAGACAACACCTTCCGA-TGGGAAGGGCAAAATAGG-AATTGACA * * 18051 ACTAGACAACACCTTTCGTCTGGGAAGGGCAA 1 ACTAGACAACACCTTCCG-ATGGGAAGGGCAA 18083 TACCGGAAAT Statistics Matches: 275, Mismatches: 33, Indels: 72 0.72 0.09 0.19 Matches are distributed among these distances: 39 3 0.01 40 58 0.21 41 29 0.11 42 7 0.03 46 20 0.07 47 79 0.29 48 25 0.09 49 53 0.19 50 1 0.00 ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16 Consensus pattern (45 bp): ACTAGACAACACCTTCCGATGGGAAGGGCAAAATAGGAATTGACA Found at i:18776 original size:32 final size:32 Alignment explanation

Indices: 18730--18793 Score: 94 Period size: 32 Copynumber: 2.0 Consensus size: 32 18720 ATTTCATCAT * * 18730 TTACTTAAAGGTTCAAT-TTTTATTTACAAAAA 1 TTACTTAAAAGTTCAATGTTTTAATTA-AAAAA 18762 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA 1 TTACTTAAAAGTTCAATGTTTTAATTAAAAAA 18794 CTCAATCATT Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 32 21 0.72 33 8 0.28 ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42 Consensus pattern (32 bp): TTACTTAAAAGTTCAATGTTTTAATTAAAAAA Found at i:18994 original size:51 final size:51 Alignment explanation

Indices: 18929--19102 Score: 180 Period size: 51 Copynumber: 3.5 Consensus size: 51 18919 AAGACCACAC * * ** 18929 TTTTATTTACAAATTAATCATCAA-TTCCATCATTTGGTTCAAAGATATCAT 1 TTTTATTTACAAATTAATCA-CAAGTTCAATCACTTAATTCAAAGATATCAT * * 18980 TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGCTCTCAT 1 TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGATATCAT * * * * * 19031 TTTTATTTGCAAATTACTTACAAGTTCAATCATTTAATTC-----TCTCAT 1 TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGATATCAT * * 19077 TTTTATTTACAAATTACTCAAAAGTT 1 TTTTATTTACAAATTAATCACAAGTT 19103 TAATTATTAG Statistics Matches: 109, Mismatches: 13, Indels: 7 0.84 0.10 0.05 Matches are distributed among these distances: 46 29 0.27 50 3 0.03 51 77 0.71 ACGTcount: A:0.35, C:0.17, G:0.05, T:0.44 Consensus pattern (51 bp): TTTTATTTACAAATTAATCACAAGTTCAATCACTTAATTCAAAGATATCAT Found at i:19498 original size:13 final size:14 Alignment explanation

Indices: 19477--19508 Score: 57 Period size: 13 Copynumber: 2.4 Consensus size: 14 19467 TCTTTTCCTC 19477 CTTTGTTTTTTTCT 1 CTTTGTTTTTTTCT 19491 CTTT-TTTTTTTCT 1 CTTTGTTTTTTTCT 19504 CTTTG 1 CTTTG 19509 CTGACTGCTT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 13 13 0.76 14 4 0.24 ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78 Consensus pattern (14 bp): CTTTGTTTTTTTCT Found at i:23830 original size:28 final size:28 Alignment explanation

Indices: 23777--23832 Score: 69 Period size: 28 Copynumber: 2.0 Consensus size: 28 23767 GGGGGCATGG * 23777 TTCTTCTTTAACTTTCCTTTATTTACTA 1 TTCTTCTTTAACTTTCCTTTAGTTACTA * * 23805 TTCTTGTTTAA-TTTCCTTGTGGTTACTA 1 TTCTTCTTTAACTTTCCTT-TAGTTACTA 23833 ACTTCTCTCC Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 27 7 0.29 28 17 0.71 ACGTcount: A:0.16, C:0.18, G:0.07, T:0.59 Consensus pattern (28 bp): TTCTTCTTTAACTTTCCTTTAGTTACTA Found at i:27480 original size:16 final size:16 Alignment explanation

Indices: 27456--27486 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 27446 GGAATGATAG * 27456 GTTTTAATCAAAGCAT 1 GTTTCAATCAAAGCAT 27472 GTTTCAATCAAAGCA 1 GTTTCAATCAAAGCA 27487 ATAGTTTTGA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32 Consensus pattern (16 bp): GTTTCAATCAAAGCAT Found at i:28069 original size:44 final size:44 Alignment explanation

Indices: 28019--28158 Score: 226 Period size: 44 Copynumber: 3.1 Consensus size: 44 28009 AGCAACGATT * * 28019 GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGGTTTGACAAAATG 1 GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG * * 28063 GTTTTCAAAAAGAGTCATTGTTTTCAAAAGGTTTTGATAAAACG 1 GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG 28107 GTTTTTCAAAAAGGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG 1 G-TTTTCAAAAA-GAGTCATGGTTTTCAAAAGGTTTTGATAAAATG 28153 GTTTTC 1 GTTTTC 28159 CAAAGTTGTG Statistics Matches: 88, Mismatches: 6, Indels: 3 0.91 0.06 0.03 Matches are distributed among these distances: 44 41 0.47 45 15 0.17 46 32 0.36 ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36 Consensus pattern (44 bp): GTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAAATG Found at i:28541 original size:32 final size:32 Alignment explanation

Indices: 28504--28574 Score: 106 Period size: 32 Copynumber: 2.2 Consensus size: 32 28494 AAAGAAATTA * * 28504 AAAAAAAAAGAAGAGAAAATTGAAAGTGAAAGT 1 AAAAAAAAA-AAGAGAAAATTGAAAGTAAAAGG * 28537 AAAAAAAAAAAGTGAAAATTGAAAGTAAAAGG 1 AAAAAAAAAAAGAGAAAATTGAAAGTAAAAGG 28569 AAAAAA 1 AAAAAA 28575 TTGAAAAGAA Statistics Matches: 35, Mismatches: 3, Indels: 1 0.90 0.08 0.03 Matches are distributed among these distances: 32 26 0.74 33 9 0.26 ACGTcount: A:0.70, C:0.00, G:0.18, T:0.11 Consensus pattern (32 bp): AAAAAAAAAAAGAGAAAATTGAAAGTAAAAGG Found at i:28564 original size:26 final size:27 Alignment explanation

Indices: 28530--28581 Score: 79 Period size: 27 Copynumber: 2.0 Consensus size: 27 28520 AAATTGAAAG 28530 TGAAAGTAAAA-AAAAAAAGTGAAAAT 1 TGAAAGTAAAAGAAAAAAAGTGAAAAT * * 28556 TGAAAGTAAAAGGAAAAAATTGAAAA 1 TGAAAGTAAAAGAAAAAAAGTGAAAA 28582 GAAAGTGAAA Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 26 11 0.48 27 12 0.52 ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15 Consensus pattern (27 bp): TGAAAGTAAAAGAAAAAAAGTGAAAAT Found at i:28566 original size:19 final size:19 Alignment explanation

Indices: 28518--28572 Score: 52 Period size: 18 Copynumber: 3.3 Consensus size: 19 28508 AAAAAGAAGA * 28518 GAAAATTGAAAGTGAAAGT 1 GAAAATTGAAAGTAAAAGT 28537 -AAAA---AAA--AAAAGT 1 GAAAATTGAAAGTAAAAGT 28550 GAAAATTGAAAGTAAAAG- 1 GAAAATTGAAAGTAAAAGT 28568 GAAAA 1 GAAAA 28573 AATTGAAAAG Statistics Matches: 29, Mismatches: 1, Indels: 13 0.67 0.02 0.30 Matches are distributed among these distances: 13 5 0.17 14 4 0.14 15 3 0.10 17 3 0.10 18 9 0.31 19 5 0.17 ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15 Consensus pattern (19 bp): GAAAATTGAAAGTAAAAGT Found at i:28585 original size:25 final size:25 Alignment explanation

Indices: 28519--28595 Score: 84 Period size: 25 Copynumber: 3.0 Consensus size: 25 28509 AAAAGAAGAG * * 28519 AAAATTGAAAGTGAAAGTAAAA-AAA 1 AAAATTGAAA-AGAAAGTAAAAGGAA * 28544 AAAAGTGAAAATTGAAAGTAAAAGGAA 1 AAAATTGAAAA--GAAAGTAAAAGGAA * 28571 AAAATTGAAAAGAAAGTGAAAGGAA 1 AAAATTGAAAAGAAAGTAAAAGGAA 28596 GGGTGAGGTT Statistics Matches: 44, Mismatches: 5, Indels: 6 0.80 0.09 0.11 Matches are distributed among these distances: 25 22 0.50 26 10 0.23 27 12 0.27 ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14 Consensus pattern (25 bp): AAAATTGAAAAGAAAGTAAAAGGAA Found at i:28935 original size:13 final size:13 Alignment explanation

Indices: 28901--28943 Score: 54 Period size: 13 Copynumber: 3.4 Consensus size: 13 28891 GTAAAAAATG 28901 AAAGAAAAA-AAA 1 AAAGAAAAAGAAA 28913 AGAAG-AAAAGAAA 1 A-AAGAAAAAGAAA * 28926 AAAGAAAAAGGAA 1 AAAGAAAAAGAAA 28939 AAAGA 1 AAAGA 28944 GGATGAAGAA Statistics Matches: 27, Mismatches: 1, Indels: 5 0.82 0.03 0.15 Matches are distributed among these distances: 12 8 0.30 13 19 0.70 ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00 Consensus pattern (13 bp): AAAGAAAAAGAAA Found at i:28942 original size:7 final size:7 Alignment explanation

Indices: 28893--28941 Score: 55 Period size: 7 Copynumber: 6.7 Consensus size: 7 28883 AAGTGCATGT 28893 AAAAAATG 1 AAAAAA-G 28901 AAAGAAA- 1 AAA-AAAG 28908 AAAAAAG 1 AAAAAAG 28915 AAGAAAAG 1 AA-AAAAG 28923 AAAAAAG 1 AAAAAAG * 28930 AAAAAGG 1 AAAAAAG 28937 AAAAA 1 AAAAA 28942 GAGGATGAAG Statistics Matches: 37, Mismatches: 1, Indels: 7 0.82 0.02 0.16 Matches are distributed among these distances: 6 3 0.08 7 21 0.57 8 10 0.27 9 3 0.08 ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02 Consensus pattern (7 bp): AAAAAAG Found at i:29290 original size:50 final size:50 Alignment explanation

Indices: 29231--29331 Score: 148 Period size: 50 Copynumber: 2.0 Consensus size: 50 29221 GAAGTTTTAT * * * * 29231 AATAAGATTGCATTTCATTTGTGAGTCCAATATCAAGATTCGATTTTCAA 1 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGATTTTCAA * * 29281 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTTGCTTTTCAA 1 AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGATTTTCAA 29331 A 1 A 29332 GGGCATTTTA Statistics Matches: 45, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 50 45 1.00 ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37 Consensus pattern (50 bp): AATAAGATTGCATTCCATTTATGAGTCCAAGATCAAAATTCGATTTTCAA Found at i:30009 original size:68 final size:68 Alignment explanation

Indices: 29853--30097 Score: 296 Period size: 68 Copynumber: 3.6 Consensus size: 68 29843 AATGCTTCGA * * * * * 29853 CTTTTCCATAAGTCAAACTCGTTTCCACACGAGTCAATTGAAGCTTTGGTTCCATCCAAGCATTC 1 CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATT-TAGCATTGGTTCCATCCAAGCA-AC * 29918 AGGGG 64 AGAGG * * * 29923 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGCCACTTTAGCCTTGGTTCCATCCAAGCAACAG 1 CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATTTAGCATTGGTTCCATCCAAGCAACAG 29988 AGG 66 AGG * ** * 29991 CTTTTCCACAAG-CTAAACTCGTTTCCATACGAGATAGTTTAAGCATTGGTTCCATCCAAGCAAC 1 CTTTTCCACAAGTC-AAACTCGTTTCCACACGAGCCAATTT-AGCATTGGTTCCATCCAAGCAAC * 30055 A-TGG 64 AGAGG * * 30059 CTTTTCCACAAGTCAAACTCGTTTCCATAAGAGCCAATT 1 CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATT 30098 CAAGTAGCAT Statistics Matches: 154, Mismatches: 18, Indels: 8 0.86 0.10 0.04 Matches are distributed among these distances: 67 1 0.01 68 74 0.48 69 44 0.29 70 35 0.23 ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28 Consensus pattern (68 bp): CTTTTCCACAAGTCAAACTCGTTTCCACACGAGCCAATTTAGCATTGGTTCCATCCAAGCAACAG AGG Found at i:30321 original size:47 final size:47 Alignment explanation

Indices: 30236--30725 Score: 560 Period size: 47 Copynumber: 10.4 Consensus size: 47 30226 ATTCAAGCAA * * 30236 TCTTCTCTCGCTTCCACGCGAGTTTGCAACTCAGTGACCAAAGTTGG 1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG ** * * * 30283 TCTTCTCTCGCTTCCATACGAATTTTCAATTTAATGACCAAAGTTGG 1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG * * * 30330 TATTCTCTCGCTTCCACGCGAGTTTGCAACTCAGTGACCAAAGTTGG 1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG * * 30377 TCTTCTCTCGCTTCCACGCGAGCTTGCAATTTATTGACCAAAGTTGG 1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG * 30424 TCTTCTCTCGCTTCCACGC-AGGTTCT-CAATTTAGTGGCCAAAGTTGG 1 TCTTCTCTCGCTTCCACGCGA-GTT-TGCAATTTAGTGACCAAAGTTGG * * 30471 -CTTTCTCTCGCTTCCACGCGAATTCT-CAATTCAGTGACCAAAGTTGG 1 TC-TTCTCTCGCTTCCACGCGAGTT-TGCAATTTAGTGACCAAAGTTGG * * 30518 TCTTCTCTCGCTTCCATGCGAGTTTGCAATTTAGTGGCCAAAGTTGG 1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG * * * * * 30565 -CATTTTCTCG-TTTCACGCGAGTTTACAGTTTGGTGACCAAAGTTGG 1 TC-TTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG * * * * * * * 30611 TCTTTTCGCGCTTCCATGCGAGTCTACAATCTAATGACCAAAGTTGG 1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG * * * * * * 30658 TCTTTTCTCGCTTCCAGGCGAGTCTACAATTTAGTGACAAAAATTGG 1 TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG * * 30705 TCTTTTATCGCTTCCACGCGA 1 TCTTCTCTCGCTTCCACGCGA 30726 ATCTGCAAGG Statistics Matches: 381, Mismatches: 53, Indels: 18 0.84 0.12 0.04 Matches are distributed among these distances: 46 41 0.11 47 337 0.88 48 3 0.01 ACGTcount: A:0.21, C:0.26, G:0.20, T:0.34 Consensus pattern (47 bp): TCTTCTCTCGCTTCCACGCGAGTTTGCAATTTAGTGACCAAAGTTGG Found at i:31631 original size:6 final size:6 Alignment explanation

Indices: 31620--31646 Score: 54 Period size: 6 Copynumber: 4.5 Consensus size: 6 31610 AAAGCAAAGC 31620 AAATCT AAATCT AAATCT AAATCT AAA 1 AAATCT AAATCT AAATCT AAATCT AAA 31647 GCAGAATTAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 21 1.00 ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30 Consensus pattern (6 bp): AAATCT Found at i:32450 original size:6 final size:6 Alignment explanation

Indices: 32439--32472 Score: 68 Period size: 6 Copynumber: 5.7 Consensus size: 6 32429 GAGATTAATT 32439 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGT 1 GTGTAA GTGTAA GTGTAA GTGTAA GTGTAA GTGT 32473 GTGATTTGTG Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 28 1.00 ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35 Consensus pattern (6 bp): GTGTAA Found at i:32618 original size:10 final size:10 Alignment explanation

Indices: 32603--32628 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 32593 GAGGACTCTA 32603 GAATTTTCTG 1 GAATTTTCTG 32613 GAATTTTCTG 1 GAATTTTCTG 32623 GAATTT 1 GAATTT 32629 GGCAGCAACT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50 Consensus pattern (10 bp): GAATTTTCTG Done.