Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_D10

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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33

Warning! 869813 characters in sequence are not A, C, G, or T


File 136 of 218

Found at i:41441538 original size:101 final size:101

Alignment explanation

Indices: 41441402--41441614 Score: 309 Period size: 101 Copynumber: 2.1 Consensus size: 101 41441392 CATAGCCTTG * * * * 41441402 CCATGGTCTTATGTTCATAGTGCCATAACCCAGTTATAGTCTTACCATCAGAATGCCATAGCCCA 1 CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATAGTCTTACCATCAAAATGCCATAACCCA * * 41441467 GCTATGGTCTTACATATAAACACTACCATGGTCTAA 66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA * ** * * 41441503 CCATTGTCTTACGTCCATAGTGTTATAACTCAGTTATGGTCTTACCATCAAAATGCCATAACCCA 1 CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATAGTCTTACCATCAAAATGCCATAACCCA * * 41441568 GCAATGGTCTTACATATATACACTGCCATGGTCCAA 66 GCAATGGTCTTACATATAAACACTACCATGGTCCAA 41441604 CCATGGTCTTA 1 CCATGGTCTTA 41441615 AATACTTCAA Statistics Matches: 98, Mismatches: 14, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 101 98 1.00 ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31 Consensus pattern (101 bp): CCATGGTCTTACGTCCATAGTGCCATAACCCAGTTATAGTCTTACCATCAAAATGCCATAACCCA GCAATGGTCTTACATATAAACACTACCATGGTCCAA Found at i:41441650 original size:27 final size:27 Alignment explanation

Indices: 41441610--41441684 Score: 141 Period size: 27 Copynumber: 2.8 Consensus size: 27 41441600 CCAACCATGG 41441610 TCTTAAATACTTCAATTTTTTTATTAT 1 TCTTAAATACTTCAATTTTTTTATTAT * 41441637 TTTTAAATACTTCAATTTTTTTATTAT 1 TCTTAAATACTTCAATTTTTTTATTAT 41441664 TCTTAAATACTTCAATTTTTT 1 TCTTAAATACTTCAATTTTTT 41441685 AATTTCTTTT Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 27 46 1.00 ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60 Consensus pattern (27 bp): TCTTAAATACTTCAATTTTTTTATTAT Found at i:41451591 original size:24 final size:25 Alignment explanation

Indices: 41451564--41451678 Score: 90 Period size: 25 Copynumber: 4.6 Consensus size: 25 41451554 GTACATGTAT * 41451564 GCTCATATGAGCTGTA-AACGGTAA 1 GCTCATATGAGCTGAATAACGGTAA * * * 41451588 GCTCCTCTGAGTTGAATAACGGTAA 1 GCTCATATGAGCTGAATAACGGTAA * ** * 41451613 GCTCCT-TCGAGAGGAATAATGGTAA 1 GCTCATAT-GAGCTGAATAACGGTAA * * * * 41451638 GCTCATACGAGTTGAGTAATGGTAA 1 GCTCATATGAGCTGAATAACGGTAA * 41451663 GCTCATAAGAGCTGAA 1 GCTCATATGAGCTGAA 41451679 ATTGGTAACC Statistics Matches: 73, Mismatches: 15, Indels: 5 0.78 0.16 0.05 Matches are distributed among these distances: 24 13 0.18 25 60 0.82 ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25 Consensus pattern (25 bp): GCTCATATGAGCTGAATAACGGTAA Found at i:41451667 original size:25 final size:25 Alignment explanation

Indices: 41451583--41451686 Score: 95 Period size: 25 Copynumber: 4.2 Consensus size: 25 41451573 AGCTGTAAAC * * 41451583 GGTAAGCTCCT-CTGAGTTGAATAAC 1 GGTAAGCTCATAC-GAGTTGAATAAT * * ** 41451608 GGTAAGCTCCTTCGAGAGGAATAAT 1 GGTAAGCTCATACGAGTTGAATAAT * 41451633 GGTAAGCTCATACGAGTTGAGTAAT 1 GGTAAGCTCATACGAGTTGAATAAT * * * 41451658 GGTAAGCTCATAAGAGCTGAA-ATT 1 GGTAAGCTCATACGAGTTGAATAAT 41451682 GGTAA 1 GGTAA 41451687 CCCTAATGAC Statistics Matches: 66, Mismatches: 12, Indels: 3 0.81 0.15 0.04 Matches are distributed among these distances: 24 7 0.11 25 58 0.88 26 1 0.02 ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26 Consensus pattern (25 bp): GGTAAGCTCATACGAGTTGAATAAT Found at i:41455329 original size:122 final size:123 Alignment explanation

Indices: 41455112--41455416 Score: 405 Period size: 122 Copynumber: 2.5 Consensus size: 123 41455102 TCGCGGTGTT * * * * * 41455112 TATGGAAAAAATACTGCTATTACTTTACCTTTTATGGCGTTTATGGGCAAAACGCCACTATTGCT 1 TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTATTGCT * 41455177 TTACCTTTTGTGGCGTTTATGGGAAAAATGCCGCTATTGC-TTACCTTTTACAGCGTG 66 TTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTACAGCGTG * * * 41455234 TATGGGAAAAACACCGCTATTGCTTTACCTTTTGTGGCATTTATGGGCAAAATGCCGCTATTGCT 1 TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTATTGCT * * * * * 41455299 TTACCTTTTGTGGCATTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGCGGTGTT 66 TTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTACAGCGTG * * * * * * * * 41455357 TATGGGCAATATACCACTATTTCTTTACCTTTTGCGGCATTTATAGGAAAAATTCCACTA 1 TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTA 41455417 ATGGTATATA Statistics Matches: 158, Mismatches: 24, Indels: 1 0.86 0.13 0.01 Matches are distributed among these distances: 122 95 0.60 123 63 0.40 ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37 Consensus pattern (123 bp): TATGGGAAAAATACCGCTATTACTTTACCTTTTGTGGCATTTATGGGCAAAATGCCACTATTGCT TTACCTTTTGTGGCATTTATGGGAAAAATGCCGCTATTGCTTTACCTTTTACAGCGTG Found at i:41455416 original size:41 final size:41 Alignment explanation

Indices: 41455109--41455409 Score: 343 Period size: 41 Copynumber: 7.4 Consensus size: 41 41455099 AATTCGCGGT ** * * * * 41455109 GTTTATGGAAAAAATACTGCTATTACTTTACCTTTTATGGC 1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC * * 41455150 GTTTATGGGCAAAACGCCACTATTGCTTTACCTTTTGTGGC 1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC * *** 41455191 GTTTATGGGAAAAATGCCGCTATTGC-TTACCTTTTACAGC 1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC * * ** 41455231 GTGTATGGGAAAAACACCGCTATTGCTTTACCTTTTGTGGC 1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC * 41455272 ATTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC 1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC * * * 41455313 ATTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGCGGT 1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC * * * * * 41455354 GTTTATGGGCAATATACCACTATTTCTTTACCTTTTGCGGC 1 GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC * * * 41455395 ATTTATAGGAAAAAT 1 GTTTATGGGCAAAAT 41455410 TCCACTAATG Statistics Matches: 222, Mismatches: 37, Indels: 2 0.85 0.14 0.01 Matches are distributed among these distances: 40 34 0.15 41 188 0.85 ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38 Consensus pattern (41 bp): GTTTATGGGCAAAATGCCGCTATTGCTTTACCTTTTGTGGC Found at i:41467001 original size:40 final size:39 Alignment explanation

Indices: 41466957--41467139 Score: 199 Period size: 40 Copynumber: 4.6 Consensus size: 39 41466947 TGACCATATT * 41466957 CGGACTAAGATCCAAAGGCATTTGTGCGAGATACTAAATC 1 CGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATC * * 41466997 CGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTT 1 CGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATC * * * 41467037 CGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC 1 CGGACTAAGTCCGAAGGCATTTGTGCGAGATACTAAATC * ** * 41467076 TGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-C 1 CGGACTAAGT-CCGAAGGCATTTGTGCGAGATACTA-AATC * 41467116 CAGG-CTATGTCCCGAAGGCATTTG 1 C-GGACTAAGT-CCGAAGGCATTTG 41467140 AACGAGGAGC Statistics Matches: 126, Mismatches: 14, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 39 33 0.26 40 89 0.71 41 4 0.03 ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26 Consensus pattern (39 bp): CGGACTAAGTCCGAAGGCATTTGTGCGAGATACTAAATC Found at i:41467062 original size:39 final size:39 Alignment explanation

Indices: 41466917--41467139 Score: 191 Period size: 40 Copynumber: 5.6 Consensus size: 39 41466907 GAATGATGTC * * * 41466917 CGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATT 1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGA-T-ACTA-ATT * * * * 41466957 CGGACTAAGATCCAAAGGCATTTGTGCGAGATACTAAATC 1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACT-AATT * * 41466997 CGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTT 1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAA-TT * * 41467037 CGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAAT 1 CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAATT * * * ** 41467075 CTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC 1 C-GGGCTAAGACCCGAAGGCATTTGTGCGAGATACTA-ATT * * * 41467116 CAGGCTATGTCCCGAAGGCATTTG 1 CGGGCTAAGACCCGAAGGCATTTG 41467140 AACGAGGAGC Statistics Matches: 158, Mismatches: 18, Indels: 14 0.83 0.09 0.07 Matches are distributed among these distances: 38 2 0.01 39 34 0.22 40 108 0.68 41 13 0.08 42 1 0.01 ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26 Consensus pattern (39 bp): CGGGCTAAGACCCGAAGGCATTTGTGCGAGATACTAATT Found at i:41467122 original size:79 final size:80 Alignment explanation

Indices: 41466971--41467139 Score: 218 Period size: 79 Copynumber: 2.1 Consensus size: 80 41466961 CTAAGATCCA * 41466971 AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATT 1 AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATA * * 41467036 TCGGGCTAAG-CCCG 66 CCAGGCTAAGTCCCG * * ** * 41467050 AAGGCATTTGTGCGAGTTACTAAATCTGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACT-AT 1 AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT * 41467113 AACCAGGCTATGTCCCG 65 -ACCAGGCTAAGTCCCG 41467130 AAGGCATTTG 1 AAGGCATTTG 41467140 AACGAGGAGC Statistics Matches: 78, Mismatches: 9, Indels: 5 0.85 0.10 0.05 Matches are distributed among these distances: 78 3 0.04 79 61 0.78 80 14 0.18 ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27 Consensus pattern (80 bp): AAGGCATTTGTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATA CCAGGCTAAGTCCCG Found at i:41467161 original size:79 final size:79 Alignment explanation

Indices: 41467008--41467162 Score: 172 Period size: 79 Copynumber: 2.0 Consensus size: 79 41466998 GGACTAAGAT ** * ** * 41467008 CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA 1 CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA * 41467073 ATCTGGGTTAAGTC 66 ATCTCGGTTAAGTC * * 41467087 CCGAAGGCATTTGTGCGAGTTACT-ATAACCAGGCTATGTCCCGAAGGCATTTGAACGAG-GAGC 1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCAGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-C * 41467150 TATATC-CGGTTAA 63 TAAATCTCGGTTAA 41467163 ATTTCGAAGG Statistics Matches: 63, Mismatches: 10, Indels: 6 0.80 0.13 0.08 Matches are distributed among these distances: 78 2 0.03 79 37 0.59 80 24 0.38 ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26 Consensus pattern (79 bp): CCGAAGGCATTTGTGCGAGATACTAATACCAGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA ATCTCGGTTAAGTC Found at i:41483099 original size:40 final size:40 Alignment explanation

Indices: 41483015--41483198 Score: 196 Period size: 40 Copynumber: 4.6 Consensus size: 40 41483005 TTGAATGCTG * * * * 41483015 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT ** * 41483054 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT 1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT * * * 41483095 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT * * 41483135 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT 41483175 TCCGGGTTAAGTCCCGAAGGCATT 1 TCCGGGTTAAGTCCCGAAGGCATT 41483199 GAATGAGTTA Statistics Matches: 123, Mismatches: 16, Indels: 10 0.83 0.11 0.07 Matches are distributed among these distances: 39 2 0.02 40 111 0.90 41 10 0.08 ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28 Consensus pattern (40 bp): TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT Found at i:41483152 original size:80 final size:81 Alignment explanation

Indices: 41483015--41483195 Score: 221 Period size: 80 Copynumber: 2.3 Consensus size: 81 41483005 TTGAATGCTG * * * 41483015 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT 1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT * * 41483079 TGTGCGAGTTATT-AAT 66 CGTGCGAGTT-TTAAAA ** 41483095 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC 1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC 41483156 ATTCGTGCGAGTTTTAAAA 63 ATTCGTGCGAGTTTTAAAA 41483175 TCCGGGTTAAGTCCCGAAGGC 1 TCCGGGTTAAGTCCCGAAGGC 41483196 ATTGAATGAG Statistics Matches: 89, Mismatches: 7, Indels: 10 0.84 0.07 0.09 Matches are distributed among these distances: 79 4 0.04 80 76 0.85 81 9 0.10 ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28 Consensus pattern (81 bp): TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT CGTGCGAGTTTTAAAA Found at i:41483219 original size:39 final size:38 Alignment explanation

Indices: 41483096--41483245 Score: 131 Period size: 40 Copynumber: 3.8 Consensus size: 38 41483086 GTTATTAATT * ** * * 41483096 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT 1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A ** * 41483136 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA 1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA * 41483175 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA 1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA * * 41483215 CCGGGCTATGTCCCGAAGGCACTTGAACGAG 1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG 41483246 GAGCTATCCG Statistics Matches: 93, Mismatches: 11, Indels: 12 0.80 0.09 0.10 Matches are distributed among these distances: 39 30 0.32 40 63 0.68 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (38 bp): CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA Found at i:41490935 original size:40 final size:40 Alignment explanation

Indices: 41490851--41491034 Score: 196 Period size: 40 Copynumber: 4.6 Consensus size: 40 41490841 TTGAATGCTG * * * * 41490851 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT ** * 41490890 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT 1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT * * * 41490931 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT * * 41490971 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT 41491011 TCCGGGTTAAGTCCCGAAGGCATT 1 TCCGGGTTAAGTCCCGAAGGCATT 41491035 GAATGAGTTA Statistics Matches: 123, Mismatches: 16, Indels: 10 0.83 0.11 0.07 Matches are distributed among these distances: 39 2 0.02 40 111 0.90 41 10 0.08 ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28 Consensus pattern (40 bp): TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT Found at i:41490988 original size:80 final size:81 Alignment explanation

Indices: 41490851--41491031 Score: 221 Period size: 80 Copynumber: 2.3 Consensus size: 81 41490841 TTGAATGCTG * * * 41490851 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT 1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT * * 41490915 TGTGCGAGTTATT-AAT 66 CGTGCGAGTT-TTAAAA ** 41490931 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC 1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC 41490992 ATTCGTGCGAGTTTTAAAA 63 ATTCGTGCGAGTTTTAAAA 41491011 TCCGGGTTAAGTCCCGAAGGC 1 TCCGGGTTAAGTCCCGAAGGC 41491032 ATTGAATGAG Statistics Matches: 89, Mismatches: 7, Indels: 10 0.84 0.07 0.09 Matches are distributed among these distances: 79 4 0.04 80 76 0.85 81 9 0.10 ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28 Consensus pattern (81 bp): TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT CGTGCGAGTTTTAAAA Found at i:41491055 original size:39 final size:38 Alignment explanation

Indices: 41490932--41491081 Score: 131 Period size: 40 Copynumber: 3.8 Consensus size: 38 41490922 GTTATTAATT * ** * * 41490932 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT 1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A ** * 41490972 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA 1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA * 41491011 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA 1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA * * 41491051 CCGGGCTATGTCCCGAAGGCACTTGAACGAG 1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG 41491082 GAGCTAATCC Statistics Matches: 93, Mismatches: 11, Indels: 12 0.80 0.09 0.10 Matches are distributed among these distances: 39 30 0.32 40 63 0.68 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (38 bp): CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA Found at i:41493131 original size:22 final size:22 Alignment explanation

Indices: 41493100--41493163 Score: 67 Period size: 22 Copynumber: 2.9 Consensus size: 22 41493090 GCCAGTAACC * 41493100 AGAATGGCTAAGAGCCATAAAT 1 AGAATAGCTAAGAGCCATAAAT * * 41493122 AGGATAGCTATA-AGCTATAAAT 1 AGAATAGCTA-AGAGCCATAAAT * * 41493144 AGAATGGCTACGAGCCATAA 1 AGAATAGCTAAGAGCCATAA 41493164 GTTCAGTAAT Statistics Matches: 33, Mismatches: 7, Indels: 4 0.75 0.16 0.09 Matches are distributed among these distances: 22 32 0.97 23 1 0.03 ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20 Consensus pattern (22 bp): AGAATAGCTAAGAGCCATAAAT Found at i:41493334 original size:27 final size:27 Alignment explanation

Indices: 41493298--41493364 Score: 91 Period size: 27 Copynumber: 2.5 Consensus size: 27 41493288 GTATCGCAAT * 41493298 AAAGCTACCAGTAACAGT-ATATGTGGC 1 AAAGCCACCAGTAACAGTGAT-TGTGGC * 41493325 CAAGCCACCAGTAACAGTGATTGTGGC 1 AAAGCCACCAGTAACAGTGATTGTGGC * 41493352 AAAACCACCAGTA 1 AAAGCCACCAGTA 41493365 TAGTACTTCC Statistics Matches: 35, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 27 33 0.94 28 2 0.06 ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18 Consensus pattern (27 bp): AAAGCCACCAGTAACAGTGATTGTGGC Found at i:41493546 original size:27 final size:26 Alignment explanation

Indices: 41493485--41493550 Score: 78 Period size: 27 Copynumber: 2.5 Consensus size: 26 41493475 AAAAAAATCA * * 41493485 ATCATTTACCCTTCAGGGGCATTACGG 1 ATCATTTACCCTCCAGAGGCATTAC-G * * 41493512 TTAATTTACCCTCCAGAGGCATTACG 1 ATCATTTACCCTCCAGAGGCATTACG 41493538 ATCATTTTACCCT 1 ATCA-TTTACCCT 41493551 ATAAGGGCAT Statistics Matches: 32, Mismatches: 6, Indels: 2 0.80 0.15 0.05 Matches are distributed among these distances: 26 3 0.09 27 29 0.91 ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33 Consensus pattern (26 bp): ATCATTTACCCTCCAGAGGCATTACG Found at i:41493571 original size:27 final size:27 Alignment explanation

Indices: 41493541--41493655 Score: 126 Period size: 27 Copynumber: 4.3 Consensus size: 27 41493531 CATTACGATC * 41493541 ATTTTACCCTATAAGGGCATTTCAGTA 1 ATTTTACCCTATAAGGGTATTTCAGTA * 41493568 ATTTTA-CCTAGTGAGGGTATTTCAGTA 1 ATTTTACCCTA-TAAGGGTATTTCAGTA * * ** 41493595 ATCTTACCC-ATCAGGGGTATTTTTGTA 1 ATTTTACCCTAT-AAGGGTATTTCAGTA * * 41493622 ATTTTACCCTTTAAGGGTATTTTAGTA 1 ATTTTACCCTATAAGGGTATTTCAGTA 41493649 ATTTTAC 1 ATTTTAC 41493656 AACCTTTCCG Statistics Matches: 73, Mismatches: 11, Indels: 8 0.79 0.12 0.09 Matches are distributed among these distances: 26 5 0.07 27 65 0.89 28 3 0.04 ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43 Consensus pattern (27 bp): ATTTTACCCTATAAGGGTATTTCAGTA Found at i:41497949 original size:9 final size:9 Alignment explanation

Indices: 41497932--41497968 Score: 65 Period size: 9 Copynumber: 4.1 Consensus size: 9 41497922 TGAGTTTTCG 41497932 AATTCGAAT 1 AATTCGAAT * 41497941 AACTCGAAT 1 AATTCGAAT 41497950 AATTCGAAT 1 AATTCGAAT 41497959 AATTCGAAT 1 AATTCGAAT 41497968 A 1 A 41497969 TCAAACTATA 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:0.46, C:0.14, G:0.11, T:0.30 Consensus pattern (9 bp): AATTCGAAT Found at i:41498216 original size:30 final size:31 Alignment explanation

Indices: 41498182--41498241 Score: 86 Period size: 30 Copynumber: 2.0 Consensus size: 31 41498172 AAACCTTTTA * 41498182 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC 1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC * * 41498212 TTTTCCCCTAAAACTTTTATTCCCTTCCCA 1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA 41498242 TCCCACCTCC Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 30 21 0.81 31 5 0.19 ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40 Consensus pattern (31 bp): TTTTCCCCCAAAACTTTTACTCCCTTCCCAC Found at i:41498368 original size:21 final size:21 Alignment explanation

Indices: 41498339--41498378 Score: 55 Period size: 20 Copynumber: 1.9 Consensus size: 21 41498329 TCCCTCAAAC 41498339 TTTTATTCCCCAAAACTTTTTA 1 TTTTATT-CCCAAAACTTTTTA * 41498361 TTTT-TTCCCTAAACTTTT 1 TTTTATTCCCAAAACTTTT 41498379 ACTTCTCACC Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 11 0.65 21 2 0.12 22 4 0.24 ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55 Consensus pattern (21 bp): TTTTATTCCCAAAACTTTTTA Found at i:41509460 original size:18 final size:18 Alignment explanation

Indices: 41509437--41509476 Score: 53 Period size: 18 Copynumber: 2.2 Consensus size: 18 41509427 GATGTGTGCT * * * 41509437 TTTGTCCTATCTCCTATC 1 TTTGTCCAAACTCCTATA 41509455 TTTGTCCAAACTCCTATA 1 TTTGTCCAAACTCCTATA 41509473 TTTG 1 TTTG 41509477 AACATCTGTC Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.17, C:0.28, G:0.07, T:0.47 Consensus pattern (18 bp): TTTGTCCAAACTCCTATA Found at i:41511552 original size:12 final size:12 Alignment explanation

Indices: 41511514--41511555 Score: 50 Period size: 12 Copynumber: 3.5 Consensus size: 12 41511504 ATTGGTCATA 41511514 GAGAGATTTGAG 1 GAGAGATTTGAG * * 41511526 GAGGGATATT-TG 1 GAGAGAT-TTGAG 41511538 GAGAGATTTGAG 1 GAGAGATTTGAG 41511550 GAGAGA 1 GAGAGA 41511556 ATATTGGGAT Statistics Matches: 24, Mismatches: 4, Indels: 4 0.75 0.12 0.12 Matches are distributed among these distances: 11 2 0.08 12 20 0.83 13 2 0.08 ACGTcount: A:0.33, C:0.00, G:0.43, T:0.24 Consensus pattern (12 bp): GAGAGATTTGAG Found at i:41511562 original size:24 final size:24 Alignment explanation

Indices: 41511514--41511560 Score: 76 Period size: 24 Copynumber: 1.9 Consensus size: 24 41511504 ATTGGTCATA * 41511514 GAGAGATTTGAGGAGGGATATTTG 1 GAGAGATTTGAGGAGGAATATTTG 41511538 GAGAGATTTGAGGAGAGAATATT 1 GAGAGATTTGAGGAG-GAATATT 41511561 GGGATTTGGG Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 24 15 0.71 25 6 0.29 ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28 Consensus pattern (24 bp): GAGAGATTTGAGGAGGAATATTTG Found at i:41514411 original size:25 final size:25 Alignment explanation

Indices: 41514383--41514461 Score: 65 Period size: 25 Copynumber: 3.3 Consensus size: 25 41514373 CTAATGGCCG 41514383 ATGTGATGAATGTGAAAGTGTATAT 1 ATGTGATGAATGTGAAAGTGTATAT * *** **** 41514408 ATGTGAT-AAGGCCTAA-TG-GCCG 1 ATGTGATGAATGTGAAAGTGTATAT 41514430 ATGTGATGAATGTGAAAGTGTATAT 1 ATGTGATGAATGTGAAAGTGTATAT 41514455 ATGTGAT 1 ATGTGAT 41514462 AAGGCCTAAT Statistics Matches: 35, Mismatches: 16, Indels: 6 0.61 0.28 0.11 Matches are distributed among these distances: 22 7 0.20 23 7 0.20 24 7 0.20 25 14 0.40 ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33 Consensus pattern (25 bp): ATGTGATGAATGTGAAAGTGTATAT Found at i:41514416 original size:47 final size:47 Alignment explanation

Indices: 41514335--41514647 Score: 521 Period size: 47 Copynumber: 6.7 Consensus size: 47 41514325 TTAGGATTCT * * * 41514335 ATGTGATGGATGATGAACA-TGCATATATGAGATAAGGCCTAATGGCCG 1 ATGTGATGAATG-TGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG 41514383 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * 41514430 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 41514477 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 41514524 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG 41514571 ATGTGATGAATGTGAAAGTG--TATA--T-ATAAGGCCTAATGGCCG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG * 41514613 ATGTGATGAATGTGAAAGTGTATAAATGTGATAAG 1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG 41514648 TCCCGAAGGG Statistics Matches: 253, Mismatches: 6, Indels: 13 0.93 0.02 0.05 Matches are distributed among these distances: 42 37 0.15 43 1 0.00 44 3 0.01 45 4 0.02 46 2 0.01 47 195 0.77 48 11 0.04 ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29 Consensus pattern (47 bp): ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG Found at i:41514822 original size:37 final size:37 Alignment explanation

Indices: 41514766--41514844 Score: 122 Period size: 37 Copynumber: 2.1 Consensus size: 37 41514756 CCGAGCTCTA * * * 41514766 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT 1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT * 41514803 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT 1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT 41514840 AAGAC 1 AAGAC 41514845 TTCGTAATAA Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25 Consensus pattern (37 bp): AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT Found at i:41516038 original size:14 final size:15 Alignment explanation

Indices: 41516011--41516049 Score: 57 Period size: 14 Copynumber: 2.8 Consensus size: 15 41516001 AATGTAAATG 41516011 ATATGCTA-ATGTGT 1 ATATGCTACATGTGT 41516025 AT-TGCTACATGTGT 1 ATATGCTACATGTGT 41516039 ATATG-TACATG 1 ATATGCTACATG 41516050 AGAATTGAGA Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 13 5 0.22 14 16 0.70 15 2 0.09 ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41 Consensus pattern (15 bp): ATATGCTACATGTGT Found at i:41516302 original size:40 final size:40 Alignment explanation

Indices: 41516059--41516290 Score: 311 Period size: 40 Copynumber: 5.8 Consensus size: 40 41516049 GAGAATTGAG * 41516059 AGTGATATATCCGGGCTATGTCCCGAAGAGCATTCGTGCT 1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT * * 41516099 AGTGATATATCCGGACTAAGTTCCGAAGAGCATTCGTGCT 1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT * * * 41516139 AGTGATATATCCAGGTTAAATCCCGAAGAGCATTCGTGCT 1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT * * * * * 41516179 AATGATGTATCCGGACTAAGTTCCAAAGAGCATTCGTGCT 1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT * ** 41516219 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT 1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT * * * 41516259 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA 1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA 41516291 ATCATGCTGG Statistics Matches: 162, Mismatches: 30, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 40 162 1.00 ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26 Consensus pattern (40 bp): AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT Found at i:41518391 original size:19 final size:19 Alignment explanation

Indices: 41518359--41518399 Score: 55 Period size: 19 Copynumber: 2.2 Consensus size: 19 41518349 CATGGGCTTA * * 41518359 GGCCGTAATGGGCCATATG 1 GGCCGAAATAGGCCATATG * 41518378 GGCCGAAATAGGCCATGTG 1 GGCCGAAATAGGCCATATG 41518397 GGC 1 GGC 41518400 TCAATGGGCT Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17 Consensus pattern (19 bp): GGCCGAAATAGGCCATATG Found at i:41518662 original size:27 final size:27 Alignment explanation

Indices: 41518632--41518847 Score: 270 Period size: 27 Copynumber: 8.0 Consensus size: 27 41518622 GATAAATTAT * 41518632 CGAAATACCCCCATAAGGTAAAATGAC 1 CGAAATACCCCCATAGGGTAAAATGAC * * 41518659 CGAAATACCTCCATAGGGTAAAATGAT 1 CGAAATACCCCCATAGGGTAAAATGAC * * 41518686 TGAAATACCCCCATAGTGTAAAATGAC 1 CGAAATACCCCCATAGGGTAAAATGAC * * * 41518713 CAAAATACCCTCATAGGGTAGAATGAC 1 CGAAATACCCCCATAGGGTAAAATGAC * 41518740 CGAAATACCCCCATAGGGTAGAATGAC 1 CGAAATACCCCCATAGGGTAAAATGAC * ** * 41518767 CAAAATACCCTTAATAGGGTAAAATGAT 1 CGAAATACCC-CCATAGGGTAAAATGAC * 41518795 CGAAATACCCTCATAGGGTAAAATGAC 1 CGAAATACCCCCATAGGGTAAAATGAC * * * 41518822 CAAAATAACCCCATAAGGTAAAATGA 1 CGAAATACCCCCATAGGGTAAAATGA 41518848 TTTTTATACC Statistics Matches: 162, Mismatches: 26, Indels: 2 0.85 0.14 0.01 Matches are distributed among these distances: 27 140 0.86 28 22 0.14 ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19 Consensus pattern (27 bp): CGAAATACCCCCATAGGGTAAAATGAC Found at i:41518719 original size:54 final size:53 Alignment explanation

Indices: 41518625--41518848 Score: 304 Period size: 54 Copynumber: 4.1 Consensus size: 53 41518615 AGAGGTCGAT * * * 41518625 AAATTATCGAAATACCCCCATAAGGTAAAATGACCGAAATACCTCCATAGGGTA 1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACC-CCATAGGGTA * * 41518679 AAATGATTGAAATACCCCCATAGTGTAAAATGACCAAAATACCCTCATAGGGTA 1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC-CATAGGGTA * * * * 41518733 GAATGACCGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTA 1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACCC--CATAGGGTA * * 41518788 AAATGATCGAAATACCCTCATAGGGTAAAATGACCAAAATAACCCCATAAGGTA 1 AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAAT-ACCCCATAGGGTA 41518842 AAATGAT 1 AAATGAT 41518849 TTTTATACCC Statistics Matches: 150, Mismatches: 17, Indels: 6 0.87 0.10 0.03 Matches are distributed among these distances: 53 1 0.01 54 100 0.67 55 45 0.30 56 4 0.03 ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20 Consensus pattern (53 bp): AAATGATCGAAATACCCCCATAGGGTAAAATGACCAAAATACCCCATAGGGTA Found at i:41518888 original size:109 final size:109 Alignment explanation

Indices: 41518632--41518847 Score: 319 Period size: 109 Copynumber: 2.0 Consensus size: 109 41518622 GATAAATTAT * * * ** * 41518632 CGAAATACCCCCATAAGGTAAAATGACCGAAATA-CCTCCATAGGGTAAAATGATTGAAATACCC 1 CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC * * * 41518696 CCATAGTGTAAAATGACCAAAATACCCTCATAGGGTAGAATGAC 66 CCATAGGGTAAAATGACCAAAATACCCTCATAAGGTAAAATGAC 41518740 CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC 1 CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC * 41518805 TCATAGGGTAAAATGACCAAAATAACCC-CATAAGGTAAAATGA 66 CCATAGGGTAAAATGACCAAAAT-ACCCTCATAAGGTAAAATGA 41518848 TTTTTATACC Statistics Matches: 96, Mismatches: 10, Indels: 3 0.88 0.09 0.03 Matches are distributed among these distances: 108 31 0.32 109 61 0.64 110 4 0.04 ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19 Consensus pattern (109 bp): CGAAATACCCCCATAGGGTAGAATGACCAAAATACCCTTAATAGGGTAAAATGATCGAAATACCC CCATAGGGTAAAATGACCAAAATACCCTCATAAGGTAAAATGAC Found at i:41519261 original size:28 final size:28 Alignment explanation

Indices: 41519216--41519363 Score: 201 Period size: 28 Copynumber: 5.3 Consensus size: 28 41519206 TGCACTGCAT 41519216 TGTTACTGTATTGGGCTAAGGCCCACAC 1 TGTTACTGTATTGGGCTAAGGCCCACAC * 41519244 TGATT-CTGTACTGGGCTAAGGCCCACAC 1 TG-TTACTGTATTGGGCTAAGGCCCACAC * * * 41519272 TAATT-CTGTATTGGGCTAAGTCCCATAC 1 T-GTTACTGTATTGGGCTAAGGCCCACAC * * 41519300 TGTTACTCTATTGGGCTAAGGCCCACAT 1 TGTTACTGTATTGGGCTAAGGCCCACAC * 41519328 TGTTACTGTATTGGGCTAAGGCCCAGAC 1 TGTTACTGTATTGGGCTAAGGCCCACAC 41519356 TGTTACTG 1 TGTTACTG 41519364 CATGCTGTTT Statistics Matches: 104, Mismatches: 13, Indels: 6 0.85 0.11 0.05 Matches are distributed among these distances: 27 2 0.02 28 100 0.96 29 2 0.02 ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31 Consensus pattern (28 bp): TGTTACTGTATTGGGCTAAGGCCCACAC Found at i:41521077 original size:14 final size:13 Alignment explanation

Indices: 41521054--41521088 Score: 52 Period size: 14 Copynumber: 2.6 Consensus size: 13 41521044 TCTAATATAT 41521054 TTTAATTTTAAAA 1 TTTAATTTTAAAA * 41521067 TTTAATATTTATAA 1 TTTAAT-TTTAAAA 41521081 TTTAATTT 1 TTTAATTT 41521089 CTAAGATACT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 13 8 0.40 14 12 0.60 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (13 bp): TTTAATTTTAAAA Found at i:41552764 original size:20 final size:20 Alignment explanation

Indices: 41552741--41552783 Score: 59 Period size: 20 Copynumber: 2.1 Consensus size: 20 41552731 GGGCACAAAT * * 41552741 GTGCAAATAGGGGCACCGTA 1 GTGCAAATAGGGACACCGAA * 41552761 GTGCGAATAGGGACACCGAA 1 GTGCAAATAGGGACACCGAA 41552781 GTG 1 GTG 41552784 TATACAGGGG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 20 20 1.00 ACGTcount: A:0.30, C:0.19, G:0.37, T:0.14 Consensus pattern (20 bp): GTGCAAATAGGGACACCGAA Found at i:41560274 original size:39 final size:39 Alignment explanation

Indices: 41560170--41560280 Score: 107 Period size: 39 Copynumber: 2.8 Consensus size: 39 41560160 TTAAAACATG * * * * 41560170 TATTAAAGATGTCCTAAACTATGACATAATT-AAAACCCT 1 TATTAATGATGTTC-AAATTATGACATAATTAAAAACCCA * * * ** * 41560209 TGTTAATGTTGTTCAGATTACCACATAATTAAAAACTCA 1 TATTAATGATGTTCAAATTATGACATAATTAAAAACCCA 41560248 TATTAATGATGTTCAAATTATGACATAAATTAA 1 TATTAATGATGTTCAAATTATGACAT-AATTAA 41560281 CTAAAGTAAC Statistics Matches: 55, Mismatches: 15, Indels: 3 0.75 0.21 0.04 Matches are distributed among these distances: 38 12 0.22 39 37 0.67 40 6 0.11 ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35 Consensus pattern (39 bp): TATTAATGATGTTCAAATTATGACATAATTAAAAACCCA Found at i:41568239 original size:27 final size:26 Alignment explanation

Indices: 41568209--41568369 Score: 169 Period size: 27 Copynumber: 6.0 Consensus size: 26 41568199 CGAATCGTGC ** 41568209 GTAAAATGACCGTATTACCCCCGAAAG 1 GTAAAATGACCAAATTACCCCC-AAAG * 41568236 GTAAAATGACCATATTACCCCCAAAGG 1 GTAAAATGACCAAATTACCCCCAAA-G * * 41568263 GTAAAATCACCAAATTACCCCCTAAAA 1 GTAAAATGACCAAATTACCCCC-AAAG * 41568290 GTAAAATGACCAAATTACCCCCGAAGG 1 GTAAAATGACCAAATTACCCCC-AAAG * * * 41568317 GTAAAATGATCGAATTACCCCCAAGG 1 GTAAAATGACCAAATTACCCCCAAAG * * * * 41568343 GTAAAATTACTAAAATACCCTCAAAG 1 GTAAAATGACCAAATTACCCCCAAAG 41568369 G 1 G 41568370 GTTAAATTAC Statistics Matches: 115, Mismatches: 17, Indels: 5 0.84 0.12 0.04 Matches are distributed among these distances: 26 27 0.23 27 85 0.74 28 3 0.03 ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19 Consensus pattern (26 bp): GTAAAATGACCAAATTACCCCCAAAG Found at i:41568268 original size:54 final size:54 Alignment explanation

Indices: 41568209--41568465 Score: 221 Period size: 54 Copynumber: 4.8 Consensus size: 54 41568199 CGAATCGTGC * * 41568209 GTAAAATGACCGTATTACCCCCGAAAGGTAAAATGACCATATTACCCCCAAAGG 1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG * * * * * 41568263 GTAAAATCACCAAATTACCCCCTAAAAGTAAAATGACCAAATTACCCCCGAAGG 1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG * * * * * * 41568317 GTAAAATGATCGAATTACCCCC-AAGGGTAAAATTACTAAAATACCCTCAAAGG 1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG * * * * * * * * * 41568370 GTTAAATTACCGAAATACCCTCGAAGGGTAAAAATTATCGAAA-TACCCTCGAAGG 1 GTAAAATGACCGAATTACCCCCGAAAGGT-AAAATGA-CCAAATTACCCCCAAAGG * * * * * * * 41568425 GTAAAATTATCAAAATACCCTCGAAGGGTAAAATTACCAAA 1 GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAA 41568466 AACCCCTAAG Statistics Matches: 172, Mismatches: 28, Indels: 7 0.83 0.14 0.03 Matches are distributed among these distances: 53 45 0.26 54 79 0.46 55 44 0.26 56 4 0.02 ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20 Consensus pattern (54 bp): GTAAAATGACCGAATTACCCCCGAAAGGTAAAATGACCAAATTACCCCCAAAGG Found at i:41568325 original size:81 final size:80 Alignment explanation

Indices: 41568209--41568465 Score: 241 Period size: 81 Copynumber: 3.2 Consensus size: 80 41568199 CGAATCGTGC ** * 41568209 GTAAAATGACCGTATTACCCCCGAAAGGTAAAATGA-CCATATTACCCCCAAAGGGTAAAATCAC 1 GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCCA-ATTACCCCC-AAGGGTAAAATCAC * 41568273 CAAATTACCCCCTAAA-A 64 CAAAATACCCCC-AAAGA * * * 41568290 GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCGAATTACCCCCAAGGGTAAAATTACTA 1 GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCCAATTACCCCCAAGGGTAAAATCACCA * * 41568355 AAATACCCTCAAAGG 66 AAATACCCCCAAAGA * * * * * * * * 41568370 GTTAAATTACCGAAA-TACCCTCGAAGGGTAAAAATTATCGAAATACCCTCGAAGGGTAAAATTA 1 GTAAAATGACC-AAATTACCCCCGAAGGGT-AAAATGATCCAATTACCC-CCAAGGGTAAAATCA * * * * 41568434 TCAAAATACCCTCGAAGG 63 CCAAAATACCCCCAAAGA * 41568452 GTAAAATTACCAAA 1 GTAAAATGACCAAA 41568466 AACCCCTAAG Statistics Matches: 152, Mismatches: 19, Indels: 10 0.84 0.10 0.06 Matches are distributed among these distances: 79 3 0.02 80 44 0.29 81 64 0.42 82 41 0.27 ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20 Consensus pattern (80 bp): GTAAAATGACCAAATTACCCCCGAAGGGTAAAATGATCCAATTACCCCCAAGGGTAAAATCACCA AAATACCCCCAAAGA Found at i:41568413 original size:28 final size:27 Alignment explanation

Indices: 41568305--41568510 Score: 206 Period size: 27 Copynumber: 7.7 Consensus size: 27 41568295 ATGACCAAAT * * * 41568305 TACCCCCGAAGGGTAAAATGATCGAAT 1 TACCCTCGAAGGGTAAAATTATCGAAA * * 41568332 TACCC-CCAAGGGTAAAATTA-CTAAAA 1 TACCCTCGAAGGGTAAAATTATC-GAAA * * * 41568358 TACCCTCAAAGGGTTAAATTACCGAAA 1 TACCCTCGAAGGGTAAAATTATCGAAA 41568385 TACCCTCGAAGGGTAAAAATTATCGAAA 1 TACCCTCGAAGGGT-AAAATTATCGAAA * 41568413 TACCCTCGAAGGGTAAAATTATCAAAA 1 TACCCTCGAAGGGTAAAATTATCGAAA * 41568440 TACCCTCGAAGGGTAAAATTA-CCAAA 1 TACCCTCGAAGGGTAAAATTATCGAAA * * * * 41568466 AACCC-CTAAGAGTAAAATTA-CTATAA 1 TACCCTCGAAGGGTAAAATTATCGA-AA * * 41568492 TACCCCCTAAGGGTAAAAT 1 TACCCTCGAAGGGTAAAAT 41568511 GATCTTTATA Statistics Matches: 155, Mismatches: 18, Indels: 12 0.84 0.10 0.06 Matches are distributed among these distances: 25 16 0.10 26 34 0.22 27 79 0.51 28 26 0.17 ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21 Consensus pattern (27 bp): TACCCTCGAAGGGTAAAATTATCGAAA Found at i:41568415 original size:55 final size:55 Alignment explanation

Indices: 41568313--41568509 Score: 201 Period size: 55 Copynumber: 3.7 Consensus size: 55 41568303 ATTACCCCCG * * * 41568313 AAGGGTAAAATGATCGAATTACCC-CCAAGGGT-AAAATTACTAAAATACCCTCA 1 AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACTAAAATACCCTCA * * * * 41568366 AAGGGTTAAATTACCGAAATACCCTCGAAGGGTAAAAATTA-TCGAAATACCCTCG 1 AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACT-AAAATACCCTCA * * * 41568421 AAGGGTAAAATTATCAAAATACCCTCGAAGGGT-AAAATTACCAAAA-ACCC-CT 1 AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACTAAAATACCCTCA * * * * 41568473 AAGAGTAAAATTA-CTATAATACCCCCTAAGGGTAAAA 1 AAGGGTAAAATTATCGA-AATACCCTCGAAGGGTAAAA 41568510 TGATCTTTAT Statistics Matches: 121, Mismatches: 17, Indels: 12 0.81 0.11 0.08 Matches are distributed among these distances: 51 2 0.02 52 27 0.22 53 27 0.22 54 18 0.15 55 47 0.39 ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21 Consensus pattern (55 bp): AAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAATTACTAAAATACCCTCA Found at i:41568521 original size:27 final size:27 Alignment explanation

Indices: 41568209--41568543 Score: 82 Period size: 27 Copynumber: 12.5 Consensus size: 27 41568199 CGAATCGTGC ** * * 41568209 GTAAAATGACCGTATTACCCCCGAA-A 1 GTAAAATGACTATAATACCCCCTAAGA * * * * 41568235 GGTAAAATGACCATATTACCCCCAAAGG 1 -GTAAAATGACTATAATACCCCCTAAGA * * * 41568263 GTAAAATCACCA-AATTACCCCCTAAAA 1 GTAAAATGACTATAA-TACCCCCTAAGA * * * 41568290 GTAAAATGACCA-AATTACCCCCGAAGG 1 GTAAAATGACTATAA-TACCCCCTAAGA * * * 41568317 GTAAAATGATCGA-ATTACCCCC-AAGG 1 GTAAAATGA-CTATAATACCCCCTAAGA * * * * * 41568343 GTAAAATTACTAAAATACCCTCAAAGG 1 GTAAAATGACTATAATACCCCCTAAGA * * * * * * 41568370 GTTAAATTACCGA-AATACCCTCGAAGG 1 GTAAAATGA-CTATAATACCCCCTAAGA * * * * * 41568397 GTAAAAATTATCGA-AATACCCTCGAAGG 1 GT-AAAATGA-CTATAATACCCCCTAAGA * * * * * 41568425 GTAAAATTA-TCAAAATACCCTCGAAGG 1 GTAAAATGACT-ATAATACCCCCTAAGA * * * 41568452 GTAAAATTACCA-AA-AACCCCTAAGA 1 GTAAAATGACTATAATACCCCCTAAGA * * 41568477 GTAAAATTACTATAATACCCCCTAAGG 1 GTAAAATGACTATAATACCCCCTAAGA * * 41568504 GTAAAATGATCT-TTATA-CCCCTAGGA 1 GTAAAATGA-CTATAATACCCCCTAAGA * 41568530 GATGAAATGACTAT 1 G-TAAAATGACTAT 41568544 TATGGCCTTA Statistics Matches: 256, Mismatches: 37, Indels: 30 0.79 0.11 0.09 Matches are distributed among these distances: 25 20 0.08 26 35 0.14 27 169 0.66 28 32 0.12 ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21 Consensus pattern (27 bp): GTAAAATGACTATAATACCCCCTAAGA Found at i:41572170 original size:13 final size:13 Alignment explanation

Indices: 41572154--41572183 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 41572144 ATATAACTGA 41572154 TTCATATAGCCAT 1 TTCATATAGCCAT * 41572167 TTCATATAGTCAT 1 TTCATATAGCCAT 41572180 TTCA 1 TTCA 41572184 AAGTGCTAAC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43 Consensus pattern (13 bp): TTCATATAGCCAT Found at i:41572172 original size:26 final size:25 Alignment explanation

Indices: 41572112--41572174 Score: 65 Period size: 26 Copynumber: 2.4 Consensus size: 25 41572102 TCCATGTAAT * 41572112 CATTTCATATAACACTTCATATAAT 1 CATTTCATATAACACTTCATATAAC * * 41572137 TATTTCCATATAACTGA-TTCATATAGC 1 CATTT-CATATAAC--ACTTCATATAAC 41572164 CATTTCATATA 1 CATTTCATATA 41572175 GTCATTTCAA Statistics Matches: 31, Mismatches: 4, Indels: 5 0.77 0.10 0.12 Matches are distributed among these distances: 25 4 0.13 26 14 0.45 27 12 0.39 28 1 0.03 ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41 Consensus pattern (25 bp): CATTTCATATAACACTTCATATAAC Found at i:41576881 original size:19 final size:19 Alignment explanation

Indices: 41576857--41576895 Score: 53 Period size: 19 Copynumber: 2.1 Consensus size: 19 41576847 AAATTAGCGG 41576857 TAATTATCGAC-TTAGTTAA 1 TAATTA-CGACTTTAGTTAA * 41576876 TAATTACTACTTTAGTTAA 1 TAATTACGACTTTAGTTAA 41576895 T 1 T 41576896 TCTAGGCTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 18 3 0.17 19 15 0.83 ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46 Consensus pattern (19 bp): TAATTACGACTTTAGTTAA Found at i:41590721 original size:27 final size:27 Alignment explanation

Indices: 41590616--41590727 Score: 138 Period size: 27 Copynumber: 4.1 Consensus size: 27 41590606 TATAACAGTC * * 41590616 ATTTTACCCTAT-GAGGGTAATTCGGTA 1 ATTTTACCCT-TCGAGGGTATTTCGATA * * 41590643 ATTTTACCCATCGAGGGTATTGT-GGTA 1 ATTTTACCCTTCGAGGGTATT-TCGATA * 41590670 AATTTACCCTTCGAGGGTATTTCGATA 1 ATTTTACCCTTCGAGGGTATTTCGATA * 41590697 ATTTTACCCTTCGAGGGTATTTCGATC 1 ATTTTACCCTTCGAGGGTATTTCGATA 41590724 ATTT 1 ATTT 41590728 AACAATCTTT Statistics Matches: 75, Mismatches: 7, Indels: 6 0.85 0.08 0.07 Matches are distributed among these distances: 26 2 0.03 27 72 0.96 28 1 0.01 ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39 Consensus pattern (27 bp): ATTTTACCCTTCGAGGGTATTTCGATA Found at i:41593320 original size:25 final size:25 Alignment explanation

Indices: 41593266--41593340 Score: 98 Period size: 25 Copynumber: 3.0 Consensus size: 25 41593256 GGTTATCGAT * 41593266 TTCAGCTCTTATGAGCTTACCGA-TA 1 TTCAGCTCATATGAGCTTACC-ATTA * 41593291 CTCAGCTCATATGAGCTTACCATTA 1 TTCAGCTCATATGAGCTTACCATTA * * 41593316 TTCAGCTCAGAGGAGCTTACCATTA 1 TTCAGCTCATATGAGCTTACCATTA 41593341 ATCATCTCGG Statistics Matches: 44, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 24 1 0.02 25 43 0.98 ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32 Consensus pattern (25 bp): TTCAGCTCATATGAGCTTACCATTA Found at i:41593353 original size:25 final size:25 Alignment explanation

Indices: 41593278--41593361 Score: 98 Period size: 25 Copynumber: 3.4 Consensus size: 25 41593268 CAGCTCTTAT * * * 41593278 GAGCTTACCGA-TACTCAGCTCATAT 1 GAGCTTACC-ATTAATCAGCTCAGAG * 41593303 GAGCTTACCATTATTCAGCTCAGAG 1 GAGCTTACCATTAATCAGCTCAGAG * * 41593328 GAGCTTACCATTAATCATCTCGGAG 1 GAGCTTACCATTAATCAGCTCAGAG 41593353 GAGCTTACC 1 GAGCTTACC 41593362 GTTTACAGCT Statistics Matches: 52, Mismatches: 6, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 24 1 0.02 25 51 0.98 ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27 Consensus pattern (25 bp): GAGCTTACCATTAATCAGCTCAGAG Found at i:41595303 original size:14 final size:14 Alignment explanation

Indices: 41595284--41595323 Score: 71 Period size: 14 Copynumber: 2.9 Consensus size: 14 41595274 GATTCAAAGA 41595284 TAAATAAAATATCC 1 TAAATAAAATATCC 41595298 TAAATAAAATATCC 1 TAAATAAAATATCC * 41595312 CAAATAAAATAT 1 TAAATAAAATAT 41595324 ATTAATAAAG Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 14 25 1.00 ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28 Consensus pattern (14 bp): TAAATAAAATATCC Found at i:41596629 original size:30 final size:30 Alignment explanation

Indices: 41596595--41596656 Score: 106 Period size: 30 Copynumber: 2.1 Consensus size: 30 41596585 CTTTACTTTA * 41596595 AACTTCTCAATATGACCATTTAAAGAGTTG 1 AACTTCTCAATATGACCAGTTAAAGAGTTG * 41596625 AACTTCTCAATATGACCGGTTAAAGAGTTG 1 AACTTCTCAATATGACCAGTTAAAGAGTTG 41596655 AA 1 AA 41596657 GAATCCTAGC Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 30 30 1.00 ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31 Consensus pattern (30 bp): AACTTCTCAATATGACCAGTTAAAGAGTTG Found at i:41603179 original size:21 final size:20 Alignment explanation

Indices: 41603149--41603191 Score: 59 Period size: 20 Copynumber: 2.1 Consensus size: 20 41603139 TTATGTTCAG * 41603149 TCTCAATTTCGTCTTTCTTTT 1 TCTCAATTTC-ACTTTCTTTT * 41603170 TCTCACTTTCACTTTCTTTT 1 TCTCAATTTCACTTTCTTTT 41603190 TC 1 TC 41603192 AATTTCTTTT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 20 11 0.55 21 9 0.45 ACGTcount: A:0.09, C:0.28, G:0.02, T:0.60 Consensus pattern (20 bp): TCTCAATTTCACTTTCTTTT Found at i:41603197 original size:12 final size:12 Alignment explanation

Indices: 41603176--41603214 Score: 51 Period size: 12 Copynumber: 3.2 Consensus size: 12 41603166 TTTTTCTCAC * 41603176 TTTCACTTTCTT 1 TTTCAATTTCTT 41603188 TTTCAATTTCTT 1 TTTCAATTTCTT ** 41603200 TTTCGTTTTCTT 1 TTTCAATTTCTT 41603212 TTT 1 TTT 41603215 AACAATCTTT Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 12 24 1.00 ACGTcount: A:0.08, C:0.18, G:0.03, T:0.72 Consensus pattern (12 bp): TTTCAATTTCTT Found at i:41603203 original size:18 final size:18 Alignment explanation

Indices: 41603182--41603284 Score: 64 Period size: 18 Copynumber: 5.6 Consensus size: 18 41603172 TCACTTTCAC 41603182 TTTCTTTTTCAATTTCTT 1 TTTCTTTTTCAATTTCTT * ** *** 41603200 TTTCGTTTTCTTTTTAAC 1 TTTCTTTTTCAATTTCTT ** * 41603218 AATCTTTTTCGA-TTCTT 1 TTTCTTTTTCAATTTCTT * * 41603235 TTCTCTCTTTCAATTTTTT 1 TT-TCTTTTTCAATTTCTT * 41603254 TTCCTCTTTTTCAATCTCTT 1 TT--TCTTTTTCAATTTCTT 41603274 TTTCTTTTTCA 1 TTTCTTTTTCA 41603285 TTACAACATG Statistics Matches: 60, Mismatches: 22, Indels: 6 0.68 0.25 0.07 Matches are distributed among these distances: 17 2 0.03 18 36 0.60 19 6 0.10 20 16 0.27 ACGTcount: A:0.12, C:0.20, G:0.02, T:0.66 Consensus pattern (18 bp): TTTCTTTTTCAATTTCTT Found at i:41603203 original size:24 final size:24 Alignment explanation

Indices: 41603176--41603277 Score: 63 Period size: 24 Copynumber: 4.2 Consensus size: 24 41603166 TTTTTCTCAC 41603176 TTTCACTTTCTTTTTCAATTTCTT 1 TTTCACTTTCTTTTTCAATTTCTT ** 41603200 TTTCGTTTTCTTTTTAACAA--TCTT 1 TTTCACTTTCTTTTT--CAATTTCTT 41603224 TTTCGATTCTTTTCTCTCTTTCAATTT-TT 1 TTTC-A--C-TTTCT-T-TTTCAATTTCTT * 41603253 TTTC-C--TCTTTTTCAATCTCTT 1 TTTCACTTTCTTTTTCAATTTCTT 41603274 TTTC 1 TTTC 41603278 TTTTTCATTA Statistics Matches: 62, Mismatches: 5, Indels: 25 0.67 0.05 0.27 Matches are distributed among these distances: 20 8 0.13 21 7 0.11 22 3 0.05 24 21 0.34 25 1 0.02 26 3 0.05 28 8 0.13 29 7 0.11 30 4 0.06 ACGTcount: A:0.12, C:0.22, G:0.02, T:0.65 Consensus pattern (24 bp): TTTCACTTTCTTTTTCAATTTCTT Found at i:41603275 original size:20 final size:18 Alignment explanation

Indices: 41603220--41603284 Score: 69 Period size: 18 Copynumber: 3.5 Consensus size: 18 41603210 TTTTTAACAA * 41603220 TCTTTTTCGATTCTTTTC 1 TCTTTTTCAATTCTTTTC * * 41603238 TCTCTTTCAATTTTTTTTCC 1 TCTTTTTCAA-TTCTTTT-C 41603258 TCTTTTTCAATCTCTTTT- 1 TCTTTTTCAAT-TCTTTTC 41603276 TCTTTTTCA 1 TCTTTTTCA 41603285 TTACAACATG Statistics Matches: 39, Mismatches: 5, Indels: 6 0.78 0.10 0.12 Matches are distributed among these distances: 18 17 0.44 19 7 0.18 20 15 0.38 ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66 Consensus pattern (18 bp): TCTTTTTCAATTCTTTTC Found at i:41608690 original size:47 final size:47 Alignment explanation

Indices: 41608615--41609203 Score: 1054 Period size: 47 Copynumber: 12.5 Consensus size: 47 41608605 TTCGGGACTC * * * * * * * 41608615 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT * 41608662 GTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41608709 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT * 41608756 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41608803 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT * 41608850 ATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT * 41608897 ATCACATATATACACTTTCATATTCATCACATCGGCCATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41608944 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41608991 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41609038 ATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41609084 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41609131 ATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT 41609180 ATCACATATATACACTTTCACATT 1 ATCACATATATACACTTTCACATT 41609204 TATTCAAATA Statistics Matches: 524, Mismatches: 15, Indels: 6 0.96 0.03 0.01 Matches are distributed among these distances: 46 46 0.09 47 431 0.82 49 47 0.09 ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33 Consensus pattern (47 bp): ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT Found at i:41612175 original size:22 final size:25 Alignment explanation

Indices: 41612127--41612175 Score: 59 Period size: 26 Copynumber: 2.0 Consensus size: 25 41612117 TGATTTTTTA * 41612127 CTTTTTCTTTTTCTTCTCCAACGTTC 1 CTTTTTCTTATTCTTCTCCAAC-TTC 41612153 CTTTTTC-TATTCTT-TCCAA-TTC 1 CTTTTTCTTATTCTTCTCCAACTTC 41612175 C 1 C 41612176 AATTTCATTT Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 22 4 0.18 24 5 0.23 25 6 0.27 26 7 0.32 ACGTcount: A:0.10, C:0.31, G:0.02, T:0.57 Consensus pattern (25 bp): CTTTTTCTTATTCTTCTCCAACTTC Found at i:41612748 original size:21 final size:21 Alignment explanation

Indices: 41612699--41612755 Score: 60 Period size: 21 Copynumber: 2.7 Consensus size: 21 41612689 CATGGGCTGC * 41612699 TCACACGGGCATGTGTCCCCT 1 TCACACGGGCATGTGGCCCCT * * ** 41612720 CCATACGGGCATGTGGGGCCT 1 TCACACGGGCATGTGGCCCCT * 41612741 TCACACGGGTATGTG 1 TCACACGGGCATGTG 41612756 TAGACCCCTA Statistics Matches: 28, Mismatches: 8, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 21 28 1.00 ACGTcount: A:0.16, C:0.30, G:0.32, T:0.23 Consensus pattern (21 bp): TCACACGGGCATGTGGCCCCT Found at i:41612795 original size:19 final size:19 Alignment explanation

Indices: 41612771--41612807 Score: 65 Period size: 19 Copynumber: 1.9 Consensus size: 19 41612761 CCCTACATGG 41612771 CTTGGGCACTTCCACACGA 1 CTTGGGCACTTCCACACGA * 41612790 CTTGGGCACTTCTACACG 1 CTTGGGCACTTCCACACG 41612808 GCCAGGGCAC Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.19, C:0.35, G:0.22, T:0.24 Consensus pattern (19 bp): CTTGGGCACTTCCACACGA Found at i:41612815 original size:19 final size:19 Alignment explanation

Indices: 41612774--41612817 Score: 52 Period size: 19 Copynumber: 2.3 Consensus size: 19 41612764 TACATGGCTT ** 41612774 GGGCACTTCCACACGACTT 1 GGGCACTTCCACACGACCA * * 41612793 GGGCACTTCTACACGGCCA 1 GGGCACTTCCACACGACCA 41612812 GGGCAC 1 GGGCAC 41612818 ACGGCCATGT Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.20, C:0.36, G:0.27, T:0.16 Consensus pattern (19 bp): GGGCACTTCCACACGACCA Found at i:41624237 original size:25 final size:26 Alignment explanation

Indices: 41624195--41624243 Score: 64 Period size: 25 Copynumber: 1.9 Consensus size: 26 41624185 AGTTGTAAAT * 41624195 TAGAAAAATGTCTCTAGA-AATTTTC 1 TAGAAAAATCTCTCTAGAGAATTTTC * * 41624220 TAGAATAATCTCTTTAGAGAATTT 1 TAGAAAAATCTCTCTAGAGAATTT 41624244 CTCTTTACAA Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 25 15 0.75 26 5 0.25 ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39 Consensus pattern (26 bp): TAGAAAAATCTCTCTAGAGAATTTTC Found at i:41626166 original size:12 final size:13 Alignment explanation

Indices: 41626142--41626170 Score: 51 Period size: 12 Copynumber: 2.3 Consensus size: 13 41626132 GAGCTATAAC 41626142 TATTGCATTTATT 1 TATTGCATTTATT 41626155 TATTGC-TTTATT 1 TATTGCATTTATT 41626167 TATT 1 TATT 41626171 CATGTATGAG Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 10 0.62 13 6 0.38 ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66 Consensus pattern (13 bp): TATTGCATTTATT Found at i:41632614 original size:2 final size:2 Alignment explanation

Indices: 41632603--41632631 Score: 51 Period size: 2 Copynumber: 15.0 Consensus size: 2 41632593 AGTACGTATG 41632603 CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 41632632 TTCACGAGCA Statistics Matches: 26, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 1 1 0.04 2 25 0.96 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): CT Found at i:41638455 original size:16 final size:15 Alignment explanation

Indices: 41638396--41638455 Score: 52 Period size: 16 Copynumber: 3.9 Consensus size: 15 41638386 CACTTTTCAT 41638396 AATT-AATTAA-TAA 1 AATTAAATTAATTAA * * * 41638409 TAATTTATTTAATTCA 1 -AATTAAATTAATTAA 41638425 AATTAAATTAGATTAA 1 AATTAAATTA-ATTAA 41638441 AATTAAAATTAATTA 1 AATT-AAATTAATTA 41638456 TATTATGAAT Statistics Matches: 37, Mismatches: 5, Indels: 6 0.77 0.10 0.12 Matches are distributed among these distances: 14 4 0.11 15 13 0.35 16 14 0.38 17 6 0.16 ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43 Consensus pattern (15 bp): AATTAAATTAATTAA Found at i:41638466 original size:22 final size:21 Alignment explanation

Indices: 41638399--41638468 Score: 65 Period size: 22 Copynumber: 3.3 Consensus size: 21 41638389 TTTTCATAAT 41638399 TAATTAATAA-TAATT-TATT- 1 TAATTAA-AATTAATTATATTA * * 41638418 TAATTCAAATTAAATTAGATTA 1 TAATTAAAATT-AATTATATTA * 41638440 AAATTAAAATTAATTATATTA 1 TAATTAAAATTAATTATATTA 41638461 TGAATTAA 1 T-AATTAA 41638469 TACAAATAAT Statistics Matches: 40, Mismatches: 6, Indels: 7 0.75 0.11 0.13 Matches are distributed among these distances: 18 2 0.05 19 7 0.17 20 4 0.10 21 12 0.30 22 15 0.38 ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44 Consensus pattern (21 bp): TAATTAAAATTAATTATATTA Found at i:41643567 original size:21 final size:18 Alignment explanation

Indices: 41643528--41643599 Score: 64 Period size: 18 Copynumber: 4.2 Consensus size: 18 41643518 TTAATACAAT 41643528 TTAATTATTTTATAAAAA 1 TTAATTATTTTATAAAAA * * 41643546 TTAATTATTTTATGACAA 1 TTAATTATTTTATAAAAA * 41643564 --AA--ATTCTATCAAAAA 1 TTAATTATTTTAT-AAAAA 41643579 TTAATTATTTTA-AATAAA 1 TTAATTATTTTATAA-AAA 41643597 TTA 1 TTA 41643600 GGTATGAAAA Statistics Matches: 42, Mismatches: 6, Indels: 12 0.70 0.10 0.20 Matches are distributed among these distances: 14 6 0.14 15 3 0.07 16 2 0.05 17 4 0.10 18 22 0.52 19 5 0.12 ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46 Consensus pattern (18 bp): TTAATTATTTTATAAAAA Found at i:41645356 original size:31 final size:31 Alignment explanation

Indices: 41645293--41645348 Score: 82 Period size: 31 Copynumber: 1.9 Consensus size: 31 41645283 TATATATCAC * 41645293 AATTATAAAAT---TATATAATATTATAAAT 1 AATTATAAAATAAATATATAATAATATAAAT 41645321 AATTATAAAATAAATATATAATAATATA 1 AATTATAAAATAAATATATAATAATATA 41645349 GGTAATTAAA Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 28 11 0.46 31 13 0.54 ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39 Consensus pattern (31 bp): AATTATAAAATAAATATATAATAATATAAAT Found at i:41646358 original size:20 final size:18 Alignment explanation

Indices: 41646311--41646401 Score: 65 Period size: 17 Copynumber: 5.3 Consensus size: 18 41646301 CAAGATAAAC 41646311 ATTAAATTAA-ATTTAAT 1 ATTAAATTAATATTTAAT 41646328 ATTAAGA-TAATCACTTTAAT 1 ATTAA-ATTAAT-A-TTTAAT * 41646348 ATTAAATTAATA--AAAT 1 ATTAAATTAATATTTAAT * 41646364 ATT--ATTAAGA--TAAGT 1 ATTAAATTAATATTTAA-T 41646379 ATTAAATTAA-ATTTAAT 1 ATTAAATTAATATTTAAT 41646396 ATTAAA 1 ATTAAA 41646402 CTATTAAAGT Statistics Matches: 61, Mismatches: 3, Indels: 20 0.73 0.04 0.24 Matches are distributed among these distances: 14 8 0.13 15 4 0.07 16 7 0.11 17 20 0.33 18 4 0.07 19 3 0.05 20 15 0.25 ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42 Consensus pattern (18 bp): ATTAAATTAATATTTAAT Found at i:41647180 original size:35 final size:35 Alignment explanation

Indices: 41647134--41647203 Score: 140 Period size: 35 Copynumber: 2.0 Consensus size: 35 41647124 CATTAACTCT 41647134 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA 1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA 41647169 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA 1 TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA 41647204 GTCATGCCAT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 35 35 1.00 ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37 Consensus pattern (35 bp): TTAATTGAGCTATGAATTCCACTGTTGCTAGTAAA Found at i:41650479 original size:33 final size:33 Alignment explanation

Indices: 41650437--41650502 Score: 132 Period size: 33 Copynumber: 2.0 Consensus size: 33 41650427 TTAAAGAGAA 41650437 AATTAAAATCTTGAGTAATTTTATTTTATTACT 1 AATTAAAATCTTGAGTAATTTTATTTTATTACT 41650470 AATTAAAATCTTGAGTAATTTTATTTTATTACT 1 AATTAAAATCTTGAGTAATTTTATTTTATTACT 41650503 CTAACATTTC Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 33 1.00 ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52 Consensus pattern (33 bp): AATTAAAATCTTGAGTAATTTTATTTTATTACT Found at i:41650783 original size:18 final size:20 Alignment explanation

Indices: 41650743--41650787 Score: 83 Period size: 20 Copynumber: 2.3 Consensus size: 20 41650733 ATAATATAAT 41650743 TATATTTAAAAATTAAAATA 1 TATATTTAAAAATTAAAATA 41650763 TATATTTAAAAATTAAAATA 1 TATATTTAAAAATTAAAATA 41650783 T-TATT 1 TATATT 41650788 ATTGTATAAA Statistics Matches: 25, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 19 4 0.16 20 21 0.84 ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44 Consensus pattern (20 bp): TATATTTAAAAATTAAAATA Found at i:41651487 original size:31 final size:31 Alignment explanation

Indices: 41651422--41651496 Score: 96 Period size: 31 Copynumber: 2.4 Consensus size: 31 41651412 TACAAAATCA * 41651422 TCACTAAATTATTTGAAAATTTTCATTTAAG 1 TCACTAAATTATTTGAAAATTTTCATTCAAG * * * 41651453 TCACTGAATTATTTGAAAATTTTTATTCATG 1 TCACTAAATTATTTGAAAATTTTCATTCAAG * * 41651484 TCACCAAACTATT 1 TCACTAAATTATT 41651497 AAGTTTTTTT Statistics Matches: 37, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 31 37 1.00 ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44 Consensus pattern (31 bp): TCACTAAATTATTTGAAAATTTTCATTCAAG Found at i:41651898 original size:3 final size:3 Alignment explanation

Indices: 41651890--41651951 Score: 117 Period size: 3 Copynumber: 21.0 Consensus size: 3 41651880 AGGTTACCTC 41651890 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 41651937 ATT ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT 41651952 TATCTGCAAT Statistics Matches: 58, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 2 2 0.03 3 56 0.97 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (3 bp): ATT Found at i:41654244 original size:100 final size:103 Alignment explanation

Indices: 41654099--41654285 Score: 218 Period size: 100 Copynumber: 1.8 Consensus size: 103 41654089 TTTCTTGTAC * * * ** * * * 41654099 TGCCAATGCCATATCCCAGATATGGTCTTACACGATAGTTCTCAT-A-TC-GGTGCCCATGCCAT 1 TGCCAACGCCATATCCCAGACATGGTCTTACACGAGACCTATCATAACTCAGATGCCAATGCCAT 41654161 GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG 66 GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG * * * 41654199 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATAACCTCAATGATGCCAATGC 1 TGCCAACGCCATATCCCAGACATGGTCTTACACGAGACCTATCATAA-CTC-A-GATGCCAATGC * 41654264 CATGTCCTAGACATGGTCTTAC 63 CATGTCCCAGACATGGTCTTAC 41654286 ATGGGATCTC Statistics Matches: 69, Mismatches: 12, Indels: 6 0.79 0.14 0.07 Matches are distributed among these distances: 100 36 0.52 101 1 0.01 103 2 0.03 106 30 0.43 ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26 Consensus pattern (103 bp): TGCCAACGCCATATCCCAGACATGGTCTTACACGAGACCTATCATAACTCAGATGCCAATGCCAT GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG Found at i:41654266 original size:56 final size:50 Alignment explanation

Indices: 41654049--41654291 Score: 186 Period size: 50 Copynumber: 4.8 Consensus size: 50 41654039 TGATAATAAC * * * * * * 41654049 ATGCCAAAGCCATGTCCCAAACATGGTCTTACATAGGA--TGT-TTCTTG 1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG * * * ** ** * * 41654096 TACTGCCAATGCCATATCCCAGATATGGTCTTACACGATAGTTCTCATATCG 1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG * * ** * 41654148 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG 1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG * * 41654198 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATAACCTCAATG 1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCAT---CTC---G * 41654254 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA 1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA 41654292 TCTCTTTACC Statistics Matches: 154, Mismatches: 31, Indels: 12 0.78 0.16 0.06 Matches are distributed among these distances: 48 1 0.01 49 29 0.19 50 80 0.52 51 2 0.01 52 3 0.02 53 3 0.02 56 36 0.23 ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27 Consensus pattern (50 bp): ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTATCATCTCG Found at i:41654667 original size:30 final size:30 Alignment explanation

Indices: 41654633--41654690 Score: 73 Period size: 30 Copynumber: 1.9 Consensus size: 30 41654623 CCTTGACTCG 41654633 AACTTTGGCAAAATTACA-TTTTTACCCCTA 1 AACTTTGGCAAAATTACACTTTTT-CCCCTA * * * 41654663 AACTTTTGCATATTTACACTTTTTCCCC 1 AACTTTGGCAAAATTACACTTTTTCCCC 41654691 AAAGCTCGGA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 30 19 0.79 31 5 0.21 ACGTcount: A:0.28, C:0.26, G:0.05, T:0.41 Consensus pattern (30 bp): AACTTTGGCAAAATTACACTTTTTCCCCTA Found at i:41657194 original size:20 final size:20 Alignment explanation

Indices: 41657166--41657218 Score: 52 Period size: 20 Copynumber: 2.6 Consensus size: 20 41657156 TTAACTTTTG * * 41657166 GAATCATAAAAATCCAACAA 1 GAATTATAAAAATCCAAAAA * * * 41657186 GAATTATAAGATTTCAAAAA 1 GAATTATAAAAATCCAAAAA * 41657206 GAATTCTAAAAAT 1 GAATTATAAAAAT 41657219 AGTCAATTTT Statistics Matches: 25, Mismatches: 8, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 20 25 1.00 ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25 Consensus pattern (20 bp): GAATTATAAAAATCCAAAAA Found at i:41663132 original size:23 final size:23 Alignment explanation

Indices: 41663106--41663151 Score: 56 Period size: 23 Copynumber: 2.0 Consensus size: 23 41663096 AATTGTTAAC * * * 41663106 TTTACATCTCAAAAATTATAAAT 1 TTTACATATAAAAAATTAAAAAT * 41663129 TTTATATATAAAAAATTAAAAAT 1 TTTACATATAAAAAATTAAAAAT 41663152 ATATATAGCA Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 23 19 1.00 ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39 Consensus pattern (23 bp): TTTACATATAAAAAATTAAAAAT Found at i:41663156 original size:22 final size:23 Alignment explanation

Indices: 41663116--41663158 Score: 61 Period size: 22 Copynumber: 1.9 Consensus size: 23 41663106 TTTACATCTC * * 41663116 AAAAATTATAAATTTTATATATA 1 AAAAATTATAAAATATATATATA 41663139 AAAAATTA-AAAATATATATA 1 AAAAATTATAAAATATATATA 41663159 GCAAACCTTA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 22 10 0.56 23 8 0.44 ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37 Consensus pattern (23 bp): AAAAATTATAAAATATATATATA Found at i:41666673 original size:139 final size:138 Alignment explanation

Indices: 41666252--41666728 Score: 408 Period size: 139 Copynumber: 3.4 Consensus size: 138 41666242 GGGTGTTACA * 41666252 GTACCCATCCACGATACA-ACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCCAT 1 GTACCTATCCACGATA-AGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCAT * * * ** * ** 41666316 CCACGATACAACTCTGAAAGGTACCTATCCATGGTATGACTTCTAACGGTACCATCCACGACATG 64 CCACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGATACA * * 41666381 ACTCCTAATA 129 ACTCCTATTG * * * * * * * * 41666391 GTAGCC-ATCCACAATAAAATTCCTAATGGTTCCCCTCCATGGTACAACTTCTAGTGGTATCCAT 1 GTA-CCTATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA-CCAT * ** * * * 41666455 CTACGACATGACTCTTAAAGGTACCTATCCATGGTATGACTCATAATAGTATTCATCCATGGCAT 64 CCACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCA-CG-AT * * 41666520 -GAA-TCCTATAG 126 ACAACTCCTATTG * * * * * * * 41666531 GTACCTACCCACGGTATGACTCCTAAAGGTACGCATCTACGGTAAAACTCCTAATGGTACCTATC 1 GTACCTATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACC-ATC * * * * 41666596 CACTACACAACTCTTAAAGGTATC-ATCCATGGTATGGCTCCTAATAGTACCCCTCCACGATACA 65 CACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTA-CCATCCACGATACA 41666660 ACTCCTATTG 129 ACTCCTATTG * * * * * ** * 41666670 GTA-CTCATCCACGATACGACTCTTAAAGGTATCTATCTATTATACAACTCCTACTGGTA 1 GTACCT-ATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTA 41666729 TTCTTTACGG Statistics Matches: 263, Mismatches: 65, Indels: 20 0.76 0.19 0.06 Matches are distributed among these distances: 137 2 0.01 138 6 0.02 139 176 0.67 140 76 0.29 141 2 0.01 142 1 0.00 ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27 Consensus pattern (138 bp): GTACCTATCCACGATAAGACTCCTAAAGGTACCCATCCATGGTACAACTCCTAATGGTACCATCC ACGACACAACTCTTAAAGGTACCTATCCATGGTATGACTCCTAATAGTACCATCCACGATACAAC TCCTATTG Found at i:41666773 original size:28 final size:28 Alignment explanation

Indices: 41666252--41666791 Score: 208 Period size: 28 Copynumber: 19.4 Consensus size: 28 41666242 GGGTGTTACA * * * 41666252 GTACCCATCCACGATACAACTCCTAAAG 1 GTACCCATCCACGGTACGACTCCTAATG * * 41666280 GTACCCATCCATGGTACAACTCCTAATG 1 GTACCCATCCACGGTACGACTCCTAATG * * * 41666308 GTACCCATCCACGATACAACT-CTGAAAG 1 GTACCCATCCACGGTACGACTCCT-AATG * * * * * 41666336 GTACCTATCCATGGTATGACTTCTAACG 1 GTACCCATCCACGGTACGACTCCTAATG ** * * 41666364 GTA-CCATCCACGACATGACTCCTAATA 1 GTACCCATCCACGGTACGACTCCTAATG * ** ** * 41666391 GTAGCCATCCACAATAAAATTCCTAATG 1 GTACCCATCCACGGTACGACTCCTAATG * * * * * * 41666419 GTTCCCCTCCATGGTACAACTTCTAGTG 1 GTACCCATCCACGGTACGACTCCTAATG * * ** * * * 41666447 GTATCCATCTACGACATGACTCTTAAAG 1 GTACCCATCCACGGTACGACTCCTAATG * * * * * 41666475 GTACCTATCCATGGTATGACTCATAATA 1 GTACCCATCCACGGTACGACTCCTAATG ** * * * * 41666503 GTATTCATCCATGGCATGAATCCT-ATAG 1 GTACCCATCCACGGTACGACTCCTAAT-G * * * * 41666531 GTACCTACCCACGGTATGACTCCTAAAG 1 GTACCCATCCACGGTACGACTCCTAATG * * ** 41666559 GTACGCATCTACGGTAAAACTCCTAATG 1 GTACCCATCCACGGTACGACTCCTAATG * *** * * * 41666587 GTACCTATCCACTACACAACTCTTAAAG 1 GTACCCATCCACGGTACGACTCCTAATG * * * * * 41666615 GTA-TCATCCATGGTATGGCTCCTAATA 1 GTACCCATCCACGGTACGACTCCTAATG * * * * 41666642 GTACCCCTCCACGATACAACTCCTATTG 1 GTACCCATCCACGGTACGACTCCTAATG * * * * 41666670 GTACTCATCCACGATACGACTCTTAAAG 1 GTACCCATCCACGGTACGACTCCTAATG * * * *** * * 41666698 GTATCTATCTATTATACAACTCCTACTG 1 GTACCCATCCACGGTACGACTCCTAATG ** ** * * 41666726 GTATTC-TTTACGGTATGACTCATAATG 1 GTACCCATCCACGGTACGACTCCTAATG 41666753 GTACCCATCCACGGTACGACTCCTAATG 1 GTACCCATCCACGGTACGACTCCTAATG * * 41666781 ATACCTATCCA 1 GTACCCATCCA 41666792 TGAAACGACT Statistics Matches: 362, Mismatches: 143, Indels: 14 0.70 0.28 0.03 Matches are distributed among these distances: 27 56 0.15 28 303 0.84 29 3 0.01 ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27 Consensus pattern (28 bp): GTACCCATCCACGGTACGACTCCTAATG Found at i:41669416 original size:30 final size:30 Alignment explanation

Indices: 41669381--41669440 Score: 120 Period size: 30 Copynumber: 2.0 Consensus size: 30 41669371 CTAAACTTAA 41669381 ATAAACTCTAATCACTTAATTAGAAAACAT 1 ATAAACTCTAATCACTTAATTAGAAAACAT 41669411 ATAAACTCTAATCACTTAATTAGAAAACAT 1 ATAAACTCTAATCACTTAATTAGAAAACAT 41669441 GAAAGAGACC Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 30 1.00 ACGTcount: A:0.50, C:0.17, G:0.03, T:0.30 Consensus pattern (30 bp): ATAAACTCTAATCACTTAATTAGAAAACAT Found at i:41675965 original size:346 final size:347 Alignment explanation

Indices: 41675328--41676025 Score: 1263 Period size: 346 Copynumber: 2.0 Consensus size: 347 41675318 GTGGAGATTT * * 41675328 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAGAAATAATCTTTTAATTAAACTTTGTTTATT 1 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTGTTTATT * 41675393 TGTTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA 66 TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA * * 41675458 TAAATAGGCTCTTTTACAACCTTAGTAAAAACATCAATTAGATTAGAACTCATAACACATTCAGA 131 TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCAATTAGATTAGAACTCATAACACATTCAGA * * 41675523 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTGTTTTTCGGGTTTTCGGGGTTTAATTTTATCTCC 196 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTCGGGGTTTAATTTTATCTCC * 41675588 ATCTTTTGTACTCTTCATTCTTTTTCCATTATAGTAAAATTATCTTTGCCCGTGG-TTTTTTATC 261 ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC 41675652 CTCTTTGGAGGGGGTTTTCCAC 326 CTCTTTGGAGGGGGTTTTCCAC * 41675674 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAGTTAAACTCTGTTTATT 1 GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTGTTTATT 41675739 TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA 66 TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA * 41675804 TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCCATTAGATTAGAACTCATAACACATTCAGA 131 TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCAATTAGATTAGAACTCATAACACATTCAGA * * 41675869 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTTGGGGTTTAGTTTTATCTCC 196 GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTCGGGGTTTAATTTTATCTCC 41675934 ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC 261 ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC ** 41675999 CTCTTTGGAGGGTTTTTTCCAC 326 CTCTTTGGAGGGGGTTTTCCAC 41676021 GTTAA 1 GTTAA 41676026 ATTTGTGTGT Statistics Matches: 337, Mismatches: 14, Indels: 1 0.96 0.04 0.00 Matches are distributed among these distances: 346 303 0.90 347 34 0.10 ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45 Consensus pattern (347 bp): GTTAAGTATGACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTGTTTATT TATTTCAGTCAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTA TAAATAGGCTCTTTTACAACCTTAGAAAAAACACCAATTAGATTAGAACTCATAACACATTCAGA GAATTTTGTGTTTACGTTTTGAGGGTTCTTTATTTTTCGAGTTTTCGGGGTTTAATTTTATCTCC ATCTTTTGTACTCTTCATTCTTTTGCCATTATAGTAAAATTATCTTTGCCCGTGGTTTTTTTATC CTCTTTGGAGGGGGTTTTCCAC Found at i:41680032 original size:27 final size:27 Alignment explanation

Indices: 41679977--41680033 Score: 71 Period size: 27 Copynumber: 2.1 Consensus size: 27 41679967 ATATACAATG * 41679977 TATTGAATGAATGTGAAAATGATTATAT 1 TATTGAATGAATGT-AAAATGATGATAT * 41680005 TATTGAATGATATGT-ATATGATGATAT 1 TATTGAATGA-ATGTAAAATGATGATAT 41680032 TA 1 TA 41680034 CAATATTTGA Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 27 12 0.46 28 10 0.38 29 4 0.15 ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42 Consensus pattern (27 bp): TATTGAATGAATGTAAAATGATGATAT Found at i:41688052 original size:9 final size:9 Alignment explanation

Indices: 41688040--41688101 Score: 61 Period size: 9 Copynumber: 6.7 Consensus size: 9 41688030 TATTAAAAGC 41688040 GAGAGAGTT 1 GAGAGAGTT * 41688049 GAGAGACTT 1 GAGAGAGTT * 41688058 GAGAGTGTTT 1 GAGAGAG-TT * 41688068 GAGAGAATTT 1 GAGAG-AGTT * * 41688078 GAAAGAATT 1 GAGAGAGTT 41688087 GAGAGAGTT 1 GAGAGAGTT 41688096 GAGAGA 1 GAGAGA 41688102 AGGATGTGAA Statistics Matches: 42, Mismatches: 9, Indels: 4 0.76 0.16 0.07 Matches are distributed among these distances: 9 29 0.69 10 13 0.31 ACGTcount: A:0.37, C:0.02, G:0.37, T:0.24 Consensus pattern (9 bp): GAGAGAGTT Found at i:41692273 original size:18 final size:16 Alignment explanation

Indices: 41692231--41692273 Score: 50 Period size: 18 Copynumber: 2.4 Consensus size: 16 41692221 TGTCGTTCTT 41692231 TTTCAAAATATTATTCA 1 TTTC-AAATATTATTCA 41692248 TTTACAAATCATTATTCAA 1 TTT-CAAAT-ATTATTC-A 41692267 TTTCAAA 1 TTTCAAA 41692274 ATGTTTTTTT Statistics Matches: 23, Mismatches: 0, Indels: 5 0.82 0.00 0.18 Matches are distributed among these distances: 17 7 0.30 18 12 0.52 19 4 0.17 ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44 Consensus pattern (16 bp): TTTCAAATATTATTCA Found at i:41692275 original size:19 final size:17 Alignment explanation

Indices: 41692231--41692275 Score: 56 Period size: 19 Copynumber: 2.5 Consensus size: 17 41692221 TGTCGTTCTT 41692231 TTTCAAAATATTATTCA 1 TTTCAAAATATTATTCA 41692248 TTT-ACAAATCATTATTCAA 1 TTTCA-AAAT-ATTATTC-A 41692267 TTTCAAAAT 1 TTTCAAAAT 41692276 GTTTTTTTTA Statistics Matches: 24, Mismatches: 0, Indels: 6 0.80 0.00 0.20 Matches are distributed among these distances: 16 1 0.04 17 7 0.29 18 7 0.29 19 8 0.33 20 1 0.04 ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44 Consensus pattern (17 bp): TTTCAAAATATTATTCA Found at i:41694019 original size:13 final size:13 Alignment explanation

Indices: 41693985--41694022 Score: 58 Period size: 15 Copynumber: 2.8 Consensus size: 13 41693975 ATCTCGAAAT 41693985 CAAAATACTTACC 1 CAAAATACTTACC 41693998 CATAAAATACTTACC 1 C--AAAATACTTACC 41694013 CAAAATACTT 1 CAAAATACTT 41694023 CAAATCGGTA Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 13 10 0.43 15 13 0.57 ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26 Consensus pattern (13 bp): CAAAATACTTACC Found at i:41702977 original size:114 final size:114 Alignment explanation

Indices: 41702836--41703066 Score: 390 Period size: 114 Copynumber: 2.0 Consensus size: 114 41702826 TCAAACATAA * * * 41702836 AAAAAAAACCTTGGATAAAGATTATATAAGTTCAATCTAATCCAATCCGAATTACTATTTAATGA 1 AAAAAAAACCTTGGATAAAGATTATATAAATTAAATCTAATCCAATCCGAATTACCATTTAATGA 41702901 TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT 66 TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT * * 41702950 AAAAAAGACCTTGGATAAAGATTATATAAATTAAATTTAATCCAATCCGAATTACCATTTAATGA 1 AAAAAAAACCTTGGATAAAGATTATATAAATTAAATCTAATCCAATCCGAATTACCATTTAATGA * * * 41703015 TATTTTAATTTTTATTTCAATTTAATTATAAAATATATAAATTTAATAT 66 TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT 41703064 AAA 1 AAA 41703067 TTTAGTTTAA Statistics Matches: 109, Mismatches: 8, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 114 109 1.00 ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40 Consensus pattern (114 bp): AAAAAAAACCTTGGATAAAGATTATATAAATTAAATCTAATCCAATCCGAATTACCATTTAATGA TATTTTAATTTTTATTTAAATTTAAATATAAAATATAAAAATTTAATAT Found at i:41706002 original size:49 final size:49 Alignment explanation

Indices: 41705892--41706004 Score: 174 Period size: 49 Copynumber: 2.3 Consensus size: 49 41705882 ATTTTTGTAG * * 41705892 GCCATGTGGGTAAGCCTTGTAGGACACACGGTCCTTTGAAATAATGCAA 1 GCCATGTGGGTAGGCCTTGTAGGACACACGGTCCTTTGAAATAAAGCAA * * 41705941 GCCATGTGGGTAGGCCTTGTAGGGCACATGG-CCGTTTGAAATAAAGCAA 1 GCCATGTGGGTAGGCCTTGTAGGACACACGGTCC-TTTGAAATAAAGCAA 41705990 GCCATGTGGGTAGGC 1 GCCATGTGGGTAGGC 41706005 GTGTGGGGCA Statistics Matches: 59, Mismatches: 4, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 48 2 0.03 49 57 0.97 ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23 Consensus pattern (49 bp): GCCATGTGGGTAGGCCTTGTAGGACACACGGTCCTTTGAAATAAAGCAA Found at i:41706718 original size:27 final size:27 Alignment explanation

Indices: 41706688--41706740 Score: 97 Period size: 27 Copynumber: 2.0 Consensus size: 27 41706678 CATTGCATGA * 41706688 TATGATATGTTATGATTTATAATATGG 1 TATGATATGGTATGATTTATAATATGG 41706715 TATGATATGGTATGATTTATAATATG 1 TATGATATGGTATGATTTATAATATG 41706741 CTTTTATATG Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47 Consensus pattern (27 bp): TATGATATGGTATGATTTATAATATGG Found at i:41707718 original size:87 final size:87 Alignment explanation

Indices: 41707534--41707740 Score: 202 Period size: 87 Copynumber: 2.4 Consensus size: 87 41707524 CAGACACTCC * * * * ** 41707534 AATTTGTAGATGAACCACCAGTGTTTGCAGATAAACTATCAGTAGGTTATGAATACACAATGTGT 1 AATTTGTGGATGAACCACTAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT ** 41707599 TTGCAAATAAAAGTTTTCAATA 66 TTGCAAATAAAAGTGCTCAATA * * * * * * * * 41707621 AGTTTTTGGATGAACCACTAGTGTTTGTAGATAAATTACCAGTGGGATGTGATTGCACAACATGT 1 AATTTGTGGATGAACCACTAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT * * 41707686 TTGCAAATAAGAGCTGCT-AGTA 66 TTGCAAATAAAAG-TGCTCAATA * * * 41707708 AATTTGTGGATAAACCATTAGTG-TTGCAAATAA 1 AATTTGTGGATGAACCACTAGTGTTTGCAGATAA 41707741 TTAAACTGCC Statistics Matches: 95, Mismatches: 24, Indels: 3 0.78 0.20 0.02 Matches are distributed among these distances: 86 8 0.08 87 85 0.89 88 2 0.02 ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32 Consensus pattern (87 bp): AATTTGTGGATGAACCACTAGTGTTTGCAGATAAACTACCAGTAGGATATGAATACACAACATGT TTGCAAATAAAAGTGCTCAATA Found at i:41719932 original size:29 final size:31 Alignment explanation

Indices: 41719899--41719965 Score: 79 Period size: 29 Copynumber: 2.3 Consensus size: 31 41719889 ATAGGGATTT 41719899 GATCAAATTTG-TCGC-TCTACTATT-AAATG 1 GATCAAATTTGATC-CTTCTACTATTAAAATG * 41719928 GATC-AATTTGATCCTTGTACTATTAAAATG 1 GATCAAATTTGATCCTTCTACTATTAAAATG * 41719958 AATCAAAT 1 GATCAAAT 41719966 AAGACCAAAT Statistics Matches: 32, Mismatches: 2, Indels: 6 0.80 0.05 0.15 Matches are distributed among these distances: 28 7 0.22 29 14 0.44 30 8 0.25 31 3 0.09 ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37 Consensus pattern (31 bp): GATCAAATTTGATCCTTCTACTATTAAAATG Found at i:41720166 original size:30 final size:30 Alignment explanation

Indices: 41720132--41720225 Score: 93 Period size: 29 Copynumber: 3.1 Consensus size: 30 41720122 GTTACAATAT * ** * * 41720132 GGACTTATTTGATTCTTTTTAATAGTATAG 1 GGACTAATTTGATTCCATTTAATAATAGAG * 41720162 GGACTAAATTGA-TCCATTTAATAATAGAG 1 GGACTAATTTGATTCCATTTAATAATAGAG * 41720191 GGACTAATTTGA-TCCAGTTTCAATAATATAG 1 GGACTAATTTGATTCCA-TTT-AATAATAGAG 41720222 GGAC 1 GGAC 41720226 CTCCTAATAC Statistics Matches: 54, Mismatches: 8, Indels: 3 0.83 0.12 0.05 Matches are distributed among these distances: 29 28 0.52 30 13 0.24 31 13 0.24 ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37 Consensus pattern (30 bp): GGACTAATTTGATTCCATTTAATAATAGAG Found at i:41720192 original size:29 final size:30 Alignment explanation

Indices: 41720149--41720225 Score: 111 Period size: 29 Copynumber: 2.6 Consensus size: 30 41720139 TTTGATTCTT * 41720149 TTTAATAGTATAGGGACTAAATTGATCCA- 1 TTTAATAATATAGGGACTAAATTGATCCAG * * 41720178 TTTAATAATAGAGGGACTAATTTGATCCAG 1 TTTAATAATATAGGGACTAAATTGATCCAG 41720208 TTTCAATAATATAGGGAC 1 TTT-AATAATATAGGGAC 41720226 CTCCTAATAC Statistics Matches: 42, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 29 26 0.62 30 3 0.07 31 13 0.31 ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34 Consensus pattern (30 bp): TTTAATAATATAGGGACTAAATTGATCCAG Found at i:41721719 original size:45 final size:45 Alignment explanation

Indices: 41721655--41721842 Score: 229 Period size: 45 Copynumber: 4.2 Consensus size: 45 41721645 TACTACGTGT * * * 41721655 ACCGGGTACCATTGATTATAAAGGCGGTTGTTGTGTACTGATTCC 1 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC * 41721700 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGTTGATTCC 1 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC * * * * 41721745 ACCGGTTA-CTATTGATTATGAAGGTGGTTGCTATGTGCTGATTCC 1 ACCGGGTATC-ATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC * * * * 41721790 ACCGAGTATCATTGACTATAAAGGTGG-TGCTATGTGCTGA-TCC 1 ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC * 41721833 ACCGTGTATC 1 ACCGGGTATC 41721843 TGTTATTATT Statistics Matches: 127, Mismatches: 14, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 43 12 0.09 44 14 0.11 45 100 0.79 46 1 0.01 ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35 Consensus pattern (45 bp): ACCGGGTATCATTGATTATAAAGGTGGTTGTTGTGTGCTGATTCC Found at i:41723957 original size:69 final size:68 Alignment explanation

Indices: 41723847--41723980 Score: 250 Period size: 69 Copynumber: 2.0 Consensus size: 68 41723837 TTGTTTTTGT * 41723847 GAAATTTGTCATAAATAAGTATCTACTTCGGTGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTT 1 GAAATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTT 41723912 GGG 66 GGG 41723915 GAAATTTGTCATAAATAAGTAATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCT 1 GAAATTTGTCATAAATAAGT-ATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCT 41723980 T 65 T 41723981 CGGTTCAAGT Statistics Matches: 64, Mismatches: 1, Indels: 1 0.97 0.02 0.02 Matches are distributed among these distances: 68 20 0.31 69 44 0.69 ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42 Consensus pattern (68 bp): GAAATTTGTCATAAATAAGTATCTACTTCGATGGTTAAGTGTTCTGATTGTGTGTTTAAAGTCTT GGG Found at i:41728440 original size:18 final size:19 Alignment explanation

Indices: 41728397--41728442 Score: 51 Period size: 18 Copynumber: 2.5 Consensus size: 19 41728387 AAAAATCTCT * * 41728397 TAAATTTTTTCCTAAATTC 1 TAAATTTTATCCTAAATTA * 41728416 T-ATTTTTAT-CTAAATTA 1 TAAATTTTATCCTAAATTA 41728433 TAAATTTTAT 1 TAAATTTTAT 41728443 TATTTTTTAT Statistics Matches: 22, Mismatches: 4, Indels: 3 0.76 0.14 0.10 Matches are distributed among these distances: 17 8 0.36 18 13 0.59 19 1 0.05 ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57 Consensus pattern (19 bp): TAAATTTTATCCTAAATTA Found at i:41728599 original size:31 final size:31 Alignment explanation

Indices: 41728564--41728622 Score: 118 Period size: 31 Copynumber: 1.9 Consensus size: 31 41728554 TCTGTCAACT 41728564 AATTGCAAATGGTAAGAATAAATTTTAAACC 1 AATTGCAAATGGTAAGAATAAATTTTAAACC 41728595 AATTGCAAATGGTAAGAATAAATTTTAA 1 AATTGCAAATGGTAAGAATAAATTTTAA 41728623 TCTTTTTAAT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 31 28 1.00 ACGTcount: A:0.49, C:0.07, G:0.14, T:0.31 Consensus pattern (31 bp): AATTGCAAATGGTAAGAATAAATTTTAAACC Found at i:41734206 original size:3 final size:3 Alignment explanation

Indices: 41734198--41734223 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 41734188 TTCCATTTCT 41734198 TTA TTA TTA TTA TTA TTA TTA TTA TT 1 TTA TTA TTA TTA TTA TTA TTA TTA TT 41734224 TTAGAATTCA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 23 1.00 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (3 bp): TTA Found at i:41740328 original size:31 final size:29 Alignment explanation

Indices: 41740291--41740356 Score: 80 Period size: 30 Copynumber: 2.2 Consensus size: 29 41740281 TAAAAGTTAC * 41740291 TATTAAAATAA-AATTTAAATATTAAATAATT 1 TATTAAAATAATAAATT--ATATT-AATAATT 41740322 TATTAAAAATAATAAATTATATTAATAATT 1 TATT-AAAATAATAAATTATATTAATAATT 41740352 TATTA 1 TATTA 41740357 TATGACTAAA Statistics Matches: 32, Mismatches: 1, Indels: 6 0.82 0.03 0.15 Matches are distributed among these distances: 29 1 0.03 30 11 0.34 31 9 0.28 32 7 0.22 33 4 0.12 ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44 Consensus pattern (29 bp): TATTAAAATAATAAATTATATTAATAATT Found at i:41741003 original size:19 final size:18 Alignment explanation

Indices: 41740976--41741011 Score: 54 Period size: 19 Copynumber: 1.9 Consensus size: 18 41740966 CATGTTAATT * 41740976 TTTTAAATTTTTTAATAC 1 TTTTAAATTTTTAAATAC 41740994 TTTTATAATTTTTAAATA 1 TTTTA-AATTTTTAAATA 41741012 TTTAATGAAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 5 0.31 19 11 0.69 ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61 Consensus pattern (18 bp): TTTTAAATTTTTAAATAC Found at i:41745899 original size:9 final size:9 Alignment explanation

Indices: 41745880--41745952 Score: 112 Period size: 9 Copynumber: 8.2 Consensus size: 9 41745870 TCGGGTATTT 41745880 TTCGG-TAA 1 TTCGGTTAA 41745888 TTCGGTTAA 1 TTCGGTTAA 41745897 TTCGGTTAA 1 TTCGGTTAA 41745906 TTCGGTTAA 1 TTCGGTTAA 41745915 TTCGGTTAA 1 TTCGGTTAA * 41745924 TTCGGGTAA 1 TTCGGTTAA * 41745933 TTCGGGTAA 1 TTCGGTTAA * 41745942 TTCGGGTAA 1 TTCGGTTAA 41745951 TT 1 TT 41745953 TTTAACCAAA Statistics Matches: 63, Mismatches: 1, Indels: 1 0.97 0.02 0.02 Matches are distributed among these distances: 8 5 0.08 9 58 0.92 ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41 Consensus pattern (9 bp): TTCGGTTAA Found at i:41747881 original size:138 final size:139 Alignment explanation

Indices: 41747589--41748117 Score: 670 Period size: 140 Copynumber: 3.8 Consensus size: 139 41747579 TTCTAGGTTT * * * * 41747589 GATTCCTCTCCTGCTCACATTTGTATTTTTTATTTCATGTTGCTTTAAGCTTTTTAATTTTTTAA 1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA * * 41747654 TTAATGTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCCTTAAG 66 TTAA-GTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAG 41747719 TCTCGAGTTG 130 TCTCGAGTTG * * * * 41747729 GATTCATCTACTACTCACATTTGTATTTTTTGTCTCATGTTGCTTCAATCTTTTTAAATTTTTAA 1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA * * * * ** 41747794 TTAA-TTTGTTAACATATTA-ATTCTTTTGTTAGATGGTTAGATAGTTATTGTTACATCTTTGAG 66 TTAAGTTTTTTAACATATTAGGTT-TTTCGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAG * 41747857 TCTCGAGTTT 130 TCTCGAGTTG * * * * 41747867 GATTTCTCTTCTACTCAAACTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA 1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA * * 41747932 TTAATGTTTTTTAACATATTAGTTTTTTCGTTAGATGGTTACATAGTTGTAATTACAT-TCTTGA 66 TTAA-GTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCT-TTGA 41747996 GTCTCGAGTTG 129 GTCTCGAGTTG * ** * * 41748007 GATTCCTCTACTAATCACATTTGTATTTTGCATTTCATGTTGCTTCAAGCTTTTTTTATTATTTT 1 GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGC-TTTTTAAAT-TTTT * * * * 41748072 AATTAA-TATTTTTAACATGTTAGCTCCTTTCGTTAGATAGTTAGAT 64 AATTAAGT-TTTTTAACATATTAGGT-TTTTCGTTAGATGGTTAGAT 41748118 GATTGCGAAT Statistics Matches: 333, Mismatches: 47, Indels: 16 0.84 0.12 0.04 Matches are distributed among these distances: 137 2 0.01 138 118 0.35 139 1 0.00 140 161 0.48 141 24 0.07 142 27 0.08 ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51 Consensus pattern (139 bp): GATTCCTCTACTACTCACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTTAAATTTTTAA TTAAGTTTTTTAACATATTAGGTTTTTCGTTAGATGGTTAGATAGTTGTAATTACATCTTTGAGT CTCGAGTTG Found at i:41748288 original size:23 final size:22 Alignment explanation

Indices: 41748231--41748289 Score: 64 Period size: 23 Copynumber: 2.5 Consensus size: 22 41748221 TTTTGATGAT 41748231 ATTTTTTAATTATTTTTATTTTTA 1 ATTTTTT-ATT-TTTTTATTTTTA * * 41748255 ATTAATGTATTTTTTTATTTTTA 1 ATT-TTTTATTTTTTTATTTTTA 41748278 ACTTTTTTATTT 1 A-TTTTTTATTT 41748290 ATAAAATCAA Statistics Matches: 29, Mismatches: 4, Indels: 5 0.76 0.11 0.13 Matches are distributed among these distances: 23 19 0.66 24 8 0.28 25 2 0.07 ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73 Consensus pattern (22 bp): ATTTTTTATTTTTTTATTTTTA Found at i:41748673 original size:135 final size:141 Alignment explanation

Indices: 41748387--41748691 Score: 326 Period size: 144 Copynumber: 2.2 Consensus size: 141 41748377 TTAATTAAAA * * * * 41748387 AAAACACTTGAAGCAACATG----AAATAAAAAATACAAATGTGAGTAGTAGATGAATCAAACTC 1 AAAA-ACTTGAAGCAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTC * ** * 41748448 CAGACTCAATTATGTAATTACAACTATCTAACCATCTAACGAAAAACTAATATGGTAAAAAAATA 65 AAGACTCAAGGATGTAATTACAACTATCTAA-CATC-AAC-AAAAACTAATATGATAAAAAAATA 41748513 TTAATTAAAAATTTT 127 TTAATTAAAAATTTT * * 41748528 AAAAACTTGAAGTAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTGA 1 AAAAACTTGAAGCAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTCA * * * * 41748593 AGCCTCAAGGATGTAATTGCAACTATCT-A-ATC-A-AAGAACTAATAT-ATTAAAAAAT-TTAA 66 AGACTCAAGGATGTAATTACAACTATCTAACATCAACAAAAACTAATATGATAAAAAAATATTAA * 41748652 TTATAAA-TTT 131 TTAAAAATTTT * * * 41748662 AAAAAGTTTGAAGCAATATGAAATAAAAAA 1 AAAAA-CTTGAAGCAACATGAAACAAAAAA 41748692 TACAAATTTA Statistics Matches: 140, Mismatches: 19, Indels: 16 0.80 0.11 0.09 Matches are distributed among these distances: 134 8 0.06 135 30 0.21 136 8 0.06 137 11 0.08 139 1 0.01 140 14 0.10 141 7 0.05 143 1 0.01 144 60 0.43 ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25 Consensus pattern (141 bp): AAAAACTTGAAGCAACATGAAACAAAAAAAAAATACAAATATGAATAGTAGAGGAATCAAACTCA AGACTCAAGGATGTAATTACAACTATCTAACATCAACAAAAACTAATATGATAAAAAAATATTAA TTAAAAATTTT Found at i:41753601 original size:26 final size:26 Alignment explanation

Indices: 41753572--41753623 Score: 95 Period size: 26 Copynumber: 2.0 Consensus size: 26 41753562 CCTGGCTGAG * 41753572 TTGTCCTTTGGATATGATCGAGTAAT 1 TTGTCCTTTGGATATGATCAAGTAAT 41753598 TTGTCCTTTGGATATGATCAAGTAAT 1 TTGTCCTTTGGATATGATCAAGTAAT 41753624 ATGCATTGAA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 25 1.00 ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42 Consensus pattern (26 bp): TTGTCCTTTGGATATGATCAAGTAAT Found at i:41764892 original size:50 final size:50 Alignment explanation

Indices: 41764753--41764893 Score: 147 Period size: 50 Copynumber: 2.8 Consensus size: 50 41764743 TTTTCTGTAC * * * * * ** 41764753 TGCCAATGTCATATCCCAGATATGATCTTACATAAAAGTTCTCATATCGG 1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG * * * ** * * 41764803 TGCCTATGCCATGTCCCAGACATAGTCTTACGGGGGACCTCTCATCTCGG 1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG * 41764853 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTC 1 TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTC 41764894 ATTCCCTTAA Statistics Matches: 70, Mismatches: 21, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 50 70 1.00 ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27 Consensus pattern (50 bp): TGCCAATGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATATCGG Found at i:41767764 original size:20 final size:20 Alignment explanation

Indices: 41767741--41767853 Score: 68 Period size: 20 Copynumber: 5.7 Consensus size: 20 41767731 GTACAGTCAT * 41767741 GGGCACCAAAGTGCGAACAG 1 GGGCACCAAAGTGCAAACAG * * * 41767761 GGGCA-GATACGTGCAAATAG 1 GGGCACCA-AAGTGCAAACAG * * * * * 41767781 GGACACCGAAGTGTATATAG 1 GGGCACCAAAGTGCAAACAG * * 41767801 GGGCACCAAAGTGCGAACAA 1 GGGCACCAAAGTGCAAACAG * 41767821 GGGCA-CATACGTGCAAACAG 1 GGGCACCA-AAGTGCAAACAG * * 41767841 GGACACCAGAGTG 1 GGGCACCAAAGTG 41767854 TATATAGGGG Statistics Matches: 66, Mismatches: 23, Indels: 8 0.68 0.24 0.08 Matches are distributed among these distances: 19 3 0.05 20 61 0.92 21 2 0.03 ACGTcount: A:0.35, C:0.21, G:0.33, T:0.11 Consensus pattern (20 bp): GGGCACCAAAGTGCAAACAG Found at i:41767805 original size:60 final size:60 Alignment explanation

Indices: 41767741--41767926 Score: 248 Period size: 60 Copynumber: 3.1 Consensus size: 60 41767731 GTACAGTCAT * 41767741 GGGCACCAAAGTGCGAACAGGGGCAGATACGTGCAAATAGGGACACC-GAAGTGTATATAG 1 GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAG-AGTGTATATAG * * 41767801 GGGCACCAAAGTGCGAACAAGGGCACATACGTGCAAACAGGGACACCAGAGTGTATATAG 1 GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATATAG *** * ** * * * 41767861 GGGCATTGAAGTGCGAACAGGAGCACAGGCGTGCAAATAGAGACACCAGAGTGTATACAT 1 GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATATAG 41767921 GGGCAC 1 GGGCAC 41767927 GCAGGGGCAC Statistics Matches: 110, Mismatches: 15, Indels: 2 0.87 0.12 0.02 Matches are distributed among these distances: 60 109 0.99 61 1 0.01 ACGTcount: A:0.35, C:0.20, G:0.32, T:0.13 Consensus pattern (60 bp): GGGCACCAAAGTGCGAACAGGGGCACATACGTGCAAATAGGGACACCAGAGTGTATATAG Found at i:41767982 original size:57 final size:56 Alignment explanation

Indices: 41767913--41768030 Score: 209 Period size: 57 Copynumber: 2.1 Consensus size: 56 41767903 ACACCAGAGT * 41767913 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAATGGCACTTCTTCATTTCC 1 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAAC-AAGGGCACTTCTTCATTTCC * 41767970 GTATACATGGGCACGTAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCC 1 GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCC 41768026 GTATA 1 GTATA 41768031 TAATGGAACT Statistics Matches: 59, Mismatches: 2, Indels: 1 0.95 0.03 0.02 Matches are distributed among these distances: 56 24 0.41 57 35 0.59 ACGTcount: A:0.26, C:0.23, G:0.25, T:0.25 Consensus pattern (56 bp): GTATACATGGGCACGCAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCC Found at i:41768113 original size:85 final size:85 Alignment explanation

Indices: 41767970--41768133 Score: 265 Period size: 85 Copynumber: 1.9 Consensus size: 85 41767960 CTTCATTTCC * * * * * 41767970 GTATACATGGGCACGTAGGGGCACAGTTGTGCAAACAAGGGCACTTCTTCATTTCCGTATATAAT 1 GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAAGAGCACTTCTTCATTTCCGTATACAAT 41768035 GGAACTCATTACATCAGAGT 66 GGAACTCATTACATCAGAGT * 41768055 GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAATAGCACTTCTTCATTTCCGTATACAAT 1 GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAAGAGCACTTCTTCATTTCCGTATACAAT * 41768120 GGAACTCGTTACAT 66 GGAACTCATTACAT 41768134 TCATAGATAA Statistics Matches: 72, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 85 72 1.00 ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26 Consensus pattern (85 bp): GTATACATGAGCACGCAGGGGCACAGTCGTGCAAACAAGAGCACTTCTTCATTTCCGTATACAAT GGAACTCATTACATCAGAGT Found at i:41769126 original size:14 final size:14 Alignment explanation

Indices: 41769107--41769133 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 41769097 ATGGACAAAT 41769107 TCTAAACCCTAAAC 1 TCTAAACCCTAAAC 41769121 TCTAAACCCTAAA 1 TCTAAACCCTAAA 41769134 TTTATAATTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22 Consensus pattern (14 bp): TCTAAACCCTAAAC Found at i:41770259 original size:16 final size:17 Alignment explanation

Indices: 41770240--41770274 Score: 63 Period size: 17 Copynumber: 2.1 Consensus size: 17 41770230 GGCCAAGCAA 41770240 ATCAAA-CCAAGATTCG 1 ATCAAAGCCAAGATTCG 41770256 ATCAAAGCCAAGATTCG 1 ATCAAAGCCAAGATTCG 41770273 AT 1 AT 41770275 GATGAATCTT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 16 6 0.33 17 12 0.67 ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20 Consensus pattern (17 bp): ATCAAAGCCAAGATTCG Found at i:41786359 original size:20 final size:18 Alignment explanation

Indices: 41786330--41786383 Score: 63 Period size: 19 Copynumber: 2.8 Consensus size: 18 41786320 TTTTAAAAAC 41786330 AATTTAACTTTGATTGAAA 1 AATTTAAC-TTGATTGAAA 41786349 AATTCTAACTTGATTGAAA 1 AATT-TAACTTGATTGAAA * 41786368 CCATTTTAACTTGATT 1 --AATTTAACTTGATT 41786384 TAAAGGTTGA Statistics Matches: 31, Mismatches: 1, Indels: 5 0.84 0.03 0.14 Matches are distributed among these distances: 19 14 0.45 20 14 0.45 21 3 0.10 ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43 Consensus pattern (18 bp): AATTTAACTTGATTGAAA Found at i:41786361 original size:19 final size:19 Alignment explanation

Indices: 41786326--41786383 Score: 73 Period size: 20 Copynumber: 2.9 Consensus size: 19 41786316 CTTGTTTTAA 41786326 AAACAATTTAACTTTGATTG 1 AAACAATTTAAC-TTGATTG 41786346 AAA-AATTCTAACTTGATTG 1 AAACAATT-TAACTTGATTG * 41786365 AAACCATTTTAACTTGATT 1 AAA-CAATTTAACTTGATT 41786384 TAAAGGTTGA Statistics Matches: 34, Mismatches: 1, Indels: 6 0.83 0.02 0.15 Matches are distributed among these distances: 19 14 0.41 20 17 0.50 21 3 0.09 ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40 Consensus pattern (19 bp): AAACAATTTAACTTGATTG Found at i:41788674 original size:20 final size:20 Alignment explanation

Indices: 41788604--41788674 Score: 81 Period size: 20 Copynumber: 3.5 Consensus size: 20 41788594 AAACCCGATA * * 41788604 GGTATCGATATTTTTTAAGAT 1 GGTATCGATA-ATTTTAAAAT 41788625 GGTATCGATAATTTTATAAAT 1 GGTATCGATAATTTTA-AAAT * * 41788646 -ATATTGATAATTTTAAAAT 1 GGTATCGATAATTTTAAAAT 41788665 GGTATCGATA 1 GGTATCGATA 41788675 CAAAATCACG Statistics Matches: 42, Mismatches: 6, Indels: 5 0.79 0.11 0.09 Matches are distributed among these distances: 19 4 0.10 20 25 0.60 21 13 0.31 ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44 Consensus pattern (20 bp): GGTATCGATAATTTTAAAAT Done.