Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr03 135709677 

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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 350 characters in sequence are not A, C, G, or T


File 116 of 438

Found at i:33857760 original size:27 final size:27

Alignment explanation

Indices: 33857722--33857851 Score: 181 Period size: 27 Copynumber: 4.8 Consensus size: 27 33857712 TTATTTACTT 33857722 GTAAAATGACCGAAATACCCCTATAGG 1 GTAAAATGACCGAAATACCCCTATAGG * 33857749 GTAAAATGACCGAAATACCCTTATAGG 1 GTAAAATGACCGAAATACCCCTATAGG * 33857776 GTAAAATGACCAAAATA-CCCTCATAGG 1 GTAAAATGACCGAAATACCCCT-ATAGG * * 33857803 GTAAAATGACCAAAATACCCCTGTAGG 1 GTAAAATGACCGAAATACCCCTATAGG * * * 33857830 GTAAAATAACTGTAATACCCCT 1 GTAAAATGACCGAAATACCCCT 33857852 GTAAGTTAAA Statistics Matches: 93, Mismatches: 8, Indels: 4 0.89 0.08 0.04 Matches are distributed among these distances: 26 3 0.03 27 86 0.92 28 4 0.04 ACGTcount: A:0.42, C:0.22, G:0.16, T:0.21 Consensus pattern (27 bp): GTAAAATGACCGAAATACCCCTATAGG Found at i:33857886 original size:27 final size:27 Alignment explanation

Indices: 33857858--33858072 Score: 188 Period size: 27 Copynumber: 8.0 Consensus size: 27 33857848 CCCTGTAAGT * * * 33857858 TAAAATAACCTTTTTGCCCTTATGTGT 1 TAAAATGACATTTTTGCCCTTATGTGG * * 33857885 TAAAATGACGATTTTT-CCTTTATGTGA 1 TAAAATGAC-ATTTTTGCCCTTATGTGG ** * 33857912 TAAAATGACGGTTTTGCTCTTATGTGG 1 TAAAATGACATTTTTGCCCTTATGTGG * * 33857939 CAAAATGAC-TGTTTTGCCCTTATGTGT 1 TAAAATGACAT-TTTTGCCCTTATGTGG * * 33857966 TAAAGTGACAGTTTTGCCCTTATGTGG 1 TAAAATGACATTTTTGCCCTTATGTGG * * 33857993 TAAAATGACGATTTTT-CTCTTATGAGG 1 TAAAATGAC-ATTTTTGCCCTTATGTGG * * 33858020 TAAAATTAC-TGTTTTGCCCTTATATGG 1 TAAAATGACAT-TTTTGCCCTTATGTGG ** 33858047 TAGGATGAC-TATTTTGCCCTTATGTG 1 TAAAATGACAT-TTTTGCCCTTATGTG 33858073 ATGTATATTT Statistics Matches: 151, Mismatches: 30, Indels: 14 0.77 0.15 0.07 Matches are distributed among these distances: 25 1 0.01 26 8 0.05 27 132 0.87 28 10 0.07 ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42 Consensus pattern (27 bp): TAAAATGACATTTTTGCCCTTATGTGG Found at i:33857916 original size:54 final size:54 Alignment explanation

Indices: 33857858--33858074 Score: 229 Period size: 54 Copynumber: 4.0 Consensus size: 54 33857848 CCCTGTAAGT * * * * * 33857858 TAAAATAACCTTTTTGCCCTTATGTGTTAAAATGACGATTTTTCCTTTATGTGA 1 TAAAATGACCGTTTTGCCCTTATGTGGTAAAATGACGATTTTGCCCTTATGTGA * * * * 33857912 TAAAATGACGGTTTTGCTCTTATGTGGCAAAATGACTG-TTTTGCCCTTATGTGT 1 TAAAATGACCGTTTTGCCCTTATGTGGTAAAATGAC-GATTTTGCCCTTATGTGA * * * * * * 33857966 TAAAGTGACAGTTTTGCCCTTATGTGGTAAAATGACGATTTTTCTCTTATGAGG 1 TAAAATGACCGTTTTGCCCTTATGTGGTAAAATGACGATTTTGCCCTTATGTGA * * * ** * 33858020 TAAAATTACTGTTTTGCCCTTATATGGTAGGATGACTATTTTGCCCTTATGTGA 1 TAAAATGACCGTTTTGCCCTTATGTGGTAAAATGACGATTTTGCCCTTATGTGA 33858074 T 1 T 33858075 GTATATTTAT Statistics Matches: 133, Mismatches: 28, Indels: 4 0.81 0.17 0.02 Matches are distributed among these distances: 53 1 0.01 54 131 0.98 55 1 0.01 ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42 Consensus pattern (54 bp): TAAAATGACCGTTTTGCCCTTATGTGGTAAAATGACGATTTTGCCCTTATGTGA Found at i:33857958 original size:81 final size:80 Alignment explanation

Indices: 33857869--33858074 Score: 268 Period size: 81 Copynumber: 2.5 Consensus size: 80 33857859 AAAATAACCT * * * 33857869 TTTTGCCCTTATGTGTTAAAATGACGATTTTTCCTTTATGTGATAAAATGACGGTTTTGCTCTTA 1 TTTTGCCCTTATGTGTTAAAATGAC-ATTTTGCCCTTATGTGATAAAATGACGATTTTGCTCTTA * 33857934 TGTGGCAAAATGACTG 65 TGAGGCAAAATGACTG * * * 33857950 TTTTGCCCTTATGTGTTAAAGTGACAGTTTTGCCCTTATGTGGTAAAATGACGATTTTTCTCTTA 1 TTTTGCCCTTATGTGTTAAAATGACA-TTTTGCCCTTATGTGATAAAATGACGATTTTGCTCTTA * * 33858015 TGAGGTAAAATTACTG 65 TGAGGCAAAATGACTG * * ** 33858031 TTTTGCCCTTATATGGTAGGATGACTATTTTGCCCTTATGTGAT 1 TTTTGCCCTTATGTGTTAAAATGAC-ATTTTGCCCTTATGTGAT 33858075 GTATATTTAT Statistics Matches: 108, Mismatches: 15, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 80 1 0.01 81 106 0.98 82 1 0.01 ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43 Consensus pattern (80 bp): TTTTGCCCTTATGTGTTAAAATGACATTTTGCCCTTATGTGATAAAATGACGATTTTGCTCTTAT GAGGCAAAATGACTG Found at i:33858432 original size:18 final size:18 Alignment explanation

Indices: 33858401--33858450 Score: 73 Period size: 18 Copynumber: 2.8 Consensus size: 18 33858391 TGCATATTGC * * 33858401 TTACTGTTATTGCACTGA 1 TTACTATTACTGCACTGA * 33858419 TTACTATTACTGCACTGT 1 TTACTATTACTGCACTGA 33858437 TTACTATTACTGCA 1 TTACTATTACTGCA 33858451 ATGGGCCAAG Statistics Matches: 29, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 18 29 1.00 ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44 Consensus pattern (18 bp): TTACTATTACTGCACTGA Found at i:33863838 original size:50 final size:50 Alignment explanation

Indices: 33863710--33863907 Score: 245 Period size: 50 Copynumber: 4.0 Consensus size: 50 33863700 TATATGTAGC * * * * * 33863710 TAGGTCGCATGTGTTGTACTAAGTGCAGGCTACTATGCGTACCCGATAACT 1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T * * * * * 33863761 TCGATCACGTGTGTAGAACTAAGTGCAGGCTACTACGTGTATCAGATAAT 1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT * * 33863811 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAAT 1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT * * * 33863861 T-GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA 1 TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA 33863908 GTTTGGCTAC Statistics Matches: 127, Mismatches: 20, Indels: 2 0.85 0.13 0.01 Matches are distributed among these distances: 49 41 0.32 50 47 0.37 51 39 0.31 ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28 Consensus pattern (50 bp): TAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAAT Found at i:33869100 original size:47 final size:48 Alignment explanation

Indices: 33868895--33869199 Score: 292 Period size: 47 Copynumber: 6.4 Consensus size: 48 33868885 GGATAAGTTA * * * 33868895 CCGATGCCATGTCCAAGACATGGTCTTACACTGGCTATCATCATTGAGG 1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG * * * 33868944 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTAT-ATACG-TG 1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTATC--ATCAT-CGAGG * * * 33868994 CTGATGCATGTCCCAGACAT-GTCTTACACTAGC-A-CAAC-TCTTA-G 1 CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATC-GAGG * * 33869038 CCGATGCATGTCCCAGACA-CGTCTTACACTGGCTATCATCATCGAGG 1 CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG * ** * * 33869085 CCGATGCATGTCCCAGACAT-GTCTTACACTGGCCCTCATC-TCTACG 1 CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG * * 33869131 CCGATGCCATGTCCCAGACATGGTCTTACACTAGC-ACTCAT-ATTGTGG 1 CCGATG-CATGTCCCAGACATGGTCTTACACTAGCTA-TCATCATCGAGG 33869179 CCGATGCATGTCCCAGACATG 1 CCGATGCATGTCCCAGACATG 33869200 TTTTATATCG Statistics Matches: 215, Mismatches: 25, Indels: 34 0.78 0.09 0.12 Matches are distributed among these distances: 43 1 0.00 44 33 0.15 45 1 0.00 46 15 0.07 47 69 0.32 48 37 0.17 49 48 0.22 50 8 0.04 51 3 0.01 ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26 Consensus pattern (48 bp): CCGATGCATGTCCCAGACATGGTCTTACACTAGCTATCATCATCGAGG Found at i:33869182 original size:141 final size:141 Alignment explanation

Indices: 33868895--33869198 Score: 395 Period size: 141 Copynumber: 2.1 Consensus size: 141 33868885 GGATAAGTTA * * * 33868895 CCGATGCCATGTCCAAGACATGGTCTTACACTGGCTATCATCATTGAGGCCGATGCCATGTCCCA 1 CCGATG-CATGTCCCAGACATCGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCA * * * 33868960 AACATGGTCTTACACTAGCTCTCGTATATACGTGCTGATGCATGTCCCAGACATGTCTTACACTA 65 AACATGGTCTTACACTAGCCCTCATATATACG-GCCGATGCATGTCCCAGACATGTCTTACACTA 33869025 GCACAACTCTTAG 129 GCACAACTCTTAG * 33869038 CCGATGCATGTCCCAGACA-CGTCTTACACTGGCTATCATCATCGAGGCCGATG-CATGTCCCAG 1 CCGATGCATGTCCCAGACATCGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCAA * * * 33869101 ACAT-GTCTTACACTGGCCCTCATCTCTAC-GCCGATGCCATGTCCCAGACATGGTCTTACACTA 66 ACATGGTCTTACACTAGCCCTCATATATACGGCCGATG-CATGTCCCAGACAT-GTCTTACACTA * 33869164 GCACTCATA-T-TGTGG 129 GCA--CA-ACTCT-TAG 33869179 CCGATGCATGTCCCAGACAT 1 CCGATGCATGTCCCAGACAT 33869199 GTTTTATATC Statistics Matches: 143, Mismatches: 11, Indels: 15 0.85 0.07 0.09 Matches are distributed among these distances: 137 6 0.04 138 14 0.10 139 34 0.24 140 14 0.10 141 56 0.39 142 13 0.09 143 6 0.04 ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26 Consensus pattern (141 bp): CCGATGCATGTCCCAGACATCGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCAA ACATGGTCTTACACTAGCCCTCATATATACGGCCGATGCATGTCCCAGACATGTCTTACACTAGC ACAACTCTTAG Found at i:33869191 original size:94 final size:92 Alignment explanation

Indices: 33868895--33869200 Score: 336 Period size: 94 Copynumber: 3.2 Consensus size: 92 33868885 GGATAAGTTA * * 33868895 CCGATGCCATGTCCAAGACATGGTCTTACACTGGCTATCATCAT-TGAGGCCGATGCCATGTCCC 1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGC-CTCATC-TCT-A-GCCGATGCCATGTCCC * * 33868959 AAACATGGTCTTACACTAGCTCTCGTATATACGT-G 60 AGACATGGTCTTACACTAGCACTC--ATAT-CGTGG * * * * 33868994 CTGATGCATGTCCCAGACATGTCTTACACTAG-CACAACTCTTAGCCGATG-CATGTCCCAGACA 1 CCGATGCATGTCCCAGACATGTCTTACACTGGCCTCATCTC-TAGCCGATGCCATGTCCCAGACA * * * 33869057 -CGTCTTACACTGGCTA-TCATCATCGAGG 65 TGGTCTTACACTAGC-ACTCAT-ATCGTGG 33869085 CCGATGCATGTCCCAGACATGTCTTACACTGGCCCTCATCTCTACGCCGATGCCATGTCCCAGAC 1 CCGATGCATGTCCCAGACATGTCTTACACTGG-CCTCATCTCTA-GCCGATGCCATGTCCCAGAC * 33869150 ATGGTCTTACACTAGCACTCATATTGTGG 64 ATGGTCTTACACTAGCACTCATATCGTGG 33869179 CCGATGCATGTCCCAGACATGT 1 CCGATGCATGTCCCAGACATGT 33869201 TTTATATCGG Statistics Matches: 177, Mismatches: 19, Indels: 27 0.79 0.09 0.12 Matches are distributed among these distances: 90 4 0.02 91 33 0.19 92 16 0.09 93 25 0.14 94 49 0.28 95 20 0.11 96 1 0.01 97 11 0.06 98 13 0.07 99 5 0.03 ACGTcount: A:0.24, C:0.31, G:0.20, T:0.26 Consensus pattern (92 bp): CCGATGCATGTCCCAGACATGTCTTACACTGGCCTCATCTCTAGCCGATGCCATGTCCCAGACAT GGTCTTACACTAGCACTCATATCGTGG Found at i:33888266 original size:47 final size:47 Alignment explanation

Indices: 33888176--33888445 Score: 173 Period size: 47 Copynumber: 5.8 Consensus size: 47 33888166 TGGGTAAGGT * * * * * 33888176 GCCGATGCCATGTCCCAGACACGGTCCTACCCTGGCTCACATCTC-AA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACT-TCATCTCGAA * * 33888223 GTCGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACT-TCATCTCGAA * * * * * 33888271 GCCGATG-CATGTCCCAAAC-TTGTCTTACACTGGCTTACGTCTCGAG 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTT-CATCTCGAA * * * 33888317 GCCGAAG-CATGTCCCCGACAT-GTCTTACACTAGCACTT-GTCTC-AA 1 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACTTCATCTCGAA * * * * * * ** 33888362 TACTGATGCCATGTCCCGGACATGGCCTTACACTGGCTCTCATAAT-GTG 1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGACT-TCAT-CTCGAA * * 33888411 GCCGAT-ACGTGTCCCAGACAT-GTCTTACACTGACT 1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGACT 33888446 CACGTAAGTG Statistics Matches: 174, Mismatches: 37, Indels: 25 0.74 0.16 0.11 Matches are distributed among these distances: 45 2 0.01 46 69 0.40 47 78 0.45 48 24 0.14 49 1 0.01 ACGTcount: A:0.22, C:0.32, G:0.20, T:0.26 Consensus pattern (47 bp): GCCGATGCCATGTCCCAGACATGGTCTTACACTGACTTCATCTCGAA Found at i:33888359 original size:46 final size:45 Alignment explanation

Indices: 33888231--33888445 Score: 143 Period size: 46 Copynumber: 4.6 Consensus size: 45 33888221 AAGTCGATGC * * 33888231 CATGTCCCAGACATGGTCTTACACTGACTATCATCTCGTAGCCGATG 1 CATGTCCCAGACAT-GTCTTACACTGACT-TCGTCTCGTAGCCGAAG * * * 33888278 CATGTCCCAAACTTGTCTTACACTGGCTTACGTCTCG-AGGCCGAAG 1 CATGTCCCAGACATGTCTTACACTGACTT-CGTCTCGTA-GCCGAAG * * * * 33888324 CATGTCCCCGACATGTCTTACACTAGCACTT-GTCTCAATA-CTGATG 1 CATGTCCCAGACATGTCTTACACT-G-ACTTCGTCTC-GTAGCCGAAG * * * * * * 33888370 CCATGTCCCGGACATGGCCTTACACTGGCTCTCATAAT-GTGGCCGATA- 1 -CATGTCCCAGACAT-GTCTTACACTGACT-TCGT-CTCGTAGCCGA-AG * 33888418 CGTGTCCCAGACATGTCTTACACTGACT 1 CATGTCCCAGACATGTCTTACACTGACT 33888446 CACGTAAGTG Statistics Matches: 130, Mismatches: 25, Indels: 27 0.71 0.14 0.15 Matches are distributed among these distances: 45 2 0.02 46 69 0.53 47 41 0.32 48 17 0.13 49 1 0.01 ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27 Consensus pattern (45 bp): CATGTCCCAGACATGTCTTACACTGACTTCGTCTCGTAGCCGAAG Found at i:33898512 original size:47 final size:47 Alignment explanation

Indices: 33898438--33898661 Score: 165 Period size: 47 Copynumber: 4.8 Consensus size: 47 33898428 GGGTAAGGTG * * * 33898438 CCGATGCCATGTCCCAAACACGATCTTACACTGGCTCACATCTC-AA 1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCGAA * * * 33898484 GTCGATGCCTTGTCCCAGACATGGTCTTACACTGACT-ATCATCTCGTAA 1 -CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-CATCTCG-AA * * * * * 33898533 CCAATG-CAAGTCCCAGACAT-GTCTTACACTGGCTTACGTCTCGAGG 1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCGA-A * * *** 33898579 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTTGTCTC-AA 1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCGAA ** * * 33898623 TGCTAATGCCATGTCCCGGACATGGCCTTACACTGGCTC 1 --CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC 33898662 TCATAATGTG Statistics Matches: 141, Mismatches: 27, Indels: 17 0.76 0.15 0.09 Matches are distributed among these distances: 45 2 0.01 46 59 0.42 47 62 0.44 48 16 0.11 49 2 0.01 ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26 Consensus pattern (47 bp): CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCTCGAA Found at i:33898620 original size:46 final size:45 Alignment explanation

Indices: 33898494--33898707 Score: 164 Period size: 46 Copynumber: 4.6 Consensus size: 45 33898484 GTCGATGCCT * 33898494 TGTCCCAGACATGGTCTTACACTGACTATCATCTCGTA-ACCAATGCA 1 TGTCCCAGACAT-GTCTTACACTGACT-TCATCTCG-AGGCCAATGCA * * * * 33898541 AGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCCGATGCA 1 TGTCCCAGACATGTCTTACACTGACTT-CATCTCGAGGCCAATGCA * * * * 33898587 TGTCCCAGACATGTCTTACACTAGCACTT-GTCTCAATGCTAATGCCA 1 TGTCCCAGACATGTCTTACACT-G-ACTTCATCTCGAGGCCAATG-CA * * * * * ** 33898634 TGTCCCGGACATGGCCTTACACTGGCTCTCATAAT-GTGGCTGATGCA 1 TGTCCCAGACAT-GTCTTACACTGACT-TCAT-CTCGAGGCCAATGCA * 33898681 TGTCCCAAACATGTCTTACACTGACTT 1 TGTCCCAGACATGTCTTACACTGACTT 33898708 ACATAAGTGA Statistics Matches: 134, Mismatches: 24, Indels: 20 0.75 0.13 0.11 Matches are distributed among these distances: 45 3 0.02 46 72 0.54 47 39 0.29 48 19 0.14 49 1 0.01 ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28 Consensus pattern (45 bp): TGTCCCAGACATGTCTTACACTGACTTCATCTCGAGGCCAATGCA Found at i:33903193 original size:20 final size:18 Alignment explanation

Indices: 33903168--33903204 Score: 56 Period size: 20 Copynumber: 1.9 Consensus size: 18 33903158 ATTGCTAAGT 33903168 TGTAAAATGAGTTGTAAATG 1 TGTAAAAT-AGTTG-AAATG 33903188 TGTAAAATAGTTGAAAT 1 TGTAAAATAGTTGAAAT 33903205 TATGAGTTGC Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 4 0.24 19 5 0.29 20 8 0.47 ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35 Consensus pattern (18 bp): TGTAAAATAGTTGAAATG Found at i:33906324 original size:46 final size:45 Alignment explanation

Indices: 33906222--33906388 Score: 185 Period size: 46 Copynumber: 3.6 Consensus size: 45 33906212 GAGATTTGTG * * * * * 33906222 TGCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGA 1 TGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGA * * 33906269 GGGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA 1 -TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA * * 33906315 TAGCCAGTGTCAGACATGTCTGGGACATGCGTCGG-CTACGAGATG- 1 T-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGA * 33906360 TGCTAGTGTAAGACATGTCTGGGACATGC 1 TGCCAGTGTAAGACATGTCTGGGACATGC 33906389 GTCAGCACGG Statistics Matches: 104, Mismatches: 13, Indels: 8 0.83 0.10 0.06 Matches are distributed among these distances: 44 26 0.25 45 3 0.03 46 52 0.50 47 12 0.12 48 11 0.11 ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23 Consensus pattern (45 bp): TGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA Found at i:33906383 original size:44 final size:44 Alignment explanation

Indices: 33906271--33906431 Score: 184 Period size: 46 Copynumber: 3.6 Consensus size: 44 33906261 TGAGACGAGG * 33906271 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAT 1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGG-CTACGAGATG-T * * 33906316 AGCCAGTGTCAGACATGTCTGGGACATGCGTCGGCTACGAGATGT 1 -GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT * * 33906361 GCTAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGT 1 GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTAC-G--AGATGT * 33906407 G-TCAGTGTAAGACCTGTCTGGGACA 1 GCT-AGTGTAAGACATGTCTGGGACA 33906432 CGGCATCGAC Statistics Matches: 102, Mismatches: 8, Indels: 10 0.85 0.07 0.08 Matches are distributed among these distances: 43 2 0.02 44 32 0.31 45 4 0.04 46 64 0.63 ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24 Consensus pattern (44 bp): GCTAGTGTAAGACATGTCTGGGACATGCGTCGGCTACGAGATGT Found at i:33909207 original size:20 final size:18 Alignment explanation

Indices: 33909182--33909218 Score: 56 Period size: 20 Copynumber: 1.9 Consensus size: 18 33909172 ATTGCTAAGT 33909182 TGTAAAATGAGTTGTAAATG 1 TGTAAAAT-AGTTG-AAATG 33909202 TGTAAAATAGTTGAAAT 1 TGTAAAATAGTTGAAAT 33909219 TATGAGTTGC Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 4 0.24 19 5 0.29 20 8 0.47 ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35 Consensus pattern (18 bp): TGTAAAATAGTTGAAATG Found at i:33914747 original size:25 final size:25 Alignment explanation

Indices: 33914719--33914766 Score: 87 Period size: 25 Copynumber: 1.9 Consensus size: 25 33914709 AAAGAGATAC * 33914719 GGAATAAGAATCAAATCCGGTGTAG 1 GGAATAAGAATCAAATCCAGTGTAG 33914744 GGAATAAGAATCAAATCCAGTGT 1 GGAATAAGAATCAAATCCAGTGT 33914767 TTTTTTATGG Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 22 1.00 ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21 Consensus pattern (25 bp): GGAATAAGAATCAAATCCAGTGTAG Found at i:33918864 original size:22 final size:19 Alignment explanation

Indices: 33918825--33918866 Score: 57 Period size: 22 Copynumber: 2.1 Consensus size: 19 33918815 TGCAAAGTTG 33918825 ATAATAATTAATATATATT 1 ATAATAATTAATATATATT 33918844 ATAATAGATATAATTATATATT 1 ATAATA-AT-TAA-TATATATT 33918866 A 1 A 33918867 AAGATTATCA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 19 6 0.30 20 2 0.10 21 3 0.15 22 9 0.45 ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45 Consensus pattern (19 bp): ATAATAATTAATATATATT Found at i:33932341 original size:114 final size:114 Alignment explanation

Indices: 33932209--33932433 Score: 432 Period size: 114 Copynumber: 2.0 Consensus size: 114 33932199 TACTAACATC 33932209 AAACTTCATAAAACTCACATTAGCAACAATAGCTTAACTCAAAATCATCAACAATTTCCAAAATT 1 AAACTTCATAAAACTCACATTAGCAACAATAGCTTAACTCAAAATCATCAACAATTTCCAAAATT 33932274 CATACATGGGCATGATAGTATACAGAGCAACGATCACAAAAACGTAAAA 66 CATACATGGGCATGATAGTATACAGAGCAACGATCACAAAAACGTAAAA * 33932323 AAACTTCATAAAACTCACATTATCAACAATAGCTTAACTCAAAATCATCAACAATTTCCAAAATT 1 AAACTTCATAAAACTCACATTAGCAACAATAGCTTAACTCAAAATCATCAACAATTTCCAAAATT * 33932388 CATACATGGGCATGATAGTATATAGAGCAACGATCACAAAAACGTA 66 CATACATGGGCATGATAGTATACAGAGCAACGATCACAAAAACGTA 33932434 TAAATTATCA Statistics Matches: 109, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 114 109 1.00 ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23 Consensus pattern (114 bp): AAACTTCATAAAACTCACATTAGCAACAATAGCTTAACTCAAAATCATCAACAATTTCCAAAATT CATACATGGGCATGATAGTATACAGAGCAACGATCACAAAAACGTAAAA Found at i:33933249 original size:22 final size:22 Alignment explanation

Indices: 33933223--33933266 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 33933213 GAAAATAATC * 33933223 AAAATTAATCAAAATTTATTAT 1 AAAATTAATCAAAATTCATTAT * 33933245 AAAATTAATTAAAATTCATTAT 1 AAAATTAATCAAAATTCATTAT 33933267 GTTAATAATT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41 Consensus pattern (22 bp): AAAATTAATCAAAATTCATTAT Found at i:33933707 original size:45 final size:46 Alignment explanation

Indices: 33933614--33933708 Score: 124 Period size: 45 Copynumber: 2.1 Consensus size: 46 33933604 CATGCCTTTA * * * 33933614 TGGCTTGCCTGTGTGGGCCTACACGCCCAGATTGGCCTTGCCCTTG 1 TGGCTTACCTGTGTGGGCCTACACGCCCAGATTAGCCTAGCCCTTG 33933660 TGGCTTACCTGTGT-GGCCTACACGCCCA-ACTTAGCCTAG-CCTGTG 1 TGGCTTACCTGTGTGGGCCTACACGCCCAGA-TTAGCCTAGCCCT-TG 33933705 TGGC 1 TGGC 33933709 CCACACAACC Statistics Matches: 44, Mismatches: 3, Indels: 5 0.85 0.06 0.10 Matches are distributed among these distances: 44 4 0.09 45 27 0.61 46 13 0.30 ACGTcount: A:0.12, C:0.33, G:0.28, T:0.27 Consensus pattern (46 bp): TGGCTTACCTGTGTGGGCCTACACGCCCAGATTAGCCTAGCCCTTG Found at i:33940544 original size:40 final size:41 Alignment explanation

Indices: 33940499--33940608 Score: 133 Period size: 39 Copynumber: 2.8 Consensus size: 41 33940489 CTGGAAATTA * * 33940499 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGGC-TAC 1 TATCCGGGCTAAGACCCGAAGGCAATTCGTGCGAGT--CATAC * 33940540 -ATCCGGGCTAAGA-CCGAAGGC-ATTCGTGCGAGTCATTC 1 TATCCGGGCTAAGACCCGAAGGCAATTCGTGCGAGTCATAC 33940578 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGC 1 TATCCGGGCTAAGACCCGAAGGCAATTCGTGC 33940609 ACGTGGTTAT Statistics Matches: 62, Mismatches: 3, Indels: 9 0.84 0.04 0.12 Matches are distributed among these distances: 37 1 0.02 38 5 0.08 39 28 0.45 40 28 0.45 ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22 Consensus pattern (41 bp): TATCCGGGCTAAGACCCGAAGGCAATTCGTGCGAGTCATAC Found at i:33940622 original size:40 final size:40 Alignment explanation

Indices: 33940496--33940624 Score: 156 Period size: 40 Copynumber: 3.2 Consensus size: 40 33940486 ATGCTGGAAA * * 33940496 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG * * ** 33940536 CTACATCCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTCA 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG * 33940575 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG 33940615 TTATATCCGG 1 TTATATCCGG 33940625 TTGTATTCCG Statistics Matches: 74, Mismatches: 12, Indels: 6 0.80 0.13 0.07 Matches are distributed among these distances: 38 3 0.04 39 30 0.41 40 41 0.55 ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG Found at i:33946081 original size:40 final size:40 Alignment explanation

Indices: 33946015--33946165 Score: 164 Period size: 40 Copynumber: 3.8 Consensus size: 40 33946005 AAATTGAATG * * * 33946015 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * *** 33946054 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * 33946094 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * 33946134 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC 33946166 ACGTGTTATA Statistics Matches: 93, Mismatches: 15, Indels: 7 0.81 0.13 0.06 Matches are distributed among these distances: 39 16 0.17 40 75 0.81 41 2 0.02 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:33954076 original size:40 final size:40 Alignment explanation

Indices: 33954010--33954153 Score: 150 Period size: 40 Copynumber: 3.6 Consensus size: 40 33954000 AAATTGAATG * * * 33954010 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * *** 33954049 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * 33954089 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * 33954129 CTATCCGGGCTAAGACCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCA 33954154 TTTGAGCACA Statistics Matches: 85, Mismatches: 16, Indels: 6 0.79 0.15 0.06 Matches are distributed among these distances: 39 16 0.19 40 69 0.81 ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:33954174 original size:40 final size:40 Alignment explanation

Indices: 33954047--33954176 Score: 145 Period size: 40 Copynumber: 3.2 Consensus size: 40 33954037 ATGCTGGAAA * * * 33954047 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG * * * ** 33954087 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG * * * 33954127 TTCTATCCGGGCTAAGACCCGAAGGCATTTGAGC-ACATGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG 33954167 TTATATCCGG 1 TTATATCCGG 33954177 TTATATTCCG Statistics Matches: 72, Mismatches: 17, Indels: 2 0.79 0.19 0.02 Matches are distributed among these distances: 39 1 0.01 40 71 0.99 ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG Found at i:33959666 original size:42 final size:42 Alignment explanation

Indices: 33959553--33959666 Score: 115 Period size: 43 Copynumber: 2.7 Consensus size: 42 33959543 AGTACCGTAC * * * * 33959553 CAATGTCATATCCCAGATATGGTCTTACATGTAATCTCGTAT 1 CAATGCCATATCCCACATATGGTCTTACACGTAATCTCATAT * * * 33959595 CGATGCCAATAGCCAAGC-TATGGTCTTACACG-AAGTCTCATAT 1 CAATGCC-ATATCCCA-CATATGGTCTTACACGTAA-TCTCATAT * 33959638 CAATTCCATATCCCACATATGGTCTTACA 1 CAATGCCATATCCCACATATGGTCTTACA 33959667 TGTTAGTCTT Statistics Matches: 57, Mismatches: 11, Indels: 8 0.75 0.14 0.11 Matches are distributed among these distances: 41 1 0.02 42 25 0.44 43 31 0.54 ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31 Consensus pattern (42 bp): CAATGCCATATCCCACATATGGTCTTACACGTAATCTCATAT Found at i:33970036 original size:27 final size:27 Alignment explanation

Indices: 33970006--33970060 Score: 92 Period size: 27 Copynumber: 2.0 Consensus size: 27 33969996 AAAAAACTAA * 33970006 ATACAATTAAACATTATTTTATAATAT 1 ATACAATTAAACATTATATTATAATAT * 33970033 ATACAATTAAATATTATATTATAATAT 1 ATACAATTAAACATTATATTATAATAT 33970060 A 1 A 33970061 CAAATTATTA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 27 26 1.00 ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44 Consensus pattern (27 bp): ATACAATTAAACATTATATTATAATAT Found at i:33970364 original size:22 final size:22 Alignment explanation

Indices: 33970339--33970381 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 33970329 AGTTAGACCT * 33970339 TTTTTTCTGTTTGT-TTTATTCA 1 TTTTTTCTATTT-TCTTTATTCA 33970361 TTTTTTCTATTTTCTTTATTC 1 TTTTTTCTATTTTCTTTATTC 33970382 TTCCCAATTC Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 21 1 0.05 22 18 0.95 ACGTcount: A:0.09, C:0.12, G:0.05, T:0.74 Consensus pattern (22 bp): TTTTTTCTATTTTCTTTATTCA Found at i:33979420 original size:30 final size:30 Alignment explanation

Indices: 33979386--33979447 Score: 88 Period size: 30 Copynumber: 2.1 Consensus size: 30 33979376 TCCTTAATAC * 33979386 AAACTTTGGAAAAATTACATTTTTGCCCCT 1 AAACTTTGGAAAAATTACACTTTTGCCCCT * * * 33979416 AAACTTTTGCATAATTACACTTTTGCCCCT 1 AAACTTTGGAAAAATTACACTTTTGCCCCT 33979446 AA 1 AA 33979448 GCTCGGGAAT Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 30 28 1.00 ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37 Consensus pattern (30 bp): AAACTTTGGAAAAATTACACTTTTGCCCCT Found at i:33984117 original size:16 final size:16 Alignment explanation

Indices: 33984098--33984133 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 33984088 ACTGTCTTTC 33984098 TGCTCGTCAATGTTAA 1 TGCTCGTCAATGTTAA ** 33984114 TGCTTTTCAATGTTAA 1 TGCTCGTCAATGTTAA 33984130 TGCT 1 TGCT 33984134 TGGATTCTCC Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44 Consensus pattern (16 bp): TGCTCGTCAATGTTAA Found at i:33984134 original size:16 final size:16 Alignment explanation

Indices: 33984104--33984134 Score: 62 Period size: 16 Copynumber: 1.9 Consensus size: 16 33984094 TTTCTGCTCG 33984104 TCAATGTTAATGCTTT 1 TCAATGTTAATGCTTT 33984120 TCAATGTTAATGCTT 1 TCAATGTTAATGCTT 33984135 GGATTCTCCG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48 Consensus pattern (16 bp): TCAATGTTAATGCTTT Found at i:33987181 original size:28 final size:28 Alignment explanation

Indices: 33987148--33987203 Score: 103 Period size: 28 Copynumber: 2.0 Consensus size: 28 33987138 AAATTAATTA * 33987148 AATTATGAATTAATACACATTTTTGGAC 1 AATTATGAATTAATACACATTTCTGGAC 33987176 AATTATGAATTAATACACATTTCTGGAC 1 AATTATGAATTAATACACATTTCTGGAC 33987204 CGTCTTAGGC Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 28 27 1.00 ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38 Consensus pattern (28 bp): AATTATGAATTAATACACATTTCTGGAC Found at i:33988450 original size:51 final size:51 Alignment explanation

Indices: 33988390--33988486 Score: 142 Period size: 51 Copynumber: 1.9 Consensus size: 51 33988380 CGGATACACG * 33988390 GTGGCCTTCACATAGCACCACCCTTGTAG-CCAAACCTATTTTATTCTCAAA 1 GTGGCCTTCACATAGCACCACACTTGT-GTCCAAACCTATTTTATTCTCAAA * ** 33988441 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC 1 GTGGCCTTCACATAGCACCACACTTGTGTCCAAACCTATTTTATTC 33988487 CTAAGGTTCA Statistics Matches: 41, Mismatches: 4, Indels: 2 0.87 0.09 0.04 Matches are distributed among these distances: 50 1 0.02 51 40 0.98 ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33 Consensus pattern (51 bp): GTGGCCTTCACATAGCACCACACTTGTGTCCAAACCTATTTTATTCTCAAA Found at i:33988566 original size:52 final size:52 Alignment explanation

Indices: 33988510--33988638 Score: 224 Period size: 52 Copynumber: 2.5 Consensus size: 52 33988500 AGAAAATTTC 33988510 TCACTTAGCACCA-TGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT 1 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT * * 33988562 TCACTTAGCACATTGCCATGGTCTTATTTCACTTAGATGCCATGGTCTTATT 1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT 33988614 TCACTTAGCACATTGCCATGGACTT 1 TCACTTAGCACATTGCCATGGACTT 33988639 TAGAATAACC Statistics Matches: 73, Mismatches: 3, Indels: 2 0.94 0.04 0.03 Matches are distributed among these distances: 51 2 0.03 52 71 0.97 ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36 Consensus pattern (52 bp): TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT Found at i:33988579 original size:28 final size:27 Alignment explanation

Indices: 33988510--33988638 Score: 171 Period size: 24 Copynumber: 4.9 Consensus size: 27 33988500 AGAAAATTTC 33988510 TCACTTAGCACCATGCCATGGACTTATT 1 TCACTTAGCA-CATGCCATGGACTTATT 33988538 TCACTTAG---ATGCCATGGACTTATT 1 TCACTTAGCACATGCCATGGACTTATT * 33988562 TCACTTAGCACATTGCCATGGTCTTATT 1 TCACTTAGCACA-TGCCATGGACTTATT * 33988590 TCACTTAG---ATGCCATGGTCTTATT 1 TCACTTAGCACATGCCATGGACTTATT 33988614 TCACTTAGCACATTGCCATGGACTT 1 TCACTTAGCACA-TGCCATGGACTT 33988639 TAGAATAACC Statistics Matches: 91, Mismatches: 2, Indels: 16 0.83 0.02 0.15 Matches are distributed among these distances: 24 47 0.52 25 1 0.01 27 2 0.02 28 41 0.45 ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36 Consensus pattern (27 bp): TCACTTAGCACATGCCATGGACTTATT Found at i:33991291 original size:51 final size:51 Alignment explanation

Indices: 33991233--33991329 Score: 151 Period size: 51 Copynumber: 1.9 Consensus size: 51 33991223 CGGATACACG * 33991233 GTGGCCTTCACATAGTACCACCCTTGTAG-CCAAACCTATTTTATTCTCAAA 1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAACCTATTTTATTCTCAAA ** 33991284 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC 1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAACCTATTTTATTC 33991330 CTAAGGTTCA Statistics Matches: 42, Mismatches: 3, Indels: 2 0.89 0.06 0.04 Matches are distributed among these distances: 50 1 0.02 51 41 0.98 ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34 Consensus pattern (51 bp): GTGGCCTTCACATAGTACCACACTTGTGTCCAAACCTATTTTATTCTCAAA Found at i:33991400 original size:24 final size:24 Alignment explanation

Indices: 33991365--33991492 Score: 157 Period size: 24 Copynumber: 5.0 Consensus size: 24 33991355 ACTTAGCACC 33991365 ATGCCATGGACTTATTTCACTTAG 1 ATGCCATGGACTTATTTCACTTAG * 33991389 ATGCCATAGACTTATTTCACTTAG 1 ATGCCATGGACTTATTTCACTTAG * 33991413 CACATTGCCATGGACTTATTTCACTTTGCAC 1 ---A-TGCCATGGACTTATTTCAC-TT--AG 33991444 ATTGCCATGGACTTATTTCACTTAG 1 A-TGCCATGGACTTATTTCACTTAG * 33991469 ATGCCATGGTCTTATTTCACTTAG 1 ATGCCATGGACTTATTTCACTTAG 33991493 CACAATTCCA Statistics Matches: 92, Mismatches: 5, Indels: 14 0.83 0.05 0.13 Matches are distributed among these distances: 24 45 0.49 25 2 0.02 27 3 0.03 28 39 0.42 29 2 0.02 31 1 0.01 ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38 Consensus pattern (24 bp): ATGCCATGGACTTATTTCACTTAG Found at i:33991409 original size:52 final size:52 Alignment explanation

Indices: 33991353--33991492 Score: 180 Period size: 52 Copynumber: 2.7 Consensus size: 52 33991343 GGGAAATTTC 33991353 TCACTTAGCACCATGCCATGGACTTATTTCACTTAGA-TGCCATAGACTTATT 1 TCACTTAGCA-CATGCCATGGACTTATTTCACTTAGATTGCCATAGACTTATT * * 33991405 TCACTTAGCACATTGCCATGGACTTATTTCACTTTGCACATTGCCATGGACTTATT 1 TCACTTAGCACA-TGCCATGGACTTATTTCAC-TT--AGATTGCCATAGACTTATT * 33991461 TCACTTAG---ATGCCATGGTCTTATTTCACTTAG 1 TCACTTAGCACATGCCATGGACTTATTTCACTTAG 33991493 CACAATTCCA Statistics Matches: 79, Mismatches: 4, Indels: 13 0.82 0.04 0.14 Matches are distributed among these distances: 49 1 0.01 51 4 0.05 52 47 0.59 53 3 0.04 55 2 0.03 56 22 0.28 ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37 Consensus pattern (52 bp): TCACTTAGCACATGCCATGGACTTATTTCACTTAGATTGCCATAGACTTATT Found at i:33991422 original size:28 final size:27 Alignment explanation

Indices: 33991353--33991496 Score: 192 Period size: 28 Copynumber: 5.4 Consensus size: 27 33991343 GGGAAATTTC 33991353 TCACTTAGCACCATGCCATGGACTTATT 1 TCACTTAGCA-CATGCCATGGACTTATT * 33991381 TCACTTAG---ATGCCATAGACTTATT 1 TCACTTAGCACATGCCATGGACTTATT 33991405 TCACTTAGCACATTGCCATGGACTTATT 1 TCACTTAGCACA-TGCCATGGACTTATT * 33991433 TCACTTTGCACATTGCCATGGACTTATT 1 TCACTTAGCACA-TGCCATGGACTTATT * 33991461 TCACTTAG---ATGCCATGGTCTTATT 1 TCACTTAGCACATGCCATGGACTTATT 33991485 TCACTTAGCACA 1 TCACTTAGCACA 33991497 ATTCCATATC Statistics Matches: 104, Mismatches: 5, Indels: 15 0.84 0.04 0.12 Matches are distributed among these distances: 24 45 0.43 25 1 0.01 27 2 0.02 28 56 0.54 ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36 Consensus pattern (27 bp): TCACTTAGCACATGCCATGGACTTATT Found at i:33998565 original size:37 final size:37 Alignment explanation

Indices: 33998515--33998587 Score: 137 Period size: 37 Copynumber: 2.0 Consensus size: 37 33998505 TTTAGCTCGA 33998515 ATAATCTCCACACGTACTCATCGGGTCTTACCCGGAC 1 ATAATCTCCACACGTACTCATCGGGTCTTACCCGGAC * 33998552 ATAATCTCCACACGTAGTCATCGGGTCTTACCCGGA 1 ATAATCTCCACACGTACTCATCGGGTCTTACCCGGA 33998588 ATATATTTCC Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 37 35 1.00 ACGTcount: A:0.25, C:0.33, G:0.18, T:0.25 Consensus pattern (37 bp): ATAATCTCCACACGTACTCATCGGGTCTTACCCGGAC Found at i:33998786 original size:48 final size:48 Alignment explanation

Indices: 33998728--33999964 Score: 2051 Period size: 48 Copynumber: 25.8 Consensus size: 48 33998718 ATATACACAC * 33998728 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 33998776 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 33998824 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 33998872 ATCTTATATATATTTCACACTAACCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 33998920 ATCTCATATATATTTCACATTGGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33998968 ATCTCACACATATTTCACACTAGCCATTCGGCTTTTCCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 33999016 ATCCCATTCATATTTCACACTACCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999064 ATATCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 33999112 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999160 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * * 33999208 ATCTTATTCATATTTCATACTAGCCATTTGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999256 ATCTTATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 33999304 ATCTCATATATATTTCACATTAGCCAGTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 33999352 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 33999400 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 33999448 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999496 ATCTCATAGATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999544 ATCTCATTCATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 33999592 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999640 ATCTTATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 33999688 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACAACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 33999736 ATCTCATACATATTTCACACTAGCCATTCGACTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 33999784 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999832 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTATCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999880 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 33999928 ATCTCATATATATTTCACATTAGCCATTCGGCTTTAC 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTAC 33999965 AACACACATA Statistics Matches: 1122, Mismatches: 67, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 48 1122 1.00 ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36 Consensus pattern (48 bp): ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT Found at i:34002505 original size:40 final size:40 Alignment explanation

Indices: 34002449--34002759 Score: 514 Period size: 40 Copynumber: 7.8 Consensus size: 40 34002439 GAATGCACAT * * * 34002449 CACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAA 1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA * 34002489 CACCAGCACGAATGCTCTTCAGGACTTAGCCCGGATATAA 1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA * * 34002529 CACCAACACGAATGCTCTTCGGGACTTAGCCCGGATATAT 1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA * * * 34002569 CACTAGCACGAATGCTCTTCAGGACTTAGCCCGGATATAT 1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA 34002609 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA 1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA * 34002649 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAT 1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA * * 34002689 CACCAGCACGAATGCTCTTTGGAACTTAGCCCGGATATAA 1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA 34002729 CACCAGCACGAATGCTCTTCGGGACTTAGCC 1 CACCAGCACGAATGCTCTTCGGGACTTAGCC 34002760 TGGCTATATA Statistics Matches: 252, Mismatches: 19, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 40 252 1.00 ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22 Consensus pattern (40 bp): CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA Found at i:34004316 original size:48 final size:48 Alignment explanation

Indices: 34004258--34005211 Score: 1613 Period size: 48 Copynumber: 19.9 Consensus size: 48 34004248 ATATACACAC * 34004258 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34004306 ATCTCATACATATTTCACACTAGCCATTCAGTTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004354 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34004402 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACTACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004450 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004498 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATTTACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34004546 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004594 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34004642 ATCTCATATATATTTCACACTAGCCATTCGGATTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 34004690 ATCTCATTCAGATTTCACACTAGCCATTCGGATTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004738 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004786 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004834 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34004882 ATCTTATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34004930 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34004978 ATCTCATACATATTTCACACTAGCCATTCAGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34005026 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34005074 ATCTCAGT-CATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCA-TACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34005122 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 34005170 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACGACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACAT 34005212 GTAACACCTT Statistics Matches: 867, Mismatches: 37, Indels: 4 0.95 0.04 0.00 Matches are distributed among these distances: 47 1 0.00 48 865 1.00 49 1 0.00 ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36 Consensus pattern (48 bp): ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT Found at i:34004723 original size:20 final size:20 Alignment explanation

Indices: 34004653--34004724 Score: 54 Period size: 20 Copynumber: 3.2 Consensus size: 20 34004643 TCTCATATAT 34004653 ATTTCACACTAGCCATTCGG 1 ATTTCACACTAGCCATTCGG * * 34004673 ATTTACCACATATACATATCTCATTCAG 1 ATTT--CAC----AC-TAGC-CATTCGG 34004701 ATTTCACACTAGCCATTCGG 1 ATTTCACACTAGCCATTCGG 34004721 ATTT 1 ATTT 34004725 ACCACATATA Statistics Matches: 40, Mismatches: 4, Indels: 16 0.67 0.07 0.27 Matches are distributed among these distances: 20 14 0.35 21 3 0.08 22 5 0.12 26 5 0.12 27 3 0.08 28 10 0.25 ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35 Consensus pattern (20 bp): ATTTCACACTAGCCATTCGG Found at i:34006637 original size:40 final size:40 Alignment explanation

Indices: 34006581--34006744 Score: 233 Period size: 40 Copynumber: 4.1 Consensus size: 40 34006571 TGGGATTTAA * * * 34006581 CCGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGC 1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC 34006621 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC 34006661 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * * * 34006701 CCGGA-ACTAGTCACTAGCGCAAATGCCTTCAGGACTTAGC 1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC 34006741 CCGG 1 CCGG 34006745 TTATCATCCA Statistics Matches: 115, Mismatches: 7, Indels: 4 0.91 0.06 0.03 Matches are distributed among these distances: 39 2 0.02 40 113 0.98 ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21 Consensus pattern (40 bp): CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC Found at i:34011069 original size:40 final size:40 Alignment explanation

Indices: 34011014--34011368 Score: 586 Period size: 40 Copynumber: 8.9 Consensus size: 40 34011004 TGCACATCAG * * * * 34011014 CAGCATGATTGCTCTTCGGGACCTAACCCGGATATAACAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC * 34011054 CAGCACGAATGCTCTTCAGGACTTAGCCCGGATATAACAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC * * 34011094 CAACACGAATGCTCTTCGGGACTTAGCCCGGATATATCAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC * 34011134 CAGCACGAATGCTCTTCAGGACTTAGCCCGGATATAACAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC * * 34011174 CAACACGAATGCTCTTCGGGACTTAGCCCGGATATATCAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC 34011214 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC * * 34011254 CAGCACGAATGCTCTTCGGAACTTAG-CCGGATATATCAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC 34011293 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC * 34011333 CAGCACGAATGCTCTTCGGGACTTAGCCCGGCTATA 1 CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA 34011369 TAACTCTCAA Statistics Matches: 293, Mismatches: 21, Indels: 2 0.93 0.07 0.01 Matches are distributed among these distances: 39 37 0.13 40 256 0.87 ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21 Consensus pattern (40 bp): CAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACAC Found at i:34012905 original size:48 final size:48 Alignment explanation

Indices: 34012847--34013653 Score: 1348 Period size: 48 Copynumber: 16.9 Consensus size: 48 34012837 ATATACACAC * 34012847 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 34012895 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA-ATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34012942 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34012990 ATCT-ATATATATTTCACACTAGCCATTCAGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34013037 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 34013085 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34013133 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34013181 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34013229 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAC 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 34013277 ATCTTATATATATTTCGCACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34013325 ATCTCATACATATTTCGCACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34013373 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * 34013421 ATCTCATTCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 34013469 ATCTCATTCATATTTCACATTAGCCATTCGGCTTTATCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 34013517 ATCGCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * 34013565 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATACAT 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT * * * 34013613 ATCTCATATATATTTCACATTAGCCATTCGGATTTACCACA 1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACA 34013654 CACATATATA Statistics Matches: 723, Mismatches: 34, Indels: 4 0.95 0.04 0.01 Matches are distributed among these distances: 47 90 0.12 48 633 0.88 ACGTcount: A:0.30, C:0.28, G:0.07, T:0.36 Consensus pattern (48 bp): ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT Found at i:34013429 original size:28 final size:28 Alignment explanation

Indices: 34013397--34013477 Score: 70 Period size: 28 Copynumber: 3.2 Consensus size: 28 34013387 TCACACTAGC 34013397 CATTCGGCTTTACCACATATACATATCT 1 CATTCGGCTTTACCACATATACATATCT *** * 34013425 CATTCATATTT--CAC----AC-TAGC- 1 CATTCGGCTTTACCACATATACATATCT 34013445 CATTCGGCTTTACCACATATACATATCT 1 CATTCGGCTTTACCACATATACATATCT 34013473 CATTC 1 CATTC 34013478 ATATTTCACA Statistics Matches: 37, Mismatches: 8, Indels: 16 0.61 0.13 0.26 Matches are distributed among these distances: 20 8 0.22 21 3 0.08 22 5 0.14 26 5 0.14 27 3 0.08 28 13 0.35 ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36 Consensus pattern (28 bp): CATTCGGCTTTACCACATATACATATCT Found at i:34022344 original size:25 final size:24 Alignment explanation

Indices: 34022316--34022407 Score: 78 Period size: 25 Copynumber: 3.8 Consensus size: 24 34022306 CCATAAAACA 34022316 GGAAGCTCATGTGAGCCATGCAATG 1 GGAAGCTCATGTGAGCCATG-AATG * * * * * 34022341 GGAAGCTCATATGGGCTATTTAACG 1 GGAAGCTCATGTGAGCCA-TGAATG * * 34022366 GGAAGCTCATGAGAGTCATG-ATCG 1 GGAAGCTCATGTGAGCCATGAAT-G * 34022390 GGAAGCTCGTGTGAGCCA 1 GGAAGCTCATGTGAGCCA 34022408 ATAACAGGTA Statistics Matches: 50, Mismatches: 15, Indels: 5 0.71 0.21 0.07 Matches are distributed among these distances: 23 1 0.02 24 17 0.34 25 31 0.62 26 1 0.02 ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22 Consensus pattern (24 bp): GGAAGCTCATGTGAGCCATGAATG Found at i:34024861 original size:17 final size:19 Alignment explanation

Indices: 34024819--34024862 Score: 56 Period size: 19 Copynumber: 2.4 Consensus size: 19 34024809 ATGAAATTTT * 34024819 AATTAGTATTATGAGATAA 1 AATTATTATTATGAGATAA * 34024838 AATTATTATTATTAGA-AA 1 AATTATTATTATGAGATAA 34024856 AA-TATTA 1 AATTATTA 34024863 CTGTATGTAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 5 0.22 18 4 0.17 19 14 0.61 ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41 Consensus pattern (19 bp): AATTATTATTATGAGATAA Found at i:34026679 original size:28 final size:28 Alignment explanation

Indices: 34026646--34026742 Score: 153 Period size: 28 Copynumber: 3.5 Consensus size: 28 34026636 GCGTAGATCA 34026646 CGAAATTACCCCTAAAGAGCAAAATTAC 1 CGAAATTACCCCTAAAGAGCAAAATTAC * 34026674 TGAAATTACCCCTAAAGAGCAAAATTAC 1 CGAAATTACCCCTAAAGAGCAAAATTAC * 34026702 CGAAATTACCCCTAAATAGCAAAATTAC 1 CGAAATTACCCCTAAAGAGCAAAATTAC 34026730 C--AATATACCCCTA 1 CGAAAT-TACCCCTA 34026743 GGGTTTAAAT Statistics Matches: 65, Mismatches: 3, Indels: 3 0.92 0.04 0.04 Matches are distributed among these distances: 26 3 0.05 27 8 0.12 28 54 0.83 ACGTcount: A:0.45, C:0.26, G:0.08, T:0.21 Consensus pattern (28 bp): CGAAATTACCCCTAAAGAGCAAAATTAC Found at i:34029157 original size:17 final size:19 Alignment explanation

Indices: 34029115--34029158 Score: 56 Period size: 19 Copynumber: 2.4 Consensus size: 19 34029105 ATGAAATTTT * 34029115 AATTAGTATTATGAGATAA 1 AATTATTATTATGAGATAA * 34029134 AATTATTATTATTAGA-AA 1 AATTATTATTATGAGATAA 34029152 AA-TATTA 1 AATTATTA 34029159 CTGTATGTAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 5 0.22 18 4 0.17 19 14 0.61 ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41 Consensus pattern (19 bp): AATTATTATTATGAGATAA Found at i:34031029 original size:28 final size:28 Alignment explanation

Indices: 34030946--34031041 Score: 151 Period size: 28 Copynumber: 3.5 Consensus size: 28 34030936 CGTAGATCAT * 34030946 GAAATTACCCCTAAAGAGCAAAATTACT 1 GAAATTACCCCTAAAGAGCAAAATTACC 34030974 GAAATTACCCCTAAAGAGCAAAATTACC 1 GAAATTACCCCTAAAGAGCAAAATTACC * 34031002 GAAATTACCCCTAAATAGCAAAATTACC 1 GAAATTACCCCTAAAGAGCAAAATTACC 34031030 --AATATACCCCTA 1 GAAAT-TACCCCTA 34031042 GGGTTTAAAT Statistics Matches: 65, Mismatches: 2, Indels: 3 0.93 0.03 0.04 Matches are distributed among these distances: 26 3 0.05 27 8 0.12 28 54 0.83 ACGTcount: A:0.46, C:0.25, G:0.08, T:0.21 Consensus pattern (28 bp): GAAATTACCCCTAAAGAGCAAAATTACC Found at i:34036295 original size:48 final size:48 Alignment explanation

Indices: 34036220--34036447 Score: 191 Period size: 48 Copynumber: 4.9 Consensus size: 48 34036210 TACATGGTAG * * * 34036220 GATGCCAAT-TCCATATCTCAAATATGGTCTTACATGGGATCACATATC 1 GATGCCAATGT-CATGTCCCAAACATGGTCTTACATGGGATCACATATC ** ** 34036268 GATGCCAATGTCATGTCCCAAACATGGTCTTACATGGGATCGTAGGTC 1 GATGCCAATGTCATGTCCCAAACATGGTCTTACATGGGATCACATATC * * * * * * 34036316 AATGCCAATGCCATGTCCCAGACATAGTCTTACATGGGATTACATGTC 1 GATGCCAATGTCATGTCCCAAACATGGTCTTACATGGGATCACATATC * * * ** ** 34036364 GATGCCGA--T-A-G-CCC-AGCTATGGTCTTACACGAAATTGCATATC 1 GATGCCAATGTCATGTCCCAAAC-ATGGTCTTACATGGGATCACATATC * * 34036407 GATGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATC 1 GATGCCAATGTCATGTCCCAAACATGGTCTTACATGGGATC 34036448 GTACATAACC Statistics Matches: 139, Mismatches: 33, Indels: 16 0.74 0.18 0.09 Matches are distributed among these distances: 42 1 0.01 43 29 0.21 44 1 0.01 45 1 0.01 46 1 0.01 47 1 0.01 48 102 0.73 49 3 0.02 ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27 Consensus pattern (48 bp): GATGCCAATGTCATGTCCCAAACATGGTCTTACATGGGATCACATATC Found at i:34039127 original size:46 final size:46 Alignment explanation

Indices: 34039077--34039248 Score: 163 Period size: 46 Copynumber: 3.7 Consensus size: 46 34039067 TGAGCATCCA * 34039077 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTG 1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG * * * * * 34039123 AACTCGTTGAGTTGAGTCCGCGTTC-GTGA--AATG-TAACTAGGCATCCG 1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG * * * 34039170 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG 1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG * * * 34039216 AGCTCGTTGAGTTGAGTCCGATTTCGCTTATGG 1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 34039249 GCGGGTTACA Statistics Matches: 101, Mismatches: 16, Indels: 18 0.75 0.12 0.13 Matches are distributed among these distances: 42 2 0.02 43 4 0.04 45 3 0.03 46 58 0.57 47 26 0.26 48 3 0.03 50 3 0.03 51 2 0.02 ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30 Consensus pattern (46 bp): AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG Found at i:34043676 original size:120 final size:120 Alignment explanation

Indices: 34043462--34043694 Score: 328 Period size: 120 Copynumber: 1.9 Consensus size: 120 34043452 TCGAATGATG * 34043462 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT 1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT * * * 34043527 GTGTGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA 66 GTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAA * * * ** 34043582 TCCGGGTTAAGTCCCGAAGGCATTTGTGCT-AGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT 1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCAT * 34043645 TTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGT 64 TTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGT 34043695 AGCTATATCT Statistics Matches: 100, Mismatches: 10, Indels: 6 0.86 0.09 0.05 Matches are distributed among these distances: 119 1 0.01 120 89 0.89 121 10 0.10 ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28 Consensus pattern (120 bp): TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT GTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAA Found at i:34043694 original size:40 final size:40 Alignment explanation

Indices: 34043462--34043687 Score: 296 Period size: 40 Copynumber: 5.7 Consensus size: 40 34043452 TCGAATGATG * * * 34043462 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * * 34043502 TCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGTTACTAAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * * 34043542 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * * * 34043582 TCCGGGTTAAGTCCCGAAGGCATTTGTGCTAGTTATTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * 34043622 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA * 34043663 -CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 34043688 AACGAGTAGC Statistics Matches: 166, Mismatches: 16, Indels: 8 0.87 0.08 0.04 Matches are distributed among these distances: 39 1 0.01 40 156 0.94 41 9 0.05 ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Found at i:34044433 original size:10 final size:10 Alignment explanation

Indices: 34044418--34044442 Score: 50 Period size: 10 Copynumber: 2.5 Consensus size: 10 34044408 CTACCTTAAA 34044418 GACAGATGCT 1 GACAGATGCT 34044428 GACAGATGCT 1 GACAGATGCT 34044438 GACAG 1 GACAG 34044443 CTGCAGTGAC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 15 1.00 ACGTcount: A:0.32, C:0.20, G:0.32, T:0.16 Consensus pattern (10 bp): GACAGATGCT Found at i:34046958 original size:70 final size:71 Alignment explanation

Indices: 34046875--34047037 Score: 310 Period size: 70 Copynumber: 2.3 Consensus size: 71 34046865 CGATTTGTCT 34046875 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 34046939 CTTTCA 66 CTTTCA * 34046945 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 34047010 CTTTCA 66 CTTTCA 34047016 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 34047038 GATACATCTC Statistics Matches: 91, Mismatches: 1, Indels: 1 0.98 0.01 0.01 Matches are distributed among these distances: 70 51 0.56 71 40 0.44 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.34 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:34047075 original size:71 final size:70 Alignment explanation

Indices: 34046875--34047071 Score: 249 Period size: 70 Copynumber: 2.8 Consensus size: 70 34046865 CGATTTGTCT * * * * 34046875 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 34046939 CTTTCA 65 CTTTCA * * * * 34046945 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 34047010 CTTTCA 65 CTTTCA * * 34047016 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 34047072 TACAGGGTGT Statistics Matches: 118, Mismatches: 7, Indels: 6 0.90 0.05 0.05 Matches are distributed among these distances: 68 22 0.19 69 1 0.01 70 52 0.44 71 43 0.36 ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:34054490 original size:70 final size:71 Alignment explanation

Indices: 34054407--34054569 Score: 319 Period size: 70 Copynumber: 2.3 Consensus size: 71 34054397 CGATTTGTCT 34054407 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 34054471 CTTTCA 66 CTTTCA 34054477 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 34054542 CTTTCA 66 CTTTCA 34054548 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 34054570 GATACATCTC Statistics Matches: 92, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 70 52 0.57 71 40 0.43 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:34054607 original size:71 final size:70 Alignment explanation

Indices: 34054407--34054603 Score: 249 Period size: 70 Copynumber: 2.8 Consensus size: 70 34054397 CGATTTGTCT * * * * 34054407 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACC-AGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 34054471 CTTTCA 65 CTTTCA * * * * 34054477 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 34054542 CTTTCA 65 CTTTCA * * 34054548 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 34054604 TACAGGGTGT Statistics Matches: 119, Mismatches: 6, Indels: 6 0.91 0.05 0.05 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 53 0.45 71 43 0.36 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:34055954 original size:24 final size:24 Alignment explanation

Indices: 34055927--34055981 Score: 67 Period size: 24 Copynumber: 2.3 Consensus size: 24 34055917 TAATAATAAT 34055927 TATATTAAGAATTTTATTAAATTA 1 TATATTAAGAATTTTATTAAATTA * ** * 34055951 TATATCATTATTTTTATTAAATTA 1 TATATTAAGAATTTTATTAAATTA 34055975 TAT-TTAA 1 TATATTAA 34055982 TAATAATTCT Statistics Matches: 25, Mismatches: 6, Indels: 1 0.78 0.19 0.03 Matches are distributed among these distances: 23 2 0.08 24 23 0.92 ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55 Consensus pattern (24 bp): TATATTAAGAATTTTATTAAATTA Found at i:34056633 original size:2 final size:2 Alignment explanation

Indices: 34056626--34056655 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 34056616 GACAACACTA 34056626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 34056656 TAAAACTGAC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:34057306 original size:150 final size:150 Alignment explanation

Indices: 34057035--34057334 Score: 528 Period size: 150 Copynumber: 2.0 Consensus size: 150 34057025 GCACACTATT * * 34057035 GATGACATTATTCTCTCAACTAACCAACATTAGTGATGAAATAAATCAAGTTATTATTTTTTCAG 1 GATGACATTATTCTCTCAACTAACCAACAATAGTGATGAAATAAATCAAGTTATTAATTTTTCAG * * 34057100 TTTAGATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAATAATTCATCGATTTTTTAAT 66 TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAACAATTCATCGATTTTTTAAT * 34057165 TTAGCTCATATTAGTTCATG 131 TTAACTCATATTAGTTCATG * * 34057185 GATGACATTATTCTCTCAACTAACTAACAATGGTGATGAAATAAATCAAGTTATTAATTTTTCAG 1 GATGACATTATTCTCTCAACTAACCAACAATAGTGATGAAATAAATCAAGTTATTAATTTTTCAG 34057250 TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAACAATTCATCGATTTTTTAAT 66 TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAACAATTCATCGATTTTTTAAT * 34057315 TTAACTTATATTAGTTCATG 131 TTAACTCATATTAGTTCATG 34057335 ACTCAACCAA Statistics Matches: 142, Mismatches: 8, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 150 142 1.00 ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39 Consensus pattern (150 bp): GATGACATTATTCTCTCAACTAACCAACAATAGTGATGAAATAAATCAAGTTATTAATTTTTCAG TTTAAATAATTCAATTAAATAAATTATAAAAAAATATTAGAAAAACAATTCATCGATTTTTTAAT TTAACTCATATTAGTTCATG Found at i:34057735 original size:27 final size:27 Alignment explanation

Indices: 34057704--34057760 Score: 73 Period size: 27 Copynumber: 2.1 Consensus size: 27 34057694 TTTTTGTGTA 34057704 TTTAAAAATAATT-TTTATATT-TTTATT 1 TTTAAAAAT-ATTATTTAT-TTATTTATT * 34057731 TTTAAAAATTTTATTTATTTATTTATT 1 TTTAAAAATATTATTTATTTATTTATT 34057758 TTT 1 TTT 34057761 TAATTTAAAA Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 26 4 0.15 27 23 0.85 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (27 bp): TTTAAAAATATTATTTATTTATTTATT Found at i:34059582 original size:21 final size:20 Alignment explanation

Indices: 34059556--34059607 Score: 77 Period size: 20 Copynumber: 2.5 Consensus size: 20 34059546 GCCCAACAGT * 34059556 AAAAAAAAAACTCTGAAAACG 1 AAAAAAAAAA-GCTGAAAACG * 34059577 AAAAAAAAAAGCTGAAAATG 1 AAAAAAAAAAGCTGAAAACG 34059597 AAAAAAAAAAG 1 AAAAAAAAAAG 34059608 GGACATGTGG Statistics Matches: 29, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 20 19 0.66 21 10 0.34 ACGTcount: A:0.73, C:0.08, G:0.12, T:0.08 Consensus pattern (20 bp): AAAAAAAAAAGCTGAAAACG Found at i:34060359 original size:150 final size:150 Alignment explanation

Indices: 34060138--34060465 Score: 446 Period size: 150 Copynumber: 2.2 Consensus size: 150 34060128 AATGTATTAT * * *** * 34060138 ATATATTTTAAAAAATAATATACG-AAAGTAAAAAATACAAATAAAGTGGTAAAATCAGGGTTAT 1 ATATATTTTAAAAAATAATATACGAAAATTAAAAAATACAAACAAAGTACCAAAATCAGAGTTAT 34060202 TTATTAAA-AAATACAAAAAACACTTAAATAATACATTTGAAACA-TAATGTACTAAAATAATAT 66 TTATTAAATAAATACAAAAAACACTTAAATAATACATTTGAAACACT-ATGTACTAAAATAATAT * 34060265 AAAGAAATAAAATATGAAAATA 130 AAA-AAATAAAATACGAAAATA * * * * * 34060287 ATATATTTTAAAAAATAAAATCCGAAAATTAAAAAATACGAACAAGGTACCAAAGTCAGAGTTAT 1 ATATATTTTAAAAAATAATATACGAAAATTAAAAAATACAAACAAAGTACCAAAATCAGAGTTAT * * * * * * 34060352 TTATTAAATTAATATAAAAAACACTTAAGTAATACATTTGAAACACTTTTTGCTAAAATAATATA 66 TTATTAAATAAATACAAAAAACACTTAAATAATACATTTGAAACACTATGTACTAAAATAATATA * 34060417 AAAAATAAAATACGTAAATA 131 AAAAATAAAATACGAAAATA 34060437 ATATATTTTAAAAAATAATATACGAAAAT 1 ATATATTTTAAAAAATAATATACGAAAAT 34060466 GTTATACTTA Statistics Matches: 155, Mismatches: 21, Indels: 5 0.86 0.12 0.03 Matches are distributed among these distances: 149 22 0.14 150 82 0.53 151 50 0.32 152 1 0.01 ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29 Consensus pattern (150 bp): ATATATTTTAAAAAATAATATACGAAAATTAAAAAATACAAACAAAGTACCAAAATCAGAGTTAT TTATTAAATAAATACAAAAAACACTTAAATAATACATTTGAAACACTATGTACTAAAATAATATA AAAAATAAAATACGAAAATA Found at i:34060763 original size:19 final size:20 Alignment explanation

Indices: 34060739--34060786 Score: 71 Period size: 19 Copynumber: 2.5 Consensus size: 20 34060729 ACATGTCCTT 34060739 TTTTTTTTTCATTTTCA-AC 1 TTTTTTTTTCATTTTCAGAC * * 34060758 TTTTTTTTTCGTTTTCAGAG 1 TTTTTTTTTCATTTTCAGAC 34060778 TTTTTTTTT 1 TTTTTTTTT 34060787 TTTACTGTTG Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 19 16 0.62 20 10 0.38 ACGTcount: A:0.10, C:0.10, G:0.06, T:0.73 Consensus pattern (20 bp): TTTTTTTTTCATTTTCAGAC Found at i:34074887 original size:28 final size:28 Alignment explanation

Indices: 34074847--34074945 Score: 112 Period size: 28 Copynumber: 3.5 Consensus size: 28 34074837 GCAATAAGCC * 34074847 CGCACACTTAGTGCTTAATAGTCGAACT 1 CGCACACTTAGTGCTTAATAATCGAACT * 34074875 CGCACACTTAGTGC-TATATAATCAAACT 1 CGCACACTTAGTGCTTA-ATAATCGAACT * * * 34074903 TGCACACTTAGTGCTGT-ATAATTTGAACC 1 CGCACACTTAGTGCT-TAATAA-TCGAACT 34074932 CGCACACTTAGTGC 1 CGCACACTTAGTGC 34074946 CAATTTGTGA Statistics Matches: 60, Mismatches: 7, Indels: 7 0.81 0.09 0.09 Matches are distributed among these distances: 27 2 0.03 28 40 0.67 29 17 0.28 30 1 0.02 ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29 Consensus pattern (28 bp): CGCACACTTAGTGCTTAATAATCGAACT Found at i:34077783 original size:39 final size:40 Alignment explanation

Indices: 34077605--34077787 Score: 181 Period size: 40 Copynumber: 4.6 Consensus size: 40 34077595 CCGCACCAAG * * * * * * * * 34077605 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * * 34077645 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAA-T 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT * 34077685 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * * * 34077725 GCCTTCGGGTCTTAACCCGGATATAATTTC-AGCATAATT 1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT * * 34077764 GTCTTCGGGGCTTAGCCCGGATAT 1 GCCTTCGGGTCTTAGCCCGGATAT 34077788 CATTCAATTT Statistics Matches: 122, Mismatches: 19, Indels: 5 0.84 0.13 0.03 Matches are distributed among these distances: 39 31 0.25 40 89 0.73 41 2 0.02 ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28 Consensus pattern (40 bp): GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT Found at i:34081354 original size:14 final size:14 Alignment explanation

Indices: 34081335--34081363 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 34081325 CTATGATATC 34081335 AGAAAAAGGTTTTA 1 AGAAAAAGGTTTTA 34081349 AGAAAAAGGTTTTA 1 AGAAAAAGGTTTTA 34081363 A 1 A 34081364 CTTGAAAAGT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.52, C:0.00, G:0.21, T:0.28 Consensus pattern (14 bp): AGAAAAAGGTTTTA Found at i:34086091 original size:37 final size:37 Alignment explanation

Indices: 34086041--34086131 Score: 155 Period size: 37 Copynumber: 2.4 Consensus size: 37 34086031 TTATTACGAA * 34086041 GTCTTACCCGGACATAATCTCCACACGTAGTCATTGG 1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG 34086078 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG 1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG * 34086115 GTCTCACCCGGAACATA 1 GTCTTACCCGG-ACATA 34086132 TTTCCAAGTT Statistics Matches: 51, Mismatches: 2, Indels: 1 0.94 0.04 0.02 Matches are distributed among these distances: 37 46 0.90 38 5 0.10 ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24 Consensus pattern (37 bp): GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG Found at i:34086274 original size:49 final size:49 Alignment explanation

Indices: 34086217--34086710 Score: 649 Period size: 49 Copynumber: 9.9 Consensus size: 49 34086207 CACACATATA * 34086217 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * * * * * 34086266 CTTCACATTCATCACATACATTAGCCATTCGGCTTTACCACATATACATATCACAC 1 TTTCACATTCAT--C--ACATTGGCCATTAGGCCTTATCACATAT--ATAT-ACAC * * * * * * 34086322 -AT-ATATT--TCACATTAGCCATTCGGCTTTACCACATATACATATCACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATAT--ATAT-ACAC * 34086370 ATATATTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC 1 -----TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * * * 34086424 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * 34086471 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC 34086520 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC 34086569 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC 34086618 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * 34086667 TTTCACATTCATCACATTGGCCATTAGGCCGTATCACATATATA 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA 34086711 CATCTCATAC Statistics Matches: 404, Mismatches: 23, Indels: 36 0.87 0.05 0.08 Matches are distributed among these distances: 47 44 0.11 48 39 0.10 49 244 0.60 50 1 0.00 51 1 0.00 52 1 0.00 53 23 0.06 54 9 0.02 55 13 0.03 56 4 0.01 57 25 0.06 ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33 Consensus pattern (49 bp): TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC Found at i:34086339 original size:48 final size:48 Alignment explanation

Indices: 34086283--34086383 Score: 202 Period size: 48 Copynumber: 2.1 Consensus size: 48 34086273 TTCATCACAT 34086283 ACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTC 1 ACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTC 34086331 ACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTC 1 ACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTC 34086379 ACATT 1 ACATT 34086384 CATCACATCG Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 48 53 1.00 ACGTcount: A:0.34, C:0.27, G:0.06, T:0.34 Consensus pattern (48 bp): ACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATTTC Found at i:34093061 original size:29 final size:29 Alignment explanation

Indices: 34093028--34093159 Score: 149 Period size: 29 Copynumber: 4.6 Consensus size: 29 34093018 GTGACGAGAT 34093028 TGGCACTAAGTGTGCGTGCTGGAAATATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA * 34093057 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA * * *** 34093086 TGGCACTAAGTGTGCGAGCTCGAAGGGTA 1 TGGCACTAAGTGTGCGTGCTGGAAATATA * * * ** 34093115 TGGCACTATGTGTGCGGGCT-TAAATCGCA 1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA 34093144 TGGCACTAAGTGTGCG 1 TGGCACTAAGTGTGCG 34093160 AAATCGAGTA Statistics Matches: 88, Mismatches: 14, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 28 2 0.02 29 86 0.98 ACGTcount: A:0.25, C:0.17, G:0.33, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCGTGCTGGAAATATA Found at i:34099760 original size:24 final size:23 Alignment explanation

Indices: 34099727--34099780 Score: 74 Period size: 25 Copynumber: 2.3 Consensus size: 23 34099717 TAGGAAGAAT 34099727 AAAGAAATGAA-AAAAAAAAAGA 1 AAAGAAATGAAGAAAAAAAAAGA * 34099749 AAGAGAATATGAAGAAAAACAAAGA 1 AA-AGAA-ATGAAGAAAAAAAAAGA 34099774 AAAGAAA 1 AAAGAAA 34099781 AAAAAGTGTT Statistics Matches: 28, Mismatches: 1, Indels: 5 0.82 0.03 0.15 Matches are distributed among these distances: 22 2 0.07 23 5 0.18 24 9 0.32 25 12 0.43 ACGTcount: A:0.76, C:0.02, G:0.17, T:0.06 Consensus pattern (23 bp): AAAGAAATGAAGAAAAAAAAAGA Found at i:34107629 original size:29 final size:25 Alignment explanation

Indices: 34107577--34107628 Score: 77 Period size: 28 Copynumber: 2.0 Consensus size: 25 34107567 GGAAGAATAA 34107577 AGAAATGAAAAAAAAAAGAAAAAAG 1 AGAAATGAAAAAAAAAAGAAAAAAG 34107602 AGAATATGAAGAAAAACAAAGAAAAAA 1 AGAA-ATGAA-AAAAA-AAAGAAAAAA 34107629 AAAAAAAGTG Statistics Matches: 24, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 25 4 0.17 26 5 0.21 27 5 0.21 28 10 0.42 ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06 Consensus pattern (25 bp): AGAAATGAAAAAAAAAAGAAAAAAG Found at i:34114015 original size:57 final size:57 Alignment explanation

Indices: 34113946--34114058 Score: 154 Period size: 57 Copynumber: 2.0 Consensus size: 57 34113936 TCGATTTTGA *** * * 34113946 AAATGGCACTTAGTGTGTGAGTTATTGAGGATGGCACTTAGTGTGCAAAACATCCAG 1 AAATGGCACTTAGTGACCGAATTATCGAGGATGGCACTTAGTGTGCAAAACATCCAG * * * 34114003 AAATGGCTCTTAGTGACCGAATTATCGAGGATGGCACTTAGTGTGCGAGACATCCA 1 AAATGGCACTTAGTGACCGAATTATCGAGGATGGCACTTAGTGTGCAAAACATCCA 34114059 CGATGGTACT Statistics Matches: 48, Mismatches: 8, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 57 48 1.00 ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27 Consensus pattern (57 bp): AAATGGCACTTAGTGACCGAATTATCGAGGATGGCACTTAGTGTGCAAAACATCCAG Found at i:34114063 original size:28 final size:28 Alignment explanation

Indices: 34113948--34114085 Score: 107 Period size: 28 Copynumber: 4.9 Consensus size: 28 34113938 GATTTTGAAA * ** ** 34113948 ATGGCACTTAGTGTGTGAGTTATTGAGG 1 ATGGCACTTAGTGTGCGAGACATCCAGG * * * 34113976 ATGGCACTTAGTGTGCAAAACATCCAGAA 1 ATGGCACTTAGTGTGCGAGACATCCAG-G * ** * * 34114005 ATGGCTCTTAGTGACCGA-ATTATCGAGG 1 ATGGCACTTAGTGTGCGAGA-CATCCAGG * 34114033 ATGGCACTTAGTGTGCGAGACATCCACG 1 ATGGCACTTAGTGTGCGAGACATCCAGG * * 34114061 ATGGTACTTAGTGTGCGATACATCC 1 ATGGCACTTAGTGTGCGAGACATCC 34114086 GTGAAGCCAC Statistics Matches: 84, Mismatches: 23, Indels: 6 0.74 0.20 0.05 Matches are distributed among these distances: 28 64 0.76 29 20 0.24 ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28 Consensus pattern (28 bp): ATGGCACTTAGTGTGCGAGACATCCAGG Found at i:34120459 original size:40 final size:40 Alignment explanation

Indices: 34120414--34120580 Score: 176 Period size: 40 Copynumber: 4.2 Consensus size: 40 34120404 CGGAATATAA 34120414 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * * 34120454 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * 34120494 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 34120534 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 34120573 CCGGATAT 1 CCGGATAT 34120581 CATTCAATTT Statistics Matches: 105, Mismatches: 21, Indels: 3 0.81 0.16 0.02 Matches are distributed among these distances: 39 14 0.13 40 91 0.87 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:34120564 original size:80 final size:79 Alignment explanation

Indices: 34120430--34120580 Score: 198 Period size: 80 Copynumber: 1.9 Consensus size: 79 34120420 ATAATCACGT * 34120430 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC 34120495 CGGATATAGCCACTA 65 CGGATATAGCCACTA * * ** * * 34120510 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC 34120573 CCGGATAT 64 CCGGATAT 34120581 CATTCAATTT Statistics Matches: 62, Mismatches: 7, Indels: 5 0.84 0.09 0.07 Matches are distributed among these distances: 79 17 0.27 80 45 0.73 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26 Consensus pattern (79 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC GGATATAGCCACTA Found at i:34128438 original size:40 final size:40 Alignment explanation

Indices: 34128393--34128557 Score: 167 Period size: 40 Copynumber: 4.2 Consensus size: 40 34128383 CGGAATATAA 34128393 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * * 34128433 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC * * * 34128473 CCGG--ATAACCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * 34128511 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 34128550 CCGGATAT 1 CCGGATAT 34128558 CATTCAATTT Statistics Matches: 103, Mismatches: 19, Indels: 7 0.80 0.15 0.05 Matches are distributed among these distances: 38 30 0.29 39 14 0.14 40 59 0.57 ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:34128514 original size:38 final size:37 Alignment explanation

Indices: 34128409--34128517 Score: 128 Period size: 38 Copynumber: 2.8 Consensus size: 37 34128399 ATAATCACGT * * 34128409 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT--AACAACTA * * 34128449 GCACGAATGCCTTCGGGCCTTAGCCCGGATAACCACTA 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAACAACTA * 34128487 GCACAATTGCCTTCGGGTCTTAACCCGGATA 1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATA 34128518 TAATTTCCAG Statistics Matches: 61, Mismatches: 7, Indels: 4 0.85 0.10 0.06 Matches are distributed among these distances: 37 2 0.03 38 31 0.51 40 28 0.46 ACGTcount: A:0.25, C:0.30, G:0.23, T:0.22 Consensus pattern (37 bp): GCACAATGCCTTCGGGTCTTAGCCCGGATAACAACTA Found at i:34128541 original size:78 final size:77 Alignment explanation

Indices: 34128409--34128556 Score: 192 Period size: 78 Copynumber: 1.9 Consensus size: 77 34128399 ATAATCACGT * 34128409 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC 34128474 CGGATAACCACTA 65 CGGATAACCACTA * * ** * * 34128487 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC 34128550 CCGGATA 64 CCGGATA 34128557 TCATTCAATT Statistics Matches: 61, Mismatches: 7, Indels: 5 0.84 0.10 0.07 Matches are distributed among these distances: 77 16 0.26 78 45 0.74 ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25 Consensus pattern (77 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC GGATAACCACTA Found at i:34129405 original size:17 final size:19 Alignment explanation

Indices: 34129382--34129427 Score: 53 Period size: 17 Copynumber: 2.5 Consensus size: 19 34129372 AAGAAGCATG 34129382 AATCATGCTCAAGAATG-C 1 AATCATGCTCAAGAATGAC * 34129400 -ATCATGGC-CAAGTATGAC 1 AATCAT-GCTCAAGAATGAC 34129418 AATCATGCTC 1 AATCATGCTC 34129428 CTTTTCAACT Statistics Matches: 23, Mismatches: 1, Indels: 7 0.74 0.03 0.23 Matches are distributed among these distances: 17 12 0.52 18 5 0.22 19 6 0.26 ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24 Consensus pattern (19 bp): AATCATGCTCAAGAATGAC Found at i:34139960 original size:563 final size:564 Alignment explanation

Indices: 34138881--34140001 Score: 1893 Period size: 563 Copynumber: 2.0 Consensus size: 564 34138871 AAACCTTTGT * * 34138881 TTTAGTAAAAATTCGTGTTTTTAGCTAGTCGTCCTAATAAATTATTAAACGAAAAATCCAAATCC 1 TTTAGTAAAAATCCGTGTTTTTAGCTAGTCGTCCTAATAAATTATTAAACAAAAAATCCAAATCC * 34138946 CAAAATTTAAGTCAACAGTACGGAGAGTCCAATTAATACAAAACTCTTAGAAATAAACCTTGAAT 66 CAAAATTTAAATCAACAGTACGGAGAGTCCAATTAATACAAAACTCTTAGAAATAAACCTTGAAT * * * * 34139011 AATAAAACCTTTAATTAAAATTAGTTCGTAGACTAATGGTCATCGCAAGACTCCGCTGCACTGAT 131 AATAAAACCTTTAATTAAAATCAATTCGTAGACTAATGGTCATCGCAAGACTCCACTGCACCGAT * * 34139076 CCGCCTAAGTCTGTGGATTACCTGTACAAAGCAGACAAACAAAAGTGGGTTTACGAAAACTCAGT 196 CCGCCTAAGTCTGTGGATTACCTGTACAAAACAGACAAACAAAAGTGAGTTTACGAAAACTCAGT * * * 34139141 GTGTAACCCAACAGAAATTGACGTGCAAAACATATAGTAACCTCATATACAGTCAGATGCAGATT 261 GTGTAACCCAACAGAAATTGACGCGAAAAACATACAGTAACCTCATATACAGTCAGATGCAGATT * ** * * 34139206 CAAACTTATGTCCATTTTAGATACAGCTAACAGAAACAGTTATGCAAATACACAGAACAAATACA 326 CAAACTTATGTCCATTTCAGATACAAATAAAAAAAACAGTTATGCAAATACACAGAACAAATACA * * * 34139271 GTGAGTCCTACCCCCATCCTCTACAGACCATCTCCGTCTATCCCATCACACTATGTGGGGTTAAA 391 GTGAGTCCTACCCCCATCCTCTACACACCATCTCCGTCCATCCCATCACACCATGTGGGGTTAAA * ** 34139336 AACACCCACCCATCCTTACACACCACATAGTGTCGATGTGACACATATCAGATAATGTGTAGCCT 456 AACACCCACCCATCCTTACACACCACATAGTGTCCATACGACACATATCAGATAATGTGTAGCCT * 34139401 AGTTGCCAGATGATAGGCGATGATCACCATAAAAAACAGTACGG 521 AGTTGCCAGATGATAGGCAATGATCACCATAAAAAACAGTACGG 34139445 TTTAGTAAAAA-CCGTGTTTTTAGCTAGTCGTCCTAATAAATTATTAAACAAAAAATCCAAATCC 1 TTTAGTAAAAATCCGTGTTTTTAGCTAGTCGTCCTAATAAATTATTAAACAAAAAATCCAAATCC * 34139509 CAAAATTTAAATCAATAGTACGGAGAGTCCAATTAATACAAAACTCTTAGAAATAAACCTTGAAT 66 CAAAATTTAAATCAACAGTACGGAGAGTCCAATTAATACAAAACTCTTAGAAATAAACCTTGAAT * * 34139574 AATAAAACCTTTAATTAAAATCAATTCGTAGACTAATGGTCATCGTAAGACTCTACTGCACCGAT 131 AATAAAACCTTTAATTAAAATCAATTCGTAGACTAATGGTCATCGCAAGACTCCACTGCACCGAT * 34139639 CCGCCTAAGTCTGTGGATTACCTGTACAAAATAGACAAACAAAAGTGAGTTTACGAAAACTCAGT 196 CCGCCTAAGTCTGTGGATTACCTGTACAAAACAGACAAACAAAAGTGAGTTTACGAAAACTCAGT * * 34139704 GTGTAACCCAACAGAAATTGACGCGAAAAACATACAGTAATCTCATATATAGTCAGATGCAGATT 261 GTGTAACCCAACAGAAATTGACGCGAAAAACATACAGTAACCTCATATACAGTCAGATGCAGATT * * * 34139769 CAGACTTATGTCCATTTCAGATACAAATAAAAAAAATAGTTATGCAAATATACAGAACAAATACA 326 CAAACTTATGTCCATTTCAGATACAAATAAAAAAAACAGTTATGCAAATACACAGAACAAATACA * * 34139834 GTGAGTCCTACCTCCTTCCTCTACACACCATCTCCGTCCATCCCATCACACCATGTGGGGTTAAA 391 GTGAGTCCTACCCCCATCCTCTACACACCATCTCCGTCCATCCCATCACACCATGTGGGGTTAAA * 34139899 AACACCCACCCATCTTTACACACCACATAGTGTCCATACGACACATATCAGATAATGTGTAGCCT 456 AACACCCACCCATCCTTACACACCACATAGTGTCCATACGACACATATCAGATAATGTGTAGCCT * * 34139964 AGTTGCCAGATGATAGGTAATGATCACCATACAAAACA 521 AGTTGCCAGATGATAGGCAATGATCACCATAAAAAACA 34140002 CTTCCTCCTT Statistics Matches: 519, Mismatches: 38, Indels: 1 0.93 0.07 0.00 Matches are distributed among these distances: 563 508 0.98 564 11 0.02 ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25 Consensus pattern (564 bp): TTTAGTAAAAATCCGTGTTTTTAGCTAGTCGTCCTAATAAATTATTAAACAAAAAATCCAAATCC CAAAATTTAAATCAACAGTACGGAGAGTCCAATTAATACAAAACTCTTAGAAATAAACCTTGAAT AATAAAACCTTTAATTAAAATCAATTCGTAGACTAATGGTCATCGCAAGACTCCACTGCACCGAT CCGCCTAAGTCTGTGGATTACCTGTACAAAACAGACAAACAAAAGTGAGTTTACGAAAACTCAGT GTGTAACCCAACAGAAATTGACGCGAAAAACATACAGTAACCTCATATACAGTCAGATGCAGATT CAAACTTATGTCCATTTCAGATACAAATAAAAAAAACAGTTATGCAAATACACAGAACAAATACA GTGAGTCCTACCCCCATCCTCTACACACCATCTCCGTCCATCCCATCACACCATGTGGGGTTAAA AACACCCACCCATCCTTACACACCACATAGTGTCCATACGACACATATCAGATAATGTGTAGCCT AGTTGCCAGATGATAGGCAATGATCACCATAAAAAACAGTACGG Found at i:34144636 original size:50 final size:49 Alignment explanation

Indices: 34144529--34144803 Score: 199 Period size: 48 Copynumber: 5.7 Consensus size: 49 34144519 GGACATGTGT * * * 34144529 GCTAGTGTAAGA-TATGTCTGGGACAT-GCATCGGCCAC-ATTAT-AAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAATATGAA-A * * * 34144575 GCCAGTGTAAGACCATCTCTGGGATATGGCATCGGCCTCGAGATATGAAA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-ATATGAAA * * * ** * * ** 34144625 GCTAGTGTAAGACCATTTTTAGGACATGGCATTAGCAC-CAACAGATGTGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGA-ATATGAAA * * * 34144675 GCCAGTGTAAGACCATGT-TGGGACATGGC-TCAGCCTCGATATATGAGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA-ATATGAAA * * * * ** 34144723 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGACCTTG-ATGTGTGA 1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAATATGAAA * * 34144771 GCCAGTGTAAGACCATGT-TCGAGACATGGCATC 1 GCTAGTGTAAGACCATGTCT-GGGACATGGCATC 34144804 AGCATCTTAC Statistics Matches: 183, Mismatches: 36, Indels: 18 0.77 0.15 0.08 Matches are distributed among these distances: 46 11 0.06 47 13 0.07 48 72 0.39 49 22 0.12 50 62 0.34 51 3 0.02 ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25 Consensus pattern (49 bp): GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAATATGAAA Found at i:34144729 original size:98 final size:97 Alignment explanation

Indices: 34144573--34144806 Score: 283 Period size: 98 Copynumber: 2.4 Consensus size: 97 34144563 CACATTATAA * * * 34144573 GAGCCAGTGTAAGACCATCTCTGGGATATGGCATCGGCCTCGAGATATGAAAGCTAGTGTAAGAC 1 GAGCCAGTGTAAGACCATGT-TGGGACATGGCATCAGCCTCGAGATATGAAAGCTAGTGTAAGAC * * 34144638 CATTTTTAGGACATGGCATTAGCACCAACA-GATGT 65 CATGTCTAGGACATGGCA-TAG-ACCAACATG-TGT * * * 34144673 GAGCCAGTGTAAGACCATGTTGGGACATGGC-TCAGCCTCGATATATGAGAGTTAGTGTAAGACC 1 GAGCCAGTGTAAGACCATGTTGGGACATGGCATCAGCCTCGAGATATGAAAGCTAGTGTAAGACC * * *** 34144737 ATGTCTGGGACATGGCATCGACCTTGATGTGT 66 ATGTCTAGGACATGGCATAGACCAACATGTGT * 34144769 GAGCCAGTGTAAGACCATGTTCGAGACATGGCATCAGC 1 GAGCCAGTGTAAGACCATGTT-GGGACATGGCATCAGC 34144807 ATCTTACCCT Statistics Matches: 117, Mismatches: 14, Indels: 8 0.84 0.10 0.06 Matches are distributed among these distances: 96 28 0.24 97 12 0.10 98 48 0.41 99 10 0.09 100 19 0.16 ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24 Consensus pattern (97 bp): GAGCCAGTGTAAGACCATGTTGGGACATGGCATCAGCCTCGAGATATGAAAGCTAGTGTAAGACC ATGTCTAGGACATGGCATAGACCAACATGTGT Found at i:34147671 original size:57 final size:57 Alignment explanation

Indices: 34147610--34147720 Score: 204 Period size: 57 Copynumber: 1.9 Consensus size: 57 34147600 ACGATAATTT * 34147610 TCCTGAAATGAATGATATGATTATGATGGTGTCGTTATGATGATGAAAGTTATGCCC 1 TCCTGAAATGAATGACATGATTATGATGGTGTCGTTATGATGATGAAAGTTATGCCC * 34147667 TCCTGAAATGAATGACATGATTGTGATGGTGTCGTTATGATGATGAAAGTTATG 1 TCCTGAAATGAATGACATGATTATGATGGTGTCGTTATGATGATGAAAGTTATG 34147721 TCATATGCAT Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 57 52 1.00 ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35 Consensus pattern (57 bp): TCCTGAAATGAATGACATGATTATGATGGTGTCGTTATGATGATGAAAGTTATGCCC Found at i:34151377 original size:50 final size:50 Alignment explanation

Indices: 34151214--34151541 Score: 289 Period size: 50 Copynumber: 6.7 Consensus size: 50 34151204 AGACATGTGT * * * * 34151214 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-A-TTATAAGA 1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAGA * * * * * * 34151260 GCCAGTGTAATACCATGTCTAGAACATGGCATAGGCATTGAG--ATGAGA 1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAGA * 34151308 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAAA 1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAGA * * * * * ** 34151358 GCTAGTGTAAGACCATGTCTAGGACATGGCATTGACATCAACAGGTGAGA 1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAGA * * * * * 34151408 CCCAGTGTAAGACCATGTCT-GTGACATGGCATCAGCCTCAATATATGAGA 1 GCTAGTGTAAGACCATGTCTAG-GACATGGCATCGGCCTCGAGATATGAGA * * * * * * 34151458 G-TCAGTGTAAGACCATATCTGGGACATGGCATCGACCT--TGATGTGTGA 1 GCT-AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAGA * * 34151506 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC 1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGC 34151542 ATCTTACCCT Statistics Matches: 227, Mismatches: 45, Indels: 18 0.78 0.16 0.06 Matches are distributed among these distances: 46 10 0.04 47 12 0.05 48 86 0.38 49 2 0.01 50 116 0.51 51 1 0.00 ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23 Consensus pattern (50 bp): GCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGATATGAGA Found at i:34155837 original size:30 final size:30 Alignment explanation

Indices: 34155803--34155859 Score: 89 Period size: 30 Copynumber: 1.9 Consensus size: 30 34155793 TTCCACACGT 34155803 GTGATCAACAAGTCC-GTGCGTGACACATAG 1 GTGATCAACAAG-CCTGTGCGTGACACATAG * 34155833 GTGATCCACAAGCCTGTGCGTGACACA 1 GTGATCAACAAGCCTGTGCGTGACACA 34155860 CGGGTAGACC Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 29 2 0.08 30 23 0.92 ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19 Consensus pattern (30 bp): GTGATCAACAAGCCTGTGCGTGACACATAG Found at i:34157028 original size:16 final size:16 Alignment explanation

Indices: 34157009--34157051 Score: 52 Period size: 16 Copynumber: 2.7 Consensus size: 16 34156999 TTTTGTTGCA * 34157009 ATTTAATTTTGTTTTT 1 ATTTACTTTTGTTTTT 34157025 ATTTACTATTT-TTTTT 1 ATTTACT-TTTGTTTTT * 34157041 CTTTACTTTTG 1 ATTTACTTTTG 34157052 GCAAGTTTTT Statistics Matches: 23, Mismatches: 2, Indels: 4 0.79 0.07 0.14 Matches are distributed among these distances: 15 3 0.13 16 17 0.74 17 3 0.13 ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72 Consensus pattern (16 bp): ATTTACTTTTGTTTTT Found at i:34163184 original size:29 final size:29 Alignment explanation

Indices: 34163054--34163176 Score: 228 Period size: 29 Copynumber: 4.2 Consensus size: 29 34163044 GTGACGAGAT 34163054 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 34163083 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 34163112 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA * 34163141 TGGCACTAAGTGTGCATGCTGGAAATAGA 1 TGGCACTAAGTGTGCATGCTGGAAATATA * 34163170 CGGCACT 1 TGGCACT 34163177 GGGTGTGCGA Statistics Matches: 92, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 29 92 1.00 ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAATATA Found at i:34163213 original size:58 final size:58 Alignment explanation

Indices: 34163055--34163205 Score: 196 Period size: 58 Copynumber: 2.6 Consensus size: 58 34163045 TGACGAGATT * * * * 34163055 GGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAATATAT 1 GGCACTAAGTGTGCATGCTCGAAAGATATGGCACTAAGTGTGCATGCTGGAAATAGAC * * 34163113 GGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAATAGAC 1 GGCACTAAGTGTGCATGCTCGAAAGATATGGCACTAAGTGTGCATGCTGGAAATAGAC ** * * 34163171 GGCACTGGGTGTGCGA-GCTCGAAGGGTATGGCACT 1 GGCACTAAGTGTGC-ATGCTCGAAAGATATGGCACT 34163206 GTGTGTGCGG Statistics Matches: 84, Mismatches: 8, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 58 83 0.99 59 1 0.01 ACGTcount: A:0.28, C:0.16, G:0.32, T:0.25 Consensus pattern (58 bp): GGCACTAAGTGTGCATGCTCGAAAGATATGGCACTAAGTGTGCATGCTGGAAATAGAC Found at i:34163231 original size:87 final size:87 Alignment explanation

Indices: 34163054--34163243 Score: 213 Period size: 87 Copynumber: 2.2 Consensus size: 87 34163044 GTGACGAGAT * * * * 34163054 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACT 1 TGGCACTAAGTGTGCATGCTGGAAATAGACGGCACTAAGTGTGCATGCTCGAAAGATATGGCACT * * 34163119 AAGTGTGCATGCTGGAAATATA 66 AAGTGTGCAGGCTGGAAATACA ** * * 34163141 TGGCACTAAGTGTGCATGCTGGAAATAGACGGCACTGGGTGTGCGA-GCTCGAAGGGTATGGCAC 1 TGGCACTAAGTGTGCATGCTGGAAATAGACGGCACTAAGTGTGC-ATGCTCGAAAGATATGGCAC ** * * * 34163205 TGTGTGTGCGGGCT-TAAATCGCA 65 TAAGTGTGCAGGCTGGAAAT-ACA 34163228 TGGCACTAAGTGTGCA 1 TGGCACTAAGTGTGCA 34163244 AAATCGAGTA Statistics Matches: 86, Mismatches: 15, Indels: 4 0.82 0.14 0.04 Matches are distributed among these distances: 86 4 0.05 87 81 0.94 88 1 0.01 ACGTcount: A:0.26, C:0.16, G:0.32, T:0.25 Consensus pattern (87 bp): TGGCACTAAGTGTGCATGCTGGAAATAGACGGCACTAAGTGTGCATGCTCGAAAGATATGGCACT AAGTGTGCAGGCTGGAAATACA Found at i:34170462 original size:39 final size:39 Alignment explanation

Indices: 34170408--34170485 Score: 156 Period size: 39 Copynumber: 2.0 Consensus size: 39 34170398 TCCTGCCCAC 34170408 ACGGGCATGTGACTCTCCAAATCAAGAAAATTTTCTAAG 1 ACGGGCATGTGACTCTCCAAATCAAGAAAATTTTCTAAG 34170447 ACGGGCATGTGACTCTCCAAATCAAGAAAATTTTCTAAG 1 ACGGGCATGTGACTCTCCAAATCAAGAAAATTTTCTAAG 34170486 TCTTCCTATT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 39 39 1.00 ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26 Consensus pattern (39 bp): ACGGGCATGTGACTCTCCAAATCAAGAAAATTTTCTAAG Found at i:34173042 original size:43 final size:43 Alignment explanation

Indices: 34172994--34173129 Score: 116 Period size: 42 Copynumber: 3.2 Consensus size: 43 34172984 TCCCGGACGT * * 34172994 GGTCTTACATGTAATTCAGTATCGATGCCTCTATCCCAAACAA 1 GGTCTTACACGTAATTCAGTATCGATGCCTATATCCCAAACAA * * * * * 34173037 GGTCTTACACGAAATT-AGATAT-GATGCCAATGTCCCAGACAT 1 GGTCTTACACGTAATTCAG-TATCGATGCCTATATCCCAAACAA * * * * * 34173079 GGTCTTACACGTAAATCTCA-AATCAAGGTCTGTATCCCAAACAA 1 GGTCTTACACGT-AAT-TCAGTATCGATGCCTATATCCCAAACAA 34173123 GGTCTTA 1 GGTCTTA 34173130 GACGATATCT Statistics Matches: 71, Mismatches: 17, Indels: 9 0.73 0.18 0.09 Matches are distributed among these distances: 42 28 0.39 43 22 0.31 44 20 0.28 45 1 0.01 ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28 Consensus pattern (43 bp): GGTCTTACACGTAATTCAGTATCGATGCCTATATCCCAAACAA Found at i:34176685 original size:117 final size:117 Alignment explanation

Indices: 34176479--34176832 Score: 397 Period size: 117 Copynumber: 3.0 Consensus size: 117 34176469 TGGGTGCATT * * * * 34176479 TTACTTTGGACGTTCCGATGAGGCATTAGGTGTCAAATGATTACTTCGACTATGTGCTGATGAGT 1 TTACTTTAGACGTTCCGATGAGGCACTAGGTGTCAAATGATTACTTCGACTACGTGTTGATGAGT * * * 34176544 GTTGGACATAATTTTTACTTCAGTCAATTGATAAGCGTTGGGTGA-AAACTAA 66 GTTGGACACAATTTTTACTTCAGTCAACTGATAAGCGTTGGG-CACAAACTAA * * * * * 34176596 TTACTTTAGACGTTCCAATGACGCACTGGGTGTCTAATGATTACTTCAACTACGTGTTGATGAGT 1 TTACTTTAGACGTTCCGATGAGGCACTAGGTGTCAAATGATTACTTCGACTACGTGTTGATGAGT * * * 34176661 ATTGGACACAATTTTTACTTCAGTCAACTGATGAGTGTTGGGCACAAACTAA 66 GTTGGACACAATTTTTACTTCAGTCAACTGATAAGCGTTGGGCACAAACTAA * * ** ** * * 34176713 TTAC-TTCGAATGTTTTGATGAGGCACTAGGTACCAAATGAATACTTCGACTACGTGTCGATGAG 1 TTACTTTAG-ACGTTCCGATGAGGCACTAGGTGTCAAATGATTACTTCGACTACGTGTTGATGAG * * * * * * * 34176777 TGTTGGGCACAATTTTTACTTCGGTCATACAGATGAGCGTAGGGCGCAATCTAA 65 TGTTGGACACAATTTTTACTTCAGTCA-ACTGATAAGCGTTGGGCACAAACTAA 34176831 TT 1 TT 34176833 TTCTTCTAAA Statistics Matches: 198, Mismatches: 36, Indels: 5 0.83 0.15 0.02 Matches are distributed among these distances: 116 4 0.02 117 171 0.86 118 23 0.12 ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33 Consensus pattern (117 bp): TTACTTTAGACGTTCCGATGAGGCACTAGGTGTCAAATGATTACTTCGACTACGTGTTGATGAGT GTTGGACACAATTTTTACTTCAGTCAACTGATAAGCGTTGGGCACAAACTAA Found at i:34180445 original size:20 final size:20 Alignment explanation

Indices: 34180420--34180494 Score: 60 Period size: 20 Copynumber: 3.5 Consensus size: 20 34180410 CTAGGAAATA 34180420 TGTGATCTGAACTCATGAGT 1 TGTGATCTGAACTCATGAGT * ** * 34180440 TGTGATTTGAGTTCATGATAT 1 TGTGATCTGAACTCATGA-GT 34180461 ATGTGACATCTGAACTCATTGAGT 1 -TGTG--ATCTGAACTCA-TGAGT * 34180485 TGTGGTCTGA 1 TGTGATCTGA 34180495 GTTCATGATA Statistics Matches: 41, Mismatches: 9, Indels: 9 0.69 0.15 0.15 Matches are distributed among these distances: 20 15 0.37 21 6 0.15 22 4 0.10 23 4 0.10 24 9 0.22 25 3 0.07 ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39 Consensus pattern (20 bp): TGTGATCTGAACTCATGAGT Found at i:34180496 original size:45 final size:44 Alignment explanation

Indices: 34180417--34180513 Score: 153 Period size: 45 Copynumber: 2.2 Consensus size: 44 34180407 TCACTAGGAA * 34180417 ATATGTG--ATCTGAACTCATGAGTTGTGATTTGAGTTCATGAT 1 ATATGTGACATCTGAACTCATGAGTTGTGATCTGAGTTCATGAT * 34180459 ATATGTGACATCTGAACTCATTGAGTTGTGGTCTGAGTTCATGAT 1 ATATGTGACATCTGAACTCA-TGAGTTGTGATCTGAGTTCATGAT 34180504 ATATGTGACA 1 ATATGTGACA 34180514 CATGTTTTGG Statistics Matches: 50, Mismatches: 2, Indels: 3 0.91 0.04 0.05 Matches are distributed among these distances: 42 7 0.14 44 11 0.22 45 32 0.64 ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38 Consensus pattern (44 bp): ATATGTGACATCTGAACTCATGAGTTGTGATCTGAGTTCATGAT Found at i:34180875 original size:2 final size:2 Alignment explanation

Indices: 34180868--34180893 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 34180858 TGTGGTAAGA 34180868 AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 34180894 GAAGATTAAG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:34185623 original size:43 final size:42 Alignment explanation

Indices: 34185565--34185721 Score: 144 Period size: 42 Copynumber: 3.7 Consensus size: 42 34185555 CAATGCCAAC * * 34185565 GTCCCAGAC-GTGGTCTTACATGTAATCAAATATCGATGCC-ACT 1 GTCCCAGACAG-GGTCTTACACGAAATCAAATA-CGATGCCGA-T * 34185608 GTCCCAGATAGGGTCTTACACGAAATCAAATACGATGCCGAT 1 GTCCCAGACAGGGTCTTACACGAAATCAAATACGATGCCGAT * * * 34185650 GTCCCAGACATGGTCTTACAC-ATAACTCTCAAAT-CGATGCCAAC 1 GTCCCAGACAGGGTCTTACACGA-AA---TCAAATACGATGCCGAT * 34185694 GTCCCAAAC-GTGGTCTTACACGAAATCA 1 GTCCCAGACAG-GGTCTTACACGAAATCA 34185722 CATATCGGAA Statistics Matches: 97, Mismatches: 9, Indels: 18 0.78 0.07 0.15 Matches are distributed among these distances: 41 4 0.04 42 29 0.30 43 28 0.29 44 29 0.30 45 7 0.07 ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24 Consensus pattern (42 bp): GTCCCAGACAGGGTCTTACACGAAATCAAATACGATGCCGAT Found at i:34185712 original size:86 final size:85 Alignment explanation

Indices: 34185565--34185721 Score: 205 Period size: 86 Copynumber: 1.8 Consensus size: 85 34185555 CAATGCCAAC * ** 34185565 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGATAGGGTCTTACACG 1 GTCCCAGACATGGTCTTACACATAATCAAATATCGATGCCACTGTCCCAGATAGGGTCTTACACG 34185630 AAATCAAATACGATGCCGAT 66 AAATCAAATACGATGCCGAT * 34185650 GTCCCAGACATGGTCTTACACATAACTCTCAA-ATCGATGCCAAC-GTCCCA-A-ACGTGGTCTT 1 GTCCCAGACATGGTCTTACACATAA-TC-AAATATCGATGCC-ACTGTCCCAGATA-G-GGTCTT 34185711 ACACGAAATCA 61 ACACGAAATCA 34185722 CATATCGGAA Statistics Matches: 63, Mismatches: 4, Indels: 9 0.83 0.05 0.12 Matches are distributed among these distances: 84 1 0.02 85 24 0.38 86 34 0.54 87 4 0.06 ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24 Consensus pattern (85 bp): GTCCCAGACATGGTCTTACACATAATCAAATATCGATGCCACTGTCCCAGATAGGGTCTTACACG AAATCAAATACGATGCCGAT Found at i:34192736 original size:43 final size:42 Alignment explanation

Indices: 34192670--34192828 Score: 176 Period size: 43 Copynumber: 3.7 Consensus size: 42 34192660 AACTCGTATA * * 34192670 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATATCG 1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATAAAATAT-G * * ** 34192713 ATGCCACTGTCCCAGACAGGGTCTTACACAAAATAAAATATG 1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATAAAATATG * * 34192755 ATGCTAATGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-TG 1 ATGCCAATGTCCCAGACATGGTCTTACACGT-AA--TAAAATATG * * * 34192799 ATGCCAATGTACGAGACGTGGTCTTACACG 1 ATGCCAATGTCCCAGACATGGTCTTACACG 34192829 AAATCATATA Statistics Matches: 97, Mismatches: 16, Indels: 5 0.82 0.14 0.04 Matches are distributed among these distances: 42 27 0.28 43 37 0.38 44 28 0.29 45 5 0.05 ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26 Consensus pattern (42 bp): ATGCCAATGTCCCAGACATGGTCTTACACGTAATAAAATATG Found at i:34210295 original size:49 final size:49 Alignment explanation

Indices: 34210232--34210509 Score: 174 Period size: 49 Copynumber: 5.9 Consensus size: 49 34210222 GCACATCAAA * * 34210232 GTCGATGCCATGTCCCAAACAGGTCTTACACTGACTTTCATATATCGAG- 1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATC-AGT * * * 34210281 GTCGATGCCGTGTCCCAGACAGGTCTTACACTAACTCTCATTTATCAGT 1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAGT * * * * * * * 34210330 GTCAATGCCCTGTCCCGGACATGTCTTACACTGACACACA-ACA--AG- 1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAGT * * * * 34210375 CT-GACGCCATGTCCCAGACAGGTCTTACACT-AGCT-TGTATATCTCGAG- 1 GTCGATGCCATGTCCCAGACAGGTCTTACACTGA-CTCT-CATATATC-AGT * * * ** 34210423 G-CTGAT-ACATGTCCCAGACATGTCTTACACT-AGCTCTC--ATCTCAAA 1 GTC-GATGCCATGTCCCAGACAGGTCTTACACTGA-CTCTCATATATCAGT * * 34210469 GTCGATG-CATGTCCCA-AGCATGTCTTACACTGGCTCTCATA 1 GTCGATGCCATGTCCCAGA-CAGGTCTTACACTGACTCTCATA 34210510 ATGTGTGTAA Statistics Matches: 180, Mismatches: 32, Indels: 35 0.73 0.13 0.14 Matches are distributed among these distances: 43 1 0.01 44 26 0.14 45 4 0.02 46 38 0.21 47 1 0.01 48 33 0.18 49 77 0.43 ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27 Consensus pattern (49 bp): GTCGATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCAGT Found at i:34211909 original size:71 final size:71 Alignment explanation

Indices: 34211823--34211986 Score: 319 Period size: 71 Copynumber: 2.3 Consensus size: 71 34211813 CGATTTGTCT 34211823 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAC 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAC 34211888 CTTTCA 66 CTTTCA * 34211894 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAC 34211959 CTTTCA 66 CTTTCA 34211965 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 34211987 GATACATCTC Statistics Matches: 92, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 71 92 1.00 ACGTcount: A:0.19, C:0.29, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAC CTTTCA Found at i:34212024 original size:71 final size:70 Alignment explanation

Indices: 34211823--34212020 Score: 267 Period size: 71 Copynumber: 2.8 Consensus size: 70 34211813 CGATTTGTCT * * * 34211823 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAC 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAC 34211888 CTTTCA 65 CTTTCA * * * * 34211894 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAC 34211959 CTTTCA 65 CTTTCA * * 34211965 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC 34212021 TACAGGGTGT Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 23 0.19 69 1 0.01 70 1 0.01 71 95 0.79 ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTACC TTTCA Found at i:34219488 original size:70 final size:71 Alignment explanation

Indices: 34219403--34219565 Score: 319 Period size: 70 Copynumber: 2.3 Consensus size: 71 34219393 CGATTTGTCT 34219403 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA- 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 34219467 CTTTCA 66 CTTTCA 34219473 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 34219538 CTTTCA 66 CTTTCA 34219544 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 34219566 GATACATCTC Statistics Matches: 92, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 70 64 0.70 71 28 0.30 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:34223409 original size:43 final size:43 Alignment explanation

Indices: 34223360--34223516 Score: 156 Period size: 43 Copynumber: 3.7 Consensus size: 43 34223350 TATCCCATAT * * * 34223360 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGAC 1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC * * * * 34223403 AGGGTCTTACACATAATCGA-TTAACGATGCCAATGTCCCAGAC 1 ATGGTCTTACACGTAATC-ACATATCGATGCCAATGTCCCAGAC * ** * 34223446 ATGGTCTTATACGTAATCACA-ATAAAATGACAATGTCCCAGAC 1 ATGGTCTTACACGTAATCACATAT-CGATGCCAATGTCCCAGAC * * * 34223489 ATGGTATTACATGTAATCACATCTCGAT 1 ATGGTCTTACACGTAATCACATATCGAT 34223517 AACCTAATGT Statistics Matches: 89, Mismatches: 21, Indels: 8 0.75 0.18 0.07 Matches are distributed among these distances: 42 2 0.02 43 85 0.96 44 2 0.02 ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28 Consensus pattern (43 bp): ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC Found at i:34227295 original size:40 final size:40 Alignment explanation

Indices: 34227236--34227443 Score: 213 Period size: 40 Copynumber: 5.2 Consensus size: 40 34227226 CATTGGAATG * * 34227236 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTAATT ** 34227276 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTAATT * * * 34227316 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTAA-C 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAG-TAATT * * * * 34227356 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTCACT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTAATT * ** * * * * * 34227396 ATAACCGGGCTTCGTCCCGAACGCATTTGAGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTAATT 34227436 ATATCCGG 1 ATATCCGG 34227444 TTAAATTCCG Statistics Matches: 138, Mismatches: 26, Indels: 8 0.80 0.15 0.05 Matches are distributed among these distances: 39 5 0.04 40 130 0.94 41 3 0.02 ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTAATT Found at i:34235209 original size:29 final size:29 Alignment explanation

Indices: 34235176--34235242 Score: 107 Period size: 29 Copynumber: 2.3 Consensus size: 29 34235166 GTGGGATCTT * 34235176 CTTCTTCATCAAGGTCTTCCTATTCCTCA 1 CTTCTTCATCAAGGTCCTCCTATTCCTCA * 34235205 CTTCTTCATCAAGGTCCTCCTTTTCCTCA 1 CTTCTTCATCAAGGTCCTCCTATTCCTCA 34235234 CTTACTTCA 1 CTT-CTTCA 34235243 ACTCGTTGCT Statistics Matches: 35, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 29 30 0.86 30 5 0.14 ACGTcount: A:0.16, C:0.36, G:0.06, T:0.42 Consensus pattern (29 bp): CTTCTTCATCAAGGTCCTCCTATTCCTCA Found at i:34236223 original size:3 final size:3 Alignment explanation

Indices: 34236215--34236241 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 34236205 TAGAAATTAA 34236215 AAT AAT AAT AAT AAT AAT AAT AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT 34236242 GAAGGAAAAG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 24 1.00 ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33 Consensus pattern (3 bp): AAT Found at i:34236804 original size:22 final size:22 Alignment explanation

Indices: 34236768--34236822 Score: 62 Period size: 22 Copynumber: 2.5 Consensus size: 22 34236758 AATTCTATGC 34236768 TAAATTGATAA-AGAT-TAATATA 1 TAAATT-ATAATAGATATAAT-TA 34236790 TAAATTATAATAGATATAATTA 1 TAAATTATAATAGATATAATTA * 34236812 TATATTA-AATA 1 TAAATTATAATA 34236823 TTATCATCTT Statistics Matches: 30, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 21 8 0.27 22 18 0.60 23 4 0.13 ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40 Consensus pattern (22 bp): TAAATTATAATAGATATAATTA Found at i:34241827 original size:18 final size:18 Alignment explanation

Indices: 34241804--34241840 Score: 74 Period size: 18 Copynumber: 2.1 Consensus size: 18 34241794 AAATGTCCTT 34241804 CCCCACAATAAACACAGG 1 CCCCACAATAAACACAGG 34241822 CCCCACAATAAACACAGG 1 CCCCACAATAAACACAGG 34241840 C 1 C 34241841 TATACTCTCA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.43, C:0.41, G:0.11, T:0.05 Consensus pattern (18 bp): CCCCACAATAAACACAGG Found at i:34248103 original size:46 final size:45 Alignment explanation

Indices: 34248050--34248177 Score: 136 Period size: 47 Copynumber: 2.7 Consensus size: 45 34248040 GGACTATTGT * 34248050 GAGCTAGTGTAAGACATGTATGGGACATGCATCAACCGCATT-ATGA 1 GAGCTAGTGTAAGACATGT-TGGGACATGCATC-ACCGCATTGACGA * * 34248096 GAGCTAGTGTAAGACCATGTTCGGGACACGGCAT--CGGCATTGAGACGA 1 GAGCTAGTGTAAGA-CATGTT-GGGACA-TGCATCACCGCATT--GACGA 34248144 GAGCTAGTGTAAGACATGTCTGGGACATGCATCA 1 GAGCTAGTGTAAGACATGT-TGGGACATGCATCA 34248178 GCTACGAGTA Statistics Matches: 69, Mismatches: 4, Indels: 16 0.78 0.04 0.18 Matches are distributed among these distances: 45 6 0.09 46 19 0.28 47 22 0.32 48 22 0.32 ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22 Consensus pattern (45 bp): GAGCTAGTGTAAGACATGTTGGGACATGCATCACCGCATTGACGA Found at i:34248225 original size:92 final size:93 Alignment explanation

Indices: 34248050--34248227 Score: 254 Period size: 92 Copynumber: 1.9 Consensus size: 93 34248040 GGACTATTGT * 34248050 GAGCTAGTGTAAGACATGTATGGGACATGCATCAACCGCATTATGAGAGCTAGTGTAAGACCATG 1 GAGCTAGTGTAAGACATGTATGGGACATGCATCAACCGCAGTA-GAGAGCTAGTGTAAGACCATG * * 34248115 TTCGGGACACGGCATCGGCATTGAGACGA 65 TCCAGGACACGGCATCGGCATTGAGACGA * * 34248144 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTACG-AGTA-A-AGCTAGTGTAAGACCAT 1 GAGCTAGTGTAAGACATGTATGGGACATGCATCAAC--CGCAGTAGAGAGCTAGTGTAAGACCAT * 34248206 GTCCAGGACATGGCATCGGCAT 64 GTCCAGGACACGGCATCGGCAT 34248228 ACTACCCCAT Statistics Matches: 76, Mismatches: 6, Indels: 6 0.86 0.07 0.07 Matches are distributed among these distances: 92 36 0.47 93 1 0.01 94 34 0.45 95 3 0.04 96 2 0.03 ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21 Consensus pattern (93 bp): GAGCTAGTGTAAGACATGTATGGGACATGCATCAACCGCAGTAGAGAGCTAGTGTAAGACCATGT CCAGGACACGGCATCGGCATTGAGACGA Found at i:34251957 original size:32 final size:32 Alignment explanation

Indices: 34251921--34251992 Score: 117 Period size: 32 Copynumber: 2.2 Consensus size: 32 34251911 ACTATGTTTT * 34251921 CTAAGATTGATTTGAGGTCTGGTTACTATCAA 1 CTAAGAGTGATTTGAGGTCTGGTTACTATCAA * * 34251953 CTAAGGGTGATTTGAGGTCTGGTTACTATCAG 1 CTAAGAGTGATTTGAGGTCTGGTTACTATCAA 34251985 CTAAGAGT 1 CTAAGAGT 34251993 TAAAGAGTAA Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 32 36 1.00 ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35 Consensus pattern (32 bp): CTAAGAGTGATTTGAGGTCTGGTTACTATCAA Done.