Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold1154

Parameters: 2 7 7 80 10 50 500

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

Length: 1159333
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30

Warning! 97731 characters in sequence are not A, C, G, or T


File 2 of 3

Found at i:8746 original size:199 final size:198

Alignment explanation

Indices: 8406--8802 Score: 785 Period size: 199 Copynumber: 2.0 Consensus size: 198 8396 AAGGCAGAAA 8406 AATTGAGATACAGCGTATTTGGATAATTTTGAAATCTATATTTGAAAGGTGCTCTTTGATTTTTG 1 AATTGAGATACAGCGTATTTGGATAATTTTGAAATCTATATTTGAAAGGTGCTCTTTGATTTTTG 8471 TACAATCTAGCATGTTATCATTCAAAATGAGTAACTTGTGTCCCGTTCATGGTAAAGACCTGAAA 66 TACAATCTAGCATGTTATCATTCAAAATGAGTAACTTGTGTCCCGTTCATGGTAAAGACCTGAAA 8536 GTTAAAGACAACTAGGTCATATCAGAAGGTCAAAGGTAAAATATAATGATTTTTTTTTTCAATTT 131 GTTAAAGACAACTAGGTCATATCAGAAGGTCAAAGGTAAAATATAATGATTTTTTTTTTCAATTT 8601 TCG 196 TCG 8604 NAATTGAGATACAGCGTATTTGGATAATTTTGAAATCTATATTTGAAAGGTGCTCTTTGATTTTT 1 -AATTGAGATACAGCGTATTTGGATAATTTTGAAATCTATATTTGAAAGGTGCTCTTTGATTTTT 8669 GTACAATCTAGCATGTTATCATTCAAAATGAGTAACTTGTGTCCCGTTCATGGTAAAGACCTGAA 65 GTACAATCTAGCATGTTATCATTCAAAATGAGTAACTTGTGTCCCGTTCATGGTAAAGACCTGAA 8734 AGTTAAAGACAACTAGGTCATATCAGAAGGTCAAAGGTAAAATATAATGATTTTTTTTTTCAATT 130 AGTTAAAGACAACTAGGTCATATCAGAAGGTCAAAGGTAAAATATAATGATTTTTTTTTTCAATT 8799 TTCG 195 TTCG 8803 CTTCCATCAA Statistics Matches: 198, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 199 198 1.00 ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37 Consensus pattern (198 bp): AATTGAGATACAGCGTATTTGGATAATTTTGAAATCTATATTTGAAAGGTGCTCTTTGATTTTTG TACAATCTAGCATGTTATCATTCAAAATGAGTAACTTGTGTCCCGTTCATGGTAAAGACCTGAAA GTTAAAGACAACTAGGTCATATCAGAAGGTCAAAGGTAAAATATAATGATTTTTTTTTTCAATTT TCG Found at i:9147 original size:11 final size:11 Alignment explanation

Indices: 9127--9167 Score: 50 Period size: 11 Copynumber: 3.7 Consensus size: 11 9117 ATACATGTGG 9127 AAAAAA-AATA 1 AAAAAATAATA 9137 AAAAAATAATA 1 AAAAAATAATA 9148 AAATAAATAA-A 1 AAA-AAATAATA 9159 AATAAAATA 1 AA-AAAATA 9168 CATACCGTTT Statistics Matches: 28, Mismatches: 0, Indels: 5 0.85 0.00 0.15 Matches are distributed among these distances: 10 6 0.21 11 15 0.54 12 7 0.25 ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17 Consensus pattern (11 bp): AAAAAATAATA Found at i:10166 original size:2 final size:2 Alignment explanation

Indices: 10159--10186 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 10149 NNNNNGGTAA 10159 AT AT AT 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 10187 GTGTGTGTTC Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:14326 original size:2 final size:2 Alignment explanation

Indices: 14319--14349 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 14309 TCAACTCAGC 14319 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 14350 CGAGCGCTTA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:18905 original size:12 final size:12 Alignment explanation

Indices: 18888--18912 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 18878 TTTTCATGTA 18888 AAAAAAAAAATC 1 AAAAAAAAAATC 18900 AAAAAAAAAATC 1 AAAAAAAAAATC 18912 A 1 A 18913 GATTATACAC Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08 Consensus pattern (12 bp): AAAAAAAAAATC Found at i:19770 original size:23 final size:23 Alignment explanation

Indices: 19744--19835 Score: 132 Period size: 23 Copynumber: 4.0 Consensus size: 23 19734 TTCTTTGTGC * 19744 TAAATAATCATTATTATATCATA 1 TAAATAATCATTATCATATCATA * * 19767 TAAATAATCATTATCATGTCAAA 1 TAAATAATCATTATCATATCATA * 19790 TAAATAATCATTATCATGTC-TAA 1 TAAATAATCATTATCATATCAT-A 19813 TAAATAATCATTATCATATCATA 1 TAAATAATCATTATCATATCATA 19836 AAAAGACGAC Statistics Matches: 62, Mismatches: 5, Indels: 4 0.87 0.07 0.06 Matches are distributed among these distances: 23 61 0.98 24 1 0.02 ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39 Consensus pattern (23 bp): TAAATAATCATTATCATATCATA Found at i:23549 original size:2 final size:2 Alignment explanation

Indices: 23542--23590 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 23532 CAGTGTACTC 23542 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 23584 CT CT CT C 1 CT CT CT C 23591 GTTAAATCAT Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:26730 original size:28 final size:28 Alignment explanation

Indices: 26690--26744 Score: 110 Period size: 28 Copynumber: 2.0 Consensus size: 28 26680 GAGGAATCTT 26690 TGATTAAGGAGTGATACTTGATAAGTAG 1 TGATTAAGGAGTGATACTTGATAAGTAG 26718 TGATTAAGGAGTGATACTTGATAAGTA 1 TGATTAAGGAGTGATACTTGATAAGTA 26745 TCTGCTATTT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 27 1.00 ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33 Consensus pattern (28 bp): TGATTAAGGAGTGATACTTGATAAGTAG Found at i:29759 original size:12 final size:12 Alignment explanation

Indices: 29742--29780 Score: 69 Period size: 12 Copynumber: 3.2 Consensus size: 12 29732 AAAATCAAGG 29742 ATATTGAATATT 1 ATATTGAATATT 29754 ATATTGAATATT 1 ATATTGAATATT * 29766 ATACTGAATATT 1 ATATTGAATATT 29778 ATA 1 ATA 29781 AGCGCTCTTT Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 12 26 1.00 ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46 Consensus pattern (12 bp): ATATTGAATATT Found at i:32161 original size:13 final size:13 Alignment explanation

Indices: 32143--32167 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 32133 TATTAACCTA 32143 GTTTTTTTTTTTT 1 GTTTTTTTTTTTT 32156 GTTTTTTTTTTT 1 GTTTTTTTTTTT 32168 ACAGAAACTG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92 Consensus pattern (13 bp): GTTTTTTTTTTTT Found at i:54875 original size:31 final size:29 Alignment explanation

Indices: 54823--54889 Score: 82 Period size: 31 Copynumber: 2.2 Consensus size: 29 54813 TACTGTGCAC * 54823 TTTTTAAATTTAAATGAAACATA-TCTTG 1 TTTTTAAATTTAAAAGAAACATATTCTTG * 54851 TTTTGTAAATGTTAAAAGACAACATATTCTTT 1 TTTT-TAAAT-TTAAAAGA-AACATATTCTTG 54883 TTTTTAA 1 TTTTTAA 54890 TTTTTCAAAC Statistics Matches: 33, Mismatches: 2, Indels: 5 0.82 0.05 0.12 Matches are distributed among these distances: 28 4 0.12 29 5 0.15 30 7 0.21 31 9 0.27 32 8 0.24 ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48 Consensus pattern (29 bp): TTTTTAAATTTAAAAGAAACATATTCTTG Found at i:54883 original size:29 final size:27 Alignment explanation

Indices: 54822--54884 Score: 65 Period size: 29 Copynumber: 2.2 Consensus size: 27 54812 TTACTGTGCA * 54822 CTTTTTAAATTTAAATGAAACATATCTT 1 CTTTTTAAATTTAAAAGAAACATA-CTT * 54850 GTTTTGTAAATGTTAAAAGACAACATA-TT 1 CTTTT-TAAAT-TTAAAAGA-AACATACTT 54879 CTTTTT 1 CTTTTT 54885 TTTAATTTTT Statistics Matches: 29, Mismatches: 3, Indels: 6 0.76 0.08 0.16 Matches are distributed among these distances: 28 5 0.17 29 11 0.38 30 7 0.24 31 6 0.21 ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46 Consensus pattern (27 bp): CTTTTTAAATTTAAAAGAAACATACTT Found at i:55366 original size:13 final size:13 Alignment explanation

Indices: 55348--55374 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 55338 AAAACCTTGC 55348 TATTTTACATAAT 1 TATTTTACATAAT 55361 TATTTTACATAAT 1 TATTTTACATAAT 55374 T 1 T 55375 TGAATTATAC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56 Consensus pattern (13 bp): TATTTTACATAAT Found at i:60775 original size:2 final size:2 Alignment explanation

Indices: 60768--60813 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 60758 NNNNNNNNNN 60768 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 60810 CT CT 1 CT CT 60814 GTTATTCGTT Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:76155 original size:21 final size:21 Alignment explanation

Indices: 76131--76210 Score: 133 Period size: 21 Copynumber: 3.8 Consensus size: 21 76121 CTTTTAAATT 76131 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA 76152 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA 76173 TCTCATAGCATAGCATACAAA 1 TCTCATAGCATAGCATACAAA * * * 76194 TCCCATACCATATCATA 1 TCTCATAGCATAGCATA 76211 GCATAAAATT Statistics Matches: 56, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 56 1.00 ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25 Consensus pattern (21 bp): TCTCATAGCATAGCATACAAA Found at i:76205 original size:26 final size:24 Alignment explanation

Indices: 76134--76219 Score: 96 Period size: 21 Copynumber: 3.8 Consensus size: 24 76124 TTAAATTTCT 76134 CATAGCATAGCATACAAAT-C-T- 1 CATAGCATAGCATACAAATCCATA 76155 CATAGCATAGCATACAAAT-C-T- 1 CATAGCATAGCATACAAATCCATA 76176 CATAGCATAGCATACAAATCCCATA 1 CATAGCATAGCATACAAAT-CCATA * 76201 CCATATCATAGCATA-AAAT 1 -CATAGCATAGCATACAAAT 76220 TGTAAAAGAT Statistics Matches: 59, Mismatches: 1, Indels: 6 0.89 0.02 0.09 Matches are distributed among these distances: 21 40 0.68 23 1 0.02 24 1 0.02 25 4 0.07 26 13 0.22 ACGTcount: A:0.44, C:0.24, G:0.08, T:0.23 Consensus pattern (24 bp): CATAGCATAGCATACAAATCCATA Found at i:78851 original size:46 final size:46 Alignment explanation

Indices: 78772--78863 Score: 112 Period size: 46 Copynumber: 2.0 Consensus size: 46 78762 TTACGTTCAG * * * * 78772 GTATCTTTACTCAAGCGACAACGAGATTTAAATCTACCCAATCTCC 1 GTATCATTACTCAAACAACAACGAGATTCAAATCTACCCAATCTCC * * * * 78818 GTATCATTACTCAAACAACACCGATATTCAAATCTAGCCGATCTCC 1 GTATCATTACTCAAACAACAACGAGATTCAAATCTACCCAATCTCC 78864 ATTCATAGTT Statistics Matches: 38, Mismatches: 8, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 46 38 1.00 ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27 Consensus pattern (46 bp): GTATCATTACTCAAACAACAACGAGATTCAAATCTACCCAATCTCC Found at i:79201 original size:26 final size:26 Alignment explanation

Indices: 79160--79226 Score: 98 Period size: 26 Copynumber: 2.6 Consensus size: 26 79150 CCTACAATAC * * 79160 CCATTGTGTTGTGGGGTTAAAAATCT 1 CCATTGTCTTGGGGGGTTAAAAATCT * * 79186 TCATTGTCTTGGGGGGTTATAAATCT 1 CCATTGTCTTGGGGGGTTAAAAATCT 79212 CCATTGTCTTGGGGG 1 CCATTGTCTTGGGGG 79227 TTCATACTGT Statistics Matches: 36, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 26 36 1.00 ACGTcount: A:0.18, C:0.13, G:0.30, T:0.39 Consensus pattern (26 bp): CCATTGTCTTGGGGGGTTAAAAATCT Found at i:80105 original size:1 final size:1 Alignment explanation

Indices: 80101--80172 Score: 126 Period size: 1 Copynumber: 72.0 Consensus size: 1 80091 GTTGTTGTGG ** 80101 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 80166 TTTTTTT 1 TTTTTTT 80173 GGCTACTAGT Statistics Matches: 69, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 1 69 1.00 ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97 Consensus pattern (1 bp): T Found at i:88788 original size:12 final size:12 Alignment explanation

Indices: 88760--88816 Score: 80 Period size: 12 Copynumber: 4.8 Consensus size: 12 88750 ATCACATTTT 88760 GTCTGTC-GTCC 1 GTCTGTCTGTCC * 88771 GTCTGTCTGTCT 1 GTCTGTCTGTCC 88783 GTCTGTCTGTCC 1 GTCTGTCTGTCC * * 88795 GTCCGTCCGTCC 1 GTCTGTCTGTCC 88807 GTCTGTCTGT 1 GTCTGTCTGT 88817 AAACTTTTCA Statistics Matches: 39, Mismatches: 6, Indels: 1 0.85 0.13 0.02 Matches are distributed among these distances: 11 7 0.18 12 32 0.82 ACGTcount: A:0.00, C:0.33, G:0.26, T:0.40 Consensus pattern (12 bp): GTCTGTCTGTCC Found at i:88814 original size:4 final size:4 Alignment explanation

Indices: 88759--88816 Score: 64 Period size: 4 Copynumber: 14.8 Consensus size: 4 88749 GATCACATTT * * * * 88759 TGTC TGTC -GTC CGTC TGTC TGTC TGTC TGTC TGTC CGTC CGTC CGTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC * 88806 CGTC TGTC TGT 1 TGTC TGTC TGT 88817 AAACTTTTCA Statistics Matches: 50, Mismatches: 3, Indels: 2 0.91 0.05 0.04 Matches are distributed among these distances: 3 3 0.06 4 47 0.94 ACGTcount: A:0.00, C:0.33, G:0.26, T:0.41 Consensus pattern (4 bp): TGTC Found at i:89343 original size:166 final size:165 Alignment explanation

Indices: 88985--89812 Score: 1128 Period size: 166 Copynumber: 5.1 Consensus size: 165 88975 AGAAATTTTC * * 88985 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATCTGG 1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * 89050 TAGTGTAGATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGGGTGGGGCCACAATGGGGGGTC 66 TAGTGTAAATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGGGTGGGGCCACAATGGGGGGTC * * * 89115 GAAGTTTTACATAGGAATATACAGAGTAAATCTTT 131 AAAGTTTTAAATAGGAATATATAGAGTAAATCTTT * 89150 GAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG 1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * * 89215 TAGTGTAAATGCTCATTTGTGAAAATCATGACCCTC-GAGGGTAGGGTGGGGCCACAATGGGGGG 66 TAGTGTAAATTCTAATTTGTGAAAATCATGACCC-CAG-GGGTAGGGTGGGGCCACAATGGGGGG 89279 TCAAAGTTTTAAATAGGAATATATAGAGTAAATCTTT 129 TCAAAGTTTTAAATAGGAATATATAGAGTAAATCTTT 89316 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAA---G---C-----T-GAA--A--CTCAGG 1 AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * * * * * 89365 TAGTGTTAATTCTAATTTGTGAAAATCATGACCCCGGGGGTAGAGTTGGGCCACAATGGGGTGTC 66 TAGTGTAAATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGGGTGGGGCCACAATGGGGGGTC * 89430 GAAG-TTTAACATAGGAATATATAGAGTAAATCTTT 131 AAAGTTTTAA-ATAGGAATATATAGAGTAAATCTTT * * * 89465 AAAAATCTTCTTCTCA-GAAAC-TAATCAGCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCA 1 AAAAATCTTCTTCTCATGAACCATAA-GA-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA * * 89528 GGTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAATGGGGG 64 GGTAGTGTAAATTCTAATTTGTGAAAATCATGA-CCCCAGGGGTAGGGTGGGGCCACAATGGGGG 89593 GTCAAAGTTTTAAATAGGAATATATAGAGTAAATCTTT 128 GTCAAAGTTTTAAATAGGAATATATAGAGTAAATCTTT * * * * * 89631 AAAAATCTTCTTCTCA-GAAAC-TAATCAGCTAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCA 1 AAAAATCTTCTTCTCATGAACCATAA-GA-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA * * 89694 GGTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAATGGGGG 64 GGTAGTGTAAATTCTAATTTGTGAAAATCATGA-CCCCAGGGGTAGGGTGGGGCCACAATGGGGG * * 89759 TTCAAAG-TTTAACAAAGGAATATATATG-GTAAATCTTT 128 GTCAAAGTTTTAA-ATAGGAATATATA-GAGTAAATCTTT 89797 AAAAATCTTCTTCTCA 1 AAAAATCTTCTTCTCA 89813 GAAACTAATC Statistics Matches: 604, Mismatches: 33, Indels: 51 0.88 0.05 0.07 Matches are distributed among these distances: 147 3 0.00 148 10 0.02 149 78 0.13 150 38 0.06 152 2 0.00 154 3 0.00 155 2 0.00 160 2 0.00 161 3 0.00 163 2 0.00 165 133 0.22 166 322 0.53 167 6 0.01 ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27 Consensus pattern (165 bp): AAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG TAGTGTAAATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGGGTGGGGCCACAATGGGGGGTC AAAGTTTTAAATAGGAATATATAGAGTAAATCTTT Found at i:89425 original size:315 final size:315 Alignment explanation

Indices: 89048--89828 Score: 1047 Period size: 315 Copynumber: 2.4 Consensus size: 315 89038 AGCATCATCT * 89048 GGTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGGGTGGGGCCACAATGGGGGG 1 GGTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGAGTGGGGCCACAATGGGGGG * * * * 89113 TCGAAGTTTTACATAGGAATATACAGAGTAAATCTTTGAAAATCTTCTTCTCATG-AAC-CATAA 66 TCGAAGTTTAACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAAACTAATCA ** * 89176 GACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATGCTCATTTGTGAAAAT 130 G-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATGCAAAGTTGTGAAAAT 89241 CATGA-CCCTC-GAGGGTAGGGTGGGGCCACAATGGGGGGTCAAAGTTTTAAATAGGAATATATA 194 CATGATCCC-CAG-GGGTAGGGTGGGGCCACAATGGGGGGTCAAAGTTTTAAATAGGAATATATA 89304 GAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTCA 257 GAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTCA * * * 89363 GGTAGTGTTA-ATTCTAATTTGTGAAAATCATGACCCCGGGGGTAGAGTTGGGCCACAATGGGGT 1 GGTAGTG-TAGATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGAGTGGGGCCACAATGGGGG * 89427 GTCGAAGTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA 65 GTCGAAGTTTAACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA * * 89492 GCCAGGAAAGCTGACACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATC 130 GCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATGCAAAGTTGTGAAAATC 89557 ATGATCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGTCAAAGTTTTAAATAGGAATATATAGAG 195 ATGATCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGTCAAAGTTTTAAATAGGAATATATAGAG * * * 89622 TAAATCTTTAAAAATCTTCTTCTCA-GAAAC-TAATCAGCTAGGAAAGCTTAAACTTGTGTGGAA 260 TAAATCTTTAAAAATCTTCTTCTCATGAACCATAA-GA-CCAGGAAAG------C-----T-GAA * 89685 GCGTCCTCA 311 ----ACTCA * * * * 89694 GGTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAATGGGGG 1 GGTAGTGTAGATTCTAATTTGTGAAAATCATGA-CCCCAGGGGTAGAGTGGGGCCACAATGGGGG * * * * 89759 TTCAAAGTTTAACAAAGGAATATATATG-GTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC 65 GTCGAAGTTTAACATAGGAATATACA-GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC 89823 AGCCAG 129 AGCCAG 89829 ATGATTCTTT Statistics Matches: 413, Mismatches: 27, Indels: 35 0.87 0.06 0.07 Matches are distributed among these distances: 313 3 0.01 314 6 0.01 315 262 0.63 316 10 0.02 321 1 0.00 326 1 0.00 327 3 0.01 330 2 0.00 331 32 0.08 332 92 0.22 333 1 0.00 ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27 Consensus pattern (315 bp): GGTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCAGGGGTAGAGTGGGGCCACAATGGGGGG TCGAAGTTTAACATAGGAATATACAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAG CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATGCAAAGTTGTGAAAATCA TGATCCCCAGGGGTAGGGTGGGGCCACAATGGGGGGTCAAAGTTTTAAATAGGAATATATAGAGT AAATCTTTAAAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTCA Found at i:93432 original size:166 final size:166 Alignment explanation

Indices: 92844--97676 Score: 6446 Period size: 166 Copynumber: 29.2 Consensus size: 166 92834 ACAAGTTTAG ** * * * * * 92844 GCTTTTCTGGCCAAATAGTCTTTAAAAAGAAGA-TATTAAAGATTTTCTCTATATATTCCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * * * * ** * * * 92908 AAAAATTCATCCCCC-ATTGTGGCCTCACCATA-CCCC-ATGACTATTATTTAAACAAACTTGAA 66 AAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAA ** * * * * 92970 TCTTTACGATCTTG-GGATGCTTCCACTTAAATTTGG 131 TCTACACTA-CCTGAGGATGCTTCCACTTTAATTTGA * * * 93006 GCTTTCCTGGCCTTATAG-TTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATA----TA--- 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * * * 93063 AAAA-TTTATCCCCC-ATTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTTGAA 66 AAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAA * * * 93126 TCTACATTATCTGAGGATGGTT--AC---AATTTGA 131 TCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * 93157 GC-TTTCTTGGCCAT-AAAG-TTTTGAAAAGAA-ATTTTTTTAAAGATTTTCTCTATATATTCCT 1 GCTTTTC-TGGCC-TGATAGTTTTTGAGAAGAAGA--TTTTTAAAGATTTTGTCTATATATTCCT * * * * * 93218 ATATAAAAATTTA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAAC 62 ATGTAAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAAC * ** * 93282 TTGAATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 126 TTGAATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** * 93323 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCGATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 93387 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 93452 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 93489 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 93554 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 93618 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** * 93655 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCGATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 93719 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 93784 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 93821 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * * 93886 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTAGCCCCGGAGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * * 93950 ATCTACACTACCTGAGGAAGCTTCCACTTTTATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * * 93987 GCTTTTCTGGCCTAATAATTTTTTAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * 94052 AAAACTTGATCCCCCC-ATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGA-CCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * * 94116 ATCTACACTACCTGAGGAAGCTTCCACTTTGATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * * * 94153 GCTTCTCTGGCCTAATAATTTTTTAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * 94218 AAAACTTGATCCCCCC-ATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGA-CCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * * 94282 ATCTACACTACCTGAGGAAGCTTCCACTTTGATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * * * 94319 GCTTCTCTGGCCTAATAATGTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * 94384 AAAACTTGATCCCCCC-ATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGA-CCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 94448 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** 94485 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCTATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 94549 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 94614 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 94651 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 94716 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 94780 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** * 94817 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCTGTATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * 94881 TAAAACATGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 94946 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 94983 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 95048 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 95112 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** * 95149 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCGATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 95213 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 95278 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 95315 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 95380 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 95444 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * ** * 95481 GCTTTTCTGGCCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAATT-TCGATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 95545 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 95610 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 95647 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 95712 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 95776 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** * 95813 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCTGTATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 95877 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 95942 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 95979 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 96044 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 96108 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** 96145 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCTATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 96209 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 96274 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 96311 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 96376 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 96440 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * * ** * 96477 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTAAAAAAAAATT-TCGATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTT-TAAAGATTTTGTCTATATATTCCTATG * * * 96541 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 96606 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 96643 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * 96708 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * ** * 96772 ATCTACACTATCTGAGGATGCTTCCACTCAAATTTAA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * *** * 96809 GCTTTTCTGACCTTATAGTTTTTGAGAAGAAGATTTTTAAAAAAAAAT-TCGATATATTCCTATG 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTGTCTATATATTCCTATG * * * 96873 TAAAACATGACCCCCCTCTTGTGGCCCCACCCTACCCCCGGGGACCATAATTTGAACAAACTTGA 65 TAAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * 96938 ATCTACACTACCTGAGGATGCTTCCATTTTAATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * 96975 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAAGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * * 97040 AAAACTTGA-TCCCCTAATTGTGGCCCCACCCTAGCCCCGGAGACCATGATTTGAACAAACTTGA 66 AAAACTTGACCCCCCT-ATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA * * 97104 ATCTACACTACCTGAGGAAGCTTCCACTTTTATTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * 97141 GCTTTTCTGGCCTCATAATATTTT-AGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATG 1 GCTTTTCTGGCCTGATAGT-TTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATG * 97205 TAAAACTTGATCCCCCC-ATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTG 65 TAAAACTTGA-CCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTG * * 97269 AATCTACACTACCTGAGGAAGCTTCCACTTTGATTTGA 129 AATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * * 97307 GCTTCTCTGGCCTAATAATGTTTT-AGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATG 1 GCTTTTCTGGCCTGATAGT-TTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATG * 97371 TAAAACTTGATCCCCCC-ATTGAGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTG 65 TAAAACTTGA-CCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTG * * * * 97435 AATCTACACTATCTGAGGAGGCTCCCATTTTAATTTGA 129 AATCTACACTACCTGAGGATGCTTCCACTTTAATTTGA * * * 97473 GCTTTTCTGGCCTGATAGTTTTTTAGAAGAAGATTTTTAAGGATTTTGTCTATATATTTCTATGT 1 GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT * * * 97538 AAAACTTGATCCCCCC-ATTGTGGCCCCTCCCTACCCCTGGGGACCATAATTTGAACAAACTTGA 66 AAAACTTGA-CCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGA ** ** 97602 ATCTACACTACCTGAGGATGCCGCCAC-ACAAGTTTGA 130 ATCTACACTACCTGAGGATGCTTCCACTTTAA-TTTGA * 97639 GCTTTTCAGGCC-GAATAGTTTTTGAGAAGAAGATTTTT 1 GCTTTTCTGGCCTG-ATAGTTTTTGAGAAGAAGATTTTT 97677 GAAAAATACC Statistics Matches: 4136, Mismatches: 460, Indels: 146 0.87 0.10 0.03 Matches are distributed among these distances: 150 4 0.00 151 27 0.01 152 24 0.01 154 25 0.01 155 10 0.00 156 35 0.01 158 2 0.00 159 8 0.00 160 4 0.00 161 77 0.02 162 36 0.01 163 2 0.00 165 116 0.03 166 3641 0.88 167 116 0.03 168 9 0.00 ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34 Consensus pattern (166 bp): GCTTTTCTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTGTCTATATATTCCTATGT AAAACTTGACCCCCCTATTGTGGCCCCACCCTACCCCCGGGGACCATGATTTGAACAAACTTGAA TCTACACTACCTGAGGATGCTTCCACTTTAATTTGA Found at i:97869 original size:18 final size:19 Alignment explanation

Indices: 97846--97893 Score: 62 Period size: 18 Copynumber: 2.5 Consensus size: 19 97836 TGAAAAGTTT * * 97846 ACAACGCCAACGCCGAC-G 1 ACAACGACAACGACGACAG 97864 ACAACGACAACGACGACAG 1 ACAACGACAACGACGACAG 97883 ACAACGGACAA 1 ACAAC-GACAA 97894 ATTGTGATCA Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 18 15 0.58 19 6 0.23 20 5 0.19 ACGTcount: A:0.44, C:0.35, G:0.21, T:0.00 Consensus pattern (19 bp): ACAACGACAACGACGACAG Found at i:107157 original size:2 final size:2 Alignment explanation

Indices: 107152--107264 Score: 208 Period size: 2 Copynumber: 56.5 Consensus size: 2 107142 ATTGCACACA * * 107152 CT CT CT CT CT CT CT CT CT AT CT CT CT AT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 107194 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 107236 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 107265 AATTTTAAAT Statistics Matches: 107, Mismatches: 4, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 107 1.00 ACGTcount: A:0.02, C:0.49, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:107565 original size:2 final size:2 Alignment explanation

Indices: 107553--107603 Score: 93 Period size: 2 Copynumber: 25.5 Consensus size: 2 107543 ACTGGAGACT * 107553 GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 107595 GA GA GA GA G 1 GA GA GA GA G 107604 GCACATAGCT Statistics Matches: 47, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): GA Found at i:107865 original size:2 final size:2 Alignment explanation

Indices: 107858--107907 Score: 91 Period size: 2 Copynumber: 25.0 Consensus size: 2 107848 GCTATGTACT 107858 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA * 107900 GA GG GA GA 1 GA GA GA GA 107908 CCATGTGGAG Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:108534 original size:2 final size:2 Alignment explanation

Indices: 108527--108569 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 108517 TTAATTGTTC 108527 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 108569 A 1 A 108570 TCCTACCTCT Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:109401 original size:2 final size:2 Alignment explanation

Indices: 109394--109470 Score: 145 Period size: 2 Copynumber: 38.5 Consensus size: 2 109384 TTAACTAGTT 109394 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * 109436 TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 109471 AGCCTTACAA Statistics Matches: 73, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 73 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): TC Found at i:113602 original size:76 final size:76 Alignment explanation

Indices: 113513--113721 Score: 244 Period size: 76 Copynumber: 2.8 Consensus size: 76 113503 TAAACACATT * * * * * 113513 AATGTAGAATATAAGTGGAGTAAAATGAGAAAATTAAAC-TAAAACTCGACGTAAAATTGGGTAT 1 AATGTGGAATATAAGTCGAGTAAAATGAG-AAATTAAACTTGAAACTCGACGTAAAATTCGATAT 113577 AA-AAACCATTTA 65 AATAAA-CATTTA * * * 113589 AATGTGGAATATAAGTCGAGTAAAATAAGTGAA-TAAACTTGAAACTCGACGTAAAATTCGATTT 1 AATGTGGAATATAAGTCGAGTAAAATGAG-AAATTAAACTTGAAACTCGACGTAAAATTCGATAT * 113653 AATAAACATTTG 65 AATAAACATTTA * * * ** 113665 TATCTGGACTATAAGTCGAGTAAAATGAGTGATTAAACTTGAAACTCGACGTAAAAT 1 AATGTGGAATATAAGTCGAGTAAAATGAGAAATTAAACTTGAAACTCGACGTAAAAT 113722 GGTGTAAAAT Statistics Matches: 114, Mismatches: 16, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 75 6 0.05 76 105 0.92 77 3 0.03 ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27 Consensus pattern (76 bp): AATGTGGAATATAAGTCGAGTAAAATGAGAAATTAAACTTGAAACTCGACGTAAAATTCGATATA ATAAACATTTA Found at i:116685 original size:16 final size:16 Alignment explanation

Indices: 116649--116691 Score: 52 Period size: 16 Copynumber: 2.7 Consensus size: 16 116639 CCGAAATGAA 116649 ATAT-AAATATAAATG 1 ATATGAAATATAAATG * * 116664 AAATGAAATATAAATT 1 ATATGAAATATAAATG 116680 ATATGATAATAT 1 ATATGA-AATAT 116692 TGTAGTGAGA Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 15 3 0.13 16 15 0.65 17 5 0.22 ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35 Consensus pattern (16 bp): ATATGAAATATAAATG Found at i:117223 original size:20 final size:21 Alignment explanation

Indices: 117198--117248 Score: 68 Period size: 20 Copynumber: 2.5 Consensus size: 21 117188 CACGACCTAG 117198 CTTTATATATATACACAATT- 1 CTTTATATATATACACAATTC *** 117218 CTTTATATATATTGGCAATTC 1 CTTTATATATATACACAATTC 117239 CTTTATATAT 1 CTTTATATAT 117249 TTAAAGCTGC Statistics Matches: 27, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 20 17 0.63 21 10 0.37 ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49 Consensus pattern (21 bp): CTTTATATATATACACAATTC Found at i:122020 original size:2 final size:2 Alignment explanation

Indices: 122015--122056 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 122005 TATAAATTGA 122015 AT AT AT AT AT AT AT AT AT AT 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 AT AT AT 122057 TTTGGTGAAT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:124291 original size:32 final size:32 Alignment explanation

Indices: 124250--124312 Score: 126 Period size: 32 Copynumber: 2.0 Consensus size: 32 124240 AAGAATTGAA 124250 AATATTGGATTATTATTAACAATTATGATGAC 1 AATATTGGATTATTATTAACAATTATGATGAC 124282 AATATTGGATTATTATTAACAATTATGATGA 1 AATATTGGATTATTATTAACAATTATGATGA 124313 AAAGCTAAGA Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 31 1.00 ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41 Consensus pattern (32 bp): AATATTGGATTATTATTAACAATTATGATGAC Found at i:126116 original size:90 final size:90 Alignment explanation

Indices: 126001--126175 Score: 251 Period size: 90 Copynumber: 1.9 Consensus size: 90 125991 ATATAAGACA * * * * * * 126001 ACAATTTTGTAAATAAAGAGAATAAATCATACACATGAATGCTATGTAAATCTGGGACTTTGTAT 1 ACAATGTTGTAAATAAAGAAAATAAACCATACACATGAATGCTATGTAAATCAGGGACGTTATAT * 126066 ATAATTTCTGATCAGATCTATGACT 66 ATAATTTCTGAGCAGATCTATGACT * * * * 126091 ACAATGTTGTAAATCAAGAAAATAAACCATACACATTAATGCTCTGTAATTCAGGGACGTTATAT 1 ACAATGTTGTAAATAAAGAAAATAAACCATACACATGAATGCTATGTAAATCAGGGACGTTATAT 126156 ATAATTTCTGAGCAGATCTA 66 ATAATTTCTGAGCAGATCTA 126176 AAAAGCCTAA Statistics Matches: 74, Mismatches: 11, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 90 74 1.00 ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33 Consensus pattern (90 bp): ACAATGTTGTAAATAAAGAAAATAAACCATACACATGAATGCTATGTAAATCAGGGACGTTATAT ATAATTTCTGAGCAGATCTATGACT Found at i:132082 original size:16 final size:16 Alignment explanation

Indices: 132063--132096 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 132053 TCACCGAGAC 132063 GAGACATCACCCTTAT 1 GAGACATCACCCTTAT * * 132079 GAGACTTCACCTTTAT 1 GAGACATCACCCTTAT 132095 GA 1 GA 132097 AACCACCTTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29 Consensus pattern (16 bp): GAGACATCACCCTTAT Found at i:132747 original size:53 final size:53 Alignment explanation

Indices: 132676--132776 Score: 121 Period size: 53 Copynumber: 1.9 Consensus size: 53 132666 ATATATTTTA * * ** * 132676 CAATATCATACAAAACAATTTCATGTGATGTGATATTATATCATATTATAAAC 1 CAATATCATACAAAACAATATCATATGATACGATATTATATAATATTATAAAC ** * * 132729 CAATATCATATTATACAATATCGTATGATACGATATTATATAATATTA 1 CAATATCATACAAAACAATATCATATGATACGATATTATATAATATTA 132777 CAGTATCTTA Statistics Matches: 39, Mismatches: 9, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 53 39 1.00 ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38 Consensus pattern (53 bp): CAATATCATACAAAACAATATCATATGATACGATATTATATAATATTATAAAC Found at i:132749 original size:15 final size:15 Alignment explanation

Indices: 132713--132769 Score: 51 Period size: 15 Copynumber: 3.6 Consensus size: 15 132703 ATGTGATATT 132713 ATATCATATTATAAACCA 1 ATATCATATTAT--A-CA 132731 ATATCATATTATACA 1 ATATCATATTATACA * * * 132746 ATATCGTATGATACG 1 ATATCATATTATACA * 132761 ATATTATAT 1 ATATCATAT 132770 AATATTACAG Statistics Matches: 34, Mismatches: 5, Indels: 3 0.81 0.12 0.07 Matches are distributed among these distances: 15 21 0.62 16 1 0.03 18 12 0.35 ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39 Consensus pattern (15 bp): ATATCATATTATACA Found at i:132847 original size:15 final size:15 Alignment explanation

Indices: 132829--132862 Score: 50 Period size: 15 Copynumber: 2.3 Consensus size: 15 132819 ACAGAAACTT * 132829 ATATCATATTATACA 1 ATATCATATGATACA * 132844 ATATCGTATGATACA 1 ATATCATATGATACA 132859 ATAT 1 ATAT 132863 TATAGAATAT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38 Consensus pattern (15 bp): ATATCATATGATACA Found at i:132983 original size:20 final size:20 Alignment explanation

Indices: 132954--133002 Score: 62 Period size: 20 Copynumber: 2.5 Consensus size: 20 132944 ATAAATTAAT * * 132954 AATACAATATAATATTATAC 1 AATACTATATAATAATATAC * * 132974 AATATTATATCATAATATAC 1 AATACTATATAATAATATAC 132994 AATACTATA 1 AATACTATA 133003 CATAACGATA Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 20 24 1.00 ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37 Consensus pattern (20 bp): AATACTATATAATAATATAC Found at i:133977 original size:162 final size:163 Alignment explanation

Indices: 133774--134380 Score: 581 Period size: 177 Copynumber: 3.5 Consensus size: 163 133764 GACCTGTTCA * * * * * 133774 AAAAAACTTAACCATATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAGCCTGCCAGG 1 AAAAACCTTAACCTTCTCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGCCTGG 133839 TGCATCAGTATCATAAGAC-GTCTGGTGAAGTTAGGACAAGTAATAACTAAGATATAATCATCAG 66 TGCATCAGTATCATAAGACAGTCTGGTGAAGTTAGGACAAGTAATAACTAAGATATAATCATCAG **** 133903 AGGGCACCTGTTTTAAAAACTTTAACCAGCTCT 131 AGGGCACCTGCAACAAAAACTTTAACCAGCTCT * * 133936 AAAAACCTTAACCTTCTCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCTGG 1 AAAAACCTTAACCTTCTCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGCCTGG * 134001 TGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTAGGACAAGTAGTAACTAA 66 TGCATCAGTATCAT-A-A-G----A--C-----AGTCTGGTGAAGTTAGGACAAGTAATAACTAA 134066 GATATAATCATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTCT 117 GATATAATCATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTCT * * * * 134113 AAAAACCTTAACCTCCTTCAGCATCTGTAACCTATAGCTCAGATTCAGCATTCAAGCCTGCCTGG 1 AAAAACCTTAACCTTCTCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGCCTGG * * * * 134178 TGCATCAGTATCATAAGACACACCATCAATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAACTT 66 TGCATCAGTATCATAAG-----------A--C-AGTCTGGTGAAGTTA-GGACAAGTAATAAC-T * * * * * * 134242 ACATGTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGATCC 115 A-A-G-ATATAAT-C-ATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTCT * * * * * 134296 AAAAACCTTAACCTCCTCCAGCATCAGAAACC-ATAAGCTCAGATTCAGCACTCAAGCCTGTCTG 1 AAAAACCTTAACCTTCTCCAGCATCTGAAACCTAT-GGCTCAGATTCAGCATTCAAGCCTGCCTG * 134360 GTGCGTCAGTATCATAAGACA 65 GTGCATCAGTATCATAAGACA 134381 CACCATCCAT Statistics Matches: 378, Mismatches: 37, Indels: 53 0.81 0.08 0.11 Matches are distributed among these distances: 162 72 0.19 163 1 0.00 164 1 0.00 165 1 0.00 169 2 0.01 170 1 0.00 171 1 0.00 172 1 0.00 174 1 0.00 175 1 0.00 176 3 0.01 177 170 0.45 178 2 0.01 179 1 0.00 180 1 0.00 181 9 0.02 182 3 0.01 183 107 0.28 ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24 Consensus pattern (163 bp): AAAAACCTTAACCTTCTCCAGCATCTGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGCCTGG TGCATCAGTATCATAAGACAGTCTGGTGAAGTTAGGACAAGTAATAACTAAGATATAATCATCAG AGGGCACCTGCAACAAAAACTTTAACCAGCTCT Found at i:134155 original size:177 final size:180 Alignment explanation

Indices: 133858--134528 Score: 837 Period size: 177 Copynumber: 3.8 Consensus size: 180 133848 ATCATAAGAC * * * **** 133858 GTCTGGTGAAGTTA-GGACAAGTAATAACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTTAAA 1 GTCTGGTGAAGTTACGGACAAGCAGTAACTAAGATATAATGCTATCAAAGGGCACCTGCAACAAA * * * * 133920 AACTTTAACCAGCTCTAAAAACCTTAACCTTCTCCAGCATCCGAAACCTATGGCTCAGATTCAGC 66 AACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTATAGCTCAGATTCAGC * * 133985 ATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACGCACCATCCATGGAA 131 ATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAA * * 134035 GTCTGGTGAAGTTA-GGACAAGTAGTAACTAAGATATAAT-C-ATCAGAGGGCACCTGCAACAAA 1 GTCTGGTGAAGTTACGGACAAGCAGTAACTAAGATATAATGCTATCAAAGGGCACCTGCAACAAA * * * 134097 AACTTTAACCAGCTCTAAAAACCTTAACCTCCTTCAGCATCTGTAACCTATAGCTCAGATTCAGC 66 AACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTATAGCTCAGATTCAGC * * 134162 ATTCAAGCCTGCCTGGTGCATCAGTATCATAAGACACACCATCAATGCAA 131 ATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAA * * * * 134212 GTTTGGTGAAG-TACGGACCAGCAGTAACTTACATGTAGATATTGCTATCAAAGGGCACCTGCAA 1 GTCTGGTGAAGTTACGGACAAGCAGTAAC-TA-A-G-ATATAATGCTATCAAAGGGCACCTGCAA * * * 134276 CAAAAACTTTAACCTGATCCAAAAACCTTAACCTCCTCCAGCATCAGAAACC-ATAAGCTCAGAT 62 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTAT-AGCTCAGAT * * 134340 TCAGCACTCAAGCCTGTCTGGTGCGTCAGTATCATAAGACACACCATCCATGCAA 126 TCAGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAA * * * * * 134395 GTTTGGTG-AGGTACGGACCAGCAGTAACTTAGATAT--TGCTGTCAAAGGGCACCTGCAACAAA 1 GTCTGGTGAAGTTACGGACAAGCAGTAACTAAGATATAATGCTATCAAAGGGCACCTGCAACAAA * * * * 134457 AACTTTAACCGGGTCCAACAACCTTAACCTCCTCCAGCATCTGAAA--TTTAGGACTCAGATTCA 66 AACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTATA-G-CTCAGATTCA * 134520 GCATCCAAG 129 GCATTCAAG 134529 TCTTTCAAGT Statistics Matches: 442, Mismatches: 40, Indels: 24 0.87 0.08 0.05 Matches are distributed among these distances: 175 1 0.00 176 4 0.01 177 269 0.61 178 2 0.00 179 4 0.01 180 2 0.00 181 6 0.01 182 6 0.01 183 148 0.33 ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24 Consensus pattern (180 bp): GTCTGGTGAAGTTACGGACAAGCAGTAACTAAGATATAATGCTATCAAAGGGCACCTGCAACAAA AACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACCTATAGCTCAGATTCAGC ATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAA Found at i:134315 original size:19 final size:19 Alignment explanation

Indices: 134276--134315 Score: 53 Period size: 19 Copynumber: 2.1 Consensus size: 19 134266 GCACCTGCAA * * 134276 CAAAAACTTTAACCTGATC 1 CAAAAACCTTAACCTCATC * 134295 CAAAAACCTTAACCTCCTC 1 CAAAAACCTTAACCTCATC 134314 CA 1 CA 134316 GCATCAGAAA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.40, C:0.35, G:0.03, T:0.23 Consensus pattern (19 bp): CAAAAACCTTAACCTCATC Found at i:134572 original size:360 final size:358 Alignment explanation

Indices: 133917--134582 Score: 867 Period size: 360 Copynumber: 1.8 Consensus size: 358 133907 CACCTGTTTT * * * * * 133917 AAAAACTTTAACCAGCTCTAAAAACCTTAACCTTCTCCAGCATCCGAAACCTATGGCTCAGATTC 1 AAAAACTTTAACCAGATCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCTATAGCTCAGATTC * * * * 133982 AGCATTCAAGCCTGTCTGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAGT 66 AGCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTCTGGTGAAGG * * 134047 TAGGACAAGTAGTAACTAAGATATAATCATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTC 131 TAGGACAAGCAGTAACTAAGATAT-ATCATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTC * * * * ** 134112 TAAAAACCTTAACCTCCTTCAGCATCTGTAACCTATAGCTCAGATTCAGCATTCAAGCCTGCCTG 195 CAAAAACCTTAACCTCCTCCAGCATCTGTAACATATAGCTCAGATTCAGCATCCAAGCCTGCCAA * * 134177 GTGCATCAGTATCATAAGACACACCATCAATGCAAGTTTGGTGAAGTACGGACCAGCAGTAACTT 260 GTCCATAAGTATCA-AAGACACACCATCAATGCAAGTTTGGTGAAGTACGGACCAGCAGTAACTT 134242 ACATGTAGATATTGCTATCAAAGGGCACCTGCAAC 324 ACATGTAGATATTGCTATCAAAGGGCACCTGCAAC * 134277 AAAAACTTTAACCTGATCCAAAAACCTTAACCTCCTCCAGCATCAGAAACC-ATAAGCTCAGATT 1 AAAAACTTTAACCAGATCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCTAT-AGCTCAGATT * * 134341 CAGCACTCAAGCCTGTCTGGTGCGTCAGTATCATAAGACACACCATCCATGCAAGTTTGGTG-AG 65 CAGCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTCTGGTGAAG * * * * 134405 GTACGGACCAGCAGTAACTTAGATAT-TGCTGTCAAAGGGCACCTGCAACAAAAACTTTAACCGG 130 GTA-GGACAAGCAGTAACTAAGATATAT-C-ATCAAAGGGCACCTGCAACAAAAACTTTAACCAG * * * * 134469 GTCCAACAACCTTAACCTCCTCCAGCATCTG-AA-ATTTAGGACTCAGATTCAGCATCCAAGTCT 192 CTCCAAAAACCTTAACCTCCTCCAGCATCTGTAACATATA-G-CTCAGATTCAGCATCCAAGCCT ** * ** * * 134532 TTCAAGTCCATAAGTAGGTC-CAGATGCATCATCCATGCAAGTTTGGTGAAG 255 GCCAAGTCCATAAGTA--TCAAAGACACACCATCAATGCAAGTTTGGTGAAG 134583 AAAGGACAAG Statistics Matches: 261, Mismatches: 37, Indels: 16 0.83 0.12 0.05 Matches are distributed among these distances: 358 4 0.02 359 10 0.04 360 245 0.94 362 2 0.01 ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24 Consensus pattern (358 bp): AAAAACTTTAACCAGATCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCTATAGCTCAGATTC AGCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTCTGGTGAAGG TAGGACAAGCAGTAACTAAGATATATCATCAAAGGGCACCTGCAACAAAAACTTTAACCAGCTCC AAAAACCTTAACCTCCTCCAGCATCTGTAACATATAGCTCAGATTCAGCATCCAAGCCTGCCAAG TCCATAAGTATCAAAGACACACCATCAATGCAAGTTTGGTGAAGTACGGACCAGCAGTAACTTAC ATGTAGATATTGCTATCAAAGGGCACCTGCAAC Found at i:134605 original size:177 final size:175 Alignment explanation

Indices: 133861--134606 Score: 759 Period size: 177 Copynumber: 4.2 Consensus size: 175 133851 ATAAGACGTC * * * **** 133861 TGGTGAAGTTAGGACAAGTAATAACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTTAAAAACT 1 TGGTGAAGTAAGGACAAGTAATAACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACT * * * * * 133924 TTAACCAGCTCTAAAAACCTTAACCTTCTCCAGCATCCGAAACCTATGGCTCAGATTCAGCATTC 64 TTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACATA-GGCTCAGATTCAGCATCC * * * 133989 AAGCCTGTCTGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTC 128 AAGCCTGTCTGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTT * * * * 134038 TGGTGAAGTTAGGACAAGTAGTAACTAAGATATAAT-C-ATCAGAGGGCACCTGCAACAAAAACT 1 TGGTGAAGTAAGGACAAGTAATAACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACT * * * * 134101 TTAACCAGCTCTAAAAACCTTAACCTCCTTCAGCATCTGTAACCTATA-GCTCAGATTCAGCATT 64 TTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTG-AAAC-ATAGGCTCAGATTCAGCATC * * 134165 CAAGCCTGCCTGGTGCATCAGTATCATAAGACACACCATCAATGCAAGTT 127 CAAGCCTGTCTGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTT * * 134215 TGGTGAAGTACGGACCAGCAGTAACTTACATGTAGATATTGCTATCAAAGGGCACCTGCAACAAA 1 TGGTGAAGTAAGGA-CA--AGTAA-TAAC-T-TAGATATTGCTATCAAAGGGCACCTGCAACAAA * * * * 134280 AACTTTAACCTGATCCAAAAACCTTAACCTCCTCCAGCATCAGAAACCATAAGCTCAGATTCAGC 60 AACTTTAACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAA-CATAGGCTCAGATTCAGC * 134345 A-CTCAAGCCTGTCTGGTGCGTCAGTATCATAAGACACACCATCCATGCAAGTT 124 ATC-CAAGCCTGTCTGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTT * * * * * * 134398 TGGTGAGGTACGGACCAGCAGTAACTTAGATATTGCTGTCAAAGGGCACCTGCAACAAAAACTTT 1 TGGTGAAGTAAGGACAAGTAATAACTTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTT * * * ** 134463 AACCGGGTCCAACAACCTTAACCTCCTCCAGCATCTGAAATTTAGGACTCAGATTCAGCATCCAA 66 AACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACATAGG-CTCAGATTCAGCATCCAA * * ** * * * ** * 134528 GTCTTTCAAGTCCATAAGTAGGTC-CAGATGCATCATCCATGCAAGTT 130 GCCTGTCTGGTGCATCAGTA--TCAAAGACACACCATCCATGCAAGTT * * 134575 TGGTGAAGAAAGGACAAGTAATAGCTTAGATA 1 TGGTGAAGTAAGGACAAGTAATAACTTAGATA 134607 CAGGACCTGC Statistics Matches: 490, Mismatches: 62, Indels: 34 0.84 0.11 0.06 Matches are distributed among these distances: 176 3 0.01 177 314 0.64 178 7 0.01 179 7 0.01 180 7 0.01 181 4 0.01 182 8 0.02 183 140 0.29 ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24 Consensus pattern (175 bp): TGGTGAAGTAAGGACAAGTAATAACTTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTT AACCAGCTCCAAAAACCTTAACCTCCTCCAGCATCTGAAACATAGGCTCAGATTCAGCATCCAAG CCTGTCTGGTGCATCAGTATCAAAGACACACCATCCATGCAAGTT Found at i:143500 original size:156 final size:159 Alignment explanation

Indices: 143124--143592 Score: 624 Period size: 168 Copynumber: 2.9 Consensus size: 159 143114 TCCACATGTT * * 143124 TGGGAGTAAAGAAGAAGATTTTTTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA 1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA * * * * 143189 CCCTAGAGCCTGAATCCCTGACACAGGAGTCATTAATTTCACAATTTTGGTAGAGGGCTTCATGG 66 CCCTAGAGCCAGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGG * 143254 ACATCATAATAATGCATTTAGTTTTTAACAAATATATA 131 ACATCATAATCATGC----A--TTTTAAC--A-ATATA ** * 143292 TGGGAGTAGAGAAG-ATTTTCTTCTAAGATTTAATACATTTTTACTATATGGCCAAATTGGCCCC 1 TGGGAGTAGAGAAGAAGATT-TTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC * * * 143356 ACCCTAGAGCCAGAACCCCTGACACAGGGGTCATGAATTTTACAATTTTTGTAGAGGGTTTCATG 65 ACCCTAGAGCCAGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATG 143421 GACATCATAATCATGCA-TTT-AC-ATATA 130 GACATCATAATCATGCATTTTAACAATATA * * * 143448 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTCACTTTTTGGCCATATTGGCCCCA 1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA * * * * 143513 CCCTAGAGACAGAACCCCTGACCCACGGGCCATGAATTTCAC-ATTTTGGTAGAGGGCTTCATGG 66 CCCTAGAGCCAGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGG * 143577 ACATCATAACCATGCA 131 ACATCATAATCATGCA 143593 ACCAGTTTTT Statistics Matches: 272, Mismatches: 27, Indels: 17 0.86 0.09 0.05 Matches are distributed among these distances: 155 35 0.13 156 97 0.36 157 3 0.01 160 2 0.01 161 3 0.01 164 1 0.00 167 3 0.01 168 128 0.47 ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31 Consensus pattern (159 bp): TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA CCCTAGAGCCAGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGG ACATCATAATCATGCATTTTAACAATATA Found at i:147961 original size:166 final size:166 Alignment explanation

Indices: 147593--148151 Score: 619 Period size: 166 Copynumber: 3.4 Consensus size: 166 147583 ATGCCACATC * * * * * * 147593 TTTAAACATTTTACCAATATAATTCTATGTTTAAAACTTTAAACACCTCTTGGGACC-CTAGTAT 1 TTTAAACATTTTCCCTATATATTTCTATG-TT-AAACTTTAAACTCCTCTTGGGGCCTC-AGTAA * * * * * 147657 TAGTCCAGGGATCACGATTTTAACAATTTAGTATCTGCATCATTTGAAGATGCTTGCATAG-TAA 63 TAGTCCAGGAATCATGATTTTAACAATTTAGTATCTACATCATTTGAGGATGCTTGCATAGTTAT 147721 ATCACAAATTGTAGCATTGTAGTTCTTCAA-AAGAAGATT 128 ATCACAAATTGTAGCATTGTAGTTCTT-AAGAAGAAGATT * 147760 TTTAAACATTTTCCCTATATATTTCTATGTTAAACTTTAAACTCCTCATGGGGCCTCAGTAATAG 1 TTTAAACATTTTCCCTATATATTTCTATGTTAAACTTTAAACTCCTCTTGGGGCCTCAGTAATAG ** * * 147825 TCCAGCCATCATGATTTTAAGAATTTAGTATCTACATCATTTGAGGATGCTTGCATAGTTATCTC 66 TCCAGGAATCATGATTTTAACAATTTAGTATCTACATCATTTGAGGATGCTTGCATAGTTATATC * 147890 ACAAATTGTAGCATTGTACTTCTTAAGAAGAAGATT 131 ACAAATTGTAGCATTGTAGTTCTTAAGAAGAAGATT * * * * ** * * * 147926 TTTAAACATTTTCCCTATTTATTTCTTTGTTAAACTCTGAACTCCTCTCAGAGCCTCAGTACTGG 1 TTTAAACATTTTCCCTATATATTTCTATGTTAAACTTTAAACTCCTCTTGGGGCCTCAGTAATAG ** * * * 147991 TCTGGGAAT--TGCAATTTTAACAATTTA-TAATCTACATCACTTGAGGATGCTTGCATAATAAT 66 TCCAGGAATCATG--ATTTTAACAATTTAGT-ATCTACATCATTTGAGGATGCTTGCATAGTTAT * * * * * 148053 ATCACAAATTGGAGCACTGCAGTTCTTGAGAGGAAGA-T 128 ATCACAAATTGTAGCATTGTAGTTCTTAAGAAGAAGATT * * * * * * * 148091 TTTAAACATTTTCTCTATATATTTCTTTGTTAAATTTTGAACCCCTTTTGGGGCCTAAGTA 1 TTTAAACATTTTCCCTATATATTTCTATGTTAAACTTTAAACTCCTCTTGGGGCCTCAGTA 148152 TTGCTCCATC Statistics Matches: 335, Mismatches: 51, Indels: 14 0.84 0.13 0.04 Matches are distributed among these distances: 164 2 0.01 165 135 0.40 166 172 0.51 167 26 0.08 ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38 Consensus pattern (166 bp): TTTAAACATTTTCCCTATATATTTCTATGTTAAACTTTAAACTCCTCTTGGGGCCTCAGTAATAG TCCAGGAATCATGATTTTAACAATTTAGTATCTACATCATTTGAGGATGCTTGCATAGTTATATC ACAAATTGTAGCATTGTAGTTCTTAAGAAGAAGATT Found at i:157352 original size:33 final size:31 Alignment explanation

Indices: 157274--157340 Score: 127 Period size: 31 Copynumber: 2.2 Consensus size: 31 157264 ACAATGGTAA 157274 CATTCTCAGCAGTTATCTCTCTTTGCCCATT 1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT 157305 CATTCTCAGCAGTTATCTCTCTTTGCCCATT 1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT 157336 C-TTCT 1 CATTCT 157341 TATGCATAGT Statistics Matches: 36, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 30 4 0.11 31 32 0.89 ACGTcount: A:0.15, C:0.33, G:0.09, T:0.43 Consensus pattern (31 bp): CATTCTCAGCAGTTATCTCTCTTTGCCCATT Found at i:157541 original size:16 final size:16 Alignment explanation

Indices: 157520--157557 Score: 67 Period size: 16 Copynumber: 2.4 Consensus size: 16 157510 ACGGAAGAGT * 157520 GACAGACGGACGGACG 1 GACAGAAGGACGGACG 157536 GACAGAAGGACGGACG 1 GACAGAAGGACGGACG 157552 GACAGA 1 GACAGA 157558 GTGATTACTA Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.37, C:0.21, G:0.42, T:0.00 Consensus pattern (16 bp): GACAGAAGGACGGACG Found at i:170473 original size:70 final size:69 Alignment explanation

Indices: 170360--170514 Score: 265 Period size: 70 Copynumber: 2.2 Consensus size: 69 170350 CAATATCTGT ** 170360 GAATATCACTGATACAGCAGCTATTACAGTTGTACCTGAGAATATCACTGATTACAACAGTTGTA 1 GAATATCACTGATACAGCAGCTATTACAAATGTACCTGAGAATATCACTGA-TACAACAGTTGTA 170425 CCTGA 65 CCTGA * 170430 GAATATCACTGATACAGCAGCTATTACAAATGTATCTGAGAATATCACTGATACAACAGTTGTAC 1 GAATATCACTGATACAGCAGCTATTACAAATGTACCTGAGAATATCACTGATACAACAGTTGTAC 170495 CTGA 66 CTGA * 170499 GAATATCAATGATACA 1 GAATATCACTGATACA 170515 ACACTTGAAC Statistics Matches: 81, Mismatches: 4, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 69 33 0.41 70 48 0.59 ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28 Consensus pattern (69 bp): GAATATCACTGATACAGCAGCTATTACAAATGTACCTGAGAATATCACTGATACAACAGTTGTAC CTGA Found at i:170499 original size:30 final size:30 Alignment explanation

Indices: 170460--170545 Score: 118 Period size: 30 Copynumber: 2.9 Consensus size: 30 170450 CTATTACAAA * * * 170460 TGTATCTGAGAATATCACTGATACAACAGT 1 TGTACCTGAGAATATCAATGATACAACACT 170490 TGTACCTGAGAATATCAATGATACAACACT 1 TGTACCTGAGAATATCAATGATACAACACT * * * 170520 TGAACCTGTGAATACCAATGATACAA 1 TGTACCTGAGAATATCAATGATACAA 170546 TACATGTAGC Statistics Matches: 50, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 50 1.00 ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27 Consensus pattern (30 bp): TGTACCTGAGAATATCAATGATACAACACT Found at i:185958 original size:44 final size:44 Alignment explanation

Indices: 185901--186004 Score: 172 Period size: 44 Copynumber: 2.4 Consensus size: 44 185891 TGAAATATTA 185901 ATAATAATTCTTTTTTGATATAATATTTTTTCAATGGATAATAT 1 ATAATAATTCTTTTTTGATATAATATTTTTTCAATGGATAATAT * 185945 ATAATAATTCTTTTTCGATATAATATTTTTTCAATGGATAATAT 1 ATAATAATTCTTTTTTGATATAATATTTTTTCAATGGATAATAT ** * 185989 ATGCTAATACTTTTTT 1 ATAATAATTCTTTTTT 186005 TAATGCATTC Statistics Matches: 55, Mismatches: 5, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 44 55 1.00 ACGTcount: A:0.35, C:0.07, G:0.07, T:0.52 Consensus pattern (44 bp): ATAATAATTCTTTTTTGATATAATATTTTTTCAATGGATAATAT Found at i:216478 original size:51 final size:51 Alignment explanation

Indices: 216417--216592 Score: 307 Period size: 51 Copynumber: 3.5 Consensus size: 51 216407 GAATCTTAGT * * 216417 GATAAAGCAGTAAAAATGCAGTACCTTTGATGCCAGTATCTAAGTGATAAA 1 GATAATGCAGTAGAAATGCAGTACCTTTGATGCCAGTATCTAAGTGATAAA 216468 GATAATGCAGTAGAAATGCAGTACCTTTGATGCCAGTATCTAAGTGATAAA 1 GATAATGCAGTAGAAATGCAGTACCTTTGATGCCAGTATCTAAGTGATAAA * 216519 GATAATGCAGTAGAAATGCAGTACCTTTGATGGCAGTATCTAAGTGATAAA 1 GATAATGCAGTAGAAATGCAGTACCTTTGATGCCAGTATCTAAGTGATAAA * * 216570 GATAATGCAGTACAAATTCAGTA 1 GATAATGCAGTAGAAATGCAGTA 216593 AACCTATGAC Statistics Matches: 120, Mismatches: 5, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 51 120 1.00 ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27 Consensus pattern (51 bp): GATAATGCAGTAGAAATGCAGTACCTTTGATGCCAGTATCTAAGTGATAAA Found at i:225763 original size:21 final size:21 Alignment explanation

Indices: 225713--225766 Score: 90 Period size: 21 Copynumber: 2.6 Consensus size: 21 225703 TCGTAATTAT * * 225713 GGGCATTTAGGTGTTTTCGAC 1 GGGCATTTCGGTGTTTTCAAC 225734 GGGCATTTCGGTGTTTTCAAC 1 GGGCATTTCGGTGTTTTCAAC 225755 GGGCATTTCGGT 1 GGGCATTTCGGT 225767 AAATCCCGGG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 21 31 1.00 ACGTcount: A:0.13, C:0.17, G:0.33, T:0.37 Consensus pattern (21 bp): GGGCATTTCGGTGTTTTCAAC Found at i:229669 original size:26 final size:24 Alignment explanation

Indices: 229640--229726 Score: 90 Period size: 21 Copynumber: 3.6 Consensus size: 24 229630 ACAACATACA 229640 TCATAGCATAGCATAGCATTGAAA- 1 TCATA-CATAGCATAGCATTGAAAT 229664 TC-T-CATAGCATAGCATTGAAAT 1 TCATACATAGCATAGCATTGAAAT * * * 229686 CTCATATCATAGCATTGCATGGAATT 1 -TCATA-CATAGCATAGCATTGAAAT 229712 TCATACCATAGCATA 1 TCATA-CATAGCATA 229727 CAATCTCATA Statistics Matches: 53, Mismatches: 5, Indels: 9 0.79 0.07 0.13 Matches are distributed among these distances: 21 18 0.34 23 3 0.06 24 3 0.06 25 13 0.25 26 16 0.30 ACGTcount: A:0.37, C:0.20, G:0.14, T:0.30 Consensus pattern (24 bp): TCATACATAGCATAGCATTGAAAT Found at i:229672 original size:21 final size:21 Alignment explanation

Indices: 229646--229702 Score: 105 Period size: 21 Copynumber: 2.7 Consensus size: 21 229636 TACATCATAG 229646 CATAGCATAGCATTGAAATCT 1 CATAGCATAGCATTGAAATCT 229667 CATAGCATAGCATTGAAATCT 1 CATAGCATAGCATTGAAATCT * 229688 CATATCATAGCATTG 1 CATAGCATAGCATTG 229703 CATGGAATTT Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 21 35 1.00 ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30 Consensus pattern (21 bp): CATAGCATAGCATTGAAATCT Found at i:229920 original size:10 final size:10 Alignment explanation

Indices: 229905--229938 Score: 50 Period size: 10 Copynumber: 3.4 Consensus size: 10 229895 GTTCAAATCT 229905 CATAGCATAC 1 CATAGCATAC * * 229915 CATAGCAAAG 1 CATAGCATAC 229925 CATAGCATAC 1 CATAGCATAC 229935 CATA 1 CATA 229939 TCATTAAGCC Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 10 20 1.00 ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18 Consensus pattern (10 bp): CATAGCATAC Found at i:229992 original size:21 final size:20 Alignment explanation

Indices: 229966--230020 Score: 65 Period size: 21 Copynumber: 2.6 Consensus size: 20 229956 TCAATTTCTT * 229966 ATAGCATAGCATACAAATCTC 1 ATAGCATAGCATA-AAATCGC * 229987 ATAGCATATCATTAAAATCGC 1 ATAGCATAGCA-TAAAATCGC * 230008 ATACCATAGCATA 1 ATAGCATAGCATA 230021 GCATTAAATT Statistics Matches: 29, Mismatches: 4, Indels: 3 0.81 0.11 0.08 Matches are distributed among these distances: 20 2 0.07 21 25 0.86 22 2 0.07 ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25 Consensus pattern (20 bp): ATAGCATAGCATAAAATCGC Found at i:245374 original size:3 final size:3 Alignment explanation

Indices: 245366--245403 Score: 76 Period size: 3 Copynumber: 12.7 Consensus size: 3 245356 CATTTCAGTC 245366 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA 1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA 245404 AAACAACATC Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32 Consensus pattern (3 bp): GAT Found at i:275055 original size:5 final size:5 Alignment explanation

Indices: 275045--275103 Score: 75 Period size: 5 Copynumber: 11.2 Consensus size: 5 275035 TGAGACAAAA 275045 CTATC CTATC CTATC CTTTATC CTGTATC CTAT- CTATC CTATC CTATC 1 CTATC CTATC CTATC C--TATC C--TATC CTATC CTATC CTATC CTATC 275093 CTATC CTATC C 1 CTATC CTATC C 275104 CATACCTTCA Statistics Matches: 50, Mismatches: 1, Indels: 6 0.88 0.02 0.11 Matches are distributed among these distances: 4 4 0.08 5 35 0.70 7 11 0.22 ACGTcount: A:0.19, C:0.37, G:0.02, T:0.42 Consensus pattern (5 bp): CTATC Found at i:275289 original size:21 final size:21 Alignment explanation

Indices: 275264--275338 Score: 116 Period size: 21 Copynumber: 3.6 Consensus size: 21 275254 GCATCGATTT * * 275264 ACCCAAAAGGAACCCAAACGG 1 ACCCAAAAGGAACACAAAAGG 275285 ACCCAAAAGGAACACAAAAGG 1 ACCCAAAAGGAACACAAAAGG 275306 ACCCAAAAGGAACACAAAAGG 1 ACCCAAAAGGAACACAAAAGG 275327 TA-CCAAAAGGAA 1 -ACCCAAAAGGAA 275339 ATTTTAATGT Statistics Matches: 51, Mismatches: 2, Indels: 2 0.93 0.04 0.04 Matches are distributed among these distances: 21 50 0.98 22 1 0.02 ACGTcount: A:0.55, C:0.25, G:0.19, T:0.01 Consensus pattern (21 bp): ACCCAAAAGGAACACAAAAGG Found at i:275290 original size:10 final size:11 Alignment explanation

Indices: 275264--275338 Score: 93 Period size: 11 Copynumber: 7.1 Consensus size: 11 275254 GCATCGATTT 275264 ACCCAAAAGGA 1 ACCCAAAAGGA * 275275 ACCCAAACGG- 1 ACCCAAAAGGA 275285 ACCCAAAAGGA 1 ACCCAAAAGGA * 275296 ACACAAAAGG- 1 ACCCAAAAGGA 275306 ACCCAAAAGGA 1 ACCCAAAAGGA * * 275317 ACACAAAAGGT 1 ACCCAAAAGGA 275328 A-CCAAAAGGA 1 ACCCAAAAGGA 275338 A 1 A 275339 ATTTTAATGT Statistics Matches: 54, Mismatches: 8, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 10 26 0.48 11 28 0.52 ACGTcount: A:0.55, C:0.25, G:0.19, T:0.01 Consensus pattern (11 bp): ACCCAAAAGGA Found at i:276498 original size:15 final size:15 Alignment explanation

Indices: 276467--276545 Score: 70 Period size: 15 Copynumber: 5.2 Consensus size: 15 276457 TGAAATTTAT * 276467 TCACAATCGGT-TAG 1 TCACATTCGGTATAG * 276481 TCACATTTGGTATAG 1 TCACATTCGGTATAG 276496 TCACATTCGGTAGATAG 1 TCACATTCGGT--ATAG ** ** 276513 AAACATTCGGTACGG 1 TCACATTCGGTATAG * 276528 TCACATTTGGTATAG 1 TCACATTCGGTATAG 276543 TCA 1 TCA 276546 TAGTCGGGAA Statistics Matches: 50, Mismatches: 12, Indels: 5 0.75 0.18 0.07 Matches are distributed among these distances: 14 9 0.18 15 28 0.56 17 13 0.26 ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32 Consensus pattern (15 bp): TCACATTCGGTATAG Found at i:278424 original size:20 final size:20 Alignment explanation

Indices: 278394--278452 Score: 68 Period size: 20 Copynumber: 3.0 Consensus size: 20 278384 TGGGTCTCAC * 278394 TAAAA-AGCGCCCGGGATAA 1 TAAAATAGCGCCCGGGAGAA * 278413 TAAAATAGCGCCCGAGGAGCA 1 TAAAATAGCGCCCG-GGAGAA 278434 -AAAATAGGCGCCCGGGAGA 1 TAAAATA-GCGCCCGGGAGA 278453 TTATTTATGT Statistics Matches: 34, Mismatches: 3, Indels: 5 0.81 0.07 0.12 Matches are distributed among these distances: 19 5 0.15 20 18 0.53 21 11 0.32 ACGTcount: A:0.39, C:0.22, G:0.31, T:0.08 Consensus pattern (20 bp): TAAAATAGCGCCCGGGAGAA Found at i:279168 original size:73 final size:67 Alignment explanation

Indices: 279087--279225 Score: 179 Period size: 67 Copynumber: 2.0 Consensus size: 67 279077 AAACTTCATT * * * * 279087 GAATTTGTAGCAAGTTGCGTTATTTTAATATGAATACATTTATTTACAAACATTTCATTATATAC 1 GAATTTGTAACAAGTTGCGTTA-TTTAA-AT--ATA-A-ATATCTACAAACATTTCACTATATAC 279152 AATAAATG 60 AATAAATG * 279160 GAATTTGTAATAAGTTGCGTTATTTAAATATAAATATCTACAAACATTTCACTATATACAATAAA 1 GAATTTGTAACAAGTTGCGTTATTTAAATATAAATATCTACAAACATTTCACTATATACAATAAA 279225 T 66 T 279226 TGTTTACATA Statistics Matches: 61, Mismatches: 5, Indels: 6 0.85 0.07 0.08 Matches are distributed among these distances: 67 30 0.49 68 1 0.02 69 3 0.05 71 2 0.03 72 5 0.08 73 20 0.33 ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40 Consensus pattern (67 bp): GAATTTGTAACAAGTTGCGTTATTTAAATATAAATATCTACAAACATTTCACTATATACAATAAA TG Found at i:293396 original size:21 final size:21 Alignment explanation

Indices: 293367--293473 Score: 124 Period size: 21 Copynumber: 5.1 Consensus size: 21 293357 GCTACACGCT * * 293367 CGCTAAACGGTTCACACGAAA 1 CGCTGAACGGTTTACACGAAA 293388 CGCTGAACGGTTTACACGAAA 1 CGCTGAACGGTTTACACGAAA * * * * * 293409 CACTGCACGCTTTGCCCGAAA 1 CGCTGAACGGTTTACACGAAA * * 293430 CGCTAAACGATTTACACGAAA 1 CGCTGAACGGTTTACACGAAA * 293451 CGCTGAACGGTTTACAAGAAA 1 CGCTGAACGGTTTACACGAAA 293472 CG 1 CG 293474 ATTCTCGCAC Statistics Matches: 70, Mismatches: 16, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 21 70 1.00 ACGTcount: A:0.35, C:0.27, G:0.21, T:0.18 Consensus pattern (21 bp): CGCTGAACGGTTTACACGAAA Found at i:293630 original size:21 final size:21 Alignment explanation

Indices: 293604--293652 Score: 89 Period size: 21 Copynumber: 2.3 Consensus size: 21 293594 ACGATTCACT * 293604 CGAAACGCTAAATGGTTTACA 1 CGAAACGCTAAACGGTTTACA 293625 CGAAACGCTAAACGGTTTACA 1 CGAAACGCTAAACGGTTTACA 293646 CGAAACG 1 CGAAACG 293653 TTTCTCGCAC Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 27 1.00 ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18 Consensus pattern (21 bp): CGAAACGCTAAACGGTTTACA Found at i:296841 original size:16 final size:16 Alignment explanation

Indices: 296820--296854 Score: 61 Period size: 16 Copynumber: 2.2 Consensus size: 16 296810 AACTGAAGTG 296820 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC * 296836 GGACAGACAGATGGAC 1 GGACAGACAGACGGAC 296852 GGA 1 GGA 296855 TGGACTGACA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.37, C:0.20, G:0.40, T:0.03 Consensus pattern (16 bp): GGACAGACAGACGGAC Found at i:296846 original size:20 final size:20 Alignment explanation

Indices: 296821--296866 Score: 56 Period size: 20 Copynumber: 2.3 Consensus size: 20 296811 ACTGAAGTGG 296821 GACAGACAGACGGACGGACA 1 GACAGACAGACGGACGGACA ** * * 296841 GACAGATGGACGGATGGACT 1 GACAGACAGACGGACGGACA 296861 GACAGA 1 GACAGA 296867 TGCAGAGGAA Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.37, C:0.20, G:0.37, T:0.07 Consensus pattern (20 bp): GACAGACAGACGGACGGACA Found at i:296867 original size:20 final size:20 Alignment explanation

Indices: 296829--296868 Score: 62 Period size: 20 Copynumber: 2.0 Consensus size: 20 296819 GGGACAGACA 296829 GACGGACGGACAGACAGATG 1 GACGGACGGACAGACAGATG * * 296849 GACGGATGGACTGACAGATG 1 GACGGACGGACAGACAGATG 296869 CAGAGGAAAG Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.33, C:0.17, G:0.40, T:0.10 Consensus pattern (20 bp): GACGGACGGACAGACAGATG Found at i:298551 original size:131 final size:130 Alignment explanation

Indices: 298395--298657 Score: 517 Period size: 131 Copynumber: 2.0 Consensus size: 130 298385 GGTAAGTACA 298395 TGTAATAATTTGATACATGTATGTGAATTTGTTATTTTAAAATTTCTCTCATGAGAAATCATAAA 1 TGTAATAATTTGATACATGTATGTGAATTTGTTATTTTAAAATTTCTCTCATGAGAAATCATAAA 298460 TATATATGAACAGAATCTATAGCAAATTTCCAATGAAAATTTACAGGTATTTGTTTTATCATTTC 66 TATATATGAACAGAATCTATAGCAAATTTCCAATGAAAATTTACAGGTATTTGTTTTATCATTTC 298525 TGNTAATAATTTGATACATGTATGTGAATTTGTTATTTTAAAATTTCTCTCATGAGAAATCATAA 1 TG-TAATAATTTGATACATGTATGTGAATTTGTTATTTTAAAATTTCTCTCATGAGAAATCATAA 298590 ATATATATGAACAGAATCTATAGCAAATTTCCAATGAAAATTTACAGGTATTTGTTTTATCATTT 65 ATATATATGAACAGAATCTATAGCAAATTTCCAATGAAAATTTACAGGTATTTGTTTTATCATTT 298655 C 130 C 298656 TG 1 TG 298658 AGTTTATTCA Statistics Matches: 132, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 130 2 0.02 131 130 0.98 ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41 Consensus pattern (130 bp): TGTAATAATTTGATACATGTATGTGAATTTGTTATTTTAAAATTTCTCTCATGAGAAATCATAAA TATATATGAACAGAATCTATAGCAAATTTCCAATGAAAATTTACAGGTATTTGTTTTATCATTTC Found at i:305306 original size:11 final size:11 Alignment explanation

Indices: 305290--305318 Score: 51 Period size: 11 Copynumber: 2.7 Consensus size: 11 305280 ATTTTAGTTT 305290 AGTATTTACCA 1 AGTATTTACCA 305301 AGTATTTACCA 1 AGTATTTACCA 305312 AGT-TTTA 1 AGTATTTA 305319 TTCCTTGAGG Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 4 0.22 11 14 0.78 ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41 Consensus pattern (11 bp): AGTATTTACCA Found at i:306117 original size:163 final size:164 Alignment explanation

Indices: 305682--306143 Score: 777 Period size: 164 Copynumber: 2.8 Consensus size: 164 305672 GTGAGGTTGG * * 305682 CCAGTTCTTGGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCCAATTTGTGTGATC 1 CCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTTGTGTGATC * * 305747 CCCATTCAAGGGAACTGTTCTTTACCAAGTTTTATTCCTTGAGGGTATCCGTAAGTGTTCAGACA 66 CCCATTCAAGGGAACTGTTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTGTTCAGACA * 305812 GTGTGTCACATTTTCAACAGGCACAGAGCAAGGC 131 GTGTGTCACATGTTCAACAGGCACAGAGCAAGGC * * 305846 CCAGTTAC-TAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTAAGCGCAAATTTGTGTGAT 1 CCAGTT-CTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTTGTGTGAT * 305910 CCCCATTCAAGGGAACTGTTCTTTACCAAGTTTTATTTCTTGAGGGTATCCATATGTGTTCAGAC 65 CCCCATTCAAGGGAACTGTTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTGTTCAGAC 305975 AGTGTGTCACATGTTCAACAGGCACAGAGCAA-GC 130 AGTGTGTCACATGTTCAACAGGCACAGAGCAAGGC * 306009 CCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCGAATTTGTGTGA-C 1 CCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTTGTGTGATC * * * 306073 CCTCATGCAAGGGAACTGTTCTTTACCAAGTTTTATTCCTTGAGGCTATCCATATGTGTTCAGAG 66 CC-CATTCAAGGGAACTGTTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTGTTCAGAC 306138 AGTGTG 130 AGTGTG 306144 CACTGGCGGA Statistics Matches: 280, Mismatches: 15, Indels: 7 0.93 0.05 0.02 Matches are distributed among these distances: 162 4 0.01 163 124 0.44 164 151 0.54 165 1 0.00 ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30 Consensus pattern (164 bp): CCAGTTCTTAGAGCCACCTTTAGTGGGACACATGAAAGACATCTTCAGCTCAAATTTGTGTGATC CCCATTCAAGGGAACTGTTCTTTACCAAGTTTTATTCCTTGAGGGTATCCATATGTGTTCAGACA GTGTGTCACATGTTCAACAGGCACAGAGCAAGGC Found at i:320360 original size:31 final size:31 Alignment explanation

Indices: 320325--320391 Score: 98 Period size: 31 Copynumber: 2.2 Consensus size: 31 320315 CTTTAGATTA * * 320325 AATAAGATACCTATGATAAATGCTCCCTGAT 1 AATAAGATAACTATAATAAATGCTCCCTGAT * 320356 AATAAGATAACTATAATGAATGCTCCCTGAT 1 AATAAGATAACTATAATAAATGCTCCCTGAT * 320387 TATAA 1 AATAA 320392 ACCAATGCAG Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30 Consensus pattern (31 bp): AATAAGATAACTATAATAAATGCTCCCTGAT Found at i:323774 original size:2 final size:2 Alignment explanation

Indices: 323767--323795 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 323757 CATCTAAAAG 323767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 323796 NNNNNNNNNN Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:349764 original size:13 final size:13 Alignment explanation

Indices: 349746--349770 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 349736 TAAACTGATG 349746 TATTTTCTATATC 1 TATTTTCTATATC 349759 TATTTTCTATAT 1 TATTTTCTATAT 349771 GGGGCATTCC Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64 Consensus pattern (13 bp): TATTTTCTATATC Found at i:351030 original size:2 final size:2 Alignment explanation

Indices: 351023--351081 Score: 118 Period size: 2 Copynumber: 29.5 Consensus size: 2 351013 NNNNNNNNNN 351023 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 351065 TG TG TG TG TG TG TG TG T 1 TG TG TG TG TG TG TG TG T 351082 TAGAAATAAA Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 57 1.00 ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51 Consensus pattern (2 bp): TG Found at i:373473 original size:13 final size:13 Alignment explanation

Indices: 373455--373479 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 373445 GGAATTGGAG 373455 GGGGGGGGGGGGT 1 GGGGGGGGGGGGT 373468 GGGGGGGGGGGG 1 GGGGGGGGGGGG 373480 GGGTTGGAGG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.00, C:0.00, G:0.96, T:0.04 Consensus pattern (13 bp): GGGGGGGGGGGGT Found at i:373473 original size:14 final size:14 Alignment explanation

Indices: 373454--373480 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 373444 TGGAATTGGA 373454 GGGGGGGGGGGGGT 1 GGGGGGGGGGGGGT 373468 GGGGGGGGGGGGG 1 GGGGGGGGGGGGG 373481 GGTTGGAGGA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.00, C:0.00, G:0.96, T:0.04 Consensus pattern (14 bp): GGGGGGGGGGGGGT Found at i:374040 original size:17 final size:17 Alignment explanation

Indices: 374018--374054 Score: 74 Period size: 17 Copynumber: 2.2 Consensus size: 17 374008 GTGGTTCTGA 374018 GAATTCGTTATAACTGG 1 GAATTCGTTATAACTGG 374035 GAATTCGTTATAACTGG 1 GAATTCGTTATAACTGG 374052 GAA 1 GAA 374055 CTCCTCGGTG Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 20 1.00 ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32 Consensus pattern (17 bp): GAATTCGTTATAACTGG Found at i:374641 original size:2 final size:2 Alignment explanation

Indices: 374636--374719 Score: 168 Period size: 2 Copynumber: 42.0 Consensus size: 2 374626 GAGATTAACA 374636 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 374678 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 374720 GGGAGAGACA Statistics Matches: 82, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 82 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:383993 original size:20 final size:20 Alignment explanation

Indices: 383970--384009 Score: 62 Period size: 20 Copynumber: 2.0 Consensus size: 20 383960 TGTCTGGCGC * 383970 AAGTCACACTTCTCTGCCAT 1 AAGTCACAATTCTCTGCCAT * 383990 AAGTCACAATTCTTTGCCAT 1 AAGTCACAATTCTCTGCCAT 384010 TATCTCTTCA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.28, C:0.30, G:0.10, T:0.33 Consensus pattern (20 bp): AAGTCACAATTCTCTGCCAT Found at i:384277 original size:2 final size:2 Alignment explanation

Indices: 384270--384324 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 384260 TCCTTAGGAA 384270 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 384312 AC AC AC AC AC AC A 1 AC AC AC AC AC AC A 384325 AAAACATCAT Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:393308 original size:1 final size:1 Alignment explanation

Indices: 393297--393326 Score: 51 Period size: 1 Copynumber: 30.0 Consensus size: 1 393287 TCAAAATACA * 393297 CCCCACCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 393327 GAGTGTGGTT Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:394603 original size:1 final size:1 Alignment explanation

Indices: 394597--394627 Score: 62 Period size: 1 Copynumber: 31.0 Consensus size: 1 394587 GAACCATCAA 394597 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 394628 TCTCGGCCTT Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 30 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:396226 original size:8 final size:8 Alignment explanation

Indices: 396213--396261 Score: 80 Period size: 8 Copynumber: 6.1 Consensus size: 8 396203 TGCTTTGTTC 396213 GTATGTGT 1 GTATGTGT * 396221 GTATGTAT 1 GTATGTGT 396229 GTATGTGT 1 GTATGTGT * 396237 GTATGTAT 1 GTATGTGT 396245 GTATGTGT 1 GTATGTGT 396253 GTATGTGT 1 GTATGTGT 396261 G 1 G 396262 CACTCCATTT Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 8 37 1.00 ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49 Consensus pattern (8 bp): GTATGTGT Found at i:396229 original size:4 final size:4 Alignment explanation

Indices: 396213--396258 Score: 65 Period size: 4 Copynumber: 11.5 Consensus size: 4 396203 TGCTTTGTTC * * * 396213 GTAT GTGT GTAT GTAT GTAT GTGT GTAT GTAT GTAT GTGT GTAT GT 1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT 396259 GTGCACTCCA Statistics Matches: 36, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 4 36 1.00 ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50 Consensus pattern (4 bp): GTAT Found at i:396234 original size:16 final size:16 Alignment explanation

Indices: 396213--396258 Score: 92 Period size: 16 Copynumber: 2.9 Consensus size: 16 396203 TGCTTTGTTC 396213 GTATGTGTGTATGTAT 1 GTATGTGTGTATGTAT 396229 GTATGTGTGTATGTAT 1 GTATGTGTGTATGTAT 396245 GTATGTGTGTATGT 1 GTATGTGTGTATGT 396259 GTGCACTCCA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 30 1.00 ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50 Consensus pattern (16 bp): GTATGTGTGTATGTAT Found at i:407238 original size:14 final size:14 Alignment explanation

Indices: 407219--407245 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 407209 GGGACATTTA 407219 TTTCTCTCTCTCTC 1 TTTCTCTCTCTCTC 407233 TTTCTCTCTCTCT 1 TTTCTCTCTCTCT 407246 AACAAAATAG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59 Consensus pattern (14 bp): TTTCTCTCTCTCTC Found at i:408710 original size:15 final size:17 Alignment explanation

Indices: 408690--408721 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 408680 ACATATATAC 408690 TGTTTG-TA-AAAAAAA 1 TGTTTGTTACAAAAAAA 408705 TGTTTGTTACAAAAAAA 1 TGTTTGTTACAAAAAAA 408722 GATAAATCTA Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 15 6 0.40 16 2 0.13 17 7 0.47 ACGTcount: A:0.50, C:0.03, G:0.12, T:0.34 Consensus pattern (17 bp): TGTTTGTTACAAAAAAA Found at i:409767 original size:15 final size:17 Alignment explanation

Indices: 409747--409778 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 409737 ACATATATAC 409747 TGTTTG-TA-AAAAAAA 1 TGTTTGTTACAAAAAAA 409762 TGTTTGTTACAAAAAAA 1 TGTTTGTTACAAAAAAA 409779 GATAAATCTA Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 15 6 0.40 16 2 0.13 17 7 0.47 ACGTcount: A:0.50, C:0.03, G:0.12, T:0.34 Consensus pattern (17 bp): TGTTTGTTACAAAAAAA Found at i:412648 original size:45 final size:45 Alignment explanation

Indices: 412584--412674 Score: 182 Period size: 45 Copynumber: 2.0 Consensus size: 45 412574 AAGTGAAAGC 412584 GCGGAAGCCTTGAAAATTAACGACGATTCCGAGGCTATTTTTTGA 1 GCGGAAGCCTTGAAAATTAACGACGATTCCGAGGCTATTTTTTGA 412629 GCGGAAGCCTTGAAAATTAACGACGATTCCGAGGCTATTTTTTGA 1 GCGGAAGCCTTGAAAATTAACGACGATTCCGAGGCTATTTTTTGA 412674 G 1 G 412675 ACGTACCGTC Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 45 46 1.00 ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29 Consensus pattern (45 bp): GCGGAAGCCTTGAAAATTAACGACGATTCCGAGGCTATTTTTTGA Found at i:418579 original size:26 final size:26 Alignment explanation

Indices: 418543--418594 Score: 104 Period size: 26 Copynumber: 2.0 Consensus size: 26 418533 GTAGTAAAGT 418543 TATGAACAGCAAAATGTGCAAATATA 1 TATGAACAGCAAAATGTGCAAATATA 418569 TATGAACAGCAAAATGTGCAAATATA 1 TATGAACAGCAAAATGTGCAAATATA 418595 AGCAGGGTTG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23 Consensus pattern (26 bp): TATGAACAGCAAAATGTGCAAATATA Found at i:424365 original size:4 final size:4 Alignment explanation

Indices: 424356--424403 Score: 64 Period size: 4 Copynumber: 12.5 Consensus size: 4 424346 TACATTTCAT * * 424356 TATC TATC TATC TATC TATC AATC -AT- TATC TATT TATC TATC TATC 1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC 424402 TA 1 TA 424404 GATAGATAGA Statistics Matches: 39, Mismatches: 3, Indels: 4 0.85 0.07 0.09 Matches are distributed among these distances: 3 4 0.10 4 35 0.90 ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50 Consensus pattern (4 bp): TATC Found at i:424388 original size:26 final size:26 Alignment explanation

Indices: 424352--424401 Score: 91 Period size: 26 Copynumber: 1.9 Consensus size: 26 424342 CGAATACATT 424352 TCATTATCTATCTATCTATCTATCAA 1 TCATTATCTATCTATCTATCTATCAA * 424378 TCATTATCTATTTATCTATCTATC 1 TCATTATCTATCTATCTATCTATC 424402 TAGATAGATA Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 23 1.00 ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50 Consensus pattern (26 bp): TCATTATCTATCTATCTATCTATCAA Found at i:424593 original size:52 final size:52 Alignment explanation

Indices: 424537--424636 Score: 155 Period size: 52 Copynumber: 1.9 Consensus size: 52 424527 ACAACAACTG * 424537 CAACAACTAACAACATGGCTCCTAAAAACTGTAAACAAGGAACTTCAAACAA 1 CAACAACTAACAACATGCCTCCTAAAAACTGTAAACAAGGAACTTCAAACAA * * * * 424589 CAACAACTAACGACATGCCTTCTGAAAACTGTCAACAAGGAACTTCAA 1 CAACAACTAACAACATGCCTCCTAAAAACTGTAAACAAGGAACTTCAA 424637 CTTCTCAATG Statistics Matches: 43, Mismatches: 5, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 52 43 1.00 ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17 Consensus pattern (52 bp): CAACAACTAACAACATGCCTCCTAAAAACTGTAAACAAGGAACTTCAAACAA Found at i:429056 original size:20 final size:20 Alignment explanation

Indices: 429027--429072 Score: 65 Period size: 20 Copynumber: 2.3 Consensus size: 20 429017 TTCCCATTAT 429027 TTCCCAGGAAATACCAGTAA 1 TTCCCAGGAAATACCAGTAA * * * 429047 TTCCCGGGAATTACCAGTAT 1 TTCCCAGGAAATACCAGTAA 429067 TTCCCA 1 TTCCCA 429073 CCGTCCAGGG Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26 Consensus pattern (20 bp): TTCCCAGGAAATACCAGTAA Found at i:432484 original size:17 final size:17 Alignment explanation

Indices: 432464--432496 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 432454 AACTCTCAGT 432464 TTAGCCGATAACTGGTC 1 TTAGCCGATAACTGGTC 432481 TTAGCCGATAACTGGT 1 TTAGCCGATAACTGGT 432497 ACAGTACCAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30 Consensus pattern (17 bp): TTAGCCGATAACTGGTC Found at i:442883 original size:178 final size:178 Alignment explanation

Indices: 442584--442939 Score: 642 Period size: 178 Copynumber: 2.0 Consensus size: 178 442574 GATGTCCTAC * * 442584 TATATCCATGAAAAAGTTTTACTCTACCACCCTAAACAAAAGAGATCTAAACACTCAAAAATTAA 1 TATATCCATGAAAAAGTTTTACTCTACCACCCAAAACAAAAGAGATCTAAAAACTCAAAAATTAA 442649 TAGATTTCCAAATACCTTGACATTTGGCCAAGACGGACGCTTCTATCCAAAGAAGTCCGAAGTCT 66 TAGATTTCCAAATACCTTGACATTTGGCCAAGACGGACGCTTCTATCCAAAGAAGTCCGAAGTCT * 442714 CTATGATAAATAATAAAAAAATT-GAAGTAATTTTATGGAAATTTGAAT 131 CTATGATAAATAAT-AAAAAATTGGAAGTAATTTTATGAAAATTTGAAT * 442762 TATATCCATGAAAAAGTTTTACTCTACCACCCAAAACAAAAGAGATCTAAAAACTCATAAATTAA 1 TATATCCATGAAAAAGTTTTACTCTACCACCCAAAACAAAAGAGATCTAAAAACTCAAAAATTAA * 442827 TAGATTTCCAAATACCTTGACATTTGGCCAAGATGGACGCTTCTATCCAAAGAAGTCCGAAGTCT 66 TAGATTTCCAAATACCTTGACATTTGGCCAAGACGGACGCTTCTATCCAAAGAAGTCCGAAGTCT * 442892 CTATGATAAATAATAAAAAATTGGAAGTAATTTTATTAAAATTTGAAT 131 CTATGATAAATAATAAAAAATTGGAAGTAATTTTATGAAAATTTGAAT 442940 ATTTCAGGGG Statistics Matches: 171, Mismatches: 6, Indels: 2 0.96 0.03 0.01 Matches are distributed among these distances: 177 8 0.05 178 163 0.95 ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29 Consensus pattern (178 bp): TATATCCATGAAAAAGTTTTACTCTACCACCCAAAACAAAAGAGATCTAAAAACTCAAAAATTAA TAGATTTCCAAATACCTTGACATTTGGCCAAGACGGACGCTTCTATCCAAAGAAGTCCGAAGTCT CTATGATAAATAATAAAAAATTGGAAGTAATTTTATGAAAATTTGAAT Found at i:448548 original size:178 final size:179 Alignment explanation

Indices: 448249--448648 Score: 712 Period size: 178 Copynumber: 2.2 Consensus size: 179 448239 NNNNNNNNNN * 448249 AGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAA 1 AGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATATAGGGTACCCTCATTGTACGGATAA * 448314 CTCCTCCTACATTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGG 66 CTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGG ** 448379 TGT-ATATTGCTAGGATTTTGATTTCCAATAATTTATGGAAAAAATACC 131 TGTCATATTGCTAGGATTTTGATTTCCAATAATTTATAAAAAAAATACC 448427 AGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATATAGGGTACCCTCATTGTACGGATAA 1 AGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATATAGGGTACCCTCATTGTACGGATAA * * 448492 CTTCTCCTACAGTTCTCAAGATAGGAAGTTGTTTTTTTGCAGATCAATTGTACATATATCAGAGG 66 CTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGG * * 448557 TGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATAAAAAAAATACT 131 TGT-CATATTGCTAGGATTTTGATTTCCAATAATTTATAAAAAAAATACC 448607 AGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATATA 1 AGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATATA 448649 CATGTAGGGT Statistics Matches: 212, Mismatches: 8, Indels: 2 0.95 0.04 0.01 Matches are distributed among these distances: 178 129 0.61 180 83 0.39 ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38 Consensus pattern (179 bp): AGCTTTTGAACTTAGTCATTTTTTGGCAAAATGTTGCATATAGGGTACCCTCATTGTACGGATAA CTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGG TGTCATATTGCTAGGATTTTGATTTCCAATAATTTATAAAAAAAATACC Found at i:450862 original size:22 final size:22 Alignment explanation

Indices: 450835--450903 Score: 93 Period size: 22 Copynumber: 3.1 Consensus size: 22 450825 ACCGATCAGA 450835 CCCAACCTAACAGAAAATAAAC 1 CCCAACCTAACAGAAAATAAAC * * 450857 CTCAACCTAACAGAAAGTAAAC 1 CCCAACCTAACAGAAAATAAAC * * * 450879 CCCAAACTAACAGAAAGTAACC 1 CCCAACCTAACAGAAAATAAAC 450901 CCC 1 CCC 450904 CAAAAAACCT Statistics Matches: 42, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 22 42 1.00 ACGTcount: A:0.49, C:0.33, G:0.07, T:0.10 Consensus pattern (22 bp): CCCAACCTAACAGAAAATAAAC Found at i:463348 original size:4 final size:4 Alignment explanation

Indices: 463339--463371 Score: 66 Period size: 4 Copynumber: 8.2 Consensus size: 4 463329 ACCCACACAT 463339 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A 1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A 463372 CAAATACGAA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 29 1.00 ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24 Consensus pattern (4 bp): ATAC Found at i:463378 original size:12 final size:12 Alignment explanation

Indices: 463333--463387 Score: 58 Period size: 12 Copynumber: 4.6 Consensus size: 12 463323 GAGTGCACCC * 463333 ACACATATACAT 1 ACACACATACAT * 463345 ACATACATACAT 1 ACACACATACAT * 463357 ACATACATACAT 1 ACACACATACAT * 463369 ACACAAATACGA- 1 ACACACATAC-AT 463381 ACACACA 1 ACACACA 463388 CACGCACGGT Statistics Matches: 37, Mismatches: 5, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 12 36 0.97 13 1 0.03 ACGTcount: A:0.53, C:0.27, G:0.02, T:0.18 Consensus pattern (12 bp): ACACACATACAT Found at i:468596 original size:44 final size:45 Alignment explanation

Indices: 468505--468596 Score: 152 Period size: 45 Copynumber: 2.1 Consensus size: 45 468495 CTTCTTTATA * 468505 ACTGTTCATTACACAGACACTAGGTTTGGTTTTATATTATCATTT 1 ACTGTTCATTACAAAGACACTAGGTTTGGTTTTATATTATCATTT 468550 ACTGTTCATTACAAAGACAC-ATGGTTT-GTTTTATATTATCATTT 1 ACTGTTCATTACAAAGACACTA-GGTTTGGTTTTATATTATCATTT 468594 ACT 1 ACT 468597 CCTGTAGTGT Statistics Matches: 45, Mismatches: 1, Indels: 3 0.92 0.02 0.06 Matches are distributed among these distances: 44 21 0.47 45 24 0.53 ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45 Consensus pattern (45 bp): ACTGTTCATTACAAAGACACTAGGTTTGGTTTTATATTATCATTT Found at i:469152 original size:18 final size:18 Alignment explanation

Indices: 469129--469165 Score: 74 Period size: 18 Copynumber: 2.1 Consensus size: 18 469119 TACATCAACA 469129 ACCTTAAGTCCATACTGT 1 ACCTTAAGTCCATACTGT 469147 ACCTTAAGTCCATACTGT 1 ACCTTAAGTCCATACTGT 469165 A 1 A 469166 TGACTTTATT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32 Consensus pattern (18 bp): ACCTTAAGTCCATACTGT Found at i:470401 original size:176 final size:175 Alignment explanation

Indices: 470047--470507 Score: 750 Period size: 176 Copynumber: 2.6 Consensus size: 175 470037 CAGTATACTT * 470047 GTATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAATT 1 GTATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAAT * * 470112 TTATTGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGC---TTACGAGGTCAATTTTTGGATAA 66 TTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTATTACAAGGTCAATTTTTGGATAA * 470174 AACGGAGTCATTGTTGTGGTCAAAGTCCCATAACTCCAACAAAAA 131 AACAGAGTCATTGTTGTGGTCAAAGTCCCATAACTCCAACAAAAA 470219 GTATCGACCAATGCTGATTTTCGAAACTTGACCGAA-GTATTAGTGGTATAAACATTTGGTATAA 1 GTATCGACCAATGCTGATTTTCG-AACTTGACC-AAGGTATTAGTGGTATAAACATTTGGTATAA * * * 470283 ATTTAATGAAAATCCGTCAAAATGTGTAGGCATGAGAGTGCTTATTACAAGGTCAATTTTTTGAT 64 ATTTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTATTACAAGGTCAATTTTTGGAT 470348 AAAACAGAGTCATTGTTGTGGTCAAAGTCCCATAACTCCAACAAAAA 129 AAAACAGAGTCATTGTTGTGGTCAAAGTCCCATAACTCCAACAAAAA * 470395 GTATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTACTTGTATAAACATTTGGT 1 GTATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGT-G-----GTATAAACATTTGGT 470460 ATAAATTTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTA 60 ATAAATTTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTA 470508 CAAAAAAGTG Statistics Matches: 267, Mismatches: 10, Indels: 15 0.91 0.03 0.05 Matches are distributed among these distances: 172 23 0.09 173 74 0.28 174 4 0.01 175 16 0.06 176 89 0.33 181 61 0.23 ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31 Consensus pattern (175 bp): GTATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAAT TTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTATTACAAGGTCAATTTTTGGATAA AACAGAGTCATTGTTGTGGTCAAAGTCCCATAACTCCAACAAAAA Found at i:476403 original size:4 final size:4 Alignment explanation

Indices: 476394--476441 Score: 60 Period size: 4 Copynumber: 12.0 Consensus size: 4 476384 TTTACCCTTG * * * * 476394 TGTC TGTC TGTC TGTC CGTC CGTC CGTC TGTC TGTC CGTC TGTC TGTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC 476442 CGTCCGTAAC Statistics Matches: 40, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 4 40 1.00 ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42 Consensus pattern (4 bp): TGTC Found at i:476424 original size:16 final size:16 Alignment explanation

Indices: 476403--476448 Score: 74 Period size: 16 Copynumber: 2.9 Consensus size: 16 476393 GTGTCTGTCT 476403 GTCTGTCCGTCCGTCC 1 GTCTGTCCGTCCGTCC * * 476419 GTCTGTCTGTCCGTCT 1 GTCTGTCCGTCCGTCC 476435 GTCTGTCCGTCCGT 1 GTCTGTCCGTCCGT 476449 AACAAAAATT Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 27 1.00 ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37 Consensus pattern (16 bp): GTCTGTCCGTCCGTCC Found at i:476432 original size:12 final size:12 Alignment explanation

Indices: 476395--476445 Score: 75 Period size: 12 Copynumber: 4.2 Consensus size: 12 476385 TTACCCTTGT * 476395 GTCTGTCTGTCT 1 GTCTGTCTGTCC * * 476407 GTCCGTCCGTCC 1 GTCTGTCTGTCC 476419 GTCTGTCTGTCC 1 GTCTGTCTGTCC 476431 GTCTGTCTGTCC 1 GTCTGTCTGTCC 476443 GTC 1 GTC 476446 CGTAACAAAA Statistics Matches: 34, Mismatches: 5, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 12 34 1.00 ACGTcount: A:0.00, C:0.35, G:0.25, T:0.39 Consensus pattern (12 bp): GTCTGTCTGTCC Found at i:477030 original size:166 final size:166 Alignment explanation

Indices: 476472--477765 Score: 1925 Period size: 166 Copynumber: 7.8 Consensus size: 166 476462 GTCGCATTTA * * 476472 TCTCAGCAACTATTTATCGCAGATGCTTGACATTTTAACACAGTGTTTGCTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTAAGGCATGCCATAT * 476537 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTT * * 476602 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGTTT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 476639 TCTCAGCAACTATTTATCGCAGATGCTTGACATTTTAACACAGTGTTTG-TGAAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCT-AAGGCATGCCATA * 476703 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTTTTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTG-TTTATT * * 476768 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGTTT 129 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 476806 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTA-AGGCATGCCATA * * 476870 TTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT * * * 476935 TTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 476972 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGCTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTAAGGCATGCCATAT * * 477037 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTTCTGTTAAATGA-GTACTTTGTTTATTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTT * * * 477101 TTTGCCAAAATTTTCAAACAAATTTCCGTCAAAGAAT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * 477138 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTAAACACACTATTTGCTTAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTAAGGCATGCCATAT * * * 477203 CGTGGGATTTATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTT 477268 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * ** 477305 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTAAACACACTATTTGTTTTGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTAAGGCATGCCATAT * * 477370 TGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTATTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTT * 477434 TTTGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * * 477471 TCTCAGCAGCTATTTATCGGAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTAAGGCATGCCATAT 477536 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTA-TT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTT * * 477599 TTAGCCAAAATGTTCAAACAAATTTTCCTCAAAGATT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * * * 477636 TCTCAGCAGCTATTTATTGCAGATGCTTGAAATTTTAATACACTATTTGTTTAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTAAGGCATGCCATAT * * * * * * * * * 477701 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAATTGCCGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT 477766 GCATATTCAC Statistics Matches: 1049, Mismatches: 68, Indels: 21 0.92 0.06 0.02 Matches are distributed among these distances: 165 145 0.14 166 470 0.45 167 432 0.41 168 2 0.00 ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38 Consensus pattern (166 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGCTAAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT Found at i:477402 original size:499 final size:498 Alignment explanation

Indices: 476472--477765 Score: 2056 Period size: 499 Copynumber: 2.6 Consensus size: 498 476462 GTCGCATTTA * 476472 TCTCAGCAACTATTTATCGCAGATGCTTGACATTTTAACACAGTGTTTGCTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGCTAAGGCATGCCATAT * 476537 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTATTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGA-GTACTTTGTTTATTT * * * 476601 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGTTTTCTCAGCAACTATTTATCGCAGATGCT 130 TTT-GCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCT * * * * 476666 TGACATTTTAACACAGTGTTTGTGAAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGG 194 TGAAATTTTAACACACTATTTGT-TAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGG * 476731 ACGTCAACTTCCTGTTAAATGACGACTTTGCTTTTTTTTTAACCAAAATTTTCAAACAAATTTTC 258 ACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTTC * * ** * 476796 GTCAAAGTTTTCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGG 323 GTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTAAACACACTATTTGTATAGG 476861 CATGCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACG-ACT 388 CATGCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGA-GTACT 476925 TTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT 452 TTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT * 476972 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGCTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGCTAAGGCATGCCATAT * * 477037 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTTCTGTTAAATGAGTACTTTGTTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTT * 477102 TTGCCAAAATTTTCAAACAAATTTCCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTG 131 TTGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTG * * * 477167 AAATTTAAACACACTATTTGCTTAGGCATGCCATATCGTGGGATTTATTTTTGTATCAATCGGAC 196 AAATTTTAACACACTATTTG-TTAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGAC * 477232 GTCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAGCCAAAATTTTCAAACAAATTTTCGT 260 GTCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTTCGT * * * 477297 CAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTAAACACACTATTTGTTTTGGCA 325 CAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTAAACACACTATTTGTATAGGCA * * 477362 TGCCATATTGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTG 390 TGCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGAGTACTTTG * * * * 477427 TTTATTTTTTGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT 455 TTTATTTTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT * * * * 477471 TCTCAGCAGCTATTTATCGGAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGCTAAGGCATGCCATAT 477536 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTA-TTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTT * * * * 477600 TAGCCAAAATGTTCAAACAAATTTTCC-TCAAAGATTTCTCAGCAGCTATTTATTGCAGATGCTT 131 TTGCCAAAATTTTCAAACAAA-TTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT * * * 477664 GAAATTTTAATACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGA 195 GAAATTTTAACACACTATTTG-TTAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGA * * * * * * 477729 TGCCAGCTTTCTGTTAATTGCCGACTTTGCTTATTTT 259 CGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 477766 GCATATTCAC Statistics Matches: 733, Mismatches: 57, Indels: 10 0.92 0.07 0.01 Matches are distributed among these distances: 498 146 0.20 499 461 0.63 500 126 0.17 ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38 Consensus pattern (498 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGCTAAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTATTTT TTGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTG AAATTTTAACACACTATTTGTTAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCGGACG TCAACTTCCTGTTAAATGACGACTTTGCTTATTTTTTAACCAAAATTTTCAAACAAATTTTCGTC AAAGATTTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTAAACACACTATTTGTATAGGCAT GCCATATTGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGAGTACTTTGT TTATTTTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGAAT Found at i:482755 original size:200 final size:200 Alignment explanation

Indices: 482407--482801 Score: 781 Period size: 200 Copynumber: 2.0 Consensus size: 200 482397 ATTTTAATTT * 482407 CACCTTGAAAACAACATGTTAAATTATCACTTGGCAATATGGAATACAATATCTGTTCTATATAG 1 CACCCTGAAAACAACATGTTAAATTATCACTTGGCAATATGGAATACAATATCTGTTCTATATAG 482472 GTAATCTAATTTGATATTTGTTACATTGTATACTTGTAGGAATAAATTATATGCATTTATGCATT 66 GTAATCTAATTTGATATTTGTTACATTGTATACTTGTAGGAATAAATTATATGCATTTATGCATT 482537 GTATGCGCATTCTAAATGAAACTGTCAAGATTCTTCAGACTCTTGAAACGCATCACCTAGACCCC 131 GTATGCGCATTCTAAATGAAACTGTCAAGATTCTTCAGACTCTTGAAACGCATCACCTAGACCCC 482602 AAGAC 196 AAGAC 482607 CACCCTGAAAACAACATGTTAAATTATCACTTGGCAATATGGAATACAATATCTGTTCTATATAG 1 CACCCTGAAAACAACATGTTAAATTATCACTTGGCAATATGGAATACAATATCTGTTCTATATAG 482672 GTAATCTAATTTGATATTTGTTACATTGTATACTTGTAGGAATAAATTATATGCATTTATGCATT 66 GTAATCTAATTTGATATTTGTTACATTGTATACTTGTAGGAATAAATTATATGCATTTATGCATT 482737 GTATGCGCATTCTAAATGAAACTGTCAAGATTCTTCAGACTCTTGAAACGCATCACCTAGACCCC 131 GTATGCGCATTCTAAATGAAACTGTCAAGATTCTTCAGACTCTTGAAACGCATCACCTAGACCCC 482802 CCGACCCCCC Statistics Matches: 194, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 200 194 1.00 ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34 Consensus pattern (200 bp): CACCCTGAAAACAACATGTTAAATTATCACTTGGCAATATGGAATACAATATCTGTTCTATATAG GTAATCTAATTTGATATTTGTTACATTGTATACTTGTAGGAATAAATTATATGCATTTATGCATT GTATGCGCATTCTAAATGAAACTGTCAAGATTCTTCAGACTCTTGAAACGCATCACCTAGACCCC AAGAC Found at i:482851 original size:1 final size:1 Alignment explanation

Indices: 482806--482831 Score: 52 Period size: 1 Copynumber: 26.0 Consensus size: 1 482796 GACCCCCCGA 482806 CCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 482832 ACCCACACAC Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 25 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:493005 original size:17 final size:18 Alignment explanation

Indices: 492970--493005 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 492960 ATATAGTCTC * 492970 CTTCTAATTGTGTTAAAA 1 CTTCTAAGTGTGTTAAAA 492988 CTTCTAAGTGTG-TAAAA 1 CTTCTAAGTGTGTTAAAA 493005 C 1 C 493006 ATTTCTATTT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 6 0.35 18 11 0.65 ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39 Consensus pattern (18 bp): CTTCTAAGTGTGTTAAAA Found at i:511437 original size:20 final size:20 Alignment explanation

Indices: 511412--511575 Score: 310 Period size: 20 Copynumber: 8.2 Consensus size: 20 511402 CAAACAAGTG 511412 GTAACAGTCTGTACAGTAAA 1 GTAACAGTCTGTACAGTAAA * 511432 GTAACAGTCTGTACAGCAAA 1 GTAACAGTCTGTACAGTAAA 511452 GTAACAGTCTGTACAGTAAA 1 GTAACAGTCTGTACAGTAAA 511472 GTAACAGTCTGTACAGTAAA 1 GTAACAGTCTGTACAGTAAA 511492 GTAACAGTCTGTACAGTAAA 1 GTAACAGTCTGTACAGTAAA 511512 GTAACAGTCTGTACAGTAAA 1 GTAACAGTCTGTACAGTAAA * 511532 ATAACAGTCTGTACAGTAAA 1 GTAACAGTCTGTACAGTAAA 511552 GTAACAGTCTGTACAGTAAA 1 GTAACAGTCTGTACAGTAAA 511572 GTAA 1 GTAA 511576 AAATTACAAA Statistics Matches: 140, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 20 140 1.00 ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24 Consensus pattern (20 bp): GTAACAGTCTGTACAGTAAA Found at i:512013 original size:42 final size:42 Alignment explanation

Indices: 511966--512548 Score: 932 Period size: 42 Copynumber: 13.6 Consensus size: 42 511956 ACTGAATTGA ** 511966 ACAAAATACCAGCGACTGTATCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 512008 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * * * 512050 ACAAAATACCAGCTAATGTATCTAACTATCCAGGAACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * 512092 ACAAAATACCAGTTACTGTATCTGACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 512134 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 512176 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * 512218 ACAAAATACCAGCTACTGTATCTAATTATAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATC------TAACTATCCAGGGACAATTC * * 512266 ACAAAATATCAGTTACTGTTTCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * 512308 ACAAAATACCAGTTACTATATCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 512350 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * 512392 ACAAAATACCAGTTACTGTATCTAATTATAACTATCCAGGAACAATTC 1 ACAAAATACCAGTTACTGTATC------TAACTATCCAGGGACAATTC 512440 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * * * 512482 AAAAAATACCAGTTACCGTAACTAACTATCCAGGGACAATTC 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 512524 ACAAAATACCAGTTACTGTATCTAA 1 ACAAAATACCAGTTACTGTATCTAA 512549 TTATAACTAT Statistics Matches: 503, Mismatches: 26, Indels: 24 0.91 0.05 0.04 Matches are distributed among these distances: 42 423 0.84 48 80 0.16 ACGTcount: A:0.39, C:0.23, G:0.11, T:0.26 Consensus pattern (42 bp): ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC Found at i:512347 original size:174 final size:174 Alignment explanation

Indices: 511966--512548 Score: 1016 Period size: 174 Copynumber: 3.4 Consensus size: 174 511956 ACTGAATTGA ** 511966 ACAAAATACCAGCGACTGTATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT * 512031 AACTATCCAGGGACAATTCACAAAATACCAGCTAATGTATC------TAACTATCCAGGAACAAT 66 AACTATCCAGGGACAATTCACAAAATACCAGCTACTGTATCTAATTATAACTATCCAGGAACAAT * 512090 TCACAAAATACCAGTTACTGTATCTGACTATCCAGGGACAATTC 131 TCACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 512134 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT * 512199 AACTATCCAGGGACAATTCACAAAATACCAGCTACTGTATCTAATTATAACTATCCAGGGACAAT 66 AACTATCCAGGGACAATTCACAAAATACCAGCTACTGTATCTAATTATAACTATCCAGGAACAAT * * 512264 TCACAAAATATCAGTTACTGTTTCTAACTATCCAGGGACAATTC 131 TCACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * 512308 ACAAAATACCAGTTACTATATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT * 512373 AACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCTAATTATAACTATCCAGGAACAAT 66 AACTATCCAGGGACAATTCACAAAATACCAGCTACTGTATCTAATTATAACTATCCAGGAACAAT 512438 TCACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC 131 TCACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC * * * 512482 AAAAAATACCAGTTACCGTAACTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT 1 ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT 512547 AA 66 AA 512549 TTATAACTAT Statistics Matches: 393, Mismatches: 16, Indels: 6 0.95 0.04 0.01 Matches are distributed among these distances: 168 103 0.26 174 290 0.74 ACGTcount: A:0.39, C:0.23, G:0.11, T:0.26 Consensus pattern (174 bp): ACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTCACAAAATACCAGTTACTGTATCT AACTATCCAGGGACAATTCACAAAATACCAGCTACTGTATCTAATTATAACTATCCAGGAACAAT TCACAAAATACCAGTTACTGTATCTAACTATCCAGGGACAATTC Found at i:516478 original size:41 final size:41 Alignment explanation

Indices: 516432--516891 Score: 773 Period size: 41 Copynumber: 11.5 Consensus size: 41 516422 TAATAAGGCT * 516432 TACATGTAACGATCATGTAACTTAGCTGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG * 516473 TACATGTAACGATCATGTAACTTAGCTGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 516514 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG * * 516555 TACATGTAACGATCATGAAACTTAGATGATGGCCTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 516596 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 516637 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 516678 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 516719 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG * 516760 TACATGTAACGATCATGTAACTAAGATGATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 516801 TACATGTAACGATCATGTAACTT--A-GA----TT--A--- 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG * * 516830 TGCATGTAACGATCATGTAACTTAGATTATGGCTTACAGCG 1 TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG 516871 TACATGTAACGATCATGTAAC 1 TACATGTAACGATCATGTAAC 516892 GTACTTATTA Statistics Matches: 397, Mismatches: 10, Indels: 24 0.92 0.02 0.06 Matches are distributed among these distances: 29 22 0.06 31 1 0.00 32 2 0.01 34 2 0.01 36 2 0.01 38 3 0.01 39 1 0.00 41 364 0.92 ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29 Consensus pattern (41 bp): TACATGTAACGATCATGTAACTTAGATGATGGCTTACAGCG Found at i:516880 original size:30 final size:29 Alignment explanation

Indices: 516803--516860 Score: 116 Period size: 29 Copynumber: 2.0 Consensus size: 29 516793 TTACAGCGTA 516803 CATGTAACGATCATGTAACTTAGATTATG 1 CATGTAACGATCATGTAACTTAGATTATG 516832 CATGTAACGATCATGTAACTTAGATTATG 1 CATGTAACGATCATGTAACTTAGATTATG 516861 GCTTACAGCG Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34 Consensus pattern (29 bp): CATGTAACGATCATGTAACTTAGATTATG Done.