Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A08

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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 2655529 characters in sequence are not A, C, G, or T


File 117 of 362

Found at i:38478136 original size:48 final size:48

Alignment explanation

Indices: 38477939--38478132 Score: 237 Period size: 48 Copynumber: 4.0 Consensus size: 48 38477929 TACATGAATC * * * * * * 38477939 CACATATCATTGTCGATGCCATGTCCCATACATGATCTAACACTGGCA 1 CACATATCATCGCCGATGCCATGTCCCAAACATGGTCTTACACAGGCA * 38477987 CACATATCATCGCCGATTCCATGTCCCAAACATGGTCTTACACTA-GCA 1 CACATATCATCGCCGATGCCATGTCCCAAACATGGTCTTACAC-AGGCA * * * 38478035 CACATATCATCGTCGATGCCATGTCCCACACATGGTCTTACACAGGAA 1 CACATATCATCGCCGATGCCATGTCCCAAACATGGTCTTACACAGGCA ** * * * 38478083 CATTTATCATCACCGATGCCATATCCCAGACATGGTCTTACACAGGCA 1 CACATATCATCGCCGATGCCATGTCCCAAACATGGTCTTACACAGGCA 38478131 CA 1 CA 38478133 TTTAGCACGG Statistics Matches: 126, Mismatches: 18, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 47 1 0.01 48 125 0.99 ACGTcount: A:0.29, C:0.31, G:0.14, T:0.25 Consensus pattern (48 bp): CACATATCATCGCCGATGCCATGTCCCAAACATGGTCTTACACAGGCA Found at i:38491866 original size:19 final size:20 Alignment explanation

Indices: 38491830--38491884 Score: 55 Period size: 20 Copynumber: 2.9 Consensus size: 20 38491820 AATTAAAATT 38491830 CATAATGTTTA-TATTTT-TAA 1 CATAAT-TTTATTATTTTAT-A 38491850 CATAATTTTATTATTTTATA 1 CATAATTTTATTATTTTATA * 38491870 -AT-ATTTAATTATTTT 1 CATAATTTTATTATTTT 38491885 TTGACAAGAA Statistics Matches: 32, Mismatches: 1, Indels: 6 0.82 0.03 0.15 Matches are distributed among these distances: 18 12 0.38 19 6 0.19 20 13 0.41 21 1 0.03 ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60 Consensus pattern (20 bp): CATAATTTTATTATTTTATA Found at i:38491880 original size:18 final size:16 Alignment explanation

Indices: 38491851--38491884 Score: 50 Period size: 18 Copynumber: 2.0 Consensus size: 16 38491841 TATTTTTAAC 38491851 ATAATTTTATTATTTT 1 ATAATTTTATTATTTT 38491867 ATAATATTTAATTATTTT 1 ATAAT-TTT-ATTATTTT 38491885 TTGACAAGAA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 5 0.31 17 3 0.19 18 8 0.50 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (16 bp): ATAATTTTATTATTTT Found at i:38496725 original size:35 final size:35 Alignment explanation

Indices: 38496686--38496758 Score: 128 Period size: 35 Copynumber: 2.1 Consensus size: 35 38496676 ACACATTCTT * 38496686 TATTCTCGTCAGATCAATCTCACATAAATAATATA 1 TATTCTCGTCAAATCAATCTCACATAAATAATATA * 38496721 TATTCTCGTTAAATCAATCTCACATAAATAATATA 1 TATTCTCGTCAAATCAATCTCACATAAATAATATA 38496756 TAT 1 TAT 38496759 ATCACATACC Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 35 36 1.00 ACGTcount: A:0.41, C:0.18, G:0.04, T:0.37 Consensus pattern (35 bp): TATTCTCGTCAAATCAATCTCACATAAATAATATA Found at i:38496775 original size:39 final size:35 Alignment explanation

Indices: 38496698--38496765 Score: 109 Period size: 35 Copynumber: 1.9 Consensus size: 35 38496688 TTCTCGTCAG * * 38496698 ATCAATCTCACATAAATAATATATATTCTCGTTAA 1 ATCAATCTCACATAAATAATATATATTCACATTAA 38496733 ATCAATCTCACATAAATAATATATATATCACAT 1 ATCAATCTCACATAAATAATATATAT-TCACAT 38496766 ACCTGAATCA Statistics Matches: 30, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 35 26 0.87 36 4 0.13 ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35 Consensus pattern (35 bp): ATCAATCTCACATAAATAATATATATTCACATTAA Found at i:38500779 original size:57 final size:58 Alignment explanation

Indices: 38500707--38500817 Score: 161 Period size: 57 Copynumber: 1.9 Consensus size: 58 38500697 GTGCCCACTG * 38500707 ACCGATCTCGAACACATAGTGCTCGGTTGAA-GAACTCGCACACACAGTGCCTCAATT 1 ACCGATCTCGAACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATT * * * * * 38500764 ACCGATCTCGCACACATAGTGCTTGGTTAAAGGAATTTGCACACATAGTGCCTC 1 ACCGATCTCGAACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTC 38500818 TAATCATTCG Statistics Matches: 47, Mismatches: 6, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 57 28 0.60 58 19 0.40 ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23 Consensus pattern (58 bp): ACCGATCTCGAACACATAGTGCTCGGTTAAAGGAACTCGCACACACAGTGCCTCAATT Found at i:38501032 original size:43 final size:43 Alignment explanation

Indices: 38500971--38501071 Score: 148 Period size: 43 Copynumber: 2.3 Consensus size: 43 38500961 CCTTACTCGA ** * * 38500971 ATCACCGGCATTAAGCCTGCTAGGCACGAAGACCCGAATATAC 1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCAAATACAC * * 38501014 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACAT 1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCAAATACAC 38501057 ATCACCGGCACGAAG 1 ATCACCGGCACGAAG 38501072 GCCCAAATAC Statistics Matches: 52, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 43 52 1.00 ACGTcount: A:0.33, C:0.32, G:0.23, T:0.13 Consensus pattern (43 bp): ATCACCGGCACGAAGCCTGCTAGGCACGAAGACCCAAATACAC Found at i:38501074 original size:27 final size:27 Alignment explanation

Indices: 38501036--38501098 Score: 99 Period size: 27 Copynumber: 2.3 Consensus size: 27 38501026 AAGCCTGCTA * 38501036 GGCACGAAGGCCCAAATACATATCACC 1 GGCACGAAGGCCCAAATACACATCACC * 38501063 GGCACGAAGGCCCAAATACACATCATC 1 GGCACGAAGGCCCAAATACACATCACC * 38501090 GGCATGAAG 1 GGCACGAAG 38501099 CCTGCTAGGC Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 27 33 1.00 ACGTcount: A:0.37, C:0.30, G:0.22, T:0.11 Consensus pattern (27 bp): GGCACGAAGGCCCAAATACACATCACC Found at i:38501110 original size:43 final size:43 Alignment explanation

Indices: 38501063--38501216 Score: 254 Period size: 43 Copynumber: 3.6 Consensus size: 43 38501053 ACATATCACC * * 38501063 GGCACGAAGGCCCAAATACACATCATCGGCATGAAGCCTGCTA 1 GGCACGAAGGCCCGAATACACATCATCGGCACGAAGCCTGCTA * * 38501106 GGCACGAAGGCCCGAATACACATCATTGGCACGGAGCCTGCTA 1 GGCACGAAGGCCCGAATACACATCATCGGCACGAAGCCTGCTA 38501149 GGCACGAAGGCCCGAATACACATCATCGGCACGAAGCCTGCTA 1 GGCACGAAGGCCCGAATACACATCATCGGCACGAAGCCTGCTA * * 38501192 GGCACGAAGGCCCCAATAGACATCA 1 GGCACGAAGGCCCGAATACACATCA 38501217 CCGAGTTTCA Statistics Matches: 103, Mismatches: 8, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 43 103 1.00 ACGTcount: A:0.31, C:0.31, G:0.25, T:0.12 Consensus pattern (43 bp): GGCACGAAGGCCCGAATACACATCATCGGCACGAAGCCTGCTA Found at i:38501138 original size:70 final size:70 Alignment explanation

Indices: 38500993--38501130 Score: 213 Period size: 70 Copynumber: 2.0 Consensus size: 70 38500983 AAGCCTGCTA * * * 38500993 GGCACGAAGACCCGAATATACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACATA 1 GGCACGAAGACCCAAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA 38501058 TCACC 66 TCACC * * * * 38501063 GGCACGAAGGCCCAAATACACATCATCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACA 1 GGCACGAAGACCCAAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA 38501128 TCA 66 TCA 38501131 TTGGCACGGA Statistics Matches: 61, Mismatches: 7, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 70 61 1.00 ACGTcount: A:0.34, C:0.32, G:0.22, T:0.12 Consensus pattern (70 bp): GGCACGAAGACCCAAATACACATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCAAATACACA TCACC Found at i:38501179 original size:113 final size:113 Alignment explanation

Indices: 38500971--38501184 Score: 338 Period size: 113 Copynumber: 1.9 Consensus size: 113 38500961 CCTTACTCGA * * 38500971 ATCACCGGCATTAAGCCTGCTAGGCACGAAGACCCGAATATACATCACCGGCACGAAGCCTGCTA 1 ATCACCGGCATGAAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACGAAGCCTGCTA * 38501036 GGCACGAAGGCCCAAATACATATCACCGGCACGAAGGCCCAAATACAC 66 GGCACGAAGGCCCAAATACACATCACCGGCACGAAGGCCCAAATACAC * * ** * 38501084 ATCATCGGCATGAAGCCTGCTAGGCACGAAGGCCCGAATACACATCATTGGCACGGAGCCTGCTA 1 ATCACCGGCATGAAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACGAAGCCTGCTA * * 38501149 GGCACGAAGGCCCGAATACACATCATCGGCACGAAG 66 GGCACGAAGGCCCAAATACACATCACCGGCACGAAG 38501185 CCTGCTAGGC Statistics Matches: 91, Mismatches: 10, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 113 91 1.00 ACGTcount: A:0.32, C:0.31, G:0.24, T:0.13 Consensus pattern (113 bp): ATCACCGGCATGAAGCCTGCTAGGCACGAAGACCCGAATACACATCACCGGCACGAAGCCTGCTA GGCACGAAGGCCCAAATACACATCACCGGCACGAAGGCCCAAATACAC Found at i:38502656 original size:35 final size:35 Alignment explanation

Indices: 38502617--38502689 Score: 146 Period size: 35 Copynumber: 2.1 Consensus size: 35 38502607 ACACATTCTT 38502617 TATTCTCGTCAGATCAATCTCACATAAATAATATA 1 TATTCTCGTCAGATCAATCTCACATAAATAATATA 38502652 TATTCTCGTCAGATCAATCTCACATAAATAATATA 1 TATTCTCGTCAGATCAATCTCACATAAATAATATA 38502687 TAT 1 TAT 38502690 ATCACATACC Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 35 38 1.00 ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36 Consensus pattern (35 bp): TATTCTCGTCAGATCAATCTCACATAAATAATATA Found at i:38507404 original size:62 final size:62 Alignment explanation

Indices: 38507307--38507431 Score: 232 Period size: 62 Copynumber: 2.0 Consensus size: 62 38507297 CTTCGCATGG * * 38507307 CCTAAGTACCTTAGCCAGATTGGCTAAGCAATCATCGTACGTATCTCCAAACGCTGAAAAGT 1 CCTAAGCACCTTAGCCAAATTGGCTAAGCAATCATCGTACGTATCTCCAAACGCTGAAAAGT 38507369 CCTAAGCACCTTAGCCAAATTGGCTAAGCAATCATCGTACGTATCTCCAAACGCTGAAAAGT 1 CCTAAGCACCTTAGCCAAATTGGCTAAGCAATCATCGTACGTATCTCCAAACGCTGAAAAGT 38507431 C 1 C 38507432 ATCCATGAAA Statistics Matches: 61, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 62 61 1.00 ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23 Consensus pattern (62 bp): CCTAAGCACCTTAGCCAAATTGGCTAAGCAATCATCGTACGTATCTCCAAACGCTGAAAAGT Found at i:38522983 original size:31 final size:31 Alignment explanation

Indices: 38522943--38523015 Score: 83 Period size: 31 Copynumber: 2.4 Consensus size: 31 38522933 ACTAACAAGA * * ** 38522943 GAGTAACTAAACTATTCAATTTTGAAAAGGT 1 GAGTGACTAAAATATTCAATTTCAAAAAGGT * * * 38522974 GAGTGACTAAAATGTTTAATTTCAAAAAGTT 1 GAGTGACTAAAATATTCAATTTCAAAAAGGT 38523005 GAGTGACTAAA 1 GAGTGACTAAA 38523016 TGAAAAAAAA Statistics Matches: 35, Mismatches: 7, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 31 35 1.00 ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32 Consensus pattern (31 bp): GAGTGACTAAAATATTCAATTTCAAAAAGGT Found at i:38523995 original size:27 final size:27 Alignment explanation

Indices: 38523965--38524076 Score: 82 Period size: 27 Copynumber: 4.1 Consensus size: 27 38523955 CATACGAACT * 38523965 ATTCCTTCAACGTTCGCCATATTTACC 1 ATTCCTTCAAAGTTCGCCATATTTACC * * ** 38523992 ATTCCTTCAAAGTTTGTCATATTTAAA 1 ATTCCTTCAAAGTTCGCCATATTTACC * * * 38524019 ATTCTTTTAGAGTTCGCCATACTTT-CC 1 ATTCCTTCAAAGTTCGCCATA-TTTACC * * * *** 38524046 ATTCTTTTAGAGTTTTTCATATTTACC 1 ATTCCTTCAAAGTTCGCCATATTTACC 38524073 ATTC 1 ATTC 38524077 TTCCCTTTCT Statistics Matches: 68, Mismatches: 15, Indels: 4 0.78 0.17 0.05 Matches are distributed among these distances: 26 3 0.04 27 62 0.91 28 3 0.04 ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46 Consensus pattern (27 bp): ATTCCTTCAAAGTTCGCCATATTTACC Found at i:38524077 original size:27 final size:27 Alignment explanation

Indices: 38523982--38524078 Score: 106 Period size: 27 Copynumber: 3.6 Consensus size: 27 38523972 CAACGTTCGC * * * 38523982 CATATTTACCATTCCTTCAAAGTTTGT 1 CATATTTACCATTCTTTTAGAGTTTGT ** * * 38524009 CATATTTAAAATTCTTTTAGAGTTCGC 1 CATATTTACCATTCTTTTAGAGTTTGT * 38524036 CATACTTT-CCATTCTTTTAGAGTTTTT 1 CATA-TTTACCATTCTTTTAGAGTTTGT 38524063 CATATTTACCATTCTT 1 CATATTTACCATTCTT 38524079 CCCTTTCTGG Statistics Matches: 56, Mismatches: 12, Indels: 4 0.78 0.17 0.06 Matches are distributed among these distances: 26 3 0.05 27 50 0.89 28 3 0.05 ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48 Consensus pattern (27 bp): CATATTTACCATTCTTTTAGAGTTTGT Found at i:38524204 original size:27 final size:27 Alignment explanation

Indices: 38524152--38524246 Score: 102 Period size: 27 Copynumber: 3.5 Consensus size: 27 38524142 ATGCACCATG * * 38524152 AAGGCATTCC-TTTCCATAGATCACCACA 1 AAGGC-TTCCATTT-CATAAATTACCACA * * * 38524180 AAGGCTTCTATTTCATATATTACCATA 1 AAGGCTTCCATTTCATAAATTACCACA ** 38524207 AAGGCTTCCATTTCATAAATTGTCACA 1 AAGGCTTCCATTTCATAAATTACCACA 38524234 AAGGCTTCCATTT 1 AAGGCTTCCATTT 38524247 TTCCAATGTG Statistics Matches: 57, Mismatches: 9, Indels: 3 0.83 0.13 0.04 Matches are distributed among these distances: 27 49 0.86 28 8 0.14 ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34 Consensus pattern (27 bp): AAGGCTTCCATTTCATAAATTACCACA Found at i:38529492 original size:42 final size:42 Alignment explanation

Indices: 38529437--38529525 Score: 106 Period size: 42 Copynumber: 2.1 Consensus size: 42 38529427 TCGAGCAAAG * ** 38529437 ACACGGGCATGTGTCTCAGCCGTGTGTGCTACATGGCCTAAA 1 ACACGAGCATGTGTCTCAGCCGTGTGTGCTACACAGCCTAAA * * ** * 38529479 ACACGAGCGTGTGTCTCGGTTGTGTGTGCTACACAGCCTAGA 1 ACACGAGCATGTGTCTCAGCCGTGTGTGCTACACAGCCTAAA 38529521 ACACG 1 ACACG 38529526 GGCACATGTC Statistics Matches: 39, Mismatches: 8, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 42 39 1.00 ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24 Consensus pattern (42 bp): ACACGAGCATGTGTCTCAGCCGTGTGTGCTACACAGCCTAAA Found at i:38529536 original size:42 final size:42 Alignment explanation

Indices: 38529458--38529546 Score: 106 Period size: 42 Copynumber: 2.1 Consensus size: 42 38529448 TGTCTCAGCC ** *** 38529458 GTGTGTGCTACATGGCCTAAAACACGAGCGTGTGTCTCGGTT 1 GTGTGTGCTACACAGCCTAAAACACGAGCACATGTCTCGGTT * * * 38529500 GTGTGTGCTACACAGCCTAGAACACGGGCACATGTCTTGGTT 1 GTGTGTGCTACACAGCCTAAAACACGAGCACATGTCTCGGTT 38529542 GTGTG 1 GTGTG 38529547 AAACTTGCAC Statistics Matches: 39, Mismatches: 8, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 42 39 1.00 ACGTcount: A:0.19, C:0.21, G:0.31, T:0.28 Consensus pattern (42 bp): GTGTGTGCTACACAGCCTAAAACACGAGCACATGTCTCGGTT Found at i:38538893 original size:48 final size:48 Alignment explanation

Indices: 38538841--38539165 Score: 300 Period size: 50 Copynumber: 6.7 Consensus size: 48 38538831 TAAGAGCCAA * * * 38538841 TGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGATGAGAGCTAG 1 TGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGAAAGCTAG * * 38538889 TGTAAGACCATGTCTAGGACATGGCATCGACCA-CGAGATATGAAAGCTAG 1 TGTAAGACCATGTCTGGGACATGGCATCG-GCATCGAG--ATGAAAGCTAG * ** * * * 38538939 TGTAAGACCATGTCTGGGACATGGCATCAGC-TTAATATG--TGTTAG 1 TGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGAAAGCTAG * * 38538984 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAAAGCCAG 1 TGTAAGACCATGTCTGGGACATGGCATCGGCATCG--AGATGAAAGCTAG * * * * 38539034 TGTAAGACCATGTCTGGGGCATGACATCGGCCTCGATATATGAAAG-TCAG 1 TGTAAGACCATGTCTGGGACATGGCATCGGCATCG--AGATGAAAGCT-AG * * * * * ** * 38539084 TGTAAGACCATGTCTGGGACATGGCATTGACTTTGATATGTGAGCCAG 1 TGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGAAAGCTAG * * 38539132 TGTAAGACCATGTCTGGGACATGGCGTCAGCATC 1 TGTAAGACCATGTCTGGGACATGGCATCGGCATC 38539166 TTACCCTATT Statistics Matches: 225, Mismatches: 41, Indels: 22 0.78 0.14 0.08 Matches are distributed among these distances: 45 34 0.15 47 3 0.01 48 73 0.32 49 4 0.02 50 111 0.49 ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24 Consensus pattern (48 bp): TGTAAGACCATGTCTGGGACATGGCATCGGCATCGAGATGAAAGCTAG Found at i:38539062 original size:145 final size:145 Alignment explanation

Indices: 38538835--38539156 Score: 427 Period size: 145 Copynumber: 2.2 Consensus size: 145 38538825 ACATTATAAG * * ** * * 38538835 AGCCAATGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACCAT 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGAAAGCCAGTGTAAGACCAT * 38538900 GTCTAGGACATGGCATCGACCACGAGATATGAAAG-CTAGTGTAAGACCATGTCTGGGACATGGC 66 GTCTAGGACATGACATCGACCACGAGATATGAAAGTC-AGTGTAAGACCATGTCTGGGACATGGC 38538964 ATCAG-C-TTAATATGT 130 AT-AGACTTTAATATGT ** 38538979 -GTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAAAGCCAGTGTAAGACC 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCG--AGATGAAAGCCAGTGTAAGACC * * * * * 38539043 ATGTCTGGGGCATGACATCGGCCTCGATATATGAAAGTCAGTGTAAGACCATGTCTGGGACATGG 64 ATGTCTAGGACATGACATCGACCACGAGATATGAAAGTCAGTGTAAGACCATGTCTGGGACATGG * * 38539108 CATTGACTTTGATATGT 129 CATAGACTTTAATATGT 38539125 GAGCCAGTGTAAGACCATGTCTGGGACATGGC 1 -AGCCAGTGTAAGACCATGTCTGGGACATGGC 38539157 GTCAGCATCT Statistics Matches: 153, Mismatches: 18, Indels: 10 0.85 0.10 0.06 Matches are distributed among these distances: 143 34 0.22 144 1 0.01 145 81 0.53 146 9 0.06 148 28 0.18 ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23 Consensus pattern (145 bp): AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGAAAGCCAGTGTAAGACCAT GTCTAGGACATGACATCGACCACGAGATATGAAAGTCAGTGTAAGACCATGTCTGGGACATGGCA TAGACTTTAATATGT Found at i:38541989 original size:30 final size:30 Alignment explanation

Indices: 38541944--38542003 Score: 86 Period size: 30 Copynumber: 2.0 Consensus size: 30 38541934 ATTTAATATG 38541944 AACTTTGGCAAAATTACA-TTTTTGCCCCTA 1 AACTTTGGCAAAATTACACTTTTT-CCCCTA * * 38541974 AACTTTTGCATAATTACACTTTTTCCCCTA 1 AACTTTGGCAAAATTACACTTTTTCCCCTA 38542004 GGCTCGGGAA Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 30 22 0.81 31 5 0.19 ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40 Consensus pattern (30 bp): AACTTTGGCAAAATTACACTTTTTCCCCTA Found at i:38548840 original size:30 final size:30 Alignment explanation

Indices: 38548795--38548854 Score: 86 Period size: 30 Copynumber: 2.0 Consensus size: 30 38548785 ATTTAATATG 38548795 AACTTTGGCAAAATTACA-TTTTTGCCCCTA 1 AACTTTGGCAAAATTACACTTTTT-CCCCTA * * 38548825 AACTTTTGCATAATTACACTTTTTCCCCTA 1 AACTTTGGCAAAATTACACTTTTTCCCCTA 38548855 GGCTCAAGAA Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 30 22 0.81 31 5 0.19 ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40 Consensus pattern (30 bp): AACTTTGGCAAAATTACACTTTTTCCCCTA Found at i:38554634 original size:50 final size:50 Alignment explanation

Indices: 38554526--38554805 Score: 274 Period size: 50 Copynumber: 5.7 Consensus size: 50 38554516 TGACATGCGT ** * 38554526 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATTTGCCAC-AT-TATGAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAGA * * * * * 38554572 GCCAGTGTAAGACTATGTATGGGATATGGCATCGGCCTCGAGATATG-GAA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAG-A * 38554622 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATAGATGAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATATATGAGA * * * 38554672 GCCAATGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATATATGAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAGA * * * * * * 38554722 G-TCAGTGTAATACCATGTCTGGGACATGGCATCGACTTTGATGT-TTA-A 1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAGA * * 38554770 GCTATTGTAAGACCATGT-TCGGGACATGGCGTCGGC 1 GCTAGTGTAAGACCATGTCT-GGGACATGGCATCGGC 38554806 ATCTTACCCT Statistics Matches: 192, Mismatches: 31, Indels: 20 0.79 0.13 0.08 Matches are distributed among these distances: 46 11 0.06 47 12 0.06 48 37 0.19 49 6 0.03 50 124 0.65 51 2 0.01 ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25 Consensus pattern (50 bp): GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATATATGAGA Found at i:38554805 original size:148 final size:146 Alignment explanation

Indices: 38554531--38554806 Score: 344 Period size: 148 Copynumber: 1.9 Consensus size: 146 38554521 TGCGTGCTAG ** * 38554531 TGTAAGACATGTCTGGGACATGCATTTGCCACATTATGAGAGCCAGTGTAAGACTATGTATGGGA 1 TGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTATGGGA * * 38554596 TATGGCATCGGCCTCGAGATATGGAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACC 66 CATGGCATCGACCTCGAGATATGGAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACC 38554661 GATAGATGAGAGCCAA 131 GATAGATGAGAGCCAA * * * * 38554677 TGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATATATGAGAGTCAGTGTAATACCATGTCT 1 TGTAAGA-CATGTCTGGGACAT-GCATCAGCCAC-AT-TATGAGAGCCAGTGTAAGACCATGTAT * * * * * 38554742 GGGACATGGCATCGACTTTGATG-T-T-TAAGCTATTGTAAGACCATGT-TCGGGACATGGCGTC 62 GGGACATGGCATCGACCTCGA-GATATGGAAGCTAGTGTAAGACCATGTCT-GGGACATGGCATC 38554803 GGCA 125 GGCA 38554807 TCTTACCCTA Statistics Matches: 110, Mismatches: 14, Indels: 10 0.82 0.10 0.07 Matches are distributed among these distances: 146 7 0.06 147 15 0.14 148 43 0.39 149 3 0.03 150 41 0.37 151 1 0.01 ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25 Consensus pattern (146 bp): TGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTATGGGA CATGGCATCGACCTCGAGATATGGAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACC GATAGATGAGAGCCAA Found at i:38559941 original size:63 final size:67 Alignment explanation

Indices: 38559873--38560008 Score: 158 Period size: 67 Copynumber: 2.1 Consensus size: 67 38559863 CTAACTTAAA * * * 38559873 TAAATGAAC-TAACACTTATGCATC-AT-TTATTTC-AGCAACTAGTTTAATTAAGAG-AAGCA- 1 TAAATGAACTTAA-ACTCATGCATCAATAATATTTCTAGCAACTAGATTAATTAAGAGCAA-CAC 38559932 TTAT 64 TTAT * * 38559936 TAAATGAACTTTAACTCATGCATCAATAAATATTTCTAGGAACTAGATTAATTAAGAGCAACACT 1 TAAATGAACTTAAACTCATGCATCAAT-AATATTTCTAGCAACTAGATTAATTAAGAGCAACACT 38560001 TAT 65 TAT 38560004 TAAAT 1 TAAAT 38560009 AAAGTTTAAC Statistics Matches: 61, Mismatches: 5, Indels: 9 0.81 0.07 0.12 Matches are distributed among these distances: 63 19 0.31 64 4 0.07 66 6 0.10 67 21 0.34 68 11 0.18 ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34 Consensus pattern (67 bp): TAAATGAACTTAAACTCATGCATCAATAATATTTCTAGCAACTAGATTAATTAAGAGCAACACTT AT Found at i:38561536 original size:24 final size:24 Alignment explanation

Indices: 38561437--38561537 Score: 157 Period size: 24 Copynumber: 4.2 Consensus size: 24 38561427 AAGTCTGTCA * 38561437 GGAGAGGATTTAGGAGTTGATAAG 1 GGAGAGGATTTAGGAGCTGATAAG * * 38561461 GGATAGGATTTAGGAGTTGATAAG 1 GGAGAGGATTTAGGAGCTGATAAG * 38561485 GGATAGGATTTAGGAGCTGATAAG 1 GGAGAGGATTTAGGAGCTGATAAG * 38561509 GGAGAGGATTTAGGAGCTGATTAG 1 GGAGAGGATTTAGGAGCTGATAAG 38561533 GGAGA 1 GGAGA 38561538 ACAGTGTTGG Statistics Matches: 73, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 24 73 1.00 ACGTcount: A:0.33, C:0.02, G:0.41, T:0.25 Consensus pattern (24 bp): GGAGAGGATTTAGGAGCTGATAAG Found at i:38563035 original size:27 final size:26 Alignment explanation

Indices: 38562947--38563051 Score: 111 Period size: 27 Copynumber: 3.9 Consensus size: 26 38562937 AAGTGTCCTA * * * * 38562947 GTGGCTATGCCATATTTATTTGATCTG 1 GTGGCTCTGCCACA-TTATCTGTTCTG * 38562974 GTGGCACTGCCACATATATCTGTTCTG 1 GTGGCTCTGCCACAT-TATCTGTTCTG 38563001 GTGGCTCTGCCACAATTATCTGTTCTG 1 GTGGCTCTGCCAC-ATTATCTGTTCTG * ** 38563028 GTGACTCTGTAACATTATCTGTTC 1 GTGGCTCTGCCACATTATCTGTTC 38563052 AGGCAGCAAT Statistics Matches: 67, Mismatches: 9, Indels: 5 0.83 0.11 0.06 Matches are distributed among these distances: 26 12 0.18 27 53 0.79 28 2 0.03 ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39 Consensus pattern (26 bp): GTGGCTCTGCCACATTATCTGTTCTG Found at i:38569421 original size:24 final size:24 Alignment explanation

Indices: 38569323--38569422 Score: 139 Period size: 24 Copynumber: 4.2 Consensus size: 24 38569313 AGTCTGTCAA * 38569323 GAGAGGATTTAGGAGTTGATAAGG 1 GAGAGGATTTAGGAGCTGATAAGG * * 38569347 GATAGGATTTAGGAGTTGATAAGG 1 GAGAGGATTTAGGAGCTGATAAGG * 38569371 GATAGGATTTCA-GAGCTGATAAGG 1 GAGAGGATTT-AGGAGCTGATAAGG * 38569395 GAGAGGATTTAGGAGCTGATTAGG 1 GAGAGGATTTAGGAGCTGATAAGG 38569419 GAGA 1 GAGA 38569423 ACAGTGTTGG Statistics Matches: 70, Mismatches: 4, Indels: 4 0.90 0.05 0.05 Matches are distributed among these distances: 23 1 0.01 24 68 0.97 25 1 0.01 ACGTcount: A:0.33, C:0.03, G:0.39, T:0.25 Consensus pattern (24 bp): GAGAGGATTTAGGAGCTGATAAGG Found at i:38570849 original size:27 final size:27 Alignment explanation

Indices: 38570810--38570910 Score: 143 Period size: 27 Copynumber: 3.8 Consensus size: 27 38570800 ACATGGGTTA * * 38570810 TGCCACATTTATCTGATCTGGTGGCTC 1 TGCCACATATATCTGTTCTGGTGGCTC 38570837 TGCCACATATATCTGTTCTGGTGGCTC 1 TGCCACATATATCTGTTCTGGTGGCTC * 38570864 TGCCACA-ATTATCTGTTCTGGTGACTC 1 TGCCACATA-TATCTGTTCTGGTGGCTC * 38570891 TGTCACAT-TATCTGTTCTGG 1 TGCCACATATATCTGTTCTGG 38570911 CAGCAATGCT Statistics Matches: 68, Mismatches: 4, Indels: 5 0.88 0.05 0.06 Matches are distributed among these distances: 26 13 0.19 27 55 0.81 ACGTcount: A:0.16, C:0.25, G:0.21, T:0.39 Consensus pattern (27 bp): TGCCACATATATCTGTTCTGGTGGCTC Found at i:38574159 original size:12 final size:12 Alignment explanation

Indices: 38574108--38574159 Score: 50 Period size: 12 Copynumber: 4.2 Consensus size: 12 38574098 CTAATTTCAA 38574108 TTTTTTTCGAAT 1 TTTTTTTCGAAT * * 38574120 ATTTTTTCCAAAT 1 -TTTTTTTCGAAT * * 38574133 TCTTTTTCGATT 1 TTTTTTTCGAAT * 38574145 TTTTTTTTGAAT 1 TTTTTTTCGAAT 38574157 TTT 1 TTT 38574160 GAACTTTTTT Statistics Matches: 30, Mismatches: 9, Indels: 1 0.75 0.22 0.03 Matches are distributed among these distances: 12 20 0.67 13 10 0.33 ACGTcount: A:0.17, C:0.10, G:0.06, T:0.67 Consensus pattern (12 bp): TTTTTTTCGAAT Found at i:38576498 original size:21 final size:22 Alignment explanation

Indices: 38576472--38576514 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 38576462 CTCTAGGACA * 38576472 GGCGTG-CCCTAGGGTCACACG 1 GGCGTGTCCCTAGGATCACACG * 38576493 GGCGTGTCCCTTGGATCACACG 1 GGCGTGTCCCTAGGATCACACG 38576515 AGCCTGTGAG Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 21 6 0.32 22 13 0.68 ACGTcount: A:0.14, C:0.33, G:0.35, T:0.19 Consensus pattern (22 bp): GGCGTGTCCCTAGGATCACACG Found at i:38579409 original size:21 final size:22 Alignment explanation

Indices: 38579375--38579417 Score: 79 Period size: 21 Copynumber: 2.0 Consensus size: 22 38579365 TAAGTAAAAC 38579375 AAAGCCATTTTTTTTACTTCAT 1 AAAGCCATTTTTTTTACTTCAT 38579397 AAAGCCA-TTTTTTTACTTCAT 1 AAAGCCATTTTTTTTACTTCAT 38579418 TCATATTTTT Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 21 14 0.67 22 7 0.33 ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49 Consensus pattern (22 bp): AAAGCCATTTTTTTTACTTCAT Found at i:38585028 original size:18 final size:18 Alignment explanation

Indices: 38585005--38585043 Score: 51 Period size: 18 Copynumber: 2.2 Consensus size: 18 38584995 GTAAATAGCT * 38585005 TAAAATAGATTTTAAAAA 1 TAAAATAGAGTTTAAAAA * * 38585023 TAAAATCGAGTTTGAAAA 1 TAAAATAGAGTTTAAAAA 38585041 TAA 1 TAA 38585044 TTGAGAAAAT Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31 Consensus pattern (18 bp): TAAAATAGAGTTTAAAAA Found at i:38587955 original size:21 final size:21 Alignment explanation

Indices: 38587931--38587999 Score: 50 Period size: 21 Copynumber: 3.1 Consensus size: 21 38587921 TGATCTGAAC 38587931 TCATTGATTTGTGGTCTGAGT 1 TCATTGATTTGTGGTCTGAGT * * * 38587952 TCATCAT-ATATGTGACATCTGAGC 1 TCAT--TGATTTGTG--GTCTGAGT * * 38587976 TCATTGAATTGTGGTCTTAGT 1 TCATTGATTTGTGGTCTGAGT 38587997 TCA 1 TCA 38588000 GGATGTATGT Statistics Matches: 35, Mismatches: 8, Indels: 10 0.66 0.15 0.19 Matches are distributed among these distances: 21 12 0.34 22 7 0.20 23 6 0.17 24 10 0.29 ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42 Consensus pattern (21 bp): TCATTGATTTGTGGTCTGAGT Found at i:38587979 original size:45 final size:45 Alignment explanation

Indices: 38587923--38588013 Score: 128 Period size: 45 Copynumber: 2.0 Consensus size: 45 38587913 GAACTATGTG * * 38587923 ATCTGAACTCATTGATTTGTGGTCTGAGTTCATCATATATGTGAC 1 ATCTGAACTCATTGAATTGTGGTCTGAGTTCAGCATATATGTGAC * * * * 38587968 ATCTGAGCTCATTGAATTGTGGTCTTAGTTCAGGATGTATGTGAC 1 ATCTGAACTCATTGAATTGTGGTCTGAGTTCAGCATATATGTGAC 38588013 A 1 A 38588014 CATGTTTTGG Statistics Matches: 40, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 45 40 1.00 ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38 Consensus pattern (45 bp): ATCTGAACTCATTGAATTGTGGTCTGAGTTCAGCATATATGTGAC Found at i:38592570 original size:18 final size:18 Alignment explanation

Indices: 38592543--38592583 Score: 55 Period size: 18 Copynumber: 2.3 Consensus size: 18 38592533 GCACAATGTG * * 38592543 TTAATTTGGTGATCTGCA 1 TTAATATGGTGAACTGCA * 38592561 TTAATATGGTGAACTGTA 1 TTAATATGGTGAACTGCA 38592579 TTAAT 1 TTAAT 38592584 TTTCCAAATT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44 Consensus pattern (18 bp): TTAATATGGTGAACTGCA Found at i:38593660 original size:37 final size:37 Alignment explanation

Indices: 38593591--38593695 Score: 111 Period size: 37 Copynumber: 2.8 Consensus size: 37 38593581 TTTGTAAAGT * * * ** 38593591 AATAGCAAACAATTTCACATGTTAATTAATTTAGTAC 1 AATAACAAACAATTTCACATATCAATTAATTTAACAC * * * 38593628 AATGACAAACAATTTCACATATCAATTTATTTAACAT 1 AATAACAAACAATTTCACATATCAATTAATTTAACAC * * * 38593665 AATAACAAACAATCTCGCATATCAATCAATT 1 AATAACAAACAATTTCACATATCAATTAATT 38593696 CAATACGGTT Statistics Matches: 55, Mismatches: 13, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 37 55 1.00 ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32 Consensus pattern (37 bp): AATAACAAACAATTTCACATATCAATTAATTTAACAC Found at i:38596213 original size:36 final size:36 Alignment explanation

Indices: 38596166--38596288 Score: 108 Period size: 36 Copynumber: 3.5 Consensus size: 36 38596156 TTGGTTATCT * * 38596166 GACTAGAGCTGGGCTCAATAATTTGTCGATTCGTTC 1 GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC * * * * * 38596202 GACTAGTGCTGGGCAGAACT-A-TCGTCGGTT-ATCC 1 GACTAGTGCTGGGCACAA-TAATTTGTCGATTCGTTC ** * * * 38596236 GGTTAGTGCTGAGCACAATAATTTTTCAATTCGTTC 1 GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC 38596272 GACTAGTGCTGGGCACA 1 GACTAGTGCTGGGCACA 38596289 CCAATGATTT Statistics Matches: 63, Mismatches: 20, Indels: 8 0.69 0.22 0.09 Matches are distributed among these distances: 33 1 0.02 34 17 0.27 35 12 0.19 36 32 0.51 37 1 0.02 ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31 Consensus pattern (36 bp): GACTAGTGCTGGGCACAATAATTTGTCGATTCGTTC Found at i:38597176 original size:28 final size:28 Alignment explanation

Indices: 38597145--38597207 Score: 72 Period size: 30 Copynumber: 2.2 Consensus size: 28 38597135 TCTCAGCTGT * 38597145 GTGTGACACACGGCTAGGCGACATAGCC 1 GTGTGACACACAGCTAGGCGACATAGCC * * * 38597173 GTGTATGACACACAGTTAGGCGACATGGCT 1 GTG--TGACACACAGCTAGGCGACATAGCC 38597203 GTGTG 1 GTGTG 38597208 TTTATTATTG Statistics Matches: 29, Mismatches: 4, Indels: 4 0.78 0.11 0.11 Matches are distributed among these distances: 28 5 0.17 30 24 0.83 ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21 Consensus pattern (28 bp): GTGTGACACACAGCTAGGCGACATAGCC Found at i:38600788 original size:18 final size:18 Alignment explanation

Indices: 38600760--38600812 Score: 72 Period size: 18 Copynumber: 2.9 Consensus size: 18 38600750 TTGGCCAATT * 38600760 CAGTAACAGTAAACAGTG 1 CAGTAATAGTAAACAGTG * 38600778 TAGTAATAGTAAACAGTG 1 CAGTAATAGTAAACAGTG 38600796 CAGT-ATCAGTAAACAGT 1 CAGTAAT-AGTAAACAGT 38600813 ATGCAAGTCC Statistics Matches: 31, Mismatches: 3, Indels: 2 0.86 0.08 0.06 Matches are distributed among these distances: 17 2 0.06 18 29 0.94 ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23 Consensus pattern (18 bp): CAGTAATAGTAAACAGTG Found at i:38605276 original size:24 final size:24 Alignment explanation

Indices: 38605248--38605299 Score: 68 Period size: 24 Copynumber: 2.2 Consensus size: 24 38605238 CCCATTTTTT * 38605248 CCTCCCCTAATCTCTCCTAAAATC 1 CCTCCCCAAATCTCTCCTAAAATC * * * 38605272 CCTCCTCAAATCTCTCTTCAAATC 1 CCTCCCCAAATCTCTCCTAAAATC 38605296 CCTC 1 CCTC 38605300 AACTGATCAC Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 24 24 1.00 ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31 Consensus pattern (24 bp): CCTCCCCAAATCTCTCCTAAAATC Found at i:38605292 original size:12 final size:12 Alignment explanation

Indices: 38605256--38605295 Score: 53 Period size: 12 Copynumber: 3.3 Consensus size: 12 38605246 TTCCTCCCCT * 38605256 AATCTCTCCTAA 1 AATCTCTCCTCA * 38605268 AATCCCTCCTCA 1 AATCTCTCCTCA * 38605280 AATCTCTCTTCA 1 AATCTCTCCTCA 38605292 AATC 1 AATC 38605296 CCTCAACTGA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 12 24 1.00 ACGTcount: A:0.30, C:0.38, G:0.00, T:0.33 Consensus pattern (12 bp): AATCTCTCCTCA Found at i:38609423 original size:13 final size:13 Alignment explanation

Indices: 38609407--38609440 Score: 59 Period size: 13 Copynumber: 2.6 Consensus size: 13 38609397 CACACGACCA * 38609407 TGTAACACAGCCG 1 TGTAACACAACCG 38609420 TGTAACACAACCG 1 TGTAACACAACCG 38609433 TGTAACAC 1 TGTAACAC 38609441 GCCCATGTCC Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 13 20 1.00 ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18 Consensus pattern (13 bp): TGTAACACAACCG Found at i:38612044 original size:46 final size:46 Alignment explanation

Indices: 38611991--38612127 Score: 184 Period size: 46 Copynumber: 3.0 Consensus size: 46 38611981 TATATATACG * * * * 38611991 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC 1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC * * * 38612037 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTATCTCATATC 1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC * * * 38612083 TAACTCATACACATTTCGCATTAGCCATTCGGCCTTACCACATAT 1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT 38612128 ATACATGTTC Statistics Matches: 78, Mismatches: 13, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 46 78 1.00 ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34 Consensus pattern (46 bp): CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC Found at i:38612161 original size:47 final size:47 Alignment explanation

Indices: 38612101--38612321 Score: 370 Period size: 47 Copynumber: 4.7 Consensus size: 47 38612091 ACACATTTCG * * * ** 38612101 CATTAGCCATTCGGCCTTACCACATATATACATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA * * 38612148 CATTGGCCATTCGGCCTTATCTCATATACGCATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA * 38612195 CATTGGCCATTCGGCCTTAGCACACATACGCATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA 38612242 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA 38612289 CATTGGCCATTCGGCCTTATCACACATACGCAT 1 CATTGGCCATTCGGCCTTATCACACATACGCAT 38612322 CACCCAAACA Statistics Matches: 165, Mismatches: 9, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 47 165 1.00 ACGTcount: A:0.26, C:0.31, G:0.13, T:0.30 Consensus pattern (47 bp): CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA Found at i:38612244 original size:23 final size:23 Alignment explanation

Indices: 38612217--38612291 Score: 57 Period size: 23 Copynumber: 3.2 Consensus size: 23 38612207 GGCCTTAGCA 38612217 CACATACGCATGTTCACATTCAT 1 CACATACGCATGTTCACATTCAT ** * * 38612240 CACATTGGCCA--TTCGGCCTT-AT 1 CACATACG-CATGTTC-ACATTCAT 38612262 CACACATACGCATGTTCACATTCAT 1 --CACATACGCATGTTCACATTCAT 38612287 CACAT 1 CACAT 38612292 TGGCCATTCG Statistics Matches: 37, Mismatches: 8, Indels: 14 0.63 0.14 0.24 Matches are distributed among these distances: 22 5 0.14 23 16 0.43 24 11 0.30 25 5 0.14 ACGTcount: A:0.28, C:0.32, G:0.11, T:0.29 Consensus pattern (23 bp): CACATACGCATGTTCACATTCAT Found at i:38614739 original size:22 final size:20 Alignment explanation

Indices: 38614685--38614737 Score: 97 Period size: 20 Copynumber: 2.6 Consensus size: 20 38614675 TAGGCTGAGG * 38614685 ACACGGGCGTGTGCCAAGTC 1 ACACAGGCGTGTGCCAAGTC 38614705 ACACAGGCGTGTGCCAAGTC 1 ACACAGGCGTGTGCCAAGTC 38614725 ACACAGGCGTGTG 1 ACACAGGCGTGTG 38614738 TGACCATACG Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 20 32 1.00 ACGTcount: A:0.23, C:0.28, G:0.34, T:0.15 Consensus pattern (20 bp): ACACAGGCGTGTGCCAAGTC Found at i:38620925 original size:20 final size:20 Alignment explanation

Indices: 38620897--38620934 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 38620887 GTAGGAACTA 38620897 TGTGATCTGAGCTCATGAGT 1 TGTGATCTGAGCTCATGAGT * * 38620917 TGTGGTCTGAGTTCATGA 1 TGTGATCTGAGCTCATGA 38620935 TATATGTGAC Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37 Consensus pattern (20 bp): TGTGATCTGAGCTCATGAGT Found at i:38623573 original size:28 final size:28 Alignment explanation

Indices: 38623541--38623596 Score: 112 Period size: 28 Copynumber: 2.0 Consensus size: 28 38623531 ATTCAAGGGT 38623541 ACCCATTAGGGCACTTAACTAAGAAACA 1 ACCCATTAGGGCACTTAACTAAGAAACA 38623569 ACCCATTAGGGCACTTAACTAAGAAACA 1 ACCCATTAGGGCACTTAACTAAGAAACA 38623597 CTCTCTCGAG Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18 Consensus pattern (28 bp): ACCCATTAGGGCACTTAACTAAGAAACA Found at i:38624334 original size:20 final size:20 Alignment explanation

Indices: 38624305--38624349 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 38624295 AGCACATGTA * 38624305 TTCATAAAATTTTACAATTT 1 TTCATAAAATTTTACAACTT * * 38624325 TTCATCAAATTTTACTACTT 1 TTCATAAAATTTTACAACTT 38624345 TTCAT 1 TTCAT 38624350 TTTAGTCACT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51 Consensus pattern (20 bp): TTCATAAAATTTTACAACTT Found at i:38625478 original size:11 final size:11 Alignment explanation

Indices: 38625462--38625487 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 38625452 CGAAGCCCAC 38625462 ATCACAATAAT 1 ATCACAATAAT 38625473 ATCACAATAAT 1 ATCACAATAAT 38625484 ATCA 1 ATCA 38625488 TACATGCAAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27 Consensus pattern (11 bp): ATCACAATAAT Found at i:38625951 original size:27 final size:27 Alignment explanation

Indices: 38625910--38625986 Score: 100 Period size: 27 Copynumber: 2.9 Consensus size: 27 38625900 AGGGAAAAAT * * 38625910 GTCATTTTACCCTACAGGGGTATGTCA 1 GTCATTTTACACTACAAGGGTATGTCA * * * 38625937 GTCATTTTACACTACAAGCGTATTTCG 1 GTCATTTTACACTACAAGGGTATGTCA * 38625964 GTAATTTTACACTACAAGGGTAT 1 GTCATTTTACACTACAAGGGTAT 38625987 TTCGATAATT Statistics Matches: 43, Mismatches: 7, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 27 43 1.00 ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35 Consensus pattern (27 bp): GTCATTTTACACTACAAGGGTATGTCA Found at i:38625987 original size:27 final size:27 Alignment explanation

Indices: 38625951--38626213 Score: 253 Period size: 27 Copynumber: 9.7 Consensus size: 27 38625941 TTTTACACTA * * 38625951 CAAGCGTATTTCGGTAATTTTAC-ACT 1 CAAGGGTATTTCGGTAATTTTACAAAT * 38625977 ACAAGGGTATTTCGATAATTTTACAAAT 1 -CAAGGGTATTTCGGTAATTTTACAAAT ** * 38626005 CGGGGGTGTTTCGGTAATTTTACAAAT 1 CAAGGGTATTTCGGTAATTTTACAAAT * 38626032 CAAGGGTATTTCGATAATTTTACAAAT 1 CAAGGGTATTTCGGTAATTTTACAAAT * * 38626059 CGAGGGTATTTCGATAATTTTACAAAT 1 CAAGGGTATTTCGGTAATTTTACAAAT * ** 38626086 -AGAGGGTGTTTCTATAATTTTACAAAT 1 CA-AGGGTATTTCGGTAATTTTACAAAT * ** * 38626113 CGATGGGTATTTTAGTAATTTCAC-AAT 1 C-AAGGGTATTTCGGTAATTTTACAAAT * * * 38626140 CGAGGGTATTTTGGTAATTTTACAAAC 1 CAAGGGTATTTCGGTAATTTTACAAAT * * * 38626167 CGAGGGTACTTCGGTAATTTTACAAAC 1 CAAGGGTATTTCGGTAATTTTACAAAT * ** 38626194 CGAGGGTATTTTAGTAATTT 1 CAAGGGTATTTCGGTAATTT 38626214 CTCTTTATTA Statistics Matches: 200, Mismatches: 31, Indels: 10 0.83 0.13 0.04 Matches are distributed among these distances: 26 18 0.09 27 164 0.82 28 17 0.09 29 1 0.00 ACGTcount: A:0.31, C:0.12, G:0.20, T:0.38 Consensus pattern (27 bp): CAAGGGTATTTCGGTAATTTTACAAAT Found at i:38626025 original size:81 final size:80 Alignment explanation

Indices: 38625951--38626213 Score: 294 Period size: 81 Copynumber: 3.2 Consensus size: 80 38625941 TTTTACACTA * * * 38625951 CAAGCGTATTTCGGTAATTTTACACTACAAGGGTATTTCGATAATTTTACAAATCGGGGGTGTTT 1 CAAGGGTATTTCGGTAATTTTACA-TACGAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTT 38626016 CGGTAATTTTACAAAT 65 CGGTAATTTTACAAAT * * * 38626032 CAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATAGAGGGTGTTT 1 CAAGGGTATTTCGGTAATTTTACATA-CGAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTT ** 38626097 CTATAATTTTACAAAT 65 CGGTAATTTTACAAAT * ** * * * * ** 38626113 CGATGGGTATTTTAGTAATTTCACA-ATCGAGGGTATTTTGGTAATTTTACAAACCGAGGGTACT 1 C-AAGGGTATTTCGGTAATTTTACATA-CGAGGGTATTTCGATAATTTTACAAATCGAGGGTGTT * 38626177 TCGGTAATTTTACAAAC 64 TCGGTAATTTTACAAAT * ** 38626194 CGAGGGTATTTTAGTAATTT 1 CAAGGGTATTTCGGTAATTT 38626214 CTCTTTATTA Statistics Matches: 156, Mismatches: 24, Indels: 5 0.84 0.13 0.03 Matches are distributed among these distances: 80 18 0.12 81 120 0.77 82 18 0.12 ACGTcount: A:0.31, C:0.12, G:0.20, T:0.38 Consensus pattern (80 bp): CAAGGGTATTTCGGTAATTTTACATACGAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTC GGTAATTTTACAAAT Found at i:38626198 original size:54 final size:54 Alignment explanation

Indices: 38625956--38626213 Score: 299 Period size: 54 Copynumber: 4.8 Consensus size: 54 38625946 CACTACAAGC * * * * 38625956 GTATTTCGGTAATTTTAC-ACTACAAGGGTATTTCGATAATTTTACAAATCGGGG 1 GTATTTCGGTAATTTTACAAAT-CGAGGGTATTTTGATAATTTTACAAATCGAGG * * * 38626010 GTGTTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGG 1 GTATTTCGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAATCGAGG * * * 38626064 GTATTTCGATAATTTTACAAATAGAGGGTGTTTCT-ATAATTTTACAAATCGATGG 1 GTATTTCGGTAATTTTACAAATCGAGGGTATTT-TGATAATTTTACAAATCGA-GG ** * * * 38626119 GTATTTTAGTAATTTCAC-AATCGAGGGTATTTTGGTAATTTTACAAACCGAGG 1 GTATTTCGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAATCGAGG * * 38626172 GTACTTCGGTAATTTTACAAACCGAGGGTATTTT-AGTAATTT 1 GTATTTCGGTAATTTTACAAATCGAGGGTATTTTGA-TAATTT 38626214 CTCTTTATTA Statistics Matches: 175, Mismatches: 23, Indels: 12 0.83 0.11 0.06 Matches are distributed among these distances: 53 17 0.10 54 140 0.80 55 18 0.10 ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38 Consensus pattern (54 bp): GTATTTCGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAATCGAGG Found at i:38626564 original size:28 final size:28 Alignment explanation

Indices: 38626528--38626591 Score: 101 Period size: 28 Copynumber: 2.3 Consensus size: 28 38626518 CGGCCCCTTT * * 38626528 AGGCCCAATCTCGTTCACATGGCCCATC 1 AGGCCCAATCACCTTCACATGGCCCATC * 38626556 AGGCCCAATCACCTTCATATGGCCCATC 1 AGGCCCAATCACCTTCACATGGCCCATC 38626584 AGGCCCAA 1 AGGCCCAA 38626592 CTACTTCCCA Statistics Matches: 33, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 28 33 1.00 ACGTcount: A:0.25, C:0.39, G:0.17, T:0.19 Consensus pattern (28 bp): AGGCCCAATCACCTTCACATGGCCCATC Found at i:38636718 original size:28 final size:28 Alignment explanation

Indices: 38636678--38636734 Score: 114 Period size: 28 Copynumber: 2.0 Consensus size: 28 38636668 AGCTTGACTA 38636678 TGGCCGAACTAGGTTTTCTTTTCTTTTT 1 TGGCCGAACTAGGTTTTCTTTTCTTTTT 38636706 TGGCCGAACTAGGTTTTCTTTTCTTTTT 1 TGGCCGAACTAGGTTTTCTTTTCTTTTT 38636734 T 1 T 38636735 CCTTTCTTAT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 29 1.00 ACGTcount: A:0.11, C:0.18, G:0.18, T:0.54 Consensus pattern (28 bp): TGGCCGAACTAGGTTTTCTTTTCTTTTT Found at i:38638204 original size:24 final size:23 Alignment explanation

Indices: 38638157--38638205 Score: 62 Period size: 24 Copynumber: 2.1 Consensus size: 23 38638147 CCAATTTTAT * * 38638157 TTTTATTTTTATTTTGTTATATG 1 TTTTATTTTTATTTTCTTACATG * 38638180 TTTTATTTTTTATTTTCTTGCATG 1 TTTTA-TTTTTATTTTCTTACATG 38638204 TT 1 TT 38638206 AATAAATTTT Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 23 5 0.23 24 17 0.77 ACGTcount: A:0.14, C:0.04, G:0.08, T:0.73 Consensus pattern (23 bp): TTTTATTTTTATTTTCTTACATG Found at i:38641332 original size:20 final size:22 Alignment explanation

Indices: 38641288--38641333 Score: 60 Period size: 20 Copynumber: 2.2 Consensus size: 22 38641278 TATAAACTAT * * 38641288 ATTTCTTAATTAATTTTTTACA 1 ATTTCTTAATTAATTTTTCAAA 38641310 ATTT-TTAATT-ATTTTTCAAA 1 ATTTCTTAATTAATTTTTCAAA 38641330 ATTT 1 ATTT 38641334 AGAACAGGGG Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 20 12 0.55 21 6 0.27 22 4 0.18 ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61 Consensus pattern (22 bp): ATTTCTTAATTAATTTTTCAAA Found at i:38656499 original size:42 final size:43 Alignment explanation

Indices: 38656420--38656521 Score: 118 Period size: 42 Copynumber: 2.4 Consensus size: 43 38656410 TCCCGGACGT * ** 38656420 GGTCTTACATGTAATTCAATATCGATGCCTCTATCCCAGACAA 1 GGTCTTACATGTAAATCAATATCGATGCCAATATCCCAGACAA * * 38656463 GGTCTTACATG-AAATCAGATAT-GATGCCAATGTCCCAGACAT 1 GGTCTTACATGTAAATCA-ATATCGATGCCAATATCCCAGACAA * * 38656505 GGTCTTATACGTAAATC 1 GGTCTTACATGTAAATC 38656522 TCAATCAAGG Statistics Matches: 50, Mismatches: 7, Indels: 4 0.82 0.11 0.07 Matches are distributed among these distances: 42 30 0.60 43 20 0.40 ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29 Consensus pattern (43 bp): GGTCTTACATGTAAATCAATATCGATGCCAATATCCCAGACAA Found at i:38663500 original size:13 final size:13 Alignment explanation

Indices: 38663482--38663545 Score: 83 Period size: 13 Copynumber: 4.9 Consensus size: 13 38663472 AGTTTGGCAA * 38663482 TGCTTTTAAAAAG 1 TGCTTTTGAAAAG * 38663495 TGCTTTTGAGAAG 1 TGCTTTTGAAAAG * * 38663508 TGCTGTGGAAAAG 1 TGCTTTTGAAAAG * 38663521 TGCTTTTGAGAAG 1 TGCTTTTGAAAAG 38663534 TGCTTTTGAAAA 1 TGCTTTTGAAAA 38663546 ATTTGGTTTA Statistics Matches: 42, Mismatches: 9, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 13 42 1.00 ACGTcount: A:0.30, C:0.08, G:0.27, T:0.36 Consensus pattern (13 bp): TGCTTTTGAAAAG Found at i:38663511 original size:26 final size:26 Alignment explanation

Indices: 38663482--38663546 Score: 94 Period size: 26 Copynumber: 2.5 Consensus size: 26 38663472 AGTTTGGCAA 38663482 TGCTTTTAAAAAGTGCTTTTGAGAAG 1 TGCTTTTAAAAAGTGCTTTTGAGAAG * ** 38663508 TGCTGTGGAAAAGTGCTTTTGAGAAG 1 TGCTTTTAAAAAGTGCTTTTGAGAAG 38663534 TGCTTTTGAAAAA 1 TGCTTTT-AAAAA 38663547 TTTGGTTTAA Statistics Matches: 32, Mismatches: 6, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 26 28 0.88 27 4 0.12 ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35 Consensus pattern (26 bp): TGCTTTTAAAAAGTGCTTTTGAGAAG Found at i:38663894 original size:21 final size:20 Alignment explanation

Indices: 38663855--38663894 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 38663845 TTGTAATTAG * 38663855 TATTTTAAAAAATATTTTTT 1 TATTTTAAAAAATAATTTTT * 38663875 TATTTTAAATTAATAATTTT 1 TATTTTAAA-AAATAATTTT 38663895 AACACATTTG Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 20 9 0.53 21 8 0.47 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (20 bp): TATTTTAAAAAATAATTTTT Found at i:38667374 original size:23 final size:23 Alignment explanation

Indices: 38667332--38667375 Score: 61 Period size: 23 Copynumber: 1.9 Consensus size: 23 38667322 AAATGGAAAC * 38667332 GCCAAAGTGCTAATAACAAGAGT 1 GCCAAAGTACTAATAACAAGAGT * * 38667355 GCCAAAGTACTCATATCAAGA 1 GCCAAAGTACTAATAACAAGA 38667376 ATCCCTTATT Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 23 18 1.00 ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18 Consensus pattern (23 bp): GCCAAAGTACTAATAACAAGAGT Found at i:38667812 original size:139 final size:140 Alignment explanation

Indices: 38667562--38667839 Score: 436 Period size: 139 Copynumber: 2.0 Consensus size: 140 38667552 TAACATAATT * * 38667562 TAATAGAAATCTCACTTCATGTATTATGCCAATATCATTTTTGTCATAAATATGGTTTTTAGCCA 1 TAATAGAAACCTCACTTCATGTATTATGCCAATATAATTTTTGTCATAAATATGGTTTTTAGCCA 38667627 TTTTGTAACACCTCAAACCCAGCATAGACATTATGGCCAGATCTGAAGGTGTCACCAT-AAATCA 66 TTTTGTAACACCTCAAACCCAGCATAGACATTATGGCCAGATCTGAAGGTGTCACCATAAAATCA 38667691 ATTGAAAACA 131 ATTGAAAACA * 38667701 TAATAGAAACCTCTCTTCATGTATTATGCCAATATAATTTCTT-TCATAAATATGGTTTTTAGCC 1 TAATAGAAACCTCACTTCATGTATTATGCCAATATAATTT-TTGTCATAAATATGGTTTTTAGCC * * * * * * 38667765 ATTTTGTAACACC-CTATACCCGGCCTAGACGTTATGGTCAGATCTGAAGGTGTTACCATAAAAT 65 ATTTTGTAACACCTC-AAACCCAGCATAGACATTATGGCCAGATCTGAAGGTGTCACCATAAAAT 38667829 CAATTGAAAAC 129 CAATTGAAAAC 38667840 CCAGAATTCG Statistics Matches: 127, Mismatches: 9, Indels: 5 0.90 0.06 0.04 Matches are distributed among these distances: 138 1 0.01 139 109 0.86 140 17 0.13 ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33 Consensus pattern (140 bp): TAATAGAAACCTCACTTCATGTATTATGCCAATATAATTTTTGTCATAAATATGGTTTTTAGCCA TTTTGTAACACCTCAAACCCAGCATAGACATTATGGCCAGATCTGAAGGTGTCACCATAAAATCA ATTGAAAACA Found at i:38672934 original size:46 final size:45 Alignment explanation

Indices: 38672804--38673069 Score: 139 Period size: 46 Copynumber: 5.6 Consensus size: 45 38672794 TGTGTGAGCT * * * * * * * 38672804 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCACAATATGAGAGCC 1 AGTGTAAGACCATGTTTGGGACATGCATCAGCCTCGAGACG-TAG-C * * 38672850 AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGACGTAAGC 1 AGTGTAAGACCATGTTTGGGACATGCATCAGCCTCGAGACGT-AGC * * * * 38672896 TAGTGTAA-AACATGTTTGGGACATGCATCAG-TTGCGAGATGTATC 1 -AGTGTAAGACCATGTTTGGGACATGCATCAGCCT-CGAGACGTAGC * * * 38672941 AGTGTAAGACCACGTTTGGGACATGACATCAG-CACG-GTTATGTGAGATC 1 AGTGTAAGACCATGTTTGGGACATG-CATCAGCCTCGAG--ACGT-AG--C ** * * * 38672990 TAGTGTAAGACCATGTCCGAGACATGGCAT-TGACCTCGAAGATGATAGCC 1 -AGTGTAAGACCATGTTTGGGACAT-GCATCAG-CCTCG-AGACG-TAG-C 38673040 AGTGTAAGACCATGTTTGGGACATGGCATC 1 AGTGTAAGACCATGTTTGGGACAT-GCATC 38673070 GGCACCCCCA Statistics Matches: 175, Mismatches: 26, Indels: 34 0.74 0.11 0.14 Matches are distributed among these distances: 44 8 0.05 45 20 0.11 46 47 0.27 47 37 0.21 49 28 0.16 50 24 0.14 51 9 0.05 52 1 0.01 53 1 0.01 ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24 Consensus pattern (45 bp): AGTGTAAGACCATGTTTGGGACATGCATCAGCCTCGAGACGTAGC Found at i:38676344 original size:19 final size:17 Alignment explanation

Indices: 38676303--38676351 Score: 53 Period size: 19 Copynumber: 2.7 Consensus size: 17 38676293 CTTTTACAAA 38676303 TATAATTTATTTTTATAT 1 TATAA-TTATTTTTATAT * 38676321 CATAATTATTTTTAAATAT 1 TATAATTATTTTT--ATAT * 38676340 TATAATAATTTT 1 TATAATTATTTT 38676352 GTATGAAAAT Statistics Matches: 26, Mismatches: 3, Indels: 3 0.81 0.09 0.09 Matches are distributed among these distances: 17 8 0.31 18 4 0.15 19 14 0.54 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59 Consensus pattern (17 bp): TATAATTATTTTTATAT Found at i:38678959 original size:49 final size:49 Alignment explanation

Indices: 38678902--38679001 Score: 182 Period size: 49 Copynumber: 2.0 Consensus size: 49 38678892 ACTATGAGAA * * 38678902 ATACCGTGATGACTATTACATAATAATCCAAGAAGCATTCTCATGGTAT 1 ATACCGTGATAACTATTACATAATAATCCAAGAAGCATTATCATGGTAT 38678951 ATACCGTGATAACTATTACATAATAATCCAAGAAGCATTATCATGGTAT 1 ATACCGTGATAACTATTACATAATAATCCAAGAAGCATTATCATGGTAT 38679000 AT 1 AT 38679002 TGTTCTTTAA Statistics Matches: 49, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 49 49 1.00 ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31 Consensus pattern (49 bp): ATACCGTGATAACTATTACATAATAATCCAAGAAGCATTATCATGGTAT Found at i:38680910 original size:6 final size:6 Alignment explanation

Indices: 38680899--38680928 Score: 60 Period size: 6 Copynumber: 5.0 Consensus size: 6 38680889 CAGAATTGTA 38680899 TGCCAT TGCCAT TGCCAT TGCCAT TGCCAT 1 TGCCAT TGCCAT TGCCAT TGCCAT TGCCAT 38680929 GCTGGTGTTG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 24 1.00 ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33 Consensus pattern (6 bp): TGCCAT Found at i:38685630 original size:12 final size:13 Alignment explanation

Indices: 38685613--38685649 Score: 51 Period size: 12 Copynumber: 3.0 Consensus size: 13 38685603 GAACCGGACA 38685613 CGAACCGAA-CTC 1 CGAACCGAAGCTC 38685625 CGAACC-AAGCTC 1 CGAACCGAAGCTC * 38685637 CGAACCGTAGCTC 1 CGAACCGAAGCTC 38685650 TGATGCCACT Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 11 2 0.09 12 15 0.68 13 5 0.23 ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11 Consensus pattern (13 bp): CGAACCGAAGCTC Found at i:38689227 original size:33 final size:32 Alignment explanation

Indices: 38689183--38689244 Score: 90 Period size: 33 Copynumber: 1.9 Consensus size: 32 38689173 AAATGAAGAT 38689183 ATAATTAATAATAAATACTTGAAAT-TAGTATAA 1 ATAATTAATAATAAATA-TT-AAATATAGTATAA * 38689216 ATAATTTATAATAAATATTAAATATAGTA 1 ATAATTAATAATAAATATTAAATATAGTA 38689245 GGTAAAAAAT Statistics Matches: 27, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 31 4 0.15 32 7 0.26 33 16 0.59 ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39 Consensus pattern (32 bp): ATAATTAATAATAAATATTAAATATAGTATAA Found at i:38689886 original size:29 final size:29 Alignment explanation

Indices: 38689845--38689900 Score: 112 Period size: 29 Copynumber: 1.9 Consensus size: 29 38689835 TTTTTTAATA 38689845 AAAAAGAGATTATCAAATTATAAATCCTT 1 AAAAAGAGATTATCAAATTATAAATCCTT 38689874 AAAAAGAGATTATCAAATTATAAATCC 1 AAAAAGAGATTATCAAATTATAAATCC 38689901 AAAATAACTT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 29 27 1.00 ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29 Consensus pattern (29 bp): AAAAAGAGATTATCAAATTATAAATCCTT Found at i:38692745 original size:16 final size:15 Alignment explanation

Indices: 38692723--38692779 Score: 55 Period size: 16 Copynumber: 3.8 Consensus size: 15 38692713 AATTGGTTGA 38692723 AAAAATTATTTAATT 1 AAAAATTATTTAATT * * 38692738 GGAAAATTAATTAATT 1 -AAAAATTATTTAATT * 38692754 AAAAATAATTTAA-T 1 AAAAATTATTTAATT 38692768 AAATAA-TATTTA 1 AAA-AATTATTTA 38692780 TTTTTAAAAA Statistics Matches: 34, Mismatches: 6, Indels: 4 0.77 0.14 0.09 Matches are distributed among these distances: 14 9 0.26 15 12 0.35 16 13 0.38 ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40 Consensus pattern (15 bp): AAAAATTATTTAATT Found at i:38695662 original size:25 final size:25 Alignment explanation

Indices: 38695625--38695672 Score: 71 Period size: 25 Copynumber: 1.9 Consensus size: 25 38695615 TTGTAAATAA 38695625 GAAAAATATCTTTAGA-AATTTTTT 1 GAAAAATATCTTTAGAGAATTTTTT * 38695649 GAAATAATTTCTTTAGAGAATTTT 1 GAAA-AATATCTTTAGAGAATTTT 38695673 CTCTCTACAA Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 24 4 0.19 25 11 0.52 26 6 0.29 ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46 Consensus pattern (25 bp): GAAAAATATCTTTAGAGAATTTTTT Found at i:38698825 original size:3 final size:3 Alignment explanation

Indices: 38698817--38698841 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 38698807 CAACCCCCTT 38698817 TAA TAA TAA TAA TAA TAA TAA TAA T 1 TAA TAA TAA TAA TAA TAA TAA TAA T 38698842 TTTATTAAAA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (3 bp): TAA Found at i:38706990 original size:18 final size:19 Alignment explanation

Indices: 38706969--38707010 Score: 54 Period size: 17 Copynumber: 2.4 Consensus size: 19 38706959 AGTTTTCATT 38706969 TATGTTATTTAATTTA-AA 1 TATGTTATTTAATTTACAA * 38706987 TATG-TATTTATTTTACAA 1 TATGTTATTTAATTTACAA 38707005 -ATGTTA 1 TATGTTA 38707011 GGATTTGAAT Statistics Matches: 21, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 17 13 0.62 18 8 0.38 ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55 Consensus pattern (19 bp): TATGTTATTTAATTTACAA Found at i:38709201 original size:30 final size:30 Alignment explanation

Indices: 38709165--38709260 Score: 92 Period size: 30 Copynumber: 3.2 Consensus size: 30 38709155 AGTTTTGGAG 38709165 TAAATTTACATGAGGCTTTAAGTACTACAC 1 TAAATTTACATGAGGCTTTAAGTACTACAC * ** 38709195 TAAATTT-CAAT-ATAGCTTTTCACCTA-TACAC 1 TAAATTTAC-ATGA-GGC-TTT-AAGTACTACAC 38709226 TAAA-TTACATGAGGCTTTAAGTACTACAC 1 TAAATTTACATGAGGCTTTAAGTACTACAC * 38709255 TTAATT 1 TAAATT 38709261 CATCCGGGTA Statistics Matches: 51, Mismatches: 7, Indels: 16 0.69 0.09 0.22 Matches are distributed among these distances: 28 3 0.06 29 13 0.25 30 18 0.35 31 14 0.27 32 3 0.06 ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36 Consensus pattern (30 bp): TAAATTTACATGAGGCTTTAAGTACTACAC Found at i:38709528 original size:331 final size:331 Alignment explanation

Indices: 38708926--38709553 Score: 1024 Period size: 331 Copynumber: 1.9 Consensus size: 331 38708916 GTACATATTC * * * * 38708926 AATTCATCCGGGTAGTACTAAGATGTATTGTGACTAAAAACAGATGTGCCAGTGGCTGGGAATAA 1 AATTCATCCGGGTAGTACTAAGATGTATTGTGACTAAAAACAAATGTACCAATGGCTGAGAATAA * * * 38708991 AATAGGAAATTTTTTACTTTGTAGCTAAATGTTTGGTATGTTAGCAAGTGAAAGCCGAACATCAG 66 AATAGGAAATTTTTGACTTTGTAGCTAAATGTTTGGTATGTTAGAAAGTGAAAGCCAAACATCAG * * 38709056 GTTCCATTTGGTTTGTTACAGTTATAAATTTATGAGATTGTTAGATTGCACAGTGTACCATTGTC 131 GTTCCATTTGGTTTGTTACAGTTATAAATTTATGAGATTGTTAGATTACACAGTGTACCACTGTC * * * 38709121 CATTATTTCTGATCGCGATCTGAGGTTTACTTCTAGTTTTGGAGTAAATTTACATGAGGCTTTAA 196 CATTATTTCTAATCGCAATCTGAGGTTTACTTCCAGTTTTGGAGTAAATTTACATGAGGCTTTAA 38709186 GTACTACACTAAATTTCAATATAGCTTTTCACCTATACACTAAATTACATGAGGCTTTAAGTACT 261 GTACTACACTAAATTTCAATATAGCTTTTCACCTATACACTAAATTACATGAGGCTTTAAGTACT 38709251 ACACTT 326 ACACTT * * * 38709257 AATTCATCCGGGTAGTACTAAGATGTATTGTGACTGAAAACAAATGTACTAATGGCTGAGAATGA 1 AATTCATCCGGGTAGTACTAAGATGTATTGTGACTAAAAACAAATGTACCAATGGCTGAGAATAA * * * * * 38709322 AATAGGAAATTTTTGACTTTGTAGCTAAGTGTTTGGTATTTTAGAAAGTGAAAGTCAAAGAT-TG 66 AATAGGAAATTTTTGACTTTGTAGCTAAATGTTTGGTATGTTAGAAAGTGAAAGCCAAACATCAG * ** 38709386 TGTTCCATTTGGTTTGTTACAGTTATACATTTATGAGATTGTTAGATTACATGGTGTACCACTGT 131 -GTTCCATTTGGTTTGTTACAGTTATAAATTTATGAGATTGTTAGATTACACAGTGTACCACTGT 38709451 CCATTATTTCTAATCGCAATCTGAGGTTTACTTCCAGTTTTGGAGTAAATTTACATGAGGCTTTA 195 CCATTATTTCTAATCGCAATCTGAGGTTTACTTCCAGTTTTGGAGTAAATTTACATGAGGCTTTA * 38709516 AGTATTACACTAAATTTCAATATAGCTTTTCACCTATA 260 AGTACTACACTAAATTTCAATATAGCTTTTCACCTATA 38709554 GACAGAAGAC Statistics Matches: 272, Mismatches: 24, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 330 1 0.00 331 271 1.00 ACGTcount: A:0.31, C:0.14, G:0.19, T:0.37 Consensus pattern (331 bp): AATTCATCCGGGTAGTACTAAGATGTATTGTGACTAAAAACAAATGTACCAATGGCTGAGAATAA AATAGGAAATTTTTGACTTTGTAGCTAAATGTTTGGTATGTTAGAAAGTGAAAGCCAAACATCAG GTTCCATTTGGTTTGTTACAGTTATAAATTTATGAGATTGTTAGATTACACAGTGTACCACTGTC CATTATTTCTAATCGCAATCTGAGGTTTACTTCCAGTTTTGGAGTAAATTTACATGAGGCTTTAA GTACTACACTAAATTTCAATATAGCTTTTCACCTATACACTAAATTACATGAGGCTTTAAGTACT ACACTT Found at i:38713547 original size:40 final size:40 Alignment explanation

Indices: 38713468--38713644 Score: 180 Period size: 40 Copynumber: 4.5 Consensus size: 40 38713458 CGGATGATAA * * ** * 38713468 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT * * * * * 38713508 CCGGGCTATGTCCCAAAGGCATTTATGCTA-ATGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATG-CTATAT * * 38713548 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT * * * 38713588 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT 38713628 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 38713645 ATACTTGGGT Statistics Matches: 116, Mismatches: 18, Indels: 7 0.82 0.13 0.05 Matches are distributed among these distances: 38 1 0.01 39 15 0.13 40 98 0.84 41 2 0.02 ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT Found at i:38713607 original size:80 final size:80 Alignment explanation

Indices: 38713468--38713644 Score: 234 Period size: 80 Copynumber: 2.2 Consensus size: 80 38713458 CGGATGATAA * * * * 38713468 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCAAAGGCATTTA 1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCAAAGGCATTTA * 38713533 TGCTA-ATGATTATAT 66 TGCGAGATG-TTATAT * * * 38713548 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTG 1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCAAAGGCATTTA * 38713613 TGCGAGTTGTTATAT 66 TGCGAGATGTTATAT 38713628 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 38713645 ATACTTGGGT Statistics Matches: 86, Mismatches: 9, Indels: 5 0.86 0.09 0.05 Matches are distributed among these distances: 78 1 0.01 79 13 0.15 80 70 0.81 81 2 0.02 ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26 Consensus pattern (80 bp): CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCAAAGGCATTTA TGCGAGATGTTATAT Found at i:38713913 original size:22 final size:22 Alignment explanation

Indices: 38713873--38713914 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 38713863 GAATGTGCAT * 38713873 ATATGAAGTTATTCATTTAGCC 1 ATATGAAGTTATACATTTAGCC 38713895 ATATGAATGTTATAC-TTTAG 1 ATATGAA-GTTATACATTTAG 38713915 TCAAAACTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 12 0.67 23 6 0.33 ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43 Consensus pattern (22 bp): ATATGAAGTTATACATTTAGCC Found at i:38721533 original size:40 final size:40 Alignment explanation

Indices: 38721454--38721630 Score: 189 Period size: 40 Copynumber: 4.5 Consensus size: 40 38721444 CGGATGATAA * * ** * 38721454 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT * * * * 38721494 CCGGGCTATGTCCCGAAGGCATTTATGCTA-ATGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATG-CTATAT * * 38721534 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT * * * 38721574 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT 38721614 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 38721631 ATACTTGGGT Statistics Matches: 118, Mismatches: 16, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 38 1 0.01 39 15 0.13 40 100 0.85 41 2 0.02 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTATGCGAGATGCTATAT Found at i:38721592 original size:80 final size:80 Alignment explanation

Indices: 38721454--38721630 Score: 243 Period size: 80 Copynumber: 2.2 Consensus size: 80 38721444 CGGATGATAA * * * * 38721454 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA 1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA * 38721519 TGCTA-ATGATTATAT 66 TGCGAGATG-TTATAT * * 38721534 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTG 1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA * 38721599 TGCGAGTTGTTATAT 66 TGCGAGATGTTATAT 38721614 CC-GGCTAA-ATCCCGAAG 1 CCGGGCTAAGA-CCCGAAG 38721631 ATACTTGGGT Statistics Matches: 87, Mismatches: 8, Indels: 5 0.87 0.08 0.05 Matches are distributed among these distances: 78 1 0.01 79 13 0.15 80 71 0.82 81 2 0.02 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (80 bp): CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA TGCGAGATGTTATAT Found at i:38721899 original size:22 final size:22 Alignment explanation

Indices: 38721859--38721900 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 38721849 GAATGTGCAT * 38721859 ATATGAAGTTATTCATTTAGCC 1 ATATGAAGTTATACATTTAGCC 38721881 ATATGAATGTTATAC-TTTAG 1 ATATGAA-GTTATACATTTAG 38721901 TCAAAACTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 12 0.67 23 6 0.33 ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43 Consensus pattern (22 bp): ATATGAAGTTATACATTTAGCC Found at i:38725527 original size:60 final size:60 Alignment explanation

Indices: 38725461--38725579 Score: 220 Period size: 60 Copynumber: 2.0 Consensus size: 60 38725451 ATAATTTAAA * 38725461 AAGTTCTTGAAAATTATTGGGCTTTAGAAATATTTATAAAAAAGATTTTAAAATTTTATT 1 AAGTTCTTGAAAATTATTGGGCTTTAGAAATATTTATAAAAAAGATTTTAAAAATTTATT * 38725521 AAGTTCTTGAAAGTTATTGGGCTTTAGAAATATTTATAAAAAAGATTTTAAAAATTTAT 1 AAGTTCTTGAAAATTATTGGGCTTTAGAAATATTTATAAAAAAGATTTTAAAAATTTAT 38725580 CTAATAAAAT Statistics Matches: 57, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 60 57 1.00 ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42 Consensus pattern (60 bp): AAGTTCTTGAAAATTATTGGGCTTTAGAAATATTTATAAAAAAGATTTTAAAAATTTATT Found at i:38726139 original size:10 final size:9 Alignment explanation

Indices: 38726046--38726139 Score: 66 Period size: 9 Copynumber: 9.9 Consensus size: 9 38726036 ATATTTTTTA 38726046 TATAAAAAT 1 TATAAAAAT * 38726055 TATTAAAAT 1 TATAAAAAT * * 38726064 GATAAAATT 1 TATAAAAAT 38726073 TATAAAAAAAT 1 TAT--AAAAAT * 38726084 TATTAAAAT 1 TATAAAAAT 38726093 T-TAAAAATTT 1 TATAAAAA--T 38726103 ATATAAAAAAT 1 -TAT-AAAAAT * 38726114 TACAAAAA- 1 TATAAAAAT 38726122 TATAAAAAT 1 TATAAAAAT 38726131 TATAGAAAA 1 TATA-AAAA 38726140 AGAATATTAA Statistics Matches: 66, Mismatches: 10, Indels: 17 0.71 0.11 0.18 Matches are distributed among these distances: 8 12 0.18 9 31 0.47 10 7 0.11 11 10 0.15 12 1 0.02 13 5 0.08 ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33 Consensus pattern (9 bp): TATAAAAAT Found at i:38726153 original size:30 final size:28 Alignment explanation

Indices: 38726043--38726167 Score: 126 Period size: 29 Copynumber: 4.3 Consensus size: 28 38726033 TTGATATTTT * * 38726043 TTATATAAAAATTATTAAAATGATAAAAT 1 TTATAAAAAAATTATTAAAAT-ATAAAAA * 38726072 TTATAAAAAAATTATTAAAATTTAAAAA 1 TTATAAAAAAATTATTAAAATATAAAAA ** 38726100 TTTATATAAAAAATTACAAAAATATAAAAA 1 -TTATA-AAAAAATTATTAAAATATAAAAA * 38726130 TTATAGAAAAAGAATATTAAAATA-ACAAAA 1 TTATA-AAAAA-ATTATTAAAATATA-AAAA * 38726160 TTAGAAAA 1 TTATAAAA 38726168 TAGTATAGAA Statistics Matches: 81, Mismatches: 11, Indels: 8 0.81 0.11 0.08 Matches are distributed among these distances: 28 5 0.06 29 39 0.48 30 37 0.46 ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31 Consensus pattern (28 bp): TTATAAAAAAATTATTAAAATATAAAAA Found at i:38726569 original size:27 final size:25 Alignment explanation

Indices: 38726532--38726590 Score: 73 Period size: 27 Copynumber: 2.3 Consensus size: 25 38726522 AAAATTGTAA * * 38726532 ATATTTTAAATTTTATATAAATTTT 1 ATATTTTAAATTCTAAATAAATTTT * 38726557 ATTATTTTAAAATTCTAAATAATTTTT 1 A-TATTTT-AAATTCTAAATAAATTTT 38726584 ATATTTT 1 ATATTTT 38726591 CTATTATAAT Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 25 1 0.03 26 12 0.41 27 16 0.55 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59 Consensus pattern (25 bp): ATATTTTAAATTCTAAATAAATTTT Found at i:38726580 original size:26 final size:26 Alignment explanation

Indices: 38726532--38726590 Score: 68 Period size: 26 Copynumber: 2.3 Consensus size: 26 38726522 AAAATTGTAA * * 38726532 ATATTTTAAATTTTATATAAA-TTTT 1 ATATTTTAAATTCTAAATAAATTTTT 38726557 ATTATTTTAAAATTCTAAAT-AATTTTT 1 A-TATTTT-AAATTCTAAATAAATTTTT 38726584 ATATTTT 1 ATATTTT 38726591 CTATTATAAT Statistics Matches: 29, Mismatches: 2, Indels: 5 0.81 0.06 0.14 Matches are distributed among these distances: 25 1 0.03 26 14 0.48 27 14 0.48 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59 Consensus pattern (26 bp): ATATTTTAAATTCTAAATAAATTTTT Found at i:38726612 original size:21 final size:21 Alignment explanation

Indices: 38726575--38726614 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 38726565 AAAATTCTAA * 38726575 ATAATTTTTATATTTTCTATT 1 ATAATTTTTATACTTTCTATT 38726596 ATAA-TTTTATGACTTTCTA 1 ATAATTTTTAT-ACTTTCTA 38726615 ATGATTTTAT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 6 0.35 21 11 0.65 ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60 Consensus pattern (21 bp): ATAATTTTTATACTTTCTATT Found at i:38734274 original size:23 final size:22 Alignment explanation

Indices: 38734242--38734285 Score: 61 Period size: 23 Copynumber: 2.0 Consensus size: 22 38734232 AAAAAATTAA * 38734242 ATATTAAATTATATTTTATATTT 1 ATATTAAATTACATTTT-TATTT * 38734265 ATATTGAATTACATTTTTATT 1 ATATTAAATTACATTTTTATT 38734286 ATAATTTAAA Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 22 4 0.21 23 15 0.79 ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59 Consensus pattern (22 bp): ATATTAAATTACATTTTTATTT Found at i:38735071 original size:9 final size:9 Alignment explanation

Indices: 38735057--38735081 Score: 50 Period size: 9 Copynumber: 2.8 Consensus size: 9 38735047 TTAGTGTTCA 38735057 AATTGATAG 1 AATTGATAG 38735066 AATTGATAG 1 AATTGATAG 38735075 AATTGAT 1 AATTGAT 38735082 TAAAAAGTAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36 Consensus pattern (9 bp): AATTGATAG Found at i:38741772 original size:30 final size:30 Alignment explanation

Indices: 38741736--38742023 Score: 142 Period size: 30 Copynumber: 9.7 Consensus size: 30 38741726 GGTTGTTTCC * 38741736 ATCCCTTTCCATAGTTCGATAGCCGAAGCT 1 ATCCCTTTTCATAGTTCGATAGCCGAAGCT * * * * 38741766 ATCCCTTTTCATAGTTCGATGGTCGCCA-CC 1 ATCCCTTTTCATAGTTCGATAGCCG-AAGCT * * ** * * 38741796 ATCCCTTTTCATTGTT-GATGGTTGCCATC- 1 ATCCCTTTTCATAGTTCGATAGCCG-AAGCT * * * * * 38741825 ATCCCTTTTCATAATTAGATAACCAAAACT 1 ATCCCTTTTCATAGTTCGATAGCCGAAGCT * ** * 38741855 ATCCTTTTTCATTTTTCGATAACCGAAGCT 1 ATCCCTTTTCATAGTTCGATAGCCGAAGCT * * * 38741885 ATCCTTTTTAATAGTTCGATAGTCGAAGCT 1 ATCCCTTTTCATAGTTCGATAGCCGAAGCT * * * * * 38741915 ATCCCTTTTCATAATTCAATGGTC-ATCA-CC 1 ATCCCTTTTCATAGTTCGATAGCCGA--AGCT * * * * * * 38741945 ATCCTTTTTCATTGTT-GATGGTCGTCA-CC 1 ATCCCTTTTCATAGTTCGATAGCCG-AAGCT * * 38741974 ATCCCTTTTCATATTTTGATAGCCGAAGCT 1 ATCCCTTTTCATAGTTCGATAGCCGAAGCT 38742004 ATCCCTTTTCACTAG-TCGAT 1 ATCCCTTTTCA-TAGTTCGAT 38742024 GATCGTCGAT Statistics Matches: 200, Mismatches: 47, Indels: 22 0.74 0.17 0.08 Matches are distributed among these distances: 29 50 0.25 30 146 0.73 31 4 0.02 ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39 Consensus pattern (30 bp): ATCCCTTTTCATAGTTCGATAGCCGAAGCT Found at i:38741952 original size:29 final size:29 Alignment explanation

Indices: 38741915--38741986 Score: 90 Period size: 29 Copynumber: 2.4 Consensus size: 29 38741905 AGTCGAAGCT 38741915 ATCCCTTTTCATAATTCAATGGTCATCACC 1 ATCCCTTTTCATAATT-AATGGTCATCACC * ** * * 38741945 ATCCTTTTTCATTGTTGATGGTCGTCACC 1 ATCCCTTTTCATAATTAATGGTCATCACC 38741974 ATCCCTTTTCATA 1 ATCCCTTTTCATA 38741987 TTTTGATAGC Statistics Matches: 35, Mismatches: 7, Indels: 1 0.81 0.16 0.02 Matches are distributed among these distances: 29 22 0.63 30 13 0.37 ACGTcount: A:0.21, C:0.28, G:0.10, T:0.42 Consensus pattern (29 bp): ATCCCTTTTCATAATTAATGGTCATCACC Found at i:38742023 original size:149 final size:149 Alignment explanation

Indices: 38741746--38742023 Score: 394 Period size: 149 Copynumber: 1.9 Consensus size: 149 38741736 ATCCCTTTCC * * * 38741746 ATAGTTCGATAGCCGAAGCTATCCCTTTTCATAGTTCGATGGTCGCCACCATCCCTTTTCATTGT 1 ATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCAATGGTCACCACCATCCCTTTTCATTGT * * * * ** 38741811 TGATGGTTGCCATCATCCCTTTTCATAATTAGATAACCAAAACTATCCTTTTTCATTTTTCGATA 66 TGATGGTCGCCACCATCCCTTTTCATAATTAGATAACCAAAACTATCCCTTTTCACTAGTCGATA 38741876 ACCGAAGCTATCCTTTTTA 131 ACCGAAGCTATCCTTTTTA * * * 38741895 ATAGTTCGATAGTCGAAGCTATCCCTTTTCATAATTCAATGGTCATCACCATCCTTTTTCATTGT 1 ATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCAATGGTCACCACCATCCCTTTTCATTGT * * * * * * 38741960 TGATGGTCGTCACCATCCCTTTTCATATTTTGATAGCCGAAGCTATCCCTTTTCACTAGTCGAT 66 TGATGGTCGCCACCATCCCTTTTCATAATTAGATAACCAAAACTATCCCTTTTCACTAGTCGAT 38742024 GATCGTCGAT Statistics Matches: 111, Mismatches: 18, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 149 111 1.00 ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38 Consensus pattern (149 bp): ATAGTTCGATAGCCGAAGCTATCCCTTTTCATAATTCAATGGTCACCACCATCCCTTTTCATTGT TGATGGTCGCCACCATCCCTTTTCATAATTAGATAACCAAAACTATCCCTTTTCACTAGTCGATA ACCGAAGCTATCCTTTTTA Found at i:38742821 original size:12 final size:13 Alignment explanation

Indices: 38742799--38742830 Score: 57 Period size: 12 Copynumber: 2.5 Consensus size: 13 38742789 TTGTTTTTGT 38742799 TTTACTTTATTTA 1 TTTACTTTATTTA 38742812 TTTA-TTTATTTA 1 TTTACTTTATTTA 38742824 TTTACTT 1 TTTACTT 38742831 AATTAACCTT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 12 12 0.67 13 6 0.33 ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72 Consensus pattern (13 bp): TTTACTTTATTTA Found at i:38743390 original size:21 final size:20 Alignment explanation

Indices: 38743359--38743398 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 20 38743349 CCCATGAAAC 38743359 AGGGCACACGC-CTGTGTGGA 1 AGGGCACACGCTC-GTGTGGA 38743379 AGGGCAACACGCTCGTGTGG 1 AGGGC-ACACGCTCGTGTGG 38743399 TCATTATAAC Statistics Matches: 18, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 20 5 0.28 21 12 0.67 22 1 0.06 ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15 Consensus pattern (20 bp): AGGGCACACGCTCGTGTGGA Found at i:38750402 original size:45 final size:44 Alignment explanation

Indices: 38750337--38750465 Score: 176 Period size: 45 Copynumber: 2.9 Consensus size: 44 38750327 TCGTACAGTA 38750337 ATATTCGGGCCTTTCAGCCTAGCAGGCTACAATGCCGGTGAAAT- 1 ATATTCGGGCC-TTCAGCCTAGCAGGCTACAATGCCGGTGAAATG 38750381 ACTATTCGGGCCTTCGAGCCTAGCAGGCTACAATGCCGGTGAAATG 1 A-TATTCGGGCCTTC-AGCCTAGCAGGCTACAATGCCGGTGAAATG * * 38750427 ATA-TCGGG-CTTCAAGCCTAGCAGGCGA-AATGTCGGTGAA 1 ATATTCGGGCCTTC-AGCCTAGCAGGCTACAATGCCGGTGAA 38750466 TGAACTCGGG Statistics Matches: 79, Mismatches: 3, Indels: 8 0.88 0.03 0.09 Matches are distributed among these distances: 42 11 0.14 43 17 0.22 44 9 0.11 45 41 0.52 46 1 0.01 ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22 Consensus pattern (44 bp): ATATTCGGGCCTTCAGCCTAGCAGGCTACAATGCCGGTGAAATG Found at i:38750487 original size:41 final size:41 Alignment explanation

Indices: 38750354--38750505 Score: 137 Period size: 41 Copynumber: 3.6 Consensus size: 41 38750344 GGCCTTTCAG ** * 38750354 CCTAGCAGGCTACAATGCCGGTGAAAT-ACTATTCGGGCCTTCGAG 1 CCTAGCAGGCTA-AATGCCGGTG-AATGA-TA-TCGGG-CTTAAAA * * 38750399 CCTAGCAGGCTACAATGCCGGTGAAATGATATCGGGCTTCAAG 1 CCTAGCAGGCTA-AATGCCGGTG-AATGATATCGGGCTTAAAA * * * 38750442 CCTAGCAGGCGAAATGTCGGTGAATGA-ACTCGGGTTTAAAA 1 CCTAGCAGGCTAAATGCCGGTGAATGATA-TCGGGCTTAAAA * 38750483 CCTAGTAGGCTAAATGCCGGTGA 1 CCTAGCAGGCTAAATGCCGGTGA 38750506 TTTGATTTAA Statistics Matches: 96, Mismatches: 9, Indels: 8 0.85 0.08 0.07 Matches are distributed among these distances: 40 1 0.01 41 34 0.35 42 9 0.09 43 17 0.18 44 5 0.05 45 29 0.30 46 1 0.01 ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22 Consensus pattern (41 bp): CCTAGCAGGCTAAATGCCGGTGAATGATATCGGGCTTAAAA Found at i:38751023 original size:16 final size:18 Alignment explanation

Indices: 38750992--38751024 Score: 52 Period size: 16 Copynumber: 1.9 Consensus size: 18 38750982 AACTCGTCAC 38750992 ACTATCTATCATTTTGGT 1 ACTATCTATCATTTTGGT 38751010 ACTA-CTAT-ATTTTGG 1 ACTATCTATCATTTTGG 38751025 AGCTAGTATG Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 7 0.47 17 4 0.27 18 4 0.27 ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48 Consensus pattern (18 bp): ACTATCTATCATTTTGGT Found at i:38755549 original size:49 final size:49 Alignment explanation

Indices: 38755460--38755682 Score: 172 Period size: 49 Copynumber: 4.7 Consensus size: 49 38755450 GGGTTAAGAC * * * * 38755460 GCCGGTGCCATGTCCCGGACACGGTCTTACACTAGCTTTCATATAGCGAG 1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTGGATTTCATATAGCGAG * * * * 38755510 GCCGATGCCATGTCCCAGACAAGTCTTACACTGGATTTCATCTATCGAT 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGATTTCATATAGCGAG * * * * * * 38755559 GTCGATGCCATGTCCTAGACAGGTCTTACACT-GA---CACACAAC-AA 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGATTTCATATAGCGAG ** * * * * * * * 38755603 GTTGACGCCATGTCTCAGACAGGTCTTACACTAGCTTGT-ATATCGTGGG 1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGATT-TCATATAGCGAG 38755652 GCCGATG-CATGTCCCAGACAGGTCTTACACT 1 GCCGATGCCATGTCCCAGACAGGTCTTACACT 38755683 ACCTCTCGTC Statistics Matches: 135, Mismatches: 32, Indels: 14 0.75 0.18 0.08 Matches are distributed among these distances: 44 29 0.21 45 5 0.04 48 27 0.20 49 55 0.41 50 19 0.14 ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26 Consensus pattern (49 bp): GCCGATGCCATGTCCCAGACAGGTCTTACACTGGATTTCATATAGCGAG Found at i:38755776 original size:46 final size:47 Alignment explanation

Indices: 38755468--38755786 Score: 192 Period size: 46 Copynumber: 6.8 Consensus size: 47 38755458 ACGCCGGTGC * * * 38755468 CATGTCCCGGACACGGTCTTACACTAGCTTTCATATAGC-GAGGCCGATG 1 CATGTCCCAGACA-GGTCTTACACTAGCTCTCATAT--CTGTGGCCGATG * * * * * 38755517 CCATGTCCCAGACAAGTCTTACACTGGATTTCATCTATC-GAT-GTCGATG 1 -CATGTCCCAGACAGGTCTTACACTAGCTCTCA--TATCTG-TGGCCGATG * * * * * * * 38755566 CCATGTCCTAGACAGGTCTTACACT-GACACACA-A-CAAGTTGACG--C 1 -CATGTCCCAGACAGGTCTTACACTAG-CTCTCATATC-TGTGGCCGATG * * * 38755611 CATGTCTCAGACAGGTCTTACACTAGCT-TGTATATCGTGGGGCCGATG 1 CATGTCCCAGACAGGTCTTACACTAGCTCT-CATATC-TGTGGCCGATG * * * ** 38755659 CATGTCCCAGACAGGTCTTACACTACCTCTCGTCTCAAT-GCCGATG 1 CATGTCCCAGACAGGTCTTACACTAGCTCTCATATCTGTGGCCGATG * ** 38755705 CATGTCCCAGACATGTCTTACACTAGCTCTCATAT-TGTGGCTAATG 1 CATGTCCCAGACAGGTCTTACACTAGCTCTCATATCTGTGGCCGATG * * * 38755751 CATGTCCCAGACATGTCTTACACTAGCACACATATC 1 CATGTCCCAGACAGGTCTTACACTAGCTCTCATATC 38755787 ACCGATTATC Statistics Matches: 210, Mismatches: 43, Indels: 35 0.73 0.15 0.12 Matches are distributed among these distances: 44 24 0.11 45 4 0.02 46 83 0.40 47 4 0.02 48 30 0.14 49 50 0.24 50 12 0.06 51 3 0.01 ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27 Consensus pattern (47 bp): CATGTCCCAGACAGGTCTTACACTAGCTCTCATATCTGTGGCCGATG Found at i:38762631 original size:46 final size:44 Alignment explanation

Indices: 38762559--38762783 Score: 141 Period size: 46 Copynumber: 4.8 Consensus size: 44 38762549 GGTTAATTGA * * * * 38762559 GTGCTAGTGTAAGATATGTCTAGGACATGCATCGGCCT-CGAGAT 1 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTACAAGAT * * 38762603 GTAAGCCAGTGTATGACATGTCTGGGACATGTATCGGCTACAAGAT 1 GT--GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGAT * * * * * 38762649 GTGTCAGTGTAAGACCATGTCTGGGACATGGCTTCAGC-ACGGATAT 1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAC-AAGAT * ** * 38762695 GTGAGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCAACTTA-ATGGAT 1 GT----GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TACA-AGAT * 38762746 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC 1 GTGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC 38762784 ATTATACCTT Statistics Matches: 146, Mismatches: 22, Indels: 23 0.76 0.12 0.12 Matches are distributed among these distances: 44 12 0.08 45 18 0.12 46 45 0.31 47 33 0.23 50 34 0.23 51 3 0.02 52 1 0.01 ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25 Consensus pattern (44 bp): GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTACAAGAT Found at i:38762715 original size:50 final size:47 Alignment explanation

Indices: 38762646--38762780 Score: 182 Period size: 47 Copynumber: 2.8 Consensus size: 47 38762636 TCGGCTACAA * * 38762646 GATGTGTCAGTGTAAGACCATGTCTGGGACATGGCTTCAGCACGGATATG 1 GATGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCA--ACGGA-ATG ** 38762696 TGA-GAGTCAGTGTAAGACCATGTCTGGGACATGGCATCAACTTAATG 1 -GATGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCAACGGAATG * 38762743 GATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC 1 GATGAGTCAGTGTAAGACCATGTCTGGGACATGGCATC 38762781 GGCATTATAC Statistics Matches: 78, Mismatches: 5, Indels: 6 0.88 0.06 0.07 Matches are distributed among these distances: 46 2 0.03 47 37 0.47 48 3 0.04 50 34 0.44 51 2 0.03 ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24 Consensus pattern (47 bp): GATGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCAACGGAATG Found at i:38785078 original size:28 final size:28 Alignment explanation

Indices: 38785023--38785078 Score: 69 Period size: 28 Copynumber: 2.0 Consensus size: 28 38785013 ACAGGGTTTT * * 38785023 TCACACGGCTTGACACATGCCCGTGTCCC 1 TCACACGGCATGACACA-GCCCATGTCCC 38785052 TCACACGGCCATGACAC-GCCCATGTCC 1 TCACACGG-CATGACACAGCCCATGTCC 38785079 TGGCCCGTGT Statistics Matches: 24, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 28 9 0.38 29 8 0.33 30 7 0.29 ACGTcount: A:0.20, C:0.43, G:0.20, T:0.18 Consensus pattern (28 bp): TCACACGGCATGACACAGCCCATGTCCC Found at i:38787908 original size:93 final size:93 Alignment explanation

Indices: 38787749--38787919 Score: 279 Period size: 93 Copynumber: 1.8 Consensus size: 93 38787739 GCCCCTAAGT * * * * 38787749 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA 38787814 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * * * 38787842 GAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA 38787907 CGAGTTCGGATGC 66 CGAGTTCGGATGC 38787920 TCAACCATCC Statistics Matches: 71, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 93 71 1.00 ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:38787909 original size:46 final size:46 Alignment explanation

Indices: 38787744--38787913 Score: 175 Period size: 46 Copynumber: 3.7 Consensus size: 46 38787734 AACCCGCCCC * * * * * * 38787744 TAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA * * * * 38787790 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C- 1 TAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC-ATTTGCATCCA * * 38787838 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA 38787883 TAAGTGAACTCGGACTCAACTCAACGAGTTC 1 TAAGTGAACTCGGACTCAACTCAACGAGTTC 38787914 GGATGCTCAA Statistics Matches: 101, Mismatches: 16, Indels: 14 0.77 0.12 0.11 Matches are distributed among these distances: 43 6 0.06 44 3 0.03 45 3 0.03 46 54 0.53 47 26 0.26 48 2 0.02 49 3 0.03 50 4 0.04 ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA Found at i:38794161 original size:21 final size:21 Alignment explanation

Indices: 38794137--38794181 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 38794127 CTACTAGTAG * 38794137 AACT-GGGAGTTCTACCGATAC 1 AACTCGGG-GTTCTACCAATAC * 38794158 AACTCTGGGTTCTACCAATAC 1 AACTCGGGGTTCTACCAATAC 38794179 AAC 1 AAC 38794182 GCAGACTTCA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 21 19 0.90 22 2 0.10 ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24 Consensus pattern (21 bp): AACTCGGGGTTCTACCAATAC Found at i:38794749 original size:20 final size:20 Alignment explanation

Indices: 38794724--38794791 Score: 136 Period size: 20 Copynumber: 3.4 Consensus size: 20 38794714 TTTAAGAGCC 38794724 ACACGCCCGTGTGGCTTGGG 1 ACACGCCCGTGTGGCTTGGG 38794744 ACACGCCCGTGTGGCTTGGG 1 ACACGCCCGTGTGGCTTGGG 38794764 ACACGCCCGTGTGGCTTGGG 1 ACACGCCCGTGTGGCTTGGG 38794784 ACACGCCC 1 ACACGCCC 38794792 CTGTAGGTAG Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 48 1.00 ACGTcount: A:0.12, C:0.34, G:0.37, T:0.18 Consensus pattern (20 bp): ACACGCCCGTGTGGCTTGGG Found at i:38796043 original size:42 final size:42 Alignment explanation

Indices: 38795931--38796134 Score: 230 Period size: 42 Copynumber: 4.8 Consensus size: 42 38795921 TACCATACCA * * * 38795931 ATGCCATATCCCAGATATGGTCTTACATG-GGATCTCGTATCG 1 ATGCCATATCCCAGATATGGTCTTACACGTAG-TCTCATATCG * * * * 38795973 ATGCCAACAGCCCAGCTATGGTCTTACACGAAGTCTCATATCG 1 ATGCC-ATATCCCAGATATGGTCTTACACGTAGTCTCATATCG ** * 38796016 ATGCCATATCTTAGATATGGTCTTACACGTAGTCTCATATTG 1 ATGCCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG * * * 38796058 ATGCCATATCCCAAATATGGTCTTATACGTAGTCTCATATTG 1 ATGCCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG * * * * 38796100 ATGCTATATCCCAGTTATGGTCCTACATGTAGTCT 1 ATGCCATATCCCAGATATGGTCTTACACGTAGTCT 38796135 TAGTAACCCT Statistics Matches: 137, Mismatches: 23, Indels: 4 0.84 0.14 0.02 Matches are distributed among these distances: 42 102 0.74 43 34 0.25 44 1 0.01 ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33 Consensus pattern (42 bp): ATGCCATATCCCAGATATGGTCTTACACGTAGTCTCATATCG Found at i:38803159 original size:43 final size:43 Alignment explanation

Indices: 38803067--38803226 Score: 128 Period size: 43 Copynumber: 3.7 Consensus size: 43 38803057 ATTAACGAGT ** 38803067 TGTGATTATATGTAAGACCATGTCTGGGAAATTGGCACCATTA 1 TGTGATTACGTGTAAGACCATGTCTGGGAAATTGGCACCATTA * * * 38803110 TGTGATTACGTGTAAGACCATGTCTGGGACATT-GCAATCGTTA 1 TGTGATTACGTGTAAGACCATGTCTGGGAAATTGGC-ACCATTA * * * ** * 38803153 TTTGATTTCGTGTGAGACCATAGT-TGGGCTATTGGCATCGA-TA 1 TGTGATTACGTGTAAGACCAT-GTCTGGGAAATTGGCA-CCATTA * * * 38803196 TGTGATATAACATGTAAGACTATATCTGGGA 1 TGTGAT-T-ACGTGTAAGACCATGTCTGGGA 38803227 TATGGCATTG Statistics Matches: 90, Mismatches: 20, Indels: 12 0.74 0.16 0.10 Matches are distributed among these distances: 42 2 0.02 43 68 0.76 44 6 0.07 45 14 0.16 ACGTcount: A:0.28, C:0.14, G:0.25, T:0.34 Consensus pattern (43 bp): TGTGATTACGTGTAAGACCATGTCTGGGAAATTGGCACCATTA Found at i:38805295 original size:18 final size:18 Alignment explanation

Indices: 38805272--38805310 Score: 78 Period size: 18 Copynumber: 2.2 Consensus size: 18 38805262 AACCCTAGGT 38805272 AAGAGAAAAGAAACTTTC 1 AAGAGAAAAGAAACTTTC 38805290 AAGAGAAAAGAAACTTTC 1 AAGAGAAAAGAAACTTTC 38805308 AAG 1 AAG 38805311 GCCTAATTGG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 21 1.00 ACGTcount: A:0.56, C:0.10, G:0.18, T:0.15 Consensus pattern (18 bp): AAGAGAAAAGAAACTTTC Found at i:38818883 original size:27 final size:27 Alignment explanation

Indices: 38818845--38818937 Score: 150 Period size: 27 Copynumber: 3.4 Consensus size: 27 38818835 TTAAGATCCC 38818845 GATTTGTAAAATTATCGAAATACCCCT 1 GATTTGTAAAATTATCGAAATACCCCT * 38818872 GATTTGTGAAATTATCGAAATACCCCT 1 GATTTGTAAAATTATCGAAATACCCCT * * 38818899 AATTTGTAAAATTATCGAAATACCCCC 1 GATTTGTAAAATTATCGAAATACCCCT * 38818926 GATTTATAAAAT 1 GATTTGTAAAAT 38818938 GACTATAATT Statistics Matches: 60, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 27 60 1.00 ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33 Consensus pattern (27 bp): GATTTGTAAAATTATCGAAATACCCCT Found at i:38818962 original size:27 final size:27 Alignment explanation

Indices: 38818932--38819129 Score: 184 Period size: 27 Copynumber: 7.3 Consensus size: 27 38818922 CCCCGATTTA ** * 38818932 TAAAATGACTATAATTA-CCCTGTAGCG 1 TAAAATGACCGTAA-TACCCCTGTAGGG * * * 38818959 TAAAATGGCTGTAATACCCCTATAGGG 1 TAAAATGACCGTAATACCCCTGTAGGG * * 38818986 TAAAATAACCGTATTACCCCTGTAGGG 1 TAAAATGACCGTAATACCCCTGTAGGG 38819013 TAAAATGACCGTAATACCCCTGTAGGG 1 TAAAATGACCGTAATACCCCTGTAGGG * * 38819040 TAAAATGACCAG-AATACCCTTATAGGG 1 TAAAATGACC-GTAATACCCCTGTAGGG ** * * 38819067 TACGATTACCGTAATACCCCTATAGGG 1 TAAAATGACCGTAATACCCCTGTAGGG * * ** ** 38819094 TAAAATAATCGTAATACCATTGTTTGG 1 TAAAATGACCGTAATACCCCTGTAGGG 38819121 TAAAATGAC 1 TAAAATGAC 38819130 GATTATGCCC Statistics Matches: 140, Mismatches: 28, Indels: 6 0.80 0.16 0.03 Matches are distributed among these distances: 26 3 0.02 27 136 0.97 28 1 0.01 ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27 Consensus pattern (27 bp): TAAAATGACCGTAATACCCCTGTAGGG Found at i:38819017 original size:81 final size:81 Alignment explanation

Indices: 38818932--38819099 Score: 205 Period size: 81 Copynumber: 2.1 Consensus size: 81 38818922 CCCCGATTTA * * * 38818932 TAAAATGACTATAATTA-CCCTGTAGCGTAAAATG-GCTGTAATACCCCTATAGGGTAAAATAAC 1 TAAAATGACCATAA-TACCCCTGTAGCGTAAAATGACCAG-AATACCCCTATAGGGTAAAATAAC * * 38818995 CGTATTACCCCTGTAGGG 64 CGTAATACCCCTATAGGG * * * ** * 38819013 TAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCAGAATACCCTTATAGGGTACGATTACCG 1 TAAAATGACCATAATACCCCTGTAGCGTAAAATGACCAGAATACCCCTATAGGGTAAAATAACCG 38819078 TAATACCCCTATAGGG 66 TAATACCCCTATAGGG 38819094 TAAAAT 1 TAAAAT 38819100 AATCGTAATA Statistics Matches: 74, Mismatches: 11, Indels: 4 0.83 0.12 0.04 Matches are distributed among these distances: 80 2 0.03 81 70 0.95 82 2 0.03 ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26 Consensus pattern (81 bp): TAAAATGACCATAATACCCCTGTAGCGTAAAATGACCAGAATACCCCTATAGGGTAAAATAACCG TAATACCCCTATAGGG Found at i:38819107 original size:81 final size:82 Alignment explanation

Indices: 38818949--38819129 Score: 213 Period size: 81 Copynumber: 2.2 Consensus size: 82 38818939 ACTATAATTA * * * * * 38818949 CCCTGTAGCGTAAAATG-GCTGTAATACCCCTATAGGGTAAAATAACCGTATTACCCCTGTAGGG 1 CCCTGTAGGGTAAAATGACCAGTAATACCCCTATAGGGTAAAATAACCGTAATACCCCTATAGGG * 38819013 TAAAATGACCGTAATAC 66 TAAAATAACCGTAATAC * ** * 38819030 CCCTGTAGGGTAAAATGACCAG-AATACCCTTATAGGGTACGATTACCGTAATACCCCTATAGGG 1 CCCTGTAGGGTAAAATGACCAGTAATACCCCTATAGGGTAAAATAACCGTAATACCCCTATAGGG * 38819094 TAAAATAATCGTAATAC 66 TAAAATAACCGTAATAC ** ** 38819111 CATTGTTTGGTAAAATGAC 1 CCCTGTAGGGTAAAATGAC 38819130 GATTATGCCC Statistics Matches: 84, Mismatches: 15, Indels: 2 0.83 0.15 0.02 Matches are distributed among these distances: 81 82 0.98 82 2 0.02 ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26 Consensus pattern (82 bp): CCCTGTAGGGTAAAATGACCAGTAATACCCCTATAGGGTAAAATAACCGTAATACCCCTATAGGG TAAAATAACCGTAATAC Found at i:38819382 original size:26 final size:26 Alignment explanation

Indices: 38819344--38819400 Score: 78 Period size: 26 Copynumber: 2.2 Consensus size: 26 38819334 TTTGCCACAT * * 38819344 TTATTGTTTCTGGTAGCTATGCTGCG 1 TTATTATTACTGGTAGCTATGCTGCG * 38819370 TTATTATTACTGGTAGCTTTGCTGCG 1 TTATTATTACTGGTAGCTATGCTGCG * 38819396 ATATT 1 TTATT 38819401 GGTGTGCTGG Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 26 27 1.00 ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47 Consensus pattern (26 bp): TTATTATTACTGGTAGCTATGCTGCG Found at i:38823741 original size:40 final size:40 Alignment explanation

Indices: 38823648--38823864 Score: 298 Period size: 40 Copynumber: 5.5 Consensus size: 40 38823638 AAGCCAAGTA * * * 38823648 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG 1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG * * 38823686 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 38823726 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * 38823766 CCTTCGGGACTTAGCCCAGATATAGTAGCTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG * * * 38823806 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG 1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG 38823846 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 38823865 TTATCATCCA Statistics Matches: 162, Mismatches: 13, Indels: 6 0.90 0.07 0.03 Matches are distributed among these distances: 38 12 0.07 39 18 0.11 40 132 0.81 ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG Found at i:38826206 original size:27 final size:27 Alignment explanation

Indices: 38826163--38826273 Score: 100 Period size: 27 Copynumber: 4.1 Consensus size: 27 38826153 GGTCGTTAAG * 38826163 ACCCC-AATTTTTAAAATTACCGAAAT 1 ACCCCTAATTTGTAAAATTACCGAAAT * 38826189 ACCCCTAATTTGTGAAATTACCGAAAT 1 ACCCCTAATTTGTAAAATTACCGAAAT * * * * ** 38826216 GCCTCTGATTTGTATAATTACAAAAAT 1 ACCCCTAATTTGTAAAATTACCGAAAT ** * 38826243 ACCCCCGATTTGTAAAATAACC-ATAAT 1 ACCCCTAATTTGTAAAATTACCGA-AAT 38826270 ACCC 1 ACCC 38826274 TTATAGGGTA Statistics Matches: 68, Mismatches: 15, Indels: 3 0.79 0.17 0.03 Matches are distributed among these distances: 26 6 0.09 27 62 0.91 ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30 Consensus pattern (27 bp): ACCCCTAATTTGTAAAATTACCGAAAT Done.