Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A13

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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 2708888 characters in sequence are not A, C, G, or T


File 3 of 332

Found at i:788484 original size:21 final size:21

Alignment explanation

Indices: 788460--788509 Score: 73 Period size: 21 Copynumber: 2.4 Consensus size: 21 788450 GTGTCATATT 788460 TCAGGCACCTCGTGTGTCGTA 1 TCAGGCACCTCGTGTGTCGTA * * 788481 TCAGGCATCTCGTGTGTCGTT 1 TCAGGCACCTCGTGTGTCGTA * 788502 TTAGGCAC 1 TCAGGCAC 788510 TTTATGTGTC Statistics Matches: 25, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 25 1.00 ACGTcount: A:0.14, C:0.26, G:0.28, T:0.32 Consensus pattern (21 bp): TCAGGCACCTCGTGTGTCGTA Found at i:788517 original size:21 final size:21 Alignment explanation

Indices: 788439--788521 Score: 60 Period size: 21 Copynumber: 3.9 Consensus size: 21 788429 TTTATCGATC * * 788439 AGGCACTTTATGTGTCATATTT 1 AGGCACTTCATGTGTCGT-TTT * * * * 788461 CAGGCACCTCGTGTGTCGTATC 1 -AGGCACTTCATGTGTCGTTTT * 788483 AGGCA-TCTCGTGTGTCGTTTT 1 AGGCACT-TCATGTGTCGTTTT * 788504 AGGCACTTTATGTGTCGT 1 AGGCACTTCATGTGTCGT 788522 ACTCTAATCA Statistics Matches: 47, Mismatches: 11, Indels: 6 0.73 0.17 0.09 Matches are distributed among these distances: 21 31 0.66 22 2 0.04 23 14 0.30 ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39 Consensus pattern (21 bp): AGGCACTTCATGTGTCGTTTT Found at i:788704 original size:18 final size:19 Alignment explanation

Indices: 788683--788723 Score: 59 Period size: 19 Copynumber: 2.2 Consensus size: 19 788673 AATGAAATGA 788683 GAAATTGA-AT-TGAGAATT 1 GAAATTGAGATATGAG-ATT 788701 GAAATTGAGATATGAGATT 1 GAAATTGAGATATGAGATT 788720 GAAA 1 GAAA 788724 ACATGAACCA Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 18 8 0.38 19 9 0.43 20 4 0.19 ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29 Consensus pattern (19 bp): GAAATTGAGATATGAGATT Found at i:788832 original size:17 final size:17 Alignment explanation

Indices: 788810--788842 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 788800 TATTGTTAAG 788810 AAGTAAAGTGTGAATAC 1 AAGTAAAGTGTGAATAC * 788827 AAGTAAATTGTGAATA 1 AAGTAAAGTGTGAATA 788843 TATTGTATAT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.48, C:0.03, G:0.21, T:0.27 Consensus pattern (17 bp): AAGTAAAGTGTGAATAC Found at i:803026 original size:19 final size:19 Alignment explanation

Indices: 803004--803041 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 802994 CCACACAGCA 803004 TAGGCTGTGACACACGGCC 1 TAGGCTGTGACACACGGCC 803023 TAGGCTGTGACACACGGCC 1 TAGGCTGTGACACACGGCC 803042 GTGTGTCCCT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.21, C:0.32, G:0.32, T:0.16 Consensus pattern (19 bp): TAGGCTGTGACACACGGCC Found at i:810134 original size:125 final size:125 Alignment explanation

Indices: 809895--810122 Score: 384 Period size: 125 Copynumber: 1.8 Consensus size: 125 809885 ATAACAACGA * * * * * 809895 ACACTCCTTAGCATCACACCTTAAATGTAAGATCATCCCTTAACATAGACAACCTAGAAACTCCG 1 ACACTCCTTAGCACCACACCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCA * 809960 AAACATTGTAGCAAAAATACTCCATAAAAACAAAAGAAACACAAAAATTAGAAATCGAGC 66 AAAAATTGTAGCAAAAATACTCCATAAAAACAAAAGAAACACAAAAATTAGAAATCGAGC * 810020 ACACTCCTTAGCACCACTCCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCA 1 ACACTCCTTAGCACCACACCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCA * 810085 AAAAATTGTAGCAAGAATACTCCATAAAAACAAAAGAA 66 AAAAATTGTAGCAAAAATACTCCATAAAAACAAAAGAA 810123 CGACGAAAAT Statistics Matches: 95, Mismatches: 8, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 125 95 1.00 ACGTcount: A:0.47, C:0.25, G:0.09, T:0.19 Consensus pattern (125 bp): ACACTCCTTAGCACCACACCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCA AAAAATTGTAGCAAAAATACTCCATAAAAACAAAAGAAACACAAAAATTAGAAATCGAGC Found at i:810140 original size:12 final size:12 Alignment explanation

Indices: 810125--810149 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 810115 CAAAAGAACG 810125 ACGAAAATTAAA 1 ACGAAAATTAAA 810137 ACGAAAATTAAA 1 ACGAAAATTAAA 810149 A 1 A 810150 ATTGAGCACA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16 Consensus pattern (12 bp): ACGAAAATTAAA Found at i:810158 original size:125 final size:124 Alignment explanation

Indices: 809902--810162 Score: 321 Period size: 125 Copynumber: 2.1 Consensus size: 124 809892 CGAACACTCC * * * * * * 809902 TTAGCATCACACCTTAAATGTAAGATCATCCCTTAACATAGACAACCTAGAAACTCCGAAACATT 1 TTAGCA-CACTCCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCAAAAAATT ** **** 809967 GTAGCAAAAATACTCCATAAAAACAAAAGAAACACAAAAATTAGAAATCGAGCACACTCC 65 GTAGCAAAAATACTCCATAAAAACAAAAGAAACACAAAAATTAGAAATCGAAAACAAAAA 810027 TTAGCACCACTCCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCAAAAAATT 1 TTAGCA-CACTCCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCAAAAAATT * * * 810092 GTAGCAAGAATACTCCATAAAAACAAAAG-AACGACGAAAATTA-AAA-CGAAAATTAAAAA 65 GTAGCAAAAATACTCCATAAAAACAAAAGAAAC-ACAAAAATTAGAAATCGAAAA-CAAAAA 810151 TTGAGCACACTC 1 TT-AGCACACTC 810163 GTTAGCATCA Statistics Matches: 117, Mismatches: 16, Indels: 7 0.84 0.11 0.05 Matches are distributed among these distances: 123 4 0.03 124 14 0.12 125 99 0.85 ACGTcount: A:0.49, C:0.23, G:0.10, T:0.19 Consensus pattern (124 bp): TTAGCACACTCCTTAAATGTAAGATCATACCTTAACACAGACAACCTAAAAACTCCAAAAAATTG TAGCAAAAATACTCCATAAAAACAAAAGAAACACAAAAATTAGAAATCGAAAACAAAAA Found at i:810959 original size:24 final size:24 Alignment explanation

Indices: 810923--810969 Score: 58 Period size: 24 Copynumber: 2.0 Consensus size: 24 810913 GCAATTTTGG ** * * 810923 ACTTTTCTTATTTTCCTTTTCTTC 1 ACTTTTCAAATTTCCCTCTTCTTC 810947 ACTTTTCAAATTTCCCTCTTCTT 1 ACTTTTCAAATTTCCCTCTTCTT 810970 TTCCTTTCCT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 24 19 1.00 ACGTcount: A:0.13, C:0.28, G:0.00, T:0.60 Consensus pattern (24 bp): ACTTTTCAAATTTCCCTCTTCTTC Found at i:812461 original size:13 final size:13 Alignment explanation

Indices: 812443--812468 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 812433 TTGCCCCTGC 812443 CACTAAAAGTCGA 1 CACTAAAAGTCGA 812456 CACTAAAAGTCGA 1 CACTAAAAGTCGA 812469 GATATAAGTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15 Consensus pattern (13 bp): CACTAAAAGTCGA Found at i:815063 original size:14 final size:14 Alignment explanation

Indices: 815044--815073 Score: 60 Period size: 14 Copynumber: 2.1 Consensus size: 14 815034 GGTAATGATG 815044 TATCAAATGAAGCC 1 TATCAAATGAAGCC 815058 TATCAAATGAAGCC 1 TATCAAATGAAGCC 815072 TA 1 TA 815074 AAACATTTTT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23 Consensus pattern (14 bp): TATCAAATGAAGCC Found at i:816395 original size:12 final size:12 Alignment explanation

Indices: 816378--816402 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 816368 TGAAAAACAT 816378 ATTTCAATGGAA 1 ATTTCAATGGAA 816390 ATTTCAATGGAA 1 ATTTCAATGGAA 816402 A 1 A 816403 CTGCCAAAGT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32 Consensus pattern (12 bp): ATTTCAATGGAA Found at i:817204 original size:17 final size:17 Alignment explanation

Indices: 817182--817216 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 817172 GAAGGGAGAA 817182 TGATTATATTACGGTAG 1 TGATTATATTACGGTAG 817199 TGATTATATTACGGTAG 1 TGATTATATTACGGTAG 817216 T 1 T 817217 ATTCACTCAA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43 Consensus pattern (17 bp): TGATTATATTACGGTAG Found at i:824128 original size:9 final size:9 Alignment explanation

Indices: 824114--824138 Score: 50 Period size: 9 Copynumber: 2.8 Consensus size: 9 824104 AATAATTCAT 824114 AAAGGAGGA 1 AAAGGAGGA 824123 AAAGGAGGA 1 AAAGGAGGA 824132 AAAGGAG 1 AAAGGAG 824139 AAGACCGGTG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00 Consensus pattern (9 bp): AAAGGAGGA Found at i:837960 original size:52 final size:48 Alignment explanation

Indices: 837875--838241 Score: 439 Period size: 46 Copynumber: 7.6 Consensus size: 48 837865 TTTGAGTACT * ** 837875 TCTGATCAAGTG--ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA 1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA * * 837921 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA 1 TCTGATCAAGTGAC-A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA * 837973 TCTGATCAAGTG--ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA 1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA * 838019 TCTGATCAAGTGAC--AAAGTGATAAGTGATAGCTTCAGCTACACTTA 1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA 838065 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA 1 TCTGATCAAGTGAC-A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA * 838117 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA 1 TCTGATCAAGTGAC-A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA * ** 838169 TCTGATCAAGAGAC--AAAGTGATAAGTGATAGCTTTAGCTACACTTA 1 TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA * * 838215 TCTGATCAA--GAAACAAAGTGATAAGTG 1 TCTGATCAAGTGACATAAAGTGATAAGTG 838242 GCTACACTTA Statistics Matches: 289, Mismatches: 16, Indels: 32 0.86 0.05 0.09 Matches are distributed among these distances: 44 2 0.01 46 150 0.52 48 1 0.00 49 2 0.01 50 1 0.00 52 133 0.46 ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29 Consensus pattern (48 bp): TCTGATCAAGTGACATAAAGTGATAAGTGATAGCTTCGGCTACACTTA Found at i:837995 original size:98 final size:97 Alignment explanation

Indices: 837875--838224 Score: 494 Period size: 98 Copynumber: 3.6 Consensus size: 97 837865 TTTGAGTACT * * 837875 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG 1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT- * 837940 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA 65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA * * 837973 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC----- 1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG * * 838033 AAAGTGATAAGTGATAGCTTCAGCTACACTTA 66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA * 838065 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA 1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA 838130 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA 60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA * * * 838169 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAG 1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAG 838225 AAACAAAGTG Statistics Matches: 226, Mismatches: 14, Indels: 24 0.86 0.05 0.09 Matches are distributed among these distances: 92 41 0.18 95 1 0.00 96 1 0.00 98 141 0.62 101 1 0.00 104 41 0.18 ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29 Consensus pattern (97 bp): TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG AAAGTGATAAGTGATAGCTTCGGCTATACTTA Found at i:838223 original size:196 final size:196 Alignment explanation

Indices: 837889--838241 Score: 598 Period size: 196 Copynumber: 1.8 Consensus size: 196 837879 ATCAAGTGAT * * * 837889 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA 1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA * * * * 837954 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA 66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA ** 838019 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG 131 TCTGATCAAGAAACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG 838084 G 196 G * * 838085 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG 1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA * 838150 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA 66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA 838215 TCTGATCAAGAAACAAAGTGATAAGTG 131 TCTGATCAAGAAACAAAGTGATAAGTG 838242 GCTACACTTA Statistics Matches: 145, Mismatches: 12, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 196 145 1.00 ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29 Consensus pattern (196 bp): AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA TCTGATCAAGAAACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG G Found at i:838249 original size:37 final size:37 Alignment explanation

Indices: 838205--838313 Score: 168 Period size: 37 Copynumber: 3.0 Consensus size: 37 838195 GATAGCTTTA 838205 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG * * 838242 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG ** 838279 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG 1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG 838314 ATCATACGTA Statistics Matches: 66, Mismatches: 6, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 35 11 0.17 36 4 0.06 37 51 0.77 ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25 Consensus pattern (37 bp): GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG Found at i:847568 original size:18 final size:18 Alignment explanation

Indices: 847542--847581 Score: 62 Period size: 18 Copynumber: 2.2 Consensus size: 18 847532 TATCAGATGA * 847542 AGAAGAAGAAACTTCTTC 1 AGAAAAAGAAACTTCTTC * 847560 AGAAAAAGAAATTTCTTC 1 AGAAAAAGAAACTTCTTC 847578 AGAA 1 AGAA 847582 GAGTCATCTT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23 Consensus pattern (18 bp): AGAAAAAGAAACTTCTTC Found at i:850763 original size:18 final size:18 Alignment explanation

Indices: 850736--850788 Score: 88 Period size: 18 Copynumber: 2.9 Consensus size: 18 850726 TGTTAATATA * 850736 GGAGTAAATCCCTGATTG 1 GGAGTAAATCCTTGATTG * 850754 GGAGTCAATCCTTGATTG 1 GGAGTAAATCCTTGATTG 850772 GGAGTAAATCCTTGATT 1 GGAGTAAATCCTTGATT 850789 AGGATTTATC Statistics Matches: 32, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 18 32 1.00 ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32 Consensus pattern (18 bp): GGAGTAAATCCTTGATTG Found at i:854198 original size:21 final size:20 Alignment explanation

Indices: 854174--854215 Score: 50 Period size: 20 Copynumber: 2.0 Consensus size: 20 854164 TTTGATAGAA 854174 ATTACAAATATAATTTT-ATTT 1 ATTACAAA-AT-ATTTTCATTT * 854195 ATTAGAAAATATTTTCATTT 1 ATTACAAAATATTTTCATTT 854215 A 1 A 854216 ATAGATTGTG Statistics Matches: 19, Mismatches: 1, Indels: 3 0.83 0.04 0.13 Matches are distributed among these distances: 19 5 0.26 20 7 0.37 21 7 0.37 ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50 Consensus pattern (20 bp): ATTACAAAATATTTTCATTT Found at i:883497 original size:1 final size:1 Alignment explanation

Indices: 883491--883515 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 883481 ATGCAAATTT 883491 AAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAA 883516 GGCAATCTAA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:886968 original size:20 final size:20 Alignment explanation

Indices: 886943--886983 Score: 82 Period size: 20 Copynumber: 2.0 Consensus size: 20 886933 ACCGACTTGT 886943 AATAAATTCAGTAGCACCTC 1 AATAAATTCAGTAGCACCTC 886963 AATAAATTCAGTAGCACCTC 1 AATAAATTCAGTAGCACCTC 886983 A 1 A 886984 CTGGCAATTA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.41, C:0.24, G:0.10, T:0.24 Consensus pattern (20 bp): AATAAATTCAGTAGCACCTC Found at i:890434 original size:49 final size:49 Alignment explanation

Indices: 890362--890458 Score: 194 Period size: 49 Copynumber: 2.0 Consensus size: 49 890352 AACAAGGTTT 890362 TAGTTTAATTAACCCATAATAAACTTTAGGGAAATGACTCAGATACATA 1 TAGTTTAATTAACCCATAATAAACTTTAGGGAAATGACTCAGATACATA 890411 TAGTTTAATTAACCCATAATAAACTTTAGGGAAATGACTCAGATACAT 1 TAGTTTAATTAACCCATAATAAACTTTAGGGAAATGACTCAGATACAT 890459 GAGAACCATC Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 49 48 1.00 ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31 Consensus pattern (49 bp): TAGTTTAATTAACCCATAATAAACTTTAGGGAAATGACTCAGATACATA Found at i:896598 original size:16 final size:17 Alignment explanation

Indices: 896573--896607 Score: 54 Period size: 16 Copynumber: 2.1 Consensus size: 17 896563 TACCAAGCAA * 896573 AAGTTTTCTATC-CTTC 1 AAGTTATCTATCTCTTC 896589 AAGTTATCTATCTCTTC 1 AAGTTATCTATCTCTTC 896606 AA 1 AA 896608 TTTTCCATCC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 11 0.65 17 6 0.35 ACGTcount: A:0.26, C:0.23, G:0.06, T:0.46 Consensus pattern (17 bp): AAGTTATCTATCTCTTC Found at i:897498 original size:15 final size:15 Alignment explanation

Indices: 897474--897527 Score: 56 Period size: 15 Copynumber: 3.6 Consensus size: 15 897464 TCTGAATTTT * 897474 AAAATATAAAGTTAGA 1 AAAAT-TAAAGTTACA * * 897490 AAAATTAAATTTATA 1 AAAATTAAAGTTACA * 897505 AAAATAAAAG-TACA 1 AAAATTAAAGTTACA 897519 AAAATTAAA 1 AAAATTAAA 897528 TTCTAAAATT Statistics Matches: 32, Mismatches: 6, Indels: 2 0.80 0.15 0.05 Matches are distributed among these distances: 14 11 0.34 15 16 0.50 16 5 0.16 ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26 Consensus pattern (15 bp): AAAATTAAAGTTACA Found at i:897501 original size:29 final size:29 Alignment explanation

Indices: 897468--897536 Score: 88 Period size: 29 Copynumber: 2.4 Consensus size: 29 897458 GTTGAATCTG * 897468 AATTTTAAAATAT-AAAGTTAGAAAAATTA 1 AATTTTAAAATATAAAAG-TACAAAAATTA 897497 AATTTATAAAA-ATAAAAGTACAAAAATTA 1 AATTT-TAAAATATAAAAGTACAAAAATTA * 897526 AATTCTAAAAT 1 AATTTTAAAAT 897537 TTTAAAAAAT Statistics Matches: 35, Mismatches: 2, Indels: 6 0.81 0.05 0.14 Matches are distributed among these distances: 28 5 0.14 29 21 0.60 30 9 0.26 ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32 Consensus pattern (29 bp): AATTTTAAAATATAAAAGTACAAAAATTA Found at i:902633 original size:35 final size:36 Alignment explanation

Indices: 902586--902658 Score: 139 Period size: 35 Copynumber: 2.1 Consensus size: 36 902576 ATCTTGAAAC 902586 TTTATTTCCTTTTTCTTCTTCTTCTTCTCCTTTTTT 1 TTTATTTCCTTTTTCTTCTTCTTCTTCTCCTTTTTT 902622 TTTA-TTCCTTTTTCTTCTTCTTCTTCTCCTTTTTT 1 TTTATTTCCTTTTTCTTCTTCTTCTTCTCCTTTTTT 902657 TT 1 TT 902659 GTTTCATTAG Statistics Matches: 37, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 35 33 0.89 36 4 0.11 ACGTcount: A:0.03, C:0.25, G:0.00, T:0.73 Consensus pattern (36 bp): TTTATTTCCTTTTTCTTCTTCTTCTTCTCCTTTTTT Found at i:905567 original size:11 final size:11 Alignment explanation

Indices: 905553--905639 Score: 86 Period size: 11 Copynumber: 8.0 Consensus size: 11 905543 ATATCCAAAC * 905553 AATAATAATAT 1 AATAATAAAAT * 905564 AATAGTAAAAT 1 AATAATAAAAT * * 905575 AGTAACAAAAT 1 AATAATAAAAT * * 905586 AGTAAGAAAAT 1 AATAATAAAAT 905597 AATAATAAAAT 1 AATAATAAAAT * * 905608 AATAACAAAAC 1 AATAATAAAAT 905619 AATAA-AAAAT 1 AATAATAAAAT * 905629 AATAAGAAAAT 1 AATAATAAAAT 905640 TTACAATTTA Statistics Matches: 64, Mismatches: 11, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 10 9 0.14 11 55 0.86 ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22 Consensus pattern (11 bp): AATAATAAAAT Found at i:905606 original size:22 final size:22 Alignment explanation

Indices: 905553--905639 Score: 97 Period size: 22 Copynumber: 4.0 Consensus size: 22 905543 ATATCCAAAC * 905553 AATAATAATATAAT-AGTAAAAT 1 AATAATAAAATAATAAG-AAAAT * * * 905575 AGTAACAAAATAGTAAGAAAAT 1 AATAATAAAATAATAAGAAAAT * * 905597 AATAATAAAATAATAACAAAAC 1 AATAATAAAATAATAAGAAAAT 905619 AATAA-AAAATAATAAGAAAAT 1 AATAATAAAATAATAAGAAAAT 905640 TTACAATTTA Statistics Matches: 53, Mismatches: 11, Indels: 3 0.79 0.16 0.04 Matches are distributed among these distances: 21 14 0.26 22 37 0.70 23 2 0.04 ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22 Consensus pattern (22 bp): AATAATAAAATAATAAGAAAAT Found at i:905606 original size:33 final size:32 Alignment explanation

Indices: 905549--905639 Score: 110 Period size: 33 Copynumber: 2.8 Consensus size: 32 905539 TACAATATCC * * * 905549 AAACAATAATAATATAATAGTAAAATAGTAACA 1 AAACAATAA-AAAATAATAATAAAATAATAACA * * 905582 AAATAGTAAGAAAATAATAATAAAATAATAACA 1 AAACAATAA-AAAATAATAATAAAATAATAACA * 905615 AAACAATAAAAAATAATAAGAAAAT 1 AAACAATAAAAAATAATAATAAAAT 905640 TTACAATTTA Statistics Matches: 49, Mismatches: 9, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 32 15 0.31 33 34 0.69 ACGTcount: A:0.69, C:0.04, G:0.05, T:0.21 Consensus pattern (32 bp): AAACAATAAAAAATAATAATAAAATAATAACA Found at i:917537 original size:12 final size:12 Alignment explanation

Indices: 917520--917546 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 917510 AAGAGAAGGA 917520 TGATGATGATGG 1 TGATGATGATGG 917532 TGATGATGATGG 1 TGATGATGATGG 917544 TGA 1 TGA 917547 GGACCTAATA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.26, C:0.00, G:0.41, T:0.33 Consensus pattern (12 bp): TGATGATGATGG Found at i:919537 original size:20 final size:20 Alignment explanation

Indices: 919475--919536 Score: 76 Period size: 20 Copynumber: 3.2 Consensus size: 20 919465 AATTTAAAAT * 919475 TTTTTATAAA-TATTTT-AA 1 TTTTTAAAAATTATTTTGAA * 919493 ATTTTAAAAATTATTTTGAA 1 TTTTTAAAAATTATTTTGAA * 919513 TTTTTGAAAATTATTTTG-A 1 TTTTTAAAAATTATTTTGAA 919532 TTTTT 1 TTTTT 919537 TTTTTTGTAA Statistics Matches: 38, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 18 8 0.21 19 12 0.32 20 18 0.47 ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60 Consensus pattern (20 bp): TTTTTAAAAATTATTTTGAA Found at i:920851 original size:18 final size:18 Alignment explanation

Indices: 920830--920866 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 920820 TTTTTTGAAT 920830 TTTTATTAACTTTTTATA 1 TTTTATTAACTTTTTATA * * 920848 TTTTATTGATTTTTTATA 1 TTTTATTAACTTTTTATA 920866 T 1 T 920867 ATATTTAATA Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70 Consensus pattern (18 bp): TTTTATTAACTTTTTATA Found at i:922829 original size:29 final size:30 Alignment explanation

Indices: 922776--922834 Score: 77 Period size: 29 Copynumber: 2.0 Consensus size: 30 922766 ATGAACATTC * 922776 TCATTTAATAATTTCCATGTACAAT-ATCA 1 TCATTTAATAATTTCCATATACAATCATCA * 922805 TCATTTCAT-ATTTCCATATATCAATCATCA 1 TCATTTAATAATTTCCATATA-CAATCATCA 922835 CGTATCGTCA Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 28 10 0.38 29 12 0.46 30 4 0.15 ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42 Consensus pattern (30 bp): TCATTTAATAATTTCCATATACAATCATCA Found at i:923540 original size:26 final size:26 Alignment explanation

Indices: 923511--923567 Score: 64 Period size: 24 Copynumber: 2.2 Consensus size: 26 923501 TTGATTATGT ** 923511 AACAAAGTTCACATTTATA-ACATTCA 1 AACAAA-TTCACACATATACACATTCA 923537 AAC-AATTCACACATATACACATTCA 1 AACAAATTCACACATATACACATTCA 923562 ATACAA 1 A-ACAA 923568 GCACATAAAT Statistics Matches: 26, Mismatches: 2, Indels: 5 0.79 0.06 0.15 Matches are distributed among these distances: 24 10 0.38 25 10 0.38 26 5 0.19 27 1 0.04 ACGTcount: A:0.49, C:0.23, G:0.02, T:0.26 Consensus pattern (26 bp): AACAAATTCACACATATACACATTCA Found at i:923572 original size:25 final size:24 Alignment explanation

Indices: 923526--923572 Score: 60 Period size: 25 Copynumber: 1.9 Consensus size: 24 923516 AGTTCACATT * 923526 TATAACATTCAAACAATTCACACA 1 TATAACATTCAAACAATGCACACA 923550 TATACACATTCAATACAA-GCACA 1 TATA-ACATTCAA-ACAATGCACA 923573 TAAATATACA Statistics Matches: 20, Mismatches: 1, Indels: 3 0.83 0.04 0.12 Matches are distributed among these distances: 24 4 0.20 25 12 0.60 26 4 0.20 ACGTcount: A:0.49, C:0.26, G:0.02, T:0.23 Consensus pattern (24 bp): TATAACATTCAAACAATGCACACA Found at i:940104 original size:51 final size:51 Alignment explanation

Indices: 940044--940143 Score: 200 Period size: 51 Copynumber: 2.0 Consensus size: 51 940034 ATTAATTTGG 940044 GTAAAAAGTATAAAAATATCTTATCTTCAACTTATTATACACCCATTCAGA 1 GTAAAAAGTATAAAAATATCTTATCTTCAACTTATTATACACCCATTCAGA 940095 GTAAAAAGTATAAAAATATCTTATCTTCAACTTATTATACACCCATTCA 1 GTAAAAAGTATAAAAATATCTTATCTTCAACTTATTATACACCCATTCA 940144 ATTACATGTT Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 51 49 1.00 ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34 Consensus pattern (51 bp): GTAAAAAGTATAAAAATATCTTATCTTCAACTTATTATACACCCATTCAGA Found at i:941164 original size:3 final size:3 Alignment explanation

Indices: 941156--941195 Score: 80 Period size: 3 Copynumber: 13.3 Consensus size: 3 941146 TTTTATAGAG 941156 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A 941196 GGTGTTATTA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 37 1.00 ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): AAT Found at i:943645 original size:3 final size:3 Alignment explanation

Indices: 943637--943662 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 943627 AATGAGTAGG 943637 TAA TAA TAA TAA TAA TAA TAA TAA TA 1 TAA TAA TAA TAA TAA TAA TAA TAA TA 943663 GGAGTAATTA 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:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (3 bp): TAA Found at i:950774 original size:24 final size:25 Alignment explanation

Indices: 950744--950792 Score: 73 Period size: 25 Copynumber: 2.0 Consensus size: 25 950734 TAGTTTGGAC * 950744 AACAACA-TTAAACTTAAAACCTAA 1 AACAACACTTAAAATTAAAACCTAA * 950768 AACAACACTTAAAATTAAAGCCTAA 1 AACAACACTTAAAATTAAAACCTAA 950793 TAAAGCAACA Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 24 7 0.32 25 15 0.68 ACGTcount: A:0.57, C:0.20, G:0.02, T:0.20 Consensus pattern (25 bp): AACAACACTTAAAATTAAAACCTAA Found at i:951751 original size:6 final size:6 Alignment explanation

Indices: 951740--951789 Score: 55 Period size: 6 Copynumber: 8.3 Consensus size: 6 951730 GTAGGTAAAG * * * * * 951740 TAGTAA TAGTAA TAGTAA TAGTAG TAGTAG TAATAA TAATAA TAATAA 1 TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA TAGTAA 951788 TA 1 TA 951790 ATAGGGATAA Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 6 41 1.00 ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34 Consensus pattern (6 bp): TAGTAA Found at i:952799 original size:8 final size:8 Alignment explanation

Indices: 952786--952815 Score: 60 Period size: 8 Copynumber: 3.8 Consensus size: 8 952776 CAGCAACATG 952786 CATGCAAC 1 CATGCAAC 952794 CATGCAAC 1 CATGCAAC 952802 CATGCAAC 1 CATGCAAC 952810 CATGCA 1 CATGCA 952816 GGAGCAAGCA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 22 1.00 ACGTcount: A:0.37, C:0.37, G:0.13, T:0.13 Consensus pattern (8 bp): CATGCAAC Found at i:967140 original size:16 final size:17 Alignment explanation

Indices: 967119--967158 Score: 55 Period size: 16 Copynumber: 2.4 Consensus size: 17 967109 TTAAATTAAT 967119 TTAAATTATTTT-TCAA 1 TTAAATTATTTTCTCAA * 967135 TTAAATAATTTTCTCAA 1 TTAAATTATTTTCTCAA * 967152 TTCAATT 1 TTAAATT 967159 CTAATCCTAA Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 16 11 0.55 17 9 0.45 ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53 Consensus pattern (17 bp): TTAAATTATTTTCTCAA Found at i:975385 original size:19 final size:19 Alignment explanation

Indices: 975361--975398 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 975351 TTGAGATTGC 975361 CAACCTATTTGCCTGAAAT 1 CAACCTATTTGCCTGAAAT 975380 CAACCTATTTGCCTGAAAT 1 CAACCTATTTGCCTGAAAT 975399 TATTCATTTC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32 Consensus pattern (19 bp): CAACCTATTTGCCTGAAAT Found at i:975492 original size:6 final size:7 Alignment explanation

Indices: 975474--975499 Score: 52 Period size: 7 Copynumber: 3.7 Consensus size: 7 975464 CACTCCCTTT 975474 TAAAAAA 1 TAAAAAA 975481 TAAAAAA 1 TAAAAAA 975488 TAAAAAA 1 TAAAAAA 975495 TAAAA 1 TAAAA 975500 TTTCAAAGCG Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15 Consensus pattern (7 bp): TAAAAAA Found at i:977496 original size:24 final size:24 Alignment explanation

Indices: 977469--977522 Score: 65 Period size: 24 Copynumber: 2.2 Consensus size: 24 977459 TTTCTTTCCT * 977469 TTGCATT-CATCCCATGCATTTGCA 1 TTGCATTGCATCACATGCA-TTGCA ** 977493 TTGCATTGCATCATGTGCATTGCA 1 TTGCATTGCATCACATGCATTGCA 977517 TTGCAT 1 TTGCAT 977523 CATTTGCATT Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 24 18 0.69 25 8 0.31 ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39 Consensus pattern (24 bp): TTGCATTGCATCACATGCATTGCA Found at i:977511 original size:19 final size:19 Alignment explanation

Indices: 977489--977532 Score: 79 Period size: 19 Copynumber: 2.3 Consensus size: 19 977479 CCCATGCATT 977489 TGCATTGCATTGCATCATG 1 TGCATTGCATTGCATCATG * 977508 TGCATTGCATTGCATCATT 1 TGCATTGCATTGCATCATG 977527 TGCATT 1 TGCATT 977533 AGATTTTCCC Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 19 24 1.00 ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41 Consensus pattern (19 bp): TGCATTGCATTGCATCATG Found at i:985756 original size:3 final size:3 Alignment explanation

Indices: 985750--985797 Score: 60 Period size: 3 Copynumber: 16.0 Consensus size: 3 985740 ATCATCATCG * * * * 985750 GAA GAA GAA GAA GAG GAG GAA GAA GAA GAA GAG GAA GAA GAA GGA GAA 1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA 985798 CCTGGAGTGG Statistics Matches: 39, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 3 39 1.00 ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00 Consensus pattern (3 bp): GAA Found at i:985770 original size:18 final size:18 Alignment explanation

Indices: 985749--985797 Score: 80 Period size: 18 Copynumber: 2.7 Consensus size: 18 985739 AATCATCATC 985749 GGAAGAAGAAGAAGAGGA 1 GGAAGAAGAAGAAGAGGA 985767 GGAAGAAGAAGAAGAGGA 1 GGAAGAAGAAGAAGAGGA * * 985785 AGAAGAAGGAGAA 1 GGAAGAAGAAGAA 985798 CCTGGAGTGG Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 29 1.00 ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00 Consensus pattern (18 bp): GGAAGAAGAAGAAGAGGA Found at i:985771 original size:15 final size:15 Alignment explanation

Indices: 985753--985792 Score: 71 Period size: 15 Copynumber: 2.7 Consensus size: 15 985743 ATCATCGGAA * 985753 GAAGAAGAAGAGGAG 1 GAAGAAGAAGAAGAG 985768 GAAGAAGAAGAAGAG 1 GAAGAAGAAGAAGAG 985783 GAAGAAGAAG 1 GAAGAAGAAG 985793 GAGAACCTGG Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 15 24 1.00 ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00 Consensus pattern (15 bp): GAAGAAGAAGAAGAG Found at i:997814 original size:20 final size:20 Alignment explanation

Indices: 997786--997835 Score: 82 Period size: 20 Copynumber: 2.5 Consensus size: 20 997776 TTGATTAAGG 997786 TATCGATACCTTGGATGTGA 1 TATCGATACCTTGGATGTGA * * 997806 TATCAATACCTTGGATGTGG 1 TATCGATACCTTGGATGTGA 997826 TATCGATACC 1 TATCGATACC 997836 AAAATTACAT Statistics Matches: 27, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 27 1.00 ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34 Consensus pattern (20 bp): TATCGATACCTTGGATGTGA Found at i:1008032 original size:13 final size:13 Alignment explanation

Indices: 1008014--1008039 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 1008004 GCTTTAGAAT 1008014 TTGGGTTTTTAAG 1 TTGGGTTTTTAAG 1008027 TTGGGTTTTTAAG 1 TTGGGTTTTTAAG 1008040 ATAATCTCGA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54 Consensus pattern (13 bp): TTGGGTTTTTAAG Found at i:1011274 original size:13 final size:14 Alignment explanation

Indices: 1011251--1011283 Score: 50 Period size: 13 Copynumber: 2.4 Consensus size: 14 1011241 ATATTACATT * 1011251 AATATATAATTTAA 1 AATATATAATTAAA 1011265 AATATA-AATTAAA 1 AATATATAATTAAA 1011278 AATATA 1 AATATA 1011284 GCAAAATAAT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 13 12 0.67 14 6 0.33 ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36 Consensus pattern (14 bp): AATATATAATTAAA Found at i:1017022 original size:18 final size:17 Alignment explanation

Indices: 1016995--1017028 Score: 50 Period size: 18 Copynumber: 1.9 Consensus size: 17 1016985 CAACAATTCA * 1016995 TCAACCAACTCCACCAT 1 TCAACCAACTCAACCAT 1017012 TCAATCCAACTCAACCA 1 TCAA-CCAACTCAACCA 1017029 CGAATGCAAA Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 4 0.27 18 11 0.73 ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18 Consensus pattern (17 bp): TCAACCAACTCAACCAT Found at i:1017864 original size:4 final size:4 Alignment explanation

Indices: 1017855--1017916 Score: 124 Period size: 4 Copynumber: 15.5 Consensus size: 4 1017845 ATAAATGAAA 1017855 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT 1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT 1017903 ATGT ATGT ATGT AT 1 ATGT ATGT ATGT AT 1017917 ACGGGAAGAA Statistics Matches: 58, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 58 1.00 ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50 Consensus pattern (4 bp): ATGT Found at i:1020645 original size:16 final size:16 Alignment explanation

Indices: 1020624--1020692 Score: 111 Period size: 16 Copynumber: 4.3 Consensus size: 16 1020614 TTGGTTTGCT 1020624 GTAATGGAATAGAGGC 1 GTAATGGAATAGAGGC * * 1020640 GTAATGGAATAAAGGT 1 GTAATGGAATAGAGGC * 1020656 GTAATGGAATAGAGGT 1 GTAATGGAATAGAGGC 1020672 GTAATGGAATAGAGGC 1 GTAATGGAATAGAGGC 1020688 GTAAT 1 GTAAT 1020693 AGCAATTCAA Statistics Matches: 49, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 16 49 1.00 ACGTcount: A:0.39, C:0.03, G:0.35, T:0.23 Consensus pattern (16 bp): GTAATGGAATAGAGGC Found at i:1020736 original size:45 final size:44 Alignment explanation

Indices: 1020671--1020768 Score: 135 Period size: 44 Copynumber: 2.2 Consensus size: 44 1020661 GGAATAGAGG * 1020671 TGTAATGGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAA 1 TGTAATGGAATAGAGACGTAATAG-AATTC-ATGTGTTTGGTTGAA * * 1020716 TGTAATGGAATAGAGACGTAATAGTATTCTTGTGTTTGGTTGAA 1 TGTAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAA * 1020760 TGGAATGGA 1 TGTAATGGA 1020769 GGTGTAATAG Statistics Matches: 48, Mismatches: 4, Indels: 3 0.87 0.07 0.05 Matches are distributed among these distances: 43 1 0.02 44 24 0.50 45 23 0.48 ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35 Consensus pattern (44 bp): TGTAATGGAATAGAGACGTAATAGAATTCATGTGTTTGGTTGAA Found at i:1020946 original size:18 final size:17 Alignment explanation

Indices: 1020925--1020959 Score: 52 Period size: 18 Copynumber: 2.0 Consensus size: 17 1020915 TTATTATTAA * 1020925 ATATATTTTAATTAAAAT 1 ATATAATTTAA-TAAAAT 1020943 ATATAATTTAATAAAAT 1 ATATAATTTAATAAAAT 1020960 TCTTAATAAT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 6 0.38 18 10 0.62 ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46 Consensus pattern (17 bp): ATATAATTTAATAAAAT Found at i:1021031 original size:25 final size:26 Alignment explanation

Indices: 1021003--1021052 Score: 66 Period size: 26 Copynumber: 2.0 Consensus size: 26 1020993 ATAATAATAT 1021003 ATGA-TACTATAAAATATAATTTAAC 1 ATGATTACTATAAAATATAATTTAAC * * * 1021028 ATGATTATTATTAAATATATTTTAA 1 ATGATTACTATAAAATATAATTTAA 1021053 TTAAAATATA Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 25 4 0.19 26 17 0.81 ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44 Consensus pattern (26 bp): ATGATTACTATAAAATATAATTTAAC Found at i:1021063 original size:18 final size:17 Alignment explanation

Indices: 1021040--1021076 Score: 51 Period size: 16 Copynumber: 2.2 Consensus size: 17 1021030 GATTATTATT 1021040 AAATATAT--TTTAATTA 1 AAATATATGATTTAA-TA 1021056 AAATATATGATTTAATA 1 AAATATATGATTTAATA 1021073 AAAT 1 AAAT 1021077 TCTTAATAAT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 16 8 0.42 17 6 0.32 18 5 0.26 ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43 Consensus pattern (17 bp): AAATATATGATTTAATA Found at i:1021125 original size:61 final size:60 Alignment explanation

Indices: 1020940--1021137 Score: 160 Period size: 60 Copynumber: 3.3 Consensus size: 60 1020930 TTTTAATTAA * * 1020940 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTT-C-ATATAAT 1 AATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAATAAT * * * * * * * * 1020998 AATATATGATACT-ATAAAATATAATTTAA-CATGATTATTATTAAAT-ATATTT--TAATTAA- 1 AATATATGAT-TTAATAAAAT-T--CTTAATAATCAATATTCTTATATGA-ATTTACTAAATAAT * * 1021057 AATATATGATTTAATAAAATTCTTAATAATCAATTTTCTTATATGAATTTACTAAAATCAT 1 AATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACT-AAATAAT ** 1021118 AATATATGATACAATAAAAT 1 AATATATGATTTAATAAAAT 1021138 ATAATTTGAA Statistics Matches: 105, Mismatches: 22, Indels: 23 0.70 0.15 0.15 Matches are distributed among these distances: 56 4 0.04 57 15 0.14 58 19 0.18 59 21 0.20 60 24 0.23 61 22 0.21 ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43 Consensus pattern (60 bp): AATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAATAAT Found at i:1021183 original size:18 final size:17 Alignment explanation

Indices: 1021160--1021196 Score: 51 Period size: 16 Copynumber: 2.2 Consensus size: 17 1021150 AATTATTATT 1021160 AAATATAT--TTTAATTA 1 AAATATATGATTTAA-TA 1021176 AAATATATGATTTAATA 1 AAATATATGATTTAATA 1021193 AAAT 1 AAAT 1021197 TTAAAATAAT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 16 8 0.42 17 6 0.32 18 5 0.26 ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43 Consensus pattern (17 bp): AAATATATGATTTAATA Found at i:1021199 original size:28 final size:29 Alignment explanation

Indices: 1021118--1021200 Score: 71 Period size: 28 Copynumber: 2.8 Consensus size: 29 1021108 CTAAAATCAT * * 1021118 AATATATGA-TACAATAAAATATAATTTGA 1 AATATATGATTA-AATAAAATTTAATTTAA * * * 1021147 AATAATTATTATTAAATATATTTTAA-TTAA 1 AAT-A-TATGATTAAATAAAATTTAATTTAA * 1021177 AATATATGATTTAATAAAATTTAA 1 AATATATGATTAAATAAAATTTAA 1021201 AATAATTATT Statistics Matches: 42, Mismatches: 9, Indels: 7 0.72 0.16 0.12 Matches are distributed among these distances: 28 16 0.38 29 4 0.10 30 7 0.17 31 13 0.31 32 2 0.05 ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42 Consensus pattern (29 bp): AATATATGATTAAATAAAATTTAATTTAA Found at i:1021206 original size:120 final size:117 Alignment explanation

Indices: 1020905--1021197 Score: 489 Period size: 117 Copynumber: 2.5 Consensus size: 117 1020895 TTAATCATAT * 1020905 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT 1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT * * 1020970 CAATATTCTTATATGAATTTCATATAATAATATATGATACTATAAAATATAA 66 CAATATTCTTATATGAATTTCAAATAATAATATATGATACAATAAAATATAA * 1021022 TTTAACATGATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT 1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT * * 1021087 CAATTTTCTTATATGAATTTACTAAAATCATAATATATGATACAATAAAATATAA 66 CAATATTCTTATATGAATTT-C--AAATAATAATATATGATACAATAAAATATAA 1021142 TTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT 1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT 1021198 TAAAATAATT Statistics Matches: 165, Mismatches: 7, Indels: 5 0.93 0.04 0.03 Matches are distributed among these distances: 117 82 0.50 118 1 0.01 120 80 0.48 121 2 0.01 ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45 Consensus pattern (117 bp): TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT CAATATTCTTATATGAATTTCAAATAATAATATATGATACAATAAAATATAA Found at i:1021247 original size:47 final size:46 Alignment explanation

Indices: 1021179--1021346 Score: 152 Period size: 47 Copynumber: 3.7 Consensus size: 46 1021169 TTAATTAAAA * 1021179 TATATG-ATTTAATAAAATTTAAAATAATTATTACTAATAAATTTTCT 1 TATATGAATTT-ATATAATTTAAAATAATTATTA-TAATAAATTTTCT * * * * 1021226 TATTTGAATTTGTATAATTTAAAATTATTATTAT--TAAATATAAT-T 1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT * * * 1021271 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT 1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT 1021317 TATATGAATTTATATAATTTAAAATAATTA 1 TATATGAATTTATATAATTTAAAATAATTA 1021347 ATATTAAATA Statistics Matches: 94, Mismatches: 15, Indels: 24 0.71 0.11 0.18 Matches are distributed among these distances: 43 3 0.03 44 20 0.21 45 10 0.11 46 9 0.10 47 45 0.48 48 7 0.07 ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48 Consensus pattern (46 bp): TATATGAATTTATATAATTTAAAATAATTATTATAATAAATTTTCT Found at i:1021286 original size:44 final size:42 Alignment explanation

Indices: 1021238--1021380 Score: 128 Period size: 44 Copynumber: 3.2 Consensus size: 42 1021228 TTTGAATTTG 1021238 TATAATTTAAAATTATTATTATTAAATATAATTTAATAATAATA 1 TATAATTTAAAATTATTA-TATTAAATATAATTTAATAAT-ATA * * * * 1021282 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA 1 TATAA-TT--TAAAATTATT-ATATTAAATATAAT-TTA-AT-AATATA * 1021329 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA 1 TATAATTTAAAATTATT-ATATTAAATATAATTTAATAAT-ATA 1021373 TATAATTT 1 TATAATTT 1021381 TATAAATTTC Statistics Matches: 79, Mismatches: 10, Indels: 20 0.72 0.09 0.18 Matches are distributed among these distances: 43 3 0.04 44 33 0.42 45 7 0.09 46 7 0.09 47 25 0.32 48 4 0.05 ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48 Consensus pattern (42 bp): TATAATTTAAAATTATTATATTAAATATAATTTAATAATATA Found at i:1021316 original size:91 final size:91 Alignment explanation

Indices: 1021204--1021419 Score: 333 Period size: 91 Copynumber: 2.4 Consensus size: 91 1021194 AATTTAAAAT * * * * * * 1021204 AATTATTACTAATAAATTTTCTTATTTGAATTTGTATAATTTAAAATTATTATTATTAAATATAA 1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA 1021269 TTTAATAATAATATATAATTTCATAA 66 TTTAATAATAATATATAATTTCATAA * 1021295 AATTCTTGATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA 1 AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA * * 1021360 TTTAATAATGATATATAATTTTATAA 66 TTTAATAATAATATATAATTTCATAA * * 1021386 ATTTCTTAATAATAAATATTCTTATATGAATTTA 1 AATTCTTAATAATAAATTTTCTTATATGAATTTA 1021420 CTAAAATCAA Statistics Matches: 113, Mismatches: 12, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 91 113 1.00 ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49 Consensus pattern (91 bp): AATTCTTAATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAA TTTAATAATAATATATAATTTCATAA Found at i:1021402 original size:47 final size:45 Alignment explanation

Indices: 1021238--1021404 Score: 139 Period size: 47 Copynumber: 3.7 Consensus size: 45 1021228 TTTGAATTTG * * * 1021238 TATAA-TTTA-AAATTATTATTATTAAATATAATTTAATAATAATA 1 TATAATTTTATAAATTCTTAATAATAAATATAATTTAATAAT-ATA * * * * 1021282 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA 1 TATAATTTTAT-AAATTCTTAATAATAAATATAAT-TTA-AT-AATATA ** * 1021329 TATAA-TTTA-AAATAATTAATATTAAATATAATTTAATAATGATA 1 TATAATTTTATAAATTCTTAATAATAAATATAATTTAATAAT-ATA 1021373 TATAATTTTATAAATTTCTTAATAATAAATAT 1 TATAATTTTATAAA-TTCTTAATAATAAATAT 1021405 TCTTATATGA Statistics Matches: 94, Mismatches: 17, Indels: 21 0.71 0.13 0.16 Matches are distributed among these distances: 43 3 0.03 44 28 0.30 45 12 0.13 46 11 0.12 47 37 0.39 48 3 0.03 ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47 Consensus pattern (45 bp): TATAATTTTATAAATTCTTAATAATAAATATAATTTAATAATATA Found at i:1024426 original size:16 final size:16 Alignment explanation

Indices: 1024362--1024429 Score: 82 Period size: 16 Copynumber: 4.2 Consensus size: 16 1024352 TTTGGTTCGC 1024362 TGTATTGGATTAGAGG 1 TGTATTGGATTAGAGG ** * * * 1024378 CATATTGAATTAAAAG 1 TGTATTGGATTAGAGG * 1024394 CGTATTGGATTAGAGG 1 TGTATTGGATTAGAGG 1024410 TGTATTGGATTAGAGG 1 TGTATTGGATTAGAGG 1024426 TGTA 1 TGTA 1024430 ATAGTAAATT Statistics Matches: 42, Mismatches: 10, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 16 42 1.00 ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35 Consensus pattern (16 bp): TGTATTGGATTAGAGG Found at i:1024686 original size:18 final size:17 Alignment explanation

Indices: 1024665--1024699 Score: 52 Period size: 18 Copynumber: 2.0 Consensus size: 17 1024655 TTATTATTAA * 1024665 ATATATTTTAATTAAAAT 1 ATATAATTTAA-TAAAAT 1024683 ATATAATTTAATAAAAT 1 ATATAATTTAATAAAAT 1024700 TCTTAATAAT Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 6 0.38 18 10 0.62 ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46 Consensus pattern (17 bp): ATATAATTTAATAAAAT Found at i:1024753 original size:157 final size:156 Alignment explanation

Indices: 1024563--1024867 Score: 565 Period size: 157 Copynumber: 1.9 Consensus size: 156 1024553 TAATATAAAA * 1024563 TTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAATAAT 1 TTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAAT * * 1024628 AAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTA 66 AAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA-TTA 1024693 ATAAAATTCTTAATAATTAGCAGAAAT 130 ATAAAATTCTTAATAATTAGCAGAAAT * 1024720 TTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAAT 1 TTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAAT 1024785 AAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTAA 66 AAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTAA 1024850 TAAAATTCTTAATAATTA 131 TAAAATTCTTAATAATTA 1024868 ATATTCTTAT Statistics Matches: 144, Mismatches: 4, Indels: 1 0.97 0.03 0.01 Matches are distributed among these distances: 156 22 0.15 157 122 0.85 ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48 Consensus pattern (156 bp): TTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAATAAT AAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTAA TAAAATTCTTAATAATTAGCAGAAAT Found at i:1024839 original size:16 final size:16 Alignment explanation

Indices: 1024802--1024843 Score: 52 Period size: 15 Copynumber: 2.7 Consensus size: 16 1024792 TTAATCATAT * 1024802 TTAAACATA-ATTATTA 1 TTAAA-ATATATTATAA 1024818 TT-AAATATATTATAA 1 TTAAAATATATTATAA 1024833 TTAAAATATAT 1 TTAAAATATAT 1024844 AATTAATAAA Statistics Matches: 23, Mismatches: 1, Indels: 4 0.82 0.04 0.14 Matches are distributed among these distances: 14 3 0.13 15 10 0.43 16 10 0.43 ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45 Consensus pattern (16 bp): TTAAAATATATTATAA Found at i:1024846 original size:13 final size:15 Alignment explanation

Indices: 1024811--1024849 Score: 55 Period size: 15 Copynumber: 2.7 Consensus size: 15 1024801 TTTAAACATA * 1024811 ATTATTATTAAATAT 1 ATTATAATTAAATAT 1024826 ATTATAATTAAA-AT 1 ATTATAATTAAATAT 1024840 A-TATAATTAA 1 ATTATAATTAA 1024850 TAAAATTCTT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 13 9 0.39 14 3 0.13 15 11 0.48 ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46 Consensus pattern (15 bp): ATTATAATTAAATAT Found at i:1025087 original size:14 final size:15 Alignment explanation

Indices: 1024919--1025089 Score: 60 Period size: 15 Copynumber: 11.6 Consensus size: 15 1024909 TGTAAATATA 1024919 AATTAACATA-ATTAT 1 AATTAA-ATATATTAT * 1024934 TATTAAATATATTAT 1 AATTAAATATATTAT * 1024949 AATTAAAATATATAATT 1 AATT-AAATATATTA-T * * 1024966 AATAAAAT-TCTTAAT 1 AATTAAATATATT-AT * 1024981 AATT-AATATTCTTAT 1 AATTAAATA-TATTAT * * * 1024996 -A-TGAATTTACTCA- 1 AATTAAATATA-TTAT * * 1025009 AATCATAATATATGAT 1 AATTA-AATATATTAT * 1025025 ACTGTAAA-ATA-TA- 1 AAT-TAAATATATTAT 1025038 AATTAACATA-ATTAT 1 AATTAA-ATATATTAT * 1025053 TATTAAATATATTAT 1 AATTAAATATATTAT 1025068 AATTAAA-ATA-TAT 1 AATTAAATATATTAT * 1025081 AATTTAATA 1 AATTAAATA 1025090 AAATTCTTAA Statistics Matches: 116, Mismatches: 21, Indels: 39 0.66 0.12 0.22 Matches are distributed among these distances: 12 3 0.03 13 15 0.13 14 24 0.21 15 42 0.36 16 27 0.23 17 5 0.04 ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43 Consensus pattern (15 bp): AATTAAATATATTAT Found at i:1025169 original size:120 final size:118 Alignment explanation

Indices: 1024805--1025196 Score: 698 Period size: 118 Copynumber: 3.3 Consensus size: 118 1024795 ATCATATTTA 1024805 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTAATAAAATTCTTAATAATTAAT 1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTAATAAAATTCTTAATAATTAAT 1024870 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATATAAATT 66 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATATAAATT 1024923 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTAATAAAATTCTTAATAATTAAT 1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTAATAAAATTCTTAATAATTAAT 1024988 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT 66 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTGT-AAATATAAATT 1025042 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA 1 AACATAATTATTATTAAATATATTATAATTAAAATATATAA-TTAATAAAATTCTTAATAATTAA * 1025107 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGA-AAATTT 65 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAT-ATAAA-TT * * 1025162 GAA-ATAATTAATATTAAATATATTTTAATTAAAAT 1 -AACATAATTATTATTAAATATATTATAATTAAAAT 1025197 TTATTGTTTA Statistics Matches: 266, Mismatches: 3, Indels: 8 0.96 0.01 0.03 Matches are distributed among these distances: 118 107 0.40 119 59 0.22 120 98 0.37 121 2 0.01 ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42 Consensus pattern (118 bp): AACATAATTATTATTAAATATATTATAATTAAAATATATAATTAATAAAATTCTTAATAATTAAT ATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATATAAATT Found at i:1028542 original size:18 final size:18 Alignment explanation

Indices: 1028515--1028549 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 1028505 TTTTCTGTTG * 1028515 TTTTTGTTTTCTTTTATT 1 TTTTTCTTTTCTTTTATT * 1028533 TTTTTCTTTTTTTTTAT 1 TTTTTCTTTTCTTTTAT 1028550 GCCAAAAAAA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.06, C:0.06, G:0.03, T:0.86 Consensus pattern (18 bp): TTTTTCTTTTCTTTTATT Found at i:1029371 original size:50 final size:50 Alignment explanation

Indices: 1029316--1029450 Score: 150 Period size: 50 Copynumber: 2.7 Consensus size: 50 1029306 TTCTGTTTTT * 1029316 AATTTTTTTTAT-TTGTTGGTTTTAAACTCTTTTACATATTATCTATATTG 1 AATTTTTTTTATATTGTTGATTTTAAACTCTTTTACATATTATCTAT-TTG * * ** * 1029366 AATTTTTATATATATTGTTTATTTTTAAA-T-TTTTATTTATTATCTATTTT 1 AATTTTT-TTTATATTGTTGA-TTTTAAACTCTTTTACATATTATCTATTTG * 1029416 AATTTTTTTATATAATGTTGATTTTAAACTCTTTT 1 AATTTTTTT-TATATTGTTGATTTTAAACTCTTTT 1029451 TATACATCAT Statistics Matches: 70, Mismatches: 9, Indels: 11 0.78 0.10 0.12 Matches are distributed among these distances: 49 8 0.11 50 26 0.37 51 23 0.33 52 6 0.09 53 7 0.10 ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63 Consensus pattern (50 bp): AATTTTTTTTATATTGTTGATTTTAAACTCTTTTACATATTATCTATTTG Found at i:1029398 original size:26 final size:25 Alignment explanation

Indices: 1029335--1029621 Score: 193 Period size: 26 Copynumber: 11.2 Consensus size: 25 1029325 TATTTGTTGG * * * 1029335 TTTTAAACTCTTTTACATATTATCTA 1 TTTTAAA-TTTTTTATATATTATTTA * * * 1029361 TATTGAATTTTTATATATATTGTTTA 1 TTTTAAATTTTT-TATATATTATTTA * * 1029387 TTTTTAAA-TTTTTATTTATTATCTA 1 -TTTTAAATTTTTTATATATTATTTA * * * * 1029412 TTTTAATTTTTTTATATAATGTTGA 1 TTTTAAATTTTTTATATATTATTTA * * 1029437 TTTTAAACTCTTTTTATACATCATTTA 1 TTTTAAA-T-TTTTTATATATTATTTA * * * * 1029464 CTTTAAAACTTTTTATGTGTTATTTA 1 -TTTTAAATTTTTTATATATTATTTA * 1029490 TTTTAAATTATTTTACATATTATTTA 1 TTTTAAATT-TTTTATATATTATTTA * * * 1029516 TTTTAAATATTTGTGTATATTATCTA 1 TTTTAAAT-TTTTTATATATTATTTA * * * 1029542 TTTTAAAGTTTTATATATATTACTTG 1 TTTTAAA-TTTTTTATATATTATTTA * * 1029568 GTTTAAATTATTTTATATGTTATTTA 1 TTTTAAATT-TTTTATATATTATTTA * * 1029594 CTTTAAATTTCTTT-TACATTA-TTA 1 TTTTAAATTT-TTTATATATTATTTA 1029618 TTTT 1 TTTT 1029622 TAAAACTGTT Statistics Matches: 198, Mismatches: 52, Indels: 24 0.72 0.19 0.09 Matches are distributed among these distances: 24 12 0.06 25 47 0.24 26 114 0.58 27 19 0.10 28 6 0.03 ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60 Consensus pattern (25 bp): TTTTAAATTTTTTATATATTATTTA Found at i:1029745 original size:26 final size:26 Alignment explanation

Indices: 1029697--1029761 Score: 87 Period size: 26 Copynumber: 2.5 Consensus size: 26 1029687 TTAAACTTTA * 1029697 TATGTCATTTTAATTTTTTTATAAAT 1 TATGTTATTTTAATTTTTTTATAAAT * 1029723 TA-GTTATTTTAGATTTTTTTATATAT 1 TATGTTATTTTA-ATTTTTTTATAAAT * 1029749 TATTTTATTTTAA 1 TATGTTATTTTAA 1029762 ATTGTTTTGT Statistics Matches: 34, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 25 8 0.24 26 18 0.53 27 8 0.24 ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65 Consensus pattern (26 bp): TATGTTATTTTAATTTTTTTATAAAT Found at i:1029756 original size:27 final size:26 Alignment explanation

Indices: 1029703--1029782 Score: 90 Period size: 27 Copynumber: 3.0 Consensus size: 26 1029693 TTTATATGTC * * 1029703 ATTTTAATTTTTTTATAAATTA-GTT 1 ATTTTAATTTTTTTATATATTATTTT 1029728 ATTTTAGATTTTTTTATATATTATTTT 1 ATTTTA-ATTTTTTTATATATTATTTT * * 1029755 ATTTTAAATTGTTTTGTATATTAATTTT 1 ATTTT-AATTTTTTTATATATT-ATTTT 1029783 TTAAAATTAT Statistics Matches: 47, Mismatches: 4, Indels: 5 0.84 0.07 0.09 Matches are distributed among these distances: 25 6 0.13 26 15 0.32 27 20 0.43 28 6 0.13 ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66 Consensus pattern (26 bp): ATTTTAATTTTTTTATATATTATTTT Found at i:1031397 original size:70 final size:70 Alignment explanation

Indices: 1031288--1031426 Score: 269 Period size: 70 Copynumber: 2.0 Consensus size: 70 1031278 GGATGGCTTG 1031288 AATTAAATTTGTTTATGATTGCTTAAATTAAAATATCATAAATAAATACTTCCTCTTGAAAGAGG 1 AATTAAATTTGTTTATGATTGCTTAAATTAAAATATCATAAATAAATACTTCCTCTTGAAAGAGG 1031353 TATTA 66 TATTA * 1031358 AATTACATTTGTTTATGATTGCTTAAATTAAAATATCATAAATAAATACTTCCTCTTGAAAGAGG 1 AATTAAATTTGTTTATGATTGCTTAAATTAAAATATCATAAATAAATACTTCCTCTTGAAAGAGG 1031423 TATT 66 TATT 1031427 TAAAATTGAT Statistics Matches: 68, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 70 68 1.00 ACGTcount: A:0.40, C:0.09, G:0.10, T:0.40 Consensus pattern (70 bp): AATTAAATTTGTTTATGATTGCTTAAATTAAAATATCATAAATAAATACTTCCTCTTGAAAGAGG TATTA Found at i:1031634 original size:14 final size:14 Alignment explanation

Indices: 1031615--1031642 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 1031605 CTATAACAAC 1031615 ATTATGATGAATTA 1 ATTATGATGAATTA 1031629 ATTATGATGAATTA 1 ATTATGATGAATTA 1031643 GTAAATTAAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43 Consensus pattern (14 bp): ATTATGATGAATTA Found at i:1032084 original size:15 final size:15 Alignment explanation

Indices: 1032064--1032093 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 1032054 CATATACAAA 1032064 TAATTATATTTATCC 1 TAATTATATTTATCC 1032079 TAATTATATTTATCC 1 TAATTATATTTATCC 1032094 GGTATAAAAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53 Consensus pattern (15 bp): TAATTATATTTATCC Found at i:1035657 original size:17 final size:17 Alignment explanation

Indices: 1035635--1035668 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 1035625 ATCCACTAAT * 1035635 CCACTACCACCAACAAC 1 CCACTACCAACAACAAC 1035652 CCACTACCAACAACAAC 1 CCACTACCAACAACAAC 1035669 AATCCACTAC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06 Consensus pattern (17 bp): CCACTACCAACAACAAC Found at i:1040295 original size:17 final size:17 Alignment explanation

Indices: 1040273--1040306 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 1040263 ATCCACTAAT * 1040273 CCACTACCACCAACAAC 1 CCACTACCAACAACAAC 1040290 CCACTACCAACAACAAC 1 CCACTACCAACAACAAC 1040307 AATCCACTAC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06 Consensus pattern (17 bp): CCACTACCAACAACAAC Found at i:1044027 original size:25 final size:27 Alignment explanation

Indices: 1043990--1044042 Score: 74 Period size: 26 Copynumber: 2.0 Consensus size: 27 1043980 TCAAACATGC 1043990 ATTTAGGTCAATTTAAC-CCTAGGGGT 1 ATTTAGGTCAATTTAACTCCTAGGGGT * * 1044016 ATTTCGGT-AATTTATCTCCTAGGGGT 1 ATTTAGGTCAATTTAACTCCTAGGGGT 1044042 A 1 A 1044043 AAACTGTAAA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 25 7 0.29 26 17 0.71 ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38 Consensus pattern (27 bp): ATTTAGGTCAATTTAACTCCTAGGGGT Found at i:1045564 original size:26 final size:26 Alignment explanation

Indices: 1045534--1045615 Score: 155 Period size: 26 Copynumber: 3.2 Consensus size: 26 1045524 TGAAATTCCC 1045534 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * 1045560 ATCATGAAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 1045586 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 1045612 ATCA 1 ATCA 1045616 ATTTGTATCA Statistics Matches: 54, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 54 1.00 ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30 Consensus pattern (26 bp): ATCATGGAACATTTACCTAACCCATT Found at i:1048905 original size:12 final size:12 Alignment explanation

Indices: 1048888--1048918 Score: 53 Period size: 12 Copynumber: 2.6 Consensus size: 12 1048878 GAGACATGAT 1048888 TTTGGGCGTGAA 1 TTTGGGCGTGAA * 1048900 TTTGGGCGTGTA 1 TTTGGGCGTGAA 1048912 TTTGGGC 1 TTTGGGC 1048919 ATAATTTTGC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.10, C:0.10, G:0.42, T:0.39 Consensus pattern (12 bp): TTTGGGCGTGAA Found at i:1051186 original size:17 final size:15 Alignment explanation

Indices: 1051151--1051180 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 1051141 GTTCATATAA 1051151 CTTTATGTAAATATT 1 CTTTATGTAAATATT * 1051166 CTTTATGTATATATT 1 CTTTATGTAAATATT 1051181 TTCTTTTCAA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57 Consensus pattern (15 bp): CTTTATGTAAATATT Found at i:1060093 original size:3 final size:3 Alignment explanation

Indices: 1060085--1060132 Score: 78 Period size: 3 Copynumber: 16.0 Consensus size: 3 1060075 AACCGTAGGT * * 1060085 AGA AGA AGA AGA AAA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA 1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA 1060133 TCAAAGCTCT Statistics Matches: 41, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 3 41 1.00 ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00 Consensus pattern (3 bp): AGA Found at i:1068693 original size:42 final size:42 Alignment explanation

Indices: 1068646--1068730 Score: 170 Period size: 42 Copynumber: 2.0 Consensus size: 42 1068636 TTTTGCTCGC 1068646 AAATGTCATAATAAAATTCTTTTTCTTCTTCATCTGAGTTTA 1 AAATGTCATAATAAAATTCTTTTTCTTCTTCATCTGAGTTTA 1068688 AAATGTCATAATAAAATTCTTTTTCTTCTTCATCTGAGTTTA 1 AAATGTCATAATAAAATTCTTTTTCTTCTTCATCTGAGTTTA 1068730 A 1 A 1068731 CTCATATTTA Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 42 43 1.00 ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47 Consensus pattern (42 bp): AAATGTCATAATAAAATTCTTTTTCTTCTTCATCTGAGTTTA Found at i:1070202 original size:9 final size:9 Alignment explanation

Indices: 1070188--1070220 Score: 59 Period size: 9 Copynumber: 3.8 Consensus size: 9 1070178 TTCCATCTTT 1070188 AATTAATCA 1 AATTAATCA 1070197 AATTAATCA 1 AATTAATCA 1070206 AATTAAT-A 1 AATTAATCA 1070214 AATTAAT 1 AATTAAT 1070221 TGTTGAAGTT Statistics Matches: 24, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 8 8 0.33 9 16 0.67 ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36 Consensus pattern (9 bp): AATTAATCA Found at i:1075223 original size:105 final size:105 Alignment explanation

Indices: 1075078--1075921 Score: 1273 Period size: 105 Copynumber: 8.0 Consensus size: 105 1075068 TACATTTTTA * * * * * 1075078 AAATAAAATAAAAAATAAAAAGGTTGATACATTAGATCAAGTTGAGATGGCTATGTCAGAAGAAC 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC * 1075143 AAATACTTAGCTTCGTCCAAAGGAATTACATTTGATCATC 66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC * * 1075183 AAATAAAATAAAAAATAAAAATGTTGACACATTGGGTCAAGCT-AGGATGGCTATGTCGGAAGAG 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGA-GATGGCTATGTCGGAAGAA * 1075247 CAAATACTTAGCTTCGTCCAAAGGAATTACATTTGATCATC 65 CAAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC * 1075288 AAATAAAATAAAAAATAAAAAGGTTGACACATTAGGTCAAGCTGAGATGGCTATGTCGGAAGAAC 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC * * 1075353 AAATACTTATCTTCGTCCGAAGGGATTACATTTGATCATC 66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC * * * 1075393 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCT-AGGATGGTTATCTCGGAAGAG 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGA-GATGGCTATGTCGGAAGAA * * 1075457 CAAATACTTAGCTTCGTCCGAAGGGATTACATTTGATCACC 65 CAAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC * * * 1075498 AAATAAAATAAAAAATAAAAAGATTGACACATTAGGTCAAGCT-AGGATGGCTATCTCGGAAGAA 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGA-GATGGCTATGTCGGAAGAA * * * 1075562 TAAATACTTAGCTTCGTCTGAAGGAATTACATTTGATCACC 65 CAAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC * 1075603 AAATAAAATAAAAAATAAAAAAGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAA- 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC 1075667 AAAGTACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC 66 AAA-TACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC * * * 1075708 AAATAAAATAAAAAATAATAAGGTTGACACATTGGGTCAAGCTGAGATGGTTATGTGGGAAGAAC 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC * * * * * 1075773 AAGTACTTAGGTTCATCCGAAGGGATTACATTTGACCATC 66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC * * 1075813 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGTTATGTTGGAAGAAC 1 AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC ** * ** 1075878 AAATACTTAGCTTCACCCGAAGGGATTACATTCAATCATC 66 AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC 1075918 AAAT 1 AAAT 1075922 TGGTCCCGTA Statistics Matches: 684, Mismatches: 49, Indels: 12 0.92 0.07 0.02 Matches are distributed among these distances: 104 5 0.01 105 675 0.99 106 4 0.01 ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25 Consensus pattern (105 bp): AAATAAAATAAAAAATAAAAAGGTTGACACATTGGGTCAAGCTGAGATGGCTATGTCGGAAGAAC AAATACTTAGCTTCGTCCGAAGGAATTACATTTGATCATC Found at i:1077671 original size:18 final size:19 Alignment explanation

Indices: 1077648--1077684 Score: 58 Period size: 19 Copynumber: 2.0 Consensus size: 19 1077638 TTATATATTT 1077648 AATAAATA-AATAATTTTA 1 AATAAATATAATAATTTTA * 1077666 AATAAATATAATAGTTTTA 1 AATAAATATAATAATTTTA 1077685 TTTTTTATCT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 18 8 0.47 19 9 0.53 ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41 Consensus pattern (19 bp): AATAAATATAATAATTTTA Found at i:1078092 original size:20 final size:20 Alignment explanation

Indices: 1078067--1078116 Score: 70 Period size: 17 Copynumber: 2.6 Consensus size: 20 1078057 TGGCTTAAAA 1078067 TTGGTAGTGGATTGTTGTTG 1 TTGGTAGTGGATTGTTGTTG 1078087 TTGGTAGTGG---GTTGTTG 1 TTGGTAGTGGATTGTTGTTG * 1078104 GTGGTAGTGGATT 1 TTGGTAGTGGATT 1078117 AGTGGATGGT Statistics Matches: 26, Mismatches: 1, Indels: 6 0.79 0.03 0.18 Matches are distributed among these distances: 17 16 0.62 20 10 0.38 ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46 Consensus pattern (20 bp): TTGGTAGTGGATTGTTGTTG Found at i:1082730 original size:20 final size:20 Alignment explanation

Indices: 1082705--1082754 Score: 70 Period size: 17 Copynumber: 2.6 Consensus size: 20 1082695 TGGCTTAAAA 1082705 TTGGTAGTGGATTGTTGTTG 1 TTGGTAGTGGATTGTTGTTG 1082725 TTGGTAGTGG---GTTGTTG 1 TTGGTAGTGGATTGTTGTTG * 1082742 GTGGTAGTGGATT 1 TTGGTAGTGGATT 1082755 AGTGGATGGT Statistics Matches: 26, Mismatches: 1, Indels: 6 0.79 0.03 0.18 Matches are distributed among these distances: 17 16 0.62 20 10 0.38 ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46 Consensus pattern (20 bp): TTGGTAGTGGATTGTTGTTG Found at i:1083631 original size:4 final size:4 Alignment explanation

Indices: 1083624--1083685 Score: 106 Period size: 4 Copynumber: 15.5 Consensus size: 4 1083614 TATAAAAAAA * * 1083624 ATGT ATGT ATGT ATGC ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT 1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT 1083672 ATGT ATGT ATGT AT 1 ATGT ATGT ATGT AT 1083686 ACAAGGAGAG Statistics Matches: 56, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 4 56 1.00 ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47 Consensus pattern (4 bp): ATGT Found at i:1084212 original size:19 final size:20 Alignment explanation

Indices: 1084177--1084216 Score: 57 Period size: 19 Copynumber: 2.0 Consensus size: 20 1084167 ACTTAAGTGA 1084177 TTTTACACCTTTCAATAATT 1 TTTTACACCTTTCAATAATT 1084197 TTTTACA-CTATT-AATAATT 1 TTTTACACCT-TTCAATAATT 1084216 T 1 T 1084217 AACAATCCAT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 19 10 0.53 20 9 0.47 ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53 Consensus pattern (20 bp): TTTTACACCTTTCAATAATT Found at i:1088994 original size:21 final size:21 Alignment explanation

Indices: 1088968--1089008 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 1088958 AGACAAGCGA * * 1088968 TACTCCACAGCAGGTGGAGTG 1 TACTCCAAAACAGGTGGAGTG 1088989 TACTCCAAAACAGGTGGAGT 1 TACTCCAAAACAGGTGGAGT 1089009 TTGAGCAGAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20 Consensus pattern (21 bp): TACTCCAAAACAGGTGGAGTG Found at i:1096029 original size:25 final size:27 Alignment explanation

Indices: 1095992--1096045 Score: 67 Period size: 26 Copynumber: 2.1 Consensus size: 27 1095982 TCAAACATGC 1095992 ATTTAGGTCAATTTAAC-CCTAGGGGT 1 ATTTAGGTCAATTTAACACCTAGGGGT * ** 1096018 ATTTCGGT-AATTTTGCACCTAGGGGT 1 ATTTAGGTCAATTTAACACCTAGGGGT 1096044 AT 1 AT 1096046 AACAGTAATT Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 25 6 0.25 26 18 0.75 ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37 Consensus pattern (27 bp): ATTTAGGTCAATTTAACACCTAGGGGT Found at i:1096053 original size:26 final size:27 Alignment explanation

Indices: 1096009--1096084 Score: 82 Period size: 26 Copynumber: 2.8 Consensus size: 27 1095999 TCAATTTAAC * * * 1096009 CCTAGGGGTATTTCGGTAATTTTGC-A 1 CCTAGGGGTATTACAGTAATTTTCCAA * 1096035 CCTAGGGGTATAACAGTAATTTTCCATA 1 CCTAGGGGTATTACAGTAATTTTCCA-A * * 1096063 CATAGGGGTATTATAGTAATTT 1 CCTAGGGGTATTACAGTAATTT 1096085 AGCTGCTTTT Statistics Matches: 41, Mismatches: 7, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 26 21 0.51 28 20 0.49 ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37 Consensus pattern (27 bp): CCTAGGGGTATTACAGTAATTTTCCAA Found at i:1097590 original size:26 final size:26 Alignment explanation

Indices: 1097534--1097590 Score: 96 Period size: 26 Copynumber: 2.2 Consensus size: 26 1097524 ATGAAATTCC 1097534 CATCATGGAACATTTACCTAACCCAT 1 CATCATGGAACATTTACCTAACCCAT * * 1097560 TATCATGGAACATTTACCTAACCTAT 1 CATCATGGAACATTTACCTAACCCAT 1097586 CATCA 1 CATCA 1097591 ATTTGTATCA Statistics Matches: 28, Mismatches: 3, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30 Consensus pattern (26 bp): CATCATGGAACATTTACCTAACCCAT Found at i:1098802 original size:16 final size:17 Alignment explanation

Indices: 1098781--1098814 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 1098771 TTATATTATA 1098781 TATTATAA-AATTATTT 1 TATTATAAGAATTATTT * 1098797 TATTATAAGTATTATTT 1 TATTATAAGAATTATTT 1098814 T 1 T 1098815 TAATTATATA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 8 0.50 17 8 0.50 ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59 Consensus pattern (17 bp): TATTATAAGAATTATTT Found at i:1098923 original size:16 final size:16 Alignment explanation

Indices: 1098883--1098925 Score: 52 Period size: 17 Copynumber: 2.6 Consensus size: 16 1098873 TCTTTTATAT 1098883 ATTATTATATTTTCAC 1 ATTATTATATTTTCAC * 1098899 ATATATTATATTTATTA- 1 AT-TATTATATTT-TCAC 1098916 ATTATTATAT 1 ATTATTATAT 1098926 ATATATTGTT Statistics Matches: 24, Mismatches: 1, Indels: 4 0.83 0.03 0.14 Matches are distributed among these distances: 16 10 0.42 17 12 0.50 18 2 0.08 ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58 Consensus pattern (16 bp): ATTATTATATTTTCAC Found at i:1099008 original size:42 final size:41 Alignment explanation

Indices: 1098948--1099040 Score: 100 Period size: 40 Copynumber: 2.2 Consensus size: 41 1098938 ATGTGTTACT * 1098948 TTATATTATATCTATTATTTTCTTAT-ATGTTTATATTACATTTTA 1 TTATA-TA-ATCTATTATTATCTT-TCAT-TTTATATTAC-TTTTA * * 1098993 TTATATAATCT-TTATTATGTTTCATTTTATATTACTTTTT 1 TTATATAATCTATTATTATCTTTCATTTTATATTACTTTTA 1099033 TTATATAA 1 TTATATAA 1099041 ATGTTATGTA Statistics Matches: 44, Mismatches: 3, Indels: 7 0.81 0.06 0.13 Matches are distributed among these distances: 40 12 0.27 41 11 0.25 42 10 0.23 43 4 0.09 44 2 0.05 45 5 0.11 ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62 Consensus pattern (41 bp): TTATATAATCTATTATTATCTTTCATTTTATATTACTTTTA Found at i:1099100 original size:21 final size:20 Alignment explanation

Indices: 1099066--1099104 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 20 1099056 TGAATCGCAA 1099066 ATTATATTATTTATGTTTATT 1 ATTATATTATTTAT-TTTATT 1099087 ATTATA-TATATTATTTTA 1 ATTATATTAT-TTATTTTA 1099105 AAAATGTAAA Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 20 7 0.41 21 10 0.59 ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64 Consensus pattern (20 bp): ATTATATTATTTATTTTATT Found at i:1111261 original size:119 final size:119 Alignment explanation

Indices: 1111050--1111281 Score: 358 Period size: 119 Copynumber: 1.9 Consensus size: 119 1111040 AATTGAAGAC * * * 1111050 AGCAGATCTAGACTTCAGACATTTATGCTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTT 1 AGCAGATCTAGACTTCAGACATTTATACTGAAACAGATCCAAGATGATTTGATATTCTTGTGTTT * * 1111115 ACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATAT 66 ACAAGAAACAAATCGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAATAT ** 1111169 AGCAGATCTA-ACTTTCAGATGTTTATACTGAAACAGATCCAAGATGATTTGATATTCTTGTGTT 1 AGCAGATCTAGAC-TTCAGACATTTATACTGAAACAGATCCAAGATGATTTGATATTCTTGTGTT * * * 1111233 TACAAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTC 65 TACAAGAAACAAATCGAGGACATAGCAGATATGACTCTCAAACGTTCTC 1111282 CAACAGACTC Statistics Matches: 102, Mismatches: 10, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 118 2 0.02 119 100 0.98 ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31 Consensus pattern (119 bp): AGCAGATCTAGACTTCAGACATTTATACTGAAACAGATCCAAGATGATTTGATATTCTTGTGTTT ACAAGAAACAAATCGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAATAT Found at i:1111313 original size:83 final size:83 Alignment explanation

Indices: 1111199--1111724 Score: 858 Period size: 83 Copynumber: 6.3 Consensus size: 83 1111189 GTTTATACTG ** * * 1111199 AAACAGA-TCCAAGATGATTTGATATTCTTGTGTTTACAAGGAACAAATCGAGGACATTGCAGAT 1 AAACAGACT-CAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGAT 1111263 ATGACTCTCAAATGTTCTC 65 ATGACTCTCAAATGTTCTC * 1111282 CAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA 1 AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA 1111347 TGACTCTCAAATGTTCTC 66 TGACTCTCAAATGTTCTC * * * 1111365 AAACAGACTCAATATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGTAGATA 1 AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA 1111430 TGACTCTCAAATGTTCTC 66 TGACTCTCAAATGTTCTC * * 1111448 AAACAGACTCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGTAGATA 1 AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA * 1111513 TAACTCTCAAATGTTCTC 66 TGACTCTCAAATGTTCTC 1111531 AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA 1 AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA * 1111596 TAACTCTCAAATGTTCTC 66 TGACTCTCAAATGTTCTC * * * 1111614 AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACGTAGTAGATA 1 AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA * * 1111679 TGATTCTCGAATGTTCTC 66 TGACTCTCAAATGTTCTC 1111697 AAAACAGACTCAA-ACTGATTTGGCATCC 1 -AAACAGACTCAAGA-TGATTTGGCATCC 1111725 CCACAAATCG Statistics Matches: 421, Mismatches: 19, Indels: 5 0.95 0.04 0.01 Matches are distributed among these distances: 83 395 0.94 84 26 0.06 ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28 Consensus pattern (83 bp): AAACAGACTCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAGGACATTGCAGATA TGACTCTCAAATGTTCTC Found at i:1113335 original size:16 final size:17 Alignment explanation

Indices: 1113314--1113347 Score: 52 Period size: 16 Copynumber: 2.1 Consensus size: 17 1113304 TTATATTATA 1113314 TATTATAA-AATTATTT 1 TATTATAAGAATTATTT * 1113330 TATTATAAGTATTATTT 1 TATTATAAGAATTATTT 1113347 T 1 T 1113348 TAATTATATA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 16 8 0.50 17 8 0.50 ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59 Consensus pattern (17 bp): TATTATAAGAATTATTT Found at i:1113540 original size:42 final size:42 Alignment explanation

Indices: 1113480--1113573 Score: 102 Period size: 42 Copynumber: 2.2 Consensus size: 42 1113470 ATGTGTTACT * 1113480 TTATATTATATCTATTATTTTCTTAT-ATGTTTATATTACATTTTA 1 TTATA-TA-ATCTATTATTATCTT-TCATGTTTATATTAC-TTTTA * * * 1113525 TTATATAATCT-TTATTATGTTTCATTTTTATATTACTTTTT 1 TTATATAATCTATTATTATCTTTCATGTTTATATTACTTTTA 1113566 TTATATAA 1 TTATATAA 1113574 ATGTTATGTA Statistics Matches: 44, Mismatches: 4, Indels: 6 0.81 0.07 0.11 Matches are distributed among these distances: 41 13 0.30 42 20 0.45 43 4 0.09 44 2 0.05 45 5 0.11 ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63 Consensus pattern (42 bp): TTATATAATCTATTATTATCTTTCATGTTTATATTACTTTTA Found at i:1113637 original size:20 final size:20 Alignment explanation

Indices: 1113599--1113637 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 1113589 TGTATCGCAA * 1113599 ATTATATTATTTATGTTTAT 1 ATTATATTATATATGTTTAT 1113619 ATTATATATATATAT-TTTA 1 ATTATAT-TATATATGTTTA 1113638 AAAATGTAAA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 20 11 0.65 21 6 0.35 ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62 Consensus pattern (20 bp): ATTATATTATATATGTTTAT Found at i:1115065 original size:26 final size:26 Alignment explanation

Indices: 1115019--1115070 Score: 61 Period size: 26 Copynumber: 2.0 Consensus size: 26 1115009 TCAAACATGC * 1115019 ATTTAGGTCAATTTAACCCTATGGGT 1 ATTTAGGTCAATTTAACCCTAAGGGT * * 1115045 ATTTCGGT-AATTTATCTCCTAAGGGT 1 ATTTAGGTCAATTTAAC-CCTAAGGGT 1115071 TAAAACTATA Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 25 7 0.32 26 15 0.68 ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40 Consensus pattern (26 bp): ATTTAGGTCAATTTAACCCTAAGGGT Found at i:1116589 original size:26 final size:26 Alignment explanation

Indices: 1116558--1116717 Score: 257 Period size: 26 Copynumber: 6.2 Consensus size: 26 1116548 ATGAAATTCC * 1116558 ATCATGGAACATTTACCTAAACCATT 1 ATCATGGAACATTTACCTAACCCATT 1116584 ATCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * * 1116610 ATCATGGAATATTTACCTAATCCATT 1 ATCATGGAACATTTACCTAACCCATT * 1116636 GTCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * * 1116662 ATCATGGAATATTTACCTAATCCATT 1 ATCATGGAACATTTACCTAACCCATT * 1116688 GTCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 1116714 ATCA 1 ATCA 1116718 ATTTGTATCA Statistics Matches: 121, Mismatches: 13, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 26 121 1.00 ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33 Consensus pattern (26 bp): ATCATGGAACATTTACCTAACCCATT Found at i:1116624 original size:52 final size:52 Alignment explanation

Indices: 1116558--1116717 Score: 293 Period size: 52 Copynumber: 3.1 Consensus size: 52 1116548 ATGAAATTCC * * * 1116558 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT 1 ATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT 1116610 ATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT 1 ATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT 1116662 ATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT 1 ATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT 1116714 ATCA 1 ATCA 1116718 ATTTGTATCA Statistics Matches: 105, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 52 105 1.00 ACGTcount: A:0.34, C:0.24, G:0.09, T:0.33 Consensus pattern (52 bp): ATCATGGAATATTTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT Found at i:1119849 original size:20 final size:18 Alignment explanation

Indices: 1119815--1119851 Score: 56 Period size: 20 Copynumber: 1.9 Consensus size: 18 1119805 GCAACTCATA 1119815 ATTTCAACTATTTTACAC 1 ATTTCAACTATTTTACAC 1119833 ATTTACAACTCATTTTACA 1 ATTT-CAACT-ATTTTACA 1119852 ACTTAGCAAT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 4 0.24 19 5 0.29 20 8 0.47 ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43 Consensus pattern (18 bp): ATTTCAACTATTTTACAC Found at i:1122018 original size:26 final size:26 Alignment explanation

Indices: 1121987--1122093 Score: 162 Period size: 26 Copynumber: 4.2 Consensus size: 26 1121977 ATGAAATTCC * 1121987 ATCATGGAACATTTACCTAAACCATT 1 ATCATGGAACATTTACCTAACCCATT 1122013 ATCATGG-ACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT * * * 1122038 ATCATGGAATAATTACCTAATCCATT 1 ATCATGGAACATTTACCTAACCCATT * 1122064 GTCATGGAACATTTACCTAACCCATT 1 ATCATGGAACATTTACCTAACCCATT 1122090 ATCA 1 ATCA 1122094 ATTTGTATCA Statistics Matches: 71, Mismatches: 9, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 25 24 0.34 26 47 0.66 ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32 Consensus pattern (26 bp): ATCATGGAACATTTACCTAACCCATT Found at i:1122063 original size:51 final size:52 Alignment explanation

Indices: 1121987--1122093 Score: 171 Period size: 51 Copynumber: 2.1 Consensus size: 52 1121977 ATGAAATTCC * 1121987 ATCATGGAACATTTACCTAAACCATTATCATGG-ACATTTACCTAACCCATT 1 ATCATGGAACAATTACCTAAACCATTATCATGGAACATTTACCTAACCCATT * * * 1122038 ATCATGGAATAATTACCTAATCCATTGTCATGGAACATTTACCTAACCCATT 1 ATCATGGAACAATTACCTAAACCATTATCATGGAACATTTACCTAACCCATT 1122090 ATCA 1 ATCA 1122094 ATTTGTATCA Statistics Matches: 51, Mismatches: 4, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 51 29 0.57 52 22 0.43 ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32 Consensus pattern (52 bp): ATCATGGAACAATTACCTAAACCATTATCATGGAACATTTACCTAACCCATT Found at i:1122565 original size:197 final size:197 Alignment explanation

Indices: 1122230--1122615 Score: 745 Period size: 197 Copynumber: 2.0 Consensus size: 197 1122220 ATTTATTTGG 1122230 CCACTTCAATTTAGCCTATAGCATTTTCAAACATTTTCACATAGGTTCTATTTCATAATTTCACC 1 CCACTTCAATTTAGCCTATAGCATTTTCAAACATTTTCACATAGGTTCTATTTCATAATTTCACC 1122295 CCTTTTTCTTATGGAACAAAAATTAACTAAAATTGCCAGGTTCTATCTTAAGCTTGGGCCTTCTA 66 CCTTTTTCTTATGGAACAAAAATTAACTAAAATTGCCAGGTTCTATCTTAAGCTTGGGCCTTCTA * 1122360 GACGCCCACTAACATAATTAAACCTATGCCAACATTCACAGGATTCTCGAAAATTGGGGTGTTAC 131 GACGCCCACTAACATAATTAAACCTATGCCAACATTCACAGGATTCCCGAAAATTGGGGTGTTAC 1122425 AT 196 AT 1122427 CCACTTCAATTTAGCCTATAGCATTTTCAAACATTTTCACATAGGTTCTATTTCATAATTTCACC 1 CCACTTCAATTTAGCCTATAGCATTTTCAAACATTTTCACATAGGTTCTATTTCATAATTTCACC * 1122492 CCTTTTTCTTATGGAACAAAAATTAACTAAAATTGCCGGGTTCTATCTTAAGCTTGGGCCTTCTA 66 CCTTTTTCTTATGGAACAAAAATTAACTAAAATTGCCAGGTTCTATCTTAAGCTTGGGCCTTCTA * 1122557 GACGCCCACTAACATAATTAAACCTATGCCAACATTCATAGGATTCCCGAAAATTGGGG 131 GACGCCCACTAACATAATTAAACCTATGCCAACATTCACAGGATTCCCGAAAATTGGGG 1122616 AATTACATAT Statistics Matches: 186, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 197 186 1.00 ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34 Consensus pattern (197 bp): CCACTTCAATTTAGCCTATAGCATTTTCAAACATTTTCACATAGGTTCTATTTCATAATTTCACC CCTTTTTCTTATGGAACAAAAATTAACTAAAATTGCCAGGTTCTATCTTAAGCTTGGGCCTTCTA GACGCCCACTAACATAATTAAACCTATGCCAACATTCACAGGATTCCCGAAAATTGGGGTGTTAC AT Found at i:1126495 original size:15 final size:14 Alignment explanation

Indices: 1126449--1126501 Score: 52 Period size: 15 Copynumber: 3.6 Consensus size: 14 1126439 CCATATAAGT 1126449 AAATTTATTAATTA 1 AAATTTATTAATTA * * * 1126463 CAATTTATCAAATAA 1 AAATTTAT-TAATTA 1126478 AAATTATATTAATTA 1 AAATT-TATTAATTA 1126493 AAATATTAT 1 AAAT-TTAT 1126502 ATTAATAAAA Statistics Matches: 30, Mismatches: 6, Indels: 5 0.73 0.15 0.12 Matches are distributed among these distances: 14 7 0.23 15 19 0.63 16 4 0.13 ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43 Consensus pattern (14 bp): AAATTTATTAATTA Done.