Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_D02

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 461372 characters in sequence are not A, C, G, or T


File 175 of 216

Found at i:54779165 original size:26 final size:26

Alignment explanation

Indices: 54779129--54779181 Score: 106 Period size: 26 Copynumber: 2.0 Consensus size: 26 54779119 TGTGCCTATC 54779129 AACGAGAATTTCCCAAATGAACACTT 1 AACGAGAATTTCCCAAATGAACACTT 54779155 AACGAGAATTTCCCAAATGAACACTT 1 AACGAGAATTTCCCAAATGAACACTT 54779181 A 1 A 54779182 CTTGAGGTAA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 27 1.00 ACGTcount: A:0.43, C:0.23, G:0.11, T:0.23 Consensus pattern (26 bp): AACGAGAATTTCCCAAATGAACACTT Found at i:54782781 original size:24 final size:23 Alignment explanation

Indices: 54782747--54782793 Score: 60 Period size: 26 Copynumber: 2.0 Consensus size: 23 54782737 TCAAACTTTT 54782747 AATTTTTTTTC-AAGTATGCTTC 1 AATTTTTTTTCAAAGTATGCTTC 54782769 AATTATTTCTTTCATAAGTATGCTT 1 AATT-TTT-TTTCA-AAGTATGCTT 54782794 TAATAAATGA Statistics Matches: 21, Mismatches: 0, Indels: 4 0.84 0.00 0.16 Matches are distributed among these distances: 22 4 0.19 23 3 0.14 24 4 0.19 26 10 0.48 ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53 Consensus pattern (23 bp): AATTTTTTTTCAAAGTATGCTTC Found at i:54785748 original size:31 final size:32 Alignment explanation

Indices: 54785712--54785776 Score: 123 Period size: 32 Copynumber: 2.1 Consensus size: 32 54785702 CTTAGATAAT 54785712 TTTAAAGAG-TTTTATTAGGATTCAATTACTC 1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC 54785743 TTTAAAGAGTTTTTATTAGGATTCAATTACTC 1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC 54785775 TT 1 TT 54785777 GTAATTTGCC Statistics Matches: 33, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 31 9 0.27 32 24 0.73 ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48 Consensus pattern (32 bp): TTTAAAGAGTTTTTATTAGGATTCAATTACTC Found at i:54786291 original size:10 final size:10 Alignment explanation

Indices: 54786270--54786392 Score: 60 Period size: 10 Copynumber: 12.4 Consensus size: 10 54786260 TTCTTTAAAT 54786270 AAAAGCAAAAA 1 AAAAGC-AAAA 54786281 AAATAGC-AAA 1 AAA-AGCAAAA * 54786291 AACAGCAAAA 1 AAAAGCAAAA 54786301 AAAAGCAAAA 1 AAAAGCAAAA * 54786311 AAAGCGCAAAA 1 AAA-AGCAAAA * * 54786322 AAGAG-TAAA 1 AAAAGCAAAA ** 54786331 AAGCGCAAAA 1 AAAAGCAAAA * 54786341 AAAGAG-TAAA 1 AAA-AGCAAAA ** 54786351 AAGCGCAAAAA 1 AAAAGC-AAAA 54786362 AAAAGC---A 1 AAAAGCAAAA 54786369 AAAAGCAAAA 1 AAAAGCAAAA ** 54786379 AATCGCAAAA 1 AAAAGCAAAA 54786389 AAAA 1 AAAA 54786393 AAAGTTTCCT Statistics Matches: 82, Mismatches: 20, Indels: 21 0.67 0.16 0.17 Matches are distributed among these distances: 7 7 0.09 9 11 0.13 10 42 0.51 11 19 0.23 12 3 0.04 ACGTcount: A:0.71, C:0.12, G:0.14, T:0.03 Consensus pattern (10 bp): AAAAGCAAAA Found at i:54786302 original size:20 final size:20 Alignment explanation

Indices: 54786277--54786380 Score: 92 Period size: 20 Copynumber: 5.3 Consensus size: 20 54786267 AATAAAAGCA * 54786277 AAAAAAATAGCAAAAACAGC 1 AAAAAAAGAGCAAAAACAGC * 54786297 AAAAAAA-AGCAAAAAAAGC 1 AAAAAAAGAGCAAAAACAGC * * 54786316 GCAAAAAAGAGTAAAAAGC-GC 1 -AAAAAAAGAGCAAAAA-CAGC * 54786337 AAAAAAAGAGTAAAAAGC-GC 1 AAAAAAAGAGCAAAAA-CAGC * 54786357 AAAAAAAAAGC-AAAA-AGC 1 AAAAAAAGAGCAAAAACAGC 54786375 AAAAAA 1 AAAAAA 54786381 TCGCAAAAAA Statistics Matches: 73, Mismatches: 7, Indels: 10 0.81 0.08 0.11 Matches are distributed among these distances: 18 8 0.11 19 15 0.21 20 41 0.56 21 9 0.12 ACGTcount: A:0.71, C:0.12, G:0.14, T:0.03 Consensus pattern (20 bp): AAAAAAAGAGCAAAAACAGC Found at i:54786392 original size:20 final size:20 Alignment explanation

Indices: 54786277--54786372 Score: 92 Period size: 21 Copynumber: 4.8 Consensus size: 20 54786267 AATAAAAGCA 54786277 AAAAAAATAGC-AAAAA-CAGC 1 AAAAAAA-AGCAAAAAAGC-GC 54786297 AAAAAAAAGCAAAAAAAGCGC 1 AAAAAAAAGC-AAAAAAGCGC * * 54786318 AAAAAAGAG-TAAAAAGCGC 1 AAAAAAAAGCAAAAAAGCGC * 54786337 AAAAAAAGAG-TAAAAAGCGC 1 AAAAAAA-AGCAAAAAAGCGC 54786357 AAAAAAAAAGCAAAAA 1 -AAAAAAAAGCAAAAA 54786373 GCAAAAAATC Statistics Matches: 66, Mismatches: 4, Indels: 11 0.81 0.05 0.14 Matches are distributed among these distances: 19 18 0.27 20 21 0.32 21 26 0.39 22 1 0.02 ACGTcount: A:0.71, C:0.11, G:0.15, T:0.03 Consensus pattern (20 bp): AAAAAAAAGCAAAAAAGCGC Found at i:54789573 original size:31 final size:32 Alignment explanation

Indices: 54789537--54789601 Score: 123 Period size: 32 Copynumber: 2.1 Consensus size: 32 54789527 CTTAGATAAT 54789537 TTTAAAGAG-TTTTATTAGGATTCAATTACTC 1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC 54789568 TTTAAAGAGTTTTTATTAGGATTCAATTACTC 1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC 54789600 TT 1 TT 54789602 GTAATTTGCC Statistics Matches: 33, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 31 9 0.27 32 24 0.73 ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48 Consensus pattern (32 bp): TTTAAAGAGTTTTTATTAGGATTCAATTACTC Found at i:54790956 original size:42 final size:42 Alignment explanation

Indices: 54790910--54791002 Score: 105 Period size: 42 Copynumber: 2.2 Consensus size: 42 54790900 GGTTGAATAA ** * 54790910 AAGCTCATAAGAGCTGAACGGAAACCCATAAGAGTTAAACTG 1 AAGCTCATAAGAGCTGAACAAAAACCCATAAGAGTTAAACGG * * * * * 54790952 AAGCTCAAAAGCGCTGAACAAAAACCTATTAGGGTTAAACGG 1 AAGCTCATAAGAGCTGAACAAAAACCCATAAGAGTTAAACGG * 54790994 AAACTCATA 1 AAGCTCATA 54791003 TGAGTTAACA Statistics Matches: 41, Mismatches: 10, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 42 41 1.00 ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17 Consensus pattern (42 bp): AAGCTCATAAGAGCTGAACAAAAACCCATAAGAGTTAAACGG Found at i:54799874 original size:15 final size:15 Alignment explanation

Indices: 54799849--54799883 Score: 54 Period size: 15 Copynumber: 2.4 Consensus size: 15 54799839 GACTCTATTT * 54799849 TAATT-ATATTAGGA 1 TAATTAATATTAAGA 54799863 TAATTAATATTAAGA 1 TAATTAATATTAAGA 54799878 TAATTA 1 TAATTA 54799884 TTAAGGATTA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 14 5 0.26 15 14 0.74 ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43 Consensus pattern (15 bp): TAATTAATATTAAGA Found at i:54806558 original size:22 final size:21 Alignment explanation

Indices: 54806509--54806568 Score: 57 Period size: 22 Copynumber: 2.8 Consensus size: 21 54806499 GCCCAGAATG * * 54806509 CCTGCAGCCAAACTACCCTATT 1 CCTGCAGCC-AACCACCCTATC * 54806531 CTTGCAGCCAACCACCCTTATC 1 CCTGCAGCCAACCACCC-TATC * * 54806553 CCTGCACCCAAGCACC 1 CCTGCAGCCAACCACC 54806569 ACCCCTCAGC Statistics Matches: 31, Mismatches: 6, Indels: 2 0.79 0.15 0.05 Matches are distributed among these distances: 21 7 0.23 22 24 0.77 ACGTcount: A:0.25, C:0.47, G:0.10, T:0.18 Consensus pattern (21 bp): CCTGCAGCCAACCACCCTATC Found at i:54807681 original size:6 final size:6 Alignment explanation

Indices: 54807670--54807728 Score: 52 Period size: 6 Copynumber: 10.2 Consensus size: 6 54807660 TTCCTAAAGC * * 54807670 ATAAAA ATAAAA ATAATAA AT--AA ATAAAA ATCAAA ATAAAT A-AAAA 1 ATAAAA ATAAAA ATAA-AA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA * * 54807716 AGAAAA AGAAAA A 1 ATAAAA ATAAAA A 54807729 GAATATAATT Statistics Matches: 45, Mismatches: 4, Indels: 8 0.79 0.07 0.14 Matches are distributed among these distances: 4 4 0.09 5 4 0.09 6 33 0.73 7 4 0.09 ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15 Consensus pattern (6 bp): ATAAAA Found at i:54807696 original size:23 final size:22 Alignment explanation

Indices: 54807670--54807733 Score: 74 Period size: 23 Copynumber: 2.8 Consensus size: 22 54807660 TTCCTAAAGC 54807670 ATAAAAATAAAAATAATAAATAA 1 ATAAAAATAAAAATAATAAA-AA * 54807693 ATAAAAATCAAAATAAATAAAAA 1 ATAAAAATAAAAAT-AATAAAAA * * * 54807716 AGAAAAAGAAAAAGAATA 1 ATAAAAATAAAAATAATA 54807734 TAATTTAGGG Statistics Matches: 35, Mismatches: 5, Indels: 3 0.81 0.12 0.07 Matches are distributed among these distances: 22 4 0.11 23 25 0.71 24 6 0.17 ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16 Consensus pattern (22 bp): ATAAAAATAAAAATAATAAAAA Found at i:54807716 original size:17 final size:17 Alignment explanation

Indices: 54807674--54807715 Score: 68 Period size: 16 Copynumber: 2.5 Consensus size: 17 54807664 TAAAGCATAA 54807674 AAATAAAAATAATAAAT 1 AAATAAAAATAATAAAT * 54807691 AAATAAAAATCA-AAAT 1 AAATAAAAATAATAAAT 54807707 AAATAAAAA 1 AAATAAAAA 54807716 AGAAAAAGAA Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 16 13 0.54 17 11 0.46 ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19 Consensus pattern (17 bp): AAATAAAAATAATAAAT Found at i:54807722 original size:17 final size:16 Alignment explanation

Indices: 54807674--54807722 Score: 53 Period size: 16 Copynumber: 2.9 Consensus size: 16 54807664 TAAAGCATAA * 54807674 AAATAAAAATAATAAAT 1 AAATAAAAA-AAAAAAT ** 54807691 AAATAAAAATCAAAAT 1 AAATAAAAAAAAAAAT 54807707 AAATAAAAAAGAAAAA 1 AAATAAAAAA-AAAAA 54807723 GAAAAAGAAT Statistics Matches: 26, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 16 13 0.50 17 13 0.50 ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16 Consensus pattern (16 bp): AAATAAAAAAAAAAAT Found at i:54808310 original size:15 final size:15 Alignment explanation

Indices: 54808285--54808319 Score: 54 Period size: 15 Copynumber: 2.4 Consensus size: 15 54808275 AACTCTATTT * 54808285 TAATT-ATATTAGGA 1 TAATTAATATTAAGA 54808299 TAATTAATATTAAGA 1 TAATTAATATTAAGA 54808314 TAATTA 1 TAATTA 54808320 TTAAGGATTA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 14 5 0.26 15 14 0.74 ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43 Consensus pattern (15 bp): TAATTAATATTAAGA Found at i:54813251 original size:5 final size:5 Alignment explanation

Indices: 54813241--54813290 Score: 100 Period size: 5 Copynumber: 10.0 Consensus size: 5 54813231 ATATGAACAT 54813241 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG 1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG 54813291 TGCTATAAGC Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 45 1.00 ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40 Consensus pattern (5 bp): ATATG Found at i:54813387 original size:35 final size:36 Alignment explanation

Indices: 54813324--54813391 Score: 102 Period size: 35 Copynumber: 1.9 Consensus size: 36 54813314 TGTGAAAGAG * * * 54813324 AATATGTGGGTATGTTATTCATGCCATGTGACATTA 1 AATACGTGAGTATGTTATTCATACCATGTGACATTA 54813360 AATACGTGAGTATGTT-TTCATACCATGTGACA 1 AATACGTGAGTATGTTATTCATACCATGTGACA 54813392 GTGATTATAA Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 35 15 0.52 36 14 0.48 ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37 Consensus pattern (36 bp): AATACGTGAGTATGTTATTCATACCATGTGACATTA Found at i:54817252 original size:51 final size:51 Alignment explanation

Indices: 54817132--54817521 Score: 425 Period size: 51 Copynumber: 7.7 Consensus size: 51 54817122 TCATTCAATA * 54817132 CACGTAGTAGCCTCCACATAGTACTACACACGTGATCAAG-TTTTACGGTT 1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACGGTT * * 54817182 CACGTAGTAGCCTTCACATAGTACTACACACATGATCAAGTTTTTATGGTT 1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACGGTT * 54817233 CACGTAGTAGCCTTAACATAGTACTACACACGTGATCAAGTTTTTACGGTT 1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACGGTT * ** * * 54817284 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAACTTTT-CGATA 1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTTACGGTT * * * * * * 54817335 CACATAGTAGCCTTCACTTAGTACTACACATGTGA-CCA-TCATTTATCGATT 1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTTA-CGGTT * * * * * 54817386 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTA 1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTTACGGTT * * * * * * * 54817437 CACATTGTAGCCTTCACTTAGTACTACACATGTGA-CCA-TCATTTATCGATT 1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTTA-CGGTT * 54817488 CACGTAGTAGCCTTCACACAGTACTACACACGTG 1 CACGTAGTAGCCTTCACATAGTACTACACACGTG 54817522 TTCATCGATA Statistics Matches: 284, Mismatches: 45, Indels: 21 0.81 0.13 0.06 Matches are distributed among these distances: 49 7 0.02 50 40 0.14 51 227 0.80 52 7 0.02 53 3 0.01 ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29 Consensus pattern (51 bp): CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACGGTT Found at i:54817343 original size:102 final size:102 Alignment explanation

Indices: 54817129--54817521 Score: 474 Period size: 102 Copynumber: 3.9 Consensus size: 102 54817119 TTATCATTCA * * * 54817129 ATACACGTAGTAGCCTCCACATAGTACTACACACGTGATCAAGT--TTTA-CGGTTCACGTAGTA 1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGA-CAA-TCATTTATCGATTCACGTAGTA * * * * * 54817191 GCCTTCACATAGTACTACACACATGATC-AAGTTTTTATG 64 GCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CG * * * * * * 54817230 GTTCACGTAGTAGCCTTAACATAGTACTACACACGTGATCAAGT-TTTTA-CGGTTCACGTAGTA 1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGA-CAA-TCATTTATCGATTCACGTAGTA * * 54817293 GCCTTCACATAGTACTACACACGTGACCAAAACTTTTCG 64 GCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCG * * * 54817332 ATACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGC 1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGACAATCATTTATCGATTCACGTAGTAGC * 54817397 CTTCACACAGTACTACACACGTGACCAAAGCTTCTCG 66 CTTCACACAGTACTACACACGTGACCAAAGCTTTTCG * * * * * 54817434 GTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGC 1 ATACACATAGTAGCCTTCACATAGTACTACACACGTGACAATCATTTATCGATTCACGTAGTAGC 54817499 CTTCACACAGTACTACACACGTG 66 CTTCACACAGTACTACACACGTG 54817522 TTCATCGATA Statistics Matches: 265, Mismatches: 23, Indels: 7 0.90 0.08 0.02 Matches are distributed among these distances: 100 1 0.00 101 46 0.17 102 212 0.80 103 6 0.02 ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29 Consensus pattern (102 bp): ATACACATAGTAGCCTTCACATAGTACTACACACGTGACAATCATTTATCGATTCACGTAGTAGC CTTCACACAGTACTACACACGTGACCAAAGCTTTTCG Found at i:54817410 original size:153 final size:151 Alignment explanation

Indices: 54817130--54817518 Score: 469 Period size: 153 Copynumber: 2.5 Consensus size: 151 54817120 TATCATTCAA * * * * 54817130 TACACGTAGTAGCCTCCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTAGCCT 1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATTTT-CGATTCACGTAGTAGCCT * * * 54817195 TCACATAGTACTACACACATGATCAAGTTTTTATGGTTCACGTAGTAGCCTTAACATAGTACTAC 65 TCACATAGTACTACACACATGATCAAGTATTTATGATTCACGTAGTAGCCTTAACACAGTACTAC * * * 54817260 ACACGTGATC-AAGTTTTTACGG 130 ACACGTGACCAAAGCTTCT-CGG * * * 54817282 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAACTTTTCGATACACATAGTAGCC 1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAA-TTTTCGATTCACGTAGTAGCC * ** * * 54817347 TTCACTTAGTACTACACATGTGA-CCA-TCATTTATCGATTCACGTAGTAGCCTTCACACAGTAC 64 TTCACATAGTACTACACACATGATCAAGT-ATTTAT-GATTCACGTAGTAGCCTTAACACAGTAC 54817410 TACACACGTGACCAAAGCTTCTCGG 127 TACACACGTGACCAAAGCTTCTCGG * * * * * 54817435 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC 1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AATTT-TCGATTCACGTAGTAGCC * 54817500 TTCACACAGTACTACACAC 64 TTCACATAGTACTACACAC 54817519 GTGTTCATCG Statistics Matches: 201, Mismatches: 29, Indels: 13 0.83 0.12 0.05 Matches are distributed among these distances: 151 1 0.00 152 47 0.23 153 143 0.71 154 10 0.05 ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29 Consensus pattern (151 bp): TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAATTTTCGATTCACGTAGTAGCCTT CACATAGTACTACACACATGATCAAGTATTTATGATTCACGTAGTAGCCTTAACACAGTACTACA CACGTGACCAAAGCTTCTCGG Found at i:54826636 original size:20 final size:20 Alignment explanation

Indices: 54826594--54826639 Score: 56 Period size: 20 Copynumber: 2.3 Consensus size: 20 54826584 TAGAAATATT * * 54826594 GATACCTTAGGAAATATAAC 1 GATACCTTAAGAAAGATAAC * * 54826614 GATACCTTAAGAAAGGTATC 1 GATACCTTAAGAAAGATAAC 54826634 GATACC 1 GATACC 54826640 GAGGATACCT Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24 Consensus pattern (20 bp): GATACCTTAAGAAAGATAAC Found at i:54830742 original size:12 final size:11 Alignment explanation

Indices: 54830725--54830758 Score: 50 Period size: 12 Copynumber: 2.9 Consensus size: 11 54830715 GCCTGTATGC 54830725 CAGGCCGTGTGG 1 CAGGCCGTGT-G 54830737 CAGGCCGTGTG 1 CAGGCCGTGTG 54830748 CTAGGCCGTGT 1 C-AGGCCGTGT 54830759 AACAACTTGA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 11 2 0.10 12 19 0.90 ACGTcount: A:0.09, C:0.26, G:0.44, T:0.21 Consensus pattern (11 bp): CAGGCCGTGTG Found at i:54834853 original size:38 final size:38 Alignment explanation

Indices: 54834810--54834930 Score: 104 Period size: 38 Copynumber: 3.2 Consensus size: 38 54834800 TTTTAGTCAA * * 54834810 AATATAAAAGACATGGAAATTAATATCCTTTTGGAAAG 1 AATATAAAAGATATGGAAATTAATATACTTTTGGAAAG * * * * ** 54834848 AATATAATTAGTATAT-GAATTTAAT-TAATTTCAGCCAA- 1 AATATAA-AAG-ATATGGAAATTAATATACTTT-TGGAAAG * * 54834886 AATATAAAAGATATGAAAATTAATATTCTTTTGGAAAG 1 AATATAAAAGATATGGAAATTAATATACTTTTGGAAAG 54834924 AATATAA 1 AATATAA 54834931 TTAATATATG Statistics Matches: 61, Mismatches: 16, Indels: 12 0.69 0.18 0.13 Matches are distributed among these distances: 36 4 0.07 37 12 0.20 38 29 0.48 39 13 0.21 40 3 0.05 ACGTcount: A:0.49, C:0.06, G:0.12, T:0.34 Consensus pattern (38 bp): AATATAAAAGATATGGAAATTAATATACTTTTGGAAAG Found at i:54834857 original size:137 final size:138 Alignment explanation

Indices: 54834578--54834869 Score: 480 Period size: 137 Copynumber: 2.1 Consensus size: 138 54834568 ACATAGATAA 54834578 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAATTATAAATA 1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAATTATAAATA ** * 54834643 TAAACAATTATATTAATTAATTTAGGTCAAAATATAAAAGATGTGGAAATTAATATTCTTTTGGA 66 TAAACAATTATATTAATTAATTTAGGTCAAAATATAAAAGACATGGAAATTAATATCCTTTTGGA 54834708 AAGAATAT 131 AAGAATAT * * * * 54834716 AATTAACATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACTGAATTTATTAATA 1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAATTATAAATA * 54834781 TAAA-AATTGTATTAATTAATTTTA-GTCAAAATATAAAAGACATGGAAATTAATATCCTTTTGG 66 TAAACAATTATATTAATTAA-TTTAGGTCAAAATATAAAAGACATGGAAATTAATATCCTTTTGG 54834844 AAAGAATAT 130 AAAGAATAT * 54834853 AATTAGTATATGAATTT 1 AATTAATATATGAATTT 54834870 AATTAATTTC Statistics Matches: 143, Mismatches: 10, Indels: 3 0.92 0.06 0.02 Matches are distributed among these distances: 137 74 0.52 138 69 0.48 ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40 Consensus pattern (138 bp): AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAAATTATAAATA TAAACAATTATATTAATTAATTTAGGTCAAAATATAAAAGACATGGAAATTAATATCCTTTTGGA AAGAATAT Found at i:54834876 original size:76 final size:76 Alignment explanation

Indices: 54834792--54834945 Score: 254 Period size: 76 Copynumber: 2.0 Consensus size: 76 54834782 AAAAATTGTA * * * 54834792 TTAATTAATTTTAGTCAAAATATAAAAGACATGGAAATTAATATCCTTTTGGAAAGAATATAATT 1 TTAATTAATTTCAGCCAAAATATAAAAGACATGAAAATTAATATCCTTTTGGAAAGAATATAATT * 54834857 AGTATATGAAT 66 AATATATGAAT * * 54834868 TTAATTAATTTCAGCCAAAATATAAAAGATATGAAAATTAATATTCTTTTGGAAAGAATATAATT 1 TTAATTAATTTCAGCCAAAATATAAAAGACATGAAAATTAATATCCTTTTGGAAAGAATATAATT 54834933 AATATATGAAT 66 AATATATGAAT 54834944 TT 1 TT 54834946 GATTCATACA Statistics Matches: 72, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 76 72 1.00 ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38 Consensus pattern (76 bp): TTAATTAATTTCAGCCAAAATATAAAAGACATGAAAATTAATATCCTTTTGGAAAGAATATAATT AATATATGAAT Found at i:54835198 original size:73 final size:73 Alignment explanation

Indices: 54835013--54835227 Score: 317 Period size: 75 Copynumber: 2.9 Consensus size: 73 54835003 ATAAAAGATA * * * 54835013 TGGAAAGAATATAATTCATTTGTCTAACTTTTCATTTGTCTTCTCTATTAAAAAGATG-ATAATC 1 TGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGA-GAATAATC 54835077 CTATATTTT 65 CTATATTTT * * 54835086 TGGGGAAATAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGGGAATAAT 1 T--GGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGAGAATAAT 54835151 CCTAT-TCTTT 64 CCTATAT-TTT * * 54835161 TGGAAAGAATATAATTCTTTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAAGAGAATAATCC 1 TGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGAGAATAATCC 54835226 TA 66 TA 54835228 GTTTTCCTTT Statistics Matches: 129, Mismatches: 9, Indels: 8 0.88 0.06 0.05 Matches are distributed among these distances: 73 63 0.49 74 2 0.02 75 64 0.50 ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44 Consensus pattern (73 bp): TGGAAAGAATATAATTCATTTTTCTAACTTTCCATTTGTCTTCTCTATTAATAAGAGAATAATCC TATATTTT Found at i:54835593 original size:33 final size:33 Alignment explanation

Indices: 54835551--54835615 Score: 121 Period size: 33 Copynumber: 2.0 Consensus size: 33 54835541 ACACCACGGG 54835551 GCATACCGGTAATCCAAAAATATGTTCCTCAAA 1 GCATACCGGTAATCCAAAAATATGTTCCTCAAA * 54835584 GCATACCGGTAATCCAAAACTATGTTCCTCAA 1 GCATACCGGTAATCCAAAAATATGTTCCTCAA 54835616 GGCAAGTTTG Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 33 31 1.00 ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25 Consensus pattern (33 bp): GCATACCGGTAATCCAAAAATATGTTCCTCAAA Found at i:54838867 original size:18 final size:20 Alignment explanation

Indices: 54838836--54838872 Score: 60 Period size: 19 Copynumber: 1.9 Consensus size: 20 54838826 ATGAGATTAT 54838836 TATTTATATTTCAA-ATATC 1 TATTTATATTTCAAGATATC 54838855 TATTTAT-TTTCAAGATAT 1 TATTTATATTTCAAGATAT 54838873 TCAACTCTCA Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 6 0.35 19 11 0.65 ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54 Consensus pattern (20 bp): TATTTATATTTCAAGATATC Found at i:54845843 original size:29 final size:29 Alignment explanation

Indices: 54845801--54845858 Score: 89 Period size: 29 Copynumber: 2.0 Consensus size: 29 54845791 CATGGAAGAA * * * 54845801 GTGAATAACTTGTTCGTTGAGAGTTCGTG 1 GTGAAGAACTTGTTCATTGAGAATTCGTG 54845830 GTGAAGAACTTGTTCATTGAGAATTCGTG 1 GTGAAGAACTTGTTCATTGAGAATTCGTG 54845859 TCAAGGTGAA Statistics Matches: 26, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 29 26 1.00 ACGTcount: A:0.24, C:0.10, G:0.29, T:0.36 Consensus pattern (29 bp): GTGAAGAACTTGTTCATTGAGAATTCGTG Found at i:54859526 original size:25 final size:24 Alignment explanation

Indices: 54859498--54859549 Score: 59 Period size: 24 Copynumber: 2.1 Consensus size: 24 54859488 ATTTTGAAAG 54859498 AAATAAAAAAGATATTTATACTAAT 1 AAATAAAAAAGATA-TTATACTAAT *** * 54859523 AAATGCTAAATATATTATACTAAT 1 AAATAAAAAAGATATTATACTAAT 54859547 AAA 1 AAA 54859550 AAACTAAATC Statistics Matches: 23, Mismatches: 4, Indels: 1 0.82 0.14 0.04 Matches are distributed among these distances: 24 13 0.57 25 10 0.43 ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33 Consensus pattern (24 bp): AAATAAAAAAGATATTATACTAAT Found at i:54859556 original size:25 final size:23 Alignment explanation

Indices: 54859509--54859558 Score: 64 Period size: 24 Copynumber: 2.1 Consensus size: 23 54859499 AATAAAAAAG ** 54859509 ATATTTATACTAATAAATGCTAA 1 ATATTTATACTAATAAAAACTAA 54859532 ATATATTATACTAATAAAAAACTAA 1 ATAT-TTATACTAAT-AAAAACTAA 54859557 AT 1 AT 54859559 CTTTTAGAAA Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 23 4 0.17 24 10 0.43 25 9 0.39 ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36 Consensus pattern (23 bp): ATATTTATACTAATAAAAACTAA Found at i:54859615 original size:17 final size:17 Alignment explanation

Indices: 54859593--54859677 Score: 98 Period size: 17 Copynumber: 4.7 Consensus size: 17 54859583 TTTAACTTGT * 54859593 CTTGCAAGTAAATTTAA 1 CTTGCAAGTAAAATTAA * 54859610 CTTGCAAGTAAAATTGA 1 CTTGCAAGTAAAATTAA 54859627 CTTGCAAGTAAACTAAATTGAA 1 CTTGCAAGT--A--AAATT-AA * 54859649 CTTGCAAGTAAAATTGA 1 CTTGCAAGTAAAATTAA 54859666 CTTGCAAGTAAA 1 CTTGCAAGTAAA 54859678 CTCTTCAAAT Statistics Matches: 59, Mismatches: 4, Indels: 10 0.81 0.05 0.14 Matches are distributed among these distances: 17 37 0.63 18 5 0.08 19 1 0.02 20 1 0.02 21 5 0.08 22 10 0.17 ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29 Consensus pattern (17 bp): CTTGCAAGTAAAATTAA Found at i:54859644 original size:39 final size:39 Alignment explanation

Indices: 54859601--54859679 Score: 149 Period size: 39 Copynumber: 2.0 Consensus size: 39 54859591 GTCTTGCAAG * 54859601 TAAATTTAACTTGCAAGTAAAATTGACTTGCAAGTAAAC 1 TAAATTGAACTTGCAAGTAAAATTGACTTGCAAGTAAAC 54859640 TAAATTGAACTTGCAAGTAAAATTGACTTGCAAGTAAAC 1 TAAATTGAACTTGCAAGTAAAATTGACTTGCAAGTAAAC 54859679 T 1 T 54859680 CTTCAAATCC Statistics Matches: 39, Mismatches: 1, Indels: 0 0.98 0.03 0.00 Matches are distributed among these distances: 39 39 1.00 ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30 Consensus pattern (39 bp): TAAATTGAACTTGCAAGTAAAATTGACTTGCAAGTAAAC Found at i:54861606 original size:30 final size:30 Alignment explanation

Indices: 54861570--54861657 Score: 167 Period size: 30 Copynumber: 2.9 Consensus size: 30 54861560 AACCTATTAC 54861570 AACCTATGGATAAACCAAGTTGCATGTTAA 1 AACCTATGGATAAACCAAGTTGCATGTTAA 54861600 AACCTATGGATAAACCAAGTTGCATGTTAA 1 AACCTATGGATAAACCAAGTTGCATGTTAA * 54861630 AACTTATGGATAAACCAAGTTGCATGTT 1 AACCTATGGATAAACCAAGTTGCATGTT 54861658 CAAGAATTAA Statistics Matches: 57, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 30 57 1.00 ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28 Consensus pattern (30 bp): AACCTATGGATAAACCAAGTTGCATGTTAA Found at i:54875798 original size:20 final size:22 Alignment explanation

Indices: 54875770--54875820 Score: 63 Period size: 22 Copynumber: 2.4 Consensus size: 22 54875760 TCAAATACAG * 54875770 ATTAAATTA-TTTTTAAAAA-A 1 ATTATATTATTTTTTAAAAATA 54875790 ATTATATTAATTTTTTAAAAATA 1 ATTATATT-ATTTTTTAAAAATA 54875813 ATT-TATTA 1 ATTATATTA 54875821 AAATCTCTTT Statistics Matches: 27, Mismatches: 1, Indels: 5 0.82 0.03 0.15 Matches are distributed among these distances: 20 7 0.26 21 2 0.07 22 14 0.52 23 4 0.15 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (22 bp): ATTATATTATTTTTTAAAAATA Found at i:54875807 original size:22 final size:22 Alignment explanation

Indices: 54875779--54875821 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 54875769 GATTAAATTA 54875779 TTTTTAAAAA-AATTATATTAAT 1 TTTTTAAAAATAATT-TATTAAT 54875801 TTTTTAAAAATAATTTATTAA 1 TTTTTAAAAATAATTTATTAA 54875822 AATCTCTTTT Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 22 16 0.80 23 4 0.20 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (22 bp): TTTTTAAAAATAATTTATTAAT Found at i:54877021 original size:5 final size:5 Alignment explanation

Indices: 54877011--54877056 Score: 92 Period size: 5 Copynumber: 9.2 Consensus size: 5 54877001 TGAGCATTCG 54877011 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A 1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A 54877057 AATTTTCAAG Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 41 1.00 ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20 Consensus pattern (5 bp): ATCGA Found at i:54878115 original size:9 final size:9 Alignment explanation

Indices: 54878079--54878112 Score: 59 Period size: 9 Copynumber: 3.8 Consensus size: 9 54878069 TATAATTTAA 54878079 TATTCGAAT 1 TATTCGAAT 54878088 TATTCGAAT 1 TATTCGAAT * 54878097 TATTCGAGT 1 TATTCGAAT 54878106 TATTCGA 1 TATTCGA 54878113 GTTTGAAAAC Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 9 24 1.00 ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44 Consensus pattern (9 bp): TATTCGAAT Found at i:54892270 original size:30 final size:30 Alignment explanation

Indices: 54892234--54892294 Score: 113 Period size: 30 Copynumber: 2.0 Consensus size: 30 54892224 TCCCAAAGCT 54892234 CATACACTTTCCTCTCACCCACATGCCCCG 1 CATACACTTTCCTCTCACCCACATGCCCCG * 54892264 CATACACTTTCCTCTCTCCCACATGCCCCG 1 CATACACTTTCCTCTCACCCACATGCCCCG 54892294 C 1 C 54892295 TTGGCAGGTA Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 30 30 1.00 ACGTcount: A:0.18, C:0.51, G:0.07, T:0.25 Consensus pattern (30 bp): CATACACTTTCCTCTCACCCACATGCCCCG Found at i:54893021 original size:9 final size:9 Alignment explanation

Indices: 54893009--54893061 Score: 54 Period size: 9 Copynumber: 5.8 Consensus size: 9 54892999 ATTTTTAAAA 54893009 ATATTTTTT 1 ATATTTTTT 54893018 ATATTTTTT 1 ATATTTTTT * * 54893027 ATA-ATTTA 1 ATATTTTTT * 54893035 ATAATTTTT 1 ATATTTTTT 54893044 ATAGTTTTTTT 1 ATA--TTTTTT 54893055 ATATTTT 1 ATATTTT 54893062 ATAAAATTAA Statistics Matches: 36, Mismatches: 5, Indels: 6 0.77 0.11 0.13 Matches are distributed among these distances: 8 6 0.17 9 22 0.61 11 8 0.22 ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70 Consensus pattern (9 bp): ATATTTTTT Found at i:54893043 original size:26 final size:27 Alignment explanation

Indices: 54893008--54893062 Score: 76 Period size: 28 Copynumber: 2.0 Consensus size: 27 54892998 AATTTTTAAA * 54893008 AATATTTTTTATA-TTTTTTATAATTT 1 AATAATTTTTATAGTTTTTTATAATTT * 54893034 AATAATTTTTATAGTTTTTTTATATTTT 1 AATAATTTTTATAG-TTTTTTATAATTT 54893062 A 1 A 54893063 TAAAATTAAT Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 26 12 0.48 28 13 0.52 ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67 Consensus pattern (27 bp): AATAATTTTTATAGTTTTTTATAATTT Found at i:54912438 original size:6 final size:6 Alignment explanation

Indices: 54912427--54912519 Score: 186 Period size: 6 Copynumber: 15.5 Consensus size: 6 54912417 TAGACATGGA 54912427 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT 1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT 54912475 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG 1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATG 54912520 CAATTGTCTC Statistics Matches: 87, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 87 1.00 ACGTcount: A:0.33, C:0.00, G:0.17, T:0.49 Consensus pattern (6 bp): ATGTAT Found at i:54913605 original size:20 final size:20 Alignment explanation

Indices: 54913568--54913605 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 54913558 TTAGGGTTAC * 54913568 AAAACATTACCATACAATCA 1 AAAACATTAACATACAATCA 54913588 AAAACATTTAACAT-CAAT 1 AAAACA-TTAACATACAAT 54913606 ATTCAATTAA Statistics Matches: 16, Mismatches: 1, Indels: 2 0.84 0.05 0.11 Matches are distributed among these distances: 20 10 0.62 21 6 0.38 ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24 Consensus pattern (20 bp): AAAACATTAACATACAATCA Found at i:54915331 original size:25 final size:25 Alignment explanation

Indices: 54915297--54915351 Score: 74 Period size: 25 Copynumber: 2.2 Consensus size: 25 54915287 ACACACCATA * 54915297 GCTCTTATGAGCGTCCCGATATTTG 1 GCTCTCATGAGCGTCCCGATATTTG * * * 54915322 GCTCTCATGAGCTTCTCGTTATTTG 1 GCTCTCATGAGCGTCCCGATATTTG 54915347 GCTCT 1 GCTCT 54915352 GCGGAGCTTC Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40 Consensus pattern (25 bp): GCTCTCATGAGCGTCCCGATATTTG Found at i:54915470 original size:49 final size:50 Alignment explanation

Indices: 54915417--54915512 Score: 131 Period size: 49 Copynumber: 1.9 Consensus size: 50 54915407 ACTTCTCGAT * ** 54915417 ATTGGCTAGCATGAGCTTCCCGAT-TACAGCTCTTATGAGCTTCCTGATA 1 ATTGGCTAGCAAGAGCTTCCCGATATACAGCTCACATGAGCTTCCTGATA * * * 54915466 ATTGGCTCGCAAGAGTTTCCCGTTATACAGCTCACATGAGCTTCCTG 1 ATTGGCTAGCAAGAGCTTCCCGATATACAGCTCACATGAGCTTCCTG 54915513 TTATATGGTT Statistics Matches: 40, Mismatches: 6, Indels: 1 0.85 0.13 0.02 Matches are distributed among these distances: 49 20 0.50 50 20 0.50 ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31 Consensus pattern (50 bp): ATTGGCTAGCAAGAGCTTCCCGATATACAGCTCACATGAGCTTCCTGATA Found at i:54915498 original size:25 final size:25 Alignment explanation

Indices: 54915470--54915517 Score: 60 Period size: 25 Copynumber: 1.9 Consensus size: 25 54915460 CTGATAATTG * * 54915470 GCTCGCAAGAGTTTCCCGTTATACA 1 GCTCACAAGAGCTTCCCGTTATACA * * 54915495 GCTCACATGAGCTTCCTGTTATA 1 GCTCACAAGAGCTTCCCGTTATA 54915518 TGGTTTGAAA Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 25 19 1.00 ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31 Consensus pattern (25 bp): GCTCACAAGAGCTTCCCGTTATACA Found at i:54925571 original size:27 final size:27 Alignment explanation

Indices: 54925479--54925572 Score: 76 Period size: 27 Copynumber: 3.6 Consensus size: 27 54925469 ATTTAATATT * ** 54925479 AATATAATAATATTATTATAA-AATTTA 1 AATAT-ATATTATTATTATAATTTTTTA 54925506 AAT-T-TATTATTA-TATAATTTTTTGA 1 AATATATATTATTATTATAATTTTTT-A 54925531 AA-ATAT-TTATTTATTCAT-ATTTTTTA 1 AATATATATTA-TTATT-ATAATTTTTTA 54925557 AATATATATTATTATT 1 AATATATATTATTATT 54925573 TCTTGTCAAC Statistics Matches: 55, Mismatches: 3, Indels: 18 0.72 0.04 0.24 Matches are distributed among these distances: 23 5 0.09 24 10 0.18 25 7 0.13 26 8 0.15 27 20 0.36 28 5 0.09 ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55 Consensus pattern (27 bp): AATATATATTATTATTATAATTTTTTA Found at i:54925811 original size:47 final size:46 Alignment explanation

Indices: 54925722--54925862 Score: 178 Period size: 46 Copynumber: 3.1 Consensus size: 46 54925712 ACTAAAATGG * * * * 54925722 TATT-TTTTTTAATCGCGCCTATCTGGCATTGC-CGAATCAATTTTT 1 TATTATTTTTTAATCGCGCCAATCTGACA-GGCGTGAATCAATTTTT * * 54925767 TATTATTTTTTTAATCGCGCCAATTTGACAGGCGTGAATTAATTTTT 1 TATTA-TTTTTTAATCGCGCCAATCTGACAGGCGTGAATCAATTTTT * * 54925814 TATTATTTTTTAATCGTGCCTATCTGACAGGCGTGAATCAATTTTT 1 TATTATTTTTTAATCGCGCCAATCTGACAGGCGTGAATCAATTTTT 54925860 TAT 1 TAT 54925863 ATTAAAAATA Statistics Matches: 83, Mismatches: 10, Indels: 5 0.85 0.10 0.05 Matches are distributed among these distances: 45 4 0.05 46 42 0.51 47 37 0.45 ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47 Consensus pattern (46 bp): TATTATTTTTTAATCGCGCCAATCTGACAGGCGTGAATCAATTTTT Found at i:54925842 original size:46 final size:46 Alignment explanation

Indices: 54925722--54925917 Score: 189 Period size: 47 Copynumber: 4.1 Consensus size: 46 54925712 ACTAAAATGG * * * 54925722 TATT-TTTTTTAATCGCGCCTATCTGGCATTGC-CGAATCAATTTTT 1 TATTATTTTTTAATCGCGCCTATCTGACA-GGCGTGAATCAATTTTT * * * 54925767 TATTATTTTTTTAATCGCGCCAATTTGACAGGCGTGAATTAATTTTT 1 TATTA-TTTTTTAATCGCGCCTATCTGACAGGCGTGAATCAATTTTT * 54925814 TATTATTTTTTAATCGTGCCTATCTGACAGGCGTGAATCAATTTTTT 1 TATTATTTTTTAATCGCGCCTATCTGACAGGCGTGAATCAA-TTTTT * ** 54925861 ATATTAAAAATATTTTTTTAATCGCGCCTACCTGACAGGCACGAATCAATTTTT 1 -TA-T-----TA-TTTTTTAATCGCGCCTATCTGACAGGCGTGAATCAATTTTT 54925915 TAT 1 TAT 54925918 ATTAAAAAAT Statistics Matches: 125, Mismatches: 14, Indels: 17 0.80 0.09 0.11 Matches are distributed among these distances: 45 4 0.03 46 34 0.27 47 42 0.34 48 2 0.02 49 1 0.01 52 1 0.01 53 2 0.02 54 7 0.06 55 32 0.26 ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44 Consensus pattern (46 bp): TATTATTTTTTAATCGCGCCTATCTGACAGGCGTGAATCAATTTTT Found at i:54925881 original size:55 final size:56 Alignment explanation

Indices: 54925819--54925935 Score: 191 Period size: 55 Copynumber: 2.1 Consensus size: 56 54925809 TTTTTTATTA * * ** 54925819 TTTTTTAATCGTGCCTATCTGACAGGCGTGAATCAATTTTTTATATT-AAAAATAT 1 TTTTTTAATCGCGCCTACCTGACAGGCACGAATCAATTTTTTATATTAAAAAATAT 54925874 TTTTTTAATCGCGCCTACCTGACAGGCACGAATCAATTTTTTATATTAAAAAATAT 1 TTTTTTAATCGCGCCTACCTGACAGGCACGAATCAATTTTTTATATTAAAAAATAT 54925930 TTTTTT 1 TTTTTT 54925936 GTTTTAAATA Statistics Matches: 57, Mismatches: 4, Indels: 1 0.92 0.06 0.02 Matches are distributed among these distances: 55 43 0.75 56 14 0.25 ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44 Consensus pattern (56 bp): TTTTTTAATCGCGCCTACCTGACAGGCACGAATCAATTTTTTATATTAAAAAATAT Found at i:54928283 original size:15 final size:15 Alignment explanation

Indices: 54928263--54928370 Score: 78 Period size: 15 Copynumber: 7.2 Consensus size: 15 54928253 TTTATGGAAA 54928263 ATCAAAGATATGGGT 1 ATCAAAGATATGGGT * * ** 54928278 ATCAAATA-ATAGAA 1 ATCAAAGATATGGGT 54928292 AGTCAAAGATATGGGT 1 A-TCAAAGATATGGGT * ** 54928308 ATCAAATAT-TGGAA 1 ATCAAAGATATGGGT 54928322 AGTCAAAGATATGGGT 1 A-TCAAAGATATGGGT * ** 54928338 ATCAAATAT-TGGAA 1 ATCAAAGATATGGGT 54928352 AGTCAAAGATATGGGT 1 A-TCAAAGATATGGGT 54928368 ATC 1 ATC 54928371 GAGATATTGG Statistics Matches: 67, Mismatches: 20, Indels: 12 0.68 0.20 0.12 Matches are distributed among these distances: 14 12 0.18 15 43 0.64 16 12 0.18 ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26 Consensus pattern (15 bp): ATCAAAGATATGGGT Found at i:54928300 original size:30 final size:30 Alignment explanation

Indices: 54928257--54928380 Score: 203 Period size: 30 Copynumber: 4.1 Consensus size: 30 54928247 TCCATATTTA * * 54928257 TGGAAAATCAAAGATATGGGTATCAAATAA 1 TGGAAAGTCAAAGATATGGGTATCAAATAT * 54928287 TAGAAAGTCAAAGATATGGGTATCAAATAT 1 TGGAAAGTCAAAGATATGGGTATCAAATAT 54928317 TGGAAAGTCAAAGATATGGGTATCAAATAT 1 TGGAAAGTCAAAGATATGGGTATCAAATAT * 54928347 TGGAAAGTCAAAGATATGGGTATCGAGATAT 1 TGGAAAGTCAAAGATATGGGTATC-AAATAT 54928378 TGG 1 TGG 54928381 CATAATAAAA Statistics Matches: 88, Mismatches: 5, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 30 80 0.91 31 8 0.09 ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26 Consensus pattern (30 bp): TGGAAAGTCAAAGATATGGGTATCAAATAT Found at i:54932974 original size:15 final size:15 Alignment explanation

Indices: 54932954--54933061 Score: 78 Period size: 15 Copynumber: 7.2 Consensus size: 15 54932944 TTTATGGAAA 54932954 ATCAAAGATATGGGT 1 ATCAAAGATATGGGT * * ** 54932969 ATCAAATA-ATAGAA 1 ATCAAAGATATGGGT 54932983 AGTCAAAGATATGGGT 1 A-TCAAAGATATGGGT * ** 54932999 ATCAAATAT-TGGAA 1 ATCAAAGATATGGGT 54933013 AGTCAAAGATATGGGT 1 A-TCAAAGATATGGGT * ** 54933029 ATCAAATAT-TGGAA 1 ATCAAAGATATGGGT 54933043 AGTCAAAGATATGGGT 1 A-TCAAAGATATGGGT 54933059 ATC 1 ATC 54933062 GAGATATTGG Statistics Matches: 67, Mismatches: 20, Indels: 12 0.68 0.20 0.12 Matches are distributed among these distances: 14 12 0.18 15 43 0.64 16 12 0.18 ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26 Consensus pattern (15 bp): ATCAAAGATATGGGT Found at i:54932991 original size:30 final size:30 Alignment explanation

Indices: 54932948--54933071 Score: 203 Period size: 30 Copynumber: 4.1 Consensus size: 30 54932938 TCCATATTTA * * 54932948 TGGAAAATCAAAGATATGGGTATCAAATAA 1 TGGAAAGTCAAAGATATGGGTATCAAATAT * 54932978 TAGAAAGTCAAAGATATGGGTATCAAATAT 1 TGGAAAGTCAAAGATATGGGTATCAAATAT 54933008 TGGAAAGTCAAAGATATGGGTATCAAATAT 1 TGGAAAGTCAAAGATATGGGTATCAAATAT * 54933038 TGGAAAGTCAAAGATATGGGTATCGAGATAT 1 TGGAAAGTCAAAGATATGGGTATC-AAATAT 54933069 TGG 1 TGG 54933072 CATAATAAAA Statistics Matches: 88, Mismatches: 5, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 30 80 0.91 31 8 0.09 ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26 Consensus pattern (30 bp): TGGAAAGTCAAAGATATGGGTATCAAATAT Found at i:54935029 original size:9 final size:9 Alignment explanation

Indices: 54935015--54935039 Score: 50 Period size: 9 Copynumber: 2.8 Consensus size: 9 54935005 AATAATATCT 54935015 ATATTTAAC 1 ATATTTAAC 54935024 ATATTTAAC 1 ATATTTAAC 54935033 ATATTTA 1 ATATTTA 54935040 TAAATAAAAT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48 Consensus pattern (9 bp): ATATTTAAC Found at i:54937147 original size:20 final size:19 Alignment explanation

Indices: 54937103--54937156 Score: 58 Period size: 20 Copynumber: 2.9 Consensus size: 19 54937093 ATCTGTTCAC * 54937103 CAAGAGATACAA-T-TGTT 1 CAAGAGATACAACTATTTT * 54937120 CAAAAGATACAACTATTTAT 1 CAAGAGATACAACTATTT-T * 54937140 CAAGAGATAGAACTATT 1 CAAGAGATACAACTATT 54937157 GTTTAATTTG Statistics Matches: 30, Mismatches: 4, Indels: 3 0.81 0.11 0.08 Matches are distributed among these distances: 17 11 0.37 18 1 0.03 19 2 0.07 20 16 0.53 ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28 Consensus pattern (19 bp): CAAGAGATACAACTATTTT Found at i:54938960 original size:41 final size:41 Alignment explanation

Indices: 54938896--54938997 Score: 143 Period size: 41 Copynumber: 2.5 Consensus size: 41 54938886 GCAGAAAGCG * 54938896 CTTCCAGCTGAAAGCTTTCTTTTGCAAATCAACTGAAAACT 1 CTTCCAGTTGAAAGCTTTCTTTTGCAAATCAACTGAAAACT * * 54938937 CTTCCAGTTGAAAG-TATTGTTTTGCAAATCAACTGAAAATT 1 CTTCCAGTTGAAAGCT-TTCTTTTGCAAATCAACTGAAAACT * 54938978 TTTCCAGTTGAAAGCGTTTC 1 CTTCCAGTTGAAAGC-TTTC 54938998 CGTAAAACCG Statistics Matches: 53, Mismatches: 5, Indels: 5 0.84 0.08 0.08 Matches are distributed among these distances: 40 1 0.02 41 49 0.92 42 2 0.04 43 1 0.02 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35 Consensus pattern (41 bp): CTTCCAGTTGAAAGCTTTCTTTTGCAAATCAACTGAAAACT Found at i:54943119 original size:21 final size:21 Alignment explanation

Indices: 54943095--54943134 Score: 80 Period size: 21 Copynumber: 1.9 Consensus size: 21 54943085 TTTTGTGTAA 54943095 AATTAACATTTATAGATCTAG 1 AATTAACATTTATAGATCTAG 54943116 AATTAACATTTATAGATCT 1 AATTAACATTTATAGATCT 54943135 TACACGTTAT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40 Consensus pattern (21 bp): AATTAACATTTATAGATCTAG Found at i:54965123 original size:18 final size:19 Alignment explanation

Indices: 54965094--54965129 Score: 56 Period size: 18 Copynumber: 1.9 Consensus size: 19 54965084 GTTTGTTTGC * 54965094 TTAAGTTGAAATGAATGAT 1 TTAAGTTGAAATCAATGAT 54965113 TTAAG-TGAAATCAATGA 1 TTAAGTTGAAATCAATGA 54965130 CCCTATATTG Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 11 0.69 19 5 0.31 ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33 Consensus pattern (19 bp): TTAAGTTGAAATCAATGAT Found at i:54967679 original size:42 final size:42 Alignment explanation

Indices: 54967632--54967752 Score: 165 Period size: 42 Copynumber: 2.9 Consensus size: 42 54967622 TTAGAGTTAC 54967632 TGAGATTACGTGTAAGACCATATCTGGGACATGGCATCGATA 1 TGAGATTACGTGTAAGACCATATCTGGGACATGGCATCGATA * * * 54967674 TGAGATTTCGTGTAAGACCATAGT-TGGG-CTATGGCACCGATG 1 TGAGATTACGTGTAAGACCATA-TCTGGGAC-ATGGCATCGATA * * 54967716 TGAGATTACATGTAAGACCATATCTGGGATATGGCAT 1 TGAGATTACGTGTAAGACCATATCTGGGACATGGCAT 54967753 TGGTATTGTG Statistics Matches: 68, Mismatches: 7, Indels: 8 0.82 0.08 0.10 Matches are distributed among these distances: 41 2 0.03 42 65 0.96 43 1 0.01 ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28 Consensus pattern (42 bp): TGAGATTACGTGTAAGACCATATCTGGGACATGGCATCGATA Found at i:54973469 original size:25 final size:25 Alignment explanation

Indices: 54973422--54973491 Score: 79 Period size: 25 Copynumber: 2.8 Consensus size: 25 54973412 GTTGTATAAT * * * 54973422 GAGAAGCTCTTGCAAGCCGTTTATC 1 GAGAAGCTCATACAAGCCATTTATC * 54973447 -AGGAATCTCATACAAGCCATTTATC 1 GA-GAAGCTCATACAAGCCATTTATC * 54973472 GAGAAGCTCATACGAGCCAT 1 GAGAAGCTCATACAAGCCAT 54973492 AAACGGGAAG Statistics Matches: 37, Mismatches: 6, Indels: 4 0.79 0.13 0.09 Matches are distributed among these distances: 24 1 0.03 25 35 0.95 26 1 0.03 ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24 Consensus pattern (25 bp): GAGAAGCTCATACAAGCCATTTATC Found at i:54978734 original size:25 final size:25 Alignment explanation

Indices: 54978706--54978775 Score: 95 Period size: 25 Copynumber: 2.8 Consensus size: 25 54978696 TCCTGTACAT * * 54978706 GTATGCTCACACAATCTGTGAATCG 1 GTATGCTCACACAAGCTGTGAATCA ** 54978731 GTATGCTCACATGAGCTGTGAATCA 1 GTATGCTCACACAAGCTGTGAATCA * 54978756 GTATGCTCACACGAGCTGTG 1 GTATGCTCACACAAGCTGTG 54978776 GGTTAGAACA Statistics Matches: 40, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 25 40 1.00 ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27 Consensus pattern (25 bp): GTATGCTCACACAAGCTGTGAATCA Found at i:54984884 original size:87 final size:87 Alignment explanation

Indices: 54984722--54984976 Score: 339 Period size: 87 Copynumber: 2.9 Consensus size: 87 54984712 TGATCTGATC * * * 54984722 TGGCAGTTTAACTATAACTTATTGGTATAGTGGTTTATCGCAGTGTACCGCTTGTACGTCAACGT 1 TGGCAGTTTAACTACAACTTATTGGTATAGTGGTTTACCGCACTGTACCGCTTGTACGTCAACGT * 54984787 TGTTGTGTACTATTATCTAATA 66 TGTTGCGTACTATTATCTAATA * * * * * 54984809 TGGCAGTTTAACTACAACTTATTAGTATAGCGGTTTACCGCACTGTACCGCTTGTACCTCATCTT 1 TGGCAGTTTAACTACAACTTATTGGTATAGTGGTTTACCGCACTGTACCGCTTGTACGTCAACGT * * 54984874 TGCTGCGTACTATTATCTAATC 66 TGTTGCGTACTATTATCTAATA ** * * * * * * 54984896 TAACAGTTTAACTGCAACTTATCGGTACAGTGGTTTACCGTACTGTACCGCATGTACGTCAGCGT 1 TGGCAGTTTAACTACAACTTATTGGTATAGTGGTTTACCGCACTGTACCGCTTGTACGTCAACGT 54984961 TGTTGCGTACTATTAT 66 TGTTGCGTACTATTAT 54984977 ATGATCTGGA Statistics Matches: 144, Mismatches: 24, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 87 144 1.00 ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37 Consensus pattern (87 bp): TGGCAGTTTAACTACAACTTATTGGTATAGTGGTTTACCGCACTGTACCGCTTGTACGTCAACGT TGTTGCGTACTATTATCTAATA Found at i:54984991 original size:87 final size:87 Alignment explanation

Indices: 54984714--54985020 Score: 319 Period size: 87 Copynumber: 3.5 Consensus size: 87 54984704 ACTAATTTTG * * * * * * * * 54984714 ATCTGATCTGGCAGTTTAACTATAACTTATTGGTATAGTGGTTTATCGCAGTGTACCGCTTGTAC 1 ATCTAATCTGGAAGTTTAACTACAACTTATCGGTACAGCGGTTTACCGCACTGTACCGCTTGTAC * 54984779 GTCAACGTTGTTGTGTACTATT 66 GTCAACGTTGTTGCGTACTATT * * ** * 54984801 ATCTAATATGGCAGTTTAACTACAACTTATTAGTATAGCGGTTTACCGCACTGTACCGCTTGTAC 1 ATCTAATCTGGAAGTTTAACTACAACTTATCGGTACAGCGGTTTACCGCACTGTACCGCTTGTAC * * * * 54984866 CTCATCTTTGCTGCGTACTATT 66 GTCAACGTTGTTGCGTACTATT * * * * * 54984888 ATCTAATCT-AACAGTTTAACTGCAACTTATCGGTACAGTGGTTTACCGTACTGTACCGCATGTA 1 ATCTAATCTGGA-AGTTTAACTACAACTTATCGGTACAGCGGTTTACCGCACTGTACCGCTTGTA * 54984952 CGTCAGCGTTGTTGCGTACTATT 65 CGTCAACGTTGTTGCGTACTATT * * * * * * 54984975 ATATGATCTGGAAGTTTAAACTGCAACATGTCTGTACAGCGGTTTA 1 ATCTAATCTGGAAGTTT-AACTACAACTTATCGGTACAGCGGTTTA 54985021 TCGTAATGCA Statistics Matches: 184, Mismatches: 33, Indels: 5 0.83 0.15 0.02 Matches are distributed among these distances: 87 159 0.86 88 25 0.14 ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36 Consensus pattern (87 bp): ATCTAATCTGGAAGTTTAACTACAACTTATCGGTACAGCGGTTTACCGCACTGTACCGCTTGTAC GTCAACGTTGTTGCGTACTATT Found at i:54986729 original size:18 final size:19 Alignment explanation

Indices: 54986692--54986730 Score: 53 Period size: 18 Copynumber: 2.1 Consensus size: 19 54986682 GTGACCCCTG * 54986692 TTTCCAAAATTTTTCAATT 1 TTTCCAAAAGTTTTCAATT * 54986711 TTTCC-AAAGTTTTCTATT 1 TTTCCAAAAGTTTTCAATT 54986729 TT 1 TT 54986731 ATTTCAAAAT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 18 13 0.72 19 5 0.28 ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56 Consensus pattern (19 bp): TTTCCAAAAGTTTTCAATT Found at i:54988004 original size:21 final size:21 Alignment explanation

Indices: 54987980--54988019 Score: 71 Period size: 21 Copynumber: 1.9 Consensus size: 21 54987970 AAAGCTAAAT 54987980 AGAAGCTCGTAAGAGCTGAAC 1 AGAAGCTCGTAAGAGCTGAAC * 54988001 AGAAGCTCGTGAGAGCTGA 1 AGAAGCTCGTAAGAGCTGA 54988020 TCCACCCAAT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.35, C:0.17, G:0.33, T:0.15 Consensus pattern (21 bp): AGAAGCTCGTAAGAGCTGAAC Found at i:54990075 original size:101 final size:102 Alignment explanation

Indices: 54989950--54990134 Score: 302 Period size: 101 Copynumber: 1.8 Consensus size: 102 54989940 AAAGTAATGG * 54989950 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT 1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGATAATGGTCACATGTGTAGT 54990013 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA 65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA * * * 54990051 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA 1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGTAGTA * 54990116 CTATGTGTAGGCTACTATG 66 CTATGTGCAGGCTACTATG 54990135 TGAACCAAAC Statistics Matches: 77, Mismatches: 5, Indels: 3 0.91 0.06 0.04 Matches are distributed among these distances: 100 4 0.05 101 40 0.52 102 33 0.43 ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31 Consensus pattern (102 bp): TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATAATGGTCACATGTGTAGTA CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA Found at i:54990080 original size:51 final size:51 Alignment explanation

Indices: 54989942--54990132 Score: 253 Period size: 51 Copynumber: 3.8 Consensus size: 51 54989932 TAAAAGTGAA 54989942 AGTAATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA- 1 AGTAATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT * * * * 54989992 A-TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT 1 AGTAAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT * * * * 54990043 AGT-TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT 1 AGTAAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT * * 54990094 GGTAATGGTCACATGTGTAGTACTATGTGTAGGCTACTA 1 AGTAATGGTCACATGTGTAGTACTATGTGCAGGCTACTA 54990133 TGTGAACCAA Statistics Matches: 120, Mismatches: 17, Indels: 7 0.83 0.12 0.05 Matches are distributed among these distances: 49 3 0.03 50 42 0.35 51 73 0.61 52 2 0.02 ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31 Consensus pattern (51 bp): AGTAATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT Found at i:54990194 original size:45 final size:45 Alignment explanation

Indices: 54990138--54990230 Score: 159 Period size: 45 Copynumber: 2.1 Consensus size: 45 54990128 TACTATGTGA * * 54990138 ACCAAACATCATTGATTAGTAAGGTGGTTTCTATGTGCTGATTCC 1 ACCAAACATCATTGATTAATAAGGTGGTTTCTATGTGCTGAATCC * 54990183 ACCAGACATCATTGATTAATAAGGTGGTTTCTATGTGCTGAATCC 1 ACCAAACATCATTGATTAATAAGGTGGTTTCTATGTGCTGAATCC 54990228 ACC 1 ACC 54990231 GAGTATCTGT Statistics Matches: 45, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 45 45 1.00 ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33 Consensus pattern (45 bp): ACCAAACATCATTGATTAATAAGGTGGTTTCTATGTGCTGAATCC Found at i:55016582 original size:3 final size:3 Alignment explanation

Indices: 55016576--55016614 Score: 71 Period size: 3 Copynumber: 13.3 Consensus size: 3 55016566 GGCAGCAGGT 55016576 GAA GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GAA G 1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G 55016615 GCAAGAAATG Statistics Matches: 35, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 2 2 0.06 3 33 0.94 ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00 Consensus pattern (3 bp): GAA Found at i:55017411 original size:93 final size:94 Alignment explanation

Indices: 55017300--55017473 Score: 269 Period size: 93 Copynumber: 1.8 Consensus size: 94 55017290 TACAAAAAAG * * * 55017300 AATGTAACTATCTGCCTAAGTTTAGATATTAGTAGCAATAATATGAAAATT-TACAAAAAAAGAA 1 AATGTAACTATCTGCCTAAGTTTAGATATTAGTAGCAATAATAGGAAAATTAAAAAAAAAAAGAA 55017364 TATGCCTAAGTTTAGAAATCAATAGCGTC 66 TATGCCTAAGTTTAGAAATCAATAGCGTC * * 55017393 AATGTAGCTATCTGCCTAAGTTTAGATATTAGTAGCAATAATAGGCAAATTAAAAAAAAAAAAAG 1 AATGTAACTATCTGCCTAAGTTTAGATATTAGTAGCAATAATAGGAAAATT--AAAAAAAAAAAG * 55017458 AATTTGCCTAAGTTTA 64 AATATGCCTAAGTTTA 55017474 AACTTCCATC Statistics Matches: 72, Mismatches: 6, Indels: 3 0.89 0.07 0.04 Matches are distributed among these distances: 93 48 0.67 96 24 0.33 ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30 Consensus pattern (94 bp): AATGTAACTATCTGCCTAAGTTTAGATATTAGTAGCAATAATAGGAAAATTAAAAAAAAAAAGAA TATGCCTAAGTTTAGAAATCAATAGCGTC Found at i:55025050 original size:3 final size:3 Alignment explanation

Indices: 55025042--55025087 Score: 83 Period size: 3 Copynumber: 15.3 Consensus size: 3 55025032 TGTTCTGTAT * 55025042 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG TTG T 1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T 55025088 CGACGATTTC Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 3 41 1.00 ACGTcount: A:0.02, C:0.00, G:0.30, T:0.67 Consensus pattern (3 bp): TTG Found at i:55028959 original size:21 final size:21 Alignment explanation

Indices: 55028930--55028976 Score: 51 Period size: 21 Copynumber: 2.2 Consensus size: 21 55028920 GTCCAACGTG * * 55028930 GCTAGTTAATAGG-CCAGGTCA 1 GCTATTTAA-AGGCCCACGTCA * 55028951 GCTATTTAACGGCCCACGTCA 1 GCTATTTAAAGGCCCACGTCA 55028972 GCTAT 1 GCTAT 55028977 CCTGTTAGGG Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 20 2 0.09 21 20 0.91 ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26 Consensus pattern (21 bp): GCTATTTAAAGGCCCACGTCA Found at i:55029058 original size:30 final size:29 Alignment explanation

Indices: 55029010--55029106 Score: 106 Period size: 30 Copynumber: 3.3 Consensus size: 29 55029000 TGGGCTCGAG ** 55029010 GTGATTGATTT-TCCATTTTTGAAAACATTA 1 GTGATTGATTTAT-CATTTTTG-AAAGTTTA * * 55029040 GTGATTGATTTATAATTTTCGTAAAGTTTA 1 GTGATTGATTTATCATTTTTG-AAAGTTTA * * 55029070 GTGATTGAGTTATCACTTTTGAAAGTTTA 1 GTGATTGATTTATCATTTTTGAAAGTTTA 55029099 GTGATTGA 1 GTGATTGA 55029107 AATGTTATTT Statistics Matches: 57, Mismatches: 9, Indels: 3 0.83 0.13 0.04 Matches are distributed among these distances: 29 16 0.28 30 40 0.70 31 1 0.02 ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46 Consensus pattern (29 bp): GTGATTGATTTATCATTTTTGAAAGTTTA Found at i:55029101 original size:29 final size:30 Alignment explanation

Indices: 55029037--55029106 Score: 99 Period size: 29 Copynumber: 2.4 Consensus size: 30 55029027 TTTGAAAACA * 55029037 TTAGTGATTGATTTATAATTTTCGTAAAGT 1 TTAGTGATTGAGTTATAATTTTCGTAAAGT * 55029067 TTAGTGATTGAGTTATCACTTTT-G-AAAGT 1 TTAGTGATTGAGTTAT-AATTTTCGTAAAGT 55029096 TTAGTGATTGA 1 TTAGTGATTGA 55029107 AATGTTATTT Statistics Matches: 37, Mismatches: 2, Indels: 3 0.88 0.05 0.07 Matches are distributed among these distances: 29 16 0.43 30 16 0.43 31 5 0.14 ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47 Consensus pattern (30 bp): TTAGTGATTGAGTTATAATTTTCGTAAAGT Found at i:55030408 original size:20 final size:21 Alignment explanation

Indices: 55030372--55030410 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 55030362 AGTCTTATTC 55030372 TCTAATATGATTATTTTTAAA 1 TCTAATATGATTATTTTTAAA 55030393 TCTATATAT-ATT-TTTTTA 1 TCTA-ATATGATTATTTTTA 55030411 TTTTTAAAAT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 20 6 0.35 21 7 0.41 22 4 0.24 ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59 Consensus pattern (21 bp): TCTAATATGATTATTTTTAAA Found at i:55032939 original size:18 final size:18 Alignment explanation

Indices: 55032896--55032939 Score: 54 Period size: 18 Copynumber: 2.4 Consensus size: 18 55032886 AGCAACCATC 55032896 AAAAAAATAAATAAATAA 1 AAAAAAATAAATAAATAA * * 55032914 AATAAAATACATAAA-AA 1 AAAAAAATAAATAAATAA 55032931 AAAACAAAT 1 AAAA-AAAT 55032940 CAAGTATATA Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 17 5 0.23 18 17 0.77 ACGTcount: A:0.80, C:0.05, G:0.00, T:0.16 Consensus pattern (18 bp): AAAAAAATAAATAAATAA Found at i:55033257 original size:28 final size:27 Alignment explanation

Indices: 55033226--55033285 Score: 77 Period size: 28 Copynumber: 2.1 Consensus size: 27 55033216 TTATAAAATA 55033226 AAAAATATAAGTA-TGTATATATATTTAT 1 AAAAATAT--GTACTGTATATATATTTAT * 55033254 AAAAATATGTACGTGTATGTATATTTAT 1 AAAAATATGTAC-TGTATATATATTTAT 55033282 AAAA 1 AAAA 55033286 GAGATACATG Statistics Matches: 29, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 26 3 0.10 28 26 0.90 ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40 Consensus pattern (27 bp): AAAAATATGTACTGTATATATATTTAT Found at i:55034882 original size:28 final size:28 Alignment explanation

Indices: 55034821--55034874 Score: 76 Period size: 28 Copynumber: 2.0 Consensus size: 28 55034811 ATATAGCTAA * * 55034821 AATAATAATAATTACATATGATAATAAT 1 AATAATAATAATTACATATGAAAAAAAT 55034849 AATAATAATAATTACAT-T-AAAAAAAT 1 AATAATAATAATTACATATGAAAAAAAT 55034875 TAACTAATTT Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 26 6 0.25 27 1 0.04 28 17 0.71 ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33 Consensus pattern (28 bp): AATAATAATAATTACATATGAAAAAAAT Found at i:55035426 original size:22 final size:21 Alignment explanation

Indices: 55035401--55035486 Score: 81 Period size: 19 Copynumber: 4.2 Consensus size: 21 55035391 TGCAAATTAA 55035401 ATCTCTAAGATTACAAAATCAT 1 ATCTCTAAGATTAC-AAATCAT * 55035423 ATCTTCTAAGATTACATATCAT 1 ATC-TCTAAGATTACAAATCAT * * 55035445 A--TCTAAGATTGCATATCAT 1 ATCTCTAAGATTACAAATCAT * * 55035464 A--TCTAAGATTGCATATCAT 1 ATCTCTAAGATTACAAATCAT 55035483 ATCT 1 ATCT 55035487 AAAATTGCAT Statistics Matches: 59, Mismatches: 2, Indels: 7 0.87 0.03 0.10 Matches are distributed among these distances: 19 37 0.63 21 1 0.02 22 10 0.17 23 11 0.19 ACGTcount: A:0.38, C:0.17, G:0.07, T:0.37 Consensus pattern (21 bp): ATCTCTAAGATTACAAATCAT Found at i:55035434 original size:23 final size:22 Alignment explanation

Indices: 55035404--55035448 Score: 72 Period size: 23 Copynumber: 2.0 Consensus size: 22 55035394 AAATTAAATC 55035404 TCTAAGATTACAAAATCATATCT 1 TCTAAGATTAC-AAATCATATCT * 55035427 TCTAAGATTACATATCATATCT 1 TCTAAGATTACAAATCATATCT 55035449 AAGATTGCAT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 22 10 0.48 23 11 0.52 ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38 Consensus pattern (22 bp): TCTAAGATTACAAATCATATCT Found at i:55035451 original size:19 final size:19 Alignment explanation

Indices: 55035427--55035499 Score: 128 Period size: 19 Copynumber: 3.8 Consensus size: 19 55035417 AATCATATCT * 55035427 TCTAAGATTACATATCATA 1 TCTAAGATTGCATATCATA 55035446 TCTAAGATTGCATATCATA 1 TCTAAGATTGCATATCATA 55035465 TCTAAGATTGCATATCATA 1 TCTAAGATTGCATATCATA * 55035484 TCTAAAATTGCATATC 1 TCTAAGATTGCATATC 55035500 CTCAAAAATT Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 19 52 1.00 ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37 Consensus pattern (19 bp): TCTAAGATTGCATATCATA Found at i:55035864 original size:44 final size:44 Alignment explanation

Indices: 55035816--55036160 Score: 173 Period size: 44 Copynumber: 7.8 Consensus size: 44 55035806 CTGTAACCAC * * 55035816 AGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGCTT 1 AGGGAGGTAAAATCTACCATCTTCAATCTACTCCACTACTGCTT * * ** * ** * 55035860 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGTTGCCT 1 AGGGAGGTAAAATCTACCATCTTCAATCTACTCCACTACTGCTT * * * * * ** 55035904 AGGGAAGTAGAAT-TACTAGCTTCAATGTACTCCACTGTAACCAC-T 1 AGGGAGGTAAAATCTACCATCTTCAATCTACTCCAC--T-ACTGCTT ** * 55035949 -GGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGCTT 1 AGGGAGGTAAAATCTACCATCTTCAATCTACTCCACTACTGCTT * * ** * * ** * 55035992 AGGGAGATAAGATCTAAAATCTTTAATCTATTCCACTGTTGCCT 1 AGGGAGGTAAAATCTACCATCTTCAATCTACTCCACTACTGCTT * * * * * ** 55036036 AGGGAAGTAGAAT-TACTAGCTTCAATGTACTCCACTGTAAC--CAC 1 AGGGAGGTAAAATCTACCATCTTCAATCTACTCCAC--T-ACTGCTT * * * ** 55036080 AGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTTTTT 1 AGGGAGGTAAAATCTACCATCTTCAATCTACTCCACTACTGCTT * * * * 55036124 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACT 1 AGGGAGGTAAAATCT-ACCATCTTCAATCTACTCCACT 55036161 GTAATGCCAA Statistics Matches: 211, Mismatches: 77, Indels: 26 0.67 0.25 0.08 Matches are distributed among these distances: 42 5 0.02 43 36 0.17 44 133 0.63 45 36 0.17 46 1 0.00 ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29 Consensus pattern (44 bp): AGGGAGGTAAAATCTACCATCTTCAATCTACTCCACTACTGCTT Found at i:55035968 original size:132 final size:132 Alignment explanation

Indices: 55035728--55036162 Score: 714 Period size: 132 Copynumber: 3.3 Consensus size: 132 55035718 CTGCAACTGC * * * * * 55035728 AGGGAGATAAGA-CTTACAATCTTCAACCTATTCCACTGCTGACTAGGG-AGATAGGATTACT-G 1 AGGGAGATAAGATC-TAAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAG-TAGAATTACTAG 55035790 ACTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTAC 64 -CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTAC 55035855 TGCTT 128 TGCTT 55035860 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTAGCT 1 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTAGCT * * 55035925 TCAATGTACTCCACTGTAACCACTGGGAGGTAAAATCCGCCATCTTCGATCTACTCCACTACTGC 66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC 55035990 TT 131 TT * 55035992 AGGGAGATAAGATCTAAAATCTTTAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTAGCT 1 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTAGCT * ** 55036057 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTTT 66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC 55036122 TT 131 TT * 55036124 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGT 1 AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGT 55036163 AATGCCAAAG Statistics Matches: 285, Mismatches: 15, Indels: 6 0.93 0.05 0.02 Matches are distributed among these distances: 132 281 0.99 133 4 0.01 ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29 Consensus pattern (132 bp): AGGGAGATAAGATCTAAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTAGCT TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC TT Found at i:55036567 original size:132 final size:133 Alignment explanation

Indices: 55036330--55036803 Score: 546 Period size: 132 Copynumber: 3.6 Consensus size: 133 55036320 CTGTCAGTGC * 55036330 AGGAAGACAGGACTTGCTAT-TTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT 1 AGGAAGACAGGACCTGCTATCTTT-GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT * * * 55036394 CTTCGATCTATTTCGCCACCAGTATGGGAAGATAAGATCTGCATCTTCTATCCACTTC-CTACCA 65 CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCA 55036458 ATAT 130 ATAT 55036462 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC 1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC * * * 55036527 TTCGATCTACTTCGCCATCATTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACTAA 66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA 55036592 TAT 131 TAT * * * * 55036595 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTGC-ATC 1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC * * * * * * * * * * * 55036659 TTTGATCCACTTC-CTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-GCCA 66 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCA * * 55036722 GTAA 130 ATAT * * * * * * * * *** * 55036726 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGC-AT 1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTT * 55036790 CTTCGATCCACTTC 65 CTTCGATCTACTTC 55036804 CTACCAATAT Statistics Matches: 301, Mismatches: 37, Indels: 8 0.87 0.11 0.02 Matches are distributed among these distances: 131 54 0.18 132 177 0.59 133 70 0.23 ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29 Consensus pattern (133 bp): AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA TAT Found at i:55036696 original size:220 final size:220 Alignment explanation

Indices: 55036367--55036836 Score: 692 Period size: 220 Copynumber: 2.1 Consensus size: 220 55036357 CTACTTCACG * * * * * * ** * 55036367 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGTATGGGAAGATAAGAT 1 CCAATATAAGAAGACAAGATCTGCTATCTTCGATCTACTTCGACACCAATACAGGAAGACAAGAT * 55036432 CTGCATCTTCTATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCA 66 CTGCATCTTCTATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA * * * * 55036497 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCATCATTATGGGAAGACAAG 131 CGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAG 55036562 ATCTGCATCTTCGATCCACTTCGCTA 196 ATCTGCATCTTCGATCCACTTC-CTA * * * * * 55036588 CTAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGAT 1 CCAATATAAGAAGACAAGATCTGCTATCTTCGATCTACTTCGACACCAATACAGGAAGACAAGAT * * 55036652 TTGCATCTT-TGATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTC 66 CTGCATCTTCT-ATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTC * 55036716 ACGCCAGTAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAA 130 ACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAA 55036781 GATCTGCATCTTCGATCCACTTCCTA 195 GATCTGCATCTTCGATCCACTTCCTA * * 55036807 CCAATATAAGAAGACATGACCTGCTATCTT 1 CCAATATAAGAAGACAAGATCTGCTATCTT 55036837 TACTGATCTG Statistics Matches: 223, Mismatches: 25, Indels: 4 0.88 0.10 0.02 Matches are distributed among these distances: 219 30 0.13 220 158 0.71 221 35 0.16 ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29 Consensus pattern (220 bp): CCAATATAAGAAGACAAGATCTGCTATCTTCGATCTACTTCGACACCAATACAGGAAGACAAGAT CTGCATCTTCTATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA CGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAG ATCTGCATCTTCGATCCACTTCCTA Found at i:55036836 original size:44 final size:44 Alignment explanation

Indices: 55036330--55036836 Score: 445 Period size: 44 Copynumber: 11.5 Consensus size: 44 55036320 CTGTCAGTGC * * * * 55036330 AGGAAGACAGGA-CTTGCTATTTTCGATCTACTTCACGCCAATAC 1 AGGAAGACAAGATC-TGCTATCTTCGATCTACTTCACACCAATAT * * * * * 55036374 ATGAAGACAAGATCTGCTTTCTTCGATCTATTTCGCCACCAGTAT 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT * * * * 55036419 GGGAAGATAAGATCTGC-ATCTTCTATCCACTTC-CTACCAATAT 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT * * * * * 55036462 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATAC 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT * * * * * 55036506 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCATCATTAT 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT * * * * 55036551 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACTAATAT 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT * * * 55036595 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATAC 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT * * * * 55036639 ATGAAGACAAGATTTGC-ATCTTTGATCCACTTC-CTACCAATAT 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT * * * * * * 55036682 AGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAGTAA 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT * * * * 55036726 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATAT 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT * * 55036771 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT 1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT * * * 55036814 AAGAAGACATGACCTGCTATCTT 1 AGGAAGACAAGATCTGCTATCTT 55036837 TACTGATCTG Statistics Matches: 362, Mismatches: 87, Indels: 28 0.76 0.18 0.06 Matches are distributed among these distances: 42 3 0.01 43 74 0.20 44 205 0.57 45 80 0.22 ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29 Consensus pattern (44 bp): AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT Found at i:55038055 original size:6 final size:6 Alignment explanation

Indices: 55038039--55038071 Score: 59 Period size: 6 Copynumber: 5.7 Consensus size: 6 55038029 GGCCTCTCCA 55038039 TTTTC- TTTTCT TTTTCT TTTTCT TTTTCT TTTT 1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT 55038072 ATCACTTTTA Statistics Matches: 27, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 5 5 0.19 6 22 0.81 ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85 Consensus pattern (6 bp): TTTTCT Found at i:55042621 original size:15 final size:15 Alignment explanation

Indices: 55042584--55042623 Score: 53 Period size: 16 Copynumber: 2.6 Consensus size: 15 55042574 ATATACAAAG * * 55042584 ATAAATATAAAAAAT 1 ATAATTATAAAAAAA 55042599 ATAGATTATAAAAAAA 1 ATA-ATTATAAAAAAA 55042615 ATAATTATA 1 ATAATTATA 55042624 TATAAATAAA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 15 9 0.41 16 13 0.59 ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30 Consensus pattern (15 bp): ATAATTATAAAAAAA Found at i:55043359 original size:22 final size:21 Alignment explanation

Indices: 55043324--55043400 Score: 77 Period size: 19 Copynumber: 3.7 Consensus size: 21 55043314 AAAGGGTATC * * 55043324 TACAAATTAAATCTCTAAGAT 1 TACAAATCATATCTCTAAGAT 55043345 TACAAAATCATATCTTCTAAGAT 1 TAC-AAATCATATC-TCTAAGAT * 55043368 TACATATCATA--TCTAAGAT 1 TACAAATCATATCTCTAAGAT * * 55043387 TGCATATCATATCT 1 TACAAATCATATCT 55043401 AAGATTGCAT Statistics Matches: 48, Mismatches: 4, Indels: 8 0.80 0.07 0.13 Matches are distributed among these distances: 19 18 0.38 21 4 0.08 22 15 0.31 23 11 0.23 ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36 Consensus pattern (21 bp): TACAAATCATATCTCTAAGAT Found at i:55043367 original size:23 final size:22 Alignment explanation

Indices: 55043324--55043381 Score: 73 Period size: 22 Copynumber: 2.6 Consensus size: 22 55043314 AAAGGGTATC * * 55043324 TACAAATTAAATC-TCTAAGAT 1 TACAAATCATATCTTCTAAGAT 55043345 TACAAAATCATATCTTCTAAGAT 1 TAC-AAATCATATCTTCTAAGAT * 55043368 TACATATCATATCT 1 TACAAATCATATCT 55043382 AAGATTGCAT Statistics Matches: 32, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 21 3 0.09 22 18 0.56 23 11 0.34 ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36 Consensus pattern (22 bp): TACAAATCATATCTTCTAAGAT Found at i:55043384 original size:19 final size:19 Alignment explanation

Indices: 55043337--55043413 Score: 91 Period size: 19 Copynumber: 3.8 Consensus size: 19 55043327 AAATTAAATC * 55043337 TCTAAGATTACAAAATCATA 1 TCTAAGATTAC-ATATCATA 55043357 TCTTCTAAGATTACATATCATA 1 ---TCTAAGATTACATATCATA * 55043379 TCTAAGATTGCATATCATA 1 TCTAAGATTACATATCATA * 55043398 TCTAAGATTGCATATC 1 TCTAAGATTACATATC 55043414 CTCAAAAATT Statistics Matches: 52, Mismatches: 2, Indels: 4 0.90 0.03 0.07 Matches are distributed among these distances: 19 34 0.65 22 7 0.13 23 11 0.21 ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36 Consensus pattern (19 bp): TCTAAGATTACATATCATA Found at i:55044505 original size:6 final size:6 Alignment explanation

Indices: 55044494--55044526 Score: 59 Period size: 6 Copynumber: 5.7 Consensus size: 6 55044484 AACGGTTCAA 55044494 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAT AAAA 1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA 55044527 TAAGATAAGA Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 5 5 0.19 6 21 0.81 ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15 Consensus pattern (6 bp): AAAAAT Found at i:55045342 original size:49 final size:49 Alignment explanation

Indices: 55045309--55045437 Score: 170 Period size: 49 Copynumber: 2.6 Consensus size: 49 55045299 ATTTAGCTTT * * * 55045309 AATTTGTTCCACTGCAACTTCAGGGAAATAAGATTTGTACCCGGTCTTC 1 AATTTGCTCCACTGCAACTTCAGGGAAATAAGATCTGTACCCAGTCTTC * * * * 55045358 AATTTGCTCCACTGCAACTTCAGGGAGATACA-ATTTGTAGCCGGTCTTC 1 AATTTGCTCCACTGCAACTTCAGGGAAATA-AGATCTGTACCCAGTCTTC * 55045407 AATTTGCTCCACTGCAACTTCAGGGAGATAA 1 AATTTGCTCCACTGCAACTTCAGGGAAATAA 55045438 AACTTATGGC Statistics Matches: 76, Mismatches: 3, Indels: 3 0.93 0.04 0.04 Matches are distributed among these distances: 48 1 0.01 49 74 0.97 50 1 0.01 ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30 Consensus pattern (49 bp): AATTTGCTCCACTGCAACTTCAGGGAAATAAGATCTGTACCCAGTCTTC Found at i:55046405 original size:42 final size:43 Alignment explanation

Indices: 55046339--55046420 Score: 112 Period size: 42 Copynumber: 1.9 Consensus size: 43 55046329 GGTATGACAA * 55046339 GATCACCACATGCCCCAATCTGAT-CAAAATTTGAGCTGCTTT 1 GATCACCACATGCCCCAATCTGATCCAAAATTTGAACTGCTTT ** * * 55046381 GATCACCTTATGCCCCATTTTGATCCAAAATTTGAACTGC 1 GATCACCACATGCCCCAATCTGATCCAAAATTTGAACTGC 55046421 CCATTCCTGG Statistics Matches: 34, Mismatches: 5, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 42 20 0.59 43 14 0.41 ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30 Consensus pattern (43 bp): GATCACCACATGCCCCAATCTGATCCAAAATTTGAACTGCTTT Found at i:55057202 original size:17 final size:17 Alignment explanation

Indices: 55057161--55057202 Score: 50 Period size: 17 Copynumber: 2.5 Consensus size: 17 55057151 AGCAACCATC 55057161 AAAAAAATAAATAAATA 1 AAAAAAATAAATAAATA * * 55057178 AATAAAATACATAAA-A 1 AAAAAAATAAATAAATA 55057194 AAAACAAAT 1 AAAA-AAAT 55057203 CAAGTATATA Statistics Matches: 21, Mismatches: 3, Indels: 2 0.81 0.12 0.08 Matches are distributed among these distances: 16 4 0.19 17 17 0.81 ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17 Consensus pattern (17 bp): AAAAAAATAAATAAATA Found at i:55057502 original size:36 final size:32 Alignment explanation

Indices: 55057423--55057491 Score: 129 Period size: 32 Copynumber: 2.2 Consensus size: 32 55057413 TGCATATATC 55057423 TAAAAATATGTAGTTATATATATAAATTATAG 1 TAAAAATATGTAGTTATATATATAAATTATAG 55057455 TAAAAATATGTAGTTATATATATAAATTATAG 1 TAAAAATATGTAGTTATATATATAAATTATAG * 55057487 GAAAA 1 TAAAA 55057492 TAAAAAATGT Statistics Matches: 36, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 36 1.00 ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38 Consensus pattern (32 bp): TAAAAATATGTAGTTATATATATAAATTATAG Found at i:55057505 original size:32 final size:32 Alignment explanation

Indices: 55057436--55057505 Score: 79 Period size: 32 Copynumber: 2.2 Consensus size: 32 55057426 AAATATGTAG *** * 55057436 TTATATATATAAATTATAGTAAAAATATGTAG 1 TTATATATATAAATTATAGTAAAAATAAAAAA * 55057468 TTATATATATAAATTATAG-GAAAATAAAAAA 1 TTATATATATAAATTATAGTAAAAATAAAAAA 55057499 TGTATAT 1 T-TATAT 55057506 GAAAATTATA Statistics Matches: 32, Mismatches: 5, Indels: 2 0.82 0.13 0.05 Matches are distributed among these distances: 31 8 0.25 32 24 0.75 ACGTcount: A:0.53, C:0.00, G:0.09, T:0.39 Consensus pattern (32 bp): TTATATATATAAATTATAGTAAAAATAAAAAA Found at i:55067989 original size:28 final size:28 Alignment explanation

Indices: 55067931--55067991 Score: 72 Period size: 28 Copynumber: 2.2 Consensus size: 28 55067921 AAAGTTTTCA * * 55067931 TTTTTTTATTTTTTTCATCATTTGAAAT 1 TTTTTTTATTTTTTTAATCATTTCAAAT * 55067959 TTTTTTTATTTTATTTAAT-ATTTC-CAT 1 TTTTTTTATTTT-TTTAATCATTTCAAAT 55067986 TTTTTT 1 TTTTTT 55067992 AGGATTTTGA Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 27 8 0.28 28 16 0.55 29 5 0.17 ACGTcount: A:0.20, C:0.07, G:0.02, T:0.72 Consensus pattern (28 bp): TTTTTTTATTTTTTTAATCATTTCAAAT Found at i:55075025 original size:16 final size:16 Alignment explanation

Indices: 55075001--55075037 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 16 55074991 TCAGGACAGT * 55075001 AGTTTAAATTCTGAAA 1 AGTTAAAATTCTGAAA * 55075017 AGTTAAAATTTTGAAA 1 AGTTAAAATTCTGAAA 55075033 AGTTA 1 AGTTA 55075038 CGCATTAGTC 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:0.46, C:0.03, G:0.14, T:0.38 Consensus pattern (16 bp): AGTTAAAATTCTGAAA Found at i:55081040 original size:21 final size:21 Alignment explanation

Indices: 55081016--55081102 Score: 88 Period size: 22 Copynumber: 4.1 Consensus size: 21 55081006 TTTTTTGCGC 55081016 TTTTTT-GCTTTTTGCTTTTT 1 TTTTTTCGCTTTTTGCTTTTT * * 55081036 TTTTTTGCGCTTTTTACTCTTT 1 TTTTTT-CGCTTTTTGCTTTTT * * * 55081058 TTTTTGCGCTTTTTAC-TCTT 1 TTTTTTCGCTTTTTGCTTTTT * 55081078 TTTTTGCGCTTTTTTGCTTTTT 1 TTTTTTCGC-TTTTTGCTTTTT 55081100 TTT 1 TTT 55081103 GTTTTTTTTG Statistics Matches: 56, Mismatches: 7, Indels: 6 0.81 0.10 0.09 Matches are distributed among these distances: 20 17 0.30 21 16 0.29 22 23 0.41 ACGTcount: A:0.02, C:0.15, G:0.10, T:0.72 Consensus pattern (21 bp): TTTTTTCGCTTTTTGCTTTTT Found at i:55081128 original size:19 final size:19 Alignment explanation

Indices: 55081087--55081130 Score: 54 Period size: 19 Copynumber: 2.3 Consensus size: 19 55081077 TTTTTTGCGC * * 55081087 TTTTTTGCTTTTTTTTGTT 1 TTTTTTGCTTGTTTTTGTA 55081106 TTTTTTGC-TGTTTTTGCTA 1 TTTTTTGCTTGTTTTTG-TA 55081125 TTTTTT 1 TTTTTT 55081131 TTTGCTTTTA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 18 7 0.32 19 15 0.68 ACGTcount: A:0.02, C:0.07, G:0.11, T:0.80 Consensus pattern (19 bp): TTTTTTGCTTGTTTTTGTA Found at i:55081139 original size:9 final size:9 Alignment explanation

Indices: 55081075--55081130 Score: 58 Period size: 10 Copynumber: 5.9 Consensus size: 9 55081065 GCTTTTTACT 55081075 CTTTTTTTG 1 CTTTTTTTG * 55081084 CGCTTTTTTG 1 C-TTTTTTTG 55081094 CTTTTTTTTG 1 C-TTTTTTTG * 55081104 TTTTTTTTG 1 CTTTTTTTG * 55081113 CTGTTTTTG 1 CTTTTTTTG 55081122 CTATTTTTT 1 CT-TTTTTT 55081131 TTTGCTTTTA Statistics Matches: 38, Mismatches: 7, Indels: 3 0.79 0.15 0.06 Matches are distributed among these distances: 9 18 0.47 10 20 0.53 ACGTcount: A:0.02, C:0.11, G:0.12, T:0.75 Consensus pattern (9 bp): CTTTTTTTG Found at i:55081139 original size:20 final size:20 Alignment explanation

Indices: 55081016--55081120 Score: 79 Period size: 21 Copynumber: 5.1 Consensus size: 20 55081006 TTTTTTGCGC * 55081016 TTTTTTGCTTTTTGCTTTTT 1 TTTTTTGCTTTTTGCTCTTT * 55081036 TTTTTTGCGCTTTTTACTCTTT 1 TTTTTT--GCTTTTTGCTCTTT * * 55081058 TTTTTGCGCTTTTTACTCTTT 1 TTTTT-TGCTTTTTGCTCTTT ** 55081079 TTTTGCGCTTTTTTGCT-TTT 1 TTTTTTGC-TTTTTGCTCTTT * * 55081099 TTTTGTT-TTTTTTGCTGTTT 1 TTTT-TTGCTTTTTGCTCTTT 55081119 TT 1 TT 55081121 GCTATTTTTT Statistics Matches: 71, Mismatches: 8, Indels: 12 0.78 0.09 0.13 Matches are distributed among these distances: 19 8 0.11 20 21 0.30 21 25 0.35 22 17 0.24 ACGTcount: A:0.02, C:0.13, G:0.11, T:0.73 Consensus pattern (20 bp): TTTTTTGCTTTTTGCTCTTT Found at i:55088638 original size:16 final size:16 Alignment explanation

Indices: 55088617--55088647 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 55088607 TTCACTATTA * 55088617 TGTCTTTTGTATTTTC 1 TGTCTTTTATATTTTC 55088633 TGTCTTTTATATTTT 1 TGTCTTTTATATTTT 55088648 GCATGCATAG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71 Consensus pattern (16 bp): TGTCTTTTATATTTTC Found at i:55089758 original size:34 final size:34 Alignment explanation

Indices: 55089720--55089802 Score: 121 Period size: 34 Copynumber: 2.4 Consensus size: 34 55089710 GAATTTTCTT * 55089720 GAAAAATTATTTTGGAAAATCTAAATGATTTTAA 1 GAAAAATTATTTTGGAAAATCTAAATGAATTTAA * * 55089754 GAAAAATTAATTTGGAAAATCTAAGTGAATTTAA 1 GAAAAATTATTTTGGAAAATCTAAATGAATTTAA * 55089788 GAAAATTTAATTTTG 1 GAAAAATT-ATTTTG 55089803 ATGAAGTAAA Statistics Matches: 43, Mismatches: 5, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 34 38 0.88 35 5 0.12 ACGTcount: A:0.47, C:0.02, G:0.13, T:0.37 Consensus pattern (34 bp): GAAAAATTATTTTGGAAAATCTAAATGAATTTAA Found at i:55090274 original size:12 final size:12 Alignment explanation

Indices: 55090240--55090345 Score: 50 Period size: 12 Copynumber: 9.2 Consensus size: 12 55090230 ATTCCAAAAA * 55090240 TAATA-TTATTT 1 TAATATTTAATT 55090251 TAATAGTTTAATAT 1 TAATA-TTTAAT-T 55090265 TAA-ATTTAATT 1 TAATATTTAATT 55090276 TAATATTT-ATCT 1 TAATATTTAAT-T * 55090288 TAATA-GT-ATT 1 TAATATTTAATT 55090298 T--TA-TTAATT 1 TAATATTTAATT * * 55090307 TAATATTAAAGT 1 TAATATTTAATT * * 55090319 GATTATCTTAATAT 1 TAATAT-TTAAT-T 55090333 TAA-ATTTAATT 1 TAATATTTAATT 55090344 TA 1 TA 55090346 TTGTTTATCT Statistics Matches: 73, Mismatches: 11, Indels: 22 0.69 0.10 0.21 Matches are distributed among these distances: 8 3 0.04 9 4 0.05 10 2 0.03 11 19 0.26 12 29 0.40 13 10 0.14 14 6 0.08 ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54 Consensus pattern (12 bp): TAATATTTAATT Found at i:55090293 original size:37 final size:36 Alignment explanation

Indices: 55090240--55090331 Score: 98 Period size: 37 Copynumber: 2.4 Consensus size: 36 55090230 ATTCCAAAAA * 55090240 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T 1 TAATATTATCTTAATAGTATT-ATATT-AATTTAATAT * 55090276 TAATATTTATCTTAATAGTATTTTATTAATTTAATAT 1 TAATA-TTATCTTAATAGTATTATATTAATTTAATAT 55090313 TAAAGTGATTATCTTAATA 1 T-AA-T-ATTATCTTAATA 55090332 TTAAATTTAA Statistics Matches: 48, Mismatches: 2, Indels: 9 0.81 0.03 0.15 Matches are distributed among these distances: 36 13 0.27 37 18 0.38 38 4 0.08 39 12 0.25 40 1 0.02 ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53 Consensus pattern (36 bp): TAATATTATCTTAATAGTATTATATTAATTTAATAT Found at i:55090315 original size:11 final size:11 Alignment explanation

Indices: 55090240--55090315 Score: 52 Period size: 11 Copynumber: 6.8 Consensus size: 11 55090230 ATTCCAAAAA * 55090240 TAATATTATTT 1 TAATATTAATT 55090251 TAATAGTTTAATAT 1 TAATA--TTAAT-T 55090265 TAA-ATTTAATT 1 TAATA-TTAATT * 55090276 TAATATTTATCT 1 TAATATTAAT-T * 55090288 TAATAGT-ATT 1 TAATATTAATT 55090298 T--TATTAATT 1 TAATATTAATT 55090307 TAATATTAA 1 TAATATTAA 55090316 AGTGATTATC Statistics Matches: 53, Mismatches: 4, Indels: 16 0.73 0.05 0.22 Matches are distributed among these distances: 8 3 0.06 9 4 0.08 10 2 0.04 11 21 0.40 12 14 0.26 13 5 0.09 14 4 0.08 ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55 Consensus pattern (11 bp): TAATATTAATT Found at i:55090335 original size:68 final size:65 Alignment explanation

Indices: 55090257--55090454 Score: 192 Period size: 68 Copynumber: 3.0 Consensus size: 65 55090247 ATTTTAATAG 55090257 TTTAATATTAAATTTAATTTAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGAT 1 TTTAATATTAAATTTAATTTAATATTTATCTT-ATAGTA-TTTATTAATTTAATATTAAAGTGAT 55090322 TA 64 TA * * * * * * 55090324 TCTTAATATTAAATTTAATTTATTGTTTATCTTGTAG-A--TA-AACATTCTATTATTTTAA-T- 1 T-TTAATATTAAATTTAATTTAATATTTATCTTATAGTATTTATTA-ATT-TAATA-TTAAAGTG * 55090383 AATA 62 ATTA * * 55090387 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGA 1 TTTAATATTAAATTTAATTTAATATTTATCTT-AT-AGTATT-TATTAATTTAATATTAAAGTGA 55090452 TTA 63 TTA 55090455 AGTTTGATCA Statistics Matches: 102, Mismatches: 16, Indels: 25 0.71 0.11 0.17 Matches are distributed among these distances: 62 29 0.28 63 10 0.10 64 6 0.06 65 5 0.05 66 5 0.05 67 9 0.09 68 37 0.36 69 1 0.01 ACGTcount: A:0.40, C:0.04, G:0.05, T:0.52 Consensus pattern (65 bp): TTTAATATTAAATTTAATTTAATATTTATCTTATAGTATTTATTAATTTAATATTAAAGTGATTA Found at i:55099436 original size:32 final size:30 Alignment explanation

Indices: 55099390--55099553 Score: 159 Period size: 30 Copynumber: 5.3 Consensus size: 30 55099380 TATGTTGTCA * * 55099390 AATTGATTTGTATATAGATATATATATTGCCG 1 AATTGATTTGTATAT-G-GATATACATTGCCG * * * * ** 55099422 AATTAATTTATATATAGATATATAAATAACCG 1 AATTGATTTGTATAT-G-GATATACATTGCCG ** 55099454 AATTGATTTGTATATGGATATACATTGCTA 1 AATTGATTTGTATATGGATATACATTGCCG * 55099484 AATT-ATTTTGTATATGGATATACATTGCTG 1 AATTGA-TTTGTATATGGATATACATTGCCG * 55099514 AATTGATTTGTATATGGATATATATTGCCG 1 AATTGATTTGTATATGGATATACATTGCCG * 55099544 AATTTATTTG 1 AATTGATTTG 55099554 AGCATTGGAT Statistics Matches: 113, Mismatches: 17, Indels: 6 0.83 0.12 0.04 Matches are distributed among these distances: 29 1 0.01 30 70 0.62 31 2 0.02 32 40 0.35 ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44 Consensus pattern (30 bp): AATTGATTTGTATATGGATATACATTGCCG Found at i:55100783 original size:31 final size:31 Alignment explanation

Indices: 55100745--55100807 Score: 126 Period size: 31 Copynumber: 2.0 Consensus size: 31 55100735 TGACATATTT 55100745 ATATATTGTGATAGTGTGATGAATTCTTGAC 1 ATATATTGTGATAGTGTGATGAATTCTTGAC 55100776 ATATATTGTGATAGTGTGATGAATTCTTGAC 1 ATATATTGTGATAGTGTGATGAATTCTTGAC 55100807 A 1 A 55100808 ATTCAAAATG Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.30, C:0.06, G:0.22, T:0.41 Consensus pattern (31 bp): ATATATTGTGATAGTGTGATGAATTCTTGAC Found at i:55105135 original size:16 final size:16 Alignment explanation

Indices: 55105116--55105175 Score: 104 Period size: 16 Copynumber: 3.8 Consensus size: 16 55105106 TGTATTGGAT 55105116 TAGAGGTGTAA-TGTAA 1 TAGAGGTGTAATTG-AA 55105132 TAGAGGTGTAATTGAA 1 TAGAGGTGTAATTGAA 55105148 TAGAGGTGTAATTGAA 1 TAGAGGTGTAATTGAA 55105164 TAGAGGTGTAAT 1 TAGAGGTGTAAT 55105176 AGCAAATCAA Statistics Matches: 43, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 16 41 0.95 17 2 0.05 ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32 Consensus pattern (16 bp): TAGAGGTGTAATTGAA Found at i:55105211 original size:45 final size:41 Alignment explanation

Indices: 55105154--55105263 Score: 107 Period size: 45 Copynumber: 2.6 Consensus size: 41 55105144 TGAATAGAGG * 55105154 TGTAATTGAATAGAGGTGTAATAGCAAATCAACTATTTGGTT 1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTATTTGG-T ** * *** 55105196 GAATGTAATGGAATAGAGACGTAATAG-TAATCTTGTATTTGGT 1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAACTATTTGGT 55105239 TG-AATGGAATAGAGGTGTAATAGCA 1 TGTAATGGAATAGAGGTGTAATAGCA 55105264 TAATGGAAAA Statistics Matches: 54, Mismatches: 10, Indels: 7 0.76 0.14 0.10 Matches are distributed among these distances: 39 19 0.35 40 2 0.04 43 1 0.02 44 11 0.20 45 21 0.39 ACGTcount: A:0.36, C:0.05, G:0.25, T:0.33 Consensus pattern (41 bp): TGTAATGGAATAGAGGTGTAATAGCAAATCAACTATTTGGT Found at i:55105426 original size:16 final size:16 Alignment explanation

Indices: 55105389--55105430 Score: 52 Period size: 15 Copynumber: 2.7 Consensus size: 16 55105379 TTAATCATAT * 55105389 TTAAACATA-ATTATTA 1 TTAAA-ATATATTATAA 55105405 TT-AAATATATTATAA 1 TTAAAATATATTATAA 55105420 TTAAAATATAT 1 TTAAAATATAT 55105431 AATTTAATAA Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 14 3 0.13 15 10 0.43 16 10 0.43 ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45 Consensus pattern (16 bp): TTAAAATATATTATAA Found at i:55105437 original size:14 final size:15 Alignment explanation

Indices: 55105398--55105439 Score: 52 Period size: 15 Copynumber: 2.9 Consensus size: 15 55105388 TTTAAACATA * 55105398 ATTATTATTAAATAT 1 ATTATAATTAAATAT 55105413 ATTATAATTAAA-AT 1 ATTATAATTAAATAT * 55105427 A-TATAATTTAATA 1 ATTATAATTAAATA 55105440 AAATTCTTAA Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 13 9 0.38 14 4 0.17 15 11 0.46 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (15 bp): ATTATAATTAAATAT Found at i:55105511 original size:107 final size:108 Alignment explanation

Indices: 55105387--55105597 Score: 397 Period size: 107 Copynumber: 2.0 Consensus size: 108 55105377 ATTTAATCAT 55105387 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA 1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA * * 55105452 ATTAATATTCTTATATGAATTTACTCAAATCATAATATAGATA 66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATAGATA 55105495 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA 1 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA 55105559 ATCAATATTCTTATATGAATTTACTAAAATCATAATATA 66 ATCAATATTCTTATATGAATTTACTAAAATCATAATATA 55105598 TAATACTATA Statistics Matches: 101, Mismatches: 2, Indels: 1 0.97 0.02 0.01 Matches are distributed among these distances: 107 97 0.96 108 4 0.04 ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44 Consensus pattern (108 bp): ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA ATCAATATTCTTATATGAATTTACTAAAATCATAATATAGATA Found at i:55105535 original size:16 final size:16 Alignment explanation

Indices: 55105492--55105537 Score: 51 Period size: 16 Copynumber: 2.9 Consensus size: 16 55105482 CATAATATAG * 55105492 ATAATTTAACATA-ATT 1 ATAA-TTAAAATATATT * 55105508 ATTATT-AAATATATT 1 ATAATTAAAATATATT 55105523 ATAATTAAAATATAT 1 ATAATTAAAATATAT 55105538 AATTTAATAA Statistics Matches: 25, Mismatches: 3, Indels: 4 0.78 0.09 0.12 Matches are distributed among these distances: 14 4 0.16 15 10 0.40 16 11 0.44 ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46 Consensus pattern (16 bp): ATAATTAAAATATATT Found at i:55105544 original size:14 final size:15 Alignment explanation

Indices: 55105492--55105546 Score: 53 Period size: 15 Copynumber: 3.7 Consensus size: 15 55105482 CATAATATAG 55105492 ATAATTTAACATA-ATT 1 ATAA-TTAA-ATATATT * 55105508 ATTATTAAATATATT 1 ATAATTAAATATATT 55105523 ATAATTAAA-ATA-T 1 ATAATTAAATATATT * 55105536 ATAATTTAATA 1 ATAATTAAATA 55105547 AAATTCTTAA Statistics Matches: 34, Mismatches: 3, Indels: 6 0.79 0.07 0.14 Matches are distributed among these distances: 13 9 0.26 14 7 0.21 15 15 0.44 16 3 0.09 ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45 Consensus pattern (15 bp): ATAATTAAATATATT Found at i:55105595 original size:37 final size:35 Alignment explanation

Indices: 55105426--55105595 Score: 100 Period size: 37 Copynumber: 4.7 Consensus size: 35 55105416 ATAATTAAAA * 55105426 TATATAATTTAATAAAATTCTTAATAATTAATATTCT 1 TATATAATTTAATAAAA-TCATAATAATTAATATT-T * * 55105463 TATATGAATTTACTCAAATCATAAT-A-TAGATAATTT 1 TATAT-AATTTAATAAAATCATAATAATTA-AT-ATTT * * * * * 55105499 AACATAATTATTATTAAATAT-ATTATAATTAA-A--A 1 TATATAA-T-TTAATAAA-ATCATAATAATTAATATTT * * 55105533 TATATAATTTAATAAAATTCTTAATAATCAATATTCT 1 TATATAATTTAATAAAA-TCATAATAATTAATATT-T * 55105570 TATATGAATTTACTAAAATCATAATA 1 TATAT-AATTTAATAAAATCATAATA 55105596 TATAATACTA Statistics Matches: 100, Mismatches: 18, Indels: 30 0.68 0.12 0.20 Matches are distributed among these distances: 31 1 0.01 32 8 0.08 33 9 0.09 34 6 0.06 35 4 0.04 36 9 0.09 37 36 0.36 38 25 0.25 39 2 0.02 ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44 Consensus pattern (35 bp): TATATAATTTAATAAAATCATAATAATTAATATTT Done.