Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr14

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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31

Warning! 4503000 characters in sequence are not A, C, G, or T


File 409 of 770

Found at i:125622090 original size:26 final size:26

Alignment explanation

Indices: 125622020--125622117 Score: 171 Period size: 26 Copynumber: 3.8 Consensus size: 26 125622010 CTCTTTTAAT * 125622020 AACTGGGGCAAAAGCCCTTTTTGATA 1 AACTGGGGCAAAAGCCCTTTTCGATA 125622046 AACTGGGG-AAAAGCCCTTTTCGATA 1 AACTGGGGCAAAAGCCCTTTTCGATA * 125622071 AACTGGGGCAAAAGCCCTTTTCGGTA 1 AACTGGGGCAAAAGCCCTTTTCGATA 125622097 AACTGGGGCAAAAGCCCTTTT 1 AACTGGGGCAAAAGCCCTTTT 125622118 TCCACTTCCT Statistics Matches: 69, Mismatches: 2, Indels: 2 0.95 0.03 0.03 Matches are distributed among these distances: 25 24 0.35 26 45 0.65 ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24 Consensus pattern (26 bp): AACTGGGGCAAAAGCCCTTTTCGATA Found at i:125624067 original size:28 final size:28 Alignment explanation

Indices: 125624035--125624133 Score: 112 Period size: 28 Copynumber: 3.5 Consensus size: 28 125624025 GCAATAAGCC * 125624035 CGCACACTTAGTGCTTAATAGTCGAACT 1 CGCACACTTAGTGCTTAATAATCGAACT * 125624063 CGCACACTTAGTGC-TATATAATCAAACT 1 CGCACACTTAGTGCTTA-ATAATCGAACT * * * 125624091 TGCACACTTAGTGCTGT-ATAATTTGAACC 1 CGCACACTTAGTGCT-TAATAA-TCGAACT 125624120 CGCACACTTAGTGC 1 CGCACACTTAGTGC 125624134 CAATTTGTGA Statistics Matches: 60, Mismatches: 7, Indels: 7 0.81 0.09 0.09 Matches are distributed among these distances: 27 2 0.03 28 40 0.67 29 17 0.28 30 1 0.02 ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29 Consensus pattern (28 bp): CGCACACTTAGTGCTTAATAATCGAACT Found at i:125628355 original size:80 final size:80 Alignment explanation

Indices: 125628271--125628419 Score: 183 Period size: 80 Copynumber: 1.9 Consensus size: 80 125628261 TATGGTAACC * * * * 125628271 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG 1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA 125628335 CCCGGATAGAATGACT 65 CCCGGATAGAATGACT * * * * * * * 125628351 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC 125628416 CCGG 66 CCGG 125628420 TTATAATTTC Statistics Matches: 57, Mismatches: 11, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 79 1 0.02 80 56 0.98 ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22 Consensus pattern (80 bp): CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC CCGGATAGAATGACT Found at i:125628361 original size:40 final size:38 Alignment explanation

Indices: 125628312--125628419 Score: 128 Period size: 40 Copynumber: 2.7 Consensus size: 38 125628302 ATCACGATTT * 125628312 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA * 125628352 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA * 125628392 GCACAATTGCCTTCGGGTCTTAACCCGG 1 GCACAA-TGCCTTCGGGTCTTAGCCCGG 125628420 TTATAATTTC Statistics Matches: 61, Mismatches: 4, Indels: 6 0.86 0.06 0.08 Matches are distributed among these distances: 38 1 0.02 39 4 0.07 40 56 0.92 ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23 Consensus pattern (38 bp): GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA Found at i:125636466 original size:80 final size:80 Alignment explanation

Indices: 125636382--125636530 Score: 183 Period size: 80 Copynumber: 1.9 Consensus size: 80 125636372 TATGGTAACC * * * * 125636382 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG 1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA 125636446 CCCGGATAGAATGACT 65 CCCGGATAGAATGACT * * * * * * * 125636462 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC 125636527 CCGG 66 CCGG 125636531 TTATAATTTC Statistics Matches: 57, Mismatches: 11, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 79 1 0.02 80 56 0.98 ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22 Consensus pattern (80 bp): CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC CCGGATAGAATGACT Found at i:125636472 original size:40 final size:38 Alignment explanation

Indices: 125636423--125636530 Score: 128 Period size: 40 Copynumber: 2.7 Consensus size: 38 125636413 ATCACGATTT * 125636423 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA * 125636463 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA * 125636503 GCACAATTGCCTTCGGGTCTTAACCCGG 1 GCACAA-TGCCTTCGGGTCTTAGCCCGG 125636531 TTATAATTTC Statistics Matches: 61, Mismatches: 4, Indels: 6 0.86 0.06 0.08 Matches are distributed among these distances: 38 1 0.02 39 4 0.07 40 56 0.92 ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23 Consensus pattern (38 bp): GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA Found at i:125652345 original size:32 final size:32 Alignment explanation

Indices: 125652303--125652369 Score: 107 Period size: 32 Copynumber: 2.1 Consensus size: 32 125652293 TACTCAATTG * * * 125652303 AATTTTCGTACATACTTGTACCATATCGTACC 1 AATTTCCGTACATACCTATACCATATCGTACC 125652335 AATTTCCGTACATACCTATACCATATCGTACC 1 AATTTCCGTACATACCTATACCATATCGTACC 125652367 AAT 1 AAT 125652370 CTCATACTCA Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 32 32 1.00 ACGTcount: A:0.31, C:0.27, G:0.07, T:0.34 Consensus pattern (32 bp): AATTTCCGTACATACCTATACCATATCGTACC Found at i:125652556 original size:42 final size:42 Alignment explanation

Indices: 125652434--125652557 Score: 169 Period size: 42 Copynumber: 3.0 Consensus size: 42 125652424 GTTACTCAGG * * * * 125652434 AATCTCACACACTAAGTGCCAATACCTAGCCGAAGCTAACTT 1 AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTT * * 125652476 AATCACGCACACTAAGTGCCAATG-ATAGCTGAAGCTATCTT 1 AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTT * * 125652517 GATCTCGCATACTAAGTGCCAATGCATAGCCGAAGCTATCT 1 AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCT 125652558 CAAATATTTC Statistics Matches: 71, Mismatches: 10, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 41 35 0.49 42 36 0.51 ACGTcount: A:0.33, C:0.27, G:0.16, T:0.23 Consensus pattern (42 bp): AATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCTT Found at i:125658497 original size:42 final size:42 Alignment explanation

Indices: 125658438--125658638 Score: 251 Period size: 42 Copynumber: 4.8 Consensus size: 42 125658428 AGGGTTACTA * * 125658438 AGACTACGTCTAAGACCATATTTGGGATATGGCATC-ACTATG 1 AGACTACGTGTAAGACCATATCTGGGATATGGCATCGA-TATG * * * * 125658480 AGACTATGTGTAAGACCATATCTAGGATATGACATCAATATG 1 AGACTACGTGTAAGACCATATCTGGGATATGGCATCGATATG 125658522 AGACTACGTGTAAGACCATATCTGGGATATGGCATCGATATG 1 AGACTACGTGTAAGACCATATCTGGGATATGGCATCGATATG * * * * * 125658564 AGACTTCTTGTAAGACCATAGCTGGGCTATTGGCATCGATACG 1 AGACTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATG * * * 125658607 AGATTACATGTAAGACCATAACTGGGATATGG 1 AGACTACGTGTAAGACCATATCTGGGATATGG 125658639 AATTGGAACA Statistics Matches: 138, Mismatches: 19, Indels: 4 0.86 0.12 0.02 Matches are distributed among these distances: 42 101 0.73 43 37 0.27 ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27 Consensus pattern (42 bp): AGACTACGTGTAAGACCATATCTGGGATATGGCATCGATATG Found at i:125663060 original size:69 final size:69 Alignment explanation

Indices: 125662897--125663388 Score: 387 Period size: 69 Copynumber: 7.1 Consensus size: 69 125662887 TGAACATTTG * * ** * * * 125662897 TTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTTGCTTTTCGCCTGTGAACT 1 TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCTCCTGCGAAC- * 125662962 TTTAA 65 CTTAA * * * * * * 125662967 TTTTATAGATGGGAGTTTTGCTCTTGCTAATTGTGCTGGAGGTTGTGGCTCTTCTCAC-GCAAAC 1 TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCTC-CTGCGAAC * 125663031 CTTAG 65 CTTAA * * * * * * * * 125663036 TTTTATAGTTGGGAGCTTTACTCTTACTAATTGTGCTGGAGGTCGCGACTCTT-TGCCTGTGAAC 1 TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCT-CCTGCGAAC 125663100 CTTAA 65 CTTAA * * * * * * * 125663105 TTTTACAGCTGGGATCTTTGCTCTCGTTAACTGTGCTAGAGGTTGCAGCTCTTCGCCTGCAAACC 1 TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCTCCTGCGAACC 125663170 TTAA 66 TTAA ** * * * 125663174 TTTTACAGCTAAGACCTTTGATCTTGCTAATTGTGCTAGAGGTCGCGGCTCTT-TACCTGCGAAC 1 TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCT-CCTGCGAAC 125663238 CTTAA 65 CTTAA * * * * * * * *** * * * 125663243 TTTTATAGCTAGGACCTTTGCTCTTGCTAACTGCGTTGGAGGTCATGGCTTTTCGCTTGCGAACC 1 TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCTCCTGCGAACC * 125663308 TTAC 66 TTAA * * *** * * * ** * 125663312 TTTTACAGCTAGGAACTTTGCTCTCATTAACTGTGCTGGAGGTGGTAGCTCTTCACCTGCGAACC 1 TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCTCCTGCGAACC 125663377 TTAA 66 TTAA 125663381 TTTTACAG 1 TTTTACAG 125663389 TTGACAATTT Statistics Matches: 340, Mismatches: 76, Indels: 13 0.79 0.18 0.03 Matches are distributed among these distances: 68 2 0.01 69 286 0.84 70 51 0.15 71 1 0.00 ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37 Consensus pattern (69 bp): TTTTACAGCTGGGAGCTTTGCTCTTGCTAATTGTGCTAGAGGTTGCGGCTCTTCTCCTGCGAACC TTAA Found at i:125663309 original size:207 final size:207 Alignment explanation

Indices: 125662897--125663388 Score: 567 Period size: 207 Copynumber: 2.4 Consensus size: 207 125662887 TGAACATTTG * * * * * 125662897 TTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTAGAGGTTGTTGCTTTTCGCCTGTGAACT 1 TTTTACAGCTGGGAACTTTGCTCTCGTTAACTGTGCTAGAGGTTGTAGCTCTTCGCCTGCGAAC- * * ** ** * * * * 125662962 TTTAATTTTATAGATGGGAGTTTTGCTCTTGCTAATTGTGCTGGAGGTTGTGGCTCTTCTCACGC 65 CTTAATTTTACAGATAAGACCTTTGATCTTGCTAATTGTGCTAGAGGTCGCGGCTCTTCTCACGC * * * * * * * 125663027 AAACCTTAGTTTTATAGTTGGGAGCTTTACTCTTACTAATTGTGCTGGAGGTCGCGACTCTTTGC 130 AAACCTTAATTTTATAGCTAGGACCTTTACTCTTACTAACTGCGCTGGAGGTCACGACTCTTTGC * 125663092 CTGTGAACCTTAA 195 CTGCGAACCTTAA * * * 125663105 TTTTACAGCTGGGATCTTTGCTCTCGTTAACTGTGCTAGAGGTTGCAGCTCTTCGCCTGCAAACC 1 TTTTACAGCTGGGAACTTTGCTCTCGTTAACTGTGCTAGAGGTTGTAGCTCTTCGCCTGCGAACC * 125663170 TTAATTTTACAGCTAAGACCTTTGATCTTGCTAATTGTGCTAGAGGTCGCGGCTCTT-T-ACCTG 66 TTAATTTTACAGATAAGACCTTTGATCTTGCTAATTGTGCTAGAGGTCGCGGCTCTTCTCA-C-G * * * * * * 125663233 CGAACCTTAATTTTATAGCTAGGACCTTTGCTCTTGCTAACTGCGTTGGAGGTCATGGCT-TTTC 129 CAAACCTTAATTTTATAGCTAGGACCTTTACTCTTACTAACTGCGCTGGAGGTCACGACTCTTT- * * 125663297 GCTTGCGAACCTTAC 193 GCCTGCGAACCTTAA * * * * * 125663312 TTTTACAGCTAGGAACTTTGCTCTCATTAACTGTGCTGGAGGTGGTAGCTCTTCACCTGCGAACC 1 TTTTACAGCTGGGAACTTTGCTCTCGTTAACTGTGCTAGAGGTTGTAGCTCTTCGCCTGCGAACC 125663377 TTAATTTTACAG 66 TTAATTTTACAG 125663389 TTGACAATTT Statistics Matches: 239, Mismatches: 42, Indels: 7 0.83 0.15 0.02 Matches are distributed among these distances: 205 1 0.00 206 5 0.02 207 176 0.74 208 57 0.24 ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37 Consensus pattern (207 bp): TTTTACAGCTGGGAACTTTGCTCTCGTTAACTGTGCTAGAGGTTGTAGCTCTTCGCCTGCGAACC TTAATTTTACAGATAAGACCTTTGATCTTGCTAATTGTGCTAGAGGTCGCGGCTCTTCTCACGCA AACCTTAATTTTATAGCTAGGACCTTTACTCTTACTAACTGCGCTGGAGGTCACGACTCTTTGCC TGCGAACCTTAA Found at i:125666233 original size:38 final size:38 Alignment explanation

Indices: 125666198--125666347 Score: 160 Period size: 38 Copynumber: 3.9 Consensus size: 38 125666188 CCGAGGCTAT * 125666198 ATGCTGGAATTATATCTGGGTTAAATCCCGCAGGCTTC 1 ATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTC * * * 125666236 GTGCTGGTAA-CATATCCGAGTTAAATCCCGCAGGCTTC 1 ATGCTGG-AATTATATCCGGGTTAAATCCCGCAGGCTTC * * * 125666274 ATGCTGGTATTATATCCGGGTTAAATTCCGCAGGCCT- 1 ATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTC * * * 125666311 AGTGCTGGTATTATATCTGAGCTTAAAGTCCCGCAGG 1 A-TGCTGGAATTATATCCG-GGTTAAA-TCCCGCAGG 125666348 TTTGTGCTGG Statistics Matches: 94, Mismatches: 13, Indels: 8 0.82 0.11 0.07 Matches are distributed among these distances: 37 2 0.02 38 76 0.81 39 8 0.09 40 8 0.09 ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30 Consensus pattern (38 bp): ATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCTTC Found at i:125666278 original size:76 final size:78 Alignment explanation

Indices: 125666171--125666347 Score: 227 Period size: 76 Copynumber: 2.3 Consensus size: 78 125666161 TTTTGATGTG * * * * 125666171 TATCCGTGCTTAAAGACCCG-AGGCTAT-ATGCTGGAATTATATCTGGGTTAAATCCCGCAGGCT 1 TATCCGAGCTTAAAGTCCCGCAGGCT-TCATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCC * 125666234 TCGTGCTGGTAACA 65 TAGTGCTGGTAACA * * 125666248 TATCCGAG-TTAAA-TCCCGCAGGCTTCATGCTGGTATTATATCCGGGTTAAATTCCGCAGGCCT 1 TATCCGAGCTTAAAGTCCCGCAGGCTTCATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCCT ** 125666311 AGTGCTGGTATTA 66 AGTGCTGGTAACA * 125666324 TATCTGAGCTTAAAGTCCCGCAGG 1 TATCCGAGCTTAAAGTCCCGCAGG 125666348 TTTGTGCTGG Statistics Matches: 86, Mismatches: 10, Indels: 7 0.83 0.10 0.07 Matches are distributed among these distances: 75 5 0.06 76 60 0.70 77 12 0.14 78 9 0.10 ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29 Consensus pattern (78 bp): TATCCGAGCTTAAAGTCCCGCAGGCTTCATGCTGGAATTATATCCGGGTTAAATCCCGCAGGCCT AGTGCTGGTAACA Found at i:125669947 original size:29 final size:29 Alignment explanation

Indices: 125669907--125670009 Score: 154 Period size: 29 Copynumber: 3.6 Consensus size: 29 125669897 GTTGAGAGAT * 125669907 TGGCACTGAGTGTGCGAGCTTGAAATGCA 1 TGGCACTAAGTGTGCGAGCTTGAAATGCA 125669936 TGGCACTAAGTGTGCGAGCTTGAAATGCA 1 TGGCACTAAGTGTGCGAGCTTGAAATGCA * ** 125669965 TGGCACTAAGTGTGCGAG-TTTAAAGTATA 1 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA 125669994 TGGCACTAAGTGTGCG 1 TGGCACTAAGTGTGCG 125670010 CGGCTGATTA Statistics Matches: 69, Mismatches: 4, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 28 5 0.07 29 64 0.93 ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCGAGCTTGAAATGCA Found at i:125677728 original size:75 final size:77 Alignment explanation

Indices: 125677589--125677756 Score: 218 Period size: 75 Copynumber: 2.2 Consensus size: 77 125677579 ATGTGCATCC * * * 125677589 GAGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTATATCCGGGTTAAATCCCGCACCTTCGTGC 1 GAGCTTAAAGTCCCGCTGGCT-TCATGCTGGAATTATATCCGGGTTAAATCCCGCACCTTAGTGC * 125677653 TGGTAATATATTT 65 TGGTAATATATCT * * * 125677666 G-GGTTAAA-TCCCGCTGGCTTCATGCTGGTATTATATCCGGGTTAAATCCCGCAGGC-TAGTGC 1 GAGCTTAAAGTCCCGCTGGCTTCATGCTGGAATTATATCCGGGTTAAATCCCGCA-CCTTAGTGC * 125677728 TGGTATTATATCT 65 TGGTAATATATCT 125677741 GAGCTTAAAGTCCCGC 1 GAGCTTAAAGTCCCGC 125677757 AGGTTTGTGC Statistics Matches: 78, Mismatches: 9, Indels: 8 0.82 0.09 0.08 Matches are distributed among these distances: 74 1 0.01 75 57 0.73 76 13 0.17 77 7 0.09 ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30 Consensus pattern (77 bp): GAGCTTAAAGTCCCGCTGGCTTCATGCTGGAATTATATCCGGGTTAAATCCCGCACCTTAGTGCT GGTAATATATCT Found at i:125677738 original size:37 final size:37 Alignment explanation

Indices: 125677600--125677770 Score: 166 Period size: 38 Copynumber: 4.5 Consensus size: 37 125677590 AGCTTAAAGA * * 125677600 CCCGCAGGCTATATGCTGGAATTATATCCGGGTTAAAT 1 CCCGCAGGCTA-GTGCTGGTATTATATCCGGGTTAAAT * * * ** 125677638 CCCGCA-CCTTCGTGCTGGTAATATATTTGGGTTAAAT 1 CCCGCAGGC-TAGTGCTGGTATTATATCCGGGTTAAAT * 125677675 CCCGCTGGCTTCA-TGCTGGTATTATATCCGGGTTAAAT 1 CCCGCAGGC-T-AGTGCTGGTATTATATCCGGGTTAAAT * * 125677713 CCCGCAGGCTAGTGCTGGTATTATATCTGAGCTTAAAGT 1 CCCGCAGGCTAGTGCTGGTATTATATCCG-GGTTAAA-T * * 125677752 CCCGCAGGTTTGTGCTGGT 1 CCCGCAGGCTAGTGCTGGT 125677771 GACTGGATTC Statistics Matches: 109, Mismatches: 18, Indels: 11 0.79 0.13 0.08 Matches are distributed among these distances: 36 1 0.01 37 44 0.40 38 46 0.42 39 18 0.17 ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32 Consensus pattern (37 bp): CCCGCAGGCTAGTGCTGGTATTATATCCGGGTTAAAT Found at i:125683291 original size:27 final size:27 Alignment explanation

Indices: 125683261--125683335 Score: 105 Period size: 27 Copynumber: 2.8 Consensus size: 27 125683251 ACCCCTGGTT 125683261 TGTAAAATTACTAAAATACCCTCGACC 1 TGTAAAATTACTAAAATACCCTCGACC * * * 125683288 TGTAAAATTATTGAAATACCCTCGACT 1 TGTAAAATTACTAAAATACCCTCGACC * * 125683315 TGTAAAATTACCAAAGTACCC 1 TGTAAAATTACTAAAATACCC 125683336 CTAATTTACA Statistics Matches: 41, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 27 41 1.00 ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28 Consensus pattern (27 bp): TGTAAAATTACTAAAATACCCTCGACC Found at i:125683348 original size:27 final size:25 Alignment explanation

Indices: 125683318--125683391 Score: 76 Period size: 27 Copynumber: 2.8 Consensus size: 25 125683308 CTCGACTTGT 125683318 AAAATTACCAAAGTACCCCTAATTTAC 1 AAAATTACCAAA-TACCCCT-ATTTAC *** 125683345 AAAATTACCGTTTTACCCTCTATTTAC 1 AAAATTACC-AAATACCC-CTATTTAC 125683372 AAAATTACCGAAATACCCCT 1 AAAATTACC-AAATACCCCT 125683392 GTAGGGAAGA Statistics Matches: 39, Mismatches: 6, Indels: 5 0.78 0.12 0.10 Matches are distributed among these distances: 26 2 0.05 27 35 0.90 28 2 0.05 ACGTcount: A:0.39, C:0.27, G:0.04, T:0.30 Consensus pattern (25 bp): AAAATTACCAAATACCCCTATTTAC Found at i:125683404 original size:27 final size:27 Alignment explanation

Indices: 125683374--125683623 Score: 331 Period size: 27 Copynumber: 9.3 Consensus size: 27 125683364 CTATTTACAA * * 125683374 AATTACCGAAATACCCCTGTAGGGAAG 1 AATTACCGAAATACCCTTGTAGGGTAG 125683401 AATTACCGAAATACCCTTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG * * * 125683428 AAATACGGAAATACCCCTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG ** * 125683455 AATTACTAAAATAACCC-TGTAAGGTAG 1 AATTACCGAAAT-ACCCTTGTAGGGTAG 125683482 AATTACCGAAATACCCTTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG * * 125683509 AAATACTGAAATACCCTTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG ** 125683536 AATTACTAAAATACCCTTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG * * 125683563 AATTACTGAAATACCCCTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAG * * * 125683590 AATTACCGAGATACCCTTGTGGGGTAA 1 AATTACCGAAATACCCTTGTAGGGTAG 125683617 AATTACC 1 AATTACC 125683624 ATTTTATGTG Statistics Matches: 198, Mismatches: 23, Indels: 4 0.88 0.10 0.02 Matches are distributed among these distances: 26 4 0.02 27 190 0.96 28 4 0.02 ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25 Consensus pattern (27 bp): AATTACCGAAATACCCTTGTAGGGTAG Found at i:125683905 original size:27 final size:26 Alignment explanation

Indices: 125683861--125683912 Score: 68 Period size: 27 Copynumber: 2.0 Consensus size: 26 125683851 CTCGCTGCAA * 125683861 TCTGGTGGCCTCGCCACATATATCTGT 1 TCTGGTGACCTCGCCACA-ATATCTGT * * 125683888 TCTGGTGACTTCGTCACAATATCTG 1 TCTGGTGACCTCGCCACAATATCTG 125683913 GCAGCCTCGC Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 26 7 0.32 27 15 0.68 ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35 Consensus pattern (26 bp): TCTGGTGACCTCGCCACAATATCTGT Found at i:125684152 original size:6 final size:6 Alignment explanation

Indices: 125684143--125684325 Score: 99 Period size: 6 Copynumber: 29.8 Consensus size: 6 125684133 TTGCATTCAC * * * * * 125684143 ATTCTG ATTCTA ATTCTG -TTACTCG ATACAG ATTCTG ATTTTG -TTACCTA 1 ATTCTG ATTCTG ATTCTG ATT-CT-G ATTCTG ATTCTG ATTCTG ATT--CTG * ** 125684193 ATTCTG ATTCTG GTTCTG ATTCTG ATTCTG -TTACCTG ACACTG ATTCTG 1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG * * * * 125684242 ATT-TG -TTACCTA ATTCTG ATTCTG ATTTTG ATTTTG ATTCTG -TCACCTG 1 ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG * * * 125684291 ATTTTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT 1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT 125684326 TGTAACGCCC Statistics Matches: 133, Mismatches: 28, Indels: 32 0.69 0.15 0.17 Matches are distributed among these distances: 4 2 0.02 5 9 0.07 6 106 0.80 7 10 0.08 8 6 0.05 ACGTcount: A:0.19, C:0.17, G:0.14, T:0.49 Consensus pattern (6 bp): ATTCTG Found at i:125684280 original size:61 final size:61 Alignment explanation

Indices: 125684143--125684305 Score: 220 Period size: 61 Copynumber: 2.7 Consensus size: 61 125684133 TTGCATTCAC * * 125684143 ATTCTGATTCTAATTCTGTTA-CTCGATACAGATTCTGATTTTGTTACCTAATTCTGATTCTG 1 ATTCTGATTCTGATTCTGTTACCT-GATACTGATTCTGA-TTTGTTACCTAATTCTGATTCTG * * 125684205 GTTCTGATTCTGATTCTGTTACCTGACACTGATTCTGATTTGTTACCTAATTCTGATTCTG 1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTTGTTACCTAATTCTGATTCTG * * * ** 125684266 ATTTTGATTTTGATTCTGTCACCTGATTTTGATTCTGATT 1 ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATT 125684306 CTGATTCTCA Statistics Matches: 89, Mismatches: 11, Indels: 3 0.86 0.11 0.03 Matches are distributed among these distances: 61 56 0.63 62 31 0.35 63 2 0.02 ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48 Consensus pattern (61 bp): ATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTTGTTACCTAATTCTGATTCTG Found at i:125686084 original size:28 final size:28 Alignment explanation

Indices: 125686044--125686108 Score: 96 Period size: 28 Copynumber: 2.3 Consensus size: 28 125686034 ATGTACTAGA * 125686044 ATACCCCTATGTATGCAAAATTACCAT-T 1 ATACCCCTATGTATGCAAAATGACC-TCT * 125686072 ATACCCCTATGTATGTAAAATGACCTCT 1 ATACCCCTATGTATGCAAAATGACCTCT 125686100 ATACCCCTA 1 ATACCCCTA 125686109 GGGTTAATTT Statistics Matches: 34, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 27 1 0.03 28 33 0.97 ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31 Consensus pattern (28 bp): ATACCCCTATGTATGCAAAATGACCTCT Found at i:125686272 original size:27 final size:27 Alignment explanation

Indices: 125686214--125686303 Score: 119 Period size: 28 Copynumber: 3.2 Consensus size: 27 125686204 AGGAAGCGTC 125686214 CTGGTGGCTA-TGCCACAAATTATCTGTT 1 CTGGTGGC-ACTGCCACAAA-TATCTGTT * * 125686242 CTGGTGGCCCTGCCACATATATCTGTT 1 CTGGTGGCACTGCCACAAATATCTGTT 125686269 CTGGTGGCACTGCCACAAAATATCTGTAT 1 CTGGTGGCACTGCCAC-AAATATCTGT-T 125686298 CTGGTG 1 CTGGTG 125686304 ACTCTATCAC Statistics Matches: 55, Mismatches: 4, Indels: 5 0.86 0.06 0.08 Matches are distributed among these distances: 27 23 0.42 28 25 0.45 29 7 0.13 ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32 Consensus pattern (27 bp): CTGGTGGCACTGCCACAAATATCTGTT Found at i:125686314 original size:29 final size:28 Alignment explanation

Indices: 125686226--125686314 Score: 81 Period size: 27 Copynumber: 3.2 Consensus size: 28 125686216 GGTGGCTATG * * * * 125686226 CCACAAATTATCTGTTCTGGTGGCCCTG 1 CCACAAAATATCTGTTCTGGTGACACTA * * * 125686254 CCAC-ATATATCTGTTCTGGTGGCACTG 1 CCACAAAATATCTGTTCTGGTGACACTA * 125686281 CCACAAAATATCTGTATCTGGTGACTCTA 1 CCACAAAATATCTGT-TCTGGTGACACTA * 125686310 TCACA 1 CCACA 125686315 TTTTCTGTAT Statistics Matches: 51, Mismatches: 8, Indels: 3 0.82 0.13 0.05 Matches are distributed among these distances: 27 24 0.47 28 13 0.25 29 14 0.27 ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31 Consensus pattern (28 bp): CCACAAAATATCTGTTCTGGTGACACTA Found at i:125686322 original size:55 final size:56 Alignment explanation

Indices: 125686214--125686328 Score: 137 Period size: 55 Copynumber: 2.1 Consensus size: 56 125686204 AGGAAGCGTC * * * 125686214 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T 1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTACCACATATATCTGTAT * * * 125686269 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTATCACAT-TTTCTGTAT 1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTACCACATATATCTGTAT 125686325 CTGG 1 CTGG 125686329 CAGCCATGCT Statistics Matches: 51, Mismatches: 6, Indels: 5 0.82 0.10 0.08 Matches are distributed among these distances: 54 1 0.02 55 30 0.59 56 20 0.39 ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35 Consensus pattern (56 bp): CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTACCACATATATCTGTAT Found at i:125698328 original size:70 final size:71 Alignment explanation

Indices: 125698245--125698407 Score: 310 Period size: 70 Copynumber: 2.3 Consensus size: 71 125698235 CGATTTGTCT 125698245 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 125698309 CTTTCA 66 CTTTCA * 125698315 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 125698380 CTTTCA 66 CTTTCA 125698386 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 125698408 GATACATCTC Statistics Matches: 91, Mismatches: 1, Indels: 1 0.98 0.01 0.01 Matches are distributed among these distances: 70 51 0.56 71 40 0.44 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:125698445 original size:71 final size:70 Alignment explanation

Indices: 125698245--125698441 Score: 249 Period size: 70 Copynumber: 2.8 Consensus size: 70 125698235 CGATTTGTCT * * * * 125698245 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 125698309 CTTTCA 65 CTTTCA * * * * 125698315 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 125698380 CTTTCA 65 CTTTCA * * 125698386 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 125698442 TACAGGGTGT Statistics Matches: 118, Mismatches: 7, Indels: 6 0.90 0.05 0.05 Matches are distributed among these distances: 68 22 0.19 69 1 0.01 70 52 0.44 71 43 0.36 ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:125700591 original size:24 final size:25 Alignment explanation

Indices: 125700563--125700626 Score: 78 Period size: 24 Copynumber: 2.6 Consensus size: 25 125700553 TCAACCGAAT * * * 125700563 TCGCACACATAGTGCTA-ATTAAGC 1 TCGCACACATAGTGCCATACTAAAC * 125700587 TCGCACACATAATGCCATACTAAAC 1 TCGCACACATAGTGCCATACTAAAC 125700612 -CGCACACATAGTGCC 1 TCGCACACATAGTGCC 125700627 TAAAATTTTC Statistics Matches: 34, Mismatches: 5, Indels: 2 0.83 0.12 0.05 Matches are distributed among these distances: 24 29 0.85 25 5 0.15 ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20 Consensus pattern (25 bp): TCGCACACATAGTGCCATACTAAAC Found at i:125700677 original size:24 final size:24 Alignment explanation

Indices: 125700650--125700699 Score: 64 Period size: 24 Copynumber: 2.1 Consensus size: 24 125700640 CATGCATCGA * 125700650 CATTCAAATCTGCACACATAGCGC 1 CATTCAAATCCGCACACATAGCGC * * * 125700674 CATTTAATTCCGCACACATAGTGC 1 CATTCAAATCCGCACACATAGCGC 125700698 CA 1 CA 125700700 ATGTTAGCTC Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 24 22 1.00 ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24 Consensus pattern (24 bp): CATTCAAATCCGCACACATAGCGC Found at i:125700772 original size:94 final size:94 Alignment explanation

Indices: 125700655--125700891 Score: 411 Period size: 94 Copynumber: 2.5 Consensus size: 94 125700645 ATCGACATTC * * * * 125700655 AAATCTGCACACATAGCGCCATTTAATTCCGCACACATAGTGCCAATGTTAGCTCATTATAATAA 1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA 125700720 GGCAATTTACTTAATTCAAATAGCATATA 66 GGCAATTTACTTAATTCAAATAGCATATA ** 125700749 AAATCTGCACACAAAGTGACATTTAATTATGCACACATAGTGCCAATGTTAACTCATTATAATAA 1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA * 125700814 GGCAATTTACTTATTTCAAATAGCATATA 66 GGCAATTTACTTAATTCAAATAGCATATA 125700843 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGT 1 AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGT 125700892 ATAAAATCTG Statistics Matches: 134, Mismatches: 9, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 94 134 1.00 ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30 Consensus pattern (94 bp): AAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATGTTAACTCATTATAATAA GGCAATTTACTTAATTCAAATAGCATATA Found at i:125700876 original size:24 final size:24 Alignment explanation

Indices: 125700849--125700936 Score: 95 Period size: 24 Copynumber: 3.5 Consensus size: 24 125700839 TATAAAATCT 125700849 GCACACAAAGTGACATTTAATTCC 1 GCACACAAAGTGACATTTAATTCC * * * * 125700873 GCACACATAGTGCCAATGTATAAAATCT 1 GCACACAAAGTGAC-AT-T-T-AATTCC 125700901 GCACACAAAGTGACATTTAATTCC 1 GCACACAAAGTGACATTTAATTCC * 125700925 GCACACATAGTG 1 GCACACAAAGTG 125700937 CCAATGTTAA Statistics Matches: 51, Mismatches: 9, Indels: 8 0.75 0.13 0.12 Matches are distributed among these distances: 24 27 0.53 25 3 0.06 26 2 0.04 27 3 0.06 28 16 0.31 ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24 Consensus pattern (24 bp): GCACACAAAGTGACATTTAATTCC Found at i:125700917 original size:52 final size:52 Alignment explanation

Indices: 125700839--125700943 Score: 210 Period size: 52 Copynumber: 2.0 Consensus size: 52 125700829 TCAAATAGCA 125700839 TATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATG 1 TATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATG 125700891 TATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATG 1 TATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATG 125700943 T 1 T 125700944 TAACTCATTA Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 52 53 1.00 ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26 Consensus pattern (52 bp): TATAAAATCTGCACACAAAGTGACATTTAATTCCGCACACATAGTGCCAATG Found at i:125711132 original size:47 final size:47 Alignment explanation

Indices: 125711078--125711175 Score: 196 Period size: 47 Copynumber: 2.1 Consensus size: 47 125711068 TGTCATGACA 125711078 TATAAGCATAACAAATAAACGGTGATATAATGATCCTACTTGAATTG 1 TATAAGCATAACAAATAAACGGTGATATAATGATCCTACTTGAATTG 125711125 TATAAGCATAACAAATAAACGGTGATATAATGATCCTACTTGAATTG 1 TATAAGCATAACAAATAAACGGTGATATAATGATCCTACTTGAATTG 125711172 TATA 1 TATA 125711176 TCGGGGTAAT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 47 51 1.00 ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31 Consensus pattern (47 bp): TATAAGCATAACAAATAAACGGTGATATAATGATCCTACTTGAATTG Found at i:125711571 original size:79 final size:80 Alignment explanation

Indices: 125711398--125711585 Score: 315 Period size: 79 Copynumber: 2.4 Consensus size: 80 125711388 GGACTAAGAT * * * * 125711398 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGATAAGTCCCGAAGGCATTTGTGTGAGTTACTA 1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGATAAGTCCCAAAGGCATTTGTGCGAGTTACTA 125711463 TATCCGGGCTAAGTC 66 TATCCGGGCTAAGTC * 125711478 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCA-TTGTGCGAGTTACTA 1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGATAAGTCCCAAAGGCATTTGTGCGAGTTACTA 125711542 TATCCGGGCTAAGTC 66 TATCCGGGCTAAGTC * 125711557 CCGAAGGCATTTGTGCGAGTTGCTATATC 1 CCGAAGGCATTTGTGCGAGTTACTATATC 125711586 TGGCTAAATC Statistics Matches: 102, Mismatches: 6, Indels: 1 0.94 0.06 0.01 Matches are distributed among these distances: 79 57 0.56 80 45 0.44 ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28 Consensus pattern (80 bp): CCGAAGGCATTTGTGCGAGTTACTATATCCGGGATAAGTCCCAAAGGCATTTGTGCGAGTTACTA TATCCGGGCTAAGTC Found at i:125711591 original size:39 final size:40 Alignment explanation

Indices: 125711398--125711602 Score: 315 Period size: 40 Copynumber: 5.2 Consensus size: 40 125711388 GGACTAAGAT * * * 125711398 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGATAAGTC 1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC * 125711438 CCGAAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTC 1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC 125711478 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC 1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC * 125711518 CCAAAGGCA-TTGTGCGAGTTACTATATCCGGGCTAAGTC 1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC * * * 125711557 CCGAAGGCATTTGTGCGAGTTGCTATAT-CTGGCTAAATC 1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC * 125711596 TCGAAGG 1 CCGAAGG 125711603 TACTTGGGTT Statistics Matches: 153, Mismatches: 11, Indels: 3 0.92 0.07 0.02 Matches are distributed among these distances: 39 53 0.35 40 100 0.65 ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28 Consensus pattern (40 bp): CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTC Found at i:125719990 original size:48 final size:47 Alignment explanation

Indices: 125719934--125720154 Score: 192 Period size: 48 Copynumber: 4.6 Consensus size: 47 125719924 ATAAGGTCTC * * * * * 125719934 GTGTAAGACTATGTTTGGGATATGGCATCACCGTTGATATCTGAGTCA 1 GTGTAAGACAATGTCTGGGACATGGCATCAGCGTTGATATGTGAG-CA * 125719982 GTGTAAGACAATGTCTGGGACATGGCATCAGGGTTGATATGTGAGCCA 1 GTGTAAGACAATGTCTGGGACATGGCATCAGCGTTGATATGTGAG-CA * * * ** * * 125720030 GTGTAACACCATGTCTAGGTTATGGCATCAGTGTGGATATGTGAGCTA 1 GTGTAAGACAATGTCTGGGACATGGCATCAGCGTTGATATGTGAGC-A * ** * * * 125720078 GTGTAAGACAATGTTTGGGACATGGCATTGGCGCTGACATGTGTGCTA 1 GTGTAAGACAATGTCTGGGACATGGCATCAGCGTTGATATGTGAGC-A * * * 125720126 GTATAAGTTCAA-GTCTGAGACATGGCATC 1 GTGTAAG-ACAATGTCTGGGACATGGCATC 125720155 GGCACAGGCA Statistics Matches: 139, Mismatches: 32, Indels: 4 0.79 0.18 0.02 Matches are distributed among these distances: 47 1 0.01 48 135 0.97 49 3 0.02 ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29 Consensus pattern (47 bp): GTGTAAGACAATGTCTGGGACATGGCATCAGCGTTGATATGTGAGCA Found at i:125726497 original size:27 final size:27 Alignment explanation

Indices: 125726424--125726531 Score: 103 Period size: 27 Copynumber: 4.0 Consensus size: 27 125726414 TGGCTGCCAC * * * 125726424 AACAGACAA-TGTGACAGAGTCACCAG 1 AACAGATAATTGTGGCAGAGCCACCAG * * ** 125726450 ATATAGATAATCGTGGCAGAGCCACCTT 1 A-ACAGATAATTGTGGCAGAGCCACCAG 125726478 AACAGA-AATATGTGGCAGAGCCACCAG 1 AACAGATAAT-TGTGGCAGAGCCACCAG * * 125726505 ATCAGATAATTGTGGCATAGCCACCAG 1 AACAGATAATTGTGGCAGAGCCACCAG 125726532 GACGCTTCCT Statistics Matches: 65, Mismatches: 13, Indels: 7 0.76 0.15 0.08 Matches are distributed among these distances: 26 4 0.06 27 45 0.69 28 16 0.25 ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18 Consensus pattern (27 bp): AACAGATAATTGTGGCAGAGCCACCAG Found at i:125726520 original size:54 final size:54 Alignment explanation

Indices: 125726424--125726529 Score: 142 Period size: 54 Copynumber: 2.0 Consensus size: 54 125726414 TGGCTGCCAC * * * 125726424 AACAGACAATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCACCTT 1 AACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCTT * * * 125726478 AACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACC 1 AACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACC 125726530 AGGACGCTTC Statistics Matches: 45, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 54 27 0.60 55 18 0.40 ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18 Consensus pattern (54 bp): AACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCTT Found at i:125726969 original size:16 final size:15 Alignment explanation

Indices: 125726948--125726977 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 125726938 AAAATACCAA 125726948 CTTTTCGGCATTTTGG 1 CTTTTCGGC-TTTTGG 125726964 CTTTTCGGCTTTTG 1 CTTTTCGGCTTTTG 125726978 CCGATCGAGT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 5 0.36 16 9 0.64 ACGTcount: A:0.03, C:0.20, G:0.23, T:0.53 Consensus pattern (15 bp): CTTTTCGGCTTTTGG Found at i:125727976 original size:24 final size:24 Alignment explanation

Indices: 125727949--125727995 Score: 76 Period size: 24 Copynumber: 2.0 Consensus size: 24 125727939 CTAGATTTCC ** 125727949 TCCCTTATCTGCTCCTAAATCCTA 1 TCCCTTATCAACTCCTAAATCCTA 125727973 TCCCTTATCAACTCCTAAATCCT 1 TCCCTTATCAACTCCTAAATCCT 125727996 CTCCTGATAG Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 24 21 1.00 ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36 Consensus pattern (24 bp): TCCCTTATCAACTCCTAAATCCTA Found at i:125733416 original size:37 final size:36 Alignment explanation

Indices: 125733331--125733450 Score: 213 Period size: 36 Copynumber: 3.3 Consensus size: 36 125733321 TATAAAAGAA * 125733331 GTCTTACCCGGACATAATCTCCACACGTAGTCATCG 1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCG 125733367 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG 1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATC-G 125733404 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCG 1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCG * 125733440 GTCTCACCCGG 1 GTCTTACCCGG 125733451 AACATATTCC Statistics Matches: 81, Mismatches: 2, Indels: 2 0.95 0.02 0.02 Matches are distributed among these distances: 36 45 0.56 37 36 0.44 ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26 Consensus pattern (36 bp): GTCTTACCCGGTCATAATCTCCACACGTAGTCATCG Found at i:125733605 original size:49 final size:49 Alignment explanation

Indices: 125733552--125733766 Score: 367 Period size: 49 Copynumber: 4.4 Consensus size: 49 125733542 TTTTACATTA * 125733552 GCCATTAGGCCTTATCATATATACATACACTTTCACATTCACCACATCG 1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG 125733601 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG 1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG * 125733650 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCACCACATCG 1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG * * * * 125733699 GCCATTAGGCCTCATCACATATACATACACTTTCACATTCATCGCATTG 1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG * 125733748 GCCATTCGGCCTTATCACA 1 GCCATTAGGCCTTATCACA 125733767 CATATATGTA Statistics Matches: 159, Mismatches: 7, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 49 159 1.00 ACGTcount: A:0.29, C:0.33, G:0.09, T:0.29 Consensus pattern (49 bp): GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG Found at i:125738063 original size:27 final size:26 Alignment explanation

Indices: 125738026--125738137 Score: 143 Period size: 27 Copynumber: 4.2 Consensus size: 26 125738016 AGCATGGCTG * * 125738026 CCAGAACAGATAATGTGACAGAGTCA 1 CCAGAACAGATAATGTGGCAGAGCCA 125738052 CCAGATACAGATAATCGTGGCAGAGCCA 1 CCAGA-ACAGATAAT-GTGGCAGAGCCA * 125738080 CCAGAACAGAAATATGTGGCAGAGCCA 1 CCAGAACAGATA-ATGTGGCAGAGCCA * * 125738107 CCAGATCAGATAATTGTGGCATAGCCA 1 CCAGAACAGATAA-TGTGGCAGAGCCA 125738134 CCAG 1 CCAG 125738138 GACGCTTCCT Statistics Matches: 76, Mismatches: 6, Indels: 7 0.85 0.07 0.08 Matches are distributed among these distances: 26 6 0.08 27 53 0.70 28 17 0.22 ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15 Consensus pattern (26 bp): CCAGAACAGATAATGTGGCAGAGCCA Found at i:125738118 original size:54 final size:54 Alignment explanation

Indices: 125738026--125738137 Score: 163 Period size: 54 Copynumber: 2.1 Consensus size: 54 125738016 AGCATGGCTG * * 125738026 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA 1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA * * * 125738080 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA 1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA 125738134 CCAG 1 CCAG 125738138 GACGCTTCCT Statistics Matches: 52, Mismatches: 5, Indels: 2 0.88 0.08 0.03 Matches are distributed among these distances: 54 34 0.65 55 18 0.35 ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15 Consensus pattern (54 bp): CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA Found at i:125739584 original size:24 final size:24 Alignment explanation

Indices: 125739557--125739603 Score: 76 Period size: 24 Copynumber: 2.0 Consensus size: 24 125739547 CTAGATTTCC ** 125739557 TCCCTTATCTGCTCCTAAATCCTA 1 TCCCTTATCAACTCCTAAATCCTA 125739581 TCCCTTATCAACTCCTAAATCCT 1 TCCCTTATCAACTCCTAAATCCT 125739604 CTCCTGACAG Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 24 21 1.00 ACGTcount: A:0.23, C:0.38, G:0.02, T:0.36 Consensus pattern (24 bp): TCCCTTATCAACTCCTAAATCCTA Found at i:125743117 original size:49 final size:47 Alignment explanation

Indices: 125742896--125743165 Score: 396 Period size: 47 Copynumber: 5.7 Consensus size: 47 125742886 CCCTTCGGGA * * * * 125742896 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * 125742943 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * 125742990 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * * * 125743037 CTTGTCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC * * 125743084 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC 125743133 CTTATCACATATATATACACTTTCACATTCATC 1 CTTATCAC--ATATATACACTTTCACATTCATC 125743166 GCGTAAAATC Statistics Matches: 209, Mismatches: 12, Indels: 2 0.94 0.05 0.01 Matches are distributed among these distances: 47 138 0.66 49 71 0.34 ACGTcount: A:0.28, C:0.31, G:0.09, T:0.33 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC Found at i:125745794 original size:40 final size:39 Alignment explanation

Indices: 125745750--125745968 Score: 217 Period size: 40 Copynumber: 5.5 Consensus size: 39 125745740 GCTCGATTGT * * * 125745750 CTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGC 1 CTTCGGGAC-TTAGCCCGGTT-TAGTAACTCGCACAAATGC * * 125745790 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC 1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC * * 125745830 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC 1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC * * * 125745870 CTTCGGGTCTTAACCCGGTTTTGGTAACTCGCACAAATGC 1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC * * * * * 125745910 CTTCAGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC 1 CTTCGGGACTTAG-CCCGG-TTTAGTAAC-TCGCACAAATGC 125745951 CTTCGGGACTTAGCCCGG 1 CTTCGGGACTTAGCCCGG 125745969 ACACCATTCG Statistics Matches: 152, Mismatches: 22, Indels: 9 0.83 0.12 0.05 Matches are distributed among these distances: 39 2 0.01 40 123 0.81 41 26 0.17 42 1 0.01 ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27 Consensus pattern (39 bp): CTTCGGGACTTAGCCCGGTTTAGTAACTCGCACAAATGC Found at i:125753881 original size:40 final size:39 Alignment explanation

Indices: 125753837--125754053 Score: 217 Period size: 40 Copynumber: 5.5 Consensus size: 39 125753827 GCTCGATTGT * * * 125753837 CTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGC 1 CTTCGGGAC-TTAGCCCGGTT-TAGTAACTCGCACAAATGC * * 125753877 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC 1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC * * 125753917 CTT--GGACTTAACCCGGTTTTGGTAACTCGCACAAATGC 1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC * * 125753955 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC 1 CTTCGGGACTTAGCCCGG-TTTAGTAACTCGCACAAATGC * * * * 125753995 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC 1 CTTCGGGACTTAG-CCCGG-TTTAGTAAC-TCGCACAAATGC 125754036 CTTCGGGACTTAGCCCGG 1 CTTCGGGACTTAGCCCGG 125754054 ACACCATTCG Statistics Matches: 152, Mismatches: 18, Indels: 13 0.83 0.10 0.07 Matches are distributed among these distances: 38 33 0.22 39 2 0.01 40 89 0.59 41 27 0.18 42 1 0.01 ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27 Consensus pattern (39 bp): CTTCGGGACTTAGCCCGGTTTAGTAACTCGCACAAATGC Found at i:125753956 original size:78 final size:80 Alignment explanation

Indices: 125753864--125754054 Score: 242 Period size: 78 Copynumber: 2.4 Consensus size: 80 125753854 GTTATAGTGA * * * * 125753864 TTCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGCCTT-GGACTTAA 1 TTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGAATTAA * * 125753928 CCCGGTTTTGGTAAC 66 CCCGGATTTAGTAAC * * * * 125753943 -TCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATTG 1 TTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC-GGAATTA * 125754007 ACCCGGATTTAGTCAC 65 ACCCGGATTTAGTAAC * * 125754023 TTAGCACAAAAGCCTTCGGGACTTAGCCCGGA 1 TTCGCACAAATGCCTTCGGGACTTAGCCCGGA 125754055 CACCATTCGA Statistics Matches: 94, Mismatches: 15, Indels: 4 0.83 0.13 0.04 Matches are distributed among these distances: 78 49 0.52 80 18 0.19 81 27 0.29 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (80 bp): TTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGAATTAA CCCGGATTTAGTAAC Found at i:125762725 original size:16 final size:17 Alignment explanation

Indices: 125762694--125762727 Score: 52 Period size: 16 Copynumber: 2.0 Consensus size: 17 125762684 TTTTTGGGTT 125762694 AATGGGCCAAAACGGGCC 1 AATGGGCC-AAACGGGCC 125762712 AATGGGCC-AACGGGCC 1 AATGGGCCAAACGGGCC 125762728 CACTTTGGTA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 8 0.50 18 8 0.50 ACGTcount: A:0.29, C:0.29, G:0.35, T:0.06 Consensus pattern (17 bp): AATGGGCCAAACGGGCC Found at i:125763114 original size:27 final size:26 Alignment explanation

Indices: 125763076--125763135 Score: 66 Period size: 27 Copynumber: 2.3 Consensus size: 26 125763066 ATATATATAT * * 125763076 ATATTTGTTCTGGTGGCCTAGCCACA 1 ATATCTGTTCTGGTGACCTAGCCACA * * * 125763102 ATATCTGTATCTGGTGACTTCGTCACA 1 ATATCTGT-TCTGGTGACCTAGCCACA 125763129 ATATCTG 1 ATATCTG 125763136 GCAGCCTCGC Statistics Matches: 28, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 26 7 0.25 27 21 0.75 ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37 Consensus pattern (26 bp): ATATCTGTTCTGGTGACCTAGCCACA Found at i:125765731 original size:40 final size:39 Alignment explanation

Indices: 125765581--125765733 Score: 243 Period size: 39 Copynumber: 3.9 Consensus size: 39 125765571 AAATGTTCGA * * 125765581 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT * 125765620 GTGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT * 125765659 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT 1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT * * 125765698 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCG 1 GTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG 125765734 GGTTACCATA Statistics Matches: 105, Mismatches: 8, Indels: 1 0.92 0.07 0.01 Matches are distributed among these distances: 39 88 0.84 40 17 0.16 ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24 Consensus pattern (39 bp): GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT Found at i:125765749 original size:40 final size:39 Alignment explanation

Indices: 125765582--125765764 Score: 240 Period size: 39 Copynumber: 4.6 Consensus size: 39 125765572 AATGTTCGAG * * * 125765582 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTG 1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA * 125765621 TGACATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA 1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA * 125765660 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTG 1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA * * * 125765699 TGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTA 1 TGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTA ** * * 125765739 CCATAACCGGGCTATGTCCCGAAGGC 1 TGATATCCGGGCTAAG-CCCGAAGGC 125765765 GTTTGAACGA Statistics Matches: 128, Mismatches: 15, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 39 87 0.68 40 41 0.32 ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23 Consensus pattern (39 bp): TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTA Found at i:125765800 original size:79 final size:79 Alignment explanation

Indices: 125765588--125765802 Score: 177 Period size: 78 Copynumber: 2.7 Consensus size: 79 125765578 CGAGTGATAT ** * * * * * * 125765588 CCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGACATCCGGGCT-AA-GCCCGAAGGCAATTG 1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCC-GGATAAACTCCCGAAGGCAATTG ** * 125765651 TGCGAGTTATGATAT 65 TGCGAGTTACCATAA ** * * * * * 125765666 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGT 1 CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT * 125765731 GCGGGTTACCATAA 66 GCGAGTTACCATAA * ** 125765745 CCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-ATATCCGGATAAACT-CCGAAGG 1 CCGGGCTAAG-CCCGAAGGCAATTGAACGAGTAG-TGATATCCGGATAAACTCCCGAAGG 125765803 TATGTGATTC Statistics Matches: 114, Mismatches: 19, Indels: 7 0.81 0.14 0.05 Matches are distributed among these distances: 77 3 0.03 78 40 0.35 79 40 0.35 80 30 0.26 81 1 0.01 ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22 Consensus pattern (79 bp): CCGGGCTAAGCCCGAAGGCAATTGAACGAGTAGTGATATCCGGATAAACTCCCGAAGGCAATTGT GCGAGTTACCATAA Found at i:125770163 original size:101 final size:98 Alignment explanation

Indices: 125769980--125770218 Score: 334 Period size: 101 Copynumber: 2.4 Consensus size: 98 125769970 GTGAGGTCAT * * * 125769980 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACTAAGT 1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT * 125770045 GCAGGCTACTATGTGTACCCGATAACTTCGATCAC 66 GCAGGCTACTACGTGTACCCGATAA-TT-GATCAC * ** * 125770080 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAG 1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT-GGTCACATGTGTAGTACTAAG * * * 125770145 TGCAGGCTACTACGTGTACCGGATAATTGGTCGC 65 TGCAGGCTACTACGTGTACCCGATAATTGATCAC * * 125770179 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA 125770219 GCATTGGCTA Statistics Matches: 123, Mismatches: 15, Indels: 3 0.87 0.11 0.02 Matches are distributed among these distances: 99 40 0.33 100 40 0.33 101 43 0.35 ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29 Consensus pattern (98 bp): GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT GCAGGCTACTACGTGTACCCGATAATTGATCAC Found at i:125770213 original size:49 final size:50 Alignment explanation

Indices: 125769981--125770218 Score: 318 Period size: 49 Copynumber: 4.8 Consensus size: 50 125769971 TGAGGTCATG * * * 125769981 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCGCA 1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACA * * * * 125770030 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCGATAACTTCGATCACG 1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TTAGGTCACA * ** * 125770081 TGTGTAGTACTAAGTGCAGGCTACTATGTGTATCAGATGGTTAGGTCACG 1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACA * * * 125770131 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCGCA 1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACA * 125770180 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA 125770219 GCATTGGCTA Statistics Matches: 166, Mismatches: 21, Indels: 4 0.87 0.11 0.02 Matches are distributed among these distances: 49 79 0.48 50 47 0.28 51 40 0.24 ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29 Consensus pattern (50 bp): TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGGTCACA Found at i:125775258 original size:49 final size:49 Alignment explanation

Indices: 125775186--125775425 Score: 259 Period size: 49 Copynumber: 4.8 Consensus size: 49 125775176 TTTGAGGTCA * 125775186 CATGTGTAGTACTAAGTACAGGCTACTATGTGTACCAGATAATTAGTCG 1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGTCG ** * * * 125775235 CATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGATAACTTCGATCA 1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TTAG-TCG ** * * * ** 125775286 TGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTTAGGTCAG 1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTA-GTC-G * * * 125775337 -GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-GAATAATTGGTCG 1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAG-ATAATTAGTCG * * 125775385 CATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAGATA 1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA 125775426 GCTTTGGGTA Statistics Matches: 157, Mismatches: 27, Indels: 14 0.79 0.14 0.07 Matches are distributed among these distances: 48 1 0.01 49 76 0.48 50 45 0.29 51 35 0.22 ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30 Consensus pattern (49 bp): CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTAGTCG Found at i:125776971 original size:43 final size:44 Alignment explanation

Indices: 125776801--125776972 Score: 115 Period size: 43 Copynumber: 4.0 Consensus size: 44 125776791 ATATAGGATC * * * ** 125776801 CGATATGTG-TTTTCATGTAACACCACGTCTGGGTTGTTGGCAT 1 CGATATTTGATTTACATGTAAGACCACGTCTGGGACGTTGGCAT * * * * * * * 125776844 C-A-ACTTATGATTTACGTGTGAGACCATGTTTGGGACATCGACAT 1 CGATA-TT-TGATTTACATGTAAGACCACGTCTGGGACGTTGGCAT * ** * * 125776888 CG-CATTTGATTT-CATGTAAGACCTTGTCTGGTATAG-TGGCAT 1 CGATATTTGATTTACATGTAAGACCACGTCTGGGA-CGTTGGCAT 125776930 CGATATTTG-TTTACATGTAAGACCACGTCTGGGACGTTGGCAT 1 CGATATTTGATTTACATGTAAGACCACGTCTGGGACGTTGGCAT 125776973 TGTACGAGCT Statistics Matches: 94, Mismatches: 26, Indels: 18 0.68 0.19 0.13 Matches are distributed among these distances: 41 1 0.01 42 28 0.30 43 38 0.40 44 26 0.28 45 1 0.01 ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35 Consensus pattern (44 bp): CGATATTTGATTTACATGTAAGACCACGTCTGGGACGTTGGCAT Found at i:125779322 original size:48 final size:47 Alignment explanation

Indices: 125779250--125779576 Score: 334 Period size: 48 Copynumber: 6.9 Consensus size: 47 125779240 GTAAGATGTT * * * * * * 125779250 GATGCCATGTCCCAGACATAGTCTTACACTAGCTCTCTTATAAATTCC 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAAAGT-C * * * * * 125779298 AATGTCATGTTCCAAACATGGTCTTA-ACTGGCTCACATATCGAGGTC 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAT-AAAGTC * * * 125779345 GAT-CCTATGTACCAGACATGGTCTTACACTAGCTCTCATATAAATGTC 1 GATGCC-ATGTTCCAAACATGGTCTTACACTAGCTCACATATAAA-GTC * * * * 125779393 AATGCCATGTTCCAAACATGGTCTTGCACTAGCTCACATATCGAGGTC 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAT-AAAGTC * * * 125779441 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGGCC 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAT-AAAGTC * * * * * 125779489 GATGCCATGTACTAGACATGGTCTTACACTAGCTCTCATATAAATGCC 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAAA-GTC * 125779537 GATGCGATGTTCCAAACATGGTCTTACACTAGCTCACATA 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA 125779577 ACCCTAATAT Statistics Matches: 230, Mismatches: 42, Indels: 14 0.80 0.15 0.05 Matches are distributed among these distances: 46 1 0.00 47 35 0.15 48 191 0.83 49 3 0.01 ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29 Consensus pattern (47 bp): GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAAAGTC Found at i:125779481 original size:96 final size:95 Alignment explanation

Indices: 125779250--125779576 Score: 379 Period size: 96 Copynumber: 3.4 Consensus size: 95 125779240 GTAAGATGTT * * * * * * 125779250 GATGCCATGTCCCAGACATAGTCTTACACTAGCTCTCTTATAAAT-TCCAATGTCATGTTCCAAA 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAAATGT-CAATGCCATGTTCCAAA * * 125779314 CATGGTCTTAACTGGCTCACATATCGAGGTC 65 CATGGTCTTCACTAGCTCACATATCGAGGTC * * * 125779345 GAT-CCTATGTACCAGACATGGTCTTACACTAGCTCTCATATAAATGTCAATGCCATGTTCCAAA 1 GATGCC-ATGTTCCAAACATGGTCTTACACTAGCTCACATATAAATGTCAATGCCATGTTCCAAA 125779409 CATGGTCTTGCACTAGCTCACATATCGAGGTC 65 CATGGTCTT-CACTAGCTCACATATCGAGGTC * * * * * * * * 125779441 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGGCCGATGCCATGTACTAGAC 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAAATGTCAATGCCATGTTCCAAAC * ** * * 125779506 ATGGTCTTACACTAGCTCTCATATAAATGCC 66 ATGGTCTT-CACTAGCTCACATATCGAGGTC * 125779537 GATGCGATGTTCCAAACATGGTCTTACACTAGCTCACATA 1 GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA 125779577 ACCCTAATAT Statistics Matches: 203, Mismatches: 25, Indels: 7 0.86 0.11 0.03 Matches are distributed among these distances: 94 2 0.01 95 64 0.32 96 135 0.67 97 2 0.01 ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29 Consensus pattern (95 bp): GATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATAAATGTCAATGCCATGTTCCAAAC ATGGTCTTCACTAGCTCACATATCGAGGTC Found at i:125779524 original size:144 final size:143 Alignment explanation

Indices: 125779303--125779576 Score: 460 Period size: 144 Copynumber: 1.9 Consensus size: 143 125779293 ATTCCAATGT * * 125779303 CATGTTCCAAACATGGTCTTAACTGGCTCACATATCGAGGTCGATCCTATGTACCAGACATGGTC 1 CATGTTCCAAACATGGTCTTAACTGGCTCACATATCAAGGCCGATCCTATGTACCAGACATGGTC * * 125779368 TTACACTAGCTCTCATATAAATGTCAATGCCATGTTCCAAACATGGTCTTGCACTAGCTCACATA 66 TTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA 125779433 TCGAGGTCGATGC 131 TCGAGGTCGATGC * 125779446 CATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGGCCGATGCC-ATGTACTAGACATGG 1 CATGTTCCAAACATGGTCTTA-ACTGGCTCACATATCAAGGCCGAT-CCTATGTACCAGACATGG * * 125779510 TCTTACACTAGCTCTCATATAAATGCCGATGCGATGTTCCAAACATGGTCTTACACTAGCTCACA 64 TCTTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACA 125779575 TA 129 TA 125779577 ACCCTAATAT Statistics Matches: 122, Mismatches: 7, Indels: 3 0.92 0.05 0.02 Matches are distributed among these distances: 143 21 0.17 144 99 0.81 145 2 0.02 ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28 Consensus pattern (143 bp): CATGTTCCAAACATGGTCTTAACTGGCTCACATATCAAGGCCGATCCTATGTACCAGACATGGTC TTACACTAGCTCTCATATAAATGCCAATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATA TCGAGGTCGATGC Found at i:125780270 original size:51 final size:51 Alignment explanation

Indices: 125780210--125780320 Score: 213 Period size: 51 Copynumber: 2.2 Consensus size: 51 125780200 CATGGCAAAA 125780210 CCCTAAAGTTTCAACCATTTGCAAAAATAACTCTCCCATTCCTACAAGGGT 1 CCCTAAAGTTTCAACCATTTGCAAAAATAACTCTCCCATTCCTACAAGGGT 125780261 CCCTAAAGTTTCAACCATTTGCAAAAATAACTCTCCCATTCCTACAAGGGT 1 CCCTAAAGTTTCAACCATTTGCAAAAATAACTCTCCCATTCCTACAAGGGT * 125780312 CCCAAAAGT 1 CCCTAAAGT 125780321 ACAAAAATTA Statistics Matches: 59, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 51 59 1.00 ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26 Consensus pattern (51 bp): CCCTAAAGTTTCAACCATTTGCAAAAATAACTCTCCCATTCCTACAAGGGT Found at i:125786127 original size:24 final size:24 Alignment explanation

Indices: 125786091--125786204 Score: 203 Period size: 24 Copynumber: 4.8 Consensus size: 24 125786081 CTTATTATGT ** 125786091 TCGCAC-CATAGTGCCATAGCGAA 1 TCGCACACATAGTGCCATAGTAAA 125786114 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125786138 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125786162 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125786186 TCGCACACATAGTGCCATA 1 TCGCACACATAGTGCCATA 125786205 TATTTCCAGC Statistics Matches: 88, Mismatches: 2, Indels: 1 0.97 0.02 0.01 Matches are distributed among these distances: 23 6 0.07 24 82 0.93 ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20 Consensus pattern (24 bp): TCGCACACATAGTGCCATAGTAAA Found at i:125789785 original size:24 final size:24 Alignment explanation

Indices: 125789749--125789886 Score: 251 Period size: 24 Copynumber: 5.8 Consensus size: 24 125789739 CTTATTATGT ** 125789749 TCGCAC-CATAGTGCCATAGCGAA 1 TCGCACACATAGTGCCATAGTAAA 125789772 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125789796 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125789820 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125789844 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125789868 TCGCACACATAGTGCCATA 1 TCGCACACATAGTGCCATA 125789887 TATTTCCAGC Statistics Matches: 112, Mismatches: 2, Indels: 1 0.97 0.02 0.01 Matches are distributed among these distances: 23 6 0.05 24 106 0.95 ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20 Consensus pattern (24 bp): TCGCACACATAGTGCCATAGTAAA Found at i:125789927 original size:28 final size:29 Alignment explanation

Indices: 125789869--125789941 Score: 130 Period size: 28 Copynumber: 2.6 Consensus size: 29 125789859 CATAGTAAAT * 125789869 CGCACACATAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 125789898 CGCACACTTAGTGCCAT-TATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 125789926 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 125789942 ATCTCGTCAC Statistics Matches: 43, Mismatches: 1, Indels: 1 0.96 0.02 0.02 Matches are distributed among these distances: 28 27 0.63 29 16 0.37 ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:125793495 original size:24 final size:24 Alignment explanation

Indices: 125793459--125793572 Score: 203 Period size: 24 Copynumber: 4.8 Consensus size: 24 125793449 CTTATTATGT ** 125793459 TCGCAC-CATAGTGCCATAGCGAA 1 TCGCACACATAGTGCCATAGTAAA 125793482 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125793506 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125793530 TCGCACACATAGTGCCATAGTAAA 1 TCGCACACATAGTGCCATAGTAAA 125793554 TCGCACACATAGTGCCATA 1 TCGCACACATAGTGCCATA 125793573 TATTTCCAGC Statistics Matches: 88, Mismatches: 2, Indels: 1 0.97 0.02 0.01 Matches are distributed among these distances: 23 6 0.07 24 82 0.93 ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20 Consensus pattern (24 bp): TCGCACACATAGTGCCATAGTAAA Found at i:125793597 original size:29 final size:29 Alignment explanation

Indices: 125793555--125793628 Score: 139 Period size: 29 Copynumber: 2.6 Consensus size: 29 125793545 CATAGTAAAT * 125793555 CGCACACATAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 125793584 CGCACACTTAGTGCCATATATTTCCAGCA 1 CGCACACTTAGTGCCATATATTTCCAGCA 125793613 CGCACACTTAGTGCCA 1 CGCACACTTAGTGCCA 125793629 ATCTCGTCAC Statistics Matches: 44, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 29 44 1.00 ACGTcount: A:0.28, C:0.32, G:0.15, T:0.24 Consensus pattern (29 bp): CGCACACTTAGTGCCATATATTTCCAGCA Found at i:125795239 original size:29 final size:29 Alignment explanation

Indices: 125795214--125795336 Score: 237 Period size: 29 Copynumber: 4.2 Consensus size: 29 125795204 TCCCACACCC * 125795214 AGTGCCGTATATTTCCAGCATGCACACTT 1 AGTGCCATATATTTCCAGCATGCACACTT 125795243 AGTGCCATATATTTCCAGCATGCACACTT 1 AGTGCCATATATTTCCAGCATGCACACTT 125795272 AGTGCCATATATTTCCAGCATGCACACTT 1 AGTGCCATATATTTCCAGCATGCACACTT 125795301 AGTGCCATATATTTCCAGCATGCACACTT 1 AGTGCCATATATTTCCAGCATGCACACTT 125795330 AGTGCCA 1 AGTGCCA 125795337 ATCTCGTCAC Statistics Matches: 93, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 29 93 1.00 ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30 Consensus pattern (29 bp): AGTGCCATATATTTCCAGCATGCACACTT Found at i:125803360 original size:29 final size:29 Alignment explanation

Indices: 125803261--125803448 Score: 238 Period size: 29 Copynumber: 6.5 Consensus size: 29 125803251 ACTCGATTTC * * ** 125803261 GCACACTTAGTGCCATGTGATTT-AAGCCC 1 GCACACTTAGTGCCATAT-ATTTCCAGCAT * *** * 125803290 GCACACATAGTGCCATACCCTTCGAGC-T 1 GCACACTTAGTGCCATATATTTCCAGCAT * * 125803318 CGCACAC-CAGTGCCGTATATTTCCAGCAT 1 -GCACACTTAGTGCCATATATTTCCAGCAT 125803347 GCACACTTAGTGCCATATATTTCCAGCAT 1 GCACACTTAGTGCCATATATTTCCAGCAT 125803376 GCACACTTAGTGCCATATATTTCCAGCAT 1 GCACACTTAGTGCCATATATTTCCAGCAT 125803405 GCACACTTAGTGCCATATATTTCCAGCAT 1 GCACACTTAGTGCCATATATTTCCAGCAT 125803434 GCACACTTAGTGCCA 1 GCACACTTAGTGCCA 125803449 ATCTCGTCAC Statistics Matches: 140, Mismatches: 15, Indels: 8 0.86 0.09 0.05 Matches are distributed among these distances: 28 22 0.16 29 118 0.84 ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27 Consensus pattern (29 bp): GCACACTTAGTGCCATATATTTCCAGCAT Found at i:125804931 original size:14 final size:14 Alignment explanation

Indices: 125804912--125804943 Score: 64 Period size: 14 Copynumber: 2.3 Consensus size: 14 125804902 TGCACTAATA 125804912 AGCCATTTAAAATT 1 AGCCATTTAAAATT 125804926 AGCCATTTAAAATT 1 AGCCATTTAAAATT 125804940 AGCC 1 AGCC 125804944 TATCATATTT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31 Consensus pattern (14 bp): AGCCATTTAAAATT Found at i:125806044 original size:29 final size:29 Alignment explanation

Indices: 125806011--125806069 Score: 109 Period size: 29 Copynumber: 2.0 Consensus size: 29 125806001 AATAAATCAT 125806011 TTGTAATACAGATTTTCAAATACTGAGCA 1 TTGTAATACAGATTTTCAAATACTGAGCA * 125806040 TTGTAATACAGATTTTCAAATGCTGAGCA 1 TTGTAATACAGATTTTCAAATACTGAGCA 125806069 T 1 T 125806070 ACTCTAGATC Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36 Consensus pattern (29 bp): TTGTAATACAGATTTTCAAATACTGAGCA Found at i:125811312 original size:48 final size:48 Alignment explanation

Indices: 125811247--125811403 Score: 188 Period size: 48 Copynumber: 3.3 Consensus size: 48 125811237 AGTTATGTGT * 125811247 GAGCCAGTGTAGGACCATGTTTGGAACATGGCATCGGCATTATTATGA 1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGA * * * * * * * 125811295 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGC 1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGA * * * * * 125811343 GAGCCAGTGTAAGACCATGTTTGAAACATGGCACCAGCATTGTTACGA 1 GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGA * 125811391 GAGCTAGTGTAAG 1 GAGCCAGTGTAAG 125811404 TGTGACAGCC Statistics Matches: 88, Mismatches: 21, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 48 88 1.00 ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24 Consensus pattern (48 bp): GAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTATTATGA Found at i:125813187 original size:39 final size:40 Alignment explanation

Indices: 125813132--125813302 Score: 233 Period size: 39 Copynumber: 4.3 Consensus size: 40 125813122 GGACTAAGAT * * 125813132 CCGAAGGCGTTCGTGCGAGTTAATAAATCCGGGTTAAG-C 1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC 125813171 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAG-C 1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC * * 125813210 CCGAAGGCATTTGTGCGAGTTACTAAACCCGGGTTAAGTC 1 CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC * * * 125813250 CCGAAGGCATTCGTGCGAGTTACTATAA-CCGGGGTT-TGTC 1 CCGAAGGCATTTGTGCGAGTTAATA-AATCC-GGGTTAAGTC 125813290 CCGAAGGCATTTG 1 CCGAAGGCATTTG 125813303 AGCTAGTCGT Statistics Matches: 122, Mismatches: 7, Indels: 5 0.91 0.05 0.04 Matches are distributed among these distances: 39 73 0.60 40 42 0.34 41 7 0.06 ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25 Consensus pattern (40 bp): CCGAAGGCATTTGTGCGAGTTAATAAATCCGGGTTAAGTC Found at i:125822404 original size:68 final size:70 Alignment explanation

Indices: 125822332--125822529 Score: 294 Period size: 71 Copynumber: 2.8 Consensus size: 70 125822322 ACACCCTGTA * * * * 125822332 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG 1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG 125822394 ATAAAT 65 ATAAAT * 125822400 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG 1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG 125822465 ATAAAT 65 ATAAAT * 125822471 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG 1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG 125822530 AGACAAATCG Statistics Matches: 121, Mismatches: 5, Indels: 5 0.92 0.04 0.04 Matches are distributed among these distances: 68 24 0.20 69 3 0.02 70 1 0.01 71 93 0.77 ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20 Consensus pattern (70 bp): GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA TAAAT Found at i:125822443 original size:41 final size:41 Alignment explanation

Indices: 125822398--125822515 Score: 98 Period size: 41 Copynumber: 3.1 Consensus size: 41 125822388 TGAAAGATAA 125822398 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC * * * * * 125822439 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A 1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 125822469 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 125822510 ATGTAG 1 ATGTAG 125822516 ACAAGAGAGC Statistics Matches: 54, Mismatches: 10, Indels: 26 0.60 0.11 0.29 Matches are distributed among these distances: 29 1 0.02 30 8 0.15 31 9 0.17 32 1 0.02 33 3 0.06 34 1 0.02 35 1 0.02 36 1 0.02 37 1 0.02 38 3 0.06 39 1 0.02 40 9 0.17 41 14 0.26 42 1 0.02 ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21 Consensus pattern (41 bp): ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC Found at i:125822455 original size:71 final size:71 Alignment explanation

Indices: 125822366--125822529 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 125822356 GAGATGTATC 125822366 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 125822431 AGGACA 66 AGGACA 125822437 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 125822502 AGGACA 66 AGGACA 125822508 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 125822530 AGACAAATCG Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA AGGACA Found at i:125829970 original size:68 final size:70 Alignment explanation

Indices: 125829898--125830095 Score: 294 Period size: 71 Copynumber: 2.8 Consensus size: 70 125829888 ACACCCTGTA * * * 125829898 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG 1 GTAGCTAGGTCACATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG 125829960 ATAAAT 65 ATAAAT * * 125829966 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG 1 GTAGCTAGGTCACATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG 125830031 ATAAAT 65 ATAAAT * 125830037 GTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG 1 GTAGCTAGGTCACATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG 125830096 AGACAAATCG Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 24 0.20 69 3 0.03 70 1 0.01 71 92 0.77 ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20 Consensus pattern (70 bp): GTAGCTAGGTCACATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA TAAAT Found at i:125830021 original size:71 final size:71 Alignment explanation

Indices: 125829932--125830095 Score: 319 Period size: 71 Copynumber: 2.3 Consensus size: 71 125829922 GAGATGTATC * 125829932 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA 125829997 AGGACA 66 AGGACA 125830003 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA 125830068 AGGACA 66 AGGACA 125830074 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 125830096 AGACAAATCG Statistics Matches: 92, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 71 92 1.00 ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGA AGGACA Found at i:125843310 original size:43 final size:44 Alignment explanation

Indices: 125843244--125843370 Score: 118 Period size: 45 Copynumber: 2.9 Consensus size: 44 125843234 TTTTCTCAAA * * * * 125843244 TCACCAGCATT-TCGCCTGTTAGGCTC-GAGGCCCGATATCAG-T- 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGA-AT-AGATC 125843286 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAG-ATC ** * * * 125843331 TCACCGGCATTATAGTTTGCCAAGCTCAAAGGCCCAAATA 1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA 125843371 ATCAAGTCAA Statistics Matches: 71, Mismatches: 9, Indels: 7 0.82 0.10 0.08 Matches are distributed among these distances: 42 12 0.17 43 15 0.21 44 9 0.13 45 35 0.49 ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24 Consensus pattern (44 bp): TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGATC Found at i:125843752 original size:43 final size:43 Alignment explanation

Indices: 125843700--125843897 Score: 342 Period size: 43 Copynumber: 4.6 Consensus size: 43 125843690 CCGGCATTAC * 125843700 GCCTGCTAGGCACGAAGGCCTGAATACACATCACCGGCACGAA 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA * * * 125843743 GCCTACTAGGTACGAAGGCCCGAATACACATCACCGACACGAA 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA * * 125843786 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACTAA 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA 125843829 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA 125843872 GCCTGCTAGGCACGAAGGCCCGAATA 1 GCCTGCTAGGCACGAAGGCCCGAATA 125843898 TAATACCAGC Statistics Matches: 144, Mismatches: 11, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 144 1.00 ACGTcount: A:0.31, C:0.33, G:0.25, T:0.12 Consensus pattern (43 bp): GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA Found at i:125843941 original size:86 final size:86 Alignment explanation

Indices: 125843700--125843921 Score: 322 Period size: 86 Copynumber: 2.6 Consensus size: 86 125843690 CCGGCATTAC * * * * * * 125843700 GCCTGCTAGGCACGAAGGCCTGAATACACATCACCGGCACGAAGCCTACTAGGTACGAAGGCCCG 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAAGCCTGCGAGGCACGAAGGCCCG 125843765 AATACACATCACCGACACGAA 66 AATACACATCACCGACACGAA * * * 125843786 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACTAAGCCTGCTAGGCACGAAGGCCCG 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAAGCCTGCGAGGCACGAAGGCCCG * 125843851 AATACACATCACCGGCACGAA 66 AATACACATCACCGACACGAA * * 125843872 GCCTGCTAGGCACGAAGGCCCGAATATA-AT-ACCAGCACTAGGCCTGCGAG 1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAAGCCTGCGAG 125843922 ATTTATCCCA Statistics Matches: 125, Mismatches: 11, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 84 16 0.13 85 2 0.02 86 107 0.86 ACGTcount: A:0.31, C:0.32, G:0.25, T:0.12 Consensus pattern (86 bp): GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACTAAGCCTGCGAGGCACGAAGGCCCG AATACACATCACCGACACGAA Found at i:125845920 original size:29 final size:29 Alignment explanation

Indices: 125845888--125845960 Score: 101 Period size: 29 Copynumber: 2.5 Consensus size: 29 125845878 CTTCGAGCTC * 125845888 GCACACCCAGTGCCGTATATTTCCAGCAT 1 GCACACCCAGTGCCATATATTTCCAGCAT ** 125845917 GCACACTTAGTGCCATATATTTCCAGCAT 1 GCACACCCAGTGCCATATATTTCCAGCAT ** 125845946 GCACACTTAGTGCCA 1 GCACACCCAGTGCCA 125845961 ATCTCGTCAC Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 29 41 1.00 ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26 Consensus pattern (29 bp): GCACACCCAGTGCCATATATTTCCAGCAT Found at i:125853965 original size:29 final size:29 Alignment explanation

Indices: 125853933--125854005 Score: 101 Period size: 29 Copynumber: 2.5 Consensus size: 29 125853923 CTTCGAGCTC * 125853933 GCACACCCAGTGCCGTATATTTCCAGCAT 1 GCACACCCAGTGCCATATATTTCCAGCAT ** 125853962 GCACACTTAGTGCCATATATTTCCAGCAT 1 GCACACCCAGTGCCATATATTTCCAGCAT ** 125853991 GCACACTTAGTGCCA 1 GCACACCCAGTGCCA 125854006 ATCTCGTCAC Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 29 41 1.00 ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26 Consensus pattern (29 bp): GCACACCCAGTGCCATATATTTCCAGCAT Found at i:125856341 original size:2 final size:2 Alignment explanation

Indices: 125856323--125856357 Score: 54 Period size: 2 Copynumber: 18.0 Consensus size: 2 125856313 CACTTTCAAA * 125856323 AT AT A- AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 125856358 TCGACTTTCA Statistics Matches: 30, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 1 1 0.03 2 29 0.97 ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46 Consensus pattern (2 bp): AT Found at i:125864792 original size:40 final size:39 Alignment explanation

Indices: 125864773--125864889 Score: 198 Period size: 40 Copynumber: 2.9 Consensus size: 39 125864763 CCGGATGTAG * 125864773 TACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAAT 1 TACCAGCACGAAGCCTGCGGGATTTAACCCGGATAT-AAT 125864813 TACCAGCACGAAGCCTGCGGGATTTAACCCGGATATACAT 1 TACCAGCACGAAGCCTGCGGGATTTAACCCGGATATA-AT * 125864853 TACCAGCACGAAGCCTGCGGGATTTAACCTGGATATA 1 TACCAGCACGAAGCCTGCGGGATTTAACCCGGATATA 125864890 TAATATATCG Statistics Matches: 74, Mismatches: 2, Indels: 2 0.95 0.03 0.03 Matches are distributed among these distances: 39 1 0.01 40 73 0.99 ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21 Consensus pattern (39 bp): TACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAAT Found at i:125870152 original size:40 final size:40 Alignment explanation

Indices: 125870108--125870224 Score: 171 Period size: 40 Copynumber: 2.9 Consensus size: 40 125870098 CCAGATATAG * * * 125870108 TACCAGCACTAAGCCTGTGGGATTTAACCCGGATATGCAT 1 TACCAGCACGAAGCCTGAGGGATTTAACCCGGATATACAT * 125870148 TACCAGCACGAAGCCTGCGGGATTTAACCCGGATATACAT 1 TACCAGCACGAAGCCTGAGGGATTTAACCCGGATATACAT * * * 125870188 TACCATCACGAAGCCTGAAGGATTTAACCCAGATATA 1 TACCAGCACGAAGCCTGAGGGATTTAACCCGGATATA 125870225 TAATATATCG Statistics Matches: 70, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 40 70 1.00 ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22 Consensus pattern (40 bp): TACCAGCACGAAGCCTGAGGGATTTAACCCGGATATACAT Found at i:125874068 original size:19 final size:20 Alignment explanation

Indices: 125874044--125874081 Score: 53 Period size: 19 Copynumber: 1.9 Consensus size: 20 125874034 GGTACCACCA 125874044 AAACAT-ATATCA-CATCTTT 1 AAACATCAT-TCATCATCTTT 125874063 AAACATCATTCATCATCTT 1 AAACATCATTCATCATCTT 125874082 ACCACCTTAT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 19 9 0.53 20 8 0.47 ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37 Consensus pattern (20 bp): AAACATCATTCATCATCTTT Found at i:125874421 original size:47 final size:46 Alignment explanation

Indices: 125874309--125874479 Score: 160 Period size: 47 Copynumber: 3.7 Consensus size: 46 125874299 TGCGCCTAAG * * * * 125874309 TGAACTCGGACTCAACTCAACAAGCTC-G--GCCGTTCGCATCCATAAA 1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCC---AA 125874355 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTC-A 1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATC-CAA * 125874402 TGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCATA 1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA-A * 125874446 GTGAACTCGGACTCAACTCAATGAGTTCGGATGC 1 -TGAACTCGGACTCAACTCAACGAGTTCGGATGC 125874480 TCAACCATCC Statistics Matches: 106, Mismatches: 6, Indels: 24 0.78 0.04 0.18 Matches are distributed among these distances: 42 3 0.03 43 5 0.05 44 2 0.02 45 29 0.27 46 25 0.24 47 32 0.30 49 3 0.03 50 4 0.04 51 3 0.03 ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23 Consensus pattern (46 bp): TGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCAA Found at i:125874438 original size:93 final size:92 Alignment explanation

Indices: 125874309--125874479 Score: 279 Period size: 93 Copynumber: 1.8 Consensus size: 92 125874299 TGCGCCTAAG * * 125874309 TGAACTCGGACTCAACTCAACAAGCTCGGCCGTTCGCATCCATAAATGAACTCGGACTCAACTCA 1 TGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCAT-AATGAACTCGGACTCAACTCA 125874374 ACGAGTTCGGATGCCTAGTTACATCTCA 65 ACGAGTTCGGATGCCTAGTTACATCTCA * * * 125874402 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAA 1 TGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAATGAACTCGGACTCAACTCAA * 125874467 TGAGTTCGGATGC 66 CGAGTTCGGATGC 125874480 TCAACCATCC Statistics Matches: 72, Mismatches: 6, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 92 33 0.46 93 39 0.54 ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23 Consensus pattern (92 bp): TGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAATGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCA Found at i:125874929 original size:30 final size:30 Alignment explanation

Indices: 125874893--125874954 Score: 90 Period size: 30 Copynumber: 2.1 Consensus size: 30 125874883 CAGCATTTAA 125874893 TAAAC-TTTGAAAAAATTACACTTTTGCCCC 1 TAAACTTTTG-AAAAATTACACTTTTGCCCC * * 125874923 TAAACTTTTGCATAATTACACTTTTGCCCC 1 TAAACTTTTGAAAAATTACACTTTTGCCCC 125874953 TA 1 TA 125874955 GGCTCGGGAA Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 30 25 0.86 31 4 0.14 ACGTcount: A:0.32, C:0.24, G:0.06, T:0.37 Consensus pattern (30 bp): TAAACTTTTGAAAAATTACACTTTTGCCCC Found at i:125882006 original size:92 final size:92 Alignment explanation

Indices: 125881849--125882017 Score: 295 Period size: 92 Copynumber: 1.8 Consensus size: 92 125881839 CGCCCTAAGT * 125881849 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAAC 1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAC 125881914 GAGTTCGGATGCCTAGTTACATCTCAC 66 GAGTTCGGATGCCTAGTTACATCTCAC * * 125881941 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAATGAACTCGGACTCAACTCAA 125882005 CGAGTTCGGATGC 65 CGAGTTCGGATGC 125882018 TCAACCATCC Statistics Matches: 73, Mismatches: 3, Indels: 2 0.94 0.04 0.03 Matches are distributed among these distances: 92 61 0.84 93 12 0.16 ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21 Consensus pattern (92 bp): GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAATGAACTCGGACTCAACTCAAC GAGTTCGGATGCCTAGTTACATCTCAC Found at i:125882014 original size:45 final size:46 Alignment explanation

Indices: 125881844--125882014 Score: 201 Period size: 45 Copynumber: 3.7 Consensus size: 46 125881834 TAACCCGCCC * * 125881844 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA * * 125881889 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C- 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA * * 125881937 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA 125881982 T-AGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 125882015 TGCTCAACCA Statistics Matches: 108, Mismatches: 8, Indels: 20 0.79 0.06 0.15 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 3 0.03 45 61 0.56 47 29 0.27 48 2 0.02 49 2 0.02 50 3 0.03 51 2 0.02 ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA Found at i:125883894 original size:27 final size:26 Alignment explanation

Indices: 125883856--125883964 Score: 121 Period size: 27 Copynumber: 4.1 Consensus size: 26 125883846 ATACTTTAGT * 125883856 TTACCAAAATACCACTGGTTTGTAAAA 1 TTACC-AAATACCCCTGGTTTGTAAAA * * * 125883883 TTACTAGAATACCCTTGGTTTATAAAA 1 TTACCA-AATACCCCTGGTTTGTAAAA * * 125883910 TCACCAAAATACCCCTGGTCTGT-AAA 1 TTACC-AAATACCCCTGGTTTGTAAAA * 125883936 TTACCAAAAACCCCTGGTTTGTAAAA 1 TTACCAAATACCCCTGGTTTGTAAAA 125883962 TTA 1 TTA 125883965 TCAATAATTG Statistics Matches: 67, Mismatches: 12, Indels: 7 0.78 0.14 0.08 Matches are distributed among these distances: 25 15 0.22 26 14 0.21 27 37 0.55 28 1 0.01 ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30 Consensus pattern (26 bp): TTACCAAATACCCCTGGTTTGTAAAA Found at i:125884015 original size:26 final size:25 Alignment explanation

Indices: 125883971--125884128 Score: 77 Period size: 26 Copynumber: 6.0 Consensus size: 25 125883961 ATTATCAATA 125883971 ATTGTAAAATTACCAAAATATCCCTG 1 ATTGTAAAATTACCAAAATA-CCCTG * ** 125883997 ATTGTGAAATTACTGAAATACCCTCG 1 ATTGTAAAATTACCAAAATACCCT-G * *** 125884023 ACCTGTAAAATT-TTGAAATACCCTG 1 A-TTGTAAAATTACCAAAATACCCTG * * 125884048 AACTTGTAGAATTACCAAAGTACCCTTG 1 -A-TTGTAAAATTACCAAAATACCC-TG * *** 125884076 ATT-TACAGCATTACCATTTTACCCTTG 1 ATTGTA-A-AATTACCAAAATACCC-TG ** 125884103 ACTTACAAAATTACCAAAATACCCTG 1 A-TTGTAAAATTACCAAAATACCCTG 125884129 TAGGGTAGAA Statistics Matches: 101, Mismatches: 22, Indels: 18 0.72 0.16 0.13 Matches are distributed among these distances: 25 7 0.07 26 44 0.44 27 44 0.44 28 5 0.05 29 1 0.01 ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31 Consensus pattern (25 bp): ATTGTAAAATTACCAAAATACCCTG Found at i:125884088 original size:27 final size:27 Alignment explanation

Indices: 125884057--125884127 Score: 79 Period size: 27 Copynumber: 2.6 Consensus size: 27 125884047 GAACTTGTAG * * * 125884057 AATTACCAAAGTACCCTTGATTTACAG 1 AATTACCAAAATACCCTTGACTTACAA * *** 125884084 CATTACCATTTTACCCTTGACTTACAA 1 AATTACCAAAATACCCTTGACTTACAA 125884111 AATTACCAAAATACCCT 1 AATTACCAAAATACCCT 125884128 GTAGGGTAGA Statistics Matches: 34, Mismatches: 10, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 27 34 1.00 ACGTcount: A:0.37, C:0.27, G:0.06, T:0.31 Consensus pattern (27 bp): AATTACCAAAATACCCTTGACTTACAA Found at i:125884149 original size:26 final size:26 Alignment explanation

Indices: 125884111--125884400 Score: 305 Period size: 26 Copynumber: 11.3 Consensus size: 26 125884101 TGACTTACAA ** 125884111 AATTACCAAAATACCCTGTAGGGTAG 1 AATTACCGGAATACCCTGTAGGGTAG 125884137 AATTACCGGAATACCCTGTAGGGTAG 1 AATTACCGGAATACCCTGTAGGGTAG 125884163 AATTACCGGAATACCCTTGTA-GGTAG 1 AATTACCGGAATACCC-TGTAGGGTAG 125884189 AATTACC-GAATATCCCTGTAGGGTAG 1 AATTACCGGAATA-CCCTGTAGGGTAG * * 125884215 AATTACCGGAATACCCCTATAAGGTAG 1 AATTACCGGAATA-CCCTGTAGGGTAG * 125884242 AATTACCAGAATACCCCTGTA-GGTAG 1 AATTACCGGAATA-CCCTGTAGGGTAG 125884268 AATTACCGGAATACCCTG-AGGGT-- 1 AATTACCGGAATACCCTGTAGGGTAG * 125884291 --TTACC-G-TTACCCTTGTAGGGTAG 1 AATTACCGGAATACCC-TGTAGGGTAG * 125884314 AATTACCGAAATACCCCTGTAGGGTAG 1 AATTACCGGAATA-CCCTGTAGGGTAG *** * 125884341 AATTACTAAAATACCCCTGTAGGGTGG 1 AATTACCGGAATA-CCCTGTAGGGTAG * * * 125884368 AATTACC-GAGATACCTTGTGGGGTAA 1 AATTACCGGA-ATACCCTGTAGGGTAG 125884394 AATTACC 1 AATTACC 125884401 ATTTTGCCCC Statistics Matches: 229, Mismatches: 20, Indels: 30 0.82 0.07 0.11 Matches are distributed among these distances: 19 5 0.02 20 3 0.01 21 10 0.04 24 1 0.00 25 22 0.10 26 101 0.44 27 84 0.37 28 3 0.01 ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25 Consensus pattern (26 bp): AATTACCGGAATACCCTGTAGGGTAG Found at i:125884382 original size:54 final size:53 Alignment explanation

Indices: 125884298--125884399 Score: 141 Period size: 54 Copynumber: 1.9 Consensus size: 53 125884288 GGTTTACCGT * * 125884298 TACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACTAAAA 1 TACCCCTGTAGGGTAGAATTACCGAAATA-CCCTGTAGGGTAAAATTACTAAAA * * * * 125884352 TACCCCTGTAGGGTGGAATTACCGAGATACCTTGTGGGGTAAAATTAC 1 TACCCCTGTAGGGTAGAATTACCGAAATACCCTGTAGGGTAAAATTAC 125884400 CATTTTGCCC Statistics Matches: 42, Mismatches: 6, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 53 16 0.38 54 26 0.62 ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26 Consensus pattern (53 bp): TACCCCTGTAGGGTAGAATTACCGAAATACCCTGTAGGGTAAAATTACTAAAA Found at i:125884871 original size:22 final size:22 Alignment explanation

Indices: 125884827--125884891 Score: 60 Period size: 22 Copynumber: 3.0 Consensus size: 22 125884817 TTAAAGCCTT * * ** 125884827 CTGATTATGGCTTTGTGTTAAC 1 CTGAATATGGCTCTGTGCCAAC 125884849 CT-ACATATGGCTCTGTGCCAAC 1 CTGA-ATATGGCTCTGTGCCAAC * * 125884871 CTGATTATGGCTGTGTGCCAA 1 CTGAATATGGCTCTGTGCCAA 125884892 ACGTATTTAC Statistics Matches: 35, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 21 1 0.03 22 33 0.94 23 1 0.03 ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35 Consensus pattern (22 bp): CTGAATATGGCTCTGTGCCAAC Found at i:125885292 original size:31 final size:31 Alignment explanation

Indices: 125885254--125885394 Score: 201 Period size: 31 Copynumber: 4.5 Consensus size: 31 125885244 TTGCATTCAC 125885254 ATTCTGATTTTGATTCTGTTACCTGATACTG 1 ATTCTGATTTTGATTCTGTTACCTGATACTG * * 125885285 ATTCTGATTTTGATTCTGTTACCTGATGCTA 1 ATTCTGATTTTGATTCTGTTACCTGATACTG * 125885316 ATTCTGATTTTGATTCGGTTACCTGATACTG 1 ATTCTGATTTTGATTCTGTTACCTGATACTG * * * * 125885347 ATTCTGATTCTGATTCTGTCACCTAATTCTG 1 ATTCTGATTTTGATTCTGTTACCTGATACTG * * 125885378 ATTCTGGTTCTGATTCT 1 ATTCTGATTTTGATTCT 125885395 AATTCTGATT Statistics Matches: 99, Mismatches: 11, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 31 99 1.00 ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48 Consensus pattern (31 bp): ATTCTGATTTTGATTCTGTTACCTGATACTG Found at i:125885293 original size:6 final size:6 Alignment explanation

Indices: 125885254--125885421 Score: 112 Period size: 6 Copynumber: 27.3 Consensus size: 6 125885244 TTGCATTCAC * * * 125885254 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG 1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG * * * * * 125885303 -TTACCTG ATGCTA ATTCTG ATTTTG ATTC-G GTTACCTG ATACTG ATTCTG 1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG * * * * 125885353 ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG GTTCTG ATTCTA ATTCTG 1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG 125885402 ATTCTG ATTCT- AGTTCTG AT 1 ATTCTG ATTCTG A-TTCTG AT 125885422 AATGTTTCTT Statistics Matches: 124, Mismatches: 24, Indels: 28 0.70 0.14 0.16 Matches are distributed among these distances: 5 9 0.07 6 100 0.81 7 10 0.08 8 5 0.04 ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48 Consensus pattern (6 bp): ATTCTG Found at i:125886611 original size:11 final size:10 Alignment explanation

Indices: 125886583--125886616 Score: 50 Period size: 10 Copynumber: 3.3 Consensus size: 10 125886573 AGCCTGTAAG 125886583 TATTCTGAAT 1 TATTCTGAAT * 125886593 TTTTCTGAAT 1 TATTCTGAAT 125886603 ATATTCTGAAT 1 -TATTCTGAAT 125886614 TAT 1 TAT 125886617 CTGTCTGTAC Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 10 12 0.57 11 9 0.43 ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53 Consensus pattern (10 bp): TATTCTGAAT Found at i:125893111 original size:28 final size:28 Alignment explanation

Indices: 125893071--125893131 Score: 104 Period size: 28 Copynumber: 2.2 Consensus size: 28 125893061 ACTAGAATAT * 125893071 CCCTATGTATGCAAAATTACCATTATAC 1 CCCTATGTATGCAAAATGACCATTATAC * 125893099 CCCTATGTATGCAAAATGACCTTTATAC 1 CCCTATGTATGCAAAATGACCATTATAC 125893127 CCCTA 1 CCCTA 125893132 GGGTTAATTT Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 28 31 1.00 ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31 Consensus pattern (28 bp): CCCTATGTATGCAAAATGACCATTATAC Found at i:125893278 original size:28 final size:27 Alignment explanation

Indices: 125893237--125893326 Score: 101 Period size: 28 Copynumber: 3.2 Consensus size: 27 125893227 AGGAAGTGTC * 125893237 CTGGTGGCTA-TGCCACAAATTATCTATT 1 CTGGTGGC-ACTGCCACAAA-TATCTGTT * ** 125893265 CTGGTGGCCCTGCCACGTATATCTGTT 1 CTGGTGGCACTGCCACAAATATCTGTT 125893292 CTGGTGGCACTGCCACAAAATATCTGTAT 1 CTGGTGGCACTGCCAC-AAATATCTGT-T 125893321 CTGGTG 1 CTGGTG 125893327 ACTCTGTCAC Statistics Matches: 52, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 27 22 0.42 28 23 0.44 29 7 0.13 ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32 Consensus pattern (27 bp): CTGGTGGCACTGCCACAAATATCTGTT Found at i:125893295 original size:27 final size:28 Alignment explanation

Indices: 125893237--125893326 Score: 103 Period size: 27 Copynumber: 3.2 Consensus size: 28 125893227 AGGAAGTGTC * * 125893237 CTGGTGGCTA-TGCCACAAATTATCTATT 1 CTGGTGGC-ACTGCCACAAAATATCTGTT * ** 125893265 CTGGTGGCCCTGCCAC-GTATATCTGTT 1 CTGGTGGCACTGCCACAAAATATCTGTT 125893292 CTGGTGGCACTGCCACAAAATATCTGTAT 1 CTGGTGGCACTGCCACAAAATATCTGT-T 125893321 CTGGTG 1 CTGGTG 125893327 ACTCTGTCAC Statistics Matches: 51, Mismatches: 8, Indels: 5 0.80 0.12 0.08 Matches are distributed among these distances: 27 22 0.43 28 22 0.43 29 7 0.14 ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32 Consensus pattern (28 bp): CTGGTGGCACTGCCACAAAATATCTGTT Found at i:125893337 original size:29 final size:28 Alignment explanation

Indices: 125893247--125893337 Score: 85 Period size: 27 Copynumber: 3.2 Consensus size: 28 125893237 CTGGTGGCTA * * * * 125893247 TGCCACAAATTATCTATTCTGGTGGCCC 1 TGCCACAAAATATCTGTTCTGGTGACAC ** * 125893275 TGCCAC-GTATATCTGTTCTGGTGGCAC 1 TGCCACAAAATATCTGTTCTGGTGACAC * 125893302 TGCCACAAAATATCTGTATCTGGTGACTC 1 TGCCACAAAATATCTGT-TCTGGTGACAC * 125893331 TGTCACA 1 TGCCACA 125893338 TTTTCTGTAT Statistics Matches: 51, Mismatches: 10, Indels: 3 0.80 0.16 0.05 Matches are distributed among these distances: 27 22 0.43 28 14 0.27 29 15 0.29 ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32 Consensus pattern (28 bp): TGCCACAAAATATCTGTTCTGGTGACAC Found at i:125893345 original size:55 final size:56 Alignment explanation

Indices: 125893237--125893351 Score: 128 Period size: 55 Copynumber: 2.1 Consensus size: 56 125893227 AGGAAGTGTC * * * 125893237 CTGGTGGCTATGCCACAAATTATCTATTCTGGTGGCCCTGCCACGTATATCTGT-T 1 CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT * * * * 125893292 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT 1 CTGGTGGCTA-TGCCACAAAATATCTAT-TCTGGTGACCCTGCCACATATATCTGTAT 125893348 CTGG 1 CTGG 125893352 CAGCCATGCT Statistics Matches: 50, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 54 1 0.02 55 29 0.58 56 20 0.40 ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35 Consensus pattern (56 bp): CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT Found at i:125912470 original size:14 final size:14 Alignment explanation

Indices: 125912448--125912477 Score: 51 Period size: 14 Copynumber: 2.1 Consensus size: 14 125912438 AAGAGAGAAT 125912448 GATGATGAATAAGG 1 GATGATGAATAAGG * 125912462 GATGCTGAATAAGG 1 GATGATGAATAAGG 125912476 GA 1 GA 125912478 ATGAAGGGGC Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.40, C:0.03, G:0.37, T:0.20 Consensus pattern (14 bp): GATGATGAATAAGG Found at i:125915611 original size:40 final size:40 Alignment explanation

Indices: 125915566--125915733 Score: 176 Period size: 40 Copynumber: 4.2 Consensus size: 40 125915556 CGGAATATAA 125915566 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC * ** * * 125915606 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 125915646 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC *** * * * * * 125915686 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC 125915726 CCGGATAT 1 CCGGATAT 125915734 CATTCAATTT Statistics Matches: 106, Mismatches: 21, Indels: 2 0.82 0.16 0.02 Matches are distributed among these distances: 39 1 0.01 40 105 0.99 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (40 bp): CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:125915716 original size:80 final size:80 Alignment explanation

Indices: 125915566--125915733 Score: 207 Period size: 80 Copynumber: 2.1 Consensus size: 80 125915556 CGGAATATAA * 125915566 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG 1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG * 125915631 CCTTCGGGTCTTAGC 66 CCTTCGGGGCTTAGC * * * ** * 125915646 CCGGATATAGCCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA 1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA * 125915708 TTGTCTTCGGGGCTTAGC 64 -TGCCTTCGGGGCTTAGC 125915726 CCGGATAT 1 CCGGATAT 125915734 CATTCAATTT Statistics Matches: 76, Mismatches: 9, Indels: 6 0.84 0.10 0.07 Matches are distributed among these distances: 79 4 0.05 80 72 0.95 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (80 bp): CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG CCTTCGGGGCTTAGC Found at i:125923714 original size:40 final size:40 Alignment explanation

Indices: 125923577--125923736 Score: 164 Period size: 40 Copynumber: 4.0 Consensus size: 40 125923567 ATAACCGGAT * * 125923577 ATAACCAGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGA 1 ATAACCA--GCACAATTGCCTTCGGGTCTTAGCCCGGATATA 125923619 ATAACTC-GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATA 1 ATAAC-CAGCAC-AATTGCCTTCGGGTCTTAGCCCGGATATA *** * * 125923659 GCCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATA 1 ATAACCAGCACAATTGCCTTCGGGTCTTAGCCCGGATATA ** * * 125923699 ATTTCCAGCATAATTGTCTTCGGG-CTTAGCCCGGATAT 1 ATAACCAGCACAATTGCCTTCGGGTCTTAGCCCGGATAT 125923737 CATTCAATTT Statistics Matches: 100, Mismatches: 14, Indels: 11 0.80 0.11 0.09 Matches are distributed among these distances: 39 15 0.15 40 77 0.77 41 2 0.02 42 5 0.05 43 1 0.01 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (40 bp): ATAACCAGCACAATTGCCTTCGGGTCTTAGCCCGGATATA Found at i:125923720 original size:80 final size:78 Alignment explanation

Indices: 125923571--125923736 Score: 201 Period size: 80 Copynumber: 2.1 Consensus size: 78 125923561 CGGAATATAA * * 125923571 CCGGATATAACCAGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGC 1 CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGC 125923636 CTTCGGGTCTTAGC 66 CTTCGGG-CTTAGC * * * ** * 125923650 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAAT 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA- * 125923713 TGTCTTCGGGCTTAGC 63 TGCCTTCGGGCTTAGC 125923729 CCGGATAT 1 CCGGATAT 125923737 CATTCAATTT Statistics Matches: 75, Mismatches: 9, Indels: 6 0.83 0.10 0.07 Matches are distributed among these distances: 79 30 0.40 80 45 0.60 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (78 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGC CTTCGGGCTTAGC Found at i:125927182 original size:12 final size:12 Alignment explanation

Indices: 125927165--125927191 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 125927155 CCTTAGCCAA 125927165 ATCTCCTTCTAG 1 ATCTCCTTCTAG 125927177 ATCTCCTTCTAG 1 ATCTCCTTCTAG 125927189 ATC 1 ATC 125927192 ATGGGCCGGC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.19, C:0.33, G:0.07, T:0.41 Consensus pattern (12 bp): ATCTCCTTCTAG Found at i:125932296 original size:46 final size:46 Alignment explanation

Indices: 125932246--125932418 Score: 194 Period size: 46 Copynumber: 3.7 Consensus size: 46 125932236 TTGAGCATCT 125932246 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC 1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC * * * 125932292 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC 1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCC * * 125932339 GAACTCGTTGAGATGAGTCCGAGTTCACTTATGGATGCGAACG-CC 1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC * * 125932384 TGAGCTCGTTGAGTTGAGTCCGAGTTCACGTATGG 1 -GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 125932419 GCGGGTTACA Statistics Matches: 106, Mismatches: 11, Indels: 20 0.77 0.08 0.15 Matches are distributed among these distances: 42 2 0.02 43 5 0.05 45 5 0.05 46 57 0.54 47 28 0.26 48 3 0.03 50 4 0.04 51 2 0.02 ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28 Consensus pattern (46 bp): GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC Found at i:125932399 original size:93 final size:93 Alignment explanation

Indices: 125932240--125932410 Score: 290 Period size: 93 Copynumber: 1.8 Consensus size: 93 125932230 GGATGGTTGA * * * 125932240 GCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGATGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT 125932305 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * 125932333 GCATCCGAACTCGTTGAGATGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG 1 GCATCCGAACTCGTTGAGATGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG 125932397 TTGAGTCCGAGTTC 65 TTGAGTCCGAGTTC 125932411 ACGTATGGGC Statistics Matches: 73, Mismatches: 4, Indels: 2 0.92 0.05 0.03 Matches are distributed among these distances: 92 2 0.03 93 71 0.97 ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGATGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:125943464 original size:40 final size:40 Alignment explanation

Indices: 125943399--125943605 Score: 316 Period size: 40 Copynumber: 5.3 Consensus size: 40 125943389 TCTTCGGAAT * ** * 125943399 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC * * * 125943438 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC 125943478 TTAGCCC-GATATAACAACTCGCACAAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC 125943517 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC 125943557 TTAGCCC-GATATAACAACTCGCAC-AATGCCTT-GGGTC 1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC 125943594 TTAGCCCGGATA 1 TTAGCCCGGATA 125943606 AATCAGCTTA Statistics Matches: 155, Mismatches: 10, Indels: 7 0.90 0.06 0.04 Matches are distributed among these distances: 37 12 0.08 38 12 0.08 39 57 0.37 40 74 0.48 ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23 Consensus pattern (40 bp): TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC Found at i:125943502 original size:79 final size:78 Alignment explanation

Indices: 125943399--125943605 Score: 326 Period size: 79 Copynumber: 2.6 Consensus size: 78 125943389 TCTTCGGAAT * * ** * * * 125943399 TTAGCCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA 1 TTAGCCCGATATAACAACTCGCACAA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACA 125943464 AATGCCTTCGGGTC 65 AATGCCTTCGGGTC 125943478 TTAGCCCGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACA 1 TTAGCCCGATATAACAACTCGCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACA 125943543 AATGCCTTCGGGTC 65 AATGCCTTCGGGTC 125943557 TTAGCCCGATATAACAACTCGCACAATGCCTT-GGGTCTTAGCCCGGATA 1 TTAGCCCGATATAACAACTCGCACAATGCCTTCGGGTCTTAGCCCGGATA 125943606 AATCAGCTTA Statistics Matches: 120, Mismatches: 7, Indels: 4 0.92 0.05 0.03 Matches are distributed among these distances: 77 17 0.14 78 8 0.07 79 93 0.77 80 2 0.02 ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23 Consensus pattern (78 bp): TTAGCCCGATATAACAACTCGCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACAA ATGCCTTCGGGTC Found at i:125957269 original size:29 final size:29 Alignment explanation

Indices: 125957236--125957367 Score: 201 Period size: 29 Copynumber: 4.6 Consensus size: 29 125957226 GTGACGAGAT 125957236 TGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA 125957265 TGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA * 125957294 TGGCACTAAGTGTGCGTGCTGGAAATATT 1 TGGCACTAAGTGTGCGTGCTGGAAATATA ** * 125957323 TGGCACTAAGTGTGCAAGCTGGAAAAATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA * ** 125957352 CGGCACTGGGTGTGCG 1 TGGCACTAAGTGTGCG 125957368 AGTTCGGAGG Statistics Matches: 94, Mismatches: 9, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 29 94 1.00 ACGTcount: A:0.27, C:0.15, G:0.33, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCGTGCTGGAAATATA Found at i:125963057 original size:28 final size:28 Alignment explanation

Indices: 125962988--125963088 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 125962978 GACAAGATTG * * * * 125962988 GCACTAAGTGTGCGGGTTTAAAATTGTACA 1 GCACTAAGTGTGCGAGTTT--GATTATATA 125963018 GCACTAAGTGTGCGAGTTTGATTATATA 1 GCACTAAGTGTGCGAGTTTGATTATATA * 125963046 GCACTAAGTGTGCGAG-TTGAATACATATA 1 GCACTAAGTGTGCGAGTTTG-AT-TATATA 125963075 GCACTAAGTGTGCG 1 GCACTAAGTGTGCG 125963089 GATTCACTAT Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 3 0.05 28 24 0.38 29 19 0.30 30 18 0.28 ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30 Consensus pattern (28 bp): GCACTAAGTGTGCGAGTTTGATTATATA Found at i:125972845 original size:42 final size:45 Alignment explanation

Indices: 125972767--125972888 Score: 110 Period size: 45 Copynumber: 2.8 Consensus size: 45 125972757 CTCAAATCAC * * * 125972767 CGGCATT-TCGCCTGTTAGGCTCGAGGCCCGATATTAGT-T-T-AT 1 CGGCATTATAGCCTGCTAGGCTCGAGGCCCGA-ATTAGTATCTCAG * 125972809 CGGCATTATAGCCTGCTAGGCTTGAAGGCCCG-ATTAGTATCTCAG 1 CGGCATTATAGCCTGCTAGGCTCG-AGGCCCGAATTAGTATCTCAG ** * * 125972854 CGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAAT 1 CGGCATTATAGCCTGCTAGGCTC-GAGGCCCGAAT 125972889 AATCAAGTCA Statistics Matches: 64, Mismatches: 9, Indels: 10 0.77 0.11 0.12 Matches are distributed among these distances: 42 13 0.20 43 14 0.22 44 8 0.12 45 27 0.42 46 2 0.03 ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29 Consensus pattern (45 bp): CGGCATTATAGCCTGCTAGGCTCGAGGCCCGAATTAGTATCTCAG Done.