Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold693

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: 92958
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:2027 original size:49 final size:49

Alignment explanation

Indices: 1972--2166 Score: 309 Period size: 49 Copynumber: 4.0 Consensus size: 49 1962 TTCGTTTTCT * * * 1972 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC * * * 2021 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC * * 2070 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC 2119 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT 1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACA-AATCACAT 2167 GTTCACATGT Statistics Matches: 137, Mismatches: 8, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 49 131 0.96 50 6 0.04 ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24 Consensus pattern (49 bp): CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC Found at i:3520 original size:37 final size:37 Alignment explanation

Indices: 3420--3527 Score: 177 Period size: 36 Copynumber: 3.0 Consensus size: 37 3410 TACGTATGAT * 3420 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC * 3455 CACCTATCACTTTGT-TCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC 3491 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC 1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC 3528 TAAAGCTATC Statistics Matches: 67, Mismatches: 3, Indels: 4 0.91 0.04 0.05 Matches are distributed among these distances: 35 9 0.13 36 37 0.55 37 21 0.31 ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35 Consensus pattern (37 bp): CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC Found at i:3570 original size:52 final size:52 Alignment explanation

Indices: 3491--3759 Score: 370 Period size: 52 Copynumber: 5.2 Consensus size: 52 3481 TAAGTGTAGC * * ** 3491 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT 1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT * * 3544 CACTTTTCACTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT 1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT 3596 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT 1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT * * 3648 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT 1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT * ** * 3694 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT 1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT 3746 CACTTTGTCACTTG 1 CACTTT-TCACTTG 3760 ATCAGAAGTA Statistics Matches: 194, Mismatches: 15, Indels: 14 0.87 0.07 0.06 Matches are distributed among these distances: 46 43 0.22 49 1 0.01 52 135 0.70 53 15 0.08 ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36 Consensus pattern (52 bp): CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT Found at i:3665 original size:46 final size:46 Alignment explanation

Indices: 3593--3765 Score: 231 Period size: 46 Copynumber: 3.7 Consensus size: 46 3583 AGCTATCACT * 3593 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGC 1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC * 3638 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC 1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC * ** 3684 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC 1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC * 3736 TACCACTTATCACTTTGTCACTTGATCAGA 1 TATCACTTATCACTTTGTCACTTGATCAGA 3766 AGTACTCAAA Statistics Matches: 113, Mismatches: 8, Indels: 13 0.84 0.06 0.10 Matches are distributed among these distances: 45 12 0.11 46 59 0.52 48 1 0.01 50 1 0.01 52 40 0.35 ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35 Consensus pattern (46 bp): TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC Found at i:3677 original size:98 final size:98 Alignment explanation

Indices: 3491--3765 Score: 415 Period size: 98 Copynumber: 2.7 Consensus size: 98 3481 TAAGTGTAGC * * 3491 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT 1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC---T---TT * 3556 GTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT 59 GTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT ** 3596 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT 1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT * 3661 GATCAGATAAGTATAGCCGAAGCTATTACTTAT 66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT * * 3694 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT 1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT 3759 GATCAGA 66 GATCAGA 3766 AGTACTCAAA Statistics Matches: 160, Mismatches: 10, Indels: 7 0.90 0.06 0.04 Matches are distributed among these distances: 98 108 0.68 101 1 0.01 104 42 0.26 105 9 0.06 ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35 Consensus pattern (98 bp): CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT GATCAGATAAGTATAGCCGAAGCTATCACTTAT Found at i:7034 original size:37 final size:37 Alignment explanation

Indices: 6970--7041 Score: 101 Period size: 37 Copynumber: 1.9 Consensus size: 37 6960 TTTTCATAAT * * * 6970 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA 1 TTCACTTTTCCACTTTCAATCAATATTCAATTCAAAA 7007 TTCACTTTTCCA-TTTCAAGTCAATATTCAATTCAA 1 TTCACTTTTCCACTTTCAA-TCAATATTCAATTCAA 7042 TTCCACATAT Statistics Matches: 31, Mismatches: 3, Indels: 2 0.86 0.08 0.06 Matches are distributed among these distances: 36 5 0.16 37 26 0.84 ACGTcount: A:0.32, C:0.22, G:0.01, T:0.44 Consensus pattern (37 bp): TTCACTTTTCCACTTTCAATCAATATTCAATTCAAAA Found at i:7195 original size:23 final size:23 Alignment explanation

Indices: 7169--7221 Score: 88 Period size: 23 Copynumber: 2.3 Consensus size: 23 7159 ATAAGTGCCA * 7169 CACTGATATGTAGCCGAAGCTAC 1 CACTGATATGTAGCCAAAGCTAC * 7192 CACTGAAATGTAGCCAAAGCTAC 1 CACTGATATGTAGCCAAAGCTAC 7215 CACTGAT 1 CACTGAT 7222 CAATAACACT Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21 Consensus pattern (23 bp): CACTGATATGTAGCCAAAGCTAC Found at i:15590 original size:42 final size:42 Alignment explanation

Indices: 15543--15626 Score: 168 Period size: 42 Copynumber: 2.0 Consensus size: 42 15533 TGCTTGCATT 15543 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC 1 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC 15585 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC 1 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC 15627 TATTTCTTCT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 42 42 1.00 ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26 Consensus pattern (42 bp): AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC Found at i:16378 original size:51 final size:51 Alignment explanation

Indices: 16265--16378 Score: 122 Period size: 52 Copynumber: 2.2 Consensus size: 51 16255 ACTTATACAG ** * * * 16265 ACAATAATGCACAAGAGGACTATGACTCATTAAACTTTATCAAAATTAAAGT 1 ACAATAATTTACAAGAGGACGATGACTCATTAAACTTTA-CAAAAGTAAAGC * * * * 16317 TCAATAATTTACAAGAGTACGATGACTCACTTATACTTTA-ATAAGTAAAGC 1 ACAATAATTTACAAGAGGACGATGACTCA-TTAAACTTTACAAAAGTAAAGC 16368 ACAATAATTTA 1 ACAATAATTTA 16379 TAAAAGGAAG Statistics Matches: 51, Mismatches: 10, Indels: 3 0.80 0.16 0.05 Matches are distributed among these distances: 51 18 0.35 52 24 0.47 53 9 0.18 ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30 Consensus pattern (51 bp): ACAATAATTTACAAGAGGACGATGACTCATTAAACTTTACAAAAGTAAAGC Found at i:29466 original size:31 final size:31 Alignment explanation

Indices: 29425--29492 Score: 91 Period size: 31 Copynumber: 2.2 Consensus size: 31 29415 TTACAATTTG * * 29425 GTCACTGAACTATTCGAAAGTTTTCATTTAA 1 GTCACTGAACTATTCAAAAATTTTCATTTAA * * * 29456 GTCATTGAACTATTTAAAAATTTTTATTTAA 1 GTCACTGAACTATTCAAAAATTTTCATTTAA 29487 GTCACT 1 GTCACT 29493 AGGTTGTTAA Statistics Matches: 31, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43 Consensus pattern (31 bp): GTCACTGAACTATTCAAAAATTTTCATTTAA Found at i:31473 original size:19 final size:18 Alignment explanation

Indices: 31418--31469 Score: 61 Period size: 19 Copynumber: 2.8 Consensus size: 18 31408 TCTTAAATAT 31418 TTATATAATTATATATAAA 1 TTATATAATTATATAT-AA * 31437 TTAT-TCAATTTTGATATAA 1 TTATAT-AATTAT-ATATAA 31456 TTATATAATTATAT 1 TTATATAATTATAT 31470 TATATTTTCT Statistics Matches: 28, Mismatches: 2, Indels: 7 0.76 0.05 0.19 Matches are distributed among these distances: 18 3 0.11 19 20 0.71 20 5 0.18 ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52 Consensus pattern (18 bp): TTATATAATTATATATAA Found at i:32408 original size:34 final size:34 Alignment explanation

Indices: 32365--32433 Score: 138 Period size: 34 Copynumber: 2.0 Consensus size: 34 32355 ATATCCAAAA 32365 TCTTGCTACCCTATTACCACCTACTGCCATCTTT 1 TCTTGCTACCCTATTACCACCTACTGCCATCTTT 32399 TCTTGCTACCCTATTACCACCTACTGCCATCTTT 1 TCTTGCTACCCTATTACCACCTACTGCCATCTTT 32433 T 1 T 32434 TTGATCTTCA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 34 35 1.00 ACGTcount: A:0.17, C:0.38, G:0.06, T:0.39 Consensus pattern (34 bp): TCTTGCTACCCTATTACCACCTACTGCCATCTTT Found at i:34712 original size:14 final size:14 Alignment explanation

Indices: 34693--34721 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 34683 TGTCTTATTG 34693 TCTTTTCAAAGCTA 1 TCTTTTCAAAGCTA 34707 TCTTTTCAAAGCTA 1 TCTTTTCAAAGCTA 34721 T 1 T 34722 TTACTAAGAC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45 Consensus pattern (14 bp): TCTTTTCAAAGCTA Found at i:35285 original size:12 final size:12 Alignment explanation

Indices: 35268--35292 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 35258 GTACAGTATC 35268 TTTCTCATTGAA 1 TTTCTCATTGAA 35280 TTTCTCATTGAA 1 TTTCTCATTGAA 35292 T 1 T 35293 GAATGCAAAT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52 Consensus pattern (12 bp): TTTCTCATTGAA Found at i:47868 original size:21 final size:21 Alignment explanation

Indices: 47844--47886 Score: 52 Period size: 21 Copynumber: 2.0 Consensus size: 21 47834 TTAATAATTT 47844 TTTATATGAAATTTTAA-TTAA 1 TTTAT-TGAAATTTTAACTTAA * * 47865 TTTATTTAATTTTTAACTTAA 1 TTTATTGAAATTTTAACTTAA 47886 T 1 T 47887 AAATTGCCTC Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 20 9 0.47 21 10 0.53 ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58 Consensus pattern (21 bp): TTTATTGAAATTTTAACTTAA Found at i:55054 original size:66 final size:66 Alignment explanation

Indices: 54948--55076 Score: 249 Period size: 66 Copynumber: 2.0 Consensus size: 66 54938 CATTTCAGAG 54948 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA 1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA 55013 T 66 T * 55014 AGCACACTCCTGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAA 1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAA 55077 TATAAACTCA Statistics Matches: 62, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 66 62 1.00 ACGTcount: A:0.27, C:0.36, G:0.18, T:0.19 Consensus pattern (66 bp): AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA T Found at i:55288 original size:57 final size:60 Alignment explanation

Indices: 55195--55342 Score: 214 Period size: 57 Copynumber: 2.5 Consensus size: 60 55185 ACCCTAATTC * * * 55195 GGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A 1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA 55253 -GATCACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA 1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA 55314 GGATCACCCGTCCGGGCTAGATCCTTTTT 1 GGATCACCCGTCCGGGCTAGATCCTTTTT 55343 ACCGTCAATT Statistics Matches: 80, Mismatches: 3, Indels: 9 0.87 0.03 0.10 Matches are distributed among these distances: 56 6 0.08 57 45 0.56 60 1 0.01 61 1 0.01 62 21 0.26 63 6 0.08 ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30 Consensus pattern (60 bp): GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA Found at i:58475 original size:41 final size:41 Alignment explanation

Indices: 58430--58622 Score: 305 Period size: 41 Copynumber: 4.7 Consensus size: 41 58420 GGTTTTAAAA 58430 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG 1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG * 58471 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG 1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG * * 58512 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG 1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG * * 58553 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTTTAAG 1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG * * 58594 CCTAACAGGGCTAAGTGCCAGTGAATCTG 1 CCTAGCA-GGCTAAGTGCCGGTG-ATCTG 58623 TTTAAATTAA Statistics Matches: 139, Mismatches: 11, Indels: 2 0.91 0.07 0.01 Matches are distributed among these distances: 41 121 0.87 42 13 0.09 43 5 0.04 ACGTcount: A:0.27, C:0.21, G:0.28, T:0.23 Consensus pattern (41 bp): CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG Found at i:62705 original size:6 final size:6 Alignment explanation

Indices: 62694--62731 Score: 69 Period size: 6 Copynumber: 6.5 Consensus size: 6 62684 AGCGCATGAA 62694 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT -GAGAT AGA 1 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGA 62732 AGTGTCAGGA Statistics Matches: 31, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 5 5 0.16 6 26 0.84 ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16 Consensus pattern (6 bp): AGAGAT Found at i:72326 original size:36 final size:36 Alignment explanation

Indices: 72279--72350 Score: 135 Period size: 36 Copynumber: 2.0 Consensus size: 36 72269 TGAGGGAAAG 72279 AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA 1 AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA * 72315 AAAACTAGTCTGTGAGCATGGAAGTAGTAAACTACA 1 AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA 72351 TAAGCTCATC Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 36 35 1.00 ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21 Consensus pattern (36 bp): AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA Found at i:73841 original size:2 final size:2 Alignment explanation

Indices: 73834--73887 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 73824 TTGGGAGAAT 73834 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 73876 AG AG AG AG AG AG 1 AG AG AG AG AG AG 73888 CGCAAAAGCA Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:78325 original size:19 final size:19 Alignment explanation

Indices: 78301--78338 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 78291 TATCAAATAA * * 78301 AAAATTCATGTGTAAAATT 1 AAAATTCATATATAAAATT 78320 AAAATTCATATATAAAATT 1 AAAATTCATATATAAAATT 78339 GCATAAAATT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37 Consensus pattern (19 bp): AAAATTCATATATAAAATT Found at i:78382 original size:31 final size:29 Alignment explanation

Indices: 78313--78395 Score: 112 Period size: 29 Copynumber: 2.8 Consensus size: 29 78303 AATTCATGTG * * 78313 TAAAATTAAAATTCATATATAAAATTGCA 1 TAAAATTAAAATTTATATATAATATTGCA * 78342 TAAAATTAAAATTTATGTATAATATTGTACA 1 TAAAATTAAAATTTATATATAATATTG--CA * 78373 TTAAATTAAAATTTATATATAAT 1 TAAAATTAAAATTTATATATAAT 78396 TTTCAGAATT Statistics Matches: 47, Mismatches: 5, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 29 24 0.51 31 23 0.49 ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41 Consensus pattern (29 bp): TAAAATTAAAATTTATATATAATATTGCA Found at i:85005 original size:18 final size:18 Alignment explanation

Indices: 84979--85013 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 84969 TAAATTATGC * 84979 ATAACAAAATAAAAATAT 1 ATAAAAAAATAAAAATAT * 84997 ATAAAAAAATGAAAATA 1 ATAAAAAAATAAAAATA 85014 GAGCATTTGT Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20 Consensus pattern (18 bp): ATAAAAAAATAAAAATAT Found at i:85676 original size:7 final size:7 Alignment explanation

Indices: 85664--85694 Score: 62 Period size: 7 Copynumber: 4.4 Consensus size: 7 85654 ATTGAACCTA 85664 AAATTTG 1 AAATTTG 85671 AAATTTG 1 AAATTTG 85678 AAATTTG 1 AAATTTG 85685 AAATTTG 1 AAATTTG 85692 AAA 1 AAA 85695 AGTAAAATGA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 24 1.00 ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39 Consensus pattern (7 bp): AAATTTG Found at i:86264 original size:5 final size:5 Alignment explanation

Indices: 86232--86261 Score: 51 Period size: 5 Copynumber: 6.0 Consensus size: 5 86222 ATAGAATTTA * 86232 GTTCG GTTCG GTTCG GTTCG GTTCG ATTCG 1 GTTCG GTTCG GTTCG GTTCG GTTCG GTTCG 86262 ATTTTGAATA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 5 24 1.00 ACGTcount: A:0.03, C:0.20, G:0.37, T:0.40 Consensus pattern (5 bp): GTTCG Found at i:86980 original size:29 final size:29 Alignment explanation

Indices: 86938--86999 Score: 79 Period size: 29 Copynumber: 2.1 Consensus size: 29 86928 TTTTATTAAA * * 86938 ATGAAGAGACTAAAAAAACTTAAAATAGT 1 ATGAAAAGACTAAAAAAACTTAAAATAAT * * * 86967 ATGAAAAGACTAAAATATCTTAGAATAAT 1 ATGAAAAGACTAAAAAAACTTAAAATAAT 86996 ATGA 1 ATGA 87000 CTAATTATAA Statistics Matches: 28, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 29 28 1.00 ACGTcount: A:0.56, C:0.06, G:0.13, T:0.24 Consensus pattern (29 bp): ATGAAAAGACTAAAAAAACTTAAAATAAT Done.