Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr09 85040211 

Parameters: 2 7 7 80 10 50 1000

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

Length: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 160 characters in sequence are not A, C, G, or T


File 98 of 292

Found at i:30039761 original size:68 final size:67

Alignment explanation

Indices: 30039689--30039838 Score: 171 Period size: 67 Copynumber: 2.2 Consensus size: 67 30039679 CATCATGTGT * * * * 30039689 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC 1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC 30039751 ATGTAG 62 ATGTAG ** * * 30039757 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT 1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT 30039822 AG 66 AG 30039824 ACAAGAGAGCTACGA 1 ACAAGAGAGCTACGA 30039839 GATAAACTGG Statistics Matches: 70, Mismatches: 9, Indels: 7 0.81 0.10 0.08 Matches are distributed among these distances: 64 20 0.29 65 7 0.10 66 4 0.06 67 26 0.37 68 13 0.19 ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21 Consensus pattern (67 bp): ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT AG Found at i:30039794 original size:64 final size:64 Alignment explanation

Indices: 30039713--30039896 Score: 194 Period size: 67 Copynumber: 2.8 Consensus size: 64 30039703 AGACATTATG * * 30039713 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT 1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA * * * * * * 30039777 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT 1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT 30039842 AA 63 AA * * * * 30039844 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC 1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC 30039897 CGAACTATAT Statistics Matches: 98, Mismatches: 17, Indels: 11 0.78 0.13 0.09 Matches are distributed among these distances: 62 1 0.01 63 19 0.19 64 21 0.21 65 8 0.08 66 16 0.16 67 31 0.32 68 2 0.02 ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23 Consensus pattern (64 bp): ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA Found at i:30040315 original size:29 final size:27 Alignment explanation

Indices: 30040282--30040345 Score: 83 Period size: 27 Copynumber: 2.3 Consensus size: 27 30040272 AAAATAGTAT * 30040282 AAATTGAATCAGAGACTGAATGAGATATC 1 AAATTAAATCAGA-A-TGAATGAGATATC ** 30040311 AAATTAAATCTTAATGAATGAGATATC 1 AAATTAAATCAGAATGAATGAGATATC 30040338 AAATTAAA 1 AAATTAAA 30040346 CCTTAATGAG Statistics Matches: 32, Mismatches: 3, Indels: 2 0.86 0.08 0.05 Matches are distributed among these distances: 27 21 0.66 28 1 0.03 29 10 0.31 ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28 Consensus pattern (27 bp): AAATTAAATCAGAATGAATGAGATATC Found at i:30040333 original size:27 final size:27 Alignment explanation

Indices: 30040298--30040354 Score: 105 Period size: 27 Copynumber: 2.1 Consensus size: 27 30040288 AATCAGAGAC * 30040298 TGAATGAGATATCAAATTAAATCTTAA 1 TGAATGAGATATCAAATTAAACCTTAA 30040325 TGAATGAGATATCAAATTAAACCTTAA 1 TGAATGAGATATCAAATTAAACCTTAA 30040352 TGA 1 TGA 30040355 GTCTATTTTC Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 27 29 1.00 ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32 Consensus pattern (27 bp): TGAATGAGATATCAAATTAAACCTTAA Found at i:30050395 original size:2 final size:2 Alignment explanation

Indices: 30050388--30050416 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 30050378 CATCCACACG 30050388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 30050417 CATTCTTTGA 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:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:30050715 original size:40 final size:38 Alignment explanation

Indices: 30050660--30050792 Score: 144 Period size: 40 Copynumber: 3.4 Consensus size: 38 30050650 GCGGGTCTCT * 30050660 AGCCCGGATAGCATTCTAGCACGAAGCCTGCGAGTCTTTA 1 AGCCCGGATAACATTC-AGCAC-AAGCCTGCGAGTCTTTA * * 30050700 AGCCCGGATAACATTCCAGCATATAGCTTGCGAGTCTTTA 1 AGCCCGGATAACATT-CAGCACA-AGCCTGCGAGTCTTTA * * * 30050740 AGCCCGGATAACATTC--CATCTAGCCTGTGGGTCTTTA 1 AGCCCGGATAACATTCAGCA-CAAGCCTGCGAGTCTTTA * 30050777 AGCTCGGATAACATTC 1 AGCCCGGATAACATTC 30050793 CTCAAGTATC Statistics Matches: 81, Mismatches: 9, Indels: 9 0.82 0.09 0.09 Matches are distributed among these distances: 37 30 0.37 39 2 0.02 40 48 0.59 41 1 0.01 ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26 Consensus pattern (38 bp): AGCCCGGATAACATTCAGCACAAGCCTGCGAGTCTTTA Found at i:30050785 original size:37 final size:37 Alignment explanation

Indices: 30050684--30050793 Score: 148 Period size: 37 Copynumber: 2.9 Consensus size: 37 30050674 TCTAGCACGA 30050684 AGCCTGCGAGTCTTTAAGCCCGGATAACATTCCAGCATAT 1 AGCCTGCGAGTCTTTAAGCCCGGATAACATT-C--CATAT * * 30050724 AGCTTGCGAGTCTTTAAGCCCGGATAACATTCCATCT 1 AGCCTGCGAGTCTTTAAGCCCGGATAACATTCCATAT * * * 30050761 AGCCTGTGGGTCTTTAAGCTCGGATAACATTCC 1 AGCCTGCGAGTCTTTAAGCCCGGATAACATTCC 30050794 TCAAGTATCA Statistics Matches: 64, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 37 33 0.52 39 1 0.02 40 30 0.47 ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28 Consensus pattern (37 bp): AGCCTGCGAGTCTTTAAGCCCGGATAACATTCCATAT Found at i:30058493 original size:40 final size:40 Alignment explanation

Indices: 30058434--30058641 Score: 218 Period size: 40 Copynumber: 5.2 Consensus size: 40 30058424 CAATTGAATG * * * * 30058434 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * * * 30058474 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 30058514 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 30058554 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * ** 30058594 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT 30058634 ATATCCGG 1 ATATCCGG 30058642 TTGTATTCCG Statistics Matches: 142, Mismatches: 26, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 40 142 1.00 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT Found at i:30058572 original size:80 final size:80 Alignment explanation

Indices: 30058435--30058641 Score: 247 Period size: 80 Copynumber: 2.6 Consensus size: 80 30058425 AATTGAATGA * * ** * * * 30058435 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA * 30058500 TTGTGCTAGT-G-AC 66 TTGTGCAAGTCGTAC * * * 30058513 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC 1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC * * 30058578 ATTTGTGCAAGTCGTTC 64 AATTGTGCAAGTCGTAC * * 30058595 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG 30058642 TTGTATTCCG Statistics Matches: 109, Mismatches: 16, Indels: 6 0.83 0.12 0.05 Matches are distributed among these distances: 78 1 0.01 80 105 0.96 81 1 0.01 82 2 0.02 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26 Consensus pattern (80 bp): TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA TTGTGCAAGTCGTAC Found at i:30061812 original size:79 final size:81 Alignment explanation

Indices: 30061711--30061895 Score: 227 Period size: 79 Copynumber: 2.3 Consensus size: 81 30061701 ACGACTCGCT ** * * 30061711 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC * * 30061774 GGGTTTAGTAACTT-GCA 64 GGATATAGTAACTTAGCA * ** 30061791 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG * 30061855 ATATAGTCACTTAGCA 66 ATATAGTAACTTAGCA 30061871 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 30061896 CATCATTCGA Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.59 80 34 0.37 ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24 Consensus pattern (81 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG ATATAGTAACTTAGCA Found at i:30061895 original size:40 final size:39 Alignment explanation

Indices: 30061704--30061895 Score: 163 Period size: 40 Copynumber: 4.8 Consensus size: 39 30061694 GGATATAACG * ** * * 30061704 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG 1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA * * * * 30061744 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA 1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA * * * 30061784 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA 1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA * * * * 30061823 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC 1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA * 30061863 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA 1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA 30061896 CATCATTCGA Statistics Matches: 121, Mismatches: 24, Indels: 14 0.76 0.15 0.09 Matches are distributed among these distances: 38 2 0.02 39 30 0.25 40 79 0.65 41 10 0.08 ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24 Consensus pattern (39 bp): ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA Found at i:30069844 original size:79 final size:81 Alignment explanation

Indices: 30069743--30069927 Score: 227 Period size: 79 Copynumber: 2.3 Consensus size: 81 30069733 ACGACTCGCT ** * * 30069743 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC * * 30069806 GGGTTTAGTAACTT-GCA 64 GGATATAGTAACTTAGCA * ** 30069823 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG * 30069887 ATATAGTCACTTAGCA 66 ATATAGTAACTTAGCA 30069903 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 30069928 CATCATTCGA Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.59 80 34 0.37 ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24 Consensus pattern (81 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG ATATAGTAACTTAGCA Found at i:30069927 original size:40 final size:39 Alignment explanation

Indices: 30069736--30069927 Score: 163 Period size: 40 Copynumber: 4.8 Consensus size: 39 30069726 GGATATAACG * ** * * 30069736 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG 1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA * * * * 30069776 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA 1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA * * * 30069816 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA 1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA * * * * 30069855 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC 1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA * 30069895 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA 1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA 30069928 CATCATTCGA Statistics Matches: 121, Mismatches: 24, Indels: 14 0.76 0.15 0.09 Matches are distributed among these distances: 38 2 0.02 39 30 0.25 40 79 0.65 41 10 0.08 ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24 Consensus pattern (39 bp): ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA Found at i:30077817 original size:39 final size:39 Alignment explanation

Indices: 30077696--30077886 Score: 170 Period size: 40 Copynumber: 4.8 Consensus size: 39 30077686 GGATATAACG * ** * 30077696 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGG-TTATAGTG 1 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATT-TAGTA * * * 30077736 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA 1 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTAGTA * * 30077776 ACTTGCACAAATGCCTTCGGGCTTAGCCCGGATTTATTA 1 ACTCGCACAAATGCCTTCGGGCTTAGCCCGGATTTAGTA * * * * * * 30077815 ACTCGCACGAATGCCTTCGGATCCTAGTCCGGATATAGTC 1 ACTCGCACAAATGCCTTCGG-GCTTAGCCCGGATTTAGTA * * 30077855 ACTTAGCACAAA-GCCTTCGGACTTAGCCCGGA 1 AC-TCGCACAAATGCCTTCGGGCTTAGCCCGGA 30077887 CATCATTCGA Statistics Matches: 124, Mismatches: 24, Indels: 7 0.80 0.15 0.05 Matches are distributed among these distances: 39 42 0.34 40 73 0.59 41 9 0.07 ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25 Consensus pattern (39 bp): ACTCGCACAAATGCCTTCGGGCTTAGCCCGGATTTAGTA Found at i:30077819 original size:79 final size:81 Alignment explanation

Indices: 30077703--30077886 Score: 216 Period size: 79 Copynumber: 2.3 Consensus size: 81 30077693 ACGACTCGCT ** * * 30077703 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGG-CTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC * * 30077766 GGGTTTAGTAACTT-GCA 64 GGATATAGTAACTTAGCA * ** 30077783 CAAATGCCTTCGGGCTTAGCCCGGATT-TATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG 1 CAAATGCCTTCGGGCTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG * 30077847 ATATAGTCACTTAGCA 66 ATATAGTAACTTAGCA * 30077863 CAAA-GCCTTCGGACTTAGCCCGGA 1 CAAATGCCTTCGGGCTTAGCCCGGA 30077887 CATCATTCGA Statistics Matches: 90, Mismatches: 11, Indels: 7 0.83 0.10 0.06 Matches are distributed among these distances: 78 3 0.03 79 64 0.71 80 23 0.26 ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24 Consensus pattern (81 bp): CAAATGCCTTCGGGCTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG ATATAGTAACTTAGCA Found at i:30091795 original size:79 final size:81 Alignment explanation

Indices: 30091694--30091878 Score: 227 Period size: 79 Copynumber: 2.3 Consensus size: 81 30091684 ACGACTCGCT ** * * 30091694 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC * * 30091757 GGGTTTAGTAACTT-GCA 64 GGATATAGTAACTTAGCA * ** 30091774 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG * 30091838 ATATAGTCACTTAGCA 66 ATATAGTAACTTAGCA 30091854 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 30091879 CATCATTCGA Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.59 80 34 0.37 ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24 Consensus pattern (81 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG ATATAGTAACTTAGCA Found at i:30091878 original size:40 final size:39 Alignment explanation

Indices: 30091687--30091878 Score: 163 Period size: 40 Copynumber: 4.8 Consensus size: 39 30091677 GGATATAACG * ** * * 30091687 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG 1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA * * * * 30091727 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA 1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA * * * 30091767 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA 1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA * * * * 30091806 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC 1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA * 30091846 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA 1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA 30091879 CATCATTCGA Statistics Matches: 121, Mismatches: 24, Indels: 14 0.76 0.15 0.09 Matches are distributed among these distances: 38 2 0.02 39 30 0.25 40 79 0.65 41 10 0.08 ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24 Consensus pattern (39 bp): ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA Found at i:30104833 original size:42 final size:41 Alignment explanation

Indices: 30104786--30104901 Score: 108 Period size: 43 Copynumber: 2.7 Consensus size: 41 30104776 AGTTTATGTG * 30104786 TAAGACCATATCTGGGATATGGAATTGGTATGAGAT-TTCATA 1 TAAGACCATAT-TGGGATATGGAATTGGTATGAGATCCT-ATA * * * * * 30104828 TAAGACCATAGTTGGGCTATTGGCATCGATATGAGATCCTATG 1 TAAGACCATA-TTGGGATA-TGGAATTGGTATGAGATCCTATA * * 30104871 TAAGATCATATTTGGGATATAGAATTGGTAT 1 TAAGACCATA-TTGGGATATGGAATTGGTAT 30104902 ATTACTATGT Statistics Matches: 58, Mismatches: 13, Indels: 6 0.75 0.17 0.08 Matches are distributed among these distances: 42 24 0.41 43 33 0.57 44 1 0.02 ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34 Consensus pattern (41 bp): TAAGACCATATTGGGATATGGAATTGGTATGAGATCCTATA Found at i:30106110 original size:20 final size:20 Alignment explanation

Indices: 30106085--30106156 Score: 135 Period size: 20 Copynumber: 3.6 Consensus size: 20 30106075 CGACTTACCT * 30106085 ACACGGGCGTGTCCCAAGCC 1 ACACGGGCGTGTCCTAAGCC 30106105 ACACGGGCGTGTCCTAAGCC 1 ACACGGGCGTGTCCTAAGCC 30106125 ACACGGGCGTGTCCTAAGCC 1 ACACGGGCGTGTCCTAAGCC 30106145 ACACGGGCGTGT 1 ACACGGGCGTGT 30106157 AACCGTTATT Statistics Matches: 51, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 20 51 1.00 ACGTcount: A:0.19, C:0.35, G:0.32, T:0.14 Consensus pattern (20 bp): ACACGGGCGTGTCCTAAGCC Found at i:30113380 original size:93 final size:93 Alignment explanation

Indices: 30113274--30113444 Score: 297 Period size: 93 Copynumber: 1.8 Consensus size: 93 30113264 ACCCATAAGT * * * 30113274 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 30113339 CGAGCTCGGATGCCTAGTTACATCTCTC 66 CGAGCTCGGATGCCTAGTTACATCTCTC * 30113367 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA * 30113432 CGAGTTCGGATGC 66 CGAGCTCGGATGC 30113445 TCAACCATCC Statistics Matches: 73, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 93 73 1.00 ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGCTCGGATGCCTAGTTACATCTCTC Found at i:30113441 original size:46 final size:46 Alignment explanation

Indices: 30113266--30113441 Score: 205 Period size: 46 Copynumber: 3.8 Consensus size: 46 30113256 TGTAACCCAC * * * 30113266 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * 30113312 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T * *** * 30113358 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT * 30113405 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA 30113442 TGCTCAACCA Statistics Matches: 110, Mismatches: 13, Indels: 14 0.80 0.09 0.10 Matches are distributed among these distances: 43 1 0.01 44 2 0.02 46 70 0.64 47 32 0.29 49 4 0.04 50 1 0.01 ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT Found at i:30115152 original size:43 final size:42 Alignment explanation

Indices: 30115073--30115185 Score: 118 Period size: 43 Copynumber: 2.7 Consensus size: 42 30115063 TAAAGTTTAT ** ** ** 30115073 GTGTAAGACCATATTTGGGATATGGCATCGGTATGAGATTTC 1 GTGTAAGACCATACCTGGGATATGGCATCAATATGAGATCCC * * 30115115 GTGTAAGACCATACCTGGGCTTTTGGCATCAATATGAGATCCC 1 GTGTAAGACCATACCTGGG-ATATGGCATCAATATGAGATCCC * * * 30115158 ATGTAAGACCATATCTAGGATATGGCAT 1 GTGTAAGACCATACCTGGGATATGGCAT 30115186 TGGTATATTA Statistics Matches: 57, Mismatches: 13, Indels: 2 0.79 0.18 0.03 Matches are distributed among these distances: 42 24 0.42 43 33 0.58 ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30 Consensus pattern (42 bp): GTGTAAGACCATACCTGGGATATGGCATCAATATGAGATCCC Found at i:30121220 original size:40 final size:40 Alignment explanation

Indices: 30121161--30121267 Score: 124 Period size: 40 Copynumber: 2.7 Consensus size: 40 30121151 CAATTGAATG * * * * 30121161 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT * * * ** 30121201 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT * 30121241 ACATCCGGGCTAAGACCCGAAGGCATT 1 ATATCCGGGCTAAGACCCGAAGGCATT 30121268 CGTGCAAGTC Statistics Matches: 55, Mismatches: 12, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 40 55 1.00 ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT Found at i:30121325 original size:39 final size:39 Alignment explanation

Indices: 30121199--30121327 Score: 154 Period size: 40 Copynumber: 3.3 Consensus size: 39 30121189 ATGCTGGAAA * * 30121199 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGA 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG * * * 30121239 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG * 30121279 TTCTATCCGGGCTAAGACCCG-AGGCATTCGTGCACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG 30121318 TTATATCCGG 1 TTATATCCGG 30121328 TTGTATTCCG Statistics Matches: 76, Mismatches: 11, Indels: 5 0.83 0.12 0.05 Matches are distributed among these distances: 38 1 0.01 39 27 0.36 40 48 0.63 ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24 Consensus pattern (39 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG Found at i:30128868 original size:40 final size:40 Alignment explanation

Indices: 30128823--30128951 Score: 165 Period size: 40 Copynumber: 3.2 Consensus size: 40 30128813 CGGAATACAA 30128823 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC * * * 30128863 CCGGATAGAACGACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC * * * 30128903 CCGGATGT-AGCACTAGCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC 30128942 CCGGATATAA 1 CCGGATATAA 30128952 TTTCCAGCAA Statistics Matches: 77, Mismatches: 9, Indels: 6 0.84 0.10 0.07 Matches are distributed among these distances: 38 2 0.03 39 32 0.42 40 43 0.56 ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22 Consensus pattern (40 bp): CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC Found at i:30128945 original size:39 final size:40 Alignment explanation

Indices: 30128839--30128948 Score: 154 Period size: 39 Copynumber: 2.8 Consensus size: 40 30128829 ATAACCACGT * 30128839 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTC 1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA * 30128879 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCACTA 1 GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACG-ACTA * 30128918 GCAC-AATTGCCTTCGGGTCTTAACCCGGATA 1 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATA 30128949 TAATTTCCAG Statistics Matches: 64, Mismatches: 3, Indels: 6 0.88 0.04 0.08 Matches are distributed among these distances: 38 3 0.05 39 31 0.48 40 30 0.47 ACGTcount: A:0.22, C:0.29, G:0.26, T:0.23 Consensus pattern (40 bp): GCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTA Found at i:30132498 original size:40 final size:39 Alignment explanation

Indices: 30132413--30132539 Score: 141 Period size: 40 Copynumber: 3.2 Consensus size: 39 30132403 CTGGAAATTA * * * 30132413 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTG-AC 1 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTGTTC 30132451 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTC 1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC * * * 30132493 TATCCGGGCTAAGACCCGAGGGCATTCGTGCACGTGGTTA 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC 30132533 TATCCGG 1 TATCCGG 30132540 TTGTATTCCG Statistics Matches: 77, Mismatches: 7, Indels: 8 0.84 0.08 0.09 Matches are distributed among these distances: 38 1 0.01 39 3 0.04 40 70 0.91 41 1 0.01 42 2 0.03 ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23 Consensus pattern (39 bp): TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGTTC Found at i:30136211 original size:40 final size:39 Alignment explanation

Indices: 30136043--30136222 Score: 161 Period size: 40 Copynumber: 4.5 Consensus size: 39 30136033 AGAAATTGAA * * 30136043 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT- 1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG * * * * * 30136083 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G * * 30136123 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG 1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG * * 30136163 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G * 30136203 TGATATCCGGG-TAAGTCCCG 1 TGATATCCGGGCTAAGACCCG 30136223 TTGGCCTTGG Statistics Matches: 115, Mismatches: 18, Indels: 15 0.78 0.12 0.10 Matches are distributed among these distances: 37 2 0.02 38 4 0.03 39 12 0.10 40 95 0.83 41 2 0.02 ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24 Consensus pattern (39 bp): TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG Found at i:30144121 original size:40 final size:41 Alignment explanation

Indices: 30144073--30144175 Score: 120 Period size: 41 Copynumber: 2.5 Consensus size: 41 30144063 AAATTGAATG * ** 30144073 ATATCCGGGCTAAGCCCCGAAGACAAT-TATGCT-GAAATTT 1 ATATCCGGGCTAAGACCCGAAGACAATGTATGCTAG-AAGCT * * * * 30144113 ATATCCGGGTTAAGACCCGAAGGCAATGTGTGCTAGTAGCT 1 ATATCCGGGCTAAGACCCGAAGACAATGTATGCTAGAAGCT 30144154 ATATCCGGGCTAAGACCCGAAG 1 ATATCCGGGCTAAGACCCGAAG 30144176 GCATTCGTGC Statistics Matches: 53, Mismatches: 8, Indels: 3 0.83 0.12 0.05 Matches are distributed among these distances: 40 24 0.45 41 28 0.53 42 1 0.02 ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22 Consensus pattern (41 bp): ATATCCGGGCTAAGACCCGAAGACAATGTATGCTAGAAGCT Found at i:30144240 original size:40 final size:40 Alignment explanation

Indices: 30144071--30144242 Score: 156 Period size: 40 Copynumber: 4.3 Consensus size: 40 30144061 AGAAATTGAA * * 30144071 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT- 1 TGATATCCGGGCTAAGACCCGAAGGCAATT-TG-TGCAAATG * * * * * 30144111 TTATATCCGGGTTAAGACCCGAAGGCAATGTGTGCTAGTAG 1 TGATATCCGGGCTAAGACCCGAAGGCAATTTGTGCAAAT-G * * 30144152 CT-ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTG 1 -TGATATCCGGGCTAAGACCCGAAGGCAATTTGTGCAA-ATG * * 30144192 TTAAATCCGGGCTAAGACCCGAAGGC-ATTTGTGCAAATCG 1 TGATATCCGGGCTAAGACCCGAAGGCAATTTGTGCAAAT-G 30144232 TGATATCCGGG 1 TGATATCCGGG 30144243 TAAAGTCCCG Statistics Matches: 108, Mismatches: 17, Indels: 14 0.78 0.12 0.10 Matches are distributed among these distances: 38 2 0.02 39 6 0.06 40 75 0.69 41 24 0.22 42 1 0.01 ACGTcount: A:0.28, C:0.22, G:0.27, T:0.24 Consensus pattern (40 bp): TGATATCCGGGCTAAGACCCGAAGGCAATTTGTGCAAATG Found at i:30148989 original size:28 final size:27 Alignment explanation

Indices: 30148956--30149011 Score: 76 Period size: 27 Copynumber: 2.0 Consensus size: 27 30148946 TTAGAATACT * 30148956 TTAGTTTACTAAAATTACCGAAATACCC 1 TTAGTTT-CTAAAAATACCGAAATACCC * * 30148984 TTAGTTTGTAAAAATACTGAAATACCC 1 TTAGTTTCTAAAAATACCGAAATACCC 30149011 T 1 T 30149012 CGATTTGTAA Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 27 18 0.72 28 7 0.28 ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34 Consensus pattern (27 bp): TTAGTTTCTAAAAATACCGAAATACCC Found at i:30148995 original size:27 final size:28 Alignment explanation

Indices: 30148965--30149064 Score: 100 Period size: 27 Copynumber: 3.7 Consensus size: 28 30148955 TTTAGTTTAC 30148965 TAAAATTACCGAAATACCCTTAG-TTTG 1 TAAAATTACCGAAATACCCTTAGATTTG * * * 30148992 TAAAAATACTGAAATACCC-TCGATTTG 1 TAAAATTACCGAAATACCCTTAGATTTG * * * * 30149019 TAAATTTACCAAAATA-CCTTCGACTTG 1 TAAAATTACCGAAATACCCTTAGATTTG 30149046 TAAAATTACC-AAAGTACCC 1 TAAAATTACCGAAA-TACCC 30149065 CCGATTTACA Statistics Matches: 60, Mismatches: 9, Indels: 7 0.79 0.12 0.09 Matches are distributed among these distances: 26 7 0.12 27 51 0.85 28 2 0.03 ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30 Consensus pattern (28 bp): TAAAATTACCGAAATACCCTTAGATTTG Found at i:30149090 original size:27 final size:27 Alignment explanation

Indices: 30149067--30149459 Score: 453 Period size: 27 Copynumber: 14.6 Consensus size: 27 30149057 AAGTACCCCC 30149067 GATTTACAGAATTACCGTTTTACCCTT 1 GATTTACAGAATTACCGTTTTACCCTT * * * 30149094 AATTTACATAATTACCGTTTTACCCCT 1 GATTTACAGAATTACCGTTTTACCCTT * * * 30149121 GATTTACATAATTATCGTTTTACCCTC 1 GATTTACAGAATTACCGTTTTACCCTT * * 30149148 GACTTACAGAATTACCGTTTTACCCCT 1 GATTTACAGAATTACCGTTTTACCCTT * * * 30149175 AATTTACATAATTACCGTTTTACCCCT 1 GATTTACAGAATTACCGTTTTACCCTT * * * 30149202 GATTTACATAATTATCGTTTTACCCTC 1 GATTTACAGAATTACCGTTTTACCCTT * * 30149229 GACTTACAGAATTACCGTTTTACCCCT 1 GATTTACAGAATTACCGTTTTACCCTT * * * * 30149256 AATTTACATAATTATCGTTTTACCCCT 1 GATTTACAGAATTACCGTTTTACCCTT * * * 30149283 GATTTACATAATTATCGTTTTACCCTC 1 GATTTACAGAATTACCGTTTTACCCTT * * * 30149310 GACTTACAGAATTACTGTTTTACCCTC 1 GATTTACAGAATTACCGTTTTACCCTT * ** 30149337 GATTTACTGAATTACTATTTTACCCTT 1 GATTTACAGAATTACCGTTTTACCCTT * ** 30149364 GATTTATAGAATTACTATTTTACCCTT 1 GATTTACAGAATTACCGTTTTACCCTT * * 30149391 GATTTATAGAATTACTGTTTTACCCTT 1 GATTTACAGAATTACCGTTTTACCCTT * * 30149418 GATTTACAGAATTACTGTTTTACCCTC 1 GATTTACAGAATTACCGTTTTACCCTT * 30149445 GATTTACAAAATTAC 1 GATTTACAGAATTAC 30149460 TAAAATACCC Statistics Matches: 321, Mismatches: 45, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 27 321 1.00 ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42 Consensus pattern (27 bp): GATTTACAGAATTACCGTTTTACCCTT Found at i:30149468 original size:27 final size:27 Alignment explanation

Indices: 30149330--30149603 Score: 108 Period size: 27 Copynumber: 10.1 Consensus size: 27 30149320 ATTACTGTTT * ** *** 30149330 TACCCTCGATTTACTGAATTACTATTT 1 TACCCTTGATTTACAAAATTACTAAAA * * *** 30149357 TACCCTTGATTTATAGAATTACTATTT 1 TACCCTTGATTTACAAAATTACTAAAA * * **** 30149384 TACCCTTGATTTATAGAATTACTGTTT 1 TACCCTTGATTTACAAAATTACTAAAA * **** 30149411 TACCCTTGATTTACAGAATTACTGTTT 1 TACCCTTGATTTACAAAATTACTAAAA * 30149438 TACCCTCGATTTACAAAATTACTAAAA 1 TACCCTTGATTTACAAAATTACTAAAA * *** ** 30149465 TACCCTTGGTTTGTGAAATTACCGAAA 1 TACCCTTGATTTACAAAATTACTAAAA ** ** * 30149492 -ACCCTCAATTTGTAAAATTACCAAAA 1 TACCCTTGATTTACAAAATTACTAAAA * * * 30149518 TACCCCTAATTTACAAAGTTAC-AGAAA 1 TACCCTTGATTTACAAAATTACTA-AAA 30149545 TA-CCTTGACTTT-CTAAAAATTA-TAGAAA 1 TACCCTTGA-TTTAC--AAAATTACTA-AAA * * * 30149573 TACCATTGGTTTACAAAATTACTGAAA 1 TACCCTTGATTTACAAAATTACTAAAA 30149600 TACC 1 TACC 30149604 TTTGGTTTGT Statistics Matches: 204, Mismatches: 34, Indels: 18 0.80 0.13 0.07 Matches are distributed among these distances: 26 27 0.13 27 155 0.76 28 17 0.08 29 5 0.02 ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37 Consensus pattern (27 bp): TACCCTTGATTTACAAAATTACTAAAA Found at i:30149472 original size:81 final size:81 Alignment explanation

Indices: 30149060--30149458 Score: 545 Period size: 81 Copynumber: 4.9 Consensus size: 81 30149050 ATTACCAAAG * * * 30149060 TACCCCCGATTTACAGAATTACCGTTTTACCCTTAATTTACATAATTACCGTTTTACCCCTGATT 1 TACCCTCGACTTACAGAATTACCGTTTTACCCTTAATTTACATAATTACTGTTTTACCCCTGATT 30149125 TACATAATTATCGTTT 66 TACATAATTATCGTTT * * 30149141 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT 1 TACCCTCGACTTACAGAATTACCGTTTTACCCTTAATTTACATAATTACTGTTTTACCCCTGATT 30149206 TACATAATTATCGTTT 66 TACATAATTATCGTTT * 30149222 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTA-TCGTTTTACCCCTGAT 1 TACCCTCGACTTACAGAATTACCGTTTTACCCTTAATTTACATAATTACT-GTTTTACCCCTGAT 30149286 TTACATAATTATCGTTT 65 TTACATAATTATCGTTT * ** * * 30149303 TACCCTCGACTTACAGAATTACTGTTTTACCCTCGATTTAC-TGAATTACTATTTTACCCTTGAT 1 TACCCTCGACTTACAGAATTACCGTTTTACCCTTAATTTACAT-AATTACTGTTTTACCCCTGAT * * * 30149367 TTATAGAATTA-CTATTT 65 TTACATAATTATC-GTTT * * * * * * 30149384 TACCCTTGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTA-CCCTCGAT 1 TACCCTCGACTTACAGAATTACCGTTTTACCCTTAATTTACATAATTACTGTTTTACCCCT-GAT * 30149448 TTACAAAATTA 65 TTACATAATTA 30149459 CTAAAATACC Statistics Matches: 290, Mismatches: 22, Indels: 12 0.90 0.07 0.04 Matches are distributed among these distances: 80 5 0.02 81 284 0.98 82 1 0.00 ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41 Consensus pattern (81 bp): TACCCTCGACTTACAGAATTACCGTTTTACCCTTAATTTACATAATTACTGTTTTACCCCTGATT TACATAATTATCGTTT Found at i:30149608 original size:27 final size:27 Alignment explanation

Indices: 30149560--30149611 Score: 79 Period size: 27 Copynumber: 1.9 Consensus size: 27 30149550 TGACTTTCTA 30149560 AAAATTATAGAAATACCATTGGTTTAC 1 AAAATTATAGAAATACCATTGGTTTAC * 30149587 AAAATTACT-GAAATACCTTTGGTTT 1 AAAATTA-TAGAAATACCATTGGTTT 30149612 GTTGATTTAC Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 27 22 0.96 28 1 0.04 ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37 Consensus pattern (27 bp): AAAATTATAGAAATACCATTGGTTTAC Found at i:30149695 original size:27 final size:27 Alignment explanation

Indices: 30149665--30149725 Score: 79 Period size: 27 Copynumber: 2.3 Consensus size: 27 30149655 ACCCCTAACA 30149665 GGTAAAAAGACCGTAA-AGCCCCTGTAG 1 GGTAAAAAGACCGTAATA-CCCCTGTAG ** * 30149692 GGTAAAGTGACCGTAATACCCCTGTAT 1 GGTAAAAAGACCGTAATACCCCTGTAG 30149719 GGTAAAA 1 GGTAAAA 30149726 CGACGAATAT Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 27 28 0.97 28 1 0.03 ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20 Consensus pattern (27 bp): GGTAAAAAGACCGTAATACCCCTGTAG Found at i:30150986 original size:9 final size:9 Alignment explanation

Indices: 30150974--30151048 Score: 60 Period size: 9 Copynumber: 7.7 Consensus size: 9 30150964 TTTGATAAAC 30150974 ATGATATGT 1 ATGATATGT * 30150983 ATGATATGCAC 1 ATGATATG--T 30150994 ATGATATGT 1 ATGATATGT * 30151003 ATGATATGCAC 1 ATGATATG--T * 30151014 ATGACATGT 1 ATGATATGT * 30151023 ATGATATGCAC 1 ATGATATG--T 30151034 ATGATATGT 1 ATGATATGT 30151043 ATGATA 1 ATGATA 30151049 CGCACACGAG Statistics Matches: 52, Mismatches: 8, Indels: 12 0.72 0.11 0.17 Matches are distributed among these distances: 9 29 0.56 11 23 0.44 ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35 Consensus pattern (9 bp): ATGATATGT Found at i:30150999 original size:11 final size:11 Alignment explanation

Indices: 30150983--30151041 Score: 63 Period size: 11 Copynumber: 5.7 Consensus size: 11 30150973 CATGATATGT 30150983 ATGATATGCAC 1 ATGATATGCAC * 30150994 ATGATATG--T 1 ATGATATGCAC 30151003 ATGATATGCAC 1 ATGATATGCAC * * 30151014 ATGACATG--T 1 ATGATATGCAC 30151023 ATGATATGCAC 1 ATGATATGCAC 30151034 ATGATATG 1 ATGATATG 30151042 TATGATACGC Statistics Matches: 38, Mismatches: 6, Indels: 8 0.73 0.12 0.15 Matches are distributed among these distances: 9 15 0.39 11 23 0.61 ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32 Consensus pattern (11 bp): ATGATATGCAC Found at i:30151062 original size:20 final size:20 Alignment explanation

Indices: 30150972--30151054 Score: 148 Period size: 20 Copynumber: 4.2 Consensus size: 20 30150962 ATTTTGATAA 30150972 ACATGATATGTATGATATGC 1 ACATGATATGTATGATATGC 30150992 ACATGATATGTATGATATGC 1 ACATGATATGTATGATATGC * 30151012 ACATGACATGTATGATATGC 1 ACATGATATGTATGATATGC * 30151032 ACATGATATGTATGATACGC 1 ACATGATATGTATGATATGC 30151052 ACA 1 ACA 30151055 CGAGATGTTC Statistics Matches: 60, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 60 1.00 ACGTcount: A:0.36, C:0.13, G:0.19, T:0.31 Consensus pattern (20 bp): ACATGATATGTATGATATGC Found at i:30151255 original size:24 final size:24 Alignment explanation

Indices: 30151108--30151248 Score: 248 Period size: 24 Copynumber: 5.9 Consensus size: 24 30151098 GAGGAAGTGA 30151108 AAAAGGGCTTATGCCCCAGTTAT- 1 AAAAGGGCTTATGCCCCAGTTATC * 30151131 TAAAGGGCTTATGCCCCAGTTATC 1 AAAAGGGCTTATGCCCCAGTTATC 30151155 AAAAGGGCTTATGCCCCAGTTATC 1 AAAAGGGCTTATGCCCCAGTTATC 30151179 AAAAGGGCTTATGCCCCAGTTATC 1 AAAAGGGCTTATGCCCCAGTTATC * 30151203 AAAAGGGCTTATGCCCCAGTTATA 1 AAAAGGGCTTATGCCCCAGTTATC * 30151227 AAAAGGGCTTTTGCCCCAGTTA 1 AAAAGGGCTTATGCCCCAGTTA 30151249 CTAAAAGAGG Statistics Matches: 113, Mismatches: 4, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 23 22 0.19 24 91 0.81 ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26 Consensus pattern (24 bp): AAAAGGGCTTATGCCCCAGTTATC Found at i:30151456 original size:42 final size:42 Alignment explanation

Indices: 30151393--30151484 Score: 123 Period size: 42 Copynumber: 2.2 Consensus size: 42 30151383 TAGTCTCCCC * ** 30151393 AAATGGGTTTGCATACATTCATTGGTATT-TCATGTGATATTG 1 AAATGGGCTTGCATACATTCATTGACATTAT-ATGTGATATTG * * 30151435 AAATGGGCTTGCATTCTTTCATTGACATTATATGTGATATTG 1 AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG 30151477 AAATGGGC 1 AAATGGGC 30151485 CTATGGGCCA Statistics Matches: 44, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 42 43 0.98 43 1 0.02 ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40 Consensus pattern (42 bp): AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG Found at i:30155348 original size:27 final size:27 Alignment explanation

Indices: 30155318--30155511 Score: 219 Period size: 27 Copynumber: 7.2 Consensus size: 27 30155308 TAATGAAATT ** * 30155318 CCCTCAATTTGTAGAATTACCATTTTA 1 CCCTCAATTTACAAAATTACCATTTTA * * * * 30155345 CCCTCGATTTATAGAATTA-CAGTTTCA 1 CCCTCAATTTACAAAATTACCA-TTTTA ** * 30155372 CCCTTGATTTACAAAATTACCGTTTTA 1 CCCTCAATTTACAAAATTACCATTTTA * * * 30155399 CCCTCGATTTATAGAATTACCATTTTA 1 CCCTCAATTTACAAAATTACCATTTTA 30155426 CCCTCAATTTACAAAATTACCATTTTA 1 CCCTCAATTTACAAAATTACCATTTTA 30155453 CCCTCAATTTACAAAATTACCATTTTA 1 CCCTCAATTTACAAAATTACCATTTTA * * ** 30155480 CCCTTAGTTTACAAAATTACTGTTTTA 1 CCCTCAATTTACAAAATTACCATTTTA 30155507 CCCTC 1 CCCTC 30155512 GATTGTGAAA Statistics Matches: 145, Mismatches: 20, Indels: 4 0.86 0.12 0.02 Matches are distributed among these distances: 26 2 0.01 27 142 0.98 28 1 0.01 ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39 Consensus pattern (27 bp): CCCTCAATTTACAAAATTACCATTTTA Found at i:30155398 original size:54 final size:53 Alignment explanation

Indices: 30155332--30155515 Score: 253 Period size: 54 Copynumber: 3.4 Consensus size: 53 30155322 CAATTTGTAG * 30155332 AATTACCATTTTACCCTCGATTTATAGAATTA-CAGTTTCACCCTTGATTTACAA 1 AATTACCATTTTACCCTCGATTTATAGAATTACCA-TTTTACCCTT-ATTTACAA * * 30155386 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAA 1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCT-TATTTACAA * * * 30155440 AATTACCATTTTACCCTCAATTTACAAAATTACCATTTTACCCTTAGTTTACAA 1 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTTA-TTTACAA ** 30155494 AATTACTGTTTTACCCTCGATT 1 AATTACCATTTTACCCTCGATT 30155516 GTGAAATTAC Statistics Matches: 116, Mismatches: 11, Indels: 6 0.87 0.08 0.05 Matches are distributed among these distances: 53 1 0.01 54 113 0.97 55 2 0.02 ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40 Consensus pattern (53 bp): AATTACCATTTTACCCTCGATTTATAGAATTACCATTTTACCCTTATTTACAA Found at i:30155685 original size:54 final size:55 Alignment explanation

Indices: 30155547--30155711 Score: 165 Period size: 54 Copynumber: 3.0 Consensus size: 55 30155537 TGTAGGATAC * * * * 30155547 AATTACCAAAATACCCCTAGTGTGTAAAATTACCAAAATACCC-CTAGTTTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAAAATTAACGAAATACCCTCTAATTTGTAA * * * * * * 30155601 AATTATCGAAATACCACTGGTTTGTGAAATTATCGAAATACCCTC-AATTTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAAAATTAACGAAATACCCTCTAATTTGTAA * ** * * 30155655 AATTACCAAAATACCCCTAATTTACAAAATTAAAGAAATACCCT-TAACTTTCTAA 1 AATTACCAAAATACCCCTAGTTTGTAAAATTAACGAAATACCCTCTAA-TTTGTAA 30155710 AA 1 AA 30155712 ATTATAGAAA Statistics Matches: 88, Mismatches: 20, Indels: 5 0.78 0.18 0.04 Matches are distributed among these distances: 54 79 0.90 55 9 0.10 ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30 Consensus pattern (55 bp): AATTACCAAAATACCCCTAGTTTGTAAAATTAACGAAATACCCTCTAATTTGTAA Found at i:30155686 original size:27 final size:27 Alignment explanation

Indices: 30155547--30155673 Score: 157 Period size: 27 Copynumber: 4.7 Consensus size: 27 30155537 TGTAGGATAC * 30155547 AATTACCAAAATACCCCTAGTGTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAA 30155574 AATTACCAAAATACCCCTAGTTTGTAA 1 AATTACCAAAATACCCCTAGTTTGTAA * * * * * 30155601 AATTATCGAAATACCACTGGTTTGTGA 1 AATTACCAAAATACCCCTAGTTTGTAA * * * 30155628 AATTATCGAAATA-CCCTCAATTTGTAA 1 AATTACCAAAATACCCCT-AGTTTGTAA 30155655 AATTACCAAAATACCCCTA 1 AATTACCAAAATACCCCTA 30155674 ATTTACAAAA Statistics Matches: 86, Mismatches: 12, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 26 3 0.03 27 79 0.92 28 4 0.05 ACGTcount: A:0.40, C:0.21, G:0.09, T:0.29 Consensus pattern (27 bp): AATTACCAAAATACCCCTAGTTTGTAA Found at i:30155693 original size:27 final size:28 Alignment explanation

Indices: 30155663--30155725 Score: 76 Period size: 29 Copynumber: 2.2 Consensus size: 28 30155653 AAAATTACCA 30155663 AAATACCCCTAA-TTT-ACAAAATTAAAG 1 AAATACCCCTAACTTTCA-AAAATTAAAG * * 30155690 AAATACCCTTAACTTTCTAAAAATTATAG 1 AAATACCCCTAACTTTC-AAAAATTAAAG 30155719 AAATACC 1 AAATACC 30155726 ATTGGTTTAC Statistics Matches: 31, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 27 11 0.35 28 3 0.10 29 16 0.52 30 1 0.03 ACGTcount: A:0.49, C:0.19, G:0.03, T:0.29 Consensus pattern (28 bp): AAATACCCCTAACTTTCAAAAATTAAAG Found at i:30156721 original size:25 final size:25 Alignment explanation

Indices: 30156688--30156757 Score: 104 Period size: 25 Copynumber: 2.8 Consensus size: 25 30156678 AGGAAGTGCT * 30156688 AAAAGGGCTCTGCCCCAGTTTACCA 1 AAAAGGGCTTTGCCCCAGTTTACCA * 30156713 AAAAGGGCTTTGCCCCAGTTTATCA 1 AAAAGGGCTTTGCCCCAGTTTACCA * * 30156738 GAAAGGGCTTTGCTCCAGTT 1 AAAAGGGCTTTGCCCCAGTT 30156758 ATTAAAAGAG Statistics Matches: 41, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 25 41 1.00 ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26 Consensus pattern (25 bp): AAAAGGGCTTTGCCCCAGTTTACCA Found at i:30156770 original size:24 final size:24 Alignment explanation

Indices: 30156688--30156770 Score: 96 Period size: 25 Copynumber: 3.4 Consensus size: 24 30156678 AGGAAGTGCT * * 30156688 AAAAGGGCTCTGCCCCAGTTTACC 1 AAAAGGGCTTTGCCCCAGTTTATC 30156712 AAAAAGGGCTTTGCCCCAGTTTATC 1 -AAAAGGGCTTTGCCCCAGTTTATC * * 30156737 AGAAAGGGCTTTGCTCCAG-TTATT 1 A-AAAGGGCTTTGCCCCAGTTTATC 30156761 AAAAGAGGCT 1 AAAAG-GGCT 30156771 AGGCCTCCAA Statistics Matches: 52, Mismatches: 4, Indels: 5 0.85 0.07 0.08 Matches are distributed among these distances: 23 4 0.08 24 10 0.19 25 38 0.73 ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25 Consensus pattern (24 bp): AAAAGGGCTTTGCCCCAGTTTATC Found at i:30159888 original size:2 final size:2 Alignment explanation

Indices: 30159881--30159920 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 30159871 TTATTGAAAG 30159881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 30159921 AAGGCTATTA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:30160102 original size:32 final size:32 Alignment explanation

Indices: 30160041--30160131 Score: 87 Period size: 32 Copynumber: 2.8 Consensus size: 32 30160031 TACTAGTGTG ** 30160041 TATATATGTGTAGTTGGATAAAGTTGAATGTC 1 TATATATGTGTAGTTGGATAAAGCCGAATGTC * 30160073 TATATATGTGT-GATTGGATATAA-CCGAATGTG 1 TATATATGTGTAG-TTGGATA-AAGCCGAATGTC * * * * 30160105 TATCTAGGTGTAGTTTGATATAGCCGA 1 TATATATGTGTAGTTGGATAAAGCCGA 30160132 TTGAGATGTA Statistics Matches: 48, Mismatches: 7, Indels: 8 0.76 0.11 0.13 Matches are distributed among these distances: 31 2 0.04 32 43 0.90 33 3 0.06 ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38 Consensus pattern (32 bp): TATATATGTGTAGTTGGATAAAGCCGAATGTC Found at i:30160185 original size:2 final size:2 Alignment explanation

Indices: 30160140--30160170 Score: 53 Period size: 2 Copynumber: 15.5 Consensus size: 2 30160130 GATTGAGATG * 30160140 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 30160171 GTGAGTTTAA Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48 Consensus pattern (2 bp): TA Found at i:30160315 original size:27 final size:26 Alignment explanation

Indices: 30160284--30160378 Score: 84 Period size: 27 Copynumber: 3.6 Consensus size: 26 30160274 TTGAGGGATA 30160284 CACTAAGTGTGCGAATTTGATACTGAG 1 CACTAAGTGTGCGAATTTGAT-CTGAG * * * * 30160311 CACTAAGTGTGCGAGTTGGATTTAAG 1 CACTAAGTGTGCGAATTTGATCTGAG * * * * 30160337 CACTATGTGCGTGAATTAAT-TTCTGAG 1 CACTAAGTGTGCGAATT--TGATCTGAG 30160364 CACTAAGTGTGCGAA 1 CACTAAGTGTGCGAA 30160379 ATCAGTTATT Statistics Matches: 51, Mismatches: 15, Indels: 4 0.73 0.21 0.06 Matches are distributed among these distances: 26 16 0.31 27 35 0.69 ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31 Consensus pattern (26 bp): CACTAAGTGTGCGAATTTGATCTGAG Found at i:30167842 original size:26 final size:26 Alignment explanation

Indices: 30167810--30167874 Score: 89 Period size: 26 Copynumber: 2.5 Consensus size: 26 30167800 ATACAAGCCA * 30167810 TAATCAGGAAGTTCACAAAGA-ACTTT 1 TAATCAGGAAGCTCACAAAGAGAC-TT * 30167836 TAATCAGGAAGCTCACGAAGAGACTT 1 TAATCAGGAAGCTCACAAAGAGACTT 30167862 TAATCA-GAAGCTC 1 TAATCAGGAAGCTC 30167875 CGGATAGCCA Statistics Matches: 36, Mismatches: 2, Indels: 3 0.88 0.05 0.07 Matches are distributed among these distances: 25 7 0.19 26 27 0.75 27 2 0.06 ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23 Consensus pattern (26 bp): TAATCAGGAAGCTCACAAAGAGACTT Found at i:30168005 original size:65 final size:65 Alignment explanation

Indices: 30167936--30168057 Score: 190 Period size: 65 Copynumber: 1.9 Consensus size: 65 30167926 AAGAACTGCA * 30167936 TTTGTGTCTGCAATATAAGCAAAATCACAACCGATCATATAACAGGACGCTCACAAAGAGCTGTG 1 TTTGTGTCCGCAATATAAGCAAAATCACAACCGATCATATAACAGGACGCTCACAAAGAGCTGTG * ** * * 30168001 TTTGTGTCCGCAATATATGCAGGATCACAACCGATCATATAGCAGGATGCTCACAAA 1 TTTGTGTCCGCAATATAAGCAAAATCACAACCGATCATATAACAGGACGCTCACAAA 30168058 AAGCCGCGGT Statistics Matches: 51, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 65 51 1.00 ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24 Consensus pattern (65 bp): TTTGTGTCCGCAATATAAGCAAAATCACAACCGATCATATAACAGGACGCTCACAAAGAGCTGTG Found at i:30178406 original size:39 final size:40 Alignment explanation

Indices: 30178323--30178488 Score: 201 Period size: 40 Copynumber: 4.2 Consensus size: 40 30178313 TGTGCATGAA 30178323 TGTGCGAATTGTGATATCCGGGCTAAGCCCCCGAAGGCAAT 1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCCGAAGGCAAT 30178364 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT 1 TGTGCGAATTGTGATATCCGGGCTAAGCCCCGAAGGCAAT ** * * * * * 30178403 TGTGCGAGCTATCATATCCGGGATAAACTCCGAAGGCAAT 1 TGTGCGAATTGTGATATCCGGGCTAAGCCCCGAAGGCAAT * * * * 30178443 TGTGC-AAGTTGTGATATACGGGTTAAGTCCCGAAGGCATT 1 TGTGCGAA-TTGTGATATCCGGGCTAAGCCCCGAAGGCAAT 30178483 TGTGCG 1 TGTGCG 30178489 GGTTATCATA Statistics Matches: 105, Mismatches: 17, Indels: 6 0.82 0.13 0.05 Matches are distributed among these distances: 39 34 0.32 40 44 0.42 41 27 0.26 ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25 Consensus pattern (40 bp): TGTGCGAATTGTGATATCCGGGCTAAGCCCCGAAGGCAAT Found at i:30178447 original size:40 final size:39 Alignment explanation

Indices: 30178352--30178447 Score: 129 Period size: 39 Copynumber: 2.4 Consensus size: 39 30178342 GGGCTAAGCC * * * * * 30178352 CCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAG 1 CCCGAAGGCAATTGTGCGAACTATCATATCCGGGATAAA * 30178391 CCCGAAGGCAATTGTGCGAGCTATCATATCCGGGATAAA 1 CCCGAAGGCAATTGTGCGAACTATCATATCCGGGATAAA 30178430 CTCCGAAGGCAATTGTGC 1 C-CCGAAGGCAATTGTGC 30178448 AAGTTGTGAT Statistics Matches: 50, Mismatches: 6, Indels: 1 0.88 0.11 0.02 Matches are distributed among these distances: 39 34 0.68 40 16 0.32 ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22 Consensus pattern (39 bp): CCCGAAGGCAATTGTGCGAACTATCATATCCGGGATAAA Found at i:30178455 original size:79 final size:80 Alignment explanation

Indices: 30178353--30178504 Score: 227 Period size: 79 Copynumber: 1.9 Consensus size: 80 30178343 GGCTAAGCCC * 30178353 CCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGCTATCA 1 CCGAAGGCAATTGTGCGAATTGTGATATACGGGCTAAGTCCCGAAGGCAATTGTGCGAGCTATCA * 30178417 TATCCGGGATAAACT 66 TAACCGGGATAAACT * * * * 30178432 CCGAAGGCAATTGTGC-AAGTTGTGATATACGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTATC 1 CCGAAGGCAATTGTGCGAA-TTGTGATATACGGGCTAAGTCCCGAAGGCAATTGTGCGAGCTATC 30178496 ATAACCGGG 65 ATAACCGGG 30178505 CTATGTCCCG Statistics Matches: 65, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 78 2 0.03 79 33 0.51 80 30 0.46 ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24 Consensus pattern (80 bp): CCGAAGGCAATTGTGCGAATTGTGATATACGGGCTAAGTCCCGAAGGCAATTGTGCGAGCTATCA TAACCGGGATAAACT Found at i:30178513 original size:40 final size:40 Alignment explanation

Indices: 30178340--30178518 Score: 166 Period size: 40 Copynumber: 4.5 Consensus size: 40 30178330 ATTGTGATAT * * * * * 30178340 CCGGGCTAAGCCCCCGAAGGCAATTGTGCGAATTGTGATAT 1 CCGGGCTAAG-TCCCGAAGGCAATTGTGCGAGTTATCATAA * * 30178381 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGCTATCATAT 1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTATCATAA * * * * * 30178420 CCGGGATAA-ACTCCGAAGGCAATTGTGCAAGTTGTGATATA 1 CCGGGCTAAGTC-CCGAAGGCAATTGTGCGAGTTATCATA-A * * * 30178461 -CGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTATCATAA 1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTATCATAA * 30178500 CCGGGCTATGTCCCGAAGG 1 CCGGGCTAAGTCCCGAAGG 30178519 TGTTTGAACG Statistics Matches: 114, Mismatches: 19, Indels: 11 0.79 0.13 0.08 Matches are distributed among these distances: 39 35 0.31 40 68 0.60 41 11 0.10 ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTATCATAA Found at i:30180192 original size:21 final size:23 Alignment explanation

Indices: 30180168--30180219 Score: 56 Period size: 21 Copynumber: 2.3 Consensus size: 23 30180158 TCAAATGGAG * 30180168 TAAAGAAAT-CTTGTA-ATGAAA 1 TAAAGAAATACTTGAACATGAAA 30180189 TAAA-AAATACTTGAACATGAAA 1 TAAAGAAATACTTGAACATGAAA * 30180211 AAAATGAAA 1 TAAA-GAAA 30180220 ATTATTCTAG Statistics Matches: 25, Mismatches: 2, Indels: 5 0.78 0.06 0.16 Matches are distributed among these distances: 20 4 0.16 21 9 0.36 22 9 0.36 24 3 0.12 ACGTcount: A:0.60, C:0.06, G:0.12, T:0.23 Consensus pattern (23 bp): TAAAGAAATACTTGAACATGAAA Found at i:30182213 original size:37 final size:37 Alignment explanation

Indices: 30182163--30182237 Score: 150 Period size: 37 Copynumber: 2.0 Consensus size: 37 30182153 GTTTCGTTTC 30182163 TTCCATATGAAAGTAGATTCATCAAGGTTCATTTACA 1 TTCCATATGAAAGTAGATTCATCAAGGTTCATTTACA 30182200 TTCCATATGAAAGTAGATTCATCAAGGTTCATTTACA 1 TTCCATATGAAAGTAGATTCATCAAGGTTCATTTACA 30182237 T 1 T 30182238 AATTTATTCA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36 Consensus pattern (37 bp): TTCCATATGAAAGTAGATTCATCAAGGTTCATTTACA Found at i:30183094 original size:40 final size:40 Alignment explanation

Indices: 30183034--30183201 Score: 178 Period size: 40 Copynumber: 4.2 Consensus size: 40 30183024 CGGGATTTAA * ** * 30183034 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC * *** * 30183074 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAGC 1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC * 30183114 CCGGATATAACAACTCACACGAA-TGCCTTCGGGTCTTAGC 1 CCGGATATAACAACTCGCAC-AATTGCCTTCGGGTCTTAGC * * * * 30183154 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGC 1 CCGGATATAA-CAACTCGCACAATTGCCTTCGGGTCTTAGC 30183194 CCGGATAT 1 CCGGATAT 30183202 CATTCAAATG Statistics Matches: 107, Mismatches: 18, Indels: 6 0.82 0.14 0.05 Matches are distributed among these distances: 39 2 0.02 40 102 0.95 41 3 0.03 ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26 Consensus pattern (40 bp): CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC Found at i:30193172 original size:40 final size:40 Alignment explanation

Indices: 30193071--30193173 Score: 161 Period size: 40 Copynumber: 2.6 Consensus size: 40 30193061 ACAATTCAGT ** * 30193071 TATGTATGGCACTTAGTGTGTAATTCGAGATAGCTTTGAC 1 TATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGAC * 30193111 TATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGC 1 TATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGAC * 30193151 TATGTATGACACTTAGTGTGCGA 1 TATGTATGGCACTTAGTGTGCGA 30193174 AATTAAAATA Statistics Matches: 58, Mismatches: 5, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 40 58 1.00 ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35 Consensus pattern (40 bp): TATGTATGGCACTTAGTGTGCGATTCGAGATAGCTTCGAC Found at i:30196272 original size:40 final size:39 Alignment explanation

Indices: 30196227--30196356 Score: 163 Period size: 40 Copynumber: 3.3 Consensus size: 39 30196217 CGGAATACAA 30196227 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC * * 30196267 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC * * * * 30196307 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC 30196347 CCGGATATAA 1 CCGGATATAA 30196357 TTTCCAGCAT Statistics Matches: 77, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 39 3 0.04 40 74 0.96 ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23 Consensus pattern (39 bp): CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC Found at i:30204413 original size:40 final size:39 Alignment explanation

Indices: 30204368--30204497 Score: 163 Period size: 40 Copynumber: 3.3 Consensus size: 39 30204358 CGGAATACAA 30204368 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC * * 30204408 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC * * * * 30204448 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC 30204488 CCGGATATAA 1 CCGGATATAA 30204498 TTTCCAGCAT Statistics Matches: 77, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 39 3 0.04 40 74 0.96 ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23 Consensus pattern (39 bp): CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC Found at i:30207116 original size:43 final size:43 Alignment explanation

Indices: 30207057--30207180 Score: 135 Period size: 43 Copynumber: 2.9 Consensus size: 43 30207047 TCACATATCG * * * 30207057 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATC-GAATA-A 1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACAATACA * * * * 30207098 TGATGGCAATGTCTCAGACATGGTCTTACATGTAATCACAATACA 1 --ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACAATACA * * 30207143 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA 1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACA 30207181 TCTAGGTAAC Statistics Matches: 70, Mismatches: 9, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 43 65 0.93 44 4 0.06 45 1 0.01 ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25 Consensus pattern (43 bp): ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACAATACA Found at i:30212661 original size:43 final size:42 Alignment explanation

Indices: 30212614--30212711 Score: 133 Period size: 42 Copynumber: 2.3 Consensus size: 42 30212604 CCCAGACGTT * * 30212614 GTCTTACATGTAATCAAATATCGATGCCAATGTCCTAGACAGG 1 GTCTTACACGTAATCAAATA-CGATACCAATGTCCTAGACAGG * * * * 30212657 GTCTTACACGAAATCAAGTACGATACCGATGTCCTAGACATG 1 GTCTTACACGTAATCAAATACGATACCAATGTCCTAGACAGG 30212699 GTCTTACACGTAA 1 GTCTTACACGTAA 30212712 ATCTCAAATC Statistics Matches: 48, Mismatches: 7, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 42 31 0.65 43 17 0.35 ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27 Consensus pattern (42 bp): GTCTTACACGTAATCAAATACGATACCAATGTCCTAGACAGG Found at i:30212702 original size:42 final size:43 Alignment explanation

Indices: 30212614--30212764 Score: 139 Period size: 43 Copynumber: 3.5 Consensus size: 43 30212604 CCCAGACGTT * * * 30212614 GTCTTACATGTAATCAAATATCGATGCCAATGTCCTAGACAGG 1 GTCTTACACGAAATCAAATATCGATACCAATGTCCTAGACAGG * * * 30212657 GTCTTACACGAAATCAAGTA-CGATACCGATGTCCTAGACATG 1 GTCTTACACGAAATCAAATATCGATACCAATGTCCTAGACAGG * ** * 30212699 GTCTTACACGTAAATCTCAA-ATCGACGCCAACGT-CTCAGAC-GTG 1 GTCTTACACG-AAATC-AAATATCGATACCAATGTCCT-AGACAG-G * 30212743 GTCTTACACGAAATCACATATC 1 GTCTTACACGAAATCAAATATC 30212765 AGAATCATAT Statistics Matches: 87, Mismatches: 15, Indels: 12 0.76 0.13 0.11 Matches are distributed among these distances: 42 30 0.34 43 33 0.38 44 24 0.28 ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25 Consensus pattern (43 bp): GTCTTACACGAAATCAAATATCGATACCAATGTCCTAGACAGG Found at i:30223887 original size:27 final size:27 Alignment explanation

Indices: 30223855--30224213 Score: 345 Period size: 27 Copynumber: 13.4 Consensus size: 27 30223845 GGCAAATCAA * * 30223855 TCATTTTACCTTACAGGGGTATTACAG 1 TCATTTTACCTTACAGGGGTATTTCGG * * * 30223882 TTATTTTATCTTACAGGGGTATTTCGA 1 TCATTTTACCTTACAGGGGTATTTCGG * 30223909 TCATTTTACCTTAAAGGGGTATTTCGG 1 TCATTTTACCTTACAGGGGTATTTCGG * 30223936 TCATTTTACC-T-CATGAGGGTATTTCTG 1 TCATTTTACCTTACA-G-GGGTATTTCGG * * 30223963 TCATTTTACCCTACGGGGGTATTTCGG 1 TCATTTTACCTTACAGGGGTATTTCGG * * * 30223990 TCATTTTACCCTACAAGGGTATTTCAG 1 TCATTTTACCTTACAGGGGTATTTCGG ** * 30224017 TCATTTTA-CTCTATGGGGGTA-TGCGG 1 TCATTTTACCT-TACAGGGGTATTTCGG * * * 30224043 CCATTTTACCCTACGGGGGTATTTCGG 1 TCATTTTACCTTACAGGGGTATTTCGG * * 30224070 TCATTTTACCTTACGGGGGTATTTCAG 1 TCATTTTACCTTACAGGGGTATTTCGG * 30224097 TTATTTTATCCTATA-A-GGGTATTTCGG 1 TCATTTTA-CCT-TACAGGGGTATTTCGG * * 30224124 TCATTTTACCCTA-TGGGGTATTTCGG 1 TCATTTTACCTTACAGGGGTATTTCGG * ** * 30224150 TCATTTCACCTTATGGGGGTATTTCAG 1 TCATTTTACCTTACAGGGGTATTTCGG * * * * 30224177 TCATTTCACCCTATAGGGGTATTTCGA 1 TCATTTTACCTTACAGGGGTATTTCGG 30224204 TCATTTTACC 1 TCATTTTACC 30224214 CTATGGGGTT Statistics Matches: 277, Mismatches: 44, Indels: 22 0.81 0.13 0.06 Matches are distributed among these distances: 25 3 0.01 26 46 0.17 27 220 0.79 28 5 0.02 29 3 0.01 ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41 Consensus pattern (27 bp): TCATTTTACCTTACAGGGGTATTTCGG Found at i:30224078 original size:80 final size:81 Alignment explanation

Indices: 30223897--30224234 Score: 398 Period size: 80 Copynumber: 4.2 Consensus size: 81 30223887 TTATCTTACA * * * 30223897 GGGGTATTTCGATCATTTTACCTTA-AAGGGGTATTTCGGTCATTTTAC-CTCATGAGGGTATTT 1 GGGGTATTTCGGTCATTTTACCTTACAA-GGGTATTTCAGTCATTTTACTCT-ATAAGGGTATTT * 30223960 CTGTCATTTTACCCTACG 64 CGGTCATTTTACCCTACG * ** * 30223978 GGGGTATTTCGGTCATTTTACCCTACAAGGGTATTTCAGTCATTTTACTCTATGGGGGTA-TGCG 1 GGGGTATTTCGGTCATTTTACCTTACAAGGGTATTTCAGTCATTTTACTCTATAAGGGTATTTCG * 30224042 GCCATTTTACCCTACG 66 GTCATTTTACCCTACG ** * 30224058 GGGGTATTTCGGTCATTTTACCTTACGGGGGTATTTCAGTTATTTTA-TCCTATAAGGGTATTTC 1 GGGGTATTTCGGTCATTTTACCTTACAAGGGTATTTCAGTCATTTTACT-CTATAAGGGTATTTC * 30224122 GGTCATTTTACCCTA-T 65 GGTCATTTTACCCTACG * *** * * * 30224138 GGGGTATTTCGGTCATTTCACCTTATGGGGGTATTTCAGTCATTTCACCCTATAGGGGTATTTCG 1 GGGGTATTTCGGTCATTTTACCTTACAAGGGTATTTCAGTCATTTTACTCTATAAGGGTATTTCG * * 30224203 ATCATTTTACCCTATG 66 GTCATTTTACCCTACG * * 30224219 GGGTTATTTCAGTCAT 1 GGGGTATTTCGGTCAT 30224235 ACATGGCCCA Statistics Matches: 225, Mismatches: 26, Indels: 12 0.86 0.10 0.05 Matches are distributed among these distances: 79 1 0.00 80 140 0.62 81 80 0.36 82 4 0.02 ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40 Consensus pattern (81 bp): GGGGTATTTCGGTCATTTTACCTTACAAGGGTATTTCAGTCATTTTACTCTATAAGGGTATTTCG GTCATTTTACCCTACG Found at i:30227699 original size:37 final size:37 Alignment explanation

Indices: 30227635--30227776 Score: 203 Period size: 37 Copynumber: 3.8 Consensus size: 37 30227625 AGCTCAGACG * * 30227635 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA * 30227672 AAATCTCCACACGTAGTCATCGAGTCTTACCCGGACA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA * * * 30227709 TACTCTCCACACGTAGTCATCGGGTCTTACCCGGGCA 1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA * * * 30227746 TACTCTCAACACGTAGTCATCGGGTCTTACC 1 AAATCTCCACACGTAGTCATCGGGTCTTACC 30227777 TAGACATAAT Statistics Matches: 97, Mismatches: 8, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 37 97 1.00 ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24 Consensus pattern (37 bp): AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA Found at i:30228233 original size:37 final size:37 Alignment explanation

Indices: 30228180--30228258 Score: 140 Period size: 37 Copynumber: 2.1 Consensus size: 37 30228170 ATCTGTACAT * 30228180 CCGGACAAAATTTCCACACGTAGTCATCGGGTCTTAC 1 CCGGACAAAATCTCCACACGTAGTCATCGGGTCTTAC * 30228217 CCGGACATAATCTCCACACGTAGTCATCGGGTCTTAC 1 CCGGACAAAATCTCCACACGTAGTCATCGGGTCTTAC 30228254 CCGGA 1 CCGGA 30228259 ATATATTTCC Statistics Matches: 40, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 37 40 1.00 ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23 Consensus pattern (37 bp): CCGGACAAAATCTCCACACGTAGTCATCGGGTCTTAC Found at i:30228517 original size:47 final size:47 Alignment explanation

Indices: 30228465--30228658 Score: 262 Period size: 47 Copynumber: 4.1 Consensus size: 47 30228455 CATACATATT * * * * * 30228465 TCACATTAGCCATTTGGCTTTACCACATATATGCATGTTCATACTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACACTCA * * * 30228512 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACACTCA * 30228559 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACACTCA * * ** * 30228606 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA 1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACACTCA 30228653 TCACAT 1 TCACAT 30228659 AAAATCCTAA Statistics Matches: 133, Mismatches: 14, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 47 133 1.00 ACGTcount: A:0.27, C:0.29, G:0.11, T:0.34 Consensus pattern (47 bp): TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACACTCA Found at i:30228537 original size:22 final size:22 Alignment explanation

Indices: 30228511--30228629 Score: 59 Period size: 23 Copynumber: 5.1 Consensus size: 22 30228501 GTTCATACTC 30228511 ATCACATTGGCCATTCGGCCTT 1 ATCACATTGGCCATTCGGCCTT * * 30228533 ATCACACATAT-G-CATGCTC-ACATT 1 AT--CACAT-TGGCCAT--TCGGCCTT 30228557 CATCACATTGGCCATTCGGCCTT 1 -ATCACATTGGCCATTCGGCCTT * * * 30228580 ATCACATATATG-CATGTTC-ACATT 1 ATCACAT-T-GGCCA--TTCGGCCTT 30228604 CATCACATTGGCCATTCGGCCTT 1 -ATCACATTGGCCATTCGGCCTT 30228627 ATC 1 ATC 30228630 TCATATATAC Statistics Matches: 71, Mismatches: 10, Indels: 32 0.63 0.09 0.28 Matches are distributed among these distances: 22 18 0.25 23 19 0.27 24 19 0.27 25 15 0.21 ACGTcount: A:0.24, C:0.30, G:0.13, T:0.32 Consensus pattern (22 bp): ATCACATTGGCCATTCGGCCTT Found at i:30232396 original size:43 final size:43 Alignment explanation

Indices: 30232348--30232519 Score: 147 Period size: 43 Copynumber: 4.0 Consensus size: 43 30232338 AACTCGTACA * * * 30232348 ATGCCAATGTCTCAGACGTGGTCTTACATGTAATCAAATATCG 1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG * ** * 30232391 ATGCCATTGTCCCAGACAAGGTCTTACACGAAATCATATAT-G 1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG * * * * 30232433 ATACCGATGTCCCAAACAGT--TCTTACACGTAAATCTCAA-ATCGG 1 ATGCCAATGTCCCAGAC-GTGGTCTTACACG-AAATC-AAATATC-G * * * 30232477 CT-CCAATGTCTCAGACGTGGTCTTACACGAAATCACATATCG 1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG 30232519 A 1 A 30232520 AATCCTATAT Statistics Matches: 99, Mismatches: 22, Indels: 17 0.72 0.16 0.12 Matches are distributed among these distances: 41 9 0.09 42 25 0.25 43 54 0.55 44 11 0.11 ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27 Consensus pattern (43 bp): ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG Found at i:30233862 original size:12 final size:12 Alignment explanation

Indices: 30233845--30233876 Score: 64 Period size: 12 Copynumber: 2.7 Consensus size: 12 30233835 TTTGTAGGCT 30233845 ATTTTCCAAGCC 1 ATTTTCCAAGCC 30233857 ATTTTCCAAGCC 1 ATTTTCCAAGCC 30233869 ATTTTCCA 1 ATTTTCCA 30233877 TCCTCAACAC Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 20 1.00 ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38 Consensus pattern (12 bp): ATTTTCCAAGCC Found at i:30237879 original size:11 final size:10 Alignment explanation

Indices: 30237847--30237892 Score: 51 Period size: 9 Copynumber: 4.7 Consensus size: 10 30237837 CATGAGATTT 30237847 TGATAT-ACA 1 TGATATGACA * 30237856 TGATTTGACA 1 TGATATGACA 30237866 TGATATGCACA 1 TGATATG-ACA * 30237877 TGATATG-TA 1 TGATATGACA 30237886 TGATATG 1 TGATATG 30237893 CACGTGATGT Statistics Matches: 32, Mismatches: 3, Indels: 4 0.82 0.08 0.10 Matches are distributed among these distances: 9 13 0.41 10 9 0.28 11 10 0.31 ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37 Consensus pattern (10 bp): TGATATGACA Found at i:30237974 original size:24 final size:25 Alignment explanation

Indices: 30237947--30238030 Score: 73 Period size: 25 Copynumber: 3.4 Consensus size: 25 30237937 GAGGAAGTGC * 30237947 AAAAGGGCTATG-CCCTAGTTACAG 1 AAAAGGGCTATGCCCCAAGTTACAG * * * 30237971 AAAAGGGCTTTGCCCCAATTTACCG 1 AAAAGGGCTATGCCCCAAGTTACAG * * * 30237996 AAAAGGGCTTTTCCCCCAGTTTATCA- 1 AAAAGGGCTATGCCCCAAG-TTA-CAG 30238022 AAAAGGGCT 1 AAAAGGGCT 30238031 TGTGACAGCC Statistics Matches: 49, Mismatches: 8, Indels: 4 0.80 0.13 0.07 Matches are distributed among these distances: 24 11 0.22 25 25 0.51 26 12 0.24 27 1 0.02 ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24 Consensus pattern (25 bp): AAAAGGGCTATGCCCCAAGTTACAG Found at i:30237999 original size:25 final size:25 Alignment explanation

Indices: 30237947--30238031 Score: 82 Period size: 26 Copynumber: 3.4 Consensus size: 25 30237937 GAGGAAGTGC * * * * 30237947 AAAAGGGCTATG-CCCTAGTTACAG 1 AAAAGGGCTTTGCCCCAATTTACCG 30237971 AAAAGGGCTTTGCCCCAATTTACCG 1 AAAAGGGCTTTGCCCCAATTTACCG * * * * 30237996 AAAAGGGCTTTTCCCCCAGTTTATCA 1 AAAAGGGC-TTTGCCCCAATTTACCG 30238022 AAAAGGGCTT 1 AAAAGGGCTT 30238032 GTGACAGCCT Statistics Matches: 51, Mismatches: 8, Indels: 3 0.82 0.13 0.05 Matches are distributed among these distances: 24 11 0.22 25 19 0.37 26 21 0.41 ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25 Consensus pattern (25 bp): AAAAGGGCTTTGCCCCAATTTACCG Found at i:30239473 original size:28 final size:28 Alignment explanation

Indices: 30239408--30239534 Score: 132 Period size: 28 Copynumber: 4.5 Consensus size: 28 30239398 TCATGAATTG * ** * 30239408 GCACTAAGTGTGCGGGTTCAAATTGTATA 1 GCACTAAGTGTGCGAGTT-TGATTATATA 30239437 GCACTAAGTGTGCGAGTTTGATTATATA 1 GCACTAAGTGTGCGAGTTTGATTATATA * 30239465 GCACTAAGTGTGCGAGTTTGACTAT-TAA 1 GCACTAAGTGTGCGAGTTTGATTATAT-A * * * 30239493 GCACTAAGTGTGCGGGCTT-ATTATACA 1 GCACTAAGTGTGCGAGTTTGATTATATA * 30239520 TGCTCTAAGTGTGCG 1 -GCACTAAGTGTGCG 30239535 GCCTTATCGA Statistics Matches: 85, Mismatches: 10, Indels: 7 0.83 0.10 0.07 Matches are distributed among these distances: 27 6 0.07 28 62 0.73 29 17 0.20 ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32 Consensus pattern (28 bp): GCACTAAGTGTGCGAGTTTGATTATATA Found at i:30242656 original size:46 final size:45 Alignment explanation

Indices: 30242513--30242656 Score: 120 Period size: 46 Copynumber: 3.1 Consensus size: 45 30242503 CCCGCCCATA * 30242513 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTA-CATCTCT 1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATC-CT * * 30242562 --CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCAT 1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCA-AC-CATCC-T * 30242605 AAGTGAACTAGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT 1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCATCCT 30242652 AGTGA 1 AGTGA 30242657 CATGTCACTT Statistics Matches: 79, Mismatches: 6, Indels: 23 0.73 0.06 0.21 Matches are distributed among these distances: 41 1 0.01 42 1 0.01 43 6 0.08 44 1 0.01 46 33 0.42 47 29 0.37 48 5 0.06 49 1 0.01 50 2 0.03 ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22 Consensus pattern (45 bp): AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCCT Found at i:30251726 original size:24 final size:25 Alignment explanation

Indices: 30251699--30251752 Score: 65 Period size: 25 Copynumber: 2.2 Consensus size: 25 30251689 AAGTGCAAAT 30251699 GGGCTATGCCCCAG-TTACAGAAAA 1 GGGCTATGCCCCAGTTTACAGAAAA * * * * 30251723 GGGCTTTGCCCTAGTTTCCCGAAAA 1 GGGCTATGCCCCAGTTTACAGAAAA 30251748 GGGCT 1 GGGCT 30251753 TTTGCCGTGT Statistics Matches: 25, Mismatches: 4, Indels: 1 0.83 0.13 0.03 Matches are distributed among these distances: 24 12 0.48 25 13 0.52 ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22 Consensus pattern (25 bp): GGGCTATGCCCCAGTTTACAGAAAA Found at i:30251751 original size:25 final size:26 Alignment explanation

Indices: 30251705--30251789 Score: 86 Period size: 25 Copynumber: 3.4 Consensus size: 26 30251695 AAATGGGCTA * * 30251705 TGCCCCAG-TTACAGAAAAGGGC-TT 1 TGCCCTAGTTTACCGAAAAGGGCTTT * 30251729 TGCCCTAGTTTCCCGAAAAGGGCTTT 1 TGCCCTAGTTTACCGAAAAGGGCTTT * * * 30251755 TGCCGT-GTTTATCAAAAAGGGCTTT 1 TGCCCTAGTTTACCGAAAAGGGCTTT * 30251780 TGCCCCAGTT 1 TGCCCTAGTT 30251790 ATTAAAAGAG Statistics Matches: 49, Mismatches: 9, Indels: 4 0.79 0.15 0.06 Matches are distributed among these distances: 24 7 0.14 25 32 0.65 26 10 0.20 ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29 Consensus pattern (26 bp): TGCCCTAGTTTACCGAAAAGGGCTTT Found at i:30252045 original size:31 final size:31 Alignment explanation

Indices: 30252010--30252096 Score: 102 Period size: 38 Copynumber: 2.6 Consensus size: 31 30252000 CATTAACAGT 30252010 AAAGGCTTCGGCCCAGTAACATGAAATATGA 1 AAAGGCTTCGGCCCAGTAACATGAAATATGA * 30252041 AAAGGCTTCGGCCCAGTGTTATGAAATATGAAATATGA 1 AAAGGCTTCGGCCCA--G---T--AACATGAAATATGA 30252079 AAAGGCTTCGGCCCAGTA 1 AAAGGCTTCGGCCCAGTA 30252097 TATGCTGAGA Statistics Matches: 48, Mismatches: 1, Indels: 14 0.76 0.02 0.22 Matches are distributed among these distances: 31 16 0.33 33 2 0.04 36 2 0.04 38 28 0.58 ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTAACATGAAATATGA Found at i:30254036 original size:47 final size:47 Alignment explanation

Indices: 30253977--30254192 Score: 378 Period size: 47 Copynumber: 4.6 Consensus size: 47 30253967 CCATTGGCAC 30253977 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG 1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG * * 30254024 TAAGACAAGGATACCATGTAAAACCATGTTTGGAACATGGCATTTTG 1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG 30254071 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG 1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG * * 30254118 TAAGACAAGGATACCATGTAAGACCATGTTAGGAACATGGAATTTGG 1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG * * 30254165 TAAGATAAGGATATCATGTAAGACCATG 1 TAAGACAAGGATACCATGTAAGACCATG 30254193 CCAAGGCATG Statistics Matches: 161, Mismatches: 8, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 47 161 1.00 ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25 Consensus pattern (47 bp): TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG Found at i:30254229 original size:54 final size:54 Alignment explanation

Indices: 30254165--30254367 Score: 194 Period size: 54 Copynumber: 3.8 Consensus size: 54 30254155 TGGAATTTGG * * * * * 30254165 TAAGATAAGGATATCATGTAAGACCATGCCAAGGCATGGTATTGATAAGTTATA 1 TAAGGTAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTATA * * * * ** * 30254219 TAAGGTAAGGAAATCATGTAAGACTATGTCAAGACATCACACTGATGAGTTACTA 1 TAAGGTAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTA-TA * * * * * 30254274 TAAGGCAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTT-CA 1 TAAGG-TAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTATA * * * 30254327 TAAGGCAAGGATACCACGTAAGACCATGTCAAGACATGGCA 1 TAAGGTAAGGATACCATGTAAGACCATGCCAAGACATGGCA 30254368 ATGGTAAGTT Statistics Matches: 119, Mismatches: 27, Indels: 7 0.78 0.18 0.05 Matches are distributed among these distances: 52 4 0.03 53 32 0.27 54 42 0.35 55 37 0.31 56 4 0.03 ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23 Consensus pattern (54 bp): TAAGGTAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTATA Found at i:30254379 original size:53 final size:54 Alignment explanation

Indices: 30254171--30254377 Score: 193 Period size: 53 Copynumber: 3.8 Consensus size: 54 30254161 TTGGTAAGAT * * * * * 30254171 AAGGATATCATGTAAGACCATGCCAAGGCATGGTATTGATAAGTTATATAAGGT 1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTACATAAGGC * * * * ** * * 30254225 AAGGAAATCATGTAAGACTATGTCAAGACATCACACTGATGAGTTACTATAAGGC 1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTAC-ATAAGGC * * * * 30254280 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTT-CATAAGGC 1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTACATAAGGC * * * * 30254333 AAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTT 1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT 30254378 CAAAAAGGAA Statistics Matches: 123, Mismatches: 27, Indels: 7 0.78 0.17 0.04 Matches are distributed among these distances: 52 4 0.03 53 41 0.33 54 38 0.31 55 36 0.29 56 4 0.03 ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23 Consensus pattern (54 bp): AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTACATAAGGC Found at i:30257795 original size:40 final size:39 Alignment explanation

Indices: 30257750--30257879 Score: 136 Period size: 40 Copynumber: 3.3 Consensus size: 39 30257740 CGGAATATAA 30257750 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC * * * * 30257790 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC * * * * * 30257830 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC 30257870 CCGGATATAA 1 CCGGATATAA 30257880 TTTCCAGCAT Statistics Matches: 72, Mismatches: 14, Indels: 8 0.77 0.15 0.09 Matches are distributed among these distances: 38 1 0.01 40 69 0.96 41 1 0.01 42 1 0.01 ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25 Consensus pattern (39 bp): CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC Found at i:30257894 original size:40 final size:40 Alignment explanation

Indices: 30257766--30257917 Score: 148 Period size: 40 Copynumber: 3.8 Consensus size: 40 30257756 ATAACCATGT * * * 30257766 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC- 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA * ** * * 30257806 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA 1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA * * 30257846 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA * * 30257886 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT 1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT 30257918 CATTCAATTT Statistics Matches: 91, Mismatches: 17, Indels: 8 0.78 0.15 0.07 Matches are distributed among these distances: 39 2 0.02 40 86 0.95 41 3 0.03 ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28 Consensus pattern (40 bp): GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA Found at i:30257900 original size:80 final size:80 Alignment explanation

Indices: 30257766--30257915 Score: 198 Period size: 80 Copynumber: 1.9 Consensus size: 80 30257756 ATAACCATGT * 30257766 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC 30257830 CCGGATGTAGCCACTA 65 CCGGATGTAGCCACTA * * * * * 30257846 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG 30257909 CCCGGAT 64 CCCGGAT 30257916 ATCATTCAAT Statistics Matches: 61, Mismatches: 6, Indels: 6 0.84 0.08 0.08 Matches are distributed among these distances: 79 3 0.05 80 57 0.93 81 1 0.02 ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27 Consensus pattern (80 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC CGGATGTAGCCACTA Found at i:30265850 original size:40 final size:40 Alignment explanation

Indices: 30265790--30265896 Score: 205 Period size: 40 Copynumber: 2.7 Consensus size: 40 30265780 ATAACCATGT * 30265790 GCACAAATGCCTTCGGGTCTTAGCCCGAATAGAATGTCTC 1 GCACGAATGCCTTCGGGTCTTAGCCCGAATAGAATGTCTC 30265830 GCACGAATGCCTTCGGGTCTTAGCCCGAATAGAATGTCTC 1 GCACGAATGCCTTCGGGTCTTAGCCCGAATAGAATGTCTC 30265870 GCACGAATGCCTTCGGGTCTTAGCCCG 1 GCACGAATGCCTTCGGGTCTTAGCCCG 30265897 GATGTAGCCA Statistics Matches: 66, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 40 66 1.00 ACGTcount: A:0.21, C:0.29, G:0.25, T:0.24 Consensus pattern (40 bp): GCACGAATGCCTTCGGGTCTTAGCCCGAATAGAATGTCTC Found at i:30269960 original size:12 final size:12 Alignment explanation

Indices: 30269943--30269967 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 30269933 TTTTGGATGA 30269943 ATTTGATTAAAT 1 ATTTGATTAAAT 30269955 ATTTGATTAAAT 1 ATTTGATTAAAT 30269967 A 1 A 30269968 AGTTTAATTT 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:0.44, C:0.00, G:0.08, T:0.48 Consensus pattern (12 bp): ATTTGATTAAAT Found at i:30271846 original size:2 final size:2 Alignment explanation

Indices: 30271839--30271868 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 30271829 TGAAATGGGT 30271839 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 30271869 AATAACTGAA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:30277139 original size:2 final size:2 Alignment explanation

Indices: 30277132--30277159 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 30277122 AACATGTGTC 30277132 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 30277160 CACGAACTCA 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:30282329 original size:26 final size:26 Alignment explanation

Indices: 30282299--30282351 Score: 97 Period size: 26 Copynumber: 2.0 Consensus size: 26 30282289 CTTTCATTCT 30282299 CAAACATGATAAACATTTCAAACGTA 1 CAAACATGATAAACATTTCAAACGTA * 30282325 CAAACATGATAAACATTTCAAGCGTA 1 CAAACATGATAAACATTTCAAACGTA 30282351 C 1 C 30282352 CTAAATTGGA Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23 Consensus pattern (26 bp): CAAACATGATAAACATTTCAAACGTA Found at i:30292562 original size:40 final size:40 Alignment explanation

Indices: 30292503--30292710 Score: 218 Period size: 40 Copynumber: 5.2 Consensus size: 40 30292493 CAATTGAATG * * * * 30292503 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * * * 30292543 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 30292583 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 30292623 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * ** 30292663 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT 30292703 ATATCCGG 1 ATATCCGG 30292711 TTGTATTCCG Statistics Matches: 142, Mismatches: 26, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 40 142 1.00 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT Found at i:30292641 original size:80 final size:80 Alignment explanation

Indices: 30292504--30292710 Score: 247 Period size: 80 Copynumber: 2.6 Consensus size: 80 30292494 AATTGAATGA * * ** * * * 30292504 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA * 30292569 TTGTGCTAGT-G-AC 66 TTGTGCAAGTCGTAC * * * 30292582 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC 1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC * * 30292647 ATTTGTGCAAGTCGTTC 64 AATTGTGCAAGTCGTAC * * 30292664 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG 1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG 30292711 TTGTATTCCG Statistics Matches: 109, Mismatches: 16, Indels: 6 0.83 0.12 0.05 Matches are distributed among these distances: 78 1 0.01 80 105 0.96 81 1 0.01 82 2 0.02 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26 Consensus pattern (80 bp): TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA TTGTGCAAGTCGTAC Found at i:30300589 original size:40 final size:40 Alignment explanation

Indices: 30300530--30300737 Score: 227 Period size: 40 Copynumber: 5.2 Consensus size: 40 30300520 CAATTGAATG * * * * 30300530 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * * * * 30300570 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 30300610 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 30300650 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT * * ** 30300690 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT 30300730 ATATCCGG 1 ATATCCGG 30300738 TTGTATTCCG Statistics Matches: 144, Mismatches: 24, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 40 144 1.00 ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT Found at i:30300668 original size:80 final size:80 Alignment explanation

Indices: 30300532--30300737 Score: 252 Period size: 80 Copynumber: 2.6 Consensus size: 80 30300522 ATTGAATGAT * * ** * * * 30300532 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAAT 1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT * 30300597 TGTGCTAGT-GACTAC 66 TGTGCAAGTCG-CTAC * * * * 30300612 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT 1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT * * 30300677 TGTGCAAGTCGTTAT 66 TGTGCAAGTCGCTAC * * 30300692 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG 1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG 30300738 TTGTATTCCG Statistics Matches: 108, Mismatches: 17, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 80 107 0.99 81 1 0.01 ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25 Consensus pattern (80 bp): ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAAT TGTGCAAGTCGCTAC Found at i:30303662 original size:43 final size:44 Alignment explanation

Indices: 30303558--30303681 Score: 146 Period size: 43 Copynumber: 2.9 Consensus size: 44 30303548 GGTTATCAAG * * 30303558 ATGTGATTACATGTAAGACCATATCTGGGACATTGGCATCGTTA 1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGATA * * * * * 30303602 AT-CGATTTCGTGCAAGACCCTATCTGGGACAATGGCATCGAT- 1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGATA * * 30303644 ATGTGATAACATGTAAGACCATATCTGGGA-TATGGCAT 1 ATGTGATTACATGTAAGACCATATCTGGGACAATGGCAT 30303682 TCTATGAGCT Statistics Matches: 65, Mismatches: 14, Indels: 4 0.78 0.17 0.05 Matches are distributed among these distances: 42 9 0.14 43 54 0.83 44 2 0.03 ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29 Consensus pattern (44 bp): ATGTGATTACATGTAAGACCATATCTGGGACAATGGCATCGATA Found at i:30305346 original size:40 final size:40 Alignment explanation

Indices: 30305290--30305428 Score: 172 Period size: 40 Copynumber: 3.4 Consensus size: 40 30305280 ATTCGATTAC * 30305290 GTATGGCACTTCGTGTGCAATTCGAGATAGCTTCAGCTAT 1 GTATGGCACTTAGTGTGCAATTCGAGATAGCTTCAGCTAT ** 30305330 GTATGGCACTTAGTGTGTGATTCGAGATAGCTTCAGCTAT 1 GTATGGCACTTAGTGTGCAATTCGAGATAGCTTCAGCTAT * * * * * 30305370 GTATGGCACTTACTATGCAAGATT-AAAATAGCTTCGGCTAT 1 GTATGGCACTTAGTGTGC-A-ATTCGAGATAGCTTCAGCTAT 30305411 GTATTGGCACTTAGTGTG 1 GTA-TGGCACTTAGTGTG 30305429 TGAGAATTCG Statistics Matches: 84, Mismatches: 12, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 40 52 0.62 41 17 0.20 42 15 0.18 ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34 Consensus pattern (40 bp): GTATGGCACTTAGTGTGCAATTCGAGATAGCTTCAGCTAT Found at i:30305587 original size:8 final size:8 Alignment explanation

Indices: 30305576--30305604 Score: 58 Period size: 8 Copynumber: 3.6 Consensus size: 8 30305566 CTTTGAATAT 30305576 AAGTTATG 1 AAGTTATG 30305584 AAGTTATG 1 AAGTTATG 30305592 AAGTTATG 1 AAGTTATG 30305600 AAGTT 1 AAGTT 30305605 TGCATATAAG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38 Consensus pattern (8 bp): AAGTTATG Found at i:30306533 original size:25 final size:25 Alignment explanation

Indices: 30306505--30306574 Score: 131 Period size: 25 Copynumber: 2.8 Consensus size: 25 30306495 CTCTTTTAAT * 30306505 AACTGGGGCAAAGCCCTTTTTGGTA 1 AACTGGGGCAAAGCCCTTTTCGGTA 30306530 AACTGGGGCAAAGCCCTTTTCGGTA 1 AACTGGGGCAAAGCCCTTTTCGGTA 30306555 AACTGGGGCAAAGCCCTTTT 1 AACTGGGGCAAAGCCCTTTT 30306575 AGCACTTCTT Statistics Matches: 44, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 25 44 1.00 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (25 bp): AACTGGGGCAAAGCCCTTTTCGGTA Found at i:30306810 original size:27 final size:27 Alignment explanation

Indices: 30306779--30306949 Score: 225 Period size: 27 Copynumber: 6.3 Consensus size: 27 30306769 AGGGCAAAAT * * * 30306779 AGTAATTTTACCCCACAAGGGTATCTC 1 AGTAATTCTACCCTACAAGGGTATTTC * * * 30306806 GGTAATTTTACCCTACAGGGGTATTTC 1 AGTAATTCTACCCTACAAGGGTATTTC * 30306833 AGTAATTCTACCCTATAAGGGTATTTC 1 AGTAATTCTACCCTACAAGGGTATTTC * 30306860 AGTAATTCTACCTTACAAGGGTATTTC 1 AGTAATTCTACCCTACAAGGGTATTTC * 30306887 AGTAATTCTACCCTACAGGGGTATTTC 1 AGTAATTCTACCCTACAAGGGTATTTC * * * 30306914 GGTAATTCTACTCTACAGGGGTATTTC 1 AGTAATTCTACCCTACAAGGGTATTTC * 30306941 AATAATTCT 1 AGTAATTCT 30306950 GTAAATCAGG Statistics Matches: 128, Mismatches: 16, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 128 1.00 ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36 Consensus pattern (27 bp): AGTAATTCTACCCTACAAGGGTATTTC Found at i:30307016 original size:27 final size:27 Alignment explanation

Indices: 30306965--30307354 Score: 356 Period size: 27 Copynumber: 14.4 Consensus size: 27 30306955 TCAGGGGTCC * * 30306965 TTTGGTAATTTTTACAAGTCTAGGGTAT 1 TTTGGTAA-TTTTACAAATCAAGGGTAT ** * 30306993 TTCAGTAATTTTACAAATTAAGGGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT ** * 30307020 TTCAGTAATTTTACAAA-CTGAGGGTAT 1 TTTGGTAATTTTACAAATC-AAGGGTAT * * 30307047 TTCGATAATTTTACAAATCAAGGGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT * 30307074 TTTGGTAATTTTACAAACTCGA-GGTAT 1 TTTGGTAATTTTACAAA-TCAAGGGTAT ** * * 30307101 TTTGGTAATTTTGTAAACCAAAGGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT * * 30307128 TTTGGTAATTTTACAAGTCGAGGGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT ** * * 30307155 TTCAGT-ATTTTCACAAATTAGGGGTAT 1 TTTGGTAATTTT-ACAAATCAAGGGTAT * * 30307182 TTTGGTAATTTTACAAGTCGAGGGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT ** * 30307209 TTCAGTAATTTTACAAATCAGGGGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT * * 30307236 TTTGGTAATTTCACAAA-CTAGGGGTAT 1 TTTGGTAATTTTACAAATC-AAGGGTAT * * * 30307263 TTTGGCAATTTTACAAACCAGGGGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT * * * 30307290 TTTGGTAATTTTACAAACCACGAGTAT 1 TTTGGTAATTTTACAAATCAAGGGTAT * ** * 30307317 TTTAGTAATTTTACAAATTGAGGGCAT 1 TTTGGTAATTTTACAAATCAAGGGTAT * 30307344 TTTAGTAATTT 1 TTTGGTAATTT 30307355 GGTAAACTAA Statistics Matches: 299, Mismatches: 55, Indels: 17 0.81 0.15 0.05 Matches are distributed among these distances: 26 8 0.03 27 275 0.92 28 16 0.05 ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40 Consensus pattern (27 bp): TTTGGTAATTTTACAAATCAAGGGTAT Found at i:30307056 original size:54 final size:54 Alignment explanation

Indices: 30306932--30307354 Score: 394 Period size: 54 Copynumber: 7.8 Consensus size: 54 30306922 TACTCTACAG * * ** * ** * 30306932 GGGTATTTCAATAATTCTGTAAATCAGGGGTCCTTTGGTAATTTTTACAAGTCT-A 1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAA-TTTTACAA-ACTGA * ** 30306987 GGGTATTTCAGTAATTTTACAAATTAAGGGTATTTCAGTAATTTTACAAACTGA 1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTGA 30307041 GGGTATTTC-GATAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTCGA 1 GGGTATTTCAG-TAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACT-GA ** ** * * * 30307096 -GGTATTTTGGTAATTTTGTAAACCAAAGGTATTTTGGTAATTTTAC-AAGTCGA 1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACT-GA * * * 30307149 GGGTATTTCAGT-ATTTTCACAAATTAGGGGTATTTTGGTAATTTTAC-AAGTCGA 1 GGGTATTTCAGTAATTTT-ACAAATCAAGGGTATTTTGGTAATTTTACAAACT-GA * * 30307203 GGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTCACAAACT-A 1 GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTGA ** * * * * 30307256 GGGGTATTTTGGCAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAAC-CA 1 -GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTGA * * ** * * 30307310 CGAGTATTTTAGTAATTTTACAAATTGAGGGCATTTTAGTAATTT 1 -GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTT 30307355 GGTAAACTAA Statistics Matches: 312, Mismatches: 46, Indels: 21 0.82 0.12 0.06 Matches are distributed among these distances: 53 15 0.05 54 255 0.82 55 42 0.13 ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39 Consensus pattern (54 bp): GGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTGGTAATTTTACAAACTGA Found at i:30309187 original size:40 final size:40 Alignment explanation

Indices: 30309142--30309271 Score: 163 Period size: 40 Copynumber: 3.2 Consensus size: 40 30309132 CGGAATATAA * 30309142 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTGGC 1 CCGGATATAACCACT-TGCACAAATGCCTTCGGGTCTTAGC * ** * * 30309182 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC * * * 30309222 CCGGATATAGCCACTTGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC 30309262 CCGGATATAA 1 CCGGATATAA 30309272 TTTCCAGCAT Statistics Matches: 74, Mismatches: 15, Indels: 2 0.81 0.16 0.02 Matches are distributed among these distances: 40 73 0.99 41 1 0.01 ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25 Consensus pattern (40 bp): CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC Found at i:30309286 original size:40 final size:40 Alignment explanation

Indices: 30309142--30309308 Score: 142 Period size: 40 Copynumber: 4.2 Consensus size: 40 30309132 CGGAATATAA *** * * 30309142 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTGGC 1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC * ** 30309182 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC * ** * 30309222 CCGGATATAGCCACTTGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC *** * * 30309262 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC 30309301 CCGGATAT 1 CCGGATAT 30309309 CATTCAATTT Statistics Matches: 102, Mismatches: 21, Indels: 9 0.77 0.16 0.07 Matches are distributed among these distances: 39 15 0.15 40 85 0.83 41 2 0.02 ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27 Consensus pattern (40 bp): CCGGATATAACCACCAGCACAATTGCCTTCGGGTCTTAGC Found at i:30309292 original size:80 final size:79 Alignment explanation

Indices: 30309142--30309308 Score: 196 Period size: 80 Copynumber: 2.1 Consensus size: 79 30309132 CGGAATATAA ** 30309142 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTGGCCCGGATAGAATGACTCGCACGAATG 1 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATG 30309207 CCTTCGGGTCTTAGC 66 CCTTCGGG-CTTAGC * * * ** * 30309222 CCGGATATAGCCACT-TGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA 1 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA * 30309284 TTGTCTTCGGGCTTAGC 64 -TGCCTTCGGGCTTAGC 30309301 CCGGATAT 1 CCGGATAT 30309309 CATTCAATTT Statistics Matches: 75, Mismatches: 9, Indels: 7 0.82 0.10 0.08 Matches are distributed among these distances: 79 17 0.23 80 57 0.76 81 1 0.01 ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27 Consensus pattern (79 bp): CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATG CCTTCGGGCTTAGC Found at i:30312519 original size:31 final size:30 Alignment explanation

Indices: 30312446--30312528 Score: 100 Period size: 29 Copynumber: 2.8 Consensus size: 30 30312436 TTCAGTCTCG * 30312446 ACATATACTGGGCCGAAGCC-TTTCATTTA 1 ACATATACTGGGCCGAAGCCTTTTCATTAA * 30312475 AC-TGTTACTGGGCCGAAGCCTTTTCA-TAA 1 ACAT-ATACTGGGCCGAAGCCTTTTCATTAA 30312504 ATCATATCACTGGGCCGAAGCCTTT 1 A-CATAT-ACTGGGCCGAAGCCTTT 30312529 ACTGTAAACG Statistics Matches: 46, Mismatches: 3, Indels: 8 0.81 0.05 0.14 Matches are distributed among these distances: 28 1 0.02 29 20 0.43 30 7 0.15 31 18 0.39 ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30 Consensus pattern (30 bp): ACATATACTGGGCCGAAGCCTTTTCATTAA Found at i:30312783 original size:25 final size:25 Alignment explanation

Indices: 30312749--30312818 Score: 106 Period size: 25 Copynumber: 2.8 Consensus size: 25 30312739 CTCTTTTAAT * 30312749 AACTGGGGCAAAGCCCTTTTTGATA 1 AACTGAGGCAAAGCCCTTTTTGATA * 30312774 AACTGAGGCAAAGCCCTTTTTGGTA 1 AACTGAGGCAAAGCCCTTTTTGATA 30312799 AACT-AGGGCAAAGCCCTTTT 1 AACTGA-GGCAAAGCCCTTTT 30312819 AACACTTCCT Statistics Matches: 42, Mismatches: 2, Indels: 2 0.91 0.04 0.04 Matches are distributed among these distances: 24 1 0.02 25 41 0.98 ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27 Consensus pattern (25 bp): AACTGAGGCAAAGCCCTTTTTGATA Found at i:30313030 original size:27 final size:27 Alignment explanation

Indices: 30312980--30313043 Score: 67 Period size: 27 Copynumber: 2.4 Consensus size: 27 30312970 CTGTCACTTG * * 30312980 CCCATAAGGGCAAAATAATCATTTAAC 1 CCCACAAGGGCAAAATAATAATTTAAC ** * 30313007 ACCCA-AAGGGCAAAATGGTAATTTTAC 1 -CCCACAAGGGCAAAATAATAATTTAAC 30313034 CCCACAAGGG 1 CCCACAAGGG 30313044 TATCTCGGTA Statistics Matches: 31, Mismatches: 4, Indels: 3 0.82 0.11 0.08 Matches are distributed among these distances: 26 4 0.13 27 23 0.74 28 4 0.13 ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19 Consensus pattern (27 bp): CCCACAAGGGCAAAATAATAATTTAAC Found at i:30313053 original size:27 final size:27 Alignment explanation

Indices: 30313024--30313191 Score: 228 Period size: 27 Copynumber: 6.2 Consensus size: 27 30313014 GGGCAAAATG * * * * 30313024 GTAATTTTACCCCACAAGGGTATCTCG 1 GTAATTCTACCCTACAAGGGTATTTCA * * * 30313051 GTAATTCTACCCTACAGGGGTGTTTTA 1 GTAATTCTACCCTACAAGGGTATTTCA * 30313078 GTAATTCTACCCTACAAGGGTATTTTA 1 GTAATTCTACCCTACAAGGGTATTTCA * 30313105 GTAATTCTACCGTACAAGGGTATTTCA 1 GTAATTCTACCCTACAAGGGTATTTCA * 30313132 GTAATTCTACCCTACAAGGGTATTTCG 1 GTAATTCTACCCTACAAGGGTATTTCA * 30313159 GTAATTCTACCCTACAGGGGTATTTCA 1 GTAATTCTACCCTACAAGGGTATTTCA * 30313186 ATAATT 1 GTAATT 30313192 TTGTAAATCG Statistics Matches: 125, Mismatches: 16, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 125 1.00 ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35 Consensus pattern (27 bp): GTAATTCTACCCTACAAGGGTATTTCA Found at i:30313206 original size:27 final size:27 Alignment explanation

Indices: 30313176--30313327 Score: 98 Period size: 27 Copynumber: 5.6 Consensus size: 27 30313166 TACCCTACAG 30313176 GGGTATTTCAATAATTTTGTAAATCGA 1 GGGTATTTCAATAATTTTGTAAATCGA ** ** * * 30313203 GGGTAAAAT-GGTAATTCTGTAAATCGG 1 GGGT-ATTTCAATAATTTTGTAAATCGA ** 30313230 GGGTACTTT-GGTAATTTT-TACAAGTCGA 1 GGGTA-TTTCAATAATTTTGTA-AA-TCGA * ** 30313258 GGGTATTTCAGTAA-TTTACAAATCGA 1 GGGTATTTCAATAATTTTGTAAATCGA * * 30313284 GGGTATTTCAATAATTTTGCAAA-CTAA 1 GGGTATTTCAATAATTTTGTAAATC-GA * 30313311 GGGTATTTCGATAATTT 1 GGGTATTTCAATAATTT 30313328 CACAAATCAG Statistics Matches: 101, Mismatches: 16, Indels: 16 0.76 0.12 0.12 Matches are distributed among these distances: 26 21 0.21 27 65 0.64 28 15 0.15 ACGTcount: A:0.32, C:0.09, G:0.22, T:0.38 Consensus pattern (27 bp): GGGTATTTCAATAATTTTGTAAATCGA Found at i:30313233 original size:54 final size:55 Alignment explanation

Indices: 30313175--30313302 Score: 122 Period size: 54 Copynumber: 2.4 Consensus size: 55 30313165 CTACCCTACA * ** 30313175 GGGGTATTTCAATAATTTTGTA-AA-TCGAGGGTAAAAT-GGTAATTCTGTAAATCG 1 GGGGTATTTCAATAATTTTGTACAAGTCGAGGGT-AAATCAGTAATT-TACAAATCG ** ** 30313229 GGGGTACTTT-GGTAATTTT-TACAAGTCGAGGGTATTTCAGTAATTTACAAATCG 1 GGGGTA-TTTCAATAATTTTGTACAAGTCGAGGGTAAATCAGTAATTTACAAATCG * 30313283 AGGGTATTTCAATAATTTTG 1 GGGGTATTTCAATAATTTTG 30313303 CAAACTAAGG Statistics Matches: 58, Mismatches: 10, Indels: 11 0.73 0.13 0.14 Matches are distributed among these distances: 53 5 0.09 54 36 0.62 55 17 0.29 ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38 Consensus pattern (55 bp): GGGGTATTTCAATAATTTTGTACAAGTCGAGGGTAAATCAGTAATTTACAAATCG Found at i:30313333 original size:27 final size:27 Alignment explanation

Indices: 30313230--30313623 Score: 302 Period size: 27 Copynumber: 14.6 Consensus size: 27 30313220 TGTAAATCGG * * * 30313230 GGGTACTTTGGTAATTTTTAC-AAGTCGA 1 GGGTATTTTGGTAA-TTTTACAAACT-AA ** * 30313258 GGGTATTTCAGTAA-TTTACAAA-TCGA 1 GGGTATTTTGGTAATTTTACAAACT-AA *** * 30313284 GGGTATTTCAATAATTTTGCAAACTAA 1 GGGTATTTTGGTAATTTTACAAACTAA * * * * 30313311 GGGTATTTCGATAATTTCACAAA-TCAG 1 GGGTATTTTGGTAATTTTACAAACT-AA 30313338 GGGTATTTTGGTAA-TTTACAAACT-A 1 GGGTATTTTGGTAATTTTACAAACTAA ** * 30313363 GGGATATTTTGGTAATTTTGTAAACCAA 1 GGG-TATTTTGGTAATTTTACAAACTAA * * 30313391 GGGTATTTTGGTAATTTTAC-AAGTCGA 1 GGGTATTTTGGTAATTTTACAAACT-AA ** * * * 30313418 GGGTATTTCAGTAACTTCACAAATTAA 1 GGGTATTTTGGTAATTTTACAAACTAA * * 30313445 GGGTATTTTGGTAATTTTAC-AAGTCGA 1 GGGTATTTTGGTAATTTTACAAACT-AA ** * * 30313472 GGGTATTTCAGTAATTTCACAAA-TCAG 1 GGGTATTTTGGTAATTTTACAAACT-AA * 30313499 GGGTATTTTGGTAATTTCACAAACTAA 1 GGGTATTTTGGTAATTTTACAAACTAA * * 30313526 GGGTATTTTGGTAATTTTAGAAACTAG 1 GGGTATTTTGGTAATTTTACAAACTAA * 30313553 GGGTATTTTGGTAATTTTACAAACTAG 1 GGGTATTTTGGTAATTTTACAAACTAA * * * 30313580 GGGTATTTTAGTAATTTTACAAATTGA 1 GGGTATTTTGGTAATTTTACAAACTAA * * 30313607 GGGCATTTTAGTAATTT 1 GGGTATTTTGGTAATTT 30313624 GGTAAACTAA Statistics Matches: 302, Mismatches: 51, Indels: 27 0.79 0.13 0.07 Matches are distributed among these distances: 25 3 0.01 26 46 0.15 27 231 0.76 28 22 0.07 ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39 Consensus pattern (27 bp): GGGTATTTTGGTAATTTTACAAACTAA Found at i:30313333 original size:54 final size:53 Alignment explanation

Indices: 30313230--30313623 Score: 336 Period size: 54 Copynumber: 7.3 Consensus size: 53 30313220 TGTAAATCGG * * * 30313230 GGGTACTTTGGTAATTTTTAC-AAGTCGAGGGTATTTCAGTAATTT-ACAAATCGA 1 GGGTATTTTGGTAA-TTTTACAAACT-AAGGGTATTTCAGTAATTTCACAAATC-A *** * 30313284 GGGTATTTCAATAATTTTGCAAACTAAGGGTATTTC-GATAATTTCACAAATCA 1 GGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAG-TAATTTCACAAATCA ** *** * 30313337 GGGGTATTTTGGTAA-TTTACAAACT-AGGGATATTTTGGTAATTTTGTAAACCAA 1 -GGGTATTTTGGTAATTTTACAAACTAAGGG-TATTTCAGTAATTTCACAAATC-A * * * * 30313391 GGGTATTTTGGTAATTTTAC-AAGTCGAGGGTATTTCAGTAACTTCACAAATTAA 1 GGGTATTTTGGTAATTTTACAAACT-AAGGGTATTTCAGTAATTTCACAAA-TCA * * 30313445 GGGTATTTTGGTAATTTTAC-AAGTCGAGGGTATTTCAGTAATTTCACAAATCA 1 GGGTATTTTGGTAATTTTACAAACT-AAGGGTATTTCAGTAATTTCACAAATCA * ** * * 30313498 GGGGTATTTTGGTAATTTCACAAACTAAGGGTATTTTGGTAATTTTAGAAA-CTA 1 -GGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAGTAATTTCACAAATC-A * * * * 30313552 GGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTTTACAAATTGA 1 -GGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAGTAATTTCACAAA-TCA * * 30313607 GGGCATTTTAGTAATTT 1 GGGTATTTTGGTAATTT 30313624 GGTAAACTAA Statistics Matches: 283, Mismatches: 41, Indels: 32 0.79 0.12 0.09 Matches are distributed among these distances: 52 5 0.02 53 66 0.23 54 204 0.72 55 8 0.03 ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39 Consensus pattern (53 bp): GGGTATTTTGGTAATTTTACAAACTAAGGGTATTTCAGTAATTTCACAAATCA Found at i:30313475 original size:81 final size:79 Alignment explanation

Indices: 30313230--30313623 Score: 373 Period size: 81 Copynumber: 4.9 Consensus size: 79 30313220 TGTAAATCGG * * * ** ** 30313230 GGGTACTTTGGTAATTTTTACAAGTC-GAGGGTATTTCAGTAATTTACAAATCGAGGGTATTTCA 1 GGGTATTTTGGTAA-TTTTACAAATCAG-GGGTATTTTAGTAATTTACAAATTAAGGGTATTTTG * * 30313294 ATAATTTTGCAAACTAA 64 GTAATTTTACAAAC-AA * * * * * 30313311 GGGTATTTCGATAATTTCACAAATCAGGGGTATTTTGGTAATTTACAAACT-AGGGATATTTTGG 1 GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTTACAAATTAAGGG-TATTTTGG ** 30313375 TAATTTTGTAAACCAA 65 TAATTTTACAAA-CAA * * * 30313391 GGGTATTTTGGTAATTTTACAAGTC-GAGGGTATTTCAGTAACTTCACAAATTAAGGGTATTTTG 1 GGGTATTTTGGTAATTTTACAAATCAG-GGGTATTTTAGTAA-TTTACAAATTAAGGGTATTTTG * * 30313455 GTAATTTTACAAGTCGA 64 GTAATTTTACAA-ACAA ** * * * 30313472 GGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTCACAAACTAAGGGTATTTTGG 1 GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTT-ACAAATTAAGGGTATTTTGG * * 30313537 TAATTTTAGAAACTAG 65 TAATTTTACAAAC-AA * * * 30313553 GGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTAGTAATTTTACAAATTGAGGGCATTTTA 1 GGGTATTTTGGTAATTTTACAAATC-AGGGGTATTTTAGTAA-TTTACAAATTAAGGGTATTTTG 30313617 GTAATTT 64 GTAATTT 30313624 GGTAAACTAA Statistics Matches: 256, Mismatches: 45, Indels: 24 0.79 0.14 0.07 Matches are distributed among these distances: 79 5 0.02 80 84 0.33 81 159 0.62 82 8 0.03 ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39 Consensus pattern (79 bp): GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTTACAAATTAAGGGTATTTTGGT AATTTTACAAACAA Found at i:30315577 original size:31 final size:30 Alignment explanation

Indices: 30315504--30315586 Score: 100 Period size: 29 Copynumber: 2.8 Consensus size: 30 30315494 TTCAGTCTCG * 30315504 ACATATACTGGGCCGAAGCC-TTTCATTGA 1 ACATATACTGGGCCGAAGCCTTTTCATTAA * 30315533 AC-TGTTACTGGGCCGAAGCCTTTTCA-TAA 1 ACAT-ATACTGGGCCGAAGCCTTTTCATTAA 30315562 ATCATATCACTGGGCCGAAGCCTTT 1 A-CATAT-ACTGGGCCGAAGCCTTT 30315587 ACTGTAAACG Statistics Matches: 46, Mismatches: 3, Indels: 8 0.81 0.05 0.14 Matches are distributed among these distances: 28 1 0.02 29 20 0.43 30 7 0.15 31 18 0.39 ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29 Consensus pattern (30 bp): ACATATACTGGGCCGAAGCCTTTTCATTAA Found at i:30315835 original size:25 final size:25 Alignment explanation

Indices: 30315807--30315876 Score: 113 Period size: 25 Copynumber: 2.8 Consensus size: 25 30315797 CTCTTTTAAT * 30315807 AACTGGGGCAAAGCCCTTTTTGATA 1 AACTGGGGCAAAGCCCTTTTCGATA * 30315832 AACTGGGGCAAAGCCCTTTTCGGTA 1 AACTGGGGCAAAGCCCTTTTCGATA * 30315857 AACTAGGGCAAAGCCCTTTT 1 AACTGGGGCAAAGCCCTTTT 30315877 AGCACTTCCT Statistics Matches: 42, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 25 42 1.00 ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26 Consensus pattern (25 bp): AACTGGGGCAAAGCCCTTTTCGATA Done.