Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A07

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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 2857347 characters in sequence are not A, C, G, or T


File 151 of 290

Found at i:48378801 original size:40 final size:39

Alignment explanation

Indices: 48378741--48378854 Score: 120 Period size: 40 Copynumber: 2.8 Consensus size: 39 48378731 TTATTTGTGA * * 48378741 CACTTAGTGTGAGATACGACATAGCTTCGGCTATATATGG 1 CACTTAGTGTGCGATTCGACATAGCTTC-GCTATATATGG ** * 48378781 CACTTAGTGTGCGATTCGACATATTTTCGATAATATATGG 1 CACTTAGTGTGCGATTCGACATAGCTTCGCT-ATATATGG * * * * 48378821 CAATTAGTGTGCGATTTGAGATAGGTTCAGCTAT 1 CACTTAGTGTGCGATTCGACATAGCTTC-GCTAT 48378855 GTACGGTACT Statistics Matches: 61, Mismatches: 11, Indels: 4 0.80 0.14 0.05 Matches are distributed among these distances: 39 2 0.03 40 57 0.93 41 2 0.03 ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34 Consensus pattern (39 bp): CACTTAGTGTGCGATTCGACATAGCTTCGCTATATATGG Found at i:48381857 original size:79 final size:82 Alignment explanation

Indices: 48381746--48381930 Score: 229 Period size: 79 Copynumber: 2.3 Consensus size: 82 48381736 GCTACTCGTT * * * 48381746 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC * * 48381809 GGATTTAGTAAC-TCGCA 65 GGATATAGTAACTTAGCA * ** 48381826 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG * * 48381889 GATATGGTCACTTAGCA 66 GATATAGTAACTTAGCA 48381906 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 48381931 CATCATTCAA Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.59 80 34 0.37 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25 Consensus pattern (82 bp): CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG GATATAGTAACTTAGCA Found at i:48381930 original size:40 final size:40 Alignment explanation

Indices: 48381727--48381930 Score: 229 Period size: 40 Copynumber: 5.1 Consensus size: 40 48381717 CGGAATTTAA ** * 48381727 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC 1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC * * * 48381767 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * 48381807 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * 48381846 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT 1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC * * * 48381886 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC 1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC 48381926 CCGGA 1 CCGGA 48381931 CATCATTCAA Statistics Matches: 139, Mismatches: 18, Indels: 14 0.81 0.11 0.08 Matches are distributed among these distances: 38 2 0.01 39 33 0.24 40 92 0.66 41 12 0.09 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC Found at i:48389156 original size:79 final size:82 Alignment explanation

Indices: 48389045--48389229 Score: 229 Period size: 79 Copynumber: 2.3 Consensus size: 82 48389035 GCTACTCGTT * * * 48389045 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC * * 48389108 GGATTTAGTAAC-TCGCA 65 GGATATAGTAACTTAGCA * ** 48389125 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG 1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG * * 48389188 GATATGGTCACTTAGCA 66 GATATAGTAACTTAGCA 48389205 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 48389230 CATCATTCAA Statistics Matches: 91, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 3 0.03 79 54 0.59 80 34 0.37 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25 Consensus pattern (82 bp): CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG GATATAGTAACTTAGCA Found at i:48389229 original size:40 final size:40 Alignment explanation

Indices: 48389026--48389229 Score: 229 Period size: 40 Copynumber: 5.1 Consensus size: 40 48389016 CGGAATTTAA ** * 48389026 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC 1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC * * * 48389066 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * 48389106 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC 1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC * * 48389145 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT 1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC * * * 48389185 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC 1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC 48389225 CCGGA 1 CCGGA 48389230 CATCATTCAA Statistics Matches: 139, Mismatches: 18, Indels: 14 0.81 0.11 0.08 Matches are distributed among these distances: 38 2 0.01 39 33 0.24 40 92 0.66 41 12 0.09 ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC Found at i:48397541 original size:45 final size:45 Alignment explanation

Indices: 48397477--48397647 Score: 260 Period size: 45 Copynumber: 3.8 Consensus size: 45 48397467 TGTACAGTAC * 48397477 TATTCAGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATAT 1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATAT 48397522 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCC-GATGAGATAT 1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAG-TGAGATAT * 48397567 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT 1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATAT * * 48397612 TATTCTGGCC-TCGAGCCTAGCAGG-TGA-AATGCCAGT 1 TATTCGGGCCTTTGAGCCTAGCAGGCT-ATAATGCCAGT 48397648 AAATGAATTC Statistics Matches: 119, Mismatches: 4, Indels: 8 0.91 0.03 0.06 Matches are distributed among these distances: 43 9 0.08 44 15 0.13 45 94 0.79 46 1 0.01 ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28 Consensus pattern (45 bp): TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCAGTGAGATAT Found at i:48407353 original size:55 final size:54 Alignment explanation

Indices: 48407266--48407520 Score: 287 Period size: 55 Copynumber: 4.8 Consensus size: 54 48407256 ATTAGGGTTT * 48407266 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC 1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC * * * * * 48407321 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC 1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC * * * 48407376 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTCAG-TTCATAAGGC 1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC * 48407429 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA--- 1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC * * 48407478 AAGGATACCACGTAAGACCATGACAAGACATGGCAA-TGGTAAG 1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG 48407521 GTACCCGCGT Statistics Matches: 173, Mismatches: 20, Indels: 20 0.81 0.09 0.09 Matches are distributed among these distances: 49 41 0.24 52 7 0.04 53 41 0.24 54 12 0.07 55 68 0.39 56 4 0.02 ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21 Consensus pattern (54 bp): AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC Found at i:48407472 original size:108 final size:110 Alignment explanation

Indices: 48407273--48407473 Score: 327 Period size: 108 Copynumber: 1.8 Consensus size: 110 48407263 TTTAAGGATA * 48407273 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA 1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA * 48407338 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC 66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC * * 48407383 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTCA-G-TTCATAAGGCAAGGATACCATGTAAG 1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG * 48407445 ACCATGTCAAGACATGGCAATGGTAAGTT 65 ACCATGTCAAGACATGGCAATGATAAGTT 48407474 TCAAAAGGAT Statistics Matches: 85, Mismatches: 5, Indels: 4 0.90 0.05 0.04 Matches are distributed among these distances: 107 3 0.04 108 48 0.56 109 7 0.08 110 27 0.32 ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22 Consensus pattern (110 bp): CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC Found at i:48410294 original size:48 final size:48 Alignment explanation

Indices: 48410208--48410434 Score: 337 Period size: 48 Copynumber: 4.7 Consensus size: 48 48410198 TCATATCGAC * * ** * 48410208 GCCATGTCCCAAACATGGTCGTACATGAAATCACATATCGATGCCAAC 1 GCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAAT * * * * 48410256 GCCATATCCCAGACATGGTCTTACGTGGGATCATATATCAATGCCAAT 1 GCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAAT 48410304 GCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAAT 1 GCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAAT * * * 48410352 GCTATGTCCCAGACATGGTCTTACATGGGATCACATATTGATTCCAAT 1 GCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAAT * 48410400 GCCATGTCCCAGACATGGTCTAACATGGGATCACA 1 GCCATGTCCCAGACATGGTCTTACATGGGATCACA 48410435 ATGCCATAGC Statistics Matches: 161, Mismatches: 18, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 48 161 1.00 ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25 Consensus pattern (48 bp): GCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCAAT Found at i:48410455 original size:37 final size:37 Alignment explanation

Indices: 48410396--48410494 Score: 103 Period size: 37 Copynumber: 2.7 Consensus size: 37 48410386 ATATTGATTC * 48410396 CAATGCCAT-GTCCCAGAC-ATGGTCTAACATGGGATCA 1 CAATGCCATAG-CCCAG-CTATGGTCTAACATGGCATCA * * * * * 48410433 CAATGCCATAGCCCATCTATGGTTTTACATGTCATTA 1 CAATGCCATAGCCCAGCTATGGTCTAACATGGCATCA * 48410470 CGATGCCATAGCCCAGCTATGGTCT 1 CAATGCCATAGCCCAGCTATGGTCT 48410495 TGCACGTACT Statistics Matches: 51, Mismatches: 9, Indels: 4 0.80 0.14 0.06 Matches are distributed among these distances: 36 1 0.02 37 49 0.96 38 1 0.02 ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27 Consensus pattern (37 bp): CAATGCCATAGCCCAGCTATGGTCTAACATGGCATCA Found at i:48412205 original size:46 final size:47 Alignment explanation

Indices: 48412099--48412414 Score: 211 Period size: 46 Copynumber: 6.7 Consensus size: 47 48412089 TATTATGAGC * * * * * 48412099 CAGTGTAAGGCCATGTCTGGGACATGACATTGGCATTGAGACG-AGAG- 1 CAGTGTAAGACCATGTCTGGGACATGGCA-TCGCCTCGAGACGTA-AGT * 48412146 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGACGTAAGG 1 C-AGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGAGACGTAAGT * * * * 48412193 CAGTGCAAGA-CATGTCTAGGACAT-GCATCGGCTACGAGATGT--GT 1 CAGTGTAAGACCATGTCTGGGACATGGCATCGCCT-CGAGACGTAAGT * * * * * * * 48412237 CAGTGTAAGACCATGTCCGGGACATGGCATCGACACAGATATGTGAGAA 1 CAGTGTAAGACCATGTCTGGGACATGGCATCGCCTC-GAGACGTAAG-T * * 48412286 CTAGTGTAAGACCATGCCTGGGACATGGCGTCAGCCTCGATGACG-ATAGT 1 C-AGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGA-GACGTA-AGT * * ** * 48412336 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGATATGAG- 1 CAGTGTAAGACCATGTCTGGGACATGGCATCGCCTCGAGACGTAAGT * * * 48412382 CTAGTGTAAGACAATGTCTAGGACATGACATCG 1 C-AGTGTAAGACCATGTCTGGGACATGGCATCG 48412415 ACATTCTACC Statistics Matches: 216, Mismatches: 36, Indels: 34 0.76 0.13 0.12 Matches are distributed among these distances: 44 10 0.05 45 17 0.08 46 60 0.28 47 49 0.23 48 14 0.06 49 29 0.13 50 30 0.14 51 7 0.03 ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22 Consensus pattern (47 bp): CAGTGTAAGACCATGTCTGGGACATGGCATCGCCTCGAGACGTAAGT Found at i:48412406 original size:146 final size:140 Alignment explanation

Indices: 48412141--48412417 Score: 351 Period size: 146 Copynumber: 1.9 Consensus size: 140 48412131 GCATTGAGAC * * 48412141 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGGCAGTGCAAGACAT 1 GAGAACTAGTGTAAGACATGCCTGGGACATGCATCAGCCTCGAGACGTAAGGCAGTGCAAGACAT * * * * * 48412206 GTCTAGGACATGCATCGGCTACGAGATGTGTCAGTGTAAGACCATGTCCGGGACATGGCATCGAC 66 GTCTAGGACATGCATCGGCTACGAGATATGGCAGTGTAAGACAATGTCCAGGACATGACATCGAC 48412271 ACAGATATGT 131 ACAGATATGT * * * 48412281 GAGAACTAGTGTAAGACCATGCCTGGGACATGGCGTCAGCCTCGATGACG-ATAGTCAGTGTAAG 1 GAGAACTAGTGTAAGA-CATGCCTGGGACAT-GCATCAGCCTCGA-GACGTA-AGGCAGTGCAAG * * * 48412345 ACCATGTCTGGGACATGGCATCGGCT-TGAGATATGAGCTAGTGTAAGACAATGTCTAGGACATG 62 A-CATGTCTAGGACAT-GCATCGGCTACGAGATATG-GC-AGTGTAAGACAATGTCCAGGACATG 48412409 ACATCGACA 123 ACATCGACA 48412418 TTCTACCCCA Statistics Matches: 116, Mismatches: 13, Indels: 10 0.83 0.09 0.07 Matches are distributed among these distances: 140 15 0.13 141 13 0.11 142 13 0.11 143 15 0.13 144 20 0.17 145 10 0.09 146 30 0.26 ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21 Consensus pattern (140 bp): GAGAACTAGTGTAAGACATGCCTGGGACATGCATCAGCCTCGAGACGTAAGGCAGTGCAAGACAT GTCTAGGACATGCATCGGCTACGAGATATGGCAGTGTAAGACAATGTCCAGGACATGACATCGAC ACAGATATGT Found at i:48421903 original size:20 final size:20 Alignment explanation

Indices: 48421878--48421922 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 48421868 AGGGACTAAA * * 48421878 ATGAAAAGTTGTAAAATTTG 1 ATGAAAAATTCTAAAATTTG * 48421898 ATGAAAAATTCTAAAATTTT 1 ATGAAAAATTCTAAAATTTG 48421918 ATGAA 1 ATGAA 48421923 TACATGTGCT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36 Consensus pattern (20 bp): ATGAAAAATTCTAAAATTTG Found at i:48425707 original size:47 final size:47 Alignment explanation

Indices: 48425629--48426314 Score: 1111 Period size: 47 Copynumber: 14.6 Consensus size: 47 48425619 CCCTTCGGGA * * * * * * 48425629 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 48425676 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * * 48425723 CTCATCACATATATACACTTTCACATTCATCACATTGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 48425770 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 48425817 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 48425866 CTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 48425913 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * * 48425960 CTTATCACATATATACACTTTCAAATTCATCACATGGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 48426007 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 48426054 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 48426101 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 48426148 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 48426195 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 48426242 CTTATCACATATATAAACTTTCACATTCATCACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 48426289 CTTATCACATATATATACATTCACAT 1 CTTATCACATATATACACTTTCACAT 48426315 CACAATTATC Statistics Matches: 596, Mismatches: 41, Indels: 4 0.93 0.06 0.01 Matches are distributed among these distances: 47 551 0.92 49 45 0.08 ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:48434460 original size:39 final size:39 Alignment explanation

Indices: 48434425--48434813 Score: 384 Period size: 39 Copynumber: 9.9 Consensus size: 39 48434415 GGATATAGTA * * * * * 48434425 CCAGTACGAAGCCTGCGGACCTTAAGTCCGAATATAGTA 1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT * * * * * 48434464 CCAGCACGAAGCCTACAGATCTTAATTCCGGAAACAATT 1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT * * * * * * 48434503 CCAGCACGAAGCCTGCGAGTCTTTATGCCCAGATATAATT 1 CCAGCACGAAGCCTGCG-GACCTTAAGTCCGGATACAATT * * * * 48434543 CCAGCACGAAGCCTGTGGGTCTTTAAGCCCGGATACAATT 1 CCAGCACGAAGCCTG-CGGACCTTAAGTCCGGATACAATT * 48434583 CCAGCACGAAGCCTGCGGACCTTAAGTCCGAATACAATT 1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT * * * * * * 48434622 CCAGCACAAAGTCTGCGGGTCTTTAAGCCCGGATATAATT 1 CCAGCACGAAGCCTGC-GGACCTTAAGTCCGGATACAATT * * * * * 48434662 CCAGCA-TATAGCCTACGGGTCTTTAAGCCCGGATACAATT 1 CCAGCACGA-AGCCTGC-GGACCTTAAGTCCGGATACAATT * * 48434702 CCAGCACGAAGCTTGCGGACCTTAAGTCCTGATACAATT 1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT * * * 48434741 CTAGCACGAAGCTTGCGGACCTTAAGTCTGGATACAATT 1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT * 48434780 CCAGCACGAAGCTTGCGGACCTTAAGTCCGGATA 1 CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATA 48434814 TACATCAAAT Statistics Matches: 292, Mismatches: 53, Indels: 10 0.82 0.15 0.03 Matches are distributed among these distances: 39 165 0.57 40 125 0.43 41 2 0.01 ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22 Consensus pattern (39 bp): CCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT Found at i:48434547 original size:79 final size:78 Alignment explanation

Indices: 48434405--48434813 Score: 340 Period size: 79 Copynumber: 5.2 Consensus size: 78 48434395 GCCTATGGGA * * * * * * * * * * * 48434405 CTTTAAGCTCGGATATAGTACCAGTACGAAGCCTGCGGACCTTAAGTCCGAATATAGTACCAGCA 1 CTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGTCTTTAAGCCCG-ATACAATTCCAGCA * * 48434470 CGAAGCCTACAGAT 65 CGAAGCCTGCGGAT ** * * * 48434484 C-TTAATTCCGGAAACAATTCCAGCACGAAGCCTGCGAGTCTTTATGCCCAGATATAATTCCAGC 1 CTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCG-GTCTTTAAGCCC-GATACAATTCCAGC * * 48434548 ACGAAGCCTGTGGGT 64 ACGAAGCCTGCGGAT * * * 48434563 CTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGAATACAATTCCAGCA 1 CTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGTCTTTAAGCCCG-ATACAATTCCAGCA * * * 48434628 CAAAGTCTGCGGGT 65 CGAAGCCTGCGGAT * * * 48434642 CTTTAAGCCCGGATATAATTCCAGCA-TATAGCCTACGGGTCTTTAAGCCCGGATACAATTCCAG 1 CTTTAAGCCCGGATACAATTCCAGCACGA-AGCCTGC-GGTCTTTAAGCCC-GATACAATTCCAG * 48434706 CACGAAGCTTGCGGA- 63 CACGAAGCCTGCGGAT * * * * * * * ** 48434721 CCTTAAGTCCTGATACAATTCTAGCACGAAGCTTGCGGACCTTAAGTCTGGATACAATTCCAGCA 1 CTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGTCTTTAAG-CCCGATACAATTCCAGCA * 48434786 CGAAGCTTGCGGA- 65 CGAAGCCTGCGGAT * * 48434799 CCTTAAGTCCGGATA 1 CTTTAAGCCCGGATA 48434814 TACATCAAAT Statistics Matches: 269, Mismatches: 52, Indels: 19 0.79 0.15 0.06 Matches are distributed among these distances: 78 79 0.29 79 122 0.45 80 67 0.25 81 1 0.00 ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23 Consensus pattern (78 bp): CTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGTCTTTAAGCCCGATACAATTCCAGCAC GAAGCCTGCGGAT Found at i:48434727 original size:158 final size:158 Alignment explanation

Indices: 48434393--48434791 Score: 453 Period size: 158 Copynumber: 2.5 Consensus size: 158 48434383 CACCAACACA * * * * * * 48434393 AAGCCTATGGGACTTTAAGCTCGGATATAGTACCAGTACGAAGCCTGCGGACCTTAAGTCCGAAT 1 AAGCCTGTGGGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGAAT * * * * ** * 48434458 ATAGTACCAGCACGAAGCCTACAGATCTTAATTCCGGAAACAATTCCAGCACGAAGCCTGCGAGT 66 ACAATTCCAGCACAAAGCCTACAGATCTTAAGCCCGGAAACAATTCCAGCACGAAGCCTACGAGT * * 48434523 CTTTATGCCCAGATATAATTCCAGCACG 131 CTTTAAGCCCAGATACAATTCCAGCACG * 48434551 AAGCCTGTGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGAAT 1 AAGCCTGTGGGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGAAT * * * * * * * * 48434616 ACAATTCCAGCACAAAGTCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCA-TATAGCCTACGG 66 ACAATTCCAGCACAAAGCCTACAGATC-TTAAGCCCGGAAACAATTCCAGCACGA-AGCCTACGA * 48434680 GTCTTTAAGCCCGGATACAATTCCAGCACG 129 GTCTTTAAGCCCAGATACAATTCCAGCACG * * * * * * * 48434710 AAG-CT-TGCGGACCTTAAGTCCTGATACAATTCTAGCACGAAGCTTGCGGACCTTAAGTCTGGA 1 AAGCCTGTG-GGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGAA * 48434773 TACAATTCCAGCACGAAGC 65 TACAATTCCAGCACAAAGC 48434792 TTGCGGACCT Statistics Matches: 203, Mismatches: 35, Indels: 6 0.83 0.14 0.02 Matches are distributed among these distances: 157 2 0.01 158 144 0.71 159 57 0.28 ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23 Consensus pattern (158 bp): AAGCCTGTGGGACTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGAAT ACAATTCCAGCACAAAGCCTACAGATCTTAAGCCCGGAAACAATTCCAGCACGAAGCCTACGAGT CTTTAAGCCCAGATACAATTCCAGCACG Found at i:48434817 original size:119 final size:116 Alignment explanation

Indices: 48434405--48434813 Score: 417 Period size: 119 Copynumber: 3.5 Consensus size: 116 48434395 GCCTATGGGA * * * * * * * * * 48434405 CTTTAAGCTCGGATATAGTACCAGTACGAAGCCTGCGGACCTTAAGTCCGAATATAGTACCAGCA 1 CTTTAAGCCCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGCCCGGATACAATTCCAGCA * * * * * * 48434470 CGAAGCCTACAGATCTTAATTCCGGAAACAATTCCAGCACGAAGCCTGCGAGT 66 CGAAGCCTGCGGACCTTAAGTCC-GATACAATTCCAGCACGAAGCTTGCG-GT * * * * * 48434523 CTTTATGCCCAGATATAATTCCAGCACGAAGCCTGTGGGTCTTTAAGCCCGGATACAATTCCAGC 1 CTTTAAGCCCGGATATAATTCCAGCACGAAGCCTG-CGGACCTTAAGCCCGGATACAATTCCAGC * 48434588 ACGAAGCCTGCGGACCTTAAGTCCGAATACAATTCCAGCACAAAG-TCTGCGGGT 65 ACGAAGCCTGCGGACCTTAAGTCCG-ATACAATTCCAGCACGAAGCT-TGC-GGT * * * * 48434642 CTTTAAGCCCGGATATAATTCCAGCA-TATAGCCTACGGGTCTTTAAGCCCGGATACAATTCCAG 1 CTTTAAGCCCGGATATAATTCCAGCACGA-AGCCTGC-GGACCTTAAGCCCGGATACAATTCCAG * * * 48434706 CACGAAGCTTGCGGACCTTAAGTCCTGATACAATTCTAGCACGAAGCTTGCGGA 64 CACGAAGCCTGCGGACCTTAAGTCC-GATACAATTCCAGCACGAAGCTTGCGGT * * * * * * 48434760 CCTTAAGTCTGGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCCGGATA 1 CTTTAAGCCCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGCCCGGATA 48434814 TACATCAAAT Statistics Matches: 242, Mismatches: 40, Indels: 19 0.80 0.13 0.06 Matches are distributed among these distances: 117 15 0.06 118 60 0.25 119 164 0.68 120 3 0.01 ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23 Consensus pattern (116 bp): CTTTAAGCCCGGATATAATTCCAGCACGAAGCCTGCGGACCTTAAGCCCGGATACAATTCCAGCA CGAAGCCTGCGGACCTTAAGTCCGATACAATTCCAGCACGAAGCTTGCGGT Found at i:48436974 original size:27 final size:26 Alignment explanation

Indices: 48436936--48437102 Score: 199 Period size: 27 Copynumber: 6.2 Consensus size: 26 48436926 CAGCATGGCT * * 48436936 ACCAGAACAGATAATGTGACAGAGTC 1 ACCAGAACAGATAATGTGGCAGAGCC 48436962 ACCAGATACAGATAATCGTGGCAGAGCC 1 ACCAGA-ACAGATAAT-GTGGCAGAGCC * 48436990 GCCAGAACAGATATATGTGGCAGAGCC 1 ACCAGAACAGATA-ATGTGGCAGAGCC * * 48437017 ATCAGATCAGATAATCGTGGCAGAGCC 1 ACCAGAACAGATAAT-GTGGCAGAGCC * 48437044 ACCAGAACAAATATATGTGGCAGAGCC 1 ACCAGAACAGATA-ATGTGGCAGAGCC * * * 48437071 ACCAGATCAGATATTTGTGGCATAGCC 1 ACCAGAACAGATA-ATGTGGCAGAGCC 48437098 ACCAG 1 ACCAG 48437103 GACGCTTCCT Statistics Matches: 123, Mismatches: 13, Indels: 9 0.85 0.09 0.06 Matches are distributed among these distances: 26 8 0.07 27 97 0.79 28 18 0.15 ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17 Consensus pattern (26 bp): ACCAGAACAGATAATGTGGCAGAGCC Found at i:48437001 original size:54 final size:54 Alignment explanation

Indices: 48436936--48437102 Score: 246 Period size: 54 Copynumber: 3.1 Consensus size: 54 48436926 CAGCATGGCT * * 48436936 ACCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCC 1 ACCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCC * * 48436990 GCCAGAACAGATATATGTGGCAGAGCCATCAGATCAGATAATCGTGGCAGAGCC 1 ACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAGAGCC * * * * 48437044 ACCAGAACAAATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCC 1 ACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAGAGCC 48437098 ACCAG 1 ACCAG 48437103 GACGCTTCCT Statistics Matches: 102, Mismatches: 10, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 54 85 0.83 55 17 0.17 ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17 Consensus pattern (54 bp): ACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAGAGCC Found at i:48443399 original size:40 final size:40 Alignment explanation

Indices: 48443293--48443494 Score: 250 Period size: 40 Copynumber: 5.1 Consensus size: 40 48443283 GGATGATAAT * * * 48443293 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC 1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATA-TC * * 48443333 CGGGCTAAG-CCCGAAGGCAATT-GTGCGAGTTATTATACC 1 CGGGCTAAGTCCCGAAGGC-ATTCGTGCGAGTTACTATATC * * * 48443372 CGGGCTAATTCCCGAAGGCATTCGTGCGAGTTATTATGTC 1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC * 48443412 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATC 1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC * * 48443452 CGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATC 1 CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTA-CTATATC 48443492 CGG 1 CGG 48443495 TTAAATTCCG Statistics Matches: 143, Mismatches: 14, Indels: 10 0.86 0.08 0.06 Matches are distributed among these distances: 39 33 0.23 40 110 0.77 ACGTcount: A:0.22, C:0.23, G:0.29, T:0.25 Consensus pattern (40 bp): CGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATATC Found at i:48452302 original size:19 final size:19 Alignment explanation

Indices: 48452278--48452315 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 48452268 CACCAGAGTT 48452278 AGAAAAGATTTACGATGTG 1 AGAAAAGATTTACGATGTG * 48452297 AGAAAAGATTTATGATGTG 1 AGAAAAGATTTACGATGTG 48452316 TTTCACGTAT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.42, C:0.03, G:0.26, T:0.29 Consensus pattern (19 bp): AGAAAAGATTTACGATGTG Found at i:48453904 original size:47 final size:46 Alignment explanation

Indices: 48453830--48454057 Score: 187 Period size: 47 Copynumber: 4.8 Consensus size: 46 48453820 TGGGGTTATG * 48453830 TGAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATTGA-GA 1 TGAG-GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGATGA * * * * * * 48453878 CGAGGGCTAGTGTAAGACGTGTCTGGGACATGCATCAGCCACATCATGA 1 TGA-GGCCAGTGTAAGACATGTCTGGGACATGCATC-GGCA-TTGATGA * * * * * 48453927 T-A-GCCCGTGTAAGACCACGTCTAGGACATGGCATCGGCGTAGA-GA 1 TGAGGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGATGA * * 48453972 TGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGA 1 TGAG-GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGATGA * 48454019 TGTTA-GCCAGTGTAAGACGTGTCTGGGACATGCATCGGC 1 TG--AGGCCAGTGTAAGACATGTCTGGGACATGCATCGGC 48454058 TAAGTTTTGT Statistics Matches: 144, Mismatches: 24, Indels: 25 0.75 0.12 0.13 Matches are distributed among these distances: 45 3 0.02 46 28 0.19 47 78 0.54 48 31 0.22 49 4 0.03 ACGTcount: A:0.25, C:0.21, G:0.32, T:0.21 Consensus pattern (46 bp): TGAGGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGATGA Found at i:48454003 original size:94 final size:95 Alignment explanation

Indices: 48453834--48454057 Score: 292 Period size: 94 Copynumber: 2.4 Consensus size: 95 48453824 GTTATGTGAG * * * * 48453834 AGCCAGTATAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACGTG 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGACGAGGGCCAGTGTAAGACATG 48453899 TCTGGGACATGCATCAGCCAC-ATCATGAT 66 TCTGGGACATGCATCAGCCACGATCATGAT * * * * * * 48453928 AGCCCGTGTAAGACCACGTCTAGGACATGGCATCGGCGTAGAGATGAGTGCCAGTGTAAGACATG 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGACGAGGGCCAGTGTAAGACATG * * * * 48453993 TCTGGGACATGCATCGGCCTCGATGATGTT 66 TCTGGGACATGCATCAGCCACGATCATGAT * 48454023 AGCCAGTGTAAGA-CGTGTCTGGGACAT-GCATCGGC 1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC 48454058 TAAGTTTTGT Statistics Matches: 111, Mismatches: 18, Indels: 3 0.84 0.14 0.02 Matches are distributed among these distances: 93 8 0.07 94 85 0.77 95 18 0.16 ACGTcount: A:0.25, C:0.22, G:0.31, T:0.21 Consensus pattern (95 bp): AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGAGACGAGGGCCAGTGTAAGACATG TCTGGGACATGCATCAGCCACGATCATGAT Found at i:48463289 original size:58 final size:57 Alignment explanation

Indices: 48463157--48463291 Score: 155 Period size: 58 Copynumber: 2.3 Consensus size: 57 48463147 TTTAATTCAT * * ** 48463157 ATAATAATTACATTAAGAATTTTATTAAATTATATATCATTTTATTAAATTATAATTA 1 ATAATAATTATATTAA-AATATGGTTAAATTATATATCATTTTATTAAATTATAATTA * * * ** 48463215 ATAATAATTATGTTAAAATATGGTTAAATTATTTATTATATTTATTAAATTATTTTTA 1 ATAATAATTATATTAAAATATGGTTAAATTATATATCAT-TTTATTAAATTATAATTA 48463273 ATAATAATCT-TATTAAAAT 1 ATAATAAT-TATATTAAAAT 48463292 TTAATAAGAA Statistics Matches: 65, Mismatches: 10, Indels: 4 0.82 0.13 0.05 Matches are distributed among these distances: 57 18 0.28 58 46 0.71 59 1 0.02 ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50 Consensus pattern (57 bp): ATAATAATTATATTAAAATATGGTTAAATTATATATCATTTTATTAAATTATAATTA Found at i:48465090 original size:89 final size:90 Alignment explanation

Indices: 48464921--48465167 Score: 288 Period size: 88 Copynumber: 2.8 Consensus size: 90 48464911 TGTAAAAAAT * * * 48464921 CTTCAAACTTTTTTAAAATAAAGTAATTAAG-CCTCTGTTTTTTTTTTTTCACTCATTTGGGTAC 1 CTTCAAACTTTTTTAAAA-AAAGCAATTAAGCCCT-TGTTTTTTTTTTATCACTCAATTGGGTAC * * 48464985 TTGAATTTTCATAATGCATCAAAAAGAC 64 TTGAACTTTCAAAATGCATC-AAAAGAC * * 48465013 CTTCAAATTTTTTTAAAAAAAGCAATTAAGCCCTTG-TTTTTTTTTAT-ATTCAATTGGGTACTT 1 CTTCAAACTTTTTTAAAAAAAGCAATTAAGCCCTTGTTTTTTTTTTATCACTCAATTGGGTACTT * 48465076 GAACTTTCAAAATGCATCAAAAGGC 66 GAACTTTCAAAATGCATCAAAAGAC * * * ** ** * 48465101 CCTCAAACTTTTTCATAAAAAGCAATTAAGCCCTTG--CCTTTTTTGGCACTCAATTAGGTACTT 1 CTTCAAACTTTTTTAAAAAAAGCAATTAAGCCCTTGTTTTTTTTTTATCACTCAATTGGGTACTT 48465164 GAAC 66 GAAC 48465168 CGCCATTAAT Statistics Matches: 135, Mismatches: 18, Indels: 8 0.84 0.11 0.05 Matches are distributed among these distances: 87 6 0.04 88 56 0.41 89 30 0.22 90 10 0.07 91 13 0.10 92 20 0.15 ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40 Consensus pattern (90 bp): CTTCAAACTTTTTTAAAAAAAGCAATTAAGCCCTTGTTTTTTTTTTATCACTCAATTGGGTACTT GAACTTTCAAAATGCATCAAAAGAC Found at i:48465231 original size:9 final size:9 Alignment explanation

Indices: 48465217--48465375 Score: 78 Period size: 9 Copynumber: 17.2 Consensus size: 9 48465207 CATTTGGCAA * 48465217 AAAAATGAT 1 AAAAATTAT 48465226 AAAAA-TA- 1 AAAAATTAT ** 48465233 AAAAACAAT 1 AAAAATTAT * 48465242 AAAAGTTAT 1 AAAAATTAT * * 48465251 AAATATGATT 1 AAAAATTA-T ** 48465261 AAATTTTAAT 1 AAAAATTA-T 48465271 AAAAA-TAT 1 AAAAATTAT 48465279 AAAAAATTAT 1 -AAAAATTAT * 48465289 AAAAATCAT 1 AAAAATTAT 48465298 AAAAATTAT 1 AAAAATTAT * 48465307 AAAAAATTGT 1 -AAAAATTAT 48465317 -AAAATCATAT 1 AAAAAT--TAT * 48465327 AAAAATCAT 1 AAAAATTAT 48465336 AAAATATTAT 1 AAAA-ATTAT 48465346 -AAAATATAT 1 AAAAAT-TAT * 48465355 AGAAA-TAT 1 AAAAATTAT 48465363 AGAACAATTAT 1 A-AA-AATTAT 48465374 AA 1 AA 48465376 CATTTTATAA Statistics Matches: 114, Mismatches: 21, Indels: 29 0.70 0.13 0.18 Matches are distributed among these distances: 7 5 0.04 8 14 0.12 9 52 0.46 10 34 0.30 11 9 0.08 ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29 Consensus pattern (9 bp): AAAAATTAT Found at i:48465299 original size:19 final size:19 Alignment explanation

Indices: 48465269--48465349 Score: 87 Period size: 19 Copynumber: 4.3 Consensus size: 19 48465259 TTAAATTTTA 48465269 ATAAAAAT-ATAAAAAATT 1 ATAAAAATCATAAAAAATT 48465287 ATAAAAATCAT-AAAAATT 1 ATAAAAATCATAAAAAATT ** * 48465305 ATAAAAAATTGTAAAATCA-T 1 AT-AAAAATCATAAAA-AATT * 48465325 ATAAAAATCATAAAATATT 1 ATAAAAATCATAAAAAATT 48465344 ATAAAA 1 ATAAAA 48465350 TATATAGAAA Statistics Matches: 52, Mismatches: 6, Indels: 9 0.78 0.09 0.13 Matches are distributed among these distances: 18 18 0.35 19 27 0.52 20 6 0.12 21 1 0.02 ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28 Consensus pattern (19 bp): ATAAAAATCATAAAAAATT Found at i:48465347 original size:10 final size:10 Alignment explanation

Indices: 48465247--48465362 Score: 77 Period size: 10 Copynumber: 12.1 Consensus size: 10 48465237 ACAATAAAAG 48465247 TTAT-AAATA 1 TTATAAAATA * * * 48465256 TGATTAAATT 1 TTATAAAATA 48465266 TTAATAAAA-A 1 TT-ATAAAATA * 48465276 -TATAAAAAA 1 TTATAAAATA 48465285 TTATAAAA-A 1 TTATAAAATA * 48465294 TCATAAAA-A 1 TTATAAAATA * 48465303 TTATAAAAAA 1 TTATAAAATA * 48465313 TTGTAAAATCA 1 TTATAAAAT-A 48465324 -TATAAAA-A 1 TTATAAAATA * 48465332 TCATAAAATA 1 TTATAAAATA 48465342 TTATAAAATA 1 TTATAAAATA 48465352 -TATAGAAATA 1 TTATA-AAATA 48465362 T 1 T 48465363 AGAACAATTA Statistics Matches: 85, Mismatches: 12, Indels: 18 0.74 0.10 0.16 Matches are distributed among these distances: 8 7 0.08 9 31 0.36 10 41 0.48 11 6 0.07 ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34 Consensus pattern (10 bp): TTATAAAATA Found at i:48465385 original size:57 final size:57 Alignment explanation

Indices: 48465230--48465407 Score: 159 Period size: 57 Copynumber: 3.1 Consensus size: 57 48465220 AATGATAAAA * * * * * 48465230 ATAAAAAACAATAAAAGTTAT-AAATATGATTAAATTTTAATAAAAAT-ATAAAAAATT 1 ATAAAAATC-ATAAAAATTATAAAAAATTATAAAATTTT-ATAAAAATCATAAAAAATT * ** * 48465287 ATAAAAATCATAAAAATTATAAAAAATTGTAAAATCATATAAAAATCATAAAATATT 1 ATAAAAATCATAAAAATTATAAAAAATTATAAAATTTTATAAAAATCATAAAAAATT * * * * 48465344 ATAAAATAT-ATAGAAA-TATAGAACAATTATAACATTTTAT-AAAGTCATAAGAAAATT 1 ATAAAA-ATCATAAAAATTATA-AAAAATTATAAAATTTTATAAAAATCATAA-AAAATT 48465401 ATAAAAA 1 ATAAAAA 48465408 ATTGTAAAGA Statistics Matches: 99, Mismatches: 17, Indels: 11 0.78 0.13 0.09 Matches are distributed among these distances: 56 32 0.32 57 65 0.66 58 2 0.02 ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30 Consensus pattern (57 bp): ATAAAAATCATAAAAATTATAAAAAATTATAAAATTTTATAAAAATCATAAAAAATT Found at i:48466135 original size:56 final size:56 Alignment explanation

Indices: 48466033--48466141 Score: 146 Period size: 56 Copynumber: 1.9 Consensus size: 56 48466023 AAACTAATTC * * * 48466033 CTATATATCAAGAGTATATCAAAACAGAAAACAAGAGCAAAGAAATTTGAAATCTT 1 CTATATATCAAGAGCACATCAAAACAGAAAACAAAAGCAAAGAAATTTGAAATCTT * ** * * 48466089 CTATATATCAGGAGCACATCAAAACAGAAGGCAAAAGTAAATAAATTTGAAAT 1 CTATATATCAAGAGCACATCAAAACAGAAAACAAAAGCAAAGAAATTTGAAAT 48466142 ACAAATAGAT Statistics Matches: 45, Mismatches: 8, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 56 45 1.00 ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22 Consensus pattern (56 bp): CTATATATCAAGAGCACATCAAAACAGAAAACAAAAGCAAAGAAATTTGAAATCTT Found at i:48470553 original size:17 final size:17 Alignment explanation

Indices: 48470531--48470564 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 48470521 CTAAGGCTTG * 48470531 TAAAGAAGCTATTTGGT 1 TAAAGAAACTATTTGGT * 48470548 TAAAGAAACTCTTTGGT 1 TAAAGAAACTATTTGGT 48470565 GAAGTAATAA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35 Consensus pattern (17 bp): TAAAGAAACTATTTGGT Found at i:48474004 original size:12 final size:12 Alignment explanation

Indices: 48473960--48474004 Score: 63 Period size: 12 Copynumber: 3.7 Consensus size: 12 48473950 AAAAAAAAGG * * 48473960 AAAAAAATTTGA 1 AAAAAAAATTCA 48473972 AAAAAAAATTCGA 1 AAAAAAAATTC-A 48473985 AAAAAAAATTCA 1 AAAAAAAATTCA 48473997 AAAAAAAA 1 AAAAAAAA 48474005 AGTTTGTATT Statistics Matches: 30, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 12 18 0.60 13 12 0.40 ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16 Consensus pattern (12 bp): AAAAAAAATTCA Found at i:48474005 original size:13 final size:13 Alignment explanation

Indices: 48473960--48474004 Score: 74 Period size: 13 Copynumber: 3.5 Consensus size: 13 48473950 AAAAAAAAGG * 48473960 AAAAAAATTTGAA 1 AAAAAAATTCGAA 48473973 AAAAAAATTCGAA 1 AAAAAAATTCGAA 48473986 AAAAAAATTC-AA 1 AAAAAAATTCGAA 48473998 AAAAAAA 1 AAAAAAA 48474005 AGTTTGTATT Statistics Matches: 31, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 12 9 0.29 13 22 0.71 ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16 Consensus pattern (13 bp): AAAAAAATTCGAA Found at i:48474107 original size:29 final size:30 Alignment explanation

Indices: 48474049--48474117 Score: 88 Period size: 30 Copynumber: 2.3 Consensus size: 30 48474039 TAGTATTGAA * ** 48474049 GAAAAAAAAGAAGAAAAAAAATTCGGAATT 1 GAAAAAAAAAAAGAAAAAAAATTCAAAATT 48474079 -AAAAAAAGAAAAGAAAAAAAA-TCAAAATT 1 GAAAAAAA-AAAAGAAAAAAAATTCAAAATT 48474108 GAAAAAAAAA 1 GAAAAAAAAA 48474118 GAGTGATTGA Statistics Matches: 34, Mismatches: 3, Indels: 5 0.81 0.07 0.12 Matches are distributed among these distances: 29 15 0.44 30 19 0.56 ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10 Consensus pattern (30 bp): GAAAAAAAAAAAGAAAAAAAATTCAAAATT Found at i:48475023 original size:17 final size:15 Alignment explanation

Indices: 48475003--48475041 Score: 51 Period size: 15 Copynumber: 2.4 Consensus size: 15 48474993 GCGAGCGAGA 48475003 AAATGAACATGAAAAAG 1 AAATGAA-A-GAAAAAG 48475020 AAATGAAAGAAAAAG 1 AAATGAAAGAAAAAG 48475035 AAGATGA 1 AA-ATGA 48475042 GTGGGACATA Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 15 9 0.43 16 5 0.24 17 7 0.33 ACGTcount: A:0.67, C:0.03, G:0.21, T:0.10 Consensus pattern (15 bp): AAATGAAAGAAAAAG Found at i:48478407 original size:6 final size:6 Alignment explanation

Indices: 48478381--48478458 Score: 74 Period size: 6 Copynumber: 13.5 Consensus size: 6 48478371 AGTGATTTCA * * * 48478381 TTTAGT TTTATGT TTTA-- TTTATT TTTATT TTTATT TGTACT TTTATT 1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT * * 48478428 TTTATT GTTATT TGT-TT TTTA-T TTTATT TTT 1 TTTATT TTTATT TTTATT TTTATT TTTATT TTT 48478459 TAAATTTATA Statistics Matches: 58, Mismatches: 9, Indels: 10 0.75 0.12 0.13 Matches are distributed among these distances: 4 4 0.07 5 9 0.16 6 40 0.69 7 5 0.09 ACGTcount: A:0.15, C:0.01, G:0.06, T:0.77 Consensus pattern (6 bp): TTTATT Found at i:48478426 original size:18 final size:17 Alignment explanation

Indices: 48478381--48478457 Score: 72 Period size: 17 Copynumber: 4.5 Consensus size: 17 48478371 AGTGATTTCA * 48478381 TTTAGTTTTATGTTTTA- 1 TTTACTTTTAT-TTTTAT * 48478398 TTTATTTTTATTTTTAT 1 TTTACTTTTATTTTTAT 48478415 TTGTACTTTTATTTTTAT 1 TT-TACTTTTATTTTTAT 48478433 TGTTA-TTTGT-TTTTTAT 1 T-TTACTTT-TATTTTTAT 48478450 TTTA-TTTT 1 TTTACTTTT 48478458 TTAAATTTAT Statistics Matches: 54, Mismatches: 2, Indels: 10 0.82 0.03 0.15 Matches are distributed among these distances: 15 1 0.02 16 11 0.20 17 23 0.43 18 18 0.33 19 1 0.02 ACGTcount: A:0.16, C:0.01, G:0.06, T:0.77 Consensus pattern (17 bp): TTTACTTTTATTTTTAT Found at i:48478430 original size:24 final size:23 Alignment explanation

Indices: 48478398--48478458 Score: 88 Period size: 24 Copynumber: 2.7 Consensus size: 23 48478388 TTATGTTTTA 48478398 TTTATTTTTATTTTTATTTGTACT 1 TTTATTTTTATTTTTATTTGT-CT * * 48478422 TTTATTTTTATTGTTATTTGTTT 1 TTTATTTTTATTTTTATTTGTCT 48478445 TTTA-TTTTATTTTT 1 TTTATTTTTATTTTT 48478459 TAAATTTATA Statistics Matches: 34, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 22 9 0.26 23 5 0.15 24 20 0.59 ACGTcount: A:0.15, C:0.02, G:0.05, T:0.79 Consensus pattern (23 bp): TTTATTTTTATTTTTATTTGTCT Found at i:48478459 original size:12 final size:12 Alignment explanation

Indices: 48478398--48478482 Score: 52 Period size: 12 Copynumber: 6.9 Consensus size: 12 48478388 TTATGTTTTA 48478398 TTTATTTT-TATT 1 TTTATTTTAT-TT * 48478410 TTTATTTGTA-CT 1 TTTATTT-TATTT 48478422 TTTATTTT-TATT 1 TTTATTTTAT-TT * * 48478434 GTTA-TTTGTTT 1 TTTATTTTATTT 48478445 TTTATTTTATTT 1 TTTATTTTATTT * 48478457 TTTAAATTTATATGT 1 TTT--ATTT-TATTT 48478472 TTTATTTTATT 1 TTTATTTTATT 48478483 ATGCACTTTC Statistics Matches: 57, Mismatches: 7, Indels: 18 0.70 0.09 0.22 Matches are distributed among these distances: 11 9 0.16 12 32 0.56 13 5 0.09 14 4 0.07 15 7 0.12 ACGTcount: A:0.19, C:0.01, G:0.05, T:0.75 Consensus pattern (12 bp): TTTATTTTATTT Found at i:48483454 original size:33 final size:33 Alignment explanation

Indices: 48483409--48483476 Score: 118 Period size: 33 Copynumber: 2.1 Consensus size: 33 48483399 AGGACACTCC 48483409 CAGATCTAATATTTTGTGGACCCACATCAAAAA 1 CAGATCTAATATTTTGTGGACCCACATCAAAAA * * 48483442 CAGATCTGATATTTTGTGGACCCACGTCAAAAA 1 CAGATCTAATATTTTGTGGACCCACATCAAAAA 48483475 CA 1 CA 48483477 TACTCTTGCC Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 33 33 1.00 ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26 Consensus pattern (33 bp): CAGATCTAATATTTTGTGGACCCACATCAAAAA Found at i:48485591 original size:20 final size:20 Alignment explanation

Indices: 48485566--48485605 Score: 62 Period size: 20 Copynumber: 2.0 Consensus size: 20 48485556 CGGTCGTGTG 48485566 GGGGTCAACAAGCCCATGTA 1 GGGGTCAACAAGCCCATGTA * * 48485586 GGGGTCAACACGCCCGTGTA 1 GGGGTCAACAAGCCCATGTA 48485606 AGAGGAGGCA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.25, C:0.28, G:0.33, T:0.15 Consensus pattern (20 bp): GGGGTCAACAAGCCCATGTA Found at i:48485688 original size:21 final size:21 Alignment explanation

Indices: 48485610--48485682 Score: 146 Period size: 21 Copynumber: 3.5 Consensus size: 21 48485600 CGTGTAAGAG 48485610 GAGGCACACGGTCGTGTGGCT 1 GAGGCACACGGTCGTGTGGCT 48485631 GAGGCACACGGTCGTGTGGCT 1 GAGGCACACGGTCGTGTGGCT 48485652 GAGGCACACGGTCGTGTGGCT 1 GAGGCACACGGTCGTGTGGCT 48485673 GAGGCACACG 1 GAGGCACACG 48485683 CCCGTGGGAG Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 52 1.00 ACGTcount: A:0.16, C:0.25, G:0.42, T:0.16 Consensus pattern (21 bp): GAGGCACACGGTCGTGTGGCT Found at i:48490278 original size:16 final size:17 Alignment explanation

Indices: 48490251--48490285 Score: 54 Period size: 16 Copynumber: 2.1 Consensus size: 17 48490241 TAGAATTAGG * 48490251 TTGAGAAAATTATTTAA 1 TTGAGAAAATTAATTAA 48490268 TTGAG-AAATTAATTAA 1 TTGAGAAAATTAATTAA 48490284 TT 1 TT 48490286 TTATTTAATT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 12 0.71 17 5 0.29 ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43 Consensus pattern (17 bp): TTGAGAAAATTAATTAA Found at i:48492042 original size:20 final size:20 Alignment explanation

Indices: 48492013--48492145 Score: 76 Period size: 20 Copynumber: 6.8 Consensus size: 20 48492003 AAGTGGTATC * 48492013 CATTACAAATTTTAATATTG 1 CATTAAAAATTTTAATATTG * * ** * 48492033 CATTAGAAATATTGGTA-TC 1 CATTAAAAATTTTAATATTG *** 48492052 CATTAAAAATTTTGGCATTG 1 CATTAAAAATTTTAATATTG * * 48492072 CATTAAAAATATTGATATTG 1 CATTAAAAATTTTAATATTG * * * * 48492092 CATTAGAGATTTTGATATTA 1 CATTAAAAATTTTAATATTG * 48492112 CGA-TAAAAATTTTAGTATT- 1 C-ATTAAAAATTTTAATATTG * 48492131 AATT-AAAATTTTAAT 1 CATTAAAAATTTTAAT 48492146 TTCGTATTAG Statistics Matches: 88, Mismatches: 22, Indels: 8 0.75 0.19 0.07 Matches are distributed among these distances: 18 11 0.12 19 16 0.18 20 60 0.68 21 1 0.01 ACGTcount: A:0.41, C:0.07, G:0.11, T:0.42 Consensus pattern (20 bp): CATTAAAAATTTTAATATTG Found at i:48492061 original size:19 final size:19 Alignment explanation

Indices: 48491977--48492085 Score: 67 Period size: 20 Copynumber: 5.6 Consensus size: 19 48491967 CAAGATGCTC * ** 48491977 TTAAAAATTTTGGTATCTG 1 TTAAAAATATTGGTATCCA * 48491996 TTAGAAAA-AGTGGTATCCA 1 TTA-AAAATATTGGTATCCA * * ** * 48492015 TTACAAATTTTAATATTGCA 1 TTAAAAATATTGGTA-TCCA * 48492035 TTAGAAATATTGGTATCCA 1 TTAAAAATATTGGTATCCA * * * 48492054 TTAAAAATTTTGGCATTGCA 1 TTAAAAATATTGGTA-TCCA 48492074 TTAAAAATATTG 1 TTAAAAATATTG 48492086 ATATTGCATT Statistics Matches: 66, Mismatches: 20, Indels: 7 0.71 0.22 0.08 Matches are distributed among these distances: 18 3 0.05 19 31 0.47 20 32 0.48 ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39 Consensus pattern (19 bp): TTAAAAATATTGGTATCCA Found at i:48492072 original size:39 final size:39 Alignment explanation

Indices: 48491977--48492085 Score: 132 Period size: 39 Copynumber: 2.8 Consensus size: 39 48491967 CAAGATGCTC * * 48491977 TTAAAAATTTTGGTATCTG--TTAGAAAAAGTGGTATCCA 1 TTAAAAATTTTGGTAT-TGCATTAGAAATATTGGTATCCA * ** 48492015 TTACAAATTTTAATATTGCATTAGAAATATTGGTATCCA 1 TTAAAAATTTTGGTATTGCATTAGAAATATTGGTATCCA * * 48492054 TTAAAAATTTTGGCATTGCATTAAAAATATTG 1 TTAAAAATTTTGGTATTGCATTAGAAATATTG 48492086 ATATTGCATT Statistics Matches: 59, Mismatches: 10, Indels: 3 0.82 0.14 0.04 Matches are distributed among these distances: 37 2 0.03 38 13 0.22 39 44 0.75 ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39 Consensus pattern (39 bp): TTAAAAATTTTGGTATTGCATTAGAAATATTGGTATCCA Found at i:48496640 original size:21 final size:21 Alignment explanation

Indices: 48496611--48496666 Score: 94 Period size: 21 Copynumber: 2.7 Consensus size: 21 48496601 CGAACACGAC * * 48496611 AACAAAAGCTCATAGGAGCTG 1 AACAGAAGCTCAAAGGAGCTG 48496632 AACAGAAGCTCAAAGGAGCTG 1 AACAGAAGCTCAAAGGAGCTG 48496653 AACAGAAGCTCAAA 1 AACAGAAGCTCAAA 48496667 AGAGTTTATC Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 21 33 1.00 ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11 Consensus pattern (21 bp): AACAGAAGCTCAAAGGAGCTG Found at i:48497237 original size:16 final size:18 Alignment explanation

Indices: 48497216--48497248 Score: 52 Period size: 16 Copynumber: 1.9 Consensus size: 18 48497206 ATTAATCATT 48497216 TTTATC-AAATA-AATAA 1 TTTATCTAAATATAATAA 48497232 TTTATCTAAATATAATA 1 TTTATCTAAATATAATA 48497249 GGCCCTCAAA Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 6 0.40 17 5 0.33 18 4 0.27 ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42 Consensus pattern (18 bp): TTTATCTAAATATAATAA Found at i:48498605 original size:9 final size:9 Alignment explanation

Indices: 48498591--48498658 Score: 111 Period size: 9 Copynumber: 7.6 Consensus size: 9 48498581 ATAAGTATAA 48498591 AATTAACCG 1 AATTAACCG 48498600 AATTAACCG 1 AATTAACCG * 48498609 AATTAATCG 1 AATTAACCG 48498618 AATTAACCG 1 AATTAACCG 48498627 AATT-ACCAG 1 AATTAACC-G 48498636 AATTAACCG 1 AATTAACCG 48498645 AATTAACCG 1 AATTAACCG 48498654 AATTA 1 AATTA 48498659 TTTGTATAAA Statistics Matches: 55, Mismatches: 2, Indels: 4 0.90 0.03 0.07 Matches are distributed among these distances: 8 3 0.05 9 49 0.89 10 3 0.05 ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25 Consensus pattern (9 bp): AATTAACCG Found at i:48498759 original size:13 final size:13 Alignment explanation

Indices: 48498743--48498767 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 48498733 AATTTTTATG 48498743 ATTGGGTTGGGTA 1 ATTGGGTTGGGTA 48498756 ATTGGGTTGGGT 1 ATTGGGTTGGGT 48498768 TGGGTACTTG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40 Consensus pattern (13 bp): ATTGGGTTGGGTA Found at i:48498894 original size:18 final size:18 Alignment explanation

Indices: 48498871--48498905 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 48498861 TTTTATTAAT * 48498871 TTTTTTTGGTTAACCGAA 1 TTTTTTCGGTTAACCGAA 48498889 TTTTTTCGGTTAACCGA 1 TTTTTTCGGTTAACCGA 48498906 TCGGTTTTGA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49 Consensus pattern (18 bp): TTTTTTCGGTTAACCGAA Found at i:48504982 original size:22 final size:23 Alignment explanation

Indices: 48504957--48505015 Score: 68 Period size: 22 Copynumber: 2.6 Consensus size: 23 48504947 TGATTAAGAT * 48504957 AATAAAAAAATAAAATA-TGAAA 1 AATAAAAAAATAAAATATTCAAA 48504979 AATAAAATAAA-AAAATATTCAAA 1 AATAAAA-AAATAAAATATTCAAA ** 48505002 AATGCAAAAATAAA 1 AATAAAAAAATAAA 48505016 TTTAAGAAAA Statistics Matches: 31, Mismatches: 3, Indels: 5 0.79 0.08 0.13 Matches are distributed among these distances: 22 16 0.52 23 15 0.48 ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19 Consensus pattern (23 bp): AATAAAAAAATAAAATATTCAAA Found at i:48504993 original size:14 final size:14 Alignment explanation

Indices: 48504960--48504993 Score: 50 Period size: 14 Copynumber: 2.4 Consensus size: 14 48504950 TTAAGATAAT 48504960 AAAAAAATAAAATA 1 AAAAAAATAAAATA ** 48504974 TGAAAAATAAAATA 1 AAAAAAATAAAATA 48504988 AAAAAA 1 AAAAAA 48504994 TATTCAAAAA Statistics Matches: 16, Mismatches: 4, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 14 16 1.00 ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15 Consensus pattern (14 bp): AAAAAAATAAAATA Found at i:48505854 original size:13 final size:13 Alignment explanation

Indices: 48505813--48505878 Score: 63 Period size: 13 Copynumber: 5.5 Consensus size: 13 48505803 TAGATTTTTC 48505813 CTAAATATTATCA 1 CTAAATATTATCA * * 48505826 -T-TATATAATC- 1 CTAAATATTATCA 48505836 CTAAATATTATCA 1 CTAAATATTATCA * 48505849 CTAAATA--AT-T 1 CTAAATATTATCA 48505859 CTAAATATTATCA 1 CTAAATATTATCA 48505872 CTAAATA 1 CTAAATA 48505879 ATTCAAAATT Statistics Matches: 41, Mismatches: 6, Indels: 12 0.69 0.10 0.20 Matches are distributed among these distances: 10 7 0.17 11 10 0.24 12 10 0.24 13 14 0.34 ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39 Consensus pattern (13 bp): CTAAATATTATCA Found at i:48505881 original size:23 final size:23 Alignment explanation

Indices: 48505813--48505887 Score: 114 Period size: 23 Copynumber: 3.3 Consensus size: 23 48505803 TAGATTTTTC * * * 48505813 CTAAATATTATCATTATATAATC 1 CTAAATATTATCACTAAATAATT 48505836 CTAAATATTATCACTAAATAATT 1 CTAAATATTATCACTAAATAATT 48505859 CTAAATATTATCACTAAATAATT 1 CTAAATATTATCACTAAATAATT * 48505882 CAAAAT 1 CTAAAT 48505888 TTTAAAATCA Statistics Matches: 48, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 23 48 1.00 ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39 Consensus pattern (23 bp): CTAAATATTATCACTAAATAATT Found at i:48506713 original size:14 final size:15 Alignment explanation

Indices: 48506675--48506745 Score: 60 Period size: 14 Copynumber: 5.0 Consensus size: 15 48506665 ATTCAATGGC * 48506675 CATATTGCAACGGTT 1 CATATTGCAACAGTT * * 48506690 -AGATTCCAAC-GTT 1 CATATTGCAACAGTT 48506703 CATATTGCAACAGTT 1 CATATTGCAACAGTT * * * 48506718 -AGATTCCAATAG-T 1 CATATTGCAACAGTT 48506731 CATATTGCAACAGTT 1 CATATTGCAACAGTT 48506746 AGATTTCAAC Statistics Matches: 42, Mismatches: 10, Indels: 8 0.70 0.17 0.13 Matches are distributed among these distances: 13 4 0.10 14 34 0.81 15 4 0.10 ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32 Consensus pattern (15 bp): CATATTGCAACAGTT Found at i:48506771 original size:28 final size:28 Alignment explanation

Indices: 48506675--48506792 Score: 130 Period size: 28 Copynumber: 4.2 Consensus size: 28 48506665 ATTCAATGGC * * 48506675 CATATTGCAACGGTTAGATTCCAACGTT 1 CATATTGCAACAGTTAGATTCCAACGAT * 48506703 CATATTGCAACAGTTAGATTCCAA-TAGT 1 CATATTGCAACAGTTAGATTCCAACGA-T * 48506731 CATATTGCAACAGTTAGATTTCAACGAT 1 CATATTGCAACAGTTAGATTCCAACGAT ** * * * * 48506759 CATATTGTGACAGTCAAATTCCAATGAC 1 CATATTGCAACAGTTAGATTCCAACGAT 48506787 CATATT 1 CATATT 48506793 TTTGCATTAG Statistics Matches: 76, Mismatches: 12, Indels: 4 0.83 0.13 0.04 Matches are distributed among these distances: 28 75 0.99 29 1 0.01 ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32 Consensus pattern (28 bp): CATATTGCAACAGTTAGATTCCAACGAT Found at i:48506791 original size:56 final size:56 Alignment explanation

Indices: 48506663--48506792 Score: 156 Period size: 56 Copynumber: 2.3 Consensus size: 56 48506653 AGTGATCCAA * * * * 48506663 AAATT-CAATGGCCATATTGCAACGGTTAGATTCCAACGTTCATATTGCAACAGTT 1 AAATTCCAATGACCATATTGCAACAGTTAGATTCCAACGATCATATTGCAACAGTC * * * ** 48506718 AGATTCCAAT-AGTCATATTGCAACAGTTAGATTTCAACGATCATATTGTGACAGTC 1 AAATTCCAATGA-CCATATTGCAACAGTTAGATTCCAACGATCATATTGCAACAGTC 48506774 AAATTCCAATGACCATATT 1 AAATTCCAATGACCATATT 48506793 TTTGCATTAG Statistics Matches: 61, Mismatches: 11, Indels: 5 0.79 0.14 0.06 Matches are distributed among these distances: 55 4 0.07 56 56 0.92 57 1 0.02 ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32 Consensus pattern (56 bp): AAATTCCAATGACCATATTGCAACAGTTAGATTCCAACGATCATATTGCAACAGTC Found at i:48507824 original size:31 final size:31 Alignment explanation

Indices: 48507786--48507876 Score: 94 Period size: 34 Copynumber: 2.8 Consensus size: 31 48507776 ATATTCTTAA 48507786 TTATTTTAATAAATAATTTAATATTAA-AATT 1 TTATTTTAAT-AATAATTTAATATTAATAATT * 48507817 TTATTTTAATAATAAATTTTAACATTAATAATT 1 TTATTTTAATAAT-AA-TTTAATATTAATAATT * * 48507850 TAAATTTTAAGTAATATTATTAATATT 1 T-TATTTTAA-TAATAAT-TTAATATT 48507877 TTATTTAAAA Statistics Matches: 50, Mismatches: 4, Indels: 9 0.79 0.06 0.14 Matches are distributed among these distances: 30 3 0.06 31 12 0.24 32 10 0.20 33 6 0.12 34 15 0.30 35 4 0.08 ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52 Consensus pattern (31 bp): TTATTTTAATAATAATTTAATATTAATAATT Found at i:48507826 original size:19 final size:18 Alignment explanation

Indices: 48507802--48507837 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 48507792 TAATAAATAA * 48507802 TTTAATATTAAAATTTTAT 1 TTTAATAAT-AAATTTTAT 48507821 TTTAATAATAAATTTTA 1 TTTAATAATAAATTTTA 48507838 ACATTAATAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 8 0.50 19 8 0.50 ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56 Consensus pattern (18 bp): TTTAATAATAAATTTTAT Found at i:48507981 original size:13 final size:13 Alignment explanation

Indices: 48507952--48507994 Score: 52 Period size: 13 Copynumber: 3.2 Consensus size: 13 48507942 ATGTTTTGTA 48507952 ATATTAAATATAGAT 1 ATATT-AATATA-AT * 48507967 ATTTTAATATAAT 1 ATATTAATATAAT 48507980 ATATTAATA-AAT 1 ATATTAATATAAT 48507992 ATA 1 ATA 48507995 ATATTTGTTT Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 12 6 0.23 13 10 0.38 14 6 0.23 15 4 0.15 ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44 Consensus pattern (13 bp): ATATTAATATAAT Found at i:48509516 original size:10 final size:10 Alignment explanation

Indices: 48509496--48509529 Score: 59 Period size: 10 Copynumber: 3.3 Consensus size: 10 48509486 TATCTGTGTT 48509496 TCTCAGTTGTA 1 TCTC-GTTGTA 48509507 TCTCGTTGTA 1 TCTCGTTGTA 48509517 TCTCGTTGTA 1 TCTCGTTGTA 48509527 TCT 1 TCT 48509530 ATTTATGTAT Statistics Matches: 23, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 10 19 0.83 11 4 0.17 ACGTcount: A:0.12, C:0.21, G:0.18, T:0.50 Consensus pattern (10 bp): TCTCGTTGTA Found at i:48516783 original size:16 final size:16 Alignment explanation

Indices: 48516764--48516797 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 48516754 ACCTTAGATT * 48516764 AGCTCCCCCTTCGAAG 1 AGCTCACCCTTCGAAG 48516780 AGCTCACCCTTCGAAG 1 AGCTCACCCTTCGAAG 48516796 AG 1 AG 48516798 TCGATCAATC Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.24, C:0.38, G:0.21, T:0.18 Consensus pattern (16 bp): AGCTCACCCTTCGAAG Found at i:48524872 original size:10 final size:10 Alignment explanation

Indices: 48524827--48524886 Score: 61 Period size: 10 Copynumber: 6.0 Consensus size: 10 48524817 TAATTTTAGG 48524827 ATTTAT-TTT 1 ATTTATCTTT 48524836 CATTTATCTTT 1 -ATTTATCTTT * 48524847 AATTATCTTT 1 ATTTATCTTT * 48524857 AATTATCTTT 1 ATTTATCTTT * 48524867 GTTTAT-TTGT 1 ATTTATCTT-T 48524877 ATTTATCTTT 1 ATTTATCTTT 48524887 TAGAATTTAA Statistics Matches: 43, Mismatches: 4, Indels: 6 0.81 0.08 0.11 Matches are distributed among these distances: 9 2 0.05 10 36 0.84 11 5 0.12 ACGTcount: A:0.22, C:0.08, G:0.03, T:0.67 Consensus pattern (10 bp): ATTTATCTTT Found at i:48525649 original size:40 final size:39 Alignment explanation

Indices: 48525571--48525646 Score: 109 Period size: 39 Copynumber: 1.9 Consensus size: 39 48525561 TTGAAATTCC * ** 48525571 AATCAAAACTTTTAATTCTGTTTTTATTTTATTTTTTCA 1 AATCAAAACTTTTAATTCTATTTTTATTAAATTTTTTCA 48525610 AATCAAAACTTTTAATTCTATTTTT-TTAAAATTTTTT 1 AATCAAAACTTTTAATTCTATTTTTATT-AAATTTTTT 48525647 TCAGGTATGC Statistics Matches: 33, Mismatches: 3, Indels: 2 0.87 0.08 0.05 Matches are distributed among these distances: 38 2 0.06 39 31 0.94 ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58 Consensus pattern (39 bp): AATCAAAACTTTTAATTCTATTTTTATTAAATTTTTTCA Found at i:48527187 original size:40 final size:40 Alignment explanation

Indices: 48527055--48527180 Score: 200 Period size: 40 Copynumber: 3.2 Consensus size: 40 48527045 AACCCAAGTA * * * 48527055 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG * * 48527094 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG 48527134 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG 1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG 48527174 CCTTCGG 1 CCTTCGG 48527181 ATCTTAGTCC Statistics Matches: 79, Mismatches: 7, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 39 13 0.16 40 66 0.84 ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG Found at i:48528611 original size:13 final size:13 Alignment explanation

Indices: 48528595--48528622 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 48528585 TTTATTATTT 48528595 TTAACACAAAATA 1 TTAACACAAAATA 48528608 TTAACACAAAATA 1 TTAACACAAAATA 48528621 TT 1 TT 48528623 TATAATATGT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29 Consensus pattern (13 bp): TTAACACAAAATA Found at i:48533839 original size:31 final size:31 Alignment explanation

Indices: 48533767--48533840 Score: 103 Period size: 31 Copynumber: 2.4 Consensus size: 31 48533757 TTAACAATAA 48533767 AATAATTAAAATTGACAACTTATTTCATAGG 1 AATAATTAAAATTGACAACTTATTTCATAGG * * * * 48533798 AGTTATTAAAATTGACAACTTATTTTATATG 1 AATAATTAAAATTGACAACTTATTTCATAGG * 48533829 AATAACTAAAAT 1 AATAATTAAAAT 48533841 AACAATTTTT Statistics Matches: 36, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 31 36 1.00 ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38 Consensus pattern (31 bp): AATAATTAAAATTGACAACTTATTTCATAGG Found at i:48535152 original size:31 final size:32 Alignment explanation

Indices: 48535112--48535186 Score: 100 Period size: 31 Copynumber: 2.4 Consensus size: 32 48535102 AAAATTTACA * ** 48535112 ATTT-AGTCATTAAATTATTTGAAAG-TTTTT 1 ATTTAAGTCATTAAACTATTCAAAAGTTTTTT * 48535142 ATTTAAGTCATTGAACTATTCAAAAGTTTTTT 1 ATTTAAGTCATTAAACTATTCAAAAGTTTTTT 48535174 ATTTAAGTCATTA 1 ATTTAAGTCATTA 48535187 GATTGTTAAG Statistics Matches: 38, Mismatches: 5, Indels: 2 0.84 0.11 0.04 Matches are distributed among these distances: 30 4 0.11 31 17 0.45 32 17 0.45 ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49 Consensus pattern (32 bp): ATTTAAGTCATTAAACTATTCAAAAGTTTTTT Found at i:48538508 original size:25 final size:25 Alignment explanation

Indices: 48538480--48538531 Score: 77 Period size: 25 Copynumber: 2.1 Consensus size: 25 48538470 TTTGGCTTGA * 48538480 CATTTACTAAGCAATATCAGATATT 1 CATTTACTAAGCAATATCAAATATT * * 48538505 CATTTATTAGGCAATATCAAATATT 1 CATTTACTAAGCAATATCAAATATT 48538530 CA 1 CA 48538532 AATTATTCTA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37 Consensus pattern (25 bp): CATTTACTAAGCAATATCAAATATT Found at i:48541786 original size:23 final size:23 Alignment explanation

Indices: 48541732--48541790 Score: 73 Period size: 23 Copynumber: 2.6 Consensus size: 23 48541722 AGGTAAGATA * 48541732 TCGTTGCGACGTCACAACTCCCC 1 TCGTCGCGACGTCACAACTCCCC * ** 48541755 TCGTTGCGACGTCACAACTCTTC 1 TCGTCGCGACGTCACAACTCCCC * 48541778 TTGTCGCGACGTC 1 TCGTCGCGACGTC 48541791 GCATGTCTGT Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 23 32 1.00 ACGTcount: A:0.15, C:0.37, G:0.20, T:0.27 Consensus pattern (23 bp): TCGTCGCGACGTCACAACTCCCC Found at i:48545176 original size:14 final size:14 Alignment explanation

Indices: 48545124--48545193 Score: 68 Period size: 15 Copynumber: 4.7 Consensus size: 14 48545114 ACGTAGTGAC 48545124 TAAAATATAATAATAT 1 TAAAATATAAT-A-AT ** 48545140 TTTAATATAAGTAAT 1 TAAAATATAA-TAAT * 48545155 TAAAATATAATATT 1 TAAAATATAATAAT * 48545169 TTAAATATAAATAAT 1 TAAAATAT-AATAAT 48545184 TAAAATATAA 1 TAAAATATAA 48545194 ACTATTATAA Statistics Matches: 44, Mismatches: 8, Indels: 6 0.76 0.14 0.10 Matches are distributed among these distances: 14 12 0.27 15 22 0.50 16 9 0.20 17 1 0.02 ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40 Consensus pattern (14 bp): TAAAATATAATAAT Found at i:48545184 original size:29 final size:29 Alignment explanation

Indices: 48545133--48545211 Score: 106 Period size: 29 Copynumber: 2.7 Consensus size: 29 48545123 CTAAAATATA * 48545133 ATAATATTTT-AATATAAGTAATTAAAAT 1 ATAATATTTTAAATATAAATAATTAAAAT 48545161 ATAATATTTTAAATATAAATAATTAAAAT 1 ATAATATTTTAAATATAAATAATTAAAAT * * 48545190 ATAAACTATTATAAATAAAAAT 1 AT-AA-TATTTTAAATATAAAT 48545212 GACTATTTTA Statistics Matches: 45, Mismatches: 3, Indels: 3 0.88 0.06 0.06 Matches are distributed among these distances: 28 10 0.22 29 19 0.42 30 2 0.04 31 14 0.31 ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39 Consensus pattern (29 bp): ATAATATTTTAAATATAAATAATTAAAAT Found at i:48545194 original size:15 final size:15 Alignment explanation

Indices: 48545143--48545194 Score: 70 Period size: 15 Copynumber: 3.5 Consensus size: 15 48545133 ATAATATTTT * 48545143 AATATAAGTAATTAA 1 AATATAAATAATTAA * * 48545158 AATAT-AATATTTTA 1 AATATAAATAATTAA 48545172 AATATAAATAATTAA 1 AATATAAATAATTAA 48545187 AATATAAA 1 AATATAAA 48545195 CTATTATAAA Statistics Matches: 31, Mismatches: 5, Indels: 2 0.82 0.13 0.05 Matches are distributed among these distances: 14 11 0.35 15 20 0.65 ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37 Consensus pattern (15 bp): AATATAAATAATTAA Found at i:48545200 original size:15 final size:14 Alignment explanation

Indices: 48545124--48545211 Score: 61 Period size: 15 Copynumber: 5.9 Consensus size: 14 48545114 ACGTAGTGAC 48545124 TAAAATATAATAATAT 1 TAAAATAT-A-AATAT ** * 48545140 TTTAATATAAGTAAT 1 TAAAATATAAAT-AT 48545155 TAAAATAT-AATATT 1 TAAAATATAAATA-T * 48545169 TTAAATATAAATAAT 1 TAAAATATAAAT-AT 48545184 TAAAATATAAACTAT 1 TAAAATATAAA-TAT * 48545199 TATAAATAAAAAT 1 TA-AAATATAAAT 48545212 GACTATTTTA Statistics Matches: 57, Mismatches: 9, Indels: 13 0.72 0.11 0.16 Matches are distributed among these distances: 13 1 0.02 14 12 0.21 15 28 0.49 16 16 0.28 ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39 Consensus pattern (14 bp): TAAAATATAAATAT Found at i:48547989 original size:15 final size:15 Alignment explanation

Indices: 48547961--48547997 Score: 56 Period size: 15 Copynumber: 2.5 Consensus size: 15 48547951 TACTAGTGCC * * 48547961 CCACCCCCTTCAAGA 1 CCACCACCTCCAAGA 48547976 CCACCACCTCCAAGA 1 CCACCACCTCCAAGA 48547991 CCACCAC 1 CCACCAC 48547998 GAGTTTCAAA Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 15 20 1.00 ACGTcount: A:0.30, C:0.57, G:0.05, T:0.08 Consensus pattern (15 bp): CCACCACCTCCAAGA Found at i:48555191 original size:158 final size:157 Alignment explanation

Indices: 48554471--48555534 Score: 1525 Period size: 158 Copynumber: 6.7 Consensus size: 157 48554461 GAGTTTTTAA * * * * * 48554471 GGTTTAGGGTTTTAATATTTTTTAAGAAAAAATTAATTTAATTAGAATTGAAGGTTAATTAATTA 1 GGTTTAGGATTTTAGTA-TTTTTAAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATTA * * 48554536 AATTAACTATGAAAAT-AAAAAAA--AATTAAATTAGGGTTTAGGGTTTTTTAAGGTTAGGATTT 65 AATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGTTT * * 48554598 TTGATAGTTTTAGGAT-TGAGGTTTTAGT 130 TTGATTGTTTTAGGATCAG-GGTTTTAGT * * * 48554626 GGTTTAGAATTTTTGTGTTTTTAAAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATTA 1 GGTTTAGGATTTTAGTATTTTT-AAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATTA * * 48554691 AATTAACTATGAAAAT-AAAAAAATAAATTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGATT 65 AATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGTTT 48554755 TTGATTGTTTTAGGATCAGGGTTTTAGT 130 TTGATTGTTTTAGGATCAGGGTTTTAGT * * * 48554783 GGTTTTGGATTTTAGCATTTTTAAGGGAAAAATTAATTTAATTAGAGTTGATGGTTAATTAATTA 1 GGTTTAGGATTTTAGTATTTTTAA-GGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATTA * * * 48554848 AATTAACTATGAAAATAAAAAAAAATTAACTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGAT 65 AATTAACTATGAAAAT-AAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGTT * ** 48554913 TTTGATTGTTTTAAGATCAAAGTTTTAGT 129 TTTGATTGTTTTAGGATCAGGGTTTTAGT * * 48554942 GGTTTTGGATTTTAGTGTTTTTTAAGGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATT 1 GGTTTAGGATTTTAGT-ATTTTTAA-GGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATT * * * * 48555007 AAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAAGTTTGTTTATGATTAAGGT 64 AAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAGGTTT-TTTAAGGTTAGGGT 48555072 TTTTGATTGTTTTAGGATCAGGGTTTTAGT 128 TTTTGATTGTTTTAGGATCAGGGTTTTAGT * * 48555102 GGTTTAGGGTTTTAGTATTTTTAAGGGAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATTAA 1 GGTTTAGGATTTTAGTATTTTTAAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATTAA * * * 48555167 ATTAACTATGAAAATAAAAAAAATCAATTAAATTAGAGTTT-AGGGTTTTTAAAGTTAGGGTTTT 66 ATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGTTTT * 48555231 TGATTGTTTTAGGATTAGGGTTTTAGT 131 TGATTGTTTTAGGATCAGGGTTTTAGT * * 48555258 GGTTTAGAATTTTTGTATTTTTTAAAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATT 1 GGTTTAGGATTTTAGTA-TTTTT-AAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATT * * * 48555323 AAATTAACTATGAAAAT-AAAAAAGTCAATTAAATTAGGGTTTAAGATTTTTTAAAGTTAGGGTT 64 AAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGTT * * 48555387 TTTGATTGTTTTAGGATTAAGGTTTTAGT 129 TTTGATTGTTTTAGGATCAGGGTTTTAGT * * 48555416 GGTTTAAGG-TTTTTGTGTTTTTTAAAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAAT 1 GGTTT-AGGATTTTAGT-ATTTTT-AAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAAT * * 48555480 TAAATTAACTATGAAATTAAAAAAAATTAATTAAATTAGGGTTT-AGGATTTTTTA 63 TAAATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAGG-TTTTTTA 48555535 GAGTTTATTA Statistics Matches: 829, Mismatches: 64, Indels: 28 0.90 0.07 0.03 Matches are distributed among these distances: 154 5 0.01 155 74 0.09 156 55 0.07 157 164 0.20 158 262 0.32 159 155 0.19 160 114 0.14 ACGTcount: A:0.37, C:0.01, G:0.19, T:0.43 Consensus pattern (157 bp): GGTTTAGGATTTTAGTATTTTTAAGGAAAAATTAATTTAATTAGAGTTGAGGGTTAATTAATTAA ATTAACTATGAAAATAAAAAAAATCAATTAAATTAGGGTTTAAGGTTTTTTAAGGTTAGGGTTTT TGATTGTTTTAGGATCAGGGTTTTAGT Found at i:48555393 original size:23 final size:23 Alignment explanation

Indices: 48555351--48555399 Score: 64 Period size: 23 Copynumber: 2.1 Consensus size: 23 48555341 AAAAAGTCAA 48555351 TTAAATTAGGGTTTAAGATT-TT 1 TTAAATTAGGGTTTAAGATTGTT ** 48555373 TTAAAGTTAGGGTTTTTGATTGTT 1 TTAAA-TTAGGGTTTAAGATTGTT 48555397 TTA 1 TTA 48555400 GGATTAAGGT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 22 5 0.22 23 13 0.57 24 5 0.22 ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53 Consensus pattern (23 bp): TTAAATTAGGGTTTAAGATTGTT Found at i:48555790 original size:125 final size:126 Alignment explanation

Indices: 48555560--48556117 Score: 888 Period size: 125 Copynumber: 4.5 Consensus size: 126 48555550 ATTAACTATT * * * 48555560 AATTACGGAAAAAAGCTCCCACGTGGATGCTCTTTTGCTATAGTAGTATCTGAAAAAATAAATTT 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT * * * * 48555625 GAGAATATGTTTCTGAACAAATAGTGTTAAAAACGCTTCAAGAAAGATGCACTGTTAGCAA 66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA * ** * 48555686 AATTACGGAAAAAAGGTCCCATATGGACGCTCTTTTGCTGCAGTAGTATCTGA-AAAATAAATTT 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT * * * 48555750 GAGAAGATGTTTCTGAACAAATAGTGTTAAAAAAGTTTCAAGAAGGATGCACTGTCAGCAA 66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA * 48555811 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAATTTT 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT * 48555876 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGTAA 66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA * * * * 48555937 AATTACGGAAAAAAGCTCCTACGTGAACGTTCTTTTGCTACAGTAGTATCTGATAAAATAATTTT 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT * * * 48556002 AAGAAGATGTTT-TGAATAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTTAGCAA 66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA 48556062 AATTACGGAAAAAAGCTCCCACGTGGACGCTC-TTTGCTACAGTAGTATCTGATAAA 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAA 48556118 GCCTTAAACT Statistics Matches: 401, Mismatches: 30, Indels: 4 0.92 0.07 0.01 Matches are distributed among these distances: 124 24 0.06 125 190 0.47 126 187 0.47 ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28 Consensus pattern (126 bp): AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGCAA Found at i:48556025 original size:251 final size:251 Alignment explanation

Indices: 48555560--48556117 Score: 886 Period size: 251 Copynumber: 2.2 Consensus size: 251 48555550 ATTAACTATT * * * 48555560 AATTACGGAAAAAAGCTCCCACGTGGATGCTCTTTTGCTATAGTAGTATCTGAAAAAATAAATTT 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT * * * 48555625 GAGAATATGTTTCTGAACAAATAGTGTTAAAAACGCTTCAAGAAAGATGCACTGTTAGCAAAATT 66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAAGATGCACTGTCAGCAAAATT * * * * * 48555690 ACGGAAAAAAGGTCCCATATGGACGCTCTTTTGCTGCAGTAGTATCTGAAAAATAAATTTGAGAA 131 ACGGAAAAAAGCTCCCACATGAACGCTCTTTTGCTACAGTAGTATCTGAAAAATAAATTTAAGAA * * 48555755 GATGTTTCTGAACAAATAGTGTTAAAAAAGTTTCAAGAAGGATGCACTGTCAGCAA 196 GATGTTTCTGAACAAATAGTGTCAAAAAAGCTTCAAGAAGGATGCACTGTCAGCAA * 48555811 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAATTTT 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT * * 48555876 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTCAGTAAAATT 66 GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAAGATGCACTGTCAGCAAAATT * * * * 48555941 ACGGAAAAAAGCTCCTACGTGAACGTTCTTTTGCTACAGTAGTATCTGATAAAATAATTTTAAGA 131 ACGGAAAAAAGCTCCCACATGAACGCTCTTTTGCTACAGTAGTATCTGA-AAAATAAATTTAAGA * * * 48556006 AGATGTTT-TGAATAAATAGTGTCAAAAACGCTTCAAGAAGGATGCACTGTTAGCAA 195 AGATGTTTCTGAACAAATAGTGTCAAAAAAGCTTCAAGAAGGATGCACTGTCAGCAA 48556062 AATTACGGAAAAAAGCTCCCACGTGGACGCTC-TTTGCTACAGTAGTATCTGATAAA 1 AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAA 48556118 GCCTTAAACT Statistics Matches: 283, Mismatches: 23, Indels: 3 0.92 0.07 0.01 Matches are distributed among these distances: 250 24 0.08 251 238 0.84 252 21 0.07 ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28 Consensus pattern (251 bp): AATTACGGAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGATAAAATAAATTT GAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTCAAGAAAGATGCACTGTCAGCAAAATT ACGGAAAAAAGCTCCCACATGAACGCTCTTTTGCTACAGTAGTATCTGAAAAATAAATTTAAGAA GATGTTTCTGAACAAATAGTGTCAAAAAAGCTTCAAGAAGGATGCACTGTCAGCAA Found at i:48559153 original size:10 final size:9 Alignment explanation

Indices: 48559134--48559165 Score: 55 Period size: 9 Copynumber: 3.4 Consensus size: 9 48559124 ATTTATATTT 48559134 TATTAAAAA 1 TATTAAAAA 48559143 TATTAAAAAA 1 TATT-AAAAA 48559153 TATTAAAAA 1 TATTAAAAA 48559162 TATT 1 TATT 48559166 TCCATAGTCA Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 9 13 0.59 10 9 0.41 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (9 bp): TATTAAAAA Found at i:48560379 original size:14 final size:14 Alignment explanation

Indices: 48560360--48560392 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 48560350 TTATATAGGT 48560360 AATACTAAATAATA 1 AATACTAAATAATA * 48560374 AATACTAAATATTA 1 AATACTAAATAATA 48560388 AATAC 1 AATAC 48560393 AAAACAACTA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30 Consensus pattern (14 bp): AATACTAAATAATA Found at i:48570910 original size:23 final size:24 Alignment explanation

Indices: 48570866--48570930 Score: 71 Period size: 23 Copynumber: 2.7 Consensus size: 24 48570856 CTGACGGGCT 48570866 TAAATAATTTTAAATTTTCTAAGTTA 1 TAAATAATTTT-AATTTTCTAA-TTA 48570892 TAAAT-ATTTTAA-TTTCTAATTA 1 TAAATAATTTTAATTTTCTAATTA * * * 48570914 TAATTCATTTTACTTTT 1 TAAATAATTTTAATTTT 48570931 ATGCAATGAC Statistics Matches: 35, Mismatches: 2, Indels: 6 0.81 0.05 0.14 Matches are distributed among these distances: 22 7 0.20 23 13 0.37 24 5 0.14 25 5 0.14 26 5 0.14 ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55 Consensus pattern (24 bp): TAAATAATTTTAATTTTCTAATTA Found at i:48573211 original size:30 final size:30 Alignment explanation

Indices: 48573154--48573211 Score: 80 Period size: 30 Copynumber: 1.9 Consensus size: 30 48573144 TTTTTGAGCA * ** 48573154 TAGGGGTAAAATGGTCATTTTGTCAAAGTT 1 TAGGGGCAAAATGGTCATTTTACCAAAGTT * 48573184 TAGGGGCAAAATGGTTATTTTACCAAAG 1 TAGGGGCAAAATGGTCATTTTACCAAAG 48573212 ACGTGAAATT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 30 24 1.00 ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33 Consensus pattern (30 bp): TAGGGGCAAAATGGTCATTTTACCAAAGTT Found at i:48573698 original size:46 final size:45 Alignment explanation

Indices: 48573554--48573768 Score: 168 Period size: 46 Copynumber: 4.6 Consensus size: 45 48573544 TTTGTGAGCT * ** * 48573554 AGTGTAAGACATGTCTGGGATATGCATCGGCC-ACATTATGAGAGCC 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGA-GATGA-AGCC * * * * 48573600 AATGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACT-AGTGCT 1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTTGAGA-TGA-AGCC * 48573648 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATGGAACCC 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGAT-GAAGCC * * * * * * 48573694 AGTGTAAGACATGTCTAGGACATGCACCGG-CTAAGAGTTG-TGTC 1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-TGAGATGAAGCC * 48573738 AGTGTAAGACCATGTCTGGGATATGGCATCG 1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG 48573769 ACACGGATAG Statistics Matches: 137, Mismatches: 23, Indels: 18 0.77 0.13 0.10 Matches are distributed among these distances: 44 10 0.07 45 16 0.12 46 60 0.44 47 28 0.20 48 21 0.15 49 2 0.01 ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24 Consensus pattern (45 bp): AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATGAAGCC Found at i:48574114 original size:21 final size:21 Alignment explanation

Indices: 48574089--48574133 Score: 90 Period size: 21 Copynumber: 2.1 Consensus size: 21 48574079 TTTATATGCA 48574089 ACTTACTAAGCTTTTATGCTT 1 ACTTACTAAGCTTTTATGCTT 48574110 ACTTACTAAGCTTTTATGCTT 1 ACTTACTAAGCTTTTATGCTT 48574131 ACT 1 ACT 48574134 CCCCTTTTCT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47 Consensus pattern (21 bp): ACTTACTAAGCTTTTATGCTT Found at i:48580873 original size:30 final size:30 Alignment explanation

Indices: 48580816--48580873 Score: 80 Period size: 30 Copynumber: 1.9 Consensus size: 30 48580806 TTTTCAAGCA * * ** 48580816 TAGGGGTAAAATGGTCATTTTGTCAAAGTC 1 TAGGGGCAAAATAGTCATTTTACCAAAGTC 48580846 TAGGGGCAAAATAGTCATTTTACCAAAG 1 TAGGGGCAAAATAGTCATTTTACCAAAG 48580874 ATGTGAAATT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 30 24 1.00 ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29 Consensus pattern (30 bp): TAGGGGCAAAATAGTCATTTTACCAAAGTC Found at i:48599513 original size:3 final size:3 Alignment explanation

Indices: 48599505--48599531 Score: 54 Period size: 3 Copynumber: 9.0 Consensus size: 3 48599495 TTTATTAACT 48599505 TAA TAA TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA 48599532 ATATATTATT 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): TAA Found at i:48599545 original size:19 final size:20 Alignment explanation

Indices: 48599523--48599561 Score: 62 Period size: 19 Copynumber: 2.0 Consensus size: 20 48599513 ATAATAATAA * 48599523 TAATAATAAATATAT-TATT 1 TAATAACAAATATATATATT 48599542 TAATAACAAATATATATATT 1 TAATAACAAATATATATATT 48599562 ACAATTGGAC Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 19 14 0.78 20 4 0.22 ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44 Consensus pattern (20 bp): TAATAACAAATATATATATT Found at i:48599966 original size:25 final size:27 Alignment explanation

Indices: 48599932--48599993 Score: 79 Period size: 30 Copynumber: 2.1 Consensus size: 27 48599922 TGGCTTTAAT * 48599932 TTAATTTAATTCATAATATGATATTTATAA 1 TTAA-TTAATTAATAATAT-AT-TTTATAA 48599962 TTAATTAATTTAATAATATATTTTATAA 1 TTAATTAA-TTAATAATATATTTTATAA 48599990 TTAA 1 TTAA 48599994 ATTATATATA Statistics Matches: 30, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 28 11 0.37 29 6 0.20 30 13 0.43 ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52 Consensus pattern (27 bp): TTAATTAATTAATAATATATTTTATAA Found at i:48600000 original size:20 final size:21 Alignment explanation

Indices: 48599967--48600007 Score: 57 Period size: 20 Copynumber: 2.0 Consensus size: 21 48599957 TATAATTAAT * 48599967 TAATTTAATAATATAT-TTTA 1 TAATTAAATAATATATATTTA * 48599987 TAATTAAATTATATATATTTA 1 TAATTAAATAATATATATTTA 48600008 CATGATTAAA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 20 14 0.78 21 4 0.22 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (21 bp): TAATTAAATAATATATATTTA Found at i:48602468 original size:21 final size:22 Alignment explanation

Indices: 48602438--48602484 Score: 60 Period size: 21 Copynumber: 2.2 Consensus size: 22 48602428 CTTAATTAAC * 48602438 TAATTAAAACATTATTAAAT-T 1 TAATTAAAACATAATTAAATAT * * 48602459 TAATTTAAACATAATTTAATAT 1 TAATTAAAACATAATTAAATAT 48602481 TAAT 1 TAAT 48602485 GGAATTCATC Statistics Matches: 22, Mismatches: 3, Indels: 1 0.85 0.12 0.04 Matches are distributed among these distances: 21 17 0.77 22 5 0.23 ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45 Consensus pattern (22 bp): TAATTAAAACATAATTAAATAT Found at i:48602859 original size:95 final size:95 Alignment explanation

Indices: 48602696--48602885 Score: 265 Period size: 95 Copynumber: 2.0 Consensus size: 95 48602686 TATCAACTCC * * * * ** ** * 48602696 GTAAATATTTCTATTTTATATTTATGGACTTGGTTTATGTTTTATGGAAATGAGGTTCTGAAATC 1 GTAAATATTCCTATTTTATATTTACGAACTTAGTTTATGTTTTACAGAAATGAAATTCTAAAATC * 48602761 ATATTTTTCAACACCATTGAAAATCGAGTT 66 ATATTTTTCAACACCATTAAAAATCGAGTT 48602791 GTAAATATTCCTATTTTATATTTACGAACTTAGTTTACTG-TTTACAGAAATGAAATTCTAAAAT 1 GTAAATATTCCTATTTTATATTTACGAACTTAGTTTA-TGTTTTACAGAAATGAAATTCTAAAAT * 48602855 CATATTTTTTAACACCATTAAAAATCGAGTT 65 CATATTTTTCAACACCATTAAAAATCGAGTT 48602886 ATTACAGATC Statistics Matches: 83, Mismatches: 11, Indels: 2 0.86 0.11 0.02 Matches are distributed among these distances: 95 81 0.98 96 2 0.02 ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43 Consensus pattern (95 bp): GTAAATATTCCTATTTTATATTTACGAACTTAGTTTATGTTTTACAGAAATGAAATTCTAAAATC ATATTTTTCAACACCATTAAAAATCGAGTT Found at i:48603145 original size:19 final size:19 Alignment explanation

Indices: 48603106--48603147 Score: 57 Period size: 19 Copynumber: 2.2 Consensus size: 19 48603096 AGTTTAGTTG * * 48603106 TATATATTAATTAATATAT 1 TATATATTAATTAAAAAAT * 48603125 TATATATTTATTAAAAAAT 1 TATATATTAATTAAAAAAT 48603144 TATA 1 TATA 48603148 ACCTTTTAAA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (19 bp): TATATATTAATTAAAAAAT Found at i:48603431 original size:24 final size:25 Alignment explanation

Indices: 48603403--48603452 Score: 84 Period size: 25 Copynumber: 2.0 Consensus size: 25 48603393 ATTAAATTGT * 48603403 AGTTTG-AAAAAAAATCATTTAAAA 1 AGTTTGAAAAAAAAACCATTTAAAA 48603427 AGTTTGAAAAAAAAACCATTTAAAA 1 AGTTTGAAAAAAAAACCATTTAAAA 48603452 A 1 A 48603453 AAACAAAAAA Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 24 6 0.25 25 18 0.75 ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26 Consensus pattern (25 bp): AGTTTGAAAAAAAAACCATTTAAAA Found at i:48613795 original size:19 final size:20 Alignment explanation

Indices: 48613749--48613796 Score: 55 Period size: 19 Copynumber: 2.4 Consensus size: 20 48613739 TTGCTTTATC * 48613749 TATTTTGTTTTCTATTTTCTG 1 TATTTTCTTTTC-ATTTTCTG 48613770 T-TGTTTCTTTTC-TTTTCTG 1 TAT-TTTCTTTTCATTTTCTG 48613789 TATTTTCT 1 TATTTTCT 48613797 ATATTTCAGG Statistics Matches: 24, Mismatches: 1, Indels: 6 0.77 0.03 0.19 Matches are distributed among these distances: 19 13 0.54 20 2 0.08 21 9 0.38 ACGTcount: A:0.06, C:0.12, G:0.08, T:0.73 Consensus pattern (20 bp): TATTTTCTTTTCATTTTCTG Found at i:48621485 original size:3 final size:3 Alignment explanation

Indices: 48621468--48621515 Score: 60 Period size: 3 Copynumber: 16.0 Consensus size: 3 48621458 CAAAACACAA * * * * 48621468 AAT AAT AAC ATT AAT AAT AAT AAT AAT GAT AAG AAT AAT AAT AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 48621516 GGGGTTACAA Statistics Matches: 37, Mismatches: 8, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 3 37 1.00 ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31 Consensus pattern (3 bp): AAT Found at i:48621485 original size:12 final size:12 Alignment explanation

Indices: 48621445--48621511 Score: 55 Period size: 12 Copynumber: 5.5 Consensus size: 12 48621435 GTTCTAATTC * 48621445 TAATATCAATAA 1 TAATAACAATAA * 48621457 TCAA-AACACAAAA 1 T-AATAACA-ATAA * 48621470 TAATAACATTAA 1 TAATAACAATAA * 48621482 TAATAATAATAA 1 TAATAACAATAA * * 48621494 TGATAAGAATAA 1 TAATAACAATAA 48621506 TAATAA 1 TAATAA 48621512 TAATGGGGTT Statistics Matches: 43, Mismatches: 9, Indels: 6 0.74 0.16 0.10 Matches are distributed among these distances: 12 33 0.77 13 10 0.23 ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27 Consensus pattern (12 bp): TAATAACAATAA Found at i:48621624 original size:18 final size:21 Alignment explanation

Indices: 48621600--48621644 Score: 58 Period size: 20 Copynumber: 2.2 Consensus size: 21 48621590 AAGGAATATG 48621600 TATATATG-TAAAAA-AATAAA 1 TATATA-GATAAAAATAATAAA * 48621620 TATATAGATAAAAATAATACA 1 TATATAGATAAAAATAATAAA 48621641 TATA 1 TATA 48621645 AAATCTAAAA Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 19 1 0.05 20 12 0.55 21 9 0.41 ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31 Consensus pattern (21 bp): TATATAGATAAAAATAATAAA Found at i:48623595 original size:44 final size:44 Alignment explanation

Indices: 48623528--48624043 Score: 302 Period size: 44 Copynumber: 11.8 Consensus size: 44 48623518 TCCACTGCAG * * * 48623528 TCTGCTCCGCTGCAACTTTAAGGAGATAAGACTTGTAACTTCAA 1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAA * * 48623572 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTTAA 1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAA * ** * * * * *** * 48623616 CCCACTCTACTGTAACTTC-AGAAAGATAGGATTTGCTGTGTTCAG 1 TCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTG-TAACTTCAA * * * * ** 48623661 TCTGCTCTATTGCAACTTCAAAGAGATAAGAATTGTAACTTTGA 1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAA * * * * * * * 48623705 TCTGCTCCACTGCAACTTTAGGGAAATGAGATTTGTAGCTTTAG 1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAA * * * * 48623749 T-TCGCTCTACTGCAACTTC-AGAGAGATAGGATTTGCTATCTTCAG 1 TCT-GCTCCACTGCAACTTCAAG-GAGATAAGATTTG-TAACTTCAA ** * * 48623794 TCTGCTTTATTGTAACTTC-AGAGAGAT-A-A---G--ACTTCAA 1 TCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTGTAACTTCAA * * * * 48623831 TCTACTCCACCGCAACTTC-AGGAAGATAAGATTTGTAATTTTCGA 1 TCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTGTAA-CTTCAA * * * 48623876 TCTACTCCACTGCAACTTCAGGGAGATAAGATCTGTAACTTCAA 1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAA * * ** ** * 48623920 TCTACTCCACTGCAACTTCAAGGAGATAAAATTCACTATTTTCGA 1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATT-TGTAACTTCAA * * * * * ** 48623965 TCTACTCCACTGCAACTTTAGGGAGATGAGATTAGTGGCTTCAA 1 TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAA * * * 48624009 TCTACTCCACTACAACTT-TAGAGAGATAAGATTTG 1 TCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTG 48624044 CCATATTCCA Statistics Matches: 361, Mismatches: 92, Indels: 38 0.74 0.19 0.08 Matches are distributed among these distances: 36 1 0.00 37 24 0.07 38 1 0.00 39 1 0.00 40 1 0.00 42 1 0.00 43 6 0.02 44 194 0.54 45 128 0.35 46 4 0.01 ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32 Consensus pattern (44 bp): TCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAA Found at i:48623766 original size:133 final size:133 Alignment explanation

Indices: 48623538--48623952 Score: 400 Period size: 133 Copynumber: 3.2 Consensus size: 133 48623528 TCTGCTCCGC * * * * 48623538 TGCAACTTTAAGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA 1 TGCAACTTCAAAGAGATAAGAATTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGA * * * 48623603 TTTGTAGCTTTAACCCACTCTACTGTAACTTCAGAAAGATAGGATTTGCTGTGTTCAGTCTGCTC 66 TTTGTAGCTTTAACCCACTCTACTGCAACTTCAGAAAGATAGGATTTGCTATCTTCAGTCTGCTC 48623668 TAT 131 TAT ** * * * 48623671 TGCAACTTCAAAGAGATAAGAATTGTAACTTTGATCTGCTCCACTGCAACTTTAGGGAAATGAGA 1 TGCAACTTCAAAGAGATAAGAATTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGA *** * * * 48623736 TTTGTAGCTTTAGTTCGCTCTACTGCAACTTCAGAGAGATAGGATTTGCTATCTTCAGTCTGCTT 66 TTTGTAGCTTTAACCCACTCTACTGCAACTTCAGAAAGATAGGATTTGCTATCTTCAGTCTGCTC 48623801 TAT 131 TAT * * * * 48623804 TGTAACTTCAGAGAGAT---AA--G--ACTTCAATCTACTCCACCGCAACTTC-AGGAAGATAAG 1 TGCAACTTCAAAGAGATAAGAATTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAA-ATAAG ** * * * * ** * * * * * 48623861 ATTTGTAATTTTCGATCTACTCCACTGCAACTTCAGGGAGATAAGATCTG-TAACTTCAATCTAC 65 ATTTGTAGCTTT-AACCCACTCTACTGCAACTTCAGAAAGATAGGATTTGCTATCTTCAGTCTGC * * 48623925 TCCAC 129 TCTAT * 48623930 TGCAACTTCAAGGAGATAA-AATT 1 TGCAACTTCAAAGAGATAAGAATT 48623953 CACTATTTTC Statistics Matches: 229, Mismatches: 47, Indels: 15 0.79 0.16 0.05 Matches are distributed among these distances: 125 4 0.02 126 62 0.27 127 28 0.12 128 3 0.01 130 2 0.01 133 130 0.57 ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32 Consensus pattern (133 bp): TGCAACTTCAAAGAGATAAGAATTGTAACTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGA TTTGTAGCTTTAACCCACTCTACTGCAACTTCAGAAAGATAGGATTTGCTATCTTCAGTCTGCTC TAT Found at i:48623894 original size:45 final size:44 Alignment explanation

Indices: 48623825--48624043 Score: 217 Period size: 45 Copynumber: 4.9 Consensus size: 44 48623815 AGAGATAAGA * 48623825 CTTCAATCTACTCCACCGCAACTTCAGGAAGATAAGATTTGTAAT 1 CTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTTGT-AT * * * * * 48623870 TTTCGATCTACTCCACTGCAACTTCAGGGAGATAAGATCTGTAA 1 CTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTTGTAT * ** 48623914 CTTCAATCTACTCCACTGCAACTTCAAGG-AGATAAAATTCACTAT 1 CTTCAATCTACTCCACTGCAACTTC-AGGAAGATAAGATT-TGTAT * * * * * * ** 48623959 TTTCGATCTACTCCACTGCAACTTTAGGGAGATGAGATTAGTGG 1 CTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTTGTAT * * 48624003 CTTCAATCTACTCCACTACAACTTTA-GAGAGATAAGATTTG 1 CTTCAATCTACTCCACTGCAACTTCAGGA-AGATAAGATTTG 48624044 CCATATTCCA Statistics Matches: 143, Mismatches: 27, Indels: 9 0.80 0.15 0.05 Matches are distributed among these distances: 43 1 0.01 44 70 0.49 45 72 0.50 ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30 Consensus pattern (44 bp): CTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTTGTAT Found at i:48623975 original size:89 final size:89 Alignment explanation

Indices: 48623824--48624026 Score: 277 Period size: 89 Copynumber: 2.3 Consensus size: 89 48623814 GAGAGATAAG * * ** 48623824 ACTTCAATCTACTCCACCGCAACTTCAGGAAGATAAGATTTGTAATTTTCGATCTACTCCACTGC 1 ACTTCAATCTACTCCACTGCAACTTCAGGAAGATAAAATTACTAATTTTCGATCTACTCCACTGC 48623889 AACTTCAGGGAGATAAGATCT-GTA 66 AACTTCAGGGAGATAAGAT-TAGTA 48623913 ACTTCAATCTACTCCACTGCAACTTCAAGG-AGATAAAATTCACT-ATTTTCGATCTACTCCACT 1 ACTTCAATCTACTCCACTGCAACTTC-AGGAAGATAAAATT-ACTAATTTTCGATCTACTCCACT * * * 48623976 GCAACTTTAGGGAGATGAGATTAGTG 64 GCAACTTCAGGGAGATAAGATTAGTA * * 48624002 GCTTCAATCTACTCCACTACAACTT 1 ACTTCAATCTACTCCACTGCAACTT 48624027 TAGAGAGATA Statistics Matches: 102, Mismatches: 9, Indels: 6 0.87 0.08 0.05 Matches are distributed among these distances: 88 1 0.01 89 97 0.95 90 4 0.04 ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30 Consensus pattern (89 bp): ACTTCAATCTACTCCACTGCAACTTCAGGAAGATAAAATTACTAATTTTCGATCTACTCCACTGC AACTTCAGGGAGATAAGATTAGTA Found at i:48627560 original size:19 final size:19 Alignment explanation

Indices: 48627538--48627581 Score: 54 Period size: 19 Copynumber: 2.3 Consensus size: 19 48627528 TTAAAAGTAT * 48627538 TAAAATTAATATAAACTT-A 1 TAAAATT-ATATAAAATTCA 48627557 TAAAAATTATATAAAATTCA 1 T-AAAATTATATAAAATTCA 48627577 TAAAA 1 TAAAA 48627582 ATTTGAATTG Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 19 14 0.64 20 8 0.36 ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34 Consensus pattern (19 bp): TAAAATTATATAAAATTCA Found at i:48627562 original size:20 final size:20 Alignment explanation

Indices: 48627518--48627584 Score: 68 Period size: 20 Copynumber: 3.5 Consensus size: 20 48627508 CATCCAAATA * * 48627518 ATAAAAGTTAT-TAAAAGT- 1 ATAAAAATTATATAAAATTC * * 48627536 ATTAAAATTAATATAAACTT- 1 ATAAAAATT-ATATAAAATTC 48627556 ATAAAAATTATATAAAATTC 1 ATAAAAATTATATAAAATTC 48627576 ATAAAAATT 1 ATAAAAATT 48627585 TGAATTGGAC Statistics Matches: 40, Mismatches: 6, Indels: 4 0.80 0.12 0.08 Matches are distributed among these distances: 18 7 0.17 19 11 0.28 20 22 0.55 ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36 Consensus pattern (20 bp): ATAAAAATTATATAAAATTC Found at i:48627574 original size:10 final size:10 Alignment explanation

Indices: 48627518--48627584 Score: 61 Period size: 10 Copynumber: 6.8 Consensus size: 10 48627508 CATCCAAATA 48627518 ATAAAAGTTAT 1 ATAAAA-TTAT * 48627529 -TAAAAGTAT 1 ATAAAATTAT 48627538 -TAAAATTAAT 1 ATAAAATT-AT * 48627548 ATAAACTTAT 1 ATAAAATTAT 48627558 A-AAAATTAT 1 ATAAAATTAT 48627567 ATAAAATTCAT 1 ATAAAATT-AT 48627578 A-AAAATT 1 ATAAAATT 48627585 TGAATTGGAC Statistics Matches: 48, Mismatches: 4, Indels: 9 0.79 0.07 0.15 Matches are distributed among these distances: 9 17 0.35 10 22 0.46 11 9 0.19 ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36 Consensus pattern (10 bp): ATAAAATTAT Found at i:48627998 original size:9 final size:9 Alignment explanation

Indices: 48627984--48628184 Score: 99 Period size: 9 Copynumber: 21.7 Consensus size: 9 48627974 TTTTATGATG 48627984 TTTTTATAA 1 TTTTTATAA 48627993 TTTTTATAA 1 TTTTTATAA * 48628002 GTTTATATCAA 1 -TTTTTAT-AA * 48628013 TTTTAAT-A 1 TTTTTATAA 48628021 TTTTTATAA 1 TTTTTATAA 48628030 CTTTTTATAA 1 -TTTTTATAA * 48628040 TTTTTATTA 1 TTTTTATAA * 48628049 TTTTTAAGAA 1 TTTTT-ATAA * * * * 48628059 TTCTAACAC 1 TTTTTATAA * 48628068 TTTTTAAAA 1 TTTTTATAA * 48628077 ATTTTA-AA 1 TTTTTATAA * 48628085 TATTTAAAATAA 1 T-TTT--TATAA * * 48628097 GTTTAATTAA 1 TTTTTA-TAA 48628107 -TTTTATAA 1 TTTTTATAA 48628115 -TTTTATAA 1 TTTTTATAA * 48628123 TATTTATAA 1 TTTTTATAA * 48628132 GTTTTCATAA 1 -TTTTTATAA * 48628142 TTTTT-TTA 1 TTTTTATAA 48628150 TATTTT-TAA 1 T-TTTTATAA 48628159 TTTTTATAAGA 1 TTTTTAT-A-A * 48628170 TTTTTATGA 1 TTTTTATAA 48628179 TTTTTA 1 TTTTTA 48628185 ATCATTATTT Statistics Matches: 149, Mismatches: 27, Indels: 32 0.72 0.13 0.15 Matches are distributed among these distances: 8 27 0.18 9 70 0.47 10 36 0.24 11 14 0.09 12 2 0.01 ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59 Consensus pattern (9 bp): TTTTTATAA Found at i:48628016 original size:28 final size:28 Alignment explanation

Indices: 48627984--48628054 Score: 90 Period size: 28 Copynumber: 2.5 Consensus size: 28 48627974 TTTTATGATG * 48627984 TTTTTATAATTTTTATAAGTTTATATCAA 1 TTTTTATAATTTTTATAACTTTATAT-AA * * 48628013 TTTTAAT-ATTTTTATAACTTTTTATAA 1 TTTTTATAATTTTTATAACTTTATATAA * 48628040 TTTTTATTATTTTTA 1 TTTTTATAATTTTTA 48628055 AGAATTCTAA Statistics Matches: 37, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 27 8 0.22 28 23 0.62 29 6 0.16 ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65 Consensus pattern (28 bp): TTTTTATAATTTTTATAACTTTATATAA Found at i:48628035 original size:19 final size:19 Alignment explanation

Indices: 48627984--48628196 Score: 85 Period size: 19 Copynumber: 11.4 Consensus size: 19 48627974 TTTTATGATG 48627984 TTTTTATAATTTTT-ATAA 1 TTTTTATAATTTTTAATAA * 48628002 GTTTATATCAA-TTTTAAT-A 1 -TTTTTAT-AATTTTTAATAA 48628021 TTTTTATAACTTTTT-ATAA 1 TTTTTATAA-TTTTTAATAA * * 48628040 TTTTTATTATTTTTAAGAA 1 TTTTTATAATTTTTAATAA * * * * 48628059 TTCTAACACTTTTTAA-AA 1 TTTTTATAATTTTTAATAA * * 48628077 ATTTTA-AATATTTAAAATAA 1 TTTTTATAAT-TTT-TAATAA * * 48628097 GTTTAATTAA-TTTT-ATAA 1 TTTTTA-TAATTTTTAATAA * 48628115 -TTTTATAATATTT-ATAA 1 TTTTTATAATTTTTAATAA * * 48628132 GTTTTCATAATTTTT--TTA 1 -TTTTTATAATTTTTAATAA 48628150 TATTTT-TAATTTTT-ATAAGA 1 T-TTTTATAATTTTTAAT-A-A * * 48628170 TTTTTATGATTTTTAATCA 1 TTTTTATAATTTTTAATAA 48628189 TTATTTAT 1 TT-TTTAT 48628197 GGAAAAATAT Statistics Matches: 147, Mismatches: 26, Indels: 41 0.69 0.12 0.19 Matches are distributed among these distances: 16 3 0.02 17 24 0.16 18 31 0.21 19 58 0.39 20 27 0.18 21 2 0.01 22 2 0.01 ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59 Consensus pattern (19 bp): TTTTTATAATTTTTAATAA Found at i:48628183 original size:36 final size:38 Alignment explanation

Indices: 48628107--48628183 Score: 104 Period size: 37 Copynumber: 2.1 Consensus size: 38 48628097 GTTTAATTAA 48628107 TTTTATAATTTTATAATATTTATAAGTTTTCATAATTT 1 TTTTATAATTTTATAATATTTATAAGTTTTCATAATTT * * * 48628145 TTTTAT-ATTTT-TAATTTTTATAAGATTTTTATGATTT 1 TTTTATAATTTTATAATATTTATAAG-TTTTCATAATTT 48628182 TT 1 TT 48628184 AATCATTATT Statistics Matches: 35, Mismatches: 3, Indels: 3 0.85 0.07 0.07 Matches are distributed among these distances: 36 12 0.34 37 17 0.49 38 6 0.17 ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65 Consensus pattern (38 bp): TTTTATAATTTTATAATATTTATAAGTTTTCATAATTT Found at i:48629921 original size:19 final size:19 Alignment explanation

Indices: 48629899--48630017 Score: 112 Period size: 19 Copynumber: 6.2 Consensus size: 19 48629889 CGTACAAAGC * 48629899 GCATACTCGCACACGAAGT 1 GCATACTAGCACACGAAGT * * * 48629918 GCATTCTAGCACACAAAGC 1 GCATACTAGCACACGAAGT * * 48629937 ACATACTGGCACACGAAGT 1 GCATACTAGCACACGAAGT * * 48629956 GCATTCTAGCGCACGAAGT 1 GCATACTAGCACACGAAGT * * * 48629975 GCATTCTAGCGCACGATGT 1 GCATACTAGCACACGAAGT * * 48629994 ACATATCTGGCACACGAAGT 1 GCATA-CTAGCACACGAAGT 48630014 GCAT 1 GCAT 48630018 CCTGACGCAT Statistics Matches: 79, Mismatches: 20, Indels: 1 0.79 0.20 0.01 Matches are distributed among these distances: 19 65 0.82 20 14 0.18 ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19 Consensus pattern (19 bp): GCATACTAGCACACGAAGT Found at i:48629990 original size:38 final size:38 Alignment explanation

Indices: 48629899--48630017 Score: 130 Period size: 38 Copynumber: 3.1 Consensus size: 38 48629889 CGTACAAAGC * * * 48629899 GCATACTCGCACACGAAGTGCATTCTAGCACACAAAGC 1 GCATACTAGCACACGAAGTGCATTCTAGCACACGAAGT * * * 48629937 ACATACTGGCACACGAAGTGCATTCTAGCGCACGAAGT 1 GCATACTAGCACACGAAGTGCATTCTAGCACACGAAGT * * * * * 48629975 GCATTCTAGCGCACGATGTACATATCTGGCACACGAAGT 1 GCATACTAGCACACGAAGTGCAT-TCTAGCACACGAAGT 48630014 GCAT 1 GCAT 48630018 CCTGACGCAT Statistics Matches: 67, Mismatches: 13, Indels: 1 0.83 0.16 0.01 Matches are distributed among these distances: 38 50 0.75 39 17 0.25 ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19 Consensus pattern (38 bp): GCATACTAGCACACGAAGTGCATTCTAGCACACGAAGT Found at i:48632613 original size:27 final size:27 Alignment explanation

Indices: 48632575--48632632 Score: 116 Period size: 27 Copynumber: 2.1 Consensus size: 27 48632565 ATAATATGAA 48632575 ATATAAATTTACAGAAAAGTAACATGC 1 ATATAAATTTACAGAAAAGTAACATGC 48632602 ATATAAATTTACAGAAAAGTAACATGC 1 ATATAAATTTACAGAAAAGTAACATGC 48632629 ATAT 1 ATAT 48632633 CATGAAATAT Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 27 31 1.00 ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28 Consensus pattern (27 bp): ATATAAATTTACAGAAAAGTAACATGC Found at i:48633049 original size:6 final size:6 Alignment explanation

Indices: 48633038--48633062 Score: 50 Period size: 6 Copynumber: 4.2 Consensus size: 6 48633028 ACCGACAAAA 48633038 CAACTC CAACTC CAACTC CAACTC C 1 CAACTC CAACTC CAACTC CAACTC C 48633063 TTCAAATTCT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 19 1.00 ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16 Consensus pattern (6 bp): CAACTC Found at i:48637295 original size:21 final size:20 Alignment explanation

Indices: 48637271--48637383 Score: 111 Period size: 20 Copynumber: 5.5 Consensus size: 20 48637261 ATTTGTCTTA * 48637271 AATCGATTCTTTGCTTATTTG 1 AATCGATTCTTTG-TTGTTTG * * 48637292 AATCGATTGTTTTGTTGATTG 1 AATCGATT-CTTTGTTGTTTG * * 48637313 ACTCAATTCTTTTTGTTGTTTG 1 AATCGATTC--TTTGTTGTTTG * * 48637335 AATCGATTGTTTATTGTTTG 1 AATCGATTCTTTGTTGTTTG 48637355 AATCGATTCTTTGTTGTTT- 1 AATCGATTCTTTGTTGTTTG 48637374 AACTCGATTC 1 AA-TCGATTC 48637384 AAACGCCAAC Statistics Matches: 75, Mismatches: 13, Indels: 9 0.77 0.13 0.09 Matches are distributed among these distances: 19 2 0.03 20 34 0.45 21 19 0.25 22 20 0.27 ACGTcount: A:0.19, C:0.12, G:0.17, T:0.53 Consensus pattern (20 bp): AATCGATTCTTTGTTGTTTG Found at i:48637364 original size:42 final size:43 Alignment explanation

Indices: 48637271--48637372 Score: 120 Period size: 42 Copynumber: 2.4 Consensus size: 43 48637261 ATTTGTCTTA * 48637271 AATCGATTC--TTTGCTTATTTGAATCGATTGTTTTGTTGATTG 1 AATCGATTCTTTTTG-TTATTTGAATCGATTGTTTTATTGATTG * * * * 48637313 ACTCAATTCTTTTTGTTGTTTGAATCGATTG-TTTATTGTTTG 1 AATCGATTCTTTTTGTTATTTGAATCGATTGTTTTATTGATTG 48637355 AATCGATTCTTTGTTGTT 1 AATCGATTCTTT-TTGTT 48637373 TAACTCGATT Statistics Matches: 50, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 42 26 0.52 43 20 0.40 44 4 0.08 ACGTcount: A:0.18, C:0.10, G:0.18, T:0.55 Consensus pattern (43 bp): AATCGATTCTTTTTGTTATTTGAATCGATTGTTTTATTGATTG Found at i:48651916 original size:24 final size:25 Alignment explanation

Indices: 48651889--48651937 Score: 64 Period size: 24 Copynumber: 2.0 Consensus size: 25 48651879 TATTTTTATG 48651889 AAATTACATATTAATA-TAATAATA 1 AAATTACATATTAATACTAATAATA * * 48651913 AAATTATATTTTAATACCTAATAAT 1 AAATTACATATTAATA-CTAATAAT 48651938 TTAAAATTTA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 24 14 0.67 26 7 0.33 ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41 Consensus pattern (25 bp): AAATTACATATTAATACTAATAATA Found at i:48656279 original size:5 final size:6 Alignment explanation

Indices: 48656259--48656289 Score: 53 Period size: 6 Copynumber: 5.0 Consensus size: 6 48656249 CGACAAAAGG 48656259 TTTCTTT TTTCTT TTTCTT TTTCTT TTTCTT 1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT 48656290 CCAAAAGGAG Statistics Matches: 24, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 6 20 0.83 7 4 0.17 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (6 bp): TTTCTT Found at i:48657845 original size:28 final size:28 Alignment explanation

Indices: 48657813--48657874 Score: 72 Period size: 28 Copynumber: 2.2 Consensus size: 28 48657803 AAATTGAAGG * 48657813 TTTAAAGATCTCT-TTTATTGTTTAACAA 1 TTTAAAAATCT-TATTTATTGTTTAACAA * * * 48657841 TTTAAAAATGTTATTTATTGTTTAATAG 1 TTTAAAAATCTTATTTATTGTTTAACAA 48657869 TTTAAA 1 TTTAAA 48657875 TTTGGCATTT Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 27 1 0.03 28 28 0.97 ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52 Consensus pattern (28 bp): TTTAAAAATCTTATTTATTGTTTAACAA Done.