Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold471

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1282308
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29

Warning! 143812 characters in sequence are not A, C, G, or T


File 3 of 4

Found at i:317820 original size:112 final size:112

Alignment explanation

Indices: 317623--317845 Score: 383 Period size: 112 Copynumber: 2.0 Consensus size: 112 317613 AACCCTGACG * * * 317623 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGTTT 1 TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT * * * 317688 TTTTTAAGTTTGACAAACAATAGACTTTAATTAGATATACATAAACC 66 TTCTTAAGTTTGACAAACAATAGACTCTAATTAGATATACACAAACC 317735 TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 1 TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT * 317800 TTCTTAAGTTTGACAAACAATAGACTCTATTTAGATATACACAAAC 66 TTCTTAAGTTTGACAAACAATAGACTCTAATTAGATATACACAAAC 317846 GAACAAAACT Statistics Matches: 104, Mismatches: 7, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 112 104 1.00 ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35 Consensus pattern (112 bp): TGCACCTAGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT TTCTTAAGTTTGACAAACAATAGACTCTAATTAGATATACACAAACC Found at i:318056 original size:2 final size:2 Alignment explanation

Indices: 318049--318100 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 318039 CAGATGAACT 318049 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 318091 GA GA GA GA GA 1 GA GA GA GA GA 318101 TATTTCACCG Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:318514 original size:21 final size:22 Alignment explanation

Indices: 318488--318539 Score: 70 Period size: 21 Copynumber: 2.4 Consensus size: 22 318478 CTTAAAGGGA 318488 GCTTAAATGCCACTTAAAGAT- 1 GCTTAAATGCCACTTAAAGATG * ** 318509 GCTTAAAGGCGGCTTAAAGATG 1 GCTTAAATGCCACTTAAAGATG 318531 GCTTAAATG 1 GCTTAAATG 318540 TGACTTTAAG Statistics Matches: 26, Mismatches: 4, Indels: 1 0.84 0.13 0.03 Matches are distributed among these distances: 21 18 0.69 22 8 0.31 ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27 Consensus pattern (22 bp): GCTTAAATGCCACTTAAAGATG Found at i:318635 original size:11 final size:11 Alignment explanation

Indices: 318619--318659 Score: 73 Period size: 11 Copynumber: 3.7 Consensus size: 11 318609 GATGGTATAT 318619 CCTTTAAGCCA 1 CCTTTAAGCCA * 318630 CCTTTACGCCA 1 CCTTTAAGCCA 318641 CCTTTAAGCCA 1 CCTTTAAGCCA 318652 CCTTTAAG 1 CCTTTAAG 318660 GACTTGCTTA Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 11 28 1.00 ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29 Consensus pattern (11 bp): CCTTTAAGCCA Found at i:319543 original size:2 final size:2 Alignment explanation

Indices: 319536--319619 Score: 161 Period size: 2 Copynumber: 42.5 Consensus size: 2 319526 TGTTAGTAAT 319536 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 319578 GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 319619 G 1 G 319620 GTGGTCAATA Statistics Matches: 81, Mismatches: 0, Indels: 2 0.98 0.00 0.02 Matches are distributed among these distances: 1 1 0.01 2 80 0.99 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:320609 original size:5 final size:5 Alignment explanation

Indices: 320590--320716 Score: 116 Period size: 5 Copynumber: 25.4 Consensus size: 5 320580 CTGTAAAGTG * * * 320590 CGAAA CGAAA TCGAAA CGAAA TCGAAA CGAAA CGAAA CCAAT CGAAA CAAAA 1 CGAAA CGAAA -CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA * * * * 320642 CGAAA CCAAT CGAAA CGAAA TTG-AA CGAAA CGAAA CGAAA CGAAA CAAAA 1 CGAAA CGAAA CGAAA CGAAA -CGAAA CGAAA CGAAA CGAAA CGAAA CGAAA * * * 320692 CCAAA --AAT CGACA CGAAA CGAAA CG 1 CGAAA CGAAA CGAAA CGAAA CGAAA CG 320717 GAAGGAATTT Statistics Matches: 98, Mismatches: 18, Indels: 12 0.77 0.14 0.09 Matches are distributed among these distances: 3 2 0.02 4 1 0.01 5 84 0.86 6 11 0.11 ACGTcount: A:0.57, C:0.22, G:0.16, T:0.06 Consensus pattern (5 bp): CGAAA Found at i:320937 original size:2 final size:2 Alignment explanation

Indices: 320930--320973 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 320920 TTCAGACGTT 320930 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 320972 GA 1 GA 320974 TGCCTTAAAA Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:321067 original size:3 final size:3 Alignment explanation

Indices: 321059--321084 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 321049 AGAGAGAGAT 321059 ATG ATG ATG ATG ATG ATG ATG ATG AT 1 ATG ATG ATG ATG ATG ATG ATG ATG AT 321085 ACTGAAGGGC 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:0.35, C:0.00, G:0.31, T:0.35 Consensus pattern (3 bp): ATG Found at i:321777 original size:18 final size:18 Alignment explanation

Indices: 321754--321804 Score: 57 Period size: 20 Copynumber: 2.7 Consensus size: 18 321744 TTTTAAAAAG 321754 TCCTATAGGAATTATATT 1 TCCTATAGGAATTATATT * * 321772 TCCTATAGGAGAAATGTATT 1 TCCTATA-G-GAATTATATT * 321792 TCCTGTAGGAATT 1 TCCTATAGGAATT 321805 TGATTCAGAC Statistics Matches: 27, Mismatches: 4, Indels: 4 0.77 0.11 0.11 Matches are distributed among these distances: 18 11 0.41 19 2 0.07 20 14 0.52 ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39 Consensus pattern (18 bp): TCCTATAGGAATTATATT Found at i:322535 original size:12 final size:12 Alignment explanation

Indices: 322518--322544 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 322508 TCTATATCTC 322518 TCTTTCTCTCTT 1 TCTTTCTCTCTT 322530 TCTTTCTCTCTT 1 TCTTTCTCTCTT 322542 TCT 1 TCT 322545 CCCAAACTTG 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:0.00, C:0.33, G:0.00, T:0.67 Consensus pattern (12 bp): TCTTTCTCTCTT Found at i:322609 original size:2 final size:2 Alignment explanation

Indices: 322602--322683 Score: 146 Period size: 2 Copynumber: 41.0 Consensus size: 2 322592 TTTTAAGGCA * 322602 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * 322644 TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 322684 AACGTCTGAA Statistics Matches: 76, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 76 1.00 ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50 Consensus pattern (2 bp): TC Found at i:322930 original size:5 final size:5 Alignment explanation

Indices: 322920--323029 Score: 71 Period size: 5 Copynumber: 21.4 Consensus size: 5 322910 GTGTAAATTC * * * 322920 CGTTT CGTTT CGTTT CGAATTTT GGTTT CGTTT CGTTT GGTTT TGTTT 1 CGTTT CGTTT CGTTT CG---TTT CGTTT CGTTT CGTTT CGTTT CGTTT * * * * * * 322968 CGTTT CGATT GGTTT CTTTT CGTTT CGATTG GGTTT -GTTT TGTTT CG-TT 1 CGTTT CGTTT CGTTT CGTTT CGTTT CG-TTT CGTTT CGTTT CGTTT CGTTT * 323017 CAATTT CGTTT CG 1 C-GTTT CGTTT CG 323030 CACTTTACAG Statistics Matches: 81, Mismatches: 17, Indels: 14 0.72 0.15 0.12 Matches are distributed among these distances: 4 7 0.09 5 64 0.79 6 6 0.07 8 4 0.05 ACGTcount: A:0.05, C:0.14, G:0.23, T:0.58 Consensus pattern (5 bp): CGTTT Found at i:322969 original size:20 final size:20 Alignment explanation

Indices: 322921--323016 Score: 104 Period size: 20 Copynumber: 4.7 Consensus size: 20 322911 TGTAAATTCC * 322921 GTTTCGTTTCGTTTCGAATTTT 1 GTTTCGTTTCGTTT-G-GTTTT 322943 GGTTTCGTTTCGTTTGGTTTT 1 -GTTTCGTTTCGTTTGGTTTT * 322964 GTTTCGTTTCGATTGGTTTCT 1 GTTTCGTTTCGTTTGGTTT-T * * 322985 -TTTCGTTTCGATTGGGTTT 1 GTTTCGTTTCGTTTGGTTTT * 323004 GTTTTGTTTCGTT 1 GTTTCGTTTCGTT 323017 CAATTTCGTT Statistics Matches: 66, Mismatches: 5, Indels: 7 0.85 0.06 0.09 Matches are distributed among these distances: 19 1 0.02 20 45 0.68 21 5 0.08 22 1 0.02 23 14 0.21 ACGTcount: A:0.04, C:0.11, G:0.24, T:0.60 Consensus pattern (20 bp): GTTTCGTTTCGTTTGGTTTT Found at i:323166 original size:8 final size:8 Alignment explanation

Indices: 323153--323191 Score: 69 Period size: 8 Copynumber: 4.9 Consensus size: 8 323143 GCCGGGCGTC 323153 CGTCCGTG 1 CGTCCGTG 323161 CGTCCGTG 1 CGTCCGTG 323169 CGTCCGTG 1 CGTCCGTG * 323177 TGTCCGTG 1 CGTCCGTG 323185 CGTCCGT 1 CGTCCGT 323192 ATGTCCGTCT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 8 29 1.00 ACGTcount: A:0.00, C:0.36, G:0.36, T:0.28 Consensus pattern (8 bp): CGTCCGTG Found at i:323196 original size:16 final size:16 Alignment explanation

Indices: 323162--323199 Score: 67 Period size: 16 Copynumber: 2.4 Consensus size: 16 323152 CCGTCCGTGC * 323162 GTCCGTGCGTCCGTGT 1 GTCCGTGCGTCCGTAT 323178 GTCCGTGCGTCCGTAT 1 GTCCGTGCGTCCGTAT 323194 GTCCGT 1 GTCCGT 323200 CTGTCACACT Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.03, C:0.32, G:0.34, T:0.32 Consensus pattern (16 bp): GTCCGTGCGTCCGTAT Found at i:323197 original size:8 final size:8 Alignment explanation

Indices: 323154--323204 Score: 57 Period size: 8 Copynumber: 6.4 Consensus size: 8 323144 CCGGGCGTCC * 323154 GTCCGTGC 1 GTCCGTGT * 323162 GTCCGTGC 1 GTCCGTGT 323170 GTCCGTGT 1 GTCCGTGT * 323178 GTCCGTGC 1 GTCCGTGT * 323186 GTCCGTAT 1 GTCCGTGT * 323194 GTCCGTCT 1 GTCCGTGT 323202 GTC 1 GTC 323205 ACACTTTTTT Statistics Matches: 38, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 8 38 1.00 ACGTcount: A:0.02, C:0.33, G:0.33, T:0.31 Consensus pattern (8 bp): GTCCGTGT Found at i:323197 original size:24 final size:24 Alignment explanation

Indices: 323149--323204 Score: 76 Period size: 24 Copynumber: 2.3 Consensus size: 24 323139 AAATGCCGGG * * 323149 CGTCCGTCCGTGCGTCCGTGCGTC 1 CGTCTGTCCGTGCGTCCGTACGTC * * 323173 CGTGTGTCCGTGCGTCCGTATGTC 1 CGTCTGTCCGTGCGTCCGTACGTC 323197 CGTCTGTC 1 CGTCTGTC 323205 ACACTTTTTT Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 24 27 1.00 ACGTcount: A:0.02, C:0.36, G:0.32, T:0.30 Consensus pattern (24 bp): CGTCTGTCCGTGCGTCCGTACGTC Found at i:323539 original size:178 final size:172 Alignment explanation

Indices: 323213--323822 Score: 1004 Period size: 172 Copynumber: 3.5 Consensus size: 172 323203 TCACACTTTT 323213 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * * * 323278 CTACTAATACTTTGGTCAACTTAGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA 66 CCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA * * 323343 CTTTGACCACATTAATGACTCCGTTTTATCCAAAAATTGACC 131 CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC * 323385 TTGTAAGCGCTCTTATACATGTACCTACAAATTTTGACGGATTTTCATTAAATTTTTACCAAATG 1 TTGTAAGCGCTC---T-CATG--CCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATG * 323450 TTGATACCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTT 60 TTTATACCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTT * 323515 ATGGGACTTTGATCACAATAATGACACCGTTTTATCCAAAAATTGACC 125 ATGGGACTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC *** 323563 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATTTAAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * * * * 323628 CCACTAATACTTTGGTCATGTTCGAAAATAAGCATTGGTTGATACTTTTTGCTGGAGTTATGGGA 66 CCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA 323693 CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC 131 CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC * * 323735 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAGTTTATACTAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * 323800 CCACTCATACTTTGGTCAAGTTC 66 CCACTAATACTTTGGTCAAGTTC 323823 TTTAAGATTG Statistics Matches: 408, Mismatches: 24, Indels: 12 0.92 0.05 0.03 Matches are distributed among these distances: 172 239 0.59 174 4 0.01 175 2 0.00 176 4 0.01 178 159 0.39 ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38 Consensus pattern (172 bp): TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA CCACTAATACTTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA CTTTGATCACAATAATGACTCCGTTTTATCCAAAAATTGACC Found at i:335351 original size:2 final size:2 Alignment explanation

Indices: 335344--335392 Score: 80 Period size: 2 Copynumber: 24.5 Consensus size: 2 335334 TGTTTATTAT * * 335344 GA GA GA GA TA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 335386 GA GA GA G 1 GA GA GA G 335393 TCAATTTCAA Statistics Matches: 44, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.51, C:0.00, G:0.47, T:0.02 Consensus pattern (2 bp): GA Found at i:336194 original size:12 final size:12 Alignment explanation

Indices: 336145--336199 Score: 67 Period size: 12 Copynumber: 4.6 Consensus size: 12 336135 ACTGTAGCTT * 336145 TCCGTCCGTCAG 1 TCCGTCCGTCTG 336157 TCCGTCCGTCTG 1 TCCGTCCGTCTG * 336169 TCTC-TCCGTATG 1 TC-CGTCCGTCTG 336181 TCCGTCCGTCTG 1 TCCGTCCGTCTG * 336193 TCTGTCC 1 TCCGTCC 336200 CACTTCAGTT Statistics Matches: 37, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 11 1 0.03 12 35 0.95 13 1 0.03 ACGTcount: A:0.04, C:0.40, G:0.22, T:0.35 Consensus pattern (12 bp): TCCGTCCGTCTG Found at i:339981 original size:15 final size:15 Alignment explanation

Indices: 339961--339989 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 339951 GGCTTATTGA 339961 TATGGTATGCTATGC 1 TATGGTATGCTATGC 339976 TATGGTATGCTATG 1 TATGGTATGCTATG 339990 AGATTAAAAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41 Consensus pattern (15 bp): TATGGTATGCTATGC Found at i:340185 original size:26 final size:26 Alignment explanation

Indices: 340156--340221 Score: 105 Period size: 26 Copynumber: 2.5 Consensus size: 26 340146 TACGAGATTG 340156 TATGCTATGGTATGAGATTCCAATGC 1 TATGCTATGGTATGAGATTCCAATGC ** 340182 TATGCTATGGTATGAGATTTTAATGC 1 TATGCTATGGTATGAGATTCCAATGC * 340208 TATGCTATGATATG 1 TATGCTATGGTATG 340222 GTGTATGTTG Statistics Matches: 37, Mismatches: 3, Indels: 0 0.93 0.08 0.00 Matches are distributed among these distances: 26 37 1.00 ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39 Consensus pattern (26 bp): TATGCTATGGTATGAGATTCCAATGC Found at i:341819 original size:2 final size:2 Alignment explanation

Indices: 341814--341868 Score: 92 Period size: 2 Copynumber: 27.5 Consensus size: 2 341804 CAATATATAT * 341814 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * 341856 TC TC CC TC TC TC T 1 TC TC TC TC TC TC T 341869 AAAATAAATT Statistics Matches: 49, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 2 49 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:360093 original size:2 final size:2 Alignment explanation

Indices: 360086--360125 Score: 53 Period size: 2 Copynumber: 20.0 Consensus size: 2 360076 GTCATTTATT * * * 360086 GA GA GA GA GA GA GA GA GA GA GA AA TA AA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 360126 TACTGTAAAT Statistics Matches: 34, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03 Consensus pattern (2 bp): GA Found at i:361114 original size:2 final size:2 Alignment explanation

Indices: 361107--361207 Score: 159 Period size: 2 Copynumber: 51.0 Consensus size: 2 361097 AATTTACAGT 361107 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * * * * 361149 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AA AA AG AA 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 361191 AG -G AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG 361208 CATATGCGTG Statistics Matches: 92, Mismatches: 6, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 1 1 0.01 2 91 0.99 ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00 Consensus pattern (2 bp): AG Found at i:361943 original size:92 final size:91 Alignment explanation

Indices: 361786--361969 Score: 359 Period size: 92 Copynumber: 2.0 Consensus size: 91 361776 TCTTTTCAAG 361786 TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTAA 1 TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTAA 361851 AAGACTGTTCCTTTGAAAGTGTGTGA 66 AAGACTGTTCCTTTGAAAGTGTGTGA 361877 NTTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTA 1 -TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTA 361942 AAAGACTGTTCCTTTGAAAGTGTGTGA 65 AAAGACTGTTCCTTTGAAAGTGTGTGA 361969 T 1 T 361970 GTTTATTCAG Statistics Matches: 92, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 91 1 0.01 92 91 0.99 ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31 Consensus pattern (91 bp): TTCATTCCAAGACAACGTGTCAAGCTCAACAACTTTTATTTGAAGAGAATCCATGAATGTAGTAA AAGACTGTTCCTTTGAAAGTGTGTGA Found at i:362409 original size:2 final size:2 Alignment explanation

Indices: 362404--362431 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 362394 GCAGTGTGTG 362404 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 362432 NNNNNNNNNN Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:370580 original size:13 final size:13 Alignment explanation

Indices: 370562--370600 Score: 51 Period size: 13 Copynumber: 2.9 Consensus size: 13 370552 TTGCCTCATT 370562 TTAATACATCTAC 1 TTAATACATCTAC * 370575 TTAATAAATCTAC 1 TTAATACATCTAC * 370588 TTATTACAGTCTA 1 TTAATACA-TCTA 370601 ATTGTATTGT Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 13 18 0.82 14 4 0.18 ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41 Consensus pattern (13 bp): TTAATACATCTAC Found at i:374116 original size:32 final size:32 Alignment explanation

Indices: 374048--374116 Score: 106 Period size: 32 Copynumber: 2.2 Consensus size: 32 374038 GTACGAAAAC 374048 AATAAGGTCTTCCTTTGAAACGGAAAACCTTT 1 AATAAGGTCTTCCTTTGAAACGGAAAACCTTT * 374080 -ATAAGGTCTTCCGTTTGAAACGGAAGA-CTTT 1 AATAAGGTCTTCC-TTTGAAACGGAAAACCTTT 374111 AATAAG 1 AATAAG 374117 AAACAGAACG Statistics Matches: 34, Mismatches: 1, Indels: 4 0.87 0.03 0.10 Matches are distributed among these distances: 31 16 0.47 32 18 0.53 ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30 Consensus pattern (32 bp): AATAAGGTCTTCCTTTGAAACGGAAAACCTTT Found at i:374141 original size:84 final size:87 Alignment explanation

Indices: 373993--374157 Score: 237 Period size: 84 Copynumber: 1.9 Consensus size: 87 373983 TACGAAAACA * * 373993 ATAAGGTCTTCCGTTGGAAACAGAAGATCTTAATAATGAGAAACAGTACGAAAACAATAAGGTC- 1 ATAAGGTCTTCCGTTGGAAACAGAAGATCTT-ATAATAAGAAACAGAACGAAAACAATAAGGTCT * 374057 TTCCTTTGAAACGGAAAACCTTT 65 TTCCTTGGAAACGGAAAACCTTT * * * 374080 ATAAGGTCTTCCGTTTGAAACGGAAGA-CTT-TAATAAGAAACAGAACGAAATCAATAAGGTCTT 1 ATAAGGTCTTCCGTTGGAAACAGAAGATCTTATAATAAGAAACAGAACGAAAACAATAAGGTCTT * 374143 TCGTTGGAAACGGAA 66 TCCTTGGAAACGGAA 374158 GACTTTAACT Statistics Matches: 70, Mismatches: 7, Indels: 4 0.86 0.09 0.05 Matches are distributed among these distances: 84 28 0.40 85 14 0.20 86 3 0.04 87 25 0.36 ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25 Consensus pattern (87 bp): ATAAGGTCTTCCGTTGGAAACAGAAGATCTTATAATAAGAAACAGAACGAAAACAATAAGGTCTT TCCTTGGAAACGGAAAACCTTT Found at i:374616 original size:2 final size:2 Alignment explanation

Indices: 374609--374675 Score: 116 Period size: 2 Copynumber: 33.5 Consensus size: 2 374599 CAAATTTGTC * 374609 AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * 374651 AG AG AG AG AC AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG A 374676 TTTTAGTGCT Statistics Matches: 61, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.49, C:0.01, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:390407 original size:194 final size:195 Alignment explanation

Indices: 390068--390464 Score: 489 Period size: 194 Copynumber: 2.0 Consensus size: 195 390058 TTATTCCTTT * * * * 390068 TAATATACAAATGATTGAATATTTTAGGGGCCAGCCCTCTAGATCCTTAATGGGGACAGACATTG 1 TAAT-TACAAATGATTAAATATTTAAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTG * * * * 390133 GTGCTTTGATTAATAGAATCGATTAAAATCATCAATGCTAACATTTTCTCTTCTACAATGCTTAT 65 GTGCTTTGATTAATAGAATAGATTAAAACCATCAATGCAAACATTTTCTCTTCTACAATGCTTAA * * * * * 390198 CAAAATATGTCTCCTTTTCTAGATAAATTGCGTCAAAATTTAAGTAATTTGG-CCCTATAAATCC 130 CAAAATATATCTCCTTCTCTAGATAAATTACGTCAAAATTAAAGTAATTTGGCCCCTAAAAATCC 390262 C 195 C * 390263 TAATTACAAATGATTAAATATTTAAGGGGCAAGCCCTGTAGATCCCTT-ATGGGGACAGAAATTG 1 TAATTACAAATGATTAAATATTTAAGGGGCAAGCCCTCTAGAT-CCTTAATGGGGACAGAAATTG * * * * ** 390327 GTG-TATTGA-TAAGTGGAATAGATTTAAACCATTAATGCAAACATTTTCTTTTCTATGATG-TC 65 GTGCT-TTGATTAA-TAGAATAGATTAAAACCATCAATGCAAACATTTTCTCTTCTACAATGCT- * * * * 390389 TAACGAAATATATCTCCTTCTCTAGATATATTACGTCAAAGTTAAAGTACTTTGGCCCCTAAAAA 127 TAACAAAATATATCTCCTTCTCTAGATAAATTACGTCAAAATTAAAGTAATTTGGCCCCTAAAAA 390454 TCCC 192 TCCC * 390458 TTATTAC 1 TAATTAC 390465 GTAATAAATG Statistics Matches: 172, Mismatches: 25, Indels: 10 0.83 0.12 0.05 Matches are distributed among these distances: 193 5 0.03 194 141 0.82 195 26 0.15 ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35 Consensus pattern (195 bp): TAATTACAAATGATTAAATATTTAAGGGGCAAGCCCTCTAGATCCTTAATGGGGACAGAAATTGG TGCTTTGATTAATAGAATAGATTAAAACCATCAATGCAAACATTTTCTCTTCTACAATGCTTAAC AAAATATATCTCCTTCTCTAGATAAATTACGTCAAAATTAAAGTAATTTGGCCCCTAAAAATCCC Found at i:391571 original size:53 final size:53 Alignment explanation

Indices: 391495--391642 Score: 197 Period size: 53 Copynumber: 2.7 Consensus size: 53 391485 AAGAAATAAG ** * * 391495 AAGAAACAGTACGAAAACAATAAGGTGTTCCGTTTGAAACAGAATACCTAAAT 1 AAGAAACAGTACGAAAACAATAAGGTCCTCCGTTGGAAACAGAAGACCTAAAT * * 391548 AAGAAACAGTACGAAAACAATAAGGTCCTCTGTTGGAAACAGAAGACCTTAAT 1 AAGAAACAGTACGAAAACAATAAGGTCCTCCGTTGGAAACAGAAGACCTAAAT * * 391601 AAGAAACAGTACAAAAACAATTACTAGGTCTTCCGTTGGAAA 1 AAGAAACAGTACGAAAACAA-TA--AGGTCCTCCGTTGGAAA 391643 GTAAAACATT Statistics Matches: 83, Mismatches: 9, Indels: 3 0.87 0.09 0.03 Matches are distributed among these distances: 53 66 0.80 54 2 0.02 56 15 0.18 ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20 Consensus pattern (53 bp): AAGAAACAGTACGAAAACAATAAGGTCCTCCGTTGGAAACAGAAGACCTAAAT Found at i:410319 original size:35 final size:35 Alignment explanation

Indices: 410273--410343 Score: 133 Period size: 35 Copynumber: 2.0 Consensus size: 35 410263 CAATCAACTT 410273 AGATAGCTTTAATCCCTAATGATGACATGTGGTGC 1 AGATAGCTTTAATCCCTAATGATGACATGTGGTGC * 410308 AGATAGCTTTAATCCCTGATGATGACATGTGGTGC 1 AGATAGCTTTAATCCCTAATGATGACATGTGGTGC 410343 A 1 A 410344 AATTATTTCA Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 35 35 1.00 ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31 Consensus pattern (35 bp): AGATAGCTTTAATCCCTAATGATGACATGTGGTGC Found at i:421457 original size:26 final size:26 Alignment explanation

Indices: 421417--421469 Score: 79 Period size: 26 Copynumber: 2.0 Consensus size: 26 421407 ACAATGCTGT * * 421417 TTGACACGACTACCCAAAGTCAAAGC 1 TTGACACAACAACCCAAAGTCAAAGC * 421443 TTGACACAACAACCCAAAGTCCAAGC 1 TTGACACAACAACCCAAAGTCAAAGC 421469 T 1 T 421470 CCTGTTAAAA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 26 24 1.00 ACGTcount: A:0.40, C:0.32, G:0.13, T:0.15 Consensus pattern (26 bp): TTGACACAACAACCCAAAGTCAAAGC Found at i:423673 original size:33 final size:33 Alignment explanation

Indices: 423636--424148 Score: 305 Period size: 33 Copynumber: 16.0 Consensus size: 33 423626 TGATCATTTT * * 423636 ACATAGGTAAATCCCTGTCCTTGTAACTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG ** * 423669 ACATAGGTAACTCCCTGTCCCTGTCCCTGTTTC 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * * * * 423702 ACATAGGTTAGGTAATTTCCTGTCCCTTTAAC----TA 1 AC--A---TAGGTAACTCCCTGTCCCTGTAACTGTTTG * 423736 ACATAGGT-A---GC--TCCCTGTAACTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * * 423763 ACATAAGTAACTCCCTGTCCCTGTAACTGTATG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * * 423796 ACATAGGTTAGGTAATTCCATGTCCCTGTAAC----TG 1 AC--A---TAGGTAACTCCCTGTCCCTGTAACTGTTTG * 423830 ACATAGGTAACT-CCTGTCCCTGTAAATGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG *** ** * * 423862 ACATACACAACTCCCTGTCTTTGTACCTGCTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * 423895 ACATAGGTAACTCCTTGTCCCTGTAACTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * * * 423928 ACATATAGATAACTTCCAGT-CCTCGTAACTGTTTG 1 AC--ATAGGTAACTCCCTGTCCCT-GTAACTGTTTG * * ** 423963 ACATAAGTTAGAATTTCT-T-CCTGTAACTGTTTG 1 ACAT-AGGTA-ACTCCCTGTCCCTGTAACTGTTTG * * * * 423996 ACCTAGGTAACTCCCTGTCCTTTTACCTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * 424029 GCATAGGTAA---CC---CCCTGTAACTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * * 424056 ACATAGATAACT-CCTGTCCCTGTACCTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG 424088 ACATAGGTAA----C--TCCCTGTAACTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG * * * * 424115 ACTTAGGTAGCTCCCTTTCCCTGTTACTGTTTG 1 ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG 424148 A 1 A 424149 TGTTAAATCA Statistics Matches: 369, Mismatches: 68, Indels: 86 0.71 0.13 0.16 Matches are distributed among these distances: 23 9 0.02 25 1 0.00 27 51 0.14 28 14 0.04 29 16 0.04 30 2 0.01 31 6 0.02 32 41 0.11 33 140 0.38 34 18 0.05 35 31 0.08 38 40 0.11 ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35 Consensus pattern (33 bp): ACATAGGTAACTCCCTGTCCCTGTAACTGTTTG Found at i:423897 original size:99 final size:96 Alignment explanation

Indices: 423636--423902 Score: 301 Period size: 94 Copynumber: 2.7 Consensus size: 96 423626 TGATCATTTT * * * 423636 ACATAGGTAAATCCCTGTCCTTGTAACTGTTTGACATAGGTAACTCCCTGTCCCTGTCCCTGTTT 1 ACATAGGT-AAT-CCTGTCCCTGTAACTGTTTGACATA-ATAACTCCCTGTCCCTGTACCTG-TT * * 423701 CACATAGGTTAGGTAATTTCCTGTCCCTTTAACTA 62 GACATAGGTTAGGTAATTTCCTGTCCCTGTAACTA * * 423736 ACATAGGT-A-GC--TCCCTGTAACTGTTTGACATAAGTAACTCCCTGTCCCTGTAACTGTATGA 1 ACATAGGTAATCCTGTCCCTGTAACTGTTTGACATAA-TAACTCCCTGTCCCTGTACCTGT-TGA * 423797 CATAGGTTAGGTAA-TTCCATGTCCCTGTAACTG 64 CATAGGTTAGGTAATTTCC-TGTCCCTGTAACTA * * ** 423830 ACATAGGTAACTCCTGTCCCTGTAAATGTTTGACATACACAACTCCCTGTCTTTGTACCTGCTTG 1 ACATAGGTAA-TCCTGTCCCTGTAACTGTTTGACATA-ATAACTCCCTGTCCCTGTACCTG-TTG 423895 ACATAGGT 63 ACATAGGT 423903 AACTCCTTGT Statistics Matches: 143, Mismatches: 14, Indels: 21 0.80 0.08 0.12 Matches are distributed among these distances: 93 5 0.03 94 76 0.53 95 1 0.01 96 1 0.01 97 1 0.01 98 1 0.01 99 48 0.34 100 10 0.07 ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34 Consensus pattern (96 bp): ACATAGGTAATCCTGTCCCTGTAACTGTTTGACATAATAACTCCCTGTCCCTGTACCTGTTGACA TAGGTTAGGTAATTTCCTGTCCCTGTAACTA Found at i:424012 original size:27 final size:27 Alignment explanation

Indices: 423982--424130 Score: 127 Period size: 27 Copynumber: 5.1 Consensus size: 27 423972 AGAATTTCTT * 423982 CCTGTAACTGTTTGACCTAGGTAACTC 1 CCTGTAACTGTTTGACATAGGTAACTC * * * 424009 CCTGTCCTTTTACCTGTTTGGCATAGGTAACCC 1 CCTG------TAACTGTTTGACATAGGTAACTC * 424042 CCTGTAACTGTTTGACATAGATAACTCCTGTC 1 CCTGTAACTGTTTGACATAGGTAA---C--TC * 424074 CCTGTACCTGTTTGACATAGGTAACTC 1 CCTGTAACTGTTTGACATAGGTAACTC * * 424101 CCTGTAACTGTTTGACTTAGGTAGCTC 1 CCTGTAACTGTTTGACATAGGTAACTC 424128 CCT 1 CCT 424131 TTCCCTGTTA Statistics Matches: 98, Mismatches: 13, Indels: 22 0.74 0.10 0.17 Matches are distributed among these distances: 27 50 0.51 29 1 0.01 30 1 0.01 32 23 0.23 33 23 0.23 ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35 Consensus pattern (27 bp): CCTGTAACTGTTTGACATAGGTAACTC Found at i:427563 original size:169 final size:165 Alignment explanation

Indices: 427099--428104 Score: 1104 Period size: 166 Copynumber: 6.0 Consensus size: 165 427089 AATTAAAGGA * * 427099 TTTTAAAGATTTACTCTA--TATATTCCTATGTATAAATTCGACCCCCATCGTGGCCCC-TACCA 1 TTTTAAAGATTTACTCTATGTATATT-CTATG-ATAAATTCAACCCCCATCGTGGCCCCAT-CCT * 427161 ACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGT 63 ACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAGT * ** * 427226 TTCAGTTTTCCTGGCCTAACAGTTTCTGAGAAAAAGAT 128 TTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT * * * * * * * 427264 TTTTAAAAATTTACTCCATGTATA-ACAATGTTAAAACTCAACCCACCATTGTGGCCCCATCCTA 1 TTTTAAAGATTTACTCTATGTATATTCTATGAT-AAATTCAACCC-CCATCGTGGCCCCATCCTA ** * * * * * 427328 ATCCCAAGGGTCATG-ATTTCAACAACTTTGAA-CTGACAATACCTGAAGATGCTTCCATACAAG 64 CCCCCAGGGGTCATGCTTTTC-ACAACTTTGAATCT-ACACTACCTGAGGATGCTTCCAGACAAG * * 427391 TTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGAC 127 TTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT * * * * 427430 TATTAAAGCTTTACTCTTACTGTATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCC-TAC 1 TTTTAAAGATTTACTC-TA-TGTATATTC-TATG-ATAAATTCAACCCCCATCGTGGCCCCAT-C * * 427494 CTACCCCCAGGGGTCATGCTTTTCACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAA 61 CTACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAA * * ** * 427559 GTTTCAGTTTTCCTGGCCCAACAGTTTCTGAGAAAAAGAT 126 GTTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT * * * * * * * 427599 TTTTAAAAATTTACTCCATGTATA-ACAATGTTAAAACTCAACCCACCATTGTGGCCCCATCCTA 1 TTTTAAAGATTTACTCTATGTATATTCTATGAT-AAATTCAACCC-CCATCGTGGCCCCATCCTA ** * * * * * 427663 ATCCCAAGGGTCATG-ATTTCAACAACTTTGAA-CTGACAATACCTGAAGATGCTTCCATACAAG 64 CCCCCAGGGGTCATGCTTTTC-ACAACTTTGAATCT-ACACTACCTGAGGATGCTTCCAGACAAG * * 427726 TTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGAC 127 TTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT * * * * 427765 TATTAAAGCTTTACTCTTACTGTATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCC-TAC 1 TTTTAAAGATTTACTC-TA-TGTATATTC-TATG-ATAAATTCAACCCCCATCGTGGCCCCAT-C * * 427829 CTACCCCCAGGGGTCATGCTTTTCACAAATTTGAATCTACACTACCTGAGGATGCTTCCA-CCTA 61 CTACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGAC-A 427893 AGTTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT 125 AGTTTCAGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT * * 427934 TTTTAAAGATTTACTCTAT-TATATTCCCATGTATAAATTCAACCCCCCCATTGTGGCCCCATCC 1 TTTTAAAGATTTACTCTATGTATATT-CTATG-ATAAATTCAA--CCCCCATCGTGGCCCCATCC * * * 427998 TACCCCAAGGGGTCATGATTTTCACAATTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAG 62 TACCCCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAG * * 428063 TTTCAGCTTTCCTTGCCTTATGG-TTCTTGAGAAGAAGAT 127 TTTCAGCTTTCCTGGCCTAATGGTTTC-TGAGAAGAAGAT 428102 TTT 1 TTT 428105 AGAAAAAAAA Statistics Matches: 697, Mismatches: 109, Indels: 67 0.80 0.12 0.08 Matches are distributed among these distances: 164 2 0.00 165 53 0.08 166 234 0.34 167 19 0.03 168 129 0.19 169 222 0.32 170 36 0.05 171 2 0.00 ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32 Consensus pattern (165 bp): TTTTAAAGATTTACTCTATGTATATTCTATGATAAATTCAACCCCCATCGTGGCCCCATCCTACC CCCAGGGGTCATGCTTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGACAAGTTTC AGCTTTCCTGGCCTAATGGTTTCTGAGAAGAAGAT Found at i:427727 original size:335 final size:335 Alignment explanation

Indices: 427117--428100 Score: 1620 Period size: 335 Copynumber: 2.9 Consensus size: 335 427107 ATTTACTCTA * * * * 427117 TATATTCCTATGTATAAATTCGACCCCCATCGTGGCCCCTACCAACCCCCAGGGGTCATGCTTTT 1 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT * 427182 CACAACTTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA 66 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA 427247 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA 131 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA 427312 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA 196 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA 427377 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT 261 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT 427442 ACTCTTACTG 326 ACTCTTACTG 427452 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT 1 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT * 427517 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCCAACA 66 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA 427582 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA 131 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA 427647 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA 196 TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA 427712 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT 261 TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT 427777 ACTCTTACTG 326 ACTCTTACTG 427787 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT 1 TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT ** * ** 427852 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCACCTAAGTTTCAGCTTTCCTGGCCTAATG 66 CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA * * * * * * 427917 GTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTAT-TATATTCCCATG-TATAAATTCAACCCC 131 GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATA--ACAATGTTA-AAACTCAA-CCC * * * * 427980 CCCATTGTGGCCCCATCCT-ACCCCAAGGGGTCATGATTTTC-ACAATTTTGAATCT-ACACTAC 192 ACCATTGTGGCCCCATCCTAATCCCAA-GGGTCATGA-TTTCAACAACTTTGAA-CTGACAATAC * * * ** 428042 CTGAGGATGCTTCCAGACAAGTTTCAGCTTTCCTTGCCTTATGG-TTCTTGAGAAGAAGA 254 CTGAAGATGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTC-TGAGAAGAAGA 428101 TTTTAGAAAA Statistics Matches: 614, Mismatches: 27, Indels: 14 0.94 0.04 0.02 Matches are distributed among these distances: 334 4 0.01 335 488 0.79 336 20 0.03 337 96 0.16 338 6 0.01 ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31 Consensus pattern (335 bp): TATATTCTTATGCATAAATTCGACCCCTATCGTGGCCCCTACCTACCCCCAGGGGTCATGCTTTT CACAAATTTGAATCTACACTACCTGAGGATGCTTCCAGATAAGTTTCAGTTTTCCTGGCCTAACA GTTTCTGAGAAAAAGATTTTTAAAAATTTACTCCATGTATAACAATGTTAAAACTCAACCCACCA TTGTGGCCCCATCCTAATCCCAAGGGTCATGATTTCAACAACTTTGAACTGACAATACCTGAAGA TGCTTCCATACAAGTTTCAGCTTTCCTGGCCAAATGGTTTCTGAGAAGAAGACTATTAAAGCTTT ACTCTTACTG Found at i:432830 original size:21 final size:21 Alignment explanation

Indices: 432804--432885 Score: 101 Period size: 21 Copynumber: 3.9 Consensus size: 21 432794 CACTTTGAAG 432804 TGTAAAATTCACAATTTAATC 1 TGTAAAATTCACAATTTAATC * 432825 TGTAAAATTCACACTTTAATC 1 TGTAAAATTCACAATTTAATC * ** * 432846 TATAAAATTTTCACTTTAATC 1 TGTAAAATTCACAATTTAATC * * 432867 TGTAAAATTTACAAGTTAA 1 TGTAAAATTCACAATTTAA 432886 AGCGTAAATT Statistics Matches: 53, Mismatches: 8, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 53 1.00 ACGTcount: A:0.41, C:0.13, G:0.05, T:0.40 Consensus pattern (21 bp): TGTAAAATTCACAATTTAATC Found at i:432906 original size:21 final size:21 Alignment explanation

Indices: 432867--433082 Score: 197 Period size: 21 Copynumber: 10.2 Consensus size: 21 432857 CACTTTAATC * 432867 TGTAAAATTTACA-AGTTAAAG 1 TGTAAATTTTACAGA-TTAAAG * * * 432888 CGTAAATTATACAGATTAAAT 1 TGTAAATTTTACAGATTAAAG * * 432909 TGTGAATTTTACAAATT-AA- 1 TGTAAATTTTACAGATTAAAG * * 432928 TGTGAATTTTACA-CTTCAAAG 1 TGTAAATTTTACAGATT-AAAG * 432949 TGTCAATTTTACAGATTAAAG 1 TGTAAATTTTACAGATTAAAG * ** 432970 TGTGAATTTTACACTTTTTAAAAG 1 TGTAAATTTTACA--GATT-AAAG * 432994 TGTAAATTTTACAGATTAAAA 1 TGTAAATTTTACAGATTAAAG * * 433015 TGTAAAATTTACAGAATAAAG 1 TGTAAATTTTACAGATTAAAG * 433036 TGTAAATTTTACAGATTAAAT 1 TGTAAATTTTACAGATTAAAG * * 433057 TGTAAAATGTACAGATTAAAG 1 TGTAAATTTTACAGATTAAAG 433078 TGTAA 1 TGTAA 433083 TGTCTTTTGT Statistics Matches: 160, Mismatches: 27, Indels: 16 0.79 0.13 0.08 Matches are distributed among these distances: 18 2 0.01 19 13 0.08 20 4 0.03 21 118 0.74 22 5 0.03 23 2 0.01 24 16 0.10 ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37 Consensus pattern (21 bp): TGTAAATTTTACAGATTAAAG Found at i:442974 original size:42 final size:42 Alignment explanation

Indices: 442915--443651 Score: 909 Period size: 42 Copynumber: 17.7 Consensus size: 42 442905 TCTTAATCTC * 442915 TGAAACTTT-AATATTTTCCTATGTCTTTATAACTTTAACCTA 1 TGAAA-TTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * * * 442957 TGAAATTTGAATATTTTCCTATATCCTTAAAATTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * * * 442999 TGAAATTTGAATATTTTGCTCTTTTTTTTTTTATATAACTTTAACCTA 1 TGAAATTTGAATATTTT-C-C---TATATCTT-TATAACTTTAACCTA * * 443047 TGAAATTTGAATATTTTCCTTTATTTTTATAACTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * * * * * 443089 T-AAAATTCAATTATTTTCTTATATCTTTATATCTTTAATCTA 1 TGAAATTTGAA-TATTTTCCTATATCTTTATAACTTTAACCTA * 443131 TGAAATTTGAATATTTTCCTACATCTTTATAACTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * 443173 TGAAATTCGAATATTTTCCTATATCTTTATAACTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * * * 443215 TGAAATTTG-ATAATTTTCCTATCTTTTTATATCTTTAACCTA 1 TGAAATTTGAAT-ATTTTCCTATATCTTTATAACTTTAACCTA * 443257 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACTTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * 443299 TGAAATTTGGATATTTTCC--TA----TAT--CTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * 443333 TGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * * * * 443375 TGAAATTTGATTATTTTCCCATATCTTTATAACCTTAACATA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA 443417 TGAAATTTGAATATTTTCC--TA----TAT--CTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * 443451 TGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * * * * * 443493 TGAAATTTGATTATTTTGCTCTTTTTTTTTTTACAACTTTAACCTA 1 TGAAATTTGAATATTTT-C-C--TATATCTTTATAACTTTAACCTA * 443539 TGAAATTTGAATATTGTCCTATATCTTTATAACTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA * * 443581 TAAAATTTGAATATTTTCCTATATCTTTATATCTTTAACCTA 1 TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA 443623 TGAAATTTGAATATTTTCCTATATCTTTA 1 TGAAATTTGAATATTTTCCTATATCTTTA 443652 CACCGAGCTC Statistics Matches: 601, Mismatches: 63, Indels: 62 0.83 0.09 0.09 Matches are distributed among these distances: 34 54 0.09 36 10 0.02 40 10 0.02 41 12 0.02 42 424 0.71 43 18 0.03 44 3 0.00 45 1 0.00 46 34 0.06 47 5 0.01 48 30 0.05 ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49 Consensus pattern (42 bp): TGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA Found at i:442977 original size:21 final size:22 Alignment explanation

Indices: 442952--443015 Score: 62 Period size: 21 Copynumber: 3.0 Consensus size: 22 442942 TATAACTTTA 442952 ACCTATGAAATTTGAATATTTT 1 ACCTATGAAATTTGAATATTTT *** * 442974 -CCTAT-ATCCTT-AAAATTTT 1 ACCTATGAAATTTGAATATTTT 442993 AACCTATGAAATTTGAATATTTT 1 -ACCTATGAAATTTGAATATTTT 443016 GCTCTTTTTT Statistics Matches: 30, Mismatches: 8, Indels: 7 0.67 0.18 0.16 Matches are distributed among these distances: 19 7 0.23 20 3 0.10 21 10 0.33 22 3 0.10 23 7 0.23 ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45 Consensus pattern (22 bp): ACCTATGAAATTTGAATATTTT Found at i:443334 original size:76 final size:76 Alignment explanation

Indices: 443242--443651 Score: 398 Period size: 76 Copynumber: 5.1 Consensus size: 76 443232 CCTATCTTTT * 443242 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACTTATGAAATTT 1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTATGAAATTT * 443307 GGATATTTTCC 66 GAATATTTTCC * 443318 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT 1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTATGAAATTT * 443383 GATTATTTTCC 66 GAATATTTTCC * * ** * * 443394 CATATCTTTATAACCT-T-AACATATGAA-A-TTT-GAATATTTTCCTATATCTTTAACCTATGA 1 TATATC-TT-TAACCTATGAA-ATTTGAATATTTTCCTATATCTT--TATAACTTTAACCTATGA 443454 AATTTGAATATTTTCC 61 AATTTGAATATTTTCC * * * * * 443470 TATATCTTTATAACTTAAACCTATGAAATTTGATTATTTTGCTCTTTTTTTTTTTACAACTTTAA 1 TATATC----T---TT-AACCTATGAAATTTGAATATTTT-C-C--TATATCTTTATAACTTTAA * 443535 CCTATGAAATTTGAATATTGTCC 54 CCTATGAAATTTGAATATTTTCC * * 443558 TATATCTTTATAACTTTAACCTATAAAATTTGAATATTTTCCTATATCTTTATATCTTTAACCTA 1 --TA----TAT--CTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTA 443623 TGAAATTTGAATATTTTCC 58 TGAAATTTGAATATTTTCC 443642 TATATCTTTA 1 TATATCTTTA 443652 CACCGAGCTC Statistics Matches: 274, Mismatches: 31, Indels: 58 0.75 0.09 0.16 Matches are distributed among these distances: 74 6 0.02 75 3 0.01 76 121 0.44 77 9 0.03 78 9 0.03 79 1 0.00 81 1 0.00 82 8 0.03 83 6 0.02 84 39 0.14 85 3 0.01 86 1 0.00 87 1 0.00 88 52 0.19 89 2 0.01 90 7 0.03 92 1 0.00 94 3 0.01 96 1 0.00 ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48 Consensus pattern (76 bp): TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTTAACCTATGAAATTT GAATATTTTCC Found at i:443373 original size:118 final size:118 Alignment explanation

Indices: 443200--443651 Score: 600 Period size: 118 Copynumber: 3.7 Consensus size: 118 443190 CCTATATCTT * * * * * 443200 TATAACTTTAACCTATGAAATTTG-ATAATTTTCCTATCTTTTTATATCTTTAACCTATGAAATT 1 TATATCTTTAACCTATGAAATTTGAAT-ATTTTCCTATATCTTTATAACTTAAACCTATGAAATT * * 443264 TGAATATTTTCCTATATCTTTATAACTTTAACTTATGAAATTTGGATATTTTCC 65 TGAATATTTTCCTATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC 443318 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT 1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT * * * 443383 GATTATTTTCCCATATCTTTATAACCTTAACATATGAAATTTGAATATTTTCC 66 GAATATTTTCCTATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC 443436 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT 1 TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT * * * * * * * 443501 GATTATTTTGCTCTTTTTTTTTTTACAACTTTAACCTATGAAATTTGAATATTGTCC 66 GAATATTTT-C-C--TATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC * * * 443558 TATATCTTTATAACTTTAACCTATAAAATTTGAATATTTTCCTATATCTTTATATCTTTAACCTA 1 --TA----TAT--CTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTA 443623 TGAAATTTGAATATTTTCCTATATCTTTA 58 TGAAATTTGAATATTTTCCTATATCTTTA 443652 CACCGAGCTC Statistics Matches: 296, Mismatches: 25, Indels: 18 0.87 0.07 0.05 Matches are distributed among these distances: 118 179 0.60 119 3 0.01 120 1 0.00 122 34 0.11 124 2 0.01 126 7 0.02 128 4 0.01 129 1 0.00 130 65 0.22 ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48 Consensus pattern (118 bp): TATATCTTTAACCTATGAAATTTGAATATTTTCCTATATCTTTATAACTTAAACCTATGAAATTT GAATATTTTCCTATATCTTTATAACTTTAACATATGAAATTTGAATATTTTCC Found at i:443601 original size:21 final size:21 Alignment explanation

Indices: 443577--443645 Score: 63 Period size: 21 Copynumber: 3.3 Consensus size: 21 443567 ATAACTTTAA 443577 CCTATAAAATTTGAATATTTT 1 CCTATAAAATTTGAATATTTT ** 443598 CCTAT-ATCTTT--ATATCTTT 1 CCTATAAAATTTGAATAT-TTT * 443617 AACCTATGAAATTTGAATATTTT 1 --CCTATAAAATTTGAATATTTT 443640 CCTATA 1 CCTATA 443646 TCTTTACACC Statistics Matches: 37, Mismatches: 5, Indels: 12 0.69 0.09 0.22 Matches are distributed among these distances: 18 4 0.11 19 3 0.08 20 4 0.11 21 15 0.41 22 4 0.11 23 3 0.08 24 4 0.11 ACGTcount: A:0.33, C:0.14, G:0.04, T:0.48 Consensus pattern (21 bp): CCTATAAAATTTGAATATTTT Found at i:445410 original size:17 final size:17 Alignment explanation

Indices: 445377--445410 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 445367 CTGTGGTTTC * 445377 ACCAATTTTCGTTGAAT 1 ACCAATTTTCGTGGAAT * 445394 ACCAATTTTTGTGGAAT 1 ACCAATTTTCGTGGAAT 445411 TCTTTTTTGA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41 Consensus pattern (17 bp): ACCAATTTTCGTGGAAT Found at i:455524 original size:30 final size:30 Alignment explanation

Indices: 455490--455548 Score: 100 Period size: 30 Copynumber: 2.0 Consensus size: 30 455480 AATTTCATCA * * 455490 TGCGATAAATGCTAAAAATGCAAATTGTCT 1 TGCGATAAATGATAAAAATGCAAACTGTCT 455520 TGCGATAAATGATAAAAATGCAAACTGTC 1 TGCGATAAATGATAAAAATGCAAACTGTC 455549 ATGCTCATAT Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27 Consensus pattern (30 bp): TGCGATAAATGATAAAAATGCAAACTGTCT Found at i:458291 original size:21 final size:20 Alignment explanation

Indices: 458265--458340 Score: 89 Period size: 21 Copynumber: 3.6 Consensus size: 20 458255 ATTTGTAACT 458265 TGCATGTAGACATAATTATCC 1 TGCATGTAGACATAATTAT-C * * 458286 TGCATGTAGACAGAATTATAT 1 TGCATGTAGACATAATTAT-C * 458307 TGCATGTAGACACAATTATC 1 TGCATGTAGACATAATTATC * 458327 TAGCATGTTGACAT 1 T-GCATGTAGACAT 458341 NNNNNNNNNN Statistics Matches: 47, Mismatches: 7, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 20 1 0.02 21 46 0.98 ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33 Consensus pattern (20 bp): TGCATGTAGACATAATTATC Found at i:462409 original size:161 final size:160 Alignment explanation

Indices: 462129--462630 Score: 686 Period size: 161 Copynumber: 3.1 Consensus size: 160 462119 AACATCCACA * * ** * * * 462129 AAGAAAATGAACGTAAACTGCAAATATTTGGAATTTTTCTAAGTCCAAGGGGCATAACTATG-CG 1 AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG * * * * * 462193 GAAATTGCTC-TATCATACCCAAAATCAAACTTGACCTAGATATTATT-TAGATAAACCTGCATA 66 AAAATTGCTCGT-TCGTACCCAATATCGAACTTGACCTAGATATTATTAT-GATAAACCTGTATA * * * 462256 CCAAATTTCATATTAATGTGTGCACCCTTTGCG 129 CCAAATTTCAT-TTAATATGTTCATCCTTTGCG * * 462289 AAGAAAATGAGCGGAAGCTGCAAGTAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG 1 AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG * * 462354 AAAATTGCCCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACT 66 AAAATTGCTCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACC * 462419 AAATTTCATTTTAATATGTTCATCCTCTGCG 131 AAATTTCA-TTTAATATGTTCATCCTTTGCG * * 462450 AAAAAAATGAGCGGAAACTGCAAATAACTCGAATTTGTCTAAGTCCAAGGGCCATAACTCTGTCG 1 AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG * * * 462515 AAAATTGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCAGTATACC 66 AAAATTGCTCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACC * * 462580 AAATTTCATTTCAATATGTTTATCCTTTGCA 131 AAATTTCATTT-AATATGTTCATCCTTTGCG * 462611 AAGAAAATGAACGGAAACTG 1 AAGAAAATGAGCGGAAACTG 462631 TTGGTGGACC Statistics Matches: 303, Mismatches: 34, Indels: 9 0.88 0.10 0.03 Matches are distributed among these distances: 160 56 0.18 161 244 0.81 162 3 0.01 ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29 Consensus pattern (160 bp): AAGAAAATGAGCGGAAACTGCAAATAACTCGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG AAAATTGCTCGTTCGTACCCAATATCGAACTTGACCTAGATATTATTATGATAAACCTGTATACC AAATTTCATTTAATATGTTCATCCTTTGCG Found at i:464825 original size:53 final size:53 Alignment explanation

Indices: 464743--464907 Score: 278 Period size: 53 Copynumber: 3.1 Consensus size: 53 464733 TAAGCAGCAC * 464743 CAAACCTTTGATACGACCATTCGTGTGACAATGTACGAACTGAATCGCAATGAA 1 CAAA-CTTTGATACGACCATTCGTTTGACAATGTACGAACTGAATCGCAATGAA * 464797 CAAACTTTGATACGACCATTCGTTTGACAATTGT-CGAGCTGAATCGCAATGAA 1 CAAACTTTGATACGACCATTCGTTTGACAA-TGTACGAACTGAATCGCAATGAA * 464850 CAAACTTTGATACGACCATTTGTTTGACAATGTACGAACTGAATCGCAATGAA 1 CAAACTTTGATACGACCATTCGTTTGACAATGTACGAACTGAATCGCAATGAA 464903 CAAAC 1 CAAAC 464908 ATAGTTTTAA Statistics Matches: 105, Mismatches: 4, Indels: 5 0.92 0.04 0.04 Matches are distributed among these distances: 52 3 0.03 53 95 0.90 54 7 0.07 ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26 Consensus pattern (53 bp): CAAACTTTGATACGACCATTCGTTTGACAATGTACGAACTGAATCGCAATGAA Found at i:469065 original size:9 final size:9 Alignment explanation

Indices: 469051--469079 Score: 51 Period size: 9 Copynumber: 3.3 Consensus size: 9 469041 TCAATATGAG 469051 AAAAGGTAA 1 AAAAGGTAA 469060 AAAAGGT-A 1 AAAAGGTAA 469068 AAAAGGTAA 1 AAAAGGTAA 469077 AAA 1 AAA 469080 CTTGTTACAA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 8 8 0.42 9 11 0.58 ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10 Consensus pattern (9 bp): AAAAGGTAA Found at i:476671 original size:6 final size:6 Alignment explanation

Indices: 476660--476697 Score: 60 Period size: 6 Copynumber: 6.3 Consensus size: 6 476650 TGCTATACCC 476660 TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TCGGCG TC 1 TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TCGGCG TC 476698 CGGACCTGGT Statistics Matches: 30, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 5 2 0.07 6 26 0.87 7 2 0.07 ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18 Consensus pattern (6 bp): TCGGCG Found at i:477044 original size:19 final size:19 Alignment explanation

Indices: 477022--477061 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 477012 TTTCGGATGC * * 477022 TGGAGGAGGTTAAGGTTTT 1 TGGAGCAGGTTAAAGTTTT 477041 TGGAGCAGGTTAAAGTTTT 1 TGGAGCAGGTTAAAGTTTT 477060 TG 1 TG 477062 TTGTGGGTGC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38 Consensus pattern (19 bp): TGGAGCAGGTTAAAGTTTT Found at i:477053 original size:177 final size:176 Alignment explanation

Indices: 476835--477714 Score: 1253 Period size: 177 Copynumber: 4.9 Consensus size: 176 476825 GGGTCCTAAA * * ** * * * 476835 TTTCAGATGCTGGAGGAGGTTAAGGTTGTGGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTT 1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT * * * * * * * 476900 GATAGCA-ATATCTTAGTTACTGCTGGTCCGTACATCACCAAATTTGCATGGATGGTGTGCCTTA 66 GAT-G-ATATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTA * * * * 476964 TGATACTGATGCACCAGACAGGCTTGAGTGCTGAATCTGAGCTATAGG 129 TGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG * * ** 477012 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAGTTTTTGTTGTGGGTGCCCAT- 1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCC-TC * * * 477076 TGATAGCA-ATATCTAAGTTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGATGCGTCTT 65 TGAT-G-ATATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTT 477140 ATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG 128 ATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG * 477189 TTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT 1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT 477254 GATGATTATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTAT 66 GATGA-TATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTAT * 477319 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGA 130 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG * * 477366 TTTCGGATGCTGGAAGAGGTTAAGGTTTTTATAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT 1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT * 477431 GATGATTATATCTTAGTTACTACTGGTCCTTACTTCACAAAACTTGTATGGATGGTGCGTCTTAT 66 GATGA-TATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTAT 477496 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG 130 GATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG * *** 477543 TTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTAAATAAAGTTTTTGAAACAGGTGCC 1 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGG-T---TAAAGTTTTTGTTGCAGGTGCC * * * ** * 477608 CTCTGATGATGATATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTC 62 CTCTGATGAT-ATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTC * * 477673 TTATGATACTGATGCACCTGACAGGCTTGAATGCTGAGTCTG 126 TTATGATACTGATGCACCTGACAAGCTTGAATGCTGAATCTG 477715 GTTTCGGATG Statistics Matches: 647, Mismatches: 47, Indels: 14 0.91 0.07 0.02 Matches are distributed among these distances: 175 1 0.00 176 2 0.00 177 526 0.81 178 2 0.00 180 1 0.00 181 115 0.18 ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34 Consensus pattern (176 bp): TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT GATGATATATCTTAGTTACTACTGGTCCTTACTTCACCAAACTTGTATGGATGGTGCGTCTTATG ATACTGATGCACCTGACAAGCTTGAATGCTGAATCTGAGCAATAGG Found at i:478396 original size:20 final size:20 Alignment explanation

Indices: 478373--478415 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 478363 TATGATATAG 478373 TATTGTATGATATGAAACAA 1 TATTGTATGATATGAAACAA * * 478393 TATTGTTTGATATGATACAA 1 TATTGTATGATATGAAACAA 478413 TAT 1 TAT 478416 GATATCATAT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42 Consensus pattern (20 bp): TATTGTATGATATGAAACAA Found at i:478691 original size:15 final size:15 Alignment explanation

Indices: 478658--478804 Score: 73 Period size: 15 Copynumber: 9.3 Consensus size: 15 478648 ATATTCTATA * ** 478658 ATATTGTATCATACA 1 ATATTGTATAATATG 478673 ATATTGTATAATATG 1 ATATTGTATAATATG 478688 ATATTGGTTTCAGTAATATAG 1 ATATT-G--T-A-TAATAT-G * * * 478709 A-ATTATATCACATG 1 ATATTGTATAATATG * * 478723 AAATTGTATTATATG 1 ATATTGTATAATATG * 478738 ATATTGTAATATTATATA 1 ATATTGT-ATA--ATATG * * 478756 ATATTGTATCATACG 1 ATATTGTATAATATG * 478771 ATATTGTATGATATG 1 ATATTGTATAATATG * 478786 ATATTGGT-TTATATG 1 ATATT-GTATAATATG 478801 ATAT 1 ATAT 478805 ATTATCTTAT Statistics Matches: 103, Mismatches: 18, Indels: 22 0.72 0.13 0.15 Matches are distributed among these distances: 14 2 0.02 15 68 0.66 16 6 0.06 17 3 0.03 18 12 0.12 19 1 0.01 20 9 0.09 21 2 0.02 ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45 Consensus pattern (15 bp): ATATTGTATAATATG Found at i:478737 original size:50 final size:46 Alignment explanation

Indices: 478675--478841 Score: 147 Period size: 50 Copynumber: 3.4 Consensus size: 46 478665 ATCATACAAT * 478675 ATTGTATAATATGATATTGGTTTCAGTAATATAGAATTATATCACATGAA 1 ATTGTATTATATGATATTGGTTT-A-TAATATA-AATT-TATCACATGAA * * * * * 478725 ATTGTATTATATGATATT-GTAATATTATATAATATTGTATCATACGAT 1 ATTGTATTATATGATATTGGT-TTATAATATAA-ATT-TATCACATGAA * * 478773 ATTGTATGATATGATATTGGTTTATATGATATATTATCTTATCACATGAA 1 ATTGTATTATATGATATTGGTTTATA--ATATA-AAT-TTATCACATGAA * 478823 GTTGTATTATATGATATTG 1 ATTGTATTATATGATATTG 478842 TAATATATAT Statistics Matches: 94, Mismatches: 16, Indels: 14 0.76 0.13 0.11 Matches are distributed among these distances: 47 1 0.01 48 37 0.39 49 5 0.05 50 50 0.53 51 1 0.01 ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46 Consensus pattern (46 bp): ATTGTATTATATGATATTGGTTTATAATATAAATTTATCACATGAA Found at i:478752 original size:18 final size:18 Alignment explanation

Indices: 478729--478763 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 478719 CATGAAATTG * 478729 TATTATATGATATTGTAA 1 TATTATATAATATTGTAA 478747 TATTATATAATATTGTA 1 TATTATATAATATTGTA 478764 TCATACGATA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51 Consensus pattern (18 bp): TATTATATAATATTGTAA Found at i:478760 original size:98 final size:97 Alignment explanation

Indices: 478641--478863 Score: 305 Period size: 98 Copynumber: 2.3 Consensus size: 97 478631 CTATGATACA * 478641 ATATTGT-ATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTCAGTA-A 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTT-A-TAGA 478704 TATAGAAT-TATATCACATGAAATTGTATTATATG 64 TATAGAATCT-TATCACATGAAATTGTATTATATG * * 478738 ATATTGTAATATTATATAATATTGTATCATACGATATTGTATGATATGATATTGGTTTATATGAT 1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTATA-GAT ** * 478803 ATATTATCTTATCACATGAAGTTGTATTATATG 65 ATAGAATCTTATCACATGAAATTGTATTATATG * 478836 ATATTGTAATA-TATAT--TATTGTGTCATA 1 ATATTGTAATATTATATAATATTGTATCATA 478864 TGATACAATA Statistics Matches: 115, Mismatches: 7, Indels: 10 0.87 0.05 0.08 Matches are distributed among these distances: 95 11 0.10 96 2 0.02 97 13 0.11 98 88 0.77 99 1 0.01 ACGTcount: A:0.36, C:0.05, G:0.12, T:0.46 Consensus pattern (97 bp): ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGGTTTATAGATA TAGAATCTTATCACATGAAATTGTATTATATG Found at i:478842 original size:15 final size:15 Alignment explanation

Indices: 478720--478868 Score: 90 Period size: 15 Copynumber: 9.4 Consensus size: 15 478710 ATTATATCAC * 478720 ATGAAATTGTATTAT 1 ATGATATTGTATTAT 478735 ATGATATTGTAATATTAT 1 ATGATATTG---TATTAT * * 478753 ATAATATTGTATCAT 1 ATGATATTGTATTAT * * 478768 ACGATATTGTATGAT 1 ATGATATTGTATTAT 478783 ATGATATTGGT-TTAT 1 ATGATATT-GTATTAT 478798 ATGATATAT-TATCTTAT 1 ATGATAT-TGTA--TTAT 478815 CACATGA-AGTTGTATTAT 1 ---ATGATA-TTGTATTAT * 478833 ATGATATTGTAATAT 1 ATGATATTGTATTAT * * 478848 AT-ATTATTGTGTCAT 1 ATGA-TATTGTATTAT 478863 ATGATA 1 ATGATA 478869 CAATATGTAT Statistics Matches: 106, Mismatches: 12, Indels: 32 0.71 0.08 0.21 Matches are distributed among these distances: 14 2 0.02 15 68 0.64 16 5 0.05 17 4 0.04 18 18 0.17 19 2 0.02 20 7 0.07 ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47 Consensus pattern (15 bp): ATGATATTGTATTAT Found at i:478893 original size:15 final size:15 Alignment explanation

Indices: 478873--478902 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 478863 ATGATACAAT 478873 ATGTATAATATAATA 1 ATGTATAATATAATA * 478888 ATGTATTATATAATA 1 ATGTATAATATAATA 478903 TTTTGCTTTA 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:0.50, C:0.00, G:0.07, T:0.43 Consensus pattern (15 bp): ATGTATAATATAATA Found at i:485836 original size:23 final size:24 Alignment explanation

Indices: 485809--485856 Score: 80 Period size: 23 Copynumber: 2.0 Consensus size: 24 485799 CCTTGCTACA * 485809 ATGATACATTTAAAAGTTG-TATG 1 ATGATACATTCAAAAGTTGTTATG 485832 ATGATACATTCAAAAGTTGTTATG 1 ATGATACATTCAAAAGTTGTTATG 485856 A 1 A 485857 CGAAACGTTT Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 23 18 0.78 24 5 0.22 ACGTcount: A:0.40, C:0.06, G:0.17, T:0.38 Consensus pattern (24 bp): ATGATACATTCAAAAGTTGTTATG Found at i:488866 original size:17 final size:18 Alignment explanation

Indices: 488827--488867 Score: 57 Period size: 17 Copynumber: 2.3 Consensus size: 18 488817 TCAGGTTAGC 488827 TCAAATTTTCAGGTCCAT 1 TCAAATTTTCAGGTCCAT * * 488845 ACAAATTTTCA-GTCCTT 1 TCAAATTTTCAGGTCCAT 488862 TCAAAT 1 TCAAAT 488868 GTTTGCGTAA Statistics Matches: 20, Mismatches: 3, Indels: 1 0.83 0.12 0.04 Matches are distributed among these distances: 17 10 0.50 18 10 0.50 ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39 Consensus pattern (18 bp): TCAAATTTTCAGGTCCAT Found at i:489034 original size:16 final size:16 Alignment explanation

Indices: 489013--489043 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 489003 GTTCATGTCA 489013 TTCAGGTCTGTAGTAT 1 TTCAGGTCTGTAGTAT * 489029 TTCAGGTCTTTAGTA 1 TTCAGGTCTGTAGTA 489044 CATGTATGTC Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45 Consensus pattern (16 bp): TTCAGGTCTGTAGTAT Found at i:494337 original size:2 final size:2 Alignment explanation

Indices: 494330--494379 Score: 91 Period size: 2 Copynumber: 25.0 Consensus size: 2 494320 AAAGAAAAAC * 494330 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 494372 GA GA GA GA 1 GA GA GA GA 494380 TTTATTTCTA Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): GA Found at i:498437 original size:21 final size:21 Alignment explanation

Indices: 498430--498502 Score: 146 Period size: 21 Copynumber: 3.5 Consensus size: 21 498420 CAATAGTAAT 498430 ATCATTATATGCAGTGCTAAC 1 ATCATTATATGCAGTGCTAAC 498451 ATCATTATATGCAGTGCTAAC 1 ATCATTATATGCAGTGCTAAC 498472 ATCATTATATGCAGTGCTAAC 1 ATCATTATATGCAGTGCTAAC 498493 ATCATTATAT 1 ATCATTATAT 498503 ACTATTATTT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 52 1.00 ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36 Consensus pattern (21 bp): ATCATTATATGCAGTGCTAAC Found at i:498460 original size:42 final size:42 Alignment explanation

Indices: 498413--498502 Score: 146 Period size: 42 Copynumber: 2.1 Consensus size: 42 498403 GGTAAATTTT * 498413 TTATATGCAATAG-TAATATCATTATATGCAGTGCTAACATCA 1 TTATATGCAAT-GCTAACATCATTATATGCAGTGCTAACATCA * 498455 TTATATGCAGTGCTAACATCATTATATGCAGTGCTAACATCA 1 TTATATGCAATGCTAACATCATTATATGCAGTGCTAACATCA 498497 TTATAT 1 TTATAT 498503 ACTATTATTT Statistics Matches: 45, Mismatches: 2, Indels: 2 0.92 0.04 0.04 Matches are distributed among these distances: 41 1 0.02 42 44 0.98 ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37 Consensus pattern (42 bp): TTATATGCAATGCTAACATCATTATATGCAGTGCTAACATCA Found at i:499651 original size:4 final size:4 Alignment explanation

Indices: 499644--499783 Score: 77 Period size: 4 Copynumber: 34.5 Consensus size: 4 499634 CAGTCAATAA * * * * 499644 TCAG TCAG ACTG TCAG TCAG TCAG TCAG TCAA TCAG TCAAT TACATG T-AG 1 TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TC-AG T-CA-G TCAG * * * * * 499694 -CTAG TCAG TCAG TCAA TCAG TCAG ACTG TCAG TCAA TCAG TCAG TTAG 1 TC-AG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG * ** * * * * * 499742 ACTT TCAG TCAG TTAG ACTG TCAG TCAG ACAG TCCG TCAG TC 1 TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TCAG TC 499784 CTGGGGTTTT Statistics Matches: 96, Mismatches: 34, Indels: 12 0.68 0.24 0.08 Matches are distributed among these distances: 3 1 0.01 4 89 0.93 5 4 0.04 6 2 0.02 ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28 Consensus pattern (4 bp): TCAG Found at i:500644 original size:21 final size:22 Alignment explanation

Indices: 500618--500702 Score: 149 Period size: 21 Copynumber: 4.0 Consensus size: 22 500608 TGCGTCTTTT 500618 TACCCCAATGA-ACCCCAATGA 1 TACCCCAATGATACCCCAATGA 500639 TACCCCAATGA-ACCCCAATGA 1 TACCCCAATGATACCCCAATGA 500660 TACCCCAATGATACCCCAATGA 1 TACCCCAATGATACCCCAATGA 500682 -ACCCCAATGATACCCCAATGA 1 TACCCCAATGATACCCCAATGA 500703 ACTTTGAAAT Statistics Matches: 63, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 21 53 0.84 22 10 0.16 ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15 Consensus pattern (22 bp): TACCCCAATGATACCCCAATGA Found at i:500645 original size:11 final size:11 Alignment explanation

Indices: 500618--500702 Score: 149 Period size: 11 Copynumber: 8.0 Consensus size: 11 500608 TGCGTCTTTT 500618 TACCCCAATGA 1 TACCCCAATGA 500629 -ACCCCAATGA 1 TACCCCAATGA 500639 TACCCCAATGA 1 TACCCCAATGA 500650 -ACCCCAATGA 1 TACCCCAATGA 500660 TACCCCAATGA 1 TACCCCAATGA 500671 TACCCCAATGA 1 TACCCCAATGA 500682 -ACCCCAATGA 1 TACCCCAATGA 500692 TACCCCAATGA 1 TACCCCAATGA 500703 ACTTTGAAAT Statistics Matches: 71, Mismatches: 0, Indels: 6 0.92 0.00 0.08 Matches are distributed among these distances: 10 30 0.42 11 41 0.58 ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15 Consensus pattern (11 bp): TACCCCAATGA Found at i:500670 original size:32 final size:32 Alignment explanation

Indices: 500618--500704 Score: 135 Period size: 32 Copynumber: 2.8 Consensus size: 32 500608 TGCGTCTTTT 500618 TACCCCAATGA-ACCCCAATGATACCCCAATGA 1 TACCCCAATGATACCCCAATGA-ACCCCAATGA 500650 -ACCCCAATGATACCCCAATGATACCCCAATGA 1 TACCCCAATGATACCCCAATGA-ACCCCAATGA 500682 -ACCCCAATGATACCCCAATGAAC 1 TACCCCAATGATACCCCAATGAAC 500705 TTTGAAATAC Statistics Matches: 54, Mismatches: 0, Indels: 3 0.95 0.00 0.05 Matches are distributed among these distances: 31 12 0.22 32 42 0.78 ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15 Consensus pattern (32 bp): TACCCCAATGATACCCCAATGAACCCCAATGA Found at i:501459 original size:11 final size:11 Alignment explanation

Indices: 501436--501593 Score: 161 Period size: 11 Copynumber: 15.0 Consensus size: 11 501426 ATTTCAAAGT * 501436 TCATTAGGGTA 1 TCATTGGGGTA * 501447 TCATTGGGATA 1 TCATTGGGGTA * 501458 TCATT-TGGTA 1 TCATTGGGGTA * 501468 TCATAGGGGTA 1 TCATTGGGGTA * * 501479 TAATTAGGTGT- 1 TCATT-GGGGTA * 501490 T--TTTGGGTA 1 TCATTGGGGTA 501499 TCATTGGGGTA 1 TCATTGGGGTA * 501510 ACATTGGGGT- 1 TCATTGGGGTA 501520 TCATTGGGGTA 1 TCATTGGGGTA 501531 TCATTGGGGT- 1 TCATTGGGGTA 501541 TCATTGGGGTA 1 TCATTGGGGTA 501552 TCATTGGGGT- 1 TCATTGGGGTA * 501562 TCATTGGAGTA 1 TCATTGGGGTA 501573 TCATTGGGGT- 1 TCATTGGGGTA * 501583 TCATTTGGGTA 1 TCATTGGGGTA 501594 AAAAGACGCA Statistics Matches: 121, Mismatches: 17, Indels: 18 0.78 0.11 0.12 Matches are distributed among these distances: 8 3 0.02 9 3 0.02 10 44 0.36 11 67 0.55 12 4 0.03 ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39 Consensus pattern (11 bp): TCATTGGGGTA Found at i:501468 original size:21 final size:20 Alignment explanation

Indices: 501434--501593 Score: 151 Period size: 21 Copynumber: 7.6 Consensus size: 20 501424 ATATTTCAAA 501434 GTTCATTAGGGTATCATTGGG 1 GTTCATT-GGGTATCATTGGG * * * 501455 ATATCATTTGGTATCATAGGG 1 GT-TCATTGGGTATCATTGGG * * * * * 501476 GTATAATTAGGTGT-TTTTGG 1 GT-TCATTGGGTATCATTGGG * 501496 GTATCATTGGGGTAACATTGGG 1 GT-TCATT-GGGTATCATTGGG 501518 GTTCATTGGGGTATCATTGGG 1 GTTCATT-GGGTATCATTGGG 501539 GTTCATTGGGGTATCATTGGG 1 GTTCATT-GGGTATCATTGGG 501560 GTTCATTGGAGTATCATTGGG 1 GTTCATTGG-GTATCATTGGG 501581 GTTCATTTGGGTA 1 GTTCA-TTGGGTA 501594 AAAAGACGCA Statistics Matches: 117, Mismatches: 17, Indels: 10 0.81 0.12 0.07 Matches are distributed among these distances: 20 12 0.10 21 90 0.77 22 15 0.13 ACGTcount: A:0.19, C:0.08, G:0.33, T:0.39 Consensus pattern (20 bp): GTTCATTGGGTATCATTGGG Found at i:502378 original size:7 final size:7 Alignment explanation

Indices: 502366--502405 Score: 62 Period size: 7 Copynumber: 5.7 Consensus size: 7 502356 ATCTGCTACC 502366 AATAAAA 1 AATAAAA 502373 AATAAAA 1 AATAAAA * 502380 ATTAAAA 1 AATAAAA 502387 AATAAAA 1 AATAAAA * 502394 AGTAAAA 1 AATAAAA 502401 AATAA 1 AATAA 502406 CAAACCACCC Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 7 29 1.00 ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17 Consensus pattern (7 bp): AATAAAA Found at i:503995 original size:10 final size:10 Alignment explanation

Indices: 503977--504031 Score: 65 Period size: 10 Copynumber: 5.3 Consensus size: 10 503967 GATTCTGATA 503977 CACGAACGAT 1 CACGAACGAT * 503987 CACGCACGAT 1 CACGAACGAT 503997 ACACGAACGAT 1 -CACGAACGAT * 504008 CACGCACGAT 1 CACGAACGAT * 504018 ACACGGACGAT 1 -CACGAACGAT 504029 CAC 1 CAC 504032 TAACTTACTG Statistics Matches: 39, Mismatches: 4, Indels: 4 0.83 0.09 0.09 Matches are distributed among these distances: 10 21 0.54 11 18 0.46 ACGTcount: A:0.36, C:0.35, G:0.20, T:0.09 Consensus pattern (10 bp): CACGAACGAT Found at i:503997 original size:21 final size:21 Alignment explanation

Indices: 503973--504031 Score: 109 Period size: 21 Copynumber: 2.8 Consensus size: 21 503963 GCACGATTCT 503973 GATACACGAACGATCACGCAC 1 GATACACGAACGATCACGCAC 503994 GATACACGAACGATCACGCAC 1 GATACACGAACGATCACGCAC * 504015 GATACACGGACGATCAC 1 GATACACGAACGATCAC 504032 TAACTTACTG Statistics Matches: 37, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 21 37 1.00 ACGTcount: A:0.37, C:0.32, G:0.20, T:0.10 Consensus pattern (21 bp): GATACACGAACGATCACGCAC Found at i:504006 original size:11 final size:11 Alignment explanation

Indices: 503973--504028 Score: 71 Period size: 11 Copynumber: 5.3 Consensus size: 11 503963 GCACGATTCT 503973 GATACACGAAC 1 GATACACGAAC * 503984 GAT-CACGCAC 1 GATACACGAAC 503994 GATACACGAAC 1 GATACACGAAC * 504005 GAT-CACGCAC 1 GATACACGAAC * 504015 GATACACGGAC 1 GATACACGAAC 504026 GAT 1 GAT 504029 CACTAACTTA Statistics Matches: 39, Mismatches: 4, Indels: 4 0.83 0.09 0.09 Matches are distributed among these distances: 10 18 0.46 11 21 0.54 ACGTcount: A:0.38, C:0.30, G:0.21, T:0.11 Consensus pattern (11 bp): GATACACGAAC Found at i:505068 original size:21 final size:21 Alignment explanation

Indices: 505043--505096 Score: 83 Period size: 21 Copynumber: 2.6 Consensus size: 21 505033 ATTTTCCTGA * 505043 TACACGCACGATC-CCGCACGT 1 TACACGAACGATCACC-CACGT 505064 TACACGAACGATCACCCACGT 1 TACACGAACGATCACCCACGT 505085 TACACGAACGAT 1 TACACGAACGAT 505097 TTAACACGAT Statistics Matches: 31, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 21 29 0.94 22 2 0.06 ACGTcount: A:0.31, C:0.37, G:0.17, T:0.15 Consensus pattern (21 bp): TACACGAACGATCACCCACGT Found at i:508193 original size:32 final size:32 Alignment explanation

Indices: 508147--508378 Score: 337 Period size: 32 Copynumber: 7.3 Consensus size: 32 508137 TGCATGTTAA * 508147 TTTAACAGTTATGCCCCAACCATTTAGGGGAC 1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC * * 508179 TTTAATAGCCATGCCCCAACCATTTAGGGGAC 1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC * 508211 TTAAACAGTCATGCCCCAACCATTTA-GGGACC 1 TTTAACAGTCATGCCCCAACCATTTAGGGGA-C 508243 TTTAACAGTCATGCCCCAACCATTTAGGGGAC 1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC * * * 508275 TTTAACAATAATGCCCCAACCATTAAGGGGAC 1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC * * 508307 TTTAACAATCATGCCTCAACCATTTAGGGGAC 1 TTTAACAGTCATGCCCCAACCATTTAGGGGAC 508339 TTTAAGC-GTCATGCCCCAACCATTTAGGGGAC 1 TTTAA-CAGTCATGCCCCAACCATTTAGGGGAC 508371 --TAACAGTC 1 TTTAACAGTC 508379 TTGGTTAAAC Statistics Matches: 181, Mismatches: 15, Indels: 10 0.88 0.07 0.05 Matches are distributed among these distances: 29 1 0.01 30 6 0.03 31 4 0.02 32 165 0.91 33 5 0.03 ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25 Consensus pattern (32 bp): TTTAACAGTCATGCCCCAACCATTTAGGGGAC Found at i:526299 original size:1 final size:1 Alignment explanation

Indices: 526293--526317 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 526283 TGTTTCCGGA 526293 GGGGGGGGGGGGGGGGGGGGGGGGG 1 GGGGGGGGGGGGGGGGGGGGGGGGG 526318 AAAGACCCGG 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:0.00, C:0.00, G:1.00, T:0.00 Consensus pattern (1 bp): G Found at i:527970 original size:42 final size:42 Alignment explanation

Indices: 527907--527992 Score: 118 Period size: 42 Copynumber: 2.0 Consensus size: 42 527897 TCTAATGTAG * * * * * 527907 TGGAACCAAGATTTTTTTTTCTTGATGTTGTTCTGTTTAGTC 1 TGGAACCAAGAGTTATCTTTCTTGATATTGTTCTGTATAGTC * 527949 TGGAACCAAGAGTTATCTTTCTTGATATTGTTTTGTATAGTC 1 TGGAACCAAGAGTTATCTTTCTTGATATTGTTCTGTATAGTC 527991 TG 1 TG 527993 AGAGTTATTC Statistics Matches: 38, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 42 38 1.00 ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49 Consensus pattern (42 bp): TGGAACCAAGAGTTATCTTTCTTGATATTGTTCTGTATAGTC Found at i:572903 original size:2 final size:2 Alignment explanation

Indices: 572896--572920 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 572886 NNNNNNNNNN 572896 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 572921 AACAAAACAA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:576423 original size:11 final size:11 Alignment explanation

Indices: 576415--576445 Score: 53 Period size: 11 Copynumber: 2.8 Consensus size: 11 576405 ACTGGAGTGG 576415 ACCCAGAGTAA 1 ACCCAGAGTAA * 576426 ACCCAAAGTAA 1 ACCCAGAGTAA 576437 ACCCAGAGT 1 ACCCAGAGT 576446 GGACACAGAG Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.45, C:0.29, G:0.16, T:0.10 Consensus pattern (11 bp): ACCCAGAGTAA Found at i:579100 original size:20 final size:21 Alignment explanation

Indices: 579060--579101 Score: 68 Period size: 22 Copynumber: 2.0 Consensus size: 21 579050 AAGCGACGAA 579060 AATCGACTCCCCCATGCGTTAG 1 AATCGACTCCCCCA-GCGTTAG 579082 AATCGACTCCCCC-GCGTTAG 1 AATCGACTCCCCCAGCGTTAG 579102 GGGTTGTTTA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 20 7 0.35 22 13 0.65 ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21 Consensus pattern (21 bp): AATCGACTCCCCCAGCGTTAG Found at i:583271 original size:18 final size:17 Alignment explanation

Indices: 583224--583271 Score: 78 Period size: 17 Copynumber: 2.8 Consensus size: 17 583214 TCTCTCGACA * 583224 GTTTTTTTTTTGCTTTT 1 GTTTTTTTTTTGTTTTT 583241 GTTTTTTTTTTGTTTTT 1 GTTTTTTTTTTGTTTTT 583258 GTTTTTTGTTTTGT 1 GTTTTTT-TTTTGT 583272 CAATTGCATT Statistics Matches: 29, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 17 23 0.79 18 6 0.21 ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83 Consensus pattern (17 bp): GTTTTTTTTTTGTTTTT Found at i:586480 original size:4 final size:4 Alignment explanation

Indices: 586471--586517 Score: 94 Period size: 4 Copynumber: 11.8 Consensus size: 4 586461 TTACATAACT 586471 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA 1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA 586518 TATATATANT Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 43 1.00 ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26 Consensus pattern (4 bp): ATAG Found at i:589209 original size:15 final size:15 Alignment explanation

Indices: 589189--589220 Score: 64 Period size: 15 Copynumber: 2.1 Consensus size: 15 589179 GCCAAAGCTA 589189 TATGAGGCGCCGTTT 1 TATGAGGCGCCGTTT 589204 TATGAGGCGCCGTTT 1 TATGAGGCGCCGTTT 589219 TA 1 TA 589221 ATATTTTTAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34 Consensus pattern (15 bp): TATGAGGCGCCGTTT Found at i:589305 original size:20 final size:20 Alignment explanation

Indices: 589277--589464 Score: 155 Period size: 20 Copynumber: 9.0 Consensus size: 20 589267 CAATAATTCG * * 589277 AATTATTGATACCAGAAAAT 1 AATTCTTGATATCAGAAAAT * 589297 AATTCTTGATATCAAAAAAT 1 AATTCTTGATATCAGAAAAT 589317 AATTCTTGATATCCA-AAAATCT 1 AATTCTTGATAT-CAGAAAA--T * * 589339 ATTTTTTGTGATATCAGAAAAT 1 A-ATTCT-TGATATCAGAAAAT * * 589361 AATTCTTGATTTCAAAAAAAT 1 AATTCTTGATATC-AGAAAAT 589382 AATTCTTGATATCA-AAAAT 1 AATTCTTGATATCAGAAAAT * * 589401 CTATTTTGTGATATCAGAAAAT 1 -AATTCT-TGATATCAGAAAAT * * * 589423 AATTTTTGATATCACAAATT 1 AATTCTTGATATCAGAAAAT * 589443 CGAATTCTTGATATCAAAAAAT 1 --AATTCTTGATATCAGAAAAT 589465 GTGATTTTCT Statistics Matches: 138, Mismatches: 18, Indels: 22 0.78 0.10 0.12 Matches are distributed among these distances: 19 5 0.04 20 56 0.41 21 36 0.26 22 26 0.19 23 5 0.04 24 10 0.07 ACGTcount: A:0.44, C:0.11, G:0.08, T:0.38 Consensus pattern (20 bp): AATTCTTGATATCAGAAAAT Found at i:589358 original size:64 final size:62 Alignment explanation

Indices: 589240--589487 Score: 270 Period size: 62 Copynumber: 3.9 Consensus size: 62 589230 AAGTATTTTC * * * * 589240 TGATATCAAAAAATAAATAT-TTGATAT-CAATAATTCGAATTAT-TGATACCAGAAAATAATTC 1 TGATATCAAAAAAT-AAT-TCTTGATATCCAA-AAATC-TATTTTGTGATATCAGAAAATAATTC 589302 T 62 T 589303 TGATATCAAAAAATAATTCTTGATATCCAAAAATCTATTTTTTGTGATATCAGAAAATAATTCT 1 TGATATCAAAAAATAATTCTTGATATCCAAAAATCTA--TTTTGTGATATCAGAAAATAATTCT * * 589367 TGATTTCAAAAAAATAATTCTTGATAT-CAAAAATCTATTTTGTGATATCAGAAAATAATTTT 1 TGATATC-AAAAAATAATTCTTGATATCCAAAAATCTATTTTGTGATATCAGAAAATAATTCT * * * * * * 589429 TGATATCACAAATTCGAATTCTTGATATCAAAAAATGTGATTTTCTGATATCACAAAAT 1 TGATATCAAAAAAT--AATTCTTGATATCCAAAAATCT-ATTTTGTGATATCAGAAAAT 589488 GGATTTTTTG Statistics Matches: 162, Mismatches: 13, Indels: 18 0.84 0.07 0.09 Matches are distributed among these distances: 61 7 0.04 62 44 0.27 63 32 0.20 64 42 0.26 65 37 0.23 ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38 Consensus pattern (62 bp): TGATATCAAAAAATAATTCTTGATATCCAAAAATCTATTTTGTGATATCAGAAAATAATTCT Found at i:589448 original size:22 final size:21 Alignment explanation

Indices: 589234--589503 Score: 83 Period size: 20 Copynumber: 12.6 Consensus size: 21 589224 TTTTTAAAGT * * * 589234 ATTTTCTGATATCAAAAAATAA 1 ATTTT-TGATATCACAAATTGA * 589256 ATATTTGATATCA-ATAATTCGA 1 ATTTTTGATATCACA-AATT-GA * * * * 589278 ATTATTGATACCAGAAAAT-A 1 ATTTTTGATATCACAAATTGA * * * 589298 ATTCTTGATATCAAAAAAT-A 1 ATTTTTGATATCACAAATTGA * * 589318 ATTCTTGATATCCAAAAATCT-A 1 ATTTTTGATAT-CACAAAT-TGA * * * 589340 TTTTTTGTGATATCAGAAAAT-A 1 -ATTTT-TGATATCACAAATTGA * * * * 589362 ATTCTTGATTTCAAAAAAAT-A 1 ATTTTTGATATC-ACAAATTGA * * 589383 ATTCTTGATATCAAAAATCT-- 1 ATTTTTGATATCACAAAT-TGA * * 589403 ATTTTGTGATATCAGAAAAT-A 1 ATTTT-TGATATCACAAATTGA 589424 ATTTTTGATATCACAAATTCGA 1 ATTTTTGATATCACAAATT-GA * * 589446 ATTCTTGATATCAAAAAATGTG- 1 ATTTTTGATATC-ACAAAT-TGA * 589468 ATTTTCTGATATCACAAAATGGA 1 ATTTT-TGATATCAC-AAATTGA * 589491 TTTTTTGATATCA 1 ATTTTTGATATCA 589504 AGAATTAAAG Statistics Matches: 198, Mismatches: 32, Indels: 36 0.74 0.12 0.14 Matches are distributed among these distances: 20 58 0.29 21 55 0.28 22 48 0.24 23 30 0.15 24 7 0.04 ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39 Consensus pattern (21 bp): ATTTTTGATATCACAAATTGA Found at i:589477 original size:23 final size:22 Alignment explanation

Indices: 589388--589504 Score: 89 Period size: 22 Copynumber: 5.4 Consensus size: 22 589378 AAATAATTCT ** * 589388 TGATATC-AAAAATCTATTTTG 1 TGATATCAAAAAATGGATTTTC * * 589409 TGATATCAGAAAAT-AATTTT- 1 TGATATCAAAAAATGGATTTTC * * * * 589429 TGATATCACAAATTCGA-ATTC 1 TGATATCAAAAAATGGATTTTC 589450 TTGATATCAAAAAATGTGATTTTC 1 -TGATATCAAAAAATG-GATTTTC * * 589474 TGATATCACAAAATGGATTTTT 1 TGATATCAAAAAATGGATTTTC 589496 TGATATCAA 1 TGATATCAA 589505 GAATTAAAGT Statistics Matches: 77, Mismatches: 13, Indels: 11 0.76 0.13 0.11 Matches are distributed among these distances: 20 14 0.18 21 13 0.17 22 31 0.40 23 16 0.21 24 3 0.04 ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39 Consensus pattern (22 bp): TGATATCAAAAAATGGATTTTC Found at i:589499 original size:45 final size:42 Alignment explanation

Indices: 589234--589504 Score: 176 Period size: 42 Copynumber: 6.4 Consensus size: 42 589224 TTTTTAAAGT * * * 589234 ATTTTCTGATATCAAAAAATAAATATTTGATATCA-ATAATTCG 1 ATTTTTTGATATCAAAAAAT-AATTTTTGATATCACA-AAATCG * * * * * * 589277 AATTATTGATACCAGAAAATAATTCTTGATATCAAAAAAT-- 1 ATTTTTTGATATCAAAAAATAATTTTTGATATCACAAAATCG * * * * * 589317 AATTCTTGATATCCAAAAATCTATTTTTTGTGATATCAGAAAAT-- 1 ATTTTTTGATAT-CAAAAA-ATA-ATTTT-TGATATCACAAAATCG * * * * * 589361 AATTCTTGATTTCAAAAAAATAATTCTTGATATCA-AAAATCT 1 ATTTTTTGATATC-AAAAAATAATTTTTGATATCACAAAATCG * * * 589403 ATTTTGTGATATCAGAAAATAATTTTTGATATCACAAATTCG 1 ATTTTTTGATATCAAAAAATAATTTTTGATATCACAAAATCG * * * * 589445 AATTCTTGATATCAAAAAATGTGATTTTCTGATATCACAAAATGG 1 ATTTTTTGATATCAAAAAA--TAATTTT-TGATATCACAAAATCG 589490 ATTTTTTGATATCAA 1 ATTTTTTGATATCAA 589505 GAATTAAAGT Statistics Matches: 180, Mismatches: 36, Indels: 22 0.76 0.15 0.09 Matches are distributed among these distances: 40 15 0.08 41 32 0.18 42 49 0.27 43 22 0.12 44 35 0.19 45 27 0.15 ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39 Consensus pattern (42 bp): ATTTTTTGATATCAAAAAATAATTTTTGATATCACAAAATCG Found at i:589580 original size:21 final size:22 Alignment explanation

Indices: 589527--589580 Score: 56 Period size: 22 Copynumber: 2.5 Consensus size: 22 589517 GGGTTTTTTA * * 589527 ATATCAAAAAATGATTTTCTTG 1 ATATCAAAAAATCATTCTCTTG ** * 589549 ATATCCGAAAATCCTTCT-TTG 1 ATATCAAAAAATCATTCTCTTG 589570 ATATCAAAAAA 1 ATATCAAAAAA 589581 ATCGTCAGAA Statistics Matches: 25, Mismatches: 7, Indels: 1 0.76 0.21 0.03 Matches are distributed among these distances: 21 12 0.48 22 13 0.52 ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35 Consensus pattern (22 bp): ATATCAAAAAATCATTCTCTTG Found at i:589657 original size:22 final size:22 Alignment explanation

Indices: 589622--589665 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 589612 AATCATTTGT * 589622 ATTTTCTGAAATCAGAAGATAA 1 ATTTTCTGAAATCAGAAAATAA * * 589644 ATTTTTTGATATCAGAAAATAA 1 ATTTTCTGAAATCAGAAAATAA 589666 GACCTACAGT Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36 Consensus pattern (22 bp): ATTTTCTGAAATCAGAAAATAA Found at i:599503 original size:32 final size:32 Alignment explanation

Indices: 599465--599539 Score: 132 Period size: 32 Copynumber: 2.3 Consensus size: 32 599455 GCCATCTTTT 599465 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC 1 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC * 599497 CCCCCGGAAAAATGGCTATATAGCAGTTTTTC 1 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC 599529 CCCCACGGAAA 1 CCCC-CGGAAA 599540 GCTGACTATA Statistics Matches: 41, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 32 35 0.85 33 6 0.15 ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23 Consensus pattern (32 bp): CCCCCGGAAAAATGGCTATATAGCAGTTCTTC Found at i:599549 original size:33 final size:32 Alignment explanation

Indices: 599465--599552 Score: 122 Period size: 32 Copynumber: 2.7 Consensus size: 32 599455 GCCATCTTTT * 599465 CCCCCGGAAAAATGGCTATATAGCAGTTCTTC 1 CCCCCGGAAAAATGACTATATAGCAGTTCTTC * * 599497 CCCCCGGAAAAATGGCTATATAGCAGTTTTTC 1 CCCCCGGAAAAATGACTATATAGCAGTTCTTC ** 599529 CCCCACGGAAAGCTGACTATATAG 1 CCCC-CGGAAAAATGACTATATAG 599553 TGGGCTTTCC Statistics Matches: 51, Mismatches: 4, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 32 35 0.69 33 16 0.31 ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24 Consensus pattern (32 bp): CCCCCGGAAAAATGACTATATAGCAGTTCTTC Found at i:600406 original size:4 final size:4 Alignment explanation

Indices: 600397--600442 Score: 83 Period size: 4 Copynumber: 11.5 Consensus size: 4 600387 AAACGTGACA * 600397 GACG GACG GACG GACG GACG GACA GACG GACG GACG GACG GACG GA 1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GA 600443 ACAGGGTAAC Statistics Matches: 40, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 4 40 1.00 ACGTcount: A:0.28, C:0.24, G:0.48, T:0.00 Consensus pattern (4 bp): GACG Found at i:617396 original size:56 final size:56 Alignment explanation

Indices: 617285--617397 Score: 127 Period size: 56 Copynumber: 2.0 Consensus size: 56 617275 CTGATATATT * * ** * * * 617285 CTCCCTCCTCTTGATTTCACTGAGCAAATATAATGGCGGTGTAATGTTCACATAAA 1 CTCCCTCCTCTTGATTTCACTCAGCAAATACAATAACGATGAAATATTCACATAAA * * * * 617341 CTCCCTCCTCTTGATTTCACTCAGCAGATGCAATAATGATGAAATATTCATATAAA 1 CTCCCTCCTCTTGATTTCACTCAGCAAATACAATAACGATGAAATATTCACATAAA 617397 C 1 C 617398 ATATAATCTA Statistics Matches: 46, Mismatches: 11, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 56 46 1.00 ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32 Consensus pattern (56 bp): CTCCCTCCTCTTGATTTCACTCAGCAAATACAATAACGATGAAATATTCACATAAA Found at i:618605 original size:36 final size:38 Alignment explanation

Indices: 618558--618652 Score: 140 Period size: 36 Copynumber: 2.5 Consensus size: 38 618548 CCAGGTAATC 618558 AGTGTGTTCGAATTGTATGAGAATTCACA-TT-TAGAT 1 AGTGTGTTCGAATTGTATGAGAATTCACATTTATAGAT * * 618594 AGTGTGTTCGAATTGTATAAGAATTTACATTTACTAGAT 1 AGTGTGTTCGAATTGTATGAGAATTCACATTTA-TAGAT * 618633 AGTGTGTTCGAACTGTATGA 1 AGTGTGTTCGAATTGTATGA 618653 AAAGTGGAAC Statistics Matches: 52, Mismatches: 4, Indels: 3 0.88 0.07 0.05 Matches are distributed among these distances: 36 27 0.52 37 2 0.04 39 23 0.44 ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39 Consensus pattern (38 bp): AGTGTGTTCGAATTGTATGAGAATTCACATTTATAGAT Found at i:627985 original size:91 final size:91 Alignment explanation

Indices: 627825--627993 Score: 241 Period size: 91 Copynumber: 1.9 Consensus size: 91 627815 ATATCGAACA * * * * * 627825 TGACCTAGATATTATCATAATGAATCTGTATACCAAATTTCATTTCAATATCCTCAACTCCTGCA 1 TGACCTAGATATTATCATAATAAATCTGAACACAAAATTTCATTTCAATATACTCAACTCCTGCA 627890 AAGAAAATGAACGAAAACTGCACACT 66 AAGAAAATGAACGAAAACTGCACACT * * * 627916 TGACCTAGATATTATCATGATAAATCTGAACACAAAATTTCATTTCAATATATTCATC-CTCTGC 1 TGACCTAGATATTATCATAATAAATCTGAACACAAAATTTCATTTCAATATACTCAACTC-CTGC * 627980 GAAGAAAATGAACG 65 AAAGAAAATGAACG 627994 GAAGCTGTTG Statistics Matches: 68, Mismatches: 9, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 90 1 0.01 91 67 0.99 ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30 Consensus pattern (91 bp): TGACCTAGATATTATCATAATAAATCTGAACACAAAATTTCATTTCAATATACTCAACTCCTGCA AAGAAAATGAACGAAAACTGCACACT Found at i:629613 original size:159 final size:159 Alignment explanation

Indices: 629324--629642 Score: 478 Period size: 159 Copynumber: 2.0 Consensus size: 159 629314 ATATTTTTTG * 629324 TCTGCTTTAATCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA 1 TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA * * * 629389 AATAACAGGAAGGATTTCACTTCACGATGTTATATTTCTTGATTAATTTATAACATTTTGTATCG 66 AATAACAGGAAGGAGTTCACTTCACGATGTTATATTTCTTGATTAATTTATAACATATTATATCG * * * 629454 TTAAGTCTAAAAAAACTACAGTATACCGA 131 TTAAGCCTAAAAAAACTACAATACACCGA * * 629483 TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAATTGCTTGAAAGCCGTTTTATGCTAAA 1 TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA * * * * * * 629548 AATAGCGGGAGGGAGTTCACTTTATGATGTTATATTTCTTGATTAATTT-TCAGCATATTATATC 66 AATAACAGGAAGGAGTTCACTTCACGATGTTATATTTCTTGATTAATTTAT-AACATATTATATC * 629612 GTTAAGCCTCAAAAAACTACAATACACCGA 130 GTTAAGCCTAAAAAAACTACAATACACCGA 629642 T 1 T 629643 AACAAATATT Statistics Matches: 143, Mismatches: 16, Indels: 2 0.89 0.10 0.01 Matches are distributed among these distances: 158 1 0.01 159 142 0.99 ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34 Consensus pattern (159 bp): TCTGCTTTAACCTGCACTGAATGTTGTCTAAAAGAAAAACTGCCTGAAAGCCGTTTTATGCTAAA AATAACAGGAAGGAGTTCACTTCACGATGTTATATTTCTTGATTAATTTATAACATATTATATCG TTAAGCCTAAAAAAACTACAATACACCGA Found at i:639471 original size:18 final size:18 Alignment explanation

Indices: 639448--639483 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 639438 CATTTTTTCA * 639448 TACAGTTATAGACCACAG 1 TACAGTTAAAGACCACAG 639466 TACAGTTAAAGACCACAG 1 TACAGTTAAAGACCACAG 639484 CCCGCATCGA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19 Consensus pattern (18 bp): TACAGTTAAAGACCACAG Found at i:652201 original size:2 final size:2 Alignment explanation

Indices: 652196--652245 Score: 82 Period size: 2 Copynumber: 25.0 Consensus size: 2 652186 ATTCTTCTTG * * 652196 AT AT AT AA AT AT AT AT AT AT AT AT NT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 652238 AT AT AT AT 1 AT AT AT AT 652246 CAATATAAAT Statistics Matches: 44, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:652251 original size:12 final size:11 Alignment explanation

Indices: 652196--652257 Score: 67 Period size: 10 Copynumber: 5.7 Consensus size: 11 652186 ATTCTTCTTG 652196 ATATATA-AAT 1 ATATATATAAT 652206 ATATATAT-AT 1 ATATATATAAT * 652216 ATATNTAT-AT 1 ATATATATAAT 652226 ATATATATATAT 1 ATATATATA-AT 652238 ATATATATCAAT 1 ATATATAT-AAT * 652250 ATAAATAT 1 ATATATAT 652258 TTACAAAGAT Statistics Matches: 45, Mismatches: 3, Indels: 6 0.83 0.06 0.11 Matches are distributed among these distances: 10 25 0.56 12 19 0.42 13 1 0.02 ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45 Consensus pattern (11 bp): ATATATATAAT Found at i:661502 original size:12 final size:12 Alignment explanation

Indices: 661485--661511 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 661475 ATAACATGAG 661485 TTTAATACAAAC 1 TTTAATACAAAC 661497 TTTAATACAAAC 1 TTTAATACAAAC 661509 TTT 1 TTT 661512 TTTGTCTCAA 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:0.44, C:0.15, G:0.00, T:0.41 Consensus pattern (12 bp): TTTAATACAAAC Found at i:665604 original size:2 final size:2 Alignment explanation

Indices: 665597--665621 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 665587 ACACCTCACG 665597 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 665622 NNNNNNNNNN Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:666386 original size:2 final size:2 Alignment explanation

Indices: 666379--666421 Score: 65 Period size: 2 Copynumber: 23.0 Consensus size: 2 666369 NNNNNNNNNN 666379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT -T 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 666418 AT AT 1 AT AT 666422 CACATAGAAC Statistics Matches: 38, Mismatches: 0, Indels: 6 0.86 0.00 0.14 Matches are distributed among these distances: 1 3 0.08 2 35 0.92 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (2 bp): AT Found at i:668219 original size:202 final size:202 Alignment explanation

Indices: 667860--668266 Score: 769 Period size: 202 Copynumber: 2.0 Consensus size: 202 667850 GCAGAAAATA 667860 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC 1 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC * 667925 TGTGCGTCATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC 66 TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC * * 667990 CGTGCCATATGCACGCATAAGTTCAAAGGCATTTTAATTGTAAAGTTGTCAGTAAACAGTACAAA 131 CGTGCCATATGCACACATAAGTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAAA 668055 AACAAAG 196 AACAAAG 668062 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC 1 TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC 668127 TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC 66 TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC * * 668192 CGTGCCATATGCACACATAATTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAGA 131 CGTGCCATATGCACACATAAGTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAAA 668257 AACAAAG 196 AACAAAG 668264 TAT 1 TAT 668267 TCCTTTTTAA Statistics Matches: 200, Mismatches: 5, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 202 200 1.00 ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25 Consensus pattern (202 bp): TATAAGCGAGGTTAAACCGGATGCTATGGGGAAAATTCAGCCTGCGCATGAGCTAGCCTGGTTCC TGTGCGTAATGGGTAGCTCAGGGAACCAGGCTAGCACACGTTTATCTGAATCGGTATCGGGATTC CGTGCCATATGCACACATAAGTTCAAAGGCATTGTAATTGTAAAGTTGTCAGTAAACAGTACAAA AACAAAG Found at i:672103 original size:168 final size:168 Alignment explanation

Indices: 671623--672445 Score: 1352 Period size: 168 Copynumber: 4.9 Consensus size: 168 671613 CATGTGTTGG * * * 671623 AGTAGAGAAGAAGATTTTTTAAGATTTAA-ATCATTTTTACTATATGGCCATATTGGCCCCACCC 1 AGTAGAGAAGAAGATTTTCTAAGATTTAATA-CATTTTTACTATTTGGCCATATTGGCCCCTCCC * * * * * * 671687 CAGAGCATGAA-CACCTTACCCAGGGGTCATGAATTTCACAATTTTA-GTAGAGAGCCTCATGGA 65 TAGAGCCTGAATC-CCTGACCCAGGGGTCATGAATTTCACAA-TTTAGGAAGAGGGCTTCATGGA * 671750 CATCATAATCATGCATTTAGTTTTTAACAAATATATATGGG 128 CATCATAATCATGCATTTAGTTTTTAACAAATATATATGGT * 671791 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCC-TGA-CGGCCCCATCC 1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCAT-ATTGGCCCC-TCC * * 671854 C-AGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGATGAGGGCTTCATGGAC 64 CTAGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGAC * * * 671918 ATCATTATCATGCATTTAGGTTTTAACAAATATATATGAT 129 ATCATAATCATGCATTTAGTTTTTAACAAATATATATGGT 671958 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT 1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT 672023 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT 66 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT 672088 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT 131 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT 672126 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT 1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT 672191 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT 66 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT 672256 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT 131 CATAATCATGCATTTAGTTTTTAACAAATATATATGGT * 672294 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCACCCT 1 AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT * * * 672359 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACAT 66 AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT * * * 672424 TATAACCATGCATTCAGTTTTT 131 CATAATCATGCATTTAGTTTTT 672446 TCCTCACATG Statistics Matches: 620, Mismatches: 27, Indels: 16 0.94 0.04 0.02 Matches are distributed among these distances: 166 4 0.01 167 147 0.24 168 468 0.75 169 1 0.00 ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32 Consensus pattern (168 bp): AGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCTCCCT AGAGCCTGAATCCCTGACCCAGGGGTCATGAATTTCACAATTTAGGAAGAGGGCTTCATGGACAT CATAATCATGCATTTAGTTTTTAACAAATATATATGGT Found at i:672660 original size:7 final size:7 Alignment explanation

Indices: 672650--672695 Score: 74 Period size: 7 Copynumber: 6.4 Consensus size: 7 672640 AAAATTGTTA 672650 ACGCACG 1 ACGCACG 672657 ACGCACAG 1 ACGCAC-G 672665 ACGCACG 1 ACGCACG 672672 ACGCACG 1 ACGCACG * 672679 ACGCACA 1 ACGCACG 672686 ACGCACG 1 ACGCACG 672693 ACG 1 ACG 672696 ACGGACGAAG Statistics Matches: 36, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 7 29 0.81 8 7 0.19 ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00 Consensus pattern (7 bp): ACGCACG Found at i:672702 original size:21 final size:22 Alignment explanation

Indices: 672650--672695 Score: 85 Period size: 22 Copynumber: 2.1 Consensus size: 22 672640 AAAATTGTTA 672650 ACGCACGACGCACAGACGCACG 1 ACGCACGACGCACAGACGCACG 672672 ACGCACGACGCACA-ACGCACG 1 ACGCACGACGCACAGACGCACG 672693 ACG 1 ACG 672696 ACGGACGAAG Statistics Matches: 24, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 21 10 0.42 22 14 0.58 ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00 Consensus pattern (22 bp): ACGCACGACGCACAGACGCACG Found at i:682857 original size:172 final size:172 Alignment explanation

Indices: 682560--683356 Score: 1452 Period size: 172 Copynumber: 4.6 Consensus size: 172 682550 GTATCGAGTC * * 682560 TATCGACCAAGGCTGATTTTCGAACTTGACCAACGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT * * 682625 TAATGAATATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGAT-AAACT 66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAC- * * * 682689 GGGGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG 130 GGAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG * 682732 TATTGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 682797 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG 66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG 682862 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG 682904 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT * 682969 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGAATAAAACG 66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG * 683034 GAGTCGTTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG 683076 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 683141 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG 66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG 683206 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG * * 683248 TATCGACCAATGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT * * 683313 TAATGAAAATCCGTCAAAATTTGTAGGCATGAAAGCGCTTACAA 66 TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAA 683357 AAAAGTGTGA Statistics Matches: 607, Mismatches: 17, Indels: 2 0.97 0.03 0.00 Matches are distributed among these distances: 172 603 0.99 173 4 0.01 ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30 Consensus pattern (172 bp): TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT TAATGAAAATCCGTCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG GAGTCATTATTGTGGTCAAAGTTCGATAACTCCAACAAAAAG Found at i:683381 original size:8 final size:8 Alignment explanation

Indices: 683370--683463 Score: 116 Period size: 8 Copynumber: 11.8 Consensus size: 8 683360 AGTGTGACGG * 683370 ACGGACGC 1 ACGGACCC * 683378 ACGGACAC 1 ACGGACCC * * 683386 ATGGACGC 1 ACGGACCC 683394 ACGGACCC 1 ACGGACCC * 683402 ACAGACCC 1 ACGGACCC * 683410 ACGGACAC 1 ACGGACCC 683418 ACGGACCC 1 ACGGACCC 683426 ACGGACCC 1 ACGGACCC * 683434 ACGGACAC 1 ACGGACCC 683442 ACGGACCC 1 ACGGACCC * 683450 ACGGACAC 1 ACGGACCC 683458 ACGGAC 1 ACGGAC 683464 GGACGCCCGG Statistics Matches: 74, Mismatches: 12, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 8 74 1.00 ACGTcount: A:0.31, C:0.41, G:0.27, T:0.01 Consensus pattern (8 bp): ACGGACCC Found at i:683397 original size:24 final size:24 Alignment explanation

Indices: 683365--683464 Score: 128 Period size: 24 Copynumber: 4.2 Consensus size: 24 683355 AAAAAAGTGT * * * 683365 GACGGACGGACGCACGGACACATG 1 GACGCACGGACCCACGGACACACG * * 683389 GACGCACGGACCCACAGACCCACG 1 GACGCACGGACCCACGGACACACG * * 683413 GACACACGGACCCACGGACCCACG 1 GACGCACGGACCCACGGACACACG * 683437 GACACACGGACCCACGGACACACG 1 GACGCACGGACCCACGGACACACG 683461 GACG 1 GACG 683465 GACGCCCGGC Statistics Matches: 67, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 24 67 1.00 ACGTcount: A:0.30, C:0.40, G:0.29, T:0.01 Consensus pattern (24 bp): GACGCACGGACCCACGGACACACG Found at i:684455 original size:2 final size:2 Alignment explanation

Indices: 684450--684475 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 684440 TCAGTGTGTT 684450 TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA 684476 NNNNNNNNNN Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:685827 original size:16 final size:16 Alignment explanation

Indices: 685806--685840 Score: 70 Period size: 16 Copynumber: 2.2 Consensus size: 16 685796 AAAATACCCG 685806 GTAATTTGTGAAACTA 1 GTAATTTGTGAAACTA 685822 GTAATTTGTGAAACTA 1 GTAATTTGTGAAACTA 685838 GTA 1 GTA 685841 TTTTTAGCAA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37 Consensus pattern (16 bp): GTAATTTGTGAAACTA Found at i:686484 original size:16 final size:17 Alignment explanation

Indices: 686463--686495 Score: 59 Period size: 16 Copynumber: 2.0 Consensus size: 17 686453 AGATAAGATT 686463 TTCCGTTTTCC-TTCCG 1 TTCCGTTTTCCGTTCCG 686479 TTCCGTTTTCCGTTCCG 1 TTCCGTTTTCCGTTCCG 686496 CGTTTTAGCA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 11 0.69 17 5 0.31 ACGTcount: A:0.00, C:0.36, G:0.15, T:0.48 Consensus pattern (17 bp): TTCCGTTTTCCGTTCCG Found at i:687289 original size:166 final size:166 Alignment explanation

Indices: 686748--687864 Score: 1460 Period size: 166 Copynumber: 6.7 Consensus size: 166 686738 TATCTCAACC * * * 686748 ACTATTTTTCGCAGATGCTTGAAATTTTTACACAGT-GTTGTGA-AGGCATGCCATATTGTGGGA 1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGT-ATAGGCATGCCATATCGTGGGA * * * 686811 TATATTTTTGTACCAATCGGACGTCAACTTCCTGTAAAATGACGACTTTGCTTATTTTTTAACCA 65 TATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTTTAGCCA * * 686876 AAATTTTCAAACAAATTTTCGTCAAA-AATTTATTAGCA 129 AAATTTTCAAACAAATTTTCGTCAAAGAA-TTCTCAGCA * * 686914 ACTATTTATCGCAGATGCTTGAAATTTCTACACAATATTTGTATAGGCATGCCATATCGTGGGAT 1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT * * * * * * * 686979 AAAATTTTGTACCAATCAGACGTCAACTTCCTGTAAAATGACGACTTTGCTTATTTTTTAACCCA 66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTTTTAGCCAA * 687044 AATTTTCAAACAAATTTTTGTCAAAGAATTCTCAGCA 130 AATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA * * 687081 ACTGTTTATCGCAGATGCTTGAAATTTTTACACAGAATTTGTATAGGCATGCCATATCGTGGGAT 1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT * * * 687146 ATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTTTGTTTATTTTTAGCAAAA 66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAA * 687211 ATTTTCAAACAAATTTTTGTCAAAGAATTCTCAGCA 131 ATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA * * * 687247 ACTGTTTATCGCAGATGTTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATATCGTGGGAT 1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT * ** * * ** 687312 GTATTTTTGTACCAATCAAACGTCAACTTCCTGTTTAATGA-GTACTTTGTTAATTTTTTTCCAA 66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCCAA * * * * 687376 AATTTTCAAACAAATTTTTGTTAAAGATTTCTCAGTA 130 AATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA * * * * * * * * 687413 ACTATTCATCGCATAAGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGAT 1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT * * * 687478 TTATTTTTGTATCAATCGGACGTCAACTCCCTGTTAAAT-ACTGACTTTGTTTA-TTTTAGCCAA 66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAC-GACTTTGTTTATTTTTAGCCAA * * 687541 AATTTTCAAACAAATTTTCCTCAAAGATTTCTCAGCA 130 AATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA * * * 687578 GCTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGT-TAAGGCATGCCATATTGTGGGA 1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTAT-AGGCATGCCATATCGTGGGA * * 687642 TATATTTTTGTACCCATCGGACGTCAACTTCCTGTTCAATGA-GTACTTTGTTTA-TTTTAGCCA 65 TATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGTTTATTTTTAGCCA * * 687705 AAATTTTCAAACAAATTTTCCTCAAAGATTTCTCAGCA 129 AAATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA * * * * * 687743 GCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATATCCTGGGAT 1 ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT * * * * * * * * 687808 ATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAAAGTCGACTTTGCTTATTTT 66 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT 687865 GCATATTCAC Statistics Matches: 849, Mismatches: 90, Indels: 24 0.88 0.09 0.02 Matches are distributed among these distances: 164 2 0.00 165 288 0.34 166 331 0.39 167 226 0.27 168 2 0.00 ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39 Consensus pattern (166 bp): ACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGAT ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCCAAA ATTTTCAAACAAATTTTCGTCAAAGAATTCTCAGCA Done.