Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A06

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 2234201 characters in sequence are not A, C, G, or T


File 252 of 345

Found at i:85667226 original size:20 final size:21

Alignment explanation

Indices: 85667198--85667241 Score: 56 Period size: 20 Copynumber: 2.1 Consensus size: 21 85667188 AATGCTTTTG * 85667198 TTTCTATTTTGTACT-TTTTCT 1 TTTCTATTTT-TACTCTTTACT 85667219 TTTC-ATTTTTACTCTTTACT 1 TTTCTATTTTTACTCTTTACT 85667239 TTT 1 TTT 85667242 TTTGGATTTT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 19 4 0.19 20 13 0.62 21 4 0.19 ACGTcount: A:0.11, C:0.16, G:0.02, T:0.70 Consensus pattern (21 bp): TTTCTATTTTTACTCTTTACT Found at i:85670357 original size:30 final size:30 Alignment explanation

Indices: 85670302--85670363 Score: 74 Period size: 31 Copynumber: 2.1 Consensus size: 30 85670292 AATTGATCAA * * 85670302 GTTTTATATACATGTATTATCCATTT-CAT 1 GTTTTATATACATGTAATATACATTTCCAT 85670331 GTTTCTATATACCATGTAATA-ACATTTCCAT 1 GTTT-TATATA-CATGTAATATACATTTCCAT 85670362 GT 1 GT 85670364 AATTCATGTG Statistics Matches: 28, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 29 4 0.14 30 11 0.39 31 13 0.46 ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47 Consensus pattern (30 bp): GTTTTATATACATGTAATATACATTTCCAT Found at i:85670583 original size:25 final size:25 Alignment explanation

Indices: 85670555--85670607 Score: 70 Period size: 25 Copynumber: 2.1 Consensus size: 25 85670545 ATGTTCATTT * * 85670555 GAGCTATAGATCGGTATGCTCTCAC 1 GAGCTAGAAATCGGTATGCTCTCAC * * 85670580 GAGCTAGAAATTGGTATGCTCTTAC 1 GAGCTAGAAATCGGTATGCTCTCAC 85670605 GAG 1 GAG 85670608 TTGTAGAGTA Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28 Consensus pattern (25 bp): GAGCTAGAAATCGGTATGCTCTCAC Found at i:85673473 original size:6 final size:6 Alignment explanation

Indices: 85673455--85673545 Score: 53 Period size: 6 Copynumber: 14.8 Consensus size: 6 85673445 AAGAAACATT * * * * 85673455 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAAA ATCAAA 1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA * * * 85673504 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT ATCAG 1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG 85673546 GTAACAGAAT Statistics Matches: 66, Mismatches: 11, Indels: 16 0.71 0.12 0.17 Matches are distributed among these distances: 5 4 0.06 6 55 0.83 7 5 0.08 8 2 0.03 ACGTcount: A:0.48, C:0.15, G:0.16, T:0.20 Consensus pattern (6 bp): ATCAGA Found at i:85673506 original size:25 final size:25 Alignment explanation

Indices: 85673472--85673539 Score: 91 Period size: 25 Copynumber: 2.7 Consensus size: 25 85673462 CTAGAATCAG * * * 85673472 AATCAGAATCAGAATTAGGTGACAA 1 AATCAAAATCAGAATCAGGTAACAA * * 85673497 AATCAAAATCAGTATCAGGTAACAG 1 AATCAAAATCAGAATCAGGTAACAA 85673522 AATCAAAATCAGAATCAG 1 AATCAAAATCAGAATCAG 85673540 TATCAGGTAA Statistics Matches: 37, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 25 37 1.00 ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19 Consensus pattern (25 bp): AATCAAAATCAGAATCAGGTAACAA Found at i:85673529 original size:31 final size:31 Alignment explanation

Indices: 85673494--85673560 Score: 116 Period size: 31 Copynumber: 2.2 Consensus size: 31 85673484 AATTAGGTGA 85673494 CAAAATCAAAATCAGTATCAGGTAACAGAAT 1 CAAAATCAAAATCAGTATCAGGTAACAGAAT * 85673525 CAAAATCAGAATCAGTATCAGGTAACAGAAT 1 CAAAATCAAAATCAGTATCAGGTAACAGAAT * 85673556 AAAAA 1 CAAAA 85673561 ATTAGAATGT Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 31 34 1.00 ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18 Consensus pattern (31 bp): CAAAATCAAAATCAGTATCAGGTAACAGAAT Found at i:85673964 original size:22 final size:22 Alignment explanation

Indices: 85673936--85674000 Score: 69 Period size: 22 Copynumber: 3.0 Consensus size: 22 85673926 GCAAATACGT * 85673936 TTGGCACACAGCCATAATCAGG 1 TTGGCACAAAGCCATAATCAGG * * 85673958 TTGGCACAGAGCCAT-ATGTAGG 1 TTGGCACAAAGCCATAAT-CAGG * * 85673980 TTGACACAAAGGCATAATCAG 1 TTGGCACAAAGCCATAATCAG 85674001 AAGGCTTTAA Statistics Matches: 35, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 21 2 0.06 22 31 0.89 23 2 0.06 ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20 Consensus pattern (22 bp): TTGGCACAAAGCCATAATCAGG Found at i:85674486 original size:27 final size:27 Alignment explanation

Indices: 85674428--85675027 Score: 650 Period size: 27 Copynumber: 23.0 Consensus size: 27 85674418 GGGGCAAAAT * * * * 85674428 GGTAATTTTACCCCACA-AGGTATCTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * * * 85674454 GATAATTCCACCCTACAGAGGTATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC * 85674481 GGTAATTCTACCCTACATGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 85674508 GGTAATTCTACCCTACAGGGGTATTAC 1 GGTAATTCTACCCTACAGGGGTATTTC * 85674535 GATAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 85674562 GATAATTCTACCTTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * * 85674589 GGTACTTCTACTCTACAGGGGTATTGC 1 GGTAATTCTACCCTACAGGGGTATTTC ** * * * 85674616 AATAATTCTACCCTATAGGGATATTTT 1 GGTAATTCTACCCTACAGGGGTATTTC 85674643 GGTAATTCTACCCTACAGGGGTA-TTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 85674669 TGATAATTCTACCCTACAGAGGTATTTC 1 -GGTAATTCTACCCTACAGGGGTATTTC * 85674697 GGTAA-T-T---CTA-A---GTATTCC 1 GGTAATTCTACCCTACAGGGGTATTTC * 85674715 AGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 85674742 GGTAATTCTACCCTACAGGGGTATTCC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 85674769 GATAATTCTACCCTACAGAGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 85674796 GGTAA-T-T---CTA-A---GTATTCC 1 GGTAATTCTACCCTACAGGGGTATTTC * 85674814 GGTAATTCTACCCTACA-AGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC 85674840 GGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC ** * 85674867 GGTAATTCTACTGTACAGGGGTATTGC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 85674894 GATAATTCTACCCTACAGGGGTATTCC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 85674921 AGTAATTCTACCCTACAGGGGTATTCC 1 GGTAATTCTACCCTACAGGGGTATTTC * ** 85674948 GGTAATTCTACCTTATGGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC 85674975 GGTAATTCTACCCTACAGGGGTATTGT- 1 GGTAATTCTACCCTACAGGGGTATT-TC * * 85675002 GATAATTCTACCCTGCAGGGGTATTT 1 GGTAATTCTACCCTACAGGGGTATTT 85675028 AAGTAATTTT Statistics Matches: 484, Mismatches: 68, Indels: 44 0.81 0.11 0.07 Matches are distributed among these distances: 18 21 0.04 19 2 0.00 20 2 0.00 21 2 0.00 22 6 0.01 23 6 0.01 24 2 0.00 25 2 0.00 26 41 0.08 27 396 0.82 28 4 0.01 ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34 Consensus pattern (27 bp): GGTAATTCTACCCTACAGGGGTATTTC Found at i:85674727 original size:45 final size:44 Alignment explanation

Indices: 85674663--85674849 Score: 232 Period size: 45 Copynumber: 4.0 Consensus size: 44 85674653 CCCTACAGGG * 85674663 GTATTCTGATAATTCTACCCTACAGAGGTATTTCGGTAATTCTAA 1 GTATTCCG-TAATTCTACCCTACAGAGGTATTTCGGTAATTCTAA * 85674708 GTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACA 1 GTATTCC-GTAATTCTACCCTACAGAGGTATTTCGGTAA-T-T---CTA-A 85674759 GGGGTATTCCGATAATTCTACCCTACAGAGGTATTTCGGTAATTCTAA 1 ---GTATTCCG-TAATTCTACCCTACAGAGGTATTTCGGTAATTCTAA 85674807 GTATTCCGGTAATTCTACCCTACA-AGGTATTTCGGTAATTCTA 1 GTATTCC-GTAATTCTACCCTACAGAGGTATTTCGGTAATTCTA 85674850 CCCTACAGGG Statistics Matches: 127, Mismatches: 3, Indels: 25 0.82 0.02 0.16 Matches are distributed among these distances: 44 19 0.15 45 57 0.45 46 3 0.02 47 1 0.01 48 1 0.01 49 3 0.02 50 3 0.02 51 1 0.01 52 1 0.01 53 2 0.02 54 36 0.28 ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35 Consensus pattern (44 bp): GTATTCCGTAATTCTACCCTACAGAGGTATTTCGGTAATTCTAA Found at i:85674751 original size:99 final size:99 Alignment explanation

Indices: 85674609--85674999 Score: 498 Period size: 99 Copynumber: 3.9 Consensus size: 99 85674599 CTCTACAGGG * * * * * 85674609 GTATTGCAATAATTCTACCCTATAGGGATATTTTGGTAATTCTACCCTACAGGGGTA-TTCTGAT 1 GTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC-GAT 85674673 AATTCTACCCTACAGAGGTATTTCGGTAATTCTAA 65 AATTCTACCCTACAGAGGTATTTCGGTAATTCTAA * 85674708 GTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTCCGATA 1 GTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATA 85674773 ATTCTACCCTACAGAGGTATTTCGGTAATTCTAA 66 ATTCTACCCTACAGAGGTATTTCGGTAATTCTAA * * * 85674807 GTATTCCGGTAATTCTACCCTACA-AGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTA 1 GTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATA ** * * * 85674871 ATTCTACTGTACAGGGGTATTGCGATAATTCTACCCTACA 66 ATTCTACCCTACAGAGGTATTTCGGTAA-T-T---CTA-A * * ** 85674911 GGGGTATTCCAGTAATTCTACCCTACAGGGGTATTCCGGTAATTCTACCTTATGGGGGTATTTCG 1 ---GTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCG * * 85674976 GTAATTCTACCCTACAGGGGTATT 63 ATAATTCTACCCTACAGAGGTATT 85675000 GTGATAATTC Statistics Matches: 258, Mismatches: 23, Indels: 13 0.88 0.08 0.04 Matches are distributed among these distances: 98 60 0.23 99 114 0.44 100 3 0.01 103 3 0.01 104 1 0.00 107 23 0.09 108 54 0.21 ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34 Consensus pattern (99 bp): GTATTCCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATA ATTCTACCCTACAGAGGTATTTCGGTAATTCTAA Found at i:85674765 original size:72 final size:72 Alignment explanation

Indices: 85674644--85674778 Score: 218 Period size: 72 Copynumber: 1.9 Consensus size: 72 85674634 GGATATTTTG * * 85674644 GTAATTCTACCCTACAGGGGTATTCTGATAATTCTACCCTACAGAGGTATTTCGGTAATTCTAAG 1 GTAATTCTACCCTACAGGGGTATTCTGATAATTCTACCCTACAGAGGTATTCCGATAATTCTAAG 85674709 TATTCCA 66 TATTCCA * * 85674716 GTAATTCTACCCTACAGGGGTATT-TCGGTAATTCTACCCTACAGGGGTATTCCGATAATTCTA 1 GTAATTCTACCCTACAGGGGTATTCT-GATAATTCTACCCTACAGAGGTATTCCGATAATTCTA 85674779 CCCTACAGAG Statistics Matches: 58, Mismatches: 4, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 71 1 0.02 72 57 0.98 ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34 Consensus pattern (72 bp): GTAATTCTACCCTACAGGGGTATTCTGATAATTCTACCCTACAGAGGTATTCCGATAATTCTAAG TATTCCA Found at i:85674816 original size:18 final size:18 Alignment explanation

Indices: 85674789--85674823 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 85674779 CCCTACAGAG * 85674789 GTATTTCGGTAATTCTAA 1 GTATTCCGGTAATTCTAA 85674807 GTATTCCGGTAATTCTA 1 GTATTCCGGTAATTCTA 85674824 CCCTACAAGG 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:0.26, C:0.14, G:0.17, T:0.43 Consensus pattern (18 bp): GTATTCCGGTAATTCTAA Found at i:85675050 original size:27 final size:27 Alignment explanation

Indices: 85675020--85675105 Score: 100 Period size: 27 Copynumber: 3.2 Consensus size: 27 85675010 TACCCTGCAG * ** 85675020 GGGTATTTAAGTAATTTTATTGATCGA 1 GGGTATTTAAGTAATTTTGTAAATCGA ** * * 85675047 GGGTATTTGGGTAATTTTGTAAACCAA 1 GGGTATTTAAGTAATTTTGTAAATCGA * 85675074 GGGTATTTCAGTAATTTTGTAAATCGA 1 GGGTATTTAAGTAATTTTGTAAATCGA 85675101 GGGTA 1 GGGTA 85675106 AAATGGTAAT Statistics Matches: 48, Mismatches: 11, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 27 48 1.00 ACGTcount: A:0.29, C:0.06, G:0.26, T:0.40 Consensus pattern (27 bp): GGGTATTTAAGTAATTTTGTAAATCGA Found at i:85675051 original size:81 final size:80 Alignment explanation

Indices: 85674807--85675062 Score: 279 Period size: 81 Copynumber: 3.2 Consensus size: 80 85674797 GTAATTCTAA * * * 85674807 GTATTCCGGTAATTCTACCCTACA-AGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTA 1 GTATTTCGGTAATTCTACCCTACAGGGGTATTT-GATAATTCTACCCTACAGGGGTATTTCGGTA * 85674871 ATTCTACTG-TAC-AGGG 65 ATTCTATTGAT-CGA-GG * * ** * 85674887 GTATTGCGATAATTCTACCCTACAGGGGTATTCCAGTAATTCTACCCTACAGGGGTATTCCGGTA 1 GTATTTCGGTAATTCTACCCTACAGGGGTATTTGA-TAATTCTACCCTACAGGGGTATTTCGGTA * 85674952 ATTCTACCTT-AT-GGGG 65 ATTCTA--TTGATCGAGG * ** 85674968 GTATTTCGGTAATTCTACCCTACAGGGGTATTGTGATAATTCTACCCTGCAGGGGTATTTAAGTA 1 GTATTTCGGTAATTCTACCCTACAGGGGTATT-TGATAATTCTACCCTACAGGGGTATTTCGGTA * 85675033 ATTTTATTGATCGAGG 65 ATTCTATTGATCGAGG * 85675049 GTATTTGGGTAATT 1 GTATTTCGGTAATT 85675063 TTGTAAACCA Statistics Matches: 147, Mismatches: 20, Indels: 17 0.80 0.11 0.09 Matches are distributed among these distances: 79 2 0.01 80 24 0.16 81 118 0.80 82 1 0.01 83 2 0.01 ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35 Consensus pattern (80 bp): GTATTTCGGTAATTCTACCCTACAGGGGTATTTGATAATTCTACCCTACAGGGGTATTTCGGTAA TTCTATTGATCGAGG Found at i:85675114 original size:27 final size:27 Alignment explanation

Indices: 85675084--85675145 Score: 106 Period size: 27 Copynumber: 2.3 Consensus size: 27 85675074 GGGTATTTCA * 85675084 GTAATTTTGTAAATCGAGGGTAAAATG 1 GTAATTCTGTAAATCGAGGGTAAAATG * 85675111 GTAATTCTGTAAATTGAGGGTAAAATG 1 GTAATTCTGTAAATCGAGGGTAAAATG 85675138 GTAATTCT 1 GTAATTCT 85675146 ATCTTATTTT Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 27 33 1.00 ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35 Consensus pattern (27 bp): GTAATTCTGTAAATCGAGGGTAAAATG Found at i:85675132 original size:54 final size:54 Alignment explanation

Indices: 85675020--85675123 Score: 129 Period size: 54 Copynumber: 1.9 Consensus size: 54 85675010 TACCCTGCAG ** ** * 85675020 GGGTATTTAAGTAATTTTATTGATCGAGGGTATTTGGGTAATTTTGTAAACCAA 1 GGGTATTTAAGTAATTTTATAAATCGAGGGTAAATGGGTAATTCTGTAAACCAA * * 85675074 GGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAAT-GGTAATTCTGTAAA 1 GGGTATTTAAGTAATTTTATAAATCGAGGGT-AAATGGGTAATTCTGTAAA 85675124 TTGAGGGTAA Statistics Matches: 42, Mismatches: 7, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 54 40 0.95 55 2 0.05 ACGTcount: A:0.32, C:0.06, G:0.24, T:0.38 Consensus pattern (54 bp): GGGTATTTAAGTAATTTTATAAATCGAGGGTAAATGGGTAATTCTGTAAACCAA Found at i:85675217 original size:28 final size:26 Alignment explanation

Indices: 85675157--85675244 Score: 95 Period size: 27 Copynumber: 3.3 Consensus size: 26 85675147 TCTTATTTTA * * 85675157 GTAATTTTACAAATCAAGGATATTTG 1 GTAATTTTACAAATCGAGGGTATTTG * * 85675183 GGAATTTTTATAAATCGAGGGTACTTTG 1 GTAA-TTTTACAAATCGAGGGTA-TTTG * * 85675211 GTAATTTTACAAGTCGAGGGTATTTCA 1 GTAATTTTACAAATCGAGGGTATTT-G 85675238 GTAATTT 1 GTAATTT 85675245 GGTAAACTAA Statistics Matches: 51, Mismatches: 8, Indels: 5 0.80 0.12 0.08 Matches are distributed among these distances: 26 6 0.12 27 38 0.75 28 7 0.14 ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40 Consensus pattern (26 bp): GTAATTTTACAAATCGAGGGTATTTG Found at i:85680466 original size:30 final size:29 Alignment explanation

Indices: 85680432--85680497 Score: 107 Period size: 30 Copynumber: 2.2 Consensus size: 29 85680422 ATGAATCGGA 85680432 AGCTTTGGCACTAAGTGTGC-ATTTTAAACT 1 AGCTTTGGCACTAAGTGTGCGA-TTT-AACT 85680462 AGCTTTGGCACTAAGTGTGCGATTTAACT 1 AGCTTTGGCACTAAGTGTGCGATTTAACT 85680491 AGCTTTG 1 AGCTTTG 85680498 TTTACTTGAG Statistics Matches: 35, Mismatches: 0, Indels: 3 0.92 0.00 0.08 Matches are distributed among these distances: 29 11 0.31 30 23 0.66 31 1 0.03 ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36 Consensus pattern (29 bp): AGCTTTGGCACTAAGTGTGCGATTTAACT Found at i:85682229 original size:8 final size:8 Alignment explanation

Indices: 85682212--85682242 Score: 53 Period size: 8 Copynumber: 3.9 Consensus size: 8 85682202 TCCTAATATG 85682212 TCAATCAT 1 TCAATCAT * 85682220 TCAATAAT 1 TCAATCAT 85682228 TCAATCAT 1 TCAATCAT 85682236 TCAATCA 1 TCAATCA 85682243 AACTAGCAAC Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35 Consensus pattern (8 bp): TCAATCAT Found at i:85711660 original size:93 final size:93 Alignment explanation

Indices: 85711548--85711719 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 85711538 CGCCCATAAG * * 85711548 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 85711613 ACGAGTTCGGATGCCTAGTTACATCTCA 66 ACGAGTTCGGATGCCTAGTTACATCTCA * 85711641 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 85711706 ACGAGTTCGGATGC 66 ACGAGTTCGGATGC 85711720 TCAACCATCC Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21 Consensus pattern (93 bp): CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA ACGAGTTCGGATGCCTAGTTACATCTCA Found at i:85711716 original size:46 final size:46 Alignment explanation

Indices: 85711541--85711716 Score: 216 Period size: 46 Copynumber: 3.8 Consensus size: 46 85711531 TGTAACCCGC * * * 85711541 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * * 85711587 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT * 85711637 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * 85711680 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA 85711717 TGCTCAACCA Statistics Matches: 111, Mismatches: 10, Indels: 18 0.80 0.07 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 2 0.02 45 2 0.02 46 63 0.57 47 29 0.26 48 2 0.02 49 2 0.02 50 3 0.03 51 2 0.02 ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20 Consensus pattern (46 bp): CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT Found at i:85718455 original size:93 final size:93 Alignment explanation

Indices: 85718343--85718514 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 85718333 CGCCCATAAG * * 85718343 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 85718408 ACGAGTTCGGATGCCTAGTTACATCTCA 66 ACGAGTTCGGATGCCTAGTTACATCTCA * 85718436 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA 85718501 ACGAGTTCGGATGC 66 ACGAGTTCGGATGC 85718515 TCAACATCCT Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21 Consensus pattern (93 bp): CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA ACGAGTTCGGATGCCTAGTTACATCTCA Found at i:85718511 original size:46 final size:46 Alignment explanation

Indices: 85718336--85718511 Score: 216 Period size: 46 Copynumber: 3.8 Consensus size: 46 85718326 TGTAACCCGC * * * 85718336 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * * 85718382 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT * 85718432 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT * 85718475 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA 85718512 TGCTCAACAT Statistics Matches: 111, Mismatches: 10, Indels: 18 0.80 0.07 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 44 2 0.02 45 2 0.02 46 63 0.57 47 29 0.26 48 2 0.02 49 2 0.02 50 3 0.03 51 2 0.02 ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20 Consensus pattern (46 bp): CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT Found at i:85727154 original size:48 final size:47 Alignment explanation

Indices: 85726987--85727303 Score: 293 Period size: 48 Copynumber: 6.7 Consensus size: 47 85726977 CGGATAACCT * ** * 85726987 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGATATTGAGCC 1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTTATATGGAGCC * * * * * 85727034 AGTGTAAGACCATGTTTGGAACATGACATCGGCATTTATAAGAGAACT 1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTTATATG-GAGCC *** * 85727082 AGTGTAAGACCATGTTTAAAACATGGCATCGGTATTTATATGAGAGCC 1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTTATATG-GAGCC * * * 85727130 AGTGTAAGACCATGTCTGGGACATGGCATCGACATTTATATTGGAGCT 1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTTATA-TGGAGCC * ** * * ** * 85727178 AATGTAAGACCATGCCTAGGACATGGCATCGGCCTCGACATATGG-GCT 1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCAT--TTATATGGAGCC ** ** 85727226 AGTGTAAGACCATGTTTGTAACATGGCATCGGCA--CCTAT--AGCC 1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTTATATGGAGCC * 85727269 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT 1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCAT 85727304 CTTACCCTTT Statistics Matches: 222, Mismatches: 42, Indels: 15 0.80 0.15 0.05 Matches are distributed among these distances: 43 33 0.15 44 4 0.02 47 35 0.16 48 142 0.64 49 5 0.02 50 3 0.01 ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26 Consensus pattern (47 bp): AGTGTAAGACCATGTTTGGGACATGGCATCGGCATTTATATGGAGCC Found at i:85733315 original size:25 final size:25 Alignment explanation

Indices: 85733269--85733316 Score: 60 Period size: 25 Copynumber: 1.9 Consensus size: 25 85733259 TTATAACATG * * * * 85733269 AAAATGACCGTTTTGCCTCTAGGTA 1 AAAATGACCATTATACCCCTAGGTA 85733294 AAAATGACCATTATACCCCTAGG 1 AAAATGACCATTATACCCCTAGG 85733317 GTTTATATAT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 25 19 1.00 ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27 Consensus pattern (25 bp): AAAATGACCATTATACCCCTAGGTA Found at i:85733395 original size:19 final size:20 Alignment explanation

Indices: 85733360--85733417 Score: 91 Period size: 19 Copynumber: 3.0 Consensus size: 20 85733350 TAAACATGGT * 85733360 ATGTATGATATGCACATGAC 1 ATGTATGATAGGCACATGAC * 85733380 ATGTATGATA-GCACATGAT 1 ATGTATGATAGGCACATGAC 85733399 ATGTATGATAGGCACATGA 1 ATGTATGATAGGCACATGA 85733418 TGTATTCATA Statistics Matches: 36, Mismatches: 1, Indels: 2 0.92 0.03 0.05 Matches are distributed among these distances: 19 18 0.50 20 18 0.50 ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29 Consensus pattern (20 bp): ATGTATGATAGGCACATGAC Found at i:85733418 original size:20 final size:19 Alignment explanation

Indices: 85733353--85733418 Score: 96 Period size: 20 Copynumber: 3.4 Consensus size: 19 85733343 ATTTTGATAA * 85733353 ACATGGTATGTATGATATGC 1 ACATGATATGTATGATA-GC * 85733373 ACATGACATGTATGATAGC 1 ACATGATATGTATGATAGC 85733392 ACATGATATGTATGATAGGC 1 ACATGATATGTATGATA-GC 85733412 ACATGAT 1 ACATGAT 85733419 GTATTCATAA Statistics Matches: 42, Mismatches: 3, Indels: 2 0.89 0.06 0.04 Matches are distributed among these distances: 19 18 0.43 20 24 0.57 ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30 Consensus pattern (19 bp): ACATGATATGTATGATAGC Found at i:85733559 original size:25 final size:24 Alignment explanation

Indices: 85733468--85733563 Score: 149 Period size: 24 Copynumber: 4.0 Consensus size: 24 85733458 GAGGAAGTGC 85733468 AAAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT 85733492 AAAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT * 85733516 AAAAGGGCTTTTGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT * 85733540 AAAAGAGGC-TAGGCCTCCAGTTAT 1 AAAAG-GGCTTATGCC-CCAGTTAT 85733564 ATGATAAAGC Statistics Matches: 67, Mismatches: 3, Indels: 3 0.92 0.04 0.04 Matches are distributed among these distances: 24 56 0.84 25 11 0.16 ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28 Consensus pattern (24 bp): AAAAGGGCTTATGCCCCAGTTATT Found at i:85735274 original size:3 final size:3 Alignment explanation

Indices: 85735266--85735308 Score: 68 Period size: 3 Copynumber: 14.3 Consensus size: 3 85735256 AATTACAATG * * 85735266 ATA ATA ATA ATG ATA ATA ATA AAA ATA ATA ATA ATA ATA ATA A 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A 85735309 CATAATGAAA Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 3 36 1.00 ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30 Consensus pattern (3 bp): ATA Found at i:85736199 original size:28 final size:29 Alignment explanation

Indices: 85736151--85736258 Score: 94 Period size: 29 Copynumber: 3.8 Consensus size: 29 85736141 TTCACATACC * * * * 85736151 TGTATCTGCCCCATTAAGCCC-AACCATA 1 TGTATATGGCCCATTAGGCCCAAACCACA * * 85736179 T-TCATATGGCCCATTAGGCCCAAATCACC 1 TGT-ATATGGCCCATTAGGCCCAAACCACA * * 85736208 TGTATATGGCCCATTAGGCCTAAATCACA 1 TGTATATGGCCCATTAGGCCCAAACCACA * * * 85736237 TTTATATAGCCCGTTAGGCCCA 1 TGTATATGGCCCATTAGGCCCA 85736259 GTCACATTCA Statistics Matches: 65, Mismatches: 12, Indels: 5 0.79 0.15 0.06 Matches are distributed among these distances: 27 1 0.02 28 16 0.25 29 47 0.72 30 1 0.02 ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27 Consensus pattern (29 bp): TGTATATGGCCCATTAGGCCCAAACCACA Found at i:85736215 original size:29 final size:29 Alignment explanation

Indices: 85736182--85736258 Score: 109 Period size: 29 Copynumber: 2.7 Consensus size: 29 85736172 AACCATATTC * 85736182 ATATGGCCCATTAGGCCCAAATCACCTGT 1 ATATGGCCCATTAGGCCCAAATCACATGT * * 85736211 ATATGGCCCATTAGGCCTAAATCACATTT 1 ATATGGCCCATTAGGCCCAAATCACATGT * * 85736240 ATATAGCCCGTTAGGCCCA 1 ATATGGCCCATTAGGCCCA 85736259 GTCACATTCA Statistics Matches: 42, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 29 42 1.00 ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26 Consensus pattern (29 bp): ATATGGCCCATTAGGCCCAAATCACATGT Found at i:85739816 original size:40 final size:40 Alignment explanation

Indices: 85739757--85739927 Score: 206 Period size: 40 Copynumber: 4.3 Consensus size: 40 85739747 CATTTGAATG * * * 85739757 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT * 85739797 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT * 85739837 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGATT * * ** * 85739877 ATA-CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT 85739916 ATATCC-GGCTAA 1 ATATCCGGGCTAA 85739928 ATTCCGAAGA Statistics Matches: 116, Mismatches: 11, Indels: 9 0.85 0.08 0.07 Matches are distributed among these distances: 38 2 0.02 39 36 0.31 40 75 0.65 41 3 0.03 ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGATT Found at i:85739895 original size:39 final size:40 Alignment explanation

Indices: 85739757--85739907 Score: 216 Period size: 40 Copynumber: 3.8 Consensus size: 40 85739747 CATTTGAATG * * * 85739757 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T * 85739797 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT * 85739837 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT * * 85739877 ATA-CCGGGTTAAGACCCGAAGGCAATTGTGC 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC 85739908 TTGTGGTTAT Statistics Matches: 102, Mismatches: 8, Indels: 3 0.90 0.07 0.03 Matches are distributed among these distances: 39 26 0.25 40 73 0.72 41 3 0.03 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT Found at i:85739919 original size:79 final size:80 Alignment explanation

Indices: 85739757--85739927 Score: 213 Period size: 79 Copynumber: 2.2 Consensus size: 80 85739747 CATTTGAATG * * * * 85739757 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA * * 85739822 TTTGTGCGAGTTGAT 66 ATTGTGCGAGTGGAT * * 85739837 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATA-CCGGGTTAAGACCCGAAGGC 1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATATCCGGGCTAAGACCCGAAGGC ** * 85739900 AATTGTGCTTGTGGTT 65 AATTGTGCGAGTGGAT 85739916 ATATCC-GGCTAA 1 ATATCCGGGCTAA 85739928 ATTCCGAAGA Statistics Matches: 79, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 78 6 0.08 79 36 0.46 80 35 0.44 81 2 0.03 ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27 Consensus pattern (80 bp): ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA ATTGTGCGAGTGGAT Found at i:85747065 original size:40 final size:40 Alignment explanation

Indices: 85747010--85747220 Score: 239 Period size: 40 Copynumber: 5.3 Consensus size: 40 85747000 ATTTGAATGA * 85747010 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT 1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT * 85747050 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT 1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT * * * 85747090 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TA 1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT * * * * 85747130 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA 1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT * * * * * * * 85747170 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA 1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT 85747210 TATCC-GGCTAA 1 TATCCGGGCTAA 85747221 ATTCCGAAGA Statistics Matches: 156, Mismatches: 12, Indels: 7 0.89 0.07 0.04 Matches are distributed among these distances: 39 7 0.04 40 146 0.94 41 3 0.02 ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28 Consensus pattern (40 bp): TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT Found at i:85750073 original size:18 final size:18 Alignment explanation

Indices: 85750050--85750084 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 85750040 CTCTCGTCCT * * 85750050 CTAAGGGGAAGCAGAAAG 1 CTAAGGGAAAGAAGAAAG 85750068 CTAAGGGAAAGAAGAAA 1 CTAAGGGAAAGAAGAAA 85750085 CCGACTAAAT Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06 Consensus pattern (18 bp): CTAAGGGAAAGAAGAAAG Found at i:85757241 original size:40 final size:40 Alignment explanation

Indices: 85757186--85757403 Score: 237 Period size: 40 Copynumber: 5.5 Consensus size: 40 85757176 GCATAAATTG * * 85757186 TATATATGGAACTTAGTGTGCAATTCGACATAGTTTCGGC 1 TATATATGGCACTTAGTGTGCAATTCGACATAGCTTCGGC * * * 85757226 TATATATGGAACTTAGTGTGCGATTCGACATAGATTCGGC 1 TATATATGGCACTTAGTGTGCAATTCGACATAGCTTCGGC * 85757266 TATATGTGGCACTTAGTGTG---TTCGACATAGCTTCGGC 1 TATATATGGCACTTAGTGTGCAATTCGACATAGCTTCGGC * * * * 85757303 TATATATGGCACTTAGTGTGTGAGA-TCCAGATAGCTTCAGC 1 TATATATGGCACTTAGTGTG-CA-ATTCGACATAGCTTCGGC * * * * * 85757344 TATATATGGTACTTAGTGTGCTATTTGAGATAGCTTCAGC 1 TATATATGGCACTTAGTGTGCAATTCGACATAGCTTCGGC * * 85757384 TATGTACGGCACTTAGTGTG 1 TATATATGGCACTTAGTGTG 85757404 AGAGATATCG Statistics Matches: 155, Mismatches: 17, Indels: 12 0.84 0.09 0.07 Matches are distributed among these distances: 37 35 0.23 39 1 0.01 40 87 0.56 41 32 0.21 ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35 Consensus pattern (40 bp): TATATATGGCACTTAGTGTGCAATTCGACATAGCTTCGGC Found at i:85759921 original size:14 final size:15 Alignment explanation

Indices: 85759902--85759930 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 85759892 AAGTGTAGTT 85759902 ATTTTGATTT-TGGG 1 ATTTTGATTTATGGG 85759916 ATTTTGATTTATGGG 1 ATTTTGATTTATGGG 85759931 TTTCGTTTTG Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 10 0.71 15 4 0.29 ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55 Consensus pattern (15 bp): ATTTTGATTTATGGG Found at i:85761743 original size:17 final size:17 Alignment explanation

Indices: 85761721--85761753 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 85761711 TATACTAAAC * 85761721 ACTGTAGTAAAACTGAG 1 ACTGTAGCAAAACTGAG 85761738 ACTGTAGCAAAACTGA 1 ACTGTAGCAAAACTGA 85761754 TAGAGACTGC Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21 Consensus pattern (17 bp): ACTGTAGCAAAACTGAG Found at i:85763297 original size:14 final size:14 Alignment explanation

Indices: 85763280--85763307 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 85763270 AATGTTCCTT 85763280 TAAAGGTCCAAGGG 1 TAAAGGTCCAAGGG 85763294 TAAAGGTCCAAGGG 1 TAAAGGTCCAAGGG 85763308 ACGATATTTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.36, C:0.14, G:0.36, T:0.14 Consensus pattern (14 bp): TAAAGGTCCAAGGG Found at i:85764995 original size:40 final size:40 Alignment explanation

Indices: 85764928--85765038 Score: 134 Period size: 40 Copynumber: 2.8 Consensus size: 40 85764918 TTAATAGTCG * * 85764928 AAGCTATCTCAACCTCGCACACTAAGTGCCATATATATCCA 1 AAGCTATCTCGA-CTCGCACACTAAGTGCCATATATAGCCA * * * 85764969 AAGCTATTTCGACTCGCACACTAAGTGCTC-TATATGGCCG 1 AAGCTATCTCGACTCGCACACTAAGTGC-CATATATAGCCA ** 85765009 AAGCTATCTCGAAACGCACACTAAGTGCCA 1 AAGCTATCTCGACTCGCACACTAAGTGCCA 85765039 AACATAGTCA Statistics Matches: 60, Mismatches: 8, Indels: 5 0.82 0.11 0.07 Matches are distributed among these distances: 39 1 0.02 40 48 0.80 41 11 0.18 ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23 Consensus pattern (40 bp): AAGCTATCTCGACTCGCACACTAAGTGCCATATATAGCCA Found at i:85778735 original size:17 final size:17 Alignment explanation

Indices: 85778715--85778748 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 85778705 TTATATTAAT * 85778715 TAAATAAAATAAGTAAA 1 TAAATAAAATAAATAAA 85778732 TAAATAAAATAAATAAA 1 TAAATAAAATAAATAAA 85778749 GACAAATGTG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24 Consensus pattern (17 bp): TAAATAAAATAAATAAA Found at i:85778892 original size:16 final size:16 Alignment explanation

Indices: 85778844--85778897 Score: 60 Period size: 16 Copynumber: 3.5 Consensus size: 16 85778834 ATTTACTATT 85778844 TATAA-AAGATATTTA 1 TATAATAAGATATTTA * 85778859 T-TAATTAAG-TAATTA 1 TATAA-TAAGATATTTA * 85778874 TATTATAAGATATTTA 1 TATAATAAGATATTTA 85778890 TATAATAA 1 TATAATAA 85778898 ATAAATTTAA Statistics Matches: 31, Mismatches: 4, Indels: 7 0.74 0.10 0.17 Matches are distributed among these distances: 14 3 0.10 15 11 0.35 16 17 0.55 ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44 Consensus pattern (16 bp): TATAATAAGATATTTA Found at i:85779693 original size:15 final size:16 Alignment explanation

Indices: 85779673--85779703 Score: 55 Period size: 15 Copynumber: 2.0 Consensus size: 16 85779663 TAATATAAAG 85779673 TGAATTGA-AATATAT 1 TGAATTGAGAATATAT 85779688 TGAATTGAGAATATAT 1 TGAATTGAGAATATAT 85779704 CTGATTAATT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 8 0.53 16 7 0.47 ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39 Consensus pattern (16 bp): TGAATTGAGAATATAT Found at i:85780088 original size:18 final size:18 Alignment explanation

Indices: 85780065--85780160 Score: 102 Period size: 18 Copynumber: 5.3 Consensus size: 18 85780055 TAAATAAAGG * 85780065 TACTGAATAATTGATTAT 1 TACTGAATAAATGATTAT * * * 85780083 TACTGAATAATTGACTGT 1 TACTGAATAAATGATTAT * * 85780101 TACTGAATAAATGACTGT 1 TACTGAATAAATGATTAT * 85780119 TATTGAATAAATGATTAT 1 TACTGAATAAATGATTAT * * * 85780137 TATTGAATAACTGATTAA 1 TACTGAATAAATGATTAT 85780155 TACTGA 1 TACTGA 85780161 TGACTGGCTG Statistics Matches: 69, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 69 1.00 ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40 Consensus pattern (18 bp): TACTGAATAAATGATTAT Found at i:85783767 original size:40 final size:40 Alignment explanation

Indices: 85783572--85783857 Score: 422 Period size: 39 Copynumber: 7.3 Consensus size: 40 85783562 GGACTAAGAT * * * ** 85783572 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGT- 1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC 85783611 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGG-TAAGTC 1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC 85783650 CC--AGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGT- 1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC 85783687 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAAGTC 1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTT-AAGTC 85783728 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC 1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC 85783768 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC 1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC * ** * * * 85783808 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC 1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC 85783847 CCGAAGGCATT 1 CCGAAGGCATT 85783858 TGAACGAGGA Statistics Matches: 230, Mismatches: 11, Indels: 12 0.91 0.04 0.05 Matches are distributed among these distances: 37 31 0.13 38 10 0.04 39 94 0.41 40 60 0.26 41 35 0.15 ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27 Consensus pattern (40 bp): CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC Found at i:85783877 original size:79 final size:80 Alignment explanation

Indices: 85783572--85783891 Score: 278 Period size: 76 Copynumber: 4.1 Consensus size: 80 85783562 GGACTAAGAT * * * * * ** ** * 85783572 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTGTTA 1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA 85783636 AATCCGGG-TAAGTC 66 AATCCGGGTTAAGTC ** * * ** ** * 85783650 CC--AGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTGTTA 1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA 85783712 AATCCGGGTTAAAGTC 66 AATCCGGGTT-AAGTC ** * * ** ** * 85783728 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA 1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA 85783793 AATCCGGGTTAAGTC 66 AATCCGGGTTAAGTC * * * 85783808 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA 1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA * * 85783872 TATCC-GGTTAAAT- 66 AATCCGGGTTAAGTC 85783885 CCGAAGG 1 CCGAAGG 85783892 TACGTGATTT Statistics Matches: 218, Mismatches: 19, Indels: 11 0.88 0.08 0.04 Matches are distributed among these distances: 76 63 0.29 77 8 0.04 78 16 0.07 79 45 0.21 80 51 0.23 81 35 0.16 ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26 Consensus pattern (80 bp): CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA AATCCGGGTTAAGTC Found at i:85790061 original size:26 final size:25 Alignment explanation

Indices: 85789930--85790187 Score: 96 Period size: 25 Copynumber: 10.3 Consensus size: 25 85789920 CAACTTAAGG * * * 85789930 TAAATAATATAAAAAACAGTTTCAAA 1 TAAATAATATATAAAATAATTT-AAA * * 85789956 TAATTAATATATAAAA-AACTTAAAA 1 TAAATAATATATAAAATAA-TTTAAA * 85789981 TAAATAATA-ATAAAATAGCA-TGAAA 1 TAAATAATATATAAAATA--ATTTAAA * 85790006 TAAACAA-ATATAAGAAT--TTTAAGA 1 TAAATAATATATAA-AATAATTTAA-A * 85790030 TGAATAATATATAAAATAATTTAAA 1 TAAATAATATATAAAATAATTTAAA * * * 85790055 TTAAATATTACACGTGAAAAT--TTAAAA 1 -TAAATAATATA--T-AAAATAATTTAAA * * * 85790082 TAGATAATATGA-AAAATAGTTAAAA 1 TAAATAATAT-ATAAAATAATTTAAA * 85790107 TAAATAATTTATAAAA-AATATCTAAGA 1 TAAATAATATATAAAATAAT-T-TAA-A * * * 85790134 TAAATGAT-T-TATAA-AAGTT-AA 1 TAAATAATATATAAAATAATTTAAA * 85790155 TAAACAATATATGAAAAT-ATTTAAAA 1 TAAATAATATAT-AAAATAATTT-AAA 85790181 TAAATAA 1 TAAATAA 85790188 AATAAGTAAG Statistics Matches: 175, Mismatches: 29, Indels: 56 0.67 0.11 0.22 Matches are distributed among these distances: 21 7 0.04 22 2 0.01 23 10 0.06 24 26 0.15 25 59 0.34 26 50 0.29 27 15 0.09 28 1 0.01 29 5 0.03 ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31 Consensus pattern (25 bp): TAAATAATATATAAAATAATTTAAA Found at i:85790124 original size:27 final size:26 Alignment explanation

Indices: 85790071--85790149 Score: 83 Period size: 27 Copynumber: 3.1 Consensus size: 26 85790061 ATTACACGTG * * 85790071 AAAAT-TTAAAATAGATAA--TATGA 1 AAAATATTAAAATAAATAATTTATAA 85790094 AAAATAGTTAAAATAAATAATTTATAA 1 AAAATA-TTAAAATAAATAATTTATAA * * 85790121 AAAATATCTAAGATAAATGATTTATAA 1 AAAATAT-TAAAATAAATAATTTATAA 85790148 AA 1 AA 85790150 GTTAATAAAC Statistics Matches: 47, Mismatches: 4, Indels: 6 0.82 0.07 0.11 Matches are distributed among these distances: 23 5 0.11 25 12 0.26 26 1 0.02 27 29 0.62 ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32 Consensus pattern (26 bp): AAAATATTAAAATAAATAATTTATAA Found at i:85791096 original size:23 final size:22 Alignment explanation

Indices: 85791070--85791117 Score: 69 Period size: 22 Copynumber: 2.1 Consensus size: 22 85791060 ATAGATTTGT * 85791070 AGAAAATGAAACAAAAAGAAACA 1 AGAAAATGAAA-AAAAAGAAAAA * 85791093 AGAAAATGAAAAGAAAGAAAAA 1 AGAAAATGAAAAAAAAGAAAAA 85791115 AGA 1 AGA 85791118 TTAAAGCAAC Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 22 12 0.52 23 11 0.48 ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04 Consensus pattern (22 bp): AGAAAATGAAAAAAAAGAAAAA Found at i:85794051 original size:16 final size:16 Alignment explanation

Indices: 85794016--85794096 Score: 71 Period size: 16 Copynumber: 5.0 Consensus size: 16 85794006 TCAAAATAAC 85794016 ATATTTTAATAA-ATT 1 ATATTTTAATAATATT 85794031 ATATTTTATATAATATT 1 ATATTTTA-ATAATATT * 85794048 -TATTTCAAATATATATT 1 ATATTT-TAATA-ATATT * 85794065 -TAAATTT-ATAAATATT 1 AT-ATTTTAAT-AATATT 85794081 ATATTTTAATAATATT 1 ATATTTTAATAATATT 85794097 CAAAATTTAG Statistics Matches: 54, Mismatches: 4, Indels: 15 0.74 0.05 0.21 Matches are distributed among these distances: 15 8 0.15 16 29 0.54 17 14 0.26 18 3 0.06 ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54 Consensus pattern (16 bp): ATATTTTAATAATATT Found at i:85796874 original size:47 final size:47 Alignment explanation

Indices: 85796803--85797027 Score: 196 Period size: 47 Copynumber: 4.8 Consensus size: 47 85796793 AGGGTATAAT 85796803 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATC-CATCAA 1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCAC-TCAA * * * 85796850 ATCGATGCCATGTCCCAGACATGGTCTTACACTAGCTT-TCACATTTTCAT 1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCAC----TCAA * * * * 85796900 GCCGATGCCATGTCCTAGACATGGTCTTACACTGAC--A-CATCTCGTA 1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCA-CTC-AA * * * * 85796946 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGC-TCTCGTCTCAA 1 ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATC-ACTCAA * * 85796991 TGCTGATGCCATGTCCCAGACATGGTCTTACACTGGC 1 -ACCGATGCCATGTCCCAGACATGGTCTTACACTGGC 85797028 ACACAAATAA Statistics Matches: 146, Mismatches: 19, Indels: 25 0.77 0.10 0.13 Matches are distributed among these distances: 44 11 0.08 45 16 0.11 46 19 0.13 47 51 0.35 48 14 0.10 49 1 0.01 50 34 0.23 ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28 Consensus pattern (47 bp): ACCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCACTCAA Found at i:85801326 original size:6 final size:6 Alignment explanation

Indices: 85801315--85801343 Score: 58 Period size: 6 Copynumber: 4.8 Consensus size: 6 85801305 ACAATAAAAG 85801315 AAATTA AAATTA AAATTA AAATTA AAATT 1 AAATTA AAATTA AAATTA AAATTA AAATT 85801344 TAAGTAATTG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 23 1.00 ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (6 bp): AAATTA Found at i:85803049 original size:17 final size:18 Alignment explanation

Indices: 85803012--85803057 Score: 58 Period size: 17 Copynumber: 2.6 Consensus size: 18 85803002 TTATCATCTA * * 85803012 TAATTATTTTATTATTCT 1 TAATTATTTTATAATTAT 85803030 TAATT-TTTTATAATTAT 1 TAATTATTTTATAATTAT * 85803047 TAAATATTTTA 1 TAATTATTTTA 85803058 AGTTATTTAG Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 17 14 0.58 18 10 0.42 ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63 Consensus pattern (18 bp): TAATTATTTTATAATTAT Found at i:85820610 original size:24 final size:24 Alignment explanation

Indices: 85820583--85820632 Score: 82 Period size: 24 Copynumber: 2.1 Consensus size: 24 85820573 AATAAAGTAT 85820583 GAGGCATTACCGGACACATACTCA 1 GAGGCATTACCGGACACATACTCA * * 85820607 GAGGCGTTACTGGACACATACTCA 1 GAGGCATTACCGGACACATACTCA 85820631 GA 1 GA 85820633 CATTTCAAAA Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 24 1.00 ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18 Consensus pattern (24 bp): GAGGCATTACCGGACACATACTCA Found at i:85820939 original size:29 final size:29 Alignment explanation

Indices: 85820889--85820944 Score: 69 Period size: 29 Copynumber: 1.9 Consensus size: 29 85820879 ACAGGGGTTT * 85820889 TCACACGGCCAAGCACACGCCCGTGTCCC 1 TCACACGGCCAAGCACACGCCCCTGTCCC * * 85820918 TCACGCGGCCTAG-ACACGGCCCCTGTC 1 TCACACGGCCAAGCACAC-GCCCCTGTC 85820945 ATTACTCGTG Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 28 4 0.17 29 19 0.83 ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12 Consensus pattern (29 bp): TCACACGGCCAAGCACACGCCCCTGTCCC Found at i:85823949 original size:16 final size:17 Alignment explanation

Indices: 85823918--85823951 Score: 52 Period size: 16 Copynumber: 2.0 Consensus size: 17 85823908 GGTAGGGGGT 85823918 ATTTATTCTTAATTGTCA 1 ATTTATTC-TAATTGTCA 85823936 ATTTATTC-AATTGTCA 1 ATTTATTCTAATTGTCA 85823952 GTAGTCAATG Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 8 0.50 18 8 0.50 ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53 Consensus pattern (17 bp): ATTTATTCTAATTGTCA Found at i:85830911 original size:27 final size:27 Alignment explanation

Indices: 85830881--85831197 Score: 458 Period size: 27 Copynumber: 11.8 Consensus size: 27 85830871 CCTTAATCGA * 85830881 TAAAATGATTATTTTGCCCTTATGAGG 1 TAAAATGACTATTTTGCCCTTATGAGG * 85830908 TAAAATGACTGTTTTGCCCTTATGAGG 1 TAAAATGACTATTTTGCCCTTATGAGG 85830935 TAAAATGACTATTTTGCCCTTAT-AGGG 1 TAAAATGACTATTTTGCCCTTATGA-GG * * * 85830962 TAAAATGTCTGTTTTGCCCTTATGAAG 1 TAAAATGACTATTTTGCCCTTATGAGG 85830989 TAAAATGACTATTTTGCCCTTATGAGG 1 TAAAATGACTATTTTGCCCTTATGAGG * * 85831016 TAAAATGATTGTTTTGCCCTTATGAGG 1 TAAAATGACTATTTTGCCCTTATGAGG * * * 85831043 TAAAATGACTCTTTTTCCCTTATGGGG 1 TAAAATGACTATTTTGCCCTTATGAGG * * 85831070 TAAAATGACTCTTTTTCCCTTATGAGG 1 TAAAATGACTATTTTGCCCTTATGAGG 85831097 TAAAATGACTA-TTTGCCCTTATGAGG 1 TAAAATGACTATTTTGCCCTTATGAGG * * 85831123 TAAAATGATTGTTTTGCCCTTATGAGG 1 TAAAATGACTATTTTGCCCTTATGAGG * 85831150 TAAAATGACTATTTTGCCCTTATGTGG 1 TAAAATGACTATTTTGCCCTTATGAGG ** 85831177 TAAAACAACTATTTTGCCCTT 1 TAAAATGACTATTTTGCCCTT 85831198 TTATGGTAAG Statistics Matches: 262, Mismatches: 25, Indels: 6 0.89 0.09 0.02 Matches are distributed among these distances: 26 24 0.09 27 237 0.90 28 1 0.00 ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39 Consensus pattern (27 bp): TAAAATGACTATTTTGCCCTTATGAGG Found at i:85831204 original size:27 final size:27 Alignment explanation

Indices: 85831134--85831206 Score: 85 Period size: 27 Copynumber: 2.7 Consensus size: 27 85831124 AAAATGATTG * ** 85831134 TTTTGCCCTTATGA-GGTAAAATGACTA 1 TTTTGCCCTT-TTATGGTAAAACAACTA * * 85831161 TTTTGCCCTTATGTGGTAAAACAACTA 1 TTTTGCCCTTTTATGGTAAAACAACTA 85831188 TTTTGCCCTTTTATGGTAA 1 TTTTGCCCTTTTATGGTAA 85831207 GATGACTGTT Statistics Matches: 38, Mismatches: 7, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 27 38 1.00 ACGTcount: A:0.26, C:0.16, G:0.16, T:0.41 Consensus pattern (27 bp): TTTTGCCCTTTTATGGTAAAACAACTA Found at i:85831549 original size:17 final size:18 Alignment explanation

Indices: 85831524--85831570 Score: 69 Period size: 17 Copynumber: 2.7 Consensus size: 18 85831514 TTGCATATTG * 85831524 TTTATTGTTACTGCACT- 1 TTTACTGTTACTGCACTA * 85831541 TTTACTGTTACCGCACTA 1 TTTACTGTTACTGCACTA 85831559 TTTACTGTTACT 1 TTTACTGTTACT 85831571 ACAATGGGCC Statistics Matches: 26, Mismatches: 3, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 17 15 0.58 18 11 0.42 ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49 Consensus pattern (18 bp): TTTACTGTTACTGCACTA Found at i:85833821 original size:27 final size:27 Alignment explanation

Indices: 85833790--85833917 Score: 150 Period size: 27 Copynumber: 4.7 Consensus size: 27 85833780 TTAGTTTACC * 85833790 AAATTACCAAAATACCCCTGATTTGTG 1 AAATTACCAAAATACCCCTGATTTGTA ** * 85833817 AAATTACTGAAATA-CCCTCGACTTGTA 1 AAATTACCAAAATACCCCT-GATTTGTA * * ** 85833844 AAATTACCAAAATACCCTTGGTTTACA 1 AAATTACCAAAATACCCCTGATTTGTA * 85833871 AAATTACCAAAATACCCCTGGTTTGTA 1 AAATTACCAAAATACCCCTGATTTGTA * 85833898 AAATTACCAAAATGCCCCTG 1 AAATTACCAAAATACCCCTG 85833918 TAGGGTAGAA Statistics Matches: 84, Mismatches: 15, Indels: 4 0.82 0.15 0.04 Matches are distributed among these distances: 26 4 0.05 27 77 0.92 28 3 0.04 ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28 Consensus pattern (27 bp): AAATTACCAAAATACCCCTGATTTGTA Found at i:85833929 original size:27 final size:27 Alignment explanation

Indices: 85833872--85834068 Score: 243 Period size: 27 Copynumber: 7.3 Consensus size: 27 85833862 TGGTTTACAA * ** * 85833872 AATTACCAAAATACCCCTGGT-TTGTAA 1 AATTACCGAAATACCCCT-GTAGGGTAG * * 85833899 AATTACCAAAATGCCCCTGTAGGGTAG 1 AATTACCGAAATACCCCTGTAGGGTAG * * 85833926 AATTACTGAAATACCCCTATAGGGTAG 1 AATTACCGAAATACCCCTGTAGGGTAG * * * 85833953 AGTTACTGAAATACCCCTGTAGAGTAG 1 AATTACCGAAATACCCCTGTAGGGTAG * 85833980 AATTACTGAAATACCCCTGTAGGGTAG 1 AATTACCGAAATACCCCTGTAGGGTAG * 85834007 AATTACCGAAATACCCTTGTAGGGTAG 1 AATTACCGAAATACCCCTGTAGGGTAG * * 85834034 AAATACCGAAATACCTCTGTAGGGTAG 1 AATTACCGAAATACCCCTGTAGGGTAG 85834061 AATTACCG 1 AATTACCG 85834069 TGATAACCTT Statistics Matches: 150, Mismatches: 19, Indels: 2 0.88 0.11 0.01 Matches are distributed among these distances: 26 2 0.01 27 148 0.99 ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25 Consensus pattern (27 bp): AATTACCGAAATACCCCTGTAGGGTAG Found at i:85834079 original size:54 final size:54 Alignment explanation

Indices: 85833899--85834090 Score: 233 Period size: 54 Copynumber: 3.6 Consensus size: 54 85833889 TGGTTTGTAA * * * * * 85833899 AATTACCAAAATGCCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCCTGTAGGGTAG * * * * * 85833953 AGTTACTGAAATACCCCTGTAGAGTAGAATTACTGAAATACCCCTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCCTGTAGGGTAG * * 85834007 AATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCTCTGTAGGGTAG 1 AATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCCTGTAGGGTAG ** * * 85834061 AATTACCGTGATAACCTTGTGGGGTA-AAAT 1 AATTACCGAAATACCCTTGTAGGGTAGAAAT 85834091 TACCATTTTG Statistics Matches: 121, Mismatches: 17, Indels: 1 0.87 0.12 0.01 Matches are distributed among these distances: 53 4 0.03 54 117 0.97 ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26 Consensus pattern (54 bp): AATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCCTGTAGGGTAG Found at i:85834085 original size:27 final size:27 Alignment explanation

Indices: 85833916--85834094 Score: 180 Period size: 27 Copynumber: 6.6 Consensus size: 27 85833906 AAAATGCCCC * * * 85833916 TGTAGGGTAGAATTACTGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATAACCT * * * * * 85833943 TATAGGGTAGAGTTACTGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATAACCT * * * * 85833970 TGTAGAGTAGAATTACTGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATAACCT * 85833997 TGTAGGGTAGAATTACCGAAATACCCT 1 TGTAGGGTAGAATTACCGAAATAACCT * 85834024 TGTAGGGTAGAAATACCGAAAT-ACCT 1 TGTAGGGTAGAATTACCGAAATAACCT ** 85834050 CTGTAGGGTAGAATTACCGTGATAACCT 1 -TGTAGGGTAGAATTACCGAAATAACCT * * 85834078 TGTGGGGTAAAATTACC 1 TGTAGGGTAGAATTACC 85834095 ATTTTGCCCC Statistics Matches: 135, Mismatches: 15, Indels: 4 0.88 0.10 0.03 Matches are distributed among these distances: 26 3 0.02 27 128 0.95 28 4 0.03 ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26 Consensus pattern (27 bp): TGTAGGGTAGAATTACCGAAATAACCT Found at i:85834086 original size:81 final size:81 Alignment explanation

Indices: 85833899--85834094 Score: 230 Period size: 81 Copynumber: 2.4 Consensus size: 81 85833889 TGGTTTGTAA * ** * ** * 85833899 AATTACCAAAATGCCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAGTTACTGAAA 1 AATTACCGAAATAACCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAA 85833964 TACCCCTGTAGAGTAG 66 TACCCCTGTAGAGTAG * * * * 85833980 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACCGAAA 1 AATTACCGAAATAACCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAA * * 85834045 TACCTCTGTAGGGTAG 66 TACCCCTGTAGAGTAG ** * * * 85834061 AATTACCGTGATAACCTTGTGGGGTAAAATTACC 1 AATTACCGAAATAACCCTGTAGGGTAGAATTACC 85834095 ATTTTGCCCC Statistics Matches: 97, Mismatches: 18, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 81 97 1.00 ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26 Consensus pattern (81 bp): AATTACCGAAATAACCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAAATACCGAAA TACCCCTGTAGAGTAG Found at i:85834222 original size:11 final size:11 Alignment explanation

Indices: 85834206--85834270 Score: 62 Period size: 11 Copynumber: 6.1 Consensus size: 11 85834196 ATATTGTTAT 85834206 ACATGATATGC 1 ACATGATATGC 85834217 ACATGATATG- 1 ACATGATATGC ** 85834227 TTATGATATGC 1 ACATGATATGC 85834238 ACATGATATGC 1 ACATGATATGC * * 85834249 -TATGATATAC 1 ACATGATATGC * * 85834259 TCATTATATGC 1 ACATGATATGC 85834270 A 1 A 85834271 TGGGTTGGGT Statistics Matches: 42, Mismatches: 10, Indels: 4 0.75 0.18 0.07 Matches are distributed among these distances: 10 16 0.38 11 26 0.62 ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35 Consensus pattern (11 bp): ACATGATATGC Found at i:85834269 original size:21 final size:21 Alignment explanation

Indices: 85834208--85834256 Score: 89 Period size: 21 Copynumber: 2.3 Consensus size: 21 85834198 ATTGTTATAC * 85834208 ATGATATGCACATGATATGTT 1 ATGATATGCACATGATATGCT 85834229 ATGATATGCACATGATATGCT 1 ATGATATGCACATGATATGCT 85834250 ATGATAT 1 ATGATAT 85834257 ACTCATTATA Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 27 1.00 ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37 Consensus pattern (21 bp): ATGATATGCACATGATATGCT Found at i:85834336 original size:24 final size:24 Alignment explanation

Indices: 85834304--85834350 Score: 60 Period size: 25 Copynumber: 2.0 Consensus size: 24 85834294 AGGAAGTGCA ** 85834304 AAAAGGGCTTTGCC-CCAGTTATT 1 AAAAGGGCTAGGCCTCCAGTTATT 85834327 AAAAGAGGCTAGGCCTCCAGTTAT 1 AAAAG-GGCTAGGCCTCCAGTTAT 85834351 ATGATAAAGC Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 23 5 0.25 24 7 0.35 25 8 0.40 ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26 Consensus pattern (24 bp): AAAAGGGCTAGGCCTCCAGTTATT Found at i:85841423 original size:29 final size:29 Alignment explanation

Indices: 85841368--85841444 Score: 102 Period size: 29 Copynumber: 2.7 Consensus size: 29 85841358 GTGAGCATGA * * 85841368 ATATGAATGTGA-CTGGGCCTAACGGGCC 1 ATATAAATGTGATTTGGGCCTAACGGGCC * 85841396 ATATAAATGTGATTTGGGCCTAATGGGCC 1 ATATAAATGTGATTTGGGCCTAACGGGCC * * 85841425 ATATACAGGTGATTTGGGCC 1 ATATAAATGTGATTTGGGCC 85841445 ATATGAATAT Statistics Matches: 43, Mismatches: 5, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 28 11 0.26 29 32 0.74 ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27 Consensus pattern (29 bp): ATATAAATGTGATTTGGGCCTAACGGGCC Found at i:85844117 original size:27 final size:27 Alignment explanation

Indices: 85844098--85844281 Score: 235 Period size: 27 Copynumber: 6.8 Consensus size: 27 85844088 CGATTTGTAG * * 85844098 AATTACCATTTTACCCTCGATTTATAG 1 AATTACCATTTTACCCTCGATTTACAA * * * 85844125 AATTACCGTTTCACCCTCGTTTTACAA 1 AATTACCATTTTACCCTCGATTTACAA ** * * 85844152 AATTACTGTTTTACCCTCGATTTATAG 1 AATTACCATTTTACCCTCGATTTACAA 85844179 AATTACCATTTTACCCTCGATTTACAA 1 AATTACCATTTTACCCTCGATTTACAA * 85844206 AATTATCATTTTACCCTCGATTTACAA 1 AATTACCATTTTACCCTCGATTTACAA * 85844233 AATTACCATTTTACCCTC-AGTTTGCAA 1 AATTACCATTTTACCCTCGA-TTTACAA * * 85844260 AATTATCGTTTTACCCTCGATT 1 AATTACCATTTTACCCTCGATT 85844282 GTGAAATTAC Statistics Matches: 136, Mismatches: 19, Indels: 4 0.86 0.12 0.03 Matches are distributed among these distances: 26 1 0.01 27 134 0.99 28 1 0.01 ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40 Consensus pattern (27 bp): AATTACCATTTTACCCTCGATTTACAA Found at i:85844303 original size:27 final size:27 Alignment explanation

Indices: 85844280--85844555 Score: 165 Period size: 27 Copynumber: 10.2 Consensus size: 27 85844270 TTACCCTCGA * * 85844280 TTGTGAAATTACTGAAATACCCCT-GT 1 TTGTAAAATTACTAAAATACCCCTAGT ** * 85844306 AGGATAGAATTA-TCAAAATACCCCTAGT 1 TTG-TAAAATTACT-AAAATACCCCTAGT * 85844334 TTGTAAAATTACCAAAATACCCCTAGT 1 TTGTAAAATTACTAAAATACCCCTAGT * 85844361 TTGTAAAATTACCAAAATA-CCCTAGT 1 TTGTAAAATTACTAAAATACCCCTAGT * * * 85844387 TTGTAAAATTA-TCGAAATACCACTGGT 1 TTGTAAAATTACT-AAAATACCCCTAGT * ** * 85844414 TTGTGAAATTACCGAAATA-CCCTCAAT 1 TTGTAAAATTACTAAAATACCCCT-AGT 85844441 TTGTAAAATTA-TCAAAATACCCCT-GAT 1 TTGTAAAATTACT-AAAATACCCCTAG-T ** * * 85844468 TTACAAAATTAC-AGAAATACCCTTGACT 1 TTGTAAAATTACTA-AAATACCCCT-AGT * ** * 85844496 TTCTAAAAATTA-TAGAAATACCATTGGT 1 TTGT-AAAATTACTA-AAATACCCCTAGT ** * * 85844524 TTACAAAATTACTAAAATACCCTTGGT 1 TTGTAAAATTACTAAAATACCCCTAGT 85844551 TTGTA 1 TTGTA 85844556 GATTTACCAA Statistics Matches: 196, Mismatches: 36, Indels: 35 0.73 0.13 0.13 Matches are distributed among these distances: 26 29 0.15 27 134 0.68 28 15 0.08 29 18 0.09 ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32 Consensus pattern (27 bp): TTGTAAAATTACTAAAATACCCCTAGT Found at i:85844354 original size:54 final size:53 Alignment explanation

Indices: 85844310--85844464 Score: 195 Period size: 53 Copynumber: 2.9 Consensus size: 53 85844300 CCCTGTAGGA * 85844310 TAGAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTG 1 TAGAATTACCAAAATA-CCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTG * * * * * 85844364 TAAAATTACCAAAATACCCTAGTTTGTAAAATTATCGAAATACCACTGGTTTG 1 TAGAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTG * * * 85844417 T-GAAATTACCGAAATACCCTCAATTTGTAAAATTATCAAAATACCCCT 1 TAG-AATTACCAAAATACCCT-AGTTTGTAAAATTACCAAAATACCCCT 85844465 GATTTACAAA Statistics Matches: 88, Mismatches: 11, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 53 50 0.57 54 38 0.43 ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31 Consensus pattern (53 bp): TAGAATTACCAAAATACCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTG Found at i:85844355 original size:80 final size:79 Alignment explanation

Indices: 85844271--85844465 Score: 205 Period size: 80 Copynumber: 2.4 Consensus size: 79 85844261 ATTATCGTTT * * * * 85844271 TACCCTCGATTGTGAAATTACTGAAATACCCCTGTAGGATAGAATTATCAAAATACCCCTAGTTT 1 TACCCTCGATTGTAAAATTACTAAAATACCCCTGTAGG-TAAAATTATCAAAATACCACTAGTTT 85844336 GTAAAATTACCAAAA 65 GTAAAATTACCAAAA * * * ** * * 85844351 TACCCCTAGTTTGTAAAATTACCAAAATA-CCCTAGTTTGTAAAATTATCGAAATACCACTGGTT 1 TA-CCCTCGATTGTAAAATTACTAAAATACCCCT-GTAGGTAAAATTATCAAAATACCACTAGTT * * 85844415 TGTGAAATTACCGAAA 64 TGTAAAATTACCAAAA * 85844431 TACCCTCAATTTGTAAAATTA-TCAAAATACCCCTG 1 TACCCTCGA-TTGTAAAATTACT-AAAATACCCCTG 85844466 ATTTACAAAA Statistics Matches: 93, Mismatches: 17, Indels: 10 0.77 0.14 0.08 Matches are distributed among these distances: 79 4 0.04 80 61 0.66 81 28 0.30 ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30 Consensus pattern (79 bp): TACCCTCGATTGTAAAATTACTAAAATACCCCTGTAGGTAAAATTATCAAAATACCACTAGTTTG TAAAATTACCAAAA Found at i:85844382 original size:107 final size:107 Alignment explanation

Indices: 85844271--85844523 Score: 239 Period size: 107 Copynumber: 2.3 Consensus size: 107 85844261 ATTATCGTTT * * * * 85844271 TACCCTCGATTGTGAAATTA-CTGAAATACCCCT-GTAGGAT-AGAATTATCAAAATACCC-CTA 1 TACCCTAGATTGTAAAATTATC-GAAATACCACTGGTAGG-TGA-AATTACCAAAATACCCTC-A * ** 85844332 GTTTGTAAAATTACCAAAATACCCCT-AGTTTGTAAAATTACCA-AAA 62 ATTTGTAAAATTACCAAAATACCCCTGA-TTTACAAAATTA-CAGAAA * ** * 85844378 TACCCTAGTTTGTAAAATTATCGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTT 1 TACCCTAGATTGTAAAATTATCGAAATACCACTGGTAGGTGAAATTACCAAAATACCCTCAATTT * 85844443 GTAAAATTATCAAAATACCCCTGATTTACAAAATTACAGAAA 66 GTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAA * * * * 85844485 TACCCTTGACTTTCTAAAAATTATAGAAATACCATTGGT 1 TACCCTAGA--TTGT-AAAATTATCGAAATACCACTGGT 85844524 TTACAAAATT Statistics Matches: 120, Mismatches: 17, Indels: 15 0.79 0.11 0.10 Matches are distributed among these distances: 106 2 0.02 107 87 0.73 108 7 0.06 109 3 0.03 110 21 0.17 ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31 Consensus pattern (107 bp): TACCCTAGATTGTAAAATTATCGAAATACCACTGGTAGGTGAAATTACCAAAATACCCTCAATTT GTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAA Found at i:85844477 original size:54 final size:53 Alignment explanation

Indices: 85844313--85844546 Score: 204 Period size: 54 Copynumber: 4.3 Consensus size: 53 85844303 TGTAGGATAG * * * * ** 85844313 AATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCT-AGTTTGTAA 1 AATTACCAAAATA-CCCTAATTTGTAAAATTATCAAAATACCACTGA-TTTACAA * * * *** 85844367 AATTACCAAAATACCCTAGTTTGTAAAATTATCGAAATACCACTGGTTTGTGA 1 AATTACCAAAATACCCTAATTTGTAAAATTATCAAAATACCACTGATTTACAA * * 85844420 AATTACCGAAATACCCTCAATTTGTAAAATTATCAAAATACCCCTGATTTACAA 1 AATTACCAAAATACCCT-AATTTGTAAAATTATCAAAATACCACTGATTTACAA * * * * 85844474 AATTA-CAGAAATACCCTTGACTTTCTAAAAATTAT-AGAAATACCATTGGTTTACAA 1 AATTACCA-AAATACCC-T-AATTTGT-AAAATTATCA-AAATACCACTGATTTACAA * 85844530 AATTACTAAAATACCCT 1 AATTACCAAAATACCCT 85844547 TGGTTTGTAG Statistics Matches: 151, Mismatches: 22, Indels: 13 0.81 0.12 0.07 Matches are distributed among these distances: 53 51 0.34 54 54 0.36 55 8 0.05 56 37 0.25 57 1 0.01 ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31 Consensus pattern (53 bp): AATTACCAAAATACCCTAATTTGTAAAATTATCAAAATACCACTGATTTACAA Found at i:85844644 original size:27 final size:27 Alignment explanation

Indices: 85844569--85844670 Score: 73 Period size: 27 Copynumber: 3.8 Consensus size: 27 85844559 TTACCAAAAC * * * * * 85844569 ACCCTTGTAGGATGAAATGACTAAAAT 1 ACCCCTGTAGGGTAAAATGACCATAAT * * 85844596 ACCCCTAATA-GGTAAAAAGACCATAA- 1 ACCCCT-GTAGGGTAAAATGACCATAAT * * 85844622 AGCCCCTGTAGGGTAAAGTGACCGTAAT 1 A-CCCCTGTAGGGTAAAATGACCATAAT * * 85844650 ACCCTTGTATGGTAAAATGAC 1 ACCCCTGTAGGGTAAAATGAC 85844671 GAATATGTCC Statistics Matches: 57, Mismatches: 14, Indels: 8 0.72 0.18 0.10 Matches are distributed among these distances: 26 3 0.05 27 51 0.89 28 3 0.05 ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23 Consensus pattern (27 bp): ACCCCTGTAGGGTAAAATGACCATAAT Found at i:85845403 original size:20 final size:20 Alignment explanation

Indices: 85845394--85845444 Score: 102 Period size: 20 Copynumber: 2.5 Consensus size: 20 85845384 TTGATATGAT 85845394 ATGCACATGATATGTATAAA 1 ATGCACATGATATGTATAAA 85845414 ATGCACATGATATGTATAAA 1 ATGCACATGATATGTATAAA 85845434 ATGCACATGAT 1 ATGCACATGAT 85845445 GTATTCATAA Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 31 1.00 ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29 Consensus pattern (20 bp): ATGCACATGATATGTATAAA Found at i:85845558 original size:52 final size:51 Alignment explanation

Indices: 85845502--85845629 Score: 208 Period size: 52 Copynumber: 2.5 Consensus size: 51 85845492 GCAAAAGGAT 85845502 TTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGC 1 TTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCGAAAAGGGC * 85845554 TTATGCCCTAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGC 1 TTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGC 85845605 TT-TGCCCCAG-TTATT-AAAAGAGGCT 1 TTATGCCCCAGTTTATTGAAAAG-GGCT 85845630 AGGCCTTCAG Statistics Matches: 73, Mismatches: 2, Indels: 5 0.91 0.03 0.06 Matches are distributed among these distances: 48 5 0.07 49 9 0.12 50 7 0.10 51 25 0.34 52 27 0.37 ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29 Consensus pattern (51 bp): TTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGC Found at i:85845591 original size:25 final size:26 Alignment explanation

Indices: 85845502--85845629 Score: 174 Period size: 26 Copynumber: 5.0 Consensus size: 26 85845492 GCAAAAGGAT 85845502 TTATGCCCCAGTTTATTGAAAAGGGC 1 TTATGCCCCAGTTTATTGAAAAGGGC ** 85845528 TTATGCCCCAGTTTACCGAAAAGGGC 1 TTATGCCCCAGTTTATTGAAAAGGGC * 85845554 TTATGCCCTAGTTTATTGAAAAGGGC 1 TTATGCCCCAGTTTATTGAAAAGGGC ** 85845580 TT-TGCCCCAGTTTACCGAAAAGGGC 1 TTATGCCCCAGTTTATTGAAAAGGGC 85845605 TT-TGCCCCAG-TTATT-AAAAGAGGC 1 TTATGCCCCAGTTTATTGAAAAG-GGC 85845629 T 1 T 85845630 AGGCCTTCAG Statistics Matches: 91, Mismatches: 10, Indels: 4 0.87 0.10 0.04 Matches are distributed among these distances: 23 5 0.05 24 7 0.08 25 30 0.33 26 49 0.54 ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29 Consensus pattern (26 bp): TTATGCCCCAGTTTATTGAAAAGGGC Found at i:85845821 original size:42 final size:42 Alignment explanation

Indices: 85845762--85845853 Score: 130 Period size: 42 Copynumber: 2.2 Consensus size: 42 85845752 TAGTCTCCCC * ** * * 85845762 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG 1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATGG * 85845804 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATGG 1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATGG 85845846 AAATGGGC 1 AAATGGGC 85845854 CTATGGGCCA Statistics Matches: 44, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 42 44 1.00 ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34 Consensus pattern (42 bp): AAATGGGCTTGCATACATCCATTGACATTACATATGATATGG Found at i:85845913 original size:31 final size:31 Alignment explanation

Indices: 85845877--85845955 Score: 122 Period size: 31 Copynumber: 2.5 Consensus size: 31 85845867 CGTTTACAGT * * 85845877 AAAGGCTTCGGCCTAGTGAAATTATTTATGA 1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA * 85845908 AAAGGCTTCGGCCCAGTGATATGATTTATGA 1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA * 85845939 AAAGGCTTCGGCTCAGT 1 AAAGGCTTCGGCCCAGT 85845956 AACCGTTAAA Statistics Matches: 44, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 31 44 1.00 ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTGAAATGATTTATGA Found at i:85855366 original size:34 final size:34 Alignment explanation

Indices: 85855323--85855405 Score: 123 Period size: 34 Copynumber: 2.5 Consensus size: 34 85855313 AGAGTGAATA * 85855323 CATTT-AGTAACAGTAGCAGTTTGGGCATTAGCC 1 CATTTCAGTAACAGTAGCAGTCTGGGCATTAGCC * * 85855356 CATTTCAGTAACAGTAGGAGTCTGGGCTTTAGCC 1 CATTTCAGTAACAGTAGCAGTCTGGGCATTAGCC * 85855390 CATTTCAGTAATAGTA 1 CATTTCAGTAACAGTA 85855406 ATTAGTGCAG Statistics Matches: 45, Mismatches: 4, Indels: 1 0.90 0.08 0.02 Matches are distributed among these distances: 33 5 0.11 34 40 0.89 ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31 Consensus pattern (34 bp): CATTTCAGTAACAGTAGCAGTCTGGGCATTAGCC Found at i:85855450 original size:18 final size:18 Alignment explanation

Indices: 85855395--85855453 Score: 64 Period size: 18 Copynumber: 3.3 Consensus size: 18 85855385 TAGCCCATTT * * 85855395 CAGTAATAGTAATTAGTG 1 CAGTAACAGTAATCAGTG * * * 85855413 CAGTAACAATAAGCAATG 1 CAGTAACAGTAATCAGTG * 85855431 CAGTAACAGTAATCGGTG 1 CAGTAACAGTAATCAGTG 85855449 CAGTA 1 CAGTA 85855454 TGCAAGCATA Statistics Matches: 32, Mismatches: 9, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 18 32 1.00 ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24 Consensus pattern (18 bp): CAGTAACAGTAATCAGTG Found at i:85855909 original size:27 final size:27 Alignment explanation

Indices: 85855797--85855909 Score: 97 Period size: 27 Copynumber: 4.2 Consensus size: 27 85855787 AACAAATCTA * ** 85855797 TCATTTTACCTTACT-A-GGTATTTTAG 1 TCATTTTACCCTA-TGAGGGTATTTCGG * * 85855823 TCATTTTACCATA-CAGGGATATTTCGG 1 TCATTTTACCCTATGAGGG-TATTTCGG * * * * * 85855850 TCGTTCTGCCCTATGGGGGTATTTCGA 1 TCATTTTACCCTATGAGGGTATTTCGG 85855877 TCATTTTACCCTATGAGGGTATTTCGG 1 TCATTTTACCCTATGAGGGTATTTCGG 85855904 TCATTT 1 TCATTT 85855910 CATCACAAAA Statistics Matches: 68, Mismatches: 15, Indels: 7 0.76 0.17 0.08 Matches are distributed among these distances: 25 1 0.01 26 14 0.21 27 50 0.74 28 3 0.04 ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42 Consensus pattern (27 bp): TCATTTTACCCTATGAGGGTATTTCGG Found at i:85856017 original size:27 final size:27 Alignment explanation

Indices: 85855903--85856019 Score: 144 Period size: 27 Copynumber: 4.3 Consensus size: 27 85855893 GGGTATTTCG * ** 85855903 GTCATTTCATCACAAAAGGGAAAAATC 1 GTCATTTTATCACATGAGGGAAAAATC * * * 85855930 ATTATTTTATCACATGAGGGAAAAATT 1 GTCATTTTATCACATGAGGGAAAAATC * 85855957 GTCGTTTTATCACATGAGGGAAAAATC 1 GTCATTTTATCACATGAGGGAAAAATC * * 85855984 GTTATTTTATCACATGAGGGGAAAATC 1 GTCATTTTATCACATGAGGGAAAAATC * 85856011 GCCATTTTA 1 GTCATTTTA 85856020 ATCCCATAGA Statistics Matches: 75, Mismatches: 15, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 27 75 1.00 ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32 Consensus pattern (27 bp): GTCATTTTATCACATGAGGGAAAAATC Found at i:85856808 original size:26 final size:26 Alignment explanation

Indices: 85856779--85856860 Score: 155 Period size: 26 Copynumber: 3.2 Consensus size: 26 85856769 TGATACAAAT 85856779 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * 85856805 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATGGGTTAGGTAAATGTTCCA 85856831 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 85856857 TGAT 1 TGAT 85856861 GGGAATTTCA Statistics Matches: 54, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 54 1.00 ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTCCA Found at i:85863895 original size:26 final size:26 Alignment explanation

Indices: 85863866--85863947 Score: 155 Period size: 26 Copynumber: 3.2 Consensus size: 26 85863856 TGATACAAAT 85863866 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA * 85863892 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATGGGTTAGGTAAATGTTCCA 85863918 TGATAATGGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTCCA 85863944 TGAT 1 TGAT 85863948 GGGAATTTCA Statistics Matches: 54, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 54 1.00 ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTCCA Found at i:85867768 original size:43 final size:43 Alignment explanation

Indices: 85867720--85867881 Score: 161 Period size: 44 Copynumber: 3.8 Consensus size: 43 85867710 AAAGCTCGTA * * 85867720 CAATGCCAACGTCCCAGACGTGGACTTACATGTAATCAAATAT 1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATAT * * * * * 85867763 CAATGCC-ACTGTCCTAAAAAG-GGTCTTATACGAAATCAAATA- 1 CAATGCCAAC-GTCC-CAGACGTGGTCTTACACGTAATCAAATAT * * * * 85867805 CAATGCCAATGTCCCAGACATGGTCTTACACATAGATCATAA-GT 1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTA-ATCA-AATAT 85867849 CAATGCCAACGTCCCAGACGTGGTCTTACACGT 1 CAATGCCAACGTCCCAGACGTGGTCTTACACGT 85867882 TAACACATAT Statistics Matches: 93, Mismatches: 19, Indels: 13 0.74 0.15 0.10 Matches are distributed among these distances: 41 2 0.02 42 23 0.25 43 33 0.35 44 35 0.38 ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23 Consensus pattern (43 bp): CAATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATAT Found at i:85872726 original size:15 final size:15 Alignment explanation

Indices: 85872682--85872751 Score: 61 Period size: 15 Copynumber: 4.7 Consensus size: 15 85872672 AGAATAGGAC * ** 85872682 AGAGTAGAACAGAGC 1 AGAGCAGAACAGAAT 85872697 AGAGCAGAACAGAAT 1 AGAGCAGAACAGAAT * 85872712 AGAGCAGAACTGAAT 1 AGAGCAGAACAGAAT * * 85872727 AGAACTA-AACAGAGT 1 AGAGC-AGAACAGAAT * 85872742 GGAGCAGAAC 1 AGAGCAGAAC 85872752 GGATCAGAGC Statistics Matches: 44, Mismatches: 9, Indels: 4 0.77 0.16 0.07 Matches are distributed among these distances: 14 1 0.02 15 42 0.95 16 1 0.02 ACGTcount: A:0.49, C:0.14, G:0.29, T:0.09 Consensus pattern (15 bp): AGAGCAGAACAGAAT Found at i:85873812 original size:29 final size:29 Alignment explanation

Indices: 85873775--85873830 Score: 94 Period size: 29 Copynumber: 1.9 Consensus size: 29 85873765 TACAGCCTGG 85873775 CACACAGCTTGGAACATGGCCATGTGGCT 1 CACACAGCTTGGAACATGGCCATGTGGCT * * 85873804 CACACAGCTTGGCATATGGCCATGTGG 1 CACACAGCTTGGAACATGGCCATGTGG 85873831 TGTCGACTAT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 29 25 1.00 ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21 Consensus pattern (29 bp): CACACAGCTTGGAACATGGCCATGTGGCT Found at i:85876620 original size:24 final size:24 Alignment explanation

Indices: 85876593--85876694 Score: 150 Period size: 24 Copynumber: 4.2 Consensus size: 24 85876583 AAGGCTGTCA * 85876593 GGAGAAGATTTAAGAGCTGATAAG 1 GGAGAAGATTTAGGAGCTGATAAG * 85876617 GGAGATGATTTAGGAGCTGATAAG 1 GGAGAAGATTTAGGAGCTGATAAG * * 85876641 GGAGAGGATGTAGGAGCTGATAAG 1 GGAGAAGATTTAGGAGCTGATAAG * * 85876665 GGAGAGGATTTAGGAGCTGATTAG 1 GGAGAAGATTTAGGAGCTGATAAG 85876689 GGAGAA 1 GGAGAA 85876695 TGGTGTTGGC Statistics Matches: 71, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 24 71 1.00 ACGTcount: A:0.35, C:0.04, G:0.40, T:0.21 Consensus pattern (24 bp): GGAGAAGATTTAGGAGCTGATAAG Found at i:85876692 original size:12 final size:12 Alignment explanation

Indices: 85876606--85876692 Score: 54 Period size: 12 Copynumber: 7.2 Consensus size: 12 85876596 GAAGATTTAA * 85876606 GAGCTGATAAGG 1 GAGCTGATTAGG * 85876618 GAGATGATTTA-G 1 GAGCTGA-TTAGG * 85876630 GAGCTGATAAGG 1 GAGCTGATTAGG ** 85876642 GAGAGGATGTA-G 1 GAGCTGAT-TAGG * 85876654 GAGCTGATAAGG 1 GAGCTGATTAGG ** 85876666 GAGAGGATTTA-G 1 GAGCTGA-TTAGG 85876678 GAGCTGATTAGG 1 GAGCTGATTAGG 85876690 GAG 1 GAG 85876693 AATGGTGTTG Statistics Matches: 54, Mismatches: 15, Indels: 12 0.67 0.19 0.15 Matches are distributed among these distances: 11 6 0.11 12 43 0.80 13 5 0.09 ACGTcount: A:0.32, C:0.05, G:0.43, T:0.21 Consensus pattern (12 bp): GAGCTGATTAGG Found at i:85878207 original size:54 final size:53 Alignment explanation

Indices: 85878123--85878233 Score: 177 Period size: 54 Copynumber: 2.1 Consensus size: 53 85878113 AGGAAGTGTC * 85878123 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTGCCACATATATCTGTT 1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGCCACAT-TATCTGTT * * * 85878177 CTGGTGGCTCTGCCACAATTATCTGTTCTGGTGACACTGTCACATTATCTGTT 1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGCCACATTATCTGTT 85878230 CTGG 1 CTGG 85878234 CAGCCATGCT Statistics Matches: 53, Mismatches: 4, Indels: 1 0.91 0.07 0.02 Matches are distributed among these distances: 53 12 0.23 54 41 0.77 ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35 Consensus pattern (53 bp): CTGGTGGCTATGCCACAATTATCTGATCTGGTGACACTGCCACATTATCTGTT Found at i:85878230 original size:26 final size:26 Alignment explanation

Indices: 85878123--85878233 Score: 143 Period size: 27 Copynumber: 4.2 Consensus size: 26 85878113 AGGAAGTGTC * 85878123 CTGGTGGCTA-TGCCACAATTATCTGAT 1 CTGGTGGC-ACTGCCAC-ATTATCTGTT 85878150 CTGGTGGCACTGCCACATATATCTGTT 1 CTGGTGGCACTGCCACAT-TATCTGTT * 85878177 CTGGTGGCTCTGCCACAATTATCTGTT 1 CTGGTGGCACTGCCAC-ATTATCTGTT * * 85878204 CTGGTGACACTGTCACATTATCTGTT 1 CTGGTGGCACTGCCACATTATCTGTT 85878230 CTGG 1 CTGG 85878234 CAGCCATGCT Statistics Matches: 76, Mismatches: 5, Indels: 7 0.86 0.06 0.08 Matches are distributed among these distances: 26 17 0.22 27 57 0.75 28 2 0.03 ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35 Consensus pattern (26 bp): CTGGTGGCACTGCCACATTATCTGTT Found at i:85879522 original size:16 final size:16 Alignment explanation

Indices: 85879498--85879531 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 85879488 TCTTTTAGTT * 85879498 TTTTTTTTTAATTTTA 1 TTTTGTTTTAATTTTA 85879514 TTTTGTTTTAATTTTA 1 TTTTGTTTTAATTTTA 85879530 TT 1 TT 85879532 AATTTAACAT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79 Consensus pattern (16 bp): TTTTGTTTTAATTTTA Found at i:85882291 original size:40 final size:39 Alignment explanation

Indices: 85882229--85882368 Score: 167 Period size: 40 Copynumber: 3.5 Consensus size: 39 85882219 TAATTATTGA * * 85882229 TGATTGCAAATAGGTGGCCCTATTTGTACTTTGGTACCCT 1 TGATTGCACATACGT-GCCCTATTTGTACTTTGGTACCCT 85882269 TGATTGCACATACGTGCTCCTATTTGTA-TGTTGGTACCCCT 1 TGATTGCACATACGTGC-CCTATTTGTACT-TTGGTA-CCCT * * 85882310 T-ATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCC 1 TGATTGCACATACGTG-CCCTATTTGTACTTTGGTACCCT * * 85882349 TGAATGCACTTACGTGCCCT 1 TGATTGCACATACGTGCCCT 85882369 TGTTTATACT Statistics Matches: 88, Mismatches: 6, Indels: 13 0.82 0.06 0.12 Matches are distributed among these distances: 39 11 0.12 40 70 0.80 41 7 0.08 ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36 Consensus pattern (39 bp): TGATTGCACATACGTGCCCTATTTGTACTTTGGTACCCT Found at i:85882379 original size:40 final size:40 Alignment explanation

Indices: 85882246--85882393 Score: 136 Period size: 40 Copynumber: 3.7 Consensus size: 40 85882236 AAATAGGTGG * * * * 85882246 CCCTATTTGTACTTTGGTACCCTTGATTGCACATACGTGC 1 CCCTATTTATACTTCGGTACCCCTGAATGCACATACGTGC * * * * * 85882286 TCCTATTTGTA-TGTTGGTACCCCTTATTGCACATACGTGC 1 CCCTATTTATACT-TCGGTACCCCTGAATGCACATACGTGC * * 85882326 CCCTATTTGTACTTCGGTACCCCTGAATGCACTTACGTGC 1 CCCTATTTATACTTCGGTACCCCTGAATGCACATACGTGC * * * * * 85882366 CCTTGTTTATACTTTGTTAACCCTGAAT 1 CCCTATTTATACTTCGGTACCCCTGAAT 85882394 CAAATAGTAT Statistics Matches: 92, Mismatches: 14, Indels: 4 0.84 0.13 0.04 Matches are distributed among these distances: 39 1 0.01 40 90 0.98 41 1 0.01 ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39 Consensus pattern (40 bp): CCCTATTTATACTTCGGTACCCCTGAATGCACATACGTGC Found at i:85884306 original size:39 final size:39 Alignment explanation

Indices: 85884219--85884453 Score: 181 Period size: 39 Copynumber: 6.0 Consensus size: 39 85884209 AATAGAAATA * * * 85884219 CAGTGATTATTTAAGCTACGTGCCTAGCAGGCTGTATTG- 1 CAGTGATTATTTGAGCTATGTGCCTAGCAGGCTGT-GTGC * 85884258 -AGGTAATTATTTGAGCTATGTGCCTAGCAGGCTGTGTGC 1 CA-GTGATTATTTGAGCTATGTGCCTAGCAGGCTGTGTGC * * * * * * 85884297 CAATGATTA-TTCAGGCTATATGCCTAGAAAGCTATGTGC 1 CAGTGATTATTTGA-GCTATGTGCCTAGCAGGCTGTGTGC * * * 85884336 CAGTGATTATTTGGGCTATTTGCCTACCAGGCTGTGTGC 1 CAGTGATTATTTGAGCTATGTGCCTAGCAGGCTGTGTGC * * * * * * 85884375 TAGTGATTA-TTCAGGCTTTGTGCCTAGTAGGATGTGTGT 1 CAGTGATTATTTGA-GCTATGTGCCTAGCAGGCTGTGTGC ** * * * * 85884414 TGGTGATTAATCGGGCTATGTGCCTAGCAGGTTGTGTGC 1 CAGTGATTATTTGAGCTATGTGCCTAGCAGGCTGTGTGC 85884453 C 1 C 85884454 GGCGTATTGA Statistics Matches: 152, Mismatches: 37, Indels: 14 0.75 0.18 0.07 Matches are distributed among these distances: 38 8 0.05 39 140 0.92 40 4 0.03 ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34 Consensus pattern (39 bp): CAGTGATTATTTGAGCTATGTGCCTAGCAGGCTGTGTGC Found at i:85884321 original size:78 final size:79 Alignment explanation

Indices: 85884239--85884453 Score: 215 Period size: 78 Copynumber: 2.8 Consensus size: 79 85884229 TTAAGCTACG * * * 85884239 TGCCTAGCAGGCTGTATTG-AGGTAATTATTTGAGCTATGTGCCTAGCAGGCTGTGTGCCAATGA 1 TGCCTAGAAGGCTGTATTGCAGGTGATTATTTGGGCTATGTGCCTAGCAGGCTGTGTGCCAATGA 85884303 TTATTCAGGCTATA 66 TTATTCAGGCTATA * * * * * 85884317 TGCCTAGAAAGC--TATGTGCCA-GTGATTATTTGGGCTATTTGCCTACCAGGCTGTGTGCTAGT 1 TGCCTAGAAGGCTGTAT-TG-CAGGTGATTATTTGGGCTATGTGCCTAGCAGGCTGTGTGCCAAT * * 85884379 GATTATTCAGGCTTTG 64 GATTATTCAGGCTATA * * * ** * * * 85884395 TGCCTAGTAGGATGT-GTGTTGGTGATTAATCGGGCTATGTGCCTAGCAGGTTGTGTGCC 1 TGCCTAGAAGGCTGTATTGCAGGTGATTATTTGGGCTATGTGCCTAGCAGGCTGTGTGCC 85884454 GGCGTATTGA Statistics Matches: 109, Mismatches: 22, Indels: 12 0.76 0.15 0.08 Matches are distributed among these distances: 76 3 0.03 77 2 0.02 78 102 0.94 79 1 0.01 80 1 0.01 ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34 Consensus pattern (79 bp): TGCCTAGAAGGCTGTATTGCAGGTGATTATTTGGGCTATGTGCCTAGCAGGCTGTGTGCCAATGA TTATTCAGGCTATA Found at i:85889667 original size:15 final size:15 Alignment explanation

Indices: 85889635--85889663 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 85889625 ATTTTCAGTG 85889635 TTTATTATGTGTGAA 1 TTTATTATGTGTGAA 85889650 TTTA-TATGTGTGAA 1 TTTATTATGTGTGAA 85889664 ATTTCCGTGC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 10 0.71 15 4 0.29 ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52 Consensus pattern (15 bp): TTTATTATGTGTGAA Found at i:85889978 original size:13 final size:13 Alignment explanation

Indices: 85889957--85889986 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 85889947 CTTTTGACTG * 85889957 AAAGTAAGAAAAT 1 AAAGAAAGAAAAT 85889970 AAAGAAAGAAAAT 1 AAAGAAAGAAAAT 85889983 AAAG 1 AAAG 85889987 CTTTAGGTAT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10 Consensus pattern (13 bp): AAAGAAAGAAAAT Found at i:85890836 original size:43 final size:44 Alignment explanation

Indices: 85890788--85890957 Score: 142 Period size: 43 Copynumber: 4.0 Consensus size: 44 85890778 AGGGTTTCCA * 85890788 ATATGTG-TTCTAGTGTAAGACCATGTCTAGGACGTTGGCATCG 1 ATATGTGATTCTAGTGTAAGACCATGTCTGGGACGTTGGCATCG * * 85890831 ATATGTGATT-TCA-AGTAAGACCATGTCTGGGACATTGGCATCG 1 ATATGTGATTCT-AGTGTAAGACCATGTCTGGGACGTTGGCATCG * * * 85890874 -TAATTGTGATTC--GTGTAAAACCCTATCTGGGACAG-TGGCATCG 1 AT-A-TGTGATTCTAGTGTAAGACCATGTCTGGGAC-GTTGGCATCG * * * * 85890917 ACATGTGA--CTACATGTAAGACCACGTCTGGAACGTTGGCAT 1 ATATGTGATTCTA-GTGTAAGACCATGTCTGGGACGTTGGCAT 85890958 TGTACGGTAT Statistics Matches: 100, Mismatches: 15, Indels: 24 0.72 0.11 0.17 Matches are distributed among these distances: 40 1 0.01 42 7 0.07 43 82 0.82 44 10 0.10 ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29 Consensus pattern (44 bp): ATATGTGATTCTAGTGTAAGACCATGTCTGGGACGTTGGCATCG Found at i:85894832 original size:27 final size:27 Alignment explanation

Indices: 85894770--85894881 Score: 129 Period size: 27 Copynumber: 4.1 Consensus size: 27 85894760 AGCATGGCTG ** * 85894770 CCAGAACAGATAA-TGTGATAGAGTCA 1 CCAGAACAGATAATTGTGGCAGAGCCA * * 85894796 CGAGATACAGATAATCGTGGCAGAGCCA 1 CCAGA-ACAGATAATTGTGGCAGAGCCA 85894824 CCAGAACAGA-AATATGTGGCAGAGCCA 1 CCAGAACAGATAAT-TGTGGCAGAGCCA * * 85894851 CCAGATCAGATAATTGTGGCATAGCCA 1 CCAGAACAGATAATTGTGGCAGAGCCA 85894878 CCAG 1 CCAG 85894882 GACGCTTCCT Statistics Matches: 73, Mismatches: 9, Indels: 7 0.82 0.10 0.08 Matches are distributed among these distances: 26 7 0.10 27 50 0.68 28 16 0.22 ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16 Consensus pattern (27 bp): CCAGAACAGATAATTGTGGCAGAGCCA Found at i:85894861 original size:54 final size:54 Alignment explanation

Indices: 85894770--85894881 Score: 145 Period size: 54 Copynumber: 2.1 Consensus size: 54 85894760 AGCATGGCTG * * * * 85894770 CCAGAACAGATAATGTGATAGAGTCACGAGATACAGATAATCGTGGCAGAGCCA 1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA * * * 85894824 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA 1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA 85894878 CCAG 1 CCAG 85894882 GACGCTTCCT Statistics Matches: 50, Mismatches: 7, Indels: 2 0.85 0.12 0.03 Matches are distributed among these distances: 54 34 0.68 55 16 0.32 ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16 Consensus pattern (54 bp): CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA Found at i:85898782 original size:41 final size:43 Alignment explanation

Indices: 85898677--85898923 Score: 240 Period size: 45 Copynumber: 5.7 Consensus size: 43 85898667 GATATGTTTT ** * 85898677 TTCGTGTAAGACCACGTCTGGGATGTTGGCATCGATATATGTGG 1 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATAT-TGA * * 85898721 TTACGTGTAAGACCATGTCTGGGACATCGGCATCG-TA-ATTGA 1 TT-CGTGTAAGACCACGTCTGGGACATTGGCATCGATATATTGA * * 85898763 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATAGATGG 1 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATA-TTGA * 85898807 TTACGTGTAAGACCATGTCTGGGACATAT-GCATCG-TAT-TTGA 1 TT-CGTGTAAGACCACGTCTGGGACAT-TGGCATCGATATATTGA * * 85898849 TTCATGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGA--GA 1 TTCGTGTAAGACCAC-GTCTGGGACATTGGCATCGATAT-ATTGA * * * * 85898891 TAGCATGTAAGACCCCGTTTGGGACATTGGCAT 1 T-TCGTGTAAGACCACGTCTGGGACATTGGCAT 85898924 TTTTGGATAT Statistics Matches: 172, Mismatches: 18, Indels: 27 0.79 0.08 0.12 Matches are distributed among these distances: 40 1 0.01 41 56 0.33 42 16 0.09 43 29 0.17 44 12 0.07 45 57 0.33 46 1 0.01 ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29 Consensus pattern (43 bp): TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATATTGA Found at i:85898822 original size:86 final size:86 Alignment explanation

Indices: 85898677--85898891 Score: 326 Period size: 86 Copynumber: 2.5 Consensus size: 86 85898667 GATATGTTTT ** 85898677 TTCGTGTAAGACCACGTCTGGGATGTTGGCATCGATATATG-TGGTTACGTGTAAGACCATGTCT 1 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATA-GATGGTTACGTGTAAGACCATGTCT * 85898741 GGGACATCGGCATCGTAATTGA 65 GGGACATAGGCATCGTAATTGA 85898763 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATAGATGGTTACGTGTAAGACCATGTCTG 1 TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATAGATGGTTACGTGTAAGACCATGTCTG * * 85898828 GGACATATGCATCGTATTTGA 66 GGACATAGGCATCGTAATTGA * * 85898849 TTCATGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGAGAT 1 TTCGTGTAAGACCAC-GTCTGGGACATTGGCATCGATAT-AGAT 85898892 AGCATGTAAG Statistics Matches: 119, Mismatches: 7, Indels: 5 0.91 0.05 0.04 Matches are distributed among these distances: 85 2 0.02 86 113 0.95 87 4 0.03 ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30 Consensus pattern (86 bp): TTCGTGTAAGACCACGTCTGGGACATTGGCATCGATATAGATGGTTACGTGTAAGACCATGTCTG GGACATAGGCATCGTAATTGA Found at i:85901866 original size:16 final size:15 Alignment explanation

Indices: 85901841--85901871 Score: 53 Period size: 16 Copynumber: 2.0 Consensus size: 15 85901831 AACATCTCAG 85901841 AAAAATAAAGAATAC 1 AAAAATAAAGAATAC 85901856 AAAACATAAAGAATAC 1 AAAA-ATAAAGAATAC 85901872 CCAAAACTCC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 4 0.27 16 11 0.73 ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13 Consensus pattern (15 bp): AAAAATAAAGAATAC Found at i:85906883 original size:27 final size:26 Alignment explanation

Indices: 85906868--85906935 Score: 82 Period size: 27 Copynumber: 2.5 Consensus size: 26 85906858 ATTAAGTCCG 85906868 CACACTCAGTGCTATATAATCAACTCA 1 CACACTCAGTGCTATAT-ATCAACTCA * * 85906895 CACACTTAGTGCTATATAATCAAACTCG 1 CACACTCAGTGCTATAT-ATC-AACTCA * 85906923 CACACTTAGTGCT 1 CACACTCAGTGCT 85906936 GTACAATTTA Statistics Matches: 38, Mismatches: 2, Indels: 1 0.93 0.05 0.02 Matches are distributed among these distances: 27 20 0.53 28 18 0.47 ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28 Consensus pattern (26 bp): CACACTCAGTGCTATATATCAACTCA Found at i:85906929 original size:28 final size:28 Alignment explanation

Indices: 85906866--85906963 Score: 126 Period size: 28 Copynumber: 3.5 Consensus size: 28 85906856 ATATTAAGTC * 85906866 CGCACACTCAGTGCTATATAATC-AACT 1 CGCACACTTAGTGCTATATAATCAAACT * 85906893 CACACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 85906921 CGCACACTTAGTGCTGTACAATTTAAACC 1 CGCACACTTAGTGCTATATAA-TCAAACT 85906950 CGCACACTTAGTGC 1 CGCACACTTAGTGC 85906964 CAATCTAATG Statistics Matches: 62, Mismatches: 7, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 27 21 0.34 28 22 0.35 29 19 0.31 ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:85911152 original size:15 final size:15 Alignment explanation

Indices: 85911120--85911148 Score: 51 Period size: 14 Copynumber: 2.0 Consensus size: 15 85911110 ACTTTCTATG 85911120 TTTATTATGTGTGAA 1 TTTATTATGTGTGAA 85911135 TTTATT-TGTGTGAA 1 TTTATTATGTGTGAA 85911149 ATTTTCGTGC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 8 0.57 15 6 0.43 ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55 Consensus pattern (15 bp): TTTATTATGTGTGAA Found at i:85912363 original size:41 final size:44 Alignment explanation

Indices: 85912260--85912441 Score: 187 Period size: 45 Copynumber: 4.2 Consensus size: 44 85912250 ATGTGTTTTT * * * * * 85912260 GTGTAAGACCGCATCTGGGACGTTGGCATCGATATATGTCGTTTT 1 GTGTAAGACCACATCTGGGACATCGGCATCGATATATGT-GATTC ** * 85912305 GTGTAAGACCATGTCTGGGACATCAGCATCG-TAT-T-TGATTC 1 GTGTAAGACCACATCTGGGACATCGGCATCGATATATGTGATTC * * * 85912346 GTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTGGTTAC 1 GTGTAAGACCACATCTGGGACATCGGCATCGATATATGTGATT-C * 85912391 GTGTAAGACCACGTCTGGGACATCGGCATCG-TAT-T-TGATTC 1 GTGTAAGACCACATCTGGGACATCGGCATCGATATATGTGATTC * 85912432 ATGTAAGACC 1 GTGTAAGACC 85912442 CTGTCTAGGA Statistics Matches: 114, Mismatches: 19, Indels: 12 0.79 0.13 0.08 Matches are distributed among these distances: 41 39 0.34 42 8 0.07 43 3 0.03 44 10 0.09 45 54 0.47 ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30 Consensus pattern (44 bp): GTGTAAGACCACATCTGGGACATCGGCATCGATATATGTGATTC Found at i:85912407 original size:86 final size:86 Alignment explanation

Indices: 85912260--85912441 Score: 301 Period size: 86 Copynumber: 2.1 Consensus size: 86 85912250 ATGTGTTTTT * ** * 85912260 GTGTAAGACCGCATCTGGGACGTTGGCATCGATATATGTCGTTTTGTGTAAGACCATGTCTGGGA 1 GTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTCGTTACGTGTAAGACCACGTCTGGGA 85912325 CATCAGCATCGTATTTGATTC 66 CATCAGCATCGTATTTGATTC * 85912346 GTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCTGGGA 1 GTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTCGTTACGTGTAAGACCACGTCTGGGA * 85912411 CATCGGCATCGTATTTGATTC 66 CATCAGCATCGTATTTGATTC * 85912432 ATGTAAGACC 1 GTGTAAGACC 85912442 CTGTCTAGGA Statistics Matches: 89, Mismatches: 7, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 86 89 1.00 ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30 Consensus pattern (86 bp): GTGTAAGACCACATCTGGGACGTTGGCATCGATATATGTCGTTACGTGTAAGACCACGTCTGGGA CATCAGCATCGTATTTGATTC Found at i:85912459 original size:86 final size:86 Alignment explanation

Indices: 85912261--85912495 Score: 273 Period size: 86 Copynumber: 2.8 Consensus size: 86 85912251 TGTGTTTTTG * * * * ** * 85912261 TGTAAGACCGCATCTGGGACGTTGGCATCGATATATGTCGTTTTGTGTAAGACCATGTCTGGGAC 1 TGTAAGACCACATCTAGGAAGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCTGGGAC * 85912326 ATCAGCATCGTATTTGATTCG 66 ATCAGCATCGTATTTGATTCA * * 85912347 TGTAAGACCACATCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCTGGGAC 1 TGTAAGACCACATCTAGGAAGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCTGGGAC * 85912412 ATCGGCATCGTATTTGATTCA 66 ATCAGCATCGTATTTGATTCA * * * * 85912433 TGTAAGACC-CTGTCTAGGATAG-TGGCATCG--ATATG-GGATAGCATGTAAGACCACATCTGG 1 TGTAAGACCAC-ATCTAGGA-AGTTGGCATCGATATATGTGGTTA-CGTGTAAGACCACGTCTGG 85912493 GAC 63 GAC 85912496 GTTGGCATTG Statistics Matches: 133, Mismatches: 13, Indels: 8 0.86 0.08 0.05 Matches are distributed among these distances: 83 4 0.03 84 25 0.19 85 1 0.01 86 102 0.77 87 1 0.01 ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29 Consensus pattern (86 bp): TGTAAGACCACATCTAGGAAGTTGGCATCGATATATGTGGTTACGTGTAAGACCACGTCTGGGAC ATCAGCATCGTATTTGATTCA Found at i:85915067 original size:27 final size:27 Alignment explanation

Indices: 85915008--85915081 Score: 87 Period size: 27 Copynumber: 2.8 Consensus size: 27 85914998 TTGGAGGAAG * 85915008 TACTG-TACTGGTGGCTTTGCCATAAC 1 TACTGTTACTGGTGGCTTTGCCACAAC * ** 85915034 TATTGTTACTGGTGGCTTTGCCACATT 1 TACTGTTACTGGTGGCTTTGCCACAAC ** 85915061 TACTGTTACTGGCAGCTTTGC 1 TACTGTTACTGGTGGCTTTGC 85915082 TGCGATATTG Statistics Matches: 40, Mismatches: 7, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 26 4 0.10 27 36 0.90 ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39 Consensus pattern (27 bp): TACTGTTACTGGTGGCTTTGCCACAAC Found at i:85936587 original size:15 final size:15 Alignment explanation

Indices: 85936567--85936609 Score: 68 Period size: 15 Copynumber: 2.9 Consensus size: 15 85936557 TAGTGTAATT * 85936567 TGGATTTCCTTATCA 1 TGGATTTCTTTATCA * 85936582 TGGATTTCTTTATCT 1 TGGATTTCTTTATCA 85936597 TGGATTTCTTTAT 1 TGGATTTCTTTAT 85936610 TCTGGGCTTC Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 26 1.00 ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56 Consensus pattern (15 bp): TGGATTTCTTTATCA Found at i:85941574 original size:42 final size:43 Alignment explanation

Indices: 85941526--85941630 Score: 142 Period size: 44 Copynumber: 2.4 Consensus size: 43 85941516 GATGCCACAA * * * * 85941526 TCCCAGAGATGGTCTTACAC-GAAATCATATA-CGATGCCTATG 1 TCCCAGATATGGTCTTACACGGAAATCACA-AGCGATGCCAACG 85941568 TCCCAGATATGGTCTTACACGGAAATCACAAGTCGATGCCAACG 1 TCCCAGATATGGTCTTACACGGAAATCACAAG-CGATGCCAACG 85941612 TCCCAGATATGGTCTTACA 1 TCCCAGATATGGTCTTACA 85941631 TGATATCACA Statistics Matches: 56, Mismatches: 4, Indels: 4 0.88 0.06 0.06 Matches are distributed among these distances: 42 20 0.36 43 8 0.14 44 28 0.50 ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25 Consensus pattern (43 bp): TCCCAGATATGGTCTTACACGGAAATCACAAGCGATGCCAACG Found at i:85941616 original size:44 final size:40 Alignment explanation

Indices: 85941484--85941630 Score: 150 Period size: 43 Copynumber: 3.5 Consensus size: 40 85941474 GGTGTTACAA * * * * 85941484 CCCAGATGTGGTCTTACATGTAATCAAATATCGATGCCACAAT 1 CCCAGATATGGTCTTACACGAAATC-AA-ATCGATGCCAC-GT * * * 85941527 CCCAGAGATGGTCTTACACGAAATCATATACGATGCCTATGT 1 CCCAGATATGGTCTTACACGAAATCAAAT-CGATGCC-ACGT 85941569 CCCAGATATGGTCTTACACGGAAATCACAAGTCGATGCCAACGT 1 CCCAGATATGGTCTTACAC-GAAATCA-AA-TCGATGCC-ACGT 85941613 CCCAGATATGGTCTTACA 1 CCCAGATATGGTCTTACA 85941631 TGATATCACA Statistics Matches: 88, Mismatches: 11, Indels: 9 0.81 0.10 0.08 Matches are distributed among these distances: 41 2 0.02 42 27 0.31 43 29 0.33 44 29 0.33 45 1 0.01 ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25 Consensus pattern (40 bp): CCCAGATATGGTCTTACACGAAATCAAATCGATGCCACGT Found at i:85953626 original size:29 final size:29 Alignment explanation

Indices: 85953579--85953650 Score: 99 Period size: 29 Copynumber: 2.5 Consensus size: 29 85953569 CACTTGGCCT * * 85953579 AATCTCATTTATATGGCCCATCAGGCCCA 1 AATCACATTCATATGGCCCATCAGGCCCA * * 85953608 ATTCACATTCATATGGCCCATTAGGCCCA 1 AATCACATTCATATGGCCCATCAGGCCCA * 85953637 AATCACATGCATAT 1 AATCACATTCATAT 85953651 TCATGCTCAC Statistics Matches: 37, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 29 37 1.00 ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28 Consensus pattern (29 bp): AATCACATTCATATGGCCCATCAGGCCCA Found at i:85957173 original size:51 final size:51 Alignment explanation

Indices: 85957084--85957183 Score: 132 Period size: 51 Copynumber: 2.0 Consensus size: 51 85957074 AGATATGTGG * 85957084 CATCCGAGCTCGTTGAGAGGTCCAAGTTCATGGTGGATGTGATT-CATGTAA 1 CATCCGAGCTCGTTGAGAGGTCCAAGTTCATAGTGGATGTG-TTACATGTAA * * * 85957135 CATCCGAGCTCGTTGAGAGGTTCGAGTTCGTTAG-GGATGTGTTACATGT 1 CATCCGAGCTCGTTGAGAGGTCCAAGTTC-ATAGTGGATGTGTTACATGT 85957184 TATGTGGTAG Statistics Matches: 43, Mismatches: 4, Indels: 4 0.84 0.08 0.08 Matches are distributed among these distances: 50 2 0.05 51 39 0.91 52 2 0.05 ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31 Consensus pattern (51 bp): CATCCGAGCTCGTTGAGAGGTCCAAGTTCATAGTGGATGTGTTACATGTAA Found at i:85958419 original size:42 final size:42 Alignment explanation

Indices: 85958373--85958505 Score: 194 Period size: 42 Copynumber: 3.2 Consensus size: 42 85958363 TGTGTCTCAA * * * 85958373 CCGTGTAGAGGACACGGCCTAGCACACGGGCGTACGCCTTGG 1 CCGTGTGGATGACACGGCCTAGCGCACGGGCGTACGCCTTGG * 85958415 CCGTGTGGATGACACGACCTAGCGCACGGGCGTACGCCTTGG 1 CCGTGTGGATGACACGGCCTAGCGCACGGGCGTACGCCTTGG * ** 85958457 CCGTGTGGATGACACAGCCTAGCGCACGGGCGTGTGCCTTGG 1 CCGTGTGGATGACACGGCCTAGCGCACGGGCGTACGCCTTGG * 85958499 CCATGTG 1 CCGTGTG 85958506 CTCCTAAATG Statistics Matches: 82, Mismatches: 9, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 42 82 1.00 ACGTcount: A:0.17, C:0.30, G:0.36, T:0.17 Consensus pattern (42 bp): CCGTGTGGATGACACGGCCTAGCGCACGGGCGTACGCCTTGG Done.