Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: At_chr10

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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31

Warning! 2980117 characters in sequence are not A, C, G, or T


File 23 of 284

Found at i:7787033 original size:86 final size:86

Alignment explanation

Indices: 7786888--7787061 Score: 321 Period size: 86 Copynumber: 2.0 Consensus size: 86 7786878 AATGTGATTT * * * 7786888 TTTAATAAAAGTTATTTTAAAGATAAAATGTGAAATTTATACTAATATAAAATTTTAACACGAAT 1 TTTAATAAAAGTTATTTTAAAGAAAAAATGTGAAATTGATACCAATATAAAATTTTAACACGAAT 7786953 ATTTTATGGCATAATTAATAA 66 ATTTTATGGCATAATTAATAA 7786974 TTTAATAAAAGTTATTTTAAAGAAAAAATGTGAAATTGATACCAATATAAAATTTTAACACGAAT 1 TTTAATAAAAGTTATTTTAAAGAAAAAATGTGAAATTGATACCAATATAAAATTTTAACACGAAT 7787039 ATTTTATGGCATAATTAATAA 66 ATTTTATGGCATAATTAATAA 7787060 TT 1 TT 7787062 CAATTTTAAT Statistics Matches: 85, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 86 85 1.00 ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39 Consensus pattern (86 bp): TTTAATAAAAGTTATTTTAAAGAAAAAATGTGAAATTGATACCAATATAAAATTTTAACACGAAT ATTTTATGGCATAATTAATAA Found at i:7787660 original size:9 final size:9 Alignment explanation

Indices: 7787646--7787682 Score: 65 Period size: 9 Copynumber: 4.1 Consensus size: 9 7787636 TATAGTTTAA 7787646 TATTTGAAT 1 TATTTGAAT 7787655 TATTTGAAT 1 TATTTGAAT * 7787664 TATTTGAGT 1 TATTTGAAT 7787673 TATTTGAAT 1 TATTTGAAT 7787682 T 1 T 7787683 CGAAAACTCA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 9 26 1.00 ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57 Consensus pattern (9 bp): TATTTGAAT Found at i:7787748 original size:9 final size:9 Alignment explanation

Indices: 7787734--7787766 Score: 57 Period size: 9 Copynumber: 3.7 Consensus size: 9 7787724 ATTCAAGTTG 7787734 ACTCGAATA 1 ACTCGAATA * 7787743 ACTCGATTA 1 ACTCGAATA 7787752 ACTCGAATA 1 ACTCGAATA 7787761 ACTCGA 1 ACTCGA 7787767 TTTGTTTAAC Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 9 22 1.00 ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24 Consensus pattern (9 bp): ACTCGAATA Found at i:7787757 original size:18 final size:18 Alignment explanation

Indices: 7787734--7787768 Score: 70 Period size: 18 Copynumber: 1.9 Consensus size: 18 7787724 ATTCAAGTTG 7787734 ACTCGAATAACTCGATTA 1 ACTCGAATAACTCGATTA 7787752 ACTCGAATAACTCGATT 1 ACTCGAATAACTCGATT 7787769 TGTTTAACCG Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29 Consensus pattern (18 bp): ACTCGAATAACTCGATTA Found at i:7788503 original size:115 final size:115 Alignment explanation

Indices: 7788301--7788530 Score: 424 Period size: 115 Copynumber: 2.0 Consensus size: 115 7788291 TCTCACTCCT 7788301 TTTGTAGAGCAATCAAAACCCTTAGGTTATCTCTCAAACCGTCCTCAAAATAAACACATTTCTCA 1 TTTGTAGAGCAATCAAAACCCTTAGGTTATCTCTCAAACCGTCCTCAAAATAAACACATTTCTCA * * 7788366 TACTCAGATGCCACCATGCCTCGGGGGTAGCAGCTTAACCTTAGAAACTC 66 TACTCAAATGCCACCATGCCTCGGGGATAGCAGCTTAACCTTAGAAACTC * 7788416 TTTGTAGAGCAATCAAAACCCTTAGGTTATCTCTCAAACCGTCCTCAAAATAGACACATTTCTCA 1 TTTGTAGAGCAATCAAAACCCTTAGGTTATCTCTCAAACCGTCCTCAAAATAAACACATTTCTCA * 7788481 TACTCAAATGCCACCATGCCTCGGGGATAGTAGCTTAACCTTAGAAACTC 66 TACTCAAATGCCACCATGCCTCGGGGATAGCAGCTTAACCTTAGAAACTC 7788531 GGCCTCATAC Statistics Matches: 111, Mismatches: 4, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 115 111 1.00 ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27 Consensus pattern (115 bp): TTTGTAGAGCAATCAAAACCCTTAGGTTATCTCTCAAACCGTCCTCAAAATAAACACATTTCTCA TACTCAAATGCCACCATGCCTCGGGGATAGCAGCTTAACCTTAGAAACTC Found at i:7789865 original size:21 final size:20 Alignment explanation

Indices: 7789840--7789885 Score: 74 Period size: 21 Copynumber: 2.2 Consensus size: 20 7789830 TCAGATACAG * 7789840 ATATCGTGCCATTACGACACC 1 ATATCGTACCATTACGACA-C 7789861 ATATCGTACCATTACGACAC 1 ATATCGTACCATTACGACAC 7789881 ATATC 1 ATATC 7789886 AGATAAAATA Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 20 6 0.25 21 18 0.75 ACGTcount: A:0.33, C:0.30, G:0.11, T:0.26 Consensus pattern (20 bp): ATATCGTACCATTACGACAC Found at i:7792651 original size:39 final size:39 Alignment explanation

Indices: 7792596--7792780 Score: 298 Period size: 39 Copynumber: 4.7 Consensus size: 39 7792586 TTCCAACCCA * * 7792596 AATGCCTTCGGAACTTAGCCCGGATATAACATCAGCACG 1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG * * 7792635 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG 1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG * 7792674 AATGCCTTCGGGACTTAGCCCGGATATAATACCAGCACG 1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG * * 7792713 AATACCATCGGGACTTAGCCCGGATATAACACCAGCACG 1 AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG * 7792752 AATACCTTCGGGACTTAGCCCGGATATAA 1 AATGCCTTCGGGACTTAGCCCGGATATAA 7792781 ATCTCACACA Statistics Matches: 139, Mismatches: 7, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 39 139 1.00 ACGTcount: A:0.30, C:0.28, G:0.22, T:0.21 Consensus pattern (39 bp): AATGCCTTCGGGACTTAGCCCGGATATAACACCAGCACG Found at i:7793888 original size:32 final size:32 Alignment explanation

Indices: 7793852--7793914 Score: 117 Period size: 32 Copynumber: 2.0 Consensus size: 32 7793842 GTAGTTGTCA 7793852 CCTATACTCTTATGCCAAATTAGCTAACATTG 1 CCTATACTCTTATGCCAAATTAGCTAACATTG * 7793884 CCTATACTCTTATGCCGAATTAGCTAACATT 1 CCTATACTCTTATGCCAAATTAGCTAACATT 7793915 TATAATCCTT Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 30 1.00 ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35 Consensus pattern (32 bp): CCTATACTCTTATGCCAAATTAGCTAACATTG Found at i:7793930 original size:29 final size:30 Alignment explanation

Indices: 7793853--7793930 Score: 88 Period size: 32 Copynumber: 2.6 Consensus size: 30 7793843 TAGTTGTCAC * * 7793853 CTATACTCTTATGCCAAATTAGCTAACATT 1 CTATAATCTTATGCCGAATTAGCTAACATT * 7793883 GCCTATACTCTTATGCCGAATTAGCTAACATT 1 --CTATAATCTTATGCCGAATTAGCTAACATT 7793915 -TATAATCCTTA-GCCGA 1 CTATAAT-CTTATGCCGA 7793931 GTGTTATTCA Statistics Matches: 43, Mismatches: 2, Indels: 5 0.86 0.04 0.10 Matches are distributed among these distances: 29 10 0.23 30 4 0.09 32 29 0.67 ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35 Consensus pattern (30 bp): CTATAATCTTATGCCGAATTAGCTAACATT Found at i:7800726 original size:39 final size:39 Alignment explanation

Indices: 7800671--7800777 Score: 196 Period size: 39 Copynumber: 2.7 Consensus size: 39 7800661 TTCCAACCCA * 7800671 AATGCCTTCGGAACTTAGCCCGGATATAACATCAGCACG 1 AATGCCTTCGGGACTTAGCCCGGATATAACATCAGCACG * 7800710 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG 1 AATGCCTTCGGGACTTAGCCCGGATATAACATCAGCACG 7800749 AATGCCTTCGGGACTTAGCCCGGATATAA 1 AATGCCTTCGGGACTTAGCCCGGATATAA 7800778 ATCTCACACA Statistics Matches: 66, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 39 66 1.00 ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22 Consensus pattern (39 bp): AATGCCTTCGGGACTTAGCCCGGATATAACATCAGCACG Found at i:7816885 original size:19 final size:18 Alignment explanation

Indices: 7816748--7816886 Score: 64 Period size: 19 Copynumber: 7.7 Consensus size: 18 7816738 TTCAACTATA 7816748 ATTAAATTTAATCACTTTAAT 1 ATTAAA-TTAAT-A-TTTAAT * 7816769 ATTAAATTAATA-TAATAT 1 ATTAAATTAATATTTA-AT * 7816787 ATTAGATTAA-ATTTAAT 1 ATTAAATTAATATTTAAT 7816804 ATTAAATCT--TA-TTAA- 1 ATTAAAT-TAATATTTAAT * * 7816819 AAT-AATATAATGTTT-AT 1 ATTAAAT-TAATATTTAAT * 7816836 CTTCTAAAATTAA-ATTTAAT 1 -AT-T-AAATTAATATTTAAT 7816856 ATTAAGA-TAATACTTTAAT 1 ATTAA-ATTAATA-TTTAAT 7816875 ATTAAATTAATA 1 ATTAAATTAATA 7816887 AACATACTAT Statistics Matches: 90, Mismatches: 11, Indels: 36 0.66 0.08 0.26 Matches are distributed among these distances: 14 4 0.04 15 2 0.02 16 6 0.07 17 19 0.21 18 18 0.20 19 22 0.24 20 10 0.11 21 9 0.10 ACGTcount: A:0.48, C:0.04, G:0.02, T:0.45 Consensus pattern (18 bp): ATTAAATTAATATTTAAT Found at i:7822568 original size:32 final size:32 Alignment explanation

Indices: 7822532--7822595 Score: 110 Period size: 32 Copynumber: 2.0 Consensus size: 32 7822522 ATATGGCTTC * 7822532 CAACTACCGAAGCATATGGAACCTTACTCATA 1 CAACTACCAAAGCATATGGAACCTTACTCATA * 7822564 CAACTACCAAAGCATATGGAACCTTTCTCATA 1 CAACTACCAAAGCATATGGAACCTTACTCATA 7822596 TGCACTCTTT Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 32 30 1.00 ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23 Consensus pattern (32 bp): CAACTACCAAAGCATATGGAACCTTACTCATA Found at i:7827229 original size:48 final size:47 Alignment explanation

Indices: 7827151--7827300 Score: 174 Period size: 48 Copynumber: 3.1 Consensus size: 47 7827141 TACATGGTAG * * * 7827151 GATGCCAATTCCATATCCTAGATATGGTCTTACATAGGATCACATATC 1 GATGCCAATGCCATGTCCTAGACATGGTCTTACAT-GGATCACATATC * *** ** 7827199 GATGCCAATGCCATGTCCTAGACATTGTCTTACATTGGATTGTAGGTC 1 GATGCCAATGCCATGTCCTAGACATGGTCTTACA-TGGATCACATATC * * 7827247 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGAATCCCCTATC 1 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGG-ATCACATATC 7827295 GATGCC 1 GATGCC 7827301 GATAGCCCAG Statistics Matches: 84, Mismatches: 16, Indels: 4 0.81 0.15 0.04 Matches are distributed among these distances: 47 3 0.04 48 80 0.95 49 1 0.01 ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30 Consensus pattern (47 bp): GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGATCACATATC Found at i:7831166 original size:12 final size:12 Alignment explanation

Indices: 7831149--7831178 Score: 51 Period size: 12 Copynumber: 2.5 Consensus size: 12 7831139 AAATAAAAAA 7831149 TTCTCTACAAAT 1 TTCTCTACAAAT * 7831161 TTCTCTACAACT 1 TTCTCTACAAAT 7831173 TTCTCT 1 TTCTCT 7831179 TGATTTCAAG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47 Consensus pattern (12 bp): TTCTCTACAAAT Found at i:7833080 original size:16 final size:16 Alignment explanation

Indices: 7833059--7833089 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 7833049 CTATGCATGC * 7833059 AAAATATAAAAGACAG 1 AAAATACAAAAGACAG 7833075 AAAATACAAAAGACA 1 AAAATACAAAAGACA 7833090 TAATAGTGAA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10 Consensus pattern (16 bp): AAAATACAAAAGACAG Found at i:7837926 original size:15 final size:14 Alignment explanation

Indices: 7837908--7837945 Score: 51 Period size: 15 Copynumber: 2.7 Consensus size: 14 7837898 AGATTATTAT 7837908 TAAATATAATTTAA 1 TAAATATAATTTAA * 7837922 CTAAATACAATTTAA 1 -TAAATATAATTTAA 7837937 TAAA-ATAAT 1 TAAATATAAT 7837946 ATATAATTTA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 13 4 0.19 14 4 0.19 15 13 0.62 ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37 Consensus pattern (14 bp): TAAATATAATTTAA Found at i:7839087 original size:30 final size:33 Alignment explanation

Indices: 7839051--7839122 Score: 96 Period size: 33 Copynumber: 2.3 Consensus size: 33 7839041 TAGAAACATG 7839051 GGCTCACACG-CCCA-TGTGACC-TGCCCGTGT 1 GGCTCACACGACCCATTGTGACCTTGCCCGTGT * * 7839081 GGCTCACATGACCCATTTTGACCTTGCCCGTGT 1 GGCTCACACGACCCATTGTGACCTTGCCCGTGT * 7839114 GGATCACAC 1 GGCTCACAC 7839123 AGCCTTGCCT Statistics Matches: 35, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 30 9 0.26 31 4 0.11 32 6 0.17 33 16 0.46 ACGTcount: A:0.17, C:0.36, G:0.24, T:0.24 Consensus pattern (33 bp): GGCTCACACGACCCATTGTGACCTTGCCCGTGT Found at i:7840892 original size:27 final size:27 Alignment explanation

Indices: 7840850--7840911 Score: 97 Period size: 27 Copynumber: 2.3 Consensus size: 27 7840840 CGACCGTGTG 7840850 GGCCCATTTGGACCGAGAAGGGCTTTA 1 GGCCCATTTGGACCGAGAAGGGCTTTA * * 7840877 GGCCCATTTGGGCCGAGAAGGGTTTTA 1 GGCCCATTTGGACCGAGAAGGGCTTTA * 7840904 AGCCCATT 1 GGCCCATT 7840912 CGTATTGTTA Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 27 32 1.00 ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24 Consensus pattern (27 bp): GGCCCATTTGGACCGAGAAGGGCTTTA Found at i:7841135 original size:54 final size:53 Alignment explanation

Indices: 7840949--7841234 Score: 308 Period size: 54 Copynumber: 5.3 Consensus size: 53 7840939 TTAGTTTACC * * * 7840949 AAATTACTGAAATACCCTC-AGTTGTAAAATTACCAAAGTACCCCCGGTTTATA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTACCAAA-TACCCACGATTTATA ** * * 7841002 AAATTACCCAAATATCCTCGATTTGTAAAATTACCACAATA-CCATCGA-TTGTA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTACCA-AATACCCA-CGATTTATA * * * 7841055 AAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAATACCCACGATTTTTA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTAC-CAAATACCCACGATTTATA * * * * * 7841109 AAATTATTGAAATACCCTCAACTTGTAAAATTACCAAAGTACCCCCGGTTTATA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTACCAAA-TACCCACGATTTATA ** * * * 7841163 AAATTACCCAAATATCCTCGATTTGTAAAATTACTGAAATACCCACGATTTTTA 1 AAATTACTGAAATACCCTCGATTTGTAAAATTAC-CAAATACCCACGATTTATA * 7841217 AAATTATTGAAATACCCT 1 AAATTACTGAAATACCCT 7841235 TGTAGGGTAG Statistics Matches: 191, Mismatches: 34, Indels: 15 0.80 0.14 0.06 Matches are distributed among these distances: 53 63 0.33 54 123 0.64 55 5 0.03 ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31 Consensus pattern (53 bp): AAATTACTGAAATACCCTCGATTTGTAAAATTACCAAATACCCACGATTTATA Found at i:7841227 original size:27 final size:27 Alignment explanation

Indices: 7840949--7841234 Score: 276 Period size: 27 Copynumber: 10.7 Consensus size: 27 7840939 TTAGTTTACC * 7840949 AAATTACTGAAATACCCTC-AGTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * * * 7840975 AAATTAC-CAAAGTACCCCCGGTTTATA 1 AAATTACTGAAA-TACCCTCGATTTGTA ** * 7841002 AAATTACCCAAATATCCTCGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * 7841029 AAATTAC-CACAATACCATCGA-TTGTA 1 AAATTACTGA-AATACCCTCGATTTGTA * 7841055 AAATTACTAAAATACCCTCGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * 7841082 AAATTACTGAAATACCCACGATTTTTA 1 AAATTACTGAAATACCCTCGATTTGTA * * * 7841109 AAATTATTGAAATACCCTCAACTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * * * 7841136 AAATTAC-CAAAGTACCCCCGGTTTATA 1 AAATTACTGAAA-TACCCTCGATTTGTA ** * 7841163 AAATTACCCAAATATCCTCGATTTGTA 1 AAATTACTGAAATACCCTCGATTTGTA * * 7841190 AAATTACTGAAATACCCACGATTTTTA 1 AAATTACTGAAATACCCTCGATTTGTA * 7841217 AAATTATTGAAATACCCT 1 AAATTACTGAAATACCCT 7841235 TGTAGGGTAG Statistics Matches: 213, Mismatches: 39, Indels: 15 0.80 0.15 0.06 Matches are distributed among these distances: 25 3 0.01 26 40 0.19 27 162 0.76 28 8 0.04 ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31 Consensus pattern (27 bp): AAATTACTGAAATACCCTCGATTTGTA Found at i:7841248 original size:27 final size:27 Alignment explanation

Indices: 7841225--7841710 Score: 571 Period size: 27 Copynumber: 18.0 Consensus size: 27 7841215 TAAAATTATT 7841225 GAAATACCCTTGTAGGGTAGAATTACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841252 AAAATACCCTTGTAGGGTAGAAATACT 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841279 AAAATACACTTGTAGGGTAGAAATACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841306 GAAATACCTTTGTAGAGTAGAATTACT 1 GAAATACCCTTGTAGGGTAGAATTACC * 7841333 GAAATACCCCTGTAGGGTAGAATTACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841360 GAAATACCCTTATAGGATAGAAATACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * 7841387 GAAATACCCCTATAGGGTAGAATTACC 1 GAAATACCCTTGTAGGGTAGAATTACC * ** 7841414 GAAATACCCTTGTAGGGTAGAAATATT 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841441 GAAATACCCTTATAGGCTAGAAATACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841468 GAAATACCCCTATAGGGTAGAATTACA 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841495 TAAATACCCCTATAGGGTAGAATTACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * * 7841522 GAAATAACCTTGTAGGGTAGAAATATC 1 GAAATACCCTTGTAGGGTAGAATTACC * * 7841549 GAAATACCCTTGTAAGGTAGAAATACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * 7841576 GAAATACCCCTGTAGGGTAGAATTACT 1 GAAATACCCTTGTAGGGTAGAATTACC * 7841603 GAAATACCCCTGT-GGGATAGAATTACC 1 GAAATACCCTTGTAGGG-TAGAATTACC * * * 7841630 GAAATACCCTTATAGGGTAAAAATACC 1 GAAATACCCTTGTAGGGTAGAATTACC * 7841657 GAAATACCCATGTAGGGTAGAATTACC 1 GAAATACCCTTGTAGGGTAGAATTACC * * 7841684 GAGATACCCTTGT-GAGGTAAAATTACC 1 GAAATACCCTTGTAG-GGTAGAATTACC 7841711 ATTTTGCCTC Statistics Matches: 394, Mismatches: 62, Indels: 6 0.85 0.13 0.01 Matches are distributed among these distances: 26 4 0.01 27 387 0.98 28 3 0.01 ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24 Consensus pattern (27 bp): GAAATACCCTTGTAGGGTAGAATTACC Found at i:7841249 original size:108 final size:108 Alignment explanation

Indices: 7841026--7841260 Score: 321 Period size: 108 Copynumber: 2.2 Consensus size: 108 7841016 TCCTCGATTT * ** * * * 7841026 GTAAAATTACCACAATACCATC-GATTGTAAAATTACTAAAATACCCTCGATTTGTAAAATTACT 1 GTAAAATTACCAAAATACCCCCGGTTTATAAAATTACCAAAATACCCTCGATTTGTAAAATTACT ** 7841090 GAAATACCCACGATTTTTAAAATTATTGAAATACCCTCAACTT 66 GAAATACCCACGATTTTTAAAATTATTGAAATACCCTCAACGG * * * 7841133 GTAAAATTACCAAAGTACCCCCGGTTTATAAAATTACCCAAATATCCTCGATTTGTAAAATTACT 1 GTAAAATTACCAAAATACCCCCGGTTTATAAAATTACCAAAATACCCTCGATTTGTAAAATTACT ** 7841198 GAAATACCCACGATTTTTAAAATTATTGAAATACCCTTGTA-GG 66 GAAATACCCACGATTTTTAAAATTATTGAAATACCC-TCAACGG * 7841241 GTAGAATTACCAAAATACCC 1 GTAAAATTACCAAAATACCC 7841261 TTGTAGGGTA Statistics Matches: 111, Mismatches: 15, Indels: 3 0.86 0.12 0.02 Matches are distributed among these distances: 107 18 0.16 108 91 0.82 109 2 0.02 ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31 Consensus pattern (108 bp): GTAAAATTACCAAAATACCCCCGGTTTATAAAATTACCAAAATACCCTCGATTTGTAAAATTACT GAAATACCCACGATTTTTAAAATTATTGAAATACCCTCAACGG Found at i:7842189 original size:22 final size:22 Alignment explanation

Indices: 7842137--7842201 Score: 78 Period size: 22 Copynumber: 3.0 Consensus size: 22 7842127 TTAAAGCCTT * * 7842137 CTGATTATGGCTTTGTGTCAAC 1 CTGATTATGGCTCTGTGCCAAC * 7842159 CT-ACATATGGCTCTGTGCCAAC 1 CTGA-TTATGGCTCTGTGCCAAC * 7842181 CTGATTATGGCTGTGTGCCAA 1 CTGATTATGGCTCTGTGCCAA 7842202 ATGTATTTGC Statistics Matches: 36, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 21 1 0.03 22 34 0.94 23 1 0.03 ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34 Consensus pattern (22 bp): CTGATTATGGCTCTGTGCCAAC Found at i:7842309 original size:18 final size:18 Alignment explanation

Indices: 7842288--7842359 Score: 82 Period size: 18 Copynumber: 4.3 Consensus size: 18 7842278 TTGCATTCAC 7842288 ATTCTGATTCTGATTCTA 1 ATTCTGATTCTGATTCTA * * 7842306 ATTCTG--TC--A-CCTG 1 ATTCTGATTCTGATTCTA 7842319 ATTCTGATTCTGATTCTA 1 ATTCTGATTCTGATTCTA * 7842337 ATTCTGATTTTGATTCTA 1 ATTCTGATTCTGATTCTA 7842355 ATTCT 1 ATTCT 7842360 AGTAATGTTT Statistics Matches: 44, Mismatches: 5, Indels: 10 0.75 0.08 0.17 Matches are distributed among these distances: 13 8 0.18 14 1 0.02 15 2 0.05 16 2 0.05 17 1 0.02 18 30 0.68 ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50 Consensus pattern (18 bp): ATTCTGATTCTGATTCTA Found at i:7842377 original size:6 final size:6 Alignment explanation

Indices: 7842288--7842359 Score: 74 Period size: 6 Copynumber: 11.8 Consensus size: 6 7842278 TTGCATTCAC * * * 7842288 ATTCTG ATTCTG ATTCTA ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTA 1 ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG * * 7842337 ATTCTG ATTTTG ATTCTA ATTCT 1 ATTCTG ATTCTG ATTCTG ATTCT 7842360 AGTAATGTTT Statistics Matches: 54, Mismatches: 9, Indels: 6 0.78 0.13 0.09 Matches are distributed among these distances: 5 1 0.02 6 49 0.91 7 3 0.06 8 1 0.02 ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50 Consensus pattern (6 bp): ATTCTG Found at i:7842383 original size:17 final size:18 Alignment explanation

Indices: 7842350--7842383 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 7842340 CTGATTTTGA 7842350 TTCTAATTCTAGTAATGT 1 TTCTAATTCTAGTAATGT * 7842368 TTCTTATTCT-GTAATG 1 TTCTAATTCTAGTAATG 7842384 GGCTAAGGCC Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 6 0.40 18 9 0.60 ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53 Consensus pattern (18 bp): TTCTAATTCTAGTAATGT Found at i:7844471 original size:80 final size:81 Alignment explanation

Indices: 7844357--7844582 Score: 240 Period size: 80 Copynumber: 2.8 Consensus size: 81 7844347 ATACCCCCAG ** * 7844357 TTGTAAAATTACTAAAGTA-CCTCCGGTTTATAAAATTACCCAAATATCCTCGATTTATAAAATT 1 TTGTAAAATTACTAAAGTACCCT-CAATTTATAAAATTACCCAAATACCCTCGATTTATAAAATT * 7844421 ACCGAAATACCATCGA- 65 ACCAAAATACCATCGAC * * ** * * 7844437 TTGTAAAATTACTAAAATACCCTCAATTTGTAAAATTACTGAGATACCCTCGATTTGTAAAATTA 1 TTGTAAAATTACTAAAGTACCCTCAATTTATAAAATTACCCAAATACCCTCGATTTATAAAATTA * * 7844502 CTAAAATACCCTCGAC 66 CCAAAATACCATCGAC * * * * **** * 7844518 TTGTAAAATTACCAAAGTACCCCCAATTTATAGAATTATCGTTTTACCCTCGATTTACAAAATTA 1 TTGTAAAATTACTAAAGTACCCTCAATTTATAAAATTACCCAAATACCCTCGATTTATAAAATTA 7844583 TTGAAATACC Statistics Matches: 120, Mismatches: 24, Indels: 3 0.82 0.16 0.02 Matches are distributed among these distances: 80 64 0.53 81 56 0.47 ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33 Consensus pattern (81 bp): TTGTAAAATTACTAAAGTACCCTCAATTTATAAAATTACCCAAATACCCTCGATTTATAAAATTA CCAAAATACCATCGAC Found at i:7844510 original size:54 final size:54 Alignment explanation

Indices: 7844336--7844529 Score: 216 Period size: 53 Copynumber: 3.6 Consensus size: 54 7844326 TTAGTTTACC * * * * * 7844336 AAATTACTGAAATACCC-CCAGTTGTAAAATTACT-AAAGTA-CCTCCGGTTTATA 1 AAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAA-TACCCT-CGATTTGTA ** * * * * 7844389 AAATTACCCAAATATCCTCGATTTATAAAATTACCGAAATACCATCGA-TTGTA 1 AAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTTGTA * * 7844442 AAATTACTAAAATACCCTCAATTTGTAAAATTACTGAGATACCCTCGATTTGTA 1 AAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTTGTA * 7844496 AAATTACTAAAATACCCTCGACTTGTAAAATTAC 1 AAATTACTAAAATACCCTCGATTTGTAAAATTAC 7844530 CAAAGTACCC Statistics Matches: 117, Mismatches: 20, Indels: 7 0.81 0.14 0.05 Matches are distributed among these distances: 53 58 0.50 54 54 0.46 55 5 0.04 ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31 Consensus pattern (54 bp): AAATTACTAAAATACCCTCGATTTGTAAAATTACTGAAATACCCTCGATTTGTA Found at i:7844592 original size:27 final size:27 Alignment explanation

Indices: 7844336--7844593 Score: 195 Period size: 27 Copynumber: 9.6 Consensus size: 27 7844326 TTAGTTTACC * * * 7844336 AAATTACTGAAATACCC-CCAGTTGTA 1 AAATTACTGAAATACCCTCGATTTATA * 7844362 AAATTACT-AAAGTA-CCTCCGGTTTATA 1 AAATTACTGAAA-TACCCT-CGATTTATA ** * 7844389 AAATTACCCAAATATCCTCGATTTATA 1 AAATTACTGAAATACCCTCGATTTATA * * * 7844416 AAATTACCGAAATACCATCGA-TTGTA 1 AAATTACTGAAATACCCTCGATTTATA * * * 7844442 AAATTACTAAAATACCCTCAATTTGTA 1 AAATTACTGAAATACCCTCGATTTATA * * 7844469 AAATTACTGAGATACCCTCGATTTGTA 1 AAATTACTGAAATACCCTCGATTTATA * * * 7844496 AAATTACTAAAATACCCTCGACTTGTA 1 AAATTACTGAAATACCCTCGATTTATA * * * 7844523 AAATTAC-CAAAGTACCCCCAATTTATA 1 AAATTACTGAAA-TACCCTCGATTTATA * *** * 7844550 GAATTA-TCGTTTTACCCTCGATTTACA 1 AAATTACT-GAAATACCCTCGATTTATA * 7844577 AAATTATTGAAATACCC 1 AAATTACTGAAATACCC 7844594 CTGTAGGGTA Statistics Matches: 185, Mismatches: 37, Indels: 19 0.77 0.15 0.08 Matches are distributed among these distances: 25 5 0.03 26 34 0.18 27 139 0.75 28 7 0.04 ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31 Consensus pattern (27 bp): AAATTACTGAAATACCCTCGATTTATA Found at i:7844608 original size:27 final size:27 Alignment explanation

Indices: 7844585--7845077 Score: 540 Period size: 27 Copynumber: 18.3 Consensus size: 27 7844575 CAAAATTATT 7844585 GAAATACCCCTGTAGGGTAGAATTACC 1 GAAATACCCCTGTAGGGTAGAATTACC * * 7844612 GAAATACCCTTGTAGGGTAGAAATACC 1 GAAATACCCCTGTAGGGTAGAATTACC * * * 7844639 GAAATACCCTTGTAGAGTAGAATTACT 1 GAAATACCCCTGTAGGGTAGAATTACC * 7844666 GAAATACCCCTATAGGGTAGAATTACC 1 GAAATACCCCTGTAGGGTAGAATTACC * * * * 7844693 GAAATACCCTTGTAGGGTAAAAATATC 1 GAAATACCCCTGTAGGGTAGAATTACC * * * * * 7844720 AAAATACCCTTATAGGCTAGAAATACC 1 GAAATACCCCTGTAGGGTAGAATTACC * 7844747 -AGAATACCCCTGTAGGGTAGAATTACT 1 GA-AATACCCCTGTAGGGTAGAATTACC * * 7844774 AAAATACCCCTATAGGGTAGAATTACC 1 GAAATACCCCTGTAGGGTAGAATTACC * * * * 7844801 GAAATACCCTTGTAGGGTAAAAATATC 1 GAAATACCCCTGTAGGGTAGAATTACC * * * * * 7844828 AAAATACCCTTATAGGCTAGAAATACC 1 GAAATACCCCTGTAGGGTAGAATTACC * 7844855 -AGAATACCCCTGTAGGGTAGAATTACT 1 GA-AATACCCCTGTAGGGTAGAATTACC * * * * 7844882 AAAATACCCCTATAGGGGAGAATTGCC 1 GAAATACCCCTGTAGGGTAGAATTACC * * * * 7844909 GAAATAGCCTTGTAGGGTAGAAATATC 1 GAAATACCCCTGTAGGGTAGAATTACC * * 7844936 GAAATACCCTTGTAGGGTAGAAATACC 1 GAAATACCCCTGTAGGGTAGAATTACC * 7844963 GAAATACCCCTGTAGGGTAGAATTACT 1 GAAATACCCCTGTAGGGTAGAATTACC * * 7844990 GAAATACCTCTGTAGGATAGAATTACC 1 GAAATACCCCTGTAGGGTAGAATTACC * * * * 7845017 GAAATACCCTTATCGGGTAGAAATACC 1 GAAATACCCCTGTAGGGTAGAATTACC 7845044 GAAATACCCCTGTAGGGTAGAATTACC 1 GAAATACCCCTGTAGGGTAGAATTACC * 7845071 GAGATAC 1 GAAATAC 7845078 TCTTGGGTAA Statistics Matches: 389, Mismatches: 73, Indels: 8 0.83 0.16 0.02 Matches are distributed among these distances: 26 2 0.01 27 385 0.99 28 2 0.01 ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24 Consensus pattern (27 bp): GAAATACCCCTGTAGGGTAGAATTACC Found at i:7844674 original size:108 final size:108 Alignment explanation

Indices: 7844585--7845077 Score: 693 Period size: 108 Copynumber: 4.6 Consensus size: 108 7844575 CAAAATTATT * * * * 7844585 GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCTT 1 GAAATACCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCT * * * 7844650 GTAGAGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACC 66 GTAGGGTAGAATTACTAAAATACCCCTATAGGGGAGAATTACC * * * * 7844693 GAAATACCCTTGTAGGGTAAAAATATCAAAATACCCTTATAGGCTAGAAATACC-AGAATACCCC 1 GAAATACCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAATACCGA-AATACCCC * 7844757 TGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTACC 65 TGTAGGGTAGAATTACTAAAATACCCCTATAGGGGAGAATTACC * * * * 7844801 GAAATACCCTTGTAGGGTAAAAATATCAAAATACCCTTATAGGCTAGAAATACC-AGAATACCCC 1 GAAATACCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAATACCGA-AATACCCC * 7844865 TGTAGGGTAGAATTACTAAAATACCCCTATAGGGGAGAATTGCC 65 TGTAGGGTAGAATTACTAAAATACCCCTATAGGGGAGAATTACC * 7844909 GAAATAGCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCT 1 GAAATACCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCT * * * ** 7844974 GTAGGGTAGAATTACTGAAATACCTCTGTAGGATAGAATTACC 66 GTAGGGTAGAATTACTAAAATACCCCTATAGGGGAGAATTACC * * * * * * 7845017 GAAATACCCTTATCGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCGAGATAC 1 GAAATACCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAATACCGAAATAC 7845078 TCTTGGGTAA Statistics Matches: 353, Mismatches: 30, Indels: 4 0.91 0.08 0.01 Matches are distributed among these distances: 107 1 0.00 108 351 0.99 109 1 0.00 ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24 Consensus pattern (108 bp): GAAATACCCTTGTAGGGTAGAAATATCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCT GTAGGGTAGAATTACTAAAATACCCCTATAGGGGAGAATTACC Found at i:7845574 original size:22 final size:22 Alignment explanation

Indices: 7845522--7845586 Score: 78 Period size: 22 Copynumber: 3.0 Consensus size: 22 7845512 TTAAAGCCTT * * 7845522 CTGATTATGGCTTTGCGCCAAC 1 CTGATTATGGCTCTGTGCCAAC * 7845544 CT-ACATATGGCTCTGTGCCAAC 1 CTGA-TTATGGCTCTGTGCCAAC * 7845566 CTGATTATGGCTGTGTGCCAA 1 CTGATTATGGCTCTGTGCCAA 7845587 ACGTATTTGC Statistics Matches: 36, Mismatches: 5, Indels: 4 0.80 0.11 0.09 Matches are distributed among these distances: 21 1 0.03 22 34 0.94 23 1 0.03 ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31 Consensus pattern (22 bp): CTGATTATGGCTCTGTGCCAAC Found at i:7848051 original size:26 final size:26 Alignment explanation

Indices: 7848007--7848094 Score: 106 Period size: 26 Copynumber: 3.4 Consensus size: 26 7847997 TGCCACGTAT * * * 7848007 TCTGTT-TAGTGGCTTTGCCACATTA 1 TCTGTTCTGGTGGCTCTGCCACAATA 7848032 TCTGTTCTGGTGGCTCTGCCACAATA 1 TCTGTTCTGGTGGCTCTGCCACAATA ** * 7848058 TCTGTATCTGGTAACTCTGTCACAATA 1 TCTGT-TCTGGTGGCTCTGCCACAATA 7848085 TCTGTTCTGG 1 TCTGTTCTGG 7848095 CAGTCATGCT Statistics Matches: 55, Mismatches: 6, Indels: 3 0.86 0.09 0.05 Matches are distributed among these distances: 25 6 0.11 26 26 0.47 27 23 0.42 ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40 Consensus pattern (26 bp): TCTGTTCTGGTGGCTCTGCCACAATA Found at i:7848075 original size:27 final size:26 Alignment explanation

Indices: 7848022--7848094 Score: 101 Period size: 27 Copynumber: 2.8 Consensus size: 26 7848012 TTAGTGGCTT * ** 7848022 TGCCACATTATCTGTTCTGGTGGCTC 1 TGCCACAATATCTGTTCTGGTAACTC 7848048 TGCCACAATATCTGTATCTGGTAACTC 1 TGCCACAATATCTGT-TCTGGTAACTC * 7848075 TGTCACAATATCTGTTCTGG 1 TGCCACAATATCTGTTCTGG 7848095 CAGTCATGCT Statistics Matches: 42, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 26 19 0.45 27 23 0.55 ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37 Consensus pattern (26 bp): TGCCACAATATCTGTTCTGGTAACTC Found at i:7848221 original size:6 final size:6 Alignment explanation

Indices: 7848212--7848297 Score: 59 Period size: 6 Copynumber: 14.0 Consensus size: 6 7848202 TTGCATTCAC * * * 7848212 ATTCTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG -TCACCTA 1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG * * * * 7848262 ATTCTG ATTCTA ATTCTC ATTTTG ATTCTA ATTCTG 1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG 7848298 GTAATGTTTC Statistics Matches: 61, Mismatches: 13, Indels: 12 0.71 0.15 0.14 Matches are distributed among these distances: 5 3 0.05 6 51 0.84 7 5 0.08 8 2 0.03 ACGTcount: A:0.21, C:0.20, G:0.12, T:0.48 Consensus pattern (6 bp): ATTCTG Found at i:7848243 original size:25 final size:25 Alignment explanation

Indices: 7848215--7848278 Score: 92 Period size: 25 Copynumber: 2.6 Consensus size: 25 7848205 CATTCACATT * * 7848215 CTGATTCTGATTCTGTTACCTGATA 1 CTGATTCTGATTCTGTCACCTAATA * 7848240 CTGATTCTGATTCTGTCACCTAATT 1 CTGATTCTGATTCTGTCACCTAATA * 7848265 CTGATTCTAATTCT 1 CTGATTCTGATTCT 7848279 CATTTTGATT Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 25 35 1.00 ACGTcount: A:0.20, C:0.22, G:0.12, T:0.45 Consensus pattern (25 bp): CTGATTCTGATTCTGTCACCTAATA Found at i:7848320 original size:17 final size:18 Alignment explanation

Indices: 7848287--7848320 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 7848277 CTCATTTTGA 7848287 TTCTAATTCTGGTAATGT 1 TTCTAATTCTGGTAATGT * 7848305 TTCTTATTCT-GTAATG 1 TTCTAATTCTGGTAATG 7848321 GGCTAAGGCT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 6 0.40 18 9 0.60 ACGTcount: A:0.21, C:0.12, G:0.15, T:0.53 Consensus pattern (18 bp): TTCTAATTCTGGTAATGT Found at i:7851638 original size:20 final size:19 Alignment explanation

Indices: 7851609--7851670 Score: 54 Period size: 20 Copynumber: 3.2 Consensus size: 19 7851599 TTAACATTTG 7851609 ATATAT-ATTATATTTTAA 1 ATATATAATTATATTTTAA * * * 7851627 ATATAATCATTACAAATTTAA 1 ATAT-ATAATTA-TATTTTAA * 7851648 ATATATAATCTATATTTGAA 1 ATATATAAT-TATATTTTAA 7851668 ATA 1 ATA 7851671 AATTTTAATA Statistics Matches: 34, Mismatches: 6, Indels: 6 0.74 0.13 0.13 Matches are distributed among these distances: 18 4 0.12 19 2 0.06 20 16 0.47 21 12 0.35 ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45 Consensus pattern (19 bp): ATATATAATTATATTTTAA Found at i:7852055 original size:10 final size:11 Alignment explanation

Indices: 7852030--7852054 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 7852020 AAACCCTACC 7852030 AAAAGAAAAAA 1 AAAAGAAAAAA 7852041 AAAAGAAAAAA 1 AAAAGAAAAAA 7852052 AAA 1 AAA 7852055 GGGGTAGTCA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00 Consensus pattern (11 bp): AAAAGAAAAAA Found at i:7865457 original size:29 final size:30 Alignment explanation

Indices: 7865400--7865457 Score: 82 Period size: 30 Copynumber: 2.0 Consensus size: 30 7865390 CTTTTGAAAA * * * 7865400 TATTTACAAAAAGAGGCATCTAATTTTTAT 1 TATTTACAAAAAGAGGCAACCAAATTTTAT 7865430 TATTTACAAAAAGA-GCAACCAAATTTTA 1 TATTTACAAAAAGAGGCAACCAAATTTTA 7865458 AAAATACTTC Statistics Matches: 25, Mismatches: 3, Indels: 1 0.86 0.10 0.03 Matches are distributed among these distances: 29 11 0.44 30 14 0.56 ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34 Consensus pattern (30 bp): TATTTACAAAAAGAGGCAACCAAATTTTAT Found at i:7874009 original size:26 final size:26 Alignment explanation

Indices: 7873962--7874011 Score: 64 Period size: 26 Copynumber: 1.9 Consensus size: 26 7873952 TATCATCCCT * * ** 7873962 ATTTTACCCCCAGTAATTTTTTGATG 1 ATTTAACCCACAGTAAAATTTTGATG 7873988 ATTTAACCCACAGTAAAATTTTGA 1 ATTTAACCCACAGTAAAATTTTGA 7874012 CAATTTTACA Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 26 20 1.00 ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40 Consensus pattern (26 bp): ATTTAACCCACAGTAAAATTTTGATG Found at i:7874017 original size:26 final size:26 Alignment explanation

Indices: 7873988--7874037 Score: 64 Period size: 26 Copynumber: 1.9 Consensus size: 26 7873978 TTTTTTGATG * 7873988 ATTTAACCCACAGTAAAATTTTGACA 1 ATTTAACACACAGTAAAATTTTGACA * ** 7874014 ATTTTACACATGGTAAAATTTTGA 1 ATTTAACACACAGTAAAATTTTGA 7874038 AAAAATTTGT Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 26 20 1.00 ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36 Consensus pattern (26 bp): ATTTAACACACAGTAAAATTTTGACA Found at i:7903995 original size:43 final size:43 Alignment explanation

Indices: 7903886--7904030 Score: 165 Period size: 43 Copynumber: 3.4 Consensus size: 43 7903876 TAAAACCCCG * 7903886 TCTGGGACATTGGCATCGA-ATTATGATTTTCATGTGAGACCACT 1 TCTGGGACAGTGGCATCGATATT-TGA-TTTCATGTGAGACCACT 7903930 TCTGGGAC-GTTGGCATCG-TATTTGATTTCATGTGAGACC-CT 1 TCTGGGACAG-TGGCATCGATATTTGATTTCATGTGAGACCACT * * * 7903971 ATCTGGGACAGTGACATCGATATTTGATTACATGTAAGACCACGT 1 -TCTGGGACAGTGGCATCGATATTTGATTTCATGTGAGACCAC-T * 7904016 T-TGGGACATTGGCAT 1 TCTGGGACAGTGGCAT 7904031 TGTACGAGCT Statistics Matches: 88, Mismatches: 6, Indels: 15 0.81 0.06 0.14 Matches are distributed among these distances: 41 2 0.02 42 29 0.33 43 35 0.40 44 21 0.24 45 1 0.01 ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33 Consensus pattern (43 bp): TCTGGGACAGTGGCATCGATATTTGATTTCATGTGAGACCACT Found at i:7911470 original size:42 final size:42 Alignment explanation

Indices: 7911343--7911513 Score: 134 Period size: 42 Copynumber: 4.0 Consensus size: 42 7911333 ACATAGGATC * * * * * 7911343 CGATATGTGTTTACGTGTAAAACCACGTTTGGGATGTTGGCAT 1 CGATAT-TGATTACATGTAAGACCACGTCTGGGACGTTGGCAT * ** * * 7911386 CAACT-TATGATTTATGTGTAAGACCACTTCTAGGACGTTGGCAT 1 CGA-TAT-TGA-TTACATGTAAGACCACGTCTGGGACGTTGGCAT * * * 7911430 CG-TATTTGATTTCGTGTAAGTCC-CTGTCTGGGACAG-TGGCAT 1 CGATA-TTGATTACATGTAAGACCAC-GTCTGGGAC-GTTGGCAT 7911472 CGATATTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT 1 CGATATTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT 7911514 TGTACAAGCT Statistics Matches: 101, Mismatches: 18, Indels: 19 0.73 0.13 0.14 Matches are distributed among these distances: 41 2 0.02 42 57 0.56 43 12 0.12 44 30 0.30 ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33 Consensus pattern (42 bp): CGATATTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT Found at i:7921984 original size:13 final size:13 Alignment explanation

Indices: 7921945--7921997 Score: 70 Period size: 13 Copynumber: 4.1 Consensus size: 13 7921935 AGTTTGGCAA 7921945 TGCTTTTGAAAAG 1 TGCTTTTGAAAAG * * * 7921958 TGCTGTGGTAAAG 1 TGCTTTTGAAAAG * 7921971 TGCTTTTGAGAAG 1 TGCTTTTGAAAAG 7921984 TGCTTTTGAAAAG 1 TGCTTTTGAAAAG 7921997 T 1 T 7921998 TTGGTTTAAA Statistics Matches: 32, Mismatches: 8, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 13 32 1.00 ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38 Consensus pattern (13 bp): TGCTTTTGAAAAG Found at i:7931097 original size:13 final size:13 Alignment explanation

Indices: 7931058--7931110 Score: 70 Period size: 13 Copynumber: 4.1 Consensus size: 13 7931048 AGTTTGGCAA 7931058 TGCTTTTGAAAAG 1 TGCTTTTGAAAAG * * * 7931071 TGCTGTGGTAAAG 1 TGCTTTTGAAAAG * 7931084 TGCTTTTGAGAAG 1 TGCTTTTGAAAAG 7931097 TGCTTTTGAAAAG 1 TGCTTTTGAAAAG 7931110 T 1 T 7931111 TTGGTTTAAA Statistics Matches: 32, Mismatches: 8, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 13 32 1.00 ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38 Consensus pattern (13 bp): TGCTTTTGAAAAG Found at i:7933258 original size:27 final size:27 Alignment explanation

Indices: 7933232--7933394 Score: 148 Period size: 28 Copynumber: 5.9 Consensus size: 27 7933222 TCCAAGAAGG * 7933232 CTTCATTTTCATAGATCGCCACAAAGG 1 CTTCATTTTCATAGATCGCCACAAAGA * * * * * * 7933259 CTTCTTTTTTAATGGATAGCCATAAATA 1 CTTC-ATTTTCATAGATCGCCACAAAGA * * 7933287 CTTTATTTTTCATAGATCACCACAAATG- 1 CTTCA-TTTTCATAGATCGCCACAAA-GA * * 7933315 CTTCCTTTTAATAGATCGCCACAAAGA 1 CTTCATTTTCATAGATCGCCACAAAGA * * 7933342 CTTCCTTTTCAAAGATCGCCACAAAGA 1 CTTCATTTTCATAGATCGCCACAAAGA * * 7933369 CTTCATTTTTTATAGATCACCACAAA 1 CTTCA-TTTTCATAGATCGCCACAAA 7933395 TGGTTCCTTT Statistics Matches: 106, Mismatches: 25, Indels: 9 0.76 0.18 0.06 Matches are distributed among these distances: 26 1 0.01 27 51 0.48 28 54 0.51 ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34 Consensus pattern (27 bp): CTTCATTTTCATAGATCGCCACAAAGA Found at i:7933402 original size:82 final size:83 Alignment explanation

Indices: 7933231--7933405 Score: 235 Period size: 82 Copynumber: 2.1 Consensus size: 83 7933221 TTCCAAGAAG * * * * * * * * * 7933231 GCTTCATTTTCATAGATCGCCACAAAGGCTTCTTTTTTAATGGATAGCCATAAATACTTTATTTT 1 GCTTCCTTTTAATAGATCGCCACAAAGACTTCCTTTTCAATAGATAGCCACAAAGACTTCATTTT 7933296 TCATAGATCACCACAAAT 66 TCATAGATCACCACAAAT * 7933314 GCTTCCTTTTAATAGATCGCCACAAAGACTTCCTTTTCAA-AGATCGCCACAAAGACTTCATTTT 1 GCTTCCTTTTAATAGATCGCCACAAAGACTTCCTTTTCAATAGATAGCCACAAAGACTTCATTTT * 7933378 TTATAGATCACCACAAAT 66 TCATAGATCACCACAAAT * 7933396 GGTTCCTTTT 1 GCTTCCTTTT 7933406 TCTAGAGTGT Statistics Matches: 80, Mismatches: 12, Indels: 1 0.86 0.13 0.01 Matches are distributed among these distances: 82 45 0.56 83 35 0.44 ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36 Consensus pattern (83 bp): GCTTCCTTTTAATAGATCGCCACAAAGACTTCCTTTTCAATAGATAGCCACAAAGACTTCATTTT TCATAGATCACCACAAAT Found at i:7939989 original size:27 final size:27 Alignment explanation

Indices: 7939951--7940004 Score: 108 Period size: 27 Copynumber: 2.0 Consensus size: 27 7939941 ACGTTCTATT 7939951 GGCCACTAGTAGGAATTCAATGCCATA 1 GGCCACTAGTAGGAATTCAATGCCATA 7939978 GGCCACTAGTAGGAATTCAATGCCATA 1 GGCCACTAGTAGGAATTCAATGCCATA 7940005 CTCTCTATTA Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 27 1.00 ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22 Consensus pattern (27 bp): GGCCACTAGTAGGAATTCAATGCCATA Found at i:7947379 original size:18 final size:18 Alignment explanation

Indices: 7947356--7947392 Score: 74 Period size: 18 Copynumber: 2.1 Consensus size: 18 7947346 AACTCAACAT 7947356 CTATTGCATCATGCACCA 1 CTATTGCATCATGCACCA 7947374 CTATTGCATCATGCACCA 1 CTATTGCATCATGCACCA 7947392 C 1 C 7947393 AAATGAGTCA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27 Consensus pattern (18 bp): CTATTGCATCATGCACCA Found at i:7947403 original size:18 final size:18 Alignment explanation

Indices: 7947360--7947397 Score: 58 Period size: 18 Copynumber: 2.1 Consensus size: 18 7947350 CAACATCTAT * * 7947360 TGCATCATGCACCACTAT 1 TGCATCATGCACCACAAA 7947378 TGCATCATGCACCACAAA 1 TGCATCATGCACCACAAA 7947396 TG 1 TG 7947398 AGTCATCGTG Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.32, C:0.32, G:0.13, T:0.24 Consensus pattern (18 bp): TGCATCATGCACCACAAA Found at i:7949822 original size:25 final size:25 Alignment explanation

Indices: 7949794--7949859 Score: 78 Period size: 25 Copynumber: 2.6 Consensus size: 25 7949784 AAATTTTTTC 7949794 GGAAGCATTTGTGGCAATTTACTTG 1 GGAAGCATTTGTGGCAATTTACTTG * * ** * 7949819 GGAAGCCTTTATGAAAATTTATTTG 1 GGAAGCATTTGTGGCAATTTACTTG * 7949844 GGAAGCTTTTGTGGCA 1 GGAAGCATTTGTGGCA 7949860 GGTTACACGT Statistics Matches: 32, Mismatches: 9, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 25 32 1.00 ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36 Consensus pattern (25 bp): GGAAGCATTTGTGGCAATTTACTTG Found at i:7951225 original size:40 final size:40 Alignment explanation

Indices: 7951165--7951348 Score: 221 Period size: 40 Copynumber: 4.6 Consensus size: 40 7951155 TATTCGAATG * 7951165 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT 1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT * * * 7951205 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT 1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT * * * * 7951245 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGCGACT 1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT * 7951285 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC 1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT * * 7951325 ATATCCGGGCTAAGACCCAAAGGC 1 ATATCCGGGCTAAGATCCGAAGGC 7951349 CTTGTGCGAG Statistics Matches: 123, Mismatches: 16, Indels: 10 0.83 0.11 0.07 Matches are distributed among these distances: 39 1 0.01 40 119 0.97 41 3 0.02 ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24 Consensus pattern (40 bp): ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT Found at i:7951298 original size:80 final size:80 Alignment explanation

Indices: 7951165--7951348 Score: 246 Period size: 80 Copynumber: 2.3 Consensus size: 80 7951155 TATTCGAATG * ** * 7951165 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC * * 7951229 ATTTGTGCGAGTTG-CT 65 ATTTATGCGAG-TGACC * * 7951245 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA * 7951310 TTTATGCTAGTGACC 66 TTTATGCGAGTGACC * 7951325 ATATCCGGGCTAAGACCCAAAGGC 1 ATATCCGGGCTAAGACCCGAAGGC 7951349 CTTGTGCGAG Statistics Matches: 92, Mismatches: 10, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 79 3 0.03 80 89 0.97 ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24 Consensus pattern (80 bp): ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA TTTATGCGAGTGACC Found at i:7951653 original size:22 final size:22 Alignment explanation

Indices: 7951611--7951654 Score: 54 Period size: 22 Copynumber: 2.0 Consensus size: 22 7951601 AAAATGTGCA * * 7951611 TATATGAAGTTATTCATTTAGC 1 TATATGAAGTTATACACTTAGC 7951633 TATATGAATGTTATAC-CTTAGC 1 TATATGAA-GTTATACACTTAGC 7951655 CGAAACTAAT Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 22 13 0.68 23 6 0.32 ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43 Consensus pattern (22 bp): TATATGAAGTTATACACTTAGC Found at i:7959446 original size:40 final size:40 Alignment explanation

Indices: 7959386--7959569 Score: 239 Period size: 40 Copynumber: 4.6 Consensus size: 40 7959376 TATTCGAATG * 7959386 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT 1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT * * * 7959426 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT 1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT * * * 7959466 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT 1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT * 7959506 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC 1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT * 7959546 ATATCCGGGCTAAGACCCGAAGGC 1 ATATCCGGGCTAAGATCCGAAGGC 7959570 CTTGTGCGAG Statistics Matches: 126, Mismatches: 13, Indels: 10 0.85 0.09 0.07 Matches are distributed among these distances: 39 1 0.01 40 122 0.97 41 3 0.02 ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24 Consensus pattern (40 bp): ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT Found at i:7959519 original size:80 final size:80 Alignment explanation

Indices: 7959386--7959569 Score: 264 Period size: 80 Copynumber: 2.3 Consensus size: 80 7959376 TATTCGAATG * * * 7959386 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC * * 7959450 ATTTGTGCGAGTTG-CT 65 ATTTATGCGAG-TGACC * * 7959466 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA * 7959531 TTTATGCTAGTGACC 66 TTTATGCGAGTGACC 7959546 ATATCCGGGCTAAGACCCGAAGGC 1 ATATCCGGGCTAAGACCCGAAGGC 7959570 CTTGTGCGAG Statistics Matches: 94, Mismatches: 8, Indels: 4 0.89 0.08 0.04 Matches are distributed among these distances: 79 3 0.03 80 91 0.97 ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24 Consensus pattern (80 bp): ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA TTTATGCGAGTGACC Found at i:7966806 original size:42 final size:42 Alignment explanation

Indices: 7966747--7966897 Score: 135 Period size: 42 Copynumber: 3.6 Consensus size: 42 7966737 AGATTACATG * 7966747 AAGACCATATCTAGGATATGGCATC-ATTATGAAAATTTGTGT 1 AAGACCATATCTAGGATATGGCATCGA-TATGAAAATTCGTGT * * * 7966789 AAGACCATATCTAGGATATGGTATCGATATGAGACTTCGTGT 1 AAGACCATATCTAGGATATGGCATCGATATGAAAATTCGTGT * * * * * * * * * 7966831 AAGACCATAGCTGGGCTATTGGCGTCGATACG-AGATCCCATAT 1 AAGACCATATCTAGGATA-TGGCATCGATATGAAAAT-TCGTGT * 7966874 AAGACCATATCTGGGATATGGCAT 1 AAGACCATATCTAGGATATGGCAT 7966898 TGGTATTGTA Statistics Matches: 87, Mismatches: 19, Indels: 6 0.78 0.17 0.05 Matches are distributed among these distances: 42 57 0.66 43 30 0.34 ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28 Consensus pattern (42 bp): AAGACCATATCTAGGATATGGCATCGATATGAAAATTCGTGT Found at i:7972127 original size:47 final size:47 Alignment explanation

Indices: 7972076--7972486 Score: 635 Period size: 47 Copynumber: 8.7 Consensus size: 47 7972066 TTAGGATTCT * * 7972076 ATGTGATGGATGTGAACA-TGCATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG 7972123 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * * 7972170 ATATGATGAATGTGAAACTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * * 7972217 ATATGATGAATGTGAAACTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * 7972264 ATATGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * * 7972311 ATATGATGAATGTGAAACTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * 7972358 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCTG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * * * * * 7972405 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * * * * 7972452 ACGTGATGGATGTGAAAGTGCATAAATGTGATAAG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG 7972487 TCCCGAAGGG Statistics Matches: 342, Mismatches: 21, Indels: 2 0.94 0.06 0.01 Matches are distributed among these distances: 46 1 0.00 47 341 1.00 ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29 Consensus pattern (47 bp): ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG Found at i:7974388 original size:40 final size:39 Alignment explanation

Indices: 7974318--7974466 Score: 199 Period size: 40 Copynumber: 3.7 Consensus size: 39 7974308 CAGTATGTTA * 7974318 TATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATG 1 TATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTGGTGATG * * * 7974358 TATCCGGGCTAAGTCCTGAACAGCAATCGTGCTGGTGATA 1 TATCCGGGCTAAGTCC-GAAGAGCATTCGTGCTGGTGATG * * 7974398 TATCCGGACTAGGTTCCGAAGAGCATTCGTGCTGGTGATG 1 TATCCGGGCTAAG-TCCGAAGAGCATTCGTGCTGGTGATG * 7974438 TATCCGGGCTAAGTTCCGAAGAGTATTCG 1 TATCCGGGCTAAG-TCCGAAGAGCATTCG 7974467 GGCTAAGTTC Statistics Matches: 95, Mismatches: 12, Indels: 4 0.86 0.11 0.04 Matches are distributed among these distances: 39 2 0.02 40 90 0.95 41 3 0.03 ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27 Consensus pattern (39 bp): TATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATG Found at i:7974468 original size:23 final size:23 Alignment explanation

Indices: 7974437--7974488 Score: 86 Period size: 23 Copynumber: 2.3 Consensus size: 23 7974427 TGCTGGTGAT * 7974437 GTATCCGGGCTAAGTTCCGAAGA 1 GTATTCGGGCTAAGTTCCGAAGA 7974460 GTATTCGGGCTAAGTTCCGAAGA 1 GTATTCGGGCTAAGTTCCGAAGA * 7974483 GCATTC 1 GTATTC 7974489 ATGCTGGTGA Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25 Consensus pattern (23 bp): GTATTCGGGCTAAGTTCCGAAGA Found at i:7974509 original size:63 final size:63 Alignment explanation

Indices: 7974410--7974529 Score: 213 Period size: 63 Copynumber: 1.9 Consensus size: 63 7974400 TCCGGACTAG * * * 7974410 GTTCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGTTCCGAAGAGTATTCGGGCTAA 1 GTTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGGGCTAA 7974473 GTTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCG 1 GTTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCG 7974530 TGCTGGTGAT Statistics Matches: 54, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 63 54 1.00 ACGTcount: A:0.23, C:0.21, G:0.31, T:0.26 Consensus pattern (63 bp): GTTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGGGCTAA Found at i:7974520 original size:40 final size:40 Alignment explanation

Indices: 7974460--7974612 Score: 238 Period size: 40 Copynumber: 3.9 Consensus size: 40 7974450 GTTCCGAAGA * * * 7974460 GTATTCGGGCTAAGTTCCGAAGAGCATTCATGCTGGTGAT 1 GTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGAT 7974500 GTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGAT 1 GTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGAT * 7974540 ATA-CTCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGAT 1 GTATC-CGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGAT * 7974580 GTATCCGGGCTAAGCCCCGAAG-GCATTCGTGCT 1 GTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT 7974613 TGGACAAAAT Statistics Matches: 105, Mismatches: 6, Indels: 5 0.91 0.05 0.04 Matches are distributed among these distances: 39 12 0.11 40 92 0.88 41 1 0.01 ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25 Consensus pattern (40 bp): GTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGAT Found at i:7974549 original size:103 final size:103 Alignment explanation

Indices: 7974357--7974569 Score: 295 Period size: 103 Copynumber: 2.1 Consensus size: 103 7974347 TGCTGGTGAT * * * * 7974357 GTATCCGGGCTAAGTCCTGAACAGCAATCGTGCTGGTGATATATCCGGACTAGGTTCCGAAGAGC 1 GTATTCGGGCTAAGTCCTGAACAGCAATCATGCTGGTGATATATCCGGACTAAGTCCCGAAGAGC * * 7974422 ATTCGTGCTGGTGATGTATCCGGGCTAAGTTCCGAAGA 66 ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGA * * * * 7974460 GTATTCGGGCTAAGTTCC-GAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAG 1 GTATTCGGGCTAAG-TCCTGAACAGCAATCATGCTGGTGATATATCCGGACTAAGTCCCGAAGAG 7974524 CATTCGTGCTGGTGATATA-CTCGGGCTAAGTCCCGAAGA 65 CATTCGTGCTGGTGATATATC-CGGGCTAAGTCCCGAAGA * 7974563 GCATTCG 1 GTATTCG 7974570 TGCTGGTGAT Statistics Matches: 97, Mismatches: 11, Indels: 4 0.87 0.10 0.04 Matches are distributed among these distances: 102 1 0.01 103 93 0.96 104 3 0.03 ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25 Consensus pattern (103 bp): GTATTCGGGCTAAGTCCTGAACAGCAATCATGCTGGTGATATATCCGGACTAAGTCCCGAAGAGC ATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGA Found at i:7974581 original size:143 final size:143 Alignment explanation

Indices: 7974323--7974593 Score: 454 Period size: 143 Copynumber: 1.9 Consensus size: 143 7974313 TGTTATATCT * * 7974323 GGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGTCCTGAACAGCAATCGT 1 GGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAACAGCAATCGT * * 7974388 GCTGGTGATATATCCGGACTAGGTTCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGTT 66 GCTGGTGATATATCCGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGTT 7974453 CCGAAGAGTATTC 131 CCGAAGAGTATTC * * * 7974466 GGGCTAAGTTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGT 1 GGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAACAGCAATCGT * 7974531 GCTGGTGATATA-CTCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAG 66 GCTGGTGATATATC-CGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAG 7974594 CCCCGAAGGC Statistics Matches: 119, Mismatches: 8, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 142 1 0.01 143 118 0.99 ACGTcount: A:0.22, C:0.21, G:0.31, T:0.25 Consensus pattern (143 bp): GGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAACAGCAATCGT GCTGGTGATATATCCGGACTAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGTT CCGAAGAGTATTC Found at i:7974599 original size:80 final size:79 Alignment explanation

Indices: 7974464--7974612 Score: 262 Period size: 80 Copynumber: 1.9 Consensus size: 79 7974454 CGAAGAGTAT * * 7974464 TCGGGCTAAGTTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTC 1 TCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGCCCCGAAG-GCATTC 7974529 GTGCTGGTGATATAC 65 GTGCTGGTGATATAC * 7974544 TCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGCCCCGAAGGCATTCG 1 TCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGCCCCGAAGGCATTCG 7974609 TGCT 66 TGCT 7974613 TGGACAAAAT Statistics Matches: 66, Mismatches: 3, Indels: 1 0.94 0.04 0.01 Matches are distributed among these distances: 79 11 0.17 80 55 0.83 ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25 Consensus pattern (79 bp): TCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGCCCCGAAGGCATTCG TGCTGGTGATATAC Found at i:7974641 original size:80 final size:79 Alignment explanation

Indices: 7974470--7974629 Score: 207 Period size: 80 Copynumber: 2.0 Consensus size: 79 7974460 GTATTCGGGC * 7974470 TAAGTTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG 1 TAAG-TCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTG * * * ** * 7974535 GTGATATACTCGGGC 65 GTGACAAAATCCAGA * * 7974550 TAAGTCCCGAAGAGCATTCGTGCTGGTGATGTATCCGGGCTAAGCCCCGAAG-GCATTCGTGCTT 1 TAAGT-CCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTG 7974614 G-GACAAAATCCAGA 65 GTGACAAAATCCAGA 7974628 TA 1 TA 7974630 TGAGGTCCGA Statistics Matches: 70, Mismatches: 9, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 78 9 0.13 79 13 0.19 80 48 0.69 ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24 Consensus pattern (79 bp): TAAGTCCGAAGAGCATTCATGCTGGTGATGTATCCGGGCTAAGCCCCGAAGAGCATTCGTGCTGG TGACAAAATCCAGA Found at i:7979114 original size:29 final size:29 Alignment explanation

Indices: 7979060--7979116 Score: 71 Period size: 29 Copynumber: 2.0 Consensus size: 29 7979050 ACATGGCTTG * * * 7979060 CCCCATGAGCATGTGTTCTTGTCGTGTGT 1 CCCCACGAGCATGTGTTCTAGCCGTGTGT 7979089 CCCCACGAGCATGTG-TCTCAGCCGTGTG 1 CCCCACGAGCATGTGTTCT-AGCCGTGTG 7979117 GATGACACAG Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 28 3 0.12 29 21 0.88 ACGTcount: A:0.12, C:0.30, G:0.28, T:0.30 Consensus pattern (29 bp): CCCCACGAGCATGTGTTCTAGCCGTGTGT Found at i:7979260 original size:83 final size:83 Alignment explanation

Indices: 7979142--7979303 Score: 270 Period size: 83 Copynumber: 2.0 Consensus size: 83 7979132 GCCATGGGCG * * 7979142 TGTGCCCTAGGCGTGTGAAGCCTGCACCTATTTTATGAAAAATCATAAATTTTAAATCGACCACA 1 TGTGCCCTAGGCGTGTGAAGCCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACA 7979207 CAGCCTAGCACACGAGCA 66 CAGCCTAGCACACGAGCA * * 7979225 TGTGCCCTGGGCGTGTGAAGTCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACA 1 TGTGCCCTAGGCGTGTGAAGCCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACA ** 7979290 TGGCCTAGCACACG 66 CAGCCTAGCACACG 7979304 GGCGTATGAC Statistics Matches: 73, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 83 73 1.00 ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25 Consensus pattern (83 bp): TGTGCCCTAGGCGTGTGAAGCCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACA CAGCCTAGCACACGAGCA Found at i:7979323 original size:83 final size:83 Alignment explanation

Indices: 7979151--7979324 Score: 249 Period size: 83 Copynumber: 2.1 Consensus size: 83 7979141 GTGTGCCCTA * * 7979151 GGCGTGTGAAGCCTGCACCTATTTTATGAAAAATCATAAATTTTAAATCGACCACACAGCCTAGC 1 GGCGTGTGAAGCCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACACAGCCTAGC * * 7979216 ACACGAGCATGTGCCCTG 66 ACACGAGCATATGACCTG * ** 7979234 GGCGTGTGAAGTCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACATGGCCTAGC 1 GGCGTGTGAAGCCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACACAGCCTAGC * * * 7979299 ACACGGGCGTATGACTTG 66 ACACGAGCATATGACCTG * 7979317 GTCGTGTG 1 GGCGTGTG 7979325 TCTTTAATTT Statistics Matches: 80, Mismatches: 11, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 83 80 1.00 ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26 Consensus pattern (83 bp): GGCGTGTGAAGCCTACACCTATTTTATGAAAAACCATAAATTTTAAATCGACCACACAGCCTAGC ACACGAGCATATGACCTG Found at i:7980657 original size:29 final size:29 Alignment explanation

Indices: 7980583--7980657 Score: 69 Period size: 29 Copynumber: 2.6 Consensus size: 29 7980573 GTTTGTGACG * 7980583 ATCTCTATTAAAAAGAAACCCTTACACCT 1 ATCTCTATTAAAAGGAAACCCTTACACCT * * * * * ** * 7980612 ATCTTTGTTTAATGGAAACCTTTGTAGCT 1 ATCTCTATTAAAAGGAAACCCTTACACCT 7980641 ATCTCTATTAAAAGGAA 1 ATCTCTATTAAAAGGAA 7980658 GCTTTTATGG Statistics Matches: 33, Mismatches: 13, Indels: 0 0.72 0.28 0.00 Matches are distributed among these distances: 29 33 1.00 ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35 Consensus pattern (29 bp): ATCTCTATTAAAAGGAAACCCTTACACCT Found at i:7983222 original size:47 final size:47 Alignment explanation

Indices: 7983080--7983224 Score: 182 Period size: 47 Copynumber: 3.1 Consensus size: 47 7983070 CCCTTCGGGA * * * * * * * 7983080 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC *** * 7983127 CCCGTCACATAGATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 7983174 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 7983221 CTTA 1 CTTA 7983225 CTATCATTTC Statistics Matches: 82, Mismatches: 16, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 47 82 1.00 ACGTcount: A:0.26, C:0.32, G:0.11, T:0.31 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:7987626 original size:20 final size:23 Alignment explanation

Indices: 7987601--7987653 Score: 60 Period size: 22 Copynumber: 2.5 Consensus size: 23 7987591 CAGTTAGTTA 7987601 GATAAG-G-ATGATA-TAGGTAT 1 GATAAGAGTATGATAGTAGGTAT * 7987621 GATAAGAGTATGATAGTTGGTAT 1 GATAAGAGTATGATAGTAGGTAT * 7987644 G-TAAGTGTAT 1 GATAAGAGTAT 7987654 ACCAAAACTG Statistics Matches: 28, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 20 6 0.21 21 1 0.04 22 14 0.50 23 7 0.25 ACGTcount: A:0.36, C:0.00, G:0.30, T:0.34 Consensus pattern (23 bp): GATAAGAGTATGATAGTAGGTAT Found at i:7988709 original size:22 final size:23 Alignment explanation

Indices: 7988668--7988710 Score: 70 Period size: 23 Copynumber: 1.9 Consensus size: 23 7988658 AACTTTGTTT 7988668 CAAACAGTTAAACAAATAAATTA 1 CAAACAGTTAAACAAATAAATTA * 7988691 CAAACATTTAAA-AAATAAAT 1 CAAACAGTTAAACAAATAAAT 7988711 CAATTCATAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 22 8 0.42 23 11 0.58 ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23 Consensus pattern (23 bp): CAAACAGTTAAACAAATAAATTA Found at i:7994631 original size:43 final size:42 Alignment explanation

Indices: 7994520--7994632 Score: 97 Period size: 42 Copynumber: 2.6 Consensus size: 42 7994510 TGTGTTTTCG * * * * ** 7994520 TGTAAGACCACGTCTGGGATGTTGTCATCGTATTTGATTTTGA 1 TGTAAGACCATGTCT-GGAAGTTGGCATCGTATTTCATTTACA * 7994563 -GTAAGACCTTGTCTGGGATAG-TGGCATCGATATTTCA-TTACA 1 TGTAAGACCATGTCT-GGA-AGTTGGCATCG-TATTTCATTTACA 7994605 TGTAAGACCATGTCTGGAACGTTGGCAT 1 TGTAAGACCATGTCTGGAA-GTTGGCAT 7994633 TGTACAAGTT Statistics Matches: 57, Mismatches: 8, Indels: 10 0.76 0.11 0.13 Matches are distributed among these distances: 41 1 0.02 42 30 0.53 43 26 0.46 ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35 Consensus pattern (42 bp): TGTAAGACCATGTCTGGAAGTTGGCATCGTATTTCATTTACA Found at i:7995184 original size:23 final size:23 Alignment explanation

Indices: 7995158--7995211 Score: 58 Period size: 23 Copynumber: 2.3 Consensus size: 23 7995148 TTTTTCCATG 7995158 TGATATGGCTTGGT-TTTTGGT-TA 1 TGATATGG-TT-GTATTTTGGTATA * 7995181 TGATTATGGTTTTATTTTGGTATA 1 TGA-TATGGTTGTATTTTGGTATA 7995205 TGATATG 1 TGATATG 7995212 TGTGATGCAA Statistics Matches: 27, Mismatches: 1, Indels: 6 0.79 0.03 0.18 Matches are distributed among these distances: 22 1 0.04 23 16 0.59 24 10 0.37 ACGTcount: A:0.19, C:0.02, G:0.26, T:0.54 Consensus pattern (23 bp): TGATATGGTTGTATTTTGGTATA Found at i:8002812 original size:93 final size:93 Alignment explanation

Indices: 8002610--8003614 Score: 1922 Period size: 93 Copynumber: 10.8 Consensus size: 93 8002600 CATAAGTGAG * * * * 8002610 CTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACT-AACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA * 8002674 GCTCGGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8002702 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8002767 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8002795 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8002860 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8002888 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8002953 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8002981 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8003046 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8003074 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8003139 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8003167 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8003232 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8003260 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8003325 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8003353 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8003418 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA 8003446 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA 8003511 GCTCAGATGCCTAGTTACATCTCTCGAA 66 GCTCAGATGCCTAGTTACATCTCTCGAA * * 8003539 CTCGGACTCAACTCAACGAATTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA 1 CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA * * 8003604 GTTCGGATGCC 66 GCTCAGATGCC 8003615 CAAATATCCT Statistics Matches: 903, Mismatches: 9, Indels: 1 0.99 0.01 0.00 Matches are distributed among these distances: 92 55 0.06 93 848 0.94 ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22 Consensus pattern (93 bp): CTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACGA GCTCAGATGCCTAGTTACATCTCTCGAA Found at i:8011335 original size:55 final size:55 Alignment explanation

Indices: 8011221--8011337 Score: 128 Period size: 55 Copynumber: 2.1 Consensus size: 55 8011211 GTTAATCTAA * ** * 8011221 CAGGTTCAACCACGGGTTCTAGACACGGGCGTGGCGAATGCCCGTGCTATTTTCT 1 CAGGTTCAACCACGGGTTCTAGACACGGACGTGGCGAACACCCGTGCTATTTTCG * * * * * * 8011276 CAGGTTCAACCA-TGGTTCTAAGACACGGACGTGTCGCACACCCGTGTTGTTTTGG 1 CAGGTTCAACCACGGGTTCT-AGACACGGACGTGGCGAACACCCGTGCTATTTTCG 8011331 CAGGTTC 1 CAGGTTC 8011338 GCCCACGGTC Statistics Matches: 51, Mismatches: 10, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 54 6 0.12 55 45 0.88 ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26 Consensus pattern (55 bp): CAGGTTCAACCACGGGTTCTAGACACGGACGTGGCGAACACCCGTGCTATTTTCG Found at i:8021341 original size:49 final size:50 Alignment explanation

Indices: 8021284--8021386 Score: 120 Period size: 49 Copynumber: 2.1 Consensus size: 50 8021274 AAACCAAACC * ** * * 8021284 AAGCCTTTGTTGTGAATTGTTT-GGAAAGTCTTTGTGGCGATTTACTT-GG 1 AAGCCTTTGTGGAAAATTGTTTGGGAAA-CCTTTGTGGCAATTTACTTGGG * * 8021333 AAGCCTTTGTGGAAAATTTTTTGGGAAACCTTTGTGGCAATTTATTTGGG 1 AAGCCTTTGTGGAAAATTGTTTGGGAAACCTTTGTGGCAATTTACTTGGG 8021383 AAGC 1 AAGC 8021387 TTTTATGGCT Statistics Matches: 45, Mismatches: 7, Indels: 3 0.82 0.13 0.05 Matches are distributed among these distances: 49 34 0.76 50 11 0.24 ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40 Consensus pattern (50 bp): AAGCCTTTGTGGAAAATTGTTTGGGAAACCTTTGTGGCAATTTACTTGGG Found at i:8021351 original size:25 final size:25 Alignment explanation

Indices: 8021303--8021386 Score: 82 Period size: 25 Copynumber: 3.4 Consensus size: 25 8021293 TTGTGAATTG * * ** 8021303 TTTGGAAAGTCTTTGTGGCGATTTA 1 TTTGGGAAGCCTTTGTGGAAATTTA * 8021328 CTT-GGAAGCCTTTGTGGAAAATTT- 1 TTTGGGAAGCCTTTGTGG-AAATTTA * * 8021352 TTTGGGAAACCTTTGTGGCAATTTA 1 TTTGGGAAGCCTTTGTGGAAATTTA 8021377 TTTGGGAAGC 1 TTTGGGAAGC 8021387 TTTTATGGCT Statistics Matches: 47, Mismatches: 9, Indels: 6 0.76 0.15 0.10 Matches are distributed among these distances: 24 19 0.40 25 28 0.60 ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39 Consensus pattern (25 bp): TTTGGGAAGCCTTTGTGGAAATTTA Found at i:8021395 original size:25 final size:24 Alignment explanation

Indices: 8021347--8021395 Score: 62 Period size: 25 Copynumber: 2.0 Consensus size: 24 8021337 CTTTGTGGAA * 8021347 AATTTTTTGGGAAACCTTTGTGGC 1 AATTTTTTGGGAAACCTTTATGGC * * 8021371 AATTTATTTGGGAAGCTTTTATGGC 1 AATTT-TTTGGGAAACCTTTATGGC 8021396 TAGTTACTTA Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 24 5 0.24 25 16 0.76 ACGTcount: A:0.22, C:0.10, G:0.24, T:0.43 Consensus pattern (24 bp): AATTTTTTGGGAAACCTTTATGGC Found at i:8025552 original size:49 final size:49 Alignment explanation

Indices: 8025441--8025759 Score: 275 Period size: 49 Copynumber: 6.6 Consensus size: 49 8025431 GCATGATGCT 8025441 GATGCCATG-CTCCAGACATGGTCTTACACTGGCTCTCA-CATCTAAGT--- 1 GATGCCATGTC-CCAGACA-GGTCTTACACTGGCTCTCATCATCT-AGTGCC * * * 8025488 GATACCATGTCCCAGACAGGTCTTACACTGACT-TCCATACATATAG-GCC 1 GATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CAT-CATCTAGTGCC * 8025537 GATGCCATGTCCCAGACAGGTCTTACACTGGCT-TCCATACATCGAG-GCC 1 GATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CAT-CATCTAGTGCC * * * * * * * 8025586 GATGCTATATGCCAAATACGTCTTACACTGGCTCTCACTCATCT-GTGTC 1 GATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCA-TCATCTAGTGCC * * * * * 8025635 GATGCCGTGTCCCAAACAGGTCTTACACTGGCTCTCATCTTC-GGTGTC 1 GATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCATCTAGTGCC * * * 8025683 GATGCCATGTCCCAGACAAGTCTTACACTGGCTCTCATCTTC-AGTTCC 1 GATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCATCTAGTGCC * * * * 8025731 AATGTCATGTCCCAGATAAGTCTTACACT 1 GATGCCATGTCCCAGACAGGTCTTACACT 8025760 AGCACACACA Statistics Matches: 230, Mismatches: 31, Indels: 21 0.82 0.11 0.07 Matches are distributed among these distances: 45 1 0.00 46 16 0.07 47 17 0.07 48 83 0.36 49 111 0.48 50 2 0.01 ACGTcount: A:0.23, C:0.30, G:0.18, T:0.28 Consensus pattern (49 bp): GATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCATCTAGTGCC Found at i:8027163 original size:43 final size:43 Alignment explanation

Indices: 8027098--8027270 Score: 195 Period size: 43 Copynumber: 4.0 Consensus size: 43 8027088 ATATGTGATG * * 8027098 TCGATATGTGATTACATCTAAGACCATGTTTGGGACATTGGCA 1 TCGATATGTGATTACATCTAAGACCACGTCTGGGACATTGGCA * * * * ** 8027141 TCGATGTGTGATTACGTGTAAGACCACGTTTGGGATGTTGGCA 1 TCGATATGTGATTACATCTAAGACCACGTCTGGGACATTGGCA * * * * * * 8027184 TCGATATGTAATTGCGTTTAAGACC-CTGTCTGGGATAGTGGCA 1 TCGATATGTGATTACATCTAAGACCAC-GTCTGGGACATTGGCA * 8027227 TCGATATGTGATTACATCTAAGACCACATCTGGGACATTGGCA 1 TCGATATGTGATTACATCTAAGACCACGTCTGGGACATTGGCA 8027270 T 1 T 8027271 TGTACAATAT Statistics Matches: 108, Mismatches: 20, Indels: 4 0.82 0.15 0.03 Matches are distributed among these distances: 42 1 0.01 43 106 0.98 44 1 0.01 ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32 Consensus pattern (43 bp): TCGATATGTGATTACATCTAAGACCACGTCTGGGACATTGGCA Found at i:8029955 original size:94 final size:91 Alignment explanation

Indices: 8029847--8030159 Score: 294 Period size: 94 Copynumber: 3.4 Consensus size: 91 8029837 ATGTGAGAGG * 8029847 CAGTGTAAGACCATGTCTGGGACATGGCATCAGTATTGAGACGAGGGCTAGTGTAAGACGTGTCT 1 CAGTGTAAGACCATGTCTGGGACATGGCATC-G-ATTGAGAC-AGTGCTAGTGTAAGACGTGTCT 8029912 GGGACATGCATCAGCCACATTATGATAGC 63 GGGACATGCATCAGCCACATTATGATAGC * * * * 8029941 CAGTGTAAGACCATGTCTGGGACATGGCACCGGCGTAGAGATCAGTGCCAGTGTAAGACGTGTCT 1 CAGTGTAAGACCATGTCTGGGACATGGCATC-G-ATTGAGA-CAGTGCTAGTGTAAGACGTGTCT * * * 8030006 GGGACATGCATCAGCCTCAATGATGGTAGC 63 GGGACATGCATCAGCCAC-ATTATGATAGC * * * * * * * * 8030036 TAGTGTAAGA-CGTGTCTGAGACAT-GCATCGACTAAG-CTTCGTGCTAGTGTAAGACATGTTTG 1 CAGTGTAAGACCATGTCTGGGACATGGCATCGATTGAGAC--AGTGCTAGTGTAAGACGTGTCTG * 8030098 GGACATGCGTCAG-CAC-TTATACACGATAGC 64 GGACATGCATCAGCCACATTAT----GATAGC * * * 8030128 TAGTGTAAAACCATGTATGGGACATGGCATCG 1 CAGTGTAAGACCATGTCTGGGACATGGCATCG 8030160 GTCTCGATGA Statistics Matches: 179, Mismatches: 30, Indels: 20 0.78 0.13 0.09 Matches are distributed among these distances: 88 3 0.02 89 1 0.01 90 2 0.01 91 33 0.18 92 15 0.08 93 15 0.08 94 91 0.51 95 19 0.11 ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24 Consensus pattern (91 bp): CAGTGTAAGACCATGTCTGGGACATGGCATCGATTGAGACAGTGCTAGTGTAAGACGTGTCTGGG ACATGCATCAGCCACATTATGATAGC Found at i:8029958 original size:47 final size:46 Alignment explanation

Indices: 8029896--8030201 Score: 171 Period size: 47 Copynumber: 6.5 Consensus size: 46 8029886 GACGAGGGCT * * 8029896 AGTGTAAGACGTGTCTGGGACATGCATCAGCCACATTATGATAGCC 1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGATAGCC * * * * * 8029942 AGTGTAAGACCATGTCTGGGACATGGCACCGGCGTAGA-GATCAGT-GCC 1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGC-CACATGATGA-TAGCC * * * * 8029990 AGTGTAAGACGTGTCTGGGACATGCATCAGCCTCAATGATGGTAGCT 1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATGATGATAGCC * * * * * 8030037 AGTGTAAGACGTGTCTGAGACATGCATC-G--ACTAAGCTTCG-T-GCT 1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATG-AT-GATAGCC * * * * * 8030081 AGTGTAAGACATGTTTGGGACATGCGTCAG-CACTTATACACGATAGCT 1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC--AT-GATGATAGCC * * * * * * 8030129 AGTGTAAAACCATGTATGGGACATGGCATCGGTCTCGATGAAGATAGCC 1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCAC-ATGATGATAGCC 8030178 AGTGTAA-ACCATGTCTGGGACATG 1 AGTGTAAGA-CATGTCTGGGACATG 8030202 GCATTGGCAA Statistics Matches: 203, Mismatches: 39, Indels: 35 0.73 0.14 0.13 Matches are distributed among these distances: 44 30 0.15 45 3 0.01 46 22 0.11 47 62 0.31 48 47 0.23 49 30 0.15 50 7 0.03 51 2 0.01 ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24 Consensus pattern (46 bp): AGTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGATAGCC Found at i:8034982 original size:47 final size:45 Alignment explanation

Indices: 8034909--8035227 Score: 213 Period size: 47 Copynumber: 6.8 Consensus size: 45 8034899 TTATGTGAGA * 8034909 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGGATTGAGATAAGG 1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGAT-A-G * * * * 8034957 GCTAGTGTAAGA-CGTTTCTGGGACATGCATCAGCCACATT-ACGATA- 1 GCCAGTGTAAGACCATGTCTGGGACATGCATC-G--GCATTGA-GATAG * 8035003 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGATGAG 1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGAT-AG * * * * 8035050 TGCCAGTGTAAGA-CGTGTCTGGGACATGCATCGGC--TAAGCTTCG 1 -GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAG-ATAG * ** ** * * 8035094 TGCTAGTGTAAGA-CATGTCTTAGACATGCATCAACACTTTACATGAG 1 -GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCA-TTGAGAT-AG * * 8035141 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGATAAAGATA- 1 -GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTG----AGATAG * 8035191 GCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCA 1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCA 8035228 ACTTAACCCA Statistics Matches: 214, Mismatches: 36, Indels: 41 0.74 0.12 0.14 Matches are distributed among these distances: 44 32 0.15 45 7 0.03 46 27 0.13 47 54 0.25 48 44 0.21 49 46 0.21 51 1 0.00 52 3 0.01 ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24 Consensus pattern (45 bp): GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAGATAG Found at i:8035022 original size:94 final size:93 Alignment explanation

Indices: 8034908--8035227 Score: 344 Period size: 94 Copynumber: 3.4 Consensus size: 93 8034898 GTTATGTGAG * * * * 8034908 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGGATTGAGATAAGGGCTAGTGTAAGACGTT 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACGTG * 8034973 TCTGGGACATGCATCAGCCACATTACGAT 66 TCTGGGACATGCATCGGCCA-ATTACGAT * * * 8035002 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGATGAGTGCCAGTGTAAGACGTG 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACGTG * 8035067 TCTGGGACATGCATCGGCTAAGCTT-CG-T 66 TCTGGGACATGCATCGGCCAA--TTACGAT * ** ** * * * 8035095 -GCTAGTGTAAGA-CATGTCTTAGACAT-GCATCAACACTTTACATGAGAGCTAGTGTAAGACCA 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-TTGAGATGAGAGCTAGTGTAAGA-CG * * * 8035157 TGTCTGGGACATGGCATCGGCCTTGATAAAGAT 64 TGTCTGGGACAT-GCATCGGCC--AATTACGAT * 8035190 AGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCA 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA 8035228 ACTTAACCCA Statistics Matches: 185, Mismatches: 29, Indels: 20 0.79 0.12 0.09 Matches are distributed among these distances: 90 7 0.04 91 30 0.16 92 24 0.13 93 11 0.06 94 80 0.43 95 4 0.02 96 11 0.06 97 12 0.06 98 6 0.03 ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24 Consensus pattern (93 bp): AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACGTG TCTGGGACATGCATCGGCCAATTACGAT Found at i:8035168 original size:139 final size:140 Alignment explanation

Indices: 8034908--8035218 Score: 369 Period size: 139 Copynumber: 2.2 Consensus size: 140 8034898 GTTATGTGAG * * * ** * * * 8034908 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGGATTGAGATAAGGGCTAGTGTAAGACGTT 1 AGCCAGTGTAAGACCATGTCTGGGACAT-GCATC-GG-CTAAGCTTCGTGCTAGTGTAAGACATG * * * 8034973 TCTGGGACATGCATCAGCCACATTACGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG 63 TCTGAGACATGCATCAGACACATTACGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG * 8035038 CATAGAG-ATGAGT 128 CATAGAGAAAGA-T * 8035051 -GCCAGTGTAAGA-CGTGTCTGGGACATGCATCGGCTAAGCTTCGTGCTAGTGTAAGACATGTCT 1 AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTAAGCTTCGTGCTAGTGTAAGACATGTCT * * * 8035114 TAGACATGCATCA-ACACTTTACATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC 66 GAGACATGCATCAGACACATTAC--GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC * * * 8035178 CTTGATAAAGAT 129 ATAGAGAAAGAT 8035190 AGCCAGTGTAAGACCATGTCTGGGACATG 1 AGCCAGTGTAAGACCATGTCTGGGACATG 8035219 GCATTGGCAA Statistics Matches: 143, Mismatches: 20, Indels: 12 0.82 0.11 0.07 Matches are distributed among these distances: 137 7 0.05 138 33 0.23 139 44 0.31 140 20 0.14 141 27 0.19 142 12 0.08 ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24 Consensus pattern (140 bp): AGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTAAGCTTCGTGCTAGTGTAAGACATGTCT GAGACATGCATCAGACACATTACGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT AGAGAAAGAT Found at i:8038516 original size:46 final size:46 Alignment explanation

Indices: 8038463--8038551 Score: 169 Period size: 46 Copynumber: 1.9 Consensus size: 46 8038453 GGAGGCAGTG * 8038463 CTGGATGATTCTAGGCCAATTTTAAGTAGTATAGAGGGAGAAGCTA 1 CTGGATGATTCTAGGCCAAATTTAAGTAGTATAGAGGGAGAAGCTA 8038509 CTGGATGATTCTAGGCCAAATTTAAGTAGTATAGAGGGAGAAG 1 CTGGATGATTCTAGGCCAAATTTAAGTAGTATAGAGGGAGAAG 8038552 TTAAGCAAGC Statistics Matches: 42, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 46 42 1.00 ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27 Consensus pattern (46 bp): CTGGATGATTCTAGGCCAAATTTAAGTAGTATAGAGGGAGAAGCTA Found at i:8041895 original size:15 final size:15 Alignment explanation

Indices: 8041863--8041891 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 8041853 ATTTTCTGTG 8041863 TTTATAATGTGTGAA 1 TTTATAATGTGTGAA 8041878 TTTAT-ATGTGTGAA 1 TTTATAATGTGTGAA 8041892 ATTTTCGTGT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 9 0.64 15 5 0.36 ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48 Consensus pattern (15 bp): TTTATAATGTGTGAA Found at i:8043046 original size:43 final size:43 Alignment explanation

Indices: 8042970--8043143 Score: 204 Period size: 43 Copynumber: 4.0 Consensus size: 43 8042960 GATATGTGAT * * * ** 8042970 ATCGATATGTGATTACGTCTAAGATCACATCTGGGACATTGGC 1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC ** * * 8043013 ATTAATATGTGATTACATTTACGACCATGTCTGGGACATTGGC 1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC * * * 8043056 ATCGTTATGTGATTACATGTAAGACCCTGTCTGGGACAGTGGC 1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC * * ** 8043099 ATCGATATATGATTACATGTAAGACCACGTCTGGGATGTTGGC 1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC 8043142 AT 1 AT 8043144 TGTACGATAT Statistics Matches: 109, Mismatches: 22, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 43 109 1.00 ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32 Consensus pattern (43 bp): ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC Found at i:8043337 original size:19 final size:18 Alignment explanation

Indices: 8043313--8043356 Score: 52 Period size: 18 Copynumber: 2.3 Consensus size: 18 8043303 GATACTAATT 8043313 ATATATGATGCAAATGAAA 1 ATATAT-ATGCAAATGAAA * * 8043332 ATATATATGTATATGAAA 1 ATATATATGCAAATGAAA 8043350 AGTATAT 1 A-TATAT 8043357 TCGGCCAAAT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 18 11 0.50 19 11 0.50 ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34 Consensus pattern (18 bp): ATATATATGCAAATGAAA Found at i:8058172 original size:12 final size:11 Alignment explanation

Indices: 8058152--8058185 Score: 50 Period size: 11 Copynumber: 3.0 Consensus size: 11 8058142 ATATAATTAC 8058152 TTTTTATTTTA 1 TTTTTATTTTA * 8058163 TTTTTAATTTA 1 TTTTTATTTTA 8058174 TGTTTTATTTTA 1 T-TTTTATTTTA 8058186 AGAATTATTT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 11 11 0.55 12 9 0.45 ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76 Consensus pattern (11 bp): TTTTTATTTTA Found at i:8058233 original size:19 final size:20 Alignment explanation

Indices: 8058209--8058247 Score: 71 Period size: 19 Copynumber: 2.0 Consensus size: 20 8058199 TCTTATTTTT 8058209 TATTTGTTTTT-TGTTTTAA 1 TATTTGTTTTTATGTTTTAA 8058228 TATTTGTTTTTATGTTTTAA 1 TATTTGTTTTTATGTTTTAA 8058248 ATGTATTTGA Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 19 11 0.58 20 8 0.42 ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72 Consensus pattern (20 bp): TATTTGTTTTTATGTTTTAA Found at i:8058265 original size:25 final size:23 Alignment explanation

Indices: 8058209--8058273 Score: 66 Period size: 19 Copynumber: 2.9 Consensus size: 23 8058199 TCTTATTTTT * 8058209 TATTTGTTTTT-TGTTTT-AA-- 1 TATTTGTTTTTATATTTTAAATG * 8058228 TATTTGTTTTTATGTTTTAAATG 1 TATTTGTTTTTATATTTTAAATG 8058251 TATTTGATTTATTATATTTTAAA 1 TATTTG-TTT-TTATATTTTAAA 8058274 GTTTTTTATT Statistics Matches: 39, Mismatches: 1, Indels: 6 0.85 0.02 0.13 Matches are distributed among these distances: 19 11 0.28 20 6 0.15 21 2 0.05 23 6 0.15 24 3 0.08 25 11 0.28 ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66 Consensus pattern (23 bp): TATTTGTTTTTATATTTTAAATG Found at i:8062932 original size:27 final size:27 Alignment explanation

Indices: 8062901--8063078 Score: 196 Period size: 27 Copynumber: 6.6 Consensus size: 27 8062891 TAAATTGTAC 8062901 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 8062928 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 8062954 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 8062982 GGCACTAAGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * * 8063010 AGCACTAAGTGTGCGATTTGATTACGA 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 8063037 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 8063064 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 8063079 GACTCAATAT Statistics Matches: 127, Mismatches: 21, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 27 104 0.82 28 23 0.18 ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:8063015 original size:82 final size:81 Alignment explanation

Indices: 8062902--8063057 Score: 240 Period size: 82 Copynumber: 1.9 Consensus size: 81 8062892 AAATTGTACA * * * 8062902 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT 1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAAGCACTAAGTGT 8062967 GCGAATTGACCATGCG 66 GCGAATTGACCATGCG ** * 8062983 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGAAGCACTAAGTG 1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAAGCACTAAGTG * 8063048 TGCGAGTTGA 65 TGCGAATTGA 8063058 TTATATAGCA Statistics Matches: 67, Mismatches: 7, Indels: 1 0.89 0.09 0.01 Matches are distributed among these distances: 81 15 0.22 82 52 0.78 ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAAGCACTAAGTGT GCGAATTGACCATGCG Found at i:8063069 original size:82 final size:81 Alignment explanation

Indices: 8062898--8063078 Score: 236 Period size: 82 Copynumber: 2.2 Consensus size: 81 8062888 GATTAAATTG * * * 8062898 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA 1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAAGCACTAA 8062963 GTGTGCGAATTGACCA 66 GTGTGCGAATTGACCA * * ** * 8062979 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGAAGCACTA 1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAAGCACTA * ** 8063044 AGTGTGCGAGTTGATTA 65 AGTGTGCGAATTGACCA * * 8063061 TATAGCACTGAGTGTGCG 1 TACAGCACTAAGTGTGCG 8063079 GACTCAATAT Statistics Matches: 84, Mismatches: 15, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 81 17 0.20 82 67 0.80 ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAAGCACTAA GTGTGCGAATTGACCA Found at i:8072605 original size:39 final size:39 Alignment explanation

Indices: 8072562--8072640 Score: 140 Period size: 39 Copynumber: 2.0 Consensus size: 39 8072552 ATGTGTGATA * 8072562 AGTAATTGAGGTATATAATTATTTATATTGTATGAGCTT 1 AGTAATTGAGGTATATAATCATTTATATTGTATGAGCTT * 8072601 AGTAATTGAGGTATGTAATCATTTATATTGTATGAGCTT 1 AGTAATTGAGGTATATAATCATTTATATTGTATGAGCTT 8072640 A 1 A 8072641 CTAAGTATTT Statistics Matches: 38, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 39 38 1.00 ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44 Consensus pattern (39 bp): AGTAATTGAGGTATATAATCATTTATATTGTATGAGCTT Found at i:8078252 original size:51 final size:50 Alignment explanation

Indices: 8078176--8078305 Score: 156 Period size: 49 Copynumber: 2.6 Consensus size: 50 8078166 GGATACCCGA * * 8078176 TGGCCTGCACATAGTACCACCCTTGTAGTCAAAGCTACCTTCTTCACAAAG 1 TGGCCTTCACATAGTACCACACTTGTAGTCAAAGCTACC-TCTTCACAAAG * * * * * 8078227 TGGCCTTCACATAGTACCACACTTGT-GACCAAGTTATCTCTTCTCAAAG 1 TGGCCTTCACATAGTACCACACTTGTAGTCAAAGCTACCTCTTCACAAAG * * 8078276 TGTCCTTGACATAGTACCACACTTG-AGTCA 1 TGGCCTTCACATAGTACCACACTTGTAGTCA 8078306 CCAGTGACAT Statistics Matches: 67, Mismatches: 11, Indels: 4 0.82 0.13 0.05 Matches are distributed among these distances: 49 35 0.52 50 8 0.12 51 24 0.36 ACGTcount: A:0.27, C:0.29, G:0.15, T:0.28 Consensus pattern (50 bp): TGGCCTTCACATAGTACCACACTTGTAGTCAAAGCTACCTCTTCACAAAG Found at i:8084195 original size:30 final size:30 Alignment explanation

Indices: 8084161--8084218 Score: 80 Period size: 30 Copynumber: 1.9 Consensus size: 30 8084151 CCTTAACTCT 8084161 AACTTTTGAAAAATTACAATTTTGCCCCTA 1 AACTTTTGAAAAATTACAATTTTGCCCCTA * * * * 8084191 AACTTTTGCATATTTACACTTTTGCCCC 1 AACTTTTGAAAAATTACAATTTTGCCCC 8084219 AAAGCTCAAA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 30 24 1.00 ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40 Consensus pattern (30 bp): AACTTTTGAAAAATTACAATTTTGCCCCTA Found at i:8092685 original size:17 final size:17 Alignment explanation

Indices: 8092663--8092696 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 8092653 GTTGGAGAGA 8092663 AAGAGAAAGCATTTCTC 1 AAGAGAAAGCATTTCTC 8092680 AAGAGAAAGCATTTCTC 1 AAGAGAAAGCATTTCTC 8092697 TTCATCATCT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24 Consensus pattern (17 bp): AAGAGAAAGCATTTCTC Found at i:8097893 original size:32 final size:32 Alignment explanation

Indices: 8097857--8097921 Score: 130 Period size: 32 Copynumber: 2.0 Consensus size: 32 8097847 ATTCATTGCC 8097857 AAAACAAGTTAAATCAACTTCATTCTTTAATT 1 AAAACAAGTTAAATCAACTTCATTCTTTAATT 8097889 AAAACAAGTTAAATCAACTTCATTCTTTAATT 1 AAAACAAGTTAAATCAACTTCATTCTTTAATT 8097921 A 1 A 8097922 CATTGAGAAT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 32 33 1.00 ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37 Consensus pattern (32 bp): AAAACAAGTTAAATCAACTTCATTCTTTAATT Found at i:8099438 original size:19 final size:19 Alignment explanation

Indices: 8099414--8099454 Score: 82 Period size: 19 Copynumber: 2.2 Consensus size: 19 8099404 GATAACTAGT 8099414 TGATGGTATCAATATTTTA 1 TGATGGTATCAATATTTTA 8099433 TGATGGTATCAATATTTTA 1 TGATGGTATCAATATTTTA 8099452 TGA 1 TGA 8099455 AAAAAAGTAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 22 1.00 ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46 Consensus pattern (19 bp): TGATGGTATCAATATTTTA Found at i:8107395 original size:49 final size:50 Alignment explanation

Indices: 8107277--8107460 Score: 162 Period size: 49 Copynumber: 3.8 Consensus size: 50 8107267 AGGGTGTAAT ** *** ** 8107277 GCCGATGCCATGTCCCAGACATGGTCTTACACT--GGCTCATTCAT-CAA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCACAAATCCGG * * * * * 8107324 GTCGATGCCATGCCCCAAACATGGTTTTACACTAACAGTCA-AAAT-CGAG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCACAAATCCG-G * * * * 8107373 GCCGATGCAATGTCCCAGACATGGTCTTACACTAACTCTCACATATCCGT 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCACAAATCCGG * * 8107423 GCCAATGCCATGTCCCAGACAGGGTCTTACACTAACAC 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAACAC 8107461 ATCTCGTAGC Statistics Matches: 108, Mismatches: 24, Indels: 7 0.78 0.17 0.05 Matches are distributed among these distances: 47 29 0.27 48 3 0.03 49 37 0.34 50 37 0.34 51 2 0.02 ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23 Consensus pattern (50 bp): GCCGATGCCATGTCCCAGACATGGTCTTACACTAACACTCACAAATCCGG Found at i:8130632 original size:12 final size:13 Alignment explanation

Indices: 8130615--8130644 Score: 53 Period size: 12 Copynumber: 2.4 Consensus size: 13 8130605 TACTGCAATT 8130615 TAATTTTTATTA- 1 TAATTTTTATTAC 8130627 TAATTTTTATTAC 1 TAATTTTTATTAC 8130640 TAATT 1 TAATT 8130645 CTTCTTTTTT Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 12 0.71 13 5 0.29 ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63 Consensus pattern (13 bp): TAATTTTTATTAC Found at i:8136523 original size:5 final size:5 Alignment explanation

Indices: 8136513--8136540 Score: 56 Period size: 5 Copynumber: 5.6 Consensus size: 5 8136503 ACACCTATTA 8136513 TTTAT TTTAT TTTAT TTTAT TTTAT TTT 1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT 8136541 TATCTCTATA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 23 1.00 ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82 Consensus pattern (5 bp): TTTAT Found at i:8140622 original size:42 final size:42 Alignment explanation

Indices: 8140575--8140680 Score: 124 Period size: 42 Copynumber: 2.5 Consensus size: 42 8140565 ACACTTGCCT * 8140575 ATGTCCTTGCCTGTGTGGCTCACACGGCCTGGACACACGCCC 1 ATGTCCTTGCCTGTGTGGCTCACACGGCCTAGACACACGCCC * * * * 8140617 GTGTCCTTAGCC-GTGTGGCTCACATGGCCTAGACACATGCTC 1 ATGTCCTT-GCCTGTGTGGCTCACACGGCCTAGACACACGCCC ** 8140659 ATGTCCTTTTTCTGTGTGGCTC 1 ATGTCC-TTGCCTGTGTGGCTC 8140681 CAAAATAAAA Statistics Matches: 53, Mismatches: 8, Indels: 5 0.80 0.12 0.08 Matches are distributed among these distances: 42 39 0.74 43 14 0.26 ACGTcount: A:0.13, C:0.32, G:0.25, T:0.29 Consensus pattern (42 bp): ATGTCCTTGCCTGTGTGGCTCACACGGCCTAGACACACGCCC Found at i:8145383 original size:45 final size:46 Alignment explanation

Indices: 8145351--8145476 Score: 186 Period size: 45 Copynumber: 2.8 Consensus size: 46 8145341 ATCATTTCAT * 8145351 CGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATCTCAC 1 CGGCATTATAGCCTGCTAGGCTCCAAAGGCCCGAATAGTATCTCAC * 8145396 CGGCATTATAGCCTGCTAGGC-CCAAAGGCCCGAATAGTGTCTCAC 1 CGGCATTATAGCCTGCTAGGCTCCAAAGGCCCGAATAGTATCTCAC * * * 8145441 CGGCATAATAGCCTGCTAGGCT-TAAAGGCTCGAATA 1 CGGCATTATAGCCTGCTAGGCTCCAAAGGCCCGAATA 8145477 TAATACCAGC Statistics Matches: 74, Mismatches: 5, Indels: 4 0.89 0.06 0.05 Matches are distributed among these distances: 44 4 0.05 45 70 0.95 ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21 Consensus pattern (46 bp): CGGCATTATAGCCTGCTAGGCTCCAAAGGCCCGAATAGTATCTCAC Found at i:8145620 original size:38 final size:38 Alignment explanation

Indices: 8145474--8145613 Score: 174 Period size: 38 Copynumber: 3.7 Consensus size: 38 8145464 AAAGGCTCGA * * * 8145474 ATATAATACCAGCACTAGGCCTGTAGGATTTAACCCAG 1 ATATAATACCAGCACGAAGCCTGTAGGATTTAACCCGG ** * 8145512 ATATAATACCAGCACGAAGCCTGCGGGAATTAACCCGG 1 ATATAATACCAGCACGAAGCCTGTAGGATTTAACCCGG * * 8145550 ATATATTACCAGCACGAAGCCTG-CGAGATTTAACCCGG 1 ATATAATACCAGCACGAAGCCTGTAG-GATTTAACCCGG * * 8145588 ATATATTACCAGCATGAAGCCTGTAG 1 ATATAATACCAGCACGAAGCCTGTAG 8145614 TCTTTAAGCC Statistics Matches: 89, Mismatches: 11, Indels: 3 0.86 0.11 0.03 Matches are distributed among these distances: 37 1 0.01 38 87 0.98 39 1 0.01 ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21 Consensus pattern (38 bp): ATATAATACCAGCACGAAGCCTGTAGGATTTAACCCGG Found at i:8146000 original size:43 final size:43 Alignment explanation

Indices: 8145898--8146032 Score: 164 Period size: 43 Copynumber: 3.1 Consensus size: 43 8145888 ACATAACATT * * * 8145898 TCATTTCACCGACATTATAGCTTGCTAGGCTCAAAGGCTCGATTAA 1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GCCCGA-T-A * * * 8145944 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAAGCCCGATA 1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGATA * 8145986 TCATTTCACCGGCATTATAGCCTGCTAGGCCCAAAGCCCGAATA 1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCG-ATA 8146030 TCA 1 TCA 8146033 CATTTCGATA Statistics Matches: 77, Mismatches: 10, Indels: 6 0.83 0.11 0.06 Matches are distributed among these distances: 42 2 0.03 43 35 0.45 44 11 0.14 45 28 0.36 46 1 0.01 ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26 Consensus pattern (43 bp): TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCGATA Found at i:8151975 original size:26 final size:27 Alignment explanation

Indices: 8151937--8151987 Score: 68 Period size: 26 Copynumber: 1.9 Consensus size: 27 8151927 CCATTAGAAT * * * 8151937 AAAAAATAGAAATTAAAAA-CCAAAAA 1 AAAAAAAACAAATAAAAAATCCAAAAA 8151963 AAAAAAAACAAATAAAAAATCCAAA 1 AAAAAAAACAAATAAAAAATCCAAA 8151988 TGTCAATGTC Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 26 16 0.76 27 5 0.24 ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10 Consensus pattern (27 bp): AAAAAAAACAAATAAAAAATCCAAAAA Found at i:8153765 original size:16 final size:16 Alignment explanation

Indices: 8153744--8153775 Score: 64 Period size: 16 Copynumber: 2.0 Consensus size: 16 8153734 TTCGTATAAC 8153744 TTTATGTAAATATTTT 1 TTTATGTAAATATTTT 8153760 TTTATGTAAATATTTT 1 TTTATGTAAATATTTT 8153776 CTTTTAAATT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62 Consensus pattern (16 bp): TTTATGTAAATATTTT Found at i:8163749 original size:90 final size:90 Alignment explanation

Indices: 8163596--8163867 Score: 535 Period size: 90 Copynumber: 3.0 Consensus size: 90 8163586 AAAATTTGGC 8163596 TTTTATTTTGTTTATTTATCAATTAATTATTAAATGATCAAAATACCCCTAACTTAAAATTATTC 1 TTTTATTTTGTTTATTTATCAATTAATTATTAAATGATCAAAATACCCCTAACTTAAAATTATTC 8163661 TATTTCACCTATTTCAGGTCCATTT 66 TATTTCACCTATTTCAGGTCCATTT 8163686 TTTTATTTTGTTTATTTATCAATTAATTATTAAATGATCAAAATACCCCTAACTTAAAATTATTC 1 TTTTATTTTGTTTATTTATCAATTAATTATTAAATGATCAAAATACCCCTAACTTAAAATTATTC 8163751 TATTTCACCTATTTCAGGTCCATTT 66 TATTTCACCTATTTCAGGTCCATTT 8163776 TTTTATTTTGTTTATTTATCAATTAATTATTAAATGATCAAAATACCCCTAACTTAAAATTATTC 1 TTTTATTTTGTTTATTTATCAATTAATTATTAAATGATCAAAATACCCCTAACTTAAAATTATTC * 8163841 TATTTCACCTATTTCATGTCCATTT 66 TATTTCACCTATTTCAGGTCCATTT 8163866 TT 1 TT 8163868 GTCCACCATC Statistics Matches: 181, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 90 181 1.00 ACGTcount: A:0.32, C:0.15, G:0.04, T:0.49 Consensus pattern (90 bp): TTTTATTTTGTTTATTTATCAATTAATTATTAAATGATCAAAATACCCCTAACTTAAAATTATTC TATTTCACCTATTTCAGGTCCATTT Found at i:8167840 original size:17 final size:18 Alignment explanation

Indices: 8167808--8167842 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 8167798 TAGTGTGGGC 8167808 TACCCGTGTGGGCCCACA 1 TACCCGTGTGGGCCCACA * 8167826 TACCTGTGT-GGCCCACA 1 TACCCGTGTGGGCCCACA 8167843 CGTCTCAATT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 8 0.50 18 8 0.50 ACGTcount: A:0.17, C:0.37, G:0.26, T:0.20 Consensus pattern (18 bp): TACCCGTGTGGGCCCACA Found at i:8168695 original size:44 final size:44 Alignment explanation

Indices: 8168632--8168717 Score: 138 Period size: 44 Copynumber: 2.0 Consensus size: 44 8168622 CAAATACAAA * 8168632 AATTAAACTTAAGCCCTTTAGG-CTAGGTTAATGCTTTACTCAAT 1 AATTAAACTTAAGCCCTTTAGGTC-AGGTTAAGGCTTTACTCAAT * 8168676 AATTAAACTTAATCCCTTTAGGTCAGGTTAAGGCTTTACTCA 1 AATTAAACTTAAGCCCTTTAGGTCAGGTTAAGGCTTTACTCA 8168718 GGAAAACACA Statistics Matches: 39, Mismatches: 2, Indels: 2 0.91 0.05 0.05 Matches are distributed among these distances: 44 38 0.97 45 1 0.03 ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36 Consensus pattern (44 bp): AATTAAACTTAAGCCCTTTAGGTCAGGTTAAGGCTTTACTCAAT Found at i:8177703 original size:35 final size:35 Alignment explanation

Indices: 8177659--8177798 Score: 131 Period size: 35 Copynumber: 4.0 Consensus size: 35 8177649 TGTGTTATGA * * * 8177659 AAGAAGTGTGATGGATGAAGTATTGATGTTGTGGC 1 AAGATGTGTGATGAATGAAGTATTGATGTTGTGGT 8177694 AAGATGTGTGAT-AAGTGAAGTATT-AGTGTTGTGGT 1 AAGATGTGTGATGAA-TGAAGTATTGA-TGTTGTGGT ** * * * 8177729 GGGATGTATGATAAATGAAGTATCGATGTTGTGGT 1 AAGATGTGTGATGAATGAAGTATTGATGTTGTGGT * * * * * 8177764 AGGATATGTTATGAAAGAAGTATTGGTGTTGTGGT 1 AAGATGTGTGATGAATGAAGTATTGATGTTGTGGT 8177799 GGGATTTGTC Statistics Matches: 86, Mismatches: 15, Indels: 8 0.79 0.14 0.07 Matches are distributed among these distances: 34 2 0.02 35 81 0.94 36 3 0.03 ACGTcount: A:0.29, C:0.01, G:0.35, T:0.35 Consensus pattern (35 bp): AAGATGTGTGATGAATGAAGTATTGATGTTGTGGT Found at i:8177786 original size:70 final size:70 Alignment explanation

Indices: 8177673--8177803 Score: 183 Period size: 70 Copynumber: 1.9 Consensus size: 70 8177663 AGTGTGATGG * * * 8177673 ATGAAGTATTGATGTTGTGGCAAGATGTGTGATAAGTGAAGTATTAGTGTTGTGGTGGGATGTAT 1 ATGAAGTATCGATGTTGTGGCAAGATATGTGATAAGAGAAGTATTAGTGTTGTGGTGGGATGTAT 8177738 GATAA 66 GATAA * * * * 8177743 ATGAAGTATCGATGTTGTGGTAGGATATGTTATGAA-AGAAGTATTGGTGTTGTGGTGGGAT 1 ATGAAGTATCGATGTTGTGGCAAGATATGTGAT-AAGAGAAGTATTAGTGTTGTGGTGGGAT 8177804 TTGTCCTTAA Statistics Matches: 53, Mismatches: 7, Indels: 2 0.85 0.11 0.03 Matches are distributed among these distances: 70 51 0.96 71 2 0.04 ACGTcount: A:0.27, C:0.02, G:0.35, T:0.36 Consensus pattern (70 bp): ATGAAGTATCGATGTTGTGGCAAGATATGTGATAAGAGAAGTATTAGTGTTGTGGTGGGATGTAT GATAA Found at i:8180267 original size:21 final size:21 Alignment explanation

Indices: 8180198--8180268 Score: 56 Period size: 21 Copynumber: 3.2 Consensus size: 21 8180188 TATCACAAAC 8180198 TCAGACCACAACTCAATGAGT 1 TCAGACCACAACTCAATGAGT * ** 8180219 TCGGACCTCACATA-T-ATTATGAAC 1 TCAGA-C-CACA-ACTCA--ATGAGT 8180243 TCAGACCACAACTCAATGAGT 1 TCAGACCACAACTCAATGAGT 8180264 TCAGA 1 TCAGA 8180269 TTTCATAATT Statistics Matches: 37, Mismatches: 6, Indels: 14 0.65 0.11 0.25 Matches are distributed among these distances: 21 14 0.38 22 7 0.19 23 7 0.19 24 9 0.24 ACGTcount: A:0.37, C:0.27, G:0.14, T:0.23 Consensus pattern (21 bp): TCAGACCACAACTCAATGAGT Found at i:8180490 original size:16 final size:16 Alignment explanation

Indices: 8180469--8180500 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 8180459 ACAACATCTC 8180469 ATTAATGATATAAATA 1 ATTAATGATATAAATA * 8180485 ATTAATTATATAAATA 1 ATTAATGATATAAATA 8180501 CTTACCATAC Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41 Consensus pattern (16 bp): ATTAATGATATAAATA Done.