Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold145

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: 1177157
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31

Warning! 98840 characters in sequence are not A, C, G, or T


File 3 of 3

Found at i:378139 original size:39 final size:40

Alignment explanation

Indices: 378072--378160 Score: 135 Period size: 39 Copynumber: 2.2 Consensus size: 40 378062 TCGAAAACTA * * 378072 TATAGTTAACGACGTTAATCTATATTTCACGTCTGTAAAC 1 TATAGTTAACGACGATAATCTATATTTCACATCTGTAAAC * * 378112 TATAGTTAACG-CGATAATCTATGTTTCACATCTGTTAAC 1 TATAGTTAACGACGATAATCTATATTTCACATCTGTAAAC 378151 TATAGTTAAC 1 TATAGTTAAC 378161 ACTGAAAACA Statistics Matches: 45, Mismatches: 4, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 39 34 0.76 40 11 0.24 ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38 Consensus pattern (40 bp): TATAGTTAACGACGATAATCTATATTTCACATCTGTAAAC Found at i:378956 original size:20 final size:20 Alignment explanation

Indices: 378933--379009 Score: 68 Period size: 20 Copynumber: 3.9 Consensus size: 20 378923 TGTTAAACAG 378933 ACGTAAACTATAGTTTACGA 1 ACGTAAACTATAGTTTACGA * * * 378953 ACGTGAATTATAGTTTA-GG 1 ACGTAAACTATAGTTTACGA * * 378972 ACGATAAACTAT-GATTAACAA 1 ACG-TAAACTATAG-TTTACGA * 378993 ACGTAAATTATAGTTTA 1 ACGTAAACTATAGTTTA 379010 TCTCTCAAAA Statistics Matches: 43, Mismatches: 10, Indels: 8 0.70 0.16 0.13 Matches are distributed among these distances: 19 5 0.12 20 34 0.79 21 4 0.09 ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32 Consensus pattern (20 bp): ACGTAAACTATAGTTTACGA Found at i:379623 original size:20 final size:20 Alignment explanation

Indices: 379600--379661 Score: 63 Period size: 21 Copynumber: 3.0 Consensus size: 20 379590 AGATGTGAAA 379600 TATAGATTAACGTCGGT-AAC 1 TATAG-TTAACGTCGGTAAAC * * 379620 TATAGTTTACGATCCGTAAAC 1 TATAGTTAACG-TCGGTAAAC * 379641 TATAGTTAACAGTCGATAAAC 1 TATAGTTAAC-GTCGGTAAAC 379662 CTAGTTTATC Statistics Matches: 34, Mismatches: 5, Indels: 5 0.77 0.11 0.11 Matches are distributed among these distances: 19 5 0.15 20 9 0.26 21 19 0.56 22 1 0.03 ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31 Consensus pattern (20 bp): TATAGTTAACGTCGGTAAAC Found at i:379650 original size:40 final size:41 Alignment explanation

Indices: 379541--379655 Score: 116 Period size: 39 Copynumber: 2.9 Consensus size: 41 379531 CAGTGTTAAA * * * * * 379541 TATAGTTTACAGATATGAAACATAGATT-A-TGGCGTTAAC 1 TATAGTTTACAGATGTGAAATATAGATTAACAGTCGGTAAC 379580 TATAGTTTACAGATGTGAAATATAGATTAAC-GTCGGTAAC 1 TATAGTTTACAGATGTGAAATATAGATTAACAGTCGGTAAC 379620 TATAGTTTAC-GATCCGT-AAACTATAG-TTAACAGTCG 1 TATAGTTTACAGAT--GTGAAA-TATAGATTAACAGTCG 379656 ATAAACCTAG Statistics Matches: 66, Mismatches: 4, Indels: 10 0.82 0.05 0.12 Matches are distributed among these distances: 39 29 0.44 40 26 0.39 41 11 0.17 ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33 Consensus pattern (41 bp): TATAGTTTACAGATGTGAAATATAGATTAACAGTCGGTAAC Found at i:381211 original size:14 final size:15 Alignment explanation

Indices: 381186--381215 Score: 53 Period size: 14 Copynumber: 2.1 Consensus size: 15 381176 TGGTAGTTAC 381186 TGATTATTGTGTTGG 1 TGATTATTGTGTTGG 381201 TGATT-TTGTGTTGG 1 TGATTATTGTGTTGG 381215 T 1 T 381216 ATATGTGGAG Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 10 0.67 15 5 0.33 ACGTcount: A:0.10, C:0.00, G:0.33, T:0.57 Consensus pattern (15 bp): TGATTATTGTGTTGG Found at i:387623 original size:84 final size:86 Alignment explanation

Indices: 387526--387691 Score: 246 Period size: 89 Copynumber: 1.9 Consensus size: 86 387516 AGATTGCCAG * * * 387526 AAAAAAATATTTTGTCTGTCC-TT-AAAAATGAATTATCAGAATGATTGATAGTTTTAATAATTG 1 AAAAAAATATTTTGCCTGTCCTTTAAAAAATGAATTATCAGAATGATTGAAAGTTTGAATAATTG 387589 GTCATACATATCAGTTAGAGA 66 GTCATACATATCAGTTAGAGA * * 387610 AAAAAAATGTTTTGCCTGTCCTTATTAAAAAAATGAATTATCAGTATGATTGAAAGTTTGAATAA 1 AAAAAAATATTTTGCCTGTCC-T-TT-AAAAAATGAATTATCAGAATGATTGAAAGTTTGAATAA 387675 TTGGTCATACATATCAG 63 TTGGTCATACATATCAG 387692 CTTGAGTTAT Statistics Matches: 72, Mismatches: 5, Indels: 5 0.88 0.06 0.06 Matches are distributed among these distances: 84 19 0.26 87 2 0.03 89 51 0.71 ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36 Consensus pattern (86 bp): AAAAAAATATTTTGCCTGTCCTTTAAAAAATGAATTATCAGAATGATTGAAAGTTTGAATAATTG GTCATACATATCAGTTAGAGA Found at i:393121 original size:10 final size:10 Alignment explanation

Indices: 393106--393133 Score: 56 Period size: 10 Copynumber: 2.8 Consensus size: 10 393096 TATATACATA 393106 AAAAAAAACC 1 AAAAAAAACC 393116 AAAAAAAACC 1 AAAAAAAACC 393126 AAAAAAAA 1 AAAAAAAA 393134 AACTCTCTCT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 18 1.00 ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00 Consensus pattern (10 bp): AAAAAAAACC Found at i:393691 original size:19 final size:19 Alignment explanation

Indices: 393667--393704 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 393657 TCCTAAATAT 393667 TGGCCCAGTTTAGTTTATG 1 TGGCCCAGTTTAGTTTATG 393686 TGGCCCAGTTTAGTTTATG 1 TGGCCCAGTTTAGTTTATG 393705 CCAAGTAGGA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42 Consensus pattern (19 bp): TGGCCCAGTTTAGTTTATG Found at i:397707 original size:21 final size:21 Alignment explanation

Indices: 397673--397841 Score: 257 Period size: 21 Copynumber: 8.0 Consensus size: 21 397663 AGGAATGTAA 397673 TCATCTCAAAGTACAGGTAGG 1 TCATCTCAAAGTACAGGTAGG * * * 397694 TCAACTCAAGGTACAGGTAGT 1 TCATCTCAAAGTACAGGTAGG 397715 TCATCTCAAAGTACAGGTAGG 1 TCATCTCAAAGTACAGGTAGG * 397736 TCAACTCAAAGTACAGGTAGG 1 TCATCTCAAAGTACAGGTAGG * * 397757 TCATCTCAAAGTATAAGTAGG 1 TCATCTCAAAGTACAGGTAGG * * 397778 TCATCTCAAAGTATAAGTAGG 1 TCATCTCAAAGTACAGGTAGG 397799 TCATCTCAAAGTACAGGTAGG 1 TCATCTCAAAGTACAGGTAGG * 397820 TCATCTCAAAGTTCAGGTAGG 1 TCATCTCAAAGTACAGGTAGG 397841 T 1 T 397842 TTTAATTAGC Statistics Matches: 135, Mismatches: 13, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 21 135 1.00 ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25 Consensus pattern (21 bp): TCATCTCAAAGTACAGGTAGG Found at i:404458 original size:161 final size:160 Alignment explanation

Indices: 403954--404442 Score: 753 Period size: 161 Copynumber: 3.0 Consensus size: 160 403944 GGTCCACCAA * * * 403954 CAGTTTCTGTTCATTTTCTTCGCAGAGTATAAACATATTGAAATGAAATTTGGTATACAGGTTTA 1 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA * * * * 404019 TCAAGATAATATCTAGGTCAGGTTTGATACTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG 66 TCATGATAATATCTAGGTCAAG-TTGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG 404084 CCCTTGGACATAGAAAAATTCCAGTTATTTG 130 CCCTTGGACATAGAAAAATTCCAGTTATTTG * * 404115 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATGGTAATGAAATTTGGTATACAGGTTTA 1 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA * 404180 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCAAGAGAGTTATGG 66 TCATGATAATATCTAGGTCAAGTT-GATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG * * 404245 CCCTTGGACTTAGAAACATTCCAGTTATTTG 130 CCCTTGGACATAGAAAAATTCCAGTTATTTG * * * 404276 CAGTTTCTGCTCATTTTCTTTGCAAAGGATGAACATATTGAAATAAAATTTGGTATACAGGTTTA 1 CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA * * * * 404341 TCATGATAATATCTAGGTCAAGTATGATTTTGGTTACAATTGAGCAATTTTCAACAGAGTTATGT 66 TCATGATAATATCTAGGTCAAGT-TGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG * * * 404406 CCCTTTGACGTAGAAAAATTGCAGTTATTTG 130 CCCTTGGACATAGAAAAATTCCAGTTATTTG 404437 CAGTTT 1 CAGTTT 404443 ACGTTAATTT Statistics Matches: 300, Mismatches: 26, Indels: 4 0.91 0.08 0.01 Matches are distributed among these distances: 160 2 0.01 161 297 0.99 162 1 0.00 ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36 Consensus pattern (160 bp): CAGTTTCTGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA TCATGATAATATCTAGGTCAAGTTGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGGC CCTTGGACATAGAAAAATTCCAGTTATTTG Found at i:416772 original size:14 final size:14 Alignment explanation

Indices: 416725--416772 Score: 71 Period size: 14 Copynumber: 3.4 Consensus size: 14 416715 CGGTCGAGGT * 416725 GCGAAGTTGCGACG 1 GCGAAGTTGCGAAG 416739 GCGAAAG-TGCGAAG 1 GCG-AAGTTGCGAAG 416753 GCGAAGTTGCGAAG 1 GCGAAGTTGCGAAG 416767 GCGAAG 1 GCGAAG 416773 AAGCAATACT Statistics Matches: 31, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 13 3 0.10 14 25 0.81 15 3 0.10 ACGTcount: A:0.29, C:0.17, G:0.44, T:0.10 Consensus pattern (14 bp): GCGAAGTTGCGAAG Found at i:420364 original size:49 final size:49 Alignment explanation

Indices: 420307--420502 Score: 326 Period size: 49 Copynumber: 4.1 Consensus size: 49 420297 TTGGTAAAAT * * 420307 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAAG 1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG 420356 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG 1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG * 420405 TAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTG--A- 1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG * * 420451 TAGACAACTAAACAAACAACAGGGAGGAATGAGGAAGGATTAGTGAAAG 1 TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG 420500 TAG 1 TAG 420503 NNNNNNNNNN Statistics Matches: 138, Mismatches: 6, Indels: 6 0.92 0.04 0.04 Matches are distributed among these distances: 46 42 0.30 47 1 0.01 48 1 0.01 49 94 0.68 ACGTcount: A:0.47, C:0.10, G:0.27, T:0.16 Consensus pattern (49 bp): TAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAAAG Found at i:420495 original size:95 final size:97 Alignment explanation

Indices: 420307--420502 Score: 324 Period size: 95 Copynumber: 2.0 Consensus size: 97 420297 TTGGTAAAAT * 420307 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAAGTAGACAACTAAACAAT 1 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTG-AAGTAGACAACTAAACAAA * 420372 CAACAGGGAGGAATGAGTAAGGATTAGTGAAAG 65 CAACAGGGAGGAATGAGGAAGGATTAGTGAAAG * * * 420405 TAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTG-A-TAGACAACTAAACAAAC 1 TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAGTAGACAACTAAACAAAC 420468 AACAGGGAGGAATGAGGAAGGATTAGTGAAAG 66 AACAGGGAGGAATGAGGAAGGATTAGTGAAAG 420500 TAG 1 TAG 420503 NNNNNNNNNN Statistics Matches: 93, Mismatches: 5, Indels: 3 0.92 0.05 0.03 Matches are distributed among these distances: 95 50 0.54 96 1 0.01 98 42 0.45 ACGTcount: A:0.47, C:0.10, G:0.27, T:0.16 Consensus pattern (97 bp): TAGACAACTAAACAATCAACAGAGAGGAATGAGTAAGGACTAGTGAAGTAGACAACTAAACAAAC AACAGGGAGGAATGAGGAAGGATTAGTGAAAG Found at i:420636 original size:49 final size:49 Alignment explanation

Indices: 420564--421077 Score: 866 Period size: 49 Copynumber: 10.5 Consensus size: 49 420554 NNNNNNNNNN * ** 420564 AGTAGACAACTAAATAATCAACAGAAAGGAATGAGTAAGGATTAGTGAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * 420613 AGTAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA ** * 420662 AGTAGACAACTAAACAATCAACAGGGAATAATGAATAAGGATTAGTGAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * 420711 AGTAGACAACTAAACAATCAACAGGGAGGAGTGAGTAAGGATTAGTGAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA 420760 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * 420809 AGTAGACAACTAAATAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * * 420858 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAAGATTAGTAAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * 420907 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTTAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * * 420956 GGTAGACAACTAAACAATCAACAGGGAGGAGTGAGTAAGGATTAGTGAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * * 421005 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAAGATTAGTTAA 1 AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA * * 421054 GGTAGACAACTAAATAATCAACAG 1 AGTAGACAACTAAACAATCAACAG 421078 CCTTTCAATT Statistics Matches: 439, Mismatches: 26, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 49 439 1.00 ACGTcount: A:0.48, C:0.10, G:0.25, T:0.18 Consensus pattern (49 bp): AGTAGACAACTAAACAATCAACAGGGAGGAATGAGTAAGGATTAGTGAA Found at i:428540 original size:10 final size:10 Alignment explanation

Indices: 428527--428556 Score: 51 Period size: 10 Copynumber: 3.0 Consensus size: 10 428517 AAAAATCGCC 428527 AGAGTTCTCT 1 AGAGTTCTCT 428537 AGAGTTCTCT 1 AGAGTTCTCT * 428547 AGAATTCTCT 1 AGAGTTCTCT 428557 GTTTAGTAGT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40 Consensus pattern (10 bp): AGAGTTCTCT Found at i:437299 original size:2 final size:2 Alignment explanation

Indices: 437294--437338 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 437284 TATATATATA 437294 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 437336 TG T 1 TG T 437339 TGGTGTAGTT Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51 Consensus pattern (2 bp): TG Found at i:441178 original size:2 final size:2 Alignment explanation

Indices: 441171--441230 Score: 113 Period size: 2 Copynumber: 30.5 Consensus size: 2 441161 TTATCTCCCT 441171 GA GA GA GA GA G- 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 441212 GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA G 441231 NNNNNNNNNN Statistics Matches: 57, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 1 1 0.02 2 56 0.98 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:452258 original size:2 final size:2 Alignment explanation

Indices: 452251--452318 Score: 118 Period size: 2 Copynumber: 34.0 Consensus size: 2 452241 CTATCTCCCT 452251 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 * * 452293 GA GA GA GA GA GA GA GA AA TA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA 452319 TTACAAGTAC Statistics Matches: 63, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 63 1.00 ACGTcount: A:0.51, C:0.00, G:0.47, T:0.01 Consensus pattern (2 bp): GA Found at i:453161 original size:2 final size:2 Alignment explanation

Indices: 453156--453216 Score: 122 Period size: 2 Copynumber: 30.5 Consensus size: 2 453146 ATTAAAATCC 453156 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 453198 AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG A 453217 TTTTCTCAAC 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:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:454748 original size:3 final size:3 Alignment explanation

Indices: 454722--454770 Score: 53 Period size: 3 Copynumber: 16.0 Consensus size: 3 454712 AATATGCATG * * * * 454722 TAT TCT TAT TAT CAT TAAT CAT TAT TAT TAT TAT CAT TAT TAT TAT 1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT 454768 TAT 1 TAT 454771 AAAGGAATAC Statistics Matches: 37, Mismatches: 8, Indels: 2 0.79 0.17 0.04 Matches are distributed among these distances: 3 35 0.95 4 2 0.05 ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59 Consensus pattern (3 bp): TAT Found at i:460033 original size:10 final size:10 Alignment explanation

Indices: 460018--460044 Score: 54 Period size: 10 Copynumber: 2.7 Consensus size: 10 460008 GAGCGTCGAG 460018 TTGAACTATA 1 TTGAACTATA 460028 TTGAACTATA 1 TTGAACTATA 460038 TTGAACT 1 TTGAACT 460045 CTGGCGTAAG Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 17 1.00 ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41 Consensus pattern (10 bp): TTGAACTATA Found at i:461888 original size:15 final size:13 Alignment explanation

Indices: 461860--461894 Score: 52 Period size: 15 Copynumber: 2.5 Consensus size: 13 461850 TATTCATTAT 461860 TTTATTTTATTTA 1 TTTATTTTATTTA 461873 TTTATTTGTAATTTA 1 TTTATTT-T-ATTTA 461888 TTTATTT 1 TTTATTT 461895 AGTGCCACTA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 13 7 0.35 14 1 0.05 15 12 0.60 ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74 Consensus pattern (13 bp): TTTATTTTATTTA Found at i:461889 original size:19 final size:18 Alignment explanation

Indices: 461856--461895 Score: 62 Period size: 19 Copynumber: 2.2 Consensus size: 18 461846 TGTTTATTCA * 461856 TTATTTTATTTTATTTAT 1 TTATTTTAATTTATTTAT 461874 TTATTTGTAATTTATTTAT 1 TTATTT-TAATTTATTTAT 461893 TTA 1 TTA 461896 GTGCCACTAT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 18 6 0.30 19 14 0.70 ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72 Consensus pattern (18 bp): TTATTTTAATTTATTTAT Found at i:464457 original size:4 final size:4 Alignment explanation

Indices: 464448--464502 Score: 110 Period size: 4 Copynumber: 13.8 Consensus size: 4 464438 TATTTGTAGT 464448 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA 1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA 464496 TCTA TCT 1 TCTA TCT 464503 GTCTGTCTGT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 51 1.00 ACGTcount: A:0.24, C:0.25, G:0.00, T:0.51 Consensus pattern (4 bp): TCTA Found at i:467468 original size:64 final size:64 Alignment explanation

Indices: 467367--467498 Score: 255 Period size: 64 Copynumber: 2.1 Consensus size: 64 467357 TTTTTCTATA * 467367 ATTAAGGTCTTCCGTTTCCAACGGAAGCCCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT 1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT 467431 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT 1 ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT 467495 ATTA 1 ATTA 467499 TTATTATTTT Statistics Matches: 67, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 64 67 1.00 ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47 Consensus pattern (64 bp): ATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATAGTGATTGTTAGGTTTTTTCTTTCTTTCTT Found at i:476638 original size:12 final size:12 Alignment explanation

Indices: 476621--476671 Score: 66 Period size: 12 Copynumber: 4.2 Consensus size: 12 476611 AGTGCCCATA * 476621 ATGGAACATTGC 1 ATGGAACATTAC * 476633 ATGGAACATTGC 1 ATGGAACATTAC * 476645 GTGGAACATTAC 1 ATGGAACATTAC * 476657 AGGGAACATTAC 1 ATGGAACATTAC 476669 ATG 1 ATG 476672 CAAACCAAAC Statistics Matches: 34, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 34 1.00 ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24 Consensus pattern (12 bp): ATGGAACATTAC Found at i:484340 original size:22 final size:22 Alignment explanation

Indices: 484315--484364 Score: 57 Period size: 22 Copynumber: 2.3 Consensus size: 22 484305 TCGCTTCTTT 484315 GCCTTTGCAA-CTTCGCACTCTC 1 GCCTTTG-AATCTTCGCACTCTC * * * 484337 GCCTTCGAATCTTCGCGCTTTC 1 GCCTTTGAATCTTCGCACTCTC 484359 GCCTTT 1 GCCTTT 484365 TTAGCTCATA Statistics Matches: 23, Mismatches: 4, Indels: 2 0.79 0.14 0.07 Matches are distributed among these distances: 21 2 0.09 22 21 0.91 ACGTcount: A:0.10, C:0.38, G:0.16, T:0.36 Consensus pattern (22 bp): GCCTTTGAATCTTCGCACTCTC Found at i:485791 original size:11 final size:11 Alignment explanation

Indices: 485761--485792 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 485751 TAAAGACGGT * 485761 CTTTAAGCCAC 1 CTTTAAGCTAC 485772 CTTTAAGCTAC 1 CTTTAAGCTAC 485783 CTTTAAGCTA 1 CTTTAAGCTA 485793 TATGTATTGC Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:485851 original size:22 final size:22 Alignment explanation

Indices: 485801--485853 Score: 70 Period size: 22 Copynumber: 2.4 Consensus size: 22 485791 TATATGTATT * 485801 GCTTAAAGGTGGCTTAAAGAAA 1 GCTTAAAGATGGCTTAAAGAAA * ** 485823 GCGTAAAGATGGCTTAAAGGCA 1 GCTTAAAGATGGCTTAAAGAAA 485845 GCTTAAAGA 1 GCTTAAAGA 485854 CTATCTTTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21 Consensus pattern (22 bp): GCTTAAAGATGGCTTAAAGAAA Found at i:485874 original size:11 final size:11 Alignment explanation

Indices: 485858--485886 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 485848 TAAAGACTAT 485858 CTTTAAGCCAC 1 CTTTAAGCCAC 485869 CTTTAAGCCAC 1 CTTTAAGCCAC 485880 CTTTAAG 1 CTTTAAG 485887 GACAACTTAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:485934 original size:11 final size:11 Alignment explanation

Indices: 485918--485971 Score: 99 Period size: 11 Copynumber: 4.9 Consensus size: 11 485908 GTCCAAACTT 485918 CTTTAAGCCAC 1 CTTTAAGCCAC 485929 CTTTAAGCCAC 1 CTTTAAGCCAC * 485940 CTTTAAGCTAC 1 CTTTAAGCCAC 485951 CTTTAAGCCAC 1 CTTTAAGCCAC 485962 CTTTAAGCCA 1 CTTTAAGCCA 485972 TTAAAAAAAA Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 41 1.00 ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:487187 original size:112 final size:112 Alignment explanation

Indices: 486990--487213 Score: 421 Period size: 112 Copynumber: 2.0 Consensus size: 112 486980 AACCCTGACG * 486990 TGCACCTGGGCAAACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 1 TGCACCTGGGCAAACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT * 487055 TTCTTAAGTTGGACAAACAATAGACTTTAATTAGATATACACAAACA 66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA * 487102 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 1 TGCACCTGGGCAAACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 487167 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA 66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA 487214 AACAAAACTA Statistics Matches: 109, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 112 109 1.00 ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33 Consensus pattern (112 bp): TGCACCTGGGCAAACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA Found at i:487434 original size:2 final size:2 Alignment explanation

Indices: 487427--487466 Score: 71 Period size: 2 Copynumber: 20.0 Consensus size: 2 487417 CGGATGAACT * 487427 GA GA GA GA GA GA AA 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 487467 TTTTTTCACC Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00 Consensus pattern (2 bp): GA Found at i:487828 original size:22 final size:22 Alignment explanation

Indices: 487800--487860 Score: 61 Period size: 22 Copynumber: 2.8 Consensus size: 22 487790 AATATTGACT * * 487800 TAAAGGCCACTTAAAGACAGTG 1 TAAAGGCCAATTAAAGACAGCG * * 487822 TAAAGG-CAGTGTAAAGAGAGCG 1 TAAAGGCCAAT-TAAAGACAGCG * 487844 TAAATGCCAATTAAAGA 1 TAAAGGCCAATTAAAGA 487861 TGCTTAAAGG Statistics Matches: 32, Mismatches: 5, Indels: 4 0.78 0.12 0.10 Matches are distributed among these distances: 21 3 0.09 22 26 0.81 23 3 0.09 ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18 Consensus pattern (22 bp): TAAAGGCCAATTAAAGACAGCG Found at i:487977 original size:11 final size:11 Alignment explanation

Indices: 487961--487990 Score: 51 Period size: 11 Copynumber: 2.7 Consensus size: 11 487951 CGTTTAAGCT * 487961 CCTTTAAGTCA 1 CCTTTAAGCCA 487972 CCTTTAAGCCA 1 CCTTTAAGCCA 487983 CCTTTAAG 1 CCTTTAAG 487991 GACTTGCTTA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33 Consensus pattern (11 bp): CCTTTAAGCCA Found at i:490503 original size:53 final size:53 Alignment explanation

Indices: 490430--490596 Score: 183 Period size: 53 Copynumber: 3.2 Consensus size: 53 490420 AAAAAATATT * * * 490430 TTATTTCAATAATGGTTGTAATGAAATGCAT-CTTTAACCACAATTGAAATAAA 1 TTATTTCAATAGTGGTTGTAATGAAATGCATAC-CTAACCACAATTGAAACAAA * ** * 490483 TTATTTCAATAGTTGTTGTAATGAAATGCATACCTAACCACTTTTGAAACAAT 1 TTATTTCAATAGTGGTTGTAATGAAATGCATACCTAACCACAATTGAAACAAA * * * * * * * * 490536 TTATTTCAATAGTGGTTATAATGAAACGGATACCCAACCACTAGTGAAATAAT 1 TTATTTCAATAGTGGTTGTAATGAAATGCATACCTAACCACAATTGAAACAAA 490589 TTATTTCA 1 TTATTTCA 490597 TTCAATATTG Statistics Matches: 98, Mismatches: 15, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 53 97 0.99 54 1 0.01 ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36 Consensus pattern (53 bp): TTATTTCAATAGTGGTTGTAATGAAATGCATACCTAACCACAATTGAAACAAA Found at i:491497 original size:17 final size:17 Alignment explanation

Indices: 491475--491509 Score: 61 Period size: 17 Copynumber: 2.1 Consensus size: 17 491465 ATTGAAATAA 491475 TTTATTTCAATAATGGT 1 TTTATTTCAATAATGGT * 491492 TTTATTTCAATAGTGGT 1 TTTATTTCAATAATGGT 491509 T 1 T 491510 GCAACAGGGA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54 Consensus pattern (17 bp): TTTATTTCAATAATGGT Found at i:497357 original size:165 final size:166 Alignment explanation

Indices: 497160--497517 Score: 456 Period size: 168 Copynumber: 2.2 Consensus size: 166 497150 GGGGCCACGA * * * 497160 ATTTCACAATTTTGGTAGAAGGCTTCATGGACATCATAATCA-TGCATTTATTTTTTAACAAATA 1 ATTTCACAATTTTGGTAGAGGGCTTAATGGACATCATAAT-ATTGCATTTAGTTTTTAACAAATA * * * * * * * 497224 TATATGGAAGTAGAGAAG-ATTGTCTACGATTTAATATATTTTAACCT-TATGGCCAT-ATTGGT 65 TATATGGAAGCAGAGAAGAATTGTCTAAGATGTAATACATTTTAA-ATATATGACCATCA-TGGC * * 497286 CCCA-CTGTAGAGCCAGAACCCCTGACAAAGGGGTCATAC 128 CCCATC-CTAGAGCCAGAACCCCTGACAAAGGGGCCATAC * 497325 ATTTCACAATATTGGTAGAGGGCTTAATGGACATCATAATATTGCATTTAGTTTTTAACAAATAT 1 ATTTCACAATTTTGGTAGAGGGCTTAATGGACATCATAATATTGCATTTAGTTTTTAACAAATAT * * 497390 ATATGGGAGCAGAGAAGAATATTTTCTAAGATGTAATACATTTTAAATATATGACCATCATGGCC 66 ATATGGAAGCAGAGAAG-A-ATTGTCTAAGATGTAATACATTTTAAATATATGACCATCATGGCC * ** * 497455 CCATCCTAGATCCAGAACCCCTGACCTAGGGGCCATGC 129 CCATCCTAGAGCCAGAACCCCTGACAAAGGGGCCATAC 497493 ATTTCACAATTTTGGTAGAGGGCTT 1 ATTTCACAATTTTGGTAGAGGGCTT 497518 CCTGGTTATC Statistics Matches: 166, Mismatches: 20, Indels: 11 0.84 0.10 0.06 Matches are distributed among these distances: 164 1 0.01 165 74 0.45 167 1 0.01 168 88 0.53 169 2 0.01 ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32 Consensus pattern (166 bp): ATTTCACAATTTTGGTAGAGGGCTTAATGGACATCATAATATTGCATTTAGTTTTTAACAAATAT ATATGGAAGCAGAGAAGAATTGTCTAAGATGTAATACATTTTAAATATATGACCATCATGGCCCC ATCCTAGAGCCAGAACCCCTGACAAAGGGGCCATAC Found at i:498240 original size:2 final size:2 Alignment explanation

Indices: 498235--498280 Score: 74 Period size: 2 Copynumber: 23.0 Consensus size: 2 498225 AAAACAGTTT * * 498235 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GG 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 498277 GA GA 1 GA GA 498281 AAGATTCAGC Statistics Matches: 42, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00 Consensus pattern (2 bp): GA Found at i:504190 original size:13 final size:13 Alignment explanation

Indices: 504172--504200 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 504162 AAAATAGTGC 504172 AACTTCAAAAGTA 1 AACTTCAAAAGTA 504185 AACTTCAAAAGTA 1 AACTTCAAAAGTA 504198 AAC 1 AAC 504201 AAAAAACCAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21 Consensus pattern (13 bp): AACTTCAAAAGTA Found at i:505166 original size:2 final size:2 Alignment explanation

Indices: 505161--505203 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 505151 GTGTGTGTGT 505161 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 505203 G 1 G 505204 NNNNNNNNNN Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:512685 original size:14 final size:13 Alignment explanation

Indices: 512666--512710 Score: 56 Period size: 14 Copynumber: 3.4 Consensus size: 13 512656 AGTTAGTTAT 512666 ATTTTTTTCTAGAC 1 ATTTTTTTCTA-AC 512680 ATTTTTTTCTAA- 1 ATTTTTTTCTAAC * 512692 ACTTTTTTCTACAC 1 ATTTTTTTCTA-AC 512706 ATTTT 1 ATTTT 512711 AAAAAAAAAA Statistics Matches: 27, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 12 10 0.37 13 2 0.07 14 15 0.56 ACGTcount: A:0.22, C:0.16, G:0.02, T:0.60 Consensus pattern (13 bp): ATTTTTTTCTAAC Found at i:521653 original size:4 final size:4 Alignment explanation

Indices: 521635--521679 Score: 63 Period size: 4 Copynumber: 11.2 Consensus size: 4 521625 AATGAGTTTT * * * 521635 TCTG TCCG TCCG TCTG TCTG TCTG TCTG TCTG TCTC TCTG TCTG T 1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG T 521680 AAACTTTTCA Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 4 37 1.00 ACGTcount: A:0.00, C:0.31, G:0.22, T:0.47 Consensus pattern (4 bp): TCTG Found at i:526764 original size:21 final size:21 Alignment explanation

Indices: 526738--526801 Score: 83 Period size: 21 Copynumber: 3.0 Consensus size: 21 526728 TTGGGGTGTT * 526738 AGATTTCAATGCTATGGTATG 1 AGATTTCAATGCTATGCTATG * 526759 AGATTTCAATGCTATACTATG 1 AGATTTCAATGCTATGCTATG * * * 526780 AAATGTCAATGATATGCTATG 1 AGATTTCAATGCTATGCTATG 526801 A 1 A 526802 TATGGTGTAT Statistics Matches: 37, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 37 1.00 ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36 Consensus pattern (21 bp): AGATTTCAATGCTATGCTATG Found at i:534142 original size:28 final size:29 Alignment explanation

Indices: 534110--534177 Score: 93 Period size: 29 Copynumber: 2.4 Consensus size: 29 534100 ATGCATGATA * * * 534110 TACTTGTATTTTG-CCGTGTAGTTCGGTG 1 TACTTGTATATTGTCCGTGTAGTACGGAG 534138 TACTTGTATATTGTCCGTGTAGTACGGAG 1 TACTTGTATATTGTCCGTGTAGTACGGAG * 534167 TATTTGTATAT 1 TACTTGTATAT 534178 CGTTTTGACG Statistics Matches: 35, Mismatches: 4, Indels: 1 0.88 0.10 0.03 Matches are distributed among these distances: 28 12 0.34 29 23 0.66 ACGTcount: A:0.18, C:0.12, G:0.25, T:0.46 Consensus pattern (29 bp): TACTTGTATATTGTCCGTGTAGTACGGAG Found at i:538318 original size:43 final size:43 Alignment explanation

Indices: 538270--538364 Score: 122 Period size: 43 Copynumber: 2.2 Consensus size: 43 538260 ATATGTTTTT 538270 TCGTAATAAAGAGATAATTAACTCGCT-ATAACGAGATCGTTTC 1 TCGTAATAAAGAGATAATTAACTCG-TAATAACGAGATCGTTTC * ** * 538313 TCGTAA-ATATGAGATAATTAACTCGTAATTTCGAGATCTTTTC 1 TCGTAATA-AAGAGATAATTAACTCGTAATAACGAGATCGTTTC 538356 TCGTAATAA 1 TCGTAATAA 538365 CGATATTTTT Statistics Matches: 45, Mismatches: 4, Indels: 6 0.82 0.07 0.11 Matches are distributed among these distances: 42 2 0.04 43 42 0.93 44 1 0.02 ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35 Consensus pattern (43 bp): TCGTAATAAAGAGATAATTAACTCGTAATAACGAGATCGTTTC Found at i:538360 original size:21 final size:21 Alignment explanation

Indices: 538300--538434 Score: 83 Period size: 21 Copynumber: 6.3 Consensus size: 21 538290 ACTCGCTATA * * 538300 ACGAGATCGTTTCTCGTAAAT 1 ACGAGATCTTTTCTCGTAATT * * ** 538321 ATGAGATAATTAACTCGTAATT 1 ACGAGAT-CTTTTCTCGTAATT * * 538343 TCGAGATCTTTTCTCGTAATA 1 ACGAGATCTTTTCTCGTAATT * * 538364 ACGATATTTTTTCTCGTAATT 1 ACGAGATCTTTTCTCGTAATT * ** ** * 538385 CCGAGAAAATTAACTCGTAATA 1 ACGAG-ATCTTTTCTCGTAATT * 538407 ACGAGATCTGTTT-TGGTAATT 1 ACGAGATCT-TTTCTCGTAATT 538428 ACGAGAT 1 ACGAGAT 538435 AATCAACTCA Statistics Matches: 81, Mismatches: 30, Indels: 6 0.69 0.26 0.05 Matches are distributed among these distances: 21 51 0.63 22 30 0.37 ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37 Consensus pattern (21 bp): ACGAGATCTTTTCTCGTAATT Found at i:538426 original size:43 final size:43 Alignment explanation

Indices: 538355--538443 Score: 108 Period size: 43 Copynumber: 2.1 Consensus size: 43 538345 GAGATCTTTT * * * * 538355 CTCGTAATAACGATATTTTTTCTCGTAATTCCGAGAAAATTAA 1 CTCGTAATAACGAGATTGTTTCTCGTAATTACGAGAAAATCAA * * 538398 CTCGTAATAACGAGATCTGTTT-TGGTAATTACGAGATAATCAA 1 CTCGTAATAACGAGAT-TGTTTCTCGTAATTACGAGAAAATCAA 538441 CTC 1 CTC 538444 ATTCGTAATT Statistics Matches: 39, Mismatches: 6, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 43 35 0.90 44 4 0.10 ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35 Consensus pattern (43 bp): CTCGTAATAACGAGATTGTTTCTCGTAATTACGAGAAAATCAA Found at i:538434 original size:107 final size:106 Alignment explanation

Indices: 538238--538443 Score: 258 Period size: 107 Copynumber: 1.9 Consensus size: 106 538228 CTTATGATAA * * 538238 CGAGATCTTTTCTTAAATTACGATATGTTTTTTCGTAATAAAGAGATAATTAACTCGCTATAACG 1 CGAGATCTTTTCTTAAATAACGATATGTTTTTTCGTAATAAAGAGAAAATTAACTCGCTATAACG * * 538303 AGATCGTTTCTCGTAAATATGAGATAATTAACTCGTAATTT 66 AGATCGTTTCTCGTAAATACGAGATAATCAACTCGTAATTT *** 538344 CGAGATCTTTTCTCGT-AATAACGATAT-TTTTTCTCGTAATTCCGAGAAAATTAACTCG-TAAT 1 CGAGATCTTTTCT--TAAATAACGATATGTTTTT-TCGTAATAAAGAGAAAATTAACTCGCT-AT * * 538406 AACGAGATCTGTTT-TGGTAATTACGAGATAATCAACTC 62 AACGAGATC-GTTTCTCGTAAATACGAGATAATCAACTC 538444 ATTCGTAATT Statistics Matches: 86, Mismatches: 9, Indels: 9 0.83 0.09 0.09 Matches are distributed among these distances: 106 19 0.22 107 62 0.72 108 5 0.06 ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37 Consensus pattern (106 bp): CGAGATCTTTTCTTAAATAACGATATGTTTTTTCGTAATAAAGAGAAAATTAACTCGCTATAACG AGATCGTTTCTCGTAAATACGAGATAATCAACTCGTAATTT Found at i:539307 original size:21 final size:21 Alignment explanation

Indices: 539283--539340 Score: 64 Period size: 21 Copynumber: 2.8 Consensus size: 21 539273 GTCATTGGGA 539283 TATCATTTGGTATCATAAGGG 1 TATCATTTGGTATCATAAGGG * * ** 539304 TATCAGTAGGTATCATTGGGG 1 TATCATTTGGTATCATAAGGG 539325 T-TCATTTGGGTATCAT 1 TATCATTT-GGTATCAT 539341 TGGAGTATTA Statistics Matches: 30, Mismatches: 6, Indels: 2 0.79 0.16 0.05 Matches are distributed among these distances: 20 4 0.13 21 26 0.87 ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40 Consensus pattern (21 bp): TATCATTTGGTATCATAAGGG Found at i:539341 original size:21 final size:21 Alignment explanation

Indices: 539312--539378 Score: 73 Period size: 21 Copynumber: 3.2 Consensus size: 21 539302 GGTATCAGTA * 539312 GGTATCATTGGGGTTCATTTG 1 GGTATCATTGGGGTTCATTGG * * 539333 GGTATCATTGGAGTATTATTGG 1 GGTATCATTGGGGT-TCATTGG * * 539355 GGT-TCATCGCGGTTCATTGG 1 GGTATCATTGGGGTTCATTGG 539375 GGTA 1 GGTA 539379 AAATGACGCA Statistics Matches: 37, Mismatches: 7, Indels: 4 0.77 0.15 0.08 Matches are distributed among these distances: 20 9 0.24 21 20 0.54 22 8 0.22 ACGTcount: A:0.16, C:0.10, G:0.34, T:0.39 Consensus pattern (21 bp): GGTATCATTGGGGTTCATTGG Found at i:539348 original size:11 final size:10 Alignment explanation

Indices: 539261--539355 Score: 70 Period size: 11 Copynumber: 9.2 Consensus size: 10 539251 TGCTCATTAT 539261 GGTATCATTG 1 GGTATCATTG 539271 TGG--TCATTG 1 -GGTATCATTG * 539280 GGATATCATTT 1 GG-TATCATTG * 539291 GGTATCATAAG 1 GGTATCAT-TG * * 539302 GGTATCAGTA 1 GGTATCATTG 539312 GGTATCATTGG 1 GGTATCATT-G 539323 GGT-TCATTTG 1 GGTATCA-TTG 539333 GGTATCATTG 1 GGTATCATTG * 539343 GAGTATTATTG 1 G-GTATCATTG 539354 GG 1 GG 539356 GTTCATCGCG Statistics Matches: 67, Mismatches: 9, Indels: 17 0.72 0.10 0.18 Matches are distributed among these distances: 8 2 0.03 9 6 0.09 10 26 0.39 11 33 0.49 ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39 Consensus pattern (10 bp): GGTATCATTG Found at i:545777 original size:10 final size:10 Alignment explanation

Indices: 545764--545949 Score: 152 Period size: 10 Copynumber: 18.2 Consensus size: 10 545754 CCCCCCCCCC 545764 AAAAAAAAC- 1 AAAAAAAACA 545773 AAAAAAAACA 1 AAAAAAAACA 545783 AAAACAAAA-A 1 AAAA-AAAACA * 545793 CAAAAACAA-A 1 -AAAAAAAACA * 545803 AACAAAAACA 1 AAAAAAAACA 545813 AAAAAAAGA-A 1 AAAAAAA-ACA 545823 CAAAAAAAACA 1 -AAAAAAAACA * 545834 AAACAAAACA 1 AAAAAAAACA 545844 AAAAAAAACA 1 AAAAAAAACA * 545854 AAACAAAACA 1 AAAAAAAACA 545864 AAACAAAAA-A 1 AAA-AAAAACA 545874 AAAAAAAACA 1 AAAAAAAACA 545884 AAAAAAAA-A 1 AAAAAAAACA 545893 AAAAAAAA-A 1 AAAAAAAACA 545902 AATGTAAAAAACCCA 1 AA---AAAAAA--CA * 545917 AAACAAAACA 1 AAAAAAAACA * * 545927 AAGTAAAACCA 1 AA-AAAAAACA * 545938 AAAAAAATCA 1 AAAAAAAACA 545948 AA 1 AA 545950 GTACTGATGT Statistics Matches: 147, Mismatches: 14, Indels: 31 0.77 0.07 0.16 Matches are distributed among these distances: 9 32 0.22 10 73 0.50 11 28 0.19 12 11 0.07 15 3 0.02 ACGTcount: A:0.83, C:0.13, G:0.02, T:0.02 Consensus pattern (10 bp): AAAAAAAACA Found at i:545787 original size:15 final size:15 Alignment explanation

Indices: 545767--545903 Score: 149 Period size: 15 Copynumber: 8.9 Consensus size: 15 545757 CCCCCCCAAA 545767 AAAAACAAAAAAAAC 1 AAAAACAAAAAAAAC 545782 AAAAACAAAAACAAAAAC 1 AAAAAC--AAA-AAAAAC * 545800 AAAAACAAAAACAAAAA 1 AAAAAC-AAAA-AAAAC 545817 AAAGAACAAAAAAAAC 1 AAA-AACAAAAAAAAC 545833 -AAAACAAAACAAAA- 1 AAAAACAAAA-AAAAC 545847 AAAAACAAAACAAAAC 1 AAAAACAAAA-AAAAC * 545863 -AAAACAAAAAAAAA 1 AAAAACAAAAAAAAC 545877 AAAAACAAAAAAAA- 1 AAAAACAAAAAAAAC 545891 AAAAA-AAAAAAAA 1 AAAAACAAAAAAAA 545904 TGTAAAAAAC Statistics Matches: 110, Mismatches: 3, Indels: 20 0.83 0.02 0.15 Matches are distributed among these distances: 13 8 0.07 14 16 0.15 15 48 0.44 16 5 0.05 17 18 0.16 18 15 0.14 ACGTcount: A:0.88, C:0.12, G:0.01, T:0.00 Consensus pattern (15 bp): AAAAACAAAAAAAAC Found at i:545912 original size:1 final size:1 Alignment explanation

Indices: 545764--545903 Score: 127 Period size: 1 Copynumber: 140.0 Consensus size: 1 545754 CCCCCCCCCC * * * * * * * * * 545764 AAAAAAAACAAAAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAAAAAGAACAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA * * * * * * * * 545829 AAACAAAACAAAACAAAAAAAAACAAAACAAAACAAAACAAAAAAAAAAAAAACAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 545894 AAAAAAAAAA 1 AAAAAAAAAA 545904 TGTAAAAAAC Statistics Matches: 105, Mismatches: 34, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 1 105 1.00 ACGTcount: A:0.88, C:0.11, G:0.01, T:0.00 Consensus pattern (1 bp): A Found at i:545912 original size:22 final size:22 Alignment explanation

Indices: 545763--545903 Score: 158 Period size: 24 Copynumber: 6.0 Consensus size: 22 545753 CCCCCCCCCC 545763 CAAAAAAAACAAAAAAAACAAAAA 1 CAAAAAAAA-AAAAAAAA-AAAAA * 545787 CAAAAACAAAAACAAAAACAAAAA 1 CAAAAA-AAAAA-AAAAAAAAAAA * * 545811 C-AAAAAAAAGAACAAAAAAAA 1 CAAAAAAAAAAAAAAAAAAAAA 545832 CAAAACAAAACAAAAAAAAACAAAA 1 CAAAA-AAAA-AAAAAAAAA-AAAA 545857 CAAAACAAAACAAAAAAAAAAAAAA 1 C-AAA-AAAA-AAAAAAAAAAAAAA 545882 CAAAAAAAAAAAAAAAAAAAAA 1 CAAAAAAAAAAAAAAAAAAAAA 545904 TGTAAAAAAC Statistics Matches: 102, Mismatches: 6, Indels: 20 0.80 0.05 0.16 Matches are distributed among these distances: 21 10 0.10 22 21 0.21 23 12 0.12 24 24 0.24 25 18 0.18 26 15 0.15 27 2 0.02 ACGTcount: A:0.87, C:0.12, G:0.01, T:0.00 Consensus pattern (22 bp): CAAAAAAAAAAAAAAAAAAAAA Found at i:546591 original size:8 final size:8 Alignment explanation

Indices: 546578--546648 Score: 78 Period size: 8 Copynumber: 9.4 Consensus size: 8 546568 TTGCCAGAGT * 546578 AAACAAAC 1 AAACAAAA * 546586 AAACAAAC 1 AAACAAAA 546594 AAA-AAAA 1 AAACAAAA 546601 AAA-AAAA 1 AAACAAAA 546608 AAACAAAA 1 AAACAAAA 546616 AAA-AAAA 1 AAACAAAA * 546623 AAAAAAAA 1 AAACAAAA 546631 AAACAAAA 1 AAACAAAA * 546639 CAA-AAAA 1 AAACAAAA 546646 AAA 1 AAA 546649 TCTAACAAAA Statistics Matches: 57, Mismatches: 4, Indels: 5 0.86 0.06 0.08 Matches are distributed among these distances: 7 26 0.46 8 31 0.54 ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00 Consensus pattern (8 bp): AAACAAAA Found at i:546614 original size:22 final size:23 Alignment explanation

Indices: 546586--546648 Score: 110 Period size: 23 Copynumber: 2.8 Consensus size: 23 546576 GTAAACAAAC 546586 AAAC-AAACAAAAAAAAAAAAAA 1 AAACAAAACAAAAAAAAAAAAAA * 546608 AAACAAAAAAAAAAAAAAAAAAA 1 AAACAAAACAAAAAAAAAAAAAA 546631 AAACAAAACAAAAAAAAA 1 AAACAAAACAAAAAAAAA 546649 TCTAACAAAA Statistics Matches: 38, Mismatches: 2, Indels: 1 0.93 0.05 0.02 Matches are distributed among these distances: 22 4 0.11 23 34 0.89 ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00 Consensus pattern (23 bp): AAACAAAACAAAAAAAAAAAAAA Found at i:546655 original size:20 final size:19 Alignment explanation

Indices: 546590--546659 Score: 79 Period size: 20 Copynumber: 3.6 Consensus size: 19 546580 ACAAACAAAC 546590 AAACAA-AAAAAAAAAAAA 1 AAACAACAAAAAAAAAAAA * 546608 AAACAAAAAAAAAAAAAAAA 1 AAAC-AACAAAAAAAAAAAA * * 546628 AAAAAACAAAACAAAAAAA 1 AAACAACAAAAAAAAAAAA * 546647 AATCTAACAAAAA 1 AAAC-AACAAAAA 546660 TTATTTTTAT Statistics Matches: 43, Mismatches: 6, Indels: 4 0.81 0.11 0.08 Matches are distributed among these distances: 18 4 0.09 19 17 0.40 20 22 0.51 ACGTcount: A:0.89, C:0.09, G:0.00, T:0.03 Consensus pattern (19 bp): AAACAACAAAAAAAAAAAA Found at i:546659 original size:1 final size:1 Alignment explanation

Indices: 546594--546648 Score: 83 Period size: 1 Copynumber: 55.0 Consensus size: 1 546584 ACAAACAAAC * * * 546594 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAACAAAACAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 546649 TCTAACAAAA Statistics Matches: 48, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 1 48 1.00 ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:560792 original size:3 final size:3 Alignment explanation

Indices: 560433--560777 Score: 268 Period size: 3 Copynumber: 114.0 Consensus size: 3 560423 GATTTGACCG * * * 560433 TAC TAC TAC TAC TTC TAC TAC TAC GAAT TAC TAC TAC TAC TAC TAC 1 TAC TAC TAC TAC TAC TAC TAC TAC -TAC TAC TAC TAC TAC TAC TAC ** * 560479 TAC TAC TAC TAC TTT TAC TAC TAT TAC TAC TAC TAC TAC TAC TAC TAC 1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC * * * * * 560527 TAC TAC TGC TAC TAC TAC TTC TAC TAC TAC TTC TAC TAC TAC AAC AAC 1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC * * * * * ** * 560575 AAC AAC AAC TTC TAC TAC TAC TAC GAC TTT TAC TAC TAT TAC TAC TAC 1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC * * * 560623 TAC TAC TAC -AC GTTATG TAC TAC TAC TAC TAA TAC TAC TAC TGC TAC 1 TAC TAC TAC TAC --TA-C TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC * * * * * ** 560670 TAC TAAC -AT TGC TAC TAC TAT TA- TCAC CAC TTC TTT TAC TAC TAC 1 TAC T-AC TAC TAC TAC TAC TAC TAC T-AC TAC TAC TAC TAC TAC TAC * * * * * 560715 TTC TAC TAC TAC ATAC T-C TAC CAA TAGC -AC CAC TAC TAC TAC TAT 1 TAC TAC TAC TAC -TAC TAC TAC TAC TA-C TAC TAC TAC TAC TAC TAC * 560760 TAC TAC AAC TAC TAC TAC 1 TAC TAC TAC TAC TAC TAC 560778 ATCCATTACT Statistics Matches: 271, Mismatches: 58, Indels: 26 0.76 0.16 0.07 Matches are distributed among these distances: 2 7 0.03 3 255 0.94 4 8 0.03 5 1 0.00 ACGTcount: A:0.32, C:0.30, G:0.02, T:0.35 Consensus pattern (3 bp): TAC Found at i:565308 original size:21 final size:21 Alignment explanation

Indices: 565284--565324 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 565274 TATTCAGTGC 565284 GTGACGGTTGGTTTTGCATCT 1 GTGACGGTTGGTTTTGCATCT ** * 565305 GTGATTGTTTGTTTTGCATC 1 GTGACGGTTGGTTTTGCATC 565325 AATGTCTGCT Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.10, C:0.12, G:0.29, T:0.49 Consensus pattern (21 bp): GTGACGGTTGGTTTTGCATCT Found at i:568874 original size:22 final size:22 Alignment explanation

Indices: 568806--568875 Score: 65 Period size: 22 Copynumber: 3.2 Consensus size: 22 568796 GTCTTAGAGT 568806 TTTTTCTCAGTGTCACTCAGGC 1 TTTTTCTCAGTGTCACTCAGGC * * * * 568828 TTTTTTTTA-TAGT--CTAAGAGT 1 TTTTTCTCAGT-GTCACTCAG-GC 568849 TTTTTCTCAGTGTCACTCAGGC 1 TTTTTCTCAGTGTCACTCAGGC 568871 TTTTT 1 TTTTT 568876 TTATAGTCTC Statistics Matches: 35, Mismatches: 8, Indels: 10 0.66 0.15 0.19 Matches are distributed among these distances: 20 4 0.11 21 11 0.31 22 16 0.46 23 4 0.11 ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50 Consensus pattern (22 bp): TTTTTCTCAGTGTCACTCAGGC Found at i:568893 original size:19 final size:19 Alignment explanation

Indices: 568829--568896 Score: 59 Period size: 19 Copynumber: 3.4 Consensus size: 19 568819 CACTCAGGCT * 568829 TTTTTTTATAGTCTAAGAG 1 TTTTTTTATAGTCTCAGAG 568848 TTTTTTCTCAGT-GTCACTCAG-G 1 TTTTTT-T-A-TAGT--CTCAGAG 568870 CTTTTTTTATAGTCTCAGAG 1 -TTTTTTTATAGTCTCAGAG 568890 TTTTTTT 1 TTTTTTT 568897 CATTACAGCA Statistics Matches: 40, Mismatches: 1, Indels: 16 0.70 0.02 0.28 Matches are distributed among these distances: 19 18 0.45 20 3 0.08 21 6 0.15 22 3 0.08 23 10 0.25 ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54 Consensus pattern (19 bp): TTTTTTTATAGTCTCAGAG Found at i:568897 original size:43 final size:42 Alignment explanation

Indices: 568766--568895 Score: 208 Period size: 43 Copynumber: 3.1 Consensus size: 42 568756 TCTCTCAGGG * * * 568766 TTTTCTCAGTGCCACTGAGGC-TTTTTTATAGTCTTAGAGTT 1 TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTAAGAGTT 568807 TTTTCTCAGTGTCACTCAGGCTTTTTTTTATAGTCTAAGAGTT 1 TTTTCTCAGTGTCACTCAGGC-TTTTTTTATAGTCTAAGAGTT * 568850 TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTCAGAGTT 1 TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTAAGAGTT 568892 TTTT 1 TTTT 568896 TCATTACAGC Statistics Matches: 83, Mismatches: 4, Indels: 3 0.92 0.04 0.03 Matches are distributed among these distances: 41 19 0.23 42 24 0.29 43 40 0.48 ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49 Consensus pattern (42 bp): TTTTCTCAGTGTCACTCAGGCTTTTTTTATAGTCTAAGAGTT Found at i:578449 original size:21 final size:21 Alignment explanation

Indices: 578423--578470 Score: 60 Period size: 21 Copynumber: 2.3 Consensus size: 21 578413 ACCATAGCAA * * 578423 AGCATAGCATTGAAATCGCAT 1 AGCATAGCACTGAAATCACAT * 578444 AGCATAGCACTGGAATCACAT 1 AGCATAGCACTGAAATCACAT * 578465 ACCATA 1 AGCATA 578471 CCATATAATC Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21 Consensus pattern (21 bp): AGCATAGCACTGAAATCACAT Found at i:578690 original size:10 final size:10 Alignment explanation

Indices: 578675--578705 Score: 53 Period size: 10 Copynumber: 3.1 Consensus size: 10 578665 CAAATCTCAC 578675 AGCATACCAT 1 AGCATACCAT * 578685 AGCATAGCAT 1 AGCATACCAT 578695 AGCATACCAT 1 AGCATACCAT 578705 A 1 A 578706 TCATTAAGCC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.42, C:0.26, G:0.13, T:0.19 Consensus pattern (10 bp): AGCATACCAT Found at i:578755 original size:21 final size:21 Alignment explanation

Indices: 578729--578808 Score: 108 Period size: 21 Copynumber: 3.8 Consensus size: 21 578719 AATTTCAATT 578729 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA 578750 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA * * 578771 TATCATAGCATATCATTA-AAA 1 TCTCATAGCATAGCA-TACAAA * * 578792 TCGCATATCATAGCATA 1 TCTCATAGCATAGCATA 578809 GCATACATTT Statistics Matches: 52, Mismatches: 6, Indels: 3 0.85 0.10 0.05 Matches are distributed among these distances: 20 2 0.04 21 48 0.92 22 2 0.04 ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28 Consensus pattern (21 bp): TCTCATAGCATAGCATACAAA Found at i:578782 original size:26 final size:25 Alignment explanation

Indices: 578732--578813 Score: 66 Period size: 26 Copynumber: 3.4 Consensus size: 25 578722 TTCAATTTCT 578732 CATAGCATAGCATACAA-ATC-T-- 1 CATAGCATAGCATACAATATCATAG 578753 CATAGCATAGCATACAAATATCATAG 1 CATAGCATAGCATAC-AATATCATAG * ** * 578779 CATATCATTAAAAT-CGCATATCATAG 1 CATAGCA-TAGCATAC-AATATCATAG 578805 CATAGCATA 1 CATAGCATA 578814 CATTTGTAAA Statistics Matches: 49, Mismatches: 6, Indels: 8 0.78 0.10 0.13 Matches are distributed among these distances: 21 15 0.31 22 2 0.04 23 3 0.06 24 1 0.02 25 2 0.04 26 22 0.45 27 4 0.08 ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26 Consensus pattern (25 bp): CATAGCATAGCATACAATATCATAG Found at i:583173 original size:27 final size:27 Alignment explanation

Indices: 583142--583194 Score: 97 Period size: 27 Copynumber: 2.0 Consensus size: 27 583132 AAAAACCAAA 583142 ATTCCCCTTCTTTATACAATCAAATAT 1 ATTCCCCTTCTTTATACAATCAAATAT * 583169 ATTCCTCTTCTTTATACAATCAAATA 1 ATTCCCCTTCTTTATACAATCAAATA 583195 GTTTGGCGTA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.34, C:0.25, G:0.00, T:0.42 Consensus pattern (27 bp): ATTCCCCTTCTTTATACAATCAAATAT Found at i:583364 original size:14 final size:14 Alignment explanation

Indices: 583345--583386 Score: 84 Period size: 14 Copynumber: 3.0 Consensus size: 14 583335 ATATCAACTG 583345 ATATAGATACAAAC 1 ATATAGATACAAAC 583359 ATATAGATACAAAC 1 ATATAGATACAAAC 583373 ATATAGATACAAAC 1 ATATAGATACAAAC 583387 TTCTATACTA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 28 1.00 ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21 Consensus pattern (14 bp): ATATAGATACAAAC Found at i:586320 original size:14 final size:14 Alignment explanation

Indices: 586301--586328 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 586291 AATCTGGTAG 586301 TACATTACTGCCAC 1 TACATTACTGCCAC 586315 TACATTACTGCCAC 1 TACATTACTGCCAC 586329 AGTGGTGCAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29 Consensus pattern (14 bp): TACATTACTGCCAC Found at i:600022 original size:20 final size:21 Alignment explanation

Indices: 599997--600047 Score: 61 Period size: 20 Copynumber: 2.5 Consensus size: 21 599987 TGAAAATGTC * 599997 ATTTTTGCTGATAAT-TCCTG 1 ATTTTTGCTGATAATATACTG * * 600017 ATTTTTACTGATATTATACTG 1 ATTTTTGCTGATAATATACTG 600038 -TTTTTGCTGA 1 ATTTTTGCTGA 600048 AGATTGCTGT Statistics Matches: 26, Mismatches: 4, Indels: 2 0.81 0.12 0.06 Matches are distributed among these distances: 20 22 0.85 21 4 0.15 ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53 Consensus pattern (21 bp): ATTTTTGCTGATAATATACTG Found at i:600119 original size:10 final size:10 Alignment explanation

Indices: 600104--600128 Score: 50 Period size: 10 Copynumber: 2.5 Consensus size: 10 600094 GTTGTTGTTT 600104 CTGATATTTA 1 CTGATATTTA 600114 CTGATATTTA 1 CTGATATTTA 600124 CTGAT 1 CTGAT 600129 GCTTTTGCTG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 15 1.00 ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48 Consensus pattern (10 bp): CTGATATTTA Found at i:602279 original size:4 final size:4 Alignment explanation

Indices: 602270--602442 Score: 253 Period size: 4 Copynumber: 44.0 Consensus size: 4 602260 CTGTTCATAT * * * * 602270 ATAG ATAG ATTG ATAG ATAG ATAA ATAC AT-G -TAG ATAG ATAG ATAA 1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG * * * 602316 AAAG AT-G ATAG ATAG ATAG TTAG ATAG ATAG ATAG ATAG ATAG ATGG 1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG 602363 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG 1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG * 602411 ATAG ATAG ATAG ATAA ATAG ATAG ATAG ATAG 1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG 602443 GGTACACTTT Statistics Matches: 151, Mismatches: 15, Indels: 6 0.88 0.09 0.03 Matches are distributed among these distances: 2 1 0.01 3 4 0.03 4 146 0.97 ACGTcount: A:0.50, C:0.01, G:0.24, T:0.26 Consensus pattern (4 bp): ATAG Found at i:602925 original size:14 final size:14 Alignment explanation

Indices: 602906--602942 Score: 56 Period size: 14 Copynumber: 2.6 Consensus size: 14 602896 ATCACTCATT 602906 AAAAAAACAGACAG 1 AAAAAAACAGACAG * * 602920 AAAAAAAAAGAGAG 1 AAAAAAACAGACAG 602934 AAAAAAACA 1 AAAAAAACA 602943 AACATAGTTT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 14 20 1.00 ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00 Consensus pattern (14 bp): AAAAAAACAGACAG Found at i:605846 original size:13 final size:12 Alignment explanation

Indices: 605814--605861 Score: 51 Period size: 12 Copynumber: 3.9 Consensus size: 12 605804 TGTTGAACTG * 605814 TTTTTTTTTTTG 1 TTTTTTTTTTTA * * 605826 GTGTTTTTTTTA 1 TTTTTTTTTTTA * 605838 TTTTATTTTATTA 1 TTTT-TTTTTTTA 605851 TTTTTTTTTTT 1 TTTTTTTTTTT 605862 GGGGGGGGGG Statistics Matches: 28, Mismatches: 7, Indels: 2 0.76 0.19 0.05 Matches are distributed among these distances: 12 17 0.61 13 11 0.39 ACGTcount: A:0.08, C:0.00, G:0.06, T:0.85 Consensus pattern (12 bp): TTTTTTTTTTTA Found at i:624512 original size:1 final size:1 Alignment explanation

Indices: 624506--624530 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 624496 CCGCGCATGG 624506 CCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCC 624531 ACCACCACAN Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:631356 original size:7 final size:7 Alignment explanation

Indices: 631341--631407 Score: 82 Period size: 7 Copynumber: 9.6 Consensus size: 7 631331 TTTAGATATT 631341 GAATCTC 1 GAATCTC * 631348 GAATTTC 1 GAATCTC 631355 GAATCTC 1 GAATCTC 631362 GAATCTC 1 GAATCTC * * 631369 GTATTTC 1 GAATCTC 631376 GAATCTC 1 GAATCTC * 631383 GTAAT-TT 1 G-AATCTC 631390 GAATCTC 1 GAATCTC 631397 GAATCTC 1 GAATCTC 631404 GAAT 1 GAAT 631408 GATCCTTCTC Statistics Matches: 50, Mismatches: 8, Indels: 4 0.81 0.13 0.06 Matches are distributed among these distances: 6 3 0.06 7 44 0.88 8 3 0.06 ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36 Consensus pattern (7 bp): GAATCTC Found at i:631366 original size:21 final size:21 Alignment explanation

Indices: 631341--631407 Score: 91 Period size: 21 Copynumber: 3.2 Consensus size: 21 631331 TTTAGATATT 631341 GAATCTCGAATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC * 631362 GAATCTCGTATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC * * 631383 GTAAT-TTGAATCTCGAATCTC 1 G-AATCTCGAATTTCGAATCTC 631404 GAAT 1 GAAT 631408 GATCCTTCTC Statistics Matches: 41, Mismatches: 4, Indels: 3 0.85 0.08 0.06 Matches are distributed among these distances: 20 3 0.07 21 35 0.85 22 3 0.07 ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36 Consensus pattern (21 bp): GAATCTCGAATTTCGAATCTC Found at i:631441 original size:16 final size:16 Alignment explanation

Indices: 631412--631448 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 16 631402 TCGAATGATC * 631412 CTTCTCGGCTTTCGTA 1 CTTCTCGGCCTTCGTA * 631428 CTTCTTGGCCTTCGTA 1 CTTCTCGGCCTTCGTA 631444 CTTCT 1 CTTCT 631449 GAATTTTTGT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.05, C:0.32, G:0.16, T:0.46 Consensus pattern (16 bp): CTTCTCGGCCTTCGTA Found at i:633771 original size:2 final size:2 Alignment explanation

Indices: 633766--633813 Score: 69 Period size: 2 Copynumber: 23.5 Consensus size: 2 633756 AAATCACACA ** 633766 AT AT AT AT AT CC ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT 633809 AT AT A 1 AT AT A 633814 ACACACAAGA Statistics Matches: 41, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 2 40 0.98 3 1 0.02 ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46 Consensus pattern (2 bp): AT Found at i:635064 original size:8 final size:8 Alignment explanation

Indices: 635051--635104 Score: 72 Period size: 8 Copynumber: 6.8 Consensus size: 8 635041 AATGCCGGGC 635051 GTCCGTGG 1 GTCCGTGG 635059 GTCCGTGG 1 GTCCGTGG * 635067 GTCCGTGT 1 GTCCGTGG * 635075 GTCTGTGG 1 GTCCGTGG * 635083 GTCCGTGC 1 GTCCGTGG * 635091 GTCCGTGT 1 GTCCGTGG 635099 GTCCGT 1 GTCCGT 635105 CCGTCACACT Statistics Matches: 40, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 8 40 1.00 ACGTcount: A:0.00, C:0.26, G:0.43, T:0.31 Consensus pattern (8 bp): GTCCGTGG Found at i:635087 original size:24 final size:24 Alignment explanation

Indices: 635055--635101 Score: 85 Period size: 24 Copynumber: 2.0 Consensus size: 24 635045 CCGGGCGTCC * 635055 GTGGGTCCGTGGGTCCGTGTGTCT 1 GTGGGTCCGTGCGTCCGTGTGTCT 635079 GTGGGTCCGTGCGTCCGTGTGTC 1 GTGGGTCCGTGCGTCCGTGTGTC 635102 CGTCCGTCAC Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.00, C:0.23, G:0.45, T:0.32 Consensus pattern (24 bp): GTGGGTCCGTGCGTCCGTGTGTCT Found at i:638229 original size:21 final size:21 Alignment explanation

Indices: 638203--638276 Score: 94 Period size: 21 Copynumber: 3.5 Consensus size: 21 638193 TAATTATTTC * 638203 GACATGCAAGATAAAGATGTT 1 GACATGCAAGATAAATATGTT * * 638224 GACATGCAAGATAATTATGTC 1 GACATGCAAGATAAATATGTT * * * 638245 AACATGCAACATAACTATGTT 1 GACATGCAAGATAAATATGTT 638266 GACATGCAAGA 1 GACATGCAAGA 638277 AAACTGCAAT Statistics Matches: 44, Mismatches: 9, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 21 44 1.00 ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24 Consensus pattern (21 bp): GACATGCAAGATAAATATGTT Found at i:638252 original size:42 final size:42 Alignment explanation

Indices: 638193--638276 Score: 123 Period size: 42 Copynumber: 2.0 Consensus size: 42 638183 ATTTTTCTAT * * * 638193 TAATTATTTCGACATGCAAGATAAAGATGTTGACATGCAAGA 1 TAATTATGTCAACATGCAACATAAAGATGTTGACATGCAAGA ** 638235 TAATTATGTCAACATGCAACATAACTATGTTGACATGCAAGA 1 TAATTATGTCAACATGCAACATAAAGATGTTGACATGCAAGA 638277 AAACTGCAAT Statistics Matches: 37, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 42 37 1.00 ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29 Consensus pattern (42 bp): TAATTATGTCAACATGCAACATAAAGATGTTGACATGCAAGA Found at i:639223 original size:21 final size:21 Alignment explanation

Indices: 639166--639225 Score: 84 Period size: 21 Copynumber: 2.9 Consensus size: 21 639156 CATAGCTATG * * * 639166 TTGCATGTTGACATAATTATT 1 TTGCATGTCGACATATTTATC * 639187 TTGCATGTCAACATATTTATC 1 TTGCATGTCGACATATTTATC 639208 TTGCATGTCGACATATTT 1 TTGCATGTCGACATATTT 639226 CATAGAAAAA Statistics Matches: 34, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 34 1.00 ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45 Consensus pattern (21 bp): TTGCATGTCGACATATTTATC Found at i:648263 original size:183 final size:176 Alignment explanation

Indices: 647833--648284 Score: 440 Period size: 167 Copynumber: 2.6 Consensus size: 176 647823 ATTGTGAAAT * * * ** 647833 TCATGGCCCCTGGGTCTA-GGGTTCAGGCTCTAGGGTGTTGCCAATATGGCCATATAGTAAAAAT 1 TCATGACCCCTGTGTC-AGGGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTAAAAAT * * * * ** * * * * 647897 ATTTTAAATATTAGAAAATCTTCACCTCTACTCCCATATCTATCTGT--------TAAA-AAGTA 65 GTATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATATATATTTGTAAAAAAAAAAAACAACTA * * * 647953 AATGGATGGTTATGATGTCCATGAAGTCCTCTACCAAAATAGTGAAC 130 AATGCATGATTATGATGTCCATGAAGCCCTCTACCAAAATAGTGAAC * * 648000 TCATGACCCCTGTGTCAGGGGTTCAGGCTCAAGGTTGCAGCCAATTTGGCCATATAGTAAAAATG 1 TCATGACCCCTGTGTCAGGGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTAAAAATG * * 648065 TTTTAAATCTTGGAAAATCTTCTTCTCTTCTCCCATATATATTTGTAAAAAAAAAAAACAACTAA 66 TATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATATATATTTGTAAAAAAAAAAAACAACTAA * * * 648130 ATGCATGATTATGATGTCCATGAGGCCCTCTATCAAAAGT-GTGAAAT 131 ATGCATGATTATGATGTCCATGAAGCCCTCTACCAAAA-TAGTG-AAC * * * ** * 648177 TCATTACCCCTGTGTCACTTTTGAGGGTTCATGCTCTAGGGTGGGGCCAATATGGCCATTTAGTA 1 TCATGACCCCTGTGTCA-----G-GGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTA * * * 648242 AAAATGTATTATATCTTGGAAAGTCTTCTTTTCTACTCCCATA 60 AAAATGTATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATA 648285 CATGTCGGCA Statistics Matches: 231, Mismatches: 36, Indels: 20 0.80 0.13 0.07 Matches are distributed among these distances: 166 1 0.00 167 94 0.41 175 3 0.01 176 41 0.18 177 19 0.08 182 1 0.00 183 72 0.31 ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33 Consensus pattern (176 bp): TCATGACCCCTGTGTCAGGGGTTCAGGCTCAAGGGTGCAGCCAATATGGCCATATAGTAAAAATG TATTAAATCTTGGAAAATCTTCTTCTCTACTCCCATATATATTTGTAAAAAAAAAAAACAACTAA ATGCATGATTATGATGTCCATGAAGCCCTCTACCAAAATAGTGAAC Found at i:649349 original size:266 final size:266 Alignment explanation

Indices: 648875--649406 Score: 1028 Period size: 266 Copynumber: 2.0 Consensus size: 266 648865 CGCGGGCGCA 648875 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT 1 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT * 648940 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGTGTCACGAAG 66 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG 649005 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC 131 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC * 649070 TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATCACAATGTCCCACAAATCCAAT 196 TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT 649135 AAAGTT 261 AAAGTT * 649141 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCTTCTGACATGCGGTGGCGCCAACT 1 ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT 649206 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG 66 TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG 649271 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC 131 CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC * 649336 TTTAAAGATCACCGCGCATTTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT 196 TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT 649401 AAAGTT 261 AAAGTT 649407 CTGGCCAGAA Statistics Matches: 262, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 266 262 1.00 ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19 Consensus pattern (266 bp): ATGACTGAATCAAAAGTGATAAAATTAAAAAATGGGAAACCGTCTGACATGCGGTGGCGCCAACT TAAGGCCCGACACGACACATTTTCGCTAAGGTCTCCAGAAGCAACCGCATCCGCGCGTCACGAAG CCATGACAAGACAACGCATGACACGCTATATCCATGAGCTAGAAAACATCATCCAGTCCCCGAAC TTTAAAGATCACCGCGCATCTGGAACATGGATGAAACAGGGATAACAATGTCCCACAAATCCAAT AAAGTT Found at i:661871 original size:12 final size:12 Alignment explanation

Indices: 661850--661884 Score: 52 Period size: 12 Copynumber: 2.9 Consensus size: 12 661840 GTCATAGTAG 661850 TTTTCCGTTCCA 1 TTTTCCGTTCCA * 661862 TTTTCTGTTCCA 1 TTTTCCGTTCCA * 661874 TTTTTCGTTCC 1 TTTTCCGTTCC 661885 GCGTTTTAGC Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 20 1.00 ACGTcount: A:0.06, C:0.29, G:0.09, T:0.57 Consensus pattern (12 bp): TTTTCCGTTCCA Found at i:669482 original size:19 final size:19 Alignment explanation

Indices: 669458--669496 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 669448 TATTCGCCAT 669458 AATTTTATTAAGGTTAAAC 1 AATTTTATTAAGGTTAAAC 669477 AATTTTATTAAGGTTAAAC 1 AATTTTATTAAGGTTAAAC 669496 A 1 A 669497 GCATCTTTAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41 Consensus pattern (19 bp): AATTTTATTAAGGTTAAAC Found at i:670787 original size:4 final size:4 Alignment explanation

Indices: 670778--670824 Score: 67 Period size: 4 Copynumber: 11.8 Consensus size: 4 670768 TTCATACCTT * * * 670778 GATA GATA GATA GATA GATA GATA GATA GATA AAGA GAGA GATA GAT 1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT 670825 GAATGCATGA Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 4 39 1.00 ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21 Consensus pattern (4 bp): GATA Found at i:688516 original size:482 final size:479 Alignment explanation

Indices: 687613--688574 Score: 1879 Period size: 482 Copynumber: 2.0 Consensus size: 479 687603 CGTCACTCTC * 687613 CGTATGCCCAGAGATTGTGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCAT 1 CGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCAT 687678 CGACCAGATAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCAAGC 66 CGACCAGATAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCAAGC * 687743 CATGTCCTAACCACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCTAAT 131 CATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCTAAT 687808 ACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTCCGT 196 ACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTCCGT 687873 CGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTTGGG 261 CGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTTGGG 687938 AAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTTCAG 326 AAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTTCAG 688003 AGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGAGTT 391 AGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGAGTT 688068 CATGCGAAAAATCTTTGAGAACAA 456 CATGCGAAAAATCTTTGAGAACAA 688092 NCGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCA 1 -CGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCA 688157 TCGACCAGATACAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCA 65 TCGACCAGAT--AGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCA 688222 AGCCATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCT 128 AGCCATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCT 688287 AATACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTC 193 AATACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTC 688352 CGTCGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTT 258 CGTCGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTT 688417 GGGAAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTT 323 GGGAAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTT 688482 CAGAGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGA 388 CAGAGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGA 688547 GTTCATGCGAAAAATCTTTGAGAACAA 453 GTTCATGCGAAAAATCTTTGAGAACAA 688574 C 1 C 688575 CATGCTGAGA Statistics Matches: 478, Mismatches: 2, Indels: 3 0.99 0.00 0.01 Matches are distributed among these distances: 480 73 0.15 481 1 0.00 482 404 0.85 ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27 Consensus pattern (479 bp): CGTATGCCCAGAGATTGCGCTTAGGTTGGGTGGTTGTAGGAGAAACATGTCTCAGCCAGTTTCAT CGACCAGATAGTCACTGTAAATAAGACCTACCTGTTACGTAATGGCAGATCATCAATATGCAAGC CATGTCCTAACAACTTTGAGATTAAGGAAGAGTTCACAACAGACTCATTTGACACAGATTCTAAT ACACCCAAGTGTGATTCAGACATTTTTGCTAGAAGAAATGATGATGACACTGTCGGACTGTCCGT CGAAGATGAAGAGTTTCTTTGTATTATGGATCAGACGGTTTCTAAAAATGCTGAAGGGTTTTGGG AAGCCCCTCTACCTTTCCGTTCTCCAAGGAGAAGACTTCCGGATAATCGAACCCAAGCCCTTCAG AGAGCTAAATCCCTGGATTTCTCCCTTCGAAAAGATGATGCGAAGAAAAATCATTTCCTGGAGTT CATGCGAAAAATCTTTGAGAACAA Found at i:688841 original size:76 final size:75 Alignment explanation

Indices: 688715--688865 Score: 293 Period size: 76 Copynumber: 2.0 Consensus size: 75 688705 TTTCATTGAA 688715 CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGTA 1 CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGTA 688780 AAGACCTTGT 66 AAGACCTTGT 688790 NCGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGT 1 -CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGT 688855 AAAGACCTTGT 65 AAAGACCTTGT 688866 TGCTATCACT Statistics Matches: 75, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 76 75 1.00 ACGTcount: A:0.19, C:0.23, G:0.23, T:0.36 Consensus pattern (75 bp): CGATGTTCTCATGACTGGACCCGATTTGATCAATAGCCTTCTTGGCGTGTTATTGCGTTTCCGTA AAGACCTTGT Found at i:689066 original size:52 final size:55 Alignment explanation

Indices: 688939--689066 Score: 163 Period size: 56 Copynumber: 2.4 Consensus size: 55 688929 CTTTTTNTGA * * * 688939 TAAGTGGTGCCAGGCTTTTGTGATTAAAGCTTATGTTAGTGTATGTACACAACAAT 1 TAAGTGGTGTCAGGCTGTGGTGATTAAAGCTTATGTTAGTGTA-GTACACAACAAT * * * 688995 TAAGTGGTGTCAGGCTGTGGTGGTTCAAGCTTATGTTAGTGTA-TA-A-AACAGT 1 TAAGTGGTGTCAGGCTGTGGTGATTAAAGCTTATGTTAGTGTAGTACACAACAAT * 689047 TGAGTGGTGTCAGGCTGTGG 1 TAAGTGGTGTCAGGCTGTGG 689067 AGGCACAATA Statistics Matches: 65, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 52 24 0.37 53 1 0.02 54 2 0.03 56 38 0.58 ACGTcount: A:0.24, C:0.11, G:0.30, T:0.34 Consensus pattern (55 bp): TAAGTGGTGTCAGGCTGTGGTGATTAAAGCTTATGTTAGTGTAGTACACAACAAT Found at i:689741 original size:53 final size:52 Alignment explanation

Indices: 689594--689760 Score: 203 Period size: 52 Copynumber: 3.2 Consensus size: 52 689584 TAGATTTTCC * * * * 689594 GTGGTGTTAGACTGTGATGACAC-AGGACTGTTTTATAGTGTGTCG-AAATTTA 1 GTGGTGTCAGACTGTGGTAACACAAGG-CTGTTTTATAGTGT-ACGAAAATTTA * * * * 689646 GTGGTGTCAGATTGTGGTGACAAAAGGCTGTTTAATAGTGTACGAAAATTTA 1 GTGGTGTCAGACTGTGGTAACACAAGGCTGTTTTATAGTGTACGAAAATTTA * * 689698 GTGGTGTCAGGACTGTGGTAACACAAGGCTGTTTTATAATGTACCAAAATTTA 1 GTGGTGTCA-GACTGTGGTAACACAAGGCTGTTTTATAGTGTACGAAAATTTA 689751 GTGGTGTCAG 1 GTGGTGTCAG 689761 GATTTTAGTA Statistics Matches: 100, Mismatches: 12, Indels: 6 0.85 0.10 0.05 Matches are distributed among these distances: 51 2 0.02 52 49 0.49 53 49 0.49 ACGTcount: A:0.28, C:0.10, G:0.29, T:0.34 Consensus pattern (52 bp): GTGGTGTCAGACTGTGGTAACACAAGGCTGTTTTATAGTGTACGAAAATTTA Found at i:689772 original size:53 final size:53 Alignment explanation

Indices: 689639--689777 Score: 199 Period size: 53 Copynumber: 2.6 Consensus size: 53 689629 TAGTGTGTCG * * * * 689639 AAATTTAGTGGTGTCA-GATTGTGGTGACAAAAGGCTGTTTAATAGTGTACGA 1 AAATTTAGTGGTGTCAGGATTGTGGTAACACAAGGCTGTTTAATAATGTACCA * * 689691 AAATTTAGTGGTGTCAGGACTGTGGTAACACAAGGCTGTTTTATAATGTACCA 1 AAATTTAGTGGTGTCAGGATTGTGGTAACACAAGGCTGTTTAATAATGTACCA * * 689744 AAATTTAGTGGTGTCAGGATTTTAGTAACACAAG 1 AAATTTAGTGGTGTCAGGATTGTGGTAACACAAG 689778 TTTATCATTT Statistics Matches: 77, Mismatches: 9, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 52 16 0.21 53 61 0.79 ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32 Consensus pattern (53 bp): AAATTTAGTGGTGTCAGGATTGTGGTAACACAAGGCTGTTTAATAATGTACCA Found at i:698211 original size:2 final size:2 Alignment explanation

Indices: 698204--698257 Score: 99 Period size: 2 Copynumber: 27.0 Consensus size: 2 698194 TACAAATTAA * 698204 TC TC TC TC TC CC 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 698246 TC TC TC TC TC TC 1 TC TC TC TC TC TC 698258 NNNNNNNNNN Statistics Matches: 50, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): TC Found at i:699195 original size:2 final size:2 Alignment explanation

Indices: 699188--699231 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 699178 NNNNNNNNNN 699188 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 699230 AG 1 AG 699232 TCAAGTGCAA Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:700872 original size:2 final size:2 Alignment explanation

Indices: 700865--700911 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 700855 ATTCTTCAAA 700865 CT CT CT CT CT 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 CT CT CT CT CT 700907 CT CT C 1 CT CT C 700912 AGGAAATGCG 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:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:708032 original size:26 final size:26 Alignment explanation

Indices: 707979--708042 Score: 74 Period size: 26 Copynumber: 2.4 Consensus size: 26 707969 TCGAAAATAG * * * 707979 ATAAATATTTATATAATATAAGAGAA 1 ATAATTATTTATATAATACAAGAAAA * * 708005 ATAATTATTTCTATAATACAATAAAA 1 ATAATTATTTATATAATACAAGAAAA 708031 ATATATTATTTA 1 ATA-ATTATTTA 708043 GTGTTGGTTC Statistics Matches: 31, Mismatches: 6, Indels: 1 0.82 0.16 0.03 Matches are distributed among these distances: 26 24 0.77 27 7 0.23 ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41 Consensus pattern (26 bp): ATAATTATTTATATAATACAAGAAAA Found at i:714987 original size:8 final size:9 Alignment explanation

Indices: 714968--715004 Score: 65 Period size: 9 Copynumber: 4.0 Consensus size: 9 714958 CATTAACACT 714968 TATAGAATA 1 TATAGAATA 714977 TATAGATATA 1 TATAGA-ATA 714987 TATAGAATA 1 TATAGAATA 714996 TATAGAATA 1 TATAGAATA 715005 GCACATAGGG Statistics Matches: 27, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 9 18 0.67 10 9 0.33 ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35 Consensus pattern (9 bp): TATAGAATA Found at i:720110 original size:13 final size:14 Alignment explanation

Indices: 720092--720121 Score: 53 Period size: 14 Copynumber: 2.2 Consensus size: 14 720082 GGTAATGTGA 720092 GTTTTC-TTGTGTT 1 GTTTTCTTTGTGTT 720105 GTTTTCTTTGTGTT 1 GTTTTCTTTGTGTT 720119 GTT 1 GTT 720122 ACTTGTTGCT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 6 0.38 14 10 0.62 ACGTcount: A:0.00, C:0.07, G:0.23, T:0.70 Consensus pattern (14 bp): GTTTTCTTTGTGTT Found at i:720318 original size:27 final size:27 Alignment explanation

Indices: 720149--720306 Score: 289 Period size: 27 Copynumber: 5.9 Consensus size: 27 720139 TTATCGCTTC 720149 TGGATTGCTGAATATTGTTGTTGTTGG 1 TGGATTGCTGAATATTGTTGTTGTTGG * 720176 TGGATTGCTGAATATTGTTGTTGTTGT 1 TGGATTGCTGAATATTGTTGTTGTTGG * 720203 TGGATTGCTGAATATTGTTGTTGTTGT 1 TGGATTGCTGAATATTGTTGTTGTTGG * 720230 TGGATTGCTGAATATTATTGTTGTTGG 1 TGGATTGCTGAATATTGTTGTTGTTGG 720257 TGGATTGCTGAATATTGTTGTTGTTGG 1 TGGATTGCTGAATATTGTTGTTGTTGG 720284 TGGATTGCTGAATATTGTTGTTG 1 TGGATTGCTGAATATTGTTGTTG 720307 CTTCAGTGTT Statistics Matches: 127, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 27 127 1.00 ACGTcount: A:0.16, C:0.04, G:0.31, T:0.49 Consensus pattern (27 bp): TGGATTGCTGAATATTGTTGTTGTTGG Found at i:720610 original size:24 final size:24 Alignment explanation

Indices: 720582--720672 Score: 155 Period size: 24 Copynumber: 3.8 Consensus size: 24 720572 TGCTACTGCT * * 720582 ATATAGTGTACTAAGGTTGTACTG 1 ATATAGTGTACTAATGTTGTACTA 720606 ATATAGTGTACTAATGTTGTACTA 1 ATATAGTGTACTAATGTTGTACTA * 720630 ATATAGTGTACTTATGTTGTACTA 1 ATATAGTGTACTAATGTTGTACTA 720654 ATATAGTGTACTAATGTTG 1 ATATAGTGTACTAATGTTG 720673 ATCTTTGTTT Statistics Matches: 63, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 24 63 1.00 ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42 Consensus pattern (24 bp): ATATAGTGTACTAATGTTGTACTA Found at i:720617 original size:13 final size:12 Alignment explanation

Indices: 720580--720666 Score: 69 Period size: 11 Copynumber: 7.2 Consensus size: 12 720570 GTTGCTACTG 720580 CTATATAGTGTA 1 CTATATAGTGTA * 720592 CTA-A-GGTTGTA 1 CTATATAG-TGTA 720603 CTGATATAGTGTA 1 CT-ATATAGTGTA 720616 CTA-AT-GTTGTA 1 CTATATAG-TGTA 720627 CTAATATAGTGTA 1 CT-ATATAGTGTA 720640 CT-TAT-GTTGTA 1 CTATATAG-TGTA 720651 CTAATATAGTGTA 1 CT-ATATAGTGTA 720664 CTA 1 CTA 720667 ATGTTGATCT Statistics Matches: 61, Mismatches: 2, Indels: 24 0.70 0.02 0.28 Matches are distributed among these distances: 10 3 0.05 11 24 0.39 12 7 0.11 13 24 0.39 14 3 0.05 ACGTcount: A:0.31, C:0.09, G:0.18, T:0.41 Consensus pattern (12 bp): CTATATAGTGTA Found at i:720667 original size:13 final size:13 Alignment explanation

Indices: 720582--720668 Score: 80 Period size: 13 Copynumber: 7.2 Consensus size: 13 720572 TGCTACTGCT 720582 ATATAGTGTACTA 1 ATATAGTGTACTA ** * 720595 AGGT--TGTACTG 1 ATATAGTGTACTA 720606 ATATAGTGTACTA 1 ATATAGTGTACTA * 720619 ATGT--TGTACTA 1 ATATAGTGTACTA 720630 ATATAGTGTACT- 1 ATATAGTGTACTA 720642 -TAT-GTTGTACTA 1 ATATAG-TGTACTA 720654 ATATAGTGTACTA 1 ATATAGTGTACTA 720667 AT 1 AT 720669 GTTGATCTTT Statistics Matches: 58, Mismatches: 8, Indels: 16 0.71 0.10 0.20 Matches are distributed among these distances: 10 1 0.02 11 27 0.47 13 29 0.50 14 1 0.02 ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41 Consensus pattern (13 bp): ATATAGTGTACTA Found at i:721294 original size:60 final size:60 Alignment explanation

Indices: 721225--721858 Score: 1124 Period size: 60 Copynumber: 10.6 Consensus size: 60 721215 AGATGGTATA * 721225 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGTTCTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * 721285 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * * * 721345 GGTCTTATAGATACAAATGAATGAAGTAACGTCATGCTTTAGAGATGGTATAGGTTTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * 721405 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * * * 721465 GGTCTTATAGATACAAATGAATGAAGTAACGTCATGCTTTAGAGATGGTATAGGTTTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * 721525 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * * * 721585 GGTCTTATAGATACAAATGAATGAAGTAACGTCATGCTTTAGAGATGGTATAGGTTTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * 721645 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGCTATAGGTCTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG 721705 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * 721765 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATTGGTCTATG 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG * 721825 GGTCTTATAGATACAAATGTATGAAGTAACGTCA 1 GGTCTTATAGATACAAATGTATGTAGTAACGTCA 721859 CCACAGTAAA Statistics Matches: 545, Mismatches: 29, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 60 545 1.00 ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35 Consensus pattern (60 bp): GGTCTTATAGATACAAATGTATGTAGTAACGTCATGCTTTAGAGATGGTATAGGTCTATG Found at i:723250 original size:15 final size:15 Alignment explanation

Indices: 723230--723263 Score: 68 Period size: 15 Copynumber: 2.3 Consensus size: 15 723220 TTCCTAGTGC 723230 ATAATGGTTAGTTTT 1 ATAATGGTTAGTTTT 723245 ATAATGGTTAGTTTT 1 ATAATGGTTAGTTTT 723260 ATAA 1 ATAA 723264 GCGTGATTTG Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50 Consensus pattern (15 bp): ATAATGGTTAGTTTT Found at i:724782 original size:53 final size:53 Alignment explanation

Indices: 724702--724809 Score: 216 Period size: 53 Copynumber: 2.0 Consensus size: 53 724692 TAAGCATGCG 724702 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC 1 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC 724755 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC 1 CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC 724808 CT 1 CT 724810 AAAGACACTT Statistics Matches: 55, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 53 55 1.00 ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21 Consensus pattern (53 bp): CTCAGGTACAGCTGAGACGTACTACGCTAACATAGGAATAAAATAATATACCC Found at i:726708 original size:2 final size:2 Alignment explanation

Indices: 726701--726735 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 726691 GGACTGCCGC 726701 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 C 726736 CGACCACACC Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:729751 original size:20 final size:20 Alignment explanation

Indices: 729728--729773 Score: 76 Period size: 20 Copynumber: 2.4 Consensus size: 20 729718 ATAACATTTA 729728 AAATTAAATACATGCATTAT 1 AAATTAAATACATGCATTAT * 729748 AAATTGAATACATGCATTAT 1 AAATTAAATACATGCATTAT 729768 -AATTAA 1 AAATTAA 729774 GATTATTTGA Statistics Matches: 24, Mismatches: 2, Indels: 1 0.89 0.07 0.04 Matches are distributed among these distances: 19 5 0.21 20 19 0.79 ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35 Consensus pattern (20 bp): AAATTAAATACATGCATTAT Found at i:731242 original size:14 final size:14 Alignment explanation

Indices: 731206--731236 Score: 53 Period size: 14 Copynumber: 2.2 Consensus size: 14 731196 CTGTTTCTTG * 731206 ATTGCTTTTTTATA 1 ATTGCTTTTTTAAA 731220 ATTGCTTTTTTAAA 1 ATTGCTTTTTTAAA 731234 ATT 1 ATT 731237 TGTTTTGCAT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61 Consensus pattern (14 bp): ATTGCTTTTTTAAA Found at i:738624 original size:25 final size:25 Alignment explanation

Indices: 738596--738646 Score: 102 Period size: 25 Copynumber: 2.0 Consensus size: 25 738586 GTAAACTGCC 738596 CCAAACCATTTTATATCGTATAAAA 1 CCAAACCATTTTATATCGTATAAAA 738621 CCAAACCATTTTATATCGTATAAAA 1 CCAAACCATTTTATATCGTATAAAA 738646 C 1 C 738647 TAAAAAATAT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31 Consensus pattern (25 bp): CCAAACCATTTTATATCGTATAAAA Found at i:745485 original size:15 final size:15 Alignment explanation

Indices: 745465--745494 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 745455 TTCGAACGAT 745465 TTTCAAACAAAATTA 1 TTTCAAACAAAATTA 745480 TTTCAAACAAAATTA 1 TTTCAAACAAAATTA 745495 AATATTAATA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33 Consensus pattern (15 bp): TTTCAAACAAAATTA Found at i:747027 original size:41 final size:41 Alignment explanation

Indices: 746970--747092 Score: 201 Period size: 41 Copynumber: 3.0 Consensus size: 41 746960 CGCTTCATTT * ** 746970 TAGCAAATATGACGCTATATCGAGCTACAACATATATCTAA 1 TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA * 747011 TAGCAAATATGTCGCTATATCGTGCTACAATTTATATCTAA 1 TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA * 747052 TAGCAAATATGTCGCTATATTGAGCTACAATTTATATCTAA 1 TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA 747093 GAGCGTAGTC Statistics Matches: 76, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 41 76 1.00 ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33 Consensus pattern (41 bp): TAGCAAATATGTCGCTATATCGAGCTACAATTTATATCTAA Found at i:747411 original size:2 final size:2 Alignment explanation

Indices: 747404--747448 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 747394 TTGTGAAAAC 747404 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 747446 AG A 1 AG A 747449 TTTTATTGAT Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:749836 original size:4 final size:4 Alignment explanation

Indices: 749827--749904 Score: 66 Period size: 4 Copynumber: 19.5 Consensus size: 4 749817 GATCAGCTGA * * * * * * 749827 CTCT CTCT CTCT GTCT CTGT CTGT CTGT CTCT CTCT CTCT TTCT GTCT 1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT * * * * 749875 CTGT CTGT CTGT CTGT CTCT CTCT CTCT CT 1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CT 749905 AAAAAAAAAC Statistics Matches: 65, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 4 65 1.00 ACGTcount: A:0.00, C:0.37, G:0.12, T:0.51 Consensus pattern (4 bp): CTCT Found at i:749853 original size:14 final size:14 Alignment explanation

Indices: 749827--749904 Score: 84 Period size: 14 Copynumber: 5.6 Consensus size: 14 749817 GATCAGCTGA 749827 CTCTCTCTCTCTGT 1 CTCTCTCTCTCTGT * * 749841 CTCTGTCTGTCTGT 1 CTCTCTCTCTCTGT * 749855 CTCTCTCTCTCTTT 1 CTCTCTCTCTCTGT * * 749869 CTGTCTCTGTCTGT 1 CTCTCTCTCTCTGT * * * 749883 CTGTCTGTCTCTCT 1 CTCTCTCTCTCTGT 749897 CTCTCTCT 1 CTCTCTCT 749905 AAAAAAAAAC Statistics Matches: 51, Mismatches: 13, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 14 51 1.00 ACGTcount: A:0.00, C:0.37, G:0.12, T:0.51 Consensus pattern (14 bp): CTCTCTCTCTCTGT Found at i:749871 original size:18 final size:18 Alignment explanation

Indices: 749840--749902 Score: 90 Period size: 18 Copynumber: 3.5 Consensus size: 18 749830 TCTCTCTCTG * 749840 TCTCTGTCTGTCTGTCTC 1 TCTCTCTCTGTCTGTCTC * 749858 TCTCTCTCTTTCTGTCTC 1 TCTCTCTCTGTCTGTCTC * * 749876 TGTCTGTCTGTCTGTCTC 1 TCTCTCTCTGTCTGTCTC 749894 TCTCTCTCT 1 TCTCTCTCT 749903 CTAAAAAAAA Statistics Matches: 38, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 18 38 1.00 ACGTcount: A:0.00, C:0.35, G:0.13, T:0.52 Consensus pattern (18 bp): TCTCTCTCTGTCTGTCTC Done.