Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold42

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: 3911082
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33

Warning! 18191 characters in sequence are not A, C, G, or T


File 22 of 24

Found at i:3342731 original size:32 final size:32

Alignment explanation

Indices: 3342687--3342757 Score: 124 Period size: 32 Copynumber: 2.2 Consensus size: 32 3342677 AGCTTCGTAG * 3342687 CGATACATTGTATCGATACAACACTTATGTAT 1 CGATACAATGTATCGATACAACACTTATGTAT * 3342719 CGATACAATGTATCGATACATCACTTATGTAT 1 CGATACAATGTATCGATACAACACTTATGTAT 3342751 CGATACA 1 CGATACA 3342758 GTTACTGTTT Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 32 37 1.00 ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32 Consensus pattern (32 bp): CGATACAATGTATCGATACAACACTTATGTAT Found at i:3342773 original size:21 final size:19 Alignment explanation

Indices: 3342695--3342757 Score: 75 Period size: 19 Copynumber: 3.6 Consensus size: 19 3342685 AGCGATACAT * 3342695 TGTATCGATACAACACTTA 1 TGTATCGATACATCACTTA 3342714 TGTATCGAT--A-CA---A 1 TGTATCGATACATCACTTA 3342727 TGTATCGATACATCACTTA 1 TGTATCGATACATCACTTA 3342746 TGTATCGATACA 1 TGTATCGATACA 3342758 GTTACTGTTT Statistics Matches: 38, Mismatches: 0, Indels: 12 0.76 0.00 0.24 Matches are distributed among these distances: 13 10 0.26 15 1 0.03 16 4 0.11 17 1 0.03 19 22 0.58 ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33 Consensus pattern (19 bp): TGTATCGATACATCACTTA Found at i:3343658 original size:49 final size:49 Alignment explanation

Indices: 3343509--3343873 Score: 249 Period size: 42 Copynumber: 7.9 Consensus size: 49 3343499 AATGACAATG * ** * * * * 3343509 TGATTCATGGCCAGTGACATTGGACTTGAAGAAG-A-ATGCCAATGTGC 1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC ** * * * 3343556 TGAGACAAGGCCAGCGACATTGGGCTTAGAA-ATGTTAAAGATGCCAATATGC 1 TGATTCAAGGCCAACGATATTGGACTTA-AAGATG---AAGATGCCAATATGC * * * 3343608 TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACCAATGTGC 1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC * * 3343657 TGATTCAAGGCCGACGACATTGGACTT-AA-A-G--G-TGCCAATATGC 1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC * * * 3343700 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGT 1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC ** * * * * 3343749 TGATTCAAGGTTAGCGACATTGG--TTTAA-A-G--G-TGCCAATATGT 1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC * * 3343791 TGATTCAAGGCCAACGATATTGG--TTTAA-A-G--G-TGCCAATATGT 1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC * * 3343833 TGATTCAAGGCCAGCGATATTGGACTT--AGAAGAAGATGCCA 1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCA 3343874 CCAACTTGTG Statistics Matches: 262, Mismatches: 36, Indels: 40 0.78 0.11 0.12 Matches are distributed among these distances: 42 71 0.27 43 35 0.13 44 6 0.02 45 2 0.01 46 4 0.02 47 34 0.13 48 5 0.02 49 66 0.25 51 3 0.01 52 36 0.14 ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25 Consensus pattern (49 bp): TGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATGCCAATATGC Found at i:3343747 original size:92 final size:91 Alignment explanation

Indices: 3343590--3343813 Score: 342 Period size: 92 Copynumber: 2.5 Consensus size: 91 3343580 CTTAGAAATG * * 3343590 TTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGATACCAATGT 1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATACCAATGT 3343655 GCTGATTCAAGGCCGA-CGACATTGGAC 66 GCTGATTCAAGG-CGAGCGACATTGG-C * * 3343682 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT 1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATACCAATGT * ** * 3343747 GTTGATTCAAGGTTAGCGACATTGGT 66 GCTGATTCAAGGCGAGCGACATTGGC * 3343773 TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGG 1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGG 3343814 TTTAAAGGTG Statistics Matches: 121, Mismatches: 10, Indels: 3 0.90 0.07 0.02 Matches are distributed among these distances: 91 40 0.33 92 81 0.67 ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26 Consensus pattern (91 bp): TTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGATACCAATGT GCTGATTCAAGGCGAGCGACATTGGC Found at i:3343800 original size:21 final size:21 Alignment explanation

Indices: 3343776--3343842 Score: 66 Period size: 21 Copynumber: 3.2 Consensus size: 21 3343766 CATTGGTTTA 3343776 AAGGTGCCAATATGTTGATTC 1 AAGGTGCCAATATGTTGATTC * * * * 3343797 AA-G-GCCAACGATATTGGTTTA 1 AAGGTGCCAA-TATGTT-GATTC 3343818 AAGGTGCCAATATGTTGATTC 1 AAGGTGCCAATATGTTGATTC 3343839 AAGG 1 AAGG 3343843 CCAGCGATAT Statistics Matches: 34, Mismatches: 8, Indels: 8 0.68 0.16 0.16 Matches are distributed among these distances: 19 5 0.15 20 5 0.15 21 14 0.41 22 5 0.15 23 5 0.15 ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30 Consensus pattern (21 bp): AAGGTGCCAATATGTTGATTC Found at i:3343852 original size:22 final size:21 Alignment explanation

Indices: 3343785--3343852 Score: 52 Period size: 21 Copynumber: 3.2 Consensus size: 21 3343775 AAAGGTGCCA 3343785 ATATGTTGATTCAAGGCCAACG 1 ATATGTTGATTCAAGGCC-ACG * * * 3343807 ATAT-TGGTTTAAAGGTGCCA-- 1 ATATGTTGATTCAA-G-GCCACG 3343827 ATATGTTGATTCAAGGCCAGCG 1 ATATGTTGATTCAAGGCCA-CG 3343849 ATAT 1 ATAT 3343853 TGGACTTAGA Statistics Matches: 34, Mismatches: 6, Indels: 12 0.65 0.12 0.23 Matches are distributed among these distances: 19 4 0.12 20 5 0.15 21 12 0.35 22 10 0.29 23 3 0.09 ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31 Consensus pattern (21 bp): ATATGTTGATTCAAGGCCACG Found at i:3343947 original size:28 final size:28 Alignment explanation

Indices: 3343882--3344349 Score: 544 Period size: 28 Copynumber: 16.4 Consensus size: 28 3343872 CACCAACTTG ** 3343882 TGTGGGCTTTTGATAGGGTTG-CACCAACT 1 TGTGGGCTTTTGA-A-GGTTGCCACTGACT * 3343911 TGTGTGCTTTTGAAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT * * 3343939 TATGGGCTTTTGAAGGTTGCCACTAACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT 3343967 TGTGGGCTTTTGAAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT * * * * 3343995 TGTGGGCTTTGGAAAAGATGCCACGGACT 1 TGTGGGCTTTTG-AAGGTTGCCACTGACT * * 3344024 CGTGGGCTTTTGAAAAGGGTGCCACTGACT 1 TGTGGGCTTTTG--AAGGTTGCCACTGACT * 3344054 TGTGGGCTTTTAAAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT * * * * 3344082 TGCGGGCTTTGGAAAAGATGCCAC-GAACT 1 TGTGGGCTTTTG-AAGGTTGCCACTG-ACT 3344111 TGTGGGCTTTTGAAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT 3344139 TGTGGGCTTTTGAAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT * * * 3344167 TGTGGGCTTTGGAAAAGATGCCACTGACT 1 TGTGGGCTTTTG-AAGGTTGCCACTGACT * * * 3344196 TGTGGGATTTGGAAAAGGGTGCCACTGACT 1 TGTGGGCTTTTG--AAGGTTGCCACTGACT * 3344226 TGTGGGCTTTTGAAAGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT * * * * 3344254 TGTGGGCTTTGGAAAAGATGCCACGGACT 1 TGTGGGCTTTTG-AAGGTTGCCACTGACT 3344283 TGTGGGCTTTTGAAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACT * * * 3344311 TGTGGGCTTTGGAAACGATGCCACTGACT 1 TGTGGGCTTTTG-AAGGTTGCCACTGACT 3344340 TGTGGGCTTT 1 TGTGGGCTTT 3344350 GAACAAGGTG Statistics Matches: 380, Mismatches: 49, Indels: 20 0.85 0.11 0.04 Matches are distributed among these distances: 27 5 0.01 28 194 0.51 29 132 0.35 30 49 0.13 ACGTcount: A:0.19, C:0.18, G:0.32, T:0.32 Consensus pattern (28 bp): TGTGGGCTTTTGAAGGTTGCCACTGACT Found at i:3343951 original size:57 final size:57 Alignment explanation

Indices: 3343882--3344349 Score: 568 Period size: 57 Copynumber: 8.2 Consensus size: 57 3343872 CACCAACTTG ** * * * 3343882 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTTTG-AAGGTTGCCACTGACT 1 TGTGGGCTTTTGA-A-GGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT * * * * 3343939 TATGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTTG-AAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT * * * * * * * 3343995 TGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGCTTTTGAAAAGGGTGCCACTGACT 1 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGC-TTTGGAAAGGATGCCACTGACT * * * 3344054 TGTGGGCTTTTAAAGGTTGCCACTGACTTGCGGGCTTTGGAAAAGATGCCAC-GAACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTG-ACT * * 3344111 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT * * * * * 3344167 TGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGATTTGGAAAAGGGTGCCACTGACT 1 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGG-AAAGGATGCCACTGACT * * * 3344226 TGTGGGCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACGGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT * 3344283 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAACGATGCCACTGACT 1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT 3344340 TGTGGGCTTT 1 TGTGGGCTTT 3344350 GAACAAGGTG Statistics Matches: 359, Mismatches: 43, Indels: 18 0.85 0.10 0.04 Matches are distributed among these distances: 55 5 0.01 56 69 0.19 57 187 0.52 58 47 0.13 59 51 0.14 ACGTcount: A:0.19, C:0.18, G:0.32, T:0.32 Consensus pattern (57 bp): TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTGACT Found at i:3344168 original size:172 final size:171 Alignment explanation

Indices: 3343928--3344350 Score: 704 Period size: 172 Copynumber: 2.5 Consensus size: 171 3343918 TTTTGAAGGT * * 3343928 TGCCACTGACTTATGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGA 1 TGCCAC-GACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGA * * 3343993 CTTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTG 65 CTTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGATTTGGAAAAGGGTGCCACTGACTTGTG 3344058 GGCTTTT-AAAGGTTGCCACTGACTTGCGGGCTTTGGAAAAGA 130 GGCTTTTGAAA-GTTGCCACTGACTTGCGGGCTTTGGAAAAGA 3344100 TGCCACGAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGA 1 TGCCACG-ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGA * * 3344165 CTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGATTTGGAAAAGGGTGCCACTGACTTGTG 65 CTTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGATTTGGAAAAGGGTGCCACTGACTTGTG * 3344230 GGCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTGGAAAAGA 130 GGCTTTTGAAAGTTGCCACTGACTTGCGGGCTTTGGAAAAGA * * * 3344272 TGCCACGGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAACGATGCCACTG 1 TGCCAC-GACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTG 3344337 ACTTGTGGGCTTTG 64 ACTTGTGGGCTTTG 3344351 AACAAGGTGA Statistics Matches: 237, Mismatches: 10, Indels: 7 0.93 0.04 0.03 Matches are distributed among these distances: 171 1 0.00 172 207 0.87 173 29 0.12 ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31 Consensus pattern (171 bp): TGCCACGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGAC TTGTGGGCTTTGGAAAAGATGCCACGGACTCGTGGGATTTGGAAAAGGGTGCCACTGACTTGTGG GCTTTTGAAAGTTGCCACTGACTTGCGGGCTTTGGAAAAGA Found at i:3345806 original size:17 final size:17 Alignment explanation

Indices: 3345786--3345821 Score: 56 Period size: 17 Copynumber: 2.1 Consensus size: 17 3345776 CTTTTTGTTG 3345786 TTGTTGTTGT-TTTTTTT 1 TTGTT-TTGTGTTTTTTT 3345803 TTGTTTTGTGTTTTTTT 1 TTGTTTTGTGTTTTTTT 3345820 TT 1 TT 3345822 TTGGGGAGGA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 16 4 0.22 17 14 0.78 ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83 Consensus pattern (17 bp): TTGTTTTGTGTTTTTTT Found at i:3345816 original size:16 final size:17 Alignment explanation

Indices: 3345786--3345820 Score: 54 Period size: 16 Copynumber: 2.1 Consensus size: 17 3345776 CTTTTTGTTG * 3345786 TTGTTGTTGTTTTTTTT 1 TTGTTGTTGTGTTTTTT 3345803 TTGTT-TTGTGTTTTTT 1 TTGTTGTTGTGTTTTTT 3345819 TT 1 TT 3345821 TTTGGGGAGG Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 12 0.71 17 5 0.29 ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83 Consensus pattern (17 bp): TTGTTGTTGTGTTTTTT Found at i:3345824 original size:19 final size:20 Alignment explanation

Indices: 3345777--3345822 Score: 69 Period size: 18 Copynumber: 2.4 Consensus size: 20 3345767 ATCCGGACCC * 3345777 TTTTTGTTGTTGTTGTTGTT 1 TTTTTTTTGTTGTTGTTGTT 3345797 TTTTTTTTGTT-TTG-TGTT 1 TTTTTTTTGTTGTTGTTGTT 3345815 TTTTTTTT 1 TTTTTTTT 3345823 TGGGGAGGAC Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 18 12 0.48 19 3 0.12 20 10 0.40 ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83 Consensus pattern (20 bp): TTTTTTTTGTTGTTGTTGTT Found at i:3361136 original size:61 final size:60 Alignment explanation

Indices: 3361035--3361159 Score: 162 Period size: 61 Copynumber: 2.1 Consensus size: 60 3361025 CCTTTTTCTT * * * * * * 3361035 TCTTAAGCCTAATATTGCTGGCCCTAGATCAGCATGTTGGCATCTTTTTCATTCTTCTCA 1 TCTTAAGCCTAATATCGCTGGCACTAGATCAGCATATTGGCACCTTTATCATTCTTCGCA * 3361095 TCTTCAAGCCTAATATCGCTGGCAGT-GAATCAGCATATTGGCACCTTTATCATTCTTCGCA 1 TCTT-AAGCCTAATATCGCTGGCACTAG-ATCAGCATATTGGCACCTTTATCATTCTTCGCA 3361156 TCTT 1 TCTT 3361160 TAAGTCCAAT Statistics Matches: 56, Mismatches: 7, Indels: 3 0.85 0.11 0.05 Matches are distributed among these distances: 60 5 0.09 61 51 0.91 ACGTcount: A:0.22, C:0.26, G:0.15, T:0.38 Consensus pattern (60 bp): TCTTAAGCCTAATATCGCTGGCACTAGATCAGCATATTGGCACCTTTATCATTCTTCGCA Found at i:3361185 original size:61 final size:61 Alignment explanation

Indices: 3361062--3361211 Score: 160 Period size: 61 Copynumber: 2.5 Consensus size: 61 3361052 CTGGCCCTAG * * * * * 3361062 ATCAGCATGTTGGCATCTTTTTCATTCTTCTCATCTTCAAGCCTAATATCGCTGGCAGTGA 1 ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTCAAGCCTAATATCGCTGACAGTGA * * * ** 3361123 ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTTAAGTCC-AATGTTGCTGACTTTGA 1 ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTCAAG-CCTAATATCGCTGACAGTGA * * * 3361184 ATCAGCACATTGACACTTTTATC-TTCTT 1 ATCAGCATATTGGCACCTTTATCATTCTT 3361212 ATCTTTAAGT Statistics Matches: 75, Mismatches: 13, Indels: 3 0.82 0.14 0.03 Matches are distributed among these distances: 60 5 0.07 61 68 0.91 62 2 0.03 ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39 Consensus pattern (61 bp): ATCAGCATATTGGCACCTTTATCATTCTTCGCATCTTCAAGCCTAATATCGCTGACAGTGA Found at i:3371042 original size:51 final size:51 Alignment explanation

Indices: 3370985--3371096 Score: 136 Period size: 51 Copynumber: 2.2 Consensus size: 51 3370975 GACAGGGTTG * * * 3370985 GAGTATCCTCGATTGTGGAAAATCAGTGTTTT-GAAAATAAAATCGAAGTTA 1 GAGTATCCCCGATTATGAAAAATCAGTGTTTTAG-AAATAAAATCGAAGTTA ** ** * 3371036 GAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAATCGGGGTTG 1 GAGTATCCCCGATTATGAAAAATCAGTGTTTTAGAAATAAAATCGAAGTTA 3371087 GAGTATCCCC 1 GAGTATCCCC 3371097 TTGGAAATAA Statistics Matches: 52, Mismatches: 8, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 51 51 0.98 52 1 0.02 ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29 Consensus pattern (51 bp): GAGTATCCCCGATTATGAAAAATCAGTGTTTTAGAAATAAAATCGAAGTTA Found at i:3371119 original size:79 final size:79 Alignment explanation

Indices: 3371036--3371254 Score: 312 Period size: 79 Copynumber: 2.8 Consensus size: 79 3371026 ATCGAAGTTA * * * * 3371036 GAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTTGG 1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG 3371101 AAATAACGGGGTTG 66 AAATAACGGGGTTG * * * * * * 3371115 GAGTATCCCTGATTGTGAGAAATTAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCGG 1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG 3371180 AAATAACGGGGTTG 66 AAATAACGGGGTTG * * * * 3371194 GAGCATCCCCGATTATGAAAAATTGATGTTTTGGATATAAAACCGAGGTTGGAGTATCCCC 1 GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC 3371255 GAGATGAAAA Statistics Matches: 120, Mismatches: 20, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 79 120 1.00 ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28 Consensus pattern (79 bp): GAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGG AAATAACGGGGTTG Found at i:3371170 original size:130 final size:130 Alignment explanation

Indices: 3370932--3371175 Score: 316 Period size: 130 Copynumber: 1.9 Consensus size: 130 3370922 AGGAAATCGA * 3370932 TGTTTTGAGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATGACAGGGTTGGAGTATCCTCGA 1 TGTTTTGAGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGA * * * 3370997 TTGTGGAAAATCAGTGTTTTGAAAATAAAATCGAAGTTAGAGTATCCCCGATTATGAAAAATGGG 66 TTGTGGAAAATCAATATTTTGAAAATAAAACCGAAGTTAGAGTATCCCCGATTATGAAAAATGGG * * * 3371062 TGTTTT-AGAAATAAAATCGGGGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCC-CT 1 TGTTTTGAG-AATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTC- * * ** * 3371125 GATTGT-GAGAAATTAATATTTT-AGAAATAAAGCCGGGGTTGGAGTATCCCC 64 GATTGTGGA-AAATCAATATTTTGA-AAATAAAACCGAAGTTAGAGTATCCCC 3371176 TCGGAAATAA Statistics Matches: 98, Mismatches: 12, Indels: 8 0.83 0.10 0.07 Matches are distributed among these distances: 129 6 0.06 130 92 0.94 ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29 Consensus pattern (130 bp): TGTTTTGAGAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGA TTGTGGAAAATCAATATTTTGAAAATAAAACCGAAGTTAGAGTATCCCCGATTATGAAAAATGGG Found at i:3371951 original size:119 final size:119 Alignment explanation

Indices: 3371739--3371979 Score: 428 Period size: 119 Copynumber: 2.0 Consensus size: 119 3371729 GGTAGGCCTG * * * 3371739 AATGGCCCAAATAGAATGCATTTTACTGACTCTAGCGTTTTTGAACAGCTTAGACTCAAAAAATC 1 AATGGCCCAAACAGAATGCATTTTACTAACTCAAGCGTTTTTGAACAGCTTAGACTCAAAAAATC 3371804 ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT 66 ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT * * 3371858 AATGGCCCAAACAGAATGCATTTTACTAACTCAAGGGTTTTTGAACAGCTTCGACTCAAAAAATC 1 AATGGCCCAAACAGAATGCATTTTACTAACTCAAGCGTTTTTGAACAGCTTAGACTCAAAAAATC * 3371923 ATAACTCTCTAGTTTGGACTAATTTGGGGGCAAACAAGACATCGTTGAAAAGAT 66 ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT 3371977 AAT 1 AAT 3371980 TCAAAGCTCT Statistics Matches: 116, Mismatches: 6, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 119 116 1.00 ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27 Consensus pattern (119 bp): AATGGCCCAAACAGAATGCATTTTACTAACTCAAGCGTTTTTGAACAGCTTAGACTCAAAAAATC ATAACTCTCTAGTTTGGACTAATCTGGGGGCAAACAAGACATCGTTGAAAAGAT Found at i:3373751 original size:13 final size:13 Alignment explanation

Indices: 3373733--3373762 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 3373723 GTAAACCCAG * 3373733 AATGTATTGATAC 1 AATGTATTGACAC 3373746 AATGTATTGACAC 1 AATGTATTGACAC 3373759 AATG 1 AATG 3373763 AACAAATTAT 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:0.40, C:0.10, G:0.17, T:0.33 Consensus pattern (13 bp): AATGTATTGACAC Found at i:3374544 original size:42 final size:43 Alignment explanation

Indices: 3374497--3374633 Score: 156 Period size: 42 Copynumber: 3.2 Consensus size: 43 3374487 AAAGGAAAAA 3374497 AGGAAAATGAAATGCGTCCTGCTCTTTGAGGAC-AAGAGAAAG 1 AGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAGAGAAAG 3374539 AGGAAAAT-AAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGAAAAG 1 AGGAAAATGAAA-TGCGTCCTGCTCTTTGAGGAC-AAAGAG-AAAG * * * * * 3374584 AAGG-GAATGAAGTGTGTCCTACTTTTTGAGGACAAAGGAGAAA- 1 -AGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAA-GAGAAAG 3374627 AGGAAAA 1 AGGAAAA 3374634 GGAGTCCTGC Statistics Matches: 81, Mismatches: 6, Indels: 15 0.79 0.06 0.15 Matches are distributed among these distances: 41 3 0.04 42 32 0.40 43 2 0.02 44 11 0.14 45 28 0.35 46 5 0.06 ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19 Consensus pattern (43 bp): AGGAAAATGAAATGCGTCCTGCTCTTTGAGGACAAAGAGAAAG Found at i:3374603 original size:45 final size:45 Alignment explanation

Indices: 3374487--3374628 Score: 168 Period size: 45 Copynumber: 3.2 Consensus size: 45 3374477 TTTCGAGGAT * * 3374487 AAAG-GAAAAAAGGAAAATGAAATGCGTCCTGCTCTTTGAGGAC- 1 AAAGAGAAAAGAGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA * 3374530 -AAGAG-AAAGAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACA 1 AAAGAGAAAAGAGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA * * * * 3374573 AAAGAGAAAAGAAGG-GAATGAAGTGTGTCCTACTTTTTGAGGACA 1 AAAGAGAAAAG-AGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA * 3374618 AAGGAGAAAAG 1 AAAGAGAAAAG 3374629 GAAAAGGAGT Statistics Matches: 85, Mismatches: 9, Indels: 8 0.83 0.09 0.08 Matches are distributed among these distances: 42 37 0.44 43 1 0.01 44 5 0.06 45 39 0.46 46 3 0.04 ACGTcount: A:0.42, C:0.11, G:0.28, T:0.18 Consensus pattern (45 bp): AAAGAGAAAAGAGGAAAATGAAGTGCGTCCTGCTCTTTGAGGACA Found at i:3374703 original size:61 final size:62 Alignment explanation

Indices: 3374624--3375460 Score: 571 Period size: 61 Copynumber: 13.5 Consensus size: 62 3374614 GACAAAGGAG * ** * 3374624 AAAAGGAAAAGG-AGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAAGTTTTA 1 AAAAGAAAAAGGCA-TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * * ** * * * 3374686 AAAAG-AAAAGGCATCCTGCTTTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA ** * * * * 3374747 AAAAGAAAAAGGTGTACTGCTCTTTGAAGACT-AAAAGTGTCACCAACTCGTGTGGGCTTTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * ** * * * * 3374808 AAAAGGAAAAGGTGTCCTGCTCCTTGAGGACT-AAAGGTGTCACCAACTCGTGTGGGCTTTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * * ** * 3374869 AAAAGAAAAAGGCATCCTGTTTTTTGAGGACTAAAGCGTGCCACCAACTCGTGTGGGC-TTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * * ** ** * * 3374930 AAAAGAAAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAG-GAAATGAAGTGCGTCCTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACT--------AAAAAGTGCCACCAACT-CGT-GTG ** 3374994 CTCTTT- 56 GGCTTTA * * *** *** * * * * ** * ** 3375000 -GAGGACAAAAGG-A----GAAATGAAAGGAATGAAACGTG--TCCTGCTC-TTTGAGGACAAAG 1 AAAAGA-AAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTG-GG-C--TT * 3375056 AA 61 TA * * * 3375058 GAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG 1 -AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * ** * * 3375121 AAAAGAAAAAAGTGTCCTGCTCTTTGAAGACT-AAAAGTGCCACCAACTCGTGTGGGCTTTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA ** * * * 3375182 AAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTA 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * ** * * * 3375244 AAAAGGAAAAGGTGTCCTGCTCATTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * ** * * * 3375305 AAAAGAAAAATGTGTCCTGCTCGTTGAGGA-TTAAAAGATGCCACCAACTTGTGTGGGCTTTA 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAG-TGCCACCAACTCGTGTGGGCTTTA * * * * * 3375367 AAAAGGAAAAGGCGTCCTCCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTG 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA * * 3375428 AAAAGAAAAAGGCGTCCTACTCTTTGAGGACTA 1 AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTA 3375461 GAAGGGCTAA Statistics Matches: 616, Mismatches: 123, Indels: 72 0.76 0.15 0.09 Matches are distributed among these distances: 53 2 0.00 54 1 0.00 55 2 0.00 56 1 0.00 57 4 0.01 58 1 0.00 59 6 0.01 60 3 0.00 61 355 0.58 62 182 0.30 63 1 0.00 64 13 0.02 65 9 0.01 66 7 0.01 67 3 0.00 68 5 0.01 69 10 0.02 70 9 0.01 71 2 0.00 ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24 Consensus pattern (62 bp): AAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTA Found at i:3374837 original size:184 final size:182 Alignment explanation

Indices: 3374623--3375465 Score: 781 Period size: 184 Copynumber: 4.5 Consensus size: 182 3374613 GGACAAAGGA * ** * 3374623 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAAGTTTTAAA 1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAA * * * * * 3374688 AAGAAAAGGCATCCTGCTTTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA 65 AAGAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGA * * 3374753 AAAAGGTGTACTGCTCTTTGAAGACTAAAAGTGTCACCAACTCGTGTGGGCTTT 129 AAAAGGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT * * * * 3374807 GAAAAGGAAAAGGTGTCCTGCTCCTTGAGGACTAAAGGTGTCACCAACTCGTGTGGGCTTTGAAA 1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA * * * 3374872 AGAAAAAGGCATCCTGTTTTTTGAGGACTAAAGCGTGCCACCAACTCGTGTGGGC-TTGAAAAGA 66 AG-AAAAGGCGTCCTGCTCTTTGAGGACTAAAG-GTGCCACCAACTCGTGTGGGCTTTGAAAAGA * * * ** ** * * ** 3374936 AAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAG-GAAATGAAGTGCGTCCTGCTCTTT 129 AAAAGGTGTCCTGCTCTTTGAAGACT---------AAAAGTGCCACCAACT-CGT-GTGGGCTTT ** * *** ** * * * ** * ** 3375000 GAGGA-CAAAAGGAGAAATG-----AAAGGAATGAAACGTG--TCCTGCTC-TTTGAGGACAAAG 1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTG-GG-C--TT * * 3375056 AAGAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG 61 TA-AAAA-GAAAAGGCGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTG * 3375121 AAAAGAAAAAAGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT 123 AAAAGAAAAAGGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT * * * * 3375181 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAA 1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTAAA * * 3375246 AAGGAAAAGGTGTCCTGCTCATTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGA 65 AA-GAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGA * * * * * 3375311 AAAATGTGTCCTGCTCGTTGAGGATTAAAAGATGCCACCAACTTGTGTGGGCTTT 129 AAAAGGTGTCCTGCTCTTTGAAGACTAAAAG-TGCCACCAACTCGTGTGGGCTTT * * * * 3375366 AAAAAGGAAAAGGCGTCCTCCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA 1 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA * 3375431 AGAAAAAGGCGTCCTACTCTTTGAGGACTAGAAGG 66 AG-AAAAGGCGTCCTGCTCTTTGAGGACTA-AAGG 3375466 GCTAAAAGAA Statistics Matches: 527, Mismatches: 97, Indels: 69 0.76 0.14 0.10 Matches are distributed among these distances: 181 9 0.02 182 17 0.03 183 68 0.13 184 190 0.36 185 88 0.17 186 8 0.02 187 17 0.03 188 7 0.01 189 6 0.01 190 51 0.10 191 40 0.08 192 17 0.03 193 9 0.02 ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24 Consensus pattern (182 bp): GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTAAAA AGAAAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAA AAGGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTT Found at i:3374992 original size:45 final size:42 Alignment explanation

Indices: 3374938--3375093 Score: 167 Period size: 46 Copynumber: 3.6 Consensus size: 42 3374928 TGAAAAGAAA * 3374938 AAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAGGAAATG 1 AAGGCGTCCTGCTCTTTGAGGACTAAAG-AAAAAAAAGG-AATG * * 3374982 AAGTGCGTCCTGCTCTTTGAGGACAAAAGGAGAAATGAAAGGAATG 1 AAG-GCGTCCTGCTCTTTGAGGACTAAA-GA-AAA-AAAAGGAATG * * * 3375028 AAACGTGTCCTGCTCTTTGAGGAC-AAAG-AAGAAAAGGAA-- 1 -AAGGCGTCCTGCTCTTTGAGGACTAAAGAAAAAAAAGGAATG 3375067 AAGGCGTCCTGCTCTTTGAGGACTAAA 1 AAGGCGTCCTGCTCTTTGAGGACTAAA 3375094 AAGTGCCACC Statistics Matches: 97, Mismatches: 9, Indels: 17 0.79 0.07 0.14 Matches are distributed among these distances: 38 21 0.22 39 3 0.03 41 7 0.07 42 2 0.02 44 4 0.04 45 26 0.27 46 27 0.28 47 7 0.07 ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19 Consensus pattern (42 bp): AAGGCGTCCTGCTCTTTGAGGACTAAAGAAAAAAAAGGAATG Found at i:3375078 original size:38 final size:40 Alignment explanation

Indices: 3374930--3375094 Score: 156 Period size: 45 Copynumber: 3.9 Consensus size: 40 3374920 TGTGGGCTTG * * 3374930 AAAA-GAAAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAA 1 AAAAGGAAAAAGGCGTCCTGCTCTTTGAGGACAAAAG--AAA 3374971 AAAAGGAAATGAAGTGCGTCCTGCTCTTTGAGGACAAAAGGAGAA 1 AAAAGGAAA--AAG-GCGTCCTGCTCTTTGAGGACAAAA-GA-AA * * * 3375016 ATGAAAGGAATGAAACGTGTCCTGCTCTTTGAGGAC-AAAGAAG 1 A--AAAGGAA--AAAGGCGTCCTGCTCTTTGAGGACAAAAGAAA 3375059 AAAAGG-AAAAGGCGTCCTGCTCTTTGAGGACTAAAA 1 AAAAGGAAAAAGGCGTCCTGCTCTTTGAGGAC-AAAA 3375095 AGTGCCACCA Statistics Matches: 105, Mismatches: 7, Indels: 25 0.77 0.05 0.18 Matches are distributed among these distances: 38 22 0.21 40 4 0.04 41 9 0.09 42 4 0.04 43 2 0.02 44 6 0.06 45 28 0.27 46 20 0.19 47 9 0.09 49 1 0.01 ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18 Consensus pattern (40 bp): AAAAGGAAAAAGGCGTCCTGCTCTTTGAGGACAAAAGAAA Found at i:3375207 original size:123 final size:123 Alignment explanation

Indices: 3374623--3375460 Score: 734 Period size: 123 Copynumber: 6.8 Consensus size: 123 3374613 GGACAAAGGA * * ** * * 3374623 GAAAAGGAAAAGGAGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTAAGTTTTAAA 1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTCGTGTGGGCTTTGAA * * * ** * * 3374688 AAG-AAAAGGCATCCTGCTTTTTGAGGATTGGAAGGTGCCACCAACTTGTGTGGGCTTT 65 AAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT * * * 3374746 GAAAAGAAAAAGGTGTACTGCTCTTTGAAGACTAAAAGTGTCACCAACTCGTGTGGGCTTTGAAA 1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA * * * * * 3374811 AGGAAAAGGTGTCCTGCTCCTTGAGGACT-AAAGGTGTCACCAACTCGTGTGGGCTTT 66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT ** * * * 3374868 GAAAAGAAAAAGGCATCCTGTTTTTTGAGGACTAAAGCGTGCCACCAACTCGTGTGGGC-TTGAA 1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAA-AGTGCCACCAACTCGTGTGGGCTTTGAA * ** ** * * ** 3374932 AAGAAAAAGGCGTCCTGCACTTTGAGGACTAAAGCAAAAAAAAG-GAAATGAAGTGCGTCCTGCT 65 AAGAAAAAGGCGTCCTGCTCTTTGAGGACT--------AAAAAGTGCCACCAACT-CGT-GTGGG 3374996 CTTT 120 CTTT * * *** ** * * * ** * 3375000 G--AGGACAAAAGGAGAAATG-----AAAGGAATGAAACGTG--TCCTGCTC-TTTGAGGACAAA 1 GAAAAGA-AAAAGGTGTCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTCGTGTG-GG-C--- *** * 3375055 GAAGAAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT 59 TTTGAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT * * 3375120 GAAAAGAAAAAAGTGTCCTGCTCTTTGAAGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA 1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA * * * * 3375185 AGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTT 66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT * * * * 3375243 AAAAAGGAAAAGGTGTCCTGCTCATTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA 1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA * * * * * 3375308 AGAAAAATGTGTCCTGCTCGTTGAGGA-TTAAAAGATGCCACCAACTTGTGTGGGCTTT 66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAG-TGCCACCAACTCGTGTGGGCTTT * * * * * 3375366 AAAAAGGAAAAGGCGTCCTCCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAA 1 GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA * 3375431 AGAAAAAGGCGTCCTACTCTTTGAGGACTA 66 AGAAAAAGGCGTCCTGCTCTTTGAGGACTA 3375461 GAAGGGCTAA Statistics Matches: 576, Mismatches: 105, Indels: 67 0.77 0.14 0.09 Matches are distributed among these distances: 120 7 0.01 121 17 0.03 122 128 0.22 123 321 0.56 124 8 0.01 125 7 0.01 126 14 0.02 127 10 0.02 128 3 0.01 129 31 0.05 130 8 0.01 131 15 0.03 132 7 0.01 ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24 Consensus pattern (123 bp): GAAAAGAAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAA AGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT Found at i:3380284 original size:79 final size:78 Alignment explanation

Indices: 3380120--3380285 Score: 219 Period size: 79 Copynumber: 2.1 Consensus size: 78 3380110 TCGGGGTTCC * * 3380120 AGAAATAAAATCAGGGTTGGAGTATCTCCTCGAAAATAACAGGGTTGGAGTATCCTTGATTATAT 1 AGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATAT * 3380185 AAAATCGGTATTT 66 AAAATCGATATTT * * * 3380198 TGAAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAAC-GAGGTTGGAGTATCCTCGATTGT 1 AG-AAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCTCGATTAT * 3380262 GA-AAAATTGATGATTT 64 -ATAAAATCGAT-ATTT 3380278 AGAAATAA 1 AGAAATAA 3380286 GGTCGGGATT Statistics Matches: 76, Mismatches: 8, Indels: 7 0.84 0.09 0.08 Matches are distributed among these distances: 78 2 0.03 79 68 0.89 80 6 0.08 ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29 Consensus pattern (78 bp): AGAAATAAAATCAGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATAT AAAATCGATATTT Found at i:3380303 original size:79 final size:79 Alignment explanation

Indices: 3380122--3380306 Score: 209 Period size: 79 Copynumber: 2.3 Consensus size: 79 3380112 GGGGTTCCAG * * 3380122 AAATAAAATCAGGG-TTGGAGTATCTCCTCGAAAATAACAGGGTTGGAGTATCCTTGATTATATA 1 AAATAAAATC-GGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATATA * * 3380186 AAATCGGTATTTTGA 65 AAATCGATATTTAGA * * 3380201 AAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAAC-GAGGTTGGAGTATCCTCGATTGTGA- 1 AAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACAG-GGTTGGAGTATCCTCGATTAT-AT * 3380264 AAAATTGATGATTTAG- 64 AAAATCGAT-ATTTAGA ** 3380280 AAATAAGGTCGGGATT-GATGTATCCCC 1 AAATAAAATCGGGATTGGA-GTATCCCC 3380307 GATTATGAGA Statistics Matches: 92, Mismatches: 9, Indels: 10 0.83 0.08 0.09 Matches are distributed among these distances: 78 6 0.07 79 80 0.87 80 6 0.07 ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29 Consensus pattern (79 bp): AAATAAAATCGGGATTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCTCGATTATATAA AATCGATATTTAGA Found at i:3380310 original size:51 final size:51 Alignment explanation

Indices: 3380243--3380525 Score: 227 Period size: 51 Copynumber: 5.5 Consensus size: 51 3380233 AATAACGAGG * * ** 3380243 TTGGAGTATCCTCGATTGTGAAAAATTGATGA-TTTAGAAATAAGGTCGGGA 1 TTGGAGTATCCCCGATTGTGAAAAATCGAT-ATTTTAGAAATAAAATCGGGA * * * * * 3380294 TT-GATGTATCCCCGATTATGAGAAATCAATATTTTGAAAAATAAAATC-AGA 1 TTGGA-GTATCCCCGATTGTGAAAAATCGATATTTT-AGAAATAAAATCGGGA * * 3380345 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGAGG- 1 -TTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCG-GGA * * ** ** 3380397 TTGGAGTATCCCCCGATTGCGATAAATCGATGCTTTAGAAATAAAATC-ATA 1 TTGGAGTAT-CCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCGGGA ** * * * * ** 3380448 CTTGGAGTATCCCCGATTAAGAAAAATTGATGTCTTGGAAATGGAATCGGGA 1 -TTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCGGGA * 3380500 TTGGAGTATCCCCGAGT-TGAAAAATC 1 TTGGAGTATCCCCGATTGTGAAAAATC 3380526 TAGAAATTTA Statistics Matches: 183, Mismatches: 38, Indels: 23 0.75 0.16 0.09 Matches are distributed among these distances: 50 10 0.05 51 92 0.50 52 78 0.43 53 3 0.02 ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30 Consensus pattern (51 bp): TTGGAGTATCCCCGATTGTGAAAAATCGATATTTTAGAAATAAAATCGGGA Found at i:3380356 original size:103 final size:104 Alignment explanation

Indices: 3380242--3380512 Score: 286 Period size: 103 Copynumber: 2.6 Consensus size: 104 3380232 AAATAACGAG * ** 3380242 GTTGGAGTATCCTCGATTGTGAAAAATTGATGA-TTTAGAAATAAGGTCG-GGATT-GATGTAT- 1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGG-TTGGA-GTATC * * 3380303 CCCCGATTATGAGAAATCAATATTTTGAAAAATAAAATCAGA 64 CCCCGATTACGAGAAATCAATACTTT-AAAAATAAAATCAGA * 3380345 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-ATTTTAGAAATAAAATCGAGGTTGGAGTATCCC 1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGGTTGGAGTATCCC * * * * * * 3380409 CCGATTGCGATAAATCGATGCTTTAGAAATAAAATCATA 66 CCGATTACGAGAAATCAATACTTTAAAAATAAAATCAGA * ** * * ** 3380448 CTTGGAGTATCCCCGATTAAGAAAAATTGATG-TCTTGGAAATGGAATCG-GGATTGGAGTATCC 1 GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGG-TTGGAGTATCC 3380511 CC 65 CC 3380513 GAGTTGAAAA Statistics Matches: 142, Mismatches: 20, Indels: 12 0.82 0.11 0.07 Matches are distributed among these distances: 102 3 0.02 103 115 0.81 104 24 0.17 ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30 Consensus pattern (104 bp): GTTGGAGTATCCCCGATTGTGAAAAATTGATGATTTTAGAAATAAAATCGAGGTTGGAGTATCCC CCGATTACGAGAAATCAATACTTTAAAAATAAAATCAGA Found at i:3382839 original size:20 final size:20 Alignment explanation

Indices: 3382814--3382929 Score: 101 Period size: 20 Copynumber: 5.8 Consensus size: 20 3382804 AAAAATGCCT * 3382814 GAATGTATTGATACATTGTA 1 GAATGTATCGATACATTGTA * 3382834 GAATGTATTGATACATTGTA 1 GAATGTATCGATACATTGTA * * * 3382854 AAATATATCGATACAATG-A 1 GAATGTATCGATACATTGTA * * 3382873 GCAATGTATCGATACAAT-AA 1 G-AATGTATCGATACATTGTA * * * 3382893 GCAATGTATCAATACAATGCA 1 G-AATGTATCGATACATTGTA * 3382914 AAATGTATCGATACAT 1 GAATGTATCGATACAT 3382930 CTGGGTAAAC Statistics Matches: 82, Mismatches: 11, Indels: 6 0.83 0.11 0.06 Matches are distributed among these distances: 19 1 0.01 20 80 0.98 21 1 0.01 ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31 Consensus pattern (20 bp): GAATGTATCGATACATTGTA Found at i:3383731 original size:134 final size:129 Alignment explanation

Indices: 3383428--3384219 Score: 683 Period size: 134 Copynumber: 6.0 Consensus size: 129 3383418 TCCTACTTTT * ** * * * * * * 3383428 AAAGGAAAAAAGGAAAACGAAATGCGTCATGCTCTTTGAAGATAAAA-GAAAAAGGAAAATAAAG 1 AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGAAAATGAAG * * * * 3383492 TGCGTCTTGCTCTTTGAGGACAAAAGGGAAAAGAAGGGAATGAAGTGTTTCTGCTCTTTGAGGAC 66 TGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTG-TCCTGCTCTTTGAGGAC * * * * * 3383557 AAATGA-AGAAA-GAAAATGAAGTGCGTCCTACTCTTTGAGGACGAAAGGGAAAAGAAGGAAATG 1 AAAGGAGA-AAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAG--GAAAATG * * * * 3383620 AAGTGTGTCCAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTG 63 AAGTGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGAAGGAAAT-GAA-GTGTCCTGCTCTTTG 3383685 AGGAC 125 AGGAC * * * 3383690 AGAGGAGAAAAGGAAAATAAAATGTGTCCTACTCTTTGAGGACAAAAGGGAAAA-GATTGGAATG 1 AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGA---AAATG * * * 3383754 AAGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCCTGCTCTTTG 63 AAGTGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGAAGGAAAT-GAA-GTGTCCTGCTCTTTG 3383819 AGGAC 125 AGGAC * * * * 3383824 AAAGGAGAAAAGGAAAATAAAGTGCGTCATGCTCTTTGAGGACAAAAGAGAAAAGGAAAAT-AAT 1 AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGAAAATGAA- * * * 3383888 GTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTCCTGCTCTTTGAGG 65 GTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGT--GTCCTGCTCTTTGAGG 3383953 ACC 128 A-C * ** * * * * 3383956 AAAGGAGAAAAAAAGG-GAATGGAACGTGTCCTGCTCTTTGAGGAC-CAAGGAGAAAAGGAAAAT 1 AAAGGAG---AAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGGAAAAT * * * 3384019 AAAGTGCATTCTACTCTTTGAGGACAAAAGGGGAAAA-AAGGAAATGAAGTGTGTCCTGCTCTTT 62 GAAGTGCGTCCTACTCTTTGAGGACAAAA-GGGAAAAGAAGGAAATGAA--GTGTCCTGCTCTTT 3384083 GAGGAC 124 GAGGAC ** * * ** * * * * 3384089 AAAAGGAGAAAA-GAAGGGAATGGAACGTGTTTTGCCCTTTAAGGA-TAAAGGAGAAAAGGAAAA 1 -AAAGGAGAAAAGGAA---AATAAAATGCGTCCTACTCTTTGAGGACAAAAGG-GAAAAGGAAAA * * * 3384152 T-ACAGTGCGTCCTACTCTTTGAGGACAAAAGAGAAGAGAA--AAATAAAGTACGTCCTGCTCTT 61 TGA-AGTGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGT--GTCCTGCTCTT 3384214 TGAGGA 123 TGAGGA 3384220 TAAGGAGGTG Statistics Matches: 560, Mismatches: 68, Indels: 67 0.81 0.10 0.10 Matches are distributed among these distances: 128 29 0.05 129 16 0.03 130 6 0.01 131 68 0.12 132 70 0.12 133 36 0.06 134 316 0.56 135 17 0.03 136 2 0.00 ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20 Consensus pattern (129 bp): AAAGGAGAAAAGGAAAATAAAATGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGGAAAATGAAG TGCGTCCTACTCTTTGAGGACAAAAGGGAAAAGAAGGAAATGAAGTGTCCTGCTCTTTGAGGAC Found at i:3383913 original size:177 final size:175 Alignment explanation

Indices: 3383457--3384219 Score: 743 Period size: 177 Copynumber: 4.3 Consensus size: 175 3383447 AAATGCGTCA * * * * * 3383457 TGCTCTTTGAAGATAAAAGA-AAAAGGAAAATAAAGTGCGTCTTGCTCTTTGAGGACAAAAGGGA 1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGA * * * * 3383521 AAA-GAAGGGAATGAAGTGT-TTCTGCTCTTTGAGGAC-AAATGAAGAAAGA-AAATGAAGTGCG 66 AAAGGAA---AATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGGA-AAAGAGGAATGAAGTGCG * * * * 3383582 TCCTACTCTTTGAGGACGAAAGG-GAAAAGAAGGAAAT-GAAGTGTGTCC 127 TCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAA-CGTGTCC ** * * 3383630 AACTCTTTGAGGACAAAAGGAGAAAA--AAAAGAAA-TGGAACGTGTCCTGCTCTTTGAGGACAG 1 TGCTCTTTGAGGAC-AAAGGAGAAAAGGAAAATAAAGT-G--C--GTCCTGCTCTTTGAGGACAA * * * * 3383692 AGGAGAAAAGGAAAATAAAATGTGTCCTACTCTTTGAGGACAAAAGGGAAAAGATTGGAATGAAG 60 AAGAGAAAAGGAAAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGGAAAAGA--GGAATGAAG * 3383757 TGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC 123 TGCGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC * 3383810 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCATGCTCTTTGAGGACAAAAGAGA 1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGA * * * 3383875 AAAGGAAAAT-AATGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGT 66 AAAGGAAAATGAA-GTGTGTCCTGCTCTTTGAGGACAAAAGGGAAAAG-AGG-AATGAAGTGCGT * * 3383939 CCTGCTCTTTGAGGACCAAAGGAGAAAAAAAGGGAATGGAACGTGTCC 128 CCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC * * * * 3383987 TGCTCTTTGAGGACCAAGGAGAAAAGGAAAATAAAGTGCATTCTACTCTTTGAGGACAAAAGGGG 1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAA---G * 3384052 AAAAAAGG-AAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACG 63 AGAAAAGGAAAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGG-GAAAAG-A-GGAAT-GAA-G ** * * * ** ** * 3384116 T--GTTTTGCCCTTTAAGGA-TAAAGGAGAAAAGGAA---AATACAGTGCGTCC 123 TGCGTCCTGCTCTTTGAGGACAAAAGGAGAAAA-GAAGGGAATGGAACGTGTCC * * * * * 3384164 TACTCTTTGAGGACAAAAGAGAAGAGAAAAATAAAGTACGTCCTGCTCTTTGAGGA 1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGA 3384220 TAAGGAGGTG Statistics Matches: 495, Mismatches: 65, Indels: 56 0.80 0.11 0.09 Matches are distributed among these distances: 172 1 0.00 173 18 0.04 174 5 0.01 175 13 0.03 176 24 0.05 177 261 0.53 178 4 0.01 179 83 0.17 180 67 0.14 181 16 0.03 182 3 0.01 ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20 Consensus pattern (175 bp): TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAGA AAAGGAAAATGAAGTGTGTCCTGCTCTTTGAGGACAAAAGGGAAAAGAGGAATGAAGTGCGTCCT GCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC Found at i:3384067 original size:311 final size:309 Alignment explanation

Indices: 3383499--3384214 Score: 1005 Period size: 311 Copynumber: 2.3 Consensus size: 309 3383489 AAGTGCGTCT * ** * 3383499 TGCTCTTTGAGGACAAAAGG-GAAAA-GAAGGGAATGAAGTGTTTCTGCTCTTTGAGGACAAATG 1 TGCTCTTTGAGGAC-AAAGGAGAAAAGGAA---AATAAAGTGCGTCTGCTCTTTGAGGACAAAAG * * * * 3383562 A-AGAAA-GAAAATGAAGTGCGTCCTACTCTTTGAGGACGAAAGGGAAAAGAAGGAAATGAAGTG 62 AGA-AAAGGAAAAT-AAGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTG * 3383625 TGTCCAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGAC 125 CGTCCAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGAC ** * 3383690 AGAGGAGAAAAGGAAAATAAAATGTGTCCTACTCTTTGAGGACAAAAGGGAAAAGATTGGAATGA 190 AGAGGAGAAAAGGAAAATAAAATGCATCCTACTCTTTGAGGACAAAAGGGAAAAGATAGGAATGA 3383755 AGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC 255 AGTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC 3383810 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCATGCTCTTTGAGGACAAAAGAGA 1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTC-TGCTCTTTGAGGACAAAAGAGA 3383875 AAAGGAAAATAATGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTC 65 AAAGGAAAATAA-GTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTC ** * * * 3383940 CTGCTCTTTGAGGACCAAAGGAGAAAAAAAGGGAATGGAACGTGTCCTGCTCTTTGAGGACCA-A 129 CAACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGA-CAGA * * 3384004 GGAGAAAAGGAAAATAAAGTGCATTCTACTCTTTGAGGACAAAAGGGGAAAA-A-AGGAAATGAA 193 GGAGAAAAGGAAAATAAAATGCATCCTACTCTTTGAGGACAAAA-GGGAAAAGATAGG-AATGAA ** 3384067 GTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTTT 256 GTGTGTCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC * * * * * 3384121 TGCCCTTTAAGGATAAAGGAGAAAAGGAAAATACAGTGCGTCCTACTCTTTGAGGACAAAAGAGA 1 TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGT-CTGCTCTTTGAGGACAAAAGAGA * * * 3384186 AGAGAAAAATAAAGTACGTCCTGCTCTTT 65 AAAGGAAAAT-AAGTGCGTCCTGCTCTTT 3384215 GAGGATAAGG Statistics Matches: 365, Mismatches: 29, Indels: 22 0.88 0.07 0.05 Matches are distributed among these distances: 309 10 0.03 310 31 0.08 311 309 0.85 312 15 0.04 ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20 Consensus pattern (309 bp): TGCTCTTTGAGGACAAAGGAGAAAAGGAAAATAAAGTGCGTCTGCTCTTTGAGGACAAAAGAGAA AAGGAAAATAAGTGCGTCCTGCTCTTTAAAGACAAAAGGGAAAAGAAGGAAATGAAGTGCGTCCA ACTCTTTGAGGACAAAAGGAGAAAAAAAAGAAATGGAACGTGTCCTGCTCTTTGAGGACAGAGGA GAAAAGGAAAATAAAATGCATCCTACTCTTTGAGGACAAAAGGGAAAAGATAGGAATGAAGTGTG TCCTGCTCTTTGAGGACAAAAGGAGAAAAGAAGGGAATGGAACGTGTCC Found at i:3384291 original size:60 final size:61 Alignment explanation

Indices: 3384204--3384889 Score: 779 Period size: 61 Copynumber: 11.4 Consensus size: 61 3384194 ATAAAGTACG * 3384204 TCCTGCTCTTTGAGGA-TAAGG-AGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCA 1 TCCTGCTCTTTGAGGACT--GGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * ** * 3384265 TCCT-TTCTTTGAGGACTGGAATGTGCCACCAACTTAAGTGGTCTTTAAAAGGAGAAA-GCA 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCA ** * * 3384325 TCCTGCTCTTTGAGGACTGGAAAATGCCCCCAACTTGTGTGGGCTCT-----G-AAAGGCA 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * ** 3384380 TCCTGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * * * * 3384441 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTCTAAAAAGAAAAATGCA 1 TCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGGAAAAGGCA * * * * 3384504 TCCTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGAGTGGTCTTTAAAAGGAAAAGGCG 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * * 3384565 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACG 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * * * 3384625 TCATGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA * * * * * 3384686 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAATGCG 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA * * * ** * * * * * 3384747 TCCTGCTCTTTAAAGACTGGAGGGTGCCACCAACTCATGTAGACTTT-GAAGGAGAAGGCG 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA ** * 3384807 TCCTGCTCTTTGAGGACTAAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA 1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA 3384868 TCCTGCTCTTTGAGGACTGGAA 1 TCCTGCTCTTTGAGGACTGGAA 3384890 AGGCTAAAAG Statistics Matches: 536, Mismatches: 73, Indels: 32 0.84 0.11 0.05 Matches are distributed among these distances: 54 3 0.01 55 46 0.09 56 1 0.00 59 2 0.00 60 173 0.32 61 211 0.39 62 69 0.13 63 31 0.06 ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25 Consensus pattern (61 bp): TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA Found at i:3384690 original size:121 final size:122 Alignment explanation

Indices: 3384204--3384889 Score: 808 Period size: 121 Copynumber: 5.7 Consensus size: 122 3384194 ATAAAGTACG * 3384204 TCCTGCTCTTTGAGGA-T-AAGGAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAGGCATC 1 TCCTGCTCTTTGAGGACTGAA--AGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATC * * ** * 3384267 CT-TTCTTTGAGGACTGGAATGTGCCACCAACTTAAGTGGTCTTTAAAAGGAGAAA-GCA 64 CTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCA * * * 3384325 TCCTGCTCTTTGAGGACTGGAAA-ATGCCCCCAACTTGTGTGGGCTCT-----G-AAAGGCATCC 1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCC * * ** 3384383 TGTTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA 65 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * * * 3384441 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTCTAAAAAGAAAAATGCATC 1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCT-TTAAAAGGAAAAGGCATC * * * * 3384506 CTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGAGTGGTCTTTAAAAGGAAAAGGCG 64 CTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * * 3384565 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCAT 1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT * * * 3384629 GCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA 66 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA * * * * 3384686 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAATGCGTCC 1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCC * * * ** * * * * * 3384750 TGCTCTTTAAAGACTGGAGGGTGCCACCAACTCATGTAGACTTT-GAAGGAGAAGGCG 65 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA * * 3384807 TCCTGCTCTTTGAGGACTAAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT 1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT 3384872 GCTCTTTGAGGACTGGAA 66 GCTCTTTGAGGACTGGAA 3384890 AGGCTAAAAG Statistics Matches: 486, Mismatches: 62, Indels: 34 0.84 0.11 0.06 Matches are distributed among these distances: 115 14 0.03 116 69 0.14 117 20 0.04 120 23 0.05 121 179 0.37 122 79 0.16 123 23 0.05 124 79 0.16 ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25 Consensus pattern (122 bp): TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCT GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA Found at i:3388955 original size:52 final size:52 Alignment explanation

Indices: 3388877--3389005 Score: 204 Period size: 52 Copynumber: 2.5 Consensus size: 52 3388867 CGAAATATGA * * ** 3388877 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC 1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTACGC * 3388929 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTACGC 1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTACGC * 3388981 AAATTTGCCTGCATGTACCGATACA 1 AAATTTGCCTGCATGTATCGATACA 3389006 AAGATCAGTG Statistics Matches: 71, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 52 71 1.00 ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34 Consensus pattern (52 bp): AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTACGC Found at i:3389018 original size:52 final size:51 Alignment explanation

Indices: 3388877--3389025 Score: 192 Period size: 52 Copynumber: 2.9 Consensus size: 51 3388867 CGAAATATGA * ** 3388877 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC 1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTACGC * * 3388929 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTACGC 1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTACGC * * 3388981 AAATTTGCCTGCATGTACCGATACA-AAGATCAGTGTATCGATACA 1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA 3389026 ATGTATCGAT Statistics Matches: 86, Mismatches: 9, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 51 2 0.02 52 84 0.98 ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33 Consensus pattern (51 bp): AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTACGC Found at i:3389032 original size:13 final size:13 Alignment explanation

Indices: 3389014--3389038 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3389004 CAAAGATCAG 3389014 TGTATCGATACAA 1 TGTATCGATACAA 3389027 TGTATCGATACA 1 TGTATCGATACA 3389039 TTTGAGTAAT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3389119 original size:13 final size:13 Alignment explanation

Indices: 3389101--3389125 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3389091 CAAAAAAATA 3389101 TGTATCGATACAT 1 TGTATCGATACAT 3389114 TGTATCGATACA 1 TGTATCGATACA 3389126 ATACTTTATG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3389485 original size:13 final size:13 Alignment explanation

Indices: 3389444--3389525 Score: 60 Period size: 13 Copynumber: 7.2 Consensus size: 13 3389434 CCGTTACAAG 3389444 CAATGTATCGATA 1 CAATGTATCGATA 3389457 CAAT-T-TC-AT- 1 CAATGTATCGATA * 3389466 C-ATGTATTGATA 1 CAATGTATCGATA 3389478 CAATGTATCGATA 1 CAATGTATCGATA * 3389491 C-A--T-T-G-TC 1 CAATGTATCGATA * 3389498 CTATGTATCGATA 1 CAATGTATCGATA 3389511 CAATGTATCGATA 1 CAATGTATCGATA 3389524 CA 1 CA 3389526 TTGTCCCATG Statistics Matches: 53, Mismatches: 5, Indels: 22 0.66 0.06 0.28 Matches are distributed among these distances: 7 2 0.04 8 4 0.08 9 3 0.06 10 5 0.09 11 5 0.09 12 4 0.08 13 30 0.57 ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35 Consensus pattern (13 bp): CAATGTATCGATA Found at i:3389505 original size:20 final size:19 Alignment explanation

Indices: 3389480--3389545 Score: 72 Period size: 20 Copynumber: 3.7 Consensus size: 19 3389470 TATTGATACA 3389480 ATGTATCGATACATTGTCC 1 ATGTATCGATACATTGTCC 3389499 TATGTATCGATACA------ 1 -ATGTATCGATACATTGTCC 3389513 ATGTATCGATACATTGTCCC 1 ATGTATCGATACATTGT-CC 3389533 ATGTATCGATACA 1 ATGTATCGATACA 3389546 ATTAGTGGTA Statistics Matches: 39, Mismatches: 0, Indels: 14 0.74 0.00 0.26 Matches are distributed among these distances: 13 13 0.33 20 26 0.67 ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35 Consensus pattern (19 bp): ATGTATCGATACATTGTCC Found at i:3389511 original size:33 final size:33 Alignment explanation

Indices: 3389444--3389547 Score: 156 Period size: 33 Copynumber: 3.1 Consensus size: 33 3389434 CCGTTACAAG * * 3389444 CAATGTATCGATACAATT-TCATCATGTATTGATA 1 CAATGTATCGATAC-ATTGTCCT-ATGTATCGATA 3389478 CAATGTATCGATACATTGTCCTATGTATCGATA 1 CAATGTATCGATACATTGTCCTATGTATCGATA * 3389511 CAATGTATCGATACATTGTCCCATGTATCGATA 1 CAATGTATCGATACATTGTCCTATGTATCGATA 3389544 CAAT 1 CAAT 3389548 TAGTGGTAGG Statistics Matches: 66, Mismatches: 3, Indels: 3 0.92 0.04 0.04 Matches are distributed among these distances: 33 49 0.74 34 17 0.26 ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36 Consensus pattern (33 bp): CAATGTATCGATACATTGTCCTATGTATCGATA Found at i:3389601 original size:20 final size:18 Alignment explanation

Indices: 3389576--3389667 Score: 78 Period size: 20 Copynumber: 4.7 Consensus size: 18 3389566 TGCCAGTTTC 3389576 ATGTATCGATACAACTGTCT 1 ATGTATCGATACAA-TG-CT 3389596 ATGTATCGATACAATGAGC- 1 ATGTATCGATACAAT--GCT * 3389615 ATGTATCGATACAAAGCAGT 1 ATGTATCGATACAATGC--T * * 3389635 ATGTATCGATACATCTGGT 1 ATGTATCGATACA-ATGCT 3389654 AGTGTATCGATACA 1 A-TGTATCGATACA 3389668 TTCAAGGGTT Statistics Matches: 61, Mismatches: 4, Indels: 14 0.77 0.05 0.18 Matches are distributed among these distances: 17 2 0.03 19 17 0.28 20 40 0.66 21 2 0.03 ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30 Consensus pattern (18 bp): ATGTATCGATACAATGCT Found at i:3390258 original size:16 final size:17 Alignment explanation

Indices: 3390219--3390260 Score: 59 Period size: 16 Copynumber: 2.5 Consensus size: 17 3390209 AATTTATATC * 3390219 TTCTCCCCCTTAAAGAAT 1 TTCT-CCCCTTAAAGAAA 3390237 TTCTCCCCTTAAA-AAA 1 TTCTCCCCTTAAAGAAA 3390253 TTCTCCCC 1 TTCTCCCC 3390261 CTTTGTCAAA Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 16 10 0.43 17 9 0.39 18 4 0.17 ACGTcount: A:0.26, C:0.38, G:0.02, T:0.33 Consensus pattern (17 bp): TTCTCCCCTTAAAGAAA Found at i:3390261 original size:17 final size:17 Alignment explanation

Indices: 3390219--3390263 Score: 65 Period size: 17 Copynumber: 2.6 Consensus size: 17 3390209 AATTTATATC * 3390219 TTCTCCCCCTTAAAGAA 1 TTCTCCCCCTTAAAAAA 3390236 TT-TCTCCCCTTAAAAAA 1 TTCTC-CCCCTTAAAAAA 3390253 TTCTCCCCCTT 1 TTCTCCCCCTT 3390264 TGTCAAATAA Statistics Matches: 25, Mismatches: 1, Indels: 4 0.83 0.03 0.13 Matches are distributed among these distances: 16 2 0.08 17 21 0.84 18 2 0.08 ACGTcount: A:0.24, C:0.38, G:0.02, T:0.36 Consensus pattern (17 bp): TTCTCCCCCTTAAAAAA Found at i:3390983 original size:13 final size:13 Alignment explanation

Indices: 3390965--3390989 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3390955 AGTAGCCAGG 3390965 GTATCGATACAAT 1 GTATCGATACAAT 3390978 GTATCGATACAA 1 GTATCGATACAA 3390990 GGAATGTTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28 Consensus pattern (13 bp): GTATCGATACAAT Found at i:3397126 original size:21 final size:21 Alignment explanation

Indices: 3397100--3397155 Score: 71 Period size: 21 Copynumber: 2.7 Consensus size: 21 3397090 ATTACAAGCA 3397100 ATGTATCGATACGATT-TCAT 1 ATGTATCGATACGATTGTCAT * 3397120 CATGTATCGATAC-ATTGTCCT 1 -ATGTATCGATACGATTGTCAT * 3397141 ATGTATTGATACGAT 1 ATGTATCGATACGAT 3397156 GTATCGATAC Statistics Matches: 31, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 20 14 0.45 21 17 0.55 ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39 Consensus pattern (21 bp): ATGTATCGATACGATTGTCAT Found at i:3397146 original size:20 final size:20 Alignment explanation

Indices: 3397100--3397186 Score: 73 Period size: 20 Copynumber: 4.7 Consensus size: 20 3397090 ATTACAAGCA * 3397100 ATGTATCGATACGATT-TCAT 1 ATGTATCGATAC-ATTGTCCT 3397120 CATGTATCGATACATTGTCCT 1 -ATGTATCGATACATTGTCCT * 3397141 ATGTATTGATAC---G---- 1 ATGTATCGATACATTGTCCT * 3397154 ATGTATCGATACATTGTCCC 1 ATGTATCGATACATTGTCCT 3397174 ATGTATCGATACA 1 ATGTATCGATACA 3397187 AATAGTGGTA Statistics Matches: 55, Mismatches: 3, Indels: 17 0.73 0.04 0.23 Matches are distributed among these distances: 13 11 0.20 16 1 0.02 17 1 0.02 20 27 0.49 21 15 0.27 ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37 Consensus pattern (20 bp): ATGTATCGATACATTGTCCT Found at i:3397163 original size:33 final size:33 Alignment explanation

Indices: 3397121--3397185 Score: 112 Period size: 33 Copynumber: 2.0 Consensus size: 33 3397111 CGATTTCATC * * 3397121 ATGTATCGATACATTGTCCTATGTATTGATACG 1 ATGTATCGATACATTGTCCCATGTATCGATACG 3397154 ATGTATCGATACATTGTCCCATGTATCGATAC 1 ATGTATCGATACATTGTCCCATGTATCGATAC 3397186 AAATAGTGGT Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 33 30 1.00 ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37 Consensus pattern (33 bp): ATGTATCGATACATTGTCCCATGTATCGATACG Found at i:3397274 original size:13 final size:13 Alignment explanation

Indices: 3397256--3397282 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 3397246 TAGAATGAGC 3397256 ATGTATCGATACA 1 ATGTATCGATACA 3397269 ATGTATCGATACA 1 ATGTATCGATACA 3397282 A 1 A 3397283 AGCAGTATGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3397298 original size:33 final size:32 Alignment explanation

Indices: 3397237--3397301 Score: 94 Period size: 33 Copynumber: 2.0 Consensus size: 32 3397227 TCAACTATCT * * 3397237 ATGTATCGATAGAATGAGCATGTATCGATACA 1 ATGTATCGATACAAAGAGCATGTATCGATACA * 3397269 ATGTATCGATACAAAGCAGTATGTATCGATACA 1 ATGTATCGATACAAAG-AGCATGTATCGATACA 3397302 TCTGGTAGTG Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 32 14 0.48 33 15 0.52 ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28 Consensus pattern (32 bp): ATGTATCGATACAAAGAGCATGTATCGATACA Found at i:3403223 original size:16 final size:17 Alignment explanation

Indices: 3403198--3403235 Score: 51 Period size: 16 Copynumber: 2.3 Consensus size: 17 3403188 TTGTGCTGTA * * 3403198 ATCATGACATC-ATGAC 1 ATCATAACATCAATAAC 3403214 ATCATAACATCAATAAC 1 ATCATAACATCAATAAC 3403231 ATCAT 1 ATCAT 3403236 TATTTGCATC Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 16 10 0.53 17 9 0.47 ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26 Consensus pattern (17 bp): ATCATAACATCAATAAC Found at i:3403390 original size:31 final size:31 Alignment explanation

Indices: 3403334--3403565 Score: 148 Period size: 31 Copynumber: 7.2 Consensus size: 31 3403324 CTTCAAATAC * * * * 3403334 CTTCTTAAAGTCCACGACTCAGTGGCAATCT 1 CTTCTCAAAGCCCACAACTCCGTGGCAATCT * * * 3403365 CTTCTCAAAGCCCATAACTCCGTGGCACTTTTTT 1 CTTCTCAAAGCCCACAACTCCGTGGCA---ATCT * * * * 3403399 CTTTTTAAAGCCCACAACTCCGTGGCACTTTTT 1 CTTCTCAAAGCCCACAACTCCGTGGCA--ATCT * * * 3403432 CCTTTTTAAAGCCCACAACTCCGTGGC-ACCTT 1 -CTTCTCAAAGCCCACAACTCCGTGGCAATC-T * * 3403464 CTTTTCAAAGCCCACAACTCCGTGGCACTCTT 1 CTTCTCAAAGCCCACAACTCCGTGGCAATC-T * * * 3403496 TTTCCCTTTTAAAGCCCACAACTCCGTGGC-ACCTT 1 CTT--C--TCAAAGCCCACAACTCCGTGGCAATC-T 3403531 CTTCTCAAAGCCCACAACTCCGTGGC-ATCT 1 CTTCTCAAAGCCCACAACTCCGTGGCAATCT 3403561 -TTCTC 1 CTTCTC 3403566 CTTCCCAAAG Statistics Matches: 166, Mismatches: 25, Indels: 22 0.78 0.12 0.10 Matches are distributed among these distances: 29 5 0.03 30 1 0.01 31 70 0.42 32 6 0.04 33 6 0.04 34 52 0.31 35 5 0.03 36 21 0.13 ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31 Consensus pattern (31 bp): CTTCTCAAAGCCCACAACTCCGTGGCAATCT Found at i:3403410 original size:34 final size:34 Alignment explanation

Indices: 3403371--3403562 Score: 243 Period size: 34 Copynumber: 5.7 Consensus size: 34 3403361 ATCTCTTCTC * 3403371 AAAGCCCATAACTCCGTGGCACTTTTTTCTTTTT 1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT * 3403405 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTTT 1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT * * 3403439 AAAGCCCACAACTCCGTGGCAC---CTTCTTTTC 1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT * 3403470 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT 1 AAAGCCCACAACTCCGTGGCACT-TTTTT-CTTTTT * * * 3403506 AAAGCCCACAACTCCGTGGCAC---CTTCTTCTC 1 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT 3403537 AAAGCCCACAACTCCGTGGCATCTTT 1 AAAGCCCACAACTCCGTGGCA-CTTT 3403563 CTCCTTCCCA Statistics Matches: 137, Mismatches: 12, Indels: 17 0.83 0.07 0.10 Matches are distributed among these distances: 31 52 0.38 32 3 0.02 34 54 0.39 35 2 0.01 36 26 0.19 ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31 Consensus pattern (34 bp): AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTT Found at i:3403523 original size:67 final size:66 Alignment explanation

Indices: 3403371--3403562 Score: 296 Period size: 67 Copynumber: 2.9 Consensus size: 66 3403361 ATCTCTTCTC * * * * 3403371 AAAGCCCATAACTCCGTGGCACTTTTTTCTTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTCCT 1 AAAGCCCACAACTCCGTGGCAC---CTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTTTTCCC 3403435 TTTT 63 TTTT 3403439 AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT 1 AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCA-TCTTTTTCCCTT 3403504 TT 65 TT * 3403506 AAAGCCCACAACTCCGTGGCACCTTCTTCTCAAAGCCCACAACTCCGTGGCATCTTT 1 AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTT 3403563 CTCCTTCCCA Statistics Matches: 117, Mismatches: 5, Indels: 6 0.91 0.04 0.05 Matches are distributed among these distances: 65 28 0.24 66 5 0.04 67 63 0.54 68 21 0.18 ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31 Consensus pattern (66 bp): AAAGCCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCATCTTTTTCCCTTT T Found at i:3403773 original size:33 final size:33 Alignment explanation

Indices: 3403572--3403960 Score: 567 Period size: 33 Copynumber: 11.9 Consensus size: 33 3403562 TCTCCTTCCC * 3403572 AAAGCCCACACAAGTCGGTGGCAACC-CTCTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT * * 3403604 AAAGCCCACACAAGTTGGTGGCAACCCTTCT-T 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT * 3403636 AAAGCCCACACAAGTTGGTGGCAACCTTTCTC- 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT * * 3403668 AAAGCCCACATAAGTCGGTGGCAACC-CTCTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT * * 3403700 AAAGCCCACACAAGTCGGTGGTAACCTTT-TTT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT * * 3403732 AAAGCCCACACAAGTCGGTGGAAACCTTTTTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT 3403765 AAAGCCCACACAAGTCGGTGGCAAACC-TTCTCT 1 AAAGCCCACACAAGTCGGTGGC-AACCTTTCTCT * 3403798 AAAGCCCACACAAGTCGGTGGCAACCTTTTTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT 3403831 AAAGCCCACACAAGTCGGTGGCAAACC-TTCTCT 1 AAAGCCCACACAAGTCGGTGGC-AACCTTTCTCT * 3403864 AAAGCCCACACAAGTCGGTGGCAACCTTTTTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT * * 3403897 AAAGCCCACACAAGTTGGTGGCAACCATTCTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT * * 3403930 AAAGCCCACACAAGTTGGTGGCAACCCTTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTTTCT 3403961 AAGCCCAATA Statistics Matches: 327, Mismatches: 21, Indels: 17 0.90 0.06 0.05 Matches are distributed among these distances: 31 4 0.01 32 142 0.43 33 173 0.53 34 8 0.02 ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21 Consensus pattern (33 bp): AAAGCCCACACAAGTCGGTGGCAACCTTTCTCT Found at i:3404028 original size:49 final size:49 Alignment explanation

Indices: 3403960--3404489 Score: 655 Period size: 49 Copynumber: 11.1 Consensus size: 49 3403950 GCAACCCTTC * * * 3403960 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT * * * * 3404009 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT * * 3404052 TAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCTTCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT * * * 3404101 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT 3404144 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT * 3404193 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT * * * 3404242 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C-- 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT * * 3404286 -AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTT * * 3404337 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT * * * 3404386 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCATCTT * * 3404438 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT 3404487 TAA 1 TAA 3404490 CATTCCTAAG Statistics Matches: 417, Mismatches: 40, Indels: 48 0.83 0.08 0.10 Matches are distributed among these distances: 43 111 0.27 45 2 0.00 46 1 0.00 47 4 0.01 48 2 0.00 49 214 0.51 50 3 0.01 51 2 0.00 52 78 0.19 ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32 Consensus pattern (49 bp): TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT Found at i:3404122 original size:92 final size:92 Alignment explanation

Indices: 3403955--3404489 Score: 587 Period size: 92 Copynumber: 5.6 Consensus size: 92 3403945 TGGTGGCAAC * * * * * * 3403955 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCTAATG 1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATA * * 3404020 TAGCTGGCCTTGAATCAGCACATTGGCA 65 TCGCTGGCCTTGAATCAGCATATTGGCA * * * * 3404048 CCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT 1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT * * 3404113 AGCTGGCCTTGAATCAGCACATTGGCA 66 CGCTGGCCTTGAATCAGCATATTGGCA * 3404140 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATAT 1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT * 3404205 CGCTAGCCTTGAATCAGCATATTGGCA 66 CGCTGGCCTTGAATCAGCATATTGGCA * * 3404232 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGTC 1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTC * 3404291 CAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCA 60 CAATATCGCTGGCCTTGAATCAGCATATT---G-----G-CA * * * 3404333 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATAT 1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT 3404398 CGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCA 66 CGCTGGCCTTGAATCAGCATATT---G-----G-CA * * 3404434 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA 1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA 3404490 CATTCCTAAG Statistics Matches: 399, Mismatches: 22, Indels: 34 0.88 0.05 0.07 Matches are distributed among these distances: 92 200 0.50 93 4 0.01 95 45 0.11 96 3 0.01 97 2 0.01 98 42 0.11 100 1 0.00 101 102 0.26 ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32 Consensus pattern (92 bp): CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATAT CGCTGGCCTTGAATCAGCATATTGGCA Found at i:3404224 original size:141 final size:141 Alignment explanation

Indices: 3403960--3404489 Score: 649 Period size: 141 Copynumber: 3.7 Consensus size: 141 3403950 GCAACCCTTC * * * * * 3403960 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCTAATGTAGCT 1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCT * 3404025 GGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCAT 60 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT * 3404084 ATTGGCACCTTCTTCTT 125 ATTGGCACCTTCATCTT * 3404101 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT 1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT * * 3404166 GAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGC 66 GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC 3404231 ACCTTCATCTT 131 ACCTTCATCTT * ** 3404242 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGCCTT 1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT * * * * * 3404307 GAATCAACATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT 66 GAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT 3404372 GGCACCTTCATCTT 128 GGCACCTTCATCTT * * * * * 3404386 CAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGTCCAATGTC 1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATT---G-----G-CACCTTTAAGTCCAATATC 3404451 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA 57 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA 3404490 CATTCCTAAG Statistics Matches: 343, Mismatches: 28, Indels: 27 0.86 0.07 0.07 Matches are distributed among these distances: 135 38 0.11 137 1 0.00 139 1 0.00 141 165 0.48 143 1 0.00 144 84 0.24 147 1 0.00 150 10 0.03 151 1 0.00 152 1 0.00 153 40 0.12 ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32 Consensus pattern (141 bp): TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC ACCTTCATCTT Found at i:3404364 original size:52 final size:52 Alignment explanation

Indices: 3404286--3404480 Score: 288 Period size: 52 Copynumber: 3.8 Consensus size: 52 3404276 TGGCACCTCC * * * 3404286 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCGCCTTTGTCATCTTT 1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT * * 3404338 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTC 1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT * ** 3404387 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTT 1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT * 3404439 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT 1 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT 3404481 CATCTTTAAC Statistics Matches: 126, Mismatches: 14, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 49 43 0.34 50 1 0.01 51 1 0.01 52 81 0.64 ACGTcount: A:0.23, C:0.27, G:0.19, T:0.32 Consensus pattern (52 bp): AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTT Found at i:3404435 original size:101 final size:101 Alignment explanation

Indices: 3404141--3404486 Score: 548 Period size: 101 Copynumber: 3.5 Consensus size: 101 3404131 ACATTGGCAC * * * 3404141 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATC 1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC * * 3404206 GCTAGCCTTGAATCAGCATATTGGC-AC-CT-TCAT 66 GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT * 3404239 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--C-TC--CAAGTCCAATATC 1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC * * 3404298 GCTGGCCTTGAATCAACATATTGGCGCCTTTGTCAT 66 GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT 3404334 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC 1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC * 3404399 GCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT 66 GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT 3404435 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT 1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT 3404487 TAACATTCCT Statistics Matches: 228, Mismatches: 11, Indels: 15 0.90 0.04 0.06 Matches are distributed among these distances: 92 35 0.15 93 1 0.00 94 3 0.01 95 46 0.20 96 1 0.00 97 1 0.00 98 40 0.18 99 2 0.01 101 99 0.43 ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32 Consensus pattern (101 bp): CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC GCTGGCCTTGAATCAGCATATTGGCGACTTTGTCAT Found at i:3405314 original size:13 final size:13 Alignment explanation

Indices: 3405296--3405320 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3405286 CATAAAGTGT 3405296 TGTATCGATACAA 1 TGTATCGATACAA 3405309 TGTATCGATACA 1 TGTATCGATACA 3405321 TATTTTTTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3405336 original size:32 final size:33 Alignment explanation

Indices: 3405276--3405341 Score: 98 Period size: 32 Copynumber: 2.0 Consensus size: 33 3405266 TTCAATGATT 3405276 TGTATCGATACATAAAGTGTTGTATCGATACAA 1 TGTATCGATACATAAAGTGTTGTATCGATACAA ** * 3405309 TGTATCGATACAT-ATTTTTTGTATCGATACAA 1 TGTATCGATACATAAAGTGTTGTATCGATACAA 3405341 T 1 T 3405342 TTAAGCTACT Statistics Matches: 30, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 32 17 0.57 33 13 0.43 ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39 Consensus pattern (33 bp): TGTATCGATACATAAAGTGTTGTATCGATACAA Found at i:3405400 original size:13 final size:13 Alignment explanation

Indices: 3405382--3405409 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 3405372 ATTACTCAAA 3405382 TGTATCGATACAT 1 TGTATCGATACAT 3405395 TGTATCGATACAT 1 TGTATCGATACAT 3405408 TG 1 TG 3405410 ATCTTTGTAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3405459 original size:52 final size:50 Alignment explanation

Indices: 3405395--3405539 Score: 209 Period size: 52 Copynumber: 2.8 Consensus size: 50 3405385 ATCGATACAT * 3405395 TGTATCGATACATTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA 1 TGTATCGATACATT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA * 3405447 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA 1 TGTATCGATACATTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA * 3405499 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAA 1 TGTATCGATACATTATT--ATGTATCGATACATGCAGGCAA 3405540 CTTTTCATAT Statistics Matches: 85, Mismatches: 5, Indels: 6 0.89 0.05 0.06 Matches are distributed among these distances: 51 2 0.02 52 83 0.98 ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30 Consensus pattern (50 bp): TGTATCGATACATTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA Found at i:3408642 original size:79 final size:78 Alignment explanation

Indices: 3408548--3408766 Score: 262 Period size: 79 Copynumber: 2.8 Consensus size: 78 3408538 CAACGGGCTA * ** 3408548 GAGTATCCCCGATTATGGAAAATCGGTGTTCTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGA 1 GAGTATCCCTGATTATGGAAAATCAATGTT-TAGAAATAAAATCGGGGTTGGAGTATCCCCTCGA 3408613 AAATAAC-AGGGTTG 65 AAATAACGA-GGTTG * * * 3408627 GAGTATCCCTGATTATAGAAAATCAATATTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCGA 1 GAGTATCCCTGATTATGGAAAATCAATGTTTAG-AAATAAAATCGGGGTTGGAGTATCCCCTCGA 3408692 AAATAACGAGGTTG 65 AAATAACGAGGTTG * * * ** * * 3408706 GAGAAT-CTTCGATTATGAAAAATCAATGATTTAGAAATAAGGTTGGGGTTGAAGTATCCCC 1 GAGTATCCCT-GATTATGGAAAATCAATG-TTTAGAAATAAAATCGGGGTTGGAGTATCCCC 3408767 GATTATGAGA Statistics Matches: 120, Mismatches: 16, Indels: 8 0.83 0.11 0.06 Matches are distributed among these distances: 78 4 0.03 79 111 0.93 80 5 0.04 ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27 Consensus pattern (78 bp): GAGTATCCCTGATTATGGAAAATCAATGTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAA AATAACGAGGTTG Found at i:3408770 original size:51 final size:51 Alignment explanation

Indices: 3408715--3408924 Score: 178 Period size: 51 Copynumber: 4.1 Consensus size: 51 3408705 GGAGAATCTT ** * 3408715 CGATTATGAAAAATCAATGA-TTTAGAAATAAGGTTGGGGTTGAAGTATCCC 1 CGATTATGAAAAATCAAT-ATTTTAGAAATAAAATTGGAGTTGAAGTATCCC * * * * 3408766 CGATTATGAGAAATCAATATTTTGGAAATAAAATTGGAGTTGGAGTATGCC 1 CGATTATGAAAAATCAATATTTTAGAAATAAAATTGGAGTTGAAGTATCCC * *** * 3408817 CGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGG-GTT-AGAGTATCCC 1 CGATTATGAAAAATCAATATTTTAGAAATAAAAT-TGGAGTTGA-AGTATCCC * * * ** * 3408868 CGATTA-CAGTAAATCGATGCTTTAGAAATAAAATCGGAGTTTG-AGTATCCC 1 CGATTATGA-AAAATCAATATTTTAGAAATAAAATTGGAG-TTGAAGTATCCC 3408919 CGATTA 1 CGATTA 3408925 AGAGAAATTG Statistics Matches: 128, Mismatches: 24, Indels: 14 0.77 0.14 0.08 Matches are distributed among these distances: 50 3 0.02 51 121 0.95 52 4 0.03 ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30 Consensus pattern (51 bp): CGATTATGAAAAATCAATATTTTAGAAATAAAATTGGAGTTGAAGTATCCC Found at i:3408821 original size:102 final size:102 Alignment explanation

Indices: 3408715--3408924 Score: 228 Period size: 102 Copynumber: 2.1 Consensus size: 102 3408705 GGAGAATCTT ** ** * 3408715 CGATTATGAAAAATCAATGA-TTTAGAAATAAGGTTGGGGTT-GAAGTATCCCCGATTATGAG-A 1 CGATTATGAAAAATCAAT-ATTTTAGAAATAAAATCAGGGTTAG-AGTATCCCCGATTA-CAGTA * * * * 3408777 AATCAATATTTTGGAAATAAAATTGGAGTTGGAGTATGCC 63 AATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCC * *** 3408817 CGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGGGTTAGAGTATCCCCGATTACAGTAAAT 1 CGATTATGAAAAATCAATATTTTAGAAATAAAATCAGGGTTAGAGTATCCCCGATTACAGTAAAT * * * 3408882 CGATGCTTTAGAAATAAAATCGGAGTTTGAGTATCCC 66 CAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCC 3408919 CGATTA 1 CGATTA 3408925 AGAGAAATTG Statistics Matches: 89, Mismatches: 16, Indels: 6 0.80 0.14 0.05 Matches are distributed among these distances: 101 3 0.03 102 85 0.96 103 1 0.01 ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30 Consensus pattern (102 bp): CGATTATGAAAAATCAATATTTTAGAAATAAAATCAGGGTTAGAGTATCCCCGATTACAGTAAAT CAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCC Found at i:3408947 original size:51 final size:50 Alignment explanation

Indices: 3408758--3408947 Score: 159 Period size: 51 Copynumber: 3.7 Consensus size: 50 3408748 TTGGGGTTGA * * * * * * 3408758 AGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAATTGGAGTTGG 1 AGTATCCCCGATTAAG-GAAATCGATATCTTAGAAATAAAATCGGAGTTAG * * * * * 3408809 AGTATGCCCGATTATGGAAAATTGGTATTTTAGAAATAAAATCAGG-GTTAG 1 AGTATCCCCGATTAAGG-AAATCGATATCTTAGAAATAAAATC-GGAGTTAG * * * 3408860 AGTATCCCCGATTACAGTAAATCGAT-GCTTTAGAAATAAAATCGGAGTTTG 1 AGTATCCCCGATTA-AGGAAATCGATATC-TTAGAAATAAAATCGGAGTTAG * * * 3408911 AGTATCCCCGATTAAGAGAAATTGATGTCTTGGAAAT 1 AGTATCCCCGATTAAG-GAAATCGATATCTTAGAAAT 3408948 GGAACCGAGA Statistics Matches: 113, Mismatches: 19, Indels: 14 0.77 0.13 0.10 Matches are distributed among these distances: 50 5 0.04 51 104 0.92 52 4 0.04 ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31 Consensus pattern (50 bp): AGTATCCCCGATTAAGGAAATCGATATCTTAGAAATAAAATCGGAGTTAG Found at i:3408947 original size:102 final size:102 Alignment explanation

Indices: 3408758--3408947 Score: 231 Period size: 102 Copynumber: 1.9 Consensus size: 102 3408748 TTGGGGTTGA * * * * * 3408758 AGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAATTGGAGTTGGAGTATGCCCGATTA 1 AGTATCCCCGATTATCAGAAATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTA * * * 3408823 TGGAAAATTGGTATTTTAGAAATAAAATCAGGGTTAG 66 AGGAAAATTGATATCTTAGAAATAAAATCAGGGTTAG * * * 3408860 AGTATCCCCGATTA-CAGTAAATCGATGCTTTAGAAATAAAATCGGAGTTTGAGTATCCCCGATT 1 AGTATCCCCGATTATCAG-AAATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATT * * 3408924 AA-GAGAAATTGATGTCTTGGAAAT 65 AAGGA-AAATTGATATCTTAGAAAT 3408948 GGAACCGAGA Statistics Matches: 73, Mismatches: 13, Indels: 4 0.81 0.14 0.04 Matches are distributed among these distances: 101 4 0.05 102 69 0.95 ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31 Consensus pattern (102 bp): AGTATCCCCGATTATCAGAAATCAATACTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTA AGGAAAATTGATATCTTAGAAATAAAATCAGGGTTAG Found at i:3411295 original size:20 final size:19 Alignment explanation

Indices: 3411265--3411338 Score: 76 Period size: 20 Copynumber: 3.7 Consensus size: 19 3411255 AAAATGCCTG * * 3411265 AATGCATCGATACATTGTAA 1 AATGTATCGATACAATG-AA * * 3411285 AATATATCGATACAATGAGC 1 AATGTATCGATACAATGA-A * 3411305 AGTGTATCGATACAATGCAA 1 AATGTATCGATACAATG-AA 3411325 AATGTATCGATACA 1 AATGTATCGATACA 3411339 TCTGGGTAAA Statistics Matches: 44, Mismatches: 8, Indels: 4 0.79 0.14 0.07 Matches are distributed among these distances: 19 1 0.02 20 42 0.95 21 1 0.02 ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27 Consensus pattern (19 bp): AATGTATCGATACAATGAA Found at i:3413874 original size:78 final size:78 Alignment explanation

Indices: 3413783--3414003 Score: 302 Period size: 78 Copynumber: 2.8 Consensus size: 78 3413773 TAAAATCAAA * * * 3413783 GTTGGAGTATCCCCGATTATGGAAATGGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCT 1 GTTGGAGTATCCCCGATTATGGAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCT * 3413848 CGA-AAATAATGGG 66 C-ATAAATAACGGG * * * * 3413861 GTTGGAGTATCCCCGATTGT-GAGAATTAATATTATAGAAATAAAGCCGGGGTTGGAGTATCCCC 1 GTTGGAGTATCCCCGATTATGGA-AATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCC 3413925 TCATAAATAACGGG 65 TCATAAATAACGGG * * * 3413939 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAATAAAGCTGGGGTTGGAGTATCCCC 1 GTTGGAGTATCCCCGATTATG-GAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCC 3414004 GAGATGAAAA Statistics Matches: 124, Mismatches: 15, Indels: 7 0.85 0.10 0.05 Matches are distributed among these distances: 77 3 0.02 78 84 0.68 79 36 0.29 80 1 0.01 ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28 Consensus pattern (78 bp): GTTGGAGTATCCCCGATTATGGAAATTGATGTTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCT CATAAATAACGGG Found at i:3416184 original size:20 final size:20 Alignment explanation

Indices: 3416159--3416209 Score: 77 Period size: 20 Copynumber: 2.5 Consensus size: 20 3416149 AAAATGCCTG * 3416159 AATGTATCGATACAATG-AGC 1 AATGTATCGATACAATGCA-A 3416179 AATGTATCGATACAATGCAA 1 AATGTATCGATACAATGCAA 3416199 AATGTATCGAT 1 AATGTATCGAT 3416210 TCATCTGGGT Statistics Matches: 29, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 20 28 0.97 21 1 0.03 ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27 Consensus pattern (20 bp): AATGTATCGATACAATGCAA Found at i:3418024 original size:65 final size:64 Alignment explanation

Indices: 3417941--3418070 Score: 152 Period size: 65 Copynumber: 2.0 Consensus size: 64 3417931 GTGGCACCCA * * * * * * 3417941 TCTCAAAGTCCACAACTTAATGGCATCTTTTTTTAAAGTCCACGACTCCGTGGCACCCTTTTTTC 1 TCTCAAAATCCACAACTTAATGGCATATCTTCTAAAAATCCACGACTCCGTGGCA-CCTTTTTTC ** * * * 3418006 TCTCAAAATCCATGACTTAGTGGCATATCTTCTAAAAATCCATGACTCTGTGGCACCTTTTTTC 1 TCTCAAAATCCACAACTTAATGGCATATCTTCTAAAAATCCACGACTCCGTGGCACCTTTTTTC 3418070 T 1 T 3418071 TTTTAAGTCC Statistics Matches: 54, Mismatches: 11, Indels: 1 0.82 0.17 0.02 Matches are distributed among these distances: 64 10 0.19 65 44 0.81 ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36 Consensus pattern (64 bp): TCTCAAAATCCACAACTTAATGGCATATCTTCTAAAAATCCACGACTCCGTGGCACCTTTTTTC Found at i:3418112 original size:33 final size:32 Alignment explanation

Indices: 3418056--3418463 Score: 256 Period size: 33 Copynumber: 12.9 Consensus size: 32 3418046 CATGACTCTG 3418056 TGGCACCTTTTTTCTTTTTAAGTCCACAACTCCA 1 TGGCACC-TTTTT-TTTTTAAGTCCACAACTCCA * * 3418090 TGGCACCCTTTTTTTTTTAAGTCCATAACTCCG 1 TGGCA-CCTTTTTTTTTTAAGTCCACAACTCCA ** * * * 3418123 TGGCACAGTTTTCTTCTAAGTCCACAACTTCA 1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA 3418155 TGGCA-CTTTTTTCTTTCTAAGTCCACAACTCCA 1 TGGCACCTTTTTT-TTT-TAAGTCCACAACTCCA * * * 3418188 TGGCACCTTTTTCCTTTTAAATCCACAACTCTA 1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA * * * * 3418221 TGACACC-----CTTTTAGGTCCACAACTCCG 1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA * ** * * * * 3418248 TGGCACCTTTTTCTTCAAAGTCTAGAACTTCT 1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA * * 3418280 TGGCACCTTTTTCTTTTTAAGTCCATAAATCCA 1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA * * * * * 3418313 TAGTACC-----CTTTTAAGTCCCCAACTCCG 1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA * * * 3418340 TGGCACCTTTTTCCTTTTAAGTTCATAACTCCA 1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA * * * * * 3418373 TAGAACCTTTTTCCTTTTAAGACCACAACTCTA 1 TGGCACCTTTTT-TTTTTAAGTCCACAACTCCA * 3418406 TGGCACC-----TTTTTAAGTCCACAACTCCG 1 TGGCACCTTTTTTTTTTAAGTCCACAACTCCA * 3418433 TGGCA-CTTTTTTCCTTTTAAGTTCACAACTC 1 TGGCACCTTTTTT--TTTTAAGTCCACAACTC 3418464 TATGAAACAT Statistics Matches: 286, Mismatches: 64, Indels: 49 0.72 0.16 0.12 Matches are distributed among these distances: 26 1 0.00 27 63 0.22 31 5 0.02 32 52 0.18 33 144 0.50 34 19 0.07 35 2 0.01 ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38 Consensus pattern (32 bp): TGGCACCTTTTTTTTTTAAGTCCACAACTCCA Found at i:3418150 original size:65 final size:64 Alignment explanation

Indices: 3418050--3418504 Score: 285 Period size: 60 Copynumber: 7.2 Consensus size: 64 3418040 AAAATCCATG * * 3418050 ACTCTGTGGCACCTTTTTTCTTTTTAAGTCCACAACTCCATGGCACCCTTTTTTTTTTAAGTCCA 1 ACTCCGTGGCACC-TTTTTC-TTCTAAGTCCACAACTCCATGGCA-CCTTTTTTTTTTAAGTCCA * 3418115 TA 63 CA ** * 3418117 ACTCCGTGGCACAGTTTTCTTCTAAGTCCACAACTTCATGGCA-CTTTTTTCTTTCTAAGTCCAC 1 ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTTT-TTT-TAAGTCCAC 3418181 A 64 A * * * * * * * 3418182 ACTCCATGGCACCTTTTTCCTTTTAAATCCACAACTCTATGACACC-----CTTTTAGGTCCACA 1 ACTCCGTGGCACCTTTTT-CTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA * * * * * * 3418242 ACTCCGTGGCACCTTTTTCTTCAAAGTCTAGAACTTCTTGGCACCTTTTTCTTTTTAAGTCCATA 1 ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTT-TTTTTAAGTCCACA * * * * * * * * * * 3418307 AATCCATAGTACC-----CTTTTAAGTCCCCAACTCCGTGGCACCTTTTTCCTTTTAAGTTCATA 1 ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTT-TTTTTAAGTCCACA * * * * * * 3418367 ACTCCATAGAACCTTTTTCCTTTTAAGACCACAACTCTATGGCACC-----TTTTTAAGTCCACA 1 ACTCCGTGGCACCTTTTT-CTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA * * * * ** * * ** * 3418427 ACTCCGTGGCACTTTTTTCCTTTTAAGTTCACAACTCTATGAAACATTTTTCTTCAAAGTCTACA 1 ACTCCGTGGCACCTTTTT-CTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA * 3418492 ACTCTGTGGCACC 1 ACTCCGTGGCACC 3418505 CTTCTTTAAA Statistics Matches: 301, Mismatches: 66, Indels: 44 0.73 0.16 0.11 Matches are distributed among these distances: 59 18 0.06 60 123 0.41 61 3 0.01 63 7 0.02 64 3 0.01 65 87 0.29 66 48 0.16 67 12 0.04 ACGTcount: A:0.23, C:0.29, G:0.11, T:0.38 Consensus pattern (64 bp): ACTCCGTGGCACCTTTTTCTTCTAAGTCCACAACTCCATGGCACCTTTTTTTTTTAAGTCCACA Found at i:3418356 original size:125 final size:127 Alignment explanation

Indices: 3418071--3418417 Score: 318 Period size: 125 Copynumber: 2.8 Consensus size: 127 3418061 CCTTTTTTCT * ** 3418071 TTTTAAGTCCACAACTCCATGGCACCCTTTTT-TTTTTAAGTCCATAACTCCGTGGCACAGTTTT 1 TTTTAAGTCCACAACTCCATGGCA-CCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTT * * * * 3418135 CTTCTAAGTCCACAACTTCATGGCACTTTTTTCTTTCTAAGTCCACAACTCCATGGCACCTTTTT 65 CTTCAAAGTCCACAACTTCATGGCACCTTTTTCTTTCTAAGTCCACAAATCCATAGCACC----T 3418200 CC 126 CC * * * * * 3418202 TTTTAAATCCACAACTCTATGACA-C-----CCTTTTAGGTCCACAACTCCGTGGCACCTTTTTC 1 TTTTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTTC * * * * * * 3418261 TTCAAAGTCTAGAACTTCTTGGCACCTTTTTCTTTTTAAGTCCATAAATCCATAGTA-C-CC 66 TTCAAAGTCCACAACTTCATGGCACCTTTTTCTTTCTAAGTCCACAAATCCATAGCACCTCC * * * * * * 3418321 TTTTAAGTCCCCAACTCCGTGGCACCTTTTTCCTTTTAAGTTCATAACTCCATAGAACCTTTTTC 1 TTTTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTT- ** * 3418386 CTTTTAAGACCACAAC-TCTATGGCACCTTTTT 65 CTTCAAAGTCCACAACTTC-ATGGCACCTTTTT 3418418 AAGTCCACAA Statistics Matches: 172, Mismatches: 35, Indels: 23 0.75 0.15 0.10 Matches are distributed among these distances: 119 21 0.12 120 1 0.01 124 1 0.01 125 104 0.60 126 23 0.13 129 1 0.01 131 21 0.12 ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38 Consensus pattern (127 bp): TTTTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAAGTCCATAACTCCGTGGCACCTTTTTC TTCAAAGTCCACAACTTCATGGCACCTTTTTCTTTCTAAGTCCACAAATCCATAGCACCTCC Found at i:3418429 original size:93 final size:93 Alignment explanation

Indices: 3418050--3418478 Score: 382 Period size: 93 Copynumber: 4.6 Consensus size: 93 3418040 AAAATCCATG * * * * * * 3418050 ACTCTGTGGCACCTTTTTTCTTTTTAAGTCCACAACTCCATGGCACCCTTTTT-TTTTTAAGTCC 1 ACTCCGTGGCACC-TTTTTCCTTTTAAGTTCACAACTCCATGG-AACCTTTTTCCTTTTAAGACC * * * * 3418114 ATAACTCCGTGGCACAGTTTTCTTCTAAGTCCACA 64 ACAACTCCATGGCAC-----CCTTTTAAGTCCACA * * * * * 3418149 ACTTCATGGCA-CTTTTTTCTTTCTAAGTCCACAACTCCATGGCACCTTTTTCCTTTTAA-ATCC 1 ACTCCGTGGCACCTTTTTCCTTT-TAAGTTCACAACTCCATGGAACCTTTTTCCTTTTAAGA-CC * * * 3418212 ACAACTCTATGACACCCTTTTAGGTCCACA 64 ACAACTCCATGGCACCCTTTTAAGTCCACA ** * * * * * * 3418242 ACTCCGTGGCACCTTTTT-CTTCAAAG-TCTAGAACTTCTTGGCACCTTTTTCTTTTTAAGTCCA 1 ACTCCGTGGCACCTTTTTCCTTTTAAGTTC-ACAACTCCATGGAACCTTTTTCCTTTTAAGACCA * * * * * 3418305 TAAATCCATAGTACCCTTTTAAGTCCCCA 65 CAACTCCATGGCACCCTTTTAAGTCCACA * * 3418334 ACTCCGTGGCACCTTTTTCCTTTTAAGTTCATAACTCCATAGAACCTTTTTCCTTTTAAGACCAC 1 ACTCCGTGGCACCTTTTTCCTTTTAAGTTCACAACTCCATGGAACCTTTTTCCTTTTAAGACCAC * * 3418399 AACTCTATGGCACCTTTTTAAGTCCACA 66 AACTCCATGGCACCCTTTTAAGTCCACA * * * * 3418427 ACTCCGTGGCACTTTTTTCCTTTTAAGTTCACAACTCTATGAAACATTTTTC 1 ACTCCGTGGCACCTTTTTCCTTTTAAGTTCACAACTCCATGGAACCTTTTTC 3418479 TTCAAAGTCT Statistics Matches: 266, Mismatches: 56, Indels: 22 0.77 0.16 0.06 Matches are distributed among these distances: 91 1 0.00 92 70 0.26 93 125 0.47 94 8 0.03 97 15 0.06 98 39 0.15 99 8 0.03 ACGTcount: A:0.23, C:0.29, G:0.10, T:0.38 Consensus pattern (93 bp): ACTCCGTGGCACCTTTTTCCTTTTAAGTTCACAACTCCATGGAACCTTTTTCCTTTTAAGACCAC AACTCCATGGCACCCTTTTAAGTCCACA Found at i:3418441 original size:26 final size:27 Alignment explanation

Indices: 3418387--3418444 Score: 80 Period size: 27 Copynumber: 2.1 Consensus size: 27 3418377 ACCTTTTTCC * 3418387 TTTTAAGACCACAACTCTATGGCACCT 1 TTTTAAGACCACAACTCCATGGCACCT * * * 3418414 TTTTAAGTCCACAACTCCGTGGCACTT 1 TTTTAAGACCACAACTCCATGGCACCT 3418441 TTTT 1 TTTT 3418445 CCTTTTAAGT Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 27 27 1.00 ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36 Consensus pattern (27 bp): TTTTAAGACCACAACTCCATGGCACCT Found at i:3418477 original size:33 final size:33 Alignment explanation

Indices: 3418319--3418495 Score: 93 Period size: 33 Copynumber: 5.6 Consensus size: 33 3418309 TCCATAGTAC * * ** * 3418319 CCTTTTAAGTCCCCAACTCCGTGGCACCTTTTT 1 CCTTTTAAGTCCACAACTCCATGAAACATTTTT * * * 3418352 CCTTTTAAGTTCATAACTCCAT-AGAACCTTTTT 1 CCTTTTAAGTCCACAACTCCATGA-AACATTTTT * * * 3418385 CCTTTTAAGACCACAACTCTATG--GCA----- 1 CCTTTTAAGTCCACAACTCCATGAAACATTTTT * ** * 3418411 CCTTTTTAAGTCCACAACTCCGTGGCACTTTTTT 1 CC-TTTTAAGTCCACAACTCCATGAAACATTTTT * * 3418445 CCTTTTAAGTTCACAACTCTATGAAACATTTTT 1 CCTTTTAAGTCCACAACTCCATGAAACATTTTT ** * 3418478 -CTTCAAAGTCTACAACTC 1 CCTTTTAAGTCCACAACTC 3418496 TGTGGCACCC Statistics Matches: 107, Mismatches: 27, Indels: 21 0.69 0.17 0.14 Matches are distributed among these distances: 26 2 0.02 27 18 0.17 29 1 0.01 31 1 0.01 32 14 0.13 33 69 0.64 34 2 0.02 ACGTcount: A:0.25, C:0.29, G:0.09, T:0.37 Consensus pattern (33 bp): CCTTTTAAGTCCACAACTCCATGAAACATTTTT Found at i:3418533 original size:32 final size:32 Alignment explanation

Indices: 3418497--3418900 Score: 229 Period size: 32 Copynumber: 12.4 Consensus size: 32 3418487 CTACAACTCT * 3418497 GTGGCACCCTTCTTTAAAGCCCACACAAGTTG 1 GTGGCACCCTTCTTTAAAGCCCACACAAGTCG * * * 3418529 GTGGCA-ACTTCTTTTAAAGCCCACACAAATTG 1 GTGGCACCCTTC-TTTAAAGCCCACACAAGTCG * ** 3418561 GTGGTAACCCTT-TCAAAAGCCCACACAAGTCG 1 GTGG-CACCCTTCTTTAAAGCCCACACAAGTCG * * * 3418593 GTGGAAACC-TCTTTCAAAAG-CC-CACAAGTTG 1 GTGGCACCCTTCTTT--AAAGCCCACACAAGTCG * * 3418624 GTGGCAACCC-TCTCTAAAGCCCACACAAGTCA 1 GTGGC-ACCCTTCTTTAAAGCCCACACAAGTCG ** * 3418656 GTGGCAACCCTTCTCAAAAGCCCACACAAGTCA 1 GTGGC-ACCCTTCTTTAAAGCCCACACAAGTCG * * * 3418689 GAGGCA-ACATCTTTCAAAAGCCCACACAAGTCG 1 GTGGCACCCTTCTTT--AAAGCCCACACAAGTCG * * 3418722 GTGGCAACC-TCTTTCAAAAGCCCACATAAGTCG 1 GTGGCACCCTTCTTT--AAAGCCCACACAAGTCG * * * 3418755 GTGGTAACCTT-TTTCAAAGCCCACACAAGTTG 1 GTGGCACCCTTCTTT-AAAGCCCACACAAGTCG * * * * 3418787 GTGGTA-ACTTCTTTTCTAAAGCCCACAAAAGTCA 1 GTGGCACCCTTC--TT-TAAAGCCCACACAAGTCG * * * * 3418821 GTGGCAACCC-CCTTCAAAAGCCCACATAAGTTG 1 GTGGC-ACCCTTCTT-TAAAGCCCACACAAGTCG * ** * * 3418854 GTGGTAACCC-TCTCAAAAGCCCACATATGTCG 1 GTGG-CACCCTTCTTTAAAGCCCACACAAGTCG 3418886 GTGGCATCTCCTTCT 1 GTGGCA-C-CCTTCT 3418901 AAGCCCAATG Statistics Matches: 300, Mismatches: 48, Indels: 46 0.76 0.12 0.12 Matches are distributed among these distances: 30 5 0.02 31 31 0.10 32 118 0.39 33 114 0.38 34 28 0.09 35 3 0.01 36 1 0.00 ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22 Consensus pattern (32 bp): GTGGCACCCTTCTTTAAAGCCCACACAAGTCG Found at i:3418612 original size:33 final size:33 Alignment explanation

Indices: 3418512--3418891 Score: 407 Period size: 33 Copynumber: 11.7 Consensus size: 33 3418502 ACCCTTCTTT * * * 3418512 AAAGCCCACACAAGTTGGTGGCAACTTCTTT-T 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * * * 3418544 AAAGCCCACACAAATTGGTGGTAACC-CTTTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * 3418576 AAAGCCCACACAAGTCGGTGGAAACCTCTTTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * * * 3418609 AAAG-CC-CACAAGTTGGTGGCAACC-CTCTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * 3418639 AAAGCCCACACAAGTCAGTGGCAACC-CTTCTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTT-TCA * * * 3418672 AAAGCCCACACAAGTCAGAGGCAACATCTTTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA 3418705 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * * * 3418738 AAAGCCCACATAAGTCGGTGGTAACCTTTTTC- 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * * * * 3418770 AAAGCCCACACAAGTTGGTGGTAACTTCTTTTCT 1 AAAGCCCACACAAGTCGGTGGCAACCTC-TTTCA * * * * 3418804 AAAGCCCACAAAAGTCAGTGGCAACCCCCTTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * * * * 3418837 AAAGCCCACATAAGTTGGTGGTAACC-CTCTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA * * 3418869 AAAGCCCACATATGTCGGTGGCA 1 AAAGCCCACACAAGTCGGTGGCA 3418892 TCTCCTTCTA Statistics Matches: 296, Mismatches: 44, Indels: 16 0.83 0.12 0.04 Matches are distributed among these distances: 30 8 0.03 31 22 0.07 32 114 0.39 33 127 0.43 34 25 0.08 ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21 Consensus pattern (33 bp): AAAGCCCACACAAGTCGGTGGCAACCTCTTTCA Found at i:3419047 original size:52 final size:52 Alignment explanation

Indices: 3418975--3419270 Score: 234 Period size: 52 Copynumber: 5.5 Consensus size: 52 3418965 CAACGTCATC * * * * ** * 3418975 GGCCTTGAATCAACACATTGGCACCTTTTTTTTTCTT-AAGTCTAATATCGTT 1 GGCCTTAAATCAGCATATTGGCACC-TTTGTCATCTTCAAGTCTAATATCGCT * ** * * 3419027 GGCCTTAAATTAGCATATTGGTGCCTTTGTCATCTTTAAGTCTAATATTGCT 1 GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT * * * * * 3419079 GGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCATCTTCAAGTCTAATGTCACT 1 GGCCTTAAATCAGCATATTGGCA-C----C--T-TTGTCATCTTCAAGTCTAATATCGCT * * * * * 3419139 GGCCTTGAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAATATCGCT 1 GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT * ** * * 3419191 GGCCTTGAATCAGCATATTGGCACCTTCATCATCTTCAAGCCTGATATCGCT 1 GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT * * * 3419243 GGCCGTAAATTAGAATATTGGCACCTTT 1 GGCCTTAAATCAGCATATTGGCACCTTT 3419271 AAGTCCAATG Statistics Matches: 193, Mismatches: 42, Indels: 18 0.76 0.17 0.07 Matches are distributed among these distances: 51 8 0.04 52 139 0.72 53 2 0.01 55 1 0.01 57 1 0.01 59 2 0.01 60 40 0.21 ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36 Consensus pattern (52 bp): GGCCTTAAATCAGCATATTGGCACCTTTGTCATCTTCAAGTCTAATATCGCT Found at i:3419142 original size:112 final size:111 Alignment explanation

Indices: 3419008--3419208 Score: 276 Period size: 112 Copynumber: 1.8 Consensus size: 111 3418998 CCTTTTTTTT ** * * ** * * * 3419008 TCTTAAGTCTAATATCGTTGGCCTTAAATTAGCATATTGGTGCCTTTGTCATCTTTAAGTCTAAT 1 TCTTAAGTCTAATATCACTGGCCTTAAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAAT * 3419073 ATTGCTGGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCA 66 ATCGCTGGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCA * * 3419119 TCTTCAAGTCTAATGTCACTGGCCTTGAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAA 1 TCTT-AAGTCTAATATCACTGGCCTTAAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAA * 3419184 TATCGCTGGCCTTGAATCAGCATAT 65 TATCGCTGGCCTTAAATCAGCATAT 3419209 TGGCACCTTC Statistics Matches: 76, Mismatches: 13, Indels: 1 0.84 0.14 0.01 Matches are distributed among these distances: 111 4 0.05 112 72 0.95 ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37 Consensus pattern (111 bp): TCTTAAGTCTAATATCACTGGCCTTAAATCAGCATATTAGCACCTTTGTCATCTTGAAGCCCAAT ATCGCTGGCCTTAAATCAGCATATCGACATCTTATCATTCTTCTCA Found at i:3420012 original size:20 final size:21 Alignment explanation

Indices: 3419964--3420017 Score: 65 Period size: 20 Copynumber: 2.6 Consensus size: 21 3419954 TTCTATAATT * * 3419964 TGTATCAATACAAATAGTAAA 1 TGTATCGATACATATAGTAAA * * 3419985 TTTATCGATACATA-AGTGAA 1 TGTATCGATACATATAGTAAA 3420005 TGTATCGATACAT 1 TGTATCGATACAT 3420018 GCTCGAAATG Statistics Matches: 28, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 20 17 0.61 21 11 0.39 ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33 Consensus pattern (21 bp): TGTATCGATACATATAGTAAA Found at i:3421540 original size:19 final size:20 Alignment explanation

Indices: 3421498--3421549 Score: 79 Period size: 19 Copynumber: 2.6 Consensus size: 20 3421488 AAGCTCAAAA * * 3421498 GTATCGATACATATTGCTTT 1 GTATCGATACATGTTGCATT 3421518 GTATCGATACATGTT-CATT 1 GTATCGATACATGTTGCATT 3421537 GTATCGATACATG 1 GTATCGATACATG 3421550 AAATTGGTAG Statistics Matches: 30, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 19 16 0.53 20 14 0.47 ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40 Consensus pattern (20 bp): GTATCGATACATGTTGCATT Found at i:3424581 original size:166 final size:166 Alignment explanation

Indices: 3424398--3424968 Score: 611 Period size: 166 Copynumber: 3.4 Consensus size: 166 3424388 CTTATTTTTA * * * 3424398 AAATACGTGTTTTTTCTTCTCTGTAAATTTTTTCGAGAGAAGTTTTCTTAATTTTTAATTTTTAA 1 AAATACG-GTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAA * ** ** 3424463 AATTCGTCAAATGTTTTTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT 65 AATTCATCAAACATCATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT 3424528 AGTTTTTGAATTTTTTCTTGAAATTTTCCTTTTTTCG 130 AGTTTTTGAATTTTTTCTTGAAATTTTCCTTTTTTCG * * * * 3424565 AAATACGGTGTTTTCTTCTTTGTAAATTTTTTTGAGTAG-ATTTTTCTTAGTTTTTAACTTTTAA 1 AAATACGGTATTTTCTTCTTTGTAAATTTTTTCGAG-AGAATTTTTCTTAATTTTTAATTTTTAA * * 3424629 AATTCATCAAACATCATTATTTATTTTGTATTAATTCTGTTTTCAAAAATTCATTCATTTTCATT 65 AATTCATCAAACATCATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATT * 3424694 CA-TTTTT-AATTTTTTCCTTGAAATTTTTCTTTTTTCG 130 -AGTTTTTGAATTTTTT-CTTGAAATTTTCCTTTTTTCG * ** * * * * * 3424731 AAATACGGTATTTTCTACTTCATAAA--TTTTCAAGGGGATTTTTCTCAGTTTTTAATTTTTAAA 1 AAATACGGTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAAA * * * * 3424794 ATTCATCAAACATCATTATTTGA-TTCATAGTT-ATTCATTTTTCAAAAAATTAATTCTTTTTCA 66 ATTCATCAAACATCATTATTT-ATTTTATA-TTAATTCAGTTTTC-AAAAATTCATTCATTTTCA * * * * * 3424857 TGAG-TTTTGAATTTTTTTTGTTGAAATTCTCCTTTTTCCC 128 TTAGTTTTTGAA--TTTTTTCTTGAAATTTTCCTTTTTTCG * * * * * * ** * 3424897 AAGAAACCGAAATTTCTTCTTTGTAAATTTTTTCGGGAGAA-TTTTCTTGATTTAGAATTTTGAA 1 AA-ATACGGTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAA * 3424961 AACTCATC 65 AATTCATC 3424969 TTGTAAGCTC Statistics Matches: 337, Mismatches: 53, Indels: 27 0.81 0.13 0.06 Matches are distributed among these distances: 163 1 0.00 164 69 0.20 165 31 0.09 166 171 0.51 167 33 0.10 168 24 0.07 169 8 0.02 ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52 Consensus pattern (166 bp): AAATACGGTATTTTCTTCTTTGTAAATTTTTTCGAGAGAATTTTTCTTAATTTTTAATTTTTAAA ATTCATCAAACATCATTATTTATTTTATATTAATTCAGTTTTCAAAAATTCATTCATTTTCATTA GTTTTTGAATTTTTTCTTGAAATTTTCCTTTTTTCG Found at i:3425742 original size:20 final size:18 Alignment explanation

Indices: 3425717--3425769 Score: 63 Period size: 17 Copynumber: 2.9 Consensus size: 18 3425707 GCTGGGTTTA 3425717 ATGTATCGATACAATGCAC 1 ATGTATCGATACAATG-AC * * 3425736 TATGTATTGATACAAT-TC 1 -ATGTATCGATACAATGAC 3425754 ATGTATCGATACAATG 1 ATGTATCGATACAATG 3425770 TATCGATACT Statistics Matches: 29, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 17 14 0.48 18 1 0.03 20 14 0.48 ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34 Consensus pattern (18 bp): ATGTATCGATACAATGAC Found at i:3425772 original size:13 final size:13 Alignment explanation

Indices: 3425754--3425778 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3425744 GATACAATTC 3425754 ATGTATCGATACA 1 ATGTATCGATACA 3425767 ATGTATCGATAC 1 ATGTATCGATAC 3425779 TAAGTGAGTT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3428982 original size:154 final size:155 Alignment explanation

Indices: 3428698--3429374 Score: 539 Period size: 154 Copynumber: 4.4 Consensus size: 155 3428688 GGTAGAATCA * * * * * * 3428698 TCATTATTTATCCTTTTAAGTCCTTTAAGGGTA-TCAGGTATTTTTACATTGAAGGTATCCGCCA 1 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGA-GTACTTTTACGTCGAAGGTATCC-CCT * * * * * * 3428762 AGGA-CATTTTCATAAATTTTCAGAACTGAGTCCTTA-GTTGTCATCGA-ATCTGCTTTTATGCT 64 AGGAGCATTTTCATAATTTTTCAAAACTAAGTCC-TAGGTTGTCATCGAGGTCCGCTTTTATGCC * * 3428824 GAAGGTAGATATTTAGGATAGGTTCATT 128 GAAGGTAGGTATTTAGGATAGGTTCATC * * 3428852 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAATACTTTTATGTCGAAGGTATCCCCTAG 1 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCTAG ** 3428917 GAGCATTTT-AGTAATTTTTCAAAA-TCAAGTCCTAGGTTGTCATCGA-GTTTG-TTTTCATGCC 66 GAGCATTTTCA-TAATTTTTCAAAACT-AAGTCCTAGGTTGTCATCGAGGTCCGCTTTT-ATGCC * * * 3428978 GAAGGTGGGTATTTAGGATACGTTCACC 128 GAAGGTAGGTATTTAGGATAGGTTCATC * * * * * * 3429006 CCATCTA--TATCCTTTTTAAGTCCTTTAGGGGTATCGGGTACTTTTACGTCAAAGTTATCTCCT 1 TCAT-TATTTATCC-TTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCT * * 3429069 AGG-GCCATTTTCATAA-TTTTCTAAAACTAAGT-CTTGAGTTGCCATC-AGGTCCGCTTTTATG 64 AGGAG-CATTTTCATAATTTTTC-AAAACTAAGTCCTAG-GTTGTCATCGAGGTCCGCTTTTATG * * * * * * 3429130 CCAAAAGTGGGCATTTAGGATAGATTCATT 126 CCGAAGGTAGGTATTTAGGATAGGTTCATC * * * * ** * * 3429160 TCATCAATAATCTTTTTAAGTCCTTTAGGGGTATTGAACACTTCTACGTCGAAGATATCCCCT-G 1 TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCTAG * * * * * ** * * * * 3429224 CAGGCATTTTGATAATTTTTTAGAA-TCGAGTTTTAGGTTATCA-CCAGGTTCGCTTTTATGCTG 66 GA-GCATTTTCATAATTTTTCAAAACT-AAGTCCTAGGTTGTCATCGAGGTCCGCTTTTATGCCG 3429287 AAGGTAGGTATTTAGGATAGGTTCATC 129 AAGGTAGGTATTTAGGATAGGTTCATC * * * * 3429314 TCATT-TATAATCTTTTTTAAGTCCTTTAGGGGTA--GCAGGTACTTTTATGTCAAAGGTATCC 1 TCATTAT-TTATC-CTTTTAAGTCCTTTAGGGGTATTG-A-GTACTTTTACGTCGAAGGTATCC 3429375 TTTAGAGGTA Statistics Matches: 421, Mismatches: 75, Indels: 53 0.77 0.14 0.10 Matches are distributed among these distances: 153 34 0.08 154 329 0.78 155 58 0.14 ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39 Consensus pattern (155 bp): TCATTATTTATCCTTTTAAGTCCTTTAGGGGTATTGAGTACTTTTACGTCGAAGGTATCCCCTAG GAGCATTTTCATAATTTTTCAAAACTAAGTCCTAGGTTGTCATCGAGGTCCGCTTTTATGCCGAA GGTAGGTATTTAGGATAGGTTCATC Found at i:3432103 original size:13 final size:13 Alignment explanation

Indices: 3432085--3432109 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3432075 CATAAAGTGT 3432085 TGTATCGATACAA 1 TGTATCGATACAA 3432098 TGTATCGATACA 1 TGTATCGATACA 3432110 TAAGTGTTGT Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3432120 original size:32 final size:33 Alignment explanation

Indices: 3432065--3432128 Score: 121 Period size: 32 Copynumber: 2.0 Consensus size: 33 3432055 TTCAACGATT 3432065 TGTATCGATACATAAAGTGTTGTATCGATACAA 1 TGTATCGATACATAAAGTGTTGTATCGATACAA 3432098 TGTATCGATACAT-AAGTGTTGTATCGATACA 1 TGTATCGATACATAAAGTGTTGTATCGATACA 3432129 TAAGTTTTGT Statistics Matches: 31, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 32 18 0.58 33 13 0.42 ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34 Consensus pattern (33 bp): TGTATCGATACATAAAGTGTTGTATCGATACAA Found at i:3432122 original size:19 final size:19 Alignment explanation

Indices: 3432064--3432147 Score: 108 Period size: 19 Copynumber: 4.7 Consensus size: 19 3432054 TTTCAACGAT 3432064 TTGTATCGATACATAAAGTG 1 TTGTATCGATACAT-AAGTG 3432084 TTGTATCGATAC--AA--- 1 TTGTATCGATACATAAGTG 3432098 -TGTATCGATACATAAGTG 1 TTGTATCGATACATAAGTG * 3432116 TTGTATCGATACATAAGTT 1 TTGTATCGATACATAAGTG 3432135 TTGTATCGATACA 1 TTGTATCGATACA 3432148 ATGTAAGCTA Statistics Matches: 57, Mismatches: 1, Indels: 13 0.80 0.01 0.18 Matches are distributed among these distances: 13 11 0.19 15 2 0.04 17 2 0.04 19 30 0.53 20 12 0.21 ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37 Consensus pattern (19 bp): TTGTATCGATACATAAGTG Found at i:3432208 original size:13 final size:13 Alignment explanation

Indices: 3432190--3432214 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3432180 ATTACTCAAA 3432190 TGTATCGATACAT 1 TGTATCGATACAT 3432203 TGTATCGATACA 1 TGTATCGATACA 3432215 CTGATCTTTG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3432264 original size:52 final size:52 Alignment explanation

Indices: 3432223--3432351 Score: 222 Period size: 52 Copynumber: 2.5 Consensus size: 52 3432213 CACTGATCTT * * 3432223 TGTATCGATATATGCAGGCAAATTTGCCTAGATGTATCGATACACTATAAAA 1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA * * 3432275 TGTATCGATACATGAAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA 1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA 3432327 TGTATCGATACATGCAGGCAAATTT 1 TGTATCGATACATGCAGGCAAATTT 3432352 TCATATTTCG Statistics Matches: 72, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 52 72 1.00 ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29 Consensus pattern (52 bp): TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA Found at i:3438715 original size:14 final size:15 Alignment explanation

Indices: 3438708--3438746 Score: 62 Period size: 15 Copynumber: 2.6 Consensus size: 15 3438698 AAAAGTCAAA 3438708 AAAAAAAAGAAGAGT 1 AAAAAAAAGAAGAGT 3438723 AAAAAAAA-AAGAGT 1 AAAAAAAAGAAGAGT 3438737 CAAAAAAAAG 1 -AAAAAAAAG 3438747 TGTAAAGGCA Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 14 6 0.27 15 16 0.73 ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05 Consensus pattern (15 bp): AAAAAAAAGAAGAGT Found at i:3438726 original size:13 final size:13 Alignment explanation

Indices: 3438709--3438752 Score: 52 Period size: 13 Copynumber: 3.2 Consensus size: 13 3438699 AAAGTCAAAA 3438709 AAAAAAAGAAGAGT 1 AAAAAAA-AAGAGT 3438723 AAAAAAAAAAGAGT 1 -AAAAAAAAAGAGT * * 3438737 CAAAAAAAAGTGT 1 AAAAAAAAAGAGT 3438750 AAA 1 AAA 3438753 GGCAAAATCA Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 13 13 0.50 14 6 0.23 15 7 0.27 ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09 Consensus pattern (13 bp): AAAAAAAAAGAGT Found at i:3438743 original size:17 final size:18 Alignment explanation

Indices: 3438701--3438745 Score: 53 Period size: 15 Copynumber: 2.7 Consensus size: 18 3438691 CACAAACAAA 3438701 AGTCAAAAAAAAAAAGAAG 1 AGTC-AAAAAAAAAAGAAG 3438720 AGT---AAAAAAAA-AAG 1 AGTCAAAAAAAAAAGAAG 3438734 AGTCAAAAAAAA 1 AGTCAAAAAAAA 3438746 GTGTAAAGGC Statistics Matches: 23, Mismatches: 0, Indels: 8 0.74 0.00 0.26 Matches are distributed among these distances: 14 6 0.26 15 8 0.35 17 6 0.26 19 3 0.13 ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07 Consensus pattern (18 bp): AGTCAAAAAAAAAAGAAG Found at i:3440095 original size:30 final size:30 Alignment explanation

Indices: 3440027--3440432 Score: 331 Period size: 31 Copynumber: 13.1 Consensus size: 30 3440017 TTCAAATACC * * * 3440027 TTCTTAAAGTCCATGACTCAGTGGCAATCTC 1 TTCTCAAAGTCCACGACTCAGTGGC-ATCTT * * 3440058 TTCTCAAAGCCCACAACTCAGTGGCAT-TT 1 TTCTCAAAGTCCACGACTCAGTGGCATCTT * * 3440087 TGTCTCAAAGTCCACGATTCTGTGGCATCCTT 1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT 3440119 TTCTTCAAAGTCCACGACTCAGTGGCAT-TT 1 TTC-TCAAAGTCCACGACTCAGTGGCATCTT * 3440149 TATCTCAAAGTCCATGACTCAGTGGCATCCGTT 1 T-TCTCAAAGTCCACGACTCAGTGGCAT-C-TT 3440182 TT-TCAAAGTCCACGACTCAGTGGCAT-TT 1 TTCTCAAAGTCCACGACTCAGTGGCATCTT * * 3440210 TGTCTCAAAGTCCACGGCTTAGTGGCATCCTT 1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT * 3440242 TTCTTCAAAGTCCACGACTCAGTGGCGT-TT 1 TTC-TCAAAGTCCACGACTCAGTGGCATCTT * 3440272 TGTCTCAAAGTCCACGACTTAGTGGCATCCTT 1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT * * * 3440304 TTCTTCAAAGTCCACAACTTC-GTGGTACCTT 1 TTC-TCAAAGTCCACGAC-TCAGTGGCATCTT ** * * 3440335 GTTCTTTGTAAGTCCACGACTCCGTGGCACCTT 1 -TTC--TCAAAGTCCACGACTCAGTGGCATCTT * * * * 3440368 CCTT-TCAAAGTCAAAGACTCCGTGGCACCTTT 1 --TTCTCAAAGTCCACGACTCAGTGGCATC-TT * * * * 3440400 TTTTCAAAGCCCACAACTCCGTGGCACTCTT 1 TTCTCAAAGTCCACGACTCAGTGGCA-TCTT 3440431 TT 1 TT 3440433 TCCCTTTTAA Statistics Matches: 312, Mismatches: 38, Indels: 50 0.78 0.09 0.12 Matches are distributed among these distances: 28 3 0.01 29 3 0.01 30 99 0.32 31 101 0.32 32 79 0.25 33 25 0.08 34 2 0.01 ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32 Consensus pattern (30 bp): TTCTCAAAGTCCACGACTCAGTGGCATCTT Found at i:3440251 original size:123 final size:122 Alignment explanation

Indices: 3440032--3440322 Score: 433 Period size: 123 Copynumber: 2.4 Consensus size: 122 3440022 ATACCTTCTT * * 3440032 AAAGTCCATGACTCAGTGGCAAT-CTCTTCTCAAAGCCCACAACTCAGTGGCATTTTGTCTCAAA 1 AAAGTCCATGACTCAGTGGC-ATCCT-TTTTCAAAGTCCACAACTCAGTGGCATTTTGTCTCAAA * 3440096 GTCCACGATTCTGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC 64 GTCCACGATTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC * 3440155 AAAGTCCATGACTCAGTGGCATCCGTTTTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCAAAG 1 AAAGTCCATGACTCAGTGGCATCC-TTTTTCAAAGTCCACAACTCAGTGGCATTTTGTCTCAAAG * * * 3440220 TCCACGGCTT-AGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCGTTTTGTCTC 65 TCCAC-GATTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC * * 3440278 AAAGTCCACGACTTAGTGGCATCCTTTTCTTCAAAGTCCACAACT 1 AAAGTCCATGACTCAGTGGCATCC-TTT-TTCAAAGTCCACAACT 3440323 TCGTGGTACC Statistics Matches: 153, Mismatches: 11, Indels: 7 0.89 0.06 0.04 Matches are distributed among these distances: 122 2 0.01 123 132 0.86 124 19 0.12 ACGTcount: A:0.24, C:0.28, G:0.18, T:0.31 Consensus pattern (122 bp): AAAGTCCATGACTCAGTGGCATCCTTTTTCAAAGTCCACAACTCAGTGGCATTTTGTCTCAAAGT CCACGATTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTATCTC Found at i:3440387 original size:31 final size:30 Alignment explanation

Indices: 3440307--3440657 Score: 211 Period size: 31 Copynumber: 10.8 Consensus size: 30 3440297 CATCCTTTTC * * * 3440307 TTCAAAGTCCACAACTTCGTGGTACCTTGTTCT 1 TTCAAAGT-CACAACTCCGTGGCACC-T-TCCT ** * 3440340 TTGTAAGTCCACGACTCCGTGGCACCTTCCT 1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT * ** 3440371 TTCAAAGTCAAAGACTCCGTGGCACCTTTTT 1 TTCAAAGTCACA-ACTCCGTGGCACCTTCCT * 3440402 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT 1 TTCAAAG-TCACAACTCCGTGGCAC-C---TT-CCT * * 3440438 TTTAAAGTCCACAACTTCGTGGCACCTTGTTCCT 1 TTCAAAGT-CACAACTCCGTGGCACC---TTCCT * * 3440472 TT-TAAGTCCACAACTCCGTGGCACCTTCTT 1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT * 3440502 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT 1 TTCAAAG-TCACAACTCCGTGGCAC-C---TT-CCT * * 3440538 TTTAAAGTCCACAACCCCGTGGCACCTTGTTCCT 1 TTCAAAGT-CACAACTCCGTGGCACC---TTCCT * * 3440572 TT-TAAGTCCACAACTCCGTGGCACCTTTCT 1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT * * ** 3440602 TTCAAAGTCCGCGACTCCGTGGCACCTTATT 1 TTCAAAGT-CACAACTCCGTGGCACCTTCCT * 3440633 TTCAAAGCCCACAACTCCGTGGCAC 1 TTCAAAG-TCACAACTCCGTGGCAC 3440658 TCTTTTTCCC Statistics Matches: 259, Mismatches: 41, Indels: 38 0.77 0.12 0.11 Matches are distributed among these distances: 30 14 0.05 31 107 0.41 32 6 0.02 33 63 0.24 34 10 0.04 35 14 0.05 36 45 0.17 ACGTcount: A:0.21, C:0.34, G:0.15, T:0.31 Consensus pattern (30 bp): TTCAAAGTCACAACTCCGTGGCACCTTCCT Found at i:3440504 original size:100 final size:99 Alignment explanation

Indices: 3440279--3440750 Score: 461 Period size: 100 Copynumber: 4.8 Consensus size: 99 3440269 TTTTGTCTCA * ** * * * 3440279 AAGTCCACGACTTAGTGGCATCCTTTTCTTCAAAGTCCACAACTTCGTGGTAC-CTTGTT--CTT 1 AAGTCCACAACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTT * * 3440341 TGT-AAGTCCACGACTCCGTGGCACC---TTCCTTTCA 64 T-TAAAGTCCACAACTCCGTGGCACCTTGTTCCTTT-T * * 3440375 AAGT-CAAAGACTCCGTGGCACCTTTTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT 1 AAGTCCACA-ACTCCGTGGCACC-TTTTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTT * 3440439 TTAAAGTCCACAACTTCGTGGCACCTTGTTCCTTTT 64 TTAAAGTCCACAACTCCGTGGCACCTTGTTCCTTTT * 3440475 AAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT 1 AAGTCCACAACTCCGTGGCACCTT-TTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTT * 3440540 TAAAGTCCACAACCCCGTGGCACCTTGTTCCTTTT 65 TAAAGTCCACAACTCCGTGGCACCTTGTTCCTTTT * * * 3440575 AAGTCCACAACTCCGTGGCACCTTTCTTTCAAAGTCCGCGACTCCGTGGCAC-C-TTAT---TTT 1 AAGTCCACAACTCCGTGGCACCTTT-TTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTT * * * 3440635 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT 65 TAAAGTCCACAACTCCGTGGCAC-CTTGTT-CCTTTT * ** * ** 3440672 AAAG-CCTATAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA-TCTTTCACC 1 -AAGTCC-ACAACTCCGTGGCACCTT-TT--TTCAAAGTCCACAACTCCGTGGCACTCTTTTTCC * 3440735 CTTTTTAAAGCCCACA 61 C-TTTTAAAGTCCACA 3440751 CAAGTCGATG Statistics Matches: 320, Mismatches: 31, Indels: 41 0.82 0.08 0.10 Matches are distributed among these distances: 95 49 0.15 96 27 0.08 97 9 0.03 98 48 0.15 99 5 0.02 100 157 0.49 101 12 0.04 105 13 0.04 ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32 Consensus pattern (99 bp): AAGTCCACAACTCCGTGGCACCTTTTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTT AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTT Found at i:3440640 original size:231 final size:231 Alignment explanation

Indices: 3440310--3440725 Score: 692 Period size: 231 Copynumber: 1.8 Consensus size: 231 3440300 CCTTTTCTTC ** * * 3440310 AAAGTCCACAACTTCGTGGTACCTTGTTCTTTGTAAGTCCACGACTCCGTGGCACCTTCCTTTCA 1 AAAGTCCACAACCCCGTGGCACCTTGTTCTTTGTAAGTCCACAACTCCGTGGCACCTTCCTTTCA * 3440375 AAGTCAAAGACTCCGTGGCACCTTTTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT 66 AAGTCAAAGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT * 3440440 TAAAGTCC-ACAACTTCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTT 131 TAAAG-CCTACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTT 3440504 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT 195 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT * 3440541 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTT-TAAGTCCACAACTCCGTGGCACCTTTCTTTC 1 AAAGTCCACAACCCCGTGGCACCTTGTT-CTTTGTAAGTCCACAACTCCGTGGCACCTTCCTTTC *** 3440605 AAAGTCCGCGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT 65 AAAGTCAAAGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT * * 3440670 TTAAAGCCTATAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA 130 TTAAAGCCTACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCA 3440726 TCTTTCACCC Statistics Matches: 171, Mismatches: 12, Indels: 4 0.91 0.06 0.02 Matches are distributed among these distances: 230 2 0.01 231 165 0.96 232 4 0.02 ACGTcount: A:0.21, C:0.33, G:0.15, T:0.32 Consensus pattern (231 bp): AAAGTCCACAACCCCGTGGCACCTTGTTCTTTGTAAGTCCACAACTCCGTGGCACCTTCCTTTCA AAGTCAAAGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT TAAAGCCTACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTC AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT Found at i:3440655 original size:62 final size:61 Alignment explanation

Indices: 3440032--3440662 Score: 419 Period size: 62 Copynumber: 9.9 Consensus size: 61 3440022 ATACCTTCTT * * * * * * * * * * 3440032 AAAGTCCATGACTCAGTGGCAATCTCTTCTCAAAGCCCACAACTCAGTGGCA-TTTTGTCTC 1 AAAGTCCACGACTCCGTGGC-ACCTTTTTTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC * * * * * * * 3440093 AAAGTCCACGATTCTGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCA-TTTTATCTC 1 AAAGTCCACGACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC * * * * * * * * 3440155 AAAGTCCATGACTCAGTGGCATCCGTTTTTCAAAGTCCACGACTCAGTGGCA-TTTTGTCTC 1 AAAGTCCACGACTCCGTGGCA-CCTTTTTTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC * ** * * ** * * 3440216 AAAGTCCACGGCTTAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGC-GTTTTGTCTC 1 AAAGTCCACGACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC ** * * * 3440278 AAAGTCCACGACTTAGTGGCATCCTTTTCTTCAAAGTCCACAACTTCGTGGTACCTTGTTCTTTG 1 AAAGTCCACGACTCCGTGGCA-CCTTTT-TTCAAAGTCCACAACTCCGTGGCACC-T-TTCTTTC * * * * 3440343 TAAGTCCACGACTCCGTGGCACCTTCCTTTCAAAGT-CAAAGACTCCGTGGCACCTTTTTTTC 1 AAAGTCCACGACTCCGTGGCACCTT-TTTTCAAAGTCCACA-ACTCCGTGGCACCTTTCTTTC * * * * 3440405 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACTTCGTGGCACCTTGTTC 1 AAAGTCCACGACTCCGTGGCAC-C--TTT---TTTCAAAGTCCACAACTCCGTGGCACC-T-TT- 3440470 CTTT- 57 CTTTC * * * 3440474 TAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT 1 AAAGTCCACGACTCCGTGGCACCTT-TTTTCAAAGTCCACAACTCCGTGGCAC-C--TTT--CTT * 3440539 TT 60 TC * * ** 3440541 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTCTTTC 1 AAAGTCCACGACTCCGTGGCACCTT-TT--TTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC * * 3440605 AAAGTCCGCGACTCCGTGGCACCTTATTTTCAAAGCCCACAACTCCGTGGCACTCTTT 1 AAAGTCCACGACTCCGTGGCACCTT-TTTTCAAAGTCCACAACTCCGTGGCAC-CTTT 3440663 TTCCCTTTTA Statistics Matches: 479, Mismatches: 64, Indels: 52 0.81 0.11 0.09 Matches are distributed among these distances: 60 1 0.00 61 77 0.16 62 178 0.37 63 9 0.02 64 75 0.16 65 28 0.06 66 12 0.03 67 46 0.10 68 6 0.01 69 44 0.09 70 3 0.01 ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31 Consensus pattern (61 bp): AAAGTCCACGACTCCGTGGCACCTTTTTTCAAAGTCCACAACTCCGTGGCACCTTTCTTTC Found at i:3440731 original size:131 final size:131 Alignment explanation

Indices: 3440311--3440725 Score: 567 Period size: 131 Copynumber: 3.2 Consensus size: 131 3440301 CTTTTCTTCA * * 3440311 AAGTCCACAACTTCGTGGTACCTTGTTCTTTGTAAGTCCACGACTCCGTGGCACCTTCCTTTCAA 1 AAGTCCACAACTTCGTGGCACCTTGTTCTTT-TAAGTCCACGACTCCGTGGCACCTTCTTTTCAA * * * * 3440376 AG-TCAAAGACTCCGTGGCAC-C-TTTT---TTTCAAAGCCCACAACTCCGTGGCACTCTTTTTC 65 AGCCCACA-ACTCCGTGGCACTCTTTTTCCCTTTTAAAG-CCACAACTCCGTGGCAC-CTTGTT- 3440435 CCTTTT 126 CCTTTT * 3440441 AAAGTCCACAACTTCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCA 1 -AAGTCCACAACTTCGTGGCACCTTGTT-CTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCA * 3440506 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACCCCGTGGCACCTTGTTCC 64 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAG-CCACAACTCCGTGGCACCTTGTTCC 3440571 TTTT 128 TTTT * * * * 3440575 AAGTCCACAACTCCGTGGCACC-T-TTCTTTCAAAGTCCGCGACTCCGTGGCACCTTATTTTCAA 1 AAGTCCACAACTTCGTGGCACCTTGTTCTTT-TAAGTCCACGACTCCGTGGCACCTTCTTTTCAA * 3440638 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCTATAACTCCGTGGCACCTTGTTCCT 65 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCC-ACAACTCCGTGGCACCTTGTTCCT 3440703 TTT 129 TTT 3440706 AAGTCCACAACTTCGTGGCA 1 AAGTCCACAACTTCGTGGCA 3440726 TCTTTCACCC Statistics Matches: 258, Mismatches: 17, Indels: 18 0.88 0.06 0.06 Matches are distributed among these distances: 130 6 0.02 131 184 0.71 132 9 0.03 133 25 0.10 134 6 0.02 135 5 0.02 136 23 0.09 ACGTcount: A:0.20, C:0.33, G:0.15, T:0.32 Consensus pattern (131 bp): AAGTCCACAACTTCGTGGCACCTTGTTCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCAAA GCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCACAACTCCGTGGCACCTTGTTCCTTT T Found at i:3440769 original size:32 final size:32 Alignment explanation

Indices: 3440740--3440875 Score: 179 Period size: 32 Copynumber: 4.3 Consensus size: 32 3440730 TCACCCTTTT 3440740 TAAAGCCCACACAAGTCGATGGCAACCCTTCC 1 TAAAGCCCACACAAGTCGATGGCAACCCTTCC * 3440772 CAAAGCCCACACAAGTC-AGTGGCAACCCTTCC 1 TAAAGCCCACACAAGTCGA-TGGCAACCCTTCC * * * * 3440804 TAAAGCCCACACAAGTTGGTGACAACCATTCTC 1 TAAAGCCCACACAAGTCGATGGCAACCCTTC-C * 3440837 TAAAGCCCACACAAGTCGGTGGCAACCCTT-C 1 TAAAGCCCACACAAGTCGATGGCAACCCTTCC 3440868 T-AAGCCCA 1 TAAAGCCCA 3440876 ATATCGCTGG Statistics Matches: 92, Mismatches: 9, Indels: 8 0.84 0.08 0.07 Matches are distributed among these distances: 30 7 0.08 31 3 0.03 32 54 0.59 33 28 0.30 ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16 Consensus pattern (32 bp): TAAAGCCCACACAAGTCGATGGCAACCCTTCC Found at i:3441030 original size:92 final size:92 Alignment explanation

Indices: 3440868--3441185 Score: 351 Period size: 92 Copynumber: 3.5 Consensus size: 92 3440858 GCAACCCTTC * 3440868 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT * * 3440933 GGCCTTGAATCAGTACATTGGCACCTG 66 AGCCTTGAATCAGCACATTGGCACCTG * * * * 3440960 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCACTGTAGCT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT * 3441025 AGCCTTGAATCAGCACATTGGCACCTT 66 AGCCTTGAATCAGCACATTGGCACCTG ** * * * * * 3441052 TAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCT 1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT * * 3441111 GGCCTTGAATCAGCATATTGGCACCTTTG 66 AGCCTTGAATCAGCACATTGGCACC--TG * * * * 3441140 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGAACATTGGCACCT 1 ----TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT 3441186 CCAAGTCTAA Statistics Matches: 197, Mismatches: 21, Indels: 14 0.85 0.09 0.06 Matches are distributed among these distances: 86 39 0.20 88 1 0.01 91 1 0.01 92 155 0.79 93 1 0.01 ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30 Consensus pattern (92 bp): TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAATCCAATGTAGCT AGCCTTGAATCAGCACATTGGCACCTG Found at i:3441192 original size:92 final size:92 Alignment explanation

Indices: 3441049--3441736 Score: 1112 Period size: 92 Copynumber: 7.4 Consensus size: 92 3441039 ACATTGGCAC * 3441049 CTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC 1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC * 3441114 CTTGAATCAGCATATTGGCACCTTTGT 66 CTTGAATCAGCATATTGGCACCTTTAT * ** * 3441141 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGAACATTGGCACCTCCAAGTCTAATATCGCTGGC 1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC * 3441206 CTTGAATCAGCATATTGGCACTTTTAT 66 CTTGAATCAGCATATTGGCACCTTTAT * * * 3441233 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATCGGCACCTTTAAGTCCAATATCGTTGGC 1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC * 3441298 CTTGAATCAGCATATTGGCACCTTTGT 66 CTTGAATCAGCATATTGGCACCTTTAT ** 3441325 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC 1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC 3441390 CTTGAATCAGCATATTGGCACCTTTAT 66 CTTGAATCAGCATATTGGCACCTTTAT * 3441417 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCACCTTTAAGTCCAATATCGCTGGC 1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC 3441482 CTTGAATCAGCATATTGGCACCTTTAT 66 CTTGAATCAGCATATTGGCACCTTTAT 3441509 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC 1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC * 3441574 CTTGAATCAGCATATTGGCACC-TCAT 66 CTTGAATCAGCATATTGGCACCTTTAT 3441600 CTTTTAAG-CCTAATGTCA-CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT 1 C-TTTAAGTCC-AATGT-AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT * * 3441663 GGCCTTGAATTAGCATATTGGCGCCTCTGTCAT 63 GGCCTTGAATCAGCATATTGGCACCT-T-T-AT * * * * 3441696 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGC 1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC 3441737 GTCTTTGTCA Statistics Matches: 553, Mismatches: 34, Indels: 15 0.92 0.06 0.02 Matches are distributed among these distances: 91 6 0.01 92 508 0.92 93 1 0.00 94 1 0.00 95 32 0.06 96 5 0.01 ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31 Consensus pattern (92 bp): CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC CTTGAATCAGCATATTGGCACCTTTAT Found at i:3441788 original size:52 final size:52 Alignment explanation

Indices: 3441644--3441778 Score: 225 Period size: 52 Copynumber: 2.6 Consensus size: 52 3441634 ACATTGGCAC * 3441644 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTCTGTCAT 1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTCTGTCAT * * * 3441696 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGTCTTTGTCAT 1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTCTGTCAT * 3441748 CTTTAAGTCCAATGTCGCTGGCCTTGAATCA 1 CTTTAAGTCCAATATCGCTGGCCTTGAATCA 3441779 ATACATTGGC Statistics Matches: 77, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 52 77 1.00 ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35 Consensus pattern (52 bp): CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTCTGTCAT Found at i:3447148 original size:15 final size:16 Alignment explanation

Indices: 3447124--3447157 Score: 52 Period size: 15 Copynumber: 2.2 Consensus size: 16 3447114 AACTATTTAT * 3447124 TTTCAGAATATTAATA 1 TTTCAGAATAGTAATA 3447140 TTTCA-AATAGTAATA 1 TTTCAGAATAGTAATA 3447155 TTT 1 TTT 3447158 TAATCATAAT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 12 0.71 16 5 0.29 ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47 Consensus pattern (16 bp): TTTCAGAATAGTAATA Found at i:3447276 original size:12 final size:11 Alignment explanation

Indices: 3447242--3447313 Score: 64 Period size: 10 Copynumber: 6.9 Consensus size: 11 3447232 TTAATTATAT 3447242 AAATATT-TTA 1 AAATATTATTA 3447252 AAATATTA-TA 1 AAATATTATTA * 3447262 ATA-ATTATTA 1 AAATATTATTA 3447272 AAATATTATT- 1 AAATATTATTA * * 3447282 -TATATTAATA 1 AAATATTATTA * 3447292 TAATTATTATTA 1 -AAATATTATTA 3447304 AAATATTATT 1 AAATATTATT 3447314 TTACAATTTT Statistics Matches: 48, Mismatches: 8, Indels: 11 0.72 0.12 0.16 Matches are distributed among these distances: 9 11 0.23 10 15 0.31 11 15 0.31 12 7 0.15 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (11 bp): AAATATTATTA Found at i:3447291 original size:15 final size:17 Alignment explanation

Indices: 3447265--3447314 Score: 52 Period size: 15 Copynumber: 3.0 Consensus size: 17 3447255 TATTATAATA 3447265 ATTATTAAAATATTATTT 1 ATTATT-AAATATTATTT * 3447283 A-TATT-AATA-TAATT 1 ATTATTAAATATTATTT 3447297 ATTATTAAAATATTATTT 1 ATTATT-AAATATTATTT 3447315 TACAATTTTT Statistics Matches: 26, Mismatches: 2, Indels: 8 0.72 0.06 0.22 Matches are distributed among these distances: 14 5 0.19 15 8 0.31 17 8 0.31 18 5 0.19 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (17 bp): ATTATTAAATATTATTT Found at i:3447356 original size:8 final size:8 Alignment explanation

Indices: 3447343--3447376 Score: 52 Period size: 8 Copynumber: 4.4 Consensus size: 8 3447333 ATATTAACAT 3447343 AAATATTA 1 AAATATTA 3447351 AAATATT- 1 AAATATTA * 3447358 AATTATTA 1 AAATATTA 3447366 AAATATTA 1 AAATATTA 3447374 AAA 1 AAA 3447377 ACTATTTATC Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 7 6 0.26 8 17 0.74 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (8 bp): AAATATTA Found at i:3447366 original size:15 final size:15 Alignment explanation

Indices: 3447346--3447374 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 3447336 TTAACATAAA 3447346 TATTAAAATATTAAT 1 TATTAAAATATTAAT 3447361 TATTAAAATATTAA 1 TATTAAAATATTAA 3447375 AAACTATTTA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45 Consensus pattern (15 bp): TATTAAAATATTAAT Found at i:3447838 original size:22 final size:21 Alignment explanation

Indices: 3447787--3447839 Score: 52 Period size: 22 Copynumber: 2.4 Consensus size: 21 3447777 AATAATAGAT * * 3447787 TATAAATACTCTATTATTAAA 1 TATAAATATTATATTATTAAA * * 3447808 AAAATAATATTATATTATTGAAA 1 TATA-AATATTATATTATT-AAA 3447831 TATAAATAT 1 TATAAATAT 3447840 GCATGTTTAA Statistics Matches: 24, Mismatches: 6, Indels: 3 0.73 0.18 0.09 Matches are distributed among these distances: 21 2 0.08 22 17 0.71 23 5 0.21 ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42 Consensus pattern (21 bp): TATAAATATTATATTATTAAA Found at i:3448785 original size:20 final size:19 Alignment explanation

Indices: 3448759--3448831 Score: 76 Period size: 20 Copynumber: 3.7 Consensus size: 19 3448749 CTGCTAGTTT * 3448759 CATGTATCGATACAATTGAG 1 CATGTATCGATACAA-TGAA * * 3448779 TATGTATCGATGCAATGAA 1 CATGTATCGATACAATGAA * 3448798 CATGTATCGATACAAAGCATA 1 CATGTATCGATACAATG-A-A 3448819 -ATGTATCGATACA 1 CATGTATCGATACA 3448832 TCTGGATGTG Statistics Matches: 45, Mismatches: 6, Indels: 4 0.82 0.11 0.07 Matches are distributed among these distances: 19 17 0.38 20 27 0.60 21 1 0.02 ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29 Consensus pattern (19 bp): CATGTATCGATACAATGAA Found at i:3448804 original size:19 final size:20 Alignment explanation

Indices: 3448759--3448812 Score: 74 Period size: 19 Copynumber: 2.8 Consensus size: 20 3448749 CTGCTAGTTT * 3448759 CATGTATCGATACAATTGAG 1 CATGTATCGATACAATTGAA * * 3448779 TATGTATCGATGCAA-TGAA 1 CATGTATCGATACAATTGAA 3448798 CATGTATCGATACAA 1 CATGTATCGATACAA 3448813 AGCATAATGT Statistics Matches: 29, Mismatches: 5, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 19 16 0.55 20 13 0.45 ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30 Consensus pattern (20 bp): CATGTATCGATACAATTGAA Found at i:3452389 original size:52 final size:52 Alignment explanation

Indices: 3452244--3452368 Score: 241 Period size: 52 Copynumber: 2.4 Consensus size: 52 3452234 ATATGAAAAT 3452244 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC 1 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC * 3452296 TTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAAC 1 TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC 3452348 TTGCCTGCATGTATCGATACA 1 TTGCCTGCATGTATCGATACA 3452369 AAGATCAGTG Statistics Matches: 72, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 52 72 1.00 ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34 Consensus pattern (52 bp): TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAAC Found at i:3452455 original size:19 final size:19 Alignment explanation

Indices: 3452431--3452512 Score: 104 Period size: 19 Copynumber: 4.6 Consensus size: 19 3452421 TAGCTCACAT * * 3452431 TGTATCAATACAAAACTTA 1 TGTATCGATACAACACTTA 3452450 TGTATCGAT---ACA--T- 1 TGTATCGATACAACACTTA 3452463 TGTATCGATACAACACTTA 1 TGTATCGATACAACACTTA 3452482 TGTATCGATACAACACTTA 1 TGTATCGATACAACACTTA 3452501 TGTATCGATACA 1 TGTATCGATACA 3452513 TTATATCGAT Statistics Matches: 55, Mismatches: 2, Indels: 12 0.80 0.03 0.17 Matches are distributed among these distances: 13 9 0.16 14 1 0.02 16 5 0.09 18 1 0.02 19 39 0.71 ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33 Consensus pattern (19 bp): TGTATCGATACAACACTTA Done.