Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold77

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1619719
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29

Warning! 197531 characters in sequence are not A, C, G, or T


File 2 of 4

Found at i:1748 original size:23 final size:23

Alignment explanation

Indices: 1721--1765 Score: 90 Period size: 23 Copynumber: 2.0 Consensus size: 23 1711 AGGTTGACTT 1721 CCATTGTTCTCGAGAACAATAGA 1 CCATTGTTCTCGAGAACAATAGA 1744 CCATTGTTCTCGAGAACAATAG 1 CCATTGTTCTCGAGAACAATAG 1766 CTCTATTGTT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 22 1.00 ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27 Consensus pattern (23 bp): CCATTGTTCTCGAGAACAATAGA Found at i:1923 original size:2 final size:2 Alignment explanation

Indices: 1916--1941 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 1906 TTTCTCTTTA 1916 TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC 1942 CTCCCTTTTA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1992 original size:1 final size:1 Alignment explanation

Indices: 1959--1984 Score: 52 Period size: 1 Copynumber: 26.0 Consensus size: 1 1949 TTATTTCCAC 1959 AAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 1985 GAGAAAAAGT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 25 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:3517 original size:200 final size:200 Alignment explanation

Indices: 3174--3573 Score: 800 Period size: 200 Copynumber: 2.0 Consensus size: 200 3164 CACCCCCACT 3174 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT 1 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT 3239 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT 66 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT 3304 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG 131 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG 3369 TGTAA 196 TGTAA 3374 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT 1 TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT 3439 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT 66 AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT 3504 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG 131 GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG 3569 TGTAA 196 TGTAA 3574 ACGTATATAT Statistics Matches: 200, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 200 200 1.00 ACGTcount: A:0.29, C:0.14, G:0.14, T:0.41 Consensus pattern (200 bp): TATACCACCAAAAAGAGTTTGTCCACTGGGACCTCTACCATGACCCTGGCATATCAGACTATTTT AGATGATGGTAAGTTTTTTATTTCCTCTGTTGACTCTGTTTTTTGAACAAAAATTTGATATTGAT GTTTAATTGAAATTAAAAATATTTGTCCCTCAGTTAAATATTTAGTTTATTCATATATTTTGTTG TGTAA Found at i:8184 original size:14 final size:13 Alignment explanation

Indices: 8165--8196 Score: 55 Period size: 14 Copynumber: 2.4 Consensus size: 13 8155 ATGTATAGTT 8165 TTTTTTTGCTATAA 1 TTTTTTTGCTAT-A 8179 TTTTTTTGCTATA 1 TTTTTTTGCTATA 8192 TTTTT 1 TTTTT 8197 CTTTCTTATT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 13 6 0.33 14 12 0.67 ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72 Consensus pattern (13 bp): TTTTTTTGCTATA Found at i:14446 original size:166 final size:166 Alignment explanation

Indices: 14155--14581 Score: 766 Period size: 166 Copynumber: 2.6 Consensus size: 166 14145 NNNNNNATTT 14155 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT 1 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT * 14220 GGTTCTTGAGAAGAAGATTTTTTAAACATTTTCCTAAGGTATATCTATGTTAAATTTGAACCCCG 66 GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCTAAGGTATATCTATGTTAAATTTGAACCCCG 14285 CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG 131 CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG * * * 14321 TTACAATTTAGAATCTTCACTATGTATACAAGCTTATGTGTAAATATTGGCATTTCTGGTGCAGT 1 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT * * 14386 GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCT-ATGTATTTCTATGTTAAACTTTGAACCCC 66 GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCTAAGGTATATCTATGTTAAA-TTTGAACCCC * 14450 GCCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTT 130 GCCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG 14487 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT 1 TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT 14552 GGTTCTTGAGAAGAAGATTTTTAAAGACAT 66 GGTTCTTGAGAAGAAGATTTTTAAA-ACAT 14582 GCACCCTATA Statistics Matches: 249, Mismatches: 10, Indels: 3 0.95 0.04 0.01 Matches are distributed among these distances: 165 16 0.06 166 229 0.92 167 4 0.02 ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37 Consensus pattern (166 bp): TTACAATTTAGAACCTTCACTATATATACAAGCTTTTGTGTAAATATTGGCATTTCTGGTGCAGT GGTTCTTGAGAAGAAGATTTTTAAAACATTTTCCTAAGGTATATCTATGTTAAATTTGAACCCCG CCTGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTG Found at i:14755 original size:4 final size:4 Alignment explanation

Indices: 14746--14791 Score: 67 Period size: 4 Copynumber: 11.8 Consensus size: 4 14736 AAAGTTTACA * * 14746 GACG GACG GACA GACA GACG GACG GACG GACG GACG GAC- GACG GAC 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GAC 14792 AACGGGTGAT Statistics Matches: 39, Mismatches: 2, Indels: 2 0.91 0.05 0.05 Matches are distributed among these distances: 3 3 0.08 4 36 0.92 ACGTcount: A:0.30, C:0.26, G:0.43, T:0.00 Consensus pattern (4 bp): GACG Found at i:14760 original size:12 final size:12 Alignment explanation

Indices: 14743--14796 Score: 67 Period size: 12 Copynumber: 4.7 Consensus size: 12 14733 TGAAAAGTTT 14743 ACAGACGGACGG 1 ACAGACGGACGG * 14755 ACAGACAGACGG 1 ACAGACGGACGG * 14767 ACGGACGGACGG 1 ACAGACGGACGG * 14779 ACGGAC-GACGG 1 ACAGACGGACGG 14790 ACA-ACGG 1 ACAGACGG 14797 GTGATCAGAA Statistics Matches: 37, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 10 2 0.05 11 8 0.22 12 27 0.73 ACGTcount: A:0.33, C:0.26, G:0.41, T:0.00 Consensus pattern (12 bp): ACAGACGGACGG Found at i:19448 original size:2 final size:2 Alignment explanation

Indices: 19441--19501 Score: 122 Period size: 2 Copynumber: 30.5 Consensus size: 2 19431 TCCAGTTCAT 19441 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 19483 GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA G 19502 CACCTGTCAC Statistics Matches: 59, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 59 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:22071 original size:44 final size:44 Alignment explanation

Indices: 21996--22914 Score: 1245 Period size: 44 Copynumber: 20.8 Consensus size: 44 21986 GATCAAGGTG * *** 21996 CATGCTTATGCTTTATAACCATACAAAGATCCCATCCAATGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * * * 22040 CATCCTTTTGCGTTATAATCATACAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * 22084 CATGCTTATGCTTTATAACCATATAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * * *** 22128 CATGCTTATGTTTTTTAACCATACAAAGATCCCATCCAATGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * ** 22172 CATGCTTATGCTTTATAACCATATAGAGATCCCATCCAGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * 22216 CATGCTTTTGCTTTATAACCATACAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * 22260 CATGCTTATGCGTTATAACCATACAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * 22304 CATGCTTTTGCTTTATAACCATACAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * 22348 CATGCTTATGTTTTATAACCATACAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * * * 22392 CATGCTTATGTTTTATAACCATACAGATATCCCATCTGGAGGGT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * ** 22436 CATGCTTATG-TGTTATAACCATATAGAGATCCCATCCAGTGGTT 1 CATGCTTATGCT-TTATAACCATACAGAGATCCCATCTGGTGGTT * * 22480 CATGCTTTTGCTTTATAACCATACAGAGATCCAATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * * * * 22524 CATGCTTATGCATTATAATCATTCAAAGATCCCATCTGGTTGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * * 22568 CATGCTTTTGCTTTATAATCATACAGAGATCCCATCTGGTGGTC 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * 22612 CATGCTTGTGCTTTATAACCATACAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * * 22656 CATGCTTTTGCTTTATATTAACTATACAAAGATCCCATCTGGTGGTT 1 CATGCTTATGC-TT-TA-TAACCATACAGAGATCCCATCTGGTGGTT * 22703 CCTGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * * * 22747 CATGCTTTTGCTTTATATTAACTATACAAAGATCCCATCTGATGGTT 1 CATGCTTATGC-TT-TA-TAACCATACAGAGATCCCATCTGGTGGTT * * * 22794 CCTGCTTATTCTTTATAACCATACAAAGATCCCATCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * * 22838 CCTGCTTATGCTTTATAACCATACAGAGATCCCTTCTGGTGGTT 1 CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT * 22882 CATGCTT-T--TTCT-TAACCATACAAAGATCCCATC 1 CATGCTTATGCTT-TATAACCATACAGAGATCCCATC 22915 AGGCATCTGG Statistics Matches: 778, Mismatches: 88, Indels: 21 0.88 0.10 0.02 Matches are distributed among these distances: 41 21 0.03 42 1 0.00 43 2 0.00 44 667 0.86 45 9 0.01 46 8 0.01 47 70 0.09 ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36 Consensus pattern (44 bp): CATGCTTATGCTTTATAACCATACAGAGATCCCATCTGGTGGTT Found at i:29460 original size:40 final size:40 Alignment explanation

Indices: 29416--29493 Score: 147 Period size: 40 Copynumber: 1.9 Consensus size: 40 29406 CTTAATGATA * 29416 ATAGTGTAAACCTAAACAGTTTCTATATTGAAATTTTATC 1 ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTATC 29456 ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTA 1 ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTA 29494 GGCAGATCTG Statistics Matches: 37, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 40 37 1.00 ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40 Consensus pattern (40 bp): ATAGTGTAAACCTAAACAGTTTATATATTGAAATTTTATC Found at i:30627 original size:10 final size:10 Alignment explanation

Indices: 30599--30630 Score: 55 Period size: 10 Copynumber: 3.2 Consensus size: 10 30589 ATACACAGTT * 30599 TATCACAAAA 1 TATCACAATA 30609 TATCACAATA 1 TATCACAATA 30619 TATCACAATA 1 TATCACAATA 30629 TA 1 TA 30631 CATACTTTAG Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 10 21 1.00 ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28 Consensus pattern (10 bp): TATCACAATA Found at i:30810 original size:6 final size:6 Alignment explanation

Indices: 30799--30842 Score: 72 Period size: 6 Copynumber: 7.3 Consensus size: 6 30789 TGCTATACCC 30799 TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TCGGCG TCGGCG TC 1 TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TCGGCG TCGGCG TC 30843 CGGACCTGGT Statistics Matches: 36, Mismatches: 0, Indels: 4 0.90 0.00 0.10 Matches are distributed among these distances: 5 2 0.06 6 32 0.89 7 2 0.06 ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18 Consensus pattern (6 bp): TCGGCG Found at i:31189 original size:19 final size:19 Alignment explanation

Indices: 31167--31206 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 31157 TTTCGGATGC * * 31167 TGGAGGAGGTTAAGGTTTT 1 TGGAGCAGGTTAAAGTTTT 31186 TGGAGCAGGTTAAAGTTTT 1 TGGAGCAGGTTAAAGTTTT 31205 TG 1 TG 31207 TTGCGGGTGC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38 Consensus pattern (19 bp): TGGAGCAGGTTAAAGTTTT Found at i:31197 original size:177 final size:176 Alignment explanation

Indices: 30985--31497 Score: 688 Period size: 177 Copynumber: 2.9 Consensus size: 176 30975 CTAAATTTTA * * * 30985 GATGCTGGAGGAGTTTAAGGTTGTTGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG 1 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG * * 31050 CAATATCTAAGTTACTGCTGGTCCGTACTTCACCAAACTTGCATGGATGGTGTGCCTTATGATAC 66 CAATATCTAAGTTACTACTGGTCC-TACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATAC * * * 31115 TGATGCACCAGACAGGCTTGAGTGCTGAATCTAAGCTATAGGTTTCG 130 TGATGCACCTGACAGGCTTGAATGCTGAATCTAAGCAATAGGTTTCG * * 31162 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCGGGTGCCCATTGATAG 1 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG * * * 31227 CAATATCTAAGTTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGATGCGTCTTATGATAC 66 CAATATCTAAGTTACTACTGGTCCT-ACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATAC * * 31292 TGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGGTTTCG 130 TGATGCACCTGACAGGCTTGAATGCTGAATCTAAGCAATAGGTTTCG ** * *** * 31339 GATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAGATAAAGTTTTTGAAACAGGTGCCCTCTG 1 GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGG-T---TAAAGTTTTTGTTGCAGGTGCCCTTTG * * * * * 31404 AT-G-ATGATATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTA 62 ATAGCA--ATATCTAAGTTACTACTGGTCC-TACTTCACCAAACTTGCATGGATGGTGTGTCTTA 31467 TGATACTGATGCACCTGACAGGCTTGAATGC 124 TGATACTGATGCACCTGACAGGCTTGAATGC 31498 ATAGTCTGGT Statistics Matches: 295, Mismatches: 33, Indels: 12 0.87 0.10 0.04 Matches are distributed among these distances: 176 1 0.00 177 190 0.64 178 1 0.00 179 1 0.00 180 1 0.00 181 100 0.34 182 1 0.00 ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33 Consensus pattern (176 bp): GATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAG CAATATCTAAGTTACTACTGGTCCTACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACT GATGCACCTGACAGGCTTGAATGCTGAATCTAAGCAATAGGTTTCG Found at i:32187 original size:20 final size:20 Alignment explanation

Indices: 32164--32206 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 32154 TATGATAAAG 32164 TATTGTATGATATGAAACAA 1 TATTGTATGATATGAAACAA * * 32184 TATTGTTTGATATGATACAA 1 TATTGTATGATATGAAACAA 32204 TAT 1 TAT 32207 GATATCATAT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42 Consensus pattern (20 bp): TATTGTATGATATGAAACAA Found at i:32317 original size:28 final size:28 Alignment explanation

Indices: 32268--32321 Score: 76 Period size: 28 Copynumber: 1.9 Consensus size: 28 32258 TCAATTTTTT 32268 TGATATTTTATGATATGATATTGTATCA 1 TGATATTTTATGATATGATATTGTATCA 32296 TGATATTGTTATG-TAT-AGTATTGTAT 1 TGATATT-TTATGATATGA-TATTGTAT 32322 ATTATGATAC Statistics Matches: 24, Mismatches: 0, Indels: 4 0.86 0.00 0.14 Matches are distributed among these distances: 27 1 0.04 28 18 0.75 29 5 0.21 ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52 Consensus pattern (28 bp): TGATATTTTATGATATGATATTGTATCA Found at i:32482 original size:15 final size:15 Alignment explanation

Indices: 32449--32582 Score: 72 Period size: 15 Copynumber: 8.4 Consensus size: 15 32439 ATATTCTATA * ** 32449 ATATTGTATCATACA 1 ATATTGTATAATATG 32464 ATATTGTATAATATG 1 ATATTGTATAATATG 32479 ATATTGGTTTCAGTAATATAG 1 ATATT-G--T-A-TAATAT-G * * * 32500 A-ATTATATCACATG 1 ATATTGTATAATATG * * 32514 AAATTGTATTATATG 1 ATATTGTATAATATG * 32529 ATATTGTAATATTATATA 1 ATATTGT-ATA--ATATG * * 32547 ATATTGTATCATACG 1 ATATTGTATAATATG * 32562 ATATTGTATGATATG 1 ATATTGTATAATATG 32577 ATATTG 1 ATATTG 32583 GTTTTTATGA Statistics Matches: 92, Mismatches: 17, Indels: 20 0.71 0.13 0.16 Matches are distributed among these distances: 14 2 0.02 15 59 0.64 16 4 0.04 17 3 0.03 18 12 0.13 19 1 0.01 20 9 0.10 21 2 0.02 ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44 Consensus pattern (15 bp): ATATTGTATAATATG Found at i:32528 original size:50 final size:47 Alignment explanation

Indices: 32466--32632 Score: 156 Period size: 50 Copynumber: 3.4 Consensus size: 47 32456 ATCATACAAT * 32466 ATTGTATAATATGATATTGGTTTCAGTAATATAGAATTATATCACATGAA 1 ATTGTATTATATGATATTGGTTT-A-TAATATA-AATTATATCACATGAA * * * * * * 32516 ATTGTATTATATGATATT-GTAATATTATATAATATTGTATCATACGAT 1 ATTGTATTATATGATATTGGT-TTATAATATAA-ATTATATCACATGAA * * * * 32564 ATTGTATGATATGATATTGGTTTTTATGATATATTATCATATCACATGAA 1 ATTGTATTATATGATATTGG--TTTATAATATA-AATTATATCACATGAA 32614 ATTGTATTATATGATATTG 1 ATTGTATTATATGATATTG 32633 TTATATATTA Statistics Matches: 94, Mismatches: 17, Indels: 12 0.76 0.14 0.10 Matches are distributed among these distances: 47 1 0.01 48 34 0.36 49 4 0.04 50 54 0.57 51 1 0.01 ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46 Consensus pattern (47 bp): ATTGTATTATATGATATTGGTTTATAATATAAATTATATCACATGAA Found at i:32543 original size:18 final size:18 Alignment explanation

Indices: 32520--32554 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 32510 CATGAAATTG * 32520 TATTATATGATATTGTAA 1 TATTATATAATATTGTAA 32538 TATTATATAATATTGTA 1 TATTATATAATATTGTA 32555 TCATACGATA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51 Consensus pattern (18 bp): TATTATATAATATTGTAA Found at i:32551 original size:98 final size:98 Alignment explanation

Indices: 32432--32643 Score: 311 Period size: 98 Copynumber: 2.2 Consensus size: 98 32422 CTATGATACA * 32432 ATATTGT-ATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGG-TTTCAGTAA 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTTCA-TAA * 32495 TATAGAATTATATCACATGAAATTGTATTATATG 65 TATAGAATCATATCACATGAAATTGTATTATATG * * * * 32529 ATATTGTAATATTATATAATATTGTATCATACGATATTGTATGATATGATATTGGTTTTTATGAT 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTTCATAAT ** 32594 ATATTATCATATCACATGAAATTGTATTATATG 66 ATAGAATCATATCACATGAAATTGTATTATATG 32627 ATATTGTTATATATTAT 1 ATATTG-TA-ATATTAT 32644 TGTGTCATAT Statistics Matches: 103, Mismatches: 8, Indels: 5 0.89 0.07 0.04 Matches are distributed among these distances: 97 7 0.07 98 83 0.81 99 6 0.06 100 7 0.07 ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47 Consensus pattern (98 bp): ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTTCATAAT ATAGAATCATATCACATGAAATTGTATTATATG Found at i:32632 original size:15 final size:15 Alignment explanation

Indices: 32511--32633 Score: 79 Period size: 15 Copynumber: 7.7 Consensus size: 15 32501 ATTATATCAC * 32511 ATGAAATTGTATTAT 1 ATGATATTGTATTAT 32526 ATGATATTGTAATATTAT 1 ATGATATTG---TATTAT * * 32544 ATAATATTGTATCAT 1 ATGATATTGTATTAT * * 32559 ACGATATTGTATGAT 1 ATGATATTGTATTAT * 32574 ATGATATTGGT-TTTT 1 ATGATATT-GTATTAT 32589 ATGATATAT-TATCATAT 1 ATGATAT-TGTAT--TAT * 32606 CACATGAAATTGTATTAT 1 ---ATGATATTGTATTAT 32624 ATGATATTGT 1 ATGATATTGT 32634 TATATATTAT Statistics Matches: 84, Mismatches: 12, Indels: 24 0.70 0.10 0.20 Matches are distributed among these distances: 14 1 0.01 15 51 0.61 16 3 0.04 17 2 0.02 18 17 0.20 19 1 0.01 20 9 0.11 ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47 Consensus pattern (15 bp): ATGATATTGTATTAT Found at i:34630 original size:20 final size:20 Alignment explanation

Indices: 34605--34644 Score: 80 Period size: 20 Copynumber: 2.0 Consensus size: 20 34595 CACAACTACC 34605 CAAAGTCCAAGCTCTTGTTA 1 CAAAGTCCAAGCTCTTGTTA 34625 CAAAGTCCAAGCTCTTGTTA 1 CAAAGTCCAAGCTCTTGTTA 34645 AAATGGTTCT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30 Consensus pattern (20 bp): CAAAGTCCAAGCTCTTGTTA Found at i:44464 original size:2 final size:2 Alignment explanation

Indices: 44457--44483 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 44447 TCCCCCGAAA 44457 AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG A 44484 ATTAGTTTTC Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:61089 original size:37 final size:38 Alignment explanation

Indices: 61048--61122 Score: 98 Period size: 37 Copynumber: 2.0 Consensus size: 38 61038 TACATAATAC * * * 61048 CTCCAATATTGCAGTAGTTCAATGT-TAGATTCAGTAT 1 CTCCAACATTGCAGTAGTTAAATGTATAAATTCAGTAT * * 61085 CTCCAACATTGTATTAGTTAAATGTATAAATTCAGTAT 1 CTCCAACATTGCAGTAGTTAAATGTATAAATTCAGTAT 61123 AGAAGGTTTA Statistics Matches: 32, Mismatches: 5, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 37 21 0.66 38 11 0.34 ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39 Consensus pattern (38 bp): CTCCAACATTGCAGTAGTTAAATGTATAAATTCAGTAT Found at i:67142 original size:12 final size:12 Alignment explanation

Indices: 67125--67170 Score: 65 Period size: 12 Copynumber: 3.8 Consensus size: 12 67115 ACCGGTTTCA * 67125 CCGTCTGTCTGT 1 CCGTCTGTCCGT 67137 CCGTCTGTCCGT 1 CCGTCTGTCCGT * 67149 CCGTCAGTCCGT 1 CCGTCTGTCCGT * 67161 CTGTCTGTCC 1 CCGTCTGTCC 67171 CACTTCAGTT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 12 30 1.00 ACGTcount: A:0.02, C:0.39, G:0.24, T:0.35 Consensus pattern (12 bp): CCGTCTGTCCGT Found at i:83564 original size:34 final size:34 Alignment explanation

Indices: 83526--83592 Score: 98 Period size: 34 Copynumber: 2.0 Consensus size: 34 83516 TTGTACACAT * * 83526 GTACATGTATGTGCAGAGAGGTGGATAGTATATA 1 GTACATGTATGTGCAGAGAAGTGGATAATATATA ** 83560 GTACATGTATGTGTGGAGAAGTGGATAATATAT 1 GTACATGTATGTGCAGAGAAGTGGATAATATAT 83593 GTGTGTGTGT Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 34 29 1.00 ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31 Consensus pattern (34 bp): GTACATGTATGTGCAGAGAAGTGGATAATATATA Found at i:83778 original size:31 final size:31 Alignment explanation

Indices: 83743--83821 Score: 104 Period size: 31 Copynumber: 2.5 Consensus size: 31 83733 CATGAAGGAG * * 83743 TGGATAGTGTATTCATGTATTTGTGGAGGTA 1 TGGATAGTGTATACATGTATTTCTGGAGGTA * * * 83774 TGGATAGTTTATACATATATTTCTGGAGGTT 1 TGGATAGTGTATACATGTATTTCTGGAGGTA * 83805 TGGATAGTGTATGCATG 1 TGGATAGTGTATACATG 83822 CATGTGTAGA Statistics Matches: 40, Mismatches: 8, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 31 40 1.00 ACGTcount: A:0.24, C:0.05, G:0.29, T:0.42 Consensus pattern (31 bp): TGGATAGTGTATACATGTATTTCTGGAGGTA Found at i:84008 original size:65 final size:65 Alignment explanation

Indices: 83933--84288 Score: 397 Period size: 67 Copynumber: 5.3 Consensus size: 65 83923 TCTGGTGGTA * * * * * * 83933 TGGATAGTGTATATATGCATATGTAAAGGGAATGAATAGTTCATAAATATGTGTATATATAGGGT 1 TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTCATAAATATATGTGTATATAGGGT * * * * * 83998 TGGATAGTGTATACATATATATGTAGAGGGAATGGATAGTTCATAAATACATGTGTATAAAAAGG 1 TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTCATAAATATATGTGTAT--ATAGG 84063 GT 64 GT * * * * * 84065 TGGGTAGTGTATACATGTATATACAAAGGTCTATTGGATAGTTCATAAATATATGTGTATATAGA 1 TGGATAGTGTATACATGTATATGCAAAGG--GAATGGATAGTTCATAAATATATGTGTATATAGG 84130 GT 64 GT * * * 84132 TGGATAGTGTATACATGCATATGAAAAGGGAATGGATAGTTCATATTAAATACATGTGTATATAG 1 TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTC--A-TAAATATATGTGTATATAG 84197 GGT 63 GGT * * * * * * 84200 TGGGTAGTTTATACATGTATATACAAAGGTCTATTGGATAGTTCATAAATATTTGTGTATATAGG 1 TGGATAGTGTATACATGTATATGCAAAGG--GAATGGATAGTTCATAAATATATGTGTATATAGG 84265 GT 64 GT * 84267 TGGGTAGTGTATACATGTATAT 1 TGGATAGTGTATACATGTATAT 84289 ATATATATAT Statistics Matches: 245, Mismatches: 37, Indels: 16 0.82 0.12 0.05 Matches are distributed among these distances: 65 61 0.25 67 102 0.42 68 45 0.18 69 26 0.11 70 11 0.04 ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36 Consensus pattern (65 bp): TGGATAGTGTATACATGTATATGCAAAGGGAATGGATAGTTCATAAATATATGTGTATATAGGGT Found at i:84250 original size:135 final size:133 Alignment explanation

Indices: 83968--84288 Score: 500 Period size: 135 Copynumber: 2.4 Consensus size: 133 83958 AAGGGAATGA * * * * * 83968 ATAGTTCATAAATATGTGTATATATAGGGTTGGATAGTGTATACATATATATGTAGAGGGAATGG 1 ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATATGAAAAGGGAATGG 84033 ATAGTTCATAAATACATGTGTATAAAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTCTA 66 ATAGTTCATAAATACATGTGTAT-AAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTCTA 84098 TTGG 130 TTGG * * 84102 ATAGTTCATAAATATATGTGTATATAGAGTTGGATAGTGTATACATGCATATGAAAAGGGAATGG 1 ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATATGAAAAGGGAATGG * * 84167 ATAGTTCATATTAAATACATGTGTAT-ATAGGGTTGGGTAGTTTATACATGTATATACAAAGGTC 66 ATAGTTC--A-TAAATACATGTGTATAAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTC 84231 TATTGG 128 TATTGG * * 84237 ATAGTTCATAAATATTTGTGTATATAGGGTTGGGTAGTGTATACATGTATAT 1 ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATAT 84289 ATATATATAT Statistics Matches: 171, Mismatches: 13, Indels: 5 0.90 0.07 0.03 Matches are distributed among these distances: 134 65 0.38 135 90 0.53 136 1 0.01 137 15 0.09 ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36 Consensus pattern (133 bp): ATAGTTCATAAATATATGTGTATATAGGGTTGGATAGTGTATACATGTATATGAAAAGGGAATGG ATAGTTCATAAATACATGTGTATAAAAGGGTTGGGTAGTGTATACATGTATATACAAAGGTCTAT TGG Found at i:84326 original size:108 final size:108 Alignment explanation

Indices: 84190--84396 Score: 265 Period size: 108 Copynumber: 1.9 Consensus size: 108 84180 AATACATGTG * * * * * 84190 TATATAGGGTTGGGTAGTTTATACATGTATATACAAAGGTCTATTGGATAGTTCATAAATAT-T- 1 TATATAGGGTTGGATAGTGTAGACATGTATATACAAAGG--GAATGGATAGTTCATAAATATGTG * * * 84253 TGTGTATATAGGGTTGGGTAGTGTATACATGTATATATATATATA 64 TGTATATATAGGGTTGGATAGCGTATACATGTATATATATATATA * * ** * 84298 TATATAGGGTTGGATCGTGTAGAGATGTATATGTAGAGGGAATGGATAGTTCATAAATATGTGTG 1 TATATAGGGTTGGATAGTGTAGACATGTATATACAAAGGGAATGGATAGTTCATAAATATGTGTG 84363 TATATATAGGGTTGGATAGCGTATACATGTATAT 66 TATATATAGGGTTGGATAGCGTATACATGTATAT 84397 GTAGAGGGAA Statistics Matches: 84, Mismatches: 13, Indels: 4 0.83 0.13 0.04 Matches are distributed among these distances: 106 19 0.23 107 1 0.01 108 64 0.76 ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38 Consensus pattern (108 bp): TATATAGGGTTGGATAGTGTAGACATGTATATACAAAGGGAATGGATAGTTCATAAATATGTGTG TATATATAGGGTTGGATAGCGTATACATGTATATATATATATA Found at i:84369 original size:67 final size:64 Alignment explanation

Indices: 84296--84513 Score: 339 Period size: 63 Copynumber: 3.4 Consensus size: 64 84286 TATATATATA * * * * 84296 TATATATAGGGTTGGATCGTGTAGAGATGTATATGTAGAGGGAATGGATAGTTCATAAATATGTG 1 TATATATAGGATTGGATAGTGTA-ACATGTATATGTAGAGGGAATGGATAGGTCATAAATA--TG 84361 TG 63 TG * * 84363 TATATATAGGGTTGGATAGCGTATACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG 1 TATATATAGGATTGGATAGTGTA-ACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG 84428 TATATATAGGATTGGATAGTGT-ACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG 1 TATATATAGGATTGGATAGTGTAACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG 84491 TATATATAGGATTGGATAGTGTA 1 TATATATAGGATTGGATAGTGTA 84514 TGAATGGATA Statistics Matches: 143, Mismatches: 7, Indels: 5 0.92 0.05 0.03 Matches are distributed among these distances: 63 63 0.44 65 24 0.17 67 56 0.39 ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34 Consensus pattern (64 bp): TATATATAGGATTGGATAGTGTAACATGTATATGTAGAGGGAATGGATAGGTCATAAATATGTG Found at i:84545 original size:48 final size:49 Alignment explanation

Indices: 84467--84563 Score: 160 Period size: 48 Copynumber: 2.0 Consensus size: 49 84457 TATGTAGAGG * 84467 GAATGGATAGGTCATAAATATGTGT-ATATATAGGATTGGATAGTGTAT 1 GAATGGATAGGTCATAAATATATGTAATATATAGGATTGGATAGTGTAT * 84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTA 1 GAATGGATAGGTCATAAATATATGT-AATATATAGGATTGGATAGTGTA 84564 CATGTATATG Statistics Matches: 46, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 48 24 0.52 50 22 0.48 ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35 Consensus pattern (49 bp): GAATGGATAGGTCATAAATATATGTAATATATAGGATTGGATAGTGTAT Found at i:84559 original size:50 final size:48 Alignment explanation

Indices: 84467--84563 Score: 176 Period size: 50 Copynumber: 2.0 Consensus size: 48 84457 TATGTAGAGG 84467 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT 1 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT 84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTA 1 GAATGGATAGGTCAT-AA-ATATGTGTATATATAGGATTGGATAGTGTA 84564 CATGTATATG Statistics Matches: 47, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 48 15 0.32 49 2 0.04 50 30 0.64 ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35 Consensus pattern (48 bp): GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT Found at i:84571 original size:243 final size:245 Alignment explanation

Indices: 84027--84637 Score: 651 Period size: 243 Copynumber: 2.5 Consensus size: 245 84017 TATGTAGAGG * * * * ** * 84027 GAATGGATAGTTCATAAATACATGTGTATAAAAAGGGTTGGGTAGTGTATACATGTATATACAAA 1 GAATGGATAG-TCATAAATATATGTGTATATATAGGGTTGGATAGTG--TACATGTATATGTAGA * * * * 84092 GGTCTATTGGATAGTTCATAAATATATGTG--TATATAGAGTTGGATAGTGTATACATGCATATG 63 GG--GAATGGATAGTTCATAAATAT-TGTGTATATATAGGGTTGGATAGTGTATACATGTATATG * * * * 84155 AAAAGGGAATGGATAGTTCATATTAAATACATGTGTATATAGGGTTGGGTAGTTTATACATGTAT 125 AAAAGGGAATGGATAGGTCA-ATTAAATACATGTATATATAGGATTGGATAG-TTATACATGTAT * * * * * * * 84220 ATACAAAGGTCTATTGGATAGTTCATAAATATTTGTGTATATAGGGTTGGGTAGTGTAT 188 ATACAAAGG-CGAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT * * * 84279 -ACAT-G-TA-T-AT--ATATA--TATATATATAGGGTTGGATCGTGTAGAGATGTATATGTAGA 1 GA-ATGGATAGTCATAAATATATGTGTATATATAGGGTTGGATAGTGT--ACATGTATATGTAGA * * 84335 GGGAATGGATAGTTCATAAATATGTGTGTATATATAGGGTTGGATAGCGTATACATGTATATGTA 63 GGGAATGGATAGTTCATAAATAT-TGTGTATATATAGGGTTGGATAGTGTATACATGTATATGAA * ** * ** 84400 GAGGGAATGGATAGGTC-A-TAAATATGTGTATATATAGGATTGGATAG-TGTACATGTATATGT 127 AAGGGAATGGATAGGTCAATTAAATACATGTATATATAGGATTGGATAGTTATACATGTATATAC * 84462 AGAGG-GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT 192 AAAGGCGAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT * 84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGG 1 GAATGGATA-GTCATAAATATATGTGTATATATAGGGTTGGATAGTGTACATGTATATGTAGAGG * * 84580 GAATGGATAGGTCATAAATA-TGTGTATATATAGGATTGGATAGTGTATACATGTATAT 65 GAATGGATAGTTCATAAATATTGTGTATATATAGGGTTGGATAGTGTATACATGTATAT 84638 ACAAAGGTCT Statistics Matches: 302, Mismatches: 42, Indels: 41 0.78 0.11 0.11 Matches are distributed among these distances: 236 43 0.14 237 2 0.01 238 18 0.06 240 25 0.08 241 63 0.21 243 117 0.39 245 25 0.08 247 2 0.01 248 1 0.00 250 2 0.01 251 2 0.01 252 2 0.01 ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35 Consensus pattern (245 bp): GAATGGATAGTCATAAATATATGTGTATATATAGGGTTGGATAGTGTACATGTATATGTAGAGGG AATGGATAGTTCATAAATATTGTGTATATATAGGGTTGGATAGTGTATACATGTATATGAAAAGG GAATGGATAGGTCAATTAAATACATGTATATATAGGATTGGATAGTTATACATGTATATACAAAG GCGAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT Found at i:84600 original size:113 final size:111 Alignment explanation

Indices: 84404--84627 Score: 430 Period size: 113 Copynumber: 2.0 Consensus size: 111 84394 TATGTAGAGG 84404 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGGGA 1 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGGGA 84469 ATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT 66 ATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT 84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGG 1 GAATGGATAGGTCAT-AA-ATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGG 84580 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT 64 GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT 84628 ACATGTATAT Statistics Matches: 111, Mismatches: 0, Indels: 2 0.98 0.00 0.02 Matches are distributed among these distances: 111 15 0.14 112 2 0.02 113 94 0.85 ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34 Consensus pattern (111 bp): GAATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTACATGTATATGTAGAGGGA ATGGATAGGTCATAAATATGTGTATATATAGGATTGGATAGTGTAT Found at i:84623 original size:63 final size:66 Alignment explanation

Indices: 84515--84637 Score: 216 Period size: 63 Copynumber: 1.9 Consensus size: 66 84505 GATAGTGTAT 84515 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTG-TACATGTATATGTAGAG 1 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGATACATGTATATGTAGAG 84579 G 66 G 84580 GAATGGATAGGTCAT-AA-ATATGTGTATATATAGGATTGGATAGTGTATACATGTATAT 1 GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTG-ATACATGTATAT 84638 ACAAAGGTCT Statistics Matches: 56, Mismatches: 0, Indels: 4 0.93 0.00 0.07 Matches are distributed among these distances: 63 28 0.50 64 2 0.04 65 26 0.46 ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35 Consensus pattern (66 bp): GAATGGATAGGTCATAAATATATGTGTATATATAGGATTGGATAGTGATACATGTATATGTAGAG G Found at i:85800 original size:35 final size:35 Alignment explanation

Indices: 85761--85962 Score: 181 Period size: 35 Copynumber: 5.5 Consensus size: 35 85751 TTATGTCAAA * 85761 GTAAGTGATACAGACCCTGTGTCTGTCATGTCCAT 1 GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT * * * 85796 GTAAGTGATGCAGACCAAGTGGTTGCCATGTTCATGTACCAGGGGG 1 GTAAGTGATGCAGACC--CT-G-TGTC-TG-TCATGT-CCA----T ** * * 85842 GTAAGTGATGCAGACCAAGTGGT-TGCCATGTTCAT 1 GTAAGTGATGCAGACCCTGT-GTCTGTCATGTCCAT * * 85877 GTAAGTGCTGCAGACCCTGTGTCTGTCATGTCCAA 1 GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT * * 85912 GTAAGTGATACAGACCCTGTGTCTGTCATGTTCAT 1 GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT 85947 GTAAGTGATGCAGACC 1 GTAAGTGATGCAGACC 85963 AAGTGGTTGT Statistics Matches: 133, Mismatches: 21, Indels: 26 0.74 0.12 0.14 Matches are distributed among these distances: 34 2 0.02 35 87 0.65 37 1 0.01 38 1 0.01 39 5 0.04 40 7 0.05 41 8 0.06 42 4 0.03 43 2 0.02 46 16 0.12 ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28 Consensus pattern (35 bp): GTAAGTGATGCAGACCCTGTGTCTGTCATGTCCAT Found at i:86093 original size:151 final size:149 Alignment explanation

Indices: 85752--86040 Score: 456 Period size: 151 Copynumber: 1.9 Consensus size: 149 85742 CAGTCCTTGT * 85752 TATGTCAAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTG 1 TATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTG * * ** 85817 GTTGCCATGTTCATGTACCAGGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATGTTCATGTAAG 66 GTTGCCATGTTCATGTACCA-GGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAG * * 85882 TGCTGCAGACCCTGTGTCTG 130 TGCTACAGACCCTGTGTCTA * 85902 TCATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTTCATGTAAGTGATGCAGACCAAGT 1 T-ATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGT * * 85967 GGTTG-TATGTTCATGTACC-GGGGGTAAGTGATGCAGACCAAGTGGTTGTCATCTCCAAATAAG 65 GGTTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAG 86030 TGCTACAGACC 130 TGCTACAGACC 86041 AAGTTGATGT Statistics Matches: 129, Mismatches: 9, Indels: 4 0.91 0.06 0.03 Matches are distributed among these distances: 148 49 0.38 150 14 0.11 151 66 0.51 ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28 Consensus pattern (149 bp): TATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTG GTTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGT GCTACAGACCCTGTGTCTA Found at i:86110 original size:151 final size:150 Alignment explanation

Indices: 85753--86113 Score: 401 Period size: 151 Copynumber: 2.4 Consensus size: 150 85743 AGTCCTTGTT * ** ** 85753 ATGTCAAAGTAAGTGATACAGACCCTGTGTCTGTCATGTCCATGTAAGTGATGCAGACCAAGTGG 1 ATGTCCAAGTAAGTGATACAGACCAAGTGTCTGTCATGTCCACATAAGTGATGCAGACCAAGTGG * * ** 85818 TTGCCATGTTCATGTACCAGGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATGTTCATGTAAGT 66 TTGCCATGTTCATGTACCA-GGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGT * * 85883 GCTGCAGACCCTGTGTCTGTC 130 GCTACAGACCCTGTGTCTATC ** * ** 85904 ATGTCCAAGTAAGTGATACAGACCCTGTGTCTGTCATGTTCATGTAAGTGATGCAGACCAAGTGG 1 ATGTCCAAGTAAGTGATACAGACCAAGTGTCTGTCATGTCCACATAAGTGATGCAGACCAAGTGG * * 85969 TTG-TATGTTCATGTACC-GGGGGTAAGTGATGCAGACCAAGTGGTTGTCATCTCCAAATAAGTG 66 TTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGTG * 86032 CTACAGACCAAGTTGATGT-TAAT- 131 CTACAGACC---CTG-TGTCT-ATC * * * * 86055 ATGTCCAAGTAAGTGTTCCAGACCAAGTG-CTTGTCATGTCCAACAT-TGTGCTGCAGACC 1 ATGTCCAAGTAAGTGATACAGACCAAGTGTC-TGTCATGTCC-ACATAAGTGATGCAGACC 86114 TTGTGTTTTT Statistics Matches: 183, Mismatches: 20, Indels: 14 0.84 0.09 0.06 Matches are distributed among these distances: 148 49 0.27 150 14 0.08 151 114 0.62 152 6 0.03 ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28 Consensus pattern (150 bp): ATGTCCAAGTAAGTGATACAGACCAAGTGTCTGTCATGTCCACATAAGTGATGCAGACCAAGTGG TTGCCATGTTCATGTACCAGGGGGTAAGTGATGCAGACCAAGTGGTTGCCATCTCCAAATAAGTG CTACAGACCCTGTGTCTATC Found at i:86158 original size:69 final size:69 Alignment explanation

Indices: 86000--86221 Score: 239 Period size: 69 Copynumber: 3.1 Consensus size: 69 85990 GTAAGTGATG * * * 86000 CAGACCAAGTGGTTGTCATCTCCAAATAAGTGCTACAGACCAAGTTGATGTTAATATGTCCAAGT 1 CAGACCAAGTGGTTGTCATGTCCAAATATGTGCTACAGACC---TTG-TGTTATTATGTCCAAGT * 86065 AAGTGTTC 62 ATGTGTTC * * * 86073 CAGACCAAGTGCTTGTCATGTCCAACAT-TGTGCTGCAGACCTTGTGTTTTTATGTCCAAGTATG 1 CAGACCAAGTGGTTGTCATGTCCAA-ATATGTGCTACAGACCTTGTGTTATTATGTCCAAGTATG 86137 TGTTC 65 TGTTC * * * ** * * 86142 CAGACCAAGTGGTTGTCATGCCCAAGTATGTGCTACACACCAAGTGGTTGTCATGTCCAAGTATG 1 CAGACCAAGTGGTTGTCATGTCCAAATATGTGCTACAGACCTTGT-GTTATTATGTCCAAGTATG * * 86207 TGCTG 65 TGTTC 86212 CAGACCAAGT 1 CAGACCAAGT 86222 TGATGTTGTG Statistics Matches: 128, Mismatches: 18, Indels: 9 0.83 0.12 0.06 Matches are distributed among these distances: 68 1 0.01 69 58 0.45 70 33 0.26 73 34 0.27 74 2 0.02 ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30 Consensus pattern (69 bp): CAGACCAAGTGGTTGTCATGTCCAAATATGTGCTACAGACCTTGTGTTATTATGTCCAAGTATGT GTTC Found at i:86235 original size:35 final size:35 Alignment explanation

Indices: 85852--86221 Score: 210 Period size: 35 Copynumber: 10.3 Consensus size: 35 85842 GTAAGTGATG * * * * * 85852 CAGACCAAGTGGTTGCCATGTTCATGTAAGTGCTG 1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA ** * * 85887 CAGACCCTGT-GTCTGTCATGTCCAAGTAAGTGATA 1 CAGACCAAGTGGT-TGTCATGTCCAAGTATGTGCTA ** * * * * * 85922 CAGACCCTGT-GTCTGTCATGTTCATGTAAGTGATG 1 CAGACCAAGTGGT-TGTCATGTCCAAGTATGTGCTA ** * * * 85957 CAGACCAAGTGGTTGTATGTTCATGTACCGGGGGTAAGTGATG 1 CAGACCAAGT-G--GT-TG-TCATGT-CC--AAGTATGTGCTA * * * 86000 CAGACCAAGTGGTTGTCATCTCCAAATAAGTGCTA 1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA * * * * 86035 CAGACCAAGTTGATGTTAAT-ATGTCCAAGTAAGTGTTC 1 CAGACCAAG-TG--GTT-GTCATGTCCAAGTATGTGCTA * * * 86073 CAGACCAAGTGCTTGTCATGTCCAA-CATTGTGCTG 1 CAGACCAAGTGGTTGTCATGTCCAAGTA-TGTGCTA ** * * * * 86108 CAGACCTTGT-GTTTTTATGTCCAAGTATGTGTTC 1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA * 86142 CAGACCAAGTGGTTGTCATGCCCAAGTATGTGCTA 1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA * * 86177 CACACCAAGTGGTTGTCATGTCCAAGTATGTGCTG 1 CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA 86212 CAGACCAAGT 1 CAGACCAAGT 86222 TGATGTTGTG Statistics Matches: 266, Mismatches: 52, Indels: 34 0.76 0.15 0.10 Matches are distributed among these distances: 34 28 0.11 35 164 0.62 36 2 0.01 37 4 0.02 38 31 0.12 39 7 0.03 40 8 0.03 41 1 0.00 42 1 0.00 43 20 0.08 ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30 Consensus pattern (35 bp): CAGACCAAGTGGTTGTCATGTCCAAGTATGTGCTA Found at i:89750 original size:26 final size:26 Alignment explanation

Indices: 89730--89975 Score: 177 Period size: 26 Copynumber: 9.7 Consensus size: 26 89720 CATCCGTTTC * 89730 GATACATTTTATCATTTATCCTGTTT 1 GATACATTTTATCATTTATCCTGTTG * * * 89756 GATACATTTTATCATTAATTCTATTG 1 GATACATTTTATCATTTATCCTGTTG * * 89782 GATACATTTTATTATTCATCCTGTTG 1 GATACATTTTATCATTTATCCTGTTG ** 89808 GATAGTTTTTATCATTTATCCTGTTG 1 GATACATTTTATCATTTATCCTGTTG ** * 89834 GATAC-TTTTGA-CATTTATTAT-TTT 1 GATACATTTT-ATCATTTATCCTGTTG * * 89858 GATACATTTTATCA---ATCATGTTT 1 GATACATTTTATCATTTATCCTGTTG * * * * 89881 GTTACATTATATCATTCA-CACGGTTG 1 GATACATTTTATCATTTATC-CTGTTG * * * * 89907 GATAC-TTTTTTGAATTTATCCTATTA 1 GATACATTTTAT-CATTTATCCTGTTG * * * 89933 GATACATTTCATGATTTATAAC-GTTG 1 GATACATTTTATCATTTAT-CCTGTTG 89959 GATACATTTTATCATTT 1 GATACATTTTATCATTT 89976 GATTGTATGA Statistics Matches: 170, Mismatches: 38, Indels: 24 0.73 0.16 0.10 Matches are distributed among these distances: 22 4 0.02 23 15 0.09 24 8 0.05 25 23 0.14 26 114 0.67 27 6 0.04 ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50 Consensus pattern (26 bp): GATACATTTTATCATTTATCCTGTTG Found at i:91011 original size:15 final size:15 Alignment explanation

Indices: 91001--91033 Score: 66 Period size: 15 Copynumber: 2.2 Consensus size: 15 90991 TATGATATTG 91001 TATCATATGATACAA 1 TATCATATGATACAA 91016 TATCATATGATACAA 1 TATCATATGATACAA 91031 TAT 1 TAT 91034 TGTATCATAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36 Consensus pattern (15 bp): TATCATATGATACAA Found at i:91114 original size:20 final size:20 Alignment explanation

Indices: 91091--91130 Score: 53 Period size: 20 Copynumber: 2.0 Consensus size: 20 91081 TTTTCTTTTC * * 91091 ATATTATACAATATCATATA 1 ATATGATACAATAGCATATA * 91111 ATATGGTACAATAGCATATA 1 ATATGATACAATAGCATATA 91131 TAATGTCTTG Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35 Consensus pattern (20 bp): ATATGATACAATAGCATATA Found at i:98226 original size:165 final size:164 Alignment explanation

Indices: 97825--98281 Score: 442 Period size: 165 Copynumber: 2.8 Consensus size: 164 97815 GTGAATATGC * * ** * * * 97825 AAAATAAGCAAAGTTGTCATTTAATAAAAAGCTGACATCCAATTGGTACAAAAAAAATACCCCAA 1 AAAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTAC-AAAAATATATCCCAA * * ** 97890 CGTATGGCATATCTAAACAAATA--GTGTTAGAATTTCAAGCATCTGCAATGAATTGTTGCTATG 65 CGTATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATGAACAGTTGCTATG * * * * * 97953 AAATTTGTGTCGAAAATTTGTTTAAAACTTATGCT 130 AAATCTGCGACGAAAATTTCTTTAAAACTTAAGCT * * * * * ** * 97988 AGAAATAAACAAAGTTGTCATTTCACAGGAAGTTGACATCTGATAGGTACAGAAATGGATCCCAC 1 A-AAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTACAAAAATATATCCCAA * * * * ** 98053 CATATGGCATGCCTAAACAAACAGTGTGTTAAAACTTCAAGCATCTGTGAT-ACACAGTTGCTGA 65 CGTATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATGA-ACAGTTGCT-A * 98117 -GAAATCCT-CGAC-AAAATTTCTTTGAAAATTTAAGCT 128 TGAAAT-CTGCGACGAAAATTTCTTT-AAAACTTAAGCT * * 98153 GAAAATAAACAAAGTTGTCATTTAACAGGAAGCTGAAATCCGATTGGTACAAAAATATATCCAAA 1 -AAAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTACAAAAATATATCCCAA * * * * 98218 TGTATGGCATATGTCTAAACAAATAGTGTGTTAATATTTTAAGCATCTG-AGATGAATAGTTGCT 65 CGTATGGC--ATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCA-ATGAACAGTTGCT 98282 TGGAAAAATG Statistics Matches: 232, Mismatches: 50, Indels: 20 0.77 0.17 0.07 Matches are distributed among these distances: 163 29 0.12 164 50 0.22 165 105 0.45 166 3 0.01 167 44 0.19 168 1 0.00 ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29 Consensus pattern (164 bp): AAAATAAACAAAGTTGTCATTTAACAGGAAGCTGACATCCGATTGGTACAAAAATATATCCCAAC GTATGGCATGTCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCAATGAACAGTTGCTATGA AATCTGCGACGAAAATTTCTTTAAAACTTAAGCT Found at i:100988 original size:18 final size:17 Alignment explanation

Indices: 100962--101018 Score: 73 Period size: 18 Copynumber: 3.4 Consensus size: 17 100952 CATCAGATCA 100962 TCGTCATCATCATCTTCT 1 TCGTCATCATCATC-TCT * 100980 TCTTCATCAT-A-CTCT 1 TCGTCATCATCATCTCT 100995 TCGTCATCATCATCCTCT 1 TCGTCATCATCAT-CTCT 101013 TCGTCA 1 TCGTCA 101019 AGAATTGACA Statistics Matches: 34, Mismatches: 2, Indels: 6 0.81 0.05 0.14 Matches are distributed among these distances: 15 12 0.35 16 2 0.06 17 1 0.03 18 19 0.56 ACGTcount: A:0.18, C:0.35, G:0.05, T:0.42 Consensus pattern (17 bp): TCGTCATCATCATCTCT Found at i:102428 original size:21 final size:21 Alignment explanation

Indices: 102404--102459 Score: 76 Period size: 21 Copynumber: 2.7 Consensus size: 21 102394 AATTGAAGTA 102404 ATCAACTGAGGAGCAGAGCTG 1 ATCAACTGAGGAGCAGAGCTG * *** 102425 ATCAGCTGAGGAATGGAGCTG 1 ATCAACTGAGGAGCAGAGCTG 102446 ATCAACTGAGGAGC 1 ATCAACTGAGGAGC 102460 TGTGTTGACT Statistics Matches: 28, Mismatches: 7, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 21 28 1.00 ACGTcount: A:0.32, C:0.18, G:0.34, T:0.16 Consensus pattern (21 bp): ATCAACTGAGGAGCAGAGCTG Found at i:105385 original size:66 final size:66 Alignment explanation

Indices: 105279--105416 Score: 197 Period size: 66 Copynumber: 2.1 Consensus size: 66 105269 GGGGAGACTC * * ** * 105279 ATTTTCTGGAACTGATTGACATTTATCATTGATGTTCCACTTAAT-ATTTTTATCCTTAACAAAA 1 ATTTTCTGCAACTGATTGACATTTATCATTCATGCCCCACTTAATGA-TTTTATCCCTAACAAAA 105343 AT 65 AT * 105345 ATTTTCTGCAACTGATTGACATTTATTATTCATGCCCCACTTAATGATTTTATCCCTAACAAAAA 1 ATTTTCTGCAACTGATTGACATTTATCATTCATGCCCCACTTAATGATTTTATCCCTAACAAAAA 105410 T 66 T * 105411 GTTTTC 1 ATTTTC 105417 CCTCATCAGG Statistics Matches: 64, Mismatches: 7, Indels: 2 0.88 0.10 0.03 Matches are distributed among these distances: 66 63 0.98 67 1 0.02 ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43 Consensus pattern (66 bp): ATTTTCTGCAACTGATTGACATTTATCATTCATGCCCCACTTAATGATTTTATCCCTAACAAAAA T Found at i:116085 original size:2 final size:2 Alignment explanation

Indices: 116078--116130 Score: 90 Period size: 2 Copynumber: 26.5 Consensus size: 2 116068 CGTGTTACCG 116078 CT CT CT CT CT CT CT CT CT CT CT C- CAT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT 116120 CT CT CT CT CT C 1 CT CT CT CT CT C 116131 ATTATTTATT Statistics Matches: 49, Mismatches: 0, Indels: 4 0.92 0.00 0.08 Matches are distributed among these distances: 1 1 0.02 2 47 0.96 3 1 0.02 ACGTcount: A:0.02, C:0.51, G:0.00, T:0.47 Consensus pattern (2 bp): CT Found at i:116755 original size:2 final size:2 Alignment explanation

Indices: 116748--116797 Score: 91 Period size: 2 Copynumber: 25.0 Consensus size: 2 116738 TGTCCATGCA * 116748 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 116790 CT CT CT CT 1 CT CT CT CT 116798 GGCACAAACA Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48 Consensus pattern (2 bp): CT Found at i:117683 original size:125 final size:125 Alignment explanation

Indices: 117458--117685 Score: 402 Period size: 125 Copynumber: 1.8 Consensus size: 125 117448 NNNNNNNNNN * * 117458 TAACAGTTGAAATTGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGATAATG 1 TAACAGTTGAAATCGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG 117523 GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCATAATAGTGCCTGTTTGGGAGGG 66 GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCATAATAGTGCCTGTTTGGGAGGG * 117583 TAACAGTTGAAATCGACACCCCGAGGAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG 1 TAACAGTTGAAATCGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG ** * 117648 GTTTTCTCGGGGTGTCAATTTCAACTGTTATCCTCCCA 66 GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCA 117686 AACAGGCACT Statistics Matches: 97, Mismatches: 6, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 125 97 1.00 ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25 Consensus pattern (125 bp): TAACAGTTGAAATCGACACCCCGAGAAAACCATTGTCAACCGACGCGAAGCGGAGGTTGACAATG GTTTTCGAGGGGTGTCAATTTCAACTGTTACCCTCCCATAATAGTGCCTGTTTGGGAGGG Found at i:125964 original size:12 final size:13 Alignment explanation

Indices: 125941--125972 Score: 57 Period size: 12 Copynumber: 2.5 Consensus size: 13 125931 GATCCTGCGC 125941 TACATATGAGTAA 1 TACATATGAGTAA 125954 TACAT-TGAGTAA 1 TACATATGAGTAA 125966 TACATAT 1 TACATAT 125973 CAACAAGATA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 12 12 0.67 13 6 0.33 ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34 Consensus pattern (13 bp): TACATATGAGTAA Found at i:142401 original size:2 final size:2 Alignment explanation

Indices: 142394--142430 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 142384 TGTATTAAAC 142394 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 142431 CAAGCACCAT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:155366 original size:2 final size:2 Alignment explanation

Indices: 155359--155414 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 155349 CGAATTAAAA 155359 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 155401 TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC 155415 CATTTTTAAG Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:160582 original size:31 final size:31 Alignment explanation

Indices: 160541--160990 Score: 519 Period size: 31 Copynumber: 16.1 Consensus size: 31 160531 CGCGCTAACA 160541 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG * 160572 CATAACACGCCGTCGCGCTAA--C-A----- 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160595 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160626 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160657 CACAACACGCCGTCGCGCTAA--C-A----- 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160680 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160711 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160742 CACAACACGCCGTCGCGCTAA--C-A----- 1 CACAACACGCCGTCGCGCTAACGCAACTTTG * 160765 CACAACACGCCGTCGCGCTAACACAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160796 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG * 160827 CATAACACGCCGTCGCGCTAA--C-A----- 1 CACAACACGCCGTCGCGCTAACGCAACTTTG * 160850 CACAACACGCCGTCGCGCTAACACAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160881 CACAACACGCCGTCGCGCTAA--C-A----- 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160904 CACAACACGCCGTCGCGCTAA--C-A----- 1 CACAACACGCCGTCGCGCTAACGCAACTTTG * 160927 CACAACACGCCGTCGCGCTAACACAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160958 CACAACACGCCGTCGCGCTAACGCAACTTTG 1 CACAACACGCCGTCGCGCTAACGCAACTTTG 160989 CA 1 CA 160991 AGTTTCACAG Statistics Matches: 373, Mismatches: 6, Indels: 80 0.81 0.01 0.17 Matches are distributed among these distances: 23 126 0.34 25 5 0.01 26 5 0.01 28 5 0.01 29 5 0.01 31 227 0.61 ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14 Consensus pattern (31 bp): CACAACACGCCGTCGCGCTAACGCAACTTTG Found at i:160612 original size:54 final size:55 Alignment explanation

Indices: 160530--160979 Score: 418 Period size: 54 Copynumber: 8.2 Consensus size: 55 160520 AAACGAGACA * 160530 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACGCAACTTTGCATAACACGCCG 1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG 160584 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCG 1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG 160638 TCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAA-C-A-----CACAACACGCCG 1 TCGCGCTAA--CAA---T-CACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG 160692 TCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCG 1 TCGCGCTAA--CAA---T-CACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG 160754 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCG 1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG * 160808 TCGCGCTAACGCAACTTTGCATAACACGCCGTCGCGCTAA-C-A-----CACAACACGCCG 1 TCGCGCTAA--CAA---T-CACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG 160862 TCGCGCTAACACAACTTTGCACAACACGCCGTCGCGCTAA-C-A-----CACAACACGCCG 1 TCGCGCT-A-ACAA---T-CACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG 160916 TCGCGCTAAC-A-CACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCG 1 TCGCGCTAACAATCACAACACGCCGTCGCGCTAAC-CAACTTTGCACAACACGCCG 160970 TCGCGCTAAC 1 TCGCGCTAAC 160980 GCAACTTTGC Statistics Matches: 358, Mismatches: 4, Indels: 68 0.83 0.01 0.16 Matches are distributed among these distances: 46 21 0.06 48 1 0.00 49 1 0.00 51 1 0.00 52 2 0.01 53 1 0.00 54 255 0.71 55 1 0.00 56 4 0.01 57 3 0.01 59 3 0.01 60 3 0.01 62 62 0.17 ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14 Consensus pattern (55 bp): TCGCGCTAACAATCACAACACGCCGTCGCGCTAACCAACTTTGCACAACACGCCG Found at i:160684 original size:85 final size:85 Alignment explanation

Indices: 160541--160990 Score: 808 Period size: 85 Copynumber: 5.4 Consensus size: 85 160531 CGCGCTAACA * 160541 CACAACACGCCGTCGCGCTAACGCAACTTTGCATAACACGCCGTCGCGCTAACACACAACACGCC 1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC * 160606 GTCGCGCTAACGCAACTTTG 66 GTCGCGCTAACACAACTTTG 160626 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC 1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC * 160691 GTCGCGCTAACGCAACTTTG 66 GTCGCGCTAACACAACTTTG 160711 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC 1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC 160776 GTCGCGCTAACACAACTTTG 66 GTCGCGCTAACACAACTTTG * 160796 CACAACACGCCGTCGCGCTAACGCAACTTTGCATAACACGCCGTCGCGCTAACACACAACACGCC 1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC 160861 GTCGCGCTAACACAACTTTG 66 GTCGCGCTAACACAACTTTG 160881 CACAACACGCCGTCGCGCTAA--C-A-----CACAACACGCCGTCGCGCTAACACACAACACGCC 1 CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC 160938 GTCGCGCTAACACAACTTTG 66 GTCGCGCTAACACAACTTTG 160958 CACAACACGCCGTCGCGCTAACGCAACTTTGCA 1 CACAACACGCCGTCGCGCTAACGCAACTTTGCA 160991 AGTTTCACAG Statistics Matches: 353, Mismatches: 4, Indels: 16 0.95 0.01 0.04 Matches are distributed among these distances: 77 74 0.21 79 1 0.00 80 1 0.00 82 1 0.00 83 1 0.00 85 275 0.78 ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14 Consensus pattern (85 bp): CACAACACGCCGTCGCGCTAACGCAACTTTGCACAACACGCCGTCGCGCTAACACACAACACGCC GTCGCGCTAACACAACTTTG Found at i:160685 original size:23 final size:23 Alignment explanation

Indices: 160657--160701 Score: 90 Period size: 23 Copynumber: 2.0 Consensus size: 23 160647 CGCAACTTTG 160657 CACAACACGCCGTCGCGCTAACA 1 CACAACACGCCGTCGCGCTAACA 160680 CACAACACGCCGTCGCGCTAAC 1 CACAACACGCCGTCGCGCTAAC 160702 GCAACTTTGC Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 22 1.00 ACGTcount: A:0.29, C:0.44, G:0.18, T:0.09 Consensus pattern (23 bp): CACAACACGCCGTCGCGCTAACA Found at i:160791 original size:21 final size:23 Alignment explanation

Indices: 160742--160789 Score: 96 Period size: 23 Copynumber: 2.1 Consensus size: 23 160732 CGCAACTTTG 160742 CACAACACGCCGTCGCGCTAACA 1 CACAACACGCCGTCGCGCTAACA 160765 CACAACACGCCGTCGCGCTAACA 1 CACAACACGCCGTCGCGCTAACA 160788 CA 1 CA 160790 ACTTTGCACA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 25 1.00 ACGTcount: A:0.31, C:0.44, G:0.17, T:0.08 Consensus pattern (23 bp): CACAACACGCCGTCGCGCTAACA Found at i:160850 original size:16 final size:16 Alignment explanation

Indices: 160768--160850 Score: 53 Period size: 16 Copynumber: 5.3 Consensus size: 16 160758 GCTAACACAC 160768 AACACGCCGTCGCGCT 1 AACACGCCGTCGCGCT ** * * * 160784 AACACAACTTTGCAC- 1 AACACGCCGTCGCGCT 160799 AACACGCCGTCGCGCT 1 AACACGCCGTCGCGCT * ** * * * 160815 AACGCAACTTTGC-AT 1 AACACGCCGTCGCGCT 160830 AACACGCCGTCGCGCT 1 AACACGCCGTCGCGCT 160846 AACAC 1 AACAC 160851 ACAACACGCC Statistics Matches: 43, Mismatches: 22, Indels: 4 0.62 0.32 0.06 Matches are distributed among these distances: 15 19 0.44 16 24 0.56 ACGTcount: A:0.28, C:0.39, G:0.18, T:0.16 Consensus pattern (16 bp): AACACGCCGTCGCGCT Found at i:160875 original size:21 final size:23 Alignment explanation

Indices: 160830--160951 Score: 102 Period size: 23 Copynumber: 5.0 Consensus size: 23 160820 AACTTTGCAT 160830 AACACGCCGTCGCGCTAACACAC 1 AACACGCCGTCGCGCTAACACAC 160853 AACACGCCGTCGCGCTAACACAAC 1 AACACGCCGTCGCGCTAACAC-AC ** * * ** 160877 TTTGCACAACACGCCGTCGCGCTA-ACACAC 1 --AACAC-GC-CGTCG-CGC-TAACACA--C 160907 AACACGCCGTCGCGCTAACACAC 1 AACACGCCGTCGCGCTAACACAC 160930 AACACGCCGTCGCGCTAACACA 1 AACACGCCGTCGCGCTAACACA 160952 ACTTTGCACA Statistics Matches: 77, Mismatches: 12, Indels: 20 0.71 0.11 0.18 Matches are distributed among these distances: 23 44 0.57 24 3 0.04 25 6 0.08 26 7 0.09 27 2 0.03 28 8 0.10 29 5 0.06 30 2 0.03 ACGTcount: A:0.30, C:0.42, G:0.17, T:0.11 Consensus pattern (23 bp): AACACGCCGTCGCGCTAACACAC Found at i:160922 original size:77 final size:77 Alignment explanation

Indices: 160830--160979 Score: 300 Period size: 77 Copynumber: 1.9 Consensus size: 77 160820 AACTTTGCAT 160830 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC 1 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC 160895 GCGCTAACACAC 66 GCGCTAACACAC 160907 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC 1 AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC 160972 GCGCTAAC 66 GCGCTAAC 160980 GCAACTTTGC Statistics Matches: 73, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 77 73 1.00 ACGTcount: A:0.29, C:0.41, G:0.17, T:0.12 Consensus pattern (77 bp): AACACGCCGTCGCGCTAACACACAACACGCCGTCGCGCTAACACAACTTTGCACAACACGCCGTC GCGCTAACACAC Found at i:160953 original size:21 final size:23 Alignment explanation

Indices: 160881--160951 Score: 142 Period size: 23 Copynumber: 3.1 Consensus size: 23 160871 CACAACTTTG 160881 CACAACACGCCGTCGCGCTAACA 1 CACAACACGCCGTCGCGCTAACA 160904 CACAACACGCCGTCGCGCTAACA 1 CACAACACGCCGTCGCGCTAACA 160927 CACAACACGCCGTCGCGCTAACA 1 CACAACACGCCGTCGCGCTAACA 160950 CA 1 CA 160952 ACTTTGCACA Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 48 1.00 ACGTcount: A:0.31, C:0.44, G:0.17, T:0.08 Consensus pattern (23 bp): CACAACACGCCGTCGCGCTAACA Found at i:161958 original size:31 final size:31 Alignment explanation

Indices: 161920--162026 Score: 149 Period size: 31 Copynumber: 3.7 Consensus size: 31 161910 GGACACGTGT 161920 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC 161951 GTTAGCGCGACGGCGTGTTGT-----G-T-- 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC * 161974 GTTAGCGCGACGGCGTGTTATGCAAAGTTGC 1 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC 162005 GTTAGCGCGACGGCGTGTTGTG 1 GTTAGCGCGACGGCGTGTTGTG 162027 TGTTAGCGCG Statistics Matches: 66, Mismatches: 2, Indels: 16 0.79 0.02 0.19 Matches are distributed among these distances: 23 20 0.30 25 1 0.02 26 1 0.02 28 1 0.02 29 1 0.02 31 42 0.64 ACGTcount: A:0.14, C:0.19, G:0.40, T:0.27 Consensus pattern (31 bp): GTTAGCGCGACGGCGTGTTGTGCAAAGTTGC Found at i:161992 original size:54 final size:54 Alignment explanation

Indices: 161916--162037 Score: 235 Period size: 54 Copynumber: 2.3 Consensus size: 54 161906 TTCCGGACAC * 161916 GTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGCGTTAGCGCGACGGCGTGTT 1 GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT 161970 GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT 1 GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT 162024 GTGTGTTAGCGCGA 1 GTGTGTTAGCGCGA 162038 TGTCTCGTTT Statistics Matches: 67, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 54 67 1.00 ACGTcount: A:0.14, C:0.18, G:0.40, T:0.28 Consensus pattern (54 bp): GTGTGTTAGCGCGACGGCGTGTTATGCAAAGTTGCGTTAGCGCGACGGCGTGTT Found at i:173903 original size:102 final size:102 Alignment explanation

Indices: 173797--174020 Score: 396 Period size: 102 Copynumber: 2.2 Consensus size: 102 173787 CAGAAAGGGG * 173797 AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACATTAGACCTCTATCTCCCTCAGA 1 AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACACTAGACCTCTATCTCCCTCAGA 173862 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA 66 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA ** * 173899 AAGAAAAAGAAGAAGAAAGGAGATGAGACTGAAGATGAAGACACTAGACCTTTATCTCCCTCAGA 1 AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACACTAGACCTCTATCTCCCTCAGA 173964 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA 66 GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA * 174001 AAGAAAAAGAAG-GGAAAGGA 1 AAGAAAAAGAAGAAGAAAGGA 174021 TGAAGAGAGG Statistics Matches: 117, Mismatches: 5, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 101 7 0.06 102 110 0.94 ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13 Consensus pattern (102 bp): AAGAAAAAGAAGAAGAAAGGAGAACAGACTGAAGATGAAGACACTAGACCTCTATCTCCCTCAGA GGATTCTATGCCAGCCACACCAACCAAAACTAAAGGA Found at i:174217 original size:27 final size:27 Alignment explanation

Indices: 174157--174226 Score: 81 Period size: 27 Copynumber: 2.7 Consensus size: 27 174147 TTCAAAGAAA * * 174157 AAGAAGAAGAA-AA-AGAAGGAAGGTG 1 AAGAAGAAGAAGAAGAGGAGGAAGATG * 174182 AAGAAGAAGAAGAGGAGGAGGAAGATG 1 AAGAAGAAGAAGAAGAGGAGGAAGATG * * 174209 ATGATGAAGAAGAAGAGG 1 AAGAAGAAGAAGAAGAGG 174227 TGTGTTCATT Statistics Matches: 37, Mismatches: 6, Indels: 2 0.82 0.13 0.04 Matches are distributed among these distances: 25 11 0.30 26 1 0.03 27 25 0.68 ACGTcount: A:0.54, C:0.00, G:0.40, T:0.06 Consensus pattern (27 bp): AAGAAGAAGAAGAAGAGGAGGAAGATG Found at i:174935 original size:32 final size:32 Alignment explanation

Indices: 174894--175007 Score: 219 Period size: 32 Copynumber: 3.6 Consensus size: 32 174884 TGTTTTATTG 174894 ATGATACAGTTTACATATGATACAGTGTATAT 1 ATGATACAGTTTACATATGATACAGTGTATAT 174926 ATGATACAGTTTACATATGATACAGTGTATAT 1 ATGATACAGTTTACATATGATACAGTGTATAT 174958 ATGATACAGTTTACATATGATACAGTGTATAT 1 ATGATACAGTTTACATATGATACAGTGTATAT * 174990 ATGATACAGTTTATATAT 1 ATGATACAGTTTACATAT 175008 ATGATAAGTT Statistics Matches: 81, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 32 81 1.00 ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39 Consensus pattern (32 bp): ATGATACAGTTTACATATGATACAGTGTATAT Found at i:175019 original size:16 final size:16 Alignment explanation

Indices: 174894--175007 Score: 174 Period size: 16 Copynumber: 7.1 Consensus size: 16 174884 TGTTTTATTG * 174894 ATGATACAGTTTACAT 1 ATGATACAGTTTATAT * 174910 ATGATACAGTGTATAT 1 ATGATACAGTTTATAT * 174926 ATGATACAGTTTACAT 1 ATGATACAGTTTATAT * 174942 ATGATACAGTGTATAT 1 ATGATACAGTTTATAT * 174958 ATGATACAGTTTACAT 1 ATGATACAGTTTATAT * 174974 ATGATACAGTGTATAT 1 ATGATACAGTTTATAT 174990 ATGATACAGTTTATAT 1 ATGATACAGTTTATAT 175006 AT 1 AT 175008 ATGATAAGTT Statistics Matches: 87, Mismatches: 11, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 87 1.00 ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39 Consensus pattern (16 bp): ATGATACAGTTTATAT Found at i:195409 original size:183 final size:181 Alignment explanation

Indices: 195075--195623 Score: 473 Period size: 178 Copynumber: 2.9 Consensus size: 181 195065 AGCTGTTGAA * * ** * * * * * ** 195075 CTCGCAGAATATTGCATAAAGGGTGCACCTATTGTAGGAGTAACTCCTCCTTCAGTTTTCAAGAT 1 CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAAGAT * * * * * * 195140 AGGAGAAAGTTGTTGTTTTGAAGATCAACTGTACATACATGTATATTAGAGATATGCATATTTCA 66 A-G-G-AA--TGTTGTTTTGCAGATCAA-AGTATATACA--TATATCAGAGATATGCATATTACT 195205 TGGATTTTGATTTTTGATAATTTATGGGAAAAAATTAATACCAGCTGTTGAACTTT-GT-TATTT 123 TGGATTTTGA-TTTTGATAATTTAT--G-AAAAA-T-ATACCAGCTGTTGAACTTTCGTCT-TTT 195268 T 181 T * * * * 195269 CTCGCAGATTATTGCATATAGGGCACCCCTATAGTAATAATAACCCCTCCTACAGTTTTCAAGGA 1 CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAA-GA * * 195334 TATGAA-GTTGTTTTGCAGATC-AA-T-TATACATATATCAGAGATATGCATATTACTTGGGTTT 65 TAGGAATGTTGTTTTGCAGATCAAAGTATATACATATATCAGAGATATGCATATTACTTGGATTT * * * * 195395 TAGATTTTGATAATTCATGAAAAATATACCTGTTATTGAA-TTTCGTCTTTTT 130 T-GATTTTGATAATTTATGAAAAATATACCAGCTGTTGAACTTTCGTCTTTTT * ** * ** * * 195447 CTCGCAGACTATTGTATACAGGGTTCCCCTATTGTGCGGATAACTCCTCCCACAGTTTTCAAGAT 1 CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAAGAT * * * 195512 AGGAAGTTGTTGTTTTGCATATCAAATGTACATATACATGTATCAGAGATATGCATATGACTTGG 66 AGGAA--TGTTGTTTTGCAGATCAAA-GT--ATATACATATATCAGAGATATGCATATTACTTGG * * * 195577 ATTTTGATTTTTATGAAATTATGAAAAATATACCAGCTGTTAAACTT 126 ATTTTGATTTTGAT-AATTTATGAAAAATATACCAGCTGTTGAACTT 195624 AGCAATGTTC Statistics Matches: 293, Mismatches: 47, Indels: 37 0.78 0.12 0.10 Matches are distributed among these distances: 177 10 0.03 178 68 0.23 179 2 0.01 180 19 0.06 181 3 0.01 183 42 0.14 184 2 0.01 185 13 0.04 186 59 0.20 187 2 0.01 188 1 0.00 189 14 0.05 192 2 0.01 193 1 0.00 194 51 0.17 195 4 0.01 ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37 Consensus pattern (181 bp): CTCGCAGACTATTGCATACAGGGCACCCCTATAGTAAGAATAACCCCTCCCACAGTTTTCAAGAT AGGAATGTTGTTTTGCAGATCAAAGTATATACATATATCAGAGATATGCATATTACTTGGATTTT GATTTTGATAATTTATGAAAAATATACCAGCTGTTGAACTTTCGTCTTTTT Found at i:196030 original size:1 final size:1 Alignment explanation

Indices: 196024--196058 Score: 52 Period size: 1 Copynumber: 35.0 Consensus size: 1 196014 CAAAATACGT * * 196024 GGGGGGGGGGGGGGGGGGGGTGGGGGCGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 196059 ATGGACACAC Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 1 30 1.00 ACGTcount: A:0.00, C:0.03, G:0.94, T:0.03 Consensus pattern (1 bp): G Found at i:202897 original size:2 final size:2 Alignment explanation

Indices: 202892--202957 Score: 132 Period size: 2 Copynumber: 33.0 Consensus size: 2 202882 TATGTGATAA 202892 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 202934 TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC 202958 ACACACACAC Statistics Matches: 64, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 64 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:202962 original size:2 final size:2 Alignment explanation

Indices: 202957--202984 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 202947 CTCTCTCTCT 202957 CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA 202985 TCATTTTGGT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): CA Found at i:205071 original size:21 final size:21 Alignment explanation

Indices: 205047--205094 Score: 62 Period size: 21 Copynumber: 2.3 Consensus size: 21 205037 TTGTACTTAT * 205047 TACTTACTTGTTGATTT-TTAA 1 TACTTACTAGTT-ATTTATTAA 205068 TACTTACTAGTTATTTATTAA 1 TACTTACTAGTTATTTATTAA * 205089 TTCTTA 1 TACTTA 205095 ATACTTACTA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 20 4 0.17 21 20 0.83 ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56 Consensus pattern (21 bp): TACTTACTAGTTATTTATTAA Found at i:205071 original size:28 final size:28 Alignment explanation

Indices: 205040--205105 Score: 78 Period size: 28 Copynumber: 2.4 Consensus size: 28 205030 TTCTTGCTTG * * * * 205040 TACTTATTACTTACTTGTTGATTTTTAA 1 TACTTACTACTTACTTATTAATTCTTAA * * 205068 TACTTACTAGTTATTTATTAATTCTTAA 1 TACTTACTACTTACTTATTAATTCTTAA 205096 TACTTACTAC 1 TACTTACTAC 205106 CTATTACTTA Statistics Matches: 31, Mismatches: 7, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 28 31 1.00 ACGTcount: A:0.29, C:0.14, G:0.05, T:0.53 Consensus pattern (28 bp): TACTTACTACTTACTTATTAATTCTTAA Found at i:205101 original size:49 final size:49 Alignment explanation

Indices: 205042--205229 Score: 157 Period size: 49 Copynumber: 3.9 Consensus size: 49 205032 CTTGCTTGTA * * 205042 CTTATTACTTACTTGTTGATT-TTTAATACTTACTAGTTATTTATTAATT 1 CTTAATACTTACTTGTT-ATTACTTAATACTTACTAGTTATTTATTAATT *** * * * * 205091 CTTAATACTTACTACCTATTACTTAATACTTGCTTGTTAATTGTTAAATT 1 CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTTATT-AATT * * * * * * 205141 -TTATTTCTTAATTGTTATTACTTATTATTTACTGGTTATTTATTAATT 1 CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTTATTAATT * ** * * 205189 CTTAATACTTATTTGTT-TTACTTGTTATTTTCTAGTTATTT 1 CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTT 205230 CTAATTTCAT Statistics Matches: 109, Mismatches: 27, Indels: 7 0.76 0.19 0.05 Matches are distributed among these distances: 48 28 0.26 49 77 0.71 50 4 0.04 ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57 Consensus pattern (49 bp): CTTAATACTTACTTGTTATTACTTAATACTTACTAGTTATTTATTAATT Found at i:206818 original size:39 final size:41 Alignment explanation

Indices: 206738--206818 Score: 121 Period size: 41 Copynumber: 2.0 Consensus size: 41 206728 AAAAAATAAG * * 206738 TCATTACAATTAAGAAATAAGTCAATATGTCCTTCCAGGGC 1 TCATAACAATTAAGAAATAAGTCAATATGTCCTCCCAGGGC * 206779 TCATAACAATTAAGAAGTAAGTC-A-ATGTCCTCCCAGGGC 1 TCATAACAATTAAGAAATAAGTCAATATGTCCTCCCAGGGC 206818 T 1 T 206819 TCCGTAATAA Statistics Matches: 37, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 39 15 0.41 40 1 0.03 41 21 0.57 ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27 Consensus pattern (41 bp): TCATAACAATTAAGAAATAAGTCAATATGTCCTCCCAGGGC Found at i:219818 original size:4 final size:4 Alignment explanation

Indices: 219809--219885 Score: 73 Period size: 4 Copynumber: 19.2 Consensus size: 4 219799 TAACAATGAA * * * * * 219809 AGAG AGAG AGAG AGAG AGAG AGAG AGAG ACAG ACAG ACAG ACAG ACAG 1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG * * * * 219857 ACAG ACAG ACAG AGAG AGAC AGAG AGAG A 1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG A 219886 ATGATTGATT Statistics Matches: 69, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 4 69 1.00 ACGTcount: A:0.51, C:0.12, G:0.38, T:0.00 Consensus pattern (4 bp): AGAG Found at i:219884 original size:12 final size:12 Alignment explanation

Indices: 219809--219885 Score: 82 Period size: 12 Copynumber: 6.2 Consensus size: 12 219799 TAACAATGAA * 219809 AGAGAGAGAGAG 1 AGAGACAGAGAG * 219821 AGAGAGAGAGAG 1 AGAGACAGAGAG * 219833 AGAGACAGACAG 1 AGAGACAGAGAG * * 219845 ACAGACAGACAG 1 AGAGACAGAGAG * 219857 ACAGACAGACAGAG 1 AGAGACAG--AGAG 219871 AGAGACAGAGAG 1 AGAGACAGAGAG 219883 AGA 1 AGA 219886 ATGATTGATT Statistics Matches: 58, Mismatches: 5, Indels: 4 0.87 0.07 0.06 Matches are distributed among these distances: 12 48 0.83 14 10 0.17 ACGTcount: A:0.51, C:0.12, G:0.38, T:0.00 Consensus pattern (12 bp): AGAGACAGAGAG Found at i:224302 original size:21 final size:21 Alignment explanation

Indices: 224276--224328 Score: 106 Period size: 21 Copynumber: 2.5 Consensus size: 21 224266 TCATTAATCT 224276 TTTGGGTCATAAAAATATTTA 1 TTTGGGTCATAAAAATATTTA 224297 TTTGGGTCATAAAAATATTTA 1 TTTGGGTCATAAAAATATTTA 224318 TTTGGGTCATA 1 TTTGGGTCATA 224329 TGAGAATGAT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 32 1.00 ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43 Consensus pattern (21 bp): TTTGGGTCATAAAAATATTTA Found at i:225445 original size:22 final size:22 Alignment explanation

Indices: 225415--225462 Score: 55 Period size: 22 Copynumber: 2.3 Consensus size: 22 225405 TCTTCAGTTA * 225415 GTCAT-AAATTAATCT-TTTGG 1 GTCATAAAAATAATCTATTTGG * * 225435 GTCATAAAAATATTTTATTTGG 1 GTCATAAAAATAATCTATTTGG 225457 GTCATA 1 GTCATA 225463 TGAGAATGAT Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 20 5 0.22 21 7 0.30 22 11 0.48 ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44 Consensus pattern (22 bp): GTCATAAAAATAATCTATTTGG Found at i:227305 original size:181 final size:180 Alignment explanation

Indices: 226699--227834 Score: 2058 Period size: 180 Copynumber: 6.3 Consensus size: 180 226689 GGCTGCCAAA * * 226699 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCC 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA 226764 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAA-TTCATGA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTC-TGA 226828 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT * 226879 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCC 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA * 226944 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA 227009 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT ** 227059 AGATTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA * 227124 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTCTGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A 227189 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT * * * 227240 AGGGTACCCTCATTTTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCATTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA * * 227305 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTATGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA 227370 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT * * 227420 AGGGTACCCTCATTTTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA * 227485 GATCAATTGTACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A 227550 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT * * 227601 AGAGTACCCTCATTGTATGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA * 227666 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA * 227731 AAAAATACCAGCTTTTGAACTTAGTCATATTTTGGCAAAATATTGCATAT 131 AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT * 227781 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGAAAGTT 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTT 227835 TGAACTGAAG Statistics Matches: 926, Mismatches: 27, Indels: 6 0.97 0.03 0.01 Matches are distributed among these distances: 180 576 0.62 181 350 0.38 ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37 Consensus pattern (180 bp): AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT Found at i:227372 original size:361 final size:360 Alignment explanation

Indices: 226699--227994 Score: 2135 Period size: 361 Copynumber: 3.5 Consensus size: 360 226689 GGCTGCCAAA * * 226699 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCC 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA 226764 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAA-TTCATGA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTC-TGA 226828 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT 130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT * 226893 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCCGATCAATTGTACAT 195 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT 226958 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT 260 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT 227023 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 325 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT ** 227059 AGATTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA * 227124 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTCTGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A 227189 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT 130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT * * * 227254 TTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCATTTGCAGATCAATTGTACAT 195 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT * * 227319 ATATCAGAGGTGTGCATATTGCTAGGATTATGATTTCTGATAATTTATGAAAAAAATACCAGCTT 260 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT 227384 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 325 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT * * 227420 AGGGTACCCTCATTTTACGGATAACTCCTCCTACAGTTTTTAAGGTAGGAAGTTGTTCTTTTGCA 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA * 227485 GATCAATTGTACATATATCAGAGGTATGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA 66 GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTG-A * 227550 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGAGTACCCTCATT 130 AAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATT * 227615 GTATGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT 195 GTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACAT 227680 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT 260 ATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTT * 227745 TTGAACTTAGTCATATTTTGGCAAAATATTGCATAT 325 TTGAACTTAGTCATTTTTTGGCAAAATATTGCATAT 227781 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGAAAGTTTGAACTGAAGT 1 AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGT----A----G----GAAG- * 227846 TTGAATTGAAAAGCTGGAACTTTTGCCGATCAATTGTACATATATCAGAGGTGTGCATATTGCTA 53 TTG---T-------T----CTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCTA * * 227911 GGATTTTGATTTCTGATAATTTATGAAAAAAATACCAGCTTTTGAACTTAGTCATTCTTTGGCAA 104 GGATTTTGATTTCTGATAATTTCTGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAA 227976 AATATTGCATATAGGGTAC 169 AATATTGCATATAGGGTAC 227995 ACCATTTCAC Statistics Matches: 875, Mismatches: 32, Indels: 31 0.93 0.03 0.03 Matches are distributed among these distances: 360 119 0.14 361 620 0.71 365 1 0.00 369 1 0.00 373 4 0.00 374 3 0.00 377 1 0.00 384 1 0.00 387 57 0.07 388 68 0.08 ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37 Consensus pattern (360 bp): AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCA GATCAATTGTACATATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTCTGAA AAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTG TACGGATAACTCCTCCTACAGTTTTCAAGGTAGGAAGTTGTTCTTTTGCAGATCAATTGTACATA TATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCTGATAATTTGTGAAAAAAATACCAGCTTT TGAACTTAGTCATTTTTTGGCAAAATATTGCATAT Found at i:236809 original size:11 final size:11 Alignment explanation

Indices: 236793--236818 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 236783 AAAGATTAAT 236793 GTGATAATTGG 1 GTGATAATTGG 236804 GTGATAATTGG 1 GTGATAATTGG 236815 GTGA 1 GTGA 236819 AATGTCAGAA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35 Consensus pattern (11 bp): GTGATAATTGG Found at i:243652 original size:13 final size:13 Alignment explanation

Indices: 243634--243659 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 243624 CTTCTTTGCG 243634 GGAGTAACTGAGC 1 GGAGTAACTGAGC 243647 GGAGTAACTGAGC 1 GGAGTAACTGAGC 243660 ATTTTATCAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15 Consensus pattern (13 bp): GGAGTAACTGAGC Found at i:245392 original size:30 final size:30 Alignment explanation

Indices: 245356--245417 Score: 124 Period size: 30 Copynumber: 2.1 Consensus size: 30 245346 AGATTTATAA 245356 ATAAAAAACATGTACACTGTACATGTACCT 1 ATAAAAAACATGTACACTGTACATGTACCT 245386 ATAAAAAACATGTACACTGTACATGTACCT 1 ATAAAAAACATGTACACTGTACATGTACCT 245416 AT 1 AT 245418 CAGCTTCTAT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 32 1.00 ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27 Consensus pattern (30 bp): ATAAAAAACATGTACACTGTACATGTACCT Found at i:255850 original size:16 final size:16 Alignment explanation

Indices: 255814--255861 Score: 69 Period size: 16 Copynumber: 2.9 Consensus size: 16 255804 GATCGGGGTT * * 255814 TCTCTCTCCTCTCCCCT 1 TCTCTCT-CTCTCTCCA 255831 TCTCTCTCTCTCTCCA 1 TCTCTCTCTCTCTCCA 255847 TCTCTCTCTCTCTCC 1 TCTCTCTCTCTCTCC 255862 TGGGAGGAGG Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 16 22 0.76 17 7 0.24 ACGTcount: A:0.02, C:0.54, G:0.00, T:0.44 Consensus pattern (16 bp): TCTCTCTCTCTCTCCA Found at i:257929 original size:27 final size:27 Alignment explanation

Indices: 257899--257956 Score: 116 Period size: 27 Copynumber: 2.1 Consensus size: 27 257889 CGAAATCCCG 257899 AGCGACCTTTCAAATACAAAGGTGACA 1 AGCGACCTTTCAAATACAAAGGTGACA 257926 AGCGACCTTTCAAATACAAAGGTGACA 1 AGCGACCTTTCAAATACAAAGGTGACA 257953 AGCG 1 AGCG 257957 TCACACGATA Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 31 1.00 ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17 Consensus pattern (27 bp): AGCGACCTTTCAAATACAAAGGTGACA Found at i:267478 original size:25 final size:25 Alignment explanation

Indices: 267432--267479 Score: 62 Period size: 25 Copynumber: 1.9 Consensus size: 25 267422 TTTGTATAAT ** 267432 ATATATTTAATAATATTTTATTTTA 1 ATATATTTAATAATATAATATTTTA 267457 ATAT-TTTATATAATATAATATTT 1 ATATATTTA-ATAATATAATATTT 267480 ATTGAGGTCA Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 24 4 0.20 25 16 0.80 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (25 bp): ATATATTTAATAATATAATATTTTA Found at i:278343 original size:2 final size:2 Alignment explanation

Indices: 278330--278368 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 278320 AGATAAAAGT * 278330 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 278369 GTATTATAAT Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54 Consensus pattern (2 bp): TC Found at i:284363 original size:32 final size:32 Alignment explanation

Indices: 284327--284455 Score: 240 Period size: 32 Copynumber: 4.0 Consensus size: 32 284317 TGCAGGAAAG * 284327 ATACAAATAATTATAAGTTTGAACAGGTTTGT 1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT 284359 ATACAAGTAATTATAAGTTTGAACAGGTTTGT 1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT 284391 ATACAAGTAATTATAAGTTTGAACAGGTTTGT 1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT * 284423 ATACAAGTAATTATAAGTTTGTACAGGTTTGT 1 ATACAAGTAATTATAAGTTTGAACAGGTTTGT 284455 A 1 A 284456 CCTGAGAGAC Statistics Matches: 95, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 32 95 1.00 ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38 Consensus pattern (32 bp): ATACAAGTAATTATAAGTTTGAACAGGTTTGT Found at i:285568 original size:51 final size:51 Alignment explanation

Indices: 285512--285616 Score: 210 Period size: 51 Copynumber: 2.1 Consensus size: 51 285502 AGTTCGGAAG 285512 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA 1 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA 285563 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA 1 CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA 285614 CAT 1 CAT 285617 TTGAATTCAA Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 51 54 1.00 ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31 Consensus pattern (51 bp): CATATATAATATGAACTTAAATATACAGAATATCAGTATTGGTACAAAATA Found at i:300386 original size:2 final size:2 Alignment explanation

Indices: 300379--300425 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 300369 NNNNNNNNNN 300379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 300421 TA TA T 1 TA TA T 300426 GGTGTTTACT Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:304610 original size:33 final size:33 Alignment explanation

Indices: 304558--304678 Score: 136 Period size: 33 Copynumber: 3.7 Consensus size: 33 304548 AATGTAAACA * * * 304558 TTGTAAAACGTACACTCGTAATTTACGTTAACG 1 TTGTAAAACATATATTCGTAATTTACGTTAACG * ** * 304591 TTGTAAAATATATATTCGTAATAAAGGTTAACG 1 TTGTAAAACATATATTCGTAATTTACGTTAACG * * * 304624 TTGTAAAACGA-ACAGTCGTAATTTACGTTAAAG 1 TTGTAAAAC-ATATATTCGTAATTTACGTTAACG 304657 TTGTAAAACATATATTCGTAAT 1 TTGTAAAACATATATTCGTAAT 304679 AAACGTCAAA Statistics Matches: 70, Mismatches: 16, Indels: 4 0.78 0.18 0.04 Matches are distributed among these distances: 32 1 0.01 33 68 0.97 34 1 0.01 ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35 Consensus pattern (33 bp): TTGTAAAACATATATTCGTAATTTACGTTAACG Found at i:304664 original size:66 final size:66 Alignment explanation

Indices: 304558--304681 Score: 212 Period size: 66 Copynumber: 1.9 Consensus size: 66 304548 AATGTAAACA * * * 304558 TTGTAAAACGTACACTCGTAATTTACGTTAACGTTGTAAAATATATATTCGTAATAAAGGTTAAC 1 TTGTAAAACGAACACTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAAGGTTAAC 304623 G 66 G * 304624 TTGTAAAACGAACAGTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAA 1 TTGTAAAACGAACACTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAA 304682 CGTCAAAACG Statistics Matches: 54, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 66 54 1.00 ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34 Consensus pattern (66 bp): TTGTAAAACGAACACTCGTAATTTACGTTAAAGTTGTAAAACATATATTCGTAATAAAGGTTAAC G Found at i:305527 original size:14 final size:14 Alignment explanation

Indices: 305508--305534 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 305498 CTACACATAC 305508 AGCTTCCGGTCTGT 1 AGCTTCCGGTCTGT 305522 AGCTTCCGGTCTG 1 AGCTTCCGGTCTG 305535 AAAAAATTCA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.07, C:0.30, G:0.30, T:0.33 Consensus pattern (14 bp): AGCTTCCGGTCTGT Found at i:309301 original size:11 final size:11 Alignment explanation

Indices: 309280--309309 Score: 51 Period size: 11 Copynumber: 2.6 Consensus size: 11 309270 TGCAAAAAAA 309280 AAAACAACAACC 1 AAAA-AACAACC 309292 AAAAAACAACC 1 AAAAAACAACC 309303 AAAAAAC 1 AAAAAAC 309310 CCCCCCCCCC Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 14 0.78 12 4 0.22 ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00 Consensus pattern (11 bp): AAAAAACAACC Found at i:314225 original size:31 final size:32 Alignment explanation

Indices: 314166--314261 Score: 158 Period size: 32 Copynumber: 3.0 Consensus size: 32 314156 AAGTAACGTA 314166 CCCTACATGTAGACCTAATGATTACTATAGGT 1 CCCTACATGTAGACCTAATGATTACTATAGGT * * 314198 CCCTACATGTAGGCCAAATG-TTACTATAGGT 1 CCCTACATGTAGACCTAATGATTACTATAGGT * 314229 TCCTACATGTAGACCTAATGATTACTATAGGT 1 CCCTACATGTAGACCTAATGATTACTATAGGT 314261 C 1 C 314262 TTACAATTAC Statistics Matches: 57, Mismatches: 6, Indels: 2 0.88 0.09 0.03 Matches are distributed among these distances: 31 28 0.49 32 29 0.51 ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31 Consensus pattern (32 bp): CCCTACATGTAGACCTAATGATTACTATAGGT Found at i:314369 original size:32 final size:32 Alignment explanation

Indices: 314319--314864 Score: 729 Period size: 32 Copynumber: 16.9 Consensus size: 32 314309 TGAAGAGATT * 314319 CATGTAGATCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 314351 CATGCAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 314383 CATGTAGACCTAATGATTACTATAGGTTCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 314415 CATGTAGACCTAATGATTACTATAGGT-CTTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA ** 314446 CATGTAGACCTAATGATTACTATAGACCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * * ** 314478 CATATAGATCTAATGATTACTATAGACCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * * * 314510 CATATAGATCTAATGATTACTATAGGCCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 314542 CATGTAGACCTAATGATTACTATAGG-CCCCA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 314573 CCATATAGACCTAATGATTACTATAGGTCCCTA 1 -CATGTAGACCTAATGATTACTATAGGTCCCTA * * 314606 CATGTAGATCTAATGATTACTATAGGTTCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA ** ** * 314638 CATGTAGATATAATGATTACTATAGACCCCTG 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * * 314670 CATATAGATCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * * 314702 CATATAGACCTAATGATTACTATAGGCCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA 314734 CATGTAGACCTAATGATTACTATANAAGTAACGTACCCTA 1 CATGTAGACCTAATGATTACTAT---AG----GT-CCCTA 314774 CATGTAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * * * 314806 CATGTAGGCCAAATG-TTACTATAGGTTCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA 314837 CATGTAGACCTAATGATTACTATAGGTC 1 CATGTAGACCTAATGATTACTATAGGTC 314865 TTACAATTAC Statistics Matches: 463, Mismatches: 39, Indels: 24 0.88 0.07 0.05 Matches are distributed among these distances: 31 60 0.13 32 364 0.79 33 6 0.01 35 2 0.00 37 2 0.00 39 1 0.00 40 28 0.06 ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31 Consensus pattern (32 bp): CATGTAGACCTAATGATTACTATAGGTCCCTA Found at i:314396 original size:64 final size:64 Alignment explanation

Indices: 314319--315303 Score: 1029 Period size: 64 Copynumber: 15.0 Consensus size: 64 314309 TGAAGAGATT * * 314319 CATGTAGATCTAATGATTACTATAGGTCCCTACATGCAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA * * 314383 CATGTAGACCTAATGATTACTATAGGTTCCTACATGTAGACCTAATGATTACTATAGGT-CTTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA ** * * ** 314446 CATGTAGACCTAATGATTACTATAGACCCCTACATATAGATCTAATGATTACTATAGACCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA * * * * 314510 CATATAGATCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATAGG-CCCCA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA * * * 314573 CCATATAGACCTAATGATTACTATAGGTCCCTACATGTAGATCTAATGATTACTATAGGTTCCTA 1 -CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA ** ** * * * 314638 CATGTAGATATAATGATTACTATAGACCCCTGCATATAGATCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA * * 314702 CATATAGACCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATANAAGTAACG 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTAT---AG----G 314767 TACCCTA 59 T-CCCTA * * * 314774 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGGCCAAATG-TTACTATAGGTTCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA * * * * 314837 CATGTAGACCTAATGATTACTATAGGTCTTACAATTACATGTAGACCTACTGATAACTATAGGCC 1 CATGTAGACCTAATGATTACTATAGGTC---C--CTACATGTAGACCTAATGATTACTATAGGTC * 314902 CCTGT 61 CCT-A * * * * ** * * * * 314907 GATGTTGA---AGA-GATT-CATGTAGATCTAATGATTACTATAGGTCCCTACATGCA-GACCTA 1 CATGTAGACCTA-ATGATTAC-TATAGGTC-CCT-A-CA-TGTA-G-ACCTA-ATG-ATTA-CTA * ** 314966 -ATGATTACTA 55 TA-GGTCCCTA * * * 314976 TAGGTCCCTACATGTAGACCTAATGATTACTATAGGTTCCTACATGTAGACCTAATGATTACTAT 1 CA--T--GT------AGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTAT * 315041 AGGT-CTTA 56 AGGTCCCTA ** * * 315049 CATGTAGACCTAATGATTACTATAGACCCCTACATATAGACCTAATGATTACTATAGGTTCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA * * * 315113 CATGTAGACCAAATGATTACTATAGGCCCCTACATATAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA 315177 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA * 315241 CATGCAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCT 1 CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCT 315304 GTGATGTTGA Statistics Matches: 776, Mismatches: 98, Indels: 94 0.80 0.10 0.10 Matches are distributed among these distances: 63 142 0.18 64 460 0.59 65 4 0.01 66 5 0.01 67 14 0.02 68 21 0.03 69 18 0.02 70 13 0.02 71 11 0.01 72 48 0.06 73 4 0.01 74 6 0.01 75 5 0.01 76 4 0.01 77 1 0.00 78 3 0.00 79 3 0.00 80 1 0.00 81 2 0.00 82 10 0.01 83 1 0.00 ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31 Consensus pattern (64 bp): CATGTAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTCCCTA Found at i:314587 original size:96 final size:95 Alignment explanation

Indices: 314323--315303 Score: 891 Period size: 96 Copynumber: 9.9 Consensus size: 95 314313 GAGATTCATG * * * * 314323 TAGATCTAATGATTACTATAGGTCCCTACATGCAGACCTAATGATTACTATAGGTCCCTACATGT 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-CCCCACATAT * * 314388 AGACCTAATGATTACTATAGGTTCCTACATG 65 AGACCTAATGATTACTATAGGTCCCTACATA * * 314419 TAGACCTAATGATTACTATAGGT-CTTACATGTAGACCTAATGATTACTATAGACCCCTACATAT 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCC-ACATAT * ** 314483 AGATCTAATGATTACTATAGACCCCTACATA 65 AGACCTAATGATTACTATAGGTCCCTACATA * * 314514 TAGATCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATAGGCCCCACCATAT 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCCA-CATAT * 314579 AGACCTAATGATTACTATAGGTCCCTACATG 65 AGACCTAATGATTACTATAGGTCCCTACATA * * ** * * 314610 TAGATCTAATGATTACTATAGGTTCCTACATGTAGATATAATGATTACTATAGACCCCTGCATAT 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCC-ACATAT * 314675 AGATCTAATGATTACTATAGGTCCCTACATA 65 AGACCTAATGATTACTATAGGTCCCTACATA * 314706 TAGACCTAATGATTACTATAGGCCCCTACATGTAGACCTAATGATTACTATANAAGTAACGTACC 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTAT---AG----G--CC * * * 314771 CTACATGTAGACCTAATGATTACTATAGGTCCCTACATG 57 CCACATATAGACCTAATGATTACTATAGGTCCCTACATA * * * ** 314810 TAGGCCAAATG-TTACTATAGGTTCCTACATGTAGACCTAATGATTACTATAGGTCTTACAATTA 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-C---C--CCA * * * * ** * 314874 CATGTAGACCTACTGATAACTATAGGCCCCTGTGATG 60 CATATAGACCTAATGATTACTATAGGTCCCT-ACATA * * * ** * * * * 314911 TTGA---AGA-GATT-CATGTAGATCTAATGATTACTATAGGTCCCTACATGCA-GACCTAATGA 1 TAGACCTA-ATGATTAC-TATAGGTC-CCT-A-CA-TGTA-G-ACCTA-ATG-ATTA-CT-AT-A ** *** * * * 314970 TTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGTTCCTACATG 53 -GGCCCCA----CATA----TAGACCTAATGATTACTATAGGTCCCTACATA * * 315022 TAGACCTAATGATTACTATAGGT-CTTACATGTAGACCTAATGATTACTATAGACCCCTACATAT 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCC-ACATAT * * 315086 AGACCTAATGATTACTATAGGTTCCTACATG 65 AGACCTAATGATTACTATAGGTCCCTACATA * * * * * 315117 TAGACCAAATGATTACTATAGGCCCCTACATATAGACCTAATGATTACTATAGGTCCCTACATGT 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-CCCCACATAT * 315182 AGACCTAATGATTACTATAGGTCCCTACATG 65 AGACCTAATGATTACTATAGGTCCCTACATA * * * 315213 TAGACCTAATGATTACTATAGGTCCCTACATGCAGACCTAATGATTACTATAGGTCCCTACATGT 1 TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGG-CCCCACATAT 315278 AGACCTAATGATTACTATAGGTCCCT 65 AGACCTAATGATTACTATAGGTCCCT 315304 GTGATGTTGA Statistics Matches: 736, Mismatches: 98, Indels: 102 0.79 0.10 0.11 Matches are distributed among these distances: 94 3 0.00 95 134 0.18 96 369 0.50 97 3 0.00 98 4 0.01 99 13 0.02 100 33 0.04 101 6 0.01 102 3 0.00 103 42 0.06 104 47 0.06 105 10 0.01 106 8 0.01 107 7 0.01 108 5 0.01 109 5 0.01 110 1 0.00 111 7 0.01 112 24 0.03 113 1 0.00 114 10 0.01 115 1 0.00 ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31 Consensus pattern (95 bp): TAGACCTAATGATTACTATAGGTCCCTACATGTAGACCTAATGATTACTATAGGCCCCACATATA GACCTAATGATTACTATAGGTCCCTACATA Found at i:314972 original size:32 final size:32 Alignment explanation

Indices: 314922--315303 Score: 649 Period size: 32 Copynumber: 12.0 Consensus size: 32 314912 TGAAGAGATT * 314922 CATGTAGATCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 314954 CATGCAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 314986 CATGTAGACCTAATGATTACTATAGGTTCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 315018 CATGTAGACCTAATGATTACTATAGGT-CTTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA ** 315049 CATGTAGACCTAATGATTACTATAGACCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * * 315081 CATATAGACCTAATGATTACTATAGGTTCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * * 315113 CATGTAGACCAAATGATTACTATAGGCCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 315145 CATATAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA 315177 CATGTAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA 315209 CATGTAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA * 315241 CATGCAGACCTAATGATTACTATAGGTCCCTA 1 CATGTAGACCTAATGATTACTATAGGTCCCTA 315273 CATGTAGACCTAATGATTACTATAGGTCCCT 1 CATGTAGACCTAATGATTACTATAGGTCCCT 315304 GTGATGTTGA Statistics Matches: 327, Mismatches: 22, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 31 28 0.09 32 299 0.91 ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31 Consensus pattern (32 bp): CATGTAGACCTAATGATTACTATAGGTCCCTA Found at i:315076 original size:18 final size:18 Alignment explanation

Indices: 315053--315105 Score: 51 Period size: 18 Copynumber: 3.2 Consensus size: 18 315043 GTCTTACATG 315053 TAGACCTAATGATTACTA 1 TAGACCTAATGATTACTA ** * 315071 TAGACC-CCT-A-CA-TA 1 TAGACCTAATGATTACTA 315085 TAGACCTAATGATTACTA 1 TAGACCTAATGATTACTA 315103 TAG 1 TAG 315106 GTTCCTACAT Statistics Matches: 25, Mismatches: 6, Indels: 8 0.64 0.15 0.21 Matches are distributed among these distances: 14 8 0.32 15 2 0.08 16 2 0.08 17 2 0.08 18 11 0.44 ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30 Consensus pattern (18 bp): TAGACCTAATGATTACTA Found at i:327327 original size:2 final size:2 Alignment explanation

Indices: 327320--327351 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 327310 ACCAGGCATA 327320 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 327352 GAGTAATTTC Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:344662 original size:22 final size:22 Alignment explanation

Indices: 344634--344677 Score: 72 Period size: 22 Copynumber: 2.0 Consensus size: 22 344624 GAGGTACGAG 344634 AGTGCGA-AGTTGCGACGGCGAA 1 AGTGCGAGAG-TGCGACGGCGAA 344656 AGTGCGAGAGTGCGACGGCGAA 1 AGTGCGAGAGTGCGACGGCGAA 344678 GGAGCAAAAG Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 22 19 0.90 23 2 0.10 ACGTcount: A:0.27, C:0.18, G:0.43, T:0.11 Consensus pattern (22 bp): AGTGCGAGAGTGCGACGGCGAA Found at i:344689 original size:22 final size:22 Alignment explanation

Indices: 344644--344692 Score: 62 Period size: 22 Copynumber: 2.2 Consensus size: 22 344634 AGTGCGAAGT * * * 344644 TGCGACGGCGAAAGTGCGAGAG 1 TGCGACGGCGAAAGAGCAAAAG * 344666 TGCGACGGCGAAGGAGCAAAAG 1 TGCGACGGCGAAAGAGCAAAAG 344688 TGCGA 1 TGCGA 344693 AGATGCGACG Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 22 23 1.00 ACGTcount: A:0.31, C:0.18, G:0.43, T:0.08 Consensus pattern (22 bp): TGCGACGGCGAAAGAGCAAAAG Found at i:344738 original size:22 final size:21 Alignment explanation

Indices: 344685--344751 Score: 107 Period size: 21 Copynumber: 3.1 Consensus size: 21 344675 GAAGGAGCAA * 344685 AAGTGCGAAGATGCGACGGCG 1 AAGTGCGAAGTTGCGACGGCG * 344706 AAGCGCGAAGTTGCGACGGCG 1 AAGTGCGAAGTTGCGACGGCG 344727 AGAGTGCGAAGTTGCGACGGCG 1 A-AGTGCGAAGTTGCGACGGCG 344749 AAG 1 AAG 344752 AAGCGATACT Statistics Matches: 42, Mismatches: 3, Indels: 2 0.89 0.06 0.04 Matches are distributed among these distances: 21 22 0.52 22 20 0.48 ACGTcount: A:0.27, C:0.19, G:0.43, T:0.10 Consensus pattern (21 bp): AAGTGCGAAGTTGCGACGGCG Found at i:344757 original size:22 final size:22 Alignment explanation

Indices: 344689--344757 Score: 88 Period size: 22 Copynumber: 3.2 Consensus size: 22 344679 GAGCAAAAGT * * 344689 GCGAAGATGCGACGGCGAAG-C 1 GCGAAGTTGCGACGGCGAAGAA * 344710 GCGAAGTTGCGACGGCG-AGAGT 1 GCGAAGTTGCGACGGCGAAGA-A 344732 GCGAAGTTGCGACGGCGAAGAA 1 GCGAAGTTGCGACGGCGAAGAA 344754 GCGA 1 GCGA 344758 TACTACTATC Statistics Matches: 42, Mismatches: 3, Indels: 5 0.84 0.06 0.10 Matches are distributed among these distances: 20 2 0.05 21 16 0.38 22 21 0.50 23 3 0.07 ACGTcount: A:0.28, C:0.20, G:0.43, T:0.09 Consensus pattern (22 bp): GCGAAGTTGCGACGGCGAAGAA Found at i:344791 original size:14 final size:14 Alignment explanation

Indices: 344766--344827 Score: 58 Period size: 14 Copynumber: 4.3 Consensus size: 14 344756 GATACTACTA 344766 TCGCACTCTCGC-CT 1 TCGCACT-TCGCACT 344780 TCGCAACTTCGCACT 1 TCGC-ACTTCGCACT 344795 CTCGC-CTTCGCATCT 1 -TCGCACTTCGCA-CT 344810 TCGCACTTTCGC-CT 1 TCGCAC-TTCGCACT 344824 TCGC 1 TCGC 344828 CTTTTTATAA Statistics Matches: 42, Mismatches: 0, Indels: 12 0.78 0.00 0.22 Matches are distributed among these distances: 14 25 0.60 15 8 0.19 16 9 0.21 ACGTcount: A:0.10, C:0.45, G:0.15, T:0.31 Consensus pattern (14 bp): TCGCACTTCGCACT Found at i:344794 original size:22 final size:22 Alignment explanation

Indices: 344766--344827 Score: 106 Period size: 22 Copynumber: 2.8 Consensus size: 22 344756 GATACTACTA 344766 TCGCACTCTCGCCTTCGCAACT 1 TCGCACTCTCGCCTTCGCAACT * 344788 TCGCACTCTCGCCTTCGCATCT 1 TCGCACTCTCGCCTTCGCAACT * 344810 TCGCACTTTCGCCTTCGC 1 TCGCACTCTCGCCTTCGC 344828 CTTTTTATAA Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 22 38 1.00 ACGTcount: A:0.10, C:0.45, G:0.15, T:0.31 Consensus pattern (22 bp): TCGCACTCTCGCCTTCGCAACT Found at i:345530 original size:22 final size:22 Alignment explanation

Indices: 345501--345558 Score: 84 Period size: 22 Copynumber: 2.7 Consensus size: 22 345491 TGCTATCAAA 345501 AAAG-GCGAAGGCGACAGTGCG 1 AAAGTGCGAAGGCGACAGTGCG 345522 AAAGTGCGAAGGCGACAGTGCG 1 AAAGTGCGAAGGCGACAGTGCG * 345544 -AAGTTGCGAAAGCGA 1 AAAG-TGCGAAGGCGA 345559 GGGAGCGATA Statistics Matches: 34, Mismatches: 1, Indels: 3 0.89 0.03 0.08 Matches are distributed among these distances: 21 7 0.21 22 27 0.79 ACGTcount: A:0.34, C:0.17, G:0.40, T:0.09 Consensus pattern (22 bp): AAAGTGCGAAGGCGACAGTGCG Found at i:345597 original size:14 final size:15 Alignment explanation

Indices: 345575--345714 Score: 68 Period size: 14 Copynumber: 9.5 Consensus size: 15 345565 GATAGTAGTA * 345575 TCGCTCCTTCGC-CT 1 TCGCACCTTCGCACT 345589 TCGCACCTTCGCACTT 1 TCGCACCTTCGCAC-T 345605 TCG--CCTTCGCATCT 1 TCGCACCTTCGCA-CT * * 345619 TCGC-GCTTCGC-CG 1 TCGCACCTTCGCACT * * 345632 TCGTATCTTCGCACTT 1 TCGCACCTTCGCAC-T * * 345648 TCGCTCCTTCGC-CG 1 TCGCACCTTCGCACT 345662 TCGCA-CTCTCGCACTT 1 TCGCACCT-TCGCAC-T 345678 TCG--CCTTCGCAACT 1 TCGCACCTTCGC-ACT 345692 TCGCA-CTCTCGCATCT 1 TCGCACCT-TCGCA-CT 345708 TCG-ACCT 1 TCGCACCT 345715 AAAGGCGAAA Statistics Matches: 97, Mismatches: 12, Indels: 32 0.69 0.09 0.23 Matches are distributed among these distances: 13 6 0.06 14 45 0.46 15 19 0.20 16 27 0.28 ACGTcount: A:0.09, C:0.44, G:0.16, T:0.32 Consensus pattern (15 bp): TCGCACCTTCGCACT Found at i:345607 original size:22 final size:22 Alignment explanation

Indices: 345582--345710 Score: 99 Period size: 22 Copynumber: 5.8 Consensus size: 22 345572 GTATCGCTCC * 345582 TTCGCCTTCGCACCTTCGCACT 1 TTCGCCTTCGCATCTTCGCACT * 345604 TTCGCCTTCGCATCTTCGCGC- 1 TTCGCCTTCGCATCTTCGCACT * * 345625 TTCGCCGTCGTATCTTCGCACT 1 TTCGCCTTCGCATCTTCGCACT * 345647 TTCGCTCCTTCGC--CGTCGCACT 1 TTCG--CCTTCGCATCTTCGCACT * 345669 CTCGCACTTTCGC--CTTCGCAAC- 1 TTCGC-C-TTCGCATCTTCGC-ACT 345691 TTCGCACTCTCGCATCTTCG 1 TTCGC-CT-TCGCATCTTCG 345711 ACCTAAAGGC Statistics Matches: 87, Mismatches: 11, Indels: 16 0.76 0.10 0.14 Matches are distributed among these distances: 20 1 0.01 21 20 0.23 22 54 0.62 23 2 0.02 24 10 0.11 ACGTcount: A:0.09, C:0.43, G:0.16, T:0.33 Consensus pattern (22 bp): TTCGCCTTCGCATCTTCGCACT Found at i:345660 original size:30 final size:30 Alignment explanation

Indices: 345624--345704 Score: 96 Period size: 30 Copynumber: 2.7 Consensus size: 30 345614 CATCTTCGCG * 345624 CTTCGCCGTCGTA-TCTTCGCACTTTCGCTC 1 CTTCGCCGTCGCACTC-TCGCACTTTCGCTC 345654 CTTCGCCGTCGCACTCTCGCACTTTCG--C 1 CTTCGCCGTCGCACTCTCGCACTTTCGCTC * 345682 CTTCGCAACTTCGCACTCTCGCA 1 CTTCGC--CGTCGCACTCTCGCA 345705 TCTTCGACCT Statistics Matches: 46, Mismatches: 2, Indels: 6 0.85 0.04 0.11 Matches are distributed among these distances: 28 7 0.15 30 37 0.80 31 2 0.04 ACGTcount: A:0.10, C:0.43, G:0.16, T:0.31 Consensus pattern (30 bp): CTTCGCCGTCGCACTCTCGCACTTTCGCTC Found at i:351047 original size:2 final size:2 Alignment explanation

Indices: 351034--351068 Score: 61 Period size: 2 Copynumber: 17.5 Consensus size: 2 351024 NNNNNNNNNN * 351034 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 351069 ATAAAATGTC Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00 Consensus pattern (2 bp): AG Found at i:370552 original size:12 final size:12 Alignment explanation

Indices: 370535--370560 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 370525 TTTTTTGTAA 370535 AAAAAAAAAAAG 1 AAAAAAAAAAAG 370547 AAAAAAAAAAAG 1 AAAAAAAAAAAG 370559 AA 1 AA 370561 GAAGAAGTCA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00 Consensus pattern (12 bp): AAAAAAAAAAAG Found at i:370553 original size:15 final size:15 Alignment explanation

Indices: 370533--370563 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 370523 TTTTTTTTGT 370533 AAAAAAAAAAAAAGA 1 AAAAAAAAAAAAAGA * 370548 AAAAAAAAAAGAAGA 1 AAAAAAAAAAAAAGA 370563 A 1 A 370564 GAAGTCATTT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00 Consensus pattern (15 bp): AAAAAAAAAAAAAGA Found at i:380468 original size:12 final size:13 Alignment explanation

Indices: 380446--380474 Score: 51 Period size: 12 Copynumber: 2.3 Consensus size: 13 380436 CATGGATAAA 380446 ATTATTAATCACT 1 ATTATTAATCACT 380459 ATTA-TAATCACT 1 ATTATTAATCACT 380471 ATTA 1 ATTA 380475 ATGGATAAAA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 12 0.75 13 4 0.25 ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45 Consensus pattern (13 bp): ATTATTAATCACT Found at i:382736 original size:29 final size:31 Alignment explanation

Indices: 382685--382745 Score: 72 Period size: 29 Copynumber: 2.0 Consensus size: 31 382675 CATTTATTTT * * 382685 ATAATCATCTTATTGTATGGTATGAT-ACAA 1 ATAATCATCATATTATATGGTATGATGACAA * * 382715 ATAAT-ATCATATTATATTGTATTATGACAA 1 ATAATCATCATATTATATGGTATGATGACAA 382745 A 1 A 382746 GCCAAAGGTA Statistics Matches: 26, Mismatches: 4, Indels: 2 0.81 0.12 0.06 Matches are distributed among these distances: 29 16 0.62 30 10 0.38 ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41 Consensus pattern (31 bp): ATAATCATCATATTATATGGTATGATGACAA Done.